Multiple sequence alignment - TraesCS2A01G120500

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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 TraesCS2A01G120500 chr2A 100.000 2946 0 0 1 2946 70654067 70657012 0.000000e+00 5441.0
1 TraesCS2A01G120500 chr2A 86.059 1492 137 34 1482 2946 70156029 70154582 0.000000e+00 1537.0
2 TraesCS2A01G120500 chr2A 86.975 952 94 16 1472 2410 70644552 70645486 0.000000e+00 1044.0
3 TraesCS2A01G120500 chr2A 77.580 1570 231 54 873 2410 70284469 70282989 0.000000e+00 837.0
4 TraesCS2A01G120500 chr2A 81.752 822 86 29 736 1527 70235248 70234461 1.930000e-176 628.0
5 TraesCS2A01G120500 chr2A 85.572 603 69 9 846 1437 70649214 70649809 1.500000e-172 616.0
6 TraesCS2A01G120500 chr2A 87.849 502 42 4 973 1471 70156775 70156290 3.290000e-159 571.0
7 TraesCS2A01G120500 chr2A 84.629 553 56 9 2401 2946 70645511 70646041 9.360000e-145 523.0
8 TraesCS2A01G120500 chr2A 87.765 425 37 8 2528 2946 70230581 70230166 1.590000e-132 483.0
9 TraesCS2A01G120500 chr2A 85.100 349 26 14 749 1084 70643752 70644087 1.690000e-87 333.0
10 TraesCS2A01G120500 chr2A 82.353 357 44 14 887 1227 70291843 70291490 2.870000e-75 292.0
11 TraesCS2A01G120500 chr2A 88.235 85 9 1 428 511 70237884 70237800 1.870000e-17 100.0
12 TraesCS2A01G120500 chr2A 86.567 67 8 1 512 577 70276023 70275957 4.070000e-09 73.1
13 TraesCS2A01G120500 chr2D 91.484 1233 61 16 723 1941 71598607 71599809 0.000000e+00 1655.0
14 TraesCS2A01G120500 chr2D 85.423 1420 173 22 1008 2410 71565718 71567120 0.000000e+00 1445.0
15 TraesCS2A01G120500 chr2D 93.388 983 50 5 1966 2946 71600086 71601055 0.000000e+00 1441.0
16 TraesCS2A01G120500 chr2D 84.626 1444 154 40 1008 2410 71578398 71579814 0.000000e+00 1375.0
17 TraesCS2A01G120500 chr2D 87.141 941 88 14 2019 2946 70672905 70671985 0.000000e+00 1037.0
18 TraesCS2A01G120500 chr2D 83.250 1194 130 31 755 1912 70674448 70673289 0.000000e+00 1033.0
19 TraesCS2A01G120500 chr2D 77.950 1610 223 70 845 2410 71404540 71406061 0.000000e+00 885.0
20 TraesCS2A01G120500 chr2D 84.787 539 57 13 2416 2946 71410344 71410865 4.350000e-143 518.0
21 TraesCS2A01G120500 chr2D 83.992 531 67 10 2416 2938 71471589 71472109 7.330000e-136 494.0
22 TraesCS2A01G120500 chr2D 81.026 643 85 23 813 1427 71399241 71399874 7.390000e-131 477.0
23 TraesCS2A01G120500 chr2D 84.519 478 59 13 1 475 71597291 71597756 2.680000e-125 459.0
24 TraesCS2A01G120500 chr2D 82.056 535 69 14 2401 2924 70635048 70635566 5.830000e-117 431.0
25 TraesCS2A01G120500 chr2D 82.812 448 61 10 2486 2925 70636919 70637358 1.280000e-103 387.0
26 TraesCS2A01G120500 chr2D 84.906 265 19 10 813 1069 71565477 71565728 6.310000e-62 248.0
27 TraesCS2A01G120500 chr2D 86.082 194 19 3 2753 2946 71465367 71465552 4.980000e-48 202.0
28 TraesCS2A01G120500 chr2D 89.167 120 11 2 459 578 71597772 71597889 6.580000e-32 148.0
29 TraesCS2A01G120500 chr2D 85.235 149 17 5 430 577 71598412 71598556 6.580000e-32 148.0
30 TraesCS2A01G120500 chr2D 87.500 72 8 1 428 498 71467053 71467124 6.770000e-12 82.4
31 TraesCS2A01G120500 chr2B 91.388 1196 75 9 1427 2619 107793870 107795040 0.000000e+00 1613.0
32 TraesCS2A01G120500 chr2B 84.285 1419 164 37 1008 2410 107783242 107784617 0.000000e+00 1330.0
33 TraesCS2A01G120500 chr2B 91.282 585 31 6 826 1395 107793118 107793697 0.000000e+00 780.0
34 TraesCS2A01G120500 chr2B 85.337 757 75 15 1850 2594 107023411 107022679 0.000000e+00 750.0
35 TraesCS2A01G120500 chr2B 83.252 824 103 21 728 1527 107576665 107577477 0.000000e+00 725.0
36 TraesCS2A01G120500 chr2B 85.353 553 65 8 2401 2946 107784642 107785185 2.560000e-155 558.0
37 TraesCS2A01G120500 chr2B 84.181 531 63 9 2416 2938 107578418 107578935 2.040000e-136 496.0
38 TraesCS2A01G120500 chr2B 88.028 284 22 6 2670 2946 107795305 107795583 2.830000e-85 326.0
39 TraesCS2A01G120500 chr2B 83.540 322 48 2 1524 1843 107038569 107038251 2.220000e-76 296.0
40 TraesCS2A01G120500 chr2B 82.216 343 31 22 749 1084 107782947 107783266 4.840000e-68 268.0
41 TraesCS2A01G120500 chr2B 81.962 316 46 6 2083 2397 107790243 107790548 1.050000e-64 257.0
42 TraesCS2A01G120500 chr2B 85.340 191 20 3 2756 2946 107574503 107574685 1.080000e-44 191.0


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 TraesCS2A01G120500 chr2A 70654067 70657012 2945 False 5441.000000 5441 100.000000 1 2946 1 chr2A.!!$F1 2945
1 TraesCS2A01G120500 chr2A 70154582 70156775 2193 True 1054.000000 1537 86.954000 973 2946 2 chr2A.!!$R4 1973
2 TraesCS2A01G120500 chr2A 70282989 70284469 1480 True 837.000000 837 77.580000 873 2410 1 chr2A.!!$R2 1537
3 TraesCS2A01G120500 chr2A 70643752 70649809 6057 False 629.000000 1044 85.569000 749 2946 4 chr2A.!!$F2 2197
4 TraesCS2A01G120500 chr2A 70230166 70237884 7718 True 403.666667 628 85.917333 428 2946 3 chr2A.!!$R5 2518
