Multiple sequence alignment - TraesCS2B01G066200

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 TraesCS2B01G066200 chr2B 100.000 2498 0 0 1 2498 33383181 33385678 0.000000e+00 4614
1 TraesCS2B01G066200 chr2B 99.870 767 1 0 1732 2498 33415127 33415893 0.000000e+00 1411
2 TraesCS2B01G066200 chr6A 91.871 1304 100 5 740 2039 3586603 3585302 0.000000e+00 1816
3 TraesCS2B01G066200 chr6A 83.594 1725 173 38 45 1708 3287653 3289328 0.000000e+00 1517
4 TraesCS2B01G066200 chr6D 87.379 1450 145 23 323 1742 3993902 3992461 0.000000e+00 1629
5 TraesCS2B01G066200 chr6D 88.336 703 54 9 686 1385 3997632 3998309 0.000000e+00 819
6 TraesCS2B01G066200 chr6D 91.892 259 21 0 1380 1638 3998472 3998730 1.830000e-96 363
7 TraesCS2B01G066200 chr3B 89.764 127 13 0 2369 2495 787889458 787889332 1.990000e-36 163
8 TraesCS2B01G066200 chr2D 89.231 130 14 0 2369 2498 553750594 553750465 1.990000e-36 163
9 TraesCS2B01G066200 chr7D 89.516 124 13 0 2369 2492 3181101 3181224 9.250000e-35 158
10 TraesCS2B01G066200 chr7B 88.800 125 14 0 2369 2493 736466369 736466245 1.200000e-33 154
11 TraesCS2B01G066200 chr7B 85.827 127 18 0 2369 2495 707891233 707891359 4.330000e-28 135
12 TraesCS2B01G066200 chr1B 86.923 130 15 1 2369 2498 152945645 152945518 7.200000e-31 145
13 TraesCS2B01G066200 chrUn 86.047 129 14 4 2369 2495 82177179 82177305 4.330000e-28 135
14 TraesCS2B01G066200 chr5B 85.606 132 16 3 2366 2495 522597929 522598059 4.330000e-28 135


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 TraesCS2B01G066200 chr2B 33383181 33385678 2497 False 4614 4614 100.000 1 2498 1 chr2B.!!$F1 2497
1 TraesCS2B01G066200 chr2B 33415127 33415893 766 False 1411 1411 99.870 1732 2498 1 chr2B.!!$F2 766
2 TraesCS2B01G066200 chr6A 3585302 3586603 1301 True 1816 1816 91.871 740 2039 1 chr6A.!!$R1 1299
3 TraesCS2B01G066200 chr6A 3287653 3289328 1675 False 1517 1517 83.594 45 1708 1 chr6A.!!$F1 1663
4 TraesCS2B01G066200 chr6D 3992461 3993902 1441 True 1629 1629 87.379 323 1742 1 chr6D.!!$R1 1419
5 TraesCS2B01G066200 chr6D 3997632 3998730 1098 False 591 819 90.114 686 1638 2 chr6D.!!$F1 952

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
296 300 0.39382 AGACCCGGCGTAAACTGAAA 59.606 50.0 6.01 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1953 0.387929 ACTCGGACAACATGACGTGT 59.612 50.0 0.0 0.0 44.84 4.49 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 8.648557 CAACGTATATGGTGATAATCATAGGG 57.351 38.462 3.73 0.00 30.56 3.53
26 27 7.361457 ACGTATATGGTGATAATCATAGGGG 57.639 40.000 0.00 0.00 30.56 4.79
