Multiple sequence alignment - TraesCS2A01G541700

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 TraesCS2A01G541700 chr2A 100.000 2588 0 0 1 2588 752918783 752916196 0.000000e+00 4780.0
1 TraesCS2A01G541700 chr2A 80.800 625 104 12 940 1558 607915203 607915817 2.330000e-130 475.0
2 TraesCS2A01G541700 chr2A 81.684 475 72 10 1116 1584 607967726 607968191 5.230000e-102 381.0
3 TraesCS2A01G541700 chr2A 95.480 177 7 1 1 176 196057347 196057171 5.450000e-72 281.0
4 TraesCS2A01G541700 chr2A 94.915 177 8 1 1 176 196060101 196059925 2.540000e-70 276.0
5 TraesCS2A01G541700 chr2A 95.050 101 5 0 697 797 752917987 752918087 2.670000e-35 159.0
6 TraesCS2A01G541700 chr2A 87.129 101 9 4 692 790 111440703 111440801 7.570000e-21 111.0
7 TraesCS2A01G541700 chr2A 88.172 93 9 2 701 793 9108529 9108619 2.720000e-20 110.0
8 TraesCS2A01G541700 chr2A 79.221 154 20 10 865 1010 607967457 607967606 2.120000e-16 97.1
9 TraesCS2A01G541700 chr2D 91.311 1830 113 20 787 2587 621118528 621116716 0.000000e+00 2457.0
10 TraesCS2A01G541700 chr2D 93.662 710 27 8 1 703 621119218 621118520 0.000000e+00 1046.0
11 TraesCS2A01G541700 chr2D 84.977 872 102 19 891 1752 621115161 621114309 0.000000e+00 857.0
12 TraesCS2A01G541700 chr2D 76.872 895 159 36 943 1825 467065264 467066122 1.810000e-126 462.0
13 TraesCS2A01G541700 chr2D 81.224 474 73 10 1116 1584 467239345 467239807 4.070000e-98 368.0
14 TraesCS2A01G541700 chr2D 80.303 132 25 1 320 450 544872775 544872906 5.890000e-17 99.0
15 TraesCS2A01G541700 chr2B 91.840 1152 59 13 788 1911 762028957 762027813 0.000000e+00 1574.0
16 TraesCS2A01G541700 chr2B 93.958 480 27 2 1 479 762043481 762043003 0.000000e+00 725.0
17 TraesCS2A01G541700 chr2B 77.539 837 145 27 934 1756 545762298 545763105 5.040000e-127 464.0
18 TraesCS2A01G541700 chr2B 81.967 488 80 7 1116 1600 546180011 546180493 8.620000e-110 407.0
19 TraesCS2A01G541700 chr2B 92.050 239 12 6 471 703 762029187 762028950 1.920000e-86 329.0
20 TraesCS2A01G541700 chr2B 81.679 131 22 2 320 450 528159617 528159489 9.790000e-20 108.0
21 TraesCS2A01G541700 chr3B 96.045 177 6 1 1 176 696746179 696746003 1.170000e-73 287.0
22 TraesCS2A01G541700 chr1B 95.480 177 7 1 1 176 116189620 116189796 5.450000e-72 281.0
23 TraesCS2A01G541700 chr1B 95.930 172 6 1 6 176 116162339 116162510 7.050000e-71 278.0
24 TraesCS2A01G541700 chr1B 94.915 177 8 1 1 176 116175483 116175659 2.540000e-70 276.0
25 TraesCS2A01G541700 chr1B 94.915 177 8 1 1 176 116248748 116248924 2.540000e-70 276.0
26 TraesCS2A01G541700 chr1B 89.691 97 6 3 698 792 190318925 190318831 1.260000e-23 121.0
