Multiple sequence alignment - TraesCS2A01G191800

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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 TraesCS2A01G191800 chr2A 100.000 2411 0 0 1 2411 158806742 158804332 0.000000e+00 4453.0
1 TraesCS2A01G191800 chr2A 96.591 440 14 1 1001 1440 62113378 62112940 0.000000e+00 728.0
2 TraesCS2A01G191800 chr2A 85.088 114 15 2 1328 1440 1359056 1358944 5.450000e-22 115.0
3 TraesCS2A01G191800 chr5B 93.876 1290 78 1 90 1379 10578834 10580122 0.000000e+00 1943.0
4 TraesCS2A01G191800 chr5B 75.726 482 86 22 1864 2337 596638275 596637817 1.880000e-51 213.0
5 TraesCS2A01G191800 chr2B 86.696 1353 173 7 91 1440 28744426 28745774 0.000000e+00 1495.0
6 TraesCS2A01G191800 chr2B 86.544 1360 177 6 90 1446 372232348 372230992 0.000000e+00 1493.0
7 TraesCS2A01G191800 chr2B 94.771 612 31 1 830 1441 53272348 53271738 0.000000e+00 952.0
8 TraesCS2A01G191800 chr2B 79.639 997 132 38 1444 2411 433716614 433715660 0.000000e+00 651.0
9 TraesCS2A01G191800 chr2B 93.979 382 20 2 447 827 53295906 53295527 2.080000e-160 575.0
10 TraesCS2A01G191800 chr2B 81.139 281 44 8 182 459 717090687 717090413 1.450000e-52 217.0
11 TraesCS2A01G191800 chr7B 84.813 935 108 15 1433 2344 477620481 477621404 0.000000e+00 909.0
12 TraesCS2A01G191800 chr7B 81.140 912 130 23 1439 2325 10054670 10055564 0.000000e+00 693.0
13 TraesCS2A01G191800 chr7B 81.317 835 90 24 1623 2411 339243082 339242268 3.410000e-173 617.0
14 TraesCS2A01G191800 chr6B 81.711 1017 122 27 1439 2411 560666625 560667621 0.000000e+00 789.0
15 TraesCS2A01G191800 chr6B 81.426 996 135 22 1439 2411 588110600 588111568 0.000000e+00 769.0
16 TraesCS2A01G191800 chr6B 75.565 929 159 39 1439 2349 144795037 144794159 1.740000e-106 396.0
17 TraesCS2A01G191800 chr1B 81.723 952 121 29 1506 2411 45063951 45064895 0.000000e+00 745.0
18 TraesCS2A01G191800 chr1B 94.419 215 12 0 1021 1235 593247101 593247315 4.970000e-87 331.0
19 TraesCS2A01G191800 chr1D 83.845 749 91 17 1622 2349 346364503 346365242 0.000000e+00 686.0
20 TraesCS2A01G191800 chr1D 87.069 116 14 1 321 435 466490319 466490434 1.950000e-26 130.0
21 TraesCS2A01G191800 chr5A 81.595 815 114 20 1566 2349 44293539 44294348 2.020000e-180 641.0
22 TraesCS2A01G191800 chr7D 82.874 689 83 15 1679 2344 453393886 453394562 9.600000e-164 586.0
23 TraesCS2A01G191800 chr7D 88.800 250 25 3 1433 1682 453393606 453393852 1.080000e-78 303.0
24 TraesCS2A01G191800 chr3D 82.390 636 82 13 1734 2344 440698155 440698785 5.900000e-146 527.0
25 TraesCS2A01G191800 chr3D 74.925 335 75 7 128 459 480415165 480414837 6.950000e-31 145.0
