Multiple sequence alignment - TraesCS3B01G030000

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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 TraesCS3B01G030000 chr3B 100.000 5389 0 0 1 5389 13813087 13818475 0.000000e+00 9952.0
1 TraesCS3B01G030000 chr3B 91.892 111 6 3 608 716 261980623 261980732 9.350000e-33 152.0
2 TraesCS3B01G030000 chr3B 87.200 125 12 4 600 721 161708739 161708616 7.280000e-29 139.0
3 TraesCS3B01G030000 chr3D 92.724 4467 297 14 735 5176 9632050 9636513 0.000000e+00 6423.0
4 TraesCS3B01G030000 chr3D 91.433 3525 284 14 874 4392 4960507 4956995 0.000000e+00 4820.0
5 TraesCS3B01G030000 chr3D 92.857 378 27 0 47 424 9631239 9631616 2.840000e-152 549.0
6 TraesCS3B01G030000 chr3D 89.835 364 28 5 874 1236 4999636 4999281 4.920000e-125 459.0
7 TraesCS3B01G030000 chr3D 94.313 211 11 1 5174 5383 9636538 9636748 6.730000e-84 322.0
8 TraesCS3B01G030000 chr3D 87.755 147 17 1 4448 4593 4956624 4956478 2.580000e-38 171.0
9 TraesCS3B01G030000 chr3D 100.000 49 0 0 478 526 9631865 9631913 2.070000e-14 91.6
10 TraesCS3B01G030000 chr3A 90.175 4580 370 21 871 5383 10885718 10881152 0.000000e+00 5891.0
11 TraesCS3B01G030000 chr3A 90.516 4091 353 19 739 4804 10690005 10685925 0.000000e+00 5373.0
12 TraesCS3B01G030000 chr3A 93.915 378 22 1 47 424 10690500 10690124 2.180000e-158 569.0
13 TraesCS3B01G030000 chr3A 90.476 336 25 6 150 483 10698050 10697720 2.300000e-118 436.0
14 TraesCS3B01G030000 chr3A 93.651 189 12 0 5195 5383 10684309 10684121 3.180000e-72 283.0
15 TraesCS3B01G030000 chr3A 95.620 137 4 1 5042 5176 10685830 10685694 9.090000e-53 219.0
16 TraesCS3B01G030000 chr3A 93.269 104 5 2 611 713 423951584 423951482 9.350000e-33 152.0
17 TraesCS3B01G030000 chrUn 90.851 3880 320 23 868 4729 35293990 35297852 0.000000e+00 5166.0
18 TraesCS3B01G030000 chrUn 90.851 3880 320 23 868 4729 229343830 229347692 0.000000e+00 5166.0
19 TraesCS3B01G030000 chrUn 91.510 3357 271 11 874 4219 284403937 284400584 0.000000e+00 4608.0
20 TraesCS3B01G030000 chrUn 91.510 3357 271 11 874 4219 284410471 284407118 0.000000e+00 4608.0
21 TraesCS3B01G030000 chrUn 91.510 3357 271 11 874 4219 302994096 302990743 0.000000e+00 4608.0
22 TraesCS3B01G030000 chrUn 90.072 3475 305 23 759 4219 257888477 257885029 0.000000e+00 4470.0
23 TraesCS3B01G030000 chrUn 86.831 486 31 6 4723 5176 208765844 208766328 3.720000e-141 512.0
24 TraesCS3B01G030000 chrUn 90.173 346 25 5 874 1218 478123132 478122795 4.950000e-120 442.0
25 TraesCS3B01G030000 chrUn 91.379 174 15 0 5179 5352 208766359 208766532 6.980000e-59 239.0
26 TraesCS3B01G030000 chrUn 80.169 237 14 15 5179 5383 285724193 285724428 4.350000e-31 147.0
27 TraesCS3B01G030000 chrUn 88.060 67 8 0 735 801 284404107 284404041 4.470000e-11 80.5
28 TraesCS3B01G030000 chrUn 88.060 67 8 0 735 801 284410641 284410575 4.470000e-11 80.5
29 TraesCS3B01G030000 chrUn 88.060 67 8 0 735 801 302994266 302994200 4.470000e-11 80.5
30 TraesCS3B01G030000 chrUn 100.000 28 0 0 590 617 319857033 319857006 1.000000e-02 52.8
31 TraesCS3B01G030000 chrUn 96.774 31 1 0 587 617 331093106 331093136 1.000000e-02 52.8
32 TraesCS3B01G030000 chr6A 95.918 98 3 1 614 711 51946467 51946563 2.010000e-34 158.0
33 TraesCS3B01G030000 chr2B 97.802 91 2 0 611 701 134499542 134499632 2.010000e-34 158.0
34 TraesCS3B01G030000 chr2B 100.000 49 0 0 1 49 720472005 720471957 2.070000e-14 91.6
35 TraesCS3B01G030000 chr2B 100.000 46 0 0 2 47 140537685 140537730 9.620000e-13 86.1
36 TraesCS3B01G030000 chr4A 92.453 106 7 1 615 720 637742382 637742278 3.360000e-32 150.0
37 TraesCS3B01G030000 chr4A 92.453 106 6 2 604 708 668943964 668943860 3.360000e-32 150.0
38 TraesCS3B01G030000 chr7B 91.667 108 7 2 607 714 171202732 171202627 1.210000e-31 148.0
39 TraesCS3B01G030000 chr7B 93.478 46 3 0 2 47 734907273 734907318 9.690000e-08 69.4
40 TraesCS3B01G030000 chr5D 90.909 110 6 3 613 721 208140841 208140947 1.560000e-30 145.0
41 TraesCS3B01G030000 chr2A 73.684 266 63 6 1102 1365 762741741 762741481 4.440000e-16 97.1
42 TraesCS3B01G030000 chr2D 97.778 45 1 0 5 49 26538732 26538688 1.610000e-10 78.7
43 TraesCS3B01G030000 chr2D 93.478 46 3 0 2 47 7202214 7202259 9.690000e-08 69.4
44 TraesCS3B01G030000 chr7A 93.478 46 3 0 2 47 558105380 558105335 9.690000e-08 69.4


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 TraesCS3B01G030000 chr3B 13813087 13818475 5388 False 9952.00 9952 100.0000 1 5389 1 chr3B.!!$F1 5388
1 TraesCS3B01G030000 chr3D 4956478 4960507 4029 True 2495.50 4820 89.5940 874 4593 2 chr3D.!!$R2 3719
2 TraesCS3B01G030000 chr3D 9631239 9636748 5509 False 1846.40 6423 94.9735 47 5383 4 chr3D.!!$F1 5336
3 TraesCS3B01G030000 chr3A 10881152 10885718 4566 True 5891.00 5891 90.1750 871 5383 1 chr3A.!!$R2 4512
4 TraesCS3B01G030000 chr3A 10684121 10690500 6379 True 1611.00 5373 93.4255 47 5383 4 chr3A.!!$R4 5336
5 TraesCS3B01G030000 chrUn 35293990 35297852 3862 False 5166.00 5166 90.8510 868 4729 1 chrUn.!!$F1 3861
6 TraesCS3B01G030000 chrUn 229343830 229347692 3862 False 5166.00 5166 90.8510 868 4729 1 chrUn.!!$F2 3861
