Multiple sequence alignment - TraesCS1A01G146000

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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 TraesCS1A01G146000 chr1A 100.000 3338 0 0 1 3338 252325295 252321958 0.000000e+00 6165.0
1 TraesCS1A01G146000 chr1D 92.188 3264 162 35 132 3338 199844637 199841410 0.000000e+00 4529.0
2 TraesCS1A01G146000 chr1D 93.846 65 1 1 3213 3277 65902448 65902509 9.860000e-16 95.3
3 TraesCS1A01G146000 chr1D 89.610 77 2 4 3201 3274 65902517 65902444 3.550000e-15 93.5
4 TraesCS1A01G146000 chr1D 91.304 69 3 2 3206 3271 437506518 437506586 1.280000e-14 91.6
5 TraesCS1A01G146000 chr1B 96.309 2330 60 11 128 2448 286613656 286611344 0.000000e+00 3803.0
6 TraesCS1A01G146000 chr1B 94.961 516 21 5 2433 2945 286611330 286610817 0.000000e+00 804.0
7 TraesCS1A01G146000 chr1B 96.127 284 8 1 2931 3211 286610770 286610487 8.440000e-126 460.0
8 TraesCS1A01G146000 chr1B 100.000 137 0 0 1 137 311683644 311683780 1.540000e-63 254.0
9 TraesCS1A01G146000 chr1B 89.474 76 5 3 3197 3271 632034064 632033991 3.550000e-15 93.5
10 TraesCS1A01G146000 chr6B 98.592 142 1 1 1 141 85852016 85852157 1.990000e-62 250.0
11 TraesCS1A01G146000 chr6B 97.260 146 2 2 1 144 637877626 637877481 2.570000e-61 246.0
12 TraesCS1A01G146000 chr6A 99.275 138 1 0 1 138 133802972 133802835 1.990000e-62 250.0
13 TraesCS1A01G146000 chr3A 99.275 138 1 0 1 138 22785664 22785801 1.990000e-62 250.0
14 TraesCS1A01G146000 chr2B 99.275 138 1 0 1 138 564821695 564821832 1.990000e-62 250.0
15 TraesCS1A01G146000 chr2B 98.582 141 2 0 1 141 635083466 635083326 1.990000e-62 250.0
16 TraesCS1A01G146000 chr2B 94.286 70 2 1 3210 3279 761990715 761990782 4.550000e-19 106.0
17 TraesCS1A01G146000 chr7A 99.270 137 1 0 1 137 529331659 529331795 7.150000e-62 248.0
18 TraesCS1A01G146000 chr7A 92.424 66 3 2 3209 3272 83786039 83786104 3.550000e-15 93.5
19 TraesCS1A01G146000 chr2A 95.484 155 5 2 1 153 46341113 46340959 2.570000e-61 246.0
20 TraesCS1A01G146000 chr2D 95.652 69 2 1 3208 3275 537496650 537496582 3.520000e-20 110.0
21 TraesCS1A01G146000 chr2D 96.774 62 0 1 3211 3272 582301488 582301429 5.890000e-18 102.0


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 TraesCS1A01G146000 chr1A 252321958 252325295 3337 True 6165 6165 100.000 1 3338 1 chr1A.!!$R1 3337
1 TraesCS1A01G146000 chr1D 199841410 199844637 3227 True 4529 4529 92.188 132 3338 1 chr1D.!!$R2 3206
2 TraesCS1A01G146000 chr1B 286610487 286613656 3169 True 1689 3803 95.799 128 3211 3 chr1B.!!$R2 3083

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
