Multiple sequence alignment - TraesCS7D01G132400

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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 TraesCS7D01G132400 chr7D 100.000 2750 0 0 1 2750 83756601 83753852 0.000000e+00 5079.0
1 TraesCS7D01G132400 chr7D 81.888 784 83 36 1980 2750 586745076 586744339 8.420000e-170 606.0
2 TraesCS7D01G132400 chr7D 87.500 544 43 13 723 1256 83664248 83663720 3.030000e-169 604.0
3 TraesCS7D01G132400 chr7D 82.267 547 66 18 1425 1953 83663563 83663030 6.990000e-121 444.0
4 TraesCS7D01G132400 chr7D 82.035 462 71 8 2292 2747 365258866 365258411 1.550000e-102 383.0
5 TraesCS7D01G132400 chr7D 87.273 110 12 2 1627 1734 130924005 130923896 1.030000e-24 124.0
6 TraesCS7D01G132400 chr7A 86.239 1279 91 39 722 1971 85413303 85412081 0.000000e+00 1308.0
7 TraesCS7D01G132400 chr7A 82.840 979 88 35 983 1891 85348028 85347060 0.000000e+00 804.0
8 TraesCS7D01G132400 chr7A 80.980 510 49 25 159 661 85413996 85413528 7.240000e-96 361.0
9 TraesCS7D01G132400 chr7A 89.381 113 11 1 1623 1734 129704239 129704127 1.030000e-29 141.0
10 TraesCS7D01G132400 chr7B 83.416 1007 110 32 983 1953 33415301 33414316 0.000000e+00 881.0
11 TraesCS7D01G132400 chr7B 86.676 713 46 25 667 1340 33529586 33528884 0.000000e+00 745.0
12 TraesCS7D01G132400 chr7B 91.709 398 26 5 1494 1885 33528730 33528334 1.860000e-151 545.0
13 TraesCS7D01G132400 chr7B 75.232 646 134 19 1978 2610 707636686 707637318 1.610000e-72 283.0
14 TraesCS7D01G132400 chr7B 88.889 216 21 2 72 284 33530127 33529912 2.100000e-66 263.0
15 TraesCS7D01G132400 chr7B 80.240 334 30 17 328 661 33529917 33529620 4.610000e-53 219.0
16 TraesCS7D01G132400 chr7B 86.567 134 15 3 1622 1752 92014634 92014501 7.940000e-31 145.0
17 TraesCS7D01G132400 chr7B 90.741 54 2 3 1983 2035 361162782 361162731 4.910000e-08 69.4
18 TraesCS7D01G132400 chr5B 84.772 788 73 22 1982 2750 644885101 644884342 0.000000e+00 747.0
19 TraesCS7D01G132400 chr5B 80.029 696 87 24 2060 2750 97513022 97513670 4.150000e-128 468.0
20 TraesCS7D01G132400 chr5B 81.329 557 74 17 2203 2750 113448669 113448134 2.530000e-115 425.0
21 TraesCS7D01G132400 chr5D 82.949 780 97 21 1978 2750 370945866 370945116 0.000000e+00 671.0
22 TraesCS7D01G132400 chr5D 80.426 705 83 27 2050 2750 92170432 92171085 1.140000e-133 486.0
23 TraesCS7D01G132400 chr3A 89.521 334 27 7 2422 2750 883957 884287 1.520000e-112 416.0
24 TraesCS7D01G132400 chr3A 96.078 51 2 0 1978 2028 736247732 736247782 1.750000e-12 84.2
25 TraesCS7D01G132400 chr3A 85.526 76 9 2 2220 2294 205685496 205685422 8.170000e-11 78.7
26 TraesCS7D01G132400 chr3D 85.156 384 49 4 2369 2747 39592962 39593342 1.190000e-103 387.0
27 TraesCS7D01G132400 chr5A 86.377 345 39 6 2412 2750 358482684 358483026 1.200000e-98 370.0
28 TraesCS7D01G132400 chr5A 94.595 37 2 0 2012 2048 695764754 695764790 1.060000e-04 58.4
29 TraesCS7D01G132400 chr3B 82.727 440 47 7 2317 2750 766800034 766800450 5.600000e-97 364.0
30 TraesCS7D01G132400 chr3B 85.882 85 12 0 2076 2160 16402251 16402167 1.050000e-14 91.6
31 TraesCS7D01G132400 chr6A 84.475 219 29 5 1978 2192 594465145 594465362 7.720000e-51 211.0
32 TraesCS7D01G132400 chr6A 75.152 165 28 10 2036 2196 19765284 19765439 6.360000e-07 65.8
33 TraesCS7D01G132400 chr2B 100.000 29 0 0 2012 2040 198641499 198641527 1.000000e-03 54.7


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 TraesCS7D01G132400 chr7D 83753852 83756601 2749 True 5079.0 5079 100.0000 1 2750 1 chr7D.!!$R1 2749
1 TraesCS7D01G132400 chr7D 586744339 586745076 737 True 606.0 606 81.8880 1980 2750 1 chr7D.!!$R4 770
2 TraesCS7D01G132400 chr7D 83663030 83664248 1218 True 524.0 604 84.8835 723 1953 2 chr7D.!!$R5 1230
3 TraesCS7D01G132400 chr7A 85412081 85413996 1915 True 834.5 1308 83.6095 159 1971 2 chr7A.!!$R3 1812
4 TraesCS7D01G132400 chr7A 85347060 85348028 968 True 804.0 804 82.8400 983 1891 1 chr7A.!!$R1 908
5 TraesCS7D01G132400 chr7B 33414316 33415301 985 True 881.0 881 83.4160 983 1953 1 chr7B.!!$R1 970
6 TraesCS7D01G132400 chr7B 33528334 33530127 1793 True 443.0 745 86.8785 72 1885 4 chr7B.!!$R4 1813
7 TraesCS7D01G132400 chr7B 707636686 707637318 632 False 283.0 283 75.2320 1978 2610 1 chr7B.!!$F1 632
8 TraesCS7D01G132400 chr5B 644884342 644885101 759 True 747.0 747 84.7720 1982 2750 1 chr5B.!!$R2 768
