Multiple sequence alignment - TraesCS2D01G442700

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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 TraesCS2D01G442700 chr2D 100.000 3917 0 0 1 3917 553254573 553250657 0.000000e+00 7234
1 TraesCS2D01G442700 chr2B 94.995 2877 101 23 309 3162 659004511 659001655 0.000000e+00 4475
2 TraesCS2D01G442700 chr2B 94.272 611 25 7 2530 3138 658997077 658996475 0.000000e+00 926
3 TraesCS2D01G442700 chr2B 89.644 309 17 8 1 307 659004865 659004570 2.860000e-101 379
4 TraesCS2D01G442700 chr2A 96.387 2159 58 10 989 3138 693429940 693427793 0.000000e+00 3537
5 TraesCS2D01G442700 chr2A 85.169 445 19 12 502 942 693430413 693430012 2.820000e-111 412
6 TraesCS2D01G442700 chr5B 92.857 770 39 6 3157 3917 208704871 208704109 0.000000e+00 1103
7 TraesCS2D01G442700 chr5B 89.833 777 51 9 3159 3912 474051570 474050799 0.000000e+00 972
8 TraesCS2D01G442700 chr5B 84.874 476 56 12 3158 3623 420574414 420574883 2.130000e-127 466
9 TraesCS2D01G442700 chr5B 84.783 322 32 6 3608 3917 420574945 420575261 1.370000e-79 307
10 TraesCS2D01G442700 chr6A 92.458 769 45 6 3158 3917 576223283 576224047 0.000000e+00 1086
11 TraesCS2D01G442700 chr6A 81.573 1297 202 22 1638 2920 493842838 493844111 0.000000e+00 1037
12 TraesCS2D01G442700 chr6A 92.493 706 40 6 3221 3917 576397482 576398183 0.000000e+00 998
13 TraesCS2D01G442700 chr6A 80.802 1297 212 20 1638 2920 493756655 493757928 0.000000e+00 981
14 TraesCS2D01G442700 chr6A 80.663 1267 210 20 1667 2920 495153701 495152457 0.000000e+00 950
15 TraesCS2D01G442700 chr6A 80.124 1293 224 17 1638 2918 494047348 494048619 0.000000e+00 933
16 TraesCS2D01G442700 chr6A 80.568 916 145 19 1641 2544 494880285 494879391 0.000000e+00 675
17 TraesCS2D01G442700 chr6A 89.732 224 22 1 1230 1453 493842509 493842731 6.410000e-73 285
18 TraesCS2D01G442700 chr6A 89.286 224 23 1 1230 1453 495154059 495153837 2.980000e-71 279
19 TraesCS2D01G442700 chr6A 90.141 213 21 0 1241 1453 493756339 493756551 1.070000e-70 278
20 TraesCS2D01G442700 chr6D 81.596 1266 196 18 1667 2918 350204727 350203485 0.000000e+00 1013
21 TraesCS2D01G442700 chr6D 81.096 1296 210 20 1638 2920 349031771 349033044 0.000000e+00 1003
22 TraesCS2D01G442700 chr6D 80.478 1296 218 22 1638 2920 348861708 348862981 0.000000e+00 959
23 TraesCS2D01G442700 chr6D 88.596 228 25 1 1225 1452 28244891 28244665 3.860000e-70 276
24 TraesCS2D01G442700 chr6D 88.839 224 24 1 1230 1453 350205043 350204821 1.390000e-69 274
25 TraesCS2D01G442700 chr6D 88.789 223 24 1 1230 1452 348861379 348861600 4.990000e-69 272
