Multiple sequence alignment - TraesCS5B01G371600

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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 TraesCS5B01G371600 chr5B 100.000 2393 0 0 1 2393 550210138 550212530 0.000000e+00 4420.0
1 TraesCS5B01G371600 chr5B 76.438 539 78 27 972 1479 550161890 550162410 1.840000e-61 246.0
2 TraesCS5B01G371600 chr5A 88.767 1914 111 39 28 1889 569468170 569470031 0.000000e+00 2248.0
3 TraesCS5B01G371600 chr5A 91.549 71 6 0 2097 2167 569470379 569470449 5.440000e-17 99.0
4 TraesCS5B01G371600 chr5A 94.340 53 2 1 2053 2104 569470320 569470268 1.970000e-11 80.5
5 TraesCS5B01G371600 chr5D 90.230 1740 117 28 324 2041 450178860 450180568 0.000000e+00 2222.0
6 TraesCS5B01G371600 chr5D 92.664 259 16 3 2136 2393 450199331 450199587 1.040000e-98 370.0
7 TraesCS5B01G371600 chr5D 93.514 185 9 3 1955 2136 450180564 450180748 3.030000e-69 272.0
8 TraesCS5B01G371600 chr5D 76.766 538 82 28 972 1479 450153428 450153952 6.560000e-66 261.0
9 TraesCS5B01G371600 chr5D 93.125 160 10 1 2234 2393 450199937 450200095 1.430000e-57 233.0
10 TraesCS5B01G371600 chr2D 72.495 549 96 26 821 1333 66867157 66867686 2.500000e-25 126.0
11 TraesCS5B01G371600 chr2B 81.132 106 18 2 1198 1302 104581306 104581202 1.520000e-12 84.2


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 TraesCS5B01G371600 chr5B 550210138 550212530 2392 False 4420.0 4420 100.0000 1 2393 1 chr5B.!!$F2 2392
1 TraesCS5B01G371600 chr5B 550161890 550162410 520 False 246.0 246 76.4380 972 1479 1 chr5B.!!$F1 507
2 TraesCS5B01G371600 chr5A 569468170 569470449 2279 False 1173.5 2248 90.1580 28 2167 2 chr5A.!!$F1 2139
3 TraesCS5B01G371600 chr5D 450178860 450180748 1888 False 1247.0 2222 91.8720 324 2136 2 chr5D.!!$F2 1812
4 TraesCS5B01G371600 chr5D 450199331 450200095 764 False 301.5 370 92.8945 2136 2393 2 chr5D.!!$F3 257
5 TraesCS5B01G371600 chr5D 450153428 450153952 524 False 261.0 261 76.7660 972 1479 1 chr5D.!!$F1 507

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
440 447 0.335019 GGGTAGAAAAGGGCCATGGT 59.665 55.0 14.67 0.0 0.00 3.55 F
1182 1241 0.539438 AAATGCCGAAGCCTGAACCA 60.539 50.0 0.00 0.0 38.69 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1416 0.039035 TCCGGCTTAGGCATTGGTTT 59.961 50.0 6.6 0.0 40.87 3.27 R
2320 2699 0.249031 GGTTCTTGGTGTGCAGTTGC 60.249 55.0 0.0 0.0 42.50 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
21 22 3.738982 TCCTTTCTCTTCAAATGCACGA 58.261 40.909 0.00 0.00 0.00 4.35
