Multiple sequence alignment - TraesCS5A01G410800

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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 TraesCS5A01G410800 chr5A 100.000 3239 0 0 1 3239 599770434 599767196 0.000000e+00 5982.0
1 TraesCS5A01G410800 chr5A 98.716 701 8 1 2539 3239 574346860 574346161 0.000000e+00 1243.0
2 TraesCS5A01G410800 chr5B 89.335 1744 117 36 733 2443 588926235 588924528 0.000000e+00 2126.0
3 TraesCS5A01G410800 chr5B 95.607 387 17 0 2853 3239 558343254 558343640 3.550000e-174 621.0
4 TraesCS5A01G410800 chr5B 84.418 507 63 12 220 713 588926791 588926288 4.860000e-133 484.0
5 TraesCS5A01G410800 chr5B 97.701 261 6 0 2539 2799 558342995 558343255 1.770000e-122 449.0
6 TraesCS5A01G410800 chr5B 100.000 35 0 0 2508 2542 588924414 588924380 7.500000e-07 65.8
7 TraesCS5A01G410800 chr5D 97.004 701 21 0 2539 3239 456608812 456609512 0.000000e+00 1179.0
8 TraesCS5A01G410800 chr5D 91.238 719 42 11 1792 2506 480560971 480560270 0.000000e+00 959.0
9 TraesCS5A01G410800 chr5D 93.094 362 19 1 1133 1494 480595452 480595097 2.860000e-145 525.0
10 TraesCS5A01G410800 chr5D 91.586 309 19 4 1490 1798 480575758 480575457 1.390000e-113 420.0
11 TraesCS5A01G410800 chr5D 85.763 295 14 8 720 1000 480595738 480595458 1.470000e-73 287.0


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 TraesCS5A01G410800 chr5A 599767196 599770434 3238 True 5982.000000 5982 100.0000 1 3239 1 chr5A.!!$R2 3238
1 TraesCS5A01G410800 chr5A 574346161 574346860 699 True 1243.000000 1243 98.7160 2539 3239 1 chr5A.!!$R1 700
2 TraesCS5A01G410800 chr5B 588924380 588926791 2411 True 891.933333 2126 91.2510 220 2542 3 chr5B.!!$R1 2322
3 TraesCS5A01G410800 chr5B 558342995 558343640 645 False 535.000000 621 96.6540 2539 3239 2 chr5B.!!$F1 700
4 TraesCS5A01G410800 chr5D 456608812 456609512 700 False 1179.000000 1179 97.0040 2539 3239 1 chr5D.!!$F1 700
5 TraesCS5A01G410800 chr5D 480560270 480560971 701 True 959.000000 959 91.2380 1792 2506 1 chr5D.!!$R1 714
6 TraesCS5A01G410800 chr5D 480595097 480595738 641 True 406.000000 525 89.4285 720 1494 2 chr5D.!!$R3 774

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
130 131 0.038166 TTTCCATCGAGGCAGGCTTT 59.962 50.0 0.0 0.0 37.29 3.51 F
1884 1972 0.103208 CACCTATGCTGGTCGTCTCC 59.897 60.0 0.0 0.0 38.45 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2143 0.041839 CAACTGCGCTCACAGACAAC 60.042 55.00 9.73 0.0 40.25 3.32 R
3129 3274 5.644902 TCACAATGTTACGCAATATACGG 57.355 39.13 3.45 0.0 34.00 4.02 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
27 28 9.689501 AATAGTAAAATCGACCAAAATAGGGAA 57.310 29.630 0.00 0.00 0.00 3.97
28 29 7.625828 AGTAAAATCGACCAAAATAGGGAAG 57.374 36.000 0.00 0.00 0.00 3.46
29 30 7.399634 AGTAAAATCGACCAAAATAGGGAAGA 58.600 34.615 0.00 0.00 0.00 2.87
30 31 6.510879 AAAATCGACCAAAATAGGGAAGAC 57.489 37.500 0.00 0.00 0.00 3.01
31 32 3.241067 TCGACCAAAATAGGGAAGACG 57.759 47.619 0.00 0.00 0.00 4.18
32 33 2.827322 TCGACCAAAATAGGGAAGACGA 59.173 45.455 0.00 0.00 0.00 4.20
33 34 3.449737 TCGACCAAAATAGGGAAGACGAT 59.550 43.478 0.00 0.00 0.00 3.73
34 35 4.081309 TCGACCAAAATAGGGAAGACGATT 60.081 41.667 0.00 0.00 0.00 3.34
35 36 4.034048 CGACCAAAATAGGGAAGACGATTG 59.966 45.833 0.00 0.00 0.00 2.67
36 37 5.174037 ACCAAAATAGGGAAGACGATTGA 57.826 39.130 0.00 0.00 0.00 2.57
37 38 5.755849 ACCAAAATAGGGAAGACGATTGAT 58.244 37.500 0.00 0.00 0.00 2.57
38 39 6.895782 ACCAAAATAGGGAAGACGATTGATA 58.104 36.000 0.00 0.00 0.00 2.15
39 40 7.343357 ACCAAAATAGGGAAGACGATTGATAA 58.657 34.615 0.00 0.00 0.00 1.75
40 41 7.832187 ACCAAAATAGGGAAGACGATTGATAAA 59.168 33.333 0.00 0.00 0.00 1.40
41 42 8.129211 CCAAAATAGGGAAGACGATTGATAAAC 58.871 37.037 0.00 0.00 0.00 2.01
42 43 7.803279 AAATAGGGAAGACGATTGATAAACC 57.197 36.000 0.00 0.00 0.00 3.27
43 44 3.793559 AGGGAAGACGATTGATAAACCG 58.206 45.455 0.00 0.00 0.00 4.44
44 45 3.449737 AGGGAAGACGATTGATAAACCGA 59.550 43.478 0.00 0.00 0.00 4.69
45 46 3.554731 GGGAAGACGATTGATAAACCGAC 59.445 47.826 0.00 0.00 0.00 4.79
46 47 3.554731 GGAAGACGATTGATAAACCGACC 59.445 47.826 0.00 0.00 0.00 4.79
47 48 4.430908 GAAGACGATTGATAAACCGACCT 58.569 43.478 0.00 0.00 0.00 3.85
48 49 5.450965 GGAAGACGATTGATAAACCGACCTA 60.451 44.000 0.00 0.00 0.00 3.08
49 50 5.184340 AGACGATTGATAAACCGACCTAG 57.816 43.478 0.00 0.00 0.00 3.02
50 51 4.885907 AGACGATTGATAAACCGACCTAGA 59.114 41.667 0.00 0.00 0.00 2.43
51 52 5.359009 AGACGATTGATAAACCGACCTAGAA 59.641 40.000 0.00 0.00 0.00 2.10
52 53 5.969423 ACGATTGATAAACCGACCTAGAAA 58.031 37.500 0.00 0.00 0.00 2.52
53 54 6.400568 ACGATTGATAAACCGACCTAGAAAA 58.599 36.000 0.00 0.00 0.00 2.29
54 55 6.875195 ACGATTGATAAACCGACCTAGAAAAA 59.125 34.615 0.00 0.00 0.00 1.94
80 81 2.047655 CGCAAGTAGCCGTGGGAA 60.048 61.111 0.00 0.00 41.38 3.97
81 82 2.100631 CGCAAGTAGCCGTGGGAAG 61.101 63.158 0.00 0.00 41.38 3.46
82 83 2.399356 GCAAGTAGCCGTGGGAAGC 61.399 63.158 0.00 0.00 37.23 3.86
