Multiple sequence alignment - TraesCS2D01G099300

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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 TraesCS2D01G099300 chr2D 100.000 3665 0 0 1 3665 51168341 51164677 0.000000e+00 6769.0
1 TraesCS2D01G099300 chr2A 87.868 2341 145 64 1 2229 52580655 52578342 0.000000e+00 2621.0
2 TraesCS2D01G099300 chr2A 94.203 1449 47 16 2249 3665 52578294 52576851 0.000000e+00 2176.0
3 TraesCS2D01G099300 chr2A 90.419 167 15 1 2877 3042 249754624 249754458 6.160000e-53 219.0
4 TraesCS2D01G099300 chr2A 78.922 204 28 8 3040 3243 52577093 52576905 1.380000e-24 124.0
5 TraesCS2D01G099300 chr2A 92.308 39 3 0 1227 1265 73180323 73180285 5.110000e-04 56.5
6 TraesCS2D01G099300 chr2B 93.240 932 60 3 1885 2814 79714641 79713711 0.000000e+00 1369.0
7 TraesCS2D01G099300 chr2B 86.945 766 51 14 1153 1880 79715448 79714694 0.000000e+00 815.0
8 TraesCS2D01G099300 chr2B 88.755 498 29 8 640 1115 79716027 79715535 5.270000e-163 584.0
9 TraesCS2D01G099300 chr2B 84.448 598 70 13 10 588 50764175 50763582 5.310000e-158 568.0
10 TraesCS2D01G099300 chr2B 91.358 162 14 0 2880 3041 76912138 76912299 4.760000e-54 222.0
11 TraesCS2D01G099300 chr1B 88.636 572 46 9 8 561 352332539 352331969 0.000000e+00 678.0
12 TraesCS2D01G099300 chr7B 88.462 572 48 8 8 561 217303887 217303316 0.000000e+00 675.0
13 TraesCS2D01G099300 chr7B 88.462 572 48 8 8 561 608187108 608187679 0.000000e+00 675.0
14 TraesCS2D01G099300 chr7B 84.797 592 70 12 14 589 15823824 15824411 8.830000e-161 577.0
15 TraesCS2D01G099300 chr5B 88.014 584 52 8 8 573 276898020 276897437 0.000000e+00 675.0
16 TraesCS2D01G099300 chr3B 88.462 572 48 8 8 561 758628266 758628837 0.000000e+00 675.0
17 TraesCS2D01G099300 chr3B 83.221 447 51 14 163 590 172725177 172724736 4.440000e-104 388.0
18 TraesCS2D01G099300 chr3B 86.452 155 19 1 904 1058 742306696 742306848 6.290000e-38 169.0
19 TraesCS2D01G099300 chrUn 88.307 573 49 8 8 562 399760414 399759842 0.000000e+00 671.0
20 TraesCS2D01G099300 chrUn 88.133 573 50 8 8 562 8241712 8241140 0.000000e+00 665.0
21 TraesCS2D01G099300 chr6D 88.328 574 47 10 8 562 420707084 420707656 0.000000e+00 671.0
22 TraesCS2D01G099300 chr6D 91.071 168 15 0 2875 3042 351233601 351233434 1.020000e-55 228.0
23 TraesCS2D01G099300 chr4B 88.475 564 47 5 17 562 424285809 424285246 0.000000e+00 665.0
24 TraesCS2D01G099300 chr4B 92.308 169 12 1 2873 3041 28724137 28724304 4.730000e-59 239.0
25 TraesCS2D01G099300 chr6B 82.051 585 73 19 20 585 299624373 299623802 1.540000e-128 470.0
