Multiple sequence alignment - TraesCS4A01G323000

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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 TraesCS4A01G323000 chr4A 100.000 4959 0 0 1 4959 611024042 611029000 0.000000e+00 9158.0
1 TraesCS4A01G323000 chr4A 84.785 1630 201 31 1503 3100 611073635 611072021 0.000000e+00 1592.0
2 TraesCS4A01G323000 chr4A 84.657 1486 203 17 1622 3100 610706864 610708331 0.000000e+00 1458.0
3 TraesCS4A01G323000 chr4A 82.392 1522 246 18 1624 3140 611203497 611201993 0.000000e+00 1306.0
4 TraesCS4A01G323000 chr4A 82.548 1507 240 18 1635 3138 610818274 610816788 0.000000e+00 1304.0
5 TraesCS4A01G323000 chr4A 82.326 1522 247 18 1624 3140 610640290 610641794 0.000000e+00 1301.0
6 TraesCS4A01G323000 chr4A 91.242 491 24 6 954 1435 610640147 610640627 0.000000e+00 651.0
7 TraesCS4A01G323000 chr4A 91.242 491 24 3 954 1435 611203640 611203160 0.000000e+00 651.0
8 TraesCS4A01G323000 chr4A 94.643 168 8 1 4279 4446 362068076 362067910 4.920000e-65 259.0
9 TraesCS4A01G323000 chr4A 80.473 338 44 10 1526 1842 610818686 610818350 6.420000e-59 239.0
10 TraesCS4A01G323000 chr4A 94.958 119 5 1 3271 3389 611027194 611027311 8.480000e-43 185.0
11 TraesCS4A01G323000 chr4A 94.958 119 5 1 3153 3270 611027312 611027430 8.480000e-43 185.0
12 TraesCS4A01G323000 chr4A 83.721 86 4 8 3179 3263 610708440 610708516 6.890000e-09 73.1
13 TraesCS4A01G323000 chr4A 97.436 39 1 0 3298 3336 610708440 610708478 3.200000e-07 67.6
14 TraesCS4A01G323000 chr4A 100.000 32 0 0 4619 4650 611028510 611028541 5.360000e-05 60.2
15 TraesCS4A01G323000 chr4A 100.000 32 0 0 4469 4500 611028660 611028691 5.360000e-05 60.2
16 TraesCS4A01G323000 chr5B 97.809 4107 67 12 872 4959 704722510 704726612 0.000000e+00 7064.0
17 TraesCS4A01G323000 chr5B 83.754 1742 220 36 1408 3100 704498094 704499821 0.000000e+00 1591.0
18 TraesCS4A01G323000 chr5B 84.869 1487 199 18 1622 3100 704760626 704759158 0.000000e+00 1476.0
19 TraesCS4A01G323000 chr5B 83.201 1512 230 13 1635 3140 704528565 704530058 0.000000e+00 1363.0
20 TraesCS4A01G323000 chr5B 82.521 1539 243 19 1609 3140 704479160 704480679 0.000000e+00 1328.0
21 TraesCS4A01G323000 chr5B 82.612 1524 238 19 1624 3140 704824478 704822975 0.000000e+00 1321.0
22 TraesCS4A01G323000 chr5B 94.390 820 29 6 1 814 704721686 704722494 0.000000e+00 1243.0
23 TraesCS4A01G323000 chr5B 91.650 491 31 2 954 1435 704824630 704824141 0.000000e+00 671.0
24 TraesCS4A01G323000 chr5B 88.283 495 45 4 954 1435 704479018 704479512 9.250000e-162 580.0
25 TraesCS4A01G323000 chr5B 81.331 541 85 7 3477 4016 704318502 704317977 4.590000e-115 425.0
26 TraesCS4A01G323000 chr5B 81.445 512 80 10 3480 3981 704530286 704530792 5.980000e-109 405.0
27 TraesCS4A01G323000 chr5B 82.173 359 51 9 1088 1435 704760634 704760278 3.750000e-76 296.0
28 TraesCS4A01G323000 chr5B 81.616 359 48 10 1499 1842 704528137 704528492 1.050000e-71 281.0
29 TraesCS4A01G323000 chr5B 94.767 172 8 1 4276 4447 27817177 27817007 2.940000e-67 267.0
30 TraesCS4A01G323000 chr5B 94.958 119 5 1 3271 3389 704724800 704724917 8.480000e-43 185.0
31 TraesCS4A01G323000 chr5B 93.333 120 6 2 3153 3270 704724918 704725037 5.100000e-40 176.0
32 TraesCS4A01G323000 chr5B 87.879 99 8 4 3392 3489 213255211 213255306 4.060000e-21 113.0
33 TraesCS4A01G323000 chr5B 86.076 79 11 0 3149 3227 704822861 704822783 8.840000e-13 86.1
34 TraesCS4A01G323000 chr5B 83.721 86 4 8 3179 3263 704499946 704500022 6.890000e-09 73.1
35 TraesCS4A01G323000 chr5B 97.436 39 1 0 3298 3336 704499946 704499984 3.200000e-07 67.6
36 TraesCS4A01G323000 chr5B 100.000 35 0 0 4616 4650 704726118 704726152 1.150000e-06 65.8
37 TraesCS4A01G323000 chr5B 100.000 32 0 0 4469 4500 704726271 704726302 5.360000e-05 60.2
38 TraesCS4A01G323000 chrUn 100.000 400 0 0 3705 4104 478707249 478706850 0.000000e+00 739.0
39 TraesCS4A01G323000 chr7A 92.857 182 11 2 4279 4460 115807688 115807509 3.810000e-66 263.0
40 TraesCS4A01G323000 chr4D 94.706 170 8 1 4278 4447 377455672 377455504 3.810000e-66 263.0