83 84 1.745489 CAAGTAGCCGTGGGAAGCC 60.745 63.158 0.00 0.00 0.00 4.35
84 85 2.221299 AAGTAGCCGTGGGAAGCCA 61.221 57.895 0.00 0.00 0.00 4.75
85 86 2.125106 GTAGCCGTGGGAAGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
86 87 4.096003 TAGCCGTGGGAAGCCAGC 62.096 66.667 0.00 0.00 0.00 4.85
89 90 4.641645 CCGTGGGAAGCCAGCACA 62.642 66.667 0.00 0.00 0.00 4.57
90 91 2.594303 CGTGGGAAGCCAGCACAA 60.594 61.111 0.00 0.00 0.00 3.33
91 92 2.192861 CGTGGGAAGCCAGCACAAA 61.193 57.895 0.00 0.00 0.00 2.83
92 93 1.733402 CGTGGGAAGCCAGCACAAAA 61.733 55.000 0.00 0.00 0.00 2.44
93 94 0.249447 GTGGGAAGCCAGCACAAAAC 60.249 55.000 0.00 0.00 0.00 2.43
94 95 0.685785 TGGGAAGCCAGCACAAAACA 60.686 50.000 0.00 0.00 0.00 2.83
95 96 0.463620 GGGAAGCCAGCACAAAACAA 59.536 50.000 0.00 0.00 0.00 2.83
96 97 1.134551 GGGAAGCCAGCACAAAACAAA 60.135 47.619 0.00 0.00 0.00 2.83
97 98 1.933181 GGAAGCCAGCACAAAACAAAC 59.067 47.619 0.00 0.00 0.00 2.93
98 99 1.587946 GAAGCCAGCACAAAACAAACG 59.412 47.619 0.00 0.00 0.00 3.60
99 100 0.814457 AGCCAGCACAAAACAAACGA 59.186 45.000 0.00 0.00 0.00 3.85
100 101 1.408702 AGCCAGCACAAAACAAACGAT 59.591 42.857 0.00 0.00 0.00 3.73
101 102 1.522258 GCCAGCACAAAACAAACGATG 59.478 47.619 0.00 0.00 0.00 3.84
102 103 1.522258 CCAGCACAAAACAAACGATGC 59.478 47.619 0.00 0.00 0.00 3.91
103 104 2.191802 CAGCACAAAACAAACGATGCA 58.808 42.857 0.00 0.00 35.51 3.96
104 105 2.216940 CAGCACAAAACAAACGATGCAG 59.783 45.455 0.00 0.00 35.51 4.41
105 106 1.522258 GCACAAAACAAACGATGCAGG 59.478 47.619 0.00 0.00 33.27 4.85
106 107 2.126467 CACAAAACAAACGATGCAGGG 58.874 47.619 0.00 0.00 0.00 4.45
107 108 1.068434 ACAAAACAAACGATGCAGGGG 59.932 47.619 0.00 0.00 0.00 4.79
108 109 0.678950 AAAACAAACGATGCAGGGGG 59.321 50.000 0.00 0.00 0.00 5.40
109 110 1.815817 AAACAAACGATGCAGGGGGC 61.816 55.000 0.00 0.00 45.13 5.80
110 111 3.451894 CAAACGATGCAGGGGGCC 61.452 66.667 0.00 0.00 43.89 5.80
111 112 3.661648 AAACGATGCAGGGGGCCT 61.662 61.111 0.84 0.00 43.89 5.19
112 113 3.224007 AAACGATGCAGGGGGCCTT 62.224 57.895 0.84 0.00 43.89 4.35
113 114 2.730129 AAACGATGCAGGGGGCCTTT 62.730 55.000 0.84 0.00 43.89 3.11
114 115 2.830370 CGATGCAGGGGGCCTTTC 60.830 66.667 0.84 0.00 43.89 2.62
115 116 2.442830 GATGCAGGGGGCCTTTCC 60.443 66.667 0.84 2.02 43.89 3.13
116 117 3.275271 ATGCAGGGGGCCTTTCCA 61.275 61.111 0.84 0.00 43.89 3.53
117 118 2.594365 GATGCAGGGGGCCTTTCCAT 62.594 60.000 0.84 1.52 43.89 3.41
118 119 2.442830 GCAGGGGGCCTTTCCATC 60.443 66.667 0.84 0.00 36.11 3.51
119 120 2.124151 CAGGGGGCCTTTCCATCG 60.124 66.667 0.84 0.00 36.21 3.84
120 121 2.286121 AGGGGGCCTTTCCATCGA 60.286 61.111 0.84 0.00 36.21 3.59
121 122 2.193248 GGGGGCCTTTCCATCGAG 59.807 66.667 0.84 0.00 36.21 4.04
122 123 2.193248 GGGGCCTTTCCATCGAGG 59.807 66.667 0.84 0.00 36.21 4.63
126 127 4.547859 CCTTTCCATCGAGGCAGG 57.452 61.111 0.00 0.00 37.29 4.85
127 128 1.821332 CCTTTCCATCGAGGCAGGC 60.821 63.158 0.00 0.00 37.29 4.85
128 129 1.222936 CTTTCCATCGAGGCAGGCT 59.777 57.895 0.00 0.00 37.29 4.58
129 130 0.393537 CTTTCCATCGAGGCAGGCTT 60.394 55.000 0.00 0.00 37.29 4.35
130 131 0.038166 TTTCCATCGAGGCAGGCTTT 59.962 50.000 0.00 0.00 37.29 3.51
131 132 0.677731 TTCCATCGAGGCAGGCTTTG 60.678 55.000 0.00 0.00 37.29 2.77
132 133 1.078214 CCATCGAGGCAGGCTTTGA 60.078 57.895 0.00 0.00 0.00 2.69
133 134 1.372087 CCATCGAGGCAGGCTTTGAC 61.372 60.000 0.00 0.00 33.75 3.18
134 135 1.078143 ATCGAGGCAGGCTTTGACC 60.078 57.895 0.00 0.00 34.24 4.02
135 136 2.543067 ATCGAGGCAGGCTTTGACCC 62.543 60.000 0.00 0.00 34.24 4.46
136 137 2.361737 GAGGCAGGCTTTGACCCC 60.362 66.667 0.00 0.00 34.24 4.95
137 138 4.351054 AGGCAGGCTTTGACCCCG 62.351 66.667 0.00 0.00 34.24 5.73
164 165 4.485834 CGCGACGGAACCGGATCA 62.486 66.667 9.46 0.00 44.69 2.92
165 166 2.106332 GCGACGGAACCGGATCAT 59.894 61.111 9.46 0.00 44.69 2.45
166 167 1.949631 GCGACGGAACCGGATCATC 60.950 63.158 9.46 6.82 44.69 2.92
167 168 1.657487 CGACGGAACCGGATCATCG 60.657 63.158 18.63 18.63 44.69 3.84
175 176 4.855105 CGGATCATCGGAGGCAAA 57.145 55.556 0.00 0.00 0.00 3.68
176 177 3.312404 CGGATCATCGGAGGCAAAT 57.688 52.632 0.00 0.00 0.00 2.32
177 178 2.455674 CGGATCATCGGAGGCAAATA 57.544 50.000 0.00 0.00 0.00 1.40
178 179 2.069273 CGGATCATCGGAGGCAAATAC 58.931 52.381 0.00 0.00 0.00 1.89
179 180 2.069273 GGATCATCGGAGGCAAATACG 58.931 52.381 0.00 0.00 0.00 3.06
180 181 1.461127 GATCATCGGAGGCAAATACGC 59.539 52.381 0.00 0.00 0.00 4.42
196 197 2.048316 GCCAACATGCGGGTTTGG 60.048 61.111 7.50 7.50 0.00 3.28
197 198 2.048316 CCAACATGCGGGTTTGGC 60.048 61.111 0.00 0.00 0.00 4.52
198 199 2.048316 CAACATGCGGGTTTGGCC 60.048 61.111 0.00 0.00 0.00 5.36
199 200 2.203625 AACATGCGGGTTTGGCCT 60.204 55.556 3.32 0.00 37.43 5.19
200 201 2.275380 AACATGCGGGTTTGGCCTC 61.275 57.895 3.32 0.00 37.43 4.70
201 202 3.451894 CATGCGGGTTTGGCCTCC 61.452 66.667 3.32 3.79 37.43 4.30
202 203 4.759205 ATGCGGGTTTGGCCTCCC 62.759 66.667 17.39 17.39 40.26 4.30