26 TraesCS2D01G099300 chr5A 80.619 614 90 16 1 593 685970057 685969452 7.220000e-122 448.0
27 TraesCS2D01G099300 chr5A 86.047 86 7 5 508 592 225774758 225774839 1.810000e-13 87.9
28 TraesCS2D01G099300 chr6A 81.657 338 43 13 263 583 558403941 558404276 2.810000e-66 263.0
29 TraesCS2D01G099300 chr6A 91.071 168 15 0 2875 3042 492096068 492096235 1.020000e-55 228.0
30 TraesCS2D01G099300 chr3D 92.405 158 12 0 2885 3042 598889737 598889894 3.680000e-55 226.0
31 TraesCS2D01G099300 chr4D 91.358 162 14 0 2880 3041 75266909 75266748 4.760000e-54 222.0
32 TraesCS2D01G099300 chr4D 77.695 269 41 9 335 585 506735267 506735534 2.950000e-31 147.0
33 TraesCS2D01G099300 chr5D 90.419 167 16 0 2880 3046 330893583 330893417 1.710000e-53 220.0


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 TraesCS2D01G099300 chr2D 51164677 51168341 3664 True 6769.000000 6769 100.000000 1 3665 1 chr2D.!!$R1 3664
1 TraesCS2D01G099300 chr2A 52576851 52580655 3804 True 1640.333333 2621 86.997667 1 3665 3 chr2A.!!$R3 3664
2 TraesCS2D01G099300 chr2B 79713711 79716027 2316 True 922.666667 1369 89.646667 640 2814 3 chr2B.!!$R2 2174
3 TraesCS2D01G099300 chr2B 50763582 50764175 593 True 568.000000 568 84.448000 10 588 1 chr2B.!!$R1 578
4 TraesCS2D01G099300 chr1B 352331969 352332539 570 True 678.000000 678 88.636000 8 561 1 chr1B.!!$R1 553
5 TraesCS2D01G099300 chr7B 217303316 217303887 571 True 675.000000 675 88.462000 8 561 1 chr7B.!!$R1 553
6 TraesCS2D01G099300 chr7B 608187108 608187679 571 False 675.000000 675 88.462000 8 561 1 chr7B.!!$F2 553
7 TraesCS2D01G099300 chr7B 15823824 15824411 587 False 577.000000 577 84.797000 14 589 1 chr7B.!!$F1 575
8 TraesCS2D01G099300 chr5B 276897437 276898020 583 True 675.000000 675 88.014000 8 573 1 chr5B.!!$R1 565
9 TraesCS2D01G099300 chr3B 758628266 758628837 571 False 675.000000 675 88.462000 8 561 1 chr3B.!!$F2 553
10 TraesCS2D01G099300 chrUn 399759842 399760414 572 True 671.000000 671 88.307000 8 562 1 chrUn.!!$R2 554
11 TraesCS2D01G099300 chrUn 8241140 8241712 572 True 665.000000 665 88.133000 8 562 1 chrUn.!!$R1 554
12 TraesCS2D01G099300 chr6D 420707084 420707656 572 False 671.000000 671 88.328000 8 562 1 chr6D.!!$F1 554
13 TraesCS2D01G099300 chr4B 424285246 424285809 563 True 665.000000 665 88.475000 17 562 1 chr4B.!!$R1 545
14 TraesCS2D01G099300 chr6B 299623802 299624373 571 True 470.000000 470 82.051000 20 585 1 chr6B.!!$R1 565
15 TraesCS2D01G099300 chr5A 685969452 685970057 605 True 448.000000 448 80.619000 1 593 1 chr5A.!!$R1 592

