Multiple sequence alignment - TraesCS4B01G325200

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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 TraesCS4B01G325200 chr4B 100.000 2418 0 0 1 2418 615836040 615833623 0.000000e+00 4466
1 TraesCS4B01G325200 chr4B 88.442 199 15 5 4 200 636687370 636687178 1.450000e-57 233
2 TraesCS4B01G325200 chr4D 91.450 2234 71 36 200 2418 484295064 484292936 0.000000e+00 2957
3 TraesCS4B01G325200 chr5A 93.269 1768 74 23 242 1993 664556013 664554275 0.000000e+00 2564
4 TraesCS4B01G325200 chr5A 95.550 427 13 2 1992 2418 664553954 664553534 0.000000e+00 678
5 TraesCS4B01G325200 chr5A 90.000 60 2 3 1 60 647805935 647805990 9.270000e-10 75
6 TraesCS4B01G325200 chr5B 83.455 411 60 7 197 603 532562768 532563174 2.270000e-100 375
7 TraesCS4B01G325200 chr5B 81.509 411 68 7 197 603 81576302 81576708 4.980000e-87 331
8 TraesCS4B01G325200 chr5B 86.782 174 18 4 1 173 494295271 494295102 3.170000e-44 189
9 TraesCS4B01G325200 chr3B 82.238 411 62 10 197 603 43924331 43923928 6.400000e-91 344
10 TraesCS4B01G325200 chr3B 82.238 411 62 10 197 603 44030145 44029742 6.400000e-91 344
11 TraesCS4B01G325200 chr3B 82.161 398 64 5 197 590 508119743 508119349 3.850000e-88 335
12 TraesCS4B01G325200 chr6A 82.857 385 59 6 197 577 524735961 524736342 2.980000e-89 339
13 TraesCS4B01G325200 chr2B 81.509 411 68 7 197 603 423280176 423280582 4.980000e-87 331
14 TraesCS4B01G325200 chr4A 85.000 180 19 5 4 182 731390345 731390173 2.470000e-40 176
15 TraesCS4B01G325200 chr5D 84.091 176 16 10 1 174 23836635 23836470 2.490000e-35 159
16 TraesCS4B01G325200 chr3A 80.198 202 29 7 1 201 594851554 594851363 9.010000e-30 141
17 TraesCS4B01G325200 chr3A 82.941 170 15 5 1 168 726299414 726299571 9.010000e-30 141


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 TraesCS4B01G325200 chr4B 615833623 615836040 2417 True 4466 4466 100.0000 1 2418 1 chr4B.!!$R1 2417
1 TraesCS4B01G325200 chr4D 484292936 484295064 2128 True 2957 2957 91.4500 200 2418 1 chr4D.!!$R1 2218
2 TraesCS4B01G325200 chr5A 664553534 664556013 2479 True 1621 2564 94.4095 242 2418 2 chr5A.!!$R1 2176

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
159 160 0.027586 AGAAACGTGCGCACAGTTTC 59.972 50.0 42.79 42.79 44.75 2.78 F
166 167 0.179059 TGCGCACAGTTTCCTCTCAA 60.179 50.0 5.66 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1015 1030 0.478072 TTGGGGTGAGTTGCATCTGT 59.522 50.0 1.0 0.0 0.0 3.41 R
1751 1777 0.674581 TGAATGGCAGCAGAGGTTCG 60.675 55.0 0.0 0.0 0.0 3.95 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
19 20 3.762293 TGCAAAATGGCACTCGCT 58.238 50.000 0.00 0.00 39.25 4.93
20 21 1.286570 TGCAAAATGGCACTCGCTG 59.713 52.632 0.00 0.00 39.25 5.18
21 22 1.444895 GCAAAATGGCACTCGCTGG 60.445 57.895 0.00 0.00 38.60 4.85
22 23 1.959085 CAAAATGGCACTCGCTGGT 59.041 52.632 0.00 0.00 38.60 4.00
23 24 1.164411 CAAAATGGCACTCGCTGGTA 58.836 50.000 0.00 0.00 38.60 3.25
24 25 1.131126 CAAAATGGCACTCGCTGGTAG 59.869 52.381 0.00 0.00 38.60 3.18
