Multiple sequence alignment - TraesCS5D01G447000

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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 TraesCS5D01G447000 chr5D 100.000 2507 0 0 1 2507 497037498 497040004 0.000000e+00 4630.0
1 TraesCS5D01G447000 chr5D 93.830 1637 82 9 882 2507 497103852 497105480 0.000000e+00 2446.0
2 TraesCS5D01G447000 chr5D 83.333 312 35 7 491 787 497019071 497019380 3.180000e-69 272.0
3 TraesCS5D01G447000 chr5D 97.059 34 1 0 484 517 528613327 528613360 9.690000e-05 58.4
4 TraesCS5D01G447000 chr5D 96.970 33 1 0 484 516 325894332 325894300 3.480000e-04 56.5
5 TraesCS5D01G447000 chrUn 93.830 1637 82 9 882 2507 302517447 302519075 0.000000e+00 2446.0
6 TraesCS5D01G447000 chrUn 93.769 1637 83 9 882 2507 68274173 68272545 0.000000e+00 2440.0
7 TraesCS5D01G447000 chr5B 92.474 1568 74 15 535 2098 615950635 615952162 0.000000e+00 2202.0
8 TraesCS5D01G447000 chr5B 91.160 1629 114 15 882 2507 616310480 616312081 0.000000e+00 2183.0
9 TraesCS5D01G447000 chr5B 91.160 1629 114 15 882 2507 616322116 616323717 0.000000e+00 2183.0
10 TraesCS5D01G447000 chr5B 90.915 1629 118 15 882 2507 616265631 616267232 0.000000e+00 2161.0
11 TraesCS5D01G447000 chr5B 90.915 1629 118 15 882 2507 616276552 616278153 0.000000e+00 2161.0
12 TraesCS5D01G447000 chr5B 90.915 1629 117 16 882 2507 616245867 616247467 0.000000e+00 2159.0
13 TraesCS5D01G447000 chr5B 90.731 1629 117 19 882 2507 616223294 616224891 0.000000e+00 2141.0
14 TraesCS5D01G447000 chr5B 85.242 393 40 6 1 392 615948284 615948659 3.020000e-104 388.0
15 TraesCS5D01G447000 chr5B 93.038 158 9 2 381 537 615950296 615950452 1.940000e-56 230.0
16 TraesCS5D01G447000 chr5A 80.311 386 44 15 612 994 621228626 621228982 1.910000e-66 263.0
17 TraesCS5D01G447000 chr5A 97.143 35 0 1 484 517 450879424 450879390 9.690000e-05 58.4
18 TraesCS5D01G447000 chr7A 100.000 31 0 0 484 514 70830140 70830110 9.690000e-05 58.4
19 TraesCS5D01G447000 chr6B 97.059 34 1 0 484 517 84048 84015 9.690000e-05 58.4
20 TraesCS5D01G447000 chr1D 97.059 34 1 0 484 517 249561626 249561593 9.690000e-05 58.4
21 TraesCS5D01G447000 chr7B 94.444 36 2 0 484 519 687105394 687105429 3.480000e-04 56.5
22 TraesCS5D01G447000 chr1A 96.970 33 1 0 483 515 499636451 499636419 3.480000e-04 56.5


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 TraesCS5D01G447000 chr5D 497037498 497040004 2506 False 4630 4630 100.000000 1 2507 1 chr5D.!!$F2 2506
1 TraesCS5D01G447000 chr5D 497103852 497105480 1628 False 2446 2446 93.830000 882 2507 1 chr5D.!!$F3 1625
