Multiple sequence alignment - TraesCS5D01G188800

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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 TraesCS5D01G188800 chr5D 100.000 3882 0 0 1 3882 291495448 291499329 0.000000e+00 7169.0
1 TraesCS5D01G188800 chr5A 94.002 1217 46 10 829 2020 383875667 383876881 0.000000e+00 1818.0
2 TraesCS5D01G188800 chr5A 95.989 1047 40 2 2837 3882 383880364 383881409 0.000000e+00 1700.0
3 TraesCS5D01G188800 chr5A 88.729 834 58 8 3 828 383874797 383875602 0.000000e+00 987.0
4 TraesCS5D01G188800 chr5A 90.654 321 23 4 2505 2819 383879952 383880271 1.670000e-113 420.0
5 TraesCS5D01G188800 chr5A 90.323 62 6 0 2003 2064 383878093 383878154 8.940000e-12 82.4
6 TraesCS5D01G188800 chr5B 96.457 875 19 6 3020 3882 332200353 332201227 0.000000e+00 1434.0
7 TraesCS5D01G188800 chr5B 90.940 883 37 18 1179 2061 332198586 332199425 0.000000e+00 1147.0
8 TraesCS5D01G188800 chr5B 84.135 561 43 13 2270 2819 332199634 332200159 5.790000e-138 501.0
9 TraesCS5D01G188800 chr5B 89.313 262 23 5 2102 2361 332199422 332199680 1.350000e-84 324.0
10 TraesCS5D01G188800 chr7A 95.349 86 4 0 2937 3022 398924517 398924432 1.880000e-28 137.0
11 TraesCS5D01G188800 chr3B 95.349 86 3 1 2943 3028 126580070 126580154 6.770000e-28 135.0
12 TraesCS5D01G188800 chr3B 92.553 94 5 2 2930 3022 680423390 680423298 2.430000e-27 134.0
13 TraesCS5D01G188800 chr2A 94.318 88 4 1 2937 3023 593655908 593655995 2.430000e-27 134.0
14 TraesCS5D01G188800 chr4A 91.667 96 6 2 2925 3020 590111642 590111549 8.750000e-27 132.0
15 TraesCS5D01G188800 chr1B 96.250 80 3 0 2943 3022 120657922 120657843 8.750000e-27 132.0
16 TraesCS5D01G188800 chr2D 95.062 81 4 0 2943 3023 299891098 299891018 1.130000e-25 128.0
17 TraesCS5D01G188800 chr7B 93.023 86 5 1 2937 3022 354257222 354257306 1.460000e-24 124.0


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 TraesCS5D01G188800 chr5D 291495448 291499329 3881 False 7169.00 7169 100.00000 1 3882 1 chr5D.!!$F1 3881
1 TraesCS5D01G188800 chr5A 383874797 383881409 6612 False 1001.48 1818 91.93940 3 3882 5 chr5A.!!$F1 3879
2 TraesCS5D01G188800 chr5B 332198586 332201227 2641 False 851.50 1434 90.21125 1179 3882 4 chr5B.!!$F1 2703

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
129 130 0.106918 TGAAGGTGGTGTTGTGGGTC 60.107 55.0 0.0 0.0 0.00 4.46 F
489 498 0.177604 CTCGGGCAGATTGAAGAGCT 59.822 55.0 0.0 0.0 0.00 4.09 F
631 640 0.258774 ACTTGGCTTGTGGTTCACCT 59.741 50.0 0.0 0.0 36.82 4.00 F
905 978 0.574922 CGAGCGTGCGTGCATTATTA 59.425 50.0 0.0 0.0 37.31 0.98 F
2473 5228 0.611714 ACACCCCTCATCAACCGTAC 59.388 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1139 1220 1.820906 GAGCATGATCGCAAGCCCA 60.821 57.895 0.0 0.0 39.44 5.36 R
2135 4810 0.179056 CAACCACGTCACCCTCTGTT 60.179 55.000 0.0 0.0 0.00 3.16 R
2586 5394 0.182775 AGGAAGTGGTTGGCGTCTTT 59.817 50.000 0.0 0.0 0.00 2.52 R
2592 5400 0.811281 GTATGCAGGAAGTGGTTGGC 59.189 55.000 0.0 0.0 0.00 4.52 R
