Multiple sequence alignment - TraesCS4D01G056900

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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 TraesCS4D01G056900 chr4D 100.000 3223 0 0 1 3223 32062441 32065663 0.000000e+00 5952
1 TraesCS4D01G056900 chr4B 91.822 3228 135 57 80 3223 46220533 46223715 0.000000e+00 4379
2 TraesCS4D01G056900 chr4A 91.489 3149 140 60 129 3223 570912879 570909805 0.000000e+00 4213
3 TraesCS4D01G056900 chr4A 91.579 190 16 0 133 322 570913615 570913426 2.470000e-66 263


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 TraesCS4D01G056900 chr4D 32062441 32065663 3222 False 5952 5952 100.000 1 3223 1 chr4D.!!$F1 3222
1 TraesCS4D01G056900 chr4B 46220533 46223715 3182 False 4379 4379 91.822 80 3223 1 chr4B.!!$F1 3143
2 TraesCS4D01G056900 chr4A 570909805 570913615 3810 True 2238 4213 91.534 129 3223 2 chr4A.!!$R1 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
77 78 0.439985 CCTCACGCACTCAAACATCG 59.560 55.0 0.0 0.0 0.0 3.84 F
366 978 1.039068 CCCCAGCATTTCACACAACA 58.961 50.0 0.0 0.0 0.0 3.33 F
1104 1751 0.751643 GGTGGCTGACTGGTTGTTGT 60.752 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1690 1.375396 CACCCGACGCCATCAGAAA 60.375 57.895 0.00 0.00 0.00 2.52 R
2132 2832 1.334869 CCGGCCTGCAACAGATTAATC 59.665 52.381 7.41 7.41 32.44 1.75 R
2917 3654 0.903454 ACAAGAGGGTACAGGTCGGG 60.903 60.000 0.00 0.00 0.00 5.14 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 3.520569 TGGTTTTGTTTTTGCTGAGAGC 58.479 40.909 0.00 0.00 42.82 4.09
37 38 2.688507 GAGAGCACTCAAATGTCCGAA 58.311 47.619 6.25 0.00 42.21 4.30
40 41 2.548057 GAGCACTCAAATGTCCGAACAA 59.452 45.455 0.00 0.00 39.30 2.83
41 42 2.549754 AGCACTCAAATGTCCGAACAAG 59.450 45.455 0.00 0.00 39.30 3.16
42 43 2.918131 GCACTCAAATGTCCGAACAAGC 60.918 50.000 0.00 0.00 39.30 4.01
43 44 2.549754 CACTCAAATGTCCGAACAAGCT 59.450 45.455 0.00 0.00 39.30 3.74
44 45 3.745975 CACTCAAATGTCCGAACAAGCTA 59.254 43.478 0.00 0.00 39.30 3.32
46 47 4.819630 ACTCAAATGTCCGAACAAGCTAAA 59.180 37.500 0.00 0.00 39.30 1.85
48 49 6.016276 ACTCAAATGTCCGAACAAGCTAAAAT 60.016 34.615 0.00 0.00 39.30 1.82
49 50 6.744112 TCAAATGTCCGAACAAGCTAAAATT 58.256 32.000 0.00 0.00 39.30 1.82
50 51 6.861055 TCAAATGTCCGAACAAGCTAAAATTC 59.139 34.615 0.00 0.00 39.30 2.17
51 52 5.957842 ATGTCCGAACAAGCTAAAATTCA 57.042 34.783 0.00 0.00 39.30 2.57
52 53 5.103290 TGTCCGAACAAGCTAAAATTCAC 57.897 39.130 0.00 0.00 30.70 3.18
53 54 4.576873 TGTCCGAACAAGCTAAAATTCACA 59.423 37.500 0.00 0.00 30.70 3.58