5 TraesCS2A01G120500 chr2D 71578398 71579814 1416 False 1375.000000 1375 84.626000 1008 2410 1 chr2D.!!$F5 1402
6 TraesCS2A01G120500 chr2D 70671985 70674448 2463 True 1035.000000 1037 85.195500 755 2946 2 chr2D.!!$R1 2191
7 TraesCS2A01G120500 chr2D 71404540 71406061 1521 False 885.000000 885 77.950000 845 2410 1 chr2D.!!$F2 1565
8 TraesCS2A01G120500 chr2D 71565477 71567120 1643 False 846.500000 1445 85.164500 813 2410 2 chr2D.!!$F8 1597
9 TraesCS2A01G120500 chr2D 71597291 71601055 3764 False 770.200000 1655 88.758600 1 2946 5 chr2D.!!$F9 2945
10 TraesCS2A01G120500 chr2D 71410344 71410865 521 False 518.000000 518 84.787000 2416 2946 1 chr2D.!!$F3 530
11 TraesCS2A01G120500 chr2D 71471589 71472109 520 False 494.000000 494 83.992000 2416 2938 1 chr2D.!!$F4 522
12 TraesCS2A01G120500 chr2D 71399241 71399874 633 False 477.000000 477 81.026000 813 1427 1 chr2D.!!$F1 614
13 TraesCS2A01G120500 chr2D 70635048 70637358 2310 False 409.000000 431 82.434000 2401 2925 2 chr2D.!!$F6 524
14 TraesCS2A01G120500 chr2B 107022679 107023411 732 True 750.000000 750 85.337000 1850 2594 1 chr2B.!!$R1 744
15 TraesCS2A01G120500 chr2B 107790243 107795583 5340 False 744.000000 1613 88.165000 826 2946 4 chr2B.!!$F3 2120
16 TraesCS2A01G120500 chr2B 107782947 107785185 2238 False 718.666667 1330 83.951333 749 2946 3 chr2B.!!$F2 2197
17 TraesCS2A01G120500 chr2B 107574503 107578935 4432 False 470.666667 725 84.257667 728 2946 3 chr2B.!!$F1 2218

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
111 112 0.031043 TTTCTTTGCTCGTCGGTCGA 59.969 50.0 0.0 0.0 46.83 4.20 F
724 725 0.035439 ATTTCGCCCGGTGACTGAAT 60.035 50.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 7257 1.134098 ACATCCATGATCACCGAACCC 60.134 52.381 0.0 0.0 0.0 4.11 R
1960 7411 2.604139 CAAAGCAAAGGGGGAGGTAAA 58.396 47.619 0.0 0.0 0.0 2.01 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
27 28 5.021033 TGGAGTTTGTTGTCAATTGCAAT 57.979 34.783 5.99 5.99 33.32 3.56
55 56 0.322726 TCCGTCGTGGATGAGGTGTA 60.323 55.000 0.00 0.00 43.74 2.90
106 107 6.969669 AAACTTAATTTTCTTTGCTCGTCG 57.030 33.333 0.00 0.00 0.00 5.12
111 112 0.031043 TTTCTTTGCTCGTCGGTCGA 59.969 50.000 0.00 0.00 46.83 4.20
150 151 4.260825 GCACTTCTCAGATCTGCATGATTG 60.261 45.833 18.36 14.52 35.14 2.67
158 159 4.023963 CAGATCTGCATGATTGATGTGGTC 60.024 45.833 10.38 0.00 35.14 4.02
162 163 2.691011 TGCATGATTGATGTGGTCCATG 59.309 45.455 0.00 0.00 32.56 3.66
178 179 4.632688 GGTCCATGGCATCAAATTTTTCAG 59.367 41.667 6.96 0.00 0.00 3.02
181 182 6.311200 GTCCATGGCATCAAATTTTTCAGTAC 59.689 38.462 6.96 0.00 0.00 2.73
182 183 6.014755 TCCATGGCATCAAATTTTTCAGTACA 60.015 34.615 6.96 0.00 0.00 2.90
189 190 8.231837 GCATCAAATTTTTCAGTACATTGCATT 58.768 29.630 0.00 0.00 0.00 3.56
190 191 9.536558 CATCAAATTTTTCAGTACATTGCATTG 57.463 29.630 7.04 7.04 0.00 2.82
192 193 8.980610 TCAAATTTTTCAGTACATTGCATTGAG 58.019 29.630 15.20 2.96 0.00 3.02
193 194 6.956299 ATTTTTCAGTACATTGCATTGAGC 57.044 33.333 15.20 7.20 45.96 4.26
194 195 5.710513 TTTTCAGTACATTGCATTGAGCT 57.289 34.783 15.20 9.13 45.94 4.09
195 196 4.690184 TTCAGTACATTGCATTGAGCTG 57.310 40.909 15.20 18.39 45.94 4.24
196 197 2.421073 TCAGTACATTGCATTGAGCTGC 59.579 45.455 15.20 0.00 45.94 5.25
207 208 4.240096 GCATTGAGCTGCAACTGTATTTT 58.760 39.130 1.02 0.00 41.87 1.82
208 209 4.687483 GCATTGAGCTGCAACTGTATTTTT 59.313 37.500 1.02 0.00 41.87 1.94
243 244 7.972832 TTATTTGGCGTGTTATCCTAATAGG 57.027 36.000 0.00 0.00 33.76 2.57
259 260 7.574607 TCCTAATAGGAATTGTTTTCCCTCTC 58.425 38.462 6.54 0.00 42.51 3.20
260 261 7.183839 TCCTAATAGGAATTGTTTTCCCTCTCA 59.816 37.037 6.54 0.00 42.51 3.27
262 263 9.243105 CTAATAGGAATTGTTTTCCCTCTCAAA 57.757 33.333 0.82 0.00 39.39 2.69
265 266 4.546570 GAATTGTTTTCCCTCTCAAACCG 58.453 43.478 0.00 0.00 32.76 4.44
266 267 1.975660 TGTTTTCCCTCTCAAACCGG 58.024 50.000 0.00 0.00 32.76 5.28
269 270 3.117963 TGTTTTCCCTCTCAAACCGGTTA 60.118 43.478 22.60 4.69 32.76 2.85
270 271 4.077108 GTTTTCCCTCTCAAACCGGTTAT 58.923 43.478 22.60 8.26 0.00 1.89
271 272 4.376225 TTTCCCTCTCAAACCGGTTATT 57.624 40.909 22.60 2.14 0.00 1.40
273 274 2.907696 TCCCTCTCAAACCGGTTATTGA 59.092 45.455 22.60 20.07 34.57 2.57
274 275 3.521937 TCCCTCTCAAACCGGTTATTGAT 59.478 43.478 22.60 0.29 35.20 2.57
275 276 3.877508 CCCTCTCAAACCGGTTATTGATC 59.122 47.826 22.60 0.00 35.20 2.92
276 277 4.513442 CCTCTCAAACCGGTTATTGATCA 58.487 43.478 22.60 9.96 35.20 2.92
279 280 6.072175 CCTCTCAAACCGGTTATTGATCAAAA 60.072 38.462 22.60 5.67 35.20 2.44
280 281 7.362920 CCTCTCAAACCGGTTATTGATCAAAAT 60.363 37.037 22.60 0.00 35.20 1.82
281 282 7.535139 TCTCAAACCGGTTATTGATCAAAATC 58.465 34.615 22.60 7.72 35.20 2.17
282 283 6.318628 TCAAACCGGTTATTGATCAAAATCG 58.681 36.000 22.60 17.63 34.39 3.34
290 291 7.850982 CGGTTATTGATCAAAATCGGTTTCTAG 59.149 37.037 13.09 0.00 34.39 2.43
295 296 6.649155 TGATCAAAATCGGTTTCTAGATGGA 58.351 36.000 8.01 0.00 34.39 3.41