7 TraesCS3B01G030000 chrUn 257885029 257888477 3448 True 4470.00 4470 90.0720 759 4219 1 chrUn.!!$R1 3460
8 TraesCS3B01G030000 chrUn 284400584 284410641 10057 True 2344.25 4608 89.7850 735 4219 4 chrUn.!!$R4 3484
9 TraesCS3B01G030000 chrUn 302990743 302994266 3523 True 2344.25 4608 89.7850 735 4219 2 chrUn.!!$R5 3484
10 TraesCS3B01G030000 chrUn 208765844 208766532 688 False 375.50 512 89.1050 4723 5352 2 chrUn.!!$F5 629

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
25 26 0.323633 TCATGGGGCATGTGTCCAAG 60.324 55.0 5.93 4.56 42.93 3.61 F
1129 1443 0.388520 CGACACTGATCTTGCCGTCA 60.389 55.0 0.00 0.00 0.00 4.35 F
1644 1965 0.034337 TCGGTAACAACAGCCTGTCC 59.966 55.0 0.00 0.00 0.00 4.02 F
1953 2274 0.393132 TCGAAGGTGTTGTGCCAACA 60.393 50.0 14.38 14.38 0.00 3.33 F
2169 2490 0.616395 TAGTCGGACCCATTCCTGCA 60.616 55.0 4.14 0.00 43.25 4.41 F
2828 3150 0.802494 CTGGCACATTACCCGTTGAC 59.198 55.0 0.00 0.00 38.20 3.18 F
3189 3512 0.947180 TGGCGCTTCACGTTTAGGAC 60.947 55.0 7.64 0.00 46.11 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1839 1.345741 CCAAGACTCTGCAGGTTCTGA 59.654 52.381 15.13 0.0 32.44 3.27 R
2562 2883 0.325933 CATCCAGGTCAAGCCACTGA 59.674 55.000 0.00 0.0 40.61 3.41 R
3155 3477 0.318120 CGCCACAAAGCCCAGAATTT 59.682 50.000 0.00 0.0 0.00 1.82 R
3911 4234 0.322816 CTGGTGCCATGTAGCCAAGT 60.323 55.000 0.00 0.0 0.00 3.16 R
3912 4235 1.033746 CCTGGTGCCATGTAGCCAAG 61.034 60.000 0.00 0.0 0.00 3.61 R
4162 4486 2.357637 CGGAAAAGTTCTGCAGGAAACA 59.642 45.455 15.13 0.0 35.51 2.83 R
4891 9471 4.216687 TCTTTTGTTTGTGACACCGTCTTT 59.783 37.500 2.45 0.0 38.18 2.52 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
19 20 1.712056 ATGGAATCATGGGGCATGTG 58.288 50.000 0.00 0.00 41.98 3.21
20 21 0.335705 TGGAATCATGGGGCATGTGT 59.664 50.000 0.00 0.00 41.98 3.72
21 22 1.035139 GGAATCATGGGGCATGTGTC 58.965 55.000 0.00 0.00 41.98 3.67
22 23 1.035139 GAATCATGGGGCATGTGTCC 58.965 55.000 0.00 0.00 41.98 4.02
23 24 0.335705 AATCATGGGGCATGTGTCCA 59.664 50.000 5.93 6.33 42.93 4.02
24 25 0.335705 ATCATGGGGCATGTGTCCAA 59.664 50.000 5.93 0.00 42.93 3.53
25 26 0.323633 TCATGGGGCATGTGTCCAAG 60.324 55.000 5.93 4.56 42.93 3.61
26 27 1.683365 ATGGGGCATGTGTCCAAGC 60.683 57.895 5.93 0.00 42.93 4.01
27 28 2.036256 GGGGCATGTGTCCAAGCT 59.964 61.111 5.93 0.00 42.93 3.74
28 29 2.345760 GGGGCATGTGTCCAAGCTG 61.346 63.158 5.93 0.00 42.93 4.24
29 30 2.345760 GGGCATGTGTCCAAGCTGG 61.346 63.158 0.00 0.00 40.23 4.85
30 31 1.303561 GGCATGTGTCCAAGCTGGA 60.304 57.895 0.00 0.00 45.98 3.86
38 39 1.304381 TCCAAGCTGGACCATTGGC 60.304 57.895 18.58 8.77 42.67 4.52
39 40 2.353610 CCAAGCTGGACCATTGGCC 61.354 63.158 12.86 0.00 40.96 5.36
40 41 1.607178 CAAGCTGGACCATTGGCCA 60.607 57.895 0.00 0.00 0.00 5.36
41 42 0.974010 CAAGCTGGACCATTGGCCAT 60.974 55.000 6.09 0.00 30.92 4.40
42 43 0.974010 AAGCTGGACCATTGGCCATG 60.974 55.000 6.09 7.26 30.92 3.66
43 44 3.085119 GCTGGACCATTGGCCATGC 62.085 63.158 6.09 16.35 30.92 4.06
171 172 0.824595 TTGCATGTGCCAGTTGCTCT 60.825 50.000 2.07 0.00 42.00 4.09
203 204 1.400888 GCGCATCAATTGTCGTGGAAA 60.401 47.619 0.30 0.00 0.00 3.13
225 226 7.093771 GGAAAAATGAATTCCACCTATGACTGT 60.094 37.037 2.27 0.00 44.70 3.55
284 285 4.518217 GCATTAGCAGCAGTAAACATACG 58.482 43.478 0.00 0.00 41.58 3.06
321 322 3.056179 TGCACATCGTCATCAGTAGGAAA 60.056 43.478 0.00 0.00 0.00 3.13
337 338 5.841783 AGTAGGAAAGAGGAAGATATGGTCC 59.158 44.000 0.00 0.00 0.00 4.46
346 347 3.499918 GGAAGATATGGTCCATGCTTTCG 59.500 47.826 15.10 0.00 0.00 3.46
387 388 9.852091 GAAATGCTGAAAGAAATGTCTTAGAAT 57.148 29.630 0.00 0.00 43.59 2.40
405 406 7.915397 TCTTAGAATGTTGAAACTGAAAGCAAC 59.085 33.333 0.00 0.00 40.62 4.17
448 667 0.804989 GTGATGGGGAGAAAGCAACG 59.195 55.000 0.00 0.00 0.00 4.10
451 670 0.539438 ATGGGGAGAAAGCAACGCAA 60.539 50.000 0.00 0.00 0.00 4.85
454 673 1.669795 GGGGAGAAAGCAACGCAAATG 60.670 52.381 0.00 0.00 0.00 2.32
457 676 2.030805 GGAGAAAGCAACGCAAATGAGT 60.031 45.455 0.00 0.00 0.00 3.41
458 677 2.975851 GAGAAAGCAACGCAAATGAGTG 59.024 45.455 0.00 0.00 0.00 3.51
459 678 2.053627 GAAAGCAACGCAAATGAGTGG 58.946 47.619 0.00 0.00 0.00 4.00
460 679 1.032014 AAGCAACGCAAATGAGTGGT 58.968 45.000 0.00 0.00 0.00 4.16
461 680 1.032014 AGCAACGCAAATGAGTGGTT 58.968 45.000 0.00 0.00 0.00 3.67
462 681 1.130955 GCAACGCAAATGAGTGGTTG 58.869 50.000 0.00 0.00 40.57 3.77
463 682 1.769733 CAACGCAAATGAGTGGTTGG 58.230 50.000 0.00 0.00 35.53 3.77
464 683 1.066908 CAACGCAAATGAGTGGTTGGT 59.933 47.619 0.00 0.00 35.53 3.67
465 684 1.398692 ACGCAAATGAGTGGTTGGTT 58.601 45.000 0.00 0.00 0.00 3.67
466 685 1.066908 ACGCAAATGAGTGGTTGGTTG 59.933 47.619 0.00 0.00 0.00 3.77
467 686 1.501169 GCAAATGAGTGGTTGGTTGC 58.499 50.000 0.00 0.00 35.13 4.17
468 687 1.202510 GCAAATGAGTGGTTGGTTGCA 60.203 47.619 0.00 0.00 40.74 4.08
469 688 2.741228 GCAAATGAGTGGTTGGTTGCAA 60.741 45.455 0.00 0.00 40.74 4.08
470 689 3.529533 CAAATGAGTGGTTGGTTGCAAA 58.470 40.909 0.00 0.00 0.00 3.68
471 690 4.128643 CAAATGAGTGGTTGGTTGCAAAT 58.871 39.130 0.00 0.00 0.00 2.32
472 691 2.886862 TGAGTGGTTGGTTGCAAATG 57.113 45.000 0.00 0.00 0.00 2.32