54 55 4.909880 GTCCGAACAAGCTAAAATTCACAC 59.090 41.667 0.00 0.00 0.00 3.82
57 58 4.319190 CGAACAAGCTAAAATTCACACGGA 60.319 41.667 0.00 0.00 0.00 4.69
58 59 4.483476 ACAAGCTAAAATTCACACGGAC 57.517 40.909 0.00 0.00 0.00 4.79
60 61 3.418684 AGCTAAAATTCACACGGACCT 57.581 42.857 0.00 0.00 0.00 3.85
61 62 3.335579 AGCTAAAATTCACACGGACCTC 58.664 45.455 0.00 0.00 0.00 3.85
62 63 3.071479 GCTAAAATTCACACGGACCTCA 58.929 45.455 0.00 0.00 0.00 3.86
63 64 3.120304 GCTAAAATTCACACGGACCTCAC 60.120 47.826 0.00 0.00 0.00 3.51
64 65 1.508632 AAATTCACACGGACCTCACG 58.491 50.000 0.00 0.00 37.36 4.35
65 66 0.949105 AATTCACACGGACCTCACGC 60.949 55.000 0.00 0.00 34.00 5.34
67 68 2.964438 TTCACACGGACCTCACGCAC 62.964 60.000 0.00 0.00 34.00 5.34
68 69 3.224324 ACACGGACCTCACGCACT 61.224 61.111 0.00 0.00 34.00 4.40
69 70 2.430921 CACGGACCTCACGCACTC 60.431 66.667 0.00 0.00 34.00 3.51
70 71 2.910479 ACGGACCTCACGCACTCA 60.910 61.111 0.00 0.00 34.00 3.41
71 72 2.338620 CGGACCTCACGCACTCAA 59.661 61.111 0.00 0.00 0.00 3.02
72 73 1.300620 CGGACCTCACGCACTCAAA 60.301 57.895 0.00 0.00 0.00 2.69
73 74 1.557443 CGGACCTCACGCACTCAAAC 61.557 60.000 0.00 0.00 0.00 2.93
74 75 0.531974 GGACCTCACGCACTCAAACA 60.532 55.000 0.00 0.00 0.00 2.83
76 77 1.461127 GACCTCACGCACTCAAACATC 59.539 52.381 0.00 0.00 0.00 3.06
77 78 0.439985 CCTCACGCACTCAAACATCG 59.560 55.000 0.00 0.00 0.00 3.84
82 83 2.666022 CACGCACTCAAACATCGTATGA 59.334 45.455 2.48 0.00 0.00 2.15
83 84 2.923655 ACGCACTCAAACATCGTATGAG 59.076 45.455 0.00 0.00 44.77 2.90
85 86 2.932614 GCACTCAAACATCGTATGAGCT 59.067 45.455 2.13 0.00 43.41 4.09
86 87 3.000724 GCACTCAAACATCGTATGAGCTC 59.999 47.826 6.82 6.82 43.41 4.09
87 88 3.241553 CACTCAAACATCGTATGAGCTCG 59.758 47.826 9.64 0.00 43.41 5.03
88 89 2.791560 CTCAAACATCGTATGAGCTCGG 59.208 50.000 9.64 0.00 34.72 4.63
89 90 1.860950 CAAACATCGTATGAGCTCGGG 59.139 52.381 9.64 0.00 0.00 5.14
90 91 1.112113 AACATCGTATGAGCTCGGGT 58.888 50.000 9.64 0.00 0.00 5.28
91 92 1.112113 ACATCGTATGAGCTCGGGTT 58.888 50.000 9.64 0.00 0.00 4.11
92 93 1.067212 ACATCGTATGAGCTCGGGTTC 59.933 52.381 9.64 0.00 0.00 3.62
95 96 1.546923 TCGTATGAGCTCGGGTTCAAA 59.453 47.619 5.74 0.00 36.35 2.69
96 97 2.028839 TCGTATGAGCTCGGGTTCAAAA 60.029 45.455 5.74 0.00 36.35 2.44
98 99 3.374058 CGTATGAGCTCGGGTTCAAAAAT 59.626 43.478 5.74 0.00 36.35 1.82
99 100 3.855689 ATGAGCTCGGGTTCAAAAATG 57.144 42.857 5.74 0.00 36.35 2.32
101 102 3.745799 TGAGCTCGGGTTCAAAAATGTA 58.254 40.909 9.64 0.00 29.96 2.29
102 103 4.331968 TGAGCTCGGGTTCAAAAATGTAT 58.668 39.130 9.64 0.00 29.96 2.29
