Multiple sequence alignment - TraesCS5D01G411300

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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 TraesCS5D01G411300 chr5D 100.000 3895 0 0 1 3895 474716117 474720011 0.000000e+00 7193
1 TraesCS5D01G411300 chr5B 90.080 2258 95 67 449 2651 581711240 581709057 0.000000e+00 2809
2 TraesCS5D01G411300 chr5B 92.503 747 36 11 3161 3895 581708376 581707638 0.000000e+00 1051
3 TraesCS5D01G411300 chr5B 84.181 531 28 28 2644 3155 581708989 581708496 7.620000e-127 464
4 TraesCS5D01G411300 chr5B 86.881 404 51 2 1 403 581711651 581711249 5.930000e-123 451
5 TraesCS5D01G411300 chr5B 76.923 247 53 4 2405 2649 415775447 415775691 1.890000e-28 137
6 TraesCS5D01G411300 chr5A 87.488 2030 106 59 672 2651 593760084 593762015 0.000000e+00 2206
7 TraesCS5D01G411300 chr5A 84.866 1229 73 45 2641 3831 593762079 593763232 0.000000e+00 1134
8 TraesCS5D01G411300 chr3B 84.196 367 42 5 38 403 668818282 668817931 3.730000e-90 342
9 TraesCS5D01G411300 chr7B 83.379 367 60 1 38 403 47614499 47614133 4.820000e-89 339
10 TraesCS5D01G411300 chr7B 83.702 362 43 5 38 398 32464550 32464204 1.040000e-85 327
11 TraesCS5D01G411300 chr6D 83.924 367 43 8 38 403 458725170 458724819 1.730000e-88 337
12 TraesCS5D01G411300 chr4A 83.924 367 43 5 38 403 672266920 672266569 1.730000e-88 337
13 TraesCS5D01G411300 chr1B 84.270 356 44 8 2302 2651 114601881 114601532 1.730000e-88 337
14 TraesCS5D01G411300 chr6B 83.651 367 44 5 38 403 212165013 212164662 8.070000e-87 331
15 TraesCS5D01G411300 chr2B 83.651 367 44 5 38 403 85697543 85697894 8.070000e-87 331
16 TraesCS5D01G411300 chr2B 83.019 318 49 5 2334 2651 473330756 473330444 2.290000e-72 283
17 TraesCS5D01G411300 chr2B 79.032 310 38 10 2328 2637 142541153 142540871 1.850000e-43 187
18 TraesCS5D01G411300 chr3D 82.880 368 43 10 39 403 472439034 472438684 2.920000e-81 313
19 TraesCS5D01G411300 chr1D 82.584 356 50 8 2302 2651 13669443 13669094 1.760000e-78 303
20 TraesCS5D01G411300 chr2D 83.796 216 33 2 2436 2651 571221884 571222097 1.830000e-48 204


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 TraesCS5D01G411300 chr5D 474716117 474720011 3894 False 7193.00 7193 100.00000 1 3895 1 chr5D.!!$F1 3894
1 TraesCS5D01G411300 chr5B 581707638 581711651 4013 True 1193.75 2809 88.41125 1 3895 4 chr5B.!!$R1 3894
2 TraesCS5D01G411300 chr5A 593760084 593763232 3148 False 1670.00 2206 86.17700 672 3831 2 chr5A.!!$F1 3159

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
237 239 0.105593 CAGTCCCATCGTCCTCCATG 59.894 60.000 0.00 0.0 0.00 3.66 F
239 241 0.179073 GTCCCATCGTCCTCCATGTG 60.179 60.000 0.00 0.0 0.00 3.21 F
270 272 0.394216 TCTCCATGGATTTGGTGGCG 60.394 55.000 16.63 0.0 38.01 5.69 F
274 276 0.680921 CATGGATTTGGTGGCGTCCT 60.681 55.000 0.00 0.0 0.00 3.85 F
624 633 1.004918 CACTCCCGCTCGTCCTTTT 60.005 57.895 0.00 0.0 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1912 0.107703 CCTTTCCTCCTGCGCACATA 60.108 55.000 5.66 0.00 0.00 2.29 R
2097 2212 3.749064 AGCACGGCGTCGATGTCT 61.749 61.111 20.03 9.44 40.11 3.41 R
2208 2323 4.457496 CTCAGCACCGCCCACGAT 62.457 66.667 0.00 0.00 43.93 3.73 R
2598 2713 4.803426 GTCCAGTCGCCGAGCAGG 62.803 72.222 0.00 0.00 44.97 4.85 R
2933 3157 1.135402 CAGTAATTGCCACGGAAAGCC 60.135 52.381 0.00 0.00 0.00 4.35 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
23 24 4.547671 TCTCTGTTATAAGTAGCAGCCCT 58.452 43.478 0.00 0.00 38.57 5.19
28 29 4.141937 TGTTATAAGTAGCAGCCCTGTCAG 60.142 45.833 0.00 0.00 0.00 3.51
95 96 2.409870 GGTCTGGCAAGGCGATTGG 61.410 63.158 2.87 0.00 39.47 3.16
123 124 2.223525 CCTAGCGGAAGAGGTTTCTACG 60.224 54.545 0.00 0.00 37.15 3.51
124 125 0.531200 AGCGGAAGAGGTTTCTACGG 59.469 55.000 0.00 0.00 35.63 4.02
133 134 3.262405 AGAGGTTTCTACGGGCACAATAA 59.738 43.478 0.00 0.00 0.00 1.40
138 139 5.048573 GGTTTCTACGGGCACAATAAAGAAA 60.049 40.000 0.00 0.00 0.00 2.52
139 140 6.440436 GTTTCTACGGGCACAATAAAGAAAA 58.560 36.000 0.00 0.00 34.37 2.29
140 141 5.873179 TCTACGGGCACAATAAAGAAAAG 57.127 39.130 0.00 0.00 0.00 2.27
146 147 5.105756 CGGGCACAATAAAGAAAAGGAAGAT 60.106 40.000 0.00 0.00 0.00 2.40
151 152 7.031975 CACAATAAAGAAAAGGAAGATGGCTC 58.968 38.462 0.00 0.00 0.00 4.70
166 168 0.105778 GGCTCTCAGGACCATAGCAC 59.894 60.000 0.00 0.00 34.85 4.40
170 172 1.751351 TCTCAGGACCATAGCACGAAG 59.249 52.381 0.00 0.00 0.00 3.79
184 186 0.317160 ACGAAGAGTGACGCCATTGA 59.683 50.000 0.00 0.00 0.00 2.57
198 200 1.942657 CCATTGATAAGGCGTCAGTGG 59.057 52.381 14.13 14.13 43.86 4.00
209 211 0.729116 CGTCAGTGGCTGCTTAATGG 59.271 55.000 0.00 0.00 0.00 3.16
211 213 2.012673 GTCAGTGGCTGCTTAATGGAG 58.987 52.381 0.00 0.00 37.17 3.86
