Multiple sequence alignment - TraesCS3D01G356000

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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 TraesCS3D01G356000 chr3D 100.000 6090 0 0 1 6090 467766144 467772233 0.000000e+00 11247.0
1 TraesCS3D01G356000 chr3D 79.949 394 63 13 2314 2694 468654506 468654896 6.010000e-70 276.0
2 TraesCS3D01G356000 chr3D 79.217 332 53 13 2356 2674 467777825 467778153 3.700000e-52 217.0
3 TraesCS3D01G356000 chr3D 75.556 270 47 14 5635 5886 104097386 104097654 1.390000e-21 115.0
4 TraesCS3D01G356000 chr3A 92.843 4569 195 44 1588 6089 610412094 610416597 0.000000e+00 6505.0
5 TraesCS3D01G356000 chr3A 93.497 1261 56 15 314 1552 610410841 610412097 0.000000e+00 1851.0
6 TraesCS3D01G356000 chr3A 74.745 784 149 36 2314 3063 610523688 610524456 7.670000e-79 305.0
7 TraesCS3D01G356000 chr3A 79.733 375 56 14 2315 2674 610424695 610425064 2.820000e-63 254.0
8 TraesCS3D01G356000 chr3A 84.091 264 12 8 2 236 610410509 610410771 1.710000e-55 228.0
9 TraesCS3D01G356000 chr3A 75.746 268 47 12 5635 5886 380925960 380926225 1.070000e-22 119.0
10 TraesCS3D01G356000 chr3B 96.267 1795 56 7 1504 3297 622079035 622080819 0.000000e+00 2933.0
11 TraesCS3D01G356000 chr3B 92.068 1349 74 17 177 1506 622077505 622078839 0.000000e+00 1868.0
12 TraesCS3D01G356000 chr3B 95.320 1047 49 0 4344 5390 622081477 622082523 0.000000e+00 1663.0
13 TraesCS3D01G356000 chr3B 94.986 718 36 0 3654 4371 622080814 622081531 0.000000e+00 1127.0
14 TraesCS3D01G356000 chr3B 78.892 379 52 18 2315 2674 622085598 622085967 1.320000e-56 231.0
15 TraesCS3D01G356000 chr3B 96.241 133 5 0 5419 5551 622082520 622082652 1.030000e-52 219.0
16 TraesCS3D01G356000 chr3B 94.783 115 5 1 5524 5637 622082652 622082766 1.740000e-40 178.0
17 TraesCS3D01G356000 chr3B 79.459 185 31 7 5675 5854 561855463 561855281 2.300000e-24 124.0
18 TraesCS3D01G356000 chr3B 73.514 185 47 2 5856 6039 800133531 800133714 1.100000e-07 69.4
19 TraesCS3D01G356000 chr5D 91.919 99 8 0 2 100 543752974 543752876 8.230000e-29 139.0
20 TraesCS3D01G356000 chr5D 72.251 382 84 17 5715 6080 425853010 425853385 1.400000e-16 99.0
21 TraesCS3D01G356000 chr5A 78.475 223 37 8 5669 5882 680622419 680622199 1.060000e-27 135.0
22 TraesCS3D01G356000 chr5A 77.674 215 39 7 5676 5882 467736260 467736047 8.290000e-24 122.0
23 TraesCS3D01G356000 chr4A 80.108 186 32 5 5669 5850 667846296 667846480 3.830000e-27 134.0
24 TraesCS3D01G356000 chr4A 76.426 263 46 11 5635 5882 665472637 665472376 1.780000e-25 128.0
25 TraesCS3D01G356000 chr1D 73.381 417 87 15 5682 6086 106293017 106292613 3.830000e-27 134.0
26 TraesCS3D01G356000 chr7A 74.332 374 67 22 5636 5986 695840791 695841158 1.380000e-26 132.0
27 TraesCS3D01G356000 chr7A 76.190 210 39 8 5635 5834 562174625 562174417 3.880000e-17 100.0
28 TraesCS3D01G356000 chr6B 77.778 216 37 8 5676 5882 161595565 161595778 8.290000e-24 122.0
29 TraesCS3D01G356000 chr2D 81.507 146 25 2 5946 6090 106856180 106856324 1.070000e-22 119.0
30 TraesCS3D01G356000 chr2D 71.429 434 107 15 5669 6089 304335622 304335193 1.400000e-16 99.0
31 TraesCS3D01G356000 chr2A 72.749 422 88 16 5681 6086 476211126 476211536 3.860000e-22 117.0
32 TraesCS3D01G356000 chr2A 72.258 310 71 9 5674 5971 717765576 717765270 1.410000e-11 82.4
33 TraesCS3D01G356000 chr7D 79.433 141 29 0 5946 6086 133887213 133887073 3.880000e-17 100.0
34 TraesCS3D01G356000 chr4D 78.873 142 29 1 5946 6086 428988234 428988093 1.810000e-15 95.3
35 TraesCS3D01G356000 chr4D 86.765 68 6 2 3406 3470 22039508 22039441 8.470000e-09 73.1
36 TraesCS3D01G356000 chr4B 78.873 142 28 2 5946 6086 527122412 527122272 1.810000e-15 95.3
37 TraesCS3D01G356000 chr4B 86.765 68 6 2 3406 3470 34056369 34056302 8.470000e-09 73.1


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 TraesCS3D01G356000 chr3D 467766144 467772233 6089 False 11247.000000 11247 100.000000 1 6090 1 chr3D.!!$F2 6089
1 TraesCS3D01G356000 chr3A 610410509 610416597 6088 False 2861.333333 6505 90.143667 2 6089 3 chr3A.!!$F4 6087
