Multiple sequence alignment - TraesCS3A01G299100

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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 TraesCS3A01G299100 chr3A 100.000 3836 0 0 1 3836 533590395 533594230 0.000000e+00 7084
1 TraesCS3A01G299100 chr3A 90.891 2536 222 7 1116 3648 709609080 709606551 0.000000e+00 3395
2 TraesCS3A01G299100 chr3A 85.742 1536 191 12 96 1628 682737496 682739006 0.000000e+00 1598
3 TraesCS3A01G299100 chr2D 92.872 3746 248 7 94 3836 78513348 78517077 0.000000e+00 5421
4 TraesCS3A01G299100 chr2D 88.263 3340 361 18 295 3628 18541016 18544330 0.000000e+00 3967
5 TraesCS3A01G299100 chr5D 93.080 3584 215 15 141 3720 325458531 325454977 0.000000e+00 5214
6 TraesCS3A01G299100 chr7D 89.768 3626 325 19 216 3836 3584388 3587972 0.000000e+00 4599
7 TraesCS3A01G299100 chr2B 90.321 2769 204 28 90 2850 461886186 461883474 0.000000e+00 3570
8 TraesCS3A01G299100 chr1D 92.447 2092 151 7 1749 3836 437519393 437517305 0.000000e+00 2981
9 TraesCS3A01G299100 chr1B 89.204 2260 240 4 1580 3836 563656840 563659098 0.000000e+00 2819
10 TraesCS3A01G299100 chr1B 96.512 86 3 0 1 86 72502835 72502920 3.990000e-30 143
11 TraesCS3A01G299100 chr1B 96.512 86 3 0 1 86 378025488 378025403 3.990000e-30 143
12 TraesCS3A01G299100 chr7A 88.710 2303 255 5 1537 3836 695988128 695985828 0.000000e+00 2808
13 TraesCS3A01G299100 chr7A 88.664 2223 246 6 1616 3836 144139139 144141357 0.000000e+00 2704
14 TraesCS3A01G299100 chr7A 79.924 1584 267 29 95 1667 311218791 311220334 0.000000e+00 1116
15 TraesCS3A01G299100 chr7A 86.084 812 95 12 101 910 34979222 34980017 0.000000e+00 857
16 TraesCS3A01G299100 chr3D 87.936 2263 264 9 1579 3836 608033141 608030883 0.000000e+00 2658
17 TraesCS3A01G299100 chr6A 86.824 2034 243 11 95 2126 24207898 24209908 0.000000e+00 2248
18 TraesCS3A01G299100 chr6A 97.674 86 2 0 1 86 69057886 69057971 8.590000e-32 148
19 TraesCS3A01G299100 chr3B 91.080 1648 130 6 120 1765 715290917 715289285 0.000000e+00 2213
20 TraesCS3A01G299100 chr1A 81.750 1326 216 17 94 1406 553737036 553735724 0.000000e+00 1085
21 TraesCS3A01G299100 chr1A 96.512 86 3 0 1 86 360865329 360865244 3.990000e-30 143
22 TraesCS3A01G299100 chr4A 92.537 670 35 8 85 752 738091728 738091072 0.000000e+00 946
23 TraesCS3A01G299100 chrUn 96.512 86 3 0 1 86 457722384 457722299 3.990000e-30 143
24 TraesCS3A01G299100 chrUn 96.512 86 3 0 1 86 463010893 463010978 3.990000e-30 143
25 TraesCS3A01G299100 chrUn 96.512 86 3 0 1 86 465657038 465656953 3.990000e-30 143
26 TraesCS3A01G299100 chr4B 96.512 86 3 0 1 86 141587897 141587982 3.990000e-30 143
27 TraesCS3A01G299100 chr4B 96.512 86 3 0 1 86 308562970 308562885 3.990000e-30 143


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 TraesCS3A01G299100 chr3A 533590395 533594230 3835 False 7084 7084 100.000 1 3836 1 chr3A.!!$F1 3835
