Multiple sequence alignment - TraesCS5D01G512400

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 TraesCS5D01G512400 chr5D 100.000 2804 0 0 1 2804 536693355 536696158 0.000000e+00 5179
1 TraesCS5D01G512400 chr5D 92.737 179 13 0 997 1175 536688058 536688236 2.770000e-65 259
2 TraesCS5D01G512400 chr4A 90.229 2487 128 37 373 2804 634510445 634508019 0.000000e+00 3140
3 TraesCS5D01G512400 chr4A 84.615 130 11 3 374 502 634525151 634525030 1.360000e-23 121
4 TraesCS5D01G512400 chr5B 90.788 2106 108 39 362 2450 677346560 677348596 0.000000e+00 2736
5 TraesCS5D01G512400 chr5B 85.429 350 47 4 2 350 677345811 677346157 7.380000e-96 361
6 TraesCS5D01G512400 chr5B 90.870 230 19 2 997 1226 677336640 677336867 9.760000e-80 307
7 TraesCS5D01G512400 chr5B 83.333 132 20 2 227 358 687210111 687209982 1.360000e-23 121
8 TraesCS5D01G512400 chr5B 82.963 135 11 9 374 505 687209873 687209748 8.210000e-21 111
9 TraesCS5D01G512400 chr5B 83.077 130 11 5 374 501 687107111 687107231 1.060000e-19 108
10 TraesCS5D01G512400 chr6A 77.649 519 88 23 2298 2804 163142609 163142107 9.830000e-75 291
11 TraesCS5D01G512400 chr7D 77.407 509 66 20 2298 2801 130225223 130224759 9.970000e-65 257
12 TraesCS5D01G512400 chr4D 76.056 284 45 20 1012 1288 333011714 333011447 2.930000e-25 126


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 TraesCS5D01G512400 chr5D 536693355 536696158 2803 False 5179.0 5179 100.0000 1 2804 1 chr5D.!!$F2 2803
1 TraesCS5D01G512400 chr4A 634508019 634510445 2426 True 3140.0 3140 90.2290 373 2804 1 chr4A.!!$R1 2431
2 TraesCS5D01G512400 chr5B 677345811 677348596 2785 False 1548.5 2736 88.1085 2 2450 2 chr5B.!!$F3 2448
3 TraesCS5D01G512400 chr6A 163142107 163142609 502 True 291.0 291 77.6490 2298 2804 1 chr6A.!!$R1 506

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
771 1212 0.035056 ACGTACGTAGGGTAGGCAGT 60.035 55.0 21.41 0.0 39.94 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 3150 0.386478 GCGATAGTACCGTTAGGGCG 60.386 60.0 0.0 0.0 39.68 6.13 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
53 54 0.038455 GCCCGAGATAGCCTAGGAGA 59.962 60.000 14.75 0.00 39.73 3.71
55 56 1.459450 CCGAGATAGCCTAGGAGAGC 58.541 60.000 14.75 1.08 39.73 4.09
56 57 1.459450 CGAGATAGCCTAGGAGAGCC 58.541 60.000 14.75 0.00 0.00 4.70
59 60 3.118038 CGAGATAGCCTAGGAGAGCCTAT 60.118 52.174 14.75 9.26 45.54 2.57
60 61 4.101898 CGAGATAGCCTAGGAGAGCCTATA 59.898 50.000 14.75 0.00 45.54 1.31
62 63 5.952387 AGATAGCCTAGGAGAGCCTATATG 58.048 45.833 14.75 0.00 45.54 1.78
