Multiple sequence alignment - TraesCS1D01G273200

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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 TraesCS1D01G273200 chr1D 100.000 3848 0 0 1 3848 367432025 367428178 0.000000e+00 7107
1 TraesCS1D01G273200 chr1B 93.061 2104 89 31 1776 3848 491983734 491981657 0.000000e+00 3024
2 TraesCS1D01G273200 chr1B 91.109 1136 54 20 283 1379 491985208 491984081 0.000000e+00 1495
3 TraesCS1D01G273200 chr1B 94.444 270 14 1 1444 1713 491984045 491983777 7.690000e-112 414
4 TraesCS1D01G273200 chr1B 93.981 216 12 1 10 224 491985726 491985511 3.710000e-85 326
5 TraesCS1D01G273200 chr1A 92.170 1954 81 32 1793 3706 466928421 466926500 0.000000e+00 2695
6 TraesCS1D01G273200 chr1A 85.296 1877 147 74 1 1812 466930248 466928436 0.000000e+00 1818
7 TraesCS1D01G273200 chr1A 89.510 143 8 5 3704 3846 466926192 466926057 1.420000e-39 174
8 TraesCS1D01G273200 chr3D 78.252 1007 157 41 1865 2848 484822376 484823343 1.190000e-164 590
9 TraesCS1D01G273200 chr3B 78.131 1006 159 40 1865 2848 647680070 647681036 1.990000e-162 582
10 TraesCS1D01G273200 chr3A 77.563 1034 174 36 1834 2848 627864195 627865189 4.310000e-159 571
11 TraesCS1D01G273200 chr3A 83.740 123 16 4 1524 1646 627863813 627863931 3.140000e-21 113
12 TraesCS1D01G273200 chr7B 73.077 702 132 40 2182 2849 427303258 427302580 3.030000e-46 196
13 TraesCS1D01G273200 chr7A 77.596 366 53 17 2509 2849 474296329 474295968 1.090000e-45 195
14 TraesCS1D01G273200 chr2B 93.388 121 8 0 2729 2849 792990050 792989930 3.050000e-41 180
15 TraesCS1D01G273200 chr2A 92.562 121 9 0 2729 2849 769223290 769223410 1.420000e-39 174
16 TraesCS1D01G273200 chr2D 91.736 121 10 0 2729 2849 644095885 644096005 6.610000e-38 169
17 TraesCS1D01G273200 chr2D 86.364 132 16 2 2500 2631 644095589 644095718 4.010000e-30 143
18 TraesCS1D01G273200 chr7D 73.333 465 102 14 2180 2643 412886077 412885634 6.660000e-33 152


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 TraesCS1D01G273200 chr1D 367428178 367432025 3847 True 7107.000000 7107 100.00000 1 3848 1 chr1D.!!$R1 3847
1 TraesCS1D01G273200 chr1B 491981657 491985726 4069 True 1314.750000 3024 93.14875 10 3848 4 chr1B.!!$R1 3838
2 TraesCS1D01G273200 chr1A 466926057 466930248 4191 True 1562.333333 2695 88.99200 1 3846 3 chr1A.!!$R1 3845
3 TraesCS1D01G273200 chr3D 484822376 484823343 967 False 590.000000 590 78.25200 1865 2848 1 chr3D.!!$F1 983
4 TraesCS1D01G273200 chr3B 647680070 647681036 966 False 582.000000 582 78.13100 1865 2848 1 chr3B.!!$F1 983