2 TraesCS3D01G356000 chr3A 610523688 610524456 768 False 305.000000 305 74.745000 2314 3063 1 chr3A.!!$F3 749
3 TraesCS3D01G356000 chr3B 622077505 622085967 8462 False 1174.142857 2933 92.651000 177 5637 7 chr3B.!!$F2 5460

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
445 513 0.179062 TTGTTTGCCATGTTGGGTGC 60.179 50.000 0.00 0.0 38.19 5.01 F
1190 1269 1.637553 ACCATGGGAGCCATATCCATC 59.362 52.381 18.09 0.0 43.15 3.51 F
1555 1847 0.529992 GTGACCTATGGCCGCAGTAC 60.530 60.000 0.00 0.0 0.00 2.73 F
2131 2424 0.254462 TGTGTGCACCAAGGAGTTCA 59.746 50.000 15.69 0.0 0.00 3.18 F
4063 4394 0.457851 CTAGAGCGGTTGGTGAGAGG 59.542 60.000 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1583 2.069273 CCTGTCAATGAGTCACCGTTC 58.931 52.381 0.00 0.0 0.00 3.95 R
2003 2296 2.362397 GGATAGAGTGATCAGGCAACGA 59.638 50.000 0.00 0.0 46.39 3.85 R
3301 3623 2.762887 CTGCTATCACTGTCCTGAAGGA 59.237 50.000 0.00 0.0 43.08 3.36 R
4117 4448 1.101635 TCCGGTCAGTATGCTCGAGG 61.102 60.000 15.58 0.0 34.23 4.63 R
5905 8457 0.037326 TGTCTTCGGTGGATCTGTGC 60.037 55.000 0.00 0.0 0.00 4.57 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
41 42 0.179073 CCGCGGAAACTCAGATCCAT 60.179 55.000 24.07 0.00 35.34 3.41
46 47 2.131023 GGAAACTCAGATCCATCCCCT 58.869 52.381 0.00 0.00 35.71 4.79
77 78 1.569072 AGGTAAAAATCCCCTCGCCAT 59.431 47.619 0.00 0.00 0.00 4.40
79 80 2.764010 GGTAAAAATCCCCTCGCCATTT 59.236 45.455 0.00 0.00 0.00 2.32
129 134 3.711190 GGCATGAAATTTTGGGATAGGGT 59.289 43.478 0.00 0.00 0.00 4.34
134 139 5.016173 TGAAATTTTGGGATAGGGTGTCTG 58.984 41.667 0.00 0.00 0.00 3.51
273 331 5.220970 GCATCCGCCAAATTAAGCTACTTTA 60.221 40.000 0.00 0.00 0.00 1.85
275 333 6.185852 TCCGCCAAATTAAGCTACTTTAAC 57.814 37.500 0.00 0.00 0.00 2.01
301 360 3.876914 CGTGGTGCTATATGTGGTGAATT 59.123 43.478 0.00 0.00 0.00 2.17
317 376 2.734606 TGAATTGCCGAAGTTGTACTCG 59.265 45.455 0.00 0.00 0.00 4.18
339 398 0.749649 TTTTGCCTTTGCGTGGATGT 59.250 45.000 0.00 0.00 41.78 3.06
401 463 1.126846 GTTTGAGGCGACAATCACTCG 59.873 52.381 0.00 0.00 32.76 4.18
441 509 2.224233 TGTGGATTGTTTGCCATGTTGG 60.224 45.455 0.00 0.00 41.55 3.77
445 513 0.179062 TTGTTTGCCATGTTGGGTGC 60.179 50.000 0.00 0.00 38.19 5.01
473 541 4.996758 GGTAGGTACGGTAAACACAAACAT 59.003 41.667 0.00 0.00 0.00 2.71
501 569 3.989817 GACATGCACAAAAAGGTTCCATC 59.010 43.478 0.00 0.00 0.00 3.51
775 849 5.401531 ACTTTTAGAGAGTTGCGGATACA 57.598 39.130 0.00 0.00 0.00 2.29
816 890 3.142174 GCAGTGCTCCACTAAGTTCTTT 58.858 45.455 8.18 0.00 43.43 2.52
952 1027 6.471233 TGACACTCATATTACTTCTCCCTG 57.529 41.667 0.00 0.00 0.00 4.45
954 1029 6.096987 TGACACTCATATTACTTCTCCCTGTC 59.903 42.308 0.00 0.00 0.00 3.51
1190 1269 1.637553 ACCATGGGAGCCATATCCATC 59.362 52.381 18.09 0.00 43.15 3.51
1279 1368 5.076873 CCTTTTCCTTTGTCCATGGACTTA 58.923 41.667 37.92 25.89 44.80 2.24
1329 1418 4.260985 TGTAATCCGTTACAGGACGTCTA 58.739 43.478 16.46 0.00 43.86 2.59
1347 1436 8.142551 GGACGTCTACAAAGTTGAATATATCCT 58.857 37.037 16.46 0.00 0.00 3.24
1349 1438 8.692710 ACGTCTACAAAGTTGAATATATCCTCA 58.307 33.333 0.00 0.00 0.00 3.86
1362 1451 9.189156 TGAATATATCCTCAAAAGGTTTTCCAG 57.811 33.333 0.00 0.00 43.82 3.86
1363 1452 9.408648 GAATATATCCTCAAAAGGTTTTCCAGA 57.591 33.333 0.00 0.00 43.82 3.86
1364 1453 9.768215 AATATATCCTCAAAAGGTTTTCCAGAA 57.232 29.630 0.00 0.00 43.82 3.02
1368 1457 5.359860 TCCTCAAAAGGTTTTCCAGAAAGTC 59.640 40.000 0.00 0.00 43.82 3.01
1453 1547 3.965292 TGAGAAGCGGTAATCTAGTCG 57.035 47.619 0.00 0.00 0.00 4.18
1489 1583 7.414540 GCACTTCATTTGGAGACTAAGTATTGG 60.415 40.741 0.00 0.00 0.00 3.16
1525 1817 1.539869 AGGTCCAGGTGTCTGCCAT 60.540 57.895 0.00 0.00 39.61 4.40
1549 1841 2.691526 TGTAACTAGTGACCTATGGCCG 59.308 50.000 7.97 0.00 0.00 6.13
1555 1847 0.529992 GTGACCTATGGCCGCAGTAC 60.530 60.000 0.00 0.00 0.00 2.73
1560 1853 1.406887 CCTATGGCCGCAGTACAGTTT 60.407 52.381 0.00 0.00 0.00 2.66
1566 1859 2.148768 GCCGCAGTACAGTTTTTACCT 58.851 47.619 0.00 0.00 0.00 3.08
1576 1869 9.715121 CAGTACAGTTTTTACCTAGTATTGGAA 57.285 33.333 0.00 0.00 0.00 3.53
1635 1928 4.074259 AGCTGCTCAAATGACACACAATA 58.926 39.130 0.00 0.00 0.00 1.90
