Multiple sequence alignment - TraesCS2A01G153800

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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 TraesCS2A01G153800 chr2A 100.000 2645 0 0 1 2645 101826105 101823461 0.000000e+00 4885
1 TraesCS2A01G153800 chr2A 83.252 412 45 17 1125 1533 101840241 101839851 9.000000e-95 357
2 TraesCS2A01G153800 chr2B 90.078 1542 81 35 516 2026 153896004 153894504 0.000000e+00 1934
3 TraesCS2A01G153800 chr2B 85.271 516 56 17 19 524 153896562 153896057 5.050000e-142 514
4 TraesCS2A01G153800 chr2B 82.324 413 47 18 1128 1533 153907832 153907439 4.220000e-88 335
5 TraesCS2A01G153800 chr2D 87.332 1563 82 41 516 2026 102647346 102645848 0.000000e+00 1683
6 TraesCS2A01G153800 chr2D 95.737 563 24 0 2083 2645 248768028 248768590 0.000000e+00 907
7 TraesCS2A01G153800 chr2D 94.336 565 30 2 2082 2645 152861566 152862129 0.000000e+00 865
8 TraesCS2A01G153800 chr2D 86.408 515 56 7 19 524 102647900 102647391 3.850000e-153 551
9 TraesCS2A01G153800 chr7D 95.922 564 23 0 2082 2645 81765023 81765586 0.000000e+00 915
10 TraesCS2A01G153800 chr7D 95.035 564 26 2 2083 2645 69553440 69552878 0.000000e+00 885
11 TraesCS2A01G153800 chr7D 94.326 564 30 2 2083 2645 338857971 338858533 0.000000e+00 863
12 TraesCS2A01G153800 chr5D 95.390 564 26 0 2082 2645 243799781 243800344 0.000000e+00 898
13 TraesCS2A01G153800 chr5D 84.706 680 38 16 1049 1712 432892929 432892300 1.040000e-173 619
14 TraesCS2A01G153800 chr1D 95.221 565 25 2 2082 2645 7481753 7482316 0.000000e+00 893
15 TraesCS2A01G153800 chr6D 94.326 564 30 2 2083 2645 19493932 19494494 0.000000e+00 863
16 TraesCS2A01G153800 chr4D 94.326 564 29 3 2083 2645 411004947 411004386 0.000000e+00 861
17 TraesCS2A01G153800 chr1B 85.644 202 14 10 1511 1712 588239879 588240065 5.770000e-47 198
18 TraesCS2A01G153800 chr1B 85.714 133 14 1 1044 1176 588239531 588239658 4.590000e-28 135
19 TraesCS2A01G153800 chr4A 85.792 183 11 8 1530 1712 358879867 358880034 2.090000e-41 180


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 TraesCS2A01G153800 chr2A 101823461 101826105 2644 True 4885 4885 100.0000 1 2645 1 chr2A.!!$R1 2644
1 TraesCS2A01G153800 chr2B 153894504 153896562 2058 True 1224 1934 87.6745 19 2026 2 chr2B.!!$R2 2007
2 TraesCS2A01G153800 chr2D 102645848 102647900 2052 True 1117 1683 86.8700 19 2026 2 chr2D.!!$R1 2007
3 TraesCS2A01G153800 chr2D 248768028 248768590 562 False 907 907 95.7370 2083 2645 1 chr2D.!!$F2 562
4 TraesCS2A01G153800 chr2D 152861566 152862129 563 False 865 865 94.3360 2082 2645 1 chr2D.!!$F1 563
5 TraesCS2A01G153800 chr7D 81765023 81765586 563 False 915 915 95.9220 2082 2645 1 chr7D.!!$F1 563
6 TraesCS2A01G153800 chr7D 69552878 69553440 562 True 885 885 95.0350 2083 2645 1 chr7D.!!$R1 562
7 TraesCS2A01G153800 chr7D 338857971 338858533 562 False 863 863 94.3260 2083 2645 1 chr7D.!!$F2 562
8 TraesCS2A01G153800 chr5D 243799781 243800344 563 False 898 898 95.3900 2082 2645 1 chr5D.!!$F1 563
