Multiple sequence alignment - TraesCS6D01G274200

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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 TraesCS6D01G274200 chr6D 100.000 6042 0 0 1 6042 382620494 382626535 0.000000e+00 11158.0
1 TraesCS6D01G274200 chr6D 89.310 290 25 5 1718 2007 291388452 291388169 5.760000e-95 359.0
2 TraesCS6D01G274200 chr6D 83.380 361 36 15 1713 2055 432969655 432970009 4.550000e-81 313.0
3 TraesCS6D01G274200 chr6A 94.608 5286 160 58 43 5280 524763143 524768351 0.000000e+00 8067.0
4 TraesCS6D01G274200 chr6A 90.186 377 22 6 5637 6008 524768736 524769102 1.520000e-130 477.0
5 TraesCS6D01G274200 chr6A 86.926 283 28 4 1718 2000 563280193 563280466 5.880000e-80 309.0
6 TraesCS6D01G274200 chr6A 85.492 193 15 7 5375 5557 524768352 524768541 7.990000e-44 189.0
7 TraesCS6D01G274200 chr6B 94.321 1796 78 15 3673 5456 572404479 572406262 0.000000e+00 2730.0
8 TraesCS6D01G274200 chr6B 95.460 1608 55 8 2067 3671 572402802 572404394 0.000000e+00 2549.0
9 TraesCS6D01G274200 chr6B 92.791 971 43 8 760 1716 572401853 572402810 0.000000e+00 1380.0
10 TraesCS6D01G274200 chr6B 85.255 746 46 23 34 764 572401120 572401816 0.000000e+00 710.0
11 TraesCS6D01G274200 chr6B 88.978 372 15 5 5637 6008 572406344 572406689 2.590000e-118 436.0
12 TraesCS6D01G274200 chr6B 83.448 145 22 2 5737 5880 664743831 664743688 3.800000e-27 134.0
13 TraesCS6D01G274200 chr6B 100.000 44 0 0 5999 6042 572406700 572406743 1.400000e-11 82.4
14 TraesCS6D01G274200 chr1B 81.758 1058 129 29 4212 5233 171619508 171620537 0.000000e+00 826.0
15 TraesCS6D01G274200 chr1B 86.174 745 76 21 986 1714 171617309 171618042 0.000000e+00 780.0
16 TraesCS6D01G274200 chr1B 90.683 483 37 4 3309 3790 171618988 171619463 2.380000e-178 636.0
17 TraesCS6D01G274200 chr1B 80.831 433 47 23 2727 3150 171618497 171618902 2.120000e-79 307.0
18 TraesCS6D01G274200 chr1D 81.488 1075 123 37 4212 5245 112353680 112354719 0.000000e+00 813.0
19 TraesCS6D01G274200 chr1D 87.372 681 64 17 1032 1701 112351364 112352033 0.000000e+00 761.0
20 TraesCS6D01G274200 chr1D 90.041 492 38 7 3309 3796 112353157 112353641 1.430000e-175 627.0
21 TraesCS6D01G274200 chr1D 80.822 438 38 19 2727 3150 112352666 112353071 9.840000e-78 302.0
22 TraesCS6D01G274200 chr1A 82.818 937 115 20 4347 5245 119495937 119496865 0.000000e+00 797.0
23 TraesCS6D01G274200 chr1A 85.904 752 72 22 986 1714 119493661 119494401 0.000000e+00 771.0
24 TraesCS6D01G274200 chr1A 90.103 485 37 8 3313 3790 119495345 119495825 2.390000e-173 619.0
25 TraesCS6D01G274200 chr1A 79.759 415 40 20 2727 3128 119494854 119495237 1.670000e-65 261.0
26 TraesCS6D01G274200 chr4D 88.857 350 30 8 1706 2051 9304099 9304443 7.240000e-114 422.0
27 TraesCS6D01G274200 chr4A 87.826 345 23 8 1706 2039 594145065 594144729 2.640000e-103 387.0
28 TraesCS6D01G274200 chr5B 87.742 310 27 9 1749 2051 111709317 111709012 9.630000e-93 351.0
29 TraesCS6D01G274200 chr7D 87.500 296 28 4 1717 2012 118445843 118445557 3.490000e-87 333.0
30 TraesCS6D01G274200 chr2A 85.014 347 28 15 1718 2051 757674181 757674516 1.260000e-86 331.0
31 TraesCS6D01G274200 chr7A 100.000 29 0 0 1728 1756 137847558 137847586 3.000000e-03 54.7
32 TraesCS6D01G274200 chr2B 100.000 29 0 0 1728 1756 520201445 520201417 3.000000e-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 TraesCS6D01G274200 chr6D 382620494 382626535 6041 False 11158.000000 11158 100.000000 1 6042 1 chr6D.!!$F1 6041
1 TraesCS6D01G274200 chr6A 524763143 524769102 5959 False 2911.000000 8067 90.095333 43 6008 3 chr6A.!!$F2 5965
2 TraesCS6D01G274200 chr6B 572401120 572406743 5623 False 1314.566667 2730 92.800833 34 6042 6 chr6B.!!$F1 6008
3 TraesCS6D01G274200 chr1B 171617309 171620537 3228 False 637.250000 826 84.861500 986 5233 4 chr1B.!!$F1 4247
4 TraesCS6D01G274200 chr1D 112351364 112354719 3355 False 625.750000 813 84.930750 1032 5245 4 chr1D.!!$F1 4213
5 TraesCS6D01G274200 chr1A 119493661 119496865 3204 False 612.000000 797 84.646000 986 5245 4 chr1A.!!$F1 4259

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
728 779 0.107831 TGTTGCTATATGCCCCCGTC 59.892 55.000 0.00 0.00 42.00 4.79 F
1123 1257 0.253894 GCTAACCCCCAATACCGTGT 59.746 55.000 0.00 0.00 0.00 4.49 F
1741 2048 0.323360 TTCAATTTGGCTCCCGGGAG 60.323 55.000 41.29 41.29 44.56 4.30 F
2057 2364 0.260230 TTCACCCAGGAGCCAAAACA 59.740 50.000 0.00 0.00 0.00 2.83 F
