Multiple sequence alignment - TraesCS3A01G448300

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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 TraesCS3A01G448300 chr3A 100.000 2923 0 0 1 2923 688419148 688422070 0.000000e+00 5398.0
1 TraesCS3A01G448300 chr3A 86.408 927 111 10 1000 1923 688065700 688064786 0.000000e+00 1000.0
2 TraesCS3A01G448300 chr3A 86.061 165 8 6 1010 1169 688134461 688134307 2.330000e-36 163.0
3 TraesCS3A01G448300 chr3A 90.123 81 6 1 639 719 646608257 646608179 1.430000e-18 104.0
4 TraesCS3A01G448300 chr3D 89.830 2173 138 41 770 2904 551206987 551209114 0.000000e+00 2712.0
5 TraesCS3A01G448300 chr3B 92.531 1513 60 22 644 2112 730782166 730783669 0.000000e+00 2119.0
6 TraesCS3A01G448300 chr3B 85.480 427 46 8 1035 1449 730384836 730384414 5.790000e-117 431.0
7 TraesCS3A01G448300 chr3B 85.246 427 47 8 1035 1449 730440253 730439831 2.690000e-115 425.0
8 TraesCS3A01G448300 chr3B 85.012 427 48 8 1035 1449 730420938 730420516 1.250000e-113 420.0
9 TraesCS3A01G448300 chr3B 81.202 516 75 11 1414 1925 730432591 730432094 2.110000e-106 396.0
10 TraesCS3A01G448300 chr7A 95.312 640 29 1 1 640 1762870 1763508 0.000000e+00 1014.0
11 TraesCS3A01G448300 chr7A 87.500 80 8 2 639 716 713327733 713327812 1.120000e-14 91.6
12 TraesCS3A01G448300 chr7A 87.500 80 8 2 639 716 713399161 713399240 1.120000e-14 91.6
13 TraesCS3A01G448300 chr7A 87.500 80 8 2 639 716 713461941 713462020 1.120000e-14 91.6
14 TraesCS3A01G448300 chr7A 87.500 80 8 2 639 716 713522374 713522453 1.120000e-14 91.6
15 TraesCS3A01G448300 chr7A 87.500 80 7 3 639 716 713607573 713607651 4.010000e-14 89.8
16 TraesCS3A01G448300 chrUn 95.000 640 31 1 1 640 313651780 313651142 0.000000e+00 1003.0
17 TraesCS3A01G448300 chr1A 93.858 635 39 0 6 640 468412974 468412340 0.000000e+00 957.0
18 TraesCS3A01G448300 chr1A 93.701 635 40 0 6 640 468464148 468463514 0.000000e+00 952.0
19 TraesCS3A01G448300 chr1A 91.456 632 54 0 9 640 276262613 276261982 0.000000e+00 869.0
20 TraesCS3A01G448300 chr1A 94.643 56 3 0 1018 1073 561761329 561761274 1.440000e-13 87.9
21 TraesCS3A01G448300 chr5A 93.228 635 43 0 6 640 502836393 502837027 0.000000e+00 935.0
22 TraesCS3A01G448300 chr6B 91.181 635 56 0 6 640 711327620 711326986 0.000000e+00 863.0
23 TraesCS3A01G448300 chr2D 91.038 636 56 1 6 640 483637704 483637069 0.000000e+00 857.0
24 TraesCS3A01G448300 chr5B 80.530 642 109 14 7 640 403924704 403925337 2.040000e-131 479.0
25 TraesCS3A01G448300 chr5B 78.221 652 121 19 1 640 227829453 227830095 5.870000e-107 398.0
