Multiple sequence alignment - TraesCS3B01G388300

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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 TraesCS3B01G388300 chr3B 100.000 2641 0 0 1 2641 611149853 611152493 0.000000e+00 4878.0
1 TraesCS3B01G388300 chr3B 82.136 487 44 25 2148 2624 611170638 611171091 6.900000e-101 377.0
2 TraesCS3B01G388300 chr3D 91.014 2604 143 39 104 2641 460930457 460933035 0.000000e+00 3428.0
3 TraesCS3B01G388300 chr3A 86.193 1282 97 44 1417 2641 603234296 603235554 0.000000e+00 1314.0
4 TraesCS3B01G388300 chr3A 86.726 904 70 24 563 1420 603233367 603234266 0.000000e+00 959.0
5 TraesCS3B01G388300 chr3A 84.457 341 32 15 580 899 603232578 603232918 1.530000e-82 316.0
6 TraesCS3B01G388300 chr6D 96.667 120 4 0 1 120 214124206 214124087 1.600000e-47 200.0
7 TraesCS3B01G388300 chr6D 97.143 35 0 1 312 346 422609828 422609861 1.020000e-04 58.4
8 TraesCS3B01G388300 chrUn 95.161 124 5 1 1 123 150562382 150562505 7.460000e-46 195.0
9 TraesCS3B01G388300 chrUn 95.161 124 5 1 1 123 166659560 166659683 7.460000e-46 195.0
10 TraesCS3B01G388300 chrUn 95.161 124 5 1 1 123 168178891 168179014 7.460000e-46 195.0
11 TraesCS3B01G388300 chr7D 94.531 128 4 2 1 126 336419815 336419689 7.460000e-46 195.0
12 TraesCS3B01G388300 chr7D 96.552 116 4 0 1 116 342805153 342805268 2.680000e-45 193.0
13 TraesCS3B01G388300 chr2B 94.531 128 4 3 1 127 54573374 54573249 7.460000e-46 195.0
14 TraesCS3B01G388300 chr7B 93.233 133 5 4 1 132 309758340 309758469 2.680000e-45 193.0
15 TraesCS3B01G388300 chr1D 90.780 141 9 4 1 139 159023935 159024073 4.490000e-43 185.0
16 TraesCS3B01G388300 chr2D 89.706 68 7 0 1417 1484 316020144 316020077 1.300000e-13 87.9
17 TraesCS3B01G388300 chr2D 96.226 53 2 0 1298 1350 316020249 316020197 1.300000e-13 87.9


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 TraesCS3B01G388300 chr3B 611149853 611152493 2640 False 4878 4878 100.000 1 2641 1 chr3B.!!$F1 2640
1 TraesCS3B01G388300 chr3D 460930457 460933035 2578 False 3428 3428 91.014 104 2641 1 chr3D.!!$F1 2537
2 TraesCS3B01G388300 chr3A 603232578 603235554 2976 False 863 1314 85.792 563 2641 3 chr3A.!!$F1 2078

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
842 1091 0.240145 TGTTACCTGTCACGCTCTCG 59.76 55.0 0.0 0.0 42.43 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 2084 0.034574 AATGTATGCTTGCCCGGTGA 60.035 50.0 0.0 0.0 0.0 4.02 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
