Multiple sequence alignment - TraesCS7B01G113400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G113400 chr7B 100.000 3299 0 0 1 3299 131375737 131379035 0.000000e+00 6093
1 TraesCS7B01G113400 chr7B 87.594 266 26 6 3036 3299 733307432 733307692 5.350000e-78 302
2 TraesCS7B01G113400 chr7B 83.036 112 17 2 2916 3026 725639906 725640016 2.090000e-17 100
3 TraesCS7B01G113400 chr7A 92.502 2934 125 43 331 3242 168811781 168814641 0.000000e+00 4111
4 TraesCS7B01G113400 chr7D 95.904 2075 55 9 462 2531 167227755 167229804 0.000000e+00 3334
5 TraesCS7B01G113400 chr7D 91.445 713 52 6 2590 3299 167245932 167246638 0.000000e+00 970
6 TraesCS7B01G113400 chr7D 91.765 85 6 1 112 195 167227442 167227526 2.080000e-22 117
7 TraesCS7B01G113400 chr6D 88.727 275 26 2 3022 3295 53605485 53605755 6.820000e-87 331
8 TraesCS7B01G113400 chr6D 86.644 292 30 6 3013 3299 2815795 2815508 6.870000e-82 315
9 TraesCS7B01G113400 chr6D 85.990 207 19 7 2051 2255 382588821 382588623 2.580000e-51 213
10 TraesCS7B01G113400 chr2D 83.073 384 31 19 2543 2921 616984840 616985194 5.310000e-83 318
11 TraesCS7B01G113400 chr2D 85.437 103 14 1 2925 3027 200777681 200777580 4.500000e-19 106
12 TraesCS7B01G113400 chr6A 86.691 278 29 5 3025 3299 161340194 161339922 5.350000e-78 302
13 TraesCS7B01G113400 chr5A 85.915 284 33 4 3018 3299 669989115 669988837 2.490000e-76 296
14 TraesCS7B01G113400 chr5A 85.246 122 16 1 2906 3027 77756460 77756579 1.240000e-24 124
15 TraesCS7B01G113400 chr5A 87.255 102 13 0 2925 3026 17369457 17369356 2.080000e-22 117
16 TraesCS7B01G113400 chr5A 85.714 98 14 0 2929 3026 536369959 536370056 1.620000e-18 104
17 TraesCS7B01G113400 chr3B 86.282 277 32 4 3024 3299 42292440 42292711 2.490000e-76 296
18 TraesCS7B01G113400 chr3B 84.091 132 17 2 1608 1735 11577032 11577163 1.240000e-24 124
19 TraesCS7B01G113400 chr1D 85.921 277 33 4 3025 3299 380611895 380612167 1.160000e-74 291
20 TraesCS7B01G113400 chr1D 85.294 102 12 3 2926 3025 69473253 69473153 5.820000e-18 102
21 TraesCS7B01G113400 chr1B 85.121 289 35 5 3012 3299 295427461 295427742 4.170000e-74 289
22 TraesCS7B01G113400 chr4A 95.588 136 4 2 2107 2241 580734809 580734675 1.990000e-52 217
23 TraesCS7B01G113400 chr4D 94.853 136 5 2 2107 2241 21775588 21775454 9.270000e-51 211
24 TraesCS7B01G113400 chr4B 94.853 136 5 2 2107 2241 32897830 32897964 9.270000e-51 211
25 TraesCS7B01G113400 chr6B 87.425 167 19 2 2088 2253 572392592 572392427 1.210000e-44 191
26 TraesCS7B01G113400 chr1A 84.971 173 12 5 2764 2922 84626259 84626431 2.630000e-36 163
27 TraesCS7B01G113400 chr5D 84.762 105 15 1 2925 3028 469506741 469506637 1.620000e-18 104
28 TraesCS7B01G113400 chr3A 83.478 115 16 3 2913 3027 475281328 475281217 1.620000e-18 104


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 TraesCS7B01G113400 chr7B 131375737 131379035 3298 False 6093.0 6093 100.0000 1 3299 1 chr7B.!!$F1 3298
1 TraesCS7B01G113400 chr7A 168811781 168814641 2860 False 4111.0 4111 92.5020 331 3242 1 chr7A.!!$F1 2911
2 TraesCS7B01G113400 chr7D 167227442 167229804 2362 False 1725.5 3334 93.8345 112 2531 2 chr7D.!!$F2 2419
