Multiple sequence alignment - TraesCS1A01G337900

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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 TraesCS1A01G337900 chr1A 100.000 2730 0 0 1 2730 527178579 527181308 0.000000e+00 5042.0
1 TraesCS1A01G337900 chr1A 93.548 62 3 1 1821 1882 351005462 351005522 1.040000e-14 91.6
2 TraesCS1A01G337900 chr1A 89.552 67 7 0 1815 1881 547968936 547968870 4.840000e-13 86.1
3 TraesCS1A01G337900 chr1D 91.520 2335 112 36 462 2730 429701724 429704038 0.000000e+00 3136.0
4 TraesCS1A01G337900 chr1D 78.094 598 80 29 1172 1730 430104942 430105527 5.630000e-87 331.0
5 TraesCS1A01G337900 chr1D 87.607 234 16 7 1 234 429699862 429700082 2.700000e-65 259.0
6 TraesCS1A01G337900 chr1D 93.694 111 6 1 369 478 429701596 429701706 6.050000e-37 165.0
7 TraesCS1A01G337900 chr1B 90.161 1433 63 27 366 1736 580637014 580638430 0.000000e+00 1794.0
8 TraesCS1A01G337900 chr1B 77.852 596 85 25 1172 1730 581099066 581099651 2.620000e-85 326.0
9 TraesCS1A01G337900 chr5D 88.991 545 54 3 2186 2730 454266213 454266751 0.000000e+00 669.0
10 TraesCS1A01G337900 chr5D 85.138 545 60 10 2186 2730 454290390 454290913 3.090000e-149 538.0
11 TraesCS1A01G337900 chr5D 87.257 463 54 2 2186 2648 454214181 454214638 8.660000e-145 523.0
12 TraesCS1A01G337900 chr5D 92.537 67 3 2 1817 1881 310276621 310276687 8.050000e-16 95.3
13 TraesCS1A01G337900 chr4B 81.107 524 75 11 2186 2705 288176591 288177094 5.480000e-107 398.0
14 TraesCS1A01G337900 chr7A 80.462 563 68 19 2186 2719 496826964 496827513 2.550000e-105 392.0
15 TraesCS1A01G337900 chr7B 89.701 301 31 0 2186 2486 389100505 389100205 4.260000e-103 385.0
16 TraesCS1A01G337900 chr7B 88.372 301 35 0 2186 2486 389097541 389097241 2.000000e-96 363.0
17 TraesCS1A01G337900 chr3B 83.879 397 57 4 2186 2582 670270386 670270775 3.320000e-99 372.0
18 TraesCS1A01G337900 chr3B 86.667 75 9 1 1807 1881 827494480 827494407 6.270000e-12 82.4
19 TraesCS1A01G337900 chr3B 86.667 75 9 1 1807 1881 830634282 830634355 6.270000e-12 82.4
20 TraesCS1A01G337900 chr4A 83.010 412 58 5 2294 2705 418659166 418659565 2.000000e-96 363.0
21 TraesCS1A01G337900 chr4A 85.366 82 8 3 1804 1882 646585281 646585361 6.270000e-12 82.4
22 TraesCS1A01G337900 chr2D 89.873 79 6 2 1803 1881 36796199 36796275 1.730000e-17 100.0
23 TraesCS1A01G337900 chr5B 93.750 64 4 0 1818 1881 538714200 538714263 2.240000e-16 97.1