167 168 1.065926 CAGGCTACTGTGCAGATTCCA 60.066 52.381 6.17 0.0 39.92 3.53 F
434 445 1.584724 CCTGCTCTAGGGGGAAAGAA 58.415 55.000 0.00 0.0 43.33 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1055 1.210722 TGGTCCACTTGTACACAGCAA 59.789 47.619 0.00 0.0 0.00 3.91 R
2378 2398 0.984995 AAACCAGGAGCCTGTAGGAC 59.015 55.000 14.97 0.0 42.15 3.85 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
28 29 9.162764 TGAGTCTACAAAGTAATAAATGAAGGC 57.837 33.333 0.00 0.00 0.00 4.35
29 30 9.162764 GAGTCTACAAAGTAATAAATGAAGGCA 57.837 33.333 0.00 0.00 0.00 4.75
30 31 9.515226 AGTCTACAAAGTAATAAATGAAGGCAA 57.485 29.630 0.00 0.00 0.00 4.52
31 32 9.556030 GTCTACAAAGTAATAAATGAAGGCAAC 57.444 33.333 0.00 0.00 0.00 4.17
46 47 3.067684 GGCAACTATGTTACCACACCT 57.932 47.619 0.00 0.00 35.03 4.00
47 48 4.210724 GGCAACTATGTTACCACACCTA 57.789 45.455 0.00 0.00 35.03 3.08
48 49 4.777463 GGCAACTATGTTACCACACCTAT 58.223 43.478 0.00 0.00 35.03 2.57
49 50 4.574828 GGCAACTATGTTACCACACCTATG 59.425 45.833 0.00 0.00 35.03 2.23
50 51 5.424757 GCAACTATGTTACCACACCTATGA 58.575 41.667 0.00 0.00 35.03 2.15
51 52 5.293569 GCAACTATGTTACCACACCTATGAC 59.706 44.000 0.00 0.00 35.03 3.06
52 53 6.403049 CAACTATGTTACCACACCTATGACA 58.597 40.000 0.00 0.00 35.03 3.58
53 54 5.974108 ACTATGTTACCACACCTATGACAC 58.026 41.667 0.00 0.00 35.03 3.67
54 55 5.720041 ACTATGTTACCACACCTATGACACT 59.280 40.000 0.00 0.00 35.03 3.55
55 56 6.893554 ACTATGTTACCACACCTATGACACTA 59.106 38.462 0.00 0.00 35.03 2.74
56 57 5.395682 TGTTACCACACCTATGACACTAC 57.604 43.478 0.00 0.00 0.00 2.73
57 58 4.221262 TGTTACCACACCTATGACACTACC 59.779 45.833 0.00 0.00 0.00 3.18
58 59 2.185387 ACCACACCTATGACACTACCC 58.815 52.381 0.00 0.00 0.00 3.69
59 60 2.184533 CCACACCTATGACACTACCCA 58.815 52.381 0.00 0.00 0.00 4.51
60 61 2.093658 CCACACCTATGACACTACCCAC 60.094 54.545 0.00 0.00 0.00 4.61
61 62 2.832129 CACACCTATGACACTACCCACT 59.168 50.000 0.00 0.00 0.00 4.00
62 63 4.021229 CACACCTATGACACTACCCACTA 58.979 47.826 0.00 0.00 0.00 2.74
63 64 4.649674 CACACCTATGACACTACCCACTAT 59.350 45.833 0.00 0.00 0.00 2.12
64 65 4.649674 ACACCTATGACACTACCCACTATG 59.350 45.833 0.00 0.00 0.00 2.23
65 66 4.893524 CACCTATGACACTACCCACTATGA 59.106 45.833 0.00 0.00 0.00 2.15
66 67 5.362717 CACCTATGACACTACCCACTATGAA 59.637 44.000 0.00 0.00 0.00 2.57
67 68 5.598830 ACCTATGACACTACCCACTATGAAG 59.401 44.000 0.00 0.00 0.00 3.02
68 69 5.011125 CCTATGACACTACCCACTATGAAGG 59.989 48.000 0.00 0.00 0.00 3.46
69 70 3.786553 TGACACTACCCACTATGAAGGT 58.213 45.455 0.00 0.00 37.69 3.50
70 71 4.938028 TGACACTACCCACTATGAAGGTA 58.062 43.478 0.00 0.00 35.02 3.08
