Multiple sequence alignment - TraesCS3D01G027100

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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 TraesCS3D01G027100 chr3D 100.000 3502 0 0 1 3502 9198558 9202059 0.000000e+00 6468.0
1 TraesCS3D01G027100 chr3D 84.398 1378 159 15 1009 2350 9243805 9245162 0.000000e+00 1303.0
2 TraesCS3D01G027100 chr3D 88.273 631 56 6 2407 3036 9245244 9245857 0.000000e+00 739.0
3 TraesCS3D01G027100 chr3D 78.811 774 118 34 1010 1765 9132068 9131323 2.450000e-131 479.0
4 TraesCS3D01G027100 chr3D 72.515 342 57 25 2402 2718 9245944 9246273 3.750000e-10 76.8
5 TraesCS3D01G027100 chr3B 84.263 1417 149 16 1009 2382 11561680 11563065 0.000000e+00 1314.0
6 TraesCS3D01G027100 chr3B 84.597 1279 122 28 574 1805 11510568 11511818 0.000000e+00 1201.0
7 TraesCS3D01G027100 chr3B 89.833 836 72 10 1795 2621 3206196 3207027 0.000000e+00 1061.0
8 TraesCS3D01G027100 chr3B 81.250 1248 111 61 577 1805 3205031 3206174 0.000000e+00 894.0
9 TraesCS3D01G027100 chr3B 88.644 634 38 7 2407 3036 11563153 11563756 0.000000e+00 741.0
10 TraesCS3D01G027100 chr3B 89.081 577 48 10 1795 2360 11511840 11512412 0.000000e+00 702.0
11 TraesCS3D01G027100 chr3B 89.279 513 51 4 1 510 637051017 637051528 1.060000e-179 640.0
12 TraesCS3D01G027100 chr3B 90.172 407 28 6 2632 3036 3210362 3210758 1.440000e-143 520.0
13 TraesCS3D01G027100 chr3B 92.347 196 15 0 3189 3384 11513151 11513346 2.660000e-71 279.0
14 TraesCS3D01G027100 chr3B 86.364 132 14 1 3049 3176 11512486 11512617 1.310000e-29 141.0
15 TraesCS3D01G027100 chr5B 89.535 516 49 5 1 512 358812557 358812043 0.000000e+00 649.0
16 TraesCS3D01G027100 chr5B 89.804 510 43 9 1 504 474442191 474442697 0.000000e+00 645.0
17 TraesCS3D01G027100 chr5B 88.867 512 53 4 1 509 681220817 681221327 8.250000e-176 627.0
18 TraesCS3D01G027100 chr5B 88.544 515 53 6 1 512 232986805 232986294 1.380000e-173 619.0
19 TraesCS3D01G027100 chr1B 89.147 516 50 6 1 512 328941630 328942143 3.810000e-179 638.0
20 TraesCS3D01G027100 chr1B 88.716 514 53 4 1 510 612171117 612171629 1.070000e-174 623.0
21 TraesCS3D01G027100 chr1A 88.911 514 52 5 1 512 462634049 462634559 2.290000e-176 628.0
22 TraesCS3D01G027100 chr4A 87.570 539 63 4 1 536 598621670 598621133 3.840000e-174 621.0
23 TraesCS3D01G027100 chr4A 74.218 799 176 25 1019 1805 656030041 656030821 1.220000e-79 307.0
24 TraesCS3D01G027100 chr4A 75.360 556 109 13 1223 1772 655659043 655659576 3.490000e-60 243.0
25 TraesCS3D01G027100 chr4A 77.202 386 59 16 2022 2399 655664159 655664523 7.670000e-47 198.0
26 TraesCS3D01G027100 chr4A 75.798 376 62 19 1802 2175 656551663 656552011 2.800000e-36 163.0
27 TraesCS3D01G027100 chr4A 77.778 270 51 6 1510 1773 656472944 656473210 1.300000e-34 158.0
28 TraesCS3D01G027100 chr4A 75.472 371 61 16 1802 2164 655659636 655659984 1.680000e-33 154.0
29 TraesCS3D01G027100 chr4A 73.000 400 82 13 1334 1717 656556644 656556255 2.210000e-22 117.0
30 TraesCS3D01G027100 chr7D 75.953 761 157 19 1019 1769 44538327 44539071 5.520000e-98 368.0
31 TraesCS3D01G027100 chr7D 73.236 822 168 38 1010 1805 43169393 43168598 5.800000e-63 252.0
32 TraesCS3D01G027100 chr7D 73.378 740 139 32 1010 1717 44656270 44655557 4.550000e-54 222.0
33 TraesCS3D01G027100 chr7D 73.378 740 139 32 1010 1717 44709078 44709791 4.550000e-54 222.0
34 TraesCS3D01G027100 chr7D 75.236 529 88 25 1875 2395 44531491 44531984 9.850000e-51 211.0
35 TraesCS3D01G027100 chr3A 75.389 772 117 32 1010 1765 11865303 11866017 4.390000e-79 305.0
36 TraesCS3D01G027100 chr7A 72.973 777 174 25 1022 1773 47225283 47224518 4.520000e-59 239.0
37 TraesCS3D01G027100 chr7A 73.826 745 131 36 1010 1717 47256357 47255640 1.620000e-58 237.0
38 TraesCS3D01G027100 chr7A 74.542 601 106 27 1803 2395 47001412 47001973 5.890000e-53 219.0
39 TraesCS3D01G027100 chr7A 75.701 428 68 19 1803 2227 47008116 47008510 7.720000e-42 182.0
40 TraesCS3D01G027100 chrUn 73.414 741 142 33 1010 1717 48987442 48986724 3.520000e-55 226.0


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 TraesCS3D01G027100 chr3D 9198558 9202059 3501 False 6468.000000 6468 100.000000 1 3502 1 chr3D.!!$F1 3501
1 TraesCS3D01G027100 chr3D 9243805 9246273 2468 False 706.266667 1303 81.728667 1009 3036 3 chr3D.!!$F2 2027
2 TraesCS3D01G027100 chr3D 9131323 9132068 745 True 479.000000 479 78.811000 1010 1765 1 chr3D.!!$R1 755
3 TraesCS3D01G027100 chr3B 11561680 11563756 2076 False 1027.500000 1314 86.453500 1009 3036 2 chr3B.!!$F4 2027
4 TraesCS3D01G027100 chr3B 3205031 3210758 5727 False 825.000000 1061 87.085000 577 3036 3 chr3B.!!$F2 2459
5 TraesCS3D01G027100 chr3B 637051017 637051528 511 False 640.000000 640 89.279000 1 510 1 chr3B.!!$F1 509
6 TraesCS3D01G027100 chr3B 11510568 11513346 2778 False 580.750000 1201 88.097250 574 3384 4 chr3B.!!$F3 2810
7 TraesCS3D01G027100 chr5B 358812043 358812557 514 True 649.000000 649 89.535000 1 512 1 chr5B.!!$R2 511
8 TraesCS3D01G027100 chr5B 474442191 474442697 506 False 645.000000 645 89.804000 1 504 1 chr5B.!!$F1 503