5 TraesCS1D01G273200 chr3A 627863813 627865189 1376 False 342.000000 571 80.65150 1524 2848 2 chr3A.!!$F1 1324

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
183 197 0.102481 GGATCGGCGCTCAAGAAGTA 59.898 55.0 13.15 0.0 0.00 2.24 F
775 1080 0.249911 GTTCCCAGCGGGCTATACTG 60.250 60.0 8.57 0.0 43.94 2.74 F
1359 1679 0.406750 TCACCTTCCCCGTGTCTCTA 59.593 55.0 0.00 0.0 32.86 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1634 0.669318 CGCAAAACTCTGGGCTCGTA 60.669 55.000 0.00 0.0 0.00 3.43 R
2604 3249 1.149148 GCTGGAAGTTCTTCACCGAC 58.851 55.000 13.44 0.0 35.30 4.79 R
3143 3812 1.067565 TCTGCTCTTTACCAGACAGCG 60.068 52.381 0.00 0.0 33.44 5.18 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
59 70 2.282958 TCCTCCCTCTTCGCGTGT 60.283 61.111 5.77 0.00 0.00 4.49
181 195 2.233654 CGGATCGGCGCTCAAGAAG 61.234 63.158 13.15 0.00 0.00 2.85
182 196 1.153549 GGATCGGCGCTCAAGAAGT 60.154 57.895 13.15 0.00 0.00 3.01
183 197 0.102481 GGATCGGCGCTCAAGAAGTA 59.898 55.000 13.15 0.00 0.00 2.24
219 234 1.588861 GTGAGTTATTTCGGCTCGAGC 59.411 52.381 29.38 29.38 37.14 5.03
228 243 3.917760 GGCTCGAGCTGCCGGTAT 61.918 66.667 34.46 0.00 41.03 2.73
251 270 3.389687 CGTCCTTGATTTGATTGACGG 57.610 47.619 0.00 0.00 41.19 4.79
254 273 2.094675 CCTTGATTTGATTGACGGGCT 58.905 47.619 0.00 0.00 0.00 5.19
361 642 6.225981 AGTTCTTGGCATCTTTTTGTTCTT 57.774 33.333 0.00 0.00 0.00 2.52
405 691 2.473816 CAAGAGTTCGTTCAGCTGTCA 58.526 47.619 14.67 0.00 0.00 3.58
661 966 2.436646 CACCGGGGTGTCTCATGC 60.437 66.667 6.32 0.00 40.91 4.06
666 971 1.524482 GGGGTGTCTCATGCTCTCC 59.476 63.158 0.00 0.00 0.00 3.71
724 1029 8.883731 CATTTCGGATGTGTAGACTATTCTTTT 58.116 33.333 0.00 0.00 32.75 2.27
729 1034 7.646130 CGGATGTGTAGACTATTCTTTTCTCTC 59.354 40.741 0.00 0.00 32.75 3.20
735 1040 6.131544 AGACTATTCTTTTCTCTCGAGCTC 57.868 41.667 7.81 2.73 0.00 4.09
737 1042 5.890334 ACTATTCTTTTCTCTCGAGCTCTG 58.110 41.667 12.85 5.69 0.00 3.35
750 1055 1.078143 GCTCTGCTCGAAATGGGGT 60.078 57.895 0.00 0.00 0.00 4.95
768 1073 1.976474 TGATTTGTTCCCAGCGGGC 60.976 57.895 8.57 0.00 43.94 6.13
770 1075 0.393808 GATTTGTTCCCAGCGGGCTA 60.394 55.000 8.57 0.00 43.94 3.93
772 1077 0.913205 TTTGTTCCCAGCGGGCTATA 59.087 50.000 8.57 0.00 43.94 1.31
775 1080 0.249911 GTTCCCAGCGGGCTATACTG 60.250 60.000 8.57 0.00 43.94 2.74
833 1151 8.624776 GCTATACTCACCAAAATTATGCTTCTT 58.375 33.333 0.00 0.00 0.00 2.52
856 1174 1.344942 CTCTCGCAGGTACACGTTGC 61.345 60.000 0.00 0.00 0.00 4.17
935 1254 2.481185 TGTAATCGCCGTTCCAAAAGAC 59.519 45.455 0.00 0.00 0.00 3.01
958 1278 2.876550 ACAGTTTAGAAAGGTTGTCGGC 59.123 45.455 0.00 0.00 0.00 5.54