77 78 7.598759 CTACCCACTATGAAGGTAGTAACAT 57.401 40.000 7.19 0.00 45.39 2.71
78 79 8.701908 CTACCCACTATGAAGGTAGTAACATA 57.298 38.462 7.19 0.00 45.39 2.29
79 80 7.598759 ACCCACTATGAAGGTAGTAACATAG 57.401 40.000 0.00 0.00 44.14 2.23
80 81 7.359849 ACCCACTATGAAGGTAGTAACATAGA 58.640 38.462 16.37 0.00 42.41 1.98
81 82 7.287235 ACCCACTATGAAGGTAGTAACATAGAC 59.713 40.741 16.37 0.00 42.41 2.59
82 83 7.506261 CCCACTATGAAGGTAGTAACATAGACT 59.494 40.741 16.37 0.00 42.41 3.24
83 84 9.570468 CCACTATGAAGGTAGTAACATAGACTA 57.430 37.037 16.37 0.00 42.41 2.59
89 90 9.964354 TGAAGGTAGTAACATAGACTAGTAACA 57.036 33.333 0.00 0.00 30.08 2.41
119 120 7.894753 ATGTTACTAGTCTAAGTTACTCCCC 57.105 40.000 0.00 0.00 31.82 4.81
120 121 6.793478 TGTTACTAGTCTAAGTTACTCCCCA 58.207 40.000 0.00 0.00 31.82 4.96
121 122 6.660949 TGTTACTAGTCTAAGTTACTCCCCAC 59.339 42.308 0.00 0.00 31.82 4.61
122 123 5.533333 ACTAGTCTAAGTTACTCCCCACT 57.467 43.478 0.00 0.00 0.00 4.00
123 124 6.649041 ACTAGTCTAAGTTACTCCCCACTA 57.351 41.667 0.00 0.00 0.00 2.74
124 125 7.223472 ACTAGTCTAAGTTACTCCCCACTAT 57.777 40.000 0.00 0.00 0.00 2.12
125 126 7.061688 ACTAGTCTAAGTTACTCCCCACTATG 58.938 42.308 0.00 0.00 0.00 2.23
126 127 6.088541 AGTCTAAGTTACTCCCCACTATGA 57.911 41.667 0.00 0.00 0.00 2.15
130 131 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
167 168 1.065926 CAGGCTACTGTGCAGATTCCA 60.066 52.381 6.17 0.00 39.92 3.53
290 291 6.776887 ATCCCATATCCTCTTCAACAATCT 57.223 37.500 0.00 0.00 0.00 2.40
311 312 6.531503 TCTGAACTATCTTCACCAGTTAGG 57.468 41.667 0.00 0.00 45.67 2.69
384 385 9.747293 GAGAGGTTAATGTAAGTCAACTATACC 57.253 37.037 0.00 0.00 0.00 2.73
405 406 4.041815 ACCACCTCCCTTTAACTTCTTCTC 59.958 45.833 0.00 0.00 0.00 2.87
408 409 4.257731 CCTCCCTTTAACTTCTTCTCTGC 58.742 47.826 0.00 0.00 0.00 4.26
411 412 4.020128 TCCCTTTAACTTCTTCTCTGCTCC 60.020 45.833 0.00 0.00 0.00 4.70
412 413 4.019771 CCCTTTAACTTCTTCTCTGCTCCT 60.020 45.833 0.00 0.00 0.00 3.69
413 414 5.187967 CCCTTTAACTTCTTCTCTGCTCCTA 59.812 44.000 0.00 0.00 0.00 2.94
414 415 6.126911 CCCTTTAACTTCTTCTCTGCTCCTAT 60.127 42.308 0.00 0.00 0.00 2.57
415 416 6.983890 CCTTTAACTTCTTCTCTGCTCCTATC 59.016 42.308 0.00 0.00 0.00 2.08
416 417 6.472686 TTAACTTCTTCTCTGCTCCTATCC 57.527 41.667 0.00 0.00 0.00 2.59
417 418 4.264373 ACTTCTTCTCTGCTCCTATCCT 57.736 45.455 0.00 0.00 0.00 3.24
418 419 3.960102 ACTTCTTCTCTGCTCCTATCCTG 59.040 47.826 0.00 0.00 0.00 3.86
419 420 2.315176 TCTTCTCTGCTCCTATCCTGC 58.685 52.381 0.00 0.00 0.00 4.85
420 421 2.091389 TCTTCTCTGCTCCTATCCTGCT 60.091 50.000 0.00 0.00 0.00 4.24
434 445 1.584724 CCTGCTCTAGGGGGAAAGAA 58.415 55.000 0.00 0.00 43.33 2.52
