Multiple sequence alignment - TraesCS4D01G204300

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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 TraesCS4D01G204300 chr4D 100.000 2546 0 0 1 2546 351736113 351738658 0.000000e+00 4702.0
1 TraesCS4D01G204300 chr4A 92.017 2593 109 45 3 2546 113506973 113504430 0.000000e+00 3552.0
2 TraesCS4D01G204300 chr4A 81.043 786 90 28 834 1582 113580110 113579347 2.840000e-159 571.0
3 TraesCS4D01G204300 chr4B 92.939 1133 43 19 834 1954 434713753 434714860 0.000000e+00 1615.0
4 TraesCS4D01G204300 chr4B 90.920 870 31 21 1 835 434712867 434713723 0.000000e+00 1125.0
5 TraesCS4D01G204300 chr4B 91.379 464 38 2 1990 2453 434722058 434722519 3.570000e-178 634.0
6 TraesCS4D01G204300 chr4B 90.000 100 7 3 2447 2544 434789524 434789622 2.660000e-25 126.0
7 TraesCS4D01G204300 chr4B 97.368 38 1 0 2351 2388 546723164 546723127 5.880000e-07 65.8
8 TraesCS4D01G204300 chr1D 85.308 211 19 7 1142 1350 20061994 20062194 9.230000e-50 207.0
9 TraesCS4D01G204300 chr3A 86.792 106 12 2 1244 1349 603895557 603895454 1.600000e-22 117.0
10 TraesCS4D01G204300 chr3A 84.167 120 15 4 1232 1349 603813806 603813689 2.070000e-21 113.0
11 TraesCS4D01G204300 chr3D 84.167 120 15 4 1232 1349 461313437 461313320 2.070000e-21 113.0
12 TraesCS4D01G204300 chr3B 85.849 106 13 2 1244 1349 612104015 612103912 7.450000e-21 111.0
13 TraesCS4D01G204300 chr3B 85.849 106 13 2 1244 1349 612360005 612359902 7.450000e-21 111.0


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 TraesCS4D01G204300 chr4D 351736113 351738658 2545 False 4702 4702 100.0000 1 2546 1 chr4D.!!$F1 2545
1 TraesCS4D01G204300 chr4A 113504430 113506973 2543 True 3552 3552 92.0170 3 2546 1 chr4A.!!$R1 2543
2 TraesCS4D01G204300 chr4A 113579347 113580110 763 True 571 571 81.0430 834 1582 1 chr4A.!!$R2 748
3 TraesCS4D01G204300 chr4B 434712867 434714860 1993 False 1370 1615 91.9295 1 1954 2 chr4B.!!$F3 1953

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
21 22 0.037790 AAGAAGTCTCACTGCGCCTC 60.038 55.0 4.18 0.0 0.00 4.70 F
562 611 0.179045 AGCCATCATCACTTACGGCC 60.179 55.0 0.00 0.0 40.49 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1248 1.112916 TGCACTCGAACACCCTCTCA 61.113 55.0 0.0 0.0 0.0 3.27 R
2153 2296 0.040204 CCCTTTCCCAGCAAGTCCAT 59.960 55.0 0.0 0.0 0.0 3.41 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