63 64 5.435041 AGATAGCCTAGGAGAGCCTATATGT 59.565 44.000 14.75 0.00 45.54 2.29
64 65 3.707316 AGCCTAGGAGAGCCTATATGTG 58.293 50.000 14.75 0.00 45.54 3.21
65 66 3.076785 AGCCTAGGAGAGCCTATATGTGT 59.923 47.826 14.75 0.00 45.54 3.72
66 67 3.194542 GCCTAGGAGAGCCTATATGTGTG 59.805 52.174 14.75 0.00 45.54 3.82
67 68 4.667573 CCTAGGAGAGCCTATATGTGTGA 58.332 47.826 1.05 0.00 45.54 3.58
68 69 5.080337 CCTAGGAGAGCCTATATGTGTGAA 58.920 45.833 1.05 0.00 45.54 3.18
69 70 5.719085 CCTAGGAGAGCCTATATGTGTGAAT 59.281 44.000 1.05 0.00 45.54 2.57
70 71 5.480642 AGGAGAGCCTATATGTGTGAATG 57.519 43.478 0.00 0.00 44.74 2.67
74 75 6.939163 GGAGAGCCTATATGTGTGAATGAAAT 59.061 38.462 0.00 0.00 0.00 2.17
85 86 6.437928 TGTGTGAATGAAATAAGCTCAACAC 58.562 36.000 0.00 0.00 36.07 3.32
87 88 5.238432 TGTGAATGAAATAAGCTCAACACGT 59.762 36.000 0.00 0.00 37.17 4.49
89 90 4.584029 ATGAAATAAGCTCAACACGTCG 57.416 40.909 0.00 0.00 0.00 5.12
95 96 1.954146 GCTCAACACGTCGCCTCAA 60.954 57.895 0.00 0.00 0.00 3.02
96 97 1.291877 GCTCAACACGTCGCCTCAAT 61.292 55.000 0.00 0.00 0.00 2.57
97 98 0.439985 CTCAACACGTCGCCTCAATG 59.560 55.000 0.00 0.00 0.00 2.82
124 125 3.912496 AATCCACAACTCATCGATGGA 57.088 42.857 24.61 14.44 43.42 3.41
138 139 4.090588 TGGAATCCCCACGTCGCC 62.091 66.667 0.00 0.00 40.82 5.54
139 140 4.090588 GGAATCCCCACGTCGCCA 62.091 66.667 0.00 0.00 34.14 5.69
141 142 4.404098 AATCCCCACGTCGCCACC 62.404 66.667 0.00 0.00 0.00 4.61
151 152 4.351938 TCGCCACCACGAAGTCCG 62.352 66.667 0.00 0.00 41.61 4.79
154 155 4.308458 CCACCACGAAGTCCGCCA 62.308 66.667 0.00 0.00 41.61 5.69
166 167 3.369400 CCGCCAAAACGCCCATGA 61.369 61.111 0.00 0.00 0.00 3.07
177 178 1.103398 CGCCCATGAGGATTTCACCC 61.103 60.000 0.00 0.00 38.99 4.61
183 184 1.452108 GAGGATTTCACCCTGGGCG 60.452 63.158 14.08 2.68 33.36 6.13
184 185 3.140814 GGATTTCACCCTGGGCGC 61.141 66.667 14.08 0.00 0.00 6.53
202 203 1.605058 GCTGGCGAGGGTGAACTAGA 61.605 60.000 0.00 0.00 0.00 2.43
220 221 5.865085 ACTAGATCACTAGAGTCTAGGCAG 58.135 45.833 27.07 17.58 46.34 4.85
267 268 3.190849 CATCGCTGCGGAGGTGTG 61.191 66.667 23.03 7.94 0.00 3.82
276 277 1.738099 CGGAGGTGTGGAGCTTTCG 60.738 63.158 0.00 0.00 0.00 3.46
297 298 2.612746 GGCACCTCCCCCACCTTA 60.613 66.667 0.00 0.00 0.00 2.69
352 353 3.404438 GACCCACCATGGCCCGTA 61.404 66.667 13.04 0.00 35.79 4.02
370 762 2.531483 TAGGGGAGGACCACAGAGCC 62.531 65.000 0.00 0.00 43.15 4.70
484 885 3.386078 GCAGACCATCAGATCCAACTCTA 59.614 47.826 0.00 0.00 0.00 2.43
