Multiple sequence alignment - TraesCS1A01G212300

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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 TraesCS1A01G212300 chr1A 100.000 3209 0 0 1 3209 375017280 375014072 0.000000e+00 5927.0
1 TraesCS1A01G212300 chr1A 74.503 302 57 14 1906 2203 369997433 369997148 2.620000e-21 113.0
2 TraesCS1A01G212300 chr1B 91.777 2031 74 28 310 2293 405712532 405710548 0.000000e+00 2739.0
3 TraesCS1A01G212300 chr1B 81.278 673 87 27 2549 3209 405710350 405709705 2.860000e-140 508.0
4 TraesCS1A01G212300 chr1B 92.537 201 13 2 2336 2535 405710534 405710335 1.460000e-73 287.0
5 TraesCS1A01G212300 chr1B 75.248 303 53 16 1906 2203 399798937 399798652 1.210000e-24 124.0
6 TraesCS1A01G212300 chr1D 92.095 1556 65 22 1 1525 300709965 300708437 0.000000e+00 2139.0
7 TraesCS1A01G212300 chr1D 94.986 1037 28 15 1512 2535 300708411 300707386 0.000000e+00 1605.0
8 TraesCS1A01G212300 chr1D 86.339 366 39 4 2734 3098 300704731 300704376 3.880000e-104 388.0
9 TraesCS1A01G212300 chr1D 89.730 185 15 4 2549 2730 300707401 300707218 1.920000e-57 233.0
10 TraesCS1A01G212300 chr1D 74.834 302 56 14 1906 2203 297378559 297378274 5.620000e-23 119.0
11 TraesCS1A01G212300 chr1D 81.651 109 13 6 135 239 65905173 65905068 2.050000e-12 84.2
12 TraesCS1A01G212300 chr3A 80.488 246 45 2 38 282 579552274 579552031 5.470000e-43 185.0
13 TraesCS1A01G212300 chr3A 80.978 184 32 2 96 278 163177138 163177319 3.340000e-30 143.0
14 TraesCS1A01G212300 chr3A 81.143 175 26 7 70 240 515827610 515827439 2.010000e-27 134.0
15 TraesCS1A01G212300 chr6D 85.897 156 22 0 1610 1765 15640547 15640702 1.980000e-37 167.0
16 TraesCS1A01G212300 chr2B 88.430 121 13 1 82 201 788023487 788023607 9.280000e-31 145.0
17 TraesCS1A01G212300 chr7D 82.353 136 20 4 86 219 89597592 89597725 7.270000e-22 115.0
18 TraesCS1A01G212300 chr5D 80.380 158 23 5 86 239 370360096 370360249 2.620000e-21 113.0
19 TraesCS1A01G212300 chr4D 82.812 128 20 2 55 180 478024804 478024677 2.620000e-21 113.0
20 TraesCS1A01G212300 chr2D 89.024 82 9 0 86 167 134117301 134117220 5.660000e-18 102.0
21 TraesCS1A01G212300 chrUn 89.610 77 8 0 1672 1748 12882458 12882382 7.330000e-17 99.0
22 TraesCS1A01G212300 chr6B 100.000 28 0 0 2753 2780 599398171 599398198 6.000000e-03 52.8


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 TraesCS1A01G212300 chr1A 375014072 375017280 3208 True 5927.00 5927 100.000000 1 3209 1 chr1A.!!$R2 3208
1 TraesCS1A01G212300 chr1B 405709705 405712532 2827 True 1178.00 2739 88.530667 310 3209 3 chr1B.!!$R2 2899
2 TraesCS1A01G212300 chr1D 300704376 300709965 5589 True 1091.25 2139 90.787500 1 3098 4 chr1D.!!$R3 3097

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
81 84 0.250901 AGGTGTAAGCACAGGGCAAG 60.251 55.0 0.0 0.0 46.95 4.01 F
92 95 0.318120 CAGGGCAAGCCGAATGTTTT 59.682 50.0 4.8 0.0 36.85 2.43 F