21 22 0.037790 AAGAAGTCTCACTGCGCCTC 60.038 55.000 4.18 0.00 0.00 4.70
236 263 2.280628 GTAGGCCAATGAAAGGAGACG 58.719 52.381 5.01 0.00 0.00 4.18
293 327 2.224137 TGAAAGCTCTCACAGTCACAGG 60.224 50.000 0.00 0.00 0.00 4.00
294 328 1.709578 AAGCTCTCACAGTCACAGGA 58.290 50.000 0.00 0.00 0.00 3.86
295 329 1.255882 AGCTCTCACAGTCACAGGAG 58.744 55.000 0.00 0.00 0.00 3.69
416 450 3.414700 GTGAACTGTGGGCGCTCG 61.415 66.667 7.64 0.00 0.00 5.03
453 502 1.134250 GGAATTCAGAGCCCTCACTCC 60.134 57.143 7.93 0.00 37.39 3.85
456 505 0.616111 TTCAGAGCCCTCACTCCTCC 60.616 60.000 0.00 0.00 37.39 4.30
470 519 0.631753 TCCTCCCAGCTAGTAGCAGT 59.368 55.000 23.77 1.17 45.56 4.40
486 535 0.896940 CAGTCCCAGTTGCTTGCCAT 60.897 55.000 0.00 0.00 0.00 4.40
556 605 4.613622 CGAACGAAAAAGCCATCATCACTT 60.614 41.667 0.00 0.00 0.00 3.16
558 607 5.296813 ACGAAAAAGCCATCATCACTTAC 57.703 39.130 0.00 0.00 0.00 2.34
559 608 4.142902 ACGAAAAAGCCATCATCACTTACG 60.143 41.667 0.00 0.00 0.00 3.18
560 609 4.662145 GAAAAAGCCATCATCACTTACGG 58.338 43.478 0.00 0.00 0.00 4.02
562 611 0.179045 AGCCATCATCACTTACGGCC 60.179 55.000 0.00 0.00 40.49 6.13
563 612 0.463654 GCCATCATCACTTACGGCCA 60.464 55.000 2.24 0.00 33.31 5.36
565 614 1.134401 CCATCATCACTTACGGCCACT 60.134 52.381 2.24 0.00 0.00 4.00
566 615 1.935873 CATCATCACTTACGGCCACTG 59.064 52.381 2.24 0.00 0.00 3.66
579 629 3.046087 CACTGAGTGGCGGCACAG 61.046 66.667 38.86 30.43 36.58 3.66
603 654 4.548991 ATCTATAGCTTCGTTCGTTCGT 57.451 40.909 0.00 0.00 0.00 3.85
605 656 5.469373 TCTATAGCTTCGTTCGTTCGTAA 57.531 39.130 0.00 0.00 0.00 3.18
606 657 5.258622 TCTATAGCTTCGTTCGTTCGTAAC 58.741 41.667 0.00 0.00 0.00 2.50
608 659 2.462889 AGCTTCGTTCGTTCGTAACAA 58.537 42.857 0.00 0.00 0.00 2.83
610 661 2.217167 GCTTCGTTCGTTCGTAACAAGT 59.783 45.455 2.67 0.00 0.00 3.16
611 662 3.421888 GCTTCGTTCGTTCGTAACAAGTA 59.578 43.478 2.67 0.00 0.00 2.24
762 814 0.748367 GGATCCGTCCCCTCTTTTGC 60.748 60.000 0.00 0.00 38.69 3.68
767 819 4.360405 TCCCCTCTTTTGCCCGCC 62.360 66.667 0.00 0.00 0.00 6.13
915 999 1.839994 TCACTCATTCAGACCCATCCC 59.160 52.381 0.00 0.00 0.00 3.85
916 1000 1.561076 CACTCATTCAGACCCATCCCA 59.439 52.381 0.00 0.00 0.00 4.37
917 1001 1.842562 ACTCATTCAGACCCATCCCAG 59.157 52.381 0.00 0.00 0.00 4.45
918 1002 0.548031 TCATTCAGACCCATCCCAGC 59.452 55.000 0.00 0.00 0.00 4.85
919 1003 0.466922 CATTCAGACCCATCCCAGCC 60.467 60.000 0.00 0.00 0.00 4.85