296 297 7.109501 TGATCAAAATCGGTTTCTAGATGGAA 58.890 34.615 8.01 0.00 34.39 3.53
299 300 5.693769 AAATCGGTTTCTAGATGGAAGGA 57.306 39.130 0.00 0.00 0.00 3.36
301 302 4.939052 TCGGTTTCTAGATGGAAGGATC 57.061 45.455 0.00 0.00 0.00 3.36
302 303 4.547671 TCGGTTTCTAGATGGAAGGATCT 58.452 43.478 0.00 0.00 36.61 2.75
305 306 6.434652 TCGGTTTCTAGATGGAAGGATCTATC 59.565 42.308 0.00 0.00 42.26 2.08
308 309 6.849085 TTCTAGATGGAAGGATCTATCAGC 57.151 41.667 0.00 0.00 43.84 4.26
309 310 5.896963 TCTAGATGGAAGGATCTATCAGCA 58.103 41.667 5.22 0.00 43.84 4.41
310 311 4.888326 AGATGGAAGGATCTATCAGCAC 57.112 45.455 5.22 0.00 43.84 4.40
314 315 5.441718 TGGAAGGATCTATCAGCACTTTT 57.558 39.130 0.00 0.00 0.00 2.27
315 316 6.560003 TGGAAGGATCTATCAGCACTTTTA 57.440 37.500 0.00 0.00 0.00 1.52
316 317 6.586344 TGGAAGGATCTATCAGCACTTTTAG 58.414 40.000 0.00 0.00 0.00 1.85
317 318 6.156949 TGGAAGGATCTATCAGCACTTTTAGT 59.843 38.462 0.00 0.00 0.00 2.24
318 319 7.051000 GGAAGGATCTATCAGCACTTTTAGTT 58.949 38.462 0.00 0.00 0.00 2.24
319 320 7.011857 GGAAGGATCTATCAGCACTTTTAGTTG 59.988 40.741 0.00 0.00 0.00 3.16
320 321 5.819901 AGGATCTATCAGCACTTTTAGTTGC 59.180 40.000 0.00 0.00 0.00 4.17
323 324 7.148171 GGATCTATCAGCACTTTTAGTTGCTTT 60.148 37.037 0.00 0.00 32.84 3.51
427 428 5.592054 TCAAGATTCATAGACCACTTAGCG 58.408 41.667 0.00 0.00 0.00 4.26
428 429 5.359860 TCAAGATTCATAGACCACTTAGCGA 59.640 40.000 0.00 0.00 0.00 4.93
429 430 5.189659 AGATTCATAGACCACTTAGCGAC 57.810 43.478 0.00 0.00 0.00 5.19
430 431 4.645136 AGATTCATAGACCACTTAGCGACA 59.355 41.667 0.00 0.00 0.00 4.35
431 432 4.794278 TTCATAGACCACTTAGCGACAA 57.206 40.909 0.00 0.00 0.00 3.18
432 433 5.339008 TTCATAGACCACTTAGCGACAAT 57.661 39.130 0.00 0.00 0.00 2.71
433 434 6.459670 TTCATAGACCACTTAGCGACAATA 57.540 37.500 0.00 0.00 0.00 1.90
436 437 6.923508 TCATAGACCACTTAGCGACAATATTG 59.076 38.462 14.01 14.01 0.00 1.90
438 439 5.109903 AGACCACTTAGCGACAATATTGAC 58.890 41.667 22.16 14.62 0.00 3.18
440 441 5.488341 ACCACTTAGCGACAATATTGACTT 58.512 37.500 22.16 9.21 0.00 3.01
442 443 6.430000 ACCACTTAGCGACAATATTGACTTTT 59.570 34.615 22.16 0.00 0.00 2.27
443 444 7.040686 ACCACTTAGCGACAATATTGACTTTTT 60.041 33.333 22.16 0.00 0.00 1.94
473 474 7.565323 AAGCAGATCTTCATGAAAATCTACC 57.435 36.000 21.13 15.51 0.00 3.18
474 475 6.897986 AGCAGATCTTCATGAAAATCTACCT 58.102 36.000 21.13 17.11 0.00 3.08
475 476 8.027524 AGCAGATCTTCATGAAAATCTACCTA 57.972 34.615 21.13 0.00 0.00 3.08
482 483 8.677300 TCTTCATGAAAATCTACCTAATTGTGC 58.323 33.333 9.88 0.00 0.00 4.57
483 484 7.936496 TCATGAAAATCTACCTAATTGTGCA 57.064 32.000 0.00 0.00 0.00 4.57
486 487 9.241317 CATGAAAATCTACCTAATTGTGCAATC 57.759 33.333 0.00 0.00 0.00 2.67
487 488 8.347004 TGAAAATCTACCTAATTGTGCAATCA 57.653 30.769 0.00 0.00 0.00 2.57
488 489 8.243426 TGAAAATCTACCTAATTGTGCAATCAC 58.757 33.333 0.00 0.00 43.40 3.06
504 505 8.385789 GTGCAATCACAATATTTTGACACTAG 57.614 34.615 6.45 0.00 42.66 2.57
505 506 8.023128 GTGCAATCACAATATTTTGACACTAGT 58.977 33.333 6.45 0.00 42.66 2.57
506 507 8.236586 TGCAATCACAATATTTTGACACTAGTC 58.763 33.333 6.45 0.00 45.19 2.59
507 508 8.454106 GCAATCACAATATTTTGACACTAGTCT 58.546 33.333 6.45 0.00 45.20 3.24
510 511 9.725019 ATCACAATATTTTGACACTAGTCTTGA 57.275 29.630 6.45 0.00 45.20 3.02
511 512 9.554395 TCACAATATTTTGACACTAGTCTTGAA 57.446 29.630 2.69 0.00 45.20 2.69
521 522 9.567848 TTGACACTAGTCTTGAAATTCAAAAAC 57.432 29.630 9.85 10.51 45.20 2.43
522 523 8.188139 TGACACTAGTCTTGAAATTCAAAAACC 58.812 33.333 9.85 0.00 45.20 3.27
524 525 8.695456 ACACTAGTCTTGAAATTCAAAAACCAT 58.305 29.630 9.85 0.38 35.73 3.55
529 530 9.533253 AGTCTTGAAATTCAAAAACCATAACTG 57.467 29.630 9.85 0.00 35.73 3.16
534 535 9.883142 TGAAATTCAAAAACCATAACTGAAACT 57.117 25.926 0.00 0.00 30.37 2.66
537 538 9.883142 AATTCAAAAACCATAACTGAAACTCAA 57.117 25.926 0.00 0.00 30.37 3.02
541 542 5.438761 AACCATAACTGAAACTCAACTGC 57.561 39.130 0.00 0.00 0.00 4.40
543 544 5.865085 ACCATAACTGAAACTCAACTGCTA 58.135 37.500 0.00 0.00 0.00 3.49
544 545 6.476378 ACCATAACTGAAACTCAACTGCTAT 58.524 36.000 0.00 0.00 0.00 2.97
547 548 9.113838 CCATAACTGAAACTCAACTGCTATTAT 57.886 33.333 0.00 0.00 0.00 1.28
551 552 8.261492 ACTGAAACTCAACTGCTATTATCTTG 57.739 34.615 0.00 0.00 0.00 3.02
552 553 7.880195 ACTGAAACTCAACTGCTATTATCTTGT 59.120 33.333 0.00 0.00 0.00 3.16
553 554 8.256611 TGAAACTCAACTGCTATTATCTTGTC 57.743 34.615 0.00 0.00 0.00 3.18
554 555 7.334421 TGAAACTCAACTGCTATTATCTTGTCC 59.666 37.037 0.00 0.00 0.00 4.02
556 557 5.127194 ACTCAACTGCTATTATCTTGTCCGA 59.873 40.000 0.00 0.00 0.00 4.55
557 558 5.972935 TCAACTGCTATTATCTTGTCCGAA 58.027 37.500 0.00 0.00 0.00 4.30
558 559 6.403049 TCAACTGCTATTATCTTGTCCGAAA 58.597 36.000 0.00 0.00 0.00 3.46
559 560 6.535150 TCAACTGCTATTATCTTGTCCGAAAG 59.465 38.462 0.00 0.00 0.00 2.62
560 561 6.222038 ACTGCTATTATCTTGTCCGAAAGA 57.778 37.500 0.00 0.00 40.36 2.52
