Multiple sequence alignment - TraesCS3D01G367800

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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 TraesCS3D01G367800 chr3D 100.000 2639 0 0 1 2639 481533435 481536073 0.000000e+00 4874.0
1 TraesCS3D01G367800 chr3D 77.228 101 19 3 85 183 560186575 560186477 3.670000e-04 56.5
2 TraesCS3D01G367800 chr3A 93.293 1670 74 14 1007 2639 624541607 624543275 0.000000e+00 2429.0
3 TraesCS3D01G367800 chr3A 89.741 1121 84 13 1532 2639 6653952 6655054 0.000000e+00 1404.0
4 TraesCS3D01G367800 chr3A 86.435 575 46 11 1019 1576 6653349 6653908 3.760000e-168 601.0
5 TraesCS3D01G367800 chr3A 89.139 267 16 3 725 978 624541347 624541613 1.180000e-83 320.0
6 TraesCS3D01G367800 chr3A 83.117 154 25 1 1960 2112 705297240 705297393 3.540000e-29 139.0
7 TraesCS3D01G367800 chr3B 92.538 1635 96 13 702 2322 642826512 642828134 0.000000e+00 2320.0
8 TraesCS3D01G367800 chr3B 86.544 654 55 19 46 695 642825842 642826466 0.000000e+00 689.0
9 TraesCS3D01G367800 chr3B 90.000 250 16 2 2399 2639 642828132 642828381 5.480000e-82 315.0
10 TraesCS3D01G367800 chr3B 83.117 154 22 2 1960 2112 760442679 760442829 1.270000e-28 137.0
11 TraesCS3D01G367800 chr4A 88.804 1313 109 15 1347 2639 16846861 16845567 0.000000e+00 1576.0
12 TraesCS3D01G367800 chr4A 78.182 165 27 7 85 243 577754668 577754507 2.160000e-16 97.1
13 TraesCS3D01G367800 chr1A 89.819 884 73 9 1739 2610 309686635 309687513 0.000000e+00 1118.0
14 TraesCS3D01G367800 chr1A 86.811 599 47 11 995 1576 309685876 309686459 7.960000e-180 640.0
15 TraesCS3D01G367800 chr1A 91.803 183 11 3 1532 1714 309686459 309686637 4.360000e-63 252.0
16 TraesCS3D01G367800 chr5A 90.618 842 61 7 1532 2371 396390664 396391489 0.000000e+00 1101.0
17 TraesCS3D01G367800 chr5A 86.477 599 48 15 995 1576 396390082 396390664 6.200000e-176 627.0
18 TraesCS3D01G367800 chr5A 86.926 283 25 6 2367 2639 396391687 396391967 9.180000e-80 307.0
19 TraesCS3D01G367800 chr2D 80.882 204 33 5 46 245 65534911 65535112 3.520000e-34 156.0
20 TraesCS3D01G367800 chr7D 80.488 164 25 5 87 245 611091411 611091572 4.610000e-23 119.0
21 TraesCS3D01G367800 chr5D 92.405 79 6 0 41 119 509672106 509672184 2.150000e-21 113.0
22 TraesCS3D01G367800 chr5D 80.000 105 17 4 85 187 219512660 219512762 1.010000e-09 75.0
23 TraesCS3D01G367800 chrUn 75.622 201 42 6 54 249 334256566 334256368 2.800000e-15 93.5