1 TraesCS3A01G299100 chr3A 709606551 709609080 2529 True 3395 3395 90.891 1116 3648 1 chr3A.!!$R1 2532
2 TraesCS3A01G299100 chr3A 682737496 682739006 1510 False 1598 1598 85.742 96 1628 1 chr3A.!!$F2 1532
3 TraesCS3A01G299100 chr2D 78513348 78517077 3729 False 5421 5421 92.872 94 3836 1 chr2D.!!$F2 3742
4 TraesCS3A01G299100 chr2D 18541016 18544330 3314 False 3967 3967 88.263 295 3628 1 chr2D.!!$F1 3333
5 TraesCS3A01G299100 chr5D 325454977 325458531 3554 True 5214 5214 93.080 141 3720 1 chr5D.!!$R1 3579
6 TraesCS3A01G299100 chr7D 3584388 3587972 3584 False 4599 4599 89.768 216 3836 1 chr7D.!!$F1 3620
7 TraesCS3A01G299100 chr2B 461883474 461886186 2712 True 3570 3570 90.321 90 2850 1 chr2B.!!$R1 2760
8 TraesCS3A01G299100 chr1D 437517305 437519393 2088 True 2981 2981 92.447 1749 3836 1 chr1D.!!$R1 2087
9 TraesCS3A01G299100 chr1B 563656840 563659098 2258 False 2819 2819 89.204 1580 3836 1 chr1B.!!$F2 2256
10 TraesCS3A01G299100 chr7A 695985828 695988128 2300 True 2808 2808 88.710 1537 3836 1 chr7A.!!$R1 2299
11 TraesCS3A01G299100 chr7A 144139139 144141357 2218 False 2704 2704 88.664 1616 3836 1 chr7A.!!$F2 2220
12 TraesCS3A01G299100 chr7A 311218791 311220334 1543 False 1116 1116 79.924 95 1667 1 chr7A.!!$F3 1572
13 TraesCS3A01G299100 chr7A 34979222 34980017 795 False 857 857 86.084 101 910 1 chr7A.!!$F1 809
14 TraesCS3A01G299100 chr3D 608030883 608033141 2258 True 2658 2658 87.936 1579 3836 1 chr3D.!!$R1 2257
15 TraesCS3A01G299100 chr6A 24207898 24209908 2010 False 2248 2248 86.824 95 2126 1 chr6A.!!$F1 2031
16 TraesCS3A01G299100 chr3B 715289285 715290917 1632 True 2213 2213 91.080 120 1765 1 chr3B.!!$R1 1645
17 TraesCS3A01G299100 chr1A 553735724 553737036 1312 True 1085 1085 81.750 94 1406 1 chr1A.!!$R2 1312
18 TraesCS3A01G299100 chr4A 738091072 738091728 656 True 946 946 92.537 85 752 1 chr4A.!!$R1 667

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
475 481 0.179111 GGACGCCGACATGATTGAGA 60.179 55.0 0.00 0.00 0.00 3.27 F
542 548 1.167851 TGTGTGCAGCTGGATTTAGC 58.832 50.0 17.12 0.22 44.01 3.09 F
2090 2128 0.033504 GTTGCGGTGACTTCTGGAGA 59.966 55.0 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2112 0.109039 GTCTCTCCAGAAGTCACCGC 60.109 60.0 0.00 0.00 0.00 5.68 R
2276 2319 0.259356 ACCGAAGAGGAGAGGGTAGG 59.741 60.0 0.00 0.00 45.00 3.18 R
3184 3232 0.315568 GACTCTGCAGTCGTCACCTT 59.684 55.0 24.14 0.78 39.91 3.50 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
20 21 2.292103 TCGTCATGCGTGATGAATGA 57.708 45.000 25.20 10.18 45.08 2.57
21 22 2.825205 TCGTCATGCGTGATGAATGAT 58.175 42.857 25.20 0.00 44.64 2.45
22 23 3.197265 TCGTCATGCGTGATGAATGATT 58.803 40.909 25.20 0.00 44.64 2.57
