Multiple sequence alignment - TraesCS7A01G187400

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 TraesCS7A01G187400 chr7A 100.000 2462 0 0 1 2462 143038795 143041256 0.000000e+00 4547
1 TraesCS7A01G187400 chr7A 93.433 335 22 0 2002 2336 143040742 143041076 4.730000e-137 497
2 TraesCS7A01G187400 chr7A 93.433 335 22 0 1948 2282 143040796 143041130 4.730000e-137 497
3 TraesCS7A01G187400 chr7A 91.901 284 23 0 2053 2336 143040739 143041022 4.930000e-107 398
4 TraesCS7A01G187400 chr7A 91.901 284 23 0 1945 2228 143040847 143041130 4.930000e-107 398
5 TraesCS7A01G187400 chr7A 90.870 230 21 0 2107 2336 143040739 143040968 2.380000e-80 309
6 TraesCS7A01G187400 chr7A 90.870 230 21 0 1945 2174 143040901 143041130 2.380000e-80 309
7 TraesCS7A01G187400 chr7A 91.860 172 14 0 2165 2336 143040743 143040914 8.800000e-60 241
8 TraesCS7A01G187400 chr7A 91.860 172 14 0 1949 2120 143040959 143041130 8.800000e-60 241
9 TraesCS7A01G187400 chr2B 95.035 866 41 1 876 1739 783011468 783012333 0.000000e+00 1360
10 TraesCS7A01G187400 chr2B 90.625 416 37 2 1734 2147 783064373 783064788 3.580000e-153 551
11 TraesCS7A01G187400 chr2B 82.133 347 35 7 2116 2462 783064595 783064914 3.120000e-69 272
12 TraesCS7A01G187400 chr6D 83.305 1168 132 38 290 1424 4692007 4693144 0.000000e+00 1018
13 TraesCS7A01G187400 chr6D 93.478 92 4 1 756 847 4692508 4692597 4.270000e-28 135
14 TraesCS7A01G187400 chr6B 91.311 702 47 4 756 1455 213159212 213159901 0.000000e+00 946
15 TraesCS7A01G187400 chr6B 88.576 639 58 7 90 727 213158511 213159135 0.000000e+00 761
16 TraesCS7A01G187400 chr6B 86.288 299 33 5 751 1044 472717774 472717479 3.950000e-83 318
17 TraesCS7A01G187400 chr3D 90.368 571 50 4 9 579 548232544 548233109 0.000000e+00 745
18 TraesCS7A01G187400 chr3D 87.601 621 72 4 1 621 548210374 548210989 0.000000e+00 715
19 TraesCS7A01G187400 chr3B 81.010 990 121 38 90 1044 534249275 534250232 0.000000e+00 725
20 TraesCS7A01G187400 chr4B 80.982 815 135 13 909 1712 497106827 497106022 1.610000e-176 628
21 TraesCS7A01G187400 chr4B 79.434 530 99 9 926 1451 14908121 14907598 1.390000e-97 366
22 TraesCS7A01G187400 chr7D 75.665 752 133 38 1203 1932 402554089 402553366 1.830000e-86 329
23 TraesCS7A01G187400 chrUn 82.105 285 51 0 2010 2294 53003071 53003355 6.800000e-61 244
24 TraesCS7A01G187400 chrUn 81.319 273 51 0 2064 2336 53003071 53003343 3.190000e-54 222
