Multiple sequence alignment - TraesCS3A01G479700

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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 TraesCS3A01G479700 chr3A 100.000 3534 0 0 1 3534 711114387 711117920 0.000000e+00 6527.0
1 TraesCS3A01G479700 chr3A 90.533 1764 129 20 878 2618 711253948 711252200 0.000000e+00 2298.0
2 TraesCS3A01G479700 chr3A 88.921 343 20 9 196 521 11288195 11288536 1.180000e-109 407.0
3 TraesCS3A01G479700 chr3A 89.091 55 6 0 140 194 694095856 694095910 6.330000e-08 69.4
4 TraesCS3A01G479700 chr3A 92.308 39 3 0 485 523 42214696 42214658 4.930000e-04 56.5
5 TraesCS3A01G479700 chr3B 91.777 1885 105 20 753 2623 766592941 766594789 0.000000e+00 2577.0
6 TraesCS3A01G479700 chr3B 91.078 1670 128 11 878 2535 766636834 766635174 0.000000e+00 2239.0
7 TraesCS3A01G479700 chr3B 93.939 990 53 3 1240 2229 766179623 766178641 0.000000e+00 1489.0
8 TraesCS3A01G479700 chr3B 89.201 1102 78 12 1740 2810 766551765 766552856 0.000000e+00 1338.0
9 TraesCS3A01G479700 chr3B 92.393 723 54 1 2811 3533 29531071 29531792 0.000000e+00 1029.0
10 TraesCS3A01G479700 chr3B 87.363 823 86 8 892 1701 766550951 766551768 0.000000e+00 928.0
11 TraesCS3A01G479700 chr3B 85.161 775 113 2 1011 1784 795194441 795193668 0.000000e+00 793.0
12 TraesCS3A01G479700 chr3B 87.234 517 41 15 740 1252 766180582 766180087 1.840000e-157 566.0
13 TraesCS3A01G479700 chr3B 89.610 77 4 2 671 747 766182276 766182204 1.040000e-15 95.3
14 TraesCS3A01G479700 chr3B 95.556 45 2 0 480 524 71975528 71975484 4.890000e-09 73.1
15 TraesCS3A01G479700 chr3B 87.273 55 7 0 140 194 740889080 740889134 2.950000e-06 63.9
16 TraesCS3A01G479700 chr4D 90.470 1511 137 5 1011 2518 494850566 494852072 0.000000e+00 1986.0
17 TraesCS3A01G479700 chr5A 90.325 1509 136 5 1011 2516 674371416 674372917 0.000000e+00 1969.0
18 TraesCS3A01G479700 chr5A 89.118 340 20 5 196 519 520224873 520224535 1.180000e-109 407.0
19 TraesCS3A01G479700 chr5A 89.634 328 19 6 196 517 671412231 671411913 1.530000e-108 403.0
20 TraesCS3A01G479700 chr5A 87.151 358 28 7 180 521 367334514 367334869 1.190000e-104 390.0
21 TraesCS3A01G479700 chr4B 90.132 1510 142 5 1011 2520 634727707 634726205 0.000000e+00 1956.0
22 TraesCS3A01G479700 chr4B 89.868 1510 149 3 1011 2520 634764863 634766368 0.000000e+00 1938.0
23 TraesCS3A01G479700 chr3D 92.091 1315 71 20 1357 2652 575631706 575633006 0.000000e+00 1821.0
24 TraesCS3A01G479700 chr3D 86.340 1552 190 17 1011 2547 592973770 592972226 0.000000e+00 1672.0
25 TraesCS3A01G479700 chr3D 92.173 1086 70 7 1539 2612 575733644 575732562 0.000000e+00 1520.0
26 TraesCS3A01G479700 chr3D 89.531 640 38 13 681 1319 575631096 575631707 0.000000e+00 784.0
27 TraesCS3A01G479700 chr3D 87.179 195 22 3 3 194 575630302 575630496 5.940000e-53 219.0
28 TraesCS3A01G479700 chr3D 89.091 55 6 0 140 194 558220906 558220960 6.330000e-08 69.4
29 TraesCS3A01G479700 chr2A 94.167 720 42 0 2814 3533 394619483 394618764 0.000000e+00 1098.0
30 TraesCS3A01G479700 chr2A 93.490 722 46 1 2813 3533 734562234 734561513 0.000000e+00 1072.0
31 TraesCS3A01G479700 chr2A 89.238 223 13 2 300 521 182038127 182038339 5.820000e-68 268.0
32 TraesCS3A01G479700 chr2A 78.261 299 34 13 228 524 694584028 694583759 2.820000e-36 163.0
33 TraesCS3A01G479700 chr2A 97.436 39 1 0 485 523 45133534 45133496 2.280000e-07 67.6
34 TraesCS3A01G479700 chr2A 94.286 35 2 0 487 521 705739951 705739985 2.000000e-03 54.7
35 TraesCS3A01G479700 chr7D 94.274 716 41 0 2818 3533 527926786 527927501 0.000000e+00 1096.0
36 TraesCS3A01G479700 chr2D 94.217 709 38 3 2825 3533 635745591 635744886 0.000000e+00 1079.0
37 TraesCS3A01G479700 chr2B 92.521 722 52 1 2814 3533 121373181 121373902 0.000000e+00 1033.0
38 TraesCS3A01G479700 chr5D 92.181 729 57 0 2805 3533 455150307 455149579 0.000000e+00 1031.0
39 TraesCS3A01G479700 chr5D 92.500 720 54 0 2814 3533 455257950 455257231 0.000000e+00 1031.0
40 TraesCS3A01G479700 chr5D 88.991 327 27 3 196 517 493411220 493411542 2.560000e-106 396.0
41 TraesCS3A01G479700 chr1B 92.149 726 55 2 2809 3533 647534368 647535092 0.000000e+00 1024.0
42 TraesCS3A01G479700 chr4A 90.691 333 21 3 196 522 45063355 45063027 5.420000e-118 435.0
43 TraesCS3A01G479700 chr7A 87.500 368 22 9 193 538 663274832 663275197 1.530000e-108 403.0
44 TraesCS3A01G479700 chr6A 92.500 280 20 1 196 474 556095171 556094892 1.980000e-107 399.0
45 TraesCS3A01G479700 chr1A 87.209 344 27 5 190 517 97163776 97164118 3.330000e-100 375.0


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 TraesCS3A01G479700 chr3A 711114387 711117920 3533 False 6527.000000 6527 100.000000 1 3534 1 chr3A.!!$F3 3533
