Multiple sequence alignment - TraesCS5D01G249600

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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 TraesCS5D01G249600 chr5D 100.000 2975 0 0 1 2975 356195777 356192803 0.000000e+00 5494.0
1 TraesCS5D01G249600 chr5D 77.640 322 54 15 1221 1533 75354251 75353939 2.360000e-41 180.0
2 TraesCS5D01G249600 chr5D 75.573 393 60 23 2198 2572 536034594 536034968 8.530000e-36 161.0
3 TraesCS5D01G249600 chr5D 83.200 125 19 2 1306 1429 352698270 352698147 2.420000e-21 113.0
4 TraesCS5D01G249600 chr5B 92.667 2100 114 20 902 2975 421166437 421164352 0.000000e+00 2988.0
5 TraesCS5D01G249600 chr5B 85.597 611 44 19 312 882 421167028 421166422 4.240000e-168 601.0
6 TraesCS5D01G249600 chr5B 87.955 357 36 3 1793 2142 405796084 405795728 5.930000e-112 414.0
7 TraesCS5D01G249600 chr5B 78.395 324 62 7 1233 1549 251917775 251918097 1.400000e-48 204.0
8 TraesCS5D01G249600 chr5B 74.474 333 72 13 1221 1545 420714437 420714764 6.690000e-27 132.0
9 TraesCS5D01G249600 chr5B 83.200 125 19 2 1306 1429 415670114 415669991 2.420000e-21 113.0
10 TraesCS5D01G249600 chr5A 95.748 1176 42 1 902 2077 457891753 457890586 0.000000e+00 1888.0
11 TraesCS5D01G249600 chr5A 86.977 837 83 13 67 882 457892569 457891738 0.000000e+00 918.0
12 TraesCS5D01G249600 chr5A 79.036 415 53 18 2216 2614 457890536 457890140 1.370000e-63 254.0
13 TraesCS5D01G249600 chr5A 78.592 341 51 19 1221 1550 70482814 70482485 3.890000e-49 206.0
14 TraesCS5D01G249600 chr5A 74.096 332 69 15 1221 1545 457516625 457516304 1.450000e-23 121.0
15 TraesCS5D01G249600 chr5A 74.675 154 32 7 2307 2457 644026155 644026006 8.900000e-06 62.1
16 TraesCS5D01G249600 chr2B 78.413 315 48 9 2152 2465 56928522 56928227 1.410000e-43 187.0
17 TraesCS5D01G249600 chr2B 77.215 316 49 19 2276 2573 470521181 470520871 2.370000e-36 163.0
18 TraesCS5D01G249600 chr2B 81.013 158 25 3 429 584 306981119 306981273 1.450000e-23 121.0
19 TraesCS5D01G249600 chr2B 76.923 182 29 10 1225 1399 141282817 141282992 1.140000e-14 91.6
20 TraesCS5D01G249600 chr2B 87.013 77 9 1 2496 2572 759601999 759601924 5.280000e-13 86.1
21 TraesCS5D01G249600 chr1D 75.443 395 71 19 2198 2572 482501059 482501447 5.100000e-38 169.0
22 TraesCS5D01G249600 chr4A 74.886 438 73 24 2152 2572 547519673 547520090 6.600000e-37 165.0
23 TraesCS5D01G249600 chr4A 81.416 113 16 5 1333 1443 84897266 84897157 1.470000e-13 87.9
24 TraesCS5D01G249600 chr7D 76.803 319 50 19 2276 2575 404377768 404377455 1.100000e-34 158.0
25 TraesCS5D01G249600 chr7D 75.472 318 56 19 2276 2575 404608689 404608376 5.170000e-28 135.0
26 TraesCS5D01G249600 chr7D 89.412 85 8 1 2490 2573 635004093 635004009 4.060000e-19 106.0
27 TraesCS5D01G249600 chrUn 75.000 384 67 17 2201 2572 82258908 82258542 1.850000e-32 150.0
