Multiple sequence alignment - TraesCS3D01G293400

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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 TraesCS3D01G293400 chr3D 100.000 2789 0 0 1 2789 403705916 403703128 0.000000e+00 5151
1 TraesCS3D01G293400 chr3D 93.600 125 6 2 2337 2460 175443102 175442979 4.740000e-43 185
2 TraesCS3D01G293400 chr3D 91.304 92 7 1 2547 2638 175443284 175443194 1.050000e-24 124
3 TraesCS3D01G293400 chr3D 98.413 63 1 0 2485 2547 403703201 403703139 8.170000e-21 111
4 TraesCS3D01G293400 chr3D 98.413 63 1 0 2716 2778 403703432 403703370 8.170000e-21 111
5 TraesCS3D01G293400 chr3A 91.602 1548 75 29 593 2094 525642269 525640731 0.000000e+00 2087
6 TraesCS3D01G293400 chr3A 96.190 315 10 2 2088 2402 525640699 525640387 5.330000e-142 514
7 TraesCS3D01G293400 chr3A 82.143 476 52 17 1 473 525647268 525646823 7.290000e-101 377
8 TraesCS3D01G293400 chr3A 93.506 231 13 2 2561 2789 525640424 525640194 2.660000e-90 342
9 TraesCS3D01G293400 chr3A 92.000 125 8 2 2337 2460 474212524 474212647 1.030000e-39 174
10 TraesCS3D01G293400 chr3B 92.270 1009 65 6 1094 2094 529808544 529807541 0.000000e+00 1419
11 TraesCS3D01G293400 chr3B 92.097 620 38 9 457 1072 529809125 529808513 0.000000e+00 863
12 TraesCS3D01G293400 chr3B 83.333 474 55 8 1 473 529809609 529809159 1.550000e-112 416
13 TraesCS3D01G293400 chr3B 95.652 253 11 0 2088 2340 529807500 529807248 9.300000e-110 407
14 TraesCS3D01G293400 chr3B 98.039 153 2 1 2638 2789 529805742 529805590 5.920000e-67 265
15 TraesCS3D01G293400 chr5A 93.600 125 6 2 2337 2460 44109791 44109668 4.740000e-43 185
16 TraesCS3D01G293400 chr1D 92.800 125 7 2 2337 2460 387563066 387563189 2.210000e-41 180
17 TraesCS3D01G293400 chr6D 92.063 126 7 3 2337 2460 102984322 102984198 1.030000e-39 174
18 TraesCS3D01G293400 chr6D 92.391 92 7 0 2547 2638 102978809 102978900 6.270000e-27 132
19 TraesCS3D01G293400 chr2D 90.435 115 9 2 2347 2460 619608952 619609065 1.730000e-32 150
20 TraesCS3D01G293400 chr2B 89.344 122 10 3 2337 2457 6060920 6060801 1.730000e-32 150
21 TraesCS3D01G293400 chr2B 90.698 86 6 2 2555 2638 572176553 572176638 2.270000e-21 113
22 TraesCS3D01G293400 chr2B 88.889 90 8 1 2549 2638 774702511 774702598 2.940000e-20 110
23 TraesCS3D01G293400 chr4A 88.793 116 9 4 2347 2460 119806398 119806511 3.750000e-29 139
24 TraesCS3D01G293400 chr7D 86.508 126 13 4 2337 2460 575406290 575406167 4.850000e-28 135
25 TraesCS3D01G293400 chr7D 87.879 99 10 2 2535 2632 40863230 40863327 6.310000e-22 115
26 TraesCS3D01G293400 chr7D 86.139 101 10 4 2540 2638 17861479 17861577 3.800000e-19 106
27 TraesCS3D01G293400 chr4B 88.298 94 9 2 2546 2638 475921549 475921457 8.170000e-21 111
28 TraesCS3D01G293400 chr6B 86.139 101 10 3 2540 2638 288424285 288424383 3.800000e-19 106


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 TraesCS3D01G293400 chr3D 403703128 403705916 2788 True 1791 5151 98.9420 1 2789 3 chr3D.!!$R2 2788
1 TraesCS3D01G293400 chr3A 525640194 525642269 2075 True 981 2087 93.7660 593 2789 3 chr3A.!!$R2 2196
2 TraesCS3D01G293400 chr3B 529805590 529809609 4019 True 674 1419 92.2782 1 2789 5 chr3B.!!$R1 2788

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
172 174 0.247460 TGAGGAGAGCATTCACGTGG 59.753 55.0 17.0 0.08 0.0 4.94 F
379 381 0.316278 CCTATGAGAGCGACGACACG 60.316 60.0 0.0 0.00 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1789 0.178981 ATGCAGTCCTTGTTGCCAGT 60.179 50.000 0.0 0.0 39.54 4.0 R
2378 2529 1.354368 CACCTAACCAGTTCACCCCAT 59.646 52.381 0.0 0.0 0.00 4.0 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
20 21 2.855180 CATCGTTTGCTGTTAAGGCTG 58.145 47.619 0.00 0.00 0.00 4.85
29 30 3.440173 TGCTGTTAAGGCTGTAATTCTGC 59.560 43.478 0.00 0.00 39.71 4.26
35 36 3.565764 AGGCTGTAATTCTGCTGCATA 57.434 42.857 1.31 0.00 40.19 3.14
64 65 4.713553 TGTTTGGACTTGCTTATGTCTCA 58.286 39.130 0.00 0.00 34.01 3.27
107 108 7.065803 CCATGTGGCTTTATTTATATAGTCGGG 59.934 40.741 0.00 0.00 0.00 5.14
113 114 8.255905 GGCTTTATTTATATAGTCGGGCTCTAA 58.744 37.037 0.00 0.00 0.00 2.10
125 126 2.619646 CGGGCTCTAACCTTCTCTCTAC 59.380 54.545 0.00 0.00 0.00 2.59
139 141 4.566004 TCTCTCTACAAAAATGGACCACG 58.434 43.478 0.00 0.00 0.00 4.94
141 143 3.074412 CTCTACAAAAATGGACCACGCT 58.926 45.455 0.00 0.00 0.00 5.07
153 155 1.947456 GACCACGCTTCAAAAGAAGGT 59.053 47.619 7.28 0.00 33.21 3.50
157 159 2.031682 CACGCTTCAAAAGAAGGTGAGG 60.032 50.000 15.51 0.00 36.43 3.86
169 171 0.534412 AGGTGAGGAGAGCATTCACG 59.466 55.000 0.00 0.00 41.57 4.35
170 172 0.247736 GGTGAGGAGAGCATTCACGT 59.752 55.000 0.00 0.00 41.57 4.49
172 174 0.247460 TGAGGAGAGCATTCACGTGG 59.753 55.000 17.00 0.08 0.00 4.94
173 175 0.532573 GAGGAGAGCATTCACGTGGA 59.467 55.000 17.00 7.58 0.00 4.02
180 182 1.983224 CATTCACGTGGAGGAGGGT 59.017 57.895 17.00 0.00 0.00 4.34
185 187 4.087892 CGTGGAGGAGGGTGGCTG 62.088 72.222 0.00 0.00 0.00 4.85
215 217 4.402474 AGGCATGTTTCTACCCAAAATAGC 59.598 41.667 0.00 0.00 0.00 2.97
219 221 4.400120 TGTTTCTACCCAAAATAGCCGTT 58.600 39.130 0.00 0.00 0.00 4.44
220 222 5.558818 TGTTTCTACCCAAAATAGCCGTTA 58.441 37.500 0.00 0.00 0.00 3.18
