Multiple sequence alignment - TraesCS4B01G215400

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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 TraesCS4B01G215400 chr4B 100.000 2791 0 0 1 2791 455012944 455010154 0.000000e+00 5155.0
1 TraesCS4B01G215400 chr4B 77.431 288 55 8 1624 1906 139106968 139107250 2.220000e-36 163.0
2 TraesCS4B01G215400 chr4B 83.117 77 13 0 1130 1206 432257596 432257520 1.390000e-08 71.3
3 TraesCS4B01G215400 chr4A 95.234 2623 108 8 112 2723 94823185 94825801 0.000000e+00 4135.0
4 TraesCS4B01G215400 chr4A 82.383 193 29 4 254 442 658230913 658230722 2.220000e-36 163.0
5 TraesCS4B01G215400 chr4A 83.140 172 27 2 272 442 657882303 657882473 3.720000e-34 156.0
6 TraesCS4B01G215400 chr4A 97.059 68 2 0 2724 2791 94825874 94825941 6.320000e-22 115.0
7 TraesCS4B01G215400 chr4D 95.695 2509 98 6 218 2722 369862748 369860246 0.000000e+00 4026.0
8 TraesCS4B01G215400 chr4D 95.417 2509 105 6 218 2722 369873832 369876334 0.000000e+00 3988.0
9 TraesCS4B01G215400 chr4D 94.512 164 8 1 27 189 369890675 369890512 4.610000e-63 252.0
10 TraesCS4B01G215400 chr4D 77.431 288 53 10 1625 1906 97383997 97384278 8.000000e-36 161.0
11 TraesCS4B01G215400 chr4D 78.113 265 47 11 1633 1893 97379113 97379370 1.030000e-34 158.0
12 TraesCS4B01G215400 chr4D 98.529 68 1 0 2724 2791 369859095 369859028 1.360000e-23 121.0
13 TraesCS4B01G215400 chr4D 98.529 68 1 0 2724 2791 369877485 369877552 1.360000e-23 121.0
14 TraesCS4B01G215400 chr4D 83.562 73 12 0 1130 1202 349410887 349410815 4.990000e-08 69.4
15 TraesCS4B01G215400 chr7D 75.108 462 95 13 254 714 45551927 45552369 6.100000e-47 198.0
16 TraesCS4B01G215400 chr7A 76.762 383 70 11 253 633 47690747 47691112 2.190000e-46 196.0
17 TraesCS4B01G215400 chr7A 81.865 193 29 5 254 442 47832633 47832443 1.030000e-34 158.0


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 TraesCS4B01G215400 chr4B 455010154 455012944 2790 True 5155.0 5155 100.0000 1 2791 1 chr4B.!!$R2 2790
1 TraesCS4B01G215400 chr4A 94823185 94825941 2756 False 2125.0 4135 96.1465 112 2791 2 chr4A.!!$F2 2679
2 TraesCS4B01G215400 chr4D 369859028 369862748 3720 True 2073.5 4026 97.1120 218 2791 2 chr4D.!!$R3 2573
3 TraesCS4B01G215400 chr4D 369873832 369877552 3720 False 2054.5 3988 96.9730 218 2791 2 chr4D.!!$F3 2573

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