26 TraesCS3A01G448300 chr2B 79.369 412 71 12 1312 1713 549539461 549539054 7.980000e-71 278.0
27 TraesCS3A01G448300 chr4D 86.170 94 11 2 639 730 72486000 72485907 1.850000e-17 100.0
28 TraesCS3A01G448300 chr1B 89.157 83 6 3 639 719 626810228 626810309 1.850000e-17 100.0
29 TraesCS3A01G448300 chr4B 90.769 65 6 0 1009 1073 553915003 553915067 1.440000e-13 87.9
30 TraesCS3A01G448300 chr7B 85.185 81 10 2 641 719 668937214 668937294 6.710000e-12 82.4


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 TraesCS3A01G448300 chr3A 688419148 688422070 2922 False 5398 5398 100.000 1 2923 1 chr3A.!!$F1 2922
1 TraesCS3A01G448300 chr3A 688064786 688065700 914 True 1000 1000 86.408 1000 1923 1 chr3A.!!$R2 923
2 TraesCS3A01G448300 chr3D 551206987 551209114 2127 False 2712 2712 89.830 770 2904 1 chr3D.!!$F1 2134
3 TraesCS3A01G448300 chr3B 730782166 730783669 1503 False 2119 2119 92.531 644 2112 1 chr3B.!!$F1 1468
4 TraesCS3A01G448300 chr7A 1762870 1763508 638 False 1014 1014 95.312 1 640 1 chr7A.!!$F1 639
5 TraesCS3A01G448300 chrUn 313651142 313651780 638 True 1003 1003 95.000 1 640 1 chrUn.!!$R1 639
6 TraesCS3A01G448300 chr1A 468412340 468412974 634 True 957 957 93.858 6 640 1 chr1A.!!$R2 634
7 TraesCS3A01G448300 chr1A 468463514 468464148 634 True 952 952 93.701 6 640 1 chr1A.!!$R3 634
8 TraesCS3A01G448300 chr1A 276261982 276262613 631 True 869 869 91.456 9 640 1 chr1A.!!$R1 631
9 TraesCS3A01G448300 chr5A 502836393 502837027 634 False 935 935 93.228 6 640 1 chr5A.!!$F1 634
10 TraesCS3A01G448300 chr6B 711326986 711327620 634 True 863 863 91.181 6 640 1 chr6B.!!$R1 634
11 TraesCS3A01G448300 chr2D 483637069 483637704 635 True 857 857 91.038 6 640 1 chr2D.!!$R1 634
12 TraesCS3A01G448300 chr5B 403924704 403925337 633 False 479 479 80.530 7 640 1 chr5B.!!$F2 633
13 TraesCS3A01G448300 chr5B 227829453 227830095 642 False 398 398 78.221 1 640 1 chr5B.!!$F1 639

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
350 351 1.077265 CATGGGGTGTTTGGCTCCT 59.923 57.895 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2260 0.384309 CGCTCTATCACCTACGGCAA 59.616 55.0 0.0 0.0 0.0 4.52 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
69 70 5.610429 AGAGGGTAGGGGTAAATTTGTTT 57.390 39.130 0.00 0.00 0.00 2.83
235 236 2.494059 CGCCTTCTTGGTTCTCTTCAA 58.506 47.619 0.00 0.00 38.35 2.69
350 351 1.077265 CATGGGGTGTTTGGCTCCT 59.923 57.895 0.00 0.00 0.00 3.69
363 364 2.123683 CTCCTAGCTCGGCTCCCA 60.124 66.667 0.00 0.00 40.44 4.37
498 503 4.626081 AACGGCCACTTGAGCGCT 62.626 61.111 11.27 11.27 0.00 5.92