221 223 5.644636 TGTTTCTACCCAAAATAGCCGTTAG 59.355 40.000 0.00 0.00 0.00 2.34
224 226 1.283905 ACCCAAAATAGCCGTTAGCCT 59.716 47.619 0.00 0.00 45.47 4.58
225 227 2.506644 ACCCAAAATAGCCGTTAGCCTA 59.493 45.455 0.00 0.00 45.47 3.93
226 228 3.139077 CCCAAAATAGCCGTTAGCCTAG 58.861 50.000 0.00 0.00 45.47 3.02
227 229 3.433173 CCCAAAATAGCCGTTAGCCTAGT 60.433 47.826 0.00 0.00 45.47 2.57
228 230 3.560068 CCAAAATAGCCGTTAGCCTAGTG 59.440 47.826 0.00 0.00 45.47 2.74
229 231 4.439057 CAAAATAGCCGTTAGCCTAGTGA 58.561 43.478 0.00 0.00 45.47 3.41
230 232 3.729862 AATAGCCGTTAGCCTAGTGAC 57.270 47.619 0.00 0.00 45.47 3.67
231 233 2.133281 TAGCCGTTAGCCTAGTGACA 57.867 50.000 0.00 0.00 45.47 3.58
232 234 1.263356 AGCCGTTAGCCTAGTGACAA 58.737 50.000 0.00 0.00 45.47 3.18
233 235 1.621814 AGCCGTTAGCCTAGTGACAAA 59.378 47.619 0.00 0.00 45.47 2.83
234 236 2.038033 AGCCGTTAGCCTAGTGACAAAA 59.962 45.455 0.00 0.00 45.47 2.44
235 237 2.809696 GCCGTTAGCCTAGTGACAAAAA 59.190 45.455 0.00 0.00 34.35 1.94
262 264 3.658757 GCAGTTAGCCCATTCACAAAA 57.341 42.857 0.00 0.00 37.23 2.44
293 295 2.633488 GTTAGTGATGTTGCCCTCCTC 58.367 52.381 0.00 0.00 0.00 3.71
309 311 5.532779 GCCCTCCTCTAATTTTGGATTGTAG 59.467 44.000 0.00 0.00 0.00 2.74
323 325 3.067742 GGATTGTAGTAACTGCTAGGCGA 59.932 47.826 0.00 0.00 0.00 5.54
364 366 3.502086 CCATCTAGTGGGGCCCTAT 57.498 57.895 25.93 14.82 44.79 2.57
365 367 0.987294 CCATCTAGTGGGGCCCTATG 59.013 60.000 25.93 17.56 44.79 2.23
379 381 0.316278 CCTATGAGAGCGACGACACG 60.316 60.000 0.00 0.00 0.00 4.49
389 391 1.584761 GCGACGACACGTGCATTTATA 59.415 47.619 17.22 0.00 41.37 0.98
390 392 2.028284 GCGACGACACGTGCATTTATAA 59.972 45.455 17.22 0.00 41.37 0.98
401 403 7.220683 ACACGTGCATTTATAATGAATTCAAGC 59.779 33.333 17.22 7.26 0.00 4.01
402 404 7.433131 CACGTGCATTTATAATGAATTCAAGCT 59.567 33.333 13.09 2.86 0.00 3.74
411 413 5.998454 AATGAATTCAAGCTCATACCTCG 57.002 39.130 13.09 0.00 31.97 4.63
412 414 4.471904 TGAATTCAAGCTCATACCTCGT 57.528 40.909 5.45 0.00 0.00 4.18
413 415 4.183865 TGAATTCAAGCTCATACCTCGTG 58.816 43.478 5.45 0.00 0.00 4.35
416 418 2.959516 TCAAGCTCATACCTCGTGTTG 58.040 47.619 0.00 0.00 0.00 3.33
419 421 1.893137 AGCTCATACCTCGTGTTGTGA 59.107 47.619 0.00 0.00 0.00 3.58
428 430 2.289547 CCTCGTGTTGTGACCGAAAAAT 59.710 45.455 0.00 0.00 31.40 1.82
430 432 4.024725 CCTCGTGTTGTGACCGAAAAATTA 60.025 41.667 0.00 0.00 31.40 1.40
433 435 5.007823 TCGTGTTGTGACCGAAAAATTACAT 59.992 36.000 0.00 0.00 0.00 2.29
435 437 5.338559 GTGTTGTGACCGAAAAATTACATCG 59.661 40.000 0.00 1.66 36.39 3.84
441 443 3.371591 ACCGAAAAATTACATCGCGCTTA 59.628 39.130 5.56 0.00 35.35 3.09
459 461 5.618561 CGCTTACAAGAAAGTATTGACACC 58.381 41.667 0.00 0.00 0.00 4.16
477 529 4.320870 ACACCCTATTTGTTCTTGTACCG 58.679 43.478 0.00 0.00 0.00 4.02
483 535 6.183360 CCCTATTTGTTCTTGTACCGTGATTC 60.183 42.308 0.00 0.00 0.00 2.52
491 543 7.811236 TGTTCTTGTACCGTGATTCTAAACTAG 59.189 37.037 0.00 0.00 0.00 2.57
496 548 5.069501 ACCGTGATTCTAAACTAGTCACC 57.930 43.478 0.00 0.00 36.68 4.02
497 549 4.103357 CCGTGATTCTAAACTAGTCACCG 58.897 47.826 0.00 0.00 36.68 4.94
505 557 2.831685 AACTAGTCACCGATGTTGCA 57.168 45.000 0.00 0.00 0.00 4.08
507 559 1.618837 ACTAGTCACCGATGTTGCACT 59.381 47.619 0.00 0.00 0.00 4.40
508 560 2.263077 CTAGTCACCGATGTTGCACTC 58.737 52.381 0.00 0.00 0.00 3.51
513 566 2.316867 CCGATGTTGCACTCACGCA 61.317 57.895 0.00 0.00 41.03 5.24
540 593 5.114081 GGTACGTTGCACTGGAAATATACT 58.886 41.667 0.00 0.00 0.00 2.12
541 594 6.275335 GGTACGTTGCACTGGAAATATACTA 58.725 40.000 0.00 0.00 0.00 1.82
542 595 6.420008 GGTACGTTGCACTGGAAATATACTAG 59.580 42.308 0.00 0.00 0.00 2.57
543 596 5.974108 ACGTTGCACTGGAAATATACTAGT 58.026 37.500 0.00 0.00 0.00 2.57
544 597 7.104043 ACGTTGCACTGGAAATATACTAGTA 57.896 36.000 4.77 4.77 0.00 1.82
545 598 7.201145 ACGTTGCACTGGAAATATACTAGTAG 58.799 38.462 8.85 0.00 0.00 2.57
546 599 6.641314 CGTTGCACTGGAAATATACTAGTAGG 59.359 42.308 8.85 0.00 0.00 3.18
547 600 7.498443 GTTGCACTGGAAATATACTAGTAGGT 58.502 38.462 8.85 0.00 0.00 3.08
548 601 7.286215 TGCACTGGAAATATACTAGTAGGTC 57.714 40.000 8.85 3.09 0.00 3.85
552 605 8.692710 CACTGGAAATATACTAGTAGGTCACAA 58.307 37.037 8.85 0.00 0.00 3.33
564 617 7.927629 ACTAGTAGGTCACAAAACATTTAACGA 59.072 33.333 1.45 0.00 0.00 3.85
569 622 4.439776 GTCACAAAACATTTAACGAGCACC 59.560 41.667 0.00 0.00 0.00 5.01
608 661 7.719871 TGATTAGGAATACCTACAGGCTATC 57.280 40.000 0.00 0.00 46.97 2.08
700 755 2.203640 TGTCACAGCCTCTCGGGT 60.204 61.111 0.00 0.00 43.12 5.28
734 790 2.667199 CGGACGTTTCCCCACCAC 60.667 66.667 0.00 0.00 38.99 4.16
735 791 2.281970 GGACGTTTCCCCACCACC 60.282 66.667 0.00 0.00 35.57 4.61
736 792 2.511900 GACGTTTCCCCACCACCA 59.488 61.111 0.00 0.00 0.00 4.17
1018 1076 3.991924 ATGTCTCTCGGCAGGCCCT 62.992 63.158 0.00 0.00 0.00 5.19
1054 1121 3.032609 CAGGCGGCGATGATCGAC 61.033 66.667 20.25 15.96 46.24 4.20
1271 1368 3.724374 CCTGTGTACAAAAACTCCGAGA 58.276 45.455 1.33 0.00 0.00 4.04
1535 1632 7.440198 TCTGATGCATTTCTGGAGTATAAGAG 58.560 38.462 0.00 0.00 0.00 2.85
1573 1670 1.670674 GCGTGTCATCTTCGGGTGTTA 60.671 52.381 0.00 0.00 0.00 2.41
1606 1703 7.864686 TGAGCAAAATCGTATTCTTATGATGG 58.135 34.615 0.00 0.00 34.86 3.51