441 452 4.520874 GCTCTAGGGGGAAAGAAATTATGC 59.479 45.833 0.00 0.00 0.00 3.14
509 520 5.941948 AGTGTAAAGAAAAATCCGTCTGG 57.058 39.130 0.00 0.00 0.00 3.86
660 679 2.296190 ACAAAGCTTCCCGAACCAAATC 59.704 45.455 0.00 0.00 0.00 2.17
662 681 2.286365 AGCTTCCCGAACCAAATCAA 57.714 45.000 0.00 0.00 0.00 2.57
752 771 5.810074 GCGAAAAACCCAGCAATATGTTAAT 59.190 36.000 0.00 0.00 0.00 1.40
805 824 3.838317 TCTGTTGGCCAGTTAGTCATAGT 59.162 43.478 5.11 0.00 42.19 2.12
816 835 7.171678 GCCAGTTAGTCATAGTTTGTATGGATC 59.828 40.741 0.00 0.00 0.00 3.36
883 903 6.316140 CACCATTTTCTTGTATAGTGCTGCTA 59.684 38.462 0.00 0.00 0.00 3.49
935 955 8.907222 AAGTGACTGGCAATGAATTTATTTTT 57.093 26.923 0.00 0.00 0.00 1.94
1809 1829 7.336161 TGAGTAGAGCTTAGTTTGGAGTATC 57.664 40.000 0.00 0.00 0.00 2.24
1828 1848 7.495934 GGAGTATCAACTGCTAAAATCTAGCAA 59.504 37.037 7.77 0.00 43.20 3.91
2226 2246 1.936547 GACACCATGAAAGAGATCGGC 59.063 52.381 0.00 0.00 0.00 5.54
2378 2398 5.972107 AGAATTTGAATTGGTGAGGTCAG 57.028 39.130 0.00 0.00 0.00 3.51
2420 2440 9.626045 GTTTGACATAAGAAAATGGTCCTTTAG 57.374 33.333 0.00 0.00 0.00 1.85
2467 2516 8.031864 AGTTTGTGACTTGTGAGATATCTACAG 58.968 37.037 4.89 2.15 33.92 2.74
2585 2637 7.175641 GGGACTTAAGATGGATGTATTGAATGG 59.824 40.741 10.09 0.00 0.00 3.16
2606 2658 4.069304 GGTTGTTGTGTGGCTATACTTGA 58.931 43.478 0.00 0.00 0.00 3.02
2868 2944 2.030363 TGCACAGCTTAAATCAAACGGG 60.030 45.455 0.00 0.00 0.00 5.28
2882 2959 0.113580 AACGGGCTATTTTGGGTGGT 59.886 50.000 0.00 0.00 0.00 4.16
2889 2966 3.194755 GGCTATTTTGGGTGGTAAAGTGG 59.805 47.826 0.00 0.00 0.00 4.00
2901 2978 4.935808 GTGGTAAAGTGGACAGTTATCAGG 59.064 45.833 0.00 0.00 0.00 3.86
2994 3132 5.486735 TTTGGCAAGACATGATCCATTTT 57.513 34.783 0.00 0.00 0.00 1.82
3038 3179 5.171476 CACCGAGTGAAGATAAACTCACAT 58.829 41.667 5.13 0.00 42.45 3.21
3211 3355 6.527722 ACACTGACGCATAATAAAATTGCAAG 59.472 34.615 4.94 0.00 36.15 4.01
3225 3375 1.255667 TGCAAGTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
3227 3377 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
3243 3415 4.625742 CCGTCCCATAATATAAGAGCAACG 59.374 45.833 0.00 0.00 0.00 4.10
3271 3443 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
3272 3444 4.687262 ATTATGGGACGGAGGGAGTATA 57.313 45.455 0.00 0.00 0.00 1.47
3286 3458 4.043812 AGGGAGTATATACCTAACAGCCGA 59.956 45.833 9.32 0.00 31.53 5.54
3307 3479 0.541863 ATGGGCTTCAGTAAGGTCGG 59.458 55.000 0.00 0.00 32.98 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.162764 GCCTTCATTTATTACTTTGTAGACTCA 57.837 33.333 0.00 0.00 0.00 3.41
3 4 9.162764 TGCCTTCATTTATTACTTTGTAGACTC 57.837 33.333 0.00 0.00 0.00 3.36