26 TraesCS2A01G191800 chr3D 74.699 332 62 18 112 434 56567669 56567987 7.000000e-26 128.0
27 TraesCS2A01G191800 chr3B 94.465 271 15 0 1026 1296 31671559 31671829 3.710000e-113 418.0
28 TraesCS2A01G191800 chr3B 89.873 158 16 0 1283 1440 31672996 31673153 1.130000e-48 204.0
29 TraesCS2A01G191800 chrUn 81.250 192 34 2 245 435 68204307 68204497 1.150000e-33 154.0
30 TraesCS2A01G191800 chrUn 83.158 95 12 4 328 420 88047482 88047574 1.540000e-12 84.2
31 TraesCS2A01G191800 chr5D 90.909 66 4 2 1380 1443 44056455 44056390 1.190000e-13 87.9


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 TraesCS2A01G191800 chr2A 158804332 158806742 2410 True 4453.0 4453 100.000 1 2411 1 chr2A.!!$R3 2410
1 TraesCS2A01G191800 chr5B 10578834 10580122 1288 False 1943.0 1943 93.876 90 1379 1 chr5B.!!$F1 1289
2 TraesCS2A01G191800 chr2B 28744426 28745774 1348 False 1495.0 1495 86.696 91 1440 1 chr2B.!!$F1 1349
3 TraesCS2A01G191800 chr2B 372230992 372232348 1356 True 1493.0 1493 86.544 90 1446 1 chr2B.!!$R3 1356
4 TraesCS2A01G191800 chr2B 53271738 53272348 610 True 952.0 952 94.771 830 1441 1 chr2B.!!$R1 611
5 TraesCS2A01G191800 chr2B 433715660 433716614 954 True 651.0 651 79.639 1444 2411 1 chr2B.!!$R4 967
6 TraesCS2A01G191800 chr7B 477620481 477621404 923 False 909.0 909 84.813 1433 2344 1 chr7B.!!$F2 911
7 TraesCS2A01G191800 chr7B 10054670 10055564 894 False 693.0 693 81.140 1439 2325 1 chr7B.!!$F1 886
8 TraesCS2A01G191800 chr7B 339242268 339243082 814 True 617.0 617 81.317 1623 2411 1 chr7B.!!$R1 788
9 TraesCS2A01G191800 chr6B 560666625 560667621 996 False 789.0 789 81.711 1439 2411 1 chr6B.!!$F1 972
10 TraesCS2A01G191800 chr6B 588110600 588111568 968 False 769.0 769 81.426 1439 2411 1 chr6B.!!$F2 972
11 TraesCS2A01G191800 chr6B 144794159 144795037 878 True 396.0 396 75.565 1439 2349 1 chr6B.!!$R1 910
12 TraesCS2A01G191800 chr1B 45063951 45064895 944 False 745.0 745 81.723 1506 2411 1 chr1B.!!$F1 905
13 TraesCS2A01G191800 chr1D 346364503 346365242 739 False 686.0 686 83.845 1622 2349 1 chr1D.!!$F1 727
14 TraesCS2A01G191800 chr5A 44293539 44294348 809 False 641.0 641 81.595 1566 2349 1 chr5A.!!$F1 783
15 TraesCS2A01G191800 chr7D 453393606 453394562 956 False 444.5 586 85.837 1433 2344 2 chr7D.!!$F1 911
16 TraesCS2A01G191800 chr3D 440698155 440698785 630 False 527.0 527 82.390 1734 2344 1 chr3D.!!$F2 610
17 TraesCS2A01G191800 chr3B 31671559 31673153 1594 False 311.0 418 92.169 1026 1440 2 chr3B.!!$F1 414

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
828 829 0.249868 TCAGACAACACCCTTCTGCG 60.25 55.0 0.0 0.0 37.31 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 3594 6.869421 AATGTTCGTGTTTCAAAAAGTCTG 57.131 33.333 0.0 0.0 0.0 3.51 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