22 23 3.498397 TCCTTTCTCTTCAAATGCACGAC 59.502 43.478 0.00 0.00 0.00 4.34
23 24 3.365364 CCTTTCTCTTCAAATGCACGACC 60.365 47.826 0.00 0.00 0.00 4.79
24 25 2.542020 TCTCTTCAAATGCACGACCA 57.458 45.000 0.00 0.00 0.00 4.02
25 26 2.844946 TCTCTTCAAATGCACGACCAA 58.155 42.857 0.00 0.00 0.00 3.67
26 27 3.210227 TCTCTTCAAATGCACGACCAAA 58.790 40.909 0.00 0.00 0.00 3.28
42 43 5.476945 ACGACCAAAAATAGGAGAATGCTTT 59.523 36.000 0.00 0.00 38.32 3.51
43 44 6.030228 CGACCAAAAATAGGAGAATGCTTTC 58.970 40.000 4.20 4.20 38.32 2.62
44 45 6.127897 CGACCAAAAATAGGAGAATGCTTTCT 60.128 38.462 14.25 14.25 44.99 2.52
87 88 8.951787 ATTTGTACAGTGTACAACTCTGTTTA 57.048 30.769 36.79 24.57 46.90 2.01
89 90 7.940178 TGTACAGTGTACAACTCTGTTTATG 57.060 36.000 29.44 1.05 46.90 1.90
90 91 7.718525 TGTACAGTGTACAACTCTGTTTATGA 58.281 34.615 29.44 5.12 46.90 2.15
91 92 8.364894 TGTACAGTGTACAACTCTGTTTATGAT 58.635 33.333 29.44 0.26 46.90 2.45
122 124 6.238648 GGGTTTTTCCTCTCTTAGTGAATGA 58.761 40.000 0.00 0.00 36.25 2.57
126 128 8.621286 GTTTTTCCTCTCTTAGTGAATGAAACA 58.379 33.333 7.63 1.87 0.00 2.83
129 131 6.459066 TCCTCTCTTAGTGAATGAAACACAG 58.541 40.000 0.00 0.00 40.25 3.66
141 143 3.360867 TGAAACACAGGAAAGAAGGCAA 58.639 40.909 0.00 0.00 0.00 4.52
172 175 7.167136 GCTGCATTTTGCTTAATTCACTAGATC 59.833 37.037 0.00 0.00 45.31 2.75
183 186 3.184382 TCACTAGATCTGTGGGTTGGA 57.816 47.619 18.91 3.20 36.21 3.53
199 206 4.503991 GGGTTGGATCAATGCTAGGTCTAG 60.504 50.000 0.00 0.85 36.29 2.43
211 218 0.535797 AGGTCTAGCCGCCAAGTTAC 59.464 55.000 0.00 0.00 43.70 2.50
218 225 3.967332 AGCCGCCAAGTTACTTAACTA 57.033 42.857 0.00 0.00 45.17 2.24
222 229 4.309099 CCGCCAAGTTACTTAACTACACA 58.691 43.478 0.00 0.00 45.17 3.72
263 270 4.864916 TCTACGTTGATGAGGTACGTAC 57.135 45.455 17.56 17.56 45.59 3.67
264 271 4.507710 TCTACGTTGATGAGGTACGTACT 58.492 43.478 24.07 11.06 45.59 2.73
266 273 4.871993 ACGTTGATGAGGTACGTACTAG 57.128 45.455 24.07 8.45 45.59 2.57
267 274 4.507710 ACGTTGATGAGGTACGTACTAGA 58.492 43.478 24.07 9.25 45.59 2.43
268 275 4.937620 ACGTTGATGAGGTACGTACTAGAA 59.062 41.667 24.07 9.13 45.59 2.10
269 276 5.163814 ACGTTGATGAGGTACGTACTAGAAC 60.164 44.000 24.07 15.88 45.59 3.01
300 307 3.480470 AGGACATGAAAGGTTGACACAG 58.520 45.455 0.00 0.00 0.00 3.66
313 320 2.582052 TGACACAGGGTTAGCAAAAGG 58.418 47.619 0.00 0.00 0.00 3.11
433 440 2.354805 CGGAGTGAAGGGTAGAAAAGGG 60.355 54.545 0.00 0.00 0.00 3.95
435 442 1.354705 AGTGAAGGGTAGAAAAGGGCC 59.645 52.381 0.00 0.00 0.00 5.80
436 443 1.074889 GTGAAGGGTAGAAAAGGGCCA 59.925 52.381 6.18 0.00 0.00 5.36