25 TraesCS7A01G187400 chrUn 83.889 180 29 0 1953 2132 53003176 53003355 3.260000e-39 172
26 TraesCS7A01G187400 chr7B 83.333 180 26 3 926 1104 603625954 603626130 1.960000e-36 163


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 TraesCS7A01G187400 chr7A 143038795 143041256 2461 False 826.333333 4547 92.903111 1 2462 9 chr7A.!!$F1 2461
1 TraesCS7A01G187400 chr2B 783011468 783012333 865 False 1360.000000 1360 95.035000 876 1739 1 chr2B.!!$F1 863
2 TraesCS7A01G187400 chr2B 783064373 783064914 541 False 411.500000 551 86.379000 1734 2462 2 chr2B.!!$F2 728
3 TraesCS7A01G187400 chr6D 4692007 4693144 1137 False 576.500000 1018 88.391500 290 1424 2 chr6D.!!$F1 1134
4 TraesCS7A01G187400 chr6B 213158511 213159901 1390 False 853.500000 946 89.943500 90 1455 2 chr6B.!!$F1 1365
5 TraesCS7A01G187400 chr3D 548232544 548233109 565 False 745.000000 745 90.368000 9 579 1 chr3D.!!$F2 570
6 TraesCS7A01G187400 chr3D 548210374 548210989 615 False 715.000000 715 87.601000 1 621 1 chr3D.!!$F1 620
7 TraesCS7A01G187400 chr3B 534249275 534250232 957 False 725.000000 725 81.010000 90 1044 1 chr3B.!!$F1 954
8 TraesCS7A01G187400 chr4B 497106022 497106827 805 True 628.000000 628 80.982000 909 1712 1 chr4B.!!$R2 803
9 TraesCS7A01G187400 chr4B 14907598 14908121 523 True 366.000000 366 79.434000 926 1451 1 chr4B.!!$R1 525
10 TraesCS7A01G187400 chr7D 402553366 402554089 723 True 329.000000 329 75.665000 1203 1932 1 chr7D.!!$R1 729

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
746 802 0.027979 CCAGACAATATGGCGTTGCG 59.972 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1835 0.035056 AGCTGGACCCATGTAACTGC 60.035 55.0 0.0 0.0 0.0 4.4 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
81 82 2.106857 GGATCTCGTCCTCCTCCTCTAA 59.893 54.545 0.00 0.00 44.16 2.10
83 84 1.914108 TCTCGTCCTCCTCCTCTAACA 59.086 52.381 0.00 0.00 0.00 2.41
141 143 0.252284 TTCCCCCTTCTCTCTTCGCT 60.252 55.000 0.00 0.00 0.00 4.93
148 150 3.193691 CCCTTCTCTCTTCGCTTGTTCTA 59.806 47.826 0.00 0.00 0.00 2.10
184 186 0.662619 CGTTTCTGCCTGTCTTGCAA 59.337 50.000 0.00 0.00 38.46 4.08
185 187 1.267806 CGTTTCTGCCTGTCTTGCAAT 59.732 47.619 0.00 0.00 38.46 3.56
192 194 1.619654 CCTGTCTTGCAATTGGGTCA 58.380 50.000 7.72 0.00 0.00 4.02
217 219 1.517832 CGGCGGAGGATCTGTCTTT 59.482 57.895 0.00 0.00 46.05 2.52
265 268 3.139077 GGCCCAGGTAGTTATTTGATCG 58.861 50.000 0.00 0.00 0.00 3.69
