Multiple sequence alignment - TraesCS3D01G506800

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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 TraesCS3D01G506800 chr3D 100.000 2690 0 0 1 2690 593639287 593636598 0.000000e+00 4968.0
1 TraesCS3D01G506800 chrUn 89.967 897 70 9 1257 2146 41853130 41852247 0.000000e+00 1140.0
2 TraesCS3D01G506800 chrUn 89.496 714 58 7 1467 2173 327318247 327317544 0.000000e+00 887.0
3 TraesCS3D01G506800 chrUn 89.496 714 58 7 1467 2173 376490547 376491250 0.000000e+00 887.0
4 TraesCS3D01G506800 chrUn 88.494 704 76 3 32 730 41849155 41848452 0.000000e+00 846.0
5 TraesCS3D01G506800 chrUn 88.873 692 72 3 32 718 41941093 41941784 0.000000e+00 846.0
6 TraesCS3D01G506800 chrUn 88.494 704 76 3 32 730 381981917 381981214 0.000000e+00 846.0
7 TraesCS3D01G506800 chrUn 88.595 491 54 2 32 520 41945862 41946352 1.780000e-166 595.0
8 TraesCS3D01G506800 chrUn 88.595 491 54 2 32 520 327943599 327944089 1.780000e-166 595.0
9 TraesCS3D01G506800 chrUn 88.595 491 54 2 32 520 328101428 328101918 1.780000e-166 595.0
10 TraesCS3D01G506800 chrUn 88.595 491 54 2 32 520 339708394 339707904 1.780000e-166 595.0
11 TraesCS3D01G506800 chrUn 90.339 383 22 5 891 1261 421971714 421971335 3.110000e-134 488.0
12 TraesCS3D01G506800 chrUn 94.096 271 7 4 997 1261 41853499 41853232 1.160000e-108 403.0
13 TraesCS3D01G506800 chrUn 94.096 271 7 4 997 1261 473211041 473210774 1.160000e-108 403.0
14 TraesCS3D01G506800 chrUn 90.431 209 16 2 1257 1465 421971233 421971029 3.410000e-69 272.0
15 TraesCS3D01G506800 chrUn 90.431 209 16 2 1257 1465 473210672 473210468 3.410000e-69 272.0
16 TraesCS3D01G506800 chrUn 91.129 124 9 2 2332 2453 41852085 41851962 1.660000e-37 167.0
17 TraesCS3D01G506800 chrUn 85.065 154 6 2 722 873 41943128 41943266 1.000000e-29 141.0
18 TraesCS3D01G506800 chrUn 85.065 154 6 2 722 873 41948333 41948195 1.000000e-29 141.0
19 TraesCS3D01G506800 chr3A 89.121 671 58 6 1517 2177 724572422 724573087 0.000000e+00 821.0
20 TraesCS3D01G506800 chr3A 90.399 552 27 11 723 1261 724571815 724572353 0.000000e+00 702.0
21 TraesCS3D01G506800 chr3A 89.003 291 30 2 441 731 724571102 724571390 2.550000e-95 359.0
22 TraesCS3D01G506800 chr3A 97.222 36 1 0 661 696 625247715 625247680 8.040000e-06 62.1
23 TraesCS3D01G506800 chr6B 97.222 36 1 0 661 696 476816470 476816505 8.040000e-06 62.1
24 TraesCS3D01G506800 chr1A 90.909 44 4 0 651 694 8156452 8156495 2.890000e-05 60.2
25 TraesCS3D01G506800 chr5D 100.000 31 0 0 665 695 544721827 544721797 1.040000e-04 58.4
26 TraesCS3D01G506800 chr6A 96.970 33 1 0 661 693 45976907 45976939 3.740000e-04 56.5


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 TraesCS3D01G506800 chr3D 593636598 593639287 2689 True 4968.000000 4968 100.000000 1 2690 1 chr3D.!!$R1 2689
1 TraesCS3D01G506800 chrUn 327317544 327318247 703 True 887.000000 887 89.496000 1467 2173 1 chrUn.!!$R2 706
2 TraesCS3D01G506800 chrUn 376490547 376491250 703 False 887.000000 887 89.496000 1467 2173 1 chrUn.!!$F3 706
3 TraesCS3D01G506800 chrUn 381981214 381981917 703 True 846.000000 846 88.494000 32 730 1 chrUn.!!$R4 698
4 TraesCS3D01G506800 chrUn 41848452 41853499 5047 True 639.000000 1140 90.921500 32 2453 4 chrUn.!!$R5 2421
5 TraesCS3D01G506800 chrUn 41941093 41946352 5259 False 527.333333 846 87.511000 32 873 3 chrUn.!!$F4 841
6 TraesCS3D01G506800 chrUn 421971029 421971714 685 True 380.000000 488 90.385000 891 1465 2 chrUn.!!$R6 574
7 TraesCS3D01G506800 chrUn 473210468 473211041 573 True 337.500000 403 92.263500 997 1465 2 chrUn.!!$R7 468
8 TraesCS3D01G506800 chr3A 724571102 724573087 1985 False 627.333333 821 89.507667 441 2177 3 chr3A.!!$F1 1736

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
180 181 0.247814 GACGACAATGGCGCTTGATG 60.248 55.0 9.06 8.61 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 4928 0.682209 CCTCCCCAATGCAGTCAAGG 60.682 60.0 0.0 0.0 0.0 3.61 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
111 112 1.411246 GGGTTTTGTTGTGGTCCCTTC 59.589 52.381 0.00 0.00 32.89 3.46
149 150 2.159142 GGTGTGAATACCCTAGTCCGTG 60.159 54.545 0.00 0.00 34.56 4.94
154 155 3.698040 TGAATACCCTAGTCCGTGTTCTC 59.302 47.826 10.53 0.00 32.95 2.87
166 167 2.202453 GTTCTCGGGCTCGACGAC 60.202 66.667 3.45 2.32 40.88 4.34
167 168 2.670592 TTCTCGGGCTCGACGACA 60.671 61.111 3.45 0.00 40.88 4.35
