Multiple sequence alignment - TraesCS3A01G040300

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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 TraesCS3A01G040300 chr3A 100.000 2471 0 0 1 2471 21176972 21174502 0.000000e+00 4564.0
1 TraesCS3A01G040300 chr3A 86.694 744 86 7 788 1520 21290948 21291689 0.000000e+00 813.0
2 TraesCS3A01G040300 chr3A 87.059 510 53 8 978 1476 21315914 21316421 4.610000e-157 564.0
3 TraesCS3A01G040300 chr3A 81.835 556 79 12 44 578 21169137 21168583 4.850000e-122 448.0
4 TraesCS3A01G040300 chr3A 83.770 382 51 6 162 533 21277616 21277996 3.910000e-93 351.0
5 TraesCS3A01G040300 chr3A 82.888 374 55 4 140 504 21148755 21148382 6.590000e-86 327.0
6 TraesCS3A01G040300 chr3A 89.500 200 21 0 788 987 21314936 21315135 1.130000e-63 254.0
7 TraesCS3A01G040300 chr3A 83.832 167 15 9 44 201 21314019 21314182 5.510000e-32 148.0
8 TraesCS3A01G040300 chr3A 94.737 95 4 1 1861 1955 21211233 21211140 1.980000e-31 147.0
9 TraesCS3A01G040300 chr1D 86.846 745 82 6 790 1521 46361431 46362172 0.000000e+00 819.0
10 TraesCS3A01G040300 chr3D 85.714 742 84 12 788 1518 15100494 15099764 0.000000e+00 763.0
11 TraesCS3A01G040300 chr3D 92.857 420 30 0 788 1207 15211219 15211638 5.840000e-171 610.0
12 TraesCS3A01G040300 chr3D 83.591 518 72 6 44 548 15123706 15123189 8.000000e-130 473.0
13 TraesCS3A01G040300 chr3D 83.205 518 71 6 44 552 15201589 15201079 6.230000e-126 460.0
14 TraesCS3A01G040300 chr3D 92.038 314 25 0 1207 1520 15212645 15212958 2.260000e-120 442.0
15 TraesCS3A01G040300 chr3D 80.743 592 76 18 836 1412 15132350 15131782 6.320000e-116 427.0
16 TraesCS3A01G040300 chr3D 88.796 357 12 6 2143 2471 15213494 15213850 1.770000e-111 412.0
17 TraesCS3A01G040300 chr3D 79.926 543 78 19 787 1317 15219564 15220087 1.080000e-98 370.0
18 TraesCS3A01G040300 chr3D 79.920 503 67 12 44 537 15218710 15219187 3.040000e-89 339.0
19 TraesCS3A01G040300 chr3D 81.159 414 69 8 44 453 15101417 15101009 8.520000e-85 324.0
20 TraesCS3A01G040300 chr3D 84.969 326 22 4 1844 2150 15213122 15213439 3.090000e-79 305.0
21 TraesCS3A01G040300 chr3D 98.485 66 1 0 1533 1598 15213055 15213120 1.550000e-22 117.0
22 TraesCS3A01G040300 chr3D 91.071 56 5 0 44 99 15209426 15209481 2.640000e-10 76.8
23 TraesCS3A01G040300 chr3B 89.590 586 38 7 788 1364 22199424 22199995 0.000000e+00 723.0
24 TraesCS3A01G040300 chr3B 84.630 527 62 11 44 552 22165283 22164758 7.890000e-140 507.0
25 TraesCS3A01G040300 chr3B 81.958 521 75 6 44 552 22179907 22179394 8.170000e-115 424.0
26 TraesCS3A01G040300 chr3B 78.166 458 62 25 796 1245 22171060 22170633 8.770000e-65 257.0
27 TraesCS3A01G040300 chr3B 84.940 166 23 2 1334 1498 22169869 22169705 1.520000e-37 167.0
28 TraesCS3A01G040300 chr3B 85.455 165 16 4 44 201 22171898 22171735 5.470000e-37 165.0
29 TraesCS3A01G040300 chr3B 80.090 221 29 6 44 249 22198945 22199165 1.530000e-32 150.0
30 TraesCS3A01G040300 chr1B 86.222 675 68 16 862 1521 65703770 65703106 0.000000e+00 708.0
31 TraesCS3A01G040300 chr1B 98.425 254 2 2 1591 1843 302760077 302759825 1.740000e-121 446.0
32 TraesCS3A01G040300 chr4A 98.431 255 3 1 1590 1843 4195258 4195004 4.850000e-122 448.0
33 TraesCS3A01G040300 chr2A 97.348 264 5 2 1582 1843 529417920 529417657 4.850000e-122 448.0
34 TraesCS3A01G040300 chr2A 98.047 256 3 2 1590 1843 265273531 265273276 6.270000e-121 444.0
35 TraesCS3A01G040300 chr2A 98.039 255 3 2 1590 1843 756365348 756365601 2.260000e-120 442.0
36 TraesCS3A01G040300 chr7A 98.795 249 2 1 1596 1843 706650934 706650686 2.260000e-120 442.0