24 TraesCS1A01G337900 chr4D 95.000 40 2 0 273 312 119235545 119235584 2.270000e-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 TraesCS1A01G337900 chr1A 527178579 527181308 2729 False 5042.000000 5042 100.000000 1 2730 1 chr1A.!!$F2 2729
1 TraesCS1A01G337900 chr1D 429699862 429704038 4176 False 1186.666667 3136 90.940333 1 2730 3 chr1D.!!$F2 2729
2 TraesCS1A01G337900 chr1D 430104942 430105527 585 False 331.000000 331 78.094000 1172 1730 1 chr1D.!!$F1 558
3 TraesCS1A01G337900 chr1B 580637014 580638430 1416 False 1794.000000 1794 90.161000 366 1736 1 chr1B.!!$F1 1370
4 TraesCS1A01G337900 chr1B 581099066 581099651 585 False 326.000000 326 77.852000 1172 1730 1 chr1B.!!$F2 558
5 TraesCS1A01G337900 chr5D 454266213 454266751 538 False 669.000000 669 88.991000 2186 2730 1 chr5D.!!$F3 544
6 TraesCS1A01G337900 chr5D 454290390 454290913 523 False 538.000000 538 85.138000 2186 2730 1 chr5D.!!$F4 544
7 TraesCS1A01G337900 chr4B 288176591 288177094 503 False 398.000000 398 81.107000 2186 2705 1 chr4B.!!$F1 519
8 TraesCS1A01G337900 chr7A 496826964 496827513 549 False 392.000000 392 80.462000 2186 2719 1 chr7A.!!$F1 533
9 TraesCS1A01G337900 chr7B 389097241 389100505 3264 True 374.000000 385 89.036500 2186 2486 2 chr7B.!!$R1 300

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
118 119 0.110823 CGAGCACGGTTGTTTGTAGC 60.111 55.0 0.0 0.0 35.72 3.58 F
293 1454 0.251430 CTCCCTCCTCCCTCCGTATC 60.251 65.0 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 2795 0.321122 GACCACTCTGCTCCCAACTG 60.321 60.0 0.0 0.0 0.00 3.16 R
2093 3634 0.327924 ATTCCAGTGGATCACGGCAA 59.672 50.0 14.0 0.0 39.64 4.52 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
118 119 0.110823 CGAGCACGGTTGTTTGTAGC 60.111 55.000 0.00 0.00 35.72 3.58
121 122 0.941542 GCACGGTTGTTTGTAGCTCA 59.058 50.000 0.00 0.00 0.00 4.26
125 126 3.805422 CACGGTTGTTTGTAGCTCAACTA 59.195 43.478 13.15 0.62 40.52 2.24
126 127 4.271533 CACGGTTGTTTGTAGCTCAACTAA 59.728 41.667 13.15 0.00 40.52 2.24
129 130 5.679792 CGGTTGTTTGTAGCTCAACTAAAAC 59.320 40.000 13.15 5.71 40.52 2.43
134 135 8.682128 TGTTTGTAGCTCAACTAAAACAAAAG 57.318 30.769 8.35 0.00 36.56 2.27
135 136 8.301002 TGTTTGTAGCTCAACTAAAACAAAAGT 58.699 29.630 8.35 0.00 36.56 2.66
155 156 9.220767 CAAAAGTTGTTTCTAGCTAGTTCCTAT 57.779 33.333 20.10 0.55 0.00 2.57
156 157 9.438228 AAAAGTTGTTTCTAGCTAGTTCCTATC 57.562 33.333 20.10 7.34 0.00 2.08
157 158 7.719871 AGTTGTTTCTAGCTAGTTCCTATCA 57.280 36.000 20.10 8.51 0.00 2.15
158 159 8.312669 AGTTGTTTCTAGCTAGTTCCTATCAT 57.687 34.615 20.10 0.00 0.00 2.45
