Multiple sequence alignment - TraesCS4D01G083200

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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 TraesCS4D01G083200 chr4D 100.000 7149 0 0 1 7149 57069141 57076289 0.000000e+00 13202.0
1 TraesCS4D01G083200 chr4B 95.320 5342 134 46 1887 7149 85697284 85702588 0.000000e+00 8373.0
2 TraesCS4D01G083200 chr4B 96.072 1731 39 9 71 1794 85695575 85697283 0.000000e+00 2793.0
3 TraesCS4D01G083200 chr4B 81.250 96 13 3 2575 2670 217854105 217854015 9.950000e-09 73.1
4 TraesCS4D01G083200 chr4A 96.085 2580 72 15 86 2643 539761463 539758891 0.000000e+00 4178.0
5 TraesCS4D01G083200 chr4A 90.211 2564 152 46 3734 6227 539757907 539755373 0.000000e+00 3253.0
6 TraesCS4D01G083200 chr4A 95.964 991 33 5 2700 3690 539758879 539757896 0.000000e+00 1602.0
7 TraesCS4D01G083200 chr4A 88.832 394 34 9 6758 7149 539754798 539754413 6.490000e-130 475.0
8 TraesCS4D01G083200 chr4A 91.045 67 6 0 1 67 539761573 539761507 2.750000e-14 91.6
9 TraesCS4D01G083200 chr4A 100.000 38 0 0 35 72 740895543 740895580 3.580000e-08 71.3
10 TraesCS4D01G083200 chr7A 85.926 270 27 4 768 1037 158289725 158289467 1.960000e-70 278.0
11 TraesCS4D01G083200 chr7A 100.000 38 0 0 35 72 45016879 45016916 3.580000e-08 71.3
12 TraesCS4D01G083200 chr7B 85.660 265 27 6 773 1037 685044802 685044549 1.180000e-67 268.0
13 TraesCS4D01G083200 chr6A 84.825 257 28 4 778 1034 189575501 189575746 1.540000e-61 248.0
14 TraesCS4D01G083200 chr1B 81.466 232 41 2 2698 2928 593220812 593221042 9.470000e-44 189.0
15 TraesCS4D01G083200 chr6B 81.061 264 23 12 770 1032 21846562 21846799 1.220000e-42 185.0
16 TraesCS4D01G083200 chr5B 80.682 264 24 12 770 1032 700927661 700927424 5.700000e-41 180.0
17 TraesCS4D01G083200 chr7D 80.534 262 24 10 770 1030 578156783 578157018 7.370000e-40 176.0
18 TraesCS4D01G083200 chr7D 82.258 124 19 3 2464 2584 606706687 606706564 3.530000e-18 104.0
19 TraesCS4D01G083200 chr7D 83.654 104 6 5 2464 2557 205549974 205550076 3.550000e-13 87.9
20 TraesCS4D01G083200 chr5A 92.593 81 5 1 2470 2549 160081910 160081990 1.630000e-21 115.0
21 TraesCS4D01G083200 chrUn 83.333 114 17 2 2470 2581 92701950 92702063 3.530000e-18 104.0
22 TraesCS4D01G083200 chr2B 82.143 112 17 3 2464 2574 689300215 689300324 7.640000e-15 93.5
23 TraesCS4D01G083200 chr5D 80.992 121 15 4 2470 2583 388328634 388328753 9.880000e-14 89.8
24 TraesCS4D01G083200 chr5D 78.218 101 14 4 2576 2670 417734486 417734584 2.790000e-04 58.4
25 TraesCS4D01G083200 chr2A 89.706 68 5 2 2470 2536 606574226 606574292 1.280000e-12 86.1