2 TraesCS5D01G447000 chrUn 302517447 302519075 1628 False 2446 2446 93.830000 882 2507 1 chrUn.!!$F1 1625
3 TraesCS5D01G447000 chrUn 68272545 68274173 1628 True 2440 2440 93.769000 882 2507 1 chrUn.!!$R1 1625
4 TraesCS5D01G447000 chr5B 616310480 616312081 1601 False 2183 2183 91.160000 882 2507 1 chr5B.!!$F5 1625
5 TraesCS5D01G447000 chr5B 616322116 616323717 1601 False 2183 2183 91.160000 882 2507 1 chr5B.!!$F6 1625
6 TraesCS5D01G447000 chr5B 616265631 616267232 1601 False 2161 2161 90.915000 882 2507 1 chr5B.!!$F3 1625
7 TraesCS5D01G447000 chr5B 616276552 616278153 1601 False 2161 2161 90.915000 882 2507 1 chr5B.!!$F4 1625
8 TraesCS5D01G447000 chr5B 616245867 616247467 1600 False 2159 2159 90.915000 882 2507 1 chr5B.!!$F2 1625
9 TraesCS5D01G447000 chr5B 616223294 616224891 1597 False 2141 2141 90.731000 882 2507 1 chr5B.!!$F1 1625
10 TraesCS5D01G447000 chr5B 615948284 615952162 3878 False 940 2202 90.251333 1 2098 3 chr5B.!!$F7 2097

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
822 2659 0.179094 CGACGGCTGGCCAACTATAA 60.179 55.0 7.01 0.0 35.37 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 3932 0.033796 TCCGGAACCTACGATGGACT 60.034 55.0 0.0 0.0 0.0 3.85 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
44 45 1.143183 ATACGGACGGATGTGTGGC 59.857 57.895 0.00 0.00 0.00 5.01
46 47 4.735132 CGGACGGATGTGTGGCGT 62.735 66.667 0.00 0.00 0.00 5.68
47 48 2.813908 GGACGGATGTGTGGCGTC 60.814 66.667 0.00 0.00 0.00 5.19
104 105 2.035237 TTAATGGAGGTAGGCGGGCG 62.035 60.000 0.00 0.00 0.00 6.13
121 122 1.813753 CGGACGGATGCCATTTCGT 60.814 57.895 6.71 6.71 38.62 3.85
124 125 1.083489 GACGGATGCCATTTCGTTGA 58.917 50.000 8.09 0.00 35.91 3.18
135 136 3.365364 CCATTTCGTTGAGGAGCAAAGAC 60.365 47.826 0.00 0.00 43.15 3.01
144 145 1.722507 GAGCAAAGACGCGTGCAAC 60.723 57.895 20.70 8.63 43.42 4.17
180 181 3.736100 CACGCCGCTTCAATGCCA 61.736 61.111 0.00 0.00 0.00 4.92
189 190 2.677836 CGCTTCAATGCCAGCTTTAGTA 59.322 45.455 3.38 0.00 33.52 1.82
207 208 1.736681 GTAAGAGGTCGTGTACGCTCT 59.263 52.381 4.67 8.20 37.35 4.09
214 215 2.875485 GTGTACGCTCTGAGCCGA 59.125 61.111 22.97 8.95 38.18 5.54
218 219 1.746787 TGTACGCTCTGAGCCGAAATA 59.253 47.619 22.97 6.18 38.18 1.40
251 252 0.677731 CCGCATCAGGCAGAAAAGGA 60.678 55.000 0.00 0.00 45.17 3.36
253 254 0.449388 GCATCAGGCAGAAAAGGACG 59.551 55.000 0.00 0.00 43.97 4.79
254 255 1.813513 CATCAGGCAGAAAAGGACGT 58.186 50.000 0.00 0.00 0.00 4.34
257 258 1.073199 AGGCAGAAAAGGACGTGGG 59.927 57.895 0.00 0.00 0.00 4.61
