Multiple sequence alignment - TraesCS5D01G513900

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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 TraesCS5D01G513900 chr5D 100.000 2538 0 0 1 2538 537752268 537749731 0.000000e+00 4687
1 TraesCS5D01G513900 chr5D 89.749 478 31 10 1998 2461 538044659 538045132 1.680000e-166 595
2 TraesCS5D01G513900 chr5D 83.307 629 62 26 816 1430 537738342 537737743 7.990000e-150 540
3 TraesCS5D01G513900 chr5D 89.175 194 14 5 1446 1636 537737691 537737502 4.220000e-58 235
4 TraesCS5D01G513900 chr5D 81.641 256 42 5 1178 1430 537676402 537676149 9.200000e-50 207
5 TraesCS5D01G513900 chr5B 88.852 1211 73 23 570 1732 678491389 678490193 0.000000e+00 1432
6 TraesCS5D01G513900 chr5B 91.258 469 22 5 1998 2451 678455716 678455252 2.770000e-174 621
7 TraesCS5D01G513900 chr5B 85.638 564 49 16 14 555 678492029 678491476 4.740000e-157 564
8 TraesCS5D01G513900 chr5B 87.917 480 38 12 1998 2461 678707851 678707376 4.770000e-152 547
9 TraesCS5D01G513900 chr5B 81.310 626 86 22 816 1430 678440341 678439736 1.770000e-131 479
10 TraesCS5D01G513900 chr5B 93.704 270 10 5 1731 1995 678489314 678489047 5.090000e-107 398
11 TraesCS5D01G513900 chr5B 87.868 272 21 6 1446 1717 678439684 678439425 2.450000e-80 309
12 TraesCS5D01G513900 chr5B 86.643 277 23 8 1731 1995 678490139 678489865 6.870000e-76 294
13 TraesCS5D01G513900 chr5B 86.364 220 23 5 1436 1653 678340191 678339977 1.520000e-57 233
14 TraesCS5D01G513900 chr5B 82.443 262 42 3 1171 1430 678340492 678340233 2.540000e-55 226
15 TraesCS5D01G513900 chr4A 84.411 1578 83 51 259 1732 631954130 631952612 0.000000e+00 1400
16 TraesCS5D01G513900 chr4A 92.336 548 15 13 2011 2538 631949078 631948538 0.000000e+00 754
17 TraesCS5D01G513900 chr4A 89.749 478 31 10 1998 2461 632231938 632232411 1.680000e-166 595
18 TraesCS5D01G513900 chr4A 86.063 287 28 7 1446 1732 631940325 631940051 5.310000e-77 298
19 TraesCS5D01G513900 chr4A 87.293 181 13 4 1825 1995 631952512 631952332 5.540000e-47 198
20 TraesCS5D01G513900 chr4A 86.628 172 16 3 1 166 631954299 631954129 1.550000e-42 183
21 TraesCS5D01G513900 chr4A 89.394 132 14 0 1178 1309 631942204 631942073 1.560000e-37 167
22 TraesCS5D01G513900 chr4A 85.714 126 13 4 1307 1430 631940499 631940377 7.370000e-26 128
23 TraesCS5D01G513900 chr2B 84.739 249 27 7 1744 1985 481052395 481052151 3.260000e-59 239
24 TraesCS5D01G513900 chr2D 82.625 259 36 6 1744 1995 405419769 405419513 1.180000e-53 220
