Multiple sequence alignment - TraesCS3A01G164500

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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 TraesCS3A01G164500 chr3A 100.000 2339 0 0 1 2339 169838469 169840807 0.000000e+00 4320
1 TraesCS3A01G164500 chr3A 96.753 154 5 0 1 154 110369236 110369389 8.290000e-65 257
2 TraesCS3A01G164500 chr3A 91.892 111 9 0 1309 1419 169838735 169838625 3.110000e-34 156
3 TraesCS3A01G164500 chr3A 82.778 180 25 5 157 333 169839887 169839711 3.110000e-34 156
4 TraesCS3A01G164500 chr5A 96.123 1264 48 1 157 1420 85661402 85660140 0.000000e+00 2061
5 TraesCS3A01G164500 chr5A 95.125 923 39 4 1421 2339 274869548 274868628 0.000000e+00 1450
6 TraesCS3A01G164500 chr5A 79.551 1247 210 16 157 1391 581576151 581574938 0.000000e+00 848
7 TraesCS3A01G164500 chr5A 97.368 152 4 0 4 155 277556547 277556396 2.310000e-65 259
8 TraesCS3A01G164500 chr5A 84.574 188 23 5 1243 1427 85661226 85661410 5.130000e-42 182
9 TraesCS3A01G164500 chr5A 84.916 179 23 3 1245 1421 589377923 589377747 6.640000e-41 178
10 TraesCS3A01G164500 chr5A 83.152 184 25 5 1241 1420 311942637 311942818 1.860000e-36 163
11 TraesCS3A01G164500 chr2A 96.356 1235 45 0 184 1418 541848311 541847077 0.000000e+00 2032
12 TraesCS3A01G164500 chr2A 95.553 922 36 3 1421 2339 42693649 42694568 0.000000e+00 1471
13 TraesCS3A01G164500 chr2A 95.103 919 42 3 1421 2339 666574067 666573152 0.000000e+00 1445
14 TraesCS3A01G164500 chr2A 95.011 922 41 3 1421 2339 491485308 491484389 0.000000e+00 1443
15 TraesCS3A01G164500 chr1A 95.570 1264 49 3 157 1419 451737049 451738306 0.000000e+00 2017
16 TraesCS3A01G164500 chr1A 95.946 1036 39 2 157 1192 327012033 327013065 0.000000e+00 1677
17 TraesCS3A01G164500 chr1A 94.902 922 40 5 1421 2339 391934422 391935339 0.000000e+00 1435
18 TraesCS3A01G164500 chr1A 97.428 311 7 1 1110 1420 327013060 327013369 1.590000e-146 529
19 TraesCS3A01G164500 chr1A 93.750 112 7 0 1309 1420 327012143 327012032 4.000000e-38 169
20 TraesCS3A01G164500 chr1A 83.060 183 25 5 154 333 451738309 451738130 6.690000e-36 161
21 TraesCS3A01G164500 chr1A 82.778 180 24 6 157 333 327013368 327013193 1.120000e-33 154
22 TraesCS3A01G164500 chr6A 95.228 922 39 3 1421 2339 176545020 176544101 0.000000e+00 1454
23 TraesCS3A01G164500 chr6A 96.753 154 3 2 1 154 186449256 186449407 2.980000e-64 255
24 TraesCS3A01G164500 chr6A 96.753 154 4 1 1 154 212746782 212746630 2.980000e-64 255
25 TraesCS3A01G164500 chr7A 95.011 922 41 3 1421 2339 187188732 187187813 0.000000e+00 1443
26 TraesCS3A01G164500 chr7A 96.753 154 5 0 1 154 447505308 447505155 8.290000e-65 257
27 TraesCS3A01G164500 chr7A 96.753 154 4 1 1 154 74360354 74360506 2.980000e-64 255