159 160 8.417884 AGTTGTTTCTAGCTAGTTCCTATCATC 58.582 37.037 20.10 9.83 0.00 2.92
160 161 7.291411 TGTTTCTAGCTAGTTCCTATCATCC 57.709 40.000 20.10 0.00 0.00 3.51
161 162 7.069986 TGTTTCTAGCTAGTTCCTATCATCCT 58.930 38.462 20.10 0.00 0.00 3.24
162 163 8.225416 TGTTTCTAGCTAGTTCCTATCATCCTA 58.775 37.037 20.10 0.00 0.00 2.94
163 164 9.250246 GTTTCTAGCTAGTTCCTATCATCCTAT 57.750 37.037 20.10 0.00 0.00 2.57
164 165 8.815565 TTCTAGCTAGTTCCTATCATCCTATG 57.184 38.462 20.10 0.00 0.00 2.23
198 199 6.970043 TCATTAAAATATTCCTTTCGCGTTGG 59.030 34.615 5.77 7.24 0.00 3.77
234 235 2.149578 CCGGGAATTCATCATCTGCTC 58.850 52.381 7.93 0.00 0.00 4.26
235 236 2.149578 CGGGAATTCATCATCTGCTCC 58.850 52.381 7.93 0.00 0.00 4.70
236 237 2.486013 CGGGAATTCATCATCTGCTCCA 60.486 50.000 7.93 0.00 0.00 3.86
237 238 3.764218 GGGAATTCATCATCTGCTCCAT 58.236 45.455 7.93 0.00 0.00 3.41
238 239 4.150359 GGGAATTCATCATCTGCTCCATT 58.850 43.478 7.93 0.00 0.00 3.16
239 240 4.587684 GGGAATTCATCATCTGCTCCATTT 59.412 41.667 7.93 0.00 0.00 2.32
240 241 5.509163 GGGAATTCATCATCTGCTCCATTTG 60.509 44.000 7.93 0.00 0.00 2.32
241 242 5.509163 GGAATTCATCATCTGCTCCATTTGG 60.509 44.000 7.93 0.00 0.00 3.28
242 243 2.304092 TCATCATCTGCTCCATTTGGC 58.696 47.619 0.00 0.00 34.44 4.52
250 251 4.279982 TCTGCTCCATTTGGCAAATCATA 58.720 39.130 22.02 9.80 38.02 2.15
263 264 4.455533 GGCAAATCATATGGCGAATACAGA 59.544 41.667 2.13 0.00 33.46 3.41
267 268 7.434897 GCAAATCATATGGCGAATACAGAAAAA 59.565 33.333 2.13 0.00 0.00 1.94
286 287 0.644937 AATGCTACTCCCTCCTCCCT 59.355 55.000 0.00 0.00 0.00 4.20
288 289 1.152419 GCTACTCCCTCCTCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
289 290 1.151908 CTACTCCCTCCTCCCTCCG 59.848 68.421 0.00 0.00 0.00 4.63
293 1454 0.251430 CTCCCTCCTCCCTCCGTATC 60.251 65.000 0.00 0.00 0.00 2.24
300 1461 4.532521 CCTCCTCCCTCCGTATCAAAATAT 59.467 45.833 0.00 0.00 0.00 1.28
303 1464 7.092846 CCTCCTCCCTCCGTATCAAAATATAAT 60.093 40.741 0.00 0.00 0.00 1.28
305 1466 8.755977 TCCTCCCTCCGTATCAAAATATAATAC 58.244 37.037 0.00 0.00 0.00 1.89
318 1479 9.175312 TCAAAATATAATACGTTTTGTAGGCCA 57.825 29.630 5.01 0.00 41.30 5.36
319 1480 9.228636 CAAAATATAATACGTTTTGTAGGCCAC 57.771 33.333 5.01 1.31 37.79 5.01
320 1481 8.741603 AAATATAATACGTTTTGTAGGCCACT 57.258 30.769 5.01 0.00 36.25 4.00
321 1482 7.958053 ATATAATACGTTTTGTAGGCCACTC 57.042 36.000 5.01 0.00 36.25 3.51
322 1483 3.975168 ATACGTTTTGTAGGCCACTCT 57.025 42.857 5.01 0.00 36.25 3.24
323 1484 2.632987 ACGTTTTGTAGGCCACTCTT 57.367 45.000 5.01 0.00 0.00 2.85