25 TraesCS5D01G513900 chr2D 84.279 229 22 8 1744 1964 27499539 27499761 7.110000e-51 211
26 TraesCS5D01G513900 chr7B 82.520 246 30 7 1745 1983 643377246 643377485 1.190000e-48 204
27 TraesCS5D01G513900 chr7D 83.111 225 30 5 1779 1995 160490025 160489801 5.540000e-47 198
28 TraesCS5D01G513900 chr5A 80.913 241 33 8 1744 1977 701891915 701891681 7.220000e-41 178


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 TraesCS5D01G513900 chr5D 537749731 537752268 2537 True 4687.00 4687 100.00000 1 2538 1 chr5D.!!$R2 2537
1 TraesCS5D01G513900 chr5D 537737502 537738342 840 True 387.50 540 86.24100 816 1636 2 chr5D.!!$R3 820
2 TraesCS5D01G513900 chr5B 678489047 678492029 2982 True 672.00 1432 88.70925 14 1995 4 chr5B.!!$R5 1981
3 TraesCS5D01G513900 chr5B 678439425 678440341 916 True 394.00 479 84.58900 816 1717 2 chr5B.!!$R4 901
4 TraesCS5D01G513900 chr5B 678339977 678340492 515 True 229.50 233 84.40350 1171 1653 2 chr5B.!!$R3 482
5 TraesCS5D01G513900 chr4A 631948538 631954299 5761 True 633.75 1400 87.66700 1 2538 4 chr4A.!!$R2 2537

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
927 1074 0.323908 AGAAGCCTACCGAGCAGTCT 60.324 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2311 1.303091 AAGGCCCACGACGCAAATAC 61.303 55.0 0.0 0.0 0.0 1.89 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
96 102 3.090037 CTCTCTCCGTCCCAAAAGTCTA 58.910 50.000 0.00 0.00 0.00 2.59
97 103 3.503365 TCTCTCCGTCCCAAAAGTCTAA 58.497 45.455 0.00 0.00 0.00 2.10
170 176 9.490379 AGATTATAAGTTTGACACCGGATAATC 57.510 33.333 9.46 12.22 34.73 1.75
171 177 9.268268 GATTATAAGTTTGACACCGGATAATCA 57.732 33.333 9.46 2.67 34.70 2.57
172 178 9.621629 ATTATAAGTTTGACACCGGATAATCAA 57.378 29.630 9.46 9.39 0.00 2.57
179 185 9.019764 GTTTGACACCGGATAATCAATAAAATG 57.980 33.333 9.46 0.00 31.45 2.32
212 218 2.064762 GTGTGAGAAGCTGTAGTGCTG 58.935 52.381 0.00 0.00 43.24 4.41
213 219 1.688735 TGTGAGAAGCTGTAGTGCTGT 59.311 47.619 0.00 0.00 43.24 4.40
214 220 2.890945 TGTGAGAAGCTGTAGTGCTGTA 59.109 45.455 0.00 0.00 43.24 2.74
238 245 3.356639 GAGCGCTGATGTGGACCGA 62.357 63.158 18.48 0.00 0.00 4.69
241 248 1.153568 CGCTGATGTGGACCGATGT 60.154 57.895 0.00 0.00 0.00 3.06
244 251 1.406069 GCTGATGTGGACCGATGTTCT 60.406 52.381 0.00 0.00 0.00 3.01
247 254 3.361786 TGATGTGGACCGATGTTCTAGA 58.638 45.455 0.00 0.00 0.00 2.43
248 255 3.381590 TGATGTGGACCGATGTTCTAGAG 59.618 47.826 0.00 0.00 0.00 2.43
250 257 3.162666 TGTGGACCGATGTTCTAGAGTT 58.837 45.455 0.00 0.00 0.00 3.01
251 258 3.056821 TGTGGACCGATGTTCTAGAGTTG 60.057 47.826 0.00 0.00 0.00 3.16
