Multiple sequence alignment - TraesCS5A01G163000

Loading Multiple Alignment...

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 TraesCS5A01G163000 chr5A 100.000 4631 0 0 1 4631 348721503 348716873 0.000000e+00 8552.0
1 TraesCS5A01G163000 chr5A 78.125 96 19 2 4442 4536 537248308 537248214 5.000000e-05 60.2
2 TraesCS5A01G163000 chr5B 93.779 3488 110 42 1195 4631 295383144 295379713 0.000000e+00 5140.0
3 TraesCS5A01G163000 chr5B 94.188 499 21 2 183 681 295385138 295384648 0.000000e+00 754.0
4 TraesCS5A01G163000 chr5B 93.658 473 25 2 674 1141 295383836 295383364 0.000000e+00 702.0
5 TraesCS5A01G163000 chr5B 88.889 54 3 3 4440 4492 611866288 611866237 3.870000e-06 63.9
6 TraesCS5A01G163000 chr5D 92.813 2087 80 33 33 2088 262843103 262841056 0.000000e+00 2959.0
7 TraesCS5A01G163000 chr5D 94.359 1631 43 16 2408 4021 262840388 262838790 0.000000e+00 2457.0
8 TraesCS5A01G163000 chr5D 98.046 614 10 1 4020 4631 262838696 262838083 0.000000e+00 1066.0
9 TraesCS5A01G163000 chr5D 97.778 225 5 0 2100 2324 262840912 262840688 5.620000e-104 388.0
10 TraesCS5A01G163000 chr5D 93.684 95 4 2 2331 2423 262840630 262840536 1.740000e-29 141.0
11 TraesCS5A01G163000 chr2A 88.679 53 3 3 4441 4492 725890649 725890599 1.390000e-05 62.1
12 TraesCS5A01G163000 chr6B 89.583 48 4 1 4442 4489 211810942 211810896 5.000000e-05 60.2
13 TraesCS5A01G163000 chr4B 94.872 39 0 2 4439 4476 237056968 237057005 5.000000e-05 60.2
14 TraesCS5A01G163000 chr1B 88.235 51 5 1 4442 4492 553454121 553454072 5.000000e-05 60.2
15 TraesCS5A01G163000 chr6D 88.000 50 3 3 4441 4489 59026466 59026513 6.470000e-04 56.5


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 TraesCS5A01G163000 chr5A 348716873 348721503 4630 True 8552.000000 8552 100.000 1 4631 1 chr5A.!!$R1 4630
1 TraesCS5A01G163000 chr5B 295379713 295385138 5425 True 2198.666667 5140 93.875 183 4631 3 chr5B.!!$R2 4448
2 TraesCS5A01G163000 chr5D 262838083 262843103 5020 True 1402.200000 2959 95.336 33 4631 5 chr5D.!!$R1 4598

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
838 1667 0.033504 ATGGACAGTGACTCGCGTTT 59.966 50.0 5.77 0.00 0.0 3.60 F
1516 2527 0.036732 AGCATTCTCGTTGGGCAAGA 59.963 50.0 0.00 0.00 0.0 3.02 F
2006 3033 0.109272 TCGTCGATGTGTCTCCTTGC 60.109 55.0 4.21 0.00 0.0 4.01 F
2956 4395 0.311790 AACAAACTCTGGCGTGCATG 59.688 50.0 0.09 0.09 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2916 0.584396 TTCGCACGTTCATTCACACC 59.416 50.0 0.00 0.00 0.00 4.16 R
2955 4394 0.179065 CGATCTTCTCCTGCCATGCA 60.179 55.0 0.00 0.00 36.92 3.96 R
3600 5039 0.179000 GGGTGTAGTGCTCCATCTGG 59.821 60.0 1.67 0.00 32.58 3.86 R
