Multiple sequence alignment - TraesCS6B01G186800

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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 TraesCS6B01G186800 chr6B 100.000 2750 0 0 1 2750 213152705 213149956 0.000000e+00 5079.0
1 TraesCS6B01G186800 chr6B 92.564 780 20 8 1602 2365 213307481 213306724 0.000000e+00 1085.0
2 TraesCS6B01G186800 chr6B 94.281 647 25 3 977 1612 213308309 213307664 0.000000e+00 979.0
3 TraesCS6B01G186800 chr6B 96.907 388 11 1 2362 2749 213306796 213306410 0.000000e+00 649.0
4 TraesCS6B01G186800 chr6B 89.423 312 17 7 1858 2154 213481114 213481424 2.000000e-101 379.0
5 TraesCS6B01G186800 chr6B 83.544 395 28 13 2362 2749 213142832 213142468 4.390000e-88 335.0
6 TraesCS6B01G186800 chr6B 100.000 179 0 0 149 327 525106238 525106416 5.680000e-87 331.0
7 TraesCS6B01G186800 chr6B 93.088 217 15 0 2150 2366 213142975 213142759 4.420000e-83 318.0
8 TraesCS6B01G186800 chr6B 87.013 231 13 8 1940 2154 213143240 213143011 7.610000e-61 244.0
9 TraesCS6B01G186800 chr6B 81.673 251 13 13 742 986 213315689 213315466 7.830000e-41 178.0
10 TraesCS6B01G186800 chr6B 97.260 73 2 0 2293 2365 213150344 213150272 1.030000e-24 124.0
11 TraesCS6B01G186800 chr6B 97.260 73 2 0 2362 2434 213150413 213150341 1.030000e-24 124.0
12 TraesCS6B01G186800 chr6D 92.933 1132 55 11 331 1446 121090172 121089050 0.000000e+00 1624.0
13 TraesCS6B01G186800 chr6D 88.039 1137 88 20 1056 2154 121300940 121299814 0.000000e+00 1303.0
14 TraesCS6B01G186800 chr6D 90.281 391 26 6 2369 2750 121298044 121297657 4.090000e-138 501.0
15 TraesCS6B01G186800 chr6D 88.487 304 19 6 2059 2361 121334697 121334409 1.210000e-93 353.0
16 TraesCS6B01G186800 chr6D 81.955 399 23 17 2362 2750 121334477 121334118 2.680000e-75 292.0
17 TraesCS6B01G186800 chr6D 94.079 152 8 1 1 152 121090317 121090167 2.130000e-56 230.0
18 TraesCS6B01G186800 chr6D 82.437 279 22 12 2478 2750 121463922 121464179 4.610000e-53 219.0
19 TraesCS6B01G186800 chr6D 90.303 165 13 1 2152 2316 121299774 121299613 2.150000e-51 213.0
20 TraesCS6B01G186800 chr6D 83.333 186 9 8 740 921 121310576 121310409 4.740000e-33 152.0
21 TraesCS6B01G186800 chr6D 83.000 100 5 6 654 741 121310704 121310605 2.270000e-11 80.5
22 TraesCS6B01G186800 chr6A 89.484 1046 75 15 749 1780 162728148 162729172 0.000000e+00 1290.0
23 TraesCS6B01G186800 chr6A 86.479 747 70 12 740 1473 162785407 162786135 0.000000e+00 791.0
24 TraesCS6B01G186800 chr6A 89.885 524 53 0 1257 1780 162549233 162549756 0.000000e+00 675.0
25 TraesCS6B01G186800 chr6A 89.423 416 37 4 846 1257 162463956 162464368 4.060000e-143 518.0
26 TraesCS6B01G186800 chr6A 93.333 300 18 2 2367 2665 162802075 162802373 2.510000e-120 442.0
27 TraesCS6B01G186800 chr6A 83.263 472 76 1 998 1469 158409052 158409520 5.440000e-117 431.0
28 TraesCS6B01G186800 chr6A 85.227 440 31 10 1748 2154 162801471 162801909 3.270000e-114 422.0
29 TraesCS6B01G186800 chr6A 83.964 449 61 7 1461 1902 158422419 158422863 1.180000e-113 420.0
30 TraesCS6B01G186800 chr6A 86.118 389 25 10 2362 2750 158305178 158305537 2.570000e-105 392.0
31 TraesCS6B01G186800 chr6A 83.375 403 55 3 1354 1750 162789729 162790125 2.010000e-96 363.0
32 TraesCS6B01G186800 chr6A 90.476 273 21 4 2414 2683 158350308 158350578 3.370000e-94 355.0
33 TraesCS6B01G186800 chr6A 88.040 301 29 4 2450 2750 158423347 158423640 1.570000e-92 350.0
34 TraesCS6B01G186800 chr6A 86.928 306 20 3 2362 2660 162549778 162550070 2.640000e-85 326.0
35 TraesCS6B01G186800 chr6A 91.729 133 11 0 1935 2067 158422856 158422988 4.680000e-43 185.0
36 TraesCS6B01G186800 chr6A 82.110 218 17 10 2150 2365 162801945 162802142 1.690000e-37 167.0
37 TraesCS6B01G186800 chr6A 96.250 80 2 1 2150 2229 158305102 158305180 2.220000e-26 130.0
38 TraesCS6B01G186800 chr6A 96.078 51 2 0 326 376 552478846 552478796 1.750000e-12 84.2
39 TraesCS6B01G186800 chr6A 85.246 61 9 0 2690 2750 162550079 162550139 2.290000e-06 63.9
40 TraesCS6B01G186800 chr7D 83.978 1086 148 17 999 2067 78262592 78263668 0.000000e+00 1018.0
41 TraesCS6B01G186800 chr7D 86.996 446 54 2 1588 2029 631729070 631728625 1.470000e-137 499.0
42 TraesCS6B01G186800 chr7D 87.692 390 19 15 2375 2750 78264020 78264394 7.040000e-116 427.0
43 TraesCS6B01G186800 chr7D 80.000 235 17 10 412 619 153970714 153970945 2.210000e-31 147.0
44 TraesCS6B01G186800 chr7B 83.868 1029 109 27 1019 2036 747942467 747943449 0.000000e+00 928.0
45 TraesCS6B01G186800 chr7B 83.746 1009 107 33 1028 2025 749331684 749332646 0.000000e+00 902.0
46 TraesCS6B01G186800 chr7B 87.728 383 25 11 2375 2750 25641658 25642025 7.040000e-116 427.0
47 TraesCS6B01G186800 chr7B 95.855 193 7 1 142 333 662001638 662001446 7.400000e-81 311.0
48 TraesCS6B01G186800 chr1A 77.394 1013 172 37 1021 2013 540413774 540414749 1.440000e-152 549.0
49 TraesCS6B01G186800 chr1A 94.118 153 7 2 1 152 527285777 527285928 5.920000e-57 231.0
50 TraesCS6B01G186800 chr1A 93.464 153 8 2 1 152 509053272 509053121 2.760000e-55 226.0
51 TraesCS6B01G186800 chr1A 93.464 153 8 2 1 152 576228908 576228757 2.760000e-55 226.0
52 TraesCS6B01G186800 chr1A 96.078 51 2 0 326 376 402475906 402475956 1.750000e-12 84.2
