Multiple sequence alignment - TraesCS2B01G383600

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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 TraesCS2B01G383600 chr2B 100.000 3485 0 0 1 3485 547056072 547059556 0.000000e+00 6436
1 TraesCS2B01G383600 chr2D 92.839 3226 123 44 316 3485 468855480 468858653 0.000000e+00 4578
2 TraesCS2B01G383600 chr2D 92.784 291 16 2 1 290 468854731 468855017 1.930000e-112 416
3 TraesCS2B01G383600 chr2A 90.945 3247 158 61 318 3485 608870354 608873543 0.000000e+00 4242
4 TraesCS2B01G383600 chr2A 91.327 196 15 2 98 292 608865638 608865832 2.060000e-67 267
5 TraesCS2B01G383600 chr6A 88.181 1396 158 7 1008 2398 426967484 426966091 0.000000e+00 1657
6 TraesCS2B01G383600 chr6B 88.037 1396 160 7 1008 2398 458486146 458487539 0.000000e+00 1646
7 TraesCS2B01G383600 chr6D 87.894 1396 162 7 1008 2398 293801968 293803361 0.000000e+00 1635


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 TraesCS2B01G383600 chr2B 547056072 547059556 3484 False 6436 6436 100.0000 1 3485 1 chr2B.!!$F1 3484
1 TraesCS2B01G383600 chr2D 468854731 468858653 3922 False 2497 4578 92.8115 1 3485 2 chr2D.!!$F1 3484
2 TraesCS2B01G383600 chr2A 608870354 608873543 3189 False 4242 4242 90.9450 318 3485 1 chr2A.!!$F2 3167
3 TraesCS2B01G383600 chr6A 426966091 426967484 1393 True 1657 1657 88.1810 1008 2398 1 chr6A.!!$R1 1390
4 TraesCS2B01G383600 chr6B 458486146 458487539 1393 False 1646 1646 88.0370 1008 2398 1 chr6B.!!$F1 1390
5 TraesCS2B01G383600 chr6D 293801968 293803361 1393 False 1635 1635 87.8940 1008 2398 1 chr6D.!!$F1 1390

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
711 1184 0.250234 CCAGAGATTCCAGAACGGCA 59.75 55.0 0.0 0.0 33.14 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 3096 1.130777 AAAGCATTGGCCCAAACAGT 58.869 45.0 0.0 0.0 42.56 3.55 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
22 23 4.096681 GGGGGAAAAGAAGATGAATGGTT 58.903 43.478 0.00 0.00 0.00 3.67
61 62 4.578928 GCCAGAACACAGAACTTCCTAAAA 59.421 41.667 0.00 0.00 0.00 1.52
103 104 1.476488 GAGAGGGAGAGTGAGACTTGC 59.524 57.143 0.00 0.00 0.00 4.01
114 115 5.698545 AGAGTGAGACTTGCAATAGACAAAC 59.301 40.000 0.00 0.00 0.00 2.93
115 116 5.368145 AGTGAGACTTGCAATAGACAAACA 58.632 37.500 0.00 0.00 0.00 2.83
116 117 5.237344 AGTGAGACTTGCAATAGACAAACAC 59.763 40.000 0.00 3.50 0.00 3.32
119 120 3.561143 ACTTGCAATAGACAAACACCCA 58.439 40.909 0.00 0.00 0.00 4.51
120 121 3.569701 ACTTGCAATAGACAAACACCCAG 59.430 43.478 0.00 0.00 0.00 4.45