47 48 7.377766 TGAATAGTTTGCACTAGAAATCACC 57.622 36.000 0.00 0.00 38.96 4.02
48 49 7.168219 TGAATAGTTTGCACTAGAAATCACCT 58.832 34.615 0.00 0.00 38.96 4.00
49 50 6.992063 ATAGTTTGCACTAGAAATCACCTG 57.008 37.500 0.00 0.00 38.96 4.00
50 51 4.973168 AGTTTGCACTAGAAATCACCTGA 58.027 39.130 0.00 0.00 0.00 3.86
51 52 4.757149 AGTTTGCACTAGAAATCACCTGAC 59.243 41.667 0.00 0.00 0.00 3.51
52 53 4.350368 TTGCACTAGAAATCACCTGACA 57.650 40.909 0.00 0.00 0.00 3.58
54 55 4.713553 TGCACTAGAAATCACCTGACAAA 58.286 39.130 0.00 0.00 0.00 2.83
56 57 6.472016 TGCACTAGAAATCACCTGACAAATA 58.528 36.000 0.00 0.00 0.00 1.40
57 58 7.112122 TGCACTAGAAATCACCTGACAAATAT 58.888 34.615 0.00 0.00 0.00 1.28
60 61 7.066163 CACTAGAAATCACCTGACAAATATGCA 59.934 37.037 0.00 0.00 0.00 3.96
63 64 6.379133 AGAAATCACCTGACAAATATGCATGT 59.621 34.615 10.16 0.00 0.00 3.21
65 66 7.828508 AATCACCTGACAAATATGCATGTAT 57.171 32.000 10.16 0.82 0.00 2.29
66 67 6.622833 TCACCTGACAAATATGCATGTATG 57.377 37.500 10.16 7.63 0.00 2.39
86 87 7.644490 TGTATGCAATATTTTTGGTCGTATCC 58.356 34.615 0.00 0.00 0.00 2.59
87 88 6.707440 ATGCAATATTTTTGGTCGTATCCA 57.293 33.333 0.00 0.00 35.49 3.41
88 89 6.516739 TGCAATATTTTTGGTCGTATCCAA 57.483 33.333 5.65 5.65 44.48 3.53
90 91 5.977129 GCAATATTTTTGGTCGTATCCAAGG 59.023 40.000 8.73 0.00 46.27 3.61
91 92 6.405397 GCAATATTTTTGGTCGTATCCAAGGT 60.405 38.462 8.73 4.13 46.27 3.50
93 94 8.342634 CAATATTTTTGGTCGTATCCAAGGTAG 58.657 37.037 8.73 0.00 46.27 3.18
94 95 4.895668 TTTTGGTCGTATCCAAGGTAGT 57.104 40.909 8.73 0.00 46.27 2.73
95 96 4.895668 TTTGGTCGTATCCAAGGTAGTT 57.104 40.909 8.73 0.00 46.27 2.24
97 98 6.549433 TTTGGTCGTATCCAAGGTAGTTAT 57.451 37.500 8.73 0.00 46.27 1.89
98 99 5.524971 TGGTCGTATCCAAGGTAGTTATG 57.475 43.478 0.00 0.00 34.24 1.90
99 100 4.957954 TGGTCGTATCCAAGGTAGTTATGT 59.042 41.667 0.00 0.00 34.24 2.29
100 101 5.068198 TGGTCGTATCCAAGGTAGTTATGTC 59.932 44.000 0.00 0.00 34.24 3.06
101 102 5.508657 GGTCGTATCCAAGGTAGTTATGTCC 60.509 48.000 0.00 0.00 0.00 4.02
102 103 5.301298 GTCGTATCCAAGGTAGTTATGTCCT 59.699 44.000 0.00 0.00 0.00 3.85
103 104 5.533903 TCGTATCCAAGGTAGTTATGTCCTC 59.466 44.000 0.00 0.00 0.00 3.71
104 105 5.301045 CGTATCCAAGGTAGTTATGTCCTCA 59.699 44.000 0.00 0.00 0.00 3.86
105 106 6.015350 CGTATCCAAGGTAGTTATGTCCTCAT 60.015 42.308 0.00 0.00 38.00 2.90
