Multiple sequence alignment - TraesCS4A01G103300

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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 TraesCS4A01G103300 chr4A 100.000 2609 0 0 1 2609 116478679 116476071 0.000000e+00 4819
1 TraesCS4A01G103300 chr4B 88.774 2699 131 52 1 2609 428963931 428966547 0.000000e+00 3147
2 TraesCS4A01G103300 chr4B 82.793 401 44 17 482 862 115554268 115554663 4.160000e-88 335
3 TraesCS4A01G103300 chr4D 90.763 1808 69 42 864 2608 348795723 348797495 0.000000e+00 2324
4 TraesCS4A01G103300 chr2A 85.337 341 36 12 533 863 110894267 110893931 8.940000e-90 340
5 TraesCS4A01G103300 chr3B 88.930 271 30 0 2 272 201848226 201848496 4.160000e-88 335
6 TraesCS4A01G103300 chr5B 83.117 385 42 17 484 857 569886747 569887119 1.940000e-86 329
7 TraesCS4A01G103300 chr6B 84.795 342 35 12 533 862 701604915 701605251 6.960000e-86 327
8 TraesCS4A01G103300 chr2B 82.687 387 49 13 487 862 388944315 388944694 6.960000e-86 327
9 TraesCS4A01G103300 chr2B 84.706 340 33 14 532 862 789967529 789967200 3.240000e-84 322
10 TraesCS4A01G103300 chr7A 89.764 254 24 2 20 272 721178158 721178410 9.010000e-85 324
11 TraesCS4A01G103300 chr3D 89.494 257 26 1 16 272 554148897 554148642 9.010000e-85 324
12 TraesCS4A01G103300 chr3A 84.848 330 41 6 534 858 565557670 565557995 9.010000e-85 324
13 TraesCS4A01G103300 chr7B 87.823 271 32 1 2 272 412092538 412092269 1.510000e-82 316
14 TraesCS4A01G103300 chr7B 86.842 190 21 3 31 219 520415202 520415388 2.630000e-50 209
15 TraesCS4A01G103300 chr5D 93.810 210 13 0 1264 1473 480618649 480618440 1.510000e-82 316
16 TraesCS4A01G103300 chr5D 82.955 264 23 8 2 265 508988991 508988750 4.370000e-53 219
17 TraesCS4A01G103300 chr2D 82.005 389 43 23 487 858 642102079 642102457 3.260000e-79 305
18 TraesCS4A01G103300 chr2D 81.912 387 45 21 487 858 598330538 598330914 1.170000e-78 303
19 TraesCS4A01G103300 chr5A 87.795 254 31 0 11 264 241136317 241136064 5.460000e-77 298
20 TraesCS4A01G103300 chr6A 91.566 166 14 0 107 272 611906813 611906648 2.020000e-56 230
21 TraesCS4A01G103300 chr6A 88.554 166 19 0 107 272 125265110 125264945 4.400000e-48 202


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 TraesCS4A01G103300 chr4A 116476071 116478679 2608 True 4819 4819 100.000 1 2609 1 chr4A.!!$R1 2608
1 TraesCS4A01G103300 chr4B 428963931 428966547 2616 False 3147 3147 88.774 1 2609 1 chr4B.!!$F2 2608
2 TraesCS4A01G103300 chr4D 348795723 348797495 1772 False 2324 2324 90.763 864 2608 1 chr4D.!!$F1 1744

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