17 18 3.142393 AGCGCCAGAGACAACAGT 58.858 55.556 2.29 0.00 0.00 3.55
18 19 1.301244 AGCGCCAGAGACAACAGTG 60.301 57.895 2.29 0.00 0.00 3.66
19 20 2.320587 GCGCCAGAGACAACAGTGG 61.321 63.158 0.00 0.00 0.00 4.00
20 21 1.367471 CGCCAGAGACAACAGTGGA 59.633 57.895 0.00 0.00 31.04 4.02
21 22 0.668706 CGCCAGAGACAACAGTGGAG 60.669 60.000 0.00 0.00 31.04 3.86
22 23 0.952984 GCCAGAGACAACAGTGGAGC 60.953 60.000 0.00 0.00 31.04 4.70
23 24 0.683973 CCAGAGACAACAGTGGAGCT 59.316 55.000 0.00 0.00 31.04 4.09
24 25 1.895798 CCAGAGACAACAGTGGAGCTA 59.104 52.381 0.00 0.00 31.04 3.32
25 26 2.300152 CCAGAGACAACAGTGGAGCTAA 59.700 50.000 0.00 0.00 31.04 3.09
26 27 3.321497 CAGAGACAACAGTGGAGCTAAC 58.679 50.000 0.00 0.00 0.00 2.34
27 28 2.300437 AGAGACAACAGTGGAGCTAACC 59.700 50.000 0.00 0.00 0.00 2.85
28 29 2.037251 GAGACAACAGTGGAGCTAACCA 59.963 50.000 0.00 0.00 37.63 3.67
29 30 2.037772 AGACAACAGTGGAGCTAACCAG 59.962 50.000 0.00 0.00 40.85 4.00
30 31 1.768870 ACAACAGTGGAGCTAACCAGT 59.231 47.619 0.00 0.00 43.46 4.00
31 32 2.969950 ACAACAGTGGAGCTAACCAGTA 59.030 45.455 1.59 0.00 41.09 2.74
32 33 3.583086 ACAACAGTGGAGCTAACCAGTAT 59.417 43.478 1.59 0.00 41.09 2.12
33 34 3.895232 ACAGTGGAGCTAACCAGTATG 57.105 47.619 1.59 1.63 41.09 2.39
34 35 3.441101 ACAGTGGAGCTAACCAGTATGA 58.559 45.455 1.59 0.00 41.09 2.15
35 36 3.195825 ACAGTGGAGCTAACCAGTATGAC 59.804 47.826 1.59 0.00 41.09 3.06
36 37 3.195610 CAGTGGAGCTAACCAGTATGACA 59.804 47.826 1.59 0.00 41.09 3.58
37 38 3.838317 AGTGGAGCTAACCAGTATGACAA 59.162 43.478 0.00 0.00 41.21 3.18
38 39 4.081420 AGTGGAGCTAACCAGTATGACAAG 60.081 45.833 0.00 0.00 41.21 3.16
39 40 3.838317 TGGAGCTAACCAGTATGACAAGT 59.162 43.478 0.00 0.00 39.69 3.16
40 41 4.286032 TGGAGCTAACCAGTATGACAAGTT 59.714 41.667 0.00 0.00 39.69 2.66
41 42 5.482526 TGGAGCTAACCAGTATGACAAGTTA 59.517 40.000 0.00 0.00 39.69 2.24
42 43 6.043411 GGAGCTAACCAGTATGACAAGTTAG 58.957 44.000 11.51 11.51 39.69 2.34
43 44 5.720261 GCTAACCAGTATGACAAGTTAGC 57.280 43.478 19.27 19.27 45.56 3.09
44 45 5.420409 GCTAACCAGTATGACAAGTTAGCT 58.580 41.667 23.06 0.00 46.67 3.32
45 46 5.292101 GCTAACCAGTATGACAAGTTAGCTG 59.708 44.000 23.06 7.09 46.67 4.24
46 47 4.891992 ACCAGTATGACAAGTTAGCTGT 57.108 40.909 0.00 0.00 39.69 4.40
47 48 5.995565 ACCAGTATGACAAGTTAGCTGTA 57.004 39.130 0.00 0.00 39.69 2.74
48 49 5.967088 ACCAGTATGACAAGTTAGCTGTAG 58.033 41.667 0.00 0.00 39.69 2.74
49 50 5.480772 ACCAGTATGACAAGTTAGCTGTAGT 59.519 40.000 0.00 0.00 39.69 2.73
50 51 5.807520 CCAGTATGACAAGTTAGCTGTAGTG 59.192 44.000 0.00 0.00 39.69 2.74