473 692 1.411977 TGAGTGGTTGGTTGCAAATGG 59.588 47.619 0.00 0.00 0.00 3.16
474 693 1.686052 GAGTGGTTGGTTGCAAATGGA 59.314 47.619 0.00 0.00 0.00 3.41
475 694 1.412343 AGTGGTTGGTTGCAAATGGAC 59.588 47.619 0.00 0.00 0.00 4.02
476 695 1.137872 GTGGTTGGTTGCAAATGGACA 59.862 47.619 0.00 0.00 0.00 4.02
477 696 1.833630 TGGTTGGTTGCAAATGGACAA 59.166 42.857 0.00 0.00 0.00 3.18
478 697 2.237143 TGGTTGGTTGCAAATGGACAAA 59.763 40.909 0.00 0.00 0.00 2.83
479 698 2.871633 GGTTGGTTGCAAATGGACAAAG 59.128 45.455 0.00 0.00 0.00 2.77
526 745 5.049886 CGGCATGTAGATGTAGAACGTACTA 60.050 44.000 1.37 0.00 31.50 1.82
539 758 9.801873 TGTAGAACGTACTACAAACTTAGTTTT 57.198 29.630 7.71 3.18 46.11 2.43
542 761 9.249457 AGAACGTACTACAAACTTAGTTTTACC 57.751 33.333 7.71 0.00 33.10 2.85
543 762 8.940768 AACGTACTACAAACTTAGTTTTACCA 57.059 30.769 7.71 0.00 33.10 3.25
544 763 8.940768 ACGTACTACAAACTTAGTTTTACCAA 57.059 30.769 7.71 0.00 33.10 3.67
545 764 9.377312 ACGTACTACAAACTTAGTTTTACCAAA 57.623 29.630 7.71 0.00 33.10 3.28
546 765 9.636965 CGTACTACAAACTTAGTTTTACCAAAC 57.363 33.333 7.71 2.54 42.48 2.93
612 831 6.127196 ACAAACTTTTGAATTGGGTCTTGCTA 60.127 34.615 8.69 0.00 40.55 3.49
613 832 6.478512 AACTTTTGAATTGGGTCTTGCTAA 57.521 33.333 0.00 0.00 0.00 3.09
614 833 6.670695 ACTTTTGAATTGGGTCTTGCTAAT 57.329 33.333 0.00 0.00 0.00 1.73
615 834 7.775053 ACTTTTGAATTGGGTCTTGCTAATA 57.225 32.000 0.00 0.00 0.00 0.98
616 835 7.602753 ACTTTTGAATTGGGTCTTGCTAATAC 58.397 34.615 0.00 0.00 0.00 1.89
617 836 7.451566 ACTTTTGAATTGGGTCTTGCTAATACT 59.548 33.333 0.00 0.00 0.00 2.12
618 837 7.391148 TTTGAATTGGGTCTTGCTAATACTC 57.609 36.000 0.00 0.00 0.00 2.59
619 838 6.313519 TGAATTGGGTCTTGCTAATACTCT 57.686 37.500 0.00 0.00 0.00 3.24
620 839 6.349300 TGAATTGGGTCTTGCTAATACTCTC 58.651 40.000 0.00 0.00 0.00 3.20
621 840 6.156949 TGAATTGGGTCTTGCTAATACTCTCT 59.843 38.462 0.00 0.00 0.00 3.10
622 841 5.599999 TTGGGTCTTGCTAATACTCTCTC 57.400 43.478 0.00 0.00 0.00 3.20
623 842 3.961408 TGGGTCTTGCTAATACTCTCTCC 59.039 47.826 0.00 0.00 0.00 3.71
624 843 3.004944 GGGTCTTGCTAATACTCTCTCCG 59.995 52.174 0.00 0.00 0.00 4.63
625 844 3.633065 GGTCTTGCTAATACTCTCTCCGT 59.367 47.826 0.00 0.00 0.00 4.69
626 845 4.098196 GGTCTTGCTAATACTCTCTCCGTT 59.902 45.833 0.00 0.00 0.00 4.44
627 846 5.275494 GTCTTGCTAATACTCTCTCCGTTC 58.725 45.833 0.00 0.00 0.00 3.95
628 847 4.338682 TCTTGCTAATACTCTCTCCGTTCC 59.661 45.833 0.00 0.00 0.00 3.62
629 848 3.628008 TGCTAATACTCTCTCCGTTCCA 58.372 45.455 0.00 0.00 0.00 3.53
630 849 4.021229 TGCTAATACTCTCTCCGTTCCAA 58.979 43.478 0.00 0.00 0.00 3.53
631 850 4.464951 TGCTAATACTCTCTCCGTTCCAAA 59.535 41.667 0.00 0.00 0.00 3.28
632 851 5.046878 TGCTAATACTCTCTCCGTTCCAAAA 60.047 40.000 0.00 0.00 0.00 2.44
633 852 6.049790 GCTAATACTCTCTCCGTTCCAAAAT 58.950 40.000 0.00 0.00 0.00 1.82
634 853 7.147794 TGCTAATACTCTCTCCGTTCCAAAATA 60.148 37.037 0.00 0.00 0.00 1.40
635 854 7.709613 GCTAATACTCTCTCCGTTCCAAAATAA 59.290 37.037 0.00 0.00 0.00 1.40
636 855 9.595823 CTAATACTCTCTCCGTTCCAAAATAAA 57.404 33.333 0.00 0.00 0.00 1.40
638 857 6.743575 ACTCTCTCCGTTCCAAAATAAATG 57.256 37.500 0.00 0.00 0.00 2.32
639 858 6.472887 ACTCTCTCCGTTCCAAAATAAATGA 58.527 36.000 0.00 0.00 0.00 2.57
640 859 6.371825 ACTCTCTCCGTTCCAAAATAAATGAC 59.628 38.462 0.00 0.00 0.00 3.06
641 860 5.646360 TCTCTCCGTTCCAAAATAAATGACC 59.354 40.000 0.00 0.00 0.00 4.02
642 861 4.703093 TCTCCGTTCCAAAATAAATGACCC 59.297 41.667 0.00 0.00 0.00 4.46
643 862 4.408276 TCCGTTCCAAAATAAATGACCCA 58.592 39.130 0.00 0.00 0.00 4.51
644 863 4.833380 TCCGTTCCAAAATAAATGACCCAA 59.167 37.500 0.00 0.00 0.00 4.12
645 864 4.926832 CCGTTCCAAAATAAATGACCCAAC 59.073 41.667 0.00 0.00 0.00 3.77
646 865 5.279256 CCGTTCCAAAATAAATGACCCAACT 60.279 40.000 0.00 0.00 0.00 3.16
647 866 6.220201 CGTTCCAAAATAAATGACCCAACTT 58.780 36.000 0.00 0.00 0.00 2.66
648 867 6.704050 CGTTCCAAAATAAATGACCCAACTTT 59.296 34.615 0.00 0.00 0.00 2.66
649 868 7.868415 CGTTCCAAAATAAATGACCCAACTTTA 59.132 33.333 0.00 0.00 0.00 1.85
650 869 9.719355 GTTCCAAAATAAATGACCCAACTTTAT 57.281 29.630 0.00 0.00 0.00 1.40
675 894 9.716531 ATACTAACTTTAGTACAAAGTTGGGTC 57.283 33.333 28.62 0.00 46.38 4.46
676 895 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
677 896 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
678 897 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
679 898 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
680 899 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
681 900 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
682 901 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
683 902 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
684 903 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
685 904 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
686 905 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
687 906 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
688 907 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
689 908 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
690 909 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