3 TraesCS7B01G113400 chr7D 167245932 167246638 706 False 970.0 970 91.4450 2590 3299 1 chr7D.!!$F1 709

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
597 666 0.677842 AGCGACGTAGGAAAACCACT 59.322 50.0 0.0 0.0 0.00 4.00 F
769 838 1.018910 CCCAACGACGAACCAAAAGT 58.981 50.0 0.0 0.0 0.00 2.66 F
1530 1599 1.076533 CCATCGTTGAGAACCCGACG 61.077 60.0 0.0 0.0 43.37 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1524 0.036294 TCGCTTCCTCGAGAGTCAGA 60.036 55.000 15.71 4.9 34.09 3.27 R
2003 2072 0.886563 GTAGTAGTCGTGTGGCCAGT 59.113 55.000 5.11 0.0 0.00 4.00 R
3266 3352 1.977009 CCAAGGCGGAGGGGAAAAC 60.977 63.158 0.00 0.0 36.56 2.43 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 3.703558 GCATGTGCATTTTGGTAAACG 57.296 42.857 0.00 0.00 41.59 3.60
29 30 2.411409 GCATGTGCATTTTGGTAAACGG 59.589 45.455 0.00 0.00 41.59 4.44
30 31 2.141535 TGTGCATTTTGGTAAACGGC 57.858 45.000 0.00 0.00 0.00 5.68
31 32 1.683917 TGTGCATTTTGGTAAACGGCT 59.316 42.857 0.00 0.00 31.61 5.52
32 33 2.058057 GTGCATTTTGGTAAACGGCTG 58.942 47.619 0.00 0.00 31.61 4.85
33 34 1.683917 TGCATTTTGGTAAACGGCTGT 59.316 42.857 0.00 0.00 31.61 4.40
34 35 2.885266 TGCATTTTGGTAAACGGCTGTA 59.115 40.909 0.00 0.00 31.61 2.74
35 36 3.508012 TGCATTTTGGTAAACGGCTGTAT 59.492 39.130 0.00 0.00 31.61 2.29
36 37 4.700692 TGCATTTTGGTAAACGGCTGTATA 59.299 37.500 0.00 0.00 31.61 1.47
37 38 5.183331 TGCATTTTGGTAAACGGCTGTATAA 59.817 36.000 0.00 0.00 31.61 0.98
38 39 5.741982 GCATTTTGGTAAACGGCTGTATAAG 59.258 40.000 0.00 0.00 0.00 1.73
50 51 2.138320 CTGTATAAGCCCACATGAGCG 58.862 52.381 0.00 0.00 0.00 5.03
51 52 1.484653 TGTATAAGCCCACATGAGCGT 59.515 47.619 0.00 0.03 0.00 5.07
52 53 2.093181 TGTATAAGCCCACATGAGCGTT 60.093 45.455 0.00 0.00 0.00 4.84
53 54 2.128771 ATAAGCCCACATGAGCGTTT 57.871 45.000 0.00 0.00 0.00 3.60
54 55 1.164411 TAAGCCCACATGAGCGTTTG 58.836 50.000 0.00 0.00 0.00 2.93
55 56 2.126346 GCCCACATGAGCGTTTGC 60.126 61.111 0.00 0.00 43.24 3.68
70 71 5.942325 GCGTTTGCTTCTCTTTTAAACAA 57.058 34.783 0.00 0.00 38.39 2.83
71 72 5.714272 GCGTTTGCTTCTCTTTTAAACAAC 58.286 37.500 0.00 0.00 38.39 3.32
72 73 5.276207 GCGTTTGCTTCTCTTTTAAACAACC 60.276 40.000 0.00 0.00 38.39 3.77
73 74 5.231357 CGTTTGCTTCTCTTTTAAACAACCC 59.769 40.000 0.00 0.00 32.36 4.11
74 75 6.338146 GTTTGCTTCTCTTTTAAACAACCCT 58.662 36.000 0.00 0.00 32.92 4.34
75 76 6.538945 TTGCTTCTCTTTTAAACAACCCTT 57.461 33.333 0.00 0.00 0.00 3.95
76 77 6.144078 TGCTTCTCTTTTAAACAACCCTTC 57.856 37.500 0.00 0.00 0.00 3.46
77 78 5.212934 GCTTCTCTTTTAAACAACCCTTCG 58.787 41.667 0.00 0.00 0.00 3.79
78 79 5.220989 GCTTCTCTTTTAAACAACCCTTCGT 60.221 40.000 0.00 0.00 0.00 3.85
79 80 6.679638 GCTTCTCTTTTAAACAACCCTTCGTT 60.680 38.462 0.00 0.00 33.90 3.85
87 88 1.529226 CAACCCTTCGTTGGTATGCA 58.471 50.000 0.00 0.00 46.89 3.96
88 89 2.091541 CAACCCTTCGTTGGTATGCAT 58.908 47.619 3.79 3.79 46.89 3.96
89 90 2.491693 CAACCCTTCGTTGGTATGCATT 59.508 45.455 3.54 0.00 46.89 3.56
90 91 2.091541 ACCCTTCGTTGGTATGCATTG 58.908 47.619 3.54 0.00 33.26 2.82
91 92 2.290641 ACCCTTCGTTGGTATGCATTGA 60.291 45.455 3.54 0.00 33.26 2.57