612 1045 2.096013 GCCTAACAAAGCGATGAAGGTC 59.904 50.000 14.30 7.52 32.87 3.85
613 1046 2.678336 CCTAACAAAGCGATGAAGGTCC 59.322 50.000 0.00 0.00 0.00 4.46
714 1155 3.517100 TCCACAGATTCTTCTTCCTCCTG 59.483 47.826 0.00 0.00 0.00 3.86
725 1166 3.882444 TCTTCCTCCTGCATTTCATCAG 58.118 45.455 0.00 0.00 0.00 2.90
760 1201 2.825189 GCAAATCGCAAAACGTACGTA 58.175 42.857 23.12 4.86 44.19 3.57
761 1202 2.830480 GCAAATCGCAAAACGTACGTAG 59.170 45.455 23.12 15.44 44.19 3.51
762 1203 3.400995 CAAATCGCAAAACGTACGTAGG 58.599 45.455 23.12 14.75 44.19 3.18
763 1204 1.632422 ATCGCAAAACGTACGTAGGG 58.368 50.000 23.12 20.79 44.19 3.53
764 1205 0.313672 TCGCAAAACGTACGTAGGGT 59.686 50.000 23.12 10.18 44.19 4.34
765 1206 1.537638 TCGCAAAACGTACGTAGGGTA 59.462 47.619 23.12 9.98 44.19 3.69
766 1207 1.913403 CGCAAAACGTACGTAGGGTAG 59.087 52.381 23.12 9.75 36.87 3.18
767 1208 2.262211 GCAAAACGTACGTAGGGTAGG 58.738 52.381 23.12 8.36 41.59 3.18
768 1209 2.262211 CAAAACGTACGTAGGGTAGGC 58.738 52.381 23.12 0.00 39.94 3.93
769 1210 1.544724 AAACGTACGTAGGGTAGGCA 58.455 50.000 23.12 0.00 39.94 4.75
770 1211 1.098050 AACGTACGTAGGGTAGGCAG 58.902 55.000 23.12 0.00 39.94 4.85
771 1212 0.035056 ACGTACGTAGGGTAGGCAGT 60.035 55.000 21.41 0.00 39.94 4.40
772 1213 1.209504 ACGTACGTAGGGTAGGCAGTA 59.790 52.381 21.41 0.00 39.94 2.74
773 1214 1.599542 CGTACGTAGGGTAGGCAGTAC 59.400 57.143 7.22 0.00 31.03 2.73
774 1215 2.643551 GTACGTAGGGTAGGCAGTACA 58.356 52.381 0.00 0.00 35.75 2.90
849 1293 2.050533 TGACGCGGTTGCATTTGC 60.051 55.556 12.47 0.00 42.97 3.68
851 1295 1.797537 GACGCGGTTGCATTTGCTC 60.798 57.895 12.47 0.00 42.97 4.26
885 1339 5.904984 AGCCCTATATAAACACATCCACA 57.095 39.130 0.00 0.00 0.00 4.17
930 1384 3.064958 CACATCTCCACAGCACATCATTC 59.935 47.826 0.00 0.00 0.00 2.67
931 1385 3.054582 ACATCTCCACAGCACATCATTCT 60.055 43.478 0.00 0.00 0.00 2.40
955 1409 1.363885 GGCCTAAGTTAACCGCGTGG 61.364 60.000 14.93 14.93 42.84 4.94
956 1410 0.390209 GCCTAAGTTAACCGCGTGGA 60.390 55.000 24.59 0.00 39.21 4.02
958 1412 1.067354 CCTAAGTTAACCGCGTGGAGT 60.067 52.381 24.59 11.67 39.21 3.85
962 1416 1.227586 TTAACCGCGTGGAGTTGCA 60.228 52.632 24.59 0.00 39.21 4.08
994 1448 1.893062 CAGGACAGATCAGTCGGCA 59.107 57.895 11.63 0.00 39.42 5.69
1832 2286 4.812814 CGTCCATCGTCTCATGCA 57.187 55.556 0.00 0.00 34.52 3.96
1833 2287 3.279285 CGTCCATCGTCTCATGCAT 57.721 52.632 0.00 0.00 34.52 3.96
1990 2446 8.496751 GGTATATCTTCGGCATTTTACTTCTTC 58.503 37.037 0.00 0.00 0.00 2.87
