Multiple sequence alignment - TraesCS2D01G081600

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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 TraesCS2D01G081600 chr2D 100.000 3101 0 0 1 3101 35035380 35032280 0.000000e+00 5727.0
1 TraesCS2D01G081600 chr2D 83.333 1572 199 41 216 1740 35231193 35229638 0.000000e+00 1393.0
2 TraesCS2D01G081600 chr2A 94.653 2899 108 15 247 3101 38341666 38338771 0.000000e+00 4451.0
3 TraesCS2D01G081600 chr2A 82.564 1646 211 42 223 1821 38590228 38591844 0.000000e+00 1380.0
4 TraesCS2D01G081600 chr2A 82.503 1646 212 42 223 1821 38348464 38346848 0.000000e+00 1375.0
5 TraesCS2D01G081600 chr2A 89.404 302 32 0 226 527 38392962 38392661 6.280000e-102 381.0
6 TraesCS2D01G081600 chr2A 80.943 488 59 22 1355 1816 38392633 38392154 3.800000e-94 355.0
7 TraesCS2D01G081600 chr2B 92.809 2058 100 25 157 2181 57791251 57789209 0.000000e+00 2937.0
8 TraesCS2D01G081600 chr2B 83.971 1647 214 33 216 1821 58086957 58085320 0.000000e+00 1533.0
9 TraesCS2D01G081600 chr2B 81.412 1657 229 47 210 1821 58602784 58604406 0.000000e+00 1280.0
10 TraesCS2D01G081600 chr2B 87.105 760 68 23 2353 3101 57789207 57788467 0.000000e+00 833.0
11 TraesCS2D01G081600 chr2B 86.331 695 89 5 226 920 58298458 58297770 0.000000e+00 752.0
12 TraesCS2D01G081600 chr2B 81.061 924 124 29 939 1821 58296638 58295725 0.000000e+00 689.0
13 TraesCS2D01G081600 chr1A 71.777 1435 300 65 266 1655 481628121 481629495 3.000000e-80 309.0
14 TraesCS2D01G081600 chr7B 73.030 901 212 20 555 1435 744032742 744033631 3.910000e-74 289.0
15 TraesCS2D01G081600 chr3A 75.878 427 89 9 1020 1435 11401277 11401700 4.050000e-49 206.0
16 TraesCS2D01G081600 chr3A 77.987 159 22 10 1709 1867 10694616 10694761 1.530000e-13 87.9
17 TraesCS2D01G081600 chr3A 87.755 49 5 1 1978 2026 11398549 11398596 4.320000e-04 56.5
18 TraesCS2D01G081600 chrUn 76.630 368 75 6 1020 1377 260318339 260318705 3.160000e-45 193.0
19 TraesCS2D01G081600 chrUn 76.359 368 76 6 1020 1377 213717494 213717860 1.470000e-43 187.0
20 TraesCS2D01G081600 chrUn 75.862 377 80 6 1026 1392 265026424 265026049 6.830000e-42 182.0
21 TraesCS2D01G081600 chrUn 76.087 368 77 6 1020 1377 287938629 287938995 6.830000e-42 182.0
22 TraesCS2D01G081600 chrUn 73.560 382 75 19 1021 1392 35360105 35359740 4.200000e-24 122.0
23 TraesCS2D01G081600 chrUn 87.302 63 8 0 1075 1137 35819488 35819426 4.290000e-09 73.1
24 TraesCS2D01G081600 chr3B 72.603 365 80 14 1022 1375 46064792 46065147 5.470000e-18 102.0


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 TraesCS2D01G081600 chr2D 35032280 35035380 3100 True 5727.0 5727 100.0000 1 3101 1 chr2D.!!$R1 3100
1 TraesCS2D01G081600 chr2D 35229638 35231193 1555 True 1393.0 1393 83.3330 216 1740 1 chr2D.!!$R2 1524
2 TraesCS2D01G081600 chr2A 38338771 38341666 2895 True 4451.0 4451 94.6530 247 3101 1 chr2A.!!$R1 2854
3 TraesCS2D01G081600 chr2A 38590228 38591844 1616 False 1380.0 1380 82.5640 223 1821 1 chr2A.!!$F1 1598
4 TraesCS2D01G081600 chr2A 38346848 38348464 1616 True 1375.0 1375 82.5030 223 1821 1 chr2A.!!$R2 1598
5 TraesCS2D01G081600 chr2A 38392154 38392962 808 True 368.0 381 85.1735 226 1816 2 chr2A.!!$R3 1590
