Multiple sequence alignment - TraesCS2D01G358300

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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 TraesCS2D01G358300 chr2D 100.000 2750 0 0 1 2750 460647891 460650640 0.000000e+00 5079
1 TraesCS2D01G358300 chr2D 88.644 317 34 2 1087 1402 125324464 125324779 4.300000e-103 385
2 TraesCS2D01G358300 chr2D 80.000 460 43 26 1935 2377 460643414 460643841 7.450000e-76 294
3 TraesCS2D01G358300 chr2B 93.699 2095 65 24 590 2663 541686592 541688640 0.000000e+00 3075
4 TraesCS2D01G358300 chr2B 84.600 513 52 12 60 546 541685823 541686334 4.120000e-133 484
5 TraesCS2D01G358300 chr2B 89.241 316 34 0 1087 1402 178338363 178338678 1.980000e-106 396
6 TraesCS2D01G358300 chr2A 95.151 1753 73 7 184 1933 603522877 603524620 0.000000e+00 2756
7 TraesCS2D01G358300 chr2A 89.387 848 32 18 1917 2750 603524835 603525638 0.000000e+00 1014
8 TraesCS2D01G358300 chr2A 88.013 317 36 2 1087 1402 131682859 131683174 9.300000e-100 374
9 TraesCS2D01G358300 chr2A 82.063 446 44 21 1935 2377 603516525 603516937 5.640000e-92 348
10 TraesCS2D01G358300 chr3D 89.420 293 31 0 1099 1391 6337870 6338162 1.200000e-98 370
11 TraesCS2D01G358300 chr3D 83.849 291 35 10 1096 1380 558292451 558292167 1.620000e-67 267
12 TraesCS2D01G358300 chr3B 88.737 293 33 0 1099 1391 7186981 7186689 2.600000e-95 359
13 TraesCS2D01G358300 chr3A 88.737 293 33 0 1099 1391 14044671 14044379 2.600000e-95 359


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 TraesCS2D01G358300 chr2D 460647891 460650640 2749 False 5079.0 5079 100.0000 1 2750 1 chr2D.!!$F3 2749
1 TraesCS2D01G358300 chr2B 541685823 541688640 2817 False 1779.5 3075 89.1495 60 2663 2 chr2B.!!$F2 2603
2 TraesCS2D01G358300 chr2A 603522877 603525638 2761 False 1885.0 2756 92.2690 184 2750 2 chr2A.!!$F3 2566

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
22 23 0.174845 TCTTAGTGCAATCCCGTCCG 59.825 55.0 0.00 0.0 0.0 4.79 F
58 59 0.322816 ACTCACATGTGTCATGGGCC 60.323 55.0 24.63 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1904 1.131315 GAAGGCAGCCTCGAAATCAAC 59.869 52.381 16.53 0.0 30.89 3.18 R
2039 2523 1.666872 GTACGCGCAGTCCTTTGGT 60.667 57.895 5.73 0.0 0.00 3.67 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
19 20 1.276622 ACCTCTTAGTGCAATCCCGT 58.723 50.000 0.00 0.00 0.00 5.28
20 21 1.207329 ACCTCTTAGTGCAATCCCGTC 59.793 52.381 0.00 0.00 0.00 4.79
21 22 1.473434 CCTCTTAGTGCAATCCCGTCC 60.473 57.143 0.00 0.00 0.00 4.79
22 23 0.174845 TCTTAGTGCAATCCCGTCCG 59.825 55.000 0.00 0.00 0.00 4.79
23 24 1.429148 CTTAGTGCAATCCCGTCCGC 61.429 60.000 0.00 0.00 0.00 5.54
24 25 1.895020 TTAGTGCAATCCCGTCCGCT 61.895 55.000 0.00 0.00 0.00 5.52
25 26 1.038681 TAGTGCAATCCCGTCCGCTA 61.039 55.000 0.00 0.00 0.00 4.26