1607 1704 7.714813 TGAGCAAAATCGTATTCTTATGATGGA 59.285 33.333 0.00 0.00 34.86 3.41
1608 1705 8.092521 AGCAAAATCGTATTCTTATGATGGAG 57.907 34.615 0.00 0.00 34.86 3.86
1609 1706 7.933577 AGCAAAATCGTATTCTTATGATGGAGA 59.066 33.333 0.00 0.00 34.86 3.71
1610 1707 8.559536 GCAAAATCGTATTCTTATGATGGAGAA 58.440 33.333 0.00 0.00 34.86 2.87
1614 1711 6.816136 TCGTATTCTTATGATGGAGAAGCAA 58.184 36.000 0.00 0.00 35.54 3.91
1615 1712 7.445121 TCGTATTCTTATGATGGAGAAGCAAT 58.555 34.615 0.00 0.00 35.54 3.56
1616 1713 7.600375 TCGTATTCTTATGATGGAGAAGCAATC 59.400 37.037 0.00 0.00 35.54 2.67
1617 1714 7.386025 CGTATTCTTATGATGGAGAAGCAATCA 59.614 37.037 0.00 0.00 35.54 2.57
1619 1716 7.506328 TTCTTATGATGGAGAAGCAATCATG 57.494 36.000 7.46 0.00 40.40 3.07
1636 1733 7.576236 GCAATCATGCGTAGATAACATTACTT 58.424 34.615 0.00 0.00 43.83 2.24
1637 1734 7.531871 GCAATCATGCGTAGATAACATTACTTG 59.468 37.037 0.00 0.00 43.83 3.16
1639 1736 6.578944 TCATGCGTAGATAACATTACTTGGT 58.421 36.000 0.00 0.00 0.00 3.67
1643 1740 6.035220 TGCGTAGATAACATTACTTGGTTTCG 59.965 38.462 0.00 0.00 0.00 3.46
1646 1743 7.276218 CGTAGATAACATTACTTGGTTTCGGAA 59.724 37.037 0.00 0.00 0.00 4.30
1655 1752 8.567948 CATTACTTGGTTTCGGAAATATATGCT 58.432 33.333 6.43 0.00 0.00 3.79
1656 1753 9.787435 ATTACTTGGTTTCGGAAATATATGCTA 57.213 29.630 6.43 0.00 0.00 3.49
1662 1759 6.255887 GGTTTCGGAAATATATGCTATCGAGG 59.744 42.308 6.43 0.00 0.00 4.63
1667 1764 6.036083 CGGAAATATATGCTATCGAGGTTTGG 59.964 42.308 0.00 0.00 0.00 3.28
1670 1767 7.482169 AATATATGCTATCGAGGTTTGGAGA 57.518 36.000 0.00 0.00 0.00 3.71
1678 1775 1.466167 CGAGGTTTGGAGAATGTGCTG 59.534 52.381 0.00 0.00 0.00 4.41
1680 1777 3.350833 GAGGTTTGGAGAATGTGCTGAT 58.649 45.455 0.00 0.00 0.00 2.90
1687 1784 4.196971 TGGAGAATGTGCTGATGAGATTG 58.803 43.478 0.00 0.00 0.00 2.67
1692 1789 5.826208 AGAATGTGCTGATGAGATTGCAATA 59.174 36.000 12.97 0.00 37.17 1.90
1870 1967 5.588246 TCAGTCTTTGTCTGTTGTTTATGCA 59.412 36.000 0.00 0.00 34.86 3.96
1884 1982 4.455533 TGTTTATGCATTCGAGTTGAGCTT 59.544 37.500 3.54 0.00 0.00 3.74
1993 2091 3.457749 GGGAACTGAAGATGAGGAGGATT 59.542 47.826 0.00 0.00 0.00 3.01
2151 2302 5.690865 TGTTCCTTGTCTCCAGTAATGTTT 58.309 37.500 0.00 0.00 0.00 2.83
2384 2535 4.561155 AGTTCGGACTGATGGGGT 57.439 55.556 0.00 0.00 33.99 4.95
2385 2536 1.983224 AGTTCGGACTGATGGGGTG 59.017 57.895 0.00 0.00 33.99 4.61
2386 2537 0.544357 AGTTCGGACTGATGGGGTGA 60.544 55.000 0.00 0.00 33.99 4.02
2387 2538 0.323629 GTTCGGACTGATGGGGTGAA 59.676 55.000 0.00 0.00 0.00 3.18
2388 2539 0.323629 TTCGGACTGATGGGGTGAAC 59.676 55.000 0.00 0.00 0.00 3.18
2390 2541 0.391661 CGGACTGATGGGGTGAACTG 60.392 60.000 0.00 0.00 0.00 3.16
2391 2542 0.035056 GGACTGATGGGGTGAACTGG 60.035 60.000 0.00 0.00 0.00 4.00
2392 2543 0.693049 GACTGATGGGGTGAACTGGT 59.307 55.000 0.00 0.00 0.00 4.00
2393 2544 1.073923 GACTGATGGGGTGAACTGGTT 59.926 52.381 0.00 0.00 0.00 3.67
2394 2545 2.304761 GACTGATGGGGTGAACTGGTTA 59.695 50.000 0.00 0.00 0.00 2.85
2395 2546 2.305927 ACTGATGGGGTGAACTGGTTAG 59.694 50.000 0.00 0.00 0.00 2.34
2396 2547 1.633432 TGATGGGGTGAACTGGTTAGG 59.367 52.381 0.00 0.00 0.00 2.69
2397 2548 1.633945 GATGGGGTGAACTGGTTAGGT 59.366 52.381 0.00 0.00 0.00 3.08
2398 2549 0.768622 TGGGGTGAACTGGTTAGGTG 59.231 55.000 0.00 0.00 0.00 4.00
2399 2550 0.608308 GGGGTGAACTGGTTAGGTGC 60.608 60.000 0.00 0.00 0.00 5.01
2400 2551 0.109723 GGGTGAACTGGTTAGGTGCA 59.890 55.000 0.00 0.00 0.00 4.57
2401 2552 1.271926 GGGTGAACTGGTTAGGTGCAT 60.272 52.381 0.00 0.00 0.00 3.96
2402 2553 2.026636 GGGTGAACTGGTTAGGTGCATA 60.027 50.000 0.00 0.00 0.00 3.14
2403 2554 3.560453 GGGTGAACTGGTTAGGTGCATAA 60.560 47.826 0.00 0.00 0.00 1.90
2404 2555 3.689649 GGTGAACTGGTTAGGTGCATAAG 59.310 47.826 0.00 0.00 0.00 1.73
2405 2556 3.127030 GTGAACTGGTTAGGTGCATAAGC 59.873 47.826 0.00 0.00 42.57 3.09
2408 2559 3.347216 ACTGGTTAGGTGCATAAGCTTG 58.653 45.455 9.86 0.00 42.74 4.01
2409 2560 2.091541 TGGTTAGGTGCATAAGCTTGC 58.908 47.619 9.86 6.29 42.74 4.01
2419 2570 2.476854 GCATAAGCTTGCAACGAAGAGG 60.477 50.000 9.86 0.00 42.31 3.69
2420 2571 2.543777 TAAGCTTGCAACGAAGAGGT 57.456 45.000 9.86 0.00 0.00 3.85
2421 2572 1.680338 AAGCTTGCAACGAAGAGGTT 58.320 45.000 0.00 0.00 0.00 3.50
2422 2573 1.230324 AGCTTGCAACGAAGAGGTTC 58.770 50.000 0.00 0.00 0.00 3.62
2423 2574 0.944386 GCTTGCAACGAAGAGGTTCA 59.056 50.000 0.00 0.00 32.36 3.18
2424 2575 1.069636 GCTTGCAACGAAGAGGTTCAG 60.070 52.381 0.00 0.00 32.36 3.02
2425 2576 1.532868 CTTGCAACGAAGAGGTTCAGG 59.467 52.381 0.00 0.00 32.36 3.86
2426 2577 0.250295 TGCAACGAAGAGGTTCAGGG 60.250 55.000 0.00 0.00 32.36 4.45
2427 2578 0.250338 GCAACGAAGAGGTTCAGGGT 60.250 55.000 0.00 0.00 32.36 4.34
2428 2579 1.814248 GCAACGAAGAGGTTCAGGGTT 60.814 52.381 0.00 0.00 32.36 4.11
2429 2580 2.143925 CAACGAAGAGGTTCAGGGTTC 58.856 52.381 0.00 0.00 32.36 3.62
2430 2581 1.420430 ACGAAGAGGTTCAGGGTTCA 58.580 50.000 0.00 0.00 32.36 3.18
2433 2584 3.211045 CGAAGAGGTTCAGGGTTCAAAA 58.789 45.455 0.00 0.00 32.36 2.44
2434 2585 3.003378 CGAAGAGGTTCAGGGTTCAAAAC 59.997 47.826 0.00 0.00 32.36 2.43
2446 2597 4.722361 GGTTCAAAACCCAGTAAACACA 57.278 40.909 0.00 0.00 46.12 3.72
2447 2598 5.074584 GGTTCAAAACCCAGTAAACACAA 57.925 39.130 0.00 0.00 46.12 3.33