106 107 0.033504 TTTAGATCGGATCGGCTGGC 59.966 55.0 12.08 0.00 0.00 4.85 F
198 204 0.456221 CACTAGTAGGTCACCTGCCG 59.544 60.0 6.61 1.55 36.92 5.69 F
1077 1084 0.550914 AAGGTGAGGCTTTGGACACA 59.449 50.0 5.75 0.00 35.33 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1058 0.693049 AAAGCCTCACCTTCACGGAT 59.307 50.0 0.0 0.0 36.31 4.18 R
1137 1144 0.965866 CTCCTCGCCAGTAGACACCA 60.966 60.0 0.0 0.0 0.00 4.17 R
2161 2172 1.632422 CGCTTGCCCAAATGATGAAC 58.368 50.0 0.0 0.0 0.00 3.18 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
17 18 2.984623 TTGCTCATGAGAGGCGCT 59.015 55.556 27.04 0.00 42.33 5.92
18 19 1.153489 TTGCTCATGAGAGGCGCTC 60.153 57.895 27.04 11.63 42.33 5.03
19 20 2.280052 GCTCATGAGAGGCGCTCC 60.280 66.667 27.04 1.80 43.26 4.70
20 21 2.027314 CTCATGAGAGGCGCTCCG 59.973 66.667 18.34 7.08 43.26 4.63
21 22 2.440247 TCATGAGAGGCGCTCCGA 60.440 61.111 15.82 9.35 43.26 4.55
22 23 2.009424 CTCATGAGAGGCGCTCCGAA 62.009 60.000 18.34 0.00 43.26 4.30
23 24 1.591059 CATGAGAGGCGCTCCGAAG 60.591 63.158 15.82 0.00 43.26 3.79
24 25 2.055042 ATGAGAGGCGCTCCGAAGT 61.055 57.895 15.82 0.00 43.26 3.01
25 26 2.202676 GAGAGGCGCTCCGAAGTG 60.203 66.667 7.64 0.00 37.69 3.16
31 32 3.041940 CGCTCCGAAGTGCCGTTT 61.042 61.111 0.00 0.00 0.00 3.60
32 33 1.735198 CGCTCCGAAGTGCCGTTTA 60.735 57.895 0.00 0.00 0.00 2.01
33 34 1.082117 CGCTCCGAAGTGCCGTTTAT 61.082 55.000 0.00 0.00 0.00 1.40
34 35 0.373716 GCTCCGAAGTGCCGTTTATG 59.626 55.000 0.00 0.00 0.00 1.90
35 36 2.004583 CTCCGAAGTGCCGTTTATGA 57.995 50.000 0.00 0.00 0.00 2.15
36 37 2.343101 CTCCGAAGTGCCGTTTATGAA 58.657 47.619 0.00 0.00 0.00 2.57
37 38 2.936498 CTCCGAAGTGCCGTTTATGAAT 59.064 45.455 0.00 0.00 0.00 2.57
38 39 3.340034 TCCGAAGTGCCGTTTATGAATT 58.660 40.909 0.00 0.00 0.00 2.17
39 40 3.126171 TCCGAAGTGCCGTTTATGAATTG 59.874 43.478 0.00 0.00 0.00 2.32
40 41 2.845967 CGAAGTGCCGTTTATGAATTGC 59.154 45.455 0.00 0.00 0.00 3.56
41 42 2.939460 AGTGCCGTTTATGAATTGCC 57.061 45.000 0.00 0.00 0.00 4.52
42 43 1.476488 AGTGCCGTTTATGAATTGCCC 59.524 47.619 0.00 0.00 0.00 5.36
43 44 1.476488 GTGCCGTTTATGAATTGCCCT 59.524 47.619 0.00 0.00 0.00 5.19
44 45 1.476085 TGCCGTTTATGAATTGCCCTG 59.524 47.619 0.00 0.00 0.00 4.45
45 46 1.476488 GCCGTTTATGAATTGCCCTGT 59.524 47.619 0.00 0.00 0.00 4.00
46 47 2.479560 GCCGTTTATGAATTGCCCTGTC 60.480 50.000 0.00 0.00 0.00 3.51
