Multiple sequence alignment - TraesCS5D01G418400

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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 TraesCS5D01G418400 chr5D 100.000 4870 0 0 1 4870 480349162 480344293 0.000000e+00 8994
1 TraesCS5D01G418400 chr5A 95.622 3152 117 10 1729 4870 598819862 598816722 0.000000e+00 5036
2 TraesCS5D01G418400 chr5A 92.323 1003 51 15 438 1430 598822632 598821646 0.000000e+00 1402
3 TraesCS5D01G418400 chr5A 94.444 234 7 5 1501 1731 598821427 598821197 6.000000e-94 355
4 TraesCS5D01G418400 chr5B 93.255 1794 86 23 3096 4866 588397901 588396120 0.000000e+00 2610
5 TraesCS5D01G418400 chr5B 92.317 1614 73 26 1502 3097 588399563 588397983 0.000000e+00 2246
6 TraesCS5D01G418400 chr5B 90.612 1406 77 30 123 1484 588401271 588399877 0.000000e+00 1814
7 TraesCS5D01G418400 chr3A 88.706 425 19 16 888 1311 158185759 158185363 4.380000e-135 492
8 TraesCS5D01G418400 chr3A 90.291 309 21 7 365 671 158197691 158197390 3.530000e-106 396
9 TraesCS5D01G418400 chr1A 97.464 276 7 0 1155 1430 45842268 45842543 5.710000e-129 472
10 TraesCS5D01G418400 chr1A 93.085 188 11 1 365 550 45841539 45841726 1.730000e-69 274
11 TraesCS5D01G418400 chr1A 81.982 222 12 15 905 1126 45841710 45841903 3.900000e-36 163


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 TraesCS5D01G418400 chr5D 480344293 480349162 4869 True 8994.000000 8994 100.000000 1 4870 1 chr5D.!!$R1 4869
1 TraesCS5D01G418400 chr5A 598816722 598822632 5910 True 2264.333333 5036 94.129667 438 4870 3 chr5A.!!$R1 4432
2 TraesCS5D01G418400 chr5B 588396120 588401271 5151 True 2223.333333 2610 92.061333 123 4866 3 chr5B.!!$R1 4743
3 TraesCS5D01G418400 chr1A 45841539 45842543 1004 False 303.000000 472 90.843667 365 1430 3 chr1A.!!$F1 1065

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
430 445 0.173481 GCCACAGCATAGACAGTCGA 59.827 55.000 0.00 0.0 39.53 4.20 F
939 972 0.471401 GCTACCCCCTAATCCCGTCT 60.471 60.000 0.00 0.0 0.00 4.18 F
2342 4420 0.040204 CCCTTTTCCACCCTGCAGAT 59.960 55.000 17.39 0.0 0.00 2.90 F
2733 4814 1.354368 ACCCTGGCATTTATATCCCCG 59.646 52.381 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 4401 0.040204 ATCTGCAGGGTGGAAAAGGG 59.960 55.000 15.13 0.00 0.00 3.95 R
2623 4704 3.733337 AGTCTGGACAAATCACACTCAC 58.267 45.455 3.51 0.00 0.00 3.51 R
3281 5447 0.025001 CGAGTTCAAATACGGCGCAG 59.975 55.000 10.83 8.25 0.00 5.18 R
3938 6108 1.227823 CTGGGTTTGAGTGCGACCA 60.228 57.895 0.00 0.00 35.11 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
25 26 6.729690 AAAAGTGATCCCATTTGTTTCAGA 57.270 33.333 0.00 0.00 0.00 3.27
26 27 6.729690 AAAGTGATCCCATTTGTTTCAGAA 57.270 33.333 0.00 0.00 0.00 3.02
27 28 6.729690 AAGTGATCCCATTTGTTTCAGAAA 57.270 33.333 0.00 0.00 0.00 2.52
28 29 6.336842 AGTGATCCCATTTGTTTCAGAAAG 57.663 37.500 0.00 0.00 0.00 2.62
