Multiple sequence alignment - TraesCS2A01G526200

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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 TraesCS2A01G526200 chr2A 100.000 4046 0 0 1 4046 746619655 746623700 0.000000e+00 7472.0
1 TraesCS2A01G526200 chr2A 92.258 2493 175 4 600 3087 748285016 748287495 0.000000e+00 3518.0
2 TraesCS2A01G526200 chr2A 92.250 2413 163 5 699 3087 748437494 748439906 0.000000e+00 3398.0
3 TraesCS2A01G526200 chr2A 89.085 2492 250 16 615 3087 748503724 748501236 0.000000e+00 3075.0
4 TraesCS2A01G526200 chr2A 93.642 1038 56 5 2529 3564 748209749 748210778 0.000000e+00 1543.0
5 TraesCS2A01G526200 chr2A 94.896 960 30 7 3089 4046 748452801 748451859 0.000000e+00 1483.0
6 TraesCS2A01G526200 chr2A 87.298 929 95 11 620 1533 748389794 748390714 0.000000e+00 1040.0
7 TraesCS2A01G526200 chr2A 95.782 403 16 1 3093 3494 748464674 748464272 0.000000e+00 649.0
8 TraesCS2A01G526200 chr2A 87.783 442 28 9 3535 3974 748464273 748463856 1.010000e-135 494.0
9 TraesCS2A01G526200 chr2A 87.989 358 25 9 3634 3974 748210783 748211139 1.350000e-109 407.0
10 TraesCS2A01G526200 chr2A 89.474 95 8 2 514 607 748284840 748284933 7.100000e-23 119.0
11 TraesCS2A01G526200 chr2A 94.737 76 3 1 3972 4046 748463813 748463738 2.560000e-22 117.0
12 TraesCS2A01G526200 chr2A 98.361 61 0 1 3972 4031 748288535 748288595 5.530000e-19 106.0
13 TraesCS2A01G526200 chr2A 88.750 80 4 2 3972 4046 748222616 748222695 4.310000e-15 93.5
14 TraesCS2A01G526200 chr2B 91.021 3397 264 25 599 3972 753931435 753928057 0.000000e+00 4545.0
15 TraesCS2A01G526200 chr2B 92.150 2981 183 18 653 3605 753792712 753795669 0.000000e+00 4161.0
16 TraesCS2A01G526200 chr2B 92.430 2140 150 8 1232 3368 753786113 753788243 0.000000e+00 3044.0
17 TraesCS2A01G526200 chr2B 93.857 879 43 2 2736 3613 753935066 753934198 0.000000e+00 1314.0
18 TraesCS2A01G526200 chr2B 90.107 374 21 8 3605 3974 753795714 753796075 4.730000e-129 472.0
19 TraesCS2A01G526200 chr2B 89.276 373 36 4 3604 3974 753934167 753933797 7.920000e-127 464.0
20 TraesCS2A01G526200 chr2B 98.667 75 1 0 3972 4046 753796118 753796192 2.540000e-27 134.0
21 TraesCS2A01G526200 chr2B 90.526 95 8 1 514 607 753792624 753792718 1.530000e-24 124.0
22 TraesCS2A01G526200 chr2B 93.421 76 4 1 3972 4046 753933754 753933679 1.190000e-20 111.0
23 TraesCS2A01G526200 chr2B 96.721 61 1 1 3972 4031 753788421 753788481 2.570000e-17 100.0
24 TraesCS2A01G526200 chr2B 91.304 69 6 0 620 688 753938796 753938728 1.200000e-15 95.3
25 TraesCS2A01G526200 chr2B 94.340 53 3 0 468 520 753792525 753792577 9.320000e-12 82.4
26 TraesCS2A01G526200 chr2D 92.555 2928 195 4 700 3605 617633781 617636707 0.000000e+00 4178.0
27 TraesCS2A01G526200 chr2D 94.025 2544 150 2 1071 3613 617760443 617762985 0.000000e+00 3855.0
28 TraesCS2A01G526200 chr2D 93.083 2501 158 5 600 3087 617546306 617548804 0.000000e+00 3646.0
29 TraesCS2A01G526200 chr2D 92.816 2436 164 5 699 3123 617538792 617541227 0.000000e+00 3518.0
30 TraesCS2A01G526200 chr2D 91.761 2391 186 8 706 3085 617909820 617907430 0.000000e+00 3314.0
31 TraesCS2A01G526200 chr2D 90.107 374 29 7 3605 3974 617763017 617763386 2.830000e-131 479.0
32 TraesCS2A01G526200 chr2D 88.705 363 30 7 3622 3974 617636896 617637257 2.230000e-117 433.0
33 TraesCS2A01G526200 chr2D 91.770 243 8 5 3809 4046 617902205 617901970 1.080000e-85 327.0
34 TraesCS2A01G526200 chr2D 90.909 77 7 0 531 607 617546127 617546203 1.990000e-18 104.0
35 TraesCS2A01G526200 chr2D 90.000 80 3 2 3972 4046 617541512 617541591 9.250000e-17 99.0
36 TraesCS2A01G526200 chr2D 94.000 50 3 0 471 520 617546028 617546077 4.340000e-10 76.8
37 TraesCS2A01G526200 chr2D 97.500 40 1 0 3178 3217 617541224 617541263 7.260000e-08 69.4
38 TraesCS2A01G526200 chr2D 93.478 46 3 0 620 665 617909941 617909896 7.260000e-08 69.4
39 TraesCS2A01G526200 chr7B 81.039 385 36 20 1 367 726149577 726149942 5.150000e-69 272.0
40 TraesCS2A01G526200 chr7B 91.954 87 6 1 521 607 726149990 726150075 1.980000e-23 121.0


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 TraesCS2A01G526200 chr2A 746619655 746623700 4045 False 7472.000000 7472 100.000000 1 4046 1 chr2A.!!$F1 4045
1 TraesCS2A01G526200 chr2A 748437494 748439906 2412 False 3398.000000 3398 92.250000 699 3087 1 chr2A.!!$F4 2388
2 TraesCS2A01G526200 chr2A 748501236 748503724 2488 True 3075.000000 3075 89.085000 615 3087 1 chr2A.!!$R2 2472
3 TraesCS2A01G526200 chr2A 748451859 748452801 942 True 1483.000000 1483 94.896000 3089 4046 1 chr2A.!!$R1 957
4 TraesCS2A01G526200 chr2A 748284840 748288595 3755 False 1247.666667 3518 93.364333 514 4031 3 chr2A.!!$F6 3517
5 TraesCS2A01G526200 chr2A 748389794 748390714 920 False 1040.000000 1040 87.298000 620 1533 1 chr2A.!!$F3 913
6 TraesCS2A01G526200 chr2A 748209749 748211139 1390 False 975.000000 1543 90.815500 2529 3974 2 chr2A.!!$F5 1445
7 TraesCS2A01G526200 chr2A 748463738 748464674 936 True 420.000000 649 92.767333 3093 4046 3 chr2A.!!$R3 953
8 TraesCS2A01G526200 chr2B 753786113 753788481 2368 False 1572.000000 3044 94.575500 1232 4031 2 chr2B.!!$F1 2799
9 TraesCS2A01G526200 chr2B 753928057 753938796 10739 True 1305.860000 4545 91.775800 599 4046 5 chr2B.!!$R1 3447
10 TraesCS2A01G526200 chr2B 753792525 753796192 3667 False 994.680000 4161 93.158000 468 4046 5 chr2B.!!$F2 3578
11 TraesCS2A01G526200 chr2D 617633781 617637257 3476 False 2305.500000 4178 90.630000 700 3974 2 chr2D.!!$F3 3274
12 TraesCS2A01G526200 chr2D 617760443 617763386 2943 False 2167.000000 3855 92.066000 1071 3974 2 chr2D.!!$F4 2903