121 122 1.885887 TGCAATAGACAAACACCCAGC 59.114 47.619 0.00 0.00 0.00 4.85
225 227 1.139095 GCGAACTCCCTCAGGTACG 59.861 63.158 0.00 0.00 0.00 3.67
227 229 0.450983 CGAACTCCCTCAGGTACGTC 59.549 60.000 0.00 0.00 0.00 4.34
232 234 1.950909 CTCCCTCAGGTACGTCAGATC 59.049 57.143 0.00 0.00 0.00 2.75
235 237 1.600013 CCTCAGGTACGTCAGATCTCG 59.400 57.143 0.00 0.00 0.00 4.04
248 250 1.745653 AGATCTCGCACGTGAATCTCA 59.254 47.619 22.23 0.00 0.00 3.27
251 253 2.328473 TCTCGCACGTGAATCTCAAAG 58.672 47.619 22.23 3.87 0.00 2.77
275 277 1.615424 GCTCCCACCACCCTCCTTA 60.615 63.158 0.00 0.00 0.00 2.69
290 292 3.090037 CTCCTTAGGGAACGACTGAGAA 58.910 50.000 0.00 0.00 41.69 2.87
291 293 3.702045 CTCCTTAGGGAACGACTGAGAAT 59.298 47.826 0.00 0.00 41.69 2.40
292 294 4.863548 TCCTTAGGGAACGACTGAGAATA 58.136 43.478 0.00 0.00 38.93 1.75
293 295 5.455872 TCCTTAGGGAACGACTGAGAATAT 58.544 41.667 0.00 0.00 38.93 1.28
294 296 5.535406 TCCTTAGGGAACGACTGAGAATATC 59.465 44.000 0.00 0.00 38.93 1.63
295 297 5.536916 CCTTAGGGAACGACTGAGAATATCT 59.463 44.000 0.00 0.00 33.58 1.98
296 298 6.715718 CCTTAGGGAACGACTGAGAATATCTA 59.284 42.308 0.00 0.00 33.58 1.98
297 299 7.230913 CCTTAGGGAACGACTGAGAATATCTAA 59.769 40.741 0.00 0.00 33.58 2.10
298 300 8.529424 TTAGGGAACGACTGAGAATATCTAAA 57.471 34.615 0.00 0.00 0.00 1.85
299 301 7.604657 AGGGAACGACTGAGAATATCTAAAT 57.395 36.000 0.00 0.00 0.00 1.40
300 302 7.437748 AGGGAACGACTGAGAATATCTAAATG 58.562 38.462 0.00 0.00 0.00 2.32
301 303 6.647067 GGGAACGACTGAGAATATCTAAATGG 59.353 42.308 0.00 0.00 0.00 3.16
302 304 7.210873 GGAACGACTGAGAATATCTAAATGGT 58.789 38.462 0.00 0.00 0.00 3.55
303 305 7.711339 GGAACGACTGAGAATATCTAAATGGTT 59.289 37.037 0.00 0.00 0.00 3.67
304 306 8.649973 AACGACTGAGAATATCTAAATGGTTC 57.350 34.615 0.00 0.00 0.00 3.62
305 307 6.918569 ACGACTGAGAATATCTAAATGGTTCG 59.081 38.462 0.00 0.00 0.00 3.95
306 308 6.129062 CGACTGAGAATATCTAAATGGTTCGC 60.129 42.308 0.00 0.00 0.00 4.70
307 309 6.821388 ACTGAGAATATCTAAATGGTTCGCT 58.179 36.000 0.00 0.00 0.00 4.93
367 806 5.883661 ACTCGAAATGTAAATCTTGCCATG 58.116 37.500 0.00 0.00 0.00 3.66
372 811 7.498900 TCGAAATGTAAATCTTGCCATGACTAT 59.501 33.333 0.00 0.00 0.00 2.12
404 850 0.947180 GGCAGCACCACAATTGCAAG 60.947 55.000 4.94 0.00 42.83 4.01
423 869 0.831307 GGCTGTAAACCCGAGATCCT 59.169 55.000 0.00 0.00 0.00 3.24
472 921 8.465273 AGGTTAAAAGTTTCAAAGATACAGCT 57.535 30.769 0.00 0.00 0.00 4.24
511 964 6.091713 CCAATGTGAAGTACTACCCGTAAAAG 59.908 42.308 0.00 0.00 0.00 2.27
528 984 7.225397 CCGTAAAAGAAATCGAGTAACAGAAC 58.775 38.462 0.00 0.00 0.00 3.01