29 30 5.244626 AGTGATCCCATTTGTTTCAGAAAGG 59.755 40.000 0.00 0.00 0.00 3.11
30 31 5.011023 GTGATCCCATTTGTTTCAGAAAGGT 59.989 40.000 0.00 0.00 0.00 3.50
31 32 5.602145 TGATCCCATTTGTTTCAGAAAGGTT 59.398 36.000 0.00 0.00 0.00 3.50
32 33 5.948742 TCCCATTTGTTTCAGAAAGGTTT 57.051 34.783 0.00 0.00 0.00 3.27
33 34 6.306643 TCCCATTTGTTTCAGAAAGGTTTT 57.693 33.333 0.00 0.00 0.00 2.43
34 35 6.345298 TCCCATTTGTTTCAGAAAGGTTTTC 58.655 36.000 0.00 0.00 0.00 2.29
35 36 6.070538 TCCCATTTGTTTCAGAAAGGTTTTCA 60.071 34.615 0.00 0.00 0.00 2.69
36 37 6.597280 CCCATTTGTTTCAGAAAGGTTTTCAA 59.403 34.615 0.00 0.00 0.00 2.69
37 38 7.282901 CCCATTTGTTTCAGAAAGGTTTTCAAT 59.717 33.333 0.00 0.00 0.00 2.57
38 39 8.676401 CCATTTGTTTCAGAAAGGTTTTCAATT 58.324 29.630 0.00 0.00 0.00 2.32
42 43 8.839310 TGTTTCAGAAAGGTTTTCAATTTTCA 57.161 26.923 0.00 0.00 33.19 2.69
43 44 9.447157 TGTTTCAGAAAGGTTTTCAATTTTCAT 57.553 25.926 0.00 0.00 33.19 2.57
60 61 9.492973 CAATTTTCATTAATCCAGAAAAGTGGT 57.507 29.630 20.84 5.44 45.71 4.16
63 64 9.541143 TTTTCATTAATCCAGAAAAGTGGTTTC 57.459 29.630 7.67 0.00 45.23 2.78
64 65 7.831691 TCATTAATCCAGAAAAGTGGTTTCA 57.168 32.000 2.00 0.00 46.98 2.69
65 66 8.243961 TCATTAATCCAGAAAAGTGGTTTCAA 57.756 30.769 2.00 0.00 46.98 2.69
66 67 8.700051 TCATTAATCCAGAAAAGTGGTTTCAAA 58.300 29.630 2.00 0.00 46.98 2.69
67 68 8.764287 CATTAATCCAGAAAAGTGGTTTCAAAC 58.236 33.333 0.00 0.00 46.98 2.93
68 69 5.930837 ATCCAGAAAAGTGGTTTCAAACA 57.069 34.783 1.93 0.00 46.98 2.83
69 70 5.930837 TCCAGAAAAGTGGTTTCAAACAT 57.069 34.783 1.93 0.00 46.98 2.71
70 71 6.293004 TCCAGAAAAGTGGTTTCAAACATT 57.707 33.333 1.93 0.00 46.98 2.71
71 72 6.706295 TCCAGAAAAGTGGTTTCAAACATTT 58.294 32.000 1.93 0.00 46.98 2.32
72 73 6.816140 TCCAGAAAAGTGGTTTCAAACATTTC 59.184 34.615 1.93 7.17 46.98 2.17
73 74 6.593382 CCAGAAAAGTGGTTTCAAACATTTCA 59.407 34.615 16.07 0.00 46.98 2.69
74 75 7.201548 CCAGAAAAGTGGTTTCAAACATTTCAG 60.202 37.037 16.07 11.07 46.98 3.02
75 76 7.545265 CAGAAAAGTGGTTTCAAACATTTCAGA 59.455 33.333 16.07 0.00 46.98 3.27
76 77 7.761249 AGAAAAGTGGTTTCAAACATTTCAGAG 59.239 33.333 16.07 0.00 46.98 3.35
77 78 6.773976 AAGTGGTTTCAAACATTTCAGAGA 57.226 33.333 1.93 0.00 0.00 3.10
78 79 6.382869 AGTGGTTTCAAACATTTCAGAGAG 57.617 37.500 1.93 0.00 0.00 3.20
79 80 6.122277 AGTGGTTTCAAACATTTCAGAGAGA 58.878 36.000 1.93 0.00 0.00 3.10
80 81 6.774656 AGTGGTTTCAAACATTTCAGAGAGAT 59.225 34.615 1.93 0.00 0.00 2.75
81 82 7.286316 AGTGGTTTCAAACATTTCAGAGAGATT 59.714 33.333 1.93 0.00 0.00 2.40
82 83 8.567948 GTGGTTTCAAACATTTCAGAGAGATTA 58.432 33.333 1.93 0.00 0.00 1.75
83 84 9.300681 TGGTTTCAAACATTTCAGAGAGATTAT 57.699 29.630 1.93 0.00 0.00 1.28
84 85 9.565213 GGTTTCAAACATTTCAGAGAGATTATG 57.435 33.333 1.93 0.00 0.00 1.90
