Multiple sequence alignment - TraesCS2A01G074400

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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 TraesCS2A01G074400 chr2A 100.000 3825 0 0 1 3825 32862403 32866227 0.000000e+00 7064.0
1 TraesCS2A01G074400 chr2A 87.087 1270 115 12 1759 2984 32875904 32877168 0.000000e+00 1391.0
2 TraesCS2A01G074400 chr2A 78.226 1511 250 56 1148 2601 32772983 32774471 0.000000e+00 894.0
3 TraesCS2A01G074400 chr2A 84.517 549 48 19 3058 3571 32877153 32877699 3.410000e-140 508.0
4 TraesCS2A01G074400 chr2A 94.839 310 16 0 1121 1430 32817734 32818043 5.750000e-133 484.0
5 TraesCS2A01G074400 chr2A 87.045 440 39 5 438 863 32817157 32817592 7.430000e-132 481.0
6 TraesCS2A01G074400 chr2A 79.883 512 85 9 1160 1659 32554173 32554678 3.630000e-95 359.0
7 TraesCS2A01G074400 chr2A 76.299 616 99 30 2158 2744 32928976 32929573 6.250000e-73 285.0
8 TraesCS2A01G074400 chr2A 76.708 571 93 24 2158 2700 32887879 32888437 8.090000e-72 281.0
9 TraesCS2A01G074400 chr2A 73.147 823 165 36 1193 1977 32886576 32887380 1.060000e-60 244.0
10 TraesCS2A01G074400 chr2A 89.759 166 14 2 140 305 32812852 32813014 3.870000e-50 209.0
11 TraesCS2A01G074400 chr2A 91.216 148 4 4 892 1039 32817554 32817692 3.900000e-45 193.0
12 TraesCS2A01G074400 chr2A 90.647 139 7 6 3621 3754 32878174 32878311 3.040000e-41 180.0
13 TraesCS2A01G074400 chr2A 78.605 215 38 7 1736 1949 32926395 32926602 6.670000e-28 135.0
14 TraesCS2A01G074400 chr2A 82.258 124 22 0 2014 2137 32887452 32887575 1.450000e-19 108.0
15 TraesCS2A01G074400 chr2A 86.047 86 12 0 2052 2137 32928587 32928672 4.070000e-15 93.5
16 TraesCS2A01G074400 chr2A 81.818 99 18 0 1241 1339 1165163 1165065 2.450000e-12 84.2
17 TraesCS2A01G074400 chr2A 92.593 54 4 0 3766 3819 32811331 32811384 1.140000e-10 78.7
18 TraesCS2A01G074400 chr2B 92.036 2323 97 32 892 3129 50410902 50413221 0.000000e+00 3184.0
19 TraesCS2A01G074400 chr2B 74.236 1669 322 62 1180 2772 50495304 50493668 5.470000e-168 601.0
20 TraesCS2A01G074400 chr2B 81.752 685 115 8 2018 2700 50524166 50523490 7.170000e-157 564.0
21 TraesCS2A01G074400 chr2B 86.395 441 44 6 438 864 50410505 50410943 5.790000e-128 468.0
22 TraesCS2A01G074400 chr2B 83.709 399 40 15 3162 3543 50413300 50413690 1.690000e-93 353.0
23 TraesCS2A01G074400 chr2B 83.582 335 49 5 1160 1488 50392704 50393038 3.710000e-80 309.0
24 TraesCS2A01G074400 chr2B 75.104 719 143 20 2016 2700 43797974 43798690 1.730000e-78 303.0
25 TraesCS2A01G074400 chr2B 90.244 164 15 1 140 303 50408424 50408586 2.990000e-51 213.0
26 TraesCS2A01G074400 chr2B 82.051 117 15 4 1226 1339 10078181 10078068 1.130000e-15 95.3
27 TraesCS2A01G074400 chr2B 91.837 49 2 1 31 79 50408261 50408307 2.470000e-07 67.6
28 TraesCS2A01G074400 chr2D 87.343 1351 111 20 1702 3006 30619219 30620555 0.000000e+00 1493.0
29 TraesCS2A01G074400 chr2D 77.546 1728 294 62 1160 2819 30611708 30613409 0.000000e+00 955.0
30 TraesCS2A01G074400 chr2D 88.657 335 32 3 1406 1734 30618741 30619075 1.650000e-108 403.0
31 TraesCS2A01G074400 chr2D 80.835 527 54 19 3031 3521 30620737 30621252 1.680000e-98 370.0
32 TraesCS2A01G074400 chr2D 87.584 298 33 4 450 745 30618313 30618608 3.660000e-90 342.0
33 TraesCS2A01G074400 chr2D 75.202 742 122 33 2014 2700 30654032 30654766 1.040000e-75 294.0
34 TraesCS2A01G074400 chr2D 97.345 113 3 0 1130 1242 30618630 30618742 3.900000e-45 193.0
35 TraesCS2A01G074400 chr2D 77.419 217 38 10 1736 1949 30653723 30653931 6.710000e-23 119.0
36 TraesCS2A01G074400 chr2D 91.111 45 4 0 1295 1339 1703317 1703273 1.150000e-05 62.1


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 TraesCS2A01G074400 chr2A 32862403 32866227 3824 False 7064.00 7064 100.000000 1 3825 1 chr2A.!!$F3 3824
1 TraesCS2A01G074400 chr2A 32772983 32774471 1488 False 894.00 894 78.226000 1148 2601 1 chr2A.!!$F2 1453
2 TraesCS2A01G074400 chr2A 32875904 32878311 2407 False 693.00 1391 87.417000 1759 3754 3 chr2A.!!$F6 1995
3 TraesCS2A01G074400 chr2A 32817157 32818043 886 False 386.00 484 91.033333 438 1430 3 chr2A.!!$F5 992
4 TraesCS2A01G074400 chr2A 32554173 32554678 505 False 359.00 359 79.883000 1160 1659 1 chr2A.!!$F1 499
5 TraesCS2A01G074400 chr2A 32886576 32888437 1861 False 211.00 281 77.371000 1193 2700 3 chr2A.!!$F7 1507
6 TraesCS2A01G074400 chr2B 50408261 50413690 5429 False 857.12 3184 88.844200 31 3543 5 chr2B.!!$F3 3512
7 TraesCS2A01G074400 chr2B 50493668 50495304 1636 True 601.00 601 74.236000 1180 2772 1 chr2B.!!$R2 1592
8 TraesCS2A01G074400 chr2B 50523490 50524166 676 True 564.00 564 81.752000 2018 2700 1 chr2B.!!$R3 682
9 TraesCS2A01G074400 chr2B 43797974 43798690 716 False 303.00 303 75.104000 2016 2700 1 chr2B.!!$F1 684
10 TraesCS2A01G074400 chr2D 30611708 30613409 1701 False 955.00 955 77.546000 1160 2819 1 chr2D.!!$F1 1659
11 TraesCS2A01G074400 chr2D 30618313 30621252 2939 False 560.20 1493 88.352800 450 3521 5 chr2D.!!$F2 3071
