Multiple sequence alignment - TraesCS5D01G466500

Loading Multiple Alignment...

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 TraesCS5D01G466500 chr5D 100.000 3463 0 0 1 3463 508997286 508993824 0.000000e+00 6396.0
1 TraesCS5D01G466500 chr5D 96.354 384 13 1 891 1273 508963222 508962839 6.310000e-177 630.0
2 TraesCS5D01G466500 chr5D 84.015 269 34 6 2173 2439 508962598 508962337 2.060000e-62 250.0
3 TraesCS5D01G466500 chr5D 84.118 170 19 7 1439 1604 508995222 508995057 1.290000e-34 158.0
4 TraesCS5D01G466500 chr5D 84.118 170 19 7 2065 2230 508995848 508995683 1.290000e-34 158.0
5 TraesCS5D01G466500 chr5B 90.952 1481 108 12 1995 3463 639607981 639606515 0.000000e+00 1969.0
6 TraesCS5D01G466500 chr5B 85.379 554 38 24 1461 2004 639610302 639609782 5.090000e-148 534.0
7 TraesCS5D01G466500 chr5B 91.768 328 27 0 946 1273 639610686 639610359 1.130000e-124 457.0
8 TraesCS5D01G466500 chr5B 85.838 346 21 6 928 1273 639556944 639556627 3.310000e-90 342.0
9 TraesCS5D01G466500 chr5B 84.262 305 40 7 439 741 639612423 639612125 1.220000e-74 291.0
10 TraesCS5D01G466500 chr5B 81.273 267 29 10 2173 2435 639556445 639556196 2.730000e-46 196.0
11 TraesCS5D01G466500 chr5B 95.000 40 1 1 2065 2104 639610357 639610319 1.040000e-05 62.1
12 TraesCS5D01G466500 chr5A 89.201 926 59 14 1643 2546 636293572 636292666 0.000000e+00 1118.0
13 TraesCS5D01G466500 chr5A 88.079 453 47 5 1 449 636298290 636297841 6.580000e-147 531.0
14 TraesCS5D01G466500 chr5A 86.427 361 20 8 927 1273 636295723 636295378 5.460000e-98 368.0
15 TraesCS5D01G466500 chr5A 90.393 229 15 6 1429 1656 636295386 636295164 9.400000e-76 294.0
16 TraesCS5D01G466500 chr5A 90.244 164 13 3 550 712 636297823 636297662 9.740000e-51 211.0
17 TraesCS5D01G466500 chr5A 78.431 153 20 6 1 152 32700393 32700533 1.710000e-13 87.9
18 TraesCS5D01G466500 chr3D 77.407 270 49 5 1 269 565195005 565195263 2.150000e-32 150.0
19 TraesCS5D01G466500 chr3D 97.143 35 1 0 1397 1431 545342756 545342790 3.730000e-05 60.2
20 TraesCS5D01G466500 chr3D 100.000 30 0 0 1397 1426 401679360 401679389 4.830000e-04 56.5
21 TraesCS5D01G466500 chr4D 92.929 99 7 0 1275 1373 62478472 62478374 1.000000e-30 145.0
22 TraesCS5D01G466500 chr7B 77.487 191 38 5 40 229 150027045 150026859 3.650000e-20 110.0
23 TraesCS5D01G466500 chr1A 84.783 92 14 0 1274 1365 553880527 553880436 3.680000e-15 93.5
24 TraesCS5D01G466500 chr1D 83.908 87 12 2 245 331 464348995 464348911 7.970000e-12 82.4
25 TraesCS5D01G466500 chr1D 96.970 33 1 0 1397 1429 328117584 328117552 4.830000e-04 56.5
26 TraesCS5D01G466500 chr3B 81.443 97 16 2 1275 1371 83956544 83956638 1.030000e-10 78.7
27 TraesCS5D01G466500 chr7A 91.111 45 4 0 1278 1322 664629352 664629396 1.040000e-05 62.1
28 TraesCS5D01G466500 chrUn 92.683 41 3 0 1397 1437 31615839 31615879 3.730000e-05 60.2
29 TraesCS5D01G466500 chr2B 97.222 36 0 1 1394 1429 132829352 132829318 3.730000e-05 60.2
30 TraesCS5D01G466500 chr6D 100.000 30 0 0 1397 1426 14681958 14681987 4.830000e-04 56.5
31 TraesCS5D01G466500 chr3A 100.000 30 0 0 1397 1426 522063828 522063857 4.830000e-04 56.5
32 TraesCS5D01G466500 chr6B 94.118 34 2 0 1263 1296 142631527 142631560 6.000000e-03 52.8


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 TraesCS5D01G466500 chr5D 508993824 508997286 3462 True 2237.333333 6396 89.4120 1 3463 3 chr5D.!!$R2 3462
1 TraesCS5D01G466500 chr5D 508962337 508963222 885 True 440.000000 630 90.1845 891 2439 2 chr5D.!!$R1 1548
2 TraesCS5D01G466500 chr5B 639606515 639612423 5908 True 662.620000 1969 89.4722 439 3463 5 chr5B.!!$R2 3024
3 TraesCS5D01G466500 chr5B 639556196 639556944 748 True 269.000000 342 83.5555 928 2435 2 chr5B.!!$R1 1507
4 TraesCS5D01G466500 chr5A 636292666 636298290 5624 True 504.400000 1118 88.8688 1 2546 5 chr5A.!!$R1 2545

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
547 552 0.034896 ACGTCCAAACCAGGCAGTAG 59.965 55.0 0.0 0.0 0.00 2.57 F
829 2768 0.108585 GGGCTTGTGTCCAACAGAGA 59.891 55.0 0.0 0.0 40.74 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 4428 0.107654 GGGATGTGTGTGGCTAGGTC 60.108 60.0 0.00 0.0 0.0 3.85 R
2683 9236 0.467384 CCATGAGTGAGTAGGGCCAG 59.533 60.0 6.18 0.0 0.0 4.85 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
18 19 3.046280 GGACTGGACGAAACGGATC 57.954 57.895 0.00 0.00 0.00 3.36
124 125 2.202756 GTCGCCGTGGACCAGATC 60.203 66.667 0.00 0.00 0.00 2.75
152 153 2.123982 CCCAAGCTCATCTGGGCC 60.124 66.667 8.28 0.00 34.28 5.80
155 156 3.801997 AAGCTCATCTGGGCCCGG 61.802 66.667 26.30 26.30 0.00 5.73
174 175 1.653151 GTAAGACCTGCGATCCCAAC 58.347 55.000 0.00 0.00 0.00 3.77
209 210 2.202623 CTACGTCGCAGAGTGGCC 60.203 66.667 0.00 0.00 36.95 5.36
210 211 2.986979 TACGTCGCAGAGTGGCCA 60.987 61.111 0.00 0.00 36.95 5.36