259 260 1.896660 GCAGAAAAGGACGTGGGCA 60.897 57.895 0.00 0.00 0.00 5.36
269 270 4.722700 CGTGGGCAAGGGAGTGGG 62.723 72.222 0.00 0.00 0.00 4.61
295 296 2.557490 GGGTACATGCCCGTGTTAAAAA 59.443 45.455 0.00 0.00 39.17 1.94
328 329 2.028476 CCGGATAGCATGGTCGGATAAA 60.028 50.000 16.15 0.00 42.94 1.40
361 362 0.966920 GGCCTAGCCTAAGCATCGTA 59.033 55.000 0.00 0.00 46.69 3.43
407 2058 9.709495 AAAAACAGTACATTGATGCAATAATGT 57.291 25.926 25.50 25.50 46.14 2.71
482 2133 5.046231 GGATAAATCATACTCCCTCTGTCCC 60.046 48.000 0.00 0.00 0.00 4.46
501 2152 5.533154 TGTCCCAACGCTTTTATATTATGGG 59.467 40.000 0.00 0.00 46.13 4.00
504 2155 5.685841 CCAACGCTTTTATATTATGGGACG 58.314 41.667 0.00 0.00 0.00 4.79
508 2159 4.630069 CGCTTTTATATTATGGGACGGAGG 59.370 45.833 0.00 0.00 0.00 4.30
523 2174 1.065418 CGGAGGGAATACTTGCCAACT 60.065 52.381 0.16 0.00 44.70 3.16
530 2181 1.442769 ATACTTGCCAACTGAGCACG 58.557 50.000 0.00 0.00 40.69 5.34
626 2462 3.004862 TGCTACAAGATGACACATGCAG 58.995 45.455 0.00 0.00 0.00 4.41
749 2585 3.756069 GCTTGACAGCTGCAGATAAAAG 58.244 45.455 20.43 15.91 43.51 2.27
750 2586 3.190118 GCTTGACAGCTGCAGATAAAAGT 59.810 43.478 20.43 4.88 43.51 2.66
751 2587 4.393062 GCTTGACAGCTGCAGATAAAAGTA 59.607 41.667 20.43 0.00 43.51 2.24
752 2588 5.672321 GCTTGACAGCTGCAGATAAAAGTAC 60.672 44.000 20.43 0.00 43.51 2.73
753 2589 4.893608 TGACAGCTGCAGATAAAAGTACA 58.106 39.130 20.43 3.36 0.00 2.90
810 2647 2.684001 TGTATTGGAAATCGACGGCT 57.316 45.000 0.00 0.00 0.00 5.52
811 2648 2.276201 TGTATTGGAAATCGACGGCTG 58.724 47.619 0.00 0.00 0.00 4.85
812 2649 1.597663 GTATTGGAAATCGACGGCTGG 59.402 52.381 0.00 0.00 0.00 4.85
813 2650 1.376609 ATTGGAAATCGACGGCTGGC 61.377 55.000 0.00 0.00 0.00 4.85
814 2651 3.202706 GGAAATCGACGGCTGGCC 61.203 66.667 0.00 0.00 0.00 5.36
815 2652 2.435938 GAAATCGACGGCTGGCCA 60.436 61.111 4.71 4.71 35.37 5.36
816 2653 2.033448 AAATCGACGGCTGGCCAA 59.967 55.556 7.01 0.00 35.37 4.52
817 2654 2.253414 GAAATCGACGGCTGGCCAAC 62.253 60.000 7.01 0.65 35.37 3.77
818 2655 2.748058 AAATCGACGGCTGGCCAACT 62.748 55.000 7.01 0.00 35.37 3.16
819 2656 1.895020 AATCGACGGCTGGCCAACTA 61.895 55.000 7.01 0.00 35.37 2.24
820 2657 1.686325 ATCGACGGCTGGCCAACTAT 61.686 55.000 7.01 0.00 35.37 2.12
821 2658 1.038681 TCGACGGCTGGCCAACTATA 61.039 55.000 7.01 0.00 35.37 1.31
822 2659 0.179094 CGACGGCTGGCCAACTATAA 60.179 55.000 7.01 0.00 35.37 0.98
823 2660 1.540363 CGACGGCTGGCCAACTATAAT 60.540 52.381 7.01 0.00 35.37 1.28
824 2661 2.572290 GACGGCTGGCCAACTATAATT 58.428 47.619 7.01 0.00 35.37 1.40
864 2701 7.120923 TGGCGAGGTACTTTTTCTCTATTAT 57.879 36.000 0.00 0.00 41.55 1.28