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
188 193 0.546598 AATAAAGGTCTCCCCGCCTG 59.453 55.0 0.00 0.0 38.74 4.85 F
499 507 1.002366 CAGTGCTTGTAGTCATCGCC 58.998 55.0 0.00 0.0 0.00 5.54 F
1594 1713 1.298859 GCCGTCGAGTCAATTTGCCT 61.299 55.0 0.00 0.0 0.00 4.75 F
2279 2505 0.312102 GTGCTCAACTTTGGTGCCTC 59.688 55.0 5.76 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1669 0.033991 TCCCTCTCTTCTCGTCCCTG 60.034 60.000 0.00 0.00 0.00 4.45 R
1613 1732 0.249868 CGAGCTGGTGGAAGACAACA 60.250 55.000 0.00 0.00 46.67 3.33 R
2658 2884 2.506231 TCCAGTGAACAACCACTACCAA 59.494 45.455 0.00 0.00 44.87 3.67 R
3212 3438 2.632512 TGAGTGGCATTGTACTCTCACA 59.367 45.455 17.86 3.15 42.86 3.58 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
116 118 5.310720 AGTCGTTTCTTTCAGTTTTGCTT 57.689 34.783 0.00 0.00 0.00 3.91
150 155 1.467734 GCTTAGGAAGACGAGACGACA 59.532 52.381 0.00 0.00 0.00 4.35
151 156 2.097791 GCTTAGGAAGACGAGACGACAT 59.902 50.000 0.00 0.00 0.00 3.06
188 193 0.546598 AATAAAGGTCTCCCCGCCTG 59.453 55.000 0.00 0.00 38.74 4.85
305 312 4.090786 TCGTTATTCGTCTACGTTCGTGTA 59.909 41.667 8.14 0.00 40.80 2.90
373 380 1.133025 GTTGCTGTTCTTGTGCACTGT 59.867 47.619 19.41 0.00 36.37 3.55
377 384 1.334869 CTGTTCTTGTGCACTGTTCCC 59.665 52.381 19.41 2.38 0.00 3.97
392 399 3.809013 CCCACGGGGCCTTAGCAT 61.809 66.667 0.00 0.00 42.56 3.79
406 413 4.384056 CCTTAGCATGATGACTTTCCGAT 58.616 43.478 0.00 0.00 0.00 4.18
461 469 2.498941 GGAGGGGCGATGACGATGA 61.499 63.158 0.00 0.00 42.66 2.92
473 481 2.202610 CGATGACGCGCCTTCTGA 60.203 61.111 5.73 0.00 0.00 3.27
499 507 1.002366 CAGTGCTTGTAGTCATCGCC 58.998 55.000 0.00 0.00 0.00 5.54
503 511 1.432270 GCTTGTAGTCATCGCCAGGC 61.432 60.000 0.00 0.00 0.00 4.85
564 589 9.000486 TCATGATTGAAGATGAATAGATCAAGC 58.000 33.333 0.00 0.00 42.54 4.01
758 790 2.041265 TCCCTCTTCCTCCCCTGC 59.959 66.667 0.00 0.00 0.00 4.85
807 841 3.104766 TCGTCGGCGATGGAGTAC 58.895 61.111 27.09 5.92 42.81 2.73
941 995 3.910490 AGCATCCTCTCGCCTCGC 61.910 66.667 0.00 0.00 0.00 5.03
977 1032 3.390521 CACCCAGCCGTCCTAGCA 61.391 66.667 0.00 0.00 0.00 3.49
983 1038 4.078516 GCCGTCCTAGCAACCCGT 62.079 66.667 0.00 0.00 0.00 5.28
1009 1064 2.117156 CCGCAAGCCATGGAGAAGG 61.117 63.158 18.40 7.63 0.00 3.46
1020 1075 3.470567 GAGAAGGCGTCGCACGTG 61.471 66.667 20.50 12.28 44.73 4.49
1108 1165 2.158623 TGCATCCTGAGTTGACCTTTGT 60.159 45.455 0.00 0.00 0.00 2.83
1115 1172 7.406031 TCCTGAGTTGACCTTTGTATACTAG 57.594 40.000 4.17 1.87 0.00 2.57
1117 1174 8.111545 TCCTGAGTTGACCTTTGTATACTAGTA 58.888 37.037 4.77 4.77 0.00 1.82