3979 5418 0.606401 GATGCACGGTCCCCATATGG 60.606 60.0 15.41 15.41 0.00 2.74 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 2.940137 GCGACGTGCGTTTAATAAGAG 58.060 47.619 0.00 0.00 43.41 2.85
26 27 2.595536 GCGACGTGCGTTTAATAAGAGA 59.404 45.455 0.00 0.00 43.41 3.10
27 28 3.059834 GCGACGTGCGTTTAATAAGAGAA 59.940 43.478 0.00 0.00 43.41 2.87
28 29 4.775083 GCGACGTGCGTTTAATAAGAGAAG 60.775 45.833 0.00 0.00 43.41 2.85
29 30 4.556135 CGACGTGCGTTTAATAAGAGAAGA 59.444 41.667 0.00 0.00 34.64 2.87
30 31 5.496657 CGACGTGCGTTTAATAAGAGAAGAC 60.497 44.000 0.00 0.00 34.64 3.01
31 32 4.322804 ACGTGCGTTTAATAAGAGAAGACG 59.677 41.667 0.00 0.00 0.00 4.18
36 37 6.308766 TGCGTTTAATAAGAGAAGACGTTACC 59.691 38.462 0.00 0.00 0.00 2.85
46 47 3.431055 ACGTTACCGTCGACCACA 58.569 55.556 10.58 0.00 46.28 4.17
51 52 1.788886 GTTACCGTCGACCACAAAGAC 59.211 52.381 10.58 0.00 0.00 3.01
54 55 4.021650 GTCGACCACAAAGACGCA 57.978 55.556 3.51 0.00 0.00 5.24
69 70 2.157668 AGACGCATGTGACGAATTTGTC 59.842 45.455 17.60 17.60 39.37 3.18
89 90 3.424529 GTCTGCGTCTGTACTGTGTTAAC 59.575 47.826 0.00 0.00 0.00 2.01
94 95 5.294799 TGCGTCTGTACTGTGTTAACAAAAT 59.705 36.000 10.51 0.00 35.37 1.82
104 105 6.083098 TGTGTTAACAAAATGGAGACATGG 57.917 37.500 10.51 0.00 41.59 3.66
117 118 2.573915 GAGACATGGGAAGGGAAAGAGT 59.426 50.000 0.00 0.00 0.00 3.24
118 119 2.307098 AGACATGGGAAGGGAAAGAGTG 59.693 50.000 0.00 0.00 0.00 3.51
126 127 0.543174 AGGGAAAGAGTGACGGCTCT 60.543 55.000 0.00 0.00 46.82 4.09
219 220 1.270550 CACACCTTGCCACCAATTCTC 59.729 52.381 0.00 0.00 0.00 2.87
227 228 1.631405 CCACCAATTCTCAAAGGGCA 58.369 50.000 0.00 0.00 0.00 5.36
291 292 1.816224 GGAGAGAGACTGTGTGTCCTC 59.184 57.143 0.00 0.00 46.46 3.71
386 387 0.805322 GCACGACTCTGATCTGCCTG 60.805 60.000 0.00 0.00 0.00 4.85
449 454 0.527385 CTGCTAAGAGACTGAGGCGC 60.527 60.000 0.00 0.00 0.00 6.53
483 488 1.203994 CACACTCCCCTACAAGGTACG 59.796 57.143 0.00 0.00 31.93 3.67
484 489 1.203100 ACACTCCCCTACAAGGTACGT 60.203 52.381 0.00 0.00 31.93 3.57
485 490 2.041620 ACACTCCCCTACAAGGTACGTA 59.958 50.000 0.00 0.00 31.93 3.57
486 491 2.424956 CACTCCCCTACAAGGTACGTAC 59.575 54.545 17.56 17.56 31.93 3.67
500 505 5.476614 AGGTACGTACTTGGAATTCACTTC 58.523 41.667 24.07 3.49 0.00 3.01
574 579 5.049405 CCTCCGTATATTGGTTGCATTTCTC 60.049 44.000 0.00 0.00 0.00 2.87
575 580 5.680619 TCCGTATATTGGTTGCATTTCTCT 58.319 37.500 0.00 0.00 0.00 3.10
576 581 5.758296 TCCGTATATTGGTTGCATTTCTCTC 59.242 40.000 0.00 0.00 0.00 3.20
577 582 5.049405 CCGTATATTGGTTGCATTTCTCTCC 60.049 44.000 0.00 0.00 0.00 3.71
632 637 2.056481 GATGCAATGCGAGCAGGTCC 62.056 60.000 0.00 0.00 46.36 4.46
634 639 2.825836 CAATGCGAGCAGGTCCCC 60.826 66.667 3.58 0.00 0.00 4.81