1653 1946 9.046296 CACACAATAATCTTTACCAGAGGATAC 57.954 37.037 0.00 0.00 33.87 2.24
1654 1947 8.768397 ACACAATAATCTTTACCAGAGGATACA 58.232 33.333 0.00 0.00 33.87 2.29
1655 1948 9.046296 CACAATAATCTTTACCAGAGGATACAC 57.954 37.037 0.00 0.00 33.87 2.90
1749 2042 6.521162 ACAAGTGAAAGGTGTTTGAAGTTTT 58.479 32.000 0.00 0.00 0.00 2.43
1763 2056 9.515020 TGTTTGAAGTTTTTCATGATACAGTTC 57.485 29.630 11.01 11.01 42.60 3.01
2125 2418 3.940209 ATATGTTTGTGTGCACCAAGG 57.060 42.857 15.69 0.00 0.00 3.61
2129 2422 1.476488 GTTTGTGTGCACCAAGGAGTT 59.524 47.619 15.69 0.00 0.00 3.01
2131 2424 0.254462 TGTGTGCACCAAGGAGTTCA 59.746 50.000 15.69 0.00 0.00 3.18
2147 2441 4.397417 GGAGTTCAAAATCATGTGAGGGAG 59.603 45.833 0.00 0.00 0.00 4.30
2180 2475 5.789643 ACTTATGTGTTGGCTGTGATTTT 57.210 34.783 0.00 0.00 0.00 1.82
2444 2739 4.270008 ACCCTGGTCGAATTAAATCCAAG 58.730 43.478 0.00 0.00 0.00 3.61
2520 2822 3.243468 GGTAAGCTCCGAAGTGATAGTCC 60.243 52.174 0.00 0.00 0.00 3.85
2662 2967 3.120511 CGCTTTGCCTACTTGTTCTCTTC 60.121 47.826 0.00 0.00 0.00 2.87
3027 3348 3.837146 AGCTCTCTTTGTCATCTCCTTGA 59.163 43.478 0.00 0.00 0.00 3.02
3269 3591 4.248058 CCTGATTTTGAAATGCACCTTCC 58.752 43.478 7.68 0.00 0.00 3.46
3270 3592 4.262549 CCTGATTTTGAAATGCACCTTCCA 60.263 41.667 7.68 0.00 0.00 3.53
3271 3593 5.484715 CTGATTTTGAAATGCACCTTCCAT 58.515 37.500 7.68 0.00 0.00 3.41
3360 3682 7.593825 AGAATTTGTCATACAACTTACAAGGC 58.406 34.615 0.00 0.00 37.90 4.35
3364 3686 2.027561 TCATACAACTTACAAGGCGGCT 60.028 45.455 5.25 5.25 0.00 5.52
3379 3701 3.891366 AGGCGGCTAAATGCTAATTGATT 59.109 39.130 11.03 0.00 42.39 2.57
3606 3928 6.493115 TGGTTTCATGGATTAGTTCATGTTGT 59.507 34.615 6.41 0.00 40.94 3.32
3626 3957 6.311690 TGTTGTTAGCTTAAGTTTTTGCCAAC 59.688 34.615 4.02 8.78 0.00 3.77
3634 3965 3.177997 AGTTTTTGCCAACGAAAGCAT 57.822 38.095 0.00 0.00 39.11 3.79
3640 3971 3.717400 TGCCAACGAAAGCATGTTTAA 57.283 38.095 0.00 0.00 33.08 1.52
3652 3983 4.597079 AGCATGTTTAACATTTATCCGCG 58.403 39.130 7.97 0.00 36.53 6.46
3656 3987 6.344936 GCATGTTTAACATTTATCCGCGATTG 60.345 38.462 8.23 0.00 36.53 2.67
3704 4035 9.152327 TGCAATGGAATTTGGTATGGATAAATA 57.848 29.630 0.00 0.00 31.22 1.40
3736 4067 5.224888 CAAAAGGACACAACCATTCTCATG 58.775 41.667 0.00 0.00 0.00 3.07
3789 4120 4.793201 ACCTCAAGAAACAAGCCTAACTT 58.207 39.130 0.00 0.00 40.05 2.66
3852 4183 6.239036 CCCTTTCGAGTGATGTGATATCTACA 60.239 42.308 3.98 7.28 0.00 2.74
3928 4259 5.817816 CCCTATAGCTTGTTTGTAAGACCAG 59.182 44.000 0.00 0.00 0.00 4.00
3958 4289 5.980715 TGTGCATTTTGCTGCTGATATAATG 59.019 36.000 0.00 0.00 45.31 1.90
3994 4325 6.699204 CCTACATACTGACATGACATCTGTTC 59.301 42.308 0.00 0.00 31.53 3.18
4063 4394 0.457851 CTAGAGCGGTTGGTGAGAGG 59.542 60.000 0.00 0.00 0.00 3.69
4135 4466 1.360551 CCTCGAGCATACTGACCGG 59.639 63.158 6.99 0.00 0.00 5.28
4241 4572 0.723981 GCAAAGGACTCGACAGCATC 59.276 55.000 0.00 0.00 0.00 3.91
4354 4685 1.541588 GCAAACACTGTCCAGAATCCC 59.458 52.381 0.40 0.00 0.00 3.85
4359 4690 1.625315 CACTGTCCAGAATCCCACTCA 59.375 52.381 0.40 0.00 0.00 3.41
4360 4691 1.905215 ACTGTCCAGAATCCCACTCAG 59.095 52.381 0.40 0.00 0.00 3.35
4361 4692 1.209019 CTGTCCAGAATCCCACTCAGG 59.791 57.143 0.00 0.00 37.03 3.86
4362 4693 1.280457 GTCCAGAATCCCACTCAGGT 58.720 55.000 0.00 0.00 34.66 4.00
4363 4694 2.225522 TGTCCAGAATCCCACTCAGGTA 60.226 50.000 0.00 0.00 34.66 3.08
4364 4695 2.838202 GTCCAGAATCCCACTCAGGTAA 59.162 50.000 0.00 0.00 34.66 2.85
4365 4696 3.263425 GTCCAGAATCCCACTCAGGTAAA 59.737 47.826 0.00 0.00 34.66 2.01
4366 4697 3.263425 TCCAGAATCCCACTCAGGTAAAC 59.737 47.826 0.00 0.00 34.66 2.01
4367 4698 3.009033 CCAGAATCCCACTCAGGTAAACA 59.991 47.826 0.00 0.00 34.66 2.83
4368 4699 4.003648 CAGAATCCCACTCAGGTAAACAC 58.996 47.826 0.00 0.00 34.66 3.32
4369 4700 3.910627 AGAATCCCACTCAGGTAAACACT 59.089 43.478 0.00 0.00 34.66 3.55
4370 4701 3.703001 ATCCCACTCAGGTAAACACTG 57.297 47.619 0.00 0.00 37.30 3.66
4371 4702 2.404559 TCCCACTCAGGTAAACACTGT 58.595 47.619 0.00 0.00 37.25 3.55
4372 4703 2.367567 TCCCACTCAGGTAAACACTGTC 59.632 50.000 0.00 0.00 37.25 3.51
