Multiple sequence alignment - TraesCS3A01G365200

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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 TraesCS3A01G365200 chr3A 100.000 3613 0 0 1 3613 614575776 614572164 0.000000e+00 6673.0
1 TraesCS3A01G365200 chr3D 92.995 2912 142 29 443 3318 471971396 471968511 0.000000e+00 4191.0
2 TraesCS3A01G365200 chr3D 95.044 343 13 3 3272 3613 471968447 471968108 1.480000e-148 536.0
3 TraesCS3A01G365200 chr3D 82.133 347 49 11 59 398 360579799 360579459 5.900000e-73 285.0
4 TraesCS3A01G365200 chr3D 83.986 281 42 3 100 377 45408156 45408436 2.140000e-67 267.0
5 TraesCS3A01G365200 chr3D 78.780 377 43 20 51 398 185228209 185228577 6.070000e-53 219.0
6 TraesCS3A01G365200 chr3B 92.263 2947 148 31 444 3342 627614423 627611509 0.000000e+00 4106.0
7 TraesCS3A01G365200 chr2D 81.944 360 51 11 51 400 526159068 526159423 3.530000e-75 292.0
8 TraesCS3A01G365200 chr2D 81.609 261 38 9 51 305 79091592 79091336 1.310000e-49 207.0
9 TraesCS3A01G365200 chr2D 100.000 30 0 0 1471 1500 28550830 28550859 5.040000e-04 56.5
10 TraesCS3A01G365200 chr5A 80.055 361 58 9 44 392 552387584 552387226 4.630000e-64 255.0
11 TraesCS3A01G365200 chr5A 100.000 39 0 0 1574 1612 340270048 340270010 5.000000e-09 73.1
12 TraesCS3A01G365200 chr6D 79.508 366 55 13 51 400 464534920 464534559 3.600000e-60 243.0
13 TraesCS3A01G365200 chr5B 80.060 336 50 13 51 378 586716494 586716820 2.170000e-57 233.0
14 TraesCS3A01G365200 chr2A 79.751 321 52 11 51 367 657000910 657000599 1.690000e-53 220.0
15 TraesCS3A01G365200 chr4B 78.552 359 53 14 51 398 653208043 653208388 7.860000e-52 215.0
16 TraesCS3A01G365200 chr4B 80.153 131 25 1 3383 3512 47447538 47447668 2.970000e-16 97.1
17 TraesCS3A01G365200 chr7A 78.729 362 36 18 44 392 467369034 467368701 1.700000e-48 204.0
18 TraesCS3A01G365200 chr7A 80.247 243 38 7 162 399 498485714 498485477 1.330000e-39 174.0
19 TraesCS3A01G365200 chr7A 79.835 243 39 7 162 399 581365811 581366048 6.200000e-38 169.0
20 TraesCS3A01G365200 chr7A 79.268 246 42 6 160 399 700430916 700431158 2.890000e-36 163.0
21 TraesCS3A01G365200 chr7A 79.012 243 42 6 163 399 498485444 498485205 1.340000e-34 158.0
22 TraesCS3A01G365200 chr7A 78.455 246 44 6 160 399 581366078 581366320 6.250000e-33 152.0
23 TraesCS3A01G365200 chr7A 78.601 243 42 7 162 399 700430649 700430886 6.250000e-33 152.0
24 TraesCS3A01G365200 chr7A 87.209 86 11 0 1527 1612 708319173 708319258 8.260000e-17 99.0
25 TraesCS3A01G365200 chr7B 85.065 154 17 5 239 392 624705497 624705350 6.250000e-33 152.0
26 TraesCS3A01G365200 chr7B 79.286 140 27 2 1474 1612 708511638 708511776 2.970000e-16 97.1
27 TraesCS3A01G365200 chr5D 94.118 51 3 0 1562 1612 255989492 255989442 1.080000e-10 78.7
28 TraesCS3A01G365200 chr6A 100.000 30 0 0 1471 1500 578887681 578887652 5.040000e-04 56.5


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 TraesCS3A01G365200 chr3A 614572164 614575776 3612 True 6673.0 6673 100.0000 1 3613 1 chr3A.!!$R1 3612
1 TraesCS3A01G365200 chr3D 471968108 471971396 3288 True 2363.5 4191 94.0195 443 3613 2 chr3D.!!$R2 3170
2 TraesCS3A01G365200 chr3B 627611509 627614423 2914 True 4106.0 4106 92.2630 444 3342 1 chr3B.!!$R1 2898

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
440 441 0.037447 GAGAGCCAAAAGGCCTCACT 59.963 55.0 5.23 0.0 34.61 3.41 F
441 442 0.251077 AGAGCCAAAAGGCCTCACTG 60.251 55.0 5.23 3.4 35.12 3.66 F
864 871 0.538746 TCGTCTCGCTGGCCCATATA 60.539 55.0 0.00 0.0 0.00 0.86 F
1695 1718 0.967380 GTGCCCCATTTCCTGTGGAG 60.967 60.0 0.00 0.0 39.12 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1695 0.318120 CACAGGAAATGGGGCACAAC 59.682 55.000 0.00 0.0 0.00 3.32 R
1722 1767 1.063469 GCGCCTTACACGTTGCATTAT 59.937 47.619 0.00 0.0 0.00 1.28 R
1916 1963 1.070758 AGTTTCGCGATAGATGCCCAT 59.929 47.619 10.88 0.0 39.76 4.00 R
3392 3562 1.133025 GCAGCATCACACACCCAATAC 59.867 52.381 0.00 0.0 0.00 1.89 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
39 40 9.891828 TTTCATTTGTATCTGTTGTAACATGTC 57.108 29.630 0.00 0.00 38.41 3.06
40 41 8.846943 TCATTTGTATCTGTTGTAACATGTCT 57.153 30.769 0.00 0.00 38.41 3.41
41 42 9.283768 TCATTTGTATCTGTTGTAACATGTCTT 57.716 29.630 0.00 0.00 38.41 3.01
42 43 9.546909 CATTTGTATCTGTTGTAACATGTCTTC 57.453 33.333 0.00 0.00 38.41 2.87
43 44 8.902540 TTTGTATCTGTTGTAACATGTCTTCT 57.097 30.769 0.00 0.00 38.41 2.85
44 45 8.902540 TTGTATCTGTTGTAACATGTCTTCTT 57.097 30.769 0.00 0.00 38.41 2.52
45 46 8.310406 TGTATCTGTTGTAACATGTCTTCTTG 57.690 34.615 0.00 0.00 38.41 3.02
46 47 8.147704 TGTATCTGTTGTAACATGTCTTCTTGA 58.852 33.333 0.00 0.00 38.41 3.02
47 48 9.155975 GTATCTGTTGTAACATGTCTTCTTGAT 57.844 33.333 0.00 1.49 38.41 2.57
49 50 9.896645 ATCTGTTGTAACATGTCTTCTTGATAT 57.103 29.630 0.00 0.00 38.41 1.63
58 59 9.927081 AACATGTCTTCTTGATATAAATCCCTT 57.073 29.630 0.00 0.00 0.00 3.95
59 60 9.927081 ACATGTCTTCTTGATATAAATCCCTTT 57.073 29.630 0.00 0.00 0.00 3.11
62 63 9.189156 TGTCTTCTTGATATAAATCCCTTTTGG 57.811 33.333 0.00 0.00 39.97 3.28