1533 1610 0.249657 GGGTAGCAATCTCGGCTCAG 60.250 60.0 0.0 0.0 42.62 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1121 0.978146 GACCAGCTAGCCTTGGAGGA 60.978 60.000 25.43 0.00 37.67 3.71 R
1805 1888 2.071540 GGTTTGCTTGGAGTACGTACC 58.928 52.381 21.80 13.02 0.00 3.34 R
3131 5722 0.035739 TGGCTTCGAAAGGGGTGTAC 59.964 55.000 0.00 0.00 0.00 2.90 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
38 41 6.220579 AGCGACGAATTGATGATGATTTAG 57.779 37.500 0.00 0.00 0.00 1.85
45 48 8.781196 ACGAATTGATGATGATTTAGGAATCTG 58.219 33.333 0.00 0.00 41.80 2.90
55 58 6.223852 TGATTTAGGAATCTGATAACGCTCC 58.776 40.000 0.00 0.00 41.80 4.70
59 62 2.540101 GGAATCTGATAACGCTCCAACG 59.460 50.000 1.35 0.00 39.50 4.10
61 64 0.459585 TCTGATAACGCTCCAACGCC 60.460 55.000 0.00 0.00 36.19 5.68
62 65 0.739462 CTGATAACGCTCCAACGCCA 60.739 55.000 0.00 0.00 36.19 5.69
73 76 1.574428 CAACGCCAGGTGTAAGCAC 59.426 57.895 5.94 0.00 44.53 4.40
81 84 0.250901 AGGTGTAAGCACAGGGCAAG 60.251 55.000 0.00 0.00 46.95 4.01
82 85 1.866853 GGTGTAAGCACAGGGCAAGC 61.867 60.000 0.00 0.00 46.95 4.01
90 93 1.228552 ACAGGGCAAGCCGAATGTT 60.229 52.632 4.80 0.00 36.85 2.71
92 95 0.318120 CAGGGCAAGCCGAATGTTTT 59.682 50.000 4.80 0.00 36.85 2.43
114 117 2.440501 GATGGCAAGTTTAATGACGCG 58.559 47.619 3.53 3.53 0.00 6.01
117 120 1.202031 GGCAAGTTTAATGACGCGAGG 60.202 52.381 15.93 0.00 0.00 4.63
125 128 1.359848 AATGACGCGAGGATGACAAC 58.640 50.000 15.93 0.00 0.00 3.32
127 130 0.388520 TGACGCGAGGATGACAACTG 60.389 55.000 15.93 0.00 0.00 3.16
130 133 1.135373 ACGCGAGGATGACAACTGTAG 60.135 52.381 15.93 0.00 0.00 2.74
199 202 7.859325 AAATTACAGTGTGTGTCAACTAACT 57.141 32.000 5.88 0.00 40.94 2.24
203 206 4.630069 ACAGTGTGTGTCAACTAACTTGTC 59.370 41.667 0.00 0.00 31.90 3.18
204 207 4.629634 CAGTGTGTGTCAACTAACTTGTCA 59.370 41.667 0.00 0.00 0.00 3.58
224 227 7.015226 TGTCATTCTTGTGTCACTAAACTTG 57.985 36.000 4.27 0.00 0.00 3.16
258 261 3.363871 CGTTTCATTTGTCATGTGCTCGA 60.364 43.478 0.00 0.00 0.00 4.04
260 263 5.156355 GTTTCATTTGTCATGTGCTCGAAT 58.844 37.500 0.00 0.00 0.00 3.34
261 264 5.375417 TTCATTTGTCATGTGCTCGAATT 57.625 34.783 0.00 0.00 0.00 2.17
263 266 5.155643 TCATTTGTCATGTGCTCGAATTTG 58.844 37.500 0.00 0.00 0.00 2.32
274 277 3.857665 TGCTCGAATTTGACGTCAGATAC 59.142 43.478 20.62 12.09 0.00 2.24
275 278 4.106197 GCTCGAATTTGACGTCAGATACT 58.894 43.478 20.62 7.44 0.00 2.12
282 285 8.210525 CGAATTTGACGTCAGATACTTATCATG 58.789 37.037 20.62 1.33 35.17 3.07
285 288 5.748592 TGACGTCAGATACTTATCATGTCG 58.251 41.667 15.76 6.47 35.17 4.35
301 304 6.173427 TCATGTCGGATGATTTATCTTGGA 57.827 37.500 0.00 0.00 36.03 3.53
303 306 6.652062 TCATGTCGGATGATTTATCTTGGATG 59.348 38.462 0.00 0.00 36.03 3.51
508 517 0.681733 GTCAGCCACAGGAACAGAGA 59.318 55.000 0.00 0.00 0.00 3.10
563 572 2.515926 TGCGTCAGAATCAGGATAGC 57.484 50.000 0.00 0.00 0.00 2.97
564 573 1.269257 TGCGTCAGAATCAGGATAGCG 60.269 52.381 0.00 0.00 0.00 4.26