1994 2450 7.272037 TCTTCGGCATTTTACTTCTTCTTTT 57.728 32.000 0.00 0.00 0.00 2.27
1995 2451 7.360361 TCTTCGGCATTTTACTTCTTCTTTTC 58.640 34.615 0.00 0.00 0.00 2.29
2001 2457 7.596621 GGCATTTTACTTCTTCTTTTCTTGAGG 59.403 37.037 0.00 0.00 0.00 3.86
2044 2500 0.392193 GCACTGGATGGAGTGTCAGG 60.392 60.000 0.00 0.00 44.53 3.86
2066 2522 6.643770 CAGGGAAATTGTCAGAAATGTCAAAG 59.356 38.462 0.00 0.00 0.00 2.77
2114 2570 1.455786 CGAAGTCGCACGTCTGAAAAT 59.544 47.619 0.00 0.00 0.00 1.82
2222 2680 3.119096 GGCCGAACGCTTCAGTCC 61.119 66.667 0.00 0.00 37.74 3.85
2284 2742 6.141462 CAGTATCCTACGACTAACGATTTCC 58.859 44.000 0.00 0.00 45.77 3.13
2318 2779 8.675504 CGACTAACTTCAAGGTCTAGATCTAAA 58.324 37.037 5.79 3.41 0.00 1.85
2327 2788 8.314751 TCAAGGTCTAGATCTAAAGGTTTTCTG 58.685 37.037 5.79 0.00 0.00 3.02
2332 2793 9.092876 GTCTAGATCTAAAGGTTTTCTGACATG 57.907 37.037 3.57 0.00 0.00 3.21
2333 2794 6.749923 AGATCTAAAGGTTTTCTGACATGC 57.250 37.500 0.00 0.00 0.00 4.06
2374 2835 8.951243 GGTGAAAATGTAGAGCTAGATCTTTTT 58.049 33.333 16.99 15.98 0.00 1.94
2452 2913 8.177663 GCAAACTCGAAGAAGATCAATAATGAA 58.822 33.333 0.00 0.00 35.65 2.57
2456 2917 8.253810 ACTCGAAGAAGATCAATAATGAAGACA 58.746 33.333 0.00 0.00 35.65 3.41
2468 2929 4.474226 AATGAAGACAAAACACGAGCTC 57.526 40.909 2.73 2.73 0.00 4.09
2513 2975 4.656575 AGAAGACCCTCTTTTATAGGCTCC 59.343 45.833 0.00 0.00 36.73 4.70
2607 3091 0.401356 TGCAATGAAGAGGAGCCACA 59.599 50.000 0.00 0.00 0.00 4.17
2608 3092 0.807496 GCAATGAAGAGGAGCCACAC 59.193 55.000 0.00 0.00 0.00 3.82
2663 3147 0.034574 TCGCCCTAACGGTACTACCA 60.035 55.000 6.06 0.00 38.47 3.25
2664 3148 0.101219 CGCCCTAACGGTACTACCAC 59.899 60.000 6.06 0.00 38.47 4.16
2665 3149 1.478631 GCCCTAACGGTACTACCACT 58.521 55.000 6.06 0.00 38.47 4.00
2666 3150 1.406898 GCCCTAACGGTACTACCACTC 59.593 57.143 6.06 0.00 38.47 3.51
2667 3151 1.672881 CCCTAACGGTACTACCACTCG 59.327 57.143 6.06 0.00 38.47 4.18
2668 3152 1.064654 CCTAACGGTACTACCACTCGC 59.935 57.143 6.06 0.00 38.47 5.03
2669 3153 1.064654 CTAACGGTACTACCACTCGCC 59.935 57.143 6.06 0.00 38.47 5.54
2670 3154 1.598701 AACGGTACTACCACTCGCCC 61.599 60.000 6.06 0.00 38.47 6.13
2671 3155 1.751927 CGGTACTACCACTCGCCCT 60.752 63.158 6.06 0.00 38.47 5.19
2672 3156 0.464373 CGGTACTACCACTCGCCCTA 60.464 60.000 6.06 0.00 38.47 3.53
2673 3157 1.767759 GGTACTACCACTCGCCCTAA 58.232 55.000 0.00 0.00 38.42 2.69
2674 3158 1.406898 GGTACTACCACTCGCCCTAAC 59.593 57.143 0.00 0.00 38.42 2.34
2675 3159 1.064654 GTACTACCACTCGCCCTAACG 59.935 57.143 0.00 0.00 0.00 3.18