92 93 2.951642 CCCTTCGTTGGTATGCATTGAT 59.048 45.455 3.54 0.00 0.00 2.57
93 94 3.381272 CCCTTCGTTGGTATGCATTGATT 59.619 43.478 3.54 0.00 0.00 2.57
94 95 4.142182 CCCTTCGTTGGTATGCATTGATTT 60.142 41.667 3.54 0.00 0.00 2.17
95 96 5.410067 CCTTCGTTGGTATGCATTGATTTT 58.590 37.500 3.54 0.00 0.00 1.82
96 97 5.516339 CCTTCGTTGGTATGCATTGATTTTC 59.484 40.000 3.54 0.00 0.00 2.29
97 98 5.895636 TCGTTGGTATGCATTGATTTTCT 57.104 34.783 3.54 0.00 0.00 2.52
98 99 5.639757 TCGTTGGTATGCATTGATTTTCTG 58.360 37.500 3.54 0.00 0.00 3.02
99 100 5.414144 TCGTTGGTATGCATTGATTTTCTGA 59.586 36.000 3.54 0.00 0.00 3.27
100 101 6.095300 TCGTTGGTATGCATTGATTTTCTGAT 59.905 34.615 3.54 0.00 0.00 2.90
101 102 7.281999 TCGTTGGTATGCATTGATTTTCTGATA 59.718 33.333 3.54 0.00 0.00 2.15
102 103 8.077991 CGTTGGTATGCATTGATTTTCTGATAT 58.922 33.333 3.54 0.00 0.00 1.63
103 104 9.188588 GTTGGTATGCATTGATTTTCTGATATG 57.811 33.333 3.54 0.00 0.00 1.78
104 105 7.372714 TGGTATGCATTGATTTTCTGATATGC 58.627 34.615 3.54 0.00 38.97 3.14
109 110 8.725405 TGCATTGATTTTCTGATATGCAAAAT 57.275 26.923 0.00 0.00 43.58 1.82
110 111 9.168451 TGCATTGATTTTCTGATATGCAAAATT 57.832 25.926 0.00 0.00 43.58 1.82
176 178 5.810074 CCCAAGTCAAACTTTTTAAGTGTGG 59.190 40.000 9.27 3.94 45.07 4.17
206 208 9.850198 ATACTAAATATAGTACTCCCTCGGATC 57.150 37.037 0.00 0.00 45.08 3.36
207 209 7.118060 ACTAAATATAGTACTCCCTCGGATCC 58.882 42.308 0.00 0.00 40.62 3.36
208 210 5.531753 AATATAGTACTCCCTCGGATCCA 57.468 43.478 13.41 0.00 0.00 3.41
209 211 5.735733 ATATAGTACTCCCTCGGATCCAT 57.264 43.478 13.41 0.00 0.00 3.41
210 212 6.843473 ATATAGTACTCCCTCGGATCCATA 57.157 41.667 13.41 0.00 0.00 2.74
211 213 5.735733 ATAGTACTCCCTCGGATCCATAT 57.264 43.478 13.41 0.00 0.00 1.78
212 214 3.702792 AGTACTCCCTCGGATCCATATG 58.297 50.000 13.41 0.00 0.00 1.78
213 215 1.944177 ACTCCCTCGGATCCATATGG 58.056 55.000 16.25 16.25 0.00 2.74
224 226 2.238084 TCCATATGGATCGGAGGGAG 57.762 55.000 20.98 0.00 39.78 4.30
225 227 1.433199 TCCATATGGATCGGAGGGAGT 59.567 52.381 20.98 0.00 39.78 3.85
226 228 2.652857 TCCATATGGATCGGAGGGAGTA 59.347 50.000 20.98 0.00 39.78 2.59
227 229 3.272285 TCCATATGGATCGGAGGGAGTAT 59.728 47.826 20.98 0.00 39.78 2.12
228 230 3.386078 CCATATGGATCGGAGGGAGTATG 59.614 52.174 17.49 0.00 37.39 2.39
229 231 4.281657 CATATGGATCGGAGGGAGTATGA 58.718 47.826 0.00 0.00 0.00 2.15
230 232 2.767644 TGGATCGGAGGGAGTATGAA 57.232 50.000 0.00 0.00 0.00 2.57
231 233 3.040655 TGGATCGGAGGGAGTATGAAA 57.959 47.619 0.00 0.00 0.00 2.69
232 234 3.380393 TGGATCGGAGGGAGTATGAAAA 58.620 45.455 0.00 0.00 0.00 2.29
233 235 3.973973 TGGATCGGAGGGAGTATGAAAAT 59.026 43.478 0.00 0.00 0.00 1.82
234 236 5.152193 TGGATCGGAGGGAGTATGAAAATA 58.848 41.667 0.00 0.00 0.00 1.40
289 291 9.823647 TTTGGTGTTGTATATGTTGATGTTTTT 57.176 25.926 0.00 0.00 0.00 1.94
318 320 9.696917 ATATTTGGTCAAACATCAAGAAGTTTC 57.303 29.630 0.88 0.00 35.90 2.78
319 321 6.522625 TTGGTCAAACATCAAGAAGTTTCA 57.477 33.333 0.88 0.00 35.90 2.69
320 322 5.890334 TGGTCAAACATCAAGAAGTTTCAC 58.110 37.500 0.88 0.00 35.90 3.18
321 323 5.163561 TGGTCAAACATCAAGAAGTTTCACC 60.164 40.000 14.39 14.39 45.53 4.02
322 324 4.970003 GTCAAACATCAAGAAGTTTCACCG 59.030 41.667 0.88 0.00 35.90 4.94