865 2702 7.562135 TGGCGAGGTACTTTTTCTCTATTATT 58.438 34.615 0.00 0.00 41.55 1.40
866 2703 8.698210 TGGCGAGGTACTTTTTCTCTATTATTA 58.302 33.333 0.00 0.00 41.55 0.98
911 2748 1.134310 TCGATGATCTTGTGCAGGCAT 60.134 47.619 0.00 0.00 0.00 4.40
959 2796 4.162888 TGGCAGTCTATCTCATTGTCACAT 59.837 41.667 0.00 0.00 0.00 3.21
1033 2871 1.469940 CGAAGCTAGCAGTAGTGGTGG 60.470 57.143 18.83 10.52 35.51 4.61
1518 3356 4.046938 CCCGTACTAGGCTATATGCATG 57.953 50.000 10.16 0.00 45.15 4.06
1599 3446 4.248058 CTGTGATAACTGCAGTGTGATCA 58.752 43.478 22.49 23.94 0.00 2.92
1600 3447 4.248058 TGTGATAACTGCAGTGTGATCAG 58.752 43.478 27.23 1.64 0.00 2.90
1612 3459 5.634439 GCAGTGTGATCAGAGATGTGATATC 59.366 44.000 0.00 0.00 37.29 1.63
1718 3566 6.764085 AGTTGTGTTATTGTACAAGCAGTGTA 59.236 34.615 14.65 0.00 41.98 2.90
1777 3626 1.067635 GGTATTTGTGCCTTGCTGTGG 60.068 52.381 0.00 0.00 0.00 4.17
1778 3627 1.067635 GTATTTGTGCCTTGCTGTGGG 60.068 52.381 0.00 0.00 0.00 4.61
1782 3631 1.363807 GTGCCTTGCTGTGGGAAAC 59.636 57.895 0.00 0.00 0.00 2.78
1784 3633 0.685785 TGCCTTGCTGTGGGAAACAA 60.686 50.000 0.00 0.00 38.67 2.83
1785 3634 0.249447 GCCTTGCTGTGGGAAACAAC 60.249 55.000 0.00 0.00 38.67 3.32
1807 3656 3.214328 CCCAGCATACATAGAAACCACC 58.786 50.000 0.00 0.00 0.00 4.61
1826 3675 5.422012 ACCACCAATCAAAGTGTCTTTCTTT 59.578 36.000 0.00 0.00 35.82 2.52
1868 3717 8.482429 CACTTGTTCTTTATGTTCTGCATTTTC 58.518 33.333 0.00 0.00 38.94 2.29
1954 3804 2.124487 AGACTCTCGCTCCCTCCG 60.124 66.667 0.00 0.00 0.00 4.63
1956 3806 4.434354 ACTCTCGCTCCCTCCGCT 62.434 66.667 0.00 0.00 0.00 5.52
2033 3883 0.494551 TCCCCTCCCAGGTTTCACTA 59.505 55.000 0.00 0.00 31.93 2.74
2042 3892 3.053693 CCCAGGTTTCACTATGGATCCAA 60.054 47.826 20.67 7.48 34.60 3.53
2068 3918 2.980233 GCGGTCCAGTGCAAGCTT 60.980 61.111 0.00 0.00 0.00 3.74
2082 3932 0.179009 AAGCTTGCTCTCAACCAGCA 60.179 50.000 0.00 0.00 45.32 4.41
2202 4052 1.466856 CATGCATGCCTGTGGTACTT 58.533 50.000 14.93 0.00 0.00 2.24
2215 4065 0.105039 GGTACTTCGGATCTGGGCAG 59.895 60.000 0.62 0.00 0.00 4.85
2257 4107 1.511613 AATCCATCGTGGTCATCCCT 58.488 50.000 4.33 0.00 39.03 4.20
2273 4123 1.291877 CCCTTCCGCTCTTGTCAACG 61.292 60.000 0.00 0.00 0.00 4.10
2280 4130 2.400399 CGCTCTTGTCAACGTTTCCTA 58.600 47.619 0.00 0.00 0.00 2.94
2305 4155 1.945354 GCGAGGACGAAGGATGGACA 61.945 60.000 0.00 0.00 42.66 4.02
2322 4172 3.199946 TGGACAAAGCTCTAATCCCGAAT 59.800 43.478 0.00 0.00 0.00 3.34
2331 4181 4.503910 CTCTAATCCCGAATGAACACACA 58.496 43.478 0.00 0.00 0.00 3.72