25 26 0.392998 AAATGGCACTCGCTGGTAGG 60.393 55.000 0.00 0.00 38.60 3.18
26 27 2.876368 AATGGCACTCGCTGGTAGGC 62.876 60.000 0.00 0.00 38.60 3.93
27 28 3.775654 GGCACTCGCTGGTAGGCT 61.776 66.667 0.00 0.00 38.60 4.58
28 29 2.510238 GCACTCGCTGGTAGGCTG 60.510 66.667 0.00 0.00 34.30 4.85
29 30 2.185350 CACTCGCTGGTAGGCTGG 59.815 66.667 0.00 0.00 0.00 4.85
30 31 2.283966 ACTCGCTGGTAGGCTGGT 60.284 61.111 0.00 0.00 0.00 4.00
31 32 2.185350 CTCGCTGGTAGGCTGGTG 59.815 66.667 0.00 0.00 0.00 4.17
32 33 2.603473 TCGCTGGTAGGCTGGTGT 60.603 61.111 0.00 0.00 0.00 4.16
33 34 2.434884 CGCTGGTAGGCTGGTGTG 60.435 66.667 0.00 0.00 0.00 3.82
34 35 2.045926 GCTGGTAGGCTGGTGTGG 60.046 66.667 0.00 0.00 0.00 4.17
35 36 2.895424 GCTGGTAGGCTGGTGTGGT 61.895 63.158 0.00 0.00 0.00 4.16
36 37 1.550130 GCTGGTAGGCTGGTGTGGTA 61.550 60.000 0.00 0.00 0.00 3.25
37 38 0.981183 CTGGTAGGCTGGTGTGGTAA 59.019 55.000 0.00 0.00 0.00 2.85
38 39 1.559682 CTGGTAGGCTGGTGTGGTAAT 59.440 52.381 0.00 0.00 0.00 1.89
39 40 1.989586 TGGTAGGCTGGTGTGGTAATT 59.010 47.619 0.00 0.00 0.00 1.40
40 41 3.182976 TGGTAGGCTGGTGTGGTAATTA 58.817 45.455 0.00 0.00 0.00 1.40
41 42 3.783642 TGGTAGGCTGGTGTGGTAATTAT 59.216 43.478 0.00 0.00 0.00 1.28
42 43 4.228666 TGGTAGGCTGGTGTGGTAATTATT 59.771 41.667 0.00 0.00 0.00 1.40
43 44 5.198207 GGTAGGCTGGTGTGGTAATTATTT 58.802 41.667 0.00 0.00 0.00 1.40
44 45 6.069556 TGGTAGGCTGGTGTGGTAATTATTTA 60.070 38.462 0.00 0.00 0.00 1.40
45 46 7.002276 GGTAGGCTGGTGTGGTAATTATTTAT 58.998 38.462 0.00 0.00 0.00 1.40
46 47 7.504574 GGTAGGCTGGTGTGGTAATTATTTATT 59.495 37.037 0.00 0.00 0.00 1.40
47 48 7.971368 AGGCTGGTGTGGTAATTATTTATTT 57.029 32.000 0.00 0.00 0.00 1.40
48 49 8.374184 AGGCTGGTGTGGTAATTATTTATTTT 57.626 30.769 0.00 0.00 0.00 1.82
49 50 8.821817 AGGCTGGTGTGGTAATTATTTATTTTT 58.178 29.630 0.00 0.00 0.00 1.94
118 119 2.288961 TTTTAGACGGATGCGAGGAC 57.711 50.000 15.49 1.71 0.00 3.85
119 120 1.471119 TTTAGACGGATGCGAGGACT 58.529 50.000 15.49 9.33 0.00 3.85
120 121 1.471119 TTAGACGGATGCGAGGACTT 58.529 50.000 15.49 0.00 0.00 3.01
121 122 1.471119 TAGACGGATGCGAGGACTTT 58.529 50.000 15.49 0.00 0.00 2.66
122 123 1.471119 AGACGGATGCGAGGACTTTA 58.529 50.000 15.49 0.00 0.00 1.85
123 124 2.032620 AGACGGATGCGAGGACTTTAT 58.967 47.619 15.49 0.00 0.00 1.40
124 125 2.128035 GACGGATGCGAGGACTTTATG 58.872 52.381 15.49 0.00 0.00 1.90
125 126 1.480954 ACGGATGCGAGGACTTTATGT 59.519 47.619 15.49 0.00 0.00 2.29
126 127 2.691526 ACGGATGCGAGGACTTTATGTA 59.308 45.455 15.49 0.00 0.00 2.29
127 128 3.321111 ACGGATGCGAGGACTTTATGTAT 59.679 43.478 15.49 0.00 0.00 2.29
128 129 4.202223 ACGGATGCGAGGACTTTATGTATT 60.202 41.667 15.49 0.00 0.00 1.89
129 130 4.750098 CGGATGCGAGGACTTTATGTATTT 59.250 41.667 0.00 0.00 0.00 1.40
130 131 5.236478 CGGATGCGAGGACTTTATGTATTTT 59.764 40.000 0.00 0.00 0.00 1.82
131 132 6.238374 CGGATGCGAGGACTTTATGTATTTTT 60.238 38.462 0.00 0.00 0.00 1.94
152 153 6.807708 TTTTTAAAAATAGAAACGTGCGCA 57.192 29.167 5.66 5.66 0.00 6.09
153 154 5.793023 TTTAAAAATAGAAACGTGCGCAC 57.207 34.783 30.42 30.42 0.00 5.34
