Multiple sequence alignment - TraesCS3A01G117000

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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 TraesCS3A01G117000 chr3A 100.000 2438 0 0 1 2438 86372907 86375344 0.000000e+00 4503
1 TraesCS3A01G117000 chr3D 90.538 2452 140 44 1 2415 73393133 73395529 0.000000e+00 3158
2 TraesCS3A01G117000 chr3B 89.872 2261 135 46 217 2418 118759179 118761404 0.000000e+00 2820
3 TraesCS3A01G117000 chr3B 92.275 233 14 3 1 233 118758934 118759162 6.500000e-86 327
4 TraesCS3A01G117000 chr2D 91.332 773 36 11 1349 2109 66077207 66076454 0.000000e+00 1027
5 TraesCS3A01G117000 chrUn 90.496 726 37 13 1398 2111 105815339 105816044 0.000000e+00 929
6 TraesCS3A01G117000 chrUn 90.496 726 38 13 1398 2111 106336592 106337298 0.000000e+00 929
7 TraesCS3A01G117000 chr5D 90.234 727 39 15 1398 2111 180244278 180244985 0.000000e+00 920
8 TraesCS3A01G117000 chr5D 90.220 726 40 12 1398 2111 187522747 187523453 0.000000e+00 918


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 TraesCS3A01G117000 chr3A 86372907 86375344 2437 False 4503.0 4503 100.0000 1 2438 1 chr3A.!!$F1 2437
1 TraesCS3A01G117000 chr3D 73393133 73395529 2396 False 3158.0 3158 90.5380 1 2415 1 chr3D.!!$F1 2414
2 TraesCS3A01G117000 chr3B 118758934 118761404 2470 False 1573.5 2820 91.0735 1 2418 2 chr3B.!!$F1 2417
3 TraesCS3A01G117000 chr2D 66076454 66077207 753 True 1027.0 1027 91.3320 1349 2109 1 chr2D.!!$R1 760
4 TraesCS3A01G117000 chrUn 105815339 105816044 705 False 929.0 929 90.4960 1398 2111 1 chrUn.!!$F1 713
5 TraesCS3A01G117000 chrUn 106336592 106337298 706 False 929.0 929 90.4960 1398 2111 1 chrUn.!!$F2 713
6 TraesCS3A01G117000 chr5D 180244278 180244985 707 False 920.0 920 90.2340 1398 2111 1 chr5D.!!$F1 713
7 TraesCS3A01G117000 chr5D 187522747 187523453 706 False 918.0 918 90.2200 1398 2111 1 chr5D.!!$F2 713

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
988 1042 0.036388 TTGATTCTCGCCACTGTCCC 60.036 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2309 0.179006 GATGCCAACCCCATCCTCTC 60.179 60.0 0.0 0.0 34.43 3.2 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
72 73 9.545611 GCATTATGAAAAACAAGCAAATAAAGG 57.454 29.630 0.00 0.00 0.00 3.11
89 90 6.969828 ATAAAGGTCACGTTCTCTTCATTC 57.030 37.500 0.00 0.00 0.00 2.67
94 95 3.619038 GTCACGTTCTCTTCATTCCCATC 59.381 47.826 0.00 0.00 0.00 3.51
97 98 4.034858 CACGTTCTCTTCATTCCCATCATG 59.965 45.833 0.00 0.00 0.00 3.07