9 TraesCS3D01G027100 chr5B 681220817 681221327 510 False 627.000000 627 88.867000 1 509 1 chr5B.!!$F2 508
10 TraesCS3D01G027100 chr5B 232986294 232986805 511 True 619.000000 619 88.544000 1 512 1 chr5B.!!$R1 511
11 TraesCS3D01G027100 chr1B 328941630 328942143 513 False 638.000000 638 89.147000 1 512 1 chr1B.!!$F1 511
12 TraesCS3D01G027100 chr1B 612171117 612171629 512 False 623.000000 623 88.716000 1 510 1 chr1B.!!$F2 509
13 TraesCS3D01G027100 chr1A 462634049 462634559 510 False 628.000000 628 88.911000 1 512 1 chr1A.!!$F1 511
14 TraesCS3D01G027100 chr4A 598621133 598621670 537 True 621.000000 621 87.570000 1 536 1 chr4A.!!$R1 535
15 TraesCS3D01G027100 chr4A 656030041 656030821 780 False 307.000000 307 74.218000 1019 1805 1 chr4A.!!$F2 786
16 TraesCS3D01G027100 chr7D 44538327 44539071 744 False 368.000000 368 75.953000 1019 1769 1 chr7D.!!$F2 750
17 TraesCS3D01G027100 chr7D 43168598 43169393 795 True 252.000000 252 73.236000 1010 1805 1 chr7D.!!$R1 795
18 TraesCS3D01G027100 chr7D 44655557 44656270 713 True 222.000000 222 73.378000 1010 1717 1 chr7D.!!$R2 707
19 TraesCS3D01G027100 chr7D 44709078 44709791 713 False 222.000000 222 73.378000 1010 1717 1 chr7D.!!$F3 707
20 TraesCS3D01G027100 chr3A 11865303 11866017 714 False 305.000000 305 75.389000 1010 1765 1 chr3A.!!$F1 755
21 TraesCS3D01G027100 chr7A 47224518 47225283 765 True 239.000000 239 72.973000 1022 1773 1 chr7A.!!$R1 751
22 TraesCS3D01G027100 chr7A 47255640 47256357 717 True 237.000000 237 73.826000 1010 1717 1 chr7A.!!$R2 707
23 TraesCS3D01G027100 chr7A 47001412 47001973 561 False 219.000000 219 74.542000 1803 2395 1 chr7A.!!$F1 592
24 TraesCS3D01G027100 chrUn 48986724 48987442 718 True 226.000000 226 73.414000 1010 1717 1 chrUn.!!$R1 707

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
568 581 0.106819 AGTGCAGCTCCATGGATTCC 60.107 55.0 16.63 6.99 0.00 3.01 F
572 585 0.466922 CAGCTCCATGGATTCCCACC 60.467 60.0 16.63 0.00 46.98 4.61 F
1627 1784 0.620410 CCCACCAGTCCACCATAGGA 60.620 60.0 0.00 0.00 34.64 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2143 0.450482 GAAACACGCCGTCAATGTCG 60.450 55.000 0.00 0.00 0.00 4.35 R
1963 2162 4.093556 GTCTTCGCTTTCCACATTTCCTAG 59.906 45.833 0.00 0.00 0.00 3.02 R
3176 7221 0.099436 AGCGAATCGATTTTGGCTGC 59.901 50.000 23.06 15.47 38.93 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
73 75 2.299013 GGGTTTGATTTCCAGGGTGAAC 59.701 50.000 0.00 0.00 0.00 3.18
113 117 0.593128 CCTCCTGCAACCTTTGAACG 59.407 55.000 0.00 0.00 0.00 3.95
349 359 5.122239 TGAGAGCTATGTTTGATTTGAACCG 59.878 40.000 0.00 0.00 0.00 4.44
392 402 8.414003 TCTATTTTATATACTATGCTGGGCGAG 58.586 37.037 0.00 0.00 0.00 5.03
406 416 2.202610 CGAGCGGACAAGATGCGA 60.203 61.111 0.00 0.00 46.80 5.10
461 471 2.106332 ATCCACGAATCCGGACGC 59.894 61.111 6.12 0.00 40.78 5.19
464 474 3.541831 CACGAATCCGGACGCACG 61.542 66.667 6.12 12.94 40.78 5.34
486 497 2.350772 CGGCTTCATTGTCACCTCAAAC 60.351 50.000 0.00 0.00 0.00 2.93
487 498 2.350772 GGCTTCATTGTCACCTCAAACG 60.351 50.000 0.00 0.00 0.00 3.60
490 501 0.240945 CATTGTCACCTCAAACGGGC 59.759 55.000 0.00 0.00 0.00 6.13
491 502 1.234615 ATTGTCACCTCAAACGGGCG 61.235 55.000 0.00 0.00 0.00 6.13
494 507 1.146485 TCACCTCAAACGGGCGAAA 59.854 52.632 0.00 0.00 0.00 3.46
497 510 0.958876 ACCTCAAACGGGCGAAATCC 60.959 55.000 0.00 0.00 0.00 3.01
514 527 2.544359 CGACAAAGCGGACGTGTG 59.456 61.111 0.00 0.00 0.00 3.82
536 549 1.173913 GCGTTGGAGTTGGCCTTATT 58.826 50.000 3.32 0.00 0.00 1.40
537 550 2.361789 GCGTTGGAGTTGGCCTTATTA 58.638 47.619 3.32 0.00 0.00 0.98
538 551 2.750712 GCGTTGGAGTTGGCCTTATTAA 59.249 45.455 3.32 0.00 0.00 1.40
539 552 3.191791 GCGTTGGAGTTGGCCTTATTAAA 59.808 43.478 3.32 0.00 0.00 1.52
540 553 4.142249 GCGTTGGAGTTGGCCTTATTAAAT 60.142 41.667 3.32 0.00 0.00 1.40
541 554 5.623596 GCGTTGGAGTTGGCCTTATTAAATT 60.624 40.000 3.32 0.00 0.00 1.82
542 555 6.033966 CGTTGGAGTTGGCCTTATTAAATTC 58.966 40.000 3.32 0.00 0.00 2.17
543 556 6.349777 CGTTGGAGTTGGCCTTATTAAATTCA 60.350 38.462 3.32 0.00 0.00 2.57
544 557 6.773976 TGGAGTTGGCCTTATTAAATTCAG 57.226 37.500 3.32 0.00 0.00 3.02
545 558 6.252995 TGGAGTTGGCCTTATTAAATTCAGT 58.747 36.000 3.32 0.00 0.00 3.41
546 559 6.377146 TGGAGTTGGCCTTATTAAATTCAGTC 59.623 38.462 3.32 0.00 0.00 3.51
547 560 6.377146 GGAGTTGGCCTTATTAAATTCAGTCA 59.623 38.462 3.32 0.00 0.00 3.41
548 561 7.093945 GGAGTTGGCCTTATTAAATTCAGTCAA 60.094 37.037 3.32 0.00 0.00 3.18
549 562 8.189119 AGTTGGCCTTATTAAATTCAGTCAAA 57.811 30.769 3.32 0.00 0.00 2.69
550 563 8.306761 AGTTGGCCTTATTAAATTCAGTCAAAG 58.693 33.333 3.32 0.00 0.00 2.77
551 564 7.775053 TGGCCTTATTAAATTCAGTCAAAGT 57.225 32.000 3.32 0.00 0.00 2.66
552 565 7.601856 TGGCCTTATTAAATTCAGTCAAAGTG 58.398 34.615 3.32 0.00 0.00 3.16
553 566 6.531594 GGCCTTATTAAATTCAGTCAAAGTGC 59.468 38.462 0.00 0.00 0.00 4.40
554 567 7.090173 GCCTTATTAAATTCAGTCAAAGTGCA 58.910 34.615 0.00 0.00 0.00 4.57
555 568 7.274250 GCCTTATTAAATTCAGTCAAAGTGCAG 59.726 37.037 0.00 0.00 0.00 4.41
556 569 7.274250 CCTTATTAAATTCAGTCAAAGTGCAGC 59.726 37.037 0.00 0.00 0.00 5.25