53 TraesCS6B01G186800 chr1D 82.589 448 65 10 1582 2020 445187658 445187215 1.550000e-102 383.0
54 TraesCS6B01G186800 chr2A 96.447 197 5 2 140 336 72943069 72943263 9.500000e-85 324.0
55 TraesCS6B01G186800 chr2A 96.078 51 2 0 326 376 227883798 227883748 1.750000e-12 84.2
56 TraesCS6B01G186800 chr2A 94.118 51 3 0 326 376 726137887 726137837 8.170000e-11 78.7
57 TraesCS6B01G186800 chr2A 100.000 29 0 0 447 475 683006594 683006622 1.000000e-03 54.7
58 TraesCS6B01G186800 chr3B 96.335 191 7 0 144 334 758070450 758070260 5.720000e-82 315.0
59 TraesCS6B01G186800 chr3B 95.876 194 6 2 139 331 18137974 18138166 2.060000e-81 313.0
60 TraesCS6B01G186800 chr5B 95.385 195 9 0 143 337 647874803 647874997 7.400000e-81 311.0
61 TraesCS6B01G186800 chr1B 95.408 196 8 1 143 338 593908844 593908650 7.400000e-81 311.0
62 TraesCS6B01G186800 chr4B 94.898 196 10 0 142 337 399038829 399038634 9.570000e-80 307.0
63 TraesCS6B01G186800 chr4B 91.304 46 4 0 430 475 505156379 505156424 2.290000e-06 63.9
64 TraesCS6B01G186800 chr3A 93.237 207 11 3 146 351 750381948 750382152 4.450000e-78 302.0
65 TraesCS6B01G186800 chr3A 94.118 153 7 2 1 152 638485878 638485727 5.920000e-57 231.0
66 TraesCS6B01G186800 chr3A 94.444 54 2 1 324 376 638485740 638485687 6.310000e-12 82.4
67 TraesCS6B01G186800 chr5A 90.547 201 14 4 145 343 79282230 79282427 7.550000e-66 261.0
68 TraesCS6B01G186800 chr5A 93.464 153 8 2 1 152 135970631 135970782 2.760000e-55 226.0
69 TraesCS6B01G186800 chr5A 93.464 153 8 2 1 152 648043839 648043688 2.760000e-55 226.0
70 TraesCS6B01G186800 chr5A 96.078 51 2 0 326 376 97674384 97674434 1.750000e-12 84.2
71 TraesCS6B01G186800 chr7A 94.118 153 7 2 1 152 40290433 40290282 5.920000e-57 231.0
72 TraesCS6B01G186800 chr7A 94.118 153 8 1 1 152 661815972 661816124 5.920000e-57 231.0
73 TraesCS6B01G186800 chr7A 96.078 51 2 0 326 376 40290292 40290242 1.750000e-12 84.2
74 TraesCS6B01G186800 chr2B 82.039 206 9 15 143 348 672575660 672575837 1.710000e-32 150.0
75 TraesCS6B01G186800 chrUn 83.000 100 13 4 1186 1283 88642927 88643024 1.360000e-13 87.9
76 TraesCS6B01G186800 chrUn 83.000 100 13 4 1186 1283 283733018 283733115 1.360000e-13 87.9


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 TraesCS6B01G186800 chr6B 213149956 213152705 2749 True 1775.666667 5079 98.173333 1 2750 3 chr6B.!!$R3 2749
1 TraesCS6B01G186800 chr6B 213306410 213308309 1899 True 904.333333 1085 94.584000 977 2749 3 chr6B.!!$R4 1772
2 TraesCS6B01G186800 chr6B 213142468 213143240 772 True 299.000000 335 87.881667 1940 2749 3 chr6B.!!$R2 809
3 TraesCS6B01G186800 chr6D 121089050 121090317 1267 True 927.000000 1624 93.506000 1 1446 2 chr6D.!!$R1 1445
4 TraesCS6B01G186800 chr6D 121297657 121300940 3283 True 672.333333 1303 89.541000 1056 2750 3 chr6D.!!$R2 1694
5 TraesCS6B01G186800 chr6D 121334118 121334697 579 True 322.500000 353 85.221000 2059 2750 2 chr6D.!!$R4 691
6 TraesCS6B01G186800 chr6A 162728148 162729172 1024 False 1290.000000 1290 89.484000 749 1780 1 chr6A.!!$F4 1031
7 TraesCS6B01G186800 chr6A 162785407 162790125 4718 False 577.000000 791 84.927000 740 1750 2 chr6A.!!$F8 1010
8 TraesCS6B01G186800 chr6A 162549233 162550139 906 False 354.966667 675 87.353000 1257 2750 3 chr6A.!!$F7 1493
9 TraesCS6B01G186800 chr6A 162801471 162802373 902 False 343.666667 442 86.890000 1748 2665 3 chr6A.!!$F9 917
10 TraesCS6B01G186800 chr6A 158422419 158423640 1221 False 318.333333 420 87.911000 1461 2750 3 chr6A.!!$F6 1289
11 TraesCS6B01G186800 chr7D 78262592 78264394 1802 False 722.500000 1018 85.835000 999 2750 2 chr7D.!!$F2 1751
12 TraesCS6B01G186800 chr7B 747942467 747943449 982 False 928.000000 928 83.868000 1019 2036 1 chr7B.!!$F2 1017
13 TraesCS6B01G186800 chr7B 749331684 749332646 962 False 902.000000 902 83.746000 1028 2025 1 chr7B.!!$F3 997
14 TraesCS6B01G186800 chr1A 540413774 540414749 975 False 549.000000 549 77.394000 1021 2013 1 chr1A.!!$F3 992

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
960 992 0.234884 GTACAACTCACGCACCAAGC 59.765 55.0 0.0 0.0 40.87 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 6602 0.676736 GGCCGACAATTGTTTTCCCA 59.323 50.0 13.36 0.0 0.0 4.37 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
56 57 8.934825 GCATTTGATTTCTGCTGGTTTATTTAA 58.065 29.630 0.00 0.00 33.15 1.52
70 71 9.981114 CTGGTTTATTTAAAAACAACAGATCCT 57.019 29.630 5.40 0.00 40.42 3.24
127 128 6.453092 AGGAGCACTTGAATTTCAAATTCTG 58.547 36.000 20.98 16.04 35.73 3.02
128 129 5.119743 GGAGCACTTGAATTTCAAATTCTGC 59.880 40.000 20.98 20.61 35.73 4.26
151 152 7.556844 TGCTGGTTTCTGTTGGTTTATTTAAA 58.443 30.769 0.00 0.00 0.00 1.52
152 153 7.708752 TGCTGGTTTCTGTTGGTTTATTTAAAG 59.291 33.333 0.00 0.00 0.00 1.85
153 154 7.170828 GCTGGTTTCTGTTGGTTTATTTAAAGG 59.829 37.037 0.00 0.00 0.00 3.11
154 155 7.501844 TGGTTTCTGTTGGTTTATTTAAAGGG 58.498 34.615 0.00 0.00 0.00 3.95
155 156 7.344871 TGGTTTCTGTTGGTTTATTTAAAGGGA 59.655 33.333 0.00 0.00 0.00 4.20
156 157 7.870954 GGTTTCTGTTGGTTTATTTAAAGGGAG 59.129 37.037 0.00 0.00 0.00 4.30