6 TraesCS2D01G081600 chr2B 57788467 57791251 2784 True 1885.0 2937 89.9570 157 3101 2 chr2B.!!$R2 2944
7 TraesCS2D01G081600 chr2B 58085320 58086957 1637 True 1533.0 1533 83.9710 216 1821 1 chr2B.!!$R1 1605
8 TraesCS2D01G081600 chr2B 58602784 58604406 1622 False 1280.0 1280 81.4120 210 1821 1 chr2B.!!$F1 1611
9 TraesCS2D01G081600 chr2B 58295725 58298458 2733 True 720.5 752 83.6960 226 1821 2 chr2B.!!$R3 1595
10 TraesCS2D01G081600 chr1A 481628121 481629495 1374 False 309.0 309 71.7770 266 1655 1 chr1A.!!$F1 1389
11 TraesCS2D01G081600 chr7B 744032742 744033631 889 False 289.0 289 73.0300 555 1435 1 chr7B.!!$F1 880

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
137 138 0.099791 CCAACACCACGTCGCTTTTT 59.900 50.0 0.00 0.00 0.00 1.94 F
153 154 0.102120 TTTTTCCTGTGCACGCAAGG 59.898 50.0 13.13 13.72 46.39 3.61 F
204 205 0.103937 CTCCCCACGAATGAGAGAGC 59.896 60.0 0.00 0.00 31.18 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 3197 4.686554 GCAACAGTAAACAAAACCACACAA 59.313 37.500 0.00 0.00 0.0 3.33 R
2048 3355 7.771183 TCCAATGCCTAGAAACATAAAACATC 58.229 34.615 0.00 0.00 0.0 3.06 R
2218 3527 1.753930 CTTGGTGCATGCTATCCACA 58.246 50.000 20.33 13.06 0.0 4.17 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
18 19 2.538790 TTGGAGGGAGTGAAGCACA 58.461 52.632 0.00 0.00 36.74 4.57
19 20 1.067295 TTGGAGGGAGTGAAGCACAT 58.933 50.000 0.00 0.00 36.74 3.21
20 21 1.951209 TGGAGGGAGTGAAGCACATA 58.049 50.000 0.00 0.00 36.74 2.29
21 22 1.833630 TGGAGGGAGTGAAGCACATAG 59.166 52.381 0.00 0.00 36.74 2.23
22 23 1.474143 GGAGGGAGTGAAGCACATAGC 60.474 57.143 0.00 0.00 46.19 2.97
31 32 3.214845 GCACATAGCAGCCCAGCC 61.215 66.667 0.00 0.00 44.79 4.85
32 33 2.517875 CACATAGCAGCCCAGCCC 60.518 66.667 0.00 0.00 34.23 5.19
33 34 3.016971 ACATAGCAGCCCAGCCCA 61.017 61.111 0.00 0.00 34.23 5.36
34 35 2.203308 CATAGCAGCCCAGCCCAG 60.203 66.667 0.00 0.00 34.23 4.45
35 36 4.201122 ATAGCAGCCCAGCCCAGC 62.201 66.667 0.00 0.00 34.23 4.85
39 40 4.809496 CAGCCCAGCCCAGCGAAT 62.809 66.667 0.00 0.00 0.00 3.34
40 41 4.052518 AGCCCAGCCCAGCGAATT 62.053 61.111 0.00 0.00 0.00 2.17
41 42 3.521796 GCCCAGCCCAGCGAATTC 61.522 66.667 0.00 0.00 0.00 2.17
42 43 2.830370 CCCAGCCCAGCGAATTCC 60.830 66.667 0.00 0.00 0.00 3.01
43 44 2.273449 CCAGCCCAGCGAATTCCT 59.727 61.111 0.00 0.00 0.00 3.36
44 45 1.526887 CCAGCCCAGCGAATTCCTA 59.473 57.895 0.00 0.00 0.00 2.94
45 46 0.107214 CCAGCCCAGCGAATTCCTAA 60.107 55.000 0.00 0.00 0.00 2.69
46 47 1.681780 CCAGCCCAGCGAATTCCTAAA 60.682 52.381 0.00 0.00 0.00 1.85
47 48 1.672881 CAGCCCAGCGAATTCCTAAAG 59.327 52.381 0.00 0.00 0.00 1.85
48 49 1.282157 AGCCCAGCGAATTCCTAAAGT 59.718 47.619 0.00 0.00 0.00 2.66
49 50 1.401905 GCCCAGCGAATTCCTAAAGTG 59.598 52.381 0.00 0.00 0.00 3.16
50 51 2.017049 CCCAGCGAATTCCTAAAGTGG 58.983 52.381 0.00 0.00 0.00 4.00
51 52 2.017049 CCAGCGAATTCCTAAAGTGGG 58.983 52.381 0.00 0.00 0.00 4.61
52 53 1.401905 CAGCGAATTCCTAAAGTGGGC 59.598 52.381 0.00 0.00 0.00 5.36
53 54 0.738975 GCGAATTCCTAAAGTGGGCC 59.261 55.000 0.00 0.00 0.00 5.80
54 55 1.014352 CGAATTCCTAAAGTGGGCCG 58.986 55.000 0.00 0.00 0.00 6.13
55 56 1.677820 CGAATTCCTAAAGTGGGCCGT 60.678 52.381 0.00 0.00 0.00 5.68
56 57 2.014857 GAATTCCTAAAGTGGGCCGTC 58.985 52.381 0.00 0.00 0.00 4.79