26 TraesCS2D01G442700 chr6B 80.603 1294 216 21 1638 2918 529890222 529891493 0.000000e+00 966
27 TraesCS2D01G442700 chr6B 80.495 1292 219 19 1641 2920 530851842 530850572 0.000000e+00 959
28 TraesCS2D01G442700 chr6B 84.744 780 87 13 3151 3913 142735767 142736531 0.000000e+00 752
29 TraesCS2D01G442700 chr6B 89.286 224 23 1 1230 1453 529889893 529890115 2.980000e-71 279
30 TraesCS2D01G442700 chrUn 85.863 771 82 12 3164 3913 928652 927888 0.000000e+00 795
31 TraesCS2D01G442700 chrUn 85.714 777 84 12 3158 3913 951049 951819 0.000000e+00 795
32 TraesCS2D01G442700 chr1A 85.863 771 82 12 3164 3913 514591872 514591108 0.000000e+00 795
33 TraesCS2D01G442700 chr1A 85.038 782 83 16 3158 3917 9965007 9965776 0.000000e+00 765
34 TraesCS2D01G442700 chr5D 88.667 450 33 6 3477 3913 294330399 294330843 2.070000e-147 532
35 TraesCS2D01G442700 chr3A 87.640 356 28 8 3576 3917 680763037 680763390 2.190000e-107 399
36 TraesCS2D01G442700 chr7A 91.379 232 17 3 3687 3917 234527842 234528071 8.170000e-82 315
37 TraesCS2D01G442700 chr7D 83.871 124 20 0 3151 3274 27507996 27508119 6.880000e-23 119


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 TraesCS2D01G442700 chr2D 553250657 553254573 3916 True 7234.0 7234 100.0000 1 3917 1 chr2D.!!$R1 3916
1 TraesCS2D01G442700 chr2B 659001655 659004865 3210 True 2427.0 4475 92.3195 1 3162 2 chr2B.!!$R2 3161
2 TraesCS2D01G442700 chr2B 658996475 658997077 602 True 926.0 926 94.2720 2530 3138 1 chr2B.!!$R1 608
3 TraesCS2D01G442700 chr2A 693427793 693430413 2620 True 1974.5 3537 90.7780 502 3138 2 chr2A.!!$R1 2636
4 TraesCS2D01G442700 chr5B 208704109 208704871 762 True 1103.0 1103 92.8570 3157 3917 1 chr5B.!!$R1 760
5 TraesCS2D01G442700 chr5B 474050799 474051570 771 True 972.0 972 89.8330 3159 3912 1 chr5B.!!$R2 753
6 TraesCS2D01G442700 chr5B 420574414 420575261 847 False 386.5 466 84.8285 3158 3917 2 chr5B.!!$F1 759
7 TraesCS2D01G442700 chr6A 576223283 576224047 764 False 1086.0 1086 92.4580 3158 3917 1 chr6A.!!$F2 759
8 TraesCS2D01G442700 chr6A 576397482 576398183 701 False 998.0 998 92.4930 3221 3917 1 chr6A.!!$F3 696
9 TraesCS2D01G442700 chr6A 494047348 494048619 1271 False 933.0 933 80.1240 1638 2918 1 chr6A.!!$F1 1280
10 TraesCS2D01G442700 chr6A 494879391 494880285 894 True 675.0 675 80.5680 1641 2544 1 chr6A.!!$R1 903
11 TraesCS2D01G442700 chr6A 493842509 493844111 1602 False 661.0 1037 85.6525 1230 2920 2 chr6A.!!$F5 1690
12 TraesCS2D01G442700 chr6A 493756339 493757928 1589 False 629.5 981 85.4715 1241 2920 2 chr6A.!!$F4 1679