157 158 8.418662 GTTTCTGTTGGTTTATTTAAAGGGAGT 58.581 33.333 0.00 0.00 0.00 3.85
158 159 9.643735 TTTCTGTTGGTTTATTTAAAGGGAGTA 57.356 29.630 0.00 0.00 0.00 2.59
159 160 8.625786 TCTGTTGGTTTATTTAAAGGGAGTAC 57.374 34.615 0.00 0.00 0.00 2.73
160 161 7.666804 TCTGTTGGTTTATTTAAAGGGAGTACC 59.333 37.037 0.00 0.00 40.67 3.34
209 210 8.424274 AATTTGGTCTCATTCACTTTGAAAAC 57.576 30.769 0.00 0.00 40.12 2.43
210 211 6.522625 TTGGTCTCATTCACTTTGAAAACA 57.477 33.333 0.00 0.00 40.12 2.83
211 212 6.522625 TGGTCTCATTCACTTTGAAAACAA 57.477 33.333 0.00 0.00 40.12 2.83
212 213 6.563422 TGGTCTCATTCACTTTGAAAACAAG 58.437 36.000 0.00 0.00 40.12 3.16
213 214 6.376864 TGGTCTCATTCACTTTGAAAACAAGA 59.623 34.615 0.00 0.00 40.12 3.02
214 215 7.093988 TGGTCTCATTCACTTTGAAAACAAGAA 60.094 33.333 0.00 0.00 40.12 2.52
215 216 7.220875 GGTCTCATTCACTTTGAAAACAAGAAC 59.779 37.037 0.00 0.00 40.12 3.01
216 217 7.754924 GTCTCATTCACTTTGAAAACAAGAACA 59.245 33.333 0.00 0.00 40.12 3.18
217 218 7.970061 TCTCATTCACTTTGAAAACAAGAACAG 59.030 33.333 0.00 0.00 40.12 3.16
218 219 7.825681 TCATTCACTTTGAAAACAAGAACAGA 58.174 30.769 0.00 0.00 40.12 3.41
219 220 8.469200 TCATTCACTTTGAAAACAAGAACAGAT 58.531 29.630 0.00 0.00 40.12 2.90
220 221 9.734620 CATTCACTTTGAAAACAAGAACAGATA 57.265 29.630 0.00 0.00 40.12 1.98
221 222 9.736023 ATTCACTTTGAAAACAAGAACAGATAC 57.264 29.630 0.00 0.00 40.12 2.24
222 223 8.275015 TCACTTTGAAAACAAGAACAGATACA 57.725 30.769 0.00 0.00 0.00 2.29
223 224 8.735315 TCACTTTGAAAACAAGAACAGATACAA 58.265 29.630 0.00 0.00 0.00 2.41
224 225 8.798153 CACTTTGAAAACAAGAACAGATACAAC 58.202 33.333 0.00 0.00 0.00 3.32
225 226 7.973944 ACTTTGAAAACAAGAACAGATACAACC 59.026 33.333 0.00 0.00 0.00 3.77
226 227 6.385649 TGAAAACAAGAACAGATACAACCC 57.614 37.500 0.00 0.00 0.00 4.11
227 228 5.888724 TGAAAACAAGAACAGATACAACCCA 59.111 36.000 0.00 0.00 0.00 4.51
228 229 5.767816 AAACAAGAACAGATACAACCCAC 57.232 39.130 0.00 0.00 0.00 4.61
229 230 3.399330 ACAAGAACAGATACAACCCACG 58.601 45.455 0.00 0.00 0.00 4.94
230 231 3.181458 ACAAGAACAGATACAACCCACGT 60.181 43.478 0.00 0.00 0.00 4.49
231 232 3.314541 AGAACAGATACAACCCACGTC 57.685 47.619 0.00 0.00 0.00 4.34
232 233 2.631062 AGAACAGATACAACCCACGTCA 59.369 45.455 0.00 0.00 0.00 4.35
233 234 2.743636 ACAGATACAACCCACGTCAG 57.256 50.000 0.00 0.00 0.00 3.51
234 235 1.337823 ACAGATACAACCCACGTCAGC 60.338 52.381 0.00 0.00 0.00 4.26
235 236 0.973632 AGATACAACCCACGTCAGCA 59.026 50.000 0.00 0.00 0.00 4.41
236 237 1.076332 GATACAACCCACGTCAGCAC 58.924 55.000 0.00 0.00 0.00 4.40
237 238 0.394938 ATACAACCCACGTCAGCACA 59.605 50.000 0.00 0.00 0.00 4.57
238 239 0.531090 TACAACCCACGTCAGCACAC 60.531 55.000 0.00 0.00 0.00 3.82
239 240 1.817520 CAACCCACGTCAGCACACA 60.818 57.895 0.00 0.00 0.00 3.72
240 241 1.817941 AACCCACGTCAGCACACAC 60.818 57.895 0.00 0.00 0.00 3.82
241 242 3.337889 CCCACGTCAGCACACACG 61.338 66.667 0.00 0.00 41.90 4.49
242 243 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
243 244 3.261216 CACGTCAGCACACACGCA 61.261 61.111 0.00 0.00 39.73 5.24
244 245 2.280119 ACGTCAGCACACACGCAT 60.280 55.556 0.00 0.00 39.73 4.73
245 246 2.310233 ACGTCAGCACACACGCATC 61.310 57.895 0.00 0.00 39.73 3.91
246 247 2.023771 CGTCAGCACACACGCATCT 61.024 57.895 0.00 0.00 0.00 2.90
247 248 1.560004 CGTCAGCACACACGCATCTT 61.560 55.000 0.00 0.00 0.00 2.40
248 249 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
249 250 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
250 251 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
251 252 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
252 253 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
253 254 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
254 255 2.545526 GCACACACGCATCTTATAGCAT 59.454 45.455 0.00 0.00 0.00 3.79
255 256 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
256 257 3.803778 CACACACGCATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
257 258 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
258 259 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
259 260 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
260 261 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
261 262 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
262 263 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
263 264 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
264 265 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
265 266 6.552629 GCATCTTATAGCATCACATCCAATG 58.447 40.000 0.00 0.00 0.00 2.82
266 267 6.373495 GCATCTTATAGCATCACATCCAATGA 59.627 38.462 0.00 0.00 0.00 2.57
267 268 7.625817 GCATCTTATAGCATCACATCCAATGAC 60.626 40.741 0.00 0.00 0.00 3.06
268 269 7.071069 TCTTATAGCATCACATCCAATGACT 57.929 36.000 0.00 0.00 0.00 3.41
269 270 8.193953 TCTTATAGCATCACATCCAATGACTA 57.806 34.615 0.00 0.00 0.00 2.59
270 271 8.819845 TCTTATAGCATCACATCCAATGACTAT 58.180 33.333 0.00 0.00 32.32 2.12
274 275 9.797642 ATAGCATCACATCCAATGACTATAAAA 57.202 29.630 0.00 0.00 0.00 1.52
275 276 8.162878 AGCATCACATCCAATGACTATAAAAG 57.837 34.615 0.00 0.00 0.00 2.27
276 277 7.230108 AGCATCACATCCAATGACTATAAAAGG 59.770 37.037 0.00 0.00 0.00 3.11
