Multiple sequence alignment - TraesCS3D01G439400

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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 TraesCS3D01G439400 chr3D 100.000 3299 0 0 1 3299 549704015 549707313 0.000000e+00 6093.0
1 TraesCS3D01G439400 chr3D 91.045 67 6 0 719 785 27934841 27934907 1.260000e-14 91.6
2 TraesCS3D01G439400 chr3D 90.323 62 5 1 726 787 594870447 594870387 2.730000e-11 80.5
3 TraesCS3D01G439400 chr3D 92.593 54 4 0 732 785 594868166 594868113 9.810000e-11 78.7
4 TraesCS3D01G439400 chr3A 96.612 1948 51 3 719 2666 686862964 686864896 0.000000e+00 3217.0
5 TraesCS3D01G439400 chr3A 90.370 405 37 1 2 406 686862188 686862590 6.270000e-147 531.0
6 TraesCS3D01G439400 chr3A 90.794 315 10 3 2979 3293 686865272 686865567 1.430000e-108 403.0
7 TraesCS3D01G439400 chr3A 79.134 254 49 4 1399 1650 542203127 542203378 4.380000e-39 172.0
8 TraesCS3D01G439400 chr3A 91.045 67 6 0 719 785 37808650 37808716 1.260000e-14 91.6
9 TraesCS3D01G439400 chr3A 95.000 40 0 1 2971 3010 13085199 13085236 9.880000e-06 62.1
10 TraesCS3D01G439400 chr3B 96.382 1603 44 3 829 2429 729414512 729416102 0.000000e+00 2627.0
11 TraesCS3D01G439400 chr3B 93.143 350 19 1 2932 3281 729416782 729417126 2.940000e-140 508.0
12 TraesCS3D01G439400 chr3B 92.000 225 18 0 2705 2929 603040905 603040681 1.910000e-82 316.0
13 TraesCS3D01G439400 chr3B 87.324 284 24 7 2658 2930 247259640 247259922 6.870000e-82 315.0
14 TraesCS3D01G439400 chr3B 93.750 176 9 1 224 399 729412637 729412810 2.520000e-66 263.0
15 TraesCS3D01G439400 chr3B 87.826 115 9 1 719 833 729413238 729413347 2.670000e-26 130.0
16 TraesCS3D01G439400 chr3B 90.000 70 3 4 718 786 13859301 13859235 1.630000e-13 87.9
17 TraesCS3D01G439400 chr5A 86.199 1681 174 33 786 2439 55018252 55019901 0.000000e+00 1766.0
18 TraesCS3D01G439400 chr5D 86.060 1693 173 38 786 2443 65753517 65755181 0.000000e+00 1760.0
19 TraesCS3D01G439400 chr5D 85.443 158 19 4 566 722 514021488 514021642 9.470000e-36 161.0
20 TraesCS3D01G439400 chr5B 85.375 1682 194 31 792 2439 65279752 65278089 0.000000e+00 1696.0
21 TraesCS3D01G439400 chr5B 88.278 273 21 3 2673 2936 55880548 55880818 1.910000e-82 316.0
22 TraesCS3D01G439400 chrUn 88.732 284 20 4 2658 2929 158465637 158465354 1.470000e-88 337.0
23 TraesCS3D01G439400 chrUn 86.667 285 26 7 2658 2930 53749047 53749331 4.140000e-79 305.0
24 TraesCS3D01G439400 chr1B 88.462 286 21 6 2657 2930 225807799 225808084 5.270000e-88 335.0
25 TraesCS3D01G439400 chr1B 80.451 266 47 5 1399 1662 576205888 576206150 7.220000e-47 198.0
26 TraesCS3D01G439400 chr1B 84.211 152 23 1 2525 2676 245953843 245953993 2.650000e-31 147.0
27 TraesCS3D01G439400 chr1B 88.060 67 2 2 656 722 22107822 22107762 1.270000e-09 75.0
28 TraesCS3D01G439400 chr6B 88.112 286 22 4 2658 2931 136907283 136907568 2.450000e-86 329.0
29 TraesCS3D01G439400 chr6B 89.754 244 21 4 2709 2951 301553204 301552964 3.200000e-80 309.0
30 TraesCS3D01G439400 chr2B 89.734 263 18 1 2676 2929 72992155 72991893 8.830000e-86 327.0
31 TraesCS3D01G439400 chr2B 82.692 104 14 4 622 723 690957476 690957375 4.530000e-14 89.8
32 TraesCS3D01G439400 chr7B 92.035 226 18 0 2705 2930 201904701 201904476 5.310000e-83 318.0
33 TraesCS3D01G439400 chr7B 86.585 82 8 1 641 722 676448040 676447962 1.630000e-13 87.9
34 TraesCS3D01G439400 chr1A 91.379 232 19 1 2705 2936 7789124 7789354 1.910000e-82 316.0
35 TraesCS3D01G439400 chr1A 85.965 285 28 6 2658 2930 10404053 10403769 8.950000e-76 294.0
36 TraesCS3D01G439400 chr1A 83.566 286 33 10 2658 2930 19500545 19500261 4.220000e-64 255.0
37 TraesCS3D01G439400 chr1A 80.451 266 47 5 1399 1662 521629506 521629768 7.220000e-47 198.0
38 TraesCS3D01G439400 chr1A 83.750 160 23 3 2525 2681 201863224 201863383 7.380000e-32 148.0
39 TraesCS3D01G439400 chr4D 88.755 249 23 5 2705 2951 505435669 505435914 1.920000e-77 300.0
40 TraesCS3D01G439400 chr4D 88.350 103 11 1 598 700 401529440 401529541 4.470000e-24 122.0
41 TraesCS3D01G439400 chr4B 86.316 285 27 6 2658 2930 8217065 8217349 1.920000e-77 300.0
42 TraesCS3D01G439400 chr4B 83.275 287 34 5 2658 2930 87455642 87455928 5.460000e-63 252.0
43 TraesCS3D01G439400 chr4B 84.810 158 24 0 564 721 141627603 141627760 3.410000e-35 159.0
44 TraesCS3D01G439400 chr4B 86.957 69 5 4 718 785 654324766 654324831 1.270000e-09 75.0
45 TraesCS3D01G439400 chr1D 80.827 266 46 5 1399 1662 426587341 426587603 1.550000e-48 204.0
46 TraesCS3D01G439400 chr1D 84.800 125 9 4 597 720 435926376 435926261 2.080000e-22 117.0
47 TraesCS3D01G439400 chr6A 88.750 160 16 2 564 722 143010038 143009880 9.340000e-46 195.0
48 TraesCS3D01G439400 chr6A 91.200 125 11 0 598 722 143009109 143008985 1.570000e-38 171.0
49 TraesCS3D01G439400 chr2D 88.608 158 18 0 565 722 126951187 126951344 3.360000e-45 193.0
50 TraesCS3D01G439400 chr7A 83.673 98 15 1 2526 2622 66224005 66223908 1.260000e-14 91.6
51 TraesCS3D01G439400 chr7A 100.000 39 0 0 2967 3005 9454524 9454486 4.570000e-09 73.1
