Multiple sequence alignment - TraesCS5A01G549200

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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 TraesCS5A01G549200 chr5A 100.000 3930 0 0 1 3930 702981419 702985348 0.000000e+00 7258.0
1 TraesCS5A01G549200 chr5A 89.410 576 48 12 1242 1812 702230033 702230600 0.000000e+00 713.0
2 TraesCS5A01G549200 chr3B 87.930 2444 200 46 952 3342 800173808 800176209 0.000000e+00 2791.0
3 TraesCS5A01G549200 chr3B 95.141 885 38 2 1 884 748423860 748422980 0.000000e+00 1391.0
4 TraesCS5A01G549200 chr3B 84.676 894 127 10 2049 2934 566190341 566189450 0.000000e+00 883.0
5 TraesCS5A01G549200 chr3B 87.768 654 72 6 1161 1810 566190985 566190336 0.000000e+00 758.0
6 TraesCS5A01G549200 chr3B 85.906 149 21 0 3749 3897 627841058 627840910 4.060000e-35 159.0
7 TraesCS5A01G549200 chr3B 93.750 48 3 0 1902 1949 795762290 795762243 5.450000e-09 73.1
8 TraesCS5A01G549200 chr4B 88.834 2221 187 30 1149 3342 664519576 664517390 0.000000e+00 2671.0
9 TraesCS5A01G549200 chr4B 86.528 193 20 3 952 1141 664525240 664525051 1.430000e-49 207.0
10 TraesCS5A01G549200 chr4B 84.393 173 23 4 3751 3921 12100099 12099929 2.430000e-37 167.0
11 TraesCS5A01G549200 chr4B 83.544 79 11 2 1872 1949 411629687 411629610 5.450000e-09 73.1
12 TraesCS5A01G549200 chr4D 92.623 1098 62 5 880 1971 506719998 506721082 0.000000e+00 1561.0
13 TraesCS5A01G549200 chr4D 95.213 940 45 0 2008 2947 506721089 506722028 0.000000e+00 1487.0
14 TraesCS5A01G549200 chr4D 87.229 462 46 12 1396 1852 506104071 506104524 7.530000e-142 514.0
15 TraesCS5A01G549200 chr4D 92.733 344 17 7 3358 3698 506722578 506722916 1.270000e-134 490.0
16 TraesCS5A01G549200 chr4D 91.176 374 12 11 3014 3368 506722023 506722394 4.560000e-134 488.0
17 TraesCS5A01G549200 chr4D 93.301 209 14 0 3721 3929 506722910 506723118 3.810000e-80 309.0
18 TraesCS5A01G549200 chr4D 84.699 183 27 1 3749 3930 414067883 414067701 8.670000e-42 182.0
19 TraesCS5A01G549200 chr1A 97.622 883 21 0 1 883 89587551 89588433 0.000000e+00 1515.0
20 TraesCS5A01G549200 chr1A 82.550 149 26 0 3749 3897 98238428 98238576 8.860000e-27 132.0
21 TraesCS5A01G549200 chr5D 95.372 886 33 5 1 885 446818389 446817511 0.000000e+00 1402.0
22 TraesCS5A01G549200 chr7B 95.362 884 34 4 1 883 595800168 595799291 0.000000e+00 1399.0
23 TraesCS5A01G549200 chr7B 81.564 179 28 3 3749 3924 530706698 530706874 4.090000e-30 143.0
24 TraesCS5A01G549200 chr7B 91.089 101 9 0 3749 3849 42182639 42182739 1.900000e-28 137.0
25 TraesCS5A01G549200 chr2A 93.311 882 53 3 1 882 759743772 759742897 0.000000e+00 1297.0
26 TraesCS5A01G549200 chr2D 91.422 886 68 5 1 884 47988231 47987352 0.000000e+00 1208.0
27 TraesCS5A01G549200 chr6D 90.508 885 76 5 1 884 461523538 461524415 0.000000e+00 1162.0