9 TraesCS2A01G153800 chr5D 432892300 432892929 629 True 619 619 84.7060 1049 1712 1 chr5D.!!$R1 663
10 TraesCS2A01G153800 chr1D 7481753 7482316 563 False 893 893 95.2210 2082 2645 1 chr1D.!!$F1 563
11 TraesCS2A01G153800 chr6D 19493932 19494494 562 False 863 863 94.3260 2083 2645 1 chr6D.!!$F1 562
12 TraesCS2A01G153800 chr4D 411004386 411004947 561 True 861 861 94.3260 2083 2645 1 chr4D.!!$R1 562

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
309 320 0.033109 CATTTTCCCACCTCCTCCCC 60.033 60.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2204 0.037326 TCGTGCTTTGAATCGGCTCT 60.037 50.0 0.0 0.0 0.0 4.09 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
88 89 4.299586 TGCAAGACAAATAGGGACATCA 57.700 40.909 0.00 0.00 0.00 3.07
248 259 1.134280 CATGAATGCTCGACCCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
273 284 4.587189 CCTCCGATCGTTCCGCCC 62.587 72.222 15.09 0.00 0.00 6.13
291 302 2.363018 CTGCCTCCGACCTCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
293 304 1.306141 TGCCTCCGACCTCCTCATT 60.306 57.895 0.00 0.00 0.00 2.57
309 320 0.033109 CATTTTCCCACCTCCTCCCC 60.033 60.000 0.00 0.00 0.00 4.81
326 337 1.537202 CCCCTTTTTCTTCTCACTGCG 59.463 52.381 0.00 0.00 0.00 5.18
327 338 2.494059 CCCTTTTTCTTCTCACTGCGA 58.506 47.619 0.00 0.00 0.00 5.10
331 342 4.023707 CCTTTTTCTTCTCACTGCGAACAT 60.024 41.667 0.00 0.00 0.00 2.71
344 363 1.927895 CGAACATTCCTCTTCCTCCG 58.072 55.000 0.00 0.00 0.00 4.63
348 367 0.466124 CATTCCTCTTCCTCCGTCCC 59.534 60.000 0.00 0.00 0.00 4.46
349 368 0.042731 ATTCCTCTTCCTCCGTCCCA 59.957 55.000 0.00 0.00 0.00 4.37
350 369 0.042731 TTCCTCTTCCTCCGTCCCAT 59.957 55.000 0.00 0.00 0.00 4.00
358 377 3.000819 TCCGTCCCATCGCCACTT 61.001 61.111 0.00 0.00 0.00 3.16
375 394 0.179000 CTTTCGAGCTAGGGTGCCAT 59.821 55.000 0.00 0.00 0.00 4.40
379 398 1.227380 GAGCTAGGGTGCCATCACG 60.227 63.158 0.00 0.00 44.03 4.35
401 420 3.065371 GCATAACAAATCCTTCACCGGAG 59.935 47.826 9.46 0.00 36.31 4.63
423 442 5.723355 AGGGGCTTATTACCACTAGTATCA 58.277 41.667 0.00 0.00 39.92 2.15
424 443 5.543020 AGGGGCTTATTACCACTAGTATCAC 59.457 44.000 0.00 0.00 39.92 3.06
439 458 2.981977 ATCACGTGCCGGTTGTCGTT 62.982 55.000 11.67 0.00 37.11 3.85
455 474 2.745884 TTGCCATCTCGCCGTTGG 60.746 61.111 0.30 0.30 35.88 3.77
500 519 0.178944 TCCTTCCACCTTCCGACTCA 60.179 55.000 0.00 0.00 0.00 3.41
530 610 3.207777 AGGCTTGTCCCTCTTCTCCTATA 59.792 47.826 0.00 0.00 34.51 1.31
532 612 3.004944 GCTTGTCCCTCTTCTCCTATACG 59.995 52.174 0.00 0.00 0.00 3.06
543 623 4.180377 TCTCCTATACGTCCAATCCAGT 57.820 45.455 0.00 0.00 0.00 4.00
556 636 4.824537 TCCAATCCAGTGTTCGAAATTTCA 59.175 37.500 17.99 2.95 0.00 2.69
560 640 8.620416 CCAATCCAGTGTTCGAAATTTCATATA 58.380 33.333 17.99 0.99 0.00 0.86
637 717 9.815936 CAGATTCAAATTAATTTCAAGCCAAAC 57.184 29.630 10.53 0.00 0.00 2.93
638 718 9.783081 AGATTCAAATTAATTTCAAGCCAAACT 57.217 25.926 10.53 0.24 0.00 2.66
698 782 6.571150 GCATGGAGATCAAAATAATAGTGGGC 60.571 42.308 0.00 0.00 0.00 5.36
