Multiple sequence alignment - TraesCS3D01G165400

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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 TraesCS3D01G165400 chr3D 100.000 3224 0 0 1 3224 137008865 137005642 0.000000e+00 5954.0
1 TraesCS3D01G165400 chr3D 82.547 212 31 4 1270 1478 137007524 137007316 7.110000e-42 182.0
2 TraesCS3D01G165400 chr3D 82.547 212 31 4 1342 1550 137007596 137007388 7.110000e-42 182.0
3 TraesCS3D01G165400 chr3D 89.381 113 12 0 1287 1399 137007432 137007320 3.350000e-30 143.0
4 TraesCS3D01G165400 chr3D 89.381 113 12 0 1434 1546 137007579 137007467 3.350000e-30 143.0
5 TraesCS3D01G165400 chr3D 87.387 111 2 1 7 117 137008813 137008911 2.030000e-22 117.0
6 TraesCS3D01G165400 chr3D 100.000 34 0 0 32 65 137008859 137008892 2.690000e-06 63.9
7 TraesCS3D01G165400 chr3B 92.094 3162 122 59 130 3224 200478189 200481289 0.000000e+00 4337.0
8 TraesCS3D01G165400 chr3B 81.567 217 31 7 1264 1475 200479409 200479621 1.540000e-38 171.0
9 TraesCS3D01G165400 chr3B 87.719 114 12 2 1287 1399 200479508 200479620 7.260000e-27 132.0
10 TraesCS3D01G165400 chr3B 84.874 119 12 2 1434 1546 200479355 200479473 7.310000e-22 115.0
11 TraesCS3D01G165400 chr3A 93.799 2935 98 33 130 3032 155056638 155059520 0.000000e+00 4335.0
12 TraesCS3D01G165400 chr3A 82.297 209 31 4 1270 1475 155057833 155058038 3.310000e-40 176.0
13 TraesCS3D01G165400 chr3A 81.308 214 19 6 3031 3224 155059667 155059879 1.550000e-33 154.0
14 TraesCS3D01G165400 chr3A 89.381 113 12 0 1287 1399 155057925 155058037 3.350000e-30 143.0
15 TraesCS3D01G165400 chr7D 98.148 54 0 1 130 182 598698253 598698200 3.420000e-15 93.5
16 TraesCS3D01G165400 chr7D 96.364 55 1 1 130 183 598597139 598597193 4.430000e-14 89.8
17 TraesCS3D01G165400 chr7D 98.077 52 0 1 130 180 599463201 599463150 4.430000e-14 89.8
18 TraesCS3D01G165400 chr7D 96.296 54 1 1 130 182 535547332 535547385 1.590000e-13 87.9
19 TraesCS3D01G165400 chr7B 98.039 51 1 0 130 180 677754260 677754310 4.430000e-14 89.8
20 TraesCS3D01G165400 chr5B 98.077 52 0 1 130 181 658458265 658458315 4.430000e-14 89.8
21 TraesCS3D01G165400 chr5B 96.296 54 1 1 130 182 658160167 658160114 1.590000e-13 87.9
22 TraesCS3D01G165400 chr1D 98.039 51 1 0 130 180 387330240 387330190 4.430000e-14 89.8


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 TraesCS3D01G165400 chr3D 137005642 137008865 3223 True 1320.80 5954 88.77120 1 3224 5 chr3D.!!$R1 3223
1 TraesCS3D01G165400 chr3B 200478189 200481289 3100 False 1188.75 4337 86.56350 130 3224 4 chr3B.!!$F1 3094
2 TraesCS3D01G165400 chr3A 155056638 155059879 3241 False 1202.00 4335 86.69625 130 3224 4 chr3A.!!$F1 3094

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
830 853 0.036875 CACCTCCACTTCCCACTTCC 59.963 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2308 1.481871 CCAAACCCCGAGCTAGTAGA 58.518 55.0 0.0 0.0 0.0 2.59 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
22 23 3.855950 CCGTCGTTTGTAGTACAATCTCC 59.144 47.826 16.26 7.82 38.00 3.71
23 24 3.541130 CGTCGTTTGTAGTACAATCTCCG 59.459 47.826 16.26 14.87 38.00 4.63
