Multiple sequence alignment - TraesCS3D01G408800

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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 TraesCS3D01G408800 chr3D 100.000 3899 0 0 1 3899 523168018 523171916 0.000000e+00 7201
1 TraesCS3D01G408800 chr3D 88.174 482 28 12 1 460 170801231 170800757 7.370000e-152 547
2 TraesCS3D01G408800 chr3B 86.541 1694 99 66 460 2095 689683014 689684636 0.000000e+00 1746
3 TraesCS3D01G408800 chr3B 92.821 1170 51 21 2116 3268 689684762 689685915 0.000000e+00 1664
4 TraesCS3D01G408800 chr3B 89.355 620 23 14 3314 3899 689685994 689686604 0.000000e+00 739
5 TraesCS3D01G408800 chr3A 90.407 1178 59 29 543 1708 657942765 657943900 0.000000e+00 1500
6 TraesCS3D01G408800 chr3A 89.649 1169 59 29 2748 3899 657945065 657946188 0.000000e+00 1432
7 TraesCS3D01G408800 chr3A 94.872 663 19 8 2098 2748 657944338 657944997 0.000000e+00 1022
8 TraesCS3D01G408800 chr3A 95.890 219 5 1 1877 2095 657944008 657944222 6.200000e-93 351
9 TraesCS3D01G408800 chr3A 82.397 267 45 2 196 460 84193470 84193204 8.430000e-57 231
10 TraesCS3D01G408800 chr6D 87.805 492 31 15 1 463 414263829 414263338 2.050000e-152 549
11 TraesCS3D01G408800 chr6D 87.759 482 33 8 1 460 372770512 372770035 1.230000e-149 540
12 TraesCS3D01G408800 chr2D 87.474 487 33 11 1 460 65658223 65658708 1.590000e-148 536
13 TraesCS3D01G408800 chr2D 87.552 482 36 8 1 460 544580977 544581456 1.590000e-148 536
14 TraesCS3D01G408800 chr2D 88.496 226 25 1 236 460 193272042 193272267 4.960000e-69 272
15 TraesCS3D01G408800 chr1D 87.295 488 33 10 1 460 447062517 447062031 7.420000e-147 531
16 TraesCS3D01G408800 chr5D 87.190 484 35 14 1 462 428668533 428668055 3.450000e-145 525
17 TraesCS3D01G408800 chr5D 85.412 473 41 12 1 445 400367286 400367758 2.120000e-127 466
18 TraesCS3D01G408800 chr5D 84.524 504 36 17 1 464 455610990 455611491 9.870000e-126 460
19 TraesCS3D01G408800 chr5D 83.681 288 27 9 197 465 434336547 434336261 1.800000e-63 254
20 TraesCS3D01G408800 chr5D 84.167 240 20 8 236 462 467618984 467619218 2.360000e-52 217
21 TraesCS3D01G408800 chr5B 86.957 483 34 11 1 460 639224485 639224009 2.080000e-142 516
22 TraesCS3D01G408800 chr2A 86.182 275 27 7 196 460 758051882 758051609 1.770000e-73 287
23 TraesCS3D01G408800 chr2B 86.017 236 30 3 196 430 549556409 549556642 2.330000e-62 250
24 TraesCS3D01G408800 chr6A 83.922 255 39 2 210 462 373999261 373999515 3.890000e-60 243
25 TraesCS3D01G408800 chr6B 82.437 279 29 13 196 460 135400511 135400783 3.920000e-55 226
26 TraesCS3D01G408800 chr1A 86.364 154 19 2 311 462 412453548 412453701 2.410000e-37 167


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 TraesCS3D01G408800 chr3D 523168018 523171916 3898 False 7201.00 7201 100.000000 1 3899 1 chr3D.!!$F1 3898
1 TraesCS3D01G408800 chr3B 689683014 689686604 3590 False 1383.00 1746 89.572333 460 3899 3 chr3B.!!$F1 3439
2 TraesCS3D01G408800 chr3A 657942765 657946188 3423 False 1076.25 1500 92.704500 543 3899 4 chr3A.!!$F1 3356
3 TraesCS3D01G408800 chr5D 455610990 455611491 501 False 460.00 460 84.524000 1 464 1 chr5D.!!$F2 463

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
948 1005 0.390866 ACAGATTCGCTCAGCACAGG 60.391 55.0 0.00 0.0 0.00 4.00 F
1180 1268 0.180878 TCGAGATGCATGGCAATGGA 59.819 50.0 2.46 0.0 43.62 3.41 F
2448 2689 0.109689 GTCTCGCAGCACGTAAGAGT 60.110 55.0 0.00 0.0 44.19 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2243 0.103208 CGTGGATGCTGTAGTCCCTC 59.897 60.0 0.0 0.0 33.45 4.30 R
2458 2699 0.734889 GGCCATCACAACTTGGATCG 59.265 55.0 0.0 0.0 34.81 3.69 R
3256 3589 0.321919 TGGATGTGGTTCTGAGCTGC 60.322 55.0 0.0 0.0 0.00 5.25 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
44 45 1.481871 GTCGGAGGAGGACATTACCA 58.518 55.000 0.00 0.00 34.56 3.25
54 55 2.904434 AGGACATTACCAAGTCGGAGTT 59.096 45.455 0.00 0.00 38.63 3.01
154 158 3.000727 CCGGCGAGTAGTTCATCTTTTT 58.999 45.455 9.30 0.00 0.00 1.94
191 214 1.380920 GGTACTACCTCTGGCCGGT 60.381 63.158 12.43 8.91 34.73 5.28
307 335 2.126965 CGCGTCCGTCTCGTTTCT 60.127 61.111 0.00 0.00 0.00 2.52
310 338 2.426183 CGTCCGTCTCGTTTCTGCG 61.426 63.158 0.00 0.00 0.00 5.18