212 214 1.065199 TCAGTGGCTGCTTAATGGAGG 60.065 52.381 0.00 0.00 34.46 4.30
213 215 0.257039 AGTGGCTGCTTAATGGAGGG 59.743 55.000 0.00 0.00 34.46 4.30
222 224 3.451178 TGCTTAATGGAGGGTACTCAGTC 59.549 47.826 0.00 0.00 45.81 3.51
225 227 0.716591 ATGGAGGGTACTCAGTCCCA 59.283 55.000 13.16 0.00 45.81 4.37
228 230 1.033574 GAGGGTACTCAGTCCCATCG 58.966 60.000 13.16 0.00 45.64 3.84
237 239 0.105593 CAGTCCCATCGTCCTCCATG 59.894 60.000 0.00 0.00 0.00 3.66
239 241 0.179073 GTCCCATCGTCCTCCATGTG 60.179 60.000 0.00 0.00 0.00 3.21
240 242 0.617535 TCCCATCGTCCTCCATGTGT 60.618 55.000 0.00 0.00 0.00 3.72
241 243 0.462581 CCCATCGTCCTCCATGTGTG 60.463 60.000 0.00 0.00 0.00 3.82
256 258 0.610174 GTGTGTCTGGCTCATCTCCA 59.390 55.000 0.00 0.00 0.00 3.86
270 272 0.394216 TCTCCATGGATTTGGTGGCG 60.394 55.000 16.63 0.00 38.01 5.69
274 276 0.680921 CATGGATTTGGTGGCGTCCT 60.681 55.000 0.00 0.00 0.00 3.85
285 287 2.870411 GGTGGCGTCCTATGTATTCAAC 59.130 50.000 0.00 0.00 0.00 3.18
289 291 4.406326 TGGCGTCCTATGTATTCAACCTTA 59.594 41.667 0.00 0.00 0.00 2.69
294 296 8.403236 GCGTCCTATGTATTCAACCTTAATTTT 58.597 33.333 0.00 0.00 0.00 1.82
309 311 7.857456 ACCTTAATTTTGTTGAGGGTTTCTTT 58.143 30.769 4.03 0.00 0.00 2.52
320 322 5.445069 TGAGGGTTTCTTTGAGACATTGAA 58.555 37.500 0.00 0.00 0.00 2.69
346 348 3.614630 CGAGGGTTCGTGGTTGTTACATA 60.615 47.826 0.00 0.00 41.84 2.29
369 371 9.872757 CATATTATGTATGTTTGTCGGGTTAAC 57.127 33.333 0.00 0.00 0.00 2.01
400 402 6.145535 GTCATGGAGTTTGTTTCTTAGCAAG 58.854 40.000 0.00 0.00 0.00 4.01
403 405 6.613755 TGGAGTTTGTTTCTTAGCAAGTAC 57.386 37.500 0.00 0.00 0.00 2.73
405 407 7.502696 TGGAGTTTGTTTCTTAGCAAGTACTA 58.497 34.615 0.00 0.00 0.00 1.82
406 408 7.988599 TGGAGTTTGTTTCTTAGCAAGTACTAA 59.011 33.333 0.00 0.00 0.00 2.24
407 409 9.000486 GGAGTTTGTTTCTTAGCAAGTACTAAT 58.000 33.333 0.00 0.00 31.90 1.73
446 448 8.928270 ATAATTGTTTTAGAGAGTAGTCCACG 57.072 34.615 0.00 0.00 0.00 4.94
447 449 5.779529 TTGTTTTAGAGAGTAGTCCACGT 57.220 39.130 0.00 0.00 0.00 4.49
455 457 3.748083 AGAGTAGTCCACGTGTGTTCTA 58.252 45.455 15.65 8.24 0.00 2.10
460 462 5.651139 AGTAGTCCACGTGTGTTCTATATGT 59.349 40.000 15.65 0.00 0.00 2.29
461 463 6.825213 AGTAGTCCACGTGTGTTCTATATGTA 59.175 38.462 15.65 0.00 0.00 2.29
462 464 6.710597 AGTCCACGTGTGTTCTATATGTAT 57.289 37.500 15.65 0.00 0.00 2.29
463 465 6.736123 AGTCCACGTGTGTTCTATATGTATC 58.264 40.000 15.65 0.00 0.00 2.24
494 496 9.796120 TTTGTCTGGTTTTCTGTTAATTAAGTG 57.204 29.630 0.00 0.00 0.00 3.16
495 497 7.936584 TGTCTGGTTTTCTGTTAATTAAGTGG 58.063 34.615 0.00 0.00 0.00 4.00
496 498 7.013846 TGTCTGGTTTTCTGTTAATTAAGTGGG 59.986 37.037 0.00 0.00 0.00 4.61
497 499 7.013942 GTCTGGTTTTCTGTTAATTAAGTGGGT 59.986 37.037 0.00 0.00 0.00 4.51
498 500 8.219178 TCTGGTTTTCTGTTAATTAAGTGGGTA 58.781 33.333 0.00 0.00 0.00 3.69
499 501 8.763984 TGGTTTTCTGTTAATTAAGTGGGTAA 57.236 30.769 0.00 0.00 0.00 2.85
535 542 9.502145 TCTTAATTACTAATTGATGCTTTTGCG 57.498 29.630 4.52 0.00 39.17 4.85
536 543 9.289303 CTTAATTACTAATTGATGCTTTTGCGT 57.711 29.630 4.52 0.00 39.17 5.24
547 554 2.754472 GCTTTTGCGTCCTTTTCCAAT 58.246 42.857 0.00 0.00 34.86 3.16
553 560 6.591313 TTTGCGTCCTTTTCCAATAAAAAC 57.409 33.333 0.00 0.00 0.00 2.43
556 563 6.106673 TGCGTCCTTTTCCAATAAAAACAAA 58.893 32.000 0.00 0.00 0.00 2.83
557 564 6.036191 TGCGTCCTTTTCCAATAAAAACAAAC 59.964 34.615 0.00 0.00 0.00 2.93
558 565 6.036191 GCGTCCTTTTCCAATAAAAACAAACA 59.964 34.615 0.00 0.00 0.00 2.83
559 566 7.413109 GCGTCCTTTTCCAATAAAAACAAACAA 60.413 33.333 0.00 0.00 0.00 2.83
560 567 7.900864 CGTCCTTTTCCAATAAAAACAAACAAC 59.099 33.333 0.00 0.00 0.00 3.32
561 568 8.178964 GTCCTTTTCCAATAAAAACAAACAACC 58.821 33.333 0.00 0.00 0.00 3.77
562 569 7.883311 TCCTTTTCCAATAAAAACAAACAACCA 59.117 29.630 0.00 0.00 0.00 3.67
563 570 8.180920 CCTTTTCCAATAAAAACAAACAACCAG 58.819 33.333 0.00 0.00 0.00 4.00
564 571 8.622948 TTTTCCAATAAAAACAAACAACCAGT 57.377 26.923 0.00 0.00 0.00 4.00
565 572 9.720769 TTTTCCAATAAAAACAAACAACCAGTA 57.279 25.926 0.00 0.00 0.00 2.74
566 573 8.934507 TTCCAATAAAAACAAACAACCAGTAG 57.065 30.769 0.00 0.00 0.00 2.57
567 574 7.493367 TCCAATAAAAACAAACAACCAGTAGG 58.507 34.615 0.00 0.00 42.21 3.18
576 583 1.091771 CAACCAGTAGGCAGCATCGG 61.092 60.000 0.00 0.00 39.06 4.18
620 629 4.436998 CCACACTCCCGCTCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
621 630 3.374402 CACACTCCCGCTCGTCCT 61.374 66.667 0.00 0.00 0.00 3.85
623 632 2.207924 ACACTCCCGCTCGTCCTTT 61.208 57.895 0.00 0.00 0.00 3.11
624 633 1.004918 CACTCCCGCTCGTCCTTTT 60.005 57.895 0.00 0.00 0.00 2.27
628 650 2.173382 CCGCTCGTCCTTTTTGCG 59.827 61.111 0.00 0.00 45.22 4.85