47 48 2.752354 CCGTTTATGAATTGCCCTGTCA 59.248 45.455 0.00 0.00 0.00 3.58
48 49 3.181497 CCGTTTATGAATTGCCCTGTCAG 60.181 47.826 0.00 0.00 0.00 3.51
49 50 3.731867 CGTTTATGAATTGCCCTGTCAGC 60.732 47.826 0.00 0.00 0.00 4.26
50 51 2.057137 TATGAATTGCCCTGTCAGCC 57.943 50.000 0.00 0.00 0.00 4.85
51 52 1.033746 ATGAATTGCCCTGTCAGCCG 61.034 55.000 0.00 0.00 0.00 5.52
52 53 2.361610 AATTGCCCTGTCAGCCGG 60.362 61.111 0.00 0.00 0.00 6.13
53 54 3.210012 AATTGCCCTGTCAGCCGGT 62.210 57.895 1.90 0.00 0.00 5.28
54 55 3.925630 ATTGCCCTGTCAGCCGGTG 62.926 63.158 1.90 0.00 0.00 4.94
70 71 0.098728 GGTGGCCGATTTTGATCACG 59.901 55.000 0.00 0.00 0.00 4.35
71 72 0.098728 GTGGCCGATTTTGATCACGG 59.901 55.000 16.03 16.03 46.74 4.94
72 73 0.322098 TGGCCGATTTTGATCACGGT 60.322 50.000 19.92 0.00 45.91 4.83
73 74 0.377203 GGCCGATTTTGATCACGGTC 59.623 55.000 19.92 15.75 45.91 4.79
74 75 1.369625 GCCGATTTTGATCACGGTCT 58.630 50.000 19.92 0.00 45.91 3.85
75 76 1.062587 GCCGATTTTGATCACGGTCTG 59.937 52.381 19.92 6.07 45.91 3.51
76 77 1.062587 CCGATTTTGATCACGGTCTGC 59.937 52.381 12.96 0.00 40.42 4.26
77 78 1.062587 CGATTTTGATCACGGTCTGCC 59.937 52.381 0.00 0.00 0.00 4.85
78 79 1.401905 GATTTTGATCACGGTCTGCCC 59.598 52.381 0.00 0.00 0.00 5.36
79 80 0.608035 TTTTGATCACGGTCTGCCCC 60.608 55.000 0.00 0.00 0.00 5.80
93 94 3.873812 CCCCGGCCCGCTTTAGAT 61.874 66.667 0.00 0.00 0.00 1.98
94 95 2.280865 CCCGGCCCGCTTTAGATC 60.281 66.667 0.00 0.00 0.00 2.75
95 96 2.661866 CCGGCCCGCTTTAGATCG 60.662 66.667 0.00 0.00 0.00 3.69
96 97 2.661866 CGGCCCGCTTTAGATCGG 60.662 66.667 0.00 0.00 44.89 4.18
102 103 2.435741 CGCTTTAGATCGGATCGGC 58.564 57.895 12.08 13.11 0.00 5.54
103 104 0.039074 CGCTTTAGATCGGATCGGCT 60.039 55.000 12.08 0.00 0.00 5.52
104 105 1.423395 GCTTTAGATCGGATCGGCTG 58.577 55.000 12.08 6.15 0.00 4.85
105 106 1.937108 GCTTTAGATCGGATCGGCTGG 60.937 57.143 12.08 4.91 0.00 4.85
106 107 0.033504 TTTAGATCGGATCGGCTGGC 59.966 55.000 12.08 0.00 0.00 4.85
107 108 1.112916 TTAGATCGGATCGGCTGGCA 61.113 55.000 12.08 0.00 0.00 4.92
108 109 1.112916 TAGATCGGATCGGCTGGCAA 61.113 55.000 12.08 0.00 0.00 4.52
109 110 2.203070 ATCGGATCGGCTGGCAAC 60.203 61.111 1.08 0.00 0.00 4.17
110 111 3.757248 ATCGGATCGGCTGGCAACC 62.757 63.158 1.08 0.00 0.00 3.77
142 143 0.747255 CCCACCTGTAGATCTCCACG 59.253 60.000 0.00 0.00 0.00 4.94
145 146 1.204704 CACCTGTAGATCTCCACGCAA 59.795 52.381 0.00 0.00 0.00 4.85