252 259 2.094182 TGGACCGATGTTCTAGAGTTGC 60.094 50.000 0.00 0.00 0.00 4.17
344 376 4.803426 GGAGGCACCTCGTCGCTG 62.803 72.222 10.52 0.00 43.59 5.18
410 444 2.125106 CCAAGGGTACGCTCTGCC 60.125 66.667 13.46 0.00 0.00 4.85
411 445 2.509336 CAAGGGTACGCTCTGCCG 60.509 66.667 13.46 0.00 0.00 5.69
412 446 4.452733 AAGGGTACGCTCTGCCGC 62.453 66.667 13.46 0.00 0.00 6.53
414 448 4.874977 GGGTACGCTCTGCCGCTC 62.875 72.222 2.05 0.00 0.00 5.03
415 449 3.827898 GGTACGCTCTGCCGCTCT 61.828 66.667 0.00 0.00 0.00 4.09
416 450 2.580867 GTACGCTCTGCCGCTCTG 60.581 66.667 0.00 0.00 0.00 3.35
417 451 4.498520 TACGCTCTGCCGCTCTGC 62.499 66.667 0.00 0.00 0.00 4.26
471 509 4.392940 ACTCTGTTTTGTGCTCTGCTTAT 58.607 39.130 0.00 0.00 0.00 1.73
472 510 5.551233 ACTCTGTTTTGTGCTCTGCTTATA 58.449 37.500 0.00 0.00 0.00 0.98
473 511 5.641209 ACTCTGTTTTGTGCTCTGCTTATAG 59.359 40.000 0.00 0.00 0.00 1.31
475 513 4.326826 TGTTTTGTGCTCTGCTTATAGCT 58.673 39.130 0.00 0.00 42.97 3.32
476 514 4.393062 TGTTTTGTGCTCTGCTTATAGCTC 59.607 41.667 0.00 0.00 42.97 4.09
477 515 3.893326 TTGTGCTCTGCTTATAGCTCA 57.107 42.857 0.00 0.00 42.97 4.26
480 518 5.535753 TGTGCTCTGCTTATAGCTCAATA 57.464 39.130 0.00 0.00 42.97 1.90
481 519 5.917462 TGTGCTCTGCTTATAGCTCAATAA 58.083 37.500 0.00 0.00 42.97 1.40
484 522 7.500227 TGTGCTCTGCTTATAGCTCAATAAAAT 59.500 33.333 0.00 0.00 42.97 1.82
485 523 8.993121 GTGCTCTGCTTATAGCTCAATAAAATA 58.007 33.333 0.00 0.00 42.97 1.40
486 524 8.993121 TGCTCTGCTTATAGCTCAATAAAATAC 58.007 33.333 0.00 0.00 42.97 1.89
487 525 8.447053 GCTCTGCTTATAGCTCAATAAAATACC 58.553 37.037 0.00 0.00 42.97 2.73
488 526 8.848474 TCTGCTTATAGCTCAATAAAATACCC 57.152 34.615 0.00 0.00 42.97 3.69
536 578 0.763035 AGTACCAAAACAGCCCTCGT 59.237 50.000 0.00 0.00 0.00 4.18
563 668 2.288825 TGTTTAGCTCCTCCGTCTGTTG 60.289 50.000 0.00 0.00 0.00 3.33
585 699 0.546122 TCTGGTGGTTCAGCACAACT 59.454 50.000 11.09 0.00 36.93 3.16
612 726 1.415659 CAGGCCATACAAGAGAGGGAG 59.584 57.143 5.01 0.00 0.00 4.30
702 843 8.033626 ACAAGTTGTTCTACAATACCTACTAGC 58.966 37.037 1.64 0.00 40.59 3.42
795 939 5.809001 TCTGTAATTCTCTGCAATTGGAGT 58.191 37.500 24.15 9.22 34.87 3.85
796 940 6.240894 TCTGTAATTCTCTGCAATTGGAGTT 58.759 36.000 24.15 14.55 34.87 3.01
797 941 6.149973 TCTGTAATTCTCTGCAATTGGAGTTG 59.850 38.462 24.15 18.06 34.87 3.16
798 942 4.796038 AATTCTCTGCAATTGGAGTTGG 57.204 40.909 24.15 15.89 34.87 3.77
800 944 3.063510 TCTCTGCAATTGGAGTTGGAG 57.936 47.619 24.15 15.36 45.51 3.86