1314 1634 2.356535 GGAGATGTGCAGGGAGATTGTT 60.357 50.000 0.00 0.00 0.00 2.83
1323 1643 0.539986 GGGAGATTGTTACGAGCCCA 59.460 55.000 0.00 0.00 34.25 5.36
1353 1673 0.955919 GAAAGCTCACCTTCCCCGTG 60.956 60.000 0.00 0.00 31.99 4.94
1359 1679 0.406750 TCACCTTCCCCGTGTCTCTA 59.593 55.000 0.00 0.00 32.86 2.43
1386 1706 4.015084 AGGTGAAATTTCTGCATCTCCTG 58.985 43.478 18.64 0.00 35.20 3.86
1415 1735 5.754890 AGCAAACCTTAAAACTGAAATGCTG 59.245 36.000 0.00 0.00 38.81 4.41
1423 1743 3.375782 AACTGAAATGCTGCCAAGAAC 57.624 42.857 0.00 0.00 0.00 3.01
1425 1745 0.597568 TGAAATGCTGCCAAGAACGG 59.402 50.000 0.00 0.00 0.00 4.44
1436 1756 3.915437 CCAAGAACGGCATTTTGTACT 57.085 42.857 0.00 0.00 0.00 2.73
1453 1773 7.484993 TTTGTACTACTACCTAGATGGCAAA 57.515 36.000 0.00 0.00 40.22 3.68
1479 1799 2.473235 GAGACTGAAGAGTGTTCGTTGC 59.527 50.000 0.00 0.00 30.16 4.17
1488 1808 1.871039 AGTGTTCGTTGCGTTGCTTAT 59.129 42.857 0.00 0.00 0.00 1.73
1511 1831 4.478206 TCTCATGCCTCTTAAGTCAAGG 57.522 45.455 1.63 3.36 34.76 3.61
1571 1891 3.661944 CCCTCGAGATGGAATGATTCAG 58.338 50.000 15.71 0.00 0.00 3.02
1595 1915 9.358123 CAGTGTTTTATAAAGCGAGATAAATCG 57.642 33.333 7.44 0.00 45.48 3.34
1643 1963 4.177026 GCCTGACTAATGGTATGCTATCG 58.823 47.826 0.00 0.00 0.00 2.92
1644 1964 4.177026 CCTGACTAATGGTATGCTATCGC 58.823 47.826 0.00 0.00 0.00 4.58
1757 2294 5.741962 TGAATTCATCATTTTGGCCTTGA 57.258 34.783 3.38 2.28 31.50 3.02
1765 2302 4.305769 TCATTTTGGCCTTGATTTTGTCG 58.694 39.130 3.32 0.00 0.00 4.35
1768 2305 0.597568 TGGCCTTGATTTTGTCGCAG 59.402 50.000 3.32 0.00 0.00 5.18
1769 2306 0.598065 GGCCTTGATTTTGTCGCAGT 59.402 50.000 0.00 0.00 0.00 4.40
1770 2307 1.666888 GGCCTTGATTTTGTCGCAGTG 60.667 52.381 0.00 0.00 0.00 3.66
1771 2308 1.001378 GCCTTGATTTTGTCGCAGTGT 60.001 47.619 0.00 0.00 0.00 3.55
1773 2310 3.300009 CCTTGATTTTGTCGCAGTGTTC 58.700 45.455 0.00 0.00 0.00 3.18
1774 2311 3.243035 CCTTGATTTTGTCGCAGTGTTCA 60.243 43.478 0.00 0.00 0.00 3.18
1775 2312 4.539870 CTTGATTTTGTCGCAGTGTTCAT 58.460 39.130 0.00 0.00 0.00 2.57
1776 2313 5.334802 CCTTGATTTTGTCGCAGTGTTCATA 60.335 40.000 0.00 0.00 0.00 2.15
1777 2314 5.029650 TGATTTTGTCGCAGTGTTCATAC 57.970 39.130 0.00 0.00 0.00 2.39
1779 2316 2.831685 TTGTCGCAGTGTTCATACCT 57.168 45.000 0.00 0.00 0.00 3.08
1780 2317 3.945981 TTGTCGCAGTGTTCATACCTA 57.054 42.857 0.00 0.00 0.00 3.08
1781 2318 3.945981 TGTCGCAGTGTTCATACCTAA 57.054 42.857 0.00 0.00 0.00 2.69
1867 2442 1.066430 GCGGTACTTGTGGAGAATGGA 60.066 52.381 0.00 0.00 0.00 3.41
2016 2591 8.548877 ACTCATGTATACTGTAACCATTTCCTT 58.451 33.333 4.17 0.00 0.00 3.36