278 281 0.958091 TTGATCGGTTGTTTGCCTGG 59.042 50.000 0.00 0.00 0.00 4.45
279 282 0.893270 TGATCGGTTGTTTGCCTGGG 60.893 55.000 0.00 0.00 0.00 4.45
284 287 1.299850 GTTGTTTGCCTGGGCGTTC 60.300 57.895 7.14 0.70 45.51 3.95
297 300 0.384230 GGCGTTCGTGATGTGTTGTG 60.384 55.000 0.00 0.00 0.00 3.33
313 322 3.321648 TGCGGGTGCTGGACTGAT 61.322 61.111 0.00 0.00 43.34 2.90
316 325 1.648467 GCGGGTGCTGGACTGATTTC 61.648 60.000 0.00 0.00 38.39 2.17
317 326 1.026718 CGGGTGCTGGACTGATTTCC 61.027 60.000 0.00 0.00 36.03 3.13
318 327 0.681243 GGGTGCTGGACTGATTTCCC 60.681 60.000 0.00 0.00 34.33 3.97
319 328 0.681243 GGTGCTGGACTGATTTCCCC 60.681 60.000 0.00 0.00 34.33 4.81
320 329 0.681243 GTGCTGGACTGATTTCCCCC 60.681 60.000 0.00 0.00 34.33 5.40
422 432 4.063967 CCGCTGCTGGTGTACGGA 62.064 66.667 0.00 0.00 46.71 4.69
423 433 2.809601 CGCTGCTGGTGTACGGAC 60.810 66.667 0.00 0.00 0.00 4.79
453 463 1.546029 GGTTTCCTTGCAGGTGATTCC 59.454 52.381 0.00 0.00 36.53 3.01
462 472 2.292126 TGCAGGTGATTCCTCTCTCTCT 60.292 50.000 0.00 0.00 46.24 3.10
463 473 2.362077 GCAGGTGATTCCTCTCTCTCTC 59.638 54.545 0.00 0.00 46.24 3.20
517 557 6.620877 AAAGGGATATGTGTTGTAGTCTGA 57.379 37.500 0.00 0.00 0.00 3.27
529 569 6.366332 GTGTTGTAGTCTGATAGTTCTTGGTG 59.634 42.308 0.00 0.00 0.00 4.17
531 571 6.665992 TGTAGTCTGATAGTTCTTGGTGTT 57.334 37.500 0.00 0.00 0.00 3.32
579 619 3.044235 TGCAGTCTGGTGATAGTTGTG 57.956 47.619 1.14 0.00 0.00 3.33
582 622 4.466015 TGCAGTCTGGTGATAGTTGTGATA 59.534 41.667 1.14 0.00 0.00 2.15
587 627 6.156949 AGTCTGGTGATAGTTGTGATATGGTT 59.843 38.462 0.00 0.00 0.00 3.67
655 695 2.637947 GGTGTGGCCATTTTGTTTTGT 58.362 42.857 9.72 0.00 37.17 2.83
659 699 3.196469 TGTGGCCATTTTGTTTTGTCTGA 59.804 39.130 9.72 0.00 0.00 3.27
661 701 4.211794 GTGGCCATTTTGTTTTGTCTGATG 59.788 41.667 9.72 0.00 0.00 3.07
662 702 3.187022 GGCCATTTTGTTTTGTCTGATGC 59.813 43.478 0.00 0.00 0.00 3.91
690 730 4.115401 TGCAGACAAGATAGCAGTACTG 57.885 45.455 18.93 18.93 32.48 2.74
692 732 4.109050 GCAGACAAGATAGCAGTACTGTC 58.891 47.826 23.44 15.50 36.80 3.51
697 737 4.711846 ACAAGATAGCAGTACTGTCATGGA 59.288 41.667 23.44 4.19 38.93 3.41
698 738 5.187772 ACAAGATAGCAGTACTGTCATGGAA 59.812 40.000 23.44 3.08 38.93 3.53
707 747 6.294176 GCAGTACTGTCATGGAATTTCAGTTT 60.294 38.462 23.44 0.00 38.23 2.66
735 791 1.895798 TCTTCTGCTCGTCCAGACAAT 59.104 47.619 7.16 0.00 41.28 2.71