28 TraesCS5A01G549200 chr6D 89.932 884 81 5 1 883 101264567 101265443 0.000000e+00 1133.0
29 TraesCS5A01G549200 chr7D 90.271 884 80 5 1 883 14570608 14571486 0.000000e+00 1151.0
30 TraesCS5A01G549200 chr3A 84.452 894 129 9 2049 2934 571809013 571808122 0.000000e+00 872.0
31 TraesCS5A01G549200 chr3A 83.203 893 142 7 2049 2934 571912688 571911797 0.000000e+00 811.0
32 TraesCS5A01G549200 chr3A 86.870 655 73 10 1161 1810 571913329 571912683 0.000000e+00 721.0
33 TraesCS5A01G549200 chr3A 85.542 664 74 11 1161 1810 571809663 571809008 0.000000e+00 676.0
34 TraesCS5A01G549200 chr3D 89.902 307 26 4 1244 1548 433427176 433426873 1.320000e-104 390.0
35 TraesCS5A01G549200 chr4A 85.475 179 25 1 3748 3925 333346186 333346008 6.710000e-43 185.0
36 TraesCS5A01G549200 chr6A 83.889 180 24 4 3750 3926 309682159 309682336 2.430000e-37 167.0
37 TraesCS5A01G549200 chr7A 81.905 105 17 2 1870 1973 554392377 554392274 1.950000e-13 87.9
38 TraesCS5A01G549200 chr7A 87.931 58 7 0 1918 1975 94486357 94486414 7.050000e-08 69.4
39 TraesCS5A01G549200 chr2B 88.679 53 6 0 1902 1954 473999125 473999073 9.120000e-07 65.8
40 TraesCS5A01G549200 chrUn 84.127 63 10 0 1906 1968 90282644 90282582 1.180000e-05 62.1


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 TraesCS5A01G549200 chr5A 702981419 702985348 3929 False 7258.0 7258 100.0000 1 3930 1 chr5A.!!$F2 3929
1 TraesCS5A01G549200 chr5A 702230033 702230600 567 False 713.0 713 89.4100 1242 1812 1 chr5A.!!$F1 570
2 TraesCS5A01G549200 chr3B 800173808 800176209 2401 False 2791.0 2791 87.9300 952 3342 1 chr3B.!!$F1 2390
3 TraesCS5A01G549200 chr3B 748422980 748423860 880 True 1391.0 1391 95.1410 1 884 1 chr3B.!!$R2 883
4 TraesCS5A01G549200 chr3B 566189450 566190985 1535 True 820.5 883 86.2220 1161 2934 2 chr3B.!!$R4 1773
5 TraesCS5A01G549200 chr4B 664517390 664519576 2186 True 2671.0 2671 88.8340 1149 3342 1 chr4B.!!$R3 2193
6 TraesCS5A01G549200 chr4D 506719998 506723118 3120 False 867.0 1561 93.0092 880 3929 5 chr4D.!!$F2 3049
7 TraesCS5A01G549200 chr1A 89587551 89588433 882 False 1515.0 1515 97.6220 1 883 1 chr1A.!!$F1 882
8 TraesCS5A01G549200 chr5D 446817511 446818389 878 True 1402.0 1402 95.3720 1 885 1 chr5D.!!$R1 884
9 TraesCS5A01G549200 chr7B 595799291 595800168 877 True 1399.0 1399 95.3620 1 883 1 chr7B.!!$R1 882
10 TraesCS5A01G549200 chr2A 759742897 759743772 875 True 1297.0 1297 93.3110 1 882 1 chr2A.!!$R1 881
11 TraesCS5A01G549200 chr2D 47987352 47988231 879 True 1208.0 1208 91.4220 1 884 1 chr2D.!!$R1 883
12 TraesCS5A01G549200 chr6D 461523538 461524415 877 False 1162.0 1162 90.5080 1 884 1 chr6D.!!$F2 883
13 TraesCS5A01G549200 chr6D 101264567 101265443 876 False 1133.0 1133 89.9320 1 883 1 chr6D.!!$F1 882