12 TraesCS2A01G074400 chr2D 30653723 30654766 1043 False 206.50 294 76.310500 1736 2700 2 chr2D.!!$F3 964

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
455 2287 0.315251 CGCGGCATCATCTTCCTCTA 59.685 55.0 0.0 0.0 0.0 2.43 F
1000 2855 0.381801 CAACAGTCCAACACCAGCAC 59.618 55.0 0.0 0.0 0.0 4.40 F
1007 2862 0.534412 CCAACACCAGCACCACAAAA 59.466 50.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 3920 0.596577 GCCTCCCCTTGTCGAAAAAC 59.403 55.000 0.0 0.0 0.00 2.43 R
1884 3994 3.264897 CGGCAGTAGACGGCATGC 61.265 66.667 9.9 9.9 44.44 4.06 R
2987 5490 3.686016 ACCACCGCTGAGTGAAATATTT 58.314 40.909 0.0 0.0 40.34 1.40 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 8.964476 ATCAAAAGAAATATAGAAAGCTCGGA 57.036 30.769 0.00 0.00 0.00 4.55
26 27 8.197988 TCAAAAGAAATATAGAAAGCTCGGAC 57.802 34.615 0.00 0.00 0.00 4.79
27 28 7.822334 TCAAAAGAAATATAGAAAGCTCGGACA 59.178 33.333 0.00 0.00 0.00 4.02
28 29 8.450964 CAAAAGAAATATAGAAAGCTCGGACAA 58.549 33.333 0.00 0.00 0.00 3.18
29 30 7.541122 AAGAAATATAGAAAGCTCGGACAAC 57.459 36.000 0.00 0.00 0.00 3.32
41 42 8.556213 AAAGCTCGGACAACTACAAAATATAA 57.444 30.769 0.00 0.00 0.00 0.98
42 43 8.556213 AAGCTCGGACAACTACAAAATATAAA 57.444 30.769 0.00 0.00 0.00 1.40
43 44 8.197988 AGCTCGGACAACTACAAAATATAAAG 57.802 34.615 0.00 0.00 0.00 1.85
72 73 2.701951 AGGACCTGAGTTACACGGAAAA 59.298 45.455 0.00 0.00 0.00 2.29
79 80 7.388437 ACCTGAGTTACACGGAAAATATACAA 58.612 34.615 0.00 0.00 0.00 2.41
80 81 7.332678 ACCTGAGTTACACGGAAAATATACAAC 59.667 37.037 0.00 0.00 0.00 3.32
81 82 7.332430 CCTGAGTTACACGGAAAATATACAACA 59.668 37.037 0.00 0.00 0.00 3.33
82 83 8.604640 TGAGTTACACGGAAAATATACAACAA 57.395 30.769 0.00 0.00 0.00 2.83
83 84 9.053840 TGAGTTACACGGAAAATATACAACAAA 57.946 29.630 0.00 0.00 0.00 2.83
84 85 9.321590 GAGTTACACGGAAAATATACAACAAAC 57.678 33.333 0.00 0.00 0.00 2.93
85 86 8.838365 AGTTACACGGAAAATATACAACAAACA 58.162 29.630 0.00 0.00 0.00 2.83
86 87 9.448294 GTTACACGGAAAATATACAACAAACAA 57.552 29.630 0.00 0.00 0.00 2.83
88 89 8.928270 ACACGGAAAATATACAACAAACAAAA 57.072 26.923 0.00 0.00 0.00 2.44
89 90 9.535878 ACACGGAAAATATACAACAAACAAAAT 57.464 25.926 0.00 0.00 0.00 1.82
91 92 9.198837 ACGGAAAATATACAACAAACAAAATCC 57.801 29.630 0.00 0.00 0.00 3.01
101 102 7.836842 ACAACAAACAAAATCCTGTAGAAAGT 58.163 30.769 0.00 0.00 0.00 2.66
102 103 8.962679 ACAACAAACAAAATCCTGTAGAAAGTA 58.037 29.630 0.00 0.00 0.00 2.24
103 104 9.450807 CAACAAACAAAATCCTGTAGAAAGTAG 57.549 33.333 0.00 0.00 0.00 2.57
104 105 8.974060 ACAAACAAAATCCTGTAGAAAGTAGA 57.026 30.769 0.00 0.00 0.00 2.59
105 106 9.403583 ACAAACAAAATCCTGTAGAAAGTAGAA 57.596 29.630 0.00 0.00 0.00 2.10
111 112 9.722184 AAAATCCTGTAGAAAGTAGAAACTACC 57.278 33.333 0.00 0.00 33.75 3.18
113 114 9.765295 AATCCTGTAGAAAGTAGAAACTACCTA 57.235 33.333 0.00 0.00 33.75 3.08
114 115 8.804912 TCCTGTAGAAAGTAGAAACTACCTAG 57.195 38.462 0.00 0.00 33.75 3.02
115 116 8.389366 TCCTGTAGAAAGTAGAAACTACCTAGT 58.611 37.037 0.00 0.00 38.39 2.57
116 117 8.676401 CCTGTAGAAAGTAGAAACTACCTAGTC 58.324 40.741 0.00 0.00 34.99 2.59
117 118 8.572855 TGTAGAAAGTAGAAACTACCTAGTCC 57.427 38.462 0.00 0.00 34.99 3.85
118 119 7.613411 TGTAGAAAGTAGAAACTACCTAGTCCC 59.387 40.741 0.00 0.00 34.99 4.46
120 121 7.247500 AGAAAGTAGAAACTACCTAGTCCCTT 58.753 38.462 0.00 0.00 34.99 3.95
121 122 6.854091 AAGTAGAAACTACCTAGTCCCTTG 57.146 41.667 0.00 0.00 34.99 3.61
122 123 5.901598 AGTAGAAACTACCTAGTCCCTTGT 58.098 41.667 0.00 0.00 34.99 3.16
123 124 6.321321 AGTAGAAACTACCTAGTCCCTTGTT 58.679 40.000 0.00 0.00 34.99 2.83
129 130 4.850386 ACTACCTAGTCCCTTGTTCCATTT 59.150 41.667 0.00 0.00 0.00 2.32
130 131 4.302559 ACCTAGTCCCTTGTTCCATTTC 57.697 45.455 0.00 0.00 0.00 2.17
132 133 4.105697 ACCTAGTCCCTTGTTCCATTTCAA 59.894 41.667 0.00 0.00 0.00 2.69
133 134 5.222337 ACCTAGTCCCTTGTTCCATTTCAAT 60.222 40.000 0.00 0.00 0.00 2.57
134 135 5.358160 CCTAGTCCCTTGTTCCATTTCAATC 59.642 44.000 0.00 0.00 0.00 2.67
135 136 4.739793 AGTCCCTTGTTCCATTTCAATCA 58.260 39.130 0.00 0.00 0.00 2.57
137 138 4.082026 GTCCCTTGTTCCATTTCAATCAGG 60.082 45.833 0.00 0.00 0.00 3.86
138 139 3.834231 CCCTTGTTCCATTTCAATCAGGT 59.166 43.478 0.00 0.00 0.00 4.00
146 203 2.655090 TTTCAATCAGGTGCCAGACA 57.345 45.000 0.00 0.00 0.00 3.41
169 226 7.398024 ACACTGGTTAAATAGAAAGAGAGCAT 58.602 34.615 0.00 0.00 0.00 3.79
171 228 9.039870 CACTGGTTAAATAGAAAGAGAGCATAG 57.960 37.037 0.00 0.00 0.00 2.23
178 235 3.037549 AGAAAGAGAGCATAGGAGTGGG 58.962 50.000 0.00 0.00 0.00 4.61
179 236 1.799933 AAGAGAGCATAGGAGTGGGG 58.200 55.000 0.00 0.00 0.00 4.96
191 248 2.039624 GTGGGGGAGGAGAGCAGA 59.960 66.667 0.00 0.00 0.00 4.26
227 284 5.760253 TCTTCAGTTAGCTTTCTCAAGTTGG 59.240 40.000 2.34 0.00 31.86 3.77
232 289 3.845781 AGCTTTCTCAAGTTGGAGTGA 57.154 42.857 2.34 0.00 36.30 3.41
246 303 1.623811 GGAGTGACTTGAGCCAGGTAA 59.376 52.381 0.00 0.00 0.00 2.85
258 315 7.286775 ACTTGAGCCAGGTAAGAAACATTAAAA 59.713 33.333 7.11 0.00 0.00 1.52
259 316 6.977213 TGAGCCAGGTAAGAAACATTAAAAC 58.023 36.000 0.00 0.00 0.00 2.43
