Multiple sequence alignment - TraesCS2A01G552600

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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 TraesCS2A01G552600 chr2A 100.000 4716 0 0 1 4716 758527681 758522966 0.000000e+00 8709.0
1 TraesCS2A01G552600 chr2A 85.998 1107 108 28 872 1937 758409204 758410304 0.000000e+00 1142.0
2 TraesCS2A01G552600 chr2A 81.755 1288 183 36 1019 2277 758583281 758584545 0.000000e+00 1029.0
3 TraesCS2A01G552600 chr2A 83.122 948 114 33 1362 2276 758516869 758515935 0.000000e+00 822.0
4 TraesCS2A01G552600 chr2A 82.099 810 121 12 1055 1849 758596582 758597382 0.000000e+00 671.0
5 TraesCS2A01G552600 chr2A 80.105 950 147 21 1359 2278 758693397 758692460 0.000000e+00 669.0
6 TraesCS2A01G552600 chr2A 75.819 1282 237 40 1056 2278 758713389 758712122 2.450000e-162 582.0
7 TraesCS2A01G552600 chr2A 76.568 303 51 13 2408 2693 758600478 758600777 1.060000e-31 148.0
8 TraesCS2A01G552600 chr2A 82.682 179 19 7 2847 3019 758687656 758687484 1.060000e-31 148.0
9 TraesCS2A01G552600 chr2A 73.270 318 55 14 2845 3150 758600831 758601130 6.500000e-14 89.8
10 TraesCS2A01G552600 chr2A 97.619 42 1 0 710 751 131708907 131708866 6.550000e-09 73.1
11 TraesCS2A01G552600 chr2B 94.263 3608 118 41 501 4073 771160862 771157309 0.000000e+00 5433.0
12 TraesCS2A01G552600 chr2B 88.141 1248 98 11 1029 2272 770745787 770746988 0.000000e+00 1439.0
13 TraesCS2A01G552600 chr2B 76.765 1317 237 37 1017 2278 771924313 771923011 0.000000e+00 673.0
14 TraesCS2A01G552600 chr2B 90.200 449 41 3 65 511 771173684 771173237 2.450000e-162 582.0
15 TraesCS2A01G552600 chr2B 79.732 671 115 17 1445 2096 771496101 771496769 2.570000e-127 466.0
16 TraesCS2A01G552600 chr2B 78.686 685 105 16 1607 2278 771822692 771822036 7.300000e-113 418.0
17 TraesCS2A01G552600 chr2B 89.474 266 18 5 4454 4716 771157029 771156771 1.270000e-85 327.0
18 TraesCS2A01G552600 chr2B 82.258 124 14 4 2847 2968 771510091 771510208 3.000000e-17 100.0
19 TraesCS2A01G552600 chr2B 85.556 90 12 1 663 752 770745453 770745541 5.020000e-15 93.5
20 TraesCS2A01G552600 chr2B 82.474 97 15 2 663 758 178712110 178712015 3.020000e-12 84.2
21 TraesCS2A01G552600 chr2B 82.653 98 14 3 2377 2473 771972290 771972195 3.020000e-12 84.2
22 TraesCS2A01G552600 chr2D 89.518 2843 177 52 1925 4716 628015343 628012571 0.000000e+00 3487.0
23 TraesCS2A01G552600 chr2D 89.399 1481 109 26 501 1951 628016806 628015344 0.000000e+00 1821.0
24 TraesCS2A01G552600 chr2D 87.571 885 80 13 1000 1862 627935504 627936380 0.000000e+00 998.0
25 TraesCS2A01G552600 chr2D 81.052 1293 193 24 1017 2278 628663229 628664500 0.000000e+00 983.0
26 TraesCS2A01G552600 chr2D 81.861 1268 129 54 1085 2286 627980938 627979706 0.000000e+00 974.0
27 TraesCS2A01G552600 chr2D 80.742 1293 198 31 1015 2277 628587891 628586620 0.000000e+00 961.0
28 TraesCS2A01G552600 chr2D 80.426 1267 207 27 1023 2277 628258354 628259591 0.000000e+00 928.0
29 TraesCS2A01G552600 chr2D 80.286 1258 176 28 1041 2278 628572767 628571562 0.000000e+00 883.0
30 TraesCS2A01G552600 chr2D 87.566 571 63 6 1039 1606 628623370 628623935 0.000000e+00 654.0
31 TraesCS2A01G552600 chr2D 76.404 1318 241 40 1017 2278 628643103 628644406 0.000000e+00 647.0
32 TraesCS2A01G552600 chr2D 90.113 354 33 2 64 415 628017654 628017301 4.300000e-125 459.0
33 TraesCS2A01G552600 chr2D 85.461 282 37 3 224 504 627958368 627958646 1.660000e-74 291.0
34 TraesCS2A01G552600 chr2D 77.570 321 51 12 2846 3153 628330002 628330314 1.740000e-39 174.0
35 TraesCS2A01G552600 chr2D 77.857 280 50 5 2878 3153 628343986 628344257 3.780000e-36 163.0
36 TraesCS2A01G552600 chr2D 83.333 168 18 6 2847 3008 628667160 628667323 3.800000e-31 147.0
37 TraesCS2A01G552600 chr1A 81.052 1293 178 33 1016 2271 551671879 551673141 0.000000e+00 968.0
38 TraesCS2A01G552600 chr4A 93.902 492 28 2 3466 3957 662711349 662711838 0.000000e+00 741.0
39 TraesCS2A01G552600 chr4A 90.110 91 6 3 4075 4162 236122126 236122216 1.070000e-21 115.0
40 TraesCS2A01G552600 chr1B 92.683 492 34 2 3466 3957 658197310 658197799 0.000000e+00 708.0
41 TraesCS2A01G552600 chr1B 86.869 99 8 4 4069 4163 508671252 508671349 6.450000e-19 106.0
42 TraesCS2A01G552600 chr7A 87.912 91 8 3 4075 4162 288878467 288878377 2.320000e-18 104.0
43 TraesCS2A01G552600 chr6B 85.859 99 10 3 4068 4165 163967941 163967846 8.350000e-18 102.0
44 TraesCS2A01G552600 chr6B 84.545 110 8 7 4072 4172 529769699 529769808 3.000000e-17 100.0