324 1485 2.218603 ACGTTTTGTAGGCCACTCTTG 58.781 47.619 5.01 0.00 0.00 3.02
325 1486 2.218603 CGTTTTGTAGGCCACTCTTGT 58.781 47.619 5.01 0.00 0.00 3.16
327 1488 3.185797 CGTTTTGTAGGCCACTCTTGTAC 59.814 47.826 5.01 0.00 0.00 2.90
342 1510 9.832445 CCACTCTTGTACTATTTTGGTACATAT 57.168 33.333 7.39 0.00 45.58 1.78
408 1797 6.961554 GCCGAGTTGTTTCTATGTATTTTCTG 59.038 38.462 0.00 0.00 0.00 3.02
481 1905 3.698539 TGAAAGAAACATGTGGCACAGAA 59.301 39.130 26.04 2.00 41.80 3.02
533 1960 2.712709 TCCTCCAAAACGTGTCACAAA 58.287 42.857 3.42 0.00 0.00 2.83
536 1963 4.158764 TCCTCCAAAACGTGTCACAAATTT 59.841 37.500 3.42 0.00 0.00 1.82
537 1964 4.867608 CCTCCAAAACGTGTCACAAATTTT 59.132 37.500 3.42 4.10 0.00 1.82
573 2000 1.401905 GTTCATGCATCCTTCCCGAAC 59.598 52.381 0.00 1.92 0.00 3.95
697 2136 3.680786 CTGACAGCGGGACCGTGA 61.681 66.667 12.83 0.00 42.09 4.35
825 2289 2.485122 CCAAGGAATTGCCGACGC 59.515 61.111 0.00 0.00 43.43 5.19
870 2334 2.523902 CCCAAGCCAAGCAACCCA 60.524 61.111 0.00 0.00 0.00 4.51
1052 2541 1.333791 GCACAAGCAACGTAACACCTC 60.334 52.381 0.00 0.00 41.58 3.85
1147 2636 4.973663 GGCCATCCGTCGTATTTTATTTTG 59.026 41.667 0.00 0.00 0.00 2.44
1254 2747 4.129737 CCGGTCACCATCTCGCGT 62.130 66.667 5.77 0.00 0.00 6.01
1446 2981 0.612453 GAGGTGGAGGACGAGGAAGT 60.612 60.000 0.00 0.00 0.00 3.01
1456 2991 1.153745 CGAGGAAGTGGAAGAGCCG 60.154 63.158 0.00 0.00 40.66 5.52
1702 3240 1.524482 GGCTGTCCACTCCATCTCC 59.476 63.158 0.00 0.00 0.00 3.71
1736 3274 1.331756 GCGGCAGAATGTAGGATTGTG 59.668 52.381 0.00 0.00 39.31 3.33
1800 3341 4.037208 CCAATTCCAGGGAAGAATCATTCG 59.963 45.833 6.91 0.00 37.56 3.34
1832 3373 9.688091 GAATCAGATGATGTATAGTACTCCCTA 57.312 37.037 0.00 0.00 34.49 3.53
1905 3446 5.584253 AGTAGTGATCTAAACGCACAGAT 57.416 39.130 0.00 0.00 35.08 2.90
1909 3450 3.932710 GTGATCTAAACGCACAGATGGAA 59.067 43.478 0.00 0.00 31.63 3.53
1915 3456 3.513680 AACGCACAGATGGAATACGTA 57.486 42.857 0.00 0.00 0.00 3.57
1980 3521 5.012251 TGTTAGGGCACTGTTGTATTACTCA 59.988 40.000 0.00 0.00 0.00 3.41
1982 3523 2.671396 GGGCACTGTTGTATTACTCACG 59.329 50.000 0.00 0.00 0.00 4.35
1993 3534 7.337184 TGTTGTATTACTCACGATCTCTCTCTT 59.663 37.037 0.00 0.00 0.00 2.85
1997 3538 6.671614 TTACTCACGATCTCTCTCTTTCTC 57.328 41.667 0.00 0.00 0.00 2.87
2107 3648 0.670546 CGTTCTTGCCGTGATCCACT 60.671 55.000 0.00 0.00 31.34 4.00
2115 3656 1.810412 GCCGTGATCCACTGGAATACC 60.810 57.143 0.66 0.00 34.34 2.73
2126 3667 2.179424 ACTGGAATACCGGATACCCTCT 59.821 50.000 9.46 0.00 44.87 3.69
2135 3676 1.683917 CGGATACCCTCTCCTTCTGTG 59.316 57.143 0.00 0.00 0.00 3.66