26 27 1.448893 GTGCAATCCCGTCCGCTAA 60.449 57.895 0.00 0.00 0.00 3.09
27 28 1.448893 TGCAATCCCGTCCGCTAAC 60.449 57.895 0.00 0.00 0.00 2.34
28 29 2.178235 GCAATCCCGTCCGCTAACC 61.178 63.158 0.00 0.00 0.00 2.85
29 30 1.219664 CAATCCCGTCCGCTAACCA 59.780 57.895 0.00 0.00 0.00 3.67
30 31 0.810031 CAATCCCGTCCGCTAACCAG 60.810 60.000 0.00 0.00 0.00 4.00
31 32 2.588856 AATCCCGTCCGCTAACCAGC 62.589 60.000 0.00 0.00 44.90 4.85
46 47 6.992063 CTAACCAGCATTTTCTACTCACAT 57.008 37.500 0.00 0.00 0.00 3.21
47 48 5.633830 AACCAGCATTTTCTACTCACATG 57.366 39.130 0.00 0.00 0.00 3.21
48 49 4.655963 ACCAGCATTTTCTACTCACATGT 58.344 39.130 0.00 0.00 0.00 3.21
49 50 4.456911 ACCAGCATTTTCTACTCACATGTG 59.543 41.667 20.18 20.18 0.00 3.21
50 51 4.456911 CCAGCATTTTCTACTCACATGTGT 59.543 41.667 24.63 9.87 0.00 3.72
51 52 5.391310 CCAGCATTTTCTACTCACATGTGTC 60.391 44.000 24.63 2.39 0.00 3.67
52 53 5.179929 CAGCATTTTCTACTCACATGTGTCA 59.820 40.000 24.63 6.40 0.00 3.58
53 54 5.942236 AGCATTTTCTACTCACATGTGTCAT 59.058 36.000 24.63 13.80 0.00 3.06
54 55 6.025896 GCATTTTCTACTCACATGTGTCATG 58.974 40.000 24.63 15.27 0.00 3.07
55 56 6.549061 CATTTTCTACTCACATGTGTCATGG 58.451 40.000 24.63 13.30 0.00 3.66
56 57 3.893326 TCTACTCACATGTGTCATGGG 57.107 47.619 24.63 9.68 0.00 4.00
57 58 2.093500 TCTACTCACATGTGTCATGGGC 60.093 50.000 24.63 0.00 0.00 5.36
58 59 0.322816 ACTCACATGTGTCATGGGCC 60.323 55.000 24.63 0.00 0.00 5.80
59 60 1.001020 TCACATGTGTCATGGGCCC 60.001 57.895 24.63 17.59 0.00 5.80
60 61 2.045045 ACATGTGTCATGGGCCCG 60.045 61.111 19.37 3.22 0.00 6.13
61 62 2.271821 CATGTGTCATGGGCCCGA 59.728 61.111 19.37 6.23 0.00 5.14
62 63 1.378382 CATGTGTCATGGGCCCGAA 60.378 57.895 19.37 0.00 0.00 4.30
63 64 1.077501 ATGTGTCATGGGCCCGAAG 60.078 57.895 19.37 9.67 0.00 3.79
64 65 1.561769 ATGTGTCATGGGCCCGAAGA 61.562 55.000 19.37 12.21 0.00 2.87
65 66 1.745489 GTGTCATGGGCCCGAAGAC 60.745 63.158 25.87 25.87 0.00 3.01
66 67 2.220586 TGTCATGGGCCCGAAGACA 61.221 57.895 29.39 29.39 36.92 3.41
67 68 1.745489 GTCATGGGCCCGAAGACAC 60.745 63.158 27.00 11.88 0.00 3.67
68 69 1.918293 TCATGGGCCCGAAGACACT 60.918 57.895 19.37 0.00 0.00 3.55
69 70 0.616395 TCATGGGCCCGAAGACACTA 60.616 55.000 19.37 0.00 0.00 2.74
70 71 0.462047 CATGGGCCCGAAGACACTAC 60.462 60.000 19.37 0.00 0.00 2.73
74 75 1.673808 GGCCCGAAGACACTACCGAT 61.674 60.000 0.00 0.00 0.00 4.18
86 87 3.149981 CACTACCGATCTATGAGAGGCA 58.850 50.000 0.00 0.00 0.00 4.75
93 94 6.591935 ACCGATCTATGAGAGGCATTAAAAA 58.408 36.000 0.00 0.00 38.44 1.94
112 113 4.779993 AAAACTAGCCTGATAGAAGGGG 57.220 45.455 0.00 0.00 37.84 4.79
114 115 2.965562 ACTAGCCTGATAGAAGGGGAC 58.034 52.381 0.00 0.00 37.84 4.46
115 116 2.247635 ACTAGCCTGATAGAAGGGGACA 59.752 50.000 0.00 0.00 37.84 4.02
136 139 3.039011 ACCCCGCTCTTATAAGTCATGT 58.961 45.455 12.19 1.81 0.00 3.21
