Multiple sequence alignment - TraesCS2B01G186400

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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 TraesCS2B01G186400 chr2B 100.000 4180 0 0 1 4180 161409712 161405533 0.000000e+00 7720
1 TraesCS2B01G186400 chr2A 89.710 1205 91 9 2462 3665 111411223 111410051 0.000000e+00 1507
2 TraesCS2B01G186400 chr2A 91.318 933 68 8 800 1725 111413236 111412310 0.000000e+00 1262
3 TraesCS2B01G186400 chr2A 90.515 738 30 15 1 702 111414003 111413270 0.000000e+00 939
4 TraesCS2B01G186400 chr2A 89.076 595 31 11 1874 2464 111411817 111411253 0.000000e+00 708
5 TraesCS2B01G186400 chr2D 89.948 1154 69 22 2521 3665 111321213 111320098 0.000000e+00 1445
6 TraesCS2B01G186400 chr2D 87.580 942 67 31 799 1716 111323472 111322557 0.000000e+00 1046
7 TraesCS2B01G186400 chr2D 91.184 794 33 15 1 765 111324258 111323473 0.000000e+00 1044
8 TraesCS2B01G186400 chr2D 91.036 502 40 4 3680 4179 339656222 339656720 0.000000e+00 673
9 TraesCS2B01G186400 chr2D 87.873 503 51 9 3680 4180 103586948 103587442 2.170000e-162 582
10 TraesCS2B01G186400 chr2D 90.278 432 29 5 1921 2351 111321931 111321512 1.700000e-153 553
11 TraesCS2B01G186400 chr7A 90.200 500 43 5 3681 4178 734469922 734470417 0.000000e+00 647
12 TraesCS2B01G186400 chr3D 89.113 496 45 9 3681 4171 456434319 456433828 3.570000e-170 608
13 TraesCS2B01G186400 chr3D 87.921 505 53 8 3679 4180 613976559 613976060 4.660000e-164 588
14 TraesCS2B01G186400 chr1D 88.800 500 47 8 3680 4176 465458096 465458589 4.620000e-169 604
15 TraesCS2B01G186400 chr1D 88.095 504 53 6 3681 4180 402719906 402720406 3.600000e-165 592
16 TraesCS2B01G186400 chr6D 88.469 503 52 6 3681 4180 29359121 29358622 1.660000e-168 603
17 TraesCS2B01G186400 chr5D 88.469 503 50 7 3680 4180 398828511 398829007 5.980000e-168 601


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 TraesCS2B01G186400 chr2B 161405533 161409712 4179 True 7720 7720 100.00000 1 4180 1 chr2B.!!$R1 4179
1 TraesCS2B01G186400 chr2A 111410051 111414003 3952 True 1104 1507 90.15475 1 3665 4 chr2A.!!$R1 3664
2 TraesCS2B01G186400 chr2D 111320098 111324258 4160 True 1022 1445 89.74750 1 3665 4 chr2D.!!$R1 3664
3 TraesCS2B01G186400 chr1D 402719906 402720406 500 False 592 592 88.09500 3681 4180 1 chr1D.!!$F1 499

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
30 31 1.022735 CCATCTCATCCAACAGCAGC 58.977 55.0 0.0 0.0 0.00 5.25 F
1368 1437 0.890683 CAGTTCACCTGCCAAATCCC 59.109 55.0 0.0 0.0 33.59 3.85 F
2781 3578 0.327480 AGGCATGGATGGAGTGGGTA 60.327 55.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 1510 0.033504 ACTACAGAGCCACCACAACG 59.966 55.0 0.00 0.0 0.0 4.10 R
2868 3665 0.249676 ACCTAGAGAGACGTCGAGCA 59.750 55.0 10.46 0.0 0.0 4.26 R
3806 4609 0.109532 TGATTTCTTCACACCCGGCA 59.890 50.0 0.00 0.0 0.0 5.69 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
30 31 1.022735 CCATCTCATCCAACAGCAGC 58.977 55.000 0.00 0.00 0.00 5.25
71 72 3.181465 ACAGCTATCATGGTAAACTCCCG 60.181 47.826 0.00 0.00 0.00 5.14
158 161 1.267121 TTAACCAGCCGAGCTCTCTT 58.733 50.000 12.85 0.00 36.40 2.85
453 466 9.467796 TGATCATATGGTTTTGGTTTGTGTATA 57.532 29.630 2.13 0.00 0.00 1.47
562 579 9.716507 GTACAGCACCTGTAATTTGTAAATATG 57.283 33.333 6.66 0.00 46.55 1.78
563 580 8.348285 ACAGCACCTGTAATTTGTAAATATGT 57.652 30.769 0.00 0.00 43.46 2.29
564 581 9.456147 ACAGCACCTGTAATTTGTAAATATGTA 57.544 29.630 0.00 0.00 43.46 2.29
565 582 9.716507 CAGCACCTGTAATTTGTAAATATGTAC 57.283 33.333 0.00 0.00 0.00 2.90
566 583 9.681062 AGCACCTGTAATTTGTAAATATGTACT 57.319 29.630 4.68 0.00 0.00 2.73
660 703 3.936372 TGTTGCTGTACCTCTCTACAC 57.064 47.619 0.00 0.00 0.00 2.90
682 728 6.039270 ACACAAGCATCTGCAAAGTAAAGTAA 59.961 34.615 4.79 0.00 45.16 2.24
683 729 7.086376 CACAAGCATCTGCAAAGTAAAGTAAT 58.914 34.615 4.79 0.00 45.16 1.89
684 730 7.596248 CACAAGCATCTGCAAAGTAAAGTAATT 59.404 33.333 4.79 0.00 45.16 1.40
685 731 8.792633 ACAAGCATCTGCAAAGTAAAGTAATTA 58.207 29.630 4.79 0.00 45.16 1.40