154 155 3.341857 AAAAATAGAAACGTGCGCACA 57.658 38.095 37.03 19.31 0.00 4.57
155 156 2.594529 AAATAGAAACGTGCGCACAG 57.405 45.000 37.03 29.88 0.00 3.66
156 157 1.508632 AATAGAAACGTGCGCACAGT 58.491 45.000 37.03 30.50 0.00 3.55
157 158 1.508632 ATAGAAACGTGCGCACAGTT 58.491 45.000 37.03 33.48 32.51 3.16
158 159 1.292061 TAGAAACGTGCGCACAGTTT 58.708 45.000 38.32 38.32 39.12 2.66
159 160 0.027586 AGAAACGTGCGCACAGTTTC 59.972 50.000 42.79 42.79 44.75 2.78
160 161 0.928451 GAAACGTGCGCACAGTTTCC 60.928 55.000 41.66 32.97 42.20 3.13
161 162 1.373590 AAACGTGCGCACAGTTTCCT 61.374 50.000 35.44 24.54 35.10 3.36
162 163 1.772063 AACGTGCGCACAGTTTCCTC 61.772 55.000 37.03 10.05 0.00 3.71
163 164 1.956170 CGTGCGCACAGTTTCCTCT 60.956 57.895 37.03 0.00 0.00 3.69
164 165 1.862806 GTGCGCACAGTTTCCTCTC 59.137 57.895 34.52 2.71 0.00 3.20
165 166 0.880278 GTGCGCACAGTTTCCTCTCA 60.880 55.000 34.52 0.00 0.00 3.27
166 167 0.179059 TGCGCACAGTTTCCTCTCAA 60.179 50.000 5.66 0.00 0.00 3.02
167 168 0.514691 GCGCACAGTTTCCTCTCAAG 59.485 55.000 0.30 0.00 0.00 3.02
168 169 0.514691 CGCACAGTTTCCTCTCAAGC 59.485 55.000 0.00 0.00 0.00 4.01
169 170 0.514691 GCACAGTTTCCTCTCAAGCG 59.485 55.000 0.00 0.00 0.00 4.68
170 171 1.151668 CACAGTTTCCTCTCAAGCGG 58.848 55.000 0.00 0.00 0.00 5.52
171 172 0.603975 ACAGTTTCCTCTCAAGCGGC 60.604 55.000 0.00 0.00 0.00 6.53
172 173 1.374758 AGTTTCCTCTCAAGCGGCG 60.375 57.895 0.51 0.51 0.00 6.46
173 174 1.668151 GTTTCCTCTCAAGCGGCGT 60.668 57.895 9.37 0.00 0.00 5.68
174 175 1.374252 TTTCCTCTCAAGCGGCGTC 60.374 57.895 9.37 0.13 0.00 5.19
175 176 2.094757 TTTCCTCTCAAGCGGCGTCA 62.095 55.000 9.37 0.00 0.00 4.35
176 177 2.765250 TTCCTCTCAAGCGGCGTCAC 62.765 60.000 9.37 0.00 0.00 3.67
177 178 2.049156 CTCTCAAGCGGCGTCACA 60.049 61.111 9.37 0.00 0.00 3.58
178 179 1.446792 CTCTCAAGCGGCGTCACAT 60.447 57.895 9.37 0.00 0.00 3.21
179 180 1.690283 CTCTCAAGCGGCGTCACATG 61.690 60.000 9.37 0.91 0.00 3.21
180 181 2.741985 TCAAGCGGCGTCACATGG 60.742 61.111 9.37 0.00 0.00 3.66
181 182 3.049674 CAAGCGGCGTCACATGGT 61.050 61.111 9.37 0.00 0.00 3.55
182 183 3.049674 AAGCGGCGTCACATGGTG 61.050 61.111 9.37 0.00 34.45 4.17
192 193 4.380945 ACATGGTGGCGCCCCAAT 62.381 61.111 31.83 22.77 44.33 3.16
193 194 3.530260 CATGGTGGCGCCCCAATC 61.530 66.667 31.83 14.01 44.33 2.67
194 195 4.059304 ATGGTGGCGCCCCAATCA 62.059 61.111 31.83 19.09 44.33 2.57
196 197 4.740822 GGTGGCGCCCCAATCACT 62.741 66.667 26.77 0.00 44.33 3.41
197 198 2.270850 GTGGCGCCCCAATCACTA 59.729 61.111 26.77 0.00 44.33 2.74
198 199 1.819632 GTGGCGCCCCAATCACTAG 60.820 63.158 26.77 0.00 44.33 2.57
284 285 5.694006 GCTTGGCAATGTAATGTTGTGTTTA 59.306 36.000 0.00 0.00 0.00 2.01
286 287 7.470289 TTGGCAATGTAATGTTGTGTTTAAC 57.530 32.000 0.00 0.00 0.00 2.01
287 288 6.573434 TGGCAATGTAATGTTGTGTTTAACA 58.427 32.000 0.00 0.00 43.93 2.41
365 367 0.681175 AAGTTTCTGCAATGTGGCCC 59.319 50.000 0.00 0.00 0.00 5.80
413 415 4.874966 TGTTTTGACCTTTCCATTGCAAAG 59.125 37.500 1.71 0.00 0.00 2.77
426 428 5.051816 CCATTGCAAAGATTGTGACAACTT 58.948 37.500 1.71 3.85 0.00 2.66