63 64 9.190317 GTCTTCTTGATATAAATCCCTTTTGGT 57.810 33.333 0.00 0.00 38.10 3.67
64 65 9.189156 TCTTCTTGATATAAATCCCTTTTGGTG 57.811 33.333 0.00 0.00 38.10 4.17
65 66 7.896383 TCTTGATATAAATCCCTTTTGGTGG 57.104 36.000 0.00 0.00 38.10 4.61
66 67 6.323739 TCTTGATATAAATCCCTTTTGGTGGC 59.676 38.462 0.00 0.00 38.10 5.01
67 68 4.898861 TGATATAAATCCCTTTTGGTGGCC 59.101 41.667 0.00 0.00 38.10 5.36
68 69 1.551452 TAAATCCCTTTTGGTGGCCG 58.449 50.000 0.00 0.00 38.10 6.13
69 70 0.178947 AAATCCCTTTTGGTGGCCGA 60.179 50.000 0.00 0.00 38.10 5.54
70 71 0.611896 AATCCCTTTTGGTGGCCGAG 60.612 55.000 0.00 0.00 38.10 4.63
71 72 3.373565 CCCTTTTGGTGGCCGAGC 61.374 66.667 0.00 0.00 38.10 5.03
72 73 2.282462 CCTTTTGGTGGCCGAGCT 60.282 61.111 0.00 0.00 34.07 4.09
73 74 2.335712 CCTTTTGGTGGCCGAGCTC 61.336 63.158 2.73 2.73 34.07 4.09
74 75 2.282180 TTTTGGTGGCCGAGCTCC 60.282 61.111 8.47 0.00 0.00 4.70
75 76 3.126703 TTTTGGTGGCCGAGCTCCA 62.127 57.895 8.47 0.00 33.12 3.86
76 77 2.424842 TTTTGGTGGCCGAGCTCCAT 62.425 55.000 8.47 0.00 35.81 3.41
77 78 3.626996 TTGGTGGCCGAGCTCCATG 62.627 63.158 8.47 0.00 35.81 3.66
78 79 4.101448 GGTGGCCGAGCTCCATGT 62.101 66.667 8.47 0.00 35.81 3.21
79 80 2.731571 GGTGGCCGAGCTCCATGTA 61.732 63.158 8.47 0.00 35.81 2.29
80 81 1.227380 GTGGCCGAGCTCCATGTAG 60.227 63.158 8.47 0.00 35.81 2.74
81 82 2.423446 GGCCGAGCTCCATGTAGG 59.577 66.667 8.47 3.22 39.47 3.18
82 83 2.435693 GGCCGAGCTCCATGTAGGT 61.436 63.158 8.47 0.00 39.02 3.08
83 84 1.068250 GCCGAGCTCCATGTAGGTC 59.932 63.158 8.47 7.39 39.97 3.85
86 87 2.506065 GAGCTCCATGTAGGTCGGT 58.494 57.895 0.87 0.00 39.02 4.69
87 88 0.824759 GAGCTCCATGTAGGTCGGTT 59.175 55.000 0.87 0.00 39.02 4.44
88 89 1.207329 GAGCTCCATGTAGGTCGGTTT 59.793 52.381 0.87 0.00 39.02 3.27
89 90 1.628846 AGCTCCATGTAGGTCGGTTTT 59.371 47.619 0.00 0.00 39.02 2.43
90 91 2.039879 AGCTCCATGTAGGTCGGTTTTT 59.960 45.455 0.00 0.00 39.02 1.94
91 92 2.161609 GCTCCATGTAGGTCGGTTTTTG 59.838 50.000 0.00 0.00 39.02 2.44
92 93 3.670625 CTCCATGTAGGTCGGTTTTTGA 58.329 45.455 0.00 0.00 39.02 2.69
93 94 4.069304 CTCCATGTAGGTCGGTTTTTGAA 58.931 43.478 0.00 0.00 39.02 2.69
94 95 4.462133 TCCATGTAGGTCGGTTTTTGAAA 58.538 39.130 0.00 0.00 39.02 2.69
95 96 4.888239 TCCATGTAGGTCGGTTTTTGAAAA 59.112 37.500 0.00 0.00 39.02 2.29
96 97 5.360144 TCCATGTAGGTCGGTTTTTGAAAAA 59.640 36.000 0.00 0.00 39.02 1.94
184 185 8.864260 GCATAATGCACAAGTGTTTAAATTTC 57.136 30.769 0.00 0.00 44.26 2.17
185 186 8.494347 GCATAATGCACAAGTGTTTAAATTTCA 58.506 29.630 0.00 0.00 44.26 2.69
188 189 8.715191 AATGCACAAGTGTTTAAATTTCAAGA 57.285 26.923 0.00 0.00 0.00 3.02
189 190 7.518731 TGCACAAGTGTTTAAATTTCAAGAC 57.481 32.000 4.63 4.63 0.00 3.01
190 191 6.252441 TGCACAAGTGTTTAAATTTCAAGACG 59.748 34.615 6.71 0.00 0.00 4.18
191 192 6.470877 GCACAAGTGTTTAAATTTCAAGACGA 59.529 34.615 6.71 0.00 0.00 4.20
192 193 7.008810 GCACAAGTGTTTAAATTTCAAGACGAA 59.991 33.333 6.71 0.00 0.00 3.85
207 208 9.611284 TTTCAAGACGAAATATGTTGAAATGAG 57.389 29.630 6.08 0.00 41.64 2.90
208 209 8.546597 TCAAGACGAAATATGTTGAAATGAGA 57.453 30.769 0.00 0.00 0.00 3.27
209 210 8.659491 TCAAGACGAAATATGTTGAAATGAGAG 58.341 33.333 0.00 0.00 0.00 3.20
210 211 7.009568 AGACGAAATATGTTGAAATGAGAGC 57.990 36.000 0.00 0.00 0.00 4.09
211 212 6.820656 AGACGAAATATGTTGAAATGAGAGCT 59.179 34.615 0.00 0.00 0.00 4.09
212 213 6.779117 ACGAAATATGTTGAAATGAGAGCTG 58.221 36.000 0.00 0.00 0.00 4.24
213 214 6.372659 ACGAAATATGTTGAAATGAGAGCTGT 59.627 34.615 0.00 0.00 0.00 4.40
214 215 6.685828 CGAAATATGTTGAAATGAGAGCTGTG 59.314 38.462 0.00 0.00 0.00 3.66
215 216 3.844577 ATGTTGAAATGAGAGCTGTGC 57.155 42.857 0.00 0.00 0.00 4.57
216 217 1.532437 TGTTGAAATGAGAGCTGTGCG 59.468 47.619 0.00 0.00 0.00 5.34
217 218 1.800586 GTTGAAATGAGAGCTGTGCGA 59.199 47.619 0.00 0.00 0.00 5.10
218 219 2.391616 TGAAATGAGAGCTGTGCGAT 57.608 45.000 0.00 0.00 0.00 4.58
219 220 2.703416 TGAAATGAGAGCTGTGCGATT 58.297 42.857 0.00 0.00 0.00 3.34
220 221 3.076621 TGAAATGAGAGCTGTGCGATTT 58.923 40.909 0.00 0.00 0.00 2.17
221 222 3.503363 TGAAATGAGAGCTGTGCGATTTT 59.497 39.130 0.00 0.00 0.00 1.82
222 223 4.022935 TGAAATGAGAGCTGTGCGATTTTT 60.023 37.500 0.00 0.00 0.00 1.94
249 250 7.928908 TTTTGAGTTTCTTAACACATGATGC 57.071 32.000 0.00 0.00 35.31 3.91
250 251 6.882610 TTGAGTTTCTTAACACATGATGCT 57.117 33.333 0.00 0.00 35.31 3.79
251 252 7.977789 TTGAGTTTCTTAACACATGATGCTA 57.022 32.000 0.00 0.00 35.31 3.49
252 253 8.565896 TTGAGTTTCTTAACACATGATGCTAT 57.434 30.769 0.00 0.00 35.31 2.97
253 254 8.565896 TGAGTTTCTTAACACATGATGCTATT 57.434 30.769 0.00 0.00 36.70 1.73
254 255 8.668353 TGAGTTTCTTAACACATGATGCTATTC 58.332 33.333 0.00 0.00 36.70 1.75
255 256 8.565896 AGTTTCTTAACACATGATGCTATTCA 57.434 30.769 0.00 0.00 36.70 2.57
256 257 9.182214 AGTTTCTTAACACATGATGCTATTCAT 57.818 29.630 0.00 0.00 35.40 2.57
257 258 9.443283 GTTTCTTAACACATGATGCTATTCATC 57.557 33.333 0.00 0.00 41.47 2.92
266 267 2.627515 TGCTATTCATCCTCACAGGC 57.372 50.000 0.00 0.00 34.61 4.85
267 268 1.141657 TGCTATTCATCCTCACAGGCC 59.858 52.381 0.00 0.00 34.61 5.19
