Multiple sequence alignment - TraesCS3A01G373800

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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 TraesCS3A01G373800 chr3A 100.000 2921 0 0 1 2921 623609042 623611962 0.000000e+00 5395.0
1 TraesCS3A01G373800 chr3A 88.901 946 94 8 1000 1939 625210613 625209673 0.000000e+00 1155.0
2 TraesCS3A01G373800 chr3A 74.268 820 165 35 1079 1878 598553493 598554286 1.320000e-78 303.0
3 TraesCS3A01G373800 chr3A 75.156 640 123 27 1075 1708 448701982 448702591 4.800000e-68 268.0
4 TraesCS3A01G373800 chr3A 71.867 814 160 53 1084 1864 484636972 484636195 1.390000e-38 171.0
5 TraesCS3A01G373800 chr3A 87.013 77 8 2 2834 2910 9355457 9355531 5.190000e-13 86.1
6 TraesCS3A01G373800 chr3B 90.831 2094 93 39 1 2032 641659620 641661676 0.000000e+00 2712.0
7 TraesCS3A01G373800 chr3B 87.553 940 110 6 987 1925 644172687 644171754 0.000000e+00 1081.0
8 TraesCS3A01G373800 chr3B 89.060 713 60 9 2119 2821 641661867 641662571 0.000000e+00 869.0
9 TraesCS3A01G373800 chr3B 74.450 818 161 38 1079 1878 602331250 602332037 2.830000e-80 309.0
10 TraesCS3A01G373800 chr3B 74.450 818 161 38 1079 1878 602352332 602353119 2.830000e-80 309.0
11 TraesCS3A01G373800 chr3B 75.039 633 118 29 1084 1708 431040220 431040820 1.040000e-64 257.0
12 TraesCS3A01G373800 chr3B 89.677 155 16 0 2222 2376 641663123 641663277 6.390000e-47 198.0
13 TraesCS3A01G373800 chr3B 95.652 115 2 1 2807 2921 641662589 641662700 6.430000e-42 182.0
14 TraesCS3A01G373800 chr3D 94.780 1590 44 20 413 1990 480841796 480843358 0.000000e+00 2440.0
15 TraesCS3A01G373800 chr3D 88.387 930 100 5 1000 1925 482191076 482190151 0.000000e+00 1112.0
16 TraesCS3A01G373800 chr3D 89.487 409 28 6 1 408 480841370 480841764 1.210000e-138 503.0
17 TraesCS3A01G373800 chr3D 74.421 821 162 37 1079 1878 455869729 455870522 2.830000e-80 309.0
18 TraesCS3A01G373800 chr3D 73.848 803 148 48 1084 1864 331657192 331657954 2.230000e-66 263.0
19 TraesCS3A01G373800 chr3D 90.000 90 8 1 2174 2262 480843663 480843752 6.610000e-22 115.0
20 TraesCS3A01G373800 chr4B 93.151 73 5 0 2830 2902 414222191 414222263 1.110000e-19 108.0
21 TraesCS3A01G373800 chr2B 92.000 75 6 0 2830 2904 288471667 288471741 3.980000e-19 106.0
22 TraesCS3A01G373800 chr2B 89.855 69 7 0 2842 2910 597549280 597549212 4.010000e-14 89.8
23 TraesCS3A01G373800 chr4D 91.781 73 6 0 2830 2902 336228741 336228813 5.150000e-18 102.0
24 TraesCS3A01G373800 chr4A 91.781 73 5 1 2830 2902 136889245 136889174 1.850000e-17 100.0
25 TraesCS3A01G373800 chr2D 86.047 86 7 5 2839 2921 650258448 650258365 1.440000e-13 87.9
26 TraesCS3A01G373800 chr2D 88.000 75 6 3 2839 2912 650237834 650237762 5.190000e-13 86.1


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 TraesCS3A01G373800 chr3A 623609042 623611962 2920 False 5395.000000 5395 100.000000 1 2921 1 chr3A.!!$F4 2920
1 TraesCS3A01G373800 chr3A 625209673 625210613 940 True 1155.000000 1155 88.901000 1000 1939 1 chr3A.!!$R2 939
