Multiple sequence alignment - TraesCS7D01G339500

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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 TraesCS7D01G339500 chr7D 100.000 2381 0 0 1 2381 433784295 433781915 0.000000e+00 4397
1 TraesCS7D01G339500 chr7D 77.152 1510 233 59 856 2296 215785662 215787128 0.000000e+00 774
2 TraesCS7D01G339500 chr7D 80.604 861 140 11 1113 1954 216132383 216133235 7.180000e-180 640
3 TraesCS7D01G339500 chr7D 78.614 1010 164 30 1338 2317 629514837 629515824 2.600000e-174 621
4 TraesCS7D01G339500 chr7D 95.787 356 14 1 1 356 637652531 637652885 7.380000e-160 573
5 TraesCS7D01G339500 chr7D 95.977 348 13 1 1 347 5551721 5552068 4.440000e-157 564
6 TraesCS7D01G339500 chr7D 81.491 389 60 9 463 846 484298844 484298463 2.300000e-80 309
7 TraesCS7D01G339500 chr7B 85.206 1406 146 29 1011 2381 451171674 451170296 0.000000e+00 1387
8 TraesCS7D01G339500 chr7B 87.546 546 60 5 355 896 451172643 451172102 2.010000e-175 625
9 TraesCS7D01G339500 chr7B 77.778 1026 168 33 508 1496 708474048 708473046 5.710000e-161 577
10 TraesCS7D01G339500 chr1B 79.926 1888 297 38 488 2326 302005170 302007024 0.000000e+00 1312
11 TraesCS7D01G339500 chr1B 79.382 1295 208 31 1006 2266 564738533 564737264 0.000000e+00 857
12 TraesCS7D01G339500 chr1B 76.404 534 104 11 1631 2151 268663027 268663551 3.900000e-68 268
13 TraesCS7D01G339500 chr1D 79.236 1912 283 54 451 2289 372520936 372522806 0.000000e+00 1227
14 TraesCS7D01G339500 chr1D 79.150 1717 258 50 581 2247 417951599 417949933 0.000000e+00 1096
15 TraesCS7D01G339500 chr1D 96.067 356 13 1 1 355 493884993 493884638 1.590000e-161 579
16 TraesCS7D01G339500 chr1D 76.230 1077 203 37 552 1598 463316946 463315893 2.710000e-144 521
17 TraesCS7D01G339500 chr1D 78.850 539 90 16 917 1439 291077171 291076641 2.270000e-90 342
18 TraesCS7D01G339500 chr1D 77.006 648 106 23 499 1115 217097125 217097760 4.910000e-87 331
19 TraesCS7D01G339500 chr4D 79.146 1827 279 56 488 2234 49160299 49162103 0.000000e+00 1170
20 TraesCS7D01G339500 chr4D 95.068 365 15 3 1 364 228188663 228189025 2.660000e-159 571
21 TraesCS7D01G339500 chr4D 78.571 770 124 24 508 1249 401867740 401866984 9.960000e-129 470
22 TraesCS7D01G339500 chr4D 80.851 470 58 15 701 1145 499593073 499593535 8.150000e-90 340
23 TraesCS7D01G339500 chr5D 82.002 1289 164 34 654 1887 539695410 539696685 0.000000e+00 1033
24 TraesCS7D01G339500 chr5D 96.067 356 12 2 1 355 300135768 300135414 1.590000e-161 579
25 TraesCS7D01G339500 chr3B 80.552 1378 205 39 941 2277 418458980 418460335 0.000000e+00 1002
26 TraesCS7D01G339500 chr3B 75.825 1878 335 61 450 2244 468001944 468000103 0.000000e+00 843
27 TraesCS7D01G339500 chr5A 81.083 1200 183 20 458 1627 676751782 676752967 0.000000e+00 918
28 TraesCS7D01G339500 chr3D 78.047 1239 219 23 941 2150 350665658 350664444 0.000000e+00 732
29 TraesCS7D01G339500 chr3D 94.340 371 19 2 1 369 588001500 588001130 3.430000e-158 568
30 TraesCS7D01G339500 chr3D 85.556 360 44 6 488 843 72243071 72243426 1.040000e-98 370
31 TraesCS7D01G339500 chr2D 80.958 919 144 14 1371 2266 641494448 641493538 0.000000e+00 699
32 TraesCS7D01G339500 chr2D 83.824 340 45 6 508 846 83812013 83811683 4.940000e-82 315
33 TraesCS7D01G339500 chr6A 78.959 922 157 18 1396 2312 495677794 495678683 5.670000e-166 593
34 TraesCS7D01G339500 chr6D 96.067 356 13 1 1 355 4223279 4222924 1.590000e-161 579
35 TraesCS7D01G339500 chr6D 96.067 356 13 1 1 355 247925885 247925530 1.590000e-161 579
36 TraesCS7D01G339500 chr6D 83.824 612 92 6 1269 1878 347704259 347703653 2.050000e-160 575
37 TraesCS7D01G339500 chr6D 79.680 812 119 19 541 1315 362214239 362213437 5.790000e-151 544
38 TraesCS7D01G339500 chr6D 73.954 956 185 42 552 1474 43196358 43197282 6.350000e-86 327
39 TraesCS7D01G339500 chrUn 96.307 352 12 1 1 351 69328065 69327714 5.710000e-161 577
40 TraesCS7D01G339500 chr4A 80.556 648 97 11 1610 2234 175492013 175492654 2.770000e-129 472
41 TraesCS7D01G339500 chr4A 83.333 360 54 5 489 846 631375074 631374719 6.350000e-86 327
42 TraesCS7D01G339500 chr3A 78.080 698 108 22 599 1262 360166423 360165737 1.330000e-107 399
43 TraesCS7D01G339500 chr3A 83.382 343 51 5 508 846 88519195 88518855 1.780000e-81 313
44 TraesCS7D01G339500 chr1A 81.429 490 61 20 491 955 580021236 580020752 8.040000e-100 374


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 TraesCS7D01G339500 chr7D 433781915 433784295 2380 True 4397 4397 100.000 1 2381 1 chr7D.!!$R1 2380
1 TraesCS7D01G339500 chr7D 215785662 215787128 1466 False 774 774 77.152 856 2296 1 chr7D.!!$F2 1440
2 TraesCS7D01G339500 chr7D 216132383 216133235 852 False 640 640 80.604 1113 1954 1 chr7D.!!$F3 841
3 TraesCS7D01G339500 chr7D 629514837 629515824 987 False 621 621 78.614 1338 2317 1 chr7D.!!$F4 979