106 107 5.871396 TCCAAGGTAGTTATGTCCTCATC 57.129 43.478 0.00 0.00 35.70 2.92
107 108 5.277250 TCCAAGGTAGTTATGTCCTCATCA 58.723 41.667 0.00 0.00 35.70 3.07
123 124 4.831155 CCTCATCAAGGTGGAATGCATATT 59.169 41.667 0.00 0.00 40.67 1.28
216 218 4.931214 GATATTTCGATGAAACCGCTACG 58.069 43.478 0.00 0.00 34.23 3.51
224 226 4.146616 CGATGAAACCGCTACGAAAGATAG 59.853 45.833 0.00 0.00 0.00 2.08
226 228 5.565592 TGAAACCGCTACGAAAGATAGTA 57.434 39.130 0.00 0.00 0.00 1.82
277 279 6.173427 TCAAATGACATATACTAGCAGGCA 57.827 37.500 0.00 0.00 0.00 4.75
293 295 4.040217 AGCAGGCAATGGACAAACATTTTA 59.960 37.500 0.00 0.00 38.94 1.52
319 321 1.886542 GTGCGATGAAAGGGGAAAGTT 59.113 47.619 0.00 0.00 0.00 2.66
348 350 6.029346 TCTTAACTTCCGTTGTTAGGTAGG 57.971 41.667 0.00 0.00 34.59 3.18
383 385 5.125900 TGCAATTGTAATCTCTGACCCAATG 59.874 40.000 7.40 0.00 0.00 2.82
477 479 4.582240 GCCCCTTCATTTCTCTATTTCCAG 59.418 45.833 0.00 0.00 0.00 3.86
486 488 9.784531 TCATTTCTCTATTTCCAGTCATAATCC 57.215 33.333 0.00 0.00 0.00 3.01
574 802 3.118542 GTGAAAGACGGTAAGACAACGT 58.881 45.455 0.00 0.00 44.35 3.99
614 842 1.872388 TTTCGAAGGAACGCACATCA 58.128 45.000 0.00 0.00 0.00 3.07
842 1091 0.240145 TGTTACCTGTCACGCTCTCG 59.760 55.000 0.00 0.00 42.43 4.04
933 1189 3.920144 CGGAAGCTACTACCGTCTG 57.080 57.895 11.56 0.00 41.47 3.51
941 1197 2.478200 GCTACTACCGTCTGTTCTCTGC 60.478 54.545 0.00 0.00 0.00 4.26
955 1211 3.614659 CTGCTCGATCTGTGCGCG 61.615 66.667 0.00 0.00 39.94 6.86
980 1251 4.671766 GCGAACAAGTTAATTAGGTGGCTG 60.672 45.833 0.00 0.00 0.00 4.85
1242 1514 2.939640 GCCGTCACATCCACTGGTAATT 60.940 50.000 0.00 0.00 0.00 1.40
1403 1677 7.010645 GTCTTAGCAAGCTAGAAACTGTATTCC 59.989 40.741 1.68 0.00 0.00 3.01
1413 1687 7.705325 GCTAGAAACTGTATTCCGAGATTGTAA 59.295 37.037 0.00 0.00 0.00 2.41
1604 1913 2.266055 CCTTCAGACCAGGCGTCC 59.734 66.667 0.00 0.00 43.08 4.79
1625 1934 1.110442 CCTCAAGGAGCTCAGACGAT 58.890 55.000 17.19 0.00 37.39 3.73
1635 1944 1.716186 CTCAGACGATAACGACGACG 58.284 55.000 5.58 5.58 42.66 5.12
1637 1946 1.059692 TCAGACGATAACGACGACGAC 59.940 52.381 15.32 0.00 42.66 4.34
1638 1947 1.060266 CAGACGATAACGACGACGACT 59.940 52.381 15.32 3.12 42.66 4.18
1639 1948 2.279921 CAGACGATAACGACGACGACTA 59.720 50.000 15.32 5.37 42.66 2.59
1641 1950 1.590238 ACGATAACGACGACGACTAGG 59.410 52.381 15.32 2.84 42.66 3.02