738 794 3.443099 TCTGCTCGTCCAGACAATATG 57.557 47.619 4.14 0.00 36.96 1.78
742 798 0.821517 TCGTCCAGACAATATGGCGT 59.178 50.000 0.00 0.00 38.04 5.68
746 802 0.027979 CCAGACAATATGGCGTTGCG 59.972 55.000 0.00 0.00 0.00 4.85
748 804 1.599071 CAGACAATATGGCGTTGCGAT 59.401 47.619 0.00 0.00 0.00 4.58
749 805 1.599071 AGACAATATGGCGTTGCGATG 59.401 47.619 0.00 0.00 0.00 3.84
777 833 1.780503 AGCATCCTTATTGGTTGGCC 58.219 50.000 0.00 0.00 36.33 5.36
779 835 2.513738 AGCATCCTTATTGGTTGGCCTA 59.486 45.455 3.32 0.00 36.33 3.93
793 880 4.566488 GGTTGGCCTATATGCTCTTATGCT 60.566 45.833 3.32 0.00 0.00 3.79
847 934 4.380531 CAAGGTCACATGTGTAGTTCAGT 58.619 43.478 24.63 1.88 0.00 3.41
848 935 5.538118 CAAGGTCACATGTGTAGTTCAGTA 58.462 41.667 24.63 0.00 0.00 2.74
869 956 4.634012 ACTGTACATACTGCAAGGGAAA 57.366 40.909 0.00 0.00 39.30 3.13
906 993 7.462571 TCTGTTTTCTTATTTAAAGGGCCTC 57.537 36.000 6.46 0.00 0.00 4.70
907 994 7.238710 TCTGTTTTCTTATTTAAAGGGCCTCT 58.761 34.615 6.46 0.00 0.00 3.69
942 1029 4.578928 TGAAGGTCTAACTTTTGTCCTTGC 59.421 41.667 6.66 1.72 33.50 4.01
946 1033 4.578928 GGTCTAACTTTTGTCCTTGCTTGA 59.421 41.667 0.00 0.00 0.00 3.02
1007 1099 1.774110 TGTGTTGGCAGGATGTTTGT 58.226 45.000 0.00 0.00 39.31 2.83
1376 1480 1.317613 TCTGTTGTTGGTGGTGATGC 58.682 50.000 0.00 0.00 0.00 3.91
1403 1507 0.602638 GCTGTGGGTGACGTCAATGA 60.603 55.000 21.95 3.49 0.00 2.57
1415 1519 0.804364 GTCAATGATGCTTCACGGCA 59.196 50.000 4.14 0.00 46.63 5.69
1506 1610 5.941647 GTGTTATCTTTGGGGTTGTTAGCTA 59.058 40.000 0.00 0.00 0.00 3.32
1531 1635 7.783042 AGTAGTTGTTTCTTTACTGAGTCTGT 58.217 34.615 7.86 7.86 0.00 3.41
1712 1835 0.443869 GCCTGACGTTATGCTGTGTG 59.556 55.000 0.29 0.00 0.00 3.82
1750 1873 5.335191 CCAGCTTCTTATTTGTCCAGTGTTC 60.335 44.000 0.00 0.00 0.00 3.18
1779 1903 2.098934 TGTTGTCTGGTTGTTGACATGC 59.901 45.455 0.00 0.00 41.93 4.06
1786 1910 1.225855 GTTGTTGACATGCCTCGTGA 58.774 50.000 0.00 0.00 0.00 4.35
1850 1974 0.107848 GGTTGATAGGTGGTCGTGGG 60.108 60.000 0.00 0.00 0.00 4.61
1851 1975 0.743345 GTTGATAGGTGGTCGTGGGC 60.743 60.000 0.00 0.00 0.00 5.36
1852 1976 2.106332 GATAGGTGGTCGTGGGCG 59.894 66.667 0.00 0.00 39.92 6.13
1853 1977 2.682494 ATAGGTGGTCGTGGGCGT 60.682 61.111 0.00 0.00 39.49 5.68
1854 1978 2.901051 GATAGGTGGTCGTGGGCGTG 62.901 65.000 0.00 0.00 39.49 5.34
1916 2048 2.483188 CCGTGGAGGTTCTAATACAGGC 60.483 54.545 0.00 0.00 34.51 4.85