323 325 4.036262 TCAAACATCAAGAAGTTTCACCGG 59.964 41.667 0.00 0.00 35.90 5.28
324 326 1.880027 ACATCAAGAAGTTTCACCGGC 59.120 47.619 0.00 0.00 0.00 6.13
325 327 1.879380 CATCAAGAAGTTTCACCGGCA 59.121 47.619 0.00 0.00 0.00 5.69
326 328 2.045561 TCAAGAAGTTTCACCGGCAA 57.954 45.000 0.00 0.00 0.00 4.52
327 329 2.370349 TCAAGAAGTTTCACCGGCAAA 58.630 42.857 0.00 0.00 0.00 3.68
328 330 2.755655 TCAAGAAGTTTCACCGGCAAAA 59.244 40.909 0.00 0.00 0.00 2.44
329 331 3.193691 TCAAGAAGTTTCACCGGCAAAAA 59.806 39.130 0.00 0.00 0.00 1.94
359 361 4.639135 AGGAGTTTGTTCTGAGCAAAAC 57.361 40.909 19.07 15.53 37.54 2.43
405 407 5.321959 CTTGAGTAGCACTGAGAATCTGA 57.678 43.478 0.00 0.00 37.51 3.27
407 409 3.698539 TGAGTAGCACTGAGAATCTGAGG 59.301 47.826 1.20 0.00 37.51 3.86
408 410 3.699038 GAGTAGCACTGAGAATCTGAGGT 59.301 47.826 1.20 0.00 38.64 3.85
409 411 3.446873 AGTAGCACTGAGAATCTGAGGTG 59.553 47.826 1.20 2.62 36.27 4.00
410 412 2.255406 AGCACTGAGAATCTGAGGTGT 58.745 47.619 1.20 0.00 34.57 4.16
438 502 9.971922 CTCTTTATTTATTTATTTGCCCTGAGG 57.028 33.333 0.00 0.00 0.00 3.86
439 503 9.487442 TCTTTATTTATTTATTTGCCCTGAGGT 57.513 29.630 0.00 0.00 34.57 3.85
441 505 9.883142 TTTATTTATTTATTTGCCCTGAGGTTG 57.117 29.630 0.00 0.00 34.57 3.77
442 506 5.930837 TTATTTATTTGCCCTGAGGTTGG 57.069 39.130 0.00 0.00 34.57 3.77
474 538 2.271173 GGGTCCCTAAGGTTGGCG 59.729 66.667 0.00 0.00 0.00 5.69
497 562 6.349363 GCGGTGAATTTTAATGGAAGAGAACT 60.349 38.462 0.00 0.00 0.00 3.01
524 592 5.039645 TGTAGGGGAGAATGGAAGAGAAAT 58.960 41.667 0.00 0.00 0.00 2.17
597 666 0.677842 AGCGACGTAGGAAAACCACT 59.322 50.000 0.00 0.00 0.00 4.00
692 761 2.203126 GCCAATCAGAGGCCTCCG 60.203 66.667 29.54 20.14 46.50 4.63
769 838 1.018910 CCCAACGACGAACCAAAAGT 58.981 50.000 0.00 0.00 0.00 2.66
995 1064 1.371635 CCAGCGGCTTTGGTTTTCG 60.372 57.895 0.00 0.00 0.00 3.46
1522 1591 3.458872 GATGGTGCCATCGTTGAGA 57.541 52.632 14.58 0.00 42.55 3.27
1530 1599 1.076533 CCATCGTTGAGAACCCGACG 61.077 60.000 0.00 0.00 43.37 5.12
1620 1689 2.184322 GACGCCGAGCTCATGGAA 59.816 61.111 15.40 0.00 0.00 3.53
1911 1980 2.203938 TTCACCCCGAGGAGCCTT 60.204 61.111 0.00 0.00 36.73 4.35
2003 2072 1.467543 GCACGTCAAGCTCGATGACTA 60.468 52.381 13.66 0.00 43.93 2.59
2061 2130 0.761802 GGATGATGGGAGGAGTGGTC 59.238 60.000 0.00 0.00 0.00 4.02
2335 2404 1.300266 CTGTCGGTGTGCATGCATGA 61.300 55.000 30.64 16.25 0.00 3.07
2365 2434 4.758251 CGTGTGGGCTCGCCATGA 62.758 66.667 10.51 0.00 37.98 3.07
2366 2435 2.359850 GTGTGGGCTCGCCATGAA 60.360 61.111 10.51 0.00 37.98 2.57
2367 2436 1.971167 GTGTGGGCTCGCCATGAAA 60.971 57.895 10.51 0.00 37.98 2.69
2368 2437 1.001020 TGTGGGCTCGCCATGAAAT 60.001 52.632 10.51 0.00 37.98 2.17
2369 2438 1.314534 TGTGGGCTCGCCATGAAATG 61.315 55.000 10.51 0.00 46.21 2.32
2444 2513 7.854557 AGTTACTTTCCTTTTTCAGTTACGT 57.145 32.000 0.00 0.00 0.00 3.57
2457 2531 4.827692 TCAGTTACGTTATGGTGCATTCT 58.172 39.130 0.00 0.00 0.00 2.40
2489 2563 2.675348 CAAGGAATTTCAGGTCGCTCTC 59.325 50.000 0.00 0.00 0.00 3.20
2562 2644 9.331282 AGTTTTCCACTTTAGATATATGTCAGC 57.669 33.333 2.04 0.00 27.32 4.26