316 344 3.827784 CTCGTTTCTGCGCCGACG 61.828 66.667 4.18 10.25 44.07 5.12
317 345 4.634133 TCGTTTCTGCGCCGACGT 62.634 61.111 4.18 0.00 42.83 4.34
348 377 1.271127 AAAAATGGGCCGGGAATGGG 61.271 55.000 2.18 0.00 0.00 4.00
405 445 3.284449 GCCGCCTTTTGTGTCCGT 61.284 61.111 0.00 0.00 0.00 4.69
406 446 1.962306 GCCGCCTTTTGTGTCCGTA 60.962 57.895 0.00 0.00 0.00 4.02
407 447 1.303091 GCCGCCTTTTGTGTCCGTAT 61.303 55.000 0.00 0.00 0.00 3.06
413 453 1.652124 CTTTTGTGTCCGTATCGACCG 59.348 52.381 0.00 0.00 31.35 4.79
430 471 2.895372 GAAACGGATGGCGCGGAT 60.895 61.111 8.83 0.00 0.00 4.18
450 491 1.004161 TGAAATGGGTCGCCTCATTGA 59.996 47.619 0.00 0.00 34.28 2.57
479 520 7.422399 TGCTCTAAACCACTTTTTATCAACAC 58.578 34.615 0.00 0.00 0.00 3.32
481 522 7.918562 GCTCTAAACCACTTTTTATCAACACAA 59.081 33.333 0.00 0.00 0.00 3.33
482 523 9.796120 CTCTAAACCACTTTTTATCAACACAAA 57.204 29.630 0.00 0.00 0.00 2.83
485 526 6.843069 ACCACTTTTTATCAACACAAATGC 57.157 33.333 0.00 0.00 0.00 3.56
486 527 5.461737 ACCACTTTTTATCAACACAAATGCG 59.538 36.000 0.00 0.00 0.00 4.73
487 528 5.461737 CCACTTTTTATCAACACAAATGCGT 59.538 36.000 0.00 0.00 0.00 5.24
488 529 6.019156 CCACTTTTTATCAACACAAATGCGTT 60.019 34.615 0.00 0.00 0.00 4.84
489 530 7.168302 CCACTTTTTATCAACACAAATGCGTTA 59.832 33.333 0.00 0.00 0.00 3.18
490 531 8.535592 CACTTTTTATCAACACAAATGCGTTAA 58.464 29.630 0.00 0.00 0.00 2.01
491 532 8.536407 ACTTTTTATCAACACAAATGCGTTAAC 58.464 29.630 0.00 0.00 0.00 2.01
492 533 8.635877 TTTTTATCAACACAAATGCGTTAACT 57.364 26.923 3.71 0.00 0.00 2.24
493 534 9.731819 TTTTTATCAACACAAATGCGTTAACTA 57.268 25.926 3.71 0.00 0.00 2.24
494 535 9.731819 TTTTATCAACACAAATGCGTTAACTAA 57.268 25.926 3.71 0.00 0.00 2.24
495 536 9.900710 TTTATCAACACAAATGCGTTAACTAAT 57.099 25.926 3.71 0.00 0.00 1.73
512 553 8.680903 GTTAACTAATACTACTAGCCAGACACA 58.319 37.037 0.00 0.00 0.00 3.72
537 578 9.330063 CAGAAGAGCATCAGGTGTAAATAAATA 57.670 33.333 0.00 0.00 37.82 1.40
549 590 9.528018 AGGTGTAAATAAATAAATCAAATGGCG 57.472 29.630 0.00 0.00 0.00 5.69
550 591 9.308318 GGTGTAAATAAATAAATCAAATGGCGT 57.692 29.630 0.00 0.00 0.00 5.68
572 614 1.067354 CCAGATCCCAAGCTTTTGTGC 60.067 52.381 0.00 0.00 0.00 4.57
612 658 3.488310 AGCATCGCGTACGTTTAATAAGG 59.512 43.478 17.90 0.00 41.18 2.69
613 659 3.486841 GCATCGCGTACGTTTAATAAGGA 59.513 43.478 17.90 1.51 41.18 3.36
669 715 8.928733 CGGTTTGATTTGATCTGATTTGATTTT 58.071 29.630 0.00 0.00 0.00 1.82
764 811 4.193334 TGAGCAGGCCGATCGACG 62.193 66.667 18.66 1.12 42.18 5.12
784 831 2.094390 CGCTAGTGGTGCACCTTTACTA 60.094 50.000 34.75 29.19 34.49 1.82
785 832 3.522553 GCTAGTGGTGCACCTTTACTAG 58.477 50.000 35.69 35.69 40.41 2.57
787 834 3.679824 AGTGGTGCACCTTTACTAGAC 57.320 47.619 34.75 21.88 34.49 2.59
813 863 2.790123 GCAACGACATGCATGATCACAG 60.790 50.000 32.75 17.20 45.70 3.66
821 871 2.439409 TGCATGATCACAGGACCTTTG 58.561 47.619 0.00 0.78 0.00 2.77
824 874 3.424703 CATGATCACAGGACCTTTGGTT 58.575 45.455 7.80 0.00 35.25 3.67
841 891 3.041508 GGTTTGTGACCTCACTACTCC 57.958 52.381 6.97 1.95 46.55 3.85
842 892 2.633481 GGTTTGTGACCTCACTACTCCT 59.367 50.000 6.97 0.00 46.55 3.69
843 893 3.071167 GGTTTGTGACCTCACTACTCCTT 59.929 47.826 6.97 0.00 46.55 3.36
844 894 4.308265 GTTTGTGACCTCACTACTCCTTC 58.692 47.826 6.97 0.00 46.55 3.46
913 967 2.606587 TTCCCTTCCTGCCTGCCTC 61.607 63.158 0.00 0.00 0.00 4.70
940 997 3.470562 GTTCGTTCAAACAGATTCGCTC 58.529 45.455 0.00 0.00 0.00 5.03
945 1002 1.800586 TCAAACAGATTCGCTCAGCAC 59.199 47.619 0.00 0.00 0.00 4.40
946 1003 1.532437 CAAACAGATTCGCTCAGCACA 59.468 47.619 0.00 0.00 0.00 4.57
947 1004 1.436600 AACAGATTCGCTCAGCACAG 58.563 50.000 0.00 0.00 0.00 3.66
948 1005 0.390866 ACAGATTCGCTCAGCACAGG 60.391 55.000 0.00 0.00 0.00 4.00
999 1058 2.880963 AGAGAAGCGATCAGTTAGCC 57.119 50.000 0.00 0.00 0.00 3.93
1142 1204 7.433131 GTCGTGTAAACGTCAATAATCCATCTA 59.567 37.037 5.14 0.00 0.00 1.98
1143 1205 7.433131 TCGTGTAAACGTCAATAATCCATCTAC 59.567 37.037 5.14 0.00 0.00 2.59
1144 1206 7.434307 CGTGTAAACGTCAATAATCCATCTACT 59.566 37.037 0.00 0.00 0.00 2.57
1167 1229 7.828712 ACTAGTAGCTTGTTAAGTTTCGAGAT 58.171 34.615 0.00 0.00 0.00 2.75