28 TraesCS5D01G249600 chrUn 74.935 387 68 17 2198 2572 82274434 82274803 1.850000e-32 150.0
29 TraesCS5D01G249600 chrUn 81.046 153 25 3 429 579 11410904 11410754 5.210000e-23 119.0
30 TraesCS5D01G249600 chrUn 87.013 77 9 1 2496 2572 23233281 23233206 5.280000e-13 86.1
31 TraesCS5D01G249600 chr6D 80.124 161 25 5 422 578 355545871 355546028 2.420000e-21 113.0
32 TraesCS5D01G249600 chr6D 79.739 153 27 3 429 579 364031878 364032028 1.130000e-19 108.0
33 TraesCS5D01G249600 chr6B 79.739 153 27 3 429 579 314648000 314648150 1.130000e-19 108.0
34 TraesCS5D01G249600 chr1A 79.870 154 25 5 429 579 280091696 280091846 1.130000e-19 108.0
35 TraesCS5D01G249600 chr1A 73.179 302 54 17 2172 2467 348854953 348855233 1.900000e-12 84.2
36 TraesCS5D01G249600 chr7A 79.605 152 27 2 429 578 201433551 201433402 4.060000e-19 106.0
37 TraesCS5D01G249600 chr2A 77.049 183 27 11 1225 1399 88299755 88299930 1.140000e-14 91.6
38 TraesCS5D01G249600 chr3A 77.885 104 22 1 2358 2460 51400912 51401015 2.480000e-06 63.9


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 TraesCS5D01G249600 chr5D 356192803 356195777 2974 True 5494.0 5494 100.000000 1 2975 1 chr5D.!!$R3 2974
1 TraesCS5D01G249600 chr5B 421164352 421167028 2676 True 1794.5 2988 89.132000 312 2975 2 chr5B.!!$R3 2663
2 TraesCS5D01G249600 chr5A 457890140 457892569 2429 True 1020.0 1888 87.253667 67 2614 3 chr5A.!!$R4 2547

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
205 207 0.034616 GGCCTCATCCCAGAATCGAG 59.965 60.0 0.0 0.0 0.0 4.04 F
829 884 1.226746 AGGCGAGAAAAGGTTGTTCG 58.773 50.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1034 1094 0.460987 GCAGTGTTCGATCTCCAGGG 60.461 60.0 0.00 0.00 0.0 4.45 R
2216 2282 0.392998 AACAATGTAGAGGCCGGCTG 60.393 55.0 28.56 16.55 0.0 4.85 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
21 22 4.880886 TCAGTGATGCATTTTATGGACG 57.119 40.909 0.00 0.00 31.88 4.79
22 23 4.260985 TCAGTGATGCATTTTATGGACGT 58.739 39.130 0.00 0.00 31.88 4.34
23 24 4.699735 TCAGTGATGCATTTTATGGACGTT 59.300 37.500 0.00 0.00 31.88 3.99
24 25 5.030295 CAGTGATGCATTTTATGGACGTTC 58.970 41.667 0.00 0.00 31.88 3.95
25 26 4.699735 AGTGATGCATTTTATGGACGTTCA 59.300 37.500 0.00 0.00 31.88 3.18
26 27 5.182950 AGTGATGCATTTTATGGACGTTCAA 59.817 36.000 0.00 0.00 31.88 2.69
27 28 6.035843 GTGATGCATTTTATGGACGTTCAAT 58.964 36.000 0.00 0.00 31.88 2.57
28 29 6.020440 GTGATGCATTTTATGGACGTTCAATG 60.020 38.462 0.00 0.62 31.88 2.82
29 30 4.742417 TGCATTTTATGGACGTTCAATGG 58.258 39.130 0.00 0.00 0.00 3.16
30 31 3.551485 GCATTTTATGGACGTTCAATGGC 59.449 43.478 0.00 0.00 0.00 4.40
31 32 3.479505 TTTTATGGACGTTCAATGGCG 57.520 42.857 0.00 0.00 0.00 5.69
32 33 2.388310 TTATGGACGTTCAATGGCGA 57.612 45.000 0.00 0.00 0.00 5.54
33 34 1.647346 TATGGACGTTCAATGGCGAC 58.353 50.000 0.00 0.00 0.00 5.19