640 646 3.813166 ACACCATTGTCGTGTTCCTTAAG 59.187 43.478 0.00 0.00 41.66 1.85
641 647 4.062293 CACCATTGTCGTGTTCCTTAAGA 58.938 43.478 3.36 0.00 0.00 2.10
642 648 4.513692 CACCATTGTCGTGTTCCTTAAGAA 59.486 41.667 3.36 0.00 0.00 2.52
701 709 2.195956 GCCCTATGAAGCCCACCC 59.804 66.667 0.00 0.00 0.00 4.61
711 719 2.282462 GCCCACCCACTGGACTTG 60.282 66.667 0.00 0.00 43.95 3.16
720 728 3.052082 CTGGACTTGCCACTGCGG 61.052 66.667 0.00 0.00 43.33 5.69
787 814 4.760047 GTGACATGAGCCGGCCGT 62.760 66.667 26.15 15.92 0.00 5.68
815 842 2.875786 GCCTGCGCGAGTAATGCTC 61.876 63.158 12.10 0.00 40.77 4.26
873 900 1.548357 ATCTGCGGTTCTGCACTCCT 61.548 55.000 1.90 0.00 40.62 3.69
884 911 2.984623 CACTCCTGCCAGCTGCTA 59.015 61.111 8.66 0.00 42.00 3.49
887 914 2.607442 TCCTGCCAGCTGCTACCA 60.607 61.111 8.66 1.29 42.00 3.25
1083 1113 1.248101 CCGGCGGAACCAAAGGAATT 61.248 55.000 24.41 0.00 39.03 2.17
1499 1533 2.047179 GCCACCAACCTCGAGTCC 60.047 66.667 12.31 0.00 0.00 3.85
1581 1615 1.668101 GAACATCTCCTCCGTCGCCT 61.668 60.000 0.00 0.00 0.00 5.52
1768 1802 3.818787 CATGGAGGCGTTGCTGGC 61.819 66.667 0.00 0.00 0.00 4.85
1935 1969 1.144057 GCCTAGGCTTCGCTTGCTA 59.856 57.895 27.17 0.00 38.26 3.49
1939 2003 0.100682 TAGGCTTCGCTTGCTACTCG 59.899 55.000 0.00 0.00 0.00 4.18
1952 2016 5.721510 GCTTGCTACTCGATTAAACTGTTCG 60.722 44.000 0.00 0.00 0.00 3.95
1953 2017 5.050644 TGCTACTCGATTAAACTGTTCGA 57.949 39.130 2.76 2.76 39.38 3.71
1962 2026 6.093219 TCGATTAAACTGTTCGAGTAGCTACT 59.907 38.462 26.35 26.35 37.01 2.57
1963 2027 6.194876 CGATTAAACTGTTCGAGTAGCTACTG 59.805 42.308 30.70 20.86 36.50 2.74
1964 2028 4.850347 AAACTGTTCGAGTAGCTACTGT 57.150 40.909 30.70 17.54 36.50 3.55
1965 2029 4.850347 AACTGTTCGAGTAGCTACTGTT 57.150 40.909 30.70 21.92 36.50 3.16
1968 2032 4.519730 ACTGTTCGAGTAGCTACTGTTCTT 59.480 41.667 30.70 5.90 36.50 2.52
1969 2033 5.009811 ACTGTTCGAGTAGCTACTGTTCTTT 59.990 40.000 30.70 5.09 36.50 2.52
1970 2034 6.206243 ACTGTTCGAGTAGCTACTGTTCTTTA 59.794 38.462 30.70 9.80 36.50 1.85
1971 2035 7.094291 ACTGTTCGAGTAGCTACTGTTCTTTAT 60.094 37.037 30.70 3.47 36.50 1.40
1972 2036 8.272545 TGTTCGAGTAGCTACTGTTCTTTATA 57.727 34.615 30.70 5.53 36.50 0.98
1974 2038 9.171701 GTTCGAGTAGCTACTGTTCTTTATATG 57.828 37.037 30.70 3.11 36.50 1.78
1975 2039 7.361127 TCGAGTAGCTACTGTTCTTTATATGC 58.639 38.462 30.70 10.31 36.50 3.14
1976 2040 7.228906 TCGAGTAGCTACTGTTCTTTATATGCT 59.771 37.037 30.70 0.68 36.50 3.79
1977 2041 8.504815 CGAGTAGCTACTGTTCTTTATATGCTA 58.495 37.037 30.70 0.00 36.50 3.49
1978 2042 9.615295 GAGTAGCTACTGTTCTTTATATGCTAC 57.385 37.037 30.70 6.34 45.92 3.58
