Multiple sequence alignment - TraesCS6A01G040000

Loading Multiple Alignment...

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 TraesCS6A01G040000 chr6A 100.000 3087 0 0 1 3087 20546374 20549460 0.000000e+00 5701
1 TraesCS6A01G040000 chr6A 86.174 745 98 4 1208 1948 405817921 405818664 0.000000e+00 800
2 TraesCS6A01G040000 chr3B 86.869 990 117 5 2109 3087 169946392 169947379 0.000000e+00 1096
3 TraesCS6A01G040000 chr3B 90.977 266 23 1 943 1207 1789853 1789588 1.050000e-94 357
4 TraesCS6A01G040000 chr3B 91.925 161 13 0 1950 2110 1789593 1789433 3.100000e-55 226
5 TraesCS6A01G040000 chr3B 84.689 209 32 0 1 209 160452991 160452783 3.120000e-50 209
6 TraesCS6A01G040000 chr3B 89.796 147 15 0 2109 2255 160452797 160452651 4.060000e-44 189
7 TraesCS6A01G040000 chr1B 89.785 744 72 3 1208 1947 29783617 29784360 0.000000e+00 950
8 TraesCS6A01G040000 chr1B 86.294 197 21 6 2893 3087 185923813 185924005 3.120000e-50 209
9 TraesCS6A01G040000 chr2A 84.359 991 128 10 2109 3082 264423757 264422777 0.000000e+00 946
10 TraesCS6A01G040000 chr2A 91.443 409 34 1 538 945 156772821 156773229 7.480000e-156 560
11 TraesCS6A01G040000 chr2A 90.954 409 36 1 538 945 156769824 156770232 1.620000e-152 549
12 TraesCS6A01G040000 chr1A 89.382 744 75 3 1207 1946 500557612 500556869 0.000000e+00 933
13 TraesCS6A01G040000 chr1A 92.020 401 30 2 544 943 513367023 513366624 2.080000e-156 562
14 TraesCS6A01G040000 chr7D 89.128 745 76 4 1208 1948 36908347 36909090 0.000000e+00 922
15 TraesCS6A01G040000 chr7D 88.172 744 80 7 1208 1947 106359334 106360073 0.000000e+00 880
16 TraesCS6A01G040000 chr7D 91.791 402 30 3 544 943 266697932 266698332 9.670000e-155 556
17 TraesCS6A01G040000 chr7D 87.819 353 35 5 203 554 439710027 439709682 1.030000e-109 407
18 TraesCS6A01G040000 chr1D 88.874 746 75 7 1208 1947 13888626 13887883 0.000000e+00 911
19 TraesCS6A01G040000 chr1D 88.188 745 82 5 1208 1947 13972257 13971514 0.000000e+00 883
20 TraesCS6A01G040000 chr1D 92.079 404 29 3 544 944 436968168 436967765 1.610000e-157 566
21 TraesCS6A01G040000 chr1D 96.981 265 8 0 943 1207 159952220 159952484 2.180000e-121 446
22 TraesCS6A01G040000 chr1D 94.410 161 9 0 1950 2110 159952479 159952639 6.610000e-62 248
23 TraesCS6A01G040000 chr1D 86.842 190 21 4 2899 3087 263890115 263889929 3.120000e-50 209
24 TraesCS6A01G040000 chr1D 83.784 148 23 1 2110 2256 166641747 166641600 4.150000e-29 139
25 TraesCS6A01G040000 chr7B 88.353 747 79 7 1207 1947 609010967 609011711 0.000000e+00 891
26 TraesCS6A01G040000 chr7B 92.442 344 21 2 203 546 651392273 651391935 1.290000e-133 486
27 TraesCS6A01G040000 chr7B 95.113 266 12 1 943 1207 651391941 651391676 4.760000e-113 418
28 TraesCS6A01G040000 chr5A 88.259 758 69 12 1208 1947 370166721 370165966 0.000000e+00 889
29 TraesCS6A01G040000 chr5A 88.372 344 35 3 203 546 592306266 592305928 2.870000e-110 409
30 TraesCS6A01G040000 chr5A 92.830 265 19 0 943 1207 194720659 194720923 4.830000e-103 385
31 TraesCS6A01G040000 chr5A 92.337 261 20 0 943 1203 592305934 592305674 3.760000e-99 372
32 TraesCS6A01G040000 chr3D 92.500 400 27 3 545 943 143130275 143129878 1.240000e-158 569
33 TraesCS6A01G040000 chr3D 90.754 411 36 2 536 945 211156897 211157306 5.820000e-152 547
34 TraesCS6A01G040000 chr3D 90.778 347 23 7 200 546 188362703 188363040 3.630000e-124 455
35 TraesCS6A01G040000 chr3D 90.504 337 25 4 211 546 93477755 93477425 3.650000e-119 438
36 TraesCS6A01G040000 chr3D 93.962 265 16 0 943 1207 93477431 93477167 4.790000e-108 401
37 TraesCS6A01G040000 chr3D 92.593 162 9 1 1950 2111 188363249 188363407 2.390000e-56 230
38 TraesCS6A01G040000 chr3D 87.065 201 20 6 2889 3087 124206414 124206610 4.010000e-54 222
39 TraesCS6A01G040000 chr3D 86.911 191 20 4 2899 3087 480655855 480656042 3.120000e-50 209
40 TraesCS6A01G040000 chr3D 85.235 149 21 1 2110 2257 385409453 385409305 5.330000e-33 152
41 TraesCS6A01G040000 chr4D 92.405 395 28 2 549 942 57150867 57150474 2.080000e-156 562
42 TraesCS6A01G040000 chr4D 91.563 403 32 2 544 944 203460391 203460793 3.480000e-154 555
43 TraesCS6A01G040000 chr4D 85.906 149 19 2 2110 2257 475457088 475456941 1.150000e-34 158
44 TraesCS6A01G040000 chr4D 84.564 149 21 2 2110 2257 475420582 475420435 2.480000e-31 147
45 TraesCS6A01G040000 chr4A 92.507 347 21 2 200 546 4888759 4889100 2.770000e-135 492
46 TraesCS6A01G040000 chr4A 95.849 265 11 0 943 1207 4889094 4889358 2.200000e-116 429
47 TraesCS6A01G040000 chr4A 95.395 152 7 0 1950 2101 4889353 4889504 3.080000e-60 243
48 TraesCS6A01G040000 chr4A 82.589 224 35 4 2865 3087 464805704 464805924 8.730000e-46 195