146 147 5.766174 GGGGTTGAAATAGTAAAGACACACA 59.234 40.000 0.00 0.00 0.00 3.72
182 183 5.971792 CAGCAAGAATTGATTGACATAGCTG 59.028 40.000 0.00 0.00 46.08 4.24
219 220 1.901833 GGGGGAAGCACAACATGAAAT 59.098 47.619 0.00 0.00 0.00 2.17
275 309 7.795734 GCAACGAGATATTCTGTAATTGATGTG 59.204 37.037 0.00 0.00 0.00 3.21
291 325 4.331108 TGATGTGGTGTTTAGCAATGCTA 58.669 39.130 11.40 11.40 40.44 3.49
369 405 2.356069 TGACGTTGTGTTTAGCAATGCA 59.644 40.909 8.35 0.00 36.59 3.96
380 416 7.384660 TGTGTTTAGCAATGCATTTTTAGAAGG 59.615 33.333 9.83 0.00 0.00 3.46
506 543 2.562912 TCGACGCTTACCCGACAC 59.437 61.111 0.00 0.00 0.00 3.67
507 544 1.968017 TCGACGCTTACCCGACACT 60.968 57.895 0.00 0.00 0.00 3.55
508 545 1.800315 CGACGCTTACCCGACACTG 60.800 63.158 0.00 0.00 0.00 3.66
509 546 1.288127 GACGCTTACCCGACACTGT 59.712 57.895 0.00 0.00 0.00 3.55
510 547 1.006571 ACGCTTACCCGACACTGTG 60.007 57.895 6.19 6.19 0.00 3.66
555 598 7.551585 TGTTTCAAGTTGTTTCCATGTAACAT 58.448 30.769 10.37 0.00 35.60 2.71
583 626 7.800155 TCATGCGATGGAAATATAGTTTTCA 57.200 32.000 0.00 0.00 37.34 2.69
585 628 8.291740 TCATGCGATGGAAATATAGTTTTCATG 58.708 33.333 7.21 0.00 37.34 3.07
587 630 6.039159 TGCGATGGAAATATAGTTTTCATGCA 59.961 34.615 14.73 14.73 37.34 3.96
591 634 8.597662 ATGGAAATATAGTTTTCATGCAATGC 57.402 30.769 0.00 0.00 46.21 3.56
601 644 8.556213 AGTTTTCATGCAATGCAATTATTTCT 57.444 26.923 13.45 3.29 46.21 2.52
669 713 6.630444 ATGTGCTGTTAGATGATCAATTCC 57.370 37.500 0.00 0.00 0.00 3.01
679 723 2.923121 TGATCAATTCCAGCCAGCTAC 58.077 47.619 0.00 0.00 0.00 3.58
824 874 7.934120 ACTTAATTAAGAAGATTCCCATCCTCG 59.066 37.037 27.92 0.38 37.08 4.63
834 884 0.179062 CCCATCCTCGGCTGAAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
841 891 2.485814 CCTCGGCTGAAGAAGAAAAAGG 59.514 50.000 0.00 0.00 0.00 3.11
864 914 5.340027 GGAGAAGATTTCCATCCTAACCCAA 60.340 44.000 0.00 0.00 34.74 4.12
867 917 5.796502 AGATTTCCATCCTAACCCAAGAA 57.203 39.130 0.00 0.00 0.00 2.52
977 1031 4.499019 CGCTACCTCCTCTTCTTGATTCTC 60.499 50.000 0.00 0.00 0.00 2.87
988 1042 0.036388 TTGATTCTCGCCACTGTCCC 60.036 55.000 0.00 0.00 0.00 4.46
1119 1193 2.868787 GACGACTTCGACGACGGC 60.869 66.667 16.77 11.01 43.02 5.68
1242 1316 1.684450 GTCCGGGAGAAGAAGAGGATC 59.316 57.143 0.00 0.00 0.00 3.36
1497 1581 4.006026 TGACCGTCGTTTCTTTTGTTTC 57.994 40.909 0.00 0.00 0.00 2.78
1499 1583 4.154556 TGACCGTCGTTTCTTTTGTTTCTT 59.845 37.500 0.00 0.00 0.00 2.52