557 570 5.772825 TTAAATTCAGTCAAAGTGCAGCT 57.227 34.783 0.00 0.00 0.00 4.24
558 571 3.911661 AATTCAGTCAAAGTGCAGCTC 57.088 42.857 0.00 0.00 0.00 4.09
559 572 1.597742 TTCAGTCAAAGTGCAGCTCC 58.402 50.000 0.00 0.00 0.00 4.70
560 573 0.469494 TCAGTCAAAGTGCAGCTCCA 59.531 50.000 0.00 0.00 0.00 3.86
561 574 1.072806 TCAGTCAAAGTGCAGCTCCAT 59.927 47.619 0.00 0.00 0.00 3.41
562 575 1.199327 CAGTCAAAGTGCAGCTCCATG 59.801 52.381 0.00 0.00 0.00 3.66
563 576 0.524862 GTCAAAGTGCAGCTCCATGG 59.475 55.000 4.97 4.97 0.00 3.66
564 577 0.401356 TCAAAGTGCAGCTCCATGGA 59.599 50.000 15.27 15.27 0.00 3.41
565 578 1.005097 TCAAAGTGCAGCTCCATGGAT 59.995 47.619 16.63 0.00 0.00 3.41
566 579 1.822990 CAAAGTGCAGCTCCATGGATT 59.177 47.619 16.63 3.75 0.00 3.01
567 580 1.760192 AAGTGCAGCTCCATGGATTC 58.240 50.000 16.63 10.44 0.00 2.52
568 581 0.106819 AGTGCAGCTCCATGGATTCC 60.107 55.000 16.63 6.99 0.00 3.01
569 582 1.105759 GTGCAGCTCCATGGATTCCC 61.106 60.000 16.63 5.32 0.00 3.97
571 584 1.105759 GCAGCTCCATGGATTCCCAC 61.106 60.000 16.63 0.00 46.98 4.61
572 585 0.466922 CAGCTCCATGGATTCCCACC 60.467 60.000 16.63 0.00 46.98 4.61
622 635 4.477975 GCTCGTCGTCCAGTCCCG 62.478 72.222 0.00 0.00 0.00 5.14
629 642 2.987547 GTCCAGTCCCGTCGACCA 60.988 66.667 10.58 0.00 43.08 4.02
630 643 2.036731 TCCAGTCCCGTCGACCAT 59.963 61.111 10.58 0.00 43.08 3.55
631 644 2.184322 CCAGTCCCGTCGACCATG 59.816 66.667 10.58 1.77 43.08 3.66
632 645 2.509336 CAGTCCCGTCGACCATGC 60.509 66.667 10.58 0.00 43.08 4.06
633 646 2.994995 AGTCCCGTCGACCATGCA 60.995 61.111 10.58 0.00 43.08 3.96
646 666 2.281692 ATGCAACAGAGCGTGCCA 60.282 55.556 0.00 0.00 37.31 4.92
673 701 0.902984 TCCTCCTCCTTTACTGCGCA 60.903 55.000 10.98 10.98 0.00 6.09
674 702 0.741221 CCTCCTCCTTTACTGCGCAC 60.741 60.000 5.66 0.00 0.00 5.34
675 703 1.078759 CTCCTCCTTTACTGCGCACG 61.079 60.000 5.66 5.54 0.00 5.34
676 704 1.080093 CCTCCTTTACTGCGCACGA 60.080 57.895 5.66 0.00 0.00 4.35
677 705 1.078759 CCTCCTTTACTGCGCACGAG 61.079 60.000 5.66 0.00 0.00 4.18
687 720 3.029564 GCGCACGAGAGACGAGACT 62.030 63.158 0.30 0.00 45.77 3.24
727 760 2.034066 TTCCCCAGCTTCGCCAAG 59.966 61.111 0.00 0.00 0.00 3.61
841 891 5.069781 CCATTCCTTTCTCTCCTCGTAATCT 59.930 44.000 0.00 0.00 0.00 2.40
948 1007 6.544038 TTATCATTCATCATGCGGTTGTAG 57.456 37.500 0.00 0.00 32.13 2.74
961 1020 6.271488 TGCGGTTGTAGTAGTAGTAATGTT 57.729 37.500 0.00 0.00 0.00 2.71
964 1023 6.587608 GCGGTTGTAGTAGTAGTAATGTTTGT 59.412 38.462 0.00 0.00 0.00 2.83
972 1031 8.535690 AGTAGTAGTAATGTTTGTTTCTCTGC 57.464 34.615 0.00 0.00 0.00 4.26
985 1044 1.061570 CTCTGCATCTTTTCCGCGC 59.938 57.895 0.00 0.00 0.00 6.86
986 1045 1.638388 CTCTGCATCTTTTCCGCGCA 61.638 55.000 8.75 0.00 0.00 6.09
995 1054 3.825160 TTTCCGCGCAAGGAGCAGT 62.825 57.895 8.75 0.00 46.13 4.40
998 1057 3.782244 CGCGCAAGGAGCAGTCAC 61.782 66.667 8.75 0.00 46.13 3.67
1113 1172 2.031163 GTCAGGAAGTGCTGGCGT 59.969 61.111 0.00 0.00 0.00 5.68
1230 1304 2.586357 GCCGCCGGAGATCAGAAC 60.586 66.667 7.68 0.00 0.00 3.01
1236 1313 1.337071 GCCGGAGATCAGAACATACGA 59.663 52.381 5.05 0.00 0.00 3.43
1238 1315 2.357952 CCGGAGATCAGAACATACGACA 59.642 50.000 0.00 0.00 0.00 4.35
1247 1324 3.096852 AGAACATACGACACATCCTCCA 58.903 45.455 0.00 0.00 0.00 3.86
1254 1331 1.467543 CGACACATCCTCCAGTACACG 60.468 57.143 0.00 0.00 0.00 4.49
1551 1692 2.190578 GGATCGGACCAGCCAAGG 59.809 66.667 0.00 0.00 35.94 3.61
1590 1737 4.083484 ACAGTTTTAGAGATTTTTCCGGCG 60.083 41.667 0.00 0.00 0.00 6.46
1624 1781 1.079825 ACTACCCACCAGTCCACCATA 59.920 52.381 0.00 0.00 0.00 2.74
1626 1783 0.914417 ACCCACCAGTCCACCATAGG 60.914 60.000 0.00 0.00 0.00 2.57
1627 1784 0.620410 CCCACCAGTCCACCATAGGA 60.620 60.000 0.00 0.00 34.64 2.94
1675 1832 1.073177 CATAACCGTGTTCGACACCC 58.927 55.000 11.01 0.00 45.93 4.61
1773 1930 4.627447 CTTGCTTTGCGCCGCACA 62.627 61.111 13.21 3.84 38.71 4.57
1912 2111 1.973281 AATGGCCGTGAGCTGTTGG 60.973 57.895 0.00 0.00 43.05 3.77
1918 2117 1.069765 CGTGAGCTGTTGGTCCAGT 59.930 57.895 0.00 0.00 39.75 4.00
1940 2139 1.878522 GTCCTGACCGTATGCTGCG 60.879 63.158 0.00 0.00 0.00 5.18
1944 2143 2.296692 CTGACCGTATGCTGCGTTGC 62.297 60.000 0.00 0.00 0.00 4.17
1956 2155 2.202171 CGTTGCGACATTGACGGC 60.202 61.111 10.32 3.89 32.29 5.68
1963 2162 0.450482 CGACATTGACGGCGTGTTTC 60.450 55.000 21.19 2.65 0.00 2.78
2306 2516 3.922240 GCTTGTGCTATCAACATTTGGTG 59.078 43.478 0.00 0.00 36.03 4.17
2370 2585 8.284945 TGAACAATTGAGCTTCTATGCTTTAT 57.715 30.769 13.59 0.00 44.17 1.40
2395 2620 2.897969 TGTTCTACTGTTCTCCCCTGTC 59.102 50.000 0.00 0.00 0.00 3.51
2463 2741 6.758593 TGTTCACTACAACGACAAGTAATC 57.241 37.500 0.00 0.00 32.64 1.75
2568 2850 7.038799 ACTGGCTTTCACCATTTCAGATAAAAT 60.039 33.333 0.00 0.00 39.54 1.82
2572 2854 8.193438 GCTTTCACCATTTCAGATAAAATAGCT 58.807 33.333 0.00 0.00 0.00 3.32
2602 2885 6.422333 TGCTACATTTATGTCCAGGATTTGA 58.578 36.000 0.00 0.00 41.97 2.69
2648 6255 9.678260 ATTATTGGAGTGCTATCTTAATCATCC 57.322 33.333 0.00 0.00 0.00 3.51
2655 6262 6.268617 AGTGCTATCTTAATCATCCTGCTGTA 59.731 38.462 0.00 0.00 0.00 2.74