37 TraesCS3A01G040300 chr7A 98.400 250 3 1 1595 1843 345951577 345951826 2.920000e-119 438.0
38 TraesCS3A01G040300 chr5A 98.795 249 2 1 1596 1843 10553510 10553758 2.260000e-120 442.0
39 TraesCS3A01G040300 chr2B 98.795 249 2 1 1596 1843 150596749 150596997 2.260000e-120 442.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G040300 chr3A 21174502 21176972 2470 True 4564.000000 4564 100.000000 1 2471 1 chr3A.!!$R3 2470
1 TraesCS3A01G040300 chr3A 21290948 21291689 741 False 813.000000 813 86.694000 788 1520 1 chr3A.!!$F2 732
2 TraesCS3A01G040300 chr3A 21168583 21169137 554 True 448.000000 448 81.835000 44 578 1 chr3A.!!$R2 534
3 TraesCS3A01G040300 chr3A 21314019 21316421 2402 False 322.000000 564 86.797000 44 1476 3 chr3A.!!$F3 1432
4 TraesCS3A01G040300 chr1D 46361431 46362172 741 False 819.000000 819 86.846000 790 1521 1 chr1D.!!$F1 731
5 TraesCS3A01G040300 chr3D 15099764 15101417 1653 True 543.500000 763 83.436500 44 1518 2 chr3D.!!$R4 1474
6 TraesCS3A01G040300 chr3D 15123189 15123706 517 True 473.000000 473 83.591000 44 548 1 chr3D.!!$R1 504
7 TraesCS3A01G040300 chr3D 15201079 15201589 510 True 460.000000 460 83.205000 44 552 1 chr3D.!!$R3 508
8 TraesCS3A01G040300 chr3D 15131782 15132350 568 True 427.000000 427 80.743000 836 1412 1 chr3D.!!$R2 576
9 TraesCS3A01G040300 chr3D 15218710 15220087 1377 False 354.500000 370 79.923000 44 1317 2 chr3D.!!$F2 1273
10 TraesCS3A01G040300 chr3D 15209426 15213850 4424 False 327.133333 610 91.369333 44 2471 6 chr3D.!!$F1 2427
11 TraesCS3A01G040300 chr3B 22164758 22165283 525 True 507.000000 507 84.630000 44 552 1 chr3B.!!$R1 508
12 TraesCS3A01G040300 chr3B 22198945 22199995 1050 False 436.500000 723 84.840000 44 1364 2 chr3B.!!$F1 1320
13 TraesCS3A01G040300 chr3B 22179394 22179907 513 True 424.000000 424 81.958000 44 552 1 chr3B.!!$R2 508
14 TraesCS3A01G040300 chr1B 65703106 65703770 664 True 708.000000 708 86.222000 862 1521 1 chr1B.!!$R1 659

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
574 878 0.09473 GCGAAGATCCGTTTGGTTCG 59.905 55.0 6.64 6.64 41.6 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 5900 0.034756 AGCAGTTGTATGTCCGTGCA 59.965 50.0 0.0 0.0 33.24 4.57 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
17 18 2.663196 GTACTCCTTGCGGGCAGT 59.337 61.111 0.00 0.00 34.39 4.40
18 19 1.741770 GTACTCCTTGCGGGCAGTG 60.742 63.158 0.00 0.00 34.39 3.66
19 20 2.214216 TACTCCTTGCGGGCAGTGT 61.214 57.895 0.00 0.00 34.39 3.55
20 21 0.901114 TACTCCTTGCGGGCAGTGTA 60.901 55.000 0.00 0.00 34.39 2.90
21 22 1.448540 CTCCTTGCGGGCAGTGTAG 60.449 63.158 0.00 0.00 34.39 2.74
22 23 2.172483 CTCCTTGCGGGCAGTGTAGT 62.172 60.000 0.00 0.00 34.39 2.73
23 24 0.901114 TCCTTGCGGGCAGTGTAGTA 60.901 55.000 0.00 0.00 34.39 1.82
24 25 0.460284 CCTTGCGGGCAGTGTAGTAG 60.460 60.000 0.00 0.00 0.00 2.57
25 26 0.460284 CTTGCGGGCAGTGTAGTAGG 60.460 60.000 0.00 0.00 0.00 3.18
26 27 2.202892 GCGGGCAGTGTAGTAGGC 60.203 66.667 0.00 0.00 0.00 3.93
27 28 3.014085 GCGGGCAGTGTAGTAGGCA 62.014 63.158 0.00 0.00 0.00 4.75
28 29 1.823295 CGGGCAGTGTAGTAGGCAT 59.177 57.895 0.00 0.00 0.00 4.40
29 30 0.530650 CGGGCAGTGTAGTAGGCATG 60.531 60.000 0.00 0.00 0.00 4.06
30 31 0.541863 GGGCAGTGTAGTAGGCATGT 59.458 55.000 0.00 0.00 0.00 3.21
31 32 1.473434 GGGCAGTGTAGTAGGCATGTC 60.473 57.143 0.00 0.00 0.00 3.06
32 33 1.560923 GCAGTGTAGTAGGCATGTCG 58.439 55.000 0.00 0.00 0.00 4.35
33 34 1.560923 CAGTGTAGTAGGCATGTCGC 58.439 55.000 0.00 0.00 41.28 5.19