179 180 1.695893 CGACGACAATGGCGCTTGAT 61.696 55.000 9.06 0.00 0.00 2.57
180 181 0.247814 GACGACAATGGCGCTTGATG 60.248 55.000 9.06 8.61 0.00 3.07
186 187 0.659427 AATGGCGCTTGATGTCATCG 59.341 50.000 7.64 0.00 0.00 3.84
225 226 2.118294 GCAGCCCTGGTCCCTTTT 59.882 61.111 0.00 0.00 0.00 2.27
234 235 2.107552 CCTGGTCCCTTTTGGTTGTAGA 59.892 50.000 0.00 0.00 38.10 2.59
236 237 3.758554 CTGGTCCCTTTTGGTTGTAGATG 59.241 47.826 0.00 0.00 38.10 2.90
258 259 2.045926 GTCACTTCGGGCATGCCT 60.046 61.111 34.70 13.48 36.10 4.75
262 263 0.676466 CACTTCGGGCATGCCTTGTA 60.676 55.000 34.70 20.00 36.10 2.41
266 267 0.676466 TCGGGCATGCCTTGTACTTG 60.676 55.000 34.70 14.74 36.10 3.16
276 277 2.412089 GCCTTGTACTTGTCTTGTAGCG 59.588 50.000 0.00 0.00 0.00 4.26
277 278 2.412089 CCTTGTACTTGTCTTGTAGCGC 59.588 50.000 0.00 0.00 0.00 5.92
284 285 2.812358 TGTCTTGTAGCGCTCTTGAA 57.188 45.000 16.34 1.21 0.00 2.69
287 289 4.065088 TGTCTTGTAGCGCTCTTGAATTT 58.935 39.130 16.34 0.00 0.00 1.82
307 309 0.460284 GCGTGGATGGTCTCGATGTT 60.460 55.000 0.00 0.00 0.00 2.71
323 325 8.784994 GTCTCGATGTTCTCCTATCTTATACAA 58.215 37.037 0.00 0.00 0.00 2.41
324 326 9.004717 TCTCGATGTTCTCCTATCTTATACAAG 57.995 37.037 0.00 0.00 0.00 3.16
330 332 6.879276 TCTCCTATCTTATACAAGTGTCCG 57.121 41.667 0.00 0.00 33.20 4.79
331 333 6.363065 TCTCCTATCTTATACAAGTGTCCGT 58.637 40.000 0.00 0.00 33.20 4.69
345 347 4.533815 AGTGTCCGTATGGTATCTCTTCA 58.466 43.478 0.00 0.00 36.30 3.02
346 348 5.141182 AGTGTCCGTATGGTATCTCTTCAT 58.859 41.667 0.00 0.00 36.30 2.57
359 361 2.169352 TCTCTTCATGGTCCTTGCTAGC 59.831 50.000 8.10 8.10 0.00 3.42
361 363 2.169352 TCTTCATGGTCCTTGCTAGCTC 59.831 50.000 17.23 1.47 0.00 4.09
362 364 1.871418 TCATGGTCCTTGCTAGCTCT 58.129 50.000 17.23 0.00 0.00 4.09
365 367 0.615331 TGGTCCTTGCTAGCTCTTGG 59.385 55.000 17.23 12.15 0.00 3.61
409 411 1.003233 GTGAGGGGGCTGTCTCAAC 60.003 63.158 6.56 0.54 41.07 3.18
413 415 1.003233 GGGGGCTGTCTCAACTGTC 60.003 63.158 0.00 0.00 0.00 3.51
426 428 0.261696 AACTGTCAGTTGGCCCCTTT 59.738 50.000 17.49 0.00 37.00 3.11
431 433 1.000896 CAGTTGGCCCCTTTCGGAT 60.001 57.895 0.00 0.00 0.00 4.18
436 438 3.140814 GCCCCTTTCGGATGTGGC 61.141 66.667 0.00 0.00 0.00 5.01
482 485 1.896660 GTGGTTTCTCAAGGCGGCA 60.897 57.895 13.08 0.00 0.00 5.69
499 502 2.113139 ACGGTTCCAGCCCTGTTG 59.887 61.111 0.00 0.00 0.00 3.33
526 532 3.071167 GTCTTGGGTGTCTCTTGTTAGGT 59.929 47.826 0.00 0.00 0.00 3.08
551 557 1.124297 CGTCTCGTGTTTTCATGGTCG 59.876 52.381 0.00 0.00 37.42 4.79
586 592 0.889994 ATTGCCGCTTGCTCAAATGA 59.110 45.000 0.00 0.00 42.00 2.57
587 593 0.889994 TTGCCGCTTGCTCAAATGAT 59.110 45.000 0.00 0.00 42.00 2.45
657 663 4.953940 ATATTGGTTTGGCAGTTTGTGT 57.046 36.364 0.00 0.00 0.00 3.72
659 665 4.744795 ATTGGTTTGGCAGTTTGTGTTA 57.255 36.364 0.00 0.00 0.00 2.41
686 692 0.690744 AAAGTGGGGCAAAAGCCTGT 60.691 50.000 6.45 0.00 0.00 4.00
704 710 7.778470 AGCCTGTTTCGAGAAAGATAATTAG 57.222 36.000 0.00 0.00 0.00 1.73
807 2253 4.052518 AGCCACACCCCTCCATGC 62.053 66.667 0.00 0.00 0.00 4.06
877 2325 5.120830 GGTGATTTTGCCGCTGAGTATATAG 59.879 44.000 0.00 0.00 0.00 1.31
878 2326 5.120830 GTGATTTTGCCGCTGAGTATATAGG 59.879 44.000 0.00 0.00 0.00 2.57
880 2328 4.521130 TTTGCCGCTGAGTATATAGGAG 57.479 45.455 0.00 0.00 0.00 3.69
884 2332 3.065648 GCCGCTGAGTATATAGGAGCTAC 59.934 52.174 0.00 0.00 0.00 3.58
947 2510 9.944376 ATAGAGTAACTAAAAAGAGCATTGACA 57.056 29.630 0.00 0.00 34.56 3.58
1041 2604 2.817396 GCGAGGAAGGTCTGCAGC 60.817 66.667 9.47 4.04 0.00 5.25
1218 4185 0.389948 CAGACAAGGTACGCAGGACC 60.390 60.000 2.09 2.09 37.22 4.46
1228 4195 2.742372 GCAGGACCATGCGTCGTT 60.742 61.111 6.75 0.00 42.99 3.85
1230 4197 1.667830 CAGGACCATGCGTCGTTGT 60.668 57.895 6.75 0.00 42.99 3.32
1231 4198 0.389296 CAGGACCATGCGTCGTTGTA 60.389 55.000 6.75 0.00 42.99 2.41
1232 4199 0.389426 AGGACCATGCGTCGTTGTAC 60.389 55.000 0.00 0.00 42.99 2.90
1284 4357 6.762702 TTATGTTACTGATGTACGTCCTCA 57.237 37.500 12.54 5.24 0.00 3.86
1309 4382 2.594303 TTGCGGCACAAGTGGAGG 60.594 61.111 0.05 0.00 33.24 4.30
1313 4386 1.227823 CGGCACAAGTGGAGGACAA 60.228 57.895 2.00 0.00 0.00 3.18
1318 4391 2.033424 GCACAAGTGGAGGACAAGAAAC 59.967 50.000 2.00 0.00 0.00 2.78
1324 4397 3.456277 AGTGGAGGACAAGAAACAAGAGT 59.544 43.478 0.00 0.00 0.00 3.24
1331 4404 0.307760 AAGAAACAAGAGTTGCGCCG 59.692 50.000 4.18 0.00 38.40 6.46