2011 2075 5.366752 CATCTTCGTTTCGAGTTCAAAGAC 58.633 41.667 0.00 0.00 37.14 3.01
2119 2191 8.129211 GCACTTTCATTGTTACAAAAGACTAGT 58.871 33.333 13.03 0.00 33.85 2.57
2165 2241 4.887655 GGTCGGGAGGATAATTGATGTTTT 59.112 41.667 0.00 0.00 0.00 2.43
2168 2244 5.588648 TCGGGAGGATAATTGATGTTTTCAC 59.411 40.000 0.00 0.00 32.84 3.18
2183 2259 5.583495 TGTTTTCACAAAATACGGTCTTGG 58.417 37.500 0.00 0.00 32.22 3.61
2184 2260 5.125739 TGTTTTCACAAAATACGGTCTTGGT 59.874 36.000 0.00 0.00 32.22 3.67
2188 2264 2.295070 ACAAAATACGGTCTTGGTTGCC 59.705 45.455 0.00 0.00 0.00 4.52
2221 2297 1.517242 CGAGGAGCTGCAGTTTTCTT 58.483 50.000 16.64 7.42 0.00 2.52
2255 2331 5.186256 TGGCCCACAAAATCTTGATAGTA 57.814 39.130 0.00 0.00 36.33 1.82
2259 2335 5.880332 GCCCACAAAATCTTGATAGTAGTGA 59.120 40.000 0.00 0.00 36.33 3.41
2265 2341 7.607991 ACAAAATCTTGATAGTAGTGAGGTTGG 59.392 37.037 0.00 0.00 36.33 3.77
2269 2345 3.959293 TGATAGTAGTGAGGTTGGTCGA 58.041 45.455 0.00 0.00 0.00 4.20
2274 2350 1.105167 AGTGAGGTTGGTCGACGTGA 61.105 55.000 9.92 0.00 0.00 4.35
2286 2362 0.248907 CGACGTGACAGTGACCACTT 60.249 55.000 14.83 8.33 40.20 3.16
2289 2365 3.650139 GACGTGACAGTGACCACTTAAT 58.350 45.455 14.83 0.00 40.20 1.40
2291 2367 4.448210 ACGTGACAGTGACCACTTAATTT 58.552 39.130 14.83 0.00 40.20 1.82
2296 2372 3.317993 ACAGTGACCACTTAATTTGTGCC 59.682 43.478 0.00 2.27 40.20 5.01
2297 2373 3.569701 CAGTGACCACTTAATTTGTGCCT 59.430 43.478 0.00 0.00 40.20 4.75
2319 2395 0.179012 TTTTTCTCCGGGTCCGCTTT 60.179 50.000 0.00 0.00 38.24 3.51
2329 2405 2.920912 TCCGCTTTGTCTCGGGGT 60.921 61.111 0.64 0.00 45.31 4.95
2332 2408 2.954611 GCTTTGTCTCGGGGTTGC 59.045 61.111 0.00 0.00 0.00 4.17
2335 2411 3.109592 TTTGTCTCGGGGTTGCGGT 62.110 57.895 0.00 0.00 0.00 5.68
2337 2413 4.754667 GTCTCGGGGTTGCGGTCC 62.755 72.222 0.00 0.00 0.00 4.46
2355 2434 2.431683 GCTCCTCTGGTGGTTGCA 59.568 61.111 0.00 0.00 0.00 4.08
2357 2436 1.757306 CTCCTCTGGTGGTTGCACT 59.243 57.895 0.00 0.00 0.00 4.40
2358 2437 0.604780 CTCCTCTGGTGGTTGCACTG 60.605 60.000 0.00 0.00 0.00 3.66
2392 2471 0.880278 CCACTCGATGGCATAACCGG 60.880 60.000 0.00 0.00 43.24 5.28
2399 2478 0.110486 ATGGCATAACCGGATGGACC 59.890 55.000 9.46 4.31 43.94 4.46
2402 2481 0.818040 GCATAACCGGATGGACCACC 60.818 60.000 9.46 0.00 39.21 4.61
2411 2490 4.348684 TGGACCACCAATCCCTGT 57.651 55.556 0.00 0.00 43.91 4.00
2471 2550 5.589050 GGGTCCATTCTCTTTATTTTAGCGT 59.411 40.000 0.00 0.00 0.00 5.07
2512 2593 7.925043 TTTTAAGCCAAACCGACATATTCTA 57.075 32.000 0.00 0.00 0.00 2.10