691 910 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
692 911 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
693 912 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
694 913 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
695 914 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
701 920 0.604578 TTTGGAACGGAGGGAGTACG 59.395 55.000 0.00 0.00 0.00 3.67
713 932 4.826183 GGAGGGAGTACGTACTTATGTCAT 59.174 45.833 27.96 13.50 36.50 3.06
750 1003 0.847670 CTTGTGTGCATGTGCGTTTG 59.152 50.000 0.00 0.00 45.83 2.93
757 1010 1.440850 CATGTGCGTTTGCTGACCG 60.441 57.895 0.00 0.00 43.34 4.79
801 1062 2.143122 GTCTTCGATGTGGAAAGCACA 58.857 47.619 0.00 0.00 36.95 4.57
802 1063 2.158449 GTCTTCGATGTGGAAAGCACAG 59.842 50.000 0.00 0.00 35.89 3.66
803 1064 2.037121 TCTTCGATGTGGAAAGCACAGA 59.963 45.455 0.00 0.00 35.89 3.41
804 1065 2.542020 TCGATGTGGAAAGCACAGAA 57.458 45.000 0.00 0.00 35.89 3.02
805 1066 2.143122 TCGATGTGGAAAGCACAGAAC 58.857 47.619 0.00 0.00 35.89 3.01
820 1081 3.131046 CACAGAACCACTTGGAAAAGCTT 59.869 43.478 1.14 0.00 38.94 3.74
821 1082 3.769300 ACAGAACCACTTGGAAAAGCTTT 59.231 39.130 5.69 5.69 38.94 3.51
822 1083 4.142160 ACAGAACCACTTGGAAAAGCTTTC 60.142 41.667 13.10 6.15 38.94 2.62
823 1084 3.384789 AGAACCACTTGGAAAAGCTTTCC 59.615 43.478 13.10 15.15 38.94 3.13
824 1085 2.745968 ACCACTTGGAAAAGCTTTCCA 58.254 42.857 19.97 19.97 46.08 3.53
855 1137 4.083217 CGTTAGGGATCTCTCCACTAATCG 60.083 50.000 0.00 0.00 44.08 3.34
965 1276 5.046014 ATCGATAAGATATCAGCCCAAAGCT 60.046 40.000 5.32 0.00 46.12 3.74
978 1289 2.602878 CCAAAGCTAAAGCATGCACTG 58.397 47.619 21.98 8.00 45.16 3.66
979 1290 2.229543 CCAAAGCTAAAGCATGCACTGA 59.770 45.455 21.98 0.00 45.16 3.41
1070 1381 0.762842 ACCCTGCTGTCCACTGTACA 60.763 55.000 0.00 0.00 0.00 2.90
1127 1441 1.738099 GCGACACTGATCTTGCCGT 60.738 57.895 5.73 0.00 0.00 5.68
1129 1443 0.388520 CGACACTGATCTTGCCGTCA 60.389 55.000 0.00 0.00 0.00 4.35
1174 1488 0.539051 CGACCCTCTCAGCATCCTTT 59.461 55.000 0.00 0.00 0.00 3.11
1203 1517 5.479124 ACTGGACTACTGGTACGAATTTT 57.521 39.130 0.00 0.00 0.00 1.82
1340 1654 5.832595 TCCTCTCCTATCTCAATCTCAACAG 59.167 44.000 0.00 0.00 0.00 3.16
1356 1670 3.322541 TCAACAGTACAAATCTCACGGGA 59.677 43.478 0.00 0.00 0.00 5.14
1487 1801 9.141400 GCTTCGTGTTCTTTCCCTATATTATAG 57.859 37.037 4.02 4.02 0.00 1.31
1518 1839 2.640826 TGGTTCAATCCCGGTAGAACTT 59.359 45.455 18.64 0.00 40.05 2.66
1644 1965 0.034337 TCGGTAACAACAGCCTGTCC 59.966 55.000 0.00 0.00 0.00 4.02
1650 1971 1.227823 CAACAGCCTGTCCGGACAA 60.228 57.895 35.36 20.35 41.33 3.18
1688 2009 3.084786 GCTCCTTACCAATGCTTGAGTT 58.915 45.455 0.00 0.00 0.00 3.01
1721 2042 1.098050 GTGAATCATTTCAGCGGCCT 58.902 50.000 0.00 0.00 42.41 5.19
1780 2101 2.206576 AATCTGGCTTGGACTGAACC 57.793 50.000 0.00 0.00 0.00 3.62
1785 2106 1.133513 TGGCTTGGACTGAACCACAAT 60.134 47.619 0.00 0.00 39.85 2.71
1837 2158 2.363788 TAGTCTACCAGCGTTGCAAG 57.636 50.000 0.00 0.00 0.00 4.01
1843 2164 0.877071 ACCAGCGTTGCAAGAGATTG 59.123 50.000 0.00 0.00 0.00 2.67
1938 2259 2.843401 TCAACCGGAATTCCTTCGAA 57.157 45.000 22.05 0.00 31.75 3.71
1953 2274 0.393132 TCGAAGGTGTTGTGCCAACA 60.393 50.000 14.38 14.38 0.00 3.33
2053 2374 1.825474 GCAACCTCACTCAGCTAGGTA 59.175 52.381 5.55 0.00 42.86 3.08
2054 2375 2.417515 GCAACCTCACTCAGCTAGGTAC 60.418 54.545 5.55 0.00 42.86 3.34
2109 2430 4.144297 CCATTCCAGAAGAGTTTGGACAA 58.856 43.478 0.00 0.00 42.93 3.18
2169 2490 0.616395 TAGTCGGACCCATTCCTGCA 60.616 55.000 4.14 0.00 43.25 4.41
2175 2496 2.050144 GGACCCATTCCTGCATCTCTA 58.950 52.381 0.00 0.00 41.95 2.43
2200 2521 6.384305 AGGTAACCTGTCTGAATTAGCATACT 59.616 38.462 0.00 0.00 29.57 2.12
2231 2552 9.454859 TTTAAACAAAAACATGTTCCTTGGATT 57.545 25.926 25.49 22.06 42.49 3.01
2385 2706 5.964758 TCAAATAATTTCACCAGTGGCATC 58.035 37.500 9.78 0.00 0.00 3.91
2464 2785 2.570442 TTTTGTTGGTGAACTTCCGC 57.430 45.000 0.00 0.00 32.79 5.54
2485 2806 5.448632 CCGCCTATGATTTCAAACCTAACAC 60.449 44.000 0.00 0.00 0.00 3.32
2487 2808 5.569413 CCTATGATTTCAAACCTAACACGC 58.431 41.667 0.00 0.00 0.00 5.34
2592 2913 4.387026 TGACCTGGATGGAAATCACTTT 57.613 40.909 0.00 0.00 39.71 2.66
2723 3045 8.247666 ACCAAGTAGAATACCTAATACTGTCC 57.752 38.462 0.00 0.00 44.47 4.02
2725 3047 7.230108 CCAAGTAGAATACCTAATACTGTCCGA 59.770 40.741 0.00 0.00 44.47 4.55
2828 3150 0.802494 CTGGCACATTACCCGTTGAC 59.198 55.000 0.00 0.00 38.20 3.18
2868 3190 4.851639 ATTTACAGCATGGACCTCTCTT 57.148 40.909 0.00 0.00 43.62 2.85
2909 3231 5.555017 AGAATCCCATATTCGATTGGACAG 58.445 41.667 10.28 0.00 34.81 3.51
2934 3256 6.313519 TCCAAATGATAGCCTACTTGAACT 57.686 37.500 0.00 0.00 0.00 3.01
2952 3274 7.489113 ACTTGAACTTGTCACACAATTCATTTC 59.511 33.333 11.57 0.00 37.48 2.17
3029 3351 6.841229 ACCTATCACATAACAATCTCTCTGGA 59.159 38.462 0.00 0.00 0.00 3.86
3030 3352 7.512058 ACCTATCACATAACAATCTCTCTGGAT 59.488 37.037 0.00 0.00 0.00 3.41
3062 3384 7.827236 CCAAAGTACCTAGTCAATTTCACCATA 59.173 37.037 0.00 0.00 0.00 2.74
3068 3390 5.829924 CCTAGTCAATTTCACCATATTGGCT 59.170 40.000 7.07 7.07 45.66 4.75
3075 3397 3.213206 TCACCATATTGGCTAGCTTGG 57.787 47.619 15.72 15.25 42.67 3.61