672 695 4.202419 ACTCTGATCCATCTAGTCGTAGCT 60.202 45.833 0.00 0.00 0.00 3.32
700 723 2.351726 CCTCCTCGTCGCCAATTAAAAG 59.648 50.000 0.00 0.00 0.00 2.27
760 785 4.719773 AGCCTTTATTCCCCAATTAAACCC 59.280 41.667 0.00 0.00 0.00 4.11
770 795 2.165641 CCAATTAAACCCTTCGCTTCCC 59.834 50.000 0.00 0.00 0.00 3.97
787 812 3.066291 TCCCAAGCTTTTAAGATGCGA 57.934 42.857 0.00 0.00 33.86 5.10
845 885 7.713507 CCGATTCCTAATAACCATTTCAGTGTA 59.286 37.037 0.00 0.00 0.00 2.90
978 1043 4.517453 CCGCCTAGCTATATATCCAGTCTC 59.483 50.000 0.00 0.00 0.00 3.36
1031 1099 2.558795 TCTCACTTTCTCTCGAACCTGG 59.441 50.000 0.00 0.00 0.00 4.45
1036 1104 1.874345 TTCTCTCGAACCTGGCCGTC 61.874 60.000 0.00 0.00 0.00 4.79
1037 1105 2.282958 TCTCGAACCTGGCCGTCT 60.283 61.111 0.00 0.00 0.00 4.18
1038 1106 2.125912 CTCGAACCTGGCCGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
1039 1107 2.915659 TCGAACCTGGCCGTCTGT 60.916 61.111 0.00 0.00 0.00 3.41
1040 1108 2.432628 CGAACCTGGCCGTCTGTC 60.433 66.667 0.00 0.00 0.00 3.51
1041 1109 2.932234 CGAACCTGGCCGTCTGTCT 61.932 63.158 0.00 0.00 0.00 3.41
1042 1110 1.374758 GAACCTGGCCGTCTGTCTG 60.375 63.158 0.00 0.00 0.00 3.51
1043 1111 3.537206 AACCTGGCCGTCTGTCTGC 62.537 63.158 0.00 0.00 0.00 4.26
1044 1112 4.767255 CCTGGCCGTCTGTCTGCC 62.767 72.222 0.00 0.75 44.90 4.85
1326 1405 2.426024 GACTTCCTCATGCTGGTACGTA 59.574 50.000 0.00 0.00 0.00 3.57
1327 1406 3.031736 ACTTCCTCATGCTGGTACGTAT 58.968 45.455 0.00 0.00 0.00 3.06
1328 1407 3.451178 ACTTCCTCATGCTGGTACGTATT 59.549 43.478 0.00 0.00 0.00 1.89
1329 1408 4.647853 ACTTCCTCATGCTGGTACGTATTA 59.352 41.667 0.00 0.00 0.00 0.98
1330 1409 5.304614 ACTTCCTCATGCTGGTACGTATTAT 59.695 40.000 0.00 0.00 0.00 1.28
1331 1410 5.801531 TCCTCATGCTGGTACGTATTATT 57.198 39.130 0.00 0.00 0.00 1.40
1332 1411 6.169557 TCCTCATGCTGGTACGTATTATTT 57.830 37.500 0.00 0.00 0.00 1.40
1333 1412 6.588204 TCCTCATGCTGGTACGTATTATTTT 58.412 36.000 0.00 0.00 0.00 1.82
1334 1413 7.051623 TCCTCATGCTGGTACGTATTATTTTT 58.948 34.615 0.00 0.00 0.00 1.94
1335 1414 7.225931 TCCTCATGCTGGTACGTATTATTTTTC 59.774 37.037 0.00 0.00 0.00 2.29
1336 1415 7.226720 CCTCATGCTGGTACGTATTATTTTTCT 59.773 37.037 0.00 0.00 0.00 2.52
1337 1416 8.500753 TCATGCTGGTACGTATTATTTTTCTT 57.499 30.769 0.00 0.00 0.00 2.52
1338 1417 8.952278 TCATGCTGGTACGTATTATTTTTCTTT 58.048 29.630 0.00 0.00 0.00 2.52
1339 1418 9.567848 CATGCTGGTACGTATTATTTTTCTTTT 57.432 29.630 0.00 0.00 0.00 2.27
1341 1420 9.400638 TGCTGGTACGTATTATTTTTCTTTTTG 57.599 29.630 0.00 0.00 0.00 2.44
1342 1421 9.615295 GCTGGTACGTATTATTTTTCTTTTTGA 57.385 29.630 0.00 0.00 0.00 2.69
1421 1526 1.601914 CCGTTTTGCCTTTTTCCTCCG 60.602 52.381 0.00 0.00 0.00 4.63
1612 1717 2.081212 GCGTCAAGTCCGTCGTCTG 61.081 63.158 0.00 0.00 0.00 3.51
1729 1840 8.910351 ATACCATCATCATCATCATCATCATC 57.090 34.615 0.00 0.00 0.00 2.92
1731 1842 7.349598 ACCATCATCATCATCATCATCATCAT 58.650 34.615 0.00 0.00 0.00 2.45
1732 1843 7.500559 ACCATCATCATCATCATCATCATCATC 59.499 37.037 0.00 0.00 0.00 2.92
1733 1844 7.307632 CCATCATCATCATCATCATCATCATCG 60.308 40.741 0.00 0.00 0.00 3.84
1734 1845 6.873997 TCATCATCATCATCATCATCATCGA 58.126 36.000 0.00 0.00 0.00 3.59
1737 1848 6.640518 TCATCATCATCATCATCATCGACAT 58.359 36.000 0.00 0.00 0.00 3.06
1738 1849 6.535150 TCATCATCATCATCATCATCGACATG 59.465 38.462 0.00 0.00 0.00 3.21
1739 1850 4.630069 TCATCATCATCATCATCGACATGC 59.370 41.667 0.00 0.00 0.00 4.06
1740 1851 3.997762 TCATCATCATCATCGACATGCA 58.002 40.909 0.00 0.00 0.00 3.96
1741 1852 3.994392 TCATCATCATCATCGACATGCAG 59.006 43.478 0.00 0.00 0.00 4.41
1745 1856 3.672767 TCATCATCGACATGCAGCTAT 57.327 42.857 0.00 0.00 0.00 2.97
1747 1858 4.383173 TCATCATCGACATGCAGCTATTT 58.617 39.130 0.00 0.00 0.00 1.40
1750 1861 4.190772 TCATCGACATGCAGCTATTTTCA 58.809 39.130 0.00 0.00 0.00 2.69
1751 1862 4.034394 TCATCGACATGCAGCTATTTTCAC 59.966 41.667 0.00 0.00 0.00 3.18
1752 1863 3.599343 TCGACATGCAGCTATTTTCACT 58.401 40.909 0.00 0.00 0.00 3.41
1753 1864 3.371898 TCGACATGCAGCTATTTTCACTG 59.628 43.478 0.00 0.00 34.48 3.66
1754 1865 3.486375 CGACATGCAGCTATTTTCACTGG 60.486 47.826 0.00 0.00 31.94 4.00
1756 1867 4.275810 ACATGCAGCTATTTTCACTGGAT 58.724 39.130 0.00 0.00 42.36 3.41
1758 1869 4.970662 TGCAGCTATTTTCACTGGATTC 57.029 40.909 0.00 0.00 31.94 2.52
1759 1870 3.696051 TGCAGCTATTTTCACTGGATTCC 59.304 43.478 0.00 0.00 31.94 3.01
1760 1871 3.696051 GCAGCTATTTTCACTGGATTCCA 59.304 43.478 5.05 5.05 31.94 3.53
1761 1872 4.158394 GCAGCTATTTTCACTGGATTCCAA 59.842 41.667 6.88 0.00 30.80 3.53
1762 1873 5.163478 GCAGCTATTTTCACTGGATTCCAAT 60.163 40.000 6.88 0.00 30.80 3.16
1763 1874 6.039717 GCAGCTATTTTCACTGGATTCCAATA 59.960 38.462 6.88 0.05 30.80 1.90
