Multiple sequence alignment - TraesCS5D01G481700

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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 TraesCS5D01G481700 chr5D 100.000 2957 0 0 1 2957 519437137 519434181 0.000000e+00 5461
1 TraesCS5D01G481700 chr5D 80.571 175 15 7 2393 2555 519428522 519428355 1.860000e-22 117
2 TraesCS5D01G481700 chr5B 95.418 1484 45 13 1486 2957 653808998 653807526 0.000000e+00 2342
3 TraesCS5D01G481700 chr5B 89.447 1393 87 26 123 1503 653810403 653809059 0.000000e+00 1703
4 TraesCS5D01G481700 chr5A 94.378 1494 56 12 1486 2957 646010355 646008868 0.000000e+00 2268
5 TraesCS5D01G481700 chr5A 89.228 1114 41 35 453 1505 646011509 646010414 0.000000e+00 1319
6 TraesCS5D01G481700 chr5A 82.133 375 41 10 2335 2688 646006628 646006259 6.200000e-77 298
7 TraesCS5D01G481700 chr5A 75.000 588 80 38 2377 2938 646007960 646007414 2.990000e-50 209
8 TraesCS5D01G481700 chr7A 89.369 602 53 7 2343 2940 649714633 649714039 0.000000e+00 747
9 TraesCS5D01G481700 chr7A 90.538 465 35 5 2343 2804 280005871 280006329 9.060000e-170 606
10 TraesCS5D01G481700 chr2B 89.920 377 30 5 2343 2716 33677135 33677506 2.060000e-131 479
11 TraesCS5D01G481700 chr2B 84.768 151 17 3 2716 2863 33677542 33677689 2.370000e-31 147
12 TraesCS5D01G481700 chr7D 84.051 395 60 2 1 394 509561216 509561608 7.740000e-101 377
13 TraesCS5D01G481700 chr4D 82.716 405 70 0 2 406 13309286 13309690 7.790000e-96 361
14 TraesCS5D01G481700 chr4D 81.373 408 72 4 1 408 479414575 479414172 2.200000e-86 329
15 TraesCS5D01G481700 chr3D 83.038 395 66 1 14 408 156729780 156729387 1.010000e-94 357
16 TraesCS5D01G481700 chr2D 82.716 405 66 2 4 408 616500427 616500027 1.010000e-94 357
17 TraesCS5D01G481700 chr1A 82.555 407 67 4 1 406 449845579 449845982 3.620000e-94 355
18 TraesCS5D01G481700 chr6D 81.373 408 76 0 1 408 337846850 337847257 1.700000e-87 333
19 TraesCS5D01G481700 chr6D 80.929 409 76 2 1 408 2900436 2900029 3.680000e-84 322
20 TraesCS5D01G481700 chr6D 89.222 167 12 2 2442 2605 67702436 67702273 1.390000e-48 204
21 TraesCS5D01G481700 chr1D 81.127 408 74 2 3 408 347407934 347408340 1.020000e-84 324


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 TraesCS5D01G481700 chr5D 519434181 519437137 2956 True 5461.0 5461 100.00000 1 2957 1 chr5D.!!$R2 2956
1 TraesCS5D01G481700 chr5B 653807526 653810403 2877 True 2022.5 2342 92.43250 123 2957 2 chr5B.!!$R1 2834
2 TraesCS5D01G481700 chr5A 646006259 646011509 5250 True 1023.5 2268 85.18475 453 2957 4 chr5A.!!$R1 2504
3 TraesCS5D01G481700 chr7A 649714039 649714633 594 True 747.0 747 89.36900 2343 2940 1 chr7A.!!$R1 597
4 TraesCS5D01G481700 chr2B 33677135 33677689 554 False 313.0 479 87.34400 2343 2863 2 chr2B.!!$F1 520

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
200 201 0.037605 AGGGTTCAACGACGATGACC 60.038 55.000 7.37 11.60 0.00 4.02 F
201 202 0.320073 GGGTTCAACGACGATGACCA 60.320 55.000 20.00 3.18 0.00 4.02 F
247 248 0.650512 ACACGTGCACGAAGACTTTG 59.349 50.000 42.94 29.67 43.02 2.77 F
307 308 1.011242 CAACAACAGTGGCACGTCG 60.011 57.895 12.71 7.58 0.00 5.12 F