28 TraesCS3A01G164500 chr4A 95.016 923 38 5 1421 2339 23968798 23969716 0.000000e+00 1443
29 TraesCS3A01G164500 chr4A 98.013 151 3 0 4 154 284584774 284584624 1.780000e-66 263
30 TraesCS3A01G164500 chr4A 98.013 151 2 1 4 154 678067692 678067543 6.410000e-66 261
31 TraesCS3A01G164500 chr2D 94.891 920 44 3 1421 2339 470892825 470891908 0.000000e+00 1435
32 TraesCS3A01G164500 chr2D 97.403 154 4 0 1 154 258936016 258935863 1.780000e-66 263
33 TraesCS3A01G164500 chr7D 80.063 1279 212 22 157 1420 612341720 612342970 0.000000e+00 909
34 TraesCS3A01G164500 chr6B 79.734 1204 210 19 157 1348 479872869 479871688 0.000000e+00 841
35 TraesCS3A01G164500 chr6B 80.118 508 92 3 743 1242 231369988 231370494 1.020000e-98 370


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 TraesCS3A01G164500 chr3A 169838469 169840807 2338 False 4320 4320 100.000 1 2339 1 chr3A.!!$F2 2338
1 TraesCS3A01G164500 chr5A 85660140 85661402 1262 True 2061 2061 96.123 157 1420 1 chr5A.!!$R1 1263
2 TraesCS3A01G164500 chr5A 274868628 274869548 920 True 1450 1450 95.125 1421 2339 1 chr5A.!!$R2 918
3 TraesCS3A01G164500 chr5A 581574938 581576151 1213 True 848 848 79.551 157 1391 1 chr5A.!!$R4 1234
4 TraesCS3A01G164500 chr2A 541847077 541848311 1234 True 2032 2032 96.356 184 1418 1 chr2A.!!$R2 1234
5 TraesCS3A01G164500 chr2A 42693649 42694568 919 False 1471 1471 95.553 1421 2339 1 chr2A.!!$F1 918
6 TraesCS3A01G164500 chr2A 666573152 666574067 915 True 1445 1445 95.103 1421 2339 1 chr2A.!!$R3 918
7 TraesCS3A01G164500 chr2A 491484389 491485308 919 True 1443 1443 95.011 1421 2339 1 chr2A.!!$R1 918
8 TraesCS3A01G164500 chr1A 451737049 451738306 1257 False 2017 2017 95.570 157 1419 1 chr1A.!!$F2 1262
9 TraesCS3A01G164500 chr1A 391934422 391935339 917 False 1435 1435 94.902 1421 2339 1 chr1A.!!$F1 918
10 TraesCS3A01G164500 chr1A 327012033 327013369 1336 False 1103 1677 96.687 157 1420 2 chr1A.!!$F3 1263
11 TraesCS3A01G164500 chr6A 176544101 176545020 919 True 1454 1454 95.228 1421 2339 1 chr6A.!!$R1 918
12 TraesCS3A01G164500 chr7A 187187813 187188732 919 True 1443 1443 95.011 1421 2339 1 chr7A.!!$R1 918
13 TraesCS3A01G164500 chr4A 23968798 23969716 918 False 1443 1443 95.016 1421 2339 1 chr4A.!!$F1 918
14 TraesCS3A01G164500 chr2D 470891908 470892825 917 True 1435 1435 94.891 1421 2339 1 chr2D.!!$R2 918
15 TraesCS3A01G164500 chr7D 612341720 612342970 1250 False 909 909 80.063 157 1420 1 chr7D.!!$F1 1263
16 TraesCS3A01G164500 chr6B 479871688 479872869 1181 True 841 841 79.734 157 1348 1 chr6B.!!$R1 1191
17 TraesCS3A01G164500 chr6B 231369988 231370494 506 False 370 370 80.118 743 1242 1 chr6B.!!$F1 499

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