24 TraesCS3D01G367800 chr5B 77.301 163 30 6 90 247 348021068 348020908 3.620000e-14 89.8


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 TraesCS3D01G367800 chr3D 481533435 481536073 2638 False 4874.000000 4874 100.000000 1 2639 1 chr3D.!!$F1 2638
1 TraesCS3D01G367800 chr3A 624541347 624543275 1928 False 1374.500000 2429 91.216000 725 2639 2 chr3A.!!$F3 1914
2 TraesCS3D01G367800 chr3A 6653349 6655054 1705 False 1002.500000 1404 88.088000 1019 2639 2 chr3A.!!$F2 1620
3 TraesCS3D01G367800 chr3B 642825842 642828381 2539 False 1108.000000 2320 89.694000 46 2639 3 chr3B.!!$F2 2593
4 TraesCS3D01G367800 chr4A 16845567 16846861 1294 True 1576.000000 1576 88.804000 1347 2639 1 chr4A.!!$R1 1292
5 TraesCS3D01G367800 chr1A 309685876 309687513 1637 False 670.000000 1118 89.477667 995 2610 3 chr1A.!!$F1 1615
6 TraesCS3D01G367800 chr5A 396390082 396391967 1885 False 678.333333 1101 88.007000 995 2639 3 chr5A.!!$F1 1644

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
365 367 0.036010 AGGCCAGGAAGACACATTCG 60.036 55.0 5.01 0.0 0.0 3.34 F
686 691 0.390472 AGCGCCTTCTAAGCACTGTC 60.390 55.0 2.29 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1533 1.777030 CGTCCTCGTCCTCCTCATCG 61.777 65.000 0.00 0.0 0.0 3.84 R
2033 2264 1.923204 CTGCAGTAGCTAACAAGCTCG 59.077 52.381 5.25 0.0 45.0 5.03 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
24 25 7.581213 TTCTTTTTCTAAGGAGCACAAATCA 57.419 32.000 0.00 0.00 0.00 2.57
25 26 7.581213 TCTTTTTCTAAGGAGCACAAATCAA 57.419 32.000 0.00 0.00 0.00 2.57
26 27 8.006298 TCTTTTTCTAAGGAGCACAAATCAAA 57.994 30.769 0.00 0.00 0.00 2.69
27 28 8.641541 TCTTTTTCTAAGGAGCACAAATCAAAT 58.358 29.630 0.00 0.00 0.00 2.32
28 29 9.912634 CTTTTTCTAAGGAGCACAAATCAAATA 57.087 29.630 0.00 0.00 0.00 1.40
31 32 9.691362 TTTCTAAGGAGCACAAATCAAATAAAC 57.309 29.630 0.00 0.00 0.00 2.01
32 33 8.635765 TCTAAGGAGCACAAATCAAATAAACT 57.364 30.769 0.00 0.00 0.00 2.66
33 34 8.730680 TCTAAGGAGCACAAATCAAATAAACTC 58.269 33.333 0.00 0.00 0.00 3.01
34 35 7.530426 AAGGAGCACAAATCAAATAAACTCT 57.470 32.000 0.00 0.00 0.00 3.24
35 36 8.635765 AAGGAGCACAAATCAAATAAACTCTA 57.364 30.769 0.00 0.00 0.00 2.43
36 37 8.814038 AGGAGCACAAATCAAATAAACTCTAT 57.186 30.769 0.00 0.00 0.00 1.98
37 38 9.905713 AGGAGCACAAATCAAATAAACTCTATA 57.094 29.630 0.00 0.00 0.00 1.31