13 TraesCS2A01G526200 chr2D 617907430 617909941 2511 True 1691.700000 3314 92.619500 620 3085 2 chr2D.!!$R2 2465
14 TraesCS2A01G526200 chr2D 617546028 617548804 2776 False 1275.600000 3646 92.664000 471 3087 3 chr2D.!!$F2 2616
15 TraesCS2A01G526200 chr2D 617538792 617541591 2799 False 1228.800000 3518 93.438667 699 4046 3 chr2D.!!$F1 3347

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
177 178 0.109412 GCAAGTGATCAGCTTGGTGC 60.109 55.0 25.76 16.25 42.44 5.01 F
226 227 0.250510 TTGGTCGCTACATGTGGCAA 60.251 50.0 30.25 13.18 36.84 4.52 F
227 228 0.250510 TGGTCGCTACATGTGGCAAA 60.251 50.0 30.25 16.96 36.84 3.68 F
291 292 0.250945 TCCCTCTGATCCGATCTCCG 60.251 60.0 9.78 0.00 38.18 4.63 F
776 7608 0.491823 TTCACCTCCTCCTTCAGGGA 59.508 55.0 0.00 0.00 43.67 4.20 F
1832 8697 1.453155 AAACGTGGACTGATGGATGC 58.547 50.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 8087 0.035458 CAGTCCAGTTCAGGTGTCCC 59.965 60.000 0.00 0.00 0.00 4.46 R
1697 8562 0.461339 TCCTTCTTTCGCATACCCGC 60.461 55.000 0.00 0.00 0.00 6.13 R
1832 8697 1.004610 CTTCGAACATGTGCATAGCCG 60.005 52.381 4.29 0.00 0.00 5.52 R
2285 9151 1.304381 GCATCAGGTTGGAGGCCAA 60.304 57.895 5.01 0.00 41.69 4.52 R
2430 9296 1.272212 CCGGAGAAAAACAACCCATGG 59.728 52.381 4.14 4.14 0.00 3.66 R
3627 10923 2.168496 ACTAAAGTGCACTAGCGGAGA 58.832 47.619 22.01 0.00 46.23 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.907741 TGAATGAATGTTTATCACTTTCGCA 58.092 32.000 0.00 0.00 40.79 5.10
42 43 7.366513 TGAATGAATGTTTATCACTTTCGCAA 58.633 30.769 0.00 0.00 40.79 4.85
44 45 6.984740 TGAATGTTTATCACTTTCGCAAAC 57.015 33.333 0.00 0.00 40.79 2.93
45 46 6.734137 TGAATGTTTATCACTTTCGCAAACT 58.266 32.000 0.00 0.00 40.79 2.66
46 47 7.199766 TGAATGTTTATCACTTTCGCAAACTT 58.800 30.769 0.00 0.00 40.79 2.66
48 49 6.371809 TGTTTATCACTTTCGCAAACTTCT 57.628 33.333 0.00 0.00 31.85 2.85
49 50 7.485418 TGTTTATCACTTTCGCAAACTTCTA 57.515 32.000 0.00 0.00 31.85 2.10
50 51 8.094798 TGTTTATCACTTTCGCAAACTTCTAT 57.905 30.769 0.00 0.00 31.85 1.98
51 52 8.227791 TGTTTATCACTTTCGCAAACTTCTATC 58.772 33.333 0.00 0.00 31.85 2.08
52 53 7.899178 TTATCACTTTCGCAAACTTCTATCA 57.101 32.000 0.00 0.00 0.00 2.15
53 54 6.801539 ATCACTTTCGCAAACTTCTATCAA 57.198 33.333 0.00 0.00 0.00 2.57
55 56 7.202016 TCACTTTCGCAAACTTCTATCAAAT 57.798 32.000 0.00 0.00 0.00 2.32
56 57 7.648142 TCACTTTCGCAAACTTCTATCAAATT 58.352 30.769 0.00 0.00 0.00 1.82
57 58 7.803189 TCACTTTCGCAAACTTCTATCAAATTC 59.197 33.333 0.00 0.00 0.00 2.17
58 59 7.591057 CACTTTCGCAAACTTCTATCAAATTCA 59.409 33.333 0.00 0.00 0.00 2.57
59 60 8.299570 ACTTTCGCAAACTTCTATCAAATTCAT 58.700 29.630 0.00 0.00 0.00 2.57
60 61 8.451687 TTTCGCAAACTTCTATCAAATTCATG 57.548 30.769 0.00 0.00 0.00 3.07
61 62 7.376435 TCGCAAACTTCTATCAAATTCATGA 57.624 32.000 0.00 0.00 0.00 3.07
62 63 7.815641 TCGCAAACTTCTATCAAATTCATGAA 58.184 30.769 11.26 11.26 32.06 2.57
63 64 7.750458 TCGCAAACTTCTATCAAATTCATGAAC 59.250 33.333 11.07 0.00 32.06 3.18
64 65 7.752239 CGCAAACTTCTATCAAATTCATGAACT 59.248 33.333 11.07 0.00 32.06 3.01
65 66 9.415544 GCAAACTTCTATCAAATTCATGAACTT 57.584 29.630 11.07 2.62 32.06 2.66
117 118 9.489393 TCAAATCGATGAATCTTTTCAATTACG 57.511 29.630 0.00 0.00 44.70 3.18
118 119 7.898725 AATCGATGAATCTTTTCAATTACGC 57.101 32.000 0.00 0.00 44.70 4.42
119 120 6.415798 TCGATGAATCTTTTCAATTACGCA 57.584 33.333 0.00 0.00 44.70 5.24
120 121 6.836953 TCGATGAATCTTTTCAATTACGCAA 58.163 32.000 0.00 0.00 44.70 4.85
121 122 7.301789 TCGATGAATCTTTTCAATTACGCAAA 58.698 30.769 0.00 0.00 44.70 3.68
123 124 7.271223 CGATGAATCTTTTCAATTACGCAAACT 59.729 33.333 0.00 0.00 44.70 2.66
124 125 8.816640 ATGAATCTTTTCAATTACGCAAACTT 57.183 26.923 0.00 0.00 44.70 2.66
125 126 8.641499 TGAATCTTTTCAATTACGCAAACTTT 57.359 26.923 0.00 0.00 38.90 2.66
126 127 9.092876 TGAATCTTTTCAATTACGCAAACTTTT 57.907 25.926 0.00 0.00 38.90 2.27
127 128 9.914923 GAATCTTTTCAATTACGCAAACTTTTT 57.085 25.926 0.00 0.00 0.00 1.94
128 129 9.701355 AATCTTTTCAATTACGCAAACTTTTTG 57.299 25.926 0.00 0.00 0.00 2.44
129 130 8.245701 TCTTTTCAATTACGCAAACTTTTTGT 57.754 26.923 0.91 0.00 0.00 2.83
130 131 8.713271 TCTTTTCAATTACGCAAACTTTTTGTT 58.287 25.926 0.91 0.00 41.29 2.83
137 138 8.649973 ATTACGCAAACTTTTTGTTAAATCCA 57.350 26.923 0.91 0.00 38.03 3.41
138 139 8.649973 TTACGCAAACTTTTTGTTAAATCCAT 57.350 26.923 0.91 0.00 38.03 3.41
139 140 6.942891 ACGCAAACTTTTTGTTAAATCCATG 58.057 32.000 0.91 0.00 38.03 3.66
140 141 6.018343 ACGCAAACTTTTTGTTAAATCCATGG 60.018 34.615 4.97 4.97 38.03 3.66
143 144 8.567104 GCAAACTTTTTGTTAAATCCATGGATT 58.433 29.630 30.64 30.64 41.05 3.01
170 171 3.648339 TTCTTTTGGCAAGTGATCAGC 57.352 42.857 0.00 0.00 0.00 4.26
172 173 3.225104 TCTTTTGGCAAGTGATCAGCTT 58.775 40.909 0.00 0.00 0.00 3.74
173 174 3.005050 TCTTTTGGCAAGTGATCAGCTTG 59.995 43.478 22.94 22.94 44.34 4.01
174 175 1.250328 TTGGCAAGTGATCAGCTTGG 58.750 50.000 25.76 15.15 42.44 3.61
175 176 0.111061 TGGCAAGTGATCAGCTTGGT 59.889 50.000 25.76 2.74 42.44 3.67
177 178 0.109412 GCAAGTGATCAGCTTGGTGC 60.109 55.000 25.76 16.25 42.44 5.01
179 180 1.816835 CAAGTGATCAGCTTGGTGCAT 59.183 47.619 21.02 0.00 45.94 3.96
180 181 1.460504 AGTGATCAGCTTGGTGCATG 58.539 50.000 0.00 0.00 45.94 4.06
182 183 0.328926 TGATCAGCTTGGTGCATGGA 59.671 50.000 0.00 0.00 45.94 3.41
184 185 2.029623 GATCAGCTTGGTGCATGGAAT 58.970 47.619 0.00 0.00 45.94 3.01
187 188 1.546923 CAGCTTGGTGCATGGAATTGA 59.453 47.619 0.00 0.00 45.94 2.57
188 189 1.547372 AGCTTGGTGCATGGAATTGAC 59.453 47.619 0.00 0.00 45.94 3.18
