Multiple sequence alignment - TraesCS7D01G164000

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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 TraesCS7D01G164000 chr7D 100.000 2339 0 0 1 2339 113441214 113438876 0.000000e+00 4320
1 TraesCS7D01G164000 chr1D 96.326 626 18 4 1718 2339 494325152 494324528 0.000000e+00 1024
2 TraesCS7D01G164000 chr6D 96.019 628 19 4 1717 2339 450512592 450513218 0.000000e+00 1016
3 TraesCS7D01G164000 chr6D 96.000 625 21 4 1718 2339 392611724 392611101 0.000000e+00 1013
4 TraesCS7D01G164000 chr2D 96.148 623 23 1 1717 2339 64174904 64174283 0.000000e+00 1016
5 TraesCS7D01G164000 chr2D 95.847 626 21 4 1717 2339 7695031 7694408 0.000000e+00 1007
6 TraesCS7D01G164000 chr2D 95.840 625 22 4 1718 2339 579562192 579562815 0.000000e+00 1007
7 TraesCS7D01G164000 chrUn 96.000 625 22 3 1717 2339 94751856 94752479 0.000000e+00 1013
8 TraesCS7D01G164000 chr5D 96.141 622 19 4 1718 2339 564934565 564935181 0.000000e+00 1011
9 TraesCS7D01G164000 chr5D 95.987 623 20 4 1718 2339 520836302 520835684 0.000000e+00 1007
10 TraesCS7D01G164000 chr7A 84.929 982 82 35 1 934 118454785 118453822 0.000000e+00 933
11 TraesCS7D01G164000 chr7A 88.542 480 33 11 972 1435 118453151 118452678 1.570000e-156 562
12 TraesCS7D01G164000 chr7B 92.268 388 20 6 972 1353 73008124 73007741 2.040000e-150 542
13 TraesCS7D01G164000 chr7B 86.313 358 19 10 581 934 73009118 73008787 1.710000e-96 363
14 TraesCS7D01G164000 chr7B 86.826 334 24 9 1392 1724 73007742 73007428 2.860000e-94 355
15 TraesCS7D01G164000 chr7B 76.574 397 45 28 7 389 73128001 73127639 8.590000e-40 174


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 TraesCS7D01G164000 chr7D 113438876 113441214 2338 True 4320.0 4320 100.0000 1 2339 1 chr7D.!!$R1 2338
1 TraesCS7D01G164000 chr1D 494324528 494325152 624 True 1024.0 1024 96.3260 1718 2339 1 chr1D.!!$R1 621
2 TraesCS7D01G164000 chr6D 450512592 450513218 626 False 1016.0 1016 96.0190 1717 2339 1 chr6D.!!$F1 622
3 TraesCS7D01G164000 chr6D 392611101 392611724 623 True 1013.0 1013 96.0000 1718 2339 1 chr6D.!!$R1 621
4 TraesCS7D01G164000 chr2D 64174283 64174904 621 True 1016.0 1016 96.1480 1717 2339 1 chr2D.!!$R2 622
5 TraesCS7D01G164000 chr2D 7694408 7695031 623 True 1007.0 1007 95.8470 1717 2339 1 chr2D.!!$R1 622
6 TraesCS7D01G164000 chr2D 579562192 579562815 623 False 1007.0 1007 95.8400 1718 2339 1 chr2D.!!$F1 621
7 TraesCS7D01G164000 chrUn 94751856 94752479 623 False 1013.0 1013 96.0000 1717 2339 1 chrUn.!!$F1 622
8 TraesCS7D01G164000 chr5D 564934565 564935181 616 False 1011.0 1011 96.1410 1718 2339 1 chr5D.!!$F1 621
9 TraesCS7D01G164000 chr5D 520835684 520836302 618 True 1007.0 1007 95.9870 1718 2339 1 chr5D.!!$R1 621