27 TraesCS2A01G541700 chr1B 87.629 97 8 3 702 796 190318831 190318925 2.720000e-20 110.0
28 TraesCS2A01G541700 chr1B 88.889 90 8 2 703 792 668672048 668672135 2.720000e-20 110.0
29 TraesCS2A01G541700 chr5D 84.397 141 15 7 326 463 339961028 339960892 5.810000e-27 132.0
30 TraesCS2A01G541700 chr7D 83.969 131 18 3 320 449 490884263 490884135 3.500000e-24 122.0
31 TraesCS2A01G541700 chr6B 83.721 129 20 1 322 450 638472841 638472714 1.260000e-23 121.0
32 TraesCS2A01G541700 chr7A 88.172 93 9 2 704 796 619632739 619632649 2.720000e-20 110.0
33 TraesCS2A01G541700 chr7A 88.043 92 9 2 702 793 48760850 48760761 9.790000e-20 108.0
34 TraesCS2A01G541700 chr7A 80.153 131 23 3 321 450 156317382 156317510 7.620000e-16 95.3
35 TraesCS2A01G541700 chr5B 89.655 87 7 2 704 790 604151592 604151508 2.720000e-20 110.0
36 TraesCS2A01G541700 chr6D 82.031 128 22 1 323 450 423479836 423479710 9.790000e-20 108.0


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 TraesCS2A01G541700 chr2A 752916196 752918783 2587 True 4780.000000 4780 100.000000 1 2588 1 chr2A.!!$R1 2587
1 TraesCS2A01G541700 chr2A 607915203 607915817 614 False 475.000000 475 80.800000 940 1558 1 chr2A.!!$F3 618
2 TraesCS2A01G541700 chr2A 196057171 196060101 2930 True 278.500000 281 95.197500 1 176 2 chr2A.!!$R2 175
3 TraesCS2A01G541700 chr2A 607967457 607968191 734 False 239.050000 381 80.452500 865 1584 2 chr2A.!!$F5 719
4 TraesCS2A01G541700 chr2D 621114309 621119218 4909 True 1453.333333 2457 89.983333 1 2587 3 chr2D.!!$R1 2586
5 TraesCS2A01G541700 chr2D 467065264 467066122 858 False 462.000000 462 76.872000 943 1825 1 chr2D.!!$F1 882
6 TraesCS2A01G541700 chr2B 762027813 762029187 1374 True 951.500000 1574 91.945000 471 1911 2 chr2B.!!$R3 1440
7 TraesCS2A01G541700 chr2B 545762298 545763105 807 False 464.000000 464 77.539000 934 1756 1 chr2B.!!$F1 822

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
213 215 0.193574 AGGAGTGAAGGGAGGGACAA 59.806 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 4031 0.179032 TGCACACCGGAGAACACATT 60.179 50.0 9.46 0.0 0.0 2.71 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
80 81 5.127845 AGTCGGAAGATTAGAATCTGAAGCA 59.872 40.000 5.55 0.00 44.67 3.91
188 190 1.004595 CACATCAGTGCCTGACATCG 58.995 55.000 7.00 0.91 43.63 3.84
213 215 0.193574 AGGAGTGAAGGGAGGGACAA 59.806 55.000 0.00 0.00 0.00 3.18
215 217 1.423921 GGAGTGAAGGGAGGGACAAAA 59.576 52.381 0.00 0.00 0.00 2.44
228 230 1.152333 ACAAAAGGGGAGGGTTGGC 60.152 57.895 0.00 0.00 0.00 4.52
318 320 9.570468 ACCTTGATATCTATAACTTAGTCGTGA 57.430 33.333 3.98 0.00 0.00 4.35