34 35 1.358725 ATGGACGTTCAATGGCGACG 61.359 55.000 0.00 0.00 42.13 5.12
35 36 1.735198 GGACGTTCAATGGCGACGA 60.735 57.895 0.00 0.00 39.85 4.20
36 37 1.414897 GACGTTCAATGGCGACGAC 59.585 57.895 0.00 0.00 39.85 4.34
37 38 1.952266 GACGTTCAATGGCGACGACC 61.952 60.000 0.00 0.00 39.85 4.79
38 39 1.736645 CGTTCAATGGCGACGACCT 60.737 57.895 0.00 0.00 38.99 3.85
39 40 0.457166 CGTTCAATGGCGACGACCTA 60.457 55.000 0.00 0.00 38.99 3.08
40 41 1.278238 GTTCAATGGCGACGACCTAG 58.722 55.000 0.00 0.00 0.00 3.02
41 42 0.174845 TTCAATGGCGACGACCTAGG 59.825 55.000 7.41 7.41 0.00 3.02
42 43 1.883084 CAATGGCGACGACCTAGGC 60.883 63.158 9.30 0.36 0.00 3.93
43 44 2.355986 AATGGCGACGACCTAGGCA 61.356 57.895 9.30 0.00 44.36 4.75
44 45 2.573609 AATGGCGACGACCTAGGCAC 62.574 60.000 9.30 2.28 43.09 5.01
45 46 3.755628 GGCGACGACCTAGGCACA 61.756 66.667 9.30 0.00 0.00 4.57
46 47 2.202623 GCGACGACCTAGGCACAG 60.203 66.667 9.30 0.00 0.00 3.66
47 48 2.202623 CGACGACCTAGGCACAGC 60.203 66.667 9.30 0.00 0.00 4.40
69 70 3.775654 CTCCCTCTGACCCGCACC 61.776 72.222 0.00 0.00 0.00 5.01
81 82 4.988598 CGCACCGGTCAACCTGCT 62.989 66.667 2.59 0.00 35.68 4.24
143 144 3.775654 GTCTCCGGCCTGGTCCTG 61.776 72.222 12.46 0.00 39.52 3.86
173 174 4.767255 CTGGGCCACTCCTCACGC 62.767 72.222 0.00 0.00 34.39 5.34
176 178 4.767255 GGCCACTCCTCACGCAGG 62.767 72.222 0.00 0.00 45.15 4.85
179 181 4.767255 CACTCCTCACGCAGGCCC 62.767 72.222 0.00 0.00 43.08 5.80
198 200 1.144936 GTCTTCGGCCTCATCCCAG 59.855 63.158 0.00 0.00 0.00 4.45
202 204 0.469917 TTCGGCCTCATCCCAGAATC 59.530 55.000 0.00 0.00 0.00 2.52
205 207 0.034616 GGCCTCATCCCAGAATCGAG 59.965 60.000 0.00 0.00 0.00 4.04
226 228 4.003648 AGTGACCCGAGCTAATTTTTCAG 58.996 43.478 0.00 0.00 0.00 3.02
227 229 4.000988 GTGACCCGAGCTAATTTTTCAGA 58.999 43.478 0.00 0.00 0.00 3.27
248 250 7.568349 TCAGATACCTGAGAAATAGCAAACAT 58.432 34.615 0.00 0.00 44.01 2.71
250 252 6.769822 AGATACCTGAGAAATAGCAAACATGG 59.230 38.462 0.00 0.00 0.00 3.66
251 253 4.019174 ACCTGAGAAATAGCAAACATGGG 58.981 43.478 0.00 0.00 0.00 4.00
263 265 5.304778 AGCAAACATGGGTTTATTTTGTCC 58.695 37.500 0.00 0.00 45.18 4.02
292 294 5.640732 CATCCATGTTTAGCCACAACTAAC 58.359 41.667 0.00 0.00 31.94 2.34
297 299 3.377485 TGTTTAGCCACAACTAACGCAAA 59.623 39.130 0.00 0.00 31.94 3.68
329 331 8.867935 GGATTGATCACTTATGAATCATAGTCG 58.132 37.037 2.98 0.00 39.27 4.18
379 381 6.758886 ACTAGATTTGCCTTCGAATGTCTTAG 59.241 38.462 0.00 0.00 0.00 2.18
406 408 2.530460 AGGGCTCATTTGGTATGCAA 57.470 45.000 0.00 0.00 0.00 4.08
412 414 5.177326 GGCTCATTTGGTATGCAAAATTCA 58.823 37.500 0.00 0.00 0.00 2.57
471 473 3.888221 GCACGTGCAAAACAGACG 58.112 55.556 34.52 0.00 41.59 4.18
550 554 9.775854 AAAACACATGAATCCAAATAAACATGA 57.224 25.926 0.00 0.00 38.55 3.07
603 624 9.700831 AAATATGCCATTAAGGTTCTTAGTCTT 57.299 29.630 0.00 0.00 40.61 3.01