23 24 3.622612 TCGTCATGCGTGATGAATGATTT 59.377 39.130 25.20 0.00 44.64 2.17
24 25 4.094739 TCGTCATGCGTGATGAATGATTTT 59.905 37.500 25.20 0.00 44.64 1.82
25 26 4.435554 CGTCATGCGTGATGAATGATTTTC 59.564 41.667 21.42 0.00 44.64 2.29
26 27 5.575957 GTCATGCGTGATGAATGATTTTCT 58.424 37.500 12.67 0.00 44.64 2.52
27 28 6.509997 CGTCATGCGTGATGAATGATTTTCTA 60.510 38.462 21.42 0.00 44.64 2.10
28 29 6.849811 GTCATGCGTGATGAATGATTTTCTAG 59.150 38.462 12.67 0.00 44.64 2.43
29 30 5.739752 TGCGTGATGAATGATTTTCTAGG 57.260 39.130 0.00 0.00 0.00 3.02
30 31 5.185454 TGCGTGATGAATGATTTTCTAGGT 58.815 37.500 0.00 0.00 0.00 3.08
31 32 5.647658 TGCGTGATGAATGATTTTCTAGGTT 59.352 36.000 0.00 0.00 0.00 3.50
32 33 6.183360 TGCGTGATGAATGATTTTCTAGGTTC 60.183 38.462 0.00 0.00 0.00 3.62
33 34 6.414079 CGTGATGAATGATTTTCTAGGTTCG 58.586 40.000 0.00 0.00 0.00 3.95
34 35 6.195165 GTGATGAATGATTTTCTAGGTTCGC 58.805 40.000 0.00 0.00 0.00 4.70
35 36 4.857871 TGAATGATTTTCTAGGTTCGCG 57.142 40.909 0.00 0.00 0.00 5.87
36 37 4.250464 TGAATGATTTTCTAGGTTCGCGT 58.750 39.130 5.77 0.00 0.00 6.01
37 38 5.412640 TGAATGATTTTCTAGGTTCGCGTA 58.587 37.500 5.77 0.00 0.00 4.42
38 39 5.518847 TGAATGATTTTCTAGGTTCGCGTAG 59.481 40.000 5.77 0.00 37.03 3.51
39 40 4.445452 TGATTTTCTAGGTTCGCGTAGT 57.555 40.909 5.77 0.00 37.02 2.73
40 41 4.813027 TGATTTTCTAGGTTCGCGTAGTT 58.187 39.130 5.77 0.00 37.02 2.24
41 42 5.232463 TGATTTTCTAGGTTCGCGTAGTTT 58.768 37.500 5.77 0.00 37.02 2.66
42 43 6.389091 TGATTTTCTAGGTTCGCGTAGTTTA 58.611 36.000 5.77 0.00 37.02 2.01
43 44 6.308766 TGATTTTCTAGGTTCGCGTAGTTTAC 59.691 38.462 5.77 0.00 37.02 2.01
44 45 4.764679 TTCTAGGTTCGCGTAGTTTACA 57.235 40.909 5.77 0.00 37.02 2.41
45 46 4.970662 TCTAGGTTCGCGTAGTTTACAT 57.029 40.909 5.77 0.00 37.02 2.29
46 47 5.314923 TCTAGGTTCGCGTAGTTTACATT 57.685 39.130 5.77 0.00 37.02 2.71
47 48 5.713025 TCTAGGTTCGCGTAGTTTACATTT 58.287 37.500 5.77 0.00 37.02 2.32
48 49 4.657075 AGGTTCGCGTAGTTTACATTTG 57.343 40.909 5.77 0.00 0.00 2.32
49 50 3.120442 AGGTTCGCGTAGTTTACATTTGC 60.120 43.478 5.77 0.00 0.00 3.68
50 51 3.120442 GGTTCGCGTAGTTTACATTTGCT 60.120 43.478 5.77 0.00 0.00 3.91
51 52 4.460505 GTTCGCGTAGTTTACATTTGCTT 58.539 39.130 5.77 0.00 0.00 3.91
52 53 4.735662 TCGCGTAGTTTACATTTGCTTT 57.264 36.364 5.77 0.00 0.00 3.51
53 54 5.098218 TCGCGTAGTTTACATTTGCTTTT 57.902 34.783 5.77 0.00 0.00 2.27
54 55 5.512473 TCGCGTAGTTTACATTTGCTTTTT 58.488 33.333 5.77 0.00 0.00 1.94
76 77 6.723298 TTTAGTTTGGTTGATTCCATGTGT 57.277 33.333 0.00 0.00 37.33 3.72
77 78 7.825331 TTTAGTTTGGTTGATTCCATGTGTA 57.175 32.000 0.00 0.00 37.33 2.90
78 79 7.825331 TTAGTTTGGTTGATTCCATGTGTAA 57.175 32.000 0.00 0.00 37.33 2.41
79 80 6.723298 AGTTTGGTTGATTCCATGTGTAAA 57.277 33.333 0.00 0.00 37.33 2.01
80 81 7.301868 AGTTTGGTTGATTCCATGTGTAAAT 57.698 32.000 0.00 0.00 37.33 1.40