88 89 9.288576 TCAAACATTTCAGAGAGATTATGTTGT 57.711 29.630 0.00 0.00 39.64 3.32
89 90 9.903682 CAAACATTTCAGAGAGATTATGTTGTT 57.096 29.630 0.00 0.00 39.64 2.83
92 93 9.288576 ACATTTCAGAGAGATTATGTTGTTTCA 57.711 29.630 0.00 0.00 31.58 2.69
115 116 2.762535 AAGTGAACACACCTATCCCG 57.237 50.000 7.68 0.00 35.39 5.14
116 117 1.933021 AGTGAACACACCTATCCCGA 58.067 50.000 7.68 0.00 35.39 5.14
117 118 1.825474 AGTGAACACACCTATCCCGAG 59.175 52.381 7.68 0.00 35.39 4.63
118 119 1.822990 GTGAACACACCTATCCCGAGA 59.177 52.381 0.00 0.00 0.00 4.04
119 120 2.431057 GTGAACACACCTATCCCGAGAT 59.569 50.000 0.00 0.00 36.44 2.75
120 121 3.635373 GTGAACACACCTATCCCGAGATA 59.365 47.826 0.00 0.00 33.67 1.98
121 122 4.281182 GTGAACACACCTATCCCGAGATAT 59.719 45.833 0.00 0.00 34.44 1.63
122 123 4.899457 TGAACACACCTATCCCGAGATATT 59.101 41.667 0.00 0.00 34.44 1.28
123 124 5.365605 TGAACACACCTATCCCGAGATATTT 59.634 40.000 0.00 0.00 34.44 1.40
124 125 5.888982 ACACACCTATCCCGAGATATTTT 57.111 39.130 0.00 0.00 34.44 1.82
125 126 6.989155 ACACACCTATCCCGAGATATTTTA 57.011 37.500 0.00 0.00 34.44 1.52
126 127 6.994221 ACACACCTATCCCGAGATATTTTAG 58.006 40.000 0.00 0.00 34.44 1.85
131 132 9.555727 CACCTATCCCGAGATATTTTAGAAAAA 57.444 33.333 0.00 0.00 34.44 1.94
148 149 8.810652 TTAGAAAAAGGATTTCAACCATTTCG 57.189 30.769 4.01 0.00 37.28 3.46
165 166 6.183360 ACCATTTCGGCGAGAATTCATTATTT 60.183 34.615 10.46 0.00 38.86 1.40
166 167 6.360681 CCATTTCGGCGAGAATTCATTATTTC 59.639 38.462 10.46 0.00 38.86 2.17
167 168 6.429791 TTTCGGCGAGAATTCATTATTTCA 57.570 33.333 10.46 0.00 38.86 2.69
168 169 6.429791 TTCGGCGAGAATTCATTATTTCAA 57.570 33.333 10.46 0.00 33.14 2.69
169 170 6.429791 TCGGCGAGAATTCATTATTTCAAA 57.570 33.333 4.99 0.00 0.00 2.69
170 171 6.847400 TCGGCGAGAATTCATTATTTCAAAA 58.153 32.000 4.99 0.00 0.00 2.44
203 204 6.061441 TGTGGTCACAACTATTTCAGACATT 58.939 36.000 0.78 0.00 38.56 2.71
225 226 6.912203 TTTTTCAATTTTTCCGGAAAGGTC 57.088 33.333 27.48 0.00 41.99 3.85
226 227 4.594123 TTCAATTTTTCCGGAAAGGTCC 57.406 40.909 27.48 0.00 41.99 4.46
230 231 2.209690 TTTTCCGGAAAGGTCCCATC 57.790 50.000 27.48 0.00 41.44 3.51
236 237 2.620367 CCGGAAAGGTCCCATCATTTCA 60.620 50.000 0.00 0.00 41.44 2.69
307 309 7.323420 TGTTGTCTCGACTTCATTATCTCAAT 58.677 34.615 0.00 0.00 0.00 2.57
311 313 9.521503 TGTCTCGACTTCATTATCTCAATAAAG 57.478 33.333 0.00 0.00 31.28 1.85
375 380 1.934956 CAGAGAATCGACGCGTCCG 60.935 63.158 31.84 25.30 42.67 4.79
426 441 2.520039 CGCGCCACAGCATAGACAG 61.520 63.158 0.00 0.00 39.83 3.51
430 445 0.173481 GCCACAGCATAGACAGTCGA 59.827 55.000 0.00 0.00 39.53 4.20
444 459 3.515286 TCGATCCTCGGTGGCGAC 61.515 66.667 0.00 0.00 40.88 5.19
586 601 1.479323 AGCTATTAACTCGCAACCGGA 59.521 47.619 9.46 0.00 34.56 5.14
588 603 1.850441 CTATTAACTCGCAACCGGACG 59.150 52.381 9.46 9.47 34.56 4.79