49 TraesCS6A01G040000 chr4A 85.340 191 17 5 2447 2626 43603086 43602896 1.460000e-43 187
50 TraesCS6A01G040000 chr4A 91.262 103 8 1 3 105 381560056 381560157 4.150000e-29 139
51 TraesCS6A01G040000 chr6D 90.988 344 24 4 203 546 32688391 32688055 1.010000e-124 457
52 TraesCS6A01G040000 chr6D 95.472 265 12 0 943 1207 48682532 48682268 1.020000e-114 424
53 TraesCS6A01G040000 chr6D 93.962 265 16 0 943 1207 32688061 32687797 4.790000e-108 401
54 TraesCS6A01G040000 chr6D 93.939 165 10 0 1950 2114 48682273 48682109 1.840000e-62 250
55 TraesCS6A01G040000 chr6D 92.121 165 10 3 1950 2112 32687802 32687639 2.390000e-56 230
56 TraesCS6A01G040000 chr6D 81.879 149 26 1 2110 2257 389318435 389318583 1.160000e-24 124
57 TraesCS6A01G040000 chr3A 91.071 336 24 4 211 545 211952314 211952644 1.690000e-122 449
58 TraesCS6A01G040000 chr3A 92.727 165 12 0 1950 2114 718370535 718370371 3.980000e-59 239
59 TraesCS6A01G040000 chr2D 86.969 353 37 6 203 554 574398102 574397758 3.730000e-104 388
60 TraesCS6A01G040000 chr2D 87.179 195 17 7 2895 3087 651024747 651024935 6.700000e-52 215
61 TraesCS6A01G040000 chr5D 94.444 162 9 0 1950 2111 29519742 29519903 1.840000e-62 250
62 TraesCS6A01G040000 chr5D 79.038 291 51 8 2801 3087 325329206 325328922 1.130000e-44 191
63 TraesCS6A01G040000 chr5B 93.827 162 10 0 1950 2111 21652845 21653006 8.550000e-61 244
64 TraesCS6A01G040000 chrUn 84.564 149 22 1 2110 2257 112013524 112013376 2.480000e-31 147


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 TraesCS6A01G040000 chr6A 20546374 20549460 3086 False 5701.000000 5701 100.000000 1 3087 1 chr6A.!!$F1 3086
1 TraesCS6A01G040000 chr6A 405817921 405818664 743 False 800.000000 800 86.174000 1208 1948 1 chr6A.!!$F2 740
2 TraesCS6A01G040000 chr3B 169946392 169947379 987 False 1096.000000 1096 86.869000 2109 3087 1 chr3B.!!$F1 978
3 TraesCS6A01G040000 chr1B 29783617 29784360 743 False 950.000000 950 89.785000 1208 1947 1 chr1B.!!$F1 739
4 TraesCS6A01G040000 chr2A 264422777 264423757 980 True 946.000000 946 84.359000 2109 3082 1 chr2A.!!$R1 973
5 TraesCS6A01G040000 chr2A 156769824 156773229 3405 False 554.500000 560 91.198500 538 945 2 chr2A.!!$F1 407
6 TraesCS6A01G040000 chr1A 500556869 500557612 743 True 933.000000 933 89.382000 1207 1946 1 chr1A.!!$R1 739
7 TraesCS6A01G040000 chr7D 36908347 36909090 743 False 922.000000 922 89.128000 1208 1948 1 chr7D.!!$F1 740
8 TraesCS6A01G040000 chr7D 106359334 106360073 739 False 880.000000 880 88.172000 1208 1947 1 chr7D.!!$F2 739
9 TraesCS6A01G040000 chr1D 13887883 13888626 743 True 911.000000 911 88.874000 1208 1947 1 chr1D.!!$R1 739
10 TraesCS6A01G040000 chr1D 13971514 13972257 743 True 883.000000 883 88.188000 1208 1947 1 chr1D.!!$R2 739
11 TraesCS6A01G040000 chr7B 609010967 609011711 744 False 891.000000 891 88.353000 1207 1947 1 chr7B.!!$F1 740
12 TraesCS6A01G040000 chr7B 651391676 651392273 597 True 452.000000 486 93.777500 203 1207 2 chr7B.!!$R1 1004
13 TraesCS6A01G040000 chr5A 370165966 370166721 755 True 889.000000 889 88.259000 1208 1947 1 chr5A.!!$R1 739
14 TraesCS6A01G040000 chr5A 592305674 592306266 592 True 390.500000 409 90.354500 203 1203 2 chr5A.!!$R2 1000
15 TraesCS6A01G040000 chr3D 93477167 93477755 588 True 419.500000 438 92.233000 211 1207 2 chr3D.!!$R3 996
16 TraesCS6A01G040000 chr3D 188362703 188363407 704 False 342.500000 455 91.685500 200 2111 2 chr3D.!!$F4 1911
17 TraesCS6A01G040000 chr4A 4888759 4889504 745 False 388.000000 492 94.583667 200 2101 3 chr4A.!!$F3 1901
18 TraesCS6A01G040000 chr6D 32687639 32688391 752 True 362.666667 457 92.357000 203 2112 3 chr6D.!!$R1 1909

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
709 3708 0.105709 GAGAGGGAGGAAGGGAGAGG 60.106 65.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 5392 0.618458 CCCCGGTTTCCTCTGAATCA 59.382 55.0 0.0 0.0 0.0 2.57 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
45 46 4.415783 GGTGAACCGGAAGCCAAT 57.584 55.556 9.46 0.00 0.00 3.16
46 47 2.180674 GGTGAACCGGAAGCCAATC 58.819 57.895 9.46 0.00 0.00 2.67
47 48 1.313091 GGTGAACCGGAAGCCAATCC 61.313 60.000 9.46 0.00 36.05 3.01
48 49 0.322546 GTGAACCGGAAGCCAATCCT 60.323 55.000 9.46 0.00 37.34 3.24
49 50 0.322456 TGAACCGGAAGCCAATCCTG 60.322 55.000 9.46 0.00 37.34 3.86
50 51 1.657751 GAACCGGAAGCCAATCCTGC 61.658 60.000 9.46 0.00 37.34 4.85
51 52 3.204827 CCGGAAGCCAATCCTGCG 61.205 66.667 0.00 0.00 37.34 5.18
52 53 3.204827 CGGAAGCCAATCCTGCGG 61.205 66.667 0.00 0.00 37.34 5.69
53 54 2.830370 GGAAGCCAATCCTGCGGG 60.830 66.667 4.71 4.71 36.50 6.13
54 55 2.272146 GAAGCCAATCCTGCGGGA 59.728 61.111 18.80 18.80 46.81 5.14