703 749 7.342194 AGTAATTATGTACGTATTTGCTTGCG 58.658 34.615 12.03 0.00 0.00 4.85
716 763 2.017782 TGCTTGCGGAAAGTGTTAACA 58.982 42.857 3.59 3.59 38.25 2.41
743 790 5.904941 TCATGCCAATGTTGATAAATGACC 58.095 37.500 0.00 0.00 35.15 4.02
744 791 5.657745 TCATGCCAATGTTGATAAATGACCT 59.342 36.000 0.00 0.00 35.15 3.85
757 805 8.648698 TGATAAATGACCTGAAGATTTGGAAA 57.351 30.769 0.00 0.00 0.00 3.13
765 813 7.016465 TGACCTGAAGATTTGGAAAATGGATTT 59.984 33.333 0.00 0.00 0.00 2.17
766 814 7.389232 ACCTGAAGATTTGGAAAATGGATTTC 58.611 34.615 0.00 0.00 45.55 2.17
767 815 7.236225 ACCTGAAGATTTGGAAAATGGATTTCT 59.764 33.333 1.47 0.00 45.57 2.52
768 816 8.098912 CCTGAAGATTTGGAAAATGGATTTCTT 58.901 33.333 1.47 0.00 45.57 2.52
777 825 9.927668 TTGGAAAATGGATTTCTTATGAGTTTC 57.072 29.630 1.47 0.00 45.57 2.78
778 826 9.312904 TGGAAAATGGATTTCTTATGAGTTTCT 57.687 29.630 0.00 0.00 45.57 2.52
779 827 9.578439 GGAAAATGGATTTCTTATGAGTTTCTG 57.422 33.333 0.00 0.00 45.57 3.02
780 828 8.992835 AAAATGGATTTCTTATGAGTTTCTGC 57.007 30.769 0.00 0.00 0.00 4.26
781 829 7.707624 AATGGATTTCTTATGAGTTTCTGCA 57.292 32.000 0.00 0.00 0.00 4.41
782 830 7.707624 ATGGATTTCTTATGAGTTTCTGCAA 57.292 32.000 0.00 0.00 0.00 4.08
783 831 7.523293 TGGATTTCTTATGAGTTTCTGCAAA 57.477 32.000 0.00 0.00 0.00 3.68
784 832 7.950512 TGGATTTCTTATGAGTTTCTGCAAAA 58.049 30.769 0.00 0.00 0.00 2.44
785 833 8.084073 TGGATTTCTTATGAGTTTCTGCAAAAG 58.916 33.333 0.00 0.00 0.00 2.27
786 834 8.084684 GGATTTCTTATGAGTTTCTGCAAAAGT 58.915 33.333 0.00 0.00 0.00 2.66
787 835 9.468532 GATTTCTTATGAGTTTCTGCAAAAGTT 57.531 29.630 0.00 0.00 0.00 2.66
790 838 9.897744 TTCTTATGAGTTTCTGCAAAAGTTATG 57.102 29.630 12.48 0.00 0.00 1.90
791 839 8.023128 TCTTATGAGTTTCTGCAAAAGTTATGC 58.977 33.333 12.48 0.00 44.08 3.14
792 840 4.870363 TGAGTTTCTGCAAAAGTTATGCC 58.130 39.130 0.00 0.00 43.16 4.40
793 841 4.340666 TGAGTTTCTGCAAAAGTTATGCCA 59.659 37.500 0.00 0.00 43.16 4.92
794 842 5.010922 TGAGTTTCTGCAAAAGTTATGCCAT 59.989 36.000 0.00 0.00 43.16 4.40
795 843 5.857268 AGTTTCTGCAAAAGTTATGCCATT 58.143 33.333 0.00 0.00 43.16 3.16
796 844 6.290605 AGTTTCTGCAAAAGTTATGCCATTT 58.709 32.000 0.00 0.00 43.16 2.32
797 845 6.424812 AGTTTCTGCAAAAGTTATGCCATTTC 59.575 34.615 0.00 0.00 43.16 2.17
804 852 7.658982 TGCAAAAGTTATGCCATTTCATTTGTA 59.341 29.630 0.00 4.84 43.16 2.41
814 862 8.613060 TGCCATTTCATTTGTATTTTAGCAAA 57.387 26.923 0.00 0.00 38.68 3.68
873 921 5.328691 CGGCAGCGTATAAATTTTTGAGAA 58.671 37.500 0.00 0.00 0.00 2.87
1019 1081 3.859414 GAGCAGCCTCCGAGCCAT 61.859 66.667 0.00 0.00 31.68 4.40
1286 1351 1.066908 GATGCTAGTGAGAGAAGCGCT 59.933 52.381 2.64 2.64 39.14 5.92
1324 1389 7.464977 GCAATTGTGATTTGGCATATCTGTTTC 60.465 37.037 17.01 5.54 0.00 2.78
1338 1403 7.543172 GCATATCTGTTTCTTGCTTTTTCATGA 59.457 33.333 0.00 0.00 0.00 3.07
1342 1407 6.974622 TCTGTTTCTTGCTTTTTCATGAAGTC 59.025 34.615 8.41 0.45 33.55 3.01
1368 1437 0.890683 CAGTTCACCTGCCAAATCCC 59.109 55.000 0.00 0.00 33.59 3.85
1392 1461 2.596904 TACTACTGGGCTTCGATTGC 57.403 50.000 2.74 2.74 0.00 3.56
1409 1478 3.641437 TTGCTCGAAATTTGGGAACTG 57.359 42.857 0.00 0.00 0.00 3.16
1441 1510 2.035442 GTCGTTGGAGGAGCTTGCC 61.035 63.158 0.00 0.00 0.00 4.52
1464 1533 0.601558 GTGGTGGCTCTGTAGTTCGA 59.398 55.000 0.00 0.00 0.00 3.71
1474 1543 5.815740 GGCTCTGTAGTTCGATCCAAAATTA 59.184 40.000 0.00 0.00 0.00 1.40
1488 1557 9.438291 CGATCCAAAATTATGTGTTTCTCATAC 57.562 33.333 0.00 0.00 0.00 2.39
1522 1591 1.728323 TGTGTCCTTGTGAGATGGGA 58.272 50.000 0.00 0.00 0.00 4.37
1523 1592 1.625315 TGTGTCCTTGTGAGATGGGAG 59.375 52.381 0.00 0.00 0.00 4.30
1524 1593 1.065854 GTGTCCTTGTGAGATGGGAGG 60.066 57.143 0.00 0.00 0.00 4.30
1567 1636 5.368145 TCTCTGTGAAGCTAATGTGTGTTT 58.632 37.500 0.00 0.00 0.00 2.83
1569 1638 6.017934 TCTCTGTGAAGCTAATGTGTGTTTTC 60.018 38.462 0.00 0.00 0.00 2.29
1573 1642 4.334203 TGAAGCTAATGTGTGTTTTCGTGT 59.666 37.500 0.00 0.00 0.00 4.49