2059 2366 1.152546 ACCCAGGAGCCAAAACACC 60.153 57.895 0.00 0.00 0.00 4.16 F
2913 3245 2.084610 TCATGTTTCTGCAGACTCGG 57.915 50.000 18.03 5.58 0.00 4.63 F
4851 5316 2.334023 GAGTGGGAGGCATCCTATCTT 58.666 52.381 18.35 1.03 45.85 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 2052 0.252835 AAAATTGGCCCCAGGAGCAT 60.253 50.000 0.00 0.0 0.00 3.79 R
2045 2352 1.600916 GAGCGGTGTTTTGGCTCCT 60.601 57.895 0.00 0.0 45.67 3.69 R
2913 3245 3.057876 CCTCACGTAGATACTCATCCAGC 60.058 52.174 0.00 0.0 0.00 4.85 R
3484 3851 7.383102 AGCAAATTACAGTTGAAGATAGTGG 57.617 36.000 0.00 0.0 0.00 4.00 R
3671 4127 8.955061 AAAATGATCAGTCAGTAATGAAAACG 57.045 30.769 0.09 0.0 37.87 3.60 R
4909 5395 0.606604 AGCAAACATAGGACGACCGT 59.393 50.000 0.00 0.0 41.83 4.83 R
5897 6599 0.902984 ACGGTGGCCACTACTCATGA 60.903 55.000 33.91 0.0 0.00 3.07 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
25 26 7.925703 TTAGGAATAGAAGATAAAGTTCGCG 57.074 36.000 0.00 0.00 0.00 5.87
26 27 6.145338 AGGAATAGAAGATAAAGTTCGCGA 57.855 37.500 3.71 3.71 0.00 5.87
27 28 6.210078 AGGAATAGAAGATAAAGTTCGCGAG 58.790 40.000 9.59 0.00 0.00 5.03
28 29 6.039493 AGGAATAGAAGATAAAGTTCGCGAGA 59.961 38.462 9.59 0.00 39.20 4.04
29 30 6.361214 GGAATAGAAGATAAAGTTCGCGAGAG 59.639 42.308 9.59 0.00 43.69 3.20
30 31 4.705337 AGAAGATAAAGTTCGCGAGAGT 57.295 40.909 9.59 0.54 43.69 3.24
31 32 5.061920 AGAAGATAAAGTTCGCGAGAGTT 57.938 39.130 9.59 7.18 43.69 3.01
32 33 5.471257 AGAAGATAAAGTTCGCGAGAGTTT 58.529 37.500 9.59 16.82 43.69 2.66
33 34 5.573669 AGAAGATAAAGTTCGCGAGAGTTTC 59.426 40.000 19.96 12.90 43.69 2.78
34 35 4.806330 AGATAAAGTTCGCGAGAGTTTCA 58.194 39.130 19.96 11.68 43.69 2.69
35 36 4.621886 AGATAAAGTTCGCGAGAGTTTCAC 59.378 41.667 19.96 10.90 43.69 3.18
36 37 1.129326 AAGTTCGCGAGAGTTTCACG 58.871 50.000 9.59 0.00 43.69 4.35
37 38 0.663568 AGTTCGCGAGAGTTTCACGG 60.664 55.000 9.59 0.00 43.69 4.94
38 39 1.372499 TTCGCGAGAGTTTCACGGG 60.372 57.895 9.59 6.63 42.66 5.28
41 42 1.219522 CGCGAGAGTTTCACGGGTTT 61.220 55.000 0.00 0.00 38.25 3.27
55 56 1.004200 GGTTTGGGATCCGACGTGT 60.004 57.895 5.45 0.00 0.00 4.49
90 92 0.915364 GGCCTGATTCTTGGAGGAGT 59.085 55.000 0.00 0.00 0.00 3.85
117 121 0.614415 TTGGGGGCAGCTAAATGTGG 60.614 55.000 0.00 0.00 0.00 4.17
141 176 2.214376 TGGGCCAGTTTTACCAGATG 57.786 50.000 0.00 0.00 0.00 2.90
142 177 1.427368 TGGGCCAGTTTTACCAGATGT 59.573 47.619 0.00 0.00 0.00 3.06
143 178 2.092323 GGGCCAGTTTTACCAGATGTC 58.908 52.381 4.39 0.00 0.00 3.06
144 179 2.290960 GGGCCAGTTTTACCAGATGTCT 60.291 50.000 4.39 0.00 0.00 3.41
145 180 2.749621 GGCCAGTTTTACCAGATGTCTG 59.250 50.000 0.00 3.01 43.40 3.51
154 189 3.658398 CAGATGTCTGGGCCAGTTT 57.342 52.632 31.60 17.94 40.20 2.66
155 190 1.915141 CAGATGTCTGGGCCAGTTTT 58.085 50.000 31.60 17.58 40.20 2.43
156 191 3.071874 CAGATGTCTGGGCCAGTTTTA 57.928 47.619 31.60 16.97 40.20 1.52
157 192 2.749621 CAGATGTCTGGGCCAGTTTTAC 59.250 50.000 31.60 22.49 40.20 2.01
158 193 2.092323 GATGTCTGGGCCAGTTTTACC 58.908 52.381 31.60 14.07 32.61 2.85
259 295 1.731969 CAGACGAACCCGACCGAAC 60.732 63.158 0.00 0.00 39.50 3.95
277 314 4.241555 ATGGGGGATCGCTGCGAC 62.242 66.667 28.41 19.64 39.18 5.19
279 316 4.241555 GGGGGATCGCTGCGACAT 62.242 66.667 28.41 12.98 39.18 3.06
280 317 2.663188 GGGGATCGCTGCGACATC 60.663 66.667 28.41 20.99 39.18 3.06
285 322 0.996229 GATCGCTGCGACATCTCTCG 60.996 60.000 28.41 0.00 39.18 4.04
286 323 2.399511 ATCGCTGCGACATCTCTCGG 62.400 60.000 28.41 0.00 39.18 4.63
306 343 2.805546 GGCTGACGATCGCCAGTA 59.194 61.111 28.39 5.41 45.59 2.74
308 345 0.249489 GGCTGACGATCGCCAGTAAT 60.249 55.000 28.39 2.41 45.59 1.89
309 346 1.000607 GGCTGACGATCGCCAGTAATA 60.001 52.381 28.39 0.00 45.59 0.98
310 347 2.352814 GGCTGACGATCGCCAGTAATAT 60.353 50.000 28.39 0.85 45.59 1.28
348 396 2.178521 CGTTCCCTCACCTCGACG 59.821 66.667 0.00 0.00 0.00 5.12
349 397 2.572284 GTTCCCTCACCTCGACGG 59.428 66.667 0.00 0.03 39.35 4.79
350 398 3.379445 TTCCCTCACCTCGACGGC 61.379 66.667 0.00 0.00 35.61 5.68
351 399 3.881019 TTCCCTCACCTCGACGGCT 62.881 63.158 0.00 0.00 35.61 5.52
352 400 3.827898 CCCTCACCTCGACGGCTC 61.828 72.222 0.00 0.00 35.61 4.70
353 401 4.180946 CCTCACCTCGACGGCTCG 62.181 72.222 0.00 0.77 41.65 5.03
354 402 3.125573 CTCACCTCGACGGCTCGA 61.126 66.667 8.38 8.38 46.85 4.04
355 403 3.384014 CTCACCTCGACGGCTCGAC 62.384 68.421 5.20 0.00 44.14 4.20
356 404 4.477975 CACCTCGACGGCTCGACC 62.478 72.222 5.20 0.00 44.14 4.79
357 405 4.719106 ACCTCGACGGCTCGACCT 62.719 66.667 5.20 0.00 44.14 3.85