4 5 9.515226 TTGCCTTCATTTATTACTTTGTAGACT 57.485 29.630 0.00 0.00 0.00 3.24
5 6 9.556030 GTTGCCTTCATTTATTACTTTGTAGAC 57.444 33.333 0.00 0.00 0.00 2.59
6 7 9.515226 AGTTGCCTTCATTTATTACTTTGTAGA 57.485 29.630 0.00 0.00 0.00 2.59
14 15 9.946165 GGTAACATAGTTGCCTTCATTTATTAC 57.054 33.333 9.36 0.00 0.00 1.89
15 16 9.688091 TGGTAACATAGTTGCCTTCATTTATTA 57.312 29.630 16.08 0.00 46.17 0.98
16 17 8.588290 TGGTAACATAGTTGCCTTCATTTATT 57.412 30.769 16.08 0.00 46.17 1.40
35 36 4.382362 GGGTAGTGTCATAGGTGTGGTAAC 60.382 50.000 0.00 0.00 0.00 2.50
36 37 3.770933 GGGTAGTGTCATAGGTGTGGTAA 59.229 47.826 0.00 0.00 0.00 2.85
37 38 3.245694 TGGGTAGTGTCATAGGTGTGGTA 60.246 47.826 0.00 0.00 0.00 3.25
38 39 2.185387 GGGTAGTGTCATAGGTGTGGT 58.815 52.381 0.00 0.00 0.00 4.16
39 40 2.093658 GTGGGTAGTGTCATAGGTGTGG 60.094 54.545 0.00 0.00 0.00 4.17
40 41 2.832129 AGTGGGTAGTGTCATAGGTGTG 59.168 50.000 0.00 0.00 0.00 3.82
41 42 3.185880 AGTGGGTAGTGTCATAGGTGT 57.814 47.619 0.00 0.00 0.00 4.16
42 43 4.893524 TCATAGTGGGTAGTGTCATAGGTG 59.106 45.833 0.00 0.00 0.00 4.00
43 44 5.138758 TCATAGTGGGTAGTGTCATAGGT 57.861 43.478 0.00 0.00 0.00 3.08
44 45 5.011125 CCTTCATAGTGGGTAGTGTCATAGG 59.989 48.000 0.00 0.00 0.00 2.57
45 46 5.598830 ACCTTCATAGTGGGTAGTGTCATAG 59.401 44.000 0.00 0.00 0.00 2.23
46 47 5.525484 ACCTTCATAGTGGGTAGTGTCATA 58.475 41.667 0.00 0.00 0.00 2.15
47 48 4.362677 ACCTTCATAGTGGGTAGTGTCAT 58.637 43.478 0.00 0.00 0.00 3.06
48 49 3.786553 ACCTTCATAGTGGGTAGTGTCA 58.213 45.455 0.00 0.00 0.00 3.58
49 50 5.517322 CTACCTTCATAGTGGGTAGTGTC 57.483 47.826 9.46 0.00 44.30 3.67
54 55 8.505246 TCTATGTTACTACCTTCATAGTGGGTA 58.495 37.037 0.00 0.00 40.01 3.69
55 56 7.287235 GTCTATGTTACTACCTTCATAGTGGGT 59.713 40.741 0.00 0.00 40.01 4.51
56 57 7.506261 AGTCTATGTTACTACCTTCATAGTGGG 59.494 40.741 0.00 0.00 40.01 4.61
57 58 8.466617 AGTCTATGTTACTACCTTCATAGTGG 57.533 38.462 0.00 0.00 40.01 4.00
63 64 9.964354 TGTTACTAGTCTATGTTACTACCTTCA 57.036 33.333 0.00 0.00 0.00 3.02
93 94 9.585369 GGGGAGTAACTTAGACTAGTAACATAT 57.415 37.037 0.00 0.00 0.00 1.78
94 95 8.560039 TGGGGAGTAACTTAGACTAGTAACATA 58.440 37.037 0.00 0.00 0.00 2.29
95 96 7.341512 GTGGGGAGTAACTTAGACTAGTAACAT 59.658 40.741 0.00 0.00 0.00 2.71
96 97 6.660949 GTGGGGAGTAACTTAGACTAGTAACA 59.339 42.308 0.00 0.00 0.00 2.41
97 98 6.889177 AGTGGGGAGTAACTTAGACTAGTAAC 59.111 42.308 0.00 0.00 0.00 2.50
98 99 7.037342 AGTGGGGAGTAACTTAGACTAGTAA 57.963 40.000 0.00 0.00 0.00 2.24
99 100 6.649041 AGTGGGGAGTAACTTAGACTAGTA 57.351 41.667 0.00 0.00 0.00 1.82
100 101 5.533333 AGTGGGGAGTAACTTAGACTAGT 57.467 43.478 0.00 0.00 0.00 2.57