2026 2601 0.462047 CCATTTCCTTCCCGGTCTCG 60.462 60.000 0.00 0.00 0.00 4.04
2044 2619 4.025229 GTCTCGTGCATTTGCGGATAATAA 60.025 41.667 0.00 0.00 45.83 1.40
2056 2632 5.715070 TGCGGATAATAAAAACCAACCTTG 58.285 37.500 0.00 0.00 0.00 3.61
2058 2634 5.575218 GCGGATAATAAAAACCAACCTTGTG 59.425 40.000 0.00 0.00 0.00 3.33
2463 3102 1.574428 CAGCTCCCGGTTTTTGTCG 59.426 57.895 0.00 0.00 0.00 4.35
2507 3152 2.815298 GCGACGAGGACGGAGAGAG 61.815 68.421 0.00 0.00 44.46 3.20
2894 3557 3.083997 AGGCGCCTTCGAGGGAAT 61.084 61.111 27.08 0.00 35.37 3.01
2899 3562 0.175760 CGCCTTCGAGGGAATGAAGA 59.824 55.000 19.27 0.00 43.34 2.87
2900 3563 1.405526 CGCCTTCGAGGGAATGAAGAA 60.406 52.381 19.27 0.00 43.34 2.52
2909 3572 5.245301 TCGAGGGAATGAAGAAAGTAGAACA 59.755 40.000 0.00 0.00 0.00 3.18
2916 3579 8.447053 GGAATGAAGAAAGTAGAACACTCATTC 58.553 37.037 11.27 11.27 39.96 2.67
2960 3624 1.852067 ATCACGGACACGCCTTTTGC 61.852 55.000 0.00 0.00 46.04 3.68
2991 3655 7.488322 TGTAATTCTGCTTTGTTTGTAGCTTT 58.512 30.769 0.00 0.00 38.22 3.51
3117 3786 4.559300 CGTCACCTTCATGATTTGCCTTTT 60.559 41.667 0.00 0.00 0.00 2.27
3118 3787 5.299949 GTCACCTTCATGATTTGCCTTTTT 58.700 37.500 0.00 0.00 0.00 1.94
3143 3812 2.961062 AGCACATTTTCTATGGATGCCC 59.039 45.455 0.00 0.00 31.94 5.36
3145 3817 1.956477 ACATTTTCTATGGATGCCCGC 59.044 47.619 0.00 0.00 34.29 6.13
3200 3873 6.625081 GCTTCTGTTCTTTTACAACTGTTGGT 60.625 38.462 23.15 11.95 34.12 3.67
3230 3907 3.766151 CATGTGTGCTTGCCTTATTCTG 58.234 45.455 0.00 0.00 0.00 3.02
3307 3990 1.152376 TCCATGCCCTTTTGGTGCA 60.152 52.632 0.00 0.00 45.22 4.57
3387 4074 1.453155 CACATGTACCTGCCACCTTC 58.547 55.000 0.00 0.00 0.00 3.46
3451 4139 4.793201 GCTACCATAATTTCTGGGAGGTT 58.207 43.478 16.73 0.00 43.89 3.50
3465 4153 2.885266 GGGAGGTTGGTTGAGTTCTTTC 59.115 50.000 0.00 0.00 0.00 2.62
3486 4174 0.835941 AGCATGGAGGAGGACACATC 59.164 55.000 0.00 0.00 0.00 3.06
3488 4176 1.211457 GCATGGAGGAGGACACATCTT 59.789 52.381 0.00 0.00 0.00 2.40
3690 4389 0.240945 CAGCGAAATGAACCCACCAC 59.759 55.000 0.00 0.00 0.00 4.16
3706 4405 3.126858 CCACCACACCAGAAAATCATACG 59.873 47.826 0.00 0.00 0.00 3.06
3707 4406 3.751175 CACCACACCAGAAAATCATACGT 59.249 43.478 0.00 0.00 0.00 3.57
3779 4787 0.741915 TGAGCGTATCGTGCATGGTA 59.258 50.000 5.98 0.00 33.85 3.25
3787 4795 4.432892 CGTATCGTGCATGGTAATCATTCG 60.433 45.833 5.98 0.00 32.92 3.34
3803 4811 4.503910 TCATTCGTTCATTCTCAATCCGT 58.496 39.130 0.00 0.00 0.00 4.69
3804 4812 4.566759 TCATTCGTTCATTCTCAATCCGTC 59.433 41.667 0.00 0.00 0.00 4.79
3806 4814 1.588404 CGTTCATTCTCAATCCGTCCG 59.412 52.381 0.00 0.00 0.00 4.79
