Multiple sequence alignment - TraesCS3A01G260800

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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 TraesCS3A01G260800 chr3A 100.000 7108 0 0 1 7108 483742295 483749402 0.000000e+00 13127.0
1 TraesCS3A01G260800 chr3A 93.256 1468 70 7 1620 3081 19283666 19282222 0.000000e+00 2135.0
2 TraesCS3A01G260800 chr3A 89.242 409 22 3 1620 2028 19282460 19282074 6.410000e-135 492.0
3 TraesCS3A01G260800 chr3A 94.928 276 10 1 5424 5695 19283428 19283153 5.090000e-116 429.0
4 TraesCS3A01G260800 chr3A 93.116 276 14 2 5424 5695 483744174 483744448 3.990000e-107 399.0
5 TraesCS3A01G260800 chr3A 98.000 200 4 0 5695 5894 483743714 483743913 1.470000e-91 348.0
6 TraesCS3A01G260800 chr3A 98.000 200 4 0 1420 1619 483747989 483748188 1.470000e-91 348.0
7 TraesCS3A01G260800 chr3A 89.610 231 21 1 931 1158 39705005 39705235 2.510000e-74 291.0
8 TraesCS3A01G260800 chr3A 87.549 257 11 2 2842 3077 483743914 483744170 1.950000e-70 278.0
9 TraesCS3A01G260800 chr3A 87.549 257 11 2 1620 1876 483745136 483745371 1.950000e-70 278.0
10 TraesCS3A01G260800 chr3A 99.324 148 1 0 5424 5571 19282222 19282075 1.180000e-67 268.0
11 TraesCS3A01G260800 chr3A 82.900 269 43 1 1063 1331 681328865 681329130 9.220000e-59 239.0
12 TraesCS3A01G260800 chr2B 99.103 2340 19 2 3086 5425 732364282 732361945 0.000000e+00 4204.0
13 TraesCS3A01G260800 chr2B 96.556 813 27 1 6297 7108 783417891 783418703 0.000000e+00 1345.0
14 TraesCS3A01G260800 chr2B 88.614 202 21 2 1 202 793131298 793131099 1.980000e-60 244.0
15 TraesCS3A01G260800 chr6B 97.055 815 23 1 6295 7108 671931826 671932640 0.000000e+00 1371.0
16 TraesCS3A01G260800 chr6B 96.564 815 25 3 6296 7108 395672548 395673361 0.000000e+00 1347.0
17 TraesCS3A01G260800 chr5B 97.277 808 21 1 6297 7103 323358162 323358969 0.000000e+00 1369.0
18 TraesCS3A01G260800 chr5B 96.556 813 26 2 6296 7106 96026907 96026095 0.000000e+00 1345.0
19 TraesCS3A01G260800 chr5B 85.903 227 27 5 936 1159 430839252 430839028 3.310000e-58 237.0
20 TraesCS3A01G260800 chr5B 83.838 99 12 4 434 531 575064069 575063974 2.730000e-14 91.6
21 TraesCS3A01G260800 chrUn 96.936 816 22 2 6296 7108 31118506 31117691 0.000000e+00 1365.0
22 TraesCS3A01G260800 chrUn 90.347 259 20 5 1785 2042 276475576 276475322 1.140000e-87 335.0
23 TraesCS3A01G260800 chrUn 92.121 165 10 3 5423 5586 243508681 243508519 5.550000e-56 230.0
24 TraesCS3A01G260800 chrUn 92.121 165 10 3 5423 5586 276475484 276475322 5.550000e-56 230.0
25 TraesCS3A01G260800 chrUn 92.121 165 10 3 5423 5586 422457399 422457237 5.550000e-56 230.0
26 TraesCS3A01G260800 chr7B 96.489 826 27 2 6285 7108 25038849 25039674 0.000000e+00 1363.0
27 TraesCS3A01G260800 chr7B 84.826 1061 119 28 2008 3048 733093384 733094422 0.000000e+00 1029.0