699 783 5.063204 TGGAGATCAAAATAATAGTGGGCG 58.937 41.667 0.00 0.00 0.00 6.13
700 784 5.063880 GGAGATCAAAATAATAGTGGGCGT 58.936 41.667 0.00 0.00 0.00 5.68
702 786 5.680619 AGATCAAAATAATAGTGGGCGTCA 58.319 37.500 0.00 0.00 0.00 4.35
703 787 5.760253 AGATCAAAATAATAGTGGGCGTCAG 59.240 40.000 0.00 0.00 0.00 3.51
704 788 5.092554 TCAAAATAATAGTGGGCGTCAGA 57.907 39.130 0.00 0.00 0.00 3.27
705 789 5.680619 TCAAAATAATAGTGGGCGTCAGAT 58.319 37.500 0.00 0.00 0.00 2.90
706 790 5.758296 TCAAAATAATAGTGGGCGTCAGATC 59.242 40.000 0.00 0.00 0.00 2.75
707 791 4.955811 AATAATAGTGGGCGTCAGATCA 57.044 40.909 0.00 0.00 0.00 2.92
708 792 2.898729 AATAGTGGGCGTCAGATCAG 57.101 50.000 0.00 0.00 0.00 2.90
710 794 2.004808 TAGTGGGCGTCAGATCAGCG 62.005 60.000 0.00 0.00 0.00 5.18
711 795 3.381983 TGGGCGTCAGATCAGCGT 61.382 61.111 0.00 0.00 0.00 5.07
712 796 2.887568 GGGCGTCAGATCAGCGTG 60.888 66.667 0.00 0.00 0.00 5.34
713 797 3.558411 GGCGTCAGATCAGCGTGC 61.558 66.667 0.00 0.00 0.00 5.34
714 798 3.906649 GCGTCAGATCAGCGTGCG 61.907 66.667 0.00 0.00 0.00 5.34
715 799 2.504899 CGTCAGATCAGCGTGCGT 60.505 61.111 0.00 0.00 0.00 5.24
734 818 2.308769 GCATGGAGATGAGAGCGCG 61.309 63.158 0.00 0.00 0.00 6.86
855 951 1.597937 CCGCGCCATTTTCTTATGCTC 60.598 52.381 0.00 0.00 0.00 4.26
867 963 3.242867 TCTTATGCTCCTCCGATCCAAT 58.757 45.455 0.00 0.00 0.00 3.16
871 967 0.665298 GCTCCTCCGATCCAATTTGC 59.335 55.000 0.00 0.00 0.00 3.68
872 968 2.018644 GCTCCTCCGATCCAATTTGCA 61.019 52.381 0.00 0.00 0.00 4.08
873 969 2.579873 CTCCTCCGATCCAATTTGCAT 58.420 47.619 0.00 0.00 0.00 3.96
874 970 2.292569 CTCCTCCGATCCAATTTGCATG 59.707 50.000 0.00 0.00 0.00 4.06
875 971 1.269413 CCTCCGATCCAATTTGCATGC 60.269 52.381 11.82 11.82 0.00 4.06
953 1049 2.277583 GTGCCAACGCGCAATAATG 58.722 52.632 5.73 0.00 45.21 1.90
980 1076 1.945394 CGTCCGCGCCTATATATACCT 59.055 52.381 0.00 0.00 0.00 3.08
981 1077 2.032204 CGTCCGCGCCTATATATACCTC 60.032 54.545 0.00 0.00 0.00 3.85
1014 1110 1.755783 CTTGCTCCCCATGCTTCCC 60.756 63.158 0.00 0.00 0.00 3.97
1040 1136 0.387878 CACAGCTCACTCACTCGTCC 60.388 60.000 0.00 0.00 0.00 4.79
1063 1164 2.036571 CCGGCCGGTTGGTTAACTC 61.037 63.158 36.64 0.00 36.99 3.01
1505 1636 1.518792 GCGGGCTTTCTACCTCGAC 60.519 63.158 0.00 0.00 0.00 4.20
1601 1732 0.668535 CGGCTGGTCATCGACTCATA 59.331 55.000 0.00 0.00 32.47 2.15
1627 1758 1.667212 TGCATGAGCTAGCAAATCGTG 59.333 47.619 18.83 17.41 42.74 4.35
1744 1885 1.665599 GTGCACATGGCTTGGCAAC 60.666 57.895 13.17 0.00 45.15 4.17
1762 1903 4.314121 GCAACAAGAATGTCTCTGACTCT 58.686 43.478 0.00 0.00 39.40 3.24
1781 1922 0.809385 TCTGTAGCTGTACTGCCGAC 59.191 55.000 19.81 17.70 0.00 4.79
1785 1926 1.945354 TAGCTGTACTGCCGACTGCC 61.945 60.000 19.81 0.00 41.27 4.85
1786 1927 2.507102 CTGTACTGCCGACTGCCG 60.507 66.667 0.00 0.00 40.16 5.69
1787 1928 2.986979 TGTACTGCCGACTGCCGA 60.987 61.111 0.00 0.00 41.76 5.54
1788 1929 2.202623 GTACTGCCGACTGCCGAG 60.203 66.667 0.00 0.00 41.76 4.63