3712 6613 0.687354 AGGCCATGAACGTTGAGACT 59.313 50.000 5.0 0.0 0.00 3.24 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
23 24 1.170290 TCCGAGTCTTCAGTGACGCA 61.170 55.000 0.00 0.00 41.47 5.24
69 70 0.451783 GCCACACCCTAAAGCATTCG 59.548 55.000 0.00 0.00 0.00 3.34
75 76 4.214119 CACACCCTAAAGCATTCGATATGG 59.786 45.833 8.86 0.00 0.00 2.74
89 90 4.780815 TCGATATGGATTTTGAAGGTGCT 58.219 39.130 0.00 0.00 0.00 4.40
95 96 5.902613 TGGATTTTGAAGGTGCTATTGAG 57.097 39.130 0.00 0.00 0.00 3.02
100 101 1.340017 TGAAGGTGCTATTGAGGGTGC 60.340 52.381 0.00 0.00 0.00 5.01
109 110 4.648626 TGAGGGTGCTGCTGGTGC 62.649 66.667 0.00 0.00 40.20 5.01
129 130 0.106918 TGAAGGTGGTGTTGTGGGTC 60.107 55.000 0.00 0.00 0.00 4.46
138 139 0.472044 TGTTGTGGGTCTTGCTGCTA 59.528 50.000 0.00 0.00 0.00 3.49
139 140 0.875059 GTTGTGGGTCTTGCTGCTAC 59.125 55.000 0.00 0.00 0.00 3.58
140 141 0.472044 TTGTGGGTCTTGCTGCTACA 59.528 50.000 0.00 0.00 0.00 2.74
170 171 0.179026 CTGATGGTGCTCAGGATGGG 60.179 60.000 0.00 0.00 42.01 4.00
184 185 3.327172 CAGGATGGGATCACTGCTATCTT 59.673 47.826 0.00 0.00 32.33 2.40
204 205 9.941664 CTATCTTTGCTATGTTAATCCAGTTTG 57.058 33.333 0.00 0.00 0.00 2.93
209 210 7.377766 TGCTATGTTAATCCAGTTTGAAGAC 57.622 36.000 0.00 0.00 0.00 3.01
222 225 6.147821 CCAGTTTGAAGACTGTGGTACTATTG 59.852 42.308 4.54 0.00 44.34 1.90
240 243 6.237901 ACTATTGTGATGTTAGCCTGTTTGA 58.762 36.000 0.00 0.00 0.00 2.69
242 245 4.829064 TGTGATGTTAGCCTGTTTGAAC 57.171 40.909 0.00 0.00 0.00 3.18
244 247 5.616270 TGTGATGTTAGCCTGTTTGAACTA 58.384 37.500 0.00 0.00 0.00 2.24
258 267 7.283127 CCTGTTTGAACTACTATGGTTATGCAT 59.717 37.037 3.79 3.79 0.00 3.96
287 296 7.168219 TGCTTATCCTATGGTTTAGCTTATGG 58.832 38.462 0.00 0.00 0.00 2.74
316 325 8.630054 TGGTTTATGCTATGATTATGGTTACC 57.370 34.615 0.00 0.00 0.00 2.85
332 341 2.438868 TACCGCTATGTATGCTGCTG 57.561 50.000 0.00 0.00 0.00 4.41
334 343 0.602106 CCGCTATGTATGCTGCTGCT 60.602 55.000 17.00 5.09 40.48 4.24
348 357 1.033746 GCTGCTGTGTGCCCATGTAT 61.034 55.000 0.00 0.00 42.00 2.29
350 359 1.133598 CTGCTGTGTGCCCATGTATTG 59.866 52.381 0.00 0.00 42.00 1.90
380 389 4.044317 TCACCACTCCTAGAAGAGGTTACT 59.956 45.833 0.00 0.00 46.76 2.24
410 419 8.349245 TCATTTGAGTTGTATGTAACCAAACAG 58.651 33.333 0.00 0.00 35.55 3.16
428 437 0.743701 AGCAGCTCTTTGCATCTCGG 60.744 55.000 0.00 0.00 46.47 4.63
434 443 3.133721 AGCTCTTTGCATCTCGGTAGAAT 59.866 43.478 0.00 0.00 45.94 2.40
441 450 3.257393 GCATCTCGGTAGAATATGCAGG 58.743 50.000 0.00 0.00 41.63 4.85
445 454 2.802816 CTCGGTAGAATATGCAGGCAAC 59.197 50.000 0.00 0.00 0.00 4.17
466 475 4.551729 ACACAGGTTCCGGTGTTG 57.448 55.556 18.87 0.00 45.39 3.33
473 482 2.664851 TTCCGGTGTTGCTGCTCG 60.665 61.111 0.00 0.00 0.00 5.03
486 495 1.982430 TGCTCGGGCAGATTGAAGA 59.018 52.632 5.44 0.00 44.28 2.87
489 498 0.177604 CTCGGGCAGATTGAAGAGCT 59.822 55.000 0.00 0.00 0.00 4.09
494 503 1.132643 GGCAGATTGAAGAGCTTGCAG 59.867 52.381 5.23 0.00 0.00 4.41
495 504 2.082231 GCAGATTGAAGAGCTTGCAGA 58.918 47.619 0.00 0.00 0.00 4.26
