Multiple sequence alignment - TraesCS5D01G362800

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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 TraesCS5D01G362800 chr5D 100.000 2354 0 0 1 2354 441119963 441117610 0.000000e+00 4348.0
1 TraesCS5D01G362800 chr5D 80.658 243 42 5 1081 1322 441261558 441261320 1.440000e-42 183.0
2 TraesCS5D01G362800 chr5A 92.186 947 54 8 364 1294 557478001 557477059 0.000000e+00 1321.0
3 TraesCS5D01G362800 chr5A 95.297 404 19 0 1951 2354 557474563 557474160 1.970000e-180 641.0
4 TraesCS5D01G362800 chr5A 95.238 63 3 0 1286 1348 557474608 557474546 1.490000e-17 100.0
5 TraesCS5D01G362800 chr6A 91.624 585 35 7 1352 1934 445522432 445523004 0.000000e+00 797.0
6 TraesCS5D01G362800 chr4D 87.395 595 60 12 1360 1951 203645899 203645317 0.000000e+00 669.0
7 TraesCS5D01G362800 chr3D 86.789 598 64 10 1360 1952 526262249 526261662 0.000000e+00 652.0
8 TraesCS5D01G362800 chr3D 86.111 576 69 8 1360 1934 58404699 58404134 5.560000e-171 610.0
9 TraesCS5D01G362800 chr7B 87.002 577 68 6 1360 1934 588074582 588074011 0.000000e+00 643.0
10 TraesCS5D01G362800 chr2D 86.979 576 60 11 1360 1934 108630365 108629804 3.300000e-178 634.0
11 TraesCS5D01G362800 chr2D 86.585 574 67 7 1361 1934 98710515 98709952 1.990000e-175 625.0
12 TraesCS5D01G362800 chr2D 85.452 598 70 8 1360 1950 388478395 388477808 7.190000e-170 606.0
13 TraesCS5D01G362800 chr7D 86.609 575 69 4 1360 1934 109517038 109516472 1.540000e-176 628.0
14 TraesCS5D01G362800 chr5B 86.501 363 48 1 4 366 536778131 536777770 4.710000e-107 398.0
15 TraesCS5D01G362800 chr5B 85.185 189 19 5 364 547 536777667 536777483 4.000000e-43 185.0
16 TraesCS5D01G362800 chr5B 78.927 261 47 4 1085 1344 536316919 536317172 1.120000e-38 171.0
17 TraesCS5D01G362800 chr1B 78.626 131 21 4 1092 1220 667050722 667050597 1.940000e-11 80.5
18 TraesCS5D01G362800 chr1B 76.978 139 25 4 1084 1220 628031352 628031485 3.250000e-09 73.1


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 TraesCS5D01G362800 chr5D 441117610 441119963 2353 True 4348.000000 4348 100.000000 1 2354 1 chr5D.!!$R1 2353
1 TraesCS5D01G362800 chr5A 557474160 557478001 3841 True 687.333333 1321 94.240333 364 2354 3 chr5A.!!$R1 1990
2 TraesCS5D01G362800 chr6A 445522432 445523004 572 False 797.000000 797 91.624000 1352 1934 1 chr6A.!!$F1 582
3 TraesCS5D01G362800 chr4D 203645317 203645899 582 True 669.000000 669 87.395000 1360 1951 1 chr4D.!!$R1 591
4 TraesCS5D01G362800 chr3D 526261662 526262249 587 True 652.000000 652 86.789000 1360 1952 1 chr3D.!!$R2 592