614 638 5.048507 GGTTCTTAGTCTTGTTCTTCGTGT 58.951 41.667 0.00 0.00 0.00 4.49
657 682 6.097412 GCTCAAAATGGATGTTAGAATCCCTT 59.903 38.462 0.91 0.00 44.88 3.95
764 819 8.600449 AGAAGAAACTTCACTTTCACTATGAG 57.400 34.615 12.86 0.00 33.26 2.90
811 866 8.652810 AATCAACTCCACAAAAATTCAAGAAG 57.347 30.769 0.00 0.00 0.00 2.85
813 868 4.948847 ACTCCACAAAAATTCAAGAAGGC 58.051 39.130 0.00 0.00 0.00 4.35
814 869 3.976169 TCCACAAAAATTCAAGAAGGCG 58.024 40.909 0.00 0.00 0.00 5.52
821 876 6.476706 ACAAAAATTCAAGAAGGCGAGAAAAG 59.523 34.615 0.00 0.00 0.00 2.27
829 884 1.226746 AGGCGAGAAAAGGTTGTTCG 58.773 50.000 0.00 0.00 0.00 3.95
882 939 4.407365 CCCAACCATAGGAAGTCAAGTTT 58.593 43.478 0.00 0.00 0.00 2.66
883 940 4.832823 CCCAACCATAGGAAGTCAAGTTTT 59.167 41.667 0.00 0.00 0.00 2.43
914 971 5.772825 TTTTTGAGACATGGGAAGTCAAG 57.227 39.130 0.00 0.00 38.46 3.02
915 972 4.437682 TTTGAGACATGGGAAGTCAAGT 57.562 40.909 0.00 0.00 38.46 3.16
916 973 4.437682 TTGAGACATGGGAAGTCAAGTT 57.562 40.909 0.00 0.00 38.46 2.66
917 974 3.743521 TGAGACATGGGAAGTCAAGTTG 58.256 45.455 0.00 0.00 38.46 3.16
918 975 2.485814 GAGACATGGGAAGTCAAGTTGC 59.514 50.000 0.00 0.00 38.46 4.17
919 976 2.158623 AGACATGGGAAGTCAAGTTGCA 60.159 45.455 0.00 0.00 38.46 4.08
929 986 1.261619 GTCAAGTTGCAGAACCACTCG 59.738 52.381 0.00 0.00 31.81 4.18
1059 1119 0.817654 AGATCGAACACTGCATCCGA 59.182 50.000 0.00 0.00 0.00 4.55
1095 1155 2.202756 GTGGAGCGCTACTTCGGG 60.203 66.667 22.67 0.00 0.00 5.14
1303 1363 1.582968 GTCTTCCACGCGTACCTCA 59.417 57.895 13.44 0.00 0.00 3.86
1910 1970 1.817099 GCCACTGCTTCCATCTCGG 60.817 63.158 0.00 0.00 33.53 4.63
1912 1972 1.078918 CACTGCTTCCATCTCGGCA 60.079 57.895 0.00 0.00 33.14 5.69
2057 2117 8.659925 TTCTGTATTTTTGTTGTTGATGCATT 57.340 26.923 0.00 0.00 0.00 3.56
2196 2262 8.867112 AAAATGAAGCATCAAACATATAGCAG 57.133 30.769 0.00 0.00 39.49 4.24
2197 2263 7.578310 AATGAAGCATCAAACATATAGCAGT 57.422 32.000 0.00 0.00 39.49 4.40
2198 2264 8.681486 AATGAAGCATCAAACATATAGCAGTA 57.319 30.769 0.00 0.00 39.49 2.74
2216 2282 4.675114 GCAGTACAAACATAACAAGCACAC 59.325 41.667 0.00 0.00 0.00 3.82
2217 2283 5.731967 GCAGTACAAACATAACAAGCACACA 60.732 40.000 0.00 0.00 0.00 3.72
2218 2284 5.909054 CAGTACAAACATAACAAGCACACAG 59.091 40.000 0.00 0.00 0.00 3.66
2242 2308 5.794894 CCGGCCTCTACATTGTTAGAATAT 58.205 41.667 0.00 0.00 0.00 1.28
2248 2314 9.197694 GCCTCTACATTGTTAGAATATACACAG 57.802 37.037 0.00 0.00 0.00 3.66
2263 2329 3.163630 ACACAGCCAACATCAACAAAC 57.836 42.857 0.00 0.00 0.00 2.93
2269 2336 3.132646 AGCCAACATCAACAAACACACAT 59.867 39.130 0.00 0.00 0.00 3.21
2300 2367 1.581602 CGCCGGCAAATAACAAAATCG 59.418 47.619 28.98 0.00 0.00 3.34
2303 2370 4.356289 GCCGGCAAATAACAAAATCGTAT 58.644 39.130 24.80 0.00 0.00 3.06