2 TraesCS3A01G373800 chr3A 598553493 598554286 793 False 303.000000 303 74.268000 1079 1878 1 chr3A.!!$F3 799
3 TraesCS3A01G373800 chr3A 448701982 448702591 609 False 268.000000 268 75.156000 1075 1708 1 chr3A.!!$F2 633
4 TraesCS3A01G373800 chr3B 644171754 644172687 933 True 1081.000000 1081 87.553000 987 1925 1 chr3B.!!$R1 938
5 TraesCS3A01G373800 chr3B 641659620 641663277 3657 False 990.250000 2712 91.305000 1 2921 4 chr3B.!!$F4 2920
6 TraesCS3A01G373800 chr3B 602331250 602332037 787 False 309.000000 309 74.450000 1079 1878 1 chr3B.!!$F2 799
7 TraesCS3A01G373800 chr3B 602352332 602353119 787 False 309.000000 309 74.450000 1079 1878 1 chr3B.!!$F3 799
8 TraesCS3A01G373800 chr3B 431040220 431040820 600 False 257.000000 257 75.039000 1084 1708 1 chr3B.!!$F1 624
9 TraesCS3A01G373800 chr3D 482190151 482191076 925 True 1112.000000 1112 88.387000 1000 1925 1 chr3D.!!$R1 925
10 TraesCS3A01G373800 chr3D 480841370 480843752 2382 False 1019.333333 2440 91.422333 1 2262 3 chr3D.!!$F3 2261
11 TraesCS3A01G373800 chr3D 455869729 455870522 793 False 309.000000 309 74.421000 1079 1878 1 chr3D.!!$F2 799
12 TraesCS3A01G373800 chr3D 331657192 331657954 762 False 263.000000 263 73.848000 1084 1864 1 chr3D.!!$F1 780

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
408 411 0.033503 TGCCCGTGATACAGGAGAGA 60.034 55.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2426 0.312102 GGCAACTGGTGTTCTTCTGC 59.688 55.0 0.0 0.0 33.52 4.26 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
161 162 3.234630 TTCAACGAGCAGTCCCGGG 62.235 63.158 16.85 16.85 0.00 5.73
173 174 2.267961 CCCGGGCTTGTCCACTAC 59.732 66.667 8.08 0.00 36.21 2.73
184 185 1.616865 TGTCCACTACACACTACAGGC 59.383 52.381 0.00 0.00 31.43 4.85
186 187 2.094649 GTCCACTACACACTACAGGCTC 60.095 54.545 0.00 0.00 0.00 4.70
191 192 2.479566 ACACACTACAGGCTCAATGG 57.520 50.000 0.00 0.00 0.00 3.16
242 243 1.909700 TGAGGGCCATTGAGTTGTTC 58.090 50.000 6.18 0.00 0.00 3.18
246 247 2.108952 AGGGCCATTGAGTTGTTCTTCT 59.891 45.455 6.18 0.00 0.00 2.85
249 250 4.522789 GGGCCATTGAGTTGTTCTTCTTTA 59.477 41.667 4.39 0.00 0.00 1.85
267 269 4.830600 TCTTTAAGTTCATTGGGTTCCACC 59.169 41.667 0.00 0.00 37.60 4.61
268 270 2.765689 AAGTTCATTGGGTTCCACCA 57.234 45.000 0.00 0.00 41.02 4.17
269 271 1.995376 AGTTCATTGGGTTCCACCAC 58.005 50.000 0.00 0.00 41.02 4.16
270 272 0.596082 GTTCATTGGGTTCCACCACG 59.404 55.000 0.00 0.00 41.02 4.94
271 273 0.474614 TTCATTGGGTTCCACCACGA 59.525 50.000 0.00 0.00 41.02 4.35
272 274 0.474614 TCATTGGGTTCCACCACGAA 59.525 50.000 0.00 0.00 41.02 3.85
299 301 9.467258 CACATTGAATTGATAAATATGGACACC 57.533 33.333 0.00 0.00 0.00 4.16
313 315 2.290008 TGGACACCTATGCGTCACAATT 60.290 45.455 0.00 0.00 33.66 2.32
316 318 3.002791 ACACCTATGCGTCACAATTCAG 58.997 45.455 0.00 0.00 0.00 3.02
317 319 2.009774 ACCTATGCGTCACAATTCAGC 58.990 47.619 0.00 0.00 0.00 4.26
332 334 0.250038 TCAGCACTGACAAGGACTGC 60.250 55.000 0.00 0.00 34.14 4.40
334 336 0.533755 AGCACTGACAAGGACTGCAC 60.534 55.000 0.00 0.00 0.00 4.57