9 TraesCS7D01G132400 chr5B 97513022 97513670 648 False 468.0 468 80.0290 2060 2750 1 chr5B.!!$F1 690
10 TraesCS7D01G132400 chr5B 113448134 113448669 535 True 425.0 425 81.3290 2203 2750 1 chr5B.!!$R1 547
11 TraesCS7D01G132400 chr5D 370945116 370945866 750 True 671.0 671 82.9490 1978 2750 1 chr5D.!!$R1 772
12 TraesCS7D01G132400 chr5D 92170432 92171085 653 False 486.0 486 80.4260 2050 2750 1 chr5D.!!$F1 700

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
44 45 0.031585 TCGAGTGGTTGGTTCGTGAG 59.968 55.0 0.0 0.0 35.9 3.51 F
45 46 0.031585 CGAGTGGTTGGTTCGTGAGA 59.968 55.0 0.0 0.0 39.2 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1717 0.036952 CCTGACATCGAAGCCTGTGT 60.037 55.0 0.00 0.0 0.0 3.72 R
1790 2185 0.458260 AACAACAAAAGCCACCGGTC 59.542 50.0 2.59 0.0 0.0 4.79 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
18 19 3.102515 CGTAGTCTGGGTTCACGTG 57.897 57.895 9.94 9.94 0.00 4.49
19 20 1.007336 CGTAGTCTGGGTTCACGTGC 61.007 60.000 11.67 0.00 0.00 5.34
20 21 1.007336 GTAGTCTGGGTTCACGTGCG 61.007 60.000 11.67 0.00 0.00 5.34
21 22 1.174078 TAGTCTGGGTTCACGTGCGA 61.174 55.000 11.67 0.00 0.00 5.10
22 23 2.022129 GTCTGGGTTCACGTGCGAG 61.022 63.158 11.67 3.96 0.00 5.03
23 24 2.029073 CTGGGTTCACGTGCGAGT 59.971 61.111 11.67 0.00 0.00 4.18
24 25 2.279851 TGGGTTCACGTGCGAGTG 60.280 61.111 11.67 5.15 43.11 3.51
25 26 2.279918 GGGTTCACGTGCGAGTGT 60.280 61.111 11.67 0.00 42.40 3.55
26 27 2.308039 GGGTTCACGTGCGAGTGTC 61.308 63.158 11.67 6.17 42.40 3.67
27 28 2.645510 GGTTCACGTGCGAGTGTCG 61.646 63.158 11.67 0.00 43.89 4.35
28 29 1.656263 GTTCACGTGCGAGTGTCGA 60.656 57.895 11.67 0.00 43.74 4.20
29 30 1.370051 TTCACGTGCGAGTGTCGAG 60.370 57.895 11.67 0.00 43.74 4.04
30 31 2.051256 CACGTGCGAGTGTCGAGT 60.051 61.111 0.82 0.00 43.74 4.18
31 32 2.051256 ACGTGCGAGTGTCGAGTG 60.051 61.111 0.00 0.00 43.74 3.51
32 33 2.801162 CGTGCGAGTGTCGAGTGG 60.801 66.667 0.00 0.00 43.74 4.00
33 34 2.335369 GTGCGAGTGTCGAGTGGT 59.665 61.111 0.00 0.00 43.74 4.16
34 35 1.299926 GTGCGAGTGTCGAGTGGTT 60.300 57.895 0.00 0.00 43.74 3.67
35 36 1.299850 TGCGAGTGTCGAGTGGTTG 60.300 57.895 0.00 0.00 43.74 3.77
36 37 2.022129 GCGAGTGTCGAGTGGTTGG 61.022 63.158 0.00 0.00 43.74 3.77
37 38 1.362717 CGAGTGTCGAGTGGTTGGT 59.637 57.895 0.00 0.00 43.74 3.67
38 39 0.249322 CGAGTGTCGAGTGGTTGGTT 60.249 55.000 0.00 0.00 43.74 3.67
39 40 1.499049 GAGTGTCGAGTGGTTGGTTC 58.501 55.000 0.00 0.00 0.00 3.62
40 41 0.249322 AGTGTCGAGTGGTTGGTTCG 60.249 55.000 0.00 0.00 35.76 3.95
41 42 0.529119 GTGTCGAGTGGTTGGTTCGT 60.529 55.000 0.00 0.00 35.90 3.85
42 43 0.528901 TGTCGAGTGGTTGGTTCGTG 60.529 55.000 0.00 0.00 35.90 4.35
43 44 0.249155 GTCGAGTGGTTGGTTCGTGA 60.249 55.000 0.00 0.00 35.90 4.35
44 45 0.031585 TCGAGTGGTTGGTTCGTGAG 59.968 55.000 0.00 0.00 35.90 3.51
45 46 0.031585 CGAGTGGTTGGTTCGTGAGA 59.968 55.000 0.00 0.00 39.20 3.27
46 47 1.499049 GAGTGGTTGGTTCGTGAGAC 58.501 55.000 0.00 0.00 41.84 3.36
47 48 1.068741 GAGTGGTTGGTTCGTGAGACT 59.931 52.381 0.00 0.00 41.84 3.24
48 49 1.068741 AGTGGTTGGTTCGTGAGACTC 59.931 52.381 0.00 0.00 41.84 3.36
49 50 0.031585 TGGTTGGTTCGTGAGACTCG 59.968 55.000 0.00 0.00 41.84 4.18
50 51 1.282930 GGTTGGTTCGTGAGACTCGC 61.283 60.000 5.91 5.91 41.84 5.03
51 52 0.596600 GTTGGTTCGTGAGACTCGCA 60.597 55.000 15.98 0.97 41.84 5.10
52 53 0.596600 TTGGTTCGTGAGACTCGCAC 60.597 55.000 15.98 7.30 41.84 5.34
53 54 1.733399 GGTTCGTGAGACTCGCACC 60.733 63.158 15.98 12.34 41.84 5.01
54 55 1.286260 GTTCGTGAGACTCGCACCT 59.714 57.895 15.98 0.00 41.84 4.00
55 56 0.520404 GTTCGTGAGACTCGCACCTA 59.480 55.000 15.98 0.00 41.84 3.08
56 57 0.803117 TTCGTGAGACTCGCACCTAG 59.197 55.000 15.98 0.00 41.84 3.02
57 58 0.321387 TCGTGAGACTCGCACCTAGT 60.321 55.000 15.98 0.00 30.67 2.57
58 59 0.097325 CGTGAGACTCGCACCTAGTC 59.903 60.000 15.98 0.00 43.06 2.59
59 60 1.166129 GTGAGACTCGCACCTAGTCA 58.834 55.000 11.19 0.00 44.77 3.41
60 61 1.746220 GTGAGACTCGCACCTAGTCAT 59.254 52.381 11.19 0.00 44.77 3.06
61 62 2.943690 GTGAGACTCGCACCTAGTCATA 59.056 50.000 11.19 0.00 44.77 2.15
62 63 3.002862 GTGAGACTCGCACCTAGTCATAG 59.997 52.174 11.19 0.00 44.77 2.23
63 64 1.950909 AGACTCGCACCTAGTCATAGC 59.049 52.381 6.06 0.00 44.77 2.97
64 65 1.676529 GACTCGCACCTAGTCATAGCA 59.323 52.381 0.00 0.00 42.43 3.49
65 66 1.678627 ACTCGCACCTAGTCATAGCAG 59.321 52.381 0.00 0.00 0.00 4.24
66 67 1.950216 CTCGCACCTAGTCATAGCAGA 59.050 52.381 0.00 0.00 0.00 4.26