5 TraesCS5D01G362800 chr3D 58404134 58404699 565 True 610.000000 610 86.111000 1360 1934 1 chr3D.!!$R1 574
6 TraesCS5D01G362800 chr7B 588074011 588074582 571 True 643.000000 643 87.002000 1360 1934 1 chr7B.!!$R1 574
7 TraesCS5D01G362800 chr2D 108629804 108630365 561 True 634.000000 634 86.979000 1360 1934 1 chr2D.!!$R2 574
8 TraesCS5D01G362800 chr2D 98709952 98710515 563 True 625.000000 625 86.585000 1361 1934 1 chr2D.!!$R1 573
9 TraesCS5D01G362800 chr2D 388477808 388478395 587 True 606.000000 606 85.452000 1360 1950 1 chr2D.!!$R3 590
10 TraesCS5D01G362800 chr7D 109516472 109517038 566 True 628.000000 628 86.609000 1360 1934 1 chr7D.!!$R1 574
11 TraesCS5D01G362800 chr5B 536777483 536778131 648 True 291.500000 398 85.843000 4 547 2 chr5B.!!$R1 543

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
170 171 0.100682 ACTATCGATGTCGCGTTGCT 59.899 50.0 8.54 0.0 39.60 3.91 F
1226 1353 0.031585 CTGGTCAACCTCGTCGTCAA 59.968 55.0 0.10 0.0 36.82 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1393 0.028242 CGTCGAGGATCTTGGAGACG 59.972 60.0 0.00 10.88 43.79 4.18 R
2311 4920 0.179113 AACAAGTTGGCCGCAAACTG 60.179 50.0 14.07 10.42 37.90 3.16 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
64 65 0.598680 GGCCGTCTGATCTTGATCGG 60.599 60.000 12.01 12.01 40.72 4.18
66 67 1.601663 GCCGTCTGATCTTGATCGGAG 60.602 57.143 19.09 11.58 40.29 4.63
70 71 3.066064 CGTCTGATCTTGATCGGAGAGTT 59.934 47.826 19.09 0.00 43.63 3.01
71 72 4.358851 GTCTGATCTTGATCGGAGAGTTG 58.641 47.826 19.09 0.00 43.63 3.16
76 77 2.233922 TCTTGATCGGAGAGTTGGAACC 59.766 50.000 0.00 0.00 43.63 3.62
79 80 0.531200 ATCGGAGAGTTGGAACCGTC 59.469 55.000 0.00 0.00 43.63 4.79
87 88 1.066136 GTTGGAACCGTCGAAGCTAC 58.934 55.000 0.00 0.00 0.00 3.58
88 89 0.387622 TTGGAACCGTCGAAGCTACG 60.388 55.000 0.40 0.40 40.01 3.51
111 112 1.147376 CACCAGGAACGACCACCAA 59.853 57.895 0.00 0.00 42.04 3.67
144 145 5.565509 TGCTACCAACATAACCATGAGAAA 58.434 37.500 0.00 0.00 35.96 2.52
146 147 5.066505 GCTACCAACATAACCATGAGAAAGG 59.933 44.000 0.00 0.00 35.96 3.11
147 148 4.998051 ACCAACATAACCATGAGAAAGGT 58.002 39.130 0.00 0.00 40.61 3.50
164 165 1.215655 GGTGCCACTATCGATGTCGC 61.216 60.000 8.54 9.11 39.60 5.19
170 171 0.100682 ACTATCGATGTCGCGTTGCT 59.899 50.000 8.54 0.00 39.60 3.91
205 206 1.071814 GCGTAACCTCACCACCCAA 59.928 57.895 0.00 0.00 0.00 4.12
208 209 1.071071 CGTAACCTCACCACCCAAGAA 59.929 52.381 0.00 0.00 0.00 2.52
209 210 2.501261 GTAACCTCACCACCCAAGAAC 58.499 52.381 0.00 0.00 0.00 3.01