803 947 2.639347 TCTGCAATTGGAGTTGGAGAGA 59.361 45.455 24.15 2.25 46.97 3.10
804 948 2.746362 CTGCAATTGGAGTTGGAGAGAC 59.254 50.000 18.09 0.00 46.62 3.36
805 949 2.106338 TGCAATTGGAGTTGGAGAGACA 59.894 45.455 7.72 0.00 0.00 3.41
806 950 2.485814 GCAATTGGAGTTGGAGAGACAC 59.514 50.000 7.72 0.00 0.00 3.67
927 1074 0.323908 AGAAGCCTACCGAGCAGTCT 60.324 55.000 0.00 0.00 0.00 3.24
936 1083 2.920645 CGAGCAGTCTGACCGTGGT 61.921 63.158 3.32 2.73 0.00 4.16
1071 1218 2.839228 AGAGAGGTGATTAAGGTGCCT 58.161 47.619 0.00 0.00 0.00 4.75
1096 1243 0.179026 CCAGATGCCATCCTCACCAG 60.179 60.000 0.00 0.00 0.00 4.00
1098 1245 1.527844 GATGCCATCCTCACCAGCC 60.528 63.158 0.00 0.00 0.00 4.85
1100 1247 2.124403 GCCATCCTCACCAGCCAG 60.124 66.667 0.00 0.00 0.00 4.85
1101 1248 2.124403 CCATCCTCACCAGCCAGC 60.124 66.667 0.00 0.00 0.00 4.85
1103 1250 2.611800 ATCCTCACCAGCCAGCCA 60.612 61.111 0.00 0.00 0.00 4.75
1121 1268 2.676076 CCATTGGTGCTTGCTGTTTAC 58.324 47.619 0.00 0.00 0.00 2.01
1138 1285 8.132362 TGCTGTTTACTACATTTTTGGTTACTG 58.868 33.333 0.00 0.00 35.85 2.74
1169 1320 9.092876 TGTTTTTGTACTTCATTTCCAATGTTC 57.907 29.630 0.00 0.00 0.00 3.18
1171 1322 8.641499 TTTTGTACTTCATTTCCAATGTTCAC 57.359 30.769 0.00 0.00 0.00 3.18
1172 1323 6.951062 TGTACTTCATTTCCAATGTTCACA 57.049 33.333 0.00 0.00 0.00 3.58
1198 1368 3.492102 TTGCTTTCACTCTAGGCTTGT 57.508 42.857 0.00 0.00 0.00 3.16
1259 1429 2.257353 GCATCCTGCGAACCTTGTT 58.743 52.632 0.00 0.00 31.71 2.83
1527 1763 3.006859 CAGAACACCAAGGGGAAATTTCC 59.993 47.826 26.41 26.41 46.82 3.13
1647 1893 5.825151 TGTCATTGGTGATGAACTACAAACA 59.175 36.000 0.00 0.00 45.96 2.83
1764 2067 5.491078 TGAGAGTGTGGATTTTTATACCCCT 59.509 40.000 0.00 0.00 0.00 4.79
1796 2099 8.287350 AGTGTACCCTCTACCTAGATAATTCAA 58.713 37.037 0.00 0.00 0.00 2.69
1802 2105 7.118390 CCCTCTACCTAGATAATTCAATTTGCG 59.882 40.741 0.00 0.00 0.00 4.85
1804 2107 8.958119 TCTACCTAGATAATTCAATTTGCGTT 57.042 30.769 0.00 0.00 0.00 4.84
1809 2112 9.817365 CCTAGATAATTCAATTTGCGTTATGAG 57.183 33.333 9.42 7.40 0.00 2.90
1814 2117 4.577687 TCAATTTGCGTTATGAGTCGTC 57.422 40.909 0.00 0.00 0.00 4.20
1819 2122 5.944049 TTTGCGTTATGAGTCGTCTTATC 57.056 39.130 0.00 0.00 0.00 1.75
1823 2126 5.297527 TGCGTTATGAGTCGTCTTATCCTTA 59.702 40.000 0.00 0.00 0.00 2.69
1875 2184 6.831353 TCCAAACAAGAGAACATTTGACCTTA 59.169 34.615 0.00 0.00 34.62 2.69
1902 2215 7.133891 ACTTTGCAGATTATACACAAGTGTC 57.866 36.000 9.42 0.00 43.74 3.67
1913 2226 9.890629 ATTATACACAAGTGTCACTCATTGTAT 57.109 29.630 23.88 23.88 43.74 2.29