66 67 0.034896 GAAAGACCTCGGTGAAGCCA 59.965 55.0 0.0 0.0 36.97 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2001 0.601558 TAGTCAACGAGTCTGCCACC 59.398 55.0 0.0 0.0 0.0 4.61 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
26 27 9.933723 AATTTTTCTGGAAATCATAAAGGAGTG 57.066 29.630 0.00 0.00 0.00 3.51
27 28 8.477419 TTTTTCTGGAAATCATAAAGGAGTGT 57.523 30.769 0.00 0.00 0.00 3.55
28 29 8.477419 TTTTCTGGAAATCATAAAGGAGTGTT 57.523 30.769 0.00 0.00 0.00 3.32
29 30 8.477419 TTTCTGGAAATCATAAAGGAGTGTTT 57.523 30.769 0.00 0.00 0.00 2.83
30 31 7.452880 TCTGGAAATCATAAAGGAGTGTTTG 57.547 36.000 0.00 0.00 0.00 2.93
31 32 7.230747 TCTGGAAATCATAAAGGAGTGTTTGA 58.769 34.615 0.00 0.00 0.00 2.69
32 33 7.723616 TCTGGAAATCATAAAGGAGTGTTTGAA 59.276 33.333 0.00 0.00 0.00 2.69
33 34 8.243961 TGGAAATCATAAAGGAGTGTTTGAAA 57.756 30.769 0.00 0.00 0.00 2.69
34 35 8.359642 TGGAAATCATAAAGGAGTGTTTGAAAG 58.640 33.333 0.00 0.00 0.00 2.62
35 36 7.814587 GGAAATCATAAAGGAGTGTTTGAAAGG 59.185 37.037 0.00 0.00 0.00 3.11
36 37 8.477419 AAATCATAAAGGAGTGTTTGAAAGGA 57.523 30.769 0.00 0.00 0.00 3.36
37 38 7.693969 ATCATAAAGGAGTGTTTGAAAGGAG 57.306 36.000 0.00 0.00 0.00 3.69
38 39 6.601332 TCATAAAGGAGTGTTTGAAAGGAGT 58.399 36.000 0.00 0.00 0.00 3.85
39 40 7.060421 TCATAAAGGAGTGTTTGAAAGGAGTT 58.940 34.615 0.00 0.00 0.00 3.01
40 41 7.559897 TCATAAAGGAGTGTTTGAAAGGAGTTT 59.440 33.333 0.00 0.00 0.00 2.66
41 42 6.605471 AAAGGAGTGTTTGAAAGGAGTTTT 57.395 33.333 0.00 0.00 0.00 2.43
42 43 6.605471 AAGGAGTGTTTGAAAGGAGTTTTT 57.395 33.333 0.00 0.00 0.00 1.94
43 44 6.208988 AGGAGTGTTTGAAAGGAGTTTTTC 57.791 37.500 0.00 0.00 37.53 2.29
44 45 5.714806 AGGAGTGTTTGAAAGGAGTTTTTCA 59.285 36.000 0.00 0.00 43.32 2.69
54 55 7.320399 TGAAAGGAGTTTTTCAAAGAAAGACC 58.680 34.615 8.87 4.71 42.39 3.85
55 56 7.178451 TGAAAGGAGTTTTTCAAAGAAAGACCT 59.822 33.333 8.87 6.38 42.39 3.85
56 57 6.701145 AGGAGTTTTTCAAAGAAAGACCTC 57.299 37.500 8.87 7.60 0.00 3.85
57 58 5.297029 AGGAGTTTTTCAAAGAAAGACCTCG 59.703 40.000 8.87 0.00 0.00 4.63
58 59 5.500645 AGTTTTTCAAAGAAAGACCTCGG 57.499 39.130 8.87 0.00 0.00 4.63
59 60 4.948004 AGTTTTTCAAAGAAAGACCTCGGT 59.052 37.500 8.87 0.00 0.00 4.69
60 61 4.893424 TTTTCAAAGAAAGACCTCGGTG 57.107 40.909 0.00 0.00 0.00 4.94
61 62 3.830744 TTCAAAGAAAGACCTCGGTGA 57.169 42.857 0.00 0.00 0.00 4.02
62 63 3.830744 TCAAAGAAAGACCTCGGTGAA 57.169 42.857 0.00 0.00 0.00 3.18
63 64 3.728845 TCAAAGAAAGACCTCGGTGAAG 58.271 45.455 0.00 0.00 0.00 3.02
64 65 2.171341 AAGAAAGACCTCGGTGAAGC 57.829 50.000 0.00 0.00 0.00 3.86
65 66 0.321996 AGAAAGACCTCGGTGAAGCC 59.678 55.000 0.00 0.00 0.00 4.35
66 67 0.034896 GAAAGACCTCGGTGAAGCCA 59.965 55.000 0.00 0.00 36.97 4.75
67 68 0.250338 AAAGACCTCGGTGAAGCCAC 60.250 55.000 0.00 0.00 42.46 5.01
68 69 1.122019 AAGACCTCGGTGAAGCCACT 61.122 55.000 0.00 0.00 42.77 4.00