437 444 2.000048 TGAAGGGTAGAAAAGGGCCAT 59.000 47.619 6.18 0.00 0.00 4.40
439 446 0.631212 AGGGTAGAAAAGGGCCATGG 59.369 55.000 7.63 7.63 0.00 3.66
440 447 0.335019 GGGTAGAAAAGGGCCATGGT 59.665 55.000 14.67 0.00 0.00 3.55
442 449 1.685180 GGTAGAAAAGGGCCATGGTCC 60.685 57.143 29.08 29.08 40.91 4.46
448 455 2.763215 GGGCCATGGTCCTTGTGA 59.237 61.111 28.98 0.00 36.84 3.58
449 456 1.076549 GGGCCATGGTCCTTGTGAA 59.923 57.895 28.98 0.00 36.84 3.18
450 457 0.541764 GGGCCATGGTCCTTGTGAAA 60.542 55.000 28.98 0.00 36.84 2.69
464 475 1.422024 TGTGAAAGAAACGGATGGGGA 59.578 47.619 0.00 0.00 0.00 4.81
494 506 2.203337 TGCACCACTGGTCCTTGC 60.203 61.111 0.00 0.00 31.02 4.01
506 518 1.363744 GTCCTTGCGACAAGAGGATG 58.636 55.000 17.53 4.54 41.33 3.51
531 543 2.137528 GCTAGAGCTGACCCTCCCC 61.138 68.421 0.00 0.00 38.21 4.81
535 547 1.001760 GAGCTGACCCTCCCCACTA 59.998 63.158 0.00 0.00 0.00 2.74
539 551 2.240162 CTGACCCTCCCCACTAACGC 62.240 65.000 0.00 0.00 0.00 4.84
565 577 6.868622 ACTCCACTACTGTCTTTGTCATATC 58.131 40.000 0.00 0.00 0.00 1.63
604 616 0.604578 GTCTGTACCTACCGGCAACA 59.395 55.000 0.00 0.00 0.00 3.33
605 617 0.604578 TCTGTACCTACCGGCAACAC 59.395 55.000 0.00 0.00 0.00 3.32
627 639 2.109538 CTCAGCACGCCACACAACAG 62.110 60.000 0.00 0.00 0.00 3.16
637 653 3.435327 CGCCACACAACAGTACAATACAT 59.565 43.478 0.00 0.00 0.00 2.29
677 702 2.059490 GGTATGGGTGCCCCTACATAA 58.941 52.381 19.55 0.00 45.70 1.90
798 823 2.356913 TGTGCCGATCCACACACG 60.357 61.111 10.56 0.00 41.67 4.49
888 913 7.929785 CCTATAAAACCACACCGTATGTATCTT 59.070 37.037 0.00 0.00 40.64 2.40
912 937 1.665916 CTCCACACAGAGCACACCG 60.666 63.158 0.00 0.00 0.00 4.94
914 939 1.956170 CCACACAGAGCACACCGAC 60.956 63.158 0.00 0.00 0.00 4.79
920 945 3.936203 GAGCACACCGACCCACCA 61.936 66.667 0.00 0.00 0.00 4.17
921 946 3.249189 AGCACACCGACCCACCAT 61.249 61.111 0.00 0.00 0.00 3.55
922 947 2.746277 GCACACCGACCCACCATC 60.746 66.667 0.00 0.00 0.00 3.51
923 948 2.046314 CACACCGACCCACCATCC 60.046 66.667 0.00 0.00 0.00 3.51
924 949 2.528127 ACACCGACCCACCATCCA 60.528 61.111 0.00 0.00 0.00 3.41
925 950 1.923395 ACACCGACCCACCATCCAT 60.923 57.895 0.00 0.00 0.00 3.41
926 951 1.153168 CACCGACCCACCATCCATC 60.153 63.158 0.00 0.00 0.00 3.51
927 952 1.306997 ACCGACCCACCATCCATCT 60.307 57.895 0.00 0.00 0.00 2.90
957 982 4.168291 AGGCTAGAAGCAGCGGCC 62.168 66.667 4.82 0.00 44.75 6.13
992 1018 2.047465 CTGCGAGCACAAGGAGCT 60.047 61.111 0.00 0.00 46.82 4.09
1182 1241 0.539438 AAATGCCGAAGCCTGAACCA 60.539 50.000 0.00 0.00 38.69 3.67