51 52 5.807520 CAGTATGACAAGTTAGCTGTAGTGG 59.192 44.000 0.00 0.00 39.69 4.00
52 53 5.715279 AGTATGACAAGTTAGCTGTAGTGGA 59.285 40.000 0.00 0.00 0.00 4.02
53 54 4.948341 TGACAAGTTAGCTGTAGTGGAA 57.052 40.909 0.00 0.00 0.00 3.53
54 55 4.883083 TGACAAGTTAGCTGTAGTGGAAG 58.117 43.478 0.00 0.00 0.00 3.46
55 56 4.587262 TGACAAGTTAGCTGTAGTGGAAGA 59.413 41.667 0.00 0.00 0.00 2.87
56 57 5.246203 TGACAAGTTAGCTGTAGTGGAAGAT 59.754 40.000 0.00 0.00 0.00 2.40
57 58 6.115448 ACAAGTTAGCTGTAGTGGAAGATT 57.885 37.500 0.00 0.00 0.00 2.40
58 59 6.534634 ACAAGTTAGCTGTAGTGGAAGATTT 58.465 36.000 0.00 0.00 0.00 2.17
59 60 6.428159 ACAAGTTAGCTGTAGTGGAAGATTTG 59.572 38.462 0.00 0.00 0.00 2.32
60 61 4.938226 AGTTAGCTGTAGTGGAAGATTTGC 59.062 41.667 0.00 0.00 0.00 3.68
61 62 3.423539 AGCTGTAGTGGAAGATTTGCA 57.576 42.857 0.00 0.00 0.00 4.08
62 63 3.754965 AGCTGTAGTGGAAGATTTGCAA 58.245 40.909 0.00 0.00 30.97 4.08
63 64 3.503748 AGCTGTAGTGGAAGATTTGCAAC 59.496 43.478 0.00 0.00 30.97 4.17
64 65 3.253188 GCTGTAGTGGAAGATTTGCAACA 59.747 43.478 0.00 0.00 30.97 3.33
65 66 4.082571 GCTGTAGTGGAAGATTTGCAACAT 60.083 41.667 0.00 0.00 30.97 2.71
66 67 5.123820 GCTGTAGTGGAAGATTTGCAACATA 59.876 40.000 0.00 0.00 30.97 2.29
67 68 6.676456 GCTGTAGTGGAAGATTTGCAACATAG 60.676 42.308 0.00 0.00 30.97 2.23
68 69 6.237901 TGTAGTGGAAGATTTGCAACATAGT 58.762 36.000 0.00 0.00 30.97 2.12
69 70 7.390823 TGTAGTGGAAGATTTGCAACATAGTA 58.609 34.615 0.00 0.00 30.97 1.82
70 71 6.992063 AGTGGAAGATTTGCAACATAGTAG 57.008 37.500 0.00 0.00 30.97 2.57
71 72 6.476378 AGTGGAAGATTTGCAACATAGTAGT 58.524 36.000 0.00 0.00 30.97 2.73
72 73 6.942576 AGTGGAAGATTTGCAACATAGTAGTT 59.057 34.615 0.00 0.00 30.97 2.24
73 74 8.100791 AGTGGAAGATTTGCAACATAGTAGTTA 58.899 33.333 0.00 0.00 30.97 2.24
74 75 8.726988 GTGGAAGATTTGCAACATAGTAGTTAA 58.273 33.333 0.00 0.00 30.97 2.01
75 76 9.290988 TGGAAGATTTGCAACATAGTAGTTAAA 57.709 29.630 0.00 0.00 0.00 1.52
81 82 9.626045 ATTTGCAACATAGTAGTTAAAAGAAGC 57.374 29.630 0.00 0.00 0.00 3.86
82 83 6.827641 TGCAACATAGTAGTTAAAAGAAGCG 58.172 36.000 0.00 0.00 0.00 4.68
83 84 6.128391 TGCAACATAGTAGTTAAAAGAAGCGG 60.128 38.462 0.00 0.00 0.00 5.52
84 85 6.091713 GCAACATAGTAGTTAAAAGAAGCGGA 59.908 38.462 0.00 0.00 0.00 5.54
85 86 7.201617 GCAACATAGTAGTTAAAAGAAGCGGAT 60.202 37.037 0.00 0.00 0.00 4.18
86 87 7.772332 ACATAGTAGTTAAAAGAAGCGGATG 57.228 36.000 0.00 0.00 0.00 3.51
87 88 7.328737 ACATAGTAGTTAAAAGAAGCGGATGT 58.671 34.615 0.00 0.00 0.00 3.06
88 89 7.822822 ACATAGTAGTTAAAAGAAGCGGATGTT 59.177 33.333 0.00 0.00 0.00 2.71
123 124 2.900528 CGGTAATTGCCGCCTCTAG 58.099 57.895 22.10 0.00 45.47 2.43