2526 2607 7.308770 CCGACATATTCTATTTGATTGGCATGT 60.309 37.037 0.00 0.00 0.00 3.21
2542 2623 0.962356 ATGTGCAAGCTACCACTGGC 60.962 55.000 15.20 0.00 37.11 4.85
2548 2629 2.491693 GCAAGCTACCACTGGCAATAAA 59.508 45.455 0.00 0.00 36.55 1.40
2553 2634 5.072741 AGCTACCACTGGCAATAAATATGG 58.927 41.667 0.00 0.00 0.00 2.74
2554 2635 4.218417 GCTACCACTGGCAATAAATATGGG 59.782 45.833 0.00 0.00 0.00 4.00
2562 2643 4.420552 TGGCAATAAATATGGGGTCCCTAA 59.579 41.667 8.15 0.00 36.94 2.69
2565 2646 6.154534 GGCAATAAATATGGGGTCCCTAATTC 59.845 42.308 8.15 0.00 36.94 2.17
2570 2651 1.607225 TGGGGTCCCTAATTCTGCAT 58.393 50.000 8.15 0.00 36.94 3.96
2576 2657 6.046643 TGGGGTCCCTAATTCTGCATATAATT 59.953 38.462 8.15 0.00 36.94 1.40
2616 2697 8.950007 TTTATTCCAGACAACCTCCTTATTTT 57.050 30.769 0.00 0.00 0.00 1.82
2624 2705 6.712547 AGACAACCTCCTTATTTTCAGACAAG 59.287 38.462 0.00 0.00 0.00 3.16
2642 2725 7.251704 AGACAAGCTGATGATATAAAAACGG 57.748 36.000 0.00 0.00 0.00 4.44
2660 2743 8.710835 AAAAACGGGTGGCATTTTAATATAAG 57.289 30.769 0.00 0.00 0.00 1.73
2670 2754 7.069331 TGGCATTTTAATATAAGGTCCAAGGTG 59.931 37.037 0.00 0.00 0.00 4.00
2695 2779 7.175467 TGAGGCTATTGGTATCATAATTGCAAG 59.825 37.037 4.94 0.00 36.97 4.01
2700 2784 5.947228 TGGTATCATAATTGCAAGCTAGC 57.053 39.130 6.62 6.62 0.00 3.42
2707 2791 6.348498 TCATAATTGCAAGCTAGCTGAGTTA 58.652 36.000 20.16 12.54 34.99 2.24
2731 2815 5.995282 AGTTTTGTTCATCGTCACAATAGGA 59.005 36.000 0.00 0.00 32.96 2.94
2734 2818 6.480524 TTGTTCATCGTCACAATAGGAAAG 57.519 37.500 0.00 0.00 0.00 2.62
2754 2838 1.007118 GGTCCATGGTTCAATCCCCTT 59.993 52.381 12.58 0.00 0.00 3.95
2755 2839 2.102578 GTCCATGGTTCAATCCCCTTG 58.897 52.381 12.58 0.00 36.09 3.61
2756 2840 1.715931 TCCATGGTTCAATCCCCTTGT 59.284 47.619 12.58 0.00 36.20 3.16
2757 2841 1.826720 CCATGGTTCAATCCCCTTGTG 59.173 52.381 2.57 0.00 36.20 3.33
2764 2848 4.403734 GTTCAATCCCCTTGTGGTCTAAA 58.596 43.478 0.00 0.00 36.20 1.85
2785 2869 0.944386 TTTTTGCTGCTCGTCAGTCC 59.056 50.000 0.00 0.00 44.66 3.85
2791 2875 0.318699 CTGCTCGTCAGTCCGACAAA 60.319 55.000 0.40 0.00 45.70 2.83
2874 2958 2.278596 CTACATGCGGACCGGACG 60.279 66.667 17.22 14.23 0.00 4.79
2890 2974 3.437395 CCGGACGGAACAAAATCAATACA 59.563 43.478 4.40 0.00 37.50 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.944311 GAGAGGTTCGCGAGTTTGCA 60.944 55.000 9.59 0.00 34.15 4.08
161 162 0.251787 AGAATTTGGCGGGCTCCTTT 60.252 50.000 2.38 0.00 0.00 3.11
263 264 0.616371 TTGTGCCTGCGGGTATAACT 59.384 50.000 14.55 0.00 34.45 2.24
350 351 2.678934 AACGTGGGAGCCGAGCTA 60.679 61.111 0.00 0.00 39.88 3.32