1474 1568 1.075659 ACAGGCTGCTTCCCTTTCC 59.924 57.895 15.89 0.00 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1555 0.323816 GGAAGGGGAAAGGGAAGCAG 60.324 60.000 0.0 0.0 0.00 4.24 R
1463 1557 1.000486 GGGAAGGGGAAAGGGAAGC 60.000 63.158 0.0 0.0 0.00 3.86 R
1464 1558 1.303282 CGGGAAGGGGAAAGGGAAG 59.697 63.158 0.0 0.0 0.00 3.46 R
1784 1959 2.044555 CCATCTGCACAGCCCACAG 61.045 63.158 0.0 0.0 0.00 3.66 R
2704 2905 0.592247 GAAAAGGCTGTGTGCGTGTG 60.592 55.000 0.0 0.0 44.05 3.82 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 4.835927 CGGATGGCTACGCTTCTT 57.164 55.556 0.00 0.00 0.00 2.52
21 22 2.594541 CGGATGGCTACGCTTCTTC 58.405 57.895 0.00 0.00 0.00 2.87
22 23 0.179111 CGGATGGCTACGCTTCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
23 24 1.539065 CGGATGGCTACGCTTCTTCAT 60.539 52.381 0.00 0.00 0.00 2.57
24 25 2.139118 GGATGGCTACGCTTCTTCATC 58.861 52.381 0.00 0.00 0.00 2.92
25 26 1.789464 GATGGCTACGCTTCTTCATCG 59.211 52.381 0.00 0.00 0.00 3.84
26 27 0.815095 TGGCTACGCTTCTTCATCGA 59.185 50.000 0.00 0.00 0.00 3.59
27 28 1.202302 TGGCTACGCTTCTTCATCGAG 60.202 52.381 0.00 0.00 0.00 4.04
28 29 1.202313 GGCTACGCTTCTTCATCGAGT 60.202 52.381 0.00 0.00 0.00 4.18
29 30 2.531206 GCTACGCTTCTTCATCGAGTT 58.469 47.619 0.00 0.00 0.00 3.01
30 31 2.924290 GCTACGCTTCTTCATCGAGTTT 59.076 45.455 0.00 0.00 0.00 2.66
31 32 3.241804 GCTACGCTTCTTCATCGAGTTTG 60.242 47.826 0.00 0.00 0.00 2.93
32 33 2.755650 ACGCTTCTTCATCGAGTTTGT 58.244 42.857 0.00 0.00 0.00 2.83
33 34 2.731976 ACGCTTCTTCATCGAGTTTGTC 59.268 45.455 0.00 0.00 0.00 3.18
34 35 2.989840 CGCTTCTTCATCGAGTTTGTCT 59.010 45.455 0.00 0.00 0.00 3.41
35 36 3.430218 CGCTTCTTCATCGAGTTTGTCTT 59.570 43.478 0.00 0.00 0.00 3.01
36 37 4.433544 CGCTTCTTCATCGAGTTTGTCTTC 60.434 45.833 0.00 0.00 0.00 2.87
37 38 4.143009 GCTTCTTCATCGAGTTTGTCTTCC 60.143 45.833 0.00 0.00 0.00 3.46
38 39 3.575630 TCTTCATCGAGTTTGTCTTCCG 58.424 45.455 0.00 0.00 0.00 4.30
39 40 2.363788 TCATCGAGTTTGTCTTCCGG 57.636 50.000 0.00 0.00 0.00 5.14
40 41 1.890489 TCATCGAGTTTGTCTTCCGGA 59.110 47.619 0.00 0.00 0.00 5.14
41 42 1.993370 CATCGAGTTTGTCTTCCGGAC 59.007 52.381 1.83 0.00 44.70 4.79
42 43 1.325355 TCGAGTTTGTCTTCCGGACT 58.675 50.000 1.83 0.00 44.74 3.85
43 44 1.268899 TCGAGTTTGTCTTCCGGACTC 59.731 52.381 1.83 5.27 44.74 3.36
44 45 1.669211 CGAGTTTGTCTTCCGGACTCC 60.669 57.143 1.83 0.00 44.74 3.85
55 56 3.752704 GGACTCCGATCCTCCTCG 58.247 66.667 0.00 0.00 35.68 4.63
56 57 1.148723 GGACTCCGATCCTCCTCGA 59.851 63.158 0.00 0.00 41.12 4.04
57 58 0.887387 GGACTCCGATCCTCCTCGAG 60.887 65.000 5.13 5.13 41.12 4.04
58 59 0.179040 GACTCCGATCCTCCTCGAGT 60.179 60.000 12.31 0.00 41.12 4.18
59 60 0.256464 ACTCCGATCCTCCTCGAGTT 59.744 55.000 12.31 0.00 41.12 3.01
60 61 0.948678 CTCCGATCCTCCTCGAGTTC 59.051 60.000 12.31 0.00 41.12 3.01
61 62 0.255033 TCCGATCCTCCTCGAGTTCA 59.745 55.000 12.31 0.00 41.12 3.18
62 63 1.133761 TCCGATCCTCCTCGAGTTCAT 60.134 52.381 12.31 0.00 41.12 2.57
63 64 1.683917 CCGATCCTCCTCGAGTTCATT 59.316 52.381 12.31 0.00 41.12 2.57
64 65 2.287909 CCGATCCTCCTCGAGTTCATTC 60.288 54.545 12.31 2.04 41.12 2.67