45 TraesCS2A01G552600 chr6B 84.762 105 6 7 4068 4163 239733826 239733723 3.880000e-16 97.1
46 TraesCS2A01G552600 chrUn 86.139 101 5 3 4073 4164 314370671 314370571 3.000000e-17 100.0
47 TraesCS2A01G552600 chr7D 84.762 105 11 3 4060 4162 600971828 600971929 3.000000e-17 100.0
48 TraesCS2A01G552600 chr4B 85.526 76 6 4 710 783 80549512 80549440 1.820000e-09 75.0
49 TraesCS2A01G552600 chr4B 85.526 76 6 4 710 783 80578836 80578764 1.820000e-09 75.0
50 TraesCS2A01G552600 chr5D 93.617 47 2 1 3833 3878 443015063 443015017 8.470000e-08 69.4
51 TraesCS2A01G552600 chr5A 97.500 40 1 0 3833 3872 559073359 559073320 8.470000e-08 69.4
52 TraesCS2A01G552600 chr4D 95.455 44 1 1 713 755 107714271 107714228 8.470000e-08 69.4


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 TraesCS2A01G552600 chr2A 758522966 758527681 4715 True 8709.000000 8709 100.000000 1 4716 1 chr2A.!!$R3 4715
1 TraesCS2A01G552600 chr2A 758409204 758410304 1100 False 1142.000000 1142 85.998000 872 1937 1 chr2A.!!$F1 1065
2 TraesCS2A01G552600 chr2A 758583281 758584545 1264 False 1029.000000 1029 81.755000 1019 2277 1 chr2A.!!$F2 1258
3 TraesCS2A01G552600 chr2A 758515935 758516869 934 True 822.000000 822 83.122000 1362 2276 1 chr2A.!!$R2 914
4 TraesCS2A01G552600 chr2A 758692460 758693397 937 True 669.000000 669 80.105000 1359 2278 1 chr2A.!!$R5 919
5 TraesCS2A01G552600 chr2A 758712122 758713389 1267 True 582.000000 582 75.819000 1056 2278 1 chr2A.!!$R6 1222
6 TraesCS2A01G552600 chr2A 758596582 758601130 4548 False 302.933333 671 77.312333 1055 3150 3 chr2A.!!$F3 2095
7 TraesCS2A01G552600 chr2B 771156771 771160862 4091 True 2880.000000 5433 91.868500 501 4716 2 chr2B.!!$R6 4215
8 TraesCS2A01G552600 chr2B 770745453 770746988 1535 False 766.250000 1439 86.848500 663 2272 2 chr2B.!!$F3 1609
9 TraesCS2A01G552600 chr2B 771923011 771924313 1302 True 673.000000 673 76.765000 1017 2278 1 chr2B.!!$R4 1261
10 TraesCS2A01G552600 chr2B 771496101 771496769 668 False 466.000000 466 79.732000 1445 2096 1 chr2B.!!$F1 651
11 TraesCS2A01G552600 chr2B 771822036 771822692 656 True 418.000000 418 78.686000 1607 2278 1 chr2B.!!$R3 671
12 TraesCS2A01G552600 chr2D 628012571 628017654 5083 True 1922.333333 3487 89.676667 64 4716 3 chr2D.!!$R4 4652
13 TraesCS2A01G552600 chr2D 627935504 627936380 876 False 998.000000 998 87.571000 1000 1862 1 chr2D.!!$F1 862
14 TraesCS2A01G552600 chr2D 627979706 627980938 1232 True 974.000000 974 81.861000 1085 2286 1 chr2D.!!$R1 1201
15 TraesCS2A01G552600 chr2D 628586620 628587891 1271 True 961.000000 961 80.742000 1015 2277 1 chr2D.!!$R3 1262
16 TraesCS2A01G552600 chr2D 628258354 628259591 1237 False 928.000000 928 80.426000 1023 2277 1 chr2D.!!$F3 1254
17 TraesCS2A01G552600 chr2D 628571562 628572767 1205 True 883.000000 883 80.286000 1041 2278 1 chr2D.!!$R2 1237
18 TraesCS2A01G552600 chr2D 628623370 628623935 565 False 654.000000 654 87.566000 1039 1606 1 chr2D.!!$F6 567
19 TraesCS2A01G552600 chr2D 628643103 628644406 1303 False 647.000000 647 76.404000 1017 2278 1 chr2D.!!$F7 1261
20 TraesCS2A01G552600 chr2D 628663229 628667323 4094 False 565.000000 983 82.192500 1017 3008 2 chr2D.!!$F8 1991
21 TraesCS2A01G552600 chr1A 551671879 551673141 1262 False 968.000000 968 81.052000 1016 2271 1 chr1A.!!$F1 1255

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
533 945 0.098025 GAAGACAGAGAGAGCCGACG 59.902 60.000 0.00 0.00 0.00 5.12 F
572 989 0.676736 GGAGAAGCGATCCGGAGATT 59.323 55.000 11.34 1.16 30.90 2.40 F
2731 6738 1.065551 AGCTTCAAACCACTTGTTCGC 59.934 47.619 0.00 0.00 35.67 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 4212 2.755655 AGGAGGTATCTGTCACTCAACG 59.244 50.000 0.00 0.0 0.0 4.10 R
2904 6921 3.815401 GGCTGAACTTGCTCTCTTTTACA 59.185 43.478 0.00 0.0 0.0 2.41 R
4202 8284 1.067283 CCAGTGCACACCAGAGTAGAG 60.067 57.143 21.04 0.0 0.0 2.43 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
20 21 3.505480 GAGGGATCTTCGGTAGTAGGA 57.495 52.381 0.00 0.00 0.00 2.94
21 22 4.036941 GAGGGATCTTCGGTAGTAGGAT 57.963 50.000 0.00 0.00 0.00 3.24
22 23 4.011698 GAGGGATCTTCGGTAGTAGGATC 58.988 52.174 0.00 0.00 34.00 3.36
23 24 3.398292 AGGGATCTTCGGTAGTAGGATCA 59.602 47.826 0.00 0.00 35.76 2.92
24 25 4.140994 AGGGATCTTCGGTAGTAGGATCAA 60.141 45.833 0.00 0.00 35.76 2.57
25 26 4.773149 GGGATCTTCGGTAGTAGGATCAAT 59.227 45.833 0.00 0.00 35.76 2.57