561 562 6.640518 ACTGCTATTATCTTGTCCGAAAGAA 58.359 36.000 0.00 0.00 39.54 2.52
565 566 7.606456 TGCTATTATCTTGTCCGAAAGAAAACT 59.394 33.333 0.00 0.00 39.54 2.66
566 567 8.117370 GCTATTATCTTGTCCGAAAGAAAACTC 58.883 37.037 0.00 0.00 39.54 3.01
567 568 4.992381 ATCTTGTCCGAAAGAAAACTCG 57.008 40.909 0.00 0.00 39.54 4.18
581 582 9.717892 GAAAGAAAACTCGGTAATAAATCCATC 57.282 33.333 0.00 0.00 0.00 3.51
582 583 7.803279 AGAAAACTCGGTAATAAATCCATCC 57.197 36.000 0.00 0.00 0.00 3.51
583 584 7.343357 AGAAAACTCGGTAATAAATCCATCCA 58.657 34.615 0.00 0.00 0.00 3.41
584 585 7.832187 AGAAAACTCGGTAATAAATCCATCCAA 59.168 33.333 0.00 0.00 0.00 3.53
585 586 7.948034 AAACTCGGTAATAAATCCATCCAAA 57.052 32.000 0.00 0.00 0.00 3.28
587 588 7.510549 ACTCGGTAATAAATCCATCCAAATG 57.489 36.000 0.00 0.00 0.00 2.32
588 589 7.287061 ACTCGGTAATAAATCCATCCAAATGA 58.713 34.615 0.00 0.00 34.61 2.57
595 596 0.695924 TCCATCCAAATGACACCCGT 59.304 50.000 0.00 0.00 34.61 5.28
598 599 1.199789 CATCCAAATGACACCCGTGTG 59.800 52.381 4.96 0.00 45.05 3.82
600 601 0.591170 CCAAATGACACCCGTGTGAC 59.409 55.000 4.63 0.00 45.76 3.67
602 603 1.002900 CAAATGACACCCGTGTGACAC 60.003 52.381 4.63 5.47 46.87 3.67
614 615 0.948623 TGTGACACGAAGCAATCCGG 60.949 55.000 0.00 0.00 0.00 5.14
615 616 0.949105 GTGACACGAAGCAATCCGGT 60.949 55.000 0.00 0.00 0.00 5.28
616 617 0.669318 TGACACGAAGCAATCCGGTC 60.669 55.000 0.00 0.00 0.00 4.79
617 618 1.359459 GACACGAAGCAATCCGGTCC 61.359 60.000 0.00 0.00 0.00 4.46
618 619 1.079127 CACGAAGCAATCCGGTCCT 60.079 57.895 0.00 0.00 0.00 3.85
620 621 1.815421 CGAAGCAATCCGGTCCTGG 60.815 63.158 0.00 0.00 0.00 4.45
621 622 2.044946 AAGCAATCCGGTCCTGGC 60.045 61.111 0.00 0.00 0.00 4.85
622 623 3.976701 AAGCAATCCGGTCCTGGCG 62.977 63.158 0.00 0.00 0.00 5.69
624 625 2.511600 CAATCCGGTCCTGGCGTC 60.512 66.667 0.00 0.00 0.00 5.19
627 628 1.838073 AATCCGGTCCTGGCGTCTTT 61.838 55.000 0.00 0.00 0.00 2.52
629 630 1.186917 TCCGGTCCTGGCGTCTTTTA 61.187 55.000 0.00 0.00 0.00 1.52
630 631 0.320946 CCGGTCCTGGCGTCTTTTAA 60.321 55.000 0.00 0.00 0.00 1.52
631 632 1.515081 CGGTCCTGGCGTCTTTTAAA 58.485 50.000 0.00 0.00 0.00 1.52
634 635 3.667360 GGTCCTGGCGTCTTTTAAACTA 58.333 45.455 0.00 0.00 0.00 2.24
635 636 4.067192 GGTCCTGGCGTCTTTTAAACTAA 58.933 43.478 0.00 0.00 0.00 2.24
636 637 4.516321 GGTCCTGGCGTCTTTTAAACTAAA 59.484 41.667 0.00 0.00 0.00 1.85
637 638 5.334646 GGTCCTGGCGTCTTTTAAACTAAAG 60.335 44.000 0.00 0.00 36.64 1.85
640 641 5.912955 CCTGGCGTCTTTTAAACTAAAGTTG 59.087 40.000 0.00 0.00 38.44 3.16
646 647 7.372657 GCGTCTTTTAAACTAAAGTTGACACTC 59.627 37.037 0.00 0.00 38.44 3.51
647 648 8.385111 CGTCTTTTAAACTAAAGTTGACACTCA 58.615 33.333 0.00 0.00 38.44 3.41
657 658 8.686334 ACTAAAGTTGACACTCAAAATTGACAT 58.314 29.630 0.00 0.00 38.22 3.06
659 660 6.455360 AGTTGACACTCAAAATTGACATGT 57.545 33.333 0.00 0.00 38.22 3.21
660 661 6.267817 AGTTGACACTCAAAATTGACATGTG 58.732 36.000 1.15 10.92 38.22 3.21
663 664 6.629128 TGACACTCAAAATTGACATGTGTTT 58.371 32.000 16.11 0.00 41.32 2.83
664 665 7.766283 TGACACTCAAAATTGACATGTGTTTA 58.234 30.769 16.11 9.34 41.32 2.01
665 666 8.412456 TGACACTCAAAATTGACATGTGTTTAT 58.588 29.630 16.11 0.00 41.32 1.40
666 667 8.578308 ACACTCAAAATTGACATGTGTTTATG 57.422 30.769 1.15 4.08 39.54 1.90
679 680 5.416862 TGTGTTTATGTCACATGTGTGTC 57.583 39.130 24.63 16.15 45.76 3.67
681 682 5.204833 GTGTTTATGTCACATGTGTGTCAC 58.795 41.667 24.63 15.86 44.22 3.67
682 683 5.007626 GTGTTTATGTCACATGTGTGTCACT 59.992 40.000 24.63 13.66 44.22 3.41
683 684 5.588246 TGTTTATGTCACATGTGTGTCACTT 59.412 36.000 24.63 15.26 44.22 3.16
684 685 6.763610 TGTTTATGTCACATGTGTGTCACTTA 59.236 34.615 24.63 14.36 44.22 2.24
685 686 7.443879 TGTTTATGTCACATGTGTGTCACTTAT 59.556 33.333 24.63 9.03 44.22 1.73
686 687 7.595311 TTATGTCACATGTGTGTCACTTATC 57.405 36.000 24.63 5.43 44.22 1.75
687 688 4.954875 TGTCACATGTGTGTCACTTATCA 58.045 39.130 24.63 0.00 45.76 2.15
688 689 4.990426 TGTCACATGTGTGTCACTTATCAG 59.010 41.667 24.63 0.00 45.76 2.90
690 691 5.347093 GTCACATGTGTGTCACTTATCAGAG 59.653 44.000 24.63 0.00 45.76 3.35
691 692 5.011023 TCACATGTGTGTCACTTATCAGAGT 59.989 40.000 24.63 0.55 45.76 3.24
692 693 5.347093 CACATGTGTGTCACTTATCAGAGTC 59.653 44.000 18.03 0.00 40.96 3.36
693 694 4.521130 TGTGTGTCACTTATCAGAGTCC 57.479 45.455 4.27 0.00 35.11 3.85
695 696 5.321927 TGTGTGTCACTTATCAGAGTCCTA 58.678 41.667 4.27 0.00 35.11 2.94
699 700 7.489757 GTGTGTCACTTATCAGAGTCCTAAATC 59.510 40.741 4.27 0.00 0.00 2.17
700 701 6.981559 GTGTCACTTATCAGAGTCCTAAATCC 59.018 42.308 0.00 0.00 0.00 3.01
703 704 8.041323 GTCACTTATCAGAGTCCTAAATCCAAA 58.959 37.037 0.00 0.00 0.00 3.28
704 705 8.041323 TCACTTATCAGAGTCCTAAATCCAAAC 58.959 37.037 0.00 0.00 0.00 2.93
705 706 7.824289 CACTTATCAGAGTCCTAAATCCAAACA 59.176 37.037 0.00 0.00 0.00 2.83
