Multiple sequence alignment - TraesCS2D01G262600

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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 TraesCS2D01G262600 chr2D 100.000 2369 0 0 1 2369 318817813 318820181 0.000000e+00 4375.0
1 TraesCS2D01G262600 chr2D 79.412 238 37 4 1944 2169 549862568 549862331 8.770000e-35 158.0
2 TraesCS2D01G262600 chr2D 98.039 51 1 0 2144 2194 318820007 318820057 3.240000e-14 89.8
3 TraesCS2D01G262600 chr2A 91.289 1171 58 16 768 1913 412034301 412033150 0.000000e+00 1557.0
4 TraesCS2D01G262600 chr2A 90.395 583 40 7 1 578 412045516 412044945 0.000000e+00 752.0
5 TraesCS2D01G262600 chr2A 90.123 162 14 2 2195 2356 412031110 412030951 2.390000e-50 209.0
6 TraesCS2D01G262600 chr2A 95.455 110 4 1 667 776 412038405 412038297 8.700000e-40 174.0
7 TraesCS2D01G262600 chr2A 90.625 128 11 1 2067 2194 412031186 412031060 4.050000e-38 169.0
8 TraesCS2D01G262600 chr2B 91.522 1038 55 16 650 1682 387202003 387203012 0.000000e+00 1399.0
9 TraesCS2D01G262600 chr2B 91.213 478 29 6 1 476 387201539 387202005 2.570000e-179 638.0
10 TraesCS2D01G262600 chr2B 92.683 164 10 1 2195 2356 207476540 207476703 3.940000e-58 235.0
11 TraesCS2D01G262600 chr2B 82.955 264 32 3 1944 2194 249221092 249220829 2.370000e-55 226.0
12 TraesCS2D01G262600 chr2B 81.887 265 31 4 1942 2194 547540112 547539853 8.580000e-50 207.0
13 TraesCS2D01G262600 chr2B 89.375 160 11 4 2195 2349 519695569 519695727 1.860000e-46 196.0
14 TraesCS2D01G262600 chr2B 89.404 151 15 1 2044 2194 207476441 207476590 3.110000e-44 189.0
15 TraesCS2D01G262600 chr2B 86.747 166 18 3 2195 2356 249220879 249220714 5.200000e-42 182.0
16 TraesCS2D01G262600 chr3B 82.117 274 34 5 1935 2194 308243660 308243388 1.100000e-53 220.0
17 TraesCS2D01G262600 chr3B 87.952 166 16 2 2195 2356 308243438 308243273 2.400000e-45 193.0
18 TraesCS2D01G262600 chr3B 90.000 80 8 0 1942 2021 56741829 56741750 1.160000e-18 104.0
19 TraesCS2D01G262600 chr7B 90.446 157 11 3 2195 2349 644221320 644221166 1.110000e-48 204.0
20 TraesCS2D01G262600 chr7B 87.963 108 13 0 2087 2194 644221377 644221270 6.870000e-26 128.0
21 TraesCS2D01G262600 chr5B 85.882 170 13 7 2196 2356 2049406 2049239 1.130000e-38 171.0
22 TraesCS2D01G262600 chr7D 86.755 151 17 3 2195 2342 575576161 575576311 5.240000e-37 165.0
23 TraesCS2D01G262600 chr3D 83.436 163 21 6 2195 2355 545226275 545226433 1.900000e-31 147.0
24 TraesCS2D01G262600 chr6D 86.458 96 9 2 13 104 277860750 277860845 4.170000e-18 102.0


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 TraesCS2D01G262600 chr2D 318817813 318820181 2368 False 2232.40 4375 99.0195 1 2369 2 chr2D.!!$F1 2368
1 TraesCS2D01G262600 chr2A 412044945 412045516 571 True 752.00 752 90.3950 1 578 1 chr2A.!!$R1 577
2 TraesCS2D01G262600 chr2A 412030951 412038405 7454 True 527.25 1557 91.8730 667 2356 4 chr2A.!!$R2 1689
3 TraesCS2D01G262600 chr2B 387201539 387203012 1473 False 1018.50 1399 91.3675 1 1682 2 chr2B.!!$F3 1681

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
477 484 0.042448 GTCGCGACCAAACTGTGTTC 60.042 55.0 28.61 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 5977 0.033011 ATAGGAGGTCTCTGCGGTGT 60.033 55.0 0.0 0.0 36.39 4.16 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
178 181 0.699399 TCTTCCTCCTCCTCTGACGT 59.301 55.000 0.00 0.00 0.00 4.34
179 182 1.099689 CTTCCTCCTCCTCTGACGTC 58.900 60.000 9.11 9.11 0.00 4.34
323 330 3.767630 AACACTTTGCGGGCGGAGT 62.768 57.895 0.00 0.00 0.00 3.85
327 334 4.770874 TTTGCGGGCGGAGTAGGC 62.771 66.667 0.00 0.00 0.00 3.93
354 361 2.890474 GATCGGCGGCATTGACGT 60.890 61.111 14.37 0.00 42.32 4.34
363 370 1.060937 GCATTGACGTGATGCCGAC 59.939 57.895 18.18 0.00 43.10 4.79
422 429 4.341487 TGACTTCGTAGGAGGAAGATTCA 58.659 43.478 14.09 6.92 41.26 2.57
430 437 5.923684 CGTAGGAGGAAGATTCATCTAAAGC 59.076 44.000 7.13 0.00 38.04 3.51
476 483 1.758319 CGTCGCGACCAAACTGTGTT 61.758 55.000 31.84 0.00 0.00 3.32
477 484 0.042448 GTCGCGACCAAACTGTGTTC 60.042 55.000 28.61 0.00 0.00 3.18
478 485 1.083657 CGCGACCAAACTGTGTTCG 60.084 57.895 0.00 0.00 0.00 3.95
493 500 1.658596 TGTTCGATCTTGATTTCGCCG 59.341 47.619 0.00 0.00 35.39 6.46
494 501 1.004927 GTTCGATCTTGATTTCGCCGG 60.005 52.381 0.00 0.00 35.39 6.13
517 524 2.791501 TTCTAAGGGTCGGCCAACGC 62.792 60.000 9.07 1.88 43.86 4.84
555 563 7.878477 TTTTACGAGTTATAAGCCGGATATG 57.122 36.000 5.05 0.00 0.00 1.78
575 583 0.825010 GGATCGGCTAGGTCCGGTTA 60.825 60.000 0.00 0.00 44.09 2.85
578 586 2.159057 GATCGGCTAGGTCCGGTTAAAA 60.159 50.000 0.00 0.00 44.09 1.52
579 587 2.320745 CGGCTAGGTCCGGTTAAAAT 57.679 50.000 0.00 0.00 45.38 1.82
580 588 1.937899 CGGCTAGGTCCGGTTAAAATG 59.062 52.381 0.00 0.00 45.38 2.32