268 269 1.141657 GCTATTCATCCTCACAGGCCA 59.858 52.381 5.01 0.00 34.61 5.36
269 270 2.224719 GCTATTCATCCTCACAGGCCAT 60.225 50.000 5.01 0.00 34.61 4.40
270 271 2.359981 ATTCATCCTCACAGGCCATG 57.640 50.000 5.01 2.37 34.61 3.66
271 272 1.288188 TTCATCCTCACAGGCCATGA 58.712 50.000 5.01 7.63 34.61 3.07
272 273 1.288188 TCATCCTCACAGGCCATGAA 58.712 50.000 5.01 0.00 34.61 2.57
273 274 1.848388 TCATCCTCACAGGCCATGAAT 59.152 47.619 5.01 0.00 34.61 2.57
274 275 2.242965 TCATCCTCACAGGCCATGAATT 59.757 45.455 5.01 0.00 34.61 2.17
275 276 2.905415 TCCTCACAGGCCATGAATTT 57.095 45.000 5.01 0.00 34.61 1.82
276 277 4.079844 TCATCCTCACAGGCCATGAATTTA 60.080 41.667 5.01 0.00 34.61 1.40
277 278 4.524802 TCCTCACAGGCCATGAATTTAT 57.475 40.909 5.01 0.00 34.61 1.40
278 279 4.464008 TCCTCACAGGCCATGAATTTATC 58.536 43.478 5.01 0.00 34.61 1.75
279 280 4.166725 TCCTCACAGGCCATGAATTTATCT 59.833 41.667 5.01 0.00 34.61 1.98
280 281 4.891756 CCTCACAGGCCATGAATTTATCTT 59.108 41.667 5.01 0.00 0.00 2.40
281 282 5.361857 CCTCACAGGCCATGAATTTATCTTT 59.638 40.000 5.01 0.00 0.00 2.52
282 283 6.127253 CCTCACAGGCCATGAATTTATCTTTT 60.127 38.462 5.01 0.00 0.00 2.27
283 284 7.243604 TCACAGGCCATGAATTTATCTTTTT 57.756 32.000 5.01 0.00 0.00 1.94
309 310 5.415415 GCAGATCGCATTTCAAGTAATCT 57.585 39.130 4.93 0.00 41.79 2.40
310 311 5.438972 GCAGATCGCATTTCAAGTAATCTC 58.561 41.667 4.93 0.00 41.79 2.75
311 312 5.007039 GCAGATCGCATTTCAAGTAATCTCA 59.993 40.000 4.93 0.00 41.79 3.27
312 313 6.293298 GCAGATCGCATTTCAAGTAATCTCAT 60.293 38.462 4.93 0.00 41.79 2.90
313 314 7.637229 CAGATCGCATTTCAAGTAATCTCATT 58.363 34.615 0.00 0.00 0.00 2.57
314 315 7.797587 CAGATCGCATTTCAAGTAATCTCATTC 59.202 37.037 0.00 0.00 0.00 2.67
315 316 7.714377 AGATCGCATTTCAAGTAATCTCATTCT 59.286 33.333 0.00 0.00 0.00 2.40
316 317 7.008440 TCGCATTTCAAGTAATCTCATTCTG 57.992 36.000 0.00 0.00 0.00 3.02
317 318 6.818142 TCGCATTTCAAGTAATCTCATTCTGA 59.182 34.615 0.00 0.00 0.00 3.27
318 319 7.334171 TCGCATTTCAAGTAATCTCATTCTGAA 59.666 33.333 0.00 0.00 0.00 3.02
319 320 7.964559 CGCATTTCAAGTAATCTCATTCTGAAA 59.035 33.333 0.00 0.00 0.00 2.69
320 321 9.798994 GCATTTCAAGTAATCTCATTCTGAAAT 57.201 29.630 0.00 0.00 34.91 2.17
335 336 9.891828 TCATTCTGAAATTTTACACACATACAC 57.108 29.630 0.00 0.00 0.00 2.90
336 337 9.676195 CATTCTGAAATTTTACACACATACACA 57.324 29.630 0.00 0.00 0.00 3.72
370 371 9.915629 TTTGTTTACTTGTACAATTGTTTCAGT 57.084 25.926 17.78 16.75 34.52 3.41
371 372 9.915629 TTGTTTACTTGTACAATTGTTTCAGTT 57.084 25.926 17.78 9.43 29.82 3.16
372 373 9.915629 TGTTTACTTGTACAATTGTTTCAGTTT 57.084 25.926 17.78 7.36 0.00 2.66
401 402 8.839310 TTTTGAAACTGAAAAGGTTTGAATCA 57.161 26.923 0.00 0.00 37.07 2.57
402 403 8.477984 TTTGAAACTGAAAAGGTTTGAATCAG 57.522 30.769 0.00 0.00 42.43 2.90
406 407 6.530019 ACTGAAAAGGTTTGAATCAGTTGT 57.470 33.333 1.13 0.00 46.22 3.32
407 408 6.332630 ACTGAAAAGGTTTGAATCAGTTGTG 58.667 36.000 1.13 0.00 46.22 3.33
408 409 6.071391 ACTGAAAAGGTTTGAATCAGTTGTGT 60.071 34.615 1.13 0.00 46.22 3.72
409 410 6.329496 TGAAAAGGTTTGAATCAGTTGTGTC 58.671 36.000 0.00 0.00 0.00 3.67
410 411 4.552166 AAGGTTTGAATCAGTTGTGTCG 57.448 40.909 0.00 0.00 0.00 4.35
411 412 3.804036 AGGTTTGAATCAGTTGTGTCGA 58.196 40.909 0.00 0.00 0.00 4.20
412 413 3.560068 AGGTTTGAATCAGTTGTGTCGAC 59.440 43.478 9.11 9.11 0.00 4.20
413 414 3.531982 GTTTGAATCAGTTGTGTCGACG 58.468 45.455 11.62 0.00 0.00 5.12
414 415 1.778334 TGAATCAGTTGTGTCGACGG 58.222 50.000 11.62 0.00 0.00 4.79
415 416 1.068474 GAATCAGTTGTGTCGACGGG 58.932 55.000 11.62 0.00 0.00 5.28
416 417 0.677288 AATCAGTTGTGTCGACGGGA 59.323 50.000 11.62 2.30 0.00 5.14
417 418 0.243907 ATCAGTTGTGTCGACGGGAG 59.756 55.000 11.62 0.00 0.00 4.30
418 419 1.372997 CAGTTGTGTCGACGGGAGG 60.373 63.158 11.62 0.00 0.00 4.30
419 420 2.737376 GTTGTGTCGACGGGAGGC 60.737 66.667 11.62 0.00 0.00 4.70
420 421 3.998672 TTGTGTCGACGGGAGGCC 61.999 66.667 11.62 0.00 0.00 5.19
435 436 3.443925 GCCGAGAGCCAAAAGGCC 61.444 66.667 2.33 0.00 41.81 5.19
436 437 2.352805 CCGAGAGCCAAAAGGCCT 59.647 61.111 0.00 0.00 35.12 5.19
437 438 1.746991 CCGAGAGCCAAAAGGCCTC 60.747 63.158 5.23 8.56 35.12 4.70
438 439 1.003355 CGAGAGCCAAAAGGCCTCA 60.003 57.895 5.23 0.00 34.34 3.86
439 440 1.301677 CGAGAGCCAAAAGGCCTCAC 61.302 60.000 5.23 0.00 34.34 3.51
440 441 0.037447 GAGAGCCAAAAGGCCTCACT 59.963 55.000 5.23 0.00 34.61 3.41
441 442 0.251077 AGAGCCAAAAGGCCTCACTG 60.251 55.000 5.23 3.40 35.12 3.66
464 465 9.247861 ACTGGAAAGAGAAACATAGCATATTTT 57.752 29.630 0.00 0.00 0.00 1.82
484 485 1.872388 TTGGAAATCAGTTGCGTCGA 58.128 45.000 0.00 0.00 0.00 4.20
486 487 1.144969 GGAAATCAGTTGCGTCGACA 58.855 50.000 17.16 0.00 0.00 4.35
487 488 1.126846 GGAAATCAGTTGCGTCGACAG 59.873 52.381 17.16 9.59 0.00 3.51
505 506 4.878397 CGACAGGAATGCTAAAAAGAGGAT 59.122 41.667 0.00 0.00 0.00 3.24
536 537 5.174943 CCGACAACAAAAGCCAAGATAAAAC 59.825 40.000 0.00 0.00 0.00 2.43
539 540 6.872920 ACAACAAAAGCCAAGATAAAACTGA 58.127 32.000 0.00 0.00 0.00 3.41
540 541 6.756542 ACAACAAAAGCCAAGATAAAACTGAC 59.243 34.615 0.00 0.00 0.00 3.51