1936 2068 1.150536 GTGCCCCTGTTTCTGGTCA 59.849 57.895 0.00 0.00 0.00 4.02
1950 2082 1.448540 GGTCATGTCTCTGGCCGTG 60.449 63.158 0.00 0.00 29.80 4.94
1998 2130 4.182433 GAGCCCAGCCAGTAGCCC 62.182 72.222 0.00 0.00 45.47 5.19
2052 2184 2.203126 GATCCCAGCCAGAAGCCG 60.203 66.667 0.00 0.00 45.47 5.52
2053 2185 3.764160 GATCCCAGCCAGAAGCCGG 62.764 68.421 0.00 0.00 45.47 6.13
2096 2228 4.845580 CCTGCCGCTGGTGCCTAG 62.846 72.222 8.11 0.00 35.36 3.02
2104 2236 1.144936 CTGGTGCCTAGCCAGTAGC 59.855 63.158 6.70 0.00 46.22 3.58
2105 2237 2.317149 CTGGTGCCTAGCCAGTAGCC 62.317 65.000 6.70 0.00 46.22 3.93
2106 2238 2.107141 GTGCCTAGCCAGTAGCCG 59.893 66.667 0.00 0.00 45.47 5.52
2107 2239 3.154473 TGCCTAGCCAGTAGCCGG 61.154 66.667 0.00 0.00 45.47 6.13
2108 2240 3.930012 GCCTAGCCAGTAGCCGGG 61.930 72.222 2.18 0.00 45.47 5.73
2115 2247 4.514577 CAGTAGCCGGGCGTGGAG 62.515 72.222 14.39 0.04 0.00 3.86
2150 2282 4.845580 CCTGCCGCTGGTGCCTAG 62.846 72.222 8.11 0.00 35.36 3.02
2158 2290 1.144936 CTGGTGCCTAGCCAGTAGC 59.855 63.158 6.70 0.00 46.22 3.58
2159 2291 2.317149 CTGGTGCCTAGCCAGTAGCC 62.317 65.000 6.70 0.00 46.22 3.93
2160 2292 2.107141 GTGCCTAGCCAGTAGCCG 59.893 66.667 0.00 0.00 45.47 5.52
2161 2293 3.154473 TGCCTAGCCAGTAGCCGG 61.154 66.667 0.00 0.00 45.47 6.13
2162 2294 3.930012 GCCTAGCCAGTAGCCGGG 61.930 72.222 2.18 0.00 45.47 5.73
2163 2295 2.444140 CCTAGCCAGTAGCCGGGT 60.444 66.667 12.58 12.58 45.47 5.28
2164 2296 2.797278 CCTAGCCAGTAGCCGGGTG 61.797 68.421 18.40 0.00 45.47 4.61
2165 2297 2.038329 TAGCCAGTAGCCGGGTGT 59.962 61.111 18.40 0.00 45.47 4.16
2166 2298 2.298158 CTAGCCAGTAGCCGGGTGTG 62.298 65.000 18.40 13.52 45.47 3.82
2167 2299 4.778143 GCCAGTAGCCGGGTGTGG 62.778 72.222 25.26 25.26 34.35 4.17
2168 2300 4.096003 CCAGTAGCCGGGTGTGGG 62.096 72.222 23.00 14.79 0.00 4.61
2169 2301 4.096003 CAGTAGCCGGGTGTGGGG 62.096 72.222 18.40 0.00 0.00 4.96
2190 2322 4.087892 CTGCTCGGTGGGTCCCTG 62.088 72.222 10.00 0.00 0.00 4.45
2264 2396 3.646715 GGTGGTGCCCAGCCAGTA 61.647 66.667 11.14 0.00 45.22 2.74
2265 2397 2.045926 GTGGTGCCCAGCCAGTAG 60.046 66.667 0.00 0.00 36.57 2.57
2266 2398 4.033776 TGGTGCCCAGCCAGTAGC 62.034 66.667 0.00 0.00 44.25 3.58
2267 2399 4.803908 GGTGCCCAGCCAGTAGCC 62.804 72.222 0.00 0.00 45.47 3.93
2319 2451 2.045926 CTGGTGCCCAGCCAGTAC 60.046 66.667 8.11 0.00 45.13 2.73
2320 2452 3.628646 CTGGTGCCCAGCCAGTACC 62.629 68.421 8.11 0.00 45.13 3.34