14 TraesCS5A01G549200 chr7D 14570608 14571486 878 False 1151.0 1151 90.2710 1 883 1 chr7D.!!$F1 882
15 TraesCS5A01G549200 chr3A 571808122 571809663 1541 True 774.0 872 84.9970 1161 2934 2 chr3A.!!$R1 1773
16 TraesCS5A01G549200 chr3A 571911797 571913329 1532 True 766.0 811 85.0365 1161 2934 2 chr3A.!!$R2 1773

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
947 951 0.037232 GTTCGCCTGTGCTCCTTAGT 60.037 55.000 0.0 0.0 34.43 2.24 F
948 952 0.246635 TTCGCCTGTGCTCCTTAGTC 59.753 55.000 0.0 0.0 34.43 2.59 F
2194 2240 1.202580 GGCGACATAGCTCTCACCAAT 60.203 52.381 0.0 0.0 37.29 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2350 0.393808 GACATGGCCACGGTAACCAT 60.394 55.0 8.16 7.98 45.08 3.55 R
2594 2646 0.603569 TCACGTGCCTCCTTCTCTTC 59.396 55.0 11.67 0.00 0.00 2.87 R
3900 4232 0.251634 TTGTCCTCACTGTGCACACA 59.748 50.0 17.42 7.77 39.32 3.72 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
119 120 3.584406 AGGTGAATTCGTGTCTCTCTG 57.416 47.619 0.04 0.00 0.00 3.35
149 150 1.014804 AGTCAGATCACCCTCCTCCT 58.985 55.000 0.00 0.00 0.00 3.69
629 631 0.756294 TGGAAGGAGCGAAACAGACA 59.244 50.000 0.00 0.00 0.00 3.41
641 643 4.436852 GCGAAACAGACAAGTTTTCACTGA 60.437 41.667 0.00 0.00 41.48 3.41
661 663 2.046892 AAAGGCTGACGCATCGCT 60.047 55.556 0.00 0.00 38.10 4.93
749 751 1.944024 CGCCGGCATTGGTTAATCTAA 59.056 47.619 28.98 0.00 0.00 2.10
874 878 2.284331 TGCTCCTGCCGGTTCCTA 60.284 61.111 1.90 0.00 38.71 2.94
909 913 5.295292 AGTCAGCAAATGAATAGACATTCCG 59.705 40.000 0.00 0.00 40.43 4.30
941 945 0.319900 TTCTGAGTTCGCCTGTGCTC 60.320 55.000 0.00 0.00 34.43 4.26
942 946 1.739562 CTGAGTTCGCCTGTGCTCC 60.740 63.158 0.00 0.00 34.43 4.70
943 947 2.164865 CTGAGTTCGCCTGTGCTCCT 62.165 60.000 0.00 0.00 34.43 3.69
944 948 1.004440 GAGTTCGCCTGTGCTCCTT 60.004 57.895 0.00 0.00 34.43 3.36
945 949 0.246635 GAGTTCGCCTGTGCTCCTTA 59.753 55.000 0.00 0.00 34.43 2.69
946 950 0.247736 AGTTCGCCTGTGCTCCTTAG 59.752 55.000 0.00 0.00 34.43 2.18
947 951 0.037232 GTTCGCCTGTGCTCCTTAGT 60.037 55.000 0.00 0.00 34.43 2.24
948 952 0.246635 TTCGCCTGTGCTCCTTAGTC 59.753 55.000 0.00 0.00 34.43 2.59
1146 1153 1.616865 GGCCTACGTCCATACATAGCA 59.383 52.381 0.00 0.00 0.00 3.49
1650 1678 3.877450 GAGGGGATGCGGATGCCA 61.877 66.667 27.71 0.00 41.92 4.92
1755 1792 2.125512 GTCGGCGTGGAGAGCAAT 60.126 61.111 6.85 0.00 36.08 3.56
1859 1903 7.707464 TCCTTTTATTTTTGAACTTTCCGGAAC 59.293 33.333 18.64 5.92 0.00 3.62
1864 1908 6.895607 TTTTTGAACTTTCCGGAACATTTC 57.104 33.333 18.64 18.57 0.00 2.17
1899 1943 6.309389 AGTACTTCCTCCATCCGTAATTTT 57.691 37.500 0.00 0.00 0.00 1.82
1900 1944 6.346896 AGTACTTCCTCCATCCGTAATTTTC 58.653 40.000 0.00 0.00 0.00 2.29
1962 2006 8.290325 TGCTAGATATATCTGTTTACACGACAG 58.710 37.037 23.03 10.11 44.54 3.51