144 147 5.819901 GCTCTTATAAGTCATGTTCTGCCTT 59.180 40.000 12.19 0.00 0.00 4.35
148 151 5.690464 ATAAGTCATGTTCTGCCTTCTCT 57.310 39.130 0.00 0.00 0.00 3.10
156 159 3.582647 TGTTCTGCCTTCTCTCATAACCA 59.417 43.478 0.00 0.00 0.00 3.67
162 165 3.629398 GCCTTCTCTCATAACCAATGTGG 59.371 47.826 0.00 0.00 45.02 4.17
170 173 6.414732 TCTCATAACCAATGTGGGACTAAAG 58.585 40.000 0.00 0.00 43.37 1.85
172 175 2.969821 ACCAATGTGGGACTAAAGCA 57.030 45.000 0.00 0.00 43.37 3.91
182 185 4.037446 GTGGGACTAAAGCAAACATGAACA 59.963 41.667 0.00 0.00 0.00 3.18
222 248 8.697846 TTGGTTAGTAGATTAGTTGTTGATCG 57.302 34.615 0.00 0.00 0.00 3.69
236 262 5.041951 TGTTGATCGTGGCAGAATAAAAC 57.958 39.130 0.00 0.00 0.00 2.43
240 266 6.993786 TGATCGTGGCAGAATAAAACATAA 57.006 33.333 0.00 0.00 0.00 1.90
363 389 3.502123 AAAAAGGTTGTCCCTCATCGA 57.498 42.857 0.00 0.00 45.47 3.59
380 406 7.761704 CCCTCATCGATTCCACTAATGTATTAG 59.238 40.741 9.50 9.50 44.07 1.73
403 429 2.290896 CCTTGCCATTGACCTAGGAACA 60.291 50.000 17.98 12.39 0.00 3.18
429 455 4.514401 ACTCTTCGTTGATACCATTTCCC 58.486 43.478 0.00 0.00 0.00 3.97
441 467 1.065491 CCATTTCCCGAGGTGACATGA 60.065 52.381 0.00 0.00 0.00 3.07
472 498 4.380531 ACAACCTCATGTGAACTGTGTAG 58.619 43.478 0.00 0.00 30.82 2.74
549 575 5.670792 TCTCCATGTTTACGACTATGGTT 57.329 39.130 0.00 0.00 37.77 3.67
588 614 5.306678 GGGAAGGAGCTATGAGGATATATGG 59.693 48.000 0.00 0.00 0.00 2.74
602 842 8.278639 TGAGGATATATGGTTTTGTGTTATGGT 58.721 33.333 0.00 0.00 0.00 3.55
671 911 4.180946 CCTCCGGACTCTGCGTCG 62.181 72.222 0.00 0.00 43.79 5.12
726 966 1.679977 TCAAGGGAATGCAGCTGGC 60.680 57.895 17.12 8.54 45.13 4.85
727 967 1.681327 CAAGGGAATGCAGCTGGCT 60.681 57.895 17.12 0.00 45.15 4.75
939 1184 1.751351 CTGCCAGTACTACTGCTGCTA 59.249 52.381 10.36 1.80 44.63 3.49
940 1185 1.751351 TGCCAGTACTACTGCTGCTAG 59.249 52.381 10.36 0.00 44.63 3.42
941 1186 1.537135 GCCAGTACTACTGCTGCTAGC 60.537 57.143 8.10 8.10 44.63 3.42
942 1187 2.028130 CCAGTACTACTGCTGCTAGCT 58.972 52.381 17.23 0.00 44.63 3.32
943 1188 3.215151 CCAGTACTACTGCTGCTAGCTA 58.785 50.000 17.23 1.31 44.63 3.32
944 1189 3.252215 CCAGTACTACTGCTGCTAGCTAG 59.748 52.174 16.84 16.84 44.63 3.42
945 1190 3.304391 CAGTACTACTGCTGCTAGCTAGC 60.304 52.174 34.20 34.20 43.39 3.42
946 1191 5.518036 CAGTACTACTGCTGCTAGCTAGCT 61.518 50.000 38.07 23.12 43.44 3.32
947 1192 6.256996 CAGTACTACTGCTGCTAGCTAGCTA 61.257 48.000 38.07 25.78 43.44 3.32
948 1193 7.993166 CAGTACTACTGCTGCTAGCTAGCTAG 61.993 50.000 37.09 37.09 43.44 3.42
970 1223 1.215382 GCCGGCCTGGACATTTTTC 59.785 57.895 18.11 0.00 42.00 2.29
1903 2156 5.034797 GCGGTTCCAGTTATTATCTTTTGC 58.965 41.667 0.00 0.00 0.00 3.68
1909 2162 8.947115 GTTCCAGTTATTATCTTTTGCTACACT 58.053 33.333 0.00 0.00 0.00 3.55
1910 2163 9.515226 TTCCAGTTATTATCTTTTGCTACACTT 57.485 29.630 0.00 0.00 0.00 3.16