649 654 4.339247 CAGGTCCCCATCATTGTATTGTTC 59.661 45.833 0.00 0.00 0.00 3.18
652 657 2.286950 CCCCATCATTGTATTGTTCGCG 60.287 50.000 0.00 0.00 0.00 5.87
778 1603 2.428530 GACATGAGAAAGCCCAAATCCC 59.571 50.000 0.00 0.00 0.00 3.85
832 1661 0.950555 TTGCGCATGGACAGTGACTC 60.951 55.000 12.75 0.00 0.00 3.36
838 1667 0.033504 ATGGACAGTGACTCGCGTTT 59.966 50.000 5.77 0.00 0.00 3.60
869 1698 1.685148 CCATCCTGCTAGGCCTTTTC 58.315 55.000 12.58 0.27 34.61 2.29
941 1770 3.736252 CCTCGTGGCTTCTATACATTTCG 59.264 47.826 0.00 0.00 0.00 3.46
1163 1993 4.773674 TGATTCCATGGTGCAAGATTTTCT 59.226 37.500 12.58 0.00 0.00 2.52
1165 1995 3.091545 TCCATGGTGCAAGATTTTCTCC 58.908 45.455 12.58 0.00 0.00 3.71
1168 1998 4.020839 CCATGGTGCAAGATTTTCTCCTTT 60.021 41.667 2.57 0.00 0.00 3.11
1277 2273 1.866063 GCGACGGGTCAGATTCAGATC 60.866 57.143 0.00 0.00 0.00 2.75
1283 2279 2.559440 GGTCAGATTCAGATCAGGCAC 58.441 52.381 0.00 0.00 34.60 5.01
1503 2514 2.059541 GCGGATACCTCGTAAGCATTC 58.940 52.381 0.00 0.00 37.18 2.67
1505 2516 3.566523 CGGATACCTCGTAAGCATTCTC 58.433 50.000 0.00 0.00 37.18 2.87
1516 2527 0.036732 AGCATTCTCGTTGGGCAAGA 59.963 50.000 0.00 0.00 0.00 3.02
1531 2542 3.002791 GGCAAGAAAATTAAAGCTGGCC 58.997 45.455 0.00 0.00 40.03 5.36
1605 2621 2.121963 TCAAGGGCCTGGTGAGGT 60.122 61.111 6.92 0.00 42.15 3.85
1733 2749 2.186384 GAGCACGAGCAGGAGCAT 59.814 61.111 7.77 0.00 45.49 3.79
1734 2750 1.449246 GAGCACGAGCAGGAGCATT 60.449 57.895 7.77 0.00 45.49 3.56
1735 2751 1.427592 GAGCACGAGCAGGAGCATTC 61.428 60.000 7.77 0.00 45.49 2.67
1737 2753 1.817099 CACGAGCAGGAGCATTCCC 60.817 63.158 0.00 0.00 45.24 3.97
1738 2754 2.293318 ACGAGCAGGAGCATTCCCA 61.293 57.895 0.00 0.00 45.24 4.37
1804 2820 1.132640 CCGCGCTGCAAGTAAGTTC 59.867 57.895 5.56 0.00 35.30 3.01
1808 2824 1.225855 CGCTGCAAGTAAGTTCCACA 58.774 50.000 0.00 0.00 35.30 4.17
1809 2825 1.195448 CGCTGCAAGTAAGTTCCACAG 59.805 52.381 0.00 0.00 35.30 3.66
1810 2826 1.068954 GCTGCAAGTAAGTTCCACAGC 60.069 52.381 0.00 0.00 41.80 4.40
1811 2827 2.498167 CTGCAAGTAAGTTCCACAGCT 58.502 47.619 0.00 0.00 0.00 4.24
1814 2830 3.077359 GCAAGTAAGTTCCACAGCTCAT 58.923 45.455 0.00 0.00 0.00 2.90
2003 3030 0.954449 ACGTCGTCGATGTGTCTCCT 60.954 55.000 19.00 0.00 40.62 3.69
2004 3031 0.168348 CGTCGTCGATGTGTCTCCTT 59.832 55.000 6.28 0.00 39.71 3.36
2005 3032 1.618861 GTCGTCGATGTGTCTCCTTG 58.381 55.000 4.21 0.00 0.00 3.61
2006 3033 0.109272 TCGTCGATGTGTCTCCTTGC 60.109 55.000 4.21 0.00 0.00 4.01
2218 3389 2.898343 GTGGTGTGTCCGCGGTTT 60.898 61.111 27.15 0.00 39.52 3.27
2279 3452 2.097444 TGCAGTACGCCATTGCATC 58.903 52.632 2.83 0.00 44.16 3.91
2318 3491 5.290643 GGATCTAACGCTCTGCATTATCATC 59.709 44.000 0.00 0.00 0.00 2.92