81 82 7.153985 AGTTTGGTTGATTCCATGTGTAAATG 58.846 34.615 0.00 0.00 37.33 2.32
92 93 4.836825 CATGTGTAAATGGACTGAGGAGT 58.163 43.478 0.00 0.00 33.98 3.85
116 117 1.076632 GAGAGGGAGAGGCGGAGAA 60.077 63.158 0.00 0.00 0.00 2.87
118 119 2.042435 AGGGAGAGGCGGAGAAGG 60.042 66.667 0.00 0.00 0.00 3.46
214 220 4.584325 AGATCCATCTGTGCTCTCTTAGTC 59.416 45.833 0.00 0.00 35.42 2.59
298 304 1.153309 CTGCCGCATGGTGAGATCA 60.153 57.895 0.00 0.00 37.67 2.92
461 467 1.366854 GGTGATTTTCTCCCGGACGC 61.367 60.000 0.73 0.00 0.00 5.19
475 481 0.179111 GGACGCCGACATGATTGAGA 60.179 55.000 0.00 0.00 0.00 3.27
511 517 6.852858 TCAAACTTGATGTTTATGACGTGA 57.147 33.333 0.00 0.00 46.11 4.35
541 547 3.486375 CGAATGTGTGCAGCTGGATTTAG 60.486 47.826 17.12 2.81 0.00 1.85
542 548 1.167851 TGTGTGCAGCTGGATTTAGC 58.832 50.000 17.12 0.22 44.01 3.09
553 559 5.175090 GCTGGATTTAGCTGGATTTACAC 57.825 43.478 0.00 0.00 40.52 2.90
582 588 3.556633 GCACCGGAGATGATTGATCTGAT 60.557 47.826 9.46 0.00 41.91 2.90
589 595 3.651423 AGATGATTGATCTGATGGAGCCA 59.349 43.478 0.00 0.00 40.19 4.75
767 779 5.230306 CGGCGTTGTTCAAAAATTCAAACTA 59.770 36.000 0.00 0.00 0.00 2.24
984 998 2.031508 CGTTTGAACACGTTATTGGGCT 60.032 45.455 0.00 0.00 35.34 5.19
1091 1105 2.762043 TGCCATCCCGATCGGACA 60.762 61.111 35.42 21.13 46.09 4.02
1192 1214 1.700042 GGACGGGCAAGGAGGATCAT 61.700 60.000 0.00 0.00 36.25 2.45
1198 1220 2.107204 GGGCAAGGAGGATCATGTATGT 59.893 50.000 0.00 0.00 36.25 2.29
1199 1221 3.435601 GGGCAAGGAGGATCATGTATGTT 60.436 47.826 0.00 0.00 36.25 2.71
1428 1451 3.716381 CGCCTAGTGGTGGGGTTA 58.284 61.111 0.00 0.00 40.05 2.85
1610 1648 3.134127 GCCGGATGAAGTGGTGCC 61.134 66.667 5.05 0.00 0.00 5.01
1614 1652 2.401766 GGATGAAGTGGTGCCGCTG 61.402 63.158 4.93 0.00 36.83 5.18
1951 1989 3.319198 ACTACCCACCGCCACCAG 61.319 66.667 0.00 0.00 0.00 4.00
2090 2128 0.033504 GTTGCGGTGACTTCTGGAGA 59.966 55.000 0.00 0.00 0.00 3.71
2205 2248 4.384098 CCTTGCTATAGATGTGGTGAACCA 60.384 45.833 3.21 0.00 45.30 3.67
2252 2295 5.534278 TGAATGAACTTTGTGACTATTGCCA 59.466 36.000 0.00 0.00 0.00 4.92
2259 2302 1.270571 TGTGACTATTGCCAACGCTCA 60.271 47.619 0.00 0.00 35.36 4.26
2321 2364 7.891183 TCCTAAGCCTGGTATTAACATTTTTGA 59.109 33.333 0.00 0.00 0.00 2.69
2411 2454 1.281419 TCCTTCCCGGCAGTAATCAA 58.719 50.000 0.00 0.00 0.00 2.57
2473 2516 1.825474 AGCTACGTGACTTAGTGCCAT 59.175 47.619 0.00 0.00 0.00 4.40
2484 2527 7.011016 CGTGACTTAGTGCCATGTAATTATCAA 59.989 37.037 0.00 0.00 0.00 2.57
2569 2613 4.706962 AGATGCATTTTCTTAAGTGGGGTC 59.293 41.667 0.00 0.00 0.00 4.46
2593 2637 0.583438 CAGAGTCACAAGCACCAACG 59.417 55.000 0.00 0.00 0.00 4.10
2595 2639 0.582005 GAGTCACAAGCACCAACGTC 59.418 55.000 0.00 0.00 0.00 4.34
2596 2640 0.107897 AGTCACAAGCACCAACGTCA 60.108 50.000 0.00 0.00 0.00 4.35