1500 1584 4.655027 ACCGTCGTTTCTTTTGTTTCTTC 58.345 39.130 0.00 0.00 0.00 2.87
1543 1629 3.322254 TCTCTGTCTCAGTTTTGGAGTCC 59.678 47.826 0.73 0.73 34.04 3.85
1625 1716 5.358160 CCAATATCATGATCAGCATCTGCAT 59.642 40.000 12.53 0.00 45.16 3.96
1638 1729 3.365064 GCATCTGCATCAATCTTCATCGG 60.365 47.826 0.00 0.00 41.59 4.18
1664 1756 4.023291 TGCCCCAAACCTTTATGAATCTC 58.977 43.478 0.00 0.00 0.00 2.75
1760 1859 7.615582 TTGCTTAGTTCCAACATCTATCAAG 57.384 36.000 0.00 0.00 0.00 3.02
1776 1877 7.275888 TCTATCAAGCATGTGAAAACAGTTT 57.724 32.000 0.00 0.00 0.00 2.66
1777 1878 7.715657 TCTATCAAGCATGTGAAAACAGTTTT 58.284 30.769 11.22 11.22 35.12 2.43
1781 1882 5.783100 AGCATGTGAAAACAGTTTTGTTG 57.217 34.783 16.21 8.70 46.54 3.33
1790 1891 6.873076 TGAAAACAGTTTTGTTGCAAGAATCT 59.127 30.769 16.21 8.93 46.54 2.40
1791 1892 8.031864 TGAAAACAGTTTTGTTGCAAGAATCTA 58.968 29.630 16.21 0.00 46.54 1.98
1792 1893 7.755582 AAACAGTTTTGTTGCAAGAATCTAC 57.244 32.000 10.13 8.83 46.54 2.59
1793 1894 6.449635 ACAGTTTTGTTGCAAGAATCTACA 57.550 33.333 10.13 0.00 32.28 2.74
1794 1895 6.498304 ACAGTTTTGTTGCAAGAATCTACAG 58.502 36.000 10.13 8.29 32.28 2.74
1795 1896 6.095440 ACAGTTTTGTTGCAAGAATCTACAGT 59.905 34.615 10.13 8.84 32.28 3.55
1798 1899 8.850156 AGTTTTGTTGCAAGAATCTACAGTAAT 58.150 29.630 10.13 0.00 0.00 1.89
1808 1909 9.713740 CAAGAATCTACAGTAATTGCAAATCTC 57.286 33.333 1.71 0.00 0.00 2.75
1814 1915 4.460382 ACAGTAATTGCAAATCTCACCAGG 59.540 41.667 1.71 0.00 0.00 4.45
1817 1918 4.525912 AATTGCAAATCTCACCAGGAAC 57.474 40.909 1.71 0.00 0.00 3.62
2055 2164 5.188751 ACCAAAAGGGATTTTCACAAAGACA 59.811 36.000 0.00 0.00 41.15 3.41
2076 2185 2.809446 TGACAGCGAAATATCTGACCG 58.191 47.619 0.00 0.00 34.57 4.79
2084 2193 4.537965 CGAAATATCTGACCGTCTACAGG 58.462 47.826 0.00 0.00 35.20 4.00
2122 2231 2.290641 ACGACAATCTGGTGAAGCAAAC 59.709 45.455 0.00 0.00 0.00 2.93
2143 2252 7.201635 GCAAACTTCATTCCATTGACAGTTTTT 60.202 33.333 0.00 0.00 36.25 1.94
2144 2253 7.775397 AACTTCATTCCATTGACAGTTTTTG 57.225 32.000 0.00 0.00 30.13 2.44
2145 2254 5.754890 ACTTCATTCCATTGACAGTTTTTGC 59.245 36.000 0.00 0.00 0.00 3.68
2146 2255 5.273674 TCATTCCATTGACAGTTTTTGCA 57.726 34.783 0.00 0.00 0.00 4.08
2168 2277 8.459521 TGCATCACAAATTAATAGAAAAACGG 57.540 30.769 0.00 0.00 0.00 4.44
2169 2278 8.085296 TGCATCACAAATTAATAGAAAAACGGT 58.915 29.630 0.00 0.00 0.00 4.83
2170 2279 8.583765 GCATCACAAATTAATAGAAAAACGGTC 58.416 33.333 0.00 0.00 0.00 4.79
2171 2280 9.072294 CATCACAAATTAATAGAAAAACGGTCC 57.928 33.333 0.00 0.00 0.00 4.46