2325 3498 3.242837 GCTCTGCATTATCATCACGCAAA 60.243 43.478 0.00 0.00 31.10 3.68
2328 3501 6.622245 GCTCTGCATTATCATCACGCAAATAT 60.622 38.462 0.00 0.00 31.10 1.28
2329 3502 7.413328 GCTCTGCATTATCATCACGCAAATATA 60.413 37.037 0.00 0.00 31.10 0.86
2373 3597 6.513180 TCCCTCTGTAAATAAGCATAAGACG 58.487 40.000 0.00 0.00 0.00 4.18
2445 3834 1.804598 CCGGTAAAAATCGGCCCAC 59.195 57.895 0.00 0.00 39.78 4.61
2466 3855 1.078567 GGACAGGAGGCTCAAGCAG 60.079 63.158 17.69 3.24 44.36 4.24
2683 4074 8.414778 AGTACTGCTACAGTTGGAGTATATTTC 58.585 37.037 16.97 6.44 42.59 2.17
2861 4264 2.014128 CGCCTCCATCCAAAACGTAAT 58.986 47.619 0.00 0.00 0.00 1.89
2862 4265 3.199677 CGCCTCCATCCAAAACGTAATA 58.800 45.455 0.00 0.00 0.00 0.98
2863 4266 3.001939 CGCCTCCATCCAAAACGTAATAC 59.998 47.826 0.00 0.00 0.00 1.89
2864 4267 4.196971 GCCTCCATCCAAAACGTAATACT 58.803 43.478 0.00 0.00 0.00 2.12
2865 4268 4.272748 GCCTCCATCCAAAACGTAATACTC 59.727 45.833 0.00 0.00 0.00 2.59
2866 4269 4.814771 CCTCCATCCAAAACGTAATACTCC 59.185 45.833 0.00 0.00 0.00 3.85
2899 4310 3.653344 TCTCTCAAGTGTCAACATTCCG 58.347 45.455 0.00 0.00 0.00 4.30
2948 4387 4.327087 GCTGACAAACAAAACAAACTCTGG 59.673 41.667 0.00 0.00 0.00 3.86
2949 4388 4.241681 TGACAAACAAAACAAACTCTGGC 58.758 39.130 0.00 0.00 0.00 4.85
2950 4389 3.249917 ACAAACAAAACAAACTCTGGCG 58.750 40.909 0.00 0.00 0.00 5.69
2951 4390 3.249917 CAAACAAAACAAACTCTGGCGT 58.750 40.909 0.00 0.00 0.00 5.68
2952 4391 2.559998 ACAAAACAAACTCTGGCGTG 57.440 45.000 0.00 0.00 0.00 5.34
2953 4392 1.199624 CAAAACAAACTCTGGCGTGC 58.800 50.000 0.00 0.00 0.00 5.34
2954 4393 0.814457 AAAACAAACTCTGGCGTGCA 59.186 45.000 0.00 0.00 0.00 4.57
2955 4394 1.032014 AAACAAACTCTGGCGTGCAT 58.968 45.000 0.00 0.00 0.00 3.96
2956 4395 0.311790 AACAAACTCTGGCGTGCATG 59.688 50.000 0.09 0.09 0.00 4.06
2957 4396 1.443194 CAAACTCTGGCGTGCATGC 60.443 57.895 22.99 22.99 0.00 4.06
2958 4397 1.898094 AAACTCTGGCGTGCATGCA 60.898 52.632 30.79 18.46 36.28 3.96
2959 4398 1.246056 AAACTCTGGCGTGCATGCAT 61.246 50.000 30.79 1.21 36.28 3.96
2960 4399 1.929806 AACTCTGGCGTGCATGCATG 61.930 55.000 31.36 31.36 36.28 4.06
3054 4493 2.283966 CTGGAGGAGTGGGTCGGT 60.284 66.667 0.00 0.00 0.00 4.69
3255 4694 2.123251 AGGGGGAGCATCGACGAT 60.123 61.111 4.05 4.05 34.37 3.73
3639 5078 2.858344 CCCTATTCGCTAGACACAAACG 59.142 50.000 0.00 0.00 0.00 3.60
3661 5100 5.236478 ACGAACTTCTTTGTAATGTGACCAG 59.764 40.000 0.00 0.00 0.00 4.00
3685 5124 2.356194 CTTGTTTGGCGGCCTTGC 60.356 61.111 21.46 10.17 0.00 4.01
3686 5125 2.837291 TTGTTTGGCGGCCTTGCT 60.837 55.556 21.46 0.00 34.52 3.91
3737 5176 1.153168 AAACTGACCGTGCTGTGCT 60.153 52.632 0.00 0.00 0.00 4.40