204 205 4.678743 GCGGGTTTGGCCTCCCTT 62.679 66.667 22.21 0.00 41.40 3.95
205 206 2.117423 CGGGTTTGGCCTCCCTTT 59.883 61.111 22.21 0.00 41.40 3.11
206 207 1.977009 CGGGTTTGGCCTCCCTTTC 60.977 63.158 22.21 3.90 41.40 2.62
207 208 1.977009 GGGTTTGGCCTCCCTTTCG 60.977 63.158 19.23 0.00 40.48 3.46
208 209 2.636412 GGTTTGGCCTCCCTTTCGC 61.636 63.158 3.32 0.00 0.00 4.70
209 210 2.671619 TTTGGCCTCCCTTTCGCG 60.672 61.111 3.32 0.00 0.00 5.87
210 211 3.485346 TTTGGCCTCCCTTTCGCGT 62.485 57.895 5.77 0.00 0.00 6.01
211 212 4.697756 TGGCCTCCCTTTCGCGTG 62.698 66.667 5.77 0.00 0.00 5.34
212 213 4.699522 GGCCTCCCTTTCGCGTGT 62.700 66.667 5.77 0.00 0.00 4.49
213 214 3.423154 GCCTCCCTTTCGCGTGTG 61.423 66.667 5.77 0.00 0.00 3.82
214 215 2.742372 CCTCCCTTTCGCGTGTGG 60.742 66.667 5.77 6.52 0.00 4.17
215 216 2.742372 CTCCCTTTCGCGTGTGGG 60.742 66.667 20.89 20.89 40.95 4.61
238 239 2.388232 CGCGAGCACTACCAAACCC 61.388 63.158 0.00 0.00 0.00 4.11
240 241 2.388232 CGAGCACTACCAAACCCGC 61.388 63.158 0.00 0.00 0.00 6.13
243 244 3.428282 CACTACCAAACCCGCCGC 61.428 66.667 0.00 0.00 0.00 6.53
257 258 2.440796 CCGCATGATGGTGGCCTT 60.441 61.111 3.32 0.00 0.00 4.35
278 279 2.740055 CGAGCCAGCAGTCCACAC 60.740 66.667 0.00 0.00 0.00 3.82
279 280 2.427320 GAGCCAGCAGTCCACACA 59.573 61.111 0.00 0.00 0.00 3.72
353 354 4.479993 CTTGGAGAGCCCCCGCAG 62.480 72.222 0.00 0.00 37.52 5.18
365 366 4.641645 CCGCAGCACTCCACCCAA 62.642 66.667 0.00 0.00 0.00 4.12
369 370 0.249447 GCAGCACTCCACCCAAAAAC 60.249 55.000 0.00 0.00 0.00 2.43
375 376 0.309612 CTCCACCCAAAAACGAACGG 59.690 55.000 0.00 0.00 0.00 4.44
376 377 0.394080 TCCACCCAAAAACGAACGGT 60.394 50.000 0.00 0.00 0.00 4.83
378 379 0.452585 CACCCAAAAACGAACGGTGT 59.547 50.000 0.00 0.00 39.33 4.16
379 380 0.734309 ACCCAAAAACGAACGGTGTC 59.266 50.000 0.00 0.00 0.00 3.67
384 385 0.877213 AAAACGAACGGTGTCGAGGG 60.877 55.000 15.87 0.00 43.86 4.30
385 386 1.737355 AAACGAACGGTGTCGAGGGA 61.737 55.000 15.87 0.00 43.86 4.20
402 403 1.936547 GGGAACTCTCGCATGCTTTAG 59.063 52.381 17.13 11.84 34.68 1.85
403 404 2.418746 GGGAACTCTCGCATGCTTTAGA 60.419 50.000 17.13 14.08 34.68 2.10
404 405 2.863137 GGAACTCTCGCATGCTTTAGAG 59.137 50.000 26.91 26.91 41.03 2.43
413 414 7.489160 TCTCGCATGCTTTAGAGAAGTAATAA 58.511 34.615 17.13 0.00 36.88 1.40
417 418 7.222805 CGCATGCTTTAGAGAAGTAATAACTCA 59.777 37.037 17.13 0.00 33.75 3.41
418 419 9.050601 GCATGCTTTAGAGAAGTAATAACTCAT 57.949 33.333 11.37 0.00 33.75 2.90
445 450 7.730364 TCACATGAGAAAAAGGTTAAGTCTC 57.270 36.000 0.00 0.00 36.17 3.36
446 451 7.509546 TCACATGAGAAAAAGGTTAAGTCTCT 58.490 34.615 0.00 0.00 36.50 3.10
455 460 5.888982 AAGGTTAAGTCTCTCTTGTTCCA 57.111 39.130 0.00 0.00 37.56 3.53
474 479 7.874940 TGTTCCATACAATTCTCAAAAGACAG 58.125 34.615 0.00 0.00 32.64 3.51
476 481 8.567948 GTTCCATACAATTCTCAAAAGACAGAA 58.432 33.333 0.00 0.00 33.18 3.02
487 492 8.225603 TCTCAAAAGACAGAAATAGCAAAACT 57.774 30.769 0.00 0.00 0.00 2.66
488 493 9.337396 TCTCAAAAGACAGAAATAGCAAAACTA 57.663 29.630 0.00 0.00 34.64 2.24
493 498 6.534634 AGACAGAAATAGCAAAACTACAGGT 58.465 36.000 0.00 0.00 32.32 4.00
499 504 9.740710 AGAAATAGCAAAACTACAGGTTTAGAT 57.259 29.630 0.00 0.00 46.18 1.98
522 527 6.605471 TTGGCATATCTCCTACGTGAATAT 57.395 37.500 0.00 0.00 0.00 1.28
534 543 9.454585 CTCCTACGTGAATATAAAATTACGTGA 57.545 33.333 10.06 0.00 43.50 4.35
548 557 7.561237 AAATTACGTGAATTTGGATCAAACG 57.439 32.000 0.00 0.00 44.44 3.60
554 563 2.629639 ATTTGGATCAAACGGCGTTC 57.370 45.000 26.96 13.50 36.13 3.95
556 565 1.570347 TTGGATCAAACGGCGTTCGG 61.570 55.000 26.96 20.42 44.45 4.30
586 595 2.230992 AGCAACAAGTTTGAGTGCACAA 59.769 40.909 21.04 3.51 41.66 3.33
591 600 6.018832 GCAACAAGTTTGAGTGCACAATAAAT 60.019 34.615 21.04 5.81 40.17 1.40
592 601 7.465781 GCAACAAGTTTGAGTGCACAATAAATT 60.466 33.333 21.04 11.56 40.17 1.82
600 609 7.288810 TGAGTGCACAATAAATTTTTCCTCT 57.711 32.000 21.04 0.00 0.00 3.69
601 610 7.147312 TGAGTGCACAATAAATTTTTCCTCTG 58.853 34.615 21.04 0.00 0.00 3.35
602 611 5.928264 AGTGCACAATAAATTTTTCCTCTGC 59.072 36.000 21.04 0.00 0.00 4.26
613 622 6.726490 ATTTTTCCTCTGCTGCATATGAAT 57.274 33.333 6.97 0.00 0.00 2.57
614 623 6.534475 TTTTTCCTCTGCTGCATATGAATT 57.466 33.333 6.97 0.00 0.00 2.17
626 635 8.530311 TGCTGCATATGAATTTCTTAGGAAAAA 58.470 29.630 6.97 0.00 43.51 1.94
652 661 4.941263 CCTAACGATTCCAATCCTGTGAAA 59.059 41.667 0.00 0.00 31.68 2.69
682 691 6.369615 CAGCCAATGTGGGAATTTTTCTTAAG 59.630 38.462 0.00 0.00 38.19 1.85
716 729 6.406692 TCCCTAGAAATCCTATGAAACTCG 57.593 41.667 0.00 0.00 0.00 4.18
718 731 7.064866 TCCCTAGAAATCCTATGAAACTCGTA 58.935 38.462 0.00 0.00 0.00 3.43
721 734 7.329717 CCTAGAAATCCTATGAAACTCGTATGC 59.670 40.741 0.00 0.00 0.00 3.14
785 831 5.296813 CTTCTTCAAGGAAAACATACCCG 57.703 43.478 0.00 0.00 0.00 5.28
790 836 3.054948 TCAAGGAAAACATACCCGGGTAG 60.055 47.826 35.39 27.65 33.77 3.18