2137 3678 1.067821 GATACCCTCTCCTTCTGTGCG 59.932 57.143 0.00 0.00 0.00 5.34
2139 3680 2.125350 CCTCTCCTTCTGTGCGCC 60.125 66.667 4.18 0.00 0.00 6.53
2207 3752 2.050918 CTCCTAACATCCCTCCCTTCC 58.949 57.143 0.00 0.00 0.00 3.46
2235 3780 4.351054 CTTGACCCCAAGCCGGCT 62.351 66.667 27.08 27.08 42.72 5.52
2300 3846 0.679505 TAGCTCAAAGTCGCAGTGGT 59.320 50.000 0.00 0.00 0.00 4.16
2413 3959 8.517056 TCATTGTTGAAGTCGATGTAGTACTTA 58.483 33.333 0.00 0.00 33.72 2.24
2419 3965 6.600427 TGAAGTCGATGTAGTACTTATGGTCA 59.400 38.462 0.00 0.00 33.72 4.02
2500 4046 2.950781 TCTTGATCGGAGCAGGTAGAT 58.049 47.619 5.27 0.00 0.00 1.98
2547 4542 2.435069 CTCTCTTGCTGATCACCTCCAT 59.565 50.000 0.00 0.00 0.00 3.41
2553 4548 2.709397 TGCTGATCACCTCCATCATCAT 59.291 45.455 0.00 0.00 29.78 2.45
2554 4549 3.905591 TGCTGATCACCTCCATCATCATA 59.094 43.478 0.00 0.00 29.78 2.15
2555 4550 4.534897 TGCTGATCACCTCCATCATCATAT 59.465 41.667 0.00 0.00 29.78 1.78
2556 4551 5.722923 TGCTGATCACCTCCATCATCATATA 59.277 40.000 0.00 0.00 29.78 0.86
2557 4552 6.214005 TGCTGATCACCTCCATCATCATATAA 59.786 38.462 0.00 0.00 29.78 0.98
2558 4553 7.092578 TGCTGATCACCTCCATCATCATATAAT 60.093 37.037 0.00 0.00 29.78 1.28
2562 4561 9.458727 GATCACCTCCATCATCATATAATTGTT 57.541 33.333 0.00 0.00 0.00 2.83
2587 6536 3.690139 CGACTGAAGTGTAGAAGCTAGGA 59.310 47.826 0.00 0.00 0.00 2.94
2588 6537 4.156190 CGACTGAAGTGTAGAAGCTAGGAA 59.844 45.833 0.00 0.00 0.00 3.36
2589 6538 5.163602 CGACTGAAGTGTAGAAGCTAGGAAT 60.164 44.000 0.00 0.00 0.00 3.01
2604 6553 5.248477 AGCTAGGAATAAGGTGACAAGACAA 59.752 40.000 0.00 0.00 0.00 3.18
2612 6701 0.951558 GTGACAAGACAACGGGCAAT 59.048 50.000 0.00 0.00 0.00 3.56
2669 6963 5.395768 CCTTCCATCGAGTCAACTTCCTTAT 60.396 44.000 0.00 0.00 0.00 1.73
2712 7006 2.188817 GGATCCCAAGACACACCTAGT 58.811 52.381 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.604171 ACAGTTCCAGCAATTATGATATCCA 58.396 36.000 0.00 0.00 0.00 3.41
43 44 6.259387 TGATGATGATCAAAGAACGATTCCAG 59.741 38.462 0.00 0.00 35.55 3.86
83 84 4.092821 CGTGCTCGAGAAAATACATGGAAA 59.907 41.667 18.75 0.00 39.71 3.13
129 130 7.497925 AGGAACTAGCTAGAAACAACTTTTG 57.502 36.000 27.45 0.00 36.02 2.44
177 178 5.883503 ACCAACGCGAAAGGAATATTTTA 57.116 34.783 15.93 0.00 0.00 1.52
198 199 1.134946 CCCGGCATGATTTGGAGAAAC 59.865 52.381 0.00 0.00 0.00 2.78
211 212 2.511659 CAGATGATGAATTCCCGGCAT 58.488 47.619 2.27 0.00 0.00 4.40
234 235 3.061322 CGCCATATGATTTGCCAAATGG 58.939 45.455 7.53 4.90 37.52 3.16