1911 2164 9.515226 TCCAGTTATTATCTTTTGCTACACTTT 57.485 29.630 0.00 0.00 0.00 2.66
1912 2165 9.559958 CCAGTTATTATCTTTTGCTACACTTTG 57.440 33.333 0.00 0.00 0.00 2.77
1976 2460 3.772387 TGGCACAATCCAGTTTATTCCA 58.228 40.909 0.00 0.00 31.92 3.53
1983 2467 7.377398 CACAATCCAGTTTATTCCACAATCAA 58.623 34.615 0.00 0.00 0.00 2.57
2014 2498 9.581099 CCGGTTAACAAAATTAATTAATCAGCT 57.419 29.630 11.08 0.00 0.00 4.24
2039 2523 7.946207 TGTAGCAATCAAAACTATTCAAACCA 58.054 30.769 0.00 0.00 0.00 3.67
2066 2551 1.979469 GACTGCGCGTACTAGCATATG 59.021 52.381 8.43 0.00 42.95 1.78
2128 2614 2.097825 GTCAGACCTTAAGCTCCCGTA 58.902 52.381 0.00 0.00 0.00 4.02
2129 2615 2.097825 TCAGACCTTAAGCTCCCGTAC 58.902 52.381 0.00 0.00 0.00 3.67
2130 2616 1.101331 AGACCTTAAGCTCCCGTACG 58.899 55.000 8.69 8.69 0.00 3.67
2131 2617 0.813821 GACCTTAAGCTCCCGTACGT 59.186 55.000 15.21 0.00 0.00 3.57
2283 2775 2.091055 AGAGCTAGGGATAAGAGTGGCA 60.091 50.000 0.00 0.00 0.00 4.92
2284 2776 2.036604 GAGCTAGGGATAAGAGTGGCAC 59.963 54.545 10.29 10.29 0.00 5.01
2285 2777 1.070914 GCTAGGGATAAGAGTGGCACC 59.929 57.143 15.27 5.99 0.00 5.01
2286 2778 2.683768 CTAGGGATAAGAGTGGCACCT 58.316 52.381 15.27 8.44 0.00 4.00
2287 2779 2.868964 AGGGATAAGAGTGGCACCTA 57.131 50.000 15.27 4.03 0.00 3.08
2288 2780 2.399580 AGGGATAAGAGTGGCACCTAC 58.600 52.381 15.27 6.49 0.00 3.18
2289 2781 2.022918 AGGGATAAGAGTGGCACCTACT 60.023 50.000 15.27 8.84 0.00 2.57
2290 2782 2.365941 GGGATAAGAGTGGCACCTACTC 59.634 54.545 15.27 5.17 43.77 2.59
2294 2786 1.219393 GAGTGGCACCTACTCTGGC 59.781 63.158 15.27 0.00 41.00 4.85
2365 2857 4.923281 TGCACAAGATACCATATTCGATCG 59.077 41.667 9.36 9.36 0.00 3.69
2384 2877 6.359883 TCGATCGAAGATATTTTTGCGAGTAG 59.640 38.462 16.99 0.00 45.12 2.57
2439 2932 8.080417 TGGCGTATGTATCTTCAAATAGTAGTC 58.920 37.037 0.00 0.00 0.00 2.59
2493 2997 0.709992 AGCTTGAGAGTCCTCCCTCT 59.290 55.000 0.00 0.00 44.44 3.69
2521 3025 3.119065 CCATGTATTGCACATTGGCTTCA 60.119 43.478 0.00 0.00 46.01 3.02
2562 3067 7.435068 AGTTAAGGCAATGTAAGTACAACAG 57.565 36.000 7.11 0.00 39.99 3.16
2608 3113 0.321298 GACGGCTAGGGCTTGTGAAA 60.321 55.000 0.00 0.00 38.73 2.69
2628 3133 0.550914 TGGCTTCTGGTGGTGTTCTT 59.449 50.000 0.00 0.00 0.00 2.52
2655 3160 1.865788 GCAGCGTTTCTTGATGCCCA 61.866 55.000 0.00 0.00 42.63 5.36
2661 3166 1.734420 TTTCTTGATGCCCACCCCCA 61.734 55.000 0.00 0.00 0.00 4.96
2663 3168 3.963124 CTTGATGCCCACCCCCACC 62.963 68.421 0.00 0.00 0.00 4.61
2705 3210 2.835764 ACGAATTAGGCTTGACCCACTA 59.164 45.455 0.00 0.00 40.58 2.74
2719 3224 5.302360 TGACCCACTATACAAAGTGTGTTC 58.698 41.667 0.00 0.00 44.45 3.18
2720 3225 5.163290 TGACCCACTATACAAAGTGTGTTCA 60.163 40.000 0.00 0.80 44.45 3.18
2737 3242 1.173913 TCAGATGATCGTCACGGTGT 58.826 50.000 17.13 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.207329 GACGGGATTGCACTAAGAGGT 59.793 52.381 0.00 0.00 0.00 3.85