38 39 9.937175 GGAGCACAAATCAAATAAACTCTATAC 57.063 33.333 0.00 0.00 0.00 1.47
95 96 1.757699 GGTGGAACTAGCCTACCAGAG 59.242 57.143 11.71 0.00 36.74 3.35
128 129 8.927411 TCCTAGACTTGACATTGATGATCATAA 58.073 33.333 8.54 0.00 0.00 1.90
180 182 0.966920 TTCGTTCAGTGGGAGGAGAC 59.033 55.000 0.00 0.00 0.00 3.36
183 185 0.244178 GTTCAGTGGGAGGAGACGTC 59.756 60.000 7.70 7.70 0.00 4.34
185 187 0.322636 TCAGTGGGAGGAGACGTCTC 60.323 60.000 32.96 32.96 42.14 3.36
197 199 1.743958 AGACGTCTCCATTGACTACGG 59.256 52.381 13.58 0.00 37.86 4.02
204 206 1.883084 CATTGACTACGGAGGCGCC 60.883 63.158 21.89 21.89 30.54 6.53
209 211 2.143594 GACTACGGAGGCGCCTATGG 62.144 65.000 32.97 23.29 0.00 2.74
236 238 5.349817 ACTTCGTCAATCAAGATGTGATGTC 59.650 40.000 10.99 0.00 46.80 3.06
251 253 3.063997 GTGATGTCGGCTCAGTATTTTGG 59.936 47.826 0.00 0.00 0.00 3.28
252 254 3.055458 TGATGTCGGCTCAGTATTTTGGA 60.055 43.478 0.00 0.00 0.00 3.53
255 257 3.197766 TGTCGGCTCAGTATTTTGGAGAT 59.802 43.478 0.00 0.00 0.00 2.75
264 266 6.764379 TCAGTATTTTGGAGATGTGTGTGTA 58.236 36.000 0.00 0.00 0.00 2.90
286 288 8.706035 GTGTACGTTCATATAAGTGAGTGTTTT 58.294 33.333 0.00 0.00 0.00 2.43
300 302 5.455525 GTGAGTGTTTTGTGTTTGTATGAGC 59.544 40.000 0.00 0.00 0.00 4.26
304 306 2.679355 TTGTGTTTGTATGAGCGCAC 57.321 45.000 11.47 3.13 0.00 5.34
305 307 1.587547 TGTGTTTGTATGAGCGCACA 58.412 45.000 10.65 10.65 34.95 4.57
316 318 0.111266 GAGCGCACACGTTTGTACTG 60.111 55.000 11.47 0.00 42.83 2.74
365 367 0.036010 AGGCCAGGAAGACACATTCG 60.036 55.000 5.01 0.00 0.00 3.34
383 387 8.144478 ACACATTCGAGCATATCTATTACAACT 58.856 33.333 0.00 0.00 0.00 3.16
422 426 6.921486 TTTATTTTTCTAGTTCCAACCCCC 57.079 37.500 0.00 0.00 0.00 5.40
429 433 1.076549 GTTCCAACCCCCATGCTCA 59.923 57.895 0.00 0.00 0.00 4.26
431 435 2.043652 CCAACCCCCATGCTCAGG 60.044 66.667 0.00 0.00 0.00 3.86
432 436 2.757099 CAACCCCCATGCTCAGGC 60.757 66.667 0.00 0.00 39.26 4.85
434 438 2.551413 AACCCCCATGCTCAGGCTT 61.551 57.895 0.00 0.00 39.59 4.35
435 439 1.214305 AACCCCCATGCTCAGGCTTA 61.214 55.000 0.00 0.00 39.59 3.09
436 440 0.995675 ACCCCCATGCTCAGGCTTAT 60.996 55.000 0.00 0.00 39.59 1.73
442 446 3.571401 CCCATGCTCAGGCTTATAAAAGG 59.429 47.826 0.00 0.00 39.59 3.11
472 476 7.415541 GCTCACTATTGCACCTTGAATCAAATA 60.416 37.037 0.00 0.00 0.00 1.40
476 480 5.643379 TTGCACCTTGAATCAAATACTCC 57.357 39.130 0.00 0.00 0.00 3.85