581 589 1.674441 GGCTAGGTCCGGTTAAAATGC 59.326 52.381 0.00 0.00 0.00 3.56
582 590 2.361789 GCTAGGTCCGGTTAAAATGCA 58.638 47.619 0.00 0.00 0.00 3.96
583 591 2.750712 GCTAGGTCCGGTTAAAATGCAA 59.249 45.455 0.00 0.00 0.00 4.08
584 592 3.191791 GCTAGGTCCGGTTAAAATGCAAA 59.808 43.478 0.00 0.00 0.00 3.68
585 593 4.321378 GCTAGGTCCGGTTAAAATGCAAAA 60.321 41.667 0.00 0.00 0.00 2.44
586 594 4.251543 AGGTCCGGTTAAAATGCAAAAG 57.748 40.909 0.00 0.00 0.00 2.27
587 595 3.892588 AGGTCCGGTTAAAATGCAAAAGA 59.107 39.130 0.00 0.00 0.00 2.52
588 596 4.342665 AGGTCCGGTTAAAATGCAAAAGAA 59.657 37.500 0.00 0.00 0.00 2.52
589 597 4.684242 GGTCCGGTTAAAATGCAAAAGAAG 59.316 41.667 0.00 0.00 0.00 2.85
590 598 4.149922 GTCCGGTTAAAATGCAAAAGAAGC 59.850 41.667 0.00 0.00 0.00 3.86
591 599 4.038642 TCCGGTTAAAATGCAAAAGAAGCT 59.961 37.500 0.00 0.00 0.00 3.74
592 600 4.150451 CCGGTTAAAATGCAAAAGAAGCTG 59.850 41.667 0.00 0.00 0.00 4.24
593 601 4.981674 CGGTTAAAATGCAAAAGAAGCTGA 59.018 37.500 0.00 0.00 0.00 4.26
594 602 5.107875 CGGTTAAAATGCAAAAGAAGCTGAC 60.108 40.000 0.00 0.00 0.00 3.51
595 603 5.177511 GGTTAAAATGCAAAAGAAGCTGACC 59.822 40.000 0.00 0.00 0.00 4.02
596 604 4.405116 AAAATGCAAAAGAAGCTGACCA 57.595 36.364 0.00 0.00 0.00 4.02
597 605 4.405116 AAATGCAAAAGAAGCTGACCAA 57.595 36.364 0.00 0.00 0.00 3.67
598 606 4.405116 AATGCAAAAGAAGCTGACCAAA 57.595 36.364 0.00 0.00 0.00 3.28
599 607 3.441496 TGCAAAAGAAGCTGACCAAAG 57.559 42.857 0.00 0.00 0.00 2.77
600 608 2.760092 TGCAAAAGAAGCTGACCAAAGT 59.240 40.909 0.00 0.00 0.00 2.66
601 609 3.195396 TGCAAAAGAAGCTGACCAAAGTT 59.805 39.130 0.00 0.00 0.00 2.66
602 610 3.798878 GCAAAAGAAGCTGACCAAAGTTC 59.201 43.478 0.00 0.00 0.00 3.01
603 611 4.677779 GCAAAAGAAGCTGACCAAAGTTCA 60.678 41.667 0.00 0.00 0.00 3.18
604 612 4.639135 AAAGAAGCTGACCAAAGTTCAC 57.361 40.909 0.00 0.00 0.00 3.18
605 613 3.281727 AGAAGCTGACCAAAGTTCACA 57.718 42.857 0.00 0.00 0.00 3.58
606 614 2.945668 AGAAGCTGACCAAAGTTCACAC 59.054 45.455 0.00 0.00 0.00 3.82
607 615 2.418368 AGCTGACCAAAGTTCACACA 57.582 45.000 0.00 0.00 0.00 3.72
608 616 2.292267 AGCTGACCAAAGTTCACACAG 58.708 47.619 0.00 0.00 0.00 3.66
609 617 2.092968 AGCTGACCAAAGTTCACACAGA 60.093 45.455 0.00 0.00 0.00 3.41
610 618 2.682856 GCTGACCAAAGTTCACACAGAA 59.317 45.455 0.00 0.00 0.00 3.02
611 619 3.128589 GCTGACCAAAGTTCACACAGAAA 59.871 43.478 0.00 0.00 38.13 2.52
612 620 4.662145 CTGACCAAAGTTCACACAGAAAC 58.338 43.478 0.00 0.00 38.13 2.78
613 621 3.442273 TGACCAAAGTTCACACAGAAACC 59.558 43.478 0.00 0.00 38.13 3.27
614 622 2.422127 ACCAAAGTTCACACAGAAACCG 59.578 45.455 0.00 0.00 38.13 4.44
615 623 2.680841 CCAAAGTTCACACAGAAACCGA 59.319 45.455 0.00 0.00 38.13 4.69
616 624 3.242739 CCAAAGTTCACACAGAAACCGAG 60.243 47.826 0.00 0.00 38.13 4.63
617 625 2.981859 AGTTCACACAGAAACCGAGT 57.018 45.000 0.00 0.00 38.13 4.18
618 626 3.261981 AGTTCACACAGAAACCGAGTT 57.738 42.857 0.00 0.00 38.13 3.01
619 627 3.606687 AGTTCACACAGAAACCGAGTTT 58.393 40.909 2.23 2.23 38.13 2.66
620 628 4.007659 AGTTCACACAGAAACCGAGTTTT 58.992 39.130 3.96 0.00 38.13 2.43
621 629 4.457949 AGTTCACACAGAAACCGAGTTTTT 59.542 37.500 3.96 0.00 38.13 1.94
647 655 6.385649 TTTTTGCGACTATGACCTCTTTTT 57.614 33.333 0.00 0.00 0.00 1.94
700 708 1.804151 GTCCACAGTCGCATTGCTTAA 59.196 47.619 7.12 0.00 0.00 1.85
839 4851 0.673644 GTTGGGTCGTGTCTGATGGG 60.674 60.000 0.00 0.00 0.00 4.00
908 4920 0.512952 GGCATATAAAGACGCAGGCG 59.487 55.000 12.71 12.71 46.03 5.52
1014 5028 4.520846 GCAATGTCGGCGCTTCGG 62.521 66.667 7.64 0.00 0.00 4.30
1125 5139 0.378962 TCCAACAAAACGGCGACAAG 59.621 50.000 16.62 2.97 0.00 3.16
1183 5197 7.472543 ACGGATTTAATCTTTTCTTTCCATCG 58.527 34.615 4.87 0.00 0.00 3.84
1191 5205 8.538409 AATCTTTTCTTTCCATCGAAATTTGG 57.462 30.769 0.00 0.00 37.36 3.28
1251 5265 0.179092 GTGTATGGACAGTACCCGGC 60.179 60.000 0.00 0.00 35.82 6.13
1360 5374 4.394712 AGGCGGCCACGAAGAAGG 62.395 66.667 23.09 0.00 44.60 3.46
1372 5386 5.665459 CCACGAAGAAGGAGACATAGATTT 58.335 41.667 0.00 0.00 0.00 2.17
1373 5387 6.683110 GCCACGAAGAAGGAGACATAGATTTA 60.683 42.308 0.00 0.00 0.00 1.40
1409 5423 8.807948 TTTTGATGAAAAAGGAGATAGTAGGG 57.192 34.615 0.00 0.00 32.72 3.53
1456 5470 5.093849 ACTAGTTATAATGGCGGTTGTGT 57.906 39.130 0.00 0.00 0.00 3.72
1457 5471 4.873827 ACTAGTTATAATGGCGGTTGTGTG 59.126 41.667 0.00 0.00 0.00 3.82
1475 5489 9.430623 GGTTGTGTGCCAAATTAGTTAATTTAT 57.569 29.630 8.97 0.00 42.26 1.40
1559 5581 4.754322 TCCTTTTTGCAGTTTGGAGTTTC 58.246 39.130 0.00 0.00 0.00 2.78
1569 5596 6.183360 TGCAGTTTGGAGTTTCTTTTCCTAAG 60.183 38.462 0.00 0.00 34.48 2.18
1572 5599 8.343366 CAGTTTGGAGTTTCTTTTCCTAAGTAC 58.657 37.037 0.00 0.00 32.53 2.73