24 25 4.479619 GTCGTTTGTAGTACAATCTCCGT 58.520 43.478 16.26 0.00 38.00 4.69
25 26 4.556523 GTCGTTTGTAGTACAATCTCCGTC 59.443 45.833 16.26 10.20 38.00 4.79
26 27 3.541130 CGTTTGTAGTACAATCTCCGTCG 59.459 47.826 16.26 8.95 38.00 5.12
27 28 4.479619 GTTTGTAGTACAATCTCCGTCGT 58.520 43.478 16.26 0.00 38.00 4.34
28 29 5.631026 GTTTGTAGTACAATCTCCGTCGTA 58.369 41.667 16.26 0.00 38.00 3.43
29 30 4.864916 TGTAGTACAATCTCCGTCGTAC 57.135 45.455 0.00 0.00 35.53 3.67
30 31 4.507710 TGTAGTACAATCTCCGTCGTACT 58.492 43.478 0.00 0.00 44.93 2.73
31 32 5.660460 TGTAGTACAATCTCCGTCGTACTA 58.340 41.667 0.00 0.00 42.01 1.82
33 34 3.553511 AGTACAATCTCCGTCGTACTACG 59.446 47.826 12.62 12.62 42.01 3.51
44 45 2.621338 TCGTACTACGACGGAGATTGT 58.379 47.619 15.58 0.00 46.73 2.71
45 46 3.780902 TCGTACTACGACGGAGATTGTA 58.219 45.455 15.58 0.00 46.73 2.41
46 47 3.551890 TCGTACTACGACGGAGATTGTAC 59.448 47.826 15.58 5.69 46.73 2.90
47 48 3.553511 CGTACTACGACGGAGATTGTACT 59.446 47.826 15.58 0.00 46.05 2.73
48 49 4.740205 CGTACTACGACGGAGATTGTACTA 59.260 45.833 15.58 0.00 46.05 1.82
49 50 5.331905 CGTACTACGACGGAGATTGTACTAC 60.332 48.000 15.58 2.93 46.05 2.73
50 51 4.507710 ACTACGACGGAGATTGTACTACA 58.492 43.478 15.58 0.00 0.00 2.74
51 52 4.937620 ACTACGACGGAGATTGTACTACAA 59.062 41.667 15.58 4.08 42.95 2.41
52 53 4.771590 ACGACGGAGATTGTACTACAAA 57.228 40.909 5.73 0.00 41.96 2.83
53 54 4.730657 ACGACGGAGATTGTACTACAAAG 58.269 43.478 5.73 0.00 41.96 2.77
54 55 4.217118 ACGACGGAGATTGTACTACAAAGT 59.783 41.667 5.73 2.45 41.96 2.66
55 56 5.159209 CGACGGAGATTGTACTACAAAGTT 58.841 41.667 5.73 0.00 41.96 2.66
56 57 5.632347 CGACGGAGATTGTACTACAAAGTTT 59.368 40.000 5.73 0.00 41.96 2.66
57 58 6.183359 CGACGGAGATTGTACTACAAAGTTTC 60.183 42.308 5.73 0.00 41.96 2.78
58 59 6.518493 ACGGAGATTGTACTACAAAGTTTCA 58.482 36.000 5.73 0.00 41.96 2.69
59 60 6.645415 ACGGAGATTGTACTACAAAGTTTCAG 59.355 38.462 5.73 5.32 41.96 3.02
60 61 6.645415 CGGAGATTGTACTACAAAGTTTCAGT 59.355 38.462 5.73 5.08 41.96 3.41
61 62 7.148787 CGGAGATTGTACTACAAAGTTTCAGTC 60.149 40.741 5.73 0.00 41.96 3.51
62 63 7.656137 GGAGATTGTACTACAAAGTTTCAGTCA 59.344 37.037 5.73 1.04 41.96 3.41
63 64 8.594881 AGATTGTACTACAAAGTTTCAGTCAG 57.405 34.615 5.73 0.00 41.96 3.51
64 65 8.421784 AGATTGTACTACAAAGTTTCAGTCAGA 58.578 33.333 5.73 0.00 41.96 3.27
65 66 7.766219 TTGTACTACAAAGTTTCAGTCAGAC 57.234 36.000 0.00 0.00 34.76 3.51
66 67 5.975344 TGTACTACAAAGTTTCAGTCAGACG 59.025 40.000 3.25 0.00 37.15 4.18
67 68 5.258456 ACTACAAAGTTTCAGTCAGACGA 57.742 39.130 0.00 0.00 29.00 4.20
68 69 5.041940 ACTACAAAGTTTCAGTCAGACGAC 58.958 41.667 0.00 0.00 35.85 4.34
69 70 6.236273 ACTACAAAGTTTCAGTCAGACGACG 61.236 44.000 0.00 0.00 39.03 5.12
70 71 9.781069 TACTACAAAGTTTCAGTCAGACGACGG 62.781 44.444 0.00 0.00 41.03 4.79
72 73 1.267261 AGTTTCAGTCAGACGACGGAG 59.733 52.381 0.00 0.00 45.29 4.63
73 74 1.266175 GTTTCAGTCAGACGACGGAGA 59.734 52.381 0.00 0.00 45.29 3.71
74 75 1.822506 TTCAGTCAGACGACGGAGAT 58.177 50.000 0.00 0.00 45.29 2.75
75 76 2.160205 TTCAGTCAGACGACGGAGATT 58.840 47.619 0.00 0.00 45.29 2.40
76 77 2.095212 TTCAGTCAGACGACGGAGATTG 60.095 50.000 0.00 1.47 45.29 2.67