69 70 1.122019 AGACCTCGGTGAAGCCACTT 61.122 55.000 0.00 0.00 42.77 3.16
70 71 0.606604 GACCTCGGTGAAGCCACTTA 59.393 55.000 0.00 0.00 42.77 2.24
71 72 0.320697 ACCTCGGTGAAGCCACTTAC 59.679 55.000 0.00 0.00 42.77 2.34
72 73 0.320374 CCTCGGTGAAGCCACTTACA 59.680 55.000 0.00 0.00 42.77 2.41
73 74 1.066143 CCTCGGTGAAGCCACTTACAT 60.066 52.381 0.00 0.00 42.77 2.29
74 75 2.167693 CCTCGGTGAAGCCACTTACATA 59.832 50.000 0.00 0.00 42.77 2.29
75 76 3.181465 CCTCGGTGAAGCCACTTACATAT 60.181 47.826 0.00 0.00 42.77 1.78
76 77 4.442706 CTCGGTGAAGCCACTTACATATT 58.557 43.478 0.00 0.00 42.77 1.28
77 78 4.188462 TCGGTGAAGCCACTTACATATTG 58.812 43.478 0.00 0.00 42.77 1.90
78 79 4.081365 TCGGTGAAGCCACTTACATATTGA 60.081 41.667 0.00 0.00 42.77 2.57
79 80 4.271049 CGGTGAAGCCACTTACATATTGAG 59.729 45.833 0.00 0.00 42.77 3.02
80 81 4.035675 GGTGAAGCCACTTACATATTGAGC 59.964 45.833 0.00 0.00 42.77 4.26
81 82 4.635765 GTGAAGCCACTTACATATTGAGCA 59.364 41.667 0.00 0.00 40.10 4.26
82 83 5.297776 GTGAAGCCACTTACATATTGAGCAT 59.702 40.000 0.00 0.00 40.10 3.79
83 84 5.528690 TGAAGCCACTTACATATTGAGCATC 59.471 40.000 0.00 0.00 0.00 3.91
84 85 8.803579 GTGAAGCCACTTACATATTGAGCATCA 61.804 40.741 0.00 0.00 41.26 3.07
113 114 8.262715 TCTATAGAGATAGATCAAGACGCTTG 57.737 38.462 11.78 11.78 39.34 4.01
114 115 8.097662 TCTATAGAGATAGATCAAGACGCTTGA 58.902 37.037 19.64 19.64 39.34 3.02
115 116 5.181690 AGAGATAGATCAAGACGCTTGAC 57.818 43.478 19.72 14.67 0.00 3.18
116 117 4.642437 AGAGATAGATCAAGACGCTTGACA 59.358 41.667 19.72 11.36 0.00 3.58
117 118 5.301551 AGAGATAGATCAAGACGCTTGACAT 59.698 40.000 19.72 14.77 0.00 3.06
118 119 6.488344 AGAGATAGATCAAGACGCTTGACATA 59.512 38.462 19.72 15.98 0.00 2.29
119 120 7.176515 AGAGATAGATCAAGACGCTTGACATAT 59.823 37.037 19.72 18.70 0.00 1.78
120 121 7.665690 AGATAGATCAAGACGCTTGACATATT 58.334 34.615 19.72 7.94 0.00 1.28
121 122 8.147058 AGATAGATCAAGACGCTTGACATATTT 58.853 33.333 19.72 14.02 0.00 1.40
122 123 6.992063 AGATCAAGACGCTTGACATATTTT 57.008 33.333 19.72 6.81 0.00 1.82
123 124 7.383102 AGATCAAGACGCTTGACATATTTTT 57.617 32.000 19.72 6.23 0.00 1.94
124 125 7.467623 AGATCAAGACGCTTGACATATTTTTC 58.532 34.615 19.72 12.79 0.00 2.29
125 126 6.552859 TCAAGACGCTTGACATATTTTTCA 57.447 33.333 15.33 0.00 0.00 2.69
126 127 6.964908 TCAAGACGCTTGACATATTTTTCAA 58.035 32.000 15.33 0.00 0.00 2.69
127 128 7.592938 TCAAGACGCTTGACATATTTTTCAAT 58.407 30.769 15.33 0.00 31.41 2.57
128 129 7.538334 TCAAGACGCTTGACATATTTTTCAATG 59.462 33.333 15.33 0.00 31.41 2.82
129 130 7.144722 AGACGCTTGACATATTTTTCAATGA 57.855 32.000 0.00 0.00 31.41 2.57
130 131 7.246311 AGACGCTTGACATATTTTTCAATGAG 58.754 34.615 0.00 0.00 31.41 2.90
131 132 6.913170 ACGCTTGACATATTTTTCAATGAGT 58.087 32.000 0.00 0.00 31.41 3.41