168 169 1.863155 AAGGGCGTTGGGACATGGAT 61.863 55.000 0.00 0.00 39.30 3.41
291 292 2.812658 CCCAAGGGAATCTTCAGCTTT 58.187 47.619 0.00 0.00 37.50 3.51
302 303 3.318017 TCTTCAGCTTTCGTACAGCTTC 58.682 45.455 3.55 0.00 45.82 3.86
418 419 1.289244 CCCTGCCCCCTCAAAGGTAT 61.289 60.000 0.00 0.00 31.93 2.73
483 484 4.085107 GCAGCAAATTTGAAACGTCGAAAT 60.085 37.500 22.31 0.00 30.69 2.17
524 525 4.527944 TGTGTTATTTGTGGACTGGAACA 58.472 39.130 0.00 0.00 0.00 3.18
670 671 0.694771 TCTCTTGCTCCAATGCCAGT 59.305 50.000 0.00 0.00 0.00 4.00
682 683 0.320374 ATGCCAGTCGGAAGAACGAA 59.680 50.000 0.00 0.00 45.38 3.85
708 709 1.079543 GCTGATGACACTCTGGCGT 60.080 57.895 0.00 0.00 0.00 5.68
713 714 1.476891 GATGACACTCTGGCGTTCCTA 59.523 52.381 0.00 0.00 0.00 2.94
720 721 1.374252 CTGGCGTTCCTAGCACGTT 60.374 57.895 12.65 0.00 39.92 3.99
743 744 2.859165 AATGAACTCACCCACGACAT 57.141 45.000 0.00 0.00 0.00 3.06
824 825 3.997021 CTGTGTATCAGACAACACCCTTC 59.003 47.826 13.06 0.00 46.27 3.46
828 829 0.249868 TCAGACAACACCCTTCTGCG 60.250 55.000 0.00 0.00 37.31 5.18
1023 1024 0.601558 TTCTCCGTAGTGACACAGGC 59.398 55.000 8.59 0.00 0.00 4.85
1191 1192 3.068732 CCCAGATGATACTTCAGAGCGAA 59.931 47.826 0.00 0.00 34.73 4.70
1326 2507 1.264749 TAGCTCGCATGGGTCAGGTT 61.265 55.000 9.86 0.61 0.00 3.50
1339 2520 0.179234 TCAGGTTGAGCAACGGACAA 59.821 50.000 7.21 0.00 42.02 3.18
1535 2726 0.973632 TGAGTGAACCACGTGGCTAT 59.026 50.000 34.26 20.65 39.64 2.97
1556 2747 7.761704 GGCTATACACTGTGTTCATAGATATGG 59.238 40.741 24.63 12.48 34.50 2.74
1595 2786 9.595823 GCCAACTCAGTTAATATAAACTACAGA 57.404 33.333 0.00 0.00 37.61 3.41
1598 2789 8.853469 ACTCAGTTAATATAAACTACAGACGC 57.147 34.615 0.00 0.00 37.61 5.19
1830 3090 9.974980 GGAACATTTTCTACAATTCCTAAACAA 57.025 29.630 0.00 0.00 34.11 2.83
2027 3351 7.367285 TGAGAACATTTTTCTGAAATTACCGG 58.633 34.615 0.00 0.00 0.00 5.28
2037 3361 4.282195 TCTGAAATTACCGGGCATTTTGTT 59.718 37.500 6.32 0.00 0.00 2.83
2047 3371 4.934602 CCGGGCATTTTGTTAAACATGAAT 59.065 37.500 0.00 0.00 0.00 2.57
2241 3576 8.364482 GTGAACAAAATTTGAAAACAAATGCAC 58.636 29.630 13.19 0.00 35.23 4.57
2286 3639 9.413048 AGACTTTTTGAAACACGAACATTTTTA 57.587 25.926 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.320587 CCACTGTTGTCTCTGGCGC 61.321 63.158 0.00 0.00 0.00 6.53
2 3 0.668706 CTCCACTGTTGTCTCTGGCG 60.669 60.000 0.00 0.00 0.00 5.69
3 4 0.952984 GCTCCACTGTTGTCTCTGGC 60.953 60.000 0.00 0.00 0.00 4.85
4 5 0.683973 AGCTCCACTGTTGTCTCTGG 59.316 55.000 0.00 0.00 0.00 3.86
5 6 3.321497 GTTAGCTCCACTGTTGTCTCTG 58.679 50.000 0.00 0.00 0.00 3.35
6 7 2.300437 GGTTAGCTCCACTGTTGTCTCT 59.700 50.000 0.00 0.00 0.00 3.10