1764 1875 7.255730 GCAGCTATTTTCACTGGATTCCAATAT 60.256 37.037 6.88 0.00 30.80 1.28
1765 1876 8.636213 CAGCTATTTTCACTGGATTCCAATATT 58.364 33.333 6.88 0.00 30.80 1.28
1766 1877 8.854117 AGCTATTTTCACTGGATTCCAATATTC 58.146 33.333 6.88 0.00 30.80 1.75
1767 1878 7.805071 GCTATTTTCACTGGATTCCAATATTCG 59.195 37.037 6.88 0.00 30.80 3.34
1768 1879 7.645058 ATTTTCACTGGATTCCAATATTCGT 57.355 32.000 6.88 0.00 30.80 3.85
1769 1880 8.746052 ATTTTCACTGGATTCCAATATTCGTA 57.254 30.769 6.88 0.00 30.80 3.43
1770 1881 7.548196 TTTCACTGGATTCCAATATTCGTAC 57.452 36.000 6.88 0.00 30.80 3.67
1771 1882 5.286438 TCACTGGATTCCAATATTCGTACG 58.714 41.667 9.53 9.53 30.80 3.67
1772 1883 5.047847 CACTGGATTCCAATATTCGTACGT 58.952 41.667 16.05 0.00 30.80 3.57
1773 1884 6.039605 TCACTGGATTCCAATATTCGTACGTA 59.960 38.462 16.05 6.02 30.80 3.57
1774 1885 6.866770 CACTGGATTCCAATATTCGTACGTAT 59.133 38.462 16.05 13.94 30.80 3.06
1775 1886 8.024865 CACTGGATTCCAATATTCGTACGTATA 58.975 37.037 16.05 15.80 30.80 1.47
1776 1887 8.025445 ACTGGATTCCAATATTCGTACGTATAC 58.975 37.037 15.58 3.07 30.80 1.47
1777 1888 7.315142 TGGATTCCAATATTCGTACGTATACC 58.685 38.462 15.58 11.19 0.00 2.73
1778 1889 7.039853 TGGATTCCAATATTCGTACGTATACCA 60.040 37.037 15.58 13.25 0.00 3.25
1779 1890 7.487189 GGATTCCAATATTCGTACGTATACCAG 59.513 40.741 15.58 9.12 0.00 4.00
1780 1891 5.702865 TCCAATATTCGTACGTATACCAGC 58.297 41.667 15.58 0.00 0.00 4.85
1781 1892 4.860907 CCAATATTCGTACGTATACCAGCC 59.139 45.833 15.58 0.00 0.00 4.85
1782 1893 5.336213 CCAATATTCGTACGTATACCAGCCT 60.336 44.000 15.58 0.00 0.00 4.58
1783 1894 5.972107 ATATTCGTACGTATACCAGCCTT 57.028 39.130 15.58 0.00 0.00 4.35
1793 1904 5.046807 ACGTATACCAGCCTTCTGTAACTTT 60.047 40.000 0.00 0.00 38.66 2.66
1795 1906 2.863809 ACCAGCCTTCTGTAACTTTGG 58.136 47.619 0.00 0.00 38.66 3.28
1797 1908 3.117663 ACCAGCCTTCTGTAACTTTGGAA 60.118 43.478 0.00 0.00 38.66 3.53
1798 1909 4.082125 CCAGCCTTCTGTAACTTTGGAAT 58.918 43.478 0.00 0.00 38.66 3.01
1799 1910 4.082571 CCAGCCTTCTGTAACTTTGGAATG 60.083 45.833 0.00 0.00 38.66 2.67
1800 1911 3.507622 AGCCTTCTGTAACTTTGGAATGC 59.492 43.478 0.00 0.00 32.38 3.56
1801 1912 3.507622 GCCTTCTGTAACTTTGGAATGCT 59.492 43.478 0.00 0.00 0.00 3.79
2097 2212 2.654877 GTCGAGTTCTTCCCCGCA 59.345 61.111 0.00 0.00 0.00 5.69
2130 2245 2.425592 CTGTCCAACGCCCTGTCA 59.574 61.111 0.00 0.00 0.00 3.58
2466 2581 2.358125 CACAACATGGCCCGACGA 60.358 61.111 0.00 0.00 0.00 4.20
2598 2713 3.116531 GACGGCTACAACCACGGC 61.117 66.667 0.00 0.00 0.00 5.68
2723 2915 2.027625 GAGTTCCAAGGACGCGGTG 61.028 63.158 12.47 2.42 0.00 4.94
2771 2964 3.209410 AGTGCTCTCTGTTTCAACTTGG 58.791 45.455 0.00 0.00 0.00 3.61
2773 2966 3.002759 GTGCTCTCTGTTTCAACTTGGTC 59.997 47.826 0.00 0.00 0.00 4.02
2775 2968 3.627577 GCTCTCTGTTTCAACTTGGTCAA 59.372 43.478 0.00 0.00 0.00 3.18
2843 3067 2.748605 CTGACTTTGTCGACAGAGCTT 58.251 47.619 30.04 15.87 34.95 3.74
2845 3069 3.531538 TGACTTTGTCGACAGAGCTTTT 58.468 40.909 30.04 14.87 34.95 2.27
2903 3127 0.250295 CCAGAGTGAAAACCTGGCGA 60.250 55.000 0.00 0.00 40.69 5.54
2932 3156 4.673403 CCTTTGGGCCGCTTTTTC 57.327 55.556 0.00 0.00 0.00 2.29
2933 3157 1.372872 CCTTTGGGCCGCTTTTTCG 60.373 57.895 0.00 0.00 0.00 3.46
2954 3179 1.135402 GCTTTCCGTGGCAATTACTGG 60.135 52.381 0.00 0.00 0.00 4.00
2992 3217 3.848582 GCTTCGTAGATTTGCTGCTTTTC 59.151 43.478 0.00 0.00 35.04 2.29
3072 3306 2.388890 GATGATGAGCCCGGGACAGG 62.389 65.000 29.31 0.00 0.00 4.00
3187 3535 4.137872 GACCGCGGGGATTCACGA 62.138 66.667 31.76 0.00 36.97 4.35
3192 3540 1.449601 GCGGGGATTCACGACACAT 60.450 57.895 0.00 0.00 0.00 3.21
3300 3654 2.565841 ACTCCGTACATAGTACCGGTC 58.434 52.381 12.40 2.55 41.17 4.79
3403 3768 2.544685 CTAGAATCAGCAACGTCCAGG 58.455 52.381 0.00 0.00 0.00 4.45
3419 3793 0.459237 CAGGCTGCTCTGGTCGTAAG 60.459 60.000 0.00 0.00 0.00 2.34
3433 3807 1.301953 GTAAGCCCAAACCGGACGT 60.302 57.895 9.46 0.00 36.56 4.34
3437 3811 2.742403 CCCAAACCGGACGTACCA 59.258 61.111 9.46 0.00 38.90 3.25
3438 3812 1.375013 CCCAAACCGGACGTACCAG 60.375 63.158 9.46 0.00 38.90 4.00
3467 3842 3.505184 GCCCCGTACCGTGCAATG 61.505 66.667 0.00 0.00 0.00 2.82
3481 3857 0.801251 GCAATGGACACACAGAGAGC 59.199 55.000 0.00 0.00 0.00 4.09
3507 3883 3.612004 GCATGCTGGTAGTAGTACGATCC 60.612 52.174 11.37 0.16 0.00 3.36
3526 3902 1.523938 GGCGGCTGATACTGTTCCC 60.524 63.158 0.00 0.00 0.00 3.97
3555 3931 3.441222 CAGATTTGCAGGTGTCATTGCTA 59.559 43.478 11.93 3.86 40.87 3.49
3556 3932 3.693085 AGATTTGCAGGTGTCATTGCTAG 59.307 43.478 11.93 0.00 40.87 3.42
3719 4099 1.417890 CGGATTTATCAGGAGGTGGCT 59.582 52.381 0.00 0.00 0.00 4.75