101 102 7.229106 GTCATAGTGGGGAGTAACTTAGACTAG 59.771 44.444 0.00 0.00 31.58 2.57
102 103 7.059156 GTCATAGTGGGGAGTAACTTAGACTA 58.941 42.308 0.00 0.00 31.58 2.59
103 104 5.892686 GTCATAGTGGGGAGTAACTTAGACT 59.107 44.000 0.00 0.00 31.58 3.24
104 105 5.068855 GGTCATAGTGGGGAGTAACTTAGAC 59.931 48.000 0.00 0.00 32.58 2.59
105 106 5.206587 GGTCATAGTGGGGAGTAACTTAGA 58.793 45.833 0.00 0.00 0.00 2.10
106 107 4.960469 TGGTCATAGTGGGGAGTAACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
107 108 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
108 109 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
109 110 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
110 111 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
111 112 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
112 113 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
113 114 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
114 115 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
115 116 0.639943 TAGGCTGGTCATAGTGGGGA 59.360 55.000 0.00 0.00 0.00 4.81
116 117 1.417890 CTTAGGCTGGTCATAGTGGGG 59.582 57.143 0.00 0.00 0.00 4.96
117 118 2.398588 TCTTAGGCTGGTCATAGTGGG 58.601 52.381 0.00 0.00 0.00 4.61
118 119 3.452627 ACTTCTTAGGCTGGTCATAGTGG 59.547 47.826 0.00 0.00 0.00 4.00
119 120 4.744795 ACTTCTTAGGCTGGTCATAGTG 57.255 45.455 0.00 0.00 0.00 2.74
120 121 5.485708 AGAAACTTCTTAGGCTGGTCATAGT 59.514 40.000 0.00 0.00 32.55 2.12
121 122 5.983540 AGAAACTTCTTAGGCTGGTCATAG 58.016 41.667 0.00 0.00 32.55 2.23
122 123 5.104900 GGAGAAACTTCTTAGGCTGGTCATA 60.105 44.000 0.00 0.00 37.73 2.15
123 124 4.323868 GGAGAAACTTCTTAGGCTGGTCAT 60.324 45.833 0.00 0.00 37.73 3.06
124 125 3.008049 GGAGAAACTTCTTAGGCTGGTCA 59.992 47.826 0.00 0.00 37.73 4.02
125 126 3.601435 GGAGAAACTTCTTAGGCTGGTC 58.399 50.000 0.00 0.00 37.73 4.02
126 127 2.306219 GGGAGAAACTTCTTAGGCTGGT 59.694 50.000 0.00 0.00 37.73 4.00
130 131 2.941860 GCCTGGGAGAAACTTCTTAGGC 60.942 54.545 18.97 18.97 44.26 3.93
167 168 2.622942 TCAACGCCAGCATTTCTCTTTT 59.377 40.909 0.00 0.00 0.00 2.27
311 312 3.815401 ACAACCACTGCTGAATACTTGAC 59.185 43.478 0.00 0.00 0.00 3.18
316 317 2.226437 CACCACAACCACTGCTGAATAC 59.774 50.000 0.00 0.00 0.00 1.89
318 319 1.321474 CACCACAACCACTGCTGAAT 58.679 50.000 0.00 0.00 0.00 2.57
384 385 5.241662 CAGAGAAGAAGTTAAAGGGAGGTG 58.758 45.833 0.00 0.00 0.00 4.00
415 416 1.584724 TTCTTTCCCCCTAGAGCAGG 58.415 55.000 0.00 0.00 45.07 4.85
416 417 3.941704 ATTTCTTTCCCCCTAGAGCAG 57.058 47.619 0.00 0.00 0.00 4.24
417 418 5.694995 CATAATTTCTTTCCCCCTAGAGCA 58.305 41.667 0.00 0.00 0.00 4.26