1574 5601 7.797038 TTGGAGTTTCTTTTCCTAAGTACAC 57.203 36.000 0.00 0.00 34.48 2.90
1577 5604 8.877195 TGGAGTTTCTTTTCCTAAGTACACTAT 58.123 33.333 0.00 0.00 34.48 2.12
1684 5713 3.943671 TTGTGTCCCCGATTCCATAAT 57.056 42.857 0.00 0.00 0.00 1.28
1764 5804 1.631388 TGGCTCGGTATTCTCCCAAAA 59.369 47.619 0.00 0.00 0.00 2.44
1765 5805 2.040545 TGGCTCGGTATTCTCCCAAAAA 59.959 45.455 0.00 0.00 0.00 1.94
1794 5834 2.637382 ACAAAGTGGGCCCTTTTAATGG 59.363 45.455 25.70 13.28 32.42 3.16
1847 5891 0.247736 GTCCATCCTCAACGAGCACT 59.752 55.000 0.00 0.00 0.00 4.40
1857 5901 3.241059 CGAGCACTAGACGCACGC 61.241 66.667 13.33 0.10 36.71 5.34
1865 5909 0.945099 CTAGACGCACGCCAGATCTA 59.055 55.000 0.00 0.00 0.00 1.98
1880 5924 4.686554 CCAGATCTAAATTACGGCAGTAGC 59.313 45.833 0.00 0.00 41.10 3.58
1885 5929 2.107950 AATTACGGCAGTAGCAGCAA 57.892 45.000 0.00 0.00 44.61 3.91
1887 5931 0.320374 TTACGGCAGTAGCAGCAACT 59.680 50.000 0.00 0.00 44.61 3.16
1889 5933 0.320374 ACGGCAGTAGCAGCAACTAA 59.680 50.000 0.00 0.00 44.61 2.24
1890 5934 1.002366 CGGCAGTAGCAGCAACTAAG 58.998 55.000 0.00 0.00 44.61 2.18
1913 5957 2.733956 CAACTCTAGCAGAGACCTCCT 58.266 52.381 16.81 0.00 45.07 3.69
1914 5958 3.096092 CAACTCTAGCAGAGACCTCCTT 58.904 50.000 16.81 1.19 45.07 3.36
1915 5959 3.466395 ACTCTAGCAGAGACCTCCTTT 57.534 47.619 16.81 0.00 45.07 3.11
1916 5960 3.785364 ACTCTAGCAGAGACCTCCTTTT 58.215 45.455 16.81 0.00 45.07 2.27
1917 5961 4.164204 ACTCTAGCAGAGACCTCCTTTTT 58.836 43.478 16.81 0.00 45.07 1.94
1938 5982 7.575332 TTTTTCTTTTCTTTTGAGAACACCG 57.425 32.000 0.00 0.00 0.00 4.94
1939 5983 4.287238 TCTTTTCTTTTGAGAACACCGC 57.713 40.909 0.00 0.00 0.00 5.68
1940 5984 3.692101 TCTTTTCTTTTGAGAACACCGCA 59.308 39.130 0.00 0.00 0.00 5.69
1941 5985 3.691049 TTTCTTTTGAGAACACCGCAG 57.309 42.857 0.00 0.00 0.00 5.18
1942 5986 2.613026 TCTTTTGAGAACACCGCAGA 57.387 45.000 0.00 0.00 0.00 4.26
1943 5987 2.483876 TCTTTTGAGAACACCGCAGAG 58.516 47.619 0.00 0.00 0.00 3.35
1944 5988 2.102420 TCTTTTGAGAACACCGCAGAGA 59.898 45.455 0.00 0.00 0.00 3.10
1945 5989 1.865865 TTTGAGAACACCGCAGAGAC 58.134 50.000 0.00 0.00 0.00 3.36
1946 5990 0.033504 TTGAGAACACCGCAGAGACC 59.966 55.000 0.00 0.00 0.00 3.85
1947 5991 0.827925 TGAGAACACCGCAGAGACCT 60.828 55.000 0.00 0.00 0.00 3.85
1948 5992 0.109039 GAGAACACCGCAGAGACCTC 60.109 60.000 0.00 0.00 0.00 3.85
1949 5993 1.079750 GAACACCGCAGAGACCTCC 60.080 63.158 0.00 0.00 0.00 4.30
1950 5994 1.534235 AACACCGCAGAGACCTCCT 60.534 57.895 0.00 0.00 0.00 3.69
1963 6007 2.172930 AGACCTCCTATGTGACGCTCTA 59.827 50.000 0.00 0.00 0.00 2.43
1976 6020 3.885777 GCTCTATGCGTCAAGTTGC 57.114 52.632 0.00 0.00 0.00 4.17
1977 6021 1.363744 GCTCTATGCGTCAAGTTGCT 58.636 50.000 0.00 0.00 0.00 3.91
1978 6022 1.061711 GCTCTATGCGTCAAGTTGCTG 59.938 52.381 0.00 0.00 0.00 4.41
1980 6024 0.097674 CTATGCGTCAAGTTGCTGCC 59.902 55.000 14.14 0.00 0.00 4.85
1981 6025 1.634757 TATGCGTCAAGTTGCTGCCG 61.635 55.000 14.14 7.80 0.00 5.69
1983 6027 3.022287 CGTCAAGTTGCTGCCGTT 58.978 55.556 0.00 0.00 0.00 4.44
1984 6028 1.355210 CGTCAAGTTGCTGCCGTTT 59.645 52.632 0.00 0.00 0.00 3.60
1987 6031 0.944386 TCAAGTTGCTGCCGTTTCTC 59.056 50.000 0.00 0.00 0.00 2.87
1988 6032 0.662619 CAAGTTGCTGCCGTTTCTCA 59.337 50.000 0.00 0.00 0.00 3.27
1989 6033 0.947244 AAGTTGCTGCCGTTTCTCAG 59.053 50.000 0.00 0.00 0.00 3.35
1990 6034 0.106708 AGTTGCTGCCGTTTCTCAGA 59.893 50.000 0.00 0.00 32.26 3.27
1991 6035 0.944386 GTTGCTGCCGTTTCTCAGAA 59.056 50.000 0.00 0.00 32.26 3.02
1992 6036 1.069636 GTTGCTGCCGTTTCTCAGAAG 60.070 52.381 0.00 0.00 32.26 2.85
1993 6037 1.230635 TGCTGCCGTTTCTCAGAAGC 61.231 55.000 0.00 0.00 32.26 3.86
1994 6038 1.784062 CTGCCGTTTCTCAGAAGCG 59.216 57.895 16.13 16.13 32.26 4.68
1995 6039 1.630244 CTGCCGTTTCTCAGAAGCGG 61.630 60.000 32.11 32.11 44.60 5.52
1996 6040 2.391389 GCCGTTTCTCAGAAGCGGG 61.391 63.158 35.16 21.24 42.34 6.13
1997 6041 1.741770 CCGTTTCTCAGAAGCGGGG 60.742 63.158 29.72 9.76 38.86 5.73
1998 6042 2.391389 CGTTTCTCAGAAGCGGGGC 61.391 63.158 15.36 0.00 0.00 5.80
1999 6043 1.003233 GTTTCTCAGAAGCGGGGCT 60.003 57.895 0.00 0.00 42.56 5.19
2007 6051 4.394712 AAGCGGGGCTTCGACTGG 62.395 66.667 0.00 0.00 46.77 4.00
2012 6056 4.785453 GGGCTTCGACTGGGCCAG 62.785 72.222 31.62 31.62 46.87 4.85
2024 6068 3.001514 GGCCAGCCCATGAAGAGA 58.998 61.111 0.00 0.00 0.00 3.10
2025 6069 1.153005 GGCCAGCCCATGAAGAGAG 60.153 63.158 0.00 0.00 0.00 3.20
2026 6070 1.823041 GCCAGCCCATGAAGAGAGC 60.823 63.158 0.00 0.00 0.00 4.09
2027 6071 1.605992 CCAGCCCATGAAGAGAGCA 59.394 57.895 0.00 0.00 0.00 4.26
2028 6072 0.034767 CCAGCCCATGAAGAGAGCAA 60.035 55.000 0.00 0.00 0.00 3.91