223 224 4.643387 GGCCACGCCTCCACTGTT 62.643 66.667 0.00 0.00 46.69 3.16
242 243 2.263227 CCGCACCATGTACACCGA 59.737 61.111 0.00 0.00 0.00 4.69
262 263 4.918201 GGATCCCGCCGCTCCTTG 62.918 72.222 0.00 0.00 0.00 3.61
349 352 2.672996 CCCACAACCCAGGCTTCG 60.673 66.667 0.00 0.00 0.00 3.79
362 365 2.167861 GCTTCGCCGGTGTGATCTC 61.168 63.158 16.01 0.00 0.00 2.75
434 439 4.310769 CCACATCGTCCTCCATATTCTTC 58.689 47.826 0.00 0.00 0.00 2.87
436 441 5.226396 CACATCGTCCTCCATATTCTTCTC 58.774 45.833 0.00 0.00 0.00 2.87
442 447 3.070734 TCCTCCATATTCTTCTCTGCAGC 59.929 47.826 9.47 0.00 0.00 5.25
462 467 0.248458 GTTGCTGGTCGTTGTGTTGG 60.248 55.000 0.00 0.00 0.00 3.77
483 488 0.518636 CTTGTGGCAGATGTGGAACG 59.481 55.000 0.00 0.00 42.39 3.95
484 489 1.514678 TTGTGGCAGATGTGGAACGC 61.515 55.000 0.00 0.00 42.39 4.84
486 491 3.134127 GGCAGATGTGGAACGCCC 61.134 66.667 0.00 0.00 42.39 6.13
527 532 3.801594 GCTTTCGGTTTGCAAGATTTTGA 59.198 39.130 0.00 0.00 36.36 2.69
529 534 5.710613 TTTCGGTTTGCAAGATTTTGAAC 57.289 34.783 0.00 0.00 36.36 3.18
531 536 3.112580 CGGTTTGCAAGATTTTGAACGT 58.887 40.909 0.00 0.00 36.36 3.99
532 537 3.179599 CGGTTTGCAAGATTTTGAACGTC 59.820 43.478 0.00 0.00 36.36 4.34
533 538 3.489416 GGTTTGCAAGATTTTGAACGTCC 59.511 43.478 0.00 0.00 36.36 4.79
534 539 4.109050 GTTTGCAAGATTTTGAACGTCCA 58.891 39.130 0.00 0.00 36.36 4.02
538 543 3.489416 GCAAGATTTTGAACGTCCAAACC 59.511 43.478 0.00 0.00 35.95 3.27
539 544 4.677584 CAAGATTTTGAACGTCCAAACCA 58.322 39.130 0.00 0.00 35.95 3.67
545 550 0.818040 GAACGTCCAAACCAGGCAGT 60.818 55.000 0.00 0.00 0.00 4.40
546 551 0.470766 AACGTCCAAACCAGGCAGTA 59.529 50.000 0.00 0.00 0.00 2.74
547 552 0.034896 ACGTCCAAACCAGGCAGTAG 59.965 55.000 0.00 0.00 0.00 2.57
548 553 0.320374 CGTCCAAACCAGGCAGTAGA 59.680 55.000 0.00 0.00 0.00 2.59
552 557 1.347707 CCAAACCAGGCAGTAGACAGA 59.652 52.381 0.00 0.00 0.00 3.41
567 572 2.942376 AGACAGACGTTTGATGCACAAA 59.058 40.909 13.73 9.46 44.79 2.83
623 628 0.806868 AAATGTGTCCGAGCAGCATG 59.193 50.000 0.00 0.00 40.87 4.06
651 656 4.536364 ACATTTACAAGCGATTCGATGG 57.464 40.909 10.88 3.18 0.00 3.51
665 670 0.249489 CGATGGATCGGGTTGGAGTC 60.249 60.000 0.88 0.00 45.93 3.36
791 2730 5.303845 AGAAGACTTTCCACGTTTACCTACT 59.696 40.000 0.00 0.00 33.64 2.57
797 2736 5.649782 TTCCACGTTTACCTACTAGGAAG 57.350 43.478 9.28 0.00 37.67 3.46
829 2768 0.108585 GGGCTTGTGTCCAACAGAGA 59.891 55.000 0.00 0.00 40.74 3.10
854 2793 1.238625 CCCGCGCAAGTTTCCCTAAA 61.239 55.000 8.75 0.00 41.68 1.85
978 3980 1.402896 GGATCGATCTGCTCCCACCA 61.403 60.000 23.96 0.00 0.00 4.17
1063 4065 0.757188 CTCCTATGACGGGAGCCAGT 60.757 60.000 0.00 0.00 42.95 4.00
1116 4118 2.890808 ATGGTACTGTGCCATACGAG 57.109 50.000 26.04 0.00 44.23 4.18
1201 4203 6.314896 CACAGTCTGGAAATACTTCAAGATCC 59.685 42.308 4.53 0.00 42.46 3.36
1213 4215 3.474798 TCAAGATCCTCACTAGGGTGT 57.525 47.619 0.00 0.00 43.84 4.16
1245 4260 2.581246 GACCCCCTTCCAGTTATCCTTT 59.419 50.000 0.00 0.00 0.00 3.11
1264 4279 5.788533 TCCTTTCACTCACCCCTCTAAATTA 59.211 40.000 0.00 0.00 0.00 1.40
1265 4280 6.447084 TCCTTTCACTCACCCCTCTAAATTAT 59.553 38.462 0.00 0.00 0.00 1.28
1266 4281 6.768381 CCTTTCACTCACCCCTCTAAATTATC 59.232 42.308 0.00 0.00 0.00 1.75
1267 4282 5.888982 TCACTCACCCCTCTAAATTATCC 57.111 43.478 0.00 0.00 0.00 2.59
1268 4283 5.538877 TCACTCACCCCTCTAAATTATCCT 58.461 41.667 0.00 0.00 0.00 3.24
1269 4284 5.970640 TCACTCACCCCTCTAAATTATCCTT 59.029 40.000 0.00 0.00 0.00 3.36
1270 4285 6.447084 TCACTCACCCCTCTAAATTATCCTTT 59.553 38.462 0.00 0.00 0.00 3.11
1271 4286 7.036863 TCACTCACCCCTCTAAATTATCCTTTT 60.037 37.037 0.00 0.00 0.00 2.27
1272 4287 7.615757 CACTCACCCCTCTAAATTATCCTTTTT 59.384 37.037 0.00 0.00 0.00 1.94
1273 4288 8.842764 ACTCACCCCTCTAAATTATCCTTTTTA 58.157 33.333 0.00 0.00 0.00 1.52
1274 4289 9.343539 CTCACCCCTCTAAATTATCCTTTTTAG 57.656 37.037 0.00 0.00 36.96 1.85
1275 4290 8.842764 TCACCCCTCTAAATTATCCTTTTTAGT 58.157 33.333 0.00 0.00 36.96 2.24
1276 4291 9.475620 CACCCCTCTAAATTATCCTTTTTAGTT 57.524 33.333 0.00 0.00 36.96 2.24
1289 4304 8.691661 ATCCTTTTTAGTTTTGCTAAGTCTCA 57.308 30.769 0.00 0.00 40.41 3.27
1290 4305 8.154649 TCCTTTTTAGTTTTGCTAAGTCTCAG 57.845 34.615 0.00 0.00 40.41 3.35
1291 4306 7.773690 TCCTTTTTAGTTTTGCTAAGTCTCAGT 59.226 33.333 0.00 0.00 40.41 3.41
1292 4307 8.070769 CCTTTTTAGTTTTGCTAAGTCTCAGTC 58.929 37.037 0.00 0.00 40.41 3.51
1293 4308 6.764877 TTTAGTTTTGCTAAGTCTCAGTCG 57.235 37.500 0.00 0.00 40.41 4.18
1294 4309 4.585955 AGTTTTGCTAAGTCTCAGTCGA 57.414 40.909 0.00 0.00 0.00 4.20
1295 4310 5.140747 AGTTTTGCTAAGTCTCAGTCGAT 57.859 39.130 0.00 0.00 0.00 3.59
1296 4311 5.542779 AGTTTTGCTAAGTCTCAGTCGATT 58.457 37.500 0.00 0.00 0.00 3.34
1297 4312 5.992217 AGTTTTGCTAAGTCTCAGTCGATTT 59.008 36.000 0.00 0.00 0.00 2.17