2631 2675 1.376037 GTGGAAGCAGGAGGAACCG 60.376 63.158 0.00 0.00 44.74 4.44
2662 2706 2.666317 CTTTGGAGAAGGTGTGGGTTT 58.334 47.619 0.00 0.00 0.00 3.27
2687 2731 3.130819 TGGCGCGCCACCTAAATG 61.131 61.111 46.88 0.00 41.89 2.32
2697 2741 3.003689 CGCCACCTAAATGGATAAAGCAG 59.996 47.826 0.00 0.00 43.02 4.24
2765 2809 2.161855 GGTTGACATGCCATTCACTCA 58.838 47.619 0.00 0.00 0.00 3.41
2859 2905 4.222810 ACACATGCTGGAGTCACTTATGTA 59.777 41.667 0.00 0.00 0.00 2.29
2912 2958 0.464373 CAGGATGGGGACGGAACATG 60.464 60.000 0.00 0.00 0.00 3.21
2989 3037 0.973632 TGATACACTGCCGGAGTTGT 59.026 50.000 5.05 6.56 29.75 3.32
3002 3050 1.631898 GGAGTTGTACAAGGGGCCTAA 59.368 52.381 8.98 0.00 0.00 2.69
3022 3070 6.295916 GCCTAATACACAGCCAGATAAGGTAT 60.296 42.308 0.00 0.00 0.00 2.73
3286 3335 0.326927 GCCCTTAGCACCCAGTTACA 59.673 55.000 0.00 0.00 42.97 2.41
3421 3470 1.229723 TAACCCCTCCACAGGACCC 60.230 63.158 0.00 0.00 43.65 4.46
3452 3501 3.721706 GGTGAGCTGGGGGTGAGG 61.722 72.222 0.00 0.00 0.00 3.86
3528 3577 3.698765 GGGGGACGACGGTTTCTA 58.301 61.111 0.00 0.00 0.00 2.10
3635 3684 1.615424 GCCCTACCCTCCTTCACCA 60.615 63.158 0.00 0.00 0.00 4.17
3666 3716 3.311110 GCGTGGGAGTCCTGACCA 61.311 66.667 9.58 0.00 0.00 4.02
3736 3786 2.660064 GGATCTGGTGTCGGCTGGT 61.660 63.158 0.00 0.00 0.00 4.00
3827 3877 2.409055 GCCATGCTTCGTCATGCCA 61.409 57.895 8.72 0.00 41.77 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.575957 AGAAAATCATTCATCACGCATGAC 58.424 37.500 0.00 0.00 41.56 3.06
4 5 5.823209 AGAAAATCATTCATCACGCATGA 57.177 34.783 0.00 0.00 39.99 3.07
5 6 6.140786 CCTAGAAAATCATTCATCACGCATG 58.859 40.000 0.00 0.00 0.00 4.06
7 8 5.185454 ACCTAGAAAATCATTCATCACGCA 58.815 37.500 0.00 0.00 0.00 5.24
8 9 5.741388 ACCTAGAAAATCATTCATCACGC 57.259 39.130 0.00 0.00 0.00 5.34
9 10 6.414079 CGAACCTAGAAAATCATTCATCACG 58.586 40.000 0.00 0.00 0.00 4.35
10 11 6.195165 GCGAACCTAGAAAATCATTCATCAC 58.805 40.000 0.00 0.00 0.00 3.06
11 12 5.006649 CGCGAACCTAGAAAATCATTCATCA 59.993 40.000 0.00 0.00 0.00 3.07
12 13 5.006746 ACGCGAACCTAGAAAATCATTCATC 59.993 40.000 15.93 0.00 0.00 2.92
13 14 4.876107 ACGCGAACCTAGAAAATCATTCAT 59.124 37.500 15.93 0.00 0.00 2.57
14 15 4.250464 ACGCGAACCTAGAAAATCATTCA 58.750 39.130 15.93 0.00 0.00 2.57
15 16 4.859629 ACGCGAACCTAGAAAATCATTC 57.140 40.909 15.93 0.00 0.00 2.67
16 17 5.416947 ACTACGCGAACCTAGAAAATCATT 58.583 37.500 15.93 0.00 0.00 2.57
17 18 5.007385 ACTACGCGAACCTAGAAAATCAT 57.993 39.130 15.93 0.00 0.00 2.45
18 19 4.445452 ACTACGCGAACCTAGAAAATCA 57.555 40.909 15.93 0.00 0.00 2.57
19 20 5.774878 AAACTACGCGAACCTAGAAAATC 57.225 39.130 15.93 0.00 0.00 2.17
20 21 6.158598 TGTAAACTACGCGAACCTAGAAAAT 58.841 36.000 15.93 0.00 0.00 1.82
21 22 5.527951 TGTAAACTACGCGAACCTAGAAAA 58.472 37.500 15.93 0.00 0.00 2.29
22 23 5.119931 TGTAAACTACGCGAACCTAGAAA 57.880 39.130 15.93 0.00 0.00 2.52