2676 3160 1.318158 ACTACCACTCGCCCTAACGG 61.318 60.000 0.00 0.00 0.00 4.44
2677 3161 1.304381 TACCACTCGCCCTAACGGT 60.304 57.895 0.00 0.00 0.00 4.83
2678 3162 0.034574 TACCACTCGCCCTAACGGTA 60.035 55.000 0.00 0.00 0.00 4.02
2679 3163 1.140375 CCACTCGCCCTAACGGTAC 59.860 63.158 0.00 0.00 0.00 3.34
2680 3164 1.318158 CCACTCGCCCTAACGGTACT 61.318 60.000 0.00 0.00 0.00 2.73
2681 3165 1.382522 CACTCGCCCTAACGGTACTA 58.617 55.000 0.00 0.00 0.00 1.82
2682 3166 1.952296 CACTCGCCCTAACGGTACTAT 59.048 52.381 0.00 0.00 0.00 2.12
2683 3167 2.031333 CACTCGCCCTAACGGTACTATC 60.031 54.545 0.00 0.00 0.00 2.08
2709 3193 1.202698 GGTTACAGCTCAGGGGCATAG 60.203 57.143 0.00 0.00 34.17 2.23
2793 3277 1.865340 GCGGTACTGCCACTTATAAGC 59.135 52.381 16.25 0.26 36.97 3.09
2801 3285 6.732896 ACTGCCACTTATAAGCTGTAGTAT 57.267 37.500 17.97 2.34 36.99 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.763897 ACATTTGCCCCTCTCATTTACAC 59.236 43.478 0.00 0.00 0.00 2.90
15 16 1.786928 GCGTCTAGCGTTCACATTTGC 60.787 52.381 8.08 0.00 43.66 3.68
53 54 7.941238 AGCTTATTTCATTCACACATATAGGCT 59.059 33.333 0.00 0.00 0.00 4.58
55 56 9.276590 TGAGCTTATTTCATTCACACATATAGG 57.723 33.333 0.00 0.00 0.00 2.57
59 60 8.236586 GTGTTGAGCTTATTTCATTCACACATA 58.763 33.333 0.00 0.00 35.46 2.29
60 61 7.086376 GTGTTGAGCTTATTTCATTCACACAT 58.914 34.615 0.00 0.00 35.46 3.21
62 63 5.565259 CGTGTTGAGCTTATTTCATTCACAC 59.435 40.000 0.00 0.00 33.58 3.82
63 64 5.238432 ACGTGTTGAGCTTATTTCATTCACA 59.762 36.000 0.00 0.00 33.50 3.58
64 65 5.689819 ACGTGTTGAGCTTATTTCATTCAC 58.310 37.500 0.00 0.00 32.07 3.18
65 66 5.389411 CGACGTGTTGAGCTTATTTCATTCA 60.389 40.000 0.00 0.00 0.00 2.57
66 67 5.015733 CGACGTGTTGAGCTTATTTCATTC 58.984 41.667 0.00 0.00 0.00 2.67
67 68 4.669197 GCGACGTGTTGAGCTTATTTCATT 60.669 41.667 0.00 0.00 0.00 2.57
68 69 3.181520 GCGACGTGTTGAGCTTATTTCAT 60.182 43.478 0.00 0.00 0.00 2.57
69 70 2.156891 GCGACGTGTTGAGCTTATTTCA 59.843 45.455 0.00 0.00 0.00 2.69
70 71 2.474032 GGCGACGTGTTGAGCTTATTTC 60.474 50.000 0.00 0.00 0.00 2.17
74 75 0.388134 GAGGCGACGTGTTGAGCTTA 60.388 55.000 0.00 0.00 0.00 3.09
95 96 2.649312 TGAGTTGTGGATTTCCTCCCAT 59.351 45.455 0.00 0.00 44.23 4.00
96 97 2.061848 TGAGTTGTGGATTTCCTCCCA 58.938 47.619 0.00 0.00 44.23 4.37
97 98 2.879103 TGAGTTGTGGATTTCCTCCC 57.121 50.000 0.00 0.00 44.23 4.30
111 112 2.126882 TGGGGATTCCATCGATGAGTT 58.873 47.619 26.86 10.09 41.46 3.01
124 125 4.404098 GGTGGCGACGTGGGGATT 62.404 66.667 0.00 0.00 0.00 3.01