57 58 0.107848 ATTCCTAAAGTGGGCCGTCG 60.108 55.000 0.00 0.00 0.00 5.12
58 59 1.474332 TTCCTAAAGTGGGCCGTCGT 61.474 55.000 0.00 0.00 0.00 4.34
59 60 0.611618 TCCTAAAGTGGGCCGTCGTA 60.612 55.000 0.00 0.00 0.00 3.43
60 61 0.462789 CCTAAAGTGGGCCGTCGTAT 59.537 55.000 0.00 0.00 0.00 3.06
61 62 1.537562 CCTAAAGTGGGCCGTCGTATC 60.538 57.143 0.00 0.00 0.00 2.24
62 63 0.461135 TAAAGTGGGCCGTCGTATCC 59.539 55.000 0.00 0.00 0.00 2.59
63 64 1.546589 AAAGTGGGCCGTCGTATCCA 61.547 55.000 0.00 0.00 0.00 3.41
64 65 1.546589 AAGTGGGCCGTCGTATCCAA 61.547 55.000 0.00 0.00 0.00 3.53
65 66 1.520787 GTGGGCCGTCGTATCCAAG 60.521 63.158 0.00 0.00 0.00 3.61
66 67 2.588034 GGGCCGTCGTATCCAAGC 60.588 66.667 0.00 0.00 0.00 4.01
67 68 2.185867 GGCCGTCGTATCCAAGCA 59.814 61.111 0.00 0.00 0.00 3.91
68 69 1.883084 GGCCGTCGTATCCAAGCAG 60.883 63.158 0.00 0.00 0.00 4.24
69 70 1.153628 GCCGTCGTATCCAAGCAGT 60.154 57.895 0.00 0.00 0.00 4.40
70 71 1.146358 GCCGTCGTATCCAAGCAGTC 61.146 60.000 0.00 0.00 0.00 3.51
71 72 0.527817 CCGTCGTATCCAAGCAGTCC 60.528 60.000 0.00 0.00 0.00 3.85
72 73 0.866061 CGTCGTATCCAAGCAGTCCG 60.866 60.000 0.00 0.00 0.00 4.79
73 74 0.172803 GTCGTATCCAAGCAGTCCGT 59.827 55.000 0.00 0.00 0.00 4.69
74 75 0.454600 TCGTATCCAAGCAGTCCGTC 59.545 55.000 0.00 0.00 0.00 4.79
75 76 0.527817 CGTATCCAAGCAGTCCGTCC 60.528 60.000 0.00 0.00 0.00 4.79
76 77 0.824759 GTATCCAAGCAGTCCGTCCT 59.175 55.000 0.00 0.00 0.00 3.85
77 78 0.824109 TATCCAAGCAGTCCGTCCTG 59.176 55.000 0.00 0.00 35.49 3.86
85 86 1.927895 CAGTCCGTCCTGCACTATTC 58.072 55.000 0.00 0.00 0.00 1.75
86 87 1.478510 CAGTCCGTCCTGCACTATTCT 59.521 52.381 0.00 0.00 0.00 2.40
87 88 2.688446 CAGTCCGTCCTGCACTATTCTA 59.312 50.000 0.00 0.00 0.00 2.10
88 89 3.319405 CAGTCCGTCCTGCACTATTCTAT 59.681 47.826 0.00 0.00 0.00 1.98
89 90 3.570550 AGTCCGTCCTGCACTATTCTATC 59.429 47.826 0.00 0.00 0.00 2.08
90 91 3.570550 GTCCGTCCTGCACTATTCTATCT 59.429 47.826 0.00 0.00 0.00 1.98
91 92 4.760715 GTCCGTCCTGCACTATTCTATCTA 59.239 45.833 0.00 0.00 0.00 1.98
92 93 5.004448 TCCGTCCTGCACTATTCTATCTAG 58.996 45.833 0.00 0.00 0.00 2.43
93 94 5.004448 CCGTCCTGCACTATTCTATCTAGA 58.996 45.833 0.00 0.00 0.00 2.43
94 95 5.123186 CCGTCCTGCACTATTCTATCTAGAG 59.877 48.000 0.00 0.00 33.21 2.43
95 96 5.391523 CGTCCTGCACTATTCTATCTAGAGC 60.392 48.000 0.00 0.00 34.58 4.09
96 97 5.013547 TCCTGCACTATTCTATCTAGAGCC 58.986 45.833 0.00 0.00 33.50 4.70
97 98 4.159506 CCTGCACTATTCTATCTAGAGCCC 59.840 50.000 0.00 0.00 33.50 5.19
98 99 4.740902 TGCACTATTCTATCTAGAGCCCA 58.259 43.478 0.00 0.00 33.50 5.36
99 100 5.147767 TGCACTATTCTATCTAGAGCCCAA 58.852 41.667 0.00 0.00 33.50 4.12
100 101 5.244851 TGCACTATTCTATCTAGAGCCCAAG 59.755 44.000 0.00 0.00 33.50 3.61
101 102 5.478679 GCACTATTCTATCTAGAGCCCAAGA 59.521 44.000 0.00 0.00 33.21 3.02
102 103 6.571537 GCACTATTCTATCTAGAGCCCAAGAC 60.572 46.154 0.00 0.00 33.21 3.01
103 104 6.491745 CACTATTCTATCTAGAGCCCAAGACA 59.508 42.308 0.00 0.00 33.21 3.41
104 105 5.799827 ATTCTATCTAGAGCCCAAGACAC 57.200 43.478 0.00 0.00 33.21 3.67
105 106 3.567397 TCTATCTAGAGCCCAAGACACC 58.433 50.000 0.00 0.00 0.00 4.16
106 107 2.254152 ATCTAGAGCCCAAGACACCA 57.746 50.000 0.00 0.00 0.00 4.17
107 108 2.024176 TCTAGAGCCCAAGACACCAA 57.976 50.000 0.00 0.00 0.00 3.67