10 TraesCS7D01G164000 chr7A 118452678 118454785 2107 True 747.5 933 86.7355 1 1435 2 chr7A.!!$R1 1434
11 TraesCS7D01G164000 chr7B 73007428 73009118 1690 True 420.0 542 88.4690 581 1724 3 chr7B.!!$R2 1143

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
85 87 0.96738 GTGTTCTGGGCTGGGATTGG 60.967 60.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 2362 0.457166 CGAACGTTCGCCAGGTATCA 60.457 55.0 34.54 0.0 44.26 2.15 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
31 32 3.692406 GGGACCGAGTGCCTTCGT 61.692 66.667 7.22 0.00 40.95 3.85
85 87 0.967380 GTGTTCTGGGCTGGGATTGG 60.967 60.000 0.00 0.00 0.00 3.16
113 115 4.263594 ACTTTTAGGCCTAAATTCGTGGGA 60.264 41.667 33.16 17.68 35.27 4.37
114 116 3.553828 TTAGGCCTAAATTCGTGGGAG 57.446 47.619 23.21 0.00 0.00 4.30
115 117 1.580059 AGGCCTAAATTCGTGGGAGA 58.420 50.000 1.29 0.00 0.00 3.71
116 118 2.127708 AGGCCTAAATTCGTGGGAGAT 58.872 47.619 1.29 0.00 0.00 2.75
117 119 2.158755 AGGCCTAAATTCGTGGGAGATG 60.159 50.000 1.29 0.00 0.00 2.90
119 121 2.158813 GCCTAAATTCGTGGGAGATGGA 60.159 50.000 0.00 0.00 0.00 3.41
120 122 3.733337 CCTAAATTCGTGGGAGATGGAG 58.267 50.000 0.00 0.00 0.00 3.86
121 123 3.134804 CCTAAATTCGTGGGAGATGGAGT 59.865 47.826 0.00 0.00 0.00 3.85
124 126 2.762535 TTCGTGGGAGATGGAGTTTC 57.237 50.000 0.00 0.00 0.00 2.78
125 127 1.639722 TCGTGGGAGATGGAGTTTCA 58.360 50.000 0.00 0.00 0.00 2.69
126 128 1.974957 TCGTGGGAGATGGAGTTTCAA 59.025 47.619 0.00 0.00 0.00 2.69
127 129 2.370519 TCGTGGGAGATGGAGTTTCAAA 59.629 45.455 0.00 0.00 0.00 2.69
128 130 3.146066 CGTGGGAGATGGAGTTTCAAAA 58.854 45.455 0.00 0.00 0.00 2.44
129 131 3.568007 CGTGGGAGATGGAGTTTCAAAAA 59.432 43.478 0.00 0.00 0.00 1.94
168 170 1.002087 AGCCCTAGTTTGTCTTGGACG 59.998 52.381 0.00 0.00 40.60 4.79
184 187 7.170320 TGTCTTGGACGAATTAGACTGTAAAAC 59.830 37.037 0.00 0.00 38.23 2.43
193 196 7.753580 CGAATTAGACTGTAAAACAAATTCCCC 59.246 37.037 8.33 0.00 32.28 4.81
222 225 8.757164 AAAAAGGAGTGTAGAAAAAGTTGTTG 57.243 30.769 0.00 0.00 0.00 3.33
227 230 8.364894 AGGAGTGTAGAAAAAGTTGTTGTTTTT 58.635 29.630 0.00 0.00 39.30 1.94
246 249 5.941555 TTTTTCAGGGCAAAGGAGTAAAA 57.058 34.783 0.00 0.00 0.00 1.52
254 257 4.814234 GGGCAAAGGAGTAAAAACCAAAAG 59.186 41.667 0.00 0.00 0.00 2.27
258 261 7.713507 GGCAAAGGAGTAAAAACCAAAAGTTAT 59.286 33.333 0.00 0.00 37.88 1.89
261 264 9.811995 AAAGGAGTAAAAACCAAAAGTTATGAC 57.188 29.630 0.00 0.00 37.88 3.06
270 273 7.692908 AACCAAAAGTTATGACGAAATTGTG 57.307 32.000 0.00 0.00 36.74 3.33
271 274 7.033530 ACCAAAAGTTATGACGAAATTGTGA 57.966 32.000 0.00 0.00 0.00 3.58
274 277 7.807433 CCAAAAGTTATGACGAAATTGTGATGA 59.193 33.333 0.00 0.00 0.00 2.92
275 278 8.843733 CAAAAGTTATGACGAAATTGTGATGAG 58.156 33.333 0.00 0.00 0.00 2.90