589 604 1.356527 ATTAACTCGCAACCGGACGC 61.357 55.000 9.46 9.44 34.56 5.19
802 827 4.752594 TAAAGCGGGGGAGGCCCT 62.753 66.667 0.00 0.00 44.66 5.19
885 918 4.323602 CACGTACACTATATATGCGGCTTG 59.676 45.833 0.00 0.00 0.00 4.01
939 972 0.471401 GCTACCCCCTAATCCCGTCT 60.471 60.000 0.00 0.00 0.00 4.18
1029 1083 2.188207 GAAGAGGAGAAGGCGGCC 59.812 66.667 12.11 12.11 0.00 6.13
1067 1121 2.364842 GCTGCAGGAGGGAGAGGA 60.365 66.667 17.12 0.00 37.05 3.71
1271 1661 3.003173 CAGGGGCCTCCACGAGAA 61.003 66.667 0.00 0.00 38.24 2.87
1458 1894 3.002759 TCGTGAAATGTGTTGCGAATTCA 59.997 39.130 6.22 0.00 0.00 2.57
1486 1922 8.761575 ATTTTGAAATGCATCTTCGTATTTGT 57.238 26.923 0.00 0.00 32.27 2.83
1488 1924 8.586570 TTTGAAATGCATCTTCGTATTTGTTT 57.413 26.923 0.00 0.00 32.27 2.83
1489 1925 7.795431 TGAAATGCATCTTCGTATTTGTTTC 57.205 32.000 0.00 0.00 32.27 2.78
1491 1927 7.864882 TGAAATGCATCTTCGTATTTGTTTCAA 59.135 29.630 0.00 0.00 32.27 2.69
1492 1928 8.586570 AAATGCATCTTCGTATTTGTTTCAAA 57.413 26.923 0.00 0.00 31.12 2.69
1493 1929 8.586570 AATGCATCTTCGTATTTGTTTCAAAA 57.413 26.923 0.00 0.00 0.00 2.44
1494 1930 8.761575 ATGCATCTTCGTATTTGTTTCAAAAT 57.238 26.923 0.00 0.00 34.24 1.82
1495 1931 8.226543 TGCATCTTCGTATTTGTTTCAAAATC 57.773 30.769 0.00 0.00 32.16 2.17
1496 1932 7.864882 TGCATCTTCGTATTTGTTTCAAAATCA 59.135 29.630 0.00 0.00 32.16 2.57
1497 1933 8.863049 GCATCTTCGTATTTGTTTCAAAATCAT 58.137 29.630 0.00 0.00 32.16 2.45
1570 2302 7.031226 TGCTTCCATCAAACAGAATAATAGC 57.969 36.000 0.00 0.00 0.00 2.97
1664 2399 5.417266 TCGAATGGGCAATTAGTTTTCATCA 59.583 36.000 0.00 0.00 0.00 3.07
1700 2435 6.884295 ACACTATGGTATCTGCAAGCTTAAAA 59.116 34.615 0.00 0.00 0.00 1.52
1746 3818 5.277601 TGAGTTTATAGAAACAACGCAGC 57.722 39.130 14.93 0.00 46.30 5.25
1800 3872 7.489574 TTTTGATTGGTAAACTGAAAATGGC 57.510 32.000 0.00 0.00 0.00 4.40
1889 3962 5.587289 TGCCAGCAAAACAGTAGTAAAAAG 58.413 37.500 0.00 0.00 0.00 2.27
1920 3993 4.660105 CAGACTAAGTTAGTGTACGAGCC 58.340 47.826 20.21 3.40 39.59 4.70
1950 4023 5.560722 TTATGACCAGAGACCTCACAAAA 57.439 39.130 0.00 0.00 0.00 2.44
1969 4042 8.690884 TCACAAAATGTCATTTCACCTTTTAGA 58.309 29.630 11.19 0.00 0.00 2.10
2162 4238 4.296690 ACTTTCACAAGTACGTCAGCTAC 58.703 43.478 0.00 0.00 41.81 3.58
2323 4401 1.376553 GTCCCTCTTCTGTGCCAGC 60.377 63.158 0.00 0.00 0.00 4.85
2325 4403 2.045536 CCTCTTCTGTGCCAGCCC 60.046 66.667 0.00 0.00 0.00 5.19
2342 4420 0.040204 CCCTTTTCCACCCTGCAGAT 59.960 55.000 17.39 0.00 0.00 2.90
2343 4421 1.550869 CCCTTTTCCACCCTGCAGATT 60.551 52.381 17.39 0.00 0.00 2.40
2344 4422 2.250924 CCTTTTCCACCCTGCAGATTT 58.749 47.619 17.39 0.00 0.00 2.17
2668 4749 4.022589 CCAAAGAGCACTTGACACATCAAT 60.023 41.667 0.00 0.00 43.92 2.57
2731 4812 4.082125 CAAGACCCTGGCATTTATATCCC 58.918 47.826 0.00 0.00 0.00 3.85