65 66 2.359214 CGATCCTCCTCGAGTTCATTCA 59.641 50.000 12.31 0.00 41.12 2.57
66 67 3.005261 CGATCCTCCTCGAGTTCATTCAT 59.995 47.826 12.31 0.00 41.12 2.57
67 68 4.555262 GATCCTCCTCGAGTTCATTCATC 58.445 47.826 12.31 0.02 0.00 2.92
68 69 3.636679 TCCTCCTCGAGTTCATTCATCT 58.363 45.455 12.31 0.00 0.00 2.90
69 70 3.382865 TCCTCCTCGAGTTCATTCATCTG 59.617 47.826 12.31 0.00 0.00 2.90
70 71 3.492309 CCTCCTCGAGTTCATTCATCTGG 60.492 52.174 12.31 0.00 0.00 3.86
71 72 3.365472 TCCTCGAGTTCATTCATCTGGA 58.635 45.455 12.31 0.00 0.00 3.86
72 73 3.131223 TCCTCGAGTTCATTCATCTGGAC 59.869 47.826 12.31 0.00 0.00 4.02
73 74 3.111838 CTCGAGTTCATTCATCTGGACG 58.888 50.000 3.62 0.00 29.38 4.79
74 75 2.492088 TCGAGTTCATTCATCTGGACGT 59.508 45.455 0.00 0.00 29.38 4.34
75 76 3.692593 TCGAGTTCATTCATCTGGACGTA 59.307 43.478 0.00 0.00 29.38 3.57
76 77 4.038361 CGAGTTCATTCATCTGGACGTAG 58.962 47.826 0.00 0.00 29.38 3.51
89 90 2.183555 CGTAGTCGTTGGAGCCCC 59.816 66.667 0.00 0.00 0.00 5.80
90 91 2.183555 GTAGTCGTTGGAGCCCCG 59.816 66.667 0.00 0.00 34.29 5.73
91 92 3.072468 TAGTCGTTGGAGCCCCGG 61.072 66.667 0.00 0.00 34.29 5.73
114 115 3.680642 CAGATTCCTGCCGTATGTTTG 57.319 47.619 0.00 0.00 33.07 2.93
115 116 2.355756 CAGATTCCTGCCGTATGTTTGG 59.644 50.000 0.00 0.00 33.07 3.28
116 117 1.676006 GATTCCTGCCGTATGTTTGGG 59.324 52.381 0.00 0.00 0.00 4.12
117 118 0.693622 TTCCTGCCGTATGTTTGGGA 59.306 50.000 0.00 0.00 0.00 4.37
118 119 0.916086 TCCTGCCGTATGTTTGGGAT 59.084 50.000 0.00 0.00 0.00 3.85
119 120 1.024271 CCTGCCGTATGTTTGGGATG 58.976 55.000 0.00 0.00 0.00 3.51
120 121 1.024271 CTGCCGTATGTTTGGGATGG 58.976 55.000 0.00 0.00 0.00 3.51
121 122 1.034838 TGCCGTATGTTTGGGATGGC 61.035 55.000 0.00 0.00 44.19 4.40
137 138 0.611714 TGGCGAGGTTAGGGTTTCTC 59.388 55.000 0.00 0.00 0.00 2.87
146 147 3.000727 GTTAGGGTTTCTCGTCATGTGG 58.999 50.000 0.00 0.00 0.00 4.17
148 149 1.305930 GGGTTTCTCGTCATGTGGCC 61.306 60.000 0.00 0.00 0.00 5.36
159 160 0.108520 CATGTGGCCAGATTTGGTGC 60.109 55.000 13.78 0.00 46.80 5.01
160 161 1.259840 ATGTGGCCAGATTTGGTGCC 61.260 55.000 10.16 0.38 46.80 5.01
166 167 0.540365 CCAGATTTGGTGCCAGGTGT 60.540 55.000 0.00 0.00 39.79 4.16
171 172 1.110442 TTTGGTGCCAGGTGTTTCAG 58.890 50.000 0.00 0.00 0.00 3.02
174 175 1.168714 GGTGCCAGGTGTTTCAGATC 58.831 55.000 0.00 0.00 0.00 2.75
177 178 3.370953 GGTGCCAGGTGTTTCAGATCTAT 60.371 47.826 0.00 0.00 0.00 1.98
190 191 7.174946 TGTTTCAGATCTATTCAAGGGTTCAAC 59.825 37.037 0.00 0.00 0.00 3.18
200 201 0.037605 AGGGTTCAACGACGATGACC 60.038 55.000 7.37 11.60 0.00 4.02
201 202 0.320073 GGGTTCAACGACGATGACCA 60.320 55.000 20.00 3.18 0.00 4.02
211 212 2.187946 GATGACCACGGCTCCAGG 59.812 66.667 0.00 0.00 0.00 4.45
212 213 2.284625 ATGACCACGGCTCCAGGA 60.285 61.111 0.00 0.00 0.00 3.86
246 247 0.928229 GACACGTGCACGAAGACTTT 59.072 50.000 42.94 18.38 43.02 2.66
247 248 0.650512 ACACGTGCACGAAGACTTTG 59.349 50.000 42.94 29.67 43.02 2.77
275 276 3.423154 CGACAAGGTCAAGCCGGC 61.423 66.667 21.89 21.89 43.70 6.13
297 298 1.903404 GGTGGGGGAGCAACAACAG 60.903 63.158 0.00 0.00 0.00 3.16
298 299 1.152756 GTGGGGGAGCAACAACAGT 60.153 57.895 0.00 0.00 0.00 3.55