34 35 0.100682 AGTGTAGTAGGCATGTCGCG 59.899 55.000 0.00 0.00 43.84 5.87
35 36 0.870307 GTGTAGTAGGCATGTCGCGG 60.870 60.000 6.13 0.00 43.84 6.46
36 37 1.299926 GTAGTAGGCATGTCGCGGG 60.300 63.158 6.13 0.00 43.84 6.13
37 38 1.454295 TAGTAGGCATGTCGCGGGA 60.454 57.895 6.13 0.00 43.84 5.14
38 39 0.826256 TAGTAGGCATGTCGCGGGAT 60.826 55.000 6.13 0.00 43.84 3.85
39 40 1.956170 GTAGGCATGTCGCGGGATG 60.956 63.158 6.13 10.12 43.84 3.51
40 41 3.163832 TAGGCATGTCGCGGGATGG 62.164 63.158 6.13 0.00 43.84 3.51
48 49 4.794648 CGCGGGATGGCAGGGAAA 62.795 66.667 0.00 0.00 0.00 3.13
84 85 2.435938 TTGTTGAGATCGGCGCCC 60.436 61.111 23.46 7.02 0.00 6.13
113 114 4.980805 GACACCGGCCAGCGTGAA 62.981 66.667 18.68 0.00 34.05 3.18
118 119 1.153449 CCGGCCAGCGTGAAATAGA 60.153 57.895 2.24 0.00 0.00 1.98
119 120 1.154205 CCGGCCAGCGTGAAATAGAG 61.154 60.000 2.24 0.00 0.00 2.43
120 121 1.766143 CGGCCAGCGTGAAATAGAGC 61.766 60.000 2.24 0.00 0.00 4.09
201 220 5.723672 AGACGAAGAAATCCTTGTACTCA 57.276 39.130 0.00 0.00 34.68 3.41
264 349 0.250727 CCGAACTCACAACCATGGGT 60.251 55.000 18.09 6.57 37.65 4.51
318 409 1.261480 AGTGGACGAAGCAGTGAGAT 58.739 50.000 0.00 0.00 0.00 2.75
323 414 0.811915 ACGAAGCAGTGAGATACGCT 59.188 50.000 0.00 0.00 39.59 5.07
361 452 2.104111 TCAAAGGTCACCTTGATGTCGT 59.896 45.455 10.77 0.00 43.92 4.34
511 614 2.882301 CGGCGTGCGGTAGGTAAC 60.882 66.667 0.00 0.00 0.00 2.50
541 644 1.444119 GGCAGCGGCGATTGGAATTA 61.444 55.000 12.98 0.00 42.47 1.40
548 708 2.884639 CGGCGATTGGAATTAGGGATTT 59.115 45.455 0.00 0.00 0.00 2.17
552 780 5.278315 GGCGATTGGAATTAGGGATTTGTAC 60.278 44.000 0.00 0.00 0.00 2.90
554 782 6.513393 GCGATTGGAATTAGGGATTTGTACTG 60.513 42.308 0.00 0.00 0.00 2.74
559 787 3.985019 TTAGGGATTTGTACTGGCGAA 57.015 42.857 0.00 0.00 0.00 4.70
563 867 2.872858 GGGATTTGTACTGGCGAAGATC 59.127 50.000 0.00 0.00 0.00 2.75
573 877 0.446616 GGCGAAGATCCGTTTGGTTC 59.553 55.000 0.00 0.00 36.30 3.62
574 878 0.094730 GCGAAGATCCGTTTGGTTCG 59.905 55.000 6.64 6.64 41.60 3.95
575 879 1.425412 CGAAGATCCGTTTGGTTCGT 58.575 50.000 3.58 0.00 38.73 3.85
577 881 2.409975 GAAGATCCGTTTGGTTCGTGA 58.590 47.619 0.00 0.00 38.73 4.35
578 882 2.762535 AGATCCGTTTGGTTCGTGAT 57.237 45.000 0.00 0.00 38.73 3.06
579 883 2.346803 AGATCCGTTTGGTTCGTGATG 58.653 47.619 0.00 0.00 38.73 3.07
580 884 2.028476 AGATCCGTTTGGTTCGTGATGA 60.028 45.455 0.00 0.00 38.73 2.92
581 885 2.465860 TCCGTTTGGTTCGTGATGAT 57.534 45.000 0.00 0.00 36.30 2.45
582 886 3.596310 TCCGTTTGGTTCGTGATGATA 57.404 42.857 0.00 0.00 36.30 2.15
583 887 3.927854 TCCGTTTGGTTCGTGATGATAA 58.072 40.909 0.00 0.00 36.30 1.75
584 888 4.509616 TCCGTTTGGTTCGTGATGATAAT 58.490 39.130 0.00 0.00 36.30 1.28
585 889 4.938832 TCCGTTTGGTTCGTGATGATAATT 59.061 37.500 0.00 0.00 36.30 1.40
586 890 5.027737 CCGTTTGGTTCGTGATGATAATTG 58.972 41.667 0.00 0.00 0.00 2.32
587 891 5.163804 CCGTTTGGTTCGTGATGATAATTGA 60.164 40.000 0.00 0.00 0.00 2.57
588 892 6.458206 CCGTTTGGTTCGTGATGATAATTGAT 60.458 38.462 0.00 0.00 0.00 2.57
589 893 6.628856 CGTTTGGTTCGTGATGATAATTGATC 59.371 38.462 0.00 0.00 34.84 2.92
590 894 5.905480 TGGTTCGTGATGATAATTGATCG 57.095 39.130 0.00 0.00 37.38 3.69
591 895 5.356426 TGGTTCGTGATGATAATTGATCGT 58.644 37.500 0.00 0.00 37.38 3.73
592 896 5.462068 TGGTTCGTGATGATAATTGATCGTC 59.538 40.000 0.00 0.00 46.85 4.20
593 897 5.107453 GGTTCGTGATGATAATTGATCGTCC 60.107 44.000 1.43 0.00 46.34 4.79
594 898 4.226761 TCGTGATGATAATTGATCGTCCG 58.773 43.478 1.43 4.87 46.34 4.79
595 899 3.981416 CGTGATGATAATTGATCGTCCGT 59.019 43.478 1.43 0.00 46.34 4.69
