Multiple sequence alignment - TraesCS3A01G349500

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 TraesCS3A01G349500 chr3A 100.000 4588 0 0 1 4588 598552609 598548022 0.000000e+00 8473
1 TraesCS3A01G349500 chr3D 92.241 3802 172 54 13 3791 455867642 455863941 0.000000e+00 5273
2 TraesCS3A01G349500 chr3D 94.625 800 37 5 3794 4588 455863899 455863101 0.000000e+00 1234
3 TraesCS3A01G349500 chr3B 94.271 2950 113 24 744 3674 602305318 602302406 0.000000e+00 4460
4 TraesCS3A01G349500 chr3B 93.000 600 32 7 3752 4342 602302320 602301722 0.000000e+00 867
5 TraesCS3A01G349500 chr3B 82.911 749 81 18 1 744 602350883 602350177 8.380000e-177 630
6 TraesCS3A01G349500 chr3B 89.412 255 22 5 493 744 602305603 602305351 2.660000e-82 316
7 TraesCS3A01G349500 chr3B 94.406 143 4 1 4450 4588 602301721 602301579 2.780000e-52 217
8 TraesCS3A01G349500 chr3B 91.667 120 6 1 4339 4454 70295864 70295983 3.670000e-36 163
9 TraesCS3A01G349500 chr7A 92.500 120 5 4 4340 4455 375886610 375886491 7.890000e-38 169
10 TraesCS3A01G349500 chr7B 90.551 127 8 1 4340 4462 383736130 383736256 1.020000e-36 165
11 TraesCS3A01G349500 chr5D 91.597 119 6 4 4339 4453 492723289 492723171 1.320000e-35 161
12 TraesCS3A01G349500 chr5D 89.844 128 8 5 4340 4462 461071761 461071634 4.750000e-35 159
13 TraesCS3A01G349500 chr5D 83.186 113 13 6 457 564 120777195 120777306 1.050000e-16 99
14 TraesCS3A01G349500 chr5A 78.731 268 37 9 396 658 131569324 131569576 1.320000e-35 161
15 TraesCS3A01G349500 chr2B 90.400 125 8 2 4340 4460 643184735 643184611 1.320000e-35 161
16 TraesCS3A01G349500 chr6B 89.764 127 9 1 4334 4456 248362100 248362226 4.750000e-35 159
17 TraesCS3A01G349500 chr4B 89.516 124 7 3 4338 4457 16060842 16060963 7.950000e-33 152
18 TraesCS3A01G349500 chr5B 76.736 288 48 15 396 679 133865480 133865752 4.780000e-30 143
19 TraesCS3A01G349500 chr6A 89.831 59 4 2 433 490 600956292 600956235 1.770000e-09 75


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 TraesCS3A01G349500 chr3A 598548022 598552609 4587 True 8473.0 8473 100.00000 1 4588 1 chr3A.!!$R1 4587
1 TraesCS3A01G349500 chr3D 455863101 455867642 4541 True 3253.5 5273 93.43300 13 4588 2 chr3D.!!$R1 4575
2 TraesCS3A01G349500 chr3B 602301579 602305603 4024 True 1465.0 4460 92.77225 493 4588 4 chr3B.!!$R2 4095
3 TraesCS3A01G349500 chr3B 602350177 602350883 706 True 630.0 630 82.91100 1 744 1 chr3B.!!$R1 743

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
304 309 0.247460 CAGGACACTCGGCAATCTCA 59.753 55.000 0.00 0.0 0.00 3.27 F
841 887 0.625849 AACAGGCCACTCCCATTAGG 59.374 55.000 5.01 0.0 34.51 2.69 F
1433 1492 1.065701 TGTGTTTGCGGCGTTGTTAAT 59.934 42.857 9.37 0.0 0.00 1.40 F
2093 2162 0.101040 CCTTCAATCGCGGGTACGTA 59.899 55.000 6.13 0.0 43.45 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1458 0.040425 AACACACGCGAAATCAAGGC 60.040 50.000 15.93 0.00 0.00 4.35 R