1917 2230 8.621532 ACACAAGTGTCACTCATTGTATAAAT 57.378 30.769 5.82 0.00 40.24 1.40
1918 2231 8.506437 ACACAAGTGTCACTCATTGTATAAATG 58.494 33.333 5.82 0.00 40.24 2.32
1919 2232 8.506437 CACAAGTGTCACTCATTGTATAAATGT 58.494 33.333 5.82 0.00 34.26 2.71
2055 5610 2.098934 ACAGAGACGATGAGACAGATGC 59.901 50.000 0.00 0.00 0.00 3.91
2119 5688 4.682714 AGGGGCCAAGGAGCTGGA 62.683 66.667 4.39 0.00 38.96 3.86
2120 5689 3.661648 GGGGCCAAGGAGCTGGAA 61.662 66.667 4.39 0.00 38.96 3.53
2128 5697 1.627834 CAAGGAGCTGGAAAGAGACCT 59.372 52.381 0.00 0.00 0.00 3.85
2142 5711 6.385766 AAAGAGACCTTGAAGGATGAAGAT 57.614 37.500 19.83 0.00 37.67 2.40
2168 5737 1.078848 CCCTTCCACTTCCAGCTCG 60.079 63.158 0.00 0.00 0.00 5.03
2268 5841 2.697229 TCATCATGACGAGGATTCAGCT 59.303 45.455 0.00 0.00 27.00 4.24
2272 5845 1.489481 TGACGAGGATTCAGCTCCAT 58.511 50.000 0.00 0.00 37.81 3.41
2286 5859 9.240734 GATTCAGCTCCATTTATTATCTGGAAT 57.759 33.333 0.00 0.00 38.55 3.01
2398 5972 4.406003 TGCTTTAGTAGGTTTTTGCCCAAA 59.594 37.500 0.00 0.00 0.00 3.28
2399 5973 5.071115 TGCTTTAGTAGGTTTTTGCCCAAAT 59.929 36.000 0.00 0.00 0.00 2.32
2400 5974 6.267928 TGCTTTAGTAGGTTTTTGCCCAAATA 59.732 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.681729 ATGGTATGACTCCATAATAACCGT 57.318 37.500 0.00 0.00 42.96 4.83
44 45 1.482593 GCTCCTGCTCTAGCCAAGTTA 59.517 52.381 0.00 0.00 41.18 2.24
96 102 9.490379 AAAACGTGTCTAGACAAATCTAAGATT 57.510 29.630 26.74 9.78 43.77 2.40
170 176 5.562248 CACCAACGACGTGTACATTTTATTG 59.438 40.000 0.00 2.21 0.00 1.90
171 177 5.236911 ACACCAACGACGTGTACATTTTATT 59.763 36.000 0.00 0.00 42.56 1.40
172 178 4.751098 ACACCAACGACGTGTACATTTTAT 59.249 37.500 0.00 0.00 42.56 1.40
179 185 1.126079 CTCACACCAACGACGTGTAC 58.874 55.000 0.00 0.00 42.49 2.90
238 245 1.630148 GACGCGCAACTCTAGAACAT 58.370 50.000 5.73 0.00 0.00 2.71
241 248 0.453950 GTCGACGCGCAACTCTAGAA 60.454 55.000 5.73 0.00 0.00 2.10
244 251 1.154282 CAGTCGACGCGCAACTCTA 60.154 57.895 5.73 0.00 0.00 2.43
247 254 3.973516 TCCAGTCGACGCGCAACT 61.974 61.111 5.73 4.10 0.00 3.16
248 255 3.764049 GTCCAGTCGACGCGCAAC 61.764 66.667 5.73 1.23 0.00 4.17
410 444 0.318275 GAGATAACCGGAGCAGAGCG 60.318 60.000 9.46 0.00 0.00 5.03
411 445 0.318275 CGAGATAACCGGAGCAGAGC 60.318 60.000 9.46 0.00 0.00 4.09
412 446 0.318275 GCGAGATAACCGGAGCAGAG 60.318 60.000 9.46 0.00 0.00 3.35
413 447 1.734137 GCGAGATAACCGGAGCAGA 59.266 57.895 9.46 0.00 0.00 4.26
414 448 1.658717 CGCGAGATAACCGGAGCAG 60.659 63.158 9.46 0.00 0.00 4.24