211 212 1.342672 ACCTCACCACCCAAGAACGT 61.343 55.000 0.00 0.00 0.00 3.99
215 216 1.147600 ACCACCCAAGAACGTCACC 59.852 57.895 0.00 0.00 0.00 4.02
223 224 2.047179 GAACGTCACCTCCCAGGC 60.047 66.667 0.00 0.00 39.63 4.85
229 230 3.775654 CACCTCCCAGGCCGACTC 61.776 72.222 0.00 0.00 39.63 3.36
246 247 2.125350 CTTCGACTCTGCCAGGGC 60.125 66.667 2.62 2.62 42.35 5.19
269 270 2.175499 CAAGGAAGATAGGATGGGGCAA 59.825 50.000 0.00 0.00 0.00 4.52
312 313 1.285078 GAGAACCTTAGGCATGGGGTT 59.715 52.381 9.04 9.04 43.66 4.11
330 331 3.875125 GGTTTAGACCCTGTCTTGATCC 58.125 50.000 1.58 0.00 40.28 3.36
342 343 2.762969 CTTGATCCAACCCGGCACCA 62.763 60.000 0.00 0.00 33.14 4.17
351 352 3.052082 CCGGCACCAGCAAGACTG 61.052 66.667 0.00 0.00 46.77 3.51
362 363 1.202698 AGCAAGACTGGACACTGGAAC 60.203 52.381 0.00 0.00 0.00 3.62
383 490 4.686437 CCCACCACCCCACCCCTA 62.686 72.222 0.00 0.00 0.00 3.53
384 491 2.533232 CCACCACCCCACCCCTAA 60.533 66.667 0.00 0.00 0.00 2.69
406 513 2.683211 AAATCCCAGCACAAGAACCT 57.317 45.000 0.00 0.00 0.00 3.50
441 548 1.153745 GAGTCCTGCACAGCCGTAG 60.154 63.158 0.00 0.00 0.00 3.51
550 662 4.467084 CGGACCCGACCACCCATG 62.467 72.222 1.54 0.00 42.83 3.66
581 693 3.849951 CCTCCGCTACCGCACCAT 61.850 66.667 0.00 0.00 35.30 3.55
615 727 3.398353 GACCGACGCCGAGAGAAGG 62.398 68.421 0.00 0.00 38.22 3.46
652 773 1.611261 CACGGGGGAGAAGGGTGTA 60.611 63.158 0.00 0.00 0.00 2.90
707 828 5.391950 CCTGTTTGGTCGAATCCATTACAAG 60.392 44.000 10.03 3.61 37.33 3.16
748 869 1.405105 GGCAGCAAGACAACAAGTTCA 59.595 47.619 0.00 0.00 0.00 3.18
791 912 7.086376 AGTGAACAGTTAATGCATGAATGAAC 58.914 34.615 15.11 5.80 0.00 3.18
794 915 8.089597 TGAACAGTTAATGCATGAATGAACAAT 58.910 29.630 15.40 1.04 0.00 2.71
795 916 8.470040 AACAGTTAATGCATGAATGAACAATC 57.530 30.769 15.40 0.00 0.00 2.67
796 917 7.833786 ACAGTTAATGCATGAATGAACAATCT 58.166 30.769 15.40 0.00 0.00 2.40
797 918 7.972277 ACAGTTAATGCATGAATGAACAATCTC 59.028 33.333 15.40 0.00 0.00 2.75
885 1011 1.480954 ACGGCCAACACGAGAAGATAT 59.519 47.619 2.24 0.00 34.93 1.63
887 1013 2.936498 CGGCCAACACGAGAAGATATTT 59.064 45.455 2.24 0.00 0.00 1.40
932 1059 5.468746 CACCGTACCGAATCAATATTTCCAT 59.531 40.000 0.00 0.00 0.00 3.41
934 1061 6.647895 ACCGTACCGAATCAATATTTCCATAC 59.352 38.462 0.00 0.00 0.00 2.39
973 1100 2.890945 CTCCCAACTTCCAACCGAATTT 59.109 45.455 0.00 0.00 0.00 1.82
990 1117 3.837213 ATTTGCTGGATTCTTGTGACG 57.163 42.857 0.00 0.00 0.00 4.35
996 1123 2.031919 ATTCTTGTGACGGCGGCA 59.968 55.556 13.60 13.60 0.00 5.69