1 2 1.473434 GGACGGGATTGCACTAAGAGG 60.473 57.143 0.00 0.00 0.00 3.69
2 3 1.802880 CGGACGGGATTGCACTAAGAG 60.803 57.143 0.00 0.00 0.00 2.85
3 4 0.174845 CGGACGGGATTGCACTAAGA 59.825 55.000 0.00 0.00 0.00 2.10
4 5 1.429148 GCGGACGGGATTGCACTAAG 61.429 60.000 0.00 0.00 0.00 2.18
5 6 1.448893 GCGGACGGGATTGCACTAA 60.449 57.895 0.00 0.00 0.00 2.24
6 7 1.038681 TAGCGGACGGGATTGCACTA 61.039 55.000 0.00 0.00 0.00 2.74
7 8 1.895020 TTAGCGGACGGGATTGCACT 61.895 55.000 0.00 0.00 0.00 4.40
8 9 1.448893 TTAGCGGACGGGATTGCAC 60.449 57.895 0.00 0.00 0.00 4.57
9 10 1.448893 GTTAGCGGACGGGATTGCA 60.449 57.895 0.00 0.00 0.00 4.08
10 11 2.178235 GGTTAGCGGACGGGATTGC 61.178 63.158 0.00 0.00 0.00 3.56
11 12 0.810031 CTGGTTAGCGGACGGGATTG 60.810 60.000 0.00 0.00 0.00 2.67
13 14 3.090219 GCTGGTTAGCGGACGGGAT 62.090 63.158 0.00 0.00 40.67 3.85
14 15 3.766691 GCTGGTTAGCGGACGGGA 61.767 66.667 0.00 0.00 40.67 5.14
23 24 6.372659 ACATGTGAGTAGAAAATGCTGGTTAG 59.627 38.462 0.00 0.00 0.00 2.34
24 25 6.149308 CACATGTGAGTAGAAAATGCTGGTTA 59.851 38.462 21.64 0.00 0.00 2.85
25 26 5.048504 CACATGTGAGTAGAAAATGCTGGTT 60.049 40.000 21.64 0.00 0.00 3.67
26 27 4.456911 CACATGTGAGTAGAAAATGCTGGT 59.543 41.667 21.64 0.00 0.00 4.00
27 28 4.456911 ACACATGTGAGTAGAAAATGCTGG 59.543 41.667 31.94 0.00 0.00 4.85
28 29 5.179929 TGACACATGTGAGTAGAAAATGCTG 59.820 40.000 31.94 0.00 0.00 4.41
29 30 5.308014 TGACACATGTGAGTAGAAAATGCT 58.692 37.500 31.94 4.57 0.00 3.79
30 31 5.611796 TGACACATGTGAGTAGAAAATGC 57.388 39.130 31.94 6.70 0.00 3.56
31 32 6.403964 CCCATGACACATGTGAGTAGAAAATG 60.404 42.308 31.94 18.90 0.00 2.32
32 33 5.649395 CCCATGACACATGTGAGTAGAAAAT 59.351 40.000 31.94 6.16 0.00 1.82
33 34 5.003160 CCCATGACACATGTGAGTAGAAAA 58.997 41.667 31.94 8.16 0.00 2.29
34 35 4.578871 CCCATGACACATGTGAGTAGAAA 58.421 43.478 31.94 9.16 0.00 2.52
35 36 3.619733 GCCCATGACACATGTGAGTAGAA 60.620 47.826 31.94 10.49 0.00 2.10
36 37 2.093500 GCCCATGACACATGTGAGTAGA 60.093 50.000 31.94 10.62 0.00 2.59
37 38 2.283298 GCCCATGACACATGTGAGTAG 58.717 52.381 31.94 17.26 0.00 2.57
38 39 1.065491 GGCCCATGACACATGTGAGTA 60.065 52.381 31.94 16.83 0.00 2.59
39 40 0.322816 GGCCCATGACACATGTGAGT 60.323 55.000 31.94 11.03 0.00 3.41
40 41 1.033746 GGGCCCATGACACATGTGAG 61.034 60.000 31.94 16.93 0.00 3.51
41 42 1.001020 GGGCCCATGACACATGTGA 60.001 57.895 31.94 11.45 0.00 3.58
42 43 2.409055 CGGGCCCATGACACATGTG 61.409 63.158 24.92 24.25 0.00 3.21
43 44 2.045045 CGGGCCCATGACACATGT 60.045 61.111 24.92 0.00 0.00 3.21
44 45 1.378382 TTCGGGCCCATGACACATG 60.378 57.895 24.92 1.11 0.00 3.21
45 46 1.077501 CTTCGGGCCCATGACACAT 60.078 57.895 24.92 0.00 0.00 3.21
46 47 2.220586 TCTTCGGGCCCATGACACA 61.221 57.895 24.92 0.00 0.00 3.72