529 985 7.115947 CCGTAAAAGAAATCGAGTAACAGAACT 59.884 37.037 0.00 0.00 0.00 3.01
535 991 8.289939 AGAAATCGAGTAACAGAACTATACCA 57.710 34.615 0.00 0.00 0.00 3.25
547 1016 4.336993 AGAACTATACCAGAAGAGTGCGAG 59.663 45.833 0.00 0.00 0.00 5.03
579 1049 2.775384 AGGATTTATACAGCCCCGAACA 59.225 45.455 0.00 0.00 0.00 3.18
711 1184 0.250234 CCAGAGATTCCAGAACGGCA 59.750 55.000 0.00 0.00 33.14 5.69
737 1220 0.826715 CTGATCCGAGACCACCACAT 59.173 55.000 0.00 0.00 0.00 3.21
751 1234 3.198068 CACCACATAAGATTCACTCCGG 58.802 50.000 0.00 0.00 0.00 5.14
781 1266 1.000171 GTTCTCCAGCCAAAAGCCAAG 60.000 52.381 0.00 0.00 45.47 3.61
783 1268 1.076024 TCTCCAGCCAAAAGCCAAGAT 59.924 47.619 0.00 0.00 45.47 2.40
784 1269 2.308570 TCTCCAGCCAAAAGCCAAGATA 59.691 45.455 0.00 0.00 45.47 1.98
813 1298 1.197055 CGTCACCACACGATATTCCG 58.803 55.000 0.00 0.00 42.69 4.30
825 1311 4.269123 CACGATATTCCGAAACGAAATCCA 59.731 41.667 10.93 0.00 0.00 3.41
827 1313 5.526111 ACGATATTCCGAAACGAAATCCAAT 59.474 36.000 10.93 0.00 0.00 3.16
852 1338 2.189499 GCCTATTTCGCCTGGCCAG 61.189 63.158 26.87 26.87 39.49 4.85
929 1426 2.743928 CAGCCTCCTCACGCCAAC 60.744 66.667 0.00 0.00 0.00 3.77
933 1430 4.680237 CTCCTCACGCCAACGCCA 62.680 66.667 0.00 0.00 45.53 5.69
934 1431 4.243008 TCCTCACGCCAACGCCAA 62.243 61.111 0.00 0.00 45.53 4.52
944 1441 1.501741 CAACGCCAATCCCGACTTG 59.498 57.895 0.00 0.00 0.00 3.16
1797 2294 2.183555 CTCAAGTCGTACGGCCCC 59.816 66.667 17.68 1.64 0.00 5.80
2152 2649 3.043713 CGCTGTTCGCCAAGCAGA 61.044 61.111 2.31 0.00 34.21 4.26
2305 2805 1.423395 CTTCTTCGCGCTCAAGAAGT 58.577 50.000 31.45 0.00 46.44 3.01
2503 3003 0.981183 ACCAATCAAGCCGGAGTACA 59.019 50.000 5.05 0.00 0.00 2.90
2526 3026 8.193953 ACATAACAAGAAATCCAGTGGAAATT 57.806 30.769 17.71 14.42 34.34 1.82
2527 3027 8.306761 ACATAACAAGAAATCCAGTGGAAATTC 58.693 33.333 23.81 23.81 34.34 2.17
2528 3028 5.376854 ACAAGAAATCCAGTGGAAATTCG 57.623 39.130 24.39 17.71 36.99 3.34
2529 3029 4.827284 ACAAGAAATCCAGTGGAAATTCGT 59.173 37.500 24.39 21.19 36.99 3.85
2530 3030 5.301805 ACAAGAAATCCAGTGGAAATTCGTT 59.698 36.000 24.39 18.66 36.99 3.85
2543 3043 4.083696 GGAAATTCGTTCGCCTTTCTGTTA 60.084 41.667 13.98 0.00 37.08 2.41
2545 3045 6.183360 GGAAATTCGTTCGCCTTTCTGTTATA 60.183 38.462 13.98 0.00 37.08 0.98
2546 3046 6.920569 AATTCGTTCGCCTTTCTGTTATAT 57.079 33.333 0.00 0.00 0.00 0.86
2548 3048 4.365723 TCGTTCGCCTTTCTGTTATATCC 58.634 43.478 0.00 0.00 0.00 2.59
2571 3077 7.783042 TCCATCTCATATGTGATCTGATCATC 58.217 38.462 22.09 15.72 42.04 2.92