52 TraesCS3D01G439400 chr7A 97.619 42 1 0 2964 3005 9645839 9645880 4.570000e-09 73.1
53 TraesCS3D01G439400 chr2A 88.406 69 7 1 718 786 334534493 334534560 7.590000e-12 82.4
54 TraesCS3D01G439400 chr4A 100.000 39 0 0 2967 3005 728786093 728786055 4.570000e-09 73.1
55 TraesCS3D01G439400 chr4A 97.619 42 1 0 2964 3005 731152666 731152707 4.570000e-09 73.1
56 TraesCS3D01G439400 chr4A 97.619 42 1 0 2964 3005 731168031 731168072 4.570000e-09 73.1


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 TraesCS3D01G439400 chr3D 549704015 549707313 3298 False 6093.000000 6093 100.00000 1 3299 1 chr3D.!!$F2 3298
1 TraesCS3D01G439400 chr3A 686862188 686865567 3379 False 1383.666667 3217 92.59200 2 3293 3 chr3A.!!$F4 3291
2 TraesCS3D01G439400 chr3B 729412637 729417126 4489 False 882.000000 2627 92.77525 224 3281 4 chr3B.!!$F2 3057
3 TraesCS3D01G439400 chr5A 55018252 55019901 1649 False 1766.000000 1766 86.19900 786 2439 1 chr5A.!!$F1 1653
4 TraesCS3D01G439400 chr5D 65753517 65755181 1664 False 1760.000000 1760 86.06000 786 2443 1 chr5D.!!$F1 1657
5 TraesCS3D01G439400 chr5B 65278089 65279752 1663 True 1696.000000 1696 85.37500 792 2439 1 chr5B.!!$R1 1647

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
128 129 0.032267 GGCGACTATCTTCCCCGAAG 59.968 60.0 0.0 0.0 40.65 3.79 F
465 466 0.040499 GGGGGAGGGTATTGTGCAAA 59.960 55.0 0.0 0.0 0.00 3.68 F
704 979 0.042581 TGTCCTGGGTGCTAGATCCA 59.957 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 3039 1.295357 CCGTCGTATGCCTTGTTGCA 61.295 55.000 0.0 0.0 46.94 4.08 R
2252 3724 3.328050 GCTATCCCAAGCCCTAACTACAT 59.672 47.826 0.0 0.0 36.45 2.29 R
2689 4608 0.032267 GAGTGCCGGTAGTAGGATGC 59.968 60.000 1.9 0.0 0.00 3.91 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
24 25 3.896317 GGATGTCGTCTAGCCATCC 57.104 57.895 12.01 12.01 45.58 3.51
29 30 1.837439 TGTCGTCTAGCCATCCCATTT 59.163 47.619 0.00 0.00 0.00 2.32
46 47 3.499918 CCATTTCCCTGATTATCTCGCAC 59.500 47.826 0.00 0.00 0.00 5.34
53 54 3.240884 CTGATTATCTCGCACGATCCAG 58.759 50.000 0.00 0.00 0.00 3.86
66 67 0.659957 GATCCAGTCGCAGCCAATTC 59.340 55.000 0.00 0.00 0.00 2.17
75 76 2.791170 CAGCCAATTCTGCTCTCCC 58.209 57.895 0.00 0.00 36.81 4.30
79 80 1.457346 CCAATTCTGCTCTCCCACAC 58.543 55.000 0.00 0.00 0.00 3.82
84 85 2.596338 TGCTCTCCCACACGACGA 60.596 61.111 0.00 0.00 0.00 4.20
86 87 2.916052 GCTCTCCCACACGACGACA 61.916 63.158 0.00 0.00 0.00 4.35
96 97 4.065281 CGACGACACCAGACCCCC 62.065 72.222 0.00 0.00 0.00 5.40
128 129 0.032267 GGCGACTATCTTCCCCGAAG 59.968 60.000 0.00 0.00 40.65 3.79
170 171 4.457496 ACAGGACGGCGATGGCAG 62.457 66.667 16.62 0.00 42.47 4.85
220 221 0.538977 TCCTTCTTCCACCTCGACGT 60.539 55.000 0.00 0.00 0.00 4.34
222 223 1.132643 CCTTCTTCCACCTCGACGTAG 59.867 57.143 0.00 0.00 0.00 3.51
225 226 2.082231 TCTTCCACCTCGACGTAGAAG 58.918 52.381 13.63 13.63 34.12 2.85
227 228 1.446907 TCCACCTCGACGTAGAAGTC 58.553 55.000 0.00 0.00 37.76 3.01
241 242 1.421646 AGAAGTCTGGACCCCACTTTG 59.578 52.381 6.61 0.00 0.00 2.77
268 269 0.399075 CAAAACGGTCCTACCTGGGT 59.601 55.000 0.00 0.00 35.66 4.51
374 375 1.637553 AGAAGATGTGTGCAAGGGGAT 59.362 47.619 0.00 0.00 0.00 3.85
376 377 0.994247 AGATGTGTGCAAGGGGATGA 59.006 50.000 0.00 0.00 0.00 2.92
448 449 9.868160 ATAAGAGAGATAACCTTTTATTTGGGG 57.132 33.333 0.00 0.00 0.00 4.96
449 450 6.673583 AGAGAGATAACCTTTTATTTGGGGG 58.326 40.000 0.00 0.00 0.00 5.40
463 464 3.422204 GGGGGAGGGTATTGTGCA 58.578 61.111 0.00 0.00 0.00 4.57
464 465 1.694856 GGGGGAGGGTATTGTGCAA 59.305 57.895 0.00 0.00 0.00 4.08
465 466 0.040499 GGGGGAGGGTATTGTGCAAA 59.960 55.000 0.00 0.00 0.00 3.68
466 467 1.551329 GGGGGAGGGTATTGTGCAAAA 60.551 52.381 0.00 0.00 0.00 2.44
467 468 2.252714 GGGGAGGGTATTGTGCAAAAA 58.747 47.619 0.00 0.00 0.00 1.94
468 469 2.233676 GGGGAGGGTATTGTGCAAAAAG 59.766 50.000 0.00 0.00 0.00 2.27
469 470 3.161866 GGGAGGGTATTGTGCAAAAAGA 58.838 45.455 0.00 0.00 0.00 2.52
470 471 3.576550 GGGAGGGTATTGTGCAAAAAGAA 59.423 43.478 0.00 0.00 0.00 2.52
471 472 4.321974 GGGAGGGTATTGTGCAAAAAGAAG 60.322 45.833 0.00 0.00 0.00 2.85
472 473 4.237724 GAGGGTATTGTGCAAAAAGAAGC 58.762 43.478 0.00 0.00 0.00 3.86
473 474 3.006859 AGGGTATTGTGCAAAAAGAAGCC 59.993 43.478 9.19 9.19 0.00 4.35
474 475 2.986479 GGTATTGTGCAAAAAGAAGCCG 59.014 45.455 0.00 0.00 0.00 5.52
475 476 2.153366 ATTGTGCAAAAAGAAGCCGG 57.847 45.000 0.00 0.00 0.00 6.13
476 477 0.820871 TTGTGCAAAAAGAAGCCGGT 59.179 45.000 1.90 0.00 0.00 5.28
477 478 0.102120 TGTGCAAAAAGAAGCCGGTG 59.898 50.000 1.90 0.00 0.00 4.94
478 479 1.067250 TGCAAAAAGAAGCCGGTGC 59.933 52.632 1.90 2.36 37.95 5.01
502 777 1.163420 AACGCTGATGCAACACGGAA 61.163 50.000 17.88 0.00 39.64 4.30
510 785 2.851263 TGCAACACGGAAAGGACTAT 57.149 45.000 0.00 0.00 0.00 2.12
543 818 6.016527 CACAGTTAGAAAACTTTTAGGACCCC 60.017 42.308 0.00 0.00 43.60 4.95
564 839 8.125978 ACCCCAATATGCATTTTCATAGTATG 57.874 34.615 3.54 3.55 32.99 2.39
565 840 7.949565 ACCCCAATATGCATTTTCATAGTATGA 59.050 33.333 3.54 8.84 37.55 2.15
566 841 8.464404 CCCCAATATGCATTTTCATAGTATGAG 58.536 37.037 12.50 3.26 40.94 2.90