67 68 1.950216 TCGCACCTAGTCATAGCAGAG 59.050 52.381 0.00 0.00 0.00 3.35
68 69 1.950216 CGCACCTAGTCATAGCAGAGA 59.050 52.381 0.00 0.00 0.00 3.10
69 70 2.287308 CGCACCTAGTCATAGCAGAGAC 60.287 54.545 0.00 0.00 35.02 3.36
70 71 2.287308 GCACCTAGTCATAGCAGAGACG 60.287 54.545 0.00 0.00 39.67 4.18
86 87 3.378427 AGAGACGCTAATTTTGGGATTGC 59.622 43.478 2.19 0.00 0.00 3.56
88 89 1.199624 CGCTAATTTTGGGATTGCGC 58.800 50.000 0.00 0.00 33.44 6.09
91 92 2.417243 GCTAATTTTGGGATTGCGCTGT 60.417 45.455 9.73 0.00 0.00 4.40
92 93 2.083167 AATTTTGGGATTGCGCTGTG 57.917 45.000 9.73 0.00 0.00 3.66
95 96 0.527113 TTTGGGATTGCGCTGTGATG 59.473 50.000 9.73 0.00 0.00 3.07
102 103 2.821366 GCGCTGTGATGGGAGGTG 60.821 66.667 0.00 0.00 0.00 4.00
105 106 1.679311 GCTGTGATGGGAGGTGTGA 59.321 57.895 0.00 0.00 0.00 3.58
185 188 1.217585 CGCGGTGGTGATCATGCTAG 61.218 60.000 0.00 0.00 0.00 3.42
199 202 9.362539 GTGATCATGCTAGTTTGAAATGAATTT 57.637 29.630 0.00 0.00 31.49 1.82
220 223 6.569179 TTTCTGATGTAGCCAAAAGTTACC 57.431 37.500 0.00 0.00 31.49 2.85
223 226 6.065374 TCTGATGTAGCCAAAAGTTACCAAA 58.935 36.000 0.00 0.00 31.49 3.28
253 257 3.060473 GTGTCTGCTGTTGACGTAGAAAC 60.060 47.826 0.00 0.00 37.26 2.78
284 338 7.309438 GGTTCATATGGCTCTTTCACTTCTTTT 60.309 37.037 2.13 0.00 0.00 2.27
286 340 7.596494 TCATATGGCTCTTTCACTTCTTTTTG 58.404 34.615 2.13 0.00 0.00 2.44
287 341 4.045636 TGGCTCTTTCACTTCTTTTTGC 57.954 40.909 0.00 0.00 0.00 3.68
288 342 3.045688 GGCTCTTTCACTTCTTTTTGCG 58.954 45.455 0.00 0.00 0.00 4.85
290 344 3.632189 CTCTTTCACTTCTTTTTGCGGG 58.368 45.455 0.00 0.00 0.00 6.13
291 345 3.020984 TCTTTCACTTCTTTTTGCGGGT 58.979 40.909 0.00 0.00 0.00 5.28
292 346 2.861462 TTCACTTCTTTTTGCGGGTG 57.139 45.000 0.00 0.00 0.00 4.61
293 347 1.028905 TCACTTCTTTTTGCGGGTGG 58.971 50.000 0.00 0.00 0.00 4.61
294 348 0.597377 CACTTCTTTTTGCGGGTGGC 60.597 55.000 0.00 0.00 43.96 5.01
296 350 0.039165 CTTCTTTTTGCGGGTGGCTC 60.039 55.000 0.00 0.00 44.05 4.70
297 351 0.467290 TTCTTTTTGCGGGTGGCTCT 60.467 50.000 0.00 0.00 44.05 4.09
298 352 0.467290 TCTTTTTGCGGGTGGCTCTT 60.467 50.000 0.00 0.00 44.05 2.85
299 353 0.389025 CTTTTTGCGGGTGGCTCTTT 59.611 50.000 0.00 0.00 44.05 2.52
300 354 0.387565 TTTTTGCGGGTGGCTCTTTC 59.612 50.000 0.00 0.00 44.05 2.62
301 355 0.753479 TTTTGCGGGTGGCTCTTTCA 60.753 50.000 0.00 0.00 44.05 2.69
302 356 1.452145 TTTGCGGGTGGCTCTTTCAC 61.452 55.000 0.00 0.00 44.05 3.18
303 357 2.281484 GCGGGTGGCTCTTTCACA 60.281 61.111 0.00 0.00 39.11 3.58
304 358 1.675641 GCGGGTGGCTCTTTCACAT 60.676 57.895 0.00 0.00 39.11 3.21
305 359 0.392461 GCGGGTGGCTCTTTCACATA 60.392 55.000 0.00 0.00 39.11 2.29
306 360 1.948611 GCGGGTGGCTCTTTCACATAA 60.949 52.381 0.00 0.00 39.11 1.90
307 361 2.432444 CGGGTGGCTCTTTCACATAAA 58.568 47.619 0.00 0.00 36.90 1.40
308 362 2.420022 CGGGTGGCTCTTTCACATAAAG 59.580 50.000 0.00 0.00 36.90 1.85
309 363 3.686016 GGGTGGCTCTTTCACATAAAGA 58.314 45.455 0.00 0.00 36.90 2.52
310 364 4.079253 GGGTGGCTCTTTCACATAAAGAA 58.921 43.478 2.20 0.00 36.01 2.52
311 365 4.522789 GGGTGGCTCTTTCACATAAAGAAA 59.477 41.667 2.20 0.00 36.01 2.52
312 366 5.010617 GGGTGGCTCTTTCACATAAAGAAAA 59.989 40.000 2.20 0.00 36.01 2.29
313 367 6.462347 GGGTGGCTCTTTCACATAAAGAAAAA 60.462 38.462 2.20 0.00 36.01 1.94
369 423 4.787598 ACAGAAGCATTTTGAGCGTTTAG 58.212 39.130 0.00 0.00 37.01 1.85
405 459 1.752833 GTGTGGGGACGGAGAAAGT 59.247 57.895 0.00 0.00 0.00 2.66
414 468 3.933332 GGGACGGAGAAAGTAATGTGAAG 59.067 47.826 0.00 0.00 0.00 3.02
421 475 5.106673 GGAGAAAGTAATGTGAAGGAAACGG 60.107 44.000 0.00 0.00 0.00 4.44
467 521 6.099341 GGCACCATTTGGAGTAACAAATTAG 58.901 40.000 3.01 0.61 45.94 1.73
468 522 6.295067 GGCACCATTTGGAGTAACAAATTAGT 60.295 38.462 3.01 1.14 45.94 2.24
470 524 7.657336 CACCATTTGGAGTAACAAATTAGTGT 58.343 34.615 3.01 5.77 45.94 3.55
471 525 8.788806 CACCATTTGGAGTAACAAATTAGTGTA 58.211 33.333 3.01 0.00 45.94 2.90
472 526 9.357161 ACCATTTGGAGTAACAAATTAGTGTAA 57.643 29.630 3.01 0.00 45.94 2.41
498 562 7.745620 ATAAAGTCTAGTGGAACCAACTTTG 57.254 36.000 21.54 9.05 40.88 2.77
499 563 3.477530 AGTCTAGTGGAACCAACTTTGC 58.522 45.455 0.00 0.00 37.80 3.68
500 564 3.136626 AGTCTAGTGGAACCAACTTTGCT 59.863 43.478 0.00 0.00 37.80 3.91
501 565 4.347000 AGTCTAGTGGAACCAACTTTGCTA 59.653 41.667 0.00 0.00 37.80 3.49
502 566 5.013183 AGTCTAGTGGAACCAACTTTGCTAT 59.987 40.000 0.00 0.00 37.80 2.97