596 900 4.088638 CGTGATGATAATTGATCGTCCGTC 59.911 45.833 1.43 0.00 46.34 4.79
597 901 4.088638 GTGATGATAATTGATCGTCCGTCG 59.911 45.833 1.43 0.00 46.34 5.12
617 921 2.609459 CGAAGCACCTATACAAAGCAGG 59.391 50.000 0.00 0.00 35.45 4.85
620 924 1.064685 GCACCTATACAAAGCAGGGGT 60.065 52.381 0.00 0.00 35.14 4.95
630 934 3.192466 CAAAGCAGGGGTATGTACGTAC 58.808 50.000 18.90 18.90 0.00 3.67
681 1054 1.001597 GCGGAATCAGACCTACCTACG 60.002 57.143 0.00 0.00 0.00 3.51
682 1055 2.295885 CGGAATCAGACCTACCTACGT 58.704 52.381 0.00 0.00 0.00 3.57
683 1056 3.470709 CGGAATCAGACCTACCTACGTA 58.529 50.000 0.00 0.00 0.00 3.57
687 1060 3.550437 TCAGACCTACCTACGTACTCC 57.450 52.381 0.00 0.00 0.00 3.85
695 1068 4.581824 CCTACCTACGTACTCCTATTGCAA 59.418 45.833 0.00 0.00 0.00 4.08
707 1080 9.219603 GTACTCCTATTGCAATCAATATAAGCA 57.780 33.333 16.86 0.00 42.43 3.91
710 1083 6.025896 CCTATTGCAATCAATATAAGCAGCG 58.974 40.000 16.86 0.00 42.43 5.18
711 1084 5.694231 ATTGCAATCAATATAAGCAGCGA 57.306 34.783 5.99 0.00 40.89 4.93
712 1085 4.737353 TGCAATCAATATAAGCAGCGAG 57.263 40.909 0.00 0.00 0.00 5.03
742 2597 4.334481 CGTCTGTAAACACCAGAAAACCTT 59.666 41.667 0.00 0.00 40.44 3.50
744 2599 6.033966 GTCTGTAAACACCAGAAAACCTTTG 58.966 40.000 0.00 0.00 40.44 2.77
745 2600 5.712917 TCTGTAAACACCAGAAAACCTTTGT 59.287 36.000 0.00 0.00 36.07 2.83
746 2601 6.885376 TCTGTAAACACCAGAAAACCTTTGTA 59.115 34.615 0.00 0.00 36.07 2.41
794 2706 3.369546 AGGTTTTCAAAACAGGATGCG 57.630 42.857 14.92 0.00 42.53 4.73
841 2753 3.307906 CGGTCCCCGTCAAGGTCA 61.308 66.667 0.00 0.00 42.73 4.02
1189 3913 1.599047 CTGGCGGACCTCAACATCT 59.401 57.895 0.00 0.00 36.63 2.90
1247 4982 0.689080 TGCCTGAGAGGGAGGATGAC 60.689 60.000 0.00 0.00 35.37 3.06
1267 5002 9.690428 GGATGACCATCTACGTGAAGACGTTAA 62.690 44.444 5.46 0.00 45.40 2.01
1296 5031 9.396022 GACAAATTCTATAATCTTGAGGTGGAA 57.604 33.333 0.00 0.00 0.00 3.53
1308 5043 0.460284 AGGTGGAAAGCGCAGATACG 60.460 55.000 11.47 0.00 0.00 3.06
1311 5046 2.545113 GGTGGAAAGCGCAGATACGATA 60.545 50.000 11.47 0.00 34.06 2.92
1381 5117 0.308993 GCAGCGCCTCATATTTGACC 59.691 55.000 2.29 0.00 0.00 4.02
1425 5161 4.330620 CGTACCTTGGCAACGTACAATATT 59.669 41.667 27.33 0.00 42.51 1.28
1512 5248 2.540101 GCACCATTAGATGTACTGTCGC 59.460 50.000 0.00 0.00 0.00 5.19
1521 5257 0.109735 TGTACTGTCGCGCTCTTCAG 60.110 55.000 5.56 10.77 0.00 3.02
1522 5258 0.798771 GTACTGTCGCGCTCTTCAGG 60.799 60.000 5.56 0.00 32.92 3.86
1523 5259 0.958876 TACTGTCGCGCTCTTCAGGA 60.959 55.000 5.56 2.22 32.92 3.86
1524 5260 1.080501 CTGTCGCGCTCTTCAGGAA 60.081 57.895 5.56 0.00 0.00 3.36
1525 5261 0.667487 CTGTCGCGCTCTTCAGGAAA 60.667 55.000 5.56 0.00 0.00 3.13
1526 5262 0.944311 TGTCGCGCTCTTCAGGAAAC 60.944 55.000 5.56 0.00 0.00 2.78
1527 5263 0.667792 GTCGCGCTCTTCAGGAAACT 60.668 55.000 5.56 0.00 46.44 2.66
1593 5413 8.514594 TGAAGCACTATTTGGAAGTTCTTAATG 58.485 33.333 2.25 2.13 31.83 1.90
1602 5422 9.628500 ATTTGGAAGTTCTTAATGTATACTCCC 57.372 33.333 4.17 0.00 0.00 4.30
1603 5423 7.989947 TGGAAGTTCTTAATGTATACTCCCT 57.010 36.000 4.17 0.00 0.00 4.20
1604 5424 8.019656 TGGAAGTTCTTAATGTATACTCCCTC 57.980 38.462 4.17 0.00 0.00 4.30
1605 5425 7.070821 TGGAAGTTCTTAATGTATACTCCCTCC 59.929 40.741 4.17 0.00 0.00 4.30
1606 5426 6.651975 AGTTCTTAATGTATACTCCCTCCG 57.348 41.667 4.17 0.00 0.00 4.63
1607 5427 6.134754 AGTTCTTAATGTATACTCCCTCCGT 58.865 40.000 4.17 0.00 0.00 4.69
1608 5428 6.610425 AGTTCTTAATGTATACTCCCTCCGTT 59.390 38.462 4.17 0.00 0.00 4.44
1609 5429 6.645790 TCTTAATGTATACTCCCTCCGTTC 57.354 41.667 4.17 0.00 0.00 3.95