2601 2683 6.869315 TTTGGATCAGTCGAATTTGTTACA 57.131 33.333 0.00 0.00 0.00 2.41
2620 2703 7.359595 TGTTACATTGATTCAGTGTGCTTTAC 58.640 34.615 21.18 12.63 35.23 2.01
2637 2720 4.442073 GCTTTACGAAACGTGTGTAAGAGA 59.558 41.667 7.05 0.00 41.39 3.10
2641 2724 3.255149 ACGAAACGTGTGTAAGAGATCCT 59.745 43.478 0.00 0.00 39.18 3.24
2723 2807 0.032912 TGATGCAGCCCCATGATGTT 60.033 50.000 0.00 0.00 0.00 2.71
2891 2976 8.341903 TGTATTTTTAGATGTTGAGTGTGTGTG 58.658 33.333 0.00 0.00 0.00 3.82
2922 3007 7.656707 TGCATGCAAGTACTACATGTATATG 57.343 36.000 27.03 15.67 42.50 1.78
3039 3124 5.461516 TCTACAATACTCCCTCTGTACCA 57.538 43.478 0.00 0.00 0.00 3.25
3053 3138 5.069119 CCTCTGTACCAGTGCATAAGTCATA 59.931 44.000 0.00 0.00 32.61 2.15
3117 3202 6.995686 TGCATTAACTCTCACCTTGTTTCTTA 59.004 34.615 0.00 0.00 0.00 2.10
3159 3244 5.768164 AGGAATCAACCAATAAGAAACGTGT 59.232 36.000 0.00 0.00 0.00 4.49
3278 3364 0.606604 TTCTCTCGTTTTCCCCTCCG 59.393 55.000 0.00 0.00 0.00 4.63
3279 3365 1.448013 CTCTCGTTTTCCCCTCCGC 60.448 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.411409 CCGTTTACCAAAATGCACATGC 59.589 45.455 0.00 0.00 42.50 4.06
9 10 2.411409 GCCGTTTACCAAAATGCACATG 59.589 45.455 0.00 0.00 31.36 3.21
10 11 2.298729 AGCCGTTTACCAAAATGCACAT 59.701 40.909 0.00 0.00 31.36 3.21
11 12 1.683917 AGCCGTTTACCAAAATGCACA 59.316 42.857 0.00 0.00 31.36 4.57
12 13 2.058057 CAGCCGTTTACCAAAATGCAC 58.942 47.619 0.00 0.00 31.36 4.57
13 14 1.683917 ACAGCCGTTTACCAAAATGCA 59.316 42.857 0.00 0.00 31.36 3.96
14 15 2.432206 ACAGCCGTTTACCAAAATGC 57.568 45.000 0.00 0.00 31.36 3.56
15 16 5.741982 GCTTATACAGCCGTTTACCAAAATG 59.258 40.000 0.00 0.00 43.65 2.32
16 17 5.886992 GCTTATACAGCCGTTTACCAAAAT 58.113 37.500 0.00 0.00 43.65 1.82
17 18 5.299582 GCTTATACAGCCGTTTACCAAAA 57.700 39.130 0.00 0.00 43.65 2.44
18 19 4.950434 GCTTATACAGCCGTTTACCAAA 57.050 40.909 0.00 0.00 43.65 3.28
30 31 2.138320 CGCTCATGTGGGCTTATACAG 58.862 52.381 3.06 0.00 0.00 2.74
31 32 1.484653 ACGCTCATGTGGGCTTATACA 59.515 47.619 11.32 0.00 0.00 2.29
32 33 2.240493 ACGCTCATGTGGGCTTATAC 57.760 50.000 11.32 0.00 0.00 1.47
33 34 2.942376 CAAACGCTCATGTGGGCTTATA 59.058 45.455 11.32 0.00 0.00 0.98
34 35 1.745087 CAAACGCTCATGTGGGCTTAT 59.255 47.619 11.32 0.00 0.00 1.73
35 36 1.164411 CAAACGCTCATGTGGGCTTA 58.836 50.000 11.32 0.00 0.00 3.09
36 37 1.959085 CAAACGCTCATGTGGGCTT 59.041 52.632 11.32 3.46 0.00 4.35
37 38 2.629656 GCAAACGCTCATGTGGGCT 61.630 57.895 11.32 0.00 0.00 5.19
38 39 2.126346 GCAAACGCTCATGTGGGC 60.126 61.111 11.32 0.00 0.00 5.36
39 40 0.109597 GAAGCAAACGCTCATGTGGG 60.110 55.000 9.98 9.98 39.40 4.61
40 41 0.877071 AGAAGCAAACGCTCATGTGG 59.123 50.000 0.00 0.00 39.40 4.17
41 42 1.802960 AGAGAAGCAAACGCTCATGTG 59.197 47.619 0.00 0.00 39.40 3.21
42 43 2.175878 AGAGAAGCAAACGCTCATGT 57.824 45.000 0.00 0.00 39.40 3.21
43 44 3.549299 AAAGAGAAGCAAACGCTCATG 57.451 42.857 0.00 0.00 39.40 3.07
44 45 5.689383 TTAAAAGAGAAGCAAACGCTCAT 57.311 34.783 0.00 0.00 39.40 2.90
45 46 5.163703 TGTTTAAAAGAGAAGCAAACGCTCA 60.164 36.000 0.00 0.00 39.40 4.26
46 47 5.270853 TGTTTAAAAGAGAAGCAAACGCTC 58.729 37.500 0.00 0.00 39.40 5.03