4 TraesCS7D01G339500 chr7B 451170296 451172643 2347 True 1006 1387 86.376 355 2381 2 chr7B.!!$R2 2026
5 TraesCS7D01G339500 chr7B 708473046 708474048 1002 True 577 577 77.778 508 1496 1 chr7B.!!$R1 988
6 TraesCS7D01G339500 chr1B 302005170 302007024 1854 False 1312 1312 79.926 488 2326 1 chr1B.!!$F2 1838
7 TraesCS7D01G339500 chr1B 564737264 564738533 1269 True 857 857 79.382 1006 2266 1 chr1B.!!$R1 1260
8 TraesCS7D01G339500 chr1B 268663027 268663551 524 False 268 268 76.404 1631 2151 1 chr1B.!!$F1 520
9 TraesCS7D01G339500 chr1D 372520936 372522806 1870 False 1227 1227 79.236 451 2289 1 chr1D.!!$F2 1838
10 TraesCS7D01G339500 chr1D 417949933 417951599 1666 True 1096 1096 79.150 581 2247 1 chr1D.!!$R2 1666
11 TraesCS7D01G339500 chr1D 463315893 463316946 1053 True 521 521 76.230 552 1598 1 chr1D.!!$R3 1046
12 TraesCS7D01G339500 chr1D 291076641 291077171 530 True 342 342 78.850 917 1439 1 chr1D.!!$R1 522
13 TraesCS7D01G339500 chr1D 217097125 217097760 635 False 331 331 77.006 499 1115 1 chr1D.!!$F1 616
14 TraesCS7D01G339500 chr4D 49160299 49162103 1804 False 1170 1170 79.146 488 2234 1 chr4D.!!$F1 1746
15 TraesCS7D01G339500 chr4D 401866984 401867740 756 True 470 470 78.571 508 1249 1 chr4D.!!$R1 741
16 TraesCS7D01G339500 chr5D 539695410 539696685 1275 False 1033 1033 82.002 654 1887 1 chr5D.!!$F1 1233
17 TraesCS7D01G339500 chr3B 418458980 418460335 1355 False 1002 1002 80.552 941 2277 1 chr3B.!!$F1 1336
18 TraesCS7D01G339500 chr3B 468000103 468001944 1841 True 843 843 75.825 450 2244 1 chr3B.!!$R1 1794
19 TraesCS7D01G339500 chr5A 676751782 676752967 1185 False 918 918 81.083 458 1627 1 chr5A.!!$F1 1169
20 TraesCS7D01G339500 chr3D 350664444 350665658 1214 True 732 732 78.047 941 2150 1 chr3D.!!$R1 1209
21 TraesCS7D01G339500 chr2D 641493538 641494448 910 True 699 699 80.958 1371 2266 1 chr2D.!!$R2 895
22 TraesCS7D01G339500 chr6A 495677794 495678683 889 False 593 593 78.959 1396 2312 1 chr6A.!!$F1 916
23 TraesCS7D01G339500 chr6D 347703653 347704259 606 True 575 575 83.824 1269 1878 1 chr6D.!!$R3 609
24 TraesCS7D01G339500 chr6D 362213437 362214239 802 True 544 544 79.680 541 1315 1 chr6D.!!$R4 774
25 TraesCS7D01G339500 chr6D 43196358 43197282 924 False 327 327 73.954 552 1474 1 chr6D.!!$F1 922
26 TraesCS7D01G339500 chr4A 175492013 175492654 641 False 472 472 80.556 1610 2234 1 chr4A.!!$F1 624
27 TraesCS7D01G339500 chr3A 360165737 360166423 686 True 399 399 78.080 599 1262 1 chr3A.!!$R2 663

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
37 38 0.039798 TGACCGTCCGAGTTTCGAAG 60.04 55.0 0.0 0.0 43.74 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2236 0.029035 GTGGTCACGTAGCGATCGAT 59.971 55.0 21.57 16.78 0.0 3.59 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
19 20 2.738521 CGAAGGGCTGTCCGTGTG 60.739 66.667 0.00 0.00 41.52 3.82
20 21 2.741092 GAAGGGCTGTCCGTGTGA 59.259 61.111 0.00 0.00 41.52 3.58
21 22 1.668151 GAAGGGCTGTCCGTGTGAC 60.668 63.158 0.00 0.00 44.72 3.67
22 23 3.178540 AAGGGCTGTCCGTGTGACC 62.179 63.158 0.00 0.00 43.78 4.02
24 25 4.295119 GGCTGTCCGTGTGACCGT 62.295 66.667 0.00 0.00 43.78 4.83
25 26 2.733593 GCTGTCCGTGTGACCGTC 60.734 66.667 0.00 0.00 43.78 4.79
26 27 2.049433 CTGTCCGTGTGACCGTCC 60.049 66.667 0.00 0.00 43.78 4.79
27 28 3.891586 CTGTCCGTGTGACCGTCCG 62.892 68.421 0.00 0.00 43.78 4.79
28 29 3.663176 GTCCGTGTGACCGTCCGA 61.663 66.667 0.00 0.00 38.09 4.55
29 30 3.359523 TCCGTGTGACCGTCCGAG 61.360 66.667 0.00 0.00 0.00 4.63
30 31 3.667282 CCGTGTGACCGTCCGAGT 61.667 66.667 0.00 0.00 0.00 4.18
31 32 2.333938 CGTGTGACCGTCCGAGTT 59.666 61.111 0.00 0.00 0.00 3.01
32 33 1.299620 CGTGTGACCGTCCGAGTTT 60.300 57.895 0.00 0.00 0.00 2.66
33 34 1.273455 CGTGTGACCGTCCGAGTTTC 61.273 60.000 0.00 0.00 0.00 2.78
34 35 1.008194 TGTGACCGTCCGAGTTTCG 60.008 57.895 0.00 0.00 40.07 3.46
35 36 1.283793 GTGACCGTCCGAGTTTCGA 59.716 57.895 0.00 0.00 43.74 3.71
36 37 0.318107 GTGACCGTCCGAGTTTCGAA 60.318 55.000 0.00 0.00 43.74 3.71
37 38 0.039798 TGACCGTCCGAGTTTCGAAG 60.040 55.000 0.00 0.00 43.74 3.79
38 39 0.731855 GACCGTCCGAGTTTCGAAGG 60.732 60.000 0.00 0.00 43.74 3.46
39 40 1.288127 CCGTCCGAGTTTCGAAGGT 59.712 57.895 0.00 0.00 43.74 3.50
40 41 0.319297 CCGTCCGAGTTTCGAAGGTT 60.319 55.000 0.00 0.00 43.74 3.50
41 42 0.782384 CGTCCGAGTTTCGAAGGTTG 59.218 55.000 0.00 0.00 43.74 3.77
42 43 1.861971 GTCCGAGTTTCGAAGGTTGT 58.138 50.000 0.00 0.00 43.74 3.32
43 44 1.791204 GTCCGAGTTTCGAAGGTTGTC 59.209 52.381 0.00 0.00 43.74 3.18
44 45 1.145803 CCGAGTTTCGAAGGTTGTCC 58.854 55.000 0.00 0.00 43.74 4.02
45 46 1.145803 CGAGTTTCGAAGGTTGTCCC 58.854 55.000 0.00 0.00 43.74 4.46
46 47 1.145803 GAGTTTCGAAGGTTGTCCCG 58.854 55.000 0.00 0.00 38.74 5.14
47 48 0.754472 AGTTTCGAAGGTTGTCCCGA 59.246 50.000 0.00 0.00 38.74 5.14
48 49 1.139455 AGTTTCGAAGGTTGTCCCGAA 59.861 47.619 0.00 0.00 36.28 4.30