41 TraesCS4A01G323000 chr3A 93.714 175 9 2 4271 4445 334179811 334179983 1.370000e-65 261.0
42 TraesCS4A01G323000 chr2D 93.678 174 9 2 4277 4450 560959482 560959653 4.920000e-65 259.0
43 TraesCS4A01G323000 chr1D 94.152 171 8 2 4279 4449 178466305 178466473 4.920000e-65 259.0
44 TraesCS4A01G323000 chr7B 92.737 179 12 1 4280 4458 82691258 82691081 1.770000e-64 257.0
45 TraesCS4A01G323000 chr2B 90.722 97 6 3 3384 3480 794694182 794694275 5.210000e-25 126.0
46 TraesCS4A01G323000 chr2B 90.722 97 6 3 3384 3480 794803083 794803176 5.210000e-25 126.0
47 TraesCS4A01G323000 chr2B 91.954 87 5 2 3392 3478 677805611 677805527 2.420000e-23 121.0
48 TraesCS4A01G323000 chr6D 90.000 90 7 2 3389 3478 39676412 39676499 1.130000e-21 115.0
49 TraesCS4A01G323000 chr5A 86.916 107 8 6 3385 3489 227928515 227928617 1.130000e-21 115.0
50 TraesCS4A01G323000 chr5D 88.172 93 9 2 3392 3484 197147183 197147093 5.250000e-20 110.0
51 TraesCS4A01G323000 chr3D 87.500 96 9 3 3389 3484 75538834 75538926 1.890000e-19 108.0
52 TraesCS4A01G323000 chr1A 78.218 101 15 6 5 103 405829639 405829544 1.930000e-04 58.4


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 TraesCS4A01G323000 chr4A 611024042 611029000 4958 False 1929.680000 9158 97.983200 1 4959 5 chr4A.!!$F3 4958
1 TraesCS4A01G323000 chr4A 611072021 611073635 1614 True 1592.000000 1592 84.785000 1503 3100 1 chr4A.!!$R2 1597
2 TraesCS4A01G323000 chr4A 611201993 611203640 1647 True 978.500000 1306 86.817000 954 3140 2 chr4A.!!$R4 2186
3 TraesCS4A01G323000 chr4A 610640147 610641794 1647 False 976.000000 1301 86.784000 954 3140 2 chr4A.!!$F1 2186
4 TraesCS4A01G323000 chr4A 610816788 610818686 1898 True 771.500000 1304 81.510500 1526 3138 2 chr4A.!!$R3 1612
5 TraesCS4A01G323000 chr4A 610706864 610708516 1652 False 532.900000 1458 88.604667 1622 3336 3 chr4A.!!$F2 1714
6 TraesCS4A01G323000 chr5B 704721686 704726612 4926 False 1465.666667 7064 96.748333 1 4959 6 chr5B.!!$F5 4958
7 TraesCS4A01G323000 chr5B 704479018 704480679 1661 False 954.000000 1328 85.402000 954 3140 2 chr5B.!!$F2 2186
8 TraesCS4A01G323000 chr5B 704759158 704760634 1476 True 886.000000 1476 83.521000 1088 3100 2 chr5B.!!$R3 2012
9 TraesCS4A01G323000 chr5B 704822783 704824630 1847 True 692.700000 1321 86.779333 954 3227 3 chr5B.!!$R4 2273
10 TraesCS4A01G323000 chr5B 704528137 704530792 2655 False 683.000000 1363 82.087333 1499 3981 3 chr5B.!!$F4 2482
11 TraesCS4A01G323000 chr5B 704498094 704500022 1928 False 577.233333 1591 88.303667 1408 3336 3 chr5B.!!$F3 1928
12 TraesCS4A01G323000 chr5B 704317977 704318502 525 True 425.000000 425 81.331000 3477 4016 1 chr5B.!!$R2 539

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
842 846 0.250467 CTGTGTGTGTGAAGAGGGGG 60.250 60.0 0.00 0.0 0.00 5.40 F
1395 1411 0.034670 ATCTTGTGCTCCAGCCCTTC 60.035 55.0 0.00 0.0 41.18 3.46 F
1403 1419 0.111253 CTCCAGCCCTTCTGTTGGTT 59.889 55.0 0.00 0.0 41.25 3.67 F
1404 1420 0.178992 TCCAGCCCTTCTGTTGGTTG 60.179 55.0 0.00 0.0 41.25 3.77 F
1621 1654 0.179084 GCATAGGCAGCGGAACAGTA 60.179 55.0 0.00 0.0 40.72 2.74 F
1859 3050 1.164411 TCACGGACCAATTGATGCAC 58.836 50.0 7.12 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 3096 1.064654 GATGGAGCACGAGATTTTGGC 59.935 52.381 0.00 0.00 0.00 4.52 R
2906 4109 2.631160 ACCAAAGGTCATGACACGAA 57.369 45.000 26.47 0.00 0.00 3.85 R
3352 4669 3.188460 GCGAGTTGGATAAAGAACAGCAA 59.812 43.478 0.00 0.00 32.05 3.91 R
3397 4714 6.349243 ACGATGTTATATTATGGGACGGAA 57.651 37.500 0.00 0.00 0.00 4.30 R
3703 5030 0.531974 TGTTGAACAGACACTCCGGC 60.532 55.000 0.00 0.00 0.00 6.13 R
4104 5431 4.496175 GGAGTACTGTAGAGAAGCGCTAAC 60.496 50.000 12.05 8.57 0.00 2.34 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
36 37 2.298610 GATAGGCTAAGGTTGGGTTGC 58.701 52.381 0.00 0.00 0.00 4.17
39 40 2.989881 GCTAAGGTTGGGTTGCCGC 61.990 63.158 0.00 0.00 0.00 6.53
175 176 4.217334 GGGTCCTAGCGGTTAGTCTTATAC 59.783 50.000 0.00 0.00 0.00 1.47
183 184 2.391879 GTTAGTCTTATACGGCAGGCG 58.608 52.381 16.06 16.06 0.00 5.52