2661 6268 2.906691 ATCATCCTGCTGTAGTCTGC 57.093 50.000 0.00 0.00 38.66 4.26
2762 6382 6.978343 TTTATTGTCTGTGGGTTTATCGAG 57.022 37.500 0.00 0.00 0.00 4.04
2774 6394 3.259064 GTTTATCGAGTTACTGCTGGCA 58.741 45.455 0.00 0.00 0.00 4.92
2813 6433 6.509418 AAGCTGTTCTTTGTCAGTTTTACA 57.491 33.333 0.00 0.00 32.82 2.41
2814 6434 6.699575 AGCTGTTCTTTGTCAGTTTTACAT 57.300 33.333 0.00 0.00 34.57 2.29
2833 6453 4.265073 ACATAAAATGAGGAGCTGGACAC 58.735 43.478 0.00 0.00 0.00 3.67
2848 6468 1.269166 GACACGTCCTATCGTTGCAG 58.731 55.000 0.00 0.00 42.27 4.41
3039 7080 8.208224 TCAGAACTGTTCTACTGTTTTCCATTA 58.792 33.333 21.65 0.00 39.78 1.90
3043 7084 8.788325 ACTGTTCTACTGTTTTCCATTATACC 57.212 34.615 0.00 0.00 0.00 2.73
3044 7085 8.380099 ACTGTTCTACTGTTTTCCATTATACCA 58.620 33.333 0.00 0.00 0.00 3.25
3053 7094 3.328382 TCCATTATACCATACGGCTGC 57.672 47.619 0.00 0.00 34.57 5.25
3056 7097 2.163818 TTATACCATACGGCTGCAGC 57.836 50.000 30.88 30.88 41.14 5.25
3075 7120 1.072159 GCTGGTGCTTGGTGTCTCT 59.928 57.895 0.00 0.00 36.03 3.10
3119 7164 9.787532 ATTGTTGGATTTATTGATTTACTCACG 57.212 29.630 0.00 0.00 32.17 4.35
3125 7170 9.046296 GGATTTATTGATTTACTCACGTCTGAT 57.954 33.333 0.00 0.00 32.17 2.90
3132 7177 8.502105 TGATTTACTCACGTCTGATCTACTAA 57.498 34.615 0.00 0.00 0.00 2.24
3164 7209 4.416505 CTTGTTGAGCTTTGCTTCCTAG 57.583 45.455 0.00 0.00 39.88 3.02
3167 7212 2.479566 TGAGCTTTGCTTCCTAGGTG 57.520 50.000 9.08 4.42 39.88 4.00
3176 7221 1.886542 GCTTCCTAGGTGTTTGGGTTG 59.113 52.381 9.08 0.00 0.00 3.77
3178 7223 0.847373 TCCTAGGTGTTTGGGTTGCA 59.153 50.000 9.08 0.00 0.00 4.08
3179 7224 1.202879 TCCTAGGTGTTTGGGTTGCAG 60.203 52.381 9.08 0.00 0.00 4.41
3180 7225 0.598065 CTAGGTGTTTGGGTTGCAGC 59.402 55.000 0.00 0.00 0.00 5.25
3188 7233 1.664873 TGGGTTGCAGCCAAAATCG 59.335 52.632 22.07 0.00 43.74 3.34
3189 7234 0.825425 TGGGTTGCAGCCAAAATCGA 60.825 50.000 22.07 0.00 43.74 3.59
3190 7235 0.532115 GGGTTGCAGCCAAAATCGAT 59.468 50.000 22.07 0.00 35.40 3.59
3191 7236 1.066929 GGGTTGCAGCCAAAATCGATT 60.067 47.619 22.07 4.39 35.40 3.34
3193 7238 1.913403 GTTGCAGCCAAAATCGATTCG 59.087 47.619 11.83 5.84 31.68 3.34
3203 7769 0.179048 AATCGATTCGCTGGCCATGA 60.179 50.000 5.51 4.46 0.00 3.07
3205 7771 1.815003 CGATTCGCTGGCCATGACA 60.815 57.895 5.51 0.00 0.00 3.58
3234 7800 2.493278 GGGTCACTGTTTGAATGGATGG 59.507 50.000 0.00 0.00 35.39 3.51
3277 7843 0.320683 GGGCTCAAACCAAACATGCC 60.321 55.000 0.00 0.00 38.28 4.40
3279 7845 1.002315 GGCTCAAACCAAACATGCCAT 59.998 47.619 0.00 0.00 38.79 4.40
3353 7919 1.736032 GCCTTCTACTACCAGCGTGTG 60.736 57.143 0.00 0.00 0.00 3.82
3374 7940 4.524328 GTGGGATGGAAGTGATTTGTCTTT 59.476 41.667 0.00 0.00 0.00 2.52
3384 7950 9.346725 GGAAGTGATTTGTCTTTCATAATGTTC 57.653 33.333 0.00 0.00 0.00 3.18
3387 7953 8.446273 AGTGATTTGTCTTTCATAATGTTCTCG 58.554 33.333 0.00 0.00 0.00 4.04
3388 7954 8.230486 GTGATTTGTCTTTCATAATGTTCTCGT 58.770 33.333 0.00 0.00 0.00 4.18
3389 7955 8.443160 TGATTTGTCTTTCATAATGTTCTCGTC 58.557 33.333 0.00 0.00 0.00 4.20
3390 7956 7.962964 TTTGTCTTTCATAATGTTCTCGTCT 57.037 32.000 0.00 0.00 0.00 4.18
3391 7957 7.582435 TTGTCTTTCATAATGTTCTCGTCTC 57.418 36.000 0.00 0.00 0.00 3.36
3392 7958 5.800438 TGTCTTTCATAATGTTCTCGTCTCG 59.200 40.000 0.00 0.00 0.00 4.04
3393 7959 5.230306 GTCTTTCATAATGTTCTCGTCTCGG 59.770 44.000 0.00 0.00 0.00 4.63
3394 7960 3.079960 TCATAATGTTCTCGTCTCGGC 57.920 47.619 0.00 0.00 0.00 5.54
3395 7961 2.425668 TCATAATGTTCTCGTCTCGGCA 59.574 45.455 0.00 0.00 0.00 5.69
3396 7962 2.561733 TAATGTTCTCGTCTCGGCAG 57.438 50.000 0.00 0.00 0.00 4.85
3397 7963 0.737715 AATGTTCTCGTCTCGGCAGC 60.738 55.000 0.00 0.00 0.00 5.25
3398 7964 1.599606 ATGTTCTCGTCTCGGCAGCT 61.600 55.000 0.00 0.00 0.00 4.24
3399 7965 1.515304 GTTCTCGTCTCGGCAGCTC 60.515 63.158 0.00 0.00 0.00 4.09
3400 7966 1.675972 TTCTCGTCTCGGCAGCTCT 60.676 57.895 0.00 0.00 0.00 4.09
3401 7967 1.927608 TTCTCGTCTCGGCAGCTCTG 61.928 60.000 0.00 0.00 0.00 3.35
3412 7978 3.802862 CAGCTCTGCCATGGATTCT 57.197 52.632 18.40 1.03 0.00 2.40
3413 7979 1.309950 CAGCTCTGCCATGGATTCTG 58.690 55.000 18.40 10.40 0.00 3.02
3414 7980 1.134189 CAGCTCTGCCATGGATTCTGA 60.134 52.381 18.40 6.59 0.00 3.27
3415 7981 1.562942 AGCTCTGCCATGGATTCTGAA 59.437 47.619 18.40 0.00 0.00 3.02
3416 7982 2.175069 AGCTCTGCCATGGATTCTGAAT 59.825 45.455 18.40 1.81 0.00 2.57
3417 7983 2.553172 GCTCTGCCATGGATTCTGAATC 59.447 50.000 18.40 19.67 37.17 2.52
3418 7984 3.748027 GCTCTGCCATGGATTCTGAATCT 60.748 47.826 24.96 8.09 38.01 2.40
3419 7985 4.462133 CTCTGCCATGGATTCTGAATCTT 58.538 43.478 24.96 13.35 38.01 2.40
3420 7986 4.863548 TCTGCCATGGATTCTGAATCTTT 58.136 39.130 24.96 13.05 38.01 2.52
3421 7987 4.643334 TCTGCCATGGATTCTGAATCTTTG 59.357 41.667 24.96 21.08 38.01 2.77
3422 7988 3.131577 TGCCATGGATTCTGAATCTTTGC 59.868 43.478 24.96 21.28 38.01 3.68
3423 7989 3.383825 GCCATGGATTCTGAATCTTTGCT 59.616 43.478 24.96 7.36 38.01 3.91
3424 7990 4.142004 GCCATGGATTCTGAATCTTTGCTT 60.142 41.667 24.96 8.16 38.01 3.91
3425 7991 5.348986 CCATGGATTCTGAATCTTTGCTTG 58.651 41.667 24.96 16.76 38.01 4.01