234 235 0.106769 TGTTGCTCCTTGTGCCTTCA 60.107 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1716 0.03601 AGCACTGCTCGGCAACTTAT 60.036 50.0 0.0 0.0 38.41 1.73 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
60 61 4.263905 ACTTGAAGTGGGATGCAATAAGGA 60.264 41.667 0.00 0.00 0.00 3.36
62 63 4.464008 TGAAGTGGGATGCAATAAGGATC 58.536 43.478 0.00 0.00 43.69 3.36
66 67 2.154462 GGGATGCAATAAGGATCGTGG 58.846 52.381 0.00 0.00 45.21 4.94
70 71 1.283613 TGCAATAAGGATCGTGGGGTT 59.716 47.619 0.00 0.00 0.00 4.11
98 99 0.184451 ACATGGCATCCCTCATCCAC 59.816 55.000 0.00 0.00 0.00 4.02
102 103 0.108207 GGCATCCCTCATCCACAGAG 59.892 60.000 0.00 0.00 0.00 3.35
106 107 2.325661 TCCCTCATCCACAGAGTTGA 57.674 50.000 0.00 0.00 0.00 3.18
111 112 4.022849 CCCTCATCCACAGAGTTGAAAAAC 60.023 45.833 0.00 0.00 0.00 2.43
140 141 9.454859 AGCTAAACTATCTGCTTCTTTATTTGT 57.545 29.630 0.00 0.00 30.96 2.83
152 153 5.834239 TCTTTATTTGTCGTTCGTCCTTC 57.166 39.130 0.00 0.00 0.00 3.46
161 162 3.803778 GTCGTTCGTCCTTCAAAGGTAAA 59.196 43.478 8.60 0.15 46.54 2.01
174 175 9.103861 CCTTCAAAGGTAAATTTGCAGTTAAAA 57.896 29.630 8.59 0.36 41.41 1.52
179 180 7.433708 AGGTAAATTTGCAGTTAAAATTGGC 57.566 32.000 8.59 0.00 37.32 4.52
181 182 7.387673 AGGTAAATTTGCAGTTAAAATTGGCTC 59.612 33.333 8.59 0.00 37.32 4.70
184 185 4.953940 TTGCAGTTAAAATTGGCTCCTT 57.046 36.364 0.00 0.00 0.00 3.36
198 199 0.676151 CTCCTTGCTGCTTGGTCTCC 60.676 60.000 0.00 0.00 0.00 3.71
226 227 4.913335 ATGCTATCATTGTTGCTCCTTG 57.087 40.909 0.00 0.00 0.00 3.61
227 228 3.689347 TGCTATCATTGTTGCTCCTTGT 58.311 40.909 0.00 0.00 0.00 3.16
228 229 3.441222 TGCTATCATTGTTGCTCCTTGTG 59.559 43.478 0.00 0.00 0.00 3.33
229 230 3.733077 GCTATCATTGTTGCTCCTTGTGC 60.733 47.826 0.00 0.00 0.00 4.57
230 231 0.961019 TCATTGTTGCTCCTTGTGCC 59.039 50.000 0.00 0.00 0.00 5.01
231 232 0.963962 CATTGTTGCTCCTTGTGCCT 59.036 50.000 0.00 0.00 0.00 4.75
232 233 1.342174 CATTGTTGCTCCTTGTGCCTT 59.658 47.619 0.00 0.00 0.00 4.35
233 234 1.032014 TTGTTGCTCCTTGTGCCTTC 58.968 50.000 0.00 0.00 0.00 3.46
234 235 0.106769 TGTTGCTCCTTGTGCCTTCA 60.107 50.000 0.00 0.00 0.00 3.02
235 236 1.251251 GTTGCTCCTTGTGCCTTCAT 58.749 50.000 0.00 0.00 0.00 2.57
236 237 1.068055 GTTGCTCCTTGTGCCTTCATG 60.068 52.381 0.00 0.00 0.00 3.07
237 238 0.111061 TGCTCCTTGTGCCTTCATGT 59.889 50.000 0.00 0.00 0.00 3.21
238 239 1.350684 TGCTCCTTGTGCCTTCATGTA 59.649 47.619 0.00 0.00 0.00 2.29
239 240 2.025981 TGCTCCTTGTGCCTTCATGTAT 60.026 45.455 0.00 0.00 0.00 2.29
278 279 2.466867 CGTCCAACGCAAGCCTTAT 58.533 52.632 0.00 0.00 45.62 1.73
280 281 1.199097 CGTCCAACGCAAGCCTTATTT 59.801 47.619 0.00 0.00 45.62 1.40