567 842 8.464404 CCCAATATGCATTTTCATAGTATGAGG 58.536 37.037 12.50 6.36 40.94 3.86
568 843 9.234827 CCAATATGCATTTTCATAGTATGAGGA 57.765 33.333 12.50 6.49 40.94 3.71
571 846 7.741027 ATGCATTTTCATAGTATGAGGACTG 57.259 36.000 12.50 10.76 40.94 3.51
572 847 6.057533 TGCATTTTCATAGTATGAGGACTGG 58.942 40.000 12.50 4.21 40.94 4.00
573 848 5.049129 GCATTTTCATAGTATGAGGACTGGC 60.049 44.000 12.50 9.50 40.94 4.85
574 849 4.689612 TTTCATAGTATGAGGACTGGCC 57.310 45.455 12.50 0.00 40.94 5.36
575 850 3.328535 TCATAGTATGAGGACTGGCCA 57.671 47.619 4.71 4.71 40.02 5.36
576 851 3.234353 TCATAGTATGAGGACTGGCCAG 58.766 50.000 31.60 31.60 40.02 4.85
577 852 2.848678 TAGTATGAGGACTGGCCAGT 57.151 50.000 38.42 38.42 45.84 4.00
578 853 2.848678 AGTATGAGGACTGGCCAGTA 57.151 50.000 37.87 23.19 42.66 2.74
579 854 2.672098 AGTATGAGGACTGGCCAGTAG 58.328 52.381 37.87 14.23 42.66 2.57
580 855 1.069358 GTATGAGGACTGGCCAGTAGC 59.931 57.143 37.87 27.36 42.66 3.58
599 874 1.276622 CCTAGTGGCAAGGGTGTAGT 58.723 55.000 0.00 0.00 0.00 2.73
600 875 1.066143 CCTAGTGGCAAGGGTGTAGTG 60.066 57.143 0.00 0.00 0.00 2.74
601 876 0.981183 TAGTGGCAAGGGTGTAGTGG 59.019 55.000 0.00 0.00 0.00 4.00
602 877 1.971695 GTGGCAAGGGTGTAGTGGC 60.972 63.158 0.00 0.00 38.26 5.01
603 878 2.746277 GGCAAGGGTGTAGTGGCG 60.746 66.667 0.00 0.00 0.00 5.69
604 879 3.431725 GCAAGGGTGTAGTGGCGC 61.432 66.667 0.00 0.00 0.00 6.53
605 880 2.347490 CAAGGGTGTAGTGGCGCT 59.653 61.111 7.64 5.62 0.00 5.92
606 881 1.302511 CAAGGGTGTAGTGGCGCTT 60.303 57.895 5.61 0.00 38.20 4.68
607 882 1.003718 AAGGGTGTAGTGGCGCTTC 60.004 57.895 5.61 0.76 33.52 3.86
608 883 2.436115 GGGTGTAGTGGCGCTTCC 60.436 66.667 5.61 6.97 0.00 3.46
609 884 2.663196 GGTGTAGTGGCGCTTCCT 59.337 61.111 5.61 3.09 35.26 3.36
610 885 1.003718 GGTGTAGTGGCGCTTCCTT 60.004 57.895 5.61 0.00 35.26 3.36
611 886 1.298859 GGTGTAGTGGCGCTTCCTTG 61.299 60.000 5.61 0.00 35.26 3.61
612 887 1.671054 TGTAGTGGCGCTTCCTTGC 60.671 57.895 5.61 0.00 35.26 4.01
613 888 1.671054 GTAGTGGCGCTTCCTTGCA 60.671 57.895 5.61 0.00 35.26 4.08
614 889 1.375908 TAGTGGCGCTTCCTTGCAG 60.376 57.895 5.61 0.00 35.26 4.41
615 890 1.826340 TAGTGGCGCTTCCTTGCAGA 61.826 55.000 5.61 0.00 35.26 4.26
616 891 2.669569 TGGCGCTTCCTTGCAGAC 60.670 61.111 7.64 0.00 35.26 3.51
617 892 2.359230 GGCGCTTCCTTGCAGACT 60.359 61.111 7.64 0.00 0.00 3.24
618 893 2.684843 GGCGCTTCCTTGCAGACTG 61.685 63.158 7.64 0.00 0.00 3.51
619 894 2.684843 GCGCTTCCTTGCAGACTGG 61.685 63.158 0.00 0.00 0.00 4.00
620 895 2.037136 CGCTTCCTTGCAGACTGGG 61.037 63.158 4.26 0.00 0.00 4.45
621 896 1.676967 GCTTCCTTGCAGACTGGGG 60.677 63.158 4.26 0.00 0.00 4.96
622 897 1.763770 CTTCCTTGCAGACTGGGGT 59.236 57.895 4.26 0.00 0.00 4.95
623 898 0.111253 CTTCCTTGCAGACTGGGGTT 59.889 55.000 4.26 0.00 0.00 4.11
624 899 0.110486 TTCCTTGCAGACTGGGGTTC 59.890 55.000 4.26 0.00 0.00 3.62
625 900 1.672356 CCTTGCAGACTGGGGTTCG 60.672 63.158 4.26 0.00 0.00 3.95
626 901 1.371183 CTTGCAGACTGGGGTTCGA 59.629 57.895 4.26 0.00 0.00 3.71
627 902 0.951040 CTTGCAGACTGGGGTTCGAC 60.951 60.000 4.26 0.00 0.00 4.20
628 903 1.407656 TTGCAGACTGGGGTTCGACT 61.408 55.000 4.26 0.00 0.00 4.18
629 904 1.079750 GCAGACTGGGGTTCGACTC 60.080 63.158 4.26 0.00 0.00 3.36
630 905 1.592223 CAGACTGGGGTTCGACTCC 59.408 63.158 0.00 0.00 39.92 3.85
631 906 1.609794 AGACTGGGGTTCGACTCCC 60.610 63.158 14.53 14.53 38.22 4.30
632 907 2.995574 ACTGGGGTTCGACTCCCG 60.996 66.667 15.88 12.87 46.03 5.14
633 908 2.995574 CTGGGGTTCGACTCCCGT 60.996 66.667 15.88 0.00 46.03 5.28
634 909 2.993264 TGGGGTTCGACTCCCGTC 60.993 66.667 15.88 6.51 46.03 4.79
642 917 2.818714 GACTCCCGTCGAGAGCGA 60.819 66.667 3.36 0.00 45.71 4.93
657 932 2.297625 GCGAATTTCCGCGATCTCA 58.702 52.632 8.23 0.00 45.86 3.27
658 933 0.042967 GCGAATTTCCGCGATCTCAC 60.043 55.000 8.23 0.00 45.86 3.51
659 934 0.577269 CGAATTTCCGCGATCTCACC 59.423 55.000 8.23 0.00 0.00 4.02
660 935 0.938008 GAATTTCCGCGATCTCACCC 59.062 55.000 8.23 0.00 0.00 4.61
661 936 0.810031 AATTTCCGCGATCTCACCCG 60.810 55.000 8.23 0.00 0.00 5.28
662 937 2.644555 ATTTCCGCGATCTCACCCGG 62.645 60.000 8.23 0.00 41.97 5.73
665 940 4.873129 CGCGATCTCACCCGGGTG 62.873 72.222 42.62 42.62 46.64 4.61
666 941 4.530857 GCGATCTCACCCGGGTGG 62.531 72.222 45.13 35.55 45.43 4.61
677 952 3.588742 CCGGGTGGGCTTCTTTTAT 57.411 52.632 0.00 0.00 0.00 1.40
678 953 2.721425 CCGGGTGGGCTTCTTTTATA 57.279 50.000 0.00 0.00 0.00 0.98
679 954 3.007473 CCGGGTGGGCTTCTTTTATAA 57.993 47.619 0.00 0.00 0.00 0.98
680 955 3.358118 CCGGGTGGGCTTCTTTTATAAA 58.642 45.455 0.00 0.00 0.00 1.40
681 956 3.764972 CCGGGTGGGCTTCTTTTATAAAA 59.235 43.478 10.16 10.16 0.00 1.52
682 957 4.221041 CCGGGTGGGCTTCTTTTATAAAAA 59.779 41.667 11.62 0.00 0.00 1.94
683 958 5.105106 CCGGGTGGGCTTCTTTTATAAAAAT 60.105 40.000 11.62 0.00 0.00 1.82
684 959 6.097129 CCGGGTGGGCTTCTTTTATAAAAATA 59.903 38.462 11.62 1.05 0.00 1.40
685 960 7.201965 CCGGGTGGGCTTCTTTTATAAAAATAT 60.202 37.037 11.62 0.00 0.00 1.28
686 961 7.651704 CGGGTGGGCTTCTTTTATAAAAATATG 59.348 37.037 11.62 6.74 0.00 1.78