49 50 1.529865 GTTTCGAAGGTTGTCCCGAAG 59.470 52.381 0.00 0.00 38.14 3.79
63 64 2.572733 CGAAGGGCTCTCTGAGTGA 58.427 57.895 10.70 0.00 31.39 3.41
64 65 0.172352 CGAAGGGCTCTCTGAGTGAC 59.828 60.000 10.70 7.46 31.39 3.67
65 66 0.534873 GAAGGGCTCTCTGAGTGACC 59.465 60.000 21.33 21.33 31.39 4.02
66 67 1.254284 AAGGGCTCTCTGAGTGACCG 61.254 60.000 22.27 2.19 31.39 4.79
67 68 1.979693 GGGCTCTCTGAGTGACCGT 60.980 63.158 15.31 0.00 31.39 4.83
68 69 1.536943 GGGCTCTCTGAGTGACCGTT 61.537 60.000 15.31 0.00 31.39 4.44
69 70 0.109039 GGCTCTCTGAGTGACCGTTC 60.109 60.000 10.70 0.00 31.39 3.95
70 71 0.455295 GCTCTCTGAGTGACCGTTCG 60.455 60.000 10.70 0.00 31.39 3.95
71 72 1.157585 CTCTCTGAGTGACCGTTCGA 58.842 55.000 4.32 0.00 0.00 3.71
72 73 1.129624 CTCTCTGAGTGACCGTTCGAG 59.870 57.143 4.32 0.00 0.00 4.04
73 74 0.875728 CTCTGAGTGACCGTTCGAGT 59.124 55.000 0.00 0.00 0.00 4.18
74 75 1.267261 CTCTGAGTGACCGTTCGAGTT 59.733 52.381 0.00 0.00 0.00 3.01
75 76 1.679680 TCTGAGTGACCGTTCGAGTTT 59.320 47.619 0.00 0.00 0.00 2.66
76 77 2.052157 CTGAGTGACCGTTCGAGTTTC 58.948 52.381 0.00 0.00 0.00 2.78
77 78 1.050767 GAGTGACCGTTCGAGTTTCG 58.949 55.000 0.00 0.00 42.10 3.46
87 88 0.886563 TCGAGTTTCGAAGGTCCTCC 59.113 55.000 0.00 0.00 46.90 4.30
88 89 0.108756 CGAGTTTCGAAGGTCCTCCC 60.109 60.000 0.00 0.00 43.74 4.30
89 90 0.108756 GAGTTTCGAAGGTCCTCCCG 60.109 60.000 0.00 7.18 38.74 5.14
90 91 0.541296 AGTTTCGAAGGTCCTCCCGA 60.541 55.000 11.08 11.08 38.74 5.14
91 92 0.319405 GTTTCGAAGGTCCTCCCGAA 59.681 55.000 19.26 19.26 36.28 4.30
92 93 0.606604 TTTCGAAGGTCCTCCCGAAG 59.393 55.000 21.01 0.84 38.14 3.79
106 107 4.373116 GAAGGGCTGTCCGCGACA 62.373 66.667 8.23 9.55 40.50 4.35
107 108 4.681978 AAGGGCTGTCCGCGACAC 62.682 66.667 8.23 4.10 37.67 3.67
126 127 4.754667 GTCCGGGGGCTGTTCGAC 62.755 72.222 0.00 0.00 0.00 4.20
135 136 4.796231 CTGTTCGACCGCCTCCCG 62.796 72.222 0.00 0.00 0.00 5.14
151 152 2.363018 CGGAGGGCTGTCTGAGGA 60.363 66.667 0.00 0.00 0.00 3.71
152 153 2.422231 CGGAGGGCTGTCTGAGGAG 61.422 68.421 0.00 0.00 0.00 3.69
153 154 2.730524 GGAGGGCTGTCTGAGGAGC 61.731 68.421 0.86 0.86 34.23 4.70
154 155 1.986757 GAGGGCTGTCTGAGGAGCA 60.987 63.158 10.00 0.00 36.90 4.26
155 156 1.958902 GAGGGCTGTCTGAGGAGCAG 61.959 65.000 10.00 0.73 46.31 4.24
163 164 2.441051 TGAGGAGCAGACGAGGGT 59.559 61.111 0.00 0.00 0.00 4.34
164 165 1.689412 TGAGGAGCAGACGAGGGTA 59.311 57.895 0.00 0.00 0.00 3.69
165 166 0.259065 TGAGGAGCAGACGAGGGTAT 59.741 55.000 0.00 0.00 0.00 2.73
166 167 1.493446 TGAGGAGCAGACGAGGGTATA 59.507 52.381 0.00 0.00 0.00 1.47
167 168 1.881324 GAGGAGCAGACGAGGGTATAC 59.119 57.143 0.00 0.00 0.00 1.47
168 169 1.214673 AGGAGCAGACGAGGGTATACA 59.785 52.381 5.01 0.00 0.00 2.29
169 170 2.158445 AGGAGCAGACGAGGGTATACAT 60.158 50.000 5.01 0.00 0.00 2.29
170 171 2.229302 GGAGCAGACGAGGGTATACATC 59.771 54.545 5.01 1.38 0.00 3.06
171 172 2.229302 GAGCAGACGAGGGTATACATCC 59.771 54.545 5.01 0.00 0.00 3.51
172 173 2.158445 AGCAGACGAGGGTATACATCCT 60.158 50.000 5.01 2.65 35.82 3.24
173 174 2.229302 GCAGACGAGGGTATACATCCTC 59.771 54.545 14.91 14.91 44.50 3.71
177 178 0.526662 GAGGGTATACATCCTCGCGG 59.473 60.000 6.13 0.00 39.95 6.46
178 179 0.178970 AGGGTATACATCCTCGCGGT 60.179 55.000 6.13 0.00 0.00 5.68
179 180 0.677842 GGGTATACATCCTCGCGGTT 59.322 55.000 6.13 0.00 0.00 4.44
180 181 1.604693 GGGTATACATCCTCGCGGTTG 60.605 57.143 6.13 0.91 36.32 3.77
181 182 1.604693 GGTATACATCCTCGCGGTTGG 60.605 57.143 6.13 6.84 34.85 3.77
182 183 0.677288 TATACATCCTCGCGGTTGGG 59.323 55.000 6.13 4.04 34.85 4.12
183 184 1.046472 ATACATCCTCGCGGTTGGGA 61.046 55.000 6.13 9.83 34.85 4.37
189 190 3.552384 TCGCGGTTGGGAGGTTGT 61.552 61.111 6.13 0.00 32.60 3.32
190 191 2.208619 TCGCGGTTGGGAGGTTGTA 61.209 57.895 6.13 0.00 32.60 2.41
191 192 1.301874 CGCGGTTGGGAGGTTGTAA 60.302 57.895 0.00 0.00 0.00 2.41
192 193 0.885596 CGCGGTTGGGAGGTTGTAAA 60.886 55.000 0.00 0.00 0.00 2.01
193 194 1.541379 GCGGTTGGGAGGTTGTAAAT 58.459 50.000 0.00 0.00 0.00 1.40
194 195 1.471287 GCGGTTGGGAGGTTGTAAATC 59.529 52.381 0.00 0.00 0.00 2.17
195 196 2.089201 CGGTTGGGAGGTTGTAAATCC 58.911 52.381 0.00 0.00 0.00 3.01
196 197 2.290705 CGGTTGGGAGGTTGTAAATCCT 60.291 50.000 0.00 0.00 36.70 3.24
197 198 3.054948 CGGTTGGGAGGTTGTAAATCCTA 60.055 47.826 0.00 0.00 33.83 2.94
198 199 4.524053 GGTTGGGAGGTTGTAAATCCTAG 58.476 47.826 0.00 0.00 33.83 3.02
199 200 3.926058 TGGGAGGTTGTAAATCCTAGC 57.074 47.619 0.00 0.00 33.83 3.42
200 201 3.460825 TGGGAGGTTGTAAATCCTAGCT 58.539 45.455 0.00 0.00 33.83 3.32
201 202 3.199946 TGGGAGGTTGTAAATCCTAGCTG 59.800 47.826 0.00 0.00 33.83 4.24
202 203 3.206964 GGAGGTTGTAAATCCTAGCTGC 58.793 50.000 0.00 0.00 33.83 5.25
203 204 2.866762 GAGGTTGTAAATCCTAGCTGCG 59.133 50.000 0.00 0.00 33.83 5.18
204 205 1.940613 GGTTGTAAATCCTAGCTGCGG 59.059 52.381 0.00 0.00 0.00 5.69
205 206 1.940613 GTTGTAAATCCTAGCTGCGGG 59.059 52.381 0.00 8.09 0.00 6.13