565 574 1.269309 GCGTCAGAATCAGGATAGCGT 60.269 52.381 0.00 0.00 0.00 5.07
566 575 2.389059 CGTCAGAATCAGGATAGCGTG 58.611 52.381 0.00 0.00 0.00 5.34
567 576 2.033424 CGTCAGAATCAGGATAGCGTGA 59.967 50.000 5.77 5.77 42.43 4.35
568 577 3.637432 GTCAGAATCAGGATAGCGTGAG 58.363 50.000 9.44 0.00 41.64 3.51
610 619 4.232221 GGCACACAAATCATCTGACTTTG 58.768 43.478 10.71 10.71 36.26 2.77
912 922 3.813724 GCCCACTGCCCTGCCTAT 61.814 66.667 0.00 0.00 0.00 2.57
913 923 2.452064 GCCCACTGCCCTGCCTATA 61.452 63.158 0.00 0.00 0.00 1.31
978 988 2.476619 CTGCCGAGTTACTTGACAAGTG 59.523 50.000 27.44 12.77 42.84 3.16
980 990 1.798813 CCGAGTTACTTGACAAGTGCC 59.201 52.381 27.44 17.90 42.84 5.01
1245 1267 3.585990 GGCGGCGCATGCTAATGT 61.586 61.111 34.36 0.00 42.25 2.71
1248 1270 1.720894 CGGCGCATGCTAATGTCAA 59.279 52.632 17.13 0.00 42.25 3.18
1522 1560 4.188462 CTGATGAAATACGTGGGTAGCAA 58.812 43.478 0.00 0.00 30.81 3.91
1533 1610 0.249657 GGGTAGCAATCTCGGCTCAG 60.250 60.000 0.00 0.00 42.62 3.35
1535 1612 1.269517 GGTAGCAATCTCGGCTCAGAG 60.270 57.143 0.00 0.00 42.62 3.35
1576 1659 4.319766 CGCATTAGTTGACTTTCTGCTTGT 60.320 41.667 9.20 0.00 0.00 3.16
1805 1888 0.381801 GCACAACCTTGACCACAGTG 59.618 55.000 0.00 0.00 0.00 3.66
1821 1904 1.271379 CAGTGGTACGTACTCCAAGCA 59.729 52.381 24.07 10.44 35.38 3.91
1855 1948 1.520342 GGTCACTGATCAGCTCCGC 60.520 63.158 22.83 8.47 0.00 5.54
1857 1950 0.527385 GTCACTGATCAGCTCCGCTC 60.527 60.000 22.83 3.17 36.40 5.03
1941 2034 0.322546 GCTCCAACCCCAACTACCTG 60.323 60.000 0.00 0.00 0.00 4.00
1965 2058 1.741770 GCTGGTGGAGTTCGCGAAT 60.742 57.895 26.23 13.87 0.00 3.34
2178 2271 2.030562 AACTGGAAGCCCGACACG 59.969 61.111 0.00 0.00 37.60 4.49
2210 2303 2.249844 AACGTCCAGTTCCGTTGATT 57.750 45.000 0.00 0.00 44.79 2.57
2301 2394 7.437793 TTGTTGAATTTTACTTACTACGGGG 57.562 36.000 0.00 0.00 0.00 5.73
2304 2397 8.320617 TGTTGAATTTTACTTACTACGGGGTAT 58.679 33.333 0.00 0.00 0.00 2.73
2305 2398 9.816354 GTTGAATTTTACTTACTACGGGGTATA 57.184 33.333 0.00 0.00 0.00 1.47
2307 2400 9.985730 TGAATTTTACTTACTACGGGGTATATG 57.014 33.333 0.00 0.00 0.00 1.78
2315 2408 0.825410 ACGGGGTATATGTTGCGTCA 59.175 50.000 0.00 0.00 0.00 4.35
2341 2434 2.721603 GCGTGTAGCTCGAAGATATGTG 59.278 50.000 0.00 0.00 44.04 3.21
2342 2435 3.792459 GCGTGTAGCTCGAAGATATGTGT 60.792 47.826 0.00 0.00 44.04 3.72
2343 2436 3.726235 CGTGTAGCTCGAAGATATGTGTG 59.274 47.826 0.00 0.00 33.89 3.82
2452 2548 0.759346 CTACCCAGCCCACTATCACC 59.241 60.000 0.00 0.00 0.00 4.02
2465 2561 4.511527 CACTATCACCAGATTCACAGCTT 58.488 43.478 0.00 0.00 35.67 3.74
2536 2633 7.251704 GGATACCAATTGTGTATTCAGTCTG 57.748 40.000 16.06 0.00 0.00 3.51
2537 2634 6.823689 GGATACCAATTGTGTATTCAGTCTGT 59.176 38.462 16.06 2.10 0.00 3.41
2538 2635 7.011482 GGATACCAATTGTGTATTCAGTCTGTC 59.989 40.741 16.06 5.91 0.00 3.51
2539 2636 5.869579 ACCAATTGTGTATTCAGTCTGTCT 58.130 37.500 4.43 0.00 0.00 3.41