1 TraesCS3A01G479700 chr3A 711252200 711253948 1748 True 2298.000000 2298 90.533000 878 2618 1 chr3A.!!$R2 1740
2 TraesCS3A01G479700 chr3B 766592941 766594789 1848 False 2577.000000 2577 91.777000 753 2623 1 chr3B.!!$F3 1870
3 TraesCS3A01G479700 chr3B 766635174 766636834 1660 True 2239.000000 2239 91.078000 878 2535 1 chr3B.!!$R2 1657
4 TraesCS3A01G479700 chr3B 766550951 766552856 1905 False 1133.000000 1338 88.282000 892 2810 2 chr3B.!!$F4 1918
5 TraesCS3A01G479700 chr3B 29531071 29531792 721 False 1029.000000 1029 92.393000 2811 3533 1 chr3B.!!$F1 722
6 TraesCS3A01G479700 chr3B 795193668 795194441 773 True 793.000000 793 85.161000 1011 1784 1 chr3B.!!$R3 773
7 TraesCS3A01G479700 chr3B 766178641 766182276 3635 True 716.766667 1489 90.261000 671 2229 3 chr3B.!!$R4 1558
8 TraesCS3A01G479700 chr4D 494850566 494852072 1506 False 1986.000000 1986 90.470000 1011 2518 1 chr4D.!!$F1 1507
9 TraesCS3A01G479700 chr5A 674371416 674372917 1501 False 1969.000000 1969 90.325000 1011 2516 1 chr5A.!!$F2 1505
10 TraesCS3A01G479700 chr4B 634726205 634727707 1502 True 1956.000000 1956 90.132000 1011 2520 1 chr4B.!!$R1 1509
11 TraesCS3A01G479700 chr4B 634764863 634766368 1505 False 1938.000000 1938 89.868000 1011 2520 1 chr4B.!!$F1 1509
12 TraesCS3A01G479700 chr3D 592972226 592973770 1544 True 1672.000000 1672 86.340000 1011 2547 1 chr3D.!!$R2 1536
13 TraesCS3A01G479700 chr3D 575732562 575733644 1082 True 1520.000000 1520 92.173000 1539 2612 1 chr3D.!!$R1 1073
14 TraesCS3A01G479700 chr3D 575630302 575633006 2704 False 941.333333 1821 89.600333 3 2652 3 chr3D.!!$F2 2649
15 TraesCS3A01G479700 chr2A 394618764 394619483 719 True 1098.000000 1098 94.167000 2814 3533 1 chr2A.!!$R2 719
16 TraesCS3A01G479700 chr2A 734561513 734562234 721 True 1072.000000 1072 93.490000 2813 3533 1 chr2A.!!$R4 720
17 TraesCS3A01G479700 chr7D 527926786 527927501 715 False 1096.000000 1096 94.274000 2818 3533 1 chr7D.!!$F1 715
18 TraesCS3A01G479700 chr2D 635744886 635745591 705 True 1079.000000 1079 94.217000 2825 3533 1 chr2D.!!$R1 708
19 TraesCS3A01G479700 chr2B 121373181 121373902 721 False 1033.000000 1033 92.521000 2814 3533 1 chr2B.!!$F1 719
20 TraesCS3A01G479700 chr5D 455149579 455150307 728 True 1031.000000 1031 92.181000 2805 3533 1 chr5D.!!$R1 728
21 TraesCS3A01G479700 chr5D 455257231 455257950 719 True 1031.000000 1031 92.500000 2814 3533 1 chr5D.!!$R2 719
22 TraesCS3A01G479700 chr1B 647534368 647535092 724 False 1024.000000 1024 92.149000 2809 3533 1 chr1B.!!$F1 724

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
377 381 0.106669 GCCGGGCCTCTTCCTTAAAT 60.107 55.000 8.12 0.0 0.00 1.40 F
876 2949 0.179045 AACTCCATCGGGCTACATGC 60.179 55.000 0.00 0.0 41.94 4.06 F
1072 3166 1.961394 TGTTCTACTGCTTCCACGTCT 59.039 47.619 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 4411 0.945813 GTCGTCGATGTAGGAGGAGG 59.054 60.000 4.21 0.0 0.00 4.30 R
2042 4644 1.594833 GGTCGTAGGTCACCATGCA 59.405 57.895 0.00 0.0 32.33 3.96 R
2947 5576 2.229675 TCAGTAGCGCATGAGATTGG 57.770 50.000 11.47 0.0 0.00 3.16 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
36 37 3.315142 CTTCTGCTACAGCCGGGCA 62.315 63.158 23.09 2.24 41.18 5.36
47 50 1.032114 AGCCGGGCAAGATTTAGCAC 61.032 55.000 23.09 0.00 0.00 4.40
67 70 4.026744 CACCCACTTCATTCTCTCTCCTA 58.973 47.826 0.00 0.00 0.00 2.94
68 71 4.653341 CACCCACTTCATTCTCTCTCCTAT 59.347 45.833 0.00 0.00 0.00 2.57
75 78 8.256605 CACTTCATTCTCTCTCCTATTTTCTCA 58.743 37.037 0.00 0.00 0.00 3.27
88 91 7.394816 TCCTATTTTCTCACCTTTCCAACTAG 58.605 38.462 0.00 0.00 0.00 2.57
118 121 3.785486 TGATATCGCACATGCTATAGCC 58.215 45.455 21.84 5.12 41.18 3.93
174 178 6.741240 GCATTGGGTGGTTGTCTCTAAAAATT 60.741 38.462 0.00 0.00 0.00 1.82
177 181 7.279750 TGGGTGGTTGTCTCTAAAAATTTAC 57.720 36.000 0.00 0.00 0.00 2.01
180 184 7.143340 GGTGGTTGTCTCTAAAAATTTACCAC 58.857 38.462 19.16 19.16 41.18 4.16
183 187 7.507616 TGGTTGTCTCTAAAAATTTACCACCAT 59.492 33.333 7.88 0.00 0.00 3.55
187 191 9.667107 TGTCTCTAAAAATTTACCACCATCTAG 57.333 33.333 0.00 0.00 0.00 2.43
188 192 9.668497 GTCTCTAAAAATTTACCACCATCTAGT 57.332 33.333 0.00 0.00 0.00 2.57
194 198 8.747538 AAAATTTACCACCATCTAGTATGACC 57.252 34.615 0.00 0.00 0.00 4.02
195 199 7.446106 AATTTACCACCATCTAGTATGACCA 57.554 36.000 4.36 0.00 0.00 4.02
196 200 7.633018 ATTTACCACCATCTAGTATGACCAT 57.367 36.000 4.36 0.00 0.00 3.55
197 201 8.736097 ATTTACCACCATCTAGTATGACCATA 57.264 34.615 4.36 0.00 0.00 2.74
198 202 7.534723 TTACCACCATCTAGTATGACCATAC 57.465 40.000 11.19 11.19 42.96 2.39
199 203 4.838986 ACCACCATCTAGTATGACCATACC 59.161 45.833 14.54 0.66 43.51 2.73
200 204 5.087323 CCACCATCTAGTATGACCATACCT 58.913 45.833 14.54 6.85 43.51 3.08