206 207 0.468226 TGTAAATCCTAGCTGCGGGG 59.532 55.000 13.06 10.36 0.00 5.73
207 208 0.756903 GTAAATCCTAGCTGCGGGGA 59.243 55.000 16.26 16.26 0.00 4.81
208 209 1.348036 GTAAATCCTAGCTGCGGGGAT 59.652 52.381 18.68 18.68 41.09 3.85
209 210 0.398318 AAATCCTAGCTGCGGGGATC 59.602 55.000 22.48 0.00 38.73 3.36
210 211 0.472734 AATCCTAGCTGCGGGGATCT 60.473 55.000 22.48 13.68 38.73 2.75
211 212 1.190833 ATCCTAGCTGCGGGGATCTG 61.191 60.000 18.68 0.00 35.16 2.90
212 213 2.030262 CTAGCTGCGGGGATCTGC 59.970 66.667 0.00 0.00 45.23 4.26
221 222 4.241555 GGGATCTGCACCGCCGAT 62.242 66.667 0.00 0.00 35.34 4.18
222 223 2.969238 GGATCTGCACCGCCGATG 60.969 66.667 0.00 0.00 32.96 3.84
223 224 2.969238 GATCTGCACCGCCGATGG 60.969 66.667 0.00 0.00 32.96 3.51
224 225 3.740128 GATCTGCACCGCCGATGGT 62.740 63.158 0.00 0.00 45.21 3.55
225 226 3.740128 ATCTGCACCGCCGATGGTC 62.740 63.158 0.00 0.00 41.38 4.02
226 227 4.758251 CTGCACCGCCGATGGTCA 62.758 66.667 0.00 0.00 41.38 4.02
227 228 4.094646 TGCACCGCCGATGGTCAT 62.095 61.111 0.00 0.00 41.38 3.06
228 229 3.272334 GCACCGCCGATGGTCATC 61.272 66.667 1.08 1.08 41.38 2.92
240 241 4.231718 GATGGTCATCGACTCTACTTCC 57.768 50.000 0.00 0.00 32.47 3.46
241 242 2.376109 TGGTCATCGACTCTACTTCCC 58.624 52.381 0.00 0.00 32.47 3.97
242 243 1.334243 GGTCATCGACTCTACTTCCCG 59.666 57.143 0.00 0.00 32.47 5.14
243 244 1.022735 TCATCGACTCTACTTCCCGC 58.977 55.000 0.00 0.00 0.00 6.13
244 245 1.025812 CATCGACTCTACTTCCCGCT 58.974 55.000 0.00 0.00 0.00 5.52
245 246 1.025812 ATCGACTCTACTTCCCGCTG 58.974 55.000 0.00 0.00 0.00 5.18
246 247 1.226717 CGACTCTACTTCCCGCTGC 60.227 63.158 0.00 0.00 0.00 5.25
247 248 1.226717 GACTCTACTTCCCGCTGCG 60.227 63.158 16.34 16.34 0.00 5.18
248 249 2.583593 CTCTACTTCCCGCTGCGC 60.584 66.667 18.00 0.00 0.00 6.09
249 250 3.068691 TCTACTTCCCGCTGCGCT 61.069 61.111 18.00 0.00 0.00 5.92
250 251 1.725557 CTCTACTTCCCGCTGCGCTA 61.726 60.000 18.00 3.19 0.00 4.26
251 252 1.589196 CTACTTCCCGCTGCGCTAC 60.589 63.158 18.00 0.00 0.00 3.58
252 253 3.405592 TACTTCCCGCTGCGCTACG 62.406 63.158 18.00 12.58 0.00 3.51
253 254 4.492160 CTTCCCGCTGCGCTACGA 62.492 66.667 18.00 5.90 0.00 3.43
254 255 4.492160 TTCCCGCTGCGCTACGAG 62.492 66.667 18.00 10.57 0.00 4.18
262 263 3.586414 GCGCTACGAGTCGCTAAC 58.414 61.111 13.59 0.00 46.92 2.34
263 264 2.277503 GCGCTACGAGTCGCTAACG 61.278 63.158 13.59 12.54 46.92 3.18
290 291 5.789643 AAATCAAACCTTGTATGCAGTGT 57.210 34.783 0.00 0.00 0.00 3.55
291 292 5.376854 AATCAAACCTTGTATGCAGTGTC 57.623 39.130 0.00 0.00 0.00 3.67
292 293 3.146066 TCAAACCTTGTATGCAGTGTCC 58.854 45.455 0.00 0.00 0.00 4.02
293 294 2.884012 CAAACCTTGTATGCAGTGTCCA 59.116 45.455 0.00 0.00 0.00 4.02
294 295 3.439857 AACCTTGTATGCAGTGTCCAT 57.560 42.857 0.00 0.00 0.00 3.41
295 296 4.568072 AACCTTGTATGCAGTGTCCATA 57.432 40.909 0.00 0.00 0.00 2.74
296 297 4.142609 ACCTTGTATGCAGTGTCCATAG 57.857 45.455 0.00 0.00 0.00 2.23
297 298 3.519510 ACCTTGTATGCAGTGTCCATAGT 59.480 43.478 0.00 0.00 0.00 2.12
298 299 3.873361 CCTTGTATGCAGTGTCCATAGTG 59.127 47.826 0.00 0.00 0.00 2.74
299 300 3.541996 TGTATGCAGTGTCCATAGTGG 57.458 47.619 0.00 0.00 39.43 4.00
300 301 2.837591 TGTATGCAGTGTCCATAGTGGT 59.162 45.455 0.00 0.00 39.03 4.16
301 302 3.263170 TGTATGCAGTGTCCATAGTGGTT 59.737 43.478 0.00 0.00 39.03 3.67
302 303 2.472695 TGCAGTGTCCATAGTGGTTC 57.527 50.000 0.00 0.00 39.03 3.62
303 304 1.977854 TGCAGTGTCCATAGTGGTTCT 59.022 47.619 0.00 0.00 39.03 3.01
304 305 2.289631 TGCAGTGTCCATAGTGGTTCTG 60.290 50.000 0.00 5.10 39.03 3.02
305 306 2.936993 GCAGTGTCCATAGTGGTTCTGG 60.937 54.545 14.15 0.00 39.03 3.86
306 307 1.909302 AGTGTCCATAGTGGTTCTGGG 59.091 52.381 0.00 0.00 39.03 4.45
307 308 0.618458 TGTCCATAGTGGTTCTGGGC 59.382 55.000 0.00 0.00 39.03 5.36
308 309 0.912486 GTCCATAGTGGTTCTGGGCT 59.088 55.000 0.00 0.00 39.03 5.19
309 310 0.911769 TCCATAGTGGTTCTGGGCTG 59.088 55.000 0.00 0.00 39.03 4.85
310 311 0.107017 CCATAGTGGTTCTGGGCTGG 60.107 60.000 0.00 0.00 31.35 4.85
311 312 0.620556 CATAGTGGTTCTGGGCTGGT 59.379 55.000 0.00 0.00 0.00 4.00
312 313 0.620556 ATAGTGGTTCTGGGCTGGTG 59.379 55.000 0.00 0.00 0.00 4.17
313 314 2.124507 TAGTGGTTCTGGGCTGGTGC 62.125 60.000 0.00 0.00 38.76 5.01
314 315 4.641645 TGGTTCTGGGCTGGTGCG 62.642 66.667 0.00 0.00 40.82 5.34
315 316 4.643387 GGTTCTGGGCTGGTGCGT 62.643 66.667 0.00 0.00 40.82 5.24
316 317 2.345991 GTTCTGGGCTGGTGCGTA 59.654 61.111 0.00 0.00 40.82 4.42
317 318 1.741770 GTTCTGGGCTGGTGCGTAG 60.742 63.158 0.00 0.00 40.82 3.51
318 319 2.954684 TTCTGGGCTGGTGCGTAGG 61.955 63.158 0.00 0.00 40.82 3.18
319 320 3.706373 CTGGGCTGGTGCGTAGGT 61.706 66.667 0.00 0.00 40.82 3.08
320 321 3.665675 CTGGGCTGGTGCGTAGGTC 62.666 68.421 0.00 0.00 40.82 3.85
321 322 4.814294 GGGCTGGTGCGTAGGTCG 62.814 72.222 0.00 0.00 40.82 4.79
322 323 4.814294 GGCTGGTGCGTAGGTCGG 62.814 72.222 0.00 0.00 40.82 4.79