2575 3081 5.958955 TCATATGTGATCTGATCATCGGAC 58.041 41.667 22.09 10.32 42.04 4.79
2576 3082 2.781945 TGTGATCTGATCATCGGACG 57.218 50.000 22.09 0.00 42.04 4.79
2589 3096 3.517602 CATCGGACGATGTTTTCCAGTA 58.482 45.455 22.64 0.00 44.93 2.74
2627 3134 1.082756 GCCGCTCTTGTGTTCGTTG 60.083 57.895 0.00 0.00 0.00 4.10
2731 3245 0.729116 GTGTGTGGATGGAATCTGCG 59.271 55.000 0.00 0.00 44.71 5.18
2836 3354 4.293415 CTGCTGAAGGTTGAATTGTTGAC 58.707 43.478 0.00 0.00 0.00 3.18
2905 3423 4.032445 CGTTTTCTCGATCGAATGGCTTTA 59.968 41.667 19.92 0.00 0.00 1.85
2906 3424 5.493735 GTTTTCTCGATCGAATGGCTTTAG 58.506 41.667 19.92 4.06 0.00 1.85
2907 3425 4.386867 TTCTCGATCGAATGGCTTTAGT 57.613 40.909 19.92 0.00 0.00 2.24
2910 3428 5.898174 TCTCGATCGAATGGCTTTAGTTTA 58.102 37.500 19.92 0.00 0.00 2.01
2912 3430 6.420903 TCTCGATCGAATGGCTTTAGTTTATG 59.579 38.462 19.92 1.03 0.00 1.90
2913 3431 6.046593 TCGATCGAATGGCTTTAGTTTATGT 58.953 36.000 16.99 0.00 0.00 2.29
2915 3433 6.238103 CGATCGAATGGCTTTAGTTTATGTGT 60.238 38.462 10.26 0.00 0.00 3.72
3001 3532 9.709495 TCTTCATTTTGATGTTCCCTAAAAATG 57.291 29.630 11.17 11.17 44.13 2.32
3026 3557 0.248866 GGGTTGGTTCTTTGTGCACG 60.249 55.000 13.13 0.00 0.00 5.34
3031 3562 1.332375 TGGTTCTTTGTGCACGCTTAC 59.668 47.619 13.13 6.38 0.00 2.34
3047 3581 6.651308 CACGCTTACATTTAGTTTACACACA 58.349 36.000 0.00 0.00 0.00 3.72
3101 3635 6.762661 CCTCACAAGAGTACTCTACCTACTAC 59.237 46.154 25.42 0.00 39.39 2.73
3169 3703 7.763071 GTCATGTAGAGATGCAGCAATCATATA 59.237 37.037 4.07 0.00 0.00 0.86
3177 3712 5.756195 TGCAGCAATCATATACAAACCTC 57.244 39.130 0.00 0.00 0.00 3.85
3190 3725 3.031013 ACAAACCTCCCTTCAGTTTTGG 58.969 45.455 0.00 0.00 31.54 3.28
3212 3747 2.421248 GCCAGAAAAGAGGGATCAGAGG 60.421 54.545 0.00 0.00 0.00 3.69
3213 3748 2.843113 CCAGAAAAGAGGGATCAGAGGT 59.157 50.000 0.00 0.00 0.00 3.85
3214 3749 4.033709 CCAGAAAAGAGGGATCAGAGGTA 58.966 47.826 0.00 0.00 0.00 3.08
3261 3796 6.712547 ACAAGCTATAATTAACCTGGAGCATC 59.287 38.462 0.00 0.00 0.00 3.91
3262 3797 6.439636 AGCTATAATTAACCTGGAGCATCA 57.560 37.500 0.00 0.00 36.25 3.07
3263 3798 7.025520 AGCTATAATTAACCTGGAGCATCAT 57.974 36.000 0.00 0.00 36.25 2.45
3264 3799 8.150827 AGCTATAATTAACCTGGAGCATCATA 57.849 34.615 0.00 0.00 36.25 2.15
3265 3800 8.043710 AGCTATAATTAACCTGGAGCATCATAC 58.956 37.037 0.00 0.00 36.25 2.39
3266 3801 8.043710 GCTATAATTAACCTGGAGCATCATACT 58.956 37.037 0.00 0.00 36.25 2.12
3278 3813 4.770795 AGCATCATACTCCTGTTGGTAAC 58.229 43.478 0.00 0.00 34.23 2.50