138 139 1.440938 TTTTGGCGGACTTCGTGGTG 61.441 55.000 0.00 0.00 41.72 4.17
139 140 1.153127 TTTTGGCGGACTTCGTGGT 60.153 52.632 0.00 0.00 41.72 4.16
141 142 1.083015 CGTTTTGGCGGACTTCGTG 60.083 57.895 0.00 0.00 41.72 4.35
144 145 2.254350 GGCGTTTTGGCGGACTTC 59.746 61.111 0.00 0.00 0.00 3.01
145 146 3.292159 GGGCGTTTTGGCGGACTT 61.292 61.111 0.00 0.00 46.04 3.01
151 152 1.322538 ATCCTCATGGGCGTTTTGGC 61.323 55.000 0.00 0.00 43.88 4.52
154 155 2.231235 GTGAAATCCTCATGGGCGTTTT 59.769 45.455 0.00 0.00 36.14 2.43
166 167 2.677228 CGCCCAGGGTGAAATCCT 59.323 61.111 14.78 0.00 34.74 3.24
183 184 1.153549 CTAGTTCACCCTCGCCAGC 60.154 63.158 0.00 0.00 0.00 4.85
184 185 1.067821 GATCTAGTTCACCCTCGCCAG 59.932 57.143 0.00 0.00 0.00 4.85
189 190 5.442391 ACTCTAGTGATCTAGTTCACCCTC 58.558 45.833 24.09 5.86 45.80 4.30
196 197 6.126594 ACTGCCTAGACTCTAGTGATCTAGTT 60.127 42.308 19.06 0.00 42.88 2.24
198 199 5.700832 CACTGCCTAGACTCTAGTGATCTAG 59.299 48.000 11.46 16.40 43.48 2.43
202 203 2.955660 GCACTGCCTAGACTCTAGTGAT 59.044 50.000 11.46 0.00 40.80 3.06
220 221 4.643387 ACACCCCTCTTGCGGCAC 62.643 66.667 0.05 0.00 0.00 5.01
235 236 2.006552 GCGATGCATGTAGGTGTCACA 61.007 52.381 2.46 0.00 0.00 3.58
237 238 0.536724 AGCGATGCATGTAGGTGTCA 59.463 50.000 2.46 0.00 0.00 3.58
259 260 4.285851 CGAAAGCTCCACACCTCC 57.714 61.111 0.00 0.00 0.00 4.30
282 283 2.666098 CGGTAAGGTGGGGGAGGTG 61.666 68.421 0.00 0.00 0.00 4.00
297 298 2.203788 TGGCTTGAGTCCCTCGGT 60.204 61.111 0.00 0.00 32.35 4.69
350 351 1.331399 GCTCTGTGGTCCTCCCCTAC 61.331 65.000 0.00 0.00 0.00 3.18
352 353 2.284995 GCTCTGTGGTCCTCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
355 356 2.665603 GTGGCTCTGTGGTCCTCC 59.334 66.667 0.00 0.00 0.00 4.30
358 359 4.008933 AGCGTGGCTCTGTGGTCC 62.009 66.667 0.00 0.00 30.62 4.46
359 360 2.740055 CAGCGTGGCTCTGTGGTC 60.740 66.667 0.00 0.00 36.40 4.02
360 361 4.320456 CCAGCGTGGCTCTGTGGT 62.320 66.667 0.00 0.00 36.40 4.16
370 762 1.455383 AAAGGGAACAAGCCAGCGTG 61.455 55.000 3.95 3.95 0.00 5.34
484 885 5.722172 TGATGGATGGAGGAAAAAGATCT 57.278 39.130 0.00 0.00 0.00 2.75
533 962 6.260050 CACACCATTACATCACTGGTATTACC 59.740 42.308 5.87 5.87 41.30 2.85
539 968 2.436417 GCACACCATTACATCACTGGT 58.564 47.619 0.00 0.00 44.02 4.00
540 969 1.398041 CGCACACCATTACATCACTGG 59.602 52.381 0.00 0.00 36.09 4.00
714 1155 7.585286 TGCACTAAATTTTCTGATGAAATGC 57.415 32.000 0.00 0.00 41.24 3.56
725 1166 5.250332 GCGATTTGCATGCACTAAATTTTC 58.750 37.500 22.58 6.63 45.45 2.29