1680 1990 5.657826 ATATGCATGGCACTACACAAAAA 57.342 34.783 10.16 0.00 43.04 1.94
1718 2028 4.849383 GTGTGTGCGTGTGTAAATAAATCC 59.151 41.667 0.00 0.00 0.00 3.01
1775 2090 0.816825 CCAGCTGGATGATTCACCGG 60.817 60.000 29.88 0.00 37.39 5.28
1779 2094 0.394216 CTGGATGATTCACCGGGCAA 60.394 55.000 6.32 0.00 0.00 4.52
1780 2095 0.394216 TGGATGATTCACCGGGCAAG 60.394 55.000 6.32 0.00 0.00 4.01
1783 2098 0.396139 ATGATTCACCGGGCAAGCAT 60.396 50.000 6.32 9.58 0.00 3.79
1784 2099 0.254462 TGATTCACCGGGCAAGCATA 59.746 50.000 6.32 0.00 0.00 3.14
1786 2101 0.034574 ATTCACCGGGCAAGCATACA 60.035 50.000 6.32 0.00 0.00 2.29
1795 2110 2.533266 GGCAAGCATACATTCAGTTGC 58.467 47.619 0.00 0.00 39.63 4.17
1808 2123 4.320608 TTCAGTTGCTTGGTCCAAAATC 57.679 40.909 5.64 0.00 0.00 2.17
1868 2183 9.314133 TCTGGAATCTTGTATGCATACTAGTAT 57.686 33.333 32.92 26.01 37.38 2.12
1894 2209 1.746322 TTGTACACGTGGCGGAGGAA 61.746 55.000 21.57 0.00 0.00 3.36
2034 2351 1.072505 GGCCCTGTCTTGTTCCGAA 59.927 57.895 0.00 0.00 0.00 4.30
2046 2363 2.627945 TGTTCCGAATCCGATCTTTGG 58.372 47.619 0.00 0.00 38.22 3.28
2082 2405 0.680280 TACTCTCTCCACACGGGCTC 60.680 60.000 0.00 0.00 36.21 4.70
2107 2434 4.250431 CGCGCCCGCCCAATTAAG 62.250 66.667 0.00 0.00 37.98 1.85
2142 2469 0.591994 TCGAACGAAACACGCGAGAA 60.592 50.000 15.93 0.00 46.94 2.87
2143 2470 0.179307 CGAACGAAACACGCGAGAAG 60.179 55.000 15.93 1.54 46.94 2.85
2144 2471 0.850856 GAACGAAACACGCGAGAAGT 59.149 50.000 15.93 2.29 46.94 3.01
2145 2472 1.257155 GAACGAAACACGCGAGAAGTT 59.743 47.619 15.93 11.04 46.94 2.66
2146 2473 1.283736 ACGAAACACGCGAGAAGTTT 58.716 45.000 15.93 17.33 46.94 2.66
2158 2503 3.871248 GAAGTTTCGTCGGCCCGGT 62.871 63.158 1.90 0.00 0.00 5.28
2213 2558 1.664151 CGGAGCTTCGTGGAATTAACC 59.336 52.381 6.14 0.00 0.00 2.85
2214 2559 1.664151 GGAGCTTCGTGGAATTAACCG 59.336 52.381 0.00 0.00 0.00 4.44
2215 2560 2.344025 GAGCTTCGTGGAATTAACCGT 58.656 47.619 0.00 0.00 0.00 4.83
2240 2585 3.200887 ATCGATCAGCCCGCGACTC 62.201 63.158 8.23 0.00 36.83 3.36
2293 2642 1.555533 GAGCTACTTGCCTACTTGGGT 59.444 52.381 0.00 0.00 44.23 4.51
2429 2785 2.045242 TCGCAGTCCCTACGAGCT 60.045 61.111 0.00 0.00 31.78 4.09
2431 2787 1.094073 TCGCAGTCCCTACGAGCTAC 61.094 60.000 0.00 0.00 31.78 3.58
2433 2789 1.094073 GCAGTCCCTACGAGCTACGA 61.094 60.000 11.64 0.00 45.77 3.43
2434 2790 0.656785 CAGTCCCTACGAGCTACGAC 59.343 60.000 11.64 0.53 45.77 4.34