323 324 3.755628 GCTGGTGCGTAGGTCGGA 61.756 66.667 0.00 0.00 40.26 4.55
324 325 2.967397 CTGGTGCGTAGGTCGGAA 59.033 61.111 0.00 0.00 42.24 4.30
325 326 1.290955 CTGGTGCGTAGGTCGGAAA 59.709 57.895 0.00 0.00 42.24 3.13
326 327 0.108329 CTGGTGCGTAGGTCGGAAAT 60.108 55.000 0.00 0.00 42.24 2.17
327 328 0.322322 TGGTGCGTAGGTCGGAAATT 59.678 50.000 0.00 0.00 42.24 1.82
328 329 1.270947 TGGTGCGTAGGTCGGAAATTT 60.271 47.619 0.00 0.00 42.24 1.82
329 330 1.808343 GGTGCGTAGGTCGGAAATTTT 59.192 47.619 0.00 0.00 42.24 1.82
330 331 2.227149 GGTGCGTAGGTCGGAAATTTTT 59.773 45.455 0.00 0.00 42.24 1.94
350 351 4.428615 TTTATTTTCTGCTGCGTTACCC 57.571 40.909 0.00 0.00 0.00 3.69
351 352 1.904287 ATTTTCTGCTGCGTTACCCA 58.096 45.000 0.00 0.00 0.00 4.51
352 353 1.904287 TTTTCTGCTGCGTTACCCAT 58.096 45.000 0.00 0.00 0.00 4.00
353 354 1.448985 TTTCTGCTGCGTTACCCATC 58.551 50.000 0.00 0.00 0.00 3.51
420 421 4.514441 GGACTCTAGAATGCCACATTCATG 59.486 45.833 19.39 12.39 0.00 3.07
434 435 3.578282 ACATTCATGGAGGGAAAACAACC 59.422 43.478 0.00 0.00 0.00 3.77
497 498 2.099652 CTCCCGCAACTGTCCAGACA 62.100 60.000 0.40 0.00 39.32 3.41
506 507 1.485066 ACTGTCCAGACAACGGAAACT 59.515 47.619 1.58 0.00 41.33 2.66
539 541 1.331399 TGTATCAATCCACGGGGCGA 61.331 55.000 0.00 0.00 0.00 5.54
583 585 4.324991 GGAGACAAACGCGGGGGT 62.325 66.667 12.47 4.50 0.00 4.95
769 789 4.423209 ACCAGGGAGGGAGGGAGC 62.423 72.222 0.00 0.00 43.89 4.70
847 867 2.814835 AAGGAACCAACTCCGGCGT 61.815 57.895 6.01 0.00 40.75 5.68
924 968 3.402681 AGAGATGCACCACCCCCG 61.403 66.667 0.00 0.00 0.00 5.73
964 1018 2.612836 CCCTCCCCCGTCTCCATA 59.387 66.667 0.00 0.00 0.00 2.74
1004 1065 0.389817 TCTTCGACCCAAGCGATGTG 60.390 55.000 0.00 0.00 37.64 3.21
1022 1377 2.432628 GAAGTCGTGGTGCTCCGG 60.433 66.667 0.00 0.00 36.30 5.14
1172 1546 3.382832 CGAGGAGGACCAGGCGTT 61.383 66.667 0.00 0.00 38.94 4.84
1309 1707 2.125912 CGGAGCGTGTGAAGGAGG 60.126 66.667 0.00 0.00 0.00 4.30
1310 1708 2.636412 CGGAGCGTGTGAAGGAGGA 61.636 63.158 0.00 0.00 0.00 3.71
1311 1709 1.079750 GGAGCGTGTGAAGGAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
1378 1780 1.599047 CACCTGCCGATGAAGGAGT 59.401 57.895 0.00 0.00 37.01 3.85
1385 1787 0.669077 CCGATGAAGGAGTAGTCGGG 59.331 60.000 4.31 0.00 45.92 5.14
1781 2222 3.048602 CAACGACCCAGACCTCGT 58.951 61.111 0.00 0.00 44.89 4.18
2135 2648 0.672342 ATGTGGTCGTCCGGTATAGC 59.328 55.000 0.00 0.00 36.30 2.97
2305 2830 1.475280 CGTTAGATGACGTCCTCCCAA 59.525 52.381 14.12 7.19 38.19 4.12
2308 2833 4.514401 GTTAGATGACGTCCTCCCAAATT 58.486 43.478 14.12 0.00 0.00 1.82
2312 2837 1.894466 TGACGTCCTCCCAAATTCGTA 59.106 47.619 14.12 0.00 0.00 3.43
2332 2857 2.202797 CACGGACCGATGCAGGAG 60.203 66.667 23.38 0.00 34.73 3.69
2339 2864 1.943340 GACCGATGCAGGAGGAAATTC 59.057 52.381 11.25 0.00 34.73 2.17
2341 2866 2.290896 ACCGATGCAGGAGGAAATTCAA 60.291 45.455 11.25 0.00 34.73 2.69
2352 2877 1.970640 GGAAATTCAAGGGTTGCCACT 59.029 47.619 0.00 0.00 0.00 4.00
2356 2881 1.691196 TTCAAGGGTTGCCACTGAAG 58.309 50.000 0.00 0.00 0.00 3.02
2360 2885 0.038744 AGGGTTGCCACTGAAGATGG 59.961 55.000 0.00 0.00 40.50 3.51
2375 2900 4.530553 TGAAGATGGCCTTACACAACTCTA 59.469 41.667 3.32 0.00 34.68 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.668151 GTCACACGGACAGCCCTTC 60.668 63.158 0.00 0.00 46.19 3.46
4 5 2.426023 GTCACACGGACAGCCCTT 59.574 61.111 0.00 0.00 46.19 3.95
11 12 3.606065 CTCGGACGGTCACACGGAC 62.606 68.421 10.76 0.00 46.20 4.79
12 13 3.359523 CTCGGACGGTCACACGGA 61.360 66.667 10.76 0.00 38.39 4.69
13 14 2.688526 AAACTCGGACGGTCACACGG 62.689 60.000 10.76 2.19 38.39 4.94
14 15 1.273455 GAAACTCGGACGGTCACACG 61.273 60.000 10.76 4.75 40.31 4.49
15 16 1.273455 CGAAACTCGGACGGTCACAC 61.273 60.000 10.76 0.00 36.00 3.82
16 17 1.008194 CGAAACTCGGACGGTCACA 60.008 57.895 10.76 0.00 36.00 3.58
17 18 0.318107 TTCGAAACTCGGACGGTCAC 60.318 55.000 10.76 0.00 40.88 3.67
18 19 0.039798 CTTCGAAACTCGGACGGTCA 60.040 55.000 10.76 0.00 40.88 4.02
19 20 0.731855 CCTTCGAAACTCGGACGGTC 60.732 60.000 0.00 0.00 40.88 4.79
20 21 1.288127 CCTTCGAAACTCGGACGGT 59.712 57.895 0.00 0.00 40.88 4.83
21 22 0.319297 AACCTTCGAAACTCGGACGG 60.319 55.000 8.07 1.53 40.88 4.79
22 23 0.782384 CAACCTTCGAAACTCGGACG 59.218 55.000 8.07 0.00 40.88 4.79
23 24 1.791204 GACAACCTTCGAAACTCGGAC 59.209 52.381 8.07 0.00 40.88 4.79
24 25 1.269936 GGACAACCTTCGAAACTCGGA 60.270 52.381 8.07 0.00 40.88 4.55
25 26 1.145803 GGACAACCTTCGAAACTCGG 58.854 55.000 0.00 0.00 40.88 4.63
26 27 1.145803 GGGACAACCTTCGAAACTCG 58.854 55.000 0.00 0.00 37.49 4.18
27 28 1.145803 CGGGACAACCTTCGAAACTC 58.854 55.000 0.00 0.00 36.97 3.01
28 29 0.754472 TCGGGACAACCTTCGAAACT 59.246 50.000 0.00 0.00 36.97 2.66
29 30 1.529865 CTTCGGGACAACCTTCGAAAC 59.470 52.381 0.00 0.00 35.83 2.78
30 31 1.541670 CCTTCGGGACAACCTTCGAAA 60.542 52.381 0.00 0.00 35.83 3.46