2733 4814 1.354368 ACCCTGGCATTTATATCCCCG 59.646 52.381 0.00 0.00 0.00 5.73
2764 4846 1.692519 GCCCACGTAGACCAGGATATT 59.307 52.381 0.00 0.00 0.00 1.28
2982 5064 5.404366 GCTATGTATTCAGCAATGCATTTGG 59.596 40.000 9.83 0.17 41.17 3.28
3026 5108 3.515071 GCTTTTCAGCAATTGCACAAG 57.485 42.857 30.89 23.81 46.49 3.16
3182 5347 6.586344 ACTTGGGAGATATGTTCACATGTAG 58.414 40.000 0.00 0.00 35.38 2.74
3203 5368 6.591062 TGTAGAACACACTTTTACTTTGACGT 59.409 34.615 0.00 0.00 30.04 4.34
3206 5371 7.458677 AGAACACACTTTTACTTTGACGTAAC 58.541 34.615 0.00 0.00 0.00 2.50
3281 5447 0.393132 GACTGGGCTGCCTAAAGGAC 60.393 60.000 19.68 8.87 37.39 3.85
3401 5567 6.040054 CCATGATGGCAAAATCATTGACTAGA 59.960 38.462 0.00 0.00 43.28 2.43
3413 5579 4.713814 TCATTGACTAGAGTTCCTGCTGAT 59.286 41.667 0.00 0.00 0.00 2.90
3476 5642 6.884836 GTGGGTATGTTCCTGAAAGAAATACT 59.115 38.462 0.00 0.00 34.07 2.12
3608 5774 3.505680 ACTTTATGAACAAGAATGCGGCA 59.494 39.130 4.58 4.58 0.00 5.69
3777 5943 1.632409 AGCTGAGGAGATTGCCAAGAA 59.368 47.619 0.00 0.00 0.00 2.52
4061 6233 2.892852 CAAGGATTTGCCCAGTTCTTCA 59.107 45.455 0.00 0.00 37.37 3.02
4482 6666 3.452474 TGGCAGGAAAACAAAACGATTG 58.548 40.909 0.00 0.00 0.00 2.67
4647 6834 5.879223 CCTTCATCTTCTTTCTGCAGTACAT 59.121 40.000 14.67 0.00 0.00 2.29
4662 6849 6.526526 TGCAGTACATTGAAGTTGGTAAGTA 58.473 36.000 0.00 0.00 0.00 2.24
4702 6889 2.484889 ACGAAGACTCCAAAGCAGTTC 58.515 47.619 0.00 0.00 0.00 3.01
4707 6894 4.640771 AGACTCCAAAGCAGTTCCATAA 57.359 40.909 0.00 0.00 0.00 1.90
4769 6956 0.252742 AGGGAAGTCGAGGAATGGGT 60.253 55.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.123355 TCTGAAACAAATGGGATCACTTTTT 57.877 32.000 6.11 0.00 0.00 1.94
2 3 6.729690 TCTGAAACAAATGGGATCACTTTT 57.270 33.333 3.07 3.07 0.00 2.27
5 6 5.244626 CCTTTCTGAAACAAATGGGATCACT 59.755 40.000 0.00 0.00 0.00 3.41
6 7 5.011023 ACCTTTCTGAAACAAATGGGATCAC 59.989 40.000 9.90 0.00 0.00 3.06
7 8 5.147032 ACCTTTCTGAAACAAATGGGATCA 58.853 37.500 9.90 0.00 0.00 2.92
8 9 5.728637 ACCTTTCTGAAACAAATGGGATC 57.271 39.130 9.90 0.00 0.00 3.36
9 10 6.499106 AAACCTTTCTGAAACAAATGGGAT 57.501 33.333 9.90 0.00 0.00 3.85
10 11 5.948742 AAACCTTTCTGAAACAAATGGGA 57.051 34.783 9.90 0.00 0.00 4.37
11 12 6.112058 TGAAAACCTTTCTGAAACAAATGGG 58.888 36.000 0.00 0.79 0.00 4.00
12 13 7.608308 TTGAAAACCTTTCTGAAACAAATGG 57.392 32.000 0.00 1.50 0.00 3.16
16 17 9.277783 TGAAAATTGAAAACCTTTCTGAAACAA 57.722 25.926 0.00 1.81 34.05 2.83
17 18 8.839310 TGAAAATTGAAAACCTTTCTGAAACA 57.161 26.923 0.00 0.00 34.05 2.83
33 34 9.709495 CCACTTTTCTGGATTAATGAAAATTGA 57.291 29.630 20.06 2.41 40.00 2.57
34 35 9.492973 ACCACTTTTCTGGATTAATGAAAATTG 57.507 29.630 15.58 15.58 38.47 2.32
37 38 9.541143 GAAACCACTTTTCTGGATTAATGAAAA 57.459 29.630 10.20 10.20 40.60 2.29
38 39 8.700051 TGAAACCACTTTTCTGGATTAATGAAA 58.300 29.630 0.00 0.00 43.70 2.69