2540 2637 5.934625 ACCAATTGTGTATTCAGTCTGTCTC 59.065 40.000 4.43 0.00 0.00 3.36
2541 2638 5.934043 CCAATTGTGTATTCAGTCTGTCTCA 59.066 40.000 4.43 0.00 0.00 3.27
2542 2639 6.427853 CCAATTGTGTATTCAGTCTGTCTCAA 59.572 38.462 4.43 4.11 0.00 3.02
2543 2640 7.041167 CCAATTGTGTATTCAGTCTGTCTCAAA 60.041 37.037 4.43 0.00 0.00 2.69
2544 2641 8.344831 CAATTGTGTATTCAGTCTGTCTCAAAA 58.655 33.333 0.00 0.00 0.00 2.44
2545 2642 7.857734 TTGTGTATTCAGTCTGTCTCAAAAA 57.142 32.000 0.00 0.00 0.00 1.94
2603 2700 8.734386 CATCATTTCTAAAAGTCCTAGTTTGCT 58.266 33.333 0.00 0.00 0.00 3.91
2615 2712 6.375455 AGTCCTAGTTTGCTATTGGTGAATTG 59.625 38.462 0.00 0.00 0.00 2.32
2618 2715 5.391312 AGTTTGCTATTGGTGAATTGACC 57.609 39.130 7.20 7.20 36.43 4.02
2628 2725 4.979335 TGGTGAATTGACCTTGTGACATA 58.021 39.130 15.47 0.00 36.88 2.29
2630 2727 6.716284 TGGTGAATTGACCTTGTGACATATA 58.284 36.000 15.47 0.00 36.88 0.86
2706 2806 1.400494 CCAATCGTTCGGGATTTGACC 59.600 52.381 0.00 0.00 34.50 4.02
2710 2810 1.276705 TCGTTCGGGATTTGACCATGA 59.723 47.619 0.00 0.00 0.00 3.07
2822 5409 2.158623 TGCCGGGAAATTATCATGCTCT 60.159 45.455 2.18 0.00 0.00 4.09
2825 5412 4.518970 GCCGGGAAATTATCATGCTCTTAA 59.481 41.667 2.18 0.00 0.00 1.85
2855 5444 5.191059 GTCATCATCGCGTCAACTAAAATC 58.809 41.667 5.77 0.00 0.00 2.17
2866 5455 6.940597 GCGTCAACTAAAATCGCAATAAAAAC 59.059 34.615 0.00 0.00 45.01 2.43
2867 5456 7.149031 GCGTCAACTAAAATCGCAATAAAAACT 60.149 33.333 0.00 0.00 45.01 2.66
2892 5482 9.656040 CTTTCAATTTATCATGGTCAAAATCCA 57.344 29.630 0.00 0.00 39.41 3.41
2898 5488 4.927978 TCATGGTCAAAATCCAAACGTT 57.072 36.364 0.00 0.00 38.52 3.99
2899 5489 4.865776 TCATGGTCAAAATCCAAACGTTC 58.134 39.130 0.00 0.00 38.52 3.95
2900 5490 4.339530 TCATGGTCAAAATCCAAACGTTCA 59.660 37.500 0.00 0.00 38.52 3.18
2901 5491 4.300189 TGGTCAAAATCCAAACGTTCAG 57.700 40.909 0.00 0.00 31.50 3.02
2914 5504 7.947282 TCCAAACGTTCAGGATTTATCTTTTT 58.053 30.769 16.03 0.00 0.00 1.94
2984 5574 3.645687 AGAGGCCAAAAATTACAAAGCCA 59.354 39.130 5.01 0.00 41.45 4.75
2993 5583 6.481954 AAAATTACAAAGCCACTACTCTCG 57.518 37.500 0.00 0.00 0.00 4.04
3024 5615 1.072489 TGACCCAAGTATTTCGCACCA 59.928 47.619 0.00 0.00 0.00 4.17
3031 5622 2.710377 AGTATTTCGCACCAGCAATGA 58.290 42.857 0.00 0.00 42.27 2.57
3061 5652 6.051074 AGCCTTGCCTCATTATTATTTTTGC 58.949 36.000 0.00 0.00 0.00 3.68
3098 5689 0.468029 CTCGCCCCAAATTGCCCTAT 60.468 55.000 0.00 0.00 0.00 2.57
3111 5702 7.926018 CCAAATTGCCCTATTCTAACATAAACC 59.074 37.037 0.00 0.00 0.00 3.27
3116 5707 7.054124 TGCCCTATTCTAACATAAACCAAGAG 58.946 38.462 0.00 0.00 0.00 2.85
3123 5714 6.779860 TCTAACATAAACCAAGAGAAAGGCT 58.220 36.000 0.00 0.00 0.00 4.58
3125 5716 6.819397 AACATAAACCAAGAGAAAGGCTAC 57.181 37.500 0.00 0.00 0.00 3.58
3131 5722 3.012518 CCAAGAGAAAGGCTACATGGTG 58.987 50.000 0.00 0.00 0.00 4.17
3135 5726 3.838317 AGAGAAAGGCTACATGGTGTACA 59.162 43.478 0.00 0.00 0.00 2.90