1671 1740 4.082125 CCTGATGGTTTGCTTCTTTACCT 58.918 43.478 0.00 0.00 0.00 3.08
1672 1741 4.082571 CCTGATGGTTTGCTTCTTTACCTG 60.083 45.833 0.00 0.00 0.00 4.00
1674 1743 5.626142 TGATGGTTTGCTTCTTTACCTGTA 58.374 37.500 0.00 0.00 0.00 2.74
1676 1745 6.719370 TGATGGTTTGCTTCTTTACCTGTATT 59.281 34.615 0.00 0.00 0.00 1.89
1678 1747 8.644374 ATGGTTTGCTTCTTTACCTGTATTTA 57.356 30.769 0.00 0.00 0.00 1.40
1686 1761 7.484959 GCTTCTTTACCTGTATTTACACAATGC 59.515 37.037 0.00 0.00 31.93 3.56
1690 1765 2.682856 CCTGTATTTACACAATGCGGCT 59.317 45.455 0.00 0.00 31.93 5.52
1701 1776 3.065786 CACAATGCGGCTGTTCTATTCAT 59.934 43.478 0.00 0.00 0.00 2.57
1711 1786 4.728882 GCTGTTCTATTCATTGCGTTCCAG 60.729 45.833 0.00 0.00 0.00 3.86
1716 1791 4.811024 TCTATTCATTGCGTTCCAGACATC 59.189 41.667 0.00 0.00 0.00 3.06
1718 1793 2.076100 TCATTGCGTTCCAGACATCAC 58.924 47.619 0.00 0.00 0.00 3.06
1720 1795 0.948623 TTGCGTTCCAGACATCACCG 60.949 55.000 0.00 0.00 0.00 4.94
1741 2111 4.143556 CCGTTTGAATGAATTCTGTTTGCG 60.144 41.667 7.05 3.86 37.67 4.85
1742 2112 4.143556 CGTTTGAATGAATTCTGTTTGCGG 60.144 41.667 7.05 0.00 37.67 5.69
1766 2160 8.347771 CGGTAGTGTAAGCTTCACATATTAGTA 58.652 37.037 22.54 8.67 38.16 1.82
1840 2234 7.218228 TCAGTCATAAAACATCAATTGCACT 57.782 32.000 0.00 0.00 0.00 4.40
1853 2383 7.718314 ACATCAATTGCACTGTGTATAGATCAT 59.282 33.333 9.86 0.00 0.00 2.45
1876 2435 8.019094 TCATGTTGATACTATAATACACGTCCG 58.981 37.037 0.00 0.00 0.00 4.79
1888 2447 1.302993 ACGTCCGGATTTTGGTGGG 60.303 57.895 7.81 0.00 0.00 4.61
1892 2451 2.350458 CCGGATTTTGGTGGGCCAG 61.350 63.158 6.40 0.00 46.91 4.85
1894 2453 1.610379 GGATTTTGGTGGGCCAGCT 60.610 57.895 33.27 15.88 46.91 4.24
1940 2592 3.973206 TGACTGGGAAATGTGTACGAT 57.027 42.857 0.00 0.00 0.00 3.73
1967 2619 6.237901 TGCATAAACAGAAGTTGTGATAGGT 58.762 36.000 7.07 0.00 40.74 3.08
1970 2622 7.538678 GCATAAACAGAAGTTGTGATAGGTTTG 59.461 37.037 7.07 0.00 40.74 2.93
2001 2654 3.091545 ACAGCTAACAATGAACCATGGG 58.908 45.455 18.09 0.00 0.00 4.00
2015 2668 1.623279 CCATGGGGGAAATTCTTGCCT 60.623 52.381 2.85 0.00 42.55 4.75
2024 2677 5.163509 GGGGAAATTCTTGCCTTCAGAATAC 60.164 44.000 0.00 0.00 42.55 1.89
2027 2680 5.573337 AATTCTTGCCTTCAGAATACAGC 57.427 39.130 0.00 0.00 32.64 4.40
2287 2940 6.372659 TCTGAATTTCCATGCTCAACTACTTC 59.627 38.462 0.00 0.00 0.00 3.01
2289 2942 6.660521 TGAATTTCCATGCTCAACTACTTCAT 59.339 34.615 0.00 0.00 0.00 2.57
2299 2952 7.806690 TGCTCAACTACTTCATTTATTGTGAC 58.193 34.615 0.00 0.00 0.00 3.67
2303 2956 9.214957 TCAACTACTTCATTTATTGTGACGATT 57.785 29.630 0.00 0.00 0.00 3.34
2331 2984 1.179152 CATGGCAGGAAGTTGCATGA 58.821 50.000 0.00 0.00 45.86 3.07
2434 3193 6.311690 CCATTTTCTTCTTCTAAGACGAGTCC 59.688 42.308 0.00 0.00 35.18 3.85
2464 3226 8.911247 AAAGAATTTATTAAAGGTAGCGCTTG 57.089 30.769 18.68 0.00 35.86 4.01
2465 3227 7.027778 AGAATTTATTAAAGGTAGCGCTTGG 57.972 36.000 18.68 0.00 0.00 3.61
2466 3228 6.826741 AGAATTTATTAAAGGTAGCGCTTGGA 59.173 34.615 18.68 0.00 0.00 3.53
2467 3229 6.619801 ATTTATTAAAGGTAGCGCTTGGAG 57.380 37.500 18.68 0.00 0.00 3.86
2473 3269 2.606519 TAGCGCTTGGAGTGGGGT 60.607 61.111 18.68 0.00 0.00 4.95
2503 3299 8.106462 TCATCCAATGTATTGTTCCTAAACTGA 58.894 33.333 4.12 0.00 36.30 3.41
2513 3309 3.616956 TCCTAAACTGAGCCAGTGATG 57.383 47.619 8.37 2.96 44.62 3.07
2514 3310 3.173151 TCCTAAACTGAGCCAGTGATGA 58.827 45.455 8.37 2.26 44.62 2.92
2515 3311 3.582647 TCCTAAACTGAGCCAGTGATGAA 59.417 43.478 8.37 0.00 44.62 2.57
2516 3312 3.686726 CCTAAACTGAGCCAGTGATGAAC 59.313 47.826 8.37 0.00 44.62 3.18
2517 3313 3.498774 AAACTGAGCCAGTGATGAACT 57.501 42.857 8.37 0.00 44.62 3.01
2562 3358 7.537596 ACCAATGGATGTCAATAAAAGTCAA 57.462 32.000 6.16 0.00 0.00 3.18
2582 3378 6.591834 AGTCAAATTGTATCTGGAACTTCTCG 59.408 38.462 0.00 0.00 0.00 4.04
2651 3447 6.842676 ACTAGGAGAACACAAAGAAGGATTT 58.157 36.000 0.00 0.00 0.00 2.17
2652 3448 7.974504 ACTAGGAGAACACAAAGAAGGATTTA 58.025 34.615 0.00 0.00 0.00 1.40
2653 3449 8.606830 ACTAGGAGAACACAAAGAAGGATTTAT 58.393 33.333 0.00 0.00 0.00 1.40