3098 3420 4.718961 ACCTGTCTTTCAACAAGCTACAT 58.281 39.130 0.00 0.00 0.00 2.29
3155 3477 5.512942 TTAGTCAACAATCCTTGATGGGA 57.487 39.130 0.00 0.00 39.95 4.37
3173 3496 1.338105 GGAAATTCTGGGCTTTGTGGC 60.338 52.381 0.00 0.00 40.96 5.01
3189 3512 0.947180 TGGCGCTTCACGTTTAGGAC 60.947 55.000 7.64 0.00 46.11 3.85
3213 3536 2.749621 CCAATGTGCCCAAGTAACTCTC 59.250 50.000 0.00 0.00 0.00 3.20
3223 3546 6.174049 GCCCAAGTAACTCTCAAAGAACTAT 58.826 40.000 0.00 0.00 0.00 2.12
3232 3555 6.721318 ACTCTCAAAGAACTATTAATGGCCA 58.279 36.000 8.56 8.56 0.00 5.36
3255 3578 3.389925 TGCTGAAAATTTTGCTCCCTG 57.610 42.857 8.47 0.00 0.00 4.45
3264 3587 2.245159 TTTGCTCCCTGCTATCATCG 57.755 50.000 0.00 0.00 43.37 3.84
3288 3611 6.092122 CGTATCAATTGGACTTGTAGCTTTCA 59.908 38.462 5.42 0.00 0.00 2.69
3339 3662 1.074405 AGAAGCAGCAAGGGATGTCAA 59.926 47.619 0.00 0.00 31.62 3.18
3400 3723 2.560981 TCTCGTACCATGAGCTTGTTCA 59.439 45.455 0.00 0.00 31.39 3.18
3401 3724 2.926200 CTCGTACCATGAGCTTGTTCAG 59.074 50.000 0.00 0.00 0.00 3.02
3572 3895 1.298863 CGTACTACGGATGGCACGG 60.299 63.158 0.26 0.00 38.08 4.94
3650 3973 2.417243 GGTGCTTCAATACATGCCCAAC 60.417 50.000 0.00 0.00 0.00 3.77
3742 4065 1.135603 CATGCTTGATGTGTCGTTGGG 60.136 52.381 0.00 0.00 0.00 4.12
3761 4084 2.565841 GGAATGGAGTATCTGCACCAC 58.434 52.381 0.00 0.00 34.07 4.16
3860 4183 1.000060 GCAGACTTTGGCATTGCAAGA 60.000 47.619 11.39 0.00 34.99 3.02
3861 4184 2.669364 CAGACTTTGGCATTGCAAGAC 58.331 47.619 11.39 6.98 0.00 3.01
3911 4234 2.747460 GCGAGCATGCCTGGAACA 60.747 61.111 15.66 0.00 0.00 3.18
3912 4235 3.044059 GCGAGCATGCCTGGAACAC 62.044 63.158 15.66 0.00 0.00 3.32
4112 4436 3.833070 TCTTCACTAGAAAGAGACCCACC 59.167 47.826 0.00 0.00 32.35 4.61
4162 4486 1.152756 GGCAGTGGGTTGTTGAGGT 60.153 57.895 0.00 0.00 0.00 3.85
4199 4523 2.849294 TCCGTGTTGTGGATGATCAA 57.151 45.000 0.00 0.00 0.00 2.57
4229 4553 1.238439 GGTCTTTTAGCTGCAGCACA 58.762 50.000 38.24 23.80 45.16 4.57
4492 8640 6.370994 GCTATGATGCAGCTGTTAAGATATGT 59.629 38.462 16.64 0.00 36.07 2.29
4497 8645 5.430886 TGCAGCTGTTAAGATATGTCACAT 58.569 37.500 16.64 0.00 0.00 3.21
4673 8831 8.335532 AGCACCGCAATATAAATACATTGTAT 57.664 30.769 3.40 3.40 35.12 2.29
4721 8879 5.437060 GCTTCCTGAAATCCTACATGGTAA 58.563 41.667 0.00 0.00 37.07 2.85
4729 8887 8.220755 TGAAATCCTACATGGTAATAAAGCAC 57.779 34.615 0.00 0.00 38.70 4.40
4833 9401 3.494398 CGGAGAAACTGACCAGAGGAAAA 60.494 47.826 3.76 0.00 0.00 2.29
4995 9709 1.652167 GCTTTGCTAGCTGCTGACCC 61.652 60.000 17.23 0.00 46.77 4.46
5176 10456 3.275617 TTAGAACCCATGTGCGCTATT 57.724 42.857 9.73 0.00 0.00 1.73
5273 11919 2.938798 AAATGGAGGGGTGGCCGA 60.939 61.111 0.00 0.00 0.00 5.54
5345 12674 4.935352 AGCAATTTCACAGGCAAAAGTA 57.065 36.364 0.00 0.00 0.00 2.24
5383 12712 5.358725 ACCACGTCAGAAATACCAACTTTTT 59.641 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.062734 ACACATGCCCCATGATTCCAT 60.063 47.619 11.78 0.00 43.81 3.41
1 2 0.335705 ACACATGCCCCATGATTCCA 59.664 50.000 11.78 0.00 43.81 3.53
2 3 1.035139 GACACATGCCCCATGATTCC 58.965 55.000 11.78 0.00 43.81 3.01
3 4 1.035139 GGACACATGCCCCATGATTC 58.965 55.000 11.78 7.10 43.81 2.52
4 5 0.335705 TGGACACATGCCCCATGATT 59.664 50.000 11.78 0.00 43.81 2.57
5 6 0.335705 TTGGACACATGCCCCATGAT 59.664 50.000 11.78 0.18 43.81 2.45
6 7 0.323633 CTTGGACACATGCCCCATGA 60.324 55.000 11.78 0.00 43.81 3.07
7 8 1.952102 GCTTGGACACATGCCCCATG 61.952 60.000 3.80 3.80 46.18 3.66
8 9 1.683365 GCTTGGACACATGCCCCAT 60.683 57.895 0.00 0.00 40.72 4.00
9 10 2.283101 GCTTGGACACATGCCCCA 60.283 61.111 0.00 0.00 40.72 4.96
10 11 2.036256 AGCTTGGACACATGCCCC 59.964 61.111 0.00 0.00 45.89 5.80
11 12 2.345760 CCAGCTTGGACACATGCCC 61.346 63.158 0.00 0.00 45.89 5.36
12 13 1.303561 TCCAGCTTGGACACATGCC 60.304 57.895 0.00 0.00 42.67 4.40
13 14 4.402851 TCCAGCTTGGACACATGC 57.597 55.556 0.00 0.00 42.67 4.06
20 21 1.304381 GCCAATGGTCCAGCTTGGA 60.304 57.895 23.28 1.82 45.98 3.53
21 22 2.353610 GGCCAATGGTCCAGCTTGG 61.354 63.158 17.01 17.01 41.92 3.61
22 23 0.974010 ATGGCCAATGGTCCAGCTTG 60.974 55.000 10.96 0.00 33.77 4.01
23 24 0.974010 CATGGCCAATGGTCCAGCTT 60.974 55.000 10.96 2.55 33.77 3.74
24 25 1.380785 CATGGCCAATGGTCCAGCT 60.381 57.895 10.96 3.15 33.77 4.24
25 26 3.085119 GCATGGCCAATGGTCCAGC 62.085 63.158 10.96 16.26 36.71 4.85
26 27 3.213264 GCATGGCCAATGGTCCAG 58.787 61.111 10.96 12.02 36.71 3.86
37 38 2.760092 TCATTCTGTTTTAGGGCATGGC 59.240 45.455 11.56 11.56 0.00 4.40
38 39 4.678840 GCTTCATTCTGTTTTAGGGCATGG 60.679 45.833 0.00 0.00 0.00 3.66
39 40 4.427312 GCTTCATTCTGTTTTAGGGCATG 58.573 43.478 0.00 0.00 0.00 4.06
40 41 3.448660 GGCTTCATTCTGTTTTAGGGCAT 59.551 43.478 0.00 0.00 0.00 4.40
41 42 2.825532 GGCTTCATTCTGTTTTAGGGCA 59.174 45.455 0.00 0.00 0.00 5.36
42 43 2.825532 TGGCTTCATTCTGTTTTAGGGC 59.174 45.455 0.00 0.00 0.00 5.19
43 44 5.665916 AATGGCTTCATTCTGTTTTAGGG 57.334 39.130 0.00 0.00 36.44 3.53
44 45 5.349543 GCAAATGGCTTCATTCTGTTTTAGG 59.650 40.000 0.00 0.00 39.95 2.69
45 46 6.399204 GCAAATGGCTTCATTCTGTTTTAG 57.601 37.500 0.00 0.00 39.95 1.85
79 80 8.251750 TCGGTGATGACTTGATAAAAGTTAAG 57.748 34.615 0.00 0.00 0.00 1.85
