Multiple sequence alignment - TraesCS3A01G191900

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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 TraesCS3A01G191900 chr3A 100.000 4621 0 0 1 4621 246045497 246040877 0.000000e+00 8534.0
1 TraesCS3A01G191900 chr3A 87.532 385 47 1 3245 3628 215479565 215479181 1.180000e-120 444.0
2 TraesCS3A01G191900 chr3A 98.340 241 4 0 3741 3981 500983517 500983277 1.540000e-114 424.0
3 TraesCS3A01G191900 chr3A 88.679 106 6 5 997 1100 215482212 215482111 1.750000e-24 124.0
4 TraesCS3A01G191900 chr3D 97.429 2645 56 7 1101 3742 185790285 185792920 0.000000e+00 4497.0
5 TraesCS3A01G191900 chr3D 96.941 425 10 2 3980 4402 185792919 185793342 0.000000e+00 710.0
6 TraesCS3A01G191900 chr3D 93.970 398 19 4 705 1100 185789831 185790225 8.560000e-167 597.0
7 TraesCS3A01G191900 chr3D 86.911 382 50 0 3245 3626 175405287 175404906 3.300000e-116 429.0
8 TraesCS3A01G191900 chr3D 96.930 228 7 0 4394 4621 185798360 185798133 2.610000e-102 383.0
9 TraesCS3A01G191900 chr3D 95.122 82 3 1 997 1078 175408287 175408207 1.350000e-25 128.0
10 TraesCS3A01G191900 chr3D 79.330 179 26 9 205 372 293809700 293809878 1.050000e-21 115.0
11 TraesCS3A01G191900 chr3B 96.979 1622 32 8 2122 3742 266565404 266567009 0.000000e+00 2708.0
12 TraesCS3A01G191900 chr3B 95.135 740 12 8 1394 2131 266564208 266564925 0.000000e+00 1146.0
13 TraesCS3A01G191900 chr3B 95.426 634 6 3 3980 4612 266567008 266567619 0.000000e+00 989.0
14 TraesCS3A01G191900 chr3B 92.133 572 19 7 764 1309 266563636 266564207 0.000000e+00 784.0
15 TraesCS3A01G191900 chr3B 87.696 382 47 0 3245 3626 254776609 254776228 3.280000e-121 446.0
16 TraesCS3A01G191900 chr3B 98.354 243 4 0 3740 3982 8013437 8013679 1.190000e-115 427.0
17 TraesCS3A01G191900 chr3B 97.510 241 6 0 3741 3981 742450159 742449919 3.330000e-111 412.0
18 TraesCS3A01G191900 chr3B 93.902 82 4 1 997 1078 254779962 254779882 6.280000e-24 122.0
19 TraesCS3A01G191900 chr3B 85.841 113 15 1 262 373 299794521 299794633 8.120000e-23 119.0
20 TraesCS3A01G191900 chr7A 90.535 729 44 11 1 706 705856614 705857340 0.000000e+00 941.0
21 TraesCS3A01G191900 chr7A 87.939 655 52 16 1 630 518149788 518150440 0.000000e+00 747.0
22 TraesCS3A01G191900 chr7A 97.531 243 6 0 3740 3982 699150274 699150516 2.570000e-112 416.0
23 TraesCS3A01G191900 chr7A 97.119 243 7 0 3740 3982 722869199 722869441 1.200000e-110 411.0
24 TraesCS3A01G191900 chr7B 86.296 737 58 18 1 706 465549088 465549812 0.000000e+00 761.0
25 TraesCS3A01G191900 chr6B 86.285 576 59 15 167 723 383571300 383571874 3.950000e-170 608.0
26 TraesCS3A01G191900 chr6B 90.066 151 4 6 1 140 383571155 383571305 7.900000e-43 185.0
27 TraesCS3A01G191900 chr2A 96.774 248 8 0 3734 3981 84977776 84977529 9.250000e-112 414.0
28 TraesCS3A01G191900 chr2A 94.574 258 14 0 3725 3982 753083147 753083404 2.590000e-107 399.0
29 TraesCS3A01G191900 chr2A 80.745 161 27 4 216 372 48408660 48408500 6.280000e-24 122.0
30 TraesCS3A01G191900 chr2B 97.119 243 7 0 3739 3981 235906877 235906635 1.200000e-110 411.0
31 TraesCS3A01G191900 chr2B 96.371 248 9 0 3738 3985 13745547 13745794 4.300000e-110 409.0
32 TraesCS3A01G191900 chr4B 87.607 234 12 8 1 218 401415595 401415363 5.930000e-64 255.0
33 TraesCS3A01G191900 chr7D 89.947 189 12 3 36 218 386520239 386520052 2.150000e-58 237.0
34 TraesCS3A01G191900 chr7D 82.222 135 22 2 240 372 4181397 4181531 1.050000e-21 115.0
35 TraesCS3A01G191900 chr5D 81.761 159 23 6 217 370 315204866 315205023 1.350000e-25 128.0
36 TraesCS3A01G191900 chr5A 94.118 34 2 0 673 706 219312348 219312315 8.000000e-03 52.8


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 TraesCS3A01G191900 chr3A 246040877 246045497 4620 True 8534.000000 8534 100.000000 1 4621 1 chr3A.!!$R1 4620
1 TraesCS3A01G191900 chr3A 215479181 215482212 3031 True 284.000000 444 88.105500 997 3628 2 chr3A.!!$R3 2631
2 TraesCS3A01G191900 chr3D 185789831 185793342 3511 False 1934.666667 4497 96.113333 705 4402 3 chr3D.!!$F2 3697
3 TraesCS3A01G191900 chr3D 175404906 175408287 3381 True 278.500000 429 91.016500 997 3626 2 chr3D.!!$R2 2629
4 TraesCS3A01G191900 chr3B 266563636 266567619 3983 False 1406.750000 2708 94.918250 764 4612 4 chr3B.!!$F3 3848
5 TraesCS3A01G191900 chr3B 254776228 254779962 3734 True 284.000000 446 90.799000 997 3626 2 chr3B.!!$R2 2629
6 TraesCS3A01G191900 chr7A 705856614 705857340 726 False 941.000000 941 90.535000 1 706 1 chr7A.!!$F3 705
7 TraesCS3A01G191900 chr7A 518149788 518150440 652 False 747.000000 747 87.939000 1 630 1 chr7A.!!$F1 629
8 TraesCS3A01G191900 chr7B 465549088 465549812 724 False 761.000000 761 86.296000 1 706 1 chr7B.!!$F1 705
9 TraesCS3A01G191900 chr6B 383571155 383571874 719 False 396.500000 608 88.175500 1 723 2 chr6B.!!$F1 722

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
699 729 0.039888 GTTACAACGCACGGGCATTT 60.040 50.000 11.77 0.00 41.24 2.32 F
700 730 0.669077 TTACAACGCACGGGCATTTT 59.331 45.000 11.77 0.00 41.24 1.82 F
1420 4178 0.796312 TCTGCCGAGTTTTGATTCGC 59.204 50.000 0.00 0.00 35.58 4.70 F