503 567 5.122396 GTCTAGTGGAACCAACTTTGCTATG 59.878 44.000 0.00 0.00 37.80 2.23
504 568 2.558359 AGTGGAACCAACTTTGCTATGC 59.442 45.455 0.00 0.00 37.80 3.14
505 569 2.558359 GTGGAACCAACTTTGCTATGCT 59.442 45.455 0.00 0.00 0.00 3.79
506 570 3.005791 GTGGAACCAACTTTGCTATGCTT 59.994 43.478 0.00 0.00 0.00 3.91
507 571 3.640967 TGGAACCAACTTTGCTATGCTTT 59.359 39.130 0.00 0.00 0.00 3.51
508 572 4.100808 TGGAACCAACTTTGCTATGCTTTT 59.899 37.500 0.00 0.00 0.00 2.27
509 573 5.056480 GGAACCAACTTTGCTATGCTTTTT 58.944 37.500 0.00 0.00 0.00 1.94
531 595 2.778299 TCTTTTCTGATGGGACCAACG 58.222 47.619 0.00 0.00 0.00 4.10
563 638 5.294552 GCTAGCCAGTAAATTAAGACCACAG 59.705 44.000 2.29 0.00 0.00 3.66
600 675 4.434520 GGCCATGTGTAGAGAAGAGTAAC 58.565 47.826 0.00 0.00 0.00 2.50
609 684 7.828223 TGTGTAGAGAAGAGTAACTAACCCTAG 59.172 40.741 0.00 0.00 0.00 3.02
638 713 1.819632 GCGGGGAATGTTCTCGCAT 60.820 57.895 20.03 0.00 43.44 4.73
647 722 2.037136 GTTCTCGCATGCTGCTGGT 61.037 57.895 17.13 0.00 42.25 4.00
651 726 1.374343 CTCGCATGCTGCTGGTTGAT 61.374 55.000 17.13 0.00 42.25 2.57
653 728 1.650314 CGCATGCTGCTGGTTGATGA 61.650 55.000 17.13 0.00 42.25 2.92
655 730 1.469251 GCATGCTGCTGGTTGATGAAG 60.469 52.381 11.37 0.00 40.96 3.02
657 732 0.537828 TGCTGCTGGTTGATGAAGCA 60.538 50.000 0.00 0.00 44.36 3.91
658 733 0.599558 GCTGCTGGTTGATGAAGCAA 59.400 50.000 0.00 0.00 45.72 3.91
659 734 1.668047 GCTGCTGGTTGATGAAGCAAC 60.668 52.381 2.86 2.86 45.72 4.17
665 740 0.603065 GTTGATGAAGCAACCCACCC 59.397 55.000 0.00 0.00 41.69 4.61
667 742 0.038166 TGATGAAGCAACCCACCCTC 59.962 55.000 0.00 0.00 0.00 4.30
668 743 0.038166 GATGAAGCAACCCACCCTCA 59.962 55.000 0.00 0.00 0.00 3.86
669 744 0.706433 ATGAAGCAACCCACCCTCAT 59.294 50.000 0.00 0.00 0.00 2.90
671 746 0.038166 GAAGCAACCCACCCTCATGA 59.962 55.000 0.00 0.00 0.00 3.07
672 747 0.038744 AAGCAACCCACCCTCATGAG 59.961 55.000 16.24 16.24 0.00 2.90
688 795 3.006003 TCATGAGGTACACGTGCTTAACA 59.994 43.478 17.22 11.35 35.92 2.41
693 800 2.613133 GGTACACGTGCTTAACAACCAA 59.387 45.455 17.22 0.00 0.00 3.67
703 810 6.270064 GTGCTTAACAACCAAAGAGCTTTTA 58.730 36.000 0.00 0.00 0.00 1.52
760 996 4.479619 GGACAGCATCAACAAAGCTAAAG 58.520 43.478 0.00 0.00 36.73 1.85
761 997 3.905784 ACAGCATCAACAAAGCTAAAGC 58.094 40.909 0.00 0.00 36.73 3.51
762 998 3.248266 CAGCATCAACAAAGCTAAAGCC 58.752 45.455 0.00 0.00 43.38 4.35
763 999 3.057033 CAGCATCAACAAAGCTAAAGCCT 60.057 43.478 0.00 0.00 43.38 4.58
764 1000 4.156556 CAGCATCAACAAAGCTAAAGCCTA 59.843 41.667 0.00 0.00 43.38 3.93
847 1105 1.425448 TCACTCCTCACTCCTCACTCA 59.575 52.381 0.00 0.00 0.00 3.41
872 1130 1.661617 CGTCTACTGAGTCACTCCTCG 59.338 57.143 1.24 0.00 34.04 4.63
936 1194 1.181098 CCTTCAACAAGGTGGCCAGG 61.181 60.000 5.11 0.00 44.11 4.45
938 1196 0.467290 TTCAACAAGGTGGCCAGGAC 60.467 55.000 5.11 0.00 0.00 3.85
939 1197 1.903404 CAACAAGGTGGCCAGGACC 60.903 63.158 5.11 3.56 0.00 4.46
940 1198 2.391130 AACAAGGTGGCCAGGACCA 61.391 57.895 5.11 0.00 35.76 4.02
941 1199 2.034687 CAAGGTGGCCAGGACCAG 59.965 66.667 5.11 0.00 41.46 4.00
942 1200 2.121963 AAGGTGGCCAGGACCAGA 60.122 61.111 5.11 0.00 41.46 3.86
951 1209 0.542938 CCAGGACCAGAGACCAGACA 60.543 60.000 0.00 0.00 0.00 3.41
973 1231 0.952984 GAAGGAGGTGCTGTGTGCTC 60.953 60.000 0.00 0.00 43.37 4.26
1005 1281 3.960102 TGTAAAAGATTCATCCCATGGCC 59.040 43.478 6.09 0.00 0.00 5.36
1072 1348 2.698797 TGGTTCCTCTTCTTCAACGTCT 59.301 45.455 0.00 0.00 0.00 4.18
1278 1584 0.445436 AAGAGTACTACACGTCGCCG 59.555 55.000 0.00 0.00 40.83 6.46
1380 1710 3.736732 GAGCGCTCCTGATGCAGCT 62.737 63.158 27.22 0.00 40.66 4.24
1382 1712 3.574445 CGCTCCTGATGCAGCTGC 61.574 66.667 31.89 31.89 42.50 5.25
1423 1804 4.373116 GGAGCGACGACAGGGCAA 62.373 66.667 0.00 0.00 0.00 4.52
1450 1831 2.278206 CGCGGACGGAGATGTCTG 60.278 66.667 0.00 0.00 45.99 3.51
1718 2111 0.321653 AAGTCCATCCTCAACCACGC 60.322 55.000 0.00 0.00 0.00 5.34
1788 2183 3.558411 GCGCATCGACACTGCTCC 61.558 66.667 0.30 0.00 37.48 4.70
1789 2184 3.250323 CGCATCGACACTGCTCCG 61.250 66.667 7.80 0.00 37.48 4.63
1790 2185 2.887568 GCATCGACACTGCTCCGG 60.888 66.667 0.00 0.00 36.68 5.14
1792 2187 1.517257 CATCGACACTGCTCCGGAC 60.517 63.158 0.00 0.00 0.00 4.79
1793 2188 2.711922 ATCGACACTGCTCCGGACC 61.712 63.158 0.00 0.00 0.00 4.46
1794 2189 4.778415 CGACACTGCTCCGGACCG 62.778 72.222 6.99 6.99 0.00 4.79
1874 2295 0.733729 CCCTAGACGAGTTGGAGACG 59.266 60.000 0.00 0.00 0.00 4.18