31 32 0.034337 CCTTCGGGACAACCTTCGAA 59.966 55.000 0.00 0.00 35.83 3.71
32 33 1.669440 CCTTCGGGACAACCTTCGA 59.331 57.895 0.00 0.00 37.25 3.71
33 34 4.278956 CCTTCGGGACAACCTTCG 57.721 61.111 0.00 0.00 37.25 3.79
42 43 2.156496 ACTCAGAGAGCCCTTCGGGA 62.156 60.000 3.79 0.00 46.48 5.14
44 45 0.967887 TCACTCAGAGAGCCCTTCGG 60.968 60.000 3.79 0.00 32.04 4.30
45 46 0.172352 GTCACTCAGAGAGCCCTTCG 59.828 60.000 3.79 0.00 32.04 3.79
46 47 0.534873 GGTCACTCAGAGAGCCCTTC 59.465 60.000 3.79 0.00 32.04 3.46
47 48 1.254284 CGGTCACTCAGAGAGCCCTT 61.254 60.000 3.79 0.00 32.04 3.95
48 49 1.680651 CGGTCACTCAGAGAGCCCT 60.681 63.158 3.79 0.00 32.04 5.19
49 50 1.536943 AACGGTCACTCAGAGAGCCC 61.537 60.000 3.79 0.00 32.04 5.19
50 51 0.109039 GAACGGTCACTCAGAGAGCC 60.109 60.000 3.79 1.56 32.04 4.70
51 52 0.455295 CGAACGGTCACTCAGAGAGC 60.455 60.000 3.79 0.00 32.04 4.09
52 53 1.129624 CTCGAACGGTCACTCAGAGAG 59.870 57.143 3.79 0.00 35.52 3.20
53 54 1.157585 CTCGAACGGTCACTCAGAGA 58.842 55.000 3.79 0.00 0.00 3.10
54 55 0.875728 ACTCGAACGGTCACTCAGAG 59.124 55.000 0.00 0.51 0.00 3.35
55 56 1.315690 AACTCGAACGGTCACTCAGA 58.684 50.000 0.00 0.00 0.00 3.27
56 57 2.052157 GAAACTCGAACGGTCACTCAG 58.948 52.381 0.00 0.00 0.00 3.35
57 58 1.598676 CGAAACTCGAACGGTCACTCA 60.599 52.381 0.00 0.00 43.74 3.41
58 59 1.050767 CGAAACTCGAACGGTCACTC 58.949 55.000 0.00 0.00 43.74 3.51
59 60 0.664761 TCGAAACTCGAACGGTCACT 59.335 50.000 0.00 0.00 46.90 3.41
60 61 3.168628 TCGAAACTCGAACGGTCAC 57.831 52.632 0.00 0.00 46.90 3.67
69 70 0.108756 GGGAGGACCTTCGAAACTCG 60.109 60.000 0.00 0.00 37.49 4.18
70 71 0.108756 CGGGAGGACCTTCGAAACTC 60.109 60.000 11.36 4.93 36.97 3.01
71 72 0.541296 TCGGGAGGACCTTCGAAACT 60.541 55.000 15.55 0.00 36.97 2.66
72 73 0.319405 TTCGGGAGGACCTTCGAAAC 59.681 55.000 22.82 0.01 37.08 2.78
73 74 0.606604 CTTCGGGAGGACCTTCGAAA 59.393 55.000 24.14 9.26 38.57 3.46
74 75 2.273908 CTTCGGGAGGACCTTCGAA 58.726 57.895 23.23 23.23 37.45 3.71
75 76 4.013702 CTTCGGGAGGACCTTCGA 57.986 61.111 14.37 14.37 36.97 3.71
89 90 4.373116 TGTCGCGGACAGCCCTTC 62.373 66.667 6.13 0.00 44.76 3.46
90 91 4.681978 GTGTCGCGGACAGCCCTT 62.682 66.667 6.13 0.00 43.57 3.95
109 110 4.754667 GTCGAACAGCCCCCGGAC 62.755 72.222 0.73 0.00 0.00 4.79
118 119 4.796231 CGGGAGGCGGTCGAACAG 62.796 72.222 0.00 0.00 0.00 3.16
133 134 3.465403 CCTCAGACAGCCCTCCGG 61.465 72.222 0.00 0.00 0.00 5.14
134 135 2.363018 TCCTCAGACAGCCCTCCG 60.363 66.667 0.00 0.00 0.00 4.63
135 136 2.730524 GCTCCTCAGACAGCCCTCC 61.731 68.421 0.00 0.00 0.00 4.30
136 137 1.958902 CTGCTCCTCAGACAGCCCTC 61.959 65.000 0.00 0.00 45.72 4.30
137 138 1.988956 CTGCTCCTCAGACAGCCCT 60.989 63.158 0.00 0.00 45.72 5.19
138 139 1.986757 TCTGCTCCTCAGACAGCCC 60.987 63.158 0.00 0.00 46.34 5.19
139 140 3.705502 TCTGCTCCTCAGACAGCC 58.294 61.111 0.00 0.00 46.34 4.85
145 146 0.394488 TACCCTCGTCTGCTCCTCAG 60.394 60.000 0.00 0.00 44.21 3.35
146 147 0.259065 ATACCCTCGTCTGCTCCTCA 59.741 55.000 0.00 0.00 0.00 3.86
147 148 1.881324 GTATACCCTCGTCTGCTCCTC 59.119 57.143 0.00 0.00 0.00 3.71
148 149 1.214673 TGTATACCCTCGTCTGCTCCT 59.785 52.381 0.00 0.00 0.00 3.69
149 150 1.688772 TGTATACCCTCGTCTGCTCC 58.311 55.000 0.00 0.00 0.00 4.70
150 151 2.229302 GGATGTATACCCTCGTCTGCTC 59.771 54.545 0.00 0.00 0.00 4.26
151 152 2.158445 AGGATGTATACCCTCGTCTGCT 60.158 50.000 0.00 0.00 0.00 4.24
152 153 2.229302 GAGGATGTATACCCTCGTCTGC 59.771 54.545 11.14 0.00 39.49 4.26
171 172 2.162338 TACAACCTCCCAACCGCGAG 62.162 60.000 8.23 0.00 0.00 5.03
172 173 1.756408 TTACAACCTCCCAACCGCGA 61.756 55.000 8.23 0.00 0.00 5.87
173 174 0.885596 TTTACAACCTCCCAACCGCG 60.886 55.000 0.00 0.00 0.00 6.46
174 175 1.471287 GATTTACAACCTCCCAACCGC 59.529 52.381 0.00 0.00 0.00 5.68
175 176 2.089201 GGATTTACAACCTCCCAACCG 58.911 52.381 0.00 0.00 0.00 4.44
176 177 3.451402 AGGATTTACAACCTCCCAACC 57.549 47.619 0.00 0.00 0.00 3.77
177 178 3.945921 GCTAGGATTTACAACCTCCCAAC 59.054 47.826 0.00 0.00 37.68 3.77
178 179 3.850173 AGCTAGGATTTACAACCTCCCAA 59.150 43.478 0.00 0.00 37.68 4.12
179 180 3.199946 CAGCTAGGATTTACAACCTCCCA 59.800 47.826 0.00 0.00 37.68 4.37
180 181 3.809905 CAGCTAGGATTTACAACCTCCC 58.190 50.000 0.00 0.00 37.68 4.30
181 182 3.206964 GCAGCTAGGATTTACAACCTCC 58.793 50.000 0.00 0.00 37.68 4.30
182 183 2.866762 CGCAGCTAGGATTTACAACCTC 59.133 50.000 0.00 0.00 37.68 3.85
183 184 2.420129 CCGCAGCTAGGATTTACAACCT 60.420 50.000 1.34 0.00 39.95 3.50
184 185 1.940613 CCGCAGCTAGGATTTACAACC 59.059 52.381 1.34 0.00 0.00 3.77
185 186 1.940613 CCCGCAGCTAGGATTTACAAC 59.059 52.381 8.84 0.00 0.00 3.32
186 187 1.134220 CCCCGCAGCTAGGATTTACAA 60.134 52.381 8.84 0.00 0.00 2.41
187 188 0.468226 CCCCGCAGCTAGGATTTACA 59.532 55.000 8.84 0.00 0.00 2.41
188 189 0.756903 TCCCCGCAGCTAGGATTTAC 59.243 55.000 8.84 0.00 0.00 2.01
189 190 1.623811 GATCCCCGCAGCTAGGATTTA 59.376 52.381 12.97 0.00 40.54 1.40