415 449 2.411701 CGCGAGATAACCGGAGCA 59.588 61.111 9.46 0.00 0.00 4.26
416 450 2.354773 CCGCGAGATAACCGGAGC 60.355 66.667 9.46 0.49 44.55 4.70
417 451 2.335369 CCCGCGAGATAACCGGAG 59.665 66.667 9.46 0.00 44.55 4.63
471 509 8.871629 TTGAACTTGGGTATTTTATTGAGCTA 57.128 30.769 0.00 0.00 0.00 3.32
472 510 7.093771 CCTTGAACTTGGGTATTTTATTGAGCT 60.094 37.037 0.00 0.00 0.00 4.09
473 511 7.035612 CCTTGAACTTGGGTATTTTATTGAGC 58.964 38.462 0.00 0.00 0.00 4.26
475 513 7.396055 CCTCCTTGAACTTGGGTATTTTATTGA 59.604 37.037 0.00 0.00 0.00 2.57
476 514 7.547227 CCTCCTTGAACTTGGGTATTTTATTG 58.453 38.462 0.00 0.00 0.00 1.90
477 515 6.154534 GCCTCCTTGAACTTGGGTATTTTATT 59.845 38.462 0.00 0.00 0.00 1.40
480 518 3.832490 GCCTCCTTGAACTTGGGTATTTT 59.168 43.478 0.00 0.00 0.00 1.82
481 519 3.431415 GCCTCCTTGAACTTGGGTATTT 58.569 45.455 0.00 0.00 0.00 1.40
484 522 0.323629 CGCCTCCTTGAACTTGGGTA 59.676 55.000 0.00 0.00 0.00 3.69
485 523 1.073199 CGCCTCCTTGAACTTGGGT 59.927 57.895 0.00 0.00 0.00 4.51
486 524 1.675641 CCGCCTCCTTGAACTTGGG 60.676 63.158 0.00 0.00 0.00 4.12
487 525 1.675641 CCCGCCTCCTTGAACTTGG 60.676 63.158 0.00 0.00 0.00 3.61
488 526 0.035056 ATCCCGCCTCCTTGAACTTG 60.035 55.000 0.00 0.00 0.00 3.16
536 578 1.608025 CGGAGGAGCTAAACAAGTGCA 60.608 52.381 0.00 0.00 0.00 4.57
563 668 1.896220 TGTGCTGAACCACCAGATTC 58.104 50.000 0.00 0.00 36.29 2.52
585 699 0.393402 CTTGTATGGCCTGCTCTGCA 60.393 55.000 3.32 0.00 36.92 4.41
612 726 4.571580 CCTCATGAACTCAGAAAGATGCTC 59.428 45.833 0.00 0.00 0.00 4.26
623 764 5.624159 ACAAACAAGATCCTCATGAACTCA 58.376 37.500 0.00 0.00 0.00 3.41
795 939 5.878406 AGAAAGAAAGAGTGTCTCTCCAA 57.122 39.130 0.00 0.00 40.28 3.53
796 940 5.878406 AAGAAAGAAAGAGTGTCTCTCCA 57.122 39.130 0.00 0.00 40.28 3.86
797 941 6.521162 AGAAAGAAAGAAAGAGTGTCTCTCC 58.479 40.000 0.00 0.00 40.28 3.71
798 942 9.535878 TTAAGAAAGAAAGAAAGAGTGTCTCTC 57.464 33.333 0.00 0.00 40.28 3.20
801 945 9.892130 TCTTTAAGAAAGAAAGAAAGAGTGTCT 57.108 29.630 0.00 0.00 44.10 3.41
936 1083 2.359354 CCAAATGGGCGTCCGTGA 60.359 61.111 0.00 0.00 35.24 4.35
1085 1232 2.124403 GGCTGGCTGGTGAGGATG 60.124 66.667 0.00 0.00 0.00 3.51
1098 1245 1.080093 CAGCAAGCACCAATGGCTG 60.080 57.895 0.00 0.00 44.91 4.85
1100 1247 0.249996 AAACAGCAAGCACCAATGGC 60.250 50.000 0.00 0.00 0.00 4.40
1101 1248 2.297033 AGTAAACAGCAAGCACCAATGG 59.703 45.455 0.00 0.00 0.00 3.16
1103 1250 4.141287 TGTAGTAAACAGCAAGCACCAAT 58.859 39.130 0.00 0.00 33.01 3.16
1121 1268 9.581099 AAACAAACTCAGTAACCAAAAATGTAG 57.419 29.630 0.00 0.00 0.00 2.74