47 48 1.745489 GTCTTCGGGCCCATGACAC 60.745 63.158 24.92 7.39 0.00 3.67
48 49 2.220586 TGTCTTCGGGCCCATGACA 61.221 57.895 27.46 27.46 35.62 3.58
49 50 1.745489 GTGTCTTCGGGCCCATGAC 60.745 63.158 24.92 24.33 0.00 3.06
50 51 0.616395 TAGTGTCTTCGGGCCCATGA 60.616 55.000 24.92 13.58 0.00 3.07
51 52 0.462047 GTAGTGTCTTCGGGCCCATG 60.462 60.000 24.92 11.16 0.00 3.66
52 53 1.623542 GGTAGTGTCTTCGGGCCCAT 61.624 60.000 24.92 0.00 0.00 4.00
53 54 2.288025 GGTAGTGTCTTCGGGCCCA 61.288 63.158 24.92 6.15 0.00 5.36
54 55 2.582978 GGTAGTGTCTTCGGGCCC 59.417 66.667 13.57 13.57 0.00 5.80
55 56 1.673808 ATCGGTAGTGTCTTCGGGCC 61.674 60.000 0.00 0.00 0.00 5.80
56 57 0.248949 GATCGGTAGTGTCTTCGGGC 60.249 60.000 0.00 0.00 0.00 6.13
57 58 1.390565 AGATCGGTAGTGTCTTCGGG 58.609 55.000 0.00 0.00 0.00 5.14
58 59 3.813724 TCATAGATCGGTAGTGTCTTCGG 59.186 47.826 0.00 0.00 0.00 4.30
59 60 4.750598 TCTCATAGATCGGTAGTGTCTTCG 59.249 45.833 0.00 0.00 0.00 3.79
60 61 5.180492 CCTCTCATAGATCGGTAGTGTCTTC 59.820 48.000 0.00 0.00 0.00 2.87
61 62 5.067273 CCTCTCATAGATCGGTAGTGTCTT 58.933 45.833 0.00 0.00 0.00 3.01
62 63 4.647611 CCTCTCATAGATCGGTAGTGTCT 58.352 47.826 0.00 0.00 0.00 3.41
63 64 3.189702 GCCTCTCATAGATCGGTAGTGTC 59.810 52.174 0.00 0.00 0.00 3.67
64 65 3.150767 GCCTCTCATAGATCGGTAGTGT 58.849 50.000 0.00 0.00 0.00 3.55
65 66 3.149981 TGCCTCTCATAGATCGGTAGTG 58.850 50.000 0.00 0.00 0.00 2.74
66 67 3.510531 TGCCTCTCATAGATCGGTAGT 57.489 47.619 0.00 0.00 0.00 2.73
67 68 6.516739 TTAATGCCTCTCATAGATCGGTAG 57.483 41.667 0.00 0.00 34.33 3.18
68 69 6.911250 TTTAATGCCTCTCATAGATCGGTA 57.089 37.500 0.00 0.00 34.33 4.02
69 70 5.808366 TTTAATGCCTCTCATAGATCGGT 57.192 39.130 0.00 0.00 34.33 4.69
93 94 3.310193 GTCCCCTTCTATCAGGCTAGTT 58.690 50.000 0.00 0.00 31.69 2.24
111 112 1.761198 ACTTATAAGAGCGGGGTGTCC 59.239 52.381 19.38 0.00 0.00 4.02
112 113 2.429610 TGACTTATAAGAGCGGGGTGTC 59.570 50.000 19.38 4.37 0.00 3.67
114 115 3.181465 ACATGACTTATAAGAGCGGGGTG 60.181 47.826 19.38 9.46 0.00 4.61
115 116 3.039011 ACATGACTTATAAGAGCGGGGT 58.961 45.455 19.38 6.49 0.00 4.95
119 122 4.210120 GGCAGAACATGACTTATAAGAGCG 59.790 45.833 19.38 6.89 32.26 5.03
136 139 4.908601 TTGGTTATGAGAGAAGGCAGAA 57.091 40.909 0.00 0.00 0.00 3.02
144 147 4.104086 AGTCCCACATTGGTTATGAGAGA 58.896 43.478 0.00 0.00 37.69 3.10
148 151 4.947388 GCTTTAGTCCCACATTGGTTATGA 59.053 41.667 0.00 0.00 37.69 2.15
156 159 4.832266 TCATGTTTGCTTTAGTCCCACATT 59.168 37.500 0.00 0.00 0.00 2.71
162 165 6.039616 TGTTTGTTCATGTTTGCTTTAGTCC 58.960 36.000 0.00 0.00 0.00 3.85
170 173 7.437862 TCTCCTTTATTGTTTGTTCATGTTTGC 59.562 33.333 0.00 0.00 0.00 3.68
212 238 4.678509 TTATTCTGCCACGATCAACAAC 57.321 40.909 0.00 0.00 0.00 3.32
380 406 1.559682 TCCTAGGTCAATGGCAAGGAC 59.440 52.381 9.08 12.03 0.00 3.85
381 407 1.965414 TCCTAGGTCAATGGCAAGGA 58.035 50.000 9.08 4.34 0.00 3.36