7 8 2.037251 TGGTTAGCTCCACTGTTGTCTC 59.963 50.000 0.00 0.00 31.96 3.36
8 9 2.037772 CTGGTTAGCTCCACTGTTGTCT 59.962 50.000 0.00 0.00 33.55 3.41
9 10 2.224305 ACTGGTTAGCTCCACTGTTGTC 60.224 50.000 0.00 0.00 33.55 3.18
10 11 1.768870 ACTGGTTAGCTCCACTGTTGT 59.231 47.619 0.00 0.00 33.55 3.32
11 12 2.550830 ACTGGTTAGCTCCACTGTTG 57.449 50.000 0.00 0.00 33.55 3.33
12 13 3.838317 TCATACTGGTTAGCTCCACTGTT 59.162 43.478 0.00 0.00 33.55 3.16
13 14 3.195825 GTCATACTGGTTAGCTCCACTGT 59.804 47.826 0.00 0.00 33.55 3.55
14 15 3.195610 TGTCATACTGGTTAGCTCCACTG 59.804 47.826 0.00 0.00 33.55 3.66
15 16 3.441101 TGTCATACTGGTTAGCTCCACT 58.559 45.455 0.00 0.00 33.55 4.00
16 17 3.887621 TGTCATACTGGTTAGCTCCAC 57.112 47.619 0.00 0.00 33.55 4.02
17 18 3.838317 ACTTGTCATACTGGTTAGCTCCA 59.162 43.478 0.00 0.00 36.00 3.86
18 19 4.473477 ACTTGTCATACTGGTTAGCTCC 57.527 45.455 0.00 0.00 0.00 4.70
22 23 6.398918 ACAGCTAACTTGTCATACTGGTTAG 58.601 40.000 0.00 0.00 40.98 2.34
23 24 6.354794 ACAGCTAACTTGTCATACTGGTTA 57.645 37.500 0.00 0.00 0.00 2.85
24 25 5.228945 ACAGCTAACTTGTCATACTGGTT 57.771 39.130 0.00 0.00 0.00 3.67
25 26 4.891992 ACAGCTAACTTGTCATACTGGT 57.108 40.909 0.00 0.00 0.00 4.00
26 27 5.807520 CACTACAGCTAACTTGTCATACTGG 59.192 44.000 0.00 0.00 0.00 4.00
27 28 5.807520 CCACTACAGCTAACTTGTCATACTG 59.192 44.000 0.00 0.00 0.00 2.74
28 29 5.715279 TCCACTACAGCTAACTTGTCATACT 59.285 40.000 0.00 0.00 0.00 2.12
29 30 5.962433 TCCACTACAGCTAACTTGTCATAC 58.038 41.667 0.00 0.00 0.00 2.39
30 31 6.436218 TCTTCCACTACAGCTAACTTGTCATA 59.564 38.462 0.00 0.00 0.00 2.15
31 32 5.246203 TCTTCCACTACAGCTAACTTGTCAT 59.754 40.000 0.00 0.00 0.00 3.06
32 33 4.587262 TCTTCCACTACAGCTAACTTGTCA 59.413 41.667 0.00 0.00 0.00 3.58
33 34 5.135508 TCTTCCACTACAGCTAACTTGTC 57.864 43.478 0.00 0.00 0.00 3.18
34 35 5.746990 ATCTTCCACTACAGCTAACTTGT 57.253 39.130 0.00 0.00 0.00 3.16
35 36 6.621596 GCAAATCTTCCACTACAGCTAACTTG 60.622 42.308 0.00 0.00 0.00 3.16
36 37 5.412904 GCAAATCTTCCACTACAGCTAACTT 59.587 40.000 0.00 0.00 0.00 2.66
37 38 4.938226 GCAAATCTTCCACTACAGCTAACT 59.062 41.667 0.00 0.00 0.00 2.24
38 39 4.695455 TGCAAATCTTCCACTACAGCTAAC 59.305 41.667 0.00 0.00 0.00 2.34
39 40 4.905429 TGCAAATCTTCCACTACAGCTAA 58.095 39.130 0.00 0.00 0.00 3.09
40 41 4.551702 TGCAAATCTTCCACTACAGCTA 57.448 40.909 0.00 0.00 0.00 3.32
41 42 3.423539 TGCAAATCTTCCACTACAGCT 57.576 42.857 0.00 0.00 0.00 4.24
42 43 3.253188 TGTTGCAAATCTTCCACTACAGC 59.747 43.478 0.00 0.00 0.00 4.40
43 44 5.633830 ATGTTGCAAATCTTCCACTACAG 57.366 39.130 0.00 0.00 0.00 2.74
44 45 6.237901 ACTATGTTGCAAATCTTCCACTACA 58.762 36.000 0.00 0.00 0.00 2.74