47 48 5.243426 TGTTTAAAAGAGAAGCAAACGCT 57.757 34.783 0.00 0.00 43.25 5.07
48 49 5.276207 GGTTGTTTAAAAGAGAAGCAAACGC 60.276 40.000 0.00 0.00 32.95 4.84
49 50 5.231357 GGGTTGTTTAAAAGAGAAGCAAACG 59.769 40.000 0.00 0.00 36.05 3.60
50 51 6.338146 AGGGTTGTTTAAAAGAGAAGCAAAC 58.662 36.000 0.00 0.00 34.89 2.93
51 52 6.538945 AGGGTTGTTTAAAAGAGAAGCAAA 57.461 33.333 0.00 0.00 30.25 3.68
52 53 6.538945 AAGGGTTGTTTAAAAGAGAAGCAA 57.461 33.333 0.00 0.00 0.00 3.91
53 54 5.220970 CGAAGGGTTGTTTAAAAGAGAAGCA 60.221 40.000 0.00 0.00 0.00 3.91
54 55 5.212934 CGAAGGGTTGTTTAAAAGAGAAGC 58.787 41.667 0.00 0.00 0.00 3.86
55 56 6.373186 ACGAAGGGTTGTTTAAAAGAGAAG 57.627 37.500 0.00 0.00 0.00 2.85
56 57 6.762702 AACGAAGGGTTGTTTAAAAGAGAA 57.237 33.333 0.00 0.00 37.50 2.87
69 70 2.491693 CAATGCATACCAACGAAGGGTT 59.508 45.455 0.00 0.00 39.85 4.11
70 71 2.091541 CAATGCATACCAACGAAGGGT 58.908 47.619 0.00 0.00 42.48 4.34
71 72 2.364632 TCAATGCATACCAACGAAGGG 58.635 47.619 0.00 0.00 0.00 3.95
72 73 4.637483 AATCAATGCATACCAACGAAGG 57.363 40.909 0.00 0.00 0.00 3.46
73 74 6.252015 CAGAAAATCAATGCATACCAACGAAG 59.748 38.462 0.00 0.00 0.00 3.79
74 75 6.072230 TCAGAAAATCAATGCATACCAACGAA 60.072 34.615 0.00 0.00 0.00 3.85
75 76 5.414144 TCAGAAAATCAATGCATACCAACGA 59.586 36.000 0.00 0.00 0.00 3.85
76 77 5.639757 TCAGAAAATCAATGCATACCAACG 58.360 37.500 0.00 0.00 0.00 4.10
77 78 9.188588 CATATCAGAAAATCAATGCATACCAAC 57.811 33.333 0.00 0.00 0.00 3.77
78 79 7.868922 GCATATCAGAAAATCAATGCATACCAA 59.131 33.333 0.00 0.00 39.53 3.67
79 80 7.014422 TGCATATCAGAAAATCAATGCATACCA 59.986 33.333 0.00 0.00 43.32 3.25
80 81 7.372714 TGCATATCAGAAAATCAATGCATACC 58.627 34.615 0.00 0.00 43.32 2.73
81 82 8.806177 TTGCATATCAGAAAATCAATGCATAC 57.194 30.769 0.00 0.00 46.31 2.39
82 83 9.819267 TTTTGCATATCAGAAAATCAATGCATA 57.181 25.926 0.00 1.98 46.31 3.14
83 84 8.725405 TTTTGCATATCAGAAAATCAATGCAT 57.275 26.923 8.44 0.00 46.31 3.96
84 85 8.725405 ATTTTGCATATCAGAAAATCAATGCA 57.275 26.923 3.83 3.83 45.65 3.96
182 184 7.118060 GGATCCGAGGGAGTACTATATTTAGT 58.882 42.308 0.00 1.35 37.52 2.24
195 197 2.238084 TCCATATGGATCCGAGGGAG 57.762 55.000 20.98 0.00 39.78 4.30
206 208 1.944177 ACTCCCTCCGATCCATATGG 58.056 55.000 16.25 16.25 0.00 2.74
207 209 4.281657 TCATACTCCCTCCGATCCATATG 58.718 47.826 0.00 0.00 0.00 1.78
208 210 4.609866 TCATACTCCCTCCGATCCATAT 57.390 45.455 0.00 0.00 0.00 1.78
209 211 4.397919 TTCATACTCCCTCCGATCCATA 57.602 45.455 0.00 0.00 0.00 2.74
210 212 3.260269 TTCATACTCCCTCCGATCCAT 57.740 47.619 0.00 0.00 0.00 3.41
211 213 2.767644 TTCATACTCCCTCCGATCCA 57.232 50.000 0.00 0.00 0.00 3.41
212 214 4.625607 ATTTTCATACTCCCTCCGATCC 57.374 45.455 0.00 0.00 0.00 3.36
213 215 6.702329 ACATATTTTCATACTCCCTCCGATC 58.298 40.000 0.00 0.00 0.00 3.69
214 216 6.688073 ACATATTTTCATACTCCCTCCGAT 57.312 37.500 0.00 0.00 0.00 4.18
215 217 6.494666 AACATATTTTCATACTCCCTCCGA 57.505 37.500 0.00 0.00 0.00 4.55
216 218 7.568199 AAAACATATTTTCATACTCCCTCCG 57.432 36.000 0.00 0.00 32.29 4.63
263 265 9.823647 AAAAACATCAACATATACAACACCAAA 57.176 25.926 0.00 0.00 0.00 3.28
292 294 9.696917 GAAACTTCTTGATGTTTGACCAAATAT 57.303 29.630 15.95 4.73 36.64 1.28