354 356 2.553086 GTGGTGGTAGTTGTCGTTCAA 58.447 47.619 0.00 0.00 0.00 2.69
370 372 1.942776 TCAATGGCCTCTGAGTCTCA 58.057 50.000 3.32 1.78 0.00 3.27
409 411 4.201871 TGTTTGAGGTGCTTTGTACTTTCG 60.202 41.667 0.00 0.00 0.00 3.46
524 527 6.286240 AGTCAATGCATGTAGAGTACAGAA 57.714 37.500 0.00 0.00 42.77 3.02
591 595 3.822167 TGTGGTCTCTACGTATTGTGACA 59.178 43.478 14.92 4.99 0.00 3.58
631 637 7.500720 ACGGTTACTTGTTAGCTAATTTGTT 57.499 32.000 9.88 0.00 0.00 2.83
632 638 7.357303 ACGGTTACTTGTTAGCTAATTTGTTG 58.643 34.615 9.88 0.63 0.00 3.33
635 641 9.524106 GGTTACTTGTTAGCTAATTTGTTGTTT 57.476 29.630 9.88 0.00 0.00 2.83
639 645 9.093970 ACTTGTTAGCTAATTTGTTGTTTTTCC 57.906 29.630 9.88 0.00 0.00 3.13
652 658 6.512297 TGTTGTTTTTCCCAGCTTAAAGATC 58.488 36.000 0.00 0.00 0.00 2.75
654 660 6.916360 TGTTTTTCCCAGCTTAAAGATCAT 57.084 33.333 0.00 0.00 0.00 2.45
655 661 8.303876 GTTGTTTTTCCCAGCTTAAAGATCATA 58.696 33.333 0.00 0.00 0.00 2.15
656 662 7.826690 TGTTTTTCCCAGCTTAAAGATCATAC 58.173 34.615 0.00 0.00 0.00 2.39
657 663 7.450014 TGTTTTTCCCAGCTTAAAGATCATACA 59.550 33.333 0.00 0.00 0.00 2.29
658 664 7.630242 TTTTCCCAGCTTAAAGATCATACAG 57.370 36.000 0.00 0.00 0.00 2.74
694 703 0.323999 AATTTGGCCCGACCCCTAAC 60.324 55.000 0.00 0.00 37.83 2.34
698 707 2.136229 GGCCCGACCCCTAACGTAT 61.136 63.158 0.00 0.00 0.00 3.06
699 708 1.365267 GCCCGACCCCTAACGTATC 59.635 63.158 0.00 0.00 0.00 2.24
700 709 1.111715 GCCCGACCCCTAACGTATCT 61.112 60.000 0.00 0.00 0.00 1.98
701 710 1.819305 GCCCGACCCCTAACGTATCTA 60.819 57.143 0.00 0.00 0.00 1.98
702 711 2.157738 CCCGACCCCTAACGTATCTAG 58.842 57.143 0.00 0.00 0.00 2.43
703 712 2.487986 CCCGACCCCTAACGTATCTAGT 60.488 54.545 0.00 0.00 0.00 2.57
704 713 3.244561 CCCGACCCCTAACGTATCTAGTA 60.245 52.174 0.00 0.00 0.00 1.82
705 714 3.748568 CCGACCCCTAACGTATCTAGTAC 59.251 52.174 0.00 0.00 0.00 2.73
706 715 4.503991 CCGACCCCTAACGTATCTAGTACT 60.504 50.000 0.00 0.00 0.00 2.73
707 716 4.688413 CGACCCCTAACGTATCTAGTACTC 59.312 50.000 0.00 0.00 0.00 2.59
708 717 4.979335 ACCCCTAACGTATCTAGTACTCC 58.021 47.826 0.00 0.00 0.00 3.85
709 718 4.202514 ACCCCTAACGTATCTAGTACTCCC 60.203 50.000 0.00 0.00 0.00 4.30
710 719 4.042684 CCCCTAACGTATCTAGTACTCCCT 59.957 50.000 0.00 0.00 0.00 4.20
711 720 5.457342 CCCCTAACGTATCTAGTACTCCCTT 60.457 48.000 0.00 0.00 0.00 3.95
712 721 6.067350 CCCTAACGTATCTAGTACTCCCTTT 58.933 44.000 0.00 0.00 0.00 3.11
713 722 6.206438 CCCTAACGTATCTAGTACTCCCTTTC 59.794 46.154 0.00 0.00 0.00 2.62
714 723 5.747951 AACGTATCTAGTACTCCCTTTCG 57.252 43.478 0.00 1.81 0.00 3.46