2435 2791 0.463474 AGTCCCTACGAGCTACGACC 60.463 60.000 11.64 0.00 45.77 4.79
2441 2797 4.554363 CGAGCTACGACCCGGCTG 62.554 72.222 0.00 0.00 45.77 4.85
2554 2918 2.661866 GTGCTGCGTGAAGACGGT 60.662 61.111 0.00 0.00 46.20 4.83
2557 2921 1.372499 GCTGCGTGAAGACGGTACA 60.372 57.895 0.00 0.00 46.20 2.90
2572 2936 2.938086 TACAAGCGAGGCGGCAGAA 61.938 57.895 13.08 0.00 34.64 3.02
2576 2940 2.512515 GCGAGGCGGCAGAAGATT 60.513 61.111 13.08 0.00 0.00 2.40
2627 2996 4.164664 CCGCTCGCCACGTACGTA 62.165 66.667 22.34 4.29 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.665559 AGGTGATTTCTAGTGCAAACTATTCAA 59.334 33.333 0.00 0.00 0.00 2.69
23 24 7.119699 CAGGTGATTTCTAGTGCAAACTATTCA 59.880 37.037 0.00 0.00 0.00 2.57
26 27 6.595716 GTCAGGTGATTTCTAGTGCAAACTAT 59.404 38.462 0.00 0.00 0.00 2.12
27 28 5.932303 GTCAGGTGATTTCTAGTGCAAACTA 59.068 40.000 0.00 0.00 0.00 2.24
28 29 4.757149 GTCAGGTGATTTCTAGTGCAAACT 59.243 41.667 0.00 0.00 0.00 2.66
29 30 4.515191 TGTCAGGTGATTTCTAGTGCAAAC 59.485 41.667 0.00 0.00 0.00 2.93
30 31 4.713553 TGTCAGGTGATTTCTAGTGCAAA 58.286 39.130 0.00 0.00 0.00 3.68
31 32 4.350368 TGTCAGGTGATTTCTAGTGCAA 57.650 40.909 0.00 0.00 0.00 4.08
32 33 4.350368 TTGTCAGGTGATTTCTAGTGCA 57.650 40.909 0.00 0.00 0.00 4.57
33 34 5.886960 ATTTGTCAGGTGATTTCTAGTGC 57.113 39.130 0.00 0.00 0.00 4.40
35 36 7.112122 TGCATATTTGTCAGGTGATTTCTAGT 58.888 34.615 0.00 0.00 0.00 2.57
36 37 7.558161 TGCATATTTGTCAGGTGATTTCTAG 57.442 36.000 0.00 0.00 0.00 2.43
37 38 7.557358 ACATGCATATTTGTCAGGTGATTTCTA 59.443 33.333 0.00 0.00 0.00 2.10
38 39 6.379133 ACATGCATATTTGTCAGGTGATTTCT 59.621 34.615 0.00 0.00 0.00 2.52
40 41 6.534475 ACATGCATATTTGTCAGGTGATTT 57.466 33.333 0.00 0.00 0.00 2.17
41 42 7.654568 CATACATGCATATTTGTCAGGTGATT 58.345 34.615 0.00 0.00 30.54 2.57
42 43 7.210718 CATACATGCATATTTGTCAGGTGAT 57.789 36.000 0.00 0.00 30.54 3.06
43 44 6.622833 CATACATGCATATTTGTCAGGTGA 57.377 37.500 0.00 0.00 30.54 4.02
60 61 8.296713 GGATACGACCAAAAATATTGCATACAT 58.703 33.333 0.00 0.00 0.00 2.29
63 64 7.809546 TGGATACGACCAAAAATATTGCATA 57.190 32.000 0.00 0.00 36.96 3.14
65 66 6.516739 TTGGATACGACCAAAAATATTGCA 57.483 33.333 9.96 0.00 45.36 4.08
75 76 5.422970 ACATAACTACCTTGGATACGACCAA 59.577 40.000 11.35 11.35 46.02 3.67
76 77 4.957954 ACATAACTACCTTGGATACGACCA 59.042 41.667 0.00 0.00 42.51 4.02