1948 2017 1.155042 CAGAGACACTTGCTTCCTGC 58.845 55.000 0.00 0.00 43.25 4.85 R
2412 2482 1.875813 GCATGTGCTCCTCGTCGAG 60.876 63.158 15.53 15.53 38.21 4.04 R
3958 4115 0.031178 GCAAACAGCTGGTGAACTGG 59.969 55.000 19.93 0.00 41.15 4.00 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
44 45 3.118038 TGCTATATGTGTCTGGGTTTCCC 60.118 47.826 0.00 0.00 45.71 3.97
104 108 4.351938 TCCGTCAACCGCCGTGAG 62.352 66.667 0.00 0.00 34.38 3.51
113 117 4.504916 CGCCGTGAGCTGGGAGAG 62.505 72.222 0.00 0.00 40.39 3.20
118 122 1.821061 CGTGAGCTGGGAGAGGTGTT 61.821 60.000 0.00 0.00 30.42 3.32
119 123 1.267121 GTGAGCTGGGAGAGGTGTTA 58.733 55.000 0.00 0.00 30.42 2.41
120 124 1.834263 GTGAGCTGGGAGAGGTGTTAT 59.166 52.381 0.00 0.00 30.42 1.89
121 125 1.833630 TGAGCTGGGAGAGGTGTTATG 59.166 52.381 0.00 0.00 30.42 1.90
134 139 3.068560 GGTGTTATGTGTTTGCCGAGTA 58.931 45.455 0.00 0.00 0.00 2.59
139 144 1.005867 GTGTTTGCCGAGTACCCGA 60.006 57.895 0.00 0.00 0.00 5.14
165 170 4.530094 TTGTTGTGTTTTCTAGTCTGCG 57.470 40.909 0.00 0.00 0.00 5.18
220 225 0.749818 TGTGCCGAGTGCTTTTTCCA 60.750 50.000 0.00 0.00 42.00 3.53
304 309 0.247460 CAGGACACTCGGCAATCTCA 59.753 55.000 0.00 0.00 0.00 3.27
313 318 1.599071 TCGGCAATCTCATCGATTTGC 59.401 47.619 19.58 19.58 40.33 3.68
323 328 3.277715 TCATCGATTTGCATAGTGCCAA 58.722 40.909 0.00 0.00 44.23 4.52
362 367 8.700722 TTCATTACACCAACAATGCATTATTC 57.299 30.769 12.53 0.00 33.14 1.75
363 368 7.264221 TCATTACACCAACAATGCATTATTCC 58.736 34.615 12.53 0.00 33.14 3.01
365 370 3.197549 ACACCAACAATGCATTATTCCCC 59.802 43.478 12.53 0.00 0.00 4.81
366 371 2.430332 ACCAACAATGCATTATTCCCCG 59.570 45.455 12.53 0.02 0.00 5.73
367 372 2.472816 CAACAATGCATTATTCCCCGC 58.527 47.619 12.53 0.00 0.00 6.13
368 373 1.774110 ACAATGCATTATTCCCCGCA 58.226 45.000 12.53 0.00 39.01 5.69
370 375 2.499289 ACAATGCATTATTCCCCGCAAA 59.501 40.909 12.53 0.00 38.01 3.68
371 376 3.055530 ACAATGCATTATTCCCCGCAAAA 60.056 39.130 12.53 0.00 38.01 2.44
372 377 2.957491 TGCATTATTCCCCGCAAAAG 57.043 45.000 0.00 0.00 0.00 2.27
373 378 2.451490 TGCATTATTCCCCGCAAAAGA 58.549 42.857 0.00 0.00 0.00 2.52
374 379 2.828520 TGCATTATTCCCCGCAAAAGAA 59.171 40.909 0.00 0.00 0.00 2.52
375 380 3.259374 TGCATTATTCCCCGCAAAAGAAA 59.741 39.130 0.00 0.00 0.00 2.52
376 381 4.249661 GCATTATTCCCCGCAAAAGAAAA 58.750 39.130 0.00 0.00 0.00 2.29
377 382 4.092821 GCATTATTCCCCGCAAAAGAAAAC 59.907 41.667 0.00 0.00 0.00 2.43
378 383 4.939052 TTATTCCCCGCAAAAGAAAACA 57.061 36.364 0.00 0.00 0.00 2.83
379 384 3.828875 ATTCCCCGCAAAAGAAAACAA 57.171 38.095 0.00 0.00 0.00 2.83
380 385 3.828875 TTCCCCGCAAAAGAAAACAAT 57.171 38.095 0.00 0.00 0.00 2.71
381 386 3.104843 TCCCCGCAAAAGAAAACAATG 57.895 42.857 0.00 0.00 0.00 2.82
382 387 1.530720 CCCCGCAAAAGAAAACAATGC 59.469 47.619 0.00 0.00 0.00 3.56
383 388 2.208431 CCCGCAAAAGAAAACAATGCA 58.792 42.857 0.00 0.00 36.84 3.96