1118 1175 8.407064 CCTGAGTTGACCTTTGTATACTAGTAG 58.593 40.741 8.85 0.00 0.00 2.57
1151 1257 7.334671 ACATATCTCGCGTCTTCTCAGATTATA 59.665 37.037 5.77 0.00 0.00 0.98
1169 1275 8.516234 CAGATTATATAGGTTGCTCGTTCTAGT 58.484 37.037 0.00 0.00 0.00 2.57
1170 1276 9.736414 AGATTATATAGGTTGCTCGTTCTAGTA 57.264 33.333 0.00 0.00 0.00 1.82
1182 1288 6.988580 TGCTCGTTCTAGTAGTATGCTTAGTA 59.011 38.462 0.00 0.00 29.76 1.82
1272 1391 3.440415 CGAAGCCCGGAAAAGCCC 61.440 66.667 0.73 0.00 33.91 5.19
1372 1491 6.834451 CCATTCCTCCTAGTAGTCAGTTTCTA 59.166 42.308 0.00 0.00 0.00 2.10
1550 1669 2.072298 GTGACTGTCATTCTCACAGCC 58.928 52.381 14.37 0.00 44.50 4.85
1586 1705 1.511305 GAAGGATGCCGTCGAGTCA 59.489 57.895 0.00 0.00 0.00 3.41
1594 1713 1.298859 GCCGTCGAGTCAATTTGCCT 61.299 55.000 0.00 0.00 0.00 4.75
1613 1732 3.879321 GCCTTGAATCCAACCTCTCCAAT 60.879 47.826 0.00 0.00 0.00 3.16
1720 1839 6.817765 TGACATCTTGGTAAAATGAAGTCC 57.182 37.500 0.00 0.00 0.00 3.85
1782 1926 6.157820 TGAATGAGGATGAGTTGGGTAACATA 59.842 38.462 0.00 0.00 39.30 2.29
1783 1927 6.770286 ATGAGGATGAGTTGGGTAACATAT 57.230 37.500 0.00 0.00 39.30 1.78
1784 1928 7.872061 ATGAGGATGAGTTGGGTAACATATA 57.128 36.000 0.00 0.00 39.30 0.86
1785 1929 7.062749 TGAGGATGAGTTGGGTAACATATAC 57.937 40.000 0.00 0.00 39.30 1.47
1786 1930 6.097915 AGGATGAGTTGGGTAACATATACG 57.902 41.667 0.00 0.00 39.30 3.06
1812 1956 2.050691 GTTAACAATGCAGCGGTTGTG 58.949 47.619 14.64 0.00 38.47 3.33
1880 2024 3.118629 GCAGAGACATGGGTACTGATTCA 60.119 47.826 12.95 0.00 35.14 2.57
1881 2025 4.444022 GCAGAGACATGGGTACTGATTCAT 60.444 45.833 12.95 0.00 35.14 2.57
1884 2028 5.426509 AGAGACATGGGTACTGATTCATTCA 59.573 40.000 0.00 0.00 0.00 2.57
1888 2081 7.616935 AGACATGGGTACTGATTCATTCATTTT 59.383 33.333 0.00 0.00 32.72 1.82
1919 2112 7.753309 TCTTAACCTTTTGCAACTTAGCATA 57.247 32.000 0.00 0.00 45.19 3.14
1920 2113 8.348285 TCTTAACCTTTTGCAACTTAGCATAT 57.652 30.769 0.00 0.00 45.19 1.78
1962 2155 8.454106 AGAACTACAATTTCATCTGTAACATGC 58.546 33.333 0.00 0.00 0.00 4.06
2133 2331 0.542333 GGGTTACAGAAGCCCTCCTC 59.458 60.000 0.00 0.00 45.89 3.71
2151 2349 5.450453 CTCCTCCCTCTACTGAAACTATCA 58.550 45.833 0.00 0.00 36.38 2.15
2169 2367 3.140325 TCAAAGTTTGGAGCGAGGATT 57.860 42.857 15.47 0.00 0.00 3.01
2175 2373 2.749621 GTTTGGAGCGAGGATTGTCAAT 59.250 45.455 0.00 0.00 0.00 2.57
2177 2375 1.278985 TGGAGCGAGGATTGTCAATGT 59.721 47.619 1.88 0.00 0.00 2.71
2210 2408 1.517257 CAGAGCTGAAGGTACGCCG 60.517 63.158 0.00 0.00 40.50 6.46
2232 2430 5.444122 CGTCAGTTGAAATTCTTTCTGACC 58.556 41.667 23.98 14.82 38.29 4.02