277 278 7.013655 GCATCACATCCAATGACTATAAAAGGT 59.986 37.037 0.00 0.00 0.00 3.50
278 279 7.864108 TCACATCCAATGACTATAAAAGGTG 57.136 36.000 0.00 0.00 0.00 4.00
279 280 7.629157 TCACATCCAATGACTATAAAAGGTGA 58.371 34.615 0.00 0.00 0.00 4.02
280 281 8.106462 TCACATCCAATGACTATAAAAGGTGAA 58.894 33.333 0.00 0.00 0.00 3.18
281 282 8.906867 CACATCCAATGACTATAAAAGGTGAAT 58.093 33.333 0.00 0.00 0.00 2.57
282 283 8.906867 ACATCCAATGACTATAAAAGGTGAATG 58.093 33.333 0.00 0.00 0.00 2.67
283 284 9.123902 CATCCAATGACTATAAAAGGTGAATGA 57.876 33.333 0.00 0.00 0.00 2.57
284 285 8.737168 TCCAATGACTATAAAAGGTGAATGAG 57.263 34.615 0.00 0.00 0.00 2.90
285 286 8.548025 TCCAATGACTATAAAAGGTGAATGAGA 58.452 33.333 0.00 0.00 0.00 3.27
286 287 8.616076 CCAATGACTATAAAAGGTGAATGAGAC 58.384 37.037 0.00 0.00 0.00 3.36
287 288 8.616076 CAATGACTATAAAAGGTGAATGAGACC 58.384 37.037 0.00 0.00 0.00 3.85
288 289 7.252612 TGACTATAAAAGGTGAATGAGACCA 57.747 36.000 0.00 0.00 35.76 4.02
289 290 7.685481 TGACTATAAAAGGTGAATGAGACCAA 58.315 34.615 0.00 0.00 35.76 3.67
290 291 8.160765 TGACTATAAAAGGTGAATGAGACCAAA 58.839 33.333 0.00 0.00 35.76 3.28
291 292 9.178758 GACTATAAAAGGTGAATGAGACCAAAT 57.821 33.333 0.00 0.00 35.76 2.32
292 293 9.533831 ACTATAAAAGGTGAATGAGACCAAATT 57.466 29.630 0.00 0.00 35.76 1.82
298 299 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
299 300 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
326 327 7.897575 CTAGATGAGTTCTAGCAAAACTGTT 57.102 36.000 0.32 0.00 45.63 3.16
327 328 8.988064 CTAGATGAGTTCTAGCAAAACTGTTA 57.012 34.615 0.32 0.00 45.63 2.41
328 329 9.593134 CTAGATGAGTTCTAGCAAAACTGTTAT 57.407 33.333 0.32 0.00 45.63 1.89
329 330 8.854614 AGATGAGTTCTAGCAAAACTGTTATT 57.145 30.769 0.32 0.00 37.10 1.40
330 331 9.289782 AGATGAGTTCTAGCAAAACTGTTATTT 57.710 29.630 0.32 0.00 37.10 1.40
331 332 9.899226 GATGAGTTCTAGCAAAACTGTTATTTT 57.101 29.630 0.32 0.00 37.10 1.82
347 348 9.250624 ACTGTTATTTTTAAATAAACAGCGCAA 57.749 25.926 23.85 0.00 41.14 4.85
363 364 2.159653 GCGCAACTTCAGTAACATGGAG 60.160 50.000 0.30 0.00 0.00 3.86
455 456 4.757149 ACTGAAGCTGTTGTTACTGATTCC 59.243 41.667 9.56 0.00 43.65 3.01
618 624 4.496927 CAATTTGGGAGCGGCGGC 62.497 66.667 9.78 8.43 40.37 6.53
647 662 0.452987 TCGTACGTGCATGTACTCCC 59.547 55.000 34.69 17.53 42.00 4.30
736 751 5.130350 AGTTTTTGTATGTACACCTGTGCT 58.870 37.500 0.00 0.00 35.64 4.40
772 787 0.392706 CCGGCAGGCTCATACATACA 59.607 55.000 0.00 0.00 0.00 2.29
901 920 0.454600 GATGGAACTACCTCGCGTGA 59.545 55.000 10.21 0.00 39.86 4.35
959 991 1.526887 CAGTACAACTCACGCACCAAG 59.473 52.381 0.00 0.00 0.00 3.61
960 992 0.234884 GTACAACTCACGCACCAAGC 59.765 55.000 0.00 0.00 40.87 4.01
962 994 2.186160 CAACTCACGCACCAAGCCA 61.186 57.895 0.00 0.00 41.38 4.75
963 995 2.186826 AACTCACGCACCAAGCCAC 61.187 57.895 0.00 0.00 41.38 5.01
964 996 3.357079 CTCACGCACCAAGCCACC 61.357 66.667 0.00 0.00 41.38 4.61
965 997 3.832237 CTCACGCACCAAGCCACCT 62.832 63.158 0.00 0.00 41.38 4.00
968 1000 2.031919 CGCACCAAGCCACCTACA 59.968 61.111 0.00 0.00 41.38 2.74
970 1002 1.228124 GCACCAAGCCACCTACACA 60.228 57.895 0.00 0.00 37.23 3.72
972 1004 1.073199 ACCAAGCCACCTACACAGC 59.927 57.895 0.00 0.00 0.00 4.40
975 1007 3.254024 AAGCCACCTACACAGCCGG 62.254 63.158 0.00 0.00 0.00 6.13
1066 1101 1.949847 CTCGCTTCCCCTCGACACAT 61.950 60.000 0.00 0.00 0.00 3.21
1133 1168 2.514824 GGAGTTCCTCATGGCCGC 60.515 66.667 0.00 0.00 31.08 6.53
1160 1195 1.066573 CATCCACTCGGTCTTCAAGCT 60.067 52.381 0.00 0.00 0.00 3.74
1492 5252 3.140814 GGGACCCAAAGGATGCGC 61.141 66.667 5.33 0.00 36.73 6.09
1581 5364 0.038599 AGGACATGGACATGCAGCAA 59.961 50.000 11.96 0.00 42.39 3.91
1904 5947 4.415150 CAGGGTCCGGCAGCACAT 62.415 66.667 0.00 0.00 0.00 3.21
2096 6198 2.834549 CCCTCGATATATGTTGAGCCCT 59.165 50.000 10.52 0.00 0.00 5.19
2108 6210 2.203337 AGCCCTTTTGTGCGCTGA 60.203 55.556 9.73 0.00 0.00 4.26
2298 6596 2.097954 TGGCACAAATCGATGAATCAGC 59.902 45.455 0.00 0.00 31.92 4.26
2299 6597 2.357009 GGCACAAATCGATGAATCAGCT 59.643 45.455 0.00 0.00 0.00 4.24
2300 6598 3.181493 GGCACAAATCGATGAATCAGCTT 60.181 43.478 0.00 0.00 0.00 3.74
2304 6602 4.940046 ACAAATCGATGAATCAGCTTCACT 59.060 37.500 0.00 0.00 46.37 3.41
2305 6603 5.163784 ACAAATCGATGAATCAGCTTCACTG 60.164 40.000 0.00 0.00 46.37 3.66
2306 6604 2.897436 TCGATGAATCAGCTTCACTGG 58.103 47.619 0.00 0.00 46.37 4.00
2307 6605 1.938577 CGATGAATCAGCTTCACTGGG 59.061 52.381 0.00 0.00 46.37 4.45
2308 6606 2.419159 CGATGAATCAGCTTCACTGGGA 60.419 50.000 0.00 0.00 46.37 4.37
2309 6607 3.614092 GATGAATCAGCTTCACTGGGAA 58.386 45.455 0.00 0.00 46.37 3.97
2310 6608 4.012374 GATGAATCAGCTTCACTGGGAAA 58.988 43.478 0.00 0.00 46.37 3.13
2311 6609 4.410099 ATGAATCAGCTTCACTGGGAAAA 58.590 39.130 0.00 0.00 46.37 2.29
2312 6610 4.219288 ATGAATCAGCTTCACTGGGAAAAC 59.781 41.667 0.00 0.00 46.37 2.43
2313 6611 6.215848 ATGAATCAGCTTCACTGGGAAAACA 61.216 40.000 0.00 0.00 46.37 2.83
2314 6612 7.645102 ATGAATCAGCTTCACTGGGAAAACAA 61.645 38.462 0.00 0.00 46.37 2.83
2315 6613 8.885052 ATGAATCAGCTTCACTGGGAAAACAAT 61.885 37.037 0.00 0.00 46.37 2.71
2316 6614 4.326504 CAGCTTCACTGGGAAAACAATT 57.673 40.909 0.00 0.00 43.19 2.32
