Multiple sequence alignment - TraesCS1B01G117400

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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 TraesCS1B01G117400 chr1B 100.000 2303 0 0 1 2303 137455077 137452775 0.000000e+00 4253.0
1 TraesCS1B01G117400 chr1B 95.545 1010 37 6 996 2002 137555531 137556535 0.000000e+00 1609.0
2 TraesCS1B01G117400 chr1B 100.000 426 0 0 2502 2927 137452576 137452151 0.000000e+00 787.0
3 TraesCS1B01G117400 chr1A 91.784 2203 106 33 1 2160 78965420 78963250 0.000000e+00 2996.0
4 TraesCS1B01G117400 chr1A 96.215 1136 34 8 995 2128 79107171 79108299 0.000000e+00 1851.0
5 TraesCS1B01G117400 chr1A 89.972 359 27 7 2504 2853 78962799 78962441 3.440000e-124 455.0
6 TraesCS1B01G117400 chr1A 95.395 152 7 0 2151 2302 78962971 78962820 2.910000e-60 243.0
7 TraesCS1B01G117400 chr1A 86.792 159 18 3 2144 2300 79108283 79108440 1.080000e-39 174.0
8 TraesCS1B01G117400 chr1A 84.746 59 7 1 1891 1947 79117024 79117082 1.130000e-04 58.4
9 TraesCS1B01G117400 chr1D 94.288 1593 69 15 543 2125 84778186 84776606 0.000000e+00 2418.0
10 TraesCS1B01G117400 chr1D 94.657 1123 43 12 995 2108 84875433 84876547 0.000000e+00 1725.0
11 TraesCS1B01G117400 chr5B 79.241 448 75 16 1474 1909 410722992 410723433 2.210000e-76 296.0
12 TraesCS1B01G117400 chr6D 82.450 302 50 3 1475 1774 414256658 414256358 8.050000e-66 261.0
13 TraesCS1B01G117400 chr5A 77.704 453 79 18 1474 1909 450541450 450541897 1.040000e-64 257.0
14 TraesCS1B01G117400 chr6A 81.063 301 56 1 1475 1774 559002658 559002358 3.770000e-59 239.0


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 TraesCS1B01G117400 chr1B 137452151 137455077 2926 True 2520.000000 4253 100.000000 1 2927 2 chr1B.!!$R1 2926
1 TraesCS1B01G117400 chr1B 137555531 137556535 1004 False 1609.000000 1609 95.545000 996 2002 1 chr1B.!!$F1 1006
2 TraesCS1B01G117400 chr1A 78962441 78965420 2979 True 1231.333333 2996 92.383667 1 2853 3 chr1A.!!$R1 2852
3 TraesCS1B01G117400 chr1A 79107171 79108440 1269 False 1012.500000 1851 91.503500 995 2300 2 chr1A.!!$F2 1305
4 TraesCS1B01G117400 chr1D 84776606 84778186 1580 True 2418.000000 2418 94.288000 543 2125 1 chr1D.!!$R1 1582
5 TraesCS1B01G117400 chr1D 84875433 84876547 1114 False 1725.000000 1725 94.657000 995 2108 1 chr1D.!!$F1 1113

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
398 426 0.038526 AAACGGGTACGACTCAGCAG 60.039 55.0 0.0 0.0 44.6 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2110 5.467035 AATCATTTGACACCGAACCAATT 57.533 34.783 0.0 0.0 0.0 2.32 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 2.818169 AAGCGCCTTGACCTGACCA 61.818 57.895 2.29 0.00 0.00 4.02
75 76 2.306847 GACCTGACCAAGCCAAAGAAA 58.693 47.619 0.00 0.00 0.00 2.52
123 126 0.105964 CCTCCATCTCCTTCCCTCGA 60.106 60.000 0.00 0.00 0.00 4.04
124 127 1.689575 CCTCCATCTCCTTCCCTCGAA 60.690 57.143 0.00 0.00 0.00 3.71
135 138 4.045462 TCCTTCCCTCGAATCCTATCCATA 59.955 45.833 0.00 0.00 0.00 2.74
150 153 5.782331 CCTATCCATATCTCTCCCTTGTCAA 59.218 44.000 0.00 0.00 0.00 3.18
153 156 4.782691 TCCATATCTCTCCCTTGTCAACAA 59.217 41.667 0.00 0.00 0.00 2.83
164 190 1.462616 TGTCAACAACAAGCAGCACT 58.537 45.000 0.00 0.00 34.03 4.40