1186 1269 0.678048 GCCGAAGCCTGAACCAGAAT 60.678 55.000 0.00 0.00 32.44 2.40
1194 1277 2.627699 GCCTGAACCAGAATCAAAACCA 59.372 45.455 0.00 0.00 32.44 3.67
1218 1301 1.079888 CAAGCCGATGCCAAAACCC 60.080 57.895 0.00 0.00 38.69 4.11
1302 1415 1.919600 CTAAGCCAGAGCCCAAGCCT 61.920 60.000 0.00 0.00 41.25 4.58
1303 1416 0.620410 TAAGCCAGAGCCCAAGCCTA 60.620 55.000 0.00 0.00 41.25 3.93
1308 1421 0.038166 CAGAGCCCAAGCCTAAACCA 59.962 55.000 0.00 0.00 41.25 3.67
1323 1436 0.039035 AACCAATGCCTAAGCCGGAA 59.961 50.000 5.05 0.00 38.69 4.30
1326 1439 1.451387 AATGCCTAAGCCGGAACCG 60.451 57.895 5.05 6.25 38.69 4.44
1344 1457 1.271163 CCGAAGCCTAAACCTGAACCA 60.271 52.381 0.00 0.00 0.00 3.67
1438 1552 3.154278 ATCGAGGAGATCATGGCCA 57.846 52.632 8.56 8.56 33.45 5.36
1563 1677 9.843334 TTCGTTACATTTACAAAGTTTCTGTTT 57.157 25.926 0.00 0.00 0.00 2.83
1603 1718 9.214957 TGAGTATCACAACCTTGTAATTGTTAG 57.785 33.333 0.00 0.00 42.56 2.34
1604 1719 8.040716 AGTATCACAACCTTGTAATTGTTAGC 57.959 34.615 0.00 0.00 39.91 3.09
1641 1756 5.073192 CGTTCAATTTTGTACGTGACTCA 57.927 39.130 12.49 0.00 43.77 3.41
1707 1822 6.038356 GCATGAATGAGTTATTTTGTCCAGG 58.962 40.000 0.00 0.00 0.00 4.45
1756 1871 5.535783 TCCATGGGATGCAGTATAACATTTG 59.464 40.000 13.02 0.00 0.00 2.32
1843 1958 9.546428 AAGTAAACTCATGAAATTTTTGGAAGG 57.454 29.630 9.29 0.00 0.00 3.46
1862 1977 8.173542 TGGAAGGTTTTATCAAAGGTAGAAAC 57.826 34.615 0.00 0.00 0.00 2.78
1864 1979 6.250344 AGGTTTTATCAAAGGTAGAAACGC 57.750 37.500 0.00 0.00 0.00 4.84
1865 1980 5.766174 AGGTTTTATCAAAGGTAGAAACGCA 59.234 36.000 0.00 0.00 0.00 5.24
1955 2247 2.033372 CATGGGCATCATTAGTGGCAA 58.967 47.619 0.00 0.00 43.28 4.52
1971 2264 6.670695 AGTGGCAAAGAATATTCCTTTTGT 57.329 33.333 21.76 7.90 32.04 2.83
1973 2266 6.930722 AGTGGCAAAGAATATTCCTTTTGTTG 59.069 34.615 21.76 13.93 32.04 3.33
1992 2285 5.875224 TGTTGAGGAACAAAGATACCATCA 58.125 37.500 0.00 0.00 39.20 3.07
2042 2418 9.275398 TCCAAATGAAATCCAAAGAAAAAGATG 57.725 29.630 0.00 0.00 0.00 2.90
2101 2478 9.003658 AGGATAGCTTATAAAACCATTCAATCG 57.996 33.333 0.00 0.00 0.00 3.34
2109 2486 3.433306 AACCATTCAATCGGTCCTGAA 57.567 42.857 0.00 0.00 33.17 3.02
2161 2539 2.718563 TCACTACATGTCGCTCTGGTA 58.281 47.619 0.00 0.00 0.00 3.25
2264 2643 7.481642 TCCGATACAAGAGATAAGAACAGAAC 58.518 38.462 0.00 0.00 0.00 3.01
2277 2656 5.914085 AGAACAGAACTTCAATTGACTCG 57.086 39.130 7.89 2.40 0.00 4.18
2284 2663 2.224281 ACTTCAATTGACTCGTCAGCCA 60.224 45.455 7.89 0.00 41.13 4.75