715 724 4.775236 ACGTATCTAGTACTCCCTTTCGT 58.225 43.478 0.00 2.47 0.00 3.85
716 725 5.918608 ACGTATCTAGTACTCCCTTTCGTA 58.081 41.667 0.00 0.00 0.00 3.43
717 726 6.349300 ACGTATCTAGTACTCCCTTTCGTAA 58.651 40.000 0.00 0.00 0.00 3.18
718 727 6.823689 ACGTATCTAGTACTCCCTTTCGTAAA 59.176 38.462 0.00 0.00 0.00 2.01
719 728 7.500559 ACGTATCTAGTACTCCCTTTCGTAAAT 59.499 37.037 0.00 0.00 0.00 1.40
720 729 8.348507 CGTATCTAGTACTCCCTTTCGTAAATT 58.651 37.037 0.00 0.00 0.00 1.82
733 742 9.940166 CCCTTTCGTAAATTAATATAAAAGCGT 57.060 29.630 0.00 0.00 0.00 5.07
785 794 9.940166 ACGCTTTTATATTAATTTACGAAAGGG 57.060 29.630 16.65 16.65 39.89 3.95
859 869 4.494199 CCAAACGATTCAGATACGGAAAGC 60.494 45.833 0.00 0.00 0.00 3.51
860 870 2.822764 ACGATTCAGATACGGAAAGCC 58.177 47.619 0.00 0.00 0.00 4.35
889 899 3.843304 GCTAGAGCACGAGCCCTA 58.157 61.111 4.95 0.00 43.56 3.53
973 1149 1.531149 CCAAACACCGCATATCGATCC 59.469 52.381 0.00 0.00 41.67 3.36
977 1574 0.319813 CACCGCATATCGATCCAGCA 60.320 55.000 0.00 0.00 41.67 4.41
1101 1778 7.560368 TGTATTTTCTTGTGTGGGAAAACAAT 58.440 30.769 0.00 0.00 41.93 2.71
1106 1783 3.237268 TGTGTGGGAAAACAATAGGCT 57.763 42.857 0.00 0.00 0.00 4.58
1117 1795 1.838077 ACAATAGGCTAGGTGACACCC 59.162 52.381 21.32 5.91 39.75 4.61
1131 2451 4.281102 ACCCAGTACACGGTGACA 57.719 55.556 16.29 0.00 0.00 3.58
1224 2751 0.374758 GCATCAACGTGCACATCGAT 59.625 50.000 18.64 11.52 44.43 3.59
1602 3551 7.119997 GCACGACATGAAACAGATAGTTAATC 58.880 38.462 0.00 0.00 40.26 1.75
1617 3578 9.220767 AGATAGTTAATCAGTGTCTTGGTTTTC 57.779 33.333 0.00 0.00 37.03 2.29
1723 3686 8.960591 AGTGGTATCTGAATTTTGTATTTCCAG 58.039 33.333 0.00 0.00 0.00 3.86
1733 3696 2.432444 TGTATTTCCAGCCCAAGAACG 58.568 47.619 0.00 0.00 0.00 3.95
1820 3784 6.434028 TGGATCCAAACTTTATTCTTCCAGTG 59.566 38.462 13.46 0.00 0.00 3.66
1838 3803 7.437713 TCCAGTGAAGATGATTATAGTGGTT 57.562 36.000 0.00 0.00 32.01 3.67
1853 3818 4.553330 AGTGGTTGATACGGAGTTGATT 57.447 40.909 0.00 0.00 37.78 2.57
1871 3836 6.763135 AGTTGATTGCGATAAGTGTATGACAT 59.237 34.615 0.00 0.00 0.00 3.06
1872 3837 7.926018 AGTTGATTGCGATAAGTGTATGACATA 59.074 33.333 0.00 0.00 0.00 2.29
1873 3838 7.637709 TGATTGCGATAAGTGTATGACATAC 57.362 36.000 17.19 17.19 36.29 2.39
1880 3845 8.851416 GCGATAAGTGTATGACATACTACAATC 58.149 37.037 22.85 20.12 36.70 2.67
1911 3876 5.526111 TCCGACTACTTTTTGAGTTTTGGAG 59.474 40.000 0.00 0.00 39.86 3.86
1913 3878 6.183360 CCGACTACTTTTTGAGTTTTGGAGTT 60.183 38.462 0.00 0.00 39.86 3.01
1985 3950 9.502091 AAGTGCACATACTATCTTTTCTAAACA 57.498 29.630 21.04 0.00 0.00 2.83