189 190 1.733389 GCTTGGTGCATGGAATTGACG 60.733 52.381 0.00 0.00 42.31 4.35
190 191 1.541147 CTTGGTGCATGGAATTGACGT 59.459 47.619 0.00 0.00 0.00 4.34
193 194 0.451783 GTGCATGGAATTGACGTCCC 59.548 55.000 14.12 7.39 33.89 4.46
194 195 0.327924 TGCATGGAATTGACGTCCCT 59.672 50.000 14.12 0.00 33.89 4.20
195 196 0.734889 GCATGGAATTGACGTCCCTG 59.265 55.000 14.12 8.07 34.79 4.45
196 197 0.734889 CATGGAATTGACGTCCCTGC 59.265 55.000 14.12 3.15 33.89 4.85
197 198 0.394352 ATGGAATTGACGTCCCTGCC 60.394 55.000 14.12 8.80 33.89 4.85
198 199 2.106683 GGAATTGACGTCCCTGCCG 61.107 63.158 14.12 0.00 0.00 5.69
200 201 3.545124 AATTGACGTCCCTGCCGCA 62.545 57.895 14.12 0.00 0.00 5.69
201 202 4.980805 TTGACGTCCCTGCCGCAC 62.981 66.667 14.12 0.00 0.00 5.34
223 224 2.078226 CGTTGGTCGCTACATGTGG 58.922 57.895 9.11 6.75 0.00 4.17
224 225 1.794222 GTTGGTCGCTACATGTGGC 59.206 57.895 23.11 23.11 0.00 5.01
225 226 0.953471 GTTGGTCGCTACATGTGGCA 60.953 55.000 30.25 16.57 36.84 4.92
226 227 0.250510 TTGGTCGCTACATGTGGCAA 60.251 50.000 30.25 13.18 36.84 4.52
227 228 0.250510 TGGTCGCTACATGTGGCAAA 60.251 50.000 30.25 16.96 36.84 3.68
228 229 0.878416 GGTCGCTACATGTGGCAAAA 59.122 50.000 30.25 14.58 36.84 2.44
229 230 1.268352 GGTCGCTACATGTGGCAAAAA 59.732 47.619 30.25 12.24 36.84 1.94
233 234 3.986572 TCGCTACATGTGGCAAAAATTTG 59.013 39.130 30.25 13.75 41.03 2.32
243 244 2.947754 CAAAAATTTGCCCGAGTTGC 57.052 45.000 0.00 0.00 0.00 4.17
245 246 2.611225 AAAATTTGCCCGAGTTGCAA 57.389 40.000 0.00 0.00 46.30 4.08
255 256 4.779475 AGTTGCAACTCACCGGAG 57.221 55.556 26.36 0.00 46.96 4.63
257 258 0.468226 AGTTGCAACTCACCGGAGAA 59.532 50.000 26.36 0.00 44.26 2.87
259 260 0.756294 TTGCAACTCACCGGAGAAGA 59.244 50.000 9.46 0.00 44.26 2.87
262 263 2.218603 GCAACTCACCGGAGAAGAAAA 58.781 47.619 9.46 0.00 44.26 2.29
263 264 2.814336 GCAACTCACCGGAGAAGAAAAT 59.186 45.455 9.46 0.00 44.26 1.82
264 265 3.365364 GCAACTCACCGGAGAAGAAAATG 60.365 47.826 9.46 0.00 44.26 2.32
265 266 3.771577 ACTCACCGGAGAAGAAAATGT 57.228 42.857 9.46 0.00 44.26 2.71
266 267 3.403038 ACTCACCGGAGAAGAAAATGTG 58.597 45.455 9.46 0.00 44.26 3.21
267 268 3.071023 ACTCACCGGAGAAGAAAATGTGA 59.929 43.478 9.46 0.00 44.26 3.58
268 269 4.256920 CTCACCGGAGAAGAAAATGTGAT 58.743 43.478 9.46 0.00 44.26 3.06
269 270 4.002982 TCACCGGAGAAGAAAATGTGATG 58.997 43.478 9.46 0.00 0.00 3.07
270 271 3.753272 CACCGGAGAAGAAAATGTGATGT 59.247 43.478 9.46 0.00 0.00 3.06
271 272 4.935205 CACCGGAGAAGAAAATGTGATGTA 59.065 41.667 9.46 0.00 0.00 2.29
272 273 5.586243 CACCGGAGAAGAAAATGTGATGTAT 59.414 40.000 9.46 0.00 0.00 2.29
273 274 5.817816 ACCGGAGAAGAAAATGTGATGTATC 59.182 40.000 9.46 0.00 0.00 2.24
274 275 5.237344 CCGGAGAAGAAAATGTGATGTATCC 59.763 44.000 0.00 0.00 0.00 2.59
275 276 5.237344 CGGAGAAGAAAATGTGATGTATCCC 59.763 44.000 0.00 0.00 0.00 3.85
277 278 6.484977 GGAGAAGAAAATGTGATGTATCCCTC 59.515 42.308 0.00 0.00 0.00 4.30
278 279 7.205515 AGAAGAAAATGTGATGTATCCCTCT 57.794 36.000 0.00 0.00 0.00 3.69
279 280 7.052873 AGAAGAAAATGTGATGTATCCCTCTG 58.947 38.462 0.00 0.00 0.00 3.35
280 281 6.566079 AGAAAATGTGATGTATCCCTCTGA 57.434 37.500 0.00 0.00 0.00 3.27
281 282 7.146715 AGAAAATGTGATGTATCCCTCTGAT 57.853 36.000 0.00 0.00 37.49 2.90
282 283 7.222872 AGAAAATGTGATGTATCCCTCTGATC 58.777 38.462 0.00 0.00 34.76 2.92
283 284 5.495926 AATGTGATGTATCCCTCTGATCC 57.504 43.478 0.00 0.00 34.76 3.36
284 285 2.893489 TGTGATGTATCCCTCTGATCCG 59.107 50.000 0.00 0.00 34.76 4.18
285 286 3.157881 GTGATGTATCCCTCTGATCCGA 58.842 50.000 0.00 0.00 34.76 4.55
286 287 3.766591 GTGATGTATCCCTCTGATCCGAT 59.233 47.826 0.00 0.00 34.76 4.18
287 288 4.019858 TGATGTATCCCTCTGATCCGATC 58.980 47.826 1.01 1.01 34.76 3.69
288 289 3.816398 TGTATCCCTCTGATCCGATCT 57.184 47.619 9.78 0.00 34.76 2.75
289 290 3.691575 TGTATCCCTCTGATCCGATCTC 58.308 50.000 9.78 0.00 34.76 2.75
290 291 2.230130 ATCCCTCTGATCCGATCTCC 57.770 55.000 9.78 0.00 0.00 3.71
291 292 0.250945 TCCCTCTGATCCGATCTCCG 60.251 60.000 9.78 0.00 38.18 4.63
301 302 1.367840 CGATCTCCGGGGATGGAAC 59.632 63.158 24.99 6.05 37.64 3.62
302 303 1.755384 GATCTCCGGGGATGGAACC 59.245 63.158 24.99 2.16 37.64 3.62
308 309 2.908796 GGGGATGGAACCGACTCC 59.091 66.667 0.00 0.00 35.88 3.85
309 310 2.499685 GGGATGGAACCGACTCCG 59.500 66.667 0.00 0.00 38.44 4.63
311 312 2.202892 GATGGAACCGACTCCGCC 60.203 66.667 0.00 0.00 38.44 6.13
313 314 2.311688 GATGGAACCGACTCCGCCAT 62.312 60.000 0.00 0.00 38.35 4.40
314 315 2.511600 GGAACCGACTCCGCCATG 60.512 66.667 0.00 0.00 0.00 3.66
315 316 2.511600 GAACCGACTCCGCCATGG 60.512 66.667 7.63 7.63 40.09 3.66
316 317 4.096003 AACCGACTCCGCCATGGG 62.096 66.667 15.13 3.37 38.76 4.00
319 320 3.550431 CGACTCCGCCATGGGGAT 61.550 66.667 29.29 14.43 43.10 3.85
320 321 2.427753 GACTCCGCCATGGGGATC 59.572 66.667 29.29 18.63 43.10 3.36
321 322 2.366837 ACTCCGCCATGGGGATCA 60.367 61.111 29.29 11.95 43.10 2.92
322 323 1.983119 GACTCCGCCATGGGGATCAA 61.983 60.000 29.29 10.97 43.10 2.57
323 324 1.228063 CTCCGCCATGGGGATCAAG 60.228 63.158 29.29 16.07 43.10 3.02
324 325 1.692395 TCCGCCATGGGGATCAAGA 60.692 57.895 29.29 14.73 39.75 3.02
325 326 1.227102 CCGCCATGGGGATCAAGAA 59.773 57.895 29.29 0.00 37.91 2.52
328 329 2.488891 CCGCCATGGGGATCAAGAAATA 60.489 50.000 29.29 0.00 37.91 1.40
332 333 4.413760 CCATGGGGATCAAGAAATAGCAT 58.586 43.478 2.85 0.00 35.59 3.79
333 334 4.219944 CCATGGGGATCAAGAAATAGCATG 59.780 45.833 2.85 0.00 35.59 4.06
335 336 5.329191 TGGGGATCAAGAAATAGCATGAT 57.671 39.130 0.00 0.00 35.33 2.45
336 337 6.452757 TGGGGATCAAGAAATAGCATGATA 57.547 37.500 0.00 0.00 32.90 2.15