1079 1206 2.535588 ACGGCGGTGACATTACAAC 58.464 52.632 13.24 0.00 0.00 3.32
1094 1221 2.751166 ACAACCCTCGACTTCATCAG 57.249 50.000 0.00 0.00 0.00 2.90
1101 1228 1.448540 CGACTTCATCAGCCGCCTT 60.449 57.895 0.00 0.00 0.00 4.35
1105 1232 3.680620 TTCATCAGCCGCCTTCCCG 62.681 63.158 0.00 0.00 0.00 5.14
1132 1259 0.828343 CCTCGGTACCATCCTCTCCC 60.828 65.000 13.54 0.00 0.00 4.30
1154 1281 2.108362 CCCCGATACCAAGGACGC 59.892 66.667 0.00 0.00 0.00 5.19
1226 1353 0.031585 CTGGTCAACCTCGTCGTCAA 59.968 55.000 0.10 0.00 36.82 3.18
1266 1393 3.630148 CATGACCGCGTCGCCATC 61.630 66.667 12.44 9.94 34.95 3.51
1319 3905 2.604686 ACGCTGCCTCTCCTTCCA 60.605 61.111 0.00 0.00 0.00 3.53
1352 3938 3.716006 CCTGCGCCGTGACTTGTG 61.716 66.667 4.18 0.00 0.00 3.33
1353 3939 2.661537 CTGCGCCGTGACTTGTGA 60.662 61.111 4.18 0.00 0.00 3.58
1354 3940 2.202946 TGCGCCGTGACTTGTGAA 60.203 55.556 4.18 0.00 0.00 3.18
1355 3941 2.162921 CTGCGCCGTGACTTGTGAAG 62.163 60.000 4.18 0.00 0.00 3.02
1356 3942 1.954146 GCGCCGTGACTTGTGAAGA 60.954 57.895 0.00 0.00 0.00 2.87
1444 4031 0.827507 AAGAATGGCGGCACAGGTTT 60.828 50.000 16.34 3.59 0.00 3.27
1445 4032 0.827507 AGAATGGCGGCACAGGTTTT 60.828 50.000 16.34 2.67 0.00 2.43
1502 4091 4.432741 GGTCTTGGCAGGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
1562 4151 2.000447 GAGTAACAAGCCGCGATCTTT 59.000 47.619 8.23 0.00 0.00 2.52
1798 4393 1.525197 TCGATGTTGCGAGTGTTTCAC 59.475 47.619 0.00 0.00 35.01 3.18
1878 4483 3.079578 CTGTGTGCATCCTTGATGTCTT 58.920 45.455 6.01 0.00 41.60 3.01
1891 4496 6.319658 TCCTTGATGTCTTTTGATATCTTGCC 59.680 38.462 3.98 0.00 44.29 4.52
1896 4501 3.938963 GTCTTTTGATATCTTGCCGGTGA 59.061 43.478 1.90 0.00 0.00 4.02
1898 4503 5.007034 TCTTTTGATATCTTGCCGGTGAAA 58.993 37.500 1.90 0.00 0.00 2.69
1944 4553 6.288941 TCGCGATATTAATCCCCTTTATCA 57.711 37.500 3.71 0.00 0.00 2.15
1963 4572 2.568090 AAAAATCTGCCTGCGCGG 59.432 55.556 9.96 9.96 43.32 6.46
1964 4573 2.268076 AAAAATCTGCCTGCGCGGT 61.268 52.632 16.49 0.00 42.47 5.68
1993 4602 1.512156 GCCATGTTCGACGGTTGGTT 61.512 55.000 0.00 0.00 0.00 3.67
2131 4740 1.801771 CGCTTGTAATGTTCCCGACAA 59.198 47.619 0.00 0.00 42.62 3.18
2206 4815 2.997315 CGAGTCAGCCCTCCACCA 60.997 66.667 0.00 0.00 0.00 4.17
2210 4819 2.930019 TCAGCCCTCCACCACCTG 60.930 66.667 0.00 0.00 0.00 4.00
2257 4866 2.809665 GCCTTGAGCTTCGATGGATCAT 60.810 50.000 7.49 0.00 38.99 2.45
2295 4904 2.065906 GATCGTCTCGCCCACTCTCC 62.066 65.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.721093 TTGGGTTGGGTCGGTTCCAT 61.721 55.000 0.00 0.00 33.82 3.41