26 27 5.336849 GGGATCTTCGGTAGTAGGATCAATG 60.337 48.000 0.00 0.00 35.76 2.82
27 28 5.477291 GGATCTTCGGTAGTAGGATCAATGA 59.523 44.000 0.00 0.00 35.76 2.57
28 29 6.349777 GGATCTTCGGTAGTAGGATCAATGAG 60.350 46.154 0.00 0.00 35.76 2.90
29 30 4.278669 TCTTCGGTAGTAGGATCAATGAGC 59.721 45.833 0.00 0.00 0.00 4.26
30 31 2.891580 TCGGTAGTAGGATCAATGAGCC 59.108 50.000 9.93 9.93 38.56 4.70
31 32 2.628178 CGGTAGTAGGATCAATGAGCCA 59.372 50.000 20.45 2.95 41.08 4.75
32 33 3.069586 CGGTAGTAGGATCAATGAGCCAA 59.930 47.826 20.45 0.00 41.08 4.52
33 34 4.442893 CGGTAGTAGGATCAATGAGCCAAA 60.443 45.833 20.45 4.34 41.08 3.28
34 35 5.437060 GGTAGTAGGATCAATGAGCCAAAA 58.563 41.667 20.45 1.64 41.08 2.44
35 36 6.064717 GGTAGTAGGATCAATGAGCCAAAAT 58.935 40.000 20.45 9.01 41.08 1.82
36 37 6.547510 GGTAGTAGGATCAATGAGCCAAAATT 59.452 38.462 20.45 0.60 41.08 1.82
37 38 6.705863 AGTAGGATCAATGAGCCAAAATTC 57.294 37.500 20.45 3.37 41.08 2.17
38 39 6.430007 AGTAGGATCAATGAGCCAAAATTCT 58.570 36.000 20.45 5.50 41.08 2.40
39 40 7.577303 AGTAGGATCAATGAGCCAAAATTCTA 58.423 34.615 20.45 0.00 41.08 2.10
40 41 6.956202 AGGATCAATGAGCCAAAATTCTAG 57.044 37.500 20.45 0.00 41.08 2.43
41 42 6.430007 AGGATCAATGAGCCAAAATTCTAGT 58.570 36.000 20.45 0.00 41.08 2.57
42 43 7.577303 AGGATCAATGAGCCAAAATTCTAGTA 58.423 34.615 20.45 0.00 41.08 1.82
43 44 7.500559 AGGATCAATGAGCCAAAATTCTAGTAC 59.499 37.037 20.45 0.00 41.08 2.73
44 45 7.500559 GGATCAATGAGCCAAAATTCTAGTACT 59.499 37.037 13.30 0.00 38.12 2.73
45 46 9.547753 GATCAATGAGCCAAAATTCTAGTACTA 57.452 33.333 1.89 1.89 0.00 1.82
46 47 8.718102 TCAATGAGCCAAAATTCTAGTACTAC 57.282 34.615 0.00 0.00 0.00 2.73
47 48 8.318412 TCAATGAGCCAAAATTCTAGTACTACA 58.682 33.333 0.00 0.00 0.00 2.74
48 49 8.391106 CAATGAGCCAAAATTCTAGTACTACAC 58.609 37.037 0.00 0.00 0.00 2.90
49 50 6.403878 TGAGCCAAAATTCTAGTACTACACC 58.596 40.000 0.00 0.00 0.00 4.16
50 51 6.014070 TGAGCCAAAATTCTAGTACTACACCA 60.014 38.462 0.00 0.00 0.00 4.17
51 52 6.775708 AGCCAAAATTCTAGTACTACACCAA 58.224 36.000 0.00 0.00 0.00 3.67
52 53 7.228590 AGCCAAAATTCTAGTACTACACCAAA 58.771 34.615 0.00 0.00 0.00 3.28
53 54 7.390718 AGCCAAAATTCTAGTACTACACCAAAG 59.609 37.037 0.00 0.00 0.00 2.77
54 55 7.389607 GCCAAAATTCTAGTACTACACCAAAGA 59.610 37.037 0.00 0.00 0.00 2.52
55 56 8.936864 CCAAAATTCTAGTACTACACCAAAGAG 58.063 37.037 0.00 0.00 0.00 2.85
56 57 9.706691 CAAAATTCTAGTACTACACCAAAGAGA 57.293 33.333 0.00 0.00 0.00 3.10
57 58 9.930693 AAAATTCTAGTACTACACCAAAGAGAG 57.069 33.333 0.00 0.00 0.00 3.20
58 59 8.880991 AATTCTAGTACTACACCAAAGAGAGA 57.119 34.615 0.00 0.00 0.00 3.10
59 60 7.684937 TTCTAGTACTACACCAAAGAGAGAC 57.315 40.000 0.00 0.00 0.00 3.36
60 61 7.018487 TCTAGTACTACACCAAAGAGAGACT 57.982 40.000 0.00 0.00 0.00 3.24
61 62 7.104939 TCTAGTACTACACCAAAGAGAGACTC 58.895 42.308 0.00 0.00 0.00 3.36
62 63 5.632118 AGTACTACACCAAAGAGAGACTCA 58.368 41.667 5.02 0.00 32.06 3.41
69 70 4.336433 CACCAAAGAGAGACTCAAAAGCAA 59.664 41.667 5.02 0.00 32.06 3.91
72 73 5.240183 CCAAAGAGAGACTCAAAAGCAATGA 59.760 40.000 5.02 0.00 32.06 2.57
78 79 5.649831 AGAGACTCAAAAGCAATGAATACCC 59.350 40.000 5.02 0.00 0.00 3.69
91 92 8.362639 AGCAATGAATACCCTATGCTTAAATTG 58.637 33.333 0.00 0.00 40.99 2.32
92 93 7.116805 GCAATGAATACCCTATGCTTAAATTGC 59.883 37.037 0.00 0.00 38.49 3.56
130 132 6.935208 GGCCGGAGATAGTTAATGAATAAACT 59.065 38.462 5.05 0.00 39.25 2.66
153 155 8.603242 ACTACTTGGTTAACTTGTATCACTTG 57.397 34.615 5.42 0.00 0.00 3.16
171 173 4.065789 ACTTGGGCTTAGTTTTTCTCTCG 58.934 43.478 0.00 0.00 0.00 4.04
177 179 4.750598 GGCTTAGTTTTTCTCTCGAACACT 59.249 41.667 0.00 0.00 31.25 3.55
180 182 7.359347 GGCTTAGTTTTTCTCTCGAACACTAAG 60.359 40.741 18.33 18.33 44.70 2.18
212 215 2.740981 CGAGAGCTCAAGATTTGCAGTT 59.259 45.455 17.77 0.00 0.00 3.16
222 225 2.629617 AGATTTGCAGTTCAGGTTTGGG 59.370 45.455 0.00 0.00 0.00 4.12
228 231 2.430694 GCAGTTCAGGTTTGGGTTTTCT 59.569 45.455 0.00 0.00 0.00 2.52
230 233 4.280929 GCAGTTCAGGTTTGGGTTTTCTAT 59.719 41.667 0.00 0.00 0.00 1.98
231 234 5.564848 GCAGTTCAGGTTTGGGTTTTCTATC 60.565 44.000 0.00 0.00 0.00 2.08
232 235 5.534654 CAGTTCAGGTTTGGGTTTTCTATCA 59.465 40.000 0.00 0.00 0.00 2.15
259 262 5.222079 TGCTGTTAAGAGTGTTGGACATA 57.778 39.130 1.12 0.00 0.00 2.29
261 264 4.093556 GCTGTTAAGAGTGTTGGACATAGC 59.906 45.833 1.12 0.00 0.00 2.97
264 267 0.108138 AGAGTGTTGGACATAGCGGC 60.108 55.000 0.00 0.00 0.00 6.53
270 273 2.279517 GGACATAGCGGCGGTCTG 60.280 66.667 17.55 19.41 0.00 3.51