77 78 4.612888 TTCAGTCAGACGACGGAGATTGT 61.613 47.826 0.00 0.00 45.29 2.71
78 79 5.337968 TTCAGTCAGACGACGGAGATTGTA 61.338 45.833 0.00 0.00 45.29 2.41
79 80 2.783333 GTCAGACGACGGAGATTGTAC 58.217 52.381 0.00 0.00 31.07 2.90
80 81 1.741706 TCAGACGACGGAGATTGTACC 59.258 52.381 0.00 0.00 0.00 3.34
81 82 1.471287 CAGACGACGGAGATTGTACCA 59.529 52.381 0.00 0.00 0.00 3.25
82 83 1.471684 AGACGACGGAGATTGTACCAC 59.528 52.381 0.00 0.00 0.00 4.16
83 84 1.200716 GACGACGGAGATTGTACCACA 59.799 52.381 0.00 0.00 0.00 4.17
84 85 1.614903 ACGACGGAGATTGTACCACAA 59.385 47.619 0.00 0.00 42.95 3.33
85 86 2.036217 ACGACGGAGATTGTACCACAAA 59.964 45.455 0.00 0.00 41.96 2.83
86 87 2.666508 CGACGGAGATTGTACCACAAAG 59.333 50.000 0.00 0.00 41.96 2.77
87 88 3.660865 GACGGAGATTGTACCACAAAGT 58.339 45.455 0.00 0.00 41.96 2.66
88 89 4.062991 GACGGAGATTGTACCACAAAGTT 58.937 43.478 0.00 0.00 41.96 2.66
89 90 4.457466 ACGGAGATTGTACCACAAAGTTT 58.543 39.130 0.00 0.00 41.96 2.66
90 91 4.514066 ACGGAGATTGTACCACAAAGTTTC 59.486 41.667 0.00 0.00 41.96 2.78
91 92 4.513692 CGGAGATTGTACCACAAAGTTTCA 59.486 41.667 0.00 0.00 41.96 2.69
92 93 5.334105 CGGAGATTGTACCACAAAGTTTCAG 60.334 44.000 0.00 0.00 41.96 3.02
93 94 5.531287 GGAGATTGTACCACAAAGTTTCAGT 59.469 40.000 0.00 0.00 41.96 3.41
94 95 6.293462 GGAGATTGTACCACAAAGTTTCAGTC 60.293 42.308 0.00 0.00 41.96 3.51
95 96 6.119536 AGATTGTACCACAAAGTTTCAGTCA 58.880 36.000 0.00 0.00 41.96 3.41
96 97 5.811399 TTGTACCACAAAGTTTCAGTCAG 57.189 39.130 0.00 0.00 34.76 3.51
97 98 5.092554 TGTACCACAAAGTTTCAGTCAGA 57.907 39.130 0.00 0.00 0.00 3.27
98 99 5.492895 TGTACCACAAAGTTTCAGTCAGAA 58.507 37.500 0.00 0.00 0.00 3.02
99 100 4.965119 ACCACAAAGTTTCAGTCAGAAC 57.035 40.909 0.00 0.00 35.56 3.01
100 101 3.694566 ACCACAAAGTTTCAGTCAGAACC 59.305 43.478 0.00 0.00 35.56 3.62
101 102 3.947834 CCACAAAGTTTCAGTCAGAACCT 59.052 43.478 0.00 0.00 35.56 3.50
102 103 4.035675 CCACAAAGTTTCAGTCAGAACCTC 59.964 45.833 0.00 0.00 35.56 3.85
103 104 4.878397 CACAAAGTTTCAGTCAGAACCTCT 59.122 41.667 0.00 0.00 35.56 3.69
104 105 5.355350 CACAAAGTTTCAGTCAGAACCTCTT 59.645 40.000 0.00 0.00 35.56 2.85
105 106 5.946377 ACAAAGTTTCAGTCAGAACCTCTTT 59.054 36.000 0.00 0.00 35.56 2.52
106 107 6.127897 ACAAAGTTTCAGTCAGAACCTCTTTG 60.128 38.462 17.58 17.58 44.31 2.77
107 108 5.104259 AGTTTCAGTCAGAACCTCTTTGT 57.896 39.130 0.00 0.00 35.56 2.83
108 109 6.235231 AGTTTCAGTCAGAACCTCTTTGTA 57.765 37.500 0.00 0.00 35.56 2.41
109 110 6.284459 AGTTTCAGTCAGAACCTCTTTGTAG 58.716 40.000 0.00 0.00 35.56 2.74
110 111 4.258702 TCAGTCAGAACCTCTTTGTAGC 57.741 45.455 0.00 0.00 0.00 3.58
111 112 3.898123 TCAGTCAGAACCTCTTTGTAGCT 59.102 43.478 0.00 0.00 0.00 3.32
112 113 5.077564 TCAGTCAGAACCTCTTTGTAGCTA 58.922 41.667 0.00 0.00 0.00 3.32
113 114 5.717178 TCAGTCAGAACCTCTTTGTAGCTAT 59.283 40.000 0.00 0.00 0.00 2.97
114 115 6.890268 TCAGTCAGAACCTCTTTGTAGCTATA 59.110 38.462 0.00 0.00 0.00 1.31
115 116 7.067615 TCAGTCAGAACCTCTTTGTAGCTATAG 59.932 40.741 0.00 0.00 0.00 1.31
116 117 5.980715 GTCAGAACCTCTTTGTAGCTATAGC 59.019 44.000 17.33 17.33 42.49 2.97