104 105 6.119536 TGAGCTCGGGTTCAAAAATGTATAT 58.880 36.000 9.64 0.00 29.96 0.86
105 106 6.601613 TGAGCTCGGGTTCAAAAATGTATATT 59.398 34.615 9.64 0.00 29.96 1.28
106 107 7.027778 AGCTCGGGTTCAAAAATGTATATTC 57.972 36.000 0.00 0.00 0.00 1.75
108 109 6.238266 GCTCGGGTTCAAAAATGTATATTCGA 60.238 38.462 0.00 0.00 0.00 3.71
109 110 7.612668 TCGGGTTCAAAAATGTATATTCGAA 57.387 32.000 0.00 0.00 0.00 3.71
110 111 8.041829 TCGGGTTCAAAAATGTATATTCGAAA 57.958 30.769 0.00 0.00 0.00 3.46
111 112 7.964011 TCGGGTTCAAAAATGTATATTCGAAAC 59.036 33.333 0.00 0.00 0.00 2.78
112 113 7.219344 CGGGTTCAAAAATGTATATTCGAAACC 59.781 37.037 0.00 12.38 35.48 3.27
113 114 8.248253 GGGTTCAAAAATGTATATTCGAAACCT 58.752 33.333 0.00 0.00 35.69 3.50
114 115 9.634163 GGTTCAAAAATGTATATTCGAAACCTT 57.366 29.630 0.00 0.00 30.22 3.50
129 130 7.972832 TCGAAACCTTACATTCTTTGTATGT 57.027 32.000 0.00 0.00 40.46 2.29
130 131 9.491675 TTCGAAACCTTACATTCTTTGTATGTA 57.508 29.630 0.00 0.00 40.46 2.29
131 132 9.146984 TCGAAACCTTACATTCTTTGTATGTAG 57.853 33.333 0.00 0.00 40.46 2.74
189 799 7.715657 TCATATCACATACAAAAAGGATTGGC 58.284 34.615 0.00 0.00 34.56 4.52
194 804 5.933463 CACATACAAAAAGGATTGGCACATT 59.067 36.000 0.00 0.00 39.30 2.71
222 832 4.039124 TCTGCTTCCGATATGCACAATCTA 59.961 41.667 8.74 0.00 34.74 1.98
223 833 4.702831 TGCTTCCGATATGCACAATCTAA 58.297 39.130 8.74 3.55 33.60 2.10
242 852 9.657419 CAATCTAAAAATAAAATCCAAGTGGCT 57.343 29.630 0.00 0.00 34.44 4.75
328 940 2.225068 AGCGACAAGAACCCATATCG 57.775 50.000 0.00 0.00 0.00 2.92
366 978 1.039068 CCCCAGCATTTCACACAACA 58.961 50.000 0.00 0.00 0.00 3.33
368 980 2.353011 CCCCAGCATTTCACACAACATC 60.353 50.000 0.00 0.00 0.00 3.06
399 1012 3.018856 TCCATTGACATCACCATGAAGC 58.981 45.455 0.00 0.00 33.72 3.86
453 1066 1.160329 AGCCAATACCGCAATCGCTC 61.160 55.000 0.00 0.00 35.30 5.03
462 1075 1.590259 GCAATCGCTCGAGGGAGAC 60.590 63.158 31.94 21.31 43.27 3.36
483 1096 4.615949 ACAGCGAGAGAGCAATAATGTAG 58.384 43.478 0.00 0.00 40.15 2.74
572 1200 3.669036 GACTTGAGCGAGCGAGCGA 62.669 63.158 1.41 0.00 43.00 4.93
573 1201 2.948648 CTTGAGCGAGCGAGCGAG 60.949 66.667 1.41 0.00 43.00 5.03
574 1202 4.482684 TTGAGCGAGCGAGCGAGG 62.483 66.667 1.41 0.00 43.00 4.63
773 1403 1.703411 CTGACCCATCTCTCTCCCTC 58.297 60.000 0.00 0.00 0.00 4.30
778 1408 1.203050 CCCATCTCTCTCCCTCTCTCC 60.203 61.905 0.00 0.00 0.00 3.71
851 1491 2.264813 CTGCATTGCTATGTGTTTGCC 58.735 47.619 10.49 0.00 34.12 4.52
893 1533 3.165124 TGTTTTCGTGCGTGTTTTTCTC 58.835 40.909 0.00 0.00 0.00 2.87