2174 2283 9.769093 CACAAATTAATAGAAAAACGGTCCTAG 57.231 33.333 0.00 0.00 0.00 3.02
2181 2290 7.902387 ATAGAAAAACGGTCCTAGAGAAAAC 57.098 36.000 0.00 0.00 0.00 2.43
2183 2292 5.990386 AGAAAAACGGTCCTAGAGAAAACTC 59.010 40.000 0.00 0.00 0.00 3.01
2184 2293 4.950205 AAACGGTCCTAGAGAAAACTCA 57.050 40.909 0.00 0.00 0.00 3.41
2186 2295 2.826725 ACGGTCCTAGAGAAAACTCAGG 59.173 50.000 0.00 0.00 0.00 3.86
2187 2296 3.090037 CGGTCCTAGAGAAAACTCAGGA 58.910 50.000 0.00 0.00 32.39 3.86
2191 2300 3.452627 TCCTAGAGAAAACTCAGGATGGC 59.547 47.826 0.00 0.00 36.16 4.40
2192 2301 3.454082 CCTAGAGAAAACTCAGGATGGCT 59.546 47.826 0.00 0.00 36.16 4.75
2193 2302 4.080638 CCTAGAGAAAACTCAGGATGGCTT 60.081 45.833 0.00 0.00 36.16 4.35
2200 2309 3.922171 ACTCAGGATGGCTTTTAGGAG 57.078 47.619 0.00 0.00 36.16 3.69
2201 2310 3.454858 ACTCAGGATGGCTTTTAGGAGA 58.545 45.455 0.00 0.00 36.16 3.71
2259 2368 3.194062 CCTCATCTCTCTTTCGAAAGGC 58.806 50.000 31.82 0.00 36.67 4.35
2278 2387 2.100916 GGCAGAGGTCGCAGTTAATCTA 59.899 50.000 0.00 0.00 0.00 1.98
2280 2389 3.376540 CAGAGGTCGCAGTTAATCTAGC 58.623 50.000 0.00 0.00 0.00 3.42
2283 2392 3.292460 AGGTCGCAGTTAATCTAGCTCT 58.708 45.455 0.00 0.00 0.00 4.09
2284 2393 3.702045 AGGTCGCAGTTAATCTAGCTCTT 59.298 43.478 0.00 0.00 0.00 2.85
2285 2394 4.160626 AGGTCGCAGTTAATCTAGCTCTTT 59.839 41.667 0.00 0.00 0.00 2.52
2286 2395 5.360144 AGGTCGCAGTTAATCTAGCTCTTTA 59.640 40.000 0.00 0.00 0.00 1.85
2287 2396 6.040878 GGTCGCAGTTAATCTAGCTCTTTAA 58.959 40.000 0.00 0.00 0.00 1.52
2288 2397 6.534079 GGTCGCAGTTAATCTAGCTCTTTAAA 59.466 38.462 0.00 0.00 0.00 1.52
2289 2398 7.254151 GGTCGCAGTTAATCTAGCTCTTTAAAG 60.254 40.741 9.04 9.04 0.00 1.85
2371 2480 0.755327 GGTTCACCACTTTGGCACCT 60.755 55.000 0.00 0.00 42.67 4.00
2373 2482 2.303175 GTTCACCACTTTGGCACCTTA 58.697 47.619 0.00 0.00 42.67 2.69
2377 2486 4.076394 TCACCACTTTGGCACCTTAATAC 58.924 43.478 0.00 0.00 42.67 1.89
2386 2495 5.715434 TGGCACCTTAATACTTTTTGTCC 57.285 39.130 0.00 0.00 0.00 4.02
2406 2515 5.105797 TGTCCATTTGCAAGTGGATTATCAC 60.106 40.000 36.93 26.25 45.57 3.06
2410 2519 6.238731 CCATTTGCAAGTGGATTATCACGTAT 60.239 38.462 31.44 0.00 42.10 3.06
2411 2520 7.041440 CCATTTGCAAGTGGATTATCACGTATA 60.041 37.037 31.44 0.00 42.10 1.47
2412 2521 6.838198 TTGCAAGTGGATTATCACGTATAC 57.162 37.500 0.00 0.00 42.10 1.47
2413 2522 6.156748 TGCAAGTGGATTATCACGTATACT 57.843 37.500 0.56 0.00 42.10 2.12