359 407 2.110967 CCTCGACGGCTCGACCTAA 61.111 63.158 5.20 0.00 44.14 2.69
360 408 1.062206 CTCGACGGCTCGACCTAAC 59.938 63.158 5.20 0.00 44.14 2.34
361 409 2.101770 CGACGGCTCGACCTAACC 59.898 66.667 1.50 0.00 43.06 2.85
364 412 2.101770 CGGCTCGACCTAACCGTC 59.898 66.667 0.00 0.00 40.77 4.79
374 422 4.424566 TAACCGTCGTCAGCCCGC 62.425 66.667 0.00 0.00 0.00 6.13
471 522 2.766400 GCTCTCGTCTGTCCCTCGG 61.766 68.421 0.00 0.00 0.00 4.63
483 534 2.190578 CCTCGGGAATCTGTGGCC 59.809 66.667 0.00 0.00 0.00 5.36
728 779 0.107831 TGTTGCTATATGCCCCCGTC 59.892 55.000 0.00 0.00 42.00 4.79
743 794 1.665679 CCCGTCCGAATTGATGTTGAG 59.334 52.381 0.00 0.00 0.00 3.02
744 795 2.616960 CCGTCCGAATTGATGTTGAGA 58.383 47.619 0.00 0.00 0.00 3.27
745 796 3.198068 CCGTCCGAATTGATGTTGAGAT 58.802 45.455 0.00 0.00 0.00 2.75
828 937 1.794116 GCATGTGTGTGGCATTCAAAC 59.206 47.619 0.00 0.00 34.18 2.93
847 956 7.523293 TCAAACCATGAATACAACAGTGATT 57.477 32.000 0.00 0.00 34.30 2.57
857 966 8.311109 TGAATACAACAGTGATTGCTAGTCTTA 58.689 33.333 0.00 0.00 32.47 2.10
978 1089 2.147387 ACCACCCAGAACGAAGGCT 61.147 57.895 0.00 0.00 0.00 4.58
990 1101 1.098050 CGAAGGCTAAGGCTGCAATT 58.902 50.000 0.50 0.00 38.81 2.32
1053 1185 1.463553 CCTCCCAAAAGCGCCAGTTT 61.464 55.000 2.29 0.00 0.00 2.66
1123 1257 0.253894 GCTAACCCCCAATACCGTGT 59.746 55.000 0.00 0.00 0.00 4.49
1324 1467 3.146847 GGGTAACTACTTTGCTGTGCTT 58.853 45.455 0.00 0.00 0.00 3.91
1327 1470 2.938956 ACTACTTTGCTGTGCTTCCT 57.061 45.000 0.00 0.00 0.00 3.36
1338 1481 3.887716 GCTGTGCTTCCTATCCATTCATT 59.112 43.478 0.00 0.00 0.00 2.57
1361 1504 4.526650 TCCCTAAAACCCTTGAGAAAATGC 59.473 41.667 0.00 0.00 0.00 3.56
1362 1505 4.485163 CCTAAAACCCTTGAGAAAATGCG 58.515 43.478 0.00 0.00 0.00 4.73
1365 1508 2.568623 ACCCTTGAGAAAATGCGACT 57.431 45.000 0.00 0.00 0.00 4.18
1409 1552 4.330074 CAGTAAGAAACCACGCTAATCCTG 59.670 45.833 0.00 0.00 0.00 3.86
1412 1555 1.398390 GAAACCACGCTAATCCTGCAG 59.602 52.381 6.78 6.78 0.00 4.41
1422 1565 2.777832 AATCCTGCAGTCTCACCTTC 57.222 50.000 13.81 0.00 0.00 3.46
1424 1567 0.827925 TCCTGCAGTCTCACCTTCGT 60.828 55.000 13.81 0.00 0.00 3.85
1528 1672 4.153475 TGCTTTGCGAGTGTTAATTAGGAC 59.847 41.667 0.00 0.00 0.00 3.85
1731 2038 6.977502 TGCATATACACGGAAATTCAATTTGG 59.022 34.615 0.00 0.00 31.47 3.28
1732 2039 6.074356 GCATATACACGGAAATTCAATTTGGC 60.074 38.462 0.00 0.00 31.47 4.52
1733 2040 5.659440 ATACACGGAAATTCAATTTGGCT 57.341 34.783 0.00 0.00 31.47 4.75
1734 2041 3.913089 ACACGGAAATTCAATTTGGCTC 58.087 40.909 0.00 0.00 31.47 4.70
1735 2042 3.253230 CACGGAAATTCAATTTGGCTCC 58.747 45.455 0.00 0.00 31.47 4.70
1736 2043 2.233676 ACGGAAATTCAATTTGGCTCCC 59.766 45.455 0.00 0.00 31.47 4.30
1737 2044 2.735126 CGGAAATTCAATTTGGCTCCCG 60.735 50.000 0.00 2.88 31.47 5.14
1738 2045 2.418609 GGAAATTCAATTTGGCTCCCGG 60.419 50.000 0.00 0.00 31.47 5.73
1739 2046 1.194218 AATTCAATTTGGCTCCCGGG 58.806 50.000 16.85 16.85 0.00 5.73
1740 2047 0.334676 ATTCAATTTGGCTCCCGGGA 59.665 50.000 25.06 25.06 0.00 5.14
1741 2048 0.323360 TTCAATTTGGCTCCCGGGAG 60.323 55.000 41.29 41.29 44.56 4.30
1941 2248 2.660552 ACCGACGAAACACCGCTG 60.661 61.111 0.00 0.00 0.00 5.18
1946 2253 3.777925 CGAAACACCGCTGCTCCG 61.778 66.667 0.00 0.00 0.00 4.63
2003 2310 6.206634 ACACCAACACGATCATCTACAATTTT 59.793 34.615 0.00 0.00 0.00 1.82
2004 2311 7.083858 CACCAACACGATCATCTACAATTTTT 58.916 34.615 0.00 0.00 0.00 1.94
2057 2364 0.260230 TTCACCCAGGAGCCAAAACA 59.740 50.000 0.00 0.00 0.00 2.83
2059 2366 1.152546 ACCCAGGAGCCAAAACACC 60.153 57.895 0.00 0.00 0.00 4.16
2116 2423 3.955771 TTTGTTGTTCGTGAGTTAGGC 57.044 42.857 0.00 0.00 0.00 3.93
2127 2434 3.372206 CGTGAGTTAGGCTTTTCCATCTG 59.628 47.826 0.00 0.00 37.29 2.90
2182 2489 6.658849 TGCTTTTCTGTATAGGGCAGATTTA 58.341 36.000 0.00 0.00 41.87 1.40
2762 3079 7.711339 TGCCAACGTATACATACATTTGTCATA 59.289 33.333 3.32 0.00 32.87 2.15
2913 3245 2.084610 TCATGTTTCTGCAGACTCGG 57.915 50.000 18.03 5.58 0.00 4.63
3024 3356 9.113876 CCTTCAATTTTCATAGTTCGTTGTTAC 57.886 33.333 0.00 0.00 0.00 2.50
4069 4527 3.876914 TCTGTTTACCACAAACTCTGCAG 59.123 43.478 7.63 7.63 33.87 4.41
4258 4719 6.212840 TGGGTGTTTATTGCCCTATATGAT 57.787 37.500 0.00 0.00 42.77 2.45
4295 4756 5.287226 TCCTACTTTTCACTCGTTGTCTTC 58.713 41.667 0.00 0.00 0.00 2.87
4664 5129 5.607119 ACTTCCATGAATTTGTACACGAC 57.393 39.130 0.00 0.00 0.00 4.34
4750 5215 3.698040 TCGGGCCAAAGTAACTAGACTAG 59.302 47.826 4.39 8.00 0.00 2.57