904 1544 4.641954 CGTGTTTTTCTCATCAGGATTCG 58.358 43.478 0.00 0.00 0.00 3.34
914 1554 1.815421 CAGGATTCGGGCTGTTCGG 60.815 63.158 0.00 0.00 0.00 4.30
924 1567 1.664965 GCTGTTCGGTCGAGCTTGT 60.665 57.895 13.48 0.00 0.00 3.16
925 1568 1.891060 GCTGTTCGGTCGAGCTTGTG 61.891 60.000 13.48 0.00 0.00 3.33
956 1599 1.167851 CTGCGATCTTTGGCTTTGGA 58.832 50.000 0.00 0.00 0.00 3.53
1043 1690 5.450412 CCAATATGGTAATTTGCTGCTCGTT 60.450 40.000 0.00 0.00 31.35 3.85
1051 1698 2.975410 TTGCTGCTCGTTTTCTGATG 57.025 45.000 0.00 0.00 0.00 3.07
1104 1751 0.751643 GGTGGCTGACTGGTTGTTGT 60.752 55.000 0.00 0.00 0.00 3.32
1105 1752 1.102978 GTGGCTGACTGGTTGTTGTT 58.897 50.000 0.00 0.00 0.00 2.83
1106 1753 1.065551 GTGGCTGACTGGTTGTTGTTC 59.934 52.381 0.00 0.00 0.00 3.18
1391 2047 2.419198 CATCCTCTCCTTCGGCGG 59.581 66.667 7.21 0.00 0.00 6.13
1392 2048 3.541713 ATCCTCTCCTTCGGCGGC 61.542 66.667 7.21 0.00 0.00 6.53
1395 2051 4.821589 CTCTCCTTCGGCGGCCAC 62.822 72.222 20.71 0.00 0.00 5.01
1530 2204 2.669569 TTCCAGCAGGTCAAGCGC 60.670 61.111 0.00 0.00 37.01 5.92
1614 2288 3.945434 CACATCATGGCCGAGCGC 61.945 66.667 0.00 0.00 0.00 5.92
2128 2824 8.498054 AATTAATTACATGGTCTCACTCACTG 57.502 34.615 0.00 0.00 0.00 3.66
2132 2832 2.235650 ACATGGTCTCACTCACTGATGG 59.764 50.000 0.00 0.00 0.00 3.51
2142 2842 6.382282 TCTCACTCACTGATGGATTAATCTGT 59.618 38.462 14.95 4.34 38.75 3.41
2271 2974 7.588497 ATTTAGAACTTTGGCTTCTGTTTCT 57.412 32.000 0.00 0.00 0.00 2.52
2326 3030 4.043561 TGGGGCTAATGAGTTTTAGGTTCA 59.956 41.667 0.00 0.00 31.19 3.18
2355 3059 2.103771 TGGTGCTTCTGATGATAGCTCC 59.896 50.000 11.39 11.39 44.65 4.70
2437 3142 2.882137 GGGTGCAGCAAAAACACTAGTA 59.118 45.455 19.06 0.00 34.70 1.82
2484 3191 5.925506 TTTGCATGGTTTGATCAGATCAT 57.074 34.783 14.11 6.18 39.39 2.45
2513 3220 2.240160 TCCTGGGAGAGAGTAGAGTGAC 59.760 54.545 0.00 0.00 0.00 3.67
2600 3307 5.662657 CCCATTTTTCATTTCTCCCCTACAT 59.337 40.000 0.00 0.00 0.00 2.29
2643 3352 2.091102 TTTTTCGACGAGAGGCCGGT 62.091 55.000 1.90 0.00 33.32 5.28
2644 3353 2.091102 TTTTCGACGAGAGGCCGGTT 62.091 55.000 1.90 0.00 33.32 4.44
2675 3386 2.368311 TCAAACCCAAACACCTACCC 57.632 50.000 0.00 0.00 0.00 3.69
2683 3394 0.184211 AAACACCTACCCTTTGCCGT 59.816 50.000 0.00 0.00 0.00 5.68
2709 3425 0.251165 AAATCCCACCACTGTTCCCG 60.251 55.000 0.00 0.00 0.00 5.14
2915 3652 5.426689 AACAGGATCAAGATTGTAGCTCA 57.573 39.130 0.00 0.00 0.00 4.26
2916 3653 5.021033 ACAGGATCAAGATTGTAGCTCAG 57.979 43.478 0.00 0.00 0.00 3.35
2917 3654 3.808726 CAGGATCAAGATTGTAGCTCAGC 59.191 47.826 0.00 0.00 0.00 4.26