26 TraesCS4D01G083200 chr2A 100.000 39 0 0 34 72 710454483 710454445 9.950000e-09 73.1
27 TraesCS4D01G083200 chr3A 100.000 39 0 0 34 72 114421039 114421001 9.950000e-09 73.1
28 TraesCS4D01G083200 chr1D 100.000 38 0 0 35 72 131144238 131144275 3.580000e-08 71.3
29 TraesCS4D01G083200 chr1D 100.000 38 0 0 35 72 427944355 427944318 3.580000e-08 71.3
30 TraesCS4D01G083200 chr3B 95.238 42 2 0 31 72 64415245 64415286 4.630000e-07 67.6
31 TraesCS4D01G083200 chr3D 83.607 61 9 1 13 72 537412304 537412364 1.000000e-03 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 TraesCS4D01G083200 chr4D 57069141 57076289 7148 False 13202.00 13202 100.0000 1 7149 1 chr4D.!!$F1 7148
1 TraesCS4D01G083200 chr4B 85695575 85702588 7013 False 5583.00 8373 95.6960 71 7149 2 chr4B.!!$F1 7078
2 TraesCS4D01G083200 chr4A 539754413 539761573 7160 True 1919.92 4178 92.4274 1 7149 5 chr4A.!!$R1 7148

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
67 68 0.249398 GTGCGTTCATAGGGGTGAGT 59.751 55.000 0.00 0.00 0.00 3.41 F
1031 1070 0.535335 GGGACACCAGATTACAGCGA 59.465 55.000 0.00 0.00 36.50 4.93 F
1285 1324 1.089920 GGTCATGAATGTGAGCGCTT 58.910 50.000 13.26 0.00 36.95 4.68 F
2183 2223 0.633921 TGGACCCCCATTATTGGTGG 59.366 55.000 3.84 3.84 45.52 4.61 F
2957 3012 1.509644 CTGTTGCGTCCAGTGCACAT 61.510 55.000 21.04 0.75 43.10 3.21 F
3796 3855 2.024464 TCCCTCCTTTCTCTCCTCTCTG 60.024 54.545 0.00 0.00 0.00 3.35 F
5354 5486 1.120530 TTCCCATACCGAAGAGCCTC 58.879 55.000 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1461 0.394192 CAGAGGTGGTCAGCACTTGA 59.606 55.000 6.99 0.0 0.00 3.02 R
2183 2223 2.246719 AGTGAAGAGTGCAAGGTGTC 57.753 50.000 0.00 0.0 0.00 3.67 R
2328 2371 2.299297 ACTTCCACTACCACTACTGTGC 59.701 50.000 0.00 0.0 42.54 4.57 R
3796 3855 1.280421 AGCCTGGACCAATCAGAAGAC 59.720 52.381 0.00 0.0 34.36 3.01 R
4799 4915 2.170187 TGCCAGGTTCAAACTGCAAAAT 59.830 40.909 0.00 0.0 34.65 1.82 R
5497 5632 5.515534 CCCTCCAGGATTCAGGTTAATATGG 60.516 48.000 0.00 0.0 38.24 2.74 R
7106 7412 0.038166 ACGAAGCCATGTCCATTGGT 59.962 50.000 1.86 0.0 0.00 3.67 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
57 58 4.368808 GTGCGTGCGTGCGTTCAT 62.369 61.111 3.11 0.00 37.81 2.57
59 60 2.020016 GCGTGCGTGCGTTCATAG 59.980 61.111 3.11 0.00 0.00 2.23
67 68 0.249398 GTGCGTTCATAGGGGTGAGT 59.751 55.000 0.00 0.00 0.00 3.41
71 72 2.102588 GCGTTCATAGGGGTGAGTGTAT 59.897 50.000 0.00 0.00 0.00 2.29
72 73 3.799232 GCGTTCATAGGGGTGAGTGTATC 60.799 52.174 0.00 0.00 0.00 2.24