429 434 9.699703 GATATGTCTTATTACCTGAGGAGAAAC 57.300 37.037 4.99 0.00 0.00 2.78
437 442 2.900546 ACCTGAGGAGAAACCACACTAG 59.099 50.000 4.99 0.00 42.04 2.57
484 493 6.308282 GTCAGTCTAGTTCATTTAGGTTCACG 59.692 42.308 0.00 0.00 0.00 4.35
487 496 6.867293 AGTCTAGTTCATTTAGGTTCACGAAC 59.133 38.462 1.12 1.12 40.45 3.95
491 500 6.725246 AGTTCATTTAGGTTCACGAACTTTG 58.275 36.000 9.63 0.00 39.93 2.77
493 502 7.228706 AGTTCATTTAGGTTCACGAACTTTGAT 59.771 33.333 9.63 0.00 39.93 2.57
494 503 8.500773 GTTCATTTAGGTTCACGAACTTTGATA 58.499 33.333 9.63 0.00 40.94 2.15
495 504 8.610248 TCATTTAGGTTCACGAACTTTGATAA 57.390 30.769 9.63 0.78 40.94 1.75
496 505 9.226606 TCATTTAGGTTCACGAACTTTGATAAT 57.773 29.630 9.63 0.00 40.94 1.28
525 555 6.463995 AGTGGTTTCTTTTGACTAATTGCA 57.536 33.333 0.00 0.00 0.00 4.08
534 564 6.488344 TCTTTTGACTAATTGCATGGTGTGTA 59.512 34.615 0.00 0.00 0.00 2.90
536 566 5.621197 TGACTAATTGCATGGTGTGTAAC 57.379 39.130 0.00 0.00 35.19 2.50
537 567 5.312895 TGACTAATTGCATGGTGTGTAACT 58.687 37.500 0.00 0.00 35.19 2.24
538 568 5.181056 TGACTAATTGCATGGTGTGTAACTG 59.819 40.000 0.00 0.00 35.19 3.16
540 570 5.767665 ACTAATTGCATGGTGTGTAACTGAA 59.232 36.000 0.00 0.00 35.19 3.02
541 571 5.726980 AATTGCATGGTGTGTAACTGAAT 57.273 34.783 0.00 0.00 35.19 2.57
542 572 4.502171 TTGCATGGTGTGTAACTGAATG 57.498 40.909 0.00 0.00 38.04 2.67
544 574 2.415893 GCATGGTGTGTAACTGAATGCC 60.416 50.000 0.00 0.00 38.04 4.40
546 576 1.202710 TGGTGTGTAACTGAATGCCGT 60.203 47.619 0.00 0.00 38.04 5.68
547 577 1.877443 GGTGTGTAACTGAATGCCGTT 59.123 47.619 0.00 0.00 38.04 4.44
548 578 2.350388 GGTGTGTAACTGAATGCCGTTG 60.350 50.000 0.00 0.00 38.04 4.10
549 579 2.289547 GTGTGTAACTGAATGCCGTTGT 59.710 45.455 0.00 0.00 38.04 3.32
550 580 2.289274 TGTGTAACTGAATGCCGTTGTG 59.711 45.455 0.00 0.00 38.04 3.33
551 581 2.289547 GTGTAACTGAATGCCGTTGTGT 59.710 45.455 0.00 0.00 0.00 3.72
561 598 5.412904 TGAATGCCGTTGTGTCATTACAATA 59.587 36.000 0.00 0.00 42.02 1.90
563 600 3.687212 TGCCGTTGTGTCATTACAATAGG 59.313 43.478 0.00 0.00 42.02 2.57
575 612 9.958180 TGTCATTACAATAGGAGATGAAGAAAA 57.042 29.630 0.00 0.00 30.91 2.29
615 654 7.647715 AGCACAACAAAATACTTGTCAACATAC 59.352 33.333 0.00 0.00 0.00 2.39
658 697 7.945033 TGCATTTGGAGTTATTTGACTTTTC 57.055 32.000 0.00 0.00 0.00 2.29
677 716 9.640963 GACTTTTCATAAGTCTTAGCTCTGTTA 57.359 33.333 9.73 0.00 42.44 2.41
726 767 3.418684 TGAGGGGAGTTTTTCTGCTAC 57.581 47.619 0.00 0.00 34.83 3.58
754 795 1.825191 CATGGCCGATTCCACCCTG 60.825 63.158 0.00 0.00 39.25 4.45
826 869 8.735315 TCCATTTAACTCATAATTTGAAGCGAA 58.265 29.630 0.00 0.00 32.78 4.70
846 889 4.385825 GAACACAATGAACTCCACCAGTA 58.614 43.478 0.00 0.00 32.30 2.74