3151 5742 0.766131 TACACCCCTTTCGAAGCCAA 59.234 50.000 0.00 0.00 0.00 4.52
3168 5759 2.687914 GCCAATCAAAGCCCTAGATGGT 60.688 50.000 0.00 0.00 0.00 3.55
3170 5761 3.624777 CAATCAAAGCCCTAGATGGTGT 58.375 45.455 0.00 0.00 0.00 4.16
3191 5782 3.512516 GCCCATGACCAGCGCTTC 61.513 66.667 7.50 4.20 0.00 3.86
3193 5784 1.377725 CCCATGACCAGCGCTTCTT 60.378 57.895 7.50 0.00 0.00 2.52
3194 5785 1.651240 CCCATGACCAGCGCTTCTTG 61.651 60.000 7.50 12.50 0.00 3.02
3196 5787 1.302752 ATGACCAGCGCTTCTTGCA 60.303 52.632 7.50 1.95 43.06 4.08
3197 5788 0.890542 ATGACCAGCGCTTCTTGCAA 60.891 50.000 7.50 0.00 43.06 4.08
3200 5791 0.249031 ACCAGCGCTTCTTGCAAAAC 60.249 50.000 7.50 0.00 43.06 2.43
3201 5792 0.031178 CCAGCGCTTCTTGCAAAACT 59.969 50.000 7.50 0.00 43.06 2.66
3202 5793 1.126079 CAGCGCTTCTTGCAAAACTG 58.874 50.000 7.50 0.00 43.06 3.16
3203 5794 0.595825 AGCGCTTCTTGCAAAACTGC 60.596 50.000 2.64 1.33 43.06 4.40
3204 5795 1.869242 GCGCTTCTTGCAAAACTGCG 61.869 55.000 22.52 22.52 43.06 5.18
3205 5796 0.592247 CGCTTCTTGCAAAACTGCGT 60.592 50.000 20.15 0.00 43.06 5.24
3206 5797 0.848305 GCTTCTTGCAAAACTGCGTG 59.152 50.000 0.00 0.00 42.31 5.34
3207 5798 1.533756 GCTTCTTGCAAAACTGCGTGA 60.534 47.619 0.00 0.00 42.31 4.35
3208 5799 2.378806 CTTCTTGCAAAACTGCGTGAG 58.621 47.619 0.00 0.00 37.69 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 41 2.540101 CGTTGGAGCGTTATCAGATTCC 59.460 50.000 0.00 0.00 0.00 3.01
45 48 1.429148 CCTGGCGTTGGAGCGTTATC 61.429 60.000 0.00 0.00 38.18 1.75
55 58 1.163420 TGTGCTTACACCTGGCGTTG 61.163 55.000 0.00 0.00 46.86 4.10
59 62 1.675641 CCCTGTGCTTACACCTGGC 60.676 63.158 0.00 0.00 46.86 4.85
61 64 0.537143 TTGCCCTGTGCTTACACCTG 60.537 55.000 0.00 0.00 46.86 4.00
62 65 0.250901 CTTGCCCTGTGCTTACACCT 60.251 55.000 0.00 0.00 46.86 4.00
73 76 0.318120 AAAACATTCGGCTTGCCCTG 59.682 50.000 6.02 4.30 0.00 4.45
81 84 0.170116 TGCCATCGAAAACATTCGGC 59.830 50.000 10.63 7.28 43.98 5.54
82 85 2.095263 ACTTGCCATCGAAAACATTCGG 60.095 45.455 10.63 0.00 43.98 4.30
90 93 4.717991 CGTCATTAAACTTGCCATCGAAA 58.282 39.130 0.00 0.00 0.00 3.46
92 95 2.095213 GCGTCATTAAACTTGCCATCGA 59.905 45.455 0.00 0.00 0.00 3.59
94 97 2.095213 TCGCGTCATTAAACTTGCCATC 59.905 45.455 5.77 0.00 0.00 3.51
105 108 2.165641 AGTTGTCATCCTCGCGTCATTA 59.834 45.455 5.77 0.00 0.00 1.90
107 110 0.532573 AGTTGTCATCCTCGCGTCAT 59.467 50.000 5.77 0.00 0.00 3.06
125 128 2.430465 AGCCATGCTTGTCAACTACAG 58.570 47.619 0.00 0.00 39.87 2.74
127 130 3.600388 AGTAGCCATGCTTGTCAACTAC 58.400 45.455 0.00 5.38 40.44 2.73
130 133 2.159653 CGAAGTAGCCATGCTTGTCAAC 60.160 50.000 0.00 0.00 40.44 3.18
134 137 1.442769 CACGAAGTAGCCATGCTTGT 58.557 50.000 0.00 0.00 41.61 3.16
135 138 0.097674 GCACGAAGTAGCCATGCTTG 59.902 55.000 0.00 0.00 41.61 4.01
139 142 3.262420 ACTAAAGCACGAAGTAGCCATG 58.738 45.455 0.00 0.00 41.61 3.66
140 143 3.611766 ACTAAAGCACGAAGTAGCCAT 57.388 42.857 0.00 0.00 41.61 4.40
