Multiple sequence alignment - TraesCS7D01G505100

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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 TraesCS7D01G505100 chr7D 100.000 2504 0 0 1 2504 610798390 610795887 0.000000e+00 4625.0
1 TraesCS7D01G505100 chr7D 91.803 122 7 2 185 303 199530089 199530210 1.540000e-37 167.0
2 TraesCS7D01G505100 chr7B 89.171 905 43 19 840 1740 699361825 699362678 0.000000e+00 1077.0
3 TraesCS7D01G505100 chr7B 89.335 647 49 9 708 1344 699524875 699524239 0.000000e+00 795.0
4 TraesCS7D01G505100 chr7B 90.186 377 28 3 968 1344 699562559 699562192 1.350000e-132 483.0
5 TraesCS7D01G505100 chr7B 84.178 493 36 14 852 1341 699354435 699354888 8.220000e-120 440.0
6 TraesCS7D01G505100 chr7B 86.893 206 19 6 192 393 82447392 82447191 9.010000e-55 224.0
7 TraesCS7D01G505100 chr7B 85.955 178 18 5 208 381 628470395 628470221 1.530000e-42 183.0
8 TraesCS7D01G505100 chr7B 93.277 119 7 1 186 303 188461500 188461382 9.210000e-40 174.0
9 TraesCS7D01G505100 chr7B 81.452 124 10 7 719 842 699361689 699361799 3.430000e-14 89.8
10 TraesCS7D01G505100 chr7B 94.545 55 2 1 1571 1625 699530396 699530343 1.600000e-12 84.2
11 TraesCS7D01G505100 chr7B 94.545 55 2 1 1571 1625 699561916 699561863 1.600000e-12 84.2
12 TraesCS7D01G505100 chr7B 97.143 35 1 0 1310 1344 699530697 699530663 2.690000e-05 60.2
13 TraesCS7D01G505100 chr3D 92.160 727 25 8 1743 2442 70707970 70707249 0.000000e+00 998.0
14 TraesCS7D01G505100 chr3D 89.694 718 39 9 1759 2449 333205134 333204425 0.000000e+00 883.0
15 TraesCS7D01G505100 chr3D 88.811 429 27 9 2033 2444 564131951 564131527 7.990000e-140 507.0
16 TraesCS7D01G505100 chr1D 91.831 710 33 3 1759 2444 159191725 159191017 0.000000e+00 966.0
17 TraesCS7D01G505100 chr1D 96.522 115 4 0 2237 2351 445251497 445251383 9.140000e-45 191.0
18 TraesCS7D01G505100 chr1D 98.750 80 1 0 2365 2444 445251519 445251598 2.600000e-30 143.0
19 TraesCS7D01G505100 chr1D 84.783 138 17 3 185 318 462751046 462750909 4.340000e-28 135.0
20 TraesCS7D01G505100 chr3A 90.371 727 42 6 1749 2448 60863487 60864212 0.000000e+00 929.0
21 TraesCS7D01G505100 chr3A 83.784 185 17 6 233 404 724639461 724639645 1.990000e-36 163.0
22 TraesCS7D01G505100 chr4A 90.379 634 28 9 1759 2360 601150613 601149981 0.000000e+00 802.0
23 TraesCS7D01G505100 chr4A 82.238 715 82 20 1759 2444 698455989 698455291 2.160000e-160 575.0
24 TraesCS7D01G505100 chr5A 89.596 644 37 7 1759 2374 15123618 15122977 0.000000e+00 791.0
25 TraesCS7D01G505100 chr5A 81.879 149 12 9 306 442 425720759 425720614 7.320000e-21 111.0
26 TraesCS7D01G505100 chr6D 85.615 716 64 15 1759 2440 29875060 29874350 0.000000e+00 715.0
27 TraesCS7D01G505100 chr2D 94.988 419 9 2 2038 2444 181585047 181585465 0.000000e+00 647.0
28 TraesCS7D01G505100 chr2D 88.433 268 18 2 1797 2052 181564875 181565141 6.730000e-81 311.0
29 TraesCS7D01G505100 chr2D 80.800 250 28 12 1342 1587 459343565 459343332 7.120000e-41 178.0
30 TraesCS7D01G505100 chr2D 97.674 43 1 0 1759 1801 181560764 181560806 9.610000e-10 75.0
31 TraesCS7D01G505100 chr7A 89.235 353 26 5 995 1344 700685334 700684991 4.950000e-117 431.0
32 TraesCS7D01G505100 chr7A 91.351 185 14 2 8 191 700686046 700685863 4.130000e-63 252.0
33 TraesCS7D01G505100 chr7A 90.566 159 10 2 1587 1740 700684751 700684593 3.260000e-49 206.0
34 TraesCS7D01G505100 chr7A 87.500 96 6 3 1452 1545 700684838 700684747 3.410000e-19 106.0
35 TraesCS7D01G505100 chr4B 88.701 177 14 5 186 357 159546452 159546627 7.020000e-51 211.0
36 TraesCS7D01G505100 chr5D 81.702 235 31 4 184 409 544282474 544282243 4.250000e-43 185.0
37 TraesCS7D01G505100 chr6A 94.017 117 6 1 185 300 78147389 78147505 2.560000e-40 176.0
38 TraesCS7D01G505100 chr6A 89.744 117 11 1 185 300 77939159 77939275 5.580000e-32 148.0
39 TraesCS7D01G505100 chr2A 80.591 237 31 9 186 407 8330735 8330971 4.280000e-38 169.0
40 TraesCS7D01G505100 chr2A 80.242 248 29 12 1346 1587 602718229 602717996 4.280000e-38 169.0
41 TraesCS7D01G505100 chr2A 86.667 120 8 3 299 412 773435933 773435816 2.610000e-25 126.0
42 TraesCS7D01G505100 chr5B 84.783 138 17 3 185 318 359154430 359154293 4.340000e-28 135.0
43 TraesCS7D01G505100 chr6B 88.785 107 6 2 306 406 567709498 567709604 2.610000e-25 126.0
44 TraesCS7D01G505100 chr3B 89.474 57 6 0 1449 1505 739889101 739889045 3.450000e-09 73.1


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 TraesCS7D01G505100 chr7D 610795887 610798390 2503 True 4625.00 4625 100.0000 1 2504 1 chr7D.!!$R1 2503
1 TraesCS7D01G505100 chr7B 699524239 699524875 636 True 795.00 795 89.3350 708 1344 1 chr7B.!!$R4 636
2 TraesCS7D01G505100 chr7B 699361689 699362678 989 False 583.40 1077 85.3115 719 1740 2 chr7B.!!$F2 1021
3 TraesCS7D01G505100 chr7B 699561863 699562559 696 True 283.60 483 92.3655 968 1625 2 chr7B.!!$R6 657
4 TraesCS7D01G505100 chr3D 70707249 70707970 721 True 998.00 998 92.1600 1743 2442 1 chr3D.!!$R1 699
5 TraesCS7D01G505100 chr3D 333204425 333205134 709 True 883.00 883 89.6940 1759 2449 1 chr3D.!!$R2 690
6 TraesCS7D01G505100 chr1D 159191017 159191725 708 True 966.00 966 91.8310 1759 2444 1 chr1D.!!$R1 685
7 TraesCS7D01G505100 chr3A 60863487 60864212 725 False 929.00 929 90.3710 1749 2448 1 chr3A.!!$F1 699
8 TraesCS7D01G505100 chr4A 601149981 601150613 632 True 802.00 802 90.3790 1759 2360 1 chr4A.!!$R1 601
9 TraesCS7D01G505100 chr4A 698455291 698455989 698 True 575.00 575 82.2380 1759 2444 1 chr4A.!!$R2 685