3756 5195 4.012319 GCTAATGCAATATGGATCTGCG 57.988 45.455 0.00 0.00 38.97 5.18
3774 5213 3.911868 TGCGAACTTTCAAAATGATGGG 58.088 40.909 0.00 0.00 0.00 4.00
3820 5259 5.936956 AGAACAAGAGAATTCAGTGATGACC 59.063 40.000 8.44 0.00 0.00 4.02
3891 5330 4.620589 ATCTCTCGAGGTCTATTCGGTA 57.379 45.455 13.56 0.00 38.54 4.02
3892 5331 4.620589 TCTCTCGAGGTCTATTCGGTAT 57.379 45.455 13.56 0.00 38.54 2.73
3905 5344 2.195741 TCGGTATATGAGTAGCCGCT 57.804 50.000 0.00 0.00 41.89 5.52
3979 5418 4.143137 CGCTTCAAGAGAGCTTCTTTTCTC 60.143 45.833 8.01 0.23 43.68 2.87
3984 5423 7.192852 TCAAGAGAGCTTCTTTTCTCCATAT 57.807 36.000 8.01 0.00 43.68 1.78
4492 6028 1.316706 CGCCGGCCCTTAAAATTCCA 61.317 55.000 23.46 0.00 0.00 3.53
4578 6114 1.343069 AAAAATTTACAGGCGGCCCA 58.657 45.000 17.02 0.00 0.00 5.36
4593 6129 2.087248 CCCACAAATCCACCCCTCT 58.913 57.895 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.587285 TTAAACGCACGTCGCCAATT 59.413 45.000 0.00 0.00 43.23 2.32
1 2 0.800012 ATTAAACGCACGTCGCCAAT 59.200 45.000 0.00 2.97 43.23 3.16
2 3 1.426423 TATTAAACGCACGTCGCCAA 58.574 45.000 0.00 1.10 43.23 4.52
3 4 1.390803 CTTATTAAACGCACGTCGCCA 59.609 47.619 0.00 0.00 43.23 5.69
4 5 1.655099 TCTTATTAAACGCACGTCGCC 59.345 47.619 0.00 0.00 43.23 5.54
5 6 2.595536 TCTCTTATTAAACGCACGTCGC 59.404 45.455 0.00 3.99 43.23 5.19
6 7 4.556135 TCTTCTCTTATTAAACGCACGTCG 59.444 41.667 0.00 5.97 45.38 5.12
7 8 5.496657 CGTCTTCTCTTATTAAACGCACGTC 60.497 44.000 0.00 0.00 0.00 4.34
8 9 4.322804 CGTCTTCTCTTATTAAACGCACGT 59.677 41.667 0.00 0.00 0.00 4.49
9 10 4.322804 ACGTCTTCTCTTATTAAACGCACG 59.677 41.667 0.00 0.00 32.25 5.34
10 11 5.758570 ACGTCTTCTCTTATTAAACGCAC 57.241 39.130 0.00 0.00 32.25 5.34
11 12 6.308766 GGTAACGTCTTCTCTTATTAAACGCA 59.691 38.462 0.00 0.00 32.25 5.24
12 13 6.690494 GGTAACGTCTTCTCTTATTAAACGC 58.310 40.000 0.00 0.00 32.25 4.84
31 32 1.788886 GTCTTTGTGGTCGACGGTAAC 59.211 52.381 9.92 5.96 0.00 2.50
43 44 0.858583 TCGTCACATGCGTCTTTGTG 59.141 50.000 0.00 0.00 43.61 3.33
46 47 3.003275 ACAAATTCGTCACATGCGTCTTT 59.997 39.130 0.00 0.00 0.00 2.52
51 52 2.498905 CAGACAAATTCGTCACATGCG 58.501 47.619 0.00 0.00 38.43 4.73
54 55 2.143122 ACGCAGACAAATTCGTCACAT 58.857 42.857 0.00 0.00 38.43 3.21
69 70 3.377439 TGTTAACACAGTACAGACGCAG 58.623 45.455 3.59 0.00 0.00 5.18
75 76 7.011950 TGTCTCCATTTTGTTAACACAGTACAG 59.988 37.037 8.07 1.42 33.22 2.74
89 90 2.762327 CCCTTCCCATGTCTCCATTTTG 59.238 50.000 0.00 0.00 0.00 2.44
94 95 1.635487 CTTTCCCTTCCCATGTCTCCA 59.365 52.381 0.00 0.00 0.00 3.86
104 105 0.673956 GCCGTCACTCTTTCCCTTCC 60.674 60.000 0.00 0.00 0.00 3.46
117 118 2.425592 CACAACCCAGAGCCGTCA 59.574 61.111 0.00 0.00 0.00 4.35