2311 2690 5.447279 CCGGTTGAATGTAACTTGTGCTATC 60.447 44.000 0.00 0.00 0.00 2.08
2320 2699 0.249073 CTTGTGCTATCGTCTCCCCG 60.249 60.000 0.00 0.00 0.00 5.73
2336 3222 2.186160 CCGCAACTGCACACCAAGA 61.186 57.895 2.12 0.00 42.21 3.02
2365 3251 3.004106 GGCACCTAATCATCTGCACATTC 59.996 47.826 0.00 0.00 0.00 2.67
2370 3256 6.645827 CACCTAATCATCTGCACATTCTAGAG 59.354 42.308 0.00 0.00 0.00 2.43
2372 3258 7.092079 CCTAATCATCTGCACATTCTAGAGAG 58.908 42.308 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.498397 GTCGTGCATTTGAAGAGAAAGGA 59.502 43.478 0.00 0.00 0.00 3.36
1 2 3.365364 GGTCGTGCATTTGAAGAGAAAGG 60.365 47.826 0.00 0.00 0.00 3.11
2 3 3.250762 TGGTCGTGCATTTGAAGAGAAAG 59.749 43.478 0.00 0.00 0.00 2.62
3 4 3.210227 TGGTCGTGCATTTGAAGAGAAA 58.790 40.909 0.00 0.00 0.00 2.52
4 5 2.844946 TGGTCGTGCATTTGAAGAGAA 58.155 42.857 0.00 0.00 0.00 2.87
5 6 2.542020 TGGTCGTGCATTTGAAGAGA 57.458 45.000 0.00 0.00 0.00 3.10
6 7 3.624326 TTTGGTCGTGCATTTGAAGAG 57.376 42.857 0.00 0.00 0.00 2.85
7 8 4.377839 TTTTTGGTCGTGCATTTGAAGA 57.622 36.364 0.00 0.00 0.00 2.87
8 9 5.345741 CCTATTTTTGGTCGTGCATTTGAAG 59.654 40.000 0.00 0.00 0.00 3.02
9 10 5.010112 TCCTATTTTTGGTCGTGCATTTGAA 59.990 36.000 0.00 0.00 0.00 2.69
10 11 4.520874 TCCTATTTTTGGTCGTGCATTTGA 59.479 37.500 0.00 0.00 0.00 2.69
11 12 4.804108 TCCTATTTTTGGTCGTGCATTTG 58.196 39.130 0.00 0.00 0.00 2.32
12 13 4.764823 TCTCCTATTTTTGGTCGTGCATTT 59.235 37.500 0.00 0.00 0.00 2.32
13 14 4.331968 TCTCCTATTTTTGGTCGTGCATT 58.668 39.130 0.00 0.00 0.00 3.56
14 15 3.950397 TCTCCTATTTTTGGTCGTGCAT 58.050 40.909 0.00 0.00 0.00 3.96
15 16 3.410631 TCTCCTATTTTTGGTCGTGCA 57.589 42.857 0.00 0.00 0.00 4.57
16 17 4.662145 CATTCTCCTATTTTTGGTCGTGC 58.338 43.478 0.00 0.00 0.00 5.34
17 18 4.396166 AGCATTCTCCTATTTTTGGTCGTG 59.604 41.667 0.00 0.00 0.00 4.35
18 19 4.589908 AGCATTCTCCTATTTTTGGTCGT 58.410 39.130 0.00 0.00 0.00 4.34
19 20 5.567138 AAGCATTCTCCTATTTTTGGTCG 57.433 39.130 0.00 0.00 0.00 4.79
20 21 7.163001 AGAAAGCATTCTCCTATTTTTGGTC 57.837 36.000 0.00 0.00 42.26 4.02
83 84 7.847096 AGGAAAAACCCCAATACATCATAAAC 58.153 34.615 0.00 0.00 40.05 2.01
85 86 7.418378 AGAGGAAAAACCCCAATACATCATAA 58.582 34.615 0.00 0.00 40.05 1.90
87 88 5.842339 AGAGGAAAAACCCCAATACATCAT 58.158 37.500 0.00 0.00 40.05 2.45
89 90 5.510430 AGAGAGGAAAAACCCCAATACATC 58.490 41.667 0.00 0.00 40.05 3.06
90 91 5.536497 AGAGAGGAAAAACCCCAATACAT 57.464 39.130 0.00 0.00 40.05 2.29
91 92 5.333566 AAGAGAGGAAAAACCCCAATACA 57.666 39.130 0.00 0.00 40.05 2.29