45 46 6.743575 ACTATGTTGCAAATCTTCCACTAC 57.256 37.500 0.00 0.00 0.00 2.73
46 47 7.620880 ACTACTATGTTGCAAATCTTCCACTA 58.379 34.615 0.00 0.00 0.00 2.74
47 48 6.476378 ACTACTATGTTGCAAATCTTCCACT 58.524 36.000 0.00 0.00 0.00 4.00
48 49 6.743575 ACTACTATGTTGCAAATCTTCCAC 57.256 37.500 0.00 0.00 0.00 4.02
49 50 8.856153 TTAACTACTATGTTGCAAATCTTCCA 57.144 30.769 0.00 0.00 0.00 3.53
55 56 9.626045 GCTTCTTTTAACTACTATGTTGCAAAT 57.374 29.630 0.00 0.00 0.00 2.32
56 57 7.801315 CGCTTCTTTTAACTACTATGTTGCAAA 59.199 33.333 0.00 0.00 0.00 3.68
57 58 7.295201 CGCTTCTTTTAACTACTATGTTGCAA 58.705 34.615 0.00 0.00 0.00 4.08
58 59 6.128391 CCGCTTCTTTTAACTACTATGTTGCA 60.128 38.462 0.00 0.00 0.00 4.08
59 60 6.091713 TCCGCTTCTTTTAACTACTATGTTGC 59.908 38.462 0.00 0.00 0.00 4.17
60 61 7.591006 TCCGCTTCTTTTAACTACTATGTTG 57.409 36.000 0.00 0.00 0.00 3.33
61 62 7.822822 ACATCCGCTTCTTTTAACTACTATGTT 59.177 33.333 0.00 0.00 0.00 2.71
62 63 7.328737 ACATCCGCTTCTTTTAACTACTATGT 58.671 34.615 0.00 0.00 0.00 2.29
63 64 7.772332 ACATCCGCTTCTTTTAACTACTATG 57.228 36.000 0.00 0.00 0.00 2.23
64 65 7.201617 GCAACATCCGCTTCTTTTAACTACTAT 60.202 37.037 0.00 0.00 0.00 2.12
65 66 6.091713 GCAACATCCGCTTCTTTTAACTACTA 59.908 38.462 0.00 0.00 0.00 1.82
66 67 5.106673 GCAACATCCGCTTCTTTTAACTACT 60.107 40.000 0.00 0.00 0.00 2.57
67 68 5.086727 GCAACATCCGCTTCTTTTAACTAC 58.913 41.667 0.00 0.00 0.00 2.73
68 69 4.155280 GGCAACATCCGCTTCTTTTAACTA 59.845 41.667 0.00 0.00 0.00 2.24
69 70 3.057526 GGCAACATCCGCTTCTTTTAACT 60.058 43.478 0.00 0.00 0.00 2.24
70 71 3.242518 GGCAACATCCGCTTCTTTTAAC 58.757 45.455 0.00 0.00 0.00 2.01
71 72 2.230266 GGGCAACATCCGCTTCTTTTAA 59.770 45.455 0.00 0.00 39.74 1.52
72 73 1.816224 GGGCAACATCCGCTTCTTTTA 59.184 47.619 0.00 0.00 39.74 1.52
73 74 0.603065 GGGCAACATCCGCTTCTTTT 59.397 50.000 0.00 0.00 39.74 2.27
74 75 0.251341 AGGGCAACATCCGCTTCTTT 60.251 50.000 0.00 0.00 39.74 2.52
75 76 0.618458 TAGGGCAACATCCGCTTCTT 59.382 50.000 0.00 0.00 39.74 2.52
76 77 0.839946 ATAGGGCAACATCCGCTTCT 59.160 50.000 0.00 0.00 39.74 2.85
77 78 1.230324 GATAGGGCAACATCCGCTTC 58.770 55.000 0.00 0.00 39.74 3.86
78 79 0.546122 TGATAGGGCAACATCCGCTT 59.454 50.000 0.00 0.00 39.74 4.68
79 80 0.179045 GTGATAGGGCAACATCCGCT 60.179 55.000 0.00 0.00 39.74 5.52
80 81 0.463654 TGTGATAGGGCAACATCCGC 60.464 55.000 0.00 0.00 39.74 5.54
81 82 2.036958 TTGTGATAGGGCAACATCCG 57.963 50.000 0.00 0.00 39.74 4.18
82 83 2.035066 GCATTGTGATAGGGCAACATCC 59.965 50.000 0.00 0.00 39.74 3.51
83 84 2.287188 CGCATTGTGATAGGGCAACATC 60.287 50.000 0.00 0.00 39.74 3.06
84 85 1.677576 CGCATTGTGATAGGGCAACAT 59.322 47.619 0.00 0.00 39.74 2.71