363 364 0.832135 TGGAGCAGGAAGAGGAACGT 60.832 55.000 0.00 0.00 0.00 3.99
711 719 4.803426 CTCCTCGTCCGCAGTGGC 62.803 72.222 0.00 0.00 37.80 5.01
720 728 1.202313 CCTGGATTTCGACTCCTCGTC 60.202 57.143 13.03 0.00 41.02 4.20
815 842 3.005901 TTTTCGACGATGCGCACGG 62.006 57.895 27.28 19.17 32.99 4.94
884 911 0.249398 GCCCACTATGACGACTTGGT 59.751 55.000 0.00 0.00 0.00 3.67
887 914 0.108138 GCTGCCCACTATGACGACTT 60.108 55.000 0.00 0.00 0.00 3.01
956 983 4.371855 TGGAACTAGCTAGTGAACGATG 57.628 45.455 26.70 0.00 36.50 3.84
1096 1126 1.481871 AAGAAAGATGCATGCAGGGG 58.518 50.000 26.69 0.00 0.00 4.79
1097 1127 2.494471 TGAAAGAAAGATGCATGCAGGG 59.506 45.455 26.69 0.00 0.00 4.45
1391 1425 1.817099 GAGGATGTCCAGCTTGCCG 60.817 63.158 1.30 0.00 38.89 5.69
1768 1802 1.471676 CGTTCTCCTTCTTCCCCATCG 60.472 57.143 0.00 0.00 0.00 3.84
1939 2003 7.028361 ACAGTAGCTACTCGAACAGTTTAATC 58.972 38.462 23.68 0.00 36.43 1.75
1952 2016 9.615295 GTAGCATATAAAGAACAGTAGCTACTC 57.385 37.037 23.68 13.01 44.95 2.59
1974 2038 7.579450 CGAAACGAAGATGCTTATTTTAGTAGC 59.421 37.037 0.00 0.00 35.50 3.58
1975 2039 8.804743 TCGAAACGAAGATGCTTATTTTAGTAG 58.195 33.333 0.00 0.00 31.06 2.57
1976 2040 8.692110 TCGAAACGAAGATGCTTATTTTAGTA 57.308 30.769 0.00 0.00 31.06 1.82
1977 2041 7.331193 ACTCGAAACGAAGATGCTTATTTTAGT 59.669 33.333 0.00 0.00 34.74 2.24
1978 2042 7.676393 ACTCGAAACGAAGATGCTTATTTTAG 58.324 34.615 0.00 0.00 34.74 1.85
1979 2043 7.591006 ACTCGAAACGAAGATGCTTATTTTA 57.409 32.000 0.00 0.00 34.74 1.52
1980 2044 6.481954 ACTCGAAACGAAGATGCTTATTTT 57.518 33.333 0.00 0.00 34.74 1.82
2011 2075 1.068474 AAGATGCCTTTTCGTCGTCG 58.932 50.000 0.00 0.00 38.55 5.12
2131 2203 2.102749 CCCGACCATTGCAATGCG 59.897 61.111 30.15 26.75 35.08 4.73
2138 2213 4.085357 TCAATTATCCTCCCGACCATTG 57.915 45.455 0.00 0.00 0.00 2.82
2165 2241 3.003897 GCAACCAAGACCGTATTTTGTGA 59.996 43.478 0.00 0.00 0.00 3.58
2168 2244 2.667171 CGGCAACCAAGACCGTATTTTG 60.667 50.000 0.00 0.00 42.01 2.44
2183 2259 1.854227 GCTCTATCACCTACGGCAAC 58.146 55.000 0.00 0.00 0.00 4.17
2184 2260 0.384309 CGCTCTATCACCTACGGCAA 59.616 55.000 0.00 0.00 0.00 4.52
2188 2264 1.801771 CTCCTCGCTCTATCACCTACG 59.198 57.143 0.00 0.00 0.00 3.51
2190 2266 1.898902 GCTCCTCGCTCTATCACCTA 58.101 55.000 0.00 0.00 35.14 3.08
2213 2289 3.005367 CCAAACATGCCCGTAAGAAAACT 59.995 43.478 0.00 0.00 43.02 2.66
2216 2292 1.271102 GCCAAACATGCCCGTAAGAAA 59.729 47.619 0.00 0.00 43.02 2.52
2236 2312 6.540189 CCTCACTACTATCAAGATTTTGTGGG 59.460 42.308 0.00 0.00 35.73 4.61
2238 2314 8.446273 CAACCTCACTACTATCAAGATTTTGTG 58.554 37.037 0.00 0.00 35.73 3.33