108 109 1.623811 TCTAGAGCCCAAGACACCAAC 59.376 52.381 0.00 0.00 0.00 3.77
109 110 1.625818 CTAGAGCCCAAGACACCAACT 59.374 52.381 0.00 0.00 0.00 3.16
110 111 0.398318 AGAGCCCAAGACACCAACTC 59.602 55.000 0.00 0.00 0.00 3.01
111 112 0.951040 GAGCCCAAGACACCAACTCG 60.951 60.000 0.00 0.00 0.00 4.18
112 113 2.617274 GCCCAAGACACCAACTCGC 61.617 63.158 0.00 0.00 0.00 5.03
113 114 1.071471 CCCAAGACACCAACTCGCT 59.929 57.895 0.00 0.00 0.00 4.93
114 115 1.230635 CCCAAGACACCAACTCGCTG 61.231 60.000 0.00 0.00 0.00 5.18
115 116 1.230635 CCAAGACACCAACTCGCTGG 61.231 60.000 0.00 0.00 42.68 4.85
116 117 1.071471 AAGACACCAACTCGCTGGG 59.929 57.895 3.52 0.00 41.16 4.45
117 118 3.050275 GACACCAACTCGCTGGGC 61.050 66.667 3.52 0.00 41.16 5.36
118 119 4.643387 ACACCAACTCGCTGGGCC 62.643 66.667 0.00 0.00 41.16 5.80
121 122 4.659172 CCAACTCGCTGGGCCCAA 62.659 66.667 28.29 10.72 32.32 4.12
122 123 3.365265 CAACTCGCTGGGCCCAAC 61.365 66.667 28.29 21.89 0.00 3.77
123 124 3.884774 AACTCGCTGGGCCCAACA 61.885 61.111 28.29 11.51 0.00 3.33
124 125 4.643387 ACTCGCTGGGCCCAACAC 62.643 66.667 28.29 17.29 0.00 3.32
129 130 4.579384 CTGGGCCCAACACCACGT 62.579 66.667 28.29 0.00 32.33 4.49
130 131 4.572571 TGGGCCCAACACCACGTC 62.573 66.667 26.33 0.00 0.00 4.34
134 135 2.590575 CCCAACACCACGTCGCTT 60.591 61.111 0.00 0.00 0.00 4.68
135 136 2.184167 CCCAACACCACGTCGCTTT 61.184 57.895 0.00 0.00 0.00 3.51
136 137 1.720694 CCCAACACCACGTCGCTTTT 61.721 55.000 0.00 0.00 0.00 2.27
137 138 0.099791 CCAACACCACGTCGCTTTTT 59.900 50.000 0.00 0.00 0.00 1.94
153 154 0.102120 TTTTTCCTGTGCACGCAAGG 59.898 50.000 13.13 13.72 46.39 3.61
154 155 0.749818 TTTTCCTGTGCACGCAAGGA 60.750 50.000 18.01 18.01 46.39 3.36
155 156 0.749818 TTTCCTGTGCACGCAAGGAA 60.750 50.000 25.55 25.55 46.39 3.36
174 175 3.304726 GGAAGAAGCGGTTCCAGAAAAAG 60.305 47.826 22.91 0.00 42.79 2.27
179 180 4.729227 AGCGGTTCCAGAAAAAGAAAAA 57.271 36.364 0.00 0.00 0.00 1.94
180 181 4.682787 AGCGGTTCCAGAAAAAGAAAAAG 58.317 39.130 0.00 0.00 0.00 2.27
181 182 4.401202 AGCGGTTCCAGAAAAAGAAAAAGA 59.599 37.500 0.00 0.00 0.00 2.52
182 183 5.105513 AGCGGTTCCAGAAAAAGAAAAAGAA 60.106 36.000 0.00 0.00 0.00 2.52
183 184 5.579119 GCGGTTCCAGAAAAAGAAAAAGAAA 59.421 36.000 0.00 0.00 0.00 2.52
195 196 4.274978 AGAAAAAGAAAACTCCCCACGAA 58.725 39.130 0.00 0.00 0.00 3.85
196 197 4.893524 AGAAAAAGAAAACTCCCCACGAAT 59.106 37.500 0.00 0.00 0.00 3.34
202 203 1.938585 AACTCCCCACGAATGAGAGA 58.061 50.000 0.00 0.00 32.93 3.10
203 204 1.479709 ACTCCCCACGAATGAGAGAG 58.520 55.000 0.00 0.00 32.93 3.20
204 205 0.103937 CTCCCCACGAATGAGAGAGC 59.896 60.000 0.00 0.00 31.18 4.09
205 206 0.324738 TCCCCACGAATGAGAGAGCT 60.325 55.000 0.00 0.00 0.00 4.09
208 209 0.820226 CCACGAATGAGAGAGCTGGA 59.180 55.000 0.00 0.00 0.00 3.86
213 214 0.831966 AATGAGAGAGCTGGAGCCAG 59.168 55.000 12.17 12.17 46.15 4.85
214 215 1.049855 ATGAGAGAGCTGGAGCCAGG 61.050 60.000 17.64 0.72 43.77 4.45
298 318 0.748367 CGACCTCCTCCGTGAGATCA 60.748 60.000 0.00 0.00 34.11 2.92
312 332 2.447379 ATCATGCTCCGCCTCCCT 60.447 61.111 0.00 0.00 0.00 4.20
314 334 2.961559 ATCATGCTCCGCCTCCCTCT 62.962 60.000 0.00 0.00 0.00 3.69
885 919 0.307760 CGACTTGTTGCAGTGGTTCC 59.692 55.000 0.00 0.00 0.00 3.62