2710 3506 2.485814 GAGCGCTGAGGTGAAAAGAAAT 59.514 45.455 18.48 0.00 0.00 2.17
2739 3536 8.758715 GGTATTCTTGCAATGCTGAAAAATATC 58.241 33.333 15.19 6.27 0.00 1.63
2744 3541 8.928733 TCTTGCAATGCTGAAAAATATCTTTTC 58.071 29.630 6.82 12.42 38.51 2.29
2781 3578 0.327480 AGGCATGGATGGAGTGGGTA 60.327 55.000 0.00 0.00 0.00 3.69
2868 3665 1.455786 CAACGAGAATTGACGCTTCGT 59.544 47.619 0.00 0.00 45.10 3.85
2871 3668 1.071605 GAGAATTGACGCTTCGTGCT 58.928 50.000 0.00 0.00 41.37 4.40
2921 3718 2.338577 AGACACTTATCCTGCATGGC 57.661 50.000 0.00 0.00 35.26 4.40
2926 3723 1.202651 ACTTATCCTGCATGGCGTACC 60.203 52.381 0.00 0.00 35.26 3.34
3048 3845 6.861144 ACTCTAAAAAGACATACCCTCGTAC 58.139 40.000 0.00 0.00 0.00 3.67
3065 3862 2.686915 CGTACTACGGAAGAGGGACATT 59.313 50.000 0.26 0.00 38.08 2.71
3077 3874 0.947244 GGGACATTATGCGCAAGAGG 59.053 55.000 17.11 10.59 43.02 3.69
3080 3877 1.869767 GACATTATGCGCAAGAGGGAG 59.130 52.381 17.11 3.41 43.02 4.30
3097 3894 2.840651 GGGAGGAGGAAGACAAGATGAA 59.159 50.000 0.00 0.00 0.00 2.57
3122 3919 4.792068 AGATCAGTAGACTTCTAGCTGCT 58.208 43.478 7.57 7.57 32.59 4.24
3218 4015 2.819608 CCGCCAATTATATCCAACCCTG 59.180 50.000 0.00 0.00 0.00 4.45
3221 4018 4.223144 GCCAATTATATCCAACCCTGGTT 58.777 43.478 0.00 0.00 43.97 3.67
3229 4027 2.344535 CAACCCTGGTTGCAGAAGG 58.655 57.895 15.59 4.78 46.92 3.46
3284 4086 5.564848 CGCACTGCAGTATATAAGGCTAAGA 60.565 44.000 21.20 0.00 0.00 2.10
3292 4094 7.472945 GCAGTATATAAGGCTAAGAGAAACCCA 60.473 40.741 0.00 0.00 0.00 4.51
3303 4105 0.261696 AGAAACCCAGCCTTGTTGGT 59.738 50.000 0.00 0.00 38.35 3.67
3364 4166 1.067283 CCTATCTGCGCTGATGTAGGG 60.067 57.143 32.43 24.17 41.96 3.53
3365 4167 0.969149 TATCTGCGCTGATGTAGGGG 59.031 55.000 32.43 2.05 39.59 4.79
3366 4168 0.760567 ATCTGCGCTGATGTAGGGGA 60.761 55.000 26.49 0.00 39.59 4.81
3367 4169 3.220222 TGCGCTGATGTAGGGGAG 58.780 61.111 9.73 0.00 39.59 4.30
3368 4170 1.685765 TGCGCTGATGTAGGGGAGT 60.686 57.895 9.73 0.00 39.59 3.85
3369 4171 1.227380 GCGCTGATGTAGGGGAGTG 60.227 63.158 0.00 0.00 39.59 3.51
3370 4172 1.676678 GCGCTGATGTAGGGGAGTGA 61.677 60.000 0.00 0.00 39.59 3.41
3371 4173 0.824109 CGCTGATGTAGGGGAGTGAA 59.176 55.000 0.00 0.00 35.81 3.18
3372 4174 1.202463 CGCTGATGTAGGGGAGTGAAG 60.202 57.143 0.00 0.00 35.81 3.02
3373 4175 1.834263 GCTGATGTAGGGGAGTGAAGT 59.166 52.381 0.00 0.00 0.00 3.01
3374 4176 2.419297 GCTGATGTAGGGGAGTGAAGTG 60.419 54.545 0.00 0.00 0.00 3.16
3389 4191 2.644299 TGAAGTGATTGTCCCATGGAGT 59.356 45.455 15.22 0.00 29.39 3.85
3439 4242 5.411831 TCAGTGCTGATTGATACAGTTCT 57.588 39.130 0.00 0.00 37.64 3.01
3453 4256 2.002586 CAGTTCTGCAGTGTAATCGGG 58.997 52.381 14.67 0.00 0.00 5.14
3570 4373 0.320946 TTACCAGCTGCGTGTAACCC 60.321 55.000 8.66 0.00 0.00 4.11
3574 4377 2.032071 GCTGCGTGTAACCCTGGT 59.968 61.111 0.00 0.00 0.00 4.00
3584 4387 2.369532 TGTAACCCTGGTCCTGTGTTAC 59.630 50.000 20.27 20.27 40.85 2.50
3586 4389 1.056660 ACCCTGGTCCTGTGTTACAG 58.943 55.000 2.05 2.05 45.53 2.74
3591 4394 3.056749 CCTGGTCCTGTGTTACAGTACTC 60.057 52.174 8.04 0.00 44.50 2.59
3611 4414 3.102972 TCTAGAAGGCAGATGAAGCAGT 58.897 45.455 0.00 0.00 0.00 4.40
3614 4417 2.039480 AGAAGGCAGATGAAGCAGTCAA 59.961 45.455 0.00 0.00 40.50 3.18
3625 4428 4.484236 TGAAGCAGTCAAGTTTGTGTTTG 58.516 39.130 0.00 0.00 31.51 2.93
3641 4444 4.287067 TGTGTTTGAGCCTAGATTCTTCCT 59.713 41.667 0.00 0.00 0.00 3.36
3645 4448 3.445008 TGAGCCTAGATTCTTCCTGTGT 58.555 45.455 0.00 0.00 0.00 3.72
3653 4456 1.488705 TTCTTCCTGTGTCCGGGCAT 61.489 55.000 14.23 0.00 37.01 4.40
3665 4468 2.752903 GTCCGGGCATTGTTTCATTACT 59.247 45.455 0.00 0.00 0.00 2.24
3666 4469 2.752354 TCCGGGCATTGTTTCATTACTG 59.248 45.455 0.00 0.00 0.00 2.74
3667 4470 2.752354 CCGGGCATTGTTTCATTACTGA 59.248 45.455 0.00 0.00 0.00 3.41
3668 4471 3.181497 CCGGGCATTGTTTCATTACTGAG 60.181 47.826 0.00 0.00 31.68 3.35
3669 4472 3.440173 CGGGCATTGTTTCATTACTGAGT 59.560 43.478 0.00 0.00 31.68 3.41