1975 2019 3.660865 ACACGACAGGTAATTTCAGACC 58.339 45.455 0.00 0.00 35.83 3.85
1980 2024 4.652822 GACAGGTAATTTCAGACCAAGGT 58.347 43.478 0.00 0.00 38.27 3.50
1984 2028 7.238710 ACAGGTAATTTCAGACCAAGGTTTAT 58.761 34.615 0.00 0.00 38.27 1.40
1987 2031 7.176690 AGGTAATTTCAGACCAAGGTTTATGTG 59.823 37.037 0.00 0.00 38.27 3.21
1988 2032 5.982890 ATTTCAGACCAAGGTTTATGTGG 57.017 39.130 0.00 0.00 38.46 4.17
1989 2033 4.715534 TTCAGACCAAGGTTTATGTGGA 57.284 40.909 0.00 0.00 36.23 4.02
1993 2039 5.249622 TCAGACCAAGGTTTATGTGGACATA 59.750 40.000 0.00 0.00 37.76 2.29
2028 2074 4.468510 TCCTCACTAAACAATACATCCGGT 59.531 41.667 0.00 0.00 0.00 5.28
2065 2111 5.361571 TGTATTTCAGATGATTGGCAATGCT 59.638 36.000 19.07 9.09 0.00 3.79
2194 2240 1.202580 GGCGACATAGCTCTCACCAAT 60.203 52.381 0.00 0.00 37.29 3.16
2330 2376 2.444624 CGTGGCCATGTCGACTTCG 61.445 63.158 17.42 4.38 41.45 3.79
2380 2426 2.419021 CCTCTTCTACGACGAGGAGTCT 60.419 54.545 10.00 0.00 46.79 3.24
2510 2556 3.297830 ACGTGAGCAAAAATAAAGCCC 57.702 42.857 0.00 0.00 0.00 5.19
2521 2573 3.728385 AATAAAGCCCTGCTCAAGTCT 57.272 42.857 0.00 0.00 38.25 3.24
2574 2626 2.564471 CCGTGGAGGTAAGACGACT 58.436 57.895 0.00 0.00 35.05 4.18
2644 2696 1.134699 GTGATCGAGGGCATTGAGACA 60.135 52.381 0.00 0.00 0.00 3.41
2696 2748 1.965930 GTGAACGCCATGGAGCACA 60.966 57.895 18.40 13.35 0.00 4.57
2872 2924 3.057456 AGACTGTGACCGTGACATTAGTC 60.057 47.826 0.00 0.00 45.19 2.59
2940 2992 5.127845 ACATGGTGGAGTGAGATTACAGTAG 59.872 44.000 0.00 0.00 0.00 2.57
2946 3056 5.011635 TGGAGTGAGATTACAGTAGCAACAA 59.988 40.000 0.00 0.00 0.00 2.83
2947 3057 5.932303 GGAGTGAGATTACAGTAGCAACAAA 59.068 40.000 0.00 0.00 0.00 2.83
2948 3058 6.595716 GGAGTGAGATTACAGTAGCAACAAAT 59.404 38.462 0.00 0.00 0.00 2.32
2949 3059 7.119846 GGAGTGAGATTACAGTAGCAACAAATT 59.880 37.037 0.00 0.00 0.00 1.82
2950 3060 9.151471 GAGTGAGATTACAGTAGCAACAAATTA 57.849 33.333 0.00 0.00 0.00 1.40
2951 3061 8.936864 AGTGAGATTACAGTAGCAACAAATTAC 58.063 33.333 0.00 0.00 0.00 1.89
2952 3062 8.717821 GTGAGATTACAGTAGCAACAAATTACA 58.282 33.333 0.00 0.00 0.00 2.41
2953 3063 9.448438 TGAGATTACAGTAGCAACAAATTACAT 57.552 29.630 0.00 0.00 0.00 2.29
2960 3070 8.792633 ACAGTAGCAACAAATTACATAATGTGT 58.207 29.630 2.15 2.15 43.96 3.72
2980 3090 9.912634 AATGTGTTGTAAATTTCGAATGAGATT 57.087 25.926 0.00 0.00 30.70 2.40
2995 3105 9.914131 TCGAATGAGATTATAGTTATGGAAGTG 57.086 33.333 0.00 0.00 0.00 3.16
2996 3106 9.914131 CGAATGAGATTATAGTTATGGAAGTGA 57.086 33.333 0.00 0.00 0.00 3.41
3002 3112 9.698309 AGATTATAGTTATGGAAGTGATCAACG 57.302 33.333 0.00 0.00 0.00 4.10
3003 3113 9.692749 GATTATAGTTATGGAAGTGATCAACGA 57.307 33.333 0.00 0.00 0.00 3.85
3004 3114 9.698309 ATTATAGTTATGGAAGTGATCAACGAG 57.302 33.333 0.00 0.00 0.00 4.18
3005 3115 5.407407 AGTTATGGAAGTGATCAACGAGT 57.593 39.130 0.00 0.00 0.00 4.18