507 516 4.114794 GAGCTTGCAGACAAACAAACAAT 58.885 39.130 0.00 0.00 34.74 2.71
508 517 5.067674 AGAGCTTGCAGACAAACAAACAATA 59.932 36.000 0.00 0.00 34.74 1.90
547 556 4.093743 TGACCTGTATTCACTTAGCCAGA 58.906 43.478 0.00 0.00 0.00 3.86
560 569 1.983224 GCCAGACTGAGTTGGGCTA 59.017 57.895 17.75 0.00 41.39 3.93
568 577 0.983467 TGAGTTGGGCTACAGATGCA 59.017 50.000 0.00 0.00 0.00 3.96
579 588 0.963962 ACAGATGCAAAGTGCCCAAG 59.036 50.000 0.00 0.00 44.23 3.61
586 595 1.474077 GCAAAGTGCCCAAGATAGGTG 59.526 52.381 0.00 0.00 37.42 4.00
610 619 3.697542 AGGTAACCAAACACACCTTGTTC 59.302 43.478 0.00 0.00 43.21 3.18
611 620 5.411184 AGGTAACCAAACACACCTTGTTCC 61.411 45.833 0.00 0.00 43.21 3.62
629 638 3.944871 CACTTGGCTTGTGGTTCAC 57.055 52.632 3.21 0.00 34.56 3.18
630 639 0.385390 CACTTGGCTTGTGGTTCACC 59.615 55.000 3.21 0.00 32.73 4.02
631 640 0.258774 ACTTGGCTTGTGGTTCACCT 59.741 50.000 0.00 0.00 36.82 4.00
632 641 1.493022 ACTTGGCTTGTGGTTCACCTA 59.507 47.619 0.00 0.00 36.82 3.08
633 642 2.092103 ACTTGGCTTGTGGTTCACCTAA 60.092 45.455 0.00 0.00 36.82 2.69
634 643 2.738587 TGGCTTGTGGTTCACCTAAA 57.261 45.000 0.00 0.00 36.82 1.85
635 644 3.019799 TGGCTTGTGGTTCACCTAAAA 57.980 42.857 0.00 0.00 36.82 1.52
636 645 3.366396 TGGCTTGTGGTTCACCTAAAAA 58.634 40.909 0.00 0.00 36.82 1.94
824 833 5.464168 CAGGTATTTCTTTGAAGCAACCTG 58.536 41.667 16.09 16.09 35.68 4.00
895 968 1.122419 GAATTGAAAGCGAGCGTGCG 61.122 55.000 0.00 0.00 40.67 5.34
905 978 0.574922 CGAGCGTGCGTGCATTATTA 59.425 50.000 0.00 0.00 37.31 0.98
907 980 1.326245 GAGCGTGCGTGCATTATTACA 59.674 47.619 0.00 0.00 37.31 2.41
908 981 1.735018 AGCGTGCGTGCATTATTACAA 59.265 42.857 0.00 0.00 37.31 2.41
909 982 1.837747 GCGTGCGTGCATTATTACAAC 59.162 47.619 0.00 0.00 34.15 3.32
923 996 3.742433 TTACAACACAATTTGGCAGGG 57.258 42.857 0.78 0.00 0.00 4.45
941 1014 2.711542 GGGATCACACACAACCCTAAG 58.288 52.381 0.00 0.00 37.75 2.18
962 1036 8.739972 CCTAAGCAAATGGAAGTACAATTAGTT 58.260 33.333 0.00 0.00 0.00 2.24
1033 1107 3.192844 AGAGAAATGTGCATGCCAAAGAG 59.807 43.478 16.68 0.00 0.00 2.85
1116 1197 3.393941 GGAGATGATTCACAAGGGATCCT 59.606 47.826 12.58 0.00 33.87 3.24
1139 1220 1.151450 CTTGGTGCTGGTCCCTTGT 59.849 57.895 0.00 0.00 0.00 3.16
1247 1328 1.003839 CAACAAGCTCGCCTGGGTA 60.004 57.895 0.00 0.00 0.00 3.69
1250 1331 1.003839 CAAGCTCGCCTGGGTACAA 60.004 57.895 0.00 0.00 0.00 2.41
1296 1394 8.463930 TCTCTTGTTGTTGATCCTGTTTAATT 57.536 30.769 0.00 0.00 0.00 1.40
1336 1434 1.908619 TGCTGGTTCTTCTGGCTGATA 59.091 47.619 0.00 0.00 0.00 2.15
1579 1677 2.668280 GGCCAAGTTCACGTCGCTC 61.668 63.158 0.00 0.00 0.00 5.03
1655 1753 1.376424 CACGCCAGCTTCCTCATGT 60.376 57.895 0.00 0.00 0.00 3.21
1855 1953 4.479993 ACCAGCTCCATGCCGCTC 62.480 66.667 4.23 0.00 44.23 5.03
1887 1985 2.050351 CGTGGACAGAACGAGCGT 60.050 61.111 0.00 0.00 43.68 5.07
1889 1987 2.081212 GTGGACAGAACGAGCGTCG 61.081 63.158 0.00 5.97 46.93 5.12
2055 3382 9.941325 AAATGAGTATGAAGCTATCTTGATAGG 57.059 33.333 16.53 2.60 30.79 2.57