132 133 8.039603 ACGCTTGACATATTTTTCAATGAGTA 57.960 30.769 0.00 0.00 31.41 2.59
133 134 7.962918 ACGCTTGACATATTTTTCAATGAGTAC 59.037 33.333 0.00 0.00 31.41 2.73
134 135 7.962373 CGCTTGACATATTTTTCAATGAGTACA 59.038 33.333 0.00 0.00 31.41 2.90
135 136 9.793252 GCTTGACATATTTTTCAATGAGTACAT 57.207 29.630 0.00 0.00 38.50 2.29
144 145 8.684386 TTTTTCAATGAGTACATACCTTGACA 57.316 30.769 0.00 0.00 35.50 3.58
145 146 8.684386 TTTTCAATGAGTACATACCTTGACAA 57.316 30.769 0.00 0.00 35.50 3.18
146 147 7.905604 TTCAATGAGTACATACCTTGACAAG 57.094 36.000 8.31 8.31 35.50 3.16
147 148 7.239763 TCAATGAGTACATACCTTGACAAGA 57.760 36.000 16.99 0.00 35.50 3.02
148 149 7.851228 TCAATGAGTACATACCTTGACAAGAT 58.149 34.615 16.99 1.19 35.50 2.40
149 150 8.321353 TCAATGAGTACATACCTTGACAAGATT 58.679 33.333 16.99 5.71 35.50 2.40
150 151 8.950210 CAATGAGTACATACCTTGACAAGATTT 58.050 33.333 16.99 3.26 35.50 2.17
151 152 9.520515 AATGAGTACATACCTTGACAAGATTTT 57.479 29.630 16.99 0.86 35.50 1.82
152 153 8.322906 TGAGTACATACCTTGACAAGATTTTG 57.677 34.615 16.99 10.29 40.24 2.44
153 154 8.154203 TGAGTACATACCTTGACAAGATTTTGA 58.846 33.333 16.99 0.00 37.73 2.69
154 155 8.553459 AGTACATACCTTGACAAGATTTTGAG 57.447 34.615 16.99 0.50 37.73 3.02
155 156 8.375506 AGTACATACCTTGACAAGATTTTGAGA 58.624 33.333 16.99 1.30 37.73 3.27
353 354 0.970427 GTGGGGCCCATTCGTCAATT 60.970 55.000 31.48 0.00 35.28 2.32
394 395 2.486203 CGACGCCTAGAGAGCATAATCT 59.514 50.000 0.00 0.00 0.00 2.40
566 571 0.618968 ATGTCTTCTTCCCCGCCTCT 60.619 55.000 0.00 0.00 0.00 3.69
599 604 2.022240 GCCGCCTCGATCTCTTCCTT 62.022 60.000 0.00 0.00 0.00 3.36
857 862 1.134848 GGACTAGAAGTGCTCTGCAGG 60.135 57.143 15.13 5.82 40.08 4.85
982 1010 0.613260 CAACGAAGGGGTCATGGAGA 59.387 55.000 0.00 0.00 0.00 3.71
1249 1356 2.368594 CAGAGGAGGGCCCCACTA 59.631 66.667 21.43 0.00 34.66 2.74
1467 1580 3.391296 ACAGTCAAAGGAGTTCTTGCCTA 59.609 43.478 0.00 0.00 35.55 3.93
1484 1597 2.351738 GCCTATGTTGCAAGGTGTGAAC 60.352 50.000 0.00 0.00 35.16 3.18
1726 1840 4.069304 CGGTTATGGAGGTGACAAAAAGA 58.931 43.478 0.00 0.00 0.00 2.52
1775 1889 4.819105 AGTTTTGACACCGATCTGGATA 57.181 40.909 10.05 0.00 42.00 2.59
1887 2001 4.332543 TGCAAAATACATACGGCTCTGAAG 59.667 41.667 0.00 0.00 0.00 3.02
1997 2113 6.697641 ATTGACTCTAGTAAACCCTTTGGA 57.302 37.500 0.00 0.00 34.81 3.53
2053 2169 8.514594 ACATAAAGATGTGAACTATTGGTGTTG 58.485 33.333 0.00 0.00 44.90 3.33
2113 2229 2.290577 GCAAGTGGGAGACTGAAGGAAT 60.291 50.000 0.00 0.00 34.02 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.933723 CACTCCTTTATGATTTCCAGAAAAATT 57.066 29.630 0.00 0.00 35.78 1.82
1 2 9.093458 ACACTCCTTTATGATTTCCAGAAAAAT 57.907 29.630 0.00 0.00 35.78 1.82
2 3 8.477419 ACACTCCTTTATGATTTCCAGAAAAA 57.523 30.769 0.00 0.00 35.78 1.94