300 301 1.903404 GGGGGAGCAACAACAGTGG 60.903 63.158 0.00 0.00 0.00 4.00
302 303 1.827789 GGGAGCAACAACAGTGGCA 60.828 57.895 0.00 0.00 34.53 4.92
305 306 1.714899 GAGCAACAACAGTGGCACGT 61.715 55.000 12.71 10.50 34.53 4.49
306 307 1.298339 GCAACAACAGTGGCACGTC 60.298 57.895 12.71 0.00 32.29 4.34
307 308 1.011242 CAACAACAGTGGCACGTCG 60.011 57.895 12.71 7.58 0.00 5.12
308 309 2.177580 AACAACAGTGGCACGTCGG 61.178 57.895 12.71 11.16 0.00 4.79
309 310 2.587753 CAACAGTGGCACGTCGGT 60.588 61.111 12.71 6.72 0.00 4.69
311 312 4.602259 ACAGTGGCACGTCGGTGG 62.602 66.667 12.71 0.00 44.54 4.61
318 319 2.256158 CACGTCGGTGGCTCGTTA 59.744 61.111 0.00 0.00 40.58 3.18
320 321 1.153901 ACGTCGGTGGCTCGTTATG 60.154 57.895 0.00 0.00 34.07 1.90
321 322 1.876714 CGTCGGTGGCTCGTTATGG 60.877 63.158 1.40 0.00 0.00 2.74
330 331 1.361793 GCTCGTTATGGCGGTTGTAA 58.638 50.000 0.00 0.00 0.00 2.41
334 335 1.268335 CGTTATGGCGGTTGTAATGGC 60.268 52.381 0.00 0.00 0.00 4.40
340 341 1.798087 CGGTTGTAATGGCCGTTCC 59.202 57.895 15.07 8.32 40.53 3.62
345 346 1.376295 GTAATGGCCGTTCCGTGGT 60.376 57.895 15.07 0.00 37.80 4.16
349 350 3.998672 GGCCGTTCCGTGGTCTCA 61.999 66.667 0.00 0.00 0.00 3.27
354 355 2.470821 CCGTTCCGTGGTCTCATAATC 58.529 52.381 0.00 0.00 0.00 1.75
364 365 6.382608 CGTGGTCTCATAATCTCGATGTAAT 58.617 40.000 0.00 0.00 0.00 1.89
394 395 6.559810 TGATGTTTCAGGTGTTTTGTACTTG 58.440 36.000 0.00 0.00 0.00 3.16
396 397 3.684103 TTCAGGTGTTTTGTACTTGCG 57.316 42.857 0.00 0.00 0.00 4.85
398 399 1.673920 CAGGTGTTTTGTACTTGCGGT 59.326 47.619 0.00 0.00 0.00 5.68
399 400 1.673920 AGGTGTTTTGTACTTGCGGTG 59.326 47.619 0.00 0.00 0.00 4.94
402 403 3.243267 GGTGTTTTGTACTTGCGGTGAAT 60.243 43.478 0.00 0.00 0.00 2.57
408 409 4.217754 TGTACTTGCGGTGAATTTTGAC 57.782 40.909 0.00 0.00 0.00 3.18
409 410 2.399396 ACTTGCGGTGAATTTTGACG 57.601 45.000 0.00 0.00 0.00 4.35
415 426 3.190327 TGCGGTGAATTTTGACGATCATT 59.810 39.130 0.00 0.00 0.00 2.57
419 430 6.515882 CGGTGAATTTTGACGATCATTTTTG 58.484 36.000 0.00 0.00 0.00 2.44
422 433 8.547069 GGTGAATTTTGACGATCATTTTTGAAA 58.453 29.630 0.00 0.00 0.00 2.69
487 498 1.996291 TGGTCCACATGGTTTATCCCA 59.004 47.619 0.00 0.00 39.27 4.37
488 499 2.380249 TGGTCCACATGGTTTATCCCAA 59.620 45.455 0.00 0.00 38.20 4.12
489 500 3.012274 TGGTCCACATGGTTTATCCCAAT 59.988 43.478 0.00 0.00 38.20 3.16
490 501 4.230733 TGGTCCACATGGTTTATCCCAATA 59.769 41.667 0.00 0.00 38.20 1.90
491 502 5.103301 TGGTCCACATGGTTTATCCCAATAT 60.103 40.000 0.00 0.00 38.20 1.28
521 543 5.048013 CCATTTGAAAACCTCTAAGTGGTCC 60.048 44.000 0.00 0.00 36.69 4.46
567 607 3.126858 CGAATTTGAATTTCGCCTCTCCA 59.873 43.478 8.92 0.00 0.00 3.86
568 608 4.379394 CGAATTTGAATTTCGCCTCTCCAA 60.379 41.667 8.92 0.00 0.00 3.53
631 678 4.811761 GTTTGATCCGTGCCGCGC 62.812 66.667 0.00 0.00 39.71 6.86
659 706 2.286732 AGCCAGGCCCAGGAGAAT 60.287 61.111 15.78 0.00 0.00 2.40
720 776 1.524008 CGTGCTCCCCACCCTTTTTC 61.524 60.000 0.00 0.00 41.53 2.29
721 777 1.155155 TGCTCCCCACCCTTTTTCC 59.845 57.895 0.00 0.00 0.00 3.13
1474 1568 1.075659 ACAGGCTGCTTCCCTTTCC 59.924 57.895 15.89 0.00 0.00 3.13