2279 2505 0.312102 GTGCTCAACTTTGGTGCCTC 59.688 55.000 5.76 0.00 0.00 4.70
2517 2743 2.661866 GTCAACTGCGTGCGTCCT 60.662 61.111 0.00 0.00 0.00 3.85
2658 2884 2.567169 TCAGACGGAGATGGTGAATGTT 59.433 45.455 0.00 0.00 0.00 2.71
2779 3005 8.809159 TTCTTGCATTTTCGACATGAATAAAA 57.191 26.923 0.00 3.12 36.22 1.52
2876 3102 6.597672 TGAAACAATTCACAGTAACACAGTCT 59.402 34.615 0.00 0.00 40.59 3.24
2900 3126 8.854117 TCTATTACTTCCTCCGTTCCTAAATAC 58.146 37.037 0.00 0.00 0.00 1.89
2903 3129 6.309389 ACTTCCTCCGTTCCTAAATACAAT 57.691 37.500 0.00 0.00 0.00 2.71
2907 3133 4.386711 CTCCGTTCCTAAATACAATCCCC 58.613 47.826 0.00 0.00 0.00 4.81
2922 3148 6.347061 ACAATCCCCTTTAGAGATTCCAAT 57.653 37.500 0.00 0.00 0.00 3.16
3000 3226 5.518848 ACATCCGTATGTTGTCCGTATTA 57.481 39.130 0.00 0.00 44.07 0.98
3005 3231 7.467557 TCCGTATGTTGTCCGTATTAAAATC 57.532 36.000 0.00 0.00 0.00 2.17
3195 3421 0.673437 ACATCCAAACCACTTTGCCG 59.327 50.000 0.00 0.00 36.22 5.69
3296 3525 3.023119 ACTGTCACACCAAGAAAATGCA 58.977 40.909 0.00 0.00 0.00 3.96
3315 3544 8.524870 AAATGCACTGAGAATACAATTTCAAC 57.475 30.769 0.00 0.00 0.00 3.18
3454 3710 5.641209 CAGTTTGAATCCCAAAACACAAACA 59.359 36.000 18.07 0.00 45.40 2.83
3538 3795 9.856488 TTTGTGTTAAGATAGCAAGTAGTAGAG 57.144 33.333 0.00 0.00 0.00 2.43
3567 3824 6.380095 ACATCTAAACCGCTTTACAACAAA 57.620 33.333 0.00 0.00 0.00 2.83
3597 3854 2.100605 AAACTGAGAGAACGATGCCC 57.899 50.000 0.00 0.00 0.00 5.36
3601 3858 1.066587 GAGAGAACGATGCCCCTCG 59.933 63.158 0.00 0.00 44.14 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 118 1.202879 CCTAAGCAGGACACAAACCCA 60.203 52.381 0.00 0.00 45.91 4.51
150 155 0.399091 TCCATCTTCAGGGAGCCGAT 60.399 55.000 0.00 0.00 0.00 4.18
151 156 0.617535 TTCCATCTTCAGGGAGCCGA 60.618 55.000 0.00 0.00 34.02 5.54
188 193 4.280019 ACCACTGAAACGGGGGCC 62.280 66.667 0.00 0.00 36.62 5.80
305 312 3.010138 TCAAAAGGATCCAACCCGAAGAT 59.990 43.478 15.82 0.00 0.00 2.40
364 371 2.203139 CCGTGGGAACAGTGCACA 60.203 61.111 21.04 0.00 44.46 4.57
377 384 1.149174 ATCATGCTAAGGCCCCGTG 59.851 57.895 0.00 0.00 37.74 4.94
392 399 5.410924 CAGTAGACAATCGGAAAGTCATCA 58.589 41.667 13.40 0.00 34.80 3.07
406 413 3.181501 GCACAACTTGTTGCAGTAGACAA 60.182 43.478 12.76 1.96 34.80 3.18
447 455 3.330853 GCGTCATCGTCATCGCCC 61.331 66.667 0.00 0.00 42.33 6.13
473 481 2.029020 TGACTACAAGCACTGAAGCGAT 60.029 45.455 0.00 0.00 40.15 4.58
575 600 9.634021 ATCCTCCCTTAATACAATCTTTTCTTC 57.366 33.333 0.00 0.00 0.00 2.87
581 606 7.013369 GCGAAAATCCTCCCTTAATACAATCTT 59.987 37.037 0.00 0.00 0.00 2.40