2058 3385 8.928448 TGAGTATGAAGCTATCTTGATAGGTTT 58.072 33.333 25.88 17.79 42.72 3.27
2064 3391 8.489489 TGAAGCTATCTTGATAGGTTTCTGAAT 58.511 33.333 25.88 10.48 42.72 2.57
2065 3392 9.336171 GAAGCTATCTTGATAGGTTTCTGAATT 57.664 33.333 25.88 9.93 42.72 2.17
2066 3393 8.674263 AGCTATCTTGATAGGTTTCTGAATTG 57.326 34.615 14.38 0.00 31.47 2.32
2068 3395 7.716998 GCTATCTTGATAGGTTTCTGAATTGGA 59.283 37.037 16.53 0.00 0.00 3.53
2069 3396 9.618890 CTATCTTGATAGGTTTCTGAATTGGAA 57.381 33.333 9.21 0.00 0.00 3.53
2070 3397 8.884124 ATCTTGATAGGTTTCTGAATTGGAAA 57.116 30.769 0.00 0.00 0.00 3.13
2071 3398 8.340618 TCTTGATAGGTTTCTGAATTGGAAAG 57.659 34.615 0.00 0.00 34.02 2.62
2072 3399 8.163408 TCTTGATAGGTTTCTGAATTGGAAAGA 58.837 33.333 0.00 0.00 34.02 2.52
2132 4807 4.491676 CATTGCTTTTCAGTTGATGGGAG 58.508 43.478 0.00 0.00 0.00 4.30
2134 4809 3.565307 TGCTTTTCAGTTGATGGGAGTT 58.435 40.909 0.00 0.00 0.00 3.01
2135 4810 4.724399 TGCTTTTCAGTTGATGGGAGTTA 58.276 39.130 0.00 0.00 0.00 2.24
2136 4811 5.136828 TGCTTTTCAGTTGATGGGAGTTAA 58.863 37.500 0.00 0.00 0.00 2.01
2137 4812 5.009610 TGCTTTTCAGTTGATGGGAGTTAAC 59.990 40.000 0.00 0.00 0.00 2.01
2138 4813 5.009610 GCTTTTCAGTTGATGGGAGTTAACA 59.990 40.000 8.61 0.00 0.00 2.41
2139 4814 6.633500 TTTTCAGTTGATGGGAGTTAACAG 57.367 37.500 8.61 0.00 0.00 3.16
2140 4815 5.560722 TTCAGTTGATGGGAGTTAACAGA 57.439 39.130 8.61 0.00 0.00 3.41
2141 4816 5.152623 TCAGTTGATGGGAGTTAACAGAG 57.847 43.478 8.61 0.00 0.00 3.35
2144 4819 2.915869 TGATGGGAGTTAACAGAGGGT 58.084 47.619 8.61 0.00 0.00 4.34
2186 4893 6.727824 TTTTAGCTAGAGTTGATGTCAAGC 57.272 37.500 0.00 0.00 36.39 4.01
2190 4897 3.368843 GCTAGAGTTGATGTCAAGCCTCA 60.369 47.826 12.87 2.92 36.39 3.86
2192 4899 3.672808 AGAGTTGATGTCAAGCCTCAAG 58.327 45.455 12.87 0.00 36.39 3.02
2238 4945 4.069304 TGGTTAAACCAGACAAATCGAGG 58.931 43.478 0.00 0.00 44.79 4.63
2240 4947 2.951229 AAACCAGACAAATCGAGGGT 57.049 45.000 0.00 0.00 32.22 4.34
2263 4970 3.628008 TCGAAAGGATGTGACTAGGCTA 58.372 45.455 0.00 0.00 0.00 3.93
2264 4971 3.380637 TCGAAAGGATGTGACTAGGCTAC 59.619 47.826 0.00 0.00 0.00 3.58
2287 4994 4.507710 TGACAACCTCAGTAGAATCATGC 58.492 43.478 0.00 0.00 0.00 4.06
2295 5002 3.376234 TCAGTAGAATCATGCTGCAAAGC 59.624 43.478 6.36 0.00 33.42 3.51
2405 5160 3.437049 GTCTTGTTAGGTTGGTCATGCTC 59.563 47.826 0.00 0.00 0.00 4.26
2428 5183 2.225491 GCTCGTTGCATTTCACTGGTTA 59.775 45.455 0.00 0.00 42.31 2.85
2449 5204 8.394121 TGGTTAAATTTTGACAAAGAACATTGC 58.606 29.630 0.00 0.00 33.52 3.56
2473 5228 0.611714 ACACCCCTCATCAACCGTAC 59.388 55.000 0.00 0.00 0.00 3.67
2482 5237 2.028476 TCATCAACCGTACTCCACCAAG 60.028 50.000 0.00 0.00 0.00 3.61
2498 5253 7.015195 ACTCCACCAAGTTTAACAAATGCTATT 59.985 33.333 0.00 0.00 0.00 1.73
2560 5368 6.095860 TGAAATAGTCCATGGAAAATCTGCTG 59.904 38.462 18.20 0.00 0.00 4.41
2586 5394 8.450964 GCAACTAGACTGCAAACTATTCATTTA 58.549 33.333 14.20 0.00 39.69 1.40
2592 5400 8.230486 AGACTGCAAACTATTCATTTAAAGACG 58.770 33.333 0.00 0.00 0.00 4.18