174 200 1.669779 CAAGCAGCACTCTATTCCAGC 59.330 52.381 0.00 0.00 0.00 4.85
177 203 1.539929 GCAGCACTCTATTCCAGCGAT 60.540 52.381 0.00 0.00 0.00 4.58
208 234 1.756561 GCAACCACAACACAGGGGT 60.757 57.895 0.00 0.00 34.43 4.95
217 243 3.706373 CACAGGGGTGGACTCGGG 61.706 72.222 0.00 0.00 41.45 5.14
249 277 3.077617 GCTTTTTGCAACAAGCCCA 57.922 47.368 31.09 0.00 44.83 5.36
253 281 2.021355 TTTTGCAACAAGCCCAGTTG 57.979 45.000 0.00 8.64 46.86 3.16
267 295 3.723104 GTTGCAATTGCGACGTCG 58.277 55.556 32.57 32.57 44.53 5.12
269 297 0.179225 GTTGCAATTGCGACGTCGAT 60.179 50.000 39.74 23.08 44.53 3.59
270 298 1.059979 GTTGCAATTGCGACGTCGATA 59.940 47.619 39.74 25.89 44.53 2.92
274 302 0.918619 AATTGCGACGTCGATAACCG 59.081 50.000 39.74 14.30 43.02 4.44
281 309 0.726827 ACGTCGATAACCGCGAGTTA 59.273 50.000 8.23 14.98 44.92 2.24
289 317 0.179108 AACCGCGAGTTAGAGATGCC 60.179 55.000 8.23 0.00 36.74 4.40
305 333 4.777384 CCTTTTGCAACAAGGCCC 57.223 55.556 20.24 0.00 34.59 5.80
306 334 2.135890 CCTTTTGCAACAAGGCCCT 58.864 52.632 20.24 0.00 34.59 5.19
307 335 0.249996 CCTTTTGCAACAAGGCCCTG 60.250 55.000 20.24 0.00 34.59 4.45
308 336 0.465287 CTTTTGCAACAAGGCCCTGT 59.535 50.000 0.00 0.00 0.00 4.00
309 337 0.908198 TTTTGCAACAAGGCCCTGTT 59.092 45.000 14.23 14.23 40.17 3.16
312 340 3.536164 CAACAAGGCCCTGTTGCA 58.464 55.556 29.38 0.00 46.95 4.08
313 341 1.821936 CAACAAGGCCCTGTTGCAA 59.178 52.632 29.38 0.00 46.95 4.08
314 342 0.393820 CAACAAGGCCCTGTTGCAAT 59.606 50.000 29.38 1.95 46.95 3.56
315 343 1.130777 AACAAGGCCCTGTTGCAATT 58.869 45.000 19.07 0.00 38.12 2.32
316 344 0.393820 ACAAGGCCCTGTTGCAATTG 59.606 50.000 0.00 3.63 36.26 2.32
317 345 0.952010 CAAGGCCCTGTTGCAATTGC 60.952 55.000 23.69 23.69 42.50 3.56
342 370 2.539302 AGGGCCTTGTTGCAATGTAAT 58.461 42.857 0.00 0.00 0.00 1.89
343 371 2.234414 AGGGCCTTGTTGCAATGTAATG 59.766 45.455 0.00 0.00 0.00 1.90
374 402 3.181522 GCAATGAGCGAAACAGAGAAGAG 60.182 47.826 0.00 0.00 0.00 2.85
378 406 2.990514 GAGCGAAACAGAGAAGAGGAAC 59.009 50.000 0.00 0.00 0.00 3.62
380 408 3.131396 GCGAAACAGAGAAGAGGAACAA 58.869 45.455 0.00 0.00 0.00 2.83
382 410 4.552961 GCGAAACAGAGAAGAGGAACAAAC 60.553 45.833 0.00 0.00 0.00 2.93
392 420 1.000171 GAGGAACAAACGGGTACGACT 60.000 52.381 0.00 0.00 44.60 4.18
394 422 1.269726 GGAACAAACGGGTACGACTCA 60.270 52.381 0.00 0.00 44.60 3.41
397 425 0.319211 CAAACGGGTACGACTCAGCA 60.319 55.000 0.00 0.00 44.60 4.41
398 426 0.038526 AAACGGGTACGACTCAGCAG 60.039 55.000 0.00 0.00 44.60 4.24
401 429 1.306148 CGGGTACGACTCAGCAGATA 58.694 55.000 0.00 0.00 44.60 1.98
408 436 3.786635 ACGACTCAGCAGATATTTGGAC 58.213 45.455 0.00 0.00 0.00 4.02
415 443 5.993055 TCAGCAGATATTTGGACAAGATCA 58.007 37.500 0.00 0.00 0.00 2.92
416 444 5.819379 TCAGCAGATATTTGGACAAGATCAC 59.181 40.000 0.00 4.26 0.00 3.06
419 447 4.512944 CAGATATTTGGACAAGATCACCCG 59.487 45.833 0.00 0.00 0.00 5.28
436 464 4.789075 GGCCGACGCTCGTAGCAA 62.789 66.667 15.56 0.00 42.58 3.91
437 465 2.582498 GCCGACGCTCGTAGCAAT 60.582 61.111 10.72 0.00 42.58 3.56
438 466 2.860628 GCCGACGCTCGTAGCAATG 61.861 63.158 10.72 0.00 42.58 2.82
442 470 3.272334 CGCTCGTAGCAATGCCCC 61.272 66.667 0.00 0.00 42.58 5.80
