Multiple sequence alignment - TraesCS3B01G254700

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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 TraesCS3B01G254700 chr3B 100.000 4064 0 0 1 4064 410776744 410772681 0.000000e+00 7505
1 TraesCS3B01G254700 chr3B 93.664 726 29 10 3356 4064 407851560 407852285 0.000000e+00 1070
2 TraesCS3B01G254700 chr3B 91.280 711 59 3 3356 4064 191977241 191976532 0.000000e+00 966
3 TraesCS3B01G254700 chr3B 85.835 713 92 9 3356 4062 185624752 185624043 0.000000e+00 749
4 TraesCS3B01G254700 chr3B 80.215 743 128 17 1803 2534 183083359 183084093 1.290000e-149 540
5 TraesCS3B01G254700 chr3B 78.039 255 52 4 2647 2899 183084175 183084427 1.510000e-34 158
6 TraesCS3B01G254700 chr3A 91.869 3419 156 56 6 3351 421722627 421719258 0.000000e+00 4662
7 TraesCS3B01G254700 chr3A 79.521 752 139 14 1803 2545 140806672 140805927 4.650000e-144 521
8 TraesCS3B01G254700 chr3A 77.455 275 54 7 2647 2917 140805852 140805582 1.510000e-34 158
9 TraesCS3B01G254700 chr3D 91.564 2667 99 50 21 2614 310681273 310683886 0.000000e+00 3563
10 TraesCS3B01G254700 chr3D 97.177 744 19 2 2612 3355 310683999 310684740 0.000000e+00 1256
11 TraesCS3B01G254700 chr3D 80.265 755 130 18 1803 2546 129025188 129025934 5.940000e-153 551
12 TraesCS3B01G254700 chr3D 79.028 782 154 9 1769 2545 6023146 6022370 1.000000e-145 527
13 TraesCS3B01G254700 chr3D 78.431 255 51 4 2647 2899 129026029 129026281 3.250000e-36 163
14 TraesCS3B01G254700 chr1B 94.780 728 19 3 3356 4064 286447028 286447755 0.000000e+00 1116
15 TraesCS3B01G254700 chr1B 94.507 710 38 1 3356 4064 580191151 580190442 0.000000e+00 1094
16 TraesCS3B01G254700 chr1B 93.939 726 27 3 3356 4064 518941145 518940420 0.000000e+00 1081
17 TraesCS3B01G254700 chr1B 93.251 726 32 10 3356 4064 519218392 519219117 0.000000e+00 1053
18 TraesCS3B01G254700 chr1B 87.838 740 90 0 1818 2557 622367012 622366273 0.000000e+00 869
19 TraesCS3B01G254700 chr1B 81.732 739 81 32 2641 3353 622365635 622364925 5.900000e-158 568
20 TraesCS3B01G254700 chr1B 77.934 784 155 14 1762 2534 212410395 212409619 1.320000e-129 473
21 TraesCS3B01G254700 chr7B 93.724 717 28 5 3365 4064 206973086 206973802 0.000000e+00 1059
22 TraesCS3B01G254700 chr2B 90.896 714 60 3 3356 4064 580771950 580772663 0.000000e+00 953
23 TraesCS3B01G254700 chr2B 73.624 781 165 35 1792 2549 594846530 594845768 3.120000e-66 263
24 TraesCS3B01G254700 chr6B 90.476 714 63 3 3356 4064 264038010 264037297 0.000000e+00 937
25 TraesCS3B01G254700 chr5B 81.983 716 109 16 3356 4062 524071205 524070501 1.260000e-164 590