707 708 9.401058 CTTATCAGAGTCCTAAATCCAAACATT 57.599 33.333 0.00 0.00 0.00 2.71
710 711 6.371548 TCAGAGTCCTAAATCCAAACATTTCG 59.628 38.462 0.00 0.00 0.00 3.46
713 714 3.445805 TCCTAAATCCAAACATTTCGCCC 59.554 43.478 0.00 0.00 0.00 6.13
714 715 2.362169 AAATCCAAACATTTCGCCCG 57.638 45.000 0.00 0.00 0.00 6.13
715 716 0.530288 AATCCAAACATTTCGCCCGG 59.470 50.000 0.00 0.00 0.00 5.73
716 717 0.610785 ATCCAAACATTTCGCCCGGT 60.611 50.000 0.00 0.00 0.00 5.28
717 718 1.080839 CCAAACATTTCGCCCGGTG 60.081 57.895 0.00 0.00 0.00 4.94
721 722 1.234615 AACATTTCGCCCGGTGACTG 61.235 55.000 0.00 4.30 0.00 3.51
723 724 0.953471 CATTTCGCCCGGTGACTGAA 60.953 55.000 0.00 0.00 0.00 3.02
724 725 0.035439 ATTTCGCCCGGTGACTGAAT 60.035 50.000 0.00 0.00 0.00 2.57
725 726 0.609151 TTTCGCCCGGTGACTGAATA 59.391 50.000 0.00 0.00 0.00 1.75
730 731 2.280628 GCCCGGTGACTGAATAAGAAG 58.719 52.381 0.00 0.00 0.00 2.85
731 732 2.354805 GCCCGGTGACTGAATAAGAAGT 60.355 50.000 0.00 0.00 0.00 3.01
733 734 4.324267 CCCGGTGACTGAATAAGAAGTTT 58.676 43.478 0.00 0.00 0.00 2.66
734 735 4.154195 CCCGGTGACTGAATAAGAAGTTTG 59.846 45.833 0.00 0.00 0.00 2.93
735 736 4.154195 CCGGTGACTGAATAAGAAGTTTGG 59.846 45.833 0.00 0.00 0.00 3.28
752 5433 6.363577 AGTTTGGTAATTATGCATGTCGAG 57.636 37.500 10.16 0.00 0.00 4.04
780 5461 2.110352 CACCATTTCCGCGTACCCC 61.110 63.158 4.92 0.00 0.00 4.95
785 5466 3.880162 TTTCCGCGTACCCCGGTTG 62.880 63.158 16.43 0.00 45.71 3.77
911 5607 0.472734 CCCCATTTCCCACAAACCCA 60.473 55.000 0.00 0.00 0.00 4.51
1260 6117 4.143333 CTCACGTACGGGGCCCTG 62.143 72.222 30.26 30.26 0.00 4.45
1300 6157 0.598942 TCTTGTGTTGCTCGCGCTTA 60.599 50.000 5.56 0.00 36.97 3.09
1316 6182 0.320771 CTTACCGTCCTGCAGCAGTT 60.321 55.000 21.26 2.67 0.00 3.16
1420 6321 1.573829 TTCCGGTCGAATTGCAGCAC 61.574 55.000 0.00 0.00 0.00 4.40
1499 6754 7.254692 GGTCTAATTAATTTCGTAGTTCAGGCC 60.255 40.741 5.91 0.00 0.00 5.19
1596 7040 9.884636 CATTTCCGAACCATTCCATATATACTA 57.115 33.333 0.00 0.00 0.00 1.82
1630 7074 5.556194 CGTTTGGTTTTGTTAGAATTGCTGC 60.556 40.000 0.00 0.00 0.00 5.25
1813 7257 3.539604 GATGTCTCAGGGAGAAATGGTG 58.460 50.000 3.70 0.00 40.59 4.17
2015 7741 6.577103 TCTGTGTGTCATATGATCTTTCTCC 58.423 40.000 9.02 0.00 0.00 3.71
2174 7917 6.585416 ACCAATGATGATTTTGCTATTTCCC 58.415 36.000 0.00 0.00 0.00 3.97
2414 8414 8.562892 AGTGAGATTGTAACATTGTTTGAGAAG 58.437 33.333 7.45 0.00 0.00 2.85
2426 8426 4.136796 TGTTTGAGAAGTCCTGTCATTGG 58.863 43.478 0.00 0.00 0.00 3.16
2484 8487 4.631131 GTTTTCAAGTTTTGGCTATGGCT 58.369 39.130 0.00 0.00 38.73 4.75
2641 13393 6.919721 ACAATTATCAACTTTTATGTGGCGT 58.080 32.000 0.00 0.00 0.00 5.68
2664 13416 6.183360 CGTTATGCCCAATACATTTTGGTAGT 60.183 38.462 2.81 0.00 43.92 2.73
2697 13449 2.017049 GCTTTGTCCACTGTTCTGTGT 58.983 47.619 8.52 0.00 36.30 3.72
2792 13554 5.687730 CAGTAAATGGACGCACATCTAGTAG 59.312 44.000 0.00 0.00 0.00 2.57
2793 13555 5.593095 AGTAAATGGACGCACATCTAGTAGA 59.407 40.000 1.45 1.45 0.00 2.59
2794 13556 3.992260 ATGGACGCACATCTAGTAGAC 57.008 47.619 0.85 0.00 0.00 2.59
2795 13557 3.000684 TGGACGCACATCTAGTAGACT 57.999 47.619 0.85 0.00 0.00 3.24
2796 13558 4.146745 TGGACGCACATCTAGTAGACTA 57.853 45.455 0.85 0.00 0.00 2.59
2797 13559 4.127907 TGGACGCACATCTAGTAGACTAG 58.872 47.826 10.00 10.00 45.57 2.57
2798 13560 4.128643 GGACGCACATCTAGTAGACTAGT 58.871 47.826 14.79 0.00 44.74 2.57
2799 13561 5.163374 TGGACGCACATCTAGTAGACTAGTA 60.163 44.000 14.79 4.53 44.74 1.82
2850 13620 0.944386 GCAGACGTGCCTTTCAGAAA 59.056 50.000 0.00 0.00 44.72 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.125685 CGCACATTGCAATTGACAACA 58.874 42.857 9.83 0.00 45.36 3.33
17 18 0.314618 ACAGCGCACATTGCAATTGA 59.685 45.000 9.83 0.00 45.36 2.57
55 56 2.771372 ACCCAGAACAAAGGCAAAACAT 59.229 40.909 0.00 0.00 0.00 2.71
102 103 1.474017 GATGTTACCATCGACCGACG 58.526 55.000 0.00 0.00 38.28 5.12
111 112 4.018960 AGAAGTGCCTTCAGATGTTACCAT 60.019 41.667 14.76 0.00 42.37 3.55
150 151 1.766494 TTGATGCCATGGACCACATC 58.234 50.000 18.40 18.30 37.84 3.06
158 159 6.164876 TGTACTGAAAAATTTGATGCCATGG 58.835 36.000 7.63 7.63 0.00 3.66
162 163 6.147492 TGCAATGTACTGAAAAATTTGATGCC 59.853 34.615 0.00 0.00 0.00 4.40
217 218 9.661563 CCTATTAGGATAACACGCCAAATAATA 57.338 33.333 3.41 0.00 37.67 0.98
219 220 7.737869 TCCTATTAGGATAACACGCCAAATAA 58.262 34.615 8.42 0.00 40.06 1.40
224 225 5.818678 ATTCCTATTAGGATAACACGCCA 57.181 39.130 13.22 0.00 45.34 5.69
225 226 5.995897 ACAATTCCTATTAGGATAACACGCC 59.004 40.000 13.22 0.00 45.34 5.68
230 231 9.642343 AGGGAAAACAATTCCTATTAGGATAAC 57.358 33.333 13.22 0.96 45.34 1.89
235 236 7.346471 TGAGAGGGAAAACAATTCCTATTAGG 58.654 38.462 3.07 3.07 38.61 2.69
236 237 8.807948 TTGAGAGGGAAAACAATTCCTATTAG 57.192 34.615 7.13 0.00 38.61 1.73
243 244 4.546570 CGGTTTGAGAGGGAAAACAATTC 58.453 43.478 0.00 0.00 37.89 2.17
245 246 2.890945 CCGGTTTGAGAGGGAAAACAAT 59.109 45.455 0.00 0.00 37.89 2.71
