Multiple sequence alignment - TraesCS1B01G195200

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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 TraesCS1B01G195200 chr1B 100.000 6331 0 0 692 7022 350391339 350397669 0.000000e+00 11692.0
1 TraesCS1B01G195200 chr1B 85.753 365 43 5 5720 6076 614794129 614794492 1.850000e-100 377.0
2 TraesCS1B01G195200 chr1B 82.793 401 53 10 3532 3920 614791638 614792034 1.880000e-90 344.0
3 TraesCS1B01G195200 chr1B 82.020 406 69 3 3072 3474 614791152 614791556 6.740000e-90 342.0
4 TraesCS1B01G195200 chr1B 85.556 270 31 1 5050 5311 614793628 614793897 6.940000e-70 276.0
5 TraesCS1B01G195200 chr1B 100.000 137 0 0 1 137 350390648 350390784 3.250000e-63 254.0
6 TraesCS1B01G195200 chr1B 87.692 130 16 0 2228 2357 614790349 614790478 1.220000e-32 152.0
7 TraesCS1B01G195200 chr1D 96.871 4346 97 15 2693 7022 261740250 261735928 0.000000e+00 7236.0
8 TraesCS1B01G195200 chr1D 96.712 1916 61 2 699 2613 261742161 261740247 0.000000e+00 3188.0
9 TraesCS1B01G195200 chr1D 78.850 922 166 14 995 1891 449274910 449275827 4.690000e-166 595.0
10 TraesCS1B01G195200 chr1D 79.927 548 88 17 3973 4504 449278301 449278842 3.970000e-102 383.0
11 TraesCS1B01G195200 chr1D 85.753 365 43 5 5720 6076 449279855 449280218 1.850000e-100 377.0
12 TraesCS1B01G195200 chr1D 83.173 416 64 5 3063 3474 449276790 449277203 6.650000e-100 375.0
13 TraesCS1B01G195200 chr1D 85.251 339 41 5 3532 3861 449277285 449277623 2.430000e-89 340.0
14 TraesCS1B01G195200 chr1D 88.462 130 15 0 2228 2357 449275986 449276115 2.620000e-34 158.0
15 TraesCS1B01G195200 chr1D 100.000 34 0 0 1 34 261742511 261742478 5.880000e-06 63.9
16 TraesCS1B01G195200 chr1A 95.037 4352 125 33 2693 7022 338584830 338589112 0.000000e+00 6756.0
17 TraesCS1B01G195200 chr1A 96.358 1922 62 4 699 2613 338582913 338584833 0.000000e+00 3155.0
18 TraesCS1B01G195200 chr1A 78.696 920 172 11 995 1891 544465521 544466439 6.070000e-165 592.0
19 TraesCS1B01G195200 chr1A 87.042 355 37 5 5720 6066 544474779 544475132 6.600000e-105 392.0
20 TraesCS1B01G195200 chr1A 82.679 433 67 7 3056 3482 544467401 544467831 1.850000e-100 377.0
21 TraesCS1B01G195200 chr1A 79.511 532 88 15 3986 4504 544468246 544468769 6.700000e-95 359.0
22 TraesCS1B01G195200 chr1A 84.615 338 41 10 3527 3854 544467900 544468236 6.790000e-85 326.0
23 TraesCS1B01G195200 chr1A 85.612 278 27 6 5037 5305 544474258 544474531 5.360000e-71 279.0
24 TraesCS1B01G195200 chr1A 99.265 136 1 0 1 136 338582271 338582406 5.440000e-61 246.0
25 TraesCS1B01G195200 chr1A 88.281 128 15 0 2228 2355 544466598 544466725 3.390000e-33 154.0