384 389 2.807392 CCCGCAAAAGAAAACAATGCAT 59.193 40.909 0.00 0.00 36.84 3.96
385 390 3.250521 CCCGCAAAAGAAAACAATGCATT 59.749 39.130 5.99 5.99 36.84 3.56
386 391 4.450419 CCCGCAAAAGAAAACAATGCATTA 59.550 37.500 12.53 0.00 36.84 1.90
387 392 5.122082 CCCGCAAAAGAAAACAATGCATTAT 59.878 36.000 12.53 0.00 36.84 1.28
388 393 6.348376 CCCGCAAAAGAAAACAATGCATTATT 60.348 34.615 12.53 3.90 36.84 1.40
389 394 7.148507 CCCGCAAAAGAAAACAATGCATTATTA 60.149 33.333 12.53 0.00 36.84 0.98
390 395 8.389603 CCGCAAAAGAAAACAATGCATTATTAT 58.610 29.630 12.53 2.54 36.84 1.28
391 396 9.757859 CGCAAAAGAAAACAATGCATTATTATT 57.242 25.926 12.53 8.46 36.84 1.40
426 431 6.042638 AGAAAAGCTATTCTAGTGTGCAGA 57.957 37.500 0.00 0.00 37.88 4.26
427 432 6.105333 AGAAAAGCTATTCTAGTGTGCAGAG 58.895 40.000 0.00 0.00 37.88 3.35
446 453 1.800805 GGATACTGTGCATGGATCCG 58.199 55.000 15.33 0.00 0.00 4.18
526 533 5.782893 TGTTTCAAAGAGTTACATTGGGG 57.217 39.130 0.00 0.00 0.00 4.96
533 541 6.609616 TCAAAGAGTTACATTGGGGTTTCTTT 59.390 34.615 0.00 0.00 34.87 2.52
589 597 2.264005 AACCGTGTATCAGCAAACCA 57.736 45.000 0.00 0.00 0.00 3.67
646 655 5.616645 GCACAACGAAACATGATGATACACA 60.617 40.000 0.00 0.00 0.00 3.72
689 699 6.253942 CGAACGAAACATTTTAAAACCAGGTT 59.746 34.615 1.97 0.00 0.00 3.50
693 703 9.251792 ACGAAACATTTTAAAACCAGGTTAATC 57.748 29.630 4.87 1.88 0.00 1.75
770 816 5.517477 CCACTCTCTATATTGCTCCCCTCTA 60.517 48.000 0.00 0.00 0.00 2.43
791 837 7.387948 CCTCTATAATTTTGTTCCGGGAGTATG 59.612 40.741 0.00 0.00 0.00 2.39
792 838 8.025270 TCTATAATTTTGTTCCGGGAGTATGA 57.975 34.615 0.00 0.00 0.00 2.15
793 839 8.487848 TCTATAATTTTGTTCCGGGAGTATGAA 58.512 33.333 0.00 0.00 0.00 2.57
794 840 5.897377 AATTTTGTTCCGGGAGTATGAAG 57.103 39.130 0.00 0.00 0.00 3.02
795 841 4.627284 TTTTGTTCCGGGAGTATGAAGA 57.373 40.909 0.00 0.00 0.00 2.87
796 842 4.627284 TTTGTTCCGGGAGTATGAAGAA 57.373 40.909 0.00 0.00 0.00 2.52
797 843 3.604875 TGTTCCGGGAGTATGAAGAAC 57.395 47.619 0.00 0.00 35.35 3.01
798 844 2.901192 TGTTCCGGGAGTATGAAGAACA 59.099 45.455 0.00 0.00 40.76 3.18
822 868 1.072331 GAAGGTTCTGTCCCTGCTTGA 59.928 52.381 0.00 0.00 30.99 3.02
834 880 1.228245 TGCTTGAACAGGCCACTCC 60.228 57.895 5.01 0.00 31.78 3.85
841 887 0.625849 AACAGGCCACTCCCATTAGG 59.374 55.000 5.01 0.00 34.51 2.69
858 904 7.360575 CCATTAGGGCGTCAATAATAGTAAC 57.639 40.000 0.00 0.00 0.00 2.50
859 905 7.159372 CCATTAGGGCGTCAATAATAGTAACT 58.841 38.462 0.00 0.00 0.00 2.24
879 925 1.804151 TGCAGAAGCCAAACGATGTAC 59.196 47.619 0.00 0.00 41.13 2.90
898 944 1.076533 CCCCTCATGTTCGTTCGTCG 61.077 60.000 0.00 0.00 41.41 5.12
932 978 4.357142 CCAAATAGTCAACTGCATGCATC 58.643 43.478 22.97 9.53 0.00 3.91
973 1019 2.336809 CGATAGAGGCCGGCACTC 59.663 66.667 30.85 28.97 39.76 3.51
1372 1427 3.857854 ACGTCGGTCGATCGTCGG 61.858 66.667 33.58 19.68 43.46 4.79
1433 1492 1.065701 TGTGTTTGCGGCGTTGTTAAT 59.934 42.857 9.37 0.00 0.00 1.40