73 74 3.550233 CGTTCATAGGGGTGAGTGTATCG 60.550 52.174 0.00 0.00 0.00 2.92
306 337 2.669569 CCAGCAACCCACCTCACG 60.670 66.667 0.00 0.00 0.00 4.35
356 387 5.974108 TGCCGCTTCTATAGAACTAGTTTT 58.026 37.500 11.24 6.74 0.00 2.43
610 644 4.003648 GCTTGCTTTCCTAAGAACTGCTA 58.996 43.478 0.00 0.00 34.55 3.49
642 676 8.488668 CATGAAATTATTCCCTTTTCCCTTCAT 58.511 33.333 0.00 0.00 34.49 2.57
699 736 6.532988 AGGACTAATTCTTGTACTGAGGAC 57.467 41.667 0.00 0.00 0.00 3.85
853 892 3.369892 CCTTCTGGGTAGATGGAAGTGTG 60.370 52.174 3.81 0.00 46.23 3.82
879 918 9.436957 GAATTCTACACAAAGGAAGATTCAGTA 57.563 33.333 0.00 0.00 0.00 2.74
888 927 7.609532 ACAAAGGAAGATTCAGTAGGATTTCTG 59.390 37.037 0.00 0.00 0.00 3.02
905 944 9.875691 AGGATTTCTGTTAGCAATTTATTTTCC 57.124 29.630 0.00 0.00 0.00 3.13
1031 1070 0.535335 GGGACACCAGATTACAGCGA 59.465 55.000 0.00 0.00 36.50 4.93
1032 1071 1.641577 GGACACCAGATTACAGCGAC 58.358 55.000 0.00 0.00 0.00 5.19
1184 1223 4.820897 GTGACACATATCTCACCTTCACA 58.179 43.478 0.00 0.00 33.77 3.58
1263 1302 4.283467 TGCTCTGTCAGTTTAGCCTCTAAA 59.717 41.667 8.99 0.00 33.99 1.85
1285 1324 1.089920 GGTCATGAATGTGAGCGCTT 58.910 50.000 13.26 0.00 36.95 4.68
1422 1461 6.240118 GGATCCCTGTAAGAAATGGAGATCAT 60.240 42.308 0.00 0.00 34.32 2.45
1500 1539 2.569404 CAGGGAAGTCTCTAGGCAGTTT 59.431 50.000 0.00 0.00 0.00 2.66
1584 1623 1.486310 GGTATGCCAGAGTGGACATCA 59.514 52.381 0.00 0.00 40.96 3.07
1632 1671 4.353777 AGTTCTTGAGGGTAGACTATGCA 58.646 43.478 0.00 0.00 0.00 3.96
1795 1834 7.114754 TCTGCAGGTTGATGATTATTTCTTCT 58.885 34.615 15.13 0.00 31.42 2.85
1849 1888 5.892160 ATTACTACGCACTACAGTTCTGA 57.108 39.130 6.83 0.00 0.00 3.27
1897 1936 8.691661 ACTACATGTCACAAGATTACCTTTTT 57.308 30.769 0.00 0.00 31.42 1.94
2068 2107 9.726438 AGATTCATATGTTATACTAAACAGGCC 57.274 33.333 1.90 0.00 42.33 5.19
2099 2138 6.442112 TCATGAACTGAAGCAGATAGTATCG 58.558 40.000 4.48 1.73 35.18 2.92
2183 2223 0.633921 TGGACCCCCATTATTGGTGG 59.366 55.000 3.84 3.84 45.52 4.61
2505 2550 9.653287 CCGTTCCATAATGTAGTGTATATTGAT 57.347 33.333 0.00 0.00 0.00 2.57
2691 2746 9.915629 TCAAATGCGGTACAAACTTATTTTTAT 57.084 25.926 0.00 0.00 0.00 1.40
2957 3012 1.509644 CTGTTGCGTCCAGTGCACAT 61.510 55.000 21.04 0.75 43.10 3.21
2967 3022 4.436050 CGTCCAGTGCACATAAAAGACATC 60.436 45.833 21.04 0.00 0.00 3.06
3186 3241 5.586643 GGCTATAAAGTTTGGTCTGAGGAAG 59.413 44.000 0.00 0.00 0.00 3.46
3442 3497 2.288013 CGTAGCACATACACTGGCG 58.712 57.895 0.00 0.00 33.65 5.69
3450 3505 3.396560 CACATACACTGGCGATGATGAT 58.603 45.455 0.00 0.00 0.00 2.45