26 TraesCS1B01G195200 chr1A 91.071 112 10 0 692 803 338582374 338582485 1.220000e-32 152.0
27 TraesCS1B01G195200 chr1A 94.203 69 4 0 66 134 338582417 338582485 9.630000e-19 106.0
28 TraesCS1B01G195200 chr5A 86.301 146 20 0 6877 7022 683231731 683231876 7.290000e-35 159.0
29 TraesCS1B01G195200 chr4D 85.616 146 21 0 6877 7022 500849981 500850126 3.390000e-33 154.0
30 TraesCS1B01G195200 chr4D 84.247 146 23 0 6877 7022 500924415 500924560 7.340000e-30 143.0
31 TraesCS1B01G195200 chr4D 84.247 146 23 0 6877 7022 500960846 500960991 7.340000e-30 143.0
32 TraesCS1B01G195200 chr4D 83.562 146 23 1 6877 7022 500886891 500887035 1.230000e-27 135.0
33 TraesCS1B01G195200 chr4D 90.291 103 9 1 2613 2715 186610463 186610362 4.420000e-27 134.0
34 TraesCS1B01G195200 chr4B 85.616 146 21 0 6877 7022 644826475 644826620 3.390000e-33 154.0
35 TraesCS1B01G195200 chr4B 94.737 95 3 1 2603 2695 507357678 507357772 5.680000e-31 147.0
36 TraesCS1B01G195200 chr4B 95.556 90 4 0 2608 2697 421577974 421577885 2.040000e-30 145.0
37 TraesCS1B01G195200 chr4B 90.654 107 10 0 2596 2702 9467704 9467810 7.340000e-30 143.0
38 TraesCS1B01G195200 chr7A 98.824 85 1 0 2611 2695 556571120 556571036 1.220000e-32 152.0
39 TraesCS1B01G195200 chrUn 84.247 146 23 0 6877 7022 317845302 317845157 7.340000e-30 143.0
40 TraesCS1B01G195200 chrUn 91.089 101 9 0 2603 2703 75308377 75308477 3.420000e-28 137.0
41 TraesCS1B01G195200 chrUn 91.837 98 8 0 2606 2703 242405300 242405203 3.420000e-28 137.0
42 TraesCS1B01G195200 chr5D 94.565 92 5 0 2603 2694 547069803 547069894 7.340000e-30 143.0
43 TraesCS1B01G195200 chr2B 88.288 111 11 2 2606 2715 682450997 682450888 1.590000e-26 132.0


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 TraesCS1B01G195200 chr1B 350390648 350397669 7021 False 5973.000000 11692 100.000000 1 7022 2 chr1B.!!$F1 7021
1 TraesCS1B01G195200 chr1B 614790349 614794492 4143 False 298.200000 377 84.762800 2228 6076 5 chr1B.!!$F2 3848
2 TraesCS1B01G195200 chr1D 261735928 261742511 6583 True 3495.966667 7236 97.861000 1 7022 3 chr1D.!!$R1 7021
3 TraesCS1B01G195200 chr1D 449274910 449280218 5308 False 371.333333 595 83.569333 995 6076 6 chr1D.!!$F1 5081
4 TraesCS1B01G195200 chr1A 338582271 338589112 6841 False 2083.000000 6756 95.186800 1 7022 5 chr1A.!!$F1 7021
5 TraesCS1B01G195200 chr1A 544465521 544468769 3248 False 361.600000 592 82.756400 995 4504 5 chr1A.!!$F2 3509
6 TraesCS1B01G195200 chr1A 544474258 544475132 874 False 335.500000 392 86.327000 5037 6066 2 chr1A.!!$F3 1029

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