13 TraesCS2D01G442700 chr6A 495152457 495154059 1602 True 614.5 950 84.9745 1230 2920 2 chr6A.!!$R2 1690
14 TraesCS2D01G442700 chr6D 349031771 349033044 1273 False 1003.0 1003 81.0960 1638 2920 1 chr6D.!!$F1 1282
15 TraesCS2D01G442700 chr6D 350203485 350205043 1558 True 643.5 1013 85.2175 1230 2918 2 chr6D.!!$R2 1688
16 TraesCS2D01G442700 chr6D 348861379 348862981 1602 False 615.5 959 84.6335 1230 2920 2 chr6D.!!$F2 1690
17 TraesCS2D01G442700 chr6B 530850572 530851842 1270 True 959.0 959 80.4950 1641 2920 1 chr6B.!!$R1 1279
18 TraesCS2D01G442700 chr6B 142735767 142736531 764 False 752.0 752 84.7440 3151 3913 1 chr6B.!!$F1 762
19 TraesCS2D01G442700 chr6B 529889893 529891493 1600 False 622.5 966 84.9445 1230 2918 2 chr6B.!!$F2 1688
20 TraesCS2D01G442700 chrUn 927888 928652 764 True 795.0 795 85.8630 3164 3913 1 chrUn.!!$R1 749
21 TraesCS2D01G442700 chrUn 951049 951819 770 False 795.0 795 85.7140 3158 3913 1 chrUn.!!$F1 755
22 TraesCS2D01G442700 chr1A 514591108 514591872 764 True 795.0 795 85.8630 3164 3913 1 chr1A.!!$R1 749
23 TraesCS2D01G442700 chr1A 9965007 9965776 769 False 765.0 765 85.0380 3158 3917 1 chr1A.!!$F1 759

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
209 210 0.179032 TTGCTCTTCAGTTTCCCGCA 60.179 50.000 0.0 0.0 0.00 5.69 F
912 981 0.985490 ATCTCACCCTCCAAGGCTCC 60.985 60.000 0.0 0.0 32.73 4.70 F
1476 1572 1.066454 GTAAGCACACACCCAAACCAC 59.934 52.381 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1279 0.755079 TTGCTCTCTATCAGCGGCAT 59.245 50.000 1.45 0.0 40.01 4.40 R
2238 2421 1.227380 GATGCTCGTCGCCCAGATT 60.227 57.895 0.00 0.0 38.05 2.40 R
2928 3114 0.026803 GTACGCCGACGAGTAACGAT 59.973 55.000 0.00 0.0 45.77 3.73 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
28 29 3.786635 CTGATGTAACAGTCAGTAGCCC 58.213 50.000 0.00 0.00 37.62 5.19
63 64 1.187087 GGATTCACAGAGACGGTCCT 58.813 55.000 4.14 0.00 0.00 3.85
65 66 0.811915 ATTCACAGAGACGGTCCTCG 59.188 55.000 4.14 0.00 45.88 4.63
174 175 2.017049 GCATTTCACCTTACCGATGCT 58.983 47.619 0.00 0.00 37.49 3.79
176 177 2.851263 TTTCACCTTACCGATGCTGT 57.149 45.000 0.00 0.00 0.00 4.40
184 185 2.157834 TACCGATGCTGTTCACGTTT 57.842 45.000 0.00 0.00 0.00 3.60
209 210 0.179032 TTGCTCTTCAGTTTCCCGCA 60.179 50.000 0.00 0.00 0.00 5.69
224 230 6.097839 AGTTTCCCGCAAGATAAGTATAGTGA 59.902 38.462 0.00 0.00 43.02 3.41
225 231 5.707242 TCCCGCAAGATAAGTATAGTGAG 57.293 43.478 0.00 0.00 43.02 3.51
234 240 7.847711 AGATAAGTATAGTGAGTTGGAGCAT 57.152 36.000 0.00 0.00 0.00 3.79
235 241 8.941995 AGATAAGTATAGTGAGTTGGAGCATA 57.058 34.615 0.00 0.00 0.00 3.14