2352 2422 4.039245 GGAAAAGGGAAAAAGACCTCAAGG 59.961 45.833 0.00 0.00 35.64 3.61
2412 2482 7.566760 TGTTCACACCAATCATATATTGACC 57.433 36.000 0.00 0.00 37.11 4.02
2414 2484 7.833682 TGTTCACACCAATCATATATTGACCTT 59.166 33.333 0.00 0.00 37.11 3.50
2461 2531 3.279434 ACAACGCCTTCAGAAAGAAAGT 58.721 40.909 0.00 0.00 35.40 2.66
2466 2536 2.349912 GCCTTCAGAAAGAAAGTGACGC 60.350 50.000 0.00 0.00 35.40 5.19
2467 2537 2.224314 CCTTCAGAAAGAAAGTGACGCC 59.776 50.000 0.00 0.00 35.40 5.68
2468 2538 2.910688 TCAGAAAGAAAGTGACGCCT 57.089 45.000 0.00 0.00 0.00 5.52
2596 2676 0.819259 GTCCTTGTGCAACTGAGGCA 60.819 55.000 0.00 0.00 39.61 4.75
2625 2708 1.537202 GCTTGGTCTGTTGCCTTACAG 59.463 52.381 4.78 4.78 45.46 2.74
2642 2725 4.162690 GCATCCCCGCGAAGACCT 62.163 66.667 8.23 0.00 0.00 3.85
2866 2955 1.140652 TGTGGAGATTGTGTGTGCTCA 59.859 47.619 0.00 0.00 0.00 4.26
2875 2964 7.255491 AGATTGTGTGTGCTCATATTGTATG 57.745 36.000 0.00 0.00 0.00 2.39
2929 3018 9.352784 CATGTTGAGTAGTTTTTCAAAAACTCA 57.647 29.630 27.73 18.71 40.88 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.260985 ACGTCCATAAAATGCATCACTGA 58.739 39.130 0.00 0.00 0.00 3.41
1 2 4.621068 ACGTCCATAAAATGCATCACTG 57.379 40.909 0.00 0.00 0.00 3.66
2 3 4.699735 TGAACGTCCATAAAATGCATCACT 59.300 37.500 0.00 0.00 0.00 3.41
3 4 4.980590 TGAACGTCCATAAAATGCATCAC 58.019 39.130 0.00 0.00 0.00 3.06
6 7 5.350633 CCATTGAACGTCCATAAAATGCAT 58.649 37.500 0.00 0.00 0.00 3.96
7 8 4.742417 CCATTGAACGTCCATAAAATGCA 58.258 39.130 0.00 0.00 0.00 3.96
9 10 3.790820 CGCCATTGAACGTCCATAAAATG 59.209 43.478 0.00 0.00 0.00 2.32
10 11 3.692101 TCGCCATTGAACGTCCATAAAAT 59.308 39.130 0.00 0.00 0.00 1.82
11 12 3.075148 TCGCCATTGAACGTCCATAAAA 58.925 40.909 0.00 0.00 0.00 1.52
12 13 2.417239 GTCGCCATTGAACGTCCATAAA 59.583 45.455 0.00 0.00 0.00 1.40
14 15 1.647346 GTCGCCATTGAACGTCCATA 58.353 50.000 0.00 0.00 0.00 2.74
15 16 1.358725 CGTCGCCATTGAACGTCCAT 61.359 55.000 0.00 0.00 0.00 3.41
16 17 2.024868 CGTCGCCATTGAACGTCCA 61.025 57.895 0.00 0.00 0.00 4.02
17 18 1.735198 TCGTCGCCATTGAACGTCC 60.735 57.895 0.00 0.00 0.00 4.79
18 19 1.414897 GTCGTCGCCATTGAACGTC 59.585 57.895 0.00 0.00 0.00 4.34
19 20 2.025418 GGTCGTCGCCATTGAACGT 61.025 57.895 1.46 0.00 0.00 3.99
20 21 0.457166 TAGGTCGTCGCCATTGAACG 60.457 55.000 8.15 0.00 0.00 3.95
21 22 1.278238 CTAGGTCGTCGCCATTGAAC 58.722 55.000 8.15 0.00 0.00 3.18
22 23 0.174845 CCTAGGTCGTCGCCATTGAA 59.825 55.000 0.00 0.00 0.00 2.69
23 24 1.813859 CCTAGGTCGTCGCCATTGA 59.186 57.895 0.00 0.00 0.00 2.57
24 25 1.883084 GCCTAGGTCGTCGCCATTG 60.883 63.158 11.31 0.00 0.00 2.82
25 26 2.355986 TGCCTAGGTCGTCGCCATT 61.356 57.895 11.31 0.00 0.00 3.16
26 27 2.758327 TGCCTAGGTCGTCGCCAT 60.758 61.111 11.31 0.00 0.00 4.40
27 28 3.755628 GTGCCTAGGTCGTCGCCA 61.756 66.667 11.31 0.00 0.00 5.69
28 29 3.701604 CTGTGCCTAGGTCGTCGCC 62.702 68.421 11.31 0.00 0.00 5.54