891 892 2.258591 CACGACTACACGCAGGCT 59.741 61.111 0.00 0.00 36.70 4.58 F
1350 1372 0.471617 CCATCCCTGCCGAGAATCTT 59.528 55.000 0.00 0.00 0.00 2.40 F
1654 1676 1.083806 ATGCTGGCGTGACATGTACG 61.084 55.000 17.82 17.82 43.93 3.67 F
2250 2291 0.680921 AGGATGGTTTCATGGGCACG 60.681 55.000 0.00 0.00 32.98 5.34 F
2626 2690 0.042131 TTGTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00 F
2628 2692 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90 F
4133 4924 3.312736 AGGCAAAAGAGAGGTTTTCCA 57.687 42.857 0.00 0.00 43.73 3.53 F
4529 5337 0.249073 ACGCTATGCTGGCTCTAACG 60.249 55.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2229 0.032813 CAGGAATGGGGCCAGACATT 60.033 55.000 16.48 16.48 39.81 2.71 R
2250 2291 0.992802 GACGTGTTTCCTCATCTCGC 59.007 55.000 0.00 0.00 0.00 5.03 R
2609 2673 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73 R
4150 4941 0.182775 GATTACCCTCGGGCCACATT 59.817 55.000 4.39 0.00 39.32 2.71 R
4507 5315 0.385751 TAGAGCCAGCATAGCGTGTC 59.614 55.000 0.00 0.00 34.64 3.67 R
4529 5337 2.929398 CTGGAACAAACCAAAACTGCAC 59.071 45.455 0.00 0.00 38.70 4.57 R
5671 6678 0.613260 TCCAGAAATACCAGCTGCGT 59.387 50.000 8.66 10.58 0.00 5.24 R
6068 7085 0.904649 TCGGCATCTCTGTTGTCCAT 59.095 50.000 0.00 0.00 0.00 3.41 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
790 791 2.445492 CTTCCACCACCAGCCCCATT 62.445 60.000 0.00 0.00 0.00 3.16
831 832 2.434359 GCCTCCGCACCACACTAC 60.434 66.667 0.00 0.00 34.03 2.73
869 870 2.401766 CCAACATGCACCTCTCCGC 61.402 63.158 0.00 0.00 0.00 5.54
887 888 4.710695 CCGCCACGACTACACGCA 62.711 66.667 0.00 0.00 36.70 5.24
891 892 2.258591 CACGACTACACGCAGGCT 59.741 61.111 0.00 0.00 36.70 4.58
895 896 3.701604 GACTACACGCAGGCTCCCG 62.702 68.421 2.85 2.85 0.00 5.14
915 916 3.129502 TCGTCGCCCTCCGTACTG 61.130 66.667 0.00 0.00 38.35 2.74
933 934 2.352805 CCGCCTTCTGCCTCCTTT 59.647 61.111 0.00 0.00 36.24 3.11
940 941 2.958355 CCTTCTGCCTCCTTTTCAAACA 59.042 45.455 0.00 0.00 0.00 2.83
975 976 4.407551 GTGCCGTATGGTACCGTC 57.592 61.111 10.72 1.74 44.38 4.79
1134 1153 2.746277 GTCGGCGGCAAGTCCAAT 60.746 61.111 6.63 0.00 34.01 3.16
1215 1237 3.841643 CACCTACGTCGTTTCCAATAGT 58.158 45.455 1.78 0.00 0.00 2.12
1243 1265 1.781025 CGTTTGGGCGCAGAACTTCA 61.781 55.000 10.83 0.00 0.00 3.02
1305 1327 2.417719 GTCAAGGACAGCGATGTCTTT 58.582 47.619 30.52 26.98 38.40 2.52
1350 1372 0.471617 CCATCCCTGCCGAGAATCTT 59.528 55.000 0.00 0.00 0.00 2.40
1362 1384 3.135530 CCGAGAATCTTCTTTCTGGGGAT 59.864 47.826 7.20 0.00 43.84 3.85
1654 1676 1.083806 ATGCTGGCGTGACATGTACG 61.084 55.000 17.82 17.82 43.93 3.67