236 242 8.798402 AGATAAGTATAGTGAGTTGGAGCATAC 58.202 37.037 0.00 0.00 0.00 2.39
237 243 8.713708 ATAAGTATAGTGAGTTGGAGCATACT 57.286 34.615 0.00 0.00 30.95 2.12
238 244 6.642707 AGTATAGTGAGTTGGAGCATACTC 57.357 41.667 0.00 0.00 42.66 2.59
239 245 6.369629 AGTATAGTGAGTTGGAGCATACTCT 58.630 40.000 0.00 0.00 42.98 3.24
240 246 7.519057 AGTATAGTGAGTTGGAGCATACTCTA 58.481 38.462 0.00 0.00 42.98 2.43
241 247 6.892658 ATAGTGAGTTGGAGCATACTCTAG 57.107 41.667 0.00 0.00 42.98 2.43
242 248 4.861196 AGTGAGTTGGAGCATACTCTAGA 58.139 43.478 0.00 0.00 42.98 2.43
243 249 5.454062 AGTGAGTTGGAGCATACTCTAGAT 58.546 41.667 0.00 0.00 42.98 1.98
244 250 6.606069 AGTGAGTTGGAGCATACTCTAGATA 58.394 40.000 0.00 0.00 42.98 1.98
245 251 7.063593 AGTGAGTTGGAGCATACTCTAGATAA 58.936 38.462 0.00 0.00 42.98 1.75
256 262 9.113838 AGCATACTCTAGATAAATTTGTGGTTG 57.886 33.333 0.00 0.00 0.00 3.77
259 265 7.383102 ACTCTAGATAAATTTGTGGTTGCAG 57.617 36.000 0.00 0.00 0.00 4.41
286 292 6.270927 TGGTTAGGATTATGCTCTCTGCTAAT 59.729 38.462 0.00 0.00 43.37 1.73
287 293 6.816140 GGTTAGGATTATGCTCTCTGCTAATC 59.184 42.308 0.00 0.00 43.37 1.75
288 294 7.382110 GTTAGGATTATGCTCTCTGCTAATCA 58.618 38.462 14.89 0.00 40.02 2.57
289 295 6.430962 AGGATTATGCTCTCTGCTAATCAA 57.569 37.500 14.89 0.00 40.02 2.57
290 296 6.229733 AGGATTATGCTCTCTGCTAATCAAC 58.770 40.000 14.89 5.79 40.02 3.18
318 381 5.112937 GCGTTTCATATACGTTTTATTGCGG 59.887 40.000 0.00 0.00 40.92 5.69
334 397 1.227380 CGGTGAGCTGGCCAGATAC 60.227 63.158 37.21 27.08 0.00 2.24
344 407 2.232452 CTGGCCAGATACTTATCCGAGG 59.768 54.545 29.88 0.00 33.17 4.63
359 422 2.298163 TCCGAGGGTGAAAGTAACAGAC 59.702 50.000 0.00 0.00 0.00 3.51
365 428 4.163458 AGGGTGAAAGTAACAGACACAGAA 59.837 41.667 0.00 0.00 33.82 3.02
379 442 2.301346 CACAGAACTTTCCTTGCTGGT 58.699 47.619 0.00 0.00 37.07 4.00
409 472 1.231958 TTGGGCGCAGTAAAGTTCCG 61.232 55.000 10.83 0.00 0.00 4.30
411 474 2.322081 GGCGCAGTAAAGTTCCGCA 61.322 57.895 10.83 0.00 45.78 5.69
414 477 1.144969 CGCAGTAAAGTTCCGCAGAA 58.855 50.000 0.00 0.00 0.00 3.02
427 490 1.661509 GCAGAAAAGTTGCCACGGC 60.662 57.895 0.00 0.00 42.35 5.68
471 534 2.590575 ACCACACGCAAAGTCCCG 60.591 61.111 0.00 0.00 0.00 5.14
487 550 1.206578 CCGTCGAACATGTTGCCAC 59.793 57.895 17.58 8.32 0.00 5.01
617 685 2.978010 GCCCGGGCGGTCATATTG 60.978 66.667 33.60 0.00 0.00 1.90
735 804 4.277476 TCATTCATTTATCCTTTGCCGGT 58.723 39.130 1.90 0.00 0.00 5.28
786 855 2.167861 GCGATCCCACTGCTTCGTC 61.168 63.158 0.00 0.00 34.24 4.20
798 867 1.773496 CTTCGTCTCGTTTGACCGC 59.227 57.895 0.00 0.00 33.70 5.68
900 969 2.016096 GCCTCTTGCTTCCATCTCACC 61.016 57.143 0.00 0.00 36.87 4.02