1298 4313 7.152645 AGTTTTGCTAAGTCTCAGTCGATTTA 58.847 34.615 0.00 0.00 0.00 1.40
1299 4314 7.329717 AGTTTTGCTAAGTCTCAGTCGATTTAG 59.670 37.037 0.00 0.00 36.71 1.85
1300 4315 6.510879 TTGCTAAGTCTCAGTCGATTTAGA 57.489 37.500 7.11 0.00 36.10 2.10
1301 4316 5.881447 TGCTAAGTCTCAGTCGATTTAGAC 58.119 41.667 12.85 12.85 36.10 2.59
1314 4329 7.366167 GTCGATTTAGACTTCGTTATGTCTC 57.634 40.000 0.00 0.00 41.92 3.36
1315 4330 6.965500 GTCGATTTAGACTTCGTTATGTCTCA 59.035 38.462 0.00 0.00 41.92 3.27
1316 4331 7.164498 GTCGATTTAGACTTCGTTATGTCTCAG 59.836 40.741 0.00 0.00 41.92 3.35
1317 4332 6.967767 CGATTTAGACTTCGTTATGTCTCAGT 59.032 38.462 0.00 0.00 41.92 3.41
1318 4333 7.485277 CGATTTAGACTTCGTTATGTCTCAGTT 59.515 37.037 0.00 0.00 41.92 3.16
1319 4334 7.869016 TTTAGACTTCGTTATGTCTCAGTTG 57.131 36.000 0.00 0.00 41.92 3.16
1320 4335 5.707242 AGACTTCGTTATGTCTCAGTTGA 57.293 39.130 0.00 0.00 39.04 3.18
1321 4336 6.274157 AGACTTCGTTATGTCTCAGTTGAT 57.726 37.500 0.00 0.00 39.04 2.57
1322 4337 7.392494 AGACTTCGTTATGTCTCAGTTGATA 57.608 36.000 0.00 0.00 39.04 2.15
1323 4338 7.827701 AGACTTCGTTATGTCTCAGTTGATAA 58.172 34.615 0.00 0.00 39.04 1.75
1324 4339 8.470805 AGACTTCGTTATGTCTCAGTTGATAAT 58.529 33.333 0.00 0.00 39.04 1.28
1325 4340 9.731819 GACTTCGTTATGTCTCAGTTGATAATA 57.268 33.333 0.00 0.00 0.00 0.98
1408 4423 7.934855 ACTATAACCTTAAAGTCTCAGTCGA 57.065 36.000 0.00 0.00 0.00 4.20
1409 4424 7.760437 ACTATAACCTTAAAGTCTCAGTCGAC 58.240 38.462 7.70 7.70 0.00 4.20
1410 4425 6.837471 ATAACCTTAAAGTCTCAGTCGACT 57.163 37.500 13.58 13.58 45.73 4.18
1411 4426 7.934855 ATAACCTTAAAGTCTCAGTCGACTA 57.065 36.000 19.57 0.00 43.14 2.59
1412 4427 6.645790 AACCTTAAAGTCTCAGTCGACTAA 57.354 37.500 19.57 1.94 43.14 2.24
1413 4428 6.256912 ACCTTAAAGTCTCAGTCGACTAAG 57.743 41.667 19.57 14.47 43.14 2.18
1414 4429 6.002704 ACCTTAAAGTCTCAGTCGACTAAGA 58.997 40.000 19.57 17.01 43.14 2.10
1415 4430 6.072563 ACCTTAAAGTCTCAGTCGACTAAGAC 60.073 42.308 33.03 33.03 43.14 3.01
1416 4431 4.769859 AAAGTCTCAGTCGACTAAGACC 57.230 45.455 35.12 21.93 41.23 3.85
1417 4432 3.706600 AGTCTCAGTCGACTAAGACCT 57.293 47.619 35.12 23.42 41.23 3.85
1418 4433 4.822685 AGTCTCAGTCGACTAAGACCTA 57.177 45.455 35.12 7.90 41.23 3.08
1419 4434 4.761975 AGTCTCAGTCGACTAAGACCTAG 58.238 47.826 35.12 15.46 41.23 3.02
1420 4435 3.310501 GTCTCAGTCGACTAAGACCTAGC 59.689 52.174 31.01 11.74 41.83 3.42
1421 4436 2.614983 CTCAGTCGACTAAGACCTAGCC 59.385 54.545 19.57 0.00 41.83 3.93
1422 4437 2.026542 TCAGTCGACTAAGACCTAGCCA 60.027 50.000 19.57 0.00 41.83 4.75
1423 4438 2.097791 CAGTCGACTAAGACCTAGCCAC 59.902 54.545 19.57 0.00 41.83 5.01
1424 4439 2.089980 GTCGACTAAGACCTAGCCACA 58.910 52.381 8.70 0.00 35.22 4.17
1425 4440 2.089980 TCGACTAAGACCTAGCCACAC 58.910 52.381 0.00 0.00 0.00 3.82
1426 4441 1.816835 CGACTAAGACCTAGCCACACA 59.183 52.381 0.00 0.00 0.00 3.72
1427 4442 2.415625 CGACTAAGACCTAGCCACACAC 60.416 54.545 0.00 0.00 0.00 3.82
1445 4460 4.709397 ACACACATCCCTTTTCTTTCACAA 59.291 37.500 0.00 0.00 0.00 3.33
1466 4481 2.039613 ACCTTCCTTTTGCCTCTCTGAG 59.960 50.000 0.00 0.00 0.00 3.35
1468 4483 3.497584 CCTTCCTTTTGCCTCTCTGAGTT 60.498 47.826 4.32 0.00 0.00 3.01
1469 4484 4.263068 CCTTCCTTTTGCCTCTCTGAGTTA 60.263 45.833 4.32 0.00 0.00 2.24
1477 4557 3.703556 TGCCTCTCTGAGTTATCTTCCTG 59.296 47.826 4.32 0.00 0.00 3.86
1479 4559 4.441356 GCCTCTCTGAGTTATCTTCCTGTG 60.441 50.000 4.32 0.00 0.00 3.66
1507 4594 6.157211 CGTGCTTCCTCCGTAATAATCTATT 58.843 40.000 0.00 0.00 0.00 1.73
1545 4632 1.489481 TCAGATGACTGATTCCCGCT 58.511 50.000 0.00 0.00 46.55 5.52
1546 4633 1.410517 TCAGATGACTGATTCCCGCTC 59.589 52.381 0.00 0.00 46.55 5.03
1547 4634 0.387202 AGATGACTGATTCCCGCTCG 59.613 55.000 0.00 0.00 0.00 5.03
1548 4635 0.103208 GATGACTGATTCCCGCTCGT 59.897 55.000 0.00 0.00 0.00 4.18
1559 4649 1.205179 TCCCGCTCGTGCATTTAGTTA 59.795 47.619 10.43 0.00 39.64 2.24
1561 4651 2.612212 CCCGCTCGTGCATTTAGTTATT 59.388 45.455 10.43 0.00 39.64 1.40
1562 4652 3.064820 CCCGCTCGTGCATTTAGTTATTT 59.935 43.478 10.43 0.00 39.64 1.40
1563 4653 4.271533 CCCGCTCGTGCATTTAGTTATTTA 59.728 41.667 10.43 0.00 39.64 1.40
1628 4723 1.064654 GCTCGTGCATTCAATCCTTCC 59.935 52.381 4.26 0.00 39.41 3.46
1645 4740 0.172578 TCCAACTACGCATCAGTCCG 59.827 55.000 0.00 0.00 0.00 4.79
1669 6368 6.094061 GTGGATTTCGGTAGCTATCTGTATC 58.906 44.000 1.81 2.09 0.00 2.24
1684 6383 2.738846 CTGTATCTGTCGTGCTTGCTTT 59.261 45.455 0.00 0.00 0.00 3.51
1694 6393 1.871039 GTGCTTGCTTTACAACCTCGA 59.129 47.619 0.00 0.00 33.68 4.04
1699 6398 1.804151 TGCTTTACAACCTCGATGTGC 59.196 47.619 0.39 0.00 32.27 4.57
1720 6420 4.858140 TGCATATGATTTTGCAGTGTTTCG 59.142 37.500 6.97 0.00 43.54 3.46
1722 6422 2.859526 TGATTTTGCAGTGTTTCGCA 57.140 40.000 0.00 0.00 36.05 5.10