4851 5316 2.334023 GAGTGGGAGGCATCCTATCTT 58.666 52.381 18.35 1.03 45.85 2.40
4857 5322 3.653352 GGGAGGCATCCTATCTTTACCTT 59.347 47.826 18.35 0.00 45.85 3.50
4887 5373 2.754946 TGCGGAAGGTATTTCTCGTT 57.245 45.000 0.00 0.00 36.03 3.85
4898 5384 7.653767 AGGTATTTCTCGTTCTGTTAACAAG 57.346 36.000 10.03 3.87 0.00 3.16
4935 5431 2.223112 CGTCCTATGTTTGCTGACATGC 60.223 50.000 13.52 0.00 40.33 4.06
5137 5635 2.325484 TCTTTAGTGGCTCACCTGTGA 58.675 47.619 0.00 0.00 34.49 3.58
5153 5651 0.179081 GTGATCTCCCCAAGGCGTAC 60.179 60.000 0.00 0.00 0.00 3.67
5155 5653 2.041206 GATCTCCCCAAGGCGTACCC 62.041 65.000 0.00 0.00 36.11 3.69
5285 5791 2.029739 TCAAGTTCTACGCGGAACATCA 60.030 45.455 23.89 2.58 45.52 3.07
5286 5792 2.279582 AGTTCTACGCGGAACATCAG 57.720 50.000 23.89 0.00 45.52 2.90
5300 5806 6.489675 CGGAACATCAGAATATTTGTTCAGG 58.510 40.000 22.83 14.65 46.12 3.86
5331 5837 9.472361 TTTCTTGTAAAGTAGTACTTGCACTAG 57.528 33.333 16.22 19.31 46.34 2.57
5345 5851 0.039618 CACTAGGCACACCCCCAATT 59.960 55.000 0.00 0.00 36.11 2.32
5366 5872 1.202927 CCTGAGAAGGTTGGGCTTGAA 60.203 52.381 0.00 0.00 0.00 2.69
5368 5874 2.751806 CTGAGAAGGTTGGGCTTGAATC 59.248 50.000 0.00 0.00 0.00 2.52
5372 5878 2.797177 AGGTTGGGCTTGAATCTCTC 57.203 50.000 0.00 0.00 0.00 3.20
5373 5879 2.273619 AGGTTGGGCTTGAATCTCTCT 58.726 47.619 0.00 0.00 0.00 3.10
5456 5962 7.063544 CAGGAGCTTGTTAATCAACTACAGTAC 59.936 40.741 0.00 0.00 35.56 2.73
5478 6007 9.657728 AGTACTATTAATCAAGGGCTAGTTAGT 57.342 33.333 0.00 0.00 0.00 2.24
5500 6029 4.859304 TTTGTACAGGAGCTCGTTAAGA 57.141 40.909 6.10 0.00 0.00 2.10
5519 6048 8.371053 CGTTAAGAGAAAAACAGTATACGAAGG 58.629 37.037 0.00 0.00 0.00 3.46
5520 6049 8.654215 GTTAAGAGAAAAACAGTATACGAAGGG 58.346 37.037 0.00 0.00 0.00 3.95
5522 6051 4.259356 AGAAAAACAGTATACGAAGGGGC 58.741 43.478 0.00 0.00 0.00 5.80
5525 6054 1.188863 ACAGTATACGAAGGGGCGTT 58.811 50.000 0.00 0.00 42.71 4.84
5526 6055 1.551883 ACAGTATACGAAGGGGCGTTT 59.448 47.619 0.00 0.00 42.71 3.60
5528 6057 2.350498 CAGTATACGAAGGGGCGTTTTG 59.650 50.000 0.00 0.00 42.71 2.44
5557 6096 1.542108 GCTCACCTGCACCTGATATCC 60.542 57.143 0.00 0.00 0.00 2.59
5558 6097 2.045524 CTCACCTGCACCTGATATCCT 58.954 52.381 0.00 0.00 0.00 3.24
5559 6098 3.234353 CTCACCTGCACCTGATATCCTA 58.766 50.000 0.00 0.00 0.00 2.94
5560 6099 3.234353 TCACCTGCACCTGATATCCTAG 58.766 50.000 0.00 0.00 0.00 3.02
5561 6100 3.117131 TCACCTGCACCTGATATCCTAGA 60.117 47.826 0.00 0.00 0.00 2.43
5562 6101 3.006323 CACCTGCACCTGATATCCTAGAC 59.994 52.174 0.00 0.00 0.00 2.59
5563 6102 2.230025 CCTGCACCTGATATCCTAGACG 59.770 54.545 0.00 0.00 0.00 4.18
5564 6103 1.613925 TGCACCTGATATCCTAGACGC 59.386 52.381 0.00 0.00 0.00 5.19
5565 6104 1.613925 GCACCTGATATCCTAGACGCA 59.386 52.381 0.00 0.00 0.00 5.24
5566 6105 2.608261 GCACCTGATATCCTAGACGCAC 60.608 54.545 0.00 0.00 0.00 5.34
5567 6106 2.623416 CACCTGATATCCTAGACGCACA 59.377 50.000 0.00 0.00 0.00 4.57
5568 6107 3.068165 CACCTGATATCCTAGACGCACAA 59.932 47.826 0.00 0.00 0.00 3.33
5569 6108 3.898123 ACCTGATATCCTAGACGCACAAT 59.102 43.478 0.00 0.00 0.00 2.71
5570 6109 4.240888 CCTGATATCCTAGACGCACAATG 58.759 47.826 0.00 0.00 0.00 2.82
5571 6110 4.262207 CCTGATATCCTAGACGCACAATGT 60.262 45.833 0.00 0.00 0.00 2.71
5572 6111 5.276461 TGATATCCTAGACGCACAATGTT 57.724 39.130 0.00 0.00 0.00 2.71
5573 6112 5.049828 TGATATCCTAGACGCACAATGTTG 58.950 41.667 0.00 0.00 0.00 3.33
5574 6113 2.831685 TCCTAGACGCACAATGTTGT 57.168 45.000 0.00 0.00 43.36 3.32
5575 6114 3.945981 TCCTAGACGCACAATGTTGTA 57.054 42.857 0.00 0.00 39.91 2.41
5576 6115 4.465632 TCCTAGACGCACAATGTTGTAT 57.534 40.909 0.00 0.00 39.91 2.29
5577 6116 4.180817 TCCTAGACGCACAATGTTGTATG 58.819 43.478 0.00 0.00 39.91 2.39
5578 6117 3.309682 CCTAGACGCACAATGTTGTATGG 59.690 47.826 0.00 0.00 39.91 2.74
5579 6118 2.083774 AGACGCACAATGTTGTATGGG 58.916 47.619 0.00 0.00 39.91 4.00
5580 6119 1.132262 GACGCACAATGTTGTATGGGG 59.868 52.381 0.00 0.00 39.91 4.96
5581 6120 1.271652 ACGCACAATGTTGTATGGGGA 60.272 47.619 0.00 0.00 39.91 4.81
5582 6121 2.023673 CGCACAATGTTGTATGGGGAT 58.976 47.619 0.00 0.00 39.91 3.85
5583 6122 2.426738 CGCACAATGTTGTATGGGGATT 59.573 45.455 0.00 0.00 39.91 3.01
5584 6123 3.489059 CGCACAATGTTGTATGGGGATTC 60.489 47.826 0.00 0.00 39.91 2.52
5585 6124 3.446873 GCACAATGTTGTATGGGGATTCA 59.553 43.478 0.00 0.00 39.91 2.57
5586 6125 4.081752 GCACAATGTTGTATGGGGATTCAA 60.082 41.667 0.00 0.00 39.91 2.69
