Multiple sequence alignment - TraesCS2A01G117900

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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 TraesCS2A01G117900 chr2A 100.000 6842 0 0 1 6842 68257209 68250368 0.000000e+00 12635.0
1 TraesCS2A01G117900 chr2A 98.790 1405 13 3 3542 4944 684243971 684242569 0.000000e+00 2497.0
2 TraesCS2A01G117900 chr2A 98.148 54 1 0 28 81 167259406 167259459 2.030000e-15 95.3
3 TraesCS2A01G117900 chr2A 85.246 61 7 1 132 192 705583780 705583838 2.060000e-05 62.1
4 TraesCS2A01G117900 chr2D 93.042 3277 126 44 285 3512 66756006 66759229 0.000000e+00 4695.0
5 TraesCS2A01G117900 chr2D 93.163 1916 94 19 4948 6842 66759226 66761125 0.000000e+00 2778.0
6 TraesCS2A01G117900 chr4B 98.293 1406 16 4 3541 4942 299463174 299464575 0.000000e+00 2457.0
7 TraesCS2A01G117900 chr4B 97.795 1406 28 2 3541 4944 241710972 241709568 0.000000e+00 2422.0
8 TraesCS2A01G117900 chr4B 97.372 1408 24 3 3541 4948 220392410 220391016 0.000000e+00 2383.0
9 TraesCS2A01G117900 chr4B 96.491 57 2 0 25 81 85730844 85730900 2.030000e-15 95.3
10 TraesCS2A01G117900 chr2B 97.653 1406 28 2 3543 4944 742033578 742032174 0.000000e+00 2409.0
11 TraesCS2A01G117900 chr2B 94.426 1489 52 12 1102 2581 104821056 104819590 0.000000e+00 2261.0
12 TraesCS2A01G117900 chr2B 97.498 1119 24 2 4948 6064 104818544 104817428 0.000000e+00 1908.0
13 TraesCS2A01G117900 chr2B 96.931 945 20 4 2580 3524 104819466 104818531 0.000000e+00 1576.0
14 TraesCS2A01G117900 chr2B 97.506 842 18 1 2671 3512 104826263 104825425 0.000000e+00 1435.0
15 TraesCS2A01G117900 chr2B 95.918 588 19 5 6034 6619 104817425 104816841 0.000000e+00 948.0
16 TraesCS2A01G117900 chr2B 80.774 879 89 36 270 1106 104821959 104821119 1.260000e-171 614.0
17 TraesCS2A01G117900 chr2B 94.675 169 9 0 6674 6842 104816835 104816667 5.260000e-66 263.0
18 TraesCS2A01G117900 chr2B 88.732 71 8 0 37 107 236042552 236042622 3.400000e-13 87.9
19 TraesCS2A01G117900 chr1B 94.968 1411 62 4 3542 4951 27293802 27292400 0.000000e+00 2204.0
20 TraesCS2A01G117900 chr1B 90.909 66 5 1 37 102 483882409 483882473 3.400000e-13 87.9
21 TraesCS2A01G117900 chr7B 94.598 1407 72 3 3541 4944 684321832 684323237 0.000000e+00 2174.0
22 TraesCS2A01G117900 chr5B 94.168 1406 64 8 3541 4946 56365390 56366777 0.000000e+00 2126.0
23 TraesCS2A01G117900 chr5B 95.000 60 2 1 22 81 318403815 318403757 7.310000e-15 93.5
24 TraesCS2A01G117900 chr5B 89.706 68 6 1 36 103 513807756 513807690 1.220000e-12 86.1
25 TraesCS2A01G117900 chr7A 92.384 1418 95 6 3528 4944 193459114 193460519 0.000000e+00 2008.0
26 TraesCS2A01G117900 chr3B 92.268 194 9 3 4748 4940 428092721 428092909 3.140000e-68 270.0
27 TraesCS2A01G117900 chr3B 91.667 60 5 0 132 191 644305366 644305307 4.400000e-12 84.2
28 TraesCS2A01G117900 chr3B 90.000 60 6 0 132 191 688120416 688120357 2.050000e-10 78.7
29 TraesCS2A01G117900 chr3B 93.878 49 3 0 132 180 214030230 214030278 2.650000e-09 75.0
30 TraesCS2A01G117900 chr4A 91.429 70 3 1 36 102 742264644 742264713 7.310000e-15 93.5
31 TraesCS2A01G117900 chr3A 93.548 62 1 2 22 83 722122367 722122425 9.450000e-14 89.8
32 TraesCS2A01G117900 chr3A 91.837 49 2 2 189 235 635393964 635393916 4.430000e-07 67.6
33 TraesCS2A01G117900 chrUn 89.706 68 6 1 36 103 316777231 316777165 1.220000e-12 86.1
34 TraesCS2A01G117900 chr4D 94.444 54 3 0 132 185 274467749 274467696 4.400000e-12 84.2
35 TraesCS2A01G117900 chr7D 86.567 67 8 1 125 190 20070938 20070872 9.520000e-09 73.1
36 TraesCS2A01G117900 chr1D 88.333 60 7 0 132 191 471283693 471283752 9.520000e-09 73.1
37 TraesCS2A01G117900 chr5D 93.617 47 3 0 244 290 482118126 482118172 3.420000e-08 71.3


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 TraesCS2A01G117900 chr2A 68250368 68257209 6841 True 12635.000000 12635 100.000000 1 6842 1 chr2A.!!$R1 6841
1 TraesCS2A01G117900 chr2A 684242569 684243971 1402 True 2497.000000 2497 98.790000 3542 4944 1 chr2A.!!$R2 1402
2 TraesCS2A01G117900 chr2D 66756006 66761125 5119 False 3736.500000 4695 93.102500 285 6842 2 chr2D.!!$F1 6557
3 TraesCS2A01G117900 chr4B 299463174 299464575 1401 False 2457.000000 2457 98.293000 3541 4942 1 chr4B.!!$F2 1401
4 TraesCS2A01G117900 chr4B 241709568 241710972 1404 True 2422.000000 2422 97.795000 3541 4944 1 chr4B.!!$R2 1403