1335 4408 1.498865 AACAAGAGTTGCGCCGTCTG 61.499 55.000 4.18 0.00 36.39 3.51
1352 4425 2.184322 GCTTCGTCGGCTGGATGA 59.816 61.111 0.00 0.00 38.91 2.92
1431 4504 6.756542 CCGAGAAAAAGAAACACAAGGAAAAT 59.243 34.615 0.00 0.00 0.00 1.82
1480 4553 0.532573 CGACCCACTGTATCAGCTGT 59.467 55.000 14.67 3.75 34.37 4.40
1481 4554 1.469940 CGACCCACTGTATCAGCTGTC 60.470 57.143 14.67 6.49 34.37 3.51
1488 4561 2.421775 ACTGTATCAGCTGTCTCGTCAG 59.578 50.000 14.67 15.49 34.37 3.51
1499 4572 4.441634 GCTGTCTCGTCAGGGTATTTATGT 60.442 45.833 7.01 0.00 36.12 2.29
1551 4624 9.257651 GTTATATATGCACTTTTCCTTACTCGT 57.742 33.333 0.00 0.00 0.00 4.18
1610 4683 4.574674 TCATGAGCTTGGTAATCCTTGT 57.425 40.909 0.00 0.00 34.23 3.16
1613 4686 4.574674 TGAGCTTGGTAATCCTTGTCAT 57.425 40.909 0.00 0.00 34.23 3.06
1727 4800 0.770499 TCAGATGGTGGAGGCAACAA 59.230 50.000 0.00 0.00 41.41 2.83
1729 4802 1.067295 AGATGGTGGAGGCAACAAGA 58.933 50.000 0.00 0.00 41.41 3.02
1800 4880 0.672401 TGGTAGCTAGTTTGCGGCAC 60.672 55.000 0.05 0.00 38.13 5.01
1846 4926 3.982701 CGTTACCACGTCATGAACTTGTA 59.017 43.478 0.00 0.00 41.84 2.41
1848 4928 5.220154 CGTTACCACGTCATGAACTTGTATC 60.220 44.000 0.00 0.00 41.84 2.24
1876 4960 1.981495 GCATTGGGGAGGAGTAGCTAT 59.019 52.381 0.00 0.00 0.00 2.97
1880 4964 5.580998 CATTGGGGAGGAGTAGCTATACTA 58.419 45.833 0.00 0.00 42.46 1.82
1888 4972 6.949463 GGAGGAGTAGCTATACTATGGAAACT 59.051 42.308 0.00 0.00 42.46 2.66
1896 4980 8.001881 AGCTATACTATGGAAACTGATATCCG 57.998 38.462 0.00 0.00 38.63 4.18
1997 5089 6.205076 TGTTTAGTATCTCGAGCCTCTGTATC 59.795 42.308 7.81 0.00 0.00 2.24
1999 5091 2.552599 ATCTCGAGCCTCTGTATCGA 57.447 50.000 7.81 0.00 42.71 3.59
2033 5125 3.603532 GACTCATGTCATGACCACACAT 58.396 45.455 22.85 7.26 42.48 3.21
2075 5167 4.406069 CGCTAATTTGTCACCATTCACAG 58.594 43.478 0.00 0.00 0.00 3.66
2078 5170 6.088824 GCTAATTTGTCACCATTCACAGAAG 58.911 40.000 0.00 0.00 0.00 2.85
2104 5196 5.570320 ACTTAAGGGTTGTATGCATGAACT 58.430 37.500 10.16 0.00 0.00 3.01
2105 5197 5.415701 ACTTAAGGGTTGTATGCATGAACTG 59.584 40.000 10.16 3.54 0.00 3.16
2106 5198 3.719268 AGGGTTGTATGCATGAACTGA 57.281 42.857 10.16 0.00 0.00 3.41
2107 5199 4.240881 AGGGTTGTATGCATGAACTGAT 57.759 40.909 10.16 0.61 0.00 2.90
2112 5204 5.696270 GGTTGTATGCATGAACTGATCGATA 59.304 40.000 10.16 0.00 0.00 2.92
2129 5221 0.990374 ATAGATGCAGAGATGGGGGC 59.010 55.000 0.00 0.00 0.00 5.80
2146 5238 1.066929 GGGCGACGTTAACCCTCTTTA 60.067 52.381 12.79 0.00 40.75 1.85
2158 5250 7.117379 CGTTAACCCTCTTTACGAGAAGAAAAT 59.883 37.037 0.00 0.00 42.62 1.82
2177 5269 1.846007 TTCACACAACCAACTTGCCT 58.154 45.000 0.00 0.00 32.41 4.75
2178 5270 1.388547 TCACACAACCAACTTGCCTC 58.611 50.000 0.00 0.00 32.41 4.70
2179 5271 1.102154 CACACAACCAACTTGCCTCA 58.898 50.000 0.00 0.00 32.41 3.86
2180 5272 1.476085 CACACAACCAACTTGCCTCAA 59.524 47.619 0.00 0.00 32.41 3.02
2181 5273 1.476488 ACACAACCAACTTGCCTCAAC 59.524 47.619 0.00 0.00 32.41 3.18
2182 5274 1.476085 CACAACCAACTTGCCTCAACA 59.524 47.619 0.00 0.00 32.41 3.33
2183 5275 1.750778 ACAACCAACTTGCCTCAACAG 59.249 47.619 0.00 0.00 32.41 3.16
2184 5276 2.023673 CAACCAACTTGCCTCAACAGA 58.976 47.619 0.00 0.00 0.00 3.41
2185 5277 1.972872 ACCAACTTGCCTCAACAGAG 58.027 50.000 0.00 0.00 0.00 3.35
2194 5286 4.662468 TGCCTCAACAGAGCTAAGATAG 57.338 45.455 0.00 0.00 0.00 2.08
2200 5292 5.414360 TCAACAGAGCTAAGATAGTTGCTG 58.586 41.667 0.00 0.00 37.02 4.41
2201 5293 3.791245 ACAGAGCTAAGATAGTTGCTGC 58.209 45.455 0.00 0.00 35.76 5.25
2202 5294 3.450457 ACAGAGCTAAGATAGTTGCTGCT 59.550 43.478 0.00 0.00 35.76 4.24
2203 5295 4.050553 CAGAGCTAAGATAGTTGCTGCTC 58.949 47.826 0.00 0.00 43.77 4.26
2204 5296 3.703556 AGAGCTAAGATAGTTGCTGCTCA 59.296 43.478 13.33 0.00 45.24 4.26
2205 5297 4.344679 AGAGCTAAGATAGTTGCTGCTCAT 59.655 41.667 13.33 0.00 45.24 2.90
2206 5298 5.538053 AGAGCTAAGATAGTTGCTGCTCATA 59.462 40.000 13.33 0.00 45.24 2.15
2208 5300 5.988561 AGCTAAGATAGTTGCTGCTCATAAC 59.011 40.000 0.00 0.00 34.19 1.89
2209 5301 5.755375 GCTAAGATAGTTGCTGCTCATAACA 59.245 40.000 0.00 0.00 0.00 2.41
2210 5302 6.258727 GCTAAGATAGTTGCTGCTCATAACAA 59.741 38.462 0.00 0.00 0.00 2.83
2211 5303 6.674694 AAGATAGTTGCTGCTCATAACAAG 57.325 37.500 0.00 0.00 0.00 3.16
2212 5304 5.738909 AGATAGTTGCTGCTCATAACAAGT 58.261 37.500 0.00 0.00 0.00 3.16
2225 5317 7.093465 TGCTCATAACAAGTAAACCTAGCTACT 60.093 37.037 0.00 0.00 0.00 2.57