3280 3815 5.045578 AGCATCATACTCCTGTTGGTAACTT 60.046 40.000 0.00 0.00 37.61 2.66
3307 3845 9.884814 ACTACTACTATTTCCTGTCTCCAATAT 57.115 33.333 0.00 0.00 0.00 1.28
3326 3864 8.198778 TCCAATATTTGTGCTCGTATACTAACA 58.801 33.333 0.56 0.00 0.00 2.41
3342 3880 1.168714 AACAGAAAGCGGGCTCAATC 58.831 50.000 0.00 0.00 0.00 2.67
3439 3983 2.587473 GCTTGCGAGCTAGCCTCC 60.587 66.667 19.25 0.00 45.65 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.607198 TCCATAACCATTCATCTTCTTTTCCC 59.393 38.462 0.00 0.00 0.00 3.97
22 23 4.380843 TCTGGCCTCTTTTTGTTCCATA 57.619 40.909 3.32 0.00 0.00 2.74
30 31 3.297134 TCTGTGTTCTGGCCTCTTTTT 57.703 42.857 3.32 0.00 0.00 1.94
75 76 2.771943 TCACTCTCCCTCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
76 77 2.774234 CTCACTCTCCCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
77 78 2.771943 TCTCACTCTCCCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
78 79 2.505819 GTCTCACTCTCCCTCTCTCTCT 59.494 54.545 0.00 0.00 0.00 3.10
103 104 1.468520 CCGCTGGGTGTTTGTCTATTG 59.531 52.381 0.00 0.00 0.00 1.90
114 115 0.036010 ATCTCTGTTTCCGCTGGGTG 60.036 55.000 0.00 0.00 33.83 4.61
115 116 0.036010 CATCTCTGTTTCCGCTGGGT 60.036 55.000 0.00 0.00 33.83 4.51
116 117 1.372087 GCATCTCTGTTTCCGCTGGG 61.372 60.000 0.00 0.00 0.00 4.45
119 120 1.271054 ACTTGCATCTCTGTTTCCGCT 60.271 47.619 0.00 0.00 0.00 5.52
120 121 1.135859 CACTTGCATCTCTGTTTCCGC 60.136 52.381 0.00 0.00 0.00 5.54
121 122 2.096069 CACACTTGCATCTCTGTTTCCG 60.096 50.000 0.00 0.00 0.00 4.30
219 221 0.733729 GTGCGAGATCTGACGTACCT 59.266 55.000 12.17 0.00 38.67 3.08
225 227 1.849219 GATTCACGTGCGAGATCTGAC 59.151 52.381 11.67 0.00 0.00 3.51
227 229 2.115595 GAGATTCACGTGCGAGATCTG 58.884 52.381 20.44 0.00 0.00 2.90
232 234 2.061773 ACTTTGAGATTCACGTGCGAG 58.938 47.619 11.67 1.66 0.00 5.03
235 237 3.545633 GAACACTTTGAGATTCACGTGC 58.454 45.455 11.67 0.00 33.74 5.34
248 250 0.818040 GTGGTGGGAGCGAACACTTT 60.818 55.000 7.45 0.00 37.72 2.66
251 253 2.668550 GGTGGTGGGAGCGAACAC 60.669 66.667 0.00 0.00 36.89 3.32
275 277 7.437748 CATTTAGATATTCTCAGTCGTTCCCT 58.562 38.462 0.00 0.00 0.00 4.20
286 288 5.466728 TGCAGCGAACCATTTAGATATTCTC 59.533 40.000 0.00 0.00 0.00 2.87
290 292 5.180117 GTGATGCAGCGAACCATTTAGATAT 59.820 40.000 0.00 0.00 0.00 1.63
291 293 4.511454 GTGATGCAGCGAACCATTTAGATA 59.489 41.667 0.00 0.00 0.00 1.98
292 294 3.313526 GTGATGCAGCGAACCATTTAGAT 59.686 43.478 0.00 0.00 0.00 1.98
293 295 2.677836 GTGATGCAGCGAACCATTTAGA 59.322 45.455 0.00 0.00 0.00 2.10
294 296 2.223340 GGTGATGCAGCGAACCATTTAG 60.223 50.000 6.59 0.00 32.69 1.85