27 28 6.326583 ACGTATATGGTGATAATCATAGGGGG 59.673 42.308 0.00 0.00 30.56 5.40
28 29 6.553476 CGTATATGGTGATAATCATAGGGGGA 59.447 42.308 0.00 0.00 30.56 4.81
29 30 7.070696 CGTATATGGTGATAATCATAGGGGGAA 59.929 40.741 0.00 0.00 30.56 3.97
30 31 4.993705 TGGTGATAATCATAGGGGGAAC 57.006 45.455 0.00 0.00 0.00 3.62
31 32 3.326588 TGGTGATAATCATAGGGGGAACG 59.673 47.826 0.00 0.00 0.00 3.95
32 33 3.581332 GGTGATAATCATAGGGGGAACGA 59.419 47.826 0.00 0.00 0.00 3.85
33 34 4.225267 GGTGATAATCATAGGGGGAACGAT 59.775 45.833 0.00 0.00 0.00 3.73
34 35 5.178797 GTGATAATCATAGGGGGAACGATG 58.821 45.833 0.00 0.00 0.00 3.84
35 36 4.844085 TGATAATCATAGGGGGAACGATGT 59.156 41.667 0.00 0.00 0.00 3.06
36 37 5.309543 TGATAATCATAGGGGGAACGATGTT 59.690 40.000 0.00 0.00 0.00 2.71
37 38 3.771577 ATCATAGGGGGAACGATGTTC 57.228 47.619 1.09 1.09 0.00 3.18
38 39 1.766496 TCATAGGGGGAACGATGTTCC 59.234 52.381 18.24 18.24 37.86 3.62
39 40 1.488812 CATAGGGGGAACGATGTTCCA 59.511 52.381 25.33 9.40 40.32 3.53
40 41 0.906775 TAGGGGGAACGATGTTCCAC 59.093 55.000 25.33 22.91 41.25 4.02
41 42 0.840722 AGGGGGAACGATGTTCCACT 60.841 55.000 25.44 19.99 41.68 4.00
42 43 0.676782 GGGGGAACGATGTTCCACTG 60.677 60.000 25.44 0.00 41.68 3.66
43 44 1.305930 GGGGAACGATGTTCCACTGC 61.306 60.000 25.33 11.28 38.92 4.40
57 58 2.124403 CTGCCATCACTCCCTGCC 60.124 66.667 0.00 0.00 0.00 4.85
73 74 0.395586 TGCCCGGCAAAGCTTGATAT 60.396 50.000 10.50 0.00 34.76 1.63
78 79 1.534595 CGGCAAAGCTTGATATGGTGC 60.535 52.381 0.00 3.84 0.00 5.01
81 82 3.184541 GCAAAGCTTGATATGGTGCTTG 58.815 45.455 0.00 0.00 43.80 4.01
91 92 8.019669 GCTTGATATGGTGCTTGATAATGTTAG 58.980 37.037 0.00 0.00 0.00 2.34
95 96 5.309323 TGGTGCTTGATAATGTTAGTTGC 57.691 39.130 0.00 0.00 0.00 4.17
96 97 4.157656 TGGTGCTTGATAATGTTAGTTGCC 59.842 41.667 0.00 0.00 0.00 4.52
99 100 4.640201 TGCTTGATAATGTTAGTTGCCTCC 59.360 41.667 0.00 0.00 0.00 4.30
102 103 6.678900 GCTTGATAATGTTAGTTGCCTCCAAG 60.679 42.308 0.00 0.00 0.00 3.61
112 113 1.367346 TGCCTCCAAGGTACATTCCA 58.633 50.000 0.00 0.00 37.80 3.53
113 114 1.004277 TGCCTCCAAGGTACATTCCAC 59.996 52.381 0.00 0.00 37.80 4.02
118 119 4.459337 CCTCCAAGGTACATTCCACTTTTC 59.541 45.833 0.00 0.00 0.00 2.29
120 121 5.070001 TCCAAGGTACATTCCACTTTTCTG 58.930 41.667 0.00 0.00 0.00 3.02
123 124 6.349611 CCAAGGTACATTCCACTTTTCTGATG 60.350 42.308 0.00 0.00 0.00 3.07
127 128 7.554118 AGGTACATTCCACTTTTCTGATGTATG 59.446 37.037 0.00 0.00 0.00 2.39
169 170 6.610075 AACCCATTGAACTTAGCATGATTT 57.390 33.333 0.00 0.00 0.00 2.17
173 174 6.351202 CCCATTGAACTTAGCATGATTTTGGA 60.351 38.462 0.00 0.00 0.00 3.53