201 205 5.047021 CCACCATCTAGTATGACCATACCTG 60.047 48.000 14.54 9.15 43.51 4.00
206 210 2.706350 AGTATGACCATACCTGGCCAT 58.294 47.619 5.51 0.00 46.25 4.40
207 211 3.056080 AGTATGACCATACCTGGCCATT 58.944 45.455 5.51 0.00 42.41 3.16
208 212 2.664402 ATGACCATACCTGGCCATTC 57.336 50.000 5.51 0.00 42.41 2.67
209 213 1.145738 ATGACCATACCTGGCCATTCC 59.854 52.381 5.51 0.00 42.41 3.01
210 214 3.240904 ATGACCATACCTGGCCATTCCT 61.241 50.000 5.51 0.00 42.41 3.36
211 215 3.733709 CCATACCTGGCCATTCCTC 57.266 57.895 5.51 0.00 35.23 3.71
212 216 0.846015 CCATACCTGGCCATTCCTCA 59.154 55.000 5.51 0.00 35.23 3.86
213 217 1.202855 CCATACCTGGCCATTCCTCAG 60.203 57.143 5.51 0.00 35.23 3.35
219 223 4.883354 GCCATTCCTCAGGCCGGG 62.883 72.222 2.18 4.49 45.18 5.73
220 224 4.883354 CCATTCCTCAGGCCGGGC 62.883 72.222 22.67 22.67 0.00 6.13
248 252 2.425592 GCCAGGCCAACCAAAACC 59.574 61.111 5.01 0.00 39.06 3.27
249 253 3.147132 CCAGGCCAACCAAAACCC 58.853 61.111 5.01 0.00 39.06 4.11
250 254 2.733945 CAGGCCAACCAAAACCCG 59.266 61.111 5.01 0.00 39.06 5.28
251 255 1.830408 CAGGCCAACCAAAACCCGA 60.830 57.895 5.01 0.00 39.06 5.14
252 256 1.830847 AGGCCAACCAAAACCCGAC 60.831 57.895 5.01 0.00 39.06 4.79
253 257 2.333581 GCCAACCAAAACCCGACG 59.666 61.111 0.00 0.00 0.00 5.12
254 258 2.333581 CCAACCAAAACCCGACGC 59.666 61.111 0.00 0.00 0.00 5.19
255 259 2.482333 CCAACCAAAACCCGACGCA 61.482 57.895 0.00 0.00 0.00 5.24
256 260 1.433879 CAACCAAAACCCGACGCAA 59.566 52.632 0.00 0.00 0.00 4.85
257 261 0.179134 CAACCAAAACCCGACGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
258 262 0.531200 AACCAAAACCCGACGCAAAA 59.469 45.000 0.00 0.00 0.00 2.44
259 263 0.531200 ACCAAAACCCGACGCAAAAA 59.469 45.000 0.00 0.00 0.00 1.94
273 277 2.600470 AAAAACCCAGGCCCGAGC 60.600 61.111 0.00 0.00 38.76 5.03
308 312 2.017049 CCGTCAGGCCTAAAAATCAGG 58.983 52.381 3.98 0.00 36.16 3.86
315 319 1.025041 CCTAAAAATCAGGCCCGAGC 58.975 55.000 0.00 0.00 38.76 5.03
327 331 4.864334 CCGAGCCTGGCCCATCAC 62.864 72.222 16.57 0.00 0.00 3.06
328 332 4.100084 CGAGCCTGGCCCATCACA 62.100 66.667 16.57 0.00 0.00 3.58
329 333 2.439156 GAGCCTGGCCCATCACAC 60.439 66.667 16.57 0.00 0.00 3.82
330 334 2.937689 AGCCTGGCCCATCACACT 60.938 61.111 16.57 0.00 0.00 3.55
331 335 1.616327 AGCCTGGCCCATCACACTA 60.616 57.895 16.57 0.00 0.00 2.74
332 336 1.207488 AGCCTGGCCCATCACACTAA 61.207 55.000 16.57 0.00 0.00 2.24
333 337 0.323360 GCCTGGCCCATCACACTAAA 60.323 55.000 7.66 0.00 0.00 1.85
334 338 1.890573 GCCTGGCCCATCACACTAAAA 60.891 52.381 7.66 0.00 0.00 1.52
335 339 2.094675 CCTGGCCCATCACACTAAAAG 58.905 52.381 0.00 0.00 0.00 2.27
336 340 1.474077 CTGGCCCATCACACTAAAAGC 59.526 52.381 0.00 0.00 0.00 3.51
337 341 0.817654 GGCCCATCACACTAAAAGCC 59.182 55.000 0.00 0.00 0.00 4.35
338 342 1.616994 GGCCCATCACACTAAAAGCCT 60.617 52.381 0.00 0.00 36.22 4.58
339 343 1.474077 GCCCATCACACTAAAAGCCTG 59.526 52.381 0.00 0.00 0.00 4.85
340 344 2.795329 CCCATCACACTAAAAGCCTGT 58.205 47.619 0.00 0.00 0.00 4.00
341 345 2.749621 CCCATCACACTAAAAGCCTGTC 59.250 50.000 0.00 0.00 0.00 3.51
342 346 2.416547 CCATCACACTAAAAGCCTGTCG 59.583 50.000 0.00 0.00 0.00 4.35
343 347 2.163818 TCACACTAAAAGCCTGTCGG 57.836 50.000 0.00 0.00 0.00 4.79
344 348 1.156736 CACACTAAAAGCCTGTCGGG 58.843 55.000 0.00 0.00 38.36 5.14
374 378 3.087906 GGCCGGGCCTCTTCCTTA 61.088 66.667 30.86 0.00 46.69 2.69
375 379 2.676265 GGCCGGGCCTCTTCCTTAA 61.676 63.158 30.86 0.00 46.69 1.85
376 380 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
377 381 0.106669 GCCGGGCCTCTTCCTTAAAT 60.107 55.000 8.12 0.00 0.00 1.40
378 382 1.680338 CCGGGCCTCTTCCTTAAATG 58.320 55.000 0.84 0.00 0.00 2.32
379 383 1.211949 CCGGGCCTCTTCCTTAAATGA 59.788 52.381 0.84 0.00 0.00 2.57
380 384 2.289565 CGGGCCTCTTCCTTAAATGAC 58.710 52.381 0.84 0.00 0.00 3.06
381 385 2.289565 GGGCCTCTTCCTTAAATGACG 58.710 52.381 0.84 0.00 0.00 4.35
382 386 2.093128 GGGCCTCTTCCTTAAATGACGA 60.093 50.000 0.84 0.00 0.00 4.20
383 387 3.606687 GGCCTCTTCCTTAAATGACGAA 58.393 45.455 0.00 0.00 0.00 3.85
384 388 4.007659 GGCCTCTTCCTTAAATGACGAAA 58.992 43.478 0.00 0.00 0.00 3.46
385 389 4.640647 GGCCTCTTCCTTAAATGACGAAAT 59.359 41.667 0.00 0.00 0.00 2.17
386 390 5.220873 GGCCTCTTCCTTAAATGACGAAATC 60.221 44.000 0.00 0.00 0.00 2.17
387 391 5.502544 GCCTCTTCCTTAAATGACGAAATCG 60.503 44.000 0.48 0.48 46.33 3.34
388 392 5.810587 CCTCTTCCTTAAATGACGAAATCGA 59.189 40.000 10.16 0.00 43.02 3.59
389 393 6.237861 CCTCTTCCTTAAATGACGAAATCGAC 60.238 42.308 10.16 3.97 43.02 4.20
390 394 5.287752 TCTTCCTTAAATGACGAAATCGACG 59.712 40.000 10.16 0.00 43.02 5.12
391 395 3.861113 TCCTTAAATGACGAAATCGACGG 59.139 43.478 10.16 0.00 43.02 4.79