233 236 1.000955 ACACTAGTTTCTGCCGTGGAG 59.999 52.381 0.00 0.00 0.00 3.86
234 237 0.608640 ACTAGTTTCTGCCGTGGAGG 59.391 55.000 0.00 0.00 44.97 4.30
235 238 0.895530 CTAGTTTCTGCCGTGGAGGA 59.104 55.000 0.00 0.00 45.00 3.71
236 239 1.482593 CTAGTTTCTGCCGTGGAGGAT 59.517 52.381 0.00 0.00 45.00 3.24
237 240 0.250513 AGTTTCTGCCGTGGAGGATC 59.749 55.000 0.00 0.00 45.00 3.36
238 241 1.084370 GTTTCTGCCGTGGAGGATCG 61.084 60.000 0.00 0.00 45.00 3.69
239 242 1.254975 TTTCTGCCGTGGAGGATCGA 61.255 55.000 0.00 0.00 45.00 3.59
240 243 1.945354 TTCTGCCGTGGAGGATCGAC 61.945 60.000 0.00 0.00 45.00 4.20
241 244 2.678580 TGCCGTGGAGGATCGACA 60.679 61.111 0.00 0.00 44.74 4.35
242 245 2.021068 CTGCCGTGGAGGATCGACAT 62.021 60.000 0.00 0.00 44.74 3.06
243 246 1.300233 GCCGTGGAGGATCGACATC 60.300 63.158 0.00 0.00 44.74 3.06
290 293 1.955663 GGCCAAAGCACGCCAAAAG 60.956 57.895 0.00 0.00 45.01 2.27
296 299 4.999939 GCACGCCAAAAGGCCGTG 63.000 66.667 19.58 19.58 39.95 4.94
319 326 4.740235 TTTTTCCCTTTTGGCGCG 57.260 50.000 0.00 0.00 38.58 6.86
379 388 6.749923 AAAGGCTAAGATCTTGTAGCTTTG 57.250 37.500 21.59 0.00 40.54 2.77
386 395 9.691624 GCTAAGATCTTGTAGCTTTGCCCAAAG 62.692 44.444 18.47 14.72 43.59 2.77
450 465 1.205893 AGCCGGAGAGCAACTAGAAAG 59.794 52.381 5.05 0.00 34.23 2.62
455 470 4.806247 CCGGAGAGCAACTAGAAAGTAATG 59.194 45.833 0.00 0.00 33.75 1.90
501 516 4.217159 GCCACCTACCGGCTACCG 62.217 72.222 0.00 0.00 46.56 4.02
572 587 2.034066 CCCGAGCAAAGCTTCCCA 59.966 61.111 0.00 0.00 39.88 4.37
604 619 2.337532 CGTGGTCGTCGTCCCTTT 59.662 61.111 6.05 0.00 0.00 3.11
605 620 1.731969 CGTGGTCGTCGTCCCTTTC 60.732 63.158 6.05 0.00 0.00 2.62
616 631 2.358737 CCCTTTCGTCTTGGCGCT 60.359 61.111 7.64 0.00 0.00 5.92
658 673 1.275291 ACATGGACGGTCAAGATTCGT 59.725 47.619 10.76 0.00 39.99 3.85
686 701 2.888464 TTTCGGGGCGGTTTCACACA 62.888 55.000 0.00 0.00 0.00 3.72
687 702 3.353836 CGGGGCGGTTTCACACAG 61.354 66.667 0.00 0.00 0.00 3.66
698 713 0.390340 TTCACACAGCGCCAGAGATC 60.390 55.000 2.29 0.00 0.00 2.75
699 714 1.079612 CACACAGCGCCAGAGATCA 60.080 57.895 2.29 0.00 0.00 2.92
700 715 1.079543 ACACAGCGCCAGAGATCAC 60.080 57.895 2.29 0.00 0.00 3.06
701 716 1.079612 CACAGCGCCAGAGATCACA 60.080 57.895 2.29 0.00 0.00 3.58
824 847 1.248486 GAAAAGCACCTCCACTTCCC 58.752 55.000 0.00 0.00 0.00 3.97
825 848 0.555769 AAAAGCACCTCCACTTCCCA 59.444 50.000 0.00 0.00 0.00 4.37
826 849 0.178990 AAAGCACCTCCACTTCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
827 850 1.062488 AAGCACCTCCACTTCCCACT 61.062 55.000 0.00 0.00 0.00 4.00
828 851 1.062488 AGCACCTCCACTTCCCACTT 61.062 55.000 0.00 0.00 0.00 3.16
830 853 0.036875 CACCTCCACTTCCCACTTCC 59.963 60.000 0.00 0.00 0.00 3.46
831 854 1.296715 CCTCCACTTCCCACTTCCG 59.703 63.158 0.00 0.00 0.00 4.30
832 855 1.296715 CTCCACTTCCCACTTCCGG 59.703 63.158 0.00 0.00 0.00 5.14
855 909 0.899019 GAGAAGTCTCCAGTCCCCAC 59.101 60.000 0.00 0.00 37.02 4.61
989 1056 1.807573 GCACACTCCACTAGCGAGC 60.808 63.158 7.23 0.00 0.00 5.03
2321 2399 6.017109 ACAAGCAATTTCAACTAGAATCGTGT 60.017 34.615 0.00 0.00 35.83 4.49
2325 2403 7.023575 GCAATTTCAACTAGAATCGTGTGAAT 58.976 34.615 0.00 0.00 35.83 2.57