1990 3955 9.755064 CACATACTATCTTTTCTAAACAAACCG 57.245 33.333 0.00 0.00 0.00 4.44
1995 3960 4.915704 TCTTTTCTAAACAAACCGCACAG 58.084 39.130 0.00 0.00 0.00 3.66
1998 3963 2.215196 TCTAAACAAACCGCACAGGAC 58.785 47.619 0.00 0.00 45.00 3.85
2016 3981 3.255149 AGGACGTATACGGATTCATCACC 59.745 47.826 27.62 15.17 44.95 4.02
2021 3986 4.560716 CGTATACGGATTCATCACCACCAT 60.561 45.833 17.61 0.00 35.37 3.55
2042 4007 6.068010 CCATATGATTAGGCCCACAAAACTA 58.932 40.000 3.65 0.00 0.00 2.24
2044 4009 7.069331 CCATATGATTAGGCCCACAAAACTAAA 59.931 37.037 3.65 0.00 0.00 1.85
2046 4011 6.926630 TGATTAGGCCCACAAAACTAAATT 57.073 33.333 0.00 0.00 0.00 1.82
2098 4063 2.921754 CGGTGTGCACTTAGTAGCTTAC 59.078 50.000 19.41 3.15 0.00 2.34
2118 4083 6.349280 GCTTACATTGCTTGAACATACTCCAA 60.349 38.462 0.00 0.00 0.00 3.53
2131 4096 2.568623 ACTCCAACGCAGAGGAAAAT 57.431 45.000 2.50 0.00 35.24 1.82
2144 4109 5.934625 GCAGAGGAAAATACAGAACTTCAGA 59.065 40.000 0.00 0.00 0.00 3.27
2171 4136 3.966979 TGTCTGCAACCCATACAATCAT 58.033 40.909 0.00 0.00 28.81 2.45
2223 4190 2.871796 TGGATCCCCCAATCTAAACCT 58.128 47.619 9.90 0.00 43.29 3.50
2250 4217 3.041940 CCCGTCTTGCGTCACCAC 61.042 66.667 0.00 0.00 39.32 4.16
2251 4218 2.279851 CCGTCTTGCGTCACCACA 60.280 61.111 0.00 0.00 39.32 4.17
2266 4233 2.942376 CACCACAATATTAGAAGCCGCA 59.058 45.455 0.00 0.00 0.00 5.69
2269 4236 4.644685 ACCACAATATTAGAAGCCGCATTT 59.355 37.500 0.00 0.00 0.00 2.32
2277 4244 0.881118 GAAGCCGCATTTCAGGACAA 59.119 50.000 0.00 0.00 0.00 3.18
2291 4258 7.446106 TTTCAGGACAATAATAGCTCCCTTA 57.554 36.000 0.00 0.00 0.00 2.69
2297 4264 3.679824 ATAATAGCTCCCTTACCGCAC 57.320 47.619 0.00 0.00 0.00 5.34
2298 4265 0.104304 AATAGCTCCCTTACCGCACG 59.896 55.000 0.00 0.00 0.00 5.34
2364 4331 4.208686 GCCGCCTTCCTCGACGAT 62.209 66.667 0.00 0.00 0.00 3.73
2367 4334 2.184322 GCCTTCCTCGACGATGCA 59.816 61.111 0.00 0.00 0.00 3.96
2368 4335 1.447838 GCCTTCCTCGACGATGCAA 60.448 57.895 0.00 0.00 0.00 4.08
2369 4336 1.019278 GCCTTCCTCGACGATGCAAA 61.019 55.000 0.00 0.00 0.00 3.68
2370 4337 1.438651 CCTTCCTCGACGATGCAAAA 58.561 50.000 0.00 0.00 0.00 2.44
2372 4339 1.394917 CTTCCTCGACGATGCAAAAGG 59.605 52.381 0.00 0.00 0.00 3.11
2373 4340 0.606096 TCCTCGACGATGCAAAAGGA 59.394 50.000 0.00 0.00 0.00 3.36
2397 4379 1.203441 AGTGAGCTGCCATTCCTCCA 61.203 55.000 0.00 0.00 0.00 3.86
2409 4391 2.575921 TTCCTCCATCACCTCCTCAT 57.424 50.000 0.00 0.00 0.00 2.90
2413 4395 2.406559 CTCCATCACCTCCTCATCCTT 58.593 52.381 0.00 0.00 0.00 3.36
2417 4399 1.153289 CACCTCCTCATCCTTGCCG 60.153 63.158 0.00 0.00 0.00 5.69
2421 4403 2.587194 CCTCATCCTTGCCGCGAG 60.587 66.667 8.23 0.00 0.00 5.03