2338 4188 2.872245 CCGAATGAACACACAGACAAGT 59.128 45.455 0.00 0.00 0.00 3.16
2380 4230 0.457853 CGCACGTACAGCTACACCAT 60.458 55.000 5.84 0.00 0.00 3.55
2382 4232 2.073816 GCACGTACAGCTACACCATTT 58.926 47.619 0.00 0.00 0.00 2.32
2393 4243 1.671054 CACCATTTGGACCGACGCT 60.671 57.895 3.01 0.00 38.94 5.07
2444 4294 3.005791 GGCCTTCTTAAGCTGCTTCAAAA 59.994 43.478 19.62 7.04 0.00 2.44
2445 4295 4.322273 GGCCTTCTTAAGCTGCTTCAAAAT 60.322 41.667 19.62 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.813908 GACGCCACACATCCGTCC 60.814 66.667 1.34 0.00 43.89 4.79
34 35 2.047655 TTCGGACGCCACACATCC 60.048 61.111 0.00 0.00 0.00 3.51
44 45 2.228343 ACCTACTTTGACTCTTCGGACG 59.772 50.000 0.00 0.00 0.00 4.79
46 47 3.257624 GGAACCTACTTTGACTCTTCGGA 59.742 47.826 0.00 0.00 0.00 4.55
47 48 3.258622 AGGAACCTACTTTGACTCTTCGG 59.741 47.826 0.00 0.00 0.00 4.30
48 49 4.487019 GAGGAACCTACTTTGACTCTTCG 58.513 47.826 0.00 0.00 0.00 3.79
50 51 3.258622 CCGAGGAACCTACTTTGACTCTT 59.741 47.826 0.00 0.00 0.00 2.85
104 105 0.098728 CAACGAAATGGCATCCGTCC 59.901 55.000 22.13 2.48 33.84 4.79
108 109 1.672881 CTCCTCAACGAAATGGCATCC 59.327 52.381 0.00 0.00 0.00 3.51
115 116 2.480419 CGTCTTTGCTCCTCAACGAAAT 59.520 45.455 0.00 0.00 35.17 2.17
121 122 1.069090 ACGCGTCTTTGCTCCTCAA 59.931 52.632 5.58 0.00 0.00 3.02
124 125 3.044305 GCACGCGTCTTTGCTCCT 61.044 61.111 9.86 0.00 35.74 3.69
163 164 3.672255 CTGGCATTGAAGCGGCGTG 62.672 63.158 9.37 0.00 34.64 5.34
164 165 3.434319 CTGGCATTGAAGCGGCGT 61.434 61.111 9.37 0.00 34.64 5.68
165 166 4.842091 GCTGGCATTGAAGCGGCG 62.842 66.667 0.51 0.51 34.64 6.46
166 167 2.496828 AAAGCTGGCATTGAAGCGGC 62.497 55.000 0.00 0.00 44.34 6.53
167 168 0.810648 TAAAGCTGGCATTGAAGCGG 59.189 50.000 0.00 0.00 44.34 5.52
178 179 3.056749 ACACGACCTCTTACTAAAGCTGG 60.057 47.826 0.00 0.00 34.37 4.85
179 180 4.175787 ACACGACCTCTTACTAAAGCTG 57.824 45.455 0.00 0.00 32.36 4.24
180 181 4.142730 CGTACACGACCTCTTACTAAAGCT 60.143 45.833 0.00 0.00 43.02 3.74
189 190 0.522180 CAGAGCGTACACGACCTCTT 59.478 55.000 5.84 0.00 43.02 2.85
214 215 1.268335 CGGTTAGCGCCGCATTTATTT 60.268 47.619 13.36 0.00 45.47 1.40
235 236 1.466167 CACGTCCTTTTCTGCCTGATG 59.534 52.381 0.00 0.00 0.00 3.07
236 237 1.611673 CCACGTCCTTTTCTGCCTGAT 60.612 52.381 0.00 0.00 0.00 2.90
238 239 1.237285 CCCACGTCCTTTTCTGCCTG 61.237 60.000 0.00 0.00 0.00 4.85
239 240 1.073199 CCCACGTCCTTTTCTGCCT 59.927 57.895 0.00 0.00 0.00 4.75
251 252 3.953775 CCACTCCCTTGCCCACGT 61.954 66.667 0.00 0.00 0.00 4.49
253 254 2.656698 AAACCCACTCCCTTGCCCAC 62.657 60.000 0.00 0.00 0.00 4.61