1726 6426 1.661498 TTTGCAGTGTTTCGCAGCCA 61.661 50.000 0.00 0.00 39.75 4.75
1733 6433 0.673333 TGTTTCGCAGCCACGATGAT 60.673 50.000 0.00 0.00 42.54 2.45
1783 6493 1.865340 GGCGATATTTCAGTTCGGACC 59.135 52.381 0.00 0.00 33.62 4.46
1784 6494 1.865340 GCGATATTTCAGTTCGGACCC 59.135 52.381 0.00 0.00 33.62 4.46
1785 6495 2.483188 GCGATATTTCAGTTCGGACCCT 60.483 50.000 0.00 0.00 33.62 4.34
1786 6496 3.123804 CGATATTTCAGTTCGGACCCTG 58.876 50.000 0.00 0.00 0.00 4.45
1787 6497 3.181479 CGATATTTCAGTTCGGACCCTGA 60.181 47.826 0.00 3.16 35.97 3.86
1788 6498 4.501571 CGATATTTCAGTTCGGACCCTGAT 60.502 45.833 7.23 0.00 37.54 2.90
1789 6499 2.472695 TTTCAGTTCGGACCCTGATG 57.527 50.000 7.23 0.00 37.54 3.07
1790 6500 1.348064 TTCAGTTCGGACCCTGATGT 58.652 50.000 7.23 0.00 37.54 3.06
1791 6501 0.608130 TCAGTTCGGACCCTGATGTG 59.392 55.000 0.00 0.00 32.93 3.21
1792 6502 1.021390 CAGTTCGGACCCTGATGTGC 61.021 60.000 0.00 0.00 0.00 4.57
1793 6503 1.003839 GTTCGGACCCTGATGTGCA 60.004 57.895 0.00 0.00 0.00 4.57
1794 6504 0.392998 GTTCGGACCCTGATGTGCAT 60.393 55.000 0.00 0.00 0.00 3.96
1902 6613 2.574006 AGGACTAGGACACACGTACA 57.426 50.000 0.00 0.00 0.00 2.90
1977 6695 1.491668 GAGAGAAGGGGGAAGGAGAC 58.508 60.000 0.00 0.00 0.00 3.36
1986 6704 1.574263 GGGAAGGAGACAGGCTAACT 58.426 55.000 0.00 0.00 0.00 2.24
1987 6705 2.626149 GGGGAAGGAGACAGGCTAACTA 60.626 54.545 0.00 0.00 0.00 2.24
1988 6706 3.310193 GGGAAGGAGACAGGCTAACTAT 58.690 50.000 0.00 0.00 0.00 2.12
1989 6707 4.481072 GGGAAGGAGACAGGCTAACTATA 58.519 47.826 0.00 0.00 0.00 1.31
2020 8548 2.978156 AATTGGCCCTTTCTCACTCA 57.022 45.000 0.00 0.00 0.00 3.41
2115 8643 9.431887 TGAATTTATCTTCCTATATAACGTGCC 57.568 33.333 0.00 0.00 0.00 5.01
2134 8662 5.336531 CGTGCCTCCTCCGTAATAATCTATT 60.337 44.000 0.00 0.00 0.00 1.73
2202 8730 6.468000 GCATTTATACTTCTTTAACCACGCAC 59.532 38.462 0.00 0.00 0.00 5.34
2220 8748 1.739466 CACCACAGTCCATGGATTTCG 59.261 52.381 19.62 9.28 39.87 3.46
2231 8759 5.185249 GTCCATGGATTTCGGTAGCTATCTA 59.815 44.000 19.62 0.00 0.00 1.98
2258 8786 2.032924 GTCGTGCTTGCTTTACAACCTT 59.967 45.455 0.00 0.00 33.68 3.50
2330 8858 0.254462 TGGCTTGGATATTCGTGGCA 59.746 50.000 0.00 0.00 0.00 4.92
2429 8957 4.036380 GTGGGATTCGGTTTCATGATAACC 59.964 45.833 20.83 20.83 41.31 2.85
2452 8980 1.988982 GAAGATCAGGGGGAGGCACC 61.989 65.000 0.00 0.00 38.08 5.01
2498 9048 3.950395 GGCTAGGATTTGTGCATTTCTCT 59.050 43.478 0.00 0.00 0.00 3.10
2522 9072 0.753848 GAGAGGGGGTCGAGAGAAGG 60.754 65.000 0.00 0.00 45.01 3.46
2524 9074 0.105913 GAGGGGGTCGAGAGAAGGAT 60.106 60.000 0.00 0.00 45.01 3.24
2536 9086 6.005198 TCGAGAGAAGGATAAAGGAGATACC 58.995 44.000 0.00 0.00 37.03 2.73
2558 9108 7.852550 ACCAGAACTAGTTACTCTAGGTTTT 57.147 36.000 8.42 0.00 45.62 2.43
2565 9115 9.310449 AACTAGTTACTCTAGGTTTTCATCTGA 57.690 33.333 6.26 0.00 43.42 3.27
2578 9128 8.797438 AGGTTTTCATCTGAAATTCTACTTTCC 58.203 33.333 6.21 0.00 42.83 3.13
2579 9129 8.576442 GGTTTTCATCTGAAATTCTACTTTCCA 58.424 33.333 6.21 0.00 42.83 3.53
2595 9145 5.186198 ACTTTCCATTACAGAAGGAATCGG 58.814 41.667 0.00 0.00 40.80 4.18
2613 9164 7.344612 AGGAATCGGCATATATATGGTTGAGTA 59.655 37.037 21.50 0.00 34.32 2.59
2677 9230 8.898792 GTTAAAAGCTTAACAGTTAAATGGTCG 58.101 33.333 7.93 0.00 44.29 4.79
2683 9236 8.071967 AGCTTAACAGTTAAATGGTCGTTTTAC 58.928 33.333 7.93 0.00 0.00 2.01
2692 9245 1.002315 TGGTCGTTTTACTGGCCCTAC 59.998 52.381 0.00 0.00 0.00 3.18
2693 9246 1.277273 GGTCGTTTTACTGGCCCTACT 59.723 52.381 0.00 0.00 0.00 2.57
2706 9260 1.410882 GCCCTACTCACTCATGGTCTC 59.589 57.143 0.00 0.00 0.00 3.36
2716 9270 3.583054 CATGGTCTCATGCCCACTT 57.417 52.632 1.32 0.00 43.44 3.16
2747 9301 0.808453 ATCATGGTCGCCCGTTAACG 60.808 55.000 20.99 20.99 39.44 3.18
2770 9324 4.037565 GGAACCCGAAGTTGTCAATTCTTT 59.962 41.667 0.00 0.00 39.40 2.52
2798 9352 3.285484 CTTGGCTCATCAGGCTTAACAT 58.715 45.455 0.00 0.00 45.75 2.71
2823 9377 2.669229 CACCGGTGCTGACATGCA 60.669 61.111 24.02 0.00 41.05 3.96
2825 9379 2.042259 ACCGGTGCTGACATGCATG 61.042 57.895 25.09 25.09 45.23 4.06
2848 9402 5.712446 TGCTTGTAATTGGCCTTGTATACAA 59.288 36.000 17.16 17.16 33.61 2.41
2852 9406 7.328277 TGTAATTGGCCTTGTATACAACATC 57.672 36.000 14.35 7.18 38.10 3.06
2855 9409 6.699575 ATTGGCCTTGTATACAACATCTTC 57.300 37.500 14.35 2.79 38.10 2.87
2857 9411 5.185454 TGGCCTTGTATACAACATCTTCTG 58.815 41.667 14.35 2.59 38.10 3.02
2896 9450 5.260140 GCGCATTTTACTACGAAATAAGCA 58.740 37.500 0.30 0.00 32.83 3.91
2947 9502 0.029267 AGCCAGGGAATCTCCATCCT 60.029 55.000 0.00 0.00 38.64 3.24
2954 9509 5.399497 CCAGGGAATCTCCATCCTAAAACAT 60.399 44.000 0.00 0.00 38.64 2.71
3034 9594 2.309755 TGGACAATGCTGGAAGGAGATT 59.690 45.455 0.00 0.00 38.10 2.40
3039 9599 4.079901 ACAATGCTGGAAGGAGATTGATCT 60.080 41.667 0.00 0.00 38.10 2.75