2328 2406 9.965824 AATTTCAACTAGAATCGTGTGAATTTT 57.034 25.926 0.00 0.00 35.83 1.82
2331 2409 5.779806 ACTAGAATCGTGTGAATTTTCCG 57.220 39.130 0.00 0.00 0.00 4.30
2332 2410 5.235516 ACTAGAATCGTGTGAATTTTCCGT 58.764 37.500 0.00 0.00 0.00 4.69
2333 2411 4.404507 AGAATCGTGTGAATTTTCCGTG 57.595 40.909 0.00 0.00 0.00 4.94
2334 2412 3.813166 AGAATCGTGTGAATTTTCCGTGT 59.187 39.130 0.00 0.00 0.00 4.49
2335 2413 3.806316 ATCGTGTGAATTTTCCGTGTC 57.194 42.857 0.00 0.00 0.00 3.67
2369 2447 4.028026 GTGTGAATTTTCCGTGTCAAAACG 60.028 41.667 0.00 0.00 43.20 3.60
2381 2459 2.483106 TGTCAAAACGTTTCACCGAACA 59.517 40.909 15.01 9.45 0.00 3.18
2514 2593 4.832266 TCTTACATGTTGGGCTCACAAAAT 59.168 37.500 2.30 0.00 31.17 1.82
2543 2622 4.684703 CCAATTACTATGTCGGTCGAATCC 59.315 45.833 0.00 0.00 0.00 3.01
2809 2891 4.330074 CGGTCACCATATCTTGTTCTTGAC 59.670 45.833 0.00 0.00 0.00 3.18
3073 3303 2.100631 GCAGATCACAACGGGACCG 61.101 63.158 9.56 9.56 46.03 4.79
3084 3315 3.069443 ACAACGGGACCGAGTTAGTTTTA 59.931 43.478 18.80 0.00 42.83 1.52
3087 3318 5.254339 ACGGGACCGAGTTAGTTTTATAG 57.746 43.478 18.80 0.00 42.83 1.31
3123 3354 9.959749 TTTATTTGTTTCAAGTGAGGATTACAC 57.040 29.630 0.00 0.00 38.38 2.90
3140 3385 1.066143 ACACCGGAAGTAGCCAATCAG 60.066 52.381 9.46 0.00 0.00 2.90
3168 3418 1.885887 TCGAAAGCACAAGGGAAATGG 59.114 47.619 0.00 0.00 0.00 3.16
3181 3432 4.808042 AGGGAAATGGCAATAAGTATGCT 58.192 39.130 0.00 0.00 43.34 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.855950 GGAGATTGTACTACAAACGACGG 59.144 47.826 5.73 0.00 41.96 4.79
1 2 3.541130 CGGAGATTGTACTACAAACGACG 59.459 47.826 5.73 9.14 41.96 5.12
2 3 4.479619 ACGGAGATTGTACTACAAACGAC 58.520 43.478 17.79 10.68 41.96 4.34
3 4 4.669965 CGACGGAGATTGTACTACAAACGA 60.670 45.833 17.79 0.00 41.96 3.85
4 5 3.541130 CGACGGAGATTGTACTACAAACG 59.459 47.826 5.73 10.21 41.96 3.60
5 6 4.479619 ACGACGGAGATTGTACTACAAAC 58.520 43.478 5.73 3.64 41.96 2.93
6 7 4.771590 ACGACGGAGATTGTACTACAAA 57.228 40.909 5.73 0.00 41.96 2.83
7 8 4.937620 AGTACGACGGAGATTGTACTACAA 59.062 41.667 4.08 4.08 44.08 2.41
8 9 4.507710 AGTACGACGGAGATTGTACTACA 58.492 43.478 0.00 0.00 44.08 2.74
10 11 4.740205 CGTAGTACGACGGAGATTGTACTA 59.260 45.833 17.85 8.37 46.05 1.82
11 12 3.553511 CGTAGTACGACGGAGATTGTACT 59.446 47.826 17.85 10.02 46.05 2.73
12 13 3.551890 TCGTAGTACGACGGAGATTGTAC 59.448 47.826 25.06 0.23 46.73 2.90
13 14 3.780902 TCGTAGTACGACGGAGATTGTA 58.219 45.455 25.06 3.72 46.73 2.41
14 15 2.621338 TCGTAGTACGACGGAGATTGT 58.379 47.619 25.06 0.00 46.73 2.71
25 26 3.553511 AGTACAATCTCCGTCGTAGTACG 59.446 47.826 16.65 16.65 44.19 3.67
26 27 5.520288 TGTAGTACAATCTCCGTCGTAGTAC 59.480 44.000 0.00 0.00 39.54 2.73
27 28 5.660460 TGTAGTACAATCTCCGTCGTAGTA 58.340 41.667 0.00 0.00 0.00 1.82
28 29 4.507710 TGTAGTACAATCTCCGTCGTAGT 58.492 43.478 0.00 0.00 0.00 2.73
29 30 5.475273 TTGTAGTACAATCTCCGTCGTAG 57.525 43.478 11.75 0.00 32.34 3.51
30 31 5.412594 ACTTTGTAGTACAATCTCCGTCGTA 59.587 40.000 16.26 0.00 38.00 3.43
31 32 4.217118 ACTTTGTAGTACAATCTCCGTCGT 59.783 41.667 16.26 2.38 38.00 4.34
32 33 4.730657 ACTTTGTAGTACAATCTCCGTCG 58.269 43.478 16.26 1.86 38.00 5.12