583 608 6.565999 CGCGAAAATCCTCCCTTAATACAATC 60.566 42.308 0.00 0.00 0.00 2.67
589 614 3.277142 ACGCGAAAATCCTCCCTTAAT 57.723 42.857 15.93 0.00 0.00 1.40
590 615 2.773993 ACGCGAAAATCCTCCCTTAA 57.226 45.000 15.93 0.00 0.00 1.85
591 616 2.745281 CAAACGCGAAAATCCTCCCTTA 59.255 45.455 15.93 0.00 0.00 2.69
592 617 1.539827 CAAACGCGAAAATCCTCCCTT 59.460 47.619 15.93 0.00 0.00 3.95
593 618 1.165270 CAAACGCGAAAATCCTCCCT 58.835 50.000 15.93 0.00 0.00 4.20
605 630 1.259544 GCAGAAACGAACCAAACGCG 61.260 55.000 3.53 3.53 0.00 6.01
634 659 0.476771 ACCAATCCGTCCCAACTGTT 59.523 50.000 0.00 0.00 0.00 3.16
722 754 2.225467 GAGACTGCTTTGCTTGGACTT 58.775 47.619 0.00 0.00 0.00 3.01
723 755 1.544314 GGAGACTGCTTTGCTTGGACT 60.544 52.381 0.00 0.00 0.00 3.85
822 856 0.834687 TACGAGTTGCCTTGGAGGGT 60.835 55.000 0.00 0.00 35.37 4.34
829 863 6.104665 GGAGTAGTATTTTACGAGTTGCCTT 58.895 40.000 0.00 0.00 0.00 4.35
844 878 8.702819 GGTTAGTAAAAGACCATGGAGTAGTAT 58.297 37.037 21.47 0.00 33.61 2.12
845 879 7.675195 TGGTTAGTAAAAGACCATGGAGTAGTA 59.325 37.037 21.47 7.00 38.47 1.82
977 1032 3.284449 GCGGAGTTGCAACGGGTT 61.284 61.111 23.21 6.34 34.15 4.11
1115 1172 7.293402 AGACGCGAGATATGTATTCTACTAC 57.707 40.000 15.93 0.00 0.00 2.73
1117 1174 6.651643 AGAAGACGCGAGATATGTATTCTACT 59.348 38.462 15.93 0.00 41.03 2.57
1118 1175 6.833839 AGAAGACGCGAGATATGTATTCTAC 58.166 40.000 15.93 0.00 41.03 2.59
1126 1214 3.887339 TCTGAGAAGACGCGAGATATG 57.113 47.619 15.93 0.00 0.00 1.78
1151 1257 6.294065 GCATACTACTAGAACGAGCAACCTAT 60.294 42.308 0.00 0.00 0.00 2.57
1169 1275 5.763355 ACAGGTCCAGTACTAAGCATACTA 58.237 41.667 0.00 0.00 31.53 1.82
1170 1276 4.611367 ACAGGTCCAGTACTAAGCATACT 58.389 43.478 0.00 0.00 32.98 2.12
1182 1288 1.352622 TGCCCAAGAACAGGTCCAGT 61.353 55.000 0.00 0.00 0.00 4.00
1372 1491 3.424703 TCCGGCAAACACTAGTAGTAGT 58.575 45.455 1.57 4.29 40.38 2.73
1520 1639 1.199615 TGACAGTCACACCTTGGACA 58.800 50.000 0.00 0.00 36.50 4.02
1522 1641 2.705658 AGAATGACAGTCACACCTTGGA 59.294 45.455 5.05 0.00 0.00 3.53
1550 1669 0.033991 TCCCTCTCTTCTCGTCCCTG 60.034 60.000 0.00 0.00 0.00 4.45
1586 1705 4.162651 AGAGGTTGGATTCAAGGCAAATT 58.837 39.130 0.00 0.00 32.92 1.82
1594 1713 4.387026 ACATTGGAGAGGTTGGATTCAA 57.613 40.909 0.00 0.00 0.00 2.69
1613 1732 0.249868 CGAGCTGGTGGAAGACAACA 60.250 55.000 0.00 0.00 46.67 3.33
1720 1839 6.092122 TGCATAAGTGACGATCTAACAAAAGG 59.908 38.462 0.00 0.00 0.00 3.11
1782 1926 4.331717 GCTGCATTGTTAACCTGTACGTAT 59.668 41.667 2.48 0.00 0.00 3.06
1783 1927 3.680937 GCTGCATTGTTAACCTGTACGTA 59.319 43.478 2.48 0.00 0.00 3.57