2240 5332 2.678324 GCTACTTGCGAGTCCCATATC 58.322 52.381 10.71 0.00 37.33 1.63
2241 5333 2.035961 GCTACTTGCGAGTCCCATATCA 59.964 50.000 10.71 0.00 37.33 2.15
2242 5334 2.898729 ACTTGCGAGTCCCATATCAG 57.101 50.000 0.00 0.00 0.00 2.90
2244 5336 0.829990 TTGCGAGTCCCATATCAGCA 59.170 50.000 0.00 0.00 0.00 4.41
2245 5337 0.829990 TGCGAGTCCCATATCAGCAA 59.170 50.000 0.00 0.00 0.00 3.91
2246 5338 1.221414 GCGAGTCCCATATCAGCAAC 58.779 55.000 0.00 0.00 0.00 4.17
2259 5375 0.041839 CAGCAACTCACGTCAGCAAC 60.042 55.000 0.00 0.00 0.00 4.17
2266 5382 0.459899 TCACGTCAGCAACTCACAGT 59.540 50.000 0.00 0.00 0.00 3.55
2269 5385 1.137086 ACGTCAGCAACTCACAGTCTT 59.863 47.619 0.00 0.00 0.00 3.01
2283 5407 2.641815 ACAGTCTTCTCCTTCCATGCTT 59.358 45.455 0.00 0.00 0.00 3.91
2285 5409 3.688673 CAGTCTTCTCCTTCCATGCTTTC 59.311 47.826 0.00 0.00 0.00 2.62
2286 5410 3.013219 GTCTTCTCCTTCCATGCTTTCC 58.987 50.000 0.00 0.00 0.00 3.13
2305 5429 1.506493 CGTATCAATCTCAGGCCAGC 58.494 55.000 5.01 0.00 0.00 4.85
2327 5451 4.899239 GCGAGCTATGCCGGTGCT 62.899 66.667 1.90 8.26 40.02 4.40
2328 5452 2.659897 CGAGCTATGCCGGTGCTC 60.660 66.667 21.94 21.94 46.73 4.26
2329 5453 2.280457 GAGCTATGCCGGTGCTCC 60.280 66.667 21.54 0.00 45.12 4.70
2330 5454 3.083349 AGCTATGCCGGTGCTCCA 61.083 61.111 1.90 0.00 38.71 3.86
2343 5467 1.000274 GTGCTCCATTCACCACCAAAC 60.000 52.381 0.00 0.00 0.00 2.93
2355 5479 4.097135 TCACCACCAAACTAACATGTGTTG 59.903 41.667 0.00 2.06 38.90 3.33
2374 5498 0.385390 GTTTGTTGTGGGTCCAGCTG 59.615 55.000 6.78 6.78 0.00 4.24
2414 5538 6.734871 GCACGGTTTAAAACTCATTCCTCTTT 60.735 38.462 1.03 0.00 0.00 2.52
2416 5540 6.544564 ACGGTTTAAAACTCATTCCTCTTTGA 59.455 34.615 1.03 0.00 0.00 2.69
2427 5551 4.591321 TTCCTCTTTGATGGTTATGGCT 57.409 40.909 0.00 0.00 0.00 4.75
2442 5566 1.259609 TGGCTGCCCATTTCTCTTTG 58.740 50.000 17.53 0.00 35.79 2.77
2443 5567 0.108472 GGCTGCCCATTTCTCTTTGC 60.108 55.000 7.66 0.00 0.00 3.68
2445 5569 1.001181 GCTGCCCATTTCTCTTTGCAA 59.999 47.619 0.00 0.00 0.00 4.08
2446 5570 2.548493 GCTGCCCATTTCTCTTTGCAAA 60.548 45.455 12.14 12.14 0.00 3.68
2450 5574 5.237048 TGCCCATTTCTCTTTGCAAATAAC 58.763 37.500 13.23 0.00 0.00 1.89
2454 5578 7.548780 GCCCATTTCTCTTTGCAAATAACATAA 59.451 33.333 13.23 3.53 0.00 1.90
2455 5579 9.090692 CCCATTTCTCTTTGCAAATAACATAAG 57.909 33.333 13.23 0.00 0.00 1.73
2456 5580 8.598075 CCATTTCTCTTTGCAAATAACATAAGC 58.402 33.333 13.23 0.00 0.00 3.09
2460 5584 8.752005 TCTCTTTGCAAATAACATAAGCCTAT 57.248 30.769 13.23 0.00 0.00 2.57
2461 5585 9.845740 TCTCTTTGCAAATAACATAAGCCTATA 57.154 29.630 13.23 0.00 0.00 1.31
2464 5588 9.132521 CTTTGCAAATAACATAAGCCTATATGC 57.867 33.333 13.23 0.00 36.87 3.14
2465 5589 8.408043 TTGCAAATAACATAAGCCTATATGCT 57.592 30.769 0.00 0.00 45.43 3.79
2485 5609 6.624352 TGCTTAAGCCAAATAGCATCTAAG 57.376 37.500 24.30 0.00 38.61 2.18
2493 5618 9.681062 AAGCCAAATAGCATCTAAGTAAAGTAA 57.319 29.630 0.00 0.00 34.23 2.24
2516 5641 9.846248 GTAAAGCTATTATGGAAAATGCATAGG 57.154 33.333 0.00 0.00 32.32 2.57
2517 5642 8.482852 AAAGCTATTATGGAAAATGCATAGGT 57.517 30.769 0.00 0.00 32.32 3.08
2529 7346 1.153086 CATAGGTGCTCCAGGGTGC 60.153 63.158 7.70 5.45 35.89 5.01
2531 7348 1.341156 ATAGGTGCTCCAGGGTGCTC 61.341 60.000 12.96 9.40 35.85 4.26
2532 7349 4.416738 GGTGCTCCAGGGTGCTCC 62.417 72.222 15.20 15.20 39.76 4.70
2550 7367 7.685849 GTGCTCCACCCCCTATATATAAATA 57.314 40.000 0.00 0.00 0.00 1.40
2552 7369 8.157476 GTGCTCCACCCCCTATATATAAATATG 58.843 40.741 0.00 0.00 30.72 1.78
2553 7370 7.168905 GCTCCACCCCCTATATATAAATATGC 58.831 42.308 0.00 0.00 30.72 3.14
2554 7371 7.202186 GCTCCACCCCCTATATATAAATATGCA 60.202 40.741 0.00 0.00 30.72 3.96
2555 7372 8.645902 TCCACCCCCTATATATAAATATGCAA 57.354 34.615 0.00 0.00 30.72 4.08
2556 7373 9.248630 TCCACCCCCTATATATAAATATGCAAT 57.751 33.333 0.00 0.00 30.72 3.56
2607 8210 8.887036 AAAACTGAAATCTTGGGACATAAAAC 57.113 30.769 0.00 0.00 39.30 2.43
2608 8211 6.590234 ACTGAAATCTTGGGACATAAAACC 57.410 37.500 0.00 0.00 39.30 3.27
2610 8213 6.209391 ACTGAAATCTTGGGACATAAAACCTG 59.791 38.462 0.00 0.00 39.30 4.00
2611 8214 5.480073 TGAAATCTTGGGACATAAAACCTGG 59.520 40.000 0.00 0.00 39.30 4.45
2612 8215 4.675063 ATCTTGGGACATAAAACCTGGT 57.325 40.909 0.00 0.00 39.30 4.00
2613 8216 3.761897 TCTTGGGACATAAAACCTGGTG 58.238 45.455 0.00 0.00 39.30 4.17
2614 8217 1.917872 TGGGACATAAAACCTGGTGC 58.082 50.000 0.00 0.00 0.00 5.01