337 338 6.851318 TGGGGATCAAGAAATAGCATGATAA 58.149 36.000 0.00 0.00 32.90 1.75
338 339 6.944290 TGGGGATCAAGAAATAGCATGATAAG 59.056 38.462 0.00 0.00 32.90 1.73
339 340 7.170965 GGGGATCAAGAAATAGCATGATAAGA 58.829 38.462 0.00 0.00 32.90 2.10
341 342 7.882271 GGGATCAAGAAATAGCATGATAAGAGT 59.118 37.037 0.00 0.00 32.90 3.24
342 343 8.719648 GGATCAAGAAATAGCATGATAAGAGTG 58.280 37.037 0.00 0.00 32.90 3.51
344 345 7.049754 TCAAGAAATAGCATGATAAGAGTGCA 58.950 34.615 0.00 0.00 41.19 4.57
346 347 5.469421 AGAAATAGCATGATAAGAGTGCAGC 59.531 40.000 0.00 0.00 41.19 5.25
347 348 4.620589 ATAGCATGATAAGAGTGCAGCT 57.379 40.909 0.00 0.00 41.19 4.24
350 351 2.287373 GCATGATAAGAGTGCAGCTCAC 59.713 50.000 15.59 7.88 46.47 3.51
357 358 3.171987 GTGCAGCTCACGTGATGG 58.828 61.111 20.40 9.72 35.76 3.51
359 360 2.046892 GCAGCTCACGTGATGGGT 60.047 61.111 20.40 11.32 0.00 4.51
360 361 2.393768 GCAGCTCACGTGATGGGTG 61.394 63.158 24.61 24.61 36.74 4.61
361 362 1.004560 CAGCTCACGTGATGGGTGT 60.005 57.895 20.40 0.00 36.76 4.16
365 366 1.005037 TCACGTGATGGGTGTGAGC 60.005 57.895 15.76 0.00 37.69 4.26
366 367 1.301637 CACGTGATGGGTGTGAGCA 60.302 57.895 10.90 0.00 35.66 4.26
368 369 2.393768 CGTGATGGGTGTGAGCAGC 61.394 63.158 0.00 0.00 41.99 5.25
374 375 2.352422 GGTGTGAGCAGCCATGGA 59.648 61.111 18.40 0.00 37.15 3.41
376 377 2.045634 TGTGAGCAGCCATGGAGC 60.046 61.111 18.40 18.64 0.00 4.70
377 378 2.045634 GTGAGCAGCCATGGAGCA 60.046 61.111 25.54 9.63 34.23 4.26
378 379 1.453379 GTGAGCAGCCATGGAGCAT 60.453 57.895 25.54 14.05 34.23 3.79
379 380 1.035932 GTGAGCAGCCATGGAGCATT 61.036 55.000 25.54 10.74 34.23 3.56
382 383 2.236766 GAGCAGCCATGGAGCATTATT 58.763 47.619 25.54 9.49 34.23 1.40
383 384 2.228343 GAGCAGCCATGGAGCATTATTC 59.772 50.000 25.54 13.65 34.23 1.75
384 385 1.068748 GCAGCCATGGAGCATTATTCG 60.069 52.381 18.40 0.00 34.23 3.34
385 386 1.068748 CAGCCATGGAGCATTATTCGC 60.069 52.381 18.40 0.00 34.23 4.70
386 387 0.953727 GCCATGGAGCATTATTCGCA 59.046 50.000 18.40 0.00 0.00 5.10
388 389 2.223782 GCCATGGAGCATTATTCGCAAA 60.224 45.455 18.40 0.00 0.00 3.68
389 390 3.635331 CCATGGAGCATTATTCGCAAAG 58.365 45.455 5.56 0.00 0.00 2.77
391 392 4.285292 CATGGAGCATTATTCGCAAAGAC 58.715 43.478 0.00 0.00 0.00 3.01
392 393 3.609853 TGGAGCATTATTCGCAAAGACT 58.390 40.909 0.00 0.00 0.00 3.24
393 394 3.623060 TGGAGCATTATTCGCAAAGACTC 59.377 43.478 0.00 0.00 0.00 3.36
394 395 3.302740 GGAGCATTATTCGCAAAGACTCG 60.303 47.826 0.00 0.00 0.00 4.18
395 396 2.609459 AGCATTATTCGCAAAGACTCGG 59.391 45.455 0.00 0.00 0.00 4.63
396 397 2.607635 GCATTATTCGCAAAGACTCGGA 59.392 45.455 0.00 0.00 0.00 4.55
397 398 3.063452 GCATTATTCGCAAAGACTCGGAA 59.937 43.478 0.00 0.00 0.00 4.30
398 399 4.436852 GCATTATTCGCAAAGACTCGGAAA 60.437 41.667 0.00 0.00 0.00 3.13
399 400 5.627172 CATTATTCGCAAAGACTCGGAAAA 58.373 37.500 0.00 0.00 0.00 2.29
400 401 5.873179 TTATTCGCAAAGACTCGGAAAAT 57.127 34.783 0.00 0.00 0.00 1.82
401 402 6.971527 TTATTCGCAAAGACTCGGAAAATA 57.028 33.333 0.00 0.00 0.00 1.40
402 403 5.873179 ATTCGCAAAGACTCGGAAAATAA 57.127 34.783 0.00 0.00 0.00 1.40
403 404 5.873179 TTCGCAAAGACTCGGAAAATAAT 57.127 34.783 0.00 0.00 0.00 1.28
404 405 6.971527 TTCGCAAAGACTCGGAAAATAATA 57.028 33.333 0.00 0.00 0.00 0.98
406 407 7.367159 TCGCAAAGACTCGGAAAATAATAAA 57.633 32.000 0.00 0.00 0.00 1.40
407 408 7.981142 TCGCAAAGACTCGGAAAATAATAAAT 58.019 30.769 0.00 0.00 0.00 1.40
408 409 8.120465 TCGCAAAGACTCGGAAAATAATAAATC 58.880 33.333 0.00 0.00 0.00 2.17
409 410 8.122952 CGCAAAGACTCGGAAAATAATAAATCT 58.877 33.333 0.00 0.00 0.00 2.40
410 411 9.226345 GCAAAGACTCGGAAAATAATAAATCTG 57.774 33.333 0.00 0.00 0.00 2.90
414 415 9.838339 AGACTCGGAAAATAATAAATCTGTGAT 57.162 29.630 0.00 0.00 0.00 3.06
415 416 9.869844 GACTCGGAAAATAATAAATCTGTGATG 57.130 33.333 0.00 0.00 0.00 3.07
416 417 8.840321 ACTCGGAAAATAATAAATCTGTGATGG 58.160 33.333 0.00 0.00 0.00 3.51
417 418 8.165239 TCGGAAAATAATAAATCTGTGATGGG 57.835 34.615 0.00 0.00 0.00 4.00
418 419 7.230510 TCGGAAAATAATAAATCTGTGATGGGG 59.769 37.037 0.00 0.00 0.00 4.96
419 420 7.014230 CGGAAAATAATAAATCTGTGATGGGGT 59.986 37.037 0.00 0.00 0.00 4.95
427 428 6.933514 AAATCTGTGATGGGGTAAAAATGT 57.066 33.333 0.00 0.00 0.00 2.71
428 429 5.920193 ATCTGTGATGGGGTAAAAATGTG 57.080 39.130 0.00 0.00 0.00 3.21
430 431 5.882040 TCTGTGATGGGGTAAAAATGTGTA 58.118 37.500 0.00 0.00 0.00 2.90
431 432 6.489603 TCTGTGATGGGGTAAAAATGTGTAT 58.510 36.000 0.00 0.00 0.00 2.29
432 433 6.376864 TCTGTGATGGGGTAAAAATGTGTATG 59.623 38.462 0.00 0.00 0.00 2.39
433 434 6.249192 TGTGATGGGGTAAAAATGTGTATGA 58.751 36.000 0.00 0.00 0.00 2.15
435 436 6.601613 GTGATGGGGTAAAAATGTGTATGAGA 59.398 38.462 0.00 0.00 0.00 3.27
436 437 7.285401 GTGATGGGGTAAAAATGTGTATGAGAT 59.715 37.037 0.00 0.00 0.00 2.75
438 439 7.403312 TGGGGTAAAAATGTGTATGAGATTG 57.597 36.000 0.00 0.00 0.00 2.67
439 440 7.178573 TGGGGTAAAAATGTGTATGAGATTGA 58.821 34.615 0.00 0.00 0.00 2.57
440 441 7.671819 TGGGGTAAAAATGTGTATGAGATTGAA 59.328 33.333 0.00 0.00 0.00 2.69
441 442 8.695456 GGGGTAAAAATGTGTATGAGATTGAAT 58.305 33.333 0.00 0.00 0.00 2.57
442 443 9.736023 GGGTAAAAATGTGTATGAGATTGAATC 57.264 33.333 0.00 0.00 0.00 2.52
448 449 8.585471 AATGTGTATGAGATTGAATCACCTTT 57.415 30.769 8.03 0.00 0.00 3.11
449 450 8.585471 ATGTGTATGAGATTGAATCACCTTTT 57.415 30.769 8.03 0.00 0.00 2.27
450 451 8.408043 TGTGTATGAGATTGAATCACCTTTTT 57.592 30.769 8.03 0.00 0.00 1.94
578 633 2.358737 GCAAGTCCACCGGTCCTG 60.359 66.667 2.59 0.00 0.00 3.86
580 635 3.637273 AAGTCCACCGGTCCTGCC 61.637 66.667 2.59 0.00 0.00 4.85