153 154 2.549754 AGATCTCCACGCAACAGTTTTG 59.450 45.455 0.00 0.00 0.00 2.44
156 157 1.034838 TCCACGCAACAGTTTTGCCT 61.035 50.000 8.37 0.00 42.10 4.75
194 200 2.158204 ACCCAACACTAGTAGGTCACCT 60.158 50.000 0.00 0.00 37.71 4.00
198 204 0.456221 CACTAGTAGGTCACCTGCCG 59.544 60.000 6.61 1.55 36.92 5.69
416 423 2.387445 CGCATTTTCTCCCGCGTGA 61.387 57.895 4.92 0.00 42.66 4.35
444 451 3.702330 CGGCATCTTCGTCAACTACATA 58.298 45.455 0.00 0.00 0.00 2.29
536 543 2.075355 TTGCCTGGGTACAACTGGGG 62.075 60.000 12.47 3.57 0.00 4.96
624 631 2.358737 GTCAACCCTGCCACGAGG 60.359 66.667 0.00 0.00 38.23 4.63
705 712 1.078778 TGCCGTGTCACCGCATTAT 60.079 52.632 13.98 0.00 0.00 1.28
741 748 0.951040 CACAGGTGCCCGAGAAAGTC 60.951 60.000 0.00 0.00 0.00 3.01
742 749 1.371183 CAGGTGCCCGAGAAAGTCA 59.629 57.895 0.00 0.00 0.00 3.41
780 787 3.056328 GTGCCCGACAAGAAGCCC 61.056 66.667 0.00 0.00 0.00 5.19
782 789 4.035102 GCCCGACAAGAAGCCCCT 62.035 66.667 0.00 0.00 0.00 4.79
794 801 2.193993 GAAGCCCCTAACACCCTTCTA 58.806 52.381 0.00 0.00 31.60 2.10
1051 1058 6.478512 AAGAATGGCAAAAGAGGTTGTTTA 57.521 33.333 0.00 0.00 0.00 2.01
1077 1084 0.550914 AAGGTGAGGCTTTGGACACA 59.449 50.000 5.75 0.00 35.33 3.72
1101 1108 3.245158 TGGCTACTATACGGCTGGATAGT 60.245 47.826 29.24 29.24 40.94 2.12
1104 1111 5.416952 GGCTACTATACGGCTGGATAGTTTA 59.583 44.000 30.98 16.13 39.19 2.01
1137 1144 3.537874 GGGTCGAGGTGGCGCTAT 61.538 66.667 7.64 0.00 0.00 2.97
1311 1318 8.713737 TTGCATCATATCTAGCACTGATAATC 57.286 34.615 0.00 0.00 36.62 1.75
1353 1360 2.496899 ACAGGATGGCAAGTACCAAG 57.503 50.000 0.00 0.00 44.65 3.61
1388 1395 6.483307 CACCAATAGATATCGAGGAAAGCAAA 59.517 38.462 11.16 0.00 0.00 3.68
1445 1452 5.071653 AGGGGTTTACTTTGCAACAATTCAT 59.928 36.000 0.00 0.00 0.00 2.57
1474 1481 9.196139 TGAATATCTATTTCGGGTTTGGATTTT 57.804 29.630 0.00 0.00 0.00 1.82
1503 1513 8.991783 AAATGAATCATGTCAGATATCTTGGT 57.008 30.769 1.33 0.00 0.00 3.67
1788 1798 6.013553 AGTGGCTTATCATCTGAATAGCTCAT 60.014 38.462 13.29 0.00 35.89 2.90
1802 1812 6.611642 TGAATAGCTCATAAGTCCAGTACCTT 59.388 38.462 0.00 0.00 0.00 3.50
1805 1815 3.451178 GCTCATAAGTCCAGTACCTTGGA 59.549 47.826 0.00 0.00 44.84 3.53
1837 1847 6.128172 CGCCCAAAGGATTATTATCAGTCATC 60.128 42.308 0.00 0.00 33.47 2.92
1900 1910 2.108075 TGATTGGGGAGCTTTCAGAACA 59.892 45.455 0.00 0.00 0.00 3.18