2615 8218 1.182667 GGGACATAAAACCTGGTGCC 58.817 55.000 0.00 0.00 34.59 5.01
2616 8219 1.182667 GGACATAAAACCTGGTGCCC 58.817 55.000 0.00 0.00 0.00 5.36
2618 8221 2.243810 GACATAAAACCTGGTGCCCAA 58.756 47.619 0.00 0.00 30.80 4.12
2619 8222 2.831526 GACATAAAACCTGGTGCCCAAT 59.168 45.455 0.00 0.00 30.80 3.16
2621 8224 2.990740 TAAAACCTGGTGCCCAATCT 57.009 45.000 0.00 0.00 30.80 2.40
2622 8225 2.990740 AAAACCTGGTGCCCAATCTA 57.009 45.000 0.00 0.00 30.80 1.98
2623 8226 3.473113 AAAACCTGGTGCCCAATCTAT 57.527 42.857 0.00 0.00 30.80 1.98
2624 8227 3.473113 AAACCTGGTGCCCAATCTATT 57.527 42.857 0.00 0.00 30.80 1.73
2626 8229 3.577805 ACCTGGTGCCCAATCTATTAC 57.422 47.619 0.00 0.00 30.80 1.89
2627 8230 2.174854 ACCTGGTGCCCAATCTATTACC 59.825 50.000 0.00 0.00 30.80 2.85
2628 8231 2.494059 CTGGTGCCCAATCTATTACCG 58.506 52.381 0.00 0.00 30.80 4.02
2629 8232 1.841277 TGGTGCCCAATCTATTACCGT 59.159 47.619 0.00 0.00 0.00 4.83
2630 8233 2.240160 TGGTGCCCAATCTATTACCGTT 59.760 45.455 0.00 0.00 0.00 4.44
2631 8234 2.876550 GGTGCCCAATCTATTACCGTTC 59.123 50.000 0.00 0.00 0.00 3.95
2632 8235 2.542595 GTGCCCAATCTATTACCGTTCG 59.457 50.000 0.00 0.00 0.00 3.95
2634 8237 3.118702 TGCCCAATCTATTACCGTTCGAA 60.119 43.478 0.00 0.00 0.00 3.71
2635 8238 3.493503 GCCCAATCTATTACCGTTCGAAG 59.506 47.826 0.00 0.00 0.00 3.79
2637 8240 5.114081 CCCAATCTATTACCGTTCGAAGTT 58.886 41.667 0.00 0.00 0.00 2.66
2639 8242 6.456449 CCCAATCTATTACCGTTCGAAGTTTG 60.456 42.308 0.00 0.00 0.00 2.93
2640 8243 6.456449 CCAATCTATTACCGTTCGAAGTTTGG 60.456 42.308 0.00 1.62 31.27 3.28
2641 8244 5.138125 TCTATTACCGTTCGAAGTTTGGT 57.862 39.130 13.72 13.72 36.72 3.67
2647 8298 3.190953 ACCGTTCGAAGTTTGGTGAAAAA 59.809 39.130 0.00 0.00 0.00 1.94
2680 8331 7.837202 AAATGTATCCGTGACGAAGAAAATA 57.163 32.000 6.54 0.00 0.00 1.40
2682 8333 9.537192 AAATGTATCCGTGACGAAGAAAATATA 57.463 29.630 6.54 0.00 0.00 0.86
2683 8334 8.744008 ATGTATCCGTGACGAAGAAAATATAG 57.256 34.615 6.54 0.00 0.00 1.31
2684 8335 6.639686 TGTATCCGTGACGAAGAAAATATAGC 59.360 38.462 6.54 0.00 0.00 2.97
2685 8336 4.365723 TCCGTGACGAAGAAAATATAGCC 58.634 43.478 6.54 0.00 0.00 3.93
2686 8337 3.493503 CCGTGACGAAGAAAATATAGCCC 59.506 47.826 6.54 0.00 0.00 5.19
2687 8338 4.369182 CGTGACGAAGAAAATATAGCCCT 58.631 43.478 0.00 0.00 0.00 5.19
2688 8339 4.209288 CGTGACGAAGAAAATATAGCCCTG 59.791 45.833 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 0.034896 GAGGGAAGCGACACCTGAAA 59.965 55.000 0.00 0.00 34.02 2.69
68 69 0.832135 AGAGGGAAGCGACACCTGAA 60.832 55.000 0.00 0.00 34.02 3.02
71 72 0.832135 TCAAGAGGGAAGCGACACCT 60.832 55.000 0.00 0.00 37.31 4.00
130 131 2.811410 ACACGGACTAGGGTATTCACA 58.189 47.619 0.00 0.00 0.00 3.58
149 150 2.202453 GTCGTCGAGCCCGAGAAC 60.202 66.667 0.00 0.00 46.52 3.01
154 155 2.885644 CCATTGTCGTCGAGCCCG 60.886 66.667 0.00 0.00 37.07 6.13
166 167 1.596220 CGATGACATCAAGCGCCATTG 60.596 52.381 15.58 2.79 0.00 2.82
167 168 0.659427 CGATGACATCAAGCGCCATT 59.341 50.000 15.58 0.00 0.00 3.16
179 180 1.900351 CCTCAAGAGGGCGATGACA 59.100 57.895 8.28 0.00 44.87 3.58
180 181 4.844420 CCTCAAGAGGGCGATGAC 57.156 61.111 8.28 0.00 44.87 3.06
209 210 1.607467 CCAAAAGGGACCAGGGCTG 60.607 63.158 0.00 0.00 40.01 4.85
215 216 3.499563 CCATCTACAACCAAAAGGGACCA 60.500 47.826 0.00 0.00 41.15 4.02
225 226 1.003118 GTGACTGGCCATCTACAACCA 59.997 52.381 5.51 0.00 0.00 3.67
234 235 2.671070 CCCGAAGTGACTGGCCAT 59.329 61.111 5.51 0.00 0.00 4.40
236 237 3.628646 ATGCCCGAAGTGACTGGCC 62.629 63.158 9.59 0.00 43.35 5.36
258 259 3.005472 AGAGCGCTACAAGACAAGTACAA 59.995 43.478 11.50 0.00 0.00 2.41
262 263 2.035961 TCAAGAGCGCTACAAGACAAGT 59.964 45.455 11.50 0.00 0.00 3.16
266 267 4.398247 CAAATTCAAGAGCGCTACAAGAC 58.602 43.478 11.50 0.00 0.00 3.01
276 277 2.523015 CATCCACGCAAATTCAAGAGC 58.477 47.619 0.00 0.00 0.00 4.09
277 278 2.489329 ACCATCCACGCAAATTCAAGAG 59.511 45.455 0.00 0.00 0.00 2.85
284 285 0.249120 TCGAGACCATCCACGCAAAT 59.751 50.000 0.00 0.00 0.00 2.32
287 289 1.141665 CATCGAGACCATCCACGCA 59.858 57.895 0.00 0.00 0.00 5.24
307 309 6.363065 ACGGACACTTGTATAAGATAGGAGA 58.637 40.000 6.19 0.00 37.36 3.71
323 325 4.533815 TGAAGAGATACCATACGGACACT 58.466 43.478 0.00 0.00 35.59 3.55
324 326 4.913335 TGAAGAGATACCATACGGACAC 57.087 45.455 0.00 0.00 35.59 3.67
330 332 6.226787 CAAGGACCATGAAGAGATACCATAC 58.773 44.000 0.00 0.00 0.00 2.39