553 557 5.876460 TGTCGACATCATCATGAATGTTCTT 59.124 36.000 15.76 0.00 36.68 2.52
630 634 2.644418 ATGCAACAACGCGTGCAT 59.356 50.000 24.14 24.14 42.37 3.96
817 821 7.381139 AGCAAACATTTAATTTACGGTTCACAG 59.619 33.333 0.00 0.00 0.00 3.66
931 935 1.401539 GCAAGTTAGCTTCCTTTGCCG 60.402 52.381 11.56 0.00 31.49 5.69
971 975 7.439157 TTGATTATGAATCGAATCCATGTCC 57.561 36.000 0.00 0.00 40.84 4.02
975 979 4.071961 TGAATCGAATCCATGTCCGAAT 57.928 40.909 0.00 0.00 34.59 3.34
1015 1030 3.025978 CCCAAAATGCAGATGGAAGCTA 58.974 45.455 14.85 0.00 36.27 3.32
1062 1077 6.441924 AGAAGAAGGACAAGGTAATCATCTGA 59.558 38.462 0.00 0.00 0.00 3.27
1111 1126 2.420628 ACAACCACATCAATGCAACG 57.579 45.000 0.00 0.00 0.00 4.10
1179 1194 5.584649 TCTTATTCATTAAGGAACACGCCAG 59.415 40.000 4.42 0.00 38.29 4.85
1241 1265 5.069318 AGAAGAAAGAAAAGAGCAAGGAGG 58.931 41.667 0.00 0.00 0.00 4.30
1242 1266 3.760738 AGAAAGAAAAGAGCAAGGAGGG 58.239 45.455 0.00 0.00 0.00 4.30
1243 1267 1.916506 AAGAAAAGAGCAAGGAGGGC 58.083 50.000 0.00 0.00 0.00 5.19
1244 1268 0.773644 AGAAAAGAGCAAGGAGGGCA 59.226 50.000 0.00 0.00 0.00 5.36
1245 1269 1.145738 AGAAAAGAGCAAGGAGGGCAA 59.854 47.619 0.00 0.00 0.00 4.52
1246 1270 1.543358 GAAAAGAGCAAGGAGGGCAAG 59.457 52.381 0.00 0.00 0.00 4.01
1247 1271 0.251519 AAAGAGCAAGGAGGGCAAGG 60.252 55.000 0.00 0.00 0.00 3.61
1248 1272 1.136329 AAGAGCAAGGAGGGCAAGGA 61.136 55.000 0.00 0.00 0.00 3.36
1249 1273 1.136329 AGAGCAAGGAGGGCAAGGAA 61.136 55.000 0.00 0.00 0.00 3.36
1516 1541 1.608590 AGTTGGTGCAGGAATTGTTCG 59.391 47.619 0.00 0.00 0.00 3.95
1527 1552 1.529438 GAATTGTTCGTTCGACTGGCA 59.471 47.619 0.00 0.00 0.00 4.92
1528 1553 1.808411 ATTGTTCGTTCGACTGGCAT 58.192 45.000 0.00 0.00 0.00 4.40
1597 1623 7.371159 CAGCATTGCATGATCATCTAGATTTT 58.629 34.615 11.91 0.00 37.00 1.82
1609 1635 5.534278 TCATCTAGATTTTGGTGCACACAAA 59.466 36.000 20.43 21.36 36.15 2.83
1610 1636 5.437289 TCTAGATTTTGGTGCACACAAAG 57.563 39.130 23.44 16.18 38.84 2.77
1611 1637 4.887071 TCTAGATTTTGGTGCACACAAAGT 59.113 37.500 23.44 22.02 38.84 2.66
1683 1709 8.802267 CCTCTTAAAGATTTTTGGTATTGGACA 58.198 33.333 0.00 0.00 0.00 4.02
1684 1710 9.626045 CTCTTAAAGATTTTTGGTATTGGACAC 57.374 33.333 0.00 0.00 0.00 3.67
1700 1726 3.563808 TGGACACGACCTTTCTTGAAATG 59.436 43.478 0.00 0.00 0.00 2.32
1733 1759 6.855914 TCGAAGTCTGCATTTGTTTTTACATC 59.144 34.615 0.00 0.00 0.00 3.06
1751 1777 3.971702 AAGTGGGGAGCAGGGTGC 61.972 66.667 0.00 0.00 45.46 5.01
1764 1790 3.426568 GGTGCGAACCTCTGCTGC 61.427 66.667 4.88 0.00 0.00 5.25
1766 1792 3.939939 TGCGAACCTCTGCTGCCA 61.940 61.111 0.00 0.00 0.00 4.92
1767 1793 2.437359 GCGAACCTCTGCTGCCAT 60.437 61.111 0.00 0.00 0.00 4.40
1769 1795 1.986575 GCGAACCTCTGCTGCCATTC 61.987 60.000 0.00 0.00 0.00 2.67
1770 1796 0.674581 CGAACCTCTGCTGCCATTCA 60.675 55.000 0.00 0.00 0.00 2.57
1771 1797 1.093159 GAACCTCTGCTGCCATTCAG 58.907 55.000 0.00 0.00 45.62 3.02
1818 1865 6.348786 GCTCACATGACAATACAATGAACTGT 60.349 38.462 0.00 0.00 0.00 3.55
1820 1867 6.072563 TCACATGACAATACAATGAACTGTGG 60.073 38.462 0.00 0.00 33.06 4.17