550 551 7.631377 GCCAAGATAAAACTGACATTATTGCCT 60.631 37.037 0.00 0.00 0.00 4.75
567 568 2.188817 GCCTAAAAGGAGGAGAGGTGA 58.811 52.381 0.00 0.00 37.67 4.02
604 605 7.637511 ACTGAGGAGAAAAGAACATCCATTAT 58.362 34.615 0.00 0.00 34.08 1.28
605 606 8.112183 ACTGAGGAGAAAAGAACATCCATTATT 58.888 33.333 0.00 0.00 34.08 1.40
606 607 9.618890 CTGAGGAGAAAAGAACATCCATTATTA 57.381 33.333 0.00 0.00 34.08 0.98
643 646 9.109393 TCTATCGAATTTGCTTTACTGCTTTAT 57.891 29.630 0.00 0.00 0.00 1.40
644 647 9.374960 CTATCGAATTTGCTTTACTGCTTTATC 57.625 33.333 0.00 0.00 0.00 1.75
645 648 7.139896 TCGAATTTGCTTTACTGCTTTATCA 57.860 32.000 0.00 0.00 0.00 2.15
646 649 7.761409 TCGAATTTGCTTTACTGCTTTATCAT 58.239 30.769 0.00 0.00 0.00 2.45
649 652 9.455847 GAATTTGCTTTACTGCTTTATCATAGG 57.544 33.333 0.00 0.00 0.00 2.57
650 653 6.377327 TTGCTTTACTGCTTTATCATAGGC 57.623 37.500 0.00 0.00 0.00 3.93
651 654 5.436175 TGCTTTACTGCTTTATCATAGGCA 58.564 37.500 0.00 0.00 0.00 4.75
652 655 5.885352 TGCTTTACTGCTTTATCATAGGCAA 59.115 36.000 0.00 0.00 34.21 4.52
653 656 6.038603 TGCTTTACTGCTTTATCATAGGCAAG 59.961 38.462 0.00 0.00 34.21 4.01
654 657 6.260936 GCTTTACTGCTTTATCATAGGCAAGA 59.739 38.462 0.00 0.00 34.21 3.02
655 658 7.040823 GCTTTACTGCTTTATCATAGGCAAGAT 60.041 37.037 0.00 0.00 34.21 2.40
656 659 7.969536 TTACTGCTTTATCATAGGCAAGATC 57.030 36.000 0.00 0.00 34.21 2.75
673 676 5.523369 CAAGATCTGCACGTATCATAGTCA 58.477 41.667 0.00 0.00 0.00 3.41
689 692 2.413837 AGTCAAACGGTCAAATCGAGG 58.586 47.619 0.00 0.00 0.00 4.63
708 711 4.572389 CGAGGTCCCAAAATTAGATCACAG 59.428 45.833 0.00 0.00 0.00 3.66
791 798 5.073144 TGGAATGAAACAGGGTTTCTAGTCT 59.927 40.000 19.12 3.53 0.00 3.24
855 862 1.941734 GCTCCGAATCGTCTCGCTG 60.942 63.158 0.82 1.01 37.51 5.18
863 870 1.188219 ATCGTCTCGCTGGCCCATAT 61.188 55.000 0.00 0.00 0.00 1.78
864 871 0.538746 TCGTCTCGCTGGCCCATATA 60.539 55.000 0.00 0.00 0.00 0.86
881 888 4.945543 CCATATAAATAACCTTACGGCCCC 59.054 45.833 0.00 0.00 0.00 5.80
886 904 2.242797 TAACCTTACGGCCCCGAAGC 62.243 60.000 14.44 0.00 42.83 3.86
887 905 3.782443 CCTTACGGCCCCGAAGCT 61.782 66.667 14.44 0.00 42.83 3.74
888 906 2.202892 CTTACGGCCCCGAAGCTC 60.203 66.667 14.44 0.00 42.83 4.09
909 929 2.035961 CTCCAGAGAGAAACACGGAACA 59.964 50.000 0.00 0.00 43.39 3.18
1275 1297 4.335647 ACGCAAGGCCCAGTCCAG 62.336 66.667 0.00 0.00 46.39 3.86
1349 1371 4.660938 GCCGCAAACCCCTGTCCT 62.661 66.667 0.00 0.00 0.00 3.85
1547 1569 3.195698 GGCGCGGAACTGGATGAC 61.196 66.667 8.83 0.00 0.00 3.06
1548 1570 3.195698 GCGCGGAACTGGATGACC 61.196 66.667 8.83 0.00 0.00 4.02
1673 1695 5.695816 GCTCTTTTCATCCATCTACTGCTAG 59.304 44.000 0.00 0.00 0.00 3.42
1694 1717 1.076549 GTGCCCCATTTCCTGTGGA 59.923 57.895 0.00 0.00 39.12 4.02
1695 1718 0.967380 GTGCCCCATTTCCTGTGGAG 60.967 60.000 0.00 0.00 39.12 3.86
1702 1725 4.444876 CCCCATTTCCTGTGGAGTATGTAG 60.445 50.000 0.00 0.00 39.12 2.74
1714 1737 3.134804 GGAGTATGTAGTCAGGTGCCAAT 59.865 47.826 0.00 0.00 0.00 3.16
1716 1739 5.179452 AGTATGTAGTCAGGTGCCAATTT 57.821 39.130 0.00 0.00 0.00 1.82
1717 1740 5.570320 AGTATGTAGTCAGGTGCCAATTTT 58.430 37.500 0.00 0.00 0.00 1.82
1718 1741 4.789012 ATGTAGTCAGGTGCCAATTTTG 57.211 40.909 0.00 0.00 0.00 2.44
1722 1767 5.594725 TGTAGTCAGGTGCCAATTTTGTTTA 59.405 36.000 0.00 0.00 0.00 2.01
1748 1793 2.477189 GCAACGTGTAAGGCGCATTATT 60.477 45.455 18.34 5.18 0.00 1.40
1901 1948 6.128090 ACCAAATGATAATATCTGCTCATGCG 60.128 38.462 1.66 0.00 43.34 4.73
1916 1963 3.507103 CATGCGATTCATGGGAACAAA 57.493 42.857 0.00 0.00 46.81 2.83
1970 2017 4.460382 AGAACCGACAATGCAATCAAGAAT 59.540 37.500 0.00 0.00 0.00 2.40
2155 2202 4.515191 TCCTGTGCAAACAGTATCTGAAAC 59.485 41.667 3.70 0.00 36.06 2.78
2159 2206 4.757149 GTGCAAACAGTATCTGAAACCTCT 59.243 41.667 3.70 0.00 35.18 3.69
2396 2443 2.439409 ACATGCTTTGCTGCTGATGTA 58.561 42.857 0.00 0.00 30.95 2.29
2724 2773 0.179134 GTGCGTGCTCCGTAGATTCT 60.179 55.000 0.00 0.00 39.32 2.40
2811 2860 2.549329 TCATTCACACTGCATCACACAC 59.451 45.455 0.00 0.00 0.00 3.82
2837 2886 1.913778 AGCTGGATGTGATTGTTGCA 58.086 45.000 0.00 0.00 0.00 4.08
2844 2893 6.418819 GCTGGATGTGATTGTTGCATTATAAC 59.581 38.462 0.00 0.00 0.00 1.89
2935 2985 6.131961 CCAAATAATGAGACTCCCCATTTCT 58.868 40.000 0.00 0.00 35.02 2.52
2991 3041 5.023533 TCCTATGATGAAGCTACCACAAC 57.976 43.478 0.00 0.00 0.00 3.32
3156 3210 7.013559 TGTCTTGCATATTAACCATCATTGAGG 59.986 37.037 0.00 0.00 0.00 3.86
3159 3213 7.275888 TGCATATTAACCATCATTGAGGTTC 57.724 36.000 18.04 8.43 44.51 3.62
3202 3256 7.606135 TTGTAATCGAATAAGTAGATCCCCA 57.394 36.000 0.00 0.00 0.00 4.96
3209 3264 6.551975 TCGAATAAGTAGATCCCCATGTTACA 59.448 38.462 0.00 0.00 0.00 2.41
3255 3310 9.924010 ATTACCCAGTAGTCCTATCATATACTC 57.076 37.037 0.00 0.00 0.00 2.59
3256 3311 7.344599 ACCCAGTAGTCCTATCATATACTCA 57.655 40.000 0.00 0.00 0.00 3.41
3257 3312 7.945278 ACCCAGTAGTCCTATCATATACTCAT 58.055 38.462 0.00 0.00 0.00 2.90
3258 3313 7.836685 ACCCAGTAGTCCTATCATATACTCATG 59.163 40.741 0.00 0.00 0.00 3.07