363 364 0.693767 CAGGAGAGGAGAAGGCCCAT 60.694 60.000 0.00 0.00 0.00 4.00
381 382 1.891150 CATCAAAGTTTCAGCTGGCCT 59.109 47.619 15.13 4.34 0.00 5.19
392 393 1.483827 CAGCTGGCCTGAGATTCTGTA 59.516 52.381 14.77 0.00 44.64 2.74
432 433 6.037726 CCATGATTGTAATGACACACCAATG 58.962 40.000 0.00 0.00 34.48 2.82
443 444 6.707440 TGACACACCAATGTTCTTGTTATT 57.293 33.333 0.00 0.00 36.72 1.40
458 459 9.489084 GTTCTTGTTATTTTTAAGCTCCCAATT 57.511 29.630 0.00 0.00 0.00 2.32
486 487 1.668751 GAACAAACACTTGAGACGCCA 59.331 47.619 0.00 0.00 36.33 5.69
592 617 5.814764 AATCTTTGTTGTGCATGCAAAAA 57.185 30.435 24.69 17.76 32.64 1.94
601 626 2.096811 GTGCATGCAAAAATTCACCACG 60.097 45.455 24.58 0.00 0.00 4.94
640 665 3.862845 AGTCGTGCCAAAACAACAAAATC 59.137 39.130 0.00 0.00 0.00 2.17
676 701 9.593134 AAATGCTTTTGTAAGTAACATGTTCAA 57.407 25.926 15.85 9.85 38.10 2.69
682 707 6.494893 TGTAAGTAACATGTTCAAGGCATC 57.505 37.500 15.85 0.79 31.43 3.91
683 708 6.000840 TGTAAGTAACATGTTCAAGGCATCA 58.999 36.000 15.85 3.32 31.43 3.07
684 709 6.658816 TGTAAGTAACATGTTCAAGGCATCAT 59.341 34.615 15.85 0.00 31.43 2.45
714 739 1.542328 CCACGTCTTCCACCAATGTGA 60.542 52.381 0.00 0.00 45.76 3.58
720 745 3.006940 TCTTCCACCAATGTGATTACGC 58.993 45.455 0.00 0.00 45.76 4.42
722 747 0.376852 CCACCAATGTGATTACGCGG 59.623 55.000 12.47 0.00 45.76 6.46
723 748 1.083489 CACCAATGTGATTACGCGGT 58.917 50.000 12.47 0.00 45.76 5.68
724 749 1.083489 ACCAATGTGATTACGCGGTG 58.917 50.000 12.47 0.00 0.00 4.94
725 750 1.338294 ACCAATGTGATTACGCGGTGA 60.338 47.619 12.47 0.00 0.00 4.02
726 751 1.735018 CCAATGTGATTACGCGGTGAA 59.265 47.619 12.47 1.23 0.00 3.18
727 752 2.354510 CCAATGTGATTACGCGGTGAAT 59.645 45.455 12.47 6.99 0.00 2.57
728 753 3.181501 CCAATGTGATTACGCGGTGAATT 60.182 43.478 12.47 0.00 0.00 2.17
729 754 4.411327 CAATGTGATTACGCGGTGAATTT 58.589 39.130 12.47 0.00 0.00 1.82
730 755 4.695217 ATGTGATTACGCGGTGAATTTT 57.305 36.364 12.47 0.00 0.00 1.82
853 879 6.571150 GCAAAATGCTCCTGATTGTAGAAACT 60.571 38.462 0.00 0.00 40.96 2.66
858 884 4.563580 GCTCCTGATTGTAGAAACTCCACA 60.564 45.833 0.00 0.00 0.00 4.17
982 1008 1.793820 AAACCAGGAGGGGAGCCAAG 61.794 60.000 0.00 0.00 42.91 3.61
1069 1095 3.003173 CCAGCCCCTTCTCCGTCA 61.003 66.667 0.00 0.00 0.00 4.35
1221 1250 2.437343 GGAGTTCGAGAAGCGCGTG 61.437 63.158 8.43 0.00 40.61 5.34
1521 1550 4.874282 TACACGATCGTCGCGGCG 62.874 66.667 29.79 29.79 45.12 6.46
1615 1644 1.132588 GAGCGGCGAATAAGCTACTG 58.867 55.000 12.98 0.00 41.84 2.74
1644 1673 2.500229 TGGTTGATTTTGGTCTCGTCC 58.500 47.619 0.00 0.00 0.00 4.79
1698 1735 1.412710 CCTCCTATAAGTTGCCGAGCA 59.587 52.381 0.00 0.00 36.47 4.26