1912 1936 7.304497 AGGTCTTTACACTACATGAAGAACT 57.696 36.000 0.00 0.82 35.40 3.01
2188 2229 7.811653 TGTTATTTTCGTTAGATGCATGTTCA 58.188 30.769 2.46 0.00 0.00 3.18
2250 2291 0.680921 AGGATGGTTTCATGGGCACG 60.681 55.000 0.00 0.00 32.98 5.34
2357 2398 1.737793 GGTGAAACAGCAGGTTATCCG 59.262 52.381 0.00 0.00 39.29 4.18
2432 2487 6.309494 TGAAACTATATGTTCACTGCACGTAC 59.691 38.462 0.00 0.00 38.03 3.67
2462 2518 8.642935 TGTGAATGGTTTCATTTATCTACCAA 57.357 30.769 0.00 0.00 43.49 3.67
2590 2654 8.565896 TCTAATCACAAAATGCAGTTCTATGT 57.434 30.769 0.00 0.00 0.00 2.29
2626 2690 0.042131 TTGTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
2628 2692 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
2636 2700 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2637 2701 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2638 2702 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
2642 2706 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
2644 2708 9.044150 CCGTCCCATAATATAAGAACGTTTTTA 57.956 33.333 13.02 13.02 0.00 1.52
2659 2723 9.154847 AGAACGTTTTTAAAACTACACTAGTGT 57.845 29.630 30.13 30.13 46.87 3.55
2661 2725 8.477984 ACGTTTTTAAAACTACACTAGTGTCA 57.522 30.769 31.11 16.36 43.74 3.58
2663 2727 9.757859 CGTTTTTAAAACTACACTAGTGTCAAA 57.242 29.630 31.11 17.93 43.74 2.69
2667 2731 9.757859 TTTAAAACTACACTAGTGTCAAAAACG 57.242 29.630 31.11 13.90 43.74 3.60
2668 2732 6.973229 AAACTACACTAGTGTCAAAAACGT 57.027 33.333 31.11 14.47 43.74 3.99
2676 2742 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
2732 2884 7.039434 TGCCATTTGTTTAACATATGAAGGTCA 60.039 33.333 23.31 12.91 39.05 4.02
2913 3065 5.253330 ACTCTTCAAACTTCACACAAGGAA 58.747 37.500 0.00 0.00 0.00 3.36
3381 3544 5.182570 TGATGCACTTCTCAAGATTGAAAGG 59.817 40.000 15.48 1.22 36.64 3.11
3507 3703 7.213678 TCAAAGTGTTTTCCTTCTTGTTTTGT 58.786 30.769 0.00 0.00 0.00 2.83
3672 3880 7.905126 TGACATTATATTCTACAGTTTGTGCG 58.095 34.615 0.00 0.00 0.00 5.34
3768 3976 5.595542 ACATACAGCTTATGTGAATGCCATT 59.404 36.000 16.04 0.00 43.80 3.16
3837 4045 5.971202 CGGTTCTTCATTTAATTGGGATTCG 59.029 40.000 0.00 0.00 0.00 3.34
4054 4845 7.596494 ACTCATGATGGTAAAATTGTTGTCTG 58.404 34.615 0.00 0.00 0.00 3.51
4132 4923 5.784578 TTAAGGCAAAAGAGAGGTTTTCC 57.215 39.130 0.00 0.00 41.05 3.13
4133 4924 3.312736 AGGCAAAAGAGAGGTTTTCCA 57.687 42.857 0.00 0.00 43.73 3.53
4150 4941 7.037873 AGGTTTTCCACATACATAGTAGTTCCA 60.038 37.037 0.00 0.00 43.73 3.53
4499 5307 9.357652 TGTGAATTTCTCTCTTGTTTTTCTTTG 57.642 29.630 0.00 0.00 0.00 2.77
4506 5314 9.981114 TTCTCTCTTGTTTTTCTTTGAAGTTTT 57.019 25.926 0.00 0.00 0.00 2.43