3259 3314 7.836685 CCCAGTAGTCCTATCATATACTCATGT 59.163 40.741 0.00 0.00 0.00 3.21
3260 3315 9.249053 CCAGTAGTCCTATCATATACTCATGTT 57.751 37.037 0.00 0.00 0.00 2.71
3264 3319 8.865420 AGTCCTATCATATACTCATGTTACGT 57.135 34.615 0.00 0.00 0.00 3.57
3265 3320 9.955102 AGTCCTATCATATACTCATGTTACGTA 57.045 33.333 0.00 0.00 0.00 3.57
3365 3535 1.916181 AGCCTTATAACCAGTGGCAGT 59.084 47.619 9.78 0.00 45.42 4.40
3381 3551 3.158676 GGCAGTGGTGGGTAAATTGTAA 58.841 45.455 0.00 0.00 0.00 2.41
3392 3562 7.094506 GGTGGGTAAATTGTAACAAGTCTAAGG 60.095 40.741 0.00 0.00 0.00 2.69
3394 3564 8.658619 TGGGTAAATTGTAACAAGTCTAAGGTA 58.341 33.333 0.00 0.00 0.00 3.08
3405 3575 4.553330 AGTCTAAGGTATTGGGTGTGTG 57.447 45.455 0.00 0.00 0.00 3.82
3437 3607 5.349543 GCAAAACATGGAATCAATCTGAACC 59.650 40.000 0.00 0.00 0.00 3.62
3464 3634 1.429148 GCGGATGGTTGAGCGGTTAG 61.429 60.000 0.00 0.00 0.00 2.34
3595 3766 4.539726 AGGTGATGTGTTTATGGCATGAT 58.460 39.130 10.98 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.891828 GACATGTTACAACAGATACAAATGAAA 57.108 29.630 0.00 0.00 43.04 2.69
14 15 9.283768 AGACATGTTACAACAGATACAAATGAA 57.716 29.630 0.00 0.00 43.04 2.57
15 16 8.846943 AGACATGTTACAACAGATACAAATGA 57.153 30.769 0.00 0.00 43.04 2.57
16 17 9.546909 GAAGACATGTTACAACAGATACAAATG 57.453 33.333 0.00 0.00 43.04 2.32
17 18 9.507329 AGAAGACATGTTACAACAGATACAAAT 57.493 29.630 0.00 0.00 43.04 2.32
18 19 8.902540 AGAAGACATGTTACAACAGATACAAA 57.097 30.769 0.00 0.00 43.04 2.83
19 20 8.773645 CAAGAAGACATGTTACAACAGATACAA 58.226 33.333 0.00 0.00 43.04 2.41
20 21 8.147704 TCAAGAAGACATGTTACAACAGATACA 58.852 33.333 0.00 0.00 43.04 2.29
21 22 8.534333 TCAAGAAGACATGTTACAACAGATAC 57.466 34.615 0.00 0.00 43.04 2.24
23 24 9.896645 ATATCAAGAAGACATGTTACAACAGAT 57.103 29.630 0.00 2.14 43.04 2.90
32 33 9.927081 AAGGGATTTATATCAAGAAGACATGTT 57.073 29.630 0.00 0.00 32.09 2.71
33 34 9.927081 AAAGGGATTTATATCAAGAAGACATGT 57.073 29.630 0.00 0.00 32.09 3.21
36 37 9.189156 CCAAAAGGGATTTATATCAAGAAGACA 57.811 33.333 0.00 0.00 40.01 3.41
37 38 9.190317 ACCAAAAGGGATTTATATCAAGAAGAC 57.810 33.333 0.00 0.00 41.15 3.01
38 39 9.189156 CACCAAAAGGGATTTATATCAAGAAGA 57.811 33.333 0.00 0.00 41.15 2.87
39 40 8.416329 CCACCAAAAGGGATTTATATCAAGAAG 58.584 37.037 0.00 0.00 41.15 2.85
40 41 7.147742 GCCACCAAAAGGGATTTATATCAAGAA 60.148 37.037 0.00 0.00 41.15 2.52
41 42 6.323739 GCCACCAAAAGGGATTTATATCAAGA 59.676 38.462 0.00 0.00 41.15 3.02
42 43 6.462909 GGCCACCAAAAGGGATTTATATCAAG 60.463 42.308 0.00 0.00 41.15 3.02
43 44 5.365314 GGCCACCAAAAGGGATTTATATCAA 59.635 40.000 0.00 0.00 41.15 2.57
44 45 4.898861 GGCCACCAAAAGGGATTTATATCA 59.101 41.667 0.00 0.00 41.15 2.15
45 46 4.022329 CGGCCACCAAAAGGGATTTATATC 60.022 45.833 2.24 0.00 41.15 1.63
46 47 3.895041 CGGCCACCAAAAGGGATTTATAT 59.105 43.478 2.24 0.00 41.15 0.86
47 48 3.053544 TCGGCCACCAAAAGGGATTTATA 60.054 43.478 2.24 0.00 41.15 0.98
48 49 2.107366 CGGCCACCAAAAGGGATTTAT 58.893 47.619 2.24 0.00 41.15 1.40
49 50 1.075698 TCGGCCACCAAAAGGGATTTA 59.924 47.619 2.24 0.00 41.15 1.40
50 51 0.178947 TCGGCCACCAAAAGGGATTT 60.179 50.000 2.24 0.00 41.15 2.17
51 52 0.611896 CTCGGCCACCAAAAGGGATT 60.612 55.000 2.24 0.00 41.15 3.01
52 53 1.000896 CTCGGCCACCAAAAGGGAT 60.001 57.895 2.24 0.00 41.15 3.85
53 54 2.434331 CTCGGCCACCAAAAGGGA 59.566 61.111 2.24 0.00 41.15 4.20
54 55 3.373565 GCTCGGCCACCAAAAGGG 61.374 66.667 2.24 0.00 44.81 3.95
55 56 2.282462 AGCTCGGCCACCAAAAGG 60.282 61.111 2.24 0.00 0.00 3.11
56 57 2.335712 GGAGCTCGGCCACCAAAAG 61.336 63.158 7.83 0.00 0.00 2.27
57 58 2.282180 GGAGCTCGGCCACCAAAA 60.282 61.111 7.83 0.00 0.00 2.44
58 59 2.905996 ATGGAGCTCGGCCACCAAA 61.906 57.895 7.83 0.00 38.48 3.28
59 60 3.329889 ATGGAGCTCGGCCACCAA 61.330 61.111 7.83 0.00 38.48 3.67
60 61 4.100084 CATGGAGCTCGGCCACCA 62.100 66.667 7.83 4.23 38.44 4.17
61 62 2.650813 CTACATGGAGCTCGGCCACC 62.651 65.000 7.83 0.00 38.44 4.61
62 63 1.227380 CTACATGGAGCTCGGCCAC 60.227 63.158 7.83 0.00 38.44 5.01
63 64 2.434843 CCTACATGGAGCTCGGCCA 61.435 63.158 7.83 0.50 40.24 5.36
64 65 2.370647 GACCTACATGGAGCTCGGCC 62.371 65.000 7.83 0.00 39.71 6.13
65 66 1.068250 GACCTACATGGAGCTCGGC 59.932 63.158 7.83 0.00 39.71 5.54
66 67 1.360551 CGACCTACATGGAGCTCGG 59.639 63.158 13.93 4.50 39.71 4.63
67 68 1.360551 CCGACCTACATGGAGCTCG 59.639 63.158 14.67 14.67 39.71 5.03
68 69 0.824759 AACCGACCTACATGGAGCTC 59.175 55.000 4.71 4.71 39.71 4.09
69 70 1.276622 AAACCGACCTACATGGAGCT 58.723 50.000 0.00 0.00 39.71 4.09
70 71 2.109425 AAAACCGACCTACATGGAGC 57.891 50.000 0.00 0.00 39.71 4.70
71 72 3.670625 TCAAAAACCGACCTACATGGAG 58.329 45.455 0.00 0.00 39.71 3.86
72 73 3.773418 TCAAAAACCGACCTACATGGA 57.227 42.857 0.00 0.00 39.71 3.41
73 74 4.839668 TTTCAAAAACCGACCTACATGG 57.160 40.909 0.00 0.00 42.93 3.66
142 143 9.158097 TGCATTATGCCTCCATGTATATCTATA 57.842 33.333 15.06 0.00 44.23 1.31
143 144 7.935755 GTGCATTATGCCTCCATGTATATCTAT 59.064 37.037 15.06 0.00 44.23 1.98
144 145 7.092935 TGTGCATTATGCCTCCATGTATATCTA 60.093 37.037 15.06 0.00 44.23 1.98