443 471 3.272334 GCTCGTAGCAATGCCCCG 61.272 66.667 0.00 4.55 41.89 5.73
445 473 1.153449 CTCGTAGCAATGCCCCGAA 60.153 57.895 15.68 3.31 32.54 4.30
446 474 1.153449 TCGTAGCAATGCCCCGAAG 60.153 57.895 13.20 0.00 30.55 3.79
474 506 6.770746 ATGCATCTAAGACATTTTTCTGCT 57.229 33.333 0.00 0.00 0.00 4.24
482 514 9.778741 TCTAAGACATTTTTCTGCTAGAAGAAA 57.221 29.630 20.28 20.28 42.89 2.52
497 529 6.018669 GCTAGAAGAAAAACATATCCTCGGTG 60.019 42.308 0.00 0.00 0.00 4.94
506 538 0.759436 TATCCTCGGTGAAGCCTCCC 60.759 60.000 0.00 0.00 34.25 4.30
520 552 1.739067 CCTCCCCGATCAACTTGTTC 58.261 55.000 0.00 0.00 0.00 3.18
524 556 4.564821 CCTCCCCGATCAACTTGTTCTAAA 60.565 45.833 0.00 0.00 0.00 1.85
528 560 5.163754 CCCCGATCAACTTGTTCTAAACATC 60.164 44.000 0.00 0.00 41.79 3.06
531 563 6.149474 CCGATCAACTTGTTCTAAACATCCTT 59.851 38.462 0.00 0.00 41.79 3.36
536 568 9.567776 TCAACTTGTTCTAAACATCCTTTGATA 57.432 29.630 0.00 0.00 41.79 2.15
833 866 7.874016 TGCACAGAATTTTCTCTTGCATTTATT 59.126 29.630 16.67 0.00 43.31 1.40
941 979 4.096833 TGCAGATAACAACCATCTCATTGC 59.903 41.667 0.00 0.00 30.18 3.56
943 981 5.575957 CAGATAACAACCATCTCATTGCAC 58.424 41.667 0.00 0.00 30.18 4.57
988 1026 1.466024 GCTACTCACTCACCTTCGTCG 60.466 57.143 0.00 0.00 0.00 5.12
1116 1154 2.111043 CAGCTGGTGAACCACGGT 59.889 61.111 5.57 0.00 42.01 4.83
1122 1160 0.836830 TGGTGAACCACGGTATCCCA 60.837 55.000 0.00 0.00 42.01 4.37
1176 1214 2.516460 GAGAGCTACCGCCTCCGA 60.516 66.667 0.00 0.00 36.60 4.55
1231 1269 1.305633 CTGGAGAGGCTGGTGGAGA 60.306 63.158 0.00 0.00 0.00 3.71
2059 2110 9.076781 CAAATATGATGTGTGGGGATAATTGTA 57.923 33.333 0.00 0.00 0.00 2.41
2078 2134 5.114785 TGTAATTGGTTCGGTGTCAAATG 57.885 39.130 0.00 0.00 0.00 2.32
2088 2144 5.873179 TCGGTGTCAAATGATTAGGAAAC 57.127 39.130 0.00 0.00 0.00 2.78
2210 2557 3.649073 TCAGTACATCGTTCCACAAGTG 58.351 45.455 0.00 0.00 0.00 3.16
2219 2566 2.738846 CGTTCCACAAGTGAGATCAAGG 59.261 50.000 0.94 0.00 0.00 3.61
2278 2625 4.646572 ACAAGAAACAGAAGATCTCCACC 58.353 43.478 0.00 0.00 0.00 4.61
2302 2649 5.659048 ACAGTCGAAAAGATCTCACAAAC 57.341 39.130 0.00 0.00 0.00 2.93
2552 2899 3.679389 ACTTCACCTTCATACAAGGCTG 58.321 45.455 0.01 0.00 41.10 4.85
2554 2901 1.350684 TCACCTTCATACAAGGCTGCA 59.649 47.619 0.50 0.00 41.10 4.41
2563 2910 2.348411 ACAAGGCTGCAGTACTGTTT 57.652 45.000 23.44 8.42 0.00 2.83
2583 2930 4.909696 TTCAACGTGAATGACAAACCAT 57.090 36.364 0.00 0.00 30.26 3.55
2669 3021 0.394192 TCCGGCCTCTGCATGATTAG 59.606 55.000 0.00 0.00 40.13 1.73
2707 3059 4.142752 ACATCAATCATGCACGTGAGAAAG 60.143 41.667 22.23 10.10 35.65 2.62
2712 3064 4.891627 TCATGCACGTGAGAAAGAAAAA 57.108 36.364 22.23 0.00 0.00 1.94
2719 3071 6.195613 TGCACGTGAGAAAGAAAAATTAAACG 59.804 34.615 22.23 0.00 0.00 3.60
2746 3098 5.638234 GGTCACAACAAAGTCATAGTAGACC 59.362 44.000 0.00 0.00 39.34 3.85
2760 3112 9.201127 GTCATAGTAGACCGAAACTTAGTTTTT 57.799 33.333 11.88 0.00 32.70 1.94
2761 3113 9.199982 TCATAGTAGACCGAAACTTAGTTTTTG 57.800 33.333 11.88 8.57 35.77 2.44
2762 3114 8.985805 CATAGTAGACCGAAACTTAGTTTTTGT 58.014 33.333 11.88 11.50 35.77 2.83
2764 3116 7.270779 AGTAGACCGAAACTTAGTTTTTGTCT 58.729 34.615 28.65 28.65 42.88 3.41