28 TraesCS3A01G260800 chr7B 85.108 1014 114 29 2008 3001 623797000 623797996 0.000000e+00 1002.0
29 TraesCS3A01G260800 chr7B 84.173 992 113 35 2003 2974 710041623 710040656 0.000000e+00 922.0
30 TraesCS3A01G260800 chr7B 83.972 992 115 35 2003 2974 710103221 710102254 0.000000e+00 911.0
31 TraesCS3A01G260800 chr7B 86.076 79 11 0 454 532 518669106 518669184 1.270000e-12 86.1
32 TraesCS3A01G260800 chr2D 96.679 813 24 3 6297 7108 526079588 526078778 0.000000e+00 1349.0
33 TraesCS3A01G260800 chr2D 85.028 895 90 19 3356 4217 94459096 94458213 0.000000e+00 870.0
34 TraesCS3A01G260800 chr2D 85.258 407 41 7 1 392 508139702 508140104 1.110000e-107 401.0
35 TraesCS3A01G260800 chr2D 87.209 86 9 2 406 490 82581258 82581174 5.870000e-16 97.1
36 TraesCS3A01G260800 chr2D 90.196 51 3 1 3569 3617 94458811 94458761 1.660000e-06 65.8
37 TraesCS3A01G260800 chr3B 96.201 816 27 4 6296 7108 685898331 685899145 0.000000e+00 1332.0
38 TraesCS3A01G260800 chr3B 95.646 735 27 4 885 1619 365498668 365499397 0.000000e+00 1175.0
39 TraesCS3A01G260800 chr3B 95.888 608 18 3 5695 6297 365499198 365499803 0.000000e+00 977.0
40 TraesCS3A01G260800 chr3B 93.117 247 15 2 1783 2028 685943259 685943014 1.880000e-95 361.0
41 TraesCS3A01G260800 chr3B 82.785 395 62 6 1 392 637650095 637649704 1.470000e-91 348.0
42 TraesCS3A01G260800 chr3B 95.333 150 5 2 5423 5571 685943163 685943015 3.310000e-58 237.0
43 TraesCS3A01G260800 chr3B 82.156 269 41 3 1063 1331 720201724 720201985 2.580000e-54 224.0
44 TraesCS3A01G260800 chr3B 90.345 145 13 1 753 897 365496086 365496229 9.410000e-44 189.0
45 TraesCS3A01G260800 chr3B 88.189 127 12 2 5551 5676 16160431 16160555 1.600000e-31 148.0
46 TraesCS3A01G260800 chr3B 95.062 81 4 0 2997 3077 685944419 685944339 2.080000e-25 128.0
47 TraesCS3A01G260800 chr3D 93.573 778 40 3 845 1619 363249473 363250243 0.000000e+00 1151.0
48 TraesCS3A01G260800 chr3D 98.496 532 8 0 1 532 363247160 363247691 0.000000e+00 939.0
49 TraesCS3A01G260800 chr3D 90.296 608 36 10 5697 6290 363250046 363250644 0.000000e+00 774.0
50 TraesCS3A01G260800 chr3D 96.012 326 12 1 537 861 363247751 363248076 4.880000e-146 529.0
51 TraesCS3A01G260800 chr3D 86.154 390 49 3 1 390 514997534 514997918 3.970000e-112 416.0
52 TraesCS3A01G260800 chr3D 83.601 311 23 6 5101 5404 275623210 275623499 4.230000e-67 267.0
53 TraesCS3A01G260800 chr3D 83.548 310 24 5 5101 5404 32157972 32158260 1.520000e-66 265.0
54 TraesCS3A01G260800 chr3D 82.156 269 45 1 1063 1331 544353485 544353750 1.990000e-55 228.0
55 TraesCS3A01G260800 chr7A 85.542 996 106 28 2007 2982 134459758 134460735 0.000000e+00 1007.0
56 TraesCS3A01G260800 chr7A 83.208 1060 145 24 2007 3046 75550254 75551300 0.000000e+00 941.0
57 TraesCS3A01G260800 chr7A 83.019 1060 146 26 2007 3046 75551476 75552521 0.000000e+00 929.0