3670 4473 4.634004 CGGGCATTGTTTCATTACTGAGTA 59.366 41.667 0.00 0.00 31.68 2.59
3671 4474 5.296780 CGGGCATTGTTTCATTACTGAGTAT 59.703 40.000 0.00 0.00 31.68 2.12
3672 4475 6.183360 CGGGCATTGTTTCATTACTGAGTATT 60.183 38.462 0.00 0.00 31.68 1.89
3673 4476 7.011950 CGGGCATTGTTTCATTACTGAGTATTA 59.988 37.037 0.00 0.00 31.68 0.98
3674 4477 8.129211 GGGCATTGTTTCATTACTGAGTATTAC 58.871 37.037 0.00 0.00 31.68 1.89
3675 4478 8.129211 GGCATTGTTTCATTACTGAGTATTACC 58.871 37.037 0.00 0.00 31.68 2.85
3676 4479 8.893727 GCATTGTTTCATTACTGAGTATTACCT 58.106 33.333 0.00 0.00 31.68 3.08
3678 4481 9.959721 ATTGTTTCATTACTGAGTATTACCTGT 57.040 29.630 0.00 0.00 31.68 4.00
3679 4482 9.787435 TTGTTTCATTACTGAGTATTACCTGTT 57.213 29.630 0.00 0.00 31.68 3.16
3685 4488 9.680315 CATTACTGAGTATTACCTGTTACTAGC 57.320 37.037 0.00 0.00 0.00 3.42
3692 4495 9.627395 GAGTATTACCTGTTACTAGCACATATG 57.373 37.037 0.00 0.00 0.00 1.78
3759 4562 8.103948 AGTTAATGAGGATTATATGTGCAAGC 57.896 34.615 0.00 0.00 0.00 4.01
3763 4566 6.381481 TGAGGATTATATGTGCAAGCAAAG 57.619 37.500 0.00 0.00 0.00 2.77
3778 4581 0.319211 CAAAGCCCTGTGTGCATGTG 60.319 55.000 0.00 0.00 0.00 3.21
3806 4609 6.635030 AAGAACATTTAGCTTCTCGGTTTT 57.365 33.333 0.00 0.00 0.00 2.43
3820 4623 1.104577 GGTTTTGCCGGGTGTGAAGA 61.105 55.000 2.18 0.00 0.00 2.87
3831 4634 3.081804 GGGTGTGAAGAAATCAATCCGT 58.918 45.455 0.00 0.00 40.50 4.69
3838 4641 9.191995 GTGTGAAGAAATCAATCCGTTATTTTT 57.808 29.630 0.00 0.00 40.50 1.94
3869 4672 4.526970 TGATGGAGGGCATTTAAGAGTTC 58.473 43.478 0.00 0.00 0.00 3.01
3875 4678 6.122964 GGAGGGCATTTAAGAGTTCTGTTAT 58.877 40.000 0.00 0.00 0.00 1.89
3876 4679 6.038714 GGAGGGCATTTAAGAGTTCTGTTATG 59.961 42.308 0.00 0.00 0.00 1.90
3882 4685 8.668353 GCATTTAAGAGTTCTGTTATGTCATCA 58.332 33.333 0.00 0.00 0.00 3.07
3887 4690 6.507900 AGAGTTCTGTTATGTCATCATACGG 58.492 40.000 0.00 0.00 36.42 4.02
3892 4695 4.620982 TGTTATGTCATCATACGGCAGAG 58.379 43.478 0.00 0.00 36.42 3.35
3936 4740 3.851098 ACTTTTCCTTTCGATCGAGGAG 58.149 45.455 21.21 19.77 42.67 3.69
3952 4756 9.130312 CGATCGAGGAGATTTTAAGGTATAAAG 57.870 37.037 10.26 0.00 40.26 1.85
4051 4856 2.013286 ACGCGAACACAATTCGAAAC 57.987 45.000 15.93 0.00 43.97 2.78
4053 4858 2.032377 ACGCGAACACAATTCGAAACAT 60.032 40.909 15.93 0.00 43.97 2.71
4056 4861 4.158384 GCGAACACAATTCGAAACATGAT 58.842 39.130 12.90 0.00 43.97 2.45
4161 4968 4.637387 TTTAGAACGGGAACATGGGTTA 57.363 40.909 0.00 0.00 37.36 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.081906 GTGCGTGCTGTCCAACATG 60.082 57.895 0.00 0.00 0.00 3.21
158 161 3.024547 CGAGTTCAGGAGGAGGTTATCA 58.975 50.000 0.00 0.00 0.00 2.15
374 377 3.609409 GCTTCTTGCGGTGTTCTAAAAGG 60.609 47.826 0.00 0.00 0.00 3.11
410 413 3.072038 TGATCAGACATCCATCCATCCAC 59.928 47.826 0.00 0.00 0.00 4.02
412 415 4.571369 ATGATCAGACATCCATCCATCC 57.429 45.455 0.09 0.00 0.00 3.51
453 466 6.044871 AGGCCATGGTTAGCTTTCTTCTATAT 59.955 38.462 14.67 0.00 0.00 0.86
565 582 9.751542 GCCAGTAAATGCTATATATACAGGTAG 57.248 37.037 0.00 0.00 0.00 3.18
566 583 9.262240 TGCCAGTAAATGCTATATATACAGGTA 57.738 33.333 0.00 0.00 0.00 3.08
627 668 5.120830 GGTACAGCAACATAGTCTTCAACTG 59.879 44.000 0.00 0.00 39.11 3.16
629 670 5.238583 AGGTACAGCAACATAGTCTTCAAC 58.761 41.667 0.00 0.00 0.00 3.18
660 703 9.793252 ATAATTACTTTACTTTGCAGATGCTTG 57.207 29.630 6.35 0.00 42.66 4.01
682 728 4.812091 TCCGCAAGCAAATACGTACATAAT 59.188 37.500 0.00 0.00 0.00 1.28
683 729 4.182339 TCCGCAAGCAAATACGTACATAA 58.818 39.130 0.00 0.00 0.00 1.90
684 730 3.783191 TCCGCAAGCAAATACGTACATA 58.217 40.909 0.00 0.00 0.00 2.29
685 731 2.623535 TCCGCAAGCAAATACGTACAT 58.376 42.857 0.00 0.00 0.00 2.29
690 736 2.241722 CACTTTCCGCAAGCAAATACG 58.758 47.619 0.00 0.00 35.65 3.06
691 737 3.282831 ACACTTTCCGCAAGCAAATAC 57.717 42.857 0.00 0.00 35.65 1.89
701 747 4.217754 TGATGTTGTTAACACTTTCCGC 57.782 40.909 8.07 0.00 45.50 5.54
703 749 4.923281 GGCATGATGTTGTTAACACTTTCC 59.077 41.667 8.07 0.00 45.50 3.13
