Multiple sequence alignment - TraesCS2D01G536000

Loading Multiple Alignment...

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 TraesCS2D01G536000 chr2D 100.000 2815 0 0 524 3338 618697630 618694816 0.000000e+00 5199
1 TraesCS2D01G536000 chr2D 100.000 188 0 0 1 188 618698153 618697966 6.850000e-92 348
2 TraesCS2D01G536000 chr3B 91.916 1868 81 41 571 2407 738320286 738318458 0.000000e+00 2549
3 TraesCS2D01G536000 chr3B 92.575 835 40 9 2405 3232 738318182 738317363 0.000000e+00 1179
4 TraesCS2D01G536000 chr3B 89.730 185 16 2 792 973 738313646 738313830 2.000000e-57 233
5 TraesCS2D01G536000 chr3B 92.308 78 5 1 102 178 738322105 738322028 3.520000e-20 110
6 TraesCS2D01G536000 chrUn 94.595 1443 50 12 533 1963 271484413 271482987 0.000000e+00 2207
7 TraesCS2D01G536000 chrUn 92.771 166 12 0 21 186 392008503 392008338 1.200000e-59 241
8 TraesCS2D01G536000 chrUn 92.771 166 12 0 21 186 392010130 392009965 1.200000e-59 241
9 TraesCS2D01G536000 chrUn 97.468 79 2 0 3228 3306 271479877 271479799 5.810000e-28 135
10 TraesCS2D01G536000 chr2B 94.595 1443 50 12 533 1963 755409460 755408034 0.000000e+00 2207
11 TraesCS2D01G536000 chr2B 97.468 79 2 0 3228 3306 755404924 755404846 5.810000e-28 135
12 TraesCS2D01G536000 chr3A 77.930 512 70 20 801 1301 740097366 740096887 2.540000e-71 279
13 TraesCS2D01G536000 chr6D 97.222 108 3 0 1409 1516 188727561 188727454 2.050000e-42 183
14 TraesCS2D01G536000 chr6D 96.296 108 2 1 1169 1274 188727666 188727559 3.420000e-40 176


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 TraesCS2D01G536000 chr2D 618694816 618698153 3337 True 2773.500000 5199 100.000000 1 3338 2 chr2D.!!$R1 3337
1 TraesCS2D01G536000 chr3B 738317363 738322105 4742 True 1279.333333 2549 92.266333 102 3232 3 chr3B.!!$R1 3130
2 TraesCS2D01G536000 chrUn 271479799 271484413 4614 True 1171.000000 2207 96.031500 533 3306 2 chrUn.!!$R1 2773
3 TraesCS2D01G536000 chrUn 392008338 392010130 1792 True 241.000000 241 92.771000 21 186 2 chrUn.!!$R2 165
4 TraesCS2D01G536000 chr2B 755404846 755409460 4614 True 1171.000000 2207 96.031500 533 3306 2 chr2B.!!$R1 2773

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
43 44 0.036294 GGAGAGTACACAAGCACCCC 60.036 60.0 0.0 0.0 0.0 4.95 F
1128 3030 0.101219 CGCAGATGACGATGAGGACA 59.899 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 3818 1.628846 AGGCAACCGGAGACAATACTT 59.371 47.619 9.46 0.0 37.17 2.24 R