55 56 1.821332 GAAGCCAATCCTGCGGGAG 60.821 63.158 21.28 7.73 45.86 4.30
56 57 2.543067 GAAGCCAATCCTGCGGGAGT 62.543 60.000 21.28 15.69 45.86 3.85
57 58 1.271840 AAGCCAATCCTGCGGGAGTA 61.272 55.000 21.28 0.00 45.86 2.59
58 59 1.227674 GCCAATCCTGCGGGAGTAG 60.228 63.158 21.28 12.11 45.86 2.57
59 60 1.227674 CCAATCCTGCGGGAGTAGC 60.228 63.158 21.28 0.00 45.86 3.58
60 61 1.592669 CAATCCTGCGGGAGTAGCG 60.593 63.158 21.28 1.53 45.86 4.26
61 62 3.447025 AATCCTGCGGGAGTAGCGC 62.447 63.158 21.28 0.00 45.86 5.92
77 78 4.893601 GCGGGCGGCTTAGGAGAC 62.894 72.222 9.56 0.00 39.11 3.36
78 79 3.458163 CGGGCGGCTTAGGAGACA 61.458 66.667 9.56 0.00 0.00 3.41
79 80 2.501610 GGGCGGCTTAGGAGACAG 59.498 66.667 9.56 0.00 0.00 3.51
80 81 2.501610 GGCGGCTTAGGAGACAGG 59.498 66.667 0.00 0.00 0.00 4.00
81 82 2.058595 GGCGGCTTAGGAGACAGGA 61.059 63.158 0.00 0.00 0.00 3.86
82 83 1.142097 GCGGCTTAGGAGACAGGAC 59.858 63.158 0.00 0.00 0.00 3.85
83 84 1.817209 CGGCTTAGGAGACAGGACC 59.183 63.158 0.00 0.00 0.00 4.46
84 85 1.817209 GGCTTAGGAGACAGGACCG 59.183 63.158 0.00 0.00 0.00 4.79
85 86 1.142097 GCTTAGGAGACAGGACCGC 59.858 63.158 0.00 0.00 0.00 5.68
86 87 1.433879 CTTAGGAGACAGGACCGCG 59.566 63.158 0.00 0.00 0.00 6.46
87 88 2.615262 CTTAGGAGACAGGACCGCGC 62.615 65.000 0.00 0.00 0.00 6.86
88 89 3.640257 TAGGAGACAGGACCGCGCT 62.640 63.158 5.56 0.00 0.00 5.92
89 90 4.803426 GGAGACAGGACCGCGCTG 62.803 72.222 5.56 5.50 0.00 5.18
90 91 4.803426 GAGACAGGACCGCGCTGG 62.803 72.222 15.19 15.25 46.41 4.85
110 111 4.819761 GCACATCCGAGCCAGCGA 62.820 66.667 0.00 0.00 0.00 4.93
111 112 2.584418 CACATCCGAGCCAGCGAG 60.584 66.667 0.00 0.00 0.00 5.03
112 113 4.521062 ACATCCGAGCCAGCGAGC 62.521 66.667 0.00 0.00 0.00 5.03
134 135 3.208335 GGCTCAGGAGACGGGTAC 58.792 66.667 0.00 0.00 0.00 3.34
136 137 2.799371 CTCAGGAGACGGGTACGC 59.201 66.667 0.00 0.00 46.04 4.42
137 138 2.034532 TCAGGAGACGGGTACGCA 59.965 61.111 10.84 0.00 46.04 5.24
138 139 1.994507 CTCAGGAGACGGGTACGCAG 61.995 65.000 10.84 5.58 46.04 5.18
139 140 2.754658 AGGAGACGGGTACGCAGG 60.755 66.667 10.84 0.00 46.04 4.85
140 141 4.509737 GGAGACGGGTACGCAGGC 62.510 72.222 10.84 5.21 46.04 4.85
141 142 4.849329 GAGACGGGTACGCAGGCG 62.849 72.222 12.71 12.71 46.04 5.52
146 147 4.530857 GGGTACGCAGGCGCAGAT 62.531 66.667 14.32 0.00 44.19 2.90
147 148 2.962253 GGTACGCAGGCGCAGATC 60.962 66.667 14.32 0.00 44.19 2.75
148 149 3.323136 GTACGCAGGCGCAGATCG 61.323 66.667 14.32 9.44 44.19 3.69
149 150 3.822192 TACGCAGGCGCAGATCGT 61.822 61.111 14.32 15.07 44.19 3.73
152 153 4.819761 GCAGGCGCAGATCGTGGA 62.820 66.667 10.83 0.00 41.07 4.02
153 154 2.584418 CAGGCGCAGATCGTGGAG 60.584 66.667 10.83 0.00 41.07 3.86
154 155 3.842923 AGGCGCAGATCGTGGAGG 61.843 66.667 10.83 0.00 41.07 4.30
155 156 3.838271 GGCGCAGATCGTGGAGGA 61.838 66.667 10.83 0.00 41.07 3.71
156 157 2.419198 GCGCAGATCGTGGAGGAT 59.581 61.111 0.30 0.00 41.07 3.24
157 158 1.227380 GCGCAGATCGTGGAGGATT 60.227 57.895 0.30 0.00 41.07 3.01
158 159 1.218230 GCGCAGATCGTGGAGGATTC 61.218 60.000 0.30 0.00 41.07 2.52
159 160 0.598680 CGCAGATCGTGGAGGATTCC 60.599 60.000 0.00 0.00 44.31 3.01
167 168 2.499685 GGAGGATTCCGGGTCGTG 59.500 66.667 0.00 0.00 32.79 4.35
168 169 2.056223 GGAGGATTCCGGGTCGTGA 61.056 63.158 0.00 0.00 32.79 4.35
169 170 1.141234 GAGGATTCCGGGTCGTGAC 59.859 63.158 0.00 0.00 0.00 3.67
178 179 4.736896 GGTCGTGACCGGCTCCAC 62.737 72.222 0.00 6.77 42.29 4.02
179 180 3.681835 GTCGTGACCGGCTCCACT 61.682 66.667 16.73 0.00 35.32 4.00
180 181 2.915659 TCGTGACCGGCTCCACTT 60.916 61.111 16.73 0.00 33.95 3.16
181 182 2.432628 CGTGACCGGCTCCACTTC 60.433 66.667 16.73 0.51 0.00 3.01
182 183 2.932234 CGTGACCGGCTCCACTTCT 61.932 63.158 16.73 0.00 0.00 2.85
183 184 1.374758 GTGACCGGCTCCACTTCTG 60.375 63.158 0.00 0.00 0.00 3.02
184 185 2.266055 GACCGGCTCCACTTCTGG 59.734 66.667 0.00 0.00 39.23 3.86
185 186 3.316573 GACCGGCTCCACTTCTGGG 62.317 68.421 0.00 0.00 38.25 4.45
186 187 3.322466 CCGGCTCCACTTCTGGGT 61.322 66.667 0.00 0.00 38.25 4.51
187 188 2.750350 CGGCTCCACTTCTGGGTT 59.250 61.111 0.00 0.00 38.25 4.11
188 189 1.672356 CGGCTCCACTTCTGGGTTG 60.672 63.158 0.00 0.00 38.25 3.77
189 190 1.456287 GGCTCCACTTCTGGGTTGT 59.544 57.895 0.00 0.00 38.25 3.32
190 191 0.178990 GGCTCCACTTCTGGGTTGTT 60.179 55.000 0.00 0.00 38.25 2.83
191 192 0.954452 GCTCCACTTCTGGGTTGTTG 59.046 55.000 0.00 0.00 38.25 3.33
192 193 1.750682 GCTCCACTTCTGGGTTGTTGT 60.751 52.381 0.00 0.00 38.25 3.32
193 194 2.222027 CTCCACTTCTGGGTTGTTGTC 58.778 52.381 0.00 0.00 38.25 3.18
194 195 1.562008 TCCACTTCTGGGTTGTTGTCA 59.438 47.619 0.00 0.00 38.25 3.58