1138 1285 8.696410 TGGAAATGAAGTACAAAAACAAACTC 57.304 30.769 0.00 0.00 0.00 3.01
1142 1289 9.442047 AACATTGGAAATGAAGTACAAAAACAA 57.558 25.926 6.96 0.00 0.00 2.83
1169 1320 2.357009 AGAGTGAAAGCAAAGCACTGTG 59.643 45.455 2.76 2.76 42.47 3.66
1171 1322 3.188048 CCTAGAGTGAAAGCAAAGCACTG 59.812 47.826 0.00 0.00 42.47 3.66
1172 1323 3.406764 CCTAGAGTGAAAGCAAAGCACT 58.593 45.455 0.00 0.00 44.87 4.40
1198 1368 3.118738 GGTCGATCTTCCCAAGCTTCTTA 60.119 47.826 0.00 0.00 0.00 2.10
1259 1429 2.048597 AGCGCCGAAACACATCGA 60.049 55.556 2.29 0.00 45.48 3.59
1505 1741 3.006859 GGAAATTTCCCCTTGGTGTTCTG 59.993 47.826 24.44 0.00 41.62 3.02
1713 1959 5.445939 GCGTGTTTCATGTTAGTATCCACAG 60.446 44.000 0.00 0.00 0.00 3.66
1764 2067 7.558640 ATCTAGGTAGAGGGTACACTGGTACA 61.559 46.154 0.00 0.00 42.44 2.90
1796 2099 5.462398 GGATAAGACGACTCATAACGCAAAT 59.538 40.000 0.00 0.00 0.00 2.32
1841 2144 7.169158 TGTTCTCTTGTTTGGAAGAAACAAT 57.831 32.000 11.91 0.00 45.56 2.71
1875 2184 8.413229 ACACTTGTGTATAATCTGCAAAGTTTT 58.587 29.630 4.42 0.00 0.00 2.43
1982 2297 7.591795 ACGACGCAAATACAATGAATGTTTAAA 59.408 29.630 0.00 0.00 43.63 1.52
1988 2303 3.785521 CCACGACGCAAATACAATGAATG 59.214 43.478 0.00 0.00 0.00 2.67
1995 2310 2.036006 GGCCCACGACGCAAATACA 61.036 57.895 0.00 0.00 0.00 2.29
1996 2311 1.303091 AAGGCCCACGACGCAAATAC 61.303 55.000 0.00 0.00 0.00 1.89
2055 5610 3.801114 TCGTCATAGTCATGTCAAGGG 57.199 47.619 0.00 0.00 33.57 3.95
2093 5662 1.574526 CCTTGGCCCCTCCTTCATCA 61.575 60.000 0.00 0.00 35.26 3.07
2119 5688 5.832539 TCTTCATCCTTCAAGGTCTCTTT 57.167 39.130 2.50 0.00 36.53 2.52
2120 5689 6.900186 TCTATCTTCATCCTTCAAGGTCTCTT 59.100 38.462 2.50 0.00 36.53 2.85
2128 5697 6.391055 AGGGGAAATCTATCTTCATCCTTCAA 59.609 38.462 0.00 0.00 29.29 2.69
2142 5711 3.523564 CTGGAAGTGGAAGGGGAAATCTA 59.476 47.826 0.00 0.00 0.00 1.98
2168 5737 4.274459 CCAGAGATGGCTGCAAATAGTAAC 59.726 45.833 0.50 0.00 34.56 2.50
2256 5829 7.064371 CAGATAATAAATGGAGCTGAATCCTCG 59.936 40.741 0.00 0.00 40.29 4.63
2343 5916 5.640147 TCTCAAACATTAAGGTGAATGGGT 58.360 37.500 0.00 0.00 40.50 4.51
2344 5917 6.588719 TTCTCAAACATTAAGGTGAATGGG 57.411 37.500 0.00 0.00 40.50 4.00
2408 5982 7.744087 AGAGTACTGTGCATTGAATAAAACA 57.256 32.000 0.00 0.00 0.00 2.83
2427 6001 9.534565 GCATGAGAGTAACAATATCAAAGAGTA 57.465 33.333 0.00 0.00 0.00 2.59
2428 6002 8.263640 AGCATGAGAGTAACAATATCAAAGAGT 58.736 33.333 0.00 0.00 0.00 3.24
2429 6003 8.659925 AGCATGAGAGTAACAATATCAAAGAG 57.340 34.615 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.