2414 4363 0.032540 GGCAGACTGTTTTGGGCAAG 59.967 55.000 3.99 0.0 0.00 4.01 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
20 21 3.833545 CTTCCCTATATGACGAGGTCG 57.166 52.381 0.00 0.00 46.33 4.79
21 22 1.531423 TCCCTATATGACGAGGTCGC 58.469 55.000 0.00 0.00 44.43 5.19
22 23 1.202842 TCCCTATATGACGAGGTCGCA 60.203 52.381 0.00 0.00 44.43 5.10
23 24 1.611977 CCCTATATGACGAGGTCGCAA 59.388 52.381 0.00 0.00 44.43 4.85
43 44 0.036294 GGAGAGTACACAAGCACCCC 60.036 60.000 0.00 0.00 0.00 4.95
118 119 4.122776 ACTCTATGTTGCTTTATCGCTGG 58.877 43.478 0.00 0.00 0.00 4.85
181 182 2.086094 TCTACATAGTTCGCACGGTGA 58.914 47.619 13.29 0.00 0.00 4.02
186 187 2.758770 TAGTTCGCACGGTGAGCCAC 62.759 60.000 13.29 8.90 34.09 5.01
187 188 4.228567 TTCGCACGGTGAGCCACA 62.229 61.111 13.29 0.00 35.86 4.17
567 2041 7.675962 TTTTCTTTATCGATTTCCTTTCGGA 57.324 32.000 1.71 0.00 37.22 4.55
658 2559 4.517453 CCAATAAGAAACGGTCCAAACAGA 59.483 41.667 0.00 0.00 0.00 3.41
668 2569 2.290577 GGTCCAAACAGAGGCTGATTCT 60.291 50.000 0.00 0.00 35.18 2.40
689 2590 0.737715 GCCCAAGTCTACTCACGCTG 60.738 60.000 0.00 0.00 0.00 5.18
760 2662 2.260743 GACAGGGGTCGACCGAAC 59.739 66.667 27.68 19.65 41.60 3.95
768 2670 0.103755 GGTCGACCGAACCCCTAATC 59.896 60.000 20.85 0.00 0.00 1.75
769 2671 0.103755 GTCGACCGAACCCCTAATCC 59.896 60.000 3.51 0.00 0.00 3.01
852 2754 1.336887 CCGAGTTCGACCACATGTTCT 60.337 52.381 0.00 0.00 43.02 3.01
1128 3030 0.101219 CGCAGATGACGATGAGGACA 59.899 55.000 0.00 0.00 0.00 4.02
1142 3056 1.007734 GGACAGCAAGACGACGACA 60.008 57.895 0.00 0.00 0.00 4.35
1339 3258 7.813852 TCAATACTAGCGTTCTTCTTTCTTC 57.186 36.000 0.00 0.00 0.00 2.87
1340 3259 7.603651 TCAATACTAGCGTTCTTCTTTCTTCT 58.396 34.615 0.00 0.00 0.00 2.85
1342 3261 4.811908 ACTAGCGTTCTTCTTTCTTCTCC 58.188 43.478 0.00 0.00 0.00 3.71
1344 3263 4.073293 AGCGTTCTTCTTTCTTCTCCAA 57.927 40.909 0.00 0.00 0.00 3.53
1345 3264 4.646572 AGCGTTCTTCTTTCTTCTCCAAT 58.353 39.130 0.00 0.00 0.00 3.16
1346 3265 4.693095 AGCGTTCTTCTTTCTTCTCCAATC 59.307 41.667 0.00 0.00 0.00 2.67
1347 3266 4.693095 GCGTTCTTCTTTCTTCTCCAATCT 59.307 41.667 0.00 0.00 0.00 2.40
1348 3267 5.390356 GCGTTCTTCTTTCTTCTCCAATCTG 60.390 44.000 0.00 0.00 0.00 2.90
1349 3268 5.928839 CGTTCTTCTTTCTTCTCCAATCTGA 59.071 40.000 0.00 0.00 0.00 3.27
1350 3269 6.593382 CGTTCTTCTTTCTTCTCCAATCTGAT 59.407 38.462 0.00 0.00 0.00 2.90
1351 3270 7.412781 CGTTCTTCTTTCTTCTCCAATCTGATG 60.413 40.741 0.00 0.00 0.00 3.07