23 24 4.764679 TGTAAACTACGCGAACCTAGAA 57.235 40.909 15.93 0.00 0.00 2.10
24 25 4.970662 ATGTAAACTACGCGAACCTAGA 57.029 40.909 15.93 0.00 0.00 2.43
25 26 5.723135 GCAAATGTAAACTACGCGAACCTAG 60.723 44.000 15.93 6.51 0.00 3.02
26 27 4.091800 GCAAATGTAAACTACGCGAACCTA 59.908 41.667 15.93 0.00 0.00 3.08
27 28 3.120442 GCAAATGTAAACTACGCGAACCT 60.120 43.478 15.93 0.00 0.00 3.50
28 29 3.120442 AGCAAATGTAAACTACGCGAACC 60.120 43.478 15.93 0.00 0.00 3.62
29 30 4.061570 AGCAAATGTAAACTACGCGAAC 57.938 40.909 15.93 1.17 0.00 3.95
30 31 4.735662 AAGCAAATGTAAACTACGCGAA 57.264 36.364 15.93 0.00 0.00 4.70
31 32 4.735662 AAAGCAAATGTAAACTACGCGA 57.264 36.364 15.93 0.00 0.00 5.87
32 33 5.799542 AAAAAGCAAATGTAAACTACGCG 57.200 34.783 3.53 3.53 0.00 6.01
51 52 7.560368 ACACATGGAATCAACCAAACTAAAAA 58.440 30.769 0.00 0.00 43.47 1.94
52 53 7.118496 ACACATGGAATCAACCAAACTAAAA 57.882 32.000 0.00 0.00 43.47 1.52
53 54 6.723298 ACACATGGAATCAACCAAACTAAA 57.277 33.333 0.00 0.00 43.47 1.85
54 55 7.825331 TTACACATGGAATCAACCAAACTAA 57.175 32.000 0.00 0.00 43.47 2.24
55 56 7.825331 TTTACACATGGAATCAACCAAACTA 57.175 32.000 0.00 0.00 43.47 2.24
56 57 6.723298 TTTACACATGGAATCAACCAAACT 57.277 33.333 0.00 0.00 43.47 2.66
57 58 6.368516 CCATTTACACATGGAATCAACCAAAC 59.631 38.462 0.00 0.00 46.18 2.93
58 59 6.462500 CCATTTACACATGGAATCAACCAAA 58.538 36.000 0.00 0.00 46.18 3.28
59 60 6.035368 CCATTTACACATGGAATCAACCAA 57.965 37.500 0.00 0.00 46.18 3.67
60 61 5.657826 CCATTTACACATGGAATCAACCA 57.342 39.130 0.00 0.00 46.18 3.67
69 70 4.194640 CTCCTCAGTCCATTTACACATGG 58.805 47.826 0.00 0.00 44.80 3.66
70 71 4.633126 CACTCCTCAGTCCATTTACACATG 59.367 45.833 0.00 0.00 0.00 3.21
71 72 4.532126 TCACTCCTCAGTCCATTTACACAT 59.468 41.667 0.00 0.00 0.00 3.21
72 73 3.901222 TCACTCCTCAGTCCATTTACACA 59.099 43.478 0.00 0.00 0.00 3.72
73 74 4.537135 TCACTCCTCAGTCCATTTACAC 57.463 45.455 0.00 0.00 0.00 2.90
74 75 4.777366 TCATCACTCCTCAGTCCATTTACA 59.223 41.667 0.00 0.00 0.00 2.41
75 76 5.127845 TCTCATCACTCCTCAGTCCATTTAC 59.872 44.000 0.00 0.00 0.00 2.01
76 77 5.272402 TCTCATCACTCCTCAGTCCATTTA 58.728 41.667 0.00 0.00 0.00 1.40
77 78 4.099633 TCTCATCACTCCTCAGTCCATTT 58.900 43.478 0.00 0.00 0.00 2.32
78 79 3.705579 CTCTCATCACTCCTCAGTCCATT 59.294 47.826 0.00 0.00 0.00 3.16
79 80 3.053019 TCTCTCATCACTCCTCAGTCCAT 60.053 47.826 0.00 0.00 0.00 3.41
80 81 2.310052 TCTCTCATCACTCCTCAGTCCA 59.690 50.000 0.00 0.00 0.00 4.02
81 82 2.951642 CTCTCTCATCACTCCTCAGTCC 59.048 54.545 0.00 0.00 0.00 3.85
82 83 2.951642 CCTCTCTCATCACTCCTCAGTC 59.048 54.545 0.00 0.00 0.00 3.51
83 84 2.358090 CCCTCTCTCATCACTCCTCAGT 60.358 54.545 0.00 0.00 0.00 3.41
84 85 2.091939 TCCCTCTCTCATCACTCCTCAG 60.092 54.545 0.00 0.00 0.00 3.35
85 86 1.925959 TCCCTCTCTCATCACTCCTCA 59.074 52.381 0.00 0.00 0.00 3.86