2918 3655 3.137533 GGATCAAGATTGTAGCTCAGCC 58.862 50.000 0.00 0.00 0.00 4.85
2919 3656 2.698855 TCAAGATTGTAGCTCAGCCC 57.301 50.000 0.00 0.00 0.00 5.19
2922 3659 0.461961 AGATTGTAGCTCAGCCCGAC 59.538 55.000 0.00 0.00 0.00 4.79
2929 3666 2.893398 CTCAGCCCGACCTGTACC 59.107 66.667 0.00 0.00 34.47 3.34
3114 3855 6.604735 AAACGATCTTGTATATTGTCCTGC 57.395 37.500 0.00 0.00 0.00 4.85
3115 3856 4.632153 ACGATCTTGTATATTGTCCTGCC 58.368 43.478 0.00 0.00 0.00 4.85
3117 3858 4.687948 CGATCTTGTATATTGTCCTGCCTG 59.312 45.833 0.00 0.00 0.00 4.85
3118 3859 4.422073 TCTTGTATATTGTCCTGCCTGG 57.578 45.455 0.00 0.00 37.10 4.45
3156 3897 9.778741 ATACTATGTATTACCTGTCCACAAATG 57.221 33.333 0.00 0.00 0.00 2.32
3158 3899 8.325787 ACTATGTATTACCTGTCCACAAATGAA 58.674 33.333 0.00 0.00 0.00 2.57
3159 3900 9.342308 CTATGTATTACCTGTCCACAAATGAAT 57.658 33.333 0.00 0.00 0.00 2.57
3185 3929 1.348036 AGATTATAAGGGCGGCACTCC 59.652 52.381 4.62 0.00 0.00 3.85
3195 3939 0.598065 GCGGCACTCCTTTGTTCATT 59.402 50.000 0.00 0.00 0.00 2.57
3205 3949 7.225341 GCACTCCTTTGTTCATTCAAAAGAATT 59.775 33.333 0.00 0.00 36.96 2.17
3215 3959 9.829637 GTTCATTCAAAAGAATTGTTAAACGAC 57.170 29.630 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.925392 TTGTTCGGACATTTGAGTGCTCTCA 62.925 44.000 14.30 14.30 40.96 3.27
19 20 2.143122 TGTTCGGACATTTGAGTGCTC 58.857 47.619 0.00 0.00 0.00 4.26
21 22 2.918131 GCTTGTTCGGACATTTGAGTGC 60.918 50.000 0.00 0.00 35.29 4.40
22 23 2.549754 AGCTTGTTCGGACATTTGAGTG 59.450 45.455 0.00 0.00 35.29 3.51
23 24 2.851195 AGCTTGTTCGGACATTTGAGT 58.149 42.857 0.00 0.00 35.29 3.41
24 25 5.356882 TTTAGCTTGTTCGGACATTTGAG 57.643 39.130 0.00 0.00 35.29 3.02
25 26 5.759506 TTTTAGCTTGTTCGGACATTTGA 57.240 34.783 0.00 0.00 35.29 2.69
26 27 6.640499 TGAATTTTAGCTTGTTCGGACATTTG 59.360 34.615 0.00 0.00 35.29 2.32
27 28 6.640907 GTGAATTTTAGCTTGTTCGGACATTT 59.359 34.615 0.00 0.00 35.29 2.32
28 29 6.149633 GTGAATTTTAGCTTGTTCGGACATT 58.850 36.000 0.00 0.00 35.29 2.71
31 32 4.909880 GTGTGAATTTTAGCTTGTTCGGAC 59.090 41.667 0.00 0.00 0.00 4.79
34 35 3.906008 CCGTGTGAATTTTAGCTTGTTCG 59.094 43.478 0.00 0.00 0.00 3.95
35 36 4.909880 GTCCGTGTGAATTTTAGCTTGTTC 59.090 41.667 0.00 0.00 0.00 3.18
37 38 3.252458 GGTCCGTGTGAATTTTAGCTTGT 59.748 43.478 0.00 0.00 0.00 3.16
40 41 3.244422 TGAGGTCCGTGTGAATTTTAGCT 60.244 43.478 0.00 0.00 0.00 3.32
41 42 3.071479 TGAGGTCCGTGTGAATTTTAGC 58.929 45.455 0.00 0.00 0.00 3.09
42 43 3.122948 CGTGAGGTCCGTGTGAATTTTAG 59.877 47.826 0.00 0.00 0.00 1.85