3810 4818 2.325393 ATTCTCAATCCGTCCGGGGC 62.325 60.000 0.00 0.00 36.01 5.80
3811 4819 3.781307 CTCAATCCGTCCGGGGCA 61.781 66.667 0.00 0.00 36.01 5.36
3814 4822 2.360726 AATCCGTCCGGGGCAAAC 60.361 61.111 0.00 0.00 36.01 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 70 1.144913 CCTGGTGGTTCCTTTCTTGGA 59.855 52.381 0.00 0.00 37.07 3.53
181 195 0.179134 ACATCAGCGCGGACTCTTAC 60.179 55.000 13.72 0.00 0.00 2.34
182 196 0.179137 CACATCAGCGCGGACTCTTA 60.179 55.000 13.72 0.00 0.00 2.10
183 197 1.446792 CACATCAGCGCGGACTCTT 60.447 57.895 13.72 0.00 0.00 2.85
224 239 5.588648 TCAATCAAATCAAGGACGGAATACC 59.411 40.000 0.00 0.00 0.00 2.73
225 240 6.487103 GTCAATCAAATCAAGGACGGAATAC 58.513 40.000 0.00 0.00 0.00 1.89
227 242 4.094887 CGTCAATCAAATCAAGGACGGAAT 59.905 41.667 0.00 0.00 42.97 3.01
228 243 3.435327 CGTCAATCAAATCAAGGACGGAA 59.565 43.478 0.00 0.00 42.97 4.30
281 300 2.248086 ATCCGGACAGTAAACGCCCC 62.248 60.000 6.12 0.00 0.00 5.80
361 642 1.984990 CGGACGAATTTAACGGACGAA 59.015 47.619 0.00 0.00 36.63 3.85
428 715 1.462283 CGAGGACAAGAACGACGACTA 59.538 52.381 0.00 0.00 0.00 2.59
735 1040 1.755179 AATCACCCCATTTCGAGCAG 58.245 50.000 0.00 0.00 0.00 4.24
737 1042 1.818674 ACAAATCACCCCATTTCGAGC 59.181 47.619 0.00 0.00 0.00 5.03
741 1046 2.903135 TGGGAACAAATCACCCCATTTC 59.097 45.455 0.00 0.00 43.46 2.17
747 1052 1.595093 CCGCTGGGAACAAATCACCC 61.595 60.000 0.00 0.00 42.06 4.61
775 1080 8.739972 ACAGACACTGGAAAACATATTAATTCC 58.260 33.333 0.00 0.00 41.37 3.01
791 1096 5.423015 AGTATAGCATGAAACAGACACTGG 58.577 41.667 0.00 0.00 35.51 4.00
833 1151 0.803117 CGTGTACCTGCGAGAGAGAA 59.197 55.000 0.00 0.00 0.00 2.87
856 1174 8.573035 GGAGTATGTCTAGGTAGAAGAAATCAG 58.427 40.741 0.00 0.00 33.47 2.90
899 1218 2.572095 TTACAGATCACGGCGGCAGG 62.572 60.000 13.24 0.00 0.00 4.85
935 1254 4.788521 GCCGACAACCTTTCTAAACTGTTG 60.789 45.833 0.00 0.00 41.47 3.33
973 1293 0.179051 AGCTAGATGCAGGCTGAAGC 60.179 55.000 20.86 11.63 45.94 3.86
1179 1499 4.851214 AGCTCGGGAGGGAGGCTC 62.851 72.222 5.78 5.78 34.56 4.70
1314 1634 0.669318 CGCAAAACTCTGGGCTCGTA 60.669 55.000 0.00 0.00 0.00 3.43
1323 1643 1.604278 GTGAGCTTTCCGCAAAACTCT 59.396 47.619 4.03 0.00 42.61 3.24
1353 1673 6.606768 CAGAAATTTCACCTGCTTTAGAGAC 58.393 40.000 19.99 0.00 0.00 3.36
1379 1699 4.313020 AAGGTTTGCTTCATCAGGAGAT 57.687 40.909 0.00 0.00 33.87 2.75
1381 1701 5.964958 TTTAAGGTTTGCTTCATCAGGAG 57.035 39.130 0.00 0.00 0.00 3.69
1383 1703 5.922544 CAGTTTTAAGGTTTGCTTCATCAGG 59.077 40.000 0.00 0.00 0.00 3.86
1386 1706 8.490355 CATTTCAGTTTTAAGGTTTGCTTCATC 58.510 33.333 0.00 0.00 0.00 2.92