4373 4704 2.550208 CCCACTCAGGTAAACACTGTCC 60.550 54.545 0.00 0.00 37.25 4.02
4374 4705 2.104111 CCACTCAGGTAAACACTGTCCA 59.896 50.000 0.00 0.00 37.25 4.02
4375 4706 3.433031 CCACTCAGGTAAACACTGTCCAA 60.433 47.826 0.00 0.00 37.25 3.53
4376 4707 4.196193 CACTCAGGTAAACACTGTCCAAA 58.804 43.478 0.00 0.00 37.25 3.28
4377 4708 4.638421 CACTCAGGTAAACACTGTCCAAAA 59.362 41.667 0.00 0.00 37.25 2.44
4378 4709 5.299279 CACTCAGGTAAACACTGTCCAAAAT 59.701 40.000 0.00 0.00 37.25 1.82
4379 4710 5.531287 ACTCAGGTAAACACTGTCCAAAATC 59.469 40.000 0.00 0.00 37.25 2.17
4380 4711 4.825085 TCAGGTAAACACTGTCCAAAATCC 59.175 41.667 0.00 0.00 37.25 3.01
4381 4712 4.827284 CAGGTAAACACTGTCCAAAATCCT 59.173 41.667 0.00 0.00 0.00 3.24
4382 4713 6.001460 CAGGTAAACACTGTCCAAAATCCTA 58.999 40.000 0.00 0.00 0.00 2.94
4383 4714 6.002082 AGGTAAACACTGTCCAAAATCCTAC 58.998 40.000 0.00 0.00 0.00 3.18
4384 4715 6.002082 GGTAAACACTGTCCAAAATCCTACT 58.998 40.000 0.00 0.00 0.00 2.57
4385 4716 6.148976 GGTAAACACTGTCCAAAATCCTACTC 59.851 42.308 0.00 0.00 0.00 2.59
4427 4758 2.594592 GCCAAACGCCAGGACACT 60.595 61.111 0.00 0.00 0.00 3.55
4590 4921 0.673333 CATCCACAGGCGCACACTAA 60.673 55.000 10.83 0.00 0.00 2.24
4659 4990 2.101917 CGTATACCCCAGTGTACCAAGG 59.898 54.545 0.00 0.00 37.30 3.61
4672 5003 1.224592 CCAAGGAGCAAGGCCGTAT 59.775 57.895 0.00 0.00 0.00 3.06
4695 5026 1.135915 CTATCCGAGTCAACAGCAGCT 59.864 52.381 0.00 0.00 0.00 4.24
4836 5167 1.349688 TCATACAACTGGGGTCCACAC 59.650 52.381 0.00 0.00 0.00 3.82
4876 5207 2.105649 TGGATATTACAATCAGCCGGCA 59.894 45.455 31.54 9.64 0.00 5.69
4967 5298 2.783510 AGGTACAATAGGAATGGGGTGG 59.216 50.000 0.00 0.00 0.00 4.61
4976 5307 1.000359 AATGGGGTGGCTACAAGGC 60.000 57.895 1.52 0.00 41.77 4.35
5048 5379 2.125350 GGTCGCAAGCCTCCTCAG 60.125 66.667 0.00 0.00 37.18 3.35
5153 5484 3.763360 CCCTTGGCTGACAAAATGTATCA 59.237 43.478 0.00 0.00 38.91 2.15
5195 5526 7.981789 TGTATGTCATCCTTCATACTTCAGTTC 59.018 37.037 13.74 0.00 43.63 3.01
5200 5531 3.504906 TCCTTCATACTTCAGTTCGTCGT 59.495 43.478 0.00 0.00 0.00 4.34
5206 5537 0.596577 CTTCAGTTCGTCGTGGAGGA 59.403 55.000 0.00 0.00 0.00 3.71
5214 5545 1.541147 TCGTCGTGGAGGAAACGTAAT 59.459 47.619 0.00 0.00 41.70 1.89
5251 5582 4.549458 AGATTTTGTGCAGAATGTTTCGG 58.451 39.130 0.00 0.00 39.31 4.30
5283 5614 4.072131 GTCACTTGAGATGCCAAACCTTA 58.928 43.478 0.00 0.00 0.00 2.69
5304 5635 1.407437 CGTTTCCCTCTTCCCTGATGG 60.407 57.143 0.00 0.00 0.00 3.51
5306 5637 2.844348 GTTTCCCTCTTCCCTGATGGTA 59.156 50.000 0.00 0.00 34.77 3.25
5401 5732 0.984995 AGCAGTGACTAGGGGTTTCC 59.015 55.000 0.00 0.00 0.00 3.13
5403 5734 1.339151 GCAGTGACTAGGGGTTTCCAG 60.339 57.143 0.00 0.00 38.24 3.86
5404 5735 1.978580 CAGTGACTAGGGGTTTCCAGT 59.021 52.381 0.00 0.00 38.24 4.00
5405 5736 1.978580 AGTGACTAGGGGTTTCCAGTG 59.021 52.381 0.00 0.00 38.24 3.66
5406 5737 1.975680 GTGACTAGGGGTTTCCAGTGA 59.024 52.381 0.00 0.00 38.24 3.41
5448 5779 9.933723 ATGCAATTTTCTAAGAAAAATGCTACT 57.066 25.926 24.58 15.13 38.51 2.57
5571 5932 3.015327 CCAAGGAGCAATGAAAGAGAGG 58.985 50.000 0.00 0.00 0.00 3.69
5664 8186 5.456173 GCAGTATAAGAACACGAGAAGTAGC 59.544 44.000 0.00 0.00 0.00 3.58
5670 8192 5.847670 AGAACACGAGAAGTAGCAAAATC 57.152 39.130 0.00 0.00 0.00 2.17
5671 8193 4.691216 AGAACACGAGAAGTAGCAAAATCC 59.309 41.667 0.00 0.00 0.00 3.01
5708 8230 3.940852 TCTAGCGACGACTACAACCATTA 59.059 43.478 0.00 0.00 0.00 1.90
5713 8235 4.478699 CGACGACTACAACCATTAGAACA 58.521 43.478 0.00 0.00 0.00 3.18
5717 8240 4.929808 CGACTACAACCATTAGAACAAGCT 59.070 41.667 0.00 0.00 0.00 3.74
5722 8245 4.520492 ACAACCATTAGAACAAGCTGAAGG 59.480 41.667 0.00 0.00 0.00 3.46
5737 8260 1.687494 GAAGGCGCGTCACTGTCATC 61.687 60.000 15.58 0.00 0.00 2.92
5743 8266 2.982130 GTCACTGTCATCGCCCCT 59.018 61.111 0.00 0.00 0.00 4.79
5747 8271 0.036010 CACTGTCATCGCCCCTTTCT 60.036 55.000 0.00 0.00 0.00 2.52
5753 8277 0.179062 CATCGCCCCTTTCTCTGGAG 60.179 60.000 0.00 0.00 0.00 3.86
5767 8291 1.977854 TCTGGAGCTGAGCAAACCTTA 59.022 47.619 7.39 0.00 0.00 2.69