2457 4439 1.141254 TCCTAAACGGTGAACTTGCCA 59.859 47.619 0.00 0.00 0.00 4.92
2462 4444 3.763671 GGTGAACTTGCCACCCAG 58.236 61.111 0.00 0.00 46.30 4.45
2476 4458 1.556911 CACCCAGGAGCACTGTCTATT 59.443 52.381 7.53 0.00 46.06 1.73
2482 4464 3.445008 AGGAGCACTGTCTATTTCCTGA 58.555 45.455 0.00 0.00 33.95 3.86
2486 4468 2.673368 GCACTGTCTATTTCCTGAACGG 59.327 50.000 0.00 0.00 0.00 4.44
2494 4476 1.750341 TTTCCTGAACGGCGTCCTCA 61.750 55.000 15.17 13.98 0.00 3.86
2527 4509 2.350895 CCATCAAGTGGGCGGTCA 59.649 61.111 0.00 0.00 44.79 4.02
2534 4516 2.511600 GTGGGCGGTCATTCCTCG 60.512 66.667 0.00 0.00 0.00 4.63
2548 4533 0.904865 TCCTCGGTCACCTCATTGCT 60.905 55.000 0.00 0.00 0.00 3.91
2555 4540 1.059098 TCACCTCATTGCTGACAGGT 58.941 50.000 4.26 0.00 31.79 4.00
2559 4544 2.286872 CCTCATTGCTGACAGGTCATC 58.713 52.381 4.26 0.00 39.13 2.92
2568 4553 1.434622 GACAGGTCATCAGCGCCATG 61.435 60.000 2.29 7.26 0.00 3.66
2587 4572 1.807226 CACTGACGTCGCCATCCTA 59.193 57.895 11.62 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 185 4.457496 CACTCCTGCCGCCGATGT 62.457 66.667 0.00 0.00 0.00 3.06
184 186 3.664025 TTCACTCCTGCCGCCGATG 62.664 63.158 0.00 0.00 0.00 3.84
188 190 4.785453 CCCTTCACTCCTGCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
213 215 3.979497 CGGCCAACCCTCCCCTTT 61.979 66.667 2.24 0.00 0.00 3.11
228 230 2.186125 GAGAAACCCTACCGCCGG 59.814 66.667 0.00 0.00 0.00 6.13
330 332 0.677288 CGACAACTACCACCACCAGA 59.323 55.000 0.00 0.00 0.00 3.86
354 356 2.194859 ACATTGAGACTCAGAGGCCAT 58.805 47.619 5.01 0.00 0.00 4.40
524 527 4.517285 CAGTTTACCTGTACATGCTCCAT 58.483 43.478 0.00 0.00 36.37 3.41
631 637 6.916360 ATGATCTTTAAGCTGGGAAAAACA 57.084 33.333 0.00 0.00 0.00 2.83
632 638 7.826690 TGTATGATCTTTAAGCTGGGAAAAAC 58.173 34.615 0.00 0.00 0.00 2.43
635 641 6.721318 ACTGTATGATCTTTAAGCTGGGAAA 58.279 36.000 0.00 0.00 0.00 3.13
694 703 6.851222 TTACGAAAGGGAGTACTAGATACG 57.149 41.667 0.00 0.95 38.97 3.06
707 716 9.940166 ACGCTTTTATATTAATTTACGAAAGGG 57.060 29.630 16.65 16.65 39.89 3.95
759 768 9.940166 CCCTTTCGTAAATTAATATAAAAGCGT 57.060 29.630 0.00 0.00 0.00 5.07
772 781 8.358895 GCTATCTAGTACTCCCTTTCGTAAATT 58.641 37.037 0.00 0.00 0.00 1.82
773 782 7.039853 GGCTATCTAGTACTCCCTTTCGTAAAT 60.040 40.741 0.00 0.00 0.00 1.40
774 783 6.264067 GGCTATCTAGTACTCCCTTTCGTAAA 59.736 42.308 0.00 0.00 0.00 2.01
775 784 5.767168 GGCTATCTAGTACTCCCTTTCGTAA 59.233 44.000 0.00 0.00 0.00 3.18
776 785 5.312079 GGCTATCTAGTACTCCCTTTCGTA 58.688 45.833 0.00 0.00 0.00 3.43
777 786 4.143543 GGCTATCTAGTACTCCCTTTCGT 58.856 47.826 0.00 0.00 0.00 3.85