2766 3118 6.110707 AGACCGAAACTTAGTTTTTGTCTGA 58.889 36.000 26.96 0.00 41.00 3.27
2834 3186 6.945435 TCAATGAGGCAAATCTTTTACCACTA 59.055 34.615 0.00 0.00 0.00 2.74
2837 3189 7.391148 TGAGGCAAATCTTTTACCACTATTC 57.609 36.000 0.00 0.00 0.00 1.75
2866 3222 8.499403 AAAAATTGTAAGCAAAACTAGGCAAA 57.501 26.923 0.00 0.00 38.21 3.68
2867 3223 7.713764 AAATTGTAAGCAAAACTAGGCAAAG 57.286 32.000 0.00 0.00 38.21 2.77
2868 3224 4.846779 TGTAAGCAAAACTAGGCAAAGG 57.153 40.909 0.00 0.00 0.00 3.11
2869 3225 2.820059 AAGCAAAACTAGGCAAAGGC 57.180 45.000 0.00 0.00 40.13 4.35
2870 3226 1.703411 AGCAAAACTAGGCAAAGGCA 58.297 45.000 0.00 0.00 43.71 4.75
2871 3227 1.615392 AGCAAAACTAGGCAAAGGCAG 59.385 47.619 0.00 0.00 43.71 4.85
2872 3228 1.337167 GCAAAACTAGGCAAAGGCAGG 60.337 52.381 0.00 0.00 43.71 4.85
2873 3229 1.273327 CAAAACTAGGCAAAGGCAGGG 59.727 52.381 0.00 0.00 43.71 4.45
2874 3230 0.777446 AAACTAGGCAAAGGCAGGGA 59.223 50.000 0.00 0.00 43.71 4.20
2875 3231 0.329596 AACTAGGCAAAGGCAGGGAG 59.670 55.000 0.00 0.00 43.71 4.30
2876 3232 1.452833 CTAGGCAAAGGCAGGGAGC 60.453 63.158 0.00 0.00 43.71 4.70
2886 3242 3.406200 CAGGGAGCAGGGAGGGTG 61.406 72.222 0.00 0.00 0.00 4.61
2887 3243 4.748798 AGGGAGCAGGGAGGGTGG 62.749 72.222 0.00 0.00 0.00 4.61
2888 3244 4.741239 GGGAGCAGGGAGGGTGGA 62.741 72.222 0.00 0.00 0.00 4.02
2889 3245 3.086600 GGAGCAGGGAGGGTGGAG 61.087 72.222 0.00 0.00 0.00 3.86
2890 3246 3.086600 GAGCAGGGAGGGTGGAGG 61.087 72.222 0.00 0.00 0.00 4.30
2891 3247 4.748798 AGCAGGGAGGGTGGAGGG 62.749 72.222 0.00 0.00 0.00 4.30
2893 3249 3.011517 CAGGGAGGGTGGAGGGTG 61.012 72.222 0.00 0.00 0.00 4.61
2894 3250 4.354943 AGGGAGGGTGGAGGGTGG 62.355 72.222 0.00 0.00 0.00 4.61
2895 3251 4.348495 GGGAGGGTGGAGGGTGGA 62.348 72.222 0.00 0.00 0.00 4.02
2896 3252 2.042930 GGAGGGTGGAGGGTGGAT 59.957 66.667 0.00 0.00 0.00 3.41
2897 3253 2.378634 GGAGGGTGGAGGGTGGATG 61.379 68.421 0.00 0.00 0.00 3.51
2898 3254 2.286425 AGGGTGGAGGGTGGATGG 60.286 66.667 0.00 0.00 0.00 3.51
2899 3255 4.129148 GGGTGGAGGGTGGATGGC 62.129 72.222 0.00 0.00 0.00 4.40
2900 3256 4.129148 GGTGGAGGGTGGATGGCC 62.129 72.222 0.00 0.00 0.00 5.36
2901 3257 3.017581 GTGGAGGGTGGATGGCCT 61.018 66.667 3.32 0.00 34.31 5.19
2902 3258 1.692749 GTGGAGGGTGGATGGCCTA 60.693 63.158 3.32 0.00 34.31 3.93
2903 3259 1.062488 GTGGAGGGTGGATGGCCTAT 61.062 60.000 3.32 0.00 34.31 2.57
2904 3260 0.570727 TGGAGGGTGGATGGCCTATA 59.429 55.000 3.32 0.00 34.31 1.31
2905 3261 1.154216 TGGAGGGTGGATGGCCTATAT 59.846 52.381 3.32 0.00 34.31 0.86
2906 3262 1.561542 GGAGGGTGGATGGCCTATATG 59.438 57.143 3.32 0.00 34.31 1.78
2907 3263 2.269940 GAGGGTGGATGGCCTATATGT 58.730 52.381 3.32 0.00 34.31 2.29
2908 3264 3.450904 GAGGGTGGATGGCCTATATGTA 58.549 50.000 3.32 0.00 34.31 2.29
2909 3265 3.182152 AGGGTGGATGGCCTATATGTAC 58.818 50.000 3.32 0.00 34.31 2.90
2910 3266 2.910319 GGGTGGATGGCCTATATGTACA 59.090 50.000 3.32 0.00 34.31 2.90
2911 3267 3.307480 GGGTGGATGGCCTATATGTACAC 60.307 52.174 3.32 1.98 34.31 2.90
2912 3268 3.307480 GGTGGATGGCCTATATGTACACC 60.307 52.174 3.32 7.65 39.01 4.16
2913 3269 3.326588 GTGGATGGCCTATATGTACACCA 59.673 47.826 3.32 0.00 34.31 4.17