2448 2599 5.666462 GGTTCAAAACCCAGTAAACACAAT 58.334 37.500 0.00 0.00 46.12 2.71
2451 2602 7.764901 GGTTCAAAACCCAGTAAACACAATAAA 59.235 33.333 0.00 0.00 46.12 1.40
2452 2603 9.320352 GTTCAAAACCCAGTAAACACAATAAAT 57.680 29.630 0.00 0.00 0.00 1.40
2458 2609 9.849166 AACCCAGTAAACACAATAAATAATTCG 57.151 29.630 0.00 0.00 0.00 3.34
2459 2610 8.463607 ACCCAGTAAACACAATAAATAATTCGG 58.536 33.333 0.00 0.00 0.00 4.30
2460 2611 7.918562 CCCAGTAAACACAATAAATAATTCGGG 59.081 37.037 0.00 0.00 0.00 5.14
2461 2612 7.918562 CCAGTAAACACAATAAATAATTCGGGG 59.081 37.037 0.00 0.00 0.00 5.73
2462 2613 8.463607 CAGTAAACACAATAAATAATTCGGGGT 58.536 33.333 0.00 0.00 0.00 4.95
2464 2615 6.844097 AACACAATAAATAATTCGGGGTGT 57.156 33.333 0.00 0.00 34.29 4.16
2465 2616 6.202516 ACACAATAAATAATTCGGGGTGTG 57.797 37.500 0.00 0.00 32.62 3.82
2466 2617 5.126384 ACACAATAAATAATTCGGGGTGTGG 59.874 40.000 0.00 0.00 32.62 4.17
2467 2618 5.358442 CACAATAAATAATTCGGGGTGTGGA 59.642 40.000 0.00 0.00 0.00 4.02
2468 2619 5.592688 ACAATAAATAATTCGGGGTGTGGAG 59.407 40.000 0.00 0.00 0.00 3.86
2469 2620 3.732048 AAATAATTCGGGGTGTGGAGT 57.268 42.857 0.00 0.00 0.00 3.85
2470 2621 4.847990 AAATAATTCGGGGTGTGGAGTA 57.152 40.909 0.00 0.00 0.00 2.59
2471 2622 5.382664 AAATAATTCGGGGTGTGGAGTAT 57.617 39.130 0.00 0.00 0.00 2.12
2472 2623 6.503560 AAATAATTCGGGGTGTGGAGTATA 57.496 37.500 0.00 0.00 0.00 1.47
2473 2624 6.503560 AATAATTCGGGGTGTGGAGTATAA 57.496 37.500 0.00 0.00 0.00 0.98
2475 2626 5.382664 AATTCGGGGTGTGGAGTATAATT 57.617 39.130 0.00 0.00 0.00 1.40
2482 3102 3.883489 GGTGTGGAGTATAATTTCCAGCC 59.117 47.826 0.00 0.47 43.80 4.85
2489 3109 3.459598 AGTATAATTTCCAGCCCTGCTCA 59.540 43.478 0.00 0.00 36.40 4.26
2490 3110 3.607490 ATAATTTCCAGCCCTGCTCAT 57.393 42.857 0.00 0.00 36.40 2.90
2491 3111 4.729552 ATAATTTCCAGCCCTGCTCATA 57.270 40.909 0.00 0.00 36.40 2.15
2492 3112 3.607490 AATTTCCAGCCCTGCTCATAT 57.393 42.857 0.00 0.00 36.40 1.78
2493 3113 3.607490 ATTTCCAGCCCTGCTCATATT 57.393 42.857 0.00 0.00 36.40 1.28
2495 3115 4.729552 TTTCCAGCCCTGCTCATATTAT 57.270 40.909 0.00 0.00 36.40 1.28
2496 3116 4.729552 TTCCAGCCCTGCTCATATTATT 57.270 40.909 0.00 0.00 36.40 1.40
2497 3117 4.729552 TCCAGCCCTGCTCATATTATTT 57.270 40.909 0.00 0.00 36.40 1.40
2500 3120 4.021719 CCAGCCCTGCTCATATTATTTTGG 60.022 45.833 0.00 0.00 36.40 3.28
2501 3121 3.575687 AGCCCTGCTCATATTATTTTGGC 59.424 43.478 0.00 0.00 30.62 4.52
2502 3122 3.575687 GCCCTGCTCATATTATTTTGGCT 59.424 43.478 0.00 0.00 32.53 4.75
2503 3123 4.560108 GCCCTGCTCATATTATTTTGGCTG 60.560 45.833 0.00 0.00 32.53 4.85
2504 3124 4.586001 CCCTGCTCATATTATTTTGGCTGT 59.414 41.667 0.00 0.00 0.00 4.40
2505 3125 5.069516 CCCTGCTCATATTATTTTGGCTGTT 59.930 40.000 0.00 0.00 0.00 3.16
2506 3126 5.981315 CCTGCTCATATTATTTTGGCTGTTG 59.019 40.000 0.00 0.00 0.00 3.33
2507 3127 6.183360 CCTGCTCATATTATTTTGGCTGTTGA 60.183 38.462 0.00 0.00 0.00 3.18
2508 3128 6.798482 TGCTCATATTATTTTGGCTGTTGAG 58.202 36.000 0.00 0.00 33.07 3.02
2509 3129 6.377996 TGCTCATATTATTTTGGCTGTTGAGT 59.622 34.615 0.00 0.00 32.63 3.41
2510 3130 6.694411 GCTCATATTATTTTGGCTGTTGAGTG 59.306 38.462 0.00 0.00 32.63 3.51
2512 3132 4.806640 ATTATTTTGGCTGTTGAGTGGG 57.193 40.909 0.00 0.00 0.00 4.61
2513 3133 0.681175 ATTTTGGCTGTTGAGTGGGC 59.319 50.000 0.00 0.00 0.00 5.36
2514 3134 1.398958 TTTTGGCTGTTGAGTGGGCC 61.399 55.000 0.00 0.00 44.31 5.80
2515 3135 2.296945 TTTGGCTGTTGAGTGGGCCT 62.297 55.000 4.53 0.00 44.36 5.19
2517 3137 2.113986 GCTGTTGAGTGGGCCTGT 59.886 61.111 4.53 0.00 0.00 4.00
2518 3138 2.263741 GCTGTTGAGTGGGCCTGTG 61.264 63.158 4.53 0.00 0.00 3.66
2519 3139 1.149174 CTGTTGAGTGGGCCTGTGT 59.851 57.895 4.53 0.00 0.00 3.72
2522 3142 0.603975 GTTGAGTGGGCCTGTGTCTC 60.604 60.000 4.53 5.78 0.00 3.36
2523 3143 1.053835 TTGAGTGGGCCTGTGTCTCA 61.054 55.000 4.53 8.29 34.08 3.27
2525 3145 0.321122 GAGTGGGCCTGTGTCTCAAG 60.321 60.000 4.53 0.00 0.00 3.02
2527 3147 0.603975 GTGGGCCTGTGTCTCAAGTC 60.604 60.000 4.53 0.00 0.00 3.01
2529 3149 1.374758 GGCCTGTGTCTCAAGTCCG 60.375 63.158 0.00 0.00 0.00 4.79
2530 3150 1.666011 GCCTGTGTCTCAAGTCCGA 59.334 57.895 0.00 0.00 0.00 4.55
2531 3151 0.033504 GCCTGTGTCTCAAGTCCGAA 59.966 55.000 0.00 0.00 0.00 4.30
2532 3152 1.937108 GCCTGTGTCTCAAGTCCGAAG 60.937 57.143 0.00 0.00 0.00 3.79
2534 3154 2.352225 CCTGTGTCTCAAGTCCGAAGAG 60.352 54.545 0.00 0.00 0.00 2.85
2535 3155 2.294791 CTGTGTCTCAAGTCCGAAGAGT 59.705 50.000 0.00 0.00 0.00 3.24
2536 3156 3.483421 TGTGTCTCAAGTCCGAAGAGTA 58.517 45.455 0.00 0.00 0.00 2.59
2537 3157 3.502595 TGTGTCTCAAGTCCGAAGAGTAG 59.497 47.826 0.00 0.00 0.00 2.57
2539 3159 2.488545 GTCTCAAGTCCGAAGAGTAGCA 59.511 50.000 0.00 0.00 0.00 3.49
2540 3160 3.057456 GTCTCAAGTCCGAAGAGTAGCAA 60.057 47.826 0.00 0.00 0.00 3.91
2541 3161 3.191581 TCTCAAGTCCGAAGAGTAGCAAG 59.808 47.826 0.00 0.00 0.00 4.01
2542 3162 3.154710 TCAAGTCCGAAGAGTAGCAAGA 58.845 45.455 0.00 0.00 0.00 3.02
2543 3163 3.764434 TCAAGTCCGAAGAGTAGCAAGAT 59.236 43.478 0.00 0.00 0.00 2.40
2544 3164 3.791973 AGTCCGAAGAGTAGCAAGATG 57.208 47.619 0.00 0.00 0.00 2.90
2545 3165 3.093057 AGTCCGAAGAGTAGCAAGATGT 58.907 45.455 0.00 0.00 0.00 3.06
2546 3166 3.511934 AGTCCGAAGAGTAGCAAGATGTT 59.488 43.478 0.00 0.00 0.00 2.71