2029 6073 1.615116 CCAGCCCATGAAGAGAGCAAA 60.615 52.381 0.00 0.00 0.00 3.68
2030 6074 2.165167 CAGCCCATGAAGAGAGCAAAA 58.835 47.619 0.00 0.00 0.00 2.44
2031 6075 2.094854 CAGCCCATGAAGAGAGCAAAAC 60.095 50.000 0.00 0.00 0.00 2.43
2032 6076 1.135575 GCCCATGAAGAGAGCAAAACG 60.136 52.381 0.00 0.00 0.00 3.60
2033 6077 1.135575 CCCATGAAGAGAGCAAAACGC 60.136 52.381 0.00 0.00 42.91 4.84
2034 6078 1.536766 CCATGAAGAGAGCAAAACGCA 59.463 47.619 0.00 0.00 46.13 5.24
2035 6079 2.578495 CATGAAGAGAGCAAAACGCAC 58.422 47.619 0.00 0.00 46.13 5.34
2036 6080 1.953559 TGAAGAGAGCAAAACGCACT 58.046 45.000 0.00 0.00 45.03 4.40
2037 6081 1.599071 TGAAGAGAGCAAAACGCACTG 59.401 47.619 0.00 0.00 42.12 3.66
2038 6082 1.599542 GAAGAGAGCAAAACGCACTGT 59.400 47.619 0.00 0.00 42.12 3.55
2039 6083 0.940126 AGAGAGCAAAACGCACTGTG 59.060 50.000 2.76 2.76 42.12 3.66
2040 6084 0.040958 GAGAGCAAAACGCACTGTGG 60.041 55.000 10.21 2.45 42.12 4.17
2041 6085 1.658409 GAGCAAAACGCACTGTGGC 60.658 57.895 10.21 3.19 46.13 5.01
2042 6086 2.658268 GCAAAACGCACTGTGGCC 60.658 61.111 10.21 0.00 41.79 5.36
2043 6087 2.804167 CAAAACGCACTGTGGCCA 59.196 55.556 0.00 0.00 0.00 5.36
2048 6092 0.179113 AACGCACTGTGGCCAAAAAG 60.179 50.000 7.24 8.58 0.00 2.27
2061 6105 6.379703 TGTGGCCAAAAAGTATATATGCAGTT 59.620 34.615 7.24 0.00 0.00 3.16
2081 8029 1.811965 TGCAAGGATTCGAACACATGG 59.188 47.619 0.00 0.00 0.00 3.66
2087 8035 1.233950 ATTCGAACACATGGCGCACA 61.234 50.000 10.83 5.20 0.00 4.57
2097 8045 3.124128 CACATGGCGCACATCTATACATC 59.876 47.826 10.83 0.00 37.84 3.06
2114 8062 3.090037 ACATCACGAGTTACTACCAGCT 58.910 45.455 0.00 0.00 0.00 4.24
2117 8065 2.486982 TCACGAGTTACTACCAGCTGAC 59.513 50.000 17.39 3.79 0.00 3.51
2135 8083 3.944476 CCTAGCAGGTGAAGCTGTT 57.056 52.632 10.90 7.63 43.33 3.16
2150 8098 5.348724 TGAAGCTGTTTAAAGAGTAGCATCG 59.651 40.000 13.37 0.00 35.54 3.84
2155 8103 4.933400 TGTTTAAAGAGTAGCATCGAACCC 59.067 41.667 0.00 0.00 0.00 4.11
2159 8107 3.252974 AGAGTAGCATCGAACCCAAAG 57.747 47.619 0.00 0.00 0.00 2.77
2176 8124 2.422276 AAGAACCAAACATTCTGCGC 57.578 45.000 0.00 0.00 36.52 6.09
2177 8125 1.317613 AGAACCAAACATTCTGCGCA 58.682 45.000 10.98 10.98 35.06 6.09
2178 8126 1.267806 AGAACCAAACATTCTGCGCAG 59.732 47.619 31.53 31.53 35.06 5.18
2179 8127 1.266718 GAACCAAACATTCTGCGCAGA 59.733 47.619 35.30 35.30 35.27 4.26
2180 8128 1.538047 ACCAAACATTCTGCGCAGAT 58.462 45.000 38.40 25.11 37.29 2.90
2181 8129 1.470098 ACCAAACATTCTGCGCAGATC 59.530 47.619 38.40 0.00 37.29 2.75
2182 8130 1.202222 CCAAACATTCTGCGCAGATCC 60.202 52.381 38.40 0.00 37.29 3.36
2183 8131 0.729116 AAACATTCTGCGCAGATCCG 59.271 50.000 38.40 29.25 37.29 4.18
2184 8132 0.108186 AACATTCTGCGCAGATCCGA 60.108 50.000 38.40 25.12 37.29 4.55
2185 8133 0.108186 ACATTCTGCGCAGATCCGAA 60.108 50.000 38.40 24.73 37.29 4.30
2186 8134 1.224075 CATTCTGCGCAGATCCGAAT 58.776 50.000 38.40 25.81 37.29 3.34
2187 8135 1.194098 CATTCTGCGCAGATCCGAATC 59.806 52.381 38.40 0.00 37.29 2.52
2188 8136 0.175531 TTCTGCGCAGATCCGAATCA 59.824 50.000 38.40 19.84 37.29 2.57
2189 8137 0.249197 TCTGCGCAGATCCGAATCAG 60.249 55.000 35.30 7.31 34.07 2.90
2190 8138 0.529337 CTGCGCAGATCCGAATCAGT 60.529 55.000 33.66 0.00 34.07 3.41
2191 8139 0.108186 TGCGCAGATCCGAATCAGTT 60.108 50.000 5.66 0.00 34.07 3.16
2192 8140 1.009829 GCGCAGATCCGAATCAGTTT 58.990 50.000 0.30 0.00 34.07 2.66
2193 8141 2.201732 GCGCAGATCCGAATCAGTTTA 58.798 47.619 0.30 0.00 34.07 2.01
2194 8142 2.802816 GCGCAGATCCGAATCAGTTTAT 59.197 45.455 0.30 0.00 34.07 1.40
2195 8143 3.987868 GCGCAGATCCGAATCAGTTTATA 59.012 43.478 0.30 0.00 34.07 0.98
2196 8144 4.090642 GCGCAGATCCGAATCAGTTTATAG 59.909 45.833 0.30 0.00 34.07 1.31
2197 8145 4.090642 CGCAGATCCGAATCAGTTTATAGC 59.909 45.833 0.00 0.00 34.07 2.97
2198 8146 4.991056 GCAGATCCGAATCAGTTTATAGCA 59.009 41.667 0.00 0.00 34.07 3.49
2199 8147 5.641209 GCAGATCCGAATCAGTTTATAGCAT 59.359 40.000 0.00 0.00 34.07 3.79
2200 8148 6.183360 GCAGATCCGAATCAGTTTATAGCATC 60.183 42.308 0.00 0.00 34.07 3.91
2201 8149 6.034363 CAGATCCGAATCAGTTTATAGCATCG 59.966 42.308 0.00 0.00 34.07 3.84
2202 8150 5.447624 TCCGAATCAGTTTATAGCATCGA 57.552 39.130 0.00 0.00 0.00 3.59
2203 8151 5.838529 TCCGAATCAGTTTATAGCATCGAA 58.161 37.500 0.00 0.00 0.00 3.71
2204 8152 5.690409 TCCGAATCAGTTTATAGCATCGAAC 59.310 40.000 0.00 0.00 0.00 3.95
2205 8153 5.107453 CCGAATCAGTTTATAGCATCGAACC 60.107 44.000 0.00 0.00 0.00 3.62
2206 8154 5.692204 CGAATCAGTTTATAGCATCGAACCT 59.308 40.000 0.00 0.00 0.00 3.50
2207 8155 6.861572 CGAATCAGTTTATAGCATCGAACCTA 59.138 38.462 0.00 0.00 0.00 3.08
2208 8156 7.381408 CGAATCAGTTTATAGCATCGAACCTAA 59.619 37.037 0.00 0.00 0.00 2.69
2209 8157 8.958119 AATCAGTTTATAGCATCGAACCTAAA 57.042 30.769 0.00 0.00 0.00 1.85