392 396 3.000925 CCTTAAATGACGAAATCGACGGG 59.999 47.826 10.16 0.00 43.02 5.28
393 397 0.725117 AAATGACGAAATCGACGGGC 59.275 50.000 10.16 0.00 43.02 6.13
394 398 1.087771 AATGACGAAATCGACGGGCC 61.088 55.000 10.16 0.00 43.02 5.80
395 399 2.889018 GACGAAATCGACGGGCCC 60.889 66.667 13.57 13.57 43.02 5.80
396 400 4.807039 ACGAAATCGACGGGCCCG 62.807 66.667 42.17 42.17 43.02 6.13
422 426 3.990466 CGGGCTTCGGGCTTAAAA 58.010 55.556 1.83 0.00 41.46 1.52
423 427 1.504900 CGGGCTTCGGGCTTAAAAC 59.495 57.895 1.83 0.00 41.46 2.43
424 428 1.888018 GGGCTTCGGGCTTAAAACC 59.112 57.895 1.83 0.00 41.46 3.27
425 429 0.611062 GGGCTTCGGGCTTAAAACCT 60.611 55.000 1.83 0.00 41.46 3.50
426 430 1.340308 GGGCTTCGGGCTTAAAACCTA 60.340 52.381 1.83 0.00 41.46 3.08
427 431 2.014857 GGCTTCGGGCTTAAAACCTAG 58.985 52.381 1.83 0.00 41.46 3.02
428 432 2.014857 GCTTCGGGCTTAAAACCTAGG 58.985 52.381 7.41 7.41 38.06 3.02
429 433 2.014857 CTTCGGGCTTAAAACCTAGGC 58.985 52.381 9.30 0.00 36.31 3.93
432 436 2.789842 GGCTTAAAACCTAGGCCCG 58.210 57.895 9.30 0.00 37.12 6.13
433 437 0.253894 GGCTTAAAACCTAGGCCCGA 59.746 55.000 9.30 0.00 37.12 5.14
434 438 1.664873 GCTTAAAACCTAGGCCCGAG 58.335 55.000 9.30 0.00 0.00 4.63
435 439 1.664873 CTTAAAACCTAGGCCCGAGC 58.335 55.000 9.30 0.00 38.76 5.03
452 456 4.820744 CCCGGCCCATGGACAAGG 62.821 72.222 15.22 9.16 0.00 3.61
453 457 4.047125 CCGGCCCATGGACAAGGT 62.047 66.667 15.22 0.00 0.00 3.50
454 458 2.438434 CGGCCCATGGACAAGGTC 60.438 66.667 15.22 0.00 0.00 3.85
455 459 2.438434 GGCCCATGGACAAGGTCG 60.438 66.667 15.22 0.00 32.65 4.79
456 460 2.438434 GCCCATGGACAAGGTCGG 60.438 66.667 15.22 0.00 32.65 4.79
457 461 2.272146 CCCATGGACAAGGTCGGG 59.728 66.667 15.22 0.00 32.65 5.14
458 462 2.438434 CCATGGACAAGGTCGGGC 60.438 66.667 5.56 0.00 32.65 6.13
459 463 2.438434 CATGGACAAGGTCGGGCC 60.438 66.667 0.00 0.00 32.65 5.80
460 464 2.933287 ATGGACAAGGTCGGGCCA 60.933 61.111 4.39 0.00 40.61 5.36
461 465 2.971598 ATGGACAAGGTCGGGCCAG 61.972 63.158 4.39 0.00 40.61 4.85
462 466 4.410400 GGACAAGGTCGGGCCAGG 62.410 72.222 4.39 0.00 40.61 4.45
480 484 3.263941 CCGGGTCAGGCTTTTTCG 58.736 61.111 0.00 0.00 0.00 3.46
481 485 2.332654 CCGGGTCAGGCTTTTTCGG 61.333 63.158 0.00 2.50 0.00 4.30
482 486 2.332654 CGGGTCAGGCTTTTTCGGG 61.333 63.158 0.00 0.00 0.00 5.14
483 487 2.636412 GGGTCAGGCTTTTTCGGGC 61.636 63.158 0.00 0.00 0.00 6.13
535 539 5.008712 GCCAGGTATAGTTAAGAACCAATGC 59.991 44.000 0.00 0.00 34.29 3.56
537 541 6.260936 CCAGGTATAGTTAAGAACCAATGCAG 59.739 42.308 0.00 0.00 34.29 4.41
538 542 6.823689 CAGGTATAGTTAAGAACCAATGCAGT 59.176 38.462 0.00 0.00 34.29 4.40
539 543 6.823689 AGGTATAGTTAAGAACCAATGCAGTG 59.176 38.462 7.29 7.29 34.29 3.66
540 544 6.038271 GGTATAGTTAAGAACCAATGCAGTGG 59.962 42.308 30.60 30.60 44.92 4.00
541 545 3.157087 AGTTAAGAACCAATGCAGTGGG 58.843 45.455 34.31 17.96 43.56 4.61
542 546 3.153919 GTTAAGAACCAATGCAGTGGGA 58.846 45.455 34.31 13.13 43.56 4.37
544 548 1.067295 AGAACCAATGCAGTGGGAGA 58.933 50.000 34.31 0.00 43.56 3.71
545 549 1.168714 GAACCAATGCAGTGGGAGAC 58.831 55.000 34.31 18.91 43.56 3.36
562 576 4.009002 GGAGACCCTATAGTAGGCTAACG 58.991 52.174 0.00 0.00 44.86 3.18
572 586 0.248289 TAGGCTAACGACACTTGGCC 59.752 55.000 0.00 0.00 45.79 5.36
573 587 2.038837 GGCTAACGACACTTGGCCC 61.039 63.158 0.00 0.00 40.94 5.80
575 589 1.019805 GCTAACGACACTTGGCCCTC 61.020 60.000 0.00 0.00 0.00 4.30
576 590 0.320374 CTAACGACACTTGGCCCTCA 59.680 55.000 0.00 0.00 0.00 3.86
577 591 0.981183 TAACGACACTTGGCCCTCAT 59.019 50.000 0.00 0.00 0.00 2.90
581 595 2.124570 CACTTGGCCCTCATCCGG 60.125 66.667 0.00 0.00 0.00 5.14
582 596 2.610859 ACTTGGCCCTCATCCGGT 60.611 61.111 0.00 0.00 0.00 5.28
583 597 2.231380 ACTTGGCCCTCATCCGGTT 61.231 57.895 0.00 0.00 0.00 4.44
584 598 1.000896 CTTGGCCCTCATCCGGTTT 60.001 57.895 0.00 0.00 0.00 3.27
585 599 0.611896 CTTGGCCCTCATCCGGTTTT 60.612 55.000 0.00 0.00 0.00 2.43
588 602 1.753078 GCCCTCATCCGGTTTTCCC 60.753 63.158 0.00 0.00 36.42 3.97
597 611 2.675423 GGTTTTCCCGGCTCCACC 60.675 66.667 0.00 0.00 0.00 4.61
598 612 2.114411 GTTTTCCCGGCTCCACCA 59.886 61.111 0.00 0.00 39.03 4.17
599 613 2.114411 TTTTCCCGGCTCCACCAC 59.886 61.111 0.00 0.00 39.03 4.16
611 625 2.335681 TCCACCACAGGAGATTGGTA 57.664 50.000 0.00 0.00 44.72 3.25
612 626 2.626785 TCCACCACAGGAGATTGGTAA 58.373 47.619 0.00 0.00 44.72 2.85
613 627 2.983192 TCCACCACAGGAGATTGGTAAA 59.017 45.455 0.00 0.00 44.72 2.01
614 628 3.396276 TCCACCACAGGAGATTGGTAAAA 59.604 43.478 0.00 0.00 44.72 1.52
615 629 4.044065 TCCACCACAGGAGATTGGTAAAAT 59.956 41.667 0.00 0.00 44.72 1.82
617 631 5.949354 CCACCACAGGAGATTGGTAAAATAA 59.051 40.000 0.00 0.00 44.72 1.40