2914 3270 4.019321 GTGGATGGCCTATATGTACACCAT 60.019 45.833 11.99 11.99 40.52 3.55
2915 3271 4.019411 TGGATGGCCTATATGTACACCATG 60.019 45.833 15.90 0.47 38.00 3.66
2916 3272 3.417069 TGGCCTATATGTACACCATGC 57.583 47.619 3.32 0.00 34.86 4.06
2917 3273 2.039746 TGGCCTATATGTACACCATGCC 59.960 50.000 3.32 14.87 38.67 4.40
2918 3274 2.039746 GGCCTATATGTACACCATGCCA 59.960 50.000 16.19 0.00 38.29 4.92
2919 3275 3.074412 GCCTATATGTACACCATGCCAC 58.926 50.000 0.00 0.00 34.86 5.01
2920 3276 3.674997 CCTATATGTACACCATGCCACC 58.325 50.000 0.00 0.00 34.86 4.61
2921 3277 3.072330 CCTATATGTACACCATGCCACCA 59.928 47.826 0.00 0.00 34.86 4.17
2922 3278 2.411628 TATGTACACCATGCCACCAC 57.588 50.000 0.00 0.00 34.86 4.16
2923 3279 0.323360 ATGTACACCATGCCACCACC 60.323 55.000 0.00 0.00 30.69 4.61
2924 3280 1.677633 GTACACCATGCCACCACCC 60.678 63.158 0.00 0.00 0.00 4.61
2925 3281 2.156774 TACACCATGCCACCACCCA 61.157 57.895 0.00 0.00 0.00 4.51
2926 3282 2.419011 TACACCATGCCACCACCCAC 62.419 60.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.673599 GCTTGGTCAGGTCAAGGC 58.326 61.111 6.06 0.00 41.21 4.35
52 53 1.610522 CTTTGGCTTGGTCAGGTCAAG 59.389 52.381 0.79 0.00 43.10 3.02
54 55 0.843309 TCTTTGGCTTGGTCAGGTCA 59.157 50.000 0.00 0.00 0.00 4.02
64 65 2.554032 CGTGTGGAGATTTCTTTGGCTT 59.446 45.455 0.00 0.00 0.00 4.35
89 90 2.044946 AGGATTGGAAGGTGCCGC 60.045 61.111 0.00 0.00 0.00 6.53
94 95 2.131023 GGAGATGGAGGATTGGAAGGT 58.869 52.381 0.00 0.00 0.00 3.50
95 96 2.416638 AGGAGATGGAGGATTGGAAGG 58.583 52.381 0.00 0.00 0.00 3.46
97 98 2.780010 GGAAGGAGATGGAGGATTGGAA 59.220 50.000 0.00 0.00 0.00 3.53
98 99 2.412591 GGAAGGAGATGGAGGATTGGA 58.587 52.381 0.00 0.00 0.00 3.53
123 126 6.579214 ACAAGGGAGAGATATGGATAGGATT 58.421 40.000 0.00 0.00 0.00 3.01
124 127 6.177663 ACAAGGGAGAGATATGGATAGGAT 57.822 41.667 0.00 0.00 0.00 3.24
135 138 4.437682 TTGTTGTTGACAAGGGAGAGAT 57.562 40.909 0.00 0.00 43.13 2.75
150 153 3.077359 GGAATAGAGTGCTGCTTGTTGT 58.923 45.455 0.00 0.00 0.00 3.32
153 156 2.938756 GCTGGAATAGAGTGCTGCTTGT 60.939 50.000 0.00 0.00 32.25 3.16
160 163 2.231215 ACATCGCTGGAATAGAGTGC 57.769 50.000 0.00 0.00 0.00 4.40
164 190 2.809446 CGACAACATCGCTGGAATAGA 58.191 47.619 0.00 0.00 45.52 1.98
177 203 0.960861 TGGTTGCAACACCGACAACA 60.961 50.000 29.55 13.57 44.27 3.33
233 259 2.354259 CAACTGGGCTTGTTGCAAAAA 58.646 42.857 0.00 0.00 45.15 1.94
242 268 1.286354 CGCAATTGCAACTGGGCTTG 61.286 55.000 28.77 7.83 42.21 4.01
249 277 1.204062 CGACGTCGCAATTGCAACT 59.796 52.632 28.77 11.63 42.21 3.16
253 281 1.591394 GGTTATCGACGTCGCAATTGC 60.591 52.381 32.19 20.76 39.60 3.56
267 295 2.981140 GCATCTCTAACTCGCGGTTATC 59.019 50.000 16.83 3.91 39.36 1.75
269 297 1.066605 GGCATCTCTAACTCGCGGTTA 59.933 52.381 6.13 12.72 39.17 2.85
270 298 0.179108 GGCATCTCTAACTCGCGGTT 60.179 55.000 6.13 12.21 41.54 4.44
274 302 2.223135 GCAAAAGGCATCTCTAACTCGC 60.223 50.000 0.00 0.00 43.97 5.03
289 317 0.465287 ACAGGGCCTTGTTGCAAAAG 59.535 50.000 16.01 7.50 0.00 2.27
298 326 0.952010 GCAATTGCAACAGGGCCTTG 60.952 55.000 25.36 14.35 41.59 3.61
310 338 0.250424 AAGGCCCTTGTTGCAATTGC 60.250 50.000 23.69 23.69 42.50 3.56