892 926 1.708993 TTGCAGTGGTTCCCAGAGCT 61.709 55.000 0.00 0.00 36.07 4.09
930 964 6.966021 TGTTCTTTACTGGCTGTTAAATCAC 58.034 36.000 1.31 0.00 0.00 3.06
949 2099 1.082117 CGCGGAAGACGGCATACTTT 61.082 55.000 0.00 0.00 44.51 2.66
1256 2429 7.936847 TGAAATACTTTTATATCTGGACGGCAT 59.063 33.333 0.00 0.00 0.00 4.40
1378 2568 5.355350 GGTGATTGTTCATCCTTAGTCCTTG 59.645 44.000 0.00 0.00 33.56 3.61
1383 2573 6.061022 TGTTCATCCTTAGTCCTTGCATTA 57.939 37.500 0.00 0.00 0.00 1.90
1902 3197 3.859411 TGTTCCTTTCAAAACGCAACT 57.141 38.095 0.00 0.00 0.00 3.16
2280 3589 5.824624 CCATTCAGCTGTTATTATCCAGTGT 59.175 40.000 14.67 0.00 0.00 3.55
2316 3626 3.018856 TGCCAAAGATGATGGTGATGAC 58.981 45.455 0.00 0.00 40.23 3.06
2339 3649 3.160269 AGGCAAAATTCCTCTCCTGTTG 58.840 45.455 0.00 0.00 0.00 3.33
2452 3762 7.179160 TGCCTAAAGCTCTCATTGATATAGCTA 59.821 37.037 14.89 0.00 42.49 3.32
2918 4249 2.462456 TGTTTTGCCAGTTGTTTGCA 57.538 40.000 0.00 0.00 0.00 4.08
2936 4267 1.385038 CATGTTCACGTGTTTGCGTC 58.615 50.000 16.51 0.63 43.83 5.19
2937 4268 0.306533 ATGTTCACGTGTTTGCGTCC 59.693 50.000 16.51 0.00 43.83 4.79
3014 4345 5.067413 AGTTCTCTTCTGTGACGTGTTTCTA 59.933 40.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.067295 ATGTGCTTCACTCCCTCCAA 58.933 50.000 0.00 0.00 35.11 3.53
1 2 1.833630 CTATGTGCTTCACTCCCTCCA 59.166 52.381 0.00 0.00 35.11 3.86
2 3 1.474143 GCTATGTGCTTCACTCCCTCC 60.474 57.143 0.00 0.00 38.95 4.30
4 5 1.209019 CTGCTATGTGCTTCACTCCCT 59.791 52.381 0.00 0.00 43.37 4.20
5 6 1.661341 CTGCTATGTGCTTCACTCCC 58.339 55.000 0.00 0.00 43.37 4.30
6 7 1.012841 GCTGCTATGTGCTTCACTCC 58.987 55.000 0.00 0.00 43.37 3.85
7 8 1.012841 GGCTGCTATGTGCTTCACTC 58.987 55.000 0.00 0.00 43.37 3.51
8 9 0.393537 GGGCTGCTATGTGCTTCACT 60.394 55.000 0.00 0.00 43.37 3.41
9 10 0.677731 TGGGCTGCTATGTGCTTCAC 60.678 55.000 0.00 0.00 43.37 3.18
10 11 0.393402 CTGGGCTGCTATGTGCTTCA 60.393 55.000 0.00 0.00 43.37 3.02
11 12 1.722636 GCTGGGCTGCTATGTGCTTC 61.723 60.000 0.00 0.00 43.37 3.86
12 13 1.751927 GCTGGGCTGCTATGTGCTT 60.752 57.895 0.00 0.00 43.37 3.91
13 14 2.124403 GCTGGGCTGCTATGTGCT 60.124 61.111 0.00 0.00 43.37 4.40
14 15 3.214845 GGCTGGGCTGCTATGTGC 61.215 66.667 0.00 0.00 43.25 4.57
15 16 2.517875 GGGCTGGGCTGCTATGTG 60.518 66.667 0.00 0.00 0.00 3.21
16 17 3.016971 TGGGCTGGGCTGCTATGT 61.017 61.111 0.00 0.00 0.00 2.29
17 18 2.203308 CTGGGCTGGGCTGCTATG 60.203 66.667 0.00 0.00 0.00 2.23
18 19 4.201122 GCTGGGCTGGGCTGCTAT 62.201 66.667 0.00 0.00 0.00 2.97
22 23 4.809496 ATTCGCTGGGCTGGGCTG 62.809 66.667 0.00 0.00 0.00 4.85
23 24 4.052518 AATTCGCTGGGCTGGGCT 62.053 61.111 0.00 0.00 0.00 5.19
24 25 3.521796 GAATTCGCTGGGCTGGGC 61.522 66.667 0.00 0.00 0.00 5.36
25 26 1.983119 TAGGAATTCGCTGGGCTGGG 61.983 60.000 0.00 0.00 0.00 4.45
26 27 0.107214 TTAGGAATTCGCTGGGCTGG 60.107 55.000 0.00 0.00 0.00 4.85
27 28 1.672881 CTTTAGGAATTCGCTGGGCTG 59.327 52.381 0.00 0.00 0.00 4.85
28 29 1.282157 ACTTTAGGAATTCGCTGGGCT 59.718 47.619 0.00 0.00 0.00 5.19
29 30 1.401905 CACTTTAGGAATTCGCTGGGC 59.598 52.381 0.00 0.00 0.00 5.36
30 31 2.017049 CCACTTTAGGAATTCGCTGGG 58.983 52.381 0.00 0.00 0.00 4.45
31 32 2.017049 CCCACTTTAGGAATTCGCTGG 58.983 52.381 0.00 0.00 0.00 4.85