141 144 3.396260 AACTAAAGCACGAAGTAGCCA 57.604 42.857 0.00 0.00 41.61 4.75
142 145 6.418585 AATAAACTAAAGCACGAAGTAGCC 57.581 37.500 0.00 0.00 41.61 3.93
143 146 8.627428 CAAAAATAAACTAAAGCACGAAGTAGC 58.373 33.333 0.00 0.00 41.61 3.58
182 185 4.827692 TGACAAGTTAGTTGACACACACT 58.172 39.130 6.80 0.00 38.60 3.55
199 202 7.120579 ACAAGTTTAGTGACACAAGAATGACAA 59.879 33.333 8.59 0.00 0.00 3.18
203 206 7.015226 TGACAAGTTTAGTGACACAAGAATG 57.985 36.000 8.59 2.45 0.00 2.67
204 207 7.807977 ATGACAAGTTTAGTGACACAAGAAT 57.192 32.000 8.59 0.00 0.00 2.40
235 238 3.606846 CGAGCACATGACAAATGAAACGT 60.607 43.478 0.00 0.00 0.00 3.99
236 239 2.904319 CGAGCACATGACAAATGAAACG 59.096 45.455 0.00 0.00 0.00 3.60
237 240 4.145876 TCGAGCACATGACAAATGAAAC 57.854 40.909 0.00 0.00 0.00 2.78
239 242 5.375417 AATTCGAGCACATGACAAATGAA 57.625 34.783 0.00 0.00 0.00 2.57
240 243 5.048852 TCAAATTCGAGCACATGACAAATGA 60.049 36.000 0.00 0.00 0.00 2.57
241 244 5.060077 GTCAAATTCGAGCACATGACAAATG 59.940 40.000 0.00 0.00 37.65 2.32
248 251 2.157474 TGACGTCAAATTCGAGCACATG 59.843 45.455 17.62 0.00 0.00 3.21
258 261 8.948631 ACATGATAAGTATCTGACGTCAAATT 57.051 30.769 20.49 12.72 33.88 1.82
260 263 6.691388 CGACATGATAAGTATCTGACGTCAAA 59.309 38.462 20.49 6.93 33.88 2.69
261 264 6.199393 CGACATGATAAGTATCTGACGTCAA 58.801 40.000 20.49 11.00 33.88 3.18
263 266 5.049612 TCCGACATGATAAGTATCTGACGTC 60.050 44.000 9.11 9.11 32.97 4.34
274 277 8.663025 CCAAGATAAATCATCCGACATGATAAG 58.337 37.037 0.00 0.00 37.75 1.73
275 278 8.374743 TCCAAGATAAATCATCCGACATGATAA 58.625 33.333 0.00 3.62 37.75 1.75
282 285 4.756642 TGCATCCAAGATAAATCATCCGAC 59.243 41.667 0.00 0.00 33.75 4.79
285 288 7.282675 CCTCTATGCATCCAAGATAAATCATCC 59.717 40.741 0.19 0.00 33.75 3.51
303 306 0.882042 CCACCGTCATGCCTCTATGC 60.882 60.000 0.00 0.00 0.00 3.14
508 517 1.376553 GGCTTCTCTTTCCAGCGCT 60.377 57.895 2.64 2.64 34.09 5.92
564 573 1.079503 GATCAAACCTCACGGCTCAC 58.920 55.000 0.00 0.00 0.00 3.51
565 574 0.036388 GGATCAAACCTCACGGCTCA 60.036 55.000 0.00 0.00 0.00 4.26
566 575 0.036388 TGGATCAAACCTCACGGCTC 60.036 55.000 0.00 0.00 0.00 4.70
567 576 0.400213 TTGGATCAAACCTCACGGCT 59.600 50.000 0.00 0.00 0.00 5.52
568 577 0.521735 GTTGGATCAAACCTCACGGC 59.478 55.000 1.00 0.00 0.00 5.68
569 578 0.796312 CGTTGGATCAAACCTCACGG 59.204 55.000 7.41 0.00 35.36 4.94
610 619 4.030452 GTCAGGCGCTGGTTGCAC 62.030 66.667 7.64 0.00 43.06 4.57
910 920 2.243810 GCATTGCCGGGGGATTTTATA 58.756 47.619 2.18 0.00 0.00 0.98
911 921 1.047801 GCATTGCCGGGGGATTTTAT 58.952 50.000 2.18 0.00 0.00 1.40
912 922 1.045911 GGCATTGCCGGGGGATTTTA 61.046 55.000 12.82 0.00 39.62 1.52
913 923 2.366393 GGCATTGCCGGGGGATTTT 61.366 57.895 12.82 0.00 39.62 1.82
937 947 1.976132 CTGTGGTCTGATGGCCGGAT 61.976 60.000 5.05 0.00 31.82 4.18
980 990 2.751166 ACTTGCACTAGTAGCCAGTG 57.249 50.000 17.28 0.00 45.08 3.66
1111 1121 0.978146 GACCAGCTAGCCTTGGAGGA 60.978 60.000 25.43 0.00 37.67 3.71