2210 8158 8.594881 ATCAGTTTATAGCATCGAACCTAAAG 57.405 34.615 0.00 0.00 0.00 1.85
2211 8159 7.778083 TCAGTTTATAGCATCGAACCTAAAGA 58.222 34.615 0.00 0.00 0.00 2.52
2212 8160 8.255206 TCAGTTTATAGCATCGAACCTAAAGAA 58.745 33.333 0.00 0.00 0.00 2.52
2213 8161 8.328864 CAGTTTATAGCATCGAACCTAAAGAAC 58.671 37.037 0.00 1.16 0.00 3.01
2214 8162 7.494952 AGTTTATAGCATCGAACCTAAAGAACC 59.505 37.037 0.00 0.00 0.00 3.62
2215 8163 3.695830 AGCATCGAACCTAAAGAACCA 57.304 42.857 0.00 0.00 0.00 3.67
2216 8164 4.015872 AGCATCGAACCTAAAGAACCAA 57.984 40.909 0.00 0.00 0.00 3.67
2217 8165 4.394729 AGCATCGAACCTAAAGAACCAAA 58.605 39.130 0.00 0.00 0.00 3.28
2218 8166 4.215613 AGCATCGAACCTAAAGAACCAAAC 59.784 41.667 0.00 0.00 0.00 2.93
2219 8167 4.023536 GCATCGAACCTAAAGAACCAAACA 60.024 41.667 0.00 0.00 0.00 2.83
2220 8168 5.335661 GCATCGAACCTAAAGAACCAAACAT 60.336 40.000 0.00 0.00 0.00 2.71
2221 8169 6.677913 CATCGAACCTAAAGAACCAAACATT 58.322 36.000 0.00 0.00 0.00 2.71
2222 8170 6.308371 TCGAACCTAAAGAACCAAACATTC 57.692 37.500 0.00 0.00 0.00 2.67
2223 8171 6.059484 TCGAACCTAAAGAACCAAACATTCT 58.941 36.000 0.00 0.00 38.05 2.40
2224 8172 6.017440 TCGAACCTAAAGAACCAAACATTCTG 60.017 38.462 0.00 0.00 36.52 3.02
2225 8173 5.453567 ACCTAAAGAACCAAACATTCTGC 57.546 39.130 0.00 0.00 36.52 4.26
2226 8174 4.023193 ACCTAAAGAACCAAACATTCTGCG 60.023 41.667 0.00 0.00 36.52 5.18
2240 8188 0.249197 TCTGCGCAGATCCGAATCAG 60.249 55.000 35.30 7.31 34.07 2.90
2260 8208 5.067273 TCAGTTTAGGAATTTCGGAAGCAA 58.933 37.500 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 182 3.352652 GGAGACGTTCTTCGATAACTCG 58.647 50.000 8.88 3.64 46.41 4.18
363 370 2.352001 CGTCGATGACCCGTAGCG 60.352 66.667 0.00 0.00 0.00 4.26
422 429 0.179145 CGACGACCACGGCTTTAGAT 60.179 55.000 0.00 0.00 46.46 1.98
447 454 3.666253 TCGCGACGAGCTTGGACA 61.666 61.111 3.71 0.00 45.59 4.02
476 483 1.151777 GCCGGCGAAATCAAGATCGA 61.152 55.000 12.58 0.00 41.43 3.59
477 484 1.276844 GCCGGCGAAATCAAGATCG 59.723 57.895 12.58 0.00 41.81 3.69
478 485 1.649267 GGCCGGCGAAATCAAGATC 59.351 57.895 22.54 0.00 0.00 2.75
509 516 3.733344 TATGAGCTCCGCGTTGGCC 62.733 63.158 12.15 0.00 37.80 5.36
535 542 3.194968 CCCATATCCGGCTTATAACTCGT 59.805 47.826 0.00 0.00 0.00 4.18
536 543 3.446161 TCCCATATCCGGCTTATAACTCG 59.554 47.826 0.00 0.00 0.00 4.18
548 556 0.747255 CCTAGCCGATCCCATATCCG 59.253 60.000 0.00 0.00 0.00 4.18
563 571 5.182380 TCTTTTGCATTTTAACCGGACCTAG 59.818 40.000 9.46 0.00 0.00 3.02
570 578 4.981674 TCAGCTTCTTTTGCATTTTAACCG 59.018 37.500 0.00 0.00 0.00 4.44
575 583 4.405116 TGGTCAGCTTCTTTTGCATTTT 57.595 36.364 0.00 0.00 0.00 1.82
578 586 3.385755 ACTTTGGTCAGCTTCTTTTGCAT 59.614 39.130 0.00 0.00 0.00 3.96
579 587 2.760092 ACTTTGGTCAGCTTCTTTTGCA 59.240 40.909 0.00 0.00 0.00 4.08
580 588 3.443099 ACTTTGGTCAGCTTCTTTTGC 57.557 42.857 0.00 0.00 0.00 3.68
581 589 4.800471 GTGAACTTTGGTCAGCTTCTTTTG 59.200 41.667 0.00 0.00 0.00 2.44
582 590 4.462483 TGTGAACTTTGGTCAGCTTCTTTT 59.538 37.500 0.00 0.00 0.00 2.27
583 591 4.016444 TGTGAACTTTGGTCAGCTTCTTT 58.984 39.130 0.00 0.00 0.00 2.52
584 592 3.378427 GTGTGAACTTTGGTCAGCTTCTT 59.622 43.478 0.00 0.00 0.00 2.52
585 593 2.945668 GTGTGAACTTTGGTCAGCTTCT 59.054 45.455 0.00 0.00 0.00 2.85
586 594 2.682856 TGTGTGAACTTTGGTCAGCTTC 59.317 45.455 0.00 0.00 0.00 3.86
587 595 2.684881 CTGTGTGAACTTTGGTCAGCTT 59.315 45.455 0.00 0.00 0.00 3.74
588 596 2.092968 TCTGTGTGAACTTTGGTCAGCT 60.093 45.455 0.00 0.00 0.00 4.24
589 597 2.288666 TCTGTGTGAACTTTGGTCAGC 58.711 47.619 0.00 0.00 0.00 4.26
590 598 4.438744 GGTTTCTGTGTGAACTTTGGTCAG 60.439 45.833 0.00 0.00 33.88 3.51
591 599 3.442273 GGTTTCTGTGTGAACTTTGGTCA 59.558 43.478 0.00 0.00 33.88 4.02
592 600 3.486875 CGGTTTCTGTGTGAACTTTGGTC 60.487 47.826 0.00 0.00 33.88 4.02
593 601 2.422127 CGGTTTCTGTGTGAACTTTGGT 59.578 45.455 0.00 0.00 33.88 3.67
594 602 2.680841 TCGGTTTCTGTGTGAACTTTGG 59.319 45.455 0.00 0.00 33.88 3.28
595 603 3.374058 ACTCGGTTTCTGTGTGAACTTTG 59.626 43.478 0.00 0.00 33.88 2.77
596 604 3.606687 ACTCGGTTTCTGTGTGAACTTT 58.393 40.909 0.00 0.00 33.88 2.66
597 605 3.261981 ACTCGGTTTCTGTGTGAACTT 57.738 42.857 0.00 0.00 33.88 2.66
598 606 2.981859 ACTCGGTTTCTGTGTGAACT 57.018 45.000 0.00 0.00 33.88 3.01
599 607 4.351131 AAAACTCGGTTTCTGTGTGAAC 57.649 40.909 3.06 0.00 34.43 3.18
624 632 6.385649 AAAAAGAGGTCATAGTCGCAAAAA 57.614 33.333 0.00 0.00 0.00 1.94
685 693 2.666508 ACGTACTTAAGCAATGCGACTG 59.333 45.455 1.29 0.00 0.00 3.51
700 708 3.196685 AGAAGGAGTACCGAGTACGTACT 59.803 47.826 27.71 27.71 43.05 2.73
751 759 5.451381 CCAACAAGTCCATATCTGTACGCTA 60.451 44.000 0.00 0.00 0.00 4.26