118 119 3.050275 GCACAACCCAGAGCCGTC 61.050 66.667 0.00 0.00 0.00 4.79
177 178 9.547753 GTGTGAAAACTGATGTCAGGTATATAT 57.452 33.333 14.05 0.00 44.43 0.86
178 179 7.985184 GGTGTGAAAACTGATGTCAGGTATATA 59.015 37.037 14.05 0.00 44.43 0.86
192 193 1.202405 GGTGGCAAGGTGTGAAAACTG 60.202 52.381 0.00 0.00 0.00 3.16
219 220 1.515081 CATTTGCAACCTGCCCTTTG 58.485 50.000 0.00 0.00 44.23 2.77
227 228 1.266867 GGATGGCCCATTTGCAACCT 61.267 55.000 0.00 0.00 34.14 3.50
365 366 0.527385 GGCAGATCAGAGTCGTGCTC 60.527 60.000 0.00 2.39 44.45 4.26
386 387 4.512914 GGAGGGGTGGCCTCATGC 62.513 72.222 3.32 0.00 36.15 4.06
403 408 1.335882 TGGAGCTGATGGCAGAGAGG 61.336 60.000 0.00 0.00 45.17 3.69
404 409 0.179078 GTGGAGCTGATGGCAGAGAG 60.179 60.000 0.00 0.00 45.17 3.20
405 410 0.906282 TGTGGAGCTGATGGCAGAGA 60.906 55.000 0.00 0.00 45.17 3.10
406 411 0.035725 TTGTGGAGCTGATGGCAGAG 60.036 55.000 0.00 0.00 45.17 3.35
449 454 2.344950 GAGTGTGCAGTGATCCAAGAG 58.655 52.381 0.00 0.00 0.00 2.85
500 505 6.099557 AGAGATGTAGATGGAGAAGAAAAGGG 59.900 42.308 0.00 0.00 0.00 3.95
506 511 6.298361 CAGAGAGAGATGTAGATGGAGAAGA 58.702 44.000 0.00 0.00 0.00 2.87
574 579 2.503061 CATCCGGAGCACTGGGAG 59.497 66.667 11.34 0.00 42.48 4.30
575 580 3.785859 GCATCCGGAGCACTGGGA 61.786 66.667 11.34 3.16 42.48 4.37
576 581 3.746949 GAGCATCCGGAGCACTGGG 62.747 68.421 22.44 0.00 42.48 4.45
577 582 2.202987 GAGCATCCGGAGCACTGG 60.203 66.667 22.44 1.96 43.52 4.00
632 637 2.354510 ACGCGAACAATACAATGATGGG 59.645 45.455 15.93 0.00 0.00 4.00
634 639 3.780279 CACACGCGAACAATACAATGATG 59.220 43.478 15.93 0.00 0.00 3.07
667 672 3.476295 TCGATGCAACAAATCAGAAGC 57.524 42.857 0.00 0.00 0.00 3.86
761 1586 2.459644 CATGGGATTTGGGCTTTCTCA 58.540 47.619 0.00 0.00 0.00 3.27
764 1589 1.137675 GAGCATGGGATTTGGGCTTTC 59.862 52.381 0.00 0.00 34.44 2.62
778 1603 4.260132 GCACGAGAAGAAATGTAGAGCATG 60.260 45.833 0.00 0.00 37.96 4.06
832 1661 1.441016 GCTCTTTGCTGGAAACGCG 60.441 57.895 3.53 3.53 38.95 6.01
838 1667 0.034767 CAGGATGGCTCTTTGCTGGA 60.035 55.000 0.00 0.00 42.39 3.86
869 1698 1.681793 ACGATCTACGGAGATGTTGGG 59.318 52.381 16.82 1.39 42.80 4.12
930 1759 3.245284 CACCGTTCAGCCGAAATGTATAG 59.755 47.826 0.00 0.00 31.43 1.31
931 1760 3.191669 CACCGTTCAGCCGAAATGTATA 58.808 45.455 0.00 0.00 31.43 1.47
941 1770 0.458260 AAACAAACCACCGTTCAGCC 59.542 50.000 0.00 0.00 0.00 4.85
1168 1998 2.653726 TGCTCTTCACCTTCTGCAAAA 58.346 42.857 0.00 0.00 0.00 2.44
1172 2002 2.075338 CTCTTGCTCTTCACCTTCTGC 58.925 52.381 0.00 0.00 0.00 4.26
1283 2279 3.898509 CTCTGCTCCTCCTCCGCG 61.899 72.222 0.00 0.00 0.00 6.46
1469 2471 3.449227 CCGCGGTAGGCTGACTGA 61.449 66.667 19.50 0.00 40.44 3.41