3826 4211 2.279937 GAAGCGCGGATGTTGACGAC 62.280 60.000 8.83 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.286707 TCTGACAGGGCTGCTACTTATAA 58.713 43.478 1.81 0.00 0.00 0.98
12 13 1.612395 GCTCTGACAGGGCTGCTACT 61.612 60.000 20.49 0.00 0.00 2.57
23 24 1.597854 CCAAGTTGCCGCTCTGACA 60.598 57.895 0.00 0.00 0.00 3.58
44 45 3.130160 CCAAGGAGGCGAGCAAGC 61.130 66.667 0.00 0.00 0.00 4.01
108 109 0.611714 TGCCCGTAGAAACCTCTTCC 59.388 55.000 0.00 0.00 32.70 3.46
109 110 1.001633 TGTGCCCGTAGAAACCTCTTC 59.998 52.381 0.00 0.00 32.70 2.87
111 112 1.053424 TTGTGCCCGTAGAAACCTCT 58.947 50.000 0.00 0.00 35.52 3.69
123 124 5.722021 TCTTCCTTTTCTTTATTGTGCCC 57.278 39.130 0.00 0.00 0.00 5.36
124 125 6.101997 CCATCTTCCTTTTCTTTATTGTGCC 58.898 40.000 0.00 0.00 0.00 5.01
133 134 4.567327 CCTGAGAGCCATCTTCCTTTTCTT 60.567 45.833 0.00 0.00 35.30 2.52
138 139 1.836802 GTCCTGAGAGCCATCTTCCTT 59.163 52.381 0.00 0.00 35.30 3.36
139 140 1.494960 GTCCTGAGAGCCATCTTCCT 58.505 55.000 0.00 0.00 35.30 3.36
140 141 0.467804 GGTCCTGAGAGCCATCTTCC 59.532 60.000 0.00 0.00 35.30 3.46
146 147 0.325577 TGCTATGGTCCTGAGAGCCA 60.326 55.000 0.00 0.00 39.89 4.75
151 152 1.751351 TCTTCGTGCTATGGTCCTGAG 59.249 52.381 0.00 0.00 0.00 3.35
166 168 1.645034 ATCAATGGCGTCACTCTTCG 58.355 50.000 0.00 0.00 0.00 3.79
170 172 1.599542 GCCTTATCAATGGCGTCACTC 59.400 52.381 0.00 0.00 39.71 3.51
178 180 1.942657 CCACTGACGCCTTATCAATGG 59.057 52.381 0.00 0.00 37.15 3.16
184 186 1.450312 GCAGCCACTGACGCCTTAT 60.450 57.895 0.00 0.00 32.44 1.73
191 193 2.012673 CTCCATTAAGCAGCCACTGAC 58.987 52.381 0.00 0.00 32.44 3.51
195 197 0.034089 ACCCTCCATTAAGCAGCCAC 60.034 55.000 0.00 0.00 0.00 5.01
198 200 2.170607 TGAGTACCCTCCATTAAGCAGC 59.829 50.000 0.00 0.00 36.86 5.25
209 211 1.033574 CGATGGGACTGAGTACCCTC 58.966 60.000 12.21 10.38 45.74 4.30
211 213 0.745468 GACGATGGGACTGAGTACCC 59.255 60.000 12.21 11.88 45.74 3.69
212 214 0.745468 GGACGATGGGACTGAGTACC 59.255 60.000 6.98 6.98 36.98 3.34
213 215 1.677052 GAGGACGATGGGACTGAGTAC 59.323 57.143 0.00 0.00 0.00 2.73
222 224 0.462581 CACACATGGAGGACGATGGG 60.463 60.000 0.00 0.00 40.59 4.00
225 227 1.205655 CAGACACACATGGAGGACGAT 59.794 52.381 0.00 0.00 0.00 3.73
228 230 0.674895 GCCAGACACACATGGAGGAC 60.675 60.000 0.00 0.00 39.02 3.85
237 239 0.610174 TGGAGATGAGCCAGACACAC 59.390 55.000 0.00 0.00 0.00 3.82
239 241 1.474677 CCATGGAGATGAGCCAGACAC 60.475 57.143 5.56 0.00 39.11 3.67
240 242 0.835276 CCATGGAGATGAGCCAGACA 59.165 55.000 5.56 0.00 39.11 3.41
241 243 1.126488 TCCATGGAGATGAGCCAGAC 58.874 55.000 11.44 0.00 39.11 3.51
256 258 0.916086 TAGGACGCCACCAAATCCAT 59.084 50.000 0.00 0.00 33.33 3.41
285 287 7.984617 TCAAAGAAACCCTCAACAAAATTAAGG 59.015 33.333 0.00 0.00 0.00 2.69
289 291 7.041721 GTCTCAAAGAAACCCTCAACAAAATT 58.958 34.615 0.00 0.00 0.00 1.82
294 296 4.229304 TGTCTCAAAGAAACCCTCAACA 57.771 40.909 0.00 0.00 0.00 3.33
309 311 1.338105 CCCTCGCACTTCAATGTCTCA 60.338 52.381 0.00 0.00 0.00 3.27
346 348 7.324354 GGTTAACCCGACAAACATACATAAT 57.676 36.000 14.16 0.00 0.00 1.28
367 369 1.056660 AACTCCATGACCTCACGGTT 58.943 50.000 0.00 0.00 45.73 4.44
369 371 1.270839 ACAAACTCCATGACCTCACGG 60.271 52.381 0.00 0.00 0.00 4.94
374 376 4.762251 GCTAAGAAACAAACTCCATGACCT 59.238 41.667 0.00 0.00 0.00 3.85
420 422 9.021863 CGTGGACTACTCTCTAAAACAATTATC 57.978 37.037 0.00 0.00 0.00 1.75
421 423 8.529476 ACGTGGACTACTCTCTAAAACAATTAT 58.471 33.333 0.00 0.00 0.00 1.28
422 424 7.811236 CACGTGGACTACTCTCTAAAACAATTA 59.189 37.037 7.95 0.00 0.00 1.40
423 425 6.645415 CACGTGGACTACTCTCTAAAACAATT 59.355 38.462 7.95 0.00 0.00 2.32
424 426 6.157211 CACGTGGACTACTCTCTAAAACAAT 58.843 40.000 7.95 0.00 0.00 2.71
425 427 5.068198 ACACGTGGACTACTCTCTAAAACAA 59.932 40.000 21.57 0.00 0.00 2.83
426 428 4.581824 ACACGTGGACTACTCTCTAAAACA 59.418 41.667 21.57 0.00 0.00 2.83
427 429 4.916249 CACACGTGGACTACTCTCTAAAAC 59.084 45.833 21.57 0.00 0.00 2.43
428 430 4.581824 ACACACGTGGACTACTCTCTAAAA 59.418 41.667 21.57 0.00 34.19 1.52
429 431 4.139786 ACACACGTGGACTACTCTCTAAA 58.860 43.478 21.57 0.00 34.19 1.85
430 432 3.748083 ACACACGTGGACTACTCTCTAA 58.252 45.455 21.57 0.00 34.19 2.10
431 433 3.413846 ACACACGTGGACTACTCTCTA 57.586 47.619 21.57 0.00 34.19 2.43
432 434 2.273538 ACACACGTGGACTACTCTCT 57.726 50.000 21.57 0.00 34.19 3.10
433 435 2.553172 AGAACACACGTGGACTACTCTC 59.447 50.000 21.57 4.71 34.19 3.20
434 436 2.584236 AGAACACACGTGGACTACTCT 58.416 47.619 21.57 9.44 34.19 3.24
435 437 4.698583 ATAGAACACACGTGGACTACTC 57.301 45.455 21.57 7.30 34.19 2.59
436 438 5.651139 ACATATAGAACACACGTGGACTACT 59.349 40.000 21.57 13.88 34.19 2.57
437 439 5.888105 ACATATAGAACACACGTGGACTAC 58.112 41.667 21.57 7.17 34.19 2.73