805 851 1.347221 GTAGACGCGGCGGATTTTG 59.653 57.895 27.37 0.00 0.00 2.44
824 879 2.257676 GCCGTCCGATCCGATACC 59.742 66.667 0.00 0.00 0.00 2.73
848 903 6.373216 CCGATACATCTCCCAACAGTTTTTAA 59.627 38.462 0.00 0.00 0.00 1.52
923 990 1.216710 CTGTGGACTCGAGCTTCCC 59.783 63.158 13.61 9.43 0.00 3.97
978 1045 4.452733 GCCCCGACGACAAGGAGG 62.453 72.222 0.00 0.00 0.00 4.30
981 1048 4.796231 CCGACGACAAGGAGGCCG 62.796 72.222 0.00 0.00 0.00 6.13
1017 1084 3.079478 AGCGATCCTGCTGCCTGA 61.079 61.111 0.00 0.00 45.28 3.86
1018 1085 2.894387 GCGATCCTGCTGCCTGAC 60.894 66.667 0.00 0.00 0.00 3.51
1019 1086 2.584418 CGATCCTGCTGCCTGACG 60.584 66.667 0.00 0.00 0.00 4.35
1021 1088 1.520342 GATCCTGCTGCCTGACGAC 60.520 63.158 0.00 0.00 0.00 4.34
1022 1089 3.362399 ATCCTGCTGCCTGACGACG 62.362 63.158 0.00 0.00 0.00 5.12
1023 1090 4.363990 CCTGCTGCCTGACGACGT 62.364 66.667 0.00 0.00 0.00 4.34
1024 1091 3.108289 CTGCTGCCTGACGACGTG 61.108 66.667 4.58 0.00 0.00 4.49
1027 1094 2.807045 CTGCCTGACGACGTGCTC 60.807 66.667 4.58 0.00 0.00 4.26
1028 1095 4.357947 TGCCTGACGACGTGCTCC 62.358 66.667 4.58 0.00 0.00 4.70
1029 1096 4.057428 GCCTGACGACGTGCTCCT 62.057 66.667 4.58 0.00 0.00 3.69
1030 1097 2.179517 CCTGACGACGTGCTCCTC 59.820 66.667 4.58 0.00 0.00 3.71
1031 1098 2.179517 CTGACGACGTGCTCCTCC 59.820 66.667 4.58 0.00 0.00 4.30
1032 1099 2.282251 TGACGACGTGCTCCTCCT 60.282 61.111 4.58 0.00 0.00 3.69
1033 1100 1.002990 TGACGACGTGCTCCTCCTA 60.003 57.895 4.58 0.00 0.00 2.94
1034 1101 0.607217 TGACGACGTGCTCCTCCTAA 60.607 55.000 4.58 0.00 0.00 2.69
1035 1102 0.524862 GACGACGTGCTCCTCCTAAA 59.475 55.000 4.58 0.00 0.00 1.85
1036 1103 0.526662 ACGACGTGCTCCTCCTAAAG 59.473 55.000 0.00 0.00 0.00 1.85
1051 1118 2.493278 CCTAAAGCCATGTCAACCAAGG 59.507 50.000 0.00 0.00 34.95 3.61
1057 1124 1.304381 ATGTCAACCAAGGGCGCAT 60.304 52.632 10.83 0.00 0.00 4.73
1060 1127 3.682885 CAACCAAGGGCGCATGCA 61.683 61.111 19.57 0.00 45.35 3.96
1080 1168 1.678627 AGGGATGAGACGATCGTCAAG 59.321 52.381 40.51 7.01 46.76 3.02
1087 1175 2.949678 CGATCGTCAAGGCGACCG 60.950 66.667 7.03 0.00 41.62 4.79
1113 1201 0.747852 GACTCCCGTTGGATCTCCTC 59.252 60.000 0.00 0.00 40.80 3.71
1116 1204 1.035932 TCCCGTTGGATCTCCTCGTC 61.036 60.000 11.21 0.00 35.03 4.20
1254 1342 4.265056 AACGGCGGCTTCAACCCT 62.265 61.111 13.24 0.00 0.00 4.34
1590 1678 1.777030 CGGACGAGATCCTCTGGACG 61.777 65.000 0.00 0.00 46.69 4.79
1664 1752 4.676951 CCCGCACCACCCACCATT 62.677 66.667 0.00 0.00 0.00 3.16
1675 1763 2.234168 CACCCACCATTCAAATCATGCA 59.766 45.455 0.00 0.00 0.00 3.96
1730 1818 1.001641 ACTGGTACGTACGCCTCCT 60.002 57.895 16.72 0.00 0.00 3.69
1737 1825 2.521224 GTACGCCTCCTCCCGGAT 60.521 66.667 0.73 0.00 39.01 4.18
1742 1830 2.516405 CCTCCTCCCGGATCTCGA 59.484 66.667 0.73 0.00 42.43 4.04
1743 1831 1.075836 CCTCCTCCCGGATCTCGAT 59.924 63.158 0.73 0.00 42.43 3.59
1744 1832 0.963355 CCTCCTCCCGGATCTCGATC 60.963 65.000 0.73 0.00 42.43 3.69
1745 1833 0.250945 CTCCTCCCGGATCTCGATCA 60.251 60.000 0.73 0.00 42.43 2.92
1746 1834 0.537600 TCCTCCCGGATCTCGATCAC 60.538 60.000 0.73 0.00 42.43 3.06
1747 1835 1.528292 CCTCCCGGATCTCGATCACC 61.528 65.000 0.73 0.00 42.43 4.02
1806 1894 2.111878 GGGGCGGTGAGGATGATG 59.888 66.667 0.00 0.00 0.00 3.07
1855 1943 1.519719 GAGCCACCTGCCACTAGAG 59.480 63.158 0.00 0.00 42.71 2.43
1858 1946 3.920059 AGCCACCTGCCACTAGAGTGA 62.920 57.143 11.31 0.00 45.30 3.41
1884 1972 0.103208 CACCTATGCTGGTCGTCTCC 59.897 60.000 0.00 0.00 38.45 3.71
2029 2117 1.376683 CCGGTTCGCTTCCATGGAA 60.377 57.895 25.53 25.53 0.00 3.53
2061 2149 2.591715 GGCACGCTGGTGTTGTCT 60.592 61.111 0.00 0.00 46.13 3.41
2136 2224 2.278596 CGCCACGGGAGACATACG 60.279 66.667 0.00 0.00 0.00 3.06
2144 2232 2.025727 GAGACATACGTCCCCGCG 59.974 66.667 0.00 0.00 43.73 6.46
2239 2327 6.012658 CTTCTTAAGCCAACTGCAATACAA 57.987 37.500 0.00 0.00 44.83 2.41
2247 2335 3.191371 CCAACTGCAATACAAGGAGGAAC 59.809 47.826 0.00 0.00 0.00 3.62
2249 2337 3.679389 ACTGCAATACAAGGAGGAACAG 58.321 45.455 0.00 0.00 0.00 3.16
2250 2338 3.012518 CTGCAATACAAGGAGGAACAGG 58.987 50.000 0.00 0.00 0.00 4.00
2251 2339 2.642311 TGCAATACAAGGAGGAACAGGA 59.358 45.455 0.00 0.00 0.00 3.86
2252 2340 3.073798 TGCAATACAAGGAGGAACAGGAA 59.926 43.478 0.00 0.00 0.00 3.36
2253 2341 4.263905 TGCAATACAAGGAGGAACAGGAAT 60.264 41.667 0.00 0.00 0.00 3.01
2254 2342 5.045213 TGCAATACAAGGAGGAACAGGAATA 60.045 40.000 0.00 0.00 0.00 1.75
2259 2347 6.636454 ACAAGGAGGAACAGGAATACAATA 57.364 37.500 0.00 0.00 0.00 1.90
2260 2348 7.213178 ACAAGGAGGAACAGGAATACAATAT 57.787 36.000 0.00 0.00 0.00 1.28
2263 2351 7.072263 AGGAGGAACAGGAATACAATATCAG 57.928 40.000 0.00 0.00 0.00 2.90
2288 2379 3.165890 CACATTTTGTACGCTCAGCATG 58.834 45.455 0.00 0.00 37.54 4.06
2300 2391 0.321919 TCAGCATGAGAGGCACCAAC 60.322 55.000 0.00 0.00 42.56 3.77
2312 2403 2.026262 AGGCACCAACGAATATGTTCCT 60.026 45.455 0.00 0.00 0.00 3.36
2339 2431 1.803334 TGGTGCGTGGAATTAGTGTC 58.197 50.000 0.00 0.00 0.00 3.67