1389 1709 6.479990 AGCATTTCAGTTTTAAGGTTTGCTTC 59.520 34.615 0.00 0.00 33.23 3.86
1396 1716 3.640967 TGGCAGCATTTCAGTTTTAAGGT 59.359 39.130 0.00 0.00 0.00 3.50
1423 1743 6.140303 TCTAGGTAGTAGTACAAAATGCCG 57.860 41.667 9.89 0.00 0.00 5.69
1425 1745 6.424207 GCCATCTAGGTAGTAGTACAAAATGC 59.576 42.308 9.89 0.34 40.61 3.56
1426 1746 7.497595 TGCCATCTAGGTAGTAGTACAAAATG 58.502 38.462 9.89 7.17 40.61 2.32
1434 1754 6.611642 TCAGATTTTGCCATCTAGGTAGTAGT 59.388 38.462 0.00 0.00 40.61 2.73
1435 1755 7.014711 TCTCAGATTTTGCCATCTAGGTAGTAG 59.985 40.741 0.00 0.00 40.61 2.57
1436 1756 6.839134 TCTCAGATTTTGCCATCTAGGTAGTA 59.161 38.462 0.00 0.00 40.61 1.82
1437 1757 5.663106 TCTCAGATTTTGCCATCTAGGTAGT 59.337 40.000 0.00 0.00 40.61 2.73
1453 1773 4.279671 ACGAACACTCTTCAGTCTCAGATT 59.720 41.667 0.00 0.00 0.00 2.40
1479 1799 3.624861 AGAGGCATGAGAAATAAGCAACG 59.375 43.478 0.00 0.00 0.00 4.10
1488 1808 5.248640 CCTTGACTTAAGAGGCATGAGAAA 58.751 41.667 10.09 0.00 41.60 2.52
1511 1831 1.180029 ACAAATGTCAGGGCAGATGC 58.820 50.000 0.00 0.00 41.14 3.91
1571 1891 9.910511 TTCGATTTATCTCGCTTTATAAAACAC 57.089 29.630 0.00 0.00 38.52 3.32
1595 1915 9.944663 CACAAGTAGAGATGATAAGTAGACTTC 57.055 37.037 0.00 0.00 37.40 3.01
1643 1963 9.609346 TGGTATACTTCTAAAGGTGAAAATAGC 57.391 33.333 2.25 0.00 0.00 2.97
1742 2279 4.931002 CGACAAAATCAAGGCCAAAATGAT 59.069 37.500 5.01 6.52 35.39 2.45
1743 2280 4.305769 CGACAAAATCAAGGCCAAAATGA 58.694 39.130 5.01 4.05 0.00 2.57
1757 2294 4.072131 AGGTATGAACACTGCGACAAAAT 58.928 39.130 0.00 0.00 0.00 1.82
1830 2404 7.391148 AGTACCGCTGATTCAAAATAAATGT 57.609 32.000 0.00 0.00 0.00 2.71
1867 2442 5.532779 CCTTTTAGCAGACAAGAGGAACTTT 59.467 40.000 0.00 0.00 41.55 2.66
2016 2591 1.375396 CAAATGCACGAGACCGGGA 60.375 57.895 6.32 0.00 43.04 5.14
2026 2601 5.578727 TGGTTTTTATTATCCGCAAATGCAC 59.421 36.000 6.18 0.00 42.21 4.57
2044 2619 5.182487 GGAAATGAACACAAGGTTGGTTTT 58.818 37.500 0.00 0.00 40.63 2.43
2056 2632 4.918810 AGTTTGACCTGGAAATGAACAC 57.081 40.909 0.00 0.00 0.00 3.32
2058 2634 4.584743 AGGAAGTTTGACCTGGAAATGAAC 59.415 41.667 0.00 0.00 34.99 3.18
2604 3249 1.149148 GCTGGAAGTTCTTCACCGAC 58.851 55.000 13.44 0.00 35.30 4.79
2866 3517 4.796231 GGCGCCTGTGTCGTCGAT 62.796 66.667 22.15 0.00 0.00 3.59
2884 3538 5.995565 TCTACTTTCTTCATTCCCTCGAA 57.004 39.130 0.00 0.00 0.00 3.71
2894 3557 6.231211 GGGAATGAGTGTTCTACTTTCTTCA 58.769 40.000 0.00 0.00 40.53 3.02
2899 3562 4.302559 GGGGGAATGAGTGTTCTACTTT 57.697 45.455 0.00 0.00 40.53 2.66
2960 3624 6.256321 ACAAACAAAGCAGAATTACAAGCAAG 59.744 34.615 0.00 0.00 0.00 4.01