2317 6615 4.053295 CAGCTTCACTGGGAAAACAATTG 58.947 43.478 3.24 3.24 43.19 2.32
2318 6616 3.706086 AGCTTCACTGGGAAAACAATTGT 59.294 39.130 4.92 4.92 34.44 2.71
2319 6617 4.051237 GCTTCACTGGGAAAACAATTGTC 58.949 43.478 12.39 0.00 34.44 3.18
2320 6618 3.980646 TCACTGGGAAAACAATTGTCG 57.019 42.857 12.39 0.00 0.00 4.35
2321 6619 2.621055 TCACTGGGAAAACAATTGTCGG 59.379 45.455 12.39 6.53 0.00 4.79
2322 6620 1.339929 ACTGGGAAAACAATTGTCGGC 59.660 47.619 12.39 3.87 0.00 5.54
2323 6621 0.676736 TGGGAAAACAATTGTCGGCC 59.323 50.000 12.39 12.53 0.00 6.13
2324 6622 0.676736 GGGAAAACAATTGTCGGCCA 59.323 50.000 12.39 0.00 0.00 5.36
2325 6623 1.275010 GGGAAAACAATTGTCGGCCAT 59.725 47.619 12.39 0.00 0.00 4.40
2326 6624 2.289382 GGGAAAACAATTGTCGGCCATT 60.289 45.455 12.39 0.00 0.00 3.16
2327 6625 2.993220 GGAAAACAATTGTCGGCCATTC 59.007 45.455 12.39 9.41 0.00 2.67
2328 6626 3.553922 GGAAAACAATTGTCGGCCATTCA 60.554 43.478 12.39 0.00 0.00 2.57
2329 6627 3.742433 AAACAATTGTCGGCCATTCAA 57.258 38.095 12.39 5.06 0.00 2.69
2330 6628 3.742433 AACAATTGTCGGCCATTCAAA 57.258 38.095 12.39 0.00 0.00 2.69
2331 6629 3.302365 ACAATTGTCGGCCATTCAAAG 57.698 42.857 4.92 4.94 0.00 2.77
2332 6630 2.627699 ACAATTGTCGGCCATTCAAAGT 59.372 40.909 4.92 5.53 0.00 2.66
2333 6631 3.244976 CAATTGTCGGCCATTCAAAGTC 58.755 45.455 2.24 0.00 0.00 3.01
2334 6632 1.974265 TTGTCGGCCATTCAAAGTCA 58.026 45.000 2.24 0.00 0.00 3.41
2335 6633 1.974265 TGTCGGCCATTCAAAGTCAA 58.026 45.000 2.24 0.00 0.00 3.18
2336 6634 1.606668 TGTCGGCCATTCAAAGTCAAC 59.393 47.619 2.24 0.00 0.00 3.18
2337 6635 1.880027 GTCGGCCATTCAAAGTCAACT 59.120 47.619 2.24 0.00 0.00 3.16
2338 6636 2.095718 GTCGGCCATTCAAAGTCAACTC 60.096 50.000 2.24 0.00 0.00 3.01
2339 6637 1.200020 CGGCCATTCAAAGTCAACTCC 59.800 52.381 2.24 0.00 0.00 3.85
2340 6638 2.519013 GGCCATTCAAAGTCAACTCCT 58.481 47.619 0.00 0.00 0.00 3.69
2341 6639 2.489722 GGCCATTCAAAGTCAACTCCTC 59.510 50.000 0.00 0.00 0.00 3.71
2342 6640 2.489722 GCCATTCAAAGTCAACTCCTCC 59.510 50.000 0.00 0.00 0.00 4.30
2343 6641 2.744202 CCATTCAAAGTCAACTCCTCCG 59.256 50.000 0.00 0.00 0.00 4.63
2344 6642 3.557054 CCATTCAAAGTCAACTCCTCCGA 60.557 47.826 0.00 0.00 0.00 4.55
2345 6643 4.256920 CATTCAAAGTCAACTCCTCCGAT 58.743 43.478 0.00 0.00 0.00 4.18
2346 6644 3.594603 TCAAAGTCAACTCCTCCGATC 57.405 47.619 0.00 0.00 0.00 3.69
2347 6645 2.233922 TCAAAGTCAACTCCTCCGATCC 59.766 50.000 0.00 0.00 0.00 3.36
2348 6646 1.938585 AAGTCAACTCCTCCGATCCA 58.061 50.000 0.00 0.00 0.00 3.41
2349 6647 1.938585 AGTCAACTCCTCCGATCCAA 58.061 50.000 0.00 0.00 0.00 3.53
2350 6648 2.257207 AGTCAACTCCTCCGATCCAAA 58.743 47.619 0.00 0.00 0.00 3.28
2351 6649 2.840651 AGTCAACTCCTCCGATCCAAAT 59.159 45.455 0.00 0.00 0.00 2.32
2352 6650 3.264450 AGTCAACTCCTCCGATCCAAATT 59.736 43.478 0.00 0.00 0.00 1.82
2353 6651 3.375299 GTCAACTCCTCCGATCCAAATTG 59.625 47.826 0.00 0.00 0.00 2.32
2354 6652 2.044123 ACTCCTCCGATCCAAATTGC 57.956 50.000 0.00 0.00 0.00 3.56
2355 6653 1.281867 ACTCCTCCGATCCAAATTGCA 59.718 47.619 0.00 0.00 0.00 4.08
2356 6654 2.290896 ACTCCTCCGATCCAAATTGCAA 60.291 45.455 0.00 0.00 0.00 4.08
2357 6655 2.357009 CTCCTCCGATCCAAATTGCAAG 59.643 50.000 4.94 0.00 0.00 4.01
2358 6656 2.026356 TCCTCCGATCCAAATTGCAAGA 60.026 45.455 4.94 0.00 0.00 3.02
2359 6657 2.754552 CCTCCGATCCAAATTGCAAGAA 59.245 45.455 4.94 0.00 0.00 2.52
2360 6658 3.193267 CCTCCGATCCAAATTGCAAGAAA 59.807 43.478 4.94 0.00 0.00 2.52
2361 6659 4.321899 CCTCCGATCCAAATTGCAAGAAAA 60.322 41.667 4.94 0.00 0.00 2.29
2362 6660 5.207110 TCCGATCCAAATTGCAAGAAAAA 57.793 34.783 4.94 0.00 0.00 1.94
2363 6661 5.792741 TCCGATCCAAATTGCAAGAAAAAT 58.207 33.333 4.94 0.00 0.00 1.82
2364 6662 6.929625 TCCGATCCAAATTGCAAGAAAAATA 58.070 32.000 4.94 0.00 0.00 1.40
2365 6663 7.382110 TCCGATCCAAATTGCAAGAAAAATAA 58.618 30.769 4.94 0.00 0.00 1.40
2366 6664 7.545265 TCCGATCCAAATTGCAAGAAAAATAAG 59.455 33.333 4.94 0.00 0.00 1.73
2373 8256 8.553696 CAAATTGCAAGAAAAATAAGCTTCACT 58.446 29.630 0.00 0.00 0.00 3.41
2407 8290 2.095718 GTCGGCCATTCAAAGTCAACTC 60.096 50.000 2.24 0.00 0.00 3.01
2422 8305 3.375299 GTCAACTCCTCCGATCCAAATTG 59.625 47.826 0.00 0.00 0.00 2.32
2438 8330 7.712264 TCCAAATTGCAAGAAAAATACTGTG 57.288 32.000 4.94 0.00 0.00 3.66
2631 8544 0.543277 CTCCCAGCTCCATGTAAGCA 59.457 55.000 16.89 0.00 42.35 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 6.773976 TTTGACTTGAGGATCTGTTGTTTT 57.226 33.333 0.00 0.00 34.92 2.43
102 103 6.585322 CAGAATTTGAAATTCAAGTGCTCCTC 59.415 38.462 26.80 1.25 37.70 3.71
127 128 7.170828 CCTTTAAATAAACCAACAGAAACCAGC 59.829 37.037 0.00 0.00 0.00 4.85
128 129 7.655732 CCCTTTAAATAAACCAACAGAAACCAG 59.344 37.037 0.00 0.00 0.00 4.00
151 152 7.475654 CATCTAGATGAGTTCTAGGTACTCCCT 60.476 44.444 25.78 16.34 44.99 4.20
152 153 6.657541 CATCTAGATGAGTTCTAGGTACTCCC 59.342 46.154 25.78 12.05 44.99 4.30
153 154 7.455058 TCATCTAGATGAGTTCTAGGTACTCC 58.545 42.308 27.93 8.04 44.99 3.85
183 184 9.528018 GTTTTCAAAGTGAATGAGACCAAATTA 57.472 29.630 0.00 0.00 36.11 1.40
184 185 8.040132 TGTTTTCAAAGTGAATGAGACCAAATT 58.960 29.630 0.00 0.00 36.11 1.82
185 186 7.555087 TGTTTTCAAAGTGAATGAGACCAAAT 58.445 30.769 0.00 0.00 36.11 2.32