478 482 4.701651 TGCACCTTGAATCAAATACTCCTG 59.298 41.667 0.00 0.00 0.00 3.86
508 512 6.016360 TGTGATCAACATCCAAAGTTCGAAAT 60.016 34.615 0.00 0.00 32.36 2.17
516 520 6.036083 ACATCCAAAGTTCGAAATCATACTCG 59.964 38.462 0.00 0.00 36.39 4.18
517 521 4.328983 TCCAAAGTTCGAAATCATACTCGC 59.671 41.667 0.00 0.00 35.04 5.03
534 539 1.788308 TCGCCTCAAGTTCGTTTTACG 59.212 47.619 0.00 0.00 44.19 3.18
603 608 2.030363 TGTTTCGCCGCATTCTCAAAAT 60.030 40.909 0.00 0.00 0.00 1.82
605 610 1.164411 TCGCCGCATTCTCAAAATGT 58.836 45.000 0.00 0.00 0.00 2.71
656 661 2.031870 AGTGACATCGCCTAGTGCATA 58.968 47.619 0.00 0.00 41.33 3.14
664 669 0.931005 GCCTAGTGCATAAGCGTGTC 59.069 55.000 0.00 0.00 46.23 3.67
678 683 1.734707 GCGTGTCTAAGCGCCTTCTAA 60.735 52.381 2.29 0.00 46.93 2.10
683 688 1.825474 TCTAAGCGCCTTCTAAGCACT 59.175 47.619 2.29 0.00 0.00 4.40
686 691 0.390472 AGCGCCTTCTAAGCACTGTC 60.390 55.000 2.29 0.00 0.00 3.51
695 700 4.552166 TCTAAGCACTGTCTTTTGCAAC 57.448 40.909 0.00 0.00 41.48 4.17
697 702 3.591196 AAGCACTGTCTTTTGCAACAA 57.409 38.095 0.00 0.00 41.48 2.83
699 704 3.253230 AGCACTGTCTTTTGCAACAAAC 58.747 40.909 0.00 0.00 41.48 2.93
703 708 3.249917 CTGTCTTTTGCAACAAACGGTT 58.750 40.909 0.00 0.00 41.47 4.44
717 722 6.680874 ACAAACGGTTGTACAAAGAATGTA 57.319 33.333 19.20 0.00 46.33 2.29
718 723 7.086230 ACAAACGGTTGTACAAAGAATGTAA 57.914 32.000 19.20 0.00 46.33 2.41
719 724 6.968335 ACAAACGGTTGTACAAAGAATGTAAC 59.032 34.615 19.20 0.00 46.33 2.50
720 725 6.680874 AACGGTTGTACAAAGAATGTAACA 57.319 33.333 10.51 0.00 43.63 2.41
722 727 6.050432 ACGGTTGTACAAAGAATGTAACAGA 58.950 36.000 10.51 0.00 43.63 3.41
723 728 6.539464 ACGGTTGTACAAAGAATGTAACAGAA 59.461 34.615 10.51 0.00 43.63 3.02
1201 1259 0.537188 GTTCATCTCCTCCTTCCGCA 59.463 55.000 0.00 0.00 0.00 5.69
1458 1533 2.677979 GGCTTTCGCGAGTGAACCC 61.678 63.158 9.59 0.00 36.88 4.11
1473 1548 1.038130 AACCCGATGAGGAGGACGAG 61.038 60.000 0.00 0.00 45.00 4.18
1557 1632 3.885814 ACCTTCTCGGTGCTGGAA 58.114 55.556 0.00 0.00 46.80 3.53
1675 1838 1.153549 GGTAGCTGCCTTCGACCAG 60.154 63.158 14.43 0.00 0.00 4.00
1676 1839 1.592223 GTAGCTGCCTTCGACCAGT 59.408 57.895 0.00 0.55 0.00 4.00
1677 1840 0.458716 GTAGCTGCCTTCGACCAGTC 60.459 60.000 0.00 0.00 0.00 3.51
1802 2012 9.046296 CGGCATTACTCTTATTTATGAACTCTT 57.954 33.333 0.00 0.00 0.00 2.85