912 981 0.985490 ATCTCACCCTCCAAGGCTCC 60.985 60.000 0.00 0.00 32.73 4.70
928 997 1.228429 TCCCACCCGAGCCAAAAAG 60.228 57.895 0.00 0.00 0.00 2.27
987 1081 6.113411 GGTTTCAGCAGCTATCTACCTTAAA 58.887 40.000 0.00 0.00 0.00 1.52
1208 1304 3.550639 CCGCTGATAGAGAGCAAGAAGAG 60.551 52.174 0.00 0.00 36.12 2.85
1453 1549 1.833630 TCTCCCTCGTCGTCTACCTTA 59.166 52.381 0.00 0.00 0.00 2.69
1476 1572 1.066454 GTAAGCACACACCCAAACCAC 59.934 52.381 0.00 0.00 0.00 4.16
1544 1658 1.577328 TAACTTGGCTGCTGCGCTTC 61.577 55.000 9.73 0.00 40.82 3.86
2150 2333 2.126031 GGAGGAGGTGACGAACGC 60.126 66.667 0.00 0.00 0.00 4.84
2598 2784 2.471255 GCAGATGCCGCAGTACTTT 58.529 52.632 0.00 0.00 34.31 2.66
2927 3113 0.907837 GTGTCGTGATCGTGATCGTG 59.092 55.000 5.46 0.93 40.63 4.35
2928 3114 0.800012 TGTCGTGATCGTGATCGTGA 59.200 50.000 5.46 3.15 40.63 4.35
2929 3115 1.400494 TGTCGTGATCGTGATCGTGAT 59.600 47.619 5.46 0.00 40.63 3.06
2930 3116 2.037649 GTCGTGATCGTGATCGTGATC 58.962 52.381 16.21 16.21 40.63 2.92
2931 3117 1.037998 CGTGATCGTGATCGTGATCG 58.962 55.000 17.30 7.66 43.10 3.69
3050 3236 7.506328 TCAAAAGGTTCTTTCTTTAGGTAGC 57.494 36.000 0.00 0.00 33.80 3.58
3051 3237 7.057894 TCAAAAGGTTCTTTCTTTAGGTAGCA 58.942 34.615 0.00 0.00 33.80 3.49
3052 3238 7.228706 TCAAAAGGTTCTTTCTTTAGGTAGCAG 59.771 37.037 0.00 0.00 33.80 4.24
3053 3239 5.827326 AGGTTCTTTCTTTAGGTAGCAGT 57.173 39.130 0.00 0.00 0.00 4.40
3054 3240 6.189036 AGGTTCTTTCTTTAGGTAGCAGTT 57.811 37.500 0.00 0.00 0.00 3.16
3114 3301 0.810426 TTACGGCAACACGCAACAGA 60.810 50.000 0.00 0.00 45.17 3.41
3116 3303 1.654137 CGGCAACACGCAACAGAAC 60.654 57.895 0.00 0.00 45.17 3.01
3123 3311 1.227853 ACGCAACAGAACCTGGGTC 60.228 57.895 2.72 2.72 33.89 4.46
3139 3327 3.764434 CTGGGTCTGTGATACTGTGTAGT 59.236 47.826 0.00 0.00 40.99 2.73
3153 3341 4.331717 ACTGTGTAGTTGTCTTCGTTTTGG 59.668 41.667 0.00 0.00 31.66 3.28
3155 3343 4.093703 TGTGTAGTTGTCTTCGTTTTGGTG 59.906 41.667 0.00 0.00 0.00 4.17
3177 3365 1.589803 AACGGTCACTTTGGTGCTAC 58.410 50.000 0.00 0.00 42.72 3.58
3184 3372 3.377172 GTCACTTTGGTGCTACAACTTGT 59.623 43.478 0.00 0.00 42.72 3.16
3253 3442 5.372343 TGATGCTAATCACACTTGGGTAT 57.628 39.130 0.00 0.00 37.91 2.73
3379 3581 6.723298 TTTTTATTTCTCACAGAAAGCCCA 57.277 33.333 5.05 0.00 46.15 5.36
3389 3591 1.539388 CAGAAAGCCCATAACAACGCA 59.461 47.619 0.00 0.00 0.00 5.24
3641 3924 4.211794 CACATTTTGCACCCACTGATTTTC 59.788 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 5.403466 GCAAATTAAGTTCAGGCTTTCAGTG 59.597 40.000 0.00 0.00 0.00 3.66
128 129 5.528043 TGCAAATTAAGTTCAGGCTTTCA 57.472 34.783 0.00 0.00 0.00 2.69