2991 3655 1.616865 CTACCGAGTCCAGTTCCAACA 59.383 52.381 0.00 0.00 0.00 3.33
3117 3786 7.041107 GGCATCCATAGAAAATGTGCTAAAAA 58.959 34.615 0.00 0.00 0.00 1.94
3118 3787 6.406849 GGGCATCCATAGAAAATGTGCTAAAA 60.407 38.462 0.00 0.00 0.00 1.52
3119 3788 5.068987 GGGCATCCATAGAAAATGTGCTAAA 59.931 40.000 0.00 0.00 0.00 1.85
3120 3789 4.584325 GGGCATCCATAGAAAATGTGCTAA 59.416 41.667 0.00 0.00 0.00 3.09
3122 3791 2.961062 GGGCATCCATAGAAAATGTGCT 59.039 45.455 0.00 0.00 0.00 4.40
3123 3792 2.287788 CGGGCATCCATAGAAAATGTGC 60.288 50.000 0.00 0.00 0.00 4.57
3124 3793 2.287788 GCGGGCATCCATAGAAAATGTG 60.288 50.000 0.00 0.00 0.00 3.21
3125 3794 1.956477 GCGGGCATCCATAGAAAATGT 59.044 47.619 0.00 0.00 0.00 2.71
3126 3795 2.030540 CAGCGGGCATCCATAGAAAATG 60.031 50.000 0.00 0.00 0.00 2.32
3127 3796 2.233271 CAGCGGGCATCCATAGAAAAT 58.767 47.619 0.00 0.00 0.00 1.82
3143 3812 1.067565 TCTGCTCTTTACCAGACAGCG 60.068 52.381 0.00 0.00 33.44 5.18
3145 3817 4.453819 CCTTTTCTGCTCTTTACCAGACAG 59.546 45.833 0.00 0.00 37.78 3.51
3230 3907 3.543548 GCGCATGATCCTCGCTAC 58.456 61.111 0.30 0.00 44.79 3.58
3307 3990 3.131933 TGCTAAAACAACATGCACCAACT 59.868 39.130 0.00 0.00 0.00 3.16
3387 4074 6.317789 TGGAACACTCAAAAGCTTATGAAG 57.682 37.500 0.00 0.00 0.00 3.02
3451 4139 2.727123 TGCTGGAAAGAACTCAACCA 57.273 45.000 0.00 0.00 0.00 3.67
3465 4153 1.222936 GTGTCCTCCTCCATGCTGG 59.777 63.158 0.00 0.00 39.43 4.85
3486 4174 8.050778 AGTACTCATCTTTCTCACTACAGAAG 57.949 38.462 0.00 0.00 33.85 2.85
3488 4176 6.600032 GGAGTACTCATCTTTCTCACTACAGA 59.400 42.308 23.91 0.00 0.00 3.41
3571 4267 2.672908 CTCAGCAGCCACCATGGA 59.327 61.111 21.47 0.00 40.96 3.41
3613 4309 7.533426 CACATGATAACTTCTTCAGGGAAAAG 58.467 38.462 0.00 0.00 0.00 2.27
3618 4314 4.521146 AGCACATGATAACTTCTTCAGGG 58.479 43.478 0.00 0.00 0.00 4.45
3690 4389 6.916387 ACTATCGTACGTATGATTTTCTGGTG 59.084 38.462 29.86 14.71 34.09 4.17
3706 4405 5.067023 AGCCACCTTTGTACTACTATCGTAC 59.933 44.000 0.00 0.00 38.13 3.67
3707 4406 5.195940 AGCCACCTTTGTACTACTATCGTA 58.804 41.667 0.00 0.00 0.00 3.43
3779 4787 5.586243 ACGGATTGAGAATGAACGAATGATT 59.414 36.000 0.00 0.00 0.00 2.57
3787 4795 1.933853 CCGGACGGATTGAGAATGAAC 59.066 52.381 4.40 0.00 37.50 3.18
3806 4814 2.047370 CATTTGCCCGTTTGCCCC 60.047 61.111 0.00 0.00 0.00 5.80
3810 4818 0.897863 TCCTCCCATTTGCCCGTTTG 60.898 55.000 0.00 0.00 0.00 2.93
3811 4819 0.178947 TTCCTCCCATTTGCCCGTTT 60.179 50.000 0.00 0.00 0.00 3.60
3814 4822 2.418083 GCTTCCTCCCATTTGCCCG 61.418 63.158 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.