1352 3271 7.250032 TCTTCTTTCTTCTCCAATCTGATGA 57.750 36.000 0.00 0.00 0.00 2.92
1353 3272 7.859540 TCTTCTTTCTTCTCCAATCTGATGAT 58.140 34.615 0.00 0.00 33.70 2.45
1354 3273 7.769507 TCTTCTTTCTTCTCCAATCTGATGATG 59.230 37.037 0.00 0.00 32.44 3.07
1355 3274 7.191593 TCTTTCTTCTCCAATCTGATGATGA 57.808 36.000 0.00 0.00 32.44 2.92
1356 3275 7.803131 TCTTTCTTCTCCAATCTGATGATGAT 58.197 34.615 0.00 0.00 32.44 2.45
1357 3276 7.715686 TCTTTCTTCTCCAATCTGATGATGATG 59.284 37.037 0.00 0.00 32.44 3.07
1358 3277 6.742559 TCTTCTCCAATCTGATGATGATGA 57.257 37.500 0.00 0.00 32.44 2.92
1376 3295 9.383519 TGATGATGATGATGATGATGATACAAG 57.616 33.333 0.00 0.00 0.00 3.16
1439 3364 1.337071 GGTCCGATGAGATACGCTTCA 59.663 52.381 0.00 0.00 0.00 3.02
1538 3465 8.773404 AGCTGTATACGAAATCTTACTGTTTT 57.227 30.769 0.00 0.00 0.00 2.43
1625 3552 2.246719 GGGATCACCTGGATTTCTCG 57.753 55.000 0.00 0.00 36.00 4.04
1699 3626 5.811100 CAGTACGTAATCCTTCCTTCTTTCC 59.189 44.000 0.00 0.00 0.00 3.13
1869 3818 4.651778 CCAAGGTGGTTGATGAAGACTTA 58.348 43.478 0.00 0.00 38.60 2.24
2067 4016 3.109847 TGGCAACACTGTCCTTTCC 57.890 52.632 0.00 0.00 46.17 3.13
2240 4189 0.821301 TTTGTGGCGTCCAAGCATGA 60.821 50.000 0.00 0.00 39.27 3.07
2342 4291 5.527951 AGACGACTATGAAGAATGATCAGC 58.472 41.667 0.09 0.00 0.00 4.26
2349 4298 3.654020 GAATGATCAGCGGCGCCC 61.654 66.667 30.40 14.23 0.00 6.13
2391 4340 0.108756 GTCGGTGTTGGAGTAGCCTC 60.109 60.000 0.00 0.00 37.63 4.70
2407 4356 7.608376 GGAGTAGCCTCAGTTATCTTTTTCTTT 59.392 37.037 0.00 0.00 39.64 2.52
2409 4358 7.939588 AGTAGCCTCAGTTATCTTTTTCTTTGT 59.060 33.333 0.00 0.00 0.00 2.83
2410 4359 6.974965 AGCCTCAGTTATCTTTTTCTTTGTG 58.025 36.000 0.00 0.00 0.00 3.33
2411 4360 6.772716 AGCCTCAGTTATCTTTTTCTTTGTGA 59.227 34.615 0.00 0.00 0.00 3.58
2412 4361 7.285401 AGCCTCAGTTATCTTTTTCTTTGTGAA 59.715 33.333 0.00 0.00 0.00 3.18
2414 4363 9.237846 CCTCAGTTATCTTTTTCTTTGTGAAAC 57.762 33.333 0.00 0.00 43.55 2.78
2431 6250 3.119173 TGAAACTTGCCCAAAACAGTCTG 60.119 43.478 0.00 0.00 0.00 3.51
2436 6255 1.075374 TGCCCAAAACAGTCTGCCTAT 59.925 47.619 0.00 0.00 0.00 2.57
2568 6568 2.264813 CCAGGCGCAATTCAAATTCAG 58.735 47.619 10.83 0.00 0.00 3.02
2679 7177 6.537566 CCAATCAAATACAAGAACTGAGACG 58.462 40.000 0.00 0.00 0.00 4.18
2682 7180 4.686091 TCAAATACAAGAACTGAGACGCTG 59.314 41.667 0.00 0.00 0.00 5.18
2695 7193 5.047943 ACTGAGACGCTGTTACACTTATTCT 60.048 40.000 0.00 0.00 0.00 2.40