3006 3116 6.525578 AGTTATGGAAGTGATCAACGAGTA 57.474 37.500 0.00 0.00 0.00 2.59
3007 3117 6.565234 AGTTATGGAAGTGATCAACGAGTAG 58.435 40.000 0.00 0.00 0.00 2.57
3008 3118 6.153000 AGTTATGGAAGTGATCAACGAGTAGT 59.847 38.462 0.00 0.00 0.00 2.73
3009 3119 4.174411 TGGAAGTGATCAACGAGTAGTG 57.826 45.455 0.00 0.00 0.00 2.74
3010 3120 3.824443 TGGAAGTGATCAACGAGTAGTGA 59.176 43.478 0.00 0.00 0.00 3.41
3011 3121 4.279922 TGGAAGTGATCAACGAGTAGTGAA 59.720 41.667 0.00 0.00 0.00 3.18
3012 3122 5.047306 TGGAAGTGATCAACGAGTAGTGAAT 60.047 40.000 0.00 0.00 0.00 2.57
3013 3123 5.517054 GGAAGTGATCAACGAGTAGTGAATC 59.483 44.000 0.00 0.00 0.00 2.52
3014 3124 5.644977 AGTGATCAACGAGTAGTGAATCA 57.355 39.130 0.00 0.00 34.31 2.57
3015 3125 6.025749 AGTGATCAACGAGTAGTGAATCAA 57.974 37.500 0.00 0.00 36.77 2.57
3016 3126 5.864474 AGTGATCAACGAGTAGTGAATCAAC 59.136 40.000 0.00 0.00 36.77 3.18
3017 3127 5.633601 GTGATCAACGAGTAGTGAATCAACA 59.366 40.000 0.00 0.00 36.77 3.33
3072 3190 1.474143 CCCCGCAAAAAGCCAGAAAAA 60.474 47.619 0.00 0.00 41.38 1.94
3134 3252 3.181490 GGCTGTTGGATCCCGAAAATAAC 60.181 47.826 9.90 5.61 0.00 1.89
3187 3305 6.690194 AGAATTCAAGAAATAATGCGAGCT 57.310 33.333 8.44 0.00 0.00 4.09
3217 3335 8.847196 GTCTGTTATACTGTAGTACATCCATGA 58.153 37.037 2.82 0.00 32.72 3.07
3259 3393 5.868801 CGGCAATGATAATTTTTGTCTTGGT 59.131 36.000 0.00 0.00 0.00 3.67
3260 3394 6.368516 CGGCAATGATAATTTTTGTCTTGGTT 59.631 34.615 0.00 0.00 0.00 3.67
3361 3497 3.481453 TGCAAAAATTTACCCCAAAGCC 58.519 40.909 0.00 0.00 0.00 4.35
3387 3717 1.288188 TCTGGCATTCCATCAGGTGA 58.712 50.000 0.00 0.00 42.51 4.02
3413 3743 8.894592 ACCCTCATATTTGATGGTCTACATTAT 58.105 33.333 7.19 0.00 44.72 1.28
3444 3774 8.421673 AGTAAATAACTGTCGAAGGATAAAGC 57.578 34.615 0.00 0.00 36.93 3.51
3445 3775 8.258708 AGTAAATAACTGTCGAAGGATAAAGCT 58.741 33.333 0.00 0.00 36.93 3.74
3447 3777 4.537135 AACTGTCGAAGGATAAAGCTCA 57.463 40.909 0.00 0.00 0.00 4.26
3451 3781 5.179555 ACTGTCGAAGGATAAAGCTCAAAAC 59.820 40.000 0.00 0.00 0.00 2.43
3452 3782 4.151689 TGTCGAAGGATAAAGCTCAAAACG 59.848 41.667 0.00 0.00 0.00 3.60
3756 4088 8.397906 TGCACTCAACTAATTTATTGTGATAGC 58.602 33.333 9.24 9.66 0.00 2.97
3757 4089 8.397906 GCACTCAACTAATTTATTGTGATAGCA 58.602 33.333 9.24 0.00 0.00 3.49
3760 4092 9.888878 CTCAACTAATTTATTGTGATAGCATGG 57.111 33.333 0.00 0.00 0.00 3.66
3778 4110 7.204243 AGCATGGCTTAATATGGATGATAGA 57.796 36.000 0.00 0.00 33.89 1.98
3825 4157 3.755810 TTTTTGGGAGCCCATTCGA 57.244 47.368 9.46 0.00 46.64 3.71
3840 4172 3.426525 CCATTCGAAAAGAACTGCAAAGC 59.573 43.478 0.00 0.00 42.39 3.51
3853 4185 1.337728 TGCAAAGCTAAGCGTGCTCTA 60.338 47.619 11.87 0.00 42.16 2.43
3900 4232 1.774254 TGACTGGGAAGTTGGTCACAT 59.226 47.619 0.00 0.00 34.38 3.21