293 295 8.690884 TGAAACTTCTTGATGTTTGACCAAATA 58.309 29.630 15.95 0.00 36.64 1.40
294 296 7.492344 GTGAAACTTCTTGATGTTTGACCAAAT 59.508 33.333 15.95 0.00 35.38 2.32
295 297 6.811170 GTGAAACTTCTTGATGTTTGACCAAA 59.189 34.615 15.95 0.00 35.38 3.28
296 298 6.329496 GTGAAACTTCTTGATGTTTGACCAA 58.671 36.000 15.95 0.00 35.38 3.67
297 299 5.890334 GTGAAACTTCTTGATGTTTGACCA 58.110 37.500 15.95 8.00 35.38 4.02
298 300 5.281727 GGTGAAACTTCTTGATGTTTGACC 58.718 41.667 23.37 23.37 46.73 4.02
299 301 4.970003 CGGTGAAACTTCTTGATGTTTGAC 59.030 41.667 15.95 16.45 38.75 3.18
300 302 4.036262 CCGGTGAAACTTCTTGATGTTTGA 59.964 41.667 15.95 7.87 36.64 2.69
301 303 4.290155 CCGGTGAAACTTCTTGATGTTTG 58.710 43.478 15.95 5.35 36.64 2.93
302 304 3.243401 GCCGGTGAAACTTCTTGATGTTT 60.243 43.478 1.90 12.40 38.84 2.83
303 305 2.293399 GCCGGTGAAACTTCTTGATGTT 59.707 45.455 1.90 0.00 36.74 2.71
304 306 1.880027 GCCGGTGAAACTTCTTGATGT 59.120 47.619 1.90 0.00 36.74 3.06
305 307 1.879380 TGCCGGTGAAACTTCTTGATG 59.121 47.619 1.90 0.00 36.74 3.07
306 308 2.270352 TGCCGGTGAAACTTCTTGAT 57.730 45.000 1.90 0.00 36.74 2.57
307 309 2.045561 TTGCCGGTGAAACTTCTTGA 57.954 45.000 1.90 0.00 36.74 3.02
308 310 2.861462 TTTGCCGGTGAAACTTCTTG 57.139 45.000 1.90 0.00 36.74 3.02
309 311 3.878160 TTTTTGCCGGTGAAACTTCTT 57.122 38.095 1.90 0.00 36.74 2.52
328 330 8.084684 GCTCAGAACAAACTCCTTGATATTTTT 58.915 33.333 0.00 0.00 38.50 1.94
329 331 7.231317 TGCTCAGAACAAACTCCTTGATATTTT 59.769 33.333 0.00 0.00 38.50 1.82
340 342 9.899226 AATTATAGTTTTGCTCAGAACAAACTC 57.101 29.630 0.00 0.00 36.77 3.01
383 385 5.321959 TCAGATTCTCAGTGCTACTCAAG 57.678 43.478 0.00 0.00 0.00 3.02
449 513 1.776063 ACCTTAGGGACCCGTCAAAAA 59.224 47.619 4.40 0.00 36.25 1.94
450 514 1.437397 ACCTTAGGGACCCGTCAAAA 58.563 50.000 4.40 0.00 36.25 2.44
451 515 1.072648 CAACCTTAGGGACCCGTCAAA 59.927 52.381 4.40 0.00 36.25 2.69
452 516 0.688487 CAACCTTAGGGACCCGTCAA 59.312 55.000 4.40 0.00 36.25 3.18
453 517 1.196104 CCAACCTTAGGGACCCGTCA 61.196 60.000 4.40 0.00 36.25 4.35
454 518 1.600638 CCAACCTTAGGGACCCGTC 59.399 63.158 4.40 0.00 36.25 4.79
455 519 2.599757 GCCAACCTTAGGGACCCGT 61.600 63.158 4.40 0.00 36.25 5.28
456 520 2.271173 GCCAACCTTAGGGACCCG 59.729 66.667 4.40 0.00 36.25 5.28
457 521 2.271173 CGCCAACCTTAGGGACCC 59.729 66.667 0.59 0.59 36.25 4.46
458 522 2.271173 CCGCCAACCTTAGGGACC 59.729 66.667 2.32 0.00 36.25 4.46
459 523 1.376812 CACCGCCAACCTTAGGGAC 60.377 63.158 2.32 0.00 36.25 4.46
460 524 1.128809 TTCACCGCCAACCTTAGGGA 61.129 55.000 2.32 0.00 36.25 4.20
465 529 4.562552 CCATTAAAATTCACCGCCAACCTT 60.563 41.667 0.00 0.00 0.00 3.50
467 531 3.056465 TCCATTAAAATTCACCGCCAACC 60.056 43.478 0.00 0.00 0.00 3.77
474 538 9.764363 AAAAGTTCTCTTCCATTAAAATTCACC 57.236 29.630 0.00 0.00 32.90 4.02
497 562 5.312178 TCTCTTCCATTCTCCCCTACAAAAA 59.688 40.000 0.00 0.00 0.00 1.94
524 592 5.723672 AAAGTCATTCTCGGACTGACTAA 57.276 39.130 19.60 0.00 46.66 2.24
617 686 3.936203 TGACGCACGGGCCTTTCT 61.936 61.111 2.82 0.00 36.38 2.52
642 711 2.125391 GGTAGGGCCGTTCCGTTC 60.125 66.667 1.81 0.00 34.28 3.95