200 201 4.338539 GTGACCGGACGCGTCTGT 62.339 66.667 37.95 32.22 34.20 3.41
219 220 2.657237 CGTCTCCATATCCGCCCC 59.343 66.667 0.00 0.00 0.00 5.80
223 224 1.843376 CTCCATATCCGCCCCAGGT 60.843 63.158 0.00 0.00 0.00 4.00
255 257 0.830648 TGGGGACTGTCGATCAATCC 59.169 55.000 1.07 6.87 41.23 3.01
288 290 4.142643 GGTCGAATTTAAATGGCGTGGTTA 60.143 41.667 17.79 2.47 0.00 2.85
339 341 1.668151 GACAGCTCGTCGGGCTTTT 60.668 57.895 19.13 7.37 38.03 2.27
340 342 1.901650 GACAGCTCGTCGGGCTTTTG 61.902 60.000 19.13 10.30 38.03 2.44
341 343 2.358737 AGCTCGTCGGGCTTTTGG 60.359 61.111 15.47 0.00 36.56 3.28
342 344 3.431725 GCTCGTCGGGCTTTTGGG 61.432 66.667 10.59 0.00 0.00 4.12
343 345 3.431725 CTCGTCGGGCTTTTGGGC 61.432 66.667 0.00 0.00 40.05 5.36
464 468 1.668419 CACCAGAATTCCCCATCGTC 58.332 55.000 0.65 0.00 0.00 4.20
597 601 4.856607 CTTCTCCTCCGCGGCGAC 62.857 72.222 25.92 0.11 0.00 5.19
679 683 1.066587 GTTCGATCTCCCTGCTCGG 59.933 63.158 0.00 0.00 35.31 4.63
745 749 1.037030 TCAAATCCATTGCCGCCTCC 61.037 55.000 0.00 0.00 38.98 4.30
842 846 0.250467 CTGTGTGTGTGAAGAGGGGG 60.250 60.000 0.00 0.00 0.00 5.40
857 861 3.197895 GGGGTTGGGGGAGGGTTT 61.198 66.667 0.00 0.00 0.00 3.27
858 862 2.119611 GGGTTGGGGGAGGGTTTG 59.880 66.667 0.00 0.00 0.00 2.93
859 863 2.119611 GGTTGGGGGAGGGTTTGG 59.880 66.667 0.00 0.00 0.00 3.28
860 864 2.119611 GTTGGGGGAGGGTTTGGG 59.880 66.667 0.00 0.00 0.00 4.12
861 865 2.037128 TTGGGGGAGGGTTTGGGA 60.037 61.111 0.00 0.00 0.00 4.37
862 866 2.167037 TTGGGGGAGGGTTTGGGAG 61.167 63.158 0.00 0.00 0.00 4.30
863 867 4.062032 GGGGGAGGGTTTGGGAGC 62.062 72.222 0.00 0.00 0.00 4.70
864 868 2.941583 GGGGAGGGTTTGGGAGCT 60.942 66.667 0.00 0.00 0.00 4.09
865 869 2.548547 GGGGAGGGTTTGGGAGCTT 61.549 63.158 0.00 0.00 0.00 3.74
866 870 1.304464 GGGAGGGTTTGGGAGCTTG 60.304 63.158 0.00 0.00 0.00 4.01
867 871 1.767692 GGAGGGTTTGGGAGCTTGA 59.232 57.895 0.00 0.00 0.00 3.02
868 872 0.322906 GGAGGGTTTGGGAGCTTGAG 60.323 60.000 0.00 0.00 0.00 3.02
869 873 0.402121 GAGGGTTTGGGAGCTTGAGT 59.598 55.000 0.00 0.00 0.00 3.41
870 874 0.853530 AGGGTTTGGGAGCTTGAGTT 59.146 50.000 0.00 0.00 0.00 3.01
1122 1138 1.135859 CAGTTTGAACCGCTGAGCATC 60.136 52.381 4.88 0.00 32.39 3.91
1324 1340 3.156511 ACTACATCAGTCATGACGCAG 57.843 47.619 19.85 13.80 38.57 5.18
1325 1341 2.755103 ACTACATCAGTCATGACGCAGA 59.245 45.455 19.85 18.22 38.57 4.26
1326 1342 2.290531 ACATCAGTCATGACGCAGAG 57.709 50.000 19.85 12.37 38.57 3.35
1327 1343 1.134877 ACATCAGTCATGACGCAGAGG 60.135 52.381 19.85 20.46 38.57 3.69
1328 1344 1.135721 CATCAGTCATGACGCAGAGGA 59.864 52.381 19.85 11.81 38.57 3.71
1329 1345 1.256812 TCAGTCATGACGCAGAGGAA 58.743 50.000 19.85 0.00 36.20 3.36
1330 1346 1.067565 TCAGTCATGACGCAGAGGAAC 60.068 52.381 19.85 0.00 36.20 3.62
1331 1347 0.247736 AGTCATGACGCAGAGGAACC 59.752 55.000 19.85 0.00 36.20 3.62
1332 1348 0.037326 GTCATGACGCAGAGGAACCA 60.037 55.000 10.69 0.00 0.00 3.67
1333 1349 0.247460 TCATGACGCAGAGGAACCAG 59.753 55.000 0.00 0.00 0.00 4.00
1334 1350 1.078848 ATGACGCAGAGGAACCAGC 60.079 57.895 0.00 0.00 0.00 4.85
1338 1354 2.659610 GCAGAGGAACCAGCGACT 59.340 61.111 0.00 0.00 0.00 4.18
1339 1355 1.739562 GCAGAGGAACCAGCGACTG 60.740 63.158 0.00 0.00 0.00 3.51
1340 1356 1.967535 CAGAGGAACCAGCGACTGA 59.032 57.895 8.20 0.00 32.44 3.41
1341 1357 0.534412 CAGAGGAACCAGCGACTGAT 59.466 55.000 8.20 0.00 32.44 2.90
1342 1358 0.820871 AGAGGAACCAGCGACTGATC 59.179 55.000 8.20 6.34 32.44 2.92
1343 1359 0.820871 GAGGAACCAGCGACTGATCT 59.179 55.000 8.20 1.41 32.44 2.75
1344 1360 0.534412 AGGAACCAGCGACTGATCTG 59.466 55.000 8.20 0.00 32.44 2.90
1345 1361 1.086634 GGAACCAGCGACTGATCTGC 61.087 60.000 8.20 0.00 32.44 4.26
1346 1362 0.108424 GAACCAGCGACTGATCTGCT 60.108 55.000 8.20 0.00 35.84 4.24
1347 1363 0.322975 AACCAGCGACTGATCTGCTT 59.677 50.000 8.20 0.00 34.05 3.91
1348 1364 0.390866 ACCAGCGACTGATCTGCTTG 60.391 55.000 8.20 0.31 34.05 4.01
1349 1365 1.088340 CCAGCGACTGATCTGCTTGG 61.088 60.000 8.20 0.00 34.05 3.61
1350 1366 0.108472 CAGCGACTGATCTGCTTGGA 60.108 55.000 0.00 0.00 34.05 3.53