249 250 2.740506 AACCGGTTTGAGAGGGAAAA 57.259 45.000 15.86 0.00 0.00 2.29
250 251 4.076394 CAATAACCGGTTTGAGAGGGAAA 58.924 43.478 27.64 2.90 0.00 3.13
251 252 3.328343 TCAATAACCGGTTTGAGAGGGAA 59.672 43.478 27.64 3.77 0.00 3.97
253 254 3.343941 TCAATAACCGGTTTGAGAGGG 57.656 47.619 27.64 8.65 0.00 4.30
255 256 6.494893 TTTGATCAATAACCGGTTTGAGAG 57.505 37.500 27.64 11.50 35.47 3.20
257 258 6.468956 CGATTTTGATCAATAACCGGTTTGAG 59.531 38.462 27.64 15.16 35.47 3.02
259 260 5.514914 CCGATTTTGATCAATAACCGGTTTG 59.485 40.000 27.64 18.92 0.00 2.93
260 261 5.184287 ACCGATTTTGATCAATAACCGGTTT 59.816 36.000 27.64 6.67 44.19 3.27
262 263 4.266714 ACCGATTTTGATCAATAACCGGT 58.733 39.130 26.85 26.85 42.19 5.28
265 266 8.889717 TCTAGAAACCGATTTTGATCAATAACC 58.110 33.333 9.40 0.84 0.00 2.85
269 270 7.775093 TCCATCTAGAAACCGATTTTGATCAAT 59.225 33.333 9.40 0.00 0.00 2.57
270 271 7.109501 TCCATCTAGAAACCGATTTTGATCAA 58.890 34.615 3.38 3.38 0.00 2.57
271 272 6.649155 TCCATCTAGAAACCGATTTTGATCA 58.351 36.000 0.00 0.00 0.00 2.92
273 274 6.543831 CCTTCCATCTAGAAACCGATTTTGAT 59.456 38.462 0.00 0.00 0.00 2.57
274 275 5.880332 CCTTCCATCTAGAAACCGATTTTGA 59.120 40.000 0.00 0.00 0.00 2.69
275 276 5.880332 TCCTTCCATCTAGAAACCGATTTTG 59.120 40.000 0.00 0.00 0.00 2.44
276 277 6.062258 TCCTTCCATCTAGAAACCGATTTT 57.938 37.500 0.00 0.00 0.00 1.82
279 280 5.151454 AGATCCTTCCATCTAGAAACCGAT 58.849 41.667 0.00 0.00 30.84 4.18
280 281 4.547671 AGATCCTTCCATCTAGAAACCGA 58.452 43.478 0.00 0.00 30.84 4.69
281 282 4.946478 AGATCCTTCCATCTAGAAACCG 57.054 45.455 0.00 0.00 30.84 4.44
282 283 7.546250 TGATAGATCCTTCCATCTAGAAACC 57.454 40.000 0.00 0.00 38.50 3.27
290 291 4.888326 AGTGCTGATAGATCCTTCCATC 57.112 45.455 0.00 0.00 0.00 3.51
292 293 5.441718 AAAAGTGCTGATAGATCCTTCCA 57.558 39.130 0.00 0.00 0.00 3.53
293 294 6.587273 ACTAAAAGTGCTGATAGATCCTTCC 58.413 40.000 0.00 0.00 0.00 3.46
295 296 6.317391 GCAACTAAAAGTGCTGATAGATCCTT 59.683 38.462 0.00 0.00 0.00 3.36
296 297 5.819901 GCAACTAAAAGTGCTGATAGATCCT 59.180 40.000 0.00 0.00 0.00 3.24
299 300 7.693969 AAAGCAACTAAAAGTGCTGATAGAT 57.306 32.000 0.00 0.00 34.49 1.98
354 355 8.586879 TGTTCATTGTATTTCCATGATTGGTA 57.413 30.769 0.00 0.00 44.06 3.25
356 357 8.951787 AATGTTCATTGTATTTCCATGATTGG 57.048 30.769 0.00 0.00 45.15 3.16
401 402 8.031864 CGCTAAGTGGTCTATGAATCTTGATAT 58.968 37.037 0.00 0.00 0.00 1.63
405 406 5.460419 GTCGCTAAGTGGTCTATGAATCTTG 59.540 44.000 0.00 0.00 0.00 3.02
406 407 5.127194 TGTCGCTAAGTGGTCTATGAATCTT 59.873 40.000 0.00 0.00 0.00 2.40
410 411 4.794278 TTGTCGCTAAGTGGTCTATGAA 57.206 40.909 0.00 0.00 0.00 2.57
412 413 6.923508 TCAATATTGTCGCTAAGTGGTCTATG 59.076 38.462 14.97 0.00 0.00 2.23
413 414 6.924060 GTCAATATTGTCGCTAAGTGGTCTAT 59.076 38.462 14.97 0.00 0.00 1.98
415 416 5.105310 AGTCAATATTGTCGCTAAGTGGTCT 60.105 40.000 14.97 0.00 0.00 3.85
416 417 5.109903 AGTCAATATTGTCGCTAAGTGGTC 58.890 41.667 14.97 0.00 0.00 4.02
417 418 5.086104 AGTCAATATTGTCGCTAAGTGGT 57.914 39.130 14.97 0.00 0.00 4.16
418 419 6.422776 AAAGTCAATATTGTCGCTAAGTGG 57.577 37.500 14.97 0.00 0.00 4.00
450 451 6.897986 AGGTAGATTTTCATGAAGATCTGCT 58.102 36.000 34.70 25.20 41.23 4.24
451 452 8.668510 TTAGGTAGATTTTCATGAAGATCTGC 57.331 34.615 34.95 33.31 40.89 4.26
456 457 8.677300 GCACAATTAGGTAGATTTTCATGAAGA 58.323 33.333 8.41 4.49 0.00 2.87
457 458 8.461222 TGCACAATTAGGTAGATTTTCATGAAG 58.539 33.333 8.41 0.00 0.00 3.02
458 459 8.347004 TGCACAATTAGGTAGATTTTCATGAA 57.653 30.769 3.38 3.38 0.00 2.57
459 460 7.936496 TGCACAATTAGGTAGATTTTCATGA 57.064 32.000 0.00 0.00 0.00 3.07
463 464 8.620533 GTGATTGCACAATTAGGTAGATTTTC 57.379 34.615 0.00 0.00 44.51 2.29
479 480 8.023128 ACTAGTGTCAAAATATTGTGATTGCAC 58.977 33.333 11.51 13.79 45.35 4.57
481 482 8.454106 AGACTAGTGTCAAAATATTGTGATTGC 58.546 33.333 11.51 5.51 45.20 3.56
495 496 9.567848 GTTTTTGAATTTCAAGACTAGTGTCAA 57.432 29.630 11.41 0.00 45.20 3.18
504 505 9.528018 TCAGTTATGGTTTTTGAATTTCAAGAC 57.472 29.630 11.41 13.23 37.70 3.01
510 511 9.883142 TGAGTTTCAGTTATGGTTTTTGAATTT 57.117 25.926 0.00 0.00 0.00 1.82
511 512 9.883142 TTGAGTTTCAGTTATGGTTTTTGAATT 57.117 25.926 0.00 0.00 0.00 2.17
512 513 9.313118 GTTGAGTTTCAGTTATGGTTTTTGAAT 57.687 29.630 0.00 0.00 0.00 2.57
515 516 7.254084 GCAGTTGAGTTTCAGTTATGGTTTTTG 60.254 37.037 0.00 0.00 0.00 2.44
518 519 5.594317 AGCAGTTGAGTTTCAGTTATGGTTT 59.406 36.000 0.00 0.00 0.00 3.27
519 520 5.133221 AGCAGTTGAGTTTCAGTTATGGTT 58.867 37.500 0.00 0.00 0.00 3.67
520 521 4.718961 AGCAGTTGAGTTTCAGTTATGGT 58.281 39.130 0.00 0.00 0.00 3.55
521 522 6.992063 ATAGCAGTTGAGTTTCAGTTATGG 57.008 37.500 0.00 0.00 0.00 2.74
524 525 9.944376 AAGATAATAGCAGTTGAGTTTCAGTTA 57.056 29.630 0.00 0.00 0.00 2.24
526 527 7.880195 ACAAGATAATAGCAGTTGAGTTTCAGT 59.120 33.333 0.00 0.00 0.00 3.41
527 528 8.261492 ACAAGATAATAGCAGTTGAGTTTCAG 57.739 34.615 0.00 0.00 0.00 3.02