2444 2563 7.233962 ACATATATCCAAAATGCATCCATGTGT 59.766 33.333 0.00 0.00 0.00 3.72
2445 2564 3.596310 TCCAAAATGCATCCATGTGTG 57.404 42.857 0.00 0.00 0.00 3.82
2446 2565 2.898612 TCCAAAATGCATCCATGTGTGT 59.101 40.909 0.00 0.00 0.00 3.72
2447 2566 3.056678 TCCAAAATGCATCCATGTGTGTC 60.057 43.478 0.00 0.00 0.00 3.67
2452 2571 1.202794 TGCATCCATGTGTGTCTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
2456 2575 1.159713 CCATGTGTGTCTGTGTGCGT 61.160 55.000 0.00 0.00 0.00 5.24
2476 2600 2.849473 GTGCGTGTGTGTTTTTGGTAAG 59.151 45.455 0.00 0.00 0.00 2.34
2494 2619 6.774673 TGGTAAGTTTCAATGACCATGTCTA 58.225 36.000 0.00 0.00 35.26 2.59
2506 2631 0.947244 CATGTCTAAATCTGCCGGCC 59.053 55.000 26.77 6.44 0.00 6.13
3129 3274 8.806146 ACAATATGATGAAATTAATAGGGTGCC 58.194 33.333 0.00 0.00 0.00 5.01
3173 3318 7.147655 TGTGAACAAAACAATCCCAAATTCCTA 60.148 33.333 0.00 0.00 0.00 2.94
3198 3344 4.084011 TGGTGAAGTGACACATTCATCA 57.916 40.909 20.46 20.46 42.67 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.689501 TTCCCTATTTTGGTCGATTTTACTATT 57.310 29.630 0.00 0.00 0.00 1.73
2 3 9.338622 CTTCCCTATTTTGGTCGATTTTACTAT 57.661 33.333 0.00 0.00 0.00 2.12
3 4 8.542080 TCTTCCCTATTTTGGTCGATTTTACTA 58.458 33.333 0.00 0.00 0.00 1.82
5 6 7.470079 GTCTTCCCTATTTTGGTCGATTTTAC 58.530 38.462 0.00 0.00 0.00 2.01
6 7 6.314400 CGTCTTCCCTATTTTGGTCGATTTTA 59.686 38.462 0.00 0.00 0.00 1.52
7 8 5.123344 CGTCTTCCCTATTTTGGTCGATTTT 59.877 40.000 0.00 0.00 0.00 1.82
8 9 4.634443 CGTCTTCCCTATTTTGGTCGATTT 59.366 41.667 0.00 0.00 0.00 2.17
9 10 4.081309 TCGTCTTCCCTATTTTGGTCGATT 60.081 41.667 0.00 0.00 0.00 3.34
10 11 3.449737 TCGTCTTCCCTATTTTGGTCGAT 59.550 43.478 0.00 0.00 0.00 3.59
11 12 2.827322 TCGTCTTCCCTATTTTGGTCGA 59.173 45.455 0.00 0.00 0.00 4.20
12 13 3.241067 TCGTCTTCCCTATTTTGGTCG 57.759 47.619 0.00 0.00 0.00 4.79
13 14 5.183228 TCAATCGTCTTCCCTATTTTGGTC 58.817 41.667 0.00 0.00 0.00 4.02
14 15 5.174037 TCAATCGTCTTCCCTATTTTGGT 57.826 39.130 0.00 0.00 0.00 3.67
15 16 7.801716 TTATCAATCGTCTTCCCTATTTTGG 57.198 36.000 0.00 0.00 0.00 3.28
16 17 8.129211 GGTTTATCAATCGTCTTCCCTATTTTG 58.871 37.037 0.00 0.00 0.00 2.44
17 18 7.012044 CGGTTTATCAATCGTCTTCCCTATTTT 59.988 37.037 0.00 0.00 31.35 1.82
18 19 6.482308 CGGTTTATCAATCGTCTTCCCTATTT 59.518 38.462 0.00 0.00 31.35 1.40
19 20 5.989777 CGGTTTATCAATCGTCTTCCCTATT 59.010 40.000 0.00 0.00 31.35 1.73
20 21 5.303589 TCGGTTTATCAATCGTCTTCCCTAT 59.696 40.000 0.00 0.00 37.78 2.57
21 22 4.646040 TCGGTTTATCAATCGTCTTCCCTA 59.354 41.667 0.00 0.00 37.78 3.53
22 23 3.449737 TCGGTTTATCAATCGTCTTCCCT 59.550 43.478 0.00 0.00 37.78 4.20
23 24 3.554731 GTCGGTTTATCAATCGTCTTCCC 59.445 47.826 0.00 0.00 37.78 3.97
24 25 3.554731 GGTCGGTTTATCAATCGTCTTCC 59.445 47.826 0.00 0.00 37.78 3.46
25 26 4.430908 AGGTCGGTTTATCAATCGTCTTC 58.569 43.478 0.00 0.00 37.78 2.87
26 27 4.467198 AGGTCGGTTTATCAATCGTCTT 57.533 40.909 0.00 0.00 37.78 3.01
27 28 4.885907 TCTAGGTCGGTTTATCAATCGTCT 59.114 41.667 0.00 0.00 37.78 4.18
28 29 5.179045 TCTAGGTCGGTTTATCAATCGTC 57.821 43.478 0.00 0.00 37.78 4.20
29 30 5.587388 TTCTAGGTCGGTTTATCAATCGT 57.413 39.130 0.00 0.00 37.78 3.73
30 31 6.897259 TTTTCTAGGTCGGTTTATCAATCG 57.103 37.500 0.00 0.00 37.91 3.34
52 53 0.958822 CTACTTGCGTGGGGCTTTTT 59.041 50.000 0.00 0.00 44.05 1.94
53 54 1.524008 GCTACTTGCGTGGGGCTTTT 61.524 55.000 0.00 0.00 44.05 2.27
54 55 1.971695 GCTACTTGCGTGGGGCTTT 60.972 57.895 0.00 0.00 44.05 3.51
55 56 2.359975 GCTACTTGCGTGGGGCTT 60.360 61.111 0.00 0.00 44.05 4.35
56 57 4.410400 GGCTACTTGCGTGGGGCT 62.410 66.667 0.00 0.00 44.05 5.19
58 59 4.388499 ACGGCTACTTGCGTGGGG 62.388 66.667 0.00 0.00 44.05 4.96
59 60 3.118454 CACGGCTACTTGCGTGGG 61.118 66.667 0.00 0.00 44.05 4.61
61 62 3.118454 CCCACGGCTACTTGCGTG 61.118 66.667 0.00 0.00 44.05 5.34
62 63 2.781595 CTTCCCACGGCTACTTGCGT 62.782 60.000 0.00 0.00 44.05 5.24
63 64 2.047655 TTCCCACGGCTACTTGCG 60.048 61.111 0.00 0.00 44.05 4.85
64 65 2.399356 GCTTCCCACGGCTACTTGC 61.399 63.158 0.00 0.00 41.94 4.01
65 66 1.745489 GGCTTCCCACGGCTACTTG 60.745 63.158 0.00 0.00 0.00 3.16
66 67 2.185310 CTGGCTTCCCACGGCTACTT 62.185 60.000 0.00 0.00 35.79 2.24
67 68 2.606519 TGGCTTCCCACGGCTACT 60.607 61.111 0.00 0.00 35.79 2.57
68 69 2.125106 CTGGCTTCCCACGGCTAC 60.125 66.667 0.00 0.00 35.79 3.58
69 70 4.096003 GCTGGCTTCCCACGGCTA 62.096 66.667 0.00 0.00 35.79 3.93
72 73 4.641645 TGTGCTGGCTTCCCACGG 62.642 66.667 0.00 0.00 35.79 4.94
73 74 1.733402 TTTTGTGCTGGCTTCCCACG 61.733 55.000 0.00 0.00 35.79 4.94
74 75 0.249447 GTTTTGTGCTGGCTTCCCAC 60.249 55.000 0.00 0.00 35.79 4.61
75 76 0.685785 TGTTTTGTGCTGGCTTCCCA 60.686 50.000 0.00 0.00 39.32 4.37
76 77 0.463620 TTGTTTTGTGCTGGCTTCCC 59.536 50.000 0.00 0.00 0.00 3.97
77 78 1.933181 GTTTGTTTTGTGCTGGCTTCC 59.067 47.619 0.00 0.00 0.00 3.46
78 79 1.587946 CGTTTGTTTTGTGCTGGCTTC 59.412 47.619 0.00 0.00 0.00 3.86