3042 9602 3.520721 TGCTGGAAGGAGATTGATCTGAA 59.479 43.478 0.00 0.00 37.25 3.02
3047 9607 3.451141 AGGAGATTGATCTGAAGCGAC 57.549 47.619 0.00 0.00 37.25 5.19
3051 9611 2.797792 AGATTGATCTGAAGCGACGAGC 60.798 50.000 0.00 0.00 40.24 5.03
3082 9642 0.523072 ATTCATGCATAATCGCCGCC 59.477 50.000 0.00 0.00 0.00 6.13
3093 9653 4.821589 CGCCGCCAAGGGACTCTC 62.822 72.222 0.00 0.00 38.49 3.20
3136 9698 3.859443 AGATTGCACAAGCTCTAGTGAG 58.141 45.455 15.56 0.00 42.74 3.51
3141 9703 3.181466 TGCACAAGCTCTAGTGAGTTCAA 60.181 43.478 15.56 0.00 42.13 2.69
3156 9718 4.037803 TGAGTTCAATTCCAACATGTGTGG 59.962 41.667 16.49 16.49 0.00 4.17
3171 9733 1.127567 TGTGGACACCCTAGCTGCTT 61.128 55.000 7.79 0.00 0.00 3.91
3190 9752 3.374367 GCTTCGGTAATTCAAGTCCCTTC 59.626 47.826 0.00 0.00 0.00 3.46
3277 9839 3.056322 CAGTCATGATCTCACCACAGTCA 60.056 47.826 0.00 0.00 0.00 3.41
3315 9877 3.344215 CGCAGCCGAGCCATCATC 61.344 66.667 0.00 0.00 36.29 2.92
3326 9888 1.415659 AGCCATCATCGAAGAAGGGAG 59.584 52.381 13.23 0.00 43.58 4.30
3340 9902 1.494960 AGGGAGCATCAACCTCTCTC 58.505 55.000 0.00 0.00 35.22 3.20
3344 9906 0.175302 AGCATCAACCTCTCTCGCAG 59.825 55.000 0.00 0.00 0.00 5.18
3347 9909 2.538437 CATCAACCTCTCTCGCAGAAG 58.462 52.381 0.00 0.00 34.09 2.85
3356 9918 0.610174 TCTCGCAGAAGGAGTTGCAT 59.390 50.000 0.00 0.00 40.28 3.96
3361 9923 1.068055 GCAGAAGGAGTTGCATGGTTG 60.068 52.381 0.00 0.00 40.02 3.77
3370 9932 1.001181 GTTGCATGGTTGGCATGACTT 59.999 47.619 0.00 0.00 41.58 3.01
3391 9953 4.156455 TGGCAGGATAACTCTTGGATTC 57.844 45.455 0.00 0.00 0.00 2.52
3393 9955 2.545946 GCAGGATAACTCTTGGATTCGC 59.454 50.000 0.00 0.00 0.00 4.70
3408 9970 0.313672 TTCGCCAAATTGACACCTGC 59.686 50.000 0.00 0.00 0.00 4.85
3409 9971 1.080569 CGCCAAATTGACACCTGCC 60.081 57.895 0.00 0.00 0.00 4.85
3449 10011 0.395724 ATCCAGGAATTCGCCAACCC 60.396 55.000 0.00 0.00 0.00 4.11
3450 10012 2.052104 CCAGGAATTCGCCAACCCC 61.052 63.158 0.00 0.00 0.00 4.95
3458 10020 0.821711 TTCGCCAACCCCTGTGAAAG 60.822 55.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.869028 GGCGTAGATCCGTTTCGTCC 60.869 60.000 0.00 0.00 0.00 4.79
8 9 3.597162 CGGCGTAGATCCGTTTCG 58.403 61.111 0.00 0.00 41.85 3.46
62 63 1.002868 CCAGCTGCTTAGGCACTGT 60.003 57.895 19.97 0.00 44.28 3.55
104 105 4.742201 CTGGTCCACGGCGACAGG 62.742 72.222 16.62 12.84 34.24 4.00
140 141 2.666596 CTTACCGGGCCCAGATGAGC 62.667 65.000 24.92 0.00 0.00 4.26
142 143 1.002403 TCTTACCGGGCCCAGATGA 59.998 57.895 24.92 10.65 0.00 2.92
152 153 1.067582 GGATCGCAGGTCTTACCGG 59.932 63.158 0.00 0.00 44.90 5.28
155 156 1.653151 GTTGGGATCGCAGGTCTTAC 58.347 55.000 12.66 3.56 0.00 2.34
209 210 3.357079 GGCAACAGTGGAGGCGTG 61.357 66.667 0.00 0.00 0.00 5.34
210 211 4.988598 CGGCAACAGTGGAGGCGT 62.989 66.667 19.94 0.00 44.84 5.68
218 219 1.072332 TACATGGTGCGGCAACAGT 59.928 52.632 26.21 23.09 33.31 3.55
220 221 1.227973 TGTACATGGTGCGGCAACA 60.228 52.632 24.57 24.57 34.75 3.33
223 224 2.359354 GGTGTACATGGTGCGGCA 60.359 61.111 0.00 0.00 0.00 5.69
294 295 3.626680 CTTCTCCCTCGCGCGACAA 62.627 63.158 31.40 15.87 0.00 3.18
331 332 2.991540 GAAGCCTGGGTTGTGGGC 60.992 66.667 17.03 0.00 45.57 5.36
442 447 0.588730 CAACACAACGACCAGCAACG 60.589 55.000 0.00 0.00 0.00 4.10
478 483 3.733960 GAGGTTTGCGGGCGTTCC 61.734 66.667 0.00 0.00 0.00 3.62
483 488 3.373565 CTTGGGAGGTTTGCGGGC 61.374 66.667 0.00 0.00 0.00 6.13
484 489 3.373565 GCTTGGGAGGTTTGCGGG 61.374 66.667 0.00 0.00 0.00 6.13
486 491 3.763671 AAGCTTGGGAGGTTTGCG 58.236 55.556 0.00 0.00 40.54 4.85
509 514 3.181495 ACGTTCAAAATCTTGCAAACCGA 60.181 39.130 0.00 0.00 32.14 4.69
510 515 3.112580 ACGTTCAAAATCTTGCAAACCG 58.887 40.909 0.00 0.00 32.14 4.44
515 520 4.109050 GTTTGGACGTTCAAAATCTTGCA 58.891 39.130 23.29 0.00 38.21 4.08
527 532 0.470766 TACTGCCTGGTTTGGACGTT 59.529 50.000 0.00 0.00 0.00 3.99
529 534 0.320374 TCTACTGCCTGGTTTGGACG 59.680 55.000 0.00 0.00 0.00 4.79
531 536 1.347707 CTGTCTACTGCCTGGTTTGGA 59.652 52.381 0.00 0.00 0.00 3.53
532 537 1.347707 TCTGTCTACTGCCTGGTTTGG 59.652 52.381 0.00 0.00 0.00 3.28
533 538 2.417719 GTCTGTCTACTGCCTGGTTTG 58.582 52.381 0.00 0.00 0.00 2.93
534 539 1.000955 CGTCTGTCTACTGCCTGGTTT 59.999 52.381 0.00 0.00 0.00 3.27
538 543 2.061773 CAAACGTCTGTCTACTGCCTG 58.938 52.381 0.00 0.00 0.00 4.85
539 544 1.961394 TCAAACGTCTGTCTACTGCCT 59.039 47.619 0.00 0.00 0.00 4.75
545 550 3.378911 TGTGCATCAAACGTCTGTCTA 57.621 42.857 0.00 0.00 0.00 2.59
546 551 2.238942 TGTGCATCAAACGTCTGTCT 57.761 45.000 0.00 0.00 0.00 3.41
547 552 3.332761 TTTGTGCATCAAACGTCTGTC 57.667 42.857 9.46 0.00 40.56 3.51
548 553 3.128589 ACTTTTGTGCATCAAACGTCTGT 59.871 39.130 13.94 7.37 42.20 3.41
567 572 5.106555 CCAGACACATTTTAGCGATTCACTT 60.107 40.000 0.00 0.00 0.00 3.16