10 TraesCS7D01G505100 chr5A 15122977 15123618 641 True 791.00 791 89.5960 1759 2374 1 chr5A.!!$R1 615
11 TraesCS7D01G505100 chr6D 29874350 29875060 710 True 715.00 715 85.6150 1759 2440 1 chr6D.!!$R1 681
12 TraesCS7D01G505100 chr7A 700684593 700686046 1453 True 248.75 431 89.6630 8 1740 4 chr7A.!!$R1 1732

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
297 298 0.108615 CCGAAAGACTGAGCCGACAT 60.109 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1748 0.316689 AAAAAGCAAGCCGACGAACG 60.317 50.0 0.0 0.0 42.18 3.95 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
64 65 2.713967 ATGCACCATTTCAGCGCCC 61.714 57.895 2.29 0.00 0.00 6.13
66 67 2.639327 GCACCATTTCAGCGCCCTT 61.639 57.895 2.29 0.00 0.00 3.95
70 71 1.271926 ACCATTTCAGCGCCCTTAAGT 60.272 47.619 2.29 0.00 0.00 2.24
94 95 2.032620 GATTAGGAGGTCTCTTCCGCA 58.967 52.381 0.00 0.00 0.00 5.69
97 98 1.066587 GGAGGTCTCTTCCGCATCG 59.933 63.158 0.00 0.00 0.00 3.84
108 109 1.847818 TCCGCATCGTTTCCTATTCG 58.152 50.000 0.00 0.00 0.00 3.34
112 113 1.071436 GCATCGTTTCCTATTCGTCGC 60.071 52.381 0.00 0.00 0.00 5.19
130 131 1.226859 CGTCACGCACGGTGGATAT 60.227 57.895 10.60 0.00 46.96 1.63
168 169 4.980903 CACCGCACGCAACTTGGC 62.981 66.667 0.00 0.00 0.00 4.52
171 172 3.047280 CGCACGCAACTTGGCCTA 61.047 61.111 3.32 0.00 0.00 3.93
173 174 2.690778 GCACGCAACTTGGCCTAGG 61.691 63.158 18.75 3.67 0.00 3.02
174 175 2.359975 ACGCAACTTGGCCTAGGC 60.360 61.111 26.55 26.55 41.06 3.93
209 210 5.943706 TTTTTAACATAGTACAGCCGCAA 57.056 34.783 0.00 0.00 0.00 4.85
210 211 5.539582 TTTTAACATAGTACAGCCGCAAG 57.460 39.130 0.00 0.00 0.00 4.01
211 212 1.369625 AACATAGTACAGCCGCAAGC 58.630 50.000 0.00 0.00 44.25 4.01
220 221 3.951332 GCCGCAAGCGCTCATATA 58.049 55.556 12.06 0.00 38.24 0.86
221 222 1.493311 GCCGCAAGCGCTCATATAC 59.507 57.895 12.06 0.00 38.24 1.47
222 223 1.221466 GCCGCAAGCGCTCATATACA 61.221 55.000 12.06 0.00 38.24 2.29
223 224 0.508641 CCGCAAGCGCTCATATACAC 59.491 55.000 12.06 0.00 38.24 2.90
224 225 0.159554 CGCAAGCGCTCATATACACG 59.840 55.000 12.06 2.00 35.30 4.49
233 234 5.606335 CGCTCATATACACGCACATATAC 57.394 43.478 0.00 0.00 0.00 1.47
234 235 5.332707 CGCTCATATACACGCACATATACT 58.667 41.667 0.00 0.00 0.00 2.12
235 236 5.452623 CGCTCATATACACGCACATATACTC 59.547 44.000 0.00 0.00 0.00 2.59
236 237 6.322491 GCTCATATACACGCACATATACTCA 58.678 40.000 0.00 0.00 0.00 3.41
237 238 6.251589 GCTCATATACACGCACATATACTCAC 59.748 42.308 0.00 0.00 0.00 3.51
238 239 6.617879 TCATATACACGCACATATACTCACC 58.382 40.000 0.00 0.00 0.00 4.02
239 240 2.596904 ACACGCACATATACTCACCC 57.403 50.000 0.00 0.00 0.00 4.61
240 241 2.108168 ACACGCACATATACTCACCCT 58.892 47.619 0.00 0.00 0.00 4.34
241 242 3.293337 ACACGCACATATACTCACCCTA 58.707 45.455 0.00 0.00 0.00 3.53
242 243 3.895656 ACACGCACATATACTCACCCTAT 59.104 43.478 0.00 0.00 0.00 2.57
243 244 4.237724 CACGCACATATACTCACCCTATG 58.762 47.826 0.00 0.00 0.00 2.23
244 245 4.022329 CACGCACATATACTCACCCTATGA 60.022 45.833 0.00 0.00 35.45 2.15
245 246 4.587262 ACGCACATATACTCACCCTATGAA 59.413 41.667 0.00 0.00 36.69 2.57
246 247 4.923871 CGCACATATACTCACCCTATGAAC 59.076 45.833 0.00 0.00 36.69 3.18
247 248 4.923871 GCACATATACTCACCCTATGAACG 59.076 45.833 0.00 0.00 36.69 3.95
248 249 4.923871 CACATATACTCACCCTATGAACGC 59.076 45.833 0.00 0.00 36.69 4.84
249 250 4.587262 ACATATACTCACCCTATGAACGCA 59.413 41.667 0.00 0.00 36.69 5.24
250 251 5.246203 ACATATACTCACCCTATGAACGCAT 59.754 40.000 0.00 0.00 36.69 4.73
251 252 6.436218 ACATATACTCACCCTATGAACGCATA 59.564 38.462 0.00 0.00 36.69 3.14
252 253 3.454371 ACTCACCCTATGAACGCATAC 57.546 47.619 0.00 0.00 36.69 2.39
253 254 2.764010 ACTCACCCTATGAACGCATACA 59.236 45.455 0.00 0.00 36.69 2.29
254 255 3.123804 CTCACCCTATGAACGCATACAC 58.876 50.000 0.00 0.00 36.69 2.90
255 256 2.498078 TCACCCTATGAACGCATACACA 59.502 45.455 0.00 0.00 35.94 3.72
256 257 2.607635 CACCCTATGAACGCATACACAC 59.392 50.000 0.00 0.00 35.94 3.82
257 258 2.235155 ACCCTATGAACGCATACACACA 59.765 45.455 0.00 0.00 35.94 3.72
258 259 2.607635 CCCTATGAACGCATACACACAC 59.392 50.000 0.00 0.00 35.94 3.82
259 260 3.521560 CCTATGAACGCATACACACACT 58.478 45.455 0.00 0.00 35.94 3.55
260 261 3.932710 CCTATGAACGCATACACACACTT 59.067 43.478 0.00 0.00 35.94 3.16
261 262 4.391830 CCTATGAACGCATACACACACTTT 59.608 41.667 0.00 0.00 35.94 2.66
262 263 5.579119 CCTATGAACGCATACACACACTTTA 59.421 40.000 0.00 0.00 35.94 1.85
263 264 4.718858 TGAACGCATACACACACTTTAC 57.281 40.909 0.00 0.00 0.00 2.01
264 265 3.495377 TGAACGCATACACACACTTTACC 59.505 43.478 0.00 0.00 0.00 2.85
265 266 2.419667 ACGCATACACACACTTTACCC 58.580 47.619 0.00 0.00 0.00 3.69
266 267 1.735571 CGCATACACACACTTTACCCC 59.264 52.381 0.00 0.00 0.00 4.95
267 268 2.614481 CGCATACACACACTTTACCCCT 60.614 50.000 0.00 0.00 0.00 4.79
268 269 3.368635 CGCATACACACACTTTACCCCTA 60.369 47.826 0.00 0.00 0.00 3.53
269 270 4.682320 CGCATACACACACTTTACCCCTAT 60.682 45.833 0.00 0.00 0.00 2.57
270 271 4.574828 GCATACACACACTTTACCCCTATG 59.425 45.833 0.00 0.00 0.00 2.23
271 272 5.628200 GCATACACACACTTTACCCCTATGA 60.628 44.000 0.00 0.00 0.00 2.15
272 273 4.553330 ACACACACTTTACCCCTATGAG 57.447 45.455 0.00 0.00 0.00 2.90
273 274 3.270877 CACACACTTTACCCCTATGAGC 58.729 50.000 0.00 0.00 0.00 4.26
274 275 2.910319 ACACACTTTACCCCTATGAGCA 59.090 45.455 0.00 0.00 0.00 4.26
275 276 3.270877 CACACTTTACCCCTATGAGCAC 58.729 50.000 0.00 0.00 0.00 4.40