331 333 5.221722 GCAAGGACCATGAAGAGATACCATA 60.222 44.000 0.00 0.00 0.00 2.74
345 347 1.211457 CCAAGAGCTAGCAAGGACCAT 59.789 52.381 18.83 0.00 0.00 3.55
346 348 0.615331 CCAAGAGCTAGCAAGGACCA 59.385 55.000 18.83 0.00 0.00 4.02
388 390 1.610673 GAGACAGCCCCCTCACTCA 60.611 63.158 0.00 0.00 0.00 3.41
391 393 1.003233 GTTGAGACAGCCCCCTCAC 60.003 63.158 0.00 0.00 38.95 3.51
398 400 2.246719 AACTGACAGTTGAGACAGCC 57.753 50.000 19.96 0.00 37.00 4.85
409 411 1.237285 CGAAAGGGGCCAACTGACAG 61.237 60.000 4.39 0.00 0.00 3.51
426 428 1.302431 CACACCAAGCCACATCCGA 60.302 57.895 0.00 0.00 0.00 4.55
431 433 1.821759 CCGAACACACCAAGCCACA 60.822 57.895 0.00 0.00 0.00 4.17
436 438 1.724623 CATCGTACCGAACACACCAAG 59.275 52.381 0.00 0.00 39.99 3.61
453 456 1.749258 GAAACCACCGGGCTCCATC 60.749 63.158 6.32 0.00 37.90 3.51
482 485 2.113139 CAACAGGGCTGGAACCGT 59.887 61.111 0.00 0.00 34.19 4.83
489 492 2.613977 CCAAGACTACTCAACAGGGCTG 60.614 54.545 0.00 0.00 0.00 4.85
492 495 1.978580 ACCCAAGACTACTCAACAGGG 59.021 52.381 0.00 0.00 40.88 4.45
499 502 3.574826 ACAAGAGACACCCAAGACTACTC 59.425 47.826 0.00 0.00 0.00 2.59
526 532 0.460459 TGAAAACACGAGACGCCACA 60.460 50.000 0.00 0.00 0.00 4.17
551 557 1.219646 CAATGCAGCAAACCAACACC 58.780 50.000 0.00 0.00 0.00 4.16
633 639 6.821388 ACACAAACTGCCAAACCAATATAAA 58.179 32.000 0.00 0.00 0.00 1.40
704 710 5.164954 TCCTTTTTGCACAACTACAAACAC 58.835 37.500 0.00 0.00 35.60 3.32
718 724 5.353956 ACTTGATTGGTGTTTTCCTTTTTGC 59.646 36.000 0.00 0.00 0.00 3.68
877 2325 3.391049 CGCCAAATACCTTAGTAGCTCC 58.609 50.000 0.00 0.00 0.00 4.70
878 2326 3.069158 TCCGCCAAATACCTTAGTAGCTC 59.931 47.826 0.00 0.00 0.00 4.09
880 2328 3.181468 ACTCCGCCAAATACCTTAGTAGC 60.181 47.826 0.00 0.00 0.00 3.58
884 2332 2.943033 CCAACTCCGCCAAATACCTTAG 59.057 50.000 0.00 0.00 0.00 2.18
934 2393 4.202151 GGTTGGAGTTTGTCAATGCTCTTT 60.202 41.667 13.80 0.00 0.00 2.52
947 2510 1.880027 GTTGATCTGCGGTTGGAGTTT 59.120 47.619 0.00 0.00 34.70 2.66
1061 2630 1.185618 AGTGAAGCTGACCTGCGGTA 61.186 55.000 0.09 0.00 35.25 4.02
1218 4185 4.090786 TGAAACATAGTACAACGACGCATG 59.909 41.667 0.00 0.00 0.00 4.06
1228 4195 8.205512 TCAAAGTAGTTGGTGAAACATAGTACA 58.794 33.333 0.00 0.00 41.61 2.90
1230 4197 9.787435 AATCAAAGTAGTTGGTGAAACATAGTA 57.213 29.630 0.00 0.00 41.61 1.82
1231 4198 8.691661 AATCAAAGTAGTTGGTGAAACATAGT 57.308 30.769 0.00 0.00 41.61 2.12
1232 4199 9.965824 AAAATCAAAGTAGTTGGTGAAACATAG 57.034 29.630 0.00 0.00 41.61 2.23
1261 4228 6.151480 TGTGAGGACGTACATCAGTAACATAA 59.849 38.462 0.00 0.00 39.99 1.90
1262 4229 5.648960 TGTGAGGACGTACATCAGTAACATA 59.351 40.000 0.00 0.00 39.99 2.29
1271 4344 2.952978 AGGATCTGTGAGGACGTACATC 59.047 50.000 0.00 0.00 0.00 3.06
1272 4345 3.019799 AGGATCTGTGAGGACGTACAT 57.980 47.619 0.00 0.00 0.00 2.29
1273 4346 2.492088 CAAGGATCTGTGAGGACGTACA 59.508 50.000 0.00 0.00 0.00 2.90
1274 4347 2.735762 GCAAGGATCTGTGAGGACGTAC 60.736 54.545 0.00 0.00 0.00 3.67
1275 4348 1.476891 GCAAGGATCTGTGAGGACGTA 59.523 52.381 0.00 0.00 0.00 3.57
1309 4382 2.376032 GCGCAACTCTTGTTTCTTGTC 58.624 47.619 0.30 0.00 33.52 3.18
1313 4386 0.814010 ACGGCGCAACTCTTGTTTCT 60.814 50.000 10.83 0.00 33.52 2.52
1318 4391 2.856032 CAGACGGCGCAACTCTTG 59.144 61.111 10.83 0.00 0.00 3.02
1331 4404 2.564553 ATCCAGCCGACGAAGCAGAC 62.565 60.000 0.00 0.00 0.00 3.51
1335 4408 1.880340 CTCATCCAGCCGACGAAGC 60.880 63.158 0.00 0.00 0.00 3.86
1422 4495 5.124617 GTGGAGGAGCTTCTTATTTTCCTTG 59.875 44.000 0.00 0.00 38.35 3.61
1431 4504 0.905357 GCAGGTGGAGGAGCTTCTTA 59.095 55.000 0.00 0.00 0.00 2.10
1470 4543 1.066303 CCCTGACGAGACAGCTGATAC 59.934 57.143 23.35 11.25 36.67 2.24
1480 4553 7.123098 TCAAGTAACATAAATACCCTGACGAGA 59.877 37.037 0.00 0.00 0.00 4.04
1481 4554 7.262772 TCAAGTAACATAAATACCCTGACGAG 58.737 38.462 0.00 0.00 0.00 4.18
1488 4561 9.174166 AGAACACATCAAGTAACATAAATACCC 57.826 33.333 0.00 0.00 0.00 3.69
1499 4572 7.210718 TCGACTAGAAGAACACATCAAGTAA 57.789 36.000 0.00 0.00 0.00 2.24
1536 4609 6.426980 AACGAAAAACGAGTAAGGAAAAGT 57.573 33.333 0.00 0.00 45.77 2.66
1542 4615 3.942739 TGCAAACGAAAAACGAGTAAGG 58.057 40.909 0.00 0.00 45.77 2.69
1551 4624 3.794028 CGATTGGAACTGCAAACGAAAAA 59.206 39.130 7.66 0.00 0.00 1.94
1595 4668 7.158099 AGTAAAATGACAAGGATTACCAAGC 57.842 36.000 0.00 0.00 38.94 4.01
1610 4683 5.063204 CCTCCTCACACACAAGTAAAATGA 58.937 41.667 0.00 0.00 0.00 2.57