618 632 6.095440 CCACCACAGGAGATTGGTAAAATAAG 59.905 42.308 0.00 0.00 44.72 1.73
619 633 6.884295 CACCACAGGAGATTGGTAAAATAAGA 59.116 38.462 0.00 0.00 44.72 2.10
620 634 7.557719 CACCACAGGAGATTGGTAAAATAAGAT 59.442 37.037 0.00 0.00 44.72 2.40
625 774 9.844257 CAGGAGATTGGTAAAATAAGATCTTCT 57.156 33.333 12.24 0.00 31.30 2.85
633 782 9.851686 TGGTAAAATAAGATCTTCTGCATATGT 57.148 29.630 12.24 0.00 0.00 2.29
637 786 4.363991 AAGATCTTCTGCATATGTCCCC 57.636 45.455 0.88 0.00 0.00 4.81
642 791 1.048160 TCTGCATATGTCCCCGCTGA 61.048 55.000 4.29 0.00 0.00 4.26
689 1132 1.664016 CCACGTGCAGCAACAGAATTC 60.664 52.381 10.91 0.00 0.00 2.17
702 1145 2.226437 ACAGAATTCATCACACGCAACC 59.774 45.455 8.44 0.00 0.00 3.77
703 1146 1.464608 AGAATTCATCACACGCAACCG 59.535 47.619 8.44 0.00 41.14 4.44
704 1147 1.463056 GAATTCATCACACGCAACCGA 59.537 47.619 0.00 0.00 38.29 4.69
705 1148 1.518325 ATTCATCACACGCAACCGAA 58.482 45.000 0.00 0.00 38.29 4.30
706 1149 1.518325 TTCATCACACGCAACCGAAT 58.482 45.000 0.00 0.00 38.29 3.34
778 2851 6.423001 ACCACATTCAGTTCGAAAGTTACTAC 59.577 38.462 0.00 0.00 33.35 2.73
780 2853 7.148787 CCACATTCAGTTCGAAAGTTACTACTC 60.149 40.741 0.00 0.00 33.35 2.59
784 2857 7.369803 TCAGTTCGAAAGTTACTACTCGTAT 57.630 36.000 13.83 2.71 31.99 3.06
786 2859 6.468319 CAGTTCGAAAGTTACTACTCGTATGG 59.532 42.308 13.83 3.37 31.99 2.74
787 2860 6.150140 AGTTCGAAAGTTACTACTCGTATGGT 59.850 38.462 13.83 0.00 31.99 3.55
788 2861 7.334421 AGTTCGAAAGTTACTACTCGTATGGTA 59.666 37.037 13.83 0.00 31.99 3.25
789 2862 7.005062 TCGAAAGTTACTACTCGTATGGTAC 57.995 40.000 13.83 0.00 31.99 3.34
867 2940 1.021390 GCCACACTCAACTCCATCGG 61.021 60.000 0.00 0.00 0.00 4.18
876 2949 0.179045 AACTCCATCGGGCTACATGC 60.179 55.000 0.00 0.00 41.94 4.06
915 2988 3.321497 GCACACTCTTCCAACTCTACAG 58.679 50.000 0.00 0.00 0.00 2.74
916 2989 3.243907 GCACACTCTTCCAACTCTACAGT 60.244 47.826 0.00 0.00 0.00 3.55
917 2990 4.551388 CACACTCTTCCAACTCTACAGTC 58.449 47.826 0.00 0.00 29.93 3.51
918 2991 4.038042 CACACTCTTCCAACTCTACAGTCA 59.962 45.833 0.00 0.00 29.93 3.41
919 2992 4.279671 ACACTCTTCCAACTCTACAGTCAG 59.720 45.833 0.00 0.00 29.93 3.51
958 3035 2.760385 CTCCTCCCCCTCGACCAC 60.760 72.222 0.00 0.00 0.00 4.16
1072 3166 1.961394 TGTTCTACTGCTTCCACGTCT 59.039 47.619 0.00 0.00 0.00 4.18
1482 4054 4.400961 GACCTGCTCCCGCTGCTT 62.401 66.667 0.00 0.00 36.97 3.91
1833 4411 4.500116 GACTCGGCGGACCTGCTC 62.500 72.222 7.21 0.00 34.52 4.26
2042 4644 2.854032 CCACCACCACCCTGGACT 60.854 66.667 0.00 0.00 40.96 3.85
2071 4684 2.360350 TACGACCCGGACGAGCTT 60.360 61.111 23.17 7.35 34.70 3.74
2299 4912 4.070265 TGGATCGGGGAGGACGGT 62.070 66.667 0.00 0.00 0.00 4.83
2307 4920 2.656069 GGGAGGACGGTAAGCTGCA 61.656 63.158 1.02 0.00 0.00 4.41
2553 5166 6.370166 AGCTGATTCAGAGTAACAAAGTTAGC 59.630 38.462 17.87 0.00 32.44 3.09
2562 5175 1.318576 ACAAAGTTAGCCTGTGTGCC 58.681 50.000 0.00 0.00 40.29 5.01
2706 5330 9.030452 AGTAAATCTCAGAGACTTGTTATGTCT 57.970 33.333 0.91 0.00 46.17 3.41
2707 5331 9.081997 GTAAATCTCAGAGACTTGTTATGTCTG 57.918 37.037 0.91 0.00 43.88 3.51
2892 5520 2.746412 TAACAGCAGGCGCCACACAT 62.746 55.000 31.54 12.52 39.83 3.21
2895 5523 3.136123 GCAGGCGCCACACATGAT 61.136 61.111 31.54 0.76 0.00 2.45
3039 5668 5.420725 TGATGCTAAGTGCTTCCTTCTTA 57.579 39.130 0.00 0.00 42.91 2.10
3077 5706 8.282592 CGAGAATCTGTCACAACTTTTATTTGA 58.717 33.333 0.00 0.00 0.00 2.69
3160 5791 9.531158 AAATACCGATATAAAGTCTAGCTAGGT 57.469 33.333 20.58 9.22 0.00 3.08
3170 5801 4.462133 AGTCTAGCTAGGTATGCTCGAAA 58.538 43.478 20.58 0.00 41.46 3.46
3365 5996 2.026636 TGGGCCTCACAACAGTATTACC 60.027 50.000 4.53 0.00 0.00 2.85
3379 6010 4.279671 CAGTATTACCTGCACCAAAACCAA 59.720 41.667 0.00 0.00 0.00 3.67
3394 6025 3.673543 AACCAACCACCACCTCTTTTA 57.326 42.857 0.00 0.00 0.00 1.52
3471 6102 5.355596 CAGTAACTTTCCAAAAACATGGCA 58.644 37.500 0.00 0.00 40.46 4.92
3484 6115 6.418057 AAAACATGGCAGATCCTTTAACAA 57.582 33.333 0.00 0.00 35.26 2.83
3524 6155 8.313292 CCCAAAAATCAAATCATTCCTCAAGTA 58.687 33.333 0.00 0.00 0.00 2.24
3533 6164 3.582647 TCATTCCTCAAGTACCAAGCTCA 59.417 43.478 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.599645 ATCTTGCCCGGCTGTAGCAG 62.600 60.000 11.61 1.37 44.36 4.24
33 34 1.839424 AGTGGGTGCTAAATCTTGCC 58.161 50.000 0.00 0.00 0.00 4.52
36 37 5.574188 AGAATGAAGTGGGTGCTAAATCTT 58.426 37.500 0.00 0.00 0.00 2.40
47 50 5.885449 AATAGGAGAGAGAATGAAGTGGG 57.115 43.478 0.00 0.00 0.00 4.61
67 70 6.200878 TCCTAGTTGGAAAGGTGAGAAAAT 57.799 37.500 0.00 0.00 42.94 1.82
68 71 5.640158 TCCTAGTTGGAAAGGTGAGAAAA 57.360 39.130 0.00 0.00 42.94 2.29
88 91 4.673580 GCATGTGCGATATCATTGGAATCC 60.674 45.833 3.12 0.00 0.00 3.01