2415 2524 6.700081 TGCAAGTGGATTATCACGTATACTTC 59.300 38.462 0.56 0.00 42.10 3.01
2417 2526 7.434492 CAAGTGGATTATCACGTATACTTCCT 58.566 38.462 0.56 0.00 42.10 3.36
2419 2528 7.659186 AGTGGATTATCACGTATACTTCCTTC 58.341 38.462 0.56 0.00 42.10 3.46
2420 2529 6.581542 GTGGATTATCACGTATACTTCCTTCG 59.418 42.308 0.56 0.00 0.00 3.79
2421 2530 6.487668 TGGATTATCACGTATACTTCCTTCGA 59.512 38.462 0.56 0.00 0.00 3.71
2422 2531 7.176165 TGGATTATCACGTATACTTCCTTCGAT 59.824 37.037 0.56 0.00 0.00 3.59
2423 2532 8.027771 GGATTATCACGTATACTTCCTTCGATT 58.972 37.037 0.56 0.00 0.00 3.34
2424 2533 8.744008 ATTATCACGTATACTTCCTTCGATTG 57.256 34.615 0.56 0.00 0.00 2.67
2425 2534 5.571784 TCACGTATACTTCCTTCGATTGT 57.428 39.130 0.56 0.00 0.00 2.71
2426 2535 6.682423 TCACGTATACTTCCTTCGATTGTA 57.318 37.500 0.56 0.00 0.00 2.41
2427 2536 7.268199 TCACGTATACTTCCTTCGATTGTAT 57.732 36.000 0.56 0.00 0.00 2.29
2428 2537 7.709947 TCACGTATACTTCCTTCGATTGTATT 58.290 34.615 0.56 0.00 0.00 1.89
2429 2538 8.839343 TCACGTATACTTCCTTCGATTGTATTA 58.161 33.333 0.56 0.00 0.00 0.98
2430 2539 9.454585 CACGTATACTTCCTTCGATTGTATTAA 57.545 33.333 0.56 0.00 0.00 1.40
2431 2540 9.674824 ACGTATACTTCCTTCGATTGTATTAAG 57.325 33.333 0.56 0.00 0.00 1.85
2432 2541 9.125906 CGTATACTTCCTTCGATTGTATTAAGG 57.874 37.037 0.56 0.00 39.93 2.69
2433 2542 9.978044 GTATACTTCCTTCGATTGTATTAAGGT 57.022 33.333 0.00 0.00 39.62 3.50
2435 2544 7.611213 ACTTCCTTCGATTGTATTAAGGTTG 57.389 36.000 0.00 0.00 39.62 3.77
2436 2545 7.391620 ACTTCCTTCGATTGTATTAAGGTTGA 58.608 34.615 0.00 0.00 39.62 3.18
2437 2546 7.549488 ACTTCCTTCGATTGTATTAAGGTTGAG 59.451 37.037 0.00 0.00 39.62 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.040147 TGGGAATGAAGAGAACGTGAC 57.960 47.619 0.00 0.00 0.00 3.67
89 90 0.747644 TACAACTGGCGCATGATGGG 60.748 55.000 10.83 4.99 0.00 4.00
94 95 0.382873 ATGCATACAACTGGCGCATG 59.617 50.000 10.83 3.13 41.54 4.06
97 98 1.064621 CCATGCATACAACTGGCGC 59.935 57.895 0.00 0.00 0.00 6.53
125 126 6.801862 GCCATGTGTGTCTTTACTATTTCAAC 59.198 38.462 0.00 0.00 0.00 3.18
146 147 3.423539 TTCTTGCTGTCACTAAGCCAT 57.576 42.857 0.00 0.00 40.06 4.40
219 220 3.378512 AGTGAAGGATCATAGCTGGACA 58.621 45.455 0.00 0.00 38.01 4.02
229 263 2.610479 GCAACGTCTGAGTGAAGGATCA 60.610 50.000 0.00 0.00 0.00 2.92
275 309 8.980143 TTCTAAAAATAGCATTGCTAAACACC 57.020 30.769 21.47 0.00 44.62 4.16
291 325 9.014297 CAACCACCTAAGATGTCTTCTAAAAAT 57.986 33.333 0.00 0.00 37.40 1.82
369 405 5.325239 ACCAGCTAAGTGCCTTCTAAAAAT 58.675 37.500 0.00 0.00 44.23 1.82