364 366 5.229260 CGACACGATTCAGACGAAATGATAA 59.771 40.000 0.00 0.00 34.01 1.75
385 387 1.906574 GGGTATCCACTCAGTTCCACA 59.093 52.381 0.00 0.00 0.00 4.17
388 390 3.941483 GGTATCCACTCAGTTCCACAATG 59.059 47.826 0.00 0.00 0.00 2.82
390 392 2.849942 TCCACTCAGTTCCACAATGTG 58.150 47.619 6.37 6.37 0.00 3.21
408 411 0.033503 TGCCCGTGATACAGGAGAGA 60.034 55.000 0.00 0.00 0.00 3.10
409 412 0.386113 GCCCGTGATACAGGAGAGAC 59.614 60.000 0.00 0.00 0.00 3.36
410 413 1.763968 CCCGTGATACAGGAGAGACA 58.236 55.000 0.00 0.00 0.00 3.41
411 414 2.100197 CCCGTGATACAGGAGAGACAA 58.900 52.381 0.00 0.00 0.00 3.18
416 446 3.099905 TGATACAGGAGAGACAACTGGG 58.900 50.000 0.00 0.00 36.57 4.45
432 462 3.976015 ACTGGGACTTCAAACTTCCAAA 58.024 40.909 0.00 0.00 0.00 3.28
490 521 1.855978 CGCGCGTATTGTGGAAAGATA 59.144 47.619 24.19 0.00 0.00 1.98
491 522 2.283086 CGCGCGTATTGTGGAAAGATAA 59.717 45.455 24.19 0.00 0.00 1.75
492 523 3.601586 CGCGCGTATTGTGGAAAGATAAG 60.602 47.826 24.19 0.00 0.00 1.73
540 579 2.395690 GCACCGAACGATTCAGCG 59.604 61.111 0.00 0.00 37.29 5.18
541 580 2.092291 GCACCGAACGATTCAGCGA 61.092 57.895 0.00 0.00 34.83 4.93
542 581 1.991430 CACCGAACGATTCAGCGAG 59.009 57.895 0.00 0.00 34.83 5.03
543 582 0.732880 CACCGAACGATTCAGCGAGT 60.733 55.000 0.00 0.00 34.83 4.18
937 983 6.376581 GGGTTCTACTGGCTATATATACACGT 59.623 42.308 0.00 0.00 0.00 4.49
992 1038 2.430332 CCAAGTTTCCAGCTTCCAACAA 59.570 45.455 0.00 0.00 0.00 2.83
1012 1058 2.712057 AACAAAGATGGCGAGCAAAG 57.288 45.000 0.00 0.00 0.00 2.77
1037 1083 1.509463 CGGCAATGCTGTTGCTCAT 59.491 52.632 21.10 0.00 44.36 2.90
1038 1084 0.108992 CGGCAATGCTGTTGCTCATT 60.109 50.000 21.10 0.00 44.36 2.57
1320 1372 3.842923 CTGCTCTCCATCGGCGGT 61.843 66.667 7.21 0.00 0.00 5.68
1942 2031 2.412847 GCTGATGTTGTTAACTGCGTCC 60.413 50.000 7.22 0.00 0.00 4.79
1996 2086 3.421231 GCGAATACTGCGTGTAGTATGTC 59.579 47.826 10.71 9.47 41.70 3.06
2000 2090 1.200474 CTGCGTGTAGTATGTCGCCG 61.200 60.000 5.98 0.00 46.57 6.46
2004 2094 1.730121 CGTGTAGTATGTCGCCGTGTT 60.730 52.381 0.00 0.00 0.00 3.32
2020 2110 6.201425 TCGCCGTGTTAAATTGTATCTTATCC 59.799 38.462 0.00 0.00 0.00 2.59
2034 2124 8.862325 TGTATCTTATCCAGAAACACAATTGT 57.138 30.769 4.92 4.92 34.16 2.71
2038 2128 6.932400 TCTTATCCAGAAACACAATTGTACGT 59.068 34.615 11.53 3.01 33.55 3.57
2039 2129 8.089597 TCTTATCCAGAAACACAATTGTACGTA 58.910 33.333 11.53 0.00 33.55 3.57
2040 2130 8.780846 TTATCCAGAAACACAATTGTACGTAT 57.219 30.769 11.53 0.00 33.55 3.06
2041 2131 9.872721 TTATCCAGAAACACAATTGTACGTATA 57.127 29.630 11.53 0.00 33.55 1.47
2042 2132 7.585286 TCCAGAAACACAATTGTACGTATAC 57.415 36.000 11.53 0.00 33.55 1.47
2043 2133 7.380536 TCCAGAAACACAATTGTACGTATACT 58.619 34.615 11.53 4.25 33.55 2.12
2044 2134 7.329962 TCCAGAAACACAATTGTACGTATACTG 59.670 37.037 11.53 14.04 33.55 2.74
2045 2135 6.953743 CAGAAACACAATTGTACGTATACTGC 59.046 38.462 11.53 0.00 33.55 4.40
2046 2136 5.444586 AACACAATTGTACGTATACTGCG 57.555 39.130 11.53 0.00 33.55 5.18
2047 2137 4.487948 ACACAATTGTACGTATACTGCGT 58.512 39.130 11.53 0.00 45.11 5.24