5784 8308 8.094798 CAAACCTTATTGCAGTAGACAGTAAA 57.905 34.615 0.00 0.00 0.00 2.01
5785 8309 7.907214 AACCTTATTGCAGTAGACAGTAAAG 57.093 36.000 0.00 0.00 0.00 1.85
5801 8352 9.066892 AGACAGTAAAGAAATCATTGTGCTAAA 57.933 29.630 0.00 0.00 0.00 1.85
5823 8374 3.764237 TCCTAAAGGACCAACACACTC 57.236 47.619 0.00 0.00 39.78 3.51
5831 8382 2.004017 GACCAACACACTCGAACAACA 58.996 47.619 0.00 0.00 0.00 3.33
5832 8383 2.417239 GACCAACACACTCGAACAACAA 59.583 45.455 0.00 0.00 0.00 2.83
5834 8385 2.427169 CAACACACTCGAACAACAACG 58.573 47.619 0.00 0.00 0.00 4.10
5835 8386 0.372334 ACACACTCGAACAACAACGC 59.628 50.000 0.00 0.00 0.00 4.84
5843 8394 1.130955 GAACAACAACGCTGCCAATG 58.869 50.000 0.00 0.00 0.00 2.82
5846 8397 1.135915 ACAACAACGCTGCCAATGAAA 59.864 42.857 0.00 0.00 0.00 2.69
5852 8403 1.336240 ACGCTGCCAATGAAAAGAAGC 60.336 47.619 0.00 0.00 0.00 3.86
5877 8428 7.155328 CACAAGGATCCAACCTATAGACATAC 58.845 42.308 15.82 0.00 39.62 2.39
5888 8439 5.123502 ACCTATAGACATACGAACATAGCCG 59.876 44.000 0.00 0.00 0.00 5.52
5890 8441 1.340248 AGACATACGAACATAGCCGGG 59.660 52.381 2.18 0.00 0.00 5.73
5891 8442 1.068127 GACATACGAACATAGCCGGGT 59.932 52.381 12.58 12.58 0.00 5.28
5901 8453 0.988832 ATAGCCGGGTGAAGGTTGAA 59.011 50.000 18.40 0.00 0.00 2.69
5904 8456 1.313091 GCCGGGTGAAGGTTGAATCC 61.313 60.000 2.18 0.00 0.00 3.01
5905 8457 1.024579 CCGGGTGAAGGTTGAATCCG 61.025 60.000 0.00 0.00 36.23 4.18
5910 8561 1.197721 GTGAAGGTTGAATCCGCACAG 59.802 52.381 0.00 0.00 37.49 3.66
5916 8567 1.398390 GTTGAATCCGCACAGATCCAC 59.602 52.381 0.00 0.00 0.00 4.02
5918 8569 1.153369 AATCCGCACAGATCCACCG 60.153 57.895 0.00 0.00 0.00 4.94
5929 8580 3.244561 ACAGATCCACCGAAGACAAACAT 60.245 43.478 0.00 0.00 0.00 2.71
5931 8582 1.790755 TCCACCGAAGACAAACATCG 58.209 50.000 0.00 0.00 39.06 3.84
5932 8583 1.341852 TCCACCGAAGACAAACATCGA 59.658 47.619 0.00 0.00 41.35 3.59
5933 8584 2.028476 TCCACCGAAGACAAACATCGAT 60.028 45.455 0.00 0.00 41.35 3.59
5934 8585 2.742053 CCACCGAAGACAAACATCGATT 59.258 45.455 0.00 0.00 41.35 3.34
5935 8586 3.424829 CCACCGAAGACAAACATCGATTG 60.425 47.826 0.00 0.00 41.35 2.67
5942 8593 6.573664 AAGACAAACATCGATTGAATTCCA 57.426 33.333 2.27 0.00 0.00 3.53
5943 8594 5.942872 AGACAAACATCGATTGAATTCCAC 58.057 37.500 2.27 0.00 0.00 4.02
5944 8595 5.473162 AGACAAACATCGATTGAATTCCACA 59.527 36.000 2.27 0.00 0.00 4.17
5962 8613 0.247460 CAAGATCCGCCAGAGACACA 59.753 55.000 0.00 0.00 0.00 3.72
5975 8626 2.203015 ACACACCTCCACACGCAC 60.203 61.111 0.00 0.00 0.00 5.34
5977 8628 1.523711 CACACCTCCACACGCACTT 60.524 57.895 0.00 0.00 0.00 3.16
5978 8629 1.095228 CACACCTCCACACGCACTTT 61.095 55.000 0.00 0.00 0.00 2.66
5984 8635 0.249699 TCCACACGCACTTTGACGAT 60.250 50.000 0.00 0.00 0.00 3.73
5997 8648 1.129809 GACGATGCGAAACACACCG 59.870 57.895 0.00 0.00 0.00 4.94
6039 8690 6.238130 GCAGTACGAACCTTATTTCATCTTCC 60.238 42.308 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.587547 GGATGGATCTGAGTTTCCGC 58.412 55.000 0.00 0.00 34.58 5.54
26 27 2.131023 AGGGGATGGATCTGAGTTTCC 58.869 52.381 0.00 0.00 0.00 3.13
28 29 2.566746 ACAGGGGATGGATCTGAGTTT 58.433 47.619 0.00 0.00 33.19 2.66
32 33 3.593328 AGAAAAACAGGGGATGGATCTGA 59.407 43.478 0.00 0.00 33.19 3.27
46 47 5.305902 GGGGATTTTTACCTGGAGAAAAACA 59.694 40.000 19.07 6.05 37.35 2.83
77 78 2.180017 GGACTAGCCGACGCGAAA 59.820 61.111 15.93 0.00 41.18 3.46
129 134 1.125093 ACCCCCACAATCGACAGACA 61.125 55.000 0.00 0.00 0.00 3.41
134 139 1.918868 GCGAAACCCCCACAATCGAC 61.919 60.000 0.00 0.00 35.65 4.20
166 172 3.737172 CGAAGCAAACGGGCCCTG 61.737 66.667 22.43 16.23 0.00 4.45
169 175 3.431725 CCTCGAAGCAAACGGGCC 61.432 66.667 0.00 0.00 0.00 5.80
170 176 3.431725 CCCTCGAAGCAAACGGGC 61.432 66.667 0.00 0.00 0.00 6.13
174 180 1.666189 GTATCAGCCCTCGAAGCAAAC 59.334 52.381 9.54 0.00 0.00 2.93
175 181 1.555075 AGTATCAGCCCTCGAAGCAAA 59.445 47.619 9.54 0.00 0.00 3.68
290 349 1.909700 ACTTCGGCAATTCACCACAT 58.090 45.000 0.00 0.00 0.00 3.21
301 360 1.290955 CCCGAGTACAACTTCGGCA 59.709 57.895 14.16 0.00 37.49 5.69
317 376 1.594021 CCACGCAAAGGCAAAACCC 60.594 57.895 0.00 0.00 40.58 4.11