97 98 0.524414 TTGTCGTCGTCATCGGTGAT 59.476 50.000 0.00 0.00 36.60 3.06
203 204 6.375455 GTCACAGTCATAGGTGGAATTCATTT 59.625 38.462 7.93 0.00 35.74 2.32
225 226 1.221566 CTCACATGGCGGGATGTCA 59.778 57.895 0.00 0.00 34.18 3.58
284 285 4.152402 CGATGTGCATTTACCCTATGCTAC 59.848 45.833 8.99 6.46 46.59 3.58
307 308 5.923733 TCTTCCTCTTTCCTACTGATGAC 57.076 43.478 0.00 0.00 0.00 3.06
321 322 3.596101 AGCATGGACCATATCTTCCTCT 58.404 45.455 6.67 0.00 32.55 3.69
337 338 1.136147 GAGCAGCACCGAAAGCATG 59.864 57.895 0.00 0.00 0.00 4.06
346 347 1.258982 CATTTCGATACGAGCAGCACC 59.741 52.381 0.00 0.00 37.14 5.01
387 388 2.828520 TGGGTTGCTTTCAGTTTCAACA 59.171 40.909 6.34 0.00 40.20 3.33
429 648 0.804989 CGTTGCTTTCTCCCCATCAC 59.195 55.000 0.00 0.00 0.00 3.06
433 652 0.753479 TTTGCGTTGCTTTCTCCCCA 60.753 50.000 0.00 0.00 0.00 4.96
448 667 1.202510 TGCAACCAACCACTCATTTGC 60.203 47.619 0.00 0.00 39.80 3.68
451 670 3.494749 CCATTTGCAACCAACCACTCATT 60.495 43.478 0.00 0.00 0.00 2.57
454 673 1.686052 TCCATTTGCAACCAACCACTC 59.314 47.619 0.00 0.00 0.00 3.51
457 676 1.489481 TGTCCATTTGCAACCAACCA 58.511 45.000 0.00 0.00 0.00 3.67
458 677 2.611225 TTGTCCATTTGCAACCAACC 57.389 45.000 0.00 0.00 0.00 3.77
459 678 3.555547 GTCTTTGTCCATTTGCAACCAAC 59.444 43.478 0.00 0.00 0.00 3.77
460 679 3.196469 TGTCTTTGTCCATTTGCAACCAA 59.804 39.130 0.00 0.00 0.00 3.67
461 680 2.762887 TGTCTTTGTCCATTTGCAACCA 59.237 40.909 0.00 0.00 0.00 3.67
462 681 3.383761 CTGTCTTTGTCCATTTGCAACC 58.616 45.455 0.00 0.00 0.00 3.77
463 682 3.383761 CCTGTCTTTGTCCATTTGCAAC 58.616 45.455 0.00 0.00 0.00 4.17
464 683 2.364970 CCCTGTCTTTGTCCATTTGCAA 59.635 45.455 0.00 0.00 0.00 4.08
465 684 1.962807 CCCTGTCTTTGTCCATTTGCA 59.037 47.619 0.00 0.00 0.00 4.08
466 685 1.337167 GCCCTGTCTTTGTCCATTTGC 60.337 52.381 0.00 0.00 0.00 3.68
467 686 1.273327 GGCCCTGTCTTTGTCCATTTG 59.727 52.381 0.00 0.00 0.00 2.32
468 687 1.147817 AGGCCCTGTCTTTGTCCATTT 59.852 47.619 0.00 0.00 0.00 2.32
469 688 0.779997 AGGCCCTGTCTTTGTCCATT 59.220 50.000 0.00 0.00 0.00 3.16
470 689 1.668826 TAGGCCCTGTCTTTGTCCAT 58.331 50.000 0.00 0.00 0.00 3.41
471 690 1.281867 CATAGGCCCTGTCTTTGTCCA 59.718 52.381 0.00 0.00 0.00 4.02
472 691 1.559682 TCATAGGCCCTGTCTTTGTCC 59.440 52.381 0.00 0.00 0.00 4.02
473 692 2.633488 GTCATAGGCCCTGTCTTTGTC 58.367 52.381 0.00 0.00 0.00 3.18
474 693 1.066143 CGTCATAGGCCCTGTCTTTGT 60.066 52.381 0.00 0.00 0.00 2.83
475 694 1.066143 ACGTCATAGGCCCTGTCTTTG 60.066 52.381 0.00 0.00 0.00 2.77
476 695 1.276622 ACGTCATAGGCCCTGTCTTT 58.723 50.000 0.00 0.00 0.00 2.52
477 696 2.154567 TACGTCATAGGCCCTGTCTT 57.845 50.000 0.00 0.00 0.00 3.01
478 697 2.154567 TTACGTCATAGGCCCTGTCT 57.845 50.000 0.00 0.00 0.00 3.41
479 698 2.288886 GGATTACGTCATAGGCCCTGTC 60.289 54.545 0.00 0.00 0.00 3.51
540 759 7.996644 CCCACATATGGTAATACTAAGTTTGGT 59.003 37.037 7.80 0.00 45.66 3.67
541 760 7.996644 ACCCACATATGGTAATACTAAGTTTGG 59.003 37.037 7.80 0.23 45.66 3.28
542 761 8.974060 ACCCACATATGGTAATACTAAGTTTG 57.026 34.615 7.80 0.00 45.66 2.93
543 762 9.984590 AAACCCACATATGGTAATACTAAGTTT 57.015 29.630 7.80 0.30 45.66 2.66
581 800 8.576442 AGACCCAATTCAAAAGTTTGTAGTATG 58.424 33.333 3.82 0.00 39.18 2.39
585 804 6.200854 GCAAGACCCAATTCAAAAGTTTGTAG 59.799 38.462 3.82 0.00 39.18 2.74
592 811 7.830739 AGTATTAGCAAGACCCAATTCAAAAG 58.169 34.615 0.00 0.00 0.00 2.27
597 816 6.587273 AGAGAGTATTAGCAAGACCCAATTC 58.413 40.000 0.00 0.00 0.00 2.17
612 831 8.893727 CATTTATTTTGGAACGGAGAGAGTATT 58.106 33.333 0.00 0.00 0.00 1.89
613 832 8.265055 TCATTTATTTTGGAACGGAGAGAGTAT 58.735 33.333 0.00 0.00 0.00 2.12
614 833 7.548075 GTCATTTATTTTGGAACGGAGAGAGTA 59.452 37.037 0.00 0.00 0.00 2.59
615 834 6.371825 GTCATTTATTTTGGAACGGAGAGAGT 59.628 38.462 0.00 0.00 0.00 3.24
616 835 6.183360 GGTCATTTATTTTGGAACGGAGAGAG 60.183 42.308 0.00 0.00 0.00 3.20
617 836 5.646360 GGTCATTTATTTTGGAACGGAGAGA 59.354 40.000 0.00 0.00 0.00 3.10
618 837 5.163652 GGGTCATTTATTTTGGAACGGAGAG 60.164 44.000 0.00 0.00 0.00 3.20
619 838 4.703093 GGGTCATTTATTTTGGAACGGAGA 59.297 41.667 0.00 0.00 0.00 3.71
620 839 4.461081 TGGGTCATTTATTTTGGAACGGAG 59.539 41.667 0.00 0.00 0.00 4.63
621 840 4.408276 TGGGTCATTTATTTTGGAACGGA 58.592 39.130 0.00 0.00 0.00 4.69
622 841 4.792521 TGGGTCATTTATTTTGGAACGG 57.207 40.909 0.00 0.00 0.00 4.44
623 842 5.778862 AGTTGGGTCATTTATTTTGGAACG 58.221 37.500 0.00 0.00 0.00 3.95
624 843 9.719355 ATAAAGTTGGGTCATTTATTTTGGAAC 57.281 29.630 0.00 0.00 0.00 3.62
649 868 9.716531 GACCCAACTTTGTACTAAAGTTAGTAT 57.283 33.333 23.56 15.20 45.57 2.12
650 869 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
651 870 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
652 871 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
653 872 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
655 874 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
656 875 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
657 876 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
658 877 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
659 878 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