58 TraesCS3A01G260800 chr7A 83.019 1060 147 24 2007 3046 75552697 75553743 0.000000e+00 929.0
59 TraesCS3A01G260800 chr7A 87.466 742 73 13 4701 5424 665316297 665317036 0.000000e+00 837.0
60 TraesCS3A01G260800 chr7A 84.431 835 91 21 3356 4162 665314611 665315434 0.000000e+00 785.0
61 TraesCS3A01G260800 chr7A 86.689 293 30 7 1791 2081 734869381 734869666 4.140000e-82 316.0
62 TraesCS3A01G260800 chr7A 87.402 127 10 5 5551 5675 75550254 75550376 2.670000e-29 141.0
63 TraesCS3A01G260800 chr7A 90.196 51 3 1 3569 3617 665314896 665314946 1.660000e-06 65.8
64 TraesCS3A01G260800 chr7D 85.185 405 46 6 1 392 424105555 424105958 3.090000e-108 403.0
65 TraesCS3A01G260800 chr7D 83.601 311 23 6 5101 5404 116819158 116818869 4.230000e-67 267.0
66 TraesCS3A01G260800 chr7D 82.958 311 25 6 5101 5404 87184685 87184974 9.150000e-64 255.0
67 TraesCS3A01G260800 chr5A 84.236 406 48 3 6 397 318098316 318097913 1.450000e-101 381.0
68 TraesCS3A01G260800 chr5A 81.047 401 70 3 1 397 510075172 510075570 1.490000e-81 315.0
69 TraesCS3A01G260800 chr5A 96.364 55 2 0 431 485 588762891 588762837 2.730000e-14 91.6
70 TraesCS3A01G260800 chr6D 83.668 398 52 2 1 386 78250885 78251281 5.240000e-96 363.0
71 TraesCS3A01G260800 chr1B 92.126 254 17 3 1771 2023 45487482 45487231 8.770000e-94 355.0
72 TraesCS3A01G260800 chr1B 91.732 254 18 3 1771 2023 45629839 45629588 4.080000e-92 350.0
73 TraesCS3A01G260800 chr1B 82.620 397 68 1 1 397 662466286 662466681 4.080000e-92 350.0
74 TraesCS3A01G260800 chr1B 82.725 411 49 15 1619 2023 45605288 45604894 5.280000e-91 346.0
75 TraesCS3A01G260800 chr1B 91.339 254 19 3 1771 2023 45513682 45513431 1.900000e-90 344.0
76 TraesCS3A01G260800 chr1B 89.956 229 23 0 931 1159 375285921 375285693 5.390000e-76 296.0
77 TraesCS3A01G260800 chr1B 92.121 165 10 3 5423 5586 45468046 45467884 5.550000e-56 230.0
78 TraesCS3A01G260800 chr1B 92.121 165 10 3 5423 5586 45584500 45584338 5.550000e-56 230.0
79 TraesCS3A01G260800 chr1B 77.733 247 51 4 1091 1335 349569543 349569787 1.600000e-31 148.0
80 TraesCS3A01G260800 chr1B 92.157 51 2 2 431 480 328799864 328799913 3.560000e-08 71.3
81 TraesCS3A01G260800 chr4B 82.946 387 62 4 1 386 100327335 100326952 5.280000e-91 346.0
82 TraesCS3A01G260800 chr5D 84.196 367 39 7 59 407 341082654 341083019 8.830000e-89 339.0
83 TraesCS3A01G260800 chr1A 89.083 229 25 0 931 1159 283223316 283223088 1.170000e-72 285.0
84 TraesCS3A01G260800 chr1A 82.022 267 38 7 1061 1322 337654999 337654738 1.200000e-52 219.0
85 TraesCS3A01G260800 chr1A 86.000 100 14 0 431 530 554935028 554935127 2.710000e-19 108.0
86 TraesCS3A01G260800 chr1D 83.601 311 23 6 5101 5404 386404244 386403955 4.230000e-67 267.0
87 TraesCS3A01G260800 chr1D 79.365 315 63 2 1018 1331 262287836 262288149 3.340000e-53 220.0