687 962 8.482943 GGGTGGGCTTCTTTTATAAAAATATGT 58.517 33.333 11.62 0.00 0.00 2.29
688 963 9.529325 GGTGGGCTTCTTTTATAAAAATATGTC 57.471 33.333 11.62 6.90 0.00 3.06
689 964 9.529325 GTGGGCTTCTTTTATAAAAATATGTCC 57.471 33.333 11.62 14.09 0.00 4.02
690 965 9.487442 TGGGCTTCTTTTATAAAAATATGTCCT 57.513 29.630 19.51 0.00 0.00 3.85
691 966 9.750125 GGGCTTCTTTTATAAAAATATGTCCTG 57.250 33.333 11.62 0.00 0.00 3.86
692 967 9.750125 GGCTTCTTTTATAAAAATATGTCCTGG 57.250 33.333 11.62 0.00 0.00 4.45
693 968 9.750125 GCTTCTTTTATAAAAATATGTCCTGGG 57.250 33.333 11.62 0.00 0.00 4.45
696 971 8.691797 TCTTTTATAAAAATATGTCCTGGGTGC 58.308 33.333 11.62 0.00 0.00 5.01
697 972 8.602472 TTTTATAAAAATATGTCCTGGGTGCT 57.398 30.769 8.20 0.00 0.00 4.40
698 973 9.702253 TTTTATAAAAATATGTCCTGGGTGCTA 57.298 29.630 8.20 0.00 0.00 3.49
699 974 8.918202 TTATAAAAATATGTCCTGGGTGCTAG 57.082 34.615 0.00 0.00 0.00 3.42
700 975 5.450818 AAAAATATGTCCTGGGTGCTAGA 57.549 39.130 0.00 0.00 0.00 2.43
701 976 5.653255 AAAATATGTCCTGGGTGCTAGAT 57.347 39.130 0.00 0.00 0.00 1.98
702 977 4.899352 AATATGTCCTGGGTGCTAGATC 57.101 45.455 0.00 0.00 0.00 2.75
703 978 1.428869 ATGTCCTGGGTGCTAGATCC 58.571 55.000 0.00 0.00 0.00 3.36
704 979 0.042581 TGTCCTGGGTGCTAGATCCA 59.957 55.000 0.00 0.00 0.00 3.41
705 980 1.204146 GTCCTGGGTGCTAGATCCAA 58.796 55.000 0.00 0.00 0.00 3.53
706 981 1.771255 GTCCTGGGTGCTAGATCCAAT 59.229 52.381 0.00 0.00 0.00 3.16
707 982 2.972713 GTCCTGGGTGCTAGATCCAATA 59.027 50.000 0.00 0.00 0.00 1.90
708 983 3.007398 GTCCTGGGTGCTAGATCCAATAG 59.993 52.174 0.00 0.00 0.00 1.73
709 984 3.116746 TCCTGGGTGCTAGATCCAATAGA 60.117 47.826 0.00 0.00 0.00 1.98
710 985 3.843027 CCTGGGTGCTAGATCCAATAGAT 59.157 47.826 0.00 0.00 38.17 1.98
747 1022 3.702045 AGTATGAGGACTAGCTTGACACC 59.298 47.826 1.04 2.77 0.00 4.16
823 1099 6.127814 GGTTAACAAAGCCATAAACCCTAGTC 60.128 42.308 8.10 0.00 32.09 2.59
975 2431 2.635856 GAGCTAAGCTGCACGTACGTG 61.636 57.143 37.44 37.44 43.43 4.49
1095 2558 0.739813 GCACGTTCGCCAAGGTCTAT 60.740 55.000 0.00 0.00 0.00 1.98
1110 2573 1.516386 CTATCTCGCGCACACGGTT 60.516 57.895 8.75 0.00 40.57 4.44
2236 3708 2.550277 TAGCTGGGATCAGTTGAGGA 57.450 50.000 0.00 0.00 42.78 3.71
2252 3724 2.996742 TGAGGATAGAGCTAGGGGATGA 59.003 50.000 0.00 0.00 0.00 2.92
2474 4393 4.724074 GGCAACCATCTGAATTCATTGA 57.276 40.909 18.47 10.50 0.00 2.57
2475 4394 4.427312 GGCAACCATCTGAATTCATTGAC 58.573 43.478 18.47 13.77 0.00 3.18
2476 4395 4.159135 GGCAACCATCTGAATTCATTGACT 59.841 41.667 18.47 5.27 0.00 3.41
2535 4454 2.903375 ACGAAGTTCTACTCCCTCCT 57.097 50.000 0.56 0.00 37.78 3.69
2600 4519 7.892609 ACTTCTTTAAGTTTGACCAAGTTTGT 58.107 30.769 0.00 0.00 43.60 2.83
2604 4523 8.889717 TCTTTAAGTTTGACCAAGTTTGTAGAG 58.110 33.333 0.00 0.00 30.16 2.43
2650 4569 8.768955 ACATCGAATTAGCTTCATTAGATTCAC 58.231 33.333 9.75 0.00 33.10 3.18
2656 4575 8.674263 ATTAGCTTCATTAGATTCACCAGAAG 57.326 34.615 0.00 0.00 37.14 2.85
2702 4621 3.139077 GGGAAAATGCATCCTACTACCG 58.861 50.000 0.00 0.00 37.14 4.02
2703 4622 3.139077 GGAAAATGCATCCTACTACCGG 58.861 50.000 0.00 0.00 33.98 5.28
2705 4624 1.128200 AATGCATCCTACTACCGGCA 58.872 50.000 0.00 0.00 35.54 5.69
2706 4625 0.393077 ATGCATCCTACTACCGGCAC 59.607 55.000 0.00 0.00 33.67 5.01
2707 4626 0.686441 TGCATCCTACTACCGGCACT 60.686 55.000 0.00 0.00 0.00 4.40
2708 4627 0.032267 GCATCCTACTACCGGCACTC 59.968 60.000 0.00 0.00 0.00 3.51
2709 4628 1.399714 CATCCTACTACCGGCACTCA 58.600 55.000 0.00 0.00 0.00 3.41
2713 4632 2.429610 TCCTACTACCGGCACTCATTTC 59.570 50.000 0.00 0.00 0.00 2.17
2714 4633 2.431057 CCTACTACCGGCACTCATTTCT 59.569 50.000 0.00 0.00 0.00 2.52
2715 4634 2.674796 ACTACCGGCACTCATTTCTC 57.325 50.000 0.00 0.00 0.00 2.87
2721 4896 4.632153 ACCGGCACTCATTTCTCATATAC 58.368 43.478 0.00 0.00 0.00 1.47
2727 4902 7.390027 GGCACTCATTTCTCATATACTACCAT 58.610 38.462 0.00 0.00 0.00 3.55
2829 5004 4.853924 AAAAGTGCAAGTGAACCCATAG 57.146 40.909 0.00 0.00 0.00 2.23
2830 5005 3.508845 AAGTGCAAGTGAACCCATAGT 57.491 42.857 0.00 0.00 0.00 2.12
2831 5006 3.508845 AGTGCAAGTGAACCCATAGTT 57.491 42.857 0.00 0.00 43.07 2.24
2832 5007 3.832527 AGTGCAAGTGAACCCATAGTTT 58.167 40.909 0.00 0.00 39.40 2.66
2833 5008 4.215109 AGTGCAAGTGAACCCATAGTTTT 58.785 39.130 0.00 0.00 39.40 2.43
2834 5009 4.037923 AGTGCAAGTGAACCCATAGTTTTG 59.962 41.667 0.00 0.00 39.40 2.44
2835 5010 3.957497 TGCAAGTGAACCCATAGTTTTGT 59.043 39.130 0.00 0.00 39.40 2.83
2836 5011 4.404073 TGCAAGTGAACCCATAGTTTTGTT 59.596 37.500 0.00 0.00 39.40 2.83
2837 5012 4.744631 GCAAGTGAACCCATAGTTTTGTTG 59.255 41.667 0.00 0.00 39.40 3.33
2838 5013 5.681179 GCAAGTGAACCCATAGTTTTGTTGT 60.681 40.000 0.00 0.00 39.40 3.32
2839 5014 6.460399 GCAAGTGAACCCATAGTTTTGTTGTA 60.460 38.462 0.00 0.00 39.40 2.41
2840 5015 7.657336 CAAGTGAACCCATAGTTTTGTTGTAT 58.343 34.615 0.00 0.00 39.40 2.29
2841 5016 7.833285 AGTGAACCCATAGTTTTGTTGTATT 57.167 32.000 0.00 0.00 39.40 1.89
2842 5017 8.245195 AGTGAACCCATAGTTTTGTTGTATTT 57.755 30.769 0.00 0.00 39.40 1.40