1817 2027 7.934855 ATGAACTCTTTATTTGAGCTGTCAT 57.065 32.000 0.00 0.00 35.12 3.06
1818 2028 7.750229 TGAACTCTTTATTTGAGCTGTCATT 57.250 32.000 0.00 0.00 35.12 2.57
1906 2119 4.415179 TGCCCCAAGAGATATGGTTTATCA 59.585 41.667 0.00 0.00 36.14 2.15
1980 2193 6.909550 TGTAAACTTGGGCATATTTTGAGT 57.090 33.333 0.00 0.00 0.00 3.41
2033 2264 6.037610 CACTTATGGAGTTGGATGCTTTACTC 59.962 42.308 0.00 0.00 36.10 2.59
2174 2406 3.493699 GGAAATGGATCATGGGTGCAATG 60.494 47.826 0.00 0.00 0.00 2.82
2243 2476 7.124599 TCAGTATTCAGGGTCCGAGTTAAATAA 59.875 37.037 0.00 0.00 0.00 1.40
2299 2533 8.739039 TCCTCGAATTTTCATTGTGATGTTTAT 58.261 29.630 0.00 0.00 34.77 1.40
2392 2833 1.400846 CAGAGATGCACAATCAGGCAC 59.599 52.381 0.00 0.00 43.75 5.01
2510 2955 6.350780 GCTGTGATTCTGGATTTCCAAAAGAT 60.351 38.462 0.18 0.00 46.97 2.40
2515 2960 6.942532 TTCTGGATTTCCAAAAGATATCGG 57.057 37.500 0.18 0.00 46.97 4.18
2568 3021 9.722056 CAAACAGAAAATATAGCTTACCATGAC 57.278 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.581213 TGATTTGTGCTCCTTAGAAAAAGAA 57.419 32.000 0.00 0.00 0.00 2.52
1 2 7.581213 TTGATTTGTGCTCCTTAGAAAAAGA 57.419 32.000 0.00 0.00 0.00 2.52
2 3 8.822652 ATTTGATTTGTGCTCCTTAGAAAAAG 57.177 30.769 0.00 0.00 0.00 2.27
5 6 9.691362 GTTTATTTGATTTGTGCTCCTTAGAAA 57.309 29.630 0.00 0.00 0.00 2.52
6 7 9.077885 AGTTTATTTGATTTGTGCTCCTTAGAA 57.922 29.630 0.00 0.00 0.00 2.10
7 8 8.635765 AGTTTATTTGATTTGTGCTCCTTAGA 57.364 30.769 0.00 0.00 0.00 2.10
8 9 8.734386 AGAGTTTATTTGATTTGTGCTCCTTAG 58.266 33.333 0.00 0.00 0.00 2.18
9 10 8.635765 AGAGTTTATTTGATTTGTGCTCCTTA 57.364 30.769 0.00 0.00 0.00 2.69
10 11 7.530426 AGAGTTTATTTGATTTGTGCTCCTT 57.470 32.000 0.00 0.00 0.00 3.36
11 12 8.814038 ATAGAGTTTATTTGATTTGTGCTCCT 57.186 30.769 0.00 0.00 0.00 3.69
12 13 9.937175 GTATAGAGTTTATTTGATTTGTGCTCC 57.063 33.333 0.00 0.00 0.00 4.70
27 28 8.861086 CCTAGGCTCAATTCAGTATAGAGTTTA 58.139 37.037 0.00 0.00 0.00 2.01
28 29 7.345914 ACCTAGGCTCAATTCAGTATAGAGTTT 59.654 37.037 9.30 0.00 0.00 2.66
29 30 6.841755 ACCTAGGCTCAATTCAGTATAGAGTT 59.158 38.462 9.30 0.00 0.00 3.01
30 31 6.377912 ACCTAGGCTCAATTCAGTATAGAGT 58.622 40.000 9.30 0.00 0.00 3.24
31 32 6.491745 TGACCTAGGCTCAATTCAGTATAGAG 59.508 42.308 9.30 0.00 0.00 2.43
32 33 6.373759 TGACCTAGGCTCAATTCAGTATAGA 58.626 40.000 9.30 0.00 0.00 1.98
33 34 6.491745 TCTGACCTAGGCTCAATTCAGTATAG 59.508 42.308 19.10 4.93 33.63 1.31