1351 1367 0.175302 AGCGACTGATCTGCTTGGAG 59.825 55.000 0.00 0.00 32.96 3.86
1352 1368 0.174389 GCGACTGATCTGCTTGGAGA 59.826 55.000 0.00 0.00 0.00 3.71
1353 1369 1.919918 CGACTGATCTGCTTGGAGAC 58.080 55.000 0.00 0.00 0.00 3.36
1354 1370 1.470632 CGACTGATCTGCTTGGAGACC 60.471 57.143 0.00 0.00 0.00 3.85
1355 1371 1.830477 GACTGATCTGCTTGGAGACCT 59.170 52.381 0.00 0.00 0.00 3.85
1356 1372 2.235898 GACTGATCTGCTTGGAGACCTT 59.764 50.000 0.00 0.00 0.00 3.50
1357 1373 2.235898 ACTGATCTGCTTGGAGACCTTC 59.764 50.000 0.00 0.00 0.00 3.46
1358 1374 1.556911 TGATCTGCTTGGAGACCTTCC 59.443 52.381 0.00 0.00 46.98 3.46
1383 1399 8.136057 CAGAGGTACTATGCTAAAATCTTGTG 57.864 38.462 0.00 0.00 42.14 3.33
1384 1400 6.763610 AGAGGTACTATGCTAAAATCTTGTGC 59.236 38.462 0.00 0.00 41.55 4.57
1385 1401 6.653989 AGGTACTATGCTAAAATCTTGTGCT 58.346 36.000 0.00 0.00 36.02 4.40
1386 1402 6.763610 AGGTACTATGCTAAAATCTTGTGCTC 59.236 38.462 0.00 0.00 36.02 4.26
1387 1403 6.017852 GGTACTATGCTAAAATCTTGTGCTCC 60.018 42.308 0.00 0.00 0.00 4.70
1388 1404 5.500234 ACTATGCTAAAATCTTGTGCTCCA 58.500 37.500 0.00 0.00 0.00 3.86
1389 1405 4.978083 ATGCTAAAATCTTGTGCTCCAG 57.022 40.909 0.00 0.00 0.00 3.86
1390 1406 2.489329 TGCTAAAATCTTGTGCTCCAGC 59.511 45.455 0.00 0.00 42.50 4.85
1391 1407 2.159324 GCTAAAATCTTGTGCTCCAGCC 60.159 50.000 0.00 0.00 41.18 4.85
1392 1408 1.260544 AAAATCTTGTGCTCCAGCCC 58.739 50.000 0.00 0.00 41.18 5.19
1393 1409 0.407139 AAATCTTGTGCTCCAGCCCT 59.593 50.000 0.00 0.00 41.18 5.19
1394 1410 0.407139 AATCTTGTGCTCCAGCCCTT 59.593 50.000 0.00 0.00 41.18 3.95
1395 1411 0.034670 ATCTTGTGCTCCAGCCCTTC 60.035 55.000 0.00 0.00 41.18 3.46
1396 1412 1.130054 TCTTGTGCTCCAGCCCTTCT 61.130 55.000 0.00 0.00 41.18 2.85
1397 1413 0.959372 CTTGTGCTCCAGCCCTTCTG 60.959 60.000 0.00 0.00 42.49 3.02
1398 1414 1.708993 TTGTGCTCCAGCCCTTCTGT 61.709 55.000 0.00 0.00 41.25 3.41
1399 1415 1.073897 GTGCTCCAGCCCTTCTGTT 59.926 57.895 0.00 0.00 41.25 3.16
1400 1416 1.073722 TGCTCCAGCCCTTCTGTTG 59.926 57.895 0.00 0.00 41.25 3.33
1401 1417 1.676967 GCTCCAGCCCTTCTGTTGG 60.677 63.158 0.00 0.00 41.25 3.77
1402 1418 1.763770 CTCCAGCCCTTCTGTTGGT 59.236 57.895 0.00 0.00 41.25 3.67
1403 1419 0.111253 CTCCAGCCCTTCTGTTGGTT 59.889 55.000 0.00 0.00 41.25 3.67
1404 1420 0.178992 TCCAGCCCTTCTGTTGGTTG 60.179 55.000 0.00 0.00 41.25 3.77
1405 1421 1.662044 CAGCCCTTCTGTTGGTTGC 59.338 57.895 0.00 0.00 38.02 4.17
1406 1422 1.108727 CAGCCCTTCTGTTGGTTGCA 61.109 55.000 0.00 0.00 38.02 4.08
1407 1423 0.825010 AGCCCTTCTGTTGGTTGCAG 60.825 55.000 0.00 0.00 35.43 4.41
1408 1424 0.823356 GCCCTTCTGTTGGTTGCAGA 60.823 55.000 0.00 0.00 40.76 4.26
1409 1425 1.915141 CCCTTCTGTTGGTTGCAGAT 58.085 50.000 0.00 0.00 41.87 2.90
1415 1431 5.705441 CCTTCTGTTGGTTGCAGATTACTAA 59.295 40.000 0.00 0.00 41.87 2.24
1423 1439 7.534085 TGGTTGCAGATTACTAATTTCTACG 57.466 36.000 0.00 0.00 0.00 3.51
1425 1441 8.252417 TGGTTGCAGATTACTAATTTCTACGTA 58.748 33.333 0.00 0.00 0.00 3.57
1435 1451 7.290857 ACTAATTTCTACGTATGTGCAACTG 57.709 36.000 0.00 0.00 38.04 3.16
1454 1470 8.668353 TGCAACTGATTTCTTATGAATACTGAC 58.332 33.333 0.00 0.00 31.56 3.51
1455 1471 8.668353 GCAACTGATTTCTTATGAATACTGACA 58.332 33.333 0.00 0.00 31.56 3.58
1457 1473 9.725019 AACTGATTTCTTATGAATACTGACACA 57.275 29.630 0.00 0.00 31.56 3.72
1478 1494 2.639839 ACCACTCCACTTGCTCTGTTAT 59.360 45.455 0.00 0.00 0.00 1.89
1488 1504 7.928167 TCCACTTGCTCTGTTATCATAATACTG 59.072 37.037 0.00 0.00 0.00 2.74
1489 1505 7.307632 CCACTTGCTCTGTTATCATAATACTGC 60.308 40.741 0.00 0.00 0.00 4.40
1491 1507 8.642432 ACTTGCTCTGTTATCATAATACTGCTA 58.358 33.333 0.00 0.00 0.00 3.49
1511 1527 9.749340 ACTGCTACTAAGGTAATTTTATTTGGT 57.251 29.630 0.00 0.00 0.00 3.67
1538 1571 2.810274 CCATATCCTCCATTGCAGTTCG 59.190 50.000 0.00 0.00 0.00 3.95
1568 1601 5.305585 GGAACATCCTCAACTTCACAACTA 58.694 41.667 0.00 0.00 32.53 2.24
1570 1603 5.290493 ACATCCTCAACTTCACAACTACA 57.710 39.130 0.00 0.00 0.00 2.74
1574 1607 3.809832 CCTCAACTTCACAACTACAGTGG 59.190 47.826 0.00 0.00 37.58 4.00
1619 1652 3.414272 GCATAGGCAGCGGAACAG 58.586 61.111 0.00 0.00 40.72 3.16