85 86 1.093972 CGCATTGTGATAGGGCAACA 58.906 50.000 0.00 0.00 39.74 3.33
86 87 0.248621 GCGCATTGTGATAGGGCAAC 60.249 55.000 0.30 0.00 40.46 4.17
87 88 1.713937 CGCGCATTGTGATAGGGCAA 61.714 55.000 8.75 0.00 40.73 4.52
88 89 2.179547 CGCGCATTGTGATAGGGCA 61.180 57.895 8.75 0.00 40.73 5.36
121 122 3.461773 GAGCTCTGCCACCCGCTA 61.462 66.667 6.43 0.00 38.78 4.26
168 169 1.602165 GCGAAGTGTTGTCGAAGGAGA 60.602 52.381 0.00 0.00 41.02 3.71
289 290 4.272100 GCGGGAAGCTGTACGAAA 57.728 55.556 8.18 0.00 44.04 3.46
300 301 1.001020 ATCATGTGCAAGGCGGGAA 60.001 52.632 0.00 0.00 0.00 3.97
302 303 1.314534 TTCATCATGTGCAAGGCGGG 61.315 55.000 0.00 0.00 0.00 6.13
378 379 1.002017 CCCCCACAATGCTTCCCAT 59.998 57.895 0.00 0.00 35.06 4.00
418 419 2.199652 CCCGCCAGGCAAAAACTCA 61.200 57.895 13.30 0.00 35.76 3.41
585 586 2.601905 GGCATGCTCCATATTTTCCCT 58.398 47.619 18.92 0.00 0.00 4.20
670 671 2.991190 GCACTTGTATTCGTTCTTCCGA 59.009 45.455 0.00 0.00 34.52 4.55
682 683 4.502016 CAGAGTGTCATCAGCACTTGTAT 58.498 43.478 0.00 0.00 45.99 2.29
720 721 3.259625 TGTCGTGGGTGAGTTCATTATGA 59.740 43.478 0.00 0.00 0.00 2.15
743 744 0.991146 TTCAATAGGTGGAGCTGGCA 59.009 50.000 0.00 0.00 0.00 4.92
824 825 1.332195 TCCTCTGTCCATATCCGCAG 58.668 55.000 0.00 0.00 0.00 5.18
828 829 4.349342 ACCATCTTTCCTCTGTCCATATCC 59.651 45.833 0.00 0.00 0.00 2.59
902 903 1.512996 CCAGCAAGCAGGTGTGACAG 61.513 60.000 7.45 0.00 44.16 3.51
1003 1004 1.204941 GCCTGTGTCACTACGGAGAAT 59.795 52.381 0.00 0.00 0.00 2.40
1023 1024 3.892588 GGTAGGAGGAGTAGATGACTTGG 59.107 52.174 0.00 0.00 39.06 3.61
1090 1091 2.225091 TGTTGATTCCTTCCAGGCATGT 60.225 45.455 0.00 0.00 34.61 3.21
1326 2507 0.464036 AGACTGTTGTCCGTTGCTCA 59.536 50.000 0.00 0.00 43.91 4.26
1475 2656 2.194460 CCCCCACACACGTTTTTGT 58.806 52.632 0.00 0.00 0.00 2.83
1490 2680 1.072505 TCTTGTGTTCGAAGCCCCC 59.927 57.895 0.00 0.00 0.00 5.40
1535 2726 7.279981 GCAAACCATATCTATGAACACAGTGTA 59.720 37.037 6.63 0.00 35.75 2.90
1556 2747 5.049828 ACTGAGTTGGCATTTTAAGCAAAC 58.950 37.500 0.00 0.00 44.42 2.93
1830 3090 8.477256 TCAGAAAAATGTCCTTGTTTCAGAAAT 58.523 29.630 0.00 0.00 33.37 2.17
1869 3172 8.359875 TCAGGAAATGTATAGGAATGCAAAAA 57.640 30.769 0.00 0.00 31.06 1.94
1983 3306 9.766277 TGTTCTCATTTTTAAATTTTGTTGTGC 57.234 25.926 0.00 0.00 0.00 4.57
2025 3349 7.769272 ATATTCATGTTTAACAAAATGCCCG 57.231 32.000 14.98 0.00 0.00 6.13
2237 3572 9.677567 GTCTGTTTAGAAATTTCATAAAGTGCA 57.322 29.630 19.99 12.96 34.01 4.57
2238 3573 9.899226 AGTCTGTTTAGAAATTTCATAAAGTGC 57.101 29.630 19.99 10.02 34.01 4.40
2259 3594 6.869421 AATGTTCGTGTTTCAAAAAGTCTG 57.131 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.