186 187 6.929625 TGTTTTCAAAGTGAATGAGACCAAA 58.070 32.000 0.00 0.00 36.11 3.28
187 188 6.522625 TGTTTTCAAAGTGAATGAGACCAA 57.477 33.333 0.00 0.00 36.11 3.67
188 189 6.376864 TCTTGTTTTCAAAGTGAATGAGACCA 59.623 34.615 0.00 0.00 39.47 4.02
189 190 6.795399 TCTTGTTTTCAAAGTGAATGAGACC 58.205 36.000 0.00 0.00 39.47 3.85
190 191 7.754924 TGTTCTTGTTTTCAAAGTGAATGAGAC 59.245 33.333 0.00 0.00 39.47 3.36
191 192 7.825681 TGTTCTTGTTTTCAAAGTGAATGAGA 58.174 30.769 0.00 0.00 39.47 3.27
192 193 7.970061 TCTGTTCTTGTTTTCAAAGTGAATGAG 59.030 33.333 0.00 0.00 39.47 2.90
193 194 7.825681 TCTGTTCTTGTTTTCAAAGTGAATGA 58.174 30.769 0.00 0.00 39.47 2.57
194 195 8.638685 ATCTGTTCTTGTTTTCAAAGTGAATG 57.361 30.769 0.00 0.00 39.47 2.67
195 196 9.736023 GTATCTGTTCTTGTTTTCAAAGTGAAT 57.264 29.630 0.00 0.00 39.47 2.57
196 197 8.735315 TGTATCTGTTCTTGTTTTCAAAGTGAA 58.265 29.630 0.00 0.00 39.47 3.18
197 198 8.275015 TGTATCTGTTCTTGTTTTCAAAGTGA 57.725 30.769 0.00 0.00 39.47 3.41
198 199 8.798153 GTTGTATCTGTTCTTGTTTTCAAAGTG 58.202 33.333 0.00 0.00 39.47 3.16
199 200 7.973944 GGTTGTATCTGTTCTTGTTTTCAAAGT 59.026 33.333 0.00 0.00 39.47 2.66
200 201 7.435192 GGGTTGTATCTGTTCTTGTTTTCAAAG 59.565 37.037 0.00 0.00 39.47 2.77
201 202 7.093727 TGGGTTGTATCTGTTCTTGTTTTCAAA 60.094 33.333 0.00 0.00 39.47 2.69
202 203 6.378564 TGGGTTGTATCTGTTCTTGTTTTCAA 59.621 34.615 0.00 0.00 38.21 2.69
203 204 5.888724 TGGGTTGTATCTGTTCTTGTTTTCA 59.111 36.000 0.00 0.00 0.00 2.69
204 205 6.206498 GTGGGTTGTATCTGTTCTTGTTTTC 58.794 40.000 0.00 0.00 0.00 2.29
205 206 5.220970 CGTGGGTTGTATCTGTTCTTGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
206 207 4.274950 CGTGGGTTGTATCTGTTCTTGTTT 59.725 41.667 0.00 0.00 0.00 2.83
207 208 3.813166 CGTGGGTTGTATCTGTTCTTGTT 59.187 43.478 0.00 0.00 0.00 2.83
208 209 3.181458 ACGTGGGTTGTATCTGTTCTTGT 60.181 43.478 0.00 0.00 0.00 3.16
209 210 3.399330 ACGTGGGTTGTATCTGTTCTTG 58.601 45.455 0.00 0.00 0.00 3.02
210 211 3.070446 TGACGTGGGTTGTATCTGTTCTT 59.930 43.478 0.00 0.00 0.00 2.52
211 212 2.631062 TGACGTGGGTTGTATCTGTTCT 59.369 45.455 0.00 0.00 0.00 3.01
212 213 2.993899 CTGACGTGGGTTGTATCTGTTC 59.006 50.000 0.00 0.00 0.00 3.18
213 214 2.870435 GCTGACGTGGGTTGTATCTGTT 60.870 50.000 0.00 0.00 0.00 3.16
214 215 1.337823 GCTGACGTGGGTTGTATCTGT 60.338 52.381 0.00 0.00 0.00 3.41
215 216 1.337728 TGCTGACGTGGGTTGTATCTG 60.338 52.381 0.00 0.00 0.00 2.90
216 217 0.973632 TGCTGACGTGGGTTGTATCT 59.026 50.000 0.00 0.00 0.00 1.98
217 218 1.076332 GTGCTGACGTGGGTTGTATC 58.924 55.000 0.00 0.00 0.00 2.24
218 219 0.394938 TGTGCTGACGTGGGTTGTAT 59.605 50.000 0.00 0.00 0.00 2.29
219 220 0.531090 GTGTGCTGACGTGGGTTGTA 60.531 55.000 0.00 0.00 0.00 2.41
220 221 1.817941 GTGTGCTGACGTGGGTTGT 60.818 57.895 0.00 0.00 0.00 3.32
221 222 1.817520 TGTGTGCTGACGTGGGTTG 60.818 57.895 0.00 0.00 0.00 3.77
222 223 1.817941 GTGTGTGCTGACGTGGGTT 60.818 57.895 0.00 0.00 0.00 4.11
223 224 2.203015 GTGTGTGCTGACGTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
224 225 3.337889 CGTGTGTGCTGACGTGGG 61.338 66.667 0.00 0.00 0.00 4.61
225 226 4.000557 GCGTGTGTGCTGACGTGG 62.001 66.667 0.00 0.00 37.89 4.94
226 227 2.484631 GATGCGTGTGTGCTGACGTG 62.485 60.000 0.00 0.00 37.89 4.49
227 228 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
228 229 1.560004 AAGATGCGTGTGTGCTGACG 61.560 55.000 0.00 0.00 38.63 4.35
229 230 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
230 231 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
231 232 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
232 233 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
233 234 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
234 235 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
235 236 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
236 237 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
237 238 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
238 239 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
239 240 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
240 241 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
241 242 6.373495 TCATTGGATGTGATGCTATAAGATGC 59.627 38.462 0.00 0.00 0.00 3.91
242 243 7.606839 AGTCATTGGATGTGATGCTATAAGATG 59.393 37.037 0.00 0.00 0.00 2.90
243 244 7.687388 AGTCATTGGATGTGATGCTATAAGAT 58.313 34.615 0.00 0.00 0.00 2.40
244 245 7.071069 AGTCATTGGATGTGATGCTATAAGA 57.929 36.000 0.00 0.00 0.00 2.10
248 249 9.797642 TTTTATAGTCATTGGATGTGATGCTAT 57.202 29.630 0.00 0.00 32.56 2.97
249 250 9.276590 CTTTTATAGTCATTGGATGTGATGCTA 57.723 33.333 0.00 0.00 0.00 3.49
250 251 7.230108 CCTTTTATAGTCATTGGATGTGATGCT 59.770 37.037 0.00 0.00 0.00 3.79
251 252 7.013655 ACCTTTTATAGTCATTGGATGTGATGC 59.986 37.037 0.00 0.00 0.00 3.91
252 253 8.347771 CACCTTTTATAGTCATTGGATGTGATG 58.652 37.037 0.00 0.00 0.00 3.07
253 254 8.274322 TCACCTTTTATAGTCATTGGATGTGAT 58.726 33.333 0.00 0.00 0.00 3.06
254 255 7.629157 TCACCTTTTATAGTCATTGGATGTGA 58.371 34.615 0.00 0.00 0.00 3.58
255 256 7.864108 TCACCTTTTATAGTCATTGGATGTG 57.136 36.000 0.00 0.00 0.00 3.21