176 177 9.158233 CATTGAACTTAGCATGATTTTGGAAAT 57.842 29.630 0.00 0.00 0.00 2.17
183 184 6.795144 AGCATGATTTTGGAAATCCATGTA 57.205 33.333 2.38 0.00 46.97 2.29
191 192 7.704578 TTTTGGAAATCCATGTAATTCGGTA 57.295 32.000 2.38 0.00 46.97 4.02
236 237 8.976353 TCTGAGCTTTTATTTTATAATGCCCAA 58.024 29.630 0.00 0.00 0.00 4.12
237 238 8.940768 TGAGCTTTTATTTTATAATGCCCAAC 57.059 30.769 0.00 0.00 0.00 3.77
285 289 2.860971 GCAAAGTTTTACAAGACCCGGC 60.861 50.000 0.00 0.00 0.00 6.13
296 300 0.393820 AGACCCGGCGTAAACTGAAA 59.606 50.000 6.01 0.00 0.00 2.69
297 301 1.202675 AGACCCGGCGTAAACTGAAAA 60.203 47.619 6.01 0.00 0.00 2.29
300 304 1.874872 CCCGGCGTAAACTGAAAAAGA 59.125 47.619 6.01 0.00 0.00 2.52
386 390 5.806818 TCAAGTATGGACATTTTAACCGGA 58.193 37.500 9.46 0.00 0.00 5.14
404 408 0.935898 GACAGAGATTGATGCCAGCG 59.064 55.000 0.00 0.00 0.00 5.18
406 410 0.463295 CAGAGATTGATGCCAGCGGT 60.463 55.000 0.00 0.00 0.00 5.68
425 429 3.057174 CGGTAAAAACCAATAGCCTTGCA 60.057 43.478 0.00 0.00 0.00 4.08
454 458 8.827177 TTCACGTATGAAATTGTCCTATATCC 57.173 34.615 0.00 0.00 41.99 2.59
455 459 8.190326 TCACGTATGAAATTGTCCTATATCCT 57.810 34.615 0.00 0.00 0.00 3.24
476 480 5.812127 TCCTAGTATATTATTGCTGCGCATG 59.188 40.000 12.24 6.51 38.76 4.06
490 494 1.560923 CGCATGCTGGTACTGTAGAC 58.439 55.000 17.13 0.00 0.00 2.59
491 495 1.135112 CGCATGCTGGTACTGTAGACA 60.135 52.381 17.13 0.00 0.00 3.41
538 544 2.040278 TCTGCCCAGATGCAAGTAAGTT 59.960 45.455 0.00 0.00 41.51 2.66
539 545 2.161855 TGCCCAGATGCAAGTAAGTTG 58.838 47.619 0.00 0.00 38.56 3.16
610 637 1.950909 AGGAAATTTTGACGCCAACGA 59.049 42.857 0.00 0.00 43.93 3.85
612 646 1.713932 GAAATTTTGACGCCAACGAGC 59.286 47.619 0.00 0.00 43.93 5.03
634 668 4.083802 GCAGTAATATCCTTGCGTGATTCC 60.084 45.833 0.00 0.00 0.00 3.01
642 676 2.483876 CTTGCGTGATTCCCGTATGAT 58.516 47.619 0.00 0.00 0.00 2.45
644 678 1.686587 TGCGTGATTCCCGTATGATCT 59.313 47.619 0.00 0.00 0.00 2.75
646 680 3.131396 GCGTGATTCCCGTATGATCTTT 58.869 45.455 0.00 0.00 0.00 2.52
647 681 3.059597 GCGTGATTCCCGTATGATCTTTG 60.060 47.826 0.00 0.00 0.00 2.77
648 682 4.119862 CGTGATTCCCGTATGATCTTTGT 58.880 43.478 0.00 0.00 0.00 2.83
651 685 4.408921 TGATTCCCGTATGATCTTTGTCCT 59.591 41.667 0.00 0.00 0.00 3.85
652 686 4.402056 TTCCCGTATGATCTTTGTCCTC 57.598 45.455 0.00 0.00 0.00 3.71
653 687 3.643237 TCCCGTATGATCTTTGTCCTCT 58.357 45.455 0.00 0.00 0.00 3.69
654 688 4.800023 TCCCGTATGATCTTTGTCCTCTA 58.200 43.478 0.00 0.00 0.00 2.43
656 690 5.839063 TCCCGTATGATCTTTGTCCTCTATT 59.161 40.000 0.00 0.00 0.00 1.73
657 691 5.928839 CCCGTATGATCTTTGTCCTCTATTG 59.071 44.000 0.00 0.00 0.00 1.90