5 TraesCS2A01G117900 chr4B 220391016 220392410 1394 True 2383.000000 2383 97.372000 3541 4948 1 chr4B.!!$R1 1407
6 TraesCS2A01G117900 chr2B 742032174 742033578 1404 True 2409.000000 2409 97.653000 3543 4944 1 chr2B.!!$R1 1401
7 TraesCS2A01G117900 chr2B 104816667 104826263 9596 True 1286.428571 2261 93.961143 270 6842 7 chr2B.!!$R2 6572
8 TraesCS2A01G117900 chr1B 27292400 27293802 1402 True 2204.000000 2204 94.968000 3542 4951 1 chr1B.!!$R1 1409
9 TraesCS2A01G117900 chr7B 684321832 684323237 1405 False 2174.000000 2174 94.598000 3541 4944 1 chr7B.!!$F1 1403
10 TraesCS2A01G117900 chr5B 56365390 56366777 1387 False 2126.000000 2126 94.168000 3541 4946 1 chr5B.!!$F1 1405
11 TraesCS2A01G117900 chr7A 193459114 193460519 1405 False 2008.000000 2008 92.384000 3528 4944 1 chr7A.!!$F1 1416

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
527 4581 0.249489 AGCACCCGAGCATATTCGAC 60.249 55.000 0.0 0.0 43.03 4.20 F
1647 5806 0.620556 TGACTTGCTCTGGGGATTCC 59.379 55.000 0.0 0.0 0.00 3.01 F
2941 7229 1.346395 ACAGGCATTTGTCGGTGTAGA 59.654 47.619 0.0 0.0 0.00 2.59 F
3625 7913 1.082954 CTTCCCCTCCTTCCCCTCA 59.917 63.158 0.0 0.0 0.00 3.86 F
4586 8884 2.637382 TGCTACACCAGTTCCAATCAGA 59.363 45.455 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 5817 0.398806 TCAATTGGGGGCATCATGGG 60.399 55.000 5.42 0.00 0.00 4.00 R
3225 7513 0.407139 AGGTGCATCTGCCTTTCCTT 59.593 50.000 0.00 0.00 41.18 3.36 R
4419 8717 1.299648 CATCAAGAGGGGAACGGCA 59.700 57.895 0.00 0.00 0.00 5.69 R
5287 9594 1.667724 CACAGCGATAAAGGCTTCCTG 59.332 52.381 0.00 5.37 39.08 3.86 R
6564 10919 0.184933 TTGTGTTTCCCCACTCCTGG 59.815 55.000 0.00 0.00 36.30 4.45 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 7.531280 CATTCGACTCATTACAAGATGAACT 57.469 36.000 0.00 0.00 35.74 3.01
25 26 7.968246 CATTCGACTCATTACAAGATGAACTT 58.032 34.615 0.00 0.00 35.74 2.66
26 27 7.962964 TTCGACTCATTACAAGATGAACTTT 57.037 32.000 0.00 0.00 35.74 2.66
27 28 7.582435 TCGACTCATTACAAGATGAACTTTC 57.418 36.000 0.00 0.00 35.74 2.62
28 29 7.151976 TCGACTCATTACAAGATGAACTTTCA 58.848 34.615 0.00 0.00 42.14 2.69
45 46 8.483758 TGAACTTTCATACTTTATACTCCCTCC 58.516 37.037 0.00 0.00 31.01 4.30
46 47 7.052142 ACTTTCATACTTTATACTCCCTCCG 57.948 40.000 0.00 0.00 0.00 4.63
47 48 6.610425 ACTTTCATACTTTATACTCCCTCCGT 59.390 38.462 0.00 0.00 0.00 4.69
48 49 6.645790 TTCATACTTTATACTCCCTCCGTC 57.354 41.667 0.00 0.00 0.00 4.79
49 50 5.075493 TCATACTTTATACTCCCTCCGTCC 58.925 45.833 0.00 0.00 0.00 4.79
50 51 2.305009 ACTTTATACTCCCTCCGTCCG 58.695 52.381 0.00 0.00 0.00 4.79
51 52 2.092212 ACTTTATACTCCCTCCGTCCGA 60.092 50.000 0.00 0.00 0.00 4.55
52 53 2.734755 TTATACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
53 54 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
57 58 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
58 59 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
60 61 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
61 62 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
62 63 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
63 64 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
64 65 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
65 66 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
67 68 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
68 69 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
69 70 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
70 71 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
71 72 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
74 75 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
82 83 9.480053 ACTTGTCATCAAAATGGATAAAAAGTG 57.520 29.630 0.00 0.00 33.42 3.16
84 85 9.829507 TTGTCATCAAAATGGATAAAAAGTGTT 57.170 25.926 0.00 0.00 33.42 3.32
85 86 9.829507 TGTCATCAAAATGGATAAAAAGTGTTT 57.170 25.926 0.00 0.00 33.42 2.83
88 89 9.796062 CATCAAAATGGATAAAAAGTGTTTTCG 57.204 29.630 0.00 0.00 38.01 3.46
89 90 8.359060 TCAAAATGGATAAAAAGTGTTTTCGG 57.641 30.769 0.00 0.00 38.01 4.30
90 91 8.198109 TCAAAATGGATAAAAAGTGTTTTCGGA 58.802 29.630 0.00 0.00 38.01 4.55
91 92 7.940178 AAATGGATAAAAAGTGTTTTCGGAC 57.060 32.000 0.00 0.00 38.01 4.79