29 30 2.202623 CTGTGCCTAGGTCGTCGC 60.203 66.667 11.31 0.39 0.00 5.19
30 31 2.202623 GCTGTGCCTAGGTCGTCG 60.203 66.667 11.31 0.00 0.00 5.12
31 32 2.184579 GGCTGTGCCTAGGTCGTC 59.815 66.667 11.31 0.00 46.69 4.20
51 52 3.775654 GTGCGGGTCAGAGGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
52 53 3.775654 GGTGCGGGTCAGAGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
64 65 4.988598 AGCAGGTTGACCGGTGCG 62.989 66.667 14.63 0.00 40.78 5.34
65 66 2.594592 AAGCAGGTTGACCGGTGC 60.595 61.111 14.63 8.40 42.08 5.01
69 70 1.738099 CGAGGAAGCAGGTTGACCG 60.738 63.158 0.00 0.00 42.08 4.79
72 73 2.172483 GAGGCGAGGAAGCAGGTTGA 62.172 60.000 0.00 0.00 39.27 3.18
79 80 4.516195 GGTCGGAGGCGAGGAAGC 62.516 72.222 0.00 0.00 0.00 3.86
113 114 2.179517 GAGACAGGGACGACGCAG 59.820 66.667 4.64 0.00 0.00 5.18
179 181 2.107141 GGGATGAGGCCGAAGACG 59.893 66.667 0.00 0.00 39.43 4.18
181 183 0.617535 TTCTGGGATGAGGCCGAAGA 60.618 55.000 0.00 0.00 0.00 2.87
192 194 1.123928 GGGTCACTCGATTCTGGGAT 58.876 55.000 0.00 0.00 0.00 3.85
193 195 1.320344 CGGGTCACTCGATTCTGGGA 61.320 60.000 0.00 0.00 0.00 4.37
198 200 1.022735 TAGCTCGGGTCACTCGATTC 58.977 55.000 0.00 0.00 36.01 2.52
202 204 2.295253 AAATTAGCTCGGGTCACTCG 57.705 50.000 0.00 0.00 0.00 4.18
205 207 4.000988 TCTGAAAAATTAGCTCGGGTCAC 58.999 43.478 0.00 0.00 0.00 3.67
226 228 6.016777 CCCATGTTTGCTATTTCTCAGGTATC 60.017 42.308 0.00 0.00 0.00 2.24
227 229 5.829924 CCCATGTTTGCTATTTCTCAGGTAT 59.170 40.000 0.00 0.00 0.00 2.73
285 287 5.746245 TCAATCCTTTTGTTTGCGTTAGTTG 59.254 36.000 0.00 0.00 0.00 3.16
292 294 4.549458 AGTGATCAATCCTTTTGTTTGCG 58.451 39.130 0.00 0.00 0.00 4.85
297 299 9.246670 TGATTCATAAGTGATCAATCCTTTTGT 57.753 29.630 0.00 0.00 33.56 2.83
327 329 6.094881 GGTGAATATTGGAGGAAAATGAACGA 59.905 38.462 0.00 0.00 0.00 3.85
329 331 7.410120 AGGTGAATATTGGAGGAAAATGAAC 57.590 36.000 0.00 0.00 0.00 3.18
437 439 6.372981 GCACGTGCATTCATATCATATTTCA 58.627 36.000 34.52 0.00 41.59 2.69
500 503 0.482446 ATTCCTGTGAACCAAGGCCA 59.518 50.000 5.01 0.00 32.13 5.36
503 506 4.935352 TTTCAATTCCTGTGAACCAAGG 57.065 40.909 0.00 0.00 34.78 3.61
550 554 9.829507 TTTCATGTGGTTTGACTTTAATTTGAT 57.170 25.926 0.00 0.00 0.00 2.57
578 582 9.125026 CAAGACTAAGAACCTTAATGGCATATT 57.875 33.333 0.00 0.00 40.22 1.28
585 606 8.436200 CGAAGAACAAGACTAAGAACCTTAATG 58.564 37.037 0.00 0.00 0.00 1.90
588 609 6.921857 CACGAAGAACAAGACTAAGAACCTTA 59.078 38.462 0.00 0.00 0.00 2.69
625 649 8.181904 TCTAACATCCATTTTGAGCTCTTTTT 57.818 30.769 16.19 0.00 0.00 1.94
657 682 6.153680 TGAACCTACTTTCAAAGGAAAAGCAA 59.846 34.615 1.31 0.00 42.18 3.91
764 819 1.271926 TGACTTTAGGGCTCCTTTGGC 60.272 52.381 0.00 0.00 34.61 4.52
811 866 0.237498 CCGAACAACCTTTTCTCGCC 59.763 55.000 0.00 0.00 0.00 5.54