569 574 4.391830 TCCAGACACATTTTAGCGATTCAC 59.608 41.667 0.00 0.00 0.00 3.18
616 621 2.460757 AAATGTTTGGACCATGCTGC 57.539 45.000 0.00 0.00 0.00 5.25
623 628 3.907894 TCGCTTGTAAATGTTTGGACC 57.092 42.857 0.00 0.00 0.00 4.46
651 656 2.202892 GGCGACTCCAACCCGATC 60.203 66.667 0.00 0.00 34.01 3.69
665 670 4.547367 GGACATTCCCTCGGGGCG 62.547 72.222 0.00 0.00 43.94 6.13
767 2703 4.684484 AGGTAAACGTGGAAAGTCTTCT 57.316 40.909 0.00 0.00 0.00 2.85
768 2704 5.536260 AGTAGGTAAACGTGGAAAGTCTTC 58.464 41.667 0.00 0.00 0.00 2.87
769 2705 5.541953 AGTAGGTAAACGTGGAAAGTCTT 57.458 39.130 0.00 0.00 0.00 3.01
791 2730 2.045340 GCGCCCCTTTGCTTCCTA 60.045 61.111 0.00 0.00 0.00 2.94
823 2762 3.900892 CGCGGGCCGTATCTCTGT 61.901 66.667 28.82 0.00 0.00 3.41
829 2768 4.770874 AACTTGCGCGGGCCGTAT 62.771 61.111 28.82 3.79 39.71 3.06
859 2798 2.914908 GCGCGTGGGGATTGTGTTT 61.915 57.895 8.43 0.00 0.00 2.83
888 2827 0.675522 TTTCGGATCTGGTTTCGGCC 60.676 55.000 0.62 0.00 0.00 6.13
889 2828 0.446616 GTTTCGGATCTGGTTTCGGC 59.553 55.000 0.62 0.00 0.00 5.54
1116 4118 3.620785 ATCCGGCGGATCTGCTCC 61.621 66.667 34.54 9.46 38.09 4.70
1213 4215 0.178903 AAGGGGGTCTGTCTAGTGCA 60.179 55.000 0.00 0.00 0.00 4.57
1245 4260 5.538877 AGGATAATTTAGAGGGGTGAGTGA 58.461 41.667 0.00 0.00 0.00 3.41
1264 4279 8.691661 TGAGACTTAGCAAAACTAAAAAGGAT 57.308 30.769 0.00 0.00 40.36 3.24
1265 4280 7.773690 ACTGAGACTTAGCAAAACTAAAAAGGA 59.226 33.333 0.00 0.00 40.36 3.36
1266 4281 7.931275 ACTGAGACTTAGCAAAACTAAAAAGG 58.069 34.615 0.00 0.00 40.36 3.11
1267 4282 7.794349 CGACTGAGACTTAGCAAAACTAAAAAG 59.206 37.037 0.00 0.00 40.36 2.27
1268 4283 7.493320 TCGACTGAGACTTAGCAAAACTAAAAA 59.507 33.333 0.00 0.00 40.36 1.94
1269 4284 6.982141 TCGACTGAGACTTAGCAAAACTAAAA 59.018 34.615 0.00 0.00 40.36 1.52
1270 4285 6.509656 TCGACTGAGACTTAGCAAAACTAAA 58.490 36.000 0.00 0.00 40.36 1.85
1271 4286 6.080648 TCGACTGAGACTTAGCAAAACTAA 57.919 37.500 0.00 0.00 38.57 2.24
1272 4287 5.700722 TCGACTGAGACTTAGCAAAACTA 57.299 39.130 0.00 0.00 0.00 2.24
1273 4288 4.585955 TCGACTGAGACTTAGCAAAACT 57.414 40.909 0.00 0.00 0.00 2.66
1274 4289 5.847670 AATCGACTGAGACTTAGCAAAAC 57.152 39.130 0.00 0.00 0.00 2.43
1275 4290 7.328737 GTCTAAATCGACTGAGACTTAGCAAAA 59.671 37.037 4.05 0.00 36.27 2.44
1276 4291 6.807230 GTCTAAATCGACTGAGACTTAGCAAA 59.193 38.462 4.05 0.00 36.27 3.68
1277 4292 6.151312 AGTCTAAATCGACTGAGACTTAGCAA 59.849 38.462 8.12 0.00 44.91 3.91
1278 4293 5.648526 AGTCTAAATCGACTGAGACTTAGCA 59.351 40.000 8.12 0.00 44.91 3.49
1279 4294 6.126568 AGTCTAAATCGACTGAGACTTAGC 57.873 41.667 8.12 0.00 44.91 3.09
1284 4299 4.972201 ACGAAGTCTAAATCGACTGAGAC 58.028 43.478 3.01 3.01 43.14 3.36
1285 4300 5.624344 AACGAAGTCTAAATCGACTGAGA 57.376 39.130 1.84 0.00 45.00 3.27
1286 4301 6.967767 ACATAACGAAGTCTAAATCGACTGAG 59.032 38.462 1.84 0.00 45.00 3.35
1287 4302 6.849502 ACATAACGAAGTCTAAATCGACTGA 58.150 36.000 1.84 0.00 45.00 3.41
1288 4303 6.967767 AGACATAACGAAGTCTAAATCGACTG 59.032 38.462 1.84 0.00 45.00 3.51
1289 4304 7.086230 AGACATAACGAAGTCTAAATCGACT 57.914 36.000 1.84 0.00 45.00 4.18
1290 4305 6.965500 TGAGACATAACGAAGTCTAAATCGAC 59.035 38.462 1.84 0.00 45.00 4.20
1291 4306 7.080353 TGAGACATAACGAAGTCTAAATCGA 57.920 36.000 1.84 0.00 45.00 3.59
1292 4307 6.967767 ACTGAGACATAACGAAGTCTAAATCG 59.032 38.462 0.00 0.00 45.00 3.34
1293 4308 8.587950 CAACTGAGACATAACGAAGTCTAAATC 58.412 37.037 0.00 0.00 45.00 2.17
1294 4309 8.304596 TCAACTGAGACATAACGAAGTCTAAAT 58.695 33.333 0.00 0.00 45.00 1.40
1295 4310 7.654568 TCAACTGAGACATAACGAAGTCTAAA 58.345 34.615 0.00 0.00 45.00 1.85
1296 4311 7.210718 TCAACTGAGACATAACGAAGTCTAA 57.789 36.000 0.00 0.00 45.00 2.10
1297 4312 6.812879 TCAACTGAGACATAACGAAGTCTA 57.187 37.500 0.00 0.00 45.00 2.59
1298 4313 5.707242 TCAACTGAGACATAACGAAGTCT 57.293 39.130 0.00 0.00 45.00 3.24
1299 4314 8.635877 ATTATCAACTGAGACATAACGAAGTC 57.364 34.615 0.00 0.00 45.00 3.01
1382 4397 9.624373 TCGACTGAGACTTTAAGGTTATAGTAT 57.376 33.333 0.00 0.00 0.00 2.12
1383 4398 8.887717 GTCGACTGAGACTTTAAGGTTATAGTA 58.112 37.037 8.70 0.00 38.09 1.82
1384 4399 7.760437 GTCGACTGAGACTTTAAGGTTATAGT 58.240 38.462 8.70 0.00 38.09 2.12
1399 4414 3.533547 GCTAGGTCTTAGTCGACTGAGA 58.466 50.000 30.05 30.05 36.42 3.27
1400 4415 2.614983 GGCTAGGTCTTAGTCGACTGAG 59.385 54.545 26.80 26.80 34.38 3.35
1401 4416 2.026542 TGGCTAGGTCTTAGTCGACTGA 60.027 50.000 28.12 19.13 36.76 3.41
1402 4417 2.097791 GTGGCTAGGTCTTAGTCGACTG 59.902 54.545 28.12 12.46 36.76 3.51
1403 4418 2.290768 TGTGGCTAGGTCTTAGTCGACT 60.291 50.000 23.66 23.66 36.76 4.18
1404 4419 2.089980 TGTGGCTAGGTCTTAGTCGAC 58.910 52.381 7.70 7.70 36.76 4.20
1405 4420 2.089980 GTGTGGCTAGGTCTTAGTCGA 58.910 52.381 0.00 0.00 36.76 4.20
1406 4421 1.816835 TGTGTGGCTAGGTCTTAGTCG 59.183 52.381 0.00 0.00 36.76 4.18