1620 1653 1.450312 GCATAGGCAGCGGAACAGT 60.450 57.895 0.00 0.00 40.72 3.55
1621 1654 0.179084 GCATAGGCAGCGGAACAGTA 60.179 55.000 0.00 0.00 40.72 2.74
1625 1658 2.399356 GGCAGCGGAACAGTAAGCC 61.399 63.158 0.00 0.00 0.00 4.35
1828 3019 7.157347 GCATTCTCATCTGTGGAGTTATATCA 58.843 38.462 0.00 0.00 34.04 2.15
1858 3049 1.744522 CATCACGGACCAATTGATGCA 59.255 47.619 7.12 0.00 40.04 3.96
1859 3050 1.164411 TCACGGACCAATTGATGCAC 58.836 50.000 7.12 0.00 0.00 4.57
1905 3096 2.435586 CCTTCCAGAGGCACTGCG 60.436 66.667 6.40 0.62 44.52 5.18
2302 3494 4.325972 TGCTGTATCATCAAGTGCAAAGA 58.674 39.130 0.00 0.00 0.00 2.52
2928 4132 3.659786 TCGTGTCATGACCTTTGGTTAG 58.340 45.455 22.85 4.25 35.25 2.34
3127 4334 4.901197 TCTTTGCTGGTACTCCATACAA 57.099 40.909 0.00 0.00 43.43 2.41
3130 4337 6.245408 TCTTTGCTGGTACTCCATACAATTT 58.755 36.000 0.00 0.00 43.43 1.82
3352 4669 9.127277 GATGGAGATACACTCTTAGACTTTACT 57.873 37.037 0.00 0.00 44.37 2.24
3397 4714 6.147328 CGCTTTGTTTTTAAGCTACTACTCCT 59.853 38.462 0.00 0.00 44.47 3.69
4184 5511 1.678101 GCTTTCAGCCTTTCACTGTGT 59.322 47.619 7.79 0.00 34.48 3.72
4217 5544 0.249868 TGCTTTCTCCCTGTGTGACG 60.250 55.000 0.00 0.00 0.00 4.35
4247 5574 8.734386 ACAAAATCAAATCACAGGTCTTATCTC 58.266 33.333 0.00 0.00 0.00 2.75
4267 5594 1.474077 CTTTTACCAGACATGCAGCCC 59.526 52.381 0.00 0.00 0.00 5.19
4268 5595 0.698238 TTTACCAGACATGCAGCCCT 59.302 50.000 0.00 0.00 0.00 5.19
4387 5714 7.665559 AGTGTAGATTTACTCATTTTTGCTCCA 59.334 33.333 0.00 0.00 0.00 3.86
4442 5769 6.159398 AGGCAAATATATAGGAATGGAGGGAG 59.841 42.308 0.00 0.00 0.00 4.30
4528 5862 0.035317 GACATCAGGTGTGGTGCTGA 59.965 55.000 0.00 0.00 42.36 4.26
4573 5907 2.185350 CGCCTGGCCAGTAGACAG 59.815 66.667 30.63 15.52 0.00 3.51
4594 5928 8.267894 AGACAGTTACCTGCATCTAACAATATT 58.732 33.333 13.42 0.00 42.81 1.28
4795 6130 2.571653 AGGCTTGTCTGGTTATGTAGCA 59.428 45.455 0.00 0.00 0.00 3.49
4937 6272 2.875933 TGTTTGCCCTGAAGAAACTACG 59.124 45.455 0.00 0.00 32.01 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.619332 CTTAGCCTATCCCCGTTCCTC 59.381 57.143 0.00 0.00 0.00 3.71
183 184 4.338539 ACAGACGCGTCCGGTCAC 62.339 66.667 34.08 9.84 39.22 3.67
203 204 1.674057 CTGGGGCGGATATGGAGAC 59.326 63.158 0.00 0.00 0.00 3.36
205 206 0.544357 TACCTGGGGCGGATATGGAG 60.544 60.000 0.00 0.00 0.00 3.86
207 208 0.253044 CATACCTGGGGCGGATATGG 59.747 60.000 0.00 0.00 0.00 2.74
219 220 2.291153 CCCCATATTCAGCCCATACCTG 60.291 54.545 0.00 0.00 0.00 4.00
223 224 2.644299 CAGTCCCCATATTCAGCCCATA 59.356 50.000 0.00 0.00 0.00 2.74
256 258 5.117897 CCATTTAAATTCGACCCAAACGTTG 59.882 40.000 0.00 0.00 0.00 4.10
257 259 5.224135 CCATTTAAATTCGACCCAAACGTT 58.776 37.500 0.00 0.00 0.00 3.99
270 272 4.525100 ACACCTAACCACGCCATTTAAATT 59.475 37.500 0.00 0.00 0.00 1.82
278 280 0.250793 CCATACACCTAACCACGCCA 59.749 55.000 0.00 0.00 0.00 5.69
288 290 2.816337 CGGACCCAAAAACCATACACCT 60.816 50.000 0.00 0.00 0.00 4.00
346 348 3.591254 AAAGCCCGACGAGCTGTCC 62.591 63.158 4.06 0.00 45.23 4.02
347 349 1.668151 AAAAGCCCGACGAGCTGTC 60.668 57.895 4.06 0.00 40.49 3.51
349 351 2.680913 CCAAAAGCCCGACGAGCTG 61.681 63.158 4.06 0.00 40.49 4.24
371 375 1.329171 TAACCGGACCACCCATACCG 61.329 60.000 9.46 0.00 44.16 4.02
564 568 2.167398 GAAGAGGTACACCGGCAGCA 62.167 60.000 0.00 0.00 42.08 4.41
601 605 4.029809 GAGGGGTTGGGGTGGTCG 62.030 72.222 0.00 0.00 0.00 4.79
602 606 3.658422 GGAGGGGTTGGGGTGGTC 61.658 72.222 0.00 0.00 0.00 4.02
610 614 1.971695 GTGAAAGGCGGAGGGGTTG 60.972 63.158 0.00 0.00 0.00 3.77
679 683 2.817844 AGAAACCAGTTGCCGGAATTAC 59.182 45.455 5.05 0.00 0.00 1.89
745 749 2.416547 CAGCGTGTACCCAGAATTTCTG 59.583 50.000 17.78 17.78 43.91 3.02
804 808 3.316588 ACAGACACAAACACACACACAAA 59.683 39.130 0.00 0.00 0.00 2.83
805 809 2.881513 ACAGACACAAACACACACACAA 59.118 40.909 0.00 0.00 0.00 3.33
806 810 2.225255 CACAGACACAAACACACACACA 59.775 45.455 0.00 0.00 0.00 3.72
807 811 2.225491 ACACAGACACAAACACACACAC 59.775 45.455 0.00 0.00 0.00 3.82
808 812 2.225255 CACACAGACACAAACACACACA 59.775 45.455 0.00 0.00 0.00 3.72