380 416 3.253188 TGTTTCATCAACCAGCTAAGTGC 59.747 43.478 0.00 0.00 36.87 4.40
441 477 3.573491 GCGCGGGGCTTGTGATAC 61.573 66.667 8.83 0.00 39.11 2.24
496 533 2.095110 CGTACATCACAGTGTCGGGTAA 60.095 50.000 0.00 0.00 33.62 2.85
505 542 4.783764 TGTTCTCATCGTACATCACAGT 57.216 40.909 0.00 0.00 0.00 3.55
506 543 5.879948 GATGTTCTCATCGTACATCACAG 57.120 43.478 0.00 0.00 44.67 3.66
555 598 9.868277 AAAACTATATTTCCATCGCATGAAAAA 57.132 25.926 0.00 0.64 0.00 1.94
583 626 4.269123 CACGCAGAAATAATTGCATTGCAT 59.731 37.500 12.95 0.58 38.76 3.96
585 628 3.858812 TCACGCAGAAATAATTGCATTGC 59.141 39.130 0.46 0.46 40.28 3.56
587 630 5.314923 ACTCACGCAGAAATAATTGCATT 57.685 34.783 0.00 0.00 40.28 3.56
590 633 6.139169 CGAATTACTCACGCAGAAATAATTGC 59.861 38.462 9.95 0.00 32.12 3.56
591 634 6.628856 CCGAATTACTCACGCAGAAATAATTG 59.371 38.462 9.95 5.59 32.12 2.32
601 644 5.866335 AATTAAACCGAATTACTCACGCA 57.134 34.783 0.00 0.00 0.00 5.24
663 707 2.093288 TGAGAGTAGCTGGCTGGAATTG 60.093 50.000 5.25 0.00 0.00 2.32
669 713 1.547820 TGAAGTGAGAGTAGCTGGCTG 59.452 52.381 5.25 0.00 0.00 4.85
773 817 8.404000 GTGAGTACTGCTAGTAAATAAGTGCTA 58.596 37.037 0.00 0.00 34.53 3.49
824 874 5.066593 TCTTCTCCTTTTTCTTCTTCAGCC 58.933 41.667 0.00 0.00 0.00 4.85
834 884 8.462811 GTTAGGATGGAAATCTTCTCCTTTTTC 58.537 37.037 3.36 0.00 36.24 2.29
841 891 5.373812 TGGGTTAGGATGGAAATCTTCTC 57.626 43.478 0.00 0.00 0.00 2.87
1119 1193 2.742372 CCGGCCTTGTCGAAGTGG 60.742 66.667 0.00 0.00 29.41 4.00
1242 1316 4.463879 CCGGTGGAGCAGAGCAGG 62.464 72.222 0.00 0.00 0.00 4.85
1497 1581 5.294552 ACGAGAAAACAAGAAACAGAGGAAG 59.705 40.000 0.00 0.00 0.00 3.46
1499 1583 4.766375 ACGAGAAAACAAGAAACAGAGGA 58.234 39.130 0.00 0.00 0.00 3.71
1500 1584 4.811557 AGACGAGAAAACAAGAAACAGAGG 59.188 41.667 0.00 0.00 0.00 3.69
1543 1629 5.894807 ACATTCCTTTTCACAGTTGTTGAG 58.105 37.500 0.00 0.00 0.00 3.02
1625 1716 2.491693 GGGCAAAACCGATGAAGATTGA 59.508 45.455 0.00 0.00 40.62 2.57
1638 1729 4.344359 TCATAAAGGTTTGGGGCAAAAC 57.656 40.909 6.51 6.51 40.90 2.43
1664 1756 1.081041 TTGCTTGCATCTTGCTGCG 60.081 52.632 0.00 0.00 45.31 5.18
1760 1859 4.142945 TGCAACAAAACTGTTTTCACATGC 60.143 37.500 22.00 22.00 30.39 4.06
1776 1877 7.083858 GCAATTACTGTAGATTCTTGCAACAA 58.916 34.615 0.00 0.00 37.89 2.83
1777 1878 6.206438 TGCAATTACTGTAGATTCTTGCAACA 59.794 34.615 15.12 0.00 42.98 3.33
1781 1882 8.186821 AGATTTGCAATTACTGTAGATTCTTGC 58.813 33.333 0.00 0.00 38.33 4.01