438 440 7.307573 CGATACATATAGAACACACGTGGACTA 60.308 40.741 21.57 16.11 34.19 2.59
439 441 6.512903 CGATACATATAGAACACACGTGGACT 60.513 42.308 21.57 14.54 34.19 3.85
440 442 5.624081 CGATACATATAGAACACACGTGGAC 59.376 44.000 21.57 7.88 34.19 4.02
441 443 5.297527 ACGATACATATAGAACACACGTGGA 59.702 40.000 21.57 0.00 34.19 4.02
442 444 5.516996 ACGATACATATAGAACACACGTGG 58.483 41.667 21.57 11.39 34.19 4.94
443 445 7.445900 AAACGATACATATAGAACACACGTG 57.554 36.000 15.48 15.48 0.00 4.49
444 446 8.470040 AAAAACGATACATATAGAACACACGT 57.530 30.769 0.00 0.00 0.00 4.49
471 473 7.013942 ACCCACTTAATTAACAGAAAACCAGAC 59.986 37.037 0.00 0.00 0.00 3.51
472 474 7.064229 ACCCACTTAATTAACAGAAAACCAGA 58.936 34.615 0.00 0.00 0.00 3.86
473 475 7.284919 ACCCACTTAATTAACAGAAAACCAG 57.715 36.000 0.00 0.00 0.00 4.00
474 476 8.763984 TTACCCACTTAATTAACAGAAAACCA 57.236 30.769 0.00 0.00 0.00 3.67
518 520 4.361451 AGGACGCAAAAGCATCAATTAG 57.639 40.909 0.00 0.00 0.00 1.73
520 522 3.665745 AAGGACGCAAAAGCATCAATT 57.334 38.095 0.00 0.00 0.00 2.32
521 523 3.665745 AAAGGACGCAAAAGCATCAAT 57.334 38.095 0.00 0.00 0.00 2.57
522 524 3.380142 GAAAAGGACGCAAAAGCATCAA 58.620 40.909 0.00 0.00 0.00 2.57
526 528 1.107114 TGGAAAAGGACGCAAAAGCA 58.893 45.000 0.00 0.00 0.00 3.91
527 529 2.217429 TTGGAAAAGGACGCAAAAGC 57.783 45.000 0.00 0.00 0.00 3.51
535 542 8.178964 GGTTGTTTGTTTTTATTGGAAAAGGAC 58.821 33.333 0.00 0.00 0.00 3.85
536 543 7.883311 TGGTTGTTTGTTTTTATTGGAAAAGGA 59.117 29.630 0.00 0.00 0.00 3.36
539 546 8.622948 ACTGGTTGTTTGTTTTTATTGGAAAA 57.377 26.923 0.00 0.00 0.00 2.29
544 551 6.758886 TGCCTACTGGTTGTTTGTTTTTATTG 59.241 34.615 0.00 0.00 35.27 1.90
547 554 5.680151 GCTGCCTACTGGTTGTTTGTTTTTA 60.680 40.000 0.00 0.00 35.27 1.52
553 560 1.317613 TGCTGCCTACTGGTTGTTTG 58.682 50.000 0.00 0.00 35.27 2.93
556 563 0.391661 CGATGCTGCCTACTGGTTGT 60.392 55.000 0.00 0.00 35.27 3.32
557 564 1.091771 CCGATGCTGCCTACTGGTTG 61.092 60.000 0.00 0.00 35.27 3.77
558 565 1.221840 CCGATGCTGCCTACTGGTT 59.778 57.895 0.00 0.00 35.27 3.67
559 566 1.680522 CTCCGATGCTGCCTACTGGT 61.681 60.000 0.00 0.00 35.27 4.00
560 567 1.068753 CTCCGATGCTGCCTACTGG 59.931 63.158 0.00 0.00 0.00 4.00
561 568 1.593750 GCTCCGATGCTGCCTACTG 60.594 63.158 0.00 0.00 0.00 2.74
562 569 2.060383 TGCTCCGATGCTGCCTACT 61.060 57.895 0.00 0.00 0.00 2.57
563 570 1.884926 GTGCTCCGATGCTGCCTAC 60.885 63.158 0.00 0.00 0.00 3.18
564 571 2.060383 AGTGCTCCGATGCTGCCTA 61.060 57.895 0.00 0.00 0.00 3.93
565 572 3.397439 AGTGCTCCGATGCTGCCT 61.397 61.111 0.00 0.00 0.00 4.75
566 573 3.200593 CAGTGCTCCGATGCTGCC 61.201 66.667 0.00 0.00 0.00 4.85
567 574 1.703438 CTTCAGTGCTCCGATGCTGC 61.703 60.000 0.00 0.00 0.00 5.25
617 626 0.668535 ACAGGAAGCGCAAAAAGGAC 59.331 50.000 11.47 0.00 0.00 3.85
618 627 0.667993 CACAGGAAGCGCAAAAAGGA 59.332 50.000 11.47 0.00 0.00 3.36
620 629 0.940991 GCCACAGGAAGCGCAAAAAG 60.941 55.000 11.47 0.00 0.00 2.27
621 630 1.067250 GCCACAGGAAGCGCAAAAA 59.933 52.632 11.47 0.00 0.00 1.94
623 632 3.294493 GGCCACAGGAAGCGCAAA 61.294 61.111 11.47 0.00 0.00 3.68
624 633 4.577677 TGGCCACAGGAAGCGCAA 62.578 61.111 11.47 0.00 0.00 4.85
628 650 1.817099 CGATCTGGCCACAGGAAGC 60.817 63.158 0.00 0.00 44.99 3.86
672 695 3.068691 CGACGAGGAGGAAGGGCA 61.069 66.667 0.00 0.00 0.00 5.36
770 795 5.446473 CCACTAGTCGCATCTTAAAAGCTTG 60.446 44.000 0.00 0.00 0.00 4.01
787 812 0.324830 GGAGAGGAGTGGCCACTAGT 60.325 60.000 37.87 27.06 42.66 2.57
845 885 0.885879 TCTCAGTTACCACGACGCAT 59.114 50.000 0.00 0.00 0.00 4.73
958 1022 4.517453 GGCGAGACTGGATATATAGCTAGG 59.483 50.000 14.84 0.00 0.00 3.02
999 1064 3.096092 AGAAAGTGAGAGGTAGCAGAGG 58.904 50.000 0.00 0.00 0.00 3.69
1043 1111 4.828296 GGATGGGTGGCAGGCAGG 62.828 72.222 0.00 0.00 0.00 4.85
1044 1112 3.292481 AAGGATGGGTGGCAGGCAG 62.292 63.158 0.00 0.00 0.00 4.85
1077 1145 0.586319 CGATCGAGCTCACTCTCCTC 59.414 60.000 15.40 0.00 41.09 3.71
1123 1202 4.154347 GCTCCTCCTCCGCCACTG 62.154 72.222 0.00 0.00 0.00 3.66
1243 1322 1.364626 CGTGAAGAGGCACATCTGGC 61.365 60.000 0.00 0.00 43.48 4.85
1244 1323 0.742281 CCGTGAAGAGGCACATCTGG 60.742 60.000 0.00 0.00 38.69 3.86
1245 1324 0.247460 TCCGTGAAGAGGCACATCTG 59.753 55.000 0.00 0.00 38.69 2.90
1330 1409 9.940166 GTACGAATACTTCCTCAAAAAGAAAAA 57.060 29.630 0.00 0.00 0.00 1.94
1331 1410 8.277713 CGTACGAATACTTCCTCAAAAAGAAAA 58.722 33.333 10.44 0.00 0.00 2.29
1332 1411 7.439056 ACGTACGAATACTTCCTCAAAAAGAAA 59.561 33.333 24.41 0.00 0.00 2.52
1333 1412 6.925165 ACGTACGAATACTTCCTCAAAAAGAA 59.075 34.615 24.41 0.00 0.00 2.52
1334 1413 6.364165 CACGTACGAATACTTCCTCAAAAAGA 59.636 38.462 24.41 0.00 0.00 2.52