1562 1621 3.557264 CCCGGATTATGGCCTTCTACTTC 60.557 52.174 0.73 0.00 0.00 3.01
1625 1684 1.729881 GGTACCTACCTACGTGCGG 59.270 63.158 4.06 0.38 43.10 5.69
1701 1768 3.391965 CTCTCTGATGCATTCCTACTGC 58.608 50.000 0.00 0.00 40.10 4.40
1739 1806 2.935042 GTGTAGACGATGATCATCCGG 58.065 52.381 26.30 17.18 34.40 5.14
1857 1924 4.084171 CGGAGCTACTAAATCACATGCATG 60.084 45.833 25.09 25.09 0.00 4.06
1858 1925 5.059161 GGAGCTACTAAATCACATGCATGA 58.941 41.667 32.75 13.48 0.00 3.07
1906 1975 8.119226 CAGTAGCAAGCAACAAGATAAGATAAC 58.881 37.037 0.00 0.00 0.00 1.89
1922 1991 4.442706 AGATAACGCTGGGTTGAGTAATG 58.557 43.478 18.95 0.00 39.75 1.90
1948 2017 2.673368 GGAGTGCCTCTGTTTCATAACG 59.327 50.000 2.79 0.00 37.06 3.18
1995 2064 1.302511 TCGTGCCTGGGAAGCTTTC 60.303 57.895 0.00 0.00 0.00 2.62
2018 2087 4.272489 TCATGTCCATCTTCCAATGGTTC 58.728 43.478 0.00 0.02 45.46 3.62
2090 2159 2.522638 CGCCTTCAATCGCGGGTAC 61.523 63.158 6.13 0.00 44.57 3.34
2091 2160 2.522638 GCCTTCAATCGCGGGTACG 61.523 63.158 6.13 0.00 44.63 3.67
2092 2161 1.153706 CCTTCAATCGCGGGTACGT 60.154 57.895 6.13 0.00 43.45 3.57
2093 2162 0.101040 CCTTCAATCGCGGGTACGTA 59.899 55.000 6.13 0.00 43.45 3.57
2134 2204 0.948623 CATGTCGCACTCCAACCGAA 60.949 55.000 0.00 0.00 32.31 4.30
2141 2211 2.215196 GCACTCCAACCGAAAACTACA 58.785 47.619 0.00 0.00 0.00 2.74
2155 2225 6.145209 CCGAAAACTACATGCTAGAGATGATG 59.855 42.308 8.71 0.00 0.00 3.07
2215 2285 3.127030 GCTTCTACCTCAATTTGAACGGG 59.873 47.826 8.94 5.83 0.00 5.28
2386 2456 1.406341 GGCATCAACGGCTACAAGGTA 60.406 52.381 0.00 0.00 0.00 3.08
2412 2482 4.499183 AGTTTCTGATCGACCAACAGATC 58.501 43.478 12.00 9.48 42.52 2.75
2441 2511 4.450122 CACATGCACGCACGCTCC 62.450 66.667 0.00 0.00 0.00 4.70
2444 2514 3.197790 ATGCACGCACGCTCCATC 61.198 61.111 0.00 0.00 0.00 3.51
2451 2521 2.887568 CACGCTCCATCCGACTGC 60.888 66.667 0.00 0.00 0.00 4.40
2453 2523 1.753078 ACGCTCCATCCGACTGCTA 60.753 57.895 0.00 0.00 0.00 3.49
3281 3351 4.134187 CACTACAAGTGGCGCGCG 62.134 66.667 28.44 28.44 42.35 6.86
3326 3396 1.315257 GCATGGCCATGTCGTTCCTT 61.315 55.000 39.08 4.85 40.80 3.36
3581 3651 2.300437 GGCCACTGTACTTGAGAAGTCT 59.700 50.000 0.00 0.00 41.77 3.24
3592 3662 1.478510 TGAGAAGTCTCGATGAAGGCC 59.521 52.381 0.00 0.00 45.72 5.19
3601 3671 1.215647 GATGAAGGCCGTCGACACT 59.784 57.895 17.16 7.48 0.00 3.55
3613 3683 0.966920 TCGACACTCAACCCTTCCTC 59.033 55.000 0.00 0.00 0.00 3.71
3631 3701 1.833630 CTCACCTGTAGATCCTGCCAA 59.166 52.381 0.00 0.00 0.00 4.52
3642 3712 2.890808 TCCTGCCAAGATGATACGAC 57.109 50.000 0.00 0.00 0.00 4.34
3643 3713 2.107366 TCCTGCCAAGATGATACGACA 58.893 47.619 0.00 0.00 0.00 4.35
3644 3714 2.700371 TCCTGCCAAGATGATACGACAT 59.300 45.455 0.00 0.00 0.00 3.06
3645 3715 3.895041 TCCTGCCAAGATGATACGACATA 59.105 43.478 0.00 0.00 0.00 2.29
3646 3716 3.990469 CCTGCCAAGATGATACGACATAC 59.010 47.826 0.00 0.00 0.00 2.39