581 636 4.640690 AGTCCACCGGTCCTGCCT 62.641 66.667 2.59 0.00 34.25 4.75
582 637 4.083862 GTCCACCGGTCCTGCCTC 62.084 72.222 2.59 0.00 34.25 4.70
585 640 4.087892 CACCGGTCCTGCCTCCTG 62.088 72.222 2.59 0.00 34.25 3.86
590 645 2.435059 GTCCTGCCTCCTGCGTTC 60.435 66.667 0.00 0.00 45.60 3.95
591 646 3.706373 TCCTGCCTCCTGCGTTCC 61.706 66.667 0.00 0.00 45.60 3.62
592 647 4.785453 CCTGCCTCCTGCGTTCCC 62.785 72.222 0.00 0.00 45.60 3.97
594 649 3.249189 TGCCTCCTGCGTTCCCTT 61.249 61.111 0.00 0.00 45.60 3.95
595 650 2.436824 GCCTCCTGCGTTCCCTTC 60.437 66.667 0.00 0.00 0.00 3.46
596 651 2.269241 CCTCCTGCGTTCCCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
597 652 2.294078 CCTCCTGCGTTCCCTTCCT 61.294 63.158 0.00 0.00 0.00 3.36
598 653 1.219393 CTCCTGCGTTCCCTTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
599 654 2.125512 CCTGCGTTCCCTTCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
600 655 2.125512 CTGCGTTCCCTTCCTCGG 60.126 66.667 0.00 0.00 0.00 4.63
601 656 4.388499 TGCGTTCCCTTCCTCGGC 62.388 66.667 0.00 0.00 0.00 5.54
660 7444 3.743636 TGACGCCACTCGATCGCA 61.744 61.111 11.09 0.00 41.67 5.10
665 7449 2.125952 CCACTCGATCGCAGTGCA 60.126 61.111 27.73 2.61 40.10 4.57
776 7608 0.491823 TTCACCTCCTCCTTCAGGGA 59.508 55.000 0.00 0.00 43.67 4.20
952 7810 4.394712 CCCGTGCTCCACCCTCAC 62.395 72.222 0.00 0.00 0.00 3.51
1208 8073 1.800681 GTACAAATGAGGCGGTGGC 59.199 57.895 0.00 0.00 38.90 5.01
1478 8343 6.420913 ACCCAACATCAGGACATATACTAC 57.579 41.667 0.00 0.00 0.00 2.73
1672 8537 2.769893 CAAAGGGCCAAAAACCTGATG 58.230 47.619 6.18 0.00 37.13 3.07
1697 8562 6.366877 GTCGTCTCCTACTCTACTATGCTTAG 59.633 46.154 5.13 5.13 0.00 2.18
1832 8697 1.453155 AAACGTGGACTGATGGATGC 58.547 50.000 0.00 0.00 0.00 3.91
1988 8853 4.647564 ATCAAGGAGTTTCACCTGACAT 57.352 40.909 0.00 0.00 37.85 3.06
1991 8856 4.593206 TCAAGGAGTTTCACCTGACATAGT 59.407 41.667 0.00 0.00 37.85 2.12
2007 8872 5.105269 TGACATAGTTGTTTACCGATGCCTA 60.105 40.000 0.00 0.00 35.79 3.93
2039 8904 4.654915 TCTTGCTCTCATGGTGATTTTGA 58.345 39.130 0.00 0.00 0.00 2.69
2285 9151 6.379703 AGAGTACTTGATGCTATGAAGTCTGT 59.620 38.462 0.00 0.96 37.82 3.41
2390 9256 5.299279 GTCTTTTCAGGGAAATGTCACTCAA 59.701 40.000 0.00 0.00 34.22 3.02
2437 9303 6.569127 TGTACAACATTATACTCCATGGGT 57.431 37.500 13.02 11.37 0.00 4.51
2444 9310 7.790782 ACATTATACTCCATGGGTTGTTTTT 57.209 32.000 13.02 1.31 0.00 1.94
2474 9340 5.221322 GGAGAACAGTTTCTGCAAAGGAAAT 60.221 40.000 3.27 0.00 46.69 2.17
3291 10303 2.231964 GGATTCATGCAACAAGAAGGCA 59.768 45.455 0.00 0.00 42.43 4.75
3368 10385 4.081406 AGATGGTTGATGCACTGCTTTTA 58.919 39.130 1.98 0.00 0.00 1.52
3526 10550 4.526262 TGCATGTAAACCTAATTTGCCACT 59.474 37.500 0.00 0.00 32.27 4.00
3576 10600 4.605183 ACCTCTCTCAACAGTAGTGCTAT 58.395 43.478 0.00 0.00 0.00 2.97
3658 10995 7.222999 GCTAGTGCACTTTAGTTAGTATTCTGG 59.777 40.741 27.06 0.00 39.41 3.86
3742 11079 8.109705 TGACTGTAAAAATACATTGCAGATGT 57.890 30.769 15.56 15.56 41.31 3.06
3745 11082 8.796475 ACTGTAAAAATACATTGCAGATGTCTT 58.204 29.630 14.94 10.55 41.31 3.01
3748 11085 9.722056 GTAAAAATACATTGCAGATGTCTTAGG 57.278 33.333 14.94 0.00 33.76 2.69
3749 11086 7.944729 AAAATACATTGCAGATGTCTTAGGT 57.055 32.000 14.94 0.00 33.76 3.08
3750 11087 7.559590 AAATACATTGCAGATGTCTTAGGTC 57.440 36.000 14.94 0.00 33.76 3.85
3751 11088 4.833478 ACATTGCAGATGTCTTAGGTCT 57.167 40.909 8.21 0.00 0.00 3.85
3752 11089 4.764172 ACATTGCAGATGTCTTAGGTCTC 58.236 43.478 8.21 0.00 0.00 3.36
3753 11090 4.469227 ACATTGCAGATGTCTTAGGTCTCT 59.531 41.667 8.21 0.00 0.00 3.10
3754 11091 4.727507 TTGCAGATGTCTTAGGTCTCTC 57.272 45.455 0.00 0.00 0.00 3.20
3755 11092 3.027412 TGCAGATGTCTTAGGTCTCTCC 58.973 50.000 0.00 0.00 0.00 3.71
3831 11200 1.226974 GCGTGAAGGATCAGCGCTA 60.227 57.895 10.99 0.00 44.82 4.26
3856 11232 1.338579 GCCATCGGGATTCTCATCTCC 60.339 57.143 0.00 0.00 35.59 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.863049 GCGAAAGTGATAAACATTCATTCATTT 58.137 29.630 0.00 0.00 36.49 2.32
15 16 8.028354 TGCGAAAGTGATAAACATTCATTCATT 58.972 29.630 0.00 0.00 36.49 2.57
16 17 7.537715 TGCGAAAGTGATAAACATTCATTCAT 58.462 30.769 0.00 0.00 36.49 2.57
18 19 7.795431 TTGCGAAAGTGATAAACATTCATTC 57.205 32.000 0.00 0.00 36.49 2.67
19 20 7.867403 AGTTTGCGAAAGTGATAAACATTCATT 59.133 29.630 0.00 0.00 36.49 2.57
20 21 7.370383 AGTTTGCGAAAGTGATAAACATTCAT 58.630 30.769 0.00 0.00 36.49 2.57
21 22 6.734137 AGTTTGCGAAAGTGATAAACATTCA 58.266 32.000 0.00 0.00 36.49 2.57
23 24 7.425606 AGAAGTTTGCGAAAGTGATAAACATT 58.574 30.769 0.00 0.00 34.58 2.71
24 25 6.970484 AGAAGTTTGCGAAAGTGATAAACAT 58.030 32.000 0.00 0.00 34.58 2.71
25 26 6.371809 AGAAGTTTGCGAAAGTGATAAACA 57.628 33.333 0.00 0.00 34.58 2.83
26 27 8.227791 TGATAGAAGTTTGCGAAAGTGATAAAC 58.772 33.333 0.00 0.00 0.00 2.01
27 28 8.317891 TGATAGAAGTTTGCGAAAGTGATAAA 57.682 30.769 0.00 0.00 0.00 1.40
28 29 7.899178 TGATAGAAGTTTGCGAAAGTGATAA 57.101 32.000 0.00 0.00 0.00 1.75
29 30 7.899178 TTGATAGAAGTTTGCGAAAGTGATA 57.101 32.000 0.00 0.00 0.00 2.15
30 31 6.801539 TTGATAGAAGTTTGCGAAAGTGAT 57.198 33.333 0.00 0.00 0.00 3.06
31 32 6.612247 TTTGATAGAAGTTTGCGAAAGTGA 57.388 33.333 0.00 0.00 0.00 3.41
33 34 7.648142 TGAATTTGATAGAAGTTTGCGAAAGT 58.352 30.769 0.00 0.00 0.00 2.66
35 36 8.296000 TCATGAATTTGATAGAAGTTTGCGAAA 58.704 29.630 0.00 0.00 0.00 3.46
36 37 7.815641 TCATGAATTTGATAGAAGTTTGCGAA 58.184 30.769 0.00 0.00 0.00 4.70
37 38 7.376435 TCATGAATTTGATAGAAGTTTGCGA 57.624 32.000 0.00 0.00 0.00 5.10
91 92 9.489393 CGTAATTGAAAAGATTCATCGATTTGA 57.511 29.630 0.00 0.00 44.70 2.69