2843 5018 9.357161 AGTGAACCCATAGTTTTGTTGTATTTA 57.643 29.630 0.00 0.00 39.40 1.40
2877 5052 8.826710 CGTACATATTTGTATGTGAAATGGAGT 58.173 33.333 10.47 0.00 40.35 3.85
2881 5056 9.616634 CATATTTGTATGTGAAATGGAGTATGC 57.383 33.333 0.00 0.00 0.00 3.14
2882 5057 7.643569 ATTTGTATGTGAAATGGAGTATGCA 57.356 32.000 0.00 0.00 44.23 3.96
2883 5058 6.435430 TTGTATGTGAAATGGAGTATGCAC 57.565 37.500 0.00 0.00 41.42 4.57
2884 5059 5.495640 TGTATGTGAAATGGAGTATGCACA 58.504 37.500 0.00 0.00 41.42 4.57
2885 5060 5.942826 TGTATGTGAAATGGAGTATGCACAA 59.057 36.000 0.00 0.00 41.42 3.33
2886 5061 5.981088 ATGTGAAATGGAGTATGCACAAA 57.019 34.783 0.00 0.00 41.42 2.83
2887 5062 5.781210 TGTGAAATGGAGTATGCACAAAA 57.219 34.783 0.00 0.00 41.42 2.44
2888 5063 6.343716 TGTGAAATGGAGTATGCACAAAAT 57.656 33.333 0.00 0.00 41.42 1.82
2889 5064 7.459795 TGTGAAATGGAGTATGCACAAAATA 57.540 32.000 0.00 0.00 41.42 1.40
2890 5065 8.065473 TGTGAAATGGAGTATGCACAAAATAT 57.935 30.769 0.00 0.00 41.42 1.28
2891 5066 7.975058 TGTGAAATGGAGTATGCACAAAATATG 59.025 33.333 0.00 0.00 41.42 1.78
2892 5067 8.190122 GTGAAATGGAGTATGCACAAAATATGA 58.810 33.333 0.00 0.00 41.42 2.15
2893 5068 8.916062 TGAAATGGAGTATGCACAAAATATGAT 58.084 29.630 0.00 0.00 41.42 2.45
2896 5071 8.922931 ATGGAGTATGCACAAAATATGATACA 57.077 30.769 0.00 0.00 41.42 2.29
2897 5072 8.922931 TGGAGTATGCACAAAATATGATACAT 57.077 30.769 0.00 0.00 0.00 2.29
3081 5256 7.593644 GTGTAATGGTTGTGTTTATCCAACTTC 59.406 37.037 0.00 0.00 40.56 3.01
3136 5311 3.076621 ACACTATGAGGTGTTCGTACGA 58.923 45.455 15.28 15.28 46.71 3.43
3137 5312 3.120060 ACACTATGAGGTGTTCGTACGAC 60.120 47.826 19.36 13.59 46.71 4.34
3138 5313 2.094894 ACTATGAGGTGTTCGTACGACG 59.905 50.000 19.36 0.00 44.19 5.12
3139 5314 0.169672 ATGAGGTGTTCGTACGACGG 59.830 55.000 19.36 0.00 42.81 4.79
3140 5315 0.884259 TGAGGTGTTCGTACGACGGA 60.884 55.000 19.36 0.00 42.81 4.69
3154 5329 1.794437 CGACGGACGGTCTGATCTTTC 60.794 57.143 23.15 8.92 43.79 2.62
3185 5360 9.875675 GCTATCATAGAAAATTTAGAGTTGCAG 57.124 33.333 0.00 0.00 0.00 4.41
3282 5457 4.186926 TGTCTTATGAGCAGTGATTGAGC 58.813 43.478 0.00 0.00 0.00 4.26
3283 5458 3.244814 GTCTTATGAGCAGTGATTGAGCG 59.755 47.826 0.00 0.00 0.00 5.03
3293 5468 5.643777 AGCAGTGATTGAGCGTTACTTTATT 59.356 36.000 0.00 0.00 0.00 1.40
3294 5469 6.149474 AGCAGTGATTGAGCGTTACTTTATTT 59.851 34.615 0.00 0.00 0.00 1.40
3295 5470 7.333423 AGCAGTGATTGAGCGTTACTTTATTTA 59.667 33.333 0.00 0.00 0.00 1.40
3296 5471 8.122952 GCAGTGATTGAGCGTTACTTTATTTAT 58.877 33.333 0.00 0.00 0.00 1.40
3297 5472 9.425893 CAGTGATTGAGCGTTACTTTATTTATG 57.574 33.333 0.00 0.00 0.00 1.90
3298 5473 8.122952 AGTGATTGAGCGTTACTTTATTTATGC 58.877 33.333 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.719709 CTAGACGACATCCGCGTGA 59.280 57.895 4.92 1.95 42.77 4.35
1 2 1.939785 GCTAGACGACATCCGCGTG 60.940 63.158 4.92 0.00 42.77 5.34
2 3 2.408022 GCTAGACGACATCCGCGT 59.592 61.111 4.92 0.00 45.79 6.01
4 5 1.364171 ATGGCTAGACGACATCCGC 59.636 57.895 0.00 0.00 36.27 5.54
24 25 3.499918 GTGCGAGATAATCAGGGAAATGG 59.500 47.826 0.00 0.00 0.00 3.16
29 30 1.687563 TCGTGCGAGATAATCAGGGA 58.312 50.000 0.00 0.00 0.00 4.20
62 63 0.976641 TCGTGTGGGAGAGCAGAATT 59.023 50.000 0.00 0.00 0.00 2.17
66 67 2.126307 CGTCGTGTGGGAGAGCAG 60.126 66.667 0.00 0.00 0.00 4.24
75 76 1.660575 GGTCTGGTGTCGTCGTGTG 60.661 63.158 0.00 0.00 0.00 3.82
79 80 4.065281 GGGGGTCTGGTGTCGTCG 62.065 72.222 0.00 0.00 0.00 5.12
84 85 2.531942 GGGAAGGGGGTCTGGTGT 60.532 66.667 0.00 0.00 0.00 4.16
86 87 2.531942 GTGGGAAGGGGGTCTGGT 60.532 66.667 0.00 0.00 0.00 4.00
116 117 4.176752 GCGGCCTTCGGGGAAGAT 62.177 66.667 0.00 0.00 41.71 2.40
144 145 2.954868 CCGTCCTGTCGCGTATGC 60.955 66.667 5.77 0.00 37.91 3.14
146 147 4.547905 CGCCGTCCTGTCGCGTAT 62.548 66.667 5.77 0.00 0.00 3.06
153 154 4.457496 CTGCCATCGCCGTCCTGT 62.457 66.667 0.00 0.00 0.00 4.00
164 165 1.374343 CGTCTGCTGATTGCTGCCAT 61.374 55.000 0.00 0.00 43.37 4.40
183 184 1.202746 GGAGGAATGAGGATGGAGCAC 60.203 57.143 0.00 0.00 0.00 4.40
220 221 2.637872 CAAAGTGGGGTCCAGACTTCTA 59.362 50.000 5.46 0.00 32.34 2.10
222 223 1.143073 ACAAAGTGGGGTCCAGACTTC 59.857 52.381 5.46 0.00 32.34 3.01
225 226 3.324207 GACAAAGTGGGGTCCAGAC 57.676 57.895 0.00 0.00 32.34 3.51
241 242 0.323957 AGGACCGTTTTGCTAGGGAC 59.676 55.000 0.00 0.00 0.00 4.46
268 269 1.065926 TCCTGACGTCTACCTTCGCTA 60.066 52.381 17.92 0.00 0.00 4.26
319 320 1.821759 CACCTTTGACGGCCACACA 60.822 57.895 2.24 0.00 0.00 3.72
320 321 2.551912 CCACCTTTGACGGCCACAC 61.552 63.158 2.24 0.00 0.00 3.82
374 375 7.559897 AGGTTTTCTCTTCTAATTTTGTGGTCA 59.440 33.333 0.00 0.00 0.00 4.02
376 377 7.898014 AGGTTTTCTCTTCTAATTTTGTGGT 57.102 32.000 0.00 0.00 0.00 4.16
422 423 9.868160 CCCCAAATAAAAGGTTATCTCTCTTAT 57.132 33.333 0.00 0.00 0.00 1.73
423 424 8.279361 CCCCCAAATAAAAGGTTATCTCTCTTA 58.721 37.037 0.00 0.00 0.00 2.10
424 425 7.126061 CCCCCAAATAAAAGGTTATCTCTCTT 58.874 38.462 0.00 0.00 0.00 2.85
425 426 6.673583 CCCCCAAATAAAAGGTTATCTCTCT 58.326 40.000 0.00 0.00 0.00 3.10
426 427 6.961360 CCCCCAAATAAAAGGTTATCTCTC 57.039 41.667 0.00 0.00 0.00 3.20