195 196 2.025793 TCCACTTCTGGGTTGTTGTCAA 60.026 45.455 0.00 0.00 38.25 3.18
196 197 2.358898 CCACTTCTGGGTTGTTGTCAAG 59.641 50.000 0.00 0.00 33.97 3.02
197 198 2.358898 CACTTCTGGGTTGTTGTCAAGG 59.641 50.000 0.00 0.00 33.97 3.61
198 199 2.241176 ACTTCTGGGTTGTTGTCAAGGA 59.759 45.455 0.00 0.00 33.97 3.36
199 200 2.638480 TCTGGGTTGTTGTCAAGGAG 57.362 50.000 0.00 0.00 33.97 3.69
200 201 1.142870 TCTGGGTTGTTGTCAAGGAGG 59.857 52.381 0.00 0.00 33.97 4.30
201 202 0.467290 TGGGTTGTTGTCAAGGAGGC 60.467 55.000 0.00 0.00 33.97 4.70
202 203 1.515521 GGGTTGTTGTCAAGGAGGCG 61.516 60.000 0.00 0.00 33.97 5.52
203 204 0.534203 GGTTGTTGTCAAGGAGGCGA 60.534 55.000 0.00 0.00 33.97 5.54
204 205 0.868406 GTTGTTGTCAAGGAGGCGAG 59.132 55.000 0.00 0.00 33.97 5.03
205 206 0.250295 TTGTTGTCAAGGAGGCGAGG 60.250 55.000 0.00 0.00 0.00 4.63
206 207 2.035442 GTTGTCAAGGAGGCGAGGC 61.035 63.158 0.00 0.00 0.00 4.70
207 208 3.589654 TTGTCAAGGAGGCGAGGCG 62.590 63.158 0.00 0.00 0.00 5.52
208 209 3.760035 GTCAAGGAGGCGAGGCGA 61.760 66.667 0.00 0.00 0.00 5.54
209 210 2.994995 TCAAGGAGGCGAGGCGAA 60.995 61.111 0.00 0.00 0.00 4.70
326 327 0.984230 ATGGGAAAGACGGAAGCTGA 59.016 50.000 0.00 0.00 0.00 4.26
377 379 7.937700 ACTTAGATCTCAATGGGGATTCTTA 57.062 36.000 0.00 0.00 0.00 2.10
388 390 7.610305 TCAATGGGGATTCTTACTCTAACAAAC 59.390 37.037 0.00 0.00 0.00 2.93
392 394 7.447238 TGGGGATTCTTACTCTAACAAACTTTG 59.553 37.037 0.00 0.00 0.00 2.77
446 448 5.200483 TCAAAATGGAGAGTTGGTCTTGTT 58.800 37.500 0.00 0.00 34.71 2.83
466 468 5.617252 TGTTCTCCAAGAGGTTTCGTTAAT 58.383 37.500 0.00 0.00 35.89 1.40
506 508 5.812642 TCTTTTGATCACGATCTTCTTAGGC 59.187 40.000 8.43 0.00 38.60 3.93
509 511 3.130516 TGATCACGATCTTCTTAGGCGTT 59.869 43.478 8.43 0.00 38.60 4.84
510 512 3.146618 TCACGATCTTCTTAGGCGTTC 57.853 47.619 0.00 0.00 32.97 3.95
511 513 2.159282 TCACGATCTTCTTAGGCGTTCC 60.159 50.000 0.00 0.00 32.97 3.62
512 514 1.822990 ACGATCTTCTTAGGCGTTCCA 59.177 47.619 0.00 0.00 31.87 3.53
528 530 2.446848 CCATCCATGGGAGCGGTCT 61.447 63.158 13.02 0.00 44.31 3.85
542 544 1.762419 CGGTCTTTCGAGACGACAAA 58.238 50.000 11.29 0.00 39.57 2.83
547 549 0.942410 TTTCGAGACGACAAAGGCCG 60.942 55.000 0.00 0.00 34.89 6.13
553 555 1.202557 AGACGACAAAGGCCGTGTTTA 60.203 47.619 15.30 0.00 39.30 2.01
559 561 3.998341 GACAAAGGCCGTGTTTAGATACA 59.002 43.478 15.30 0.00 0.00 2.29
565 567 4.221262 AGGCCGTGTTTAGATACACTAACA 59.779 41.667 0.00 0.00 44.85 2.41
566 568 4.328169 GGCCGTGTTTAGATACACTAACAC 59.672 45.833 0.00 0.00 44.85 3.32
568 570 5.406175 GCCGTGTTTAGATACACTAACACAA 59.594 40.000 14.81 0.00 44.85 3.33
605 3604 9.368674 GAGTTAGATTCTAACCTTGAACTAACC 57.631 37.037 25.81 4.05 37.89 2.85
620 3619 7.463961 TGAACTAACCCTGAACTAACTCTAG 57.536 40.000 0.00 0.00 0.00 2.43
657 3656 0.461548 TGGCAGAGTTAGATGGAGCG 59.538 55.000 0.00 0.00 0.00 5.03
665 3664 1.000607 GTTAGATGGAGCGCGGATACA 60.001 52.381 8.83 0.00 0.00 2.29
709 3708 0.105709 GAGAGGGAGGAAGGGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
718 3717 0.458260 GAAGGGAGAGGACGAGAAGC 59.542 60.000 0.00 0.00 0.00 3.86
739 3738 2.359967 CGAGGAAGTGGGGAGGGAC 61.360 68.421 0.00 0.00 0.00 4.46
766 3766 3.059188 TGCGGCGAAAGTAAGAGAAAAAG 60.059 43.478 12.98 0.00 0.00 2.27
867 3867 4.202631 TGCATCTAACCCAAACTAACCCTT 60.203 41.667 0.00 0.00 0.00 3.95
875 3875 4.211920 CCCAAACTAACCCTTCTGTTTGA 58.788 43.478 15.97 0.00 46.90 2.69
876 3876 4.647399 CCCAAACTAACCCTTCTGTTTGAA 59.353 41.667 15.97 0.00 46.90 2.69
885 3885 9.423061 CTAACCCTTCTGTTTGAATATTTTTGG 57.577 33.333 0.00 0.00 33.71 3.28
975 3975 3.645212 TCATAGCTGGAGGGAATGAGAAG 59.355 47.826 0.00 0.00 0.00 2.85
1045 4046 1.019278 CGGTCTAACACTGGCGCAAT 61.019 55.000 10.83 0.00 0.00 3.56
1183 4184 9.502145 TTCATTATGCTTGTGATTTCGTTATTC 57.498 29.630 0.00 0.00 0.00 1.75
1202 4203 7.491372 CGTTATTCCTAGATTTGAGCACTGTAA 59.509 37.037 0.00 0.00 0.00 2.41
1203 4204 9.331282 GTTATTCCTAGATTTGAGCACTGTAAT 57.669 33.333 0.00 0.00 0.00 1.89
1215 4216 4.446371 AGCACTGTAATAGGTCAAGATGC 58.554 43.478 0.00 0.00 0.00 3.91
1260 4261 0.486879 TTGCCTTCCCAAACCCATCT 59.513 50.000 0.00 0.00 0.00 2.90
1319 4333 1.448893 TACGCGGGGCTAGCTTTTG 60.449 57.895 15.72 3.62 0.00 2.44
1326 4340 2.877691 GCTAGCTTTTGGCCCGTG 59.122 61.111 7.70 0.00 43.05 4.94
1363 4377 4.784177 AGTTTTCTAAACCCACGAGGAAA 58.216 39.130 0.00 0.00 39.89 3.13
1518 4533 2.716217 AGCAGCCTCAAAGTTGGATAC 58.284 47.619 0.00 0.00 0.00 2.24
1531 4546 0.611200 TGGATACCGTGTTCCACCAG 59.389 55.000 1.84 0.00 37.10 4.00
1536 4551 0.395173 ACCGTGTTCCACCAGCTTTT 60.395 50.000 0.00 0.00 0.00 2.27
1544 4559 2.676748 TCCACCAGCTTTTCACCAATT 58.323 42.857 0.00 0.00 0.00 2.32