1180 1268 0.180878 TCGAGATGCATGGCAATGGA 59.819 50.000 2.46 0.00 43.62 3.41
1184 1272 2.626266 GAGATGCATGGCAATGGAATGA 59.374 45.455 2.46 0.00 43.62 2.57
1189 1277 1.727511 ATGGCAATGGAATGACGCGG 61.728 55.000 12.47 0.00 0.00 6.46
1191 1279 2.112198 GCAATGGAATGACGCGGGA 61.112 57.895 12.47 0.00 0.00 5.14
1192 1280 2.016961 CAATGGAATGACGCGGGAG 58.983 57.895 12.47 0.00 0.00 4.30
1193 1281 0.744414 CAATGGAATGACGCGGGAGT 60.744 55.000 12.47 0.00 0.00 3.85
1197 1285 1.222115 GGAATGACGCGGGAGTATGC 61.222 60.000 12.47 0.00 0.00 3.14
1198 1286 0.529773 GAATGACGCGGGAGTATGCA 60.530 55.000 12.47 0.00 0.00 3.96
1201 1289 1.067416 GACGCGGGAGTATGCATGA 59.933 57.895 12.47 0.00 0.00 3.07
1202 1290 0.941463 GACGCGGGAGTATGCATGAG 60.941 60.000 12.47 0.00 0.00 2.90
1203 1291 2.313172 CGCGGGAGTATGCATGAGC 61.313 63.158 10.16 4.78 42.57 4.26
1517 1606 4.026744 AGCTAGGCTGACTCAATGACTTA 58.973 43.478 0.00 0.00 37.57 2.24
1518 1607 4.467795 AGCTAGGCTGACTCAATGACTTAA 59.532 41.667 0.00 0.00 37.57 1.85
1519 1608 5.130145 AGCTAGGCTGACTCAATGACTTAAT 59.870 40.000 0.00 0.00 37.57 1.40
1520 1609 6.325028 AGCTAGGCTGACTCAATGACTTAATA 59.675 38.462 0.00 0.00 37.57 0.98
1538 1627 8.859517 ACTTAATAAGAGCTTCGTGACTAATC 57.140 34.615 7.06 0.00 0.00 1.75
1543 1632 8.804688 ATAAGAGCTTCGTGACTAATCATAAC 57.195 34.615 0.00 0.00 37.14 1.89
1545 1634 4.360563 AGCTTCGTGACTAATCATAACGG 58.639 43.478 0.00 0.00 37.14 4.44
1546 1635 4.097437 AGCTTCGTGACTAATCATAACGGA 59.903 41.667 0.00 0.00 37.14 4.69
1547 1636 4.441415 GCTTCGTGACTAATCATAACGGAG 59.559 45.833 0.00 0.00 37.14 4.63
1548 1637 5.732528 GCTTCGTGACTAATCATAACGGAGA 60.733 44.000 6.01 0.00 37.14 3.71
1549 1638 5.823209 TCGTGACTAATCATAACGGAGAA 57.177 39.130 0.00 0.00 37.14 2.87
1568 1657 1.656652 AGAGAACGAAATGCATCCGG 58.343 50.000 20.61 0.00 0.00 5.14
1586 1675 1.641577 GGCACGTCCTCACTGATTAC 58.358 55.000 0.00 0.00 0.00 1.89
1693 1782 1.153568 CTTCATTCTGCTCGGCGGA 60.154 57.895 7.21 3.61 42.66 5.54
1708 1797 0.246635 GCGGAAGAGCACTCAAGGTA 59.753 55.000 0.00 0.00 37.05 3.08
1710 1799 1.732732 CGGAAGAGCACTCAAGGTACG 60.733 57.143 0.00 0.00 0.00 3.67
1711 1800 1.272769 GGAAGAGCACTCAAGGTACGT 59.727 52.381 0.00 0.00 0.00 3.57
1712 1801 2.490903 GGAAGAGCACTCAAGGTACGTA 59.509 50.000 0.00 0.00 0.00 3.57
1713 1802 3.130693 GGAAGAGCACTCAAGGTACGTAT 59.869 47.826 0.00 0.00 0.00 3.06
1714 1803 4.337555 GGAAGAGCACTCAAGGTACGTATA 59.662 45.833 0.00 0.00 0.00 1.47
1715 1804 5.163581 GGAAGAGCACTCAAGGTACGTATAA 60.164 44.000 0.00 0.00 0.00 0.98
1716 1805 6.461231 GGAAGAGCACTCAAGGTACGTATAAT 60.461 42.308 0.00 0.00 0.00 1.28
1718 1807 7.578310 AGAGCACTCAAGGTACGTATAATTA 57.422 36.000 0.00 0.00 0.00 1.40
1719 1808 7.424001 AGAGCACTCAAGGTACGTATAATTAC 58.576 38.462 0.00 0.00 0.00 1.89
1731 1821 4.806330 CGTATAATTACGGAGCCATCACT 58.194 43.478 0.00 0.00 45.86 3.41
1735 1825 4.323553 AATTACGGAGCCATCACTACTC 57.676 45.455 0.00 0.00 0.00 2.59
1737 1827 1.107114 ACGGAGCCATCACTACTCTG 58.893 55.000 0.00 0.00 41.62 3.35
1740 1830 2.292016 CGGAGCCATCACTACTCTGTAG 59.708 54.545 3.49 3.49 33.08 2.74
1764 1887 8.773404 AGTAGTAACATTTTCCATAGACACAC 57.227 34.615 0.00 0.00 0.00 3.82
1765 1888 8.372459 AGTAGTAACATTTTCCATAGACACACA 58.628 33.333 0.00 0.00 0.00 3.72
1767 1890 7.871853 AGTAACATTTTCCATAGACACACAAC 58.128 34.615 0.00 0.00 0.00 3.32
1768 1891 6.707440 AACATTTTCCATAGACACACAACA 57.293 33.333 0.00 0.00 0.00 3.33
1771 1894 8.402798 ACATTTTCCATAGACACACAACAATA 57.597 30.769 0.00 0.00 0.00 1.90
1772 1895 9.023962 ACATTTTCCATAGACACACAACAATAT 57.976 29.630 0.00 0.00 0.00 1.28
1776 1899 9.733556 TTTCCATAGACACACAACAATATTACT 57.266 29.630 0.00 0.00 0.00 2.24
1777 1900 8.716646 TCCATAGACACACAACAATATTACTG 57.283 34.615 0.00 0.00 0.00 2.74
1778 1901 7.279981 TCCATAGACACACAACAATATTACTGC 59.720 37.037 0.00 0.00 0.00 4.40
1779 1902 7.280876 CCATAGACACACAACAATATTACTGCT 59.719 37.037 0.00 0.00 0.00 4.24
1780 1903 6.727824 AGACACACAACAATATTACTGCTC 57.272 37.500 0.00 0.00 0.00 4.26
1781 1904 5.643777 AGACACACAACAATATTACTGCTCC 59.356 40.000 0.00 0.00 0.00 4.70
1782 1905 5.312895 ACACACAACAATATTACTGCTCCA 58.687 37.500 0.00 0.00 0.00 3.86