862 4874 0.942962 CTGCCCATCGATCAAGCTTC 59.057 55.000 0.00 0.00 0.00 3.86
979 4991 4.317671 TTGCTAGCTATCTACGGGTTTC 57.682 45.455 17.23 0.00 0.00 2.78
1191 5205 6.810182 TCACGCTTAGAGGAAAAATACAGTAC 59.190 38.462 0.00 0.00 0.00 2.73
1251 5265 3.324930 TCCTCTGCACCCAGCCTG 61.325 66.667 0.00 0.00 44.83 4.85
1482 5496 9.710979 ATCAAACCATAATTAAACGTTCGTATG 57.289 29.630 0.00 7.29 0.00 2.39
1578 5605 9.012161 GGGACAGAAATCGTACTACTCTATATT 57.988 37.037 0.00 0.00 0.00 1.28
1579 5606 7.333921 CGGGACAGAAATCGTACTACTCTATAT 59.666 40.741 0.00 0.00 0.00 0.86
1580 5607 6.648310 CGGGACAGAAATCGTACTACTCTATA 59.352 42.308 0.00 0.00 0.00 1.31
1581 5608 5.469421 CGGGACAGAAATCGTACTACTCTAT 59.531 44.000 0.00 0.00 0.00 1.98
1582 5609 4.813161 CGGGACAGAAATCGTACTACTCTA 59.187 45.833 0.00 0.00 0.00 2.43
1583 5610 3.626670 CGGGACAGAAATCGTACTACTCT 59.373 47.826 0.00 0.00 0.00 3.24
1584 5611 3.791455 GCGGGACAGAAATCGTACTACTC 60.791 52.174 0.00 0.00 0.00 2.59
1585 5612 2.098770 GCGGGACAGAAATCGTACTACT 59.901 50.000 0.00 0.00 0.00 2.57
1586 5613 2.159338 TGCGGGACAGAAATCGTACTAC 60.159 50.000 0.00 0.00 0.00 2.73
1764 5804 4.231273 AGGGCCCACTTTGTTAGAAATTT 58.769 39.130 27.56 0.00 0.00 1.82
1765 5805 3.856900 AGGGCCCACTTTGTTAGAAATT 58.143 40.909 27.56 0.00 0.00 1.82
1766 5806 3.542969 AGGGCCCACTTTGTTAGAAAT 57.457 42.857 27.56 0.00 0.00 2.17
1769 5809 3.322191 AAAAGGGCCCACTTTGTTAGA 57.678 42.857 27.56 0.00 40.36 2.10
1772 5812 3.072330 CCATTAAAAGGGCCCACTTTGTT 59.928 43.478 27.56 7.02 40.36 2.83
1780 5820 1.207089 GTGCTTCCATTAAAAGGGCCC 59.793 52.381 16.46 16.46 0.00 5.80
1847 5891 1.385528 TTAGATCTGGCGTGCGTCTA 58.614 50.000 5.18 0.00 0.00 2.59
1857 5901 4.686554 GCTACTGCCGTAATTTAGATCTGG 59.313 45.833 5.18 0.00 0.00 3.86
1865 5909 2.107950 TGCTGCTACTGCCGTAATTT 57.892 45.000 0.00 0.00 38.71 1.82
1880 5924 3.616379 GCTAGAGTTGCTCTTAGTTGCTG 59.384 47.826 3.87 0.00 41.50 4.41
1885 5929 4.398044 GTCTCTGCTAGAGTTGCTCTTAGT 59.602 45.833 3.87 0.00 42.83 2.24
1887 5931 3.697045 GGTCTCTGCTAGAGTTGCTCTTA 59.303 47.826 3.87 0.00 42.83 2.10
1889 5933 2.099405 GGTCTCTGCTAGAGTTGCTCT 58.901 52.381 11.37 4.02 42.83 4.09
1890 5934 2.099098 GAGGTCTCTGCTAGAGTTGCTC 59.901 54.545 11.37 0.00 42.83 4.26
1914 5958 6.090223 GCGGTGTTCTCAAAAGAAAAGAAAAA 59.910 34.615 0.00 0.00 43.04 1.94
1915 5959 5.575218 GCGGTGTTCTCAAAAGAAAAGAAAA 59.425 36.000 0.00 0.00 43.04 2.29
1916 5960 5.099575 GCGGTGTTCTCAAAAGAAAAGAAA 58.900 37.500 0.00 0.00 43.04 2.52
1917 5961 4.156922 TGCGGTGTTCTCAAAAGAAAAGAA 59.843 37.500 0.00 0.00 43.04 2.52
1918 5962 3.692101 TGCGGTGTTCTCAAAAGAAAAGA 59.308 39.130 0.00 0.00 43.04 2.52
1919 5963 4.027572 TGCGGTGTTCTCAAAAGAAAAG 57.972 40.909 0.00 0.00 43.04 2.27
1920 5964 3.692101 TCTGCGGTGTTCTCAAAAGAAAA 59.308 39.130 0.00 0.00 43.04 2.29
1921 5965 3.275143 TCTGCGGTGTTCTCAAAAGAAA 58.725 40.909 0.00 0.00 43.04 2.52
1922 5966 2.872245 CTCTGCGGTGTTCTCAAAAGAA 59.128 45.455 0.00 0.00 39.22 2.52
1923 5967 2.102420 TCTCTGCGGTGTTCTCAAAAGA 59.898 45.455 0.00 0.00 0.00 2.52
1924 5968 2.221981 GTCTCTGCGGTGTTCTCAAAAG 59.778 50.000 0.00 0.00 0.00 2.27
1925 5969 2.210116 GTCTCTGCGGTGTTCTCAAAA 58.790 47.619 0.00 0.00 0.00 2.44
1926 5970 1.540363 GGTCTCTGCGGTGTTCTCAAA 60.540 52.381 0.00 0.00 0.00 2.69
1927 5971 0.033504 GGTCTCTGCGGTGTTCTCAA 59.966 55.000 0.00 0.00 0.00 3.02
1928 5972 0.827925 AGGTCTCTGCGGTGTTCTCA 60.828 55.000 0.00 0.00 0.00 3.27
1929 5973 0.109039 GAGGTCTCTGCGGTGTTCTC 60.109 60.000 0.00 0.00 0.00 2.87
1930 5974 1.536943 GGAGGTCTCTGCGGTGTTCT 61.537 60.000 0.00 0.00 0.00 3.01
1931 5975 1.079750 GGAGGTCTCTGCGGTGTTC 60.080 63.158 0.00 0.00 0.00 3.18
1932 5976 0.251653 TAGGAGGTCTCTGCGGTGTT 60.252 55.000 0.00 0.00 36.39 3.32
1933 5977 0.033011 ATAGGAGGTCTCTGCGGTGT 60.033 55.000 0.00 0.00 36.39 4.16
1934 5978 0.387202 CATAGGAGGTCTCTGCGGTG 59.613 60.000 0.00 0.00 36.39 4.94
1935 5979 0.033011 ACATAGGAGGTCTCTGCGGT 60.033 55.000 0.00 0.00 36.39 5.68
1936 5980 0.387202 CACATAGGAGGTCTCTGCGG 59.613 60.000 0.00 0.00 36.39 5.69
1937 5981 1.066303 GTCACATAGGAGGTCTCTGCG 59.934 57.143 0.00 0.00 36.39 5.18
1938 5982 1.066303 CGTCACATAGGAGGTCTCTGC 59.934 57.143 0.00 0.00 0.00 4.26
1939 5983 1.066303 GCGTCACATAGGAGGTCTCTG 59.934 57.143 0.00 0.00 0.00 3.35
1940 5984 1.064314 AGCGTCACATAGGAGGTCTCT 60.064 52.381 0.00 0.00 0.00 3.10
1941 5985 1.335496 GAGCGTCACATAGGAGGTCTC 59.665 57.143 0.00 0.00 0.00 3.36
1942 5986 1.064314 AGAGCGTCACATAGGAGGTCT 60.064 52.381 0.00 0.00 0.00 3.85
1943 5987 1.394618 AGAGCGTCACATAGGAGGTC 58.605 55.000 0.00 0.00 0.00 3.85
1944 5988 2.730934 TAGAGCGTCACATAGGAGGT 57.269 50.000 0.00 0.00 0.00 3.85
1945 5989 2.352225 GCATAGAGCGTCACATAGGAGG 60.352 54.545 0.00 0.00 0.00 4.30