281 284 0.390472 GGCGGTCTGGTTCTCTTCTG 60.390 60.000 0.00 0.00 0.00 3.02
287 290 3.394719 GTCTGGTTCTCTTCTGGAACAC 58.605 50.000 8.49 0.44 43.20 3.32
291 294 2.879026 GGTTCTCTTCTGGAACACCAAC 59.121 50.000 8.49 0.00 43.20 3.77
292 295 3.433740 GGTTCTCTTCTGGAACACCAACT 60.434 47.826 8.49 0.00 43.20 3.16
293 296 4.200092 GTTCTCTTCTGGAACACCAACTT 58.800 43.478 0.00 0.00 41.64 2.66
332 335 5.822519 ACTTGTTTAGCAACTCTCACATTGA 59.177 36.000 0.00 0.00 33.58 2.57
334 337 6.245115 TGTTTAGCAACTCTCACATTGATG 57.755 37.500 0.00 0.00 33.58 3.07
350 353 6.764560 CACATTGATGTAGTGATCCAGAATGA 59.235 38.462 0.00 0.00 37.27 2.57
360 363 7.020827 AGTGATCCAGAATGAAAAGGTAGAA 57.979 36.000 0.00 0.00 39.69 2.10
372 375 5.012148 TGAAAAGGTAGAAGAGAAGGAGTGG 59.988 44.000 0.00 0.00 0.00 4.00
383 386 1.420138 GAAGGAGTGGAGGTTCACCAA 59.580 52.381 0.00 0.00 39.22 3.67
415 418 8.063200 TGAAGAGTCGACAAGATATAAAAGGA 57.937 34.615 19.50 0.00 0.00 3.36
416 419 8.528643 TGAAGAGTCGACAAGATATAAAAGGAA 58.471 33.333 19.50 0.00 0.00 3.36
417 420 9.367444 GAAGAGTCGACAAGATATAAAAGGAAA 57.633 33.333 19.50 0.00 0.00 3.13
418 421 9.720769 AAGAGTCGACAAGATATAAAAGGAAAA 57.279 29.630 19.50 0.00 0.00 2.29
433 436 9.836864 ATAAAAGGAAAAATAGATGGGAATTGC 57.163 29.630 0.00 0.00 0.00 3.56
434 437 7.500629 AAAGGAAAAATAGATGGGAATTGCT 57.499 32.000 0.00 0.00 0.00 3.91
435 438 6.475596 AGGAAAAATAGATGGGAATTGCTG 57.524 37.500 0.00 0.00 0.00 4.41
436 439 6.197168 AGGAAAAATAGATGGGAATTGCTGA 58.803 36.000 0.00 0.00 0.00 4.26
437 440 6.669154 AGGAAAAATAGATGGGAATTGCTGAA 59.331 34.615 0.00 0.00 0.00 3.02
439 442 7.364144 GGAAAAATAGATGGGAATTGCTGAAGT 60.364 37.037 0.00 0.00 0.00 3.01
440 443 8.593945 AAAAATAGATGGGAATTGCTGAAGTA 57.406 30.769 0.00 0.00 0.00 2.24
441 444 8.773033 AAAATAGATGGGAATTGCTGAAGTAT 57.227 30.769 0.00 0.00 0.00 2.12
459 462 7.681939 GAAGTATTCGAGGAGAGAGTATGAT 57.318 40.000 0.00 0.00 34.17 2.45
461 464 9.221933 GAAGTATTCGAGGAGAGAGTATGATTA 57.778 37.037 0.00 0.00 34.17 1.75
462 465 9.747898 AAGTATTCGAGGAGAGAGTATGATTAT 57.252 33.333 0.00 0.00 0.00 1.28
463 466 9.391006 AGTATTCGAGGAGAGAGTATGATTATC 57.609 37.037 0.00 0.00 0.00 1.75
464 467 9.391006 GTATTCGAGGAGAGAGTATGATTATCT 57.609 37.037 0.00 0.00 0.00 1.98
465 468 8.877864 ATTCGAGGAGAGAGTATGATTATCTT 57.122 34.615 0.00 0.00 0.00 2.40
466 469 8.698973 TTCGAGGAGAGAGTATGATTATCTTT 57.301 34.615 0.00 0.00 0.00 2.52
467 470 8.105097 TCGAGGAGAGAGTATGATTATCTTTG 57.895 38.462 0.00 0.00 0.00 2.77
469 472 7.003402 AGGAGAGAGTATGATTATCTTTGGC 57.997 40.000 0.00 0.00 0.00 4.52
470 473 6.786959 AGGAGAGAGTATGATTATCTTTGGCT 59.213 38.462 0.00 0.00 0.00 4.75
472 475 7.039082 GGAGAGAGTATGATTATCTTTGGCTCT 60.039 40.741 0.00 0.00 34.04 4.09
474 477 7.289782 AGAGAGTATGATTATCTTTGGCTCTGT 59.710 37.037 11.18 7.18 31.86 3.41
476 479 5.762218 AGTATGATTATCTTTGGCTCTGTGC 59.238 40.000 0.00 0.00 41.94 4.57
486 489 1.223487 GCTCTGTGCCGGGGATTTA 59.777 57.895 2.18 0.00 35.15 1.40
487 490 0.393808 GCTCTGTGCCGGGGATTTAA 60.394 55.000 2.18 0.00 35.15 1.52
488 491 1.953311 GCTCTGTGCCGGGGATTTAAA 60.953 52.381 2.18 0.00 35.15 1.52
490 493 2.358898 CTCTGTGCCGGGGATTTAAATG 59.641 50.000 5.17 0.00 0.00 2.32
491 494 2.025793 TCTGTGCCGGGGATTTAAATGA 60.026 45.455 5.17 0.00 0.00 2.57
492 495 2.358898 CTGTGCCGGGGATTTAAATGAG 59.641 50.000 5.17 0.00 0.00 2.90
493 496 2.025793 TGTGCCGGGGATTTAAATGAGA 60.026 45.455 5.17 0.00 0.00 3.27
494 497 3.222603 GTGCCGGGGATTTAAATGAGAT 58.777 45.455 5.17 0.00 0.00 2.75
495 498 3.636764 GTGCCGGGGATTTAAATGAGATT 59.363 43.478 5.17 0.00 0.00 2.40
496 499 3.888930 TGCCGGGGATTTAAATGAGATTC 59.111 43.478 5.17 0.00 0.00 2.52
497 500 4.145052 GCCGGGGATTTAAATGAGATTCT 58.855 43.478 5.17 0.00 0.00 2.40
498 501 4.584743 GCCGGGGATTTAAATGAGATTCTT 59.415 41.667 5.17 0.00 0.00 2.52
499 502 5.507985 GCCGGGGATTTAAATGAGATTCTTG 60.508 44.000 5.17 0.00 0.00 3.02
530 942 0.738389 GAGGAAGACAGAGAGAGCCG 59.262 60.000 0.00 0.00 0.00 5.52
531 943 0.329931 AGGAAGACAGAGAGAGCCGA 59.670 55.000 0.00 0.00 0.00 5.54
533 945 0.098025 GAAGACAGAGAGAGCCGACG 59.902 60.000 0.00 0.00 0.00 5.12
545 961 1.019278 AGCCGACGCCACTACATTTG 61.019 55.000 0.00 0.00 34.57 2.32
551 967 3.807622 CGACGCCACTACATTTGGAATAT 59.192 43.478 0.00 0.00 36.02 1.28
572 989 0.676736 GGAGAAGCGATCCGGAGATT 59.323 55.000 11.34 1.16 30.90 2.40
580 997 2.681706 CGATCCGGAGATTCATTCCTG 58.318 52.381 11.34 0.00 30.90 3.86