1685 1860 1.127343 GATGTCAAGGAGGAGGAGGG 58.873 60.000 0.00 0.00 0.00 4.30
1784 1959 2.671682 GGAGGTCAAGGTGGAGGC 59.328 66.667 0.00 0.00 0.00 4.70
2145 2326 8.499288 TGTATATACACCCTTCAATATGGTCA 57.501 34.615 11.62 0.00 0.00 4.02
2169 2350 0.320683 TCGATGCCAAGGATATGCCG 60.321 55.000 0.00 0.00 43.43 5.69
2318 2499 7.508296 ACTCCTGAAGTGGTAGTAGTTAAGAAA 59.492 37.037 0.00 0.00 36.65 2.52
2452 2634 5.313712 TGTCCAGGTTCAGTTATTTTCCTC 58.686 41.667 0.00 0.00 0.00 3.71
2479 2666 5.171339 AGCTCTGTTTTATGTCATGTCCT 57.829 39.130 0.00 0.00 0.00 3.85
2480 2667 4.940046 AGCTCTGTTTTATGTCATGTCCTG 59.060 41.667 0.00 0.00 0.00 3.86
2481 2668 4.095483 GCTCTGTTTTATGTCATGTCCTGG 59.905 45.833 0.00 0.00 0.00 4.45
2596 2790 4.628333 AGAATTTGGCAATTTGCTTCATCG 59.372 37.500 20.06 0.00 44.28 3.84
2675 2869 4.898829 TTGTGGTTTGAGTTCAGATGTG 57.101 40.909 0.00 0.00 0.00 3.21
2684 2878 6.395426 TTGAGTTCAGATGTGCTCATTTTT 57.605 33.333 2.26 0.00 37.74 1.94
2685 2879 7.509141 TTGAGTTCAGATGTGCTCATTTTTA 57.491 32.000 2.26 0.00 37.74 1.52
2697 2898 7.532571 TGTGCTCATTTTTATCTTCACATCTG 58.467 34.615 0.00 0.00 0.00 2.90
2709 2913 3.942539 TCACATCTGAAAACACACACG 57.057 42.857 0.00 0.00 0.00 4.49
2863 3111 2.224499 TGCTATGTGCTTGTCTCACCAA 60.224 45.455 0.00 0.00 43.37 3.67
2905 3156 1.203441 ATCAGTCTGAGGGGCTGCAA 61.203 55.000 8.82 0.00 0.00 4.08
2917 3168 2.743664 GGGGCTGCAAAATTTCATCAAC 59.256 45.455 0.50 0.00 0.00 3.18
2920 3171 4.309099 GGCTGCAAAATTTCATCAACTGA 58.691 39.130 0.50 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.921021 ACAAACTCGATGAAGAAGCGTAG 59.079 43.478 0.00 0.00 0.00 3.51
11 12 3.909430 ACAAACTCGATGAAGAAGCGTA 58.091 40.909 0.00 0.00 0.00 4.42
12 13 2.731976 GACAAACTCGATGAAGAAGCGT 59.268 45.455 0.00 0.00 0.00 5.07
13 14 2.989840 AGACAAACTCGATGAAGAAGCG 59.010 45.455 0.00 0.00 0.00 4.68
14 15 4.143009 GGAAGACAAACTCGATGAAGAAGC 60.143 45.833 0.00 0.00 0.00 3.86
15 16 4.090642 CGGAAGACAAACTCGATGAAGAAG 59.909 45.833 0.00 0.00 0.00 2.85
16 17 3.987868 CGGAAGACAAACTCGATGAAGAA 59.012 43.478 0.00 0.00 0.00 2.52
17 18 3.575630 CGGAAGACAAACTCGATGAAGA 58.424 45.455 0.00 0.00 0.00 2.87
18 19 2.668457 CCGGAAGACAAACTCGATGAAG 59.332 50.000 0.00 0.00 0.00 3.02
19 20 2.297880 TCCGGAAGACAAACTCGATGAA 59.702 45.455 0.00 0.00 0.00 2.57
20 21 1.890489 TCCGGAAGACAAACTCGATGA 59.110 47.619 0.00 0.00 0.00 2.92
21 22 1.993370 GTCCGGAAGACAAACTCGATG 59.007 52.381 5.23 0.00 45.55 3.84
22 23 2.365408 GTCCGGAAGACAAACTCGAT 57.635 50.000 5.23 0.00 45.55 3.59
23 24 3.879912 GTCCGGAAGACAAACTCGA 57.120 52.632 5.23 0.00 45.55 4.04
38 39 0.887387 CTCGAGGAGGATCGGAGTCC 60.887 65.000 3.91 0.00 42.93 3.85
39 40 0.179040 ACTCGAGGAGGATCGGAGTC 60.179 60.000 18.41 0.00 42.93 3.36
40 41 0.256464 AACTCGAGGAGGATCGGAGT 59.744 55.000 18.41 0.00 42.93 3.85
41 42 0.948678 GAACTCGAGGAGGATCGGAG 59.051 60.000 18.41 0.00 42.93 4.63
42 43 0.255033 TGAACTCGAGGAGGATCGGA 59.745 55.000 18.41 0.00 42.93 4.55
43 44 1.323412 ATGAACTCGAGGAGGATCGG 58.677 55.000 18.41 0.00 42.93 4.18
44 45 2.359214 TGAATGAACTCGAGGAGGATCG 59.641 50.000 18.41 0.00 44.07 3.69
45 46 4.280677 AGATGAATGAACTCGAGGAGGATC 59.719 45.833 18.41 9.80 33.35 3.36