1789 1930 2.675423 TACTGCCGACTGCCGAGT 60.675 61.111 0.00 0.00 41.76 4.18
1790 1931 2.989881 TACTGCCGACTGCCGAGTG 61.990 63.158 0.00 0.00 41.76 3.51
1832 1973 3.301706 GGCAACTTGCGATTCGTTTTTA 58.698 40.909 8.03 0.00 46.21 1.52
1881 2022 0.817634 TGTACGTGCTGCTGGCTTTT 60.818 50.000 4.97 0.00 42.39 2.27
2027 2169 3.124270 CGCGCCCACTGCACATAA 61.124 61.111 0.00 0.00 41.33 1.90
2028 2170 2.472059 CGCGCCCACTGCACATAAT 61.472 57.895 0.00 0.00 41.33 1.28
2029 2171 1.064621 GCGCCCACTGCACATAATG 59.935 57.895 0.00 0.00 41.33 1.90
2037 2179 4.696078 GCACATAATGCGTGGCTG 57.304 55.556 0.00 0.00 46.55 4.85
2038 2180 2.097444 GCACATAATGCGTGGCTGA 58.903 52.632 0.00 0.00 46.55 4.26
2039 2181 0.451383 GCACATAATGCGTGGCTGAA 59.549 50.000 0.00 0.00 46.55 3.02
2040 2182 1.795162 GCACATAATGCGTGGCTGAAC 60.795 52.381 0.00 0.00 46.55 3.18
2041 2183 1.468127 CACATAATGCGTGGCTGAACA 59.532 47.619 0.00 0.00 0.00 3.18
2042 2184 2.095314 CACATAATGCGTGGCTGAACAA 60.095 45.455 0.00 0.00 0.00 2.83
2043 2185 2.556189 ACATAATGCGTGGCTGAACAAA 59.444 40.909 0.00 0.00 0.00 2.83
2044 2186 2.697431 TAATGCGTGGCTGAACAAAC 57.303 45.000 0.00 0.00 0.00 2.93
2045 2187 0.317770 AATGCGTGGCTGAACAAACG 60.318 50.000 0.00 0.00 39.00 3.60
2047 2189 3.022287 CGTGGCTGAACAAACGCT 58.978 55.556 0.00 0.00 0.00 5.07
2048 2190 1.369209 CGTGGCTGAACAAACGCTG 60.369 57.895 0.00 0.00 0.00 5.18
2049 2191 1.771073 CGTGGCTGAACAAACGCTGA 61.771 55.000 0.00 0.00 0.00 4.26
2050 2192 0.380378 GTGGCTGAACAAACGCTGAA 59.620 50.000 0.00 0.00 0.00 3.02
2051 2193 0.662619 TGGCTGAACAAACGCTGAAG 59.337 50.000 0.00 0.00 0.00 3.02
2052 2194 0.040067 GGCTGAACAAACGCTGAAGG 60.040 55.000 0.00 0.00 0.00 3.46
2053 2195 0.661483 GCTGAACAAACGCTGAAGGC 60.661 55.000 0.00 0.00 37.64 4.35
2054 2196 0.947244 CTGAACAAACGCTGAAGGCT 59.053 50.000 0.00 0.00 39.13 4.58
2055 2197 0.662619 TGAACAAACGCTGAAGGCTG 59.337 50.000 0.00 0.00 39.13 4.85
2056 2198 0.944386 GAACAAACGCTGAAGGCTGA 59.056 50.000 0.00 0.00 39.13 4.26
2057 2199 0.947244 AACAAACGCTGAAGGCTGAG 59.053 50.000 0.00 0.00 39.13 3.35
2058 2200 0.106708 ACAAACGCTGAAGGCTGAGA 59.893 50.000 0.00 0.00 39.13 3.27
2059 2201 0.795085 CAAACGCTGAAGGCTGAGAG 59.205 55.000 0.00 0.00 39.13 3.20
2060 2202 0.321122 AAACGCTGAAGGCTGAGAGG 60.321 55.000 0.00 0.00 39.13 3.69
2061 2203 1.188219 AACGCTGAAGGCTGAGAGGA 61.188 55.000 0.00 0.00 39.13 3.71
2062 2204 1.188219 ACGCTGAAGGCTGAGAGGAA 61.188 55.000 0.00 0.00 39.13 3.36
2063 2205 0.459934 CGCTGAAGGCTGAGAGGAAG 60.460 60.000 0.00 0.00 39.13 3.46
2064 2206 0.901124 GCTGAAGGCTGAGAGGAAGA 59.099 55.000 0.00 0.00 38.06 2.87
2065 2207 1.134729 GCTGAAGGCTGAGAGGAAGAG 60.135 57.143 0.00 0.00 38.06 2.85
2066 2208 0.901124 TGAAGGCTGAGAGGAAGAGC 59.099 55.000 0.00 0.00 0.00 4.09
2068 2210 2.498726 GGCTGAGAGGAAGAGCCG 59.501 66.667 0.00 0.00 42.84 5.52
2069 2211 2.055042 GGCTGAGAGGAAGAGCCGA 61.055 63.158 0.00 0.00 42.84 5.54
2070 2212 1.398958 GGCTGAGAGGAAGAGCCGAT 61.399 60.000 0.00 0.00 42.84 4.18
2071 2213 0.463620 GCTGAGAGGAAGAGCCGATT 59.536 55.000 0.00 0.00 43.43 3.34