1407 4422 2.561419 TGTGTGTGGCTAGGTCTTAGTC 59.439 50.000 0.00 0.00 34.46 2.59
1408 4423 2.605257 TGTGTGTGGCTAGGTCTTAGT 58.395 47.619 0.00 0.00 0.00 2.24
1409 4424 3.430929 GGATGTGTGTGGCTAGGTCTTAG 60.431 52.174 0.00 0.00 0.00 2.18
1410 4425 2.500098 GGATGTGTGTGGCTAGGTCTTA 59.500 50.000 0.00 0.00 0.00 2.10
1411 4426 1.279271 GGATGTGTGTGGCTAGGTCTT 59.721 52.381 0.00 0.00 0.00 3.01
1412 4427 0.905357 GGATGTGTGTGGCTAGGTCT 59.095 55.000 0.00 0.00 0.00 3.85
1413 4428 0.107654 GGGATGTGTGTGGCTAGGTC 60.108 60.000 0.00 0.00 0.00 3.85
1414 4429 0.547712 AGGGATGTGTGTGGCTAGGT 60.548 55.000 0.00 0.00 0.00 3.08
1415 4430 0.620556 AAGGGATGTGTGTGGCTAGG 59.379 55.000 0.00 0.00 0.00 3.02
1416 4431 2.496899 AAAGGGATGTGTGTGGCTAG 57.503 50.000 0.00 0.00 0.00 3.42
1417 4432 2.375174 AGAAAAGGGATGTGTGTGGCTA 59.625 45.455 0.00 0.00 0.00 3.93
1418 4433 1.145738 AGAAAAGGGATGTGTGTGGCT 59.854 47.619 0.00 0.00 0.00 4.75
1419 4434 1.620822 AGAAAAGGGATGTGTGTGGC 58.379 50.000 0.00 0.00 0.00 5.01
1420 4435 3.636300 TGAAAGAAAAGGGATGTGTGTGG 59.364 43.478 0.00 0.00 0.00 4.17
1421 4436 4.097741 TGTGAAAGAAAAGGGATGTGTGTG 59.902 41.667 0.00 0.00 0.00 3.82
1422 4437 4.277476 TGTGAAAGAAAAGGGATGTGTGT 58.723 39.130 0.00 0.00 0.00 3.72
1423 4438 4.916983 TGTGAAAGAAAAGGGATGTGTG 57.083 40.909 0.00 0.00 0.00 3.82
1424 4439 4.099419 GGTTGTGAAAGAAAAGGGATGTGT 59.901 41.667 0.00 0.00 0.00 3.72
1425 4440 4.342092 AGGTTGTGAAAGAAAAGGGATGTG 59.658 41.667 0.00 0.00 0.00 3.21
1426 4441 4.546674 AGGTTGTGAAAGAAAAGGGATGT 58.453 39.130 0.00 0.00 0.00 3.06
1427 4442 5.509670 GGAAGGTTGTGAAAGAAAAGGGATG 60.510 44.000 0.00 0.00 0.00 3.51
1445 4460 2.039613 CTCAGAGAGGCAAAAGGAAGGT 59.960 50.000 0.00 0.00 0.00 3.50
1466 4481 4.243270 AGCACGTTACACAGGAAGATAAC 58.757 43.478 0.00 0.00 0.00 1.89
1468 4483 4.491676 GAAGCACGTTACACAGGAAGATA 58.508 43.478 0.00 0.00 0.00 1.98
1469 4484 3.326747 GAAGCACGTTACACAGGAAGAT 58.673 45.455 0.00 0.00 0.00 2.40
1477 4557 0.319297 ACGGAGGAAGCACGTTACAC 60.319 55.000 0.00 0.00 37.61 2.90
1479 4559 2.352503 TTACGGAGGAAGCACGTTAC 57.647 50.000 0.00 0.00 41.53 2.50
1534 4621 1.091771 AATGCACGAGCGGGAATCAG 61.092 55.000 0.00 0.00 46.23 2.90
1645 4740 4.323553 ACAGATAGCTACCGAAATCCAC 57.676 45.455 0.00 0.00 0.00 4.02
1669 6368 2.639751 GTTGTAAAGCAAGCACGACAG 58.360 47.619 0.00 0.00 37.83 3.51
1684 6383 4.664150 TCATATGCACATCGAGGTTGTA 57.336 40.909 0.00 0.00 0.00 2.41
1694 6393 5.333299 ACACTGCAAAATCATATGCACAT 57.667 34.783 0.00 0.00 46.87 3.21
1699 6398 4.858140 TGCGAAACACTGCAAAATCATATG 59.142 37.500 0.00 0.00 38.34 1.78
1783 6493 3.715638 ATAGGGATCATGCACATCAGG 57.284 47.619 9.21 0.00 0.00 3.86
1784 6494 5.985911 TGATATAGGGATCATGCACATCAG 58.014 41.667 9.21 0.00 30.75 2.90
1785 6495 6.570654 ATGATATAGGGATCATGCACATCA 57.429 37.500 9.21 0.00 43.45 3.07
1793 6503 4.353191 GCCCCATCATGATATAGGGATCAT 59.647 45.833 29.20 0.00 45.51 2.45
1794 6504 3.718434 GCCCCATCATGATATAGGGATCA 59.282 47.826 29.20 0.00 42.25 2.92
1815 6525 5.064707 TGGTATGAGAGCAAAAACGATAAGC 59.935 40.000 0.00 0.00 30.90 3.09
1902 6613 1.927527 AGTGCCTCCCCTTGAGCAT 60.928 57.895 0.00 0.00 39.98 3.79
1967 6685 1.574263 AGTTAGCCTGTCTCCTTCCC 58.426 55.000 0.00 0.00 0.00 3.97
1969 6687 9.689501 ACTATATATAGTTAGCCTGTCTCCTTC 57.310 37.037 18.01 0.00 40.54 3.46
1988 6706 9.930158 AGAAAGGGCCAATTAAACAACTATATA 57.070 29.630 6.18 0.00 0.00 0.86
1989 6707 8.838649 AGAAAGGGCCAATTAAACAACTATAT 57.161 30.769 6.18 0.00 0.00 0.86
2020 8548 2.202236 ATCCATCTGCGTGGGCACTT 62.202 55.000 3.17 0.00 46.21 3.16
2147 8675 9.566432 AGAGTAGAATCAAACATCTGAGTTTTT 57.434 29.630 0.00 0.00 39.55 1.94
2171 8699 7.820386 TGGTTAAAGAAGTATAAATGCACGAGA 59.180 33.333 0.00 0.00 0.00 4.04
2202 8730 1.340017 ACCGAAATCCATGGACTGTGG 60.340 52.381 18.99 18.75 38.11 4.17
2220 8748 6.622549 AGCACGACAAATATAGATAGCTACC 58.377 40.000 0.00 0.00 0.00 3.18
2231 8759 5.621197 TGTAAAGCAAGCACGACAAATAT 57.379 34.783 0.00 0.00 0.00 1.28
2258 8786 4.078537 ACTGCAAAACCATATACACAGCA 58.921 39.130 0.00 0.00 0.00 4.41
2304 8832 5.240891 CACGAATATCCAAGCCATCATAGT 58.759 41.667 0.00 0.00 0.00 2.12
2330 8858 5.989477 TCAGGATTCCAGTTGAAATATCGT 58.011 37.500 5.29 0.00 36.33 3.73
2429 8957 0.755686 CCTCCCCCTGATCTTCTTCG 59.244 60.000 0.00 0.00 0.00 3.79
2452 8980 1.082169 CACACCATTCAACCGTGCG 60.082 57.895 0.00 0.00 0.00 5.34
2457 9007 2.362077 GCCATATCCACACCATTCAACC 59.638 50.000 0.00 0.00 0.00 3.77
2461 9011 3.327757 TCCTAGCCATATCCACACCATTC 59.672 47.826 0.00 0.00 0.00 2.67
2498 9048 0.917821 TCTCGACCCCCTCTCTACCA 60.918 60.000 0.00 0.00 0.00 3.25
2511 9061 6.072342 GGTATCTCCTTTATCCTTCTCTCGAC 60.072 46.154 0.00 0.00 0.00 4.20
2524 9074 9.406113 GAGTAACTAGTTCTGGTATCTCCTTTA 57.594 37.037 12.39 0.00 37.07 1.85