94 97 9.306253 CAGGCTATAGCATGTGCGATATCATTG 62.306 44.444 27.08 0.71 46.46 2.82
95 98 7.399098 CAGGCTATAGCATGTGCGATATCATT 61.399 42.308 27.08 0.00 46.46 2.57
99 102 3.790091 CAGGCTATAGCATGTGCGATAT 58.210 45.455 27.08 1.24 46.46 1.63
100 103 3.236632 CAGGCTATAGCATGTGCGATA 57.763 47.619 27.08 7.44 46.46 2.92
118 121 2.559440 GGAGCAAGTCCTATTGAGCAG 58.441 52.381 0.00 0.00 42.99 4.24
174 178 6.495872 GGTATGGTCATACTAGATGGTGGTAA 59.504 42.308 17.39 0.00 42.42 2.85
177 181 5.047021 CAGGTATGGTCATACTAGATGGTGG 60.047 48.000 17.39 0.00 42.42 4.61
180 184 5.667539 CCAGGTATGGTCATACTAGATGG 57.332 47.826 17.39 15.61 42.42 3.51
194 198 1.202855 CCTGAGGAATGGCCAGGTATG 60.203 57.143 13.05 0.00 41.81 2.39
195 199 1.143813 CCTGAGGAATGGCCAGGTAT 58.856 55.000 13.05 0.00 41.81 2.73
196 200 1.635817 GCCTGAGGAATGGCCAGGTA 61.636 60.000 13.05 0.00 46.86 3.08
197 201 2.988839 GCCTGAGGAATGGCCAGGT 61.989 63.158 13.05 0.12 46.86 4.00
203 207 4.883354 GCCCGGCCTGAGGAATGG 62.883 72.222 0.65 0.00 0.00 3.16
204 208 4.883354 GGCCCGGCCTGAGGAATG 62.883 72.222 22.31 0.00 46.69 2.67
231 235 2.425592 GGTTTTGGTTGGCCTGGC 59.574 61.111 11.05 11.05 35.27 4.85
232 236 2.866726 CGGGTTTTGGTTGGCCTGG 61.867 63.158 3.32 0.00 35.27 4.45
233 237 1.830408 TCGGGTTTTGGTTGGCCTG 60.830 57.895 3.32 0.00 35.27 4.85
234 238 1.830847 GTCGGGTTTTGGTTGGCCT 60.831 57.895 3.32 0.00 35.27 5.19
235 239 2.732016 GTCGGGTTTTGGTTGGCC 59.268 61.111 0.00 0.00 0.00 5.36
236 240 2.333581 CGTCGGGTTTTGGTTGGC 59.666 61.111 0.00 0.00 0.00 4.52
237 241 2.005960 TTGCGTCGGGTTTTGGTTGG 62.006 55.000 0.00 0.00 0.00 3.77
238 242 0.179134 TTTGCGTCGGGTTTTGGTTG 60.179 50.000 0.00 0.00 0.00 3.77
239 243 0.531200 TTTTGCGTCGGGTTTTGGTT 59.469 45.000 0.00 0.00 0.00 3.67
240 244 0.531200 TTTTTGCGTCGGGTTTTGGT 59.469 45.000 0.00 0.00 0.00 3.67
241 245 3.347411 TTTTTGCGTCGGGTTTTGG 57.653 47.368 0.00 0.00 0.00 3.28
256 260 2.600470 GCTCGGGCCTGGGTTTTT 60.600 61.111 14.54 0.00 0.00 1.94
288 292 2.017049 CCTGATTTTTAGGCCTGACGG 58.983 52.381 17.99 0.00 0.00 4.79
296 300 1.025041 GCTCGGGCCTGATTTTTAGG 58.975 55.000 16.52 2.12 38.39 2.69
310 314 4.864334 GTGATGGGCCAGGCTCGG 62.864 72.222 13.78 0.00 0.00 4.63
311 315 4.100084 TGTGATGGGCCAGGCTCG 62.100 66.667 13.78 0.00 0.00 5.03
312 316 1.626356 TAGTGTGATGGGCCAGGCTC 61.626 60.000 13.78 8.27 0.00 4.70
313 317 1.207488 TTAGTGTGATGGGCCAGGCT 61.207 55.000 13.78 7.78 0.00 4.58
314 318 0.323360 TTTAGTGTGATGGGCCAGGC 60.323 55.000 13.78 1.26 0.00 4.85
315 319 2.094675 CTTTTAGTGTGATGGGCCAGG 58.905 52.381 13.78 0.00 0.00 4.45
316 320 1.474077 GCTTTTAGTGTGATGGGCCAG 59.526 52.381 13.78 0.00 0.00 4.85
317 321 1.544724 GCTTTTAGTGTGATGGGCCA 58.455 50.000 9.61 9.61 0.00 5.36
318 322 0.817654 GGCTTTTAGTGTGATGGGCC 59.182 55.000 0.00 0.00 0.00 5.80
319 323 1.474077 CAGGCTTTTAGTGTGATGGGC 59.526 52.381 0.00 0.00 0.00 5.36
320 324 2.749621 GACAGGCTTTTAGTGTGATGGG 59.250 50.000 0.00 0.00 0.00 4.00
321 325 2.416547 CGACAGGCTTTTAGTGTGATGG 59.583 50.000 0.00 0.00 0.00 3.51
322 326 2.416547 CCGACAGGCTTTTAGTGTGATG 59.583 50.000 0.00 0.00 0.00 3.07
323 327 2.615493 CCCGACAGGCTTTTAGTGTGAT 60.615 50.000 0.00 0.00 35.76 3.06
324 328 1.270625 CCCGACAGGCTTTTAGTGTGA 60.271 52.381 0.00 0.00 35.76 3.58
325 329 1.156736 CCCGACAGGCTTTTAGTGTG 58.843 55.000 0.00 0.00 35.76 3.82
326 330 3.625745 CCCGACAGGCTTTTAGTGT 57.374 52.632 0.00 0.00 35.76 3.55
358 362 0.106669 ATTTAAGGAAGAGGCCCGGC 60.107 55.000 0.00 0.00 0.00 6.13
359 363 1.211949 TCATTTAAGGAAGAGGCCCGG 59.788 52.381 0.00 0.00 0.00 5.73
360 364 2.289565 GTCATTTAAGGAAGAGGCCCG 58.710 52.381 0.00 0.00 0.00 6.13
361 365 2.093128 TCGTCATTTAAGGAAGAGGCCC 60.093 50.000 0.00 0.00 0.00 5.80
362 366 3.261981 TCGTCATTTAAGGAAGAGGCC 57.738 47.619 0.00 0.00 0.00 5.19
363 367 5.502544 CGATTTCGTCATTTAAGGAAGAGGC 60.503 44.000 0.00 0.00 34.11 4.70
364 368 5.810587 TCGATTTCGTCATTTAAGGAAGAGG 59.189 40.000 0.00 0.00 40.80 3.69
365 369 6.506513 CGTCGATTTCGTCATTTAAGGAAGAG 60.507 42.308 0.00 0.00 40.80 2.85
366 370 5.287752 CGTCGATTTCGTCATTTAAGGAAGA 59.712 40.000 0.00 0.00 40.80 2.87
367 371 5.481472 CGTCGATTTCGTCATTTAAGGAAG 58.519 41.667 0.00 0.00 40.80 3.46
368 372 4.327898 CCGTCGATTTCGTCATTTAAGGAA 59.672 41.667 0.00 0.00 40.80 3.36
369 373 3.861113 CCGTCGATTTCGTCATTTAAGGA 59.139 43.478 0.00 0.00 40.80 3.36
370 374 3.000925 CCCGTCGATTTCGTCATTTAAGG 59.999 47.826 0.00 0.00 40.80 2.69
371 375 3.543460 GCCCGTCGATTTCGTCATTTAAG 60.543 47.826 0.00 0.00 40.80 1.85
372 376 2.349275 GCCCGTCGATTTCGTCATTTAA 59.651 45.455 0.00 0.00 40.80 1.52
373 377 1.928503 GCCCGTCGATTTCGTCATTTA 59.071 47.619 0.00 0.00 40.80 1.40
374 378 0.725117 GCCCGTCGATTTCGTCATTT 59.275 50.000 0.00 0.00 40.80 2.32