1550 4565 5.990996 CACCAGCTTTTCACCAATTTAACAT 59.009 36.000 0.00 0.00 0.00 2.71
1553 4568 6.307800 CCAGCTTTTCACCAATTTAACATACG 59.692 38.462 0.00 0.00 0.00 3.06
1571 4588 7.316544 ACATACGGATTTATCTTTGGACAAC 57.683 36.000 0.00 0.00 0.00 3.32
1582 4599 3.575256 TCTTTGGACAACGGAACTAGCTA 59.425 43.478 0.00 0.00 0.00 3.32
1600 4617 7.384477 ACTAGCTAATCTTTCAAGTAACGGTT 58.616 34.615 0.00 0.00 0.00 4.44
1707 4726 2.345124 AGAGAATGAGCAAGATGGCC 57.655 50.000 0.00 0.00 0.00 5.36
1799 4820 1.073373 TTTCGGGTTCGGGCATTGA 59.927 52.632 0.00 0.00 36.95 2.57
1800 4821 0.537600 TTTCGGGTTCGGGCATTGAA 60.538 50.000 0.00 0.00 36.95 2.69
1897 4918 2.370849 GCCCATCCTCGTTCCCTAATAA 59.629 50.000 0.00 0.00 0.00 1.40
1948 4969 2.048444 GCTCCATTGCCATCTTGAGA 57.952 50.000 0.00 0.00 0.00 3.27
1949 4970 2.372264 GCTCCATTGCCATCTTGAGAA 58.628 47.619 0.00 0.00 0.00 2.87
1963 4984 6.405176 CCATCTTGAGAAATAGGGAAGCAAAC 60.405 42.308 0.00 0.00 0.00 2.93
1978 4999 5.278463 GGAAGCAAACAAAGTAGCTCATGAA 60.278 40.000 0.00 0.00 36.07 2.57
2063 5084 9.559958 AAATTGTAATGATCTTGACAAACGATC 57.440 29.630 13.93 9.44 35.56 3.69
2120 5141 1.975680 TCAGTAAAAAGGAGGCGAGGT 59.024 47.619 0.00 0.00 0.00 3.85
2187 5208 0.884704 GCAAGACCGGCTTCAAGACA 60.885 55.000 0.00 0.00 33.60 3.41
2243 5264 2.520536 AAGGGCGGCTCAGTCAAGT 61.521 57.895 9.56 0.00 0.00 3.16
2246 5267 2.031163 GCGGCTCAGTCAAGTGGT 59.969 61.111 0.00 0.00 0.00 4.16
2344 5365 1.066605 GATTAGTTACGCTGGCGAGGA 59.933 52.381 21.77 3.65 42.83 3.71
2345 5366 0.171903 TTAGTTACGCTGGCGAGGAC 59.828 55.000 21.77 14.84 42.83 3.85
2346 5367 0.961857 TAGTTACGCTGGCGAGGACA 60.962 55.000 21.77 1.09 42.83 4.02
2353 5374 2.601666 TGGCGAGGACAGCTCAGT 60.602 61.111 0.00 0.00 34.52 3.41
2371 5392 0.905337 GTACAGTGGAGGAGCAGGGT 60.905 60.000 0.00 0.00 0.00 4.34
2377 5398 0.547471 TGGAGGAGCAGGGTGATTCA 60.547 55.000 0.00 0.00 0.00 2.57
2389 5410 1.679032 GGTGATTCAGAGGAAACCGGG 60.679 57.143 6.32 0.00 36.43 5.73
2395 5416 4.468689 GAGGAAACCGGGGGCTCG 62.469 72.222 6.32 0.00 0.00 5.03
2540 5572 1.536284 GCCGTATCCTCTTCTTGGTCG 60.536 57.143 0.00 0.00 0.00 4.79
2545 5577 1.420430 TCCTCTTCTTGGTCGTGGTT 58.580 50.000 0.00 0.00 0.00 3.67
2553 5585 2.169769 TCTTGGTCGTGGTTCACTTCTT 59.830 45.455 0.00 0.00 31.34 2.52
2570 5602 6.024049 CACTTCTTGATCGTGGCTATTTTTC 58.976 40.000 0.00 0.00 0.00 2.29
2621 5657 1.411493 GGCGTCACGTCTTCGATTCC 61.411 60.000 0.00 0.00 40.62 3.01
2628 5664 5.341617 GTCACGTCTTCGATTCCTTATTCT 58.658 41.667 0.00 0.00 40.62 2.40
2643 5679 9.725019 ATTCCTTATTCTTTCCAAATTGGTTTC 57.275 29.630 12.28 0.00 39.03 2.78
2644 5680 8.256356 TCCTTATTCTTTCCAAATTGGTTTCA 57.744 30.769 12.28 0.00 39.03 2.69
2649 5685 6.399639 TCTTTCCAAATTGGTTTCACTACC 57.600 37.500 12.28 0.00 39.03 3.18
2676 5712 3.660111 AAACTTGCAGCGGCCGAC 61.660 61.111 33.48 20.78 40.13 4.79
2697 5733 3.007398 ACCTGTTTGCTTGGTTTTTGACA 59.993 39.130 0.00 0.00 0.00 3.58
2725 5761 1.497722 CGGCGACTTCTTGCTTTCC 59.502 57.895 0.00 0.00 0.00 3.13
2734 5770 2.450609 TCTTGCTTTCCTCGGTACAC 57.549 50.000 0.00 0.00 0.00 2.90
2738 5774 1.145803 GCTTTCCTCGGTACACACAC 58.854 55.000 0.00 0.00 0.00 3.82
2742 5778 2.050714 CTCGGTACACACACGCGT 60.051 61.111 5.58 5.58 0.00 6.01
2772 5808 2.133553 CACGCATCCAGAATCTAGCAG 58.866 52.381 0.00 0.00 0.00 4.24
2796 5832 1.135831 TGCATTGGTTTGTGTATCGCG 60.136 47.619 0.00 0.00 0.00 5.87
2818 5854 0.179004 TTTGACGGCCACCACAGATT 60.179 50.000 2.24 0.00 0.00 2.40
2849 5885 4.933330 TCGTAGAGATTATCTGTTGTGGC 58.067 43.478 0.00 0.00 39.20 5.01
2914 5951 8.452868 AGAACTGATATAGACCCTTCTGTATCT 58.547 37.037 15.34 1.30 46.11 1.98
2938 5975 4.379813 GCTCTTCTTCATCCGAAAATTGCA 60.380 41.667 0.00 0.00 0.00 4.08
2946 5983 5.841810 TCATCCGAAAATTGCAAACTTCTT 58.158 33.333 1.71 0.00 0.00 2.52
2954 5991 7.412891 CGAAAATTGCAAACTTCTTGAAAACCT 60.413 33.333 1.71 0.00 0.00 3.50
2988 6025 1.746220 TCCAAAAACTCAACACCACCG 59.254 47.619 0.00 0.00 0.00 4.94
2992 6029 1.381165 AAACTCAACACCACCGTGCC 61.381 55.000 0.00 0.00 44.40 5.01
3019 6056 1.456705 ACGGTGGGTGCCAATTGTT 60.457 52.632 4.43 0.00 34.18 2.83
3035 6072 0.665835 TGTTGTGGATTTGTCACGGC 59.334 50.000 0.00 0.00 37.91 5.68
3042 6079 1.812571 GGATTTGTCACGGCAGATGTT 59.187 47.619 0.00 0.00 0.00 2.71
3051 6088 2.413112 CACGGCAGATGTTCTTAGTGTG 59.587 50.000 0.00 0.00 0.00 3.82
3057 6094 4.322349 GCAGATGTTCTTAGTGTGAGGACT 60.322 45.833 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.195334 CGCCCCTGCTATTGGCCT 62.195 66.667 3.32 0.00 42.29 5.19
4 5 4.545706 TCGCCGCCCCTGCTATTG 62.546 66.667 0.00 0.00 34.43 1.90
5 6 4.547367 GTCGCCGCCCCTGCTATT 62.547 66.667 0.00 0.00 34.43 1.73