716 763 7.493320 GTCATTTATCAACATTGGCATGATGTT 59.507 33.333 10.92 10.92 45.80 2.71
735 782 8.313292 CCATTTTCCAAATCTTCAGGTCATTTA 58.687 33.333 0.00 0.00 0.00 1.40
757 805 7.707624 TGCAGAAACTCATAAGAAATCCATT 57.292 32.000 0.00 0.00 0.00 3.16
765 813 8.023128 GCATAACTTTTGCAGAAACTCATAAGA 58.977 33.333 0.00 0.00 39.90 2.10
766 814 7.274250 GGCATAACTTTTGCAGAAACTCATAAG 59.726 37.037 6.55 0.00 41.95 1.73
767 815 7.090173 GGCATAACTTTTGCAGAAACTCATAA 58.910 34.615 6.55 0.00 41.95 1.90
768 816 6.208402 TGGCATAACTTTTGCAGAAACTCATA 59.792 34.615 6.55 0.00 41.95 2.15
769 817 5.010922 TGGCATAACTTTTGCAGAAACTCAT 59.989 36.000 6.55 0.00 41.95 2.90
770 818 4.340666 TGGCATAACTTTTGCAGAAACTCA 59.659 37.500 6.55 0.00 41.95 3.41
771 819 4.870363 TGGCATAACTTTTGCAGAAACTC 58.130 39.130 6.55 0.00 41.95 3.01
772 820 4.935352 TGGCATAACTTTTGCAGAAACT 57.065 36.364 6.55 0.00 41.95 2.66
773 821 6.202570 TGAAATGGCATAACTTTTGCAGAAAC 59.797 34.615 0.00 0.00 41.95 2.78
774 822 6.286758 TGAAATGGCATAACTTTTGCAGAAA 58.713 32.000 0.00 0.00 41.95 2.52
775 823 5.851720 TGAAATGGCATAACTTTTGCAGAA 58.148 33.333 0.00 0.00 41.95 3.02
776 824 5.465532 TGAAATGGCATAACTTTTGCAGA 57.534 34.783 0.00 0.00 41.95 4.26
777 825 6.730960 AATGAAATGGCATAACTTTTGCAG 57.269 33.333 0.00 0.00 41.95 4.41
778 826 6.485984 ACAAATGAAATGGCATAACTTTTGCA 59.514 30.769 25.85 10.57 41.95 4.08
779 827 6.901265 ACAAATGAAATGGCATAACTTTTGC 58.099 32.000 25.85 6.31 39.41 3.68
786 834 9.881649 TGCTAAAATACAAATGAAATGGCATAA 57.118 25.926 0.00 0.00 0.00 1.90
787 835 9.881649 TTGCTAAAATACAAATGAAATGGCATA 57.118 25.926 0.00 0.00 0.00 3.14
788 836 8.789825 TTGCTAAAATACAAATGAAATGGCAT 57.210 26.923 0.00 0.00 0.00 4.40
789 837 8.613060 TTTGCTAAAATACAAATGAAATGGCA 57.387 26.923 0.00 0.00 31.09 4.92
873 921 4.625742 CGGTGACACGTTGATAAATTCTCT 59.374 41.667 0.00 0.00 0.00 3.10
964 1012 1.003051 GCAGGGGTTAGGGGAGAGA 59.997 63.158 0.00 0.00 0.00 3.10
966 1014 2.365105 CGCAGGGGTTAGGGGAGA 60.365 66.667 0.00 0.00 0.00 3.71
1019 1081 3.992641 TGTGGAGGAGGGCGGAGA 61.993 66.667 0.00 0.00 0.00 3.71
1249 1314 0.038159 ATCGTAGGCCATAGCTTCGC 60.038 55.000 5.01 0.00 39.73 4.70
1265 1330 1.752753 CGCTTCTCTCACTAGCATCG 58.247 55.000 0.00 0.00 34.62 3.84
1304 1369 5.517770 GCAAGAAACAGATATGCCAAATCAC 59.482 40.000 0.00 0.00 0.00 3.06
1324 1389 3.667261 CAGCGACTTCATGAAAAAGCAAG 59.333 43.478 22.34 14.38 0.00 4.01
1338 1403 2.086054 GGTGAACTGATCAGCGACTT 57.914 50.000 22.83 9.30 45.70 3.01
1368 1437 4.592485 ATCGAAGCCCAGTAGTATCAAG 57.408 45.455 0.00 0.00 0.00 3.02
1392 1461 3.857010 GCAACCAGTTCCCAAATTTCGAG 60.857 47.826 0.00 0.00 0.00 4.04
1407 1476 2.699954 ACGACCAAATCTAGCAACCAG 58.300 47.619 0.00 0.00 0.00 4.00
1409 1478 2.161609 CCAACGACCAAATCTAGCAACC 59.838 50.000 0.00 0.00 0.00 3.77
1441 1510 0.033504 ACTACAGAGCCACCACAACG 59.966 55.000 0.00 0.00 0.00 4.10
1474 1543 7.411486 AGTGCTACTAGTATGAGAAACACAT 57.589 36.000 2.33 0.00 0.00 3.21
1488 1557 7.649705 CACAAGGACACATTATAGTGCTACTAG 59.350 40.741 0.00 0.00 43.23 2.57
1522 1591 7.676468 AGAGAAAATTCTAAGACCACTCTACCT 59.324 37.037 0.00 0.00 37.73 3.08
1523 1592 7.762159 CAGAGAAAATTCTAAGACCACTCTACC 59.238 40.741 0.00 0.00 37.73 3.18
1524 1593 8.308207 ACAGAGAAAATTCTAAGACCACTCTAC 58.692 37.037 0.00 0.00 37.73 2.59
1567 1636 3.462483 TCCAGCTCTACAAAACACGAA 57.538 42.857 0.00 0.00 0.00 3.85
1569 1638 3.058914 CCTTTCCAGCTCTACAAAACACG 60.059 47.826 0.00 0.00 0.00 4.49
1573 1642 4.335416 CATCCCTTTCCAGCTCTACAAAA 58.665 43.478 0.00 0.00 0.00 2.44
1671 1740 3.078097 ACAGCCGCATTGTGTAAATACA 58.922 40.909 0.00 0.00 0.00 2.29
1672 1741 3.757745 ACAGCCGCATTGTGTAAATAC 57.242 42.857 0.00 0.00 0.00 1.89
1674 1743 2.819608 AGAACAGCCGCATTGTGTAAAT 59.180 40.909 0.00 0.00 0.00 1.40
1676 1745 1.890876 AGAACAGCCGCATTGTGTAA 58.109 45.000 0.00 0.00 0.00 2.41
1678 1747 2.113860 ATAGAACAGCCGCATTGTGT 57.886 45.000 0.00 0.00 0.00 3.72
1686 1761 1.665679 ACGCAATGAATAGAACAGCCG 59.334 47.619 0.00 0.00 0.00 5.52