88 TraesCS3A01G260800 chr1D 81.091 275 44 7 1052 1322 262310718 262310988 5.590000e-51 213.0
89 TraesCS3A01G260800 chr6A 82.581 310 27 5 5101 5404 20170572 20170860 1.530000e-61 248.0
90 TraesCS3A01G260800 chr6A 83.200 125 21 0 407 531 436849288 436849164 1.620000e-21 115.0
91 TraesCS3A01G260800 chr4A 82.581 310 26 6 5101 5404 224881483 224881196 1.530000e-61 248.0
92 TraesCS3A01G260800 chr4A 84.921 126 18 1 5552 5676 149048624 149048499 7.490000e-25 126.0
93 TraesCS3A01G260800 chr2A 88.889 54 5 1 3259 3312 355451002 355450950 1.660000e-06 65.8


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 TraesCS3A01G260800 chr3A 483742295 483749402 7107 False 13127.000000 13127 100.000000 1 7108 1 chr3A.!!$F2 7107
1 TraesCS3A01G260800 chr3A 19282074 19283666 1592 True 831.000000 2135 94.187500 1620 5695 4 chr3A.!!$R1 4075
2 TraesCS3A01G260800 chr3A 483743714 483748188 4474 False 330.200000 399 92.842800 1420 5894 5 chr3A.!!$F4 4474
3 TraesCS3A01G260800 chr2B 732361945 732364282 2337 True 4204.000000 4204 99.103000 3086 5425 1 chr2B.!!$R1 2339
4 TraesCS3A01G260800 chr2B 783417891 783418703 812 False 1345.000000 1345 96.556000 6297 7108 1 chr2B.!!$F1 811
5 TraesCS3A01G260800 chr6B 671931826 671932640 814 False 1371.000000 1371 97.055000 6295 7108 1 chr6B.!!$F2 813
6 TraesCS3A01G260800 chr6B 395672548 395673361 813 False 1347.000000 1347 96.564000 6296 7108 1 chr6B.!!$F1 812
7 TraesCS3A01G260800 chr5B 323358162 323358969 807 False 1369.000000 1369 97.277000 6297 7103 1 chr5B.!!$F1 806
8 TraesCS3A01G260800 chr5B 96026095 96026907 812 True 1345.000000 1345 96.556000 6296 7106 1 chr5B.!!$R1 810
9 TraesCS3A01G260800 chrUn 31117691 31118506 815 True 1365.000000 1365 96.936000 6296 7108 1 chrUn.!!$R1 812
10 TraesCS3A01G260800 chr7B 25038849 25039674 825 False 1363.000000 1363 96.489000 6285 7108 1 chr7B.!!$F1 823
11 TraesCS3A01G260800 chr7B 733093384 733094422 1038 False 1029.000000 1029 84.826000 2008 3048 1 chr7B.!!$F4 1040
12 TraesCS3A01G260800 chr7B 623797000 623797996 996 False 1002.000000 1002 85.108000 2008 3001 1 chr7B.!!$F3 993
13 TraesCS3A01G260800 chr7B 710040656 710041623 967 True 922.000000 922 84.173000 2003 2974 1 chr7B.!!$R1 971
14 TraesCS3A01G260800 chr7B 710102254 710103221 967 True 911.000000 911 83.972000 2003 2974 1 chr7B.!!$R2 971
15 TraesCS3A01G260800 chr2D 526078778 526079588 810 True 1349.000000 1349 96.679000 6297 7108 1 chr2D.!!$R2 811
16 TraesCS3A01G260800 chr2D 94458213 94459096 883 True 467.900000 870 87.612000 3356 4217 2 chr2D.!!$R3 861
17 TraesCS3A01G260800 chr3B 685898331 685899145 814 False 1332.000000 1332 96.201000 6296 7108 1 chr3B.!!$F2 812
18 TraesCS3A01G260800 chr3B 365496086 365499803 3717 False 780.333333 1175 93.959667 753 6297 3 chr3B.!!$F4 5544