1783 1906 5.767665 ACACACAACAATATTACTGCTCCAA 59.232 36.000 0.00 0.00 0.00 3.53
1784 1907 6.264292 ACACACAACAATATTACTGCTCCAAA 59.736 34.615 0.00 0.00 0.00 3.28
1785 1908 7.039784 ACACACAACAATATTACTGCTCCAAAT 60.040 33.333 0.00 0.00 0.00 2.32
1786 1909 7.814107 CACACAACAATATTACTGCTCCAAATT 59.186 33.333 0.00 0.00 0.00 1.82
1787 1910 7.814107 ACACAACAATATTACTGCTCCAAATTG 59.186 33.333 0.00 0.00 0.00 2.32
1788 1911 7.276218 CACAACAATATTACTGCTCCAAATTGG 59.724 37.037 5.48 5.48 39.43 3.16
1789 1912 7.039082 ACAACAATATTACTGCTCCAAATTGGT 60.039 33.333 12.28 0.00 39.03 3.67
1790 1913 7.480760 ACAATATTACTGCTCCAAATTGGTT 57.519 32.000 12.28 0.00 39.03 3.67
1791 1914 7.322664 ACAATATTACTGCTCCAAATTGGTTG 58.677 34.615 12.28 7.41 39.03 3.77
1792 1915 7.178274 ACAATATTACTGCTCCAAATTGGTTGA 59.822 33.333 12.28 0.00 39.87 3.18
1793 1916 7.902920 ATATTACTGCTCCAAATTGGTTGAT 57.097 32.000 12.28 0.00 39.87 2.57
1794 1917 6.610075 ATTACTGCTCCAAATTGGTTGATT 57.390 33.333 12.28 0.00 39.87 2.57
1795 1918 7.716799 ATTACTGCTCCAAATTGGTTGATTA 57.283 32.000 12.28 0.00 39.87 1.75
1799 1922 8.133024 ACTGCTCCAAATTGGTTGATTAATTA 57.867 30.769 12.28 0.00 39.87 1.40
1854 1977 5.724903 GCAACTTGCACGATTAACTTAAC 57.275 39.130 8.97 0.00 44.26 2.01
1861 1984 7.227116 ACTTGCACGATTAACTTAACTAACCAA 59.773 33.333 0.00 0.00 0.00 3.67
1898 2025 2.335011 GTGCGTTGCTTTCCACCC 59.665 61.111 0.00 0.00 0.00 4.61
1899 2026 3.283684 TGCGTTGCTTTCCACCCG 61.284 61.111 0.00 0.00 0.00 5.28
1900 2027 4.700365 GCGTTGCTTTCCACCCGC 62.700 66.667 0.00 0.00 37.04 6.13
1901 2028 3.283684 CGTTGCTTTCCACCCGCA 61.284 61.111 0.00 0.00 0.00 5.69
1933 2060 2.432628 GCGGAGTTCACCCAGACG 60.433 66.667 0.00 0.00 0.00 4.18
2018 2145 2.745308 CCCACCATCTCCGCCATGA 61.745 63.158 0.00 0.00 0.00 3.07
2107 2234 4.487412 GACGGCCGGTCGAACGAT 62.487 66.667 38.47 13.04 35.61 3.73
2108 2235 4.487412 ACGGCCGGTCGAACGATC 62.487 66.667 38.47 15.44 35.47 3.69
2118 2245 2.026301 GAACGATCGGAGCGGGAG 59.974 66.667 20.98 0.00 0.00 4.30
2126 2367 2.043248 GGAGCGGGAGGGACTACA 60.043 66.667 0.00 0.00 44.82 2.74
2127 2368 2.128507 GGAGCGGGAGGGACTACAG 61.129 68.421 0.00 0.00 44.82 2.74
2236 2477 3.685214 GATCCAGTCGACGCTGCGT 62.685 63.158 29.37 29.37 45.10 5.24
2359 2600 4.549516 GCCGCGTCCGAGTACCTC 62.550 72.222 4.92 0.00 36.29 3.85
2444 2685 0.796870 CATCGTCTCGCAGCACGTAA 60.797 55.000 3.90 0.00 44.19 3.18
2446 2687 1.154282 CGTCTCGCAGCACGTAAGA 60.154 57.895 0.00 0.00 44.19 2.10
2448 2689 0.109689 GTCTCGCAGCACGTAAGAGT 60.110 55.000 0.00 0.00 44.19 3.24
2450 2691 1.808343 TCTCGCAGCACGTAAGAGTAA 59.192 47.619 0.00 0.00 44.19 2.24
2452 2693 3.119602 TCTCGCAGCACGTAAGAGTAATT 60.120 43.478 0.00 0.00 44.19 1.40
2455 2696 3.366724 CGCAGCACGTAAGAGTAATTTCA 59.633 43.478 0.00 0.00 43.62 2.69
2457 2698 5.613795 CGCAGCACGTAAGAGTAATTTCAAA 60.614 40.000 0.00 0.00 43.62 2.69
2458 2699 5.564127 GCAGCACGTAAGAGTAATTTCAAAC 59.436 40.000 0.00 0.00 43.62 2.93
2459 2700 5.783654 CAGCACGTAAGAGTAATTTCAAACG 59.216 40.000 0.00 0.00 43.62 3.60
2460 2701 5.693104 AGCACGTAAGAGTAATTTCAAACGA 59.307 36.000 9.77 0.00 43.62 3.85
2814 3135 0.318275 GCATCATCGTCGTCTCCTCC 60.318 60.000 0.00 0.00 0.00 4.30
2944 3265 1.270465 CGGCAGGATGATGATGCAGTA 60.270 52.381 0.00 0.00 41.78 2.74
2980 3301 6.127897 ACCGTGACATAACAGTTACTACTACC 60.128 42.308 0.00 0.00 31.96 3.18
3041 3362 2.570169 CGTTAACATGCCAAACGTGAG 58.430 47.619 15.68 0.00 40.69 3.51
3044 3365 0.951558 AACATGCCAAACGTGAGACC 59.048 50.000 0.00 0.00 38.75 3.85
3045 3366 0.179032 ACATGCCAAACGTGAGACCA 60.179 50.000 0.00 0.00 38.75 4.02
3046 3367 0.950836 CATGCCAAACGTGAGACCAA 59.049 50.000 0.00 0.00 37.49 3.67
3076 3397 7.737972 AGCAGTACTCATAGTCATAGTAGTG 57.262 40.000 10.71 10.71 44.51 2.74
3131 3452 1.457346 AGAAGCAGCTTCCATTTCGG 58.543 50.000 28.34 0.00 40.98 4.30
3132 3453 1.003580 AGAAGCAGCTTCCATTTCGGA 59.996 47.619 28.34 0.00 40.98 4.55
3208 3541 0.108520 GGGCGGATTTGTACAGACGA 60.109 55.000 12.58 0.00 0.00 4.20
3251 3584 3.085533 CAAACATATCCCGGGTGAAACA 58.914 45.455 22.86 0.00 39.98 2.83
3252 3585 3.443145 AACATATCCCGGGTGAAACAA 57.557 42.857 22.86 0.00 39.98 2.83
3253 3586 3.443145 ACATATCCCGGGTGAAACAAA 57.557 42.857 22.86 0.00 39.98 2.83