260 317 6.547880 TGAGCCAGGTAAGAAACATTAAAACA 59.452 34.615 0.00 0.00 0.00 2.83
306 363 4.532834 GGGGGTGCTTATATGTTTTCTCA 58.467 43.478 0.00 0.00 0.00 3.27
308 365 5.067805 GGGGGTGCTTATATGTTTTCTCAAG 59.932 44.000 0.00 0.00 0.00 3.02
309 366 5.652452 GGGGTGCTTATATGTTTTCTCAAGT 59.348 40.000 0.00 0.00 0.00 3.16
310 367 6.152831 GGGGTGCTTATATGTTTTCTCAAGTT 59.847 38.462 0.00 0.00 0.00 2.66
311 368 7.338449 GGGGTGCTTATATGTTTTCTCAAGTTA 59.662 37.037 0.00 0.00 0.00 2.24
312 369 8.398665 GGGTGCTTATATGTTTTCTCAAGTTAG 58.601 37.037 0.00 0.00 0.00 2.34
313 370 7.910683 GGTGCTTATATGTTTTCTCAAGTTAGC 59.089 37.037 0.00 0.00 0.00 3.09
314 371 8.669243 GTGCTTATATGTTTTCTCAAGTTAGCT 58.331 33.333 0.00 0.00 0.00 3.32
315 372 9.231297 TGCTTATATGTTTTCTCAAGTTAGCTT 57.769 29.630 0.00 0.00 34.82 3.74
355 2141 3.730761 GCAGACGGGCAGTTGCAG 61.731 66.667 15.58 2.12 44.36 4.41
363 2149 2.684843 GGCAGTTGCAGCTTCTCCG 61.685 63.158 0.00 0.00 44.36 4.63
365 2151 2.740055 AGTTGCAGCTTCTCCGCG 60.740 61.111 0.00 0.00 34.40 6.46
401 2187 1.000717 GTTACAACGCCCATGTGCTTT 60.001 47.619 0.00 0.00 32.27 3.51
402 2188 0.595588 TACAACGCCCATGTGCTTTG 59.404 50.000 15.98 15.98 43.73 2.77
446 2278 4.552365 CCCCTGTCGCGGCATCAT 62.552 66.667 16.48 0.00 0.00 2.45
448 2280 2.107750 CCTGTCGCGGCATCATCT 59.892 61.111 16.48 0.00 0.00 2.90
449 2281 1.522355 CCTGTCGCGGCATCATCTT 60.522 57.895 16.48 0.00 0.00 2.40
451 2283 1.493950 CTGTCGCGGCATCATCTTCC 61.494 60.000 16.48 0.00 0.00 3.46
454 2286 1.068753 CGCGGCATCATCTTCCTCT 59.931 57.895 0.00 0.00 0.00 3.69
455 2287 0.315251 CGCGGCATCATCTTCCTCTA 59.685 55.000 0.00 0.00 0.00 2.43
457 2289 1.606737 GCGGCATCATCTTCCTCTACC 60.607 57.143 0.00 0.00 0.00 3.18
458 2290 1.967066 CGGCATCATCTTCCTCTACCT 59.033 52.381 0.00 0.00 0.00 3.08
482 2324 1.062880 CCTACGTCGTCAGCTCTTCTC 59.937 57.143 0.00 0.00 0.00 2.87
494 2336 0.820871 CTCTTCTCTCCTTCGGTGGG 59.179 60.000 0.00 0.00 0.00 4.61
540 2382 2.429250 TCACTCTCGTCACAAGTTGGAA 59.571 45.455 7.96 0.00 0.00 3.53
548 2390 1.673920 TCACAAGTTGGAAGCGAAACC 59.326 47.619 7.96 0.00 0.00 3.27
586 2428 2.494918 GGTAGTCCAGATGCGCGT 59.505 61.111 8.43 0.00 0.00 6.01
595 2437 4.223964 GATGCGCGTCGGCCTTTC 62.224 66.667 14.88 0.00 35.02 2.62
617 2459 0.894141 GTGGCAAGAGAGAGCAGAGA 59.106 55.000 0.00 0.00 0.00 3.10
621 2463 2.233431 GGCAAGAGAGAGCAGAGAAGAA 59.767 50.000 0.00 0.00 0.00 2.52
660 2502 2.515005 TCCATGATGATCCCCACACAAT 59.485 45.455 0.00 0.00 0.00 2.71
675 2517 4.040217 CCACACAATGATGAAGGGGAAAAA 59.960 41.667 0.00 0.00 32.70 1.94
712 2554 2.890371 CCGGGTTTCTCGGTCGAT 59.110 61.111 0.00 0.00 42.33 3.59
725 2567 3.293337 TCGGTCGATGATAAGGAAAGGA 58.707 45.455 0.00 0.00 0.00 3.36
787 2642 1.140407 GGCGAAAGACGAGATCGGTG 61.140 60.000 7.22 0.00 45.77 4.94
864 2719 7.085052 AGTTGAAACTTAGTTGTGAAGTTCC 57.915 36.000 0.00 0.00 44.43 3.62
865 2720 5.728351 TGAAACTTAGTTGTGAAGTTCCG 57.272 39.130 0.00 0.00 44.43 4.30
866 2721 5.180271 TGAAACTTAGTTGTGAAGTTCCGT 58.820 37.500 0.00 0.00 44.43 4.69
867 2722 5.644636 TGAAACTTAGTTGTGAAGTTCCGTT 59.355 36.000 0.00 0.00 44.43 4.44
868 2723 6.149807 TGAAACTTAGTTGTGAAGTTCCGTTT 59.850 34.615 0.00 0.00 44.43 3.60
869 2724 5.729974 ACTTAGTTGTGAAGTTCCGTTTC 57.270 39.130 0.00 0.00 33.25 2.78
870 2725 4.269363 ACTTAGTTGTGAAGTTCCGTTTCG 59.731 41.667 0.00 0.00 33.25 3.46
871 2726 2.896168 AGTTGTGAAGTTCCGTTTCGA 58.104 42.857 0.00 0.00 0.00 3.71
872 2727 3.264104 AGTTGTGAAGTTCCGTTTCGAA 58.736 40.909 0.00 0.00 0.00 3.71
873 2728 3.685756 AGTTGTGAAGTTCCGTTTCGAAA 59.314 39.130 6.47 6.47 0.00 3.46
874 2729 4.154556 AGTTGTGAAGTTCCGTTTCGAAAA 59.845 37.500 13.10 0.00 0.00 2.29
875 2730 4.681835 TGTGAAGTTCCGTTTCGAAAAA 57.318 36.364 13.10 0.28 0.00 1.94
906 2761 9.662947 ACTTAGTTGTGAAGTAAACTTAGTTGT 57.337 29.630 0.00 0.00 41.16 3.32
907 2762 9.916397 CTTAGTTGTGAAGTAAACTTAGTTGTG 57.084 33.333 0.00 0.00 37.74 3.33
908 2763 9.656040 TTAGTTGTGAAGTAAACTTAGTTGTGA 57.344 29.630 0.00 0.00 37.74 3.58
909 2764 8.556213 AGTTGTGAAGTAAACTTAGTTGTGAA 57.444 30.769 0.00 0.00 36.11 3.18
910 2765 8.665685 AGTTGTGAAGTAAACTTAGTTGTGAAG 58.334 33.333 0.00 0.00 36.11 3.02
911 2766 8.448615 GTTGTGAAGTAAACTTAGTTGTGAAGT 58.551 33.333 0.00 0.00 38.81 3.01
912 2767 9.656040 TTGTGAAGTAAACTTAGTTGTGAAGTA 57.344 29.630 0.00 0.00 36.10 2.24
913 2768 9.656040 TGTGAAGTAAACTTAGTTGTGAAGTAA 57.344 29.630 0.00 0.00 36.10 2.24
923 2778 9.662947 ACTTAGTTGTGAAGTAAACTTAGTTGT 57.337 29.630 0.00 0.00 41.16 3.32
924 2779 9.916397 CTTAGTTGTGAAGTAAACTTAGTTGTG 57.084 33.333 0.00 0.00 37.74 3.33
925 2780 9.656040 TTAGTTGTGAAGTAAACTTAGTTGTGA 57.344 29.630 0.00 0.00 37.74 3.58
926 2781 8.556213 AGTTGTGAAGTAAACTTAGTTGTGAA 57.444 30.769 0.00 0.00 36.11 3.18
927 2782 8.665685 AGTTGTGAAGTAAACTTAGTTGTGAAG 58.334 33.333 0.00 0.00 36.11 3.02
928 2783 8.448615 GTTGTGAAGTAAACTTAGTTGTGAAGT 58.551 33.333 0.00 0.00 38.81 3.01
929 2784 8.556213 TGTGAAGTAAACTTAGTTGTGAAGTT 57.444 30.769 0.00 0.00 46.57 2.66