3426 7992 5.105473 CCATGGATTCTGAATCTTTGCTTGT 60.105 40.000 24.96 5.03 38.01 3.16
3427 7993 6.395629 CATGGATTCTGAATCTTTGCTTGTT 58.604 36.000 24.96 2.87 38.01 2.83
3428 7994 5.775686 TGGATTCTGAATCTTTGCTTGTTG 58.224 37.500 24.96 0.00 38.01 3.33
3429 7995 5.302568 TGGATTCTGAATCTTTGCTTGTTGT 59.697 36.000 24.96 0.00 38.01 3.32
3430 7996 6.183360 TGGATTCTGAATCTTTGCTTGTTGTT 60.183 34.615 24.96 0.00 38.01 2.83
3431 7997 6.364435 GGATTCTGAATCTTTGCTTGTTGTTC 59.636 38.462 24.96 4.56 38.01 3.18
3432 7998 6.455360 TTCTGAATCTTTGCTTGTTGTTCT 57.545 33.333 0.00 0.00 0.00 3.01
3433 7999 5.824429 TCTGAATCTTTGCTTGTTGTTCTG 58.176 37.500 0.00 0.00 0.00 3.02
3434 8000 5.589855 TCTGAATCTTTGCTTGTTGTTCTGA 59.410 36.000 0.00 0.00 0.00 3.27
3435 8001 6.095300 TCTGAATCTTTGCTTGTTGTTCTGAA 59.905 34.615 0.00 0.00 0.00 3.02
3436 8002 6.629128 TGAATCTTTGCTTGTTGTTCTGAAA 58.371 32.000 0.00 0.00 0.00 2.69
3437 8003 6.531240 TGAATCTTTGCTTGTTGTTCTGAAAC 59.469 34.615 0.00 0.00 35.85 2.78
3438 8004 5.384063 TCTTTGCTTGTTGTTCTGAAACA 57.616 34.783 0.00 0.00 43.58 2.83
3439 8005 5.964758 TCTTTGCTTGTTGTTCTGAAACAT 58.035 33.333 0.00 0.00 44.59 2.71
3440 8006 7.094508 TCTTTGCTTGTTGTTCTGAAACATA 57.905 32.000 0.00 0.00 44.59 2.29
3441 8007 6.972328 TCTTTGCTTGTTGTTCTGAAACATAC 59.028 34.615 0.00 0.00 44.59 2.39
3442 8008 4.843147 TGCTTGTTGTTCTGAAACATACG 58.157 39.130 0.00 0.00 44.59 3.06
3443 8009 4.219033 GCTTGTTGTTCTGAAACATACGG 58.781 43.478 0.00 0.00 44.59 4.02
3444 8010 4.261031 GCTTGTTGTTCTGAAACATACGGT 60.261 41.667 0.00 0.00 44.59 4.83
3445 8011 5.412526 TTGTTGTTCTGAAACATACGGTC 57.587 39.130 0.00 0.00 44.59 4.79
3446 8012 4.443621 TGTTGTTCTGAAACATACGGTCA 58.556 39.130 0.00 0.00 44.59 4.02
3447 8013 4.271533 TGTTGTTCTGAAACATACGGTCAC 59.728 41.667 0.00 0.00 44.59 3.67
3448 8014 4.061357 TGTTCTGAAACATACGGTCACA 57.939 40.909 0.00 0.00 40.45 3.58
3449 8015 3.805422 TGTTCTGAAACATACGGTCACAC 59.195 43.478 0.00 0.00 40.45 3.82
3450 8016 4.056050 GTTCTGAAACATACGGTCACACT 58.944 43.478 0.00 0.00 35.36 3.55
3451 8017 4.330944 TCTGAAACATACGGTCACACTT 57.669 40.909 0.00 0.00 0.00 3.16
3452 8018 4.699637 TCTGAAACATACGGTCACACTTT 58.300 39.130 0.00 0.00 0.00 2.66
3453 8019 5.120399 TCTGAAACATACGGTCACACTTTT 58.880 37.500 0.00 0.00 0.00 2.27
3454 8020 5.587043 TCTGAAACATACGGTCACACTTTTT 59.413 36.000 0.00 0.00 0.00 1.94
3455 8021 5.812652 TGAAACATACGGTCACACTTTTTC 58.187 37.500 0.00 0.00 0.00 2.29
3456 8022 5.587043 TGAAACATACGGTCACACTTTTTCT 59.413 36.000 0.00 0.00 0.00 2.52
3457 8023 5.418310 AACATACGGTCACACTTTTTCTG 57.582 39.130 0.00 0.00 0.00 3.02
3458 8024 4.699637 ACATACGGTCACACTTTTTCTGA 58.300 39.130 0.00 0.00 0.00 3.27
3459 8025 5.120399 ACATACGGTCACACTTTTTCTGAA 58.880 37.500 0.00 0.00 0.00 3.02
3460 8026 5.007332 ACATACGGTCACACTTTTTCTGAAC 59.993 40.000 0.00 0.00 0.00 3.18
3461 8027 2.681344 ACGGTCACACTTTTTCTGAACC 59.319 45.455 0.00 0.00 0.00 3.62
3462 8028 2.286184 CGGTCACACTTTTTCTGAACCG 60.286 50.000 0.00 0.00 0.00 4.44
3463 8029 2.681344 GGTCACACTTTTTCTGAACCGT 59.319 45.455 0.00 0.00 0.00 4.83
3464 8030 3.486875 GGTCACACTTTTTCTGAACCGTG 60.487 47.826 9.84 9.84 0.00 4.94
3465 8031 2.096819 TCACACTTTTTCTGAACCGTGC 59.903 45.455 10.83 0.00 0.00 5.34
3466 8032 2.097466 CACACTTTTTCTGAACCGTGCT 59.903 45.455 10.83 0.60 0.00 4.40
3467 8033 2.752903 ACACTTTTTCTGAACCGTGCTT 59.247 40.909 10.83 0.00 0.00 3.91
3468 8034 3.192633 ACACTTTTTCTGAACCGTGCTTT 59.807 39.130 10.83 0.00 0.00 3.51
3469 8035 3.791353 CACTTTTTCTGAACCGTGCTTTC 59.209 43.478 0.00 0.00 0.00 2.62
3470 8036 3.181490 ACTTTTTCTGAACCGTGCTTTCC 60.181 43.478 0.00 0.00 0.00 3.13
3471 8037 1.314730 TTTCTGAACCGTGCTTTCCC 58.685 50.000 0.00 0.00 0.00 3.97
3472 8038 0.536460 TTCTGAACCGTGCTTTCCCC 60.536 55.000 0.00 0.00 0.00 4.81
3473 8039 1.073199 CTGAACCGTGCTTTCCCCT 59.927 57.895 0.00 0.00 0.00 4.79
3474 8040 0.955919 CTGAACCGTGCTTTCCCCTC 60.956 60.000 0.00 0.00 0.00 4.30
3475 8041 1.375326 GAACCGTGCTTTCCCCTCT 59.625 57.895 0.00 0.00 0.00 3.69
3476 8042 0.250770 GAACCGTGCTTTCCCCTCTT 60.251 55.000 0.00 0.00 0.00 2.85
3477 8043 0.185175 AACCGTGCTTTCCCCTCTTT 59.815 50.000 0.00 0.00 0.00 2.52
3478 8044 0.250770 ACCGTGCTTTCCCCTCTTTC 60.251 55.000 0.00 0.00 0.00 2.62
3479 8045 0.960861 CCGTGCTTTCCCCTCTTTCC 60.961 60.000 0.00 0.00 0.00 3.13
3480 8046 0.250727 CGTGCTTTCCCCTCTTTCCA 60.251 55.000 0.00 0.00 0.00 3.53
3481 8047 1.614317 CGTGCTTTCCCCTCTTTCCAT 60.614 52.381 0.00 0.00 0.00 3.41
3482 8048 2.529632 GTGCTTTCCCCTCTTTCCATT 58.470 47.619 0.00 0.00 0.00 3.16
3483 8049 2.493675 GTGCTTTCCCCTCTTTCCATTC 59.506 50.000 0.00 0.00 0.00 2.67
3484 8050 2.103373 GCTTTCCCCTCTTTCCATTCC 58.897 52.381 0.00 0.00 0.00 3.01
3485 8051 2.291865 GCTTTCCCCTCTTTCCATTCCT 60.292 50.000 0.00 0.00 0.00 3.36
3486 8052 3.819388 GCTTTCCCCTCTTTCCATTCCTT 60.819 47.826 0.00 0.00 0.00 3.36
3487 8053 4.420206 CTTTCCCCTCTTTCCATTCCTTT 58.580 43.478 0.00 0.00 0.00 3.11
3488 8054 4.485653 TTCCCCTCTTTCCATTCCTTTT 57.514 40.909 0.00 0.00 0.00 2.27
3489 8055 4.485653 TCCCCTCTTTCCATTCCTTTTT 57.514 40.909 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 0.100682 GCATGCTCAGGCTCAACATG 59.899 55.000 11.37 13.22 40.80 3.21