692 761 1.166531 GGGTAATGTCCATCCAGCGC 61.167 60.000 0.00 0.00 0.00 5.92
704 773 2.026641 CTGATTGGCTGGTGGGTAATG 58.973 52.381 0.00 0.00 0.00 1.90
760 829 4.490743 GTGTGTACTTTGCACTTTTGGTT 58.509 39.130 0.00 0.00 37.70 3.67
769 838 1.813212 CGCGTCGTGTGTACTTTGCA 61.813 55.000 0.00 0.00 0.00 4.08
830 899 4.654724 GGGTCTAGGTTTATAGCAGAAGGT 59.345 45.833 0.00 0.00 0.00 3.50
923 992 2.431260 TACTCCGTTTCACCGCGC 60.431 61.111 0.00 0.00 0.00 6.86
924 993 2.442188 GCTACTCCGTTTCACCGCG 61.442 63.158 0.00 0.00 0.00 6.46
995 1064 1.372087 CCCCGAGCAGCTCATCAAAC 61.372 60.000 22.49 0.00 0.00 2.93
1371 1440 0.939577 CCGTCTCCACGTCACACTTG 60.940 60.000 0.00 0.00 45.17 3.16
1389 1458 2.757917 AGCAGCTCCTCCTCGTCC 60.758 66.667 0.00 0.00 0.00 4.79
1455 1524 0.036294 TCGCTTCCTCGAGAGTCAGA 60.036 55.000 15.71 4.90 34.09 3.27
1518 1587 2.154798 CTGGCTTCGTCGGGTTCTCA 62.155 60.000 0.00 0.00 0.00 3.27
1522 1591 3.626924 AGCTGGCTTCGTCGGGTT 61.627 61.111 0.00 0.00 0.00 4.11
1620 1689 4.155733 TCCATGTCCGCGGCGAAT 62.156 61.111 25.92 10.94 0.00 3.34
1738 1807 1.107114 TCGATCTCCAGCTTGACTCC 58.893 55.000 0.00 0.00 0.00 3.85
1911 1980 3.435566 CTCGTAGTTTAGATTGAGCGCA 58.564 45.455 11.47 0.00 0.00 6.09
2003 2072 0.886563 GTAGTAGTCGTGTGGCCAGT 59.113 55.000 5.11 0.00 0.00 4.00
2335 2404 3.933722 ACACGCAGCCTGCAGAGT 61.934 61.111 17.39 11.10 45.36 3.24
2353 2422 3.122850 CCATTTCATGGCGAGCCC 58.877 61.111 12.05 0.00 44.70 5.19
2382 2451 2.173964 GACGAGTTGTTTTGTGTGTGC 58.826 47.619 0.00 0.00 0.00 4.57
2457 2531 5.178096 TGAAATTCCTTGGATACTCAGCA 57.822 39.130 0.00 0.00 37.61 4.41
2542 2624 5.864474 GTCGGCTGACATATATCTAAAGTGG 59.136 44.000 21.02 0.00 44.82 4.00
2559 2641 6.155827 TCCAAAATAAAAATTCAGTCGGCTG 58.844 36.000 11.77 11.77 43.87 4.85
2562 2644 8.028938 ACTGATCCAAAATAAAAATTCAGTCGG 58.971 33.333 0.00 0.00 38.46 4.79
2575 2657 9.004717 TGTAACAAATTCGACTGATCCAAAATA 57.995 29.630 0.00 0.00 0.00 1.40
2599 2681 4.754618 TCGTAAAGCACACTGAATCAATGT 59.245 37.500 0.00 0.00 0.00 2.71
2601 2683 5.940192 TTCGTAAAGCACACTGAATCAAT 57.060 34.783 0.00 0.00 0.00 2.57
2620 2703 3.834610 AGGATCTCTTACACACGTTTCG 58.165 45.455 0.00 0.00 0.00 3.46
2641 2724 3.959293 ACAGCATCAGTCAAATCCATGA 58.041 40.909 0.00 0.00 0.00 3.07
2657 2740 7.552687 AGGAAATCGACTGAATAAATAACAGCA 59.447 33.333 0.00 0.00 35.38 4.41
2778 2862 2.287909 GGAAAAAGGCATGCACGTACAA 60.288 45.455 21.36 0.00 0.00 2.41
2891 2976 6.603237 TGTAGTACTTGCATGCATACATTC 57.397 37.500 25.67 17.48 32.87 2.67
2922 3007 8.763601 ACTATATTATGAAATGGAGGGAGTAGC 58.236 37.037 0.00 0.00 0.00 3.58
2964 3049 6.143758 TCAAAGTGCGCAAAATTTGACTTATC 59.856 34.615 28.63 9.07 36.89 1.75
3033 3118 6.921307 CGTAATATGACTTATGCACTGGTACA 59.079 38.462 0.00 0.00 0.00 2.90
3039 3124 7.551262 TGGTTTTCGTAATATGACTTATGCACT 59.449 33.333 0.00 0.00 0.00 4.40
3159 3244 6.960468 TCAAGTCATTAAAAACATACACGCA 58.040 32.000 0.00 0.00 0.00 5.24
3252 3338 6.351626 GGAGGGGAAAACGAGAGAACTTAATA 60.352 42.308 0.00 0.00 0.00 0.98
3266 3352 1.977009 CCAAGGCGGAGGGGAAAAC 60.977 63.158 0.00 0.00 36.56 2.43


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

AutoCloner maintained by Alex Coulton.