658 692 6.463049 CCCGTATGATCTTTGTCCTCTATTGT 60.463 42.308 0.00 0.00 0.00 2.71
659 693 7.255836 CCCGTATGATCTTTGTCCTCTATTGTA 60.256 40.741 0.00 0.00 0.00 2.41
660 694 7.595502 CCGTATGATCTTTGTCCTCTATTGTAC 59.404 40.741 0.00 0.00 0.00 2.90
661 695 8.135529 CGTATGATCTTTGTCCTCTATTGTACA 58.864 37.037 0.00 0.00 0.00 2.90
717 773 3.635331 TGCAAGTACGTACAGAGTGAAC 58.365 45.455 26.55 8.18 0.00 3.18
720 776 3.802722 AGTACGTACAGAGTGAACGTC 57.197 47.619 26.55 0.00 46.04 4.34
771 827 1.609061 CCGTGACTGCCACTTCAATCT 60.609 52.381 0.00 0.00 43.53 2.40
778 834 0.807496 GCCACTTCAATCTGAGCCAC 59.193 55.000 0.00 0.00 0.00 5.01
783 839 2.234661 ACTTCAATCTGAGCCACGATGA 59.765 45.455 0.00 0.00 0.00 2.92
819 875 3.499918 ACTTCTAGCAACTTCACATGTGC 59.500 43.478 21.38 8.31 0.00 4.57
840 896 6.247229 TGCCTTGCACTCTATAAATAGGAA 57.753 37.500 0.00 0.00 31.71 3.36
863 919 2.426024 CCAAGTTCATCCATCCAAGCAG 59.574 50.000 0.00 0.00 0.00 4.24
894 950 9.426837 CAGAAAATAGAAATTCAAATTCCAGCA 57.573 29.630 0.00 0.00 0.00 4.41
904 960 5.885230 TCAAATTCCAGCAACATAGACAG 57.115 39.130 0.00 0.00 0.00 3.51
908 964 2.910199 TCCAGCAACATAGACAGCATC 58.090 47.619 0.00 0.00 0.00 3.91
910 966 3.011818 CCAGCAACATAGACAGCATCAA 58.988 45.455 0.00 0.00 0.00 2.57
921 977 2.615912 GACAGCATCAACATTAGAGGGC 59.384 50.000 0.00 0.00 0.00 5.19
957 1013 1.896465 AGTTGAGGGTTCTCTTCTCCG 59.104 52.381 0.00 0.00 40.58 4.63
1008 1064 8.571336 GCAAGTAAGTGATAATCAATGGCTTAT 58.429 33.333 0.00 0.00 0.00 1.73
1049 1105 1.726853 AGGACTTCCAATTTCGAGCG 58.273 50.000 0.00 0.00 38.89 5.03
1258 1317 7.875041 TCAAAGTAGAGAGAGATGTTGAAAAGG 59.125 37.037 0.00 0.00 0.00 3.11
1277 1336 9.131791 TGAAAAGGTAAAAGAGTTGATAAAGCT 57.868 29.630 0.00 0.00 0.00 3.74
1326 1385 1.903877 AAGGCCACGAGACCCATGAG 61.904 60.000 5.01 0.00 0.00 2.90
1503 1730 2.147958 TGCTACCGTCCATGAACAAAC 58.852 47.619 0.00 0.00 0.00 2.93
1553 1780 3.689161 AGCTGCTACGTATTTGCATTTCA 59.311 39.130 0.00 0.00 36.07 2.69
1595 1822 8.786937 ACTGTAATGAATAAAATTATGCGCTG 57.213 30.769 9.73 0.00 0.00 5.18
1598 1825 8.563732 TGTAATGAATAAAATTATGCGCTGCTA 58.436 29.630 9.73 0.00 0.00 3.49
1624 1851 5.742453 CAGCGTATAATGTTGTACGAGTCTT 59.258 40.000 21.02 3.32 46.69 3.01
1625 1852 5.742453 AGCGTATAATGTTGTACGAGTCTTG 59.258 40.000 21.02 0.00 46.69 3.02
1631 1858 0.038892 TTGTACGAGTCTTGGTCGGC 60.039 55.000 0.00 0.00 41.88 5.54
1638 1865 0.896940 AGTCTTGGTCGGCCGAGTTA 60.897 55.000 31.97 15.37 44.89 2.24
1641 1868 1.006832 CTTGGTCGGCCGAGTTATTG 58.993 55.000 31.97 13.08 40.67 1.90
1650 1877 2.351726 GGCCGAGTTATTGTAGCAACAG 59.648 50.000 0.00 0.00 36.83 3.16