3 4 8.477419 AACACTCCTTTATGATTTCCAGAAAA 57.523 30.769 0.00 0.00 35.78 2.29
4 5 8.359642 CAAACACTCCTTTATGATTTCCAGAAA 58.640 33.333 0.00 0.00 35.04 2.52
5 6 7.723616 TCAAACACTCCTTTATGATTTCCAGAA 59.276 33.333 0.00 0.00 0.00 3.02
6 7 7.230747 TCAAACACTCCTTTATGATTTCCAGA 58.769 34.615 0.00 0.00 0.00 3.86
7 8 7.452880 TCAAACACTCCTTTATGATTTCCAG 57.547 36.000 0.00 0.00 0.00 3.86
8 9 7.831691 TTCAAACACTCCTTTATGATTTCCA 57.168 32.000 0.00 0.00 0.00 3.53
9 10 7.814587 CCTTTCAAACACTCCTTTATGATTTCC 59.185 37.037 0.00 0.00 0.00 3.13
10 11 8.576442 TCCTTTCAAACACTCCTTTATGATTTC 58.424 33.333 0.00 0.00 0.00 2.17
11 12 8.477419 TCCTTTCAAACACTCCTTTATGATTT 57.523 30.769 0.00 0.00 0.00 2.17
12 13 7.725844 ACTCCTTTCAAACACTCCTTTATGATT 59.274 33.333 0.00 0.00 0.00 2.57
13 14 7.234355 ACTCCTTTCAAACACTCCTTTATGAT 58.766 34.615 0.00 0.00 0.00 2.45
14 15 6.601332 ACTCCTTTCAAACACTCCTTTATGA 58.399 36.000 0.00 0.00 0.00 2.15
15 16 6.884280 ACTCCTTTCAAACACTCCTTTATG 57.116 37.500 0.00 0.00 0.00 1.90
16 17 7.898014 AAACTCCTTTCAAACACTCCTTTAT 57.102 32.000 0.00 0.00 0.00 1.40
17 18 7.712204 AAAACTCCTTTCAAACACTCCTTTA 57.288 32.000 0.00 0.00 0.00 1.85
18 19 6.605471 AAAACTCCTTTCAAACACTCCTTT 57.395 33.333 0.00 0.00 0.00 3.11
19 20 6.210584 TGAAAAACTCCTTTCAAACACTCCTT 59.789 34.615 0.00 0.00 41.25 3.36
20 21 5.714806 TGAAAAACTCCTTTCAAACACTCCT 59.285 36.000 0.00 0.00 41.25 3.69
21 22 5.961272 TGAAAAACTCCTTTCAAACACTCC 58.039 37.500 0.00 0.00 41.25 3.85
29 30 7.178451 AGGTCTTTCTTTGAAAAACTCCTTTCA 59.822 33.333 0.00 0.00 42.21 2.69
30 31 7.548097 AGGTCTTTCTTTGAAAAACTCCTTTC 58.452 34.615 0.00 0.00 36.11 2.62
31 32 7.482169 AGGTCTTTCTTTGAAAAACTCCTTT 57.518 32.000 0.00 0.00 0.00 3.11
32 33 6.183360 CGAGGTCTTTCTTTGAAAAACTCCTT 60.183 38.462 11.09 0.00 0.00 3.36
33 34 5.297029 CGAGGTCTTTCTTTGAAAAACTCCT 59.703 40.000 11.09 0.00 0.00 3.69
34 35 5.505819 CCGAGGTCTTTCTTTGAAAAACTCC 60.506 44.000 11.09 0.00 0.00 3.85
35 36 5.066117 ACCGAGGTCTTTCTTTGAAAAACTC 59.934 40.000 0.00 0.00 0.00 3.01
36 37 4.948004 ACCGAGGTCTTTCTTTGAAAAACT 59.052 37.500 0.00 0.00 0.00 2.66
37 38 5.034797 CACCGAGGTCTTTCTTTGAAAAAC 58.965 41.667 0.00 0.00 0.00 2.43
38 39 4.944930 TCACCGAGGTCTTTCTTTGAAAAA 59.055 37.500 0.00 0.00 0.00 1.94
39 40 4.519213 TCACCGAGGTCTTTCTTTGAAAA 58.481 39.130 0.00 0.00 0.00 2.29
40 41 4.145365 TCACCGAGGTCTTTCTTTGAAA 57.855 40.909 0.00 0.00 0.00 2.69
41 42 3.830744 TCACCGAGGTCTTTCTTTGAA 57.169 42.857 0.00 0.00 0.00 2.69
42 43 3.728845 CTTCACCGAGGTCTTTCTTTGA 58.271 45.455 0.00 0.00 0.00 2.69
43 44 2.224314 GCTTCACCGAGGTCTTTCTTTG 59.776 50.000 0.00 0.00 0.00 2.77
44 45 2.495084 GCTTCACCGAGGTCTTTCTTT 58.505 47.619 0.00 0.00 0.00 2.52
45 46 1.270893 GGCTTCACCGAGGTCTTTCTT 60.271 52.381 0.00 0.00 0.00 2.52