2048 2138 4.325204 ACACAATTGTACGTATACTGCGTG 59.675 41.667 11.53 5.60 42.87 5.34
2049 2139 4.325204 CACAATTGTACGTATACTGCGTGT 59.675 41.667 11.53 0.00 42.87 4.49
2050 2140 5.512434 CACAATTGTACGTATACTGCGTGTA 59.488 40.000 11.53 0.00 42.87 2.90
2051 2141 5.740569 ACAATTGTACGTATACTGCGTGTAG 59.259 40.000 9.97 0.00 42.87 2.74
2052 2142 4.944962 TTGTACGTATACTGCGTGTAGT 57.055 40.909 0.00 0.00 42.87 2.73
2053 2143 6.603237 ATTGTACGTATACTGCGTGTAGTA 57.397 37.500 0.00 0.29 42.87 1.82
2054 2144 6.603237 TTGTACGTATACTGCGTGTAGTAT 57.397 37.500 13.80 13.80 44.04 2.12
2055 2145 5.977731 TGTACGTATACTGCGTGTAGTATG 58.022 41.667 17.46 7.19 42.31 2.39
2056 2146 3.881795 ACGTATACTGCGTGTAGTATGC 58.118 45.455 17.46 15.37 42.31 3.14
2057 2147 3.231965 CGTATACTGCGTGTAGTATGCC 58.768 50.000 17.46 9.14 42.31 4.40
2068 2158 4.552572 CGTGTAGTATGCCGATTGTACGTA 60.553 45.833 0.00 0.00 0.00 3.57
2075 2165 3.120041 TGCCGATTGTACGTATGACATG 58.880 45.455 0.00 0.00 0.00 3.21
2076 2166 3.120792 GCCGATTGTACGTATGACATGT 58.879 45.455 0.00 0.00 0.00 3.21
2081 2171 6.183360 CCGATTGTACGTATGACATGTTTTGA 60.183 38.462 0.00 0.00 0.00 2.69
2082 2172 7.230914 CGATTGTACGTATGACATGTTTTGAA 58.769 34.615 0.00 0.00 0.00 2.69
2083 2173 7.742525 CGATTGTACGTATGACATGTTTTGAAA 59.257 33.333 0.00 0.00 0.00 2.69
2084 2174 9.554724 GATTGTACGTATGACATGTTTTGAAAT 57.445 29.630 0.00 0.00 0.00 2.17
2085 2175 9.906660 ATTGTACGTATGACATGTTTTGAAATT 57.093 25.926 0.00 0.00 0.00 1.82
2099 2287 8.749841 TGTTTTGAAATTGTATTTGGTATCCG 57.250 30.769 0.00 0.00 0.00 4.18
2101 2289 9.072294 GTTTTGAAATTGTATTTGGTATCCGAG 57.928 33.333 0.00 0.00 0.00 4.63
2110 2298 5.720371 ATTTGGTATCCGAGATCTCTCTG 57.280 43.478 20.26 8.97 40.75 3.35
2117 2305 3.826524 TCCGAGATCTCTCTGTTATGCT 58.173 45.455 20.26 0.00 40.75 3.79
2134 2344 9.499479 CTGTTATGCTTACTATTCCAGAATGAT 57.501 33.333 3.10 0.00 39.69 2.45
2216 2426 3.243168 CGGGTCAATGAACAATATGGCTG 60.243 47.826 0.00 0.00 0.00 4.85
2225 2435 4.156556 TGAACAATATGGCTGCAGAAGAAC 59.843 41.667 20.43 0.00 0.00 3.01
2265 2475 6.038603 CAGAACCATCAAGAGACAACAAAGAA 59.961 38.462 0.00 0.00 0.00 2.52
2293 2503 3.629398 ACTCAAGTGCTCAAGTCCTTTTG 59.371 43.478 0.00 0.00 0.00 2.44
2294 2504 2.951642 TCAAGTGCTCAAGTCCTTTTGG 59.048 45.455 0.00 0.00 42.21 3.28
2313 2523 3.624777 TGGAGGAATGGAGCTCAATTTC 58.375 45.455 17.57 15.62 0.00 2.17
2317 2527 5.163571 GGAGGAATGGAGCTCAATTTCTTTC 60.164 44.000 23.31 15.57 0.00 2.62
2318 2528 5.578073 AGGAATGGAGCTCAATTTCTTTCT 58.422 37.500 17.88 8.30 0.00 2.52
2319 2529 6.015282 AGGAATGGAGCTCAATTTCTTTCTT 58.985 36.000 17.88 6.59 0.00 2.52
2323 2533 4.082125 GGAGCTCAATTTCTTTCTTGGGA 58.918 43.478 17.19 0.00 0.00 4.37
2324 2534 4.708909 GGAGCTCAATTTCTTTCTTGGGAT 59.291 41.667 17.19 0.00 0.00 3.85
2326 2536 6.378280 GGAGCTCAATTTCTTTCTTGGGATTA 59.622 38.462 17.19 0.00 0.00 1.75
2377 2594 3.169355 GCAATTGGCATTTCGAATCCT 57.831 42.857 7.72 0.00 43.97 3.24
2379 2596 4.874970 GCAATTGGCATTTCGAATCCTAT 58.125 39.130 7.72 0.99 43.97 2.57
2380 2597 6.012658 GCAATTGGCATTTCGAATCCTATA 57.987 37.500 7.72 0.00 43.97 1.31