1721 1758 5.049828 AGTGCTGTAAAAACTGAAATTGCC 58.950 37.500 0.00 0.00 0.00 4.52
1793 1861 2.943036 TTTACCCCACTTCCACACTC 57.057 50.000 0.00 0.00 0.00 3.51
1798 1866 1.675552 CCCACTTCCACACTCGTTTT 58.324 50.000 0.00 0.00 0.00 2.43
1799 1867 1.602377 CCCACTTCCACACTCGTTTTC 59.398 52.381 0.00 0.00 0.00 2.29
1808 1876 6.833342 TCCACACTCGTTTTCTTTTACTAC 57.167 37.500 0.00 0.00 0.00 2.73
1897 1971 1.291877 GCCGTGTGTAGCTGTTGAGG 61.292 60.000 0.00 0.00 0.00 3.86
1899 1973 1.540363 CCGTGTGTAGCTGTTGAGGTT 60.540 52.381 0.00 0.00 0.00 3.50
1928 2002 1.473257 GGCATTGCTACCGAGATGTGA 60.473 52.381 8.82 0.00 0.00 3.58
1937 2011 2.897436 ACCGAGATGTGATGATGTGTG 58.103 47.619 0.00 0.00 0.00 3.82
1958 2032 5.149977 GTGCTTGCACTTGTAGATTTTCTC 58.850 41.667 17.36 0.00 0.00 2.87
1979 2053 3.109619 CTCTCGGATCGTCTTAAACAGC 58.890 50.000 0.00 0.00 0.00 4.40
2018 2092 3.368948 GGACAAACAAGGAGCCAAACAAA 60.369 43.478 0.00 0.00 0.00 2.83
2097 2175 1.325355 GCAGGGGACATGAATGATGG 58.675 55.000 0.00 0.00 36.23 3.51
2121 2203 3.001414 TGTGTCTGCGTAGTCTACTCTC 58.999 50.000 8.37 0.00 0.00 3.20
2133 2215 3.020274 GTCTACTCTCATCCACAGCTCA 58.980 50.000 0.00 0.00 0.00 4.26
2139 2221 0.320683 TCATCCACAGCTCAACCACG 60.321 55.000 0.00 0.00 0.00 4.94
2140 2222 1.672356 ATCCACAGCTCAACCACGC 60.672 57.895 0.00 0.00 0.00 5.34
2141 2223 3.357079 CCACAGCTCAACCACGCC 61.357 66.667 0.00 0.00 0.00 5.68
2142 2224 2.591429 CACAGCTCAACCACGCCA 60.591 61.111 0.00 0.00 0.00 5.69
2143 2225 1.968017 CACAGCTCAACCACGCCAT 60.968 57.895 0.00 0.00 0.00 4.40
2144 2226 1.672356 ACAGCTCAACCACGCCATC 60.672 57.895 0.00 0.00 0.00 3.51
2145 2227 2.045926 AGCTCAACCACGCCATCC 60.046 61.111 0.00 0.00 0.00 3.51
2146 2228 2.359850 GCTCAACCACGCCATCCA 60.360 61.111 0.00 0.00 0.00 3.41
2168 2250 2.659428 AGAGCTGGGCATAATTTCCAC 58.341 47.619 0.00 0.00 0.00 4.02
2293 2375 4.161189 CAGATCACAGGTGGACTTGACTAT 59.839 45.833 0.00 0.00 0.00 2.12
2294 2376 5.360999 CAGATCACAGGTGGACTTGACTATA 59.639 44.000 0.00 0.00 0.00 1.31
2307 2389 2.871133 TGACTATAACGCACAAGACGG 58.129 47.619 0.00 0.00 34.00 4.79
2342 2440 2.351157 GCTGCTGCTTACTTTTCCACTG 60.351 50.000 8.53 0.00 36.03 3.66
2344 2442 1.608590 GCTGCTTACTTTTCCACTGCA 59.391 47.619 0.00 0.00 0.00 4.41
2349 2447 3.005791 GCTTACTTTTCCACTGCACCATT 59.994 43.478 0.00 0.00 0.00 3.16
2376 2474 2.258286 GGCAATGCCGAACACACC 59.742 61.111 9.14 0.00 39.62 4.16
2537 2644 1.867233 CGTATCCCATCTGCTTTTCCG 59.133 52.381 0.00 0.00 0.00 4.30
2556 2663 1.265905 CGGACCAACAACTAGGCAAAC 59.734 52.381 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.622811 GGGATGCCATGTTTGGTTTCA 59.377 47.619 0.00 0.00 45.57 2.69