19 TraesCS3A01G260800 chr3B 685943014 685944419 1405 True 242.000000 361 94.504000 1783 5571 3 chr3B.!!$R2 3788
20 TraesCS3A01G260800 chr3D 363247160 363250644 3484 False 848.250000 1151 94.594250 1 6290 4 chr3D.!!$F5 6289
21 TraesCS3A01G260800 chr7A 134459758 134460735 977 False 1007.000000 1007 85.542000 2007 2982 1 chr7A.!!$F1 975
22 TraesCS3A01G260800 chr7A 75550254 75553743 3489 False 735.000000 941 84.162000 2007 5675 4 chr7A.!!$F3 3668
23 TraesCS3A01G260800 chr7A 665314611 665317036 2425 False 562.600000 837 87.364333 3356 5424 3 chr7A.!!$F4 2068

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
997 4918 0.041833 AAGGCTCCCTCTGCACTCTA 59.958 55.000 0.0 0.0 30.89 2.43 F
1026 4950 0.684805 GAGGAGGAGAAGGAGGCGAA 60.685 60.000 0.0 0.0 0.00 4.70 F
1418 5349 1.902508 AGACATGAGACATCGGTTGGT 59.097 47.619 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
6011 13175 4.680537 ACCTCCTCCACGGCGTCT 62.681 66.667 10.85 0.0 0.0 4.18 R
6038 13202 2.849162 TCCATGATCCTCCCGGCC 60.849 66.667 0.00 0.0 0.0 6.13 R
6169 13334 4.377021 TCTCTTTATTCAACACGCACACT 58.623 39.130 0.00 0.0 0.0 3.55 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
27 28 1.071542 TGGTCAGGTTTGCTCGAATCA 59.928 47.619 0.00 0.00 0.00 2.57
107 108 4.019174 CAAGGTCATGTTAAGAAGCCCAT 58.981 43.478 0.00 0.00 0.00 4.00
201 202 1.068333 GTTGCAGCGATCACCATTGTT 60.068 47.619 0.00 0.00 0.00 2.83
289 290 4.837896 TGAGCTACTATCTGATTGACGG 57.162 45.455 6.11 0.00 0.00 4.79
410 411 8.970859 AGAATGTCTAGAATTTGGAGTAATGG 57.029 34.615 0.00 0.00 0.00 3.16
414 415 7.282585 TGTCTAGAATTTGGAGTAATGGGATG 58.717 38.462 0.00 0.00 0.00 3.51
501 502 0.179004 TGAGAATGTTGTGGCGGGTT 60.179 50.000 0.00 0.00 0.00 4.11
532 533 3.634448 AGGAACGTGAGTGATCCTATCAG 59.366 47.826 2.33 0.00 46.67 2.90
535 536 2.952978 ACGTGAGTGATCCTATCAGACC 59.047 50.000 0.00 0.00 46.97 3.85
780 836 1.284785 TGCCACCTATTCCTTTCCTGG 59.715 52.381 0.00 0.00 0.00 4.45
782 838 1.923148 CCACCTATTCCTTTCCTGGGT 59.077 52.381 0.00 0.00 0.00 4.51
924 4845 5.602978 AGAAACCGGATTATATCACCTGAGT 59.397 40.000 9.46 0.00 0.00 3.41
933 4854 2.236223 ATCACCTGAGTGGCTGAGCG 62.236 60.000 0.00 0.00 44.64 5.03
941 4862 0.890542 AGTGGCTGAGCGCAAAATCA 60.891 50.000 11.47 3.03 41.67 2.57
997 4918 0.041833 AAGGCTCCCTCTGCACTCTA 59.958 55.000 0.00 0.00 30.89 2.43
1026 4950 0.684805 GAGGAGGAGAAGGAGGCGAA 60.685 60.000 0.00 0.00 0.00 4.70
1050 4974 2.666862 CTGTTGGGCGCGTGGTTA 60.667 61.111 8.43 0.00 0.00 2.85
1140 5064 2.389020 CCTGCAGCACAAGAGCGAG 61.389 63.158 8.66 0.00 40.15 5.03
1161 5085 2.600729 CCTGCTCAGCTCCAACCCT 61.601 63.158 0.00 0.00 0.00 4.34
1404 5335 4.201753 CCGTAAAATCAGCAGACAGACATG 60.202 45.833 0.00 0.00 0.00 3.21
1405 5336 4.627035 CGTAAAATCAGCAGACAGACATGA 59.373 41.667 0.00 0.00 0.00 3.07