276 277 2.238898 ACACTTTACCCCTATGAGCACC 59.761 50.000 0.00 0.00 0.00 5.01
277 278 2.505819 CACTTTACCCCTATGAGCACCT 59.494 50.000 0.00 0.00 0.00 4.00
278 279 2.772515 ACTTTACCCCTATGAGCACCTC 59.227 50.000 0.00 0.00 0.00 3.85
279 280 1.802553 TTACCCCTATGAGCACCTCC 58.197 55.000 0.00 0.00 0.00 4.30
280 281 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
281 282 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
282 283 1.048724 CCCCTATGAGCACCTCCGAA 61.049 60.000 0.00 0.00 0.00 4.30
283 284 0.830648 CCCTATGAGCACCTCCGAAA 59.169 55.000 0.00 0.00 0.00 3.46
284 285 1.202580 CCCTATGAGCACCTCCGAAAG 60.203 57.143 0.00 0.00 0.00 2.62
285 286 1.757118 CCTATGAGCACCTCCGAAAGA 59.243 52.381 0.00 0.00 0.00 2.52
286 287 2.482142 CCTATGAGCACCTCCGAAAGAC 60.482 54.545 0.00 0.00 0.00 3.01
287 288 1.270907 ATGAGCACCTCCGAAAGACT 58.729 50.000 0.00 0.00 0.00 3.24
288 289 0.318441 TGAGCACCTCCGAAAGACTG 59.682 55.000 0.00 0.00 0.00 3.51
289 290 0.603569 GAGCACCTCCGAAAGACTGA 59.396 55.000 0.00 0.00 0.00 3.41
290 291 0.605589 AGCACCTCCGAAAGACTGAG 59.394 55.000 0.00 0.00 0.00 3.35
291 292 1.016653 GCACCTCCGAAAGACTGAGC 61.017 60.000 0.00 0.00 0.00 4.26
292 293 0.390472 CACCTCCGAAAGACTGAGCC 60.390 60.000 0.00 0.00 0.00 4.70
293 294 1.153745 CCTCCGAAAGACTGAGCCG 60.154 63.158 0.00 0.00 0.00 5.52
294 295 1.595993 CCTCCGAAAGACTGAGCCGA 61.596 60.000 0.00 0.00 0.00 5.54
295 296 0.456995 CTCCGAAAGACTGAGCCGAC 60.457 60.000 0.00 0.00 0.00 4.79
296 297 1.176619 TCCGAAAGACTGAGCCGACA 61.177 55.000 0.00 0.00 0.00 4.35
297 298 0.108615 CCGAAAGACTGAGCCGACAT 60.109 55.000 0.00 0.00 0.00 3.06
298 299 1.134367 CCGAAAGACTGAGCCGACATA 59.866 52.381 0.00 0.00 0.00 2.29
299 300 2.223829 CCGAAAGACTGAGCCGACATAT 60.224 50.000 0.00 0.00 0.00 1.78
300 301 3.046390 CGAAAGACTGAGCCGACATATC 58.954 50.000 0.00 0.00 0.00 1.63
301 302 3.489229 CGAAAGACTGAGCCGACATATCA 60.489 47.826 0.00 0.00 0.00 2.15
302 303 4.626042 GAAAGACTGAGCCGACATATCAT 58.374 43.478 0.00 0.00 0.00 2.45
303 304 3.657015 AGACTGAGCCGACATATCATG 57.343 47.619 0.00 0.00 0.00 3.07
316 317 5.551305 ACATATCATGTCGGAAATCCTGA 57.449 39.130 0.00 0.00 39.92 3.86
317 318 5.928976 ACATATCATGTCGGAAATCCTGAA 58.071 37.500 0.00 0.00 39.92 3.02
318 319 6.356556 ACATATCATGTCGGAAATCCTGAAA 58.643 36.000 0.00 0.00 39.92 2.69
319 320 7.000472 ACATATCATGTCGGAAATCCTGAAAT 59.000 34.615 0.00 0.00 39.92 2.17
320 321 8.156820 ACATATCATGTCGGAAATCCTGAAATA 58.843 33.333 0.00 0.00 39.92 1.40
321 322 9.002600 CATATCATGTCGGAAATCCTGAAATAA 57.997 33.333 0.00 0.00 0.00 1.40
322 323 7.880160 ATCATGTCGGAAATCCTGAAATAAA 57.120 32.000 0.00 0.00 0.00 1.40
323 324 7.880160 TCATGTCGGAAATCCTGAAATAAAT 57.120 32.000 0.00 0.00 0.00 1.40
324 325 8.292444 TCATGTCGGAAATCCTGAAATAAATT 57.708 30.769 0.00 0.00 0.00 1.82
325 326 8.405531 TCATGTCGGAAATCCTGAAATAAATTC 58.594 33.333 0.00 0.00 38.60 2.17
326 327 7.695480 TGTCGGAAATCCTGAAATAAATTCA 57.305 32.000 0.00 0.00 45.71 2.57
340 341 9.734620 TGAAATAAATTCAGGAATAAATGCGAG 57.265 29.630 0.00 0.00 43.08 5.03
341 342 8.579682 AAATAAATTCAGGAATAAATGCGAGC 57.420 30.769 0.00 0.00 0.00 5.03
342 343 5.581126 AAATTCAGGAATAAATGCGAGCA 57.419 34.783 0.00 0.00 0.00 4.26
343 344 4.558538 ATTCAGGAATAAATGCGAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
344 345 2.288666 TCAGGAATAAATGCGAGCACC 58.711 47.619 0.00 0.00 0.00 5.01
345 346 2.016318 CAGGAATAAATGCGAGCACCA 58.984 47.619 0.00 0.00 0.00 4.17
346 347 2.017049 AGGAATAAATGCGAGCACCAC 58.983 47.619 0.00 0.00 0.00 4.16
347 348 1.268032 GGAATAAATGCGAGCACCACG 60.268 52.381 0.00 0.00 0.00 4.94
348 349 1.663643 GAATAAATGCGAGCACCACGA 59.336 47.619 0.00 0.00 0.00 4.35
349 350 1.953559 ATAAATGCGAGCACCACGAT 58.046 45.000 0.00 0.00 0.00 3.73
350 351 1.732941 TAAATGCGAGCACCACGATT 58.267 45.000 0.00 0.00 0.00 3.34
351 352 0.881118 AAATGCGAGCACCACGATTT 59.119 45.000 0.00 0.00 0.00 2.17
352 353 0.168788 AATGCGAGCACCACGATTTG 59.831 50.000 0.00 0.00 0.00 2.32
353 354 0.673333 ATGCGAGCACCACGATTTGA 60.673 50.000 0.00 0.00 0.00 2.69
354 355 0.882484 TGCGAGCACCACGATTTGAA 60.882 50.000 0.00 0.00 0.00 2.69
355 356 0.452784 GCGAGCACCACGATTTGAAC 60.453 55.000 0.00 0.00 0.00 3.18
356 357 0.165944 CGAGCACCACGATTTGAACC 59.834 55.000 0.00 0.00 0.00 3.62
357 358 1.523758 GAGCACCACGATTTGAACCT 58.476 50.000 0.00 0.00 0.00 3.50
358 359 1.880027 GAGCACCACGATTTGAACCTT 59.120 47.619 0.00 0.00 0.00 3.50
359 360 1.608590 AGCACCACGATTTGAACCTTG 59.391 47.619 0.00 0.00 0.00 3.61
360 361 1.606668 GCACCACGATTTGAACCTTGA 59.393 47.619 0.00 0.00 0.00 3.02
361 362 2.228822 GCACCACGATTTGAACCTTGAT 59.771 45.455 0.00 0.00 0.00 2.57
362 363 3.438781 GCACCACGATTTGAACCTTGATA 59.561 43.478 0.00 0.00 0.00 2.15
363 364 4.437390 GCACCACGATTTGAACCTTGATAG 60.437 45.833 0.00 0.00 0.00 2.08
365 366 3.065371 CCACGATTTGAACCTTGATAGGC 59.935 47.826 0.00 0.00 46.22 3.93
366 367 3.941483 CACGATTTGAACCTTGATAGGCT 59.059 43.478 0.00 0.00 46.22 4.58
367 368 3.941483 ACGATTTGAACCTTGATAGGCTG 59.059 43.478 0.00 0.00 46.22 4.85
368 369 3.313526 CGATTTGAACCTTGATAGGCTGG 59.686 47.826 0.00 0.00 46.22 4.85
369 370 2.806945 TTGAACCTTGATAGGCTGGG 57.193 50.000 0.00 0.00 46.22 4.45
370 371 1.965414 TGAACCTTGATAGGCTGGGA 58.035 50.000 0.00 0.00 46.22 4.37
371 372 2.492025 TGAACCTTGATAGGCTGGGAT 58.508 47.619 0.00 0.00 46.22 3.85
372 373 3.664320 TGAACCTTGATAGGCTGGGATA 58.336 45.455 0.00 0.00 46.22 2.59