584 1001 1.139654 CCGGAGATTCATTCCTGCTCA 59.860 52.381 0.00 0.00 32.34 4.26
621 1038 4.517952 TTTCATTCATCGCAAACACCAT 57.482 36.364 0.00 0.00 0.00 3.55
623 1040 3.080319 TCATTCATCGCAAACACCATCA 58.920 40.909 0.00 0.00 0.00 3.07
641 1059 4.352001 CCATCATAGGGAGAGGAATTCCAA 59.648 45.833 26.22 3.16 38.89 3.53
645 1063 6.209774 TCATAGGGAGAGGAATTCCAAGTTA 58.790 40.000 26.22 10.77 38.89 2.24
650 1068 6.101881 AGGGAGAGGAATTCCAAGTTATAAGG 59.898 42.308 26.22 0.00 38.89 2.69
652 1070 7.072076 GGGAGAGGAATTCCAAGTTATAAGGTA 59.928 40.741 26.22 0.00 38.89 3.08
658 1076 7.501559 GGAATTCCAAGTTATAAGGTAAGGGTC 59.498 40.741 20.04 0.00 35.64 4.46
678 1096 4.982295 GGTCCGATTTTTCTTTTGTCAAGG 59.018 41.667 0.00 0.00 0.00 3.61
682 1100 5.687285 CCGATTTTTCTTTTGTCAAGGACTG 59.313 40.000 0.00 0.00 33.15 3.51
703 1121 3.327464 TGATCCTCTGTCAAATCACCACA 59.673 43.478 0.00 0.00 0.00 4.17
1011 1472 1.524393 CCACAGAGCAGCACACACA 60.524 57.895 0.00 0.00 0.00 3.72
2193 4165 5.379003 CGTCACACGTATATTGCAACTTTT 58.621 37.500 0.00 0.00 36.74 2.27
2204 4176 3.077229 TGCAACTTTTCACCATCGTTG 57.923 42.857 0.00 0.00 38.31 4.10
2240 4212 3.251004 CAGTGTCAAGTGGTAAGCTTTCC 59.749 47.826 14.83 14.83 0.00 3.13
2375 6060 4.927978 ACTTCGCTGCATTCTAGATAGT 57.072 40.909 0.00 0.00 0.00 2.12
2731 6738 1.065551 AGCTTCAAACCACTTGTTCGC 59.934 47.619 0.00 0.00 35.67 4.70
2904 6921 4.260702 GCGAGAGACTAATAGTTGCGTACT 60.261 45.833 0.00 0.00 41.04 2.73
3162 7204 1.154207 CGTCGTCGACAGTGATGCT 60.154 57.895 24.13 0.00 39.71 3.79
3285 7331 2.035632 GAGCCAGAGTAGCAGTACCAT 58.964 52.381 0.00 0.00 0.00 3.55
3307 7353 3.310860 ATCCACGACGACCAAGGGC 62.311 63.158 0.00 0.00 0.00 5.19
3573 7642 8.200792 AGTAGACATTCATCTGAGTTAACATCC 58.799 37.037 8.61 0.00 0.00 3.51
3588 7657 7.651808 AGTTAACATCCAGTTTTTGTCTGATG 58.348 34.615 8.61 0.00 41.64 3.07
3694 7766 4.010349 GTTGAGTAGAAATTCCCAGTGGG 58.990 47.826 23.57 23.57 46.11 4.61
4087 8169 1.495574 AGCATAGTACTCCCTCCGTCT 59.504 52.381 0.00 0.00 0.00 4.18
4098 8180 5.186198 ACTCCCTCCGTCTCAAAATAAATG 58.814 41.667 0.00 0.00 0.00 2.32
4100 8182 6.070424 ACTCCCTCCGTCTCAAAATAAATGTA 60.070 38.462 0.00 0.00 0.00 2.29
4101 8183 6.895782 TCCCTCCGTCTCAAAATAAATGTAT 58.104 36.000 0.00 0.00 0.00 2.29
4154 8236 3.071892 TGAGACACTTATTTTGGGACGGT 59.928 43.478 0.00 0.00 0.00 4.83
4174 8256 6.891388 ACGGTGGGAGTATTTGATTATAACA 58.109 36.000 0.00 0.00 0.00 2.41
4195 8277 9.802039 ATAACATCTGTTACCTTAAAAGGACAA 57.198 29.630 15.65 6.18 43.76 3.18
4196 8278 9.802039 TAACATCTGTTACCTTAAAAGGACAAT 57.198 29.630 15.65 4.74 42.70 2.71
4353 8443 2.469826 TGACACGTGTTCATCTGTCAC 58.530 47.619 24.26 6.19 38.45 3.67
4363 8453 6.127403 GTGTTCATCTGTCACGTTTTAACTC 58.873 40.000 0.00 0.00 0.00 3.01
4392 8482 9.968743 GATTCGGTACTGAAACTACAAATTTAG 57.031 33.333 20.64 0.00 0.00 1.85
4397 8487 8.164790 GGTACTGAAACTACAAATTTAGTACGC 58.835 37.037 13.49 6.82 39.84 4.42
4401 8491 7.569297 TGAAACTACAAATTTAGTACGCACTG 58.431 34.615 0.00 0.00 36.14 3.66
4416 8506 2.516923 GCACTGTACTGTACTGCTACG 58.483 52.381 20.46 10.60 30.03 3.51
4436 8526 9.063615 TGCTACGTTTACTGAATAGATAGATGA 57.936 33.333 0.00 0.00 0.00 2.92
4509 8603 6.803807 GTCAAGTCAATTAACTGCTTCATTCC 59.196 38.462 0.00 0.00 0.00 3.01
4516 8610 1.985473 ACTGCTTCATTCCTTGCACA 58.015 45.000 0.00 0.00 0.00 4.57
4550 8645 2.502142 TCACTCAGCTACCGACCTTA 57.498 50.000 0.00 0.00 0.00 2.69
4683 8784 2.307098 AGCTAAAGAGGATGTGCAAGGT 59.693 45.455 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.505480 TCCTACTACCGAAGATCCCTC 57.495 52.381 0.00 0.00 0.00 4.30
2 3 3.764218 TGATCCTACTACCGAAGATCCC 58.236 50.000 0.00 0.00 0.00 3.85
3 4 5.477291 TCATTGATCCTACTACCGAAGATCC 59.523 44.000 0.00 0.00 0.00 3.36
4 5 6.576662 TCATTGATCCTACTACCGAAGATC 57.423 41.667 0.00 0.00 0.00 2.75
5 6 5.047660 GCTCATTGATCCTACTACCGAAGAT 60.048 44.000 0.00 0.00 0.00 2.40
6 7 4.278669 GCTCATTGATCCTACTACCGAAGA 59.721 45.833 0.00 0.00 0.00 2.87
8 9 3.321111 GGCTCATTGATCCTACTACCGAA 59.679 47.826 0.00 0.00 0.00 4.30
9 10 2.891580 GGCTCATTGATCCTACTACCGA 59.108 50.000 0.00 0.00 0.00 4.69
10 11 2.628178 TGGCTCATTGATCCTACTACCG 59.372 50.000 7.97 0.00 0.00 4.02
11 12 4.689612 TTGGCTCATTGATCCTACTACC 57.310 45.455 7.97 0.00 0.00 3.18
12 13 7.500559 AGAATTTTGGCTCATTGATCCTACTAC 59.499 37.037 7.97 0.00 0.00 2.73
13 14 7.577303 AGAATTTTGGCTCATTGATCCTACTA 58.423 34.615 7.97 0.00 0.00 1.82
14 15 6.430007 AGAATTTTGGCTCATTGATCCTACT 58.570 36.000 7.97 0.00 0.00 2.57