77 78 5.508657 GGACATAACTACCTTGGATACGACC 60.509 48.000 0.00 0.00 42.51 4.79
78 79 5.301298 AGGACATAACTACCTTGGATACGAC 59.699 44.000 0.00 0.00 42.51 4.34
79 80 5.452255 AGGACATAACTACCTTGGATACGA 58.548 41.667 0.00 0.00 42.51 3.43
80 81 5.301045 TGAGGACATAACTACCTTGGATACG 59.699 44.000 0.00 0.00 34.54 3.06
81 82 6.726490 TGAGGACATAACTACCTTGGATAC 57.274 41.667 0.00 0.00 33.89 2.24
82 83 7.073208 TGATGAGGACATAACTACCTTGGATA 58.927 38.462 0.00 0.00 36.82 2.59
83 84 5.905331 TGATGAGGACATAACTACCTTGGAT 59.095 40.000 0.00 0.00 36.82 3.41
84 85 5.277250 TGATGAGGACATAACTACCTTGGA 58.723 41.667 0.00 0.00 36.82 3.53
101 102 7.176165 ACATAATATGCATTCCACCTTGATGAG 59.824 37.037 3.54 0.00 0.00 2.90
102 103 7.005902 ACATAATATGCATTCCACCTTGATGA 58.994 34.615 3.54 0.00 0.00 2.92
103 104 7.223260 ACATAATATGCATTCCACCTTGATG 57.777 36.000 3.54 0.00 0.00 3.07
104 105 7.613022 CCTACATAATATGCATTCCACCTTGAT 59.387 37.037 3.54 0.00 0.00 2.57
105 106 6.942005 CCTACATAATATGCATTCCACCTTGA 59.058 38.462 3.54 0.00 0.00 3.02
106 107 6.942005 TCCTACATAATATGCATTCCACCTTG 59.058 38.462 3.54 0.00 0.00 3.61
107 108 7.090319 TCCTACATAATATGCATTCCACCTT 57.910 36.000 3.54 0.00 0.00 3.50
175 176 9.290483 GAAATATCGGAACCATTTCTTTTCTTC 57.710 33.333 12.28 0.00 36.29 2.87
251 253 7.555914 TGCCTGCTAGTATATGTCATTTGAAAA 59.444 33.333 0.00 0.00 0.00 2.29
252 254 7.053498 TGCCTGCTAGTATATGTCATTTGAAA 58.947 34.615 0.00 0.00 0.00 2.69
272 274 6.857777 TTTAAAATGTTTGTCCATTGCCTG 57.142 33.333 0.00 0.00 35.30 4.85
313 315 4.930405 CGGAAGTTAAGAGAGGGAACTTTC 59.070 45.833 1.18 0.00 42.10 2.62
348 350 9.362539 AGAGATTACAATTGCATCAAAATTCAC 57.637 29.630 16.69 0.00 0.00 3.18
383 385 4.513318 GGTCTAGCATTATTGTTCTCAGCC 59.487 45.833 0.00 0.00 0.00 4.85
433 435 8.841757 AGGGGCCCAATTATAGTTTAAAAATTT 58.158 29.630 27.72 0.00 0.00 1.82
435 437 8.400619 AAGGGGCCCAATTATAGTTTAAAAAT 57.599 30.769 27.72 0.00 0.00 1.82
454 456 4.536765 TGGAAATAGAGAAATGAAGGGGC 58.463 43.478 0.00 0.00 0.00 5.80
455 457 5.760131 ACTGGAAATAGAGAAATGAAGGGG 58.240 41.667 0.00 0.00 0.00 4.79
477 479 6.515272 ACAAATTGGTGTGAGGATTATGAC 57.485 37.500 0.00 0.00 0.00 3.06
486 488 6.718454 TTTTCACAAACAAATTGGTGTGAG 57.282 33.333 23.89 2.08 42.95 3.51
537 539 5.927115 GTCTTTCACCAATTCTTAGTCGAGT 59.073 40.000 0.00 0.00 0.00 4.18
574 802 1.670791 AAACGGCAAAGAAAGGACGA 58.329 45.000 0.00 0.00 37.89 4.20
614 842 1.663702 CGAACCTTTGCGACCGTCT 60.664 57.895 0.00 0.00 0.00 4.18