373 374 3.391296 TGAACCTTGATAGGCTGGGATAC 59.609 47.826 0.00 0.00 46.22 2.24
387 388 2.622064 GGATACCACAGTCACCATCC 57.378 55.000 0.00 0.00 0.00 3.51
388 389 1.837439 GGATACCACAGTCACCATCCA 59.163 52.381 0.00 0.00 30.60 3.41
389 390 2.238646 GGATACCACAGTCACCATCCAA 59.761 50.000 0.00 0.00 30.60 3.53
390 391 2.851263 TACCACAGTCACCATCCAAC 57.149 50.000 0.00 0.00 0.00 3.77
391 392 0.110486 ACCACAGTCACCATCCAACC 59.890 55.000 0.00 0.00 0.00 3.77
392 393 0.110295 CCACAGTCACCATCCAACCA 59.890 55.000 0.00 0.00 0.00 3.67
393 394 1.238439 CACAGTCACCATCCAACCAC 58.762 55.000 0.00 0.00 0.00 4.16
394 395 0.843309 ACAGTCACCATCCAACCACA 59.157 50.000 0.00 0.00 0.00 4.17
395 396 1.202806 ACAGTCACCATCCAACCACAG 60.203 52.381 0.00 0.00 0.00 3.66
396 397 0.401738 AGTCACCATCCAACCACAGG 59.598 55.000 0.00 0.00 0.00 4.00
397 398 0.110486 GTCACCATCCAACCACAGGT 59.890 55.000 0.00 0.00 37.65 4.00
407 408 4.025401 CCACAGGTTGGTTCGCGC 62.025 66.667 0.00 0.00 41.10 6.86
444 445 2.504367 ACGTGTCTTTCTTCCATTGGG 58.496 47.619 2.09 0.00 0.00 4.12
445 446 1.812571 CGTGTCTTTCTTCCATTGGGG 59.187 52.381 2.09 0.00 38.37 4.96
446 447 2.814097 CGTGTCTTTCTTCCATTGGGGT 60.814 50.000 2.09 0.00 38.11 4.95
447 448 3.230976 GTGTCTTTCTTCCATTGGGGTT 58.769 45.455 2.09 0.00 38.11 4.11
448 449 3.641436 GTGTCTTTCTTCCATTGGGGTTT 59.359 43.478 2.09 0.00 38.11 3.27
449 450 4.830600 GTGTCTTTCTTCCATTGGGGTTTA 59.169 41.667 2.09 0.00 38.11 2.01
450 451 5.048013 GTGTCTTTCTTCCATTGGGGTTTAG 60.048 44.000 2.09 0.00 38.11 1.85
451 452 4.462834 GTCTTTCTTCCATTGGGGTTTAGG 59.537 45.833 2.09 0.00 38.11 2.69
452 453 4.355588 TCTTTCTTCCATTGGGGTTTAGGA 59.644 41.667 2.09 0.00 38.11 2.94
453 454 4.750833 TTCTTCCATTGGGGTTTAGGAA 57.249 40.909 2.09 0.00 38.11 3.36
455 456 3.466395 TTCCATTGGGGTTTAGGAAGG 57.534 47.619 2.09 0.00 38.11 3.46
458 459 3.096852 CCATTGGGGTTTAGGAAGGTTC 58.903 50.000 0.00 0.00 0.00 3.62
494 495 9.996554 CCATAAACTGGGTTTTCTTTTCTATTT 57.003 29.630 0.99 0.00 41.82 1.40
522 534 8.307921 TGTTTTTACCAGCTTTTTACGTTTTT 57.692 26.923 0.00 0.00 0.00 1.94
598 616 1.780806 TGTTTTTCATGCATGTGCCG 58.219 45.000 25.43 0.12 41.18 5.69
607 625 2.356913 CATGTGCCGTCGTGTCCA 60.357 61.111 0.00 0.00 0.00 4.02
625 643 2.260869 ATGCGTGTGCCTTGTGACC 61.261 57.895 0.00 0.00 41.78 4.02
634 652 3.071479 GTGCCTTGTGACCGAAAATAGA 58.929 45.455 0.00 0.00 0.00 1.98
647 665 8.240682 TGACCGAAAATAGAATACAACATTTGG 58.759 33.333 0.00 0.00 34.12 3.28
656 674 5.185828 AGAATACAACATTTGGAAAGGGAGC 59.814 40.000 0.00 0.00 34.12 4.70
675 695 1.462616 CTTCCACGCATGATTCCCAA 58.537 50.000 0.00 0.00 0.00 4.12
676 696 2.026641 CTTCCACGCATGATTCCCAAT 58.973 47.619 0.00 0.00 0.00 3.16
711 731 1.655484 TGCCAAGCTATCATCACGTG 58.345 50.000 9.94 9.94 0.00 4.49
722 742 1.001706 TCATCACGTGCTCCTATACGC 60.002 52.381 11.67 0.00 43.63 4.42
739 759 0.806868 CGCTGTAGACACCGGAACTA 59.193 55.000 9.46 5.66 0.00 2.24
770 790 1.680338 GGACTGTTGCAACCAAGTCT 58.320 50.000 32.31 12.62 30.84 3.24
780 800 2.704572 CAACCAAGTCTGAGTCCCATC 58.295 52.381 0.00 0.00 0.00 3.51
788 808 4.469657 AGTCTGAGTCCCATCAGTAGATC 58.530 47.826 3.84 0.00 45.70 2.75
813 833 1.036707 CGAGTCCTTCTCCATCTCCC 58.963 60.000 0.00 0.00 39.84 4.30
818 838 1.366082 TCCTTCTCCATCTCCCCTTCA 59.634 52.381 0.00 0.00 0.00 3.02
868 948 1.226575 CGGATTGTACGAGAGCGCA 60.227 57.895 11.47 0.00 42.48 6.09
874 954 2.293677 TGTACGAGAGCGCATCAATT 57.706 45.000 11.47 0.00 42.48 2.32
875 955 1.926510 TGTACGAGAGCGCATCAATTG 59.073 47.619 11.47 0.00 42.48 2.32
876 956 1.927174 GTACGAGAGCGCATCAATTGT 59.073 47.619 11.47 2.80 42.48 2.71
878 958 1.001624 CGAGAGCGCATCAATTGTCA 58.998 50.000 11.47 0.00 0.00 3.58
879 959 1.394572 CGAGAGCGCATCAATTGTCAA 59.605 47.619 11.47 0.00 0.00 3.18
880 960 2.536329 CGAGAGCGCATCAATTGTCAAG 60.536 50.000 11.47 0.00 0.00 3.02
881 961 1.131883 AGAGCGCATCAATTGTCAAGC 59.868 47.619 11.47 7.82 0.00 4.01
882 962 0.171903 AGCGCATCAATTGTCAAGCC 59.828 50.000 11.47 1.30 0.00 4.35
883 963 0.109179 GCGCATCAATTGTCAAGCCA 60.109 50.000 0.30 0.00 0.00 4.75
946 1031 0.667453 TCGCACATCAGCAAGCAAAA 59.333 45.000 0.00 0.00 0.00 2.44
959 1048 0.465460 AGCAAAACGAGCAAGTCCCA 60.465 50.000 0.00 0.00 0.00 4.37
1075 1164 1.683790 CGGCGACAAACTCGTGATCC 61.684 60.000 0.00 0.00 44.92 3.36
1376 1561 1.081641 CAAAGAGGCAGCAACGCAG 60.082 57.895 0.00 0.00 0.00 5.18
1516 1703 4.674475 GTTGAAGTAGTGCTAGCTAGACC 58.326 47.826 25.15 12.91 0.00 3.85
1518 1705 4.537751 TGAAGTAGTGCTAGCTAGACCAT 58.462 43.478 25.15 8.93 0.00 3.55
1519 1706 4.339530 TGAAGTAGTGCTAGCTAGACCATG 59.660 45.833 25.15 0.00 0.00 3.66
1520 1707 3.904717 AGTAGTGCTAGCTAGACCATGT 58.095 45.455 25.15 7.91 0.00 3.21
1521 1708 5.050126 AGTAGTGCTAGCTAGACCATGTA 57.950 43.478 25.15 7.03 0.00 2.29
1522 1709 5.636123 AGTAGTGCTAGCTAGACCATGTAT 58.364 41.667 25.15 5.59 0.00 2.29
1523 1710 6.780901 AGTAGTGCTAGCTAGACCATGTATA 58.219 40.000 25.15 4.75 0.00 1.47
1524 1711 6.882140 AGTAGTGCTAGCTAGACCATGTATAG 59.118 42.308 25.15 0.00 31.41 1.31
1554 1745 7.665559 TGCTTCAACATATTTGTAGACTTTCCT 59.334 33.333 7.78 0.00 34.06 3.36
1558 1749 8.717821 TCAACATATTTGTAGACTTTCCTTTCG 58.282 33.333 0.00 0.00 34.06 3.46
1632 1823 7.073883 GGTTTTTAAACAAGTGTACTCGATCC 58.926 38.462 7.57 0.00 40.63 3.36
1710 1902 9.056005 CCTTGGATCTCTATCTCTATTCTATCG 57.944 40.741 0.00 0.00 32.29 2.92
1714 1906 9.996554 GGATCTCTATCTCTATTCTATCGATGA 57.003 37.037 8.54 0.57 32.29 2.92