92 93 8.255143 GCGTAATTGAAAAGATTCATCGATTTG 58.745 33.333 0.00 0.00 44.70 2.32
94 95 7.471721 TGCGTAATTGAAAAGATTCATCGATT 58.528 30.769 0.00 0.00 44.70 3.34
96 97 6.415798 TGCGTAATTGAAAAGATTCATCGA 57.584 33.333 0.00 0.00 44.70 3.59
99 100 8.816640 AAGTTTGCGTAATTGAAAAGATTCAT 57.183 26.923 0.00 0.00 44.70 2.57
100 101 8.641499 AAAGTTTGCGTAATTGAAAAGATTCA 57.359 26.923 0.00 0.00 43.70 2.57
103 104 8.878769 ACAAAAAGTTTGCGTAATTGAAAAGAT 58.121 25.926 3.95 0.00 0.00 2.40
104 105 8.245701 ACAAAAAGTTTGCGTAATTGAAAAGA 57.754 26.923 3.95 0.00 0.00 2.52
105 106 8.873242 AACAAAAAGTTTGCGTAATTGAAAAG 57.127 26.923 3.95 0.00 37.03 2.27
114 115 7.169982 CCATGGATTTAACAAAAAGTTTGCGTA 59.830 33.333 5.56 0.00 41.64 4.42
115 116 6.018343 CCATGGATTTAACAAAAAGTTTGCGT 60.018 34.615 5.56 0.00 41.64 5.24
117 118 7.489574 TCCATGGATTTAACAAAAAGTTTGC 57.510 32.000 11.44 0.00 41.64 3.68
144 145 7.171337 GCTGATCACTTGCCAAAAGAATAAAAA 59.829 33.333 0.00 0.00 0.00 1.94
145 146 6.646240 GCTGATCACTTGCCAAAAGAATAAAA 59.354 34.615 0.00 0.00 0.00 1.52
146 147 6.015180 AGCTGATCACTTGCCAAAAGAATAAA 60.015 34.615 2.04 0.00 0.00 1.40
147 148 5.477984 AGCTGATCACTTGCCAAAAGAATAA 59.522 36.000 2.04 0.00 0.00 1.40
149 150 3.830755 AGCTGATCACTTGCCAAAAGAAT 59.169 39.130 2.04 0.00 0.00 2.40
151 152 2.867624 AGCTGATCACTTGCCAAAAGA 58.132 42.857 2.04 0.00 0.00 2.52
152 153 3.314553 CAAGCTGATCACTTGCCAAAAG 58.685 45.455 18.62 0.00 38.23 2.27
153 154 2.036217 CCAAGCTGATCACTTGCCAAAA 59.964 45.455 22.35 0.00 42.57 2.44
154 155 1.614903 CCAAGCTGATCACTTGCCAAA 59.385 47.619 22.35 0.00 42.57 3.28
155 156 1.250328 CCAAGCTGATCACTTGCCAA 58.750 50.000 22.35 0.00 42.57 4.52
158 159 0.109412 GCACCAAGCTGATCACTTGC 60.109 55.000 22.35 12.92 42.57 4.01
159 160 1.241165 TGCACCAAGCTGATCACTTG 58.759 50.000 21.47 21.47 45.94 3.16
160 161 1.816835 CATGCACCAAGCTGATCACTT 59.183 47.619 0.00 0.00 45.94 3.16
161 162 1.460504 CATGCACCAAGCTGATCACT 58.539 50.000 0.00 0.00 45.94 3.41
162 163 0.454600 CCATGCACCAAGCTGATCAC 59.545 55.000 0.00 0.00 45.94 3.06
163 164 0.328926 TCCATGCACCAAGCTGATCA 59.671 50.000 0.00 0.00 45.94 2.92
164 165 1.466856 TTCCATGCACCAAGCTGATC 58.533 50.000 0.00 0.00 45.94 2.92
166 167 1.546923 CAATTCCATGCACCAAGCTGA 59.453 47.619 0.00 0.00 45.94 4.26
168 169 1.547372 GTCAATTCCATGCACCAAGCT 59.453 47.619 0.00 0.00 45.94 3.74
170 171 1.541147 ACGTCAATTCCATGCACCAAG 59.459 47.619 0.00 0.00 0.00 3.61
172 173 1.164411 GACGTCAATTCCATGCACCA 58.836 50.000 11.55 0.00 0.00 4.17
173 174 0.451783 GGACGTCAATTCCATGCACC 59.548 55.000 18.91 0.00 32.82 5.01
174 175 0.451783 GGGACGTCAATTCCATGCAC 59.548 55.000 18.91 0.00 34.45 4.57
175 176 0.327924 AGGGACGTCAATTCCATGCA 59.672 50.000 18.91 0.00 34.45 3.96
177 178 0.734889 GCAGGGACGTCAATTCCATG 59.265 55.000 18.91 9.23 45.82 3.66
179 180 1.002624 GGCAGGGACGTCAATTCCA 60.003 57.895 18.91 0.00 34.45 3.53
180 181 2.106683 CGGCAGGGACGTCAATTCC 61.107 63.158 18.91 9.24 0.00 3.01
182 183 2.746277 GCGGCAGGGACGTCAATT 60.746 61.111 18.91 0.00 35.91 2.32
184 185 4.980805 GTGCGGCAGGGACGTCAA 62.981 66.667 18.91 0.00 35.91 3.18
205 206 1.966493 GCCACATGTAGCGACCAACG 61.966 60.000 0.00 0.00 45.66 4.10
206 207 0.953471 TGCCACATGTAGCGACCAAC 60.953 55.000 11.67 0.00 0.00 3.77
208 209 0.250510 TTTGCCACATGTAGCGACCA 60.251 50.000 11.67 0.00 0.00 4.02
209 210 0.878416 TTTTGCCACATGTAGCGACC 59.122 50.000 11.67 0.00 0.00 4.79
210 211 2.697431 TTTTTGCCACATGTAGCGAC 57.303 45.000 11.67 0.00 0.00 5.19
211 212 3.932545 AATTTTTGCCACATGTAGCGA 57.067 38.095 11.67 6.95 0.00 4.93
212 213 4.310675 CAAATTTTTGCCACATGTAGCG 57.689 40.909 11.67 0.00 0.00 4.26
224 225 2.208431 TGCAACTCGGGCAAATTTTTG 58.792 42.857 0.00 0.00 38.54 2.44
225 226 2.611225 TGCAACTCGGGCAAATTTTT 57.389 40.000 0.00 0.00 38.54 1.94
240 241 0.756294 TCTTCTCCGGTGAGTTGCAA 59.244 50.000 6.29 0.00 39.75 4.08
243 244 3.815401 ACATTTTCTTCTCCGGTGAGTTG 59.185 43.478 6.29 2.14 39.75 3.16
245 246 3.071023 TCACATTTTCTTCTCCGGTGAGT 59.929 43.478 6.29 0.00 39.75 3.41
246 247 3.664107 TCACATTTTCTTCTCCGGTGAG 58.336 45.455 6.29 0.91 40.17 3.51
247 248 3.762407 TCACATTTTCTTCTCCGGTGA 57.238 42.857 0.00 0.06 0.00 4.02
248 249 3.753272 ACATCACATTTTCTTCTCCGGTG 59.247 43.478 0.00 0.00 0.00 4.94
251 252 5.237344 GGGATACATCACATTTTCTTCTCCG 59.763 44.000 0.00 0.00 39.74 4.63
252 253 6.360618 AGGGATACATCACATTTTCTTCTCC 58.639 40.000 0.00 0.00 39.74 3.71
267 268 4.277476 GAGATCGGATCAGAGGGATACAT 58.723 47.826 19.47 0.00 36.56 2.29
268 269 3.562393 GGAGATCGGATCAGAGGGATACA 60.562 52.174 19.47 0.00 36.56 2.29
269 270 3.020984 GGAGATCGGATCAGAGGGATAC 58.979 54.545 19.47 0.00 36.00 2.24
270 271 2.356227 CGGAGATCGGATCAGAGGGATA 60.356 54.545 19.47 0.00 36.00 2.59
271 272 1.615651 CGGAGATCGGATCAGAGGGAT 60.616 57.143 19.47 0.00 39.53 3.85
272 273 0.250945 CGGAGATCGGATCAGAGGGA 60.251 60.000 19.47 0.00 34.75 4.20
273 274 2.262183 CGGAGATCGGATCAGAGGG 58.738 63.158 19.47 1.26 34.75 4.30
283 284 1.367840 GTTCCATCCCCGGAGATCG 59.632 63.158 0.73 0.00 36.12 3.69
284 285 1.755384 GGTTCCATCCCCGGAGATC 59.245 63.158 0.73 0.00 36.12 2.75
285 286 2.140792 CGGTTCCATCCCCGGAGAT 61.141 63.158 0.73 0.00 40.54 2.75
286 287 2.762459 CGGTTCCATCCCCGGAGA 60.762 66.667 0.73 0.00 40.54 3.71
287 288 2.762459 TCGGTTCCATCCCCGGAG 60.762 66.667 0.73 0.00 44.32 4.63
288 289 3.078836 GTCGGTTCCATCCCCGGA 61.079 66.667 0.73 0.00 44.32 5.14
289 290 3.081409 AGTCGGTTCCATCCCCGG 61.081 66.667 0.00 0.00 44.32 5.73
290 291 2.499685 GAGTCGGTTCCATCCCCG 59.500 66.667 0.00 0.00 45.55 5.73