93 94 4.815308 TGGATAAAAAGTGTTTTCGGACGA 59.185 37.500 0.00 0.00 38.01 4.20
94 95 5.296283 TGGATAAAAAGTGTTTTCGGACGAA 59.704 36.000 2.62 2.62 38.01 3.85
95 96 5.849604 GGATAAAAAGTGTTTTCGGACGAAG 59.150 40.000 7.25 0.00 38.01 3.79
96 97 3.685836 AAAAGTGTTTTCGGACGAAGG 57.314 42.857 7.25 0.00 35.38 3.46
97 98 1.589803 AAGTGTTTTCGGACGAAGGG 58.410 50.000 7.25 0.00 35.38 3.95
98 99 0.754472 AGTGTTTTCGGACGAAGGGA 59.246 50.000 7.25 0.00 35.38 4.20
99 100 1.145803 GTGTTTTCGGACGAAGGGAG 58.854 55.000 7.25 0.00 35.38 4.30
100 101 0.754472 TGTTTTCGGACGAAGGGAGT 59.246 50.000 7.25 0.00 35.38 3.85
101 102 1.962807 TGTTTTCGGACGAAGGGAGTA 59.037 47.619 7.25 0.00 35.38 2.59
103 104 3.763360 TGTTTTCGGACGAAGGGAGTATA 59.237 43.478 7.25 0.00 35.38 1.47
106 107 5.603170 TTTCGGACGAAGGGAGTATATTT 57.397 39.130 7.25 0.00 35.38 1.40
107 108 4.579454 TCGGACGAAGGGAGTATATTTG 57.421 45.455 0.00 0.00 0.00 2.32
108 109 3.319972 TCGGACGAAGGGAGTATATTTGG 59.680 47.826 0.00 0.00 0.00 3.28
109 110 3.069158 CGGACGAAGGGAGTATATTTGGT 59.931 47.826 0.00 0.00 0.00 3.67
110 111 4.279169 CGGACGAAGGGAGTATATTTGGTA 59.721 45.833 0.00 0.00 0.00 3.25
111 112 5.047519 CGGACGAAGGGAGTATATTTGGTAT 60.048 44.000 0.00 0.00 0.00 2.73
112 113 6.396450 GGACGAAGGGAGTATATTTGGTATC 58.604 44.000 0.00 0.00 0.00 2.24
113 114 6.356186 ACGAAGGGAGTATATTTGGTATCC 57.644 41.667 0.00 0.00 0.00 2.59
114 115 5.842328 ACGAAGGGAGTATATTTGGTATCCA 59.158 40.000 0.00 0.00 0.00 3.41
115 116 6.500751 ACGAAGGGAGTATATTTGGTATCCAT 59.499 38.462 0.00 0.00 31.53 3.41
116 117 7.017254 ACGAAGGGAGTATATTTGGTATCCATT 59.983 37.037 0.00 0.00 31.53 3.16
117 118 7.883311 CGAAGGGAGTATATTTGGTATCCATTT 59.117 37.037 0.00 0.00 31.53 2.32
120 121 8.732854 AGGGAGTATATTTGGTATCCATTTTGA 58.267 33.333 0.00 0.00 31.53 2.69
183 184 9.672086 TTTGATAACAAGTATTTTTGGACGAAG 57.328 29.630 0.00 0.00 37.32 3.79
184 185 8.610248 TGATAACAAGTATTTTTGGACGAAGA 57.390 30.769 0.00 0.00 32.32 2.87
185 186 9.058174 TGATAACAAGTATTTTTGGACGAAGAA 57.942 29.630 0.00 0.00 32.32 2.52
187 188 9.893305 ATAACAAGTATTTTTGGACGAAGAAAG 57.107 29.630 0.00 0.00 32.32 2.62
188 189 7.329588 ACAAGTATTTTTGGACGAAGAAAGT 57.670 32.000 0.00 0.00 32.32 2.66
189 190 8.441312 ACAAGTATTTTTGGACGAAGAAAGTA 57.559 30.769 0.00 0.00 32.32 2.24
190 191 9.063615 ACAAGTATTTTTGGACGAAGAAAGTAT 57.936 29.630 0.00 0.00 32.32 2.12
196 197 9.855021 ATTTTTGGACGAAGAAAGTATATTTGG 57.145 29.630 0.00 0.00 0.00 3.28
197 198 7.989416 TTTGGACGAAGAAAGTATATTTGGT 57.011 32.000 0.00 0.00 0.00 3.67
198 199 9.504708 TTTTGGACGAAGAAAGTATATTTGGTA 57.495 29.630 0.00 0.00 0.00 3.25
199 200 9.675464 TTTGGACGAAGAAAGTATATTTGGTAT 57.325 29.630 0.00 0.00 0.00 2.73
200 201 8.882415 TGGACGAAGAAAGTATATTTGGTATC 57.118 34.615 0.00 0.00 0.00 2.24
201 202 7.650504 TGGACGAAGAAAGTATATTTGGTATCG 59.349 37.037 0.00 0.00 0.00 2.92
203 204 9.669353 GACGAAGAAAGTATATTTGGTATCGTA 57.331 33.333 9.61 0.00 38.56 3.43
237 238 8.611051 AGTTATCTCTAATAACTTGGTGACCT 57.389 34.615 2.11 0.00 40.72 3.85
238 239 9.047947 AGTTATCTCTAATAACTTGGTGACCTT 57.952 33.333 2.11 0.00 40.72 3.50
239 240 9.668497 GTTATCTCTAATAACTTGGTGACCTTT 57.332 33.333 2.11 0.00 33.11 3.11
376 4414 0.608130 AGTGTCCTAGATGCACGCAA 59.392 50.000 0.00 0.00 38.10 4.85
406 4447 2.376518 GGGATGATATTGGGAAGCTCCA 59.623 50.000 0.00 0.00 38.64 3.86
417 4458 3.966665 TGGGAAGCTCCAAAAACAAAGAT 59.033 39.130 0.00 0.00 38.64 2.40
423 4464 7.329471 GGAAGCTCCAAAAACAAAGATACAATC 59.671 37.037 0.00 0.00 36.28 2.67
485 4539 2.920724 TCAAAGAACCACGGATGTCA 57.079 45.000 0.00 0.00 0.00 3.58
496 4550 2.615447 CACGGATGTCATCTTGGAATGG 59.385 50.000 12.54 0.00 0.00 3.16
527 4581 0.249489 AGCACCCGAGCATATTCGAC 60.249 55.000 0.00 0.00 43.03 4.20
529 4583 1.299926 ACCCGAGCATATTCGACGC 60.300 57.895 0.00 0.00 43.03 5.19
541 4595 1.930567 TTCGACGCCCAAATAGTAGC 58.069 50.000 0.00 0.00 0.00 3.58
546 4600 3.303132 CGACGCCCAAATAGTAGCAATTC 60.303 47.826 0.00 0.00 0.00 2.17
551 4605 7.165485 ACGCCCAAATAGTAGCAATTCATATA 58.835 34.615 0.00 0.00 0.00 0.86
552 4606 7.829211 ACGCCCAAATAGTAGCAATTCATATAT 59.171 33.333 0.00 0.00 0.00 0.86
638 4698 5.545658 TTTTCGATTCTCCTTTTCCATCG 57.454 39.130 0.00 0.00 38.46 3.84
712 4774 2.767496 CCTCCCCTCCAGCTCCAG 60.767 72.222 0.00 0.00 0.00 3.86
737 4799 2.704190 TCTCACCTCACCTTCTTCCT 57.296 50.000 0.00 0.00 0.00 3.36