2602 5410 3.886505 TCATTTAAAGACGCCAACCACTT 59.113 39.130 0.00 0.00 0.00 3.16
2603 5411 3.974871 TTTAAAGACGCCAACCACTTC 57.025 42.857 0.00 0.00 0.00 3.01
2618 5426 2.684881 CCACTTCCTGCATACCATCAAC 59.315 50.000 0.00 0.00 0.00 3.18
2636 5444 5.715439 TCAACTTCCAGGATCCAATACAT 57.285 39.130 15.82 0.00 0.00 2.29
2642 5450 5.449297 TCCAGGATCCAATACATTGACAA 57.551 39.130 15.82 0.00 40.14 3.18
2694 5502 8.044908 TGATGTACTAGGAATTACCAAAAGGTC 58.955 37.037 0.00 0.00 42.04 3.85
2700 5508 9.154632 ACTAGGAATTACCAAAAGGTCAAAAAT 57.845 29.630 0.00 0.00 42.04 1.82
2733 5543 2.092914 GCCCACCTAACAGACTAGCAAT 60.093 50.000 0.00 0.00 0.00 3.56
2940 5829 9.953565 TGAATACTATAGGCATAAAATGGTACC 57.046 33.333 4.43 4.43 0.00 3.34
2966 5855 8.433126 CACCTCTGTAACTTTTTATAAGACGTG 58.567 37.037 0.00 0.00 0.00 4.49
2982 5871 3.572682 AGACGTGTTTAGAGTCCATGACA 59.427 43.478 0.00 0.00 34.60 3.58
2988 5877 4.343814 TGTTTAGAGTCCATGACAGTGTCA 59.656 41.667 27.35 27.35 46.90 3.58
3017 5906 8.868635 AACGTCTTATATTAAGTTACAGAGGC 57.131 34.615 0.00 0.00 0.00 4.70
3027 5916 4.657436 AGTTACAGAGGCAGTAGCATAC 57.343 45.455 0.00 0.00 44.61 2.39
3041 5930 5.902051 GTAGCATACGAAAACATAGGGTC 57.098 43.478 0.00 0.00 0.00 4.46
3049 5938 8.765219 CATACGAAAACATAGGGTCATAAGAAG 58.235 37.037 0.00 0.00 0.00 2.85
3457 6358 2.112190 TGGTGCACCGGTATAATCTCA 58.888 47.619 30.07 5.67 39.43 3.27
3676 6577 1.682257 GAGGGCCTTCTTGCTGACT 59.318 57.895 7.89 0.00 0.00 3.41
3712 6613 1.070758 GTCAGAACCTCAGTGAAGGCA 59.929 52.381 8.13 0.00 40.34 4.75
3850 6751 1.349627 GCCGACAAGCATGATGACG 59.650 57.895 13.71 13.71 36.09 4.35
3853 6754 2.742774 CCGACAAGCATGATGACGATA 58.257 47.619 19.36 0.00 38.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.068194 GTCACTGAAGACTCGGACCTG 60.068 57.143 0.00 0.00 35.65 4.00
1 2 1.249407 GTCACTGAAGACTCGGACCT 58.751 55.000 0.00 0.00 35.65 3.85
6 7 0.730834 CCTGCGTCACTGAAGACTCG 60.731 60.000 0.00 0.00 36.38 4.18
17 18 1.672030 CACCTCAATGCCTGCGTCA 60.672 57.895 0.00 0.00 0.00 4.35
23 24 2.036256 GCCACCACCTCAATGCCT 59.964 61.111 0.00 0.00 0.00 4.75
59 60 8.352201 CCTTCAAAATCCATATCGAATGCTTTA 58.648 33.333 0.00 0.00 0.00 1.85
69 70 8.169977 TCAATAGCACCTTCAAAATCCATATC 57.830 34.615 0.00 0.00 0.00 1.63
75 76 4.706962 ACCCTCAATAGCACCTTCAAAATC 59.293 41.667 0.00 0.00 0.00 2.17
89 90 0.035152 CACCAGCAGCACCCTCAATA 60.035 55.000 0.00 0.00 0.00 1.90
95 96 4.648626 TCAGCACCAGCAGCACCC 62.649 66.667 0.00 0.00 45.49 4.61
100 101 1.970114 CCACCTTCAGCACCAGCAG 60.970 63.158 0.00 0.00 45.49 4.24
109 110 0.106719 ACCCACAACACCACCTTCAG 60.107 55.000 0.00 0.00 0.00 3.02
129 130 0.392193 CCACCCTCTGTAGCAGCAAG 60.392 60.000 0.00 0.00 0.00 4.01
138 139 1.681666 CATCAGCACCACCCTCTGT 59.318 57.895 0.00 0.00 0.00 3.41
139 140 1.077930 CCATCAGCACCACCCTCTG 60.078 63.158 0.00 0.00 0.00 3.35
140 141 1.539869 ACCATCAGCACCACCCTCT 60.540 57.895 0.00 0.00 0.00 3.69
170 171 6.857777 AACATAGCAAAGATAGCAGTGATC 57.142 37.500 0.00 0.00 0.00 2.92