33 34 6.643770 TGAAACTTTGTAGTACAATCTCCGTC 59.356 38.462 16.26 9.79 38.00 4.79
34 35 6.518493 TGAAACTTTGTAGTACAATCTCCGT 58.482 36.000 16.26 6.59 38.00 4.69
35 36 6.645415 ACTGAAACTTTGTAGTACAATCTCCG 59.355 38.462 16.26 9.31 38.00 4.63
36 37 7.656137 TGACTGAAACTTTGTAGTACAATCTCC 59.344 37.037 16.26 6.34 38.00 3.71
37 38 8.589335 TGACTGAAACTTTGTAGTACAATCTC 57.411 34.615 16.26 10.66 38.00 2.75
38 39 8.421784 TCTGACTGAAACTTTGTAGTACAATCT 58.578 33.333 16.26 2.22 38.00 2.40
39 40 8.488764 GTCTGACTGAAACTTTGTAGTACAATC 58.511 37.037 16.26 11.18 38.00 2.67
40 41 7.169308 CGTCTGACTGAAACTTTGTAGTACAAT 59.831 37.037 16.26 1.55 38.00 2.71
41 42 6.474427 CGTCTGACTGAAACTTTGTAGTACAA 59.526 38.462 11.75 11.75 36.11 2.41
42 43 5.975344 CGTCTGACTGAAACTTTGTAGTACA 59.025 40.000 6.21 0.00 33.17 2.90
43 44 6.142002 GTCGTCTGACTGAAACTTTGTAGTAC 59.858 42.308 6.21 0.00 42.08 2.73
44 45 6.204359 GTCGTCTGACTGAAACTTTGTAGTA 58.796 40.000 6.21 0.00 42.08 1.82
45 46 5.041940 GTCGTCTGACTGAAACTTTGTAGT 58.958 41.667 6.21 0.00 42.08 2.73
46 47 4.146616 CGTCGTCTGACTGAAACTTTGTAG 59.853 45.833 6.21 0.00 43.21 2.74
47 48 4.039703 CGTCGTCTGACTGAAACTTTGTA 58.960 43.478 6.21 0.00 43.21 2.41
48 49 2.858344 CGTCGTCTGACTGAAACTTTGT 59.142 45.455 6.21 0.00 43.21 2.83
49 50 2.218759 CCGTCGTCTGACTGAAACTTTG 59.781 50.000 6.21 0.00 43.21 2.77
50 51 2.100252 TCCGTCGTCTGACTGAAACTTT 59.900 45.455 6.21 0.00 43.21 2.66
51 52 1.679680 TCCGTCGTCTGACTGAAACTT 59.320 47.619 6.21 0.00 43.21 2.66
52 53 1.267261 CTCCGTCGTCTGACTGAAACT 59.733 52.381 6.21 0.00 43.21 2.66
53 54 1.266175 TCTCCGTCGTCTGACTGAAAC 59.734 52.381 6.21 0.00 43.21 2.78
54 55 1.601166 TCTCCGTCGTCTGACTGAAA 58.399 50.000 6.21 0.00 43.21 2.69
55 56 1.822506 ATCTCCGTCGTCTGACTGAA 58.177 50.000 6.21 0.00 43.21 3.02
56 57 1.468914 CAATCTCCGTCGTCTGACTGA 59.531 52.381 6.21 2.48 43.21 3.41
57 58 1.200252 ACAATCTCCGTCGTCTGACTG 59.800 52.381 6.21 0.01 43.21 3.51
58 59 1.535833 ACAATCTCCGTCGTCTGACT 58.464 50.000 6.21 0.00 43.21 3.41
59 60 2.477525 GGTACAATCTCCGTCGTCTGAC 60.478 54.545 0.00 0.00 41.91 3.51
60 61 1.741706 GGTACAATCTCCGTCGTCTGA 59.258 52.381 0.00 0.00 0.00 3.27
61 62 1.471287 TGGTACAATCTCCGTCGTCTG 59.529 52.381 0.00 0.00 31.92 3.51
62 63 1.471684 GTGGTACAATCTCCGTCGTCT 59.528 52.381 0.00 0.00 44.16 4.18
63 64 1.200716 TGTGGTACAATCTCCGTCGTC 59.799 52.381 0.00 0.00 44.16 4.20
64 65 1.250328 TGTGGTACAATCTCCGTCGT 58.750 50.000 0.00 0.00 44.16 4.34
65 66 2.357327 TTGTGGTACAATCTCCGTCG 57.643 50.000 0.00 0.00 44.16 5.12
66 67 3.660865 ACTTTGTGGTACAATCTCCGTC 58.339 45.455 0.00 0.00 44.16 4.79
67 68 3.764237 ACTTTGTGGTACAATCTCCGT 57.236 42.857 0.00 0.00 44.16 4.69
68 69 4.513692 TGAAACTTTGTGGTACAATCTCCG 59.486 41.667 0.00 0.00 44.16 4.63
69 70 5.531287 ACTGAAACTTTGTGGTACAATCTCC 59.469 40.000 0.00 0.00 44.16 3.71
70 71 6.260050 TGACTGAAACTTTGTGGTACAATCTC 59.740 38.462 0.00 0.00 44.16 2.75
71 72 6.119536 TGACTGAAACTTTGTGGTACAATCT 58.880 36.000 0.00 0.00 44.16 2.40
72 73 6.260050 TCTGACTGAAACTTTGTGGTACAATC 59.740 38.462 0.00 0.00 44.16 2.67
73 74 6.119536 TCTGACTGAAACTTTGTGGTACAAT 58.880 36.000 0.00 0.00 44.16 2.71