145 146 6.118170 GTGCATTATGCCTCCATGTATATCT 58.882 40.000 15.06 0.00 44.23 1.98
146 147 5.882000 TGTGCATTATGCCTCCATGTATATC 59.118 40.000 15.06 0.00 44.23 1.63
147 148 5.818887 TGTGCATTATGCCTCCATGTATAT 58.181 37.500 15.06 0.00 44.23 0.86
148 149 5.240013 TGTGCATTATGCCTCCATGTATA 57.760 39.130 15.06 0.00 44.23 1.47
149 150 4.103013 TGTGCATTATGCCTCCATGTAT 57.897 40.909 15.06 0.00 44.23 2.29
150 151 3.574354 TGTGCATTATGCCTCCATGTA 57.426 42.857 15.06 0.00 44.23 2.29
151 152 2.440517 TGTGCATTATGCCTCCATGT 57.559 45.000 15.06 0.00 44.23 3.21
152 153 2.691526 ACTTGTGCATTATGCCTCCATG 59.308 45.455 15.06 12.23 44.23 3.66
153 154 2.691526 CACTTGTGCATTATGCCTCCAT 59.308 45.455 15.06 0.00 44.23 3.41
154 155 2.093890 CACTTGTGCATTATGCCTCCA 58.906 47.619 15.06 6.01 44.23 3.86
155 156 2.094675 ACACTTGTGCATTATGCCTCC 58.905 47.619 15.06 3.38 44.23 4.30
156 157 3.855689 AACACTTGTGCATTATGCCTC 57.144 42.857 15.06 8.44 44.23 4.70
157 158 5.720371 TTAAACACTTGTGCATTATGCCT 57.280 34.783 15.06 0.00 44.23 4.75
158 159 6.966435 ATTTAAACACTTGTGCATTATGCC 57.034 33.333 15.06 6.72 44.23 4.40
159 160 8.494347 TGAAATTTAAACACTTGTGCATTATGC 58.506 29.630 10.65 10.65 45.29 3.14
162 163 9.809096 TCTTGAAATTTAAACACTTGTGCATTA 57.191 25.926 0.10 0.00 0.00 1.90
163 164 8.603181 GTCTTGAAATTTAAACACTTGTGCATT 58.397 29.630 0.10 0.00 0.00 3.56
164 165 7.043458 CGTCTTGAAATTTAAACACTTGTGCAT 60.043 33.333 0.10 0.00 0.00 3.96
165 166 6.252441 CGTCTTGAAATTTAAACACTTGTGCA 59.748 34.615 0.10 0.00 0.00 4.57
166 167 6.470877 TCGTCTTGAAATTTAAACACTTGTGC 59.529 34.615 0.10 0.00 0.00 4.57
167 168 7.962934 TCGTCTTGAAATTTAAACACTTGTG 57.037 32.000 0.00 0.00 0.00 3.33
168 169 8.973835 TTTCGTCTTGAAATTTAAACACTTGT 57.026 26.923 0.00 0.00 41.59 3.16
182 183 8.998377 TCTCATTTCAACATATTTCGTCTTGAA 58.002 29.630 0.00 0.00 33.85 2.69
183 184 8.546597 TCTCATTTCAACATATTTCGTCTTGA 57.453 30.769 0.00 0.00 0.00 3.02
184 185 7.427606 GCTCTCATTTCAACATATTTCGTCTTG 59.572 37.037 0.00 0.00 0.00 3.02
185 186 7.335422 AGCTCTCATTTCAACATATTTCGTCTT 59.665 33.333 0.00 0.00 0.00 3.01
186 187 6.820656 AGCTCTCATTTCAACATATTTCGTCT 59.179 34.615 0.00 0.00 0.00 4.18
187 188 6.904011 CAGCTCTCATTTCAACATATTTCGTC 59.096 38.462 0.00 0.00 0.00 4.20
188 189 6.372659 ACAGCTCTCATTTCAACATATTTCGT 59.627 34.615 0.00 0.00 0.00 3.85
189 190 6.685828 CACAGCTCTCATTTCAACATATTTCG 59.314 38.462 0.00 0.00 0.00 3.46
190 191 6.471519 GCACAGCTCTCATTTCAACATATTTC 59.528 38.462 0.00 0.00 0.00 2.17
191 192 6.327934 GCACAGCTCTCATTTCAACATATTT 58.672 36.000 0.00 0.00 0.00 1.40
192 193 5.448225 CGCACAGCTCTCATTTCAACATATT 60.448 40.000 0.00 0.00 0.00 1.28
193 194 4.034858 CGCACAGCTCTCATTTCAACATAT 59.965 41.667 0.00 0.00 0.00 1.78
194 195 3.371898 CGCACAGCTCTCATTTCAACATA 59.628 43.478 0.00 0.00 0.00 2.29
195 196 2.161012 CGCACAGCTCTCATTTCAACAT 59.839 45.455 0.00 0.00 0.00 2.71
196 197 1.532437 CGCACAGCTCTCATTTCAACA 59.468 47.619 0.00 0.00 0.00 3.33
197 198 1.800586 TCGCACAGCTCTCATTTCAAC 59.199 47.619 0.00 0.00 0.00 3.18
198 199 2.168326 TCGCACAGCTCTCATTTCAA 57.832 45.000 0.00 0.00 0.00 2.69
199 200 2.391616 ATCGCACAGCTCTCATTTCA 57.608 45.000 0.00 0.00 0.00 2.69
200 201 3.754188 AAATCGCACAGCTCTCATTTC 57.246 42.857 0.00 0.00 0.00 2.17
201 202 4.510038 AAAAATCGCACAGCTCTCATTT 57.490 36.364 0.00 0.00 0.00 2.32
224 225 8.196771 AGCATCATGTGTTAAGAAACTCAAAAA 58.803 29.630 0.00 0.00 41.12 1.94
225 226 7.715657 AGCATCATGTGTTAAGAAACTCAAAA 58.284 30.769 0.00 0.00 41.12 2.44
226 227 7.275888 AGCATCATGTGTTAAGAAACTCAAA 57.724 32.000 0.00 0.00 41.12 2.69
227 228 6.882610 AGCATCATGTGTTAAGAAACTCAA 57.117 33.333 0.00 0.00 41.12 3.02
228 229 8.565896 AATAGCATCATGTGTTAAGAAACTCA 57.434 30.769 0.00 0.00 41.76 3.41
229 230 8.668353 TGAATAGCATCATGTGTTAAGAAACTC 58.332 33.333 0.00 0.00 36.51 3.01
230 231 8.565896 TGAATAGCATCATGTGTTAAGAAACT 57.434 30.769 0.00 0.00 36.51 2.66
246 247 2.224719 GGCCTGTGAGGATGAATAGCAT 60.225 50.000 0.00 0.00 37.67 3.79
247 248 1.141657 GGCCTGTGAGGATGAATAGCA 59.858 52.381 0.00 0.00 37.67 3.49
248 249 1.141657 TGGCCTGTGAGGATGAATAGC 59.858 52.381 3.32 0.00 37.67 2.97
249 250 3.072038 TCATGGCCTGTGAGGATGAATAG 59.928 47.826 3.32 0.00 37.67 1.73
250 251 3.047857 TCATGGCCTGTGAGGATGAATA 58.952 45.455 3.32 0.00 37.67 1.75
251 252 1.848388 TCATGGCCTGTGAGGATGAAT 59.152 47.619 3.32 0.00 37.67 2.57
252 253 1.288188 TCATGGCCTGTGAGGATGAA 58.712 50.000 3.32 0.00 37.67 2.57
253 254 1.288188 TTCATGGCCTGTGAGGATGA 58.712 50.000 3.32 0.00 37.67 2.92
254 255 2.359981 ATTCATGGCCTGTGAGGATG 57.640 50.000 3.32 0.00 37.67 3.51
255 256 3.393426 AAATTCATGGCCTGTGAGGAT 57.607 42.857 3.32 0.00 37.67 3.24
256 257 2.905415 AAATTCATGGCCTGTGAGGA 57.095 45.000 3.32 0.00 37.67 3.71
257 258 4.467769 AGATAAATTCATGGCCTGTGAGG 58.532 43.478 3.32 0.00 38.80 3.86
258 259 6.461110 AAAGATAAATTCATGGCCTGTGAG 57.539 37.500 3.32 0.00 0.00 3.51
259 260 6.855763 AAAAGATAAATTCATGGCCTGTGA 57.144 33.333 3.32 5.72 0.00 3.58
287 288 5.007039 TGAGATTACTTGAAATGCGATCTGC 59.993 40.000 3.07 3.07 46.70 4.26
288 289 6.594284 TGAGATTACTTGAAATGCGATCTG 57.406 37.500 0.00 0.00 0.00 2.90