798 1047 1.612463 CGGGGAGGTAGAAATAGACGG 59.388 57.143 0.00 0.00 0.00 4.79
801 1050 1.713297 GGCGGGGAGGTAGAAATAGA 58.287 55.000 0.00 0.00 0.00 1.98
842 1091 2.227089 ATCGCGGGGAGTGAACTGAC 62.227 60.000 6.13 0.00 43.33 3.51
925 1181 0.803117 CGAGCAGAGAACAGACGGTA 59.197 55.000 0.00 0.00 0.00 4.02
933 1189 1.276415 GCACAGATCGAGCAGAGAAC 58.724 55.000 2.38 0.00 0.00 3.01
955 1211 3.128068 CCACCTAATTAACTTGTTCGCCC 59.872 47.826 0.00 0.00 0.00 6.13
956 1212 3.427098 GCCACCTAATTAACTTGTTCGCC 60.427 47.826 0.00 0.00 0.00 5.54
998 1269 1.437573 GATGAGTCGTCGGCCATGA 59.562 57.895 2.24 0.00 0.00 3.07
1071 1342 0.883814 GCATGCGCTAGCCTCTCAAT 60.884 55.000 9.73 0.00 44.33 2.57
1242 1514 0.900182 ATGTGAGAGTGGACGGAGCA 60.900 55.000 0.00 0.00 0.00 4.26
1403 1677 4.627035 TGACATGCTGAAGTTACAATCTCG 59.373 41.667 0.00 0.00 0.00 4.04
1413 1687 5.106396 GCTAAACAGATTGACATGCTGAAGT 60.106 40.000 10.90 0.00 33.94 3.01
1604 1913 0.108898 CGTCTGAGCTCCTTGAGGTG 60.109 60.000 12.15 0.00 40.67 4.00
1625 1934 1.369091 GCCCCTAGTCGTCGTCGTTA 61.369 60.000 1.33 0.00 38.33 3.18
1635 1944 1.536662 ATGGATCCGGCCCCTAGTC 60.537 63.158 7.39 0.00 0.00 2.59
1637 1946 3.072476 CATGGATCCGGCCCCTAG 58.928 66.667 7.39 2.71 0.00 3.02
1638 1947 3.249189 GCATGGATCCGGCCCCTA 61.249 66.667 15.46 0.00 0.00 3.53
1641 1950 0.546122 TATATGCATGGATCCGGCCC 59.454 55.000 21.50 0.13 0.00 5.80
1680 1990 7.710907 ACACGCACACACTCTCATATATTTTAT 59.289 33.333 0.00 0.00 0.00 1.40
1694 2004 5.334569 GGATTTATTTACACACGCACACACT 60.335 40.000 0.00 0.00 0.00 3.55
1702 2012 5.277345 GCTAGCTGGGATTTATTTACACACG 60.277 44.000 7.70 0.00 0.00 4.49
1769 2084 0.034574 AATGTATGCTTGCCCGGTGA 60.035 50.000 0.00 0.00 0.00 4.02
1775 2090 2.165030 AGCAACTGAATGTATGCTTGCC 59.835 45.455 0.00 0.00 46.36 4.52
1780 2095 3.428045 GGACCAAGCAACTGAATGTATGC 60.428 47.826 0.00 0.00 39.06 3.14
1783 2098 3.500448 TGGACCAAGCAACTGAATGTA 57.500 42.857 0.00 0.00 0.00 2.29
1784 2099 2.363306 TGGACCAAGCAACTGAATGT 57.637 45.000 0.00 0.00 0.00 2.71
1786 2101 4.559300 CGATTTTGGACCAAGCAACTGAAT 60.559 41.667 7.07 2.45 0.00 2.57
1795 2110 6.446318 TGAATCTTTTCGATTTTGGACCAAG 58.554 36.000 7.07 0.00 42.31 3.61
1808 2123 5.814783 GATTGGTGATCCTGAATCTTTTCG 58.185 41.667 0.00 0.00 35.24 3.46
1821 2136 0.815615 GCTCCGGTGGATTGGTGATC 60.816 60.000 0.00 0.00 0.00 2.92