295 297 1.742831 GGTGATGCAGCGAACCATTTA 59.257 47.619 6.59 0.00 32.69 1.40
296 298 0.527565 GGTGATGCAGCGAACCATTT 59.472 50.000 6.59 0.00 32.69 2.32
297 299 0.608856 TGGTGATGCAGCGAACCATT 60.609 50.000 9.90 0.00 37.77 3.16
298 300 0.394762 ATGGTGATGCAGCGAACCAT 60.395 50.000 18.43 18.43 45.95 3.55
299 301 1.002257 ATGGTGATGCAGCGAACCA 60.002 52.632 15.59 15.59 46.26 3.67
300 302 0.745845 AGATGGTGATGCAGCGAACC 60.746 55.000 4.58 4.58 34.27 3.62
301 303 0.654683 GAGATGGTGATGCAGCGAAC 59.345 55.000 0.00 0.00 34.27 3.95
302 304 0.538584 AGAGATGGTGATGCAGCGAA 59.461 50.000 0.00 0.00 34.27 4.70
303 305 1.339291 CTAGAGATGGTGATGCAGCGA 59.661 52.381 0.00 0.00 34.27 4.93
304 306 1.339291 TCTAGAGATGGTGATGCAGCG 59.661 52.381 0.00 0.00 34.27 5.18
305 307 2.288948 CCTCTAGAGATGGTGATGCAGC 60.289 54.545 21.76 0.00 0.00 5.25
306 308 2.288948 GCCTCTAGAGATGGTGATGCAG 60.289 54.545 21.76 0.73 0.00 4.41
307 309 1.690893 GCCTCTAGAGATGGTGATGCA 59.309 52.381 21.76 0.00 0.00 3.96
360 799 5.114764 TGGAATCTTGATAGTCATGGCAA 57.885 39.130 0.00 0.00 0.00 4.52
367 806 4.070716 CTGCCCATGGAATCTTGATAGTC 58.929 47.826 15.22 0.00 0.00 2.59
372 811 0.332293 TGCTGCCCATGGAATCTTGA 59.668 50.000 15.22 0.00 0.00 3.02
404 850 0.831307 AGGATCTCGGGTTTACAGCC 59.169 55.000 0.00 0.00 37.19 4.85
423 869 5.029807 TGATGACACTTATTAATGCCCGA 57.970 39.130 0.00 0.00 0.00 5.14
437 886 8.696410 TTGAAACTTTTAACCTTTGATGACAC 57.304 30.769 0.00 0.00 0.00 3.67
472 921 0.888736 CATTGGCACGTTGGGACTGA 60.889 55.000 0.00 0.00 0.00 3.41
511 964 8.404000 TCTGGTATAGTTCTGTTACTCGATTTC 58.596 37.037 0.00 0.00 0.00 2.17
528 984 4.902443 TTCTCGCACTCTTCTGGTATAG 57.098 45.455 0.00 0.00 0.00 1.31
529 985 4.705507 AGTTTCTCGCACTCTTCTGGTATA 59.294 41.667 0.00 0.00 0.00 1.47
535 991 2.094442 GGCTAGTTTCTCGCACTCTTCT 60.094 50.000 0.00 0.00 0.00 2.85
547 1016 6.017026 GGCTGTATAAATCCTTGGCTAGTTTC 60.017 42.308 0.00 0.00 0.00 2.78
579 1049 7.324935 ACTATTTCGGTTTGTTTTTGGAGTTT 58.675 30.769 0.00 0.00 0.00 2.66
672 1145 3.581770 TGGATTCTGGAGATCATAGCTGG 59.418 47.826 0.00 0.00 0.00 4.85
711 1184 4.458829 TCTCGGATCAGGGGCGGT 62.459 66.667 0.00 0.00 0.00 5.68
737 1220 1.682451 CCCGCCCGGAGTGAATCTTA 61.682 60.000 0.73 0.00 37.50 2.10
798 1283 2.094597 TCGTTTCGGAATATCGTGTGGT 60.095 45.455 0.00 0.00 0.00 4.16
813 1298 2.222953 CGGACGGATTGGATTTCGTTTC 60.223 50.000 0.00 0.00 35.91 2.78
825 1311 0.878961 GCGAAATAGGCGGACGGATT 60.879 55.000 0.00 0.00 0.00 3.01
827 1313 2.105528 GCGAAATAGGCGGACGGA 59.894 61.111 0.00 0.00 0.00 4.69