39 40 8.243961 TGAAACCACTTTTCTGGATTAATGAA 57.756 30.769 0.00 0.00 43.70 2.57
40 41 7.831691 TGAAACCACTTTTCTGGATTAATGA 57.168 32.000 0.00 0.00 43.70 2.57
41 42 8.764287 GTTTGAAACCACTTTTCTGGATTAATG 58.236 33.333 0.00 0.00 43.70 1.90
42 43 8.482128 TGTTTGAAACCACTTTTCTGGATTAAT 58.518 29.630 5.50 0.00 43.70 1.40
43 44 7.841956 TGTTTGAAACCACTTTTCTGGATTAA 58.158 30.769 5.50 0.00 43.70 1.40
44 45 7.411486 TGTTTGAAACCACTTTTCTGGATTA 57.589 32.000 5.50 0.00 43.70 1.75
45 46 6.293004 TGTTTGAAACCACTTTTCTGGATT 57.707 33.333 5.50 0.00 43.70 3.01
46 47 5.930837 TGTTTGAAACCACTTTTCTGGAT 57.069 34.783 5.50 0.00 43.70 3.41
47 48 5.930837 ATGTTTGAAACCACTTTTCTGGA 57.069 34.783 5.50 0.00 43.70 3.86
48 49 6.593382 TGAAATGTTTGAAACCACTTTTCTGG 59.407 34.615 5.50 0.00 43.70 3.86
49 50 7.545265 TCTGAAATGTTTGAAACCACTTTTCTG 59.455 33.333 5.50 12.15 43.70 3.02
50 51 7.610865 TCTGAAATGTTTGAAACCACTTTTCT 58.389 30.769 5.50 0.00 43.70 2.52
51 52 7.759433 TCTCTGAAATGTTTGAAACCACTTTTC 59.241 33.333 5.50 9.80 43.63 2.29
52 53 7.610865 TCTCTGAAATGTTTGAAACCACTTTT 58.389 30.769 5.50 1.04 0.00 2.27
53 54 7.122650 TCTCTCTGAAATGTTTGAAACCACTTT 59.877 33.333 5.50 3.22 0.00 2.66
54 55 6.603201 TCTCTCTGAAATGTTTGAAACCACTT 59.397 34.615 5.50 0.00 0.00 3.16
55 56 6.122277 TCTCTCTGAAATGTTTGAAACCACT 58.878 36.000 5.50 0.00 0.00 4.00
56 57 6.377327 TCTCTCTGAAATGTTTGAAACCAC 57.623 37.500 5.50 0.00 0.00 4.16
57 58 7.587037 AATCTCTCTGAAATGTTTGAAACCA 57.413 32.000 5.50 0.00 0.00 3.67
58 59 9.565213 CATAATCTCTCTGAAATGTTTGAAACC 57.435 33.333 5.50 0.00 0.00 3.27
62 63 9.288576 ACAACATAATCTCTCTGAAATGTTTGA 57.711 29.630 0.00 0.00 40.37 2.69
63 64 9.903682 AACAACATAATCTCTCTGAAATGTTTG 57.096 29.630 0.00 0.00 40.37 2.93
66 67 9.288576 TGAAACAACATAATCTCTCTGAAATGT 57.711 29.630 0.00 0.00 37.11 2.71
93 94 3.818773 CGGGATAGGTGTGTTCACTTTTT 59.181 43.478 4.59 0.00 43.41 1.94
94 95 3.071892 TCGGGATAGGTGTGTTCACTTTT 59.928 43.478 4.59 0.00 43.41 2.27
95 96 2.635915 TCGGGATAGGTGTGTTCACTTT 59.364 45.455 4.59 0.00 43.41 2.66
96 97 2.233922 CTCGGGATAGGTGTGTTCACTT 59.766 50.000 4.59 0.00 43.41 3.16
97 98 1.825474 CTCGGGATAGGTGTGTTCACT 59.175 52.381 4.59 0.00 43.41 3.41
98 99 1.822990 TCTCGGGATAGGTGTGTTCAC 59.177 52.381 0.00 0.00 43.19 3.18
99 100 2.225382 TCTCGGGATAGGTGTGTTCA 57.775 50.000 0.00 0.00 0.00 3.18
100 101 5.470047 AATATCTCGGGATAGGTGTGTTC 57.530 43.478 11.36 0.00 37.78 3.18
101 102 5.888982 AAATATCTCGGGATAGGTGTGTT 57.111 39.130 11.36 0.00 37.78 3.32
102 103 5.888982 AAAATATCTCGGGATAGGTGTGT 57.111 39.130 11.36 0.00 37.78 3.72
103 104 7.228314 TCTAAAATATCTCGGGATAGGTGTG 57.772 40.000 11.36 1.65 37.78 3.82
104 105 7.850935 TTCTAAAATATCTCGGGATAGGTGT 57.149 36.000 11.36 0.00 37.78 4.16
105 106 9.555727 TTTTTCTAAAATATCTCGGGATAGGTG 57.444 33.333 11.36 0.00 37.78 4.00