401 463 1.153765 GAAAAAGCTCCCATGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
441 509 1.758862 ACCGTACCTACCATTAGCACC 59.241 52.381 0.00 0.00 0.00 5.01
445 513 5.964758 TGTGTTTACCGTACCTACCATTAG 58.035 41.667 0.00 0.00 0.00 1.73
473 541 4.406456 ACCTTTTTGTGCATGTCCTATCA 58.594 39.130 0.00 0.00 0.00 2.15
501 569 0.606401 ATCACTGCCCAAGTCAACGG 60.606 55.000 0.00 0.00 36.83 4.44
767 841 3.531538 TGAGAGAACCAAATGTATCCGC 58.468 45.455 0.00 0.00 0.00 5.54
885 960 5.872617 AGTTACAAGTACAATGATTGCGCTA 59.127 36.000 9.73 0.00 0.00 4.26
888 963 7.148639 ACACTAGTTACAAGTACAATGATTGCG 60.149 37.037 4.84 0.00 0.00 4.85
952 1027 8.510505 AGAAACATAAGATCAAGCAAGAAAGAC 58.489 33.333 0.00 0.00 0.00 3.01
954 1029 9.339492 GAAGAAACATAAGATCAAGCAAGAAAG 57.661 33.333 0.00 0.00 0.00 2.62
1091 1167 6.202570 CAGCTCCTTAATTGCAGATAGTCTTC 59.797 42.308 0.00 0.00 0.00 2.87
1142 1218 6.996282 CCAAAGGAGTAAGTTACCTTTCAAGA 59.004 38.462 12.43 0.00 46.73 3.02
1190 1269 7.977293 TGTCAATATCAGGCTCATTTTCAAATG 59.023 33.333 5.99 5.99 45.49 2.32
1329 1418 9.533831 ACCTTTTGAGGATATATTCAACTTTGT 57.466 29.630 0.00 0.00 33.36 2.83
1347 1436 8.413229 CAATAGACTTTCTGGAAAACCTTTTGA 58.587 33.333 14.39 0.00 31.20 2.69
1349 1438 8.306313 ACAATAGACTTTCTGGAAAACCTTTT 57.694 30.769 0.00 0.00 0.00 2.27
1363 1452 9.682465 GGGTTCTTTAGGAATACAATAGACTTT 57.318 33.333 0.00 0.00 36.24 2.66
1364 1453 9.059023 AGGGTTCTTTAGGAATACAATAGACTT 57.941 33.333 0.00 0.00 36.24 3.01
1489 1583 2.069273 CCTGTCAATGAGTCACCGTTC 58.931 52.381 0.00 0.00 0.00 3.95
1525 1817 4.081309 GGCCATAGGTCACTAGTTACACAA 60.081 45.833 9.34 0.00 31.54 3.33
1549 1841 7.820872 TCCAATACTAGGTAAAAACTGTACTGC 59.179 37.037 0.00 0.00 0.00 4.40
1566 1859 8.815565 TTGCCATATGACTTTTTCCAATACTA 57.184 30.769 3.65 0.00 0.00 1.82
1576 1869 9.537192 CAAATCACATATTGCCATATGACTTTT 57.463 29.630 21.26 14.05 43.68 2.27
1580 1873 6.939551 GCAAATCACATATTGCCATATGAC 57.060 37.500 21.26 0.00 43.68 3.06
1723 2016 4.764823 ACTTCAAACACCTTTCACTTGTCA 59.235 37.500 0.00 0.00 0.00 3.58
1724 2017 5.310720 ACTTCAAACACCTTTCACTTGTC 57.689 39.130 0.00 0.00 0.00 3.18
1725 2018 5.722021 AACTTCAAACACCTTTCACTTGT 57.278 34.783 0.00 0.00 0.00 3.16
1749 2042 7.218228 AGCAACATTTGAACTGTATCATGAA 57.782 32.000 0.00 0.00 0.00 2.57
1763 2056 7.652909 TGAGAAAATCAGGTAAAGCAACATTTG 59.347 33.333 0.00 0.00 32.77 2.32
2003 2296 2.362397 GGATAGAGTGATCAGGCAACGA 59.638 50.000 0.00 0.00 46.39 3.85
2125 2418 4.142513 GCTCCCTCACATGATTTTGAACTC 60.143 45.833 0.00 0.00 0.00 3.01
2129 2422 3.438216 TGCTCCCTCACATGATTTTGA 57.562 42.857 0.00 0.00 0.00 2.69
2131 2424 3.972133 TGATGCTCCCTCACATGATTTT 58.028 40.909 0.00 0.00 0.00 1.82
2147 2441 5.973565 GCCAACACATAAGTTAGAATGATGC 59.026 40.000 0.00 0.00 0.00 3.91
2411 2706 3.433343 TCGACCAGGGTAGTTATCAACA 58.567 45.455 0.00 0.00 0.00 3.33
2444 2739 7.068839 TCCAAAGTACTGATCCAGTAGAAGATC 59.931 40.741 7.03 0.00 45.88 2.75
2520 2822 5.712152 ACTAGAAAAACCCATCAGCAAAG 57.288 39.130 0.00 0.00 0.00 2.77
2727 3034 6.969473 GCATCAGAAAGGTAAGCAAAAGATAC 59.031 38.462 0.00 0.00 0.00 2.24
2744 3051 8.833493 CACATGTCTCAAAATATAGCATCAGAA 58.167 33.333 0.00 0.00 0.00 3.02
3301 3623 2.762887 CTGCTATCACTGTCCTGAAGGA 59.237 50.000 0.00 0.00 43.08 3.36
3303 3625 4.462508 TTCTGCTATCACTGTCCTGAAG 57.537 45.455 0.00 0.00 0.00 3.02
3503 3825 6.226787 TGTAACCCCAGCAAAATAAACAATG 58.773 36.000 0.00 0.00 0.00 2.82
3558 3880 6.348540 CCAAGGGATTAGCATATTTAGCGAAC 60.349 42.308 0.00 0.00 37.01 3.95
3606 3928 5.502153 TCGTTGGCAAAAACTTAAGCTAA 57.498 34.783 0.00 0.00 0.00 3.09
3626 3957 6.291060 GCGGATAAATGTTAAACATGCTTTCG 60.291 38.462 0.00 0.00 37.97 3.46
3634 3965 5.031578 GCAATCGCGGATAAATGTTAAACA 58.968 37.500 6.13 0.00 0.00 2.83
3640 3971 2.560504 TGAGCAATCGCGGATAAATGT 58.439 42.857 6.13 0.00 45.49 2.71
3652 3983 3.966154 CTCATCCAGCAAATGAGCAATC 58.034 45.455 9.24 0.00 42.54 2.67
3704 4035 5.600484 TGGTTGTGTCCTTTTGGTATCAAAT 59.400 36.000 1.11 0.00 41.84 2.32
3789 4120 9.409312 CAAAACTGCAAACAATATAAGATCACA 57.591 29.630 0.00 0.00 0.00 3.58