3648 3718 3.316868 TGCCAAGATGATACGACATACGA 59.683 43.478 0.00 0.00 45.77 3.43
3705 3821 2.126467 CTGCAATTGTTGGTCGTTTGG 58.874 47.619 7.40 0.00 0.00 3.28
3727 3843 6.353323 TGGTGTAGAATGAACAGACTTTTCA 58.647 36.000 6.51 6.51 37.38 2.69
3729 3845 7.012327 TGGTGTAGAATGAACAGACTTTTCAAG 59.988 37.037 8.07 0.00 36.57 3.02
3736 3852 3.885484 ACAGACTTTTCAAGCATGTCG 57.115 42.857 0.00 0.00 33.40 4.35
3744 3860 1.317613 TCAAGCATGTCGGCAGTTTT 58.682 45.000 0.00 0.00 35.83 2.43
3749 3865 0.240945 CATGTCGGCAGTTTTCCACC 59.759 55.000 0.00 0.00 0.00 4.61
3764 3880 6.151648 AGTTTTCCACCATGATCAACTATGTG 59.848 38.462 0.00 3.19 0.00 3.21
3791 3907 7.593273 GTGCAAATGTACAATACAAAGCTAACA 59.407 33.333 0.00 0.00 42.76 2.41
3810 3965 3.067106 ACAATAGCAAACAGAGTGACCG 58.933 45.455 0.00 0.00 0.00 4.79
3850 4005 4.226427 TGAATCAACAGATCAAGGAGGG 57.774 45.455 0.00 0.00 0.00 4.30
3851 4006 3.845992 TGAATCAACAGATCAAGGAGGGA 59.154 43.478 0.00 0.00 0.00 4.20
3853 4008 3.920231 TCAACAGATCAAGGAGGGATG 57.080 47.619 0.00 0.00 0.00 3.51
3870 4025 2.756760 GGATGATGTGCATTTGAGGTGT 59.243 45.455 0.00 0.00 37.34 4.16
3884 4039 3.754965 TGAGGTGTGGGAATCAAGAAAG 58.245 45.455 0.00 0.00 0.00 2.62
3906 4063 9.404348 GAAAGAGATAGCTTTTTCAAGAAAAGG 57.596 33.333 16.61 11.63 42.03 3.11
3910 4067 9.186323 GAGATAGCTTTTTCAAGAAAAGGAAAC 57.814 33.333 18.02 6.86 40.83 2.78
3915 4072 3.300239 TTCAAGAAAAGGAAACCCCGA 57.700 42.857 0.00 0.00 40.87 5.14
3958 4115 2.490903 AGATGTGCAACTGATTTCTGCC 59.509 45.455 0.00 0.00 38.04 4.85
4011 4168 2.289072 TGGAGCTTTTCTTCAGACCTCG 60.289 50.000 0.00 0.00 0.00 4.63
4027 4184 1.472552 CCTCGACCACACAACACTTGA 60.473 52.381 0.00 0.00 0.00 3.02
4035 4192 2.095969 CACACAACACTTGACAACACGT 60.096 45.455 0.00 0.00 0.00 4.49
4100 4258 9.177608 AGAATAAAAAGCATGCATACAAGTAGA 57.822 29.630 21.98 0.00 0.00 2.59
4120 4278 2.308722 GGGCCTCCCAACTCCATGA 61.309 63.158 0.84 0.00 44.65 3.07
4191 4353 7.044181 TCAACCATCACAATTTAAAGCAACAA 58.956 30.769 0.00 0.00 0.00 2.83
4352 4515 0.547553 GTCTCCTACTCCCTCCGTCT 59.452 60.000 0.00 0.00 0.00 4.18
4359 4522 1.258676 ACTCCCTCCGTCTGAGAAAC 58.741 55.000 0.00 0.00 44.42 2.78
4368 4531 1.344763 CGTCTGAGAAACCTTGTCCCT 59.655 52.381 0.00 0.00 0.00 4.20
4390 4553 5.416952 CCTAGCTTGTCTTTCAAATGGATGT 59.583 40.000 0.00 0.00 35.48 3.06
4391 4554 6.599244 CCTAGCTTGTCTTTCAAATGGATGTA 59.401 38.462 0.00 0.00 35.48 2.29
4396 4559 8.341173 GCTTGTCTTTCAAATGGATGTATCTAG 58.659 37.037 0.00 0.00 35.48 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.867174 TGTCTGTCGATACAAGGTTTACATG 59.133 40.000 0.00 0.00 34.49 3.21
59 63 4.163552 GACAATGTTATCGTGTCTGTCGA 58.836 43.478 0.00 0.00 41.45 4.20
72 76 2.369203 TGACGGAGGGTTGACAATGTTA 59.631 45.455 0.00 0.00 0.00 2.41
104 108 1.279271 ACACATAACACCTCTCCCAGC 59.721 52.381 0.00 0.00 0.00 4.85
106 110 3.750371 CAAACACATAACACCTCTCCCA 58.250 45.455 0.00 0.00 0.00 4.37