3254 3587 3.086282 ACATATCCCGGGTGAAACAAAC 58.914 45.455 22.86 0.00 39.98 2.93
3256 3589 0.891904 ATCCCGGGTGAAACAAACGG 60.892 55.000 22.86 0.00 45.52 4.44
3257 3590 2.333581 CCGGGTGAAACAAACGGC 59.666 61.111 0.00 0.00 41.66 5.68
3258 3591 2.482333 CCGGGTGAAACAAACGGCA 61.482 57.895 0.00 0.00 41.66 5.69
3259 3592 1.008995 CGGGTGAAACAAACGGCAG 60.009 57.895 0.00 0.00 39.98 4.85
3260 3593 1.299850 GGGTGAAACAAACGGCAGC 60.300 57.895 0.00 0.00 39.98 5.25
3261 3594 1.733526 GGTGAAACAAACGGCAGCT 59.266 52.632 0.00 0.00 39.98 4.24
3262 3595 0.317854 GGTGAAACAAACGGCAGCTC 60.318 55.000 0.00 0.00 39.98 4.09
3308 3680 1.018910 GCAAGTACCACACACGGTTT 58.981 50.000 0.00 0.00 40.67 3.27
3343 3715 3.002759 AGCAGCAGTTTCTCGTTTTTCTC 59.997 43.478 0.00 0.00 0.00 2.87
3354 3726 6.373186 TCTCGTTTTTCTCTTCTTTTTCCC 57.627 37.500 0.00 0.00 0.00 3.97
3355 3727 6.120220 TCTCGTTTTTCTCTTCTTTTTCCCT 58.880 36.000 0.00 0.00 0.00 4.20
3357 3729 7.122204 TCTCGTTTTTCTCTTCTTTTTCCCTTT 59.878 33.333 0.00 0.00 0.00 3.11
3617 4022 3.443045 CCAGCAACGCCACCCATC 61.443 66.667 0.00 0.00 0.00 3.51
3618 4023 2.672651 CAGCAACGCCACCCATCA 60.673 61.111 0.00 0.00 0.00 3.07
3622 4027 2.360350 AACGCCACCCATCAGCAG 60.360 61.111 0.00 0.00 0.00 4.24
3672 4077 3.131046 GCTTTATTCTGGTGGTGATTGGG 59.869 47.826 0.00 0.00 0.00 4.12
3678 4083 2.438434 GTGGTGATTGGGCTCCGG 60.438 66.667 0.00 0.00 0.00 5.14
3739 4144 2.102578 AGGTCTGCAAAGCAAACACTT 58.897 42.857 0.00 0.00 38.41 3.16
3740 4145 2.497273 AGGTCTGCAAAGCAAACACTTT 59.503 40.909 0.00 0.00 40.49 2.66
3741 4146 3.055891 AGGTCTGCAAAGCAAACACTTTT 60.056 39.130 0.00 0.00 37.78 2.27
3742 4147 3.062504 GGTCTGCAAAGCAAACACTTTTG 59.937 43.478 0.00 0.00 44.42 2.44
3745 4150 5.347364 GTCTGCAAAGCAAACACTTTTGTTA 59.653 36.000 0.00 0.00 45.69 2.41
3749 4154 7.680062 TGCAAAGCAAACACTTTTGTTATTAC 58.320 30.769 0.00 0.00 45.69 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.207590 GTCGTTTTCCAACTCCGACTT 58.792 47.619 0.00 0.00 43.24 3.01
54 55 3.713858 TCAACTACTCGTCGTTTTCCA 57.286 42.857 0.00 0.00 0.00 3.53
118 119 1.988015 CCGGGGTGGCCGATAATAT 59.012 57.895 0.00 0.00 0.00 1.28
128 132 3.366739 GAACTACTCGCCGGGGTGG 62.367 68.421 22.52 16.56 42.50 4.61
163 167 4.656112 CCAGAGGTAGTACCAAGGATCAAT 59.344 45.833 21.49 0.00 41.95 2.57
191 214 3.458163 CGCCTCCTTAGTCGGCCA 61.458 66.667 2.24 0.00 40.70 5.36
220 248 1.225704 CCTCTCCCCATCCAACAGC 59.774 63.158 0.00 0.00 0.00 4.40
221 249 1.918253 CCCTCTCCCCATCCAACAG 59.082 63.158 0.00 0.00 0.00 3.16
291 319 2.717809 GCAGAAACGAGACGGACGC 61.718 63.158 0.00 0.00 0.00 5.19
296 324 3.827784 CGGCGCAGAAACGAGACG 61.828 66.667 10.83 0.00 34.06 4.18
304 332 1.079875 GGATTTACGTCGGCGCAGAA 61.080 55.000 12.98 1.53 42.83 3.02
307 335 2.881827 CGGATTTACGTCGGCGCA 60.882 61.111 10.50 0.00 42.83 6.09
398 438 1.262882 GTTTCGGTCGATACGGACAC 58.737 55.000 11.67 0.15 38.70 3.67
413 453 2.895372 ATCCGCGCCATCCGTTTC 60.895 61.111 0.00 0.00 39.71 2.78
419 459 1.283793 CCATTTCATCCGCGCCATC 59.716 57.895 0.00 0.00 0.00 3.51
421 461 2.828095 CCCATTTCATCCGCGCCA 60.828 61.111 0.00 0.00 0.00 5.69
430 471 1.004161 TCAATGAGGCGACCCATTTCA 59.996 47.619 0.00 0.00 31.25 2.69
450 491 8.232913 TGATAAAAAGTGGTTTAGAGCAACTT 57.767 30.769 0.00 0.00 34.60 2.66
479 520 8.485591 GGCTAGTAGTATTAGTTAACGCATTTG 58.514 37.037 0.00 0.00 0.00 2.32
481 522 7.719483 TGGCTAGTAGTATTAGTTAACGCATT 58.281 34.615 0.00 0.00 0.00 3.56
482 523 7.230108 TCTGGCTAGTAGTATTAGTTAACGCAT 59.770 37.037 0.00 0.00 0.00 4.73
483 524 6.543465 TCTGGCTAGTAGTATTAGTTAACGCA 59.457 38.462 0.00 0.00 0.00 5.24
484 525 6.855403 GTCTGGCTAGTAGTATTAGTTAACGC 59.145 42.308 0.00 0.00 0.00 4.84
485 526 7.854916 GTGTCTGGCTAGTAGTATTAGTTAACG 59.145 40.741 0.00 0.00 0.00 3.18
486 527 8.680903 TGTGTCTGGCTAGTAGTATTAGTTAAC 58.319 37.037 0.00 0.00 0.00 2.01
487 528 8.812513 TGTGTCTGGCTAGTAGTATTAGTTAA 57.187 34.615 0.00 0.00 0.00 2.01
488 529 8.270030 TCTGTGTCTGGCTAGTAGTATTAGTTA 58.730 37.037 0.00 0.00 0.00 2.24
489 530 7.117397 TCTGTGTCTGGCTAGTAGTATTAGTT 58.883 38.462 0.00 0.00 0.00 2.24
490 531 6.660800 TCTGTGTCTGGCTAGTAGTATTAGT 58.339 40.000 0.00 0.00 0.00 2.24