920 1004 0.920763 ATTCAGACCCATCCCAGCCA 60.921 55.000 0.00 0.00 0.00 4.75
940 1024 4.790962 AGCACCTGGCCATCAGCG 62.791 66.667 5.51 0.00 46.50 5.18
991 1084 1.603236 CCGGTCTTCTGCTCTGCTCT 61.603 60.000 0.00 0.00 0.00 4.09
1530 1653 4.891727 CTCGCCGTGGGATTCCGG 62.892 72.222 0.00 0.00 46.90 5.14
1631 1766 5.686159 ATACTATTTGCATTGAGCTGCTC 57.314 39.130 22.38 22.38 45.94 4.26
1679 1814 1.457303 GAAATGCTGGCTCGCGTATAG 59.543 52.381 5.77 0.00 0.00 1.31
1680 1815 0.389391 AATGCTGGCTCGCGTATAGT 59.611 50.000 5.77 0.00 0.00 2.12
1681 1816 1.244816 ATGCTGGCTCGCGTATAGTA 58.755 50.000 5.77 0.73 0.00 1.82
1683 1818 2.429478 TGCTGGCTCGCGTATAGTATA 58.571 47.619 5.77 0.00 0.00 1.47
1684 1819 2.815503 TGCTGGCTCGCGTATAGTATAA 59.184 45.455 5.77 0.00 0.00 0.98
1685 1820 3.169733 GCTGGCTCGCGTATAGTATAAC 58.830 50.000 5.77 0.00 0.00 1.89
1686 1821 3.365666 GCTGGCTCGCGTATAGTATAACA 60.366 47.826 5.77 0.00 0.00 2.41
1824 1967 3.959535 TTTTTATGCTCCTTGGCCTTG 57.040 42.857 3.32 0.00 0.00 3.61
1841 1984 4.442375 CCTTGAGGCATATCTACTACGG 57.558 50.000 0.00 0.00 0.00 4.02
1842 1985 4.079970 CCTTGAGGCATATCTACTACGGA 58.920 47.826 0.00 0.00 0.00 4.69
1843 1986 4.156922 CCTTGAGGCATATCTACTACGGAG 59.843 50.000 0.00 0.00 0.00 4.63
1880 2023 4.879067 GTTGTAAACCTCTCGAATTACGC 58.121 43.478 0.00 0.00 42.21 4.42
2035 2178 2.887783 TGAAGCCGCTTGGATTAAACAA 59.112 40.909 11.20 0.00 42.67 2.83
2038 2181 1.613270 CCGCTTGGATTAAACAACGC 58.387 50.000 10.07 8.65 33.02 4.84
2043 2186 1.982660 TGGATTAAACAACGCCCACA 58.017 45.000 0.00 0.00 0.00 4.17
2058 2201 0.320421 CCACACTCGAAATGGGACGT 60.320 55.000 0.11 0.00 0.00 4.34
2059 2202 1.068474 CACACTCGAAATGGGACGTC 58.932 55.000 7.13 7.13 0.00 4.34
2093 2236 2.266055 CAGGTCCTTGTCGGAGGC 59.734 66.667 0.00 0.00 44.20 4.70
2122 2265 2.774951 CGGTTCGTCGTGATGTCGC 61.775 63.158 0.00 0.00 0.00 5.19
2143 2286 2.198304 GATGAACGAGGGGCTGGGTT 62.198 60.000 0.00 0.00 0.00 4.11
2149 2292 1.301293 GAGGGGCTGGGTTGAGAAG 59.699 63.158 0.00 0.00 0.00 2.85
2150 2293 2.203549 GAGGGGCTGGGTTGAGAAGG 62.204 65.000 0.00 0.00 0.00 3.46
2151 2294 2.231380 GGGGCTGGGTTGAGAAGGA 61.231 63.158 0.00 0.00 0.00 3.36
2152 2295 1.301293 GGGCTGGGTTGAGAAGGAG 59.699 63.158 0.00 0.00 0.00 3.69
2153 2296 1.201429 GGGCTGGGTTGAGAAGGAGA 61.201 60.000 0.00 0.00 0.00 3.71
2154 2297 0.915364 GGCTGGGTTGAGAAGGAGAT 59.085 55.000 0.00 0.00 0.00 2.75
2155 2298 1.407989 GGCTGGGTTGAGAAGGAGATG 60.408 57.143 0.00 0.00 0.00 2.90