2893 6271 1.676916 CCCTGCTCAATGTGACGTCAT 60.677 52.381 23.12 3.16 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 4472 1.876156 ACCTCAAAGCAAAGAGAAGCG 59.124 47.619 0.00 0.00 33.74 4.68 R
1948 4744 5.803552 TGATGGTAATGTTCAGTGATGACA 58.196 37.500 0.24 0.24 0.00 3.58 R
2931 6309 0.672401 GCGAAACCACTTGATCCGGA 60.672 55.000 6.61 6.61 0.00 5.14 R
3753 7131 0.040425 GCGGGCGCACTATATTTTGG 60.040 55.000 8.62 0.00 41.49 3.28 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
151 163 2.816087 GTGACAACATTGGCTGACTGAT 59.184 45.455 0.00 0.00 37.03 2.90
153 165 3.503363 TGACAACATTGGCTGACTGATTC 59.497 43.478 0.00 0.00 37.03 2.52
415 436 3.750371 CACAGGTCCTGATGTGGTAAAA 58.250 45.455 26.18 0.00 42.46 1.52
485 515 1.208535 CACCGTTATGTGCTCCCCTAA 59.791 52.381 0.00 0.00 0.00 2.69
527 557 3.064324 GCAAACCGAGGCTGCCAT 61.064 61.111 22.65 5.85 0.00 4.40
543 573 1.663695 CCATATGGTGTTGGACGGTC 58.336 55.000 14.09 0.00 34.81 4.79
568 598 3.695606 ACGACACAGCCGAGGCAT 61.696 61.111 17.18 0.64 44.88 4.40
604 634 7.986085 AATCTTAGGCAATAAATGATAGCGT 57.014 32.000 0.00 0.00 0.00 5.07
605 635 7.986085 ATCTTAGGCAATAAATGATAGCGTT 57.014 32.000 0.00 0.00 0.00 4.84
606 636 7.801716 TCTTAGGCAATAAATGATAGCGTTT 57.198 32.000 3.34 3.34 37.09 3.60
607 637 8.220755 TCTTAGGCAATAAATGATAGCGTTTT 57.779 30.769 3.10 0.00 35.06 2.43
608 638 8.342634 TCTTAGGCAATAAATGATAGCGTTTTC 58.657 33.333 3.10 0.00 35.06 2.29
609 639 6.449635 AGGCAATAAATGATAGCGTTTTCA 57.550 33.333 3.10 0.00 35.06 2.69
610 640 7.042797 AGGCAATAAATGATAGCGTTTTCAT 57.957 32.000 3.10 0.00 35.06 2.57
611 641 6.919662 AGGCAATAAATGATAGCGTTTTCATG 59.080 34.615 3.10 2.73 35.06 3.07
612 642 6.697019 GGCAATAAATGATAGCGTTTTCATGT 59.303 34.615 3.10 3.62 35.06 3.21
613 643 7.096477 GGCAATAAATGATAGCGTTTTCATGTC 60.096 37.037 3.10 0.00 35.06 3.06
614 644 7.356719 GCAATAAATGATAGCGTTTTCATGTCG 60.357 37.037 3.10 0.00 35.06 4.35
618 648 4.933483 GCGTTTTCATGTCGCCAA 57.067 50.000 13.03 0.00 43.41 4.52
619 649 3.171705 GCGTTTTCATGTCGCCAAA 57.828 47.368 13.03 0.00 43.41 3.28
620 650 1.482278 GCGTTTTCATGTCGCCAAAA 58.518 45.000 13.03 1.81 43.41 2.44
621 651 2.058057 GCGTTTTCATGTCGCCAAAAT 58.942 42.857 13.03 0.00 43.41 1.82
622 652 3.238441 GCGTTTTCATGTCGCCAAAATA 58.762 40.909 13.03 0.00 43.41 1.40
623 653 3.058913 GCGTTTTCATGTCGCCAAAATAC 59.941 43.478 13.03 0.00 43.41 1.89
624 654 4.222886 CGTTTTCATGTCGCCAAAATACA 58.777 39.130 0.00 0.00 0.00 2.29
625 655 4.087930 CGTTTTCATGTCGCCAAAATACAC 59.912 41.667 0.00 0.00 0.00 2.90
626 656 4.837896 TTTCATGTCGCCAAAATACACA 57.162 36.364 0.00 0.00 0.00 3.72
627 657 5.384063 TTTCATGTCGCCAAAATACACAT 57.616 34.783 0.00 0.00 0.00 3.21
628 658 4.354071 TCATGTCGCCAAAATACACATG 57.646 40.909 4.32 4.32 43.79 3.21
629 659 4.354071 CATGTCGCCAAAATACACATGA 57.646 40.909 0.00 0.00 44.76 3.07
630 660 4.639755 TCATGTCGCCAAAATACACATGAT 59.360 37.500 0.00 0.00 45.28 2.45
631 661 5.125257 TCATGTCGCCAAAATACACATGATT 59.875 36.000 0.00 0.00 45.28 2.57
632 662 6.317391 TCATGTCGCCAAAATACACATGATTA 59.683 34.615 0.00 0.00 45.28 1.75
633 663 6.691754 TGTCGCCAAAATACACATGATTAT 57.308 33.333 0.00 0.00 0.00 1.28
634 664 7.094508 TGTCGCCAAAATACACATGATTATT 57.905 32.000 0.00 0.00 0.00 1.40
635 665 7.542890 TGTCGCCAAAATACACATGATTATTT 58.457 30.769 0.00 5.18 30.69 1.40
636 666 8.031864 TGTCGCCAAAATACACATGATTATTTT 58.968 29.630 16.61 16.61 38.05 1.82
637 667 8.868916 GTCGCCAAAATACACATGATTATTTTT 58.131 29.630 18.40 8.38 36.28 1.94
660 690 7.462109 TTTTCTTCAATCGTTGGTTTCATTG 57.538 32.000 0.00 0.00 0.00 2.82
661 691 4.545610 TCTTCAATCGTTGGTTTCATTGC 58.454 39.130 0.00 0.00 0.00 3.56
662 692 3.296322 TCAATCGTTGGTTTCATTGCC 57.704 42.857 0.00 0.00 0.00 4.52
663 693 2.625314 TCAATCGTTGGTTTCATTGCCA 59.375 40.909 0.00 0.00 0.00 4.92
664 694 3.257873 TCAATCGTTGGTTTCATTGCCAT 59.742 39.130 0.00 0.00 34.37 4.40
665 695 2.721274 TCGTTGGTTTCATTGCCATG 57.279 45.000 0.00 0.00 34.37 3.66
666 696 2.234143 TCGTTGGTTTCATTGCCATGA 58.766 42.857 0.00 0.00 37.67 3.07
667 697 2.824936 TCGTTGGTTTCATTGCCATGAT 59.175 40.909 0.64 0.00 39.28 2.45
668 698 4.013050 TCGTTGGTTTCATTGCCATGATA 58.987 39.130 0.64 0.00 39.28 2.15
669 699 4.096231 TCGTTGGTTTCATTGCCATGATAG 59.904 41.667 0.64 0.00 39.28 2.08
670 700 4.142403 CGTTGGTTTCATTGCCATGATAGT 60.142 41.667 0.64 0.00 39.28 2.12
671 701 4.987408 TGGTTTCATTGCCATGATAGTG 57.013 40.909 0.64 0.00 39.28 2.74
672 702 4.343231 TGGTTTCATTGCCATGATAGTGT 58.657 39.130 0.64 0.00 39.28 3.55
673 703 4.158209 TGGTTTCATTGCCATGATAGTGTG 59.842 41.667 0.64 0.00 39.28 3.82
674 704 4.158394 GGTTTCATTGCCATGATAGTGTGT 59.842 41.667 0.64 0.00 39.28 3.72
675 705 5.335127 GTTTCATTGCCATGATAGTGTGTC 58.665 41.667 0.64 0.00 39.28 3.67
676 706 4.492494 TCATTGCCATGATAGTGTGTCT 57.508 40.909 0.00 0.00 34.22 3.41
677 707 4.445453 TCATTGCCATGATAGTGTGTCTC 58.555 43.478 0.00 0.00 34.22 3.36
678 708 4.162888 TCATTGCCATGATAGTGTGTCTCT 59.837 41.667 0.00 0.00 34.22 3.10
679 709 3.808466 TGCCATGATAGTGTGTCTCTC 57.192 47.619 0.00 0.00 0.00 3.20