1522 1560 2.499289 ACATGTTTCTCTGAGCCGAGAT 59.501 45.455 0.00 0.00 39.60 2.75
1533 1610 3.481467 GCGCTACACGTAACATGTTTCTC 60.481 47.826 17.78 7.16 46.11 2.87
1535 1612 2.156117 TGCGCTACACGTAACATGTTTC 59.844 45.455 17.78 10.94 46.11 2.78
1576 1659 3.591023 TGACGCATCGTATCTGGAAAAA 58.409 40.909 0.00 0.00 41.37 1.94
1805 1888 2.071540 GGTTTGCTTGGAGTACGTACC 58.928 52.381 21.80 13.02 0.00 3.34
1821 1904 2.081585 GACCAGAGCCCCAAGGGTTT 62.082 60.000 4.11 0.00 46.45 3.27
1941 2034 4.643387 AACTCCACCAGCACGGCC 62.643 66.667 0.00 0.00 39.03 6.13
2210 2303 2.808315 GATCGGAAGCTCGGAGCA 59.192 61.111 29.88 10.95 45.56 4.26
2238 2331 5.346822 ACACTGTACCGAATTAATCAACGTC 59.653 40.000 0.00 0.00 0.00 4.34
2248 2341 3.407698 TGCATTCACACTGTACCGAATT 58.592 40.909 0.00 0.00 0.00 2.17
2293 2386 2.034124 ACGCAACATATACCCCGTAGT 58.966 47.619 0.00 0.00 0.00 2.73
2295 2388 2.030371 TGACGCAACATATACCCCGTA 58.970 47.619 0.00 0.00 0.00 4.02
2297 2390 2.066262 GATGACGCAACATATACCCCG 58.934 52.381 0.00 0.00 0.00 5.73
2299 2392 2.475111 CACGATGACGCAACATATACCC 59.525 50.000 0.00 0.00 43.96 3.69
2300 2393 2.096909 GCACGATGACGCAACATATACC 60.097 50.000 0.00 0.00 43.96 2.73
2301 2394 2.408487 CGCACGATGACGCAACATATAC 60.408 50.000 0.00 0.00 43.96 1.47
2304 2397 0.734597 ACGCACGATGACGCAACATA 60.735 50.000 0.00 0.00 43.96 2.29
2305 2398 2.027073 ACGCACGATGACGCAACAT 61.027 52.632 0.00 0.00 43.96 2.71
2306 2399 2.660224 ACGCACGATGACGCAACA 60.660 55.556 0.00 0.00 43.96 3.33
2307 2400 1.610715 TACACGCACGATGACGCAAC 61.611 55.000 0.00 0.00 43.96 4.17
2337 2430 1.285962 CCTCCTTCCATTCCCACACAT 59.714 52.381 0.00 0.00 0.00 3.21
2341 2434 0.332972 AAGCCTCCTTCCATTCCCAC 59.667 55.000 0.00 0.00 0.00 4.61
2342 2435 1.084018 AAAGCCTCCTTCCATTCCCA 58.916 50.000 0.00 0.00 0.00 4.37
2343 2436 2.937519 CTAAAGCCTCCTTCCATTCCC 58.062 52.381 0.00 0.00 0.00 3.97
2546 2643 9.850628 CATCTGATTGACTGAATACACAATTTT 57.149 29.630 0.00 0.00 33.92 1.82
2547 2644 7.972277 GCATCTGATTGACTGAATACACAATTT 59.028 33.333 0.00 0.00 33.92 1.82
2548 2645 7.338703 AGCATCTGATTGACTGAATACACAATT 59.661 33.333 0.00 0.00 33.92 2.32
2549 2646 6.827251 AGCATCTGATTGACTGAATACACAAT 59.173 34.615 0.00 0.00 35.99 2.71
2550 2647 6.175471 AGCATCTGATTGACTGAATACACAA 58.825 36.000 0.00 0.00 0.00 3.33
2551 2648 5.737860 AGCATCTGATTGACTGAATACACA 58.262 37.500 0.00 0.00 0.00 3.72
2552 2649 5.236047 GGAGCATCTGATTGACTGAATACAC 59.764 44.000 0.00 0.00 33.73 2.90
2553 2650 5.363101 GGAGCATCTGATTGACTGAATACA 58.637 41.667 0.00 0.00 33.73 2.29
2554 2651 4.754114 GGGAGCATCTGATTGACTGAATAC 59.246 45.833 0.00 0.00 33.73 1.89
2555 2652 4.409901 TGGGAGCATCTGATTGACTGAATA 59.590 41.667 0.00 0.00 33.73 1.75
2556 2653 3.201487 TGGGAGCATCTGATTGACTGAAT 59.799 43.478 0.00 0.00 33.73 2.57
2557 2654 2.573009 TGGGAGCATCTGATTGACTGAA 59.427 45.455 0.00 0.00 33.73 3.02