15 16 6.705863 AGAATTTTGGCTCATTGATCCTAC 57.294 37.500 7.97 0.00 0.00 3.18
16 17 7.577303 ACTAGAATTTTGGCTCATTGATCCTA 58.423 34.615 7.97 0.00 0.00 2.94
17 18 6.430007 ACTAGAATTTTGGCTCATTGATCCT 58.570 36.000 7.97 0.00 0.00 3.24
18 19 6.705863 ACTAGAATTTTGGCTCATTGATCC 57.294 37.500 0.00 0.00 0.00 3.36
19 20 8.443953 AGTACTAGAATTTTGGCTCATTGATC 57.556 34.615 0.00 0.00 0.00 2.92
20 21 9.331282 GTAGTACTAGAATTTTGGCTCATTGAT 57.669 33.333 1.87 0.00 0.00 2.57
21 22 8.318412 TGTAGTACTAGAATTTTGGCTCATTGA 58.682 33.333 1.87 0.00 0.00 2.57
22 23 8.391106 GTGTAGTACTAGAATTTTGGCTCATTG 58.609 37.037 1.87 0.00 0.00 2.82
23 24 7.553044 GGTGTAGTACTAGAATTTTGGCTCATT 59.447 37.037 1.87 0.00 0.00 2.57
24 25 7.048512 GGTGTAGTACTAGAATTTTGGCTCAT 58.951 38.462 1.87 0.00 0.00 2.90
25 26 6.014070 TGGTGTAGTACTAGAATTTTGGCTCA 60.014 38.462 1.87 0.00 0.00 4.26
26 27 6.403878 TGGTGTAGTACTAGAATTTTGGCTC 58.596 40.000 1.87 0.00 0.00 4.70
27 28 6.368779 TGGTGTAGTACTAGAATTTTGGCT 57.631 37.500 1.87 0.00 0.00 4.75
28 29 7.389607 TCTTTGGTGTAGTACTAGAATTTTGGC 59.610 37.037 1.87 0.00 0.00 4.52
29 30 8.842358 TCTTTGGTGTAGTACTAGAATTTTGG 57.158 34.615 1.87 0.00 0.00 3.28
30 31 9.706691 TCTCTTTGGTGTAGTACTAGAATTTTG 57.293 33.333 1.87 0.00 0.00 2.44
31 32 9.930693 CTCTCTTTGGTGTAGTACTAGAATTTT 57.069 33.333 1.87 0.00 0.00 1.82
32 33 9.310449 TCTCTCTTTGGTGTAGTACTAGAATTT 57.690 33.333 1.87 0.00 0.00 1.82
33 34 8.741841 GTCTCTCTTTGGTGTAGTACTAGAATT 58.258 37.037 1.87 0.00 0.00 2.17
34 35 8.110908 AGTCTCTCTTTGGTGTAGTACTAGAAT 58.889 37.037 1.87 0.00 0.00 2.40
35 36 7.460071 AGTCTCTCTTTGGTGTAGTACTAGAA 58.540 38.462 1.87 0.00 0.00 2.10
36 37 7.018487 AGTCTCTCTTTGGTGTAGTACTAGA 57.982 40.000 1.87 0.00 0.00 2.43
37 38 6.879993 TGAGTCTCTCTTTGGTGTAGTACTAG 59.120 42.308 1.87 0.00 0.00 2.57
38 39 6.776744 TGAGTCTCTCTTTGGTGTAGTACTA 58.223 40.000 0.00 0.00 0.00 1.82
39 40 5.632118 TGAGTCTCTCTTTGGTGTAGTACT 58.368 41.667 0.00 0.00 0.00 2.73
40 41 5.961396 TGAGTCTCTCTTTGGTGTAGTAC 57.039 43.478 0.65 0.00 0.00 2.73
41 42 6.971726 TTTGAGTCTCTCTTTGGTGTAGTA 57.028 37.500 0.65 0.00 0.00 1.82
42 43 5.871396 TTTGAGTCTCTCTTTGGTGTAGT 57.129 39.130 0.65 0.00 0.00 2.73
43 44 5.178438 GCTTTTGAGTCTCTCTTTGGTGTAG 59.822 44.000 0.65 0.00 0.00 2.74
44 45 5.057149 GCTTTTGAGTCTCTCTTTGGTGTA 58.943 41.667 0.65 0.00 0.00 2.90
45 46 3.879892 GCTTTTGAGTCTCTCTTTGGTGT 59.120 43.478 0.65 0.00 0.00 4.16
46 47 3.879295 TGCTTTTGAGTCTCTCTTTGGTG 59.121 43.478 0.65 0.00 0.00 4.17
47 48 4.156455 TGCTTTTGAGTCTCTCTTTGGT 57.844 40.909 0.65 0.00 0.00 3.67
48 49 5.240183 TCATTGCTTTTGAGTCTCTCTTTGG 59.760 40.000 0.65 0.00 0.00 3.28
49 50 6.309712 TCATTGCTTTTGAGTCTCTCTTTG 57.690 37.500 0.65 0.00 0.00 2.77
50 51 6.949352 TTCATTGCTTTTGAGTCTCTCTTT 57.051 33.333 0.65 0.00 0.00 2.52
51 52 7.120432 GGTATTCATTGCTTTTGAGTCTCTCTT 59.880 37.037 0.65 0.00 0.00 2.85
52 53 6.597280 GGTATTCATTGCTTTTGAGTCTCTCT 59.403 38.462 0.65 0.00 0.00 3.10
53 54 6.183360 GGGTATTCATTGCTTTTGAGTCTCTC 60.183 42.308 0.65 0.00 0.00 3.20
54 55 5.649831 GGGTATTCATTGCTTTTGAGTCTCT 59.350 40.000 0.65 0.00 0.00 3.10
55 56 5.649831 AGGGTATTCATTGCTTTTGAGTCTC 59.350 40.000 0.00 0.00 0.00 3.36
56 57 5.574188 AGGGTATTCATTGCTTTTGAGTCT 58.426 37.500 0.00 0.00 0.00 3.24
57 58 5.904362 AGGGTATTCATTGCTTTTGAGTC 57.096 39.130 0.00 0.00 0.00 3.36
58 59 6.183360 GCATAGGGTATTCATTGCTTTTGAGT 60.183 38.462 0.00 0.00 0.00 3.41
59 60 6.040166 AGCATAGGGTATTCATTGCTTTTGAG 59.960 38.462 0.00 0.00 37.12 3.02
60 61 5.893255 AGCATAGGGTATTCATTGCTTTTGA 59.107 36.000 0.00 0.00 37.12 2.69
61 62 6.152932 AGCATAGGGTATTCATTGCTTTTG 57.847 37.500 0.00 0.00 37.12 2.44
62 63 6.796785 AAGCATAGGGTATTCATTGCTTTT 57.203 33.333 2.35 0.00 45.32 2.27
69 70 6.071952 CGGCAATTTAAGCATAGGGTATTCAT 60.072 38.462 0.00 0.00 0.00 2.57
72 73 4.522789 CCGGCAATTTAAGCATAGGGTATT 59.477 41.667 0.00 0.00 0.00 1.89
78 79 3.705604 CAACCCGGCAATTTAAGCATAG 58.294 45.455 0.00 0.00 0.00 2.23
130 132 6.938030 CCCAAGTGATACAAGTTAACCAAGTA 59.062 38.462 0.88 3.60 0.00 2.24
171 173 4.863491 TCGTGGTAGACAACTTAGTGTTC 58.137 43.478 0.00 0.00 36.63 3.18
177 179 3.418995 AGCTCTCGTGGTAGACAACTTA 58.581 45.455 0.00 0.00 0.00 2.24
180 182 1.540267 TGAGCTCTCGTGGTAGACAAC 59.460 52.381 16.19 0.00 0.00 3.32
212 215 7.610580 AAATTGATAGAAAACCCAAACCTGA 57.389 32.000 0.00 0.00 0.00 3.86
228 231 8.081633 CCAACACTCTTAACAGCAAAATTGATA 58.918 33.333 0.00 0.00 0.00 2.15
230 233 6.096141 TCCAACACTCTTAACAGCAAAATTGA 59.904 34.615 0.00 0.00 0.00 2.57