235 236 3.979948 TCGCCATATGATTTGCCAAATG 58.020 40.909 7.53 0.00 0.00 2.32
236 237 4.669206 TTCGCCATATGATTTGCCAAAT 57.331 36.364 1.47 1.47 0.00 2.32
237 238 4.669206 ATTCGCCATATGATTTGCCAAA 57.331 36.364 3.65 0.00 0.00 3.28
238 239 4.582240 TGTATTCGCCATATGATTTGCCAA 59.418 37.500 3.65 0.00 0.00 4.52
239 240 4.140536 TGTATTCGCCATATGATTTGCCA 58.859 39.130 3.65 0.00 0.00 4.92
240 241 4.455533 TCTGTATTCGCCATATGATTTGCC 59.544 41.667 3.65 0.00 0.00 4.52
241 242 5.611796 TCTGTATTCGCCATATGATTTGC 57.388 39.130 3.65 0.00 0.00 3.68
242 243 8.854979 TTTTTCTGTATTCGCCATATGATTTG 57.145 30.769 3.65 0.00 0.00 2.32
267 268 0.644937 AGGGAGGAGGGAGTAGCATT 59.355 55.000 0.00 0.00 0.00 3.56
268 269 0.189822 GAGGGAGGAGGGAGTAGCAT 59.810 60.000 0.00 0.00 0.00 3.79
269 270 1.621377 GAGGGAGGAGGGAGTAGCA 59.379 63.158 0.00 0.00 0.00 3.49
270 271 1.152419 GGAGGGAGGAGGGAGTAGC 60.152 68.421 0.00 0.00 0.00 3.58
271 272 1.151908 CGGAGGGAGGAGGGAGTAG 59.848 68.421 0.00 0.00 0.00 2.57
272 273 0.327867 TACGGAGGGAGGAGGGAGTA 60.328 60.000 0.00 0.00 0.00 2.59
273 274 1.000041 ATACGGAGGGAGGAGGGAGT 61.000 60.000 0.00 0.00 0.00 3.85
274 275 0.251430 GATACGGAGGGAGGAGGGAG 60.251 65.000 0.00 0.00 0.00 4.30
275 276 0.997307 TGATACGGAGGGAGGAGGGA 60.997 60.000 0.00 0.00 0.00 4.20
278 279 5.746990 ATATTTTGATACGGAGGGAGGAG 57.253 43.478 0.00 0.00 0.00 3.69
279 280 7.808279 ATTATATTTTGATACGGAGGGAGGA 57.192 36.000 0.00 0.00 0.00 3.71
280 281 7.705325 CGTATTATATTTTGATACGGAGGGAGG 59.295 40.741 7.11 0.00 42.77 4.30
281 282 8.630278 CGTATTATATTTTGATACGGAGGGAG 57.370 38.462 7.11 0.00 42.77 4.30
293 1454 9.228636 GTGGCCTACAAAACGTATTATATTTTG 57.771 33.333 3.32 8.60 44.93 2.44
300 1461 5.410355 AGAGTGGCCTACAAAACGTATTA 57.590 39.130 3.32 0.00 0.00 0.98
303 1464 3.181463 ACAAGAGTGGCCTACAAAACGTA 60.181 43.478 3.32 0.00 0.00 3.57
305 1466 2.218603 ACAAGAGTGGCCTACAAAACG 58.781 47.619 3.32 0.00 0.00 3.60
310 1471 6.170506 CAAAATAGTACAAGAGTGGCCTACA 58.829 40.000 3.32 0.00 0.00 2.74
313 1474 4.042934 ACCAAAATAGTACAAGAGTGGCCT 59.957 41.667 3.32 0.00 0.00 5.19
314 1475 4.332828 ACCAAAATAGTACAAGAGTGGCC 58.667 43.478 0.00 0.00 0.00 5.36
315 1476 5.935789 TGTACCAAAATAGTACAAGAGTGGC 59.064 40.000 1.45 0.00 45.28 5.01
375 1764 0.938168 AAACAACTCGGCGTCGTCTC 60.938 55.000 10.18 0.00 37.69 3.36
376 1765 0.938168 GAAACAACTCGGCGTCGTCT 60.938 55.000 10.18 0.00 37.69 4.18
408 1797 3.927142 GTCTTGTGTACATACTGTGCTCC 59.073 47.826 0.00 0.00 33.97 4.70
437 1827 4.624024 CACATGAAGAAATGGTTGCATGAC 59.376 41.667 0.00 0.00 37.24 3.06