28 29 1.313091 GGATTGGCTTCCGGTTCACC 61.313 60.000 0.00 0.00 0.00 4.02
29 30 0.322546 AGGATTGGCTTCCGGTTCAC 60.323 55.000 0.00 0.00 40.94 3.18
30 31 0.322456 CAGGATTGGCTTCCGGTTCA 60.322 55.000 0.00 0.00 40.94 3.18
31 32 1.657751 GCAGGATTGGCTTCCGGTTC 61.658 60.000 0.00 0.00 40.94 3.62
32 33 1.678970 GCAGGATTGGCTTCCGGTT 60.679 57.895 0.00 0.00 40.94 4.44
33 34 2.044946 GCAGGATTGGCTTCCGGT 60.045 61.111 0.00 0.00 40.94 5.28
34 35 3.204827 CGCAGGATTGGCTTCCGG 61.205 66.667 0.00 0.00 40.94 5.14
60 61 4.893601 GTCTCCTAAGCCGCCCGC 62.894 72.222 0.00 0.00 37.98 6.13
61 62 3.432051 CTGTCTCCTAAGCCGCCCG 62.432 68.421 0.00 0.00 0.00 6.13
62 63 2.501610 CTGTCTCCTAAGCCGCCC 59.498 66.667 0.00 0.00 0.00 6.13
63 64 2.058595 TCCTGTCTCCTAAGCCGCC 61.059 63.158 0.00 0.00 0.00 6.13
64 65 1.142097 GTCCTGTCTCCTAAGCCGC 59.858 63.158 0.00 0.00 0.00 6.53
65 66 1.817209 GGTCCTGTCTCCTAAGCCG 59.183 63.158 0.00 0.00 0.00 5.52
66 67 1.817209 CGGTCCTGTCTCCTAAGCC 59.183 63.158 0.00 0.00 0.00 4.35
67 68 1.142097 GCGGTCCTGTCTCCTAAGC 59.858 63.158 0.00 0.00 0.00 3.09
68 69 1.433879 CGCGGTCCTGTCTCCTAAG 59.566 63.158 0.00 0.00 0.00 2.18
69 70 2.707849 GCGCGGTCCTGTCTCCTAA 61.708 63.158 8.83 0.00 0.00 2.69
70 71 3.138798 GCGCGGTCCTGTCTCCTA 61.139 66.667 8.83 0.00 0.00 2.94
72 73 4.803426 CAGCGCGGTCCTGTCTCC 62.803 72.222 8.38 0.00 0.00 3.71
73 74 4.803426 CCAGCGCGGTCCTGTCTC 62.803 72.222 8.38 0.00 0.00 3.36
93 94 4.819761 TCGCTGGCTCGGATGTGC 62.820 66.667 0.48 0.00 0.00 4.57
94 95 2.584418 CTCGCTGGCTCGGATGTG 60.584 66.667 0.48 0.00 0.00 3.21
95 96 4.521062 GCTCGCTGGCTCGGATGT 62.521 66.667 0.48 0.00 0.00 3.06
116 117 2.439701 TACCCGTCTCCTGAGCCG 60.440 66.667 0.00 0.00 0.00 5.52
117 118 2.772691 CGTACCCGTCTCCTGAGCC 61.773 68.421 0.00 0.00 0.00 4.70
118 119 2.799371 CGTACCCGTCTCCTGAGC 59.201 66.667 0.00 0.00 0.00 4.26
119 120 1.994507 CTGCGTACCCGTCTCCTGAG 61.995 65.000 0.00 0.00 36.15 3.35
120 121 2.034532 TGCGTACCCGTCTCCTGA 59.965 61.111 0.00 0.00 36.15 3.86
121 122 2.490217 CTGCGTACCCGTCTCCTG 59.510 66.667 0.00 0.00 36.15 3.86
122 123 2.754658 CCTGCGTACCCGTCTCCT 60.755 66.667 0.00 0.00 36.15 3.69
123 124 4.509737 GCCTGCGTACCCGTCTCC 62.510 72.222 0.00 0.00 36.15 3.71
124 125 4.849329 CGCCTGCGTACCCGTCTC 62.849 72.222 2.83 0.00 36.15 3.36
135 136 4.819761 TCCACGATCTGCGCCTGC 62.820 66.667 4.18 0.00 46.04 4.85
136 137 2.584418 CTCCACGATCTGCGCCTG 60.584 66.667 4.18 0.00 46.04 4.85
137 138 3.842923 CCTCCACGATCTGCGCCT 61.843 66.667 4.18 0.00 46.04 5.52
138 139 2.650813 AATCCTCCACGATCTGCGCC 62.651 60.000 4.18 0.00 46.04 6.53
139 140 1.218230 GAATCCTCCACGATCTGCGC 61.218 60.000 0.00 0.00 46.04 6.09
140 141 0.598680 GGAATCCTCCACGATCTGCG 60.599 60.000 0.00 0.00 41.96 5.18
141 142 0.598680 CGGAATCCTCCACGATCTGC 60.599 60.000 0.00 0.00 42.58 4.26
142 143 0.032678 CCGGAATCCTCCACGATCTG 59.967 60.000 0.00 0.00 42.58 2.90
143 144 1.115930 CCCGGAATCCTCCACGATCT 61.116 60.000 0.73 0.00 42.58 2.75
144 145 1.367840 CCCGGAATCCTCCACGATC 59.632 63.158 0.73 0.00 42.58 3.69
145 146 1.382695 ACCCGGAATCCTCCACGAT 60.383 57.895 0.73 0.00 42.58 3.73
146 147 2.038329 ACCCGGAATCCTCCACGA 59.962 61.111 0.73 0.00 42.58 4.35
147 148 2.499685 GACCCGGAATCCTCCACG 59.500 66.667 0.73 0.00 42.58 4.94
148 149 2.356780 ACGACCCGGAATCCTCCAC 61.357 63.158 0.73 0.00 42.58 4.02
149 150 2.038329 ACGACCCGGAATCCTCCA 59.962 61.111 0.73 0.00 42.58 3.86
150 151 2.056223 TCACGACCCGGAATCCTCC 61.056 63.158 0.73 0.00 38.52 4.30
151 152 1.141234 GTCACGACCCGGAATCCTC 59.859 63.158 0.73 0.00 0.00 3.71
152 153 2.356780 GGTCACGACCCGGAATCCT 61.357 63.158 0.73 0.00 45.68 3.24
153 154 2.186125 GGTCACGACCCGGAATCC 59.814 66.667 0.73 0.00 45.68 3.01
162 163 3.222354 AAGTGGAGCCGGTCACGAC 62.222 63.158 1.90 1.84 44.60 4.34
163 164 2.915659 AAGTGGAGCCGGTCACGA 60.916 61.111 1.90 0.00 44.60 4.35
164 165 2.432628 GAAGTGGAGCCGGTCACG 60.433 66.667 1.90 0.00 38.77 4.35
165 166 1.374758 CAGAAGTGGAGCCGGTCAC 60.375 63.158 1.90 9.90 0.00 3.67
166 167 3.059982 CAGAAGTGGAGCCGGTCA 58.940 61.111 1.90 0.00 0.00 4.02
173 174 5.751670 CTTGACAACAACCCAGAAGTGGAG 61.752 50.000 0.00 0.00 37.69 3.86
174 175 3.935180 CTTGACAACAACCCAGAAGTGGA 60.935 47.826 0.00 0.00 37.69 4.02
175 176 2.051334 TGACAACAACCCAGAAGTGG 57.949 50.000 0.00 0.00 44.56 4.00
176 177 2.358898 CCTTGACAACAACCCAGAAGTG 59.641 50.000 0.00 0.00 32.27 3.16
177 178 2.241176 TCCTTGACAACAACCCAGAAGT 59.759 45.455 0.00 0.00 32.27 3.01
178 179 2.880890 CTCCTTGACAACAACCCAGAAG 59.119 50.000 0.00 0.00 32.27 2.85
179 180 2.422803 CCTCCTTGACAACAACCCAGAA 60.423 50.000 0.00 0.00 32.27 3.02