113 117 1.463444 CCCGATGAAACTCGACAAACC 59.537 52.381 0.00 0.00 41.12 3.27
233 238 8.810990 ACCCAATCAAAATTTATTTGCATGAT 57.189 26.923 0.00 0.00 30.30 2.45
283 289 7.292292 CAATCGAAATTTGTTTGCATGACAAT 58.708 30.769 14.57 3.28 38.31 2.71
392 402 1.145759 TTCGATCGCATCTTGTCCGC 61.146 55.000 11.09 0.00 0.00 5.54
461 471 1.154413 GTGACAATGAAGCCGCGTG 60.154 57.895 4.92 0.00 0.00 5.34
464 474 0.955428 TGAGGTGACAATGAAGCCGC 60.955 55.000 0.00 0.00 0.00 6.53
487 498 1.136774 GCTTTGTCGGATTTCGCCC 59.863 57.895 0.00 0.00 39.05 6.13
497 510 2.544359 CACACGTCCGCTTTGTCG 59.456 61.111 0.00 0.00 0.00 4.35
518 531 5.576447 ATTTAATAAGGCCAACTCCAACG 57.424 39.130 5.01 0.00 0.00 4.10
536 549 4.216257 GGAGCTGCACTTTGACTGAATTTA 59.784 41.667 0.00 0.00 0.00 1.40
537 550 3.005155 GGAGCTGCACTTTGACTGAATTT 59.995 43.478 0.00 0.00 0.00 1.82
538 551 2.555757 GGAGCTGCACTTTGACTGAATT 59.444 45.455 0.00 0.00 0.00 2.17
539 552 2.157738 GGAGCTGCACTTTGACTGAAT 58.842 47.619 0.00 0.00 0.00 2.57
540 553 1.134128 TGGAGCTGCACTTTGACTGAA 60.134 47.619 2.72 0.00 0.00 3.02
541 554 0.469494 TGGAGCTGCACTTTGACTGA 59.531 50.000 2.72 0.00 0.00 3.41
542 555 1.199327 CATGGAGCTGCACTTTGACTG 59.801 52.381 11.23 0.00 0.00 3.51
543 556 1.531423 CATGGAGCTGCACTTTGACT 58.469 50.000 11.23 0.00 0.00 3.41
544 557 0.524862 CCATGGAGCTGCACTTTGAC 59.475 55.000 11.23 0.00 0.00 3.18
545 558 0.401356 TCCATGGAGCTGCACTTTGA 59.599 50.000 11.23 1.64 0.00 2.69
546 559 1.471119 ATCCATGGAGCTGCACTTTG 58.529 50.000 21.33 5.04 0.00 2.77
547 560 2.097825 GAATCCATGGAGCTGCACTTT 58.902 47.619 21.33 6.63 0.00 2.66
548 561 1.684248 GGAATCCATGGAGCTGCACTT 60.684 52.381 21.33 7.43 0.00 3.16
549 562 0.106819 GGAATCCATGGAGCTGCACT 60.107 55.000 21.33 0.00 0.00 4.40
550 563 1.105759 GGGAATCCATGGAGCTGCAC 61.106 60.000 21.33 0.00 0.00 4.57
551 564 1.228228 GGGAATCCATGGAGCTGCA 59.772 57.895 21.33 11.44 0.00 4.41
552 565 1.105759 GTGGGAATCCATGGAGCTGC 61.106 60.000 21.33 14.43 46.09 5.25
553 566 0.466922 GGTGGGAATCCATGGAGCTG 60.467 60.000 21.33 0.00 46.09 4.24
554 567 0.625683 AGGTGGGAATCCATGGAGCT 60.626 55.000 21.33 9.84 46.09 4.09
555 568 1.072965 CTAGGTGGGAATCCATGGAGC 59.927 57.143 21.33 14.26 46.09 4.70
556 569 1.072965 GCTAGGTGGGAATCCATGGAG 59.927 57.143 21.33 3.21 46.09 3.86
557 570 1.140312 GCTAGGTGGGAATCCATGGA 58.860 55.000 18.88 18.88 46.09 3.41
558 571 1.143813 AGCTAGGTGGGAATCCATGG 58.856 55.000 4.97 4.97 46.09 3.66
559 572 2.304180 CCTAGCTAGGTGGGAATCCATG 59.696 54.545 28.90 1.25 46.09 3.66
560 573 2.625639 CCTAGCTAGGTGGGAATCCAT 58.374 52.381 28.90 0.00 46.09 3.41
561 574 2.040144 GCCTAGCTAGGTGGGAATCCA 61.040 57.143 34.85 0.00 45.42 3.41
562 575 0.687920 GCCTAGCTAGGTGGGAATCC 59.312 60.000 34.85 16.11 45.42 3.01
563 576 1.346068 CAGCCTAGCTAGGTGGGAATC 59.654 57.143 34.85 19.56 45.42 2.52
564 577 1.428869 CAGCCTAGCTAGGTGGGAAT 58.571 55.000 34.85 15.38 45.42 3.01
565 578 1.338136 GCAGCCTAGCTAGGTGGGAA 61.338 60.000 34.85 0.00 45.42 3.97
566 579 1.762460 GCAGCCTAGCTAGGTGGGA 60.762 63.158 34.85 0.00 45.42 4.37
567 580 2.825264 GCAGCCTAGCTAGGTGGG 59.175 66.667 34.85 25.62 45.42 4.61
568 581 2.419198 CGCAGCCTAGCTAGGTGG 59.581 66.667 34.85 27.75 45.42 4.61
622 635 1.790387 GCTCTGTTGCATGGTCGAC 59.210 57.895 7.13 7.13 0.00 4.20
629 642 2.281692 TGGCACGCTCTGTTGCAT 60.282 55.556 0.00 0.00 0.00 3.96
630 643 3.279116 GTGGCACGCTCTGTTGCA 61.279 61.111 0.00 0.00 35.02 4.08
631 644 4.030452 GGTGGCACGCTCTGTTGC 62.030 66.667 12.17 0.00 39.78 4.17
632 645 3.357079 GGGTGGCACGCTCTGTTG 61.357 66.667 25.48 0.00 35.72 3.33
633 646 3.196207 ATGGGTGGCACGCTCTGTT 62.196 57.895 30.89 11.36 41.85 3.16
646 666 0.423544 AAAGGAGGAGGAGGATGGGT 59.576 55.000 0.00 0.00 0.00 4.51
673 701 1.022451 GCTGGAGTCTCGTCTCTCGT 61.022 60.000 0.00 0.00 40.80 4.18
674 702 1.021920 TGCTGGAGTCTCGTCTCTCG 61.022 60.000 0.00 0.00 41.41 4.04
675 703 1.388547 ATGCTGGAGTCTCGTCTCTC 58.611 55.000 0.00 0.00 35.11 3.20
676 704 1.476085 CAATGCTGGAGTCTCGTCTCT 59.524 52.381 0.00 0.00 35.11 3.10
677 705 1.919918 CAATGCTGGAGTCTCGTCTC 58.080 55.000 0.00 0.00 0.00 3.36
687 720 1.679977 GAGCCTTGGCAATGCTGGA 60.680 57.895 30.37 0.00 34.99 3.86
771 821 3.672338 ATTTACCTTGGGGCGGGGC 62.672 63.158 0.00 0.00 35.63 5.80
772 822 1.455032 GATTTACCTTGGGGCGGGG 60.455 63.158 0.00 0.00 35.63 5.73
773 823 1.455032 GGATTTACCTTGGGGCGGG 60.455 63.158 0.00 0.00 35.63 6.13
795 845 1.234615 TTGAAAGCGGGGAAGAAGCG 61.235 55.000 0.00 0.00 35.78 4.68
797 847 2.164422 GGATTTGAAAGCGGGGAAGAAG 59.836 50.000 0.00 0.00 0.00 2.85
841 891 4.499865 GCCTCAGCGATCTAGTACAAATCA 60.500 45.833 0.00 0.00 0.00 2.57
948 1007 8.306680 TGCAGAGAAACAAACATTACTACTAC 57.693 34.615 0.00 0.00 0.00 2.73
961 1020 3.304659 GCGGAAAAGATGCAGAGAAACAA 60.305 43.478 0.00 0.00 0.00 2.83
964 1023 1.464608 CGCGGAAAAGATGCAGAGAAA 59.535 47.619 0.00 0.00 0.00 2.52
970 1029 1.209898 CTTGCGCGGAAAAGATGCA 59.790 52.632 15.55 0.00 0.00 3.96
972 1031 0.097674 CTCCTTGCGCGGAAAAGATG 59.902 55.000 15.55 1.67 31.44 2.90