1928 1938 6.373005 TGAGATTATTCCTTCACTGGTTGA 57.627 37.500 0.00 0.00 0.00 3.18
2006 2016 8.517878 CCAGAAGTTTAATCAGATTGATGTTGT 58.482 33.333 5.85 0.00 37.15 3.32
2031 2041 6.126623 TGGGGTTTTATTTTTGGAAAGAGCTT 60.127 34.615 0.00 0.00 0.00 3.74
2076 2087 7.383687 TCAAAGAAGTCGCTAGAAAATAGGAA 58.616 34.615 0.00 0.00 0.00 3.36
2114 2125 9.136323 ACAGAACTTACTCAGAATTTCCATTTT 57.864 29.630 0.00 0.00 0.00 1.82
2157 2168 5.101648 TGTGCACCTGATCATCTTATGAA 57.898 39.130 15.69 0.00 43.50 2.57
2161 2172 5.928264 TGCACCTGATCATCTTATGAATACG 59.072 40.000 0.00 0.00 43.50 3.06
2242 2253 5.996669 ATTGTTTCTTCGTCTACGGTTTT 57.003 34.783 2.24 0.00 40.29 2.43
2262 2273 7.535997 GGTTTTAATACCAGGACATGTTCTTC 58.464 38.462 3.05 0.00 38.12 2.87
2367 2379 3.788227 AGTCAAATTCTGCACCCTACA 57.212 42.857 0.00 0.00 0.00 2.74
2527 2539 1.277326 TCAGTTCATGTCGCGTATGC 58.723 50.000 17.21 0.00 37.91 3.14
2591 2603 1.961133 TCCAAAACCGGGACTATCCT 58.039 50.000 6.32 0.00 36.57 3.24
2696 2708 5.755861 GGAGCAGTCATAACAGAAACCTATC 59.244 44.000 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153489 GAGCGCCTCTCATGAGCAA 60.153 57.895 18.36 0.52 41.51 3.91
1 2 2.498248 GAGCGCCTCTCATGAGCA 59.502 61.111 18.36 6.29 41.51 4.26
2 3 2.280052 GGAGCGCCTCTCATGAGC 60.280 66.667 18.36 6.82 43.70 4.26
3 4 2.009424 TTCGGAGCGCCTCTCATGAG 62.009 60.000 17.07 17.07 43.70 2.90
4 5 2.009424 CTTCGGAGCGCCTCTCATGA 62.009 60.000 2.29 0.00 43.70 3.07
5 6 1.591059 CTTCGGAGCGCCTCTCATG 60.591 63.158 2.29 0.00 43.70 3.07
6 7 2.055042 ACTTCGGAGCGCCTCTCAT 61.055 57.895 2.29 0.00 43.70 2.90
7 8 2.676822 ACTTCGGAGCGCCTCTCA 60.677 61.111 2.29 0.00 43.70 3.27
8 9 2.202676 CACTTCGGAGCGCCTCTC 60.203 66.667 2.29 0.00 41.15 3.20
9 10 4.443266 GCACTTCGGAGCGCCTCT 62.443 66.667 2.29 0.00 0.00 3.69
14 15 1.082117 ATAAACGGCACTTCGGAGCG 61.082 55.000 0.00 0.00 32.36 5.03
15 16 0.373716 CATAAACGGCACTTCGGAGC 59.626 55.000 0.00 0.00 0.00 4.70
16 17 2.004583 TCATAAACGGCACTTCGGAG 57.995 50.000 0.00 0.00 0.00 4.63
17 18 2.459060 TTCATAAACGGCACTTCGGA 57.541 45.000 0.00 0.00 0.00 4.55
18 19 3.425404 CAATTCATAAACGGCACTTCGG 58.575 45.455 0.00 0.00 0.00 4.30
19 20 2.845967 GCAATTCATAAACGGCACTTCG 59.154 45.455 0.00 0.00 0.00 3.79
20 21 3.179048 GGCAATTCATAAACGGCACTTC 58.821 45.455 0.00 0.00 0.00 3.01
21 22 2.094234 GGGCAATTCATAAACGGCACTT 60.094 45.455 0.00 0.00 0.00 3.16