2156 2299 1.407989 GCTGGGTTGAGAAGGAGATGG 60.408 57.143 0.00 0.00 0.00 3.51
2157 2300 2.191400 CTGGGTTGAGAAGGAGATGGA 58.809 52.381 0.00 0.00 0.00 3.41
2158 2301 1.909302 TGGGTTGAGAAGGAGATGGAC 59.091 52.381 0.00 0.00 0.00 4.02
2159 2302 2.192263 GGGTTGAGAAGGAGATGGACT 58.808 52.381 0.00 0.00 0.00 3.85
2160 2303 2.573915 GGGTTGAGAAGGAGATGGACTT 59.426 50.000 0.00 0.00 0.00 3.01
2161 2304 3.604582 GGTTGAGAAGGAGATGGACTTG 58.395 50.000 0.00 0.00 0.00 3.16
2162 2305 3.006247 GTTGAGAAGGAGATGGACTTGC 58.994 50.000 0.00 0.00 0.00 4.01
2163 2306 2.544721 TGAGAAGGAGATGGACTTGCT 58.455 47.619 0.00 0.00 0.00 3.91
2167 2310 0.252881 AGGAGATGGACTTGCTGGGA 60.253 55.000 0.00 0.00 0.00 4.37
2195 2338 2.039084 TGGTTGGAAGAGGAAGAAGAGC 59.961 50.000 0.00 0.00 0.00 4.09
2216 2359 3.426292 GCTGTTGGCTAGAAAAATCGACC 60.426 47.826 0.00 0.00 38.06 4.79
2220 2363 2.028839 TGGCTAGAAAAATCGACCGACA 60.029 45.455 0.00 0.00 0.00 4.35
2227 2370 3.948196 AAAATCGACCGACACGAAAAA 57.052 38.095 0.00 0.00 42.80 1.94
2235 2378 4.486025 CGACCGACACGAAAAATTTTATCG 59.514 41.667 22.46 22.46 42.05 2.92
2259 2402 6.753279 CGTACGACTTACAAAATCAATCCCTA 59.247 38.462 10.44 0.00 0.00 3.53
2297 2440 1.286880 GCTCGCATGCCAAAACACT 59.713 52.632 13.15 0.00 0.00 3.55
2319 2462 8.630037 ACACTAGATTGTCCTTTTTGGTTTAAG 58.370 33.333 0.00 0.00 37.07 1.85
2353 2496 1.138459 CGATGCTCGTCTGCAGACT 59.862 57.895 36.78 22.64 46.71 3.24
2373 2516 0.942410 AGAAGTTGTCGCGCGCTTTA 60.942 50.000 30.48 11.81 0.00 1.85
2396 2539 0.787787 TGCCGTTCTTCGTTCATTCG 59.212 50.000 0.00 0.00 37.94 3.34
2397 2540 0.094730 GCCGTTCTTCGTTCATTCGG 59.905 55.000 0.00 0.00 39.52 4.30
2439 2582 4.558226 TCATTGCTGATCACTAGGTTGT 57.442 40.909 0.00 0.00 0.00 3.32
2453 2596 8.882415 TCACTAGGTTGTGAACTTTAGTTAAG 57.118 34.615 0.00 0.00 43.08 1.85
2458 2601 5.529800 GGTTGTGAACTTTAGTTAAGCTGGA 59.470 40.000 0.00 0.00 38.56 3.86
2460 2603 5.925509 TGTGAACTTTAGTTAAGCTGGACT 58.074 37.500 7.34 7.34 38.56 3.85
2463 2606 4.868314 ACTTTAGTTAAGCTGGACTCGT 57.132 40.909 5.58 1.01 37.37 4.18
2464 2607 4.557205 ACTTTAGTTAAGCTGGACTCGTG 58.443 43.478 5.58 1.46 37.37 4.35
2465 2608 2.649331 TAGTTAAGCTGGACTCGTGC 57.351 50.000 5.58 0.00 0.00 5.34
2479 2623 1.939934 CTCGTGCTTTTCCTTGTGACA 59.060 47.619 0.00 0.00 0.00 3.58
2480 2624 2.354510 CTCGTGCTTTTCCTTGTGACAA 59.645 45.455 0.00 0.00 0.00 3.18