1850 1902 4.223320 ACGATGAACACACACAAAATCC 57.777 40.909 0.00 0.00 0.00 3.01
1932 1984 0.321671 TTTCAGTGGGAGGAGCTTCG 59.678 55.000 0.00 0.00 0.00 3.79
1968 2020 7.984617 CCAAAATTCCAAGGTTTCAAAGAGTTA 59.015 33.333 0.00 0.00 0.00 2.24
1974 2026 7.712797 TCCAAGGTTTCAAAGAGTTAAATGAC 58.287 34.615 0.00 0.00 0.00 3.06
2365 2739 4.341235 TCCTTCATGGTATCGAAGTACTGG 59.659 45.833 0.00 0.00 37.52 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.132834 CAGCGAGTGCCATTTTGCATA 59.867 47.619 0.00 0.00 44.30 3.14
1 2 0.108992 CAGCGAGTGCCATTTTGCAT 60.109 50.000 0.00 0.00 44.30 3.96
2 3 1.286570 CAGCGAGTGCCATTTTGCA 59.713 52.632 0.00 0.00 44.31 4.08
3 4 1.444895 CCAGCGAGTGCCATTTTGC 60.445 57.895 0.00 0.00 44.31 3.68
4 5 1.131126 CTACCAGCGAGTGCCATTTTG 59.869 52.381 0.00 0.00 44.31 2.44
5 6 1.453155 CTACCAGCGAGTGCCATTTT 58.547 50.000 0.00 0.00 44.31 1.82
6 7 0.392998 CCTACCAGCGAGTGCCATTT 60.393 55.000 0.00 0.00 44.31 2.32
7 8 1.221840 CCTACCAGCGAGTGCCATT 59.778 57.895 0.00 0.00 44.31 3.16
8 9 2.903357 CCTACCAGCGAGTGCCAT 59.097 61.111 0.00 0.00 44.31 4.40
9 10 4.082523 GCCTACCAGCGAGTGCCA 62.083 66.667 0.00 0.00 44.31 4.92
10 11 3.775654 AGCCTACCAGCGAGTGCC 61.776 66.667 0.00 0.00 44.31 5.01
11 12 2.510238 CAGCCTACCAGCGAGTGC 60.510 66.667 0.00 0.00 43.24 4.40
12 13 2.185350 CCAGCCTACCAGCGAGTG 59.815 66.667 0.00 0.00 38.01 3.51
13 14 2.283966 ACCAGCCTACCAGCGAGT 60.284 61.111 0.00 0.00 38.01 4.18
14 15 2.185350 CACCAGCCTACCAGCGAG 59.815 66.667 0.00 0.00 38.01 5.03
15 16 2.603473 ACACCAGCCTACCAGCGA 60.603 61.111 0.00 0.00 38.01 4.93
16 17 2.434884 CACACCAGCCTACCAGCG 60.435 66.667 0.00 0.00 38.01 5.18
17 18 1.550130 TACCACACCAGCCTACCAGC 61.550 60.000 0.00 0.00 0.00 4.85
18 19 0.981183 TTACCACACCAGCCTACCAG 59.019 55.000 0.00 0.00 0.00 4.00
19 20 1.663911 ATTACCACACCAGCCTACCA 58.336 50.000 0.00 0.00 0.00 3.25
20 21 2.801077 AATTACCACACCAGCCTACC 57.199 50.000 0.00 0.00 0.00 3.18
21 22 8.459911 AATAAATAATTACCACACCAGCCTAC 57.540 34.615 0.00 0.00 0.00 3.18
22 23 9.482175 AAAATAAATAATTACCACACCAGCCTA 57.518 29.630 0.00 0.00 0.00 3.93
23 24 7.971368 AAATAAATAATTACCACACCAGCCT 57.029 32.000 0.00 0.00 0.00 4.58
98 99 2.232941 AGTCCTCGCATCCGTCTAAAAA 59.767 45.455 0.00 0.00 35.54 1.94
99 100 1.822990 AGTCCTCGCATCCGTCTAAAA 59.177 47.619 0.00 0.00 35.54 1.52
100 101 1.471119 AGTCCTCGCATCCGTCTAAA 58.529 50.000 0.00 0.00 35.54 1.85
101 102 1.471119 AAGTCCTCGCATCCGTCTAA 58.529 50.000 0.00 0.00 35.54 2.10
102 103 1.471119 AAAGTCCTCGCATCCGTCTA 58.529 50.000 0.00 0.00 35.54 2.59
103 104 1.471119 TAAAGTCCTCGCATCCGTCT 58.529 50.000 0.00 0.00 35.54 4.18
104 105 2.128035 CATAAAGTCCTCGCATCCGTC 58.872 52.381 0.00 0.00 35.54 4.79
105 106 1.480954 ACATAAAGTCCTCGCATCCGT 59.519 47.619 0.00 0.00 35.54 4.69
106 107 2.225068 ACATAAAGTCCTCGCATCCG 57.775 50.000 0.00 0.00 0.00 4.18
107 108 6.619801 AAAATACATAAAGTCCTCGCATCC 57.380 37.500 0.00 0.00 0.00 3.51
129 130 6.252869 TGTGCGCACGTTTCTATTTTTAAAAA 59.747 30.769 33.22 15.38 0.00 1.94
130 131 5.742453 TGTGCGCACGTTTCTATTTTTAAAA 59.258 32.000 33.22 8.57 0.00 1.52