2381 2598 6.624423 GCAATTGGCATTTCGAATCCTATAT 58.376 36.000 7.72 0.00 43.97 0.86
2383 2600 8.408601 GCAATTGGCATTTCGAATCCTATATAT 58.591 33.333 7.72 0.00 43.97 0.86
2384 2601 9.941664 CAATTGGCATTTCGAATCCTATATATC 57.058 33.333 0.00 0.00 0.00 1.63
2507 2724 4.606457 AGTTTGATCTACTTGCATTCGC 57.394 40.909 0.00 0.00 39.24 4.70
2514 2731 2.235155 TCTACTTGCATTCGCCCTACAA 59.765 45.455 0.00 0.00 37.32 2.41
2521 2738 2.014128 CATTCGCCCTACAAACGGAAT 58.986 47.619 0.00 0.00 0.00 3.01
2537 2754 4.331968 ACGGAATTTCTCTACCATGCAAA 58.668 39.130 0.00 0.00 0.00 3.68
2541 2758 5.521372 GGAATTTCTCTACCATGCAAAATGC 59.479 40.000 0.00 0.00 45.29 3.56
2591 2808 8.789825 AATCACATTGCATTTAAATTAAGGCA 57.210 26.923 6.79 6.79 0.00 4.75
2625 2842 8.770438 TTTTCATGTTAAGAGTTTTTGCTTGT 57.230 26.923 0.00 0.00 0.00 3.16
2626 2843 7.754069 TTCATGTTAAGAGTTTTTGCTTGTG 57.246 32.000 0.00 0.00 0.00 3.33
2627 2844 6.862209 TCATGTTAAGAGTTTTTGCTTGTGT 58.138 32.000 0.00 0.00 0.00 3.72
2628 2845 6.751425 TCATGTTAAGAGTTTTTGCTTGTGTG 59.249 34.615 0.00 0.00 0.00 3.82
2675 2894 8.792830 ACCATAAGGACCATTAGTATTCTACA 57.207 34.615 0.00 0.00 38.69 2.74
2680 2899 8.964476 AAGGACCATTAGTATTCTACACAATG 57.036 34.615 0.00 0.00 35.17 2.82
2696 2915 9.733556 TCTACACAATGTTTAAAGACCATATGT 57.266 29.630 1.24 9.87 0.00 2.29
2706 2925 7.639113 TTAAAGACCATATGTCCAATTCCAC 57.361 36.000 1.24 0.00 45.68 4.02
2715 2934 7.147932 CCATATGTCCAATTCCACAATAACACA 60.148 37.037 1.24 0.00 0.00 3.72
2722 2941 2.513753 TCCACAATAACACAAGGGCAG 58.486 47.619 0.00 0.00 0.00 4.85
2738 2957 4.519213 AGGGCAGCGTCTAGTATATCTAG 58.481 47.826 0.00 0.00 45.37 2.43
2761 2980 9.747898 CTAGATAGTTGATCCCTACTAACTCAT 57.252 37.037 10.65 0.88 36.10 2.90
2762 2981 8.644374 AGATAGTTGATCCCTACTAACTCATC 57.356 38.462 0.00 0.00 35.05 2.92
2763 2982 8.228206 AGATAGTTGATCCCTACTAACTCATCA 58.772 37.037 0.00 0.00 35.05 3.07
2766 2985 8.095452 AGTTGATCCCTACTAACTCATCAATT 57.905 34.615 0.00 0.00 33.89 2.32
2767 2986 9.213777 AGTTGATCCCTACTAACTCATCAATTA 57.786 33.333 0.00 0.00 33.89 1.40
2795 3014 2.243810 TGCAACTACCCCAATTCAACC 58.756 47.619 0.00 0.00 0.00 3.77
2796 3015 2.243810 GCAACTACCCCAATTCAACCA 58.756 47.619 0.00 0.00 0.00 3.67
2805 3024 2.419021 CCCAATTCAACCACCATCATGC 60.419 50.000 0.00 0.00 0.00 4.06
2812 3063 3.200605 TCAACCACCATCATGCATACTCT 59.799 43.478 0.00 0.00 0.00 3.24
2847 3098 5.402997 TCTTTCAACATGCCATTATGCAA 57.597 34.783 0.00 0.00 45.84 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.181451 TGGCCCTAGCTAGATGTTTGATG 60.181 47.826 22.70 1.70 39.73 3.07
21 22 1.981495 GGATGGCCCTAGCTAGATGTT 59.019 52.381 22.70 2.77 39.73 2.71
22 23 1.650528 GGATGGCCCTAGCTAGATGT 58.349 55.000 22.70 3.26 39.73 3.06
49 50 2.092211 GGCTAAACACGACGATGAACAG 59.908 50.000 0.00 0.00 0.00 3.16
161 162 3.318017 CTGTAGTGTGTAGTGGACAAGC 58.682 50.000 0.00 0.00 40.66 4.01
173 174 1.089920 GCCATTGAGCCTGTAGTGTG 58.910 55.000 0.00 0.00 0.00 3.82
184 185 4.627611 ATTCAACGATTCAGCCATTGAG 57.372 40.909 0.00 0.00 37.07 3.02