2321 2453 4.426313 GGTGCCCAGCCAGTACCC 62.426 72.222 0.00 0.00 34.23 3.69
2322 2454 4.778143 GTGCCCAGCCAGTACCCG 62.778 72.222 0.00 0.00 0.00 5.28
2342 2474 4.764771 CATGGGGGTGCACCTGGG 62.765 72.222 33.91 16.02 40.03 4.45
2405 2537 3.261951 CGTTATGTGCCTCGCCGG 61.262 66.667 0.00 0.00 0.00 6.13
2432 2564 1.071857 GGGTTTCCTTCTTCTGGACGT 59.928 52.381 0.00 0.00 32.65 4.34
2434 2566 1.531578 GTTTCCTTCTTCTGGACGTGC 59.468 52.381 0.00 0.00 32.65 5.34
2435 2567 0.319555 TTCCTTCTTCTGGACGTGCG 60.320 55.000 1.60 0.00 32.65 5.34
2447 2579 2.803670 CGTGCGTGTACGTCCCTG 60.804 66.667 6.27 0.00 42.22 4.45
2454 2586 1.473677 CGTGTACGTCCCTGTCCATTA 59.526 52.381 0.00 0.00 34.11 1.90
2457 2589 1.117150 TACGTCCCTGTCCATTAGCC 58.883 55.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 2.600769 AGGAGGACGAACGGCTGT 60.601 61.111 0.00 0.00 0.00 4.40
83 84 3.441290 CGAGGAGGACGAACGGCT 61.441 66.667 0.00 0.00 0.00 5.52
141 143 5.407407 AAGAGAAGAGGCGAATAGAACAA 57.593 39.130 0.00 0.00 0.00 2.83
148 150 3.870633 AACGTAAGAGAAGAGGCGAAT 57.129 42.857 0.00 0.00 43.62 3.34
238 241 2.561209 TAACTACCTGGGCCATCTCA 57.439 50.000 6.72 0.00 0.00 3.27
265 268 2.693250 GAACGCCCAGGCAAACAACC 62.693 60.000 9.78 0.00 42.06 3.77
278 281 0.384230 CACAACACATCACGAACGCC 60.384 55.000 0.00 0.00 0.00 5.68
279 282 0.991770 GCACAACACATCACGAACGC 60.992 55.000 0.00 0.00 0.00 4.84
284 287 2.250939 ACCCGCACAACACATCACG 61.251 57.895 0.00 0.00 0.00 4.35
297 300 1.648467 GAAATCAGTCCAGCACCCGC 61.648 60.000 0.00 0.00 38.99 6.13
318 327 0.403271 CCTAAGCAGATCCATGGGGG 59.597 60.000 13.02 0.01 38.37 5.40
319 328 1.143813 ACCTAAGCAGATCCATGGGG 58.856 55.000 13.02 3.99 0.00 4.96
320 329 3.303351 AAACCTAAGCAGATCCATGGG 57.697 47.619 13.02 0.00 0.00 4.00
418 427 1.745320 AAACCAGCGAGACAGTCCGT 61.745 55.000 11.55 0.00 0.00 4.69
422 432 0.759346 AAGGAAACCAGCGAGACAGT 59.241 50.000 0.00 0.00 0.00 3.55
423 433 1.151668 CAAGGAAACCAGCGAGACAG 58.848 55.000 0.00 0.00 0.00 3.51
453 463 2.489275 GGCCAGGCGAGAGAGAGAG 61.489 68.421 5.00 0.00 0.00 3.20
540 580 5.698089 ACTGCAACTATCATCAATATCCGTG 59.302 40.000 0.00 0.00 0.00 4.94
541 581 5.858381 ACTGCAACTATCATCAATATCCGT 58.142 37.500 0.00 0.00 0.00 4.69
542 582 6.090493 CAGACTGCAACTATCATCAATATCCG 59.910 42.308 0.00 0.00 0.00 4.18
551 591 4.767578 ATCACCAGACTGCAACTATCAT 57.232 40.909 0.00 0.00 0.00 2.45
582 622 9.965824 CTTCTAAAAGACAACAACAATAACCAT 57.034 29.630 0.00 0.00 34.14 3.55