79 80 1.203523 TCGTTTGTTTTGTGCTGGCTT 59.796 42.857 0.00 0.00 0.00 4.35
80 81 0.814457 TCGTTTGTTTTGTGCTGGCT 59.186 45.000 0.00 0.00 0.00 4.75
81 82 1.522258 CATCGTTTGTTTTGTGCTGGC 59.478 47.619 0.00 0.00 0.00 4.85
82 83 1.522258 GCATCGTTTGTTTTGTGCTGG 59.478 47.619 0.00 0.00 0.00 4.85
83 84 2.191802 TGCATCGTTTGTTTTGTGCTG 58.808 42.857 0.00 0.00 33.95 4.41
84 85 2.462889 CTGCATCGTTTGTTTTGTGCT 58.537 42.857 0.00 0.00 33.95 4.40
85 86 1.522258 CCTGCATCGTTTGTTTTGTGC 59.478 47.619 0.00 0.00 0.00 4.57
86 87 2.126467 CCCTGCATCGTTTGTTTTGTG 58.874 47.619 0.00 0.00 0.00 3.33
87 88 1.068434 CCCCTGCATCGTTTGTTTTGT 59.932 47.619 0.00 0.00 0.00 2.83
88 89 1.605202 CCCCCTGCATCGTTTGTTTTG 60.605 52.381 0.00 0.00 0.00 2.44
89 90 0.678950 CCCCCTGCATCGTTTGTTTT 59.321 50.000 0.00 0.00 0.00 2.43
90 91 1.815817 GCCCCCTGCATCGTTTGTTT 61.816 55.000 0.00 0.00 40.77 2.83
91 92 2.275380 GCCCCCTGCATCGTTTGTT 61.275 57.895 0.00 0.00 40.77 2.83
92 93 2.676471 GCCCCCTGCATCGTTTGT 60.676 61.111 0.00 0.00 40.77 2.83
93 94 3.451894 GGCCCCCTGCATCGTTTG 61.452 66.667 0.00 0.00 43.89 2.93
94 95 2.730129 AAAGGCCCCCTGCATCGTTT 62.730 55.000 0.00 0.00 43.89 3.60
95 96 3.224007 AAAGGCCCCCTGCATCGTT 62.224 57.895 0.00 0.00 43.89 3.85
96 97 3.645268 GAAAGGCCCCCTGCATCGT 62.645 63.158 0.00 0.00 43.89 3.73
97 98 2.830370 GAAAGGCCCCCTGCATCG 60.830 66.667 0.00 0.00 43.89 3.84
98 99 2.442830 GGAAAGGCCCCCTGCATC 60.443 66.667 0.00 0.00 43.89 3.91
99 100 2.594365 GATGGAAAGGCCCCCTGCAT 62.594 60.000 0.00 0.15 43.89 3.96
100 101 3.275271 ATGGAAAGGCCCCCTGCA 61.275 61.111 0.00 0.00 43.89 4.41
101 102 2.442830 GATGGAAAGGCCCCCTGC 60.443 66.667 0.00 0.00 40.16 4.85
102 103 2.124151 CGATGGAAAGGCCCCCTG 60.124 66.667 0.00 0.00 32.13 4.45
103 104 2.286121 TCGATGGAAAGGCCCCCT 60.286 61.111 0.00 0.00 34.97 4.79
104 105 2.193248 CTCGATGGAAAGGCCCCC 59.807 66.667 0.00 0.00 34.97 5.40
105 106 2.193248 CCTCGATGGAAAGGCCCC 59.807 66.667 0.00 0.00 38.35 5.80
109 110 1.821332 GCCTGCCTCGATGGAAAGG 60.821 63.158 13.83 13.83 41.53 3.11
110 111 0.393537 AAGCCTGCCTCGATGGAAAG 60.394 55.000 5.24 2.35 38.35 2.62
111 112 0.038166 AAAGCCTGCCTCGATGGAAA 59.962 50.000 5.24 0.00 38.35 3.13
112 113 0.677731 CAAAGCCTGCCTCGATGGAA 60.678 55.000 5.24 0.00 38.35 3.53
113 114 1.078214 CAAAGCCTGCCTCGATGGA 60.078 57.895 5.24 0.00 38.35 3.41
114 115 1.078214 TCAAAGCCTGCCTCGATGG 60.078 57.895 0.00 0.00 39.35 3.51
115 116 1.372087 GGTCAAAGCCTGCCTCGATG 61.372 60.000 0.00 0.00 0.00 3.84
116 117 1.078143 GGTCAAAGCCTGCCTCGAT 60.078 57.895 0.00 0.00 0.00 3.59
117 118 2.347490 GGTCAAAGCCTGCCTCGA 59.653 61.111 0.00 0.00 0.00 4.04
118 119 2.747855 GGGTCAAAGCCTGCCTCG 60.748 66.667 0.00 0.00 31.81 4.63
119 120 2.361737 GGGGTCAAAGCCTGCCTC 60.362 66.667 0.00 0.00 35.71 4.70
120 121 4.351054 CGGGGTCAAAGCCTGCCT 62.351 66.667 0.00 0.00 35.07 4.75
147 148 3.768185 ATGATCCGGTTCCGTCGCG 62.768 63.158 10.02 0.00 0.00 5.87
148 149 1.949631 GATGATCCGGTTCCGTCGC 60.950 63.158 10.02 0.00 0.00 5.19
149 150 1.657487 CGATGATCCGGTTCCGTCG 60.657 63.158 17.48 17.48 0.00 5.12
150 151 1.299926 CCGATGATCCGGTTCCGTC 60.300 63.158 10.02 7.36 44.23 4.79
151 152 2.812499 CCGATGATCCGGTTCCGT 59.188 61.111 10.02 0.00 44.23 4.69
158 159 2.069273 GTATTTGCCTCCGATGATCCG 58.931 52.381 0.00 0.00 0.00 4.18
159 160 2.069273 CGTATTTGCCTCCGATGATCC 58.931 52.381 0.00 0.00 0.00 3.36
160 161 1.461127 GCGTATTTGCCTCCGATGATC 59.539 52.381 0.00 0.00 0.00 2.92
161 162 1.512926 GCGTATTTGCCTCCGATGAT 58.487 50.000 0.00 0.00 0.00 2.45
162 163 2.986311 GCGTATTTGCCTCCGATGA 58.014 52.632 0.00 0.00 0.00 2.92
179 180 2.048316 CCAAACCCGCATGTTGGC 60.048 61.111 0.00 0.00 0.00 4.52
180 181 2.048316 GCCAAACCCGCATGTTGG 60.048 61.111 7.50 7.50 0.00 3.77
181 182 2.048316 GGCCAAACCCGCATGTTG 60.048 61.111 0.00 0.00 0.00 3.33
182 183 2.203625 AGGCCAAACCCGCATGTT 60.204 55.556 5.01 0.00 40.58 2.71
183 184 2.676471 GAGGCCAAACCCGCATGT 60.676 61.111 5.01 0.00 40.58 3.21
184 185 3.451894 GGAGGCCAAACCCGCATG 61.452 66.667 5.01 0.00 40.58 4.06
185 186 4.759205 GGGAGGCCAAACCCGCAT 62.759 66.667 15.15 0.00 40.58 4.73
189 190 1.977009 CGAAAGGGAGGCCAAACCC 60.977 63.158 20.50 20.50 45.88 4.11
190 191 2.636412 GCGAAAGGGAGGCCAAACC 61.636 63.158 5.01 3.43 39.61 3.27
191 192 2.962569 GCGAAAGGGAGGCCAAAC 59.037 61.111 5.01 0.00 0.00 2.93
216 217 3.964221 TTGGTAGTGCTCGCGCTCG 62.964 63.158 8.41 0.00 37.92 5.03
217 218 1.736645 TTTGGTAGTGCTCGCGCTC 60.737 57.895 8.41 0.00 37.92 5.03
218 219 2.027625 GTTTGGTAGTGCTCGCGCT 61.028 57.895 5.56 10.08 40.24 5.92
224 225 2.033602 GGCGGGTTTGGTAGTGCT 59.966 61.111 0.00 0.00 0.00 4.40
240 241 2.440796 AAGGCCACCATCATGCGG 60.441 61.111 5.01 0.00 0.00 5.69
243 244 1.378882 CGGTCAAGGCCACCATCATG 61.379 60.000 5.01 0.00 32.89 3.07
256 257 2.343758 GACTGCTGGCTCGGTCAA 59.656 61.111 12.29 0.00 40.99 3.18
257 258 3.695606 GGACTGCTGGCTCGGTCA 61.696 66.667 16.85 0.00 42.63 4.02