186 187 4.735985 TCAATTCAACGATTCAGCCATTG 58.264 39.130 0.00 0.00 0.00 2.82
191 192 5.972973 TGCATTATCAATTCAACGATTCAGC 59.027 36.000 0.00 0.00 0.00 4.26
193 194 7.148272 TGTCTGCATTATCAATTCAACGATTCA 60.148 33.333 0.00 0.00 0.00 2.57
194 195 7.164826 GTGTCTGCATTATCAATTCAACGATTC 59.835 37.037 0.00 0.00 0.00 2.52
195 196 6.968904 GTGTCTGCATTATCAATTCAACGATT 59.031 34.615 0.00 0.00 0.00 3.34
196 197 6.317140 AGTGTCTGCATTATCAATTCAACGAT 59.683 34.615 0.00 0.00 0.00 3.73
197 198 5.643348 AGTGTCTGCATTATCAATTCAACGA 59.357 36.000 0.00 0.00 0.00 3.85
198 199 5.872635 AGTGTCTGCATTATCAATTCAACG 58.127 37.500 0.00 0.00 0.00 4.10
199 200 7.809331 TCAAAGTGTCTGCATTATCAATTCAAC 59.191 33.333 0.00 0.00 0.00 3.18
242 243 6.447162 GTGGAACCCAATGAACTTAAAGAAG 58.553 40.000 0.00 0.00 34.18 2.85
268 270 9.734620 CCATATTTATCAATTCAATGTGTTCGT 57.265 29.630 0.00 0.00 0.00 3.85
269 271 9.949174 TCCATATTTATCAATTCAATGTGTTCG 57.051 29.630 0.00 0.00 0.00 3.95
299 301 2.674852 AGTGCTGAATTGTGACGCATAG 59.325 45.455 0.00 0.00 32.75 2.23
313 315 0.250038 GCAGTCCTTGTCAGTGCTGA 60.250 55.000 0.00 0.00 37.25 4.26
316 318 1.835483 CGTGCAGTCCTTGTCAGTGC 61.835 60.000 0.00 0.00 40.16 4.40
317 319 0.249447 TCGTGCAGTCCTTGTCAGTG 60.249 55.000 0.00 0.00 0.00 3.66
332 334 2.104901 CTGAATCGTGTCGATCTCGTG 58.895 52.381 5.15 0.00 46.30 4.35
334 336 2.367772 GTCTGAATCGTGTCGATCTCG 58.632 52.381 5.15 0.00 46.30 4.04
364 366 2.188817 GTGGAACTGAGTGGATACCCT 58.811 52.381 0.00 0.00 0.00 4.34
385 387 0.908910 TCCTGTATCACGGGCACATT 59.091 50.000 0.00 0.00 44.40 2.71
388 390 0.103208 CTCTCCTGTATCACGGGCAC 59.897 60.000 0.00 0.00 44.40 5.01
390 392 0.386113 GTCTCTCCTGTATCACGGGC 59.614 60.000 0.00 0.00 44.40 6.13
408 411 3.288092 GGAAGTTTGAAGTCCCAGTTGT 58.712 45.455 0.00 0.00 0.00 3.32
409 412 3.287222 TGGAAGTTTGAAGTCCCAGTTG 58.713 45.455 0.00 0.00 0.00 3.16
410 413 3.662759 TGGAAGTTTGAAGTCCCAGTT 57.337 42.857 0.00 0.00 0.00 3.16
411 414 3.662759 TTGGAAGTTTGAAGTCCCAGT 57.337 42.857 0.00 0.00 0.00 4.00
416 446 7.931275 ACTTATCTGTTTGGAAGTTTGAAGTC 58.069 34.615 0.00 0.00 0.00 3.01
432 462 8.498054 TTTGCTACGTACTAGTACTTATCTGT 57.502 34.615 26.36 18.65 34.04 3.41
445 475 6.403878 AGTATGACCAAATTTGCTACGTACT 58.596 36.000 22.07 22.07 0.00 2.73
490 521 0.684153 AATACTGCCGCAATGCCCTT 60.684 50.000 0.00 0.00 0.00 3.95
491 522 0.182537 TAATACTGCCGCAATGCCCT 59.817 50.000 0.00 0.00 0.00 5.19
492 523 0.310854 GTAATACTGCCGCAATGCCC 59.689 55.000 0.00 0.00 0.00 5.36
540 579 6.197364 TCTCCTATGAAGTTTCTTCGACTC 57.803 41.667 5.28 0.00 0.00 3.36
541 580 6.015350 TGTTCTCCTATGAAGTTTCTTCGACT 60.015 38.462 5.28 0.00 0.00 4.18
542 581 6.157211 TGTTCTCCTATGAAGTTTCTTCGAC 58.843 40.000 5.28 0.00 0.00 4.20
543 582 6.340962 TGTTCTCCTATGAAGTTTCTTCGA 57.659 37.500 5.28 0.00 0.00 3.71
682 722 1.902765 ATGACGGTGCAGGCTGATCA 61.903 55.000 20.86 12.80 0.00 2.92
937 983 2.334977 TGCTGGAGAAGGTTCTTGGTA 58.665 47.619 0.00 0.00 37.73 3.25
992 1038 2.362077 ACTTTGCTCGCCATCTTTGTTT 59.638 40.909 0.00 0.00 0.00 2.83