930 2785 8.447833 TGTGAAGTAAACTTAGTTGTGAAGTTG 58.552 33.333 0.00 0.00 44.43 3.16
997 2852 2.631160 TACCAACAGTCCAACACCAG 57.369 50.000 0.00 0.00 0.00 4.00
999 2854 0.751277 CCAACAGTCCAACACCAGCA 60.751 55.000 0.00 0.00 0.00 4.41
1000 2855 0.381801 CAACAGTCCAACACCAGCAC 59.618 55.000 0.00 0.00 0.00 4.40
1002 2857 1.152984 CAGTCCAACACCAGCACCA 60.153 57.895 0.00 0.00 0.00 4.17
1003 2858 1.152963 AGTCCAACACCAGCACCAC 60.153 57.895 0.00 0.00 0.00 4.16
1004 2859 1.453015 GTCCAACACCAGCACCACA 60.453 57.895 0.00 0.00 0.00 4.17
1007 2862 0.534412 CCAACACCAGCACCACAAAA 59.466 50.000 0.00 0.00 0.00 2.44
1047 2902 0.747644 CACAGACACAGGCCACACAA 60.748 55.000 5.01 0.00 0.00 3.33
1079 2935 4.839121 TGTCTAATCGTAGCACCCAAAAT 58.161 39.130 0.00 0.00 0.00 1.82
1082 2938 6.879993 TGTCTAATCGTAGCACCCAAAATTTA 59.120 34.615 0.00 0.00 0.00 1.40
1117 2973 2.103094 CCTCTCCACAGTTGACAGTTCA 59.897 50.000 0.00 0.00 0.00 3.18
1119 2975 2.158957 TCTCCACAGTTGACAGTTCACC 60.159 50.000 0.00 0.00 0.00 4.02
1387 3262 0.742505 ACGTGTGTCGGAGTTCTTCA 59.257 50.000 0.00 0.00 44.69 3.02
1757 3866 2.283101 TGAATGGCCACCACCAGC 60.283 61.111 8.16 0.00 44.71 4.85
1792 3902 0.762418 TTTCTCCTCAAAGTCGGGCA 59.238 50.000 0.00 0.00 0.00 5.36
1810 3920 1.338579 GCAGTTGGAAGGAGAGGTCTG 60.339 57.143 0.00 0.00 0.00 3.51
1884 3994 2.069273 GACTGGTTTGATGACAGACGG 58.931 52.381 0.00 0.00 36.17 4.79
1949 4060 7.553881 AAACTGATTTCATAATGAGGTACCG 57.446 36.000 6.18 0.00 30.24 4.02
1950 4061 5.611374 ACTGATTTCATAATGAGGTACCGG 58.389 41.667 6.18 0.00 30.24 5.28
2140 4301 0.110486 AGGGGTGTACCTTGCAACTG 59.890 55.000 0.00 0.00 37.69 3.16
2781 5268 4.441634 GGTCTACTCATGTTTATCGCCTGT 60.442 45.833 0.00 0.00 0.00 4.00
2870 5357 3.135225 CTGTTGTACGGACATGAAACCA 58.865 45.455 0.00 0.00 34.86 3.67
2967 5470 7.945134 ACAACCCATATGCATTTCTTATTCTC 58.055 34.615 3.54 0.00 0.00 2.87
2984 5487 8.213679 TCTTATTCTCTTTCATCTACATTGGGG 58.786 37.037 0.00 0.00 0.00 4.96
2987 5490 4.782691 TCTCTTTCATCTACATTGGGGACA 59.217 41.667 0.00 0.00 39.83 4.02
3051 5714 4.653341 TCAATTTGGTGGTTGGTTTCATCT 59.347 37.500 0.00 0.00 0.00 2.90
3065 5728 9.196552 GTTGGTTTCATCTTGATTTTTCCTTAG 57.803 33.333 0.00 0.00 0.00 2.18
3081 5744 0.328258 TTAGTTTGGGCTCCTGCTCC 59.672 55.000 0.00 0.00 39.40 4.70
3129 5796 5.665916 AACCTTCCCAAGAAATATGCTTG 57.334 39.130 10.24 10.24 41.77 4.01
3131 5798 4.706962 ACCTTCCCAAGAAATATGCTTGTC 59.293 41.667 14.16 0.00 40.79 3.18
3132 5799 4.098501 CCTTCCCAAGAAATATGCTTGTCC 59.901 45.833 14.16 0.00 40.79 4.02
3134 5801 4.272489 TCCCAAGAAATATGCTTGTCCAG 58.728 43.478 14.16 3.29 40.79 3.86
3135 5802 4.018506 TCCCAAGAAATATGCTTGTCCAGA 60.019 41.667 14.16 6.09 40.79 3.86
3136 5803 4.706476 CCCAAGAAATATGCTTGTCCAGAA 59.294 41.667 14.16 0.00 40.79 3.02
3137 5804 5.185635 CCCAAGAAATATGCTTGTCCAGAAA 59.814 40.000 14.16 0.00 40.79 2.52
3138 5805 6.127253 CCCAAGAAATATGCTTGTCCAGAAAT 60.127 38.462 14.16 0.00 40.79 2.17
3139 5806 7.068593 CCCAAGAAATATGCTTGTCCAGAAATA 59.931 37.037 14.16 0.00 40.79 1.40
3143 5810 7.504911 AGAAATATGCTTGTCCAGAAATATGCT 59.495 33.333 0.00 0.00 0.00 3.79
3144 5811 7.592885 AATATGCTTGTCCAGAAATATGCTT 57.407 32.000 0.00 0.00 0.00 3.91
3148 5815 7.734924 TGCTTGTCCAGAAATATGCTTATAG 57.265 36.000 0.00 0.00 0.00 1.31
3149 5816 7.508687 TGCTTGTCCAGAAATATGCTTATAGA 58.491 34.615 0.00 0.00 0.00 1.98
3150 5817 8.159447 TGCTTGTCCAGAAATATGCTTATAGAT 58.841 33.333 0.00 0.00 0.00 1.98
3153 5820 9.851686 TTGTCCAGAAATATGCTTATAGATTGT 57.148 29.630 0.00 0.00 0.00 2.71
3154 5821 9.494271 TGTCCAGAAATATGCTTATAGATTGTC 57.506 33.333 0.00 0.00 0.00 3.18
3155 5822 8.940952 GTCCAGAAATATGCTTATAGATTGTCC 58.059 37.037 0.00 0.00 0.00 4.02
3189 5903 7.170393 ACTGTTTTTCCTATTATTTCTGGCC 57.830 36.000 0.00 0.00 0.00 5.36
3191 5905 6.930731 TGTTTTTCCTATTATTTCTGGCCAC 58.069 36.000 0.00 0.00 0.00 5.01
3198 5912 6.708949 TCCTATTATTTCTGGCCACGTAATTC 59.291 38.462 0.00 0.00 0.00 2.17
3222 5936 5.003804 TGGCTTATTTTCTGTCCTGAGTTC 58.996 41.667 0.00 0.00 0.00 3.01
3255 5969 1.321474 CCTGAACTTCAGCTTTGCCA 58.679 50.000 12.69 0.00 42.98 4.92
3278 5992 1.423584 TGGAAACACTCTGAGCAGGA 58.576 50.000 4.19 0.00 33.40 3.86
3280 5994 1.609320 GGAAACACTCTGAGCAGGACC 60.609 57.143 4.19 0.12 0.00 4.46
3282 5996 1.428869 AACACTCTGAGCAGGACCTT 58.571 50.000 4.19 0.00 0.00 3.50
3320 6045 2.036256 CTTGGGCCTTGGAGGGTG 59.964 66.667 4.53 0.00 35.37 4.61
3328 6053 0.250513 CCTTGGAGGGTGAGCAGTAC 59.749 60.000 0.00 0.00 0.00 2.73
3329 6054 1.270907 CTTGGAGGGTGAGCAGTACT 58.729 55.000 0.00 0.00 0.00 2.73
3336 6061 4.184629 GAGGGTGAGCAGTACTATTTGTG 58.815 47.826 0.00 0.00 0.00 3.33
3343 6068 7.237173 GTGAGCAGTACTATTTGTGTGAAATC 58.763 38.462 0.00 0.00 0.00 2.17
3438 6163 4.201532 CGACTTTGAGCATGTAGAAACTCG 60.202 45.833 0.00 0.00 31.64 4.18
3441 6171 5.864474 ACTTTGAGCATGTAGAAACTCGTAG 59.136 40.000 0.00 0.00 31.64 3.51
3602 6449 4.314740 TTGCGTTTTTGAAATAGGCTGT 57.685 36.364 12.67 0.00 0.00 4.40