122 124 2.099098 CGTTGCCTTCTTTCCTGTGTTT 59.901 45.455 0.00 0.00 0.00 2.83
126 128 0.179018 AGCGTTGCCTTCTTTCCTGT 60.179 50.000 0.00 0.00 0.00 4.00
129 131 1.081175 GCAGCGTTGCCTTCTTTCC 60.081 57.895 13.92 0.00 44.74 3.13
172 175 1.843368 AGCATTGATCCAACCCACAG 58.157 50.000 0.00 0.00 0.00 3.66
199 206 3.124128 GTGTAGTTAAGTAACTTGGCGGC 59.876 47.826 8.92 0.00 43.57 6.53
211 218 8.692710 TGGATAGGTAAGATGTGTGTAGTTAAG 58.307 37.037 0.00 0.00 0.00 1.85
218 225 8.938883 AGAAATATGGATAGGTAAGATGTGTGT 58.061 33.333 0.00 0.00 0.00 3.72
222 229 9.310449 ACGTAGAAATATGGATAGGTAAGATGT 57.690 33.333 0.00 0.00 0.00 3.06
266 273 8.793592 ACCTTTCATGTCCTTTTTACTATGTTC 58.206 33.333 0.00 0.00 0.00 3.18
267 274 8.706322 ACCTTTCATGTCCTTTTTACTATGTT 57.294 30.769 0.00 0.00 0.00 2.71
268 275 8.576442 CAACCTTTCATGTCCTTTTTACTATGT 58.424 33.333 0.00 0.00 0.00 2.29
269 276 8.792633 TCAACCTTTCATGTCCTTTTTACTATG 58.207 33.333 0.00 0.00 0.00 2.23
283 290 2.586425 ACCCTGTGTCAACCTTTCATG 58.414 47.619 0.00 0.00 0.00 3.07
300 307 1.611977 ACGCTTTCCTTTTGCTAACCC 59.388 47.619 0.00 0.00 0.00 4.11
313 320 0.235926 GTTGGACTGCTCACGCTTTC 59.764 55.000 0.00 0.00 36.97 2.62
433 440 1.909700 TCTTTCACAAGGACCATGGC 58.090 50.000 13.04 4.47 0.00 4.40
435 442 3.304659 CCGTTTCTTTCACAAGGACCATG 60.305 47.826 0.00 0.00 0.00 3.66
436 443 2.884639 CCGTTTCTTTCACAAGGACCAT 59.115 45.455 0.00 0.00 0.00 3.55
437 444 2.092861 TCCGTTTCTTTCACAAGGACCA 60.093 45.455 0.00 0.00 0.00 4.02
439 446 3.058224 CCATCCGTTTCTTTCACAAGGAC 60.058 47.826 0.00 0.00 0.00 3.85
440 447 3.146066 CCATCCGTTTCTTTCACAAGGA 58.854 45.455 0.00 0.00 0.00 3.36
442 449 2.228822 CCCCATCCGTTTCTTTCACAAG 59.771 50.000 0.00 0.00 0.00 3.16
444 451 1.422024 TCCCCATCCGTTTCTTTCACA 59.578 47.619 0.00 0.00 0.00 3.58
445 452 2.084546 CTCCCCATCCGTTTCTTTCAC 58.915 52.381 0.00 0.00 0.00 3.18
446 453 1.702957 ACTCCCCATCCGTTTCTTTCA 59.297 47.619 0.00 0.00 0.00 2.69
447 454 2.290071 TGACTCCCCATCCGTTTCTTTC 60.290 50.000 0.00 0.00 0.00 2.62
448 455 1.702957 TGACTCCCCATCCGTTTCTTT 59.297 47.619 0.00 0.00 0.00 2.52
449 456 1.358152 TGACTCCCCATCCGTTTCTT 58.642 50.000 0.00 0.00 0.00 2.52
450 457 1.584724 ATGACTCCCCATCCGTTTCT 58.415 50.000 0.00 0.00 0.00 2.52
464 475 1.333619 GTGGTGCACACGAAAATGACT 59.666 47.619 20.43 0.00 40.85 3.41
494 506 0.249073 CTACGGGCATCCTCTTGTCG 60.249 60.000 0.00 0.00 0.00 4.35
523 535 0.974525 GTAGCGTTAGTGGGGAGGGT 60.975 60.000 0.00 0.00 0.00 4.34
531 543 3.439476 ACAGTAGTGGAGTAGCGTTAGTG 59.561 47.826 1.92 0.00 0.00 2.74