778 787 3.506844 GGGCTATCTAGTACTCCCTTTCG 59.493 52.174 0.00 0.00 0.00 3.46
779 788 3.833650 GGGGCTATCTAGTACTCCCTTTC 59.166 52.174 13.29 0.00 34.28 2.62
780 789 3.754500 CGGGGCTATCTAGTACTCCCTTT 60.754 52.174 13.29 0.00 34.28 3.11
781 790 2.225066 CGGGGCTATCTAGTACTCCCTT 60.225 54.545 13.29 0.00 34.28 3.95
782 791 1.355043 CGGGGCTATCTAGTACTCCCT 59.645 57.143 13.29 0.00 34.28 4.20
783 792 1.075212 ACGGGGCTATCTAGTACTCCC 59.925 57.143 0.00 2.06 0.00 4.30
784 793 2.583024 ACGGGGCTATCTAGTACTCC 57.417 55.000 0.00 0.00 0.00 3.85
785 794 2.819019 GGAACGGGGCTATCTAGTACTC 59.181 54.545 0.00 0.00 0.00 2.59
786 795 2.874014 GGAACGGGGCTATCTAGTACT 58.126 52.381 0.00 0.00 0.00 2.73
863 873 4.129737 TGCTCTAGCCGGACACGC 62.130 66.667 5.05 0.13 41.18 5.34
973 1149 0.957395 AGGAACAATGGCGAGTGCTG 60.957 55.000 0.00 0.00 42.25 4.41
977 1574 0.389948 GTCGAGGAACAATGGCGAGT 60.390 55.000 0.00 0.00 0.00 4.18
1031 1636 4.557301 TCGCTATTACGATCATGCATAACG 59.443 41.667 0.00 8.29 37.09 3.18
1101 1778 3.300032 CTGGGTGTCACCTAGCCTA 57.700 57.895 21.12 1.86 40.04 3.93
1106 1783 1.250328 CGTGTACTGGGTGTCACCTA 58.750 55.000 21.40 14.94 38.64 3.08
1131 2451 2.126071 CCGTCGACGCTGGTGATT 60.126 61.111 31.73 0.00 38.18 2.57
1224 2751 1.695242 ACGATCTGGTTGTGGGTGTTA 59.305 47.619 0.00 0.00 0.00 2.41
1723 3686 3.754850 ACTATAAAACACCGTTCTTGGGC 59.245 43.478 0.00 0.00 0.00 5.36
1733 3696 7.865706 ACATTCAGATCCACTATAAAACACC 57.134 36.000 0.00 0.00 0.00 4.16
1820 3784 8.304596 TCCGTATCAACCACTATAATCATCTTC 58.695 37.037 0.00 0.00 0.00 2.87
1838 3803 2.951457 TCGCAATCAACTCCGTATCA 57.049 45.000 0.00 0.00 0.00 2.15
1853 3818 7.266922 TGTAGTATGTCATACACTTATCGCA 57.733 36.000 22.13 8.13 38.21 5.10
1880 3845 6.214399 ACTCAAAAAGTAGTCGGACAACTAG 58.786 40.000 11.27 0.00 36.07 2.57
1985 3950 1.733389 CGTATACGTCCTGTGCGGTTT 60.733 52.381 17.16 0.00 34.11 3.27
1990 3955 2.223641 TGAATCCGTATACGTCCTGTGC 60.224 50.000 22.87 7.04 37.74 4.57
1995 3960 3.005050 TGGTGATGAATCCGTATACGTCC 59.995 47.826 22.87 9.82 37.74 4.79
1996 3961 3.979495 GTGGTGATGAATCCGTATACGTC 59.021 47.826 22.87 14.65 37.74 4.34
1998 3963 3.243602 TGGTGGTGATGAATCCGTATACG 60.244 47.826 18.40 18.40 39.44 3.06
2016 3981 3.507162 TGTGGGCCTAATCATATGGTG 57.493 47.619 4.53 0.00 0.00 4.17
2021 3986 8.602472 AATTTAGTTTTGTGGGCCTAATCATA 57.398 30.769 4.53 0.00 0.00 2.15
2044 4009 9.853177 ACATTAGGTTAAAGCTAGCTATTGAAT 57.147 29.630 19.70 8.69 34.03 2.57
2046 4011 8.265055 ACACATTAGGTTAAAGCTAGCTATTGA 58.735 33.333 19.70 8.64 34.03 2.57
2060 4025 3.579586 ACACCGGAGAACACATTAGGTTA 59.420 43.478 9.46 0.00 0.00 2.85