491 532 7.499563 TCTTCTGTGTCTGGCTAGTAGTATTAG 59.500 40.741 0.00 0.00 0.00 1.73
492 533 7.344134 TCTTCTGTGTCTGGCTAGTAGTATTA 58.656 38.462 0.00 0.00 0.00 0.98
493 534 6.188407 TCTTCTGTGTCTGGCTAGTAGTATT 58.812 40.000 0.00 0.00 0.00 1.89
494 535 5.756918 TCTTCTGTGTCTGGCTAGTAGTAT 58.243 41.667 0.00 0.00 0.00 2.12
495 536 5.175388 TCTTCTGTGTCTGGCTAGTAGTA 57.825 43.478 0.00 0.00 0.00 1.82
512 553 9.905713 TTATTTATTTACACCTGATGCTCTTCT 57.094 29.630 0.00 0.00 0.00 2.85
537 578 3.131046 GGATCTGGAACGCCATTTGATTT 59.869 43.478 0.00 0.00 44.91 2.17
540 581 1.681780 GGGATCTGGAACGCCATTTGA 60.682 52.381 0.00 0.00 44.91 2.69
541 582 0.740737 GGGATCTGGAACGCCATTTG 59.259 55.000 0.00 0.00 44.91 2.32
542 583 0.331278 TGGGATCTGGAACGCCATTT 59.669 50.000 0.00 0.00 44.91 2.32
544 585 0.107017 CTTGGGATCTGGAACGCCAT 60.107 55.000 0.00 0.00 44.91 4.40
545 586 1.299648 CTTGGGATCTGGAACGCCA 59.700 57.895 0.00 0.00 43.47 5.69
546 587 2.115291 GCTTGGGATCTGGAACGCC 61.115 63.158 0.00 0.00 0.00 5.68
547 588 0.678048 AAGCTTGGGATCTGGAACGC 60.678 55.000 0.00 0.00 0.00 4.84
548 589 1.826385 AAAGCTTGGGATCTGGAACG 58.174 50.000 0.00 0.00 0.00 3.95
549 590 2.893489 ACAAAAGCTTGGGATCTGGAAC 59.107 45.455 0.00 0.00 36.82 3.62
550 591 2.892852 CACAAAAGCTTGGGATCTGGAA 59.107 45.455 0.00 0.00 38.31 3.53
551 592 2.517959 CACAAAAGCTTGGGATCTGGA 58.482 47.619 0.00 0.00 38.31 3.86
552 593 1.067354 GCACAAAAGCTTGGGATCTGG 60.067 52.381 0.00 0.00 38.31 3.86
572 614 2.257691 CTCCTCCAGCAATGGATCAG 57.742 55.000 0.00 0.00 37.34 2.90
596 642 7.220683 TGTGATAGTTCCTTATTAAACGTACGC 59.779 37.037 16.72 0.00 0.00 4.42
597 643 8.619146 TGTGATAGTTCCTTATTAAACGTACG 57.381 34.615 15.01 15.01 0.00 3.67
612 658 5.496387 CAGCGAAATGTGATGTGATAGTTC 58.504 41.667 0.00 0.00 0.00 3.01
613 659 4.201851 GCAGCGAAATGTGATGTGATAGTT 60.202 41.667 0.00 0.00 0.00 2.24
714 761 1.282875 GTACGTACGTATCCGGCCC 59.717 63.158 29.05 12.14 38.78 5.80
764 811 2.474410 AGTAAAGGTGCACCACTAGC 57.526 50.000 36.39 21.19 38.89 3.42
784 831 1.003355 CATGTCGTTGCCAGGGTCT 60.003 57.895 0.00 0.00 0.00 3.85
785 832 2.690778 GCATGTCGTTGCCAGGGTC 61.691 63.158 0.00 0.00 36.60 4.46
787 834 2.048023 ATGCATGTCGTTGCCAGGG 61.048 57.895 0.00 0.00 42.06 4.45
837 887 4.951094 GCCCAGATATATAGACGAAGGAGT 59.049 45.833 0.00 0.00 0.00 3.85
841 891 3.378742 AGCGCCCAGATATATAGACGAAG 59.621 47.826 2.29 0.00 0.00 3.79
842 892 3.353557 AGCGCCCAGATATATAGACGAA 58.646 45.455 2.29 0.00 0.00 3.85
843 893 3.000684 AGCGCCCAGATATATAGACGA 57.999 47.619 2.29 0.00 0.00 4.20
844 894 6.371825 TCATATAGCGCCCAGATATATAGACG 59.628 42.308 2.29 0.00 41.09 4.18
913 967 3.396260 TCTGTTTGAACGAACCTAGGG 57.604 47.619 14.81 0.00 0.00 3.53
940 997 3.117171 GTCGAGCTGCCTGTGCTG 61.117 66.667 0.00 0.00 41.30 4.41
945 1002 2.904747 CTACGTCGTCGAGCTGCCTG 62.905 65.000 9.47 0.00 40.62 4.85
946 1003 2.745100 TACGTCGTCGAGCTGCCT 60.745 61.111 9.47 0.00 40.62 4.75
947 1004 2.277373 CTACGTCGTCGAGCTGCC 60.277 66.667 9.47 0.00 40.62 4.85
948 1005 2.945066 GCTACGTCGTCGAGCTGC 60.945 66.667 9.47 3.66 40.62 5.25
999 1058 3.842923 AGCGACGAGGAGGCCATG 61.843 66.667 5.01 0.00 0.00 3.66
1142 1204 7.211966 TCTCGAAACTTAACAAGCTACTAGT 57.788 36.000 0.00 0.00 0.00 2.57
1143 1205 7.253817 GCATCTCGAAACTTAACAAGCTACTAG 60.254 40.741 0.00 0.00 0.00 2.57
1144 1206 6.530534 GCATCTCGAAACTTAACAAGCTACTA 59.469 38.462 0.00 0.00 0.00 1.82
1167 1229 0.456628 CGTCATTCCATTGCCATGCA 59.543 50.000 0.00 0.00 36.47 3.96
1180 1268 0.106708 ATGCATACTCCCGCGTCATT 59.893 50.000 4.92 0.00 0.00 2.57
1184 1272 1.068083 CTCATGCATACTCCCGCGT 59.932 57.895 4.92 0.00 0.00 6.01
1203 1291 1.068402 TGCCATGAATCTGCAAACGTG 60.068 47.619 0.00 0.00 30.85 4.49
1204 1292 1.200716 CTGCCATGAATCTGCAAACGT 59.799 47.619 0.00 0.00 34.06 3.99
1445 1533 4.088056 ACTCTGGCTAGAACGATAGCTA 57.912 45.455 0.00 0.00 46.10 3.32
1446 1534 2.938838 ACTCTGGCTAGAACGATAGCT 58.061 47.619 0.00 0.00 46.10 3.32
1447 1535 3.719173 AACTCTGGCTAGAACGATAGC 57.281 47.619 0.00 9.54 46.13 2.97
1448 1536 5.508200 AGAAACTCTGGCTAGAACGATAG 57.492 43.478 0.00 0.00 46.19 2.08
1449 1537 5.916661 AAGAAACTCTGGCTAGAACGATA 57.083 39.130 0.00 0.00 31.21 2.92