1610 5430 5.537674 TCTTAATGTATACTCCCTCCGTTCC 59.462 44.000 4.17 0.00 0.00 3.62
1611 5431 2.832643 TGTATACTCCCTCCGTTCCA 57.167 50.000 4.17 0.00 0.00 3.53
1612 5432 2.381911 TGTATACTCCCTCCGTTCCAC 58.618 52.381 4.17 0.00 0.00 4.02
1613 5433 2.291735 TGTATACTCCCTCCGTTCCACA 60.292 50.000 4.17 0.00 0.00 4.17
1614 5434 1.946984 ATACTCCCTCCGTTCCACAA 58.053 50.000 0.00 0.00 0.00 3.33
1615 5435 1.946984 TACTCCCTCCGTTCCACAAT 58.053 50.000 0.00 0.00 0.00 2.71
1616 5436 0.324943 ACTCCCTCCGTTCCACAATG 59.675 55.000 0.00 0.00 0.00 2.82
1617 5437 0.324943 CTCCCTCCGTTCCACAATGT 59.675 55.000 0.00 0.00 0.00 2.71
1618 5438 1.553248 CTCCCTCCGTTCCACAATGTA 59.447 52.381 0.00 0.00 0.00 2.29
1619 5439 1.553248 TCCCTCCGTTCCACAATGTAG 59.447 52.381 0.00 0.00 0.00 2.74
1620 5440 1.369625 CCTCCGTTCCACAATGTAGC 58.630 55.000 0.00 0.00 0.00 3.58
1621 5441 0.999406 CTCCGTTCCACAATGTAGCG 59.001 55.000 0.00 0.00 0.00 4.26
1622 5442 1.017177 TCCGTTCCACAATGTAGCGC 61.017 55.000 0.00 0.00 0.00 5.92
1623 5443 1.295357 CCGTTCCACAATGTAGCGCA 61.295 55.000 11.47 0.00 0.00 6.09
1624 5444 0.726827 CGTTCCACAATGTAGCGCAT 59.273 50.000 11.47 0.00 40.03 4.73
1625 5445 1.930503 CGTTCCACAATGTAGCGCATA 59.069 47.619 11.47 0.00 36.67 3.14
1626 5446 2.543848 CGTTCCACAATGTAGCGCATAT 59.456 45.455 11.47 0.00 36.67 1.78
1627 5447 3.738791 CGTTCCACAATGTAGCGCATATA 59.261 43.478 11.47 0.00 36.67 0.86
1628 5448 4.143326 CGTTCCACAATGTAGCGCATATAG 60.143 45.833 11.47 0.00 36.67 1.31
1629 5449 4.864704 TCCACAATGTAGCGCATATAGA 57.135 40.909 11.47 0.00 36.67 1.98
1630 5450 5.405935 TCCACAATGTAGCGCATATAGAT 57.594 39.130 11.47 0.00 36.67 1.98
1631 5451 5.410924 TCCACAATGTAGCGCATATAGATC 58.589 41.667 11.47 0.00 36.67 2.75
1632 5452 5.185828 TCCACAATGTAGCGCATATAGATCT 59.814 40.000 11.47 0.00 36.67 2.75
1633 5453 5.871524 CCACAATGTAGCGCATATAGATCTT 59.128 40.000 11.47 0.00 36.67 2.40
1634 5454 6.369890 CCACAATGTAGCGCATATAGATCTTT 59.630 38.462 11.47 0.00 36.67 2.52
1635 5455 7.095060 CCACAATGTAGCGCATATAGATCTTTT 60.095 37.037 11.47 0.00 36.67 2.27
1636 5456 8.285394 CACAATGTAGCGCATATAGATCTTTTT 58.715 33.333 11.47 0.00 36.67 1.94
1637 5457 9.489084 ACAATGTAGCGCATATAGATCTTTTTA 57.511 29.630 11.47 0.00 36.67 1.52
1638 5458 9.964253 CAATGTAGCGCATATAGATCTTTTTAG 57.036 33.333 11.47 0.00 36.67 1.85
1639 5459 9.929180 AATGTAGCGCATATAGATCTTTTTAGA 57.071 29.630 11.47 0.00 36.67 2.10
1640 5460 9.929180 ATGTAGCGCATATAGATCTTTTTAGAA 57.071 29.630 11.47 0.00 35.74 2.10
1641 5461 9.411801 TGTAGCGCATATAGATCTTTTTAGAAG 57.588 33.333 11.47 0.00 0.00 2.85
1642 5462 9.413048 GTAGCGCATATAGATCTTTTTAGAAGT 57.587 33.333 11.47 0.00 0.00 3.01
1643 5463 8.527567 AGCGCATATAGATCTTTTTAGAAGTC 57.472 34.615 11.47 0.00 0.00 3.01
1644 5464 8.144478 AGCGCATATAGATCTTTTTAGAAGTCA 58.856 33.333 11.47 0.00 0.00 3.41
1645 5465 8.765219 GCGCATATAGATCTTTTTAGAAGTCAA 58.235 33.333 0.30 0.00 0.00 3.18
1679 5499 7.696992 ACTTTGACCAAGTTTGTAGAGAAAA 57.303 32.000 0.00 0.00 43.89 2.29
1680 5500 8.293699 ACTTTGACCAAGTTTGTAGAGAAAAT 57.706 30.769 0.00 0.00 43.89 1.82
1681 5501 8.406297 ACTTTGACCAAGTTTGTAGAGAAAATC 58.594 33.333 0.00 0.00 43.89 2.17
1682 5502 7.873719 TTGACCAAGTTTGTAGAGAAAATCA 57.126 32.000 0.00 0.00 0.00 2.57
1683 5503 8.463930 TTGACCAAGTTTGTAGAGAAAATCAT 57.536 30.769 0.00 0.00 0.00 2.45
1684 5504 9.567776 TTGACCAAGTTTGTAGAGAAAATCATA 57.432 29.630 0.00 0.00 0.00 2.15
1685 5505 9.739276 TGACCAAGTTTGTAGAGAAAATCATAT 57.261 29.630 0.00 0.00 0.00 1.78
1710 5530 9.692749 ATACATCTAGAATACCAAATACGTGTG 57.307 33.333 0.00 0.00 0.00 3.82