5587 6126 5.653507 CACAATGTTGTATGGGGATTCAAG 58.346 41.667 0.00 0.00 39.91 3.02
5588 6127 4.711355 ACAATGTTGTATGGGGATTCAAGG 59.289 41.667 0.00 0.00 40.16 3.61
5589 6128 4.879295 ATGTTGTATGGGGATTCAAGGA 57.121 40.909 0.00 0.00 0.00 3.36
5590 6129 4.879295 TGTTGTATGGGGATTCAAGGAT 57.121 40.909 0.00 0.00 0.00 3.24
5591 6130 5.985175 TGTTGTATGGGGATTCAAGGATA 57.015 39.130 0.00 0.00 0.00 2.59
5592 6131 5.690865 TGTTGTATGGGGATTCAAGGATAC 58.309 41.667 0.00 0.00 0.00 2.24
5593 6132 4.617253 TGTATGGGGATTCAAGGATACG 57.383 45.455 0.00 0.00 46.39 3.06
5594 6133 3.971305 TGTATGGGGATTCAAGGATACGT 59.029 43.478 0.00 0.00 46.39 3.57
5595 6134 3.771577 ATGGGGATTCAAGGATACGTC 57.228 47.619 0.00 0.00 46.39 4.34
5596 6135 2.473070 TGGGGATTCAAGGATACGTCA 58.527 47.619 0.00 0.00 46.39 4.35
5597 6136 2.434336 TGGGGATTCAAGGATACGTCAG 59.566 50.000 0.00 0.00 46.39 3.51
5598 6137 2.434702 GGGGATTCAAGGATACGTCAGT 59.565 50.000 0.00 0.00 46.39 3.41
5599 6138 3.640029 GGGGATTCAAGGATACGTCAGTA 59.360 47.826 0.00 0.00 46.39 2.74
5600 6139 4.100498 GGGGATTCAAGGATACGTCAGTAA 59.900 45.833 0.00 0.00 46.39 2.24
5601 6140 5.048507 GGGATTCAAGGATACGTCAGTAAC 58.951 45.833 0.00 0.00 46.39 2.50
5618 6157 0.818040 AACAAGACAGGGTTCGTGCC 60.818 55.000 0.00 0.00 0.00 5.01
5627 6166 1.009335 GGTTCGTGCCGTGGAAAAC 60.009 57.895 0.00 0.00 0.00 2.43
5660 6358 7.041303 ACGCGTACATCTCTCTCTAATTGATTA 60.041 37.037 11.67 0.00 0.00 1.75
5754 6452 1.577468 GTTTGGCAAAACTTTCCCGG 58.423 50.000 15.29 0.00 42.09 5.73
5861 6563 5.313712 AGAGTTTAATTTGGTGTGATCCGT 58.686 37.500 0.00 0.00 0.00 4.69
5897 6599 1.474077 GCAATCGCCTCAAGTTTCCAT 59.526 47.619 0.00 0.00 0.00 3.41
5904 6606 3.350833 GCCTCAAGTTTCCATCATGAGT 58.649 45.455 0.09 0.00 36.61 3.41
5923 6625 4.065281 GTGGCCACCGTAGTCGCT 62.065 66.667 26.31 0.00 35.54 4.93
5953 6656 0.038159 CGGATTGAGGATCTACGGGC 60.038 60.000 0.00 0.00 35.02 6.13
5965 6668 4.262894 GGATCTACGGGCAATTCTAATGGA 60.263 45.833 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.192774 TCGCGAACTTTATCTTCTATTCCTAAA 58.807 33.333 6.20 0.00 0.00 1.85
1 2 7.709947 TCGCGAACTTTATCTTCTATTCCTAA 58.290 34.615 6.20 0.00 0.00 2.69
2 3 7.228108 TCTCGCGAACTTTATCTTCTATTCCTA 59.772 37.037 11.33 0.00 0.00 2.94
3 4 6.039493 TCTCGCGAACTTTATCTTCTATTCCT 59.961 38.462 11.33 0.00 0.00 3.36
6 7 6.797454 ACTCTCGCGAACTTTATCTTCTATT 58.203 36.000 11.33 0.00 0.00 1.73
7 8 6.380095 ACTCTCGCGAACTTTATCTTCTAT 57.620 37.500 11.33 0.00 0.00 1.98
8 9 5.814764 ACTCTCGCGAACTTTATCTTCTA 57.185 39.130 11.33 0.00 0.00 2.10
9 10 4.705337 ACTCTCGCGAACTTTATCTTCT 57.295 40.909 11.33 0.00 0.00 2.85
10 11 5.345202 TGAAACTCTCGCGAACTTTATCTTC 59.655 40.000 11.33 5.96 0.00 2.87
11 12 5.118817 GTGAAACTCTCGCGAACTTTATCTT 59.881 40.000 11.33 0.00 0.00 2.40
12 13 4.621886 GTGAAACTCTCGCGAACTTTATCT 59.378 41.667 11.33 0.00 0.00 1.98
13 14 4.872339 GTGAAACTCTCGCGAACTTTATC 58.128 43.478 11.33 5.42 0.00 1.75
14 15 4.905412 GTGAAACTCTCGCGAACTTTAT 57.095 40.909 11.33 0.00 0.00 1.40
23 24 0.234884 CAAACCCGTGAAACTCTCGC 59.765 55.000 0.00 0.00 32.67 5.03
24 25 0.865769 CCAAACCCGTGAAACTCTCG 59.134 55.000 0.00 0.00 33.67 4.04
25 26 1.202722 TCCCAAACCCGTGAAACTCTC 60.203 52.381 0.00 0.00 31.75 3.20
26 27 0.841289 TCCCAAACCCGTGAAACTCT 59.159 50.000 0.00 0.00 31.75 3.24
27 28 1.810755 GATCCCAAACCCGTGAAACTC 59.189 52.381 0.00 0.00 31.75 3.01
28 29 1.546998 GGATCCCAAACCCGTGAAACT 60.547 52.381 0.00 0.00 31.75 2.66
29 30 0.885879 GGATCCCAAACCCGTGAAAC 59.114 55.000 0.00 0.00 0.00 2.78
30 31 0.606944 CGGATCCCAAACCCGTGAAA 60.607 55.000 6.06 0.00 38.55 2.69
31 32 1.003112 CGGATCCCAAACCCGTGAA 60.003 57.895 6.06 0.00 38.55 3.18
32 33 1.914263 TCGGATCCCAAACCCGTGA 60.914 57.895 6.06 0.00 43.40 4.35
33 34 1.743995 GTCGGATCCCAAACCCGTG 60.744 63.158 6.06 0.00 43.40 4.94
34 35 2.666812 GTCGGATCCCAAACCCGT 59.333 61.111 6.06 0.00 43.40 5.28
35 36 2.510691 CGTCGGATCCCAAACCCG 60.511 66.667 6.06 0.00 44.22 5.28
36 37 1.743995 CACGTCGGATCCCAAACCC 60.744 63.158 6.06 0.00 0.00 4.11
37 38 1.004200 ACACGTCGGATCCCAAACC 60.004 57.895 6.06 0.00 0.00 3.27
38 39 1.017701 GGACACGTCGGATCCCAAAC 61.018 60.000 6.06 1.21 0.00 2.93
41 42 2.283316 TGGACACGTCGGATCCCA 60.283 61.111 6.06 0.00 0.00 4.37
90 92 2.689175 CTGCCCCCAAGCCCATTA 59.311 61.111 0.00 0.00 0.00 1.90
117 121 1.254026 GGTAAAACTGGCCCAGAACC 58.746 55.000 19.90 14.65 35.18 3.62
140 175 0.847373 TGGTAAAACTGGCCCAGACA 59.153 50.000 19.90 3.48 35.18 3.41