184 185 7.665559 AGTCTTCAAACTGGATTAACATAGCAA 59.334 33.333 0.00 0.00 0.00 3.91
204 205 6.398918 ACATCACAATAGTACCACAGTCTTC 58.601 40.000 0.00 0.00 0.00 2.87
209 210 5.523916 GGCTAACATCACAATAGTACCACAG 59.476 44.000 0.00 0.00 0.00 3.66
222 225 5.701290 AGTAGTTCAAACAGGCTAACATCAC 59.299 40.000 0.43 0.00 0.00 3.06
316 325 0.511653 CAGCAGCAGCATACATAGCG 59.488 55.000 3.17 0.00 45.49 4.26
332 341 0.457035 CCAATACATGGGCACACAGC 59.543 55.000 0.00 0.00 46.27 4.40
350 359 3.097342 TCTAGGAGTGGTGAGGTTACC 57.903 52.381 0.00 0.00 41.24 2.85
380 389 9.508642 TTGGTTACATACAACTCAAATGATGTA 57.491 29.630 0.74 0.74 33.24 2.29
410 419 1.023513 ACCGAGATGCAAAGAGCTGC 61.024 55.000 0.00 0.00 45.94 5.25
428 437 4.157656 TGTTTGGTTGCCTGCATATTCTAC 59.842 41.667 0.00 0.00 0.00 2.59
434 443 1.612950 CTGTGTTTGGTTGCCTGCATA 59.387 47.619 0.00 0.00 0.00 3.14
441 450 0.248866 CGGAACCTGTGTTTGGTTGC 60.249 55.000 2.67 5.08 46.59 4.17
445 454 0.750182 ACACCGGAACCTGTGTTTGG 60.750 55.000 9.46 0.00 40.54 3.28
473 482 0.455005 GCAAGCTCTTCAATCTGCCC 59.545 55.000 0.00 0.00 0.00 5.36
483 492 3.193267 TGTTTGTTTGTCTGCAAGCTCTT 59.807 39.130 0.00 0.00 36.86 2.85
486 495 3.591196 TTGTTTGTTTGTCTGCAAGCT 57.409 38.095 0.00 0.00 36.86 3.74
489 498 5.354767 TGCATATTGTTTGTTTGTCTGCAA 58.645 33.333 0.00 0.00 34.48 4.08
508 517 9.777297 ATACAGGTCAAAAATTAAGTTTTGCAT 57.223 25.926 27.74 19.92 44.56 3.96
520 529 6.719370 TGGCTAAGTGAATACAGGTCAAAAAT 59.281 34.615 0.00 0.00 0.00 1.82
529 538 5.105554 ACTCAGTCTGGCTAAGTGAATACAG 60.106 44.000 0.00 0.00 0.00 2.74
540 549 1.983224 GCCCAACTCAGTCTGGCTA 59.017 57.895 9.78 0.00 39.05 3.93
547 556 1.065854 GCATCTGTAGCCCAACTCAGT 60.066 52.381 0.00 0.00 0.00 3.41
568 577 1.075374 TGCACCTATCTTGGGCACTTT 59.925 47.619 0.00 0.00 31.61 2.66
579 588 3.439129 GTGTTTGGTTACCTGCACCTATC 59.561 47.826 2.07 0.00 35.07 2.08
586 595 1.687563 AGGTGTGTTTGGTTACCTGC 58.312 50.000 2.07 0.00 41.76 4.85
611 620 0.385390 GGTGAACCACAAGCCAAGTG 59.615 55.000 0.00 0.00 35.86 3.16
614 623 2.738587 TTAGGTGAACCACAAGCCAA 57.261 45.000 1.62 0.00 38.89 4.52
636 645 4.499019 CGTACATCCACAAGCCAAGTTTTT 60.499 41.667 0.00 0.00 0.00 1.94
637 646 3.004315 CGTACATCCACAAGCCAAGTTTT 59.996 43.478 0.00 0.00 0.00 2.43
638 647 2.552315 CGTACATCCACAAGCCAAGTTT 59.448 45.455 0.00 0.00 0.00 2.66
639 648 2.151202 CGTACATCCACAAGCCAAGTT 58.849 47.619 0.00 0.00 0.00 2.66
640 649 1.808411 CGTACATCCACAAGCCAAGT 58.192 50.000 0.00 0.00 0.00 3.16
641 650 0.447801 GCGTACATCCACAAGCCAAG 59.552 55.000 0.00 0.00 0.00 3.61
642 651 0.250510 TGCGTACATCCACAAGCCAA 60.251 50.000 0.00 0.00 0.00 4.52
643 652 0.035534 ATGCGTACATCCACAAGCCA 60.036 50.000 0.00 0.00 0.00 4.75
644 653 0.378257 CATGCGTACATCCACAAGCC 59.622 55.000 0.00 0.00 32.87 4.35
645 654 1.086696 ACATGCGTACATCCACAAGC 58.913 50.000 0.00 0.00 32.87 4.01
646 655 2.095853 GGAACATGCGTACATCCACAAG 59.904 50.000 0.00 0.00 32.87 3.16
647 656 2.080693 GGAACATGCGTACATCCACAA 58.919 47.619 0.00 0.00 32.87 3.33