32 33 1.401905 GCCCACTTTAGGAATTCGCTG 59.598 52.381 0.00 0.00 0.00 5.18
33 34 1.682087 GGCCCACTTTAGGAATTCGCT 60.682 52.381 0.00 0.72 0.00 4.93
34 35 0.738975 GGCCCACTTTAGGAATTCGC 59.261 55.000 0.00 0.00 0.00 4.70
35 36 1.014352 CGGCCCACTTTAGGAATTCG 58.986 55.000 0.00 0.00 0.00 3.34
36 37 2.014857 GACGGCCCACTTTAGGAATTC 58.985 52.381 0.00 0.00 0.00 2.17
37 38 1.677820 CGACGGCCCACTTTAGGAATT 60.678 52.381 0.00 0.00 0.00 2.17
38 39 0.107848 CGACGGCCCACTTTAGGAAT 60.108 55.000 0.00 0.00 0.00 3.01
39 40 1.294138 CGACGGCCCACTTTAGGAA 59.706 57.895 0.00 0.00 0.00 3.36
40 41 0.611618 TACGACGGCCCACTTTAGGA 60.612 55.000 0.00 0.00 0.00 2.94
41 42 0.462789 ATACGACGGCCCACTTTAGG 59.537 55.000 0.00 0.00 0.00 2.69
42 43 1.537562 GGATACGACGGCCCACTTTAG 60.538 57.143 0.00 0.00 0.00 1.85
43 44 0.461135 GGATACGACGGCCCACTTTA 59.539 55.000 0.00 0.00 0.00 1.85
44 45 1.219935 GGATACGACGGCCCACTTT 59.780 57.895 0.00 0.00 0.00 2.66
45 46 1.546589 TTGGATACGACGGCCCACTT 61.547 55.000 0.00 0.00 42.51 3.16
46 47 1.956629 CTTGGATACGACGGCCCACT 61.957 60.000 0.00 0.00 42.51 4.00
47 48 1.520787 CTTGGATACGACGGCCCAC 60.521 63.158 0.00 0.00 42.51 4.61
48 49 2.897207 CTTGGATACGACGGCCCA 59.103 61.111 0.00 0.05 42.51 5.36
49 50 2.588034 GCTTGGATACGACGGCCC 60.588 66.667 0.00 0.00 42.51 5.80
50 51 1.883084 CTGCTTGGATACGACGGCC 60.883 63.158 0.00 0.00 42.51 6.13
51 52 1.146358 GACTGCTTGGATACGACGGC 61.146 60.000 0.00 0.00 42.51 5.68
52 53 0.527817 GGACTGCTTGGATACGACGG 60.528 60.000 0.00 0.00 42.51 4.79
53 54 0.866061 CGGACTGCTTGGATACGACG 60.866 60.000 0.00 0.00 42.51 5.12
54 55 0.172803 ACGGACTGCTTGGATACGAC 59.827 55.000 0.00 0.00 42.51 4.34
55 56 0.454600 GACGGACTGCTTGGATACGA 59.545 55.000 0.00 0.00 42.51 3.43
56 57 0.527817 GGACGGACTGCTTGGATACG 60.528 60.000 0.00 0.00 42.51 3.06
57 58 0.824759 AGGACGGACTGCTTGGATAC 59.175 55.000 0.00 0.00 0.00 2.24
58 59 0.824109 CAGGACGGACTGCTTGGATA 59.176 55.000 0.00 0.00 0.00 2.59
59 60 1.599047 CAGGACGGACTGCTTGGAT 59.401 57.895 0.00 0.00 0.00 3.41
60 61 3.059982 CAGGACGGACTGCTTGGA 58.940 61.111 0.00 0.00 0.00 3.53
68 69 3.570550 AGATAGAATAGTGCAGGACGGAC 59.429 47.826 0.00 0.00 35.88 4.79
69 70 3.833732 AGATAGAATAGTGCAGGACGGA 58.166 45.455 0.00 0.00 0.00 4.69
70 71 5.004448 TCTAGATAGAATAGTGCAGGACGG 58.996 45.833 0.00 0.00 0.00 4.79
71 72 5.391523 GCTCTAGATAGAATAGTGCAGGACG 60.392 48.000 0.00 0.00 38.81 4.79
72 73 5.105917 GGCTCTAGATAGAATAGTGCAGGAC 60.106 48.000 0.00 0.00 40.06 3.85
73 74 5.013547 GGCTCTAGATAGAATAGTGCAGGA 58.986 45.833 0.00 0.00 40.06 3.86
74 75 4.159506 GGGCTCTAGATAGAATAGTGCAGG 59.840 50.000 0.00 0.00 40.06 4.85
75 76 4.769488 TGGGCTCTAGATAGAATAGTGCAG 59.231 45.833 0.00 0.00 40.06 4.41
76 77 4.740902 TGGGCTCTAGATAGAATAGTGCA 58.259 43.478 0.00 0.00 40.06 4.57
77 78 5.478679 TCTTGGGCTCTAGATAGAATAGTGC 59.521 44.000 0.00 0.00 38.44 4.40
78 79 6.491745 TGTCTTGGGCTCTAGATAGAATAGTG 59.508 42.308 0.00 0.00 0.00 2.74
79 80 6.492087 GTGTCTTGGGCTCTAGATAGAATAGT 59.508 42.308 0.00 0.00 0.00 2.12
80 81 6.071616 GGTGTCTTGGGCTCTAGATAGAATAG 60.072 46.154 0.00 0.00 0.00 1.73
81 82 5.775701 GGTGTCTTGGGCTCTAGATAGAATA 59.224 44.000 0.00 0.00 0.00 1.75
82 83 4.591072 GGTGTCTTGGGCTCTAGATAGAAT 59.409 45.833 0.00 0.00 0.00 2.40