660 879 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
661 880 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
662 881 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
663 882 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
664 883 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
665 884 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
666 885 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
667 886 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
668 887 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
669 888 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
670 889 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
671 890 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
672 891 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
673 892 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
674 893 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
675 894 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
676 895 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
677 896 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
678 897 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
679 898 3.119029 CGTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
680 899 2.354403 CGTACTCCCTCCGTTCCAAAAT 60.354 50.000 0.00 0.00 0.00 1.82
681 900 1.001181 CGTACTCCCTCCGTTCCAAAA 59.999 52.381 0.00 0.00 0.00 2.44
682 901 0.604578 CGTACTCCCTCCGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
683 902 0.540365 ACGTACTCCCTCCGTTCCAA 60.540 55.000 0.00 0.00 0.00 3.53
684 903 0.327924 TACGTACTCCCTCCGTTCCA 59.672 55.000 0.00 0.00 36.12 3.53
685 904 0.735471 GTACGTACTCCCTCCGTTCC 59.265 60.000 18.47 0.00 36.12 3.62
686 905 1.743996 AGTACGTACTCCCTCCGTTC 58.256 55.000 22.45 0.00 36.12 3.95
687 906 2.206576 AAGTACGTACTCCCTCCGTT 57.793 50.000 27.51 7.56 34.99 4.44
688 907 3.209410 CATAAGTACGTACTCCCTCCGT 58.791 50.000 27.51 13.18 34.99 4.69
689 908 3.209410 ACATAAGTACGTACTCCCTCCG 58.791 50.000 27.51 15.09 34.99 4.63
690 909 4.202441 TGACATAAGTACGTACTCCCTCC 58.798 47.826 27.51 16.79 34.99 4.30
691 910 6.388435 AATGACATAAGTACGTACTCCCTC 57.612 41.667 27.51 18.48 34.99 4.30
692 911 9.750783 ATATAATGACATAAGTACGTACTCCCT 57.249 33.333 27.51 15.31 34.99 4.20
727 946 0.238025 CGCACATGCACACAAGCTTA 59.762 50.000 0.00 0.00 42.21 3.09
737 990 1.008652 GTCAGCAAACGCACATGCA 60.009 52.632 4.49 0.00 44.95 3.96
750 1003 1.221414 GTCAATCTATGCCGGTCAGC 58.779 55.000 1.90 0.00 0.00 4.26
757 1010 1.599542 GACTTGCGGTCAATCTATGCC 59.400 52.381 5.00 0.00 43.94 4.40
801 1062 3.384789 GGAAAGCTTTTCCAAGTGGTTCT 59.615 43.478 14.05 0.00 38.45 3.01
802 1063 3.132111 TGGAAAGCTTTTCCAAGTGGTTC 59.868 43.478 20.99 3.53 44.90 3.62
803 1064 3.103742 TGGAAAGCTTTTCCAAGTGGTT 58.896 40.909 20.99 0.00 44.90 3.67
804 1065 2.745968 TGGAAAGCTTTTCCAAGTGGT 58.254 42.857 20.99 0.00 44.90 4.16
820 1081 2.189676 TCCCTAACGGCATTAGTGGAA 58.810 47.619 7.72 0.00 39.01 3.53
821 1082 1.868713 TCCCTAACGGCATTAGTGGA 58.131 50.000 6.49 6.49 39.01 4.02
822 1083 2.368875 AGATCCCTAACGGCATTAGTGG 59.631 50.000 0.00 1.16 39.01 4.00
823 1084 3.322254 AGAGATCCCTAACGGCATTAGTG 59.678 47.826 0.00 0.00 39.01 2.74
824 1085 3.574826 GAGAGATCCCTAACGGCATTAGT 59.425 47.826 0.00 0.00 39.01 2.24
828 1089 1.343069 GGAGAGATCCCTAACGGCAT 58.657 55.000 0.00 0.00 0.00 4.40
830 1091 0.389757 GTGGAGAGATCCCTAACGGC 59.610 60.000 0.00 0.00 0.00 5.68
855 1137 6.307077 GGTGCTTTCGGTGTAATATTTTTGTC 59.693 38.462 0.00 0.00 0.00 3.18
907 1210 6.183361 CCATCTTAATATGGTGAGAAGGGTCA 60.183 42.308 10.94 0.00 41.38 4.02
916 1220 6.102468 TCCATTCACCCATCTTAATATGGTGA 59.898 38.462 16.35 15.62 44.29 4.02
933 1237 6.478344 GGCTGATATCTTATCGATCCATTCAC 59.522 42.308 0.00 0.00 33.48 3.18
965 1276 3.937079 CAGAGATGTCAGTGCATGCTTTA 59.063 43.478 20.33 0.00 0.00 1.85
978 1289 4.832248 TGTATGTTTGGGACAGAGATGTC 58.168 43.478 0.00 0.00 42.62 3.06
979 1290 4.908601 TGTATGTTTGGGACAGAGATGT 57.091 40.909 0.00 0.00 42.62 3.06
1070 1381 2.569404 GGACCAGGAGAAGAAGATGTGT 59.431 50.000 0.00 0.00 0.00 3.72
1188 1502 4.214545 CAGTGGCAAAAATTCGTACCAGTA 59.785 41.667 0.00 0.00 29.82 2.74
1191 1505 2.294791 CCAGTGGCAAAAATTCGTACCA 59.705 45.455 0.00 0.00 0.00 3.25
1203 1517 2.499214 GACACCAAACCAGTGGCAA 58.501 52.632 9.78 0.00 43.15 4.52
1340 1654 3.536956 TGGATCCCGTGAGATTTGTAC 57.463 47.619 9.90 0.00 0.00 2.90
1356 1670 3.264450 GTCCTAAATCATCGGGGATGGAT 59.736 47.826 5.83 0.00 40.15 3.41
1487 1801 3.416156 GGGATTGAACCAGATAGATGGC 58.584 50.000 0.00 0.00 44.80 4.40
1518 1839 1.345741 CCAAGACTCTGCAGGTTCTGA 59.654 52.381 15.13 0.00 32.44 3.27
1644 1965 5.505654 GCCAATACAAGATGGTATTTGTCCG 60.506 44.000 0.00 0.00 40.92 4.79
1650 1971 5.653255 AGGAGCCAATACAAGATGGTATT 57.347 39.130 0.00 0.00 42.99 1.89
1688 2009 8.125580 TGAAATGATTCACTTGAAGGTCAAGGA 61.126 37.037 19.31 11.99 43.39 3.36
1721 2042 6.147473 TGGTTGAATATGGATGGAGGTACTA 58.853 40.000 0.00 0.00 41.55 1.82
1759 2080 2.229784 GGTTCAGTCCAAGCCAGATTTG 59.770 50.000 0.00 0.00 0.00 2.32