231 234 6.198966 GTCCAACACTCTTAACAGCAAAATTG 59.801 38.462 0.00 0.00 0.00 2.32
232 235 6.127479 TGTCCAACACTCTTAACAGCAAAATT 60.127 34.615 0.00 0.00 0.00 1.82
259 262 4.070552 GAGAACCAGACCGCCGCT 62.071 66.667 0.00 0.00 0.00 5.52
261 264 1.446272 GAAGAGAACCAGACCGCCG 60.446 63.158 0.00 0.00 0.00 6.46
264 267 1.257743 TCCAGAAGAGAACCAGACCG 58.742 55.000 0.00 0.00 0.00 4.79
270 273 2.879026 GTTGGTGTTCCAGAAGAGAACC 59.121 50.000 1.53 0.00 45.22 3.62
291 294 1.995376 AGTTTAGGCCAACCACCAAG 58.005 50.000 5.01 0.00 39.06 3.61
292 295 2.035632 CAAGTTTAGGCCAACCACCAA 58.964 47.619 5.01 0.00 39.06 3.67
293 296 1.063567 ACAAGTTTAGGCCAACCACCA 60.064 47.619 5.01 0.00 39.06 4.17
332 335 6.725364 ACCTTTTCATTCTGGATCACTACAT 58.275 36.000 0.00 0.00 0.00 2.29
334 337 7.556844 TCTACCTTTTCATTCTGGATCACTAC 58.443 38.462 0.00 0.00 0.00 2.73
350 353 5.155905 TCCACTCCTTCTCTTCTACCTTTT 58.844 41.667 0.00 0.00 0.00 2.27
360 363 2.252714 GTGAACCTCCACTCCTTCTCT 58.747 52.381 0.00 0.00 34.38 3.10
372 375 6.881602 ACTCTTCATAGAAATTGGTGAACCTC 59.118 38.462 0.37 0.00 36.82 3.85
415 418 7.486407 ACTTCAGCAATTCCCATCTATTTTT 57.514 32.000 0.00 0.00 0.00 1.94
416 419 8.773033 ATACTTCAGCAATTCCCATCTATTTT 57.227 30.769 0.00 0.00 0.00 1.82
417 420 8.773033 AATACTTCAGCAATTCCCATCTATTT 57.227 30.769 0.00 0.00 0.00 1.40
418 421 7.173907 CGAATACTTCAGCAATTCCCATCTATT 59.826 37.037 0.00 0.00 0.00 1.73
421 424 4.818546 CGAATACTTCAGCAATTCCCATCT 59.181 41.667 0.00 0.00 0.00 2.90
423 426 4.780815 TCGAATACTTCAGCAATTCCCAT 58.219 39.130 0.00 0.00 0.00 4.00
424 427 4.191544 CTCGAATACTTCAGCAATTCCCA 58.808 43.478 0.00 0.00 0.00 4.37
425 428 3.561725 CCTCGAATACTTCAGCAATTCCC 59.438 47.826 0.00 0.00 0.00 3.97
427 430 5.352284 TCTCCTCGAATACTTCAGCAATTC 58.648 41.667 0.00 0.00 0.00 2.17
428 431 5.127845 TCTCTCCTCGAATACTTCAGCAATT 59.872 40.000 0.00 0.00 0.00 2.32
429 432 4.646945 TCTCTCCTCGAATACTTCAGCAAT 59.353 41.667 0.00 0.00 0.00 3.56
430 433 4.017126 TCTCTCCTCGAATACTTCAGCAA 58.983 43.478 0.00 0.00 0.00 3.91
432 435 3.630312 ACTCTCTCCTCGAATACTTCAGC 59.370 47.826 0.00 0.00 0.00 4.26
433 436 6.708502 TCATACTCTCTCCTCGAATACTTCAG 59.291 42.308 0.00 0.00 0.00 3.02
434 437 6.592870 TCATACTCTCTCCTCGAATACTTCA 58.407 40.000 0.00 0.00 0.00 3.02
435 438 7.681939 ATCATACTCTCTCCTCGAATACTTC 57.318 40.000 0.00 0.00 0.00 3.01
436 439 9.747898 ATAATCATACTCTCTCCTCGAATACTT 57.252 33.333 0.00 0.00 0.00 2.24
437 440 9.391006 GATAATCATACTCTCTCCTCGAATACT 57.609 37.037 0.00 0.00 0.00 2.12
439 442 9.967451 AAGATAATCATACTCTCTCCTCGAATA 57.033 33.333 0.00 0.00 0.00 1.75
440 443 8.877864 AAGATAATCATACTCTCTCCTCGAAT 57.122 34.615 0.00 0.00 0.00 3.34
441 444 8.572185 CAAAGATAATCATACTCTCTCCTCGAA 58.428 37.037 0.00 0.00 0.00 3.71
443 446 7.312154 CCAAAGATAATCATACTCTCTCCTCG 58.688 42.308 0.00 0.00 0.00 4.63
445 448 6.786959 AGCCAAAGATAATCATACTCTCTCCT 59.213 38.462 0.00 0.00 0.00 3.69
447 450 7.814107 CAGAGCCAAAGATAATCATACTCTCTC 59.186 40.741 0.00 0.00 29.85 3.20
448 451 7.289782 ACAGAGCCAAAGATAATCATACTCTCT 59.710 37.037 0.00 0.00 29.85 3.10
449 452 7.384660 CACAGAGCCAAAGATAATCATACTCTC 59.615 40.741 0.00 0.00 29.85 3.20
450 453 7.215789 CACAGAGCCAAAGATAATCATACTCT 58.784 38.462 0.00 0.00 32.40 3.24
451 454 6.073331 GCACAGAGCCAAAGATAATCATACTC 60.073 42.308 0.00 0.00 37.23 2.59
452 455 5.762218 GCACAGAGCCAAAGATAATCATACT 59.238 40.000 0.00 0.00 37.23 2.12
453 456 5.995055 GCACAGAGCCAAAGATAATCATAC 58.005 41.667 0.00 0.00 37.23 2.39
469 472 2.122783 TTTAAATCCCCGGCACAGAG 57.877 50.000 0.00 0.00 0.00 3.35
470 473 2.025793 TCATTTAAATCCCCGGCACAGA 60.026 45.455 0.00 0.00 0.00 3.41
472 475 2.025793 TCTCATTTAAATCCCCGGCACA 60.026 45.455 0.00 0.00 0.00 4.57
474 477 3.593442 ATCTCATTTAAATCCCCGGCA 57.407 42.857 0.00 0.00 0.00 5.69
476 479 5.827797 TCAAGAATCTCATTTAAATCCCCGG 59.172 40.000 0.00 0.00 0.00 5.73
477 480 6.016777 CCTCAAGAATCTCATTTAAATCCCCG 60.017 42.308 0.00 0.00 0.00 5.73
478 481 6.239148 GCCTCAAGAATCTCATTTAAATCCCC 60.239 42.308 0.00 0.00 0.00 4.81
479 482 6.514048 CGCCTCAAGAATCTCATTTAAATCCC 60.514 42.308 0.00 0.00 0.00 3.85
482 485 6.599244 TGTCGCCTCAAGAATCTCATTTAAAT 59.401 34.615 0.00 0.00 0.00 1.40
484 487 5.487433 TGTCGCCTCAAGAATCTCATTTAA 58.513 37.500 0.00 0.00 0.00 1.52
486 489 3.942829 TGTCGCCTCAAGAATCTCATTT 58.057 40.909 0.00 0.00 0.00 2.32
487 490 3.616956 TGTCGCCTCAAGAATCTCATT 57.383 42.857 0.00 0.00 0.00 2.57