1901 2098 6.485984 ACCGTGGTATCTCTAATACTGTAGTG 59.514 42.308 0.00 0.00 0.00 2.74
1989 2203 2.639065 GCCCGTTGATGTCCAGATTAA 58.361 47.619 0.00 0.00 0.00 1.40
1990 2204 3.013921 GCCCGTTGATGTCCAGATTAAA 58.986 45.455 0.00 0.00 0.00 1.52
2061 2276 0.887933 AATTCGCTGGTTGCCGATTT 59.112 45.000 0.00 0.00 38.78 2.17
2263 2505 1.547372 ACTGCTGATTGATTTGGCCAC 59.453 47.619 3.88 0.00 0.00 5.01
2264 2506 1.546923 CTGCTGATTGATTTGGCCACA 59.453 47.619 3.88 0.00 0.00 4.17
2315 2560 3.747529 GCAAAACAATAGCAGCCAAACAT 59.252 39.130 0.00 0.00 0.00 2.71
2444 2691 6.151144 CCAAAACTATACTGCCAAACTAAGCT 59.849 38.462 0.00 0.00 0.00 3.74
2448 2695 5.875359 ACTATACTGCCAAACTAAGCTTCAC 59.125 40.000 0.00 0.00 0.00 3.18
2449 2696 1.873591 ACTGCCAAACTAAGCTTCACG 59.126 47.619 0.00 0.00 0.00 4.35
2450 2697 2.143122 CTGCCAAACTAAGCTTCACGA 58.857 47.619 0.00 0.00 0.00 4.35
2451 2698 2.744202 CTGCCAAACTAAGCTTCACGAT 59.256 45.455 0.00 0.00 0.00 3.73
2452 2699 3.146066 TGCCAAACTAAGCTTCACGATT 58.854 40.909 0.00 0.00 0.00 3.34
2453 2700 3.568007 TGCCAAACTAAGCTTCACGATTT 59.432 39.130 0.00 0.00 0.00 2.17
2454 2701 4.757657 TGCCAAACTAAGCTTCACGATTTA 59.242 37.500 0.00 0.00 0.00 1.40
2455 2702 5.239744 TGCCAAACTAAGCTTCACGATTTAA 59.760 36.000 0.00 0.00 0.00 1.52
2456 2703 6.146898 GCCAAACTAAGCTTCACGATTTAAA 58.853 36.000 0.00 0.00 0.00 1.52
2457 2704 6.639279 GCCAAACTAAGCTTCACGATTTAAAA 59.361 34.615 0.00 0.00 0.00 1.52
2458 2705 7.168469 GCCAAACTAAGCTTCACGATTTAAAAA 59.832 33.333 0.00 0.00 0.00 1.94
2459 2706 8.690840 CCAAACTAAGCTTCACGATTTAAAAAG 58.309 33.333 0.00 0.00 0.00 2.27
2460 2707 9.445786 CAAACTAAGCTTCACGATTTAAAAAGA 57.554 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.735857 GGCACGGTAAGTCGCGTT 60.736 61.111 5.77 0.00 0.00 4.84
52 53 1.468054 GCACTTAAGGGCGCTGAAATG 60.468 52.381 15.17 4.21 0.00 2.32
53 54 0.811281 GCACTTAAGGGCGCTGAAAT 59.189 50.000 15.17 0.00 0.00 2.17
64 65 3.385111 AGACCTCCTAATCGGCACTTAAG 59.615 47.826 0.00 0.00 0.00 1.85
66 67 2.957006 GAGACCTCCTAATCGGCACTTA 59.043 50.000 0.00 0.00 0.00 2.24
70 71 2.032620 GAAGAGACCTCCTAATCGGCA 58.967 52.381 0.00 0.00 0.00 5.69
94 95 1.202222 ACGCGACGAATAGGAAACGAT 60.202 47.619 15.93 0.00 0.00 3.73
97 98 1.319669 GTGACGCGACGAATAGGAAAC 59.680 52.381 15.93 0.00 0.00 2.78
112 113 1.226859 ATATCCACCGTGCGTGACG 60.227 57.895 0.00 0.00 46.20 4.35
119 120 0.248054 GCGTTTGCATATCCACCGTG 60.248 55.000 0.00 0.00 42.15 4.94
120 121 2.094904 GCGTTTGCATATCCACCGT 58.905 52.632 0.00 0.00 42.15 4.83
187 188 5.618195 GCTTGCGGCTGTACTATGTTAAAAA 60.618 40.000 0.00 0.00 38.06 1.94
188 189 4.142773 GCTTGCGGCTGTACTATGTTAAAA 60.143 41.667 0.00 0.00 38.06 1.52
189 190 3.372822 GCTTGCGGCTGTACTATGTTAAA 59.627 43.478 0.00 0.00 38.06 1.52
190 191 2.933906 GCTTGCGGCTGTACTATGTTAA 59.066 45.455 0.00 0.00 38.06 2.01
191 192 2.546778 GCTTGCGGCTGTACTATGTTA 58.453 47.619 0.00 0.00 38.06 2.41
192 193 1.369625 GCTTGCGGCTGTACTATGTT 58.630 50.000 0.00 0.00 38.06 2.71
193 194 0.806102 CGCTTGCGGCTGTACTATGT 60.806 55.000 7.16 0.00 39.13 2.29
194 195 1.927210 CGCTTGCGGCTGTACTATG 59.073 57.895 7.16 0.00 39.13 2.23
195 196 1.883084 GCGCTTGCGGCTGTACTAT 60.883 57.895 16.79 0.00 39.13 2.12
196 197 2.508439 GCGCTTGCGGCTGTACTA 60.508 61.111 16.79 0.00 39.13 1.82
197 198 4.379243 AGCGCTTGCGGCTGTACT 62.379 61.111 16.79 1.17 45.69 2.73
198 199 3.854459 GAGCGCTTGCGGCTGTAC 61.854 66.667 13.26 0.00 45.69 2.90
199 200 2.291457 TATGAGCGCTTGCGGCTGTA 62.291 55.000 13.26 6.37 45.69 2.74
200 201 2.930385 ATATGAGCGCTTGCGGCTGT 62.930 55.000 13.26 7.76 45.69 4.40
201 202 0.945743 TATATGAGCGCTTGCGGCTG 60.946 55.000 13.26 0.00 45.69 4.85
202 203 0.946221 GTATATGAGCGCTTGCGGCT 60.946 55.000 13.26 13.34 45.69 5.52
203 204 1.221466 TGTATATGAGCGCTTGCGGC 61.221 55.000 13.26 0.00 45.69 6.53
204 205 0.508641 GTGTATATGAGCGCTTGCGG 59.491 55.000 13.26 0.00 45.69 5.69
205 206 0.159554 CGTGTATATGAGCGCTTGCG 59.840 55.000 13.26 10.90 45.69 4.85
206 207 0.111089 GCGTGTATATGAGCGCTTGC 60.111 55.000 13.26 0.00 45.48 4.01
211 212 5.332707 AGTATATGTGCGTGTATATGAGCG 58.667 41.667 0.00 0.00 0.00 5.03
212 213 6.251589 GTGAGTATATGTGCGTGTATATGAGC 59.748 42.308 0.00 0.00 0.00 4.26
213 214 6.747739 GGTGAGTATATGTGCGTGTATATGAG 59.252 42.308 0.00 0.00 0.00 2.90
214 215 6.349860 GGGTGAGTATATGTGCGTGTATATGA 60.350 42.308 0.00 0.00 0.00 2.15
215 216 5.805486 GGGTGAGTATATGTGCGTGTATATG 59.195 44.000 0.00 0.00 0.00 1.78
216 217 5.715279 AGGGTGAGTATATGTGCGTGTATAT 59.285 40.000 0.00 0.00 0.00 0.86
217 218 5.074804 AGGGTGAGTATATGTGCGTGTATA 58.925 41.667 0.00 0.00 0.00 1.47
218 219 3.895656 AGGGTGAGTATATGTGCGTGTAT 59.104 43.478 0.00 0.00 0.00 2.29
219 220 3.293337 AGGGTGAGTATATGTGCGTGTA 58.707 45.455 0.00 0.00 0.00 2.90
220 221 2.108168 AGGGTGAGTATATGTGCGTGT 58.892 47.619 0.00 0.00 0.00 4.49
221 222 2.890808 AGGGTGAGTATATGTGCGTG 57.109 50.000 0.00 0.00 0.00 5.34
222 223 4.149598 TCATAGGGTGAGTATATGTGCGT 58.850 43.478 0.00 0.00 31.80 5.24
223 224 4.783764 TCATAGGGTGAGTATATGTGCG 57.216 45.455 0.00 0.00 31.80 5.34
224 225 4.923871 CGTTCATAGGGTGAGTATATGTGC 59.076 45.833 0.00 0.00 38.29 4.57
225 226 4.923871 GCGTTCATAGGGTGAGTATATGTG 59.076 45.833 0.00 0.00 38.29 3.21
226 227 4.587262 TGCGTTCATAGGGTGAGTATATGT 59.413 41.667 0.00 0.00 38.29 2.29
227 228 5.134202 TGCGTTCATAGGGTGAGTATATG 57.866 43.478 0.00 0.00 38.29 1.78
228 229 6.436218 TGTATGCGTTCATAGGGTGAGTATAT 59.564 38.462 0.00 0.00 38.29 0.86