86 87 2.174639 TCTCCCTCTCTCATCACTCCTC 59.825 54.545 0.00 0.00 0.00 3.71
87 88 2.175499 CTCTCCCTCTCTCATCACTCCT 59.825 54.545 0.00 0.00 0.00 3.69
88 89 2.586425 CTCTCCCTCTCTCATCACTCC 58.414 57.143 0.00 0.00 0.00 3.85
89 90 2.586425 CCTCTCCCTCTCTCATCACTC 58.414 57.143 0.00 0.00 0.00 3.51
90 91 1.411501 GCCTCTCCCTCTCTCATCACT 60.412 57.143 0.00 0.00 0.00 3.41
91 92 1.039856 GCCTCTCCCTCTCTCATCAC 58.960 60.000 0.00 0.00 0.00 3.06
92 93 0.467106 CGCCTCTCCCTCTCTCATCA 60.467 60.000 0.00 0.00 0.00 3.07
298 304 1.000993 ATCGTGCCTCCTCCTGTCT 59.999 57.895 0.00 0.00 0.00 3.41
461 467 9.658799 ATTTAATACCTATCTCAATCATGTCGG 57.341 33.333 0.00 0.00 0.00 4.79
511 517 0.672889 TGCACACATTCGCCAACAAT 59.327 45.000 0.00 0.00 0.00 2.71
541 547 1.379527 CCTTCGGGTGTAAATCCAGC 58.620 55.000 0.00 0.00 0.00 4.85
542 548 1.339631 TGCCTTCGGGTGTAAATCCAG 60.340 52.381 0.00 0.00 37.45 3.86
543 549 0.693622 TGCCTTCGGGTGTAAATCCA 59.306 50.000 0.00 0.00 37.45 3.41
544 550 1.092348 GTGCCTTCGGGTGTAAATCC 58.908 55.000 0.00 0.00 37.45 3.01
545 551 1.092348 GGTGCCTTCGGGTGTAAATC 58.908 55.000 0.00 0.00 37.45 2.17
546 552 0.675522 CGGTGCCTTCGGGTGTAAAT 60.676 55.000 0.00 0.00 37.45 1.40
547 553 1.301874 CGGTGCCTTCGGGTGTAAA 60.302 57.895 0.00 0.00 37.45 2.01
548 554 2.344500 CGGTGCCTTCGGGTGTAA 59.656 61.111 0.00 0.00 37.45 2.41
549 555 3.697747 CCGGTGCCTTCGGGTGTA 61.698 66.667 0.00 0.00 43.45 2.90
553 559 3.470888 ATCTCCGGTGCCTTCGGG 61.471 66.667 0.00 1.30 46.78 5.14
582 588 2.722094 GTGTATGAACCATTGGCTCCA 58.278 47.619 1.54 0.00 0.00 3.86
589 595 1.406341 CCCGGTCGTGTATGAACCATT 60.406 52.381 0.00 0.00 0.00 3.16
767 779 2.275380 GCTTCATGGCCGGTTTGGT 61.275 57.895 1.90 0.00 41.21 3.67
960 974 3.249080 CCCAATAACGTGTTCAAACGAGT 59.751 43.478 3.45 0.00 46.49 4.18
984 998 2.611800 ATCCAGCTCAGGCCCACA 60.612 61.111 0.00 0.00 39.73 4.17
1091 1105 1.282248 GCGGCGATACATGCACGTAT 61.282 55.000 12.98 4.87 34.75 3.06
1192 1214 2.413963 GCCATGCCGCCAACATACA 61.414 57.895 0.00 0.00 0.00 2.29
1255 1277 0.315251 GCCAGGAGAAAAAGTGCCAC 59.685 55.000 0.00 0.00 0.00 5.01
1262 1284 1.493854 TAGCCCCGCCAGGAGAAAAA 61.494 55.000 0.00 0.00 41.02 1.94
1266 1288 4.075793 ACTAGCCCCGCCAGGAGA 62.076 66.667 0.00 0.00 41.02 3.71
1327 1349 4.409218 GCGTAGTGGCACGACCGA 62.409 66.667 22.48 0.68 44.69 4.69
1384 1406 2.443016 GGCCAACACCACCCACAA 60.443 61.111 0.00 0.00 0.00 3.33
1446 1469 3.665971 CCTTGGAGGGGGCAAGCT 61.666 66.667 0.00 0.00 0.00 3.74
1481 1519 2.358737 CCGACTCAGGGTTGCACC 60.359 66.667 0.00 0.00 37.60 5.01
1482 1520 2.358737 CCCGACTCAGGGTTGCAC 60.359 66.667 0.00 0.00 46.38 4.57
1501 1539 3.524648 GACGAAACACCCCAGCCGA 62.525 63.158 0.00 0.00 0.00 5.54
1535 1573 1.153086 GAACCAGATGCATCGCCCT 60.153 57.895 20.67 7.52 0.00 5.19