680 710 2.099756 TGCCATGATAGTGTGTCTCTCG 59.900 50.000 0.00 0.00 0.00 4.04
681 711 2.099921 GCCATGATAGTGTGTCTCTCGT 59.900 50.000 0.00 0.00 0.00 4.18
682 712 3.429547 GCCATGATAGTGTGTCTCTCGTT 60.430 47.826 0.00 0.00 0.00 3.85
683 713 4.202020 GCCATGATAGTGTGTCTCTCGTTA 60.202 45.833 0.00 0.00 0.00 3.18
684 714 5.274718 CCATGATAGTGTGTCTCTCGTTAC 58.725 45.833 0.00 0.00 0.00 2.50
685 715 5.163652 CCATGATAGTGTGTCTCTCGTTACA 60.164 44.000 0.00 0.00 0.00 2.41
686 716 5.952526 TGATAGTGTGTCTCTCGTTACAA 57.047 39.130 0.00 0.00 0.00 2.41
687 717 5.696822 TGATAGTGTGTCTCTCGTTACAAC 58.303 41.667 0.00 0.00 0.00 3.32
696 726 3.339464 CGTTACAACGCACGGGCA 61.339 61.111 11.77 0.00 46.06 5.36
697 727 2.673114 CGTTACAACGCACGGGCAT 61.673 57.895 11.77 0.00 46.06 4.40
698 728 1.577421 GTTACAACGCACGGGCATT 59.423 52.632 11.77 0.00 41.24 3.56
699 729 0.039888 GTTACAACGCACGGGCATTT 60.040 50.000 11.77 0.00 41.24 2.32
700 730 0.669077 TTACAACGCACGGGCATTTT 59.331 45.000 11.77 0.00 41.24 1.82
701 731 0.669077 TACAACGCACGGGCATTTTT 59.331 45.000 11.77 0.00 41.24 1.94
741 771 3.869272 GCAAGTGCTGATCCGGCG 61.869 66.667 0.00 0.00 38.82 6.46
748 778 3.197790 CTGATCCGGCGCCAACAG 61.198 66.667 28.98 22.99 0.00 3.16
812 842 8.314021 TGTTACGAGAGAATATTATGCCATCAT 58.686 33.333 0.00 0.00 36.73 2.45
967 1001 2.285743 GCCACCTTCCTCCCTCCT 60.286 66.667 0.00 0.00 0.00 3.69
1184 1339 4.294416 ACTATCTGTTGGATCGTTCTCG 57.706 45.455 0.00 0.00 35.98 4.04
1198 1353 2.000447 GTTCTCGGTTTTGAGGGATCG 59.000 52.381 0.00 0.00 36.61 3.69
1353 4111 3.621461 CGTAGCTTGATTGGGGGTAAACT 60.621 47.826 0.00 0.00 0.00 2.66
1383 4141 3.461061 TCGCTTGATCCATCATCAGTTC 58.539 45.455 0.00 0.00 42.76 3.01
1420 4178 0.796312 TCTGCCGAGTTTTGATTCGC 59.204 50.000 0.00 0.00 35.58 4.70
1648 4444 4.313682 CGCAAAATTGTACGTCGTAGTTTG 59.686 41.667 5.08 13.75 0.00 2.93
1676 4472 6.291377 TGGATGATAGTGTTATCCAAAGAGC 58.709 40.000 10.48 0.00 46.61 4.09
1948 4744 4.058817 GCCTCTATTACGTGCATAGCTTT 58.941 43.478 0.00 0.00 0.00 3.51
2067 4863 3.791353 GTGTTTTCCTTTTCGTTCTGCAG 59.209 43.478 7.63 7.63 0.00 4.41
2099 4895 8.442632 TCTGATAGCAAATTCAATAAGTGGAG 57.557 34.615 0.00 0.00 0.00 3.86
2845 6223 6.986904 AGAGCTTTATAAAAGAAAGGACGG 57.013 37.500 3.63 0.00 34.97 4.79
2865 6243 2.126307 CTACTGCGCGACTGCTGT 60.126 61.111 12.10 4.52 46.76 4.40
2893 6271 1.676916 CCCTGCTCAATGTGACGTCAT 60.677 52.381 23.12 3.16 0.00 3.06
3028 6406 4.384940 GTGGAAGAAATAGATGGAGCCTC 58.615 47.826 0.00 0.00 0.00 4.70
3112 6490 5.163343 TGTCTAGTGAGTGTAAGCAAGGTTT 60.163 40.000 0.00 0.00 0.00 3.27
3590 6968 6.933216 TGGTGATGGCCAGATCAACTATGAT 61.933 44.000 21.98 0.00 40.25 2.45
3657 7035 3.198635 TGAGGGAAGCTTCAGTAATCAGG 59.801 47.826 27.02 0.00 0.00 3.86
3691 7069 2.307496 ATCCAGGTGCCATTTTGTGA 57.693 45.000 0.00 0.00 0.00 3.58
3744 7122 3.032017 ACACTGTGCTGTGTCATACTC 57.968 47.619 7.90 0.00 46.90 2.59
3745 7123 2.289072 ACACTGTGCTGTGTCATACTCC 60.289 50.000 7.90 0.00 46.90 3.85
3746 7124 1.276421 ACTGTGCTGTGTCATACTCCC 59.724 52.381 0.00 0.00 0.00 4.30
3747 7125 1.552337 CTGTGCTGTGTCATACTCCCT 59.448 52.381 0.00 0.00 0.00 4.20
3748 7126 1.550524 TGTGCTGTGTCATACTCCCTC 59.449 52.381 0.00 0.00 0.00 4.30
3749 7127 1.134670 GTGCTGTGTCATACTCCCTCC 60.135 57.143 0.00 0.00 0.00 4.30
3750 7128 0.103208 GCTGTGTCATACTCCCTCCG 59.897 60.000 0.00 0.00 0.00 4.63
3751 7129 1.475403 CTGTGTCATACTCCCTCCGT 58.525 55.000 0.00 0.00 0.00 4.69
3752 7130 1.825474 CTGTGTCATACTCCCTCCGTT 59.175 52.381 0.00 0.00 0.00 4.44
3753 7131 1.822990 TGTGTCATACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
3754 7132 1.136500 GTGTCATACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
3755 7133 1.272816 TGTCATACTCCCTCCGTTCCA 60.273 52.381 0.00 0.00 0.00 3.53
3756 7134 1.829222 GTCATACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
3757 7135 2.235402 GTCATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
3758 7136 2.907696 TCATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
3759 7137 3.521937 TCATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
3760 7138 4.717778 TCATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
3761 7139 5.368523 TCATACTCCCTCCGTTCCAAAATAT 59.631 40.000 0.00 0.00 0.00 1.28
3762 7140 6.555738 TCATACTCCCTCCGTTCCAAAATATA 59.444 38.462 0.00 0.00 0.00 0.86
3763 7141 5.291905 ACTCCCTCCGTTCCAAAATATAG 57.708 43.478 0.00 0.00 0.00 1.31
3764 7142 4.720273 ACTCCCTCCGTTCCAAAATATAGT 59.280 41.667 0.00 0.00 0.00 2.12
3765 7143 5.031066 TCCCTCCGTTCCAAAATATAGTG 57.969 43.478 0.00 0.00 0.00 2.74
3766 7144 3.564225 CCCTCCGTTCCAAAATATAGTGC 59.436 47.826 0.00 0.00 0.00 4.40
3767 7145 3.247648 CCTCCGTTCCAAAATATAGTGCG 59.752 47.826 0.00 0.00 0.00 5.34
3768 7146 2.610374 TCCGTTCCAAAATATAGTGCGC 59.390 45.455 0.00 0.00 0.00 6.09
3769 7147 2.286772 CCGTTCCAAAATATAGTGCGCC 60.287 50.000 4.18 0.00 0.00 6.53
3770 7148 2.286772 CGTTCCAAAATATAGTGCGCCC 60.287 50.000 4.18 0.00 0.00 6.13
3771 7149 1.588674 TCCAAAATATAGTGCGCCCG 58.411 50.000 4.18 0.00 0.00 6.13
3772 7150 0.040425 CCAAAATATAGTGCGCCCGC 60.040 55.000 4.18 5.60 42.35 6.13