311 339 1.515081 CAAGGCCCTTGTTGCAATTG 58.485 50.000 15.63 0.00 36.79 2.32
320 348 0.393820 ACATTGCAACAAGGCCCTTG 59.606 50.000 21.95 21.95 45.85 3.61
321 349 2.008242 TACATTGCAACAAGGCCCTT 57.992 45.000 0.00 0.00 0.00 3.95
322 350 2.008242 TTACATTGCAACAAGGCCCT 57.992 45.000 0.00 0.00 0.00 5.19
323 351 2.620242 CATTACATTGCAACAAGGCCC 58.380 47.619 0.00 0.00 0.00 5.80
324 352 2.028203 ACCATTACATTGCAACAAGGCC 60.028 45.455 0.00 0.00 0.00 5.19
325 353 3.056607 AGACCATTACATTGCAACAAGGC 60.057 43.478 0.00 0.00 0.00 4.35
326 354 4.789012 AGACCATTACATTGCAACAAGG 57.211 40.909 0.00 0.76 0.00 3.61
342 370 2.984562 TCGCTCATTGCAATAAGACCA 58.015 42.857 14.10 0.00 43.06 4.02
343 371 4.098416 GTTTCGCTCATTGCAATAAGACC 58.902 43.478 14.10 0.00 43.06 3.85
356 384 2.239400 TCCTCTTCTCTGTTTCGCTCA 58.761 47.619 0.00 0.00 0.00 4.26
369 397 2.064014 CGTACCCGTTTGTTCCTCTTC 58.936 52.381 0.00 0.00 0.00 2.87
374 402 1.269726 TGAGTCGTACCCGTTTGTTCC 60.270 52.381 0.00 0.00 35.01 3.62
378 406 0.319211 TGCTGAGTCGTACCCGTTTG 60.319 55.000 0.00 0.00 35.01 2.93
380 408 0.892358 TCTGCTGAGTCGTACCCGTT 60.892 55.000 0.00 0.00 35.01 4.44
382 410 1.306148 TATCTGCTGAGTCGTACCCG 58.694 55.000 0.00 0.00 0.00 5.28
392 420 5.819379 GTGATCTTGTCCAAATATCTGCTGA 59.181 40.000 0.00 0.00 0.00 4.26
394 422 5.128919 GGTGATCTTGTCCAAATATCTGCT 58.871 41.667 0.00 0.00 0.00 4.24
397 425 4.444876 CCGGGTGATCTTGTCCAAATATCT 60.445 45.833 0.00 0.00 0.00 1.98
398 426 3.815401 CCGGGTGATCTTGTCCAAATATC 59.185 47.826 0.00 0.00 0.00 1.63
401 429 1.955208 GCCGGGTGATCTTGTCCAAAT 60.955 52.381 2.18 0.00 0.00 2.32
408 436 2.511600 GTCGGCCGGGTGATCTTG 60.512 66.667 27.83 0.00 0.00 3.02
419 447 4.789075 TTGCTACGAGCGTCGGCC 62.789 66.667 14.71 0.00 46.26 6.13
436 464 1.265236 TGCATTTTTCTTCGGGGCAT 58.735 45.000 0.00 0.00 0.00 4.40
437 465 1.204467 GATGCATTTTTCTTCGGGGCA 59.796 47.619 0.00 0.00 0.00 5.36
438 466 1.478105 AGATGCATTTTTCTTCGGGGC 59.522 47.619 0.00 0.00 0.00 5.80
442 470 8.679288 AAATGTCTTAGATGCATTTTTCTTCG 57.321 30.769 0.00 0.00 39.04 3.79
474 506 7.177832 TCACCGAGGATATGTTTTTCTTCTA 57.822 36.000 0.00 0.00 0.00 2.10
482 514 2.505819 AGGCTTCACCGAGGATATGTTT 59.494 45.455 0.00 0.00 46.52 2.83
497 529 0.253327 AAGTTGATCGGGGAGGCTTC 59.747 55.000 0.00 0.00 0.00 3.86
506 538 5.643777 AGGATGTTTAGAACAAGTTGATCGG 59.356 40.000 10.54 0.00 45.86 4.18
579 611 1.930251 TGGGTCTGGTCTCTGAAGAG 58.070 55.000 0.58 0.58 43.36 2.85
740 773 2.793585 CGATGTTGTTGGATGCTCATGC 60.794 50.000 0.00 0.00 40.20 4.06
833 866 4.552355 TCGAGACATTCTCTGCGTAAAAA 58.448 39.130 1.88 0.00 41.26 1.94
839 872 0.735471 TCCTCGAGACATTCTCTGCG 59.265 55.000 15.71 0.00 41.26 5.18
941 979 2.960384 AGGCTCTGATCTGATCTCTGTG 59.040 50.000 17.82 10.10 0.00 3.66
943 981 3.507233 GGTAGGCTCTGATCTGATCTCTG 59.493 52.174 17.82 8.82 0.00 3.35
988 1026 2.814336 GGACAACCATGGTGAAGTTCTC 59.186 50.000 20.60 6.14 35.97 2.87
1116 1154 2.501723 GTCAAGAAGCTCCAGTGGGATA 59.498 50.000 9.92 0.00 43.91 2.59
1122 1160 1.004440 GCGGTCAAGAAGCTCCAGT 60.004 57.895 0.00 0.00 0.00 4.00
1962 2010 6.759497 AAAACAAAGCCAGCTAATAGGTAG 57.241 37.500 0.00 0.00 0.00 3.18
1963 2011 7.169591 TGTAAAACAAAGCCAGCTAATAGGTA 58.830 34.615 0.00 0.00 0.00 3.08