174 175 3.625764 AGAGCAAGCTTAAAACGTGAACA 59.374 39.130 0.00 0.00 0.00 3.18
176 177 4.334203 TGAAGAGCAAGCTTAAAACGTGAA 59.666 37.500 0.00 0.00 0.00 3.18
184 185 3.821033 GGGAAACTGAAGAGCAAGCTTAA 59.179 43.478 0.00 0.00 0.00 1.85
209 210 7.661536 TGCTCCAACTCACTATACTTATCTT 57.338 36.000 0.00 0.00 0.00 2.40
224 230 9.553064 CAAATTTATCTAGAGTATGCTCCAACT 57.447 33.333 7.25 0.00 42.59 3.16
225 231 9.331282 ACAAATTTATCTAGAGTATGCTCCAAC 57.669 33.333 7.25 0.00 42.59 3.77
234 240 7.065803 GCTGCAACCACAAATTTATCTAGAGTA 59.934 37.037 0.00 0.00 0.00 2.59
235 241 6.127897 GCTGCAACCACAAATTTATCTAGAGT 60.128 38.462 0.00 0.00 0.00 3.24
236 242 6.094603 AGCTGCAACCACAAATTTATCTAGAG 59.905 38.462 1.02 0.00 0.00 2.43
237 243 5.945784 AGCTGCAACCACAAATTTATCTAGA 59.054 36.000 1.02 0.00 0.00 2.43
238 244 6.032094 CAGCTGCAACCACAAATTTATCTAG 58.968 40.000 0.00 0.00 0.00 2.43
239 245 5.105797 CCAGCTGCAACCACAAATTTATCTA 60.106 40.000 8.66 0.00 0.00 1.98
240 246 4.322198 CCAGCTGCAACCACAAATTTATCT 60.322 41.667 8.66 0.00 0.00 1.98
241 247 3.928375 CCAGCTGCAACCACAAATTTATC 59.072 43.478 8.66 0.00 0.00 1.75
242 248 3.324556 ACCAGCTGCAACCACAAATTTAT 59.675 39.130 8.66 0.00 0.00 1.40
243 249 2.697751 ACCAGCTGCAACCACAAATTTA 59.302 40.909 8.66 0.00 0.00 1.40
244 250 1.485895 ACCAGCTGCAACCACAAATTT 59.514 42.857 8.66 0.00 0.00 1.82
245 251 1.122227 ACCAGCTGCAACCACAAATT 58.878 45.000 8.66 0.00 0.00 1.82
256 262 2.810852 GAGCATAATCCTAACCAGCTGC 59.189 50.000 8.66 0.00 0.00 5.25
259 265 4.314121 CAGAGAGCATAATCCTAACCAGC 58.686 47.826 0.00 0.00 0.00 4.85
289 295 5.520022 AAAACGTATATGAAACGCTTCGT 57.480 34.783 0.00 0.00 44.04 3.85
290 296 7.355354 GCAATAAAACGTATATGAAACGCTTCG 60.355 37.037 0.00 0.00 44.04 3.79
307 313 1.732405 GCCAGCTCACCGCAATAAAAC 60.732 52.381 0.00 0.00 42.61 2.43
318 381 3.556004 GGATAAGTATCTGGCCAGCTCAC 60.556 52.174 28.91 22.60 33.28 3.51
323 386 2.232452 CCTCGGATAAGTATCTGGCCAG 59.768 54.545 27.87 27.87 39.12 4.85
329 392 5.209659 ACTTTCACCCTCGGATAAGTATCT 58.790 41.667 0.00 0.00 33.28 1.98
334 397 5.080969 TGTTACTTTCACCCTCGGATAAG 57.919 43.478 0.00 0.00 0.00 1.73
344 407 5.116882 AGTTCTGTGTCTGTTACTTTCACC 58.883 41.667 0.00 0.00 0.00 4.02
359 422 2.033801 CACCAGCAAGGAAAGTTCTGTG 59.966 50.000 1.83 0.00 41.22 3.66
365 428 0.396974 TTGGCACCAGCAAGGAAAGT 60.397 50.000 1.83 0.00 44.61 2.66
409 472 1.661509 GCCGTGGCAACTTTTCTGC 60.662 57.895 5.89 0.00 41.49 4.26
411 474 2.551912 CCGCCGTGGCAACTTTTCT 61.552 57.895 12.06 0.00 42.06 2.52
457 520 2.632136 TTCGACGGGACTTTGCGTGT 62.632 55.000 0.00 0.00 0.00 4.49