393 419 3.833070 ACGAAGAGTTGATGTTCCTAGGT 59.167 43.478 9.08 0.00 0.00 3.08
429 455 0.390340 CCACCACTCATGTCACCTCG 60.390 60.000 0.00 0.00 0.00 4.63
441 467 0.538057 CATGAGGTTGTGCCACCACT 60.538 55.000 0.00 0.00 42.54 4.00
485 511 2.024176 GCTAGTGCTCCGAAATTCCA 57.976 50.000 0.00 0.00 36.03 3.53
530 556 4.266976 GTCGAACCATAGTCGTAAACATGG 59.733 45.833 0.00 0.00 40.00 3.66
532 558 4.100529 CGTCGAACCATAGTCGTAAACAT 58.899 43.478 0.00 0.00 0.00 2.71
549 575 4.772231 CCCCCTCCCCTTCGTCGA 62.772 72.222 0.00 0.00 0.00 4.20
602 842 3.371168 GTTCGCTTTGAGATTTGTGCAA 58.629 40.909 0.00 0.00 0.00 4.08
671 911 2.044832 GATGGCTGTGTGCATCGCTC 62.045 60.000 0.00 0.00 45.15 5.03
726 966 9.154847 CCTTATTTCCCTGCTCAAAATTAAAAG 57.845 33.333 0.00 0.00 0.00 2.27
727 967 8.655901 ACCTTATTTCCCTGCTCAAAATTAAAA 58.344 29.630 0.00 0.00 0.00 1.52
945 1190 2.521950 TCCAGGCCGGCTAGCTAG 60.522 66.667 28.56 16.84 33.14 3.42
946 1191 2.838225 GTCCAGGCCGGCTAGCTA 60.838 66.667 28.56 5.61 33.14 3.32
948 1193 2.893682 AAATGTCCAGGCCGGCTAGC 62.894 60.000 28.56 10.16 33.14 3.42
949 1194 0.394352 AAAATGTCCAGGCCGGCTAG 60.394 55.000 28.56 18.78 33.14 3.42
950 1195 0.039035 AAAAATGTCCAGGCCGGCTA 59.961 50.000 28.56 6.83 33.14 3.93
951 1196 1.228862 AAAAATGTCCAGGCCGGCT 60.229 52.632 28.56 9.77 33.14 5.52
952 1197 1.215382 GAAAAATGTCCAGGCCGGC 59.785 57.895 21.18 21.18 33.14 6.13
953 1198 0.527565 CAGAAAAATGTCCAGGCCGG 59.472 55.000 0.00 0.00 0.00 6.13
970 1223 1.593296 GCTGCCCCTCTTTTGCTCAG 61.593 60.000 0.00 0.00 0.00 3.35
1651 1904 1.131315 GAAGGCAGCCTCGAAATCAAC 59.869 52.381 16.53 0.00 30.89 3.18
1909 2162 9.220635 CATCGCTCGAATATTTCATTAAACAAA 57.779 29.630 0.00 0.00 0.00 2.83
1910 2163 8.394877 ACATCGCTCGAATATTTCATTAAACAA 58.605 29.630 0.00 0.00 0.00 2.83
1911 2164 7.850492 CACATCGCTCGAATATTTCATTAAACA 59.150 33.333 0.00 0.00 0.00 2.83
1912 2165 7.149288 GCACATCGCTCGAATATTTCATTAAAC 60.149 37.037 0.00 0.00 37.77 2.01
1976 2460 6.642707 TTTGTTAACCGGAGATTTGATTGT 57.357 33.333 9.46 0.00 0.00 2.71
2014 2498 7.865385 GTGGTTTGAATAGTTTTGATTGCTACA 59.135 33.333 0.00 0.00 0.00 2.74
2039 2523 1.666872 GTACGCGCAGTCCTTTGGT 60.667 57.895 5.73 0.00 0.00 3.67
2066 2551 4.102035 CAGGCTTTGCACTAGGAAAATC 57.898 45.455 0.00 0.00 34.53 2.17
2128 2614 6.112734 TCATTGCTTAGATTAACCATGACGT 58.887 36.000 0.00 0.00 0.00 4.34
2129 2615 6.603237 TCATTGCTTAGATTAACCATGACG 57.397 37.500 0.00 0.00 0.00 4.35
2130 2616 8.213518 TCTTCATTGCTTAGATTAACCATGAC 57.786 34.615 0.00 0.00 0.00 3.06
2131 2617 8.806429 TTCTTCATTGCTTAGATTAACCATGA 57.194 30.769 0.00 0.00 0.00 3.07
2152 2638 5.544176 TGAGGACAACTTGGATACTCTTCTT 59.456 40.000 0.00 0.00 37.61 2.52
2153 2639 5.046950 GTGAGGACAACTTGGATACTCTTCT 60.047 44.000 0.00 0.00 37.61 2.85
2252 2744 3.458044 TCCCTAGCTCTCTCACAGAAA 57.542 47.619 0.00 0.00 0.00 2.52