1888 2309 2.616842 TGGAGACGCAACCTTTTTCTTC 59.383 45.455 0.00 0.00 0.00 2.87
1903 2329 6.323996 CCTTTTTCTTCCTTTTGTTCCCTACT 59.676 38.462 0.00 0.00 0.00 2.57
1905 2331 7.812690 TTTTCTTCCTTTTGTTCCCTACTAC 57.187 36.000 0.00 0.00 0.00 2.73
1907 2333 6.110411 TCTTCCTTTTGTTCCCTACTACTG 57.890 41.667 0.00 0.00 0.00 2.74
1909 2335 3.908103 TCCTTTTGTTCCCTACTACTGCT 59.092 43.478 0.00 0.00 0.00 4.24
1910 2336 4.003648 CCTTTTGTTCCCTACTACTGCTG 58.996 47.826 0.00 0.00 0.00 4.41
1946 2372 2.011947 TCAGAGGCAAAAGCATCGATG 58.988 47.619 21.27 21.27 0.00 3.84
2008 2434 2.276732 TCTCCAGAGGCCAAAAACAG 57.723 50.000 5.01 0.00 0.00 3.16
2017 2443 1.070601 GGCCAAAAACAGTGCTCCAAT 59.929 47.619 0.00 0.00 0.00 3.16
2056 2497 4.762289 AAAGATTTACATCTCCGCCTCT 57.238 40.909 0.00 0.00 39.00 3.69
2057 2498 4.762289 AAGATTTACATCTCCGCCTCTT 57.238 40.909 0.00 0.00 39.00 2.85
2081 2522 7.727578 TGGAGATGTAAACTATACCACTTCA 57.272 36.000 0.00 0.00 0.00 3.02
2121 2562 1.804748 CAACTCCAGGAGGCGTAAAAC 59.195 52.381 21.31 0.00 31.17 2.43
2162 2603 0.537371 CAACCGCCACTTCTTTCCCT 60.537 55.000 0.00 0.00 0.00 4.20
2170 2611 0.108019 ACTTCTTTCCCTTTCCGCGT 59.892 50.000 4.92 0.00 0.00 6.01
2176 2617 2.281208 CCCTTTCCGCGTGACCAA 60.281 61.111 4.92 0.00 0.00 3.67
2205 2646 2.858974 CTCCCACCCACCCACCTT 60.859 66.667 0.00 0.00 0.00 3.50
2422 2928 1.603739 GCCGCAAAGAAGAAGGGGT 60.604 57.895 0.00 0.00 37.64 4.95
2517 3024 0.670239 CGGCAAAAATGTCCAAGCCC 60.670 55.000 0.00 0.00 38.90 5.19
2597 3107 1.142748 GTGCTCCTCATCCACCTCG 59.857 63.158 0.00 0.00 0.00 4.63
2671 3185 5.989551 TCCAATGTGTTCGATGATATGTG 57.010 39.130 0.00 0.00 0.00 3.21
2672 3186 4.273235 TCCAATGTGTTCGATGATATGTGC 59.727 41.667 0.00 0.00 0.00 4.57
2673 3187 4.035441 CCAATGTGTTCGATGATATGTGCA 59.965 41.667 0.00 0.00 0.00 4.57
2676 3190 5.220557 TGTGTTCGATGATATGTGCAAAG 57.779 39.130 0.00 0.00 0.00 2.77
2678 3192 4.094887 GTGTTCGATGATATGTGCAAAGGT 59.905 41.667 0.00 0.00 0.00 3.50
2679 3193 5.293324 GTGTTCGATGATATGTGCAAAGGTA 59.707 40.000 0.00 0.00 0.00 3.08
2713 3227 2.165437 TGTGCACTTCTTTGTTGTTCCC 59.835 45.455 19.41 0.00 0.00 3.97
2714 3228 1.403679 TGCACTTCTTTGTTGTTCCCG 59.596 47.619 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.007336 GCACGTGAACCCAGACTACG 61.007 60.000 22.23 0.00 40.30 3.51
1 2 1.007336 CGCACGTGAACCCAGACTAC 61.007 60.000 22.23 0.00 0.00 2.73
2 3 1.174078 TCGCACGTGAACCCAGACTA 61.174 55.000 22.23 0.00 0.00 2.59
3 4 2.029073 CGCACGTGAACCCAGACT 59.971 61.111 22.23 0.00 0.00 3.24
4 5 2.022129 CTCGCACGTGAACCCAGAC 61.022 63.158 22.23 0.00 0.00 3.51
5 6 2.338620 CTCGCACGTGAACCCAGA 59.661 61.111 22.23 6.89 0.00 3.86
6 7 2.029073 ACTCGCACGTGAACCCAG 59.971 61.111 22.23 8.79 0.00 4.45
7 8 2.279851 CACTCGCACGTGAACCCA 60.280 61.111 22.23 0.00 37.06 4.51
8 9 2.279918 ACACTCGCACGTGAACCC 60.280 61.111 22.23 0.00 38.27 4.11
9 10 2.645510 CGACACTCGCACGTGAACC 61.646 63.158 22.23 0.00 38.27 3.62
10 11 1.597700 CTCGACACTCGCACGTGAAC 61.598 60.000 22.23 0.56 40.21 3.18
11 12 1.370051 CTCGACACTCGCACGTGAA 60.370 57.895 22.23 5.20 40.21 3.18
12 13 2.251371 CTCGACACTCGCACGTGA 59.749 61.111 22.23 0.00 40.21 4.35
13 14 2.051256 ACTCGACACTCGCACGTG 60.051 61.111 12.28 12.28 40.21 4.49
14 15 2.051256 CACTCGACACTCGCACGT 60.051 61.111 0.00 0.00 40.21 4.49
15 16 2.801162 CCACTCGACACTCGCACG 60.801 66.667 0.00 0.00 40.21 5.34
16 17 1.299926 AACCACTCGACACTCGCAC 60.300 57.895 0.00 0.00 40.21 5.34
17 18 1.299850 CAACCACTCGACACTCGCA 60.300 57.895 0.00 0.00 40.21 5.10
18 19 2.022129 CCAACCACTCGACACTCGC 61.022 63.158 0.00 0.00 40.21 5.03
19 20 0.249322 AACCAACCACTCGACACTCG 60.249 55.000 0.00 0.00 42.10 4.18
20 21 1.499049 GAACCAACCACTCGACACTC 58.501 55.000 0.00 0.00 0.00 3.51
21 22 0.249322 CGAACCAACCACTCGACACT 60.249 55.000 0.00 0.00 34.52 3.55
22 23 0.529119 ACGAACCAACCACTCGACAC 60.529 55.000 0.00 0.00 36.45 3.67
23 24 0.528901 CACGAACCAACCACTCGACA 60.529 55.000 0.00 0.00 36.45 4.35
24 25 0.249155 TCACGAACCAACCACTCGAC 60.249 55.000 0.00 0.00 36.45 4.20
25 26 0.031585 CTCACGAACCAACCACTCGA 59.968 55.000 0.00 0.00 36.45 4.04
26 27 0.031585 TCTCACGAACCAACCACTCG 59.968 55.000 0.00 0.00 38.53 4.18
27 28 1.068741 AGTCTCACGAACCAACCACTC 59.931 52.381 0.00 0.00 0.00 3.51
28 29 1.068741 GAGTCTCACGAACCAACCACT 59.931 52.381 0.00 0.00 0.00 4.00
29 30 1.499049 GAGTCTCACGAACCAACCAC 58.501 55.000 0.00 0.00 0.00 4.16