1012 1058 0.031994 AACAGCATTGCCGGAAACAC 59.968 50.000 5.05 0.00 0.00 3.32
1037 1083 3.361158 CGGCCATTGTCACCGCAA 61.361 61.111 2.24 0.00 40.55 4.85
1302 1354 3.531207 CCGCCGATGGAGAGCAGA 61.531 66.667 0.00 0.00 0.00 4.26
1942 2031 1.583967 GATCGACGTGCTCCTGACG 60.584 63.158 0.00 0.00 42.62 4.35
1996 2086 6.018588 TGGATAAGATACAATTTAACACGGCG 60.019 38.462 4.80 4.80 0.00 6.46
2020 2110 6.953743 GCAGTATACGTACAATTGTGTTTCTG 59.046 38.462 21.42 17.62 39.30 3.02
2032 2122 5.558844 GCATACTACACGCAGTATACGTACA 60.559 44.000 0.00 0.00 41.61 2.90
2033 2123 4.842911 GCATACTACACGCAGTATACGTAC 59.157 45.833 0.00 0.00 41.61 3.67
2034 2124 4.083855 GGCATACTACACGCAGTATACGTA 60.084 45.833 0.00 0.00 41.61 3.57
2036 2126 3.231965 GGCATACTACACGCAGTATACG 58.768 50.000 0.00 0.00 41.61 3.06
2038 2128 3.140623 TCGGCATACTACACGCAGTATA 58.859 45.455 5.03 0.00 41.61 1.47
2039 2129 1.951602 TCGGCATACTACACGCAGTAT 59.048 47.619 0.42 0.42 41.61 2.12
2040 2130 1.381522 TCGGCATACTACACGCAGTA 58.618 50.000 0.00 0.00 41.61 2.74
2042 2132 1.522676 CAATCGGCATACTACACGCAG 59.477 52.381 0.00 0.00 0.00 5.18
2043 2133 1.134936 ACAATCGGCATACTACACGCA 60.135 47.619 0.00 0.00 0.00 5.24
2044 2134 1.567504 ACAATCGGCATACTACACGC 58.432 50.000 0.00 0.00 0.00 5.34
2045 2135 2.717519 CGTACAATCGGCATACTACACG 59.282 50.000 0.00 0.00 0.00 4.49
2046 2136 3.699067 ACGTACAATCGGCATACTACAC 58.301 45.455 0.00 0.00 34.94 2.90
2047 2137 5.239087 TCATACGTACAATCGGCATACTACA 59.761 40.000 0.00 0.00 34.94 2.74
2048 2138 5.566774 GTCATACGTACAATCGGCATACTAC 59.433 44.000 0.00 0.00 34.94 2.73
2049 2139 5.239087 TGTCATACGTACAATCGGCATACTA 59.761 40.000 0.00 0.00 34.94 1.82
2050 2140 4.037089 TGTCATACGTACAATCGGCATACT 59.963 41.667 0.00 0.00 34.94 2.12
2051 2141 4.292599 TGTCATACGTACAATCGGCATAC 58.707 43.478 0.00 0.00 34.94 2.39
2052 2142 4.571372 TGTCATACGTACAATCGGCATA 57.429 40.909 0.00 0.00 34.94 3.14
2053 2143 3.446310 TGTCATACGTACAATCGGCAT 57.554 42.857 0.00 0.00 34.94 4.40
2054 2144 2.943449 TGTCATACGTACAATCGGCA 57.057 45.000 0.00 0.00 34.94 5.69
2055 2145 3.120792 ACATGTCATACGTACAATCGGC 58.879 45.455 0.00 0.00 34.94 5.54
2056 2146 5.712217 AAACATGTCATACGTACAATCGG 57.288 39.130 0.00 0.00 34.94 4.18
2057 2147 6.757162 TCAAAACATGTCATACGTACAATCG 58.243 36.000 0.00 0.00 0.00 3.34
2068 2158 9.558396 ACCAAATACAATTTCAAAACATGTCAT 57.442 25.926 0.00 0.00 0.00 3.06
2075 2165 8.973835 TCGGATACCAAATACAATTTCAAAAC 57.026 30.769 0.00 0.00 0.00 2.43
2076 2166 9.015367 TCTCGGATACCAAATACAATTTCAAAA 57.985 29.630 0.00 0.00 0.00 2.44
2081 2171 8.432805 AGAGATCTCGGATACCAAATACAATTT 58.567 33.333 16.97 0.00 34.09 1.82
2082 2172 7.967908 AGAGATCTCGGATACCAAATACAATT 58.032 34.615 16.97 0.00 34.09 2.32
2083 2173 7.546250 AGAGATCTCGGATACCAAATACAAT 57.454 36.000 16.97 0.00 34.09 2.71
2084 2174 6.978674 AGAGATCTCGGATACCAAATACAA 57.021 37.500 16.97 0.00 34.09 2.41
2085 2175 6.576662 GAGAGATCTCGGATACCAAATACA 57.423 41.667 16.97 0.00 32.78 2.29
2099 2287 9.840427 GAATAGTAAGCATAACAGAGAGATCTC 57.160 37.037 15.29 15.29 43.17 2.75