2699 7197 6.398918 AGACGCTGTTACACTTATTCTTCAT 58.601 36.000 0.00 0.00 0.00 2.57
2700 7198 7.544622 AGACGCTGTTACACTTATTCTTCATA 58.455 34.615 0.00 0.00 0.00 2.15
2701 7199 8.198109 AGACGCTGTTACACTTATTCTTCATAT 58.802 33.333 0.00 0.00 0.00 1.78
2702 7200 9.459640 GACGCTGTTACACTTATTCTTCATATA 57.540 33.333 0.00 0.00 0.00 0.86
2703 7201 9.464714 ACGCTGTTACACTTATTCTTCATATAG 57.535 33.333 0.00 0.00 0.00 1.31
2704 7202 8.428536 CGCTGTTACACTTATTCTTCATATAGC 58.571 37.037 0.00 0.00 0.00 2.97
2705 7203 8.428536 GCTGTTACACTTATTCTTCATATAGCG 58.571 37.037 0.00 0.00 0.00 4.26
2706 7204 8.294341 TGTTACACTTATTCTTCATATAGCGC 57.706 34.615 0.00 0.00 0.00 5.92
2707 7205 8.141909 TGTTACACTTATTCTTCATATAGCGCT 58.858 33.333 17.26 17.26 0.00 5.92
2728 7226 6.364976 GCGCTTAATTAAACTGTGTTCCAAAT 59.635 34.615 0.00 0.00 0.00 2.32
2738 7236 5.256474 ACTGTGTTCCAAATATCTCCCTTG 58.744 41.667 0.00 0.00 0.00 3.61
2743 7241 2.791179 TCCAAATATCTCCCTTGGCCAT 59.209 45.455 6.09 0.00 39.61 4.40
2748 7246 5.865977 AATATCTCCCTTGGCCATATTGA 57.134 39.130 6.09 2.01 0.00 2.57
2755 7253 3.431207 CCCTTGGCCATATTGAAAGCTTG 60.431 47.826 6.09 0.00 0.00 4.01
2780 7278 9.349713 TGTCCTAGCTCTTTATTTTGAGAAAAA 57.650 29.630 0.00 0.00 33.47 1.94
2787 7285 9.186323 GCTCTTTATTTTGAGAAAAAGGTTCTC 57.814 33.333 8.78 8.78 43.85 2.87
2888 7386 4.465512 GTTCACCATGCGCTGCCG 62.466 66.667 9.73 0.00 37.57 5.69
2946 7444 3.117888 GGACTGGGCTCTGAAATTGGATA 60.118 47.826 0.00 0.00 0.00 2.59
2971 7469 3.310435 GGGGACTAGAGTTTCCTCCCTTA 60.310 52.174 11.10 0.00 38.58 2.69
2977 7475 5.717654 ACTAGAGTTTCCTCCCTTACAGAAG 59.282 44.000 0.00 0.00 38.58 2.85
2980 7478 5.247337 AGAGTTTCCTCCCTTACAGAAGAAG 59.753 44.000 0.00 0.00 38.58 2.85
2992 7491 6.492156 CTTACAGAAGAAGAGGGCTTTTGCA 61.492 44.000 0.00 0.00 40.32 4.08
3049 7548 7.856145 AGGAAACTTTCTGATGCATTACTAG 57.144 36.000 0.00 0.00 37.44 2.57
3167 7666 3.175710 ACCCAACCACGCCCTTCT 61.176 61.111 0.00 0.00 0.00 2.85
3176 7675 0.176680 CACGCCCTTCTCTGTAGCAT 59.823 55.000 0.00 0.00 0.00 3.79
3179 7678 1.808133 CGCCCTTCTCTGTAGCATTCC 60.808 57.143 0.00 0.00 0.00 3.01
3292 7813 1.978617 CCTGTTGGGGCCACATGTC 60.979 63.158 9.55 3.06 0.00 3.06
3306 7827 2.746904 CACATGTCCACCAGCGATTTTA 59.253 45.455 0.00 0.00 0.00 1.52
3307 7828 3.378112 CACATGTCCACCAGCGATTTTAT 59.622 43.478 0.00 0.00 0.00 1.40
3309 7830 5.065859 CACATGTCCACCAGCGATTTTATTA 59.934 40.000 0.00 0.00 0.00 0.98
3310 7831 5.827797 ACATGTCCACCAGCGATTTTATTAT 59.172 36.000 0.00 0.00 0.00 1.28