2547 3167 3.614616 GTCCGAAGAGTAGCAAGATGTTG 59.385 47.826 0.00 0.00 36.67 3.33
2548 3168 3.258372 TCCGAAGAGTAGCAAGATGTTGT 59.742 43.478 4.33 0.00 35.92 3.32
2550 3170 3.614616 CGAAGAGTAGCAAGATGTTGTCC 59.385 47.826 4.33 0.00 35.92 4.02
2551 3171 4.569943 GAAGAGTAGCAAGATGTTGTCCA 58.430 43.478 4.33 0.00 35.92 4.02
2552 3172 4.199432 AGAGTAGCAAGATGTTGTCCAG 57.801 45.455 4.33 0.00 35.92 3.86
2553 3173 2.675348 GAGTAGCAAGATGTTGTCCAGC 59.325 50.000 4.33 0.00 35.92 4.85
2554 3174 1.740025 GTAGCAAGATGTTGTCCAGCC 59.260 52.381 4.33 0.00 35.92 4.85
2555 3175 0.610232 AGCAAGATGTTGTCCAGCCC 60.610 55.000 4.33 0.00 35.92 5.19
2558 3178 1.004044 CAAGATGTTGTCCAGCCCTCT 59.996 52.381 0.00 0.00 0.00 3.69
2559 3179 0.908198 AGATGTTGTCCAGCCCTCTC 59.092 55.000 0.00 0.00 0.00 3.20
2560 3180 0.107459 GATGTTGTCCAGCCCTCTCC 60.107 60.000 0.00 0.00 0.00 3.71
2561 3181 1.566298 ATGTTGTCCAGCCCTCTCCC 61.566 60.000 0.00 0.00 0.00 4.30
2562 3182 2.206900 TTGTCCAGCCCTCTCCCA 59.793 61.111 0.00 0.00 0.00 4.37
2563 3183 1.229951 TTGTCCAGCCCTCTCCCAT 60.230 57.895 0.00 0.00 0.00 4.00
2564 3184 0.044092 TTGTCCAGCCCTCTCCCATA 59.956 55.000 0.00 0.00 0.00 2.74
2565 3185 0.399091 TGTCCAGCCCTCTCCCATAG 60.399 60.000 0.00 0.00 0.00 2.23
2567 3187 0.343372 TCCAGCCCTCTCCCATAGTT 59.657 55.000 0.00 0.00 0.00 2.24
2569 3189 0.390860 CAGCCCTCTCCCATAGTTCG 59.609 60.000 0.00 0.00 0.00 3.95
2570 3190 0.760945 AGCCCTCTCCCATAGTTCGG 60.761 60.000 0.00 0.00 0.00 4.30
2571 3191 0.759436 GCCCTCTCCCATAGTTCGGA 60.759 60.000 0.00 0.00 0.00 4.55
2572 3192 1.041437 CCCTCTCCCATAGTTCGGAC 58.959 60.000 0.00 0.00 0.00 4.79
2573 3193 1.688311 CCCTCTCCCATAGTTCGGACA 60.688 57.143 0.00 0.00 0.00 4.02
2583 3203 4.512944 CCATAGTTCGGACATTTGGATGAG 59.487 45.833 0.00 0.00 36.73 2.90
2585 3205 3.600388 AGTTCGGACATTTGGATGAGTC 58.400 45.455 0.00 0.00 36.73 3.36
2615 3235 6.096001 GGAGCATGAATTCAATATGGTATCCC 59.904 42.308 13.09 6.26 33.19 3.85
2619 3239 7.039504 GCATGAATTCAATATGGTATCCCAGTT 60.040 37.037 13.09 0.00 46.15 3.16
2625 3245 7.316393 TCAATATGGTATCCCAGTTAAGAGG 57.684 40.000 0.00 0.00 46.15 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.562505 GCATATGCAGCAGAATTACAGC 58.437 45.455 22.84 0.00 41.59 4.40
35 36 3.756933 AGCAAGTCCAAACATTTGCAT 57.243 38.095 10.23 0.00 46.20 3.96
41 42 5.316167 TGAGACATAAGCAAGTCCAAACAT 58.684 37.500 0.00 0.00 35.38 2.71
46 47 5.316167 ACAAATGAGACATAAGCAAGTCCA 58.684 37.500 0.00 0.00 35.38 4.02
64 65 6.342906 CCACATGGCAAGATCAAATACAAAT 58.657 36.000 0.00 0.00 0.00 2.32
100 101 2.241685 AGAGAAGGTTAGAGCCCGACTA 59.758 50.000 0.00 0.00 0.00 2.59
103 104 1.285373 AGAGAGAAGGTTAGAGCCCGA 59.715 52.381 0.00 0.00 0.00 5.14
107 108 7.065204 CCATTTTTGTAGAGAGAAGGTTAGAGC 59.935 40.741 0.00 0.00 0.00 4.09
113 114 5.073144 TGGTCCATTTTTGTAGAGAGAAGGT 59.927 40.000 0.00 0.00 0.00 3.50
125 126 2.791383 TGAAGCGTGGTCCATTTTTG 57.209 45.000 0.00 0.00 0.00 2.44
141 143 3.136443 TGCTCTCCTCACCTTCTTTTGAA 59.864 43.478 0.00 0.00 36.89 2.69
153 155 0.247460 CCACGTGAATGCTCTCCTCA 59.753 55.000 19.30 0.00 0.00 3.86
157 159 0.532573 TCCTCCACGTGAATGCTCTC 59.467 55.000 19.30 0.00 0.00 3.20
169 171 4.416738 GCAGCCACCCTCCTCCAC 62.417 72.222 0.00 0.00 0.00 4.02
170 172 4.980592 TGCAGCCACCCTCCTCCA 62.981 66.667 0.00 0.00 0.00 3.86
172 174 0.613012 AAATTGCAGCCACCCTCCTC 60.613 55.000 0.00 0.00 0.00 3.71
173 175 0.704076 TAAATTGCAGCCACCCTCCT 59.296 50.000 0.00 0.00 0.00 3.69
180 182 1.559368 ACATGCCTAAATTGCAGCCA 58.441 45.000 0.00 0.00 42.92 4.75
185 187 4.159506 TGGGTAGAAACATGCCTAAATTGC 59.840 41.667 0.00 0.00 0.00 3.56
234 236 6.014669 TGTGAATGGGCTAACTGCTAATTTTT 60.015 34.615 0.00 0.00 42.39 1.94
235 237 5.480073 TGTGAATGGGCTAACTGCTAATTTT 59.520 36.000 0.00 0.00 42.39 1.82
236 238 5.016173 TGTGAATGGGCTAACTGCTAATTT 58.984 37.500 0.00 0.00 42.39 1.82
237 239 4.599041 TGTGAATGGGCTAACTGCTAATT 58.401 39.130 0.00 0.00 42.39 1.40
238 240 4.235079 TGTGAATGGGCTAACTGCTAAT 57.765 40.909 0.00 0.00 42.39 1.73
239 241 3.712016 TGTGAATGGGCTAACTGCTAA 57.288 42.857 0.00 0.00 42.39 3.09
240 242 3.712016 TTGTGAATGGGCTAACTGCTA 57.288 42.857 0.00 0.00 42.39 3.49
241 243 2.584835 TTGTGAATGGGCTAACTGCT 57.415 45.000 0.00 0.00 42.39 4.24
242 244 3.658757 TTTTGTGAATGGGCTAACTGC 57.341 42.857 0.00 0.00 41.94 4.40
262 264 6.238648 GGCAACATCACTAACGGCTATATTTT 60.239 38.462 0.00 0.00 0.00 1.82
309 311 2.507643 GCGATCGCCTAGCAGTTAC 58.492 57.895 29.48 0.00 34.56 2.50
353 355 2.832498 GCTCTCATAGGGCCCCAC 59.168 66.667 21.43 0.00 0.00 4.61
354 356 2.844362 CGCTCTCATAGGGCCCCA 60.844 66.667 21.43 4.63 0.00 4.96
355 357 2.524394 TCGCTCTCATAGGGCCCC 60.524 66.667 21.43 0.00 38.04 5.80
356 358 2.737830 GTCGCTCTCATAGGGCCC 59.262 66.667 16.46 16.46 38.04 5.80
360 362 0.316278 CGTGTCGTCGCTCTCATAGG 60.316 60.000 0.00 0.00 0.00 2.57
364 366 2.251371 CACGTGTCGTCGCTCTCA 59.749 61.111 7.58 0.00 38.32 3.27
365 367 3.166630 GCACGTGTCGTCGCTCTC 61.167 66.667 18.38 0.00 38.32 3.20
379 381 8.861033 TGAGCTTGAATTCATTATAAATGCAC 57.139 30.769 9.40 4.04 0.00 4.57
389 391 5.295292 CACGAGGTATGAGCTTGAATTCATT 59.705 40.000 9.40 0.00 35.72 2.57
390 392 4.813161 CACGAGGTATGAGCTTGAATTCAT 59.187 41.667 9.40 0.00 37.73 2.57