1335 1414 6.522761 CACGTACGAATACTTCCTCAAAAAG 58.477 40.000 24.41 0.00 0.00 2.27
1336 1415 5.107375 GCACGTACGAATACTTCCTCAAAAA 60.107 40.000 24.41 0.00 0.00 1.94
1337 1416 4.386652 GCACGTACGAATACTTCCTCAAAA 59.613 41.667 24.41 0.00 0.00 2.44
1338 1417 3.922240 GCACGTACGAATACTTCCTCAAA 59.078 43.478 24.41 0.00 0.00 2.69
1339 1418 3.504863 GCACGTACGAATACTTCCTCAA 58.495 45.455 24.41 0.00 0.00 3.02
1340 1419 2.159338 GGCACGTACGAATACTTCCTCA 60.159 50.000 24.41 0.00 0.00 3.86
1341 1420 2.098770 AGGCACGTACGAATACTTCCTC 59.901 50.000 24.41 0.00 0.00 3.71
1342 1421 2.097825 AGGCACGTACGAATACTTCCT 58.902 47.619 24.41 12.91 0.00 3.36
1343 1422 2.573941 AGGCACGTACGAATACTTCC 57.426 50.000 24.41 10.95 0.00 3.46
1344 1423 4.019919 TGTAGGCACGTACGAATACTTC 57.980 45.455 24.41 11.92 0.00 3.01
1345 1424 3.691118 TCTGTAGGCACGTACGAATACTT 59.309 43.478 24.41 6.84 0.00 2.24
1346 1425 3.273434 TCTGTAGGCACGTACGAATACT 58.727 45.455 24.41 15.65 0.00 2.12
1347 1426 3.680642 TCTGTAGGCACGTACGAATAC 57.319 47.619 24.41 17.18 0.00 1.89
1348 1427 3.439825 TGTTCTGTAGGCACGTACGAATA 59.560 43.478 24.41 5.87 0.00 1.75
1421 1526 2.415512 AGCGACAGGAAATTAAACGAGC 59.584 45.455 0.00 0.00 0.00 5.03
1707 1818 7.307632 CGATGATGATGATGATGATGATGATGG 60.308 40.741 0.00 0.00 0.00 3.51
1710 1821 6.757010 GTCGATGATGATGATGATGATGATGA 59.243 38.462 0.00 0.00 0.00 2.92
1722 1833 2.140717 GCTGCATGTCGATGATGATGA 58.859 47.619 10.67 0.00 0.00 2.92
1723 1834 2.143925 AGCTGCATGTCGATGATGATG 58.856 47.619 10.67 4.45 0.00 3.07
1725 1836 3.672767 ATAGCTGCATGTCGATGATGA 57.327 42.857 10.67 0.00 0.00 2.92
1726 1837 4.744136 AAATAGCTGCATGTCGATGATG 57.256 40.909 1.02 0.00 0.00 3.07
1727 1838 4.818005 TGAAAATAGCTGCATGTCGATGAT 59.182 37.500 1.02 0.00 0.00 2.45
1728 1839 4.034394 GTGAAAATAGCTGCATGTCGATGA 59.966 41.667 1.02 0.00 0.00 2.92
1729 1840 4.034858 AGTGAAAATAGCTGCATGTCGATG 59.965 41.667 1.02 0.00 0.00 3.84
1731 1842 3.371898 CAGTGAAAATAGCTGCATGTCGA 59.628 43.478 1.02 0.00 0.00 4.20
1732 1843 3.486375 CCAGTGAAAATAGCTGCATGTCG 60.486 47.826 1.02 0.00 0.00 4.35
1733 1844 3.691118 TCCAGTGAAAATAGCTGCATGTC 59.309 43.478 1.02 0.00 0.00 3.06
1734 1845 3.689347 TCCAGTGAAAATAGCTGCATGT 58.311 40.909 1.02 0.00 0.00 3.21
1737 1848 3.696051 GGAATCCAGTGAAAATAGCTGCA 59.304 43.478 1.02 0.00 0.00 4.41
1738 1849 3.696051 TGGAATCCAGTGAAAATAGCTGC 59.304 43.478 0.00 0.00 0.00 5.25
1739 1850 5.902613 TTGGAATCCAGTGAAAATAGCTG 57.097 39.130 0.86 0.00 33.81 4.24
1740 1851 8.773033 AATATTGGAATCCAGTGAAAATAGCT 57.227 30.769 7.61 0.00 33.81 3.32
1741 1852 7.805071 CGAATATTGGAATCCAGTGAAAATAGC 59.195 37.037 7.61 0.00 33.81 2.97
1745 1856 7.201574 CGTACGAATATTGGAATCCAGTGAAAA 60.202 37.037 10.44 0.00 33.81 2.29
1747 1858 5.751509 CGTACGAATATTGGAATCCAGTGAA 59.248 40.000 10.44 0.00 33.81 3.18
1750 1861 5.272283 ACGTACGAATATTGGAATCCAGT 57.728 39.130 24.41 1.54 33.81 4.00
1751 1862 7.487189 GGTATACGTACGAATATTGGAATCCAG 59.513 40.741 24.41 0.00 33.81 3.86
1752 1863 7.039853 TGGTATACGTACGAATATTGGAATCCA 60.040 37.037 24.41 0.00 0.00 3.41
1753 1864 7.315142 TGGTATACGTACGAATATTGGAATCC 58.685 38.462 24.41 8.64 0.00 3.01
1754 1865 7.008992 GCTGGTATACGTACGAATATTGGAATC 59.991 40.741 24.41 0.00 0.00 2.52
1756 1867 6.151691 GCTGGTATACGTACGAATATTGGAA 58.848 40.000 24.41 0.00 0.00 3.53
1758 1869 4.860907 GGCTGGTATACGTACGAATATTGG 59.139 45.833 24.41 8.04 0.00 3.16
1759 1870 5.706916 AGGCTGGTATACGTACGAATATTG 58.293 41.667 24.41 7.30 0.00 1.90
1760 1871 5.972107 AGGCTGGTATACGTACGAATATT 57.028 39.130 24.41 0.61 0.00 1.28
1761 1872 5.709164 AGAAGGCTGGTATACGTACGAATAT 59.291 40.000 24.41 12.70 0.00 1.28
1762 1873 5.049198 CAGAAGGCTGGTATACGTACGAATA 60.049 44.000 24.41 5.00 38.51 1.75
1763 1874 3.887716 AGAAGGCTGGTATACGTACGAAT 59.112 43.478 24.41 2.35 0.00 3.34
1764 1875 3.065786 CAGAAGGCTGGTATACGTACGAA 59.934 47.826 24.41 3.79 38.51 3.85
1765 1876 2.615447 CAGAAGGCTGGTATACGTACGA 59.385 50.000 24.41 6.04 38.51 3.43
1766 1877 2.357009 ACAGAAGGCTGGTATACGTACG 59.643 50.000 15.01 15.01 46.60 3.67
1767 1878 5.067023 AGTTACAGAAGGCTGGTATACGTAC 59.933 44.000 0.00 0.00 46.60 3.67
1768 1879 5.195940 AGTTACAGAAGGCTGGTATACGTA 58.804 41.667 0.00 0.00 46.60 3.57
1769 1880 4.021916 AGTTACAGAAGGCTGGTATACGT 58.978 43.478 0.00 0.00 46.60 3.57
1770 1881 4.650754 AGTTACAGAAGGCTGGTATACG 57.349 45.455 0.00 0.00 46.60 3.06
1771 1882 5.585047 CCAAAGTTACAGAAGGCTGGTATAC 59.415 44.000 0.00 0.00 46.60 1.47
1772 1883 5.486063 TCCAAAGTTACAGAAGGCTGGTATA 59.514 40.000 0.00 0.00 46.60 1.47
1773 1884 4.288626 TCCAAAGTTACAGAAGGCTGGTAT 59.711 41.667 0.00 0.00 46.60 2.73
1774 1885 3.649023 TCCAAAGTTACAGAAGGCTGGTA 59.351 43.478 0.00 0.00 46.60 3.25