291 292 2.908796 GGAGTCGGTTCCATCCCC 59.091 66.667 1.80 0.00 37.20 4.81
292 293 2.499685 CGGAGTCGGTTCCATCCC 59.500 66.667 6.87 0.00 37.05 3.85
293 294 2.202892 GCGGAGTCGGTTCCATCC 60.203 66.667 6.87 0.00 37.05 3.51
294 295 2.202892 GGCGGAGTCGGTTCCATC 60.203 66.667 6.87 0.00 37.05 3.51
296 297 3.000819 ATGGCGGAGTCGGTTCCA 61.001 61.111 6.87 0.00 37.05 3.53
297 298 2.511600 CATGGCGGAGTCGGTTCC 60.512 66.667 0.00 0.00 36.79 3.62
298 299 2.511600 CCATGGCGGAGTCGGTTC 60.512 66.667 0.00 0.00 36.56 3.62
299 300 4.096003 CCCATGGCGGAGTCGGTT 62.096 66.667 6.09 0.00 36.56 4.44
302 303 3.521529 GATCCCCATGGCGGAGTCG 62.522 68.421 21.88 2.10 36.56 4.18
303 304 1.983119 TTGATCCCCATGGCGGAGTC 61.983 60.000 21.88 18.63 36.56 3.36
304 305 1.987807 CTTGATCCCCATGGCGGAGT 61.988 60.000 21.88 13.00 36.56 3.85
305 306 1.228063 CTTGATCCCCATGGCGGAG 60.228 63.158 21.88 9.07 36.56 4.63
307 308 0.395586 TTTCTTGATCCCCATGGCGG 60.396 55.000 6.09 9.67 0.00 6.13
308 309 1.696063 ATTTCTTGATCCCCATGGCG 58.304 50.000 6.09 0.00 0.00 5.69
309 310 2.560105 GCTATTTCTTGATCCCCATGGC 59.440 50.000 6.09 0.00 0.00 4.40
311 312 5.074804 TCATGCTATTTCTTGATCCCCATG 58.925 41.667 0.00 0.00 0.00 3.66
313 314 4.794311 TCATGCTATTTCTTGATCCCCA 57.206 40.909 0.00 0.00 0.00 4.96
314 315 7.170965 TCTTATCATGCTATTTCTTGATCCCC 58.829 38.462 0.00 0.00 34.19 4.81
315 316 7.882271 ACTCTTATCATGCTATTTCTTGATCCC 59.118 37.037 0.00 0.00 34.19 3.85
316 317 8.719648 CACTCTTATCATGCTATTTCTTGATCC 58.280 37.037 0.00 0.00 34.19 3.36
317 318 8.229137 GCACTCTTATCATGCTATTTCTTGATC 58.771 37.037 0.00 0.00 36.40 2.92
318 319 7.718314 TGCACTCTTATCATGCTATTTCTTGAT 59.282 33.333 0.00 0.00 40.13 2.57
319 320 7.049754 TGCACTCTTATCATGCTATTTCTTGA 58.950 34.615 0.00 0.00 40.13 3.02
320 321 7.255491 TGCACTCTTATCATGCTATTTCTTG 57.745 36.000 0.00 0.00 40.13 3.02
321 322 6.017275 GCTGCACTCTTATCATGCTATTTCTT 60.017 38.462 0.00 0.00 40.13 2.52
322 323 5.469421 GCTGCACTCTTATCATGCTATTTCT 59.531 40.000 0.00 0.00 40.13 2.52
323 324 5.469421 AGCTGCACTCTTATCATGCTATTTC 59.531 40.000 1.02 0.00 40.13 2.17
324 325 5.374921 AGCTGCACTCTTATCATGCTATTT 58.625 37.500 1.02 0.00 40.13 1.40
325 326 4.970711 AGCTGCACTCTTATCATGCTATT 58.029 39.130 1.02 0.00 40.13 1.73
328 329 2.169978 TGAGCTGCACTCTTATCATGCT 59.830 45.455 14.60 4.05 46.41 3.79
332 333 1.546029 ACGTGAGCTGCACTCTTATCA 59.454 47.619 14.60 0.00 46.41 2.15
333 334 1.923204 CACGTGAGCTGCACTCTTATC 59.077 52.381 10.90 0.00 46.41 1.75
335 336 0.958822 TCACGTGAGCTGCACTCTTA 59.041 50.000 15.76 0.00 46.41 2.10
336 337 0.319728 ATCACGTGAGCTGCACTCTT 59.680 50.000 24.41 0.00 46.41 2.85
337 338 0.389556 CATCACGTGAGCTGCACTCT 60.390 55.000 24.41 0.00 46.41 3.24
338 339 1.357258 CCATCACGTGAGCTGCACTC 61.357 60.000 24.41 8.75 45.49 3.51
339 340 1.375140 CCATCACGTGAGCTGCACT 60.375 57.895 24.41 1.61 45.49 4.40
341 342 2.046988 CCCATCACGTGAGCTGCA 60.047 61.111 24.41 0.00 0.00 4.41
342 343 2.046892 ACCCATCACGTGAGCTGC 60.047 61.111 24.41 0.00 0.00 5.25
344 345 1.004560 CACACCCATCACGTGAGCT 60.005 57.895 24.41 4.95 35.17 4.09
347 348 1.005037 GCTCACACCCATCACGTGA 60.005 57.895 22.48 22.48 37.33 4.35
350 351 2.393768 GCTGCTCACACCCATCACG 61.394 63.158 0.00 0.00 0.00 4.35
351 352 2.042831 GGCTGCTCACACCCATCAC 61.043 63.158 0.00 0.00 0.00 3.06
352 353 1.855441 ATGGCTGCTCACACCCATCA 61.855 55.000 0.00 0.00 37.67 3.07
354 355 1.379443 CATGGCTGCTCACACCCAT 60.379 57.895 0.00 0.00 42.03 4.00
356 357 2.753043 CCATGGCTGCTCACACCC 60.753 66.667 0.00 0.00 0.00 4.61
357 358 1.748122 CTCCATGGCTGCTCACACC 60.748 63.158 6.96 0.00 0.00 4.16
359 360 2.045634 GCTCCATGGCTGCTCACA 60.046 61.111 18.35 0.00 0.00 3.58
360 361 1.035932 AATGCTCCATGGCTGCTCAC 61.036 55.000 23.46 4.03 0.00 3.51
361 362 0.547553 TAATGCTCCATGGCTGCTCA 59.452 50.000 23.46 10.93 0.00 4.26
364 365 1.068748 CGAATAATGCTCCATGGCTGC 60.069 52.381 18.67 18.67 0.00 5.25
365 366 1.068748 GCGAATAATGCTCCATGGCTG 60.069 52.381 6.96 3.33 0.00 4.85
366 367 1.242076 GCGAATAATGCTCCATGGCT 58.758 50.000 6.96 0.00 0.00 4.75
368 369 3.316029 TCTTTGCGAATAATGCTCCATGG 59.684 43.478 4.97 4.97 0.00 3.66
369 370 4.036027 AGTCTTTGCGAATAATGCTCCATG 59.964 41.667 0.00 0.00 0.00 3.66
370 371 4.202441 AGTCTTTGCGAATAATGCTCCAT 58.798 39.130 0.00 0.00 0.00 3.41
371 372 3.609853 AGTCTTTGCGAATAATGCTCCA 58.390 40.909 0.00 0.00 0.00 3.86
372 373 3.302740 CGAGTCTTTGCGAATAATGCTCC 60.303 47.826 0.00 0.00 0.00 4.70
373 374 3.302740 CCGAGTCTTTGCGAATAATGCTC 60.303 47.826 0.00 0.00 0.00 4.26
374 375 2.609459 CCGAGTCTTTGCGAATAATGCT 59.391 45.455 0.00 0.00 0.00 3.79
376 377 4.857871 TTCCGAGTCTTTGCGAATAATG 57.142 40.909 0.00 0.00 0.00 1.90
377 378 5.873179 TTTTCCGAGTCTTTGCGAATAAT 57.127 34.783 0.00 0.00 0.00 1.28
378 379 5.873179 ATTTTCCGAGTCTTTGCGAATAA 57.127 34.783 0.00 0.00 0.00 1.40
379 380 6.971527 TTATTTTCCGAGTCTTTGCGAATA 57.028 33.333 0.00 0.00 0.00 1.75
382 383 6.971527 TTATTATTTTCCGAGTCTTTGCGA 57.028 33.333 0.00 0.00 0.00 5.10
383 384 8.122952 AGATTTATTATTTTCCGAGTCTTTGCG 58.877 33.333 0.00 0.00 0.00 4.85
384 385 9.226345 CAGATTTATTATTTTCCGAGTCTTTGC 57.774 33.333 0.00 0.00 0.00 3.68
388 389 9.838339 ATCACAGATTTATTATTTTCCGAGTCT 57.162 29.630 0.00 0.00 0.00 3.24
389 390 9.869844 CATCACAGATTTATTATTTTCCGAGTC 57.130 33.333 0.00 0.00 0.00 3.36
391 392 8.292448 CCCATCACAGATTTATTATTTTCCGAG 58.708 37.037 0.00 0.00 0.00 4.63
392 393 7.230510 CCCCATCACAGATTTATTATTTTCCGA 59.769 37.037 0.00 0.00 0.00 4.55
393 394 7.014230 ACCCCATCACAGATTTATTATTTTCCG 59.986 37.037 0.00 0.00 0.00 4.30