771 4845 1.219664 CCGCCGAGGTACCAAATCA 59.780 57.895 15.94 0.00 34.51 2.57
797 4874 2.293251 CCCCTAAACTCCCTCCTTCTCT 60.293 54.545 0.00 0.00 0.00 3.10
881 4958 0.817634 CGCCGCCCATTTATCCTTCA 60.818 55.000 0.00 0.00 0.00 3.02
956 5033 4.384247 CAGCTGTTTTCTACTCTCTTGTCG 59.616 45.833 5.25 0.00 0.00 4.35
975 5052 2.688446 TCGGTGTGATGGTAGTCTCATC 59.312 50.000 0.00 0.00 40.85 2.92
1065 5146 2.467826 GCTCTCGGCTTGTCATGGC 61.468 63.158 0.00 0.00 38.06 4.40
1148 5299 4.082787 TCCTCAAATGAATTCCAAGAACGC 60.083 41.667 2.27 0.00 0.00 4.84
1170 5321 5.051907 CGCGTTAACTAATTCAGTAGCGATT 60.052 40.000 10.36 0.00 43.43 3.34
1221 5373 4.023365 GCCATGATTGGAGAAAGCATAGAC 60.023 45.833 0.00 0.00 42.97 2.59
1235 5387 4.302455 AGCATAGACGAATATCAGTGCAC 58.698 43.478 9.40 9.40 35.12 4.57
1287 5439 0.983378 GGAGAGAAAGGGGGCAGCTA 60.983 60.000 0.00 0.00 0.00 3.32
1325 5479 2.379005 CCCTGCTCCCTGTAAATTTCC 58.621 52.381 0.00 0.00 0.00 3.13
1445 5599 5.048713 CCAAACATCTGGAGAAAGTTGTACC 60.049 44.000 0.00 0.00 38.96 3.34
1482 5636 4.082026 CAGAAAAGGAAATTAGGTGGCTGG 60.082 45.833 0.00 0.00 0.00 4.85
1493 5647 2.203480 TGGCTGGCAGTTGGAACC 60.203 61.111 17.16 7.99 0.00 3.62
1647 5806 0.620556 TGACTTGCTCTGGGGATTCC 59.379 55.000 0.00 0.00 0.00 3.01
1658 5817 1.490490 TGGGGATTCCACTAGCATCAC 59.510 52.381 6.49 0.00 41.46 3.06
1705 5864 7.854557 TTAGCTGCCATATCTAAGCATTATG 57.145 36.000 0.00 0.00 38.14 1.90
1773 5932 1.923204 GCTTGACAGATCTAGTGCGTG 59.077 52.381 0.00 0.00 31.09 5.34
1953 6114 8.680903 ACATGAGAATAGGTGAAATTGAATCAC 58.319 33.333 0.00 0.86 45.08 3.06
2086 6247 2.242043 ACTTGTGCTAAAAGCTGCCAT 58.758 42.857 0.00 0.00 42.97 4.40
2117 6280 3.940852 GGCAAAAATCAATTGGGGTCATC 59.059 43.478 5.42 0.00 0.00 2.92
2122 6285 7.553760 GCAAAAATCAATTGGGGTCATCTATTT 59.446 33.333 5.42 0.00 0.00 1.40
2145 6308 7.432350 TTTGTTTGCTTTCAGTTTGTTCAAT 57.568 28.000 0.00 0.00 0.00 2.57
2228 6391 3.811497 TGATCTTCTGCACTTGTGTTCAG 59.189 43.478 2.61 2.93 38.49 3.02
2236 6399 2.859806 GCACTTGTGTTCAGGATTGCAC 60.860 50.000 2.61 0.00 0.00 4.57
2297 6460 5.177326 GCAGAGTTCTCTGTCAAGAATCAT 58.823 41.667 24.56 0.00 37.59 2.45
2354 6517 1.831106 ACCATCGTGGAGTATGCTTCA 59.169 47.619 10.46 0.00 40.96 3.02
2415 6578 5.840243 CATGTCATGCTTTCTAAATGGGA 57.160 39.130 0.00 0.00 0.00 4.37
2416 6579 5.828747 CATGTCATGCTTTCTAAATGGGAG 58.171 41.667 0.00 0.00 0.00 4.30
2417 6580 3.696051 TGTCATGCTTTCTAAATGGGAGC 59.304 43.478 0.00 0.00 0.00 4.70
2419 6582 4.036144 GTCATGCTTTCTAAATGGGAGCTC 59.964 45.833 4.71 4.71 34.56 4.09
2941 7229 1.346395 ACAGGCATTTGTCGGTGTAGA 59.654 47.619 0.00 0.00 0.00 2.59
3037 7325 6.013206 TGCTTCTAGTATTCCCAGTTAAACCA 60.013 38.462 0.00 0.00 0.00 3.67
3054 7342 8.296713 AGTTAAACCAGTATGCTTTATGTGTTG 58.703 33.333 0.00 0.00 31.97 3.33
3074 7362 7.095060 TGTGTTGCTATTCTGATTTCTTGAGTC 60.095 37.037 0.00 0.00 0.00 3.36
3082 7370 5.240891 TCTGATTTCTTGAGTCACATGTCC 58.759 41.667 0.00 0.00 0.00 4.02
3094 7382 8.684386 TGAGTCACATGTCCTTTATGTTTTAA 57.316 30.769 0.00 0.00 36.67 1.52
3508 7796 5.280727 CCAGACTCTTAATTCCTTCCAGGTT 60.281 44.000 0.00 0.00 36.53 3.50
3509 7797 6.070194 CCAGACTCTTAATTCCTTCCAGGTTA 60.070 42.308 0.00 0.00 36.53 2.85
3510 7798 7.366011 CCAGACTCTTAATTCCTTCCAGGTTAT 60.366 40.741 0.00 0.00 36.53 1.89
3511 7799 8.705594 CAGACTCTTAATTCCTTCCAGGTTATA 58.294 37.037 0.00 0.00 36.53 0.98
3512 7800 9.453830 AGACTCTTAATTCCTTCCAGGTTATAT 57.546 33.333 0.00 0.00 36.53 0.86
3521 7809 8.760980 TTCCTTCCAGGTTATATAAATTGTGG 57.239 34.615 0.00 2.63 36.53 4.17
3522 7810 7.878495 TCCTTCCAGGTTATATAAATTGTGGT 58.122 34.615 0.00 0.00 36.53 4.16
3523 7811 7.996644 TCCTTCCAGGTTATATAAATTGTGGTC 59.003 37.037 0.00 0.00 36.53 4.02
3524 7812 7.777910 CCTTCCAGGTTATATAAATTGTGGTCA 59.222 37.037 0.00 0.00 0.00 4.02
3525 7813 9.184523 CTTCCAGGTTATATAAATTGTGGTCAA 57.815 33.333 0.00 0.00 37.98 3.18
3526 7814 8.746052 TCCAGGTTATATAAATTGTGGTCAAG 57.254 34.615 0.00 0.00 36.97 3.02
3527 7815 8.553153 TCCAGGTTATATAAATTGTGGTCAAGA 58.447 33.333 0.00 0.00 36.97 3.02
3528 7816 9.184523 CCAGGTTATATAAATTGTGGTCAAGAA 57.815 33.333 0.00 0.00 36.97 2.52
3539 7827 9.829507 AAATTGTGGTCAAGAAACATTATTTCA 57.170 25.926 2.51 0.00 36.97 2.69
3617 7905 2.543637 TCCCCTCCTTCCCCTCCT 60.544 66.667 0.00 0.00 0.00 3.69