131 132 5.271625 TGTGCGCACGTTTCTATTTTTAAA 58.728 33.333 33.22 8.97 0.00 1.52
132 133 4.845387 TGTGCGCACGTTTCTATTTTTAA 58.155 34.783 33.22 9.66 0.00 1.52
133 134 4.024725 ACTGTGCGCACGTTTCTATTTTTA 60.025 37.500 33.22 11.78 0.00 1.52
134 135 3.242936 ACTGTGCGCACGTTTCTATTTTT 60.243 39.130 33.22 7.38 0.00 1.94
135 136 2.289547 ACTGTGCGCACGTTTCTATTTT 59.710 40.909 33.22 8.04 0.00 1.82
136 137 1.871039 ACTGTGCGCACGTTTCTATTT 59.129 42.857 33.22 8.22 0.00 1.40
137 138 1.508632 ACTGTGCGCACGTTTCTATT 58.491 45.000 33.22 8.15 0.00 1.73
138 139 1.508632 AACTGTGCGCACGTTTCTAT 58.491 45.000 33.22 16.19 0.00 1.98
139 140 1.259507 GAAACTGTGCGCACGTTTCTA 59.740 47.619 42.48 27.70 43.23 2.10
140 141 0.027586 GAAACTGTGCGCACGTTTCT 59.972 50.000 42.48 31.60 43.23 2.52
141 142 0.928451 GGAAACTGTGCGCACGTTTC 60.928 55.000 42.46 42.46 44.30 2.78
142 143 1.063488 GGAAACTGTGCGCACGTTT 59.937 52.632 38.32 38.32 39.12 3.60
143 144 1.772063 GAGGAAACTGTGCGCACGTT 61.772 55.000 33.22 31.86 44.43 3.99
144 145 2.203015 AGGAAACTGTGCGCACGT 60.203 55.556 33.22 28.71 41.13 4.49
145 146 1.891060 GAGAGGAAACTGTGCGCACG 61.891 60.000 33.22 28.09 44.43 5.34
146 147 0.880278 TGAGAGGAAACTGTGCGCAC 60.880 55.000 33.11 33.11 44.43 5.34
147 148 0.179059 TTGAGAGGAAACTGTGCGCA 60.179 50.000 5.66 5.66 44.43 6.09
148 149 0.514691 CTTGAGAGGAAACTGTGCGC 59.485 55.000 0.00 0.00 44.43 6.09
149 150 0.514691 GCTTGAGAGGAAACTGTGCG 59.485 55.000 0.00 0.00 44.43 5.34
150 151 0.514691 CGCTTGAGAGGAAACTGTGC 59.485 55.000 0.00 0.00 44.43 4.57
151 152 1.151668 CCGCTTGAGAGGAAACTGTG 58.848 55.000 0.00 0.00 44.43 3.66
152 153 0.603975 GCCGCTTGAGAGGAAACTGT 60.604 55.000 4.87 0.00 44.43 3.55
153 154 1.630244 CGCCGCTTGAGAGGAAACTG 61.630 60.000 4.87 0.00 44.43 3.16
155 156 1.627550 GACGCCGCTTGAGAGGAAAC 61.628 60.000 4.87 0.00 37.14 2.78
156 157 1.374252 GACGCCGCTTGAGAGGAAA 60.374 57.895 4.87 0.00 37.14 3.13
157 158 2.261671 GACGCCGCTTGAGAGGAA 59.738 61.111 4.87 0.00 37.14 3.36
158 159 2.989253 TGACGCCGCTTGAGAGGA 60.989 61.111 4.87 0.00 37.14 3.71
159 160 2.811317 GTGACGCCGCTTGAGAGG 60.811 66.667 0.00 0.00 38.10 3.69
160 161 1.446792 ATGTGACGCCGCTTGAGAG 60.447 57.895 0.00 0.00 0.00 3.20
161 162 1.737735 CATGTGACGCCGCTTGAGA 60.738 57.895 0.00 0.00 31.81 3.27
162 163 2.743752 CCATGTGACGCCGCTTGAG 61.744 63.158 0.00 0.00 31.81 3.02
163 164 2.741985 CCATGTGACGCCGCTTGA 60.742 61.111 0.00 0.00 31.81 3.02
164 165 3.049674 ACCATGTGACGCCGCTTG 61.050 61.111 0.00 0.00 0.00 4.01
165 166 3.049674 CACCATGTGACGCCGCTT 61.050 61.111 0.00 0.00 35.23 4.68
175 176 4.380945 ATTGGGGCGCCACCATGT 62.381 61.111 29.74 20.93 42.05 3.21
176 177 3.530260 GATTGGGGCGCCACCATG 61.530 66.667 29.74 0.00 42.05 3.66
177 178 4.059304 TGATTGGGGCGCCACCAT 62.059 61.111 29.74 24.55 42.05 3.55
179 180 3.338275 TAGTGATTGGGGCGCCACC 62.338 63.158 29.43 25.52 37.93 4.61
180 181 1.819632 CTAGTGATTGGGGCGCCAC 60.820 63.158 30.85 28.40 0.00 5.01
181 182 0.978667 TACTAGTGATTGGGGCGCCA 60.979 55.000 30.85 20.22 0.00 5.69