3924 4256 0.308993 GCACAGTGAGGACAAAGTGC 59.691 55.000 4.15 0.00 44.86 4.40
3929 4261 1.961394 AGTGAGGACAAAGTGCGTAGA 59.039 47.619 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.192317 GGTGATCTGACTAATGTGGTTCC 58.808 47.826 0.00 0.00 0.00 3.62
149 150 3.138304 CGAATGGTGTCTTCTTGGTCAA 58.862 45.455 0.00 0.00 0.00 3.18
629 631 4.462483 TCAGCCTTTGTTCAGTGAAAACTT 59.538 37.500 7.25 0.00 0.00 2.66
641 643 1.868997 CGATGCGTCAGCCTTTGTT 59.131 52.632 6.75 0.00 44.33 2.83
749 751 7.255942 CCACAAAAGACCAATCAACCTAGAATT 60.256 37.037 0.00 0.00 0.00 2.17
909 913 6.359883 GGCGAACTCAGAACAAAAATAGTTTC 59.640 38.462 0.00 0.00 0.00 2.78
922 926 4.361253 GCACAGGCGAACTCAGAA 57.639 55.556 0.00 0.00 0.00 3.02
941 945 6.239064 CGCCAGGCTATATATAAGGACTAAGG 60.239 46.154 10.54 0.00 0.00 2.69
942 946 6.239064 CCGCCAGGCTATATATAAGGACTAAG 60.239 46.154 10.54 0.00 0.00 2.18
943 947 5.597182 CCGCCAGGCTATATATAAGGACTAA 59.403 44.000 10.54 0.00 0.00 2.24
944 948 5.138276 CCGCCAGGCTATATATAAGGACTA 58.862 45.833 10.54 0.00 0.00 2.59
945 949 3.961408 CCGCCAGGCTATATATAAGGACT 59.039 47.826 10.54 0.00 0.00 3.85
946 950 3.705072 ACCGCCAGGCTATATATAAGGAC 59.295 47.826 10.54 0.00 42.76 3.85
947 951 3.990369 ACCGCCAGGCTATATATAAGGA 58.010 45.455 10.54 0.00 42.76 3.36
948 952 4.694339 GAACCGCCAGGCTATATATAAGG 58.306 47.826 10.54 1.97 42.76 2.69
1050 1054 2.496817 GCGCAGAGGACGAGGAAT 59.503 61.111 0.30 0.00 0.00 3.01
1146 1153 2.677037 GCTGCCGTTGGTAGTAAGTGAT 60.677 50.000 2.91 0.00 37.73 3.06
1498 1526 2.306805 AGAAGTGGATCTGCATGTCCAA 59.693 45.455 18.62 4.34 45.50 3.53
1605 1633 2.600729 CCAGCTCCAGAAGGGCAGT 61.601 63.158 0.00 0.00 34.63 4.40
1755 1792 3.903932 CTGCTGCTCGTCTGTGCGA 62.904 63.158 0.00 0.00 37.41 5.10
1859 1903 6.035758 GGAAGTACTAAGTAAGCACGGAAATG 59.964 42.308 0.00 0.00 0.00 2.32
1864 1908 4.439837 GGAGGAAGTACTAAGTAAGCACGG 60.440 50.000 0.00 0.00 0.00 4.94
1867 1911 5.363005 GGATGGAGGAAGTACTAAGTAAGCA 59.637 44.000 0.00 0.00 0.00 3.91
1938 1982 8.784994 ACCTGTCGTGTAAACAGATATATCTAG 58.215 37.037 14.92 11.62 45.64 2.43
1954 1998 3.070446 TGGTCTGAAATTACCTGTCGTGT 59.930 43.478 0.00 0.00 36.67 4.49
1955 1999 3.659786 TGGTCTGAAATTACCTGTCGTG 58.340 45.455 0.00 0.00 36.67 4.35
1962 2006 7.312899 CACATAAACCTTGGTCTGAAATTACC 58.687 38.462 0.00 0.00 36.24 2.85
2017 2063 3.802948 GTCAGACAGACCGGATGTATT 57.197 47.619 9.46 1.87 41.56 1.89
2028 2074 6.405278 TCTGAAATACAGTTGTCAGACAGA 57.595 37.500 2.82 0.00 45.86 3.41
2065 2111 1.302511 GAAGAGGGACGGCAAAGCA 60.303 57.895 0.00 0.00 0.00 3.91
2194 2240 1.444933 AGGTTCCCATGTTCTCCACA 58.555 50.000 0.00 0.00 40.71 4.17
2304 2350 0.393808 GACATGGCCACGGTAACCAT 60.394 55.000 8.16 7.98 45.08 3.55
2510 2556 3.260740 GGAATCTGACAGACTTGAGCAG 58.739 50.000 7.47 0.00 34.16 4.24