102 103 9.331106 GCAGATAGTTTAGCTAAGTTTTTCAAC 57.669 33.333 6.24 0.00 32.72 3.18
106 107 9.508642 AGAAGCAGATAGTTTAGCTAAGTTTTT 57.491 29.630 6.24 0.00 36.07 1.94
152 153 9.662545 CCAATTTTAACTGCAAATTTACCTTTG 57.337 29.630 0.00 0.00 38.79 2.77
161 162 5.488262 AGGAGCCAATTTTAACTGCAAAT 57.512 34.783 0.00 0.00 0.00 2.32
179 180 0.676151 GGAGACCAAGCAGCAAGGAG 60.676 60.000 9.93 0.00 0.00 3.69
181 182 3.993535 GGAGACCAAGCAGCAAGG 58.006 61.111 0.00 0.00 0.00 3.61
220 221 4.125703 GAGATACATGAAGGCACAAGGAG 58.874 47.826 0.00 0.00 0.00 3.69
221 222 3.118261 GGAGATACATGAAGGCACAAGGA 60.118 47.826 0.00 0.00 0.00 3.36
222 223 3.118112 AGGAGATACATGAAGGCACAAGG 60.118 47.826 0.00 0.00 0.00 3.61
223 224 4.148128 AGGAGATACATGAAGGCACAAG 57.852 45.455 0.00 0.00 0.00 3.16
224 225 4.019411 TCAAGGAGATACATGAAGGCACAA 60.019 41.667 0.00 0.00 0.00 3.33
225 226 3.519107 TCAAGGAGATACATGAAGGCACA 59.481 43.478 0.00 0.00 0.00 4.57
226 227 4.142609 TCAAGGAGATACATGAAGGCAC 57.857 45.455 0.00 0.00 0.00 5.01
227 228 6.499106 TTATCAAGGAGATACATGAAGGCA 57.501 37.500 0.00 0.00 38.90 4.75
228 229 7.992754 AATTATCAAGGAGATACATGAAGGC 57.007 36.000 0.00 0.00 38.90 4.35
229 230 8.295288 GCAAATTATCAAGGAGATACATGAAGG 58.705 37.037 0.00 0.00 38.90 3.46
230 231 9.064706 AGCAAATTATCAAGGAGATACATGAAG 57.935 33.333 0.00 0.00 38.90 3.02
231 232 8.985315 AGCAAATTATCAAGGAGATACATGAA 57.015 30.769 0.00 0.00 38.90 2.57
232 233 8.985315 AAGCAAATTATCAAGGAGATACATGA 57.015 30.769 0.00 0.00 38.90 3.07
233 234 8.013947 CGAAGCAAATTATCAAGGAGATACATG 58.986 37.037 0.00 0.00 38.90 3.21
234 235 8.092521 CGAAGCAAATTATCAAGGAGATACAT 57.907 34.615 0.00 0.00 38.90 2.29
235 236 7.482654 CGAAGCAAATTATCAAGGAGATACA 57.517 36.000 0.00 0.00 38.90 2.29
297 298 9.646427 TGCAAGGCGTTTATAAAGATTTTTATT 57.354 25.926 6.55 0.00 39.55 1.40
298 299 9.816354 ATGCAAGGCGTTTATAAAGATTTTTAT 57.184 25.926 6.49 6.49 41.27 1.40
299 300 9.646427 AATGCAAGGCGTTTATAAAGATTTTTA 57.354 25.926 0.00 0.00 33.67 1.52
363 364 1.133823 TCAGGCCAGCTGAAACTTTGA 60.134 47.619 17.39 7.20 0.00 2.69
381 382 5.163405 GGCCACATCTAAGTACAGAATCTCA 60.163 44.000 0.00 0.00 0.00 3.27
411 412 6.489700 AGAACATTGGTGTGTCATTACAATCA 59.510 34.615 0.00 0.00 38.92 2.57
432 433 9.489084 AATTGGGAGCTTAAAAATAACAAGAAC 57.511 29.630 0.00 0.00 0.00 3.01
443 444 6.001460 TCGAGAGAAAATTGGGAGCTTAAAA 58.999 36.000 0.00 0.00 37.03 1.52
551 576 9.743057 CAAAGATTTGTTAAAGTATGTCACCAA 57.257 29.630 0.00 0.00 33.59 3.67
573 598 5.452944 GTGAATTTTTGCATGCACAACAAAG 59.547 36.000 22.58 0.00 34.97 2.77