2072 2214 1.537990 GCTGAGAGGAAGAGCCGATTC 60.538 57.143 0.00 0.00 43.43 2.52
2073 2215 1.753649 CTGAGAGGAAGAGCCGATTCA 59.246 52.381 0.00 0.00 43.43 2.57
2074 2216 2.167281 CTGAGAGGAAGAGCCGATTCAA 59.833 50.000 0.00 0.00 43.43 2.69
2075 2217 2.567169 TGAGAGGAAGAGCCGATTCAAA 59.433 45.455 0.00 0.00 43.43 2.69
2076 2218 3.194062 GAGAGGAAGAGCCGATTCAAAG 58.806 50.000 0.00 0.00 43.43 2.77
2077 2219 1.668237 GAGGAAGAGCCGATTCAAAGC 59.332 52.381 0.00 0.00 43.43 3.51
2078 2220 1.003580 AGGAAGAGCCGATTCAAAGCA 59.996 47.619 0.00 0.00 43.43 3.91
2079 2221 1.131315 GGAAGAGCCGATTCAAAGCAC 59.869 52.381 0.00 0.00 0.00 4.40
2080 2222 0.798776 AAGAGCCGATTCAAAGCACG 59.201 50.000 0.00 0.00 0.00 5.34
2105 2247 5.951747 AGAGTTAATTGCATGTTGGTACCAT 59.048 36.000 17.17 0.00 0.00 3.55
2133 2275 3.566322 GGCATCTACTCACGAGTCAGTAT 59.434 47.826 2.26 0.00 42.54 2.12
2139 2281 6.818233 TCTACTCACGAGTCAGTATCACTAT 58.182 40.000 2.26 0.00 42.54 2.12
2235 2377 4.203076 ACCGCGTATCCGACAGGC 62.203 66.667 4.92 0.00 37.47 4.85
2374 2516 0.043485 GTTCCCCTCTCCCTCTCCTT 59.957 60.000 0.00 0.00 0.00 3.36
2388 2530 1.671901 CTCCTTCCCGTGCTCCTCTC 61.672 65.000 0.00 0.00 0.00 3.20
2397 2539 1.203287 CGTGCTCCTCTCTGTCAATGA 59.797 52.381 0.00 0.00 0.00 2.57
2516 2658 3.411517 CCAGGATTGGCCGAGGGT 61.412 66.667 0.00 0.00 43.43 4.34
2550 2692 2.176273 TCGTACTACTCGAGCGGCC 61.176 63.158 13.61 0.00 33.38 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 6.874134 GTGTATAGACAGACATTGGTGAAACT 59.126 38.462 0.00 0.00 35.82 2.66
159 160 7.347117 TAAGAGGTCTTAGCATGTGTGCAATC 61.347 42.308 3.03 0.00 44.09 2.67
273 284 3.151022 GAGGAGGTCGGAGGCAGG 61.151 72.222 0.00 0.00 0.00 4.85
283 294 1.636003 GAGGTGGGAAAATGAGGAGGT 59.364 52.381 0.00 0.00 0.00 3.85
286 297 1.916181 GAGGAGGTGGGAAAATGAGGA 59.084 52.381 0.00 0.00 0.00 3.71
291 302 0.178801 AGGGGAGGAGGTGGGAAAAT 60.179 55.000 0.00 0.00 0.00 1.82
293 304 0.404346 AAAGGGGAGGAGGTGGGAAA 60.404 55.000 0.00 0.00 0.00 3.13
309 320 4.536364 TGTTCGCAGTGAGAAGAAAAAG 57.464 40.909 9.77 0.00 0.00 2.27
326 337 2.418884 GGACGGAGGAAGAGGAATGTTC 60.419 54.545 0.00 0.00 0.00 3.18
327 338 1.555533 GGACGGAGGAAGAGGAATGTT 59.444 52.381 0.00 0.00 0.00 2.71
331 342 0.042731 ATGGGACGGAGGAAGAGGAA 59.957 55.000 0.00 0.00 0.00 3.36
344 363 1.079405 TCGAAAGTGGCGATGGGAC 60.079 57.895 0.00 0.00 32.09 4.46
348 367 1.203928 CTAGCTCGAAAGTGGCGATG 58.796 55.000 0.00 0.00 37.13 3.84
349 368 0.103208 CCTAGCTCGAAAGTGGCGAT 59.897 55.000 0.00 0.00 37.13 4.58
350 369 1.511305 CCTAGCTCGAAAGTGGCGA 59.489 57.895 0.00 0.00 36.44 5.54
358 377 0.975556 TGATGGCACCCTAGCTCGAA 60.976 55.000 0.00 0.00 34.17 3.71
375 394 3.438781 GGTGAAGGATTTGTTATGCGTGA 59.561 43.478 0.00 0.00 0.00 4.35
379 398 3.013921 TCCGGTGAAGGATTTGTTATGC 58.986 45.455 0.00 0.00 34.92 3.14
382 401 2.026636 CCCTCCGGTGAAGGATTTGTTA 60.027 50.000 9.25 0.00 39.96 2.41
401 420 5.566230 CGTGATACTAGTGGTAATAAGCCCC 60.566 48.000 5.39 0.00 33.74 5.80