2558 2655 2.190538 TGGGAGCATCTGATTGACTGA 58.809 47.619 0.00 0.00 33.73 3.41
2559 2656 2.704464 TGGGAGCATCTGATTGACTG 57.296 50.000 0.00 0.00 33.73 3.51
2560 2657 2.775960 TGATGGGAGCATCTGATTGACT 59.224 45.455 0.00 0.00 33.73 3.41
2561 2658 3.204306 TGATGGGAGCATCTGATTGAC 57.796 47.619 0.00 0.00 33.73 3.18
2562 2659 4.448720 AATGATGGGAGCATCTGATTGA 57.551 40.909 0.00 0.00 33.73 2.57
2563 2660 4.827835 AGAAATGATGGGAGCATCTGATTG 59.172 41.667 0.00 0.00 33.73 2.67
2603 2700 5.380900 TGTCACAAGGTCAATTCACCAATA 58.619 37.500 0.00 0.00 39.16 1.90
2653 2751 4.202284 GCATCCCTAATGATGTGGCAAATT 60.202 41.667 0.00 0.00 43.28 1.82
2654 2752 3.322828 GCATCCCTAATGATGTGGCAAAT 59.677 43.478 0.00 0.00 43.28 2.32
2655 2753 2.694628 GCATCCCTAATGATGTGGCAAA 59.305 45.455 0.00 0.00 43.28 3.68
2658 2756 1.251251 GGCATCCCTAATGATGTGGC 58.749 55.000 3.28 0.00 43.28 5.01
2659 2757 1.527034 CGGCATCCCTAATGATGTGG 58.473 55.000 3.28 0.00 43.28 4.17
2661 2759 1.140312 ACCGGCATCCCTAATGATGT 58.860 50.000 0.00 0.00 43.28 3.06
2662 2760 3.244561 ACTTACCGGCATCCCTAATGATG 60.245 47.826 0.00 0.00 44.02 3.07
2663 2761 2.979678 ACTTACCGGCATCCCTAATGAT 59.020 45.455 0.00 0.00 37.59 2.45
2731 5314 8.815565 TGCCATAGTCAGGAAACATAAATTAA 57.184 30.769 0.00 0.00 0.00 1.40
2732 5315 8.815565 TTGCCATAGTCAGGAAACATAAATTA 57.184 30.769 0.00 0.00 0.00 1.40
2744 5327 5.294552 GCTAACTAAACTTGCCATAGTCAGG 59.705 44.000 0.00 0.00 0.00 3.86
2838 5427 2.713927 GCGATTTTAGTTGACGCGAT 57.286 45.000 15.93 0.00 39.90 4.58
2866 5455 9.656040 TGGATTTTGACCATGATAAATTGAAAG 57.344 29.630 0.00 0.00 32.03 2.62
2871 5461 8.093927 ACGTTTGGATTTTGACCATGATAAATT 58.906 29.630 0.00 0.00 37.26 1.82
2984 5574 3.764434 TCAGATTTTGCCTCGAGAGTAGT 59.236 43.478 15.71 0.00 0.00 2.73
2993 5583 2.519013 ACTTGGGTCAGATTTTGCCTC 58.481 47.619 0.00 0.00 0.00 4.70
3024 5615 0.883833 CAAGGCTTTCGGTCATTGCT 59.116 50.000 0.00 0.00 0.00 3.91
3031 5622 0.251341 AATGAGGCAAGGCTTTCGGT 60.251 50.000 0.00 0.00 0.00 4.69
3061 5652 0.689623 AGCAGAGTTCCAGGGTCTTG 59.310 55.000 0.00 0.00 0.00 3.02
3098 5689 7.231467 AGCCTTTCTCTTGGTTTATGTTAGAA 58.769 34.615 0.00 0.00 0.00 2.10
3111 5702 3.679389 ACACCATGTAGCCTTTCTCTTG 58.321 45.455 0.00 0.00 0.00 3.02
3131 5722 0.035739 TGGCTTCGAAAGGGGTGTAC 59.964 55.000 0.00 0.00 0.00 2.90
3135 5726 0.404040 TGATTGGCTTCGAAAGGGGT 59.596 50.000 0.00 0.00 0.00 4.95
3139 5730 2.599659 GGCTTTGATTGGCTTCGAAAG 58.400 47.619 0.00 0.00 0.00 2.62
3142 5733 0.038166 AGGGCTTTGATTGGCTTCGA 59.962 50.000 0.00 0.00 0.00 3.71
3143 5734 1.672881 CTAGGGCTTTGATTGGCTTCG 59.327 52.381 0.00 0.00 0.00 3.79
3144 5735 3.004752 TCTAGGGCTTTGATTGGCTTC 57.995 47.619 0.00 0.00 0.00 3.86
3151 5742 2.092212 CCACACCATCTAGGGCTTTGAT 60.092 50.000 0.00 0.00 43.89 2.57
3168 5759 3.660571 CTGGTCATGGGCCCCACA 61.661 66.667 22.27 10.04 35.80 4.17


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

AutoCloner maintained by Alex Coulton.