3773 7151 0.384230 CAAAATATAGTGCGCCCGCG 60.384 55.000 4.18 4.36 45.51 6.46
3796 7174 2.928416 CGGAGGTCCAACTTTGACC 58.072 57.895 4.16 4.16 39.18 4.02
3797 7175 0.107831 CGGAGGTCCAACTTTGACCA 59.892 55.000 13.24 0.00 41.22 4.02
3798 7176 1.271379 CGGAGGTCCAACTTTGACCAT 60.271 52.381 13.24 0.72 41.22 3.55
3799 7177 2.027561 CGGAGGTCCAACTTTGACCATA 60.028 50.000 13.24 0.00 41.22 2.74
3800 7178 3.558321 CGGAGGTCCAACTTTGACCATAA 60.558 47.826 13.24 0.00 41.22 1.90
3801 7179 4.403734 GGAGGTCCAACTTTGACCATAAA 58.596 43.478 13.24 0.00 41.22 1.40
3802 7180 5.016831 GGAGGTCCAACTTTGACCATAAAT 58.983 41.667 13.24 0.00 41.22 1.40
3803 7181 5.480422 GGAGGTCCAACTTTGACCATAAATT 59.520 40.000 13.24 0.00 41.22 1.82
3804 7182 6.014584 GGAGGTCCAACTTTGACCATAAATTT 60.015 38.462 13.24 0.00 41.22 1.82
3805 7183 7.177744 GGAGGTCCAACTTTGACCATAAATTTA 59.822 37.037 13.24 0.00 41.22 1.40
3806 7184 8.485578 AGGTCCAACTTTGACCATAAATTTAA 57.514 30.769 13.24 0.00 41.22 1.52
3807 7185 8.364894 AGGTCCAACTTTGACCATAAATTTAAC 58.635 33.333 13.24 0.00 41.22 2.01
3808 7186 7.601130 GGTCCAACTTTGACCATAAATTTAACC 59.399 37.037 1.21 0.00 38.76 2.85
3809 7187 8.145122 GTCCAACTTTGACCATAAATTTAACCA 58.855 33.333 1.21 0.00 0.00 3.67
3810 7188 8.705594 TCCAACTTTGACCATAAATTTAACCAA 58.294 29.630 1.21 2.19 0.00 3.67
3811 7189 9.500785 CCAACTTTGACCATAAATTTAACCAAT 57.499 29.630 1.21 0.00 0.00 3.16
3814 7192 9.927668 ACTTTGACCATAAATTTAACCAATGAG 57.072 29.630 1.21 3.35 0.00 2.90
3816 7194 9.921637 TTTGACCATAAATTTAACCAATGAGAC 57.078 29.630 1.21 0.00 0.00 3.36
3817 7195 8.062065 TGACCATAAATTTAACCAATGAGACC 57.938 34.615 1.21 0.00 0.00 3.85
3818 7196 7.671819 TGACCATAAATTTAACCAATGAGACCA 59.328 33.333 1.21 0.00 0.00 4.02
3819 7197 8.429237 ACCATAAATTTAACCAATGAGACCAA 57.571 30.769 1.21 0.00 0.00 3.67
3820 7198 8.311109 ACCATAAATTTAACCAATGAGACCAAC 58.689 33.333 1.21 0.00 0.00 3.77
3821 7199 8.531146 CCATAAATTTAACCAATGAGACCAACT 58.469 33.333 1.21 0.00 0.00 3.16
3822 7200 9.357652 CATAAATTTAACCAATGAGACCAACTG 57.642 33.333 1.21 0.00 0.00 3.16
3823 7201 4.846779 TTTAACCAATGAGACCAACTGC 57.153 40.909 0.00 0.00 0.00 4.40
3824 7202 1.238439 AACCAATGAGACCAACTGCG 58.762 50.000 0.00 0.00 0.00 5.18
3825 7203 0.606401 ACCAATGAGACCAACTGCGG 60.606 55.000 0.00 0.00 0.00 5.69
3826 7204 1.503542 CAATGAGACCAACTGCGGC 59.496 57.895 0.00 0.00 0.00 6.53
3827 7205 2.034879 AATGAGACCAACTGCGGCG 61.035 57.895 0.51 0.51 0.00 6.46
3828 7206 3.958147 ATGAGACCAACTGCGGCGG 62.958 63.158 9.78 7.39 0.00 6.13
3833 7211 4.697756 CCAACTGCGGCGGGAGAA 62.698 66.667 19.55 0.00 35.29 2.87
3834 7212 2.668212 CAACTGCGGCGGGAGAAA 60.668 61.111 19.55 0.00 35.29 2.52
3835 7213 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
3836 7214 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
3894 7272 9.520204 AATTCACTGATATAATTTTTGCTTCCG 57.480 29.630 0.00 0.00 0.00 4.30
3895 7273 6.494842 TCACTGATATAATTTTTGCTTCCGC 58.505 36.000 0.00 0.00 0.00 5.54
3896 7274 5.687285 CACTGATATAATTTTTGCTTCCGCC 59.313 40.000 0.00 0.00 34.43 6.13
3897 7275 4.854399 TGATATAATTTTTGCTTCCGCCG 58.146 39.130 0.00 0.00 34.43 6.46
3898 7276 1.921243 ATAATTTTTGCTTCCGCCGC 58.079 45.000 0.00 0.00 34.43 6.53
3899 7277 0.598562 TAATTTTTGCTTCCGCCGCA 59.401 45.000 0.00 0.00 35.22 5.69
3900 7278 0.249657 AATTTTTGCTTCCGCCGCAA 60.250 45.000 0.00 0.00 44.83 4.85
3901 7279 0.037419 ATTTTTGCTTCCGCCGCAAT 60.037 45.000 5.33 0.00 45.67 3.56
3902 7280 0.665972 TTTTTGCTTCCGCCGCAATC 60.666 50.000 5.33 0.00 45.67 2.67
3903 7281 2.794627 TTTTGCTTCCGCCGCAATCG 62.795 55.000 5.33 0.00 45.67 3.34
3914 7292 3.436001 CGCAATCGGTCTTGGTAGT 57.564 52.632 0.00 0.00 0.00 2.73
3915 7293 1.722011 CGCAATCGGTCTTGGTAGTT 58.278 50.000 0.00 0.00 0.00 2.24
3916 7294 2.883574 CGCAATCGGTCTTGGTAGTTA 58.116 47.619 0.00 0.00 0.00 2.24
3917 7295 3.255725 CGCAATCGGTCTTGGTAGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
3918 7296 3.680937 CGCAATCGGTCTTGGTAGTTAAA 59.319 43.478 0.00 0.00 0.00 1.52
3919 7297 4.331717 CGCAATCGGTCTTGGTAGTTAAAT 59.668 41.667 0.00 0.00 0.00 1.40
3920 7298 5.163794 CGCAATCGGTCTTGGTAGTTAAATT 60.164 40.000 0.00 0.00 0.00 1.82
3921 7299 6.617879 GCAATCGGTCTTGGTAGTTAAATTT 58.382 36.000 0.00 0.00 0.00 1.82
3922 7300 7.413219 CGCAATCGGTCTTGGTAGTTAAATTTA 60.413 37.037 0.00 0.00 0.00 1.40
3923 7301 7.695201 GCAATCGGTCTTGGTAGTTAAATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
3924 7302 6.949578 TCGGTCTTGGTAGTTAAATTTACG 57.050 37.500 0.00 0.00 0.00 3.18
3925 7303 5.868801 TCGGTCTTGGTAGTTAAATTTACGG 59.131 40.000 0.00 0.00 0.00 4.02
3926 7304 5.639082 CGGTCTTGGTAGTTAAATTTACGGT 59.361 40.000 0.00 0.00 0.00 4.83
3927 7305 6.183360 CGGTCTTGGTAGTTAAATTTACGGTC 60.183 42.308 0.00 0.00 0.00 4.79
3928 7306 6.650390 GGTCTTGGTAGTTAAATTTACGGTCA 59.350 38.462 0.00 0.00 0.00 4.02
3929 7307 7.173047 GGTCTTGGTAGTTAAATTTACGGTCAA 59.827 37.037 0.00 0.00 0.00 3.18
3930 7308 8.558700 GTCTTGGTAGTTAAATTTACGGTCAAA 58.441 33.333 0.00 0.00 0.00 2.69
3931 7309 8.776470 TCTTGGTAGTTAAATTTACGGTCAAAG 58.224 33.333 0.00 0.00 0.00 2.77