455 474 4.214758 AGTCAACAACAACGGTTATTAGGC 59.785 41.667 0.00 0.00 34.87 3.93
462 481 2.285977 GAGGAGTCAACAACAACGGTT 58.714 47.619 0.00 0.00 37.87 4.44
500 519 1.675641 GGGACAAGCCTGCGACAAT 60.676 57.895 0.00 0.00 36.66 2.71
530 610 0.677288 TCGAACACTGGATTGGACGT 59.323 50.000 0.00 0.00 0.00 4.34
532 612 4.766404 AATTTCGAACACTGGATTGGAC 57.234 40.909 0.00 0.00 0.00 4.02
556 636 8.257602 GGTCCCACCAAATTACCAAAATATAT 57.742 34.615 0.00 0.00 38.42 0.86
560 640 4.901197 GGTCCCACCAAATTACCAAAAT 57.099 40.909 0.00 0.00 38.42 1.82
587 667 9.176460 CTGGCCCAAAATTTTGATATTACAAAT 57.824 29.630 28.44 0.00 40.55 2.32
670 750 8.636213 CCACTATTATTTTGATCTCCATGCTTT 58.364 33.333 0.00 0.00 0.00 3.51
698 782 2.504899 ACGCACGCTGATCTGACG 60.505 61.111 3.42 8.95 0.00 4.35
699 783 3.075998 CACGCACGCTGATCTGAC 58.924 61.111 3.42 0.00 0.00 3.51
700 784 2.810887 GCACGCACGCTGATCTGA 60.811 61.111 3.42 0.00 0.00 3.27
702 786 2.125391 ATGCACGCACGCTGATCT 60.125 55.556 0.00 0.00 0.00 2.75
703 787 2.022346 CATGCACGCACGCTGATC 59.978 61.111 0.00 0.00 0.00 2.92
704 788 3.502455 CCATGCACGCACGCTGAT 61.502 61.111 0.00 0.00 0.00 2.90
705 789 4.678499 TCCATGCACGCACGCTGA 62.678 61.111 0.00 0.00 0.00 4.26
706 790 4.156622 CTCCATGCACGCACGCTG 62.157 66.667 0.00 0.00 0.00 5.18
707 791 3.670637 ATCTCCATGCACGCACGCT 62.671 57.895 0.00 0.00 0.00 5.07
708 792 3.197790 ATCTCCATGCACGCACGC 61.198 61.111 0.00 0.00 0.00 5.34
710 794 0.460811 TCTCATCTCCATGCACGCAC 60.461 55.000 0.00 0.00 0.00 5.34
711 795 0.179092 CTCTCATCTCCATGCACGCA 60.179 55.000 0.00 0.00 0.00 5.24
712 796 1.497223 GCTCTCATCTCCATGCACGC 61.497 60.000 0.00 0.00 0.00 5.34
713 797 1.213733 CGCTCTCATCTCCATGCACG 61.214 60.000 0.00 0.00 0.00 5.34
714 798 1.497223 GCGCTCTCATCTCCATGCAC 61.497 60.000 0.00 0.00 0.00 4.57
715 799 1.227468 GCGCTCTCATCTCCATGCA 60.227 57.895 0.00 0.00 0.00 3.96
734 818 7.192232 GCATGCATATAATTTAGCTTAGCTCC 58.808 38.462 11.09 0.00 40.44 4.70
855 951 1.269413 GCATGCAAATTGGATCGGAGG 60.269 52.381 14.21 0.00 0.00 4.30
915 1011 1.812571 CATGGGGAAGAAAGAACCGTG 59.187 52.381 0.00 0.00 32.52 4.94
916 1012 1.423921 ACATGGGGAAGAAAGAACCGT 59.576 47.619 0.00 0.00 0.00 4.83
918 1014 1.546029 GCACATGGGGAAGAAAGAACC 59.454 52.381 0.00 0.00 0.00 3.62
919 1015 1.546029 GGCACATGGGGAAGAAAGAAC 59.454 52.381 0.00 0.00 0.00 3.01
920 1016 1.146774 TGGCACATGGGGAAGAAAGAA 59.853 47.619 0.00 0.00 0.00 2.52
921 1017 0.776810 TGGCACATGGGGAAGAAAGA 59.223 50.000 0.00 0.00 0.00 2.52
922 1018 1.273327 GTTGGCACATGGGGAAGAAAG 59.727 52.381 0.00 0.00 39.30 2.62
923 1019 1.337118 GTTGGCACATGGGGAAGAAA 58.663 50.000 0.00 0.00 39.30 2.52
924 1020 0.893270 CGTTGGCACATGGGGAAGAA 60.893 55.000 0.00 0.00 39.30 2.52
925 1021 1.303236 CGTTGGCACATGGGGAAGA 60.303 57.895 0.00 0.00 39.30 2.87
926 1022 2.993471 GCGTTGGCACATGGGGAAG 61.993 63.158 0.00 0.00 39.30 3.46
927 1023 2.988684 GCGTTGGCACATGGGGAA 60.989 61.111 0.00 0.00 39.30 3.97
1601 1732 1.687563 TGCTAGCTCATGCATGCATT 58.312 45.000 30.32 18.29 41.76 3.56