1 2 2.346284 CTTGGGTTGGGTCGGTTCCA 62.346 60.000 0.00 0.00 0.00 3.53
2 3 1.602605 CTTGGGTTGGGTCGGTTCC 60.603 63.158 0.00 0.00 0.00 3.62
7 8 1.378514 CCATCCTTGGGTTGGGTCG 60.379 63.158 5.92 0.00 38.52 4.79
49 50 4.358851 CAACTCTCCGATCAAGATCAGAC 58.641 47.826 10.39 0.00 37.69 3.51
52 53 3.365472 TCCAACTCTCCGATCAAGATCA 58.635 45.455 10.39 0.00 37.69 2.92
53 54 4.116238 GTTCCAACTCTCCGATCAAGATC 58.884 47.826 0.00 0.00 34.56 2.75
64 65 1.699343 CTTCGACGGTTCCAACTCTC 58.301 55.000 0.00 0.00 0.00 3.20
66 67 0.319641 AGCTTCGACGGTTCCAACTC 60.320 55.000 0.00 0.00 0.00 3.01
70 71 1.210931 CGTAGCTTCGACGGTTCCA 59.789 57.895 6.96 0.00 36.66 3.53
71 72 1.503542 TCGTAGCTTCGACGGTTCC 59.496 57.895 11.71 0.00 40.70 3.62
79 80 0.793478 CTGGTGTCGTCGTAGCTTCG 60.793 60.000 6.38 6.38 0.00 3.79
87 88 1.728426 GTCGTTCCTGGTGTCGTCG 60.728 63.158 0.00 0.00 0.00 5.12
88 89 1.372623 GGTCGTTCCTGGTGTCGTC 60.373 63.158 0.00 0.00 0.00 4.20
90 91 1.663702 GTGGTCGTTCCTGGTGTCG 60.664 63.158 0.00 0.00 37.07 4.35
92 93 1.628238 TTGGTGGTCGTTCCTGGTGT 61.628 55.000 0.00 0.00 37.07 4.16
111 112 2.609747 TGTTGGTAGCAAGAGGAGAGT 58.390 47.619 7.79 0.00 0.00 3.24
144 145 0.385751 CGACATCGATAGTGGCACCT 59.614 55.000 15.27 1.28 43.02 4.00
146 147 1.540607 CGCGACATCGATAGTGGCAC 61.541 60.000 23.49 10.29 40.19 5.01
147 148 1.299089 CGCGACATCGATAGTGGCA 60.299 57.895 23.49 0.00 40.19 4.92
170 171 3.192230 CATTTGGCTACGCGGCGA 61.192 61.111 30.94 11.74 42.02 5.54
177 178 2.095372 GTGAGGTTACGCATTTGGCTAC 59.905 50.000 0.00 0.00 41.67 3.58
181 182 1.199097 GTGGTGAGGTTACGCATTTGG 59.801 52.381 0.00 0.00 0.00 3.28
188 189 0.682852 TCTTGGGTGGTGAGGTTACG 59.317 55.000 0.00 0.00 0.00 3.18
190 191 1.071071 CGTTCTTGGGTGGTGAGGTTA 59.929 52.381 0.00 0.00 0.00 2.85
205 206 2.584391 GCCTGGGAGGTGACGTTCT 61.584 63.158 0.00 0.00 37.80 3.01
211 212 4.316823 AGTCGGCCTGGGAGGTGA 62.317 66.667 0.00 0.00 37.80 4.02
215 216 2.896443 GAAGAGTCGGCCTGGGAG 59.104 66.667 0.00 0.00 0.00 4.30
229 230 2.125350 GCCCTGGCAGAGTCGAAG 60.125 66.667 17.94 0.00 41.49 3.79
239 240 0.255890 TATCTTCCTTGTGCCCTGGC 59.744 55.000 0.00 0.00 42.35 4.85
246 247 2.487986 GCCCCATCCTATCTTCCTTGTG 60.488 54.545 0.00 0.00 0.00 3.33
253 254 1.922447 TGTGTTGCCCCATCCTATCTT 59.078 47.619 0.00 0.00 0.00 2.40
269 270 0.819259 GCATGGGTCGGCATATGTGT 60.819 55.000 4.29 0.00 0.00 3.72
274 275 2.203001 CACGCATGGGTCGGCATA 60.203 61.111 13.22 0.00 0.00 3.14
312 313 3.263425 GGTTGGATCAAGACAGGGTCTAA 59.737 47.826 0.00 0.00 42.59 2.10