853 899 2.897969 TGAACTCCACCAGTACCTTCTC 59.102 50.000 0.00 0.00 32.30 2.87
900 948 2.124403 CTCCAGCAGCCCATGGAC 60.124 66.667 15.22 0.00 40.70 4.02
934 983 2.412770 GCAGCTTGCGCACATTTTTAAT 59.587 40.909 11.12 0.00 39.10 1.40
935 984 3.120580 GCAGCTTGCGCACATTTTTAATT 60.121 39.130 11.12 0.00 39.10 1.40
936 985 4.611130 GCAGCTTGCGCACATTTTTAATTT 60.611 37.500 11.12 0.00 39.10 1.82
937 986 5.442402 CAGCTTGCGCACATTTTTAATTTT 58.558 33.333 11.12 0.00 39.10 1.82
938 987 6.588552 CAGCTTGCGCACATTTTTAATTTTA 58.411 32.000 11.12 0.00 39.10 1.52
939 988 7.068341 CAGCTTGCGCACATTTTTAATTTTAA 58.932 30.769 11.12 0.00 39.10 1.52
940 989 7.058241 CAGCTTGCGCACATTTTTAATTTTAAC 59.942 33.333 11.12 0.00 39.10 2.01
941 990 6.848296 GCTTGCGCACATTTTTAATTTTAACA 59.152 30.769 11.12 0.00 35.78 2.41
942 991 7.374491 GCTTGCGCACATTTTTAATTTTAACAA 59.626 29.630 11.12 0.00 35.78 2.83
1340 2058 2.125912 CACCGTCGGCTTCTGAGG 60.126 66.667 12.28 0.00 0.00 3.86
1344 2062 1.153939 CGTCGGCTTCTGAGGTCTG 60.154 63.158 0.00 0.00 0.00 3.51
1362 2080 3.808174 GTCTGGTCGACCTAATTAATGGC 59.192 47.826 33.39 11.96 36.62 4.40
1363 2081 2.800544 CTGGTCGACCTAATTAATGGCG 59.199 50.000 33.39 4.00 36.82 5.69
1364 2082 2.168936 TGGTCGACCTAATTAATGGCGT 59.831 45.455 33.39 0.00 36.82 5.68
1388 2106 0.879090 GGCCGTGAAAGGGTTTACTG 59.121 55.000 0.00 0.00 45.59 2.74
1391 2109 2.418976 GCCGTGAAAGGGTTTACTGATC 59.581 50.000 0.00 0.00 45.59 2.92
1392 2110 3.868754 GCCGTGAAAGGGTTTACTGATCT 60.869 47.826 0.00 0.00 45.59 2.75
1403 2121 5.944007 GGGTTTACTGATCTTGTTGGTGTAT 59.056 40.000 0.00 0.00 0.00 2.29
1404 2122 6.128007 GGGTTTACTGATCTTGTTGGTGTATG 60.128 42.308 0.00 0.00 0.00 2.39
1473 2199 2.051879 GGAAAGCCGCAAACTCTTTC 57.948 50.000 5.63 5.63 42.81 2.62
1474 2200 1.609072 GGAAAGCCGCAAACTCTTTCT 59.391 47.619 11.98 0.00 42.99 2.52
1475 2201 2.034685 GGAAAGCCGCAAACTCTTTCTT 59.965 45.455 11.98 0.00 42.99 2.52
1476 2202 3.490933 GGAAAGCCGCAAACTCTTTCTTT 60.491 43.478 11.98 0.00 42.99 2.52
1477 2203 3.801114 AAGCCGCAAACTCTTTCTTTT 57.199 38.095 0.00 0.00 0.00 2.27
1478 2204 3.355626 AGCCGCAAACTCTTTCTTTTC 57.644 42.857 0.00 0.00 0.00 2.29
1479 2205 2.952310 AGCCGCAAACTCTTTCTTTTCT 59.048 40.909 0.00 0.00 0.00 2.52
1480 2206 3.045688 GCCGCAAACTCTTTCTTTTCTG 58.954 45.455 0.00 0.00 0.00 3.02
1481 2207 3.045688 CCGCAAACTCTTTCTTTTCTGC 58.954 45.455 0.00 0.00 0.00 4.26
1482 2208 3.045688 CGCAAACTCTTTCTTTTCTGCC 58.954 45.455 0.00 0.00 0.00 4.85
1483 2209 3.384668 GCAAACTCTTTCTTTTCTGCCC 58.615 45.455 0.00 0.00 0.00 5.36
1484 2210 3.068732 GCAAACTCTTTCTTTTCTGCCCT 59.931 43.478 0.00 0.00 0.00 5.19
1506 2232 6.208644 CCTTTTCTAGTGTGTTTTGGTGATG 58.791 40.000 0.00 0.00 0.00 3.07
1518 2244 6.691388 GTGTTTTGGTGATGTTTAGTTCTGTC 59.309 38.462 0.00 0.00 0.00 3.51