375 379 1.087771 GGCCCGTCGATTTCGTCATT 61.088 55.000 0.00 0.00 40.80 2.57
376 380 1.520787 GGCCCGTCGATTTCGTCAT 60.521 57.895 0.00 0.00 40.80 3.06
377 381 2.125832 GGCCCGTCGATTTCGTCA 60.126 61.111 0.00 0.00 40.80 4.35
378 382 2.889018 GGGCCCGTCGATTTCGTC 60.889 66.667 5.69 0.00 40.80 4.20
379 383 4.807039 CGGGCCCGTCGATTTCGT 62.807 66.667 36.64 0.00 40.80 3.85
405 409 1.504900 GTTTTAAGCCCGAAGCCCG 59.495 57.895 0.00 0.00 45.47 6.13
406 410 0.611062 AGGTTTTAAGCCCGAAGCCC 60.611 55.000 0.00 0.00 45.47 5.19
407 411 2.014857 CTAGGTTTTAAGCCCGAAGCC 58.985 52.381 0.00 0.00 45.47 4.35
408 412 2.014857 CCTAGGTTTTAAGCCCGAAGC 58.985 52.381 0.00 0.00 44.25 3.86
409 413 2.014857 GCCTAGGTTTTAAGCCCGAAG 58.985 52.381 11.31 0.00 0.00 3.79
410 414 1.340308 GGCCTAGGTTTTAAGCCCGAA 60.340 52.381 11.31 0.00 37.66 4.30
411 415 0.253894 GGCCTAGGTTTTAAGCCCGA 59.746 55.000 11.31 0.00 37.66 5.14
412 416 2.789842 GGCCTAGGTTTTAAGCCCG 58.210 57.895 11.31 0.00 37.66 6.13
414 418 0.253894 TCGGGCCTAGGTTTTAAGCC 59.746 55.000 11.31 2.81 43.09 4.35
415 419 1.664873 CTCGGGCCTAGGTTTTAAGC 58.335 55.000 11.31 0.00 0.00 3.09
416 420 1.664873 GCTCGGGCCTAGGTTTTAAG 58.335 55.000 11.31 3.50 0.00 1.85
417 421 3.867549 GCTCGGGCCTAGGTTTTAA 57.132 52.632 11.31 0.00 0.00 1.52
435 439 4.820744 CCTTGTCCATGGGCCGGG 62.821 72.222 15.27 12.08 0.00 5.73
436 440 3.995506 GACCTTGTCCATGGGCCGG 62.996 68.421 15.27 16.66 0.00 6.13
437 441 2.438434 GACCTTGTCCATGGGCCG 60.438 66.667 15.27 4.70 0.00 6.13
438 442 2.438434 CGACCTTGTCCATGGGCC 60.438 66.667 15.27 4.53 30.24 5.80
439 443 2.438434 CCGACCTTGTCCATGGGC 60.438 66.667 10.20 10.20 0.00 5.36
440 444 2.272146 CCCGACCTTGTCCATGGG 59.728 66.667 13.02 0.00 0.00 4.00
441 445 2.438434 GCCCGACCTTGTCCATGG 60.438 66.667 4.97 4.97 0.00 3.66
442 446 2.438434 GGCCCGACCTTGTCCATG 60.438 66.667 0.00 0.00 34.51 3.66
443 447 2.933287 TGGCCCGACCTTGTCCAT 60.933 61.111 0.00 0.00 40.22 3.41
444 448 3.636231 CTGGCCCGACCTTGTCCA 61.636 66.667 0.00 0.00 40.22 4.02
445 449 4.410400 CCTGGCCCGACCTTGTCC 62.410 72.222 0.00 0.00 40.22 4.02
463 467 2.332654 CCGAAAAAGCCTGACCCGG 61.333 63.158 0.00 0.00 0.00 5.73
464 468 2.332654 CCCGAAAAAGCCTGACCCG 61.333 63.158 0.00 0.00 0.00 5.28
465 469 2.636412 GCCCGAAAAAGCCTGACCC 61.636 63.158 0.00 0.00 0.00 4.46
466 470 2.636412 GGCCCGAAAAAGCCTGACC 61.636 63.158 0.00 0.00 46.14 4.02
467 471 2.962569 GGCCCGAAAAAGCCTGAC 59.037 61.111 0.00 0.00 46.14 3.51
505 509 3.650942 TCTTAACTATACCTGGCCATGGG 59.349 47.826 20.97 16.10 0.00 4.00
506 510 4.974645 TCTTAACTATACCTGGCCATGG 57.025 45.455 5.51 13.05 0.00 3.66
507 511 5.063880 GGTTCTTAACTATACCTGGCCATG 58.936 45.833 5.51 6.06 0.00 3.66
508 512 4.724798 TGGTTCTTAACTATACCTGGCCAT 59.275 41.667 5.51 0.00 0.00 4.40
509 513 4.105577 TGGTTCTTAACTATACCTGGCCA 58.894 43.478 4.71 4.71 0.00 5.36
510 514 4.765813 TGGTTCTTAACTATACCTGGCC 57.234 45.455 0.00 0.00 0.00 5.36
511 515 5.008712 GCATTGGTTCTTAACTATACCTGGC 59.991 44.000 0.00 0.00 0.00 4.85
512 516 6.119536 TGCATTGGTTCTTAACTATACCTGG 58.880 40.000 0.00 0.00 0.00 4.45
513 517 6.823689 ACTGCATTGGTTCTTAACTATACCTG 59.176 38.462 0.00 0.00 0.00 4.00
514 518 6.823689 CACTGCATTGGTTCTTAACTATACCT 59.176 38.462 0.00 0.00 0.00 3.08
515 519 6.038271 CCACTGCATTGGTTCTTAACTATACC 59.962 42.308 14.75 0.00 0.00 2.73
516 520 6.038271 CCCACTGCATTGGTTCTTAACTATAC 59.962 42.308 20.56 0.00 34.44 1.47
517 521 6.069905 TCCCACTGCATTGGTTCTTAACTATA 60.070 38.462 20.56 0.00 34.44 1.31
518 522 4.949856 CCCACTGCATTGGTTCTTAACTAT 59.050 41.667 20.56 0.00 34.44 2.12
519 523 4.042311 TCCCACTGCATTGGTTCTTAACTA 59.958 41.667 20.56 0.00 34.44 2.24
545 549 4.396522 AGTGTCGTTAGCCTACTATAGGG 58.603 47.826 4.43 0.00 46.32 3.53
552 566 1.356938 GCCAAGTGTCGTTAGCCTAC 58.643 55.000 0.00 0.00 0.00 3.18
558 572 0.981183 ATGAGGGCCAAGTGTCGTTA 59.019 50.000 6.18 0.00 0.00 3.18
562 576 1.450312 CGGATGAGGGCCAAGTGTC 60.450 63.158 6.18 0.00 0.00 3.67
581 595 2.114411 TGGTGGAGCCGGGAAAAC 59.886 61.111 2.18 0.00 41.21 2.43
582 596 2.114411 GTGGTGGAGCCGGGAAAA 59.886 61.111 2.18 0.00 41.21 2.29
583 597 3.172106 TGTGGTGGAGCCGGGAAA 61.172 61.111 2.18 0.00 41.21 3.13
584 598 3.636231 CTGTGGTGGAGCCGGGAA 61.636 66.667 2.18 0.00 41.21 3.97
592 606 3.180449 ACCAATCTCCTGTGGTGGA 57.820 52.632 0.00 0.00 46.53 4.02
597 611 8.970859 AGATCTTATTTTACCAATCTCCTGTG 57.029 34.615 0.00 0.00 0.00 3.66
598 612 9.620259 GAAGATCTTATTTTACCAATCTCCTGT 57.380 33.333 8.25 0.00 0.00 4.00
599 613 9.844257 AGAAGATCTTATTTTACCAATCTCCTG 57.156 33.333 8.25 0.00 0.00 3.86
602 616 9.113838 TGCAGAAGATCTTATTTTACCAATCTC 57.886 33.333 8.25 0.00 0.00 2.75
603 617 9.638176 ATGCAGAAGATCTTATTTTACCAATCT 57.362 29.630 8.25 0.00 0.00 2.40