1690 1765 4.391830 GTCTGGAACGCAATGAATAGAACA 59.608 41.667 0.00 0.00 0.00 3.18
1701 1776 0.948623 CGGTGATGTCTGGAACGCAA 60.949 55.000 0.00 0.00 0.00 4.85
1711 1786 5.796935 CAGAATTCATTCAAACGGTGATGTC 59.203 40.000 8.44 0.00 39.23 3.06
1716 1791 5.332506 GCAAACAGAATTCATTCAAACGGTG 60.333 40.000 8.44 0.00 39.23 4.94
1718 1793 4.143556 CGCAAACAGAATTCATTCAAACGG 60.144 41.667 8.44 0.00 39.23 4.44
1720 1795 4.744631 ACCGCAAACAGAATTCATTCAAAC 59.255 37.500 8.44 0.00 39.23 2.93
1795 2189 8.213518 ACTGAATCCACATCATACAACAATAC 57.786 34.615 0.00 0.00 0.00 1.89
1853 2383 6.486320 TCCGGACGTGTATTATAGTATCAACA 59.514 38.462 0.00 0.00 0.00 3.33
1869 2399 1.582610 CCCACCAAAATCCGGACGTG 61.583 60.000 6.12 8.36 0.00 4.49
1872 2431 2.348104 GGCCCACCAAAATCCGGAC 61.348 63.158 6.12 0.00 35.26 4.79
1888 2447 0.251354 TGAGGAATCAGACAGCTGGC 59.749 55.000 19.93 16.91 42.53 4.85
1892 2451 3.325293 TGAGTTGAGGAATCAGACAGC 57.675 47.619 0.00 0.00 0.00 4.40
1894 2453 4.713814 AGCTATGAGTTGAGGAATCAGACA 59.286 41.667 0.00 0.00 0.00 3.41
1940 2592 7.549134 CCTATCACAACTTCTGTTTATGCAGTA 59.451 37.037 0.00 0.00 35.47 2.74
2001 2654 5.418840 TGTATTCTGAAGGCAAGAATTTCCC 59.581 40.000 13.15 3.84 34.55 3.97
2027 2680 9.683069 ATGAATTTACTTTAAAAGCAGTGTCTG 57.317 29.630 0.00 0.00 34.12 3.51
2113 2766 6.423182 TCCCTTACCATCATAAACTTTGAGG 58.577 40.000 0.00 0.00 0.00 3.86
2287 2940 8.180920 TGTACCATCAAATCGTCACAATAAATG 58.819 33.333 0.00 0.00 0.00 2.32
2289 2942 7.674471 TGTACCATCAAATCGTCACAATAAA 57.326 32.000 0.00 0.00 0.00 1.40
2299 2952 2.291465 CCTGCCATGTACCATCAAATCG 59.709 50.000 0.00 0.00 0.00 3.34
2303 2956 2.308570 ACTTCCTGCCATGTACCATCAA 59.691 45.455 0.00 0.00 0.00 2.57
2406 3165 6.755206 TCGTCTTAGAAGAAGAAAATGGTCA 58.245 36.000 5.57 0.00 39.89 4.02
2409 3168 6.311690 GGACTCGTCTTAGAAGAAGAAAATGG 59.688 42.308 8.85 1.20 41.71 3.16
2441 3203 6.826741 TCCAAGCGCTACCTTTAATAAATTCT 59.173 34.615 12.05 0.00 0.00 2.40
2455 3217 2.125106 CCCCACTCCAAGCGCTAC 60.125 66.667 12.05 0.00 0.00 3.58
2460 3222 2.507407 TGATAAACCCCACTCCAAGC 57.493 50.000 0.00 0.00 0.00 4.01
2464 3226 3.662759 TTGGATGATAAACCCCACTCC 57.337 47.619 0.00 0.00 0.00 3.85
2465 3227 4.536765 ACATTGGATGATAAACCCCACTC 58.463 43.478 0.00 0.00 0.00 3.51
2466 3228 4.608170 ACATTGGATGATAAACCCCACT 57.392 40.909 0.00 0.00 0.00 4.00
2467 3229 6.323739 ACAATACATTGGATGATAAACCCCAC 59.676 38.462 6.87 0.00 41.96 4.61
2513 3309 5.357878 TGTTCCTGAATGCCATTATCAGTTC 59.642 40.000 5.83 0.00 39.10 3.01
2514 3310 5.263599 TGTTCCTGAATGCCATTATCAGTT 58.736 37.500 5.83 0.00 39.10 3.16
2515 3311 4.858850 TGTTCCTGAATGCCATTATCAGT 58.141 39.130 5.83 0.00 39.10 3.41
2516 3312 5.450965 GGTTGTTCCTGAATGCCATTATCAG 60.451 44.000 0.24 0.24 40.17 2.90
2517 3313 4.402155 GGTTGTTCCTGAATGCCATTATCA 59.598 41.667 0.00 0.00 0.00 2.15
2518 3314 4.402155 TGGTTGTTCCTGAATGCCATTATC 59.598 41.667 0.00 0.00 37.07 1.75
2519 3315 4.352009 TGGTTGTTCCTGAATGCCATTAT 58.648 39.130 0.00 0.00 37.07 1.28
2520 3316 3.772387 TGGTTGTTCCTGAATGCCATTA 58.228 40.909 0.00 0.00 37.07 1.90
2562 3358 5.794894 ACACGAGAAGTTCCAGATACAATT 58.205 37.500 0.00 0.00 0.00 2.32
2566 3362 6.132791 TGATACACGAGAAGTTCCAGATAC 57.867 41.667 0.00 0.00 0.00 2.24
2569 3365 6.961360 ATATGATACACGAGAAGTTCCAGA 57.039 37.500 0.00 0.00 0.00 3.86
2610 3406 9.696572 TTCTCCTAGTTACACAATAGACAGTAT 57.303 33.333 0.00 0.00 0.00 2.12
2710 3506 3.954200 TCAGCATTGCAAGAATACCTCA 58.046 40.909 11.91 0.00 0.00 3.86
2739 3536 3.077359 AGAAGCCTGATTGACGGAAAAG 58.923 45.455 0.00 0.00 0.00 2.27
2744 3541 1.649664 CTGAGAAGCCTGATTGACGG 58.350 55.000 0.00 0.00 0.00 4.79
2868 3665 0.249676 ACCTAGAGAGACGTCGAGCA 59.750 55.000 10.46 0.00 0.00 4.26
2921 3718 5.063060 GCAGTTCTAAGTAAACCATGGTACG 59.937 44.000 20.12 6.92 0.00 3.67
2926 3723 5.245531 TCCAGCAGTTCTAAGTAAACCATG 58.754 41.667 0.00 0.00 0.00 3.66
3048 3845 3.654414 GCATAATGTCCCTCTTCCGTAG 58.346 50.000 0.00 0.00 0.00 3.51
3065 3862 1.402896 CCTCCTCCCTCTTGCGCATA 61.403 60.000 12.75 0.92 0.00 3.14