3852 4183 5.733620 TCTTCTTAAACTGACCCGTGTAT 57.266 39.130 0.00 0.00 0.00 2.29
3958 4289 7.120923 TGTCAGTATGTAGGGTAAATTCTCC 57.879 40.000 0.00 0.00 37.40 3.71
3994 4325 5.455392 TCTTCGACCTAAACAAGAGTAACG 58.545 41.667 0.00 0.00 0.00 3.18
4063 4394 1.349357 CTAGCAATTAGGAGGAGCCCC 59.651 57.143 0.00 0.00 37.37 5.80
4117 4448 1.101635 TCCGGTCAGTATGCTCGAGG 61.102 60.000 15.58 0.00 34.23 4.63
4135 4466 3.250040 ACAACATTGCCAGTAAGTCGTTC 59.750 43.478 0.00 0.00 0.00 3.95
4219 4550 1.289066 CTGTCGAGTCCTTTGCGGA 59.711 57.895 0.00 0.00 40.30 5.54
4241 4572 3.118738 ACCTTAGCTCCCACGTTGATTAG 60.119 47.826 0.00 0.00 0.00 1.73
4354 4685 3.469008 TGGACAGTGTTTACCTGAGTG 57.531 47.619 0.00 0.00 0.00 3.51
4359 4690 5.061721 AGGATTTTGGACAGTGTTTACCT 57.938 39.130 0.00 0.00 0.00 3.08
4360 4691 6.002082 AGTAGGATTTTGGACAGTGTTTACC 58.998 40.000 0.00 0.00 0.00 2.85
4361 4692 6.708949 TGAGTAGGATTTTGGACAGTGTTTAC 59.291 38.462 0.00 0.00 0.00 2.01
4362 4693 6.833041 TGAGTAGGATTTTGGACAGTGTTTA 58.167 36.000 0.00 0.00 0.00 2.01
4363 4694 5.690865 TGAGTAGGATTTTGGACAGTGTTT 58.309 37.500 0.00 0.00 0.00 2.83
4364 4695 5.304686 TGAGTAGGATTTTGGACAGTGTT 57.695 39.130 0.00 0.00 0.00 3.32
4365 4696 4.899502 CTGAGTAGGATTTTGGACAGTGT 58.100 43.478 0.00 0.00 0.00 3.55
4380 4711 3.951037 AGTATCAGTGCTCACCTGAGTAG 59.049 47.826 4.26 0.00 43.85 2.57
4381 4712 3.696548 CAGTATCAGTGCTCACCTGAGTA 59.303 47.826 4.26 0.00 43.85 2.59
4382 4713 2.495270 CAGTATCAGTGCTCACCTGAGT 59.505 50.000 4.26 0.00 43.85 3.41
4383 4714 2.738000 GCAGTATCAGTGCTCACCTGAG 60.738 54.545 0.00 0.00 41.22 3.35
4384 4715 1.205655 GCAGTATCAGTGCTCACCTGA 59.794 52.381 7.19 0.00 41.22 3.86
4385 4716 1.066645 TGCAGTATCAGTGCTCACCTG 60.067 52.381 7.44 0.00 44.61 4.00
4392 4723 2.176273 CGCCCTGCAGTATCAGTGC 61.176 63.158 13.81 2.69 44.57 4.40
4427 4758 2.698797 GAGGAGGGTCATGATTTCGGTA 59.301 50.000 0.00 0.00 0.00 4.02
4620 4951 2.210116 ACGCCGGTTGATGATTATGAC 58.790 47.619 1.90 0.00 0.00 3.06
4659 4990 3.586892 GGATAGTAATACGGCCTTGCTC 58.413 50.000 0.00 0.00 0.00 4.26
4672 5003 3.428999 GCTGCTGTTGACTCGGATAGTAA 60.429 47.826 0.00 0.00 39.07 2.24
4695 5026 2.554893 GTTTGGAACCCGCTTGTATGAA 59.445 45.455 0.00 0.00 0.00 2.57
4836 5167 1.942657 CATTCTGGTATTGTCCTGGCG 59.057 52.381 0.00 0.00 0.00 5.69
4876 5207 2.981784 TGATCCTTGGCCTGCAGTATAT 59.018 45.455 13.81 0.00 0.00 0.86
5048 5379 4.517815 TCGCCATTCCGTACGGCC 62.518 66.667 29.64 12.99 43.17 6.13
5133 5464 5.633830 ACTGATACATTTTGTCAGCCAAG 57.366 39.130 1.81 0.00 42.33 3.61
5153 5484 7.848223 TGACATACATCATGAAATCGAAACT 57.152 32.000 0.00 0.00 38.10 2.66
5195 5526 1.652124 CATTACGTTTCCTCCACGACG 59.348 52.381 0.00 0.00 40.20 5.12
5214 5545 7.984050 TGCACAAAATCTTTTTAGTGGAAATCA 59.016 29.630 12.65 4.57 29.70 2.57
5226 5557 6.018832 CCGAAACATTCTGCACAAAATCTTTT 60.019 34.615 0.00 0.00 0.00 2.27
5251 5582 4.142816 GCATCTCAAGTGACATTACACCAC 60.143 45.833 0.00 0.00 41.12 4.16
5283 5614 1.279271 CATCAGGGAAGAGGGAAACGT 59.721 52.381 0.00 0.00 0.00 3.99
5304 5635 2.685100 AGGCAACAACGCTCTAGTTAC 58.315 47.619 0.00 0.00 41.41 2.50
5306 5637 2.256117 AAGGCAACAACGCTCTAGTT 57.744 45.000 0.00 0.00 41.41 2.24
5401 5732 5.006358 GCATTTACGGGTACACTAATCACTG 59.994 44.000 0.00 0.00 0.00 3.66
5403 5734 4.871557 TGCATTTACGGGTACACTAATCAC 59.128 41.667 0.00 0.00 0.00 3.06
5404 5735 5.087391 TGCATTTACGGGTACACTAATCA 57.913 39.130 0.00 0.00 0.00 2.57
5405 5736 6.613755 ATTGCATTTACGGGTACACTAATC 57.386 37.500 0.00 0.00 0.00 1.75
5406 5737 7.399245 AAATTGCATTTACGGGTACACTAAT 57.601 32.000 0.00 0.00 0.00 1.73
5447 5778 5.355071 TCAAGGCAAAAGCAGTGATATGTAG 59.645 40.000 0.00 0.00 0.00 2.74
5448 5779 5.252547 TCAAGGCAAAAGCAGTGATATGTA 58.747 37.500 0.00 0.00 0.00 2.29
5449 5780 4.081406 TCAAGGCAAAAGCAGTGATATGT 58.919 39.130 0.00 0.00 0.00 2.29
5571 5932 8.200120 CCCCATTTTCCTTTTGATCTATTTCTC 58.800 37.037 0.00 0.00 0.00 2.87
5664 8186 3.605634 TGGTCTACGGACATGGATTTTG 58.394 45.455 0.00 0.00 43.77 2.44
5670 8192 2.029828 GCTAGATGGTCTACGGACATGG 60.030 54.545 0.00 0.00 43.77 3.66
5671 8193 2.350868 CGCTAGATGGTCTACGGACATG 60.351 54.545 0.00 0.00 43.77 3.21