2521 2573 0.984230 GGGACAGTGGGAATCTGACA 59.016 55.000 0.00 0.00 36.81 3.58
2594 2646 0.603569 TCACGTGCCTCCTTCTCTTC 59.396 55.000 11.67 0.00 0.00 2.87
2644 2696 3.181454 ACTTGACCATTTCTGTTCCGTCT 60.181 43.478 0.00 0.00 0.00 4.18
2710 2762 4.752879 GCCAGTTCACGCCCGCTA 62.753 66.667 0.00 0.00 0.00 4.26
2719 2771 2.284331 TAGCTCCCCGCCAGTTCA 60.284 61.111 0.00 0.00 40.39 3.18
2954 3064 9.912634 AATCTCATTCGAAATTTACAACACATT 57.087 25.926 0.00 0.00 0.00 2.71
2969 3079 9.914131 CACTTCCATAACTATAATCTCATTCGA 57.086 33.333 0.00 0.00 0.00 3.71
2970 3080 9.914131 TCACTTCCATAACTATAATCTCATTCG 57.086 33.333 0.00 0.00 0.00 3.34
2976 3086 9.698309 CGTTGATCACTTCCATAACTATAATCT 57.302 33.333 0.00 0.00 0.00 2.40
2977 3087 9.692749 TCGTTGATCACTTCCATAACTATAATC 57.307 33.333 0.00 0.00 0.00 1.75
2978 3088 9.698309 CTCGTTGATCACTTCCATAACTATAAT 57.302 33.333 0.00 0.00 0.00 1.28
2979 3089 8.692710 ACTCGTTGATCACTTCCATAACTATAA 58.307 33.333 0.00 0.00 0.00 0.98
2980 3090 8.234136 ACTCGTTGATCACTTCCATAACTATA 57.766 34.615 0.00 0.00 0.00 1.31
2981 3091 7.113658 ACTCGTTGATCACTTCCATAACTAT 57.886 36.000 0.00 0.00 0.00 2.12
2982 3092 6.525578 ACTCGTTGATCACTTCCATAACTA 57.474 37.500 0.00 0.00 0.00 2.24
2983 3093 5.407407 ACTCGTTGATCACTTCCATAACT 57.593 39.130 0.00 0.00 0.00 2.24
2984 3094 6.253727 CACTACTCGTTGATCACTTCCATAAC 59.746 42.308 0.00 0.00 0.00 1.89
2985 3095 6.152154 TCACTACTCGTTGATCACTTCCATAA 59.848 38.462 0.00 0.00 0.00 1.90
2986 3096 5.650703 TCACTACTCGTTGATCACTTCCATA 59.349 40.000 0.00 0.00 0.00 2.74
2987 3097 4.462834 TCACTACTCGTTGATCACTTCCAT 59.537 41.667 0.00 0.00 0.00 3.41
2988 3098 3.824443 TCACTACTCGTTGATCACTTCCA 59.176 43.478 0.00 0.00 0.00 3.53
2989 3099 4.436242 TCACTACTCGTTGATCACTTCC 57.564 45.455 0.00 0.00 0.00 3.46
2990 3100 6.093404 TGATTCACTACTCGTTGATCACTTC 58.907 40.000 0.00 0.00 0.00 3.01
2991 3101 6.025749 TGATTCACTACTCGTTGATCACTT 57.974 37.500 0.00 0.00 0.00 3.16
2992 3102 5.644977 TGATTCACTACTCGTTGATCACT 57.355 39.130 0.00 0.00 0.00 3.41
2993 3103 5.633601 TGTTGATTCACTACTCGTTGATCAC 59.366 40.000 0.00 0.00 29.16 3.06
2994 3104 5.778862 TGTTGATTCACTACTCGTTGATCA 58.221 37.500 0.00 0.00 0.00 2.92
2995 3105 6.366332 ACTTGTTGATTCACTACTCGTTGATC 59.634 38.462 0.00 0.00 0.00 2.92
2996 3106 6.223852 ACTTGTTGATTCACTACTCGTTGAT 58.776 36.000 0.00 0.00 0.00 2.57
2997 3107 5.597806 ACTTGTTGATTCACTACTCGTTGA 58.402 37.500 0.00 0.00 0.00 3.18
2998 3108 5.907197 ACTTGTTGATTCACTACTCGTTG 57.093 39.130 0.00 0.00 0.00 4.10
2999 3109 6.641314 CACTACTTGTTGATTCACTACTCGTT 59.359 38.462 0.00 0.00 0.00 3.85
3000 3110 6.016527 TCACTACTTGTTGATTCACTACTCGT 60.017 38.462 0.00 0.00 0.00 4.18
3001 3111 6.305877 GTCACTACTTGTTGATTCACTACTCG 59.694 42.308 0.00 0.00 0.00 4.18
3002 3112 6.586844 GGTCACTACTTGTTGATTCACTACTC 59.413 42.308 0.00 0.00 0.00 2.59