592 617 4.635765 CACCTATGTGATTTCGTGGTGAAT 59.364 41.667 0.00 0.00 45.76 2.57
622 647 5.466393 AGCTATGATTTTGTTGTTTTGGCAC 59.534 36.000 0.00 0.00 0.00 5.01
699 724 3.006940 GCGTAATCACATTGGTGGAAGA 58.993 45.455 0.00 0.00 45.32 2.87
714 739 3.290308 TGCAAAAATTCACCGCGTAAT 57.710 38.095 4.92 0.00 0.00 1.89
720 745 2.133553 TGTGCATGCAAAAATTCACCG 58.866 42.857 24.58 0.00 0.00 4.94
722 747 4.533225 TGTTGTGCATGCAAAAATTCAC 57.467 36.364 24.69 13.31 0.00 3.18
723 748 5.106436 TGTTTGTTGTGCATGCAAAAATTCA 60.106 32.000 24.69 15.62 34.47 2.57
724 749 5.330295 TGTTTGTTGTGCATGCAAAAATTC 58.670 33.333 24.69 13.18 34.47 2.17
725 750 5.306532 TGTTTGTTGTGCATGCAAAAATT 57.693 30.435 24.69 0.00 34.47 1.82
726 751 4.959596 TGTTTGTTGTGCATGCAAAAAT 57.040 31.818 24.69 0.00 34.47 1.82
727 752 4.959596 ATGTTTGTTGTGCATGCAAAAA 57.040 31.818 24.69 17.76 34.47 1.94
728 753 4.959596 AATGTTTGTTGTGCATGCAAAA 57.040 31.818 24.58 21.90 34.47 2.44
729 754 4.659088 CAAATGTTTGTTGTGCATGCAAA 58.341 34.783 24.58 15.92 33.59 3.68
730 755 4.274421 CAAATGTTTGTTGTGCATGCAA 57.726 36.364 24.58 10.26 33.59 4.08
814 840 3.493176 GCATTTTGCTCCTGGTTTGAACT 60.493 43.478 0.00 0.00 40.96 3.01
842 868 3.370527 CGGGGATGTGGAGTTTCTACAAT 60.371 47.826 0.00 0.00 41.18 2.71
843 869 2.027561 CGGGGATGTGGAGTTTCTACAA 60.028 50.000 0.00 0.00 41.18 2.41
853 879 0.986019 ATTGTAGGCGGGGATGTGGA 60.986 55.000 0.00 0.00 0.00 4.02
858 884 0.923358 TGGAAATTGTAGGCGGGGAT 59.077 50.000 0.00 0.00 0.00 3.85
1221 1250 3.123620 CGGGACTTCAGCTGCAGC 61.124 66.667 31.53 31.53 42.49 5.25
1467 1496 2.746277 GGCGCCTGGTGGTACTTG 60.746 66.667 22.15 0.00 35.27 3.16
1521 1550 2.025418 CTTGACGTACACGGTGCCC 61.025 63.158 8.30 0.00 44.95 5.36
1615 1644 3.321968 ACCAAAATCAACCAAGAAGAGCC 59.678 43.478 0.00 0.00 0.00 4.70
1644 1673 5.811399 TTACAAAATGGAAGCATCCTACG 57.189 39.130 9.78 0.00 46.70 3.51
1684 1716 0.036010 AGCACTGCTCGGCAACTTAT 60.036 50.000 0.00 0.00 38.41 1.73
1685 1717 0.950555 CAGCACTGCTCGGCAACTTA 60.951 55.000 0.00 0.00 38.41 2.24
1686 1718 2.111878 AGCACTGCTCGGCAACTT 59.888 55.556 0.00 0.00 38.41 2.66
1698 1735 5.049828 GGCAATTTCAGTTTTTACAGCACT 58.950 37.500 0.00 0.00 0.00 4.40
1721 1758 3.595709 TTTTTGAACTCGCGTGGTTAG 57.404 42.857 13.32 1.28 0.00 2.34
1744 1781 5.353123 GGTCAGGCGATTGTAAGAAAACATA 59.647 40.000 0.00 0.00 0.00 2.29
1779 1822 1.602377 GAAAACGAGTGTGGAAGTGGG 59.398 52.381 0.00 0.00 0.00 4.61
1793 1861 7.325338 TCTCATCTCACGTAGTAAAAGAAAACG 59.675 37.037 0.00 0.00 41.61 3.60
1798 1866 8.051901 TCAATCTCATCTCACGTAGTAAAAGA 57.948 34.615 0.00 0.00 41.61 2.52
1799 1867 8.689251 TTCAATCTCATCTCACGTAGTAAAAG 57.311 34.615 0.00 0.00 41.61 2.27