46 47 4.039004 CAGATGAATGAACTCGAGGAGGAT 59.961 45.833 18.41 0.00 33.35 3.24
47 48 3.382865 CAGATGAATGAACTCGAGGAGGA 59.617 47.826 18.41 0.00 33.35 3.71
48 49 3.492309 CCAGATGAATGAACTCGAGGAGG 60.492 52.174 18.41 0.00 33.35 4.30
49 50 3.382865 TCCAGATGAATGAACTCGAGGAG 59.617 47.826 18.41 0.00 35.52 3.69
50 51 3.131223 GTCCAGATGAATGAACTCGAGGA 59.869 47.826 18.41 0.00 0.00 3.71
51 52 3.452474 GTCCAGATGAATGAACTCGAGG 58.548 50.000 18.41 0.00 0.00 4.63
52 53 3.111838 CGTCCAGATGAATGAACTCGAG 58.888 50.000 11.84 11.84 0.00 4.04
53 54 2.492088 ACGTCCAGATGAATGAACTCGA 59.508 45.455 0.00 0.00 0.00 4.04
54 55 2.881074 ACGTCCAGATGAATGAACTCG 58.119 47.619 0.00 0.00 0.00 4.18
55 56 5.000012 ACTACGTCCAGATGAATGAACTC 58.000 43.478 0.00 0.00 0.00 3.01
56 57 4.438880 CGACTACGTCCAGATGAATGAACT 60.439 45.833 0.00 0.00 34.56 3.01
57 58 3.791887 CGACTACGTCCAGATGAATGAAC 59.208 47.826 0.00 0.00 34.56 3.18
58 59 4.028852 CGACTACGTCCAGATGAATGAA 57.971 45.455 0.00 0.00 34.56 2.57
59 60 3.692791 CGACTACGTCCAGATGAATGA 57.307 47.619 0.00 0.00 34.56 2.57
72 73 2.183555 GGGGCTCCAACGACTACG 59.816 66.667 0.00 0.00 45.75 3.51
73 74 2.183555 CGGGGCTCCAACGACTAC 59.816 66.667 1.96 0.00 0.00 2.73
74 75 3.072468 CCGGGGCTCCAACGACTA 61.072 66.667 1.96 0.00 0.00 2.59
94 95 2.355756 CCAAACATACGGCAGGAATCTG 59.644 50.000 0.00 0.00 43.64 2.90
95 96 2.643551 CCAAACATACGGCAGGAATCT 58.356 47.619 0.00 0.00 0.00 2.40
96 97 1.676006 CCCAAACATACGGCAGGAATC 59.324 52.381 0.00 0.00 0.00 2.52
97 98 1.283613 TCCCAAACATACGGCAGGAAT 59.716 47.619 0.00 0.00 0.00 3.01
98 99 0.693622 TCCCAAACATACGGCAGGAA 59.306 50.000 0.00 0.00 0.00 3.36
99 100 0.916086 ATCCCAAACATACGGCAGGA 59.084 50.000 0.00 0.00 0.00 3.86
100 101 1.024271 CATCCCAAACATACGGCAGG 58.976 55.000 0.00 0.00 0.00 4.85
101 102 1.024271 CCATCCCAAACATACGGCAG 58.976 55.000 0.00 0.00 0.00 4.85
102 103 1.034838 GCCATCCCAAACATACGGCA 61.035 55.000 0.00 0.00 37.98 5.69
103 104 1.733526 GCCATCCCAAACATACGGC 59.266 57.895 0.00 0.00 0.00 5.68
104 105 0.462937 TCGCCATCCCAAACATACGG 60.463 55.000 0.00 0.00 0.00 4.02
105 106 0.937304 CTCGCCATCCCAAACATACG 59.063 55.000 0.00 0.00 0.00 3.06
106 107 1.308998 CCTCGCCATCCCAAACATAC 58.691 55.000 0.00 0.00 0.00 2.39
107 108 0.916086 ACCTCGCCATCCCAAACATA 59.084 50.000 0.00 0.00 0.00 2.29
108 109 0.039618 AACCTCGCCATCCCAAACAT 59.960 50.000 0.00 0.00 0.00 2.71
109 110 0.693622 TAACCTCGCCATCCCAAACA 59.306 50.000 0.00 0.00 0.00 2.83
110 111 1.379527 CTAACCTCGCCATCCCAAAC 58.620 55.000 0.00 0.00 0.00 2.93
111 112 0.254747 CCTAACCTCGCCATCCCAAA 59.745 55.000 0.00 0.00 0.00 3.28
112 113 1.632018 CCCTAACCTCGCCATCCCAA 61.632 60.000 0.00 0.00 0.00 4.12
113 114 2.070039 CCCTAACCTCGCCATCCCA 61.070 63.158 0.00 0.00 0.00 4.37
114 115 1.632965 AACCCTAACCTCGCCATCCC 61.633 60.000 0.00 0.00 0.00 3.85
115 116 0.255033 AAACCCTAACCTCGCCATCC 59.745 55.000 0.00 0.00 0.00 3.51
116 117 1.209747 AGAAACCCTAACCTCGCCATC 59.790 52.381 0.00 0.00 0.00 3.51
117 118 1.209747 GAGAAACCCTAACCTCGCCAT 59.790 52.381 0.00 0.00 0.00 4.40
118 119 0.611714 GAGAAACCCTAACCTCGCCA 59.388 55.000 0.00 0.00 0.00 5.69