1534 2260 2.005451 CTGTCTTTGCTTGGATCTCCG 58.995 52.381 0.00 0.00 39.43 4.63
1536 2262 2.003301 GTCTTTGCTTGGATCTCCGTC 58.997 52.381 0.00 0.00 39.43 4.79
1567 2294 6.513180 TGTAAAATCCGGCTCTACTCAATAG 58.487 40.000 0.00 0.00 0.00 1.73
1571 2298 7.540474 AAATCCGGCTCTACTCAATAGATTA 57.460 36.000 0.00 0.00 39.28 1.75
1577 2304 7.971168 CCGGCTCTACTCAATAGATTATAAGTG 59.029 40.741 0.00 0.00 39.28 3.16
1605 2332 1.390123 CCGTGCGACACAACTATTCTG 59.610 52.381 9.95 0.00 33.40 3.02
1607 2334 2.342651 CGTGCGACACAACTATTCTGAG 59.657 50.000 9.95 0.00 33.40 3.35
1609 2336 3.121944 GTGCGACACAACTATTCTGAGTG 59.878 47.826 5.30 0.00 34.08 3.51
1619 2346 4.074259 ACTATTCTGAGTGCATGCAAACA 58.926 39.130 24.58 22.46 0.00 2.83
1622 2349 4.325028 TTCTGAGTGCATGCAAACATTT 57.675 36.364 24.58 3.82 32.87 2.32
1708 2435 1.194781 AGAGCCACACGGTCCAGATT 61.195 55.000 0.00 0.00 40.01 2.40
1733 2460 7.974504 TCAAAGGATCACTAGTAGAAAAAGGT 58.025 34.615 3.59 0.00 0.00 3.50
1746 2473 2.668144 AAAAGGTCCATTTGTCCCGA 57.332 45.000 0.00 0.00 0.00 5.14
1804 2531 4.807834 GGACTAAAGGGTCGTTACTAATGC 59.192 45.833 0.00 0.00 37.12 3.56
1811 2538 2.036862 GGTCGTTACTAATGCCCTAGGG 59.963 54.545 24.89 24.89 38.57 3.53
1892 2619 2.674220 CCCAGGCAGGAGACCCTTC 61.674 68.421 0.00 0.00 42.02 3.46
1925 2652 1.906333 GCACCAACCGGGACCAATT 60.906 57.895 6.32 0.00 41.15 2.32
2208 2943 1.770294 AGTGATCGACCTCTCCTTCC 58.230 55.000 0.00 0.00 0.00 3.46
2236 2971 5.007724 AGAGATTGGTCGAACAACAAGTTTC 59.992 40.000 20.01 11.09 41.51 2.78
2318 3054 3.955471 TCCCCTAGCATTTGAACTCAAG 58.045 45.455 0.00 0.00 37.15 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 5.645067 ACGAATTTAGGCCTAAAAGTACACC 59.355 40.000 35.41 19.53 38.38 4.16
135 137 2.026169 ACTAGGGCTTAGTTTGGGCTTC 60.026 50.000 3.07 0.00 39.64 3.86
144 146 3.908103 TCCAAGACAAACTAGGGCTTAGT 59.092 43.478 3.07 3.07 44.55 2.24
168 170 8.803235 AGGGGAATTTGTTTTACAGTCTAATTC 58.197 33.333 0.00 0.00 34.87 2.17
227 230 3.639561 GGTTTTTACTCCTTTGCCCTGAA 59.360 43.478 0.00 0.00 0.00 3.02
228 231 3.227614 GGTTTTTACTCCTTTGCCCTGA 58.772 45.455 0.00 0.00 0.00 3.86
229 232 2.962421 TGGTTTTTACTCCTTTGCCCTG 59.038 45.455 0.00 0.00 0.00 4.45
234 237 9.810545 TCATAACTTTTGGTTTTTACTCCTTTG 57.189 29.630 0.00 0.00 39.17 2.77
243 246 9.157104 ACAATTTCGTCATAACTTTTGGTTTTT 57.843 25.926 0.00 0.00 39.17 1.94
246 249 7.484975 TCACAATTTCGTCATAACTTTTGGTT 58.515 30.769 0.00 0.00 41.54 3.67
254 257 8.728088 AAAACTCATCACAATTTCGTCATAAC 57.272 30.769 0.00 0.00 0.00 1.89
308 312 5.632959 AGAACAAATGTTTCGTTTCGACAA 58.367 33.333 0.00 0.00 38.56 3.18
389 393 8.971032 ATAAGACATATCTTCTCTGGGAGAAT 57.029 34.615 9.92 0.72 45.84 2.40