111 115 2.147958 TCGGCAAACACATAACACCTC 58.852 47.619 0.00 0.00 0.00 3.85
113 117 1.877443 ACTCGGCAAACACATAACACC 59.123 47.619 0.00 0.00 0.00 4.16
118 122 1.404449 CGGGTACTCGGCAAACACATA 60.404 52.381 7.42 0.00 0.00 2.29
119 123 0.672401 CGGGTACTCGGCAAACACAT 60.672 55.000 7.42 0.00 0.00 3.21
120 124 1.301087 CGGGTACTCGGCAAACACA 60.301 57.895 7.42 0.00 0.00 3.72
121 125 1.005867 TCGGGTACTCGGCAAACAC 60.006 57.895 16.55 0.00 0.00 3.32
134 139 2.413310 AACACAACAAAGAGTCGGGT 57.587 45.000 0.00 0.00 0.00 5.28
139 144 6.183360 GCAGACTAGAAAACACAACAAAGAGT 60.183 38.462 0.00 0.00 0.00 3.24
148 153 2.526304 AGCGCAGACTAGAAAACACA 57.474 45.000 11.47 0.00 0.00 3.72
165 170 1.247567 TAGTCTTGCCTTTGCCAAGC 58.752 50.000 0.00 0.00 36.33 4.01
181 186 3.149196 CAAAGCCAACACTCACCATAGT 58.851 45.455 0.00 0.00 0.00 2.12
184 189 1.682854 CACAAAGCCAACACTCACCAT 59.317 47.619 0.00 0.00 0.00 3.55
237 242 1.115326 GGCACTCAACAAAGGCCCTT 61.115 55.000 0.00 0.00 38.70 3.95
346 351 2.802774 GCGGGGAATAATGCATTGTTGG 60.803 50.000 24.00 12.11 0.00 3.77
362 367 1.530720 GCATTGTTTTCTTTTGCGGGG 59.469 47.619 0.00 0.00 0.00 5.73
363 368 2.208431 TGCATTGTTTTCTTTTGCGGG 58.792 42.857 0.00 0.00 36.11 6.13
365 370 9.757859 AATAATAATGCATTGTTTTCTTTTGCG 57.242 25.926 23.95 0.00 36.11 4.85
400 405 6.467677 TGCACACTAGAATAGCTTTTCTCTT 58.532 36.000 20.81 8.22 44.39 2.85
418 423 1.338105 TGCACAGTATCCTCTGCACAC 60.338 52.381 0.00 0.00 37.64 3.82
426 431 1.345741 CGGATCCATGCACAGTATCCT 59.654 52.381 13.41 0.00 35.06 3.24
427 432 1.070758 ACGGATCCATGCACAGTATCC 59.929 52.381 13.41 8.47 34.08 2.59
446 453 1.197721 CTCAAAGCAACCATGGACGAC 59.802 52.381 21.47 4.66 0.00 4.34
565 573 4.026310 GGTTTGCTGATACACGGTTATACG 60.026 45.833 0.00 0.00 40.31 3.06
589 597 8.496707 AAAAAGAATGCACTTGTTTTGAATCT 57.503 26.923 13.46 1.41 38.85 2.40
646 655 4.796312 CGTTCGGTTTTGTCTTGTTTCAAT 59.204 37.500 0.00 0.00 0.00 2.57
689 699 7.392393 GGGCTACTTTTTAGGTTGTCAAGATTA 59.608 37.037 0.00 0.00 0.00 1.75
693 703 4.083484 CGGGCTACTTTTTAGGTTGTCAAG 60.083 45.833 0.00 0.00 0.00 3.02
770 816 7.343357 TCTTCATACTCCCGGAACAAAATTAT 58.657 34.615 0.73 0.00 0.00 1.28
798 844 1.349357 GCAGGGACAGAACCTTCTTCT 59.651 52.381 0.00 0.00 35.78 2.85
822 868 0.625849 CCTAATGGGAGTGGCCTGTT 59.374 55.000 3.32 0.00 37.23 3.16
834 880 7.117812 CAGTTACTATTATTGACGCCCTAATGG 59.882 40.741 0.00 0.00 37.09 3.16
841 887 5.047847 TCTGCAGTTACTATTATTGACGCC 58.952 41.667 14.67 0.00 0.00 5.68
858 904 0.877071 ACATCGTTTGGCTTCTGCAG 59.123 50.000 7.63 7.63 41.91 4.41
859 905 1.804151 GTACATCGTTTGGCTTCTGCA 59.196 47.619 0.00 0.00 41.91 4.41
879 925 1.076533 CGACGAACGAACATGAGGGG 61.077 60.000 0.00 0.00 45.77 4.79
898 944 3.117888 TGACTATTTGGGAATGGAGGAGC 60.118 47.826 0.00 0.00 0.00 4.70
937 983 1.216977 CCCAGGTTGTGCATGCATG 59.783 57.895 25.64 22.70 0.00 4.06