256 257 8.906867 CATTCACCTTTTATAGTCATTGGATGT 58.093 33.333 0.00 0.00 0.00 3.06
257 258 9.123902 TCATTCACCTTTTATAGTCATTGGATG 57.876 33.333 0.00 0.00 0.00 3.51
258 259 9.347240 CTCATTCACCTTTTATAGTCATTGGAT 57.653 33.333 0.00 0.00 0.00 3.41
259 260 8.548025 TCTCATTCACCTTTTATAGTCATTGGA 58.452 33.333 0.00 0.00 0.00 3.53
260 261 8.616076 GTCTCATTCACCTTTTATAGTCATTGG 58.384 37.037 0.00 0.00 0.00 3.16
261 262 8.616076 GGTCTCATTCACCTTTTATAGTCATTG 58.384 37.037 0.00 0.00 0.00 2.82
262 263 8.328758 TGGTCTCATTCACCTTTTATAGTCATT 58.671 33.333 0.00 0.00 34.66 2.57
263 264 7.861629 TGGTCTCATTCACCTTTTATAGTCAT 58.138 34.615 0.00 0.00 34.66 3.06
264 265 7.252612 TGGTCTCATTCACCTTTTATAGTCA 57.747 36.000 0.00 0.00 34.66 3.41
265 266 8.561738 TTTGGTCTCATTCACCTTTTATAGTC 57.438 34.615 0.00 0.00 34.66 2.59
266 267 9.533831 AATTTGGTCTCATTCACCTTTTATAGT 57.466 29.630 0.00 0.00 34.66 2.12
272 273 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
273 274 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
274 275 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
275 276 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
303 304 9.944376 AATAACAGTTTTGCTAGAACTCATCTA 57.056 29.630 0.00 0.00 39.71 1.98
304 305 8.854614 AATAACAGTTTTGCTAGAACTCATCT 57.145 30.769 0.00 0.00 42.48 2.90
305 306 9.899226 AAAATAACAGTTTTGCTAGAACTCATC 57.101 29.630 0.00 0.00 35.26 2.92
320 321 9.250624 TGCGCTGTTTATTTAAAAATAACAGTT 57.749 25.926 25.18 0.00 39.75 3.16
321 322 8.804688 TGCGCTGTTTATTTAAAAATAACAGT 57.195 26.923 25.18 2.15 39.75 3.55
322 323 9.511022 GTTGCGCTGTTTATTTAAAAATAACAG 57.489 29.630 22.88 22.88 39.75 3.16
323 324 9.250624 AGTTGCGCTGTTTATTTAAAAATAACA 57.749 25.926 9.73 10.68 39.75 2.41
326 327 9.464714 TGAAGTTGCGCTGTTTATTTAAAAATA 57.535 25.926 9.73 0.00 0.00 1.40
327 328 8.359060 TGAAGTTGCGCTGTTTATTTAAAAAT 57.641 26.923 9.73 0.00 0.00 1.82
328 329 7.489757 ACTGAAGTTGCGCTGTTTATTTAAAAA 59.510 29.630 9.73 0.00 0.00 1.94
329 330 6.975772 ACTGAAGTTGCGCTGTTTATTTAAAA 59.024 30.769 9.73 0.00 0.00 1.52
330 331 6.500041 ACTGAAGTTGCGCTGTTTATTTAAA 58.500 32.000 9.73 0.00 0.00 1.52
331 332 6.067263 ACTGAAGTTGCGCTGTTTATTTAA 57.933 33.333 9.73 0.00 0.00 1.52
332 333 5.682943 ACTGAAGTTGCGCTGTTTATTTA 57.317 34.783 9.73 0.00 0.00 1.40
333 334 4.568152 ACTGAAGTTGCGCTGTTTATTT 57.432 36.364 9.73 0.00 0.00 1.40
334 335 5.008217 TGTTACTGAAGTTGCGCTGTTTATT 59.992 36.000 9.73 0.00 0.00 1.40
347 348 5.625656 GCTCTTAGCTCCATGTTACTGAAGT 60.626 44.000 0.00 0.00 38.45 3.01
363 364 2.531206 CACGTAGGTTCTGCTCTTAGC 58.469 52.381 0.00 0.00 42.82 3.09
455 456 7.148853 GCACTGAAATTAACAGCAGAATTTGAG 60.149 37.037 11.01 5.40 40.18 3.02
618 624 3.379445 ACGTACGACCCAGCCTGG 61.379 66.667 24.41 2.91 37.25 4.45
619 625 2.126071 CACGTACGACCCAGCCTG 60.126 66.667 24.41 2.74 0.00 4.85
647 662 3.965347 TCCCTCCTTTCCTAAATACTCCG 59.035 47.826 0.00 0.00 0.00 4.63
721 736 1.623311 AGCACAGCACAGGTGTACATA 59.377 47.619 0.00 0.00 42.60 2.29
736 751 1.600107 GGATACGAACCCCAGCACA 59.400 57.895 0.00 0.00 0.00 4.57
772 787 3.159472 TCTGAATTTGCTGGTTCATGCT 58.841 40.909 0.00 0.00 34.18 3.79
834 853 0.667487 CGGGCGATGCTGACGATAAT 60.667 55.000 0.00 0.00 0.00 1.28
880 899 1.310933 ACGCGAGGTAGTTCCATCGT 61.311 55.000 15.93 3.08 38.31 3.73
901 920 1.838077 AGCTAGATAACAAAGCCCCGT 59.162 47.619 0.00 0.00 36.92 5.28
959 991 3.702048 TCCGGCTGTGTAGGTGGC 61.702 66.667 0.00 0.00 0.00 5.01
960 992 2.264794 GTCCGGCTGTGTAGGTGG 59.735 66.667 0.00 0.00 0.00 4.61
962 994 4.065281 GCGTCCGGCTGTGTAGGT 62.065 66.667 0.00 0.00 39.11 3.08
963 995 3.371097 ATGCGTCCGGCTGTGTAGG 62.371 63.158 0.00 0.00 44.05 3.18
964 996 2.167219 CATGCGTCCGGCTGTGTAG 61.167 63.158 0.00 0.00 44.05 2.74
965 997 2.125713 CATGCGTCCGGCTGTGTA 60.126 61.111 0.00 0.00 44.05 2.90
972 1004 2.126888 GTTTGTGCATGCGTCCGG 60.127 61.111 14.09 0.00 0.00 5.14
975 1007 2.800746 GCCGTTTGTGCATGCGTC 60.801 61.111 14.09 9.43 0.00 5.19
986 1018 2.186826 GCCATGGATAGCGCCGTTT 61.187 57.895 18.40 0.00 0.00 3.60
1066 1101 3.615509 GATGGAACGGGCGGAACCA 62.616 63.158 14.11 14.11 42.05 3.67
1133 1168 4.227134 CCGAGTGGATGGCCGGAG 62.227 72.222 5.05 0.00 44.29 4.63
1451 5211 0.102481 GATGTACACGATCCGGCAGT 59.898 55.000 0.00 0.00 0.00 4.40
1492 5252 0.882474 AAGAACCACGAGGAGACGAG 59.118 55.000 5.68 0.00 38.69 4.18
1541 5318 0.169672 GTCGGCTCGTGCTAGTGTTA 59.830 55.000 9.61 0.00 39.59 2.41
1794 5794 3.394836 GGCCGCCTCTTCCTCACT 61.395 66.667 0.71 0.00 0.00 3.41
2067 6154 7.114866 TCAACATATATCGAGGGTACAACAA 57.885 36.000 0.00 0.00 0.00 2.83
2096 6198 0.953727 ATCAAGCTCAGCGCACAAAA 59.046 45.000 11.47 0.00 42.61 2.44
2120 6222 6.895040 CACGACAAGCTTTATTTCGAGTTATC 59.105 38.462 18.42 0.00 33.87 1.75
2298 6596 4.290155 CGACAATTGTTTTCCCAGTGAAG 58.710 43.478 13.36 0.00 33.63 3.02
2299 6597 3.067461 CCGACAATTGTTTTCCCAGTGAA 59.933 43.478 13.36 0.00 0.00 3.18
2300 6598 2.621055 CCGACAATTGTTTTCCCAGTGA 59.379 45.455 13.36 0.00 0.00 3.41
2302 6600 1.339929 GCCGACAATTGTTTTCCCAGT 59.660 47.619 13.36 0.00 0.00 4.00
2304 6602 0.676736 GGCCGACAATTGTTTTCCCA 59.323 50.000 13.36 0.00 0.00 4.37
2305 6603 0.676736 TGGCCGACAATTGTTTTCCC 59.323 50.000 13.36 11.27 0.00 3.97