1627 1758 3.428870 CGCATGATTACAGTATCGGGAAC 59.571 47.826 0.00 0.00 0.00 3.62
1712 1847 2.322422 GCACGCATGACTCATCGC 59.678 61.111 0.00 6.94 0.00 4.58
1713 1848 1.346197 GTGCACGCATGACTCATCG 59.654 57.895 0.00 8.46 0.00 3.84
1744 1885 5.389859 ACAGAGAGTCAGAGACATTCTTG 57.610 43.478 0.00 0.62 34.60 3.02
1753 1894 4.332543 CAGTACAGCTACAGAGAGTCAGAG 59.667 50.000 0.00 0.00 0.00 3.35
1754 1895 4.257731 CAGTACAGCTACAGAGAGTCAGA 58.742 47.826 0.00 0.00 0.00 3.27
1762 1903 0.809385 GTCGGCAGTACAGCTACAGA 59.191 55.000 10.30 2.76 34.17 3.41
1785 1926 2.792543 CGCACGCAAAAGCACTCG 60.793 61.111 0.00 0.00 0.00 4.18
1786 1927 0.865639 AAACGCACGCAAAAGCACTC 60.866 50.000 0.00 0.00 0.00 3.51
1787 1928 0.378962 TAAACGCACGCAAAAGCACT 59.621 45.000 0.00 0.00 0.00 4.40
1788 1929 1.404477 ATAAACGCACGCAAAAGCAC 58.596 45.000 0.00 0.00 0.00 4.40
1789 1930 1.783711 CAATAAACGCACGCAAAAGCA 59.216 42.857 0.00 0.00 0.00 3.91
1790 1931 2.047769 TCAATAAACGCACGCAAAAGC 58.952 42.857 0.00 0.00 0.00 3.51
1791 1932 2.656422 CCTCAATAAACGCACGCAAAAG 59.344 45.455 0.00 0.00 0.00 2.27
1844 1985 0.319383 CAGCACAGTCTCTGCGTCTT 60.319 55.000 0.00 0.00 39.79 3.01
1845 1986 1.288439 CAGCACAGTCTCTGCGTCT 59.712 57.895 0.00 0.00 39.79 4.18
1846 1987 0.241213 TACAGCACAGTCTCTGCGTC 59.759 55.000 0.00 0.00 39.79 5.19
1847 1988 0.039074 GTACAGCACAGTCTCTGCGT 60.039 55.000 0.00 0.00 39.79 5.24
1849 1990 0.039074 ACGTACAGCACAGTCTCTGC 60.039 55.000 0.00 0.00 34.37 4.26
1850 1991 1.691127 CACGTACAGCACAGTCTCTG 58.309 55.000 0.00 0.00 37.52 3.35
1851 1992 0.039074 GCACGTACAGCACAGTCTCT 60.039 55.000 2.66 0.00 0.00 3.10
1857 1998 1.955663 CAGCAGCACGTACAGCACA 60.956 57.895 5.92 0.00 0.00 4.57
1881 2022 4.121317 ACCGAACGTCAATGAAACAAGTA 58.879 39.130 0.00 0.00 0.00 2.24
1955 2097 0.944386 AATTGTGTCGTGGTGTGCTC 59.056 50.000 0.00 0.00 0.00 4.26
1995 2137 4.222589 GCGCGCACATGCATACGT 62.223 61.111 29.10 0.00 42.21 3.57
2026 2168 0.317770 CGTTTGTTCAGCCACGCATT 60.318 50.000 0.00 0.00 0.00 3.56
2027 2169 1.282570 CGTTTGTTCAGCCACGCAT 59.717 52.632 0.00 0.00 0.00 4.73
2028 2170 2.712539 CGTTTGTTCAGCCACGCA 59.287 55.556 0.00 0.00 0.00 5.24
2030 2172 1.369209 CAGCGTTTGTTCAGCCACG 60.369 57.895 0.00 0.00 35.71 4.94
2031 2173 0.380378 TTCAGCGTTTGTTCAGCCAC 59.620 50.000 0.00 0.00 0.00 5.01
2032 2174 0.662619 CTTCAGCGTTTGTTCAGCCA 59.337 50.000 0.00 0.00 0.00 4.75
2033 2175 0.040067 CCTTCAGCGTTTGTTCAGCC 60.040 55.000 0.00 0.00 0.00 4.85
2034 2176 0.661483 GCCTTCAGCGTTTGTTCAGC 60.661 55.000 0.00 0.00 0.00 4.26
2035 2177 3.461843 GCCTTCAGCGTTTGTTCAG 57.538 52.632 0.00 0.00 0.00 3.02
2045 2187 0.901124 TCTTCCTCTCAGCCTTCAGC 59.099 55.000 0.00 0.00 44.25 4.26
2046 2188 1.134729 GCTCTTCCTCTCAGCCTTCAG 60.135 57.143 0.00 0.00 0.00 3.02
2047 2189 0.901124 GCTCTTCCTCTCAGCCTTCA 59.099 55.000 0.00 0.00 0.00 3.02
2048 2190 3.758715 GCTCTTCCTCTCAGCCTTC 57.241 57.895 0.00 0.00 0.00 3.46
2052 2194 0.463620 AATCGGCTCTTCCTCTCAGC 59.536 55.000 0.00 0.00 0.00 4.26