1407 5338 4.548451 AAATCAGCAGACAGACATGAGA 57.452 40.909 0.00 0.00 0.00 3.27
1408 5339 3.523606 ATCAGCAGACAGACATGAGAC 57.476 47.619 0.00 0.00 0.00 3.36
1409 5340 2.242043 TCAGCAGACAGACATGAGACA 58.758 47.619 0.00 0.00 0.00 3.41
1410 5341 2.830321 TCAGCAGACAGACATGAGACAT 59.170 45.455 0.00 0.00 0.00 3.06
1411 5342 3.119209 TCAGCAGACAGACATGAGACATC 60.119 47.826 0.00 0.00 0.00 3.06
1412 5343 2.159268 AGCAGACAGACATGAGACATCG 60.159 50.000 0.00 0.00 0.00 3.84
1413 5344 2.807044 CAGACAGACATGAGACATCGG 58.193 52.381 0.00 0.00 0.00 4.18
1414 5345 2.165234 CAGACAGACATGAGACATCGGT 59.835 50.000 0.00 0.00 0.00 4.69
1415 5346 2.828520 AGACAGACATGAGACATCGGTT 59.171 45.455 0.00 0.00 0.00 4.44
1416 5347 2.926200 GACAGACATGAGACATCGGTTG 59.074 50.000 0.00 0.00 0.00 3.77
1417 5348 2.274437 CAGACATGAGACATCGGTTGG 58.726 52.381 0.00 0.00 0.00 3.77
1418 5349 1.902508 AGACATGAGACATCGGTTGGT 59.097 47.619 0.00 0.00 0.00 3.67
6038 13202 2.801631 GGAGGAGGTGATGCCCGAG 61.802 68.421 0.00 0.00 38.26 4.63
6268 13446 4.848357 AGTGGAACAATTCAGTGGGATAG 58.152 43.478 0.00 0.00 44.16 2.08
6273 13451 2.027192 ACAATTCAGTGGGATAGCACGT 60.027 45.455 0.00 0.00 0.00 4.49
6279 13457 1.831106 AGTGGGATAGCACGTTGATGA 59.169 47.619 0.00 0.00 0.00 2.92
6373 13552 5.009631 CCAATGACCCAAGACAACATTCTA 58.990 41.667 0.00 0.00 0.00 2.10
6428 13607 7.980662 CCAATGGTCTTAAAATGCATGTATGAA 59.019 33.333 0.00 0.00 0.00 2.57
6638 13817 6.551736 CCCATTACTGATTTTCGTTACCAAG 58.448 40.000 0.00 0.00 0.00 3.61
6791 13971 8.915871 AGGTCACAATAATTTTCATGAAATCG 57.084 30.769 21.10 8.98 36.96 3.34
6924 14108 4.771127 GCATCGGCGAATCCCTTA 57.229 55.556 15.93 0.00 0.00 2.69
6983 14167 1.353804 GGTGTCGCGCAAAGTTCAA 59.646 52.632 8.75 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.154877 TCCATTTCCAATGCATGTAATCAAGT 59.845 34.615 0.00 0.00 0.00 3.16
107 108 3.822167 TGCAACTGCTTCAAGAATGATGA 59.178 39.130 2.95 0.00 42.66 2.92
201 202 1.531365 CCTTCAGCCAGCCCAACAA 60.531 57.895 0.00 0.00 0.00 2.83
289 290 4.597940 AGGTAGCCCAAGGAGGATAAATAC 59.402 45.833 0.00 0.00 41.22 1.89
501 502 4.963373 TCACTCACGTTCCTAAATCCAAA 58.037 39.130 0.00 0.00 0.00 3.28
526 527 4.174411 TGTTCGTGAGTTGGTCTGATAG 57.826 45.455 0.00 0.00 0.00 2.08
532 533 5.292589 TCTTTTAGTTGTTCGTGAGTTGGTC 59.707 40.000 0.00 0.00 0.00 4.02
535 536 7.000575 TCTTCTTTTAGTTGTTCGTGAGTTG 57.999 36.000 0.00 0.00 0.00 3.16
574 630 9.965902 AATATTTTGTCTCTCTTAACTGTCCAT 57.034 29.630 0.00 0.00 0.00 3.41
576 632 9.436957 TCAATATTTTGTCTCTCTTAACTGTCC 57.563 33.333 0.00 0.00 34.32 4.02
637 693 5.105063 GGAGTTCAAATGCTTAAATGGAGC 58.895 41.667 0.00 0.00 40.53 4.70
640 696 3.859386 GCGGAGTTCAAATGCTTAAATGG 59.141 43.478 0.00 0.00 0.00 3.16
648 704 0.449388 CTCCTGCGGAGTTCAAATGC 59.551 55.000 14.22 0.00 44.25 3.56
694 750 1.995484 CCTAGCTCATGTTGTGTCACG 59.005 52.381 0.00 0.00 0.00 4.35