2239 2315 7.607991 CCAACCTCACTACTATCAAGATTTTGT 59.392 37.037 0.00 0.00 35.73 2.83
2255 2331 1.105167 TCACGTCGACCAACCTCACT 61.105 55.000 10.58 0.00 0.00 3.41
2259 2335 1.362717 CTGTCACGTCGACCAACCT 59.637 57.895 10.58 0.00 44.71 3.50
2265 2341 0.933509 GTGGTCACTGTCACGTCGAC 60.934 60.000 5.18 5.18 45.61 4.20
2269 2345 3.746045 ATTAAGTGGTCACTGTCACGT 57.254 42.857 4.22 0.00 41.58 4.49
2274 2350 3.317993 GGCACAAATTAAGTGGTCACTGT 59.682 43.478 4.22 0.00 41.58 3.55
2278 2354 5.606348 AAAAGGCACAAATTAAGTGGTCA 57.394 34.783 11.54 0.00 37.46 4.02
2319 2395 3.998672 GACCGCAACCCCGAGACA 61.999 66.667 0.00 0.00 0.00 3.41
2332 2408 4.135153 CACCAGAGGAGCGGACCG 62.135 72.222 10.29 10.29 34.73 4.79
2335 2411 2.203788 AACCACCAGAGGAGCGGA 60.204 61.111 0.00 0.00 0.00 5.54
2337 2413 2.743928 GCAACCACCAGAGGAGCG 60.744 66.667 0.00 0.00 0.00 5.03
2342 2421 1.102809 TTGCAGTGCAACCACCAGAG 61.103 55.000 26.36 0.00 43.99 3.35
2392 2471 0.625849 ACAGGGATTGGTGGTCCATC 59.374 55.000 0.00 0.00 43.91 3.51
2399 2478 1.750778 GGTTATGCACAGGGATTGGTG 59.249 52.381 0.00 0.00 38.05 4.17
2402 2481 3.257873 TGTTTGGTTATGCACAGGGATTG 59.742 43.478 0.00 0.00 0.00 2.67
2407 2486 4.517952 TTCATGTTTGGTTATGCACAGG 57.482 40.909 0.00 0.00 0.00 4.00
2408 2487 5.472148 ACATTCATGTTTGGTTATGCACAG 58.528 37.500 0.00 0.00 37.90 3.66
2443 2522 7.503902 GCTAAAATAAAGAGAATGGACCCTGAT 59.496 37.037 0.00 0.00 0.00 2.90
2444 2523 6.828785 GCTAAAATAAAGAGAATGGACCCTGA 59.171 38.462 0.00 0.00 0.00 3.86
2445 2524 6.238484 CGCTAAAATAAAGAGAATGGACCCTG 60.238 42.308 0.00 0.00 0.00 4.45
2446 2525 5.823045 CGCTAAAATAAAGAGAATGGACCCT 59.177 40.000 0.00 0.00 0.00 4.34
2448 2527 6.679327 ACGCTAAAATAAAGAGAATGGACC 57.321 37.500 0.00 0.00 0.00 4.46
2449 2528 7.692705 GTGAACGCTAAAATAAAGAGAATGGAC 59.307 37.037 0.00 0.00 0.00 4.02
2450 2529 7.148306 GGTGAACGCTAAAATAAAGAGAATGGA 60.148 37.037 0.00 0.00 0.00 3.41
2451 2530 6.967199 GGTGAACGCTAAAATAAAGAGAATGG 59.033 38.462 0.00 0.00 0.00 3.16
2452 2531 7.693951 CAGGTGAACGCTAAAATAAAGAGAATG 59.306 37.037 0.00 0.00 0.00 2.67
2471 2550 1.859302 AAAAACTGTGGGCAGGTGAA 58.141 45.000 0.00 0.00 42.84 3.18
2494 2573 6.371809 TCAAATAGAATATGTCGGTTTGGC 57.628 37.500 0.00 0.00 36.72 4.52
2502 2583 7.327761 GCACATGCCAATCAAATAGAATATGTC 59.672 37.037 0.00 0.00 34.31 3.06
2503 2584 7.149973 GCACATGCCAATCAAATAGAATATGT 58.850 34.615 0.00 0.00 34.31 2.29
2507 2588 5.601583 TGCACATGCCAATCAAATAGAAT 57.398 34.783 0.49 0.00 41.18 2.40
2512 2593 2.027561 AGCTTGCACATGCCAATCAAAT 60.028 40.909 0.49 0.00 41.18 2.32