2485 2629 3.698539 TGCTTTTCCTTGTGACAATGTCA 59.301 39.130 12.63 12.63 40.50 3.58
2506 2650 6.039717 TGTCATCCTTAGCTTTTATTGGATGC 59.960 38.462 13.18 9.76 46.09 3.91
2508 2652 3.882888 TCCTTAGCTTTTATTGGATGCGG 59.117 43.478 0.00 0.00 0.00 5.69
2513 2657 3.319122 AGCTTTTATTGGATGCGGGATTC 59.681 43.478 0.00 0.00 0.00 2.52
2514 2658 3.068024 GCTTTTATTGGATGCGGGATTCA 59.932 43.478 0.00 0.00 0.00 2.57
2532 2676 5.449177 GGATTCAGACATAAAGGAAAAGGCG 60.449 44.000 0.00 0.00 0.00 5.52
2542 2686 1.818674 AGGAAAAGGCGGTGCTTATTG 59.181 47.619 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 111 2.271800 CAGCTACCTCCAACTTTAGCG 58.728 52.381 0.00 0.00 41.56 4.26
236 263 6.327177 TCGAAAAGATAACGAACATAGTGC 57.673 37.500 0.00 0.00 33.20 4.40
293 327 2.552315 TCCTTTTCATGGTCGTTTGCTC 59.448 45.455 0.00 0.00 0.00 4.26
294 328 2.582052 TCCTTTTCATGGTCGTTTGCT 58.418 42.857 0.00 0.00 0.00 3.91
295 329 3.501950 GATCCTTTTCATGGTCGTTTGC 58.498 45.455 0.00 0.00 0.00 3.68
416 450 1.131638 TCCTATGCCCACTGATCCAC 58.868 55.000 0.00 0.00 0.00 4.02
453 502 1.036707 GGACTGCTACTAGCTGGGAG 58.963 60.000 16.73 4.61 43.38 4.30
456 505 0.749649 CTGGGACTGCTACTAGCTGG 59.250 60.000 16.73 0.00 43.38 4.85
470 519 1.607178 CCATGGCAAGCAACTGGGA 60.607 57.895 0.00 0.00 0.00 4.37
486 535 6.490040 GCTGCTTTTCCATAGGATATAAACCA 59.510 38.462 0.00 0.00 0.00 3.67
562 611 3.046087 CTGTGCCGCCACTCAGTG 61.046 66.667 0.00 0.00 42.54 3.66
563 612 4.996434 GCTGTGCCGCCACTCAGT 62.996 66.667 0.00 0.00 42.54 3.41
565 614 2.578163 GATAGCTGTGCCGCCACTCA 62.578 60.000 0.00 0.00 42.54 3.41
566 615 1.884926 GATAGCTGTGCCGCCACTC 60.885 63.158 0.00 0.00 42.54 3.51
579 629 4.550362 CGAACGAACGAAGCTATAGATAGC 59.450 45.833 12.72 12.72 44.31 2.97
602 653 1.225289 GCGCGTGCGTACTTGTTAC 60.225 57.895 16.27 0.00 42.09 2.50
603 654 3.149092 GCGCGTGCGTACTTGTTA 58.851 55.556 16.27 0.00 42.09 2.41
767 819 3.520862 GTGACGGCATGCATGGGG 61.521 66.667 27.34 3.29 0.00 4.96
918 1002 1.186917 TGATGGCCAGGTGCTTTTGG 61.187 55.000 13.05 0.00 40.92 3.28
919 1003 0.245539 CTGATGGCCAGGTGCTTTTG 59.754 55.000 13.05 0.00 39.23 2.44
920 1004 1.538687 GCTGATGGCCAGGTGCTTTT 61.539 55.000 13.05 0.00 43.13 2.27
940 1024 4.021016 TGAGACAAAGCTAGGAGAAGGAAC 60.021 45.833 0.00 0.00 0.00 3.62
991 1084 1.342874 CCCATGGGCCATTAGTCCAAA 60.343 52.381 20.41 0.00 33.90 3.28
1143 1248 1.112916 TGCACTCGAACACCCTCTCA 61.113 55.000 0.00 0.00 0.00 3.27