1711 5531 6.479001 ACATCTAGAATACCAAATACGTGTGC 59.521 38.462 0.00 0.00 0.00 4.57
1712 5532 6.216801 TCTAGAATACCAAATACGTGTGCT 57.783 37.500 0.00 0.00 0.00 4.40
1713 5533 6.636705 TCTAGAATACCAAATACGTGTGCTT 58.363 36.000 0.00 0.00 0.00 3.91
1714 5534 7.774134 TCTAGAATACCAAATACGTGTGCTTA 58.226 34.615 0.00 0.00 0.00 3.09
1715 5535 6.903883 AGAATACCAAATACGTGTGCTTAG 57.096 37.500 0.00 0.00 0.00 2.18
1716 5536 6.636705 AGAATACCAAATACGTGTGCTTAGA 58.363 36.000 0.00 0.00 0.00 2.10
1717 5537 7.272978 AGAATACCAAATACGTGTGCTTAGAT 58.727 34.615 0.00 0.00 0.00 1.98
1718 5538 8.418662 AGAATACCAAATACGTGTGCTTAGATA 58.581 33.333 0.00 0.00 0.00 1.98
1719 5539 7.941795 ATACCAAATACGTGTGCTTAGATAC 57.058 36.000 0.00 0.00 0.00 2.24
1720 5540 5.726397 ACCAAATACGTGTGCTTAGATACA 58.274 37.500 0.00 0.00 0.00 2.29
1721 5541 6.346096 ACCAAATACGTGTGCTTAGATACAT 58.654 36.000 0.00 0.00 0.00 2.29
1722 5542 6.479001 ACCAAATACGTGTGCTTAGATACATC 59.521 38.462 0.00 0.00 0.00 3.06
1723 5543 6.478673 CCAAATACGTGTGCTTAGATACATCA 59.521 38.462 0.00 0.00 0.00 3.07
1724 5544 7.337718 CAAATACGTGTGCTTAGATACATCAC 58.662 38.462 0.00 0.00 0.00 3.06
1725 5545 4.450082 ACGTGTGCTTAGATACATCACA 57.550 40.909 0.00 0.00 35.57 3.58
1726 5546 4.816392 ACGTGTGCTTAGATACATCACAA 58.184 39.130 0.00 0.00 39.07 3.33
1727 5547 4.625742 ACGTGTGCTTAGATACATCACAAC 59.374 41.667 0.00 0.00 39.07 3.32
1728 5548 4.625311 CGTGTGCTTAGATACATCACAACA 59.375 41.667 0.00 0.00 39.07 3.33
1729 5549 5.444613 CGTGTGCTTAGATACATCACAACAC 60.445 44.000 0.00 0.00 39.07 3.32
1730 5550 5.408299 GTGTGCTTAGATACATCACAACACA 59.592 40.000 0.00 0.00 39.07 3.72
1731 5551 6.092670 GTGTGCTTAGATACATCACAACACAT 59.907 38.462 0.00 0.00 39.07 3.21
1732 5552 7.277760 GTGTGCTTAGATACATCACAACACATA 59.722 37.037 0.00 0.00 39.07 2.29
1733 5553 7.277760 TGTGCTTAGATACATCACAACACATAC 59.722 37.037 0.00 0.00 35.08 2.39
1734 5554 7.492669 GTGCTTAGATACATCACAACACATACT 59.507 37.037 0.00 0.00 0.00 2.12
1735 5555 8.040727 TGCTTAGATACATCACAACACATACTT 58.959 33.333 0.00 0.00 0.00 2.24
1736 5556 8.883731 GCTTAGATACATCACAACACATACTTT 58.116 33.333 0.00 0.00 0.00 2.66
1738 5558 9.936759 TTAGATACATCACAACACATACTTTCA 57.063 29.630 0.00 0.00 0.00 2.69
1833 5653 7.851508 TGACTTTGTAGAAAATCTATATGCGC 58.148 34.615 0.00 0.00 30.76 6.09
1834 5654 7.710907 TGACTTTGTAGAAAATCTATATGCGCT 59.289 33.333 9.73 0.00 30.76 5.92
1835 5655 9.193133 GACTTTGTAGAAAATCTATATGCGCTA 57.807 33.333 9.73 0.00 30.76 4.26
1836 5656 8.979574 ACTTTGTAGAAAATCTATATGCGCTAC 58.020 33.333 9.73 0.00 30.76 3.58
1837 5657 8.880878 TTTGTAGAAAATCTATATGCGCTACA 57.119 30.769 9.73 0.63 36.25 2.74
1838 5658 9.489084 TTTGTAGAAAATCTATATGCGCTACAT 57.511 29.630 9.73 1.21 43.18 2.29
1839 5659 9.489084 TTGTAGAAAATCTATATGCGCTACATT 57.511 29.630 9.73 0.00 40.38 2.71
1840 5660 9.489084 TGTAGAAAATCTATATGCGCTACATTT 57.511 29.630 9.73 1.93 40.38 2.32
1841 5661 9.746711 GTAGAAAATCTATATGCGCTACATTTG 57.253 33.333 9.73 0.00 40.38 2.32
1842 5662 7.810658 AGAAAATCTATATGCGCTACATTTGG 58.189 34.615 9.73 0.00 40.38 3.28
1859 5679 7.200778 ACATTTGGTATTTTGAATTGTTGGC 57.799 32.000 0.00 0.00 0.00 4.52
1889 5709 6.907741 TGATTTTCAGTATCATTTTGCGTGA 58.092 32.000 0.00 0.00 0.00 4.35
1890 5710 7.537715 TGATTTTCAGTATCATTTTGCGTGAT 58.462 30.769 0.00 0.00 39.50 3.06
1903 5723 4.857871 TTGCGTGATAGCTACAATGAAC 57.142 40.909 0.00 0.00 38.13 3.18
1909 5729 3.199727 TGATAGCTACAATGAACTGGCCA 59.800 43.478 4.71 4.71 0.00 5.36
1967 5787 1.296577 GTGTTGCGACGTGTGTGTG 60.297 57.895 0.00 0.00 0.00 3.82