254 255 1.955458 AAAACCCACTCCCTTGCCCA 61.955 55.000 0.00 0.00 0.00 5.36
257 258 1.471829 CCCAAAACCCACTCCCTTGC 61.472 60.000 0.00 0.00 0.00 4.01
259 260 1.146359 GTACCCAAAACCCACTCCCTT 59.854 52.381 0.00 0.00 0.00 3.95
288 289 2.098258 CGGACGCGTTTTGCTTTTTAAC 60.098 45.455 15.53 0.00 43.27 2.01
291 292 0.868177 CCGGACGCGTTTTGCTTTTT 60.868 50.000 15.53 0.00 43.27 1.94
295 296 1.079681 TATCCGGACGCGTTTTGCT 60.080 52.632 15.53 1.07 43.27 3.91
348 349 3.809832 ACATCAATGTACGATGCTTAGGC 59.190 43.478 8.60 0.00 43.36 3.93
361 362 2.897271 TTGGCAGGGTACATCAATGT 57.103 45.000 0.70 0.70 44.48 2.71
385 2036 7.553760 TCAGACATTATTGCATCAATGTACTGT 59.446 33.333 26.51 13.28 43.58 3.55
386 2037 7.922837 TCAGACATTATTGCATCAATGTACTG 58.077 34.615 24.71 24.71 43.58 2.74
399 2050 4.795268 GCATCATGCCTCAGACATTATTG 58.205 43.478 0.00 0.00 37.42 1.90
437 2088 2.663879 CGTTGTGAGCAGCTGAAACATC 60.664 50.000 20.43 14.71 0.00 3.06
482 2133 5.467399 TCCGTCCCATAATATAAAAGCGTTG 59.533 40.000 0.00 0.00 0.00 4.10
501 2152 0.539986 TGGCAAGTATTCCCTCCGTC 59.460 55.000 0.00 0.00 0.00 4.79
502 2153 0.988832 TTGGCAAGTATTCCCTCCGT 59.011 50.000 0.00 0.00 0.00 4.69
504 2155 2.026262 TCAGTTGGCAAGTATTCCCTCC 60.026 50.000 7.35 0.00 0.00 4.30
508 2159 2.162408 GTGCTCAGTTGGCAAGTATTCC 59.838 50.000 7.35 0.00 41.54 3.01
523 2174 3.226712 CGTGTTAACGCGTGCTCA 58.773 55.556 28.64 9.59 43.98 4.26
611 2447 2.305635 TGGTACCTGCATGTGTCATCTT 59.694 45.455 14.36 0.00 0.00 2.40
626 2462 2.858344 CGTCATTTGATCTCGTGGTACC 59.142 50.000 4.43 4.43 0.00 3.34
760 2596 5.584649 CGTTAGAATAAGTCAAGCCAATGGA 59.415 40.000 2.05 0.00 0.00 3.41
763 2599 4.881850 CCCGTTAGAATAAGTCAAGCCAAT 59.118 41.667 0.00 0.00 0.00 3.16
764 2600 4.258543 CCCGTTAGAATAAGTCAAGCCAA 58.741 43.478 0.00 0.00 0.00 4.52
817 2654 9.341899 GCCAAATTATAGTTCGCCAAATTATAG 57.658 33.333 0.00 0.00 0.00 1.31
818 2655 8.018520 CGCCAAATTATAGTTCGCCAAATTATA 58.981 33.333 0.00 0.00 0.00 0.98
819 2656 6.861055 CGCCAAATTATAGTTCGCCAAATTAT 59.139 34.615 0.00 0.00 0.00 1.28
820 2657 6.038382 TCGCCAAATTATAGTTCGCCAAATTA 59.962 34.615 0.00 0.00 0.00 1.40
821 2658 5.040635 CGCCAAATTATAGTTCGCCAAATT 58.959 37.500 0.00 0.00 0.00 1.82
822 2659 4.336993 TCGCCAAATTATAGTTCGCCAAAT 59.663 37.500 0.00 0.00 0.00 2.32
823 2660 3.690139 TCGCCAAATTATAGTTCGCCAAA 59.310 39.130 0.00 0.00 0.00 3.28
824 2661 3.271729 TCGCCAAATTATAGTTCGCCAA 58.728 40.909 0.00 0.00 0.00 4.52
829 2666 7.549615 AAAGTACCTCGCCAAATTATAGTTC 57.450 36.000 0.00 0.00 0.00 3.01
864 2701 7.504238 TGGCTTCTCTAAACATGGAAACTTTAA 59.496 33.333 0.00 0.00 0.00 1.52