22 23 1.476488 GGGCAATTCATAAACGGCACT 59.524 47.619 0.00 0.00 0.00 4.40
23 24 1.476488 AGGGCAATTCATAAACGGCAC 59.524 47.619 0.00 0.00 0.00 5.01
24 25 1.476085 CAGGGCAATTCATAAACGGCA 59.524 47.619 0.00 0.00 0.00 5.69
25 26 1.476488 ACAGGGCAATTCATAAACGGC 59.524 47.619 0.00 0.00 0.00 5.68
26 27 2.752354 TGACAGGGCAATTCATAAACGG 59.248 45.455 0.00 0.00 0.00 4.44
27 28 3.731867 GCTGACAGGGCAATTCATAAACG 60.732 47.826 4.26 0.00 0.00 3.60
28 29 3.429410 GGCTGACAGGGCAATTCATAAAC 60.429 47.826 4.26 0.00 0.00 2.01
29 30 2.760092 GGCTGACAGGGCAATTCATAAA 59.240 45.455 4.26 0.00 0.00 1.40
30 31 2.378038 GGCTGACAGGGCAATTCATAA 58.622 47.619 4.26 0.00 0.00 1.90
31 32 1.746861 CGGCTGACAGGGCAATTCATA 60.747 52.381 4.26 0.00 0.00 2.15
32 33 1.033746 CGGCTGACAGGGCAATTCAT 61.034 55.000 4.26 0.00 0.00 2.57
33 34 1.675310 CGGCTGACAGGGCAATTCA 60.675 57.895 4.26 0.00 0.00 2.57
34 35 2.409870 CCGGCTGACAGGGCAATTC 61.410 63.158 4.26 0.00 0.00 2.17
35 36 2.361610 CCGGCTGACAGGGCAATT 60.362 61.111 4.26 0.00 0.00 2.32
36 37 3.650950 ACCGGCTGACAGGGCAAT 61.651 61.111 0.00 0.00 0.00 3.56
37 38 4.641645 CACCGGCTGACAGGGCAA 62.642 66.667 0.00 0.00 0.00 4.52
51 52 0.098728 CGTGATCAAAATCGGCCACC 59.901 55.000 2.24 0.00 34.39 4.61
52 53 0.098728 CCGTGATCAAAATCGGCCAC 59.901 55.000 9.27 0.00 36.68 5.01
53 54 0.322098 ACCGTGATCAAAATCGGCCA 60.322 50.000 19.25 0.00 45.76 5.36
54 55 0.377203 GACCGTGATCAAAATCGGCC 59.623 55.000 19.25 7.58 45.76 6.13
55 56 1.062587 CAGACCGTGATCAAAATCGGC 59.937 52.381 19.25 13.13 45.76 5.54
56 57 1.062587 GCAGACCGTGATCAAAATCGG 59.937 52.381 18.09 18.09 46.98 4.18
57 58 1.062587 GGCAGACCGTGATCAAAATCG 59.937 52.381 0.00 0.00 34.39 3.34
58 59 1.401905 GGGCAGACCGTGATCAAAATC 59.598 52.381 0.00 0.00 36.48 2.17
59 60 1.463674 GGGCAGACCGTGATCAAAAT 58.536 50.000 0.00 0.00 36.48 1.82
60 61 0.608035 GGGGCAGACCGTGATCAAAA 60.608 55.000 0.00 0.00 41.60 2.44
61 62 1.002624 GGGGCAGACCGTGATCAAA 60.003 57.895 0.00 0.00 41.60 2.69
62 63 2.668632 GGGGCAGACCGTGATCAA 59.331 61.111 0.00 0.00 41.60 2.57
76 77 3.826926 GATCTAAAGCGGGCCGGGG 62.827 68.421 29.48 0.00 0.00 5.73
77 78 2.280865 GATCTAAAGCGGGCCGGG 60.281 66.667 29.48 0.00 0.00 5.73
78 79 2.661866 CGATCTAAAGCGGGCCGG 60.662 66.667 29.48 10.74 0.00 6.13
84 85 0.039074 AGCCGATCCGATCTAAAGCG 60.039 55.000 6.81 0.00 0.00 4.68
85 86 1.423395 CAGCCGATCCGATCTAAAGC 58.577 55.000 6.81 4.56 0.00 3.51