229 230 5.771165 TGTATGCGTTCATAGGGTGAGTATA 59.229 40.000 0.00 0.00 38.29 1.47
230 231 4.587262 TGTATGCGTTCATAGGGTGAGTAT 59.413 41.667 0.00 0.00 38.29 2.12
231 232 3.955551 TGTATGCGTTCATAGGGTGAGTA 59.044 43.478 0.00 0.00 38.29 2.59
232 233 2.764010 TGTATGCGTTCATAGGGTGAGT 59.236 45.455 0.00 0.00 38.29 3.41
233 234 3.123804 GTGTATGCGTTCATAGGGTGAG 58.876 50.000 0.00 0.00 38.29 3.51
234 235 2.498078 TGTGTATGCGTTCATAGGGTGA 59.502 45.455 0.00 0.00 35.96 4.02
235 236 2.607635 GTGTGTATGCGTTCATAGGGTG 59.392 50.000 0.00 0.00 35.96 4.61
236 237 2.235155 TGTGTGTATGCGTTCATAGGGT 59.765 45.455 0.00 0.00 35.96 4.34
237 238 2.607635 GTGTGTGTATGCGTTCATAGGG 59.392 50.000 0.00 0.00 35.96 3.53
238 239 3.521560 AGTGTGTGTATGCGTTCATAGG 58.478 45.455 0.00 0.00 35.96 2.57
239 240 5.530519 AAAGTGTGTGTATGCGTTCATAG 57.469 39.130 0.00 0.00 35.96 2.23
240 241 5.349270 GGTAAAGTGTGTGTATGCGTTCATA 59.651 40.000 0.00 0.00 34.22 2.15
241 242 4.153475 GGTAAAGTGTGTGTATGCGTTCAT 59.847 41.667 0.00 0.00 36.73 2.57
242 243 3.495377 GGTAAAGTGTGTGTATGCGTTCA 59.505 43.478 0.00 0.00 0.00 3.18
243 244 3.120442 GGGTAAAGTGTGTGTATGCGTTC 60.120 47.826 0.00 0.00 0.00 3.95
244 245 2.809696 GGGTAAAGTGTGTGTATGCGTT 59.190 45.455 0.00 0.00 0.00 4.84
245 246 2.419667 GGGTAAAGTGTGTGTATGCGT 58.580 47.619 0.00 0.00 0.00 5.24
246 247 1.735571 GGGGTAAAGTGTGTGTATGCG 59.264 52.381 0.00 0.00 0.00 4.73
247 248 3.067684 AGGGGTAAAGTGTGTGTATGC 57.932 47.619 0.00 0.00 0.00 3.14
248 249 5.984725 TCATAGGGGTAAAGTGTGTGTATG 58.015 41.667 0.00 0.00 0.00 2.39
249 250 5.396436 GCTCATAGGGGTAAAGTGTGTGTAT 60.396 44.000 0.00 0.00 0.00 2.29
250 251 4.081309 GCTCATAGGGGTAAAGTGTGTGTA 60.081 45.833 0.00 0.00 0.00 2.90
251 252 3.307480 GCTCATAGGGGTAAAGTGTGTGT 60.307 47.826 0.00 0.00 0.00 3.72
252 253 3.270877 GCTCATAGGGGTAAAGTGTGTG 58.729 50.000 0.00 0.00 0.00 3.82
253 254 2.910319 TGCTCATAGGGGTAAAGTGTGT 59.090 45.455 0.00 0.00 0.00 3.72
254 255 3.270877 GTGCTCATAGGGGTAAAGTGTG 58.729 50.000 0.00 0.00 0.00 3.82
255 256 2.238898 GGTGCTCATAGGGGTAAAGTGT 59.761 50.000 0.00 0.00 0.00 3.55
256 257 2.505819 AGGTGCTCATAGGGGTAAAGTG 59.494 50.000 0.00 0.00 0.00 3.16
257 258 2.772515 GAGGTGCTCATAGGGGTAAAGT 59.227 50.000 0.00 0.00 0.00 2.66
258 259 2.104963 GGAGGTGCTCATAGGGGTAAAG 59.895 54.545 0.00 0.00 31.08 1.85
259 260 2.124411 GGAGGTGCTCATAGGGGTAAA 58.876 52.381 0.00 0.00 31.08 2.01
260 261 1.802553 GGAGGTGCTCATAGGGGTAA 58.197 55.000 0.00 0.00 31.08 2.85
261 262 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
262 263 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
263 264 1.048724 TTCGGAGGTGCTCATAGGGG 61.049 60.000 0.00 0.00 31.08 4.79
264 265 0.830648 TTTCGGAGGTGCTCATAGGG 59.169 55.000 0.00 0.00 31.08 3.53
265 266 1.757118 TCTTTCGGAGGTGCTCATAGG 59.243 52.381 0.00 0.00 31.08 2.57
266 267 2.428890 AGTCTTTCGGAGGTGCTCATAG 59.571 50.000 0.00 0.00 31.08 2.23
267 268 2.166459 CAGTCTTTCGGAGGTGCTCATA 59.834 50.000 0.00 0.00 31.08 2.15
268 269 1.066573 CAGTCTTTCGGAGGTGCTCAT 60.067 52.381 0.00 0.00 31.08 2.90
269 270 0.318441 CAGTCTTTCGGAGGTGCTCA 59.682 55.000 0.00 0.00 31.08 4.26
270 271 0.603569 TCAGTCTTTCGGAGGTGCTC 59.396 55.000 0.00 0.00 0.00 4.26
271 272 0.605589 CTCAGTCTTTCGGAGGTGCT 59.394 55.000 0.00 0.00 35.32 4.40
272 273 1.016653 GCTCAGTCTTTCGGAGGTGC 61.017 60.000 0.00 0.00 38.48 5.01
273 274 0.390472 GGCTCAGTCTTTCGGAGGTG 60.390 60.000 0.00 0.00 38.48 4.00
274 275 1.878656 CGGCTCAGTCTTTCGGAGGT 61.879 60.000 0.00 0.00 38.48 3.85
275 276 1.153745 CGGCTCAGTCTTTCGGAGG 60.154 63.158 0.00 0.00 38.48 4.30
276 277 0.456995 GTCGGCTCAGTCTTTCGGAG 60.457 60.000 0.00 0.00 40.44 4.63
277 278 1.176619 TGTCGGCTCAGTCTTTCGGA 61.177 55.000 0.00 0.00 0.00 4.55
278 279 0.108615 ATGTCGGCTCAGTCTTTCGG 60.109 55.000 0.00 0.00 0.00 4.30
279 280 2.561733 TATGTCGGCTCAGTCTTTCG 57.438 50.000 0.00 0.00 0.00 3.46
280 281 4.046938 TGATATGTCGGCTCAGTCTTTC 57.953 45.455 0.00 0.00 0.00 2.62
281 282 4.141846 ACATGATATGTCGGCTCAGTCTTT 60.142 41.667 0.00 0.00 39.92 2.52
282 283 3.386078 ACATGATATGTCGGCTCAGTCTT 59.614 43.478 0.00 0.00 39.92 3.01
283 284 2.961741 ACATGATATGTCGGCTCAGTCT 59.038 45.455 0.00 0.00 39.92 3.24
284 285 3.377346 ACATGATATGTCGGCTCAGTC 57.623 47.619 0.00 0.00 39.92 3.51
295 296 6.866010 TTTCAGGATTTCCGACATGATATG 57.134 37.500 0.00 0.00 42.08 1.78
296 297 9.573166 TTTATTTCAGGATTTCCGACATGATAT 57.427 29.630 0.00 0.00 42.08 1.63
297 298 8.972458 TTTATTTCAGGATTTCCGACATGATA 57.028 30.769 0.00 0.00 42.08 2.15
298 299 7.880160 TTTATTTCAGGATTTCCGACATGAT 57.120 32.000 0.00 0.00 42.08 2.45
299 300 7.880160 ATTTATTTCAGGATTTCCGACATGA 57.120 32.000 0.00 0.00 42.08 3.07
300 301 8.190122 TGAATTTATTTCAGGATTTCCGACATG 58.810 33.333 0.00 0.00 39.44 3.21
301 302 8.292444 TGAATTTATTTCAGGATTTCCGACAT 57.708 30.769 0.00 0.00 39.44 3.06
302 303 7.695480 TGAATTTATTTCAGGATTTCCGACA 57.305 32.000 0.00 0.00 39.44 4.35
314 315 9.734620 CTCGCATTTATTCCTGAATTTATTTCA 57.265 29.630 0.00 0.00 42.09 2.69
315 316 8.694394 GCTCGCATTTATTCCTGAATTTATTTC 58.306 33.333 0.00 0.00 34.72 2.17
316 317 8.196771 TGCTCGCATTTATTCCTGAATTTATTT 58.803 29.630 0.00 0.00 32.50 1.40
317 318 7.649306 GTGCTCGCATTTATTCCTGAATTTATT 59.351 33.333 0.00 0.00 32.50 1.40
318 319 7.141363 GTGCTCGCATTTATTCCTGAATTTAT 58.859 34.615 0.00 0.00 32.50 1.40
319 320 6.459573 GGTGCTCGCATTTATTCCTGAATTTA 60.460 38.462 0.00 0.00 32.50 1.40
320 321 5.343249 GTGCTCGCATTTATTCCTGAATTT 58.657 37.500 0.00 0.00 32.50 1.82