535 547 2.792878 AGACAGTAGTGGAGTAGCGTT 58.207 47.619 1.92 0.00 0.00 4.84
539 551 5.707242 TGACAAAGACAGTAGTGGAGTAG 57.293 43.478 1.92 0.00 0.00 2.57
565 577 4.811024 AGACCGACATGCATACAAACATAG 59.189 41.667 0.00 0.00 0.00 2.23
604 616 4.240103 TGTGGCGTGCTGAGCAGT 62.240 61.111 7.71 0.00 40.08 4.40
605 617 3.720193 GTGTGGCGTGCTGAGCAG 61.720 66.667 7.71 3.21 40.08 4.24
677 702 3.199190 CACGCCACACCACACGTT 61.199 61.111 0.00 0.00 36.45 3.99
762 787 4.336433 GCACAGCAACATATCCAGTAACAT 59.664 41.667 0.00 0.00 0.00 2.71
888 913 1.069204 GTGCTCTGTGTGGAGAAGTGA 59.931 52.381 0.00 0.00 35.52 3.41
912 937 2.338809 TGGATAGATGGATGGTGGGTC 58.661 52.381 0.00 0.00 0.00 4.46
914 939 2.240667 GGATGGATAGATGGATGGTGGG 59.759 54.545 0.00 0.00 0.00 4.61
920 945 4.045736 CCTGGATGGATGGATAGATGGAT 58.954 47.826 0.00 0.00 38.35 3.41
921 946 3.457836 CCTGGATGGATGGATAGATGGA 58.542 50.000 0.00 0.00 38.35 3.41
922 947 2.092538 GCCTGGATGGATGGATAGATGG 60.093 54.545 0.00 0.00 38.35 3.51
923 948 2.844966 AGCCTGGATGGATGGATAGATG 59.155 50.000 0.00 0.00 38.35 2.90
924 949 3.217768 AGCCTGGATGGATGGATAGAT 57.782 47.619 0.00 0.00 38.35 1.98
925 950 2.729383 AGCCTGGATGGATGGATAGA 57.271 50.000 0.00 0.00 38.35 1.98
926 951 3.717576 TCTAGCCTGGATGGATGGATAG 58.282 50.000 0.00 0.00 36.79 2.08
927 952 3.852858 TCTAGCCTGGATGGATGGATA 57.147 47.619 0.00 0.00 36.79 2.59
957 982 0.250901 AGCTAGGGGTGCACTTGTTG 60.251 55.000 17.98 6.10 0.00 3.33
1102 1128 0.038159 AGGTCCGCAAACTTCTCGAG 60.038 55.000 5.93 5.93 0.00 4.04
1182 1241 3.494924 GCTTGGGCTTTGGTTTTGATTCT 60.495 43.478 0.00 0.00 35.22 2.40
1186 1269 0.467804 GGCTTGGGCTTTGGTTTTGA 59.532 50.000 0.00 0.00 38.73 2.69
1194 1277 3.070576 GGCATCGGCTTGGGCTTT 61.071 61.111 0.00 0.00 40.87 3.51
1218 1301 3.373565 GGCTTGGGCTTGGGTTCG 61.374 66.667 0.00 0.00 38.73 3.95
1302 1415 1.282447 TCCGGCTTAGGCATTGGTTTA 59.718 47.619 6.60 0.00 40.87 2.01
1303 1416 0.039035 TCCGGCTTAGGCATTGGTTT 59.961 50.000 6.60 0.00 40.87 3.27
1308 1421 1.451387 CGGTTCCGGCTTAGGCATT 60.451 57.895 6.60 0.00 40.87 3.56
1323 1436 1.271217 GGTTCAGGTTTAGGCTTCGGT 60.271 52.381 0.00 0.00 0.00 4.69
1326 1439 4.500887 GGTTTTGGTTCAGGTTTAGGCTTC 60.501 45.833 0.00 0.00 0.00 3.86
1344 1457 1.280457 TTGGTGGTGGCTTTGGTTTT 58.720 45.000 0.00 0.00 0.00 2.43
1409 1523 3.876274 TCTCCTCGATCCTTCAGTTTG 57.124 47.619 0.00 0.00 0.00 2.93
1438 1552 2.533266 AATATCGCGATTGTGGCTCT 57.467 45.000 28.81 2.01 0.00 4.09
1568 1682 4.968719 AGGTTGTGATACTCATCATGGGTA 59.031 41.667 0.00 0.00 43.03 3.69