3625 7913 1.082954 CTTCCCCTCCTTCCCCTCA 59.917 63.158 0.00 0.00 0.00 3.86
4586 8884 2.637382 TGCTACACCAGTTCCAATCAGA 59.363 45.455 0.00 0.00 0.00 3.27
5039 9346 5.129320 AGCTGTTGATTTTTCCCTTCAAACT 59.871 36.000 0.00 0.00 31.66 2.66
5266 9573 3.192633 GGTATACCTTGGGCACAAACTTG 59.807 47.826 15.09 0.00 35.89 3.16
5287 9594 6.152831 ACTTGTAAATATGCTTTCCAACTCCC 59.847 38.462 0.00 0.00 0.00 4.30
5490 9806 7.313731 TCCTAGTTCTAACATTATCCCCATCT 58.686 38.462 0.00 0.00 0.00 2.90
5496 9812 7.406031 TCTAACATTATCCCCATCTATCGTC 57.594 40.000 0.00 0.00 0.00 4.20
5628 9944 1.330903 GCGTTGAGCGATTACGTAAGC 60.331 52.381 13.46 13.46 44.77 3.09
5634 9950 3.066203 TGAGCGATTACGTAAGCATCTCA 59.934 43.478 27.25 27.25 45.62 3.27
5662 9978 2.159476 ACATCATCATGACAAAGCACGC 60.159 45.455 0.00 0.00 33.72 5.34
5664 9980 0.522626 CATCATGACAAAGCACGCCA 59.477 50.000 0.00 0.00 0.00 5.69
6032 10385 6.604396 TGAGAACATTGCCATGAAATGTCTAT 59.396 34.615 20.34 12.72 45.25 1.98
6096 10449 6.982724 CACTTGAGAAAAAGAGGCAAATTCTT 59.017 34.615 0.00 0.00 36.49 2.52
6157 10510 3.181469 ACCTTTCACAGCAGTTAGAACGA 60.181 43.478 0.00 0.00 0.00 3.85
6305 10658 9.768215 TGGACAAAAGGAAAAATCCTCTAATAT 57.232 29.630 0.00 0.00 39.65 1.28
6388 10743 6.835819 AACCAAAGAAAACCTTATCCTAGC 57.164 37.500 0.00 0.00 34.00 3.42
6413 10768 7.214381 CCGATAAATACAAAGTGGGTGATCTA 58.786 38.462 0.00 0.00 0.00 1.98
6490 10845 0.510359 CAGCAGTTGAACAGCGTCTC 59.490 55.000 7.06 0.00 35.63 3.36
6513 10868 3.807622 CCTTTCGCAATACGGTATGTGAT 59.192 43.478 0.58 0.00 43.89 3.06
6564 10919 4.816385 CCATGGAGTGTAATGTATGGTCAC 59.184 45.833 5.56 0.00 32.44 3.67
6599 10954 0.767375 ACAAGCCTGGCTGAGAGAAA 59.233 50.000 24.16 0.00 39.62 2.52
6601 10956 2.233271 CAAGCCTGGCTGAGAGAAAAA 58.767 47.619 24.16 0.00 39.62 1.94
6612 10967 4.321718 CTGAGAGAAAAATGCTGGTCTGA 58.678 43.478 0.00 0.00 0.00 3.27
6614 10969 4.516698 TGAGAGAAAAATGCTGGTCTGAAC 59.483 41.667 0.00 0.00 0.00 3.18
6693 11054 1.296056 GCAACACTGCCCGTTCGTAT 61.296 55.000 0.00 0.00 43.26 3.06
6694 11055 1.153353 CAACACTGCCCGTTCGTATT 58.847 50.000 0.00 0.00 0.00 1.89
6743 11104 1.418097 TTTGCCAGGGTCTGCTCTCA 61.418 55.000 0.00 0.00 0.00 3.27
6798 11159 2.954989 TGCGATCTCTATCAGCTTCACT 59.045 45.455 0.00 0.00 34.69 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.151976 TGAAAGTTCATCTTGTAATGAGTCGA 58.848 34.615 0.00 0.00 37.01 4.20
4 5 7.351414 TGAAAGTTCATCTTGTAATGAGTCG 57.649 36.000 0.00 0.00 37.01 4.18
19 20 8.483758 GGAGGGAGTATAAAGTATGAAAGTTCA 58.516 37.037 0.00 0.00 42.14 3.18
20 21 7.652507 CGGAGGGAGTATAAAGTATGAAAGTTC 59.347 40.741 0.00 0.00 0.00 3.01
21 22 7.125356 ACGGAGGGAGTATAAAGTATGAAAGTT 59.875 37.037 0.00 0.00 0.00 2.66
23 24 7.052142 ACGGAGGGAGTATAAAGTATGAAAG 57.948 40.000 0.00 0.00 0.00 2.62
24 25 6.041296 GGACGGAGGGAGTATAAAGTATGAAA 59.959 42.308 0.00 0.00 0.00 2.69
25 26 5.537674 GGACGGAGGGAGTATAAAGTATGAA 59.462 44.000 0.00 0.00 0.00 2.57
26 27 5.075493 GGACGGAGGGAGTATAAAGTATGA 58.925 45.833 0.00 0.00 0.00 2.15
27 28 4.082895 CGGACGGAGGGAGTATAAAGTATG 60.083 50.000 0.00 0.00 0.00 2.39
28 29 4.077822 CGGACGGAGGGAGTATAAAGTAT 58.922 47.826 0.00 0.00 0.00 2.12
30 31 2.092212 TCGGACGGAGGGAGTATAAAGT 60.092 50.000 0.00 0.00 0.00 2.66
31 32 2.579873 TCGGACGGAGGGAGTATAAAG 58.420 52.381 0.00 0.00 0.00 1.85
33 34 2.734755 TTCGGACGGAGGGAGTATAA 57.265 50.000 0.00 0.00 0.00 0.98
34 35 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
36 37 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
37 38 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
40 41 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
41 42 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
43 44 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
44 45 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
45 46 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
46 47 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
47 48 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
48 49 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
49 50 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
57 58 9.480053 ACACTTTTTATCCATTTTGATGACAAG 57.520 29.630 0.00 0.00 37.32 3.16
58 59 9.829507 AACACTTTTTATCCATTTTGATGACAA 57.170 25.926 0.00 0.00 0.00 3.18