985 1044 1.310933 GGCATGGTGACTGCTCCTTG 61.311 60.000 0.00 0.00 39.60 3.61
986 1045 1.001641 GGCATGGTGACTGCTCCTT 60.002 57.895 0.00 0.00 39.60 3.36
995 1054 2.601702 ATGGTGTCCGGCATGGTGA 61.602 57.895 0.00 0.00 39.52 4.02
998 1057 3.520862 GCATGGTGTCCGGCATGG 61.521 66.667 17.94 4.23 40.09 3.66
1230 1304 3.380320 TGTACTGGAGGATGTGTCGTATG 59.620 47.826 0.00 0.00 0.00 2.39
1236 1313 0.246635 GCGTGTACTGGAGGATGTGT 59.753 55.000 0.00 0.00 0.00 3.72
1238 1315 1.511305 CGCGTGTACTGGAGGATGT 59.489 57.895 0.00 0.00 0.00 3.06
1247 1324 4.547905 CGGGATCGCGCGTGTACT 62.548 66.667 30.98 10.42 44.37 2.73
1254 1331 3.122323 TTGGAAACGGGATCGCGC 61.122 61.111 29.53 15.11 40.63 6.86
1551 1692 1.577328 CTGTCGGCCATTGGACACAC 61.577 60.000 9.76 5.00 38.19 3.82
1738 1895 1.519455 GGTCGCCACCAAGATCGAG 60.519 63.158 0.00 0.00 43.17 4.04
1933 2132 1.154169 CAATGTCGCAACGCAGCAT 60.154 52.632 0.00 0.00 0.00 3.79
1936 2135 1.507713 CGTCAATGTCGCAACGCAG 60.508 57.895 0.00 0.00 0.00 5.18
1940 2139 2.202171 CGCCGTCAATGTCGCAAC 60.202 61.111 0.00 0.00 0.00 4.17
1944 2143 0.450482 GAAACACGCCGTCAATGTCG 60.450 55.000 0.00 0.00 0.00 4.35
1956 2155 5.682943 TTTCCACATTTCCTAGAAACACG 57.317 39.130 0.00 0.00 0.00 4.49
1963 2162 4.093556 GTCTTCGCTTTCCACATTTCCTAG 59.906 45.833 0.00 0.00 0.00 3.02
2353 2568 8.260818 AGAACAGTTATAAAGCATAGAAGCTCA 58.739 33.333 0.00 0.00 45.89 4.26
2370 2585 4.527038 CAGGGGAGAACAGTAGAACAGTTA 59.473 45.833 0.00 0.00 27.59 2.24
2383 2598 5.046520 ACAGTTAACATAGACAGGGGAGAAC 60.047 44.000 8.61 0.00 0.00 3.01
2395 2620 6.149308 TGAGCACCAAATCACAGTTAACATAG 59.851 38.462 8.61 0.00 0.00 2.23
2486 2768 4.574013 AGCTGTATTGAAGTAGCAATCAGC 59.426 41.667 20.74 20.74 46.02 4.26
2568 2850 5.192927 ACATAAATGTAGCAGCCAAAGCTA 58.807 37.500 0.00 0.00 43.51 3.32
2572 2854 4.339748 TGGACATAAATGTAGCAGCCAAA 58.660 39.130 0.00 0.00 41.95 3.28
2622 6228 9.678260 GGATGATTAAGATAGCACTCCAATAAT 57.322 33.333 0.00 0.00 0.00 1.28
2643 6250 1.479730 CAGCAGACTACAGCAGGATGA 59.520 52.381 0.00 0.00 39.69 2.92
2648 6255 1.405256 CCTTCCAGCAGACTACAGCAG 60.405 57.143 0.00 0.00 0.00 4.24
2655 6262 1.845205 ACCAGCCTTCCAGCAGACT 60.845 57.895 0.00 0.00 34.23 3.24
2661 6268 1.004044 AGACAATCACCAGCCTTCCAG 59.996 52.381 0.00 0.00 0.00 3.86
2712 6330 5.586243 GCAAAAGAGACAGCCATATTACAGA 59.414 40.000 0.00 0.00 0.00 3.41
2762 6382 0.890996 AGCCAAGTGCCAGCAGTAAC 60.891 55.000 0.00 0.00 42.71 2.50
2774 6394 1.528129 GCTTAACAGCAGAGCCAAGT 58.472 50.000 0.00 0.00 46.49 3.16
2813 6433 3.055094 ACGTGTCCAGCTCCTCATTTTAT 60.055 43.478 0.00 0.00 0.00 1.40
2814 6434 2.301870 ACGTGTCCAGCTCCTCATTTTA 59.698 45.455 0.00 0.00 0.00 1.52
2833 6453 0.460284 AAGCCTGCAACGATAGGACG 60.460 55.000 0.00 0.00 43.77 4.79
2911 6531 3.501950 GCCATCGAAATTGTTCAGTTCC 58.498 45.455 0.00 0.00 32.89 3.62
3039 7080 1.300931 CGCTGCAGCCGTATGGTAT 60.301 57.895 32.07 0.00 37.91 2.73
3043 7084 3.933498 CAGCGCTGCAGCCGTATG 61.933 66.667 32.07 22.39 37.91 2.39
3117 7162 7.378995 GCGAAAATGTATTAGTAGATCAGACGT 59.621 37.037 0.00 0.00 0.00 4.34
3119 7164 8.804688 AGCGAAAATGTATTAGTAGATCAGAC 57.195 34.615 0.00 0.00 0.00 3.51
3125 7170 8.766000 TCAACAAGCGAAAATGTATTAGTAGA 57.234 30.769 0.00 0.00 0.00 2.59
3154 7199 1.497286 ACCCAAACACCTAGGAAGCAA 59.503 47.619 17.98 0.00 0.00 3.91
3159 7204 0.847373 TGCAACCCAAACACCTAGGA 59.153 50.000 17.98 0.00 0.00 2.94
3163 7208 2.133641 GGCTGCAACCCAAACACCT 61.134 57.895 0.50 0.00 0.00 4.00
3164 7209 1.965754 TTGGCTGCAACCCAAACACC 61.966 55.000 14.31 0.00 39.29 4.16
3176 7221 0.099436 AGCGAATCGATTTTGGCTGC 59.901 50.000 23.06 15.47 38.93 5.25
3178 7223 0.734889 CCAGCGAATCGATTTTGGCT 59.265 50.000 20.01 20.01 40.71 4.75
3179 7224 0.867329 GCCAGCGAATCGATTTTGGC 60.867 55.000 29.76 29.76 0.00 4.52
3180 7225 0.248621 GGCCAGCGAATCGATTTTGG 60.249 55.000 22.75 22.75 0.00 3.28
3187 7232 1.368345 TTGTCATGGCCAGCGAATCG 61.368 55.000 13.05 0.00 0.00 3.34
3188 7233 0.810648 TTTGTCATGGCCAGCGAATC 59.189 50.000 13.05 0.00 0.00 2.52
3189 7234 1.255882 TTTTGTCATGGCCAGCGAAT 58.744 45.000 13.05 0.00 0.00 3.34
3190 7235 1.035923 TTTTTGTCATGGCCAGCGAA 58.964 45.000 13.05 7.44 0.00 4.70
3191 7236 2.725811 TTTTTGTCATGGCCAGCGA 58.274 47.368 13.05 7.70 0.00 4.93
3217 7783 3.663995 TTGCCATCCATTCAAACAGTG 57.336 42.857 0.00 0.00 0.00 3.66
3221 7787 8.042944 ACAAAAATATTGCCATCCATTCAAAC 57.957 30.769 0.00 0.00 0.00 2.93
3225 7791 8.891671 ACATACAAAAATATTGCCATCCATTC 57.108 30.769 0.00 0.00 0.00 2.67
3226 7792 8.484575 TGACATACAAAAATATTGCCATCCATT 58.515 29.630 0.00 0.00 0.00 3.16
3277 7843 1.318158 GCCCAAGAGAGTTGCCCATG 61.318 60.000 0.00 0.00 0.00 3.66
3279 7845 2.436109 GCCCAAGAGAGTTGCCCA 59.564 61.111 0.00 0.00 0.00 5.36
3329 7895 1.739371 CGCTGGTAGTAGAAGGCAACC 60.739 57.143 0.00 0.00 37.17 3.77
3340 7906 1.596934 CATCCCACACGCTGGTAGT 59.403 57.895 0.00 0.00 38.60 2.73
3353 7919 4.766891 TGAAAGACAAATCACTTCCATCCC 59.233 41.667 0.00 0.00 0.00 3.85
3374 7940 2.425668 TGCCGAGACGAGAACATTATGA 59.574 45.455 0.00 0.00 0.00 2.15
3384 7950 2.101965 CAGAGCTGCCGAGACGAG 59.898 66.667 0.00 0.00 0.00 4.18