74 75 5.492895 TCTGACTGAAACTTTGTGGTACAA 58.507 37.500 0.00 0.00 44.16 2.41
75 76 5.092554 TCTGACTGAAACTTTGTGGTACA 57.907 39.130 0.00 0.00 0.00 2.90
76 77 5.220796 GGTTCTGACTGAAACTTTGTGGTAC 60.221 44.000 3.04 0.00 39.22 3.34
77 78 4.879545 GGTTCTGACTGAAACTTTGTGGTA 59.120 41.667 3.04 0.00 39.22 3.25
78 79 3.694566 GGTTCTGACTGAAACTTTGTGGT 59.305 43.478 3.04 0.00 39.22 4.16
79 80 4.292977 GGTTCTGACTGAAACTTTGTGG 57.707 45.455 3.04 0.00 39.22 4.17
86 87 5.050023 GCTACAAAGAGGTTCTGACTGAAAC 60.050 44.000 2.04 2.04 42.49 2.78
87 88 5.057149 GCTACAAAGAGGTTCTGACTGAAA 58.943 41.667 0.00 0.00 36.30 2.69
88 89 4.345257 AGCTACAAAGAGGTTCTGACTGAA 59.655 41.667 0.00 0.00 0.00 3.02
89 90 3.898123 AGCTACAAAGAGGTTCTGACTGA 59.102 43.478 0.00 0.00 0.00 3.41
90 91 4.264460 AGCTACAAAGAGGTTCTGACTG 57.736 45.455 0.00 0.00 0.00 3.51
91 92 6.183360 GCTATAGCTACAAAGAGGTTCTGACT 60.183 42.308 17.75 0.00 38.21 3.41
92 93 5.980715 GCTATAGCTACAAAGAGGTTCTGAC 59.019 44.000 17.75 0.00 38.21 3.51
93 94 6.150396 GCTATAGCTACAAAGAGGTTCTGA 57.850 41.667 17.75 0.00 38.21 3.27
109 110 7.382759 GGTGAGATTGTACTACAAAGCTATAGC 59.617 40.741 17.33 17.33 41.96 2.97
110 111 7.868415 GGGTGAGATTGTACTACAAAGCTATAG 59.132 40.741 5.73 0.00 41.96 1.31
111 112 7.469594 CGGGTGAGATTGTACTACAAAGCTATA 60.470 40.741 5.73 0.00 41.96 1.31
112 113 6.583562 GGGTGAGATTGTACTACAAAGCTAT 58.416 40.000 5.73 0.00 41.96 2.97
113 114 5.393787 CGGGTGAGATTGTACTACAAAGCTA 60.394 44.000 5.73 0.00 41.96 3.32
114 115 4.620803 CGGGTGAGATTGTACTACAAAGCT 60.621 45.833 5.73 6.56 41.96 3.74
115 116 3.617263 CGGGTGAGATTGTACTACAAAGC 59.383 47.826 5.73 2.15 41.96 3.51
116 117 5.068234 TCGGGTGAGATTGTACTACAAAG 57.932 43.478 5.73 0.00 41.96 2.77
117 118 4.768448 TCTCGGGTGAGATTGTACTACAAA 59.232 41.667 5.73 0.00 46.25 2.83
118 119 4.338012 TCTCGGGTGAGATTGTACTACAA 58.662 43.478 4.08 4.08 46.25 2.41
119 120 3.959293 TCTCGGGTGAGATTGTACTACA 58.041 45.455 0.00 0.00 46.25 2.74
178 181 4.933400 GTGCCTGTTAATCGAGGACTAAAA 59.067 41.667 0.00 0.00 0.00 1.52
182 185 1.899814 TGTGCCTGTTAATCGAGGACT 59.100 47.619 0.00 0.00 0.00 3.85
183 186 2.271800 CTGTGCCTGTTAATCGAGGAC 58.728 52.381 0.00 0.00 0.00 3.85
237 240 0.664466 CGGGGTGATGATCGATGTCG 60.664 60.000 0.54 0.00 41.45 4.35
238 241 0.389391 ACGGGGTGATGATCGATGTC 59.611 55.000 0.54 1.09 0.00 3.06
239 242 0.389391 GACGGGGTGATGATCGATGT 59.611 55.000 0.54 0.00 0.00 3.06
240 243 0.319900 GGACGGGGTGATGATCGATG 60.320 60.000 0.54 0.00 0.00 3.84
241 244 0.470080 AGGACGGGGTGATGATCGAT 60.470 55.000 0.00 0.00 0.00 3.59
242 245 1.076265 AGGACGGGGTGATGATCGA 60.076 57.895 0.00 0.00 0.00 3.59
243 246 1.068083 CAGGACGGGGTGATGATCG 59.932 63.158 0.00 0.00 0.00 3.69
319 326 4.103103 GTTCCGCTTTGGCTCGCC 62.103 66.667 0.00 0.00 37.80 5.54
379 388 4.093743 TCTATTTTCCTTTCCCTTTGGGC 58.906 43.478 0.00 0.00 43.94 5.36
422 437 0.818296 TGCTCTCCGGCTTAAGAGAC 59.182 55.000 19.32 11.84 41.28 3.36
455 470 7.213678 CAGGAGTAGGTTAATTTGATCTCTCC 58.786 42.308 9.79 9.79 38.27 3.71
572 587 0.036388 CCACGCCAATGGACAGTACT 60.036 55.000 2.05 0.00 43.02 2.73