34 35 6.373759 TCTGACCTAGGCTCAATTCAGTATA 58.626 40.000 19.10 3.65 33.63 1.47
35 36 5.211973 TCTGACCTAGGCTCAATTCAGTAT 58.788 41.667 19.10 0.00 33.63 2.12
36 37 4.610333 TCTGACCTAGGCTCAATTCAGTA 58.390 43.478 19.10 8.09 33.63 2.74
37 38 3.445008 TCTGACCTAGGCTCAATTCAGT 58.555 45.455 19.10 0.00 33.63 3.41
38 39 4.378774 CATCTGACCTAGGCTCAATTCAG 58.621 47.826 9.30 13.21 33.26 3.02
39 40 3.135348 CCATCTGACCTAGGCTCAATTCA 59.865 47.826 9.30 2.80 0.00 2.57
40 41 3.135530 ACCATCTGACCTAGGCTCAATTC 59.864 47.826 9.30 0.00 0.00 2.17
41 42 3.118531 ACCATCTGACCTAGGCTCAATT 58.881 45.455 9.30 0.05 0.00 2.32
42 43 2.769209 ACCATCTGACCTAGGCTCAAT 58.231 47.619 9.30 6.09 0.00 2.57
43 44 2.254152 ACCATCTGACCTAGGCTCAA 57.746 50.000 9.30 4.18 0.00 3.02
44 45 2.254152 AACCATCTGACCTAGGCTCA 57.746 50.000 9.30 10.96 0.00 4.26
45 46 3.301274 ACTAACCATCTGACCTAGGCTC 58.699 50.000 9.30 6.55 0.00 4.70
46 47 3.406512 ACTAACCATCTGACCTAGGCT 57.593 47.619 9.30 0.00 0.00 4.58
47 48 4.162509 AGAAACTAACCATCTGACCTAGGC 59.837 45.833 9.30 2.11 0.00 3.93
48 49 5.941555 AGAAACTAACCATCTGACCTAGG 57.058 43.478 7.41 7.41 0.00 3.02
141 142 8.845942 AACGAACATTACCAAAAAGACTAAAC 57.154 30.769 0.00 0.00 0.00 2.01
147 148 6.459024 CCACTGAACGAACATTACCAAAAAGA 60.459 38.462 0.00 0.00 0.00 2.52
153 154 2.369203 TCCCACTGAACGAACATTACCA 59.631 45.455 0.00 0.00 0.00 3.25
156 157 2.901192 TCCTCCCACTGAACGAACATTA 59.099 45.455 0.00 0.00 0.00 1.90
185 187 1.883084 GCGCCTCCGTAGTCAATGG 60.883 63.158 0.00 0.00 36.67 3.16
192 194 2.201022 ACCATAGGCGCCTCCGTAG 61.201 63.158 36.73 20.46 40.77 3.51
195 197 3.536917 TCACCATAGGCGCCTCCG 61.537 66.667 36.73 24.86 40.77 4.63
197 199 0.530870 GAAGTCACCATAGGCGCCTC 60.531 60.000 36.73 17.40 0.00 4.70
236 238 3.310774 CACATCTCCAAAATACTGAGCCG 59.689 47.826 0.00 0.00 0.00 5.52
251 253 7.701078 ACTTATATGAACGTACACACACATCTC 59.299 37.037 0.00 0.00 0.00 2.75
252 254 7.488150 CACTTATATGAACGTACACACACATCT 59.512 37.037 0.00 0.00 0.00 2.90
255 257 6.679843 TCACTTATATGAACGTACACACACA 58.320 36.000 0.00 0.00 0.00 3.72
264 266 7.225931 ACACAAAACACTCACTTATATGAACGT 59.774 33.333 0.00 0.00 0.00 3.99
286 288 1.262950 GTGTGCGCTCATACAAACACA 59.737 47.619 16.02 0.10 38.20 3.72
300 302 0.648441 ACACAGTACAAACGTGTGCG 59.352 50.000 5.39 0.00 44.51 5.34
339 341 1.271379 TGTCTTCCTGGCCTGCTTTAC 60.271 52.381 3.32 0.46 0.00 2.01