2306 6604 2.741759 ATGGCCGACAATTGTTTTCC 57.258 45.000 13.36 13.56 0.00 3.13
2307 6605 3.648009 TGAATGGCCGACAATTGTTTTC 58.352 40.909 13.36 9.63 0.00 2.29
2308 6606 3.742433 TGAATGGCCGACAATTGTTTT 57.258 38.095 13.36 0.61 0.00 2.43
2309 6607 3.742433 TTGAATGGCCGACAATTGTTT 57.258 38.095 13.36 1.23 0.00 2.83
2310 6608 3.069443 ACTTTGAATGGCCGACAATTGTT 59.931 39.130 13.36 0.00 0.00 2.83
2311 6609 2.627699 ACTTTGAATGGCCGACAATTGT 59.372 40.909 11.78 11.78 0.00 2.71
2312 6610 3.244976 GACTTTGAATGGCCGACAATTG 58.755 45.455 3.24 3.24 0.00 2.32
2313 6611 2.890311 TGACTTTGAATGGCCGACAATT 59.110 40.909 0.00 0.00 0.00 2.32
2314 6612 2.513753 TGACTTTGAATGGCCGACAAT 58.486 42.857 0.00 0.00 0.00 2.71
2315 6613 1.974265 TGACTTTGAATGGCCGACAA 58.026 45.000 0.00 1.19 0.00 3.18
2316 6614 1.606668 GTTGACTTTGAATGGCCGACA 59.393 47.619 0.00 0.00 0.00 4.35
2317 6615 1.880027 AGTTGACTTTGAATGGCCGAC 59.120 47.619 0.00 0.00 0.00 4.79
2318 6616 2.151202 GAGTTGACTTTGAATGGCCGA 58.849 47.619 0.00 0.00 0.00 5.54
2319 6617 1.200020 GGAGTTGACTTTGAATGGCCG 59.800 52.381 0.00 0.00 0.00 6.13
2320 6618 2.489722 GAGGAGTTGACTTTGAATGGCC 59.510 50.000 0.00 0.00 0.00 5.36
2321 6619 2.489722 GGAGGAGTTGACTTTGAATGGC 59.510 50.000 0.00 0.00 0.00 4.40
2322 6620 2.744202 CGGAGGAGTTGACTTTGAATGG 59.256 50.000 0.00 0.00 0.00 3.16
2323 6621 3.664107 TCGGAGGAGTTGACTTTGAATG 58.336 45.455 0.00 0.00 0.00 2.67
2324 6622 4.508662 GATCGGAGGAGTTGACTTTGAAT 58.491 43.478 0.00 0.00 0.00 2.57
2325 6623 3.306780 GGATCGGAGGAGTTGACTTTGAA 60.307 47.826 0.00 0.00 0.00 2.69
2326 6624 2.233922 GGATCGGAGGAGTTGACTTTGA 59.766 50.000 0.00 0.00 0.00 2.69
2327 6625 2.028112 TGGATCGGAGGAGTTGACTTTG 60.028 50.000 0.00 0.00 0.00 2.77
2328 6626 2.257207 TGGATCGGAGGAGTTGACTTT 58.743 47.619 0.00 0.00 0.00 2.66
2329 6627 1.938585 TGGATCGGAGGAGTTGACTT 58.061 50.000 0.00 0.00 0.00 3.01
2330 6628 1.938585 TTGGATCGGAGGAGTTGACT 58.061 50.000 0.00 0.00 0.00 3.41
2331 6629 2.762535 TTTGGATCGGAGGAGTTGAC 57.237 50.000 0.00 0.00 0.00 3.18
2332 6630 3.609853 CAATTTGGATCGGAGGAGTTGA 58.390 45.455 0.00 0.00 0.00 3.18
2333 6631 2.098117 GCAATTTGGATCGGAGGAGTTG 59.902 50.000 0.00 0.00 0.00 3.16
2334 6632 2.290896 TGCAATTTGGATCGGAGGAGTT 60.291 45.455 0.00 0.00 0.00 3.01
2335 6633 1.281867 TGCAATTTGGATCGGAGGAGT 59.718 47.619 0.00 0.00 0.00 3.85
2336 6634 2.042686 TGCAATTTGGATCGGAGGAG 57.957 50.000 0.00 0.00 0.00 3.69
2337 6635 2.026356 TCTTGCAATTTGGATCGGAGGA 60.026 45.455 0.00 0.00 0.00 3.71
2338 6636 2.368439 TCTTGCAATTTGGATCGGAGG 58.632 47.619 0.00 0.00 0.00 4.30
2339 6637 4.439305 TTTCTTGCAATTTGGATCGGAG 57.561 40.909 0.00 0.00 0.00 4.63
2340 6638 4.862902 TTTTCTTGCAATTTGGATCGGA 57.137 36.364 0.00 0.00 0.00 4.55
2341 6639 7.593875 TTATTTTTCTTGCAATTTGGATCGG 57.406 32.000 0.00 0.00 0.00 4.18
2342 6640 7.063780 AGCTTATTTTTCTTGCAATTTGGATCG 59.936 33.333 0.00 0.00 0.00 3.69
2343 6641 8.260270 AGCTTATTTTTCTTGCAATTTGGATC 57.740 30.769 0.00 0.00 0.00 3.36
2344 6642 8.625786 AAGCTTATTTTTCTTGCAATTTGGAT 57.374 26.923 0.00 0.00 0.00 3.41
2345 6643 7.714377 TGAAGCTTATTTTTCTTGCAATTTGGA 59.286 29.630 0.00 0.00 0.00 3.53
2346 6644 7.799914 GTGAAGCTTATTTTTCTTGCAATTTGG 59.200 33.333 0.00 0.00 0.00 3.28
2347 6645 8.553696 AGTGAAGCTTATTTTTCTTGCAATTTG 58.446 29.630 0.00 0.00 0.00 2.32
2348 6646 8.667076 AGTGAAGCTTATTTTTCTTGCAATTT 57.333 26.923 0.00 0.00 0.00 1.82
2349 6647 9.415544 CTAGTGAAGCTTATTTTTCTTGCAATT 57.584 29.630 0.00 0.00 0.00 2.32
2350 6648 8.031277 CCTAGTGAAGCTTATTTTTCTTGCAAT 58.969 33.333 0.00 0.00 0.00 3.56
2351 6649 7.230510 TCCTAGTGAAGCTTATTTTTCTTGCAA 59.769 33.333 0.00 0.00 0.00 4.08
2352 6650 6.714810 TCCTAGTGAAGCTTATTTTTCTTGCA 59.285 34.615 0.00 0.00 0.00 4.08
2353 6651 7.145932 TCCTAGTGAAGCTTATTTTTCTTGC 57.854 36.000 0.00 0.00 0.00 4.01
2354 6652 9.965824 TTTTCCTAGTGAAGCTTATTTTTCTTG 57.034 29.630 0.00 0.00 33.63 3.02
2355 6653 9.967346 GTTTTCCTAGTGAAGCTTATTTTTCTT 57.033 29.630 0.00 0.00 33.63 2.52
2356 6654 9.131791 TGTTTTCCTAGTGAAGCTTATTTTTCT 57.868 29.630 0.00 0.00 33.63 2.52
2357 6655 9.744468 TTGTTTTCCTAGTGAAGCTTATTTTTC 57.256 29.630 0.00 0.00 33.63 2.29
2360 6658 9.696917 CAATTGTTTTCCTAGTGAAGCTTATTT 57.303 29.630 0.00 0.00 33.63 1.40
2361 6659 8.860088 ACAATTGTTTTCCTAGTGAAGCTTATT 58.140 29.630 4.92 0.00 33.63 1.40
2362 6660 8.409358 ACAATTGTTTTCCTAGTGAAGCTTAT 57.591 30.769 4.92 0.00 33.63 1.73
2363 6661 7.307751 CGACAATTGTTTTCCTAGTGAAGCTTA 60.308 37.037 13.36 0.00 33.63 3.09
2364 6662 6.513393 CGACAATTGTTTTCCTAGTGAAGCTT 60.513 38.462 13.36 0.00 33.63 3.74
2365 6663 5.049405 CGACAATTGTTTTCCTAGTGAAGCT 60.049 40.000 13.36 0.00 33.63 3.74
2366 6664 5.147162 CGACAATTGTTTTCCTAGTGAAGC 58.853 41.667 13.36 0.00 33.63 3.86
2373 8256 2.865079 TGGCCGACAATTGTTTTCCTA 58.135 42.857 13.36 3.10 0.00 2.94
2407 8290 2.368439 TCTTGCAATTTGGATCGGAGG 58.632 47.619 0.00 0.00 0.00 4.30
2498 8404 4.984785 GCGAGATTAGCATCTGTGATGTAA 59.015 41.667 8.98 7.05 40.14 2.41
2631 8544 3.595819 GCTGCCGGCAAGAAGATT 58.404 55.556 32.09 0.00 41.35 2.40


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

AutoCloner maintained by Alex Coulton.