1450 1538 4.810191 AAGAAACTCTGGCTAGAACGAT 57.190 40.909 0.00 0.00 31.21 3.73
1451 1539 4.602340 AAAGAAACTCTGGCTAGAACGA 57.398 40.909 0.00 0.00 31.21 3.85
1452 1540 5.674933 AAAAAGAAACTCTGGCTAGAACG 57.325 39.130 0.00 0.00 31.21 3.95
1517 1606 9.250624 GTTATGATTAGTCACGAAGCTCTTATT 57.749 33.333 0.00 0.00 37.14 1.40
1518 1607 7.591795 CGTTATGATTAGTCACGAAGCTCTTAT 59.408 37.037 0.00 0.00 37.14 1.73
1519 1608 6.910972 CGTTATGATTAGTCACGAAGCTCTTA 59.089 38.462 0.00 0.00 37.14 2.10
1520 1609 5.744345 CGTTATGATTAGTCACGAAGCTCTT 59.256 40.000 0.00 0.00 37.14 2.85
1538 1627 5.500931 GCATTTCGTTCTCTTCTCCGTTATG 60.501 44.000 0.00 0.00 0.00 1.90
1543 1632 2.337583 TGCATTTCGTTCTCTTCTCCG 58.662 47.619 0.00 0.00 0.00 4.63
1545 1634 3.000724 CGGATGCATTTCGTTCTCTTCTC 59.999 47.826 0.00 0.00 0.00 2.87
1546 1635 2.932614 CGGATGCATTTCGTTCTCTTCT 59.067 45.455 0.00 0.00 0.00 2.85
1547 1636 2.030946 CCGGATGCATTTCGTTCTCTTC 59.969 50.000 17.80 0.00 0.00 2.87
1548 1637 2.009774 CCGGATGCATTTCGTTCTCTT 58.990 47.619 17.80 0.00 0.00 2.85
1549 1638 1.656652 CCGGATGCATTTCGTTCTCT 58.343 50.000 17.80 0.00 0.00 3.10
1568 1657 1.269166 CGTAATCAGTGAGGACGTGC 58.731 55.000 17.28 0.00 0.00 5.34
1586 1675 4.440987 CGCACAGCAAGCAGAGCG 62.441 66.667 13.60 13.60 36.49 5.03
1693 1782 5.909621 TTATACGTACCTTGAGTGCTCTT 57.090 39.130 0.00 0.00 0.00 2.85
1710 1799 6.921914 AGTAGTGATGGCTCCGTAATTATAC 58.078 40.000 0.00 0.00 0.00 1.47
1711 1800 6.946583 AGAGTAGTGATGGCTCCGTAATTATA 59.053 38.462 0.00 0.00 0.00 0.98
1712 1801 5.775701 AGAGTAGTGATGGCTCCGTAATTAT 59.224 40.000 0.00 0.00 0.00 1.28
1713 1802 5.009710 CAGAGTAGTGATGGCTCCGTAATTA 59.990 44.000 0.00 0.00 0.00 1.40
1714 1803 3.961408 AGAGTAGTGATGGCTCCGTAATT 59.039 43.478 0.00 0.00 0.00 1.40
1715 1804 3.319405 CAGAGTAGTGATGGCTCCGTAAT 59.681 47.826 0.00 0.00 0.00 1.89
1716 1805 2.688446 CAGAGTAGTGATGGCTCCGTAA 59.312 50.000 0.00 0.00 0.00 3.18
1718 1807 1.107114 CAGAGTAGTGATGGCTCCGT 58.893 55.000 0.00 0.00 0.00 4.69
1719 1808 1.107114 ACAGAGTAGTGATGGCTCCG 58.893 55.000 0.00 0.00 0.00 4.63
1720 1809 3.292460 ACTACAGAGTAGTGATGGCTCC 58.708 50.000 8.88 0.00 32.65 4.70
1737 1827 9.865321 TGTGTCTATGGAAAATGTTACTACTAC 57.135 33.333 0.00 0.00 0.00 2.73
1740 1830 8.542497 TGTGTGTCTATGGAAAATGTTACTAC 57.458 34.615 0.00 0.00 0.00 2.73
1743 1833 7.644490 TGTTGTGTGTCTATGGAAAATGTTAC 58.356 34.615 0.00 0.00 0.00 2.50
1745 1835 6.707440 TGTTGTGTGTCTATGGAAAATGTT 57.293 33.333 0.00 0.00 0.00 2.71
1746 1836 6.707440 TTGTTGTGTGTCTATGGAAAATGT 57.293 33.333 0.00 0.00 0.00 2.71
1747 1837 9.859427 AATATTGTTGTGTGTCTATGGAAAATG 57.141 29.630 0.00 0.00 0.00 2.32
1758 1881 5.411361 TGGAGCAGTAATATTGTTGTGTGTC 59.589 40.000 0.00 0.00 0.00 3.67
1764 1887 7.322664 ACCAATTTGGAGCAGTAATATTGTTG 58.677 34.615 22.19 0.00 40.96 3.33
1765 1888 7.480760 ACCAATTTGGAGCAGTAATATTGTT 57.519 32.000 22.19 0.00 40.96 2.83
1767 1890 7.546358 TCAACCAATTTGGAGCAGTAATATTG 58.454 34.615 22.19 11.17 40.96 1.90
1768 1891 7.716799 TCAACCAATTTGGAGCAGTAATATT 57.283 32.000 22.19 0.00 40.96 1.28
1771 1894 6.610075 AATCAACCAATTTGGAGCAGTAAT 57.390 33.333 22.19 3.10 40.96 1.89
1772 1895 7.531857 TTAATCAACCAATTTGGAGCAGTAA 57.468 32.000 22.19 10.65 40.96 2.24
1774 1897 6.610075 ATTAATCAACCAATTTGGAGCAGT 57.390 33.333 22.19 6.47 40.96 4.40
1775 1898 8.253113 ACTAATTAATCAACCAATTTGGAGCAG 58.747 33.333 22.19 8.32 40.96 4.24
1776 1899 8.133024 ACTAATTAATCAACCAATTTGGAGCA 57.867 30.769 22.19 5.07 40.96 4.26
1777 1900 8.872845 CAACTAATTAATCAACCAATTTGGAGC 58.127 33.333 22.19 0.00 40.96 4.70
1786 1909 9.685276 ACTCATGATCAACTAATTAATCAACCA 57.315 29.630 0.00 0.00 32.31 3.67
1799 1922 7.876936 ATGCTATTTTGACTCATGATCAACT 57.123 32.000 15.66 10.92 35.82 3.16
1851 1974 3.245754 CGCACGTTGACTTTGGTTAGTTA 59.754 43.478 0.00 0.00 0.00 2.24
1853 1976 1.595794 CGCACGTTGACTTTGGTTAGT 59.404 47.619 0.00 0.00 0.00 2.24
1854 1977 1.595794 ACGCACGTTGACTTTGGTTAG 59.404 47.619 0.00 0.00 0.00 2.34
1861 1984 2.888534 ACGCACGCACGTTGACTT 60.889 55.556 0.00 0.00 45.75 3.01
1899 2026 4.309347 CGCTGATCGCCTGCATGC 62.309 66.667 11.82 11.82 39.38 4.06
2100 2227 3.808771 CTCCCGCTCCGATCGTTCG 62.809 68.421 15.09 13.28 45.08 3.95