401 403 2.607187 GGTCACAACACGAGGTATGAG 58.393 52.381 0.00 0.00 0.00 2.90
402 404 1.068125 CGGTCACAACACGAGGTATGA 60.068 52.381 0.00 0.00 0.00 2.15
411 413 5.338559 CGATGTAATTTTTCGGTCACAACAC 59.661 40.000 0.00 0.00 0.00 3.32
412 414 5.444983 CGATGTAATTTTTCGGTCACAACA 58.555 37.500 0.00 0.00 0.00 3.33
413 415 4.319901 GCGATGTAATTTTTCGGTCACAAC 59.680 41.667 0.00 0.00 33.62 3.32
416 418 3.088552 CGCGATGTAATTTTTCGGTCAC 58.911 45.455 0.00 0.00 33.62 3.67
419 421 1.735571 AGCGCGATGTAATTTTTCGGT 59.264 42.857 12.10 0.00 33.62 4.69
428 430 3.991773 ACTTTCTTGTAAGCGCGATGTAA 59.008 39.130 12.10 0.00 0.00 2.41
430 432 2.413837 ACTTTCTTGTAAGCGCGATGT 58.586 42.857 12.10 0.00 0.00 3.06
433 435 4.090930 GTCAATACTTTCTTGTAAGCGCGA 59.909 41.667 12.10 0.00 0.00 5.87
435 437 5.080068 GTGTCAATACTTTCTTGTAAGCGC 58.920 41.667 0.00 0.00 0.00 5.92
441 443 7.724061 ACAAATAGGGTGTCAATACTTTCTTGT 59.276 33.333 0.00 0.00 0.00 3.16
459 461 6.594159 AGAATCACGGTACAAGAACAAATAGG 59.406 38.462 0.00 0.00 0.00 2.57
477 529 6.331061 ACATCGGTGACTAGTTTAGAATCAC 58.669 40.000 0.65 0.00 39.16 3.06
483 535 4.091509 GTGCAACATCGGTGACTAGTTTAG 59.908 45.833 0.65 0.00 36.32 1.85
491 543 0.512952 GTGAGTGCAACATCGGTGAC 59.487 55.000 0.65 0.00 41.43 3.67
496 548 3.243128 TGCGTGAGTGCAACATCG 58.757 55.556 0.00 0.75 43.02 3.84
505 557 2.050714 CGTACCGTGTGCGTGAGT 60.051 61.111 6.41 0.00 36.93 3.41
513 566 1.593209 CCAGTGCAACGTACCGTGT 60.593 57.895 0.00 0.00 45.86 4.49
522 575 7.498443 ACCTACTAGTATATTTCCAGTGCAAC 58.502 38.462 2.33 0.00 0.00 4.17
540 593 7.095523 GCTCGTTAAATGTTTTGTGACCTACTA 60.096 37.037 0.00 0.00 0.00 1.82
541 594 6.293244 GCTCGTTAAATGTTTTGTGACCTACT 60.293 38.462 0.00 0.00 0.00 2.57
542 595 5.849604 GCTCGTTAAATGTTTTGTGACCTAC 59.150 40.000 0.00 0.00 0.00 3.18
543 596 5.527951 TGCTCGTTAAATGTTTTGTGACCTA 59.472 36.000 0.00 0.00 0.00 3.08
544 597 4.336993 TGCTCGTTAAATGTTTTGTGACCT 59.663 37.500 0.00 0.00 0.00 3.85
545 598 4.439776 GTGCTCGTTAAATGTTTTGTGACC 59.560 41.667 0.00 0.00 0.00 4.02
546 599 4.439776 GGTGCTCGTTAAATGTTTTGTGAC 59.560 41.667 0.00 0.00 0.00 3.67
547 600 4.602995 GGTGCTCGTTAAATGTTTTGTGA 58.397 39.130 0.00 0.00 0.00 3.58
548 601 3.420576 CGGTGCTCGTTAAATGTTTTGTG 59.579 43.478 0.00 0.00 0.00 3.33
552 605 1.068816 GCCGGTGCTCGTTAAATGTTT 60.069 47.619 1.90 0.00 37.11 2.83
562 615 2.353607 GAGTATCGCCGGTGCTCG 60.354 66.667 11.05 0.54 38.88 5.03
564 617 1.037493 TAATGAGTATCGCCGGTGCT 58.963 50.000 11.05 2.54 38.61 4.40
569 622 5.891451 TCCTAATCATAATGAGTATCGCCG 58.109 41.667 0.00 0.00 38.61 6.46
608 661 1.074319 GATGGTGTGCATTGCAAGCG 61.074 55.000 13.94 0.00 41.47 4.68
1271 1368 0.815734 CTCCAAGGTACGGACACGAT 59.184 55.000 0.00 0.00 44.60 3.73
1535 1632 1.168714 GCCACTTCCTTCACACATCC 58.831 55.000 0.00 0.00 0.00 3.51
1573 1670 2.372264 ACGATTTTGCTCATCAGCCAT 58.628 42.857 0.00 0.00 46.26 4.40
1614 1711 7.217200 ACCAAGTAATGTTATCTACGCATGAT 58.783 34.615 0.00 0.00 0.00 2.45
1615 1712 6.578944 ACCAAGTAATGTTATCTACGCATGA 58.421 36.000 0.00 0.00 0.00 3.07
1616 1713 6.844696 ACCAAGTAATGTTATCTACGCATG 57.155 37.500 0.00 0.00 0.00 4.06
1617 1714 7.254319 CGAAACCAAGTAATGTTATCTACGCAT 60.254 37.037 0.00 0.00 0.00 4.73
1619 1716 6.408428 CGAAACCAAGTAATGTTATCTACGC 58.592 40.000 0.00 0.00 0.00 4.42
1622 1719 9.675464 ATTTCCGAAACCAAGTAATGTTATCTA 57.325 29.630 0.00 0.00 0.00 1.98
1634 1731 7.330946 TCGATAGCATATATTTCCGAAACCAAG 59.669 37.037 0.00 0.00 0.00 3.61
1636 1733 6.693466 TCGATAGCATATATTTCCGAAACCA 58.307 36.000 0.00 0.00 0.00 3.67
1637 1734 6.255887 CCTCGATAGCATATATTTCCGAAACC 59.744 42.308 0.00 0.00 0.00 3.27
1639 1736 6.931838 ACCTCGATAGCATATATTTCCGAAA 58.068 36.000 0.00 0.00 0.00 3.46
1643 1740 7.103641 TCCAAACCTCGATAGCATATATTTCC 58.896 38.462 0.00 0.00 0.00 3.13
1646 1743 7.482169 TCTCCAAACCTCGATAGCATATATT 57.518 36.000 0.00 0.00 0.00 1.28
1651 1748 4.141620 ACATTCTCCAAACCTCGATAGCAT 60.142 41.667 0.00 0.00 0.00 3.79
1655 1752 3.197766 AGCACATTCTCCAAACCTCGATA 59.802 43.478 0.00 0.00 0.00 2.92
1656 1753 2.026822 AGCACATTCTCCAAACCTCGAT 60.027 45.455 0.00 0.00 0.00 3.59
1662 1759 4.005650 TCTCATCAGCACATTCTCCAAAC 58.994 43.478 0.00 0.00 0.00 2.93
1667 1764 3.626217 TGCAATCTCATCAGCACATTCTC 59.374 43.478 0.00 0.00 31.05 2.87
1670 1767 5.593095 AGTATTGCAATCTCATCAGCACATT 59.407 36.000 16.86 0.00 36.62 2.71
1678 1775 4.906065 TTGCCAGTATTGCAATCTCATC 57.094 40.909 16.86 4.70 43.36 2.92
1687 1784 2.095059 CAGTCCTTGTTGCCAGTATTGC 60.095 50.000 0.00 0.00 0.00 3.56
1692 1789 0.178981 ATGCAGTCCTTGTTGCCAGT 60.179 50.000 0.00 0.00 39.54 4.00
1870 1967 3.409026 AGACCAAAGCTCAACTCGAAT 57.591 42.857 0.00 0.00 0.00 3.34
1884 1982 6.680810 CAAAAATCAGCACATCTAAGACCAA 58.319 36.000 0.00 0.00 0.00 3.67
1993 2091 5.184671 TGTCAGCAACACCAAAATATATGCA 59.815 36.000 0.00 0.00 34.89 3.96
2303 2454 9.354673 AGTCCAGAACTAAATTGAAAAGAATCA 57.645 29.630 0.00 0.00 36.07 2.57
2377 2528 1.633945 ACCTAACCAGTTCACCCCATC 59.366 52.381 0.00 0.00 0.00 3.51
2378 2529 1.354368 CACCTAACCAGTTCACCCCAT 59.646 52.381 0.00 0.00 0.00 4.00
2379 2530 0.768622 CACCTAACCAGTTCACCCCA 59.231 55.000 0.00 0.00 0.00 4.96
2382 2533 2.200373 ATGCACCTAACCAGTTCACC 57.800 50.000 0.00 0.00 0.00 4.02