182 183 0.179468 TTACTAGTGATTGGGGCGCC 59.821 55.000 21.18 21.18 0.00 6.53
183 184 1.134491 ACTTACTAGTGATTGGGGCGC 60.134 52.381 5.39 0.00 31.99 6.53
184 185 2.981859 ACTTACTAGTGATTGGGGCG 57.018 50.000 5.39 0.00 31.99 6.13
185 186 4.080751 TGGTAACTTACTAGTGATTGGGGC 60.081 45.833 5.39 0.00 34.01 5.80
186 187 5.687166 TGGTAACTTACTAGTGATTGGGG 57.313 43.478 5.39 0.00 34.01 4.96
187 188 7.827236 TCAAATGGTAACTTACTAGTGATTGGG 59.173 37.037 5.39 0.00 34.01 4.12
188 189 8.665685 GTCAAATGGTAACTTACTAGTGATTGG 58.334 37.037 5.39 0.00 34.01 3.16
189 190 8.665685 GGTCAAATGGTAACTTACTAGTGATTG 58.334 37.037 5.39 0.00 34.01 2.67
190 191 8.380099 TGGTCAAATGGTAACTTACTAGTGATT 58.620 33.333 5.39 0.00 34.01 2.57
191 192 7.822822 GTGGTCAAATGGTAACTTACTAGTGAT 59.177 37.037 5.39 0.00 34.01 3.06
192 193 7.156673 GTGGTCAAATGGTAACTTACTAGTGA 58.843 38.462 5.39 0.00 34.01 3.41
193 194 6.370718 GGTGGTCAAATGGTAACTTACTAGTG 59.629 42.308 5.39 0.00 34.01 2.74
194 195 6.043474 TGGTGGTCAAATGGTAACTTACTAGT 59.957 38.462 0.00 0.00 35.68 2.57
195 196 6.370718 GTGGTGGTCAAATGGTAACTTACTAG 59.629 42.308 0.00 0.00 37.61 2.57
196 197 6.232692 GTGGTGGTCAAATGGTAACTTACTA 58.767 40.000 0.00 0.00 37.61 1.82
197 198 5.067954 GTGGTGGTCAAATGGTAACTTACT 58.932 41.667 0.00 0.00 37.61 2.24
198 199 4.083696 CGTGGTGGTCAAATGGTAACTTAC 60.084 45.833 0.00 0.00 37.61 2.34
261 262 7.223582 TGTTAAACACAACATTACATTGCCAAG 59.776 33.333 0.00 0.00 33.55 3.61
294 295 2.426024 CCCTTGAAAGACATGATGGCTG 59.574 50.000 0.00 0.00 31.94 4.85
365 367 1.271934 TCGTGCAATGGGTTTGATTGG 59.728 47.619 0.00 0.00 37.53 3.16
398 400 4.687483 GTCACAATCTTTGCAATGGAAAGG 59.313 41.667 23.49 12.43 32.26 3.11
413 415 7.119846 AGGCAAGACTAATAAGTTGTCACAATC 59.880 37.037 0.00 0.00 35.56 2.67
607 611 1.233950 ACGCGTTGTTGCATCCATCA 61.234 50.000 5.58 0.00 34.15 3.07
817 821 5.857822 AAGTGTAAATAAGCTTCGACACC 57.142 39.130 20.61 9.83 38.32 4.16
931 935 8.635765 TCATAATCAATAAATTCAGGGGTAGC 57.364 34.615 0.00 0.00 0.00 3.58
971 975 1.845809 GCAGGGCGGATTAGCATTCG 61.846 60.000 0.00 0.00 39.27 3.34
975 979 2.190313 CAGCAGGGCGGATTAGCA 59.810 61.111 0.00 0.00 39.27 3.49
1015 1030 0.478072 TTGGGGTGAGTTGCATCTGT 59.522 50.000 1.00 0.00 0.00 3.41
1086 1101 3.004629 TGCATTGATGTGGTTGTTGAGAC 59.995 43.478 0.00 0.00 0.00 3.36
1111 1126 6.709145 TTTCTGCATTTTTATGACATGCAC 57.291 33.333 1.95 0.00 46.53 4.57
1149 1164 8.106348 CGTGTTCCTTAATGAATAAGAACGTAC 58.894 37.037 0.00 0.00 43.16 3.67
1241 1265 3.891977 ACCTTCTCTTTCTTTTCCTTGCC 59.108 43.478 0.00 0.00 0.00 4.52
1242 1266 4.319839 CGACCTTCTCTTTCTTTTCCTTGC 60.320 45.833 0.00 0.00 0.00 4.01
1243 1267 4.214332 CCGACCTTCTCTTTCTTTTCCTTG 59.786 45.833 0.00 0.00 0.00 3.61
1244 1268 4.102681 TCCGACCTTCTCTTTCTTTTCCTT 59.897 41.667 0.00 0.00 0.00 3.36
1245 1269 3.646637 TCCGACCTTCTCTTTCTTTTCCT 59.353 43.478 0.00 0.00 0.00 3.36
1246 1270 3.997681 CTCCGACCTTCTCTTTCTTTTCC 59.002 47.826 0.00 0.00 0.00 3.13
1247 1271 4.884247 TCTCCGACCTTCTCTTTCTTTTC 58.116 43.478 0.00 0.00 0.00 2.29
1248 1272 4.262678 CCTCTCCGACCTTCTCTTTCTTTT 60.263 45.833 0.00 0.00 0.00 2.27