1790 1891 5.647658 CCTGGTGAGATTTGCAATTACTGTA 59.352 40.000 0.00 0.00 0.00 2.74
1791 1892 4.460382 CCTGGTGAGATTTGCAATTACTGT 59.540 41.667 0.00 0.00 0.00 3.55
1792 1893 4.701651 TCCTGGTGAGATTTGCAATTACTG 59.298 41.667 0.00 0.00 0.00 2.74
1793 1894 4.922206 TCCTGGTGAGATTTGCAATTACT 58.078 39.130 0.00 0.00 0.00 2.24
1794 1895 5.183904 AGTTCCTGGTGAGATTTGCAATTAC 59.816 40.000 0.00 0.00 0.00 1.89
1795 1896 5.183713 CAGTTCCTGGTGAGATTTGCAATTA 59.816 40.000 0.00 0.00 0.00 1.40
1798 1899 2.886523 CAGTTCCTGGTGAGATTTGCAA 59.113 45.455 0.00 0.00 0.00 4.08
1808 1909 1.002888 AGTGATGAGCAGTTCCTGGTG 59.997 52.381 0.00 0.00 42.53 4.17
1814 1915 5.353678 AGAGCATAAAAGTGATGAGCAGTTC 59.646 40.000 0.00 0.00 39.20 3.01
1817 1918 5.117584 AGAGAGCATAAAAGTGATGAGCAG 58.882 41.667 0.00 0.00 0.00 4.24
1822 1923 8.484641 TCTGTAAAGAGAGCATAAAAGTGATG 57.515 34.615 0.00 0.00 0.00 3.07
2055 2164 3.181475 ACGGTCAGATATTTCGCTGTCAT 60.181 43.478 0.00 0.00 33.90 3.06
2076 2185 5.295787 TGTTGTGTGTGAATTTCCTGTAGAC 59.704 40.000 0.00 0.00 0.00 2.59
2084 2193 4.407818 TGTCGTTGTTGTGTGTGAATTTC 58.592 39.130 0.00 0.00 0.00 2.17
2122 2231 5.754406 TGCAAAAACTGTCAATGGAATGAAG 59.246 36.000 0.00 0.00 0.00 3.02
2143 2252 8.085296 ACCGTTTTTCTATTAATTTGTGATGCA 58.915 29.630 0.00 0.00 0.00 3.96
2144 2253 8.460831 ACCGTTTTTCTATTAATTTGTGATGC 57.539 30.769 0.00 0.00 0.00 3.91
2145 2254 9.072294 GGACCGTTTTTCTATTAATTTGTGATG 57.928 33.333 0.00 0.00 0.00 3.07
2146 2255 9.020731 AGGACCGTTTTTCTATTAATTTGTGAT 57.979 29.630 0.00 0.00 0.00 3.06
2159 2268 5.926663 AGTTTTCTCTAGGACCGTTTTTCT 58.073 37.500 0.00 0.00 0.00 2.52
2166 2275 3.090037 TCCTGAGTTTTCTCTAGGACCG 58.910 50.000 10.17 0.00 46.30 4.79
2167 2276 4.141824 CCATCCTGAGTTTTCTCTAGGACC 60.142 50.000 13.92 0.00 46.37 4.46
2168 2277 4.682050 GCCATCCTGAGTTTTCTCTAGGAC 60.682 50.000 13.92 4.33 46.37 3.85
2169 2278 3.452627 GCCATCCTGAGTTTTCTCTAGGA 59.547 47.826 13.97 13.97 46.92 2.94
2170 2279 3.454082 AGCCATCCTGAGTTTTCTCTAGG 59.546 47.826 0.00 0.00 46.30 3.02
2171 2280 4.751767 AGCCATCCTGAGTTTTCTCTAG 57.248 45.455 0.00 0.00 46.30 2.43
2174 2283 5.124617 CCTAAAAGCCATCCTGAGTTTTCTC 59.875 44.000 0.00 0.00 46.33 2.87
2176 2285 5.010282 TCCTAAAAGCCATCCTGAGTTTTC 58.990 41.667 0.00 0.00 0.00 2.29
2177 2286 4.998051 TCCTAAAAGCCATCCTGAGTTTT 58.002 39.130 0.00 0.00 0.00 2.43
2178 2287 4.289672 TCTCCTAAAAGCCATCCTGAGTTT 59.710 41.667 0.00 0.00 0.00 2.66
2179 2288 3.846588 TCTCCTAAAAGCCATCCTGAGTT 59.153 43.478 0.00 0.00 0.00 3.01