809 813 2.225491 ACACACAGACACAAACACACAC 59.775 45.455 0.00 0.00 0.00 3.82
810 814 2.225255 CACACACAGACACAAACACACA 59.775 45.455 0.00 0.00 0.00 3.72
811 815 2.225491 ACACACACAGACACAAACACAC 59.775 45.455 0.00 0.00 0.00 3.82
812 816 2.225255 CACACACACAGACACAAACACA 59.775 45.455 0.00 0.00 0.00 3.72
813 817 2.482336 TCACACACACAGACACAAACAC 59.518 45.455 0.00 0.00 0.00 3.32
814 818 2.772287 TCACACACACAGACACAAACA 58.228 42.857 0.00 0.00 0.00 2.83
815 819 3.435327 TCTTCACACACACAGACACAAAC 59.565 43.478 0.00 0.00 0.00 2.93
816 820 3.669536 TCTTCACACACACAGACACAAA 58.330 40.909 0.00 0.00 0.00 2.83
817 821 3.261580 CTCTTCACACACACAGACACAA 58.738 45.455 0.00 0.00 0.00 3.33
818 822 2.418609 CCTCTTCACACACACAGACACA 60.419 50.000 0.00 0.00 0.00 3.72
819 823 2.205074 CCTCTTCACACACACAGACAC 58.795 52.381 0.00 0.00 0.00 3.67
820 824 1.138859 CCCTCTTCACACACACAGACA 59.861 52.381 0.00 0.00 0.00 3.41
821 825 1.541233 CCCCTCTTCACACACACAGAC 60.541 57.143 0.00 0.00 0.00 3.51
822 826 0.758734 CCCCTCTTCACACACACAGA 59.241 55.000 0.00 0.00 0.00 3.41
823 827 0.250467 CCCCCTCTTCACACACACAG 60.250 60.000 0.00 0.00 0.00 3.66
842 846 2.119611 CCAAACCCTCCCCCAACC 59.880 66.667 0.00 0.00 0.00 3.77
844 848 2.037128 TCCCAAACCCTCCCCCAA 60.037 61.111 0.00 0.00 0.00 4.12
845 849 2.534272 CTCCCAAACCCTCCCCCA 60.534 66.667 0.00 0.00 0.00 4.96
846 850 4.062032 GCTCCCAAACCCTCCCCC 62.062 72.222 0.00 0.00 0.00 5.40
848 852 1.304464 CAAGCTCCCAAACCCTCCC 60.304 63.158 0.00 0.00 0.00 4.30
849 853 0.322906 CTCAAGCTCCCAAACCCTCC 60.323 60.000 0.00 0.00 0.00 4.30
850 854 0.402121 ACTCAAGCTCCCAAACCCTC 59.598 55.000 0.00 0.00 0.00 4.30
851 855 0.853530 AACTCAAGCTCCCAAACCCT 59.146 50.000 0.00 0.00 0.00 4.34
852 856 1.202940 AGAACTCAAGCTCCCAAACCC 60.203 52.381 0.00 0.00 0.00 4.11
853 857 2.278332 AGAACTCAAGCTCCCAAACC 57.722 50.000 0.00 0.00 0.00 3.27
854 858 5.003804 TCATAAGAACTCAAGCTCCCAAAC 58.996 41.667 0.00 0.00 0.00 2.93
855 859 5.241403 TCATAAGAACTCAAGCTCCCAAA 57.759 39.130 0.00 0.00 0.00 3.28
856 860 4.908601 TCATAAGAACTCAAGCTCCCAA 57.091 40.909 0.00 0.00 0.00 4.12
857 861 4.908601 TTCATAAGAACTCAAGCTCCCA 57.091 40.909 0.00 0.00 0.00 4.37
858 862 6.765915 ATTTTCATAAGAACTCAAGCTCCC 57.234 37.500 0.00 0.00 32.39 4.30
859 863 8.084684 ACAAATTTTCATAAGAACTCAAGCTCC 58.915 33.333 0.00 0.00 32.39 4.70
860 864 9.468532 AACAAATTTTCATAAGAACTCAAGCTC 57.531 29.630 0.00 0.00 32.39 4.09
1237 1253 3.007506 TCGTTTGCTGTAATTCCCTCAGA 59.992 43.478 0.00 0.00 0.00 3.27
1239 1255 3.410631 TCGTTTGCTGTAATTCCCTCA 57.589 42.857 0.00 0.00 0.00 3.86
1321 1337 1.739562 CAGTCGCTGGTTCCTCTGC 60.740 63.158 0.00 0.00 0.00 4.26
1322 1338 0.534412 ATCAGTCGCTGGTTCCTCTG 59.466 55.000 6.95 0.00 31.51 3.35
1323 1339 0.820871 GATCAGTCGCTGGTTCCTCT 59.179 55.000 6.95 0.00 31.51 3.69
1324 1340 0.820871 AGATCAGTCGCTGGTTCCTC 59.179 55.000 0.00 0.00 31.51 3.71
1325 1341 0.534412 CAGATCAGTCGCTGGTTCCT 59.466 55.000 0.00 0.00 31.51 3.36
1326 1342 1.086634 GCAGATCAGTCGCTGGTTCC 61.087 60.000 0.00 0.00 32.83 3.62
1327 1343 0.108424 AGCAGATCAGTCGCTGGTTC 60.108 55.000 0.00 5.30 39.60 3.62
1328 1344 0.322975 AAGCAGATCAGTCGCTGGTT 59.677 50.000 0.00 0.00 45.03 3.67
1329 1345 0.390866 CAAGCAGATCAGTCGCTGGT 60.391 55.000 0.00 0.00 43.96 4.00
1330 1346 1.088340 CCAAGCAGATCAGTCGCTGG 61.088 60.000 0.00 0.00 35.47 4.85
1331 1347 0.108472 TCCAAGCAGATCAGTCGCTG 60.108 55.000 0.00 1.02 35.47 5.18
1332 1348 0.175302 CTCCAAGCAGATCAGTCGCT 59.825 55.000 0.00 0.00 36.34 4.93
1333 1349 0.174389 TCTCCAAGCAGATCAGTCGC 59.826 55.000 0.00 0.00 0.00 5.19
1334 1350 1.470632 GGTCTCCAAGCAGATCAGTCG 60.471 57.143 0.00 0.00 0.00 4.18
1335 1351 1.830477 AGGTCTCCAAGCAGATCAGTC 59.170 52.381 0.00 0.00 0.00 3.51
1336 1352 1.949799 AGGTCTCCAAGCAGATCAGT 58.050 50.000 0.00 0.00 0.00 3.41
1337 1353 2.419851 GGAAGGTCTCCAAGCAGATCAG 60.420 54.545 0.00 0.00 44.67 2.90
1338 1354 1.556911 GGAAGGTCTCCAAGCAGATCA 59.443 52.381 0.00 0.00 44.67 2.92
1339 1355 2.323968 GGAAGGTCTCCAAGCAGATC 57.676 55.000 0.00 0.00 44.67 2.75
1354 1370 7.731054 AGATTTTAGCATAGTACCTCTGGAAG 58.269 38.462 0.00 0.00 0.00 3.46