1613 4686 4.764050 TCCTCCTCACACACAAGTAAAA 57.236 40.909 0.00 0.00 0.00 1.52
1727 4800 4.340381 GCTTCCATGCATAGTTCCATTTCT 59.660 41.667 0.00 0.00 0.00 2.52
1729 4802 3.067180 CGCTTCCATGCATAGTTCCATTT 59.933 43.478 0.00 0.00 0.00 2.32
1846 4926 1.002069 TCCCCAATGCAGTCAAGGAT 58.998 50.000 0.00 0.00 0.00 3.24
1848 4928 0.682209 CCTCCCCAATGCAGTCAAGG 60.682 60.000 0.00 0.00 0.00 3.61
1876 4960 7.068962 TGTTCACGGATATCAGTTTCCATAGTA 59.931 37.037 5.70 0.00 31.99 1.82
1880 4964 5.097742 TGTTCACGGATATCAGTTTCCAT 57.902 39.130 5.70 0.00 31.99 3.41
1888 4972 3.243602 CGGTACCATGTTCACGGATATCA 60.244 47.826 13.54 0.00 0.00 2.15
1895 4979 0.869068 TTTGCGGTACCATGTTCACG 59.131 50.000 13.54 0.00 0.00 4.35
1896 4980 3.569250 ATTTTGCGGTACCATGTTCAC 57.431 42.857 13.54 0.00 0.00 3.18
1984 5076 5.179742 ACTTAATACTCGATACAGAGGCTCG 59.820 44.000 9.22 6.83 42.31 5.03
2104 5196 3.446516 CCCATCTCTGCATCTATCGATCA 59.553 47.826 0.00 0.00 0.00 2.92
2105 5197 3.181477 CCCCATCTCTGCATCTATCGATC 60.181 52.174 0.00 0.00 0.00 3.69
2106 5198 2.765135 CCCCATCTCTGCATCTATCGAT 59.235 50.000 2.16 2.16 0.00 3.59
2107 5199 2.174360 CCCCATCTCTGCATCTATCGA 58.826 52.381 0.00 0.00 0.00 3.59
2112 5204 2.815945 CGCCCCCATCTCTGCATCT 61.816 63.158 0.00 0.00 0.00 2.90
2129 5221 3.120199 TCTCGTAAAGAGGGTTAACGTCG 60.120 47.826 0.00 0.00 46.82 5.12
2146 5238 4.638421 TGGTTGTGTGAATTTTCTTCTCGT 59.362 37.500 0.00 0.00 0.00 4.18
2158 5250 1.748493 GAGGCAAGTTGGTTGTGTGAA 59.252 47.619 4.75 0.00 38.55 3.18
2177 5269 5.414360 CAGCAACTATCTTAGCTCTGTTGA 58.586 41.667 13.59 0.00 37.53 3.18
2178 5270 4.033817 GCAGCAACTATCTTAGCTCTGTTG 59.966 45.833 0.00 0.00 38.13 3.33
2179 5271 4.081198 AGCAGCAACTATCTTAGCTCTGTT 60.081 41.667 0.00 0.00 34.61 3.16
2180 5272 3.450457 AGCAGCAACTATCTTAGCTCTGT 59.550 43.478 0.00 0.00 34.61 3.41
2181 5273 4.050553 GAGCAGCAACTATCTTAGCTCTG 58.949 47.826 0.00 0.00 42.60 3.35
2182 5274 3.703556 TGAGCAGCAACTATCTTAGCTCT 59.296 43.478 12.03 0.00 45.24 4.09
2183 5275 4.052159 TGAGCAGCAACTATCTTAGCTC 57.948 45.455 0.00 0.00 45.23 4.09
2184 5276 4.686191 ATGAGCAGCAACTATCTTAGCT 57.314 40.909 0.00 0.00 37.95 3.32
2185 5277 5.755375 TGTTATGAGCAGCAACTATCTTAGC 59.245 40.000 0.00 0.00 0.00 3.09
2194 5286 5.048713 AGGTTTACTTGTTATGAGCAGCAAC 60.049 40.000 0.00 0.00 0.00 4.17
2200 5292 7.266400 AGTAGCTAGGTTTACTTGTTATGAGC 58.734 38.462 0.00 0.00 0.00 4.26
2201 5293 9.088512 CAAGTAGCTAGGTTTACTTGTTATGAG 57.911 37.037 21.58 3.25 45.85 2.90
2202 5294 8.997621 CAAGTAGCTAGGTTTACTTGTTATGA 57.002 34.615 21.58 0.00 45.85 2.15
2209 5301 4.220163 ACTCGCAAGTAGCTAGGTTTACTT 59.780 41.667 0.00 1.65 40.16 2.24
2210 5302 3.762823 ACTCGCAAGTAGCTAGGTTTACT 59.237 43.478 0.00 0.00 40.16 2.24
2211 5303 4.104066 GACTCGCAAGTAGCTAGGTTTAC 58.896 47.826 0.00 0.00 40.16 2.01
2212 5304 3.129988 GGACTCGCAAGTAGCTAGGTTTA 59.870 47.826 0.00 0.00 40.16 2.01
2225 5317 0.829990 TGCTGATATGGGACTCGCAA 59.170 50.000 0.00 0.00 0.00 4.85
2227 5319 1.202580 AGTTGCTGATATGGGACTCGC 60.203 52.381 0.00 0.00 0.00 5.03
2246 5338 1.135046 CTGTGAGTTGCTGACGTGAG 58.865 55.000 0.00 0.00 0.00 3.51
2259 5375 3.859443 CATGGAAGGAGAAGACTGTGAG 58.141 50.000 0.00 0.00 0.00 3.51
2266 5382 2.355108 CGGAAAGCATGGAAGGAGAAGA 60.355 50.000 0.00 0.00 0.00 2.87
2269 5385 0.984230 ACGGAAAGCATGGAAGGAGA 59.016 50.000 0.00 0.00 0.00 3.71
2283 5407 2.103094 CTGGCCTGAGATTGATACGGAA 59.897 50.000 3.32 0.00 0.00 4.30
2285 5409 1.875576 GCTGGCCTGAGATTGATACGG 60.876 57.143 14.77 0.00 0.00 4.02
2286 5410 1.506493 GCTGGCCTGAGATTGATACG 58.494 55.000 14.77 0.00 0.00 3.06
2310 5434 4.899239 AGCACCGGCATAGCTCGC 62.899 66.667 0.00 0.00 44.61 5.03
2311 5435 2.659897 GAGCACCGGCATAGCTCG 60.660 66.667 18.78 0.00 44.37 5.03
2313 5437 1.987807 AATGGAGCACCGGCATAGCT 61.988 55.000 0.00 6.12 44.61 3.32
2314 5438 1.510480 GAATGGAGCACCGGCATAGC 61.510 60.000 0.00 0.00 44.61 2.97
2315 5439 0.179048 TGAATGGAGCACCGGCATAG 60.179 55.000 0.00 0.00 44.61 2.23
2316 5440 0.463654 GTGAATGGAGCACCGGCATA 60.464 55.000 0.00 0.00 44.61 3.14
2317 5441 1.750399 GTGAATGGAGCACCGGCAT 60.750 57.895 0.00 0.00 44.61 4.40
2318 5442 2.359850 GTGAATGGAGCACCGGCA 60.360 61.111 0.00 0.00 44.61 5.69
2319 5443 3.134127 GGTGAATGGAGCACCGGC 61.134 66.667 0.00 0.00 45.50 6.13
2323 5447 1.000274 GTTTGGTGGTGAATGGAGCAC 60.000 52.381 0.00 0.00 42.46 4.40