3610 6457 7.481798 CGTTTTTGAAATAGGCTGTCACTAATC 59.518 37.037 0.00 0.00 0.00 1.75
3629 6785 7.587757 CACTAATCTTATTGGTTCTAATTGCGC 59.412 37.037 0.00 0.00 0.00 6.09
3632 6788 4.335315 TCTTATTGGTTCTAATTGCGCTGG 59.665 41.667 9.73 0.00 0.00 4.85
3754 6915 4.716784 TCTATGATGGCTTGTCAGGTTACT 59.283 41.667 0.00 0.00 0.00 2.24
3755 6916 3.057969 TGATGGCTTGTCAGGTTACTG 57.942 47.619 0.00 0.00 46.30 2.74
3756 6917 2.371841 TGATGGCTTGTCAGGTTACTGT 59.628 45.455 0.00 0.00 45.14 3.55
3757 6918 3.181445 TGATGGCTTGTCAGGTTACTGTT 60.181 43.478 0.00 0.00 45.14 3.16
3758 6919 2.571212 TGGCTTGTCAGGTTACTGTTG 58.429 47.619 0.00 0.00 45.14 3.33
3759 6920 1.266989 GGCTTGTCAGGTTACTGTTGC 59.733 52.381 0.00 0.00 45.14 4.17
3760 6921 1.946768 GCTTGTCAGGTTACTGTTGCA 59.053 47.619 0.00 0.00 45.14 4.08
3761 6922 2.554032 GCTTGTCAGGTTACTGTTGCAT 59.446 45.455 0.00 0.00 45.14 3.96
3762 6923 3.004734 GCTTGTCAGGTTACTGTTGCATT 59.995 43.478 0.00 0.00 45.14 3.56
3763 6924 4.499696 GCTTGTCAGGTTACTGTTGCATTT 60.500 41.667 0.00 0.00 45.14 2.32
3764 6925 4.566545 TGTCAGGTTACTGTTGCATTTG 57.433 40.909 0.00 0.00 45.14 2.32
3765 6926 3.317711 TGTCAGGTTACTGTTGCATTTGG 59.682 43.478 0.00 0.00 45.14 3.28
3766 6927 3.317993 GTCAGGTTACTGTTGCATTTGGT 59.682 43.478 0.00 0.00 45.14 3.67
3767 6928 4.517453 GTCAGGTTACTGTTGCATTTGGTA 59.483 41.667 0.00 0.00 45.14 3.25
3768 6929 4.517453 TCAGGTTACTGTTGCATTTGGTAC 59.483 41.667 0.00 0.00 45.14 3.34
3769 6930 4.518970 CAGGTTACTGTTGCATTTGGTACT 59.481 41.667 0.00 0.00 39.92 2.73
3770 6931 4.760204 AGGTTACTGTTGCATTTGGTACTC 59.240 41.667 0.00 0.00 0.00 2.59
3771 6932 4.517453 GGTTACTGTTGCATTTGGTACTCA 59.483 41.667 0.00 0.00 0.00 3.41
3772 6933 5.009210 GGTTACTGTTGCATTTGGTACTCAA 59.991 40.000 0.00 0.00 0.00 3.02
3773 6934 4.836125 ACTGTTGCATTTGGTACTCAAG 57.164 40.909 0.00 0.00 36.62 3.02
3774 6935 3.004734 ACTGTTGCATTTGGTACTCAAGC 59.995 43.478 0.00 0.00 36.62 4.01
3775 6936 2.954989 TGTTGCATTTGGTACTCAAGCA 59.045 40.909 0.00 0.49 35.59 3.91
3776 6937 3.573538 TGTTGCATTTGGTACTCAAGCAT 59.426 39.130 9.93 0.00 36.73 3.79
3777 6938 4.039004 TGTTGCATTTGGTACTCAAGCATT 59.961 37.500 9.93 0.00 36.73 3.56
3778 6939 4.870123 TGCATTTGGTACTCAAGCATTT 57.130 36.364 0.00 0.00 33.45 2.32
3779 6940 4.558178 TGCATTTGGTACTCAAGCATTTG 58.442 39.130 0.00 0.00 33.45 2.32
3780 6941 4.039004 TGCATTTGGTACTCAAGCATTTGT 59.961 37.500 0.00 0.00 33.45 2.83
3781 6942 5.242615 TGCATTTGGTACTCAAGCATTTGTA 59.757 36.000 0.00 0.00 33.45 2.41
3782 6943 6.071447 TGCATTTGGTACTCAAGCATTTGTAT 60.071 34.615 0.00 0.00 33.45 2.29
3783 6944 6.473455 GCATTTGGTACTCAAGCATTTGTATC 59.527 38.462 0.00 0.00 36.62 2.24
3784 6945 7.537715 CATTTGGTACTCAAGCATTTGTATCA 58.462 34.615 0.00 0.00 36.62 2.15
3785 6946 6.741992 TTGGTACTCAAGCATTTGTATCAG 57.258 37.500 0.00 0.00 35.03 2.90
3786 6947 6.048732 TGGTACTCAAGCATTTGTATCAGA 57.951 37.500 0.00 0.00 35.73 3.27
3787 6948 6.472016 TGGTACTCAAGCATTTGTATCAGAA 58.528 36.000 0.00 0.00 35.73 3.02
3788 6949 6.371548 TGGTACTCAAGCATTTGTATCAGAAC 59.628 38.462 0.00 0.00 35.73 3.01
3789 6950 6.371548 GGTACTCAAGCATTTGTATCAGAACA 59.628 38.462 0.00 0.00 35.73 3.18
3790 6951 6.882610 ACTCAAGCATTTGTATCAGAACAA 57.117 33.333 0.00 0.00 37.58 2.83
3791 6952 7.458409 ACTCAAGCATTTGTATCAGAACAAT 57.542 32.000 0.00 0.00 39.04 2.71
3792 6953 7.889469 ACTCAAGCATTTGTATCAGAACAATT 58.111 30.769 0.00 0.00 39.04 2.32
3793 6954 8.362639 ACTCAAGCATTTGTATCAGAACAATTT 58.637 29.630 0.00 0.00 39.04 1.82
3794 6955 8.523523 TCAAGCATTTGTATCAGAACAATTTG 57.476 30.769 0.00 0.00 39.04 2.32
3795 6956 8.143193 TCAAGCATTTGTATCAGAACAATTTGT 58.857 29.630 0.00 0.00 39.04 2.83
3796 6957 9.409312 CAAGCATTTGTATCAGAACAATTTGTA 57.591 29.630 1.76 0.00 39.04 2.41
3824 6985 8.542497 TTGTCATCTACCTACATGTTAACAAC 57.458 34.615 13.23 1.95 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.831550 GTCCGAGCTTTCTATATTTCTTTTGAT 58.168 33.333 0.00 0.00 0.00 2.57
1 2 7.822334 TGTCCGAGCTTTCTATATTTCTTTTGA 59.178 33.333 0.00 0.00 0.00 2.69
2 3 7.974675 TGTCCGAGCTTTCTATATTTCTTTTG 58.025 34.615 0.00 0.00 0.00 2.44
4 5 7.824779 AGTTGTCCGAGCTTTCTATATTTCTTT 59.175 33.333 0.00 0.00 0.00 2.52
5 6 7.331791 AGTTGTCCGAGCTTTCTATATTTCTT 58.668 34.615 0.00 0.00 0.00 2.52
6 7 6.879400 AGTTGTCCGAGCTTTCTATATTTCT 58.121 36.000 0.00 0.00 0.00 2.52
7 8 7.705325 TGTAGTTGTCCGAGCTTTCTATATTTC 59.295 37.037 0.00 0.00 0.00 2.17
8 9 7.553334 TGTAGTTGTCCGAGCTTTCTATATTT 58.447 34.615 0.00 0.00 0.00 1.40
9 10 7.108841 TGTAGTTGTCCGAGCTTTCTATATT 57.891 36.000 0.00 0.00 0.00 1.28
10 11 6.710597 TGTAGTTGTCCGAGCTTTCTATAT 57.289 37.500 0.00 0.00 0.00 0.86
11 12 6.519679 TTGTAGTTGTCCGAGCTTTCTATA 57.480 37.500 0.00 0.00 0.00 1.31
12 13 5.401531 TTGTAGTTGTCCGAGCTTTCTAT 57.598 39.130 0.00 0.00 0.00 1.98
13 14 4.859304 TTGTAGTTGTCCGAGCTTTCTA 57.141 40.909 0.00 0.00 0.00 2.10
14 15 3.746045 TTGTAGTTGTCCGAGCTTTCT 57.254 42.857 0.00 0.00 0.00 2.52
15 16 4.806342 TTTTGTAGTTGTCCGAGCTTTC 57.194 40.909 0.00 0.00 0.00 2.62