30 31 0.031585 CGAGTCTCACGAACCAACCA 59.968 55.000 0.00 0.00 0.00 3.67
31 32 1.282930 GCGAGTCTCACGAACCAACC 61.283 60.000 0.00 0.00 0.00 3.77
32 33 0.596600 TGCGAGTCTCACGAACCAAC 60.597 55.000 0.00 0.00 0.00 3.77
33 34 0.596600 GTGCGAGTCTCACGAACCAA 60.597 55.000 0.00 0.00 33.72 3.67
34 35 1.007734 GTGCGAGTCTCACGAACCA 60.008 57.895 0.00 0.00 33.72 3.67
35 36 3.843985 GTGCGAGTCTCACGAACC 58.156 61.111 0.00 0.00 33.72 3.62
36 37 0.520404 TAGGTGCGAGTCTCACGAAC 59.480 55.000 7.15 0.00 38.42 3.95
37 38 0.803117 CTAGGTGCGAGTCTCACGAA 59.197 55.000 7.15 0.00 35.39 3.85
38 39 0.321387 ACTAGGTGCGAGTCTCACGA 60.321 55.000 7.15 0.00 35.39 4.35
39 40 0.097325 GACTAGGTGCGAGTCTCACG 59.903 60.000 7.15 0.00 40.23 4.35
40 41 1.166129 TGACTAGGTGCGAGTCTCAC 58.834 55.000 4.61 4.61 43.19 3.51
41 42 2.130272 ATGACTAGGTGCGAGTCTCA 57.870 50.000 0.00 0.00 43.19 3.27
42 43 2.031508 GCTATGACTAGGTGCGAGTCTC 60.032 54.545 4.57 0.00 43.19 3.36
43 44 1.950909 GCTATGACTAGGTGCGAGTCT 59.049 52.381 4.57 0.00 43.19 3.24
44 45 1.676529 TGCTATGACTAGGTGCGAGTC 59.323 52.381 0.00 0.00 43.10 3.36
45 46 1.678627 CTGCTATGACTAGGTGCGAGT 59.321 52.381 0.00 0.00 0.00 4.18
46 47 1.950216 TCTGCTATGACTAGGTGCGAG 59.050 52.381 0.00 0.00 0.00 5.03
47 48 1.950216 CTCTGCTATGACTAGGTGCGA 59.050 52.381 0.00 0.00 0.00 5.10
48 49 1.950216 TCTCTGCTATGACTAGGTGCG 59.050 52.381 0.00 0.00 0.00 5.34
49 50 2.287308 CGTCTCTGCTATGACTAGGTGC 60.287 54.545 0.00 0.00 0.00 5.01
50 51 2.287308 GCGTCTCTGCTATGACTAGGTG 60.287 54.545 0.00 0.00 0.00 4.00
51 52 1.950909 GCGTCTCTGCTATGACTAGGT 59.049 52.381 0.00 0.00 0.00 3.08
52 53 2.226330 AGCGTCTCTGCTATGACTAGG 58.774 52.381 0.00 0.00 45.14 3.02
53 54 5.621197 ATTAGCGTCTCTGCTATGACTAG 57.379 43.478 0.00 0.00 46.19 2.57
54 55 6.392625 AAATTAGCGTCTCTGCTATGACTA 57.607 37.500 0.00 0.00 46.19 2.59
55 56 4.927978 AATTAGCGTCTCTGCTATGACT 57.072 40.909 0.00 0.00 46.19 3.41
56 57 5.277058 CCAAAATTAGCGTCTCTGCTATGAC 60.277 44.000 0.00 0.00 46.19 3.06
57 58 4.811024 CCAAAATTAGCGTCTCTGCTATGA 59.189 41.667 0.00 0.00 46.19 2.15
58 59 4.024556 CCCAAAATTAGCGTCTCTGCTATG 60.025 45.833 0.00 0.00 46.19 2.23
59 60 4.130118 CCCAAAATTAGCGTCTCTGCTAT 58.870 43.478 0.00 0.00 46.19 2.97
60 61 3.196901 TCCCAAAATTAGCGTCTCTGCTA 59.803 43.478 0.00 0.00 45.14 3.49
62 63 2.356135 TCCCAAAATTAGCGTCTCTGC 58.644 47.619 0.00 0.00 0.00 4.26
63 64 4.731773 GCAATCCCAAAATTAGCGTCTCTG 60.732 45.833 0.00 0.00 0.00 3.35
64 65 3.378427 GCAATCCCAAAATTAGCGTCTCT 59.622 43.478 0.00 0.00 0.00 3.10
65 66 3.695816 GCAATCCCAAAATTAGCGTCTC 58.304 45.455 0.00 0.00 0.00 3.36
66 67 2.097466 CGCAATCCCAAAATTAGCGTCT 59.903 45.455 0.00 0.00 34.48 4.18
67 68 2.450160 CGCAATCCCAAAATTAGCGTC 58.550 47.619 0.00 0.00 34.48 5.19
68 69 1.469079 GCGCAATCCCAAAATTAGCGT 60.469 47.619 0.30 0.00 37.89 5.07
69 70 1.199624 GCGCAATCCCAAAATTAGCG 58.800 50.000 0.30 0.00 38.26 4.26
70 71 2.195922 CAGCGCAATCCCAAAATTAGC 58.804 47.619 11.47 0.00 0.00 3.09
77 78 1.314534 CCATCACAGCGCAATCCCAA 61.315 55.000 11.47 0.00 0.00 4.12
79 80 2.484062 CCCATCACAGCGCAATCCC 61.484 63.158 11.47 0.00 0.00 3.85
86 87 1.742880 CACACCTCCCATCACAGCG 60.743 63.158 0.00 0.00 0.00 5.18
88 89 3.135348 ACATATCACACCTCCCATCACAG 59.865 47.826 0.00 0.00 0.00 3.66
91 92 5.190726 TGTTTACATATCACACCTCCCATCA 59.809 40.000 0.00 0.00 0.00 3.07
92 93 5.680619 TGTTTACATATCACACCTCCCATC 58.319 41.667 0.00 0.00 0.00 3.51
95 96 6.588204 TGTATGTTTACATATCACACCTCCC 58.412 40.000 5.92 0.00 40.53 4.30
185 188 7.814107 TGGCTACATCAGAAATTCATTTCAAAC 59.186 33.333 13.50 0.00 46.50 2.93
199 202 5.235850 TGGTAACTTTTGGCTACATCAGA 57.764 39.130 0.00 0.00 37.61 3.27
220 223 6.197096 GTCAACAGCAGACACTTTGTAATTTG 59.803 38.462 0.00 0.00 36.06 2.32
223 226 4.024893 CGTCAACAGCAGACACTTTGTAAT 60.025 41.667 0.00 0.00 35.77 1.89
253 257 3.853355 AAGAGCCATATGAACCTGGAG 57.147 47.619 3.65 0.00 34.24 3.86
284 338 1.896660 GTGAAAGAGCCACCCGCAA 60.897 57.895 0.00 0.00 41.38 4.85
286 340 0.392461 TATGTGAAAGAGCCACCCGC 60.392 55.000 0.00 0.00 33.80 6.13
287 341 2.107950 TTATGTGAAAGAGCCACCCG 57.892 50.000 0.00 0.00 33.80 5.28
288 342 3.686016 TCTTTATGTGAAAGAGCCACCC 58.314 45.455 0.00 0.00 32.90 4.61
336 390 9.362539 CTCAAAATGCTTCTGTTTTATGCTTAT 57.637 29.630 0.00 0.00 0.00 1.73
337 391 7.329226 GCTCAAAATGCTTCTGTTTTATGCTTA 59.671 33.333 0.00 0.00 0.00 3.09
338 392 6.146673 GCTCAAAATGCTTCTGTTTTATGCTT 59.853 34.615 0.00 0.00 0.00 3.91