3312 7833 6.130298 TGTCCACCAGCGATTTTATTATTG 57.870 37.500 0.00 0.00 0.00 1.90
3313 7834 5.883115 TGTCCACCAGCGATTTTATTATTGA 59.117 36.000 0.00 0.00 0.00 2.57
3314 7835 6.183360 TGTCCACCAGCGATTTTATTATTGAC 60.183 38.462 0.00 0.00 0.00 3.18
3315 7836 5.007234 TCCACCAGCGATTTTATTATTGACG 59.993 40.000 0.00 0.00 0.00 4.35
3316 7837 4.670621 CACCAGCGATTTTATTATTGACGC 59.329 41.667 0.00 0.00 43.84 5.19
3318 7839 5.163703 ACCAGCGATTTTATTATTGACGCAA 60.164 36.000 0.00 0.00 45.47 4.85
3319 7840 5.914635 CCAGCGATTTTATTATTGACGCAAT 59.085 36.000 0.00 9.46 45.47 3.56
3320 7841 6.129378 CCAGCGATTTTATTATTGACGCAATG 60.129 38.462 0.00 0.00 45.47 2.82
3321 7842 6.632434 CAGCGATTTTATTATTGACGCAATGA 59.368 34.615 0.00 7.23 45.47 2.57
3322 7843 6.632834 AGCGATTTTATTATTGACGCAATGAC 59.367 34.615 0.00 0.00 45.47 3.06
3323 7844 6.396454 GCGATTTTATTATTGACGCAATGACG 60.396 38.462 13.17 6.79 43.18 4.35
3336 7857 5.806286 ACGCAATGACGTAATTTCATTAGG 58.194 37.500 0.00 2.84 46.19 2.69
3337 7858 5.204833 CGCAATGACGTAATTTCATTAGGG 58.795 41.667 0.00 4.50 40.92 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.095161 GCGACCTCGTCATATAGGGAAG 60.095 54.545 0.00 0.00 42.22 3.46
2 3 1.202842 TGCGACCTCGTCATATAGGGA 60.203 52.381 0.00 0.00 42.22 4.20
3 4 1.244816 TGCGACCTCGTCATATAGGG 58.755 55.000 0.00 0.00 42.22 3.53
4 5 2.351835 CCTTGCGACCTCGTCATATAGG 60.352 54.545 0.00 0.00 42.22 2.57
5 6 2.552743 TCCTTGCGACCTCGTCATATAG 59.447 50.000 0.00 0.00 42.22 1.31
6 7 2.552743 CTCCTTGCGACCTCGTCATATA 59.447 50.000 0.00 0.00 42.22 0.86
7 8 1.338337 CTCCTTGCGACCTCGTCATAT 59.662 52.381 0.00 0.00 42.22 1.78
8 9 0.738975 CTCCTTGCGACCTCGTCATA 59.261 55.000 0.00 0.00 42.22 2.15
9 10 0.965866 TCTCCTTGCGACCTCGTCAT 60.966 55.000 0.00 0.00 42.22 3.06
10 11 1.587043 CTCTCCTTGCGACCTCGTCA 61.587 60.000 0.00 0.00 42.22 4.35
11 12 1.137825 CTCTCCTTGCGACCTCGTC 59.862 63.158 0.00 0.00 42.22 4.20
12 13 0.322277 TACTCTCCTTGCGACCTCGT 60.322 55.000 0.00 0.00 42.22 4.18
13 14 0.099082 GTACTCTCCTTGCGACCTCG 59.901 60.000 0.00 0.00 43.27 4.63
14 15 1.135344 GTGTACTCTCCTTGCGACCTC 60.135 57.143 0.00 0.00 0.00 3.85
15 16 0.889306 GTGTACTCTCCTTGCGACCT 59.111 55.000 0.00 0.00 0.00 3.85
16 17 0.601558 TGTGTACTCTCCTTGCGACC 59.398 55.000 0.00 0.00 0.00 4.79
17 18 2.329379 CTTGTGTACTCTCCTTGCGAC 58.671 52.381 0.00 0.00 0.00 5.19
18 19 1.336887 GCTTGTGTACTCTCCTTGCGA 60.337 52.381 0.00 0.00 0.00 5.10