2053 2195 1.753649 TGAATCGGCTCTTCCTCTCAG 59.246 52.381 0.00 0.00 0.00 3.35
2054 2196 1.852633 TGAATCGGCTCTTCCTCTCA 58.147 50.000 0.00 0.00 0.00 3.27
2055 2197 2.969628 TTGAATCGGCTCTTCCTCTC 57.030 50.000 0.00 0.00 0.00 3.20
2056 2198 2.679349 GCTTTGAATCGGCTCTTCCTCT 60.679 50.000 0.00 0.00 0.00 3.69
2057 2199 1.668237 GCTTTGAATCGGCTCTTCCTC 59.332 52.381 0.00 0.00 0.00 3.71
2058 2200 1.003580 TGCTTTGAATCGGCTCTTCCT 59.996 47.619 0.00 0.00 0.00 3.36
2059 2201 1.131315 GTGCTTTGAATCGGCTCTTCC 59.869 52.381 0.00 0.00 0.00 3.46
2060 2202 1.201965 CGTGCTTTGAATCGGCTCTTC 60.202 52.381 0.00 0.00 0.00 2.87
2061 2203 0.798776 CGTGCTTTGAATCGGCTCTT 59.201 50.000 0.00 0.00 0.00 2.85
2062 2204 0.037326 TCGTGCTTTGAATCGGCTCT 60.037 50.000 0.00 0.00 0.00 4.09
2063 2205 0.371645 CTCGTGCTTTGAATCGGCTC 59.628 55.000 0.00 0.00 0.00 4.70
2064 2206 0.037326 TCTCGTGCTTTGAATCGGCT 60.037 50.000 0.00 0.00 0.00 5.52
2065 2207 0.371645 CTCTCGTGCTTTGAATCGGC 59.628 55.000 0.00 0.00 0.00 5.54
2066 2208 1.714794 ACTCTCGTGCTTTGAATCGG 58.285 50.000 0.00 0.00 0.00 4.18
2067 2209 4.903638 TTAACTCTCGTGCTTTGAATCG 57.096 40.909 0.00 0.00 0.00 3.34
2068 2210 5.509622 GCAATTAACTCTCGTGCTTTGAATC 59.490 40.000 0.00 0.00 32.43 2.52
2069 2211 5.048782 TGCAATTAACTCTCGTGCTTTGAAT 60.049 36.000 0.00 0.00 36.18 2.57
2070 2212 4.274705 TGCAATTAACTCTCGTGCTTTGAA 59.725 37.500 0.00 0.00 36.18 2.69
2071 2213 3.812609 TGCAATTAACTCTCGTGCTTTGA 59.187 39.130 0.00 0.00 36.18 2.69
2072 2214 4.145876 TGCAATTAACTCTCGTGCTTTG 57.854 40.909 0.00 0.00 36.18 2.77
2073 2215 4.216257 ACATGCAATTAACTCTCGTGCTTT 59.784 37.500 0.00 0.00 36.18 3.51
2074 2216 3.753272 ACATGCAATTAACTCTCGTGCTT 59.247 39.130 0.00 0.00 36.18 3.91
2075 2217 3.338249 ACATGCAATTAACTCTCGTGCT 58.662 40.909 0.00 0.00 36.18 4.40
2076 2218 3.747099 ACATGCAATTAACTCTCGTGC 57.253 42.857 0.00 0.00 35.75 5.34
2077 2219 4.083324 ACCAACATGCAATTAACTCTCGTG 60.083 41.667 0.00 0.00 0.00 4.35
2078 2220 4.072131 ACCAACATGCAATTAACTCTCGT 58.928 39.130 0.00 0.00 0.00 4.18
2079 2221 4.685169 ACCAACATGCAATTAACTCTCG 57.315 40.909 0.00 0.00 0.00 4.04
2080 2222 5.414454 TGGTACCAACATGCAATTAACTCTC 59.586 40.000 13.60 0.00 0.00 3.20
2105 2247 2.688446 CTCGTGAGTAGATGCCCAAGTA 59.312 50.000 0.00 0.00 0.00 2.24
2111 2253 1.746220 ACTGACTCGTGAGTAGATGCC 59.254 52.381 1.83 0.00 42.66 4.40
2115 2257 5.087391 AGTGATACTGACTCGTGAGTAGA 57.913 43.478 1.83 0.00 42.66 2.59
2162 2304 0.984230 CCACTTAGGCCCTGAGTTGA 59.016 55.000 5.25 0.00 27.61 3.18
2235 2377 2.124320 CCTAACATGTGGGCCCGG 60.124 66.667 19.37 9.27 0.00 5.73
2249 2391 4.063967 CGGCCAGCGTGTCACCTA 62.064 66.667 2.24 0.00 0.00 3.08
2374 2516 1.679305 GACAGAGAGGAGCACGGGA 60.679 63.158 0.00 0.00 0.00 5.14
2388 2530 1.006825 TTCGCCGTCGTCATTGACAG 61.007 55.000 16.61 9.40 38.84 3.51
2489 2631 1.452651 CAATCCTGGGTGCGCATCT 60.453 57.895 21.95 0.00 0.00 2.90
2550 2692 1.409381 GGCCTCCTCCATTTCTTCCTG 60.409 57.143 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.