119 120 0.459759 CGAGAAACCCTAACCTCGCC 60.460 60.000 0.00 0.00 41.31 5.54
120 121 3.046280 CGAGAAACCCTAACCTCGC 57.954 57.895 0.00 0.00 41.31 5.03
137 138 0.452987 CCAAATCTGGCCACATGACG 59.547 55.000 0.00 0.00 35.39 4.35
148 149 1.331214 AACACCTGGCACCAAATCTG 58.669 50.000 0.00 0.00 0.00 2.90
159 160 5.587844 CCTTGAATAGATCTGAAACACCTGG 59.412 44.000 5.18 0.00 0.00 4.45
160 161 5.587844 CCCTTGAATAGATCTGAAACACCTG 59.412 44.000 5.18 0.00 0.00 4.00
166 167 6.371548 CGTTGAACCCTTGAATAGATCTGAAA 59.628 38.462 5.18 0.00 0.00 2.69
171 172 4.267928 CGTCGTTGAACCCTTGAATAGATC 59.732 45.833 0.00 0.00 0.00 2.75
174 175 3.581755 TCGTCGTTGAACCCTTGAATAG 58.418 45.455 0.00 0.00 0.00 1.73
177 178 2.139917 CATCGTCGTTGAACCCTTGAA 58.860 47.619 0.00 0.00 0.00 2.69
190 191 2.579787 GAGCCGTGGTCATCGTCG 60.580 66.667 0.00 0.00 0.00 5.12
211 212 3.950232 TCCCTATGGACCAGCGTC 58.050 61.111 0.00 0.00 35.03 5.19
222 223 0.108804 CTTCGTGCACGTGTCCCTAT 60.109 55.000 35.74 0.00 40.80 2.57
223 224 1.174078 TCTTCGTGCACGTGTCCCTA 61.174 55.000 35.74 14.71 40.80 3.53
246 247 0.320683 CCTTGTCGATGACAGCCACA 60.321 55.000 0.00 0.00 43.69 4.17
247 248 0.320771 ACCTTGTCGATGACAGCCAC 60.321 55.000 0.00 0.00 43.69 5.01
282 283 1.903404 CCACTGTTGTTGCTCCCCC 60.903 63.158 0.00 0.00 0.00 5.40
290 291 2.177580 CCGACGTGCCACTGTTGTT 61.178 57.895 0.00 0.00 0.00 2.83
291 292 2.587753 CCGACGTGCCACTGTTGT 60.588 61.111 0.00 0.00 0.00 3.32
300 301 3.902162 TAACGAGCCACCGACGTGC 62.902 63.158 0.00 0.00 40.10 5.34
302 303 1.153901 CATAACGAGCCACCGACGT 60.154 57.895 0.00 0.00 41.97 4.34
305 306 2.185867 GCCATAACGAGCCACCGA 59.814 61.111 0.00 0.00 0.00 4.69
306 307 3.261951 CGCCATAACGAGCCACCG 61.262 66.667 0.00 0.00 34.06 4.94
307 308 2.895372 CCGCCATAACGAGCCACC 60.895 66.667 0.00 0.00 34.06 4.61
308 309 1.743995 AACCGCCATAACGAGCCAC 60.744 57.895 0.00 0.00 34.06 5.01
309 310 1.743623 CAACCGCCATAACGAGCCA 60.744 57.895 0.00 0.00 34.06 4.75
310 311 0.460635 TACAACCGCCATAACGAGCC 60.461 55.000 0.00 0.00 34.06 4.70
311 312 1.361793 TTACAACCGCCATAACGAGC 58.638 50.000 0.00 0.00 34.06 5.03
312 313 2.286833 CCATTACAACCGCCATAACGAG 59.713 50.000 0.00 0.00 34.06 4.18
318 319 2.118404 CGGCCATTACAACCGCCAT 61.118 57.895 2.24 0.00 41.71 4.40
340 341 4.230314 ACATCGAGATTATGAGACCACG 57.770 45.455 0.00 0.00 0.00 4.94
370 371 6.559810 CAAGTACAAAACACCTGAAACATCA 58.440 36.000 0.00 0.00 0.00 3.07
371 372 5.458779 GCAAGTACAAAACACCTGAAACATC 59.541 40.000 0.00 0.00 0.00 3.06
378 379 1.673920 ACCGCAAGTACAAAACACCTG 59.326 47.619 0.00 0.00 0.00 4.00
384 385 5.517054 GTCAAAATTCACCGCAAGTACAAAA 59.483 36.000 0.00 0.00 0.00 2.44
386 387 4.602995 GTCAAAATTCACCGCAAGTACAA 58.397 39.130 0.00 0.00 0.00 2.41
394 395 2.892373 TGATCGTCAAAATTCACCGC 57.108 45.000 0.00 0.00 0.00 5.68
396 397 7.636259 TCAAAAATGATCGTCAAAATTCACC 57.364 32.000 0.00 0.00 0.00 4.02
398 399 9.526713 TCTTTCAAAAATGATCGTCAAAATTCA 57.473 25.926 0.00 0.00 0.00 2.57
438 449 8.779354 CTAGAAGCATCTAGTAACCAGTTTTT 57.221 34.615 16.21 0.00 46.77 1.94
512 534 3.958798 CGGAGGATAAGAAGGACCACTTA 59.041 47.826 11.66 11.66 40.21 2.24