752 1193 0.035056 ACTGCCTACCCTACGTACGT 60.035 55.000 25.98 25.98 0.00 3.57
753 1194 1.599542 GTACTGCCTACCCTACGTACG 59.400 57.143 15.01 15.01 0.00 3.67
754 1195 2.643551 TGTACTGCCTACCCTACGTAC 58.356 52.381 0.00 0.00 0.00 3.67
755 1196 3.282021 CTTGTACTGCCTACCCTACGTA 58.718 50.000 0.00 0.00 0.00 3.57
756 1197 2.097825 CTTGTACTGCCTACCCTACGT 58.902 52.381 0.00 0.00 0.00 3.57
757 1198 2.097825 ACTTGTACTGCCTACCCTACG 58.902 52.381 0.00 0.00 0.00 3.51
758 1199 4.019174 TGTACTTGTACTGCCTACCCTAC 58.981 47.826 11.53 0.00 0.00 3.18
760 1201 3.179902 TGTACTTGTACTGCCTACCCT 57.820 47.619 11.53 0.00 0.00 4.34
761 1202 3.260128 AGTTGTACTTGTACTGCCTACCC 59.740 47.826 11.53 0.00 0.00 3.69
762 1203 4.243270 CAGTTGTACTTGTACTGCCTACC 58.757 47.826 11.53 0.00 33.63 3.18
768 1209 5.403766 CAGAGAAGCAGTTGTACTTGTACTG 59.596 44.000 11.53 11.24 41.64 2.74
769 1210 5.509840 CCAGAGAAGCAGTTGTACTTGTACT 60.510 44.000 11.53 0.00 0.00 2.73
770 1211 4.686554 CCAGAGAAGCAGTTGTACTTGTAC 59.313 45.833 4.14 4.14 0.00 2.90
771 1212 4.587262 TCCAGAGAAGCAGTTGTACTTGTA 59.413 41.667 0.00 0.00 0.00 2.41
772 1213 3.388024 TCCAGAGAAGCAGTTGTACTTGT 59.612 43.478 0.00 0.00 0.00 3.16
773 1214 3.995199 TCCAGAGAAGCAGTTGTACTTG 58.005 45.455 0.00 0.00 0.00 3.16
774 1215 4.284490 TGATCCAGAGAAGCAGTTGTACTT 59.716 41.667 0.00 0.00 0.00 2.24
849 1293 2.365408 AGGGCTTCGTTTACTTCGAG 57.635 50.000 0.00 0.00 38.52 4.04
851 1295 7.436080 TGTTTATATAGGGCTTCGTTTACTTCG 59.564 37.037 0.00 0.00 0.00 3.79
898 1352 4.353737 CTGTGGAGATGTGTGTTGTTTTG 58.646 43.478 0.00 0.00 0.00 2.44
930 1384 2.004733 CGGTTAACTTAGGCCGGAAAG 58.995 52.381 5.05 7.94 40.45 2.62
931 1385 1.945355 GCGGTTAACTTAGGCCGGAAA 60.945 52.381 5.05 0.00 43.90 3.13
966 1420 3.046087 CTGTCCTGCACAGCACCG 61.046 66.667 0.00 0.00 46.30 4.94
980 1434 0.176680 GGTGATGCCGACTGATCTGT 59.823 55.000 4.73 4.73 0.00 3.41
982 1436 1.126488 ATGGTGATGCCGACTGATCT 58.874 50.000 0.00 0.00 41.21 2.75
985 1439 0.108186 GACATGGTGATGCCGACTGA 60.108 55.000 0.00 0.00 41.21 3.41
994 1448 2.021068 CTCGGCCTCGACATGGTGAT 62.021 60.000 0.00 0.00 40.88 3.06
1113 1567 4.498520 AGCGCGTCCTGGATGTCG 62.499 66.667 20.80 20.80 0.00 4.35
1254 1708 1.875813 GCTGAGCATGACGTCGAGG 60.876 63.158 11.62 3.03 0.00 4.63
1710 2164 3.329542 GATGAAGCCCGCCTGGTCA 62.330 63.158 0.00 0.00 36.04 4.02
1990 2446 3.753272 TGCCGAAGATTCCTCAAGAAAAG 59.247 43.478 0.00 0.00 38.21 2.27
1994 2450 3.634397 AATGCCGAAGATTCCTCAAGA 57.366 42.857 0.00 0.00 0.00 3.02