1584 1698 4.917415 GCAGCTAACAATTACAAGGTTGTG 59.083 41.667 5.59 0.00 42.31 3.33
1587 1701 5.301805 ACAAGCAGCTAACAATTACAAGGTT 59.698 36.000 0.00 0.00 0.00 3.50
1590 1704 5.630680 CCAACAAGCAGCTAACAATTACAAG 59.369 40.000 0.00 0.00 0.00 3.16
1603 1718 0.661020 AACGTACACCAACAAGCAGC 59.339 50.000 0.00 0.00 0.00 5.25
1604 1719 1.937223 TGAACGTACACCAACAAGCAG 59.063 47.619 0.00 0.00 0.00 4.24
1707 1822 1.819632 CAACATAGCCTGCGGTCCC 60.820 63.158 0.00 0.00 0.00 4.46
1717 1832 4.462483 TCCCATGGAGAAAAACAACATAGC 59.538 41.667 15.22 0.00 0.00 2.97
1756 1871 4.439289 GCTCCAGTGCAATATTCTCCAAAC 60.439 45.833 0.00 0.00 0.00 2.93
1843 1958 5.567915 GCTGCGTTTCTACCTTTGATAAAAC 59.432 40.000 0.00 0.00 0.00 2.43
1862 1977 2.143122 TGACTTTACAAAGGAGCTGCG 58.857 47.619 0.00 0.00 40.31 5.18
1864 1979 6.566197 ATTCTTGACTTTACAAAGGAGCTG 57.434 37.500 0.00 0.00 40.31 4.24
1865 1980 6.881602 CCTATTCTTGACTTTACAAAGGAGCT 59.118 38.462 6.66 0.00 40.31 4.09
1916 2207 2.764269 TGGCCCAAGCTACTTAGATCT 58.236 47.619 0.00 0.00 39.73 2.75
1971 2264 5.357878 GCATGATGGTATCTTTGTTCCTCAA 59.642 40.000 0.00 0.00 0.00 3.02
1973 2266 4.883585 TGCATGATGGTATCTTTGTTCCTC 59.116 41.667 0.00 0.00 0.00 3.71
1992 2285 5.481473 AGTTTTGGTGGATGTTAAGATGCAT 59.519 36.000 9.99 0.00 0.00 3.96
2042 2418 6.655425 GTGGAAGGGGTTTATAAGCTATCATC 59.345 42.308 0.00 0.00 0.00 2.92
2044 2420 5.670361 AGTGGAAGGGGTTTATAAGCTATCA 59.330 40.000 0.00 0.00 0.00 2.15
2101 2478 3.208747 TGGACTTCAAACTTCAGGACC 57.791 47.619 0.00 0.00 0.00 4.46
2167 2545 2.516906 GTGGTATTCCCCCGTTTTGAA 58.483 47.619 0.00 0.00 0.00 2.69
2170 2548 0.322726 CGGTGGTATTCCCCCGTTTT 60.323 55.000 4.07 0.00 40.30 2.43
2176 2554 0.396556 AAATGCCGGTGGTATTCCCC 60.397 55.000 1.90 0.00 37.03 4.81
2184 2562 0.528901 CATGATGCAAATGCCGGTGG 60.529 55.000 1.90 0.00 41.18 4.61
2261 2640 3.120511 GGCTGACGAGTCAATTGAAGTTC 60.121 47.826 10.35 7.65 39.39 3.01
2264 2643 2.416747 TGGCTGACGAGTCAATTGAAG 58.583 47.619 10.35 7.45 39.39 3.02
2277 2656 0.958822 ATTCAACCGGTTTGGCTGAC 59.041 50.000 19.55 0.00 42.50 3.51
2284 2663 4.735283 GCACAAGTTACATTCAACCGGTTT 60.735 41.667 19.55 5.23 0.00 3.27
2311 2690 4.680237 TGCAGTTGCGGGGAGACG 62.680 66.667 0.00 0.00 45.83 4.18
2320 2699 0.249031 GGTTCTTGGTGTGCAGTTGC 60.249 55.000 0.00 0.00 42.50 4.17
2336 3222 4.747931 GCAGATGATTAGGTGCCTATGGTT 60.748 45.833 0.00 0.00 0.00 3.67
2365 3251 7.987750 TGTATCTATACTTGGTGCTCTCTAG 57.012 40.000 2.07 0.00 34.41 2.43


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

AutoCloner maintained by Alex Coulton.