1676 1908 1.295792 GTCTGTCCGCAGTTTGTTGA 58.704 50.000 0.00 0.00 43.05 3.18
1725 1957 4.864916 ATTATGTGCTTCTTGCTACACG 57.135 40.909 0.00 0.00 43.37 4.49
1727 1959 1.497991 TGTGCTTCTTGCTACACGTC 58.502 50.000 0.00 0.00 43.37 4.34
2085 2319 8.066612 TGGGAAGAATTTAAATCATCCTGTTC 57.933 34.615 18.69 10.50 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.710907 CCCCTATGATTATCACCATATACGTTG 59.289 40.741 0.00 0.00 0.00 4.10
1 2 7.147549 CCCCCTATGATTATCACCATATACGTT 60.148 40.741 0.00 0.00 0.00 3.99
3 4 6.553476 TCCCCCTATGATTATCACCATATACG 59.447 42.308 0.00 0.00 0.00 3.06
4 5 7.931015 TCCCCCTATGATTATCACCATATAC 57.069 40.000 0.00 0.00 0.00 1.47
5 6 7.070696 CGTTCCCCCTATGATTATCACCATATA 59.929 40.741 0.00 0.00 0.00 0.86
6 7 6.126768 CGTTCCCCCTATGATTATCACCATAT 60.127 42.308 0.00 0.00 0.00 1.78
7 8 5.188948 CGTTCCCCCTATGATTATCACCATA 59.811 44.000 0.00 0.00 0.00 2.74
8 9 4.019321 CGTTCCCCCTATGATTATCACCAT 60.019 45.833 0.00 0.00 0.00 3.55
9 10 3.326588 CGTTCCCCCTATGATTATCACCA 59.673 47.826 0.00 0.00 0.00 4.17
10 11 3.581332 TCGTTCCCCCTATGATTATCACC 59.419 47.826 0.00 0.00 0.00 4.02
11 12 4.884668 TCGTTCCCCCTATGATTATCAC 57.115 45.455 0.00 0.00 0.00 3.06
12 13 4.844085 ACATCGTTCCCCCTATGATTATCA 59.156 41.667 0.00 0.00 0.00 2.15
13 14 5.422214 ACATCGTTCCCCCTATGATTATC 57.578 43.478 0.00 0.00 0.00 1.75
14 15 5.280521 GGAACATCGTTCCCCCTATGATTAT 60.281 44.000 13.84 0.00 32.48 1.28
15 16 4.041198 GGAACATCGTTCCCCCTATGATTA 59.959 45.833 13.84 0.00 32.48 1.75
16 17 3.181443 GGAACATCGTTCCCCCTATGATT 60.181 47.826 13.84 0.00 32.48 2.57
17 18 2.372172 GGAACATCGTTCCCCCTATGAT 59.628 50.000 13.84 0.00 32.48 2.45
18 19 1.766496 GGAACATCGTTCCCCCTATGA 59.234 52.381 13.84 0.00 32.48 2.15
19 20 1.488812 TGGAACATCGTTCCCCCTATG 59.511 52.381 20.32 0.00 37.79 2.23
20 21 1.489230 GTGGAACATCGTTCCCCCTAT 59.511 52.381 20.32 0.00 44.52 2.57
21 22 0.906775 GTGGAACATCGTTCCCCCTA 59.093 55.000 20.32 2.07 44.52 3.53
22 23 0.840722 AGTGGAACATCGTTCCCCCT 60.841 55.000 20.32 14.04 44.52 4.79
23 24 0.676782 CAGTGGAACATCGTTCCCCC 60.677 60.000 20.32 12.31 44.52 5.40
24 25 1.305930 GCAGTGGAACATCGTTCCCC 61.306 60.000 20.32 11.19 44.52 4.81
25 26 1.305930 GGCAGTGGAACATCGTTCCC 61.306 60.000 20.32 12.85 44.52 3.97
26 27 0.605319 TGGCAGTGGAACATCGTTCC 60.605 55.000 17.21 17.21 44.52 3.62
27 28 1.398390 GATGGCAGTGGAACATCGTTC 59.602 52.381 0.00 0.00 44.52 3.95
28 29 1.271325 TGATGGCAGTGGAACATCGTT 60.271 47.619 0.00 0.00 44.52 3.85
29 30 0.324614 TGATGGCAGTGGAACATCGT 59.675 50.000 0.00 0.00 44.52 3.73
30 31 0.729116 GTGATGGCAGTGGAACATCG 59.271 55.000 0.00 0.00 44.52 3.84