488 491 3.133542 TCATGTCGCCTCAAGAATCTCAT 59.866 43.478 0.00 0.00 0.00 2.90
490 493 3.122297 CTCATGTCGCCTCAAGAATCTC 58.878 50.000 0.00 0.00 0.00 2.75
491 494 2.762887 TCTCATGTCGCCTCAAGAATCT 59.237 45.455 0.00 0.00 0.00 2.40
492 495 3.122297 CTCTCATGTCGCCTCAAGAATC 58.878 50.000 0.00 0.00 0.00 2.52
493 496 2.158986 CCTCTCATGTCGCCTCAAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
494 497 1.205655 CCTCTCATGTCGCCTCAAGAA 59.794 52.381 0.00 0.00 0.00 2.52
495 498 0.820226 CCTCTCATGTCGCCTCAAGA 59.180 55.000 0.00 0.00 0.00 3.02
496 499 0.820226 TCCTCTCATGTCGCCTCAAG 59.180 55.000 0.00 0.00 0.00 3.02
497 500 1.205655 CTTCCTCTCATGTCGCCTCAA 59.794 52.381 0.00 0.00 0.00 3.02
498 501 0.820226 CTTCCTCTCATGTCGCCTCA 59.180 55.000 0.00 0.00 0.00 3.86
499 502 1.107114 TCTTCCTCTCATGTCGCCTC 58.893 55.000 0.00 0.00 0.00 4.70
530 942 5.408604 CCTATATTCCAAATGTAGTGGCGTC 59.591 44.000 3.72 0.00 35.99 5.19
531 943 5.071250 TCCTATATTCCAAATGTAGTGGCGT 59.929 40.000 3.72 0.00 35.99 5.68
533 945 6.769512 TCTCCTATATTCCAAATGTAGTGGC 58.230 40.000 3.72 0.00 35.99 5.01
545 961 3.181485 CCGGATCGCTTCTCCTATATTCC 60.181 52.174 0.00 0.00 0.00 3.01
551 967 0.472898 TCTCCGGATCGCTTCTCCTA 59.527 55.000 3.57 0.00 0.00 2.94
572 989 2.573009 TGGAGTGAATGAGCAGGAATGA 59.427 45.455 0.00 0.00 0.00 2.57
580 997 4.996788 AATGGAAATGGAGTGAATGAGC 57.003 40.909 0.00 0.00 0.00 4.26
584 1001 7.484993 TGAATGAAATGGAAATGGAGTGAAT 57.515 32.000 0.00 0.00 0.00 2.57
621 1038 4.635473 ACTTGGAATTCCTCTCCCTATGA 58.365 43.478 24.73 0.00 36.82 2.15
623 1040 8.814448 TTATAACTTGGAATTCCTCTCCCTAT 57.186 34.615 24.73 14.89 36.82 2.57
641 1059 6.819947 AAATCGGACCCTTACCTTATAACT 57.180 37.500 0.00 0.00 0.00 2.24
645 1063 6.323210 AGAAAAATCGGACCCTTACCTTAT 57.677 37.500 0.00 0.00 0.00 1.73
650 1068 6.080648 ACAAAAGAAAAATCGGACCCTTAC 57.919 37.500 0.00 0.00 0.00 2.34
652 1070 4.647399 TGACAAAAGAAAAATCGGACCCTT 59.353 37.500 0.00 0.00 0.00 3.95
658 1076 5.687285 CAGTCCTTGACAAAAGAAAAATCGG 59.313 40.000 0.00 0.00 34.60 4.18
682 1100 3.942829 TGTGGTGATTTGACAGAGGATC 58.057 45.455 0.00 0.00 0.00 3.36
907 1368 3.493524 GGGCTGCAGAATACTCCTAGTTC 60.494 52.174 20.43 0.00 0.00 3.01
2193 4165 3.247442 GTGACGATAACAACGATGGTGA 58.753 45.455 0.00 0.00 34.70 4.02
2240 4212 2.755655 AGGAGGTATCTGTCACTCAACG 59.244 50.000 0.00 0.00 0.00 4.10
2904 6921 3.815401 GGCTGAACTTGCTCTCTTTTACA 59.185 43.478 0.00 0.00 0.00 2.41
3285 7331 0.948623 CTTGGTCGTCGTGGATGCAA 60.949 55.000 0.00 0.00 0.00 4.08
3307 7353 0.608130 TCACTCATCCAACCCTGACG 59.392 55.000 0.00 0.00 0.00 4.35
3505 7574 7.936847 TGAATACCAATCTTATACACCATGGAC 59.063 37.037 21.47 0.00 0.00 4.02
3573 7642 8.870160 TTGATTTTACCATCAGACAAAAACTG 57.130 30.769 0.00 0.00 34.59 3.16
3588 7657 5.170748 CAGGCAAATGACCTTGATTTTACC 58.829 41.667 0.00 0.00 34.42 2.85
3618 7687 9.574516 AACTCATTCCAAAGTCTACTAAAACAT 57.425 29.630 0.00 0.00 0.00 2.71
3619 7688 8.836413 CAACTCATTCCAAAGTCTACTAAAACA 58.164 33.333 0.00 0.00 0.00 2.83
3718 7790 4.504858 ACTTGCCAAGTAGTACTGCATAC 58.495 43.478 8.67 0.00 40.69 2.39
4007 8086 9.643652 CTAGAAAGAGTCATAAAAATTCATCGC 57.356 33.333 0.00 0.00 0.00 4.58
4126 8208 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
4195 8277 6.381420 AGTGCACACCAGAGTAGAGTAAATAT 59.619 38.462 21.04 0.00 0.00 1.28
4196 8278 5.715279 AGTGCACACCAGAGTAGAGTAAATA 59.285 40.000 21.04 0.00 0.00 1.40
4197 8279 4.528596 AGTGCACACCAGAGTAGAGTAAAT 59.471 41.667 21.04 0.00 0.00 1.40
4202 8284 1.067283 CCAGTGCACACCAGAGTAGAG 60.067 57.143 21.04 0.00 0.00 2.43
4307 8397 9.350951 AGATAGATCATTGCTTTTCAATCATCA 57.649 29.630 4.75 0.00 42.82 3.07
4309 8399 9.350951 TCAGATAGATCATTGCTTTTCAATCAT 57.649 29.630 0.00 0.00 43.21 2.45
4353 8443 6.309494 TCAGTACCGAATCATGAGTTAAAACG 59.691 38.462 0.09 0.00 0.00 3.60
4363 8453 6.961359 TTGTAGTTTCAGTACCGAATCATG 57.039 37.500 3.39 0.00 0.00 3.07
4397 8487 3.826236 ACGTAGCAGTACAGTACAGTG 57.174 47.619 13.37 4.69 0.00 3.66
4401 8491 5.931532 TCAGTAAACGTAGCAGTACAGTAC 58.068 41.667 2.05 2.05 0.00 2.73
4436 8526 6.887626 AATGCCAAGAAAAATGCAAGAAAT 57.112 29.167 0.00 0.00 37.27 2.17
4472 8566 2.571212 TGACTTGACGAAAATGCTGGT 58.429 42.857 0.00 0.00 0.00 4.00
4550 8645 2.813754 CCAATTGTGGTCTTCGACACAT 59.186 45.455 7.33 0.00 40.42 3.21
4582 8677 1.399714 TATCGGTCATGACTCGCCTT 58.600 50.000 24.50 15.21 0.00 4.35
4683 8784 1.573857 TGGTACTCTAGCCCCTCATCA 59.426 52.381 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.