648 657 1.277842 AGGAACATGCGTACATCCACA 59.722 47.619 0.00 0.00 32.87 4.17
649 658 2.024176 AGGAACATGCGTACATCCAC 57.976 50.000 0.00 0.00 32.87 4.02
650 659 2.779755 AAGGAACATGCGTACATCCA 57.220 45.000 0.00 0.00 32.87 3.41
651 660 4.439057 TCTTAAGGAACATGCGTACATCC 58.561 43.478 1.85 0.00 32.87 3.51
798 807 5.010617 GGTTGCTTCAAAGAAATACCTGGAA 59.989 40.000 0.00 0.00 0.00 3.53
839 912 6.978080 GCGGATTTCCAGCTAATTAAATGAAA 59.022 34.615 0.00 0.00 34.38 2.69
895 968 6.146837 TGCCAAATTGTGTTGTAATAATGCAC 59.853 34.615 0.00 0.00 0.00 4.57
905 978 1.786937 TCCCTGCCAAATTGTGTTGT 58.213 45.000 0.00 0.00 0.00 3.32
907 980 2.299867 GTGATCCCTGCCAAATTGTGTT 59.700 45.455 0.00 0.00 0.00 3.32
908 981 1.895131 GTGATCCCTGCCAAATTGTGT 59.105 47.619 0.00 0.00 0.00 3.72
909 982 1.894466 TGTGATCCCTGCCAAATTGTG 59.106 47.619 0.00 0.00 0.00 3.33
923 996 2.778299 TGCTTAGGGTTGTGTGTGATC 58.222 47.619 0.00 0.00 0.00 2.92
962 1036 3.118811 TGATGATGGCACGAGATTGTACA 60.119 43.478 0.00 0.00 0.00 2.90
1033 1107 5.654650 TCTTCTCTTCTAGTCTTGTGATCCC 59.345 44.000 0.00 0.00 0.00 3.85
1116 1197 4.898607 GACCAGCACCAAGTCCAA 57.101 55.556 0.00 0.00 0.00 3.53
1124 1205 2.282462 CCACAAGGGACCAGCACC 60.282 66.667 0.00 0.00 40.01 5.01
1139 1220 1.820906 GAGCATGATCGCAAGCCCA 60.821 57.895 0.00 0.00 39.44 5.36
1296 1394 6.267817 CAGCACTGATCACAGAAAAGAAAAA 58.732 36.000 0.00 0.00 46.03 1.94
1309 1407 2.289882 CCAGAAGAACCAGCACTGATCA 60.290 50.000 0.00 0.00 0.00 2.92
1579 1677 2.125350 GCCAGGAAGCAGACGAGG 60.125 66.667 0.00 0.00 0.00 4.63
1707 1805 4.659172 CCCAGAAGTTGCCGCCCA 62.659 66.667 0.00 0.00 0.00 5.36
1855 1953 1.891919 CACGAACTGGTGGTGGTGG 60.892 63.158 0.00 0.00 34.27 4.61
2109 4784 3.258872 TCCCATCAACTGAAAAGCAATGG 59.741 43.478 0.00 0.00 33.53 3.16
2132 4807 1.069668 ACCACGTCACCCTCTGTTAAC 59.930 52.381 0.00 0.00 0.00 2.01
2134 4809 1.069513 CAACCACGTCACCCTCTGTTA 59.930 52.381 0.00 0.00 0.00 2.41
2135 4810 0.179056 CAACCACGTCACCCTCTGTT 60.179 55.000 0.00 0.00 0.00 3.16
2136 4811 1.445942 CAACCACGTCACCCTCTGT 59.554 57.895 0.00 0.00 0.00 3.41
2137 4812 1.961277 GCAACCACGTCACCCTCTG 60.961 63.158 0.00 0.00 0.00 3.35
2138 4813 2.426023 GCAACCACGTCACCCTCT 59.574 61.111 0.00 0.00 0.00 3.69
2139 4814 2.668550 GGCAACCACGTCACCCTC 60.669 66.667 0.00 0.00 0.00 4.30
2140 4815 2.829384 ATGGCAACCACGTCACCCT 61.829 57.895 0.00 0.00 35.80 4.34
2141 4816 2.282180 ATGGCAACCACGTCACCC 60.282 61.111 0.00 0.00 35.80 4.61
2144 4819 1.107114 AAAACATGGCAACCACGTCA 58.893 45.000 0.00 0.00 35.80 4.35
2186 4893 8.783833 TTTCTGAAGTTTAGATGATCTTGAGG 57.216 34.615 0.00 0.00 0.00 3.86
2235 4942 3.385111 AGTCACATCCTTTCGATACCCTC 59.615 47.826 0.00 0.00 0.00 4.30
2238 4945 4.796618 GCCTAGTCACATCCTTTCGATACC 60.797 50.000 0.00 0.00 0.00 2.73
2240 4947 4.215908 AGCCTAGTCACATCCTTTCGATA 58.784 43.478 0.00 0.00 0.00 2.92
2287 4994 4.861389 TGTTGTTTGAAATGCTTTGCAG 57.139 36.364 0.00 0.00 43.65 4.41
2295 5002 9.919348 CTGAGGTTTAAATTGTTGTTTGAAATG 57.081 29.630 0.00 0.00 0.00 2.32