1984 5804 2.675844 GTGTGCATGACGCCAATTAGTA 59.324 45.455 0.00 0.00 41.33 1.82
2051 5890 1.366111 TTACTTTCATGCCGCGAGCC 61.366 55.000 8.23 0.00 42.71 4.70
2061 5900 0.671781 GCCGCGAGCCAATCTATGAT 60.672 55.000 8.23 0.00 34.35 2.45
2074 5913 4.871933 ATCTATGATGCACGGACATACA 57.128 40.909 0.00 0.00 0.00 2.29
2079 5918 1.062587 GATGCACGGACATACAACTGC 59.937 52.381 0.00 0.00 0.00 4.40
2085 5924 3.062639 CACGGACATACAACTGCTTGATC 59.937 47.826 0.00 0.00 0.00 2.92
2086 5925 2.609459 CGGACATACAACTGCTTGATCC 59.391 50.000 0.00 0.00 0.00 3.36
2105 5944 8.669394 TTGATCCGATAATATATAATAGCGCG 57.331 34.615 9.46 0.00 30.14 6.86
2110 5949 8.130469 TCCGATAATATATAATAGCGCGACAAA 58.870 33.333 12.10 0.00 30.14 2.83
2111 5950 8.912658 CCGATAATATATAATAGCGCGACAAAT 58.087 33.333 12.10 0.00 30.14 2.32
2112 5951 9.924408 CGATAATATATAATAGCGCGACAAATC 57.076 33.333 12.10 0.00 0.00 2.17
2143 5982 4.997905 TGCATGAAAGAGAAGAAAGACG 57.002 40.909 0.00 0.00 0.00 4.18
2144 5983 4.380531 TGCATGAAAGAGAAGAAAGACGT 58.619 39.130 0.00 0.00 0.00 4.34
2150 5989 6.055588 TGAAAGAGAAGAAAGACGTTTCCAT 58.944 36.000 0.00 0.00 42.84 3.41
2151 5990 6.542370 TGAAAGAGAAGAAAGACGTTTCCATT 59.458 34.615 0.00 0.00 42.84 3.16
2167 6071 9.280174 ACGTTTCCATTAAGAAGAACAGAATTA 57.720 29.630 0.00 0.00 0.00 1.40
2245 6150 0.320334 CACCGCCACACTACACATCA 60.320 55.000 0.00 0.00 0.00 3.07
2256 6162 6.757010 CCACACTACACATCATAAAGGTCTAC 59.243 42.308 0.00 0.00 0.00 2.59
2275 6181 2.406559 ACTCCTCAAGATAGCCTGCAT 58.593 47.619 0.00 0.00 0.00 3.96
2348 6271 7.385205 TCTGAACTAGTGAAGCTTTATTGTCAC 59.615 37.037 0.00 2.77 40.56 3.67
2412 6339 4.371624 AGACCAACAATCAGAATGGTGA 57.628 40.909 4.95 0.00 45.85 4.02
2432 6361 6.098124 TGGTGACCACATCTTTTCTTTTCATT 59.902 34.615 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.460284 CCTACTACACTGCCCGCAAG 60.460 60.000 0.00 0.00 0.00 4.01
7 8 1.594833 CCTACTACACTGCCCGCAA 59.405 57.895 0.00 0.00 0.00 4.85
8 9 3.014085 GCCTACTACACTGCCCGCA 62.014 63.158 0.00 0.00 0.00 5.69
9 10 2.202892 GCCTACTACACTGCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
10 11 0.530650 CATGCCTACTACACTGCCCG 60.531 60.000 0.00 0.00 0.00 6.13
11 12 0.541863 ACATGCCTACTACACTGCCC 59.458 55.000 0.00 0.00 0.00 5.36
12 13 1.802880 CGACATGCCTACTACACTGCC 60.803 57.143 0.00 0.00 0.00 4.85
13 14 1.560923 CGACATGCCTACTACACTGC 58.439 55.000 0.00 0.00 0.00 4.40
14 15 1.560923 GCGACATGCCTACTACACTG 58.439 55.000 0.00 0.00 37.76 3.66
15 16 0.100682 CGCGACATGCCTACTACACT 59.899 55.000 0.00 0.00 42.08 3.55
16 17 0.870307 CCGCGACATGCCTACTACAC 60.870 60.000 8.23 0.00 42.08 2.90
17 18 1.435925 CCGCGACATGCCTACTACA 59.564 57.895 8.23 0.00 42.08 2.74
18 19 1.299926 CCCGCGACATGCCTACTAC 60.300 63.158 8.23 0.00 42.08 2.73
19 20 0.826256 ATCCCGCGACATGCCTACTA 60.826 55.000 8.23 0.00 42.08 1.82
20 21 2.134287 ATCCCGCGACATGCCTACT 61.134 57.895 8.23 0.00 42.08 2.57
21 22 1.956170 CATCCCGCGACATGCCTAC 60.956 63.158 8.23 0.00 42.08 3.18
22 23 2.421314 CATCCCGCGACATGCCTA 59.579 61.111 8.23 0.00 42.08 3.93
23 24 4.552365 CCATCCCGCGACATGCCT 62.552 66.667 8.23 0.00 42.08 4.75
26 27 3.274586 CTGCCATCCCGCGACATG 61.275 66.667 8.23 9.11 0.00 3.21
27 28 4.552365 CCTGCCATCCCGCGACAT 62.552 66.667 8.23 0.00 0.00 3.06
31 32 4.794648 TTTCCCTGCCATCCCGCG 62.795 66.667 0.00 0.00 0.00 6.46
32 33 2.362375 TTTTCCCTGCCATCCCGC 60.362 61.111 0.00 0.00 0.00 6.13
33 34 2.052104 GGTTTTCCCTGCCATCCCG 61.052 63.158 0.00 0.00 0.00 5.14
34 35 1.078347 TGGTTTTCCCTGCCATCCC 59.922 57.895 0.00 0.00 39.73 3.85