2526 2607 0.251297 ATTGCCAGTGGTAGCTTGCA 60.251 50.000 11.74 0.00 35.70 4.08
2542 2623 7.093771 GCAGAATTAGGGACCCCATATTTATTG 60.094 40.741 7.00 6.33 38.92 1.90
2548 2629 3.335748 TGCAGAATTAGGGACCCCATAT 58.664 45.455 7.00 0.00 38.92 1.78
2553 2634 7.406104 AGAATTATATGCAGAATTAGGGACCC 58.594 38.462 0.59 0.59 0.00 4.46
2554 2635 7.278868 CGAGAATTATATGCAGAATTAGGGACC 59.721 40.741 0.00 0.00 0.00 4.46
2562 2643 8.147058 AGTTGTCTCGAGAATTATATGCAGAAT 58.853 33.333 18.55 0.00 0.00 2.40
2565 2646 7.706281 AAGTTGTCTCGAGAATTATATGCAG 57.294 36.000 18.55 0.00 0.00 4.41
2576 2657 7.974501 GTCTGGAATAAATAAGTTGTCTCGAGA 59.025 37.037 12.08 12.08 0.00 4.04
2598 2679 5.997746 TGTCTGAAAATAAGGAGGTTGTCTG 59.002 40.000 0.00 0.00 0.00 3.51
2624 2705 4.556699 GCCACCCGTTTTTATATCATCAGC 60.557 45.833 0.00 0.00 0.00 4.26
2628 2709 6.478512 AAATGCCACCCGTTTTTATATCAT 57.521 33.333 0.00 0.00 28.26 2.45
2641 2724 5.836358 TGGACCTTATATTAAAATGCCACCC 59.164 40.000 0.00 0.00 0.00 4.61
2642 2725 6.969993 TGGACCTTATATTAAAATGCCACC 57.030 37.500 0.00 0.00 0.00 4.61
2660 2743 1.408822 CCAATAGCCTCACCTTGGACC 60.409 57.143 0.00 0.00 40.48 4.46
2670 2754 7.452880 TTGCAATTATGATACCAATAGCCTC 57.547 36.000 0.00 0.00 0.00 4.70
2695 2779 5.924475 TGAACAAAACTAACTCAGCTAGC 57.076 39.130 6.62 6.62 0.00 3.42
2700 2784 6.019075 TGTGACGATGAACAAAACTAACTCAG 60.019 38.462 0.00 0.00 0.00 3.35
2707 2791 5.995282 TCCTATTGTGACGATGAACAAAACT 59.005 36.000 0.00 0.00 39.57 2.66
2731 2815 2.559705 GGGGATTGAACCATGGACCTTT 60.560 50.000 21.47 0.85 0.00 3.11
2734 2818 0.631212 AGGGGATTGAACCATGGACC 59.369 55.000 21.47 9.99 0.00 4.46
2741 2825 1.075536 AGACCACAAGGGGATTGAACC 59.924 52.381 0.00 0.00 41.83 3.62
2791 2875 2.359848 GGCCTACCACACGTTTCTTTTT 59.640 45.455 0.00 0.00 35.26 1.94
2822 2906 2.445682 TTTCATTTATCCCCCGGGTG 57.554 50.000 21.85 8.67 36.47 4.61
2823 2907 3.476485 TTTTTCATTTATCCCCCGGGT 57.524 42.857 21.85 2.88 36.47 5.28
2847 2931 3.181469 GGTCCGCATGTAGTTCTTGGATA 60.181 47.826 0.00 0.00 0.00 2.59
2848 2932 2.420129 GGTCCGCATGTAGTTCTTGGAT 60.420 50.000 0.00 0.00 0.00 3.41
2849 2933 1.066430 GGTCCGCATGTAGTTCTTGGA 60.066 52.381 0.00 0.00 0.00 3.53
2850 2934 1.369625 GGTCCGCATGTAGTTCTTGG 58.630 55.000 0.00 0.00 0.00 3.61
2851 2935 0.999406 CGGTCCGCATGTAGTTCTTG 59.001 55.000 0.00 0.00 0.00 3.02
2852 2936 0.108329 CCGGTCCGCATGTAGTTCTT 60.108 55.000 5.50 0.00 0.00 2.52
2853 2937 0.968901 TCCGGTCCGCATGTAGTTCT 60.969 55.000 5.50 0.00 0.00 3.01
2854 2938 0.804933 GTCCGGTCCGCATGTAGTTC 60.805 60.000 5.50 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.