141 176 1.073284 TCTGGTAAAACTGGCCCAGAC 59.927 52.381 19.90 4.57 46.45 3.51
143 178 2.514458 ATCTGGTAAAACTGGCCCAG 57.486 50.000 9.83 9.83 44.74 4.45
144 179 2.990740 AATCTGGTAAAACTGGCCCA 57.009 45.000 0.00 0.00 0.00 5.36
145 180 3.864540 GCAAAATCTGGTAAAACTGGCCC 60.865 47.826 0.00 0.00 0.00 5.80
146 181 3.325870 GCAAAATCTGGTAAAACTGGCC 58.674 45.455 0.00 0.00 0.00 5.36
147 182 2.986479 CGCAAAATCTGGTAAAACTGGC 59.014 45.455 0.00 0.00 0.00 4.85
148 183 3.980775 CACGCAAAATCTGGTAAAACTGG 59.019 43.478 0.00 0.00 0.00 4.00
149 184 3.980775 CCACGCAAAATCTGGTAAAACTG 59.019 43.478 0.00 0.00 0.00 3.16
150 185 3.005367 CCCACGCAAAATCTGGTAAAACT 59.995 43.478 0.00 0.00 0.00 2.66
151 186 3.313690 CCCACGCAAAATCTGGTAAAAC 58.686 45.455 0.00 0.00 0.00 2.43
152 187 2.288518 GCCCACGCAAAATCTGGTAAAA 60.289 45.455 0.00 0.00 34.03 1.52
153 188 1.271102 GCCCACGCAAAATCTGGTAAA 59.729 47.619 0.00 0.00 34.03 2.01
154 189 0.885196 GCCCACGCAAAATCTGGTAA 59.115 50.000 0.00 0.00 34.03 2.85
155 190 0.037590 AGCCCACGCAAAATCTGGTA 59.962 50.000 0.00 0.00 37.52 3.25
156 191 1.228552 AGCCCACGCAAAATCTGGT 60.229 52.632 0.00 0.00 37.52 4.00
157 192 1.213537 CAGCCCACGCAAAATCTGG 59.786 57.895 0.00 0.00 37.52 3.86
158 193 1.213537 CCAGCCCACGCAAAATCTG 59.786 57.895 0.00 0.00 37.52 2.90
249 285 4.483243 CCCCCATGTTCGGTCGGG 62.483 72.222 0.00 0.00 38.52 5.14
259 295 4.240103 TCGCAGCGATCCCCCATG 62.240 66.667 15.11 0.00 0.00 3.66
277 314 1.227205 GTCAGCCAGCCGAGAGATG 60.227 63.158 0.00 0.00 0.00 2.90
279 316 3.443925 CGTCAGCCAGCCGAGAGA 61.444 66.667 0.00 0.00 0.00 3.10
280 317 2.676016 GATCGTCAGCCAGCCGAGAG 62.676 65.000 0.00 0.00 33.66 3.20
306 343 7.402054 GGGTTTGAGATTTTGGGGAAAATATT 58.598 34.615 0.00 0.00 32.92 1.28
308 345 5.046950 CGGGTTTGAGATTTTGGGGAAAATA 60.047 40.000 0.00 0.00 32.92 1.40
309 346 4.262851 CGGGTTTGAGATTTTGGGGAAAAT 60.263 41.667 0.00 0.00 35.26 1.82
310 347 3.070302 CGGGTTTGAGATTTTGGGGAAAA 59.930 43.478 0.00 0.00 0.00 2.29
353 401 1.153881 GGCTGACGACGGTTAGGTC 60.154 63.158 0.00 2.26 30.83 3.85
354 402 2.643232 GGGCTGACGACGGTTAGGT 61.643 63.158 0.00 0.00 30.83 3.08
355 403 2.183555 GGGCTGACGACGGTTAGG 59.816 66.667 0.00 0.00 30.83 2.69
356 404 2.202570 CGGGCTGACGACGGTTAG 60.203 66.667 0.00 0.00 35.47 2.34
357 405 4.424566 GCGGGCTGACGACGGTTA 62.425 66.667 0.00 0.00 35.47 2.85
408 456 4.173924 GAGCAGAGAGGGCAGGGC 62.174 72.222 0.00 0.00 0.00 5.19
409 457 3.478274 GGAGCAGAGAGGGCAGGG 61.478 72.222 0.00 0.00 0.00 4.45
410 458 2.365370 AGGAGCAGAGAGGGCAGG 60.365 66.667 0.00 0.00 0.00 4.85
453 501 2.766400 CCGAGGGACAGACGAGAGC 61.766 68.421 0.00 0.00 0.00 4.09
471 522 3.134127 GTGCCGGCCACAGATTCC 61.134 66.667 26.77 0.00 44.06 3.01
575 626 2.364970 CTGATGCTTCTCTTCCCGATCT 59.635 50.000 0.88 0.00 0.00 2.75
828 937 5.571784 AGCAATCACTGTTGTATTCATGG 57.428 39.130 0.00 0.00 0.00 3.66
847 956 8.311109 TCACTGTTGTATTCATTAAGACTAGCA 58.689 33.333 0.00 0.00 0.00 3.49
903 1012 7.697352 TGCATACAAATTTGAACAAGACAAG 57.303 32.000 24.64 3.81 0.00 3.16
990 1101 2.281139 TTGTTCATCACGCCGGCA 60.281 55.556 28.98 7.49 0.00 5.69
1053 1185 2.705658 CAGGGAATAGATACCTGCACCA 59.294 50.000 0.00 0.00 44.55 4.17
1123 1257 3.771071 ACCCTAGTTAGCTACCCTTCA 57.229 47.619 0.00 0.00 0.00 3.02
1324 1467 6.411554 GGGTTTTAGGGAATGAATGGATAGGA 60.412 42.308 0.00 0.00 0.00 2.94
1327 1470 6.606241 AGGGTTTTAGGGAATGAATGGATA 57.394 37.500 0.00 0.00 0.00 2.59
1338 1481 4.526650 GCATTTTCTCAAGGGTTTTAGGGA 59.473 41.667 0.00 0.00 0.00 4.20
1361 1504 2.094906 TCACCCAACATCGTAGAAGTCG 60.095 50.000 0.00 0.00 37.54 4.18
1362 1505 3.587797 TCACCCAACATCGTAGAAGTC 57.412 47.619 0.00 0.00 37.54 3.01
1365 1508 3.181453 TGGTTTCACCCAACATCGTAGAA 60.181 43.478 0.00 0.00 37.57 2.10
1395 1538 0.108138 GACTGCAGGATTAGCGTGGT 60.108 55.000 19.93 0.00 33.10 4.16
1409 1552 0.598562 TCTGACGAAGGTGAGACTGC 59.401 55.000 0.00 0.00 31.08 4.40
1412 1555 5.312120 TCTTTATCTGACGAAGGTGAGAC 57.688 43.478 0.00 0.00 39.26 3.36
1422 1565 2.455032 CAGGACGCTCTTTATCTGACG 58.545 52.381 0.00 0.00 0.00 4.35
1424 1567 2.457598 ACCAGGACGCTCTTTATCTGA 58.542 47.619 0.00 0.00 0.00 3.27
1528 1672 7.418408 GGAACTACCAAAAACTCTTCTTCTTG 58.582 38.462 0.00 0.00 38.79 3.02
1545 1689 2.022934 CAGGACTACCTCGGAACTACC 58.977 57.143 0.00 0.00 45.94 3.18
1716 2023 2.735126 CGGGAGCCAAATTGAATTTCCG 60.735 50.000 11.56 11.56 31.41 4.30
1742 2049 2.866523 ATTGGCCCCAGGAGCATGTG 62.867 60.000 0.00 0.00 0.00 3.21