3528 3583 6.095580 AGCTCTTACTTGACGACATCTCAATA 59.904 38.462 0.00 0.00 0.00 1.90
3621 3676 4.696455 TGCGATCAGAAATAAGATGCTCA 58.304 39.130 0.00 0.00 0.00 4.26
3689 3744 6.265196 TCCAGTGAAGTCAAAATAAATGTGCT 59.735 34.615 0.00 0.00 0.00 4.40
3796 3855 2.024464 TCCCTCCTTTCTCTCCTCTCTG 60.024 54.545 0.00 0.00 0.00 3.35
3840 3899 7.432148 TTTCTGTGCTCCAGTCCTTAATATA 57.568 36.000 4.27 0.00 42.19 0.86
4420 4503 5.580691 CCGAGCAATCAAGTAATACAAGACA 59.419 40.000 0.00 0.00 0.00 3.41
4421 4504 6.237942 CCGAGCAATCAAGTAATACAAGACAG 60.238 42.308 0.00 0.00 0.00 3.51
4422 4505 6.237942 CGAGCAATCAAGTAATACAAGACAGG 60.238 42.308 0.00 0.00 0.00 4.00
4423 4506 6.476378 AGCAATCAAGTAATACAAGACAGGT 58.524 36.000 0.00 0.00 0.00 4.00
4424 4507 6.942576 AGCAATCAAGTAATACAAGACAGGTT 59.057 34.615 0.00 0.00 0.00 3.50
4425 4508 7.448469 AGCAATCAAGTAATACAAGACAGGTTT 59.552 33.333 0.00 0.00 0.00 3.27
4426 4509 7.750903 GCAATCAAGTAATACAAGACAGGTTTC 59.249 37.037 0.00 0.00 0.00 2.78
4427 4510 9.003658 CAATCAAGTAATACAAGACAGGTTTCT 57.996 33.333 0.00 0.00 0.00 2.52
4458 4562 3.198872 CAAGAAAGGCGGATAAGAGACC 58.801 50.000 0.00 0.00 0.00 3.85
4674 4788 7.160547 TCTGTTTTGATACTGTATACGGTCA 57.839 36.000 20.60 10.97 36.70 4.02
4675 4789 7.031372 TCTGTTTTGATACTGTATACGGTCAC 58.969 38.462 20.60 15.33 36.70 3.67
5354 5486 1.120530 TTCCCATACCGAAGAGCCTC 58.879 55.000 0.00 0.00 0.00 4.70
5359 5494 2.160205 CATACCGAAGAGCCTCCGATA 58.840 52.381 0.00 0.00 0.00 2.92
5497 5632 3.753797 AGAATGAGAAAAGGAGCGAAACC 59.246 43.478 0.00 0.00 0.00 3.27
5675 5810 7.816031 AGCAAAAGAATGTATTGTGGAATTCTG 59.184 33.333 5.23 0.00 38.91 3.02
6022 6157 0.651031 GGGTGATTTTAGCGAGCGAC 59.349 55.000 0.00 0.00 0.00 5.19
6109 6244 1.098050 GAGATGTTCCATGTGCCACC 58.902 55.000 0.00 0.00 0.00 4.61
6175 6312 1.517694 GATGCCGCATGGTGCAAAG 60.518 57.895 11.49 0.00 45.36 2.77
6201 6338 5.470098 ACAGGTGTTTTACTCATGACACATC 59.530 40.000 13.25 3.41 43.06 3.06
6235 6409 1.269831 GGCGCCGATCTGATCTAAACT 60.270 52.381 12.58 0.00 0.00 2.66
6260 6434 2.158827 GCCAAGGGGTTCAACAATGTTT 60.159 45.455 0.00 0.00 36.17 2.83
6293 6509 6.936279 GCTGTTGGCTATCTGGAACTATATA 58.064 40.000 0.00 0.00 38.06 0.86
6371 6624 5.133941 TGCCTGTGGTAGTTTTATTTCACA 58.866 37.500 0.00 0.00 34.54 3.58
6399 6652 5.243426 ACATATTTTTGCGGATGTACCAC 57.757 39.130 0.00 0.00 38.90 4.16
6449 6707 1.118838 TGCACACTTCAAAAAGGGGG 58.881 50.000 0.00 0.00 42.67 5.40
6470 6728 4.508662 GGAAAGGATCCTGAGTGTACAAG 58.491 47.826 17.02 0.00 45.56 3.16
6517 6775 5.567138 AGCCATCATGCTTTTAAGTGTAC 57.433 39.130 0.00 0.00 38.85 2.90