1995 2451 4.708726 AAAATGCCGAAGATTCCTCAAG 57.291 40.909 0.00 0.00 0.00 3.02
2001 2457 6.195165 CAGCTTAGTAAAATGCCGAAGATTC 58.805 40.000 0.00 0.00 0.00 2.52
2044 2500 5.928264 CCCTTTGACATTTCTGACAATTTCC 59.072 40.000 0.00 0.00 37.01 3.13
2066 2522 3.032459 CCCACTCTAACTCTAGGTTCCC 58.968 54.545 0.55 0.00 39.17 3.97
2114 2570 1.598962 GTCTGCCAGCTGCTGTTCA 60.599 57.895 26.41 21.17 42.00 3.18
2222 2680 4.135153 CGGTCTGAGAGGTGCCCG 62.135 72.222 0.00 0.00 0.00 6.13
2284 2742 4.164294 CCTTGAAGTTAGTCGTACCGAAG 58.836 47.826 0.00 0.00 37.72 3.79
2327 2788 5.064452 CACCTATCACTTTCTTCTGCATGTC 59.936 44.000 0.00 0.00 0.00 3.06
2332 2793 6.560253 TTTTCACCTATCACTTTCTTCTGC 57.440 37.500 0.00 0.00 0.00 4.26
2333 2794 8.103948 ACATTTTCACCTATCACTTTCTTCTG 57.896 34.615 0.00 0.00 0.00 3.02
2347 2808 7.430760 AAGATCTAGCTCTACATTTTCACCT 57.569 36.000 0.00 0.00 0.00 4.00
2409 2870 5.259632 AGTTTGCTATCTTTCAATGCCTCT 58.740 37.500 0.00 0.00 0.00 3.69
2452 2913 2.158957 TCCTTGAGCTCGTGTTTTGTCT 60.159 45.455 9.64 0.00 0.00 3.41
2456 2917 4.894784 TCTTATCCTTGAGCTCGTGTTTT 58.105 39.130 9.64 0.00 0.00 2.43
2513 2975 3.824443 GGATATAACGGTTGGATTTGGGG 59.176 47.826 3.07 0.00 0.00 4.96
2560 3022 3.434319 GGTACACCGTCCGAGCGA 61.434 66.667 0.00 0.00 0.00 4.93
2634 3118 1.064654 CGTTAGGGCGAGTGGTAGTAC 59.935 57.143 0.00 0.00 0.00 2.73
2663 3147 2.225467 GATAGTACCGTTAGGGCGAGT 58.775 52.381 0.00 0.00 43.47 4.18
2664 3148 1.196354 CGATAGTACCGTTAGGGCGAG 59.804 57.143 0.00 0.00 43.47 5.03
2665 3149 1.229428 CGATAGTACCGTTAGGGCGA 58.771 55.000 0.00 0.00 43.47 5.54
2666 3150 0.386478 GCGATAGTACCGTTAGGGCG 60.386 60.000 0.00 0.00 39.68 6.13
2667 3151 0.957362 AGCGATAGTACCGTTAGGGC 59.043 55.000 0.00 0.00 39.68 5.19
2668 3152 1.952296 ACAGCGATAGTACCGTTAGGG 59.048 52.381 0.00 0.00 39.68 3.53
2669 3153 2.287427 CCACAGCGATAGTACCGTTAGG 60.287 54.545 0.00 0.00 40.85 2.69
2670 3154 2.357009 ACCACAGCGATAGTACCGTTAG 59.643 50.000 0.00 0.00 39.35 2.34
2671 3155 2.368439 ACCACAGCGATAGTACCGTTA 58.632 47.619 0.00 0.00 39.35 3.18
2672 3156 1.180029 ACCACAGCGATAGTACCGTT 58.820 50.000 0.00 0.00 39.35 4.44
2673 3157 1.180029 AACCACAGCGATAGTACCGT 58.820 50.000 0.00 0.00 39.35 4.83
2674 3158 2.097954 TGTAACCACAGCGATAGTACCG 59.902 50.000 0.00 0.00 39.35 4.02
2675 3159 3.703420 CTGTAACCACAGCGATAGTACC 58.297 50.000 0.00 0.00 45.44 3.34
2709 3193 2.448542 TGGCCTGCCCTATCTCCC 60.449 66.667 3.32 0.00 34.56 4.30


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

AutoCloner maintained by Alex Coulton.