346 348 0.036010 CGAATGTGTCTTCCTGGCCT 60.036 55.000 3.32 0.00 0.00 5.19
347 349 0.036388 TCGAATGTGTCTTCCTGGCC 60.036 55.000 0.00 0.00 0.00 5.36
348 350 1.363744 CTCGAATGTGTCTTCCTGGC 58.636 55.000 0.00 0.00 0.00 4.85
349 351 1.338105 TGCTCGAATGTGTCTTCCTGG 60.338 52.381 0.00 0.00 0.00 4.45
350 352 2.084610 TGCTCGAATGTGTCTTCCTG 57.915 50.000 0.00 0.00 0.00 3.86
396 400 9.038072 GGGGGTTGGAACTAGAAAAATAAAATA 57.962 33.333 0.00 0.00 0.00 1.40
400 404 5.966684 TGGGGGTTGGAACTAGAAAAATAA 58.033 37.500 0.00 0.00 0.00 1.40
411 415 0.967380 CTGAGCATGGGGGTTGGAAC 60.967 60.000 0.00 0.00 0.00 3.62
422 426 5.504665 CGTTCCTTTTATAAGCCTGAGCATG 60.505 44.000 0.00 0.00 43.56 4.06
429 433 3.939592 GTGAGCGTTCCTTTTATAAGCCT 59.060 43.478 0.00 0.00 0.00 4.58
431 435 6.846325 ATAGTGAGCGTTCCTTTTATAAGC 57.154 37.500 0.00 0.00 0.00 3.09
432 436 7.126398 GCAATAGTGAGCGTTCCTTTTATAAG 58.874 38.462 0.00 0.00 0.00 1.73
434 438 6.036735 GTGCAATAGTGAGCGTTCCTTTTATA 59.963 38.462 0.00 0.00 0.00 0.98
435 439 4.941263 TGCAATAGTGAGCGTTCCTTTTAT 59.059 37.500 0.00 0.00 0.00 1.40
436 440 4.153475 GTGCAATAGTGAGCGTTCCTTTTA 59.847 41.667 0.00 0.00 0.00 1.52
442 446 1.726853 AGGTGCAATAGTGAGCGTTC 58.273 50.000 0.00 0.00 0.00 3.95
472 476 4.422073 TGTTGATCACAAACTCAGGAGT 57.578 40.909 0.00 0.00 44.94 3.85
476 480 5.694231 TTGGATGTTGATCACAAACTCAG 57.306 39.130 0.00 0.00 39.50 3.35
478 482 6.076981 ACTTTGGATGTTGATCACAAACTC 57.923 37.500 0.00 0.00 39.50 3.01
508 512 1.816835 ACGAACTTGAGGCGAGTATGA 59.183 47.619 0.00 0.00 0.00 2.15
573 578 1.463056 TGCGGCGAAACAAATAGTCTG 59.537 47.619 12.98 0.00 0.00 3.51
574 579 1.803334 TGCGGCGAAACAAATAGTCT 58.197 45.000 12.98 0.00 0.00 3.24
587 592 1.261989 CACATTTTGAGAATGCGGCG 58.738 50.000 0.51 0.51 0.00 6.46
625 630 5.003804 AGGCGATGTCACTTCAACTTTATT 58.996 37.500 0.00 0.00 0.00 1.40
627 632 4.002906 AGGCGATGTCACTTCAACTTTA 57.997 40.909 0.00 0.00 0.00 1.85
628 633 2.851195 AGGCGATGTCACTTCAACTTT 58.149 42.857 0.00 0.00 0.00 2.66
629 634 2.550830 AGGCGATGTCACTTCAACTT 57.449 45.000 0.00 0.00 0.00 2.66
664 669 1.929836 CAGTGCTTAGAAGGCGCTTAG 59.070 52.381 7.64 0.00 46.53 2.18
671 676 3.565482 TGCAAAAGACAGTGCTTAGAAGG 59.435 43.478 0.00 0.00 41.48 3.46
672 677 4.818534 TGCAAAAGACAGTGCTTAGAAG 57.181 40.909 0.00 0.00 41.48 2.85
673 678 4.397730 TGTTGCAAAAGACAGTGCTTAGAA 59.602 37.500 0.00 0.00 41.48 2.10