3394 7960 1.134189 TCAGAATCCATGGCAGAGCTG 60.134 52.381 6.96 9.86 0.00 4.24
3395 7961 1.210538 TCAGAATCCATGGCAGAGCT 58.789 50.000 6.96 0.00 0.00 4.09
3396 7962 2.048444 TTCAGAATCCATGGCAGAGC 57.952 50.000 6.96 0.00 0.00 4.09
3397 7963 4.088056 AGATTCAGAATCCATGGCAGAG 57.912 45.455 18.11 0.00 38.71 3.35
3398 7964 4.515028 AAGATTCAGAATCCATGGCAGA 57.485 40.909 18.11 0.00 38.71 4.26
3399 7965 4.736759 GCAAAGATTCAGAATCCATGGCAG 60.737 45.833 18.11 4.74 38.71 4.85
3400 7966 3.131577 GCAAAGATTCAGAATCCATGGCA 59.868 43.478 18.11 0.00 38.71 4.92
3401 7967 3.383825 AGCAAAGATTCAGAATCCATGGC 59.616 43.478 18.11 15.97 38.71 4.40
3402 7968 5.105473 ACAAGCAAAGATTCAGAATCCATGG 60.105 40.000 18.11 4.97 38.71 3.66
3403 7969 5.962433 ACAAGCAAAGATTCAGAATCCATG 58.038 37.500 18.11 17.12 38.71 3.66
3404 7970 6.014840 ACAACAAGCAAAGATTCAGAATCCAT 60.015 34.615 18.11 6.40 38.71 3.41
3405 7971 5.302568 ACAACAAGCAAAGATTCAGAATCCA 59.697 36.000 18.11 0.00 38.71 3.41
3406 7972 5.776744 ACAACAAGCAAAGATTCAGAATCC 58.223 37.500 18.11 4.56 38.71 3.01
3407 7973 7.114529 CAGAACAACAAGCAAAGATTCAGAATC 59.885 37.037 14.56 14.56 38.20 2.52
3408 7974 6.921857 CAGAACAACAAGCAAAGATTCAGAAT 59.078 34.615 0.00 0.00 0.00 2.40
3409 7975 6.095300 TCAGAACAACAAGCAAAGATTCAGAA 59.905 34.615 0.00 0.00 0.00 3.02
3410 7976 5.589855 TCAGAACAACAAGCAAAGATTCAGA 59.410 36.000 0.00 0.00 0.00 3.27
3411 7977 5.824429 TCAGAACAACAAGCAAAGATTCAG 58.176 37.500 0.00 0.00 0.00 3.02
3412 7978 5.833406 TCAGAACAACAAGCAAAGATTCA 57.167 34.783 0.00 0.00 0.00 2.57
3413 7979 6.531240 TGTTTCAGAACAACAAGCAAAGATTC 59.469 34.615 0.00 0.00 42.54 2.52
3414 7980 6.397272 TGTTTCAGAACAACAAGCAAAGATT 58.603 32.000 0.00 0.00 42.54 2.40
3415 7981 5.964758 TGTTTCAGAACAACAAGCAAAGAT 58.035 33.333 0.00 0.00 42.54 2.40
3416 7982 5.384063 TGTTTCAGAACAACAAGCAAAGA 57.616 34.783 0.00 0.00 42.54 2.52
3428 7994 4.056050 AGTGTGACCGTATGTTTCAGAAC 58.944 43.478 0.00 0.00 36.29 3.01
3429 7995 4.330944 AGTGTGACCGTATGTTTCAGAA 57.669 40.909 0.00 0.00 0.00 3.02
3430 7996 4.330944 AAGTGTGACCGTATGTTTCAGA 57.669 40.909 0.00 0.00 0.00 3.27
3431 7997 5.418310 AAAAGTGTGACCGTATGTTTCAG 57.582 39.130 0.00 0.00 0.00 3.02
3432 7998 5.587043 AGAAAAAGTGTGACCGTATGTTTCA 59.413 36.000 0.00 0.00 0.00 2.69
3433 7999 5.907391 CAGAAAAAGTGTGACCGTATGTTTC 59.093 40.000 0.00 0.00 0.00 2.78
3434 8000 5.587043 TCAGAAAAAGTGTGACCGTATGTTT 59.413 36.000 0.00 0.00 0.00 2.83
3435 8001 5.120399 TCAGAAAAAGTGTGACCGTATGTT 58.880 37.500 0.00 0.00 0.00 2.71
3436 8002 4.699637 TCAGAAAAAGTGTGACCGTATGT 58.300 39.130 0.00 0.00 0.00 2.29
3437 8003 5.440685 GTTCAGAAAAAGTGTGACCGTATG 58.559 41.667 0.00 0.00 0.00 2.39
3438 8004 4.514066 GGTTCAGAAAAAGTGTGACCGTAT 59.486 41.667 0.00 0.00 0.00 3.06
3439 8005 3.872771 GGTTCAGAAAAAGTGTGACCGTA 59.127 43.478 0.00 0.00 0.00 4.02
3440 8006 2.681344 GGTTCAGAAAAAGTGTGACCGT 59.319 45.455 0.00 0.00 0.00 4.83
3441 8007 2.286184 CGGTTCAGAAAAAGTGTGACCG 60.286 50.000 0.00 0.00 37.62 4.79
3442 8008 2.681344 ACGGTTCAGAAAAAGTGTGACC 59.319 45.455 0.00 0.00 0.00 4.02
3443 8009 3.680789 CACGGTTCAGAAAAAGTGTGAC 58.319 45.455 5.99 0.00 0.00 3.67
3444 8010 2.096819 GCACGGTTCAGAAAAAGTGTGA 59.903 45.455 12.64 0.00 32.74 3.58
3445 8011 2.097466 AGCACGGTTCAGAAAAAGTGTG 59.903 45.455 12.64 6.50 32.74 3.82
3446 8012 2.365582 AGCACGGTTCAGAAAAAGTGT 58.634 42.857 12.64 1.93 32.74 3.55
3447 8013 3.420839 AAGCACGGTTCAGAAAAAGTG 57.579 42.857 8.69 8.69 0.00 3.16
3448 8014 3.181490 GGAAAGCACGGTTCAGAAAAAGT 60.181 43.478 0.00 0.00 0.00 2.66
3449 8015 3.372060 GGAAAGCACGGTTCAGAAAAAG 58.628 45.455 0.00 0.00 0.00 2.27
3450 8016 2.100087 GGGAAAGCACGGTTCAGAAAAA 59.900 45.455 0.00 0.00 0.00 1.94
3451 8017 1.679153 GGGAAAGCACGGTTCAGAAAA 59.321 47.619 0.00 0.00 0.00 2.29
3452 8018 1.314730 GGGAAAGCACGGTTCAGAAA 58.685 50.000 0.00 0.00 0.00 2.52
3453 8019 0.536460 GGGGAAAGCACGGTTCAGAA 60.536 55.000 0.00 0.00 0.00 3.02
3454 8020 1.072505 GGGGAAAGCACGGTTCAGA 59.927 57.895 0.00 0.00 0.00 3.27
3455 8021 0.955919 GAGGGGAAAGCACGGTTCAG 60.956 60.000 0.00 0.00 0.00 3.02
3456 8022 1.072505 GAGGGGAAAGCACGGTTCA 59.927 57.895 0.00 0.00 0.00 3.18
3457 8023 0.250770 AAGAGGGGAAAGCACGGTTC 60.251 55.000 0.00 0.00 0.00 3.62
3458 8024 0.185175 AAAGAGGGGAAAGCACGGTT 59.815 50.000 0.00 0.00 0.00 4.44
3459 8025 0.250770 GAAAGAGGGGAAAGCACGGT 60.251 55.000 0.00 0.00 0.00 4.83
3460 8026 0.960861 GGAAAGAGGGGAAAGCACGG 60.961 60.000 0.00 0.00 0.00 4.94
3461 8027 0.250727 TGGAAAGAGGGGAAAGCACG 60.251 55.000 0.00 0.00 0.00 5.34
3462 8028 2.222227 ATGGAAAGAGGGGAAAGCAC 57.778 50.000 0.00 0.00 0.00 4.40
3463 8029 2.557452 GGAATGGAAAGAGGGGAAAGCA 60.557 50.000 0.00 0.00 0.00 3.91
3464 8030 2.103373 GGAATGGAAAGAGGGGAAAGC 58.897 52.381 0.00 0.00 0.00 3.51
3465 8031 3.746792 AGGAATGGAAAGAGGGGAAAG 57.253 47.619 0.00 0.00 0.00 2.62
3466 8032 4.485653 AAAGGAATGGAAAGAGGGGAAA 57.514 40.909 0.00 0.00 0.00 3.13
3467 8033 4.485653 AAAAGGAATGGAAAGAGGGGAA 57.514 40.909 0.00 0.00 0.00 3.97
3468 8034 4.485653 AAAAAGGAATGGAAAGAGGGGA 57.514 40.909 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.