320 321 1.002624 GCCGGGTTGGATCAAGACA 60.003 57.895 2.18 0.00 42.00 3.41
322 323 1.002624 GTGCCGGGTTGGATCAAGA 60.003 57.895 2.18 0.00 42.00 3.02
323 324 2.046285 GGTGCCGGGTTGGATCAAG 61.046 63.158 2.18 0.00 42.00 3.02
330 331 3.673484 CTTGCTGGTGCCGGGTTG 61.673 66.667 2.18 0.00 38.71 3.77
342 343 1.131638 TTCCAGTGTCCAGTCTTGCT 58.868 50.000 0.00 0.00 0.00 3.91
345 346 1.417890 CCTGTTCCAGTGTCCAGTCTT 59.582 52.381 0.00 0.00 0.00 3.01
351 352 2.034221 GGGCCTGTTCCAGTGTCC 59.966 66.667 0.84 0.00 0.00 4.02
381 488 6.378280 AGGTTCTTGTGCTGGGATTTTATTAG 59.622 38.462 0.00 0.00 0.00 1.73
382 489 6.252995 AGGTTCTTGTGCTGGGATTTTATTA 58.747 36.000 0.00 0.00 0.00 0.98
383 490 5.086621 AGGTTCTTGTGCTGGGATTTTATT 58.913 37.500 0.00 0.00 0.00 1.40
384 491 4.677182 AGGTTCTTGTGCTGGGATTTTAT 58.323 39.130 0.00 0.00 0.00 1.40
406 513 2.203972 CTCGGGCGACTAACGGTGAA 62.204 60.000 0.00 0.00 42.83 3.18
549 661 3.240134 GAGGCTCACCCTTGCGACA 62.240 63.158 10.25 0.00 46.60 4.35
550 662 2.435059 GAGGCTCACCCTTGCGAC 60.435 66.667 10.25 0.00 46.60 5.19
569 681 4.830765 TGGCGATGGTGCGGTAGC 62.831 66.667 0.00 0.00 45.41 3.58
581 693 1.717194 GGTCTATGACGTTTTGGCGA 58.283 50.000 0.00 0.00 32.65 5.54
652 773 2.359900 CTTGCAATACGCCTTTCTCCT 58.640 47.619 0.00 0.00 41.33 3.69
707 828 2.953466 TATACGTTGTGGTCCAGAGC 57.047 50.000 0.00 0.00 0.00 4.09
748 869 9.429359 CTGTTCACTTGTCTTGAAGTTATATCT 57.571 33.333 0.00 0.00 33.75 1.98
791 912 9.223099 TGTTGTGCCATCTAATATATGAGATTG 57.777 33.333 9.62 8.06 29.73 2.67
866 992 2.225068 ATATCTTCTCGTGTTGGCCG 57.775 50.000 0.00 0.00 0.00 6.13
887 1013 4.035208 GTGCGTCCTCAAGAAGAAAGAAAA 59.965 41.667 0.00 0.00 0.00 2.29
891 1017 1.801178 GGTGCGTCCTCAAGAAGAAAG 59.199 52.381 0.00 0.00 0.00 2.62
932 1059 1.066430 GTCCCGGTGCTTTGATCAGTA 60.066 52.381 0.00 0.00 0.00 2.74
934 1061 0.036010 AGTCCCGGTGCTTTGATCAG 60.036 55.000 0.00 0.00 0.00 2.90
973 1100 0.955428 GCCGTCACAAGAATCCAGCA 60.955 55.000 0.00 0.00 0.00 4.41
996 1123 2.202932 GCCACATCGTCCATCGCT 60.203 61.111 0.00 0.00 39.67 4.93
1072 1199 4.759782 CTGATGAAGTCGAGGGTTGTAAT 58.240 43.478 0.00 0.00 0.00 1.89
1079 1206 4.844420 GGCTGATGAAGTCGAGGG 57.156 61.111 0.00 0.00 0.00 4.30
1118 1245 1.481615 GGAGGAGGGAGAGGATGGTAC 60.482 61.905 0.00 0.00 0.00 3.34
1132 1259 0.105658 TCCTTGGTATCGGGGAGGAG 60.106 60.000 0.00 0.00 32.91 3.69
1160 1287 1.273455 CGACGACAGAACGGTTGTCC 61.273 60.000 15.74 0.00 45.44 4.02
1208 1335 0.249155 GTTGACGACGAGGTTGACCA 60.249 55.000 0.00 0.00 38.89 4.02