3932 7310 8.449251 TTGGTAGTTAAATTTACGGTCAAAGT 57.551 30.769 0.00 0.00 0.00 2.66
3933 7311 8.449251 TGGTAGTTAAATTTACGGTCAAAGTT 57.551 30.769 0.00 0.00 31.36 2.66
3934 7312 8.344098 TGGTAGTTAAATTTACGGTCAAAGTTG 58.656 33.333 0.00 0.00 29.44 3.16
3935 7313 8.558700 GGTAGTTAAATTTACGGTCAAAGTTGA 58.441 33.333 0.00 0.00 34.20 3.18
3936 7314 9.934190 GTAGTTAAATTTACGGTCAAAGTTGAA 57.066 29.630 0.00 0.00 39.21 2.69
3938 7316 7.646526 AGTTAAATTTACGGTCAAAGTTGAAGC 59.353 33.333 0.00 0.00 39.21 3.86
3939 7317 5.508200 AATTTACGGTCAAAGTTGAAGCA 57.492 34.783 0.00 0.00 39.21 3.91
3940 7318 3.955771 TTACGGTCAAAGTTGAAGCAC 57.044 42.857 0.00 0.00 39.21 4.40
3941 7319 0.655733 ACGGTCAAAGTTGAAGCACG 59.344 50.000 0.00 2.00 39.21 5.34
3942 7320 0.655733 CGGTCAAAGTTGAAGCACGT 59.344 50.000 0.00 0.00 39.21 4.49
3943 7321 1.594518 CGGTCAAAGTTGAAGCACGTG 60.595 52.381 12.28 12.28 39.21 4.49
3944 7322 1.268539 GGTCAAAGTTGAAGCACGTGG 60.269 52.381 18.88 0.00 39.21 4.94
3945 7323 1.668751 GTCAAAGTTGAAGCACGTGGA 59.331 47.619 18.88 0.00 39.21 4.02
3946 7324 2.290641 GTCAAAGTTGAAGCACGTGGAT 59.709 45.455 18.88 0.00 39.21 3.41
3947 7325 3.496884 GTCAAAGTTGAAGCACGTGGATA 59.503 43.478 18.88 0.00 39.21 2.59
3948 7326 3.745975 TCAAAGTTGAAGCACGTGGATAG 59.254 43.478 18.88 0.00 33.55 2.08
3949 7327 3.678056 AAGTTGAAGCACGTGGATAGA 57.322 42.857 18.88 0.00 0.00 1.98
3950 7328 3.238108 AGTTGAAGCACGTGGATAGAG 57.762 47.619 18.88 0.00 0.00 2.43
3951 7329 2.093973 AGTTGAAGCACGTGGATAGAGG 60.094 50.000 18.88 0.00 0.00 3.69
3952 7330 1.847328 TGAAGCACGTGGATAGAGGA 58.153 50.000 18.88 0.00 0.00 3.71
3953 7331 2.176045 TGAAGCACGTGGATAGAGGAA 58.824 47.619 18.88 0.00 0.00 3.36
3954 7332 2.166459 TGAAGCACGTGGATAGAGGAAG 59.834 50.000 18.88 0.00 0.00 3.46
3955 7333 0.461961 AGCACGTGGATAGAGGAAGC 59.538 55.000 18.88 0.00 0.00 3.86
3956 7334 0.175760 GCACGTGGATAGAGGAAGCA 59.824 55.000 18.88 0.00 0.00 3.91
3957 7335 1.927895 CACGTGGATAGAGGAAGCAC 58.072 55.000 7.95 0.00 0.00 4.40
3958 7336 1.478510 CACGTGGATAGAGGAAGCACT 59.521 52.381 7.95 0.00 0.00 4.40
3959 7337 2.688446 CACGTGGATAGAGGAAGCACTA 59.312 50.000 7.95 0.00 0.00 2.74
3960 7338 2.688958 ACGTGGATAGAGGAAGCACTAC 59.311 50.000 0.00 0.00 0.00 2.73
3961 7339 2.688446 CGTGGATAGAGGAAGCACTACA 59.312 50.000 0.00 0.00 0.00 2.74
3962 7340 3.319405 CGTGGATAGAGGAAGCACTACAT 59.681 47.826 0.00 0.00 0.00 2.29
3963 7341 4.202161 CGTGGATAGAGGAAGCACTACATT 60.202 45.833 0.00 0.00 0.00 2.71
3964 7342 5.009710 CGTGGATAGAGGAAGCACTACATTA 59.990 44.000 0.00 0.00 0.00 1.90
3965 7343 6.294787 CGTGGATAGAGGAAGCACTACATTAT 60.295 42.308 0.00 0.00 0.00 1.28
3966 7344 6.870965 GTGGATAGAGGAAGCACTACATTATG 59.129 42.308 0.00 0.00 0.00 1.90
3967 7345 6.014242 TGGATAGAGGAAGCACTACATTATGG 60.014 42.308 0.00 0.00 0.00 2.74
3968 7346 6.211584 GGATAGAGGAAGCACTACATTATGGA 59.788 42.308 0.00 0.00 0.00 3.41
3969 7347 5.957771 AGAGGAAGCACTACATTATGGAA 57.042 39.130 0.00 0.00 0.00 3.53
3970 7348 6.506538 AGAGGAAGCACTACATTATGGAAT 57.493 37.500 0.00 0.00 0.00 3.01
3971 7349 6.294473 AGAGGAAGCACTACATTATGGAATG 58.706 40.000 0.00 0.00 46.77 2.67
3972 7350 5.380043 AGGAAGCACTACATTATGGAATGG 58.620 41.667 0.00 0.00 45.83 3.16
3973 7351 5.132648 AGGAAGCACTACATTATGGAATGGA 59.867 40.000 0.00 0.00 45.83 3.41
3979 7357 5.832539 CTACATTATGGAATGGAGGGAGT 57.167 43.478 2.44 0.00 46.58 3.85
3980 7358 6.935240 CTACATTATGGAATGGAGGGAGTA 57.065 41.667 2.44 0.00 46.58 2.59
4054 7432 5.532779 GGTCTTTCTGATTTTGTCTGTTCCT 59.467 40.000 0.00 0.00 0.00 3.36
4140 7518 8.442632 AACTATATGTCAGTGTTCCATGATTG 57.557 34.615 0.00 0.00 0.00 2.67
4321 7701 8.579682 AGATTGTTTTCTTGCTTTGTCAATAC 57.420 30.769 0.00 0.00 0.00 1.89
4378 7758 0.108520 GTGCCTGCCCAAACATCATG 60.109 55.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 230 7.568199 AAAAAGAATTCAGGAACGAAGAGAA 57.432 32.000 8.44 0.00 0.00 2.87
363 384 1.404843 GCTCCACGATCTACTCCCTT 58.595 55.000 0.00 0.00 0.00 3.95
415 436 3.326297 GCATCTAGTCTAGGGCATCCTTT 59.674 47.826 15.41 0.00 41.56 3.11
527 557 1.592743 CCGACCGTCCAACACCATA 59.407 57.895 0.00 0.00 0.00 2.74
543 573 3.414700 GCTGTGTCGTGAAGCCCG 61.415 66.667 0.00 0.00 0.00 6.13
602 632 4.087930 GTGTATTTTGGCGACATGAAAACG 59.912 41.667 0.00 0.80 42.32 3.60
603 633 4.979197 TGTGTATTTTGGCGACATGAAAAC 59.021 37.500 0.00 0.00 42.32 2.43
604 634 5.188327 TGTGTATTTTGGCGACATGAAAA 57.812 34.783 0.00 0.00 42.32 2.29
605 635 4.837896 TGTGTATTTTGGCGACATGAAA 57.162 36.364 0.00 0.00 42.32 2.69
606 636 4.457257 TCATGTGTATTTTGGCGACATGAA 59.543 37.500 9.98 0.00 46.10 2.57
607 637 4.006319 TCATGTGTATTTTGGCGACATGA 58.994 39.130 0.00 0.00 46.62 3.07
608 638 4.354071 TCATGTGTATTTTGGCGACATG 57.646 40.909 0.00 0.00 43.43 3.21
609 639 5.581126 AATCATGTGTATTTTGGCGACAT 57.419 34.783 0.00 0.00 42.32 3.06
610 640 6.691754 ATAATCATGTGTATTTTGGCGACA 57.308 33.333 0.00 0.00 39.83 4.35
611 641 7.985634 AAATAATCATGTGTATTTTGGCGAC 57.014 32.000 9.28 0.00 0.00 5.19
612 642 8.994429 AAAAATAATCATGTGTATTTTGGCGA 57.006 26.923 20.12 0.00 38.99 5.54