446 447 0.040499 TTTGCACAATACCCTCCCCC 59.960 55.000 0.00 0.00 0.00 5.40
447 448 1.931635 TTTTGCACAATACCCTCCCC 58.068 50.000 0.00 0.00 0.00 4.81
448 449 3.161866 TCTTTTTGCACAATACCCTCCC 58.838 45.455 0.00 0.00 0.00 4.30
449 450 4.809673 CTTCTTTTTGCACAATACCCTCC 58.190 43.478 0.00 0.00 0.00 4.30
450 451 4.237724 GCTTCTTTTTGCACAATACCCTC 58.762 43.478 0.00 0.00 0.00 4.30
451 452 3.006859 GGCTTCTTTTTGCACAATACCCT 59.993 43.478 0.00 0.00 0.00 4.34
452 453 3.325870 GGCTTCTTTTTGCACAATACCC 58.674 45.455 0.00 0.00 0.00 3.69
453 454 2.986479 CGGCTTCTTTTTGCACAATACC 59.014 45.455 0.00 0.00 0.00 2.73
454 455 2.986479 CCGGCTTCTTTTTGCACAATAC 59.014 45.455 0.00 0.00 0.00 1.89
455 456 2.625790 ACCGGCTTCTTTTTGCACAATA 59.374 40.909 0.00 0.00 0.00 1.90
456 457 1.412343 ACCGGCTTCTTTTTGCACAAT 59.588 42.857 0.00 0.00 0.00 2.71
457 458 0.820871 ACCGGCTTCTTTTTGCACAA 59.179 45.000 0.00 0.00 0.00 3.33
458 459 0.102120 CACCGGCTTCTTTTTGCACA 59.898 50.000 0.00 0.00 0.00 4.57
459 460 1.215014 GCACCGGCTTCTTTTTGCAC 61.215 55.000 0.00 0.00 36.96 4.57
460 461 1.067250 GCACCGGCTTCTTTTTGCA 59.933 52.632 0.00 0.00 36.96 4.08
461 462 0.940991 CTGCACCGGCTTCTTTTTGC 60.941 55.000 0.00 0.97 41.91 3.68
462 463 0.385390 ACTGCACCGGCTTCTTTTTG 59.615 50.000 0.00 0.00 41.91 2.44
463 464 0.668535 GACTGCACCGGCTTCTTTTT 59.331 50.000 0.00 0.00 41.91 1.94
464 465 0.465460 TGACTGCACCGGCTTCTTTT 60.465 50.000 0.00 0.00 41.91 2.27
465 466 0.465460 TTGACTGCACCGGCTTCTTT 60.465 50.000 0.00 0.00 41.91 2.52
466 467 1.148273 TTGACTGCACCGGCTTCTT 59.852 52.632 0.00 0.00 41.91 2.52
467 468 1.598130 GTTGACTGCACCGGCTTCT 60.598 57.895 0.00 0.00 41.91 2.85
468 469 2.946762 GTTGACTGCACCGGCTTC 59.053 61.111 0.00 0.00 41.91 3.86
469 470 2.972505 CGTTGACTGCACCGGCTT 60.973 61.111 0.00 0.00 41.91 4.35
472 473 3.716006 CAGCGTTGACTGCACCGG 61.716 66.667 0.00 0.00 29.89 5.28
473 474 2.029288 ATCAGCGTTGACTGCACCG 61.029 57.895 3.33 0.00 37.59 4.94
474 475 1.499056 CATCAGCGTTGACTGCACC 59.501 57.895 3.33 0.00 37.59 5.01
475 476 1.154338 GCATCAGCGTTGACTGCAC 60.154 57.895 22.09 3.47 37.57 4.57
476 477 1.165284 TTGCATCAGCGTTGACTGCA 61.165 50.000 24.22 24.22 46.23 4.41
477 478 0.727122 GTTGCATCAGCGTTGACTGC 60.727 55.000 21.02 21.02 46.23 4.40
478 479 0.587768 TGTTGCATCAGCGTTGACTG 59.412 50.000 3.33 5.78 46.23 3.51
502 777 1.909302 CTGTGTCACCCCATAGTCCTT 59.091 52.381 0.00 0.00 0.00 3.36
510 785 3.201266 AGTTTTCTAACTGTGTCACCCCA 59.799 43.478 0.00 0.00 42.91 4.96
522 797 6.964807 TTGGGGTCCTAAAAGTTTTCTAAC 57.035 37.500 3.60 1.72 34.36 2.34
580 855 1.066143 CACTACACCCTTGCCACTAGG 60.066 57.143 0.00 0.00 38.23 3.02
581 856 1.066143 CCACTACACCCTTGCCACTAG 60.066 57.143 0.00 0.00 0.00 2.57
582 857 0.981183 CCACTACACCCTTGCCACTA 59.019 55.000 0.00 0.00 0.00 2.74
583 858 1.761174 CCACTACACCCTTGCCACT 59.239 57.895 0.00 0.00 0.00 4.00
584 859 1.971695 GCCACTACACCCTTGCCAC 60.972 63.158 0.00 0.00 0.00 5.01
585 860 2.434331 GCCACTACACCCTTGCCA 59.566 61.111 0.00 0.00 0.00 4.92
586 861 2.746277 CGCCACTACACCCTTGCC 60.746 66.667 0.00 0.00 0.00 4.52
587 862 3.431725 GCGCCACTACACCCTTGC 61.432 66.667 0.00 0.00 0.00 4.01
588 863 1.298859 GAAGCGCCACTACACCCTTG 61.299 60.000 2.29 0.00 0.00 3.61
589 864 1.003718 GAAGCGCCACTACACCCTT 60.004 57.895 2.29 0.00 0.00 3.95
590 865 2.663196 GAAGCGCCACTACACCCT 59.337 61.111 2.29 0.00 0.00 4.34
591 866 2.436115 GGAAGCGCCACTACACCC 60.436 66.667 2.29 0.00 36.34 4.61
592 867 1.003718 AAGGAAGCGCCACTACACC 60.004 57.895 2.29 0.00 40.02 4.16
593 868 1.912371 GCAAGGAAGCGCCACTACAC 61.912 60.000 2.29 0.00 40.02 2.90
594 869 1.671054 GCAAGGAAGCGCCACTACA 60.671 57.895 2.29 0.00 40.02 2.74
595 870 1.639298 CTGCAAGGAAGCGCCACTAC 61.639 60.000 2.29 0.00 40.02 2.73
596 871 1.375908 CTGCAAGGAAGCGCCACTA 60.376 57.895 2.29 0.00 40.02 2.74
597 872 2.670934 CTGCAAGGAAGCGCCACT 60.671 61.111 2.29 0.00 40.02 4.00
598 873 2.669569 TCTGCAAGGAAGCGCCAC 60.670 61.111 2.29 0.00 40.02 5.01
599 874 2.669569 GTCTGCAAGGAAGCGCCA 60.670 61.111 2.29 0.00 40.02 5.69
600 875 2.359230 AGTCTGCAAGGAAGCGCC 60.359 61.111 2.29 0.00 37.31 6.53
601 876 2.684843 CCAGTCTGCAAGGAAGCGC 61.685 63.158 0.00 0.00 37.31 5.92
602 877 2.037136 CCCAGTCTGCAAGGAAGCG 61.037 63.158 0.00 0.00 37.31 4.68
603 878 1.676967 CCCCAGTCTGCAAGGAAGC 60.677 63.158 0.00 0.00 0.00 3.86
604 879 0.111253 AACCCCAGTCTGCAAGGAAG 59.889 55.000 8.37 0.00 0.00 3.46
605 880 0.110486 GAACCCCAGTCTGCAAGGAA 59.890 55.000 8.37 0.00 0.00 3.36
606 881 1.761174 GAACCCCAGTCTGCAAGGA 59.239 57.895 8.37 0.00 0.00 3.36
607 882 1.672356 CGAACCCCAGTCTGCAAGG 60.672 63.158 0.00 0.00 0.00 3.61
608 883 0.951040 GTCGAACCCCAGTCTGCAAG 60.951 60.000 0.00 0.00 0.00 4.01
609 884 1.070786 GTCGAACCCCAGTCTGCAA 59.929 57.895 0.00 0.00 0.00 4.08
610 885 1.816863 GAGTCGAACCCCAGTCTGCA 61.817 60.000 0.00 0.00 0.00 4.41
611 886 1.079750 GAGTCGAACCCCAGTCTGC 60.080 63.158 0.00 0.00 0.00 4.26
612 887 1.592223 GGAGTCGAACCCCAGTCTG 59.408 63.158 0.00 0.00 0.00 3.51
613 888 1.609794 GGGAGTCGAACCCCAGTCT 60.610 63.158 16.23 0.00 42.24 3.24