607 621 9.851686 ACATATGCAGAAGATCTTATTTTACCA 57.148 29.630 8.25 0.00 0.00 3.25
610 624 9.507329 GGGACATATGCAGAAGATCTTATTTTA 57.493 33.333 8.25 0.00 0.00 1.52
611 625 7.449704 GGGGACATATGCAGAAGATCTTATTTT 59.550 37.037 8.25 0.00 0.00 1.82
612 626 6.944862 GGGGACATATGCAGAAGATCTTATTT 59.055 38.462 8.25 0.00 0.00 1.40
613 627 6.479884 GGGGACATATGCAGAAGATCTTATT 58.520 40.000 8.25 0.00 0.00 1.40
614 628 5.337894 CGGGGACATATGCAGAAGATCTTAT 60.338 44.000 8.25 1.36 0.00 1.73
615 629 4.021104 CGGGGACATATGCAGAAGATCTTA 60.021 45.833 8.25 0.00 0.00 2.10
617 631 2.301296 CGGGGACATATGCAGAAGATCT 59.699 50.000 1.58 0.00 0.00 2.75
618 632 2.693069 CGGGGACATATGCAGAAGATC 58.307 52.381 1.58 0.00 0.00 2.75
619 633 1.271054 GCGGGGACATATGCAGAAGAT 60.271 52.381 1.58 0.00 0.00 2.40
620 634 0.106708 GCGGGGACATATGCAGAAGA 59.893 55.000 1.58 0.00 0.00 2.87
625 774 0.254462 TTTCAGCGGGGACATATGCA 59.746 50.000 1.58 0.00 0.00 3.96
653 802 7.869937 GCTGCACGTGGATATATTCTCATATAT 59.130 37.037 18.88 0.00 40.11 0.86
666 815 0.320050 TCTGTTGCTGCACGTGGATA 59.680 50.000 18.88 3.71 0.00 2.59
689 1132 0.795698 TCATTCGGTTGCGTGTGATG 59.204 50.000 0.00 0.00 0.00 3.07
702 1145 2.754472 TGTGACAGGTGAGTTCATTCG 58.246 47.619 0.00 0.00 0.00 3.34
703 1146 5.482908 ACTATGTGACAGGTGAGTTCATTC 58.517 41.667 0.00 0.00 0.00 2.67
704 1147 5.489792 ACTATGTGACAGGTGAGTTCATT 57.510 39.130 0.00 0.00 0.00 2.57
705 1148 5.393135 CGTACTATGTGACAGGTGAGTTCAT 60.393 44.000 4.62 0.00 0.00 2.57
706 1149 4.082949 CGTACTATGTGACAGGTGAGTTCA 60.083 45.833 4.62 0.00 0.00 3.18
757 2829 6.581542 ACGAGTAGTAACTTTCGAACTGAATG 59.418 38.462 0.00 0.00 35.56 2.67
763 2835 6.317857 ACCATACGAGTAGTAACTTTCGAAC 58.682 40.000 0.00 0.00 39.04 3.95
852 2925 0.824109 TAGCCCGATGGAGTTGAGTG 59.176 55.000 0.00 0.00 0.00 3.51
854 2927 0.824109 TGTAGCCCGATGGAGTTGAG 59.176 55.000 0.00 0.00 0.00 3.02
857 2930 0.179045 GCATGTAGCCCGATGGAGTT 60.179 55.000 0.00 0.00 37.23 3.01
867 2940 1.338973 CCAACATCCATGCATGTAGCC 59.661 52.381 24.58 0.00 44.83 3.93
876 2949 0.108520 GCCAAGTGCCAACATCCATG 60.109 55.000 0.00 0.00 0.00 3.66
900 2973 4.278669 GTGACTGACTGTAGAGTTGGAAGA 59.721 45.833 0.00 0.00 30.16 2.87
915 2988 0.889186 AACCGCCAATGGTGACTGAC 60.889 55.000 15.40 0.00 42.89 3.51
916 2989 0.888736 CAACCGCCAATGGTGACTGA 60.889 55.000 15.40 0.00 42.89 3.41
917 2990 1.580942 CAACCGCCAATGGTGACTG 59.419 57.895 15.40 7.05 42.89 3.51
918 2991 2.268076 GCAACCGCCAATGGTGACT 61.268 57.895 15.40 0.00 42.89 3.41
919 2992 2.258286 GCAACCGCCAATGGTGAC 59.742 61.111 15.40 0.00 42.89 3.67
999 3093 1.134280 AGGAAGGAGAATGACGGCATG 60.134 52.381 3.39 0.00 34.26 4.06
1003 3097 1.066303 CTCGAGGAAGGAGAATGACGG 59.934 57.143 3.91 0.00 33.27 4.79
1008 3102 3.535280 GAAAGCTCGAGGAAGGAGAAT 57.465 47.619 15.58 0.00 33.27 2.40
1072 3166 1.896660 GGTTCTTGCGCTTGGACCA 60.897 57.895 20.62 0.00 0.00 4.02
1230 3326 1.740380 GCCGTGAAGAAGAGCTGCATA 60.740 52.381 1.02 0.00 33.76 3.14
1264 3836 3.771160 GGTGAGGACGTGGCGGAT 61.771 66.667 0.00 0.00 0.00 4.18
1627 4199 2.104132 CATGGCGTCGTCGATGGA 59.896 61.111 15.93 0.00 39.71 3.41
1679 4251 2.203337 GCACCAGCTTCCACCACA 60.203 61.111 0.00 0.00 37.91 4.17
1704 4276 2.838225 CGCTCATACCCGACCCCT 60.838 66.667 0.00 0.00 0.00 4.79
1833 4411 0.945813 GTCGTCGATGTAGGAGGAGG 59.054 60.000 4.21 0.00 0.00 4.30
2042 4644 1.594833 GGTCGTAGGTCACCATGCA 59.405 57.895 0.00 0.00 32.33 3.96
2553 5166 3.699894 AGAGAGCGGGCACACAGG 61.700 66.667 0.00 0.00 0.00 4.00
2658 5275 9.788889 TTACTAAGATCTCACGAATATACCAGA 57.211 33.333 0.00 0.00 0.00 3.86
2706 5330 2.943033 TCTCACGAATCTAGCATCGACA 59.057 45.455 19.53 7.74 41.43 4.35
2707 5331 3.610786 TCTCACGAATCTAGCATCGAC 57.389 47.619 19.53 0.00 41.43 4.20
2915 5543 9.692749 TTAGTTTCGATAATAGATGTGATGGTC 57.307 33.333 0.00 0.00 0.00 4.02
2947 5576 2.229675 TCAGTAGCGCATGAGATTGG 57.770 50.000 11.47 0.00 0.00 3.16
3005 5634 4.397103 CACTTAGCATCATCAGGCTTTTGA 59.603 41.667 0.00 0.00 41.41 2.69
3008 5637 2.686915 GCACTTAGCATCATCAGGCTTT 59.313 45.455 0.00 0.00 44.79 3.51
3039 5668 3.957497 ACAGATTCTCGCTCATAGACCTT 59.043 43.478 0.00 0.00 0.00 3.50
3077 5706 2.618053 CGTTCGTGGCTTCTTTCCTAT 58.382 47.619 0.00 0.00 0.00 2.57
3152 5783 3.568853 GGAGTTTCGAGCATACCTAGCTA 59.431 47.826 0.00 0.00 43.58 3.32
3160 5791 1.922570 GAAGCGGAGTTTCGAGCATA 58.077 50.000 0.00 0.00 38.10 3.14
3170 5801 1.296715 GGTGTGGATGAAGCGGAGT 59.703 57.895 0.00 0.00 0.00 3.85
3365 5996 0.179086 GGTGGTTGGTTTTGGTGCAG 60.179 55.000 0.00 0.00 0.00 4.41
3379 6010 4.245251 ACAAAGTAAAAGAGGTGGTGGT 57.755 40.909 0.00 0.00 0.00 4.16
3484 6115 7.147958 TGATTTTTGGGGAAGGAAAAGAAAT 57.852 32.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.