31 32 2.012673 GAGTGATGGCAGTGGAACATC 58.987 52.381 0.00 0.00 44.52 3.06
32 33 1.340405 GGAGTGATGGCAGTGGAACAT 60.340 52.381 0.00 0.00 44.52 2.71
33 34 0.036732 GGAGTGATGGCAGTGGAACA 59.963 55.000 0.00 0.00 41.43 3.18
34 35 0.678048 GGGAGTGATGGCAGTGGAAC 60.678 60.000 0.00 0.00 0.00 3.62
35 36 0.842030 AGGGAGTGATGGCAGTGGAA 60.842 55.000 0.00 0.00 0.00 3.53
36 37 1.229625 AGGGAGTGATGGCAGTGGA 60.230 57.895 0.00 0.00 0.00 4.02
37 38 1.077930 CAGGGAGTGATGGCAGTGG 60.078 63.158 0.00 0.00 0.00 4.00
38 39 1.748122 GCAGGGAGTGATGGCAGTG 60.748 63.158 0.00 0.00 0.00 3.66
39 40 2.673523 GCAGGGAGTGATGGCAGT 59.326 61.111 0.00 0.00 0.00 4.40
40 41 2.124403 GGCAGGGAGTGATGGCAG 60.124 66.667 0.00 0.00 41.35 4.85
41 42 3.731728 GGGCAGGGAGTGATGGCA 61.732 66.667 0.00 0.00 43.35 4.92
42 43 4.864334 CGGGCAGGGAGTGATGGC 62.864 72.222 0.00 0.00 41.01 4.40
43 44 4.181010 CCGGGCAGGGAGTGATGG 62.181 72.222 0.00 0.00 35.97 3.51
57 58 1.066002 CACCATATCAAGCTTTGCCGG 59.934 52.381 0.00 0.00 0.00 6.13
73 74 4.157656 GGCAACTAACATTATCAAGCACCA 59.842 41.667 0.00 0.00 0.00 4.17
91 92 2.092323 GGAATGTACCTTGGAGGCAAC 58.908 52.381 0.00 0.00 39.63 4.17
95 96 3.721087 AAGTGGAATGTACCTTGGAGG 57.279 47.619 0.00 0.00 42.49 4.30
96 97 5.182001 CAGAAAAGTGGAATGTACCTTGGAG 59.818 44.000 0.00 0.00 0.00 3.86
99 100 6.207417 ACATCAGAAAAGTGGAATGTACCTTG 59.793 38.462 0.00 0.00 0.00 3.61
102 103 7.552687 TCATACATCAGAAAAGTGGAATGTACC 59.447 37.037 0.00 0.00 0.00 3.34
142 143 5.716228 TCATGCTAAGTTCAATGGGTTTCAT 59.284 36.000 0.00 0.00 37.79 2.57
145 146 6.610075 AATCATGCTAAGTTCAATGGGTTT 57.390 33.333 0.00 0.00 0.00 3.27
148 149 5.813672 CCAAAATCATGCTAAGTTCAATGGG 59.186 40.000 0.00 0.00 0.00 4.00
154 155 7.322664 TGGATTTCCAAAATCATGCTAAGTTC 58.677 34.615 12.91 0.00 44.35 3.01
173 174 9.635404 TTATCCTTTACCGAATTACATGGATTT 57.365 29.630 0.00 0.00 34.22 2.17
261 265 4.440940 CCGGGTCTTGTAAAACTTTGCTTT 60.441 41.667 0.00 0.00 0.00 3.51
263 267 2.621526 CCGGGTCTTGTAAAACTTTGCT 59.378 45.455 0.00 0.00 0.00 3.91
264 268 2.860971 GCCGGGTCTTGTAAAACTTTGC 60.861 50.000 2.18 0.00 0.00 3.68
265 269 2.603652 CGCCGGGTCTTGTAAAACTTTG 60.604 50.000 2.18 0.00 0.00 2.77
266 270 1.605232 CGCCGGGTCTTGTAAAACTTT 59.395 47.619 2.18 0.00 0.00 2.66
267 271 1.232119 CGCCGGGTCTTGTAAAACTT 58.768 50.000 2.18 0.00 0.00 2.66
269 273 1.794512 TACGCCGGGTCTTGTAAAAC 58.205 50.000 2.18 0.00 0.00 2.43
271 275 2.142319 GTTTACGCCGGGTCTTGTAAA 58.858 47.619 2.18 4.23 35.18 2.01
272 276 1.344114 AGTTTACGCCGGGTCTTGTAA 59.656 47.619 2.18 0.00 0.00 2.41