2384 2535 3.009033 AGCTTATGCACCTAACCAGTTCA 59.991 43.478 3.16 0.00 42.74 3.18
2385 2536 3.610911 AGCTTATGCACCTAACCAGTTC 58.389 45.455 3.16 0.00 42.74 3.01
2386 2537 3.721087 AGCTTATGCACCTAACCAGTT 57.279 42.857 3.16 0.00 42.74 3.16
2387 2538 3.347216 CAAGCTTATGCACCTAACCAGT 58.653 45.455 0.00 0.00 42.74 4.00
2388 2539 2.098117 GCAAGCTTATGCACCTAACCAG 59.902 50.000 5.50 0.00 45.70 4.00
2390 2541 2.851805 GCAAGCTTATGCACCTAACC 57.148 50.000 5.50 0.00 45.70 2.85
2398 2549 2.476854 CCTCTTCGTTGCAAGCTTATGC 60.477 50.000 0.00 0.00 46.58 3.14
2399 2550 2.744202 ACCTCTTCGTTGCAAGCTTATG 59.256 45.455 0.00 0.00 0.00 1.90
2400 2551 3.059352 ACCTCTTCGTTGCAAGCTTAT 57.941 42.857 0.00 0.00 0.00 1.73
2401 2552 2.543777 ACCTCTTCGTTGCAAGCTTA 57.456 45.000 0.00 0.00 0.00 3.09
2402 2553 1.604278 GAACCTCTTCGTTGCAAGCTT 59.396 47.619 0.00 0.00 0.00 3.74
2403 2554 1.230324 GAACCTCTTCGTTGCAAGCT 58.770 50.000 0.00 0.00 0.00 3.74
2404 2555 0.944386 TGAACCTCTTCGTTGCAAGC 59.056 50.000 0.00 0.00 0.00 4.01
2405 2556 1.532868 CCTGAACCTCTTCGTTGCAAG 59.467 52.381 0.00 0.00 0.00 4.01
2408 2559 0.250338 ACCCTGAACCTCTTCGTTGC 60.250 55.000 0.00 0.00 0.00 4.17
2409 2560 2.143925 GAACCCTGAACCTCTTCGTTG 58.856 52.381 0.00 0.00 0.00 4.10
2410 2561 1.766496 TGAACCCTGAACCTCTTCGTT 59.234 47.619 0.00 0.00 0.00 3.85
2411 2562 1.420430 TGAACCCTGAACCTCTTCGT 58.580 50.000 0.00 0.00 0.00 3.85
2412 2563 2.543777 TTGAACCCTGAACCTCTTCG 57.456 50.000 0.00 0.00 0.00 3.79
2413 2564 3.318275 GGTTTTGAACCCTGAACCTCTTC 59.682 47.826 0.00 0.00 46.12 2.87
2415 2566 2.945456 GGTTTTGAACCCTGAACCTCT 58.055 47.619 0.00 0.00 46.12 3.69
2426 2577 8.705048 TTTATTGTGTTTACTGGGTTTTGAAC 57.295 30.769 0.00 0.00 0.00 3.18
2433 2584 8.463607 CCGAATTATTTATTGTGTTTACTGGGT 58.536 33.333 0.00 0.00 0.00 4.51
2434 2585 7.918562 CCCGAATTATTTATTGTGTTTACTGGG 59.081 37.037 0.00 0.00 0.00 4.45
2436 2587 8.463607 ACCCCGAATTATTTATTGTGTTTACTG 58.536 33.333 0.00 0.00 0.00 2.74
2438 2589 8.245491 ACACCCCGAATTATTTATTGTGTTTAC 58.755 33.333 0.00 0.00 30.00 2.01
2439 2590 8.244802 CACACCCCGAATTATTTATTGTGTTTA 58.755 33.333 0.00 0.00 31.16 2.01
2440 2591 7.093992 CACACCCCGAATTATTTATTGTGTTT 58.906 34.615 0.00 0.00 31.16 2.83
2441 2592 6.350612 CCACACCCCGAATTATTTATTGTGTT 60.351 38.462 0.00 0.00 31.16 3.32
2443 2594 5.358442 TCCACACCCCGAATTATTTATTGTG 59.642 40.000 0.00 0.00 0.00 3.33
2444 2595 5.511363 TCCACACCCCGAATTATTTATTGT 58.489 37.500 0.00 0.00 0.00 2.71
2445 2596 5.592688 ACTCCACACCCCGAATTATTTATTG 59.407 40.000 0.00 0.00 0.00 1.90
2446 2597 5.762279 ACTCCACACCCCGAATTATTTATT 58.238 37.500 0.00 0.00 0.00 1.40
2447 2598 5.382664 ACTCCACACCCCGAATTATTTAT 57.617 39.130 0.00 0.00 0.00 1.40
2448 2599 4.847990 ACTCCACACCCCGAATTATTTA 57.152 40.909 0.00 0.00 0.00 1.40
2451 2602 6.697641 ATTATACTCCACACCCCGAATTAT 57.302 37.500 0.00 0.00 0.00 1.28
2452 2603 6.503560 AATTATACTCCACACCCCGAATTA 57.496 37.500 0.00 0.00 0.00 1.40
2453 2604 5.382664 AATTATACTCCACACCCCGAATT 57.617 39.130 0.00 0.00 0.00 2.17
2454 2605 5.374071 GAAATTATACTCCACACCCCGAAT 58.626 41.667 0.00 0.00 0.00 3.34
2455 2606 4.384427 GGAAATTATACTCCACACCCCGAA 60.384 45.833 0.00 0.00 0.00 4.30
2456 2607 3.135167 GGAAATTATACTCCACACCCCGA 59.865 47.826 0.00 0.00 0.00 5.14
2457 2608 3.118186 TGGAAATTATACTCCACACCCCG 60.118 47.826 0.00 0.00 36.79 5.73
2458 2609 4.461198 CTGGAAATTATACTCCACACCCC 58.539 47.826 0.00 0.00 36.79 4.95
2459 2610 3.883489 GCTGGAAATTATACTCCACACCC 59.117 47.826 0.00 0.00 36.79 4.61
2460 2611 3.883489 GGCTGGAAATTATACTCCACACC 59.117 47.826 0.00 0.00 36.79 4.16
2461 2612 3.883489 GGGCTGGAAATTATACTCCACAC 59.117 47.826 0.00 0.00 36.79 3.82
2462 2613 3.785887 AGGGCTGGAAATTATACTCCACA 59.214 43.478 0.00 0.00 36.79 4.17
2464 2615 3.435026 GCAGGGCTGGAAATTATACTCCA 60.435 47.826 0.00 0.00 39.47 3.86
2465 2616 3.149981 GCAGGGCTGGAAATTATACTCC 58.850 50.000 0.00 0.00 0.00 3.85
2466 2617 4.068599 GAGCAGGGCTGGAAATTATACTC 58.931 47.826 0.00 0.00 39.88 2.59
2467 2618 3.459598 TGAGCAGGGCTGGAAATTATACT 59.540 43.478 0.00 0.00 39.88 2.12
2468 2619 3.820557 TGAGCAGGGCTGGAAATTATAC 58.179 45.455 0.00 0.00 39.88 1.47
2469 2620 4.729552 ATGAGCAGGGCTGGAAATTATA 57.270 40.909 0.00 0.00 39.88 0.98
2470 2621 3.607490 ATGAGCAGGGCTGGAAATTAT 57.393 42.857 0.00 0.00 39.88 1.28
2471 2622 4.729552 ATATGAGCAGGGCTGGAAATTA 57.270 40.909 0.00 0.00 39.88 1.40
2472 2623 3.607490 ATATGAGCAGGGCTGGAAATT 57.393 42.857 0.00 0.00 39.88 1.82
2473 2624 3.607490 AATATGAGCAGGGCTGGAAAT 57.393 42.857 0.00 0.00 39.88 2.17
2475 2626 4.729552 AATAATATGAGCAGGGCTGGAA 57.270 40.909 0.00 0.00 39.88 3.53
2482 3102 5.779529 ACAGCCAAAATAATATGAGCAGG 57.220 39.130 0.00 0.00 0.00 4.85
2489 3109 5.163416 GCCCACTCAACAGCCAAAATAATAT 60.163 40.000 0.00 0.00 0.00 1.28
2490 3110 4.159506 GCCCACTCAACAGCCAAAATAATA 59.840 41.667 0.00 0.00 0.00 0.98
2491 3111 3.055891 GCCCACTCAACAGCCAAAATAAT 60.056 43.478 0.00 0.00 0.00 1.28
2492 3112 2.298729 GCCCACTCAACAGCCAAAATAA 59.701 45.455 0.00 0.00 0.00 1.40
2493 3113 1.892474 GCCCACTCAACAGCCAAAATA 59.108 47.619 0.00 0.00 0.00 1.40
2495 3115 1.398958 GGCCCACTCAACAGCCAAAA 61.399 55.000 0.00 0.00 45.07 2.44