3077 3874 4.163078 TCATTCATCTTGTCTTCCTCCTCC 59.837 45.833 0.00 0.00 0.00 4.30
3080 3877 5.350504 TCTCATTCATCTTGTCTTCCTCC 57.649 43.478 0.00 0.00 0.00 4.30
3097 3894 5.241506 GCAGCTAGAAGTCTACTGATCTCAT 59.758 44.000 15.91 0.00 33.46 2.90
3122 3919 3.706594 CTGTATCTAACTCAAGCCCCTCA 59.293 47.826 0.00 0.00 0.00 3.86
3218 4015 1.228552 TTCCAGGCCTTCTGCAACC 60.229 57.895 0.00 0.00 43.89 3.77
3221 4018 1.719063 AACCTTCCAGGCCTTCTGCA 61.719 55.000 0.00 0.00 43.89 4.41
3222 4019 0.540597 AAACCTTCCAGGCCTTCTGC 60.541 55.000 0.00 0.00 39.63 4.26
3229 4027 0.889186 TTCAGCGAAACCTTCCAGGC 60.889 55.000 0.00 0.00 39.63 4.85
3284 4086 0.261696 ACCAACAAGGCTGGGTTTCT 59.738 50.000 2.38 0.00 43.14 2.52
3292 4094 2.038557 ACTAATCGTGACCAACAAGGCT 59.961 45.455 0.00 0.00 43.14 4.58
3323 4125 5.501156 AGGATTTCCTGATCCAACAGTTAC 58.499 41.667 0.00 0.00 46.61 2.50
3364 4166 2.859165 TGGGACAATCACTTCACTCC 57.141 50.000 0.00 0.00 31.92 3.85
3389 4191 3.053991 CACTTCACTCCCTCCTCTCTCTA 60.054 52.174 0.00 0.00 0.00 2.43
3439 4242 0.251916 CCTTCCCCGATTACACTGCA 59.748 55.000 0.00 0.00 0.00 4.41
3453 4256 2.686915 CAAGTCTTGCATCCATCCTTCC 59.313 50.000 0.00 0.00 0.00 3.46
3484 4287 7.476540 AACAAGTATACACACCTGATAGTCA 57.523 36.000 5.50 0.00 0.00 3.41
3533 4336 0.324943 AACAGCGCCTGAATACCACT 59.675 50.000 2.29 0.00 35.18 4.00
3584 4387 5.735922 GCTTCATCTGCCTTCTAGAGTACTG 60.736 48.000 0.00 0.00 0.00 2.74
3586 4389 4.098654 TGCTTCATCTGCCTTCTAGAGTAC 59.901 45.833 0.00 0.00 0.00 2.73
3591 4394 3.118847 TGACTGCTTCATCTGCCTTCTAG 60.119 47.826 0.00 0.00 0.00 2.43
3611 4414 4.776349 TCTAGGCTCAAACACAAACTTGA 58.224 39.130 0.00 0.00 0.00 3.02
3614 4417 5.625150 AGAATCTAGGCTCAAACACAAACT 58.375 37.500 0.00 0.00 0.00 2.66
3625 4428 3.181470 GGACACAGGAAGAATCTAGGCTC 60.181 52.174 0.00 0.00 0.00 4.70
3641 4444 0.466372 TGAAACAATGCCCGGACACA 60.466 50.000 0.73 0.00 0.00 3.72
3645 4448 2.752354 CAGTAATGAAACAATGCCCGGA 59.248 45.455 0.73 0.00 0.00 5.14
3653 4456 9.787435 AACAGGTAATACTCAGTAATGAAACAA 57.213 29.630 0.00 0.00 0.00 2.83
3665 4468 7.655521 ATGTGCTAGTAACAGGTAATACTCA 57.344 36.000 6.56 0.00 34.37 3.41
3666 4469 9.627395 CATATGTGCTAGTAACAGGTAATACTC 57.373 37.037 6.56 0.00 34.37 2.59
3685 4488 1.062365 CAACGCACGGGCATATGTG 59.938 57.895 11.77 0.00 41.24 3.21
3739 4542 6.516194 GCTTTGCTTGCACATATAATCCTCAT 60.516 38.462 0.00 0.00 0.00 2.90
3744 4547 4.038402 AGGGCTTTGCTTGCACATATAATC 59.962 41.667 0.00 0.00 36.08 1.75
3759 4562 0.319211 CACATGCACACAGGGCTTTG 60.319 55.000 0.00 0.00 0.00 2.77
3763 4566 0.388659 TTTTCACATGCACACAGGGC 59.611 50.000 0.00 0.00 0.00 5.19
3784 4587 5.562890 GCAAAACCGAGAAGCTAAATGTTCT 60.563 40.000 0.00 0.00 35.67 3.01
3806 4609 0.109532 TGATTTCTTCACACCCGGCA 59.890 50.000 0.00 0.00 0.00 5.69
3838 4641 3.385314 TGCCCTCCATCAATGAATGAA 57.615 42.857 0.00 0.00 42.54 2.57
3839 4642 3.605726 ATGCCCTCCATCAATGAATGA 57.394 42.857 0.00 0.00 43.67 2.57
3851 4654 3.956744 ACAGAACTCTTAAATGCCCTCC 58.043 45.455 0.00 0.00 0.00 4.30
3852 4655 6.599638 ACATAACAGAACTCTTAAATGCCCTC 59.400 38.462 0.00 0.00 0.00 4.30
3869 4672 4.620982 TCTGCCGTATGATGACATAACAG 58.379 43.478 0.00 0.00 40.13 3.16
3875 4678 2.101415 CCTTCTCTGCCGTATGATGACA 59.899 50.000 0.00 0.00 0.00 3.58
3876 4679 2.748605 CCTTCTCTGCCGTATGATGAC 58.251 52.381 0.00 0.00 0.00 3.06
3887 4690 6.639632 TGAATAATTTATGGCCTTCTCTGC 57.360 37.500 3.32 0.00 0.00 4.26
3908 4712 6.627243 TCGATCGAAAGGAAAAGTAGATTGA 58.373 36.000 16.99 0.00 0.00 2.57
3925 4729 6.896021 ATACCTTAAAATCTCCTCGATCGA 57.104 37.500 18.32 18.32 0.00 3.59
3926 4730 9.130312 CTTTATACCTTAAAATCTCCTCGATCG 57.870 37.037 9.36 9.36 0.00 3.69
3927 4731 9.984190 ACTTTATACCTTAAAATCTCCTCGATC 57.016 33.333 0.00 0.00 0.00 3.69
4032 4837 1.328069 TGTTTCGAATTGTGTTCGCGT 59.672 42.857 5.77 0.00 41.30 6.01
4144 4951 4.587584 TTTTTAACCCATGTTCCCGTTC 57.412 40.909 0.00 0.00 35.87 3.95


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

AutoCloner maintained by Alex Coulton.