1743 2050 2.172229 AATTGGCCCCAGGAGCATGT 62.172 55.000 0.00 0.00 0.00 3.21
1744 2051 0.979187 AAATTGGCCCCAGGAGCATG 60.979 55.000 0.00 0.00 0.00 4.06
1745 2052 0.252835 AAAATTGGCCCCAGGAGCAT 60.253 50.000 0.00 0.00 0.00 3.79
1746 2053 0.473501 AAAAATTGGCCCCAGGAGCA 60.474 50.000 0.00 0.00 0.00 4.26
1941 2248 3.244976 CAATTTTCATGTGGAACGGAGC 58.755 45.455 0.00 0.00 42.39 4.70
1946 2253 3.187022 GCTTGGCAATTTTCATGTGGAAC 59.813 43.478 0.00 0.00 34.56 3.62
2045 2352 1.600916 GAGCGGTGTTTTGGCTCCT 60.601 57.895 0.00 0.00 45.67 3.69
2116 2423 5.865552 CCAAAGCATTACACAGATGGAAAAG 59.134 40.000 0.00 0.00 30.36 2.27
2182 2489 4.970662 CTGCCAAACAGTAGCAATGTAT 57.029 40.909 0.00 0.00 41.86 2.29
2762 3079 9.203163 AGTATAAGCAGAATCACCTACTAGTTT 57.797 33.333 0.00 0.00 0.00 2.66
2913 3245 3.057876 CCTCACGTAGATACTCATCCAGC 60.058 52.174 0.00 0.00 0.00 4.85
3484 3851 7.383102 AGCAAATTACAGTTGAAGATAGTGG 57.617 36.000 0.00 0.00 0.00 4.00
3671 4127 8.955061 AAAATGATCAGTCAGTAATGAAAACG 57.045 30.769 0.09 0.00 37.87 3.60
4069 4527 5.562113 GCAAACAACATGTAACCTACAGGAC 60.562 44.000 0.00 0.00 42.63 3.85
4142 4600 4.119862 GCAATACGAAGGATGTCAGCTTA 58.880 43.478 0.00 0.00 0.00 3.09
4258 4719 6.950041 TGAAAAGTAGGAAGCTAGGTACTACA 59.050 38.462 25.79 12.52 41.75 2.74
4664 5129 2.119801 ACTCTGGCCTTTGCACATAG 57.880 50.000 3.32 0.00 40.13 2.23
4715 5180 2.421739 CCCGATCGTCCATCACCC 59.578 66.667 15.09 0.00 0.00 4.61
4750 5215 1.325943 GACAGCAGCGAATTCAGTAGC 59.674 52.381 6.22 3.83 0.00 3.58
4851 5316 3.126831 CCGCAAAACAAATGCAAGGTAA 58.873 40.909 0.00 0.00 44.01 2.85
4857 5322 1.137872 ACCTTCCGCAAAACAAATGCA 59.862 42.857 0.00 0.00 44.01 3.96
4887 5373 4.393680 GTGTGTGGTTCACTTGTTAACAGA 59.606 41.667 8.56 0.00 46.27 3.41
4898 5384 1.485032 GACGACCGTGTGTGGTTCAC 61.485 60.000 0.00 0.00 44.01 3.18
4909 5395 0.606604 AGCAAACATAGGACGACCGT 59.393 50.000 0.00 0.00 41.83 4.83
4935 5431 0.654683 GCCTCGCTGCATAAACAGAG 59.345 55.000 0.00 0.00 40.25 3.35
5008 5506 3.187699 CTCGATGTCCTCCTCGGCG 62.188 68.421 0.00 0.00 35.64 6.46
5137 5635 2.070650 GGGTACGCCTTGGGGAGAT 61.071 63.158 10.75 0.00 36.25 2.75
5185 5683 3.189910 ACATGAGTAACTAGTTCGTGCGA 59.810 43.478 12.39 0.00 32.42 5.10
5186 5684 3.499048 ACATGAGTAACTAGTTCGTGCG 58.501 45.455 12.39 0.57 32.42 5.34
5274 5780 4.536364 ACAAATATTCTGATGTTCCGCG 57.464 40.909 0.00 0.00 0.00 6.46
5285 5791 9.211485 CAAGAAAAATGCCTGAACAAATATTCT 57.789 29.630 0.00 0.00 0.00 2.40
5286 5792 8.992073 ACAAGAAAAATGCCTGAACAAATATTC 58.008 29.630 0.00 0.00 0.00 1.75
5300 5806 8.902735 GCAAGTACTACTTTACAAGAAAAATGC 58.097 33.333 0.00 0.00 36.03 3.56
5331 5837 1.984026 CAGGAATTGGGGGTGTGCC 60.984 63.158 0.00 0.00 0.00 5.01
5339 5845 2.450476 CCAACCTTCTCAGGAATTGGG 58.550 52.381 0.00 0.00 44.19 4.12
5345 5851 0.401738 CAAGCCCAACCTTCTCAGGA 59.598 55.000 0.00 0.00 44.19 3.86
5366 5872 2.630580 GAGGCGGTGGAATAAGAGAGAT 59.369 50.000 0.00 0.00 0.00 2.75
5368 5874 2.035321 GAGAGGCGGTGGAATAAGAGAG 59.965 54.545 0.00 0.00 0.00 3.20
5372 5878 2.035632 AGAGAGAGGCGGTGGAATAAG 58.964 52.381 0.00 0.00 0.00 1.73
5373 5879 2.160721 AGAGAGAGGCGGTGGAATAA 57.839 50.000 0.00 0.00 0.00 1.40
5418 5924 2.464157 AGCTCCTGTACAACTGAAGC 57.536 50.000 0.00 2.03 0.00 3.86
5478 6007 5.010314 TCTCTTAACGAGCTCCTGTACAAAA 59.990 40.000 8.47 0.00 39.70 2.44
5482 6011 4.698583 TTCTCTTAACGAGCTCCTGTAC 57.301 45.455 8.47 0.00 39.70 2.90
5500 6029 4.259356 GCCCCTTCGTATACTGTTTTTCT 58.741 43.478 0.56 0.00 0.00 2.52
5501 6030 3.063045 CGCCCCTTCGTATACTGTTTTTC 59.937 47.826 0.56 0.00 0.00 2.29
5504 6033 1.551883 ACGCCCCTTCGTATACTGTTT 59.448 47.619 0.56 0.00 41.36 2.83
5512 6041 0.885596 CACCAAAACGCCCCTTCGTA 60.886 55.000 0.00 0.00 42.46 3.43
5513 6042 2.190841 CACCAAAACGCCCCTTCGT 61.191 57.895 0.00 0.00 45.58 3.85
5514 6043 2.642700 CACCAAAACGCCCCTTCG 59.357 61.111 0.00 0.00 0.00 3.79
5516 6045 3.230990 GGCACCAAAACGCCCCTT 61.231 61.111 0.00 0.00 42.82 3.95
5522 6051 1.165907 TGAGCTGAGGCACCAAAACG 61.166 55.000 0.00 0.00 41.70 3.60
5524 6053 2.719376 GTGAGCTGAGGCACCAAAA 58.281 52.632 0.00 0.00 41.70 2.44
5525 6054 4.481195 GTGAGCTGAGGCACCAAA 57.519 55.556 0.00 0.00 41.70 3.28
5534 6073 1.838396 TCAGGTGCAGGTGAGCTGA 60.838 57.895 16.83 0.00 43.81 4.26
5535 6074 0.538584 TATCAGGTGCAGGTGAGCTG 59.461 55.000 7.39 7.39 39.76 4.24
5557 6096 3.309682 CCCATACAACATTGTGCGTCTAG 59.690 47.826 7.53 0.00 42.31 2.43
5558 6097 3.266636 CCCATACAACATTGTGCGTCTA 58.733 45.455 7.53 0.00 42.31 2.59