614 889 2.979649 GGGAGTCGAACCCCAGTC 59.020 66.667 16.23 0.00 42.24 3.51
615 890 2.995574 CGGGAGTCGAACCCCAGT 60.996 66.667 19.76 0.00 44.09 4.00
616 891 2.995574 ACGGGAGTCGAACCCCAG 60.996 66.667 19.76 15.04 44.09 4.45
627 902 0.179134 AAATTCGCTCTCGACGGGAG 60.179 55.000 20.65 20.65 45.43 4.30
628 903 0.179145 GAAATTCGCTCTCGACGGGA 60.179 55.000 0.00 0.00 45.43 5.14
629 904 1.146358 GGAAATTCGCTCTCGACGGG 61.146 60.000 0.00 0.00 45.43 5.28
630 905 1.472276 CGGAAATTCGCTCTCGACGG 61.472 60.000 0.00 0.00 45.43 4.79
631 906 1.910880 CGGAAATTCGCTCTCGACG 59.089 57.895 0.00 0.00 45.43 5.12
640 915 0.577269 GGTGAGATCGCGGAAATTCG 59.423 55.000 6.13 0.00 0.00 3.34
641 916 0.938008 GGGTGAGATCGCGGAAATTC 59.062 55.000 6.13 0.00 0.00 2.17
642 917 0.810031 CGGGTGAGATCGCGGAAATT 60.810 55.000 6.13 0.00 39.47 1.82
643 918 1.227263 CGGGTGAGATCGCGGAAAT 60.227 57.895 6.13 0.00 39.47 2.17
644 919 2.183300 CGGGTGAGATCGCGGAAA 59.817 61.111 6.13 0.00 39.47 3.13
659 934 2.721425 TATAAAAGAAGCCCACCCGG 57.279 50.000 0.00 0.00 0.00 5.73
660 935 5.394224 TTTTTATAAAAGAAGCCCACCCG 57.606 39.130 10.40 0.00 0.00 5.28
661 936 8.482943 ACATATTTTTATAAAAGAAGCCCACCC 58.517 33.333 10.40 0.00 0.00 4.61
662 937 9.529325 GACATATTTTTATAAAAGAAGCCCACC 57.471 33.333 10.40 0.00 0.00 4.61
663 938 9.529325 GGACATATTTTTATAAAAGAAGCCCAC 57.471 33.333 10.40 1.73 0.00 4.61
664 939 9.487442 AGGACATATTTTTATAAAAGAAGCCCA 57.513 29.630 10.40 0.00 0.00 5.36
665 940 9.750125 CAGGACATATTTTTATAAAAGAAGCCC 57.250 33.333 10.40 9.09 0.00 5.19
666 941 9.750125 CCAGGACATATTTTTATAAAAGAAGCC 57.250 33.333 10.40 8.85 0.00 4.35
667 942 9.750125 CCCAGGACATATTTTTATAAAAGAAGC 57.250 33.333 10.40 1.33 0.00 3.86
670 945 8.691797 GCACCCAGGACATATTTTTATAAAAGA 58.308 33.333 10.40 4.31 0.00 2.52
671 946 8.695456 AGCACCCAGGACATATTTTTATAAAAG 58.305 33.333 10.40 2.66 0.00 2.27
672 947 8.602472 AGCACCCAGGACATATTTTTATAAAA 57.398 30.769 6.54 6.54 0.00 1.52
673 948 9.349713 CTAGCACCCAGGACATATTTTTATAAA 57.650 33.333 0.00 0.00 0.00 1.40
674 949 8.719596 TCTAGCACCCAGGACATATTTTTATAA 58.280 33.333 0.00 0.00 0.00 0.98
675 950 8.270137 TCTAGCACCCAGGACATATTTTTATA 57.730 34.615 0.00 0.00 0.00 0.98
676 951 7.149202 TCTAGCACCCAGGACATATTTTTAT 57.851 36.000 0.00 0.00 0.00 1.40
677 952 6.569127 TCTAGCACCCAGGACATATTTTTA 57.431 37.500 0.00 0.00 0.00 1.52
678 953 5.450818 TCTAGCACCCAGGACATATTTTT 57.549 39.130 0.00 0.00 0.00 1.94
679 954 5.456763 GGATCTAGCACCCAGGACATATTTT 60.457 44.000 0.00 0.00 0.00 1.82
680 955 4.042187 GGATCTAGCACCCAGGACATATTT 59.958 45.833 0.00 0.00 0.00 1.40
681 956 3.584848 GGATCTAGCACCCAGGACATATT 59.415 47.826 0.00 0.00 0.00 1.28
682 957 3.177228 GGATCTAGCACCCAGGACATAT 58.823 50.000 0.00 0.00 0.00 1.78
683 958 2.090775 TGGATCTAGCACCCAGGACATA 60.091 50.000 0.00 0.00 0.00 2.29
684 959 1.344393 TGGATCTAGCACCCAGGACAT 60.344 52.381 0.00 0.00 0.00 3.06
685 960 0.042581 TGGATCTAGCACCCAGGACA 59.957 55.000 0.00 0.00 0.00 4.02
686 961 1.204146 TTGGATCTAGCACCCAGGAC 58.796 55.000 0.00 0.00 0.00 3.85
687 962 2.196742 ATTGGATCTAGCACCCAGGA 57.803 50.000 0.00 0.00 0.00 3.86
688 963 3.242867 TCTATTGGATCTAGCACCCAGG 58.757 50.000 0.00 0.00 0.00 4.45
689 964 5.083533 GATCTATTGGATCTAGCACCCAG 57.916 47.826 2.96 0.00 45.38 4.45
719 994 9.197306 TGTCAAGCTAGTCCTCATACTATTAAA 57.803 33.333 0.00 0.00 31.70 1.52
720 995 8.630917 GTGTCAAGCTAGTCCTCATACTATTAA 58.369 37.037 0.00 0.00 31.70 1.40
721 996 7.230913 GGTGTCAAGCTAGTCCTCATACTATTA 59.769 40.741 0.00 0.00 31.70 0.98
722 997 6.041069 GGTGTCAAGCTAGTCCTCATACTATT 59.959 42.308 0.00 0.00 31.70 1.73
723 998 5.536916 GGTGTCAAGCTAGTCCTCATACTAT 59.463 44.000 0.00 0.00 31.70 2.12
724 999 4.888239 GGTGTCAAGCTAGTCCTCATACTA 59.112 45.833 0.00 0.00 0.00 1.82
725 1000 3.702045 GGTGTCAAGCTAGTCCTCATACT 59.298 47.826 0.00 0.00 0.00 2.12
726 1001 3.181474 GGGTGTCAAGCTAGTCCTCATAC 60.181 52.174 0.00 0.00 0.00 2.39
727 1002 3.031736 GGGTGTCAAGCTAGTCCTCATA 58.968 50.000 0.00 0.00 0.00 2.15
728 1003 1.834263 GGGTGTCAAGCTAGTCCTCAT 59.166 52.381 0.00 0.00 0.00 2.90
729 1004 1.203187 AGGGTGTCAAGCTAGTCCTCA 60.203 52.381 0.00 0.00 0.00 3.86
730 1005 1.478916 GAGGGTGTCAAGCTAGTCCTC 59.521 57.143 0.00 0.00 33.57 3.71
738 1013 1.207329 ACTATTCGGAGGGTGTCAAGC 59.793 52.381 0.00 0.00 0.00 4.01
747 1022 5.581085 CACAAGTCCTAAAACTATTCGGAGG 59.419 44.000 0.00 0.00 0.00 4.30
823 1099 5.636121 TGGCTGTGTAGTTGTTTAGATAACG 59.364 40.000 0.00 0.00 32.72 3.18
1095 2558 2.429571 GTAACCGTGTGCGCGAGA 60.430 61.111 12.10 0.00 36.67 4.04
1431 2894 1.448717 GAGGAGGTTCTGCGGCTTC 60.449 63.158 0.00 0.00 0.00 3.86
1576 3039 1.295357 CCGTCGTATGCCTTGTTGCA 61.295 55.000 0.00 0.00 46.94 4.08
2236 3708 5.544441 ACTACATCATCCCCTAGCTCTAT 57.456 43.478 0.00 0.00 0.00 1.98
2252 3724 3.328050 GCTATCCCAAGCCCTAACTACAT 59.672 47.826 0.00 0.00 36.45 2.29
2473 4392 8.987890 CGTAGGTCCTACTATCTTTACTTAGTC 58.012 40.741 23.74 0.00 35.06 2.59
2474 4393 8.709308 TCGTAGGTCCTACTATCTTTACTTAGT 58.291 37.037 23.74 0.00 35.06 2.24