86 87 1.937108 GCCAGCCGATCCGATCTAAAG 60.937 57.143 6.81 0.00 0.00 1.85
87 88 0.033504 GCCAGCCGATCCGATCTAAA 59.966 55.000 6.81 0.00 0.00 1.85
88 89 1.112916 TGCCAGCCGATCCGATCTAA 61.113 55.000 6.81 0.00 0.00 2.10
89 90 1.112916 TTGCCAGCCGATCCGATCTA 61.113 55.000 6.81 0.00 0.00 1.98
90 91 2.434843 TTGCCAGCCGATCCGATCT 61.435 57.895 6.81 0.00 0.00 2.75
91 92 2.108976 TTGCCAGCCGATCCGATC 59.891 61.111 0.00 0.00 0.00 3.69
92 93 2.203070 GTTGCCAGCCGATCCGAT 60.203 61.111 0.00 0.00 0.00 4.18
93 94 4.467084 GGTTGCCAGCCGATCCGA 62.467 66.667 0.00 0.00 0.00 4.55
94 95 4.473520 AGGTTGCCAGCCGATCCG 62.474 66.667 0.00 0.00 0.00 4.18
95 96 2.825836 CAGGTTGCCAGCCGATCC 60.826 66.667 0.00 0.00 0.00 3.36
96 97 2.825836 CCAGGTTGCCAGCCGATC 60.826 66.667 0.00 0.00 0.00 3.69
105 106 2.125106 CCGTCTAGGCCAGGTTGC 60.125 66.667 5.01 0.00 0.00 4.17
120 121 1.742768 GAGATCTACAGGTGGGCCG 59.257 63.158 0.00 0.00 40.50 6.13
165 166 4.212636 CCTACTAGTGTTGGGTTTTGTTCG 59.787 45.833 5.39 0.00 35.83 3.95
210 216 1.729149 GCAGATCGAAAACAAAGGGCG 60.729 52.381 0.00 0.00 0.00 6.13
214 220 1.197721 AGGCGCAGATCGAAAACAAAG 59.802 47.619 10.83 0.00 41.67 2.77
402 409 1.301401 CACCTCACGCGGGAGAAAA 60.301 57.895 38.82 2.50 37.05 2.29
536 543 2.487762 TGATCCACAATTGGCTCGAAAC 59.512 45.455 10.83 0.27 40.45 2.78
705 712 2.290367 CTGTGGAATCGCAAACACTTGA 59.710 45.455 0.00 0.00 34.14 3.02
741 748 1.613437 GGTTGTGGTTGGACTGGAATG 59.387 52.381 0.00 0.00 0.00 2.67
742 749 1.216678 TGGTTGTGGTTGGACTGGAAT 59.783 47.619 0.00 0.00 0.00 3.01
780 787 1.558294 GTGGGGTAGAAGGGTGTTAGG 59.442 57.143 0.00 0.00 0.00 2.69
782 789 2.158127 TCAGTGGGGTAGAAGGGTGTTA 60.158 50.000 0.00 0.00 0.00 2.41
794 801 1.489230 ACGAGAAAAACTCAGTGGGGT 59.511 47.619 0.00 0.00 45.14 4.95
1051 1058 0.693049 AAAGCCTCACCTTCACGGAT 59.307 50.000 0.00 0.00 36.31 4.18
1077 1084 1.133575 TCCAGCCGTATAGTAGCCACT 60.134 52.381 0.00 0.00 38.91 4.00
1123 1130 2.758327 ACCATAGCGCCACCTCGA 60.758 61.111 2.29 0.00 0.00 4.04
1137 1144 0.965866 CTCCTCGCCAGTAGACACCA 60.966 60.000 0.00 0.00 0.00 4.17
1196 1203 4.413495 TGTAAGCCTTTTTACGATGCAC 57.587 40.909 0.00 0.00 36.54 4.57
1198 1205 5.992489 CTTTGTAAGCCTTTTTACGATGC 57.008 39.130 0.00 0.00 36.54 3.91
1311 1318 9.994432 CTGTAAGAATAACCTGCAAATAAGAAG 57.006 33.333 0.00 0.00 34.07 2.85
1330 1337 3.178046 TGGTACTTGCCATCCTGTAAGA 58.822 45.455 0.00 0.00 31.10 2.10