321 322 4.202050 GGTGCTCGCATTTATTCCTGAATT 60.202 41.667 0.00 0.00 32.50 2.17
322 323 3.316308 GGTGCTCGCATTTATTCCTGAAT 59.684 43.478 0.00 0.00 34.93 2.57
323 324 2.682856 GGTGCTCGCATTTATTCCTGAA 59.317 45.455 0.00 0.00 0.00 3.02
324 325 2.288666 GGTGCTCGCATTTATTCCTGA 58.711 47.619 0.00 0.00 0.00 3.86
325 326 2.016318 TGGTGCTCGCATTTATTCCTG 58.984 47.619 0.00 0.00 0.00 3.86
326 327 2.017049 GTGGTGCTCGCATTTATTCCT 58.983 47.619 0.00 0.00 0.00 3.36
327 328 1.268032 CGTGGTGCTCGCATTTATTCC 60.268 52.381 0.00 0.00 0.00 3.01
328 329 1.663643 TCGTGGTGCTCGCATTTATTC 59.336 47.619 0.00 0.00 0.00 1.75
329 330 1.732941 TCGTGGTGCTCGCATTTATT 58.267 45.000 0.00 0.00 0.00 1.40
330 331 1.953559 ATCGTGGTGCTCGCATTTAT 58.046 45.000 0.00 0.00 0.00 1.40
331 332 1.732941 AATCGTGGTGCTCGCATTTA 58.267 45.000 0.00 0.00 0.00 1.40
332 333 0.881118 AAATCGTGGTGCTCGCATTT 59.119 45.000 0.00 0.00 0.00 2.32
333 334 0.168788 CAAATCGTGGTGCTCGCATT 59.831 50.000 0.00 0.00 0.00 3.56
334 335 0.673333 TCAAATCGTGGTGCTCGCAT 60.673 50.000 0.00 0.00 0.00 4.73
335 336 0.882484 TTCAAATCGTGGTGCTCGCA 60.882 50.000 0.00 0.00 0.00 5.10
336 337 0.452784 GTTCAAATCGTGGTGCTCGC 60.453 55.000 0.00 0.00 0.00 5.03
337 338 0.165944 GGTTCAAATCGTGGTGCTCG 59.834 55.000 0.00 0.00 0.00 5.03
338 339 1.523758 AGGTTCAAATCGTGGTGCTC 58.476 50.000 0.00 0.00 0.00 4.26
339 340 1.608590 CAAGGTTCAAATCGTGGTGCT 59.391 47.619 0.00 0.00 0.00 4.40
340 341 1.606668 TCAAGGTTCAAATCGTGGTGC 59.393 47.619 0.00 0.00 0.00 5.01
341 342 4.094887 CCTATCAAGGTTCAAATCGTGGTG 59.905 45.833 0.00 0.00 38.19 4.17
342 343 4.261801 CCTATCAAGGTTCAAATCGTGGT 58.738 43.478 0.00 0.00 38.19 4.16
343 344 3.065371 GCCTATCAAGGTTCAAATCGTGG 59.935 47.826 0.00 0.00 45.64 4.94
344 345 3.941483 AGCCTATCAAGGTTCAAATCGTG 59.059 43.478 0.00 0.00 45.64 4.35
345 346 3.941483 CAGCCTATCAAGGTTCAAATCGT 59.059 43.478 0.00 0.00 45.64 3.73
346 347 3.313526 CCAGCCTATCAAGGTTCAAATCG 59.686 47.826 0.00 0.00 45.64 3.34
347 348 3.633986 CCCAGCCTATCAAGGTTCAAATC 59.366 47.826 0.00 0.00 45.64 2.17
348 349 3.269381 TCCCAGCCTATCAAGGTTCAAAT 59.731 43.478 0.00 0.00 45.64 2.32
349 350 2.647299 TCCCAGCCTATCAAGGTTCAAA 59.353 45.455 0.00 0.00 45.64 2.69
350 351 2.274542 TCCCAGCCTATCAAGGTTCAA 58.725 47.619 0.00 0.00 45.64 2.69
351 352 1.965414 TCCCAGCCTATCAAGGTTCA 58.035 50.000 0.00 0.00 45.64 3.18
352 353 3.244596 GGTATCCCAGCCTATCAAGGTTC 60.245 52.174 0.00 0.00 45.64 3.62
353 354 2.711547 GGTATCCCAGCCTATCAAGGTT 59.288 50.000 0.00 0.00 45.64 3.50
354 355 2.339769 GGTATCCCAGCCTATCAAGGT 58.660 52.381 0.00 0.00 45.64 3.50
355 356 2.039084 GTGGTATCCCAGCCTATCAAGG 59.961 54.545 0.00 0.00 42.94 3.61
356 357 2.705658 TGTGGTATCCCAGCCTATCAAG 59.294 50.000 0.00 0.00 42.94 3.02
357 358 2.705658 CTGTGGTATCCCAGCCTATCAA 59.294 50.000 0.00 0.00 42.94 2.57
358 359 2.329267 CTGTGGTATCCCAGCCTATCA 58.671 52.381 0.00 0.00 42.94 2.15
359 360 2.300437 GACTGTGGTATCCCAGCCTATC 59.700 54.545 0.00 0.00 42.94 2.08
360 361 2.330216 GACTGTGGTATCCCAGCCTAT 58.670 52.381 0.00 0.00 42.94 2.57
361 362 1.007842 TGACTGTGGTATCCCAGCCTA 59.992 52.381 0.00 0.00 42.94 3.93
362 363 0.252696 TGACTGTGGTATCCCAGCCT 60.253 55.000 0.00 0.00 42.94 4.58
363 364 0.107654 GTGACTGTGGTATCCCAGCC 60.108 60.000 0.00 0.00 42.94 4.85
364 365 0.107654 GGTGACTGTGGTATCCCAGC 60.108 60.000 0.00 0.00 42.94 4.85
365 366 1.275666 TGGTGACTGTGGTATCCCAG 58.724 55.000 0.00 0.00 42.94 4.45
366 367 1.837439 GATGGTGACTGTGGTATCCCA 59.163 52.381 0.00 0.00 38.87 4.37
367 368 1.141053 GGATGGTGACTGTGGTATCCC 59.859 57.143 0.00 0.00 0.00 3.85
368 369 1.837439 TGGATGGTGACTGTGGTATCC 59.163 52.381 0.00 0.00 35.72 2.59
369 370 3.270877 GTTGGATGGTGACTGTGGTATC 58.729 50.000 0.00 0.00 0.00 2.24
370 371 2.026262 GGTTGGATGGTGACTGTGGTAT 60.026 50.000 0.00 0.00 0.00 2.73
371 372 1.349688 GGTTGGATGGTGACTGTGGTA 59.650 52.381 0.00 0.00 0.00 3.25
372 373 0.110486 GGTTGGATGGTGACTGTGGT 59.890 55.000 0.00 0.00 0.00 4.16
373 374 0.110295 TGGTTGGATGGTGACTGTGG 59.890 55.000 0.00 0.00 0.00 4.17
374 375 1.238439 GTGGTTGGATGGTGACTGTG 58.762 55.000 0.00 0.00 0.00 3.66
375 376 0.843309 TGTGGTTGGATGGTGACTGT 59.157 50.000 0.00 0.00 0.00 3.55
376 377 1.527034 CTGTGGTTGGATGGTGACTG 58.473 55.000 0.00 0.00 0.00 3.51
377 378 0.401738 CCTGTGGTTGGATGGTGACT 59.598 55.000 0.00 0.00 0.00 3.41
378 379 0.110486 ACCTGTGGTTGGATGGTGAC 59.890 55.000 0.00 0.00 27.29 3.67
379 380 0.850100 AACCTGTGGTTGGATGGTGA 59.150 50.000 0.71 0.00 45.07 4.02
380 381 3.437642 AACCTGTGGTTGGATGGTG 57.562 52.632 0.71 0.00 45.07 4.17
391 392 4.025401 GGCGCGAACCAACCTGTG 62.025 66.667 12.10 0.00 0.00 3.66
392 393 3.842925 ATGGCGCGAACCAACCTGT 62.843 57.895 12.10 0.00 44.65 4.00
393 394 2.625823 AATGGCGCGAACCAACCTG 61.626 57.895 12.10 0.00 44.65 4.00
394 395 2.282180 AATGGCGCGAACCAACCT 60.282 55.556 12.10 0.00 44.65 3.50
395 396 2.126502 CAATGGCGCGAACCAACC 60.127 61.111 12.10 0.00 44.65 3.77
396 397 1.729131 CACAATGGCGCGAACCAAC 60.729 57.895 12.10 0.00 44.65 3.77
397 398 2.642129 CACAATGGCGCGAACCAA 59.358 55.556 12.10 0.00 44.65 3.67
398 399 3.361158 CCACAATGGCGCGAACCA 61.361 61.111 12.10 9.63 45.82 3.67
425 426 1.812571 CCCCAATGGAAGAAAGACACG 59.187 52.381 0.00 0.00 35.39 4.49
432 433 4.750833 TTCCTAAACCCCAATGGAAGAA 57.249 40.909 0.00 0.00 38.00 2.52
438 439 4.047627 AGAACCTTCCTAAACCCCAATG 57.952 45.455 0.00 0.00 0.00 2.82
440 441 4.505367 TCTAGAACCTTCCTAAACCCCAA 58.495 43.478 0.00 0.00 0.00 4.12