190 191 0.398318 GATCCCCGCAGCTAGGATTT 59.602 55.000 12.97 0.00 40.54 2.17
191 192 0.472734 AGATCCCCGCAGCTAGGATT 60.473 55.000 12.97 3.18 40.54 3.01
192 193 1.157276 AGATCCCCGCAGCTAGGAT 59.843 57.895 11.86 11.86 43.18 3.24
193 194 1.834378 CAGATCCCCGCAGCTAGGA 60.834 63.158 8.84 2.90 0.00 2.94
194 195 2.739784 CAGATCCCCGCAGCTAGG 59.260 66.667 0.61 0.61 0.00 3.02
195 196 2.030262 GCAGATCCCCGCAGCTAG 59.970 66.667 0.00 0.00 0.00 3.42
196 197 2.763710 TGCAGATCCCCGCAGCTA 60.764 61.111 0.00 0.00 33.34 3.32
197 198 4.479993 GTGCAGATCCCCGCAGCT 62.480 66.667 2.52 0.00 39.20 4.24
204 205 4.241555 ATCGGCGGTGCAGATCCC 62.242 66.667 7.21 0.00 39.00 3.85
205 206 2.969238 CATCGGCGGTGCAGATCC 60.969 66.667 7.44 0.00 41.08 3.36
206 207 2.969238 CCATCGGCGGTGCAGATC 60.969 66.667 16.12 0.00 41.08 2.75
207 208 3.740128 GACCATCGGCGGTGCAGAT 62.740 63.158 16.12 0.00 43.52 2.90
208 209 4.451150 GACCATCGGCGGTGCAGA 62.451 66.667 16.12 0.00 40.22 4.26
209 210 4.758251 TGACCATCGGCGGTGCAG 62.758 66.667 16.12 4.55 40.22 4.41
210 211 4.094646 ATGACCATCGGCGGTGCA 62.095 61.111 16.12 8.93 40.22 4.57
211 212 3.272334 GATGACCATCGGCGGTGC 61.272 66.667 16.12 2.25 40.22 5.01
219 220 3.004944 GGGAAGTAGAGTCGATGACCATC 59.995 52.174 0.00 0.04 32.18 3.51
220 221 2.959707 GGGAAGTAGAGTCGATGACCAT 59.040 50.000 0.00 0.00 32.18 3.55
221 222 2.376109 GGGAAGTAGAGTCGATGACCA 58.624 52.381 0.00 0.00 32.18 4.02
222 223 1.334243 CGGGAAGTAGAGTCGATGACC 59.666 57.143 0.00 0.00 32.18 4.02
223 224 1.268640 GCGGGAAGTAGAGTCGATGAC 60.269 57.143 0.00 0.00 0.00 3.06
224 225 1.022735 GCGGGAAGTAGAGTCGATGA 58.977 55.000 0.00 0.00 0.00 2.92
225 226 1.025812 AGCGGGAAGTAGAGTCGATG 58.974 55.000 0.00 0.00 0.00 3.84
226 227 1.025812 CAGCGGGAAGTAGAGTCGAT 58.974 55.000 0.00 0.00 0.00 3.59
227 228 1.654954 GCAGCGGGAAGTAGAGTCGA 61.655 60.000 0.00 0.00 0.00 4.20
228 229 1.226717 GCAGCGGGAAGTAGAGTCG 60.227 63.158 0.00 0.00 0.00 4.18
229 230 1.226717 CGCAGCGGGAAGTAGAGTC 60.227 63.158 7.00 0.00 0.00 3.36
230 231 2.885861 CGCAGCGGGAAGTAGAGT 59.114 61.111 7.00 0.00 0.00 3.24
246 247 1.346197 TCGTTAGCGACTCGTAGCG 59.654 57.895 0.00 5.81 42.81 4.26
266 267 6.581712 ACACTGCATACAAGGTTTGATTTTT 58.418 32.000 0.00 0.00 0.00 1.94
267 268 6.160576 ACACTGCATACAAGGTTTGATTTT 57.839 33.333 0.00 0.00 0.00 1.82
268 269 5.278957 GGACACTGCATACAAGGTTTGATTT 60.279 40.000 0.00 0.00 0.00 2.17
269 270 4.218417 GGACACTGCATACAAGGTTTGATT 59.782 41.667 0.00 0.00 0.00 2.57
270 271 3.758554 GGACACTGCATACAAGGTTTGAT 59.241 43.478 0.00 0.00 0.00 2.57
271 272 3.146066 GGACACTGCATACAAGGTTTGA 58.854 45.455 0.00 0.00 0.00 2.69
272 273 2.884012 TGGACACTGCATACAAGGTTTG 59.116 45.455 0.00 0.00 0.00 2.93
273 274 3.222173 TGGACACTGCATACAAGGTTT 57.778 42.857 0.00 0.00 0.00 3.27
274 275 2.949177 TGGACACTGCATACAAGGTT 57.051 45.000 0.00 0.00 0.00 3.50
275 276 3.519510 ACTATGGACACTGCATACAAGGT 59.480 43.478 0.00 0.00 29.08 3.50
276 277 3.873361 CACTATGGACACTGCATACAAGG 59.127 47.826 0.00 0.00 29.08 3.61
277 278 3.873361 CCACTATGGACACTGCATACAAG 59.127 47.826 0.00 0.00 40.96 3.16
278 279 3.263170 ACCACTATGGACACTGCATACAA 59.737 43.478 0.84 0.00 40.96 2.41
279 280 2.837591 ACCACTATGGACACTGCATACA 59.162 45.455 0.84 0.00 40.96 2.29
280 281 3.543680 ACCACTATGGACACTGCATAC 57.456 47.619 0.84 0.00 40.96 2.39
281 282 3.774766 AGAACCACTATGGACACTGCATA 59.225 43.478 0.84 0.00 40.96 3.14
282 283 2.573462 AGAACCACTATGGACACTGCAT 59.427 45.455 0.84 0.00 40.96 3.96
283 284 1.977854 AGAACCACTATGGACACTGCA 59.022 47.619 0.84 0.00 40.96 4.41
284 285 2.350522 CAGAACCACTATGGACACTGC 58.649 52.381 0.84 0.00 40.96 4.40
285 286 2.355108 CCCAGAACCACTATGGACACTG 60.355 54.545 0.84 7.57 40.96 3.66
286 287 1.909302 CCCAGAACCACTATGGACACT 59.091 52.381 0.84 0.00 40.96 3.55
287 288 1.679032 GCCCAGAACCACTATGGACAC 60.679 57.143 0.84 0.00 40.96 3.67
288 289 0.618458 GCCCAGAACCACTATGGACA 59.382 55.000 0.84 0.00 40.96 4.02
289 290 0.912486 AGCCCAGAACCACTATGGAC 59.088 55.000 0.84 0.00 40.96 4.02
290 291 0.911769 CAGCCCAGAACCACTATGGA 59.088 55.000 0.84 0.00 40.96 3.41
291 292 0.107017 CCAGCCCAGAACCACTATGG 60.107 60.000 0.00 0.00 45.02 2.74
292 293 0.620556 ACCAGCCCAGAACCACTATG 59.379 55.000 0.00 0.00 0.00 2.23
293 294 0.620556 CACCAGCCCAGAACCACTAT 59.379 55.000 0.00 0.00 0.00 2.12
294 295 2.066340 CACCAGCCCAGAACCACTA 58.934 57.895 0.00 0.00 0.00 2.74
295 296 2.839098 CACCAGCCCAGAACCACT 59.161 61.111 0.00 0.00 0.00 4.00
296 297 2.985847 GCACCAGCCCAGAACCAC 60.986 66.667 0.00 0.00 33.58 4.16
297 298 4.641645 CGCACCAGCCCAGAACCA 62.642 66.667 0.00 0.00 37.52 3.67
298 299 3.248446 TACGCACCAGCCCAGAACC 62.248 63.158 0.00 0.00 37.52 3.62
299 300 1.741770 CTACGCACCAGCCCAGAAC 60.742 63.158 0.00 0.00 37.52 3.01
300 301 2.662596 CTACGCACCAGCCCAGAA 59.337 61.111 0.00 0.00 37.52 3.02
301 302 3.390521 CCTACGCACCAGCCCAGA 61.391 66.667 0.00 0.00 37.52 3.86