2536 9086 9.575783 GATGAAAACCTAGAGTAACTAGTTCTG 57.424 37.037 12.39 0.00 45.01 3.02
2558 9108 9.958180 TGTAATGGAAAGTAGAATTTCAGATGA 57.042 29.630 4.99 0.00 40.29 2.92
2565 9115 9.807921 TTCCTTCTGTAATGGAAAGTAGAATTT 57.192 29.630 0.00 0.00 36.98 1.82
2578 9128 9.770097 ATATATATGCCGATTCCTTCTGTAATG 57.230 33.333 0.00 0.00 0.00 1.90
2579 9129 9.770097 CATATATATGCCGATTCCTTCTGTAAT 57.230 33.333 9.75 0.00 0.00 1.89
2580 9130 8.204160 CCATATATATGCCGATTCCTTCTGTAA 58.796 37.037 16.08 0.00 32.40 2.41
2581 9131 7.344612 ACCATATATATGCCGATTCCTTCTGTA 59.655 37.037 16.08 0.00 32.40 2.74
2582 9132 6.156949 ACCATATATATGCCGATTCCTTCTGT 59.843 38.462 16.08 2.68 32.40 3.41
2613 9164 5.065914 ACTGTTACTGCAGTGAATCATTGT 58.934 37.500 29.57 13.13 46.72 2.71
2666 9217 4.478699 GGCCAGTAAAACGACCATTTAAC 58.521 43.478 0.00 0.00 0.00 2.01
2677 9230 3.007614 TGAGTGAGTAGGGCCAGTAAAAC 59.992 47.826 6.18 0.00 0.00 2.43
2683 9236 0.467384 CCATGAGTGAGTAGGGCCAG 59.533 60.000 6.18 0.00 0.00 4.85
2706 9260 1.884579 GCATCCATCTAAGTGGGCATG 59.115 52.381 0.00 0.00 39.80 4.06
2716 9270 3.667360 CGACCATGATTGCATCCATCTA 58.333 45.455 0.00 0.00 30.68 1.98
2747 9301 3.146847 AGAATTGACAACTTCGGGTTCC 58.853 45.455 0.00 0.00 35.74 3.62
2753 9307 7.630924 AGTGTCTAAAAGAATTGACAACTTCG 58.369 34.615 0.00 0.00 40.47 3.79
2758 9312 6.321181 AGCCAAGTGTCTAAAAGAATTGACAA 59.679 34.615 0.00 0.00 40.47 3.18
2759 9313 5.827797 AGCCAAGTGTCTAAAAGAATTGACA 59.172 36.000 0.00 0.00 37.14 3.58
2770 9324 2.355108 GCCTGATGAGCCAAGTGTCTAA 60.355 50.000 0.00 0.00 0.00 2.10
2820 9374 1.559368 AGGCCAATTACAAGCATGCA 58.441 45.000 21.98 0.00 0.00 3.96
2823 9377 5.890985 TGTATACAAGGCCAATTACAAGCAT 59.109 36.000 5.01 0.00 0.00 3.79
2825 9379 5.828299 TGTATACAAGGCCAATTACAAGC 57.172 39.130 5.01 0.00 0.00 4.01
2848 9402 3.245016 TGAAGCATTCCCACAGAAGATGT 60.245 43.478 0.00 0.00 46.93 3.06
2852 9406 2.426024 CCATGAAGCATTCCCACAGAAG 59.574 50.000 0.00 0.00 46.93 2.85
2855 9409 0.458669 GCCATGAAGCATTCCCACAG 59.541 55.000 0.00 0.00 46.93 3.66
2857 9411 1.434696 CGCCATGAAGCATTCCCAC 59.565 57.895 0.00 0.00 46.93 4.61
2919 9473 5.143369 GGAGATTCCCTGGCTTCATTATTT 58.857 41.667 0.00 0.00 0.00 1.40
2931 9485 5.116084 TGTTTTAGGATGGAGATTCCCTG 57.884 43.478 0.00 0.00 35.03 4.45
3022 9582 4.128643 GCTTCAGATCAATCTCCTTCCAG 58.871 47.826 0.00 0.00 34.22 3.86
3034 9594 4.794164 GCTCGTCGCTTCAGATCA 57.206 55.556 0.00 0.00 35.14 2.92
3047 9607 2.530177 TGAATGCGTTCTTAGAGCTCG 58.470 47.619 19.09 0.00 35.33 5.03
3082 9642 3.601443 ATTGAAGTCGAGAGTCCCTTG 57.399 47.619 0.00 0.00 0.00 3.61
3092 9652 6.821160 TCTTGCAATGGTATTATTGAAGTCGA 59.179 34.615 0.00 0.00 39.79 4.20
3093 9653 7.015226 TCTTGCAATGGTATTATTGAAGTCG 57.985 36.000 0.00 0.00 39.79 4.18
3130 9692 6.017192 CACACATGTTGGAATTGAACTCACTA 60.017 38.462 0.00 0.00 0.00 2.74
3133 9695 4.037803 CCACACATGTTGGAATTGAACTCA 59.962 41.667 17.28 0.00 0.00 3.41
3136 9698 4.202101 TGTCCACACATGTTGGAATTGAAC 60.202 41.667 23.00 14.58 33.01 3.18
3156 9718 1.153549 CCGAAGCAGCTAGGGTGTC 60.154 63.158 8.61 0.00 33.19 3.67
3210 9772 0.608130 ATCTGCTCTACGCACCACAA 59.392 50.000 0.00 0.00 45.47 3.33
3250 9812 0.179034 GTGAGATCATGACTGGGGCC 60.179 60.000 0.00 0.00 0.00 5.80
3251 9813 0.179034 GGTGAGATCATGACTGGGGC 60.179 60.000 0.00 0.00 0.00 5.80
3252 9814 1.134280 GTGGTGAGATCATGACTGGGG 60.134 57.143 0.00 0.00 0.00 4.96
3253 9815 1.556451 TGTGGTGAGATCATGACTGGG 59.444 52.381 0.00 0.00 0.00 4.45
3277 9839 0.606401 CTGGGGCTGTCGTTCACAAT 60.606 55.000 0.00 0.00 33.31 2.71
3298 9860 3.344215 GATGATGGCTCGGCTGCG 61.344 66.667 0.00 0.00 0.00 5.18
3299 9861 3.344215 CGATGATGGCTCGGCTGC 61.344 66.667 0.00 0.00 32.58 5.25
3314 9876 1.066143 GGTTGATGCTCCCTTCTTCGA 60.066 52.381 0.00 0.00 0.00 3.71
3315 9877 1.065854 AGGTTGATGCTCCCTTCTTCG 60.066 52.381 0.00 0.00 0.00 3.79
3326 9888 0.174389 TCTGCGAGAGAGGTTGATGC 59.826 55.000 0.00 0.00 0.00 3.91
3340 9902 0.957395 ACCATGCAACTCCTTCTGCG 60.957 55.000 0.00 0.00 41.63 5.18
3344 9906 0.244721 GCCAACCATGCAACTCCTTC 59.755 55.000 0.00 0.00 0.00 3.46
3347 9909 0.108520 CATGCCAACCATGCAACTCC 60.109 55.000 0.00 0.00 44.34 3.85
3356 9918 1.152589 TGCCAAGTCATGCCAACCA 60.153 52.632 0.00 0.00 0.00 3.67
3361 9923 1.678101 GTTATCCTGCCAAGTCATGCC 59.322 52.381 0.00 0.00 0.00 4.40
3370 9932 3.432186 CGAATCCAAGAGTTATCCTGCCA 60.432 47.826 0.00 0.00 0.00 4.92
3391 9953 1.080569 GGCAGGTGTCAATTTGGCG 60.081 57.895 0.00 0.00 0.00 5.69
3393 9955 1.001181 CCAAGGCAGGTGTCAATTTGG 59.999 52.381 0.00 0.00 0.00 3.28
3408 9970 0.533951 GCTCCAAGGAAATGCCAAGG 59.466 55.000 0.00 0.00 40.02 3.61
3409 9971 1.067354 GTGCTCCAAGGAAATGCCAAG 60.067 52.381 0.00 0.00 40.02 3.61


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

AutoCloner maintained by Alex Coulton.