1784 1928 2.482721 GCTGCATTGTTAACCTGTACGT 59.517 45.455 2.48 0.00 0.00 3.57
1785 1929 2.473868 CGCTGCATTGTTAACCTGTACG 60.474 50.000 2.48 4.24 0.00 3.67
1786 1930 2.159572 CCGCTGCATTGTTAACCTGTAC 60.160 50.000 2.48 0.00 0.00 2.90
1812 1956 1.739562 CTCGTCTGCTGCAACTCCC 60.740 63.158 3.02 0.00 0.00 4.30
1893 2086 7.049799 TGCTAAGTTGCAAAAGGTTAAGATT 57.950 32.000 0.00 0.00 40.29 2.40
1898 2091 9.771534 AAAAATATGCTAAGTTGCAAAAGGTTA 57.228 25.926 0.00 0.00 46.61 2.85
1962 2155 7.064609 CACTGAACATTGGTGGTACTAAGTATG 59.935 40.741 0.00 0.00 0.00 2.39
2151 2349 2.814336 GACAATCCTCGCTCCAAACTTT 59.186 45.455 0.00 0.00 0.00 2.66
2156 2354 2.290260 ACATTGACAATCCTCGCTCCAA 60.290 45.455 0.00 0.00 0.00 3.53
2157 2355 1.278985 ACATTGACAATCCTCGCTCCA 59.721 47.619 0.00 0.00 0.00 3.86
2169 2367 1.003580 GCAAGGGAGGAGACATTGACA 59.996 52.381 0.00 0.00 0.00 3.58
2175 2373 1.533033 TGACGCAAGGGAGGAGACA 60.533 57.895 0.00 0.00 46.39 3.41
2177 2375 0.967887 CTCTGACGCAAGGGAGGAGA 60.968 60.000 0.00 0.00 46.39 3.71
2232 2430 2.732412 AACTCACTGACTGTGGATCG 57.268 50.000 12.00 2.64 46.20 3.69
2279 2505 0.807667 CTCGTTCGGCATTCTCTGGG 60.808 60.000 0.00 0.00 0.00 4.45
2517 2743 2.599281 TCGGTCCTGACGAAGCCA 60.599 61.111 0.00 0.00 37.42 4.75
2658 2884 2.506231 TCCAGTGAACAACCACTACCAA 59.494 45.455 0.00 0.00 44.87 3.67
2876 3102 8.537728 TGTATTTAGGAACGGAGGAAGTAATA 57.462 34.615 0.00 0.00 0.00 0.98
2900 3126 7.395489 CCATATTGGAATCTCTAAAGGGGATTG 59.605 40.741 0.00 0.00 40.96 2.67
2903 3129 6.157536 TCCATATTGGAATCTCTAAAGGGGA 58.842 40.000 0.00 0.00 45.00 4.81
2922 3148 3.232720 TGGCTCCGTATGTAGTCCATA 57.767 47.619 0.00 0.00 34.86 2.74
2929 3155 3.449377 TCACTCATTTGGCTCCGTATGTA 59.551 43.478 0.00 0.00 0.00 2.29
3013 3239 5.605488 TCCCTCCGTTTCTAAATATAAGCCT 59.395 40.000 0.00 0.00 0.00 4.58
3195 3421 4.745125 TCTCACATTTACTGCGCTATTAGC 59.255 41.667 9.73 5.56 38.02 3.09
3212 3438 2.632512 TGAGTGGCATTGTACTCTCACA 59.367 45.455 17.86 3.15 42.86 3.58
3296 3525 6.998074 TCACCAGTTGAAATTGTATTCTCAGT 59.002 34.615 0.00 0.00 0.00 3.41
3369 3598 6.179906 AGTAGCGGTACCTAACTACTATGA 57.820 41.667 25.73 0.66 42.61 2.15
3454 3710 8.608185 ACCCATCATAATAAAGGAACACAAAT 57.392 30.769 0.00 0.00 0.00 2.32
3538 3795 5.407387 TGTAAAGCGGTTTAGATGTTCAGTC 59.593 40.000 19.43 5.28 0.00 3.51
3567 3824 5.624738 CGTTCTCTCAGTTTTACTGGGCTAT 60.625 44.000 6.96 0.00 46.17 2.97
3597 3854 9.582431 TTAAATCTGTTTAACTAGTGATCGAGG 57.418 33.333 0.00 0.00 35.45 4.63


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

AutoCloner maintained by Alex Coulton.