2496 3116 1.832167 GGCCCACTCAACAGCCAAA 60.832 57.895 0.00 0.00 45.07 3.28
2497 3117 2.203480 GGCCCACTCAACAGCCAA 60.203 61.111 0.00 0.00 45.07 4.52
2500 3120 2.113986 ACAGGCCCACTCAACAGC 59.886 61.111 0.00 0.00 0.00 4.40
2501 3121 0.886490 GACACAGGCCCACTCAACAG 60.886 60.000 0.00 0.00 0.00 3.16
2502 3122 1.148273 GACACAGGCCCACTCAACA 59.852 57.895 0.00 0.00 0.00 3.33
2503 3123 0.603975 GAGACACAGGCCCACTCAAC 60.604 60.000 0.00 0.00 0.00 3.18
2504 3124 1.053835 TGAGACACAGGCCCACTCAA 61.054 55.000 0.00 0.00 35.20 3.02
2505 3125 1.053835 TTGAGACACAGGCCCACTCA 61.054 55.000 0.00 4.97 36.11 3.41
2506 3126 0.321122 CTTGAGACACAGGCCCACTC 60.321 60.000 0.00 2.11 0.00 3.51
2507 3127 1.056700 ACTTGAGACACAGGCCCACT 61.057 55.000 0.00 0.00 0.00 4.00
2508 3128 0.603975 GACTTGAGACACAGGCCCAC 60.604 60.000 0.00 0.00 0.00 4.61
2509 3129 1.754745 GACTTGAGACACAGGCCCA 59.245 57.895 0.00 0.00 0.00 5.36
2510 3130 1.003233 GGACTTGAGACACAGGCCC 60.003 63.158 0.00 0.00 0.00 5.80
2512 3132 0.033504 TTCGGACTTGAGACACAGGC 59.966 55.000 0.00 0.00 0.00 4.85
2513 3133 1.613925 TCTTCGGACTTGAGACACAGG 59.386 52.381 0.00 0.00 0.00 4.00
2514 3134 2.294791 ACTCTTCGGACTTGAGACACAG 59.705 50.000 8.29 0.00 0.00 3.66
2515 3135 2.307768 ACTCTTCGGACTTGAGACACA 58.692 47.619 8.29 0.00 0.00 3.72
2517 3137 2.488545 GCTACTCTTCGGACTTGAGACA 59.511 50.000 8.29 0.00 0.00 3.41
2518 3138 2.488545 TGCTACTCTTCGGACTTGAGAC 59.511 50.000 8.29 0.90 0.00 3.36
2519 3139 2.791655 TGCTACTCTTCGGACTTGAGA 58.208 47.619 8.29 0.00 0.00 3.27
2522 3142 3.577649 TCTTGCTACTCTTCGGACTTG 57.422 47.619 0.00 0.00 0.00 3.16
2523 3143 3.511934 ACATCTTGCTACTCTTCGGACTT 59.488 43.478 0.00 0.00 0.00 3.01
2525 3145 3.512033 ACATCTTGCTACTCTTCGGAC 57.488 47.619 0.00 0.00 0.00 4.79
2527 3147 3.589988 ACAACATCTTGCTACTCTTCGG 58.410 45.455 0.00 0.00 0.00 4.30
2529 3149 4.569943 TGGACAACATCTTGCTACTCTTC 58.430 43.478 0.00 0.00 0.00 2.87
2530 3150 4.573900 CTGGACAACATCTTGCTACTCTT 58.426 43.478 0.00 0.00 0.00 2.85
2531 3151 3.618507 GCTGGACAACATCTTGCTACTCT 60.619 47.826 0.00 0.00 0.00 3.24
2532 3152 2.675348 GCTGGACAACATCTTGCTACTC 59.325 50.000 0.00 0.00 0.00 2.59
2534 3154 1.740025 GGCTGGACAACATCTTGCTAC 59.260 52.381 0.00 0.00 0.00 3.58
2535 3155 1.340017 GGGCTGGACAACATCTTGCTA 60.340 52.381 0.00 0.00 0.00 3.49
2536 3156 0.610232 GGGCTGGACAACATCTTGCT 60.610 55.000 0.00 0.00 0.00 3.91
2537 3157 0.610232 AGGGCTGGACAACATCTTGC 60.610 55.000 0.00 0.00 0.00 4.01
2539 3159 1.280421 GAGAGGGCTGGACAACATCTT 59.720 52.381 0.00 0.00 0.00 2.40
2540 3160 0.908198 GAGAGGGCTGGACAACATCT 59.092 55.000 0.00 0.00 0.00 2.90
2541 3161 0.107459 GGAGAGGGCTGGACAACATC 60.107 60.000 0.00 0.00 0.00 3.06
2542 3162 1.566298 GGGAGAGGGCTGGACAACAT 61.566 60.000 0.00 0.00 0.00 2.71
2543 3163 2.224159 GGGAGAGGGCTGGACAACA 61.224 63.158 0.00 0.00 0.00 3.33
2544 3164 1.566298 ATGGGAGAGGGCTGGACAAC 61.566 60.000 0.00 0.00 0.00 3.32
2545 3165 0.044092 TATGGGAGAGGGCTGGACAA 59.956 55.000 0.00 0.00 0.00 3.18
2546 3166 0.399091 CTATGGGAGAGGGCTGGACA 60.399 60.000 0.00 0.00 0.00 4.02
2547 3167 0.399233 ACTATGGGAGAGGGCTGGAC 60.399 60.000 0.00 0.00 0.00 4.02
2548 3168 0.343372 AACTATGGGAGAGGGCTGGA 59.657 55.000 0.00 0.00 0.00 3.86
2550 3170 0.390860 CGAACTATGGGAGAGGGCTG 59.609 60.000 0.00 0.00 0.00 4.85
2551 3171 0.760945 CCGAACTATGGGAGAGGGCT 60.761 60.000 0.00 0.00 0.00 5.19
2552 3172 0.759436 TCCGAACTATGGGAGAGGGC 60.759 60.000 0.00 0.00 0.00 5.19
2553 3173 1.041437 GTCCGAACTATGGGAGAGGG 58.959 60.000 0.00 0.00 33.66 4.30
2554 3174 1.776662 TGTCCGAACTATGGGAGAGG 58.223 55.000 0.00 0.00 33.66 3.69
2555 3175 4.122776 CAAATGTCCGAACTATGGGAGAG 58.877 47.826 0.00 0.00 33.66 3.20
2558 3178 2.841266 TCCAAATGTCCGAACTATGGGA 59.159 45.455 0.00 0.00 0.00 4.37
2559 3179 3.275617 TCCAAATGTCCGAACTATGGG 57.724 47.619 0.00 0.00 0.00 4.00
2560 3180 4.450976 TCATCCAAATGTCCGAACTATGG 58.549 43.478 0.00 0.00 34.32 2.74
2561 3181 5.118990 ACTCATCCAAATGTCCGAACTATG 58.881 41.667 0.00 0.00 34.32 2.23
2562 3182 5.359194 ACTCATCCAAATGTCCGAACTAT 57.641 39.130 0.00 0.00 34.32 2.12
2563 3183 4.676986 CGACTCATCCAAATGTCCGAACTA 60.677 45.833 0.00 0.00 34.32 2.24
2564 3184 3.600388 GACTCATCCAAATGTCCGAACT 58.400 45.455 0.00 0.00 34.32 3.01
2565 3185 2.348666 CGACTCATCCAAATGTCCGAAC 59.651 50.000 0.00 0.00 34.32 3.95
2567 3187 1.134818 CCGACTCATCCAAATGTCCGA 60.135 52.381 0.00 0.00 34.32 4.55
2569 3189 1.017387 GCCGACTCATCCAAATGTCC 58.983 55.000 0.00 0.00 34.32 4.02
2570 3190 1.667724 CAGCCGACTCATCCAAATGTC 59.332 52.381 0.00 0.00 34.32 3.06
2571 3191 1.679944 CCAGCCGACTCATCCAAATGT 60.680 52.381 0.00 0.00 34.32 2.71
2572 3192 1.019673 CCAGCCGACTCATCCAAATG 58.980 55.000 0.00 0.00 0.00 2.32
2573 3193 0.911769 TCCAGCCGACTCATCCAAAT 59.088 50.000 0.00 0.00 0.00 2.32
2583 3203 0.659957 GAATTCATGCTCCAGCCGAC 59.340 55.000 0.00 0.00 41.18 4.79
2585 3205 1.097232 TTGAATTCATGCTCCAGCCG 58.903 50.000 9.40 0.00 41.18 5.52
2619 3239 8.489489 AGAGCATATTGAATTCAAGACCTCTTA 58.511 33.333 26.38 15.44 36.54 2.10
2625 3245 7.416022 CCAGAAGAGCATATTGAATTCAAGAC 58.584 38.462 24.17 13.77 39.47 3.01


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

AutoCloner maintained by Alex Coulton.