19 20 1.071605 GCTTGTGTACTCTCCTTGCG 58.928 55.000 0.00 0.00 0.00 4.85
20 21 1.801178 GTGCTTGTGTACTCTCCTTGC 59.199 52.381 0.00 0.00 0.00 4.01
21 22 2.417719 GGTGCTTGTGTACTCTCCTTG 58.582 52.381 0.00 0.00 0.00 3.61
22 23 1.348036 GGGTGCTTGTGTACTCTCCTT 59.652 52.381 0.00 0.00 0.00 3.36
23 24 0.977395 GGGTGCTTGTGTACTCTCCT 59.023 55.000 0.00 0.00 0.00 3.69
67 68 1.133025 GCTCGCTGGCAATTATGTTGT 59.867 47.619 0.00 0.00 0.00 3.32
76 77 2.510012 CAGATCGCTCGCTGGCAA 60.510 61.111 0.00 0.00 0.00 4.52
118 119 7.800767 TCATAATGAGCGAGATTTAGCATTTC 58.199 34.615 0.00 0.00 35.48 2.17
621 2522 7.961283 CGTTTCTTATTGGGCTAAAGTTCTTAC 59.039 37.037 0.00 0.00 0.00 2.34
668 2569 1.972198 CGTGAGTAGACTTGGGCCA 59.028 57.895 0.00 0.00 0.00 5.36
689 2590 2.914289 CTCACCAGGCCAGATCCC 59.086 66.667 5.01 0.00 0.00 3.85
745 2646 4.078516 GGGTTCGGTCGACCCCTG 62.079 72.222 28.52 15.05 42.77 4.45
769 2671 2.689813 GAGGTTGGGGATTGGGGG 59.310 66.667 0.00 0.00 0.00 5.40
925 2827 1.492133 TTCCTCTTGGGTGGGCTCTG 61.492 60.000 0.00 0.00 36.25 3.35
1128 3030 2.429236 CGCTGTCGTCGTCTTGCT 60.429 61.111 0.00 0.00 0.00 3.91
1142 3056 4.664677 GTGTCCACGGTCTGCGCT 62.665 66.667 9.73 0.00 0.00 5.92
1339 3258 7.106239 TCATCATCATCATCATCAGATTGGAG 58.894 38.462 0.00 0.00 30.20 3.86
1340 3259 7.016153 TCATCATCATCATCATCAGATTGGA 57.984 36.000 0.00 0.00 30.20 3.53
1342 3261 8.498054 TCATCATCATCATCATCATCAGATTG 57.502 34.615 0.00 0.00 30.20 2.67
1344 3263 8.489489 TCATCATCATCATCATCATCATCAGAT 58.511 33.333 0.00 0.00 33.87 2.90
1345 3264 7.851228 TCATCATCATCATCATCATCATCAGA 58.149 34.615 0.00 0.00 0.00 3.27
1346 3265 8.674263 ATCATCATCATCATCATCATCATCAG 57.326 34.615 0.00 0.00 0.00 2.90
1347 3266 9.547753 GTATCATCATCATCATCATCATCATCA 57.452 33.333 0.00 0.00 0.00 3.07
1348 3267 9.547753 TGTATCATCATCATCATCATCATCATC 57.452 33.333 0.00 0.00 0.00 2.92
1349 3268 9.905713 TTGTATCATCATCATCATCATCATCAT 57.094 29.630 0.00 0.00 0.00 2.45
1350 3269 9.383519 CTTGTATCATCATCATCATCATCATCA 57.616 33.333 0.00 0.00 0.00 3.07
1351 3270 9.384764 ACTTGTATCATCATCATCATCATCATC 57.615 33.333 0.00 0.00 0.00 2.92
1352 3271 9.167311 CACTTGTATCATCATCATCATCATCAT 57.833 33.333 0.00 0.00 0.00 2.45
1353 3272 7.606456 CCACTTGTATCATCATCATCATCATCA 59.394 37.037 0.00 0.00 0.00 3.07
1354 3273 7.606839 ACCACTTGTATCATCATCATCATCATC 59.393 37.037 0.00 0.00 0.00 2.92
1355 3274 7.459234 ACCACTTGTATCATCATCATCATCAT 58.541 34.615 0.00 0.00 0.00 2.45