106 107 9.780186 CTTTTTCTAAAATATCTCGGGATAGGT 57.220 33.333 11.36 0.00 37.78 3.08
107 108 9.220767 CCTTTTTCTAAAATATCTCGGGATAGG 57.779 37.037 11.36 0.00 37.78 2.57
108 109 9.998106 TCCTTTTTCTAAAATATCTCGGGATAG 57.002 33.333 11.36 0.00 37.78 2.08
110 111 9.868160 AATCCTTTTTCTAAAATATCTCGGGAT 57.132 29.630 1.91 1.91 36.07 3.85
111 112 9.695155 AAATCCTTTTTCTAAAATATCTCGGGA 57.305 29.630 0.00 0.00 0.00 5.14
112 113 9.952188 GAAATCCTTTTTCTAAAATATCTCGGG 57.048 33.333 0.00 0.00 0.00 5.14
122 123 9.255304 CGAAATGGTTGAAATCCTTTTTCTAAA 57.745 29.630 0.42 0.00 34.16 1.85
123 124 7.870445 CCGAAATGGTTGAAATCCTTTTTCTAA 59.130 33.333 0.00 0.00 34.16 2.10
124 125 7.375053 CCGAAATGGTTGAAATCCTTTTTCTA 58.625 34.615 0.00 0.00 34.16 2.10
125 126 6.223120 CCGAAATGGTTGAAATCCTTTTTCT 58.777 36.000 0.00 0.00 34.16 2.52
126 127 5.107104 GCCGAAATGGTTGAAATCCTTTTTC 60.107 40.000 0.00 0.00 41.21 2.29
131 132 1.472480 CGCCGAAATGGTTGAAATCCT 59.528 47.619 0.00 0.00 41.21 3.24
170 171 6.976934 ATAGTTGTGACCACATTCCTTTTT 57.023 33.333 3.47 0.00 41.52 1.94
175 176 5.705441 TCTGAAATAGTTGTGACCACATTCC 59.295 40.000 3.47 0.00 41.52 3.01
176 177 6.204688 TGTCTGAAATAGTTGTGACCACATTC 59.795 38.462 3.47 5.31 41.52 2.67
177 178 6.061441 TGTCTGAAATAGTTGTGACCACATT 58.939 36.000 3.47 0.00 41.52 2.71
178 179 5.620206 TGTCTGAAATAGTTGTGACCACAT 58.380 37.500 3.47 0.00 41.52 3.21
179 180 5.029807 TGTCTGAAATAGTTGTGACCACA 57.970 39.130 0.00 0.00 39.98 4.17
203 204 5.361427 GGACCTTTCCGGAAAAATTGAAAA 58.639 37.500 28.62 5.18 36.31 2.29
215 216 2.024414 GAAATGATGGGACCTTTCCGG 58.976 52.381 0.00 0.00 43.94 5.14
265 266 9.179552 CGAGACAACAATTTTGTGAATATGAAA 57.820 29.630 9.70 0.00 41.31 2.69
269 270 8.099364 AGTCGAGACAACAATTTTGTGAATAT 57.901 30.769 5.99 0.00 41.31 1.28
288 290 8.586570 AGCTTTATTGAGATAATGAAGTCGAG 57.413 34.615 0.00 0.00 0.00 4.04
404 412 4.529219 TATGCTGTGGCGCGAGGG 62.529 66.667 12.10 0.00 42.25 4.30
405 413 2.963854 CTATGCTGTGGCGCGAGG 60.964 66.667 12.10 0.00 42.25 4.63
635 652 3.818787 AGTACGTACGGCCAGGCG 61.819 66.667 21.06 12.45 0.00 5.52
649 666 1.513158 GCTTCTCCTGCTCGCAGTA 59.487 57.895 16.82 1.03 42.15 2.74
802 827 0.718904 CGGCGTTCATTTGATCGACA 59.281 50.000 15.08 0.00 43.43 4.35
804 829 0.996462 GACGGCGTTCATTTGATCGA 59.004 50.000 16.19 0.00 38.99 3.59
885 918 4.141144 CCACACGATACCATGGCC 57.859 61.111 13.04 0.00 0.00 5.36
892 925 2.890474 CAGCCGGCCACACGATAC 60.890 66.667 26.15 0.00 35.47 2.24
893 926 4.155733 CCAGCCGGCCACACGATA 62.156 66.667 26.15 0.00 35.47 2.92
983 1016 0.249031 CATGATCGACCAGCTGCGTA 60.249 55.000 8.66 0.00 0.00 4.42
1054 1108 1.454847 CCTCGTCCTCTCCCTCCTG 60.455 68.421 0.00 0.00 0.00 3.86
1536 2268 9.806203 TCTGTTTGATGGAAGCAATTATATTTG 57.194 29.630 3.47 3.47 44.33 2.32