2101 2228 2.026301 CTCCCGCTCCGATCGTTC 59.974 66.667 15.09 1.44 0.00 3.95
2102 2229 3.528370 CCTCCCGCTCCGATCGTT 61.528 66.667 15.09 0.00 0.00 3.85
2106 2233 2.764737 TAGTCCCTCCCGCTCCGAT 61.765 63.158 0.00 0.00 0.00 4.18
2107 2234 3.414193 TAGTCCCTCCCGCTCCGA 61.414 66.667 0.00 0.00 0.00 4.55
2108 2235 3.217743 GTAGTCCCTCCCGCTCCG 61.218 72.222 0.00 0.00 0.00 4.63
2109 2236 2.043248 TGTAGTCCCTCCCGCTCC 60.043 66.667 0.00 0.00 0.00 4.70
2111 2238 2.760385 GCTGTAGTCCCTCCCGCT 60.760 66.667 0.00 0.00 0.00 5.52
2112 2239 2.370647 GATGCTGTAGTCCCTCCCGC 62.371 65.000 0.00 0.00 0.00 6.13
2113 2240 1.742768 GATGCTGTAGTCCCTCCCG 59.257 63.158 0.00 0.00 0.00 5.14
2114 2241 0.691078 TGGATGCTGTAGTCCCTCCC 60.691 60.000 0.00 0.00 33.45 4.30
2115 2242 0.466124 GTGGATGCTGTAGTCCCTCC 59.534 60.000 0.00 0.00 33.45 4.30
2116 2243 0.103208 CGTGGATGCTGTAGTCCCTC 59.897 60.000 0.00 0.00 33.45 4.30
2118 2245 1.144057 CCGTGGATGCTGTAGTCCC 59.856 63.158 0.00 0.00 33.45 4.46
2142 2383 3.894547 TTGAACGCCTTCTCCGCCC 62.895 63.158 0.00 0.00 0.00 6.13
2359 2600 4.101448 CCGGAGAGCTGGTTGGGG 62.101 72.222 0.00 0.00 35.70 4.96
2444 2685 7.228706 ACAACTTGGATCGTTTGAAATTACTCT 59.771 33.333 0.00 0.00 0.00 3.24
2446 2687 7.012894 TCACAACTTGGATCGTTTGAAATTACT 59.987 33.333 0.00 0.00 0.00 2.24
2448 2689 7.265647 TCACAACTTGGATCGTTTGAAATTA 57.734 32.000 0.00 0.00 0.00 1.40
2450 2691 5.766150 TCACAACTTGGATCGTTTGAAAT 57.234 34.783 0.00 0.00 0.00 2.17
2452 2693 4.023279 CCATCACAACTTGGATCGTTTGAA 60.023 41.667 0.00 0.00 34.81 2.69
2455 2696 2.228822 GCCATCACAACTTGGATCGTTT 59.771 45.455 0.00 0.00 34.81 3.60
2457 2698 1.453155 GCCATCACAACTTGGATCGT 58.547 50.000 0.00 0.00 34.81 3.73
2458 2699 0.734889 GGCCATCACAACTTGGATCG 59.265 55.000 0.00 0.00 34.81 3.69
2459 2700 1.474077 GTGGCCATCACAACTTGGATC 59.526 52.381 9.72 0.00 45.39 3.36
2460 2701 1.549203 GTGGCCATCACAACTTGGAT 58.451 50.000 9.72 0.00 45.39 3.41
2980 3301 1.375908 CGATGGTCTGGTGGTGGTG 60.376 63.158 0.00 0.00 0.00 4.17
3145 3477 9.489084 GGGGAAGTGGCATTATTTTATTTTATC 57.511 33.333 0.00 0.00 0.00 1.75
3180 3512 2.114670 AAATCCGCCCGCAGTGATG 61.115 57.895 0.00 0.00 0.00 3.07
3251 3584 1.148273 TGGTTCTGAGCTGCCGTTT 59.852 52.632 0.00 0.00 0.00 3.60
3252 3585 1.598130 GTGGTTCTGAGCTGCCGTT 60.598 57.895 0.00 0.00 0.00 4.44
3253 3586 2.031163 GTGGTTCTGAGCTGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
3254 3587 1.364626 GATGTGGTTCTGAGCTGCCG 61.365 60.000 0.00 0.00 0.00 5.69
3256 3589 0.321919 TGGATGTGGTTCTGAGCTGC 60.322 55.000 0.00 0.00 0.00 5.25
3257 3590 2.414994 ATGGATGTGGTTCTGAGCTG 57.585 50.000 0.00 0.00 0.00 4.24
3258 3591 3.457380 ACATATGGATGTGGTTCTGAGCT 59.543 43.478 7.80 0.00 44.90 4.09
3259 3592 3.813443 ACATATGGATGTGGTTCTGAGC 58.187 45.455 7.80 0.00 44.90 4.26
3260 3593 5.755375 GTGTACATATGGATGTGGTTCTGAG 59.245 44.000 7.80 0.00 46.11 3.35
3261 3594 5.188751 TGTGTACATATGGATGTGGTTCTGA 59.811 40.000 7.80 0.00 46.11 3.27
3262 3595 5.294306 GTGTGTACATATGGATGTGGTTCTG 59.706 44.000 7.80 0.00 46.11 3.02
3563 3962 0.738762 CACTGGACGATGGACTGCAG 60.739 60.000 13.48 13.48 0.00 4.41
3604 4009 2.672651 TGCTGATGGGTGGCGTTG 60.673 61.111 0.00 0.00 0.00 4.10
3617 4022 0.883833 GGTGGTTTGGATCACTGCTG 59.116 55.000 0.00 0.00 34.57 4.41
3618 4023 0.478072 TGGTGGTTTGGATCACTGCT 59.522 50.000 0.00 0.00 34.57 4.24
3622 4027 1.000274 GCAAGTGGTGGTTTGGATCAC 60.000 52.381 0.00 0.00 0.00 3.06
3672 4077 4.802051 TGCCCAATCTGCCGGAGC 62.802 66.667 5.05 0.00 40.48 4.70
3678 4083 0.394762 TGGAGTCATGCCCAATCTGC 60.395 55.000 0.00 0.00 0.00 4.26
3740 4145 8.867935 CGGCATCAAAATCATTTGTAATAACAA 58.132 29.630 1.69 0.00 45.02 2.83
3741 4146 8.246871 TCGGCATCAAAATCATTTGTAATAACA 58.753 29.630 1.69 0.00 45.02 2.41
3742 4147 8.531530 GTCGGCATCAAAATCATTTGTAATAAC 58.468 33.333 1.69 0.00 45.02 1.89
3745 4150 5.743398 CGTCGGCATCAAAATCATTTGTAAT 59.257 36.000 1.69 0.00 45.02 1.89
3749 4154 3.500982 ACGTCGGCATCAAAATCATTTG 58.499 40.909 0.00 0.00 45.92 2.32
3757 4162 1.002251 GGTTGAAACGTCGGCATCAAA 60.002 47.619 10.03 0.00 33.93 2.69
3762 4167 2.181521 GTGGGTTGAAACGTCGGCA 61.182 57.895 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.