1868 2183 2.622965 CCACGTGTACAACATGGCA 58.377 52.632 15.65 0.00 39.36 4.92
1887 2202 1.076332 GACGTCCACATTTTCCTCCG 58.924 55.000 3.51 0.00 0.00 4.63
1894 2209 1.189524 TCCTCCGGACGTCCACATTT 61.190 55.000 32.80 0.00 35.14 2.32
2034 2351 1.227383 GCCACCCCAAAGATCGGAT 59.773 57.895 0.00 0.00 0.00 4.18
2046 2363 2.998670 GAGTACGTAGAAAAAGCCACCC 59.001 50.000 0.00 0.00 0.00 4.61
2098 2425 0.742990 TCGCCGACAGCTTAATTGGG 60.743 55.000 0.00 0.00 40.39 4.12
2099 2426 1.261619 GATCGCCGACAGCTTAATTGG 59.738 52.381 0.00 0.00 40.39 3.16
2101 2428 2.309528 TGATCGCCGACAGCTTAATT 57.690 45.000 0.00 0.00 40.39 1.40
2102 2429 2.309528 TTGATCGCCGACAGCTTAAT 57.690 45.000 0.00 0.00 40.39 1.40
2104 2431 2.201732 GATTTGATCGCCGACAGCTTA 58.798 47.619 0.00 0.00 40.39 3.09
2105 2432 1.009829 GATTTGATCGCCGACAGCTT 58.990 50.000 0.00 0.00 40.39 3.74
2106 2433 1.148157 CGATTTGATCGCCGACAGCT 61.148 55.000 0.00 0.00 46.55 4.24
2107 2434 1.273887 CGATTTGATCGCCGACAGC 59.726 57.895 0.00 0.00 46.55 4.40
2142 2469 4.675029 CACCGGGCCGACGAAACT 62.675 66.667 30.79 0.00 35.47 2.66
2158 2503 2.338620 CGCAGACGTCCAACTCCA 59.661 61.111 13.01 0.00 33.53 3.86
2194 2539 1.664151 CGGTTAATTCCACGAAGCTCC 59.336 52.381 0.00 0.00 0.00 4.70
2208 2553 1.727511 ATCGATCGGGCGACGGTTAA 61.728 55.000 16.41 0.00 43.79 2.01
2209 2554 2.121564 GATCGATCGGGCGACGGTTA 62.122 60.000 16.41 0.00 43.79 2.85
2210 2555 3.480225 GATCGATCGGGCGACGGTT 62.480 63.158 16.41 0.00 43.79 4.44
2211 2556 3.962421 GATCGATCGGGCGACGGT 61.962 66.667 16.41 0.00 43.79 4.83
2213 2558 2.427575 CTGATCGATCGGGCGACG 60.428 66.667 24.09 0.00 43.79 5.12
2214 2559 2.731348 GCTGATCGATCGGGCGAC 60.731 66.667 30.46 13.76 43.79 5.19
2215 2560 3.978491 GGCTGATCGATCGGGCGA 61.978 66.667 36.00 12.82 46.64 5.54
2293 2642 1.616865 CGCAGGGACGGAATAATCCTA 59.383 52.381 0.00 0.00 44.17 2.94
2394 2749 1.948145 CGACCTGAAGCCGAGTATAGT 59.052 52.381 0.00 0.00 0.00 2.12
2435 2791 4.760047 CGTTCCTGTCCCAGCCGG 62.760 72.222 0.00 0.00 0.00 6.13
2471 2827 4.207841 GCTCCGTGTACGTAAAATATCCAC 59.792 45.833 0.00 0.00 37.74 4.02
2547 2911 1.080025 GCCTCGCTTGTACCGTCTT 60.080 57.895 0.00 0.00 0.00 3.01
2552 2916 4.752879 TGCCGCCTCGCTTGTACC 62.753 66.667 0.00 0.00 0.00 3.34
2554 2918 2.835701 CTTCTGCCGCCTCGCTTGTA 62.836 60.000 0.00 0.00 0.00 2.41
2557 2921 2.527951 AATCTTCTGCCGCCTCGCTT 62.528 55.000 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.