1503 2514 4.385748 GCTTTAATTTTCTTGCCCAACGAG 59.614 41.667 0.00 0.00 0.00 4.18
1505 2516 4.150451 CAGCTTTAATTTTCTTGCCCAACG 59.850 41.667 0.00 0.00 0.00 4.10
1516 2527 2.029380 GGACACGGCCAGCTTTAATTTT 60.029 45.455 2.24 0.00 0.00 1.82
1531 2542 1.068748 ACAGCGTTACTACAGGACACG 60.069 52.381 0.00 0.00 0.00 4.49
1724 2740 2.109126 GTCGTGGGAATGCTCCTGC 61.109 63.158 0.00 0.00 42.05 4.85
1727 2743 2.511600 CCGTCGTGGGAATGCTCC 60.512 66.667 0.00 0.00 41.59 4.70
1733 2749 3.315140 TCCATGCCGTCGTGGGAA 61.315 61.111 4.61 0.00 46.96 3.97
1734 2750 4.077184 GTCCATGCCGTCGTGGGA 62.077 66.667 4.61 0.00 46.96 4.37
1845 2864 1.662608 CGCAGAGTGACCAGTGAGT 59.337 57.895 0.00 0.00 0.00 3.41
1846 2865 1.080230 CCGCAGAGTGACCAGTGAG 60.080 63.158 0.00 0.00 0.00 3.51
1847 2866 3.051210 CCGCAGAGTGACCAGTGA 58.949 61.111 0.00 0.00 0.00 3.41
1848 2867 2.740055 GCCGCAGAGTGACCAGTG 60.740 66.667 0.00 0.00 0.00 3.66
1849 2868 4.363990 CGCCGCAGAGTGACCAGT 62.364 66.667 0.00 0.00 0.00 4.00
1893 2916 0.584396 TTCGCACGTTCATTCACACC 59.416 50.000 0.00 0.00 0.00 4.16
1962 2989 1.209127 CGCTGCCAACTTTAACCCG 59.791 57.895 0.00 0.00 0.00 5.28
2218 3389 1.475280 CTACGCTACAGGCTACCAACA 59.525 52.381 0.00 0.00 39.13 3.33
2279 3452 3.473093 AGATCCGTAGAATGATACGCG 57.527 47.619 3.53 3.53 45.56 6.01
2329 3502 9.160412 AGAGGGAATAGTGCTTTGTACTATATT 57.840 33.333 8.33 0.00 39.74 1.28
2335 3559 4.833390 ACAGAGGGAATAGTGCTTTGTAC 58.167 43.478 0.00 0.00 0.00 2.90
2343 3567 9.778741 TTATGCTTATTTACAGAGGGAATAGTG 57.221 33.333 0.00 0.00 0.00 2.74
2445 3834 1.601171 CTTGAGCCTCCTGTCCTGG 59.399 63.158 0.00 0.00 0.00 4.45
2466 3855 5.695816 AGTACTATTCTCGGATCTGTACGAC 59.304 44.000 0.42 0.00 35.29 4.34
2671 4062 7.728981 AGAGGAGGAATAACGAAATATACTCCA 59.271 37.037 19.91 0.00 39.57 3.86
2683 4074 3.553922 GCATGAGGAGAGGAGGAATAACG 60.554 52.174 0.00 0.00 0.00 3.18
2861 4264 6.826632 TGAGAGATTACTGGAGTAGGAGTA 57.173 41.667 0.00 0.00 0.00 2.59
2862 4265 5.718801 TGAGAGATTACTGGAGTAGGAGT 57.281 43.478 0.00 0.00 0.00 3.85
2863 4266 6.039270 CACTTGAGAGATTACTGGAGTAGGAG 59.961 46.154 0.00 0.00 0.00 3.69
2864 4267 5.888724 CACTTGAGAGATTACTGGAGTAGGA 59.111 44.000 0.00 0.00 0.00 2.94
2865 4268 5.654650 ACACTTGAGAGATTACTGGAGTAGG 59.345 44.000 0.00 0.00 0.00 3.18
2866 4269 6.375736 TGACACTTGAGAGATTACTGGAGTAG 59.624 42.308 0.00 0.00 0.00 2.57
2948 4387 4.865761 CCTGCCATGCATGCACGC 62.866 66.667 25.37 26.32 38.13 5.34
2949 4388 3.120979 CTCCTGCCATGCATGCACG 62.121 63.158 25.37 16.18 38.13 5.34
2950 4389 1.317431 TTCTCCTGCCATGCATGCAC 61.317 55.000 25.37 15.25 38.13 4.57
2951 4390 1.000646 TTCTCCTGCCATGCATGCA 60.001 52.632 25.04 25.04 38.13 3.96