395 399 9.083422 TCAGGTAATAAGACATATCTTCTCTGG 57.917 37.037 0.00 0.00 41.63 3.86
407 411 5.783360 TGGTTTCTCCTCAGGTAATAAGACA 59.217 40.000 0.00 0.00 37.07 3.41
409 413 5.783360 TGTGGTTTCTCCTCAGGTAATAAGA 59.217 40.000 0.00 0.00 35.16 2.10
429 434 7.856145 AAGCAATTCTAGAATTCTAGTGTGG 57.144 36.000 31.97 22.63 44.74 4.17
437 442 9.766277 CTGACAAGTAAAGCAATTCTAGAATTC 57.234 33.333 24.72 18.91 38.84 2.17
500 509 8.001881 TGCAATTAGTCAAAAGAAACCACTAA 57.998 30.769 0.00 0.00 34.80 2.24
502 511 6.463995 TGCAATTAGTCAAAAGAAACCACT 57.536 33.333 0.00 0.00 0.00 4.00
503 512 6.146021 CCATGCAATTAGTCAAAAGAAACCAC 59.854 38.462 0.00 0.00 0.00 4.16
504 513 6.183360 ACCATGCAATTAGTCAAAAGAAACCA 60.183 34.615 0.00 0.00 0.00 3.67
505 514 6.146021 CACCATGCAATTAGTCAAAAGAAACC 59.854 38.462 0.00 0.00 0.00 3.27
506 515 6.701400 ACACCATGCAATTAGTCAAAAGAAAC 59.299 34.615 0.00 0.00 0.00 2.78
507 516 6.700960 CACACCATGCAATTAGTCAAAAGAAA 59.299 34.615 0.00 0.00 0.00 2.52
508 517 6.183360 ACACACCATGCAATTAGTCAAAAGAA 60.183 34.615 0.00 0.00 0.00 2.52
509 518 5.301551 ACACACCATGCAATTAGTCAAAAGA 59.698 36.000 0.00 0.00 0.00 2.52
510 519 5.531634 ACACACCATGCAATTAGTCAAAAG 58.468 37.500 0.00 0.00 0.00 2.27
525 555 2.083774 CGGCATTCAGTTACACACCAT 58.916 47.619 0.00 0.00 0.00 3.55
534 564 1.674359 TGACACAACGGCATTCAGTT 58.326 45.000 0.00 0.00 0.00 3.16
536 566 2.995466 AATGACACAACGGCATTCAG 57.005 45.000 0.00 0.00 0.00 3.02
537 567 3.142174 TGTAATGACACAACGGCATTCA 58.858 40.909 0.00 0.00 34.41 2.57
538 568 3.822594 TGTAATGACACAACGGCATTC 57.177 42.857 0.00 0.00 34.41 2.67
540 570 4.335315 CCTATTGTAATGACACAACGGCAT 59.665 41.667 0.00 0.00 41.02 4.40
541 571 3.687212 CCTATTGTAATGACACAACGGCA 59.313 43.478 0.00 0.00 41.02 5.69
542 572 3.936453 TCCTATTGTAATGACACAACGGC 59.064 43.478 0.00 0.00 41.02 5.68
544 574 6.756542 TCATCTCCTATTGTAATGACACAACG 59.243 38.462 0.00 0.00 41.02 4.10
546 576 8.539544 TCTTCATCTCCTATTGTAATGACACAA 58.460 33.333 0.00 0.00 42.32 3.33
547 577 8.078060 TCTTCATCTCCTATTGTAATGACACA 57.922 34.615 0.00 0.00 34.48 3.72
548 578 8.948631 TTCTTCATCTCCTATTGTAATGACAC 57.051 34.615 0.00 0.00 34.48 3.67
549 579 9.958180 TTTTCTTCATCTCCTATTGTAATGACA 57.042 29.630 0.00 0.00 0.00 3.58
561 598 3.676324 CGCCGTACTTTTCTTCATCTCCT 60.676 47.826 0.00 0.00 0.00 3.69
563 600 3.508762 TCGCCGTACTTTTCTTCATCTC 58.491 45.455 0.00 0.00 0.00 2.75
575 612 0.037697 TGTGCTCAAATCGCCGTACT 60.038 50.000 0.00 0.00 0.00 2.73
579 616 0.040514 TTGTTGTGCTCAAATCGCCG 60.041 50.000 2.18 0.00 35.20 6.46
688 727 9.907229 CTCCCCTCATAGAATAACTAAACTTTT 57.093 33.333 0.00 0.00 34.56 2.27
696 735 8.049721 CAGAAAAACTCCCCTCATAGAATAACT 58.950 37.037 0.00 0.00 0.00 2.24
697 736 7.201741 GCAGAAAAACTCCCCTCATAGAATAAC 60.202 40.741 0.00 0.00 0.00 1.89