487 550 4.547367 GGGAGGGGATCGCCAACG 62.547 72.222 28.74 0.00 37.03 4.10
500 563 4.504916 CTGCGCGACTCCAGGGAG 62.505 72.222 12.10 13.74 46.91 4.30
520 583 2.594303 CCCTGCGGTTGTGCTTGA 60.594 61.111 0.00 0.00 35.36 3.02
524 587 1.734388 AAGTTTCCCTGCGGTTGTGC 61.734 55.000 0.00 0.00 0.00 4.57
617 685 2.159462 GCTGTGGTCGTAGTGGTACTAC 60.159 54.545 0.19 0.19 45.71 2.73
786 855 2.186076 GAGATACTGCGGTCAAACGAG 58.814 52.381 0.00 0.00 35.47 4.18
798 867 1.735376 CGGGTCCCGGTGAGATACTG 61.735 65.000 23.59 0.00 44.15 2.74
857 926 3.705072 AGAGCACCGGGGCTTATATATAC 59.295 47.826 35.93 17.77 45.99 1.47
858 927 3.704566 CAGAGCACCGGGGCTTATATATA 59.295 47.826 35.93 0.00 45.99 0.86
859 928 2.501723 CAGAGCACCGGGGCTTATATAT 59.498 50.000 35.93 8.83 45.99 0.86
900 969 3.732849 GGGTGGGAGCCTTGGAGG 61.733 72.222 0.00 0.00 38.80 4.30
912 981 3.365535 CCTTTTTGGCTCGGGTGG 58.634 61.111 0.00 0.00 0.00 4.61
987 1081 1.647545 CGTCCATTGCTGCACCGATT 61.648 55.000 0.00 0.00 0.00 3.34
1135 1231 1.134367 GCCCCGGCTCTGTAAAAATTC 59.866 52.381 0.00 0.00 38.26 2.17
1183 1279 0.755079 TTGCTCTCTATCAGCGGCAT 59.245 50.000 1.45 0.00 40.01 4.40
1227 1323 4.351938 TCGAACCCGAGCACCACG 62.352 66.667 0.00 0.00 40.30 4.94
1453 1549 1.960689 GTTTGGGTGTGTGCTTACCAT 59.039 47.619 0.00 0.00 38.74 3.55
1476 1572 1.580942 CACGCCATGTCAAGGGTTG 59.419 57.895 0.00 0.00 0.00 3.77
1544 1658 1.000283 GCATCATACCCTGGAGAGACG 60.000 57.143 0.00 0.00 0.00 4.18
1719 1896 4.415332 TCGTCGAACTGCTCCGCC 62.415 66.667 0.00 0.00 0.00 6.13
2238 2421 1.227380 GATGCTCGTCGCCCAGATT 60.227 57.895 0.00 0.00 38.05 2.40
2927 3113 0.301687 TACGCCGACGAGTAACGATC 59.698 55.000 0.00 0.00 45.77 3.69
2928 3114 0.026803 GTACGCCGACGAGTAACGAT 59.973 55.000 0.00 0.00 45.77 3.73
2929 3115 1.288419 TGTACGCCGACGAGTAACGA 61.288 55.000 0.00 0.00 45.77 3.85
2931 3117 2.737467 TATGTACGCCGACGAGTAAC 57.263 50.000 0.00 0.00 43.93 2.50
3076 3263 6.459024 GCCGTAATTGCATCATACCAAACTAA 60.459 38.462 0.00 0.00 0.00 2.24
3114 3301 2.303022 CACAGTATCACAGACCCAGGTT 59.697 50.000 0.00 0.00 0.00 3.50
3116 3303 1.902508 ACACAGTATCACAGACCCAGG 59.097 52.381 0.00 0.00 0.00 4.45
3123 3311 5.569441 CGAAGACAACTACACAGTATCACAG 59.431 44.000 0.00 0.00 33.48 3.66
3184 3372 1.818060 GCACCAGTTCATTGTATGCCA 59.182 47.619 0.00 0.00 0.00 4.92
3253 3442 1.739466 GCCAAGTCAGCATCGATTTCA 59.261 47.619 0.00 0.00 0.00 2.69
3309 3505 2.494530 GGCCGCAGACCTCCTCTAG 61.495 68.421 0.00 0.00 0.00 2.43
3389 3591 2.300723 TCAAAATGAAATGGCAGCTGCT 59.699 40.909 35.82 18.48 41.70 4.24


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

AutoCloner maintained by Alex Coulton.