1335 1342 2.496899 ACTTGGTACTTGCCATCCTG 57.503 50.000 0.00 0.00 38.48 3.86
1388 1395 1.095228 CCAGACAAGGTTGTGCACGT 61.095 55.000 13.13 2.00 42.43 4.49
1445 1452 7.513856 TCCAAACCCGAAATAGATATTCATCA 58.486 34.615 0.00 0.00 33.21 3.07
1503 1513 6.769134 AAGATCAATGTGATGCTTCAATGA 57.231 33.333 3.51 9.55 37.20 2.57
1598 1608 3.133362 CCCCATTGGTTCCATCTTCATTG 59.867 47.826 1.20 0.00 0.00 2.82
1788 1798 6.127535 CGTAATCTTCCAAGGTACTGGACTTA 60.128 42.308 3.39 1.20 40.86 2.24
1802 1812 1.631388 TCCTTTGGGCGTAATCTTCCA 59.369 47.619 0.00 0.00 0.00 3.53
1805 1815 7.942341 TGATAATAATCCTTTGGGCGTAATCTT 59.058 33.333 0.00 0.00 0.00 2.40
1900 1910 5.826737 CCAGTGAAGGAATAATCTCAAGCAT 59.173 40.000 0.00 0.00 0.00 3.79
1928 1938 4.164988 CACCTAAATCTCCAGATCCCAACT 59.835 45.833 0.00 0.00 32.75 3.16
2006 2016 5.368230 AGCTCTTTCCAAAAATAAAACCCCA 59.632 36.000 0.00 0.00 0.00 4.96
2031 2041 7.879677 TCTTTGAATTCTCACTTCTATGCTTCA 59.120 33.333 7.05 0.00 0.00 3.02
2076 2087 5.374071 AGTAAGTTCTGTCCAATTCGGTTT 58.626 37.500 0.00 0.00 35.57 3.27
2114 2125 8.851145 TGCACAAAATAACCAAGATAGTTTACA 58.149 29.630 0.00 0.00 0.00 2.41
2122 2133 4.832266 TCAGGTGCACAAAATAACCAAGAT 59.168 37.500 20.43 0.00 35.01 2.40
2123 2134 4.211125 TCAGGTGCACAAAATAACCAAGA 58.789 39.130 20.43 0.00 35.01 3.02
2157 2168 3.181487 GCTTGCCCAAATGATGAACGTAT 60.181 43.478 0.00 0.00 0.00 3.06
2161 2172 1.632422 CGCTTGCCCAAATGATGAAC 58.368 50.000 0.00 0.00 0.00 3.18
2242 2253 7.252612 TGAAGAAGAACATGTCCTGGTATTA 57.747 36.000 0.00 0.00 0.00 0.98
2262 2273 5.088739 GCGTGACCAAAAATAGACATGAAG 58.911 41.667 0.00 0.00 0.00 3.02
2367 2379 4.405680 TCGGACACATCACCATAGATTTCT 59.594 41.667 0.00 0.00 0.00 2.52
2527 2539 7.534239 GCTTCAGAAACTAATTTACGAAACTGG 59.466 37.037 0.00 0.00 0.00 4.00
2567 2579 4.577693 GGATAGTCCCGGTTTTGGAATTAC 59.422 45.833 0.00 0.00 32.59 1.89
2570 2582 2.850568 AGGATAGTCCCGGTTTTGGAAT 59.149 45.455 0.00 0.00 37.19 3.01
2591 2603 9.952030 TTTGACAATTCAAGGTACATAGACATA 57.048 29.630 0.00 0.00 42.79 2.29
2631 2643 5.813513 AGAACCATTGAAGGAAAATTGCT 57.186 34.783 0.00 0.00 0.00 3.91
2640 2652 6.646240 CCAAATTTGTGTAGAACCATTGAAGG 59.354 38.462 16.73 0.00 0.00 3.46
2696 2708 1.733389 GCAATTGTCTCAATGCACGGG 60.733 52.381 7.40 0.00 38.63 5.28


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

AutoCloner maintained by Alex Coulton.