35 36 0.541764 TGTGGTTTTCCCTGCCATCC 60.542 55.000 0.00 0.00 39.73 3.51
36 37 0.890683 CTGTGGTTTTCCCTGCCATC 59.109 55.000 0.00 0.00 39.73 3.51
37 38 1.187567 GCTGTGGTTTTCCCTGCCAT 61.188 55.000 0.00 0.00 39.73 4.40
38 39 1.832167 GCTGTGGTTTTCCCTGCCA 60.832 57.895 0.00 0.00 39.73 4.92
39 40 2.919494 CGCTGTGGTTTTCCCTGCC 61.919 63.158 0.00 0.00 39.73 4.85
40 41 0.887387 TACGCTGTGGTTTTCCCTGC 60.887 55.000 0.00 0.00 39.73 4.85
41 42 1.156736 CTACGCTGTGGTTTTCCCTG 58.843 55.000 0.00 0.00 39.73 4.45
42 43 0.763035 ACTACGCTGTGGTTTTCCCT 59.237 50.000 0.00 0.00 39.73 4.20
48 49 2.612212 CAACAAAGACTACGCTGTGGTT 59.388 45.455 0.02 0.00 0.00 3.67
113 114 2.093106 CCTACCGCTATCCGCTCTATT 58.907 52.381 0.00 0.00 36.13 1.73
118 119 2.600769 CCCCTACCGCTATCCGCT 60.601 66.667 0.00 0.00 36.13 5.52
119 120 4.374645 GCCCCTACCGCTATCCGC 62.375 72.222 0.00 0.00 35.03 5.54
120 121 2.600769 AGCCCCTACCGCTATCCG 60.601 66.667 0.00 0.00 33.91 4.18
201 220 4.473520 CCATTCACCGGCGGCTCT 62.474 66.667 28.71 3.00 0.00 4.09
298 389 1.040646 TCTCACTGCTTCGTCCACTT 58.959 50.000 0.00 0.00 0.00 3.16
327 418 3.589654 CTTTGAGCTCGCCGACCCA 62.590 63.158 9.64 0.00 0.00 4.51
342 433 2.930826 ACGACATCAAGGTGACCTTT 57.069 45.000 15.48 0.00 41.69 3.11
361 452 1.228124 CCGTCACCAGCCAAAGGAA 60.228 57.895 0.00 0.00 0.00 3.36
504 603 4.197498 GCTCGCCCGCGTTACCTA 62.197 66.667 4.92 0.00 40.74 3.08
541 644 1.906574 TCTTCGCCAGTACAAATCCCT 59.093 47.619 0.00 0.00 0.00 4.20
548 708 0.892755 AACGGATCTTCGCCAGTACA 59.107 50.000 0.00 0.00 0.00 2.90
552 780 0.673644 ACCAAACGGATCTTCGCCAG 60.674 55.000 0.00 0.00 0.00 4.85
554 782 0.446616 GAACCAAACGGATCTTCGCC 59.553 55.000 0.00 0.00 0.00 5.54
559 787 2.028476 TCATCACGAACCAAACGGATCT 60.028 45.455 0.00 0.00 34.93 2.75
563 867 4.875544 ATTATCATCACGAACCAAACGG 57.124 40.909 0.00 0.00 34.93 4.44
573 877 3.981416 ACGGACGATCAATTATCATCACG 59.019 43.478 0.00 0.00 33.87 4.35
574 878 4.088638 CGACGGACGATCAATTATCATCAC 59.911 45.833 0.00 0.00 45.77 3.06
575 879 4.023536 TCGACGGACGATCAATTATCATCA 60.024 41.667 0.00 0.00 46.45 3.07
577 881 4.499037 TCGACGGACGATCAATTATCAT 57.501 40.909 0.00 0.00 46.45 2.45
578 882 3.974871 TCGACGGACGATCAATTATCA 57.025 42.857 0.00 0.00 46.45 2.15
589 893 0.659427 TATAGGTGCTTCGACGGACG 59.341 55.000 7.45 0.00 44.09 4.79
590 894 1.402968 TGTATAGGTGCTTCGACGGAC 59.597 52.381 4.91 4.91 0.00 4.79
591 895 1.753930 TGTATAGGTGCTTCGACGGA 58.246 50.000 0.00 0.00 0.00 4.69
592 896 2.572191 TTGTATAGGTGCTTCGACGG 57.428 50.000 0.00 0.00 0.00 4.79
593 897 2.281762 GCTTTGTATAGGTGCTTCGACG 59.718 50.000 0.00 0.00 0.00 5.12
594 898 3.259064 TGCTTTGTATAGGTGCTTCGAC 58.741 45.455 0.00 0.00 0.00 4.20
595 899 3.521560 CTGCTTTGTATAGGTGCTTCGA 58.478 45.455 0.00 0.00 0.00 3.71
596 900 2.609459 CCTGCTTTGTATAGGTGCTTCG 59.391 50.000 0.00 0.00 0.00 3.79
597 901 2.945668 CCCTGCTTTGTATAGGTGCTTC 59.054 50.000 0.00 0.00 0.00 3.86
598 902 2.357154 CCCCTGCTTTGTATAGGTGCTT 60.357 50.000 0.00 0.00 0.00 3.91
599 903 1.212935 CCCCTGCTTTGTATAGGTGCT 59.787 52.381 0.00 0.00 0.00 4.40
600 904 1.064685 ACCCCTGCTTTGTATAGGTGC 60.065 52.381 0.00 0.00 0.00 5.01
601 905 4.141482 ACATACCCCTGCTTTGTATAGGTG 60.141 45.833 0.00 0.00 0.00 4.00
602 906 4.045022 ACATACCCCTGCTTTGTATAGGT 58.955 43.478 0.00 0.00 0.00 3.08
617 921 2.454055 GCTTCGTGTACGTACATACCC 58.546 52.381 29.58 16.38 38.63 3.69
641 984 4.201685 CCGCTGTTCCGATTACAACTAAAG 60.202 45.833 0.00 0.00 0.00 1.85
681 1054 9.219603 TGCTTATATTGATTGCAATAGGAGTAC 57.780 33.333 12.97 0.00 46.80 2.73
682 1055 9.440773 CTGCTTATATTGATTGCAATAGGAGTA