587 627 6.775629 AGCCCTTCTAAAAGACAACAACAATA 59.224 34.615 0.00 0.00 34.14 1.90
597 637 4.855715 AGCAAAAGCCCTTCTAAAAGAC 57.144 40.909 0.00 0.00 34.14 3.01
642 682 4.634199 AGGCATCAGACAAAACAAAATGG 58.366 39.130 0.00 0.00 0.00 3.16
655 695 4.961438 TGTCTGCATATAAGGCATCAGA 57.039 40.909 3.26 0.00 41.06 3.27
659 699 5.879223 GCTATCTTGTCTGCATATAAGGCAT 59.121 40.000 8.41 0.04 41.06 4.40
661 701 5.240891 TGCTATCTTGTCTGCATATAAGGC 58.759 41.667 8.41 5.42 0.00 4.35
662 702 6.462500 ACTGCTATCTTGTCTGCATATAAGG 58.538 40.000 8.41 0.00 34.79 2.69
697 737 9.822185 AGCAGAAGAAAATACAAAACTGAAATT 57.178 25.926 0.00 0.00 0.00 1.82
698 738 9.468532 GAGCAGAAGAAAATACAAAACTGAAAT 57.531 29.630 0.00 0.00 0.00 2.17
707 747 4.637276 TGGACGAGCAGAAGAAAATACAA 58.363 39.130 0.00 0.00 0.00 2.41
719 759 2.477825 CCATATTGTCTGGACGAGCAG 58.522 52.381 0.00 0.00 35.70 4.24
735 791 0.105778 TCCATCATCGCAACGCCATA 59.894 50.000 0.00 0.00 0.00 2.74
738 794 1.369091 AACTCCATCATCGCAACGCC 61.369 55.000 0.00 0.00 0.00 5.68
742 798 2.689553 TGCTAACTCCATCATCGCAA 57.310 45.000 0.00 0.00 0.00 4.85
746 802 6.373774 CCAATAAGGATGCTAACTCCATCATC 59.626 42.308 4.08 0.00 40.60 2.92
748 804 5.132648 ACCAATAAGGATGCTAACTCCATCA 59.867 40.000 4.08 0.00 40.60 3.07
749 805 5.625150 ACCAATAAGGATGCTAACTCCATC 58.375 41.667 0.00 0.00 41.22 3.51
847 934 5.247564 AGTTTCCCTTGCAGTATGTACAGTA 59.752 40.000 0.33 0.00 39.31 2.74
848 935 4.041691 AGTTTCCCTTGCAGTATGTACAGT 59.958 41.667 0.33 0.00 39.31 3.55
906 993 4.686191 AGACCTTCATGATTCAGGCTAG 57.314 45.455 11.22 0.00 0.00 3.42
907 994 5.663106 AGTTAGACCTTCATGATTCAGGCTA 59.337 40.000 11.22 10.46 0.00 3.93
1007 1099 3.493129 GTGCACATAAGAACAACTCACGA 59.507 43.478 13.17 0.00 0.00 4.35
1285 1386 4.013728 AGCTCTCGATAGGTCATCATACC 58.986 47.826 0.00 0.00 40.06 2.73
1320 1421 0.452784 GCGAGGCTGCTAAAACAACG 60.453 55.000 0.00 0.00 0.00 4.10
1376 1480 1.002990 TCACCCACAGCAGCAGATG 60.003 57.895 0.00 0.00 37.14 2.90
1432 1536 0.687354 CAGGCTGTAGACACCAACCT 59.313 55.000 6.28 0.00 0.00 3.50
1506 1610 7.783042 ACAGACTCAGTAAAGAAACAACTACT 58.217 34.615 0.00 0.00 0.00 2.57
1531 1635 7.375834 ACACAACGATCTGAATGTAGACTAAA 58.624 34.615 0.00 0.00 0.00 1.85
1534 1638 5.392767 ACACAACGATCTGAATGTAGACT 57.607 39.130 0.00 0.00 0.00 3.24
1712 1835 0.035056 AGCTGGACCCATGTAACTGC 60.035 55.000 0.00 0.00 0.00 4.40