1946 5990 2.940147 GCATAGAGCGTCACATAGGAG 58.060 52.381 0.00 0.00 0.00 3.69
1963 6007 2.956987 GGCAGCAACTTGACGCAT 59.043 55.556 0.00 0.00 0.00 4.73
1970 6014 0.947244 CTGAGAAACGGCAGCAACTT 59.053 50.000 0.00 0.00 0.00 2.66
1972 6016 0.944386 TTCTGAGAAACGGCAGCAAC 59.056 50.000 0.00 0.00 32.27 4.17
1973 6017 1.229428 CTTCTGAGAAACGGCAGCAA 58.771 50.000 0.00 0.00 32.27 3.91
1974 6018 1.230635 GCTTCTGAGAAACGGCAGCA 61.231 55.000 0.00 0.00 42.21 4.41
1975 6019 1.499502 GCTTCTGAGAAACGGCAGC 59.500 57.895 0.00 0.00 37.04 5.25
1976 6020 1.630244 CCGCTTCTGAGAAACGGCAG 61.630 60.000 22.07 6.87 37.05 4.85
1977 6021 1.667830 CCGCTTCTGAGAAACGGCA 60.668 57.895 22.07 0.00 37.05 5.69
1978 6022 2.391389 CCCGCTTCTGAGAAACGGC 61.391 63.158 26.73 12.31 42.49 5.68
1980 6024 2.391389 GCCCCGCTTCTGAGAAACG 61.391 63.158 10.76 10.76 0.00 3.60
1981 6025 0.606673 AAGCCCCGCTTCTGAGAAAC 60.607 55.000 0.00 0.00 46.77 2.78
1983 6027 3.483587 AAGCCCCGCTTCTGAGAA 58.516 55.556 0.00 0.00 46.77 2.87
1995 6039 4.785453 CTGGCCCAGTCGAAGCCC 62.785 72.222 1.39 0.00 46.55 5.19
2007 6051 1.153005 CTCTCTTCATGGGCTGGCC 60.153 63.158 14.23 14.23 0.00 5.36
2008 6052 1.823041 GCTCTCTTCATGGGCTGGC 60.823 63.158 0.00 0.00 0.00 4.85
2009 6053 0.034767 TTGCTCTCTTCATGGGCTGG 60.035 55.000 0.00 0.00 0.00 4.85
2010 6054 1.830279 TTTGCTCTCTTCATGGGCTG 58.170 50.000 0.00 0.00 0.00 4.85
2011 6055 2.165998 GTTTTGCTCTCTTCATGGGCT 58.834 47.619 0.00 0.00 0.00 5.19
2012 6056 1.135575 CGTTTTGCTCTCTTCATGGGC 60.136 52.381 0.00 0.00 0.00 5.36
2013 6057 1.135575 GCGTTTTGCTCTCTTCATGGG 60.136 52.381 0.00 0.00 41.73 4.00
2014 6058 1.536766 TGCGTTTTGCTCTCTTCATGG 59.463 47.619 0.00 0.00 46.63 3.66
2015 6059 2.225019 AGTGCGTTTTGCTCTCTTCATG 59.775 45.455 0.00 0.00 43.68 3.07
2016 6060 2.225019 CAGTGCGTTTTGCTCTCTTCAT 59.775 45.455 0.00 0.00 45.22 2.57
2017 6061 1.599071 CAGTGCGTTTTGCTCTCTTCA 59.401 47.619 0.00 0.00 45.22 3.02
2018 6062 1.599542 ACAGTGCGTTTTGCTCTCTTC 59.400 47.619 0.00 0.00 45.22 2.87
2019 6063 1.331756 CACAGTGCGTTTTGCTCTCTT 59.668 47.619 0.00 0.00 45.22 2.85
2020 6064 0.940126 CACAGTGCGTTTTGCTCTCT 59.060 50.000 0.00 0.00 45.22 3.10
2021 6065 0.040958 CCACAGTGCGTTTTGCTCTC 60.041 55.000 0.00 0.00 45.22 3.20
2023 6067 1.658409 GCCACAGTGCGTTTTGCTC 60.658 57.895 0.00 0.00 46.63 4.26
2024 6068 2.412937 GCCACAGTGCGTTTTGCT 59.587 55.556 0.00 0.00 46.63 3.91
2025 6069 2.658268 GGCCACAGTGCGTTTTGC 60.658 61.111 0.00 0.00 46.70 3.68
2026 6070 0.459237 TTTGGCCACAGTGCGTTTTG 60.459 50.000 3.88 0.00 0.00 2.44
2027 6071 0.247736 TTTTGGCCACAGTGCGTTTT 59.752 45.000 3.88 0.00 0.00 2.43
2028 6072 0.247736 TTTTTGGCCACAGTGCGTTT 59.752 45.000 3.88 0.00 0.00 3.60
2029 6073 0.179113 CTTTTTGGCCACAGTGCGTT 60.179 50.000 3.88 0.00 0.00 4.84
2030 6074 1.319614 ACTTTTTGGCCACAGTGCGT 61.320 50.000 3.88 0.00 0.00 5.24
2031 6075 0.665835 TACTTTTTGGCCACAGTGCG 59.334 50.000 18.01 3.61 0.00 5.34
2032 6076 4.718940 ATATACTTTTTGGCCACAGTGC 57.281 40.909 18.01 0.00 0.00 4.40
2033 6077 6.183360 TGCATATATACTTTTTGGCCACAGTG 60.183 38.462 18.01 7.40 0.00 3.66
2034 6078 5.890985 TGCATATATACTTTTTGGCCACAGT 59.109 36.000 3.88 11.01 0.00 3.55
2035 6079 6.039717 ACTGCATATATACTTTTTGGCCACAG 59.960 38.462 3.88 6.82 0.00 3.66
2036 6080 5.890985 ACTGCATATATACTTTTTGGCCACA 59.109 36.000 3.88 0.00 0.00 4.17
2037 6081 6.391227 ACTGCATATATACTTTTTGGCCAC 57.609 37.500 3.88 0.00 0.00 5.01
2038 6082 6.682611 GCAACTGCATATATACTTTTTGGCCA 60.683 38.462 0.00 0.00 41.59 5.36
2039 6083 5.691754 GCAACTGCATATATACTTTTTGGCC 59.308 40.000 0.00 0.00 41.59 5.36
2040 6084 6.753897 GCAACTGCATATATACTTTTTGGC 57.246 37.500 0.00 0.00 41.59 4.52
2061 6105 1.811965 CCATGTGTTCGAATCCTTGCA 59.188 47.619 0.00 0.00 0.00 4.08
2064 6108 1.086696 CGCCATGTGTTCGAATCCTT 58.913 50.000 0.00 0.00 0.00 3.36
2065 6109 1.369091 GCGCCATGTGTTCGAATCCT 61.369 55.000 0.00 0.00 0.00 3.24
2071 8019 1.226101 GATGTGCGCCATGTGTTCG 60.226 57.895 14.84 0.00 32.56 3.95
2081 8029 2.658802 CTCGTGATGTATAGATGTGCGC 59.341 50.000 0.00 0.00 0.00 6.09
2087 8035 7.094720 GCTGGTAGTAACTCGTGATGTATAGAT 60.095 40.741 0.00 0.00 0.00 1.98
2097 8045 2.415625 GGTCAGCTGGTAGTAACTCGTG 60.416 54.545 15.13 0.00 0.00 4.35
2117 8065 2.191128 AAACAGCTTCACCTGCTAGG 57.809 50.000 0.00 1.16 42.49 3.02
2131 8079 5.063564 GGGTTCGATGCTACTCTTTAAACAG 59.936 44.000 0.00 0.00 0.00 3.16
2132 8080 4.933400 GGGTTCGATGCTACTCTTTAAACA 59.067 41.667 0.00 0.00 0.00 2.83
2133 8081 4.933400 TGGGTTCGATGCTACTCTTTAAAC 59.067 41.667 0.00 0.00 0.00 2.01
2134 8082 5.155278 TGGGTTCGATGCTACTCTTTAAA 57.845 39.130 0.00 0.00 0.00 1.52
2135 8083 4.811969 TGGGTTCGATGCTACTCTTTAA 57.188 40.909 0.00 0.00 0.00 1.52