1614 1652 3.136791 GGTGCCTTAGCTGCTGGC 61.137 66.667 20.68 20.68 46.26 4.85
1951 1989 1.738099 CCATATCCGTAGCAGGCGC 60.738 63.158 0.00 0.00 38.99 6.53
2074 2112 0.109039 GTCTCTCCAGAAGTCACCGC 60.109 60.000 0.00 0.00 0.00 5.68
2090 2128 3.322254 CGTGCCATCCCTAGATTTAGTCT 59.678 47.826 0.00 0.00 41.11 3.24
2259 2302 4.722700 GCCCCGGTCACATGCTGT 62.723 66.667 0.00 0.00 0.00 4.40
2276 2319 0.259356 ACCGAAGAGGAGAGGGTAGG 59.741 60.000 0.00 0.00 45.00 3.18
2291 2334 2.170012 AATACCAGGCTTAGGACCGA 57.830 50.000 0.00 0.00 0.00 4.69
2321 2364 5.930135 ACATCAACTCTTTACAACAGACCT 58.070 37.500 0.00 0.00 0.00 3.85
2334 2377 5.059833 GGTGTCTCAAAGAACATCAACTCT 58.940 41.667 0.00 0.00 0.00 3.24
2411 2454 5.011329 TCGGTCAACTGTCCATTAGTAACTT 59.989 40.000 0.00 0.00 0.00 2.66
2473 2516 6.832900 TGTTCCAGATGCCATTGATAATTACA 59.167 34.615 0.00 0.00 0.00 2.41
2484 2527 4.574674 TTCTAACTGTTCCAGATGCCAT 57.425 40.909 0.00 0.00 35.18 4.40
2506 2549 3.978610 AGTCCACCTTATAAGTCCGACT 58.021 45.455 11.50 13.56 0.00 4.18
2510 2553 5.431179 TGGAAAGTCCACCTTATAAGTCC 57.569 43.478 11.50 9.12 42.67 3.85
2569 2613 2.005451 GGTGCTTGTGACTCTGCATAG 58.995 52.381 0.00 0.00 37.76 2.23
2631 2675 1.652947 TCTCCAAAGGTGTACCCTCC 58.347 55.000 3.68 0.00 45.47 4.30
2662 2706 2.046796 TGGCGCGCCATAGAAACA 60.047 55.556 46.88 24.04 41.89 2.83
2697 2741 3.495753 CCAAGCTCCAAGCAATCAAAAAC 59.504 43.478 1.29 0.00 45.56 2.43
2765 2809 0.957395 CCTCGCAACTCCTTGTGCAT 60.957 55.000 0.00 0.00 37.74 3.96
2835 2881 2.645838 AAGTGACTCCAGCATGTGTT 57.354 45.000 0.00 0.00 0.00 3.32
2859 2905 6.150976 CAGTATCCTCGATCTCAAGCTCTAAT 59.849 42.308 0.00 0.00 0.00 1.73
2907 2953 2.771943 AGTCGTATCCATGTCCCATGTT 59.228 45.455 3.75 0.00 0.00 2.71
2912 2958 1.341531 CCTCAGTCGTATCCATGTCCC 59.658 57.143 0.00 0.00 0.00 4.46
2939 2987 4.514577 CCTGATTCTCGGGCGCGT 62.515 66.667 23.19 2.97 35.89 6.01
2989 3037 2.171870 GCTGTGTATTAGGCCCCTTGTA 59.828 50.000 0.00 0.00 0.00 2.41
3002 3050 9.548631 AACTATATACCTTATCTGGCTGTGTAT 57.451 33.333 0.00 0.00 0.00 2.29
3022 3070 3.069158 GGCGCCTCTTTGGTAGAACTATA 59.931 47.826 22.15 0.00 38.35 1.31
3142 3190 1.669115 GCAACTCAAGCTCCGCTGA 60.669 57.895 0.00 0.00 39.62 4.26
3184 3232 0.315568 GACTCTGCAGTCGTCACCTT 59.684 55.000 24.14 0.78 39.91 3.50
3271 3320 1.732941 CGCATGTAACTGGGTGCTAA 58.267 50.000 0.00 0.00 35.52 3.09
3286 3335 1.153549 GAAGAGAAGTCGGGCGCAT 60.154 57.895 10.83 0.00 0.00 4.73
3333 3382 1.004440 AAGTGAGAGGAACGCCAGC 60.004 57.895 0.00 0.00 36.29 4.85
3437 3486 2.930019 CACCTCACCCCCAGCTCA 60.930 66.667 0.00 0.00 0.00 4.26
3635 3684 1.520666 CACGCCCTCCCTTATCGTT 59.479 57.895 0.00 0.00 0.00 3.85
3723 3773 3.702048 GCCTACCAGCCGACACCA 61.702 66.667 0.00 0.00 0.00 4.17
3736 3786 2.048597 CGGTTGCTGACACGCCTA 60.049 61.111 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.