418 419 4.520874 GCATAATTTCTTTCCCCCTAGAGC 59.479 45.833 0.00 0.00 0.00 4.09
419 420 5.767168 CAGCATAATTTCTTTCCCCCTAGAG 59.233 44.000 0.00 0.00 0.00 2.43
420 421 5.694995 CAGCATAATTTCTTTCCCCCTAGA 58.305 41.667 0.00 0.00 0.00 2.43
434 445 5.125900 TGCATTACAAGACAGCAGCATAATT 59.874 36.000 0.00 0.00 0.00 1.40
441 452 4.227512 TGTTTGCATTACAAGACAGCAG 57.772 40.909 0.08 0.00 40.06 4.24
469 480 8.842358 TTTACACTTGAAGGATCGATAAGTTT 57.158 30.769 7.61 5.19 29.78 2.66
600 619 9.533253 GCTAACTTCAAAATGCCAATATATTGT 57.467 29.630 21.20 3.36 36.06 2.71
615 634 4.640789 TTTGCCGAAAGCTAACTTCAAA 57.359 36.364 0.00 0.00 44.23 2.69
728 747 3.230743 ACATATTGCTGGGTTTTTCGC 57.769 42.857 0.00 0.00 0.00 4.70
816 835 8.091449 GGTAATCCTCCTGTATGAAATAGTGAG 58.909 40.741 0.00 0.00 0.00 3.51
883 903 5.111293 GCAGGCAAATTATTTATGTGCTGT 58.889 37.500 8.93 0.00 45.33 4.40
891 911 7.930865 AGTCACTTTTTGCAGGCAAATTATTTA 59.069 29.630 18.97 1.70 44.14 1.40
893 913 6.203338 CAGTCACTTTTTGCAGGCAAATTATT 59.797 34.615 18.97 3.93 44.14 1.40
938 958 9.630098 CAATGTTACAACAGCTTTCAGATTAAT 57.370 29.630 0.84 0.00 43.04 1.40
1035 1055 1.210722 TGGTCCACTTGTACACAGCAA 59.789 47.619 0.00 0.00 0.00 3.91
2226 2246 2.421073 TGCAGAAGATTTGGATGAAGCG 59.579 45.455 0.00 0.00 0.00 4.68
2378 2398 0.984995 AAACCAGGAGCCTGTAGGAC 59.015 55.000 14.97 0.00 42.15 3.85
2420 2440 2.542178 TCACACAATATTATCACGCGCC 59.458 45.455 5.73 0.00 0.00 6.53
2545 2597 1.856629 AGTCCCCATGCTCCATTTTG 58.143 50.000 0.00 0.00 0.00 2.44
2585 2637 4.378459 GCTCAAGTATAGCCACACAACAAC 60.378 45.833 0.00 0.00 33.73 3.32
2606 2658 7.231317 TGTGGAAACATTATTTTCTCAGAAGCT 59.769 33.333 0.00 0.00 46.14 3.74
2706 2758 3.686726 GTGCTAGTGAGGAAATTCAGTGG 59.313 47.826 0.00 0.00 33.05 4.00
2809 2862 6.599244 AGTTAATGATCCACGAACATTGATGT 59.401 34.615 7.23 0.00 44.20 3.06
2868 2944 4.082408 GTCCACTTTACCACCCAAAATAGC 60.082 45.833 0.00 0.00 0.00 2.97
2882 2959 7.786046 TCTTACCTGATAACTGTCCACTTTA 57.214 36.000 0.00 0.00 0.00 1.85
2933 3071 7.665974 AGTTATAGCCTTGCTAACTCTTTTTGT 59.334 33.333 0.00 0.00 44.62 2.83
2994 3132 4.395854 GTGTCTGAAATGATATGTGGTGCA 59.604 41.667 0.00 0.00 0.00 4.57
3038 3179 5.521696 ACAATGATCCAATGATCCCTTCAA 58.478 37.500 0.46 0.00 45.74 2.69
3211 3355 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
3243 3415 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
3271 3443 3.162666 CCCATCTCGGCTGTTAGGTATA 58.837 50.000 0.00 0.00 0.00 1.47
3272 3444 1.971357 CCCATCTCGGCTGTTAGGTAT 59.029 52.381 0.00 0.00 0.00 2.73
3286 3458 1.482593 CGACCTTACTGAAGCCCATCT 59.517 52.381 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.