62 63 9.796062 CGAAAACACTTTTTATCCATTTTGATG 57.204 29.630 0.00 0.00 34.94 3.07
63 64 8.987890 CCGAAAACACTTTTTATCCATTTTGAT 58.012 29.630 0.00 0.00 34.94 2.57
64 65 8.198109 TCCGAAAACACTTTTTATCCATTTTGA 58.802 29.630 0.00 0.00 34.94 2.69
65 66 8.272866 GTCCGAAAACACTTTTTATCCATTTTG 58.727 33.333 0.00 0.00 34.94 2.44
67 68 6.639279 CGTCCGAAAACACTTTTTATCCATTT 59.361 34.615 0.00 0.00 34.94 2.32
68 69 6.016943 TCGTCCGAAAACACTTTTTATCCATT 60.017 34.615 0.00 0.00 34.94 3.16
69 70 5.470777 TCGTCCGAAAACACTTTTTATCCAT 59.529 36.000 0.00 0.00 34.94 3.41
70 71 4.815308 TCGTCCGAAAACACTTTTTATCCA 59.185 37.500 0.00 0.00 34.94 3.41
71 72 5.347012 TCGTCCGAAAACACTTTTTATCC 57.653 39.130 0.00 0.00 34.94 2.59
74 75 4.035441 CCCTTCGTCCGAAAACACTTTTTA 59.965 41.667 3.52 0.00 34.94 1.52
76 77 2.356695 CCCTTCGTCCGAAAACACTTTT 59.643 45.455 3.52 0.00 33.34 2.27
78 79 1.139455 TCCCTTCGTCCGAAAACACTT 59.861 47.619 3.52 0.00 33.34 3.16
79 80 0.754472 TCCCTTCGTCCGAAAACACT 59.246 50.000 3.52 0.00 33.34 3.55
80 81 1.145803 CTCCCTTCGTCCGAAAACAC 58.854 55.000 3.52 0.00 33.34 3.32
81 82 0.754472 ACTCCCTTCGTCCGAAAACA 59.246 50.000 3.52 0.00 33.34 2.83
82 83 2.730550 TACTCCCTTCGTCCGAAAAC 57.269 50.000 3.52 0.00 33.34 2.43
84 85 5.353938 CAAATATACTCCCTTCGTCCGAAA 58.646 41.667 3.52 0.00 33.34 3.46
85 86 4.202182 CCAAATATACTCCCTTCGTCCGAA 60.202 45.833 1.81 1.81 0.00 4.30
86 87 3.319972 CCAAATATACTCCCTTCGTCCGA 59.680 47.826 0.00 0.00 0.00 4.55
87 88 3.069158 ACCAAATATACTCCCTTCGTCCG 59.931 47.826 0.00 0.00 0.00 4.79
88 89 4.684484 ACCAAATATACTCCCTTCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
89 90 6.014840 TGGATACCAAATATACTCCCTTCGTC 60.015 42.308 0.00 0.00 0.00 4.20
90 91 5.842328 TGGATACCAAATATACTCCCTTCGT 59.158 40.000 0.00 0.00 0.00 3.85
91 92 6.354794 TGGATACCAAATATACTCCCTTCG 57.645 41.667 0.00 0.00 0.00 3.79
93 94 9.367160 CAAAATGGATACCAAATATACTCCCTT 57.633 33.333 0.00 0.00 36.95 3.95
94 95 8.732854 TCAAAATGGATACCAAATATACTCCCT 58.267 33.333 0.00 0.00 36.95 4.20
95 96 8.934023 TCAAAATGGATACCAAATATACTCCC 57.066 34.615 0.00 0.00 36.95 4.30
158 159 9.058174 TCTTCGTCCAAAAATACTTGTTATCAA 57.942 29.630 0.00 0.00 0.00 2.57
160 161 9.887406 TTTCTTCGTCCAAAAATACTTGTTATC 57.113 29.630 0.00 0.00 0.00 1.75
170 171 9.855021 CCAAATATACTTTCTTCGTCCAAAAAT 57.145 29.630 0.00 0.00 0.00 1.82
171 172 8.852135 ACCAAATATACTTTCTTCGTCCAAAAA 58.148 29.630 0.00 0.00 0.00 1.94
172 173 8.398878 ACCAAATATACTTTCTTCGTCCAAAA 57.601 30.769 0.00 0.00 0.00 2.44
173 174 7.989416 ACCAAATATACTTTCTTCGTCCAAA 57.011 32.000 0.00 0.00 0.00 3.28
174 175 9.321562 GATACCAAATATACTTTCTTCGTCCAA 57.678 33.333 0.00 0.00 0.00 3.53
176 177 7.650903 ACGATACCAAATATACTTTCTTCGTCC 59.349 37.037 0.00 0.00 29.97 4.79
177 178 8.571461 ACGATACCAAATATACTTTCTTCGTC 57.429 34.615 0.00 0.00 29.97 4.20
211 212 9.710818 AGGTCACCAAGTTATTAGAGATAACTA 57.289 33.333 10.77 0.00 42.19 2.24
212 213 8.611051 AGGTCACCAAGTTATTAGAGATAACT 57.389 34.615 0.00 5.78 44.16 2.24
213 214 9.668497 AAAGGTCACCAAGTTATTAGAGATAAC 57.332 33.333 0.00 1.64 35.36 1.89
252 253 9.770097 CTCCATCCGTTCTATAATATAATGCAT 57.230 33.333 0.00 0.00 0.00 3.96
253 254 8.758829 ACTCCATCCGTTCTATAATATAATGCA 58.241 33.333 0.00 0.00 0.00 3.96
264 265 8.937207 ACTATTTACTACTCCATCCGTTCTAT 57.063 34.615 0.00 0.00 0.00 1.98
265 266 9.851686 TTACTATTTACTACTCCATCCGTTCTA 57.148 33.333 0.00 0.00 0.00 2.10
266 267 8.757982 TTACTATTTACTACTCCATCCGTTCT 57.242 34.615 0.00 0.00 0.00 3.01
268 269 8.975295 ACTTTACTATTTACTACTCCATCCGTT 58.025 33.333 0.00 0.00 0.00 4.44
332 4368 6.442952 TGCATTTTCGGCGCTATATATTTTT 58.557 32.000 7.64 0.00 0.00 1.94
334 4370 5.621197 TGCATTTTCGGCGCTATATATTT 57.379 34.783 7.64 0.00 0.00 1.40
335 4371 5.181245 ACTTGCATTTTCGGCGCTATATATT 59.819 36.000 7.64 0.00 0.00 1.28
336 4372 4.695455 ACTTGCATTTTCGGCGCTATATAT 59.305 37.500 7.64 0.00 0.00 0.86
337 4373 4.062293 ACTTGCATTTTCGGCGCTATATA 58.938 39.130 7.64 0.00 0.00 0.86
340 4376 1.094785 ACTTGCATTTTCGGCGCTAT 58.905 45.000 7.64 0.00 0.00 2.97
345 4381 0.598065 AGGACACTTGCATTTTCGGC 59.402 50.000 0.00 0.00 0.00 5.54
376 4414 7.473795 GCTTCCCAATATCATCCCATGAAATTT 60.474 37.037 0.00 0.00 43.50 1.82
411 4452 9.825972 TTTTCGAAGCTTTAGATTGTATCTTTG 57.174 29.630 0.00 0.00 40.76 2.77