2101 2289 8.580720 TGGAATAGTAAGCATAACAGAGAGATC 58.419 37.037 0.00 0.00 0.00 2.75
2117 2305 8.264347 TGTAGCACAATCATTCTGGAATAGTAA 58.736 33.333 0.00 0.00 0.00 2.24
2134 2344 2.942376 CAACCAGTTGACTGTAGCACAA 59.058 45.455 4.47 0.00 42.93 3.33
2216 2426 0.312102 GGCAACTGGTGTTCTTCTGC 59.688 55.000 0.00 0.00 33.52 4.26
2225 2435 1.021202 TTCTGAAACGGCAACTGGTG 58.979 50.000 0.00 0.00 0.00 4.17
2265 2475 4.314121 GACTTGAGCACTTGAGTTCATCT 58.686 43.478 0.00 0.00 0.00 2.90
2293 2503 3.895998 AGAAATTGAGCTCCATTCCTCC 58.104 45.455 13.03 4.39 0.00 4.30
2294 2504 5.651576 AGAAAGAAATTGAGCTCCATTCCTC 59.348 40.000 13.03 8.44 0.00 3.71
2298 2508 5.046807 CCCAAGAAAGAAATTGAGCTCCATT 60.047 40.000 12.15 9.45 0.00 3.16
2304 2514 9.440773 AAAATAATCCCAAGAAAGAAATTGAGC 57.559 29.630 0.00 0.00 0.00 4.26
2405 2622 9.579932 AATTAGAGGTATTGGAAATCATTCTCC 57.420 33.333 0.00 0.00 35.79 3.71
2505 2722 2.081462 AGAAATTCCGTTTGTAGGGCG 58.919 47.619 0.00 0.00 0.00 6.13
2507 2724 4.874396 GGTAGAGAAATTCCGTTTGTAGGG 59.126 45.833 0.00 0.00 0.00 3.53
2514 2731 3.950397 TGCATGGTAGAGAAATTCCGTT 58.050 40.909 0.00 0.00 0.00 4.44
2586 2803 8.789825 TTAACATGAAAATTTATGCATGCCTT 57.210 26.923 16.68 5.27 41.25 4.35
2587 2804 8.259411 TCTTAACATGAAAATTTATGCATGCCT 58.741 29.630 16.68 8.18 41.25 4.75
2637 2854 8.343168 TGGTCCTTATGGTTTAAACTATGTTG 57.657 34.615 23.14 13.88 32.12 3.33
2638 2855 9.541884 AATGGTCCTTATGGTTTAAACTATGTT 57.458 29.630 23.14 4.76 32.12 2.71
2651 2868 8.647796 TGTGTAGAATACTAATGGTCCTTATGG 58.352 37.037 0.00 0.00 43.54 2.74
2674 2893 7.825681 TGGACATATGGTCTTTAAACATTGTG 58.174 34.615 7.80 0.33 46.16 3.33
2675 2894 8.415950 TTGGACATATGGTCTTTAAACATTGT 57.584 30.769 7.80 1.87 46.16 2.71
2680 2899 7.973944 GTGGAATTGGACATATGGTCTTTAAAC 59.026 37.037 7.80 0.00 46.16 2.01
2685 2904 5.191727 TGTGGAATTGGACATATGGTCTT 57.808 39.130 7.80 0.00 46.16 3.01
2687 2906 7.068103 TGTTATTGTGGAATTGGACATATGGTC 59.932 37.037 7.80 2.47 46.20 4.02
2696 2915 4.526262 CCCTTGTGTTATTGTGGAATTGGA 59.474 41.667 0.00 0.00 0.00 3.53
2706 2925 0.881118 ACGCTGCCCTTGTGTTATTG 59.119 50.000 0.00 0.00 0.00 1.90
2715 2934 3.768878 AGATATACTAGACGCTGCCCTT 58.231 45.455 0.00 0.00 0.00 3.95
2738 2957 8.410673 TGATGAGTTAGTAGGGATCAACTATC 57.589 38.462 0.00 0.00 31.57 2.08
2761 2980 8.664992 TGGGGTAGTTGCATATTAGATAATTGA 58.335 33.333 0.00 0.00 0.00 2.57
2762 2981 8.862325 TGGGGTAGTTGCATATTAGATAATTG 57.138 34.615 0.00 0.00 0.00 2.32
2766 2985 8.664992 TGAATTGGGGTAGTTGCATATTAGATA 58.335 33.333 0.00 0.00 0.00 1.98
2767 2986 7.526041 TGAATTGGGGTAGTTGCATATTAGAT 58.474 34.615 0.00 0.00 0.00 1.98
2768 2987 6.905736 TGAATTGGGGTAGTTGCATATTAGA 58.094 36.000 0.00 0.00 0.00 2.10
2769 2988 7.425606 GTTGAATTGGGGTAGTTGCATATTAG 58.574 38.462 0.00 0.00 0.00 1.73
2784 3003 2.419021 GCATGATGGTGGTTGAATTGGG 60.419 50.000 0.00 0.00 0.00 4.12
2789 3008 3.947196 GAGTATGCATGATGGTGGTTGAA 59.053 43.478 10.16 0.00 0.00 2.69
2847 3098 5.652452 GCATATTAAGGTGTGTCTTTTCCCT 59.348 40.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.