2150 8098 5.049828 CAGAATGTTTGGTTCTTTGGGTTC 58.950 41.667 0.00 0.00 33.82 3.62
2155 8103 2.472488 GCGCAGAATGTTTGGTTCTTTG 59.528 45.455 0.30 0.00 39.31 2.77
2159 8107 1.266718 TCTGCGCAGAATGTTTGGTTC 59.733 47.619 36.62 0.00 39.31 3.62
2176 8124 6.034363 CGATGCTATAAACTGATTCGGATCTG 59.966 42.308 8.92 8.92 37.29 2.90
2177 8125 6.071896 TCGATGCTATAAACTGATTCGGATCT 60.072 38.462 5.06 0.00 33.28 2.75
2178 8126 6.093404 TCGATGCTATAAACTGATTCGGATC 58.907 40.000 0.00 0.00 0.00 3.36
2179 8127 6.025749 TCGATGCTATAAACTGATTCGGAT 57.974 37.500 0.00 0.00 0.00 4.18
2180 8128 5.447624 TCGATGCTATAAACTGATTCGGA 57.552 39.130 0.00 0.00 0.00 4.55
2181 8129 5.107453 GGTTCGATGCTATAAACTGATTCGG 60.107 44.000 0.00 0.00 0.00 4.30
2182 8130 5.692204 AGGTTCGATGCTATAAACTGATTCG 59.308 40.000 0.00 0.00 0.00 3.34
2183 8131 8.589335 TTAGGTTCGATGCTATAAACTGATTC 57.411 34.615 0.00 0.00 0.00 2.52
2184 8132 8.958119 TTTAGGTTCGATGCTATAAACTGATT 57.042 30.769 0.00 0.00 0.00 2.57
2185 8133 8.421784 TCTTTAGGTTCGATGCTATAAACTGAT 58.578 33.333 0.00 0.00 0.00 2.90
2186 8134 7.778083 TCTTTAGGTTCGATGCTATAAACTGA 58.222 34.615 0.00 0.00 0.00 3.41
2187 8135 8.328864 GTTCTTTAGGTTCGATGCTATAAACTG 58.671 37.037 0.00 0.00 0.00 3.16
2188 8136 7.494952 GGTTCTTTAGGTTCGATGCTATAAACT 59.505 37.037 0.00 0.00 0.00 2.66
2189 8137 7.279313 TGGTTCTTTAGGTTCGATGCTATAAAC 59.721 37.037 0.00 0.00 0.00 2.01
2190 8138 7.332557 TGGTTCTTTAGGTTCGATGCTATAAA 58.667 34.615 0.00 0.00 0.00 1.40
2191 8139 6.880484 TGGTTCTTTAGGTTCGATGCTATAA 58.120 36.000 0.00 0.00 0.00 0.98
2192 8140 6.474140 TGGTTCTTTAGGTTCGATGCTATA 57.526 37.500 0.00 0.00 0.00 1.31
2193 8141 5.353394 TGGTTCTTTAGGTTCGATGCTAT 57.647 39.130 0.00 0.00 0.00 2.97
2194 8142 4.811969 TGGTTCTTTAGGTTCGATGCTA 57.188 40.909 0.00 0.00 0.00 3.49
2195 8143 3.695830 TGGTTCTTTAGGTTCGATGCT 57.304 42.857 0.00 0.00 0.00 3.79
2196 8144 4.023536 TGTTTGGTTCTTTAGGTTCGATGC 60.024 41.667 0.00 0.00 0.00 3.91
2197 8145 5.682943 TGTTTGGTTCTTTAGGTTCGATG 57.317 39.130 0.00 0.00 0.00 3.84
2198 8146 6.715264 AGAATGTTTGGTTCTTTAGGTTCGAT 59.285 34.615 0.00 0.00 32.17 3.59
2199 8147 6.017440 CAGAATGTTTGGTTCTTTAGGTTCGA 60.017 38.462 0.00 0.00 33.82 3.71
2200 8148 6.142817 CAGAATGTTTGGTTCTTTAGGTTCG 58.857 40.000 0.00 0.00 33.82 3.95
2201 8149 5.920840 GCAGAATGTTTGGTTCTTTAGGTTC 59.079 40.000 0.00 0.00 39.31 3.62
2202 8150 5.507315 CGCAGAATGTTTGGTTCTTTAGGTT 60.507 40.000 0.00 0.00 39.31 3.50
2203 8151 4.023193 CGCAGAATGTTTGGTTCTTTAGGT 60.023 41.667 0.00 0.00 39.31 3.08
2204 8152 4.475944 CGCAGAATGTTTGGTTCTTTAGG 58.524 43.478 0.00 0.00 39.31 2.69
2205 8153 3.914364 GCGCAGAATGTTTGGTTCTTTAG 59.086 43.478 0.30 0.00 39.31 1.85
2206 8154 3.316588 TGCGCAGAATGTTTGGTTCTTTA 59.683 39.130 5.66 0.00 39.31 1.85
2207 8155 2.100584 TGCGCAGAATGTTTGGTTCTTT 59.899 40.909 5.66 0.00 39.31 2.52
2208 8156 1.680735 TGCGCAGAATGTTTGGTTCTT 59.319 42.857 5.66 0.00 39.31 2.52
2209 8157 1.267806 CTGCGCAGAATGTTTGGTTCT 59.732 47.619 33.66 0.00 39.31 3.01
2210 8158 1.266718 TCTGCGCAGAATGTTTGGTTC 59.733 47.619 36.62 0.00 39.31 3.62
2211 8159 1.317613 TCTGCGCAGAATGTTTGGTT 58.682 45.000 36.62 0.00 39.31 3.67
2212 8160 1.470098 GATCTGCGCAGAATGTTTGGT 59.530 47.619 40.83 23.76 41.36 3.67
2213 8161 1.202222 GGATCTGCGCAGAATGTTTGG 60.202 52.381 40.83 12.82 41.36 3.28
2214 8162 1.530441 CGGATCTGCGCAGAATGTTTG 60.530 52.381 40.83 23.50 41.36 2.93
2215 8163 0.729116 CGGATCTGCGCAGAATGTTT 59.271 50.000 40.83 26.06 41.36 2.83
2216 8164 0.108186 TCGGATCTGCGCAGAATGTT 60.108 50.000 40.83 26.45 41.36 2.71
2217 8165 0.108186 TTCGGATCTGCGCAGAATGT 60.108 50.000 40.83 26.84 41.36 2.71
2218 8166 1.194098 GATTCGGATCTGCGCAGAATG 59.806 52.381 40.83 30.84 41.36 2.67
2219 8167 1.202568 TGATTCGGATCTGCGCAGAAT 60.203 47.619 40.83 29.37 41.36 2.40
2220 8168 0.175531 TGATTCGGATCTGCGCAGAA 59.824 50.000 40.83 26.08 41.36 3.02
2221 8169 0.249197 CTGATTCGGATCTGCGCAGA 60.249 55.000 39.63 39.63 42.37 4.26
2222 8170 0.529337 ACTGATTCGGATCTGCGCAG 60.529 55.000 31.53 31.53 35.35 5.18
2223 8171 0.108186 AACTGATTCGGATCTGCGCA 60.108 50.000 10.98 10.98 35.35 6.09
2224 8172 1.009829 AAACTGATTCGGATCTGCGC 58.990 50.000 10.31 0.00 35.35 6.09
2225 8173 2.797156 CCTAAACTGATTCGGATCTGCG 59.203 50.000 10.31 0.00 35.35 5.18
2226 8174 4.060038 TCCTAAACTGATTCGGATCTGC 57.940 45.455 10.31 0.00 35.35 4.26
2240 8188 7.652300 AAAATTGCTTCCGAAATTCCTAAAC 57.348 32.000 0.00 0.00 27.90 2.01
2285 8233 2.510874 TGAAAGTGTTTGCGTTTCACG 58.489 42.857 0.00 0.00 45.88 4.35
2294 8242 9.105206 CTTTGTTCACAAATTTGAAAGTGTTTG 57.895 29.630 24.64 9.66 43.92 2.93


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

AutoCloner maintained by Alex Coulton.