83 84 3.961408 GGTGTCTTGGGCTCTAGATAGAA 59.039 47.826 0.00 0.00 0.00 2.10
84 85 3.052869 TGGTGTCTTGGGCTCTAGATAGA 60.053 47.826 0.00 0.00 0.00 1.98
85 86 3.300388 TGGTGTCTTGGGCTCTAGATAG 58.700 50.000 0.00 0.00 0.00 2.08
86 87 3.398318 TGGTGTCTTGGGCTCTAGATA 57.602 47.619 0.00 0.00 0.00 1.98
87 88 2.237392 GTTGGTGTCTTGGGCTCTAGAT 59.763 50.000 0.00 0.00 0.00 1.98
88 89 1.623811 GTTGGTGTCTTGGGCTCTAGA 59.376 52.381 0.00 0.00 0.00 2.43
89 90 1.625818 AGTTGGTGTCTTGGGCTCTAG 59.374 52.381 0.00 0.00 0.00 2.43
90 91 1.623811 GAGTTGGTGTCTTGGGCTCTA 59.376 52.381 0.00 0.00 0.00 2.43
91 92 0.398318 GAGTTGGTGTCTTGGGCTCT 59.602 55.000 0.00 0.00 0.00 4.09
92 93 0.951040 CGAGTTGGTGTCTTGGGCTC 60.951 60.000 0.00 0.00 0.00 4.70
93 94 1.071471 CGAGTTGGTGTCTTGGGCT 59.929 57.895 0.00 0.00 0.00 5.19
94 95 2.617274 GCGAGTTGGTGTCTTGGGC 61.617 63.158 0.00 0.00 0.00 5.36
95 96 1.071471 AGCGAGTTGGTGTCTTGGG 59.929 57.895 0.00 0.00 0.00 4.12
96 97 1.230635 CCAGCGAGTTGGTGTCTTGG 61.231 60.000 8.72 0.00 44.68 3.61
97 98 1.230635 CCCAGCGAGTTGGTGTCTTG 61.231 60.000 8.72 0.00 44.68 3.02
98 99 1.071471 CCCAGCGAGTTGGTGTCTT 59.929 57.895 8.72 0.00 44.68 3.01
99 100 2.743718 CCCAGCGAGTTGGTGTCT 59.256 61.111 8.72 0.00 44.68 3.41
100 101 3.050275 GCCCAGCGAGTTGGTGTC 61.050 66.667 8.72 0.00 44.68 3.67
101 102 4.643387 GGCCCAGCGAGTTGGTGT 62.643 66.667 8.72 0.00 44.68 4.16
104 105 4.659172 TTGGGCCCAGCGAGTTGG 62.659 66.667 26.87 0.00 38.00 3.77
105 106 3.365265 GTTGGGCCCAGCGAGTTG 61.365 66.667 26.87 0.00 0.00 3.16
106 107 3.884774 TGTTGGGCCCAGCGAGTT 61.885 61.111 30.81 0.00 0.00 3.01
107 108 4.643387 GTGTTGGGCCCAGCGAGT 62.643 66.667 30.81 0.00 0.00 4.18
112 113 4.579384 ACGTGGTGTTGGGCCCAG 62.579 66.667 26.87 14.33 0.00 4.45
113 114 4.572571 GACGTGGTGTTGGGCCCA 62.573 66.667 24.45 24.45 0.00 5.36
117 118 1.720694 AAAAGCGACGTGGTGTTGGG 61.721 55.000 0.00 0.00 32.08 4.12
118 119 0.099791 AAAAAGCGACGTGGTGTTGG 59.900 50.000 0.00 0.00 32.08 3.77
119 120 3.615099 AAAAAGCGACGTGGTGTTG 57.385 47.368 0.00 0.00 34.83 3.33
134 135 0.102120 CCTTGCGTGCACAGGAAAAA 59.898 50.000 18.64 0.50 0.00 1.94
135 136 0.749818 TCCTTGCGTGCACAGGAAAA 60.750 50.000 19.26 7.47 33.56 2.29
136 137 0.749818 TTCCTTGCGTGCACAGGAAA 60.750 50.000 26.58 14.84 38.72 3.13
137 138 1.153066 TTCCTTGCGTGCACAGGAA 60.153 52.632 25.55 25.55 39.02 3.36
138 139 1.597854 CTTCCTTGCGTGCACAGGA 60.598 57.895 18.01 18.01 34.16 3.86
139 140 1.165907 TTCTTCCTTGCGTGCACAGG 61.166 55.000 18.64 16.15 0.00 4.00
140 141 0.236711 CTTCTTCCTTGCGTGCACAG 59.763 55.000 18.64 10.86 0.00 3.66
141 142 1.785041 GCTTCTTCCTTGCGTGCACA 61.785 55.000 18.64 0.00 0.00 4.57
142 143 1.081840 GCTTCTTCCTTGCGTGCAC 60.082 57.895 6.82 6.82 0.00 4.57
143 144 2.606961 CGCTTCTTCCTTGCGTGCA 61.607 57.895 0.00 0.00 44.00 4.57
144 145 2.174349 CGCTTCTTCCTTGCGTGC 59.826 61.111 0.00 0.00 44.00 5.34
148 149 0.889186 TGGAACCGCTTCTTCCTTGC 60.889 55.000 5.74 0.00 38.46 4.01
149 150 1.160137 CTGGAACCGCTTCTTCCTTG 58.840 55.000 5.74 0.00 38.46 3.61
150 151 1.056660 TCTGGAACCGCTTCTTCCTT 58.943 50.000 5.74 0.00 38.46 3.36
151 152 1.056660 TTCTGGAACCGCTTCTTCCT 58.943 50.000 5.74 0.00 38.46 3.36
152 153 1.892209 TTTCTGGAACCGCTTCTTCC 58.108 50.000 0.00 0.00 38.18 3.46