339 393 5.636543 GCTCAAAATGCTTCTGTTTTATGCT 59.363 36.000 0.00 0.00 0.00 3.79
340 394 5.443693 CGCTCAAAATGCTTCTGTTTTATGC 60.444 40.000 0.00 0.00 0.00 3.14
341 395 5.630680 ACGCTCAAAATGCTTCTGTTTTATG 59.369 36.000 0.00 0.00 0.00 1.90
342 396 5.772521 ACGCTCAAAATGCTTCTGTTTTAT 58.227 33.333 0.00 0.00 0.00 1.40
343 397 5.181690 ACGCTCAAAATGCTTCTGTTTTA 57.818 34.783 0.00 0.00 0.00 1.52
344 398 4.045636 ACGCTCAAAATGCTTCTGTTTT 57.954 36.364 0.00 0.00 0.00 2.43
345 399 3.715628 ACGCTCAAAATGCTTCTGTTT 57.284 38.095 0.00 0.00 0.00 2.83
346 400 3.715628 AACGCTCAAAATGCTTCTGTT 57.284 38.095 0.00 0.00 0.00 3.16
347 401 3.715628 AAACGCTCAAAATGCTTCTGT 57.284 38.095 0.00 0.00 0.00 3.41
369 423 1.474879 CACGTCCTCTCTTCCCTTCTC 59.525 57.143 0.00 0.00 0.00 2.87
405 459 5.424252 AGATCCTACCGTTTCCTTCACATTA 59.576 40.000 0.00 0.00 0.00 1.90
414 468 2.484889 GCATCAGATCCTACCGTTTCC 58.515 52.381 0.00 0.00 0.00 3.13
421 475 2.866762 GGTTTGACGCATCAGATCCTAC 59.133 50.000 0.00 0.00 35.83 3.18
467 521 8.611654 TGGTTCCACTAGACTTTATTTTACAC 57.388 34.615 0.00 0.00 0.00 2.90
468 522 9.059260 GTTGGTTCCACTAGACTTTATTTTACA 57.941 33.333 0.00 0.00 0.00 2.41
470 524 9.856162 AAGTTGGTTCCACTAGACTTTATTTTA 57.144 29.630 0.00 0.00 0.00 1.52
471 525 8.762481 AAGTTGGTTCCACTAGACTTTATTTT 57.238 30.769 0.00 0.00 0.00 1.82
472 526 8.630037 CAAAGTTGGTTCCACTAGACTTTATTT 58.370 33.333 14.83 0.00 36.06 1.40
473 527 7.255486 GCAAAGTTGGTTCCACTAGACTTTATT 60.255 37.037 14.83 0.00 36.06 1.40
474 528 6.206829 GCAAAGTTGGTTCCACTAGACTTTAT 59.793 38.462 14.83 0.00 36.06 1.40
475 529 5.529800 GCAAAGTTGGTTCCACTAGACTTTA 59.470 40.000 14.83 0.00 36.06 1.85
476 530 4.338400 GCAAAGTTGGTTCCACTAGACTTT 59.662 41.667 11.35 11.35 37.70 2.66
477 531 3.883489 GCAAAGTTGGTTCCACTAGACTT 59.117 43.478 0.00 2.06 0.00 3.01
478 532 3.136626 AGCAAAGTTGGTTCCACTAGACT 59.863 43.478 0.00 0.00 34.89 3.24
479 533 3.477530 AGCAAAGTTGGTTCCACTAGAC 58.522 45.455 0.00 0.00 34.89 2.59
480 534 3.857157 AGCAAAGTTGGTTCCACTAGA 57.143 42.857 0.00 0.00 34.89 2.43
481 535 4.142600 GCATAGCAAAGTTGGTTCCACTAG 60.143 45.833 0.45 0.00 39.88 2.57
507 571 5.451242 CGTTGGTCCCATCAGAAAAGAAAAA 60.451 40.000 0.00 0.00 0.00 1.94
508 572 4.037446 CGTTGGTCCCATCAGAAAAGAAAA 59.963 41.667 0.00 0.00 0.00 2.29
509 573 3.568007 CGTTGGTCCCATCAGAAAAGAAA 59.432 43.478 0.00 0.00 0.00 2.52
510 574 3.146066 CGTTGGTCCCATCAGAAAAGAA 58.854 45.455 0.00 0.00 0.00 2.52
511 575 2.105821 ACGTTGGTCCCATCAGAAAAGA 59.894 45.455 0.00 0.00 0.00 2.52
512 576 2.504367 ACGTTGGTCCCATCAGAAAAG 58.496 47.619 0.00 0.00 0.00 2.27
517 581 0.606401 AGCAACGTTGGTCCCATCAG 60.606 55.000 26.30 0.00 32.71 2.90
521 585 0.958382 GCATAGCAACGTTGGTCCCA 60.958 55.000 33.88 19.03 39.88 4.37
600 675 4.320788 CCGCGGATTAACTACTAGGGTTAG 60.321 50.000 24.07 0.00 31.94 2.34
609 684 2.140717 CATTCCCCGCGGATTAACTAC 58.859 52.381 30.73 0.00 38.24 2.73
638 713 0.537828 TGCTTCATCAACCAGCAGCA 60.538 50.000 0.00 0.00 38.65 4.41
647 722 0.482446 AGGGTGGGTTGCTTCATCAA 59.518 50.000 0.00 0.00 0.00 2.57
651 726 0.251297 CATGAGGGTGGGTTGCTTCA 60.251 55.000 0.00 0.00 0.00 3.02
653 728 0.038744 CTCATGAGGGTGGGTTGCTT 59.961 55.000 15.38 0.00 0.00 3.91
655 730 1.379044 CCTCATGAGGGTGGGTTGC 60.379 63.158 31.14 0.00 44.87 4.17
665 740 2.370281 AAGCACGTGTACCTCATGAG 57.630 50.000 18.38 16.24 36.90 2.90
667 742 3.322369 TGTTAAGCACGTGTACCTCATG 58.678 45.455 18.38 0.00 38.86 3.07
668 743 3.671008 TGTTAAGCACGTGTACCTCAT 57.329 42.857 18.38 0.00 0.00 2.90
669 744 3.125316 GTTGTTAAGCACGTGTACCTCA 58.875 45.455 18.38 8.87 0.00 3.86
671 746 2.158928 TGGTTGTTAAGCACGTGTACCT 60.159 45.455 18.38 2.52 33.29 3.08
672 747 2.211806 TGGTTGTTAAGCACGTGTACC 58.788 47.619 18.38 12.85 33.29 3.34
688 795 3.749609 ACGCGTATAAAAGCTCTTTGGTT 59.250 39.130 11.67 0.00 38.10 3.67
693 800 5.006358 CCATTGTACGCGTATAAAAGCTCTT 59.994 40.000 28.21 10.61 0.00 2.85
703 810 0.457035 ACGTCCCATTGTACGCGTAT 59.543 50.000 23.56 4.41 42.74 3.06
731 967 3.394674 TGTTGATGCTGTCCGTAAAGA 57.605 42.857 0.00 0.00 0.00 2.52
732 968 4.466828 CTTTGTTGATGCTGTCCGTAAAG 58.533 43.478 0.00 0.00 0.00 1.85
793 1029 4.760715 AGTGTGGCGTATATGTAGGAGTAG 59.239 45.833 0.00 0.00 0.00 2.57
828 1072 1.916506 TGAGTGAGGAGTGAGGAGTG 58.083 55.000 0.00 0.00 0.00 3.51
847 1105 0.733729 GTGACTCAGTAGACGGCGAT 59.266 55.000 16.62 3.89 0.00 4.58
872 1130 2.435059 GGCCGTTGAGTGAGGAGC 60.435 66.667 0.00 0.00 0.00 4.70