1249 1273 3.259625 CCTCTCCGACCTTCTCTTTCTTT 59.740 47.826 0.00 0.00 0.00 2.52
1327 1351 1.355066 GCTTCTTCGCCTTCAGGTCG 61.355 60.000 0.00 0.00 37.57 4.79
1516 1541 6.147821 AGCACAATAATATATGCCAGTCGAAC 59.852 38.462 5.98 0.00 38.92 3.95
1597 1623 0.814457 GGACAACTTTGTGTGCACCA 59.186 50.000 15.69 9.21 42.43 4.17
1609 1635 5.010282 GGATTTGATACAAGGTGGACAACT 58.990 41.667 0.00 0.00 0.00 3.16
1610 1636 4.142687 CGGATTTGATACAAGGTGGACAAC 60.143 45.833 0.00 0.00 0.00 3.32
1611 1637 4.006989 CGGATTTGATACAAGGTGGACAA 58.993 43.478 0.00 0.00 0.00 3.18
1683 1709 3.815401 CTCCACATTTCAAGAAAGGTCGT 59.185 43.478 9.59 0.00 42.49 4.34
1684 1710 3.815401 ACTCCACATTTCAAGAAAGGTCG 59.185 43.478 9.59 4.51 42.49 4.79
1700 1726 2.941453 TGCAGACTTCGATACTCCAC 57.059 50.000 0.00 0.00 0.00 4.02
1733 1759 2.034687 CACCCTGCTCCCCACTTG 59.965 66.667 0.00 0.00 0.00 3.16
1751 1777 0.674581 TGAATGGCAGCAGAGGTTCG 60.675 55.000 0.00 0.00 0.00 3.95
1764 1790 5.562307 GCTTGTTATGCTCTATGCTGAATGG 60.562 44.000 0.00 0.00 43.37 3.16
1766 1792 5.238868 CAGCTTGTTATGCTCTATGCTGAAT 59.761 40.000 0.00 0.00 46.40 2.57
1767 1793 4.573607 CAGCTTGTTATGCTCTATGCTGAA 59.426 41.667 0.00 0.00 46.40 3.02
1769 1795 3.303857 GCAGCTTGTTATGCTCTATGCTG 60.304 47.826 0.00 0.00 46.28 4.41
1770 1796 2.877168 GCAGCTTGTTATGCTCTATGCT 59.123 45.455 0.00 0.00 43.37 3.79
1771 1797 2.349249 CGCAGCTTGTTATGCTCTATGC 60.349 50.000 0.00 0.00 40.34 3.14
1772 1798 2.222678 CCGCAGCTTGTTATGCTCTATG 59.777 50.000 0.00 0.00 40.34 2.23
1773 1799 2.487934 CCGCAGCTTGTTATGCTCTAT 58.512 47.619 0.00 0.00 40.34 1.98
1774 1800 1.939974 CCGCAGCTTGTTATGCTCTA 58.060 50.000 0.00 0.00 40.34 2.43
1775 1801 1.372087 GCCGCAGCTTGTTATGCTCT 61.372 55.000 0.00 0.00 40.34 4.09
1776 1802 1.063166 GCCGCAGCTTGTTATGCTC 59.937 57.895 0.00 0.00 40.34 4.26
1777 1803 3.190878 GCCGCAGCTTGTTATGCT 58.809 55.556 0.00 0.00 40.34 3.79
1787 1813 1.651240 ATTGTCATGTGAGCCGCAGC 61.651 55.000 0.00 0.00 40.32 5.25
1788 1814 1.328680 GTATTGTCATGTGAGCCGCAG 59.671 52.381 0.00 0.00 0.00 5.18
1838 1890 9.267084 GTTATTTGGTATTTGGATTTTGTGTGT 57.733 29.630 0.00 0.00 0.00 3.72
1867 1919 9.623350 AGTTTCTCGTTCTTACTACTTAATGAC 57.377 33.333 0.00 0.00 0.00 3.06
1932 1984 5.012046 ACCTTGGAATTTTGGAGATTGTTCC 59.988 40.000 0.00 0.00 36.52 3.62
1968 2020 9.502091 TCTATGTTGCTACTAGTTTTGTCATTT 57.498 29.630 0.00 0.00 0.00 2.32
2089 2463 1.588674 CTTGGGTTGTGCAACTCGTA 58.411 50.000 13.78 2.96 44.56 3.43
2096 2470 1.028905 GTACTTGCTTGGGTTGTGCA 58.971 50.000 0.00 0.00 34.69 4.57
2144 2518 2.889512 ACTATGTGTGAGGTGAGGTGA 58.110 47.619 0.00 0.00 0.00 4.02
2145 2519 6.321435 TCTTATACTATGTGTGAGGTGAGGTG 59.679 42.308 0.00 0.00 0.00 4.00
2146 2520 6.432581 TCTTATACTATGTGTGAGGTGAGGT 58.567 40.000 0.00 0.00 0.00 3.85
2147 2521 6.961360 TCTTATACTATGTGTGAGGTGAGG 57.039 41.667 0.00 0.00 0.00 3.86
2365 2739 4.097892 GTCATGGATATGGTTTTGGTGACC 59.902 45.833 0.00 0.00 37.69 4.02


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

AutoCloner maintained by Alex Coulton.