6564 6835 3.578282 TGTTGCTGATCTGTGGAGTTAGA 59.422 43.478 1.27 0.00 0.00 2.10
6603 6874 4.647611 TGATCGTAGTTCCAATTTGGTGT 58.352 39.130 14.98 4.13 39.03 4.16
6623 6894 5.972107 TGTAGACCTACACAACTCTTACC 57.028 43.478 5.82 0.00 40.77 2.85
6624 6895 5.387788 TGTAGACCTACACAACTCTTACCA 58.612 41.667 5.82 0.00 40.77 3.25
6626 6897 5.470047 AGACCTACACAACTCTTACCAAG 57.530 43.478 0.00 0.00 0.00 3.61
6671 6944 5.118729 TGGTCAGGACTTTTTGGTTCTTA 57.881 39.130 0.00 0.00 0.00 2.10
6675 6948 6.127980 GGTCAGGACTTTTTGGTTCTTATAGC 60.128 42.308 0.00 0.00 0.00 2.97
6720 6995 0.393077 CGCTCTCGGGGAATGGTTAT 59.607 55.000 0.00 0.00 0.00 1.89
6748 7036 8.728088 ATCACATTAAACTTAAAGTGCTTTCG 57.272 30.769 11.05 0.00 40.32 3.46
6818 7123 2.102420 AGCACTTTACAGCCAAAAACCC 59.898 45.455 0.00 0.00 0.00 4.11
6909 7214 6.314784 GTTATGTCTGCAACATCCTTTACAC 58.685 40.000 14.94 3.23 45.78 2.90
6912 7217 3.568007 GTCTGCAACATCCTTTACACCAA 59.432 43.478 0.00 0.00 0.00 3.67
7015 7321 0.916086 ACACTGGTGACAACAAGGGA 59.084 50.000 7.78 0.00 42.06 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.488341 GCACCTCCAAGATACTGACTTAAA 58.512 41.667 0.00 0.00 0.00 1.52
8 9 3.130516 CGCACCTCCAAGATACTGACTTA 59.869 47.826 0.00 0.00 0.00 2.24
9 10 2.093973 CGCACCTCCAAGATACTGACTT 60.094 50.000 0.00 0.00 0.00 3.01
12 13 0.824109 CCGCACCTCCAAGATACTGA 59.176 55.000 0.00 0.00 0.00 3.41
57 58 2.812836 TGTCGATACACTCACCCCTA 57.187 50.000 0.00 0.00 0.00 3.53
59 60 1.739371 GCTTGTCGATACACTCACCCC 60.739 57.143 0.00 0.00 34.61 4.95
67 68 5.654603 TTTCTCCTAAGCTTGTCGATACA 57.345 39.130 9.86 0.00 0.00 2.29
71 72 7.972832 TTTAATTTTCTCCTAAGCTTGTCGA 57.027 32.000 9.86 0.39 0.00 4.20
72 73 9.278734 GATTTTAATTTTCTCCTAAGCTTGTCG 57.721 33.333 9.86 0.00 0.00 4.35
73 74 9.574458 GGATTTTAATTTTCTCCTAAGCTTGTC 57.426 33.333 9.86 0.00 0.00 3.18
306 337 1.993370 CGGTGGATTCAAAGAGTCGAC 59.007 52.381 7.70 7.70 0.00 4.20
414 446 0.603707 ACACAAGCCTGTCACCATCG 60.604 55.000 0.00 0.00 31.64 3.84
610 644 3.290710 AGGGAATAATTTCATGCAGCGT 58.709 40.909 0.00 0.00 33.23 5.07
757 796 3.399305 AGTGAGATTTCCCTTCCAAACCT 59.601 43.478 0.00 0.00 0.00 3.50
846 885 6.861065 TCCTTTGTGTAGAATTCACACTTC 57.139 37.500 26.73 14.93 45.26 3.01
853 892 8.329203 ACTGAATCTTCCTTTGTGTAGAATTC 57.671 34.615 0.00 0.00 0.00 2.17
879 918 9.875691 GGAAAATAAATTGCTAACAGAAATCCT 57.124 29.630 0.00 0.00 0.00 3.24
903 942 9.073475 ACATTTACTTTTAGCAACATGTAAGGA 57.927 29.630 0.00 0.00 0.00 3.36
904 943 9.341899 GACATTTACTTTTAGCAACATGTAAGG 57.658 33.333 0.00 0.00 0.00 2.69