1210 1337 0.249155 TGGTTGACGACGAGGTTGAC 60.249 55.000 0.00 0.00 0.00 3.18
1258 1385 0.103208 ATCTTGGAGACGATGGCGAC 59.897 55.000 0.00 0.00 41.64 5.19
1266 1393 0.028242 CGTCGAGGATCTTGGAGACG 59.972 60.000 0.00 10.88 43.79 4.18
1272 1399 1.078759 GGTGCACGTCGAGGATCTTG 61.079 60.000 12.85 0.41 0.00 3.02
1339 3925 0.934496 TTTCTTCACAAGTCACGGCG 59.066 50.000 4.80 4.80 0.00 6.46
1344 3930 6.655003 ACTTTCTTCACTTTCTTCACAAGTCA 59.345 34.615 0.00 0.00 31.83 3.41
1345 3931 7.078011 ACTTTCTTCACTTTCTTCACAAGTC 57.922 36.000 0.00 0.00 31.83 3.01
1346 3932 6.655003 TGACTTTCTTCACTTTCTTCACAAGT 59.345 34.615 0.00 0.00 34.67 3.16
1347 3933 7.076842 TGACTTTCTTCACTTTCTTCACAAG 57.923 36.000 0.00 0.00 0.00 3.16
1348 3934 7.415541 CCATGACTTTCTTCACTTTCTTCACAA 60.416 37.037 0.00 0.00 0.00 3.33
1349 3935 6.038603 CCATGACTTTCTTCACTTTCTTCACA 59.961 38.462 0.00 0.00 0.00 3.58
1350 3936 6.038714 ACCATGACTTTCTTCACTTTCTTCAC 59.961 38.462 0.00 0.00 0.00 3.18
1351 3937 6.038603 CACCATGACTTTCTTCACTTTCTTCA 59.961 38.462 0.00 0.00 0.00 3.02
1352 3938 6.433766 CACCATGACTTTCTTCACTTTCTTC 58.566 40.000 0.00 0.00 0.00 2.87
1353 3939 5.300286 CCACCATGACTTTCTTCACTTTCTT 59.700 40.000 0.00 0.00 0.00 2.52
1354 3940 4.823989 CCACCATGACTTTCTTCACTTTCT 59.176 41.667 0.00 0.00 0.00 2.52
1355 3941 4.557496 GCCACCATGACTTTCTTCACTTTC 60.557 45.833 0.00 0.00 0.00 2.62
1356 3942 3.319122 GCCACCATGACTTTCTTCACTTT 59.681 43.478 0.00 0.00 0.00 2.66
1502 4091 2.978010 GTCCACCTGTGTTGCCGG 60.978 66.667 0.00 0.00 0.00 6.13
1549 4138 0.462047 CACCCTAAAGATCGCGGCTT 60.462 55.000 6.13 7.87 0.00 4.35
1798 4393 1.269936 ACAAAGAACCCGTCGTAGTGG 60.270 52.381 0.00 0.00 0.00 4.00
1878 4483 4.157656 CCTTTTCACCGGCAAGATATCAAA 59.842 41.667 0.00 0.00 0.00 2.69
1896 4501 6.357367 AGATATCAATTACACTCGGCCTTTT 58.643 36.000 5.32 0.00 0.00 2.27
1898 4503 5.552870 AGATATCAATTACACTCGGCCTT 57.447 39.130 5.32 0.00 0.00 4.35
1964 4573 4.634703 AACATGGCGTGGCGGTCA 62.635 61.111 12.05 0.00 0.00 4.02
1973 4582 2.474266 CAACCGTCGAACATGGCG 59.526 61.111 0.00 0.09 33.80 5.69
2063 4672 2.665185 AAACGGAGCACAGACGGC 60.665 61.111 0.00 0.00 0.00 5.68
2131 4740 3.430374 CCGAGGGAAACAGACGTAATCAT 60.430 47.826 0.00 0.00 0.00 2.45
2178 4787 0.179124 GCTGACTCGGAGATGGTGAC 60.179 60.000 12.86 0.00 33.89 3.67
2266 4875 0.572590 CGAGACGATCCGAATGTTGC 59.427 55.000 0.00 0.00 0.00 4.17
2311 4920 0.179113 AACAAGTTGGCCGCAAACTG 60.179 50.000 14.07 10.42 37.90 3.16


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

AutoCloner maintained by Alex Coulton.