43 44 3.061322 CGTGAGGTCCGTGTGAATTTTA 58.939 45.455 0.00 0.00 0.00 1.52
44 45 1.871039 CGTGAGGTCCGTGTGAATTTT 59.129 47.619 0.00 0.00 0.00 1.82
46 47 0.949105 GCGTGAGGTCCGTGTGAATT 60.949 55.000 0.00 0.00 0.00 2.17
48 49 2.028484 GCGTGAGGTCCGTGTGAA 59.972 61.111 0.00 0.00 0.00 3.18
49 50 3.220658 TGCGTGAGGTCCGTGTGA 61.221 61.111 0.00 0.00 0.00 3.58
50 51 3.036084 GTGCGTGAGGTCCGTGTG 61.036 66.667 0.00 0.00 0.00 3.82
51 52 3.208884 GAGTGCGTGAGGTCCGTGT 62.209 63.158 0.00 0.00 0.00 4.49
52 53 2.430921 GAGTGCGTGAGGTCCGTG 60.431 66.667 0.00 0.00 0.00 4.94
53 54 2.023414 TTTGAGTGCGTGAGGTCCGT 62.023 55.000 0.00 0.00 0.00 4.69
54 55 1.300620 TTTGAGTGCGTGAGGTCCG 60.301 57.895 0.00 0.00 0.00 4.79
57 58 1.512926 GATGTTTGAGTGCGTGAGGT 58.487 50.000 0.00 0.00 0.00 3.85
58 59 0.439985 CGATGTTTGAGTGCGTGAGG 59.560 55.000 0.00 0.00 0.00 3.86
60 61 2.425578 TACGATGTTTGAGTGCGTGA 57.574 45.000 0.00 0.00 36.51 4.35
61 62 2.666022 TCATACGATGTTTGAGTGCGTG 59.334 45.455 0.00 0.00 36.51 5.34
62 63 2.923655 CTCATACGATGTTTGAGTGCGT 59.076 45.455 8.62 0.00 37.04 5.24
63 64 2.285256 GCTCATACGATGTTTGAGTGCG 60.285 50.000 15.48 0.00 41.38 5.34
64 65 2.932614 AGCTCATACGATGTTTGAGTGC 59.067 45.455 15.48 6.45 41.38 4.40
65 66 3.241553 CGAGCTCATACGATGTTTGAGTG 59.758 47.826 15.40 5.96 41.38 3.51
67 68 2.791560 CCGAGCTCATACGATGTTTGAG 59.208 50.000 15.40 11.49 41.92 3.02
68 69 2.481276 CCCGAGCTCATACGATGTTTGA 60.481 50.000 15.40 0.00 0.00 2.69
69 70 1.860950 CCCGAGCTCATACGATGTTTG 59.139 52.381 15.40 0.00 0.00 2.93
70 71 1.480954 ACCCGAGCTCATACGATGTTT 59.519 47.619 15.40 0.00 0.00 2.83
71 72 1.112113 ACCCGAGCTCATACGATGTT 58.888 50.000 15.40 0.00 0.00 2.71
72 73 1.067212 GAACCCGAGCTCATACGATGT 59.933 52.381 15.40 0.00 0.00 3.06
73 74 1.067060 TGAACCCGAGCTCATACGATG 59.933 52.381 15.40 0.00 0.00 3.84
74 75 1.399714 TGAACCCGAGCTCATACGAT 58.600 50.000 15.40 0.00 0.00 3.73
76 77 2.004583 TTTGAACCCGAGCTCATACG 57.995 50.000 15.40 0.00 0.00 3.06
77 78 4.156008 ACATTTTTGAACCCGAGCTCATAC 59.844 41.667 15.40 0.70 0.00 2.39
82 83 6.238374 CGAATATACATTTTTGAACCCGAGCT 60.238 38.462 0.00 0.00 0.00 4.09
83 84 5.907391 CGAATATACATTTTTGAACCCGAGC 59.093 40.000 0.00 0.00 0.00 5.03
85 86 7.612668 TTCGAATATACATTTTTGAACCCGA 57.387 32.000 0.00 0.00 0.00 5.14
86 87 7.219344 GGTTTCGAATATACATTTTTGAACCCG 59.781 37.037 0.00 0.00 0.00 5.28
87 88 8.248253 AGGTTTCGAATATACATTTTTGAACCC 58.752 33.333 0.00 2.63 0.00 4.11
88 89 9.634163 AAGGTTTCGAATATACATTTTTGAACC 57.366 29.630 0.00 0.00 0.00 3.62