2180 2289 3.454082 CTCTCCTAAAAGCCATCCTGAGT 59.546 47.826 0.00 0.00 0.00 3.41
2181 2290 3.708631 TCTCTCCTAAAAGCCATCCTGAG 59.291 47.826 0.00 0.00 0.00 3.35
2183 2292 3.181456 CCTCTCTCCTAAAAGCCATCCTG 60.181 52.174 0.00 0.00 0.00 3.86
2184 2293 3.044894 CCTCTCTCCTAAAAGCCATCCT 58.955 50.000 0.00 0.00 0.00 3.24
2186 2295 4.504689 CCATCCTCTCTCCTAAAAGCCATC 60.505 50.000 0.00 0.00 0.00 3.51
2187 2296 3.393941 CCATCCTCTCTCCTAAAAGCCAT 59.606 47.826 0.00 0.00 0.00 4.40
2191 2300 3.388913 ACCCCATCCTCTCTCCTAAAAG 58.611 50.000 0.00 0.00 0.00 2.27
2192 2301 3.508952 ACCCCATCCTCTCTCCTAAAA 57.491 47.619 0.00 0.00 0.00 1.52
2193 2302 3.115390 CAACCCCATCCTCTCTCCTAAA 58.885 50.000 0.00 0.00 0.00 1.85
2200 2309 0.179006 GATGCCAACCCCATCCTCTC 60.179 60.000 0.00 0.00 34.43 3.20
2201 2310 0.920763 TGATGCCAACCCCATCCTCT 60.921 55.000 0.00 0.00 38.61 3.69
2259 2368 3.067461 AGCTAGATTAACTGCGACCTCTG 59.933 47.826 0.00 0.00 0.00 3.35
2278 2387 7.470147 GCCTCTTGGTTTAAACTTTAAAGAGCT 60.470 37.037 26.73 7.77 35.27 4.09
2280 2389 7.712797 TGCCTCTTGGTTTAAACTTTAAAGAG 58.287 34.615 26.03 26.03 35.27 2.85
2283 2392 8.700973 AGATTGCCTCTTGGTTTAAACTTTAAA 58.299 29.630 17.50 3.04 35.27 1.52
2284 2393 8.245195 AGATTGCCTCTTGGTTTAAACTTTAA 57.755 30.769 17.50 9.81 35.27 1.52
2285 2394 7.833285 AGATTGCCTCTTGGTTTAAACTTTA 57.167 32.000 17.50 2.79 35.27 1.85
2286 2395 6.731292 AGATTGCCTCTTGGTTTAAACTTT 57.269 33.333 17.50 0.00 35.27 2.66
2287 2396 6.731292 AAGATTGCCTCTTGGTTTAAACTT 57.269 33.333 17.50 0.00 42.76 2.66
2318 2427 3.192212 CAGCCCTTTTCTTTGATGGAGAC 59.808 47.826 0.00 0.00 0.00 3.36
2371 2480 9.039870 CACTTGCAAATGGACAAAAAGTATTAA 57.960 29.630 0.00 0.00 0.00 1.40
2373 2482 6.482973 CCACTTGCAAATGGACAAAAAGTATT 59.517 34.615 22.28 0.00 38.34 1.89
2377 2486 4.440880 TCCACTTGCAAATGGACAAAAAG 58.559 39.130 25.05 0.00 40.17 2.27
2386 2495 4.985413 ACGTGATAATCCACTTGCAAATG 58.015 39.130 0.00 0.00 35.02 2.32
2406 2515 9.125906 CCTTAATACAATCGAAGGAAGTATACG 57.874 37.037 0.00 0.00 40.88 3.06
2410 2519 8.533657 TCAACCTTAATACAATCGAAGGAAGTA 58.466 33.333 6.52 0.00 40.88 2.24
2411 2520 7.391620 TCAACCTTAATACAATCGAAGGAAGT 58.608 34.615 6.52 0.00 40.88 3.01
2412 2521 7.843490 TCAACCTTAATACAATCGAAGGAAG 57.157 36.000 6.52 0.00 40.88 3.46
2413 2522 7.843490 CTCAACCTTAATACAATCGAAGGAA 57.157 36.000 6.52 0.00 40.88 3.36


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

AutoCloner maintained by Alex Coulton.