635 665 7.465245 GCAATGAAACCAACGATTGAAGAAAAA 60.465 33.333 0.00 0.00 0.00 1.94
636 666 6.019156 GCAATGAAACCAACGATTGAAGAAAA 60.019 34.615 0.00 0.00 0.00 2.29
637 667 5.461737 GCAATGAAACCAACGATTGAAGAAA 59.538 36.000 0.00 0.00 0.00 2.52
638 668 4.981674 GCAATGAAACCAACGATTGAAGAA 59.018 37.500 0.00 0.00 0.00 2.52
639 669 4.545610 GCAATGAAACCAACGATTGAAGA 58.454 39.130 0.00 0.00 0.00 2.87
640 670 3.674753 GGCAATGAAACCAACGATTGAAG 59.325 43.478 0.00 0.00 0.00 3.02
641 671 3.068732 TGGCAATGAAACCAACGATTGAA 59.931 39.130 0.00 0.00 31.46 2.69
642 672 2.625314 TGGCAATGAAACCAACGATTGA 59.375 40.909 0.00 0.00 31.46 2.57
643 673 3.023946 TGGCAATGAAACCAACGATTG 57.976 42.857 0.00 0.00 31.46 2.67
644 674 3.257873 TCATGGCAATGAAACCAACGATT 59.742 39.130 0.00 0.00 39.92 3.34
645 675 2.824936 TCATGGCAATGAAACCAACGAT 59.175 40.909 0.00 0.00 39.92 3.73
646 676 2.234143 TCATGGCAATGAAACCAACGA 58.766 42.857 0.00 0.00 39.92 3.85
647 677 2.721274 TCATGGCAATGAAACCAACG 57.279 45.000 0.00 0.00 39.92 4.10
648 678 5.104374 CACTATCATGGCAATGAAACCAAC 58.896 41.667 8.12 0.00 45.81 3.77
649 679 4.771577 ACACTATCATGGCAATGAAACCAA 59.228 37.500 8.12 0.00 45.81 3.67
650 680 4.158209 CACACTATCATGGCAATGAAACCA 59.842 41.667 8.12 0.00 45.81 3.67
651 681 4.158394 ACACACTATCATGGCAATGAAACC 59.842 41.667 8.12 0.00 45.81 3.27
652 682 5.124457 AGACACACTATCATGGCAATGAAAC 59.876 40.000 8.12 0.00 45.81 2.78
653 683 5.255687 AGACACACTATCATGGCAATGAAA 58.744 37.500 8.12 0.00 45.81 2.69
654 684 4.847198 AGACACACTATCATGGCAATGAA 58.153 39.130 8.12 0.00 45.81 2.57
655 685 4.162888 AGAGACACACTATCATGGCAATGA 59.837 41.667 6.16 6.16 46.71 2.57
656 686 4.449131 AGAGACACACTATCATGGCAATG 58.551 43.478 0.00 0.00 34.88 2.82
657 687 4.701765 GAGAGACACACTATCATGGCAAT 58.298 43.478 0.00 0.00 36.90 3.56
658 688 3.429410 CGAGAGACACACTATCATGGCAA 60.429 47.826 0.00 0.00 36.74 4.52
659 689 2.099756 CGAGAGACACACTATCATGGCA 59.900 50.000 0.00 0.00 36.74 4.92
660 690 2.099921 ACGAGAGACACACTATCATGGC 59.900 50.000 0.00 0.00 36.74 4.40
661 691 4.377839 AACGAGAGACACACTATCATGG 57.622 45.455 0.00 0.00 36.74 3.66
662 692 5.880341 TGTAACGAGAGACACACTATCATG 58.120 41.667 0.00 0.00 36.74 3.07
663 693 6.323266 GTTGTAACGAGAGACACACTATCAT 58.677 40.000 0.00 0.00 36.74 2.45
664 694 5.696822 GTTGTAACGAGAGACACACTATCA 58.303 41.667 0.00 0.00 36.74 2.15
680 710 0.039888 AAATGCCCGTGCGTTGTAAC 60.040 50.000 0.00 0.00 45.88 2.50
681 711 0.669077 AAAATGCCCGTGCGTTGTAA 59.331 45.000 0.00 0.00 45.88 2.41
682 712 0.669077 AAAAATGCCCGTGCGTTGTA 59.331 45.000 0.00 0.00 45.88 2.41
683 713 1.439644 AAAAATGCCCGTGCGTTGT 59.560 47.368 0.00 0.00 45.88 3.32
684 714 4.334837 AAAAATGCCCGTGCGTTG 57.665 50.000 0.00 0.00 45.88 4.10
731 761 3.197790 CTGTTGGCGCCGGATCAG 61.198 66.667 23.90 21.22 0.00 2.90
967 1001 4.137615 TCGGAGATGGCGAGGGGA 62.138 66.667 0.00 0.00 0.00 4.81
1184 1339 0.463833 ATCCGCGATCCCTCAAAACC 60.464 55.000 8.23 0.00 0.00 3.27
1205 1360 1.811266 CGTGCAGACCAGGAATCGG 60.811 63.158 0.00 0.00 0.00 4.18
1281 4039 3.376078 CAAGCATTGCCGGCAGGT 61.376 61.111 30.75 21.86 40.39 4.00
1383 4141 0.527817 GACCTCTATCCGTTGGCACG 60.528 60.000 0.00 0.00 46.71 5.34
1420 4178 0.106719 AAATCACGGCCTATGGGTGG 60.107 55.000 0.00 0.00 34.45 4.61
1676 4472 1.876156 ACCTCAAAGCAAAGAGAAGCG 59.124 47.619 0.00 0.00 33.74 4.68
1948 4744 5.803552 TGATGGTAATGTTCAGTGATGACA 58.196 37.500 0.24 0.24 0.00 3.58
2107 4903 8.170730 ACTTCAAATCCTACCTAGGTTGAATTT 58.829 33.333 22.11 17.01 42.53 1.82
2548 5841 7.496529 TTGTCTTCTGTTGACCTAAAATCAG 57.503 36.000 0.00 0.00 33.83 2.90
2893 6271 5.920903 TGATTATGATGAGTGAGCATGTGA 58.079 37.500 0.00 0.00 31.51 3.58
2931 6309 0.672401 GCGAAACCACTTGATCCGGA 60.672 55.000 6.61 6.61 0.00 5.14
3028 6406 7.307396 CGTGATGGCTATCAAATTAGTAAGTGG 60.307 40.741 14.99 0.00 44.49 4.00
3425 6803 0.036010 CACGGAATGCCTCCTTGAGT 60.036 55.000 3.08 0.00 44.58 3.41
3590 6968 6.014755 TGGCCATCATGACTTTAACAAATTCA 60.015 34.615 0.00 0.00 35.04 2.57
3691 7069 5.717078 TCGGTTTAATACGATAGCCATCT 57.283 39.130 0.00 0.00 42.67 2.90
3742 7120 5.057149 CACTATATTTTGGAACGGAGGGAG 58.943 45.833 0.00 0.00 0.00 4.30
3743 7121 4.685030 GCACTATATTTTGGAACGGAGGGA 60.685 45.833 0.00 0.00 0.00 4.20
3744 7122 3.564225 GCACTATATTTTGGAACGGAGGG 59.436 47.826 0.00 0.00 0.00 4.30
3745 7123 3.247648 CGCACTATATTTTGGAACGGAGG 59.752 47.826 0.00 0.00 0.00 4.30
3746 7124 3.303132 GCGCACTATATTTTGGAACGGAG 60.303 47.826 0.30 0.00 0.00 4.63
3747 7125 2.610374 GCGCACTATATTTTGGAACGGA 59.390 45.455 0.30 0.00 0.00 4.69
3748 7126 2.286772 GGCGCACTATATTTTGGAACGG 60.287 50.000 10.83 0.00 0.00 4.44
3749 7127 2.286772 GGGCGCACTATATTTTGGAACG 60.287 50.000 10.83 0.00 0.00 3.95
3750 7128 2.286772 CGGGCGCACTATATTTTGGAAC 60.287 50.000 8.62 0.00 0.00 3.62
3751 7129 1.944024 CGGGCGCACTATATTTTGGAA 59.056 47.619 8.62 0.00 0.00 3.53
3752 7130 1.588674 CGGGCGCACTATATTTTGGA 58.411 50.000 8.62 0.00 0.00 3.53
3753 7131 0.040425 GCGGGCGCACTATATTTTGG 60.040 55.000 8.62 0.00 41.49 3.28
3754 7132 0.384230 CGCGGGCGCACTATATTTTG 60.384 55.000 8.62 0.00 42.06 2.44