528 529 7.334421 GGACAAGATAATAGCAGTTGAGTTTCA 59.666 37.037 0.00 0.00 0.00 2.69
529 530 7.464710 CGGACAAGATAATAGCAGTTGAGTTTC 60.465 40.741 0.00 0.00 0.00 2.78
531 532 5.812642 CGGACAAGATAATAGCAGTTGAGTT 59.187 40.000 0.00 0.00 0.00 3.01
533 534 5.592054 TCGGACAAGATAATAGCAGTTGAG 58.408 41.667 0.00 0.00 0.00 3.02
534 535 5.592104 TCGGACAAGATAATAGCAGTTGA 57.408 39.130 0.00 0.00 0.00 3.18
535 536 6.535150 TCTTTCGGACAAGATAATAGCAGTTG 59.465 38.462 0.00 0.00 0.00 3.16
537 538 6.222038 TCTTTCGGACAAGATAATAGCAGT 57.778 37.500 0.00 0.00 0.00 4.40
541 542 8.321716 CGAGTTTTCTTTCGGACAAGATAATAG 58.678 37.037 4.32 0.00 32.69 1.73
543 544 7.061752 CGAGTTTTCTTTCGGACAAGATAAT 57.938 36.000 4.32 0.00 32.69 1.28
544 545 6.462073 CGAGTTTTCTTTCGGACAAGATAA 57.538 37.500 4.32 3.92 32.69 1.75
554 555 7.745015 TGGATTTATTACCGAGTTTTCTTTCG 58.255 34.615 0.00 0.00 36.62 3.46
556 557 8.683615 GGATGGATTTATTACCGAGTTTTCTTT 58.316 33.333 0.00 0.00 0.00 2.52
557 558 7.832187 TGGATGGATTTATTACCGAGTTTTCTT 59.168 33.333 0.00 0.00 0.00 2.52
558 559 7.343357 TGGATGGATTTATTACCGAGTTTTCT 58.657 34.615 0.00 0.00 0.00 2.52
559 560 7.562454 TGGATGGATTTATTACCGAGTTTTC 57.438 36.000 0.00 0.00 0.00 2.29
560 561 7.948034 TTGGATGGATTTATTACCGAGTTTT 57.052 32.000 0.00 0.00 0.00 2.43
561 562 7.948034 TTTGGATGGATTTATTACCGAGTTT 57.052 32.000 0.00 0.00 0.00 2.66
565 566 7.012894 GTGTCATTTGGATGGATTTATTACCGA 59.987 37.037 0.00 0.00 33.93 4.69
566 567 7.138736 GTGTCATTTGGATGGATTTATTACCG 58.861 38.462 0.00 0.00 33.93 4.02
567 568 7.433680 GGTGTCATTTGGATGGATTTATTACC 58.566 38.462 0.00 0.00 33.93 2.85
568 569 7.433680 GGGTGTCATTTGGATGGATTTATTAC 58.566 38.462 0.00 0.00 33.93 1.89
569 570 6.264292 CGGGTGTCATTTGGATGGATTTATTA 59.736 38.462 0.00 0.00 33.93 0.98
570 571 5.068987 CGGGTGTCATTTGGATGGATTTATT 59.931 40.000 0.00 0.00 33.93 1.40
571 572 4.584325 CGGGTGTCATTTGGATGGATTTAT 59.416 41.667 0.00 0.00 33.93 1.40
574 575 2.291540 ACGGGTGTCATTTGGATGGATT 60.292 45.455 0.00 0.00 33.93 3.01
575 576 1.284785 ACGGGTGTCATTTGGATGGAT 59.715 47.619 0.00 0.00 33.93 3.41
577 578 0.810648 CACGGGTGTCATTTGGATGG 59.189 55.000 0.00 0.00 33.93 3.51
581 582 0.591170 GTCACACGGGTGTCATTTGG 59.409 55.000 19.06 0.00 45.45 3.28
582 583 1.002900 GTGTCACACGGGTGTCATTTG 60.003 52.381 20.28 0.00 43.18 2.32
583 584 1.305201 GTGTCACACGGGTGTCATTT 58.695 50.000 20.28 0.00 43.18 2.32
584 585 3.000815 GTGTCACACGGGTGTCATT 57.999 52.632 20.28 0.00 43.18 2.57
585 586 4.771127 GTGTCACACGGGTGTCAT 57.229 55.556 20.28 0.00 43.18 3.06
595 596 0.948623 CCGGATTGCTTCGTGTCACA 60.949 55.000 0.00 0.00 0.00 3.58
598 599 1.359459 GGACCGGATTGCTTCGTGTC 61.359 60.000 9.46 0.00 0.00 3.67
600 601 1.079127 AGGACCGGATTGCTTCGTG 60.079 57.895 9.46 0.00 0.00 4.35
601 602 1.079127 CAGGACCGGATTGCTTCGT 60.079 57.895 9.46 0.00 0.00 3.85
602 603 1.815421 CCAGGACCGGATTGCTTCG 60.815 63.158 9.46 0.00 0.00 3.79
603 604 2.115291 GCCAGGACCGGATTGCTTC 61.115 63.158 9.46 0.00 0.00 3.86
604 605 2.044946 GCCAGGACCGGATTGCTT 60.045 61.111 9.46 0.00 0.00 3.91
605 606 4.473520 CGCCAGGACCGGATTGCT 62.474 66.667 9.46 0.00 0.00 3.91
606 607 4.778143 ACGCCAGGACCGGATTGC 62.778 66.667 9.46 1.93 0.00 3.56
607 608 2.511600 GACGCCAGGACCGGATTG 60.512 66.667 9.46 2.67 0.00 2.67
610 611 1.186917 TAAAAGACGCCAGGACCGGA 61.187 55.000 9.46 0.00 0.00 5.14
611 612 0.320946 TTAAAAGACGCCAGGACCGG 60.321 55.000 0.00 0.00 0.00 5.28
612 613 1.196127 GTTTAAAAGACGCCAGGACCG 59.804 52.381 0.00 0.00 0.00 4.79
614 615 5.237996 ACTTTAGTTTAAAAGACGCCAGGAC 59.762 40.000 3.51 0.00 38.50 3.85
615 616 5.370679 ACTTTAGTTTAAAAGACGCCAGGA 58.629 37.500 3.51 0.00 38.50 3.86
616 617 5.684550 ACTTTAGTTTAAAAGACGCCAGG 57.315 39.130 3.51 0.00 38.50 4.45
617 618 6.631636 GTCAACTTTAGTTTAAAAGACGCCAG 59.368 38.462 3.51 0.00 38.50 4.85
618 619 6.093771 TGTCAACTTTAGTTTAAAAGACGCCA 59.906 34.615 3.51 0.00 38.50 5.69
620 621 7.184779 AGTGTCAACTTTAGTTTAAAAGACGC 58.815 34.615 12.17 12.17 38.50 5.19
621 622 8.385111 TGAGTGTCAACTTTAGTTTAAAAGACG 58.615 33.333 3.51 0.00 38.50 4.18
629 630 9.353999 GTCAATTTTGAGTGTCAACTTTAGTTT 57.646 29.630 0.00 0.00 35.89 2.66
630 631 8.519526 TGTCAATTTTGAGTGTCAACTTTAGTT 58.480 29.630 0.00 0.00 35.89 2.24
631 632 8.050778 TGTCAATTTTGAGTGTCAACTTTAGT 57.949 30.769 0.00 0.00 35.89 2.24
634 635 7.276218 CACATGTCAATTTTGAGTGTCAACTTT 59.724 33.333 0.00 0.00 35.89 2.66
635 636 6.753279 CACATGTCAATTTTGAGTGTCAACTT 59.247 34.615 0.00 0.00 35.89 2.66
636 637 6.127647 ACACATGTCAATTTTGAGTGTCAACT 60.128 34.615 0.00 0.00 38.78 3.16
637 638 6.035843 ACACATGTCAATTTTGAGTGTCAAC 58.964 36.000 0.00 0.00 38.78 3.18
640 641 8.693504 CATAAACACATGTCAATTTTGAGTGTC 58.306 33.333 13.76 0.00 40.78 3.67
665 666 4.954875 TGATAAGTGACACACATGTGACA 58.045 39.130 31.94 22.65 44.62 3.58
669 670 5.473931 GACTCTGATAAGTGACACACATGT 58.526 41.667 8.59 0.00 43.71 3.21