3003 3113 6.456501 GGTCACTACTTGTTGATTCACTACT 58.543 40.000 0.00 0.00 0.00 2.57
3004 3114 5.638234 GGGTCACTACTTGTTGATTCACTAC 59.362 44.000 0.00 0.00 0.00 2.73
3005 3115 5.305902 TGGGTCACTACTTGTTGATTCACTA 59.694 40.000 0.00 0.00 0.00 2.74
3006 3116 4.102524 TGGGTCACTACTTGTTGATTCACT 59.897 41.667 0.00 0.00 0.00 3.41
3007 3117 4.385825 TGGGTCACTACTTGTTGATTCAC 58.614 43.478 0.00 0.00 0.00 3.18
3008 3118 4.698201 TGGGTCACTACTTGTTGATTCA 57.302 40.909 0.00 0.00 0.00 2.57
3009 3119 6.206634 TCAATTGGGTCACTACTTGTTGATTC 59.793 38.462 5.42 0.00 0.00 2.52
3010 3120 6.068010 TCAATTGGGTCACTACTTGTTGATT 58.932 36.000 5.42 0.00 0.00 2.57
3011 3121 5.630121 TCAATTGGGTCACTACTTGTTGAT 58.370 37.500 5.42 0.00 0.00 2.57
3012 3122 5.042463 TCAATTGGGTCACTACTTGTTGA 57.958 39.130 5.42 0.00 0.00 3.18
3013 3123 5.707298 AGATCAATTGGGTCACTACTTGTTG 59.293 40.000 5.42 0.00 0.00 3.33
3014 3124 5.707298 CAGATCAATTGGGTCACTACTTGTT 59.293 40.000 5.42 0.00 0.00 2.83
3015 3125 5.248640 CAGATCAATTGGGTCACTACTTGT 58.751 41.667 5.42 0.00 0.00 3.16
3016 3126 4.095483 GCAGATCAATTGGGTCACTACTTG 59.905 45.833 5.42 0.05 0.00 3.16
3017 3127 4.018960 AGCAGATCAATTGGGTCACTACTT 60.019 41.667 5.42 0.00 0.00 2.24
3134 3252 2.093553 ACATCAAATCATTTTGGGCCGG 60.094 45.455 0.00 0.00 42.10 6.13
3260 3394 7.551585 TGCACTTCCTTTCAGATTTACAAAAA 58.448 30.769 0.00 0.00 0.00 1.94
3341 3475 3.481453 TGGCTTTGGGGTAAATTTTTGC 58.519 40.909 0.00 0.00 0.00 3.68
3342 3476 6.127619 TGTTTTGGCTTTGGGGTAAATTTTTG 60.128 34.615 0.00 0.00 0.00 2.44
3420 3750 8.421673 AGCTTTATCCTTCGACAGTTATTTAC 57.578 34.615 0.00 0.00 0.00 2.01
3436 3766 1.134367 GGGGCGTTTTGAGCTTTATCC 59.866 52.381 0.00 0.00 34.52 2.59
3477 3809 2.283298 GCATGTGGATTCATCGAGTGT 58.717 47.619 0.00 0.00 0.00 3.55
3639 3971 8.192110 GCCGTTTTCCCAATAAATATGAAACTA 58.808 33.333 0.00 0.00 0.00 2.24
3640 3972 7.039270 GCCGTTTTCCCAATAAATATGAAACT 58.961 34.615 0.00 0.00 0.00 2.66
3656 3988 2.606717 CGGACTTTTAGCCGTTTTCC 57.393 50.000 0.00 0.00 42.49 3.13
3756 4088 9.539825 GTAGTCTATCATCCATATTAAGCCATG 57.460 37.037 0.00 0.00 0.00 3.66
3757 4089 9.499369 AGTAGTCTATCATCCATATTAAGCCAT 57.501 33.333 0.00 0.00 0.00 4.40
3766 4098 9.987726 ATTGATCTGAGTAGTCTATCATCCATA 57.012 33.333 13.56 3.60 30.57 2.74
3825 4157 3.066760 ACGCTTAGCTTTGCAGTTCTTTT 59.933 39.130 1.76 0.00 0.00 2.27
3840 4172 2.710760 CTCGAAGTAGAGCACGCTTAG 58.289 52.381 0.00 0.00 0.00 2.18
3853 4185 3.057315 CCCATGTTGAAATTGCTCGAAGT 60.057 43.478 0.00 0.00 0.00 3.01
3870 4202 0.692476 TTCCCAGTCAGTCACCCATG 59.308 55.000 0.00 0.00 0.00 3.66
3900 4232 0.251634 TTGTCCTCACTGTGCACACA 59.748 50.000 17.42 7.77 39.32 3.72


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

AutoCloner maintained by Alex Coulton.