3755 7133 1.938861 CGCGGGCGCACTATATTTT 59.061 52.632 8.62 0.00 42.06 1.82
3756 7134 3.637714 CGCGGGCGCACTATATTT 58.362 55.556 8.62 0.00 42.06 1.40
3771 7149 4.388499 TTGGACCTCCGGAAGCGC 62.388 66.667 5.23 0.00 39.43 5.92
3772 7150 2.434359 GTTGGACCTCCGGAAGCG 60.434 66.667 5.23 0.00 39.43 4.68
3773 7151 0.250770 AAAGTTGGACCTCCGGAAGC 60.251 55.000 5.23 0.00 39.43 3.86
3774 7152 1.071699 TCAAAGTTGGACCTCCGGAAG 59.928 52.381 5.23 0.57 39.43 3.46
3775 7153 1.133363 TCAAAGTTGGACCTCCGGAA 58.867 50.000 5.23 0.00 39.43 4.30
3776 7154 0.395312 GTCAAAGTTGGACCTCCGGA 59.605 55.000 2.93 2.93 39.43 5.14
3777 7155 2.928416 GTCAAAGTTGGACCTCCGG 58.072 57.895 0.00 0.00 39.43 5.14
3783 7161 8.145122 TGGTTAAATTTATGGTCAAAGTTGGAC 58.855 33.333 1.31 1.31 29.44 4.02
3784 7162 8.251383 TGGTTAAATTTATGGTCAAAGTTGGA 57.749 30.769 0.00 0.00 29.44 3.53
3785 7163 8.894768 TTGGTTAAATTTATGGTCAAAGTTGG 57.105 30.769 0.00 0.00 29.44 3.77
3788 7166 9.927668 CTCATTGGTTAAATTTATGGTCAAAGT 57.072 29.630 0.00 0.00 0.00 2.66
3790 7168 9.921637 GTCTCATTGGTTAAATTTATGGTCAAA 57.078 29.630 0.00 0.00 0.00 2.69
3791 7169 8.527810 GGTCTCATTGGTTAAATTTATGGTCAA 58.472 33.333 0.00 2.87 0.00 3.18
3792 7170 7.671819 TGGTCTCATTGGTTAAATTTATGGTCA 59.328 33.333 0.00 0.00 0.00 4.02
3793 7171 8.062065 TGGTCTCATTGGTTAAATTTATGGTC 57.938 34.615 0.00 0.00 0.00 4.02
3794 7172 8.311109 GTTGGTCTCATTGGTTAAATTTATGGT 58.689 33.333 0.00 0.00 0.00 3.55
3795 7173 8.531146 AGTTGGTCTCATTGGTTAAATTTATGG 58.469 33.333 0.00 0.00 0.00 2.74
3796 7174 9.357652 CAGTTGGTCTCATTGGTTAAATTTATG 57.642 33.333 0.00 0.00 0.00 1.90
3797 7175 8.034804 GCAGTTGGTCTCATTGGTTAAATTTAT 58.965 33.333 0.00 0.00 0.00 1.40
3798 7176 7.375053 GCAGTTGGTCTCATTGGTTAAATTTA 58.625 34.615 0.00 0.00 0.00 1.40
3799 7177 6.223120 GCAGTTGGTCTCATTGGTTAAATTT 58.777 36.000 0.00 0.00 0.00 1.82
3800 7178 5.564651 CGCAGTTGGTCTCATTGGTTAAATT 60.565 40.000 0.00 0.00 0.00 1.82
3801 7179 4.082787 CGCAGTTGGTCTCATTGGTTAAAT 60.083 41.667 0.00 0.00 0.00 1.40
3802 7180 3.252215 CGCAGTTGGTCTCATTGGTTAAA 59.748 43.478 0.00 0.00 0.00 1.52
3803 7181 2.811431 CGCAGTTGGTCTCATTGGTTAA 59.189 45.455 0.00 0.00 0.00 2.01
3804 7182 2.422597 CGCAGTTGGTCTCATTGGTTA 58.577 47.619 0.00 0.00 0.00 2.85
3805 7183 1.238439 CGCAGTTGGTCTCATTGGTT 58.762 50.000 0.00 0.00 0.00 3.67
3806 7184 0.606401 CCGCAGTTGGTCTCATTGGT 60.606 55.000 0.00 0.00 0.00 3.67
3807 7185 1.926511 GCCGCAGTTGGTCTCATTGG 61.927 60.000 0.00 0.00 0.00 3.16
3808 7186 1.503542 GCCGCAGTTGGTCTCATTG 59.496 57.895 0.00 0.00 0.00 2.82
3809 7187 2.034879 CGCCGCAGTTGGTCTCATT 61.035 57.895 0.00 0.00 0.00 2.57
3810 7188 2.434884 CGCCGCAGTTGGTCTCAT 60.435 61.111 0.00 0.00 0.00 2.90
3811 7189 4.680237 CCGCCGCAGTTGGTCTCA 62.680 66.667 0.00 0.00 0.00 3.27
3816 7194 4.697756 TTCTCCCGCCGCAGTTGG 62.698 66.667 0.00 0.00 0.00 3.77
3817 7195 1.791103 TTTTTCTCCCGCCGCAGTTG 61.791 55.000 0.00 0.00 0.00 3.16
3818 7196 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
3819 7197 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
3868 7246 9.520204 CGGAAGCAAAAATTATATCAGTGAATT 57.480 29.630 0.00 0.00 0.00 2.17
3896 7274 1.722011 AACTACCAAGACCGATTGCG 58.278 50.000 0.00 0.00 37.24 4.85
3897 7275 5.813080 ATTTAACTACCAAGACCGATTGC 57.187 39.130 0.00 0.00 0.00 3.56
3898 7276 7.901377 CGTAAATTTAACTACCAAGACCGATTG 59.099 37.037 0.00 0.00 0.00 2.67
3899 7277 7.064966 CCGTAAATTTAACTACCAAGACCGATT 59.935 37.037 0.00 0.00 0.00 3.34
3900 7278 6.536224 CCGTAAATTTAACTACCAAGACCGAT 59.464 38.462 0.00 0.00 0.00 4.18
3901 7279 5.868801 CCGTAAATTTAACTACCAAGACCGA 59.131 40.000 0.00 0.00 0.00 4.69
3902 7280 5.639082 ACCGTAAATTTAACTACCAAGACCG 59.361 40.000 0.00 0.00 0.00 4.79
3903 7281 6.650390 TGACCGTAAATTTAACTACCAAGACC 59.350 38.462 0.00 0.00 0.00 3.85
3904 7282 7.656707 TGACCGTAAATTTAACTACCAAGAC 57.343 36.000 0.00 0.00 0.00 3.01
3905 7283 8.674263 TTTGACCGTAAATTTAACTACCAAGA 57.326 30.769 0.00 0.00 0.00 3.02
3906 7284 8.562052 ACTTTGACCGTAAATTTAACTACCAAG 58.438 33.333 0.00 2.45 0.00 3.61
3907 7285 8.449251 ACTTTGACCGTAAATTTAACTACCAA 57.551 30.769 0.00 0.00 0.00 3.67
3908 7286 8.344098 CAACTTTGACCGTAAATTTAACTACCA 58.656 33.333 0.00 0.00 0.00 3.25
3909 7287 8.558700 TCAACTTTGACCGTAAATTTAACTACC 58.441 33.333 0.00 0.00 31.01 3.18
3910 7288 9.934190 TTCAACTTTGACCGTAAATTTAACTAC 57.066 29.630 0.00 0.00 36.83 2.73
3912 7290 7.646526 GCTTCAACTTTGACCGTAAATTTAACT 59.353 33.333 0.00 0.00 36.83 2.24
3913 7291 7.432838 TGCTTCAACTTTGACCGTAAATTTAAC 59.567 33.333 0.00 0.00 36.83 2.01
3914 7292 7.432838 GTGCTTCAACTTTGACCGTAAATTTAA 59.567 33.333 0.00 0.00 36.83 1.52
3915 7293 6.913673 GTGCTTCAACTTTGACCGTAAATTTA 59.086 34.615 0.00 0.00 36.83 1.40
3916 7294 5.746721 GTGCTTCAACTTTGACCGTAAATTT 59.253 36.000 0.00 0.00 36.83 1.82
3917 7295 5.278604 GTGCTTCAACTTTGACCGTAAATT 58.721 37.500 0.00 0.00 36.83 1.82
3918 7296 4.553938 CGTGCTTCAACTTTGACCGTAAAT 60.554 41.667 0.00 0.00 36.83 1.40
3919 7297 3.242478 CGTGCTTCAACTTTGACCGTAAA 60.242 43.478 0.00 0.00 36.83 2.01
3920 7298 2.285756 CGTGCTTCAACTTTGACCGTAA 59.714 45.455 0.00 0.00 36.83 3.18