1356 3275 6.834107 ACCACTTGTATCATCATCATCATCA 58.166 36.000 0.00 0.00 0.00 3.07
1357 3276 8.093307 ACTACCACTTGTATCATCATCATCATC 58.907 37.037 0.00 0.00 0.00 2.92
1358 3277 7.971201 ACTACCACTTGTATCATCATCATCAT 58.029 34.615 0.00 0.00 0.00 2.45
1376 3295 5.672421 AGTAGTTTGGGTCATACTACCAC 57.328 43.478 18.20 4.41 44.20 4.16
1439 3364 4.151121 TGTCATCACCACCAAATTCACAT 58.849 39.130 0.00 0.00 0.00 3.21
1538 3465 6.403092 CCATATTGTCACGCATAAACTTGACA 60.403 38.462 0.00 0.00 44.27 3.58
1571 3498 6.071560 TCACGCCATAGACCTCGATATTATTT 60.072 38.462 0.00 0.00 0.00 1.40
1625 3552 2.345341 GCAATGGAAAATGTAGTTGCGC 59.655 45.455 0.00 0.00 33.61 6.09
1869 3818 1.628846 AGGCAACCGGAGACAATACTT 59.371 47.619 9.46 0.00 37.17 2.24
2067 4016 1.573108 TGAAGGAGTAGGAGCCTTGG 58.427 55.000 0.00 0.00 44.23 3.61
2112 4061 5.335651 TCCCGCTGGATGGTATAAAACCC 62.336 52.174 0.00 0.00 41.13 4.11
2127 4076 0.597568 TTTGAATGTGCTTCCCGCTG 59.402 50.000 0.00 0.00 40.11 5.18
2240 4189 3.448686 CGATACATTTGCTCCTCTTCGT 58.551 45.455 0.00 0.00 0.00 3.85
2342 4291 1.371635 CTTTGAAAACTGGGCGCCG 60.372 57.895 22.54 10.51 0.00 6.46
2349 4298 4.907879 AAGGAGCTGACTTTGAAAACTG 57.092 40.909 0.00 0.00 0.00 3.16
2407 4356 2.564947 ACTGTTTTGGGCAAGTTTCACA 59.435 40.909 0.00 0.00 0.00 3.58
2409 4358 3.096092 AGACTGTTTTGGGCAAGTTTCA 58.904 40.909 0.00 0.00 0.00 2.69
2410 4359 3.447742 CAGACTGTTTTGGGCAAGTTTC 58.552 45.455 0.00 0.00 0.00 2.78
2411 4360 2.418609 GCAGACTGTTTTGGGCAAGTTT 60.419 45.455 3.99 0.00 0.00 2.66
2412 4361 1.136891 GCAGACTGTTTTGGGCAAGTT 59.863 47.619 3.99 0.00 0.00 2.66
2414 4363 0.032540 GGCAGACTGTTTTGGGCAAG 59.967 55.000 3.99 0.00 0.00 4.01
2415 4364 0.396974 AGGCAGACTGTTTTGGGCAA 60.397 50.000 3.99 0.00 0.00 4.52
2495 6320 8.190122 TCATAAGAGCGCAAAACATAATTCATT 58.810 29.630 11.47 0.00 0.00 2.57
2544 6544 3.951775 ATTTGAATTGCGCCTGGTTTA 57.048 38.095 4.18 0.00 0.00 2.01
2557 6557 8.169977 ACACATGAGTTACACTGAATTTGAAT 57.830 30.769 0.00 0.00 0.00 2.57
2568 6568 8.311650 ACAGAGATAAAACACATGAGTTACAC 57.688 34.615 9.01 2.49 0.00 2.90
2606 6606 6.208599 TGTCAAACACAAGTTTTCCTTCTCTT 59.791 34.615 0.00 0.00 45.32 2.85
2679 7177 8.428536 CGCTATATGAAGAATAAGTGTAACAGC 58.571 37.037 0.00 0.00 41.43 4.40
2682 7180 8.522178 AGCGCTATATGAAGAATAAGTGTAAC 57.478 34.615 8.99 0.00 0.00 2.50
2695 7193 9.104965 ACACAGTTTAATTAAGCGCTATATGAA 57.895 29.630 12.05 3.65 0.00 2.57
2699 7197 7.549842 TGGAACACAGTTTAATTAAGCGCTATA 59.450 33.333 12.05 1.02 0.00 1.31