1964 2012 6.007703 TGTAAAACAAAGCCAGCTAATAGGT 58.992 36.000 0.00 0.00 0.00 3.08
1965 2013 6.509418 TGTAAAACAAAGCCAGCTAATAGG 57.491 37.500 0.00 0.00 0.00 2.57
1966 2014 8.243426 TCATTGTAAAACAAAGCCAGCTAATAG 58.757 33.333 0.00 0.00 41.96 1.73
2002 2051 7.806014 GCGTCTGAATAAACTCCAAAAATACAA 59.194 33.333 0.00 0.00 0.00 2.41
2059 2110 5.467035 AATCATTTGACACCGAACCAATT 57.533 34.783 0.00 0.00 0.00 2.32
2078 2134 9.717892 GAAAAATCCATACTTCGTTTCCTAATC 57.282 33.333 0.00 0.00 0.00 1.75
2128 2184 7.454225 AGCAGATACTTTCAATATTACCCCTC 58.546 38.462 0.00 0.00 0.00 4.30
2144 2201 9.066892 TCAAACAATGTAAAGAAAGCAGATACT 57.933 29.630 0.00 0.00 0.00 2.12
2252 2599 6.260936 GTGGAGATCTTCTGTTTCTTGTCAAA 59.739 38.462 1.86 0.00 0.00 2.69
2278 2625 5.657470 TTGTGAGATCTTTTCGACTGTTG 57.343 39.130 0.00 0.00 0.00 3.33
2501 2848 0.178973 TTCGGGACAGTCCACAGAGA 60.179 55.000 21.75 9.03 38.64 3.10
2502 2849 0.898320 ATTCGGGACAGTCCACAGAG 59.102 55.000 21.75 6.89 38.64 3.35
2552 2899 3.936902 TTCACGTTGAAACAGTACTGC 57.063 42.857 22.90 7.39 32.71 4.40
2554 2901 5.113383 TGTCATTCACGTTGAAACAGTACT 58.887 37.500 0.00 0.00 40.12 2.73
2563 2910 6.567687 AATATGGTTTGTCATTCACGTTGA 57.432 33.333 0.00 0.00 0.00 3.18
2638 2985 2.639839 AGAGGCCGGATGTGCTTATTAT 59.360 45.455 5.05 0.00 0.00 1.28
2640 2987 0.839946 AGAGGCCGGATGTGCTTATT 59.160 50.000 5.05 0.00 0.00 1.40
2643 2990 2.270205 CAGAGGCCGGATGTGCTT 59.730 61.111 5.05 0.00 0.00 3.91
2645 2992 4.783621 TGCAGAGGCCGGATGTGC 62.784 66.667 18.68 18.68 40.13 4.57
2646 2993 2.184830 CATGCAGAGGCCGGATGTG 61.185 63.158 5.05 2.10 40.13 3.21
2648 2995 0.536687 AATCATGCAGAGGCCGGATG 60.537 55.000 5.05 0.00 40.13 3.51
2652 3004 0.394192 TCCTAATCATGCAGAGGCCG 59.606 55.000 0.00 0.00 40.13 6.13
2669 3021 1.337703 TGATGTTGCTTGTGTGCTTCC 59.662 47.619 0.00 0.00 0.00 3.46
2707 3059 3.630101 TGTGACCGGCGTTTAATTTTTC 58.370 40.909 6.01 0.00 0.00 2.29
2712 3064 1.595466 TGTTGTGACCGGCGTTTAAT 58.405 45.000 6.01 0.00 0.00 1.40
2719 3071 0.951558 ATGACTTTGTTGTGACCGGC 59.048 50.000 0.00 0.00 0.00 6.13
2806 3158 7.603784 GTGGTAAAAGATTTGCCTCATTGATTT 59.396 33.333 10.57 0.00 0.00 2.17
2816 3168 6.431198 TCGAATAGTGGTAAAAGATTTGCC 57.569 37.500 3.36 3.36 0.00 4.52
2853 3209 1.273327 CCCTGCCTTTGCCTAGTTTTG 59.727 52.381 0.00 0.00 36.33 2.44
2854 3210 1.146982 TCCCTGCCTTTGCCTAGTTTT 59.853 47.619 0.00 0.00 36.33 2.43
2855 3211 0.777446 TCCCTGCCTTTGCCTAGTTT 59.223 50.000 0.00 0.00 36.33 2.66
2856 3212 0.329596 CTCCCTGCCTTTGCCTAGTT 59.670 55.000 0.00 0.00 36.33 2.24
2857 3213 1.994463 CTCCCTGCCTTTGCCTAGT 59.006 57.895 0.00 0.00 36.33 2.57
2858 3214 1.452833 GCTCCCTGCCTTTGCCTAG 60.453 63.158 0.00 0.00 36.33 3.02
2859 3215 2.202236 CTGCTCCCTGCCTTTGCCTA 62.202 60.000 0.00 0.00 42.00 3.93
2860 3216 3.580604 CTGCTCCCTGCCTTTGCCT 62.581 63.158 0.00 0.00 42.00 4.75
2861 3217 3.066814 CTGCTCCCTGCCTTTGCC 61.067 66.667 0.00 0.00 42.00 4.52
2862 3218 3.066814 CCTGCTCCCTGCCTTTGC 61.067 66.667 0.00 0.00 42.00 3.68
2863 3219 2.362120 CCCTGCTCCCTGCCTTTG 60.362 66.667 0.00 0.00 42.00 2.77
2864 3220 2.532715 TCCCTGCTCCCTGCCTTT 60.533 61.111 0.00 0.00 42.00 3.11