3921 7299 1.862201 CGTGCTTCAACTTTGACCGTA 59.138 47.619 0.00 0.00 36.83 4.02
3922 7300 0.655733 CGTGCTTCAACTTTGACCGT 59.344 50.000 0.00 0.00 36.83 4.83
3923 7301 0.655733 ACGTGCTTCAACTTTGACCG 59.344 50.000 0.00 0.00 36.83 4.79
3924 7302 1.268539 CCACGTGCTTCAACTTTGACC 60.269 52.381 10.91 0.00 36.83 4.02
3925 7303 1.668751 TCCACGTGCTTCAACTTTGAC 59.331 47.619 10.91 0.00 36.83 3.18
3926 7304 2.031258 TCCACGTGCTTCAACTTTGA 57.969 45.000 10.91 0.00 34.92 2.69
3927 7305 3.745975 TCTATCCACGTGCTTCAACTTTG 59.254 43.478 10.91 0.00 0.00 2.77
3928 7306 3.997021 CTCTATCCACGTGCTTCAACTTT 59.003 43.478 10.91 0.00 0.00 2.66
3929 7307 3.589988 CTCTATCCACGTGCTTCAACTT 58.410 45.455 10.91 0.00 0.00 2.66
3930 7308 2.093973 CCTCTATCCACGTGCTTCAACT 60.094 50.000 10.91 0.00 0.00 3.16
3931 7309 2.094182 TCCTCTATCCACGTGCTTCAAC 60.094 50.000 10.91 0.00 0.00 3.18
3932 7310 2.176045 TCCTCTATCCACGTGCTTCAA 58.824 47.619 10.91 0.00 0.00 2.69
3933 7311 1.847328 TCCTCTATCCACGTGCTTCA 58.153 50.000 10.91 0.00 0.00 3.02
3934 7312 2.815478 CTTCCTCTATCCACGTGCTTC 58.185 52.381 10.91 0.00 0.00 3.86
3935 7313 1.134670 GCTTCCTCTATCCACGTGCTT 60.135 52.381 10.91 1.47 0.00 3.91
3936 7314 0.461961 GCTTCCTCTATCCACGTGCT 59.538 55.000 10.91 1.67 0.00 4.40
3937 7315 0.175760 TGCTTCCTCTATCCACGTGC 59.824 55.000 10.91 0.00 0.00 5.34
3938 7316 1.478510 AGTGCTTCCTCTATCCACGTG 59.521 52.381 9.08 9.08 0.00 4.49
3939 7317 1.853963 AGTGCTTCCTCTATCCACGT 58.146 50.000 0.00 0.00 0.00 4.49
3940 7318 2.688446 TGTAGTGCTTCCTCTATCCACG 59.312 50.000 0.00 0.00 0.00 4.94
3941 7319 4.946478 ATGTAGTGCTTCCTCTATCCAC 57.054 45.455 0.00 0.00 0.00 4.02
3942 7320 6.014242 CCATAATGTAGTGCTTCCTCTATCCA 60.014 42.308 0.00 0.00 0.00 3.41
3943 7321 6.211584 TCCATAATGTAGTGCTTCCTCTATCC 59.788 42.308 0.00 0.00 0.00 2.59
3944 7322 7.233389 TCCATAATGTAGTGCTTCCTCTATC 57.767 40.000 0.00 0.00 0.00 2.08
3945 7323 7.618019 TTCCATAATGTAGTGCTTCCTCTAT 57.382 36.000 0.00 0.00 0.00 1.98
3946 7324 7.445121 CATTCCATAATGTAGTGCTTCCTCTA 58.555 38.462 0.00 0.00 38.15 2.43
3947 7325 5.957771 TTCCATAATGTAGTGCTTCCTCT 57.042 39.130 0.00 0.00 0.00 3.69
3948 7326 5.471456 CCATTCCATAATGTAGTGCTTCCTC 59.529 44.000 0.00 0.00 40.84 3.71
3949 7327 5.132648 TCCATTCCATAATGTAGTGCTTCCT 59.867 40.000 0.00 0.00 40.84 3.36
3950 7328 5.376625 TCCATTCCATAATGTAGTGCTTCC 58.623 41.667 0.00 0.00 40.84 3.46
3951 7329 5.471456 CCTCCATTCCATAATGTAGTGCTTC 59.529 44.000 0.00 0.00 40.84 3.86
3952 7330 5.380043 CCTCCATTCCATAATGTAGTGCTT 58.620 41.667 0.00 0.00 40.84 3.91
3953 7331 4.202503 CCCTCCATTCCATAATGTAGTGCT 60.203 45.833 0.00 0.00 40.84 4.40
3954 7332 4.074970 CCCTCCATTCCATAATGTAGTGC 58.925 47.826 0.00 0.00 40.84 4.40
3955 7333 5.072329 ACTCCCTCCATTCCATAATGTAGTG 59.928 44.000 0.00 0.00 40.84 2.74
3956 7334 5.227593 ACTCCCTCCATTCCATAATGTAGT 58.772 41.667 0.00 0.00 40.84 2.73
3957 7335 5.832539 ACTCCCTCCATTCCATAATGTAG 57.167 43.478 0.00 0.00 40.84 2.74
3958 7336 6.792473 ACATACTCCCTCCATTCCATAATGTA 59.208 38.462 0.00 0.00 40.84 2.29
3959 7337 5.612688 ACATACTCCCTCCATTCCATAATGT 59.387 40.000 0.00 0.00 40.84 2.71
3960 7338 6.131972 ACATACTCCCTCCATTCCATAATG 57.868 41.667 0.00 0.00 41.90 1.90
3961 7339 6.103205 ACAACATACTCCCTCCATTCCATAAT 59.897 38.462 0.00 0.00 0.00 1.28
3962 7340 5.431731 ACAACATACTCCCTCCATTCCATAA 59.568 40.000 0.00 0.00 0.00 1.90
3963 7341 4.975147 ACAACATACTCCCTCCATTCCATA 59.025 41.667 0.00 0.00 0.00 2.74
3964 7342 3.788142 ACAACATACTCCCTCCATTCCAT 59.212 43.478 0.00 0.00 0.00 3.41
3965 7343 3.189606 ACAACATACTCCCTCCATTCCA 58.810 45.455 0.00 0.00 0.00 3.53
3966 7344 3.933861 ACAACATACTCCCTCCATTCC 57.066 47.619 0.00 0.00 0.00 3.01
3967 7345 4.743955 GCCTACAACATACTCCCTCCATTC 60.744 50.000 0.00 0.00 0.00 2.67
3968 7346 3.136626 GCCTACAACATACTCCCTCCATT 59.863 47.826 0.00 0.00 0.00 3.16
3969 7347 2.706190 GCCTACAACATACTCCCTCCAT 59.294 50.000 0.00 0.00 0.00 3.41
3970 7348 2.116238 GCCTACAACATACTCCCTCCA 58.884 52.381 0.00 0.00 0.00 3.86
3971 7349 2.116238 TGCCTACAACATACTCCCTCC 58.884 52.381 0.00 0.00 0.00 4.30
3972 7350 3.906720 TTGCCTACAACATACTCCCTC 57.093 47.619 0.00 0.00 0.00 4.30
3973 7351 3.780294 TCATTGCCTACAACATACTCCCT 59.220 43.478 0.00 0.00 38.99 4.20
3974 7352 4.150897 TCATTGCCTACAACATACTCCC 57.849 45.455 0.00 0.00 38.99 4.30
3975 7353 5.590259 ACAATCATTGCCTACAACATACTCC 59.410 40.000 0.00 0.00 38.99 3.85
3976 7354 6.683974 ACAATCATTGCCTACAACATACTC 57.316 37.500 0.00 0.00 38.99 2.59
3977 7355 7.315142 CAAACAATCATTGCCTACAACATACT 58.685 34.615 0.00 0.00 38.99 2.12
3978 7356 6.034898 GCAAACAATCATTGCCTACAACATAC 59.965 38.462 0.00 0.00 45.73 2.39
3979 7357 6.098679 GCAAACAATCATTGCCTACAACATA 58.901 36.000 0.00 0.00 45.73 2.29
3980 7358 4.931002 GCAAACAATCATTGCCTACAACAT 59.069 37.500 0.00 0.00 45.73 2.71
4140 7518 4.354587 GGTAAATTGTGAGCTAGCAATGC 58.645 43.478 18.83 0.00 35.72 3.56
4378 7758 3.855858 TGTTTTGGCCTCTCAAAAACAC 58.144 40.909 21.03 3.64 44.81 3.32


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

AutoCloner maintained by Alex Coulton.