986 1032 0.108138 CTCCATCGATTATCGCCCCC 60.108 60.000 10.02 0.00 40.21 5.40
1256 1311 2.718073 CGGGTGAAGGGGACGTAGG 61.718 68.421 0.00 0.00 0.00 3.18
1361 1416 0.597637 ATTCATGGCCGACGATCGAC 60.598 55.000 24.34 15.51 43.74 4.20
1372 1427 1.873069 CGAGCAGAGGAGATTCATGGC 60.873 57.143 0.00 0.00 0.00 4.40
1399 1458 0.040425 AACACACGCGAAATCAAGGC 60.040 50.000 15.93 0.00 0.00 4.35
1433 1492 1.835531 GACCCGAACCCTCCTAATCAA 59.164 52.381 0.00 0.00 0.00 2.57
1562 1621 0.173481 TTCCGACGAAGCTGATGAGG 59.827 55.000 0.00 0.00 0.00 3.86
1625 1684 4.355543 TCAAGTTTTATCTCATTGGCGC 57.644 40.909 0.00 0.00 0.00 6.53
1739 1806 3.723348 GGAAACGTCAGCCGGTGC 61.723 66.667 1.90 0.00 42.24 5.01
1881 1950 7.010552 CGTTATCTTATCTTGTTGCTTGCTACT 59.989 37.037 8.43 0.00 0.00 2.57
1906 1975 1.382522 ATGCATTACTCAACCCAGCG 58.617 50.000 0.00 0.00 0.00 5.18
1948 2017 1.155042 CAGAGACACTTGCTTCCTGC 58.845 55.000 0.00 0.00 43.25 4.85
2090 2159 8.088365 TGTAGAATGATGGATGGATAAGTTACG 58.912 37.037 0.00 0.00 0.00 3.18
2091 2160 9.950496 ATGTAGAATGATGGATGGATAAGTTAC 57.050 33.333 0.00 0.00 0.00 2.50
2092 2161 9.948964 CATGTAGAATGATGGATGGATAAGTTA 57.051 33.333 0.00 0.00 0.00 2.24
2093 2162 8.443176 ACATGTAGAATGATGGATGGATAAGTT 58.557 33.333 0.00 0.00 0.00 2.66
2134 2204 7.069208 TCACTCATCATCTCTAGCATGTAGTTT 59.931 37.037 0.00 0.00 0.00 2.66
2141 2211 5.070714 AGCTTTCACTCATCATCTCTAGCAT 59.929 40.000 0.00 0.00 0.00 3.79
2155 2225 4.332819 ACACAACACAAGTAGCTTTCACTC 59.667 41.667 0.00 0.00 0.00 3.51
2386 2456 3.005050 TGTTGGTCGATCAGAAACTACGT 59.995 43.478 0.00 0.00 0.00 3.57
2412 2482 1.875813 GCATGTGCTCCTCGTCGAG 60.876 63.158 15.53 15.53 38.21 4.04
2441 2511 6.293081 CCTGAAATTACATTAGCAGTCGGATG 60.293 42.308 0.00 0.00 0.00 3.51
2444 2514 4.876107 ACCTGAAATTACATTAGCAGTCGG 59.124 41.667 0.00 0.00 0.00 4.79
2451 2521 5.799936 CGCCAAACACCTGAAATTACATTAG 59.200 40.000 0.00 0.00 0.00 1.73
2453 2523 4.555262 CGCCAAACACCTGAAATTACATT 58.445 39.130 0.00 0.00 0.00 2.71
3281 3351 2.174319 GCTCGGGATGAAGTTCCGC 61.174 63.158 0.00 0.00 43.10 5.54
3282 3352 1.878522 CGCTCGGGATGAAGTTCCG 60.879 63.158 0.00 0.00 44.59 4.30
3449 3519 1.330655 GGATGGAGAAGAGCCCGTCA 61.331 60.000 0.00 0.00 39.61 4.35
3581 3651 2.337246 TGTCGACGGCCTTCATCGA 61.337 57.895 11.62 11.54 42.27 3.59
3592 3662 0.666577 GGAAGGGTTGAGTGTCGACG 60.667 60.000 11.62 0.00 31.46 5.12
3601 3671 2.158219 TCTACAGGTGAGGAAGGGTTGA 60.158 50.000 0.00 0.00 0.00 3.18
3613 3683 1.833630 TCTTGGCAGGATCTACAGGTG 59.166 52.381 0.00 0.00 0.00 4.00
3631 3701 3.805971 TGTCGTCGTATGTCGTATCATCT 59.194 43.478 1.64 0.00 40.80 2.90
3642 3712 5.344207 TCACTAGATCATGTCGTCGTATG 57.656 43.478 0.00 0.00 0.00 2.39
3643 3713 6.183360 GCTATCACTAGATCATGTCGTCGTAT 60.183 42.308 0.00 0.00 35.67 3.06
3644 3714 5.120363 GCTATCACTAGATCATGTCGTCGTA 59.880 44.000 0.00 0.00 35.67 3.43
3645 3715 4.083749 GCTATCACTAGATCATGTCGTCGT 60.084 45.833 0.00 0.00 35.67 4.34