16 17 8.556213 TTATATTTTGTAGTTGTCCGAGCTTT 57.444 30.769 0.00 0.00 0.00 3.51
17 18 8.556213 TTTATATTTTGTAGTTGTCCGAGCTT 57.444 30.769 0.00 0.00 0.00 3.74
18 19 8.038944 TCTTTATATTTTGTAGTTGTCCGAGCT 58.961 33.333 0.00 0.00 0.00 4.09
19 20 8.114905 GTCTTTATATTTTGTAGTTGTCCGAGC 58.885 37.037 0.00 0.00 0.00 5.03
20 21 9.367444 AGTCTTTATATTTTGTAGTTGTCCGAG 57.633 33.333 0.00 0.00 0.00 4.63
21 22 9.146984 CAGTCTTTATATTTTGTAGTTGTCCGA 57.853 33.333 0.00 0.00 0.00 4.55
22 23 8.932791 ACAGTCTTTATATTTTGTAGTTGTCCG 58.067 33.333 0.00 0.00 0.00 4.79
41 42 5.601313 TGTAACTCAGGTCCTAAACAGTCTT 59.399 40.000 0.00 0.00 0.00 3.01
42 43 5.010820 GTGTAACTCAGGTCCTAAACAGTCT 59.989 44.000 0.00 0.00 0.00 3.24
43 44 5.228665 GTGTAACTCAGGTCCTAAACAGTC 58.771 45.833 0.00 0.00 0.00 3.51
79 80 8.974060 TCTACTTTCTACAGGATTTTGTTTGT 57.026 30.769 0.00 0.00 32.56 2.83
82 83 9.628500 AGTTTCTACTTTCTACAGGATTTTGTT 57.372 29.630 0.00 0.00 32.56 2.83
85 86 9.722184 GGTAGTTTCTACTTTCTACAGGATTTT 57.278 33.333 6.83 0.00 35.77 1.82
86 87 9.102453 AGGTAGTTTCTACTTTCTACAGGATTT 57.898 33.333 6.83 0.00 35.77 2.17
88 89 9.411189 CTAGGTAGTTTCTACTTTCTACAGGAT 57.589 37.037 6.83 0.00 35.77 3.24
89 90 8.389366 ACTAGGTAGTTTCTACTTTCTACAGGA 58.611 37.037 6.83 0.00 35.77 3.86
90 91 8.578448 ACTAGGTAGTTTCTACTTTCTACAGG 57.422 38.462 6.83 0.00 35.77 4.00
91 92 8.676401 GGACTAGGTAGTTTCTACTTTCTACAG 58.324 40.741 6.83 0.00 36.50 2.74
93 94 7.833682 AGGGACTAGGTAGTTTCTACTTTCTAC 59.166 40.741 6.83 0.00 36.02 2.59
94 95 7.937591 AGGGACTAGGTAGTTTCTACTTTCTA 58.062 38.462 6.83 1.01 36.02 2.10
95 96 6.803017 AGGGACTAGGTAGTTTCTACTTTCT 58.197 40.000 6.83 0.04 36.02 2.52
96 97 7.039152 ACAAGGGACTAGGTAGTTTCTACTTTC 60.039 40.741 6.83 0.00 38.49 2.62
98 99 6.321321 ACAAGGGACTAGGTAGTTTCTACTT 58.679 40.000 6.83 2.57 38.49 2.24
99 100 5.901598 ACAAGGGACTAGGTAGTTTCTACT 58.098 41.667 6.83 0.00 38.49 2.57
101 102 5.718607 GGAACAAGGGACTAGGTAGTTTCTA 59.281 44.000 0.00 0.00 38.49 2.10
102 103 4.531339 GGAACAAGGGACTAGGTAGTTTCT 59.469 45.833 0.00 0.00 38.49 2.52
103 104 4.285260 TGGAACAAGGGACTAGGTAGTTTC 59.715 45.833 0.00 0.00 38.49 2.78
104 105 4.237018 TGGAACAAGGGACTAGGTAGTTT 58.763 43.478 0.00 0.00 38.49 2.66
105 106 3.865571 TGGAACAAGGGACTAGGTAGTT 58.134 45.455 0.00 0.00 38.49 2.24
106 107 3.555117 TGGAACAAGGGACTAGGTAGT 57.445 47.619 0.00 0.00 38.49 2.73
121 122 2.562298 TGGCACCTGATTGAAATGGAAC 59.438 45.455 0.00 0.00 0.00 3.62
122 123 2.827322 CTGGCACCTGATTGAAATGGAA 59.173 45.455 0.00 0.00 0.00 3.53
123 124 2.041485 TCTGGCACCTGATTGAAATGGA 59.959 45.455 0.00 0.00 0.00 3.41
129 130 3.631453 GTGTCTGGCACCTGATTGA 57.369 52.632 0.00 0.00 42.10 2.57
146 203 8.207545 CCTATGCTCTCTTTCTATTTAACCAGT 58.792 37.037 0.00 0.00 0.00 4.00
153 210 6.183361 CCCACTCCTATGCTCTCTTTCTATTT 60.183 42.308 0.00 0.00 0.00 1.40
169 226 1.950748 GCTCTCCTCCCCCACTCCTA 61.951 65.000 0.00 0.00 0.00 2.94
171 228 2.766229 GCTCTCCTCCCCCACTCC 60.766 72.222 0.00 0.00 0.00 3.85
178 235 1.134551 GTCACATTCTGCTCTCCTCCC 60.135 57.143 0.00 0.00 0.00 4.30
179 236 1.830477 AGTCACATTCTGCTCTCCTCC 59.170 52.381 0.00 0.00 0.00 4.30
191 248 7.416964 AGCTAACTGAAGAGATAGTCACATT 57.583 36.000 0.00 0.00 29.32 2.71
227 284 2.563179 TCTTACCTGGCTCAAGTCACTC 59.437 50.000 0.00 0.00 0.00 3.51
232 289 3.857157 TGTTTCTTACCTGGCTCAAGT 57.143 42.857 0.00 0.00 0.00 3.16
287 344 7.910683 GCTAACTTGAGAAAACATATAAGCACC 59.089 37.037 0.00 0.00 0.00 5.01
297 354 5.270853 GCGAAAAGCTAACTTGAGAAAACA 58.729 37.500 0.00 0.00 44.04 2.83
313 370 2.186076 CTGCGACCTACTAGCGAAAAG 58.814 52.381 0.00 0.00 0.00 2.27
314 371 1.734707 GCTGCGACCTACTAGCGAAAA 60.735 52.381 0.00 0.00 0.00 2.29
315 372 0.179145 GCTGCGACCTACTAGCGAAA 60.179 55.000 0.00 0.00 0.00 3.46
317 374 3.108343 GCTGCGACCTACTAGCGA 58.892 61.111 0.00 0.00 0.00 4.93
365 2151 2.775032 TAACAACCGCACGAGGCTCC 62.775 60.000 9.32 0.00 41.67 4.70
369 2155 0.233848 GTTGTAACAACCGCACGAGG 59.766 55.000 0.00 0.00 37.30 4.63
372 2158 1.719766 GCGTTGTAACAACCGCACG 60.720 57.895 13.35 8.92 45.12 5.34
377 2163 0.955905 ACATGGGCGTTGTAACAACC 59.044 50.000 0.00 1.98 0.00 3.77
378 2164 1.928595 GCACATGGGCGTTGTAACAAC 60.929 52.381 3.02 0.00 0.00 3.32
383 2169 0.595588 CAAAGCACATGGGCGTTGTA 59.404 50.000 32.35 0.00 44.60 2.41
401 2187 3.369052 CGCCTACAACCTCTTTATGACCA 60.369 47.826 0.00 0.00 0.00 4.02
402 2188 3.195661 CGCCTACAACCTCTTTATGACC 58.804 50.000 0.00 0.00 0.00 4.02
434 2266 1.218230 GAGGAAGATGATGCCGCGAC 61.218 60.000 8.23 0.00 0.00 5.19
437 2269 1.606737 GGTAGAGGAAGATGATGCCGC 60.607 57.143 0.00 0.00 0.00 6.53
438 2270 1.967066 AGGTAGAGGAAGATGATGCCG 59.033 52.381 0.00 0.00 0.00 5.69
439 2271 2.301583 GGAGGTAGAGGAAGATGATGCC 59.698 54.545 0.00 0.00 0.00 4.40
440 2272 3.238597 AGGAGGTAGAGGAAGATGATGC 58.761 50.000 0.00 0.00 0.00 3.91
441 2273 3.831911 GGAGGAGGTAGAGGAAGATGATG 59.168 52.174 0.00 0.00 0.00 3.07
442 2274 3.732204 AGGAGGAGGTAGAGGAAGATGAT 59.268 47.826 0.00 0.00 0.00 2.45