567 607 4.584743 ACTTGGCTCGGAAGAAAGAAATTT 59.415 37.500 0.00 0.00 41.32 1.82
568 608 4.145052 ACTTGGCTCGGAAGAAAGAAATT 58.855 39.130 0.00 0.00 41.32 1.82
631 678 3.610669 CCTGGCTCGGGAGGATCG 61.611 72.222 0.00 0.00 34.37 3.69
632 679 3.934962 GCCTGGCTCGGGAGGATC 61.935 72.222 12.43 0.00 29.82 3.36
720 776 3.716204 GAGGCGGGGGCTAAAAGGG 62.716 68.421 0.00 0.00 38.98 3.95
721 777 2.124278 GAGGCGGGGGCTAAAAGG 60.124 66.667 0.00 0.00 38.98 3.11
825 881 1.356738 GGCTAGGGTTAGGGTTTGGTT 59.643 52.381 0.00 0.00 0.00 3.67
1451 1545 2.674380 GGAAGCAGCCTGTGGTGG 60.674 66.667 0.00 0.00 40.37 4.61
1452 1546 2.674380 GGGAAGCAGCCTGTGGTG 60.674 66.667 0.00 0.00 42.91 4.17
1453 1547 2.011617 AAAGGGAAGCAGCCTGTGGT 62.012 55.000 0.00 0.00 39.08 4.16
1454 1548 1.228675 AAAGGGAAGCAGCCTGTGG 60.229 57.895 0.00 0.00 0.00 4.17
1455 1549 1.246737 GGAAAGGGAAGCAGCCTGTG 61.247 60.000 0.00 0.00 0.00 3.66
1456 1550 1.075659 GGAAAGGGAAGCAGCCTGT 59.924 57.895 0.00 0.00 0.00 4.00
1457 1551 1.680314 GGGAAAGGGAAGCAGCCTG 60.680 63.158 0.00 0.00 0.00 4.85
1458 1552 2.766660 GGGAAAGGGAAGCAGCCT 59.233 61.111 0.00 0.00 0.00 4.58
1459 1553 2.363018 GGGGAAAGGGAAGCAGCC 60.363 66.667 0.00 0.00 0.00 4.85
1460 1554 0.967887 GAAGGGGAAAGGGAAGCAGC 60.968 60.000 0.00 0.00 0.00 5.25
1461 1555 0.323816 GGAAGGGGAAAGGGAAGCAG 60.324 60.000 0.00 0.00 0.00 4.24
1462 1556 1.774300 GGAAGGGGAAAGGGAAGCA 59.226 57.895 0.00 0.00 0.00 3.91
1463 1557 1.000486 GGGAAGGGGAAAGGGAAGC 60.000 63.158 0.00 0.00 0.00 3.86
1464 1558 1.303282 CGGGAAGGGGAAAGGGAAG 59.697 63.158 0.00 0.00 0.00 3.46
1563 1738 2.515757 GGCTTAGCTGGCAGAGGC 60.516 66.667 20.86 15.45 40.13 4.70
1784 1959 2.044555 CCATCTGCACAGCCCACAG 61.045 63.158 0.00 0.00 0.00 3.66
1857 2035 2.483014 TTCGTTTCCCGGTGATCATT 57.517 45.000 0.00 0.00 37.11 2.57
2145 2326 4.256920 GCATATCCTTGGCATCGACTATT 58.743 43.478 0.00 0.00 0.00 1.73
2169 2350 4.300803 TCAGTTTCATTGCACATCAAAGC 58.699 39.130 0.00 0.00 38.34 3.51
2318 2499 8.964772 CATTCTAAAAGGAAAGACCATCTCAAT 58.035 33.333 0.00 0.00 42.04 2.57
2452 2634 7.369803 ACATGACATAAAACAGAGCTTACAG 57.630 36.000 0.00 0.00 0.00 2.74
2579 2773 2.161855 ACTCGATGAAGCAAATTGCCA 58.838 42.857 15.04 6.86 46.52 4.92
2596 2790 4.398247 CGCAGATTTCAGCTACAAAACTC 58.602 43.478 0.00 0.00 0.00 3.01
2675 2869 9.630098 TTTTCAGATGTGAAGATAAAAATGAGC 57.370 29.630 5.34 0.00 43.66 4.26
2684 2878 6.073819 CGTGTGTGTTTTCAGATGTGAAGATA 60.074 38.462 5.34 0.00 43.66 1.98
2685 2879 5.277490 CGTGTGTGTTTTCAGATGTGAAGAT 60.277 40.000 5.34 0.00 43.66 2.40
2697 2898 1.534028 CTGTGTGCGTGTGTGTTTTC 58.466 50.000 0.00 0.00 0.00 2.29
2702 2903 1.992233 AAAGGCTGTGTGCGTGTGTG 61.992 55.000 0.00 0.00 44.05 3.82
2703 2904 1.312371 AAAAGGCTGTGTGCGTGTGT 61.312 50.000 0.00 0.00 44.05 3.72
2704 2905 0.592247 GAAAAGGCTGTGTGCGTGTG 60.592 55.000 0.00 0.00 44.05 3.82
2709 2913 2.036236 AGCAGAAAAGGCTGTGTGC 58.964 52.632 11.35 11.35 40.80 4.57
2761 3005 7.363431 CAAGACTCCAAATCTTTCTACCAAAC 58.637 38.462 0.00 0.00 34.08 2.93
2863 3111 3.705051 ACATGAGATTTGTTGGCCAGAT 58.295 40.909 5.11 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.