2952 4391 0.750546 TCTTCTCCTGCCATGCATGC 60.751 55.000 21.69 11.82 38.13 4.06
2953 4392 1.880675 GATCTTCTCCTGCCATGCATG 59.119 52.381 20.19 20.19 38.13 4.06
2954 4393 1.542767 CGATCTTCTCCTGCCATGCAT 60.543 52.381 0.00 0.00 38.13 3.96
2955 4394 0.179065 CGATCTTCTCCTGCCATGCA 60.179 55.000 0.00 0.00 36.92 3.96
2956 4395 0.883814 CCGATCTTCTCCTGCCATGC 60.884 60.000 0.00 0.00 0.00 4.06
2957 4396 0.883814 GCCGATCTTCTCCTGCCATG 60.884 60.000 0.00 0.00 0.00 3.66
2958 4397 1.340399 TGCCGATCTTCTCCTGCCAT 61.340 55.000 0.00 0.00 0.00 4.40
2959 4398 1.340399 ATGCCGATCTTCTCCTGCCA 61.340 55.000 0.00 0.00 0.00 4.92
2960 4399 0.602372 GATGCCGATCTTCTCCTGCC 60.602 60.000 0.00 0.00 0.00 4.85
3054 4493 1.667830 CTTGTCGAAGGGCTGCGAA 60.668 57.895 0.00 0.00 38.36 4.70
3161 4600 3.017314 CGTAGCCGTCGTCATCGC 61.017 66.667 0.00 0.00 36.96 4.58
3247 4686 2.107750 CTGCAGCCCATCGTCGAT 59.892 61.111 0.00 0.75 0.00 3.59
3279 4718 2.204029 TACCCCGGGAAAGCCACT 60.204 61.111 26.32 0.00 35.15 4.00
3519 4958 4.175489 CTCGACGGCGTCATCGGT 62.175 66.667 35.62 1.56 38.86 4.69
3600 5039 0.179000 GGGTGTAGTGCTCCATCTGG 59.821 60.000 1.67 0.00 32.58 3.86
3639 5078 6.430451 CACTGGTCACATTACAAAGAAGTTC 58.570 40.000 0.00 0.00 0.00 3.01
3680 5119 0.823460 GACCCAGAGAGAGAGCAAGG 59.177 60.000 0.00 0.00 0.00 3.61
3685 5124 1.005332 TGGTCAGACCCAGAGAGAGAG 59.995 57.143 17.59 0.00 37.50 3.20
3686 5125 1.076438 TGGTCAGACCCAGAGAGAGA 58.924 55.000 17.59 0.00 37.50 3.10
3737 5176 5.308014 AGTTCGCAGATCCATATTGCATTA 58.692 37.500 4.94 0.00 37.69 1.90
3756 5195 3.674753 CACGCCCATCATTTTGAAAGTTC 59.325 43.478 0.00 0.00 0.00 3.01
3774 5213 1.605500 CATGTTGTATGTGCACACGC 58.394 50.000 24.37 17.96 39.24 5.34
3877 5316 6.038492 GGCTACTCATATACCGAATAGACCTC 59.962 46.154 0.00 0.00 0.00 3.85
3891 5330 2.495270 CTGGATCAGCGGCTACTCATAT 59.505 50.000 0.26 0.00 0.00 1.78
3892 5331 1.889170 CTGGATCAGCGGCTACTCATA 59.111 52.381 0.26 0.00 0.00 2.15
3905 5344 0.694771 AGGAGTTTGCTGCTGGATCA 59.305 50.000 0.00 0.00 42.01 2.92
3979 5418 0.606401 GATGCACGGTCCCCATATGG 60.606 60.000 15.41 15.41 0.00 2.74
3984 5423 1.001120 TCTAGATGCACGGTCCCCA 59.999 57.895 0.00 0.00 0.00 4.96
3992 5431 5.105716 TGAGGAACTTGTAGTCTAGATGCAC 60.106 44.000 0.00 0.00 41.55 4.57
4107 5641 2.635427 GAGTTTCACTCCTTCCCTCACT 59.365 50.000 0.00 0.00 39.28 3.41
4492 6028 1.743772 CGGAGATCCTGCAAAACGGAT 60.744 52.381 4.95 4.95 42.55 4.18
4520 6056 1.204146 TAGTGGATCTGTTCAGGCCC 58.796 55.000 0.00 2.97 0.00 5.80
4578 6114 0.995024 CTCCAGAGGGGTGGATTTGT 59.005 55.000 0.00 0.00 45.87 2.83
4593 6129 2.631062 CAACCCCGTACATATAGCTCCA 59.369 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.