443 2275 3.135279 AGGAGGAGGTAGAGGAAGATGA 58.865 50.000 0.00 0.00 0.00 2.92
446 2278 2.438763 CGTAGGAGGAGGTAGAGGAAGA 59.561 54.545 0.00 0.00 0.00 2.87
448 2280 2.172293 GACGTAGGAGGAGGTAGAGGAA 59.828 54.545 0.00 0.00 0.00 3.36
449 2281 1.767681 GACGTAGGAGGAGGTAGAGGA 59.232 57.143 0.00 0.00 0.00 3.71
451 2283 1.138661 ACGACGTAGGAGGAGGTAGAG 59.861 57.143 0.00 0.00 0.00 2.43
454 2286 0.904649 TGACGACGTAGGAGGAGGTA 59.095 55.000 0.00 0.00 0.00 3.08
455 2287 0.392729 CTGACGACGTAGGAGGAGGT 60.393 60.000 0.00 0.00 0.00 3.85
457 2289 0.745128 AGCTGACGACGTAGGAGGAG 60.745 60.000 0.00 0.00 0.00 3.69
458 2290 0.743701 GAGCTGACGACGTAGGAGGA 60.744 60.000 0.00 0.00 0.00 3.71
526 2368 0.934496 TTCGCTTCCAACTTGTGACG 59.066 50.000 0.00 0.00 0.00 4.35
540 2382 2.809601 CGCTGCTACGGTTTCGCT 60.810 61.111 0.00 0.00 40.63 4.93
595 2437 0.391395 CTGCTCTCTCTTGCCACCAG 60.391 60.000 0.00 0.00 0.00 4.00
617 2459 1.215647 CCGTCCTAGCACGCTTCTT 59.784 57.895 0.00 0.00 38.52 2.52
660 2502 4.957954 CCATCTCATTTTTCCCCTTCATCA 59.042 41.667 0.00 0.00 0.00 3.07
675 2517 2.035632 GTCCTCTCGTTCCCATCTCAT 58.964 52.381 0.00 0.00 0.00 2.90
712 2554 6.463053 TTCCCTTTCTTCCTTTCCTTATCA 57.537 37.500 0.00 0.00 0.00 2.15
725 2567 0.106419 TGCCACCGTTTCCCTTTCTT 60.106 50.000 0.00 0.00 0.00 2.52
771 2626 0.806492 GGCCACCGATCTCGTCTTTC 60.806 60.000 0.00 0.00 37.74 2.62
787 2642 0.395724 AAGGATTTCCATGTCGGGCC 60.396 55.000 0.00 0.00 38.89 5.80
880 2735 9.662947 ACAACTAAGTTTACTTCACAACTAAGT 57.337 29.630 0.00 0.00 40.25 2.24
881 2736 9.916397 CACAACTAAGTTTACTTCACAACTAAG 57.084 33.333 0.00 0.00 37.40 2.18
882 2737 9.656040 TCACAACTAAGTTTACTTCACAACTAA 57.344 29.630 0.00 0.00 37.40 2.24
883 2738 9.656040 TTCACAACTAAGTTTACTTCACAACTA 57.344 29.630 0.00 0.00 37.40 2.24
884 2739 8.556213 TTCACAACTAAGTTTACTTCACAACT 57.444 30.769 0.00 0.00 37.40 3.16
885 2740 8.448615 ACTTCACAACTAAGTTTACTTCACAAC 58.551 33.333 0.00 0.00 33.39 3.32
886 2741 8.556213 ACTTCACAACTAAGTTTACTTCACAA 57.444 30.769 0.00 0.00 33.39 3.33
887 2742 9.656040 TTACTTCACAACTAAGTTTACTTCACA 57.344 29.630 0.00 0.00 38.18 3.58
897 2752 9.662947 ACAACTAAGTTTACTTCACAACTAAGT 57.337 29.630 0.00 0.00 40.25 2.24
898 2753 9.916397 CACAACTAAGTTTACTTCACAACTAAG 57.084 33.333 0.00 0.00 37.40 2.18
899 2754 9.656040 TCACAACTAAGTTTACTTCACAACTAA 57.344 29.630 0.00 0.00 37.40 2.24
900 2755 9.656040 TTCACAACTAAGTTTACTTCACAACTA 57.344 29.630 0.00 0.00 37.40 2.24
901 2756 8.556213 TTCACAACTAAGTTTACTTCACAACT 57.444 30.769 0.00 0.00 37.40 3.16
902 2757 8.448615 ACTTCACAACTAAGTTTACTTCACAAC 58.551 33.333 0.00 0.00 33.39 3.32
903 2758 8.556213 ACTTCACAACTAAGTTTACTTCACAA 57.444 30.769 0.00 0.00 33.39 3.33
904 2759 8.447833 CAACTTCACAACTAAGTTTACTTCACA 58.552 33.333 0.00 0.00 42.97 3.58
905 2760 8.662141 TCAACTTCACAACTAAGTTTACTTCAC 58.338 33.333 0.00 0.00 42.97 3.18
906 2761 8.780846 TCAACTTCACAACTAAGTTTACTTCA 57.219 30.769 0.00 0.00 42.97 3.02
907 2762 9.486857 GTTCAACTTCACAACTAAGTTTACTTC 57.513 33.333 0.00 0.00 42.97 3.01
908 2763 9.227777 AGTTCAACTTCACAACTAAGTTTACTT 57.772 29.630 0.29 0.29 42.97 2.24
909 2764 8.788325 AGTTCAACTTCACAACTAAGTTTACT 57.212 30.769 0.00 0.00 42.97 2.24
912 2767 9.227777 AGTAAGTTCAACTTCACAACTAAGTTT 57.772 29.630 5.92 0.00 42.97 2.66
913 2768 8.788325 AGTAAGTTCAACTTCACAACTAAGTT 57.212 30.769 5.92 0.00 45.64 2.66
914 2769 8.665685 CAAGTAAGTTCAACTTCACAACTAAGT 58.334 33.333 5.92 0.00 39.51 2.24
915 2770 8.665685 ACAAGTAAGTTCAACTTCACAACTAAG 58.334 33.333 5.92 4.30 39.51 2.18
916 2771 8.447833 CACAAGTAAGTTCAACTTCACAACTAA 58.552 33.333 5.92 0.00 39.51 2.24
917 2772 7.820386 TCACAAGTAAGTTCAACTTCACAACTA 59.180 33.333 5.92 0.00 39.51 2.24
918 2773 6.653320 TCACAAGTAAGTTCAACTTCACAACT 59.347 34.615 5.92 1.58 39.51 3.16
919 2774 6.837992 TCACAAGTAAGTTCAACTTCACAAC 58.162 36.000 5.92 0.00 39.51 3.32
920 2775 7.174253 ACTTCACAAGTAAGTTCAACTTCACAA 59.826 33.333 5.92 0.00 40.69 3.33
921 2776 6.653320 ACTTCACAAGTAAGTTCAACTTCACA 59.347 34.615 5.92 0.00 40.69 3.58
922 2777 7.073342 ACTTCACAAGTAAGTTCAACTTCAC 57.927 36.000 5.92 4.14 40.69 3.18
923 2778 8.780846 TTACTTCACAAGTAAGTTCAACTTCA 57.219 30.769 5.92 0.00 46.13 3.02
997 2852 1.170290 AGTACGCCCTTTTGTGGTGC 61.170 55.000 0.00 0.00 36.85 5.01
999 2854 0.763035 AGAGTACGCCCTTTTGTGGT 59.237 50.000 0.00 0.00 0.00 4.16
1000 2855 1.270625 TGAGAGTACGCCCTTTTGTGG 60.271 52.381 0.00 0.00 0.00 4.17
1002 2857 2.922740 TTGAGAGTACGCCCTTTTGT 57.077 45.000 0.00 0.00 0.00 2.83
1003 2858 4.935808 ACTATTTGAGAGTACGCCCTTTTG 59.064 41.667 0.00 0.00 0.00 2.44
1004 2859 5.161943 ACTATTTGAGAGTACGCCCTTTT 57.838 39.130 0.00 0.00 0.00 2.27
1007 2862 2.694109 GGACTATTTGAGAGTACGCCCT 59.306 50.000 0.00 0.00 0.00 5.19
1047 2902 3.717400 ACGATTAGACATCAGATGCGT 57.283 42.857 10.59 7.87 0.00 5.24
1079 2935 2.587889 GCAGGCGGCTAGGGTAAA 59.412 61.111 12.74 0.00 40.25 2.01
1117 2973 1.681229 AGTGGAGAGAGAGAGAGGGT 58.319 55.000 0.00 0.00 0.00 4.34
1119 2975 2.025416 TGGAAGTGGAGAGAGAGAGAGG 60.025 54.545 0.00 0.00 0.00 3.69