2363 5116 9.541143 ACAAGACTGTTTCAAAAGAAAAGAAAA 57.459 25.926 0.00 0.00 33.54 2.29
2367 5120 9.076596 CCTAACAAGACTGTTTCAAAAGAAAAG 57.923 33.333 0.00 0.00 43.45 2.27
2368 5121 8.581578 ACCTAACAAGACTGTTTCAAAAGAAAA 58.418 29.630 0.00 0.00 43.45 2.29
2373 5126 6.209788 ACCAACCTAACAAGACTGTTTCAAAA 59.790 34.615 0.00 0.00 43.45 2.44
2383 5136 3.412386 AGCATGACCAACCTAACAAGAC 58.588 45.455 0.00 0.00 0.00 3.01
2428 5183 7.224362 TCGATGCAATGTTCTTTGTCAAAATTT 59.776 29.630 0.00 0.00 0.00 1.82
2449 5204 1.656652 GTTGATGAGGGGTGTCGATG 58.343 55.000 0.00 0.00 0.00 3.84
2473 5228 5.200368 AGCATTTGTTAAACTTGGTGGAG 57.800 39.130 0.00 0.00 0.00 3.86
2513 5318 9.545105 TTTCAATGATTTCTTGTGTTTAATGCT 57.455 25.926 0.00 0.00 0.00 3.79
2527 5335 9.874205 TTTTCCATGGACTATTTCAATGATTTC 57.126 29.630 15.91 0.00 37.84 2.17
2543 5351 2.219080 TGCAGCAGATTTTCCATGGA 57.781 45.000 11.44 11.44 0.00 3.41
2555 5363 3.222053 TGCAGTCTAGTTGCAGCAG 57.778 52.632 16.90 0.00 45.89 4.24
2560 5368 5.862924 TGAATAGTTTGCAGTCTAGTTGC 57.137 39.130 12.92 12.92 41.86 4.17
2586 5394 0.182775 AGGAAGTGGTTGGCGTCTTT 59.817 50.000 0.00 0.00 0.00 2.52
2592 5400 0.811281 GTATGCAGGAAGTGGTTGGC 59.189 55.000 0.00 0.00 0.00 4.52
2602 5410 2.575735 TGGAAGTTGATGGTATGCAGGA 59.424 45.455 0.00 0.00 0.00 3.86
2603 5411 2.947652 CTGGAAGTTGATGGTATGCAGG 59.052 50.000 0.00 0.00 0.00 4.85
2618 5426 5.439721 TGTCAATGTATTGGATCCTGGAAG 58.560 41.667 14.23 0.00 38.30 3.46
2636 5444 7.455641 TCAGAACTGTAAAGGTTTTTGTCAA 57.544 32.000 1.73 0.00 0.00 3.18
2642 5450 8.040727 AGCAAATTTCAGAACTGTAAAGGTTTT 58.959 29.630 1.73 0.00 0.00 2.43
2694 5502 6.830838 AGGTGGGCTTAGAAGATCTATTTTTG 59.169 38.462 0.00 0.00 0.00 2.44
2700 5508 5.525484 TGTTAGGTGGGCTTAGAAGATCTA 58.475 41.667 0.00 0.00 0.00 1.98
2702 5510 4.406003 TCTGTTAGGTGGGCTTAGAAGATC 59.594 45.833 0.00 0.00 0.00 2.75
2741 5551 4.325028 TGGAATCATGTTGCATATTGCC 57.675 40.909 0.00 0.00 44.23 4.52
2937 5826 9.933723 GTCTTATAAAAAGTTACAGAGGTGGTA 57.066 33.333 0.00 0.00 0.00 3.25
2940 5829 8.433126 CACGTCTTATAAAAAGTTACAGAGGTG 58.567 37.037 0.00 0.00 39.45 4.00
2966 5855 4.883083 TGACACTGTCATGGACTCTAAAC 58.117 43.478 7.84 0.00 37.67 2.01
3017 5906 5.357257 ACCCTATGTTTTCGTATGCTACTG 58.643 41.667 0.00 0.00 0.00 2.74
3027 5916 5.584649 TGCTTCTTATGACCCTATGTTTTCG 59.415 40.000 0.00 0.00 0.00 3.46
3041 5930 6.150318 GCATTGAAGATCCATGCTTCTTATG 58.850 40.000 11.36 13.49 41.71 1.90
3049 5938 5.234329 CAGAATTTGCATTGAAGATCCATGC 59.766 40.000 8.90 8.90 38.60 4.06
3457 6358 2.751816 GCCTCCTAACCTGGTTGTTTGT 60.752 50.000 22.04 0.00 0.00 2.83
3676 6577 5.527951 GGTTCTGACTCAGATCTATCGTGTA 59.472 44.000 9.63 0.00 40.39 2.90
3712 6613 0.687354 AGGCCATGAACGTTGAGACT 59.313 50.000 5.00 0.00 0.00 3.24
3850 6751 4.083643 CGGGATCACACAGATGCAAATATC 60.084 45.833 0.00 0.00 45.99 1.63
3853 6754 2.019249 CGGGATCACACAGATGCAAAT 58.981 47.619 0.00 0.00 45.99 2.32


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

AutoCloner maintained by Alex Coulton.