46 47 0.321996 GGCTTCACCGAGGTCTTTCT 59.678 55.000 0.00 0.00 0.00 2.52
47 48 0.034896 TGGCTTCACCGAGGTCTTTC 59.965 55.000 0.00 0.00 43.94 2.62
48 49 0.250338 GTGGCTTCACCGAGGTCTTT 60.250 55.000 0.00 0.00 43.94 2.52
49 50 1.122019 AGTGGCTTCACCGAGGTCTT 61.122 55.000 0.00 0.00 43.94 3.01
50 51 1.122019 AAGTGGCTTCACCGAGGTCT 61.122 55.000 0.00 0.00 43.94 3.85
51 52 0.606604 TAAGTGGCTTCACCGAGGTC 59.393 55.000 0.00 0.00 43.94 3.85
52 53 0.320697 GTAAGTGGCTTCACCGAGGT 59.679 55.000 0.00 0.00 43.94 3.85
53 54 0.320374 TGTAAGTGGCTTCACCGAGG 59.680 55.000 0.00 0.00 43.94 4.63
54 55 2.386661 ATGTAAGTGGCTTCACCGAG 57.613 50.000 0.00 0.00 43.94 4.63
55 56 4.081365 TCAATATGTAAGTGGCTTCACCGA 60.081 41.667 0.00 0.00 43.94 4.69
56 57 4.188462 TCAATATGTAAGTGGCTTCACCG 58.812 43.478 0.00 0.00 43.94 4.94
57 58 4.035675 GCTCAATATGTAAGTGGCTTCACC 59.964 45.833 0.00 0.00 42.13 4.02
58 59 4.635765 TGCTCAATATGTAAGTGGCTTCAC 59.364 41.667 0.00 0.00 41.51 3.18
59 60 4.842574 TGCTCAATATGTAAGTGGCTTCA 58.157 39.130 0.00 0.00 0.00 3.02
60 61 5.528690 TGATGCTCAATATGTAAGTGGCTTC 59.471 40.000 0.00 0.00 0.00 3.86
61 62 5.439721 TGATGCTCAATATGTAAGTGGCTT 58.560 37.500 0.00 0.00 0.00 4.35
62 63 5.039920 TGATGCTCAATATGTAAGTGGCT 57.960 39.130 0.00 0.00 0.00 4.75
63 64 5.528690 TCTTGATGCTCAATATGTAAGTGGC 59.471 40.000 0.08 0.00 35.59 5.01
64 65 7.660617 AGATCTTGATGCTCAATATGTAAGTGG 59.339 37.037 0.00 0.00 35.59 4.00
65 66 8.604640 AGATCTTGATGCTCAATATGTAAGTG 57.395 34.615 0.00 0.00 35.59 3.16
75 76 9.972106 TCTATCTCTATAGATCTTGATGCTCAA 57.028 33.333 0.00 0.00 41.71 3.02
88 89 8.097662 TCAAGCGTCTTGATCTATCTCTATAGA 58.902 37.037 15.33 1.69 46.31 1.98
89 90 8.175069 GTCAAGCGTCTTGATCTATCTCTATAG 58.825 40.741 20.08 0.00 37.08 1.31
90 91 7.661847 TGTCAAGCGTCTTGATCTATCTCTATA 59.338 37.037 20.08 0.00 0.00 1.31
91 92 6.488344 TGTCAAGCGTCTTGATCTATCTCTAT 59.512 38.462 20.08 0.00 0.00 1.98
92 93 5.823045 TGTCAAGCGTCTTGATCTATCTCTA 59.177 40.000 20.08 0.00 0.00 2.43
93 94 4.642437 TGTCAAGCGTCTTGATCTATCTCT 59.358 41.667 20.08 0.00 0.00 3.10
94 95 4.926244 TGTCAAGCGTCTTGATCTATCTC 58.074 43.478 20.08 9.82 0.00 2.75
95 96 4.991153 TGTCAAGCGTCTTGATCTATCT 57.009 40.909 20.08 0.00 0.00 1.98
96 97 7.881643 AATATGTCAAGCGTCTTGATCTATC 57.118 36.000 20.08 10.86 0.00 2.08
97 98 8.668510 AAAATATGTCAAGCGTCTTGATCTAT 57.331 30.769 20.08 16.62 0.00 1.98
98 99 8.492673 AAAAATATGTCAAGCGTCTTGATCTA 57.507 30.769 20.08 15.57 0.00 1.98
99 100 6.992063 AAAATATGTCAAGCGTCTTGATCT 57.008 33.333 20.08 14.39 0.00 2.75
100 101 7.243487 TGAAAAATATGTCAAGCGTCTTGATC 58.757 34.615 20.08 15.18 0.00 2.92
101 102 7.144722 TGAAAAATATGTCAAGCGTCTTGAT 57.855 32.000 20.08 11.23 0.00 2.57
102 103 6.552859 TGAAAAATATGTCAAGCGTCTTGA 57.447 33.333 15.33 15.33 0.00 3.02