302 303 3.665675 GACCTACGCACCAGCCCAG 62.666 68.421 0.00 0.00 37.52 4.45
303 304 3.702048 GACCTACGCACCAGCCCA 61.702 66.667 0.00 0.00 37.52 5.36
304 305 4.814294 CGACCTACGCACCAGCCC 62.814 72.222 0.00 0.00 37.52 5.19
305 306 4.814294 CCGACCTACGCACCAGCC 62.814 72.222 0.00 0.00 41.07 4.85
306 307 2.775032 TTTCCGACCTACGCACCAGC 62.775 60.000 0.00 0.00 41.07 4.85
307 308 0.108329 ATTTCCGACCTACGCACCAG 60.108 55.000 0.00 0.00 41.07 4.00
308 309 0.322322 AATTTCCGACCTACGCACCA 59.678 50.000 0.00 0.00 41.07 4.17
309 310 1.445871 AAATTTCCGACCTACGCACC 58.554 50.000 0.00 0.00 41.07 5.01
310 311 3.547649 AAAAATTTCCGACCTACGCAC 57.452 42.857 0.00 0.00 41.07 5.34
327 328 5.221263 TGGGTAACGCAGCAGAAAATAAAAA 60.221 36.000 0.00 0.00 37.60 1.94
328 329 4.278669 TGGGTAACGCAGCAGAAAATAAAA 59.721 37.500 0.00 0.00 37.60 1.52
329 330 3.821600 TGGGTAACGCAGCAGAAAATAAA 59.178 39.130 0.00 0.00 37.60 1.40
330 331 3.413327 TGGGTAACGCAGCAGAAAATAA 58.587 40.909 0.00 0.00 37.60 1.40
331 332 3.060736 TGGGTAACGCAGCAGAAAATA 57.939 42.857 0.00 0.00 37.60 1.40
332 333 1.904287 TGGGTAACGCAGCAGAAAAT 58.096 45.000 0.00 0.00 37.60 1.82
333 334 1.810151 GATGGGTAACGCAGCAGAAAA 59.190 47.619 0.00 0.00 33.03 2.29
334 335 1.271108 TGATGGGTAACGCAGCAGAAA 60.271 47.619 0.00 0.00 37.76 2.52
335 336 0.323302 TGATGGGTAACGCAGCAGAA 59.677 50.000 0.00 0.00 37.76 3.02
336 337 0.323302 TTGATGGGTAACGCAGCAGA 59.677 50.000 0.00 0.00 42.94 4.26
337 338 0.447801 GTTGATGGGTAACGCAGCAG 59.552 55.000 0.00 0.00 42.94 4.24
338 339 0.250510 TGTTGATGGGTAACGCAGCA 60.251 50.000 0.00 0.00 40.66 4.41
339 340 0.878416 TTGTTGATGGGTAACGCAGC 59.122 50.000 0.00 0.00 33.40 5.25
340 341 3.004315 AGTTTTGTTGATGGGTAACGCAG 59.996 43.478 0.00 0.00 37.60 5.18
341 342 2.952978 AGTTTTGTTGATGGGTAACGCA 59.047 40.909 0.00 0.00 37.60 5.24
342 343 3.003897 TGAGTTTTGTTGATGGGTAACGC 59.996 43.478 0.00 0.00 37.60 4.84
343 344 4.822036 TGAGTTTTGTTGATGGGTAACG 57.178 40.909 0.00 0.00 37.60 3.18
344 345 5.048991 ACGATGAGTTTTGTTGATGGGTAAC 60.049 40.000 0.00 0.00 0.00 2.50
345 346 5.049060 CACGATGAGTTTTGTTGATGGGTAA 60.049 40.000 0.00 0.00 0.00 2.85
346 347 4.454161 CACGATGAGTTTTGTTGATGGGTA 59.546 41.667 0.00 0.00 0.00 3.69
347 348 3.253188 CACGATGAGTTTTGTTGATGGGT 59.747 43.478 0.00 0.00 0.00 4.51
348 349 3.366273 CCACGATGAGTTTTGTTGATGGG 60.366 47.826 0.00 0.00 0.00 4.00
349 350 3.501828 TCCACGATGAGTTTTGTTGATGG 59.498 43.478 0.00 0.00 0.00 3.51
350 351 4.747540 TCCACGATGAGTTTTGTTGATG 57.252 40.909 0.00 0.00 0.00 3.07
351 352 4.821805 AGTTCCACGATGAGTTTTGTTGAT 59.178 37.500 0.00 0.00 0.00 2.57
352 353 4.196193 AGTTCCACGATGAGTTTTGTTGA 58.804 39.130 0.00 0.00 0.00 3.18
353 354 4.552166 AGTTCCACGATGAGTTTTGTTG 57.448 40.909 0.00 0.00 0.00 3.33
420 421 5.303333 TGTTTATTCTGGTTGTTTTCCCTCC 59.697 40.000 0.00 0.00 0.00 4.30
434 435 5.882557 AGATGCCCTAGTGTTGTTTATTCTG 59.117 40.000 0.00 0.00 0.00 3.02
506 507 1.887854 TGATACAGGTCGACGTTGGAA 59.112 47.619 18.97 9.81 0.00 3.53
539 541 1.067582 GGAGAAATCGCGTCCGGAT 59.932 57.895 7.81 0.00 34.56 4.18
745 755 0.618680 CTCCCTCCCTGGTCACATCA 60.619 60.000 0.00 0.00 0.00 3.07
964 1018 4.423209 GGAGGGAGGGGCTCAGGT 62.423 72.222 0.00 0.00 31.08 4.00
1004 1065 2.432628 CGGAGCACCACGACTTCC 60.433 66.667 0.00 0.00 35.59 3.46
1022 1377 2.027751 GTACTCCGCCTGCCGATC 59.972 66.667 0.00 0.00 40.02 3.69
1183 1581 2.356667 CTTGAGGAGTTGGGGCCC 59.643 66.667 18.17 18.17 0.00 5.80
1184 1582 2.231380 TCCTTGAGGAGTTGGGGCC 61.231 63.158 0.00 0.00 39.78 5.80
1361 1763 1.115467 CTACTCCTTCATCGGCAGGT 58.885 55.000 0.00 0.00 0.00 4.00
1385 1787 3.512516 GATTGTGCTGGGGCGAGC 61.513 66.667 0.39 0.39 42.25 5.03
1572 1978 2.110006 GGCGGCATCTCCTCCTTC 59.890 66.667 3.07 0.00 36.76 3.46
1646 2080 3.680786 CAGACACGACGGCCCTCA 61.681 66.667 0.00 0.00 0.00 3.86
1781 2222 4.429212 CGATCACCCACACGGCGA 62.429 66.667 16.62 0.00 33.26 5.54
1795 2236 0.029035 GTGGTCACGTAGCGATCGAT 59.971 55.000 21.57 16.78 0.00 3.59
1875 2323 1.937108 GCAGTTGCTAAGCGACACTCT 60.937 52.381 0.00 0.00 44.70 3.24
2117 2630 1.717791 CGCTATACCGGACGACCACA 61.718 60.000 9.46 0.00 35.59 4.17
2206 2730 8.356000 ACCGGATGGATTTCATTTAAGTTTAA 57.644 30.769 9.46 0.00 39.21 1.52
2247 2771 3.540617 GGCCAACAATTTGAACCAACTT 58.459 40.909 0.00 0.00 34.24 2.66
2312 2837 1.153369 CCTGCATCGGTCCGTGAAT 60.153 57.895 11.88 0.00 0.00 2.57
2322 2847 2.357009 CCTTGAATTTCCTCCTGCATCG 59.643 50.000 0.00 0.00 0.00 3.84
2332 2857 1.970640 AGTGGCAACCCTTGAATTTCC 59.029 47.619 0.00 0.00 0.00 3.13
2339 2864 1.542915 CATCTTCAGTGGCAACCCTTG 59.457 52.381 0.00 0.00 0.00 3.61
2341 2866 0.038744 CCATCTTCAGTGGCAACCCT 59.961 55.000 0.00 0.00 0.00 4.34
2352 2877 3.327757 AGAGTTGTGTAAGGCCATCTTCA 59.672 43.478 5.01 0.00 36.93 3.02


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

AutoCloner maintained by Alex Coulton.