3646 3716 4.083802 TGCTATCACTAGATCATGTCGTCG 60.084 45.833 0.00 0.00 35.67 5.12
3647 3717 5.363979 TGCTATCACTAGATCATGTCGTC 57.636 43.478 0.00 0.00 35.67 4.20
3648 3718 5.242615 ACATGCTATCACTAGATCATGTCGT 59.757 40.000 0.00 0.00 41.86 4.34
3727 3843 0.598065 GGAAAACTGCCGACATGCTT 59.402 50.000 0.00 0.00 0.00 3.91
3729 3845 0.387239 GTGGAAAACTGCCGACATGC 60.387 55.000 0.00 0.00 0.00 4.06
3736 3852 2.170166 TGATCATGGTGGAAAACTGCC 58.830 47.619 0.00 0.00 0.00 4.85
3744 3860 3.523157 ACCACATAGTTGATCATGGTGGA 59.477 43.478 25.57 0.00 38.99 4.02
3749 3865 4.968812 TTGCACCACATAGTTGATCATG 57.031 40.909 0.00 0.00 0.00 3.07
3764 3880 5.469479 AGCTTTGTATTGTACATTTGCACC 58.531 37.500 0.00 0.00 38.68 5.01
3791 3907 3.067106 CACGGTCACTCTGTTTGCTATT 58.933 45.455 0.00 0.00 32.67 1.73
3810 3965 4.944619 TCATCTGATCCACTATGGTCAC 57.055 45.455 0.00 0.00 39.03 3.67
3850 4005 3.428452 CCACACCTCAAATGCACATCATC 60.428 47.826 0.00 0.00 33.40 2.92
3851 4006 2.494471 CCACACCTCAAATGCACATCAT 59.506 45.455 0.00 0.00 36.87 2.45
3853 4008 1.203052 CCCACACCTCAAATGCACATC 59.797 52.381 0.00 0.00 0.00 3.06
3870 4025 5.965033 AGCTATCTCTTTCTTGATTCCCA 57.035 39.130 0.00 0.00 0.00 4.37
3884 4039 9.186323 GTTTCCTTTTCTTGAAAAAGCTATCTC 57.814 33.333 9.41 0.00 36.26 2.75
3900 4055 3.243636 GGTTTCTTCGGGGTTTCCTTTTC 60.244 47.826 0.00 0.00 0.00 2.29
3905 4062 1.694844 TTGGTTTCTTCGGGGTTTCC 58.305 50.000 0.00 0.00 0.00 3.13
3906 4063 2.953648 TCTTTGGTTTCTTCGGGGTTTC 59.046 45.455 0.00 0.00 0.00 2.78
3910 4067 1.611977 GGTTCTTTGGTTTCTTCGGGG 59.388 52.381 0.00 0.00 0.00 5.73
3915 4072 4.803452 TCATCAGGGTTCTTTGGTTTCTT 58.197 39.130 0.00 0.00 0.00 2.52
3958 4115 0.031178 GCAAACAGCTGGTGAACTGG 59.969 55.000 19.93 0.00 41.15 4.00
3981 4138 1.072965 AGAAAAGCTCCAGTGTCAGGG 59.927 52.381 0.00 0.00 0.00 4.45
4011 4168 2.486203 TGTTGTCAAGTGTTGTGTGGTC 59.514 45.455 0.00 0.00 0.00 4.02
4027 4184 7.066645 TGTGCTCTATAGAATAGTACGTGTTGT 59.933 37.037 3.57 0.00 0.00 3.32
4035 4192 9.131791 TGATTGTGTGTGCTCTATAGAATAGTA 57.868 33.333 3.57 0.00 0.00 1.82
4100 4258 1.544917 ATGGAGTTGGGAGGCCCTT 60.545 57.895 0.00 0.00 45.70 3.95
4120 4278 5.321102 TGTTATGTTGGCAGGAGTTTACAT 58.679 37.500 4.37 4.37 0.00 2.29
4203 4365 4.265904 TGAAGTTGTCTTATTGGCTCGA 57.734 40.909 0.00 0.00 33.64 4.04
4352 4515 2.621070 AGCTAGGGACAAGGTTTCTCA 58.379 47.619 0.00 0.00 0.00 3.27
4359 4522 3.244561 TGAAAGACAAGCTAGGGACAAGG 60.245 47.826 0.00 0.00 0.00 3.61
4368 4531 8.049117 AGATACATCCATTTGAAAGACAAGCTA 58.951 33.333 0.00 0.00 39.77 3.32
4390 4553 7.891498 TGTATCACCAAGTTAGTGCTAGATA 57.109 36.000 0.00 0.00 35.14 1.98
4391 4554 6.791867 TGTATCACCAAGTTAGTGCTAGAT 57.208 37.500 0.00 0.00 35.14 1.98
4396 4559 4.513442 TGGATGTATCACCAAGTTAGTGC 58.487 43.478 0.00 0.00 35.14 4.40


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

AutoCloner maintained by Alex Coulton.