698 737 6.828785 GCAGAAAAACTCCCCTCATAGAATAA 59.171 38.462 0.00 0.00 0.00 1.40
700 739 5.044550 AGCAGAAAAACTCCCCTCATAGAAT 60.045 40.000 0.00 0.00 0.00 2.40
701 740 4.289672 AGCAGAAAAACTCCCCTCATAGAA 59.710 41.667 0.00 0.00 0.00 2.10
703 742 4.227864 AGCAGAAAAACTCCCCTCATAG 57.772 45.455 0.00 0.00 0.00 2.23
705 744 3.308473 GGTAGCAGAAAAACTCCCCTCAT 60.308 47.826 0.00 0.00 0.00 2.90
706 745 2.039879 GGTAGCAGAAAAACTCCCCTCA 59.960 50.000 0.00 0.00 0.00 3.86
707 746 2.039879 TGGTAGCAGAAAAACTCCCCTC 59.960 50.000 0.00 0.00 0.00 4.30
709 748 2.579410 TGGTAGCAGAAAAACTCCCC 57.421 50.000 0.00 0.00 0.00 4.81
726 767 3.319755 GAATCGGCCATGCAAATAATGG 58.680 45.455 2.24 0.00 46.29 3.16
754 795 2.038557 TGTTGTTCTAGGAAGGACAGCC 59.961 50.000 0.00 0.00 42.35 4.85
826 869 3.496160 GGTACTGGTGGAGTTCATTGTGT 60.496 47.826 0.00 0.00 35.96 3.72
846 889 1.207791 ATTGCCCAGATCGAGAAGGT 58.792 50.000 0.00 0.00 0.00 3.50
853 899 3.567164 AGCTATTGAAATTGCCCAGATCG 59.433 43.478 5.95 0.00 37.78 3.69
1344 2062 2.542595 CACGCCATTAATTAGGTCGACC 59.457 50.000 27.67 27.67 0.00 4.79
1353 2071 1.381165 GGCCGACCACGCCATTAATT 61.381 55.000 0.00 0.00 38.29 1.40
1354 2072 1.822186 GGCCGACCACGCCATTAAT 60.822 57.895 0.00 0.00 38.29 1.40
1355 2073 2.437002 GGCCGACCACGCCATTAA 60.437 61.111 0.00 0.00 38.29 1.40
1356 2074 4.823419 CGGCCGACCACGCCATTA 62.823 66.667 24.07 0.00 36.21 1.90
1362 2080 3.411351 CTTTCACGGCCGACCACG 61.411 66.667 35.90 14.32 39.43 4.94
1363 2081 3.047877 CCTTTCACGGCCGACCAC 61.048 66.667 35.90 0.00 34.57 4.16
1364 2082 4.323477 CCCTTTCACGGCCGACCA 62.323 66.667 35.90 12.22 34.57 4.02
1388 2106 3.119849 GCCACACATACACCAACAAGATC 60.120 47.826 0.00 0.00 0.00 2.75
1391 2109 1.952990 TGCCACACATACACCAACAAG 59.047 47.619 0.00 0.00 0.00 3.16
1392 2110 1.678627 GTGCCACACATACACCAACAA 59.321 47.619 0.00 0.00 34.08 2.83
1423 2149 4.382291 AGCACACCTTCGTATGTACAAAA 58.618 39.130 0.00 0.00 0.00 2.44
1467 2193 5.781210 AGAAAAGGGCAGAAAAGAAAGAG 57.219 39.130 0.00 0.00 0.00 2.85
1468 2194 6.263168 CACTAGAAAAGGGCAGAAAAGAAAGA 59.737 38.462 0.00 0.00 0.00 2.52
1469 2195 6.039829 ACACTAGAAAAGGGCAGAAAAGAAAG 59.960 38.462 0.00 0.00 28.14 2.62
1471 2197 5.299279 CACACTAGAAAAGGGCAGAAAAGAA 59.701 40.000 0.00 0.00 28.14 2.52
1472 2198 4.821805 CACACTAGAAAAGGGCAGAAAAGA 59.178 41.667 0.00 0.00 28.14 2.52
1473 2199 4.580580 ACACACTAGAAAAGGGCAGAAAAG 59.419 41.667 0.00 0.00 28.14 2.27
1474 2200 4.532834 ACACACTAGAAAAGGGCAGAAAA 58.467 39.130 0.00 0.00 28.14 2.29
1475 2201 4.164843 ACACACTAGAAAAGGGCAGAAA 57.835 40.909 0.00 0.00 28.14 2.52
1476 2202 3.857157 ACACACTAGAAAAGGGCAGAA 57.143 42.857 0.00 0.00 28.14 3.02
1477 2203 3.857157 AACACACTAGAAAAGGGCAGA 57.143 42.857 0.00 0.00 28.14 4.26