103 104 7.538334 TCATTGAAAAATATGTCAAGCGTCTTG 59.462 33.333 11.78 11.78 37.19 3.02
104 105 7.592938 TCATTGAAAAATATGTCAAGCGTCTT 58.407 30.769 3.87 0.00 37.19 3.01
105 106 7.094634 ACTCATTGAAAAATATGTCAAGCGTCT 60.095 33.333 3.87 0.00 37.19 4.18
106 107 7.023575 ACTCATTGAAAAATATGTCAAGCGTC 58.976 34.615 3.87 0.00 37.19 5.19
107 108 6.913170 ACTCATTGAAAAATATGTCAAGCGT 58.087 32.000 3.87 0.00 37.19 5.07
108 109 7.962373 TGTACTCATTGAAAAATATGTCAAGCG 59.038 33.333 0.00 0.00 37.19 4.68
109 110 9.793252 ATGTACTCATTGAAAAATATGTCAAGC 57.207 29.630 0.00 0.00 37.19 4.01
118 119 9.295825 TGTCAAGGTATGTACTCATTGAAAAAT 57.704 29.630 12.10 0.00 35.70 1.82
119 120 8.684386 TGTCAAGGTATGTACTCATTGAAAAA 57.316 30.769 12.10 3.36 35.70 1.94
120 121 8.684386 TTGTCAAGGTATGTACTCATTGAAAA 57.316 30.769 12.10 11.02 35.70 2.29
121 122 8.154203 TCTTGTCAAGGTATGTACTCATTGAAA 58.846 33.333 12.66 7.00 35.70 2.69
122 123 7.676004 TCTTGTCAAGGTATGTACTCATTGAA 58.324 34.615 12.66 2.26 35.70 2.69
123 124 7.239763 TCTTGTCAAGGTATGTACTCATTGA 57.760 36.000 12.66 8.41 35.70 2.57
124 125 8.498054 AATCTTGTCAAGGTATGTACTCATTG 57.502 34.615 12.66 0.00 35.70 2.82
125 126 9.520515 AAAATCTTGTCAAGGTATGTACTCATT 57.479 29.630 12.66 0.00 35.70 2.57
126 127 8.950210 CAAAATCTTGTCAAGGTATGTACTCAT 58.050 33.333 12.66 0.00 38.00 2.90
127 128 8.154203 TCAAAATCTTGTCAAGGTATGTACTCA 58.846 33.333 12.66 0.00 33.94 3.41
128 129 8.547967 TCAAAATCTTGTCAAGGTATGTACTC 57.452 34.615 12.66 0.00 33.94 2.59
129 130 8.375506 TCTCAAAATCTTGTCAAGGTATGTACT 58.624 33.333 12.66 0.00 33.94 2.73
130 131 8.547967 TCTCAAAATCTTGTCAAGGTATGTAC 57.452 34.615 12.66 0.00 33.94 2.90
131 132 9.567776 TTTCTCAAAATCTTGTCAAGGTATGTA 57.432 29.630 12.66 0.00 33.94 2.29
132 133 8.463930 TTTCTCAAAATCTTGTCAAGGTATGT 57.536 30.769 12.66 0.00 33.94 2.29
133 134 9.748708 TTTTTCTCAAAATCTTGTCAAGGTATG 57.251 29.630 12.66 8.64 33.94 2.39
353 354 0.719015 AGGAGGAGAGTGGGGATTCA 59.281 55.000 0.00 0.00 0.00 2.57
394 395 1.370587 GGCGGCATAAACCAAGCGTA 61.371 55.000 3.07 0.00 0.00 4.42
1005 1035 1.453155 CAGCCACCACGCTAAAATCT 58.547 50.000 0.00 0.00 36.82 2.40
1040 1070 1.202568 CGAGCCTGGCATTGTCATCTA 60.203 52.381 22.65 0.00 0.00 1.98
1361 1471 2.224917 GGTTCACATAACCCCCTGAACA 60.225 50.000 10.60 0.00 42.84 3.18
1467 1580 3.023119 TCAAGTTCACACCTTGCAACAT 58.977 40.909 0.00 0.00 39.30 2.71
1775 1889 5.954752 TGTATCCAGATTGAGACTCAGAGTT 59.045 40.000 4.05 0.00 0.00 3.01
1887 2001 0.601558 TAGTCAACGAGTCTGCCACC 59.398 55.000 0.00 0.00 0.00 4.61
2232 2348 6.069615 AGGCATACTAGGGACACTATGTTTTT 60.070 38.462 0.00 0.00 0.00 1.94
2239 2355 4.664064 AGTAGAGGCATACTAGGGACACTA 59.336 45.833 0.00 0.00 34.21 2.74


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

AutoCloner maintained by Alex Coulton.