289 290 7.714377 AGAATGAGATTACTTGAAATGCGATCT 59.286 33.333 0.00 0.00 0.00 2.75
290 291 7.797587 CAGAATGAGATTACTTGAAATGCGATC 59.202 37.037 0.00 0.00 39.69 3.69
291 292 7.496920 TCAGAATGAGATTACTTGAAATGCGAT 59.503 33.333 0.00 0.00 42.56 4.58
292 293 6.818142 TCAGAATGAGATTACTTGAAATGCGA 59.182 34.615 0.00 0.00 42.56 5.10
293 294 7.008440 TCAGAATGAGATTACTTGAAATGCG 57.992 36.000 0.00 0.00 42.56 4.73
310 311 9.676195 TGTGTATGTGTGTAAAATTTCAGAATG 57.324 29.630 0.00 0.00 37.54 2.67
344 345 9.915629 ACTGAAACAATTGTACAAGTAAACAAA 57.084 25.926 12.39 0.00 38.95 2.83
345 346 9.915629 AACTGAAACAATTGTACAAGTAAACAA 57.084 25.926 12.39 0.00 39.73 2.83
346 347 9.915629 AAACTGAAACAATTGTACAAGTAAACA 57.084 25.926 12.39 8.78 0.00 2.83
375 376 9.277783 TGATTCAAACCTTTTCAGTTTCAAAAA 57.722 25.926 0.00 0.00 35.28 1.94
376 377 8.839310 TGATTCAAACCTTTTCAGTTTCAAAA 57.161 26.923 0.00 0.00 35.28 2.44
377 378 8.093927 ACTGATTCAAACCTTTTCAGTTTCAAA 58.906 29.630 0.00 0.00 43.24 2.69
378 379 7.610865 ACTGATTCAAACCTTTTCAGTTTCAA 58.389 30.769 0.00 0.00 43.24 2.69
379 380 7.169158 ACTGATTCAAACCTTTTCAGTTTCA 57.831 32.000 0.00 0.00 43.24 2.69
383 384 6.071391 ACACAACTGATTCAAACCTTTTCAGT 60.071 34.615 0.00 0.00 46.62 3.41
384 385 6.332630 ACACAACTGATTCAAACCTTTTCAG 58.667 36.000 0.00 0.00 39.70 3.02
385 386 6.279513 ACACAACTGATTCAAACCTTTTCA 57.720 33.333 0.00 0.00 0.00 2.69
386 387 5.455525 CGACACAACTGATTCAAACCTTTTC 59.544 40.000 0.00 0.00 0.00 2.29
387 388 5.124776 TCGACACAACTGATTCAAACCTTTT 59.875 36.000 0.00 0.00 0.00 2.27
388 389 4.638421 TCGACACAACTGATTCAAACCTTT 59.362 37.500 0.00 0.00 0.00 3.11
389 390 4.035208 GTCGACACAACTGATTCAAACCTT 59.965 41.667 11.55 0.00 0.00 3.50
390 391 3.560068 GTCGACACAACTGATTCAAACCT 59.440 43.478 11.55 0.00 0.00 3.50
391 392 3.603857 CGTCGACACAACTGATTCAAACC 60.604 47.826 17.16 0.00 0.00 3.27
392 393 3.531982 CGTCGACACAACTGATTCAAAC 58.468 45.455 17.16 0.00 0.00 2.93
393 394 2.542178 CCGTCGACACAACTGATTCAAA 59.458 45.455 17.16 0.00 0.00 2.69
394 395 2.131972 CCGTCGACACAACTGATTCAA 58.868 47.619 17.16 0.00 0.00 2.69
395 396 1.604438 CCCGTCGACACAACTGATTCA 60.604 52.381 17.16 0.00 0.00 2.57
396 397 1.068474 CCCGTCGACACAACTGATTC 58.932 55.000 17.16 0.00 0.00 2.52
397 398 0.677288 TCCCGTCGACACAACTGATT 59.323 50.000 17.16 0.00 0.00 2.57
398 399 0.243907 CTCCCGTCGACACAACTGAT 59.756 55.000 17.16 0.00 0.00 2.90
399 400 1.658114 CTCCCGTCGACACAACTGA 59.342 57.895 17.16 1.31 0.00 3.41
400 401 1.372997 CCTCCCGTCGACACAACTG 60.373 63.158 17.16 0.00 0.00 3.16
401 402 3.048602 CCTCCCGTCGACACAACT 58.951 61.111 17.16 0.00 0.00 3.16
402 403 2.737376 GCCTCCCGTCGACACAAC 60.737 66.667 17.16 0.00 0.00 3.32
403 404 3.998672 GGCCTCCCGTCGACACAA 61.999 66.667 17.16 0.00 0.00 3.33
426 427 1.615392 CTTTCCAGTGAGGCCTTTTGG 59.385 52.381 19.73 19.73 44.18 3.28
427 428 2.555757 CTCTTTCCAGTGAGGCCTTTTG 59.444 50.000 6.77 5.87 37.29 2.44
428 429 2.443255 TCTCTTTCCAGTGAGGCCTTTT 59.557 45.455 6.77 0.00 37.29 2.27
429 430 2.057922 TCTCTTTCCAGTGAGGCCTTT 58.942 47.619 6.77 0.00 37.29 3.11
430 431 1.734655 TCTCTTTCCAGTGAGGCCTT 58.265 50.000 6.77 0.00 37.29 4.35
431 432 1.734655 TTCTCTTTCCAGTGAGGCCT 58.265 50.000 3.86 3.86 37.29 5.19
432 433 2.155279 GTTTCTCTTTCCAGTGAGGCC 58.845 52.381 0.00 0.00 37.29 5.19
433 434 2.851195 TGTTTCTCTTTCCAGTGAGGC 58.149 47.619 0.00 0.00 37.29 4.70
434 435 4.633565 GCTATGTTTCTCTTTCCAGTGAGG 59.366 45.833 0.00 0.00 39.47 3.86
435 436 5.240891 TGCTATGTTTCTCTTTCCAGTGAG 58.759 41.667 0.00 0.00 0.00 3.51
436 437 5.227569 TGCTATGTTTCTCTTTCCAGTGA 57.772 39.130 0.00 0.00 0.00 3.41
437 438 7.798596 ATATGCTATGTTTCTCTTTCCAGTG 57.201 36.000 0.00 0.00 0.00 3.66
438 439 8.814038 AAATATGCTATGTTTCTCTTTCCAGT 57.186 30.769 0.00 0.00 0.00 4.00
464 465 2.032377 GTCGACGCAACTGATTTCCAAA 60.032 45.455 0.00 0.00 0.00 3.28
465 466 1.529438 GTCGACGCAACTGATTTCCAA 59.471 47.619 0.00 0.00 0.00 3.53
468 469 1.126846 CCTGTCGACGCAACTGATTTC 59.873 52.381 11.62 0.00 0.00 2.17
472 473 0.317160 ATTCCTGTCGACGCAACTGA 59.683 50.000 11.62 0.00 0.00 3.41
478 479 1.355971 TTTAGCATTCCTGTCGACGC 58.644 50.000 11.62 6.92 0.00 5.19
484 485 7.200434 TCTATCCTCTTTTTAGCATTCCTGT 57.800 36.000 0.00 0.00 0.00 4.00
486 487 7.230027 CCATCTATCCTCTTTTTAGCATTCCT 58.770 38.462 0.00 0.00 0.00 3.36
487 488 6.072230 GCCATCTATCCTCTTTTTAGCATTCC 60.072 42.308 0.00 0.00 0.00 3.01
505 506 1.810151 GCTTTTGTTGTCGGCCATCTA 59.190 47.619 2.24 0.00 0.00 1.98
536 537 6.122277 TCCTCCTTTTAGGCAATAATGTCAG 58.878 40.000 0.00 0.00 36.51 3.51
539 540 6.327386 TCTCCTCCTTTTAGGCAATAATGT 57.673 37.500 0.00 0.00 36.51 2.71
540 541 5.767168 CCTCTCCTCCTTTTAGGCAATAATG 59.233 44.000 0.00 0.00 36.51 1.90
550 551 3.165087 TCGTCACCTCTCCTCCTTTTA 57.835 47.619 0.00 0.00 0.00 1.52
567 568 3.869065 TCTCCTCAGTTTTGTTGTTCGT 58.131 40.909 0.00 0.00 0.00 3.85
623 626 9.455847 CCTATGATAAAGCAGTAAAGCAAATTC 57.544 33.333 0.00 0.00 36.85 2.17
650 653 5.523369 TGACTATGATACGTGCAGATCTTG 58.477 41.667 0.00 0.00 0.00 3.02