274 278 0.601841 CAGTTTACGCCGGGTCTTGT 60.602 55.000 2.18 0.00 0.00 3.16
275 279 0.320073 TCAGTTTACGCCGGGTCTTG 60.320 55.000 2.18 0.00 0.00 3.02
276 280 0.393820 TTCAGTTTACGCCGGGTCTT 59.606 50.000 2.18 0.00 0.00 3.01
277 281 0.393820 TTTCAGTTTACGCCGGGTCT 59.606 50.000 2.18 0.00 0.00 3.85
285 289 9.511144 ACACCTTATTTTCTTTTTCAGTTTACG 57.489 29.630 0.00 0.00 0.00 3.18
336 340 8.102676 TGAATGAAATAAGACCAACAGAGATGA 58.897 33.333 0.00 0.00 0.00 2.92
371 375 3.934068 TCTCTGTCCGGTTAAAATGTCC 58.066 45.455 0.00 0.00 0.00 4.02
378 382 3.531538 GCATCAATCTCTGTCCGGTTAA 58.468 45.455 0.00 0.00 0.00 2.01
386 390 0.463295 CCGCTGGCATCAATCTCTGT 60.463 55.000 0.00 0.00 0.00 3.41
404 408 4.529109 TGCAAGGCTATTGGTTTTTACC 57.471 40.909 0.00 0.00 0.00 2.85
406 410 5.991933 TCATGCAAGGCTATTGGTTTTTA 57.008 34.783 0.00 0.00 0.00 1.52
425 429 8.908786 ATAGGACAATTTCATACGTGAATCAT 57.091 30.769 0.00 0.00 43.49 2.45
476 480 5.049612 GGAAAAACTTGTCTACAGTACCAGC 60.050 44.000 0.00 0.00 0.00 4.85
517 523 1.630369 ACTTACTTGCATCTGGGCAGA 59.370 47.619 0.00 0.00 45.88 4.26
538 544 1.202830 ACACGTGCCCCATTACTTTCA 60.203 47.619 17.22 0.00 0.00 2.69
539 545 1.530323 ACACGTGCCCCATTACTTTC 58.470 50.000 17.22 0.00 0.00 2.62
596 623 1.092921 ACTGCTCGTTGGCGTCAAAA 61.093 50.000 2.85 0.00 39.49 2.44
610 637 3.819564 TCACGCAAGGATATTACTGCT 57.180 42.857 0.00 0.00 46.39 4.24
612 646 4.452455 GGGAATCACGCAAGGATATTACTG 59.548 45.833 0.00 0.00 46.39 2.74
634 668 6.516718 ACAATAGAGGACAAAGATCATACGG 58.483 40.000 0.00 0.00 0.00 4.02
642 676 7.770366 TGTACTGTACAATAGAGGACAAAGA 57.230 36.000 17.74 0.00 39.67 2.52
647 681 8.979574 GCAATAATGTACTGTACAATAGAGGAC 58.020 37.037 23.03 7.01 42.76 3.85
648 682 8.924303 AGCAATAATGTACTGTACAATAGAGGA 58.076 33.333 23.03 1.70 42.76 3.71
651 685 7.441157 GGCAGCAATAATGTACTGTACAATAGA 59.559 37.037 23.03 10.06 42.76 1.98
652 686 7.307989 GGGCAGCAATAATGTACTGTACAATAG 60.308 40.741 23.03 10.39 42.76 1.73
653 687 6.485313 GGGCAGCAATAATGTACTGTACAATA 59.515 38.462 23.03 19.19 42.76 1.90
654 688 5.299279 GGGCAGCAATAATGTACTGTACAAT 59.701 40.000 23.03 17.69 42.76 2.71
656 690 4.196193 GGGCAGCAATAATGTACTGTACA 58.804 43.478 21.68 21.68 43.80 2.90
657 691 4.196193 TGGGCAGCAATAATGTACTGTAC 58.804 43.478 10.98 10.98 32.65 2.90
658 692 4.495690 TGGGCAGCAATAATGTACTGTA 57.504 40.909 0.00 0.00 32.65 2.74
659 693 3.364460 TGGGCAGCAATAATGTACTGT 57.636 42.857 0.00 0.00 32.65 3.55
660 694 5.049198 CAGTATGGGCAGCAATAATGTACTG 60.049 44.000 0.00 0.00 33.17 2.74
661 695 5.065914 CAGTATGGGCAGCAATAATGTACT 58.934 41.667 0.00 0.00 0.00 2.73