2475 4394 9.553064 TTCGTAGGTCCTACTATCTTTACTTAG 57.447 37.037 23.74 6.47 35.06 2.18
2476 4395 9.905713 TTTCGTAGGTCCTACTATCTTTACTTA 57.094 33.333 23.74 0.00 35.06 2.24
2676 4595 7.364762 CGGTAGTAGGATGCATTTTCCCTATAT 60.365 40.741 13.39 9.09 34.21 0.86
2678 4597 5.280011 CGGTAGTAGGATGCATTTTCCCTAT 60.280 44.000 13.39 7.06 34.21 2.57
2679 4598 4.039973 CGGTAGTAGGATGCATTTTCCCTA 59.960 45.833 0.00 4.04 33.45 3.53
2680 4599 3.181454 CGGTAGTAGGATGCATTTTCCCT 60.181 47.826 0.00 5.17 33.45 4.20
2681 4600 3.139077 CGGTAGTAGGATGCATTTTCCC 58.861 50.000 0.00 0.00 33.45 3.97
2682 4601 3.139077 CCGGTAGTAGGATGCATTTTCC 58.861 50.000 0.00 0.00 0.00 3.13
2683 4602 2.548480 GCCGGTAGTAGGATGCATTTTC 59.452 50.000 1.90 0.00 0.00 2.29
2685 4604 1.488812 TGCCGGTAGTAGGATGCATTT 59.511 47.619 1.90 0.00 0.00 2.32
2686 4605 1.128200 TGCCGGTAGTAGGATGCATT 58.872 50.000 1.90 0.00 0.00 3.56
2687 4606 0.393077 GTGCCGGTAGTAGGATGCAT 59.607 55.000 1.90 0.00 0.00 3.96
2688 4607 0.686441 AGTGCCGGTAGTAGGATGCA 60.686 55.000 1.90 0.00 0.00 3.96
2689 4608 0.032267 GAGTGCCGGTAGTAGGATGC 59.968 60.000 1.90 0.00 0.00 3.91
2690 4609 1.399714 TGAGTGCCGGTAGTAGGATG 58.600 55.000 1.90 0.00 0.00 3.51
2691 4610 2.383442 ATGAGTGCCGGTAGTAGGAT 57.617 50.000 1.90 0.00 0.00 3.24
2693 4612 2.431057 AGAAATGAGTGCCGGTAGTAGG 59.569 50.000 1.90 0.00 0.00 3.18
2694 4613 3.130516 TGAGAAATGAGTGCCGGTAGTAG 59.869 47.826 1.90 0.00 0.00 2.57
2696 4615 1.899814 TGAGAAATGAGTGCCGGTAGT 59.100 47.619 1.90 0.00 0.00 2.73
2697 4616 2.672961 TGAGAAATGAGTGCCGGTAG 57.327 50.000 1.90 0.00 0.00 3.18
2698 4617 4.955811 ATATGAGAAATGAGTGCCGGTA 57.044 40.909 1.90 0.00 0.00 4.02
2699 4618 3.845781 ATATGAGAAATGAGTGCCGGT 57.154 42.857 1.90 0.00 0.00 5.28
2700 4619 4.887748 AGTATATGAGAAATGAGTGCCGG 58.112 43.478 0.00 0.00 0.00 6.13
2702 4621 6.759272 TGGTAGTATATGAGAAATGAGTGCC 58.241 40.000 0.00 0.00 0.00 5.01
2703 4622 7.875041 ACATGGTAGTATATGAGAAATGAGTGC 59.125 37.037 0.00 0.00 0.00 4.40
2705 4624 8.370940 CCACATGGTAGTATATGAGAAATGAGT 58.629 37.037 0.00 0.00 0.00 3.41
2706 4625 8.768957 CCACATGGTAGTATATGAGAAATGAG 57.231 38.462 0.00 0.00 0.00 2.90
2807 4982 4.649218 ACTATGGGTTCACTTGCACTTTTT 59.351 37.500 0.00 0.00 0.00 1.94
2808 4983 4.215109 ACTATGGGTTCACTTGCACTTTT 58.785 39.130 0.00 0.00 0.00 2.27
2809 4984 3.832527 ACTATGGGTTCACTTGCACTTT 58.167 40.909 0.00 0.00 0.00 2.66
2810 4985 3.508845 ACTATGGGTTCACTTGCACTT 57.491 42.857 0.00 0.00 0.00 3.16
2811 4986 3.508845 AACTATGGGTTCACTTGCACT 57.491 42.857 0.00 0.00 31.69 4.40
2812 4987 4.202111 ACAAAACTATGGGTTCACTTGCAC 60.202 41.667 0.00 0.00 37.12 4.57
2813 4988 3.957497 ACAAAACTATGGGTTCACTTGCA 59.043 39.130 0.00 0.00 37.12 4.08
2814 4989 4.584327 ACAAAACTATGGGTTCACTTGC 57.416 40.909 0.00 0.00 37.12 4.01
2815 4990 5.901552 ACAACAAAACTATGGGTTCACTTG 58.098 37.500 0.00 0.00 37.12 3.16
2816 4991 7.833285 ATACAACAAAACTATGGGTTCACTT 57.167 32.000 0.00 0.00 37.12 3.16
2817 4992 7.833285 AATACAACAAAACTATGGGTTCACT 57.167 32.000 0.00 0.00 37.12 3.41
2855 5030 9.616634 GCATACTCCATTTCACATACAAATATG 57.383 33.333 0.00 0.00 43.46 1.78
2856 5031 9.353431 TGCATACTCCATTTCACATACAAATAT 57.647 29.630 0.00 0.00 0.00 1.28
2857 5032 8.620416 GTGCATACTCCATTTCACATACAAATA 58.380 33.333 0.00 0.00 0.00 1.40
2858 5033 7.122501 TGTGCATACTCCATTTCACATACAAAT 59.877 33.333 0.00 0.00 30.58 2.32
2859 5034 6.432472 TGTGCATACTCCATTTCACATACAAA 59.568 34.615 0.00 0.00 30.58 2.83
2860 5035 5.942826 TGTGCATACTCCATTTCACATACAA 59.057 36.000 0.00 0.00 30.58 2.41
2861 5036 5.495640 TGTGCATACTCCATTTCACATACA 58.504 37.500 0.00 0.00 30.58 2.29
2862 5037 6.435430 TTGTGCATACTCCATTTCACATAC 57.565 37.500 0.00 0.00 34.88 2.39
2863 5038 7.459795 TTTTGTGCATACTCCATTTCACATA 57.540 32.000 0.00 0.00 34.88 2.29
2864 5039 5.981088 TTTGTGCATACTCCATTTCACAT 57.019 34.783 0.00 0.00 34.88 3.21
2865 5040 5.781210 TTTTGTGCATACTCCATTTCACA 57.219 34.783 0.00 0.00 33.29 3.58
2866 5041 8.190122 TCATATTTTGTGCATACTCCATTTCAC 58.810 33.333 0.00 0.00 0.00 3.18
2867 5042 8.291191 TCATATTTTGTGCATACTCCATTTCA 57.709 30.769 0.00 0.00 0.00 2.69
2870 5045 9.353431 TGTATCATATTTTGTGCATACTCCATT 57.647 29.630 0.00 0.00 0.00 3.16
2871 5046 8.922931 TGTATCATATTTTGTGCATACTCCAT 57.077 30.769 0.00 0.00 0.00 3.41
2872 5047 8.922931 ATGTATCATATTTTGTGCATACTCCA 57.077 30.769 0.00 0.00 0.00 3.86
3081 5256 7.228507 TCCTCATATTAAAATCACCACCGATTG 59.771 37.037 0.00 0.00 35.77 2.67
3129 5304 2.048222 AGACCGTCCGTCGTACGA 60.048 61.111 15.28 15.28 46.05 3.43
3136 5311 1.546961 AGAAAGATCAGACCGTCCGT 58.453 50.000 0.00 0.00 0.00 4.69
3137 5312 2.683867 ACTAGAAAGATCAGACCGTCCG 59.316 50.000 0.00 0.00 0.00 4.79
3138 5313 3.735514 GCACTAGAAAGATCAGACCGTCC 60.736 52.174 0.00 0.00 0.00 4.79
3139 5314 3.129638 AGCACTAGAAAGATCAGACCGTC 59.870 47.826 0.00 0.00 0.00 4.79
3140 5315 3.093057 AGCACTAGAAAGATCAGACCGT 58.907 45.455 0.00 0.00 0.00 4.83
3185 5360 6.015940 ACCTCATGTTTGAAAGGTCAATCTTC 60.016 38.462 0.00 0.00 43.29 2.87


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

AutoCloner maintained by Alex Coulton.