1780 2101 4.772100 AGGGATTGGACCAGTTAAATTGTG 59.228 41.667 0.00 0.00 0.00 3.33
1785 2106 5.586155 TGTTAGGGATTGGACCAGTTAAA 57.414 39.130 0.00 0.00 0.00 1.52
1837 2158 2.645838 TTGCTATCCAGGCCAATCTC 57.354 50.000 5.01 0.00 0.00 2.75
1843 2164 4.006319 GTGAATCTATTGCTATCCAGGCC 58.994 47.826 0.00 0.00 0.00 5.19
2005 2326 3.431486 GCAACAGGAATTGGACCAACAAA 60.431 43.478 9.67 0.00 33.48 2.83
2062 2383 0.828677 GACAGGTTACAGGCCGGTAT 59.171 55.000 16.85 0.85 34.68 2.73
2094 2415 4.145052 GGTCCAATTGTCCAAACTCTTCT 58.855 43.478 4.43 0.00 0.00 2.85
2109 2430 2.951642 CAACACAGTGAGTTGGTCCAAT 59.048 45.455 21.57 0.00 41.92 3.16
2169 2490 7.014808 GCTAATTCAGACAGGTTACCTAGAGAT 59.985 40.741 2.52 0.00 29.64 2.75
2175 2496 5.700402 ATGCTAATTCAGACAGGTTACCT 57.300 39.130 0.00 0.00 0.00 3.08
2200 2521 8.329203 AGGAACATGTTTTTGTTTAAAAGCAA 57.671 26.923 13.36 0.00 45.69 3.91
2205 2526 9.454859 AATCCAAGGAACATGTTTTTGTTTAAA 57.545 25.926 23.70 11.82 39.85 1.52
2217 2538 3.696045 TGGTACCAATCCAAGGAACATG 58.304 45.455 13.60 0.00 31.50 3.21
2231 2552 3.653836 ACTACCAATTGTTCCTGGTACCA 59.346 43.478 15.39 15.39 44.28 3.25
2254 2575 4.439057 TCAATACGAACCATAGAGTTGGC 58.561 43.478 0.00 0.00 40.68 4.52
2385 2706 2.172717 CAGGTTCCCCACATAGTTAGGG 59.827 54.545 0.00 0.00 42.44 3.53
2420 2741 7.509141 TTGTTCTTAGATGCACTGAAAATCA 57.491 32.000 0.00 0.00 0.00 2.57
2464 2785 5.448632 GGCGTGTTAGGTTTGAAATCATAGG 60.449 44.000 0.00 0.00 0.00 2.57
2487 2808 7.605449 TCTTTGAAAAATCTAGCCATTCAAGG 58.395 34.615 12.04 12.04 40.07 3.61
2526 2847 7.981142 TCATCATGATGGATTCTGGAATCTTA 58.019 34.615 30.54 7.10 44.90 2.10
2562 2883 0.325933 CATCCAGGTCAAGCCACTGA 59.674 55.000 0.00 0.00 40.61 3.41
2608 2929 5.456548 TTCTTGAGCATTGCAATTTGAGA 57.543 34.783 9.83 6.44 0.00 3.27
2613 2934 7.286087 TGTCCTATATTCTTGAGCATTGCAATT 59.714 33.333 9.83 0.00 0.00 2.32
2671 2992 1.852965 ACCAATCCCCTCTGGTATTGG 59.147 52.381 12.77 12.77 46.50 3.16
2723 3045 7.307989 GGGATAATTGATGATAACTGGTTGTCG 60.308 40.741 5.92 0.00 34.04 4.35
2725 3047 7.353525 TGGGATAATTGATGATAACTGGTTGT 58.646 34.615 0.00 0.00 0.00 3.32
2767 3089 1.476085 CTAGCTGGAGGACACTGTCAG 59.524 57.143 11.34 0.00 33.68 3.51
2828 3150 6.817641 TGTAAATTTGCTTCAAATAGCCCATG 59.182 34.615 7.80 0.00 42.32 3.66
2888 3210 4.074970 GCTGTCCAATCGAATATGGGATT 58.925 43.478 13.38 0.00 37.31 3.01
2909 3231 4.708177 TCAAGTAGGCTATCATTTGGAGC 58.292 43.478 0.00 0.00 35.39 4.70
2994 3316 7.681939 TGTTATGTGATAGGTCCAAACTTTC 57.318 36.000 0.00 0.00 0.00 2.62
3029 3351 9.975218 AAATTGACTAGGTACTTTGGTATTGAT 57.025 29.630 0.00 0.00 41.75 2.57
3030 3352 9.444600 GAAATTGACTAGGTACTTTGGTATTGA 57.555 33.333 0.00 0.00 41.75 2.57
3062 3384 0.995024 ACAGGTCCAAGCTAGCCAAT 59.005 50.000 12.13 0.00 0.00 3.16
3068 3390 3.135712 TGTTGAAAGACAGGTCCAAGCTA 59.864 43.478 0.00 0.00 0.00 3.32
3075 3397 4.127171 TGTAGCTTGTTGAAAGACAGGTC 58.873 43.478 0.00 0.00 0.00 3.85
3155 3477 0.318120 CGCCACAAAGCCCAGAATTT 59.682 50.000 0.00 0.00 0.00 1.82
3173 3496 2.864882 TGGAAGTCCTAAACGTGAAGCG 60.865 50.000 0.00 0.00 41.02 4.68
3189 3512 3.157087 AGTTACTTGGGCACATTGGAAG 58.843 45.455 0.00 0.00 0.00 3.46
3213 3536 5.750067 GCATGTGGCCATTAATAGTTCTTTG 59.250 40.000 9.72 0.00 36.11 2.77
3223 3546 4.822685 ATTTTCAGCATGTGGCCATTAA 57.177 36.364 9.72 0.00 46.50 1.40
3232 3555 3.325716 AGGGAGCAAAATTTTCAGCATGT 59.674 39.130 13.78 0.00 37.40 3.21
3255 3578 6.425114 ACAAGTCCAATTGATACGATGATAGC 59.575 38.462 7.12 0.00 34.20 2.97
3264 3587 7.377766 TGAAAGCTACAAGTCCAATTGATAC 57.622 36.000 7.12 4.91 34.20 2.24
3314 3637 5.116084 ACATCCCTTGCTGCTTCTTTATA 57.884 39.130 0.00 0.00 0.00 0.98
3317 3640 2.165998 GACATCCCTTGCTGCTTCTTT 58.834 47.619 0.00 0.00 0.00 2.52
3339 3662 1.553704 GTCAACCATACCGGGAGAAGT 59.446 52.381 6.32 0.00 40.22 3.01
3400 3723 6.317391 GCTCTCACTAAAATTATCAGTTGCCT 59.683 38.462 0.00 0.00 0.00 4.75
3401 3724 6.094048 TGCTCTCACTAAAATTATCAGTTGCC 59.906 38.462 0.00 0.00 0.00 4.52
3572 3895 1.953559 TCCTCATTAGATTGCGGTGC 58.046 50.000 0.00 0.00 0.00 5.01
3650 3973 0.599728 GGAGCATCTCTAAGCTGCCG 60.600 60.000 0.00 0.00 42.50 5.69
3742 4065 2.159099 TCGTGGTGCAGATACTCCATTC 60.159 50.000 0.00 0.00 35.77 2.67
3761 4084 0.879765 AGACCACCTCGTAGTGTTCG 59.120 55.000 6.79 0.00 34.62 3.95
3860 4183 4.090090 AGCTGTCATCACCTAGTAACAGT 58.910 43.478 0.00 0.00 37.15 3.55
3861 4184 4.400884 AGAGCTGTCATCACCTAGTAACAG 59.599 45.833 0.00 0.00 37.70 3.16
3911 4234 0.322816 CTGGTGCCATGTAGCCAAGT 60.323 55.000 0.00 0.00 0.00 3.16
3912 4235 1.033746 CCTGGTGCCATGTAGCCAAG 61.034 60.000 0.00 0.00 0.00 3.61
4162 4486 2.357637 CGGAAAAGTTCTGCAGGAAACA 59.642 45.455 15.13 0.00 35.51 2.83
4199 4523 5.569026 GCAGCTAAAAGACCCTTGTAGTAGT 60.569 44.000 5.97 0.00 0.00 2.73
4492 8640 7.962995 AGAAGGTTCTAGTCTATTCATGTGA 57.037 36.000 0.00 0.00 35.34 3.58
4891 9471 4.216687 TCTTTTGTTTGTGACACCGTCTTT 59.783 37.500 2.45 0.00 38.18 2.52
5201 11847 2.289444 CGCTTGGTGAAGAGGTTAGGAA 60.289 50.000 0.00 0.00 0.00 3.36
5297 11943 4.090761 TCACAGGAAAAATGAGCTCACT 57.909 40.909 20.97 4.71 0.00 3.41


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

AutoCloner maintained by Alex Coulton.