2865 3221 3.013932 CTCCCTGCTCCCTGCCTT 61.014 66.667 0.00 0.00 42.00 4.35
2869 3225 3.406200 CACCCTCCCTGCTCCCTG 61.406 72.222 0.00 0.00 0.00 4.45
2870 3226 4.748798 CCACCCTCCCTGCTCCCT 62.749 72.222 0.00 0.00 0.00 4.20
2871 3227 4.741239 TCCACCCTCCCTGCTCCC 62.741 72.222 0.00 0.00 0.00 4.30
2872 3228 3.086600 CTCCACCCTCCCTGCTCC 61.087 72.222 0.00 0.00 0.00 4.70
2873 3229 3.086600 CCTCCACCCTCCCTGCTC 61.087 72.222 0.00 0.00 0.00 4.26
2874 3230 4.748798 CCCTCCACCCTCCCTGCT 62.749 72.222 0.00 0.00 0.00 4.24
2876 3232 3.011517 CACCCTCCACCCTCCCTG 61.012 72.222 0.00 0.00 0.00 4.45
2877 3233 4.354943 CCACCCTCCACCCTCCCT 62.355 72.222 0.00 0.00 0.00 4.20
2878 3234 3.660092 ATCCACCCTCCACCCTCCC 62.660 68.421 0.00 0.00 0.00 4.30
2879 3235 2.042930 ATCCACCCTCCACCCTCC 59.957 66.667 0.00 0.00 0.00 4.30
2880 3236 2.378634 CCATCCACCCTCCACCCTC 61.379 68.421 0.00 0.00 0.00 4.30
2881 3237 2.286425 CCATCCACCCTCCACCCT 60.286 66.667 0.00 0.00 0.00 4.34
2882 3238 4.129148 GCCATCCACCCTCCACCC 62.129 72.222 0.00 0.00 0.00 4.61
2883 3239 4.129148 GGCCATCCACCCTCCACC 62.129 72.222 0.00 0.00 0.00 4.61
2884 3240 1.062488 ATAGGCCATCCACCCTCCAC 61.062 60.000 5.01 0.00 32.65 4.02
2885 3241 0.570727 TATAGGCCATCCACCCTCCA 59.429 55.000 5.01 0.00 32.65 3.86
2886 3242 1.561542 CATATAGGCCATCCACCCTCC 59.438 57.143 5.01 0.00 32.65 4.30
2887 3243 2.269940 ACATATAGGCCATCCACCCTC 58.730 52.381 5.01 0.00 32.65 4.30
2888 3244 2.440494 ACATATAGGCCATCCACCCT 57.560 50.000 5.01 0.00 35.22 4.34
2889 3245 2.910319 TGTACATATAGGCCATCCACCC 59.090 50.000 5.01 0.00 33.74 4.61
2890 3246 3.307480 GGTGTACATATAGGCCATCCACC 60.307 52.174 5.01 5.57 33.78 4.61
2891 3247 3.326588 TGGTGTACATATAGGCCATCCAC 59.673 47.826 5.01 0.00 33.74 4.02
2892 3248 3.592865 TGGTGTACATATAGGCCATCCA 58.407 45.455 5.01 0.00 33.74 3.41
2893 3249 4.517285 CATGGTGTACATATAGGCCATCC 58.483 47.826 5.01 0.00 37.84 3.51
2894 3250 3.941483 GCATGGTGTACATATAGGCCATC 59.059 47.826 5.01 3.67 37.84 3.51
2895 3251 3.308402 GGCATGGTGTACATATAGGCCAT 60.308 47.826 20.47 14.74 41.90 4.40
2896 3252 2.039746 GGCATGGTGTACATATAGGCCA 59.960 50.000 20.47 13.36 41.90 5.36
2897 3253 2.039746 TGGCATGGTGTACATATAGGCC 59.960 50.000 19.30 19.30 42.36 5.19
2898 3254 3.074412 GTGGCATGGTGTACATATAGGC 58.926 50.000 0.00 1.93 37.84 3.93
2899 3255 3.072330 TGGTGGCATGGTGTACATATAGG 59.928 47.826 0.00 0.00 37.84 2.57
2900 3256 4.065088 GTGGTGGCATGGTGTACATATAG 58.935 47.826 0.00 0.00 37.84 1.31
2901 3257 3.181449 GGTGGTGGCATGGTGTACATATA 60.181 47.826 0.00 0.00 37.84 0.86
2902 3258 2.422803 GGTGGTGGCATGGTGTACATAT 60.423 50.000 0.00 0.00 37.84 1.78
2903 3259 1.065053 GGTGGTGGCATGGTGTACATA 60.065 52.381 0.00 0.00 37.84 2.29
2904 3260 0.323360 GGTGGTGGCATGGTGTACAT 60.323 55.000 0.00 0.00 41.57 2.29
2905 3261 1.074072 GGTGGTGGCATGGTGTACA 59.926 57.895 0.00 0.00 0.00 2.90
2906 3262 1.677633 GGGTGGTGGCATGGTGTAC 60.678 63.158 0.00 0.00 0.00 2.90
2907 3263 2.156774 TGGGTGGTGGCATGGTGTA 61.157 57.895 0.00 0.00 0.00 2.90
2908 3264 3.506743 TGGGTGGTGGCATGGTGT 61.507 61.111 0.00 0.00 0.00 4.16
2909 3265 2.990967 GTGGGTGGTGGCATGGTG 60.991 66.667 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.