695 751 2.996621 GTCCTAGCTCATGTTGTGTCAC 59.003 50.000 0.00 0.00 0.00 3.67
780 836 1.186030 CGTCAGCGTTGTCGTATACC 58.814 55.000 10.40 0.00 39.49 2.73
782 838 1.733912 ACTCGTCAGCGTTGTCGTATA 59.266 47.619 16.91 0.00 37.20 1.47
933 4854 5.723492 AGTGCTTTCTTGTTTGATTTTGC 57.277 34.783 0.00 0.00 0.00 3.68
941 4862 5.648092 AGACTTGTGTAGTGCTTTCTTGTTT 59.352 36.000 0.00 0.00 37.17 2.83
997 4918 0.252881 TCTCCTCCTCCTGCCATTGT 60.253 55.000 0.00 0.00 0.00 2.71
1036 4960 3.358707 GCTTAACCACGCGCCCAA 61.359 61.111 5.73 0.00 0.00 4.12
1048 4972 1.632018 CGGATCACCCAGGGGCTTAA 61.632 60.000 11.37 0.00 39.32 1.85
1050 4974 3.411517 CGGATCACCCAGGGGCTT 61.412 66.667 11.37 0.00 39.32 4.35
1120 5044 2.256591 CGCTCTTGTGCTGCAGGTT 61.257 57.895 17.12 0.00 0.00 3.50
1140 5064 1.744741 GTTGGAGCTGAGCAGGAGC 60.745 63.158 7.39 0.00 42.56 4.70
1161 5085 4.898607 GGGACCTTCTTGTGCACA 57.101 55.556 17.42 17.42 0.00 4.57
1404 5335 3.122445 GTCGTAAAACCAACCGATGTCTC 59.878 47.826 0.00 0.00 0.00 3.36
1405 5336 3.062042 GTCGTAAAACCAACCGATGTCT 58.938 45.455 0.00 0.00 0.00 3.41
1407 5338 3.116079 AGTCGTAAAACCAACCGATGT 57.884 42.857 0.00 0.00 0.00 3.06
1408 5339 3.805823 CAAGTCGTAAAACCAACCGATG 58.194 45.455 0.00 0.00 0.00 3.84
1409 5340 2.224784 GCAAGTCGTAAAACCAACCGAT 59.775 45.455 0.00 0.00 0.00 4.18
1410 5341 1.598601 GCAAGTCGTAAAACCAACCGA 59.401 47.619 0.00 0.00 0.00 4.69
1411 5342 1.600485 AGCAAGTCGTAAAACCAACCG 59.400 47.619 0.00 0.00 0.00 4.44
1412 5343 2.614983 TCAGCAAGTCGTAAAACCAACC 59.385 45.455 0.00 0.00 0.00 3.77
1413 5344 3.955771 TCAGCAAGTCGTAAAACCAAC 57.044 42.857 0.00 0.00 0.00 3.77
1414 5345 4.819630 AGATTCAGCAAGTCGTAAAACCAA 59.180 37.500 0.00 0.00 0.00 3.67
1415 5346 4.213270 CAGATTCAGCAAGTCGTAAAACCA 59.787 41.667 0.00 0.00 0.00 3.67
1416 5347 4.213482 ACAGATTCAGCAAGTCGTAAAACC 59.787 41.667 0.00 0.00 0.00 3.27
1417 5348 5.140177 CACAGATTCAGCAAGTCGTAAAAC 58.860 41.667 0.00 0.00 0.00 2.43
1418 5349 4.814234 ACACAGATTCAGCAAGTCGTAAAA 59.186 37.500 0.00 0.00 0.00 1.52
6011 13175 4.680537 ACCTCCTCCACGGCGTCT 62.681 66.667 10.85 0.00 0.00 4.18
6038 13202 2.849162 TCCATGATCCTCCCGGCC 60.849 66.667 0.00 0.00 0.00 6.13
6169 13334 4.377021 TCTCTTTATTCAACACGCACACT 58.623 39.130 0.00 0.00 0.00 3.55
6268 13446 8.786937 ATAAATAAATCATGTCATCAACGTGC 57.213 30.769 0.00 0.00 43.43 5.34
6428 13607 7.692460 TCTTTCATGATTGAAGTGTAGCATT 57.308 32.000 0.00 0.00 42.60 3.56
6638 13817 6.021596 CCGTGCATGTATGTTTAGAAGAAAC 58.978 40.000 4.96 0.00 0.00 2.78
6791 13971 5.576447 AACAAATTCCGAATCATACACCC 57.424 39.130 0.00 0.00 0.00 4.61
6888 14072 2.302733 TGCTGTCAGGTGTGTGTATGAT 59.697 45.455 1.14 0.00 0.00 2.45
6924 14108 4.050553 CGTGTGGCATTGTGAAAGATTTT 58.949 39.130 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.