678 683 3.253230 GTTTGTTGCAAAAGACAGTGCT 58.747 40.909 0.00 0.00 41.48 4.40
683 688 3.305398 AACCGTTTGTTGCAAAAGACA 57.695 38.095 10.63 0.00 35.31 3.41
695 700 6.967767 TGTTACATTCTTTGTACAACCGTTTG 59.032 34.615 8.07 5.61 40.53 2.93
697 702 6.539464 TCTGTTACATTCTTTGTACAACCGTT 59.461 34.615 8.07 0.00 40.53 4.44
699 704 6.533819 TCTGTTACATTCTTTGTACAACCG 57.466 37.500 8.07 2.71 40.53 4.44
761 803 2.000447 GATCCGTGCAGTACTTTCACC 59.000 52.381 15.57 2.85 0.00 4.02
931 985 0.650476 CGTATTTGCGATTGACGGCG 60.650 55.000 4.80 4.80 42.83 6.46
944 998 0.108709 TAACGTCTGGCGCCGTATTT 60.109 50.000 23.90 13.28 46.11 1.40
948 1002 3.980989 TGTAACGTCTGGCGCCGT 61.981 61.111 23.90 13.24 46.11 5.68
988 1046 4.957684 ATCCATGGCGAGCGCGAG 62.958 66.667 15.92 0.19 43.06 5.03
989 1047 4.950062 GATCCATGGCGAGCGCGA 62.950 66.667 15.92 5.30 43.06 5.87
1201 1259 4.043100 GGGGCTAGGGTTTGCGGT 62.043 66.667 0.00 0.00 0.00 5.68
1443 1510 2.729455 TCGGGTTCACTCGCGAAA 59.271 55.556 11.33 0.00 46.38 3.46
1458 1533 1.777030 CGTCCTCGTCCTCCTCATCG 61.777 65.000 0.00 0.00 0.00 3.84
1473 1548 2.107953 GGCAGCATCTCCTCGTCC 59.892 66.667 0.00 0.00 0.00 4.79
1675 1838 7.524294 AATTCAAACACACAAACTCAATGAC 57.476 32.000 0.00 0.00 0.00 3.06
1676 1839 9.814899 AATAATTCAAACACACAAACTCAATGA 57.185 25.926 0.00 0.00 0.00 2.57
1751 1961 4.350368 TGGTGAGTGATACAACACACAT 57.650 40.909 7.11 0.00 41.65 3.21
1884 2097 4.985538 TGATAAACCATATCTCTTGGGGC 58.014 43.478 0.00 0.00 38.64 5.80
1906 2119 7.369551 TCGGAATGTAACCATAGTAAGGATT 57.630 36.000 0.00 0.00 0.00 3.01
1955 2168 7.906327 ACTCAAAATATGCCCAAGTTTACATT 58.094 30.769 0.00 0.00 0.00 2.71
1980 2193 7.663905 AGTGCAAAGTAATCTACACCACAATAA 59.336 33.333 0.00 0.00 0.00 1.40
2025 2256 3.254892 AGCTAACAAGCTCGAGTAAAGC 58.745 45.455 15.13 13.79 42.12 3.51
2033 2264 1.923204 CTGCAGTAGCTAACAAGCTCG 59.077 52.381 5.25 0.00 45.00 5.03
2365 2604 4.124970 TGATTGTGCATCTCTGACATAGC 58.875 43.478 0.00 0.00 32.34 2.97
2455 2900 3.005897 ACCTGACGATCTGGCATACATAC 59.994 47.826 9.66 0.00 38.86 2.39
2510 2955 2.842457 TCGACAGCTAAGCTACCGATA 58.158 47.619 0.00 0.00 36.40 2.92
2515 2960 6.034591 TGAACTATTTCGACAGCTAAGCTAC 58.965 40.000 0.00 0.00 33.61 3.58
2581 3034 8.739972 AGGCAACAAGTGTTCCTTAATAATAAG 58.260 33.333 8.49 0.00 36.23 1.73


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

AutoCloner maintained by Alex Coulton.