1750 1873 0.320421 AACCAGACAACATCGTCCCG 60.320 55.000 0.00 0.00 36.52 5.14
1786 1910 1.292223 CCACGAGACACAACCGGAT 59.708 57.895 9.46 0.00 0.00 4.18
1870 2001 2.707849 CCCCGTCCACGACCAGTAG 61.708 68.421 0.00 0.00 43.02 2.57
1916 2048 2.672996 CCAGAAACAGGGGCACGG 60.673 66.667 0.00 0.00 0.00 4.94
1936 2068 4.457496 CCGCACGGCCAGAGACAT 62.457 66.667 2.24 0.00 0.00 3.06
2098 2230 4.514577 CTCCACGCCCGGCTACTG 62.515 72.222 8.05 0.00 0.00 2.74
2133 2265 4.845580 CTAGGCACCAGCGGCAGG 62.846 72.222 10.16 10.16 43.41 4.85
2141 2273 2.367202 GGCTACTGGCTAGGCACCA 61.367 63.158 16.16 4.90 45.58 4.17
2142 2274 2.506472 GGCTACTGGCTAGGCACC 59.494 66.667 16.16 11.40 45.58 5.01
2143 2275 2.107141 CGGCTACTGGCTAGGCAC 59.893 66.667 16.16 5.44 46.42 5.01
2144 2276 3.154473 CCGGCTACTGGCTAGGCA 61.154 66.667 19.10 19.10 46.42 4.75
2145 2277 3.930012 CCCGGCTACTGGCTAGGC 61.930 72.222 9.85 9.85 43.32 3.93
2146 2278 2.444140 ACCCGGCTACTGGCTAGG 60.444 66.667 0.85 0.00 41.46 3.02
2147 2279 2.058595 ACACCCGGCTACTGGCTAG 61.059 63.158 0.00 0.00 41.46 3.42
2148 2280 2.038329 ACACCCGGCTACTGGCTA 59.962 61.111 0.00 0.00 41.46 3.93
2149 2281 3.706373 CACACCCGGCTACTGGCT 61.706 66.667 0.00 0.00 41.46 4.75
2150 2282 4.778143 CCACACCCGGCTACTGGC 62.778 72.222 0.00 0.00 40.90 4.85
2151 2283 4.096003 CCCACACCCGGCTACTGG 62.096 72.222 0.00 0.00 0.00 4.00
2152 2284 4.096003 CCCCACACCCGGCTACTG 62.096 72.222 0.00 0.00 0.00 2.74
2173 2305 4.087892 CAGGGACCCACCGAGCAG 62.088 72.222 14.60 0.00 40.11 4.24
2196 2328 4.803908 GGCTACTGGCTGGGCACC 62.804 72.222 11.89 0.00 44.11 5.01
2250 2382 4.803908 GGCTACTGGCTGGGCACC 62.804 72.222 11.89 0.00 44.11 5.01
2305 2437 4.778143 CGGGTACTGGCTGGGCAC 62.778 72.222 0.00 0.00 0.00 5.01
2314 2446 4.189580 CCCCATGCCCGGGTACTG 62.190 72.222 24.63 16.98 45.80 2.74
2325 2457 4.764771 CCCAGGTGCACCCCCATG 62.765 72.222 32.29 22.56 36.42 3.66
2345 2477 4.838152 CATCCGTCAGGGGTGGCG 62.838 72.222 0.00 0.00 43.76 5.69
2359 2491 1.078426 CCAGGGACCAACGGACATC 60.078 63.158 0.00 0.00 0.00 3.06
2405 2537 1.535896 GAAGAAGGAAACCCAACGAGC 59.464 52.381 0.00 0.00 0.00 5.03
2432 2564 2.646719 GACAGGGACGTACACGCA 59.353 61.111 0.00 0.00 44.43 5.24
2434 2566 0.245539 AATGGACAGGGACGTACACG 59.754 55.000 0.00 0.00 46.33 4.49
2435 2567 2.737679 GCTAATGGACAGGGACGTACAC 60.738 54.545 0.00 0.00 30.82 2.90


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

AutoCloner maintained by Alex Coulton.