4507 5315 9.410556 TCTCTCTTGTTTTTCTTTGAAGTTTTG 57.589 29.630 0.00 0.00 0.00 2.44
4529 5337 0.249073 ACGCTATGCTGGCTCTAACG 60.249 55.000 0.00 0.00 0.00 3.18
4555 5363 5.623596 GCAGTTTTGGTTTGTTCCAGTAAGT 60.624 40.000 0.00 0.00 38.80 2.24
4753 5727 1.136305 CTGGCCCTTTGCAGATGAATG 59.864 52.381 0.00 0.00 43.89 2.67
4758 5741 2.086869 CCTTTGCAGATGAATGACGGT 58.913 47.619 0.00 0.00 0.00 4.83
4912 5896 3.681417 GCCTTTGGATGAACAATTGAAGC 59.319 43.478 13.59 0.00 0.00 3.86
4978 5962 7.899648 TTTTTGTGGGGATAGTTTGAACTTA 57.100 32.000 1.20 0.00 40.37 2.24
5039 6023 7.057894 ACTAGTTGTTGGGACATGAAACTTAA 58.942 34.615 0.00 0.00 39.30 1.85
5040 6024 6.144078 AGTTGTTGGGACATGAAACTTAAC 57.856 37.500 0.00 1.11 39.30 2.01
5290 6282 4.924305 TTCAAGTTCAAGCTGCTGAATT 57.076 36.364 1.35 3.65 37.63 2.17
5399 6391 3.403968 TGTTATGCGTTGCTTAGAACCA 58.596 40.909 0.00 0.00 0.00 3.67
5466 6458 1.133407 GAGAGACTGCCTCCAACTACG 59.867 57.143 0.00 0.00 42.97 3.51
5532 6533 9.512435 AAACTATAGACACGTAATGACACATAC 57.488 33.333 6.78 0.00 0.00 2.39
5622 6625 3.356290 ACAGCAGTGAAAAAGGTTGTCT 58.644 40.909 0.00 0.00 0.00 3.41
5631 6634 7.176690 CAGTGAAAAAGGTTGTCTGGGTATATT 59.823 37.037 0.00 0.00 0.00 1.28
6068 7085 5.570205 TGTTGGTGACTTCTTGGGTATTA 57.430 39.130 0.00 0.00 0.00 0.98
6222 7241 1.118838 CTGCCTTTTGGTTGTTCCCA 58.881 50.000 0.00 0.00 42.99 4.37
6268 7287 7.786046 TTACATGTATTCGGTCCCTGTATAT 57.214 36.000 6.36 0.00 0.00 0.86
6406 7425 5.212532 TGCAAAACTGTAAATGCATCCTT 57.787 34.783 0.00 0.00 43.32 3.36
6411 7430 5.376854 AACTGTAAATGCATCCTTCACAC 57.623 39.130 0.00 0.00 0.00 3.82
6444 7463 1.367471 GTTGGGCCTTGGTTTGCTC 59.633 57.895 4.53 0.00 0.00 4.26
6538 7560 1.205417 GAACCACCATCATGCCTTTGG 59.795 52.381 0.00 0.00 36.56 3.28
6539 7561 0.615544 ACCACCATCATGCCTTTGGG 60.616 55.000 7.79 0.00 34.72 4.12
6595 7618 7.067372 CAGAGAAATGCATGTTAAAGGGATGTA 59.933 37.037 0.00 0.00 0.00 2.29
6853 7877 8.715088 CATTCATTCAGATCAGTATAATTGCGA 58.285 33.333 0.00 0.00 0.00 5.10
6946 7970 0.532573 TGAAGGTGGAGCTGTCGATC 59.467 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
691 692 0.555769 GGATGGGGCTGGTAATGGAA 59.444 55.000 0.00 0.00 0.00 3.53
692 693 1.360393 GGGATGGGGCTGGTAATGGA 61.360 60.000 0.00 0.00 0.00 3.41
693 694 1.153756 GGGATGGGGCTGGTAATGG 59.846 63.158 0.00 0.00 0.00 3.16
694 695 0.111253 GAGGGATGGGGCTGGTAATG 59.889 60.000 0.00 0.00 0.00 1.90
695 696 1.418908 CGAGGGATGGGGCTGGTAAT 61.419 60.000 0.00 0.00 0.00 1.89
696 697 2.070039 CGAGGGATGGGGCTGGTAA 61.070 63.158 0.00 0.00 0.00 2.85
697 698 2.445845 CGAGGGATGGGGCTGGTA 60.446 66.667 0.00 0.00 0.00 3.25