2700 7198 6.373216 TGGAACACAGTTTAATTAAGCGCTAT 59.627 34.615 12.05 0.00 0.00 2.97
2701 7199 5.701750 TGGAACACAGTTTAATTAAGCGCTA 59.298 36.000 12.05 0.00 0.00 4.26
2702 7200 4.517453 TGGAACACAGTTTAATTAAGCGCT 59.483 37.500 2.64 2.64 0.00 5.92
2703 7201 4.789784 TGGAACACAGTTTAATTAAGCGC 58.210 39.130 0.00 0.00 0.00 5.92
2704 7202 7.867445 ATTTGGAACACAGTTTAATTAAGCG 57.133 32.000 6.43 4.86 39.29 4.68
2728 7226 5.634118 CTTTCAATATGGCCAAGGGAGATA 58.366 41.667 10.96 0.00 0.00 1.98
2738 7236 3.026694 AGGACAAGCTTTCAATATGGCC 58.973 45.455 0.00 0.00 39.60 5.36
2755 7253 9.833182 CTTTTTCTCAAAATAAAGAGCTAGGAC 57.167 33.333 0.00 0.00 31.28 3.85
2764 7262 8.349983 TCCGAGAACCTTTTTCTCAAAATAAAG 58.650 33.333 13.10 0.00 43.78 1.85
2769 7267 7.255346 GGTTATCCGAGAACCTTTTTCTCAAAA 60.255 37.037 16.28 0.31 43.78 2.44
2780 7278 2.547990 ACCTTGGTTATCCGAGAACCT 58.452 47.619 22.37 3.00 45.72 3.50
2787 7285 6.354794 TCCTATGATTACCTTGGTTATCCG 57.645 41.667 13.95 5.20 36.30 4.18
2888 7386 7.649306 TCTTATCTGAAACAAAAGCAAGAAAGC 59.351 33.333 0.00 0.00 0.00 3.51
2889 7387 9.688592 ATCTTATCTGAAACAAAAGCAAGAAAG 57.311 29.630 0.00 0.00 0.00 2.62
2971 7469 2.234143 GCAAAAGCCCTCTTCTTCTGT 58.766 47.619 0.00 0.00 0.00 3.41
2977 7475 4.379652 TCAATTTTGCAAAAGCCCTCTTC 58.620 39.130 27.08 0.00 0.00 2.87
2980 7478 2.481568 GCTCAATTTTGCAAAAGCCCTC 59.518 45.455 27.08 13.70 0.00 4.30
2992 7491 5.360714 TGAAAACTGGAGTGAGCTCAATTTT 59.639 36.000 20.19 14.00 43.37 1.82
3167 7666 2.256306 TGTCAGGTGGAATGCTACAGA 58.744 47.619 0.00 0.00 0.00 3.41
3176 7675 4.715534 TGGATAAACTTGTCAGGTGGAA 57.284 40.909 0.00 0.00 0.00 3.53
3179 7678 5.964958 ATGTTGGATAAACTTGTCAGGTG 57.035 39.130 0.00 0.00 39.70 4.00
3292 7813 5.204833 CGTCAATAATAAAATCGCTGGTGG 58.795 41.667 0.00 0.00 0.00 4.61
3306 7827 7.468441 TGAAATTACGTCATTGCGTCAATAAT 58.532 30.769 8.92 2.83 44.55 1.28
3307 7828 6.832804 TGAAATTACGTCATTGCGTCAATAA 58.167 32.000 8.92 0.93 44.55 1.40
3309 7830 5.289917 TGAAATTACGTCATTGCGTCAAT 57.710 34.783 8.92 0.09 44.55 2.57
3310 7831 4.733972 TGAAATTACGTCATTGCGTCAA 57.266 36.364 8.92 0.00 44.55 3.18
3312 7833 5.901884 CCTAATGAAATTACGTCATTGCGTC 59.098 40.000 12.21 0.00 43.76 5.19
3313 7834 5.220777 CCCTAATGAAATTACGTCATTGCGT 60.221 40.000 12.21 10.17 43.76 5.24
3314 7835 5.204833 CCCTAATGAAATTACGTCATTGCG 58.795 41.667 12.21 5.37 43.76 4.85


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

AutoCloner maintained by Alex Coulton.