180 181 1.142870 CCTCCTTGACAACAACCCAGA 59.857 52.381 0.00 0.00 32.27 3.86
181 182 1.609208 CCTCCTTGACAACAACCCAG 58.391 55.000 0.00 0.00 32.27 4.45
182 183 0.467290 GCCTCCTTGACAACAACCCA 60.467 55.000 0.00 0.00 32.27 4.51
183 184 1.515521 CGCCTCCTTGACAACAACCC 61.516 60.000 0.00 0.00 32.27 4.11
184 185 0.534203 TCGCCTCCTTGACAACAACC 60.534 55.000 0.00 0.00 32.27 3.77
185 186 0.868406 CTCGCCTCCTTGACAACAAC 59.132 55.000 0.00 0.00 32.27 3.32
186 187 0.250295 CCTCGCCTCCTTGACAACAA 60.250 55.000 0.00 0.00 34.65 2.83
187 188 1.371183 CCTCGCCTCCTTGACAACA 59.629 57.895 0.00 0.00 0.00 3.33
188 189 2.035442 GCCTCGCCTCCTTGACAAC 61.035 63.158 0.00 0.00 0.00 3.32
189 190 2.347490 GCCTCGCCTCCTTGACAA 59.653 61.111 0.00 0.00 0.00 3.18
190 191 4.069232 CGCCTCGCCTCCTTGACA 62.069 66.667 0.00 0.00 0.00 3.58
191 192 2.579684 ATTCGCCTCGCCTCCTTGAC 62.580 60.000 0.00 0.00 0.00 3.18
192 193 2.359169 ATTCGCCTCGCCTCCTTGA 61.359 57.895 0.00 0.00 0.00 3.02
193 194 2.176273 CATTCGCCTCGCCTCCTTG 61.176 63.158 0.00 0.00 0.00 3.61
194 195 2.185310 AACATTCGCCTCGCCTCCTT 62.185 55.000 0.00 0.00 0.00 3.36
195 196 2.660064 AACATTCGCCTCGCCTCCT 61.660 57.895 0.00 0.00 0.00 3.69
196 197 2.125106 AACATTCGCCTCGCCTCC 60.125 61.111 0.00 0.00 0.00 4.30
197 198 2.464459 CCAACATTCGCCTCGCCTC 61.464 63.158 0.00 0.00 0.00 4.70
198 199 2.436646 CCAACATTCGCCTCGCCT 60.437 61.111 0.00 0.00 0.00 5.52
199 200 2.435938 TCCAACATTCGCCTCGCC 60.436 61.111 0.00 0.00 0.00 5.54
200 201 0.459585 TACTCCAACATTCGCCTCGC 60.460 55.000 0.00 0.00 0.00 5.03
201 202 2.128035 GATACTCCAACATTCGCCTCG 58.872 52.381 0.00 0.00 0.00 4.63
202 203 3.460857 AGATACTCCAACATTCGCCTC 57.539 47.619 0.00 0.00 0.00 4.70
203 204 3.961408 AGTAGATACTCCAACATTCGCCT 59.039 43.478 0.00 0.00 0.00 5.52
204 205 4.323553 AGTAGATACTCCAACATTCGCC 57.676 45.455 0.00 0.00 0.00 5.54
205 206 6.074544 AGTAGTAGATACTCCAACATTCGC 57.925 41.667 0.00 0.00 40.99 4.70
356 358 7.309091 AGAGTAAGAATCCCCATTGAGATCTA 58.691 38.462 0.00 0.00 0.00 1.98
388 390 7.095910 TGGGTGATAATGCATTAACAACAAAG 58.904 34.615 32.85 0.00 35.28 2.77
392 394 6.042143 CCTTGGGTGATAATGCATTAACAAC 58.958 40.000 27.71 27.71 33.53 3.32
446 448 5.740290 AGATTAACGAAACCTCTTGGAGA 57.260 39.130 0.00 0.00 37.04 3.71
511 513 0.107017 AAAGACCGCTCCCATGGATG 60.107 55.000 15.22 6.44 0.00 3.51
512 514 0.181350 GAAAGACCGCTCCCATGGAT 59.819 55.000 15.22 0.00 0.00 3.41
528 530 0.942410 CGGCCTTTGTCGTCTCGAAA 60.942 55.000 0.00 0.00 37.72 3.46
595 3594 6.742559 AGAGTTAGTTCAGGGTTAGTTCAA 57.257 37.500 0.00 0.00 0.00 2.69
597 3596 6.331845 GCTAGAGTTAGTTCAGGGTTAGTTC 58.668 44.000 0.00 0.00 0.00 3.01
605 3604 5.407407 TCTTTGGCTAGAGTTAGTTCAGG 57.593 43.478 0.00 0.00 0.00 3.86
620 3619 1.273327 CCATCCAAACACCTCTTTGGC 59.727 52.381 5.91 0.00 46.88 4.52
640 3639 1.211818 CGCGCTCCATCTAACTCTGC 61.212 60.000 5.56 0.00 0.00 4.26
700 3699 0.040499 AGCTTCTCGTCCTCTCCCTT 59.960 55.000 0.00 0.00 0.00 3.95
709 3708 1.200484 ACTTCCTCGAAGCTTCTCGTC 59.800 52.381 23.50 0.00 42.79 4.20
718 3717 1.617947 CCCTCCCCACTTCCTCGAAG 61.618 65.000 0.00 0.00 44.37 3.79
739 3738 1.970917 CTTACTTTCGCCGCAGCAGG 61.971 60.000 0.00 0.00 39.83 4.85
789 3789 5.641155 AGAGGTGCTTATTTGGGTTAGTTT 58.359 37.500 0.00 0.00 0.00 2.66
841 3841 4.035208 GGTTAGTTTGGGTTAGATGCATCG 59.965 45.833 20.67 0.00 0.00 3.84
867 3867 9.757227 CAACTAACCCAAAAATATTCAAACAGA 57.243 29.630 0.00 0.00 0.00 3.41
875 3875 8.485578 TTGGACTCAACTAACCCAAAAATATT 57.514 30.769 0.00 0.00 34.33 1.28
876 3876 8.664669 ATTGGACTCAACTAACCCAAAAATAT 57.335 30.769 0.00 0.00 39.91 1.28
975 3975 4.913376 ACACATCTGCGCAAAAATCTATC 58.087 39.130 13.05 0.00 0.00 2.08
1083 4084 5.825593 TCATAGTATCAATCCCCTCCAAC 57.174 43.478 0.00 0.00 0.00 3.77
1091 4092 7.768120 GTCCTCCATCATTCATAGTATCAATCC 59.232 40.741 0.00 0.00 0.00 3.01
1183 4184 6.821388 ACCTATTACAGTGCTCAAATCTAGG 58.179 40.000 0.00 0.00 0.00 3.02
1202 4203 1.134098 CCCGTTGGCATCTTGACCTAT 60.134 52.381 0.00 0.00 0.00 2.57
1203 4204 0.251916 CCCGTTGGCATCTTGACCTA 59.748 55.000 0.00 0.00 0.00 3.08
1204 4205 1.002134 CCCGTTGGCATCTTGACCT 60.002 57.895 0.00 0.00 0.00 3.85
1205 4206 2.046285 CCCCGTTGGCATCTTGACC 61.046 63.158 0.00 0.00 0.00 4.02
1215 4216 0.324275 ATGGGTTTCATCCCCGTTGG 60.324 55.000 0.00 0.00 45.86 3.77
1326 4340 4.200092 AGAAAACTCGATGGATTTAGGGC 58.800 43.478 0.00 0.00 0.00 5.19
1334 4348 4.320870 GTGGGTTTAGAAAACTCGATGGA 58.679 43.478 2.84 0.00 0.00 3.41
1363 4377 1.628238 TATGCCGATTTCCCCGTGGT 61.628 55.000 0.00 0.00 0.00 4.16
1531 4546 6.383415 TCCGTATGTTAAATTGGTGAAAAGC 58.617 36.000 0.00 0.00 0.00 3.51
1536 4551 9.621629 AGATAAATCCGTATGTTAAATTGGTGA 57.378 29.630 0.00 0.00 0.00 4.02