455 456 5.429130 CCAGTTTATGGGAGGTTCTAGAAC 58.571 45.833 24.73 24.73 46.36 3.01
493 494 8.307921 ACGTAAAAAGCTGGTAAAAACAAAAA 57.692 26.923 0.00 0.00 0.00 1.94
494 495 7.886405 ACGTAAAAAGCTGGTAAAAACAAAA 57.114 28.000 0.00 0.00 0.00 2.44
495 496 7.886405 AACGTAAAAAGCTGGTAAAAACAAA 57.114 28.000 0.00 0.00 0.00 2.83
496 497 7.886405 AAACGTAAAAAGCTGGTAAAAACAA 57.114 28.000 0.00 0.00 0.00 2.83
573 591 5.277876 GGCACATGCATGAAAAACATTTTCA 60.278 36.000 32.75 17.59 44.36 2.69
575 593 4.319622 CGGCACATGCATGAAAAACATTTT 60.320 37.500 32.75 3.33 44.36 1.82
576 594 3.186817 CGGCACATGCATGAAAAACATTT 59.813 39.130 32.75 4.13 44.36 2.32
577 595 2.737783 CGGCACATGCATGAAAAACATT 59.262 40.909 32.75 4.93 44.36 2.71
581 599 1.665448 CGACGGCACATGCATGAAAAA 60.665 47.619 32.75 0.00 44.36 1.94
598 616 2.853210 CACACGCATGGACACGAC 59.147 61.111 0.00 0.00 0.00 4.34
607 625 2.260869 GGTCACAAGGCACACGCAT 61.261 57.895 0.00 0.00 41.24 4.73
634 652 5.086621 AGCTCCCTTTCCAAATGTTGTATT 58.913 37.500 0.00 0.00 0.00 1.89
647 665 0.678048 ATGCGTGGAAGCTCCCTTTC 60.678 55.000 0.00 0.00 35.03 2.62
651 669 0.749454 AATCATGCGTGGAAGCTCCC 60.749 55.000 5.98 0.00 35.03 4.30
656 674 1.462616 TTGGGAATCATGCGTGGAAG 58.537 50.000 5.98 0.00 0.00 3.46
681 701 7.451566 TGATGATAGCTTGGCATCTACTAAGTA 59.548 37.037 18.10 0.00 39.24 2.24
682 702 6.268617 TGATGATAGCTTGGCATCTACTAAGT 59.731 38.462 18.10 0.00 39.24 2.24
683 703 6.589523 GTGATGATAGCTTGGCATCTACTAAG 59.410 42.308 18.10 0.00 39.24 2.18
684 704 6.459066 GTGATGATAGCTTGGCATCTACTAA 58.541 40.000 18.10 2.27 39.24 2.24
685 705 5.335976 CGTGATGATAGCTTGGCATCTACTA 60.336 44.000 18.10 0.00 39.24 1.82
686 706 4.560311 CGTGATGATAGCTTGGCATCTACT 60.560 45.833 18.10 0.00 39.24 2.57
687 707 3.677121 CGTGATGATAGCTTGGCATCTAC 59.323 47.826 18.10 14.34 39.24 2.59
688 708 3.321968 ACGTGATGATAGCTTGGCATCTA 59.678 43.478 18.10 0.00 39.24 1.98
689 709 2.103771 ACGTGATGATAGCTTGGCATCT 59.896 45.455 18.10 0.00 39.24 2.90
690 710 2.222678 CACGTGATGATAGCTTGGCATC 59.777 50.000 10.90 13.23 39.02 3.91
691 711 2.216046 CACGTGATGATAGCTTGGCAT 58.784 47.619 10.90 0.00 0.00 4.40
711 731 2.030981 GGTGTCTACAGCGTATAGGAGC 60.031 54.545 0.00 0.00 34.50 4.70
722 742 3.427773 GCTTCTAGTTCCGGTGTCTACAG 60.428 52.174 0.00 1.86 0.00 2.74
770 790 2.952310 CACGATCTACTGATGGGACTCA 59.048 50.000 0.00 0.00 33.49 3.41
788 808 1.241990 TGGAGAAGGACTCGGACACG 61.242 60.000 0.00 0.00 45.76 4.49
813 833 1.359848 GTCCGCACACTGTATGAAGG 58.640 55.000 0.00 0.00 0.00 3.46
818 838 1.596934 CTGGGTCCGCACACTGTAT 59.403 57.895 0.00 0.00 0.00 2.29
874 954 8.135529 GCGTGTATATATAGATATGGCTTGACA 58.864 37.037 0.00 0.00 30.57 3.58
875 955 7.595502 GGCGTGTATATATAGATATGGCTTGAC 59.404 40.741 11.17 0.00 30.57 3.18
876 956 7.505923 AGGCGTGTATATATAGATATGGCTTGA 59.494 37.037 14.17 0.00 30.57 3.02
878 958 7.255977 CCAGGCGTGTATATATAGATATGGCTT 60.256 40.741 16.44 3.88 30.57 4.35
879 959 6.209589 CCAGGCGTGTATATATAGATATGGCT 59.790 42.308 14.17 14.17 30.57 4.75
880 960 6.015350 ACCAGGCGTGTATATATAGATATGGC 60.015 42.308 10.65 10.65 30.57 4.40
881 961 7.371159 CACCAGGCGTGTATATATAGATATGG 58.629 42.308 5.57 2.74 37.73 2.74
882 962 7.371159 CCACCAGGCGTGTATATATAGATATG 58.629 42.308 5.57 0.00 41.26 1.78
883 963 6.493802 CCCACCAGGCGTGTATATATAGATAT 59.506 42.308 5.57 0.00 41.26 1.63
946 1031 3.575351 GAGCGTGGGACTTGCTCGT 62.575 63.158 0.00 0.00 43.54 4.18
1035 1124 1.137872 GGATCATTGCTGTCGAGGAGT 59.862 52.381 0.00 0.00 0.00 3.85
1075 1164 2.126071 ATTGGCGTCGTCGAGGTG 60.126 61.111 15.66 1.14 39.71 4.00
1516 1703 9.740239 AAATATGTTGAAGCAAAGCTATACATG 57.260 29.630 16.78 0.00 38.25 3.21
1518 1705 8.739039 ACAAATATGTTGAAGCAAAGCTATACA 58.261 29.630 0.00 0.00 34.97 2.29
1521 1708 9.177608 TCTACAAATATGTTGAAGCAAAGCTAT 57.822 29.630 0.00 0.00 38.35 2.97
1522 1709 8.450964 GTCTACAAATATGTTGAAGCAAAGCTA 58.549 33.333 0.00 0.00 41.75 3.32
1523 1710 7.175641 AGTCTACAAATATGTTGAAGCAAAGCT 59.824 33.333 5.11 0.00 41.75 3.74
1524 1711 7.308435 AGTCTACAAATATGTTGAAGCAAAGC 58.692 34.615 5.11 0.00 41.75 3.51
1525 1712 9.683069 AAAGTCTACAAATATGTTGAAGCAAAG 57.317 29.630 5.11 0.00 41.75 2.77
1554 1745 1.155424 AAGCAAGCCGACGAACGAAA 61.155 50.000 0.00 0.00 45.77 3.46
1557 1748 0.316689 AAAAAGCAAGCCGACGAACG 60.317 50.000 0.00 0.00 42.18 3.95
1558 1749 2.304413 GTAAAAAGCAAGCCGACGAAC 58.696 47.619 0.00 0.00 0.00 3.95
1710 1902 9.935241 TTATCCATTATTCTGCTCTAAGTCATC 57.065 33.333 0.00 0.00 0.00 2.92
1753 1949 1.125711 ACTCCCAAACGCACCTAGGT 61.126 55.000 9.21 9.21 0.00 3.08
1754 1950 0.673644 CACTCCCAAACGCACCTAGG 60.674 60.000 7.41 7.41 0.00 3.02
1755 1951 0.320374 TCACTCCCAAACGCACCTAG 59.680 55.000 0.00 0.00 0.00 3.02
1756 1952 0.981183 ATCACTCCCAAACGCACCTA 59.019 50.000 0.00 0.00 0.00 3.08
1757 1953 0.606401 CATCACTCCCAAACGCACCT 60.606 55.000 0.00 0.00 0.00 4.00
1831 2028 6.569179 TTAAGCCAAACACCTCAAAGTATC 57.431 37.500 0.00 0.00 0.00 2.24
1863 2060 5.680594 ATACCACGGTATCTTAAACCACA 57.319 39.130 2.74 0.00 36.69 4.17
1878 2075 7.493743 ACACTACAGTATTAGAGATACCACG 57.506 40.000 0.00 0.00 0.00 4.94
1990 2204 2.684927 CGGAGGCTCCCATCAGATTTTT 60.685 50.000 27.36 0.00 31.13 1.94
2003 2217 1.073284 AGATAGAGGAGTCGGAGGCTC 59.927 57.143 5.78 5.78 40.46 4.70
2061 2276 2.915604 AGAAGCCCAGAATCCAGAAAGA 59.084 45.455 0.00 0.00 0.00 2.52
2315 2560 1.133407 GTTTTGACAAGTCCACCGCAA 59.867 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.