1355 1371 7.676683 AGATTTTAGCATAGTACCTCTGGAA 57.323 36.000 0.00 0.00 0.00 3.53
1356 1372 7.125811 ACAAGATTTTAGCATAGTACCTCTGGA 59.874 37.037 0.00 0.00 0.00 3.86
1357 1373 7.225538 CACAAGATTTTAGCATAGTACCTCTGG 59.774 40.741 0.00 0.00 0.00 3.86
1358 1374 7.254590 GCACAAGATTTTAGCATAGTACCTCTG 60.255 40.741 0.00 0.00 0.00 3.35
1359 1375 6.763610 GCACAAGATTTTAGCATAGTACCTCT 59.236 38.462 0.00 0.00 0.00 3.69
1360 1376 6.763610 AGCACAAGATTTTAGCATAGTACCTC 59.236 38.462 0.00 0.00 0.00 3.85
1361 1377 6.653989 AGCACAAGATTTTAGCATAGTACCT 58.346 36.000 0.00 0.00 0.00 3.08
1362 1378 6.017852 GGAGCACAAGATTTTAGCATAGTACC 60.018 42.308 0.00 0.00 0.00 3.34
1363 1379 6.538742 TGGAGCACAAGATTTTAGCATAGTAC 59.461 38.462 0.00 0.00 0.00 2.73
1364 1380 6.649155 TGGAGCACAAGATTTTAGCATAGTA 58.351 36.000 0.00 0.00 0.00 1.82
1365 1381 5.500234 TGGAGCACAAGATTTTAGCATAGT 58.500 37.500 0.00 0.00 0.00 2.12
1366 1382 5.505324 GCTGGAGCACAAGATTTTAGCATAG 60.505 44.000 0.00 0.00 41.59 2.23
1367 1383 4.336433 GCTGGAGCACAAGATTTTAGCATA 59.664 41.667 0.00 0.00 41.59 3.14
1368 1384 3.129988 GCTGGAGCACAAGATTTTAGCAT 59.870 43.478 0.00 0.00 41.59 3.79
1369 1385 2.489329 GCTGGAGCACAAGATTTTAGCA 59.511 45.455 0.00 0.00 41.59 3.49
1370 1386 2.159324 GGCTGGAGCACAAGATTTTAGC 60.159 50.000 0.20 0.00 44.36 3.09
1371 1387 2.424956 GGGCTGGAGCACAAGATTTTAG 59.575 50.000 0.20 0.00 45.57 1.85
1372 1388 2.446435 GGGCTGGAGCACAAGATTTTA 58.554 47.619 0.20 0.00 45.57 1.52
1373 1389 1.260544 GGGCTGGAGCACAAGATTTT 58.739 50.000 0.20 0.00 45.57 1.82
1374 1390 2.967270 GGGCTGGAGCACAAGATTT 58.033 52.632 0.20 0.00 45.57 2.17
1375 1391 4.751431 GGGCTGGAGCACAAGATT 57.249 55.556 0.20 0.00 45.57 2.40
1388 1404 0.825010 CTGCAACCAACAGAAGGGCT 60.825 55.000 0.00 0.00 37.32 5.19
1389 1405 0.823356 TCTGCAACCAACAGAAGGGC 60.823 55.000 0.00 0.00 41.10 5.19
1390 1406 1.915141 ATCTGCAACCAACAGAAGGG 58.085 50.000 0.00 0.00 46.63 3.95
1391 1407 4.074970 AGTAATCTGCAACCAACAGAAGG 58.925 43.478 0.00 0.00 46.63 3.46
1392 1408 6.801539 TTAGTAATCTGCAACCAACAGAAG 57.198 37.500 0.00 0.00 46.63 2.85
1393 1409 7.759489 AATTAGTAATCTGCAACCAACAGAA 57.241 32.000 0.00 0.00 46.63 3.02
1395 1411 7.820648 AGAAATTAGTAATCTGCAACCAACAG 58.179 34.615 0.00 0.00 36.44 3.16
1396 1412 7.759489 AGAAATTAGTAATCTGCAACCAACA 57.241 32.000 0.00 0.00 0.00 3.33
1397 1413 7.903431 CGTAGAAATTAGTAATCTGCAACCAAC 59.097 37.037 0.00 0.00 0.00 3.77
1398 1414 7.604927 ACGTAGAAATTAGTAATCTGCAACCAA 59.395 33.333 0.00 0.00 0.00 3.67
1399 1415 7.101054 ACGTAGAAATTAGTAATCTGCAACCA 58.899 34.615 0.00 0.00 0.00 3.67
1400 1416 7.535489 ACGTAGAAATTAGTAATCTGCAACC 57.465 36.000 0.00 0.00 0.00 3.77
1402 1418 9.811995 ACATACGTAGAAATTAGTAATCTGCAA 57.188 29.630 0.08 0.00 0.00 4.08
1403 1419 9.244799 CACATACGTAGAAATTAGTAATCTGCA 57.755 33.333 0.08 0.00 0.00 4.41
1404 1420 8.215132 GCACATACGTAGAAATTAGTAATCTGC 58.785 37.037 0.08 0.00 0.00 4.26
1405 1421 9.244799 TGCACATACGTAGAAATTAGTAATCTG 57.755 33.333 0.08 0.00 0.00 2.90
1406 1422 9.811995 TTGCACATACGTAGAAATTAGTAATCT 57.188 29.630 0.08 0.00 0.00 2.40
1407 1423 9.845305 GTTGCACATACGTAGAAATTAGTAATC 57.155 33.333 0.08 0.00 0.00 1.75
1408 1424 9.595823 AGTTGCACATACGTAGAAATTAGTAAT 57.404 29.630 0.08 0.00 0.00 1.89
1409 1425 8.865978 CAGTTGCACATACGTAGAAATTAGTAA 58.134 33.333 0.08 0.00 0.00 2.24
1415 1431 6.985188 AATCAGTTGCACATACGTAGAAAT 57.015 33.333 0.08 0.00 0.00 2.17
1425 1441 9.182214 AGTATTCATAAGAAATCAGTTGCACAT 57.818 29.630 0.00 0.00 37.29 3.21
1435 1451 8.391106 GTGGTGTGTCAGTATTCATAAGAAATC 58.609 37.037 0.00 0.00 37.29 2.17
1450 1466 1.586422 CAAGTGGAGTGGTGTGTCAG 58.414 55.000 0.00 0.00 0.00 3.51
1454 1470 0.107456 AGAGCAAGTGGAGTGGTGTG 59.893 55.000 0.00 0.00 0.00 3.82
1455 1471 0.107456 CAGAGCAAGTGGAGTGGTGT 59.893 55.000 0.00 0.00 0.00 4.16
1457 1473 0.839946 AACAGAGCAAGTGGAGTGGT 59.160 50.000 0.00 0.00 0.00 4.16
1501 1517 8.977412 GGAGGATATGGAGAAAACCAAATAAAA 58.023 33.333 0.00 0.00 43.47 1.52
1502 1518 8.119246 TGGAGGATATGGAGAAAACCAAATAAA 58.881 33.333 0.00 0.00 43.47 1.40