865 2702 7.001674 TGGCTTCTCTAAACATGGAAACTTTA 58.998 34.615 0.00 0.00 0.00 1.85
866 2703 5.833131 TGGCTTCTCTAAACATGGAAACTTT 59.167 36.000 0.00 0.00 0.00 2.66
877 2714 5.537188 AGATCATCGATGGCTTCTCTAAAC 58.463 41.667 24.61 1.67 0.00 2.01
878 2715 5.798125 AGATCATCGATGGCTTCTCTAAA 57.202 39.130 24.61 2.04 0.00 1.85
1544 3386 6.847956 TTTATTTATGCAATACGCCGTACT 57.152 33.333 0.00 0.00 41.33 2.73
1587 3434 2.564062 TCACATCTCTGATCACACTGCA 59.436 45.455 0.00 0.00 0.00 4.41
1588 3435 3.242549 TCACATCTCTGATCACACTGC 57.757 47.619 0.00 0.00 0.00 4.40
1599 3446 8.317679 GGCTGGTTAATTAGATATCACATCTCT 58.682 37.037 5.32 0.00 0.00 3.10
1600 3447 7.276658 CGGCTGGTTAATTAGATATCACATCTC 59.723 40.741 5.32 0.00 0.00 2.75
1612 3459 1.164041 CCGGCCGGCTGGTTAATTAG 61.164 60.000 41.29 17.25 37.68 1.73
1753 3601 3.696051 ACAGCAAGGCACAAATACCATAG 59.304 43.478 0.00 0.00 0.00 2.23
1777 3626 1.917872 TGTATGCTGGGGTTGTTTCC 58.082 50.000 0.00 0.00 0.00 3.13
1778 3627 4.523083 TCTATGTATGCTGGGGTTGTTTC 58.477 43.478 0.00 0.00 0.00 2.78
1782 3631 3.632145 GGTTTCTATGTATGCTGGGGTTG 59.368 47.826 0.00 0.00 0.00 3.77
1784 3633 2.849943 TGGTTTCTATGTATGCTGGGGT 59.150 45.455 0.00 0.00 0.00 4.95
1785 3634 3.214328 GTGGTTTCTATGTATGCTGGGG 58.786 50.000 0.00 0.00 0.00 4.96
1826 3675 6.595326 AGAACAAGTGCGAGATGATAAAATGA 59.405 34.615 0.00 0.00 0.00 2.57
2033 3883 2.919043 GGCCGGAGTTGGATCCAT 59.081 61.111 17.06 0.06 39.53 3.41
2068 3918 1.372683 GGACTGCTGGTTGAGAGCA 59.627 57.895 0.00 0.00 44.22 4.26
2075 3925 0.537188 CCTACGATGGACTGCTGGTT 59.463 55.000 0.00 0.00 0.00 3.67
2082 3932 0.033796 TCCGGAACCTACGATGGACT 60.034 55.000 0.00 0.00 0.00 3.85
2202 4052 0.977627 ATCACACTGCCCAGATCCGA 60.978 55.000 1.69 0.00 0.00 4.55
2215 4065 0.721718 GTACTGCCGCTCAATCACAC 59.278 55.000 0.00 0.00 0.00 3.82
2257 4107 1.595794 GAAACGTTGACAAGAGCGGAA 59.404 47.619 0.00 0.00 0.00 4.30
2273 4123 5.288827 TCGTCCTCGCCTGAATAGGAAAC 62.289 52.174 0.00 0.00 46.38 2.78
2280 4130 0.970937 TCCTTCGTCCTCGCCTGAAT 60.971 55.000 0.00 0.00 36.96 2.57
2305 4155 4.636206 GTGTTCATTCGGGATTAGAGCTTT 59.364 41.667 0.00 0.00 0.00 3.51
2322 4172 4.693283 CTCCTTACTTGTCTGTGTGTTCA 58.307 43.478 0.00 0.00 0.00 3.18
2331 4181 4.851639 ATTGATGGCTCCTTACTTGTCT 57.148 40.909 0.00 0.00 0.00 3.41
2338 4188 4.695455 GCGCTAATAATTGATGGCTCCTTA 59.305 41.667 0.00 0.00 0.00 2.69
2380 4230 3.235481 TCCCAGCGTCGGTCCAAA 61.235 61.111 0.00 0.00 0.00 3.28
2393 4243 2.045708 GCGCACCATTGATGTCCCA 61.046 57.895 0.30 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.