2283 2775 0.707616 AGAGAGGTGCCAGAGTAGGT 59.292 55.000 0.00 0.00 0.00 3.08
2284 2776 1.341482 TGAGAGAGGTGCCAGAGTAGG 60.341 57.143 0.00 0.00 0.00 3.18
2285 2777 1.748493 GTGAGAGAGGTGCCAGAGTAG 59.252 57.143 0.00 0.00 0.00 2.57
2286 2778 1.075536 TGTGAGAGAGGTGCCAGAGTA 59.924 52.381 0.00 0.00 0.00 2.59
2287 2779 0.178950 TGTGAGAGAGGTGCCAGAGT 60.179 55.000 0.00 0.00 0.00 3.24
2288 2780 0.972134 TTGTGAGAGAGGTGCCAGAG 59.028 55.000 0.00 0.00 0.00 3.35
2289 2781 1.277273 CATTGTGAGAGAGGTGCCAGA 59.723 52.381 0.00 0.00 0.00 3.86
2290 2782 1.277273 TCATTGTGAGAGAGGTGCCAG 59.723 52.381 0.00 0.00 0.00 4.85
2291 2783 1.002430 GTCATTGTGAGAGAGGTGCCA 59.998 52.381 0.00 0.00 0.00 4.92
2292 2784 1.677217 GGTCATTGTGAGAGAGGTGCC 60.677 57.143 0.00 0.00 0.00 5.01
2293 2785 1.677217 GGGTCATTGTGAGAGAGGTGC 60.677 57.143 0.00 0.00 0.00 5.01
2294 2786 1.905215 AGGGTCATTGTGAGAGAGGTG 59.095 52.381 0.00 0.00 0.00 4.00
2365 2857 6.017934 TGCCATCTACTCGCAAAAATATCTTC 60.018 38.462 0.00 0.00 0.00 2.87
2439 2932 7.755582 ACATTTTTCTTTGAAAAGGACTTCG 57.244 32.000 3.08 0.00 34.81 3.79
2493 2997 2.785540 TGTGCAATACATGGAGAGCA 57.214 45.000 3.10 3.10 33.42 4.26
2562 3067 6.259608 CCATGAAGGTGTGATCTATTTCAGAC 59.740 42.308 0.00 0.00 38.74 3.51
2608 3113 0.773644 AGAACACCACCAGAAGCCAT 59.226 50.000 0.00 0.00 0.00 4.40
2670 3175 0.833287 ATTCGTGACTCATGAGGGGG 59.167 55.000 26.08 12.37 30.69 5.40
2671 3176 2.698855 AATTCGTGACTCATGAGGGG 57.301 50.000 26.08 12.04 30.69 4.79
2672 3177 3.722147 CCTAATTCGTGACTCATGAGGG 58.278 50.000 26.08 12.38 30.69 4.30
2673 3178 3.126831 GCCTAATTCGTGACTCATGAGG 58.873 50.000 26.08 8.89 30.69 3.86
2674 3179 4.052159 AGCCTAATTCGTGACTCATGAG 57.948 45.455 21.37 21.37 30.69 2.90
2675 3180 4.081697 TCAAGCCTAATTCGTGACTCATGA 60.082 41.667 0.00 0.00 0.00 3.07
2676 3181 4.033358 GTCAAGCCTAATTCGTGACTCATG 59.967 45.833 5.00 0.00 39.00 3.07
2677 3182 4.184629 GTCAAGCCTAATTCGTGACTCAT 58.815 43.478 5.00 0.00 39.00 2.90
2678 3183 3.585862 GTCAAGCCTAATTCGTGACTCA 58.414 45.455 5.00 0.00 39.00 3.41
2679 3184 2.930682 GGTCAAGCCTAATTCGTGACTC 59.069 50.000 10.12 0.77 40.87 3.36
2680 3185 2.354805 GGGTCAAGCCTAATTCGTGACT 60.355 50.000 10.12 0.00 40.87 3.41
2681 3186 2.007608 GGGTCAAGCCTAATTCGTGAC 58.992 52.381 3.97 3.97 40.53 3.67
2682 3187 1.626321 TGGGTCAAGCCTAATTCGTGA 59.374 47.619 0.00 0.00 37.43 4.35
2683 3188 1.737793 GTGGGTCAAGCCTAATTCGTG 59.262 52.381 0.00 0.00 37.43 4.35
2684 3189 1.628846 AGTGGGTCAAGCCTAATTCGT 59.371 47.619 0.00 0.00 37.43 3.85
2705 3210 6.166279 ACGATCATCTGAACACACTTTGTAT 58.834 36.000 0.00 0.00 37.51 2.29
2719 3224 1.920574 GAACACCGTGACGATCATCTG 59.079 52.381 6.54 0.00 0.00 2.90
2720 3225 1.544246 TGAACACCGTGACGATCATCT 59.456 47.619 6.54 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.