153 154 3.564225 TCTTTTTCTGGAACCGCTTCTTC 59.436 43.478 0.00 0.00 0.00 2.87
154 155 3.551846 TCTTTTTCTGGAACCGCTTCTT 58.448 40.909 0.00 0.00 0.00 2.52
155 156 3.208747 TCTTTTTCTGGAACCGCTTCT 57.791 42.857 0.00 0.00 0.00 2.85
174 175 4.642445 TTCGTGGGGAGTTTTCTTTTTC 57.358 40.909 0.00 0.00 0.00 2.29
179 180 2.637872 TCTCATTCGTGGGGAGTTTTCT 59.362 45.455 0.00 0.00 0.00 2.52
180 181 3.003480 CTCTCATTCGTGGGGAGTTTTC 58.997 50.000 0.00 0.00 0.00 2.29
181 182 2.637872 TCTCTCATTCGTGGGGAGTTTT 59.362 45.455 0.00 0.00 0.00 2.43
182 183 2.234908 CTCTCTCATTCGTGGGGAGTTT 59.765 50.000 0.00 0.00 0.00 2.66
183 184 1.827969 CTCTCTCATTCGTGGGGAGTT 59.172 52.381 0.00 0.00 0.00 3.01
195 196 1.049855 CCTGGCTCCAGCTCTCTCAT 61.050 60.000 10.37 0.00 42.35 2.90
196 197 1.685077 CCTGGCTCCAGCTCTCTCA 60.685 63.158 10.37 0.00 42.35 3.27
204 205 4.809496 ATTGGCGCCTGGCTCCAG 62.809 66.667 27.54 8.66 44.43 3.86
312 332 3.569361 AAGGGAGGAGGGCTGCAGA 62.569 63.158 20.43 0.00 0.00 4.26
314 334 3.011517 GAAGGGAGGAGGGCTGCA 61.012 66.667 0.50 0.00 0.00 4.41
372 392 1.303091 CGGTGAATTTGGGGTCGACC 61.303 60.000 27.04 27.04 39.11 4.79
845 874 3.574396 CGAACCTGAATATGGAGCCTCTA 59.426 47.826 0.00 0.00 0.00 2.43
885 919 0.984230 TACCAACAAGGGAGCTCTGG 59.016 55.000 14.64 14.39 43.89 3.86
892 926 6.488683 CAGTAAAGAACATTACCAACAAGGGA 59.511 38.462 0.00 0.00 43.89 4.20
930 964 1.082117 AAAGTATGCCGTCTTCCGCG 61.082 55.000 0.00 0.00 34.38 6.46
949 2099 7.175104 AGGCTTTGTCTATCCAAATCAAACTA 58.825 34.615 0.00 0.00 34.07 2.24
1065 2221 5.795972 TGAATGTTATGGTAACGGTGAGAA 58.204 37.500 0.00 0.00 42.51 2.87
1256 2429 8.525316 TCGACTTAAGTTGAACCATATAGACAA 58.475 33.333 21.09 0.00 35.62 3.18
1439 2635 7.865706 AAGTCAGTGAACACTTAAGAATTGT 57.134 32.000 10.09 0.00 40.20 2.71
1467 2674 7.406104 AGGAAAGAGGCAATCATTAACTTAGT 58.594 34.615 0.00 0.00 0.00 2.24
1470 2677 6.319911 GCTAGGAAAGAGGCAATCATTAACTT 59.680 38.462 0.00 0.00 0.00 2.66
1483 2723 4.810191 AACAGTACAGCTAGGAAAGAGG 57.190 45.455 0.00 0.00 0.00 3.69
1623 2903 9.809096 TCATTTGACATTTGCTTTTACACTAAA 57.191 25.926 0.00 0.00 0.00 1.85
1902 3197 4.686554 GCAACAGTAAACAAAACCACACAA 59.313 37.500 0.00 0.00 0.00 3.33
2048 3355 7.771183 TCCAATGCCTAGAAACATAAAACATC 58.229 34.615 0.00 0.00 0.00 3.06
2215 3524 2.025898 TGGTGCATGCTATCCACATTG 58.974 47.619 20.33 0.00 0.00 2.82
2218 3527 1.753930 CTTGGTGCATGCTATCCACA 58.246 50.000 20.33 13.06 0.00 4.17
2280 3589 8.747471 TCATCTTTGGCATATGTGTTATTTCAA 58.253 29.630 4.29 0.00 0.00 2.69
2316 3626 3.160269 ACAGGAGAGGAATTTTGCCTTG 58.840 45.455 0.00 0.00 35.44 3.61
2339 3649 4.444056 GGTTGTCATTTATGCACAACACAC 59.556 41.667 23.57 12.95 43.04 3.82
2452 3762 7.995488 CCCTTCCAGTTTATCTATTCAGAACAT 59.005 37.037 0.00 0.00 33.50 2.71
2469 3779 3.971971 ACTACTAACACAACCCTTCCAGT 59.028 43.478 0.00 0.00 0.00 4.00
2690 4000 6.851222 AATGCTGAACCTAATCGAACATAG 57.149 37.500 0.00 0.00 0.00 2.23
2847 4170 7.160049 AGACTAAGGAAAACACTAACTAAGGC 58.840 38.462 0.00 0.00 0.00 4.35
2936 4267 5.009410 AGGTATCTTACGTAGTTGATTCGGG 59.991 44.000 11.23 0.00 37.78 5.14
2937 4268 6.069684 AGGTATCTTACGTAGTTGATTCGG 57.930 41.667 11.23 0.00 37.78 4.30
3014 4345 7.228706 ACAGAACTTACAGTCGGAAATGAAAAT 59.771 33.333 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.