1775 1886 2.441750 TCCAAAGTTACAGAAGGCTGGT 59.558 45.455 0.00 0.00 46.60 4.00
1776 1887 3.140325 TCCAAAGTTACAGAAGGCTGG 57.860 47.619 0.00 0.00 46.60 4.85
1778 1889 3.507622 GCATTCCAAAGTTACAGAAGGCT 59.492 43.478 10.21 0.00 41.44 4.58
1779 1890 3.507622 AGCATTCCAAAGTTACAGAAGGC 59.492 43.478 9.71 9.71 44.10 4.35
1780 1891 6.375455 ACATAGCATTCCAAAGTTACAGAAGG 59.625 38.462 0.00 0.00 0.00 3.46
1781 1892 7.246311 CACATAGCATTCCAAAGTTACAGAAG 58.754 38.462 0.00 0.00 0.00 2.85
1782 1893 6.349280 GCACATAGCATTCCAAAGTTACAGAA 60.349 38.462 0.00 0.00 44.79 3.02
1783 1894 5.123820 GCACATAGCATTCCAAAGTTACAGA 59.876 40.000 0.00 0.00 44.79 3.41
1793 1904 1.096967 CCTGCGCACATAGCATTCCA 61.097 55.000 5.66 0.00 46.13 3.53
1795 1906 0.585357 CTCCTGCGCACATAGCATTC 59.415 55.000 5.66 0.00 46.13 2.67
1797 1908 1.227764 CCTCCTGCGCACATAGCAT 60.228 57.895 5.66 0.00 46.13 3.79
1798 1909 1.898330 TTCCTCCTGCGCACATAGCA 61.898 55.000 5.66 0.00 46.13 3.49
1799 1910 0.744414 TTTCCTCCTGCGCACATAGC 60.744 55.000 5.66 0.00 40.87 2.97
1800 1911 1.293924 CTTTCCTCCTGCGCACATAG 58.706 55.000 5.66 3.70 0.00 2.23
1801 1912 0.107703 CCTTTCCTCCTGCGCACATA 60.108 55.000 5.66 0.00 0.00 2.29
2097 2212 3.749064 AGCACGGCGTCGATGTCT 61.749 61.111 20.03 9.44 40.11 3.41
2130 2245 4.681978 GCCAGGAACGTGCCGAGT 62.682 66.667 7.01 0.00 0.00 4.18
2208 2323 4.457496 CTCAGCACCGCCCACGAT 62.457 66.667 0.00 0.00 43.93 3.73
2598 2713 4.803426 GTCCAGTCGCCGAGCAGG 62.803 72.222 0.00 0.00 44.97 4.85
2673 2865 3.357079 GGAACACTGGCACGGCAG 61.357 66.667 18.15 18.15 39.14 4.85
2723 2915 1.135803 ACGTACGGCAAAATGTGATGC 60.136 47.619 21.06 0.00 41.82 3.91
2771 2964 3.553511 CCGCACATCTATCTGAACTTGAC 59.446 47.826 0.00 0.00 0.00 3.18
2773 2966 3.525537 ACCGCACATCTATCTGAACTTG 58.474 45.455 0.00 0.00 0.00 3.16
2775 2968 3.895232 AACCGCACATCTATCTGAACT 57.105 42.857 0.00 0.00 0.00 3.01
2848 3072 5.447279 GCTCTGTCGACAAGTTTCTCAAAAA 60.447 40.000 20.49 0.00 0.00 1.94
2850 3074 3.555956 GCTCTGTCGACAAGTTTCTCAAA 59.444 43.478 20.49 0.00 0.00 2.69
2851 3075 3.123804 GCTCTGTCGACAAGTTTCTCAA 58.876 45.455 20.49 0.00 0.00 3.02
2852 3076 2.362397 AGCTCTGTCGACAAGTTTCTCA 59.638 45.455 20.49 0.00 0.00 3.27
2853 3077 2.728839 CAGCTCTGTCGACAAGTTTCTC 59.271 50.000 20.49 6.89 0.00 2.87
2854 3078 2.362397 TCAGCTCTGTCGACAAGTTTCT 59.638 45.455 20.49 9.33 0.00 2.52
2855 3079 2.728839 CTCAGCTCTGTCGACAAGTTTC 59.271 50.000 20.49 7.21 0.00 2.78
2856 3080 2.101582 ACTCAGCTCTGTCGACAAGTTT 59.898 45.455 20.49 9.56 0.00 2.66
2857 3081 1.683917 ACTCAGCTCTGTCGACAAGTT 59.316 47.619 20.49 14.15 0.00 2.66
2858 3082 1.323412 ACTCAGCTCTGTCGACAAGT 58.677 50.000 20.49 15.52 0.00 3.16
2859 3083 2.730715 GCTACTCAGCTCTGTCGACAAG 60.731 54.545 20.49 18.89 44.93 3.16
2933 3157 1.135402 CAGTAATTGCCACGGAAAGCC 60.135 52.381 0.00 0.00 0.00 4.35
2946 3171 4.017126 GGCCTAAGTTTCAGCCAGTAATT 58.983 43.478 0.00 0.00 45.07 1.40
2954 3179 0.960861 AAGCGGGCCTAAGTTTCAGC 60.961 55.000 0.84 0.00 0.00 4.26
2964 3189 0.462047 CAAATCTACGAAGCGGGCCT 60.462 55.000 0.84 0.00 0.00 5.19
3003 3228 2.202892 GGAAGGGGATGCGTCGAC 60.203 66.667 5.18 5.18 0.00 4.20
3175 3523 2.223947 TGATATGTGTCGTGAATCCCCG 60.224 50.000 0.00 0.00 0.00 5.73
3186 3534 2.604914 CTGTTGTCGGCTGATATGTGTC 59.395 50.000 0.00 0.00 0.00 3.67
3187 3535 2.233676 TCTGTTGTCGGCTGATATGTGT 59.766 45.455 0.00 0.00 0.00 3.72
3192 3540 0.894835 TGCTCTGTTGTCGGCTGATA 59.105 50.000 0.00 0.00 0.00 2.15
3308 3662 2.665649 AACTCGACATATGCGGTGAA 57.334 45.000 16.01 1.01 0.00 3.18
3309 3663 2.665649 AAACTCGACATATGCGGTGA 57.334 45.000 16.01 3.91 0.00 4.02
3310 3664 3.124466 TGAAAAACTCGACATATGCGGTG 59.876 43.478 16.01 12.51 0.00 4.94
3403 3768 1.811679 GGCTTACGACCAGAGCAGC 60.812 63.158 0.00 0.00 38.14 5.25
3419 3793 2.743538 GGTACGTCCGGTTTGGGC 60.744 66.667 0.00 0.00 39.78 5.36
3433 3807 2.441750 GGGGCCAATCATTACTCTGGTA 59.558 50.000 4.39 0.00 0.00 3.25
3437 3811 1.213296 ACGGGGCCAATCATTACTCT 58.787 50.000 4.39 0.00 0.00 3.24
3438 3812 2.490991 GTACGGGGCCAATCATTACTC 58.509 52.381 4.39 0.00 0.00 2.59
3467 3842 1.080995 GCATCGCTCTCTGTGTGTCC 61.081 60.000 0.00 0.00 0.00 4.02
3481 3857 2.515926 ACTACTACCAGCATGCATCG 57.484 50.000 21.98 8.82 31.97 3.84
3507 3883 1.883084 GGAACAGTATCAGCCGCCG 60.883 63.158 0.00 0.00 0.00 6.46
3526 3902 1.349627 CCTGCAAATCTGTAGCGCG 59.650 57.895 0.00 0.00 34.18 6.86
3573 3949 1.267121 TACTGCCAGGGAGTTCAGTC 58.733 55.000 20.29 0.00 40.01 3.51
3615 3995 2.046700 TCAATTCGCCGTGACCCC 60.047 61.111 0.00 0.00 0.00 4.95
3868 4253 4.699522 GGTCGACCAGGGCACACC 62.700 72.222 29.75 0.00 40.67 4.16


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

AutoCloner maintained by Alex Coulton.