2062 4027 1.975680 ACACCGGAGAACACATTAGGT 59.024 47.619 9.46 0.00 0.00 3.08
2066 4031 0.179032 TGCACACCGGAGAACACATT 60.179 50.000 9.46 0.00 0.00 2.71
2067 4032 0.884704 GTGCACACCGGAGAACACAT 60.885 55.000 13.17 0.00 0.00 3.21
2098 4063 4.406069 CGTTGGAGTATGTTCAAGCAATG 58.594 43.478 0.00 0.00 0.00 2.82
2118 4083 4.273148 AGTTCTGTATTTTCCTCTGCGT 57.727 40.909 0.00 0.00 0.00 5.24
2131 4096 3.248024 ACATGGGGTCTGAAGTTCTGTA 58.752 45.455 4.17 0.00 0.00 2.74
2144 4109 1.803453 ATGGGTTGCAGACATGGGGT 61.803 55.000 0.00 0.00 0.00 4.95
2218 4185 3.703127 GGGGAGTCGCCGAGGTTT 61.703 66.667 10.92 0.00 37.63 3.27
2242 4209 3.245284 CGGCTTCTAATATTGTGGTGACG 59.755 47.826 0.00 0.00 0.00 4.35
2250 4217 5.239306 TCCTGAAATGCGGCTTCTAATATTG 59.761 40.000 0.00 0.00 0.00 1.90
2251 4218 5.239525 GTCCTGAAATGCGGCTTCTAATATT 59.760 40.000 0.00 0.00 0.00 1.28
2266 4233 6.521527 AGGGAGCTATTATTGTCCTGAAAT 57.478 37.500 0.00 0.00 0.00 2.17
2269 4236 5.307196 GGTAAGGGAGCTATTATTGTCCTGA 59.693 44.000 0.00 0.00 0.00 3.86
2277 4244 2.029290 CGTGCGGTAAGGGAGCTATTAT 60.029 50.000 0.00 0.00 0.00 1.28
2350 4317 1.019278 TTTGCATCGTCGAGGAAGGC 61.019 55.000 21.22 21.22 0.00 4.35
2358 4325 3.432252 ACTTAACTCCTTTTGCATCGTCG 59.568 43.478 0.00 0.00 0.00 5.12
2364 4331 3.565482 CAGCTCACTTAACTCCTTTTGCA 59.435 43.478 0.00 0.00 0.00 4.08
2367 4334 3.149981 GGCAGCTCACTTAACTCCTTTT 58.850 45.455 0.00 0.00 0.00 2.27
2368 4335 2.106511 TGGCAGCTCACTTAACTCCTTT 59.893 45.455 0.00 0.00 0.00 3.11
2369 4336 1.699634 TGGCAGCTCACTTAACTCCTT 59.300 47.619 0.00 0.00 0.00 3.36
2370 4337 1.352083 TGGCAGCTCACTTAACTCCT 58.648 50.000 0.00 0.00 0.00 3.69
2372 4339 2.680339 GGAATGGCAGCTCACTTAACTC 59.320 50.000 0.00 0.00 0.00 3.01
2373 4340 2.307098 AGGAATGGCAGCTCACTTAACT 59.693 45.455 0.00 0.00 0.00 2.24
2397 4379 0.842635 GGCAAGGATGAGGAGGTGAT 59.157 55.000 0.00 0.00 0.00 3.06
2421 4403 3.050275 GAAGGTGACGGTGCTGCC 61.050 66.667 0.00 0.00 0.00 4.85
2449 4431 2.116125 GCTCCTGGGTGGCAAGTT 59.884 61.111 0.00 0.00 35.26 2.66
2450 4432 3.177884 TGCTCCTGGGTGGCAAGT 61.178 61.111 7.27 0.00 35.26 3.16
2457 4439 1.958288 AATAGACAGTGCTCCTGGGT 58.042 50.000 8.50 0.00 46.06 4.51
2462 4444 3.895232 TCAGGAAATAGACAGTGCTCC 57.105 47.619 0.00 0.00 0.00 4.70
2476 4458 2.204461 TGAGGACGCCGTTCAGGAA 61.204 57.895 0.00 0.00 45.00 3.36
2527 4509 1.407437 GCAATGAGGTGACCGAGGAAT 60.407 52.381 0.00 0.00 0.00 3.01
2548 4533 1.902765 ATGGCGCTGATGACCTGTCA 61.903 55.000 7.64 1.93 44.59 3.58


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

AutoCloner maintained by Alex Coulton.