1544 4559 9.451002 TTGTCCAAAGATAAATCCGTATGTTAA 57.549 29.630 0.00 0.00 0.00 2.01
1550 4565 4.871557 CCGTTGTCCAAAGATAAATCCGTA 59.128 41.667 0.00 0.00 0.00 4.02
1553 4568 5.414765 AGTTCCGTTGTCCAAAGATAAATCC 59.585 40.000 0.00 0.00 0.00 3.01
1571 4588 7.253684 CGTTACTTGAAAGATTAGCTAGTTCCG 60.254 40.741 0.00 0.00 0.00 4.30
1582 4599 6.708949 TGAGCTAAACCGTTACTTGAAAGATT 59.291 34.615 0.00 0.00 0.00 2.40
1600 4617 9.334947 CATCTTTTAGGATGAAATCTGAGCTAA 57.665 33.333 0.00 0.00 44.71 3.09
1642 4659 7.984422 ATGTCACTCTTCAATGAACATGTTA 57.016 32.000 11.95 0.61 0.00 2.41
1707 4726 4.236147 GAGAGTGATGATGATCATGGACG 58.764 47.826 14.30 0.00 40.78 4.79
1743 4764 9.485591 CGTCAAAATACTACAATAAGCGAATTT 57.514 29.630 0.00 0.00 0.00 1.82
1747 4768 5.521010 CCCGTCAAAATACTACAATAAGCGA 59.479 40.000 0.00 0.00 0.00 4.93
1794 4815 4.048504 GGTTCAAACCCGTTTCTTCAATG 58.951 43.478 0.10 0.00 43.43 2.82
1897 4918 2.034532 CCCCGCGGGTTTTTACCT 59.965 61.111 40.52 0.00 38.25 3.08
1948 4969 5.775195 AGCTACTTTGTTTGCTTCCCTATTT 59.225 36.000 0.00 0.00 30.96 1.40
1949 4970 5.325239 AGCTACTTTGTTTGCTTCCCTATT 58.675 37.500 0.00 0.00 30.96 1.73
1963 4984 5.871524 TCTAGCAAGTTCATGAGCTACTTTG 59.128 40.000 12.88 8.40 38.47 2.77
2004 5025 3.664107 TCCTCAAACCAATCAGAAGTCG 58.336 45.455 0.00 0.00 0.00 4.18
2103 5124 2.467566 TCACCTCGCCTCCTTTTTAC 57.532 50.000 0.00 0.00 0.00 2.01
2104 5125 3.606687 GATTCACCTCGCCTCCTTTTTA 58.393 45.455 0.00 0.00 0.00 1.52
2120 5141 0.846015 AAGATGCGGGGATGGATTCA 59.154 50.000 0.00 0.00 0.00 2.57
2147 5168 4.803426 CGCCTGTGAGCCTCGTCC 62.803 72.222 0.00 0.00 0.00 4.79
2151 5172 4.154347 CCTCCGCCTGTGAGCCTC 62.154 72.222 0.00 0.00 0.00 4.70
2158 5179 4.021925 GGTCTTGCCTCCGCCTGT 62.022 66.667 0.00 0.00 0.00 4.00
2344 5365 1.203063 TCCTCCACTGTACTGAGCTGT 60.203 52.381 6.77 0.00 0.00 4.40
2345 5366 1.476085 CTCCTCCACTGTACTGAGCTG 59.524 57.143 6.77 0.00 0.00 4.24
2346 5367 1.846007 CTCCTCCACTGTACTGAGCT 58.154 55.000 6.77 0.00 0.00 4.09
2353 5374 0.904865 CACCCTGCTCCTCCACTGTA 60.905 60.000 0.00 0.00 0.00 2.74
2371 5392 0.618458 CCCCGGTTTCCTCTGAATCA 59.382 55.000 0.00 0.00 0.00 2.57
2377 5398 3.009714 GAGCCCCCGGTTTCCTCT 61.010 66.667 0.00 0.00 0.00 3.69
2511 5543 2.836360 GGATACGGCCCGGACTCA 60.836 66.667 8.57 0.00 0.00 3.41
2540 5572 2.480419 CCACGATCAAGAAGTGAACCAC 59.520 50.000 9.59 0.00 40.50 4.16
2545 5577 4.471904 AATAGCCACGATCAAGAAGTGA 57.528 40.909 9.59 0.00 41.67 3.41
2553 5585 4.988540 CGGATAGAAAAATAGCCACGATCA 59.011 41.667 0.00 0.00 30.28 2.92
2570 5602 1.777101 GCTGCTAGCAAGTCGGATAG 58.223 55.000 19.86 4.63 41.89 2.08
2628 5664 4.888239 TCGGTAGTGAAACCAATTTGGAAA 59.112 37.500 22.19 1.66 40.96 3.13
2643 5679 3.438297 AGTTTGATCCGATCGGTAGTG 57.562 47.619 32.15 8.04 36.47 2.74
2644 5680 3.782046 CAAGTTTGATCCGATCGGTAGT 58.218 45.455 32.15 19.76 36.47 2.73
2647 5683 1.338674 TGCAAGTTTGATCCGATCGGT 60.339 47.619 32.15 20.11 36.47 4.69
2649 5685 1.267732 GCTGCAAGTTTGATCCGATCG 60.268 52.381 8.51 8.51 35.30 3.69
2676 5712 3.594134 TGTCAAAAACCAAGCAAACAGG 58.406 40.909 0.00 0.00 0.00 4.00
2697 5733 2.075979 GAAGTCGCCGGTTACTTCTT 57.924 50.000 29.06 15.71 45.26 2.52
2725 5761 2.050714 ACGCGTGTGTGTACCGAG 60.051 61.111 12.93 0.00 36.97 4.63
2742 5778 0.321475 TGGATGCGTGTGATTCTGCA 60.321 50.000 0.00 0.00 42.22 4.41
2772 5808 2.810439 TACACAAACCAATGCAAGCC 57.190 45.000 0.00 0.00 0.00 4.35
2818 5854 9.667107 AACAGATAATCTCTACGAATTTTTCCA 57.333 29.630 0.00 0.00 31.13 3.53
2829 5865 4.504461 CACGCCACAACAGATAATCTCTAC 59.496 45.833 0.00 0.00 31.13 2.59
2863 5900 4.551388 ACTCGTGAGTTCAGATCAAAGAC 58.449 43.478 0.00 0.00 38.83 3.01
2879 5916 6.202937 GGTCTATATCAGTTCTCAACTCGTG 58.797 44.000 0.00 0.00 40.46 4.35
2897 5934 5.073437 AGAGCAGATACAGAAGGGTCTAT 57.927 43.478 0.00 0.00 34.85 1.98
2914 5951 4.379813 GCAATTTTCGGATGAAGAAGAGCA 60.380 41.667 0.00 0.00 35.06 4.26
2938 5975 5.719563 TCTTCCCAAGGTTTTCAAGAAGTTT 59.280 36.000 0.00 0.00 32.89 2.66
2973 6010 1.381165 GGCACGGTGGTGTTGAGTTT 61.381 55.000 10.60 0.00 46.13 2.66
3009 6046 3.133542 TGACAAATCCACAACAATTGGCA 59.866 39.130 10.83 0.00 36.71 4.92
3015 6052 1.066303 GCCGTGACAAATCCACAACAA 59.934 47.619 0.00 0.00 34.36 2.83
3019 6056 0.107643 TCTGCCGTGACAAATCCACA 59.892 50.000 0.00 0.00 34.36 4.17
3035 6072 5.398603 AGTCCTCACACTAAGAACATCTG 57.601 43.478 0.00 0.00 0.00 2.90
3042 6079 5.048921 CACGACTAAAGTCCTCACACTAAGA 60.049 44.000 4.58 0.00 41.86 2.10
3051 6088 1.135053 GGCCTCACGACTAAAGTCCTC 60.135 57.143 0.00 0.00 41.86 3.71
3057 6094 0.947180 GCGTTGGCCTCACGACTAAA 60.947 55.000 26.38 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.