394 395 8.250143 ACCCCATCACAGATTTATTATTTTCC 57.750 34.615 0.00 0.00 0.00 3.13
401 402 9.045745 ACATTTTTACCCCATCACAGATTTATT 57.954 29.630 0.00 0.00 0.00 1.40
402 403 8.477256 CACATTTTTACCCCATCACAGATTTAT 58.523 33.333 0.00 0.00 0.00 1.40
403 404 7.453126 ACACATTTTTACCCCATCACAGATTTA 59.547 33.333 0.00 0.00 0.00 1.40
404 405 6.269769 ACACATTTTTACCCCATCACAGATTT 59.730 34.615 0.00 0.00 0.00 2.17
406 407 5.332743 ACACATTTTTACCCCATCACAGAT 58.667 37.500 0.00 0.00 0.00 2.90
407 408 4.735369 ACACATTTTTACCCCATCACAGA 58.265 39.130 0.00 0.00 0.00 3.41
408 409 6.376864 TCATACACATTTTTACCCCATCACAG 59.623 38.462 0.00 0.00 0.00 3.66
409 410 6.249192 TCATACACATTTTTACCCCATCACA 58.751 36.000 0.00 0.00 0.00 3.58
410 411 6.601613 TCTCATACACATTTTTACCCCATCAC 59.398 38.462 0.00 0.00 0.00 3.06
414 415 7.178573 TCAATCTCATACACATTTTTACCCCA 58.821 34.615 0.00 0.00 0.00 4.96
415 416 7.639113 TCAATCTCATACACATTTTTACCCC 57.361 36.000 0.00 0.00 0.00 4.95
416 417 9.736023 GATTCAATCTCATACACATTTTTACCC 57.264 33.333 0.00 0.00 0.00 3.69
421 422 8.585471 AGGTGATTCAATCTCATACACATTTT 57.415 30.769 0.00 0.00 0.00 1.82
423 424 8.585471 AAAGGTGATTCAATCTCATACACATT 57.415 30.769 0.00 0.00 33.51 2.71
424 425 8.585471 AAAAGGTGATTCAATCTCATACACAT 57.415 30.769 0.00 0.00 0.00 3.21
425 426 8.408043 AAAAAGGTGATTCAATCTCATACACA 57.592 30.769 0.00 0.00 0.00 3.72
448 449 2.106566 TGCTCCCTTTCAAGCACAAAA 58.893 42.857 0.00 0.00 43.30 2.44
449 450 1.774110 TGCTCCCTTTCAAGCACAAA 58.226 45.000 0.00 0.00 43.30 2.83
450 451 3.511362 TGCTCCCTTTCAAGCACAA 57.489 47.368 0.00 0.00 43.30 3.33
453 454 2.101249 CACTTTTGCTCCCTTTCAAGCA 59.899 45.455 0.00 0.00 46.31 3.91
455 456 2.747436 GCACTTTTGCTCCCTTTCAAG 58.253 47.619 0.00 0.00 46.17 3.02
456 457 2.888834 GCACTTTTGCTCCCTTTCAA 57.111 45.000 0.00 0.00 46.17 2.69
560 615 3.637273 AGGACCGGTGGACTTGCC 61.637 66.667 14.63 4.60 37.10 4.52
561 616 2.358737 CAGGACCGGTGGACTTGC 60.359 66.667 14.63 0.00 0.00 4.01
562 617 2.358737 GCAGGACCGGTGGACTTG 60.359 66.667 14.63 5.53 0.00 3.16
564 619 4.640690 AGGCAGGACCGGTGGACT 62.641 66.667 14.63 5.79 46.52 3.85
565 620 4.083862 GAGGCAGGACCGGTGGAC 62.084 72.222 14.63 2.79 46.52 4.02
572 627 3.959991 GAACGCAGGAGGCAGGACC 62.960 68.421 0.00 0.00 45.17 4.46
573 628 2.435059 GAACGCAGGAGGCAGGAC 60.435 66.667 0.00 0.00 45.17 3.85
574 629 3.706373 GGAACGCAGGAGGCAGGA 61.706 66.667 0.00 0.00 45.17 3.86
575 630 4.785453 GGGAACGCAGGAGGCAGG 62.785 72.222 0.00 0.00 45.17 4.85
578 633 2.436824 GAAGGGAACGCAGGAGGC 60.437 66.667 0.00 0.00 39.90 4.70
580 635 1.219393 GAGGAAGGGAACGCAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
581 636 2.646175 CGAGGAAGGGAACGCAGGA 61.646 63.158 0.00 0.00 0.00 3.86
582 637 2.125512 CGAGGAAGGGAACGCAGG 60.126 66.667 0.00 0.00 0.00 4.85
583 638 2.125512 CCGAGGAAGGGAACGCAG 60.126 66.667 0.00 0.00 0.00 5.18
584 639 4.388499 GCCGAGGAAGGGAACGCA 62.388 66.667 0.00 0.00 0.00 5.24
586 641 4.814294 CCGCCGAGGAAGGGAACG 62.814 72.222 0.00 0.00 45.00 3.95
660 7444 2.210013 TCCGCTGAAGAGGTGCACT 61.210 57.895 17.98 2.27 36.33 4.40
665 7449 3.303135 TGCGTCCGCTGAAGAGGT 61.303 61.111 13.31 0.00 42.51 3.85
869 7727 1.064783 GCTTGGCCTAGCAATTCGC 59.935 57.895 30.78 5.45 40.89 4.70
1153 8018 1.407989 CCCCTTGAGGAGATTGCTGAC 60.408 57.143 0.00 0.00 38.24 3.51
1208 8073 4.020617 TCCCGTGGAGCAGCAAGG 62.021 66.667 0.00 0.00 0.00 3.61
1222 8087 0.035458 CAGTCCAGTTCAGGTGTCCC 59.965 60.000 0.00 0.00 0.00 4.46
1478 8343 3.198635 AGCGGAATATCCATGTATCAGGG 59.801 47.826 0.00 0.00 35.91 4.45
1672 8537 4.634199 AGCATAGTAGAGTAGGAGACGAC 58.366 47.826 0.00 0.00 36.03 4.34
1697 8562 0.461339 TCCTTCTTTCGCATACCCGC 60.461 55.000 0.00 0.00 0.00 6.13
1832 8697 1.004610 CTTCGAACATGTGCATAGCCG 60.005 52.381 4.29 0.00 0.00 5.52
1988 8853 5.186409 AGAACTAGGCATCGGTAAACAACTA 59.814 40.000 0.00 0.00 0.00 2.24
1991 8856 4.250464 CAGAACTAGGCATCGGTAAACAA 58.750 43.478 0.00 0.00 0.00 2.83
2007 8872 2.050144 TGAGAGCAAGAACCCAGAACT 58.950 47.619 0.00 0.00 0.00 3.01
2039 8904 5.776716 TCAGAAATCAATTCCTTGGCTTTCT 59.223 36.000 9.21 9.21 40.92 2.52
2285 9151 1.304381 GCATCAGGTTGGAGGCCAA 60.304 57.895 5.01 0.00 41.69 4.52
2430 9296 1.272212 CCGGAGAAAAACAACCCATGG 59.728 52.381 4.14 4.14 0.00 3.66
2431 9297 1.272212 CCCGGAGAAAAACAACCCATG 59.728 52.381 0.73 0.00 0.00 3.66
2444 9310 1.618837 CAGAAACTGTTCTCCCGGAGA 59.381 52.381 13.54 13.54 42.45 3.71
2474 9340 5.469760 CCACTTGCATTCATCGTATGGAATA 59.530 40.000 0.00 0.00 33.70 1.75
2492 9358 1.315257 GCCCACTGGTATGCCACTTG 61.315 60.000 0.00 0.00 40.46 3.16
3291 10303 3.144657 TGTGTTGCACTCCTTGATCAT 57.855 42.857 0.00 0.00 35.11 2.45
3368 10385 8.554490 AATAGTAACTATCATCAACAGAGGGT 57.446 34.615 0.00 0.00 0.00 4.34
3515 10539 6.101150 ACCAGGATATCACTAGTGGCAAATTA 59.899 38.462 22.48 1.68 0.00 1.40
3627 10923 2.168496 ACTAAAGTGCACTAGCGGAGA 58.832 47.619 22.01 0.00 46.23 3.71
3658 10995 6.148948 TCAAAACATGCTTAGCACATAACAC 58.851 36.000 9.82 0.00 43.04 3.32
3742 11079 4.581309 TTCTTACCGGAGAGACCTAAGA 57.419 45.455 9.46 6.39 35.22 2.10
3745 11082 7.909485 AAATATTTCTTACCGGAGAGACCTA 57.091 36.000 9.46 5.38 36.31 3.08
3746 11083 6.809976 AAATATTTCTTACCGGAGAGACCT 57.190 37.500 9.46 3.27 36.31 3.85
3747 11084 6.927936 GGTAAATATTTCTTACCGGAGAGACC 59.072 42.308 9.46 2.59 39.11 3.85
3748 11085 7.943413 GGTAAATATTTCTTACCGGAGAGAC 57.057 40.000 9.46 0.00 39.11 3.36
3831 11200 2.329267 TGAGAATCCCGATGGCAGTAT 58.671 47.619 0.00 0.00 0.00 2.12
3856 11232 7.143340 CCTAGAATGCACCATGACAAATATTG 58.857 38.462 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.