813 868 2.415512 GGATCCGAACAACCTTTTCTCG 59.584 50.000 0.00 0.00 0.00 4.04
814 869 3.408634 TGGATCCGAACAACCTTTTCTC 58.591 45.455 7.39 0.00 0.00 2.87
821 876 3.329929 AGTAGTTGGATCCGAACAACC 57.670 47.619 21.54 12.50 46.07 3.77
829 884 5.338365 CACGTTAGTGTAGTAGTTGGATCC 58.662 45.833 4.20 4.20 43.15 3.36
892 949 5.200483 ACTTGACTTCCCATGTCTCAAAAA 58.800 37.500 0.00 0.00 35.63 1.94
893 950 4.792068 ACTTGACTTCCCATGTCTCAAAA 58.208 39.130 0.00 0.00 35.63 2.44
894 951 4.437682 ACTTGACTTCCCATGTCTCAAA 57.562 40.909 0.00 0.00 35.63 2.69
895 952 4.136796 CAACTTGACTTCCCATGTCTCAA 58.863 43.478 0.00 0.00 35.63 3.02
896 953 3.743521 CAACTTGACTTCCCATGTCTCA 58.256 45.455 0.00 0.00 35.63 3.27
897 954 2.485814 GCAACTTGACTTCCCATGTCTC 59.514 50.000 0.00 0.00 35.63 3.36
898 955 2.158623 TGCAACTTGACTTCCCATGTCT 60.159 45.455 0.00 0.00 35.63 3.41
899 956 2.227388 CTGCAACTTGACTTCCCATGTC 59.773 50.000 0.00 0.00 35.21 3.06
900 957 2.158623 TCTGCAACTTGACTTCCCATGT 60.159 45.455 0.00 0.00 0.00 3.21
901 958 2.507484 TCTGCAACTTGACTTCCCATG 58.493 47.619 0.00 0.00 0.00 3.66
902 959 2.887152 GTTCTGCAACTTGACTTCCCAT 59.113 45.455 0.00 0.00 0.00 4.00
903 960 2.297701 GTTCTGCAACTTGACTTCCCA 58.702 47.619 0.00 0.00 0.00 4.37
904 961 1.609072 GGTTCTGCAACTTGACTTCCC 59.391 52.381 0.00 0.00 32.50 3.97
905 962 2.033424 GTGGTTCTGCAACTTGACTTCC 59.967 50.000 0.00 0.00 32.50 3.46
906 963 2.945668 AGTGGTTCTGCAACTTGACTTC 59.054 45.455 0.00 0.00 32.50 3.01
907 964 2.945668 GAGTGGTTCTGCAACTTGACTT 59.054 45.455 0.00 0.00 29.75 3.01
908 965 2.565841 GAGTGGTTCTGCAACTTGACT 58.434 47.619 0.00 0.00 29.75 3.41
909 966 1.261619 CGAGTGGTTCTGCAACTTGAC 59.738 52.381 0.00 0.00 34.97 3.18
910 967 1.134521 ACGAGTGGTTCTGCAACTTGA 60.135 47.619 9.28 0.00 36.27 3.02
911 968 1.261619 GACGAGTGGTTCTGCAACTTG 59.738 52.381 1.82 1.82 38.31 3.16
912 969 1.583054 GACGAGTGGTTCTGCAACTT 58.417 50.000 0.00 0.00 29.75 2.66
913 970 0.249911 GGACGAGTGGTTCTGCAACT 60.250 55.000 0.00 0.00 33.05 3.16
914 971 1.557443 CGGACGAGTGGTTCTGCAAC 61.557 60.000 0.00 0.00 0.00 4.17
915 972 1.300620 CGGACGAGTGGTTCTGCAA 60.301 57.895 0.00 0.00 0.00 4.08
916 973 2.338620 CGGACGAGTGGTTCTGCA 59.661 61.111 0.00 0.00 0.00 4.41
917 974 3.112709 GCGGACGAGTGGTTCTGC 61.113 66.667 0.00 0.00 0.00 4.26
918 975 2.432628 GGCGGACGAGTGGTTCTG 60.433 66.667 0.00 0.00 0.00 3.02
919 976 2.504274 TTGGCGGACGAGTGGTTCT 61.504 57.895 0.00 0.00 0.00 3.01
980 1040 2.179517 GTCGACGGGAGCTCTGTG 59.820 66.667 14.64 6.27 34.56 3.66
1034 1094 0.460987 GCAGTGTTCGATCTCCAGGG 60.461 60.000 0.00 0.00 0.00 4.45
1059 1119 1.521681 GCGGCCGCTCTTGAATACT 60.522 57.895 41.71 0.00 38.26 2.12
1217 1277 1.067071 CGAGGACGGGTAGCTTCTTTT 60.067 52.381 0.00 0.00 35.72 2.27
1218 1278 0.531200 CGAGGACGGGTAGCTTCTTT 59.469 55.000 0.00 0.00 35.72 2.52
1910 1970 1.291877 ATCGTCGCAGGTGAAGTTGC 61.292 55.000 0.00 0.00 36.97 4.17