651 654 5.774498 TGACTATGATACGTGCAGATCTT 57.226 39.130 0.00 0.00 0.00 2.40
652 655 5.774498 TTGACTATGATACGTGCAGATCT 57.226 39.130 0.00 0.00 0.00 2.75
653 656 5.108217 CGTTTGACTATGATACGTGCAGATC 60.108 44.000 0.00 0.00 0.00 2.75
654 657 4.740205 CGTTTGACTATGATACGTGCAGAT 59.260 41.667 0.00 0.00 0.00 2.90
655 658 4.102649 CGTTTGACTATGATACGTGCAGA 58.897 43.478 0.00 0.00 0.00 4.26
656 659 3.242944 CCGTTTGACTATGATACGTGCAG 59.757 47.826 0.00 0.00 0.00 4.41
660 663 4.707030 TGACCGTTTGACTATGATACGT 57.293 40.909 0.00 0.00 0.00 3.57
661 664 6.559703 CGATTTGACCGTTTGACTATGATACG 60.560 42.308 0.00 0.00 0.00 3.06
668 671 3.006110 ACCTCGATTTGACCGTTTGACTA 59.994 43.478 0.00 0.00 0.00 2.59
673 676 1.609841 GGGACCTCGATTTGACCGTTT 60.610 52.381 0.00 0.00 0.00 3.60
689 692 5.642063 TCGTTCTGTGATCTAATTTTGGGAC 59.358 40.000 0.00 0.00 0.00 4.46
708 711 5.816919 TCTTGAAAGTTGTTCCATTCGTTC 58.183 37.500 0.00 0.00 0.00 3.95
774 778 6.261603 CCGTAAAAAGACTAGAAACCCTGTTT 59.738 38.462 0.00 0.00 0.00 2.83
791 798 2.653234 TGCCTTGTACCCCGTAAAAA 57.347 45.000 0.00 0.00 0.00 1.94
839 846 2.798689 CCAGCGAGACGATTCGGA 59.201 61.111 11.29 0.00 40.79 4.55
887 905 2.287977 TCCGTGTTTCTCTCTGGAGA 57.712 50.000 0.20 0.20 45.75 3.71
888 906 2.035961 TGTTCCGTGTTTCTCTCTGGAG 59.964 50.000 0.00 0.00 40.73 3.86
909 929 5.531287 GTCCACTGGTTAGTCAACATTTTCT 59.469 40.000 0.00 0.00 36.29 2.52
1349 1371 1.605165 GAATGGTTCGGTTGGGGCA 60.605 57.895 0.00 0.00 0.00 5.36
1411 1433 2.202703 AGATAACGCGCCGGTGAC 60.203 61.111 21.76 9.37 0.00 3.67
1649 1671 4.450053 AGCAGTAGATGGATGAAAAGAGC 58.550 43.478 0.00 0.00 0.00 4.09
1673 1695 0.318120 CACAGGAAATGGGGCACAAC 59.682 55.000 0.00 0.00 0.00 3.32
1694 1717 4.844349 AATTGGCACCTGACTACATACT 57.156 40.909 0.00 0.00 0.00 2.12
1695 1718 5.183140 ACAAAATTGGCACCTGACTACATAC 59.817 40.000 0.00 0.00 0.00 2.39
1702 1725 7.412891 GCATTATAAACAAAATTGGCACCTGAC 60.413 37.037 0.00 0.00 0.00 3.51
1714 1737 7.115095 GCCTTACACGTTGCATTATAAACAAAA 59.885 33.333 6.01 0.00 0.00 2.44
1716 1739 6.087522 GCCTTACACGTTGCATTATAAACAA 58.912 36.000 0.00 0.00 0.00 2.83
1717 1740 5.632959 GCCTTACACGTTGCATTATAAACA 58.367 37.500 0.00 0.00 0.00 2.83
1718 1741 4.726704 CGCCTTACACGTTGCATTATAAAC 59.273 41.667 0.00 0.00 0.00 2.01
1722 1767 1.063469 GCGCCTTACACGTTGCATTAT 59.937 47.619 0.00 0.00 0.00 1.28
1748 1793 7.825331 TGTCCATAATTCTAACAACAAACCA 57.175 32.000 0.00 0.00 0.00 3.67
1901 1948 2.500910 TGCCCATTTGTTCCCATGAATC 59.499 45.455 0.00 0.00 31.98 2.52
1916 1963 1.070758 AGTTTCGCGATAGATGCCCAT 59.929 47.619 10.88 0.00 39.76 4.00
1970 2017 3.449018 GCCTCAGAGTAGAATTCCAGTGA 59.551 47.826 0.65 0.00 0.00 3.41
2396 2443 1.072015 CCATGGCCACATTTGTTTGGT 59.928 47.619 8.16 0.00 34.35 3.67
2724 2773 3.009033 AGCTGGAAGTAACACATGCCTTA 59.991 43.478 0.00 0.00 35.30 2.69
2811 2860 3.181475 ACAATCACATCCAGCTACCTACG 60.181 47.826 0.00 0.00 0.00 3.51
2844 2893 8.732531 TGGAATGTAATTAGTTTTAGGGTTTCG 58.267 33.333 0.00 0.00 36.07 3.46
2863 2912 7.166851 TGGCACAATAATTTGAAATGGAATGT 58.833 30.769 0.00 0.00 36.64 2.71
2991 3041 7.156876 TGGTCTATTTTATTGAGCCAAACTG 57.843 36.000 0.00 0.00 32.80 3.16
3185 3239 6.755206 TGTAACATGGGGATCTACTTATTCG 58.245 40.000 0.00 0.00 0.00 3.34
3202 3256 4.821260 TGAACTGAAGTGCACATGTAACAT 59.179 37.500 21.04 0.00 0.00 2.71
3209 3264 7.362920 GGGTAATAAATGAACTGAAGTGCACAT 60.363 37.037 21.04 7.05 36.19 3.21
3253 3308 9.955208 TGGTTAATAGTACATACGTAACATGAG 57.045 33.333 0.00 0.00 30.95 2.90
3257 3312 9.920133 TGTTTGGTTAATAGTACATACGTAACA 57.080 29.630 0.00 0.00 30.95 2.41
3259 3314 9.071221 CGTGTTTGGTTAATAGTACATACGTAA 57.929 33.333 0.00 0.00 0.00 3.18
3260 3315 8.240682 ACGTGTTTGGTTAATAGTACATACGTA 58.759 33.333 0.00 0.00 0.00 3.57
3261 3316 7.062138 CACGTGTTTGGTTAATAGTACATACGT 59.938 37.037 7.58 0.00 0.00 3.57
3262 3317 7.062138 ACACGTGTTTGGTTAATAGTACATACG 59.938 37.037 17.22 0.00 0.00 3.06
3263 3318 8.164153 CACACGTGTTTGGTTAATAGTACATAC 58.836 37.037 20.79 0.00 0.00 2.39
3264 3319 7.331440 CCACACGTGTTTGGTTAATAGTACATA 59.669 37.037 20.79 0.00 0.00 2.29
3265 3320 6.148150 CCACACGTGTTTGGTTAATAGTACAT 59.852 38.462 20.79 0.00 0.00 2.29
3365 3535 5.697067 AGACTTGTTACAATTTACCCACCA 58.303 37.500 0.00 0.00 0.00 4.17
3381 3551 4.349930 ACACACCCAATACCTTAGACTTGT 59.650 41.667 0.00 0.00 0.00 3.16
3392 3562 1.133025 GCAGCATCACACACCCAATAC 59.867 52.381 0.00 0.00 0.00 1.89
3394 3564 1.588824 CGCAGCATCACACACCCAAT 61.589 55.000 0.00 0.00 0.00 3.16
3464 3634 1.753073 CCTGGCTGATCCAAAACATCC 59.247 52.381 0.00 0.00 46.01 3.51
3483 3653 5.221244 CCACTAATATAAAAAGCACCAGCCC 60.221 44.000 0.00 0.00 43.56 5.19
3484 3654 5.592688 TCCACTAATATAAAAAGCACCAGCC 59.407 40.000 0.00 0.00 43.56 4.85
3486 3656 8.682936 ATCTCCACTAATATAAAAAGCACCAG 57.317 34.615 0.00 0.00 0.00 4.00
3516 3686 3.035363 TGGGAAGATGTCTACCGCAATA 58.965 45.455 0.00 0.00 0.00 1.90
3557 3727 2.165641 TCACCTCATGTTCGCTCGTTAT 59.834 45.455 0.00 0.00 0.00 1.89
3558 3728 1.542472 TCACCTCATGTTCGCTCGTTA 59.458 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.