104 105 8.385898 ACATACAAAGAATGTAAGGTTTCGAA 57.614 30.769 0.00 0.00 43.63 3.71
105 106 7.972832 ACATACAAAGAATGTAAGGTTTCGA 57.027 32.000 0.00 0.00 43.63 3.71
106 107 8.932791 ACTACATACAAAGAATGTAAGGTTTCG 58.067 33.333 0.00 0.00 43.63 3.46
155 763 7.790823 TTTGTATGTGATATGAGATGGTGTG 57.209 36.000 0.00 0.00 0.00 3.82
189 799 7.064966 TGCATATCGGAAGCAGATATAAATGTG 59.935 37.037 0.00 0.00 38.75 3.21
194 804 6.036577 TGTGCATATCGGAAGCAGATATAA 57.963 37.500 0.00 0.00 38.75 0.98
222 832 9.051679 GTGTTAAGCCACTTGGATTTTATTTTT 57.948 29.630 3.69 0.00 41.76 1.94
223 833 7.659799 GGTGTTAAGCCACTTGGATTTTATTTT 59.340 33.333 3.69 0.00 41.76 1.82
242 852 2.885894 GGTTGTTCGGGAATGGTGTTAA 59.114 45.455 0.00 0.00 0.00 2.01
244 854 1.324383 GGTTGTTCGGGAATGGTGTT 58.676 50.000 0.00 0.00 0.00 3.32
366 978 1.144503 GTCAATGGAGATGGGGCAGAT 59.855 52.381 0.00 0.00 0.00 2.90
368 980 0.256752 TGTCAATGGAGATGGGGCAG 59.743 55.000 0.00 0.00 0.00 4.85
399 1012 4.916983 TTTAATTCGCTGGGATGGATTG 57.083 40.909 0.00 0.00 0.00 2.67
453 1066 1.436195 CTCTCTCGCTGTCTCCCTCG 61.436 65.000 0.00 0.00 0.00 4.63
462 1075 3.986572 CCTACATTATTGCTCTCTCGCTG 59.013 47.826 0.00 0.00 0.00 5.18
483 1096 7.155328 AGTAGCATTATGTCAAGCATACTACC 58.845 38.462 0.00 0.00 39.57 3.18
533 1158 4.830765 TATCCCGCTGCACCGTGC 62.831 66.667 16.93 16.93 45.29 5.34
534 1159 2.586079 CTATCCCGCTGCACCGTG 60.586 66.667 0.00 0.00 0.00 4.94
535 1160 3.849951 CCTATCCCGCTGCACCGT 61.850 66.667 0.00 0.00 0.00 4.83
536 1161 3.849951 ACCTATCCCGCTGCACCG 61.850 66.667 0.00 0.00 0.00 4.94
538 1163 1.521681 GTCACCTATCCCGCTGCAC 60.522 63.158 0.00 0.00 0.00 4.57
539 1164 1.264749 AAGTCACCTATCCCGCTGCA 61.265 55.000 0.00 0.00 0.00 4.41
540 1165 0.811616 CAAGTCACCTATCCCGCTGC 60.812 60.000 0.00 0.00 0.00 5.25
541 1166 0.824109 TCAAGTCACCTATCCCGCTG 59.176 55.000 0.00 0.00 0.00 5.18
542 1167 1.115467 CTCAAGTCACCTATCCCGCT 58.885 55.000 0.00 0.00 0.00 5.52
544 1169 0.249073 CGCTCAAGTCACCTATCCCG 60.249 60.000 0.00 0.00 0.00 5.14
572 1200 2.943265 AATGGTGGCTGCCTCCCT 60.943 61.111 30.88 21.62 36.43 4.20
573 1201 2.757099 CAATGGTGGCTGCCTCCC 60.757 66.667 30.88 24.18 36.43 4.30
574 1202 2.757099 CCAATGGTGGCTGCCTCC 60.757 66.667 28.41 28.41 38.35 4.30
773 1403 1.421646 GGGAGAGAGAGAGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
778 1408 1.287739 ACCTTGGGAGAGAGAGAGAGG 59.712 57.143 0.00 0.00 0.00 3.69
851 1491 2.645411 GCAGTTAGCATTGCGCAAG 58.355 52.632 28.62 19.92 46.13 4.01
893 1533 1.303309 GAACAGCCCGAATCCTGATG 58.697 55.000 0.00 0.00 33.40 3.07