932 1190 0.542938 TGTCTGGTCTCTGGTCCTGG 60.543 60.000 0.00 0.00 0.00 4.45
936 1194 0.251832 TCCCTGTCTGGTCTCTGGTC 60.252 60.000 0.00 0.00 0.00 4.02
938 1196 0.901124 CTTCCCTGTCTGGTCTCTGG 59.099 60.000 0.00 0.00 0.00 3.86
939 1197 0.901124 CCTTCCCTGTCTGGTCTCTG 59.099 60.000 0.00 0.00 0.00 3.35
940 1198 0.787084 TCCTTCCCTGTCTGGTCTCT 59.213 55.000 0.00 0.00 0.00 3.10
941 1199 1.190643 CTCCTTCCCTGTCTGGTCTC 58.809 60.000 0.00 0.00 0.00 3.36
942 1200 0.252467 CCTCCTTCCCTGTCTGGTCT 60.252 60.000 0.00 0.00 0.00 3.85
951 1209 1.462238 ACACAGCACCTCCTTCCCT 60.462 57.895 0.00 0.00 0.00 4.20
973 1231 7.711339 GGGATGAATCTTTTACAGTACAGGTAG 59.289 40.741 0.00 0.00 0.00 3.18
1045 1321 1.755393 AAGAAGAGGAACCACGCCGT 61.755 55.000 0.00 0.00 0.00 5.68
1117 1393 4.271816 CCGCCTCGACATCTCCGG 62.272 72.222 0.00 0.00 0.00 5.14
1128 1404 3.844090 GTGAGCCTCCTCCGCCTC 61.844 72.222 0.00 0.00 37.29 4.70
1256 1532 1.202121 GCGACGTGTAGTACTCTTCCC 60.202 57.143 0.00 0.00 0.00 3.97
1258 1534 2.171127 GGCGACGTGTAGTACTCTTC 57.829 55.000 0.00 0.59 0.00 2.87
1278 1584 0.930726 TCTCCTCTCCTCCCTCTTCC 59.069 60.000 0.00 0.00 0.00 3.46
1347 1677 2.278206 CTCGGTGTCGATGGAGCG 60.278 66.667 7.17 7.17 45.04 5.03
1380 1710 1.374631 CGAAGCCTGTGTAGCTGCA 60.375 57.895 0.00 0.00 40.49 4.41
1382 1712 1.284657 CATCGAAGCCTGTGTAGCTG 58.715 55.000 0.00 0.00 40.49 4.24
1383 1713 0.898320 ACATCGAAGCCTGTGTAGCT 59.102 50.000 0.00 0.00 44.19 3.32
1385 1715 2.534298 CTGACATCGAAGCCTGTGTAG 58.466 52.381 0.00 0.00 0.00 2.74
1386 1716 1.204704 CCTGACATCGAAGCCTGTGTA 59.795 52.381 0.00 0.00 0.00 2.90
1387 1717 0.036952 CCTGACATCGAAGCCTGTGT 60.037 55.000 0.00 0.00 0.00 3.72
1450 1831 1.153086 ACGCATCTCCCAAGCATCC 60.153 57.895 0.00 0.00 0.00 3.51
1531 1921 4.388499 CGTAGCACCCTTGGCGGT 62.388 66.667 0.00 0.00 36.18 5.68
1752 2145 3.479269 GGCGAGCCGTGAACGAAG 61.479 66.667 4.03 0.00 43.02 3.79
1788 2183 2.190841 AACAAAAGCCACCGGTCCG 61.191 57.895 2.59 3.60 0.00 4.79
1789 2184 1.362355 CAACAAAAGCCACCGGTCC 59.638 57.895 2.59 0.00 0.00 4.46
1790 2185 0.458260 AACAACAAAAGCCACCGGTC 59.542 50.000 2.59 0.00 0.00 4.79
1792 2187 0.529555 CCAACAACAAAAGCCACCGG 60.530 55.000 0.00 0.00 0.00 5.28
1793 2188 1.151172 GCCAACAACAAAAGCCACCG 61.151 55.000 0.00 0.00 0.00 4.94
1794 2189 1.151172 CGCCAACAACAAAAGCCACC 61.151 55.000 0.00 0.00 0.00 4.61
1795 2190 0.459411 ACGCCAACAACAAAAGCCAC 60.459 50.000 0.00 0.00 0.00 5.01
1874 2295 5.064707 GGAACAAAAGGAAGAAAAAGGTTGC 59.935 40.000 0.00 0.00 0.00 4.17
1888 2309 4.003648 CAGCAGTAGTAGGGAACAAAAGG 58.996 47.826 0.00 0.00 0.00 3.11
1960 2386 7.552050 AAAGGTAGAGATGCTCTTATGCTAT 57.448 36.000 1.88 0.00 41.50 2.97
1971 2397 3.563390 GGAGATGCAAAAGGTAGAGATGC 59.437 47.826 0.00 0.00 37.52 3.91
1972 2398 4.774124 TGGAGATGCAAAAGGTAGAGATG 58.226 43.478 0.00 0.00 0.00 2.90
1973 2399 4.718774 TCTGGAGATGCAAAAGGTAGAGAT 59.281 41.667 0.00 0.00 0.00 2.75
1974 2400 4.096681 TCTGGAGATGCAAAAGGTAGAGA 58.903 43.478 0.00 0.00 0.00 3.10
1975 2401 4.440880 CTCTGGAGATGCAAAAGGTAGAG 58.559 47.826 0.00 0.00 0.00 2.43
1976 2402 3.198635 CCTCTGGAGATGCAAAAGGTAGA 59.801 47.826 0.00 0.00 0.00 2.59
2008 2434 6.462500 ACATCTACATCATCTATTGGAGCAC 58.538 40.000 0.00 0.00 0.00 4.40
2038 2464 3.134458 CCAAGAGGCGGAGATGTAAATC 58.866 50.000 0.00 0.00 0.00 2.17
2040 2466 2.184533 TCCAAGAGGCGGAGATGTAAA 58.815 47.619 0.00 0.00 33.74 2.01
2056 2497 8.038944 GTGAAGTGGTATAGTTTACATCTCCAA 58.961 37.037 0.00 0.00 30.72 3.53
2057 2498 7.553334 GTGAAGTGGTATAGTTTACATCTCCA 58.447 38.462 0.00 0.00 30.72 3.86
2081 2522 3.417101 TGGAGATGTAAATTTGCACCGT 58.583 40.909 11.35 0.00 0.00 4.83
2147 2588 0.881796 GGAAAGGGAAAGAAGTGGCG 59.118 55.000 0.00 0.00 0.00 5.69
2162 2603 2.181521 GTGGTTGGTCACGCGGAAA 61.182 57.895 12.47 0.00 0.00 3.13
2654 3168 4.094739 CCTTTGCACATATCATCGAACACA 59.905 41.667 0.00 0.00 0.00 3.72
2686 3200 6.449635 ACAACAAAGAAGTGCACAAGAATA 57.550 33.333 21.04 0.00 0.00 1.75
2688 3202 4.782019 ACAACAAAGAAGTGCACAAGAA 57.218 36.364 21.04 0.00 0.00 2.52
2698 3212 3.691498 GACAACGGGAACAACAAAGAAG 58.309 45.455 0.00 0.00 0.00 2.85
2713 3227 5.063438 ACACATTCTATTGGAATCGACAACG 59.937 40.000 0.00 0.00 42.20 4.10
2714 3228 6.422776 ACACATTCTATTGGAATCGACAAC 57.577 37.500 0.00 0.00 42.20 3.32


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

AutoCloner maintained by Alex Coulton.