720 776 2.814280 AGAACACTAAGGACGTGTGG 57.186 50.000 0.00 0.00 44.25 4.17
771 827 0.246360 AATCGTGTCATCGTGGCTCA 59.754 50.000 0.00 0.00 0.00 4.26
778 834 1.059692 GTGCTCACAATCGTGTCATCG 59.940 52.381 0.00 0.00 44.02 3.84
783 839 2.533266 AGAAGTGCTCACAATCGTGT 57.467 45.000 2.63 0.00 44.02 4.49
819 875 7.054124 TGGTTTCCTATTTATAGAGTGCAAGG 58.946 38.462 0.00 0.00 32.05 3.61
840 896 2.827921 GCTTGGATGGATGAACTTGGTT 59.172 45.455 0.00 0.00 0.00 3.67
863 919 9.091784 GAATTTGAATTTCTATTTTCTGAGGCC 57.908 33.333 0.00 0.00 0.00 5.19
894 950 6.765036 CCTCTAATGTTGATGCTGTCTATGTT 59.235 38.462 0.00 0.00 0.00 2.71
895 951 6.286758 CCTCTAATGTTGATGCTGTCTATGT 58.713 40.000 0.00 0.00 0.00 2.29
904 960 0.947244 CCGCCCTCTAATGTTGATGC 59.053 55.000 0.00 0.00 0.00 3.91
908 964 1.376609 GCACCCGCCCTCTAATGTTG 61.377 60.000 0.00 0.00 0.00 3.33
910 966 2.257409 CTGCACCCGCCCTCTAATGT 62.257 60.000 0.00 0.00 37.32 2.71
957 1013 0.949105 TGAAGAACTTCGGCGCCTTC 60.949 55.000 26.68 20.76 42.28 3.46
1008 1064 0.615331 CTCCTGCCAGTGGAAGCTTA 59.385 55.000 15.20 0.00 32.61 3.09
1010 1066 1.422161 AACTCCTGCCAGTGGAAGCT 61.422 55.000 15.20 0.00 32.61 3.74
1049 1105 3.620821 GCTGTTTGATGGAAGCTCTCTAC 59.379 47.826 0.00 0.00 32.82 2.59
1244 1303 8.621286 TCAACTCTTTTACCTTTTCAACATCTC 58.379 33.333 0.00 0.00 0.00 2.75
1258 1317 7.334671 AGGCAGTAGCTTTATCAACTCTTTTAC 59.665 37.037 0.00 0.00 41.70 2.01
1277 1336 4.245660 CTCAGAAATTTCACGAGGCAGTA 58.754 43.478 19.99 0.00 0.00 2.74
1343 1402 4.613925 TCCATGTTCCTGCTCAGATATC 57.386 45.455 0.00 0.00 0.00 1.63
1345 1404 3.969312 TGATCCATGTTCCTGCTCAGATA 59.031 43.478 0.00 0.00 0.00 1.98
1503 1730 0.605319 TAACTCCAGGGCTTGTTGCG 60.605 55.000 0.00 0.00 44.05 4.85
1531 1758 3.689161 TGAAATGCAAATACGTAGCAGCT 59.311 39.130 12.70 0.00 42.14 4.24
1534 1761 6.918892 AGTATGAAATGCAAATACGTAGCA 57.081 33.333 10.02 10.02 43.14 3.49
1571 1798 7.592533 AGCAGCGCATAATTTTATTCATTACAG 59.407 33.333 11.47 0.00 0.00 2.74
1595 1822 4.143597 CGTACAACATTATACGCTGCTAGC 60.144 45.833 8.10 8.10 37.91 3.42
1598 1825 4.036567 TCGTACAACATTATACGCTGCT 57.963 40.909 0.00 0.00 43.02 4.24
1624 1851 1.135527 CTACAATAACTCGGCCGACCA 59.864 52.381 27.28 12.70 34.57 4.02
1625 1852 1.849097 CTACAATAACTCGGCCGACC 58.151 55.000 27.28 0.00 0.00 4.79
1631 1858 3.370978 CACCTGTTGCTACAATAACTCGG 59.629 47.826 1.93 0.94 32.92 4.63
1650 1877 2.358615 TGCGGACAGACATGCACC 60.359 61.111 0.00 0.00 31.31 5.01
1721 1953 0.387929 ACTCGGACAACATGACGTGT 59.612 50.000 0.00 0.00 44.84 4.49
1725 1957 1.997669 GAGGACTCGGACAACATGAC 58.002 55.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.