1530 1653 3.785122 AAGTCAACCACCACGGGGC 62.785 63.158 1.73 0.00 40.22 5.80
1631 1766 1.419374 CAAGGGTCGTTGACTTCTCG 58.581 55.000 0.00 0.00 32.47 4.04
1679 1814 7.226918 GCCCCTGAGACTTTAGAAATGTTATAC 59.773 40.741 0.00 0.00 0.00 1.47
1680 1815 7.092623 TGCCCCTGAGACTTTAGAAATGTTATA 60.093 37.037 0.00 0.00 0.00 0.98
1681 1816 6.122964 GCCCCTGAGACTTTAGAAATGTTAT 58.877 40.000 0.00 0.00 0.00 1.89
1683 1818 4.202567 TGCCCCTGAGACTTTAGAAATGTT 60.203 41.667 0.00 0.00 0.00 2.71
1684 1819 3.330701 TGCCCCTGAGACTTTAGAAATGT 59.669 43.478 0.00 0.00 0.00 2.71
1685 1820 3.944015 CTGCCCCTGAGACTTTAGAAATG 59.056 47.826 0.00 0.00 0.00 2.32
1686 1821 3.054065 CCTGCCCCTGAGACTTTAGAAAT 60.054 47.826 0.00 0.00 0.00 2.17
1824 1967 4.329528 CGTACTCCGTAGTAGATATGCCTC 59.670 50.000 0.00 0.00 38.89 4.70
1859 2002 3.609373 CGCGTAATTCGAGAGGTTTACAA 59.391 43.478 0.00 0.00 41.61 2.41
1977 2120 2.125106 CCCTTCCTGTGCGGCTAC 60.125 66.667 0.00 0.00 0.00 3.58
1978 2121 1.774894 AAACCCTTCCTGTGCGGCTA 61.775 55.000 0.00 0.00 0.00 3.93
2035 2178 1.671054 CCATTTCGAGTGTGGGCGT 60.671 57.895 5.23 0.00 0.00 5.68
2043 2186 1.445582 GCGACGTCCCATTTCGAGT 60.446 57.895 10.58 0.00 34.62 4.18
2122 2265 2.202932 CAGCCCCTCGTTCATCGG 60.203 66.667 0.00 0.00 40.32 4.18
2143 2286 2.235650 CAGCAAGTCCATCTCCTTCTCA 59.764 50.000 0.00 0.00 0.00 3.27
2149 2292 0.620556 TTCCCAGCAAGTCCATCTCC 59.379 55.000 0.00 0.00 0.00 3.71
2150 2293 2.363683 CTTTCCCAGCAAGTCCATCTC 58.636 52.381 0.00 0.00 0.00 2.75
2151 2294 1.005215 CCTTTCCCAGCAAGTCCATCT 59.995 52.381 0.00 0.00 0.00 2.90
2152 2295 1.467920 CCTTTCCCAGCAAGTCCATC 58.532 55.000 0.00 0.00 0.00 3.51
2153 2296 0.040204 CCCTTTCCCAGCAAGTCCAT 59.960 55.000 0.00 0.00 0.00 3.41
2154 2297 1.065410 TCCCTTTCCCAGCAAGTCCA 61.065 55.000 0.00 0.00 0.00 4.02
2155 2298 0.332972 ATCCCTTTCCCAGCAAGTCC 59.667 55.000 0.00 0.00 0.00 3.85
2156 2299 1.467920 CATCCCTTTCCCAGCAAGTC 58.532 55.000 0.00 0.00 0.00 3.01
2157 2300 0.040204 CCATCCCTTTCCCAGCAAGT 59.960 55.000 0.00 0.00 0.00 3.16
2158 2301 0.040204 ACCATCCCTTTCCCAGCAAG 59.960 55.000 0.00 0.00 0.00 4.01
2159 2302 0.486879 AACCATCCCTTTCCCAGCAA 59.513 50.000 0.00 0.00 0.00 3.91
2160 2303 0.251742 CAACCATCCCTTTCCCAGCA 60.252 55.000 0.00 0.00 0.00 4.41
2161 2304 0.972471 CCAACCATCCCTTTCCCAGC 60.972 60.000 0.00 0.00 0.00 4.85
2162 2305 0.704076 TCCAACCATCCCTTTCCCAG 59.296 55.000 0.00 0.00 0.00 4.45