1808 1876 6.898716 CGAAAGAAATTCAATCTCATCTCACG 59.101 38.462 0.00 0.00 37.96 4.35
1897 1971 4.188462 GGTAGCAATGCCCCAAAAATAAC 58.812 43.478 0.00 0.00 0.00 1.89
1899 1973 2.428890 CGGTAGCAATGCCCCAAAAATA 59.571 45.455 0.00 0.00 0.00 1.40
1937 2011 5.411053 AGAGAGAAAATCTACAAGTGCAAGC 59.589 40.000 0.00 0.00 38.84 4.01
1958 2032 3.109619 GCTGTTTAAGACGATCCGAGAG 58.890 50.000 0.00 0.00 0.00 3.20
2003 2077 0.385390 AGCGTTTGTTTGGCTCCTTG 59.615 50.000 0.00 0.00 29.31 3.61
2004 2078 0.385390 CAGCGTTTGTTTGGCTCCTT 59.615 50.000 0.00 0.00 34.13 3.36
2005 2079 2.032981 CAGCGTTTGTTTGGCTCCT 58.967 52.632 0.00 0.00 34.13 3.69
2018 2092 4.681978 GAGGACCAACGGCAGCGT 62.682 66.667 0.00 0.00 0.00 5.07
2058 2136 1.308998 GTTGGGCAGAATATGGTCCG 58.691 55.000 0.00 0.00 0.00 4.79
2089 2167 1.129251 CGCAGACACACACCATCATTC 59.871 52.381 0.00 0.00 0.00 2.67
2097 2175 2.225963 AGTAGACTACGCAGACACACAC 59.774 50.000 6.98 0.00 0.00 3.82
2121 2203 1.915614 GCGTGGTTGAGCTGTGGATG 61.916 60.000 0.00 0.00 0.00 3.51
2133 2215 1.244019 GCTCTTTGGATGGCGTGGTT 61.244 55.000 0.00 0.00 0.00 3.67
2139 2221 2.421399 GCCCAGCTCTTTGGATGGC 61.421 63.158 0.00 0.00 40.99 4.40
2140 2222 0.396695 ATGCCCAGCTCTTTGGATGG 60.397 55.000 0.00 0.00 40.87 3.51
2141 2223 2.353357 TATGCCCAGCTCTTTGGATG 57.647 50.000 0.00 0.00 40.87 3.51
2142 2224 3.607490 ATTATGCCCAGCTCTTTGGAT 57.393 42.857 0.00 0.00 40.87 3.41
2143 2225 3.386932 AATTATGCCCAGCTCTTTGGA 57.613 42.857 0.00 0.00 40.87 3.53
2144 2226 3.181472 GGAAATTATGCCCAGCTCTTTGG 60.181 47.826 0.00 0.00 38.00 3.28
2145 2227 3.448301 TGGAAATTATGCCCAGCTCTTTG 59.552 43.478 0.00 0.00 0.00 2.77
2146 2228 3.448660 GTGGAAATTATGCCCAGCTCTTT 59.551 43.478 0.00 0.00 0.00 2.52
2228 2310 1.487482 CGACGATGCGTATCATTGGT 58.513 50.000 14.06 3.01 41.37 3.67
2293 2375 1.004320 ATGCCCGTCTTGTGCGTTA 60.004 52.632 0.00 0.00 0.00 3.18
2294 2376 2.281484 ATGCCCGTCTTGTGCGTT 60.281 55.556 0.00 0.00 0.00 4.84
2307 2389 0.537600 AGCAGCTCATGATGGATGCC 60.538 55.000 18.34 4.64 34.24 4.40
2368 2466 1.219646 TAAAAGTCCGCGGTGTGTTC 58.780 50.000 27.15 9.74 0.00 3.18
2376 2474 1.326245 TGCATCGAATAAAAGTCCGCG 59.674 47.619 0.00 0.00 0.00 6.46
2510 2608 0.038526 CAGATGGGATACGGTACCGC 60.039 60.000 33.62 17.59 44.19 5.68
2511 2609 0.038526 GCAGATGGGATACGGTACCG 60.039 60.000 32.22 32.22 46.03 4.02
2512 2610 1.339097 AGCAGATGGGATACGGTACC 58.661 55.000 0.16 0.16 37.60 3.34
2537 2644 2.583143 AGTTTGCCTAGTTGTTGGTCC 58.417 47.619 0.00 0.00 0.00 4.46
2556 2663 8.635877 ATTAAAGCGACTTGTCTTCACTATAG 57.364 34.615 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.