443 1833 7.492020 TGTTTCTTTCACATGAAGAAATGGTTG 59.508 33.333 18.45 8.62 35.64 3.77
481 1905 7.148373 ACGTGTTTACTGTTTACAATGACACTT 60.148 33.333 0.00 0.00 0.00 3.16
487 1911 7.728580 ACAAACGTGTTTACTGTTTACAATG 57.271 32.000 0.00 0.00 32.58 2.82
554 1981 1.281867 AGTTCGGGAAGGATGCATGAA 59.718 47.619 2.46 0.00 0.00 2.57
573 2000 1.333347 CGTAGAATCGCTCCGTCTGAG 60.333 57.143 0.00 0.00 44.47 3.35
585 2012 4.261197 GCCCAACAATTCCATCGTAGAATC 60.261 45.833 0.00 0.00 43.58 2.52
587 2014 3.013921 GCCCAACAATTCCATCGTAGAA 58.986 45.455 0.00 0.00 43.58 2.10
697 2136 1.525995 CGGCACCTGGTGACTGTTT 60.526 57.895 30.23 0.00 39.83 2.83
835 2299 3.777925 CGGGAAGAACACGCGCAG 61.778 66.667 5.73 0.55 38.98 5.18
870 2334 1.974875 GGGAAAACGTGCGGGGAAT 60.975 57.895 0.00 0.00 0.00 3.01
1124 2613 4.823790 AAATAAAATACGACGGATGGCC 57.176 40.909 0.00 0.00 0.00 5.36
1294 2787 4.717629 CTCCCAACTGCGCGACGA 62.718 66.667 12.10 0.00 0.00 4.20
1299 2792 3.123620 CTCTGCTCCCAACTGCGC 61.124 66.667 0.00 0.00 0.00 6.09
1300 2793 2.031516 CACTCTGCTCCCAACTGCG 61.032 63.158 0.00 0.00 0.00 5.18
1301 2794 1.673665 CCACTCTGCTCCCAACTGC 60.674 63.158 0.00 0.00 0.00 4.40
1302 2795 0.321122 GACCACTCTGCTCCCAACTG 60.321 60.000 0.00 0.00 0.00 3.16
1303 2796 1.484444 GGACCACTCTGCTCCCAACT 61.484 60.000 0.00 0.00 0.00 3.16
1306 2799 1.610673 GAGGACCACTCTGCTCCCA 60.611 63.158 0.00 0.00 43.14 4.37
1446 2981 2.364317 CCTCCTCCGGCTCTTCCA 60.364 66.667 0.00 0.00 34.01 3.53
1456 2991 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1652 3190 3.681835 GGACACGAGGAGCACCGT 61.682 66.667 0.00 0.00 41.83 4.83
1736 3274 1.617740 GCACAAGGCAGAAAATACGC 58.382 50.000 0.00 0.00 43.97 4.42
1760 3301 2.795231 TGGGAAGAAGGAGAAGCATG 57.205 50.000 0.00 0.00 0.00 4.06
1764 3305 4.268359 CTGGAATTGGGAAGAAGGAGAAG 58.732 47.826 0.00 0.00 0.00 2.85
1800 3341 7.251321 ACTATACATCATCTGATTCTTCCCC 57.749 40.000 0.00 0.00 31.21 4.81
1881 3422 6.694877 TCTGTGCGTTTAGATCACTACTAT 57.305 37.500 0.00 0.00 0.00 2.12
1897 3438 3.079960 ACTACGTATTCCATCTGTGCG 57.920 47.619 0.00 0.00 0.00 5.34
1905 3446 6.996509 ACAAGAAAACCTACTACGTATTCCA 58.003 36.000 0.00 0.00 0.00 3.53
1909 3450 6.372659 TCGAGACAAGAAAACCTACTACGTAT 59.627 38.462 0.00 0.00 0.00 3.06
1915 3456 4.320348 CGAGTCGAGACAAGAAAACCTACT 60.320 45.833 6.73 0.00 0.00 2.57
1932 3473 2.169789 CATGCTCCTTGCCGAGTCG 61.170 63.158 5.29 5.29 42.00 4.18
1957 3498 5.350640 GTGAGTAATACAACAGTGCCCTAAC 59.649 44.000 0.00 0.00 0.00 2.34