2163 2306 1.077005 CTTCCAACCATCCCTTTCCCA 59.923 52.381 0.00 0.00 0.00 4.37
2167 2310 2.358258 TCCTCTTCCAACCATCCCTTT 58.642 47.619 0.00 0.00 0.00 3.11
2195 2338 3.181520 CGGTCGATTTTTCTAGCCAACAG 60.182 47.826 0.00 0.00 0.00 3.16
2204 2347 2.427232 TCGTGTCGGTCGATTTTTCT 57.573 45.000 0.00 0.00 32.30 2.52
2213 2356 5.376537 ACGATAAAATTTTTCGTGTCGGTC 58.623 37.500 25.91 7.85 43.80 4.79
2216 2359 6.187306 GTCGTACGATAAAATTTTTCGTGTCG 59.813 38.462 29.97 29.36 44.95 4.35
2220 2363 8.698854 TGTAAGTCGTACGATAAAATTTTTCGT 58.301 29.630 27.68 27.68 46.72 3.85
2235 2378 6.980051 AGGGATTGATTTTGTAAGTCGTAC 57.020 37.500 0.00 0.00 0.00 3.67
2239 2382 9.087424 GCAATTTAGGGATTGATTTTGTAAGTC 57.913 33.333 2.04 0.00 38.93 3.01
2259 2402 1.527736 CAAACACGCATGCTGCAATTT 59.472 42.857 17.13 6.32 45.36 1.82
2273 2416 0.597118 TTTGGCATGCGAGCAAACAC 60.597 50.000 12.44 0.00 35.83 3.32
2297 2440 8.754991 TGTCTTAAACCAAAAAGGACAATCTA 57.245 30.769 0.00 0.00 41.22 1.98
2319 2462 3.806521 AGCATCGCTCAAATCTGTATGTC 59.193 43.478 0.00 0.00 30.62 3.06
2353 2496 0.942410 AAAGCGCGCGACAACTTCTA 60.942 50.000 37.18 0.00 0.00 2.10
2381 2524 4.663636 ATGAACCGAATGAACGAAGAAC 57.336 40.909 0.00 0.00 35.09 3.01
2396 2539 9.657419 AATGATAATTCCACAAGAAAATGAACC 57.343 29.630 0.00 0.00 38.21 3.62
2439 2582 5.221382 ACGAGTCCAGCTTAACTAAAGTTCA 60.221 40.000 0.00 0.00 39.31 3.18
2444 2587 3.006537 AGCACGAGTCCAGCTTAACTAAA 59.993 43.478 0.00 0.00 34.37 1.85
2453 2596 0.603975 AGGAAAAGCACGAGTCCAGC 60.604 55.000 0.00 0.00 32.19 4.85
2458 2601 1.940613 GTCACAAGGAAAAGCACGAGT 59.059 47.619 0.00 0.00 0.00 4.18
2460 2603 2.031258 TGTCACAAGGAAAAGCACGA 57.969 45.000 0.00 0.00 0.00 4.35
2463 2606 3.698539 TGACATTGTCACAAGGAAAAGCA 59.301 39.130 15.41 0.00 37.67 3.91
2464 2607 4.305989 TGACATTGTCACAAGGAAAAGC 57.694 40.909 15.41 0.00 37.67 3.51
2465 2608 5.242393 AGGATGACATTGTCACAAGGAAAAG 59.758 40.000 21.19 0.00 45.65 2.27
2479 2623 8.773033 ATCCAATAAAAGCTAAGGATGACATT 57.227 30.769 0.00 0.00 34.75 2.71
2485 2629 4.520492 CCGCATCCAATAAAAGCTAAGGAT 59.480 41.667 0.00 0.00 36.35 3.24
2506 2650 5.066505 CCTTTTCCTTTATGTCTGAATCCCG 59.933 44.000 0.00 0.00 0.00 5.14
2508 2652 5.449177 CGCCTTTTCCTTTATGTCTGAATCC 60.449 44.000 0.00 0.00 0.00 3.01
2513 2657 3.081804 ACCGCCTTTTCCTTTATGTCTG 58.918 45.455 0.00 0.00 0.00 3.51
2514 2658 3.081804 CACCGCCTTTTCCTTTATGTCT 58.918 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.