5708 8230 2.320587 CGCGCCTTCAGCTTGTTCT 61.321 57.895 0.00 0.00 40.39 3.01
5713 8235 3.044305 GTGACGCGCCTTCAGCTT 61.044 61.111 5.73 0.00 40.39 3.74
5717 8240 2.355837 GACAGTGACGCGCCTTCA 60.356 61.111 5.73 1.14 0.00 3.02
5722 8245 4.196826 GCGATGACAGTGACGCGC 62.197 66.667 5.73 14.23 41.49 6.86
5737 8260 2.124942 GCTCCAGAGAAAGGGGCG 60.125 66.667 0.00 0.00 43.86 6.13
5743 8266 2.498167 GTTTGCTCAGCTCCAGAGAAA 58.502 47.619 0.00 0.00 35.09 2.52
5747 8271 0.767375 AAGGTTTGCTCAGCTCCAGA 59.233 50.000 0.00 0.00 0.00 3.86
5767 8291 8.798859 ATGATTTCTTTACTGTCTACTGCAAT 57.201 30.769 0.00 0.00 0.00 3.56
5773 8297 8.034058 AGCACAATGATTTCTTTACTGTCTAC 57.966 34.615 0.00 0.00 0.00 2.59
5776 8300 9.677567 TTTTAGCACAATGATTTCTTTACTGTC 57.322 29.630 0.00 0.00 0.00 3.51
5780 8304 9.860898 AGGATTTTAGCACAATGATTTCTTTAC 57.139 29.630 0.00 0.00 0.00 2.01
5785 8309 9.305925 CCTTTAGGATTTTAGCACAATGATTTC 57.694 33.333 0.00 0.00 37.39 2.17
5803 8354 2.036733 CGAGTGTGTTGGTCCTTTAGGA 59.963 50.000 0.00 0.00 43.08 2.94
5814 8365 2.427169 CGTTGTTGTTCGAGTGTGTTG 58.573 47.619 0.00 0.00 0.00 3.33
5822 8373 1.369839 TTGGCAGCGTTGTTGTTCGA 61.370 50.000 0.00 0.00 0.00 3.71
5823 8374 0.317770 ATTGGCAGCGTTGTTGTTCG 60.318 50.000 0.00 0.00 0.00 3.95
5831 8382 2.863704 GCTTCTTTTCATTGGCAGCGTT 60.864 45.455 0.00 0.00 0.00 4.84
5832 8383 1.336240 GCTTCTTTTCATTGGCAGCGT 60.336 47.619 0.00 0.00 0.00 5.07
5834 8385 2.064014 GTGCTTCTTTTCATTGGCAGC 58.936 47.619 0.00 0.00 0.00 5.25
5835 8386 3.374220 TGTGCTTCTTTTCATTGGCAG 57.626 42.857 0.00 0.00 0.00 4.85
5843 8394 4.550422 GTTGGATCCTTGTGCTTCTTTTC 58.450 43.478 14.23 0.00 0.00 2.29
5846 8397 2.108952 AGGTTGGATCCTTGTGCTTCTT 59.891 45.455 14.23 0.00 33.52 2.52
5852 8403 5.614324 TGTCTATAGGTTGGATCCTTGTG 57.386 43.478 14.23 0.00 38.86 3.33
5877 8428 0.810031 CCTTCACCCGGCTATGTTCG 60.810 60.000 0.00 0.00 0.00 3.95
5888 8439 0.608035 TGCGGATTCAACCTTCACCC 60.608 55.000 0.00 0.00 0.00 4.61
5890 8441 1.197721 CTGTGCGGATTCAACCTTCAC 59.802 52.381 0.00 0.00 34.31 3.18
5891 8442 1.071542 TCTGTGCGGATTCAACCTTCA 59.928 47.619 0.00 0.00 0.00 3.02
5901 8453 1.613317 TTCGGTGGATCTGTGCGGAT 61.613 55.000 0.00 0.00 0.00 4.18
5904 8456 1.078759 GTCTTCGGTGGATCTGTGCG 61.079 60.000 0.00 0.00 0.00 5.34
5905 8457 0.037326 TGTCTTCGGTGGATCTGTGC 60.037 55.000 0.00 0.00 0.00 4.57
5910 8561 2.348666 CGATGTTTGTCTTCGGTGGATC 59.651 50.000 0.00 0.00 39.15 3.36
5916 8567 4.661993 TTCAATCGATGTTTGTCTTCGG 57.338 40.909 0.00 0.00 41.79 4.30
5918 8569 6.524586 GTGGAATTCAATCGATGTTTGTCTTC 59.475 38.462 7.93 2.94 0.00 2.87
5929 8580 3.871006 CGGATCTTGTGGAATTCAATCGA 59.129 43.478 7.93 0.00 0.00 3.59
5931 8582 3.243201 GGCGGATCTTGTGGAATTCAATC 60.243 47.826 7.93 0.00 0.00 2.67
5932 8583 2.689983 GGCGGATCTTGTGGAATTCAAT 59.310 45.455 7.93 0.00 0.00 2.57
5933 8584 2.091541 GGCGGATCTTGTGGAATTCAA 58.908 47.619 7.93 0.00 0.00 2.69
5934 8585 1.004161 TGGCGGATCTTGTGGAATTCA 59.996 47.619 7.93 0.00 0.00 2.57
5935 8586 1.672881 CTGGCGGATCTTGTGGAATTC 59.327 52.381 0.00 0.00 0.00 2.17
5942 8593 0.247736 GTGTCTCTGGCGGATCTTGT 59.752 55.000 0.00 0.00 0.00 3.16
5943 8594 0.247460 TGTGTCTCTGGCGGATCTTG 59.753 55.000 0.00 0.00 0.00 3.02
5944 8595 0.247736 GTGTGTCTCTGGCGGATCTT 59.752 55.000 0.00 0.00 0.00 2.40
5962 8613 0.814010 GTCAAAGTGCGTGTGGAGGT 60.814 55.000 0.00 0.00 0.00 3.85
5975 8626 2.298300 GTGTGTTTCGCATCGTCAAAG 58.702 47.619 0.00 0.00 0.00 2.77
5977 8628 0.584396 GGTGTGTTTCGCATCGTCAA 59.416 50.000 0.00 0.00 0.00 3.18
5978 8629 1.553195 CGGTGTGTTTCGCATCGTCA 61.553 55.000 7.63 0.00 42.50 4.35
5997 8648 1.376848 GCCTAGCCCCTATCCTTGC 59.623 63.158 0.00 0.00 0.00 4.01
5999 8650 0.269173 ACTGCCTAGCCCCTATCCTT 59.731 55.000 0.00 0.00 0.00 3.36
6005 8656 1.001248 TTCGTACTGCCTAGCCCCT 59.999 57.895 0.00 0.00 0.00 4.79
6008 8659 0.535797 AAGGTTCGTACTGCCTAGCC 59.464 55.000 0.00 0.00 31.43 3.93
6009 8660 3.729862 ATAAGGTTCGTACTGCCTAGC 57.270 47.619 0.00 0.00 31.43 3.42


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

AutoCloner maintained by Alex Coulton.