26 TraesCS3B01G254700 chr5B 95.129 349 14 3 3355 3700 238195650 238195998 7.680000e-152 547
27 TraesCS3B01G254700 chr1D 78.526 787 145 19 1762 2534 137968343 137967567 2.820000e-136 496
28 TraesCS3B01G254700 chr1A 78.543 755 139 18 1803 2544 154700642 154701386 3.680000e-130 475
29 TraesCS3B01G254700 chr1A 77.092 729 150 14 1782 2502 578356412 578355693 4.890000e-109 405
30 TraesCS3B01G254700 chr2A 74.036 778 167 30 1792 2549 651609564 651608802 6.650000e-73 285
31 TraesCS3B01G254700 chr2D 73.813 779 167 32 1792 2549 506792298 506791536 1.440000e-69 274


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 TraesCS3B01G254700 chr3B 410772681 410776744 4063 True 7505.0 7505 100.0000 1 4064 1 chr3B.!!$R3 4063
1 TraesCS3B01G254700 chr3B 407851560 407852285 725 False 1070.0 1070 93.6640 3356 4064 1 chr3B.!!$F1 708
2 TraesCS3B01G254700 chr3B 191976532 191977241 709 True 966.0 966 91.2800 3356 4064 1 chr3B.!!$R2 708
3 TraesCS3B01G254700 chr3B 185624043 185624752 709 True 749.0 749 85.8350 3356 4062 1 chr3B.!!$R1 706
4 TraesCS3B01G254700 chr3B 183083359 183084427 1068 False 349.0 540 79.1270 1803 2899 2 chr3B.!!$F2 1096
5 TraesCS3B01G254700 chr3A 421719258 421722627 3369 True 4662.0 4662 91.8690 6 3351 1 chr3A.!!$R1 3345
6 TraesCS3B01G254700 chr3A 140805582 140806672 1090 True 339.5 521 78.4880 1803 2917 2 chr3A.!!$R2 1114
7 TraesCS3B01G254700 chr3D 310681273 310684740 3467 False 2409.5 3563 94.3705 21 3355 2 chr3D.!!$F2 3334
8 TraesCS3B01G254700 chr3D 6022370 6023146 776 True 527.0 527 79.0280 1769 2545 1 chr3D.!!$R1 776
9 TraesCS3B01G254700 chr3D 129025188 129026281 1093 False 357.0 551 79.3480 1803 2899 2 chr3D.!!$F1 1096
10 TraesCS3B01G254700 chr1B 286447028 286447755 727 False 1116.0 1116 94.7800 3356 4064 1 chr1B.!!$F1 708
11 TraesCS3B01G254700 chr1B 580190442 580191151 709 True 1094.0 1094 94.5070 3356 4064 1 chr1B.!!$R3 708
12 TraesCS3B01G254700 chr1B 518940420 518941145 725 True 1081.0 1081 93.9390 3356 4064 1 chr1B.!!$R2 708
13 TraesCS3B01G254700 chr1B 519218392 519219117 725 False 1053.0 1053 93.2510 3356 4064 1 chr1B.!!$F2 708
14 TraesCS3B01G254700 chr1B 622364925 622367012 2087 True 718.5 869 84.7850 1818 3353 2 chr1B.!!$R4 1535
15 TraesCS3B01G254700 chr1B 212409619 212410395 776 True 473.0 473 77.9340 1762 2534 1 chr1B.!!$R1 772
16 TraesCS3B01G254700 chr7B 206973086 206973802 716 False 1059.0 1059 93.7240 3365 4064 1 chr7B.!!$F1 699
17 TraesCS3B01G254700 chr2B 580771950 580772663 713 False 953.0 953 90.8960 3356 4064 1 chr2B.!!$F1 708
18 TraesCS3B01G254700 chr2B 594845768 594846530 762 True 263.0 263 73.6240 1792 2549 1 chr2B.!!$R1 757
19 TraesCS3B01G254700 chr6B 264037297 264038010 713 True 937.0 937 90.4760 3356 4064 1 chr6B.!!$R1 708
20 TraesCS3B01G254700 chr5B 524070501 524071205 704 True 590.0 590 81.9830 3356 4062 1 chr5B.!!$R1 706
21 TraesCS3B01G254700 chr1D 137967567 137968343 776 True 496.0 496 78.5260 1762 2534 1 chr1D.!!$R1 772
22 TraesCS3B01G254700 chr1A 154700642 154701386 744 False 475.0 475 78.5430 1803 2544 1 chr1A.!!$F1 741
23 TraesCS3B01G254700 chr1A 578355693 578356412 719 True 405.0 405 77.0920 1782 2502 1 chr1A.!!$R1 720
24 TraesCS3B01G254700 chr2A 651608802 651609564 762 True 285.0 285 74.0360 1792 2549 1 chr2A.!!$R1 757
25 TraesCS3B01G254700 chr2D 506791536 506792298 762 True 274.0 274 73.8130 1792 2549 1 chr2D.!!$R1 757

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
699 718 0.107945 CCTAGCTGCAACCTGACTCC 60.108 60.0 1.02 0.0 0.0 3.85 F
1070 1128 0.172352 GAGCAGTCGTCCAGAGAAGG 59.828 60.0 0.00 0.0 0.0 3.46 F
1767 1840 0.738389 CCTTTTCTGTTGCGTGTGGT 59.262 50.0 0.00 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1829 0.248458 CCTGAACAACCACACGCAAC 60.248 55.000 0.00 0.0 0.00 4.17 R
3016 3665 0.179161 GACGGATCGGTGTCTGTGAG 60.179 60.000 11.07 0.0 37.82 3.51 R
3319 4003 1.815003 GACCAATTCTGCAAGGTCCAG 59.185 52.381 9.53 0.0 43.67 3.86 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
31 32 4.686091 TGCTAGCTGTATATCGCAAACATC 59.314 41.667 17.23 0.00 0.00 3.06
40 41 5.663795 ATATCGCAAACATCACAGTGATC 57.336 39.130 13.53 1.24 34.28 2.92
48 49 3.193263 ACATCACAGTGATCATTCTCGC 58.807 45.455 13.53 0.00 34.28 5.03
70 71 4.226761 CCACAAGTCAAAAACCTTATCGC 58.773 43.478 0.00 0.00 0.00 4.58
77 78 6.119536 AGTCAAAAACCTTATCGCATCCATA 58.880 36.000 0.00 0.00 0.00 2.74
79 80 7.936847 AGTCAAAAACCTTATCGCATCCATATA 59.063 33.333 0.00 0.00 0.00 0.86
159 160 0.602905 CAGTTTCCACACGGGTCTCC 60.603 60.000 0.00 0.00 38.11 3.71
160 161 1.302271 GTTTCCACACGGGTCTCCC 60.302 63.158 0.00 0.00 41.09 4.30
172 173 3.351794 GGGTCTCCCGATTCTTCTTTT 57.648 47.619 0.00 0.00 32.13 2.27
173 174 3.687125 GGGTCTCCCGATTCTTCTTTTT 58.313 45.455 0.00 0.00 32.13 1.94
274 279 2.159476 ACGTAGTACACATGCGTACCTG 60.159 50.000 18.15 11.69 41.94 4.00
323 328 4.956582 AGGTACTTATTCCACCCTACTGT 58.043 43.478 0.00 0.00 27.25 3.55
324 329 4.961099 AGGTACTTATTCCACCCTACTGTC 59.039 45.833 0.00 0.00 27.25 3.51
359 371 3.966154 ACTACCATAGAACAAGATCGCG 58.034 45.455 0.00 0.00 0.00 5.87
629 648 0.827507 GCTTTGGAGCTTTCCCACCA 60.828 55.000 0.00 0.00 45.65 4.17
644 663 2.234296 ACCAGGGCCAAGCTAAGCT 61.234 57.895 6.18 0.00 42.56 3.74
645 664 0.914417 ACCAGGGCCAAGCTAAGCTA 60.914 55.000 6.18 0.00 38.25 3.32
646 665 0.179034 CCAGGGCCAAGCTAAGCTAG 60.179 60.000 6.18 0.00 38.25 3.42
692 711 2.512515 CCGAGCCTAGCTGCAACC 60.513 66.667 1.02 0.00 39.88 3.77
695 714 1.599047 GAGCCTAGCTGCAACCTGA 59.401 57.895 1.02 0.00 39.88 3.86
696 715 0.742635 GAGCCTAGCTGCAACCTGAC 60.743 60.000 1.02 0.00 39.88 3.51
697 716 1.197430 AGCCTAGCTGCAACCTGACT 61.197 55.000 1.02 0.00 37.57 3.41
699 718 0.107945 CCTAGCTGCAACCTGACTCC 60.108 60.000 1.02 0.00 0.00 3.85
700 719 0.459237 CTAGCTGCAACCTGACTCCG 60.459 60.000 1.02 0.00 0.00 4.63
701 720 0.898326 TAGCTGCAACCTGACTCCGA 60.898 55.000 1.02 0.00 0.00 4.55
702 721 1.078848 GCTGCAACCTGACTCCGAT 60.079 57.895 0.00 0.00 0.00 4.18
705 724 1.204704 CTGCAACCTGACTCCGATACA 59.795 52.381 0.00 0.00 0.00 2.29
708 727 2.881074 CAACCTGACTCCGATACACTG 58.119 52.381 0.00 0.00 0.00 3.66
711 730 0.733150 CTGACTCCGATACACTGCGA 59.267 55.000 0.00 0.00 0.00 5.10
712 731 0.733150 TGACTCCGATACACTGCGAG 59.267 55.000 0.00 0.00 0.00 5.03
713 732 0.592754 GACTCCGATACACTGCGAGC 60.593 60.000 0.00 0.00 0.00 5.03
714 733 1.032657 ACTCCGATACACTGCGAGCT 61.033 55.000 0.00 0.00 0.00 4.09
727 746 4.577246 GAGCTAGGGCGCACCGAG 62.577 72.222 5.73 13.25 46.96 4.63
729 748 4.143333 GCTAGGGCGCACCGAGAA 62.143 66.667 22.62 5.94 44.05 2.87
739 762 1.215655 GCACCGAGAAATCGATCCGG 61.216 60.000 19.83 19.83 45.09 5.14
756 780 0.872388 CGGTTGTCCTGTTGTTAGGC 59.128 55.000 0.00 0.00 37.76 3.93
757 781 0.872388 GGTTGTCCTGTTGTTAGGCG 59.128 55.000 0.00 0.00 37.76 5.52
758 782 1.541670 GGTTGTCCTGTTGTTAGGCGA 60.542 52.381 0.00 0.00 37.76 5.54
759 783 1.798813 GTTGTCCTGTTGTTAGGCGAG 59.201 52.381 0.00 0.00 37.76 5.03
761 785 1.080093 TCCTGTTGTTAGGCGAGCG 60.080 57.895 0.00 0.00 37.76 5.03
767 791 0.315886 TTGTTAGGCGAGCGAGAACA 59.684 50.000 0.00 4.65 0.00 3.18
771 795 0.601558 TAGGCGAGCGAGAACAGTTT 59.398 50.000 0.00 0.00 0.00 2.66
783 807 4.443063 CGAGAACAGTTTACGATTCACACA 59.557 41.667 7.10 0.00 0.00 3.72
784 808 5.609696 CGAGAACAGTTTACGATTCACACAC 60.610 44.000 7.10 0.00 0.00 3.82
785 809 5.357257 AGAACAGTTTACGATTCACACACT 58.643 37.500 0.00 0.00 0.00 3.55
806 846 8.353684 CACACTAGTCCAGGTAAGAATATACTG 58.646 40.741 0.00 0.00 0.00 2.74
891 934 4.024048 CGAATTGGTGTATCTGGTATTGCC 60.024 45.833 0.00 0.00 37.90 4.52
913 956 5.471456 GCCATACTTGATTATGTCCTTCTGG 59.529 44.000 0.00 0.00 0.00 3.86
937 994 3.814842 TCATTATTATGTTCCAGCAGCGG 59.185 43.478 0.00 0.00 33.34 5.52
973 1030 2.296471 ACTGGAGCACTACTGTGTGTAC 59.704 50.000 10.52 0.00 45.44 2.90
1047 1105 1.380246 CCAAATGGGCAGCCAGCTA 60.380 57.895 15.19 0.00 44.79 3.32
1048 1106 1.389609 CCAAATGGGCAGCCAGCTAG 61.390 60.000 15.19 0.00 44.79 3.42
1070 1128 0.172352 GAGCAGTCGTCCAGAGAAGG 59.828 60.000 0.00 0.00 0.00 3.46
1098 1156 1.300963 GCTGCTCATCCAGGTTCCA 59.699 57.895 0.00 0.00 33.44 3.53
1524 1582 4.083862 AAGACCTTCTCCGGCCGC 62.084 66.667 22.85 2.73 0.00 6.53
1694 1757 2.369532 TCAGGGTAAGTAAGCAACGGTT 59.630 45.455 0.00 0.00 0.00 4.44
1726 1795 1.123077 TGTCAGTGACCTTCAGCTGT 58.877 50.000 20.43 0.00 31.83 4.40
1727 1796 1.202568 TGTCAGTGACCTTCAGCTGTG 60.203 52.381 20.43 8.01 31.83 3.66
1749 1822 1.162698 GCTAACGGTTGGGTCTTTCC 58.837 55.000 3.07 0.00 0.00 3.13
1755 1828 2.092049 ACGGTTGGGTCTTTCCTTTTCT 60.092 45.455 0.00 0.00 36.25 2.52
1756 1829 2.293399 CGGTTGGGTCTTTCCTTTTCTG 59.707 50.000 0.00 0.00 36.25 3.02
1757 1830 3.296854 GGTTGGGTCTTTCCTTTTCTGT 58.703 45.455 0.00 0.00 36.25 3.41
1758 1831 3.704566 GGTTGGGTCTTTCCTTTTCTGTT 59.295 43.478 0.00 0.00 36.25 3.16
1759 1832 4.441495 GGTTGGGTCTTTCCTTTTCTGTTG 60.441 45.833 0.00 0.00 36.25 3.33
1760 1833 2.693074 TGGGTCTTTCCTTTTCTGTTGC 59.307 45.455 0.00 0.00 36.25 4.17
1761 1834 2.287608 GGGTCTTTCCTTTTCTGTTGCG 60.288 50.000 0.00 0.00 36.25 4.85
1762 1835 2.357952 GGTCTTTCCTTTTCTGTTGCGT 59.642 45.455 0.00 0.00 0.00 5.24
1763 1836 3.363178 GTCTTTCCTTTTCTGTTGCGTG 58.637 45.455 0.00 0.00 0.00 5.34
1764 1837 3.013921 TCTTTCCTTTTCTGTTGCGTGT 58.986 40.909 0.00 0.00 0.00 4.49
1765 1838 2.842208 TTCCTTTTCTGTTGCGTGTG 57.158 45.000 0.00 0.00 0.00 3.82
1766 1839 1.021202 TCCTTTTCTGTTGCGTGTGG 58.979 50.000 0.00 0.00 0.00 4.17
1767 1840 0.738389 CCTTTTCTGTTGCGTGTGGT 59.262 50.000 0.00 0.00 0.00 4.16
1786 1859 1.122632 TTGTTCAGGCCACGGAGGTA 61.123 55.000 5.01 0.00 40.61 3.08
1879 1952 2.437359 GTGAGCAGCCAGGCGATT 60.437 61.111 5.55 0.00 39.27 3.34
2401 2480 2.590575 CCCACCAACGTCACGCTT 60.591 61.111 0.00 0.00 0.00 4.68
2437 2516 1.272769 CCGGTCTTCTTCCTCTTCGTT 59.727 52.381 0.00 0.00 0.00 3.85
2530 2609 1.446907 ACTTCATTGCGCTCTTCCTG 58.553 50.000 9.73 0.00 0.00 3.86
2931 3580 2.800250 CCCAAGTTCAGCAAGATCCTT 58.200 47.619 0.00 0.00 0.00 3.36
3016 3665 2.026301 CCGACTCCGATTCCTCGC 59.974 66.667 0.00 0.00 43.66 5.03
3067 3731 3.372554 AAAGCCGAGCCGTAGAGCC 62.373 63.158 0.00 0.00 0.00 4.70
3276 3960 5.163844 CGTAGGTCGATCCATCTGTGTATAG 60.164 48.000 0.00 0.00 42.86 1.31
3286 3970 4.215827 CCATCTGTGTATAGGTCTACGGAC 59.784 50.000 0.00 0.00 41.43 4.79
3292 3976 6.301486 TGTGTATAGGTCTACGGACATGTAT 58.699 40.000 0.00 0.00 43.77 2.29
3293 3977 7.452562 TGTGTATAGGTCTACGGACATGTATA 58.547 38.462 0.00 0.00 43.77 1.47
3319 4003 8.419076 ACAGAAATAAACCAACAAACATTGTC 57.581 30.769 0.00 0.00 44.59 3.18
3339 4023 1.815003 CTGGACCTTGCAGAATTGGTC 59.185 52.381 13.06 13.06 45.86 4.02
3363 4047 1.565759 TGATTCAGCATAGCCTGGGTT 59.434 47.619 2.65 0.00 33.64 4.11
3450 4134 1.408822 GGGAGAGATCGTGGGCAATTT 60.409 52.381 0.00 0.00 0.00 1.82
3826 4551 3.140225 CTCCGCCGAGGCTTCTACC 62.140 68.421 12.70 0.00 40.77 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.106475 GCGATATACAGCTAGCAGACTAACT 60.106 44.000 18.83 0.00 0.00 2.24
1 2 5.090083 GCGATATACAGCTAGCAGACTAAC 58.910 45.833 18.83 4.55 0.00 2.34
2 3 4.760204 TGCGATATACAGCTAGCAGACTAA 59.240 41.667 18.83 0.00 0.00 2.24
4 5 3.149981 TGCGATATACAGCTAGCAGACT 58.850 45.455 18.83 4.56 0.00 3.24
16 17 5.966636 TCACTGTGATGTTTGCGATATAC 57.033 39.130 6.36 0.00 0.00 1.47
19 20 4.502962 TGATCACTGTGATGTTTGCGATA 58.497 39.130 26.71 0.00 37.20 2.92
31 32 1.662629 GTGGCGAGAATGATCACTGTG 59.337 52.381 0.00 0.17 0.00 3.66
40 41 3.624326 TTTTGACTTGTGGCGAGAATG 57.376 42.857 0.00 0.00 0.00 2.67
48 49 4.226761 GCGATAAGGTTTTTGACTTGTGG 58.773 43.478 0.00 0.00 0.00 4.17
70 71 6.591448 ACGATGCAACATGTACTATATGGATG 59.409 38.462 0.00 0.00 0.00 3.51
77 78 4.119862 GGACACGATGCAACATGTACTAT 58.880 43.478 0.00 0.00 0.00 2.12
79 80 2.346803 GGACACGATGCAACATGTACT 58.653 47.619 0.00 0.00 0.00 2.73
170 171 3.801307 GGAGACCCTTACCCTCAAAAA 57.199 47.619 0.00 0.00 0.00 1.94
185 186 0.393448 GGCCCTTAGAATCGGGAGAC 59.607 60.000 0.00 0.00 43.44 3.36
307 312 1.483415 GGCGACAGTAGGGTGGAATAA 59.517 52.381 0.00 0.00 0.00 1.40
308 313 1.117150 GGCGACAGTAGGGTGGAATA 58.883 55.000 0.00 0.00 0.00 1.75
316 321 1.226603 GCACTACGGCGACAGTAGG 60.227 63.158 16.62 6.64 44.20 3.18
317 322 0.523546 CAGCACTACGGCGACAGTAG 60.524 60.000 16.62 15.67 45.11 2.57
319 324 1.239296 TACAGCACTACGGCGACAGT 61.239 55.000 16.62 13.71 39.27 3.55
320 325 0.797249 GTACAGCACTACGGCGACAG 60.797 60.000 16.62 12.98 39.27 3.51
323 328 3.157727 TAGTACAGCACTACGGCGA 57.842 52.632 16.62 0.00 38.80 5.54
558 570 3.797507 CTGGTGGTGCCTGCCAGTT 62.798 63.158 17.72 0.00 43.42 3.16
629 648 2.043227 CTACTAGCTTAGCTTGGCCCT 58.957 52.381 13.44 0.00 40.44 5.19
644 663 6.315714 AGGTGCTGGATTTATAGAGCTACTA 58.684 40.000 0.00 0.00 35.42 1.82
645 664 5.151454 AGGTGCTGGATTTATAGAGCTACT 58.849 41.667 0.00 0.00 32.41 2.57
646 665 5.245075 AGAGGTGCTGGATTTATAGAGCTAC 59.755 44.000 0.00 0.00 32.41 3.58
682 701 0.898326 TCGGAGTCAGGTTGCAGCTA 60.898 55.000 0.00 0.00 0.00 3.32
692 711 0.733150 TCGCAGTGTATCGGAGTCAG 59.267 55.000 0.00 0.00 0.00 3.51
695 714 1.032657 AGCTCGCAGTGTATCGGAGT 61.033 55.000 0.00 0.00 0.00 3.85
696 715 0.945099 TAGCTCGCAGTGTATCGGAG 59.055 55.000 0.00 0.00 0.00 4.63
697 716 0.945099 CTAGCTCGCAGTGTATCGGA 59.055 55.000 0.00 0.00 0.00 4.55
699 718 0.039978 CCCTAGCTCGCAGTGTATCG 60.040 60.000 0.00 0.00 0.00 2.92
700 719 0.319125 GCCCTAGCTCGCAGTGTATC 60.319 60.000 0.00 0.00 35.50 2.24
701 720 1.742768 GCCCTAGCTCGCAGTGTAT 59.257 57.895 0.00 0.00 35.50 2.29
702 721 2.771639 CGCCCTAGCTCGCAGTGTA 61.772 63.158 0.00 0.00 36.60 2.90
712 731 2.925162 ATTTCTCGGTGCGCCCTAGC 62.925 60.000 11.56 0.00 37.71 3.42
713 732 0.876342 GATTTCTCGGTGCGCCCTAG 60.876 60.000 11.56 8.88 0.00 3.02
714 733 1.143183 GATTTCTCGGTGCGCCCTA 59.857 57.895 11.56 0.00 0.00 3.53
724 743 1.852895 GACAACCGGATCGATTTCTCG 59.147 52.381 9.46 2.03 46.41 4.04
727 746 1.933853 CAGGACAACCGGATCGATTTC 59.066 52.381 9.46 0.00 41.83 2.17
729 748 0.902531 ACAGGACAACCGGATCGATT 59.097 50.000 9.46 0.00 41.83 3.34
739 762 1.798813 CTCGCCTAACAACAGGACAAC 59.201 52.381 0.00 0.00 38.00 3.32
756 780 1.959747 TCGTAAACTGTTCTCGCTCG 58.040 50.000 10.78 3.74 0.00 5.03
757 781 3.918591 TGAATCGTAAACTGTTCTCGCTC 59.081 43.478 10.78 10.16 0.00 5.03
758 782 3.673809 GTGAATCGTAAACTGTTCTCGCT 59.326 43.478 10.78 1.70 0.00 4.93
759 783 3.427528 TGTGAATCGTAAACTGTTCTCGC 59.572 43.478 10.78 2.63 0.00 5.03
761 785 5.462398 AGTGTGTGAATCGTAAACTGTTCTC 59.538 40.000 0.00 0.00 0.00 2.87
767 791 5.010314 TGGACTAGTGTGTGAATCGTAAACT 59.990 40.000 0.00 0.00 0.00 2.66
771 795 3.442625 CCTGGACTAGTGTGTGAATCGTA 59.557 47.826 0.00 0.00 0.00 3.43
783 807 7.593653 ACCAGTATATTCTTACCTGGACTAGT 58.406 38.462 10.74 0.00 34.83 2.57
784 808 9.233649 CTACCAGTATATTCTTACCTGGACTAG 57.766 40.741 10.74 0.00 34.83 2.57
785 809 8.168725 CCTACCAGTATATTCTTACCTGGACTA 58.831 40.741 10.74 0.00 34.83 2.59
806 846 5.128827 TGCCATATCGATCCTAAATCCTACC 59.871 44.000 0.00 0.00 0.00 3.18
891 934 7.770433 TGAACCAGAAGGACATAATCAAGTATG 59.230 37.037 0.00 0.00 38.69 2.39
913 956 5.207768 CGCTGCTGGAACATAATAATGAAC 58.792 41.667 0.00 0.00 38.20 3.18
973 1030 3.264947 TCGAGAAACCTGCAGAATCATG 58.735 45.455 17.39 0.00 0.00 3.07
1047 1105 3.753434 CTGGACGACTGCTCGCCT 61.753 66.667 0.00 0.00 44.33 5.52
1048 1106 3.691744 CTCTGGACGACTGCTCGCC 62.692 68.421 0.00 0.00 44.33 5.54
1070 1128 2.945398 GATGAGCAGCGACGGGAGAC 62.945 65.000 0.00 0.00 0.00 3.36
1694 1757 2.016318 CACTGACACAGTTCAAGGCAA 58.984 47.619 1.46 0.00 42.59 4.52
1699 1768 3.055458 TGAAGGTCACTGACACAGTTCAA 60.055 43.478 11.34 0.00 42.59 2.69
1726 1795 0.834687 AGACCCAACCGTTAGCCTCA 60.835 55.000 0.00 0.00 0.00 3.86
1727 1796 0.323957 AAGACCCAACCGTTAGCCTC 59.676 55.000 0.00 0.00 0.00 4.70
1749 1822 2.184448 CAACCACACGCAACAGAAAAG 58.816 47.619 0.00 0.00 0.00 2.27
1755 1828 0.449786 CTGAACAACCACACGCAACA 59.550 50.000 0.00 0.00 0.00 3.33
1756 1829 0.248458 CCTGAACAACCACACGCAAC 60.248 55.000 0.00 0.00 0.00 4.17
1757 1830 1.999071 GCCTGAACAACCACACGCAA 61.999 55.000 0.00 0.00 0.00 4.85
1758 1831 2.477176 GCCTGAACAACCACACGCA 61.477 57.895 0.00 0.00 0.00 5.24
1759 1832 2.331451 GCCTGAACAACCACACGC 59.669 61.111 0.00 0.00 0.00 5.34
1760 1833 1.821759 TGGCCTGAACAACCACACG 60.822 57.895 3.32 0.00 0.00 4.49
1761 1834 4.251246 TGGCCTGAACAACCACAC 57.749 55.556 3.32 0.00 0.00 3.82
1764 1837 2.203280 CCGTGGCCTGAACAACCA 60.203 61.111 3.32 0.00 0.00 3.67
1765 1838 1.966451 CTCCGTGGCCTGAACAACC 60.966 63.158 3.32 0.00 0.00 3.77
1766 1839 1.966451 CCTCCGTGGCCTGAACAAC 60.966 63.158 3.32 0.00 0.00 3.32
1767 1840 1.122632 TACCTCCGTGGCCTGAACAA 61.123 55.000 3.32 0.00 40.22 2.83
1879 1952 2.343758 GCCAGCGTCTTCCACAGA 59.656 61.111 0.00 0.00 0.00 3.41
2218 2297 4.329545 GCCACCTTGGACAGCCGA 62.330 66.667 0.00 0.00 40.96 5.54
2401 2480 2.610859 GGGTGGAGCTCCTTGGGA 60.611 66.667 32.28 10.16 36.82 4.37
2506 2585 0.539051 AGAGCGCAATGAAGTAGGCT 59.461 50.000 11.47 0.00 0.00 4.58
2530 2609 4.168760 GGTTACGTACCAGTGACATGTAC 58.831 47.826 0.00 0.00 46.92 2.90
2621 3065 5.645067 TCATCACAGACACAAATCAGAATCC 59.355 40.000 0.00 0.00 0.00 3.01
2727 3376 0.316772 ACGTTATGGTCGCGATCGAG 60.317 55.000 21.57 17.16 46.46 4.04
2931 3580 4.742201 GAGGAGCGGAAGTGCGCA 62.742 66.667 19.35 5.66 40.67 6.09
3016 3665 0.179161 GACGGATCGGTGTCTGTGAG 60.179 60.000 11.07 0.00 37.82 3.51
3276 3960 5.762825 TCTGTTATACATGTCCGTAGACC 57.237 43.478 0.00 0.00 42.81 3.85
3292 3976 9.877178 ACAATGTTTGTTGGTTTATTTCTGTTA 57.123 25.926 0.00 0.00 42.22 2.41
3293 3977 8.785329 ACAATGTTTGTTGGTTTATTTCTGTT 57.215 26.923 0.00 0.00 42.22 3.16
3319 4003 1.815003 GACCAATTCTGCAAGGTCCAG 59.185 52.381 9.53 0.00 43.67 3.86
3339 4023 2.483106 CCAGGCTATGCTGAATCATTCG 59.517 50.000 0.00 0.00 0.00 3.34
3363 4047 6.551975 TGGATACGGAGTTAGATTTGGTATGA 59.448 38.462 0.00 0.00 37.78 2.15
3450 4134 6.303021 ACGTTACGCCTTTCTTGATTAAAA 57.697 33.333 4.09 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.