5559 6098 2.083774 CCCATACAACATTGTGCGTCT 58.916 47.619 7.53 0.00 42.31 4.18
5560 6099 1.132262 CCCCATACAACATTGTGCGTC 59.868 52.381 7.53 0.00 42.31 5.19
5561 6100 1.173043 CCCCATACAACATTGTGCGT 58.827 50.000 7.53 0.00 42.31 5.24
5562 6101 1.458398 TCCCCATACAACATTGTGCG 58.542 50.000 7.53 0.00 42.31 5.34
5563 6102 3.446873 TGAATCCCCATACAACATTGTGC 59.553 43.478 7.53 0.00 42.31 4.57
5564 6103 5.394443 CCTTGAATCCCCATACAACATTGTG 60.394 44.000 7.53 0.00 42.31 3.33
5565 6104 4.711355 CCTTGAATCCCCATACAACATTGT 59.289 41.667 2.32 2.32 44.86 2.71
5566 6105 4.955450 TCCTTGAATCCCCATACAACATTG 59.045 41.667 0.00 0.00 0.00 2.82
5567 6106 5.205517 TCCTTGAATCCCCATACAACATT 57.794 39.130 0.00 0.00 0.00 2.71
5568 6107 4.879295 TCCTTGAATCCCCATACAACAT 57.121 40.909 0.00 0.00 0.00 2.71
5569 6108 4.879295 ATCCTTGAATCCCCATACAACA 57.121 40.909 0.00 0.00 0.00 3.33
5570 6109 4.755123 CGTATCCTTGAATCCCCATACAAC 59.245 45.833 0.00 0.00 0.00 3.32
5571 6110 4.410883 ACGTATCCTTGAATCCCCATACAA 59.589 41.667 0.00 0.00 0.00 2.41
5572 6111 3.971305 ACGTATCCTTGAATCCCCATACA 59.029 43.478 0.00 0.00 0.00 2.29
5573 6112 4.039973 TGACGTATCCTTGAATCCCCATAC 59.960 45.833 0.00 0.00 0.00 2.39
5574 6113 4.228010 TGACGTATCCTTGAATCCCCATA 58.772 43.478 0.00 0.00 0.00 2.74
5575 6114 3.045634 TGACGTATCCTTGAATCCCCAT 58.954 45.455 0.00 0.00 0.00 4.00
5576 6115 2.434336 CTGACGTATCCTTGAATCCCCA 59.566 50.000 0.00 0.00 0.00 4.96
5577 6116 2.434702 ACTGACGTATCCTTGAATCCCC 59.565 50.000 0.00 0.00 0.00 4.81
5578 6117 3.821421 ACTGACGTATCCTTGAATCCC 57.179 47.619 0.00 0.00 0.00 3.85
5579 6118 5.657474 TGTTACTGACGTATCCTTGAATCC 58.343 41.667 0.00 0.00 0.00 3.01
5580 6119 7.009357 GTCTTGTTACTGACGTATCCTTGAATC 59.991 40.741 0.00 0.00 0.00 2.52
5581 6120 6.812160 GTCTTGTTACTGACGTATCCTTGAAT 59.188 38.462 0.00 0.00 0.00 2.57
5582 6121 6.154445 GTCTTGTTACTGACGTATCCTTGAA 58.846 40.000 0.00 0.00 0.00 2.69
5583 6122 5.242171 TGTCTTGTTACTGACGTATCCTTGA 59.758 40.000 0.00 0.00 36.10 3.02
5584 6123 5.466819 TGTCTTGTTACTGACGTATCCTTG 58.533 41.667 0.00 0.00 36.10 3.61
5585 6124 5.336531 CCTGTCTTGTTACTGACGTATCCTT 60.337 44.000 0.00 0.00 36.10 3.36
5586 6125 4.158025 CCTGTCTTGTTACTGACGTATCCT 59.842 45.833 0.00 0.00 36.10 3.24
5587 6126 4.421948 CCTGTCTTGTTACTGACGTATCC 58.578 47.826 0.00 0.00 36.10 2.59
5588 6127 4.082354 ACCCTGTCTTGTTACTGACGTATC 60.082 45.833 0.00 0.00 36.10 2.24
5589 6128 3.830755 ACCCTGTCTTGTTACTGACGTAT 59.169 43.478 0.00 0.00 36.10 3.06
5590 6129 3.225104 ACCCTGTCTTGTTACTGACGTA 58.775 45.455 0.00 0.00 36.10 3.57
5591 6130 2.037144 ACCCTGTCTTGTTACTGACGT 58.963 47.619 0.00 0.00 36.10 4.34
5592 6131 2.814280 ACCCTGTCTTGTTACTGACG 57.186 50.000 5.14 0.00 36.10 4.35
5593 6132 3.057734 CGAACCCTGTCTTGTTACTGAC 58.942 50.000 3.12 3.12 0.00 3.51
5594 6133 2.696707 ACGAACCCTGTCTTGTTACTGA 59.303 45.455 0.00 0.00 0.00 3.41
5595 6134 2.800544 CACGAACCCTGTCTTGTTACTG 59.199 50.000 0.00 0.00 0.00 2.74
5596 6135 2.805657 GCACGAACCCTGTCTTGTTACT 60.806 50.000 0.00 0.00 0.00 2.24
5597 6136 1.529865 GCACGAACCCTGTCTTGTTAC 59.470 52.381 0.00 0.00 0.00 2.50
5598 6137 1.541670 GGCACGAACCCTGTCTTGTTA 60.542 52.381 0.00 0.00 0.00 2.41
5599 6138 0.818040 GGCACGAACCCTGTCTTGTT 60.818 55.000 0.00 0.00 0.00 2.83
5600 6139 1.227853 GGCACGAACCCTGTCTTGT 60.228 57.895 0.00 0.00 0.00 3.16
5601 6140 3.655481 GGCACGAACCCTGTCTTG 58.345 61.111 0.00 0.00 0.00 3.02
5631 6170 1.328069 AGAGAGAGATGTACGCGTTCG 59.672 52.381 20.78 0.00 42.43 3.95
5632 6171 4.533225 TTAGAGAGAGATGTACGCGTTC 57.467 45.455 20.78 14.31 0.00 3.95
5633 6172 5.066117 TCAATTAGAGAGAGATGTACGCGTT 59.934 40.000 20.78 0.00 0.00 4.84
5634 6173 4.575236 TCAATTAGAGAGAGATGTACGCGT 59.425 41.667 19.17 19.17 0.00 6.01
5635 6174 5.096954 TCAATTAGAGAGAGATGTACGCG 57.903 43.478 3.53 3.53 0.00 6.01
5660 6358 1.330521 CACGCCGTTGCTAAGCATATT 59.669 47.619 0.00 0.00 38.76 1.28
5754 6452 3.842732 AAAAGGCACGCACTTATAACC 57.157 42.857 0.00 0.00 0.00 2.85
5861 6563 4.329545 GCCTCCTCCGTGCAACCA 62.330 66.667 0.00 0.00 0.00 3.67
5893 6595 1.486310 GTGGCCACTACTCATGATGGA 59.514 52.381 29.12 0.00 33.80 3.41
5897 6599 0.902984 ACGGTGGCCACTACTCATGA 60.903 55.000 33.91 0.00 0.00 3.07
5904 6606 2.703798 GCGACTACGGTGGCCACTA 61.704 63.158 33.91 19.09 40.51 2.74
5953 6656 3.627123 TCGCATGTGGTCCATTAGAATTG 59.373 43.478 6.39 0.00 0.00 2.32
5982 6685 2.126071 CACGCGAAGATGGTCCGT 60.126 61.111 15.93 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.