604 619 2.258591 GTCTGAGCGCCAAGACGA 59.741 61.111 20.40 3.56 34.06 4.20
605 620 3.175240 CGTCTGAGCGCCAAGACG 61.175 66.667 33.89 33.89 45.89 4.18
616 631 2.649190 CTGGATCTCTTCTCCGTCTGA 58.351 52.381 0.00 0.00 35.41 3.27
658 673 4.060038 GCCCCGAAAGTCGACCGA 62.060 66.667 13.01 0.00 43.74 4.69
686 701 1.079543 GTGTGTGATCTCTGGCGCT 60.080 57.895 7.64 0.00 0.00 5.92
687 702 1.374631 TGTGTGTGATCTCTGGCGC 60.375 57.895 0.00 0.00 0.00 6.53
698 713 0.597637 GACCGACCTCTGTGTGTGTG 60.598 60.000 0.00 0.00 0.00 3.82
699 714 1.040893 TGACCGACCTCTGTGTGTGT 61.041 55.000 0.00 0.00 0.00 3.72
700 715 0.597637 GTGACCGACCTCTGTGTGTG 60.598 60.000 0.00 0.00 0.00 3.82
701 716 0.755698 AGTGACCGACCTCTGTGTGT 60.756 55.000 0.00 0.00 0.00 3.72
824 847 2.672414 ACTTCTCCTCCCGGAAGTG 58.328 57.895 0.73 0.00 46.76 3.16
826 849 1.107945 GAGACTTCTCCTCCCGGAAG 58.892 60.000 0.73 0.00 43.02 3.46
827 850 3.284711 GAGACTTCTCCTCCCGGAA 57.715 57.895 0.73 0.00 39.29 4.30
836 859 0.899019 GTGGGGACTGGAGACTTCTC 59.101 60.000 0.00 0.00 42.14 2.87
837 860 0.545548 GGTGGGGACTGGAGACTTCT 60.546 60.000 0.00 0.00 0.00 2.85
838 861 1.554583 GGGTGGGGACTGGAGACTTC 61.555 65.000 0.00 0.00 0.00 3.01
839 862 1.539124 GGGTGGGGACTGGAGACTT 60.539 63.158 0.00 0.00 0.00 3.01
840 863 2.122954 GGGTGGGGACTGGAGACT 59.877 66.667 0.00 0.00 0.00 3.24
842 865 4.348495 GGGGGTGGGGACTGGAGA 62.348 72.222 0.00 0.00 0.00 3.71
989 1056 2.353607 GCGGCATCGTACTCCTCG 60.354 66.667 0.00 0.00 38.89 4.63
2190 2263 2.355986 AAGCACCCTGCCGTCGATA 61.356 57.895 0.00 0.00 46.52 2.92
2233 2308 1.481871 CCAAACCCCGAGCTAGTAGA 58.518 55.000 0.00 0.00 0.00 2.59
2236 2311 2.298661 CCCCAAACCCCGAGCTAGT 61.299 63.158 0.00 0.00 0.00 2.57
2321 2399 6.128661 CGATTCTAGTTGACACGGAAAATTCA 60.129 38.462 0.00 0.00 0.00 2.57
2325 2403 4.446385 CACGATTCTAGTTGACACGGAAAA 59.554 41.667 0.00 0.00 0.00 2.29
2328 2406 2.555325 ACACGATTCTAGTTGACACGGA 59.445 45.455 0.00 0.00 0.00 4.69
2331 2409 6.467723 AATTCACACGATTCTAGTTGACAC 57.532 37.500 0.00 0.00 0.00 3.67
2332 2410 7.307751 GGAAAATTCACACGATTCTAGTTGACA 60.308 37.037 0.00 0.00 0.00 3.58
2333 2411 7.015877 GGAAAATTCACACGATTCTAGTTGAC 58.984 38.462 0.00 0.00 0.00 3.18
2334 2412 6.128661 CGGAAAATTCACACGATTCTAGTTGA 60.129 38.462 0.00 0.00 0.00 3.18
2335 2413 6.015504 CGGAAAATTCACACGATTCTAGTTG 58.984 40.000 0.00 0.00 0.00 3.16
2369 2447 6.889019 TTACCAAATTTTGTTCGGTGAAAC 57.111 33.333 8.26 0.00 0.00 2.78
2514 2593 5.657474 GACCGACATAGTAATTGGTCTTCA 58.343 41.667 13.57 0.00 42.00 3.02
2543 2622 8.424918 ACCATGAACTATTCTATTAGAGGTGTG 58.575 37.037 0.00 0.00 0.00 3.82
2809 2891 5.059833 GGATAGTACTGATGCTCTTTTGGG 58.940 45.833 5.39 0.00 0.00 4.12
3108 3339 3.262420 CTTCCGGTGTAATCCTCACTTG 58.738 50.000 0.00 0.00 36.25 3.16
3109 3340 2.904434 ACTTCCGGTGTAATCCTCACTT 59.096 45.455 0.00 0.00 36.25 3.16
3123 3354 1.482593 AGTCTGATTGGCTACTTCCGG 59.517 52.381 0.00 0.00 0.00 5.14
3140 3385 4.454504 TCCCTTGTGCTTTCGATTTTAGTC 59.545 41.667 0.00 0.00 0.00 2.59
3168 3418 2.032054 TGCAAGCGAGCATACTTATTGC 59.968 45.455 1.83 8.39 40.11 3.56


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

AutoCloner maintained by Alex Coulton.