417 4458 7.551262 TGCCTATTTTCGAAGCTTTAGATTGTA 59.449 33.333 0.00 0.00 0.00 2.41
423 4464 9.567848 TTAAAATGCCTATTTTCGAAGCTTTAG 57.432 29.630 0.00 0.00 43.52 1.85
472 4526 1.628340 TCCAAGATGACATCCGTGGTT 59.372 47.619 24.78 7.95 36.70 3.67
496 4550 1.635663 CGGGTGCTCGTGTGGAATTC 61.636 60.000 0.00 0.00 0.00 2.17
527 4581 4.836125 ATGAATTGCTACTATTTGGGCG 57.164 40.909 0.00 0.00 0.00 6.13
551 4605 8.543862 ACGGACTAGTAAATTCGAAAAAGAAT 57.456 30.769 0.00 0.00 42.13 2.40
552 4606 7.951530 ACGGACTAGTAAATTCGAAAAAGAA 57.048 32.000 0.00 0.00 34.31 2.52
571 4625 5.464030 TCTGCTTCCCTATAAATACGGAC 57.536 43.478 0.00 0.00 0.00 4.79
587 4641 4.959399 GCCTCAGCTCATCTGCTT 57.041 55.556 0.00 0.00 41.98 3.91
615 4669 5.648092 ACGATGGAAAAGGAGAATCGAAAAT 59.352 36.000 10.03 0.00 41.98 1.82
712 4774 2.569404 AGAAGGTGAGGTGAGATTGGAC 59.431 50.000 0.00 0.00 0.00 4.02
737 4799 2.274104 GGCGGCTGGAAATGGGTA 59.726 61.111 0.00 0.00 0.00 3.69
771 4845 0.044397 GAGGGAGTTTAGGGGAGGGT 59.956 60.000 0.00 0.00 0.00 4.34
797 4874 1.072331 GTGAGCAGAACAAGAAGGGGA 59.928 52.381 0.00 0.00 0.00 4.81
956 5033 2.766263 TGGATGAGACTACCATCACACC 59.234 50.000 0.00 0.00 41.52 4.16
975 5052 2.593725 CAGGGCGCATCTCCATGG 60.594 66.667 10.83 4.97 32.21 3.66
1148 5299 6.292168 CCCAATCGCTACTGAATTAGTTAACG 60.292 42.308 0.00 0.00 40.89 3.18
1170 5321 5.183713 CAGAATGAATTCAGTAAACAGCCCA 59.816 40.000 14.54 0.00 39.69 5.36
1221 5373 3.786955 GCGTGTGCACTGATATTCG 57.213 52.632 19.41 11.54 42.15 3.34
1235 5387 1.269726 ACCTTTTGAAATGCCTGCGTG 60.270 47.619 0.00 0.00 0.00 5.34
1325 5479 1.915141 ACAGGCAATCAGAACTTGGG 58.085 50.000 0.00 0.00 0.00 4.12
1361 5515 7.744087 AGTGCATTCAATTAGTTCAGTTGTA 57.256 32.000 0.00 0.00 0.00 2.41
1445 5599 4.580167 TCCTTTTCTGTCCACACAAAGATG 59.420 41.667 7.70 0.00 29.82 2.90
1482 5636 3.249687 CCAGGTAGGTTCCAACTGC 57.750 57.895 0.00 0.00 0.00 4.40
1493 5647 4.360951 TTGTTAACAAGGGACCAGGTAG 57.639 45.455 17.01 0.00 0.00 3.18
1502 5656 6.701400 CCAGAACTTCATTTTGTTAACAAGGG 59.299 38.462 19.72 13.54 37.15 3.95
1604 5763 3.058224 GCTCCACAACAGTACAATGGTTC 60.058 47.826 0.00 0.00 0.00 3.62
1658 5817 0.398806 TCAATTGGGGGCATCATGGG 60.399 55.000 5.42 0.00 0.00 4.00
1705 5864 4.972440 GTCTTTTGCTGTGAATCACTGAAC 59.028 41.667 21.76 7.51 35.76 3.18
1773 5932 7.852971 TTAGGTTAAGTGCCATATGTTGTAC 57.147 36.000 1.24 0.00 0.00 2.90
1852 6012 7.221452 GCAAGTGGATAACTGAAAATATTGCAG 59.779 37.037 13.99 13.99 39.81 4.41
1953 6114 3.801114 GCCAAGTTAAAAGGGCATAGG 57.199 47.619 7.45 0.00 45.70 2.57
2086 6247 7.418827 CCCCAATTGATTTTTGCCTGTCATATA 60.419 37.037 7.12 0.00 0.00 0.86
2117 6280 8.655092 TGAACAAACTGAAAGCAAACAAAATAG 58.345 29.630 0.00 0.00 37.60 1.73
2122 6285 7.432350 AATTGAACAAACTGAAAGCAAACAA 57.568 28.000 0.00 0.00 37.60 2.83
2145 6308 6.969828 ACATTTACGCCAAGAAAAACAAAA 57.030 29.167 0.00 0.00 0.00 2.44
2354 6517 8.854614 AATGAGAATAAGTTCAACTTACAGCT 57.145 30.769 12.33 9.60 42.78 4.24
2414 6577 4.428615 AGACAAAGACGAACTAGAGCTC 57.571 45.455 5.27 5.27 0.00 4.09
2415 6578 4.278669 TCAAGACAAAGACGAACTAGAGCT 59.721 41.667 0.00 0.00 0.00 4.09
2416 6579 4.547532 TCAAGACAAAGACGAACTAGAGC 58.452 43.478 0.00 0.00 0.00 4.09
2417 6580 7.087639 AGATTCAAGACAAAGACGAACTAGAG 58.912 38.462 0.00 0.00 0.00 2.43
2419 6582 7.169982 ACAAGATTCAAGACAAAGACGAACTAG 59.830 37.037 0.00 0.00 0.00 2.57
2552 6715 4.645535 TGAATGGAAGAGAACAGTTGGAG 58.354 43.478 0.00 0.00 0.00 3.86
2634 6922 2.515926 TGGCGAGCATCTTGATAGAC 57.484 50.000 0.00 0.00 31.99 2.59
3037 7325 7.770433 TCAGAATAGCAACACATAAAGCATACT 59.230 33.333 0.00 0.00 0.00 2.12
3054 7342 6.974932 TGTGACTCAAGAAATCAGAATAGC 57.025 37.500 0.00 0.00 0.00 2.97
3074 7362 9.810231 GCAAATTTAAAACATAAAGGACATGTG 57.190 29.630 1.15 0.00 36.74 3.21
3082 7370 9.801714 CTGAGCAAGCAAATTTAAAACATAAAG 57.198 29.630 0.00 0.00 0.00 1.85
3094 7382 1.409790 TGCACACTGAGCAAGCAAATT 59.590 42.857 0.00 0.00 39.39 1.82
3224 7512 1.203100 AGGTGCATCTGCCTTTCCTTT 60.203 47.619 0.00 0.00 41.18 3.11
3225 7513 0.407139 AGGTGCATCTGCCTTTCCTT 59.593 50.000 0.00 0.00 41.18 3.36
3226 7514 0.407139 AAGGTGCATCTGCCTTTCCT 59.593 50.000 0.00 0.00 41.93 3.36
3411 7699 0.677731 GTGCACAGAAGGCAGCCATA 60.678 55.000 15.80 0.00 42.85 2.74
3513 7801 9.829507 TGAAATAATGTTTCTTGACCACAATTT 57.170 25.926 4.22 0.00 35.37 1.82