929 1426 3.508840 GGCAAGTCGGGATTGGCG 61.509 66.667 6.11 0.00 42.36 5.69
931 1428 0.609131 AACTGGCAAGTCGGGATTGG 60.609 55.000 0.00 0.00 34.77 3.16
932 1429 0.804989 GAACTGGCAAGTCGGGATTG 59.195 55.000 0.00 0.00 34.77 2.67
933 1430 0.322546 GGAACTGGCAAGTCGGGATT 60.323 55.000 0.00 0.00 34.77 3.01
934 1431 1.299976 GGAACTGGCAAGTCGGGAT 59.700 57.895 0.00 0.00 34.77 3.85
944 1441 1.447838 TTCAGCGATCGGAACTGGC 60.448 57.895 18.30 0.00 32.19 4.85
1051 1548 1.217244 GGTAGTCCGTGGCGTTCAT 59.783 57.895 0.00 0.00 0.00 2.57
1052 1549 1.904865 AGGTAGTCCGTGGCGTTCA 60.905 57.895 0.00 0.00 39.05 3.18
1299 1796 4.601621 GAAGAAGTGCTTCCCGATAAAC 57.398 45.455 0.00 0.00 45.90 2.01
1797 2294 4.856801 CCGTTGATGCTCCCGGGG 62.857 72.222 23.50 13.02 36.84 5.73
1878 2375 1.210931 CTTCCCGAACAGCGTCGTA 59.789 57.895 6.72 0.00 39.43 3.43
2013 2510 3.608662 ACCCACGCCGAGACGAAA 61.609 61.111 0.00 0.00 36.70 3.46
2149 2646 3.283751 AGATCTCCTCCACGTACTTCTG 58.716 50.000 0.00 0.00 0.00 3.02
2152 2649 3.204526 CGTAGATCTCCTCCACGTACTT 58.795 50.000 0.00 0.00 0.00 2.24
2503 3003 7.176690 ACGAATTTCCACTGGATTTCTTGTTAT 59.823 33.333 14.74 0.00 0.00 1.89
2526 3026 4.142116 TGGATATAACAGAAAGGCGAACGA 60.142 41.667 0.00 0.00 0.00 3.85
2527 3027 4.116961 TGGATATAACAGAAAGGCGAACG 58.883 43.478 0.00 0.00 0.00 3.95
2528 3028 5.992217 AGATGGATATAACAGAAAGGCGAAC 59.008 40.000 0.00 0.00 0.00 3.95
2529 3029 6.174720 AGATGGATATAACAGAAAGGCGAA 57.825 37.500 0.00 0.00 0.00 4.70
2530 3030 5.304357 TGAGATGGATATAACAGAAAGGCGA 59.696 40.000 0.00 0.00 0.00 5.54
2543 3043 9.435570 TGATCAGATCACATATGAGATGGATAT 57.564 33.333 18.80 8.03 38.57 1.63
2545 3045 7.735326 TGATCAGATCACATATGAGATGGAT 57.265 36.000 18.80 18.64 38.57 3.41
2546 3046 7.416438 CGATGATCAGATCACATATGAGATGGA 60.416 40.741 18.80 15.46 43.01 3.41
2548 3048 6.697892 CCGATGATCAGATCACATATGAGATG 59.302 42.308 18.80 8.55 43.01 2.90
2571 3077 2.666508 CAGTACTGGAAAACATCGTCCG 59.333 50.000 15.49 0.00 36.65 4.79
2575 3081 4.320202 CCCAAACAGTACTGGAAAACATCG 60.320 45.833 26.12 4.70 34.35 3.84
2576 3082 4.558697 GCCCAAACAGTACTGGAAAACATC 60.559 45.833 26.12 5.37 34.35 3.06
2579 3086 2.035449 GGCCCAAACAGTACTGGAAAAC 59.965 50.000 26.12 10.94 34.35 2.43
2586 3093 1.203050 AGCATTGGCCCAAACAGTACT 60.203 47.619 0.00 0.00 42.56 2.73
2589 3096 1.130777 AAAGCATTGGCCCAAACAGT 58.869 45.000 0.00 0.00 42.56 3.55
2758 3276 6.018832 CAGAATTCCACCACAAAAATGACAAC 60.019 38.462 0.65 0.00 0.00 3.32
2836 3354 2.483188 GGCCCGTACTAGAGGACAAATG 60.483 54.545 0.00 0.00 0.00 2.32