1570 2302 7.362662 AGCATGTGTAATTGTGTAAGTGAAAG 58.637 34.615 0.00 0.00 0.00 2.62
1664 2399 6.599244 CAGATACCATAGTGTTTCACAACCAT 59.401 38.462 2.80 0.00 36.74 3.55
1731 3803 6.683974 AATTATCTGCTGCGTTGTTTCTAT 57.316 33.333 0.00 0.00 0.00 1.98
1798 3870 1.094785 ACGACATGCTAATTGGTGCC 58.905 50.000 0.00 0.00 0.00 5.01
1800 3872 4.418013 TTTCACGACATGCTAATTGGTG 57.582 40.909 0.00 0.00 0.00 4.17
1847 3919 6.972901 GCTGGCATATGTTAGTTAAAGGAAAC 59.027 38.462 4.29 0.00 0.00 2.78
1920 3993 6.268617 TGAGGTCTCTGGTCATAAATAGATGG 59.731 42.308 0.00 0.00 0.00 3.51
2036 4109 9.579932 TTTAATGGTATTGGCCTTTCAATTTTT 57.420 25.926 3.32 0.00 38.24 1.94
2037 4110 9.579932 TTTTAATGGTATTGGCCTTTCAATTTT 57.420 25.926 3.32 0.00 38.24 1.82
2038 4111 9.752228 ATTTTAATGGTATTGGCCTTTCAATTT 57.248 25.926 3.32 0.00 38.24 1.82
2141 4217 3.361053 CGTAGCTGACGTACTTGTGAAAG 59.639 47.826 0.00 0.00 46.86 2.62
2323 4401 0.040204 ATCTGCAGGGTGGAAAAGGG 59.960 55.000 15.13 0.00 0.00 3.95
2325 4403 4.341366 AAAAATCTGCAGGGTGGAAAAG 57.659 40.909 15.13 0.00 0.00 2.27
2623 4704 3.733337 AGTCTGGACAAATCACACTCAC 58.267 45.455 3.51 0.00 0.00 3.51
2745 4826 4.417426 AAAATATCCTGGTCTACGTGGG 57.583 45.455 0.00 0.00 0.00 4.61
2858 4940 4.157289 AGCTGCTGAAAATGAAATCGATGT 59.843 37.500 0.00 0.00 0.00 3.06
2951 5033 6.129273 GCATTGCTGAATACATAGCGAATTTG 60.129 38.462 0.16 0.00 42.74 2.32
3026 5108 6.966066 GCTCAATGTCTTCTTCTAGCAATTTC 59.034 38.462 0.00 0.00 0.00 2.17
3182 5347 7.235777 TGTTACGTCAAAGTAAAAGTGTGTTC 58.764 34.615 0.00 0.00 38.19 3.18
3206 5371 8.960591 ACAATATTTATCCAAGTCAGTCCTTTG 58.039 33.333 0.00 0.00 0.00 2.77
3281 5447 0.025001 CGAGTTCAAATACGGCGCAG 59.975 55.000 10.83 8.25 0.00 5.18
3401 5567 4.830046 ACATCTCGTATATCAGCAGGAACT 59.170 41.667 0.00 0.00 43.88 3.01
3413 5579 5.009710 GGTCATCCAGTCAACATCTCGTATA 59.990 44.000 0.00 0.00 0.00 1.47
3476 5642 4.540099 AGGATTCCTTCAAGAACCCATACA 59.460 41.667 0.00 0.00 30.90 2.29
3777 5943 4.624913 TCCTCTGGATTAATCTCCACTGT 58.375 43.478 14.95 0.00 40.43 3.55
3815 5981 6.825721 CAGAGGCTTCTACCAAATACAATCTT 59.174 38.462 0.00 0.00 30.73 2.40
3938 6108 1.227823 CTGGGTTTGAGTGCGACCA 60.228 57.895 0.00 0.00 35.11 4.02
4061 6233 5.192923 TGCTTGGAAGGTACTATAAATGGGT 59.807 40.000 0.00 0.00 38.49 4.51
4415 6599 2.158623 TCTGGTCTTTGCTCACCATTGT 60.159 45.455 0.00 0.00 41.97 2.71
4426 6610 1.321474 TTGCTTGCCTCTGGTCTTTG 58.679 50.000 0.00 0.00 0.00 2.77
4662 6849 4.110482 CGTAAGCTAGTAAATTCGCTGGT 58.890 43.478 0.00 0.00 32.22 4.00
4732 6919 9.678941 GACTTCCCTTACAAAAAGAGTTTTATG 57.321 33.333 0.00 0.00 35.12 1.90
4753 6940 3.132289 TGATGTACCCATTCCTCGACTTC 59.868 47.826 0.00 0.00 0.00 3.01
4769 6956 8.995027 AGGATTTAAATACCAATGCTGATGTA 57.005 30.769 6.80 0.00 30.54 2.29


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

AutoCloner maintained by Alex Coulton.