670 671 4.867047 GGACTCTGATAAGTGACACACATG 59.133 45.833 8.59 0.00 36.74 3.21
671 672 4.774726 AGGACTCTGATAAGTGACACACAT 59.225 41.667 8.59 0.00 36.74 3.21
672 673 4.152647 AGGACTCTGATAAGTGACACACA 58.847 43.478 8.59 1.97 36.74 3.72
673 674 4.792521 AGGACTCTGATAAGTGACACAC 57.207 45.455 8.59 0.00 34.10 3.82
675 676 6.981559 GGATTTAGGACTCTGATAAGTGACAC 59.018 42.308 0.00 0.00 0.00 3.67
676 677 6.667848 TGGATTTAGGACTCTGATAAGTGACA 59.332 38.462 0.00 0.00 0.00 3.58
679 680 7.824289 TGTTTGGATTTAGGACTCTGATAAGTG 59.176 37.037 0.00 0.00 0.00 3.16
681 682 8.970859 ATGTTTGGATTTAGGACTCTGATAAG 57.029 34.615 0.00 0.00 0.00 1.73
682 683 9.753674 AAATGTTTGGATTTAGGACTCTGATAA 57.246 29.630 0.00 0.00 0.00 1.75
683 684 9.396022 GAAATGTTTGGATTTAGGACTCTGATA 57.604 33.333 0.00 0.00 0.00 2.15
684 685 7.066284 CGAAATGTTTGGATTTAGGACTCTGAT 59.934 37.037 0.00 0.00 0.00 2.90
685 686 6.371548 CGAAATGTTTGGATTTAGGACTCTGA 59.628 38.462 0.00 0.00 0.00 3.27
686 687 6.546395 CGAAATGTTTGGATTTAGGACTCTG 58.454 40.000 0.00 0.00 0.00 3.35
687 688 5.123979 GCGAAATGTTTGGATTTAGGACTCT 59.876 40.000 0.00 0.00 0.00 3.24
688 689 5.332707 GCGAAATGTTTGGATTTAGGACTC 58.667 41.667 0.00 0.00 0.00 3.36
690 691 4.421058 GGCGAAATGTTTGGATTTAGGAC 58.579 43.478 0.00 0.00 0.00 3.85
691 692 3.445805 GGGCGAAATGTTTGGATTTAGGA 59.554 43.478 0.00 0.00 0.00 2.94
692 693 3.733684 CGGGCGAAATGTTTGGATTTAGG 60.734 47.826 0.00 0.00 0.00 2.69
693 694 3.434637 CGGGCGAAATGTTTGGATTTAG 58.565 45.455 0.00 0.00 0.00 1.85
695 696 1.067213 CCGGGCGAAATGTTTGGATTT 60.067 47.619 0.00 0.00 0.00 2.17
699 700 1.080839 CACCGGGCGAAATGTTTGG 60.081 57.895 6.32 0.00 0.00 3.28
700 701 0.386731 GTCACCGGGCGAAATGTTTG 60.387 55.000 6.32 0.00 0.00 2.93
703 704 1.671054 CAGTCACCGGGCGAAATGT 60.671 57.895 6.32 0.00 0.00 2.71
704 705 0.953471 TTCAGTCACCGGGCGAAATG 60.953 55.000 6.32 4.92 0.00 2.32
705 706 0.035439 ATTCAGTCACCGGGCGAAAT 60.035 50.000 6.32 0.00 0.00 2.17
707 708 0.609151 TTATTCAGTCACCGGGCGAA 59.391 50.000 6.32 0.70 0.00 4.70
710 711 2.280628 CTTCTTATTCAGTCACCGGGC 58.719 52.381 6.32 0.00 0.00 6.13
713 714 4.755123 ACCAAACTTCTTATTCAGTCACCG 59.245 41.667 0.00 0.00 0.00 4.94
714 715 7.739498 TTACCAAACTTCTTATTCAGTCACC 57.261 36.000 0.00 0.00 0.00 4.02
724 725 8.394877 CGACATGCATAATTACCAAACTTCTTA 58.605 33.333 0.00 0.00 0.00 2.10
725 726 7.120579 TCGACATGCATAATTACCAAACTTCTT 59.879 33.333 0.00 0.00 0.00 2.52
730 731 6.119144 ACTCGACATGCATAATTACCAAAC 57.881 37.500 0.00 0.00 0.00 2.93
731 732 5.006261 CGACTCGACATGCATAATTACCAAA 59.994 40.000 0.00 0.00 0.00 3.28
733 734 4.048504 CGACTCGACATGCATAATTACCA 58.951 43.478 0.00 0.00 0.00 3.25
734 735 3.428870 CCGACTCGACATGCATAATTACC 59.571 47.826 0.00 0.00 0.00 2.85
735 736 3.428870 CCCGACTCGACATGCATAATTAC 59.571 47.826 0.00 0.00 0.00 1.89
752 5433 1.305930 GGAAATGGTGAGTGCCCGAC 61.306 60.000 0.00 0.00 0.00 4.79
785 5466 1.892391 GGATGCGGATTCGGGTTCC 60.892 63.158 0.00 0.00 36.79 3.62
927 5652 3.636231 CGGAGTGGTTGGGCTGGA 61.636 66.667 0.00 0.00 0.00 3.86
1224 6081 1.983224 CGCCTGGAGGAAGAGGAAA 59.017 57.895 0.00 0.00 37.39 3.13
1260 6117 2.726832 AGTTGTAGACGCAGACCTTC 57.273 50.000 0.00 0.00 0.00 3.46
1300 6157 2.031163 GAACTGCTGCAGGACGGT 59.969 61.111 31.00 10.05 35.51 4.83
1420 6321 5.505181 AATGATAACCCTGGCCTATGTAG 57.495 43.478 3.32 0.00 0.00 2.74
1596 7040 5.017294 ACAAAACCAAACGGATGAACATT 57.983 34.783 0.00 0.00 0.00 2.71
1609 7053 4.376146 GGCAGCAATTCTAACAAAACCAA 58.624 39.130 0.00 0.00 0.00 3.67
1813 7257 1.134098 ACATCCATGATCACCGAACCC 60.134 52.381 0.00 0.00 0.00 4.11
1960 7411 2.604139 CAAAGCAAAGGGGGAGGTAAA 58.396 47.619 0.00 0.00 0.00 2.01
2148 7888 8.203485 GGGAAATAGCAAAATCATCATTGGTTA 58.797 33.333 0.00 0.00 38.19 2.85
2174 7917 5.242171 TGAATGCTAATATGCAATGACCAGG 59.758 40.000 0.00 0.00 46.61 4.45
2414 8414 3.699538 GGGGAAATTACCAATGACAGGAC 59.300 47.826 0.00 0.00 0.00 3.85
2594 13110 2.841442 AAGAACTAGAGGTGTGCCAC 57.159 50.000 0.00 0.00 37.19 5.01
2697 13449 6.980593 ACAGCATAAAAGCATTAAACTGTGA 58.019 32.000 14.34 0.00 34.74 3.58
2792 13554 4.271661 AGCACCACCTTAGAGTACTAGTC 58.728 47.826 0.00 0.00 0.00 2.59
2793 13555 4.319037 AGCACCACCTTAGAGTACTAGT 57.681 45.455 0.00 0.00 0.00 2.57
2794 13556 5.241949 CCATAGCACCACCTTAGAGTACTAG 59.758 48.000 0.00 0.00 0.00 2.57
2795 13557 5.138276 CCATAGCACCACCTTAGAGTACTA 58.862 45.833 0.00 0.00 0.00 1.82
2796 13558 3.961408 CCATAGCACCACCTTAGAGTACT 59.039 47.826 0.00 0.00 0.00 2.73
2797 13559 3.492829 GCCATAGCACCACCTTAGAGTAC 60.493 52.174 0.00 0.00 39.53 2.73
2798 13560 2.698797 GCCATAGCACCACCTTAGAGTA 59.301 50.000 0.00 0.00 39.53 2.59
2799 13561 1.486726 GCCATAGCACCACCTTAGAGT 59.513 52.381 0.00 0.00 39.53 3.24
2850 13620 4.344968 ACTTGCAAGGCCAGAAATTAACTT 59.655 37.500 29.18 0.25 0.00 2.66


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

AutoCloner maintained by Alex Coulton.