278 279 2.543012 CTCGCTTCAGCTGTCCATTATG 59.457 50.000 14.67 0.00 39.32 1.90
279 280 2.169352 ACTCGCTTCAGCTGTCCATTAT 59.831 45.455 14.67 0.00 39.32 1.28
288 289 2.569134 GGACGACTCGCTTCAGCT 59.431 61.111 0.00 0.00 39.32 4.24
291 292 3.744719 CCCGGACGACTCGCTTCA 61.745 66.667 0.73 0.00 0.00 3.02
319 320 2.202987 GCCGTCTGATCTGGCTGG 60.203 66.667 10.21 9.94 45.40 4.85
353 354 0.741915 TTCGTTTTTGGGTGGAGTGC 59.258 50.000 0.00 0.00 0.00 4.40
354 355 1.268335 CGTTCGTTTTTGGGTGGAGTG 60.268 52.381 0.00 0.00 0.00 3.51
359 360 3.243855 CACCGTTCGTTTTTGGGTG 57.756 52.632 0.00 0.00 41.81 4.61
365 366 0.877213 CCCTCGACACCGTTCGTTTT 60.877 55.000 0.00 0.00 40.07 2.43
369 370 1.731969 GTTCCCTCGACACCGTTCG 60.732 63.158 0.00 0.00 40.53 3.95
384 385 3.775202 TCTCTAAAGCATGCGAGAGTTC 58.225 45.455 30.04 1.84 37.34 3.01
385 386 3.876274 TCTCTAAAGCATGCGAGAGTT 57.124 42.857 30.04 17.41 37.34 3.01
417 418 8.237811 ACTTAACCTTTTTCTCATGTGAACAT 57.762 30.769 9.65 0.00 36.96 2.71
418 419 7.556275 AGACTTAACCTTTTTCTCATGTGAACA 59.444 33.333 9.65 1.04 0.00 3.18
419 420 7.931275 AGACTTAACCTTTTTCTCATGTGAAC 58.069 34.615 9.65 0.00 0.00 3.18
476 481 8.739972 CCAATCTAAACCTGTAGTTTTGCTATT 58.260 33.333 0.00 0.00 46.79 1.73
487 492 6.558775 AGGAGATATGCCAATCTAAACCTGTA 59.441 38.462 0.00 0.00 36.33 2.74
488 493 5.370880 AGGAGATATGCCAATCTAAACCTGT 59.629 40.000 0.00 0.00 36.33 4.00
493 498 6.266786 TCACGTAGGAGATATGCCAATCTAAA 59.733 38.462 0.00 0.00 36.33 1.85
499 504 4.955811 ATTCACGTAGGAGATATGCCAA 57.044 40.909 0.00 0.00 0.00 4.52
522 527 9.119329 CGTTTGATCCAAATTCACGTAATTTTA 57.881 29.630 10.87 5.76 43.75 1.52
531 540 2.250188 CGCCGTTTGATCCAAATTCAC 58.750 47.619 0.00 0.00 35.74 3.18
534 543 2.667171 CGAACGCCGTTTGATCCAAATT 60.667 45.455 11.83 0.00 35.74 1.82
541 550 1.283736 GATACCGAACGCCGTTTGAT 58.716 50.000 18.56 3.73 36.31 2.57
547 556 1.405461 CTATGTGATACCGAACGCCG 58.595 55.000 0.00 0.00 38.18 6.46
548 557 1.137513 GCTATGTGATACCGAACGCC 58.862 55.000 0.00 0.00 0.00 5.68
554 563 5.121611 TCAAACTTGTTGCTATGTGATACCG 59.878 40.000 0.00 0.00 0.00 4.02
556 565 7.017645 CACTCAAACTTGTTGCTATGTGATAC 58.982 38.462 0.00 0.00 0.00 2.24
586 595 8.241497 TCATATGCAGCAGAGGAAAAATTTAT 57.759 30.769 0.98 0.00 0.00 1.40
591 600 6.534475 AATTCATATGCAGCAGAGGAAAAA 57.466 33.333 19.97 0.00 29.75 1.94
592 601 6.379133 AGAAATTCATATGCAGCAGAGGAAAA 59.621 34.615 19.97 0.00 29.75 2.29
600 609 7.643569 TTTCCTAAGAAATTCATATGCAGCA 57.356 32.000 0.00 0.00 37.07 4.41
601 610 8.931385 TTTTTCCTAAGAAATTCATATGCAGC 57.069 30.769 0.00 0.00 41.55 5.25
626 635 5.104527 TCACAGGATTGGAATCGTTAGGAAT 60.105 40.000 0.00 0.00 36.27 3.01
652 661 1.786937 TTCCCACATTGGCTGTTTGT 58.213 45.000 0.00 0.00 35.29 2.83
654 663 4.436113 AAAATTCCCACATTGGCTGTTT 57.564 36.364 0.00 0.00 35.29 2.83
655 664 4.102996 AGAAAAATTCCCACATTGGCTGTT 59.897 37.500 0.00 0.00 35.29 3.16
659 668 5.643348 CCTTAAGAAAAATTCCCACATTGGC 59.357 40.000 3.36 0.00 35.79 4.52
690 699 7.934120 CGAGTTTCATAGGATTTCTAGGGATTT 59.066 37.037 0.00 0.00 31.22 2.17
695 708 7.329717 GCATACGAGTTTCATAGGATTTCTAGG 59.670 40.741 0.00 0.00 0.00 3.02
696 709 7.867909 TGCATACGAGTTTCATAGGATTTCTAG 59.132 37.037 0.00 0.00 0.00 2.43
699 712 6.844696 TGCATACGAGTTTCATAGGATTTC 57.155 37.500 0.00 0.00 0.00 2.17
710 723 1.076332 GACGCCTTGCATACGAGTTT 58.924 50.000 10.07 0.00 0.00 2.66
713 726 1.148157 CTGGACGCCTTGCATACGAG 61.148 60.000 10.07 0.00 0.00 4.18
715 728 2.813179 GCTGGACGCCTTGCATACG 61.813 63.158 0.00 0.00 0.00 3.06
716 729 1.709147 CTGCTGGACGCCTTGCATAC 61.709 60.000 13.54 0.00 38.05 2.39
718 731 2.749044 CTGCTGGACGCCTTGCAT 60.749 61.111 13.54 0.00 38.05 3.96
773 819 2.543641 CGTCTACCCGGGTATGTTTTC 58.456 52.381 33.26 17.35 0.00 2.29
785 831 3.728279 AAATCCGCCGCGTCTACCC 62.728 63.158 12.58 0.00 0.00 3.69
790 836 4.174129 CCCAAAATCCGCCGCGTC 62.174 66.667 12.58 0.00 0.00 5.19
805 851 2.987547 TATCGGATCGGACGGCCC 60.988 66.667 0.00 0.00 0.00 5.80
824 879 5.880054 AAAAACTGTTGGGAGATGTATCG 57.120 39.130 0.00 0.00 0.00 2.92
848 903 3.383185 GGAGATCTGATCGAGTTGTCCTT 59.617 47.826 11.73 0.00 33.02 3.36
1005 1072 4.056125 CGTCGTCAGGCAGCAGGA 62.056 66.667 0.00 0.00 0.00 3.86
1012 1079 3.973267 GAGGAGCACGTCGTCAGGC 62.973 68.421 0.00 0.00 39.48 4.85
1014 1081 1.025113 TAGGAGGAGCACGTCGTCAG 61.025 60.000 0.00 0.00 41.16 3.51
1015 1082 0.607217 TTAGGAGGAGCACGTCGTCA 60.607 55.000 0.00 0.00 41.16 4.35
1016 1083 0.524862 TTTAGGAGGAGCACGTCGTC 59.475 55.000 0.00 0.00 39.05 4.20
1017 1084 0.526662 CTTTAGGAGGAGCACGTCGT 59.473 55.000 0.00 0.00 34.32 4.34
1018 1085 0.802607 GCTTTAGGAGGAGCACGTCG 60.803 60.000 0.00 0.00 38.73 5.12
1019 1086 0.460459 GGCTTTAGGAGGAGCACGTC 60.460 60.000 0.00 0.00 40.63 4.34
1021 1088 0.179000 ATGGCTTTAGGAGGAGCACG 59.821 55.000 0.00 0.00 40.63 5.34
1022 1089 1.065126 ACATGGCTTTAGGAGGAGCAC 60.065 52.381 0.00 0.00 40.63 4.40
1023 1090 1.210478 GACATGGCTTTAGGAGGAGCA 59.790 52.381 0.00 0.00 40.63 4.26