904 1544 3.591254 AAGCTCGACCGAACAGCCC 62.591 63.158 0.00 0.00 0.00 5.19
941 1584 0.453390 CGCCTCCAAAGCCAAAGATC 59.547 55.000 0.00 0.00 0.00 2.75
956 1599 2.352032 CCCTCGAAACTCCTCGCCT 61.352 63.158 0.00 0.00 38.73 5.52
964 1607 2.574399 GCTCGCTCCCTCGAAACT 59.426 61.111 0.00 0.00 38.08 2.66
1043 1690 1.375396 CACCCGACGCCATCAGAAA 60.375 57.895 0.00 0.00 0.00 2.52
1051 1698 2.104253 CACCATTACACCCGACGCC 61.104 63.158 0.00 0.00 0.00 5.68
1104 1751 2.037053 CACGCCACCAAACCATGAA 58.963 52.632 0.00 0.00 0.00 2.57
1105 1752 2.560119 GCACGCCACCAAACCATGA 61.560 57.895 0.00 0.00 0.00 3.07
1106 1753 2.049248 GCACGCCACCAAACCATG 60.049 61.111 0.00 0.00 0.00 3.66
1530 2204 1.878522 GACCATGGCGTCGTAGCTG 60.879 63.158 13.04 0.00 37.29 4.24
2128 2824 3.005155 GGCCTGCAACAGATTAATCCATC 59.995 47.826 11.92 0.00 32.44 3.51
2132 2832 1.334869 CCGGCCTGCAACAGATTAATC 59.665 52.381 7.41 7.41 32.44 1.75
2171 2871 1.924731 TCCTGACGATGTCCTTGACT 58.075 50.000 0.00 0.00 33.15 3.41
2285 2989 2.498167 CCAAATCCTCGAGGCTAATGG 58.502 52.381 27.39 24.36 34.44 3.16
2355 3059 2.282462 GTGTGGGGGACTGCAAGG 60.282 66.667 0.00 0.00 39.30 3.61
2437 3142 6.971932 AAAGGGAGAGGGTAGAAGTAATTT 57.028 37.500 0.00 0.00 0.00 1.82
2484 3191 2.191400 CTCTCTCCCAGGAACATGGAA 58.809 52.381 7.08 0.00 43.57 3.53
2600 3307 4.229582 ACAGGGTGAAAAGGGCTATATTGA 59.770 41.667 0.00 0.00 0.00 2.57
2675 3386 1.740025 GGATTTGAGAGGACGGCAAAG 59.260 52.381 0.00 0.00 35.29 2.77
2683 3394 1.630369 CAGTGGTGGGATTTGAGAGGA 59.370 52.381 0.00 0.00 0.00 3.71
2709 3425 4.336713 GTCCACAGATATTTGAAGCCTTCC 59.663 45.833 1.21 0.00 0.00 3.46
2915 3652 2.363925 GAGGGTACAGGTCGGGCT 60.364 66.667 0.00 0.00 0.00 5.19
2916 3653 1.988406 AAGAGGGTACAGGTCGGGC 60.988 63.158 0.00 0.00 0.00 6.13
2917 3654 0.903454 ACAAGAGGGTACAGGTCGGG 60.903 60.000 0.00 0.00 0.00 5.14
2918 3655 0.974383 AACAAGAGGGTACAGGTCGG 59.026 55.000 0.00 0.00 0.00 4.79
2919 3656 2.413837 CAAACAAGAGGGTACAGGTCG 58.586 52.381 0.00 0.00 0.00 4.79
2922 3659 2.554032 CAAGCAAACAAGAGGGTACAGG 59.446 50.000 0.00 0.00 0.00 4.00
2929 3666 3.921119 TGTATGCAAGCAAACAAGAGG 57.079 42.857 0.00 0.00 0.00 3.69
3156 3897 6.821665 TGCCGCCCTTATAATCTTGTATATTC 59.178 38.462 0.00 0.00 0.00 1.75
3158 3899 6.070194 AGTGCCGCCCTTATAATCTTGTATAT 60.070 38.462 0.00 0.00 0.00 0.86
3159 3900 5.247564 AGTGCCGCCCTTATAATCTTGTATA 59.752 40.000 0.00 0.00 0.00 1.47
3195 3939 9.232082 CTCAATGTCGTTTAACAATTCTTTTGA 57.768 29.630 0.00 0.00 31.81 2.69


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

AutoCloner maintained by Alex Coulton.