907 946 9.502091 AGAGACATTTACTTTTAGCAACATGTA 57.498 29.630 0.00 0.00 0.00 2.29
908 947 8.292448 CAGAGACATTTACTTTTAGCAACATGT 58.708 33.333 0.00 0.00 0.00 3.21
909 948 7.272084 GCAGAGACATTTACTTTTAGCAACATG 59.728 37.037 0.00 0.00 0.00 3.21
1184 1223 1.004044 CCTCAGCATCCACAGAAGGTT 59.996 52.381 0.00 0.00 0.00 3.50
1263 1302 1.741732 GCGCTCACATTCATGACCTCT 60.742 52.381 0.00 0.00 0.00 3.69
1422 1461 0.394192 CAGAGGTGGTCAGCACTTGA 59.606 55.000 6.99 0.00 0.00 3.02
1500 1539 3.055819 GTCCTTCTGTGGCTGAGAATGTA 60.056 47.826 0.19 0.00 0.00 2.29
1632 1671 1.094785 CCCGGACTTCATTGCGAATT 58.905 50.000 0.73 0.00 31.69 2.17
1795 1834 6.998074 TCTGAAGAAGAATTTTAGGAACAGCA 59.002 34.615 0.00 0.00 29.54 4.41
1897 1936 7.724061 ACTGGAAGCAAGGAGTTAGATTAAAAA 59.276 33.333 0.00 0.00 37.60 1.94
1902 1941 4.917906 ACTGGAAGCAAGGAGTTAGATT 57.082 40.909 0.00 0.00 37.60 2.40
1911 1950 8.738645 AAGAAGTTATTATACTGGAAGCAAGG 57.261 34.615 0.00 0.00 37.60 3.61
1942 1981 5.520288 TCAGCTTAATTCGACAGCATACTTC 59.480 40.000 7.59 0.00 35.88 3.01
2068 2107 6.673154 TCTGCTTCAGTTCATGATATTGTG 57.327 37.500 0.00 0.00 37.89 3.33
2099 2138 6.223852 TCACCTCTCTTGATTACACAAACTC 58.776 40.000 0.00 0.00 0.00 3.01
2183 2223 2.246719 AGTGAAGAGTGCAAGGTGTC 57.753 50.000 0.00 0.00 0.00 3.67
2257 2297 4.559862 AGTAGTGCCACTAAGCAGATTT 57.440 40.909 6.06 0.00 45.14 2.17
2328 2371 2.299297 ACTTCCACTACCACTACTGTGC 59.701 50.000 0.00 0.00 42.54 4.57
2557 2611 8.367911 GTCTCATGATTATGTAGTTGGTATCCA 58.632 37.037 0.00 0.00 35.73 3.41
2559 2613 9.935241 ATGTCTCATGATTATGTAGTTGGTATC 57.065 33.333 0.00 0.00 35.73 2.24
3186 3241 4.451096 TCTTGTACGCAAAGGACATCTTTC 59.549 41.667 0.00 0.00 44.53 2.62
3450 3505 7.996644 AGTGGAAGGAAAAACTCTAACACATAA 59.003 33.333 0.00 0.00 0.00 1.90
3621 3676 9.254133 CATGAACTAATAGAAACATCAGACGAT 57.746 33.333 0.00 0.00 0.00 3.73
3707 3762 2.796032 GCCAGTTGCTCAACACTGTTTC 60.796 50.000 14.32 0.00 43.47 2.78
3796 3855 1.280421 AGCCTGGACCAATCAGAAGAC 59.720 52.381 0.00 0.00 34.36 3.01
3951 4031 5.647658 CAGTACAATACAAGGAAATGAGCCA 59.352 40.000 0.00 0.00 0.00 4.75
4458 4562 5.486526 AGAATCTAGTGCTGAAGAAACCTG 58.513 41.667 0.00 0.00 0.00 4.00
4799 4915 2.170187 TGCCAGGTTCAAACTGCAAAAT 59.830 40.909 0.00 0.00 34.65 1.82
5354 5486 6.285790 TCGATGTTCAACATTCATTATCGG 57.714 37.500 4.04 0.00 39.27 4.18
5359 5494 7.041167 TCAGAACTTCGATGTTCAACATTCATT 60.041 33.333 33.02 15.33 46.19 2.57
5497 5632 5.515534 CCCTCCAGGATTCAGGTTAATATGG 60.516 48.000 0.00 0.00 38.24 2.74
6022 6157 0.883814 GGCATTCCTGGAGATCAGCG 60.884 60.000 0.00 0.00 42.05 5.18