2324 5448 1.133513 AGTTTGGTGGTGAATGGAGCA 60.134 47.619 0.00 0.00 0.00 4.26
2325 5449 1.620822 AGTTTGGTGGTGAATGGAGC 58.379 50.000 0.00 0.00 0.00 4.70
2326 5450 4.141287 TGTTAGTTTGGTGGTGAATGGAG 58.859 43.478 0.00 0.00 0.00 3.86
2327 5451 4.171878 TGTTAGTTTGGTGGTGAATGGA 57.828 40.909 0.00 0.00 0.00 3.41
2328 5452 4.280677 ACATGTTAGTTTGGTGGTGAATGG 59.719 41.667 0.00 0.00 0.00 3.16
2329 5453 5.221224 ACACATGTTAGTTTGGTGGTGAATG 60.221 40.000 0.00 0.00 33.91 2.67
2330 5454 4.892934 ACACATGTTAGTTTGGTGGTGAAT 59.107 37.500 0.00 0.00 33.91 2.57
2355 5479 0.385390 CAGCTGGACCCACAACAAAC 59.615 55.000 5.57 0.00 0.00 2.93
2414 5538 0.557238 ATGGGCAGCCATAACCATCA 59.443 50.000 15.19 0.00 39.41 3.07
2416 5540 2.041701 GAAATGGGCAGCCATAACCAT 58.958 47.619 15.19 3.83 45.18 3.55
2427 5551 5.221601 TGTTATTTGCAAAGAGAAATGGGCA 60.222 36.000 18.19 3.41 0.00 5.36
2455 5579 5.415701 TGCTATTTGGCTTAAGCATATAGGC 59.584 40.000 27.83 22.08 44.36 3.93
2463 5587 6.625873 ACTTAGATGCTATTTGGCTTAAGC 57.374 37.500 19.53 19.53 41.14 3.09
2465 5589 9.681062 ACTTTACTTAGATGCTATTTGGCTTAA 57.319 29.630 0.00 0.00 0.00 1.85
2467 5591 9.681062 TTACTTTACTTAGATGCTATTTGGCTT 57.319 29.630 0.00 0.00 0.00 4.35
2493 5618 7.889469 CACCTATGCATTTTCCATAATAGCTT 58.111 34.615 3.54 0.00 0.00 3.74
2511 5636 1.153086 GCACCCTGGAGCACCTATG 60.153 63.158 0.71 0.00 37.04 2.23
2512 5637 1.307343 AGCACCCTGGAGCACCTAT 60.307 57.895 8.32 0.00 37.04 2.57
2514 5639 3.325753 GAGCACCCTGGAGCACCT 61.326 66.667 8.32 0.00 37.04 4.00
2515 5640 4.416738 GGAGCACCCTGGAGCACC 62.417 72.222 8.32 7.30 35.78 5.01
2516 5641 3.640407 TGGAGCACCCTGGAGCAC 61.640 66.667 8.32 1.58 34.21 4.40
2517 5642 3.640407 GTGGAGCACCCTGGAGCA 61.640 66.667 8.32 0.00 34.21 4.26
2529 7346 8.275187 TGCATATTTATATATAGGGGGTGGAG 57.725 38.462 0.00 0.00 0.00 3.86
2531 7348 9.881773 AATTGCATATTTATATATAGGGGGTGG 57.118 33.333 0.00 0.00 0.00 4.61
2550 7367 9.675464 ATTTTCATGGTATCTTTTGAATTGCAT 57.325 25.926 0.00 0.00 0.00 3.96
2585 8188 6.209391 CAGGTTTTATGTCCCAAGATTTCAGT 59.791 38.462 0.00 0.00 0.00 3.41
2586 8189 6.350445 CCAGGTTTTATGTCCCAAGATTTCAG 60.350 42.308 0.00 0.00 0.00 3.02
2587 8190 5.480073 CCAGGTTTTATGTCCCAAGATTTCA 59.520 40.000 0.00 0.00 0.00 2.69
2588 8191 5.480422 ACCAGGTTTTATGTCCCAAGATTTC 59.520 40.000 0.00 0.00 0.00 2.17
2589 8192 5.245977 CACCAGGTTTTATGTCCCAAGATTT 59.754 40.000 0.00 0.00 0.00 2.17
2590 8193 4.772100 CACCAGGTTTTATGTCCCAAGATT 59.228 41.667 0.00 0.00 0.00 2.40
2591 8194 4.344104 CACCAGGTTTTATGTCCCAAGAT 58.656 43.478 0.00 0.00 0.00 2.40
2592 8195 3.761897 CACCAGGTTTTATGTCCCAAGA 58.238 45.455 0.00 0.00 0.00 3.02
2593 8196 2.231235 GCACCAGGTTTTATGTCCCAAG 59.769 50.000 0.00 0.00 0.00 3.61
2594 8197 2.243810 GCACCAGGTTTTATGTCCCAA 58.756 47.619 0.00 0.00 0.00 4.12
2595 8198 1.549037 GGCACCAGGTTTTATGTCCCA 60.549 52.381 0.00 0.00 0.00 4.37
2596 8199 1.182667 GGCACCAGGTTTTATGTCCC 58.817 55.000 0.00 0.00 0.00 4.46
2611 8214 2.542595 CGAACGGTAATAGATTGGGCAC 59.457 50.000 0.00 0.00 0.00 5.01
2612 8215 2.431419 TCGAACGGTAATAGATTGGGCA 59.569 45.455 0.00 0.00 0.00 5.36
2613 8216 3.102052 TCGAACGGTAATAGATTGGGC 57.898 47.619 0.00 0.00 0.00 5.36
2614 8217 4.690122 ACTTCGAACGGTAATAGATTGGG 58.310 43.478 0.00 0.00 0.00 4.12
2615 8218 6.456449 CCAAACTTCGAACGGTAATAGATTGG 60.456 42.308 0.00 0.00 31.99 3.16
2616 8219 6.091713 ACCAAACTTCGAACGGTAATAGATTG 59.908 38.462 0.00 0.00 0.00 2.67
2618 8221 5.579511 CACCAAACTTCGAACGGTAATAGAT 59.420 40.000 0.00 0.00 0.00 1.98
2619 8222 4.925054 CACCAAACTTCGAACGGTAATAGA 59.075 41.667 0.00 0.00 0.00 1.98
2621 8224 4.880759 TCACCAAACTTCGAACGGTAATA 58.119 39.130 0.00 0.00 0.00 0.98
2622 8225 3.731089 TCACCAAACTTCGAACGGTAAT 58.269 40.909 0.00 0.00 0.00 1.89
2623 8226 3.176552 TCACCAAACTTCGAACGGTAA 57.823 42.857 0.00 0.00 0.00 2.85
2624 8227 2.886862 TCACCAAACTTCGAACGGTA 57.113 45.000 0.00 0.00 0.00 4.02
2626 8229 3.408288 TTTTCACCAAACTTCGAACGG 57.592 42.857 0.00 0.00 0.00 4.44
2658 8309 7.328737 GCTATATTTTCTTCGTCACGGATACAT 59.671 37.037 0.00 0.00 0.00 2.29
2659 8310 6.639686 GCTATATTTTCTTCGTCACGGATACA 59.360 38.462 0.00 0.00 0.00 2.29
2664 8315 3.493503 GGGCTATATTTTCTTCGTCACGG 59.506 47.826 0.00 0.00 0.00 4.94
2665 8316 4.209288 CAGGGCTATATTTTCTTCGTCACG 59.791 45.833 0.00 0.00 0.00 4.35
2666 8317 5.357257 TCAGGGCTATATTTTCTTCGTCAC 58.643 41.667 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.