1980 3521 5.996644 TCCTAAGAGAAAGAGAGAGATCGT 58.003 41.667 0.00 0.00 0.00 3.73
1982 3523 8.695456 ACAATTCCTAAGAGAAAGAGAGAGATC 58.305 37.037 0.00 0.00 0.00 2.75
1993 3534 6.769512 ACACTTGCTACAATTCCTAAGAGAA 58.230 36.000 0.00 0.00 0.00 2.87
1997 3538 5.874810 TGCTACACTTGCTACAATTCCTAAG 59.125 40.000 0.00 0.00 0.00 2.18
2093 3634 0.327924 ATTCCAGTGGATCACGGCAA 59.672 50.000 14.00 0.00 39.64 4.52
2107 3648 2.492196 GGAGAGGGTATCCGGTATTCCA 60.492 54.545 0.00 0.00 38.33 3.53
2115 3656 1.683917 CACAGAAGGAGAGGGTATCCG 59.316 57.143 0.00 0.00 42.02 4.18
2137 3678 1.661112 CTGCAACTACTTAAGCGAGGC 59.339 52.381 1.29 1.25 0.00 4.70
2179 3720 1.707427 GGGATGTTAGGAGCCATGGAT 59.293 52.381 18.40 10.08 0.00 3.41
2181 3722 1.072965 GAGGGATGTTAGGAGCCATGG 59.927 57.143 7.63 7.63 0.00 3.66
2207 3752 1.969923 TGGGGTCAAGCCAAATTTCAG 59.030 47.619 0.01 0.00 39.65 3.02
2235 3780 1.341187 ACCCGAACAGTTTTTGGTGGA 60.341 47.619 2.45 0.00 0.00 4.02
2373 3919 3.489180 ACAATGACTACTTCCTCGACG 57.511 47.619 0.00 0.00 0.00 5.12
2413 3959 1.577328 CGCAAGGCTTCGTTGACCAT 61.577 55.000 0.00 0.00 31.88 3.55
2419 3965 2.954753 CTTCGCGCAAGGCTTCGTT 61.955 57.895 8.75 0.00 40.44 3.85
2462 4008 4.350816 TCAAGAACATTCTCAAGGAGGGAA 59.649 41.667 0.00 0.00 36.28 3.97
2500 4046 1.409521 GCCATGGGTGTTATAGTGCCA 60.410 52.381 15.13 0.00 0.00 4.92
2547 4542 8.940768 TTCAGTCGTCAACAATTATATGATGA 57.059 30.769 5.54 5.54 36.91 2.92
2553 4548 8.517056 TCTACACTTCAGTCGTCAACAATTATA 58.483 33.333 0.00 0.00 0.00 0.98
2554 4549 7.375834 TCTACACTTCAGTCGTCAACAATTAT 58.624 34.615 0.00 0.00 0.00 1.28
2555 4550 6.741109 TCTACACTTCAGTCGTCAACAATTA 58.259 36.000 0.00 0.00 0.00 1.40
2556 4551 5.597806 TCTACACTTCAGTCGTCAACAATT 58.402 37.500 0.00 0.00 0.00 2.32
2557 4552 5.196341 TCTACACTTCAGTCGTCAACAAT 57.804 39.130 0.00 0.00 0.00 2.71
2558 4553 4.642445 TCTACACTTCAGTCGTCAACAA 57.358 40.909 0.00 0.00 0.00 2.83
2562 4561 2.885266 AGCTTCTACACTTCAGTCGTCA 59.115 45.455 0.00 0.00 0.00 4.35
2587 6536 3.408634 CCCGTTGTCTTGTCACCTTATT 58.591 45.455 0.00 0.00 0.00 1.40
2588 6537 2.874457 GCCCGTTGTCTTGTCACCTTAT 60.874 50.000 0.00 0.00 0.00 1.73
2589 6538 1.541670 GCCCGTTGTCTTGTCACCTTA 60.542 52.381 0.00 0.00 0.00 2.69
2604 6553 1.683943 CCATGATCTTGATTGCCCGT 58.316 50.000 10.07 0.00 0.00 5.28
2612 6701 0.462581 GAGGTGCGCCATGATCTTGA 60.463 55.000 20.59 0.00 37.19 3.02
2669 6963 1.340889 GAGGGCTTGCATTGTTGTTGA 59.659 47.619 0.00 0.00 0.00 3.18
2712 7006 2.887360 GACCTACGCCGCTACCAA 59.113 61.111 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.