780 781 4.883354 GCCGAGGAATGGGGCTGG 62.883 72.222 0.00 0.00 43.52 4.85
825 826 0.744874 CATCGACGATGGGGTAGTGT 59.255 55.000 26.65 0.00 36.51 3.55
876 877 2.202623 GGAGCCTGCGTGTAGTCG 60.203 66.667 0.00 0.00 0.00 4.18
895 896 3.434319 TACGGAGGGCGACGACAC 61.434 66.667 1.63 0.00 0.00 3.67
915 916 3.927481 AAAGGAGGCAGAAGGCGGC 62.927 63.158 0.00 0.00 46.16 6.53
920 921 3.633986 ACTGTTTGAAAAGGAGGCAGAAG 59.366 43.478 0.00 0.00 0.00 2.85
933 934 1.144708 TGCATCCCTCCACTGTTTGAA 59.855 47.619 0.00 0.00 0.00 2.69
940 941 0.622738 ACCATCTGCATCCCTCCACT 60.623 55.000 0.00 0.00 0.00 4.00
984 985 2.678580 ATGCTGCCATGCTGTGCA 60.679 55.556 0.00 0.00 44.86 4.57
985 986 2.202743 CATGCTGCCATGCTGTGC 60.203 61.111 0.00 0.00 42.08 4.57
1134 1153 1.810151 GGGTCGCTTGTCATTTTAGCA 59.190 47.619 0.00 0.00 34.62 3.49
1266 1288 1.337817 CGACGAACTCAACCTCAGCG 61.338 60.000 0.00 0.00 0.00 5.18
1320 1342 1.852157 AGGGATGGCCACAGTTCCA 60.852 57.895 21.89 0.00 36.70 3.53
1350 1372 3.976654 CCTCAATCCTATCCCCAGAAAGA 59.023 47.826 0.00 0.00 0.00 2.52
1362 1384 1.700955 GGTAGACGCCCTCAATCCTA 58.299 55.000 0.00 0.00 0.00 2.94
1407 1429 1.976132 ATACAGCACCAGGAGCGCAT 61.976 55.000 11.47 0.00 37.01 4.73
1671 1693 1.135517 ACAATGTAAATCAACCGCCGC 60.136 47.619 0.00 0.00 0.00 6.53
1929 1953 5.778161 TGCAAGATATGTTGTTCGTGTAG 57.222 39.130 13.58 0.00 0.00 2.74
1934 1958 6.803320 AGTTTGAATGCAAGATATGTTGTTCG 59.197 34.615 13.58 0.00 35.04 3.95
2029 2068 4.098349 ACAGCAACAAACATATATGGGCTG 59.902 41.667 24.12 24.12 46.00 4.85
2106 2146 9.914131 TCCTCTCGATATTGTTTATATGACAAG 57.086 33.333 10.83 0.96 40.04 3.16
2184 2225 1.478105 GAATGGGGCCAGACATTGAAC 59.522 52.381 20.08 6.44 37.43 3.18
2188 2229 0.032813 CAGGAATGGGGCCAGACATT 60.033 55.000 16.48 16.48 39.81 2.71
2250 2291 0.992802 GACGTGTTTCCTCATCTCGC 59.007 55.000 0.00 0.00 0.00 5.03
2462 2518 6.101734 ACATCCAAGGATACATAAGTCATGGT 59.898 38.462 0.40 0.00 34.10 3.55
2523 2587 3.153919 GGCCAAACAGTGAACCTATTCA 58.846 45.455 0.00 0.00 42.73 2.57
2609 2673 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2614 2678 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2636 2700 8.477984 TGACACTAGTGTAGTTTTAAAAACGT 57.522 30.769 27.98 0.00 45.05 3.99
2637 2701 9.757859 TTTGACACTAGTGTAGTTTTAAAAACG 57.242 29.630 27.98 0.00 45.05 3.60
2642 2706 8.934825 ACGTTTTTGACACTAGTGTAGTTTTAA 58.065 29.630 27.98 14.27 45.05 1.52
2644 2708 7.368480 ACGTTTTTGACACTAGTGTAGTTTT 57.632 32.000 27.98 4.69 45.05 2.43
2646 2710 6.815142 AGAACGTTTTTGACACTAGTGTAGTT 59.185 34.615 27.98 21.29 45.05 2.24
2647 2711 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