1912 1972 1.291877 GCATCGTCGCAGGTGAAGTT 61.292 55.000 0.00 0.00 0.00 2.66
1944 2004 1.971167 GAACCTGGCAATGGCGTCA 60.971 57.895 1.51 0.00 42.47 4.35
2057 2117 2.576191 ACCGATCAATCTTCTTCCCCAA 59.424 45.455 0.00 0.00 0.00 4.12
2098 2158 3.296322 TCAAATCCAATTCGGCACAAC 57.704 42.857 0.00 0.00 33.14 3.32
2186 2252 8.612619 GCTTGTTATGTTTGTACTGCTATATGT 58.387 33.333 0.00 0.00 0.00 2.29
2190 2256 6.429692 TGTGCTTGTTATGTTTGTACTGCTAT 59.570 34.615 0.00 0.00 0.00 2.97
2196 2262 4.675114 GCTGTGTGCTTGTTATGTTTGTAC 59.325 41.667 0.00 0.00 38.95 2.90
2197 2263 4.261405 GGCTGTGTGCTTGTTATGTTTGTA 60.261 41.667 0.00 0.00 42.39 2.41
2198 2264 3.490761 GGCTGTGTGCTTGTTATGTTTGT 60.491 43.478 0.00 0.00 42.39 2.83
2211 2277 4.082523 TAGAGGCCGGCTGTGTGC 62.083 66.667 28.56 8.41 41.94 4.57
2216 2282 0.392998 AACAATGTAGAGGCCGGCTG 60.393 55.000 28.56 16.55 0.00 4.85
2217 2283 1.139058 CTAACAATGTAGAGGCCGGCT 59.861 52.381 28.56 12.77 0.00 5.52
2218 2284 1.138266 TCTAACAATGTAGAGGCCGGC 59.862 52.381 21.18 21.18 0.00 6.13
2242 2308 3.696548 TGTTTGTTGATGTTGGCTGTGTA 59.303 39.130 0.00 0.00 0.00 2.90
2248 2314 2.886081 TGTGTGTTTGTTGATGTTGGC 58.114 42.857 0.00 0.00 0.00 4.52
2263 2329 2.908009 CGGCGTGTTTTATTCATGTGTG 59.092 45.455 0.00 0.00 0.00 3.82
2269 2336 0.952280 TTGCCGGCGTGTTTTATTCA 59.048 45.000 23.90 0.00 0.00 2.57
2300 2367 8.290325 GCTTTAGGCATAGTTTTGGTCATATAC 58.710 37.037 0.00 0.00 41.35 1.47
2303 2370 5.295787 CGCTTTAGGCATAGTTTTGGTCATA 59.704 40.000 0.00 0.00 41.91 2.15
2473 2553 4.314740 AGTCTTTGATAGTCAGATCCGC 57.685 45.455 0.00 0.00 0.00 5.54
2486 2566 9.877178 GATGAAAACCTAGAATCTAGTCTTTGA 57.123 33.333 15.40 9.04 0.00 2.69
2511 2591 4.341366 TGCTCAGACTTGTTCTTCATGA 57.659 40.909 0.00 0.00 28.96 3.07
2582 2662 0.819259 GACCTTGCCTCAGTTGCACA 60.819 55.000 0.00 0.00 38.72 4.57
2596 2676 1.071471 CAGACCAAGCACGGACCTT 59.929 57.895 0.00 0.00 0.00 3.50
2625 2708 2.792947 TAGGTCTTCGCGGGGATGC 61.793 63.158 6.13 0.00 0.00 3.91
2642 2725 2.617308 GGCGATACACTAGCTGACAGTA 59.383 50.000 3.99 0.00 0.00 2.74
2649 2732 2.857744 GCGGGGCGATACACTAGCT 61.858 63.158 0.00 0.00 0.00 3.32
2652 2735 1.755395 AGTGCGGGGCGATACACTA 60.755 57.895 0.00 0.00 41.41 2.74
2769 2858 1.283613 TGGGGACGAAATGTAGCCAAT 59.716 47.619 0.00 0.00 0.00 3.16
2845 2934 1.802960 GAGCACACACAATCTCCACAG 59.197 52.381 0.00 0.00 0.00 3.66
2849 2938 4.637534 ACAATATGAGCACACACAATCTCC 59.362 41.667 0.00 0.00 0.00 3.71
2857 2946 4.754322 ACGACATACAATATGAGCACACA 58.246 39.130 2.88 0.00 0.00 3.72
2858 2947 5.492854 CAACGACATACAATATGAGCACAC 58.507 41.667 2.88 0.00 0.00 3.82
2866 2955 5.756195 ATGCAAGCAACGACATACAATAT 57.244 34.783 0.00 0.00 0.00 1.28
2875 2964 2.132740 TTTGGAATGCAAGCAACGAC 57.867 45.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.