1024 1091 1.210478 TGACATGGCTTTAGGAGGAGC 59.790 52.381 0.00 0.00 38.17 4.70
1025 1092 3.274288 GTTGACATGGCTTTAGGAGGAG 58.726 50.000 0.00 0.00 0.00 3.69
1026 1093 2.026262 GGTTGACATGGCTTTAGGAGGA 60.026 50.000 0.00 0.00 0.00 3.71
1027 1094 2.290896 TGGTTGACATGGCTTTAGGAGG 60.291 50.000 0.00 0.00 0.00 4.30
1028 1095 3.071874 TGGTTGACATGGCTTTAGGAG 57.928 47.619 0.00 0.00 0.00 3.69
1029 1096 3.420893 CTTGGTTGACATGGCTTTAGGA 58.579 45.455 0.00 0.00 0.00 2.94
1030 1097 2.493278 CCTTGGTTGACATGGCTTTAGG 59.507 50.000 0.00 0.00 37.55 2.69
1031 1098 2.493278 CCCTTGGTTGACATGGCTTTAG 59.507 50.000 0.00 0.00 41.77 1.85
1032 1099 2.524306 CCCTTGGTTGACATGGCTTTA 58.476 47.619 0.00 0.00 41.77 1.85
1033 1100 1.341080 CCCTTGGTTGACATGGCTTT 58.659 50.000 0.00 0.00 41.77 3.51
1034 1101 1.187567 GCCCTTGGTTGACATGGCTT 61.188 55.000 0.00 0.00 41.61 4.35
1035 1102 1.607467 GCCCTTGGTTGACATGGCT 60.607 57.895 0.00 0.00 41.61 4.75
1036 1103 2.973082 GCCCTTGGTTGACATGGC 59.027 61.111 0.00 0.00 41.77 4.40
1051 1118 3.285215 CTCATCCCTGCATGCGCC 61.285 66.667 14.09 0.00 37.32 6.53
1057 1124 1.037579 ACGATCGTCTCATCCCTGCA 61.038 55.000 16.60 0.00 0.00 4.41
1060 1127 1.678627 CTTGACGATCGTCTCATCCCT 59.321 52.381 39.10 9.25 44.80 4.20
1101 1189 3.928343 CTCGACGAGGAGATCCAAC 57.072 57.895 17.27 0.00 38.89 3.77
1288 1376 4.329545 GGAACTGCCGTCCCAGCA 62.330 66.667 0.00 0.00 36.29 4.41
1422 1510 1.087771 GTAAAGGATGGCGGTCGTGG 61.088 60.000 0.00 0.00 0.00 4.94
1503 1591 0.110823 CGAACTTGTTGCAGCCGTAC 60.111 55.000 0.00 0.00 0.00 3.67
1590 1678 1.369448 CCGCGACGAGTAGATCTGC 60.369 63.158 8.23 3.54 0.00 4.26
1648 1736 3.061848 GAATGGTGGGTGGTGCGG 61.062 66.667 0.00 0.00 0.00 5.69
1664 1752 2.083774 GGGAGTCGTTGCATGATTTGA 58.916 47.619 0.00 0.00 0.00 2.69
1675 1763 3.622826 CACGGGGTGGGAGTCGTT 61.623 66.667 0.00 0.00 33.31 3.85
1730 1818 1.107538 GTGGTGATCGAGATCCGGGA 61.108 60.000 0.00 0.00 37.02 5.14
1742 1830 2.261671 GGTCGTGCTCGTGGTGAT 59.738 61.111 8.17 0.00 38.33 3.06
1743 1831 2.910479 AGGTCGTGCTCGTGGTGA 60.910 61.111 8.17 0.00 38.33 4.02
1744 1832 2.734723 CAGGTCGTGCTCGTGGTG 60.735 66.667 8.17 0.60 38.33 4.17
1806 1894 4.021925 AAGTCCCACGGCAGCTCC 62.022 66.667 0.00 0.00 0.00 4.70
1855 1943 1.328680 CAGCATAGGTGTCGCATTCAC 59.671 52.381 0.00 0.00 35.36 3.18
1858 1946 0.253044 ACCAGCATAGGTGTCGCATT 59.747 50.000 0.00 0.00 41.30 3.56
1859 1947 0.179073 GACCAGCATAGGTGTCGCAT 60.179 55.000 0.00 0.00 43.38 4.73
1860 1948 1.218047 GACCAGCATAGGTGTCGCA 59.782 57.895 0.00 0.00 43.38 5.10
1930 2018 2.769617 CGACAACGTCCACATCGC 59.230 61.111 0.00 0.00 34.56 4.58
2055 2143 0.041839 CAACTGCGCTCACAGACAAC 60.042 55.000 9.73 0.00 40.25 3.32
2061 2149 4.254709 AGCCCAACTGCGCTCACA 62.255 61.111 9.73 0.00 36.02 3.58
2144 2232 2.373524 AATGTCGTGCACGCACACAC 62.374 55.000 31.91 25.77 46.47 3.82
2236 2324 4.993705 TTGTATTCCTGTTCCTCCTTGT 57.006 40.909 0.00 0.00 0.00 3.16
2239 2327 6.043706 CCTGATATTGTATTCCTGTTCCTCCT 59.956 42.308 0.00 0.00 0.00 3.69
2247 2335 3.187227 GTGCGCCTGATATTGTATTCCTG 59.813 47.826 4.18 0.00 0.00 3.86
2249 2337 3.138304 TGTGCGCCTGATATTGTATTCC 58.862 45.455 4.18 0.00 0.00 3.01
2250 2338 5.362556 AATGTGCGCCTGATATTGTATTC 57.637 39.130 4.18 0.00 0.00 1.75
2251 2339 5.772825 AAATGTGCGCCTGATATTGTATT 57.227 34.783 4.18 0.00 0.00 1.89
2252 2340 5.067674 ACAAAATGTGCGCCTGATATTGTAT 59.932 36.000 4.18 0.00 0.00 2.29
2253 2341 4.397730 ACAAAATGTGCGCCTGATATTGTA 59.602 37.500 4.18 0.00 0.00 2.41
2254 2342 3.193267 ACAAAATGTGCGCCTGATATTGT 59.807 39.130 4.18 6.84 0.00 2.71
2259 2347 2.919666 GTACAAAATGTGCGCCTGAT 57.080 45.000 4.18 0.00 0.00 2.90
2288 2379 2.906354 ACATATTCGTTGGTGCCTCTC 58.094 47.619 0.00 0.00 0.00 3.20
2300 2391 5.520288 CACCAAGTGTAGAGGAACATATTCG 59.480 44.000 0.00 0.00 35.48 3.34
2312 2403 0.753867 TTCCACGCACCAAGTGTAGA 59.246 50.000 0.00 0.00 39.40 2.59
2427 2519 3.924073 CAGACACACATGGATGCATTTTG 59.076 43.478 0.00 0.26 0.00 2.44
2444 2563 3.261216 CACGCACGCACACAGACA 61.261 61.111 0.00 0.00 0.00 3.41
2445 2564 3.261951 ACACGCACGCACACAGAC 61.262 61.111 0.00 0.00 0.00 3.51
2446 2565 3.261216 CACACGCACGCACACAGA 61.261 61.111 0.00 0.00 0.00 3.41
2447 2566 3.563088 ACACACGCACGCACACAG 61.563 61.111 0.00 0.00 0.00 3.66
2452 2571 1.067743 CAAAAACACACACGCACGCA 61.068 50.000 0.00 0.00 0.00 5.24
2456 2575 2.488545 ACTTACCAAAAACACACACGCA 59.511 40.909 0.00 0.00 0.00 5.24
2476 2600 6.749118 GCAGATTTAGACATGGTCATTGAAAC 59.251 38.462 0.00 0.00 34.60 2.78
2494 2619 0.261696 AAATAGGGGCCGGCAGATTT 59.738 50.000 30.85 22.16 0.00 2.17
2506 2631 6.204108 GGTGATCACGTAAACCATAAATAGGG 59.796 42.308 19.33 0.00 32.69 3.53
3129 3274 5.644902 TCACAATGTTACGCAATATACGG 57.355 39.130 3.45 0.00 34.00 4.02
3173 3318 5.850557 TGAATGTGTCACTTCACCATTTT 57.149 34.783 4.27 0.00 37.51 1.82


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

AutoCloner maintained by Alex Coulton.