2656 2720 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
2657 2721 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
2659 2723 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
2661 2725 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
2663 2727 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
2664 2728 7.289317 TCCTCTGTCCCATAATATAAGAACGTT 59.711 37.037 0.00 0.00 0.00 3.99
2666 2730 7.228314 TCCTCTGTCCCATAATATAAGAACG 57.772 40.000 0.00 0.00 0.00 3.95
2667 2731 8.652290 ACTTCCTCTGTCCCATAATATAAGAAC 58.348 37.037 0.00 0.00 0.00 3.01
2668 2732 8.798975 ACTTCCTCTGTCCCATAATATAAGAA 57.201 34.615 0.00 0.00 0.00 2.52
2676 2742 4.069312 TGGTACTTCCTCTGTCCCATAA 57.931 45.455 0.00 0.00 37.07 1.90
2678 2744 2.642171 TGGTACTTCCTCTGTCCCAT 57.358 50.000 0.00 0.00 37.07 4.00
2732 2884 3.641436 GGTTCCTGTTTCCTGGTTTTCAT 59.359 43.478 0.00 0.00 0.00 2.57
2913 3065 8.806146 ACAGCAAAGTTTGGATTGTAATAATCT 58.194 29.630 17.11 0.00 0.00 2.40
3001 3153 4.520874 TGAGAAACTGAACCAACACACAAA 59.479 37.500 0.00 0.00 0.00 2.83
3054 3211 5.593095 ACAAAAGGTTCCTACTCCTCAAAAC 59.407 40.000 0.00 0.00 33.09 2.43
3404 3567 7.739022 TTGTCGCTAAAATAAATTGCATCAG 57.261 32.000 0.00 0.00 0.00 2.90
3507 3703 4.774726 ACTAAGAGAGTTGAATGCCTGAGA 59.225 41.667 0.00 0.00 33.13 3.27
3549 3747 5.047590 TGAGTCAATAGAGCGAAACACCTAA 60.048 40.000 0.00 0.00 0.00 2.69
3672 3880 5.633601 GCCAAAATAAAAGTGTTAGTCAGCC 59.366 40.000 0.00 0.00 0.00 4.85
3768 3976 1.068948 TAAAGTGTTGGGCTGCCCTA 58.931 50.000 35.80 27.60 45.70 3.53
3837 4045 8.462016 AGAACATGCTTACCAATATCTTTGTTC 58.538 33.333 0.00 0.00 39.46 3.18
4054 4845 2.525368 ACCAAATTGTTAGCCCCTGAC 58.475 47.619 0.00 0.00 0.00 3.51
4132 4923 6.017934 GCCACATTGGAACTACTATGTATGTG 60.018 42.308 0.00 0.00 40.96 3.21
4133 4924 6.055588 GCCACATTGGAACTACTATGTATGT 58.944 40.000 0.00 0.00 40.96 2.29
4150 4941 0.182775 GATTACCCTCGGGCCACATT 59.817 55.000 4.39 0.00 39.32 2.71
4396 5201 4.997565 TGCCAAGACAAAAGAAGTTCAAG 58.002 39.130 5.50 0.00 0.00 3.02
4499 5307 3.482786 CAGCATAGCGTGTCAAAACTTC 58.517 45.455 0.00 0.00 0.00 3.01
4506 5314 1.153568 GAGCCAGCATAGCGTGTCA 60.154 57.895 0.00 0.00 34.64 3.58
4507 5315 0.385751 TAGAGCCAGCATAGCGTGTC 59.614 55.000 0.00 0.00 34.64 3.67
4529 5337 2.929398 CTGGAACAAACCAAAACTGCAC 59.071 45.455 0.00 0.00 38.70 4.57
4555 5363 7.106439 TGATTGAAAGCTAAACCAGTTCAAA 57.894 32.000 10.58 0.00 0.00 2.69
4753 5727 6.645790 TTAAGAACTAGGGATATGACCGTC 57.354 41.667 0.00 0.00 0.00 4.79
4876 5860 2.229784 CCAAAGGCCTGTCTTAAGCAAG 59.770 50.000 5.69 0.00 0.00 4.01
4912 5896 3.899835 TCAACATAACTCGCGAAATCG 57.100 42.857 11.33 0.00 43.27 3.34