1503 1519 7.647827 TGGAGGATATGGAGAAAACCAAATAA 58.352 34.615 0.00 0.00 43.47 1.40
1504 1520 7.219601 TGGAGGATATGGAGAAAACCAAATA 57.780 36.000 0.00 0.00 43.47 1.40
1505 1521 6.091076 TGGAGGATATGGAGAAAACCAAAT 57.909 37.500 0.00 0.00 43.47 2.32
1506 1522 5.528600 TGGAGGATATGGAGAAAACCAAA 57.471 39.130 0.00 0.00 43.47 3.28
1508 1524 5.448654 CAATGGAGGATATGGAGAAAACCA 58.551 41.667 0.00 0.00 44.41 3.67
1509 1525 4.279420 GCAATGGAGGATATGGAGAAAACC 59.721 45.833 0.00 0.00 0.00 3.27
1510 1526 4.889409 TGCAATGGAGGATATGGAGAAAAC 59.111 41.667 0.00 0.00 0.00 2.43
1511 1527 5.128033 TGCAATGGAGGATATGGAGAAAA 57.872 39.130 0.00 0.00 0.00 2.29
1512 1528 4.166725 ACTGCAATGGAGGATATGGAGAAA 59.833 41.667 6.73 0.00 35.51 2.52
1513 1529 3.718434 ACTGCAATGGAGGATATGGAGAA 59.282 43.478 6.73 0.00 35.51 2.87
1514 1530 3.321039 ACTGCAATGGAGGATATGGAGA 58.679 45.455 6.73 0.00 35.51 3.71
1516 1532 3.494924 CGAACTGCAATGGAGGATATGGA 60.495 47.826 6.73 0.00 0.00 3.41
1518 1534 2.810274 CCGAACTGCAATGGAGGATATG 59.190 50.000 6.73 0.00 0.00 1.78
1519 1535 2.705658 TCCGAACTGCAATGGAGGATAT 59.294 45.455 6.73 0.00 0.00 1.63
1521 1537 0.911769 TCCGAACTGCAATGGAGGAT 59.088 50.000 6.73 0.00 0.00 3.24
1523 1539 1.402968 CATTCCGAACTGCAATGGAGG 59.597 52.381 6.73 0.00 0.00 4.30
1524 1540 2.838386 CATTCCGAACTGCAATGGAG 57.162 50.000 0.00 0.00 0.00 3.86
1538 1571 2.024941 AGTTGAGGATGTTCCCCATTCC 60.025 50.000 0.00 0.00 37.19 3.01
1568 1601 3.909662 GCAATGATCGGCCACTGT 58.090 55.556 2.24 0.00 0.00 3.55
1574 1607 0.313043 CTTGGATGGCAATGATCGGC 59.687 55.000 0.00 0.00 0.00 5.54
1604 1637 1.473434 GCTTACTGTTCCGCTGCCTAT 60.473 52.381 0.00 0.00 0.00 2.57
1605 1638 0.108329 GCTTACTGTTCCGCTGCCTA 60.108 55.000 0.00 0.00 0.00 3.93
1625 1658 1.337817 CTCAACGGTTCGAGCTGACG 61.338 60.000 15.62 4.98 0.00 4.35
1683 2874 2.336945 TCGATGGAATGCTTCATGCT 57.663 45.000 0.00 0.00 43.37 3.79
1846 3037 4.679639 GCTGATTCATGTGCATCAATTGGT 60.680 41.667 5.42 0.00 27.98 3.67
1858 3049 4.449131 ACAGATCAATCGCTGATTCATGT 58.551 39.130 0.00 5.21 45.23 3.21
1859 3050 5.419760 AACAGATCAATCGCTGATTCATG 57.580 39.130 0.00 0.00 45.23 3.07
1905 3096 1.064654 GATGGAGCACGAGATTTTGGC 59.935 52.381 0.00 0.00 0.00 4.52
2302 3494 7.721402 TGTGGTGCTAAATCAAAAACTAATGT 58.279 30.769 0.00 0.00 0.00 2.71
2906 4109 2.631160 ACCAAAGGTCATGACACGAA 57.369 45.000 26.47 0.00 0.00 3.85
3352 4669 3.188460 GCGAGTTGGATAAAGAACAGCAA 59.812 43.478 0.00 0.00 32.05 3.91
3397 4714 6.349243 ACGATGTTATATTATGGGACGGAA 57.651 37.500 0.00 0.00 0.00 4.30
3703 5030 0.531974 TGTTGAACAGACACTCCGGC 60.532 55.000 0.00 0.00 0.00 6.13
4104 5431 4.496175 GGAGTACTGTAGAGAAGCGCTAAC 60.496 50.000 12.05 8.57 0.00 2.34
4184 5511 5.360714 GGGAGAAAGCATATGTCATCCAAAA 59.639 40.000 4.29 0.00 0.00 2.44
4217 5544 6.970484 AGACCTGTGATTTGATTTTGTACAC 58.030 36.000 0.00 0.00 0.00 2.90
4247 5574 1.474077 GGGCTGCATGTCTGGTAAAAG 59.526 52.381 0.50 0.00 0.00 2.27
4267 5594 4.220163 ACGGAGGGAGTAAAACAACTAGAG 59.780 45.833 0.00 0.00 0.00 2.43
4268 5595 4.154942 ACGGAGGGAGTAAAACAACTAGA 58.845 43.478 0.00 0.00 0.00 2.43
4371 5698 9.625747 TGAATACATATGGAGCAAAAATGAGTA 57.374 29.630 7.80 0.00 0.00 2.59
4394 5721 8.352942 GCCTTTCTAGAGATTTCAAAAAGTGAA 58.647 33.333 0.00 0.00 44.74 3.18
4396 5723 7.651808 TGCCTTTCTAGAGATTTCAAAAAGTG 58.348 34.615 0.00 0.00 0.00 3.16
4419 5746 6.963322 ACTCCCTCCATTCCTATATATTTGC 58.037 40.000 0.00 0.00 0.00 3.68
4427 5754 8.582891 AAAAATACTACTCCCTCCATTCCTAT 57.417 34.615 0.00 0.00 0.00 2.57
4453 5780 1.822990 CAAGTAGGAGACGGCAAGGTA 59.177 52.381 0.00 0.00 0.00 3.08
4528 5862 0.250381 TTGTGCGACCGGGTAACATT 60.250 50.000 6.32 0.00 39.74 2.71
4573 5907 7.026631 TGCAATATTGTTAGATGCAGGTAAC 57.973 36.000 16.61 12.13 41.67 2.50
4594 5928 9.208022 GTATAGTAATATTGTGCTCAAGATGCA 57.792 33.333 9.20 0.00 35.94 3.96
4814 6149 3.799366 ACATACGGACTGTCAAACACAA 58.201 40.909 10.38 0.00 33.31 3.33
4829 6164 1.529438 ACAGCGGTGTTTTGACATACG 59.471 47.619 15.81 0.00 30.30 3.06


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

AutoCloner maintained by Alex Coulton.