3514 7802 9.480053 CTGAAATAATGTTTCTTGACCACAATT 57.520 29.630 4.22 0.00 35.37 2.32
3515 7803 8.859090 TCTGAAATAATGTTTCTTGACCACAAT 58.141 29.630 4.22 0.00 35.37 2.71
3516 7804 8.231692 TCTGAAATAATGTTTCTTGACCACAA 57.768 30.769 4.22 0.00 34.65 3.33
3517 7805 7.522073 GCTCTGAAATAATGTTTCTTGACCACA 60.522 37.037 4.22 0.00 0.00 4.17
3518 7806 6.803807 GCTCTGAAATAATGTTTCTTGACCAC 59.196 38.462 4.22 0.00 0.00 4.16
3519 7807 6.071952 GGCTCTGAAATAATGTTTCTTGACCA 60.072 38.462 4.22 0.00 0.00 4.02
3520 7808 6.325596 GGCTCTGAAATAATGTTTCTTGACC 58.674 40.000 4.22 0.00 0.00 4.02
3521 7809 6.325596 GGGCTCTGAAATAATGTTTCTTGAC 58.674 40.000 4.22 0.00 0.00 3.18
3522 7810 5.418840 GGGGCTCTGAAATAATGTTTCTTGA 59.581 40.000 4.22 2.45 0.00 3.02
3523 7811 5.394553 GGGGGCTCTGAAATAATGTTTCTTG 60.395 44.000 4.22 0.00 0.00 3.02
3524 7812 4.711846 GGGGGCTCTGAAATAATGTTTCTT 59.288 41.667 4.22 0.00 0.00 2.52
3525 7813 4.281657 GGGGGCTCTGAAATAATGTTTCT 58.718 43.478 4.22 0.00 0.00 2.52
3526 7814 3.066760 CGGGGGCTCTGAAATAATGTTTC 59.933 47.826 0.00 0.00 0.00 2.78
3527 7815 3.023832 CGGGGGCTCTGAAATAATGTTT 58.976 45.455 0.00 0.00 0.00 2.83
3528 7816 2.654863 CGGGGGCTCTGAAATAATGTT 58.345 47.619 0.00 0.00 0.00 2.71
3529 7817 1.750682 GCGGGGGCTCTGAAATAATGT 60.751 52.381 0.00 0.00 0.00 2.71
3530 7818 0.954452 GCGGGGGCTCTGAAATAATG 59.046 55.000 0.00 0.00 0.00 1.90
3531 7819 0.535102 CGCGGGGGCTCTGAAATAAT 60.535 55.000 0.00 0.00 0.00 1.28
3532 7820 1.153249 CGCGGGGGCTCTGAAATAA 60.153 57.895 0.00 0.00 0.00 1.40
3533 7821 2.306255 GACGCGGGGGCTCTGAAATA 62.306 60.000 12.47 0.00 0.00 1.40
3534 7822 3.682292 GACGCGGGGGCTCTGAAAT 62.682 63.158 12.47 0.00 0.00 2.17
3535 7823 4.388499 GACGCGGGGGCTCTGAAA 62.388 66.667 12.47 0.00 0.00 2.69
4419 8717 1.299648 CATCAAGAGGGGAACGGCA 59.700 57.895 0.00 0.00 0.00 5.69
4586 8884 2.597510 GCGGGTGAAAAGCAGGGT 60.598 61.111 0.00 0.00 0.00 4.34
4956 9263 6.657541 GGTGTTAGGAATTTGATACAAGACCA 59.342 38.462 0.00 0.00 30.52 4.02
5011 9318 5.833131 TGAAGGGAAAAATCAACAGCTTACT 59.167 36.000 0.00 0.00 0.00 2.24
5030 9337 5.982356 TGATCTGTGGATAGAGTTTGAAGG 58.018 41.667 0.00 0.00 31.46 3.46
5039 9346 2.625314 CCGAGCTTGATCTGTGGATAGA 59.375 50.000 1.22 0.00 31.46 1.98
5266 9573 5.067805 CCTGGGAGTTGGAAAGCATATTTAC 59.932 44.000 0.00 0.00 0.00 2.01
5287 9594 1.667724 CACAGCGATAAAGGCTTCCTG 59.332 52.381 0.00 5.37 39.08 3.86
5490 9806 4.387598 GAGAGGCACCTAGTAAGACGATA 58.612 47.826 0.00 0.00 0.00 2.92
5496 9812 5.540337 TCAATATGGAGAGGCACCTAGTAAG 59.460 44.000 0.00 0.00 0.00 2.34
5628 9944 2.943033 TGATGATGTTGCTGCTGAGATG 59.057 45.455 0.00 0.00 0.00 2.90
5634 9950 2.718563 TGTCATGATGATGTTGCTGCT 58.281 42.857 0.00 0.00 0.00 4.24
5662 9978 1.536922 CGACAATGGAGACCTCGATGG 60.537 57.143 0.00 0.00 42.93 3.51
5664 9980 1.678627 CTCGACAATGGAGACCTCGAT 59.321 52.381 0.00 0.00 33.20 3.59
5732 10048 6.701145 TCTGCACTAAATTGGTGTTAACAA 57.299 33.333 10.51 0.00 37.07 2.83
5952 10270 6.580788 ACATCTGTATAGATATCTGCATGGC 58.419 40.000 15.79 1.25 41.71 4.40
5978 10296 3.627577 TCTGCTTTATTTCCCAGATTCGC 59.372 43.478 0.00 0.00 30.00 4.70
6055 10408 3.390967 TCAAGTGTGGGTCAGATTTCAGA 59.609 43.478 0.00 0.00 0.00 3.27
6305 10658 7.963532 AGAGTTGTCTTGTAAGTAAATCCTGA 58.036 34.615 0.00 0.00 0.00 3.86
6311 10664 9.153721 TCGAAAAAGAGTTGTCTTGTAAGTAAA 57.846 29.630 0.00 0.00 42.59 2.01
6388 10743 6.055588 AGATCACCCACTTTGTATTTATCGG 58.944 40.000 0.00 0.00 0.00 4.18
6490 10845 2.286833 CACATACCGTATTGCGAAAGGG 59.713 50.000 0.00 0.00 44.77 3.95
6564 10919 0.184933 TTGTGTTTCCCCACTCCTGG 59.815 55.000 0.00 0.00 36.30 4.45
6612 10967 1.202698 GGTGAGTGCTTCTCTGTGGTT 60.203 52.381 9.94 0.00 43.13 3.67
6614 10969 0.321122 GGGTGAGTGCTTCTCTGTGG 60.321 60.000 9.94 0.00 43.13 4.17
6616 10971 1.115930 ACGGGTGAGTGCTTCTCTGT 61.116 55.000 9.94 2.77 43.13 3.41
6617 10972 0.389166 GACGGGTGAGTGCTTCTCTG 60.389 60.000 9.94 2.29 43.13 3.35
6693 11054 3.806507 GCAGGTTTGAATTTGATGGCCAA 60.807 43.478 10.96 0.00 0.00 4.52
6694 11055 2.289569 GCAGGTTTGAATTTGATGGCCA 60.290 45.455 8.56 8.56 0.00 5.36
6743 11104 0.389948 GTCGATGCCCACGAGAAACT 60.390 55.000 0.00 0.00 40.37 2.66
6798 11159 1.765904 TGCACAGTGGGAAGTCTTACA 59.234 47.619 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.