2905 3423 7.330208 GTCAGGAACATACGTAACACATAAACT 59.670 37.037 0.00 0.00 0.00 2.66
2906 3424 7.450627 GTCAGGAACATACGTAACACATAAAC 58.549 38.462 0.00 0.00 0.00 2.01
2907 3425 6.308524 CGTCAGGAACATACGTAACACATAAA 59.691 38.462 0.00 0.00 34.76 1.40
2910 3428 4.171005 CGTCAGGAACATACGTAACACAT 58.829 43.478 0.00 0.00 34.76 3.21
2912 3430 3.568538 ACGTCAGGAACATACGTAACAC 58.431 45.455 0.00 0.00 46.83 3.32
2913 3431 3.921119 ACGTCAGGAACATACGTAACA 57.079 42.857 0.00 0.00 46.83 2.41
3001 3532 3.089284 CACAAAGAACCAACCCCCTATC 58.911 50.000 0.00 0.00 0.00 2.08
3026 3557 8.339714 TCAGTTGTGTGTAAACTAAATGTAAGC 58.660 33.333 0.00 0.00 35.70 3.09
3031 3562 6.133392 CCGTCAGTTGTGTGTAAACTAAATG 58.867 40.000 0.00 0.00 35.70 2.32
3047 3581 1.624336 TGTAGGTGTAGCCGTCAGTT 58.376 50.000 0.00 0.00 43.70 3.16
3101 3635 2.423538 CGGCTCATTTAAAACAGGGAGG 59.576 50.000 0.00 0.00 0.00 4.30
3155 3689 4.580167 GGAGGTTTGTATATGATTGCTGCA 59.420 41.667 0.00 0.00 0.00 4.41
3169 3703 3.031013 CCAAAACTGAAGGGAGGTTTGT 58.969 45.455 9.54 0.00 45.50 2.83
3177 3712 0.178964 TCTGGCCCAAAACTGAAGGG 60.179 55.000 0.00 0.00 45.68 3.95
3190 3725 1.561542 TCTGATCCCTCTTTTCTGGCC 59.438 52.381 0.00 0.00 0.00 5.36
3212 3747 8.292448 TGTACTACTAGCACAGTTTTGTACTAC 58.708 37.037 18.27 0.00 37.69 2.73
3213 3748 8.394971 TGTACTACTAGCACAGTTTTGTACTA 57.605 34.615 18.27 0.00 37.69 1.82
3214 3749 7.281040 TGTACTACTAGCACAGTTTTGTACT 57.719 36.000 18.27 0.00 37.69 2.73
3261 3796 8.064336 AGTAGTAAGTTACCAACAGGAGTATG 57.936 38.462 9.46 0.00 0.00 2.39
3262 3797 9.183368 GTAGTAGTAAGTTACCAACAGGAGTAT 57.817 37.037 9.46 0.00 0.00 2.12
3263 3798 8.386264 AGTAGTAGTAAGTTACCAACAGGAGTA 58.614 37.037 9.46 0.00 0.00 2.59
3264 3799 7.237255 AGTAGTAGTAAGTTACCAACAGGAGT 58.763 38.462 9.46 0.18 0.00 3.85
3265 3800 7.700022 AGTAGTAGTAAGTTACCAACAGGAG 57.300 40.000 9.46 0.00 0.00 3.69
3266 3801 9.759473 AATAGTAGTAGTAAGTTACCAACAGGA 57.241 33.333 9.46 0.00 0.00 3.86
3278 3813 8.749026 TGGAGACAGGAAATAGTAGTAGTAAG 57.251 38.462 0.00 0.00 35.01 2.34
3307 3845 6.090358 GCTTTCTGTTAGTATACGAGCACAAA 59.910 38.462 0.00 1.74 0.00 2.83
3326 3864 1.386533 CATGATTGAGCCCGCTTTCT 58.613 50.000 0.00 0.00 0.00 2.52
3435 3979 0.322008 GGCAACTTGGTGAGAGGAGG 60.322 60.000 0.00 0.00 0.00 4.30
3436 3980 0.671781 CGGCAACTTGGTGAGAGGAG 60.672 60.000 0.00 0.00 0.00 3.69
3439 3983 1.294659 GCTCGGCAACTTGGTGAGAG 61.295 60.000 7.05 7.05 0.00 3.20


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

AutoCloner maintained by Alex Coulton.