6109 6244 1.334243 CTACTACCCGAAGAAGCTCCG 59.666 57.143 0.00 0.00 0.00 4.63
6175 6312 3.563808 TGTCATGAGTAAAACACCTGTGC 59.436 43.478 0.00 0.00 0.00 4.57
6201 6338 2.404789 CGCCACGCTAAAGCCATG 59.595 61.111 0.00 0.00 37.91 3.66
6309 6525 1.196012 AGTAGCCCACTCAGGTAAGC 58.804 55.000 0.00 0.00 28.33 3.09
6399 6652 5.670485 TGCCACAATTCACTGGTATACTAG 58.330 41.667 14.21 14.21 0.00 2.57
6449 6707 3.935828 GCTTGTACACTCAGGATCCTTTC 59.064 47.826 13.00 0.00 0.00 2.62
6507 6765 5.136816 TGCCACATACTCGTACACTTAAA 57.863 39.130 0.00 0.00 0.00 1.52
6509 6767 3.760151 ACTGCCACATACTCGTACACTTA 59.240 43.478 0.00 0.00 0.00 2.24
6517 6775 3.002791 ACATGAAACTGCCACATACTCG 58.997 45.455 0.00 0.00 0.00 4.18
6564 6835 8.904834 ACTACGATCAGTCAAATAGTAATCACT 58.095 33.333 0.00 0.00 38.91 3.41
6603 6874 6.309357 TCTTGGTAAGAGTTGTGTAGGTCTA 58.691 40.000 0.00 0.00 32.71 2.59
6642 6915 5.222130 ACCAAAAAGTCCTGACCAGTATGAT 60.222 40.000 0.00 0.00 39.69 2.45
6644 6917 4.398319 ACCAAAAAGTCCTGACCAGTATG 58.602 43.478 0.00 0.00 0.00 2.39
6671 6944 8.621532 TTGACTTCAGTTTCTACAAATGCTAT 57.378 30.769 0.00 0.00 0.00 2.97
6675 6948 6.963796 AGCTTGACTTCAGTTTCTACAAATG 58.036 36.000 0.00 0.00 0.00 2.32
6701 6976 0.393077 ATAACCATTCCCCGAGAGCG 59.607 55.000 0.00 0.00 37.24 5.03
6703 6978 3.838244 TTCATAACCATTCCCCGAGAG 57.162 47.619 0.00 0.00 0.00 3.20
6705 6980 3.815401 GTGATTCATAACCATTCCCCGAG 59.185 47.826 0.00 0.00 0.00 4.63
6737 7024 9.612620 CTTATTTAGTCATTTCGAAAGCACTTT 57.387 29.630 22.70 13.94 35.14 2.66
6776 7081 7.037438 GTGCTGTCATGAAATTTGATATTGGT 58.963 34.615 0.00 0.00 0.00 3.67
6778 7083 8.697846 AAGTGCTGTCATGAAATTTGATATTG 57.302 30.769 0.00 0.00 0.00 1.90
6780 7085 9.793252 GTAAAGTGCTGTCATGAAATTTGATAT 57.207 29.630 0.00 0.00 0.00 1.63
6818 7123 0.813184 ATTTGCATGTTCCCGCTCTG 59.187 50.000 0.00 0.00 0.00 3.35
6909 7214 6.090129 CGGTTCATACTTATTTGGTTGTTGG 58.910 40.000 0.00 0.00 0.00 3.77
6912 7217 5.562635 TCCGGTTCATACTTATTTGGTTGT 58.437 37.500 0.00 0.00 0.00 3.32
6976 7281 5.125417 AGTGTGTTTGTCATTACAGCAAAGT 59.875 36.000 0.00 0.00 36.83 2.66
6977 7282 5.456497 CAGTGTGTTTGTCATTACAGCAAAG 59.544 40.000 0.00 0.00 36.83 2.77
6978 7283 5.339177 CAGTGTGTTTGTCATTACAGCAAA 58.661 37.500 0.00 0.00 36.83 3.68
7015 7321 2.363306 TGACTTGAACAAGGTGCCAT 57.637 45.000 17.05 0.00 42.53 4.40
7103 7409 0.680921 AAGCCATGTCCATTGGTCCG 60.681 55.000 1.86 0.00 0.00 4.79
7106 7412 0.038166 ACGAAGCCATGTCCATTGGT 59.962 50.000 1.86 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.