1478 2204 4.499696 CCAAAACACACTAGAAAAGGGCAG 60.500 45.833 0.00 0.00 28.14 4.85
1479 2205 3.383185 CCAAAACACACTAGAAAAGGGCA 59.617 43.478 0.00 0.00 28.14 5.36
1480 2206 3.383505 ACCAAAACACACTAGAAAAGGGC 59.616 43.478 0.00 0.00 28.14 5.19
1481 2207 4.642885 TCACCAAAACACACTAGAAAAGGG 59.357 41.667 0.00 0.00 33.39 3.95
1482 2208 5.828299 TCACCAAAACACACTAGAAAAGG 57.172 39.130 0.00 0.00 0.00 3.11
1483 2209 6.795399 ACATCACCAAAACACACTAGAAAAG 58.205 36.000 0.00 0.00 0.00 2.27
1484 2210 6.767524 ACATCACCAAAACACACTAGAAAA 57.232 33.333 0.00 0.00 0.00 2.29
1506 2232 5.751243 TCCAAGCAAAGACAGAACTAAAC 57.249 39.130 0.00 0.00 0.00 2.01
1518 2244 1.339055 TGGACGGAGATCCAAGCAAAG 60.339 52.381 0.00 0.00 46.08 2.77
1534 2260 4.134563 AGCCGGATTTTACATACATGGAC 58.865 43.478 5.05 0.00 0.00 4.02
1536 2262 4.389374 AGAGCCGGATTTTACATACATGG 58.611 43.478 5.05 0.00 0.00 3.66
1582 2309 2.380084 ATAGTTGTGTCGCACGGATT 57.620 45.000 5.69 0.00 37.14 3.01
1631 2358 2.817901 ACGTTCGCCAGGTATCATTAC 58.182 47.619 0.00 0.00 0.00 1.89
1632 2359 3.450578 GAACGTTCGCCAGGTATCATTA 58.549 45.455 13.36 0.00 0.00 1.90
1633 2360 2.277084 GAACGTTCGCCAGGTATCATT 58.723 47.619 13.36 0.00 0.00 2.57
1634 2361 1.801395 CGAACGTTCGCCAGGTATCAT 60.801 52.381 34.54 0.00 44.26 2.45
1635 2362 0.457166 CGAACGTTCGCCAGGTATCA 60.457 55.000 34.54 0.00 44.26 2.15
1655 2382 1.081892 CGTTGGGATCTCACTTGCAG 58.918 55.000 0.00 0.00 0.00 4.41
1659 2386 1.939838 GCGTTCGTTGGGATCTCACTT 60.940 52.381 0.00 0.00 0.00 3.16
1708 2435 7.974504 ACCTTTTTCTACTAGTGATCCTTTGA 58.025 34.615 5.39 0.00 0.00 2.69
1733 2460 4.460263 CCTTATGAATCGGGACAAATGGA 58.540 43.478 0.00 0.00 0.00 3.41
1746 2473 2.108952 GGGACAGATGGGCCTTATGAAT 59.891 50.000 19.57 0.00 0.00 2.57
1804 2531 1.132500 CCAGGACTAAAGCCCTAGGG 58.868 60.000 24.89 24.89 38.57 3.53
1811 2538 7.710044 GGTTAGTATAAGAACCAGGACTAAAGC 59.290 40.741 10.77 0.00 43.91 3.51
1886 2613 2.526046 CCAACCGGGACTGAAGGGT 61.526 63.158 6.32 0.00 40.01 4.34
1892 2619 4.263572 TGCCACCAACCGGGACTG 62.264 66.667 6.32 0.00 41.15 3.51
1991 2726 7.731235 ACACCTTAATTAACCATACAAAACCCT 59.269 33.333 0.00 0.00 0.00 4.34
2064 2799 2.690497 CCAAGCACGGAGATAAGAGAGA 59.310 50.000 0.00 0.00 0.00 3.10
2208 2943 0.530744 TGTTCGACCAATCTCTCGGG 59.469 55.000 0.00 0.00 0.00 5.14
2236 2971 4.569966 AGTAGCGTCGGATAGATAATACGG 59.430 45.833 0.00 0.00 42.62 4.02
2281 3016 8.917414 TGCTAGGGGATTGTAAGAGATATTAT 57.083 34.615 0.00 0.00 0.00 1.28
2285 3020 7.292356 TCAAATGCTAGGGGATTGTAAGAGATA 59.708 37.037 0.00 0.00 33.82 1.98
2318 3054 1.636988 CGGAGAATACCACGTGGAAC 58.363 55.000 40.21 24.66 38.94 3.62


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

AutoCloner maintained by Alex Coulton.