1268 3143 2.665000 CGAGAAGGGCCTTGCAGA 59.335 61.111 26.47 0.00 0.00 4.26
1757 3866 4.984161 AGGAGAAAACATGCAAATCAAACG 59.016 37.500 0.00 0.00 0.00 3.60
1792 3902 2.407340 ACAGACCTCTCCTTCCAACT 57.593 50.000 0.00 0.00 0.00 3.16
1810 3920 0.596577 GCCTCCCCTTGTCGAAAAAC 59.403 55.000 0.00 0.00 0.00 2.43
1884 3994 3.264897 CGGCAGTAGACGGCATGC 61.265 66.667 9.90 9.90 44.44 4.06
2140 4301 5.819270 AGACGAGACGTTTTAAAAGTAGC 57.181 39.130 0.00 0.00 41.37 3.58
2199 4647 6.418057 TTGTTATGCTTCAAGACCCAATTT 57.582 33.333 0.00 0.00 0.00 1.82
2775 5262 3.932710 TGCTAATAAGACTGAAACAGGCG 59.067 43.478 0.00 0.00 45.59 5.52
2967 5470 6.780457 ATTTGTCCCCAATGTAGATGAAAG 57.220 37.500 0.00 0.00 0.00 2.62
2984 5487 4.437390 CCACCGCTGAGTGAAATATTTGTC 60.437 45.833 5.17 0.53 40.34 3.18
2987 5490 3.686016 ACCACCGCTGAGTGAAATATTT 58.314 40.909 0.00 0.00 40.34 1.40
3012 5534 6.058827 CAAATTGATTGGGGAAACAACAAC 57.941 37.500 0.00 0.00 35.27 3.32
3038 5560 6.524734 AGGAAAAATCAAGATGAAACCAACC 58.475 36.000 0.00 0.00 0.00 3.77
3051 5714 5.011635 GGAGCCCAAACTAAGGAAAAATCAA 59.988 40.000 0.00 0.00 0.00 2.57
3065 5728 2.747855 CGGAGCAGGAGCCCAAAC 60.748 66.667 0.00 0.00 43.56 2.93
3081 5744 7.715265 AGATCAAAGTAACACAATATAGGCG 57.285 36.000 0.00 0.00 0.00 5.52
3109 5776 4.098501 GGACAAGCATATTTCTTGGGAAGG 59.901 45.833 15.21 0.00 43.77 3.46
3129 5796 8.940952 GGACAATCTATAAGCATATTTCTGGAC 58.059 37.037 0.00 0.00 0.00 4.02
3131 5798 8.105829 AGGGACAATCTATAAGCATATTTCTGG 58.894 37.037 0.00 0.00 0.00 3.86
3148 5815 9.841880 GAAAAACAGTTTCTTATAGGGACAATC 57.158 33.333 0.00 0.00 0.00 2.67
3149 5816 8.803235 GGAAAAACAGTTTCTTATAGGGACAAT 58.197 33.333 0.00 0.00 0.00 2.71
3150 5817 8.002459 AGGAAAAACAGTTTCTTATAGGGACAA 58.998 33.333 0.00 0.00 0.00 3.18
3152 5819 7.997773 AGGAAAAACAGTTTCTTATAGGGAC 57.002 36.000 0.00 0.00 0.00 4.46
3189 5903 6.842163 ACAGAAAATAAGCCAGAATTACGTG 58.158 36.000 0.00 0.00 0.00 4.49
3191 5905 6.316390 AGGACAGAAAATAAGCCAGAATTACG 59.684 38.462 0.00 0.00 0.00 3.18
3198 5912 4.583871 ACTCAGGACAGAAAATAAGCCAG 58.416 43.478 0.00 0.00 0.00 4.85
3222 5936 2.026822 AGTTCAGGGGCATTACAGACTG 60.027 50.000 0.00 0.00 0.00 3.51
3255 5969 1.421268 TGCTCAGAGTGTTTCCACCAT 59.579 47.619 0.00 0.00 42.88 3.55
3276 5990 3.441500 ACATTTCTCTTCCCAAGGTCC 57.558 47.619 0.00 0.00 0.00 4.46
3278 5992 4.811063 GCCTTACATTTCTCTTCCCAAGGT 60.811 45.833 0.00 0.00 34.95 3.50
3280 5994 3.375299 CGCCTTACATTTCTCTTCCCAAG 59.625 47.826 0.00 0.00 0.00 3.61
3282 5996 2.939640 GCGCCTTACATTTCTCTTCCCA 60.940 50.000 0.00 0.00 0.00 4.37
3320 6045 7.237173 GTGATTTCACACAAATAGTACTGCTC 58.763 38.462 5.39 0.00 45.75 4.26
3336 6061 2.921754 CGACTAGGAACGGTGATTTCAC 59.078 50.000 1.99 1.99 45.72 3.18
3438 6163 5.385509 TTCAGGCCAACTTAATTTGCTAC 57.614 39.130 5.01 0.00 0.00 3.58
3441 6171 2.995939 GCTTCAGGCCAACTTAATTTGC 59.004 45.455 5.01 0.00 34.27 3.68
3575 6422 9.081997 CAGCCTATTTCAAAAACGCAAATATAA 57.918 29.630 0.00 0.00 0.00 0.98
3597 6444 6.116126 AGAACCAATAAGATTAGTGACAGCC 58.884 40.000 1.81 0.00 30.85 4.85
3602 6449 8.826710 CGCAATTAGAACCAATAAGATTAGTGA 58.173 33.333 1.81 0.00 30.85 3.41
3610 6457 4.096382 ACCAGCGCAATTAGAACCAATAAG 59.904 41.667 11.47 0.00 0.00 1.73
3717 6878 7.529555 AGCCATCATAGAAATGGGAAGAATTA 58.470 34.615 4.44 0.00 43.32 1.40
3754 6915 2.954989 TGCTTGAGTACCAAATGCAACA 59.045 40.909 0.00 0.00 34.36 3.33
3755 6916 3.641437 TGCTTGAGTACCAAATGCAAC 57.359 42.857 0.00 0.00 34.36 4.17
3756 6917 4.870123 AATGCTTGAGTACCAAATGCAA 57.130 36.364 11.94 0.00 38.75 4.08
3757 6918 4.039004 ACAAATGCTTGAGTACCAAATGCA 59.961 37.500 10.94 10.94 39.32 3.96
3758 6919 4.559153 ACAAATGCTTGAGTACCAAATGC 58.441 39.130 0.00 0.00 36.33 3.56
3759 6920 7.537715 TGATACAAATGCTTGAGTACCAAATG 58.462 34.615 0.00 0.00 36.33 2.32
3760 6921 7.611467 TCTGATACAAATGCTTGAGTACCAAAT 59.389 33.333 0.00 0.00 36.33 2.32
3761 6922 6.939730 TCTGATACAAATGCTTGAGTACCAAA 59.060 34.615 0.00 0.00 36.33 3.28
3762 6923 6.472016 TCTGATACAAATGCTTGAGTACCAA 58.528 36.000 0.00 0.00 36.33 3.67
3763 6924 6.048732 TCTGATACAAATGCTTGAGTACCA 57.951 37.500 0.00 0.00 36.33 3.25
3764 6925 6.371548 TGTTCTGATACAAATGCTTGAGTACC 59.628 38.462 0.00 0.00 36.33 3.34
3765 6926 7.364522 TGTTCTGATACAAATGCTTGAGTAC 57.635 36.000 0.00 0.00 36.33 2.73
3766 6927 7.977789 TTGTTCTGATACAAATGCTTGAGTA 57.022 32.000 0.00 0.00 35.22 2.59
3767 6928 6.882610 TTGTTCTGATACAAATGCTTGAGT 57.117 33.333 0.00 0.00 35.22 3.41
3768 6929 8.644619 CAAATTGTTCTGATACAAATGCTTGAG 58.355 33.333 8.65 0.00 41.02 3.02
3769 6930 8.143193 ACAAATTGTTCTGATACAAATGCTTGA 58.857 29.630 0.00 0.00 41.02 3.02
3770 6931 8.301730 ACAAATTGTTCTGATACAAATGCTTG 57.698 30.769 0.00 10.77 41.02 4.01
3798 6959 9.162764 GTTGTTAACATGTAGGTAGATGACAAT 57.837 33.333 9.56 0.00 30.08 2.71
3799 6960 8.542497 GTTGTTAACATGTAGGTAGATGACAA 57.458 34.615 9.56 0.00 31.97 3.18


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

AutoCloner maintained by Alex Coulton.