4921 5905 3.273434 TGGCAGAGCATCAACATAACTC 58.727 45.455 0.00 0.00 37.82 3.01
4978 5962 8.268850 ACTAGTGAAAATTCAAATACTGCGAT 57.731 30.769 0.00 0.00 39.21 4.58
5025 6009 7.649057 AGCAAGTAAAGTTAAGTTTCATGTCC 58.351 34.615 11.53 0.00 0.00 4.02
5039 6023 6.317391 GCTTGATCCTGAATAGCAAGTAAAGT 59.683 38.462 0.00 0.00 38.48 2.66
5040 6024 6.541641 AGCTTGATCCTGAATAGCAAGTAAAG 59.458 38.462 0.00 0.00 38.48 1.85
5113 6097 8.601476 CCAATGATCACATATTCATCATCTACG 58.399 37.037 0.00 0.00 36.45 3.51
5399 6391 6.040842 AGGTGAAACAATTGTAATGAAGCAGT 59.959 34.615 12.39 0.00 39.98 4.40
5532 6533 4.699735 TGTAGAATTGCCACCAACAGTATG 59.300 41.667 0.00 0.00 46.00 2.39
5622 6625 8.633724 ACCCTAAGAGATGAGATAATATACCCA 58.366 37.037 0.00 0.00 0.00 4.51
5666 6673 3.871006 CAGAAATACCAGCTGCGTCATAA 59.129 43.478 8.66 0.00 0.00 1.90
5667 6674 3.457234 CAGAAATACCAGCTGCGTCATA 58.543 45.455 8.66 0.00 0.00 2.15
5668 6675 2.283298 CAGAAATACCAGCTGCGTCAT 58.717 47.619 8.66 0.00 0.00 3.06
5669 6676 1.675714 CCAGAAATACCAGCTGCGTCA 60.676 52.381 8.66 0.00 0.00 4.35
5670 6677 1.009829 CCAGAAATACCAGCTGCGTC 58.990 55.000 8.66 0.21 0.00 5.19
5671 6678 0.613260 TCCAGAAATACCAGCTGCGT 59.387 50.000 8.66 10.58 0.00 5.24
5672 6679 1.959042 ATCCAGAAATACCAGCTGCG 58.041 50.000 8.66 4.27 0.00 5.18
6068 7085 0.904649 TCGGCATCTCTGTTGTCCAT 59.095 50.000 0.00 0.00 0.00 3.41
6191 7210 4.590222 ACCAAAAGGCAGAAATGACTTGAT 59.410 37.500 0.00 0.00 37.20 2.57
6268 7287 6.233434 GGATCCAGCATGTAATCATCTTACA 58.767 40.000 6.95 0.74 38.99 2.41
6373 7392 9.301153 CATTTACAGTTTTGCACTAGAAACTTT 57.699 29.630 10.78 8.17 42.47 2.66
6406 7425 5.181811 CCAACATTGCTTCAGAATAGTGTGA 59.818 40.000 0.00 0.00 0.00 3.58
6411 7430 3.181483 GGCCCAACATTGCTTCAGAATAG 60.181 47.826 0.00 0.00 0.00 1.73
6444 7463 5.186409 ACCAATTTCCATTGATGACAAGAGG 59.814 40.000 0.00 0.00 42.35 3.69
6595 7618 9.874205 CTGTTTGTTGATTATTATGAAACCCAT 57.126 29.630 0.00 0.00 39.25 4.00
6813 7837 8.037382 TCTGAATGAATGAATCAACTCAACTC 57.963 34.615 3.07 4.31 42.54 3.01
6814 7838 7.991084 TCTGAATGAATGAATCAACTCAACT 57.009 32.000 3.07 0.00 42.54 3.16
6815 7839 8.456471 TGATCTGAATGAATGAATCAACTCAAC 58.544 33.333 3.07 2.52 42.54 3.18
6816 7840 8.570068 TGATCTGAATGAATGAATCAACTCAA 57.430 30.769 3.07 0.00 42.54 3.02
6817 7841 7.827729 ACTGATCTGAATGAATGAATCAACTCA 59.172 33.333 6.60 1.64 42.54 3.41
6853 7877 1.813513 CGCAAGTCTGAAATGACCCT 58.186 50.000 0.00 0.00 37.66 4.34
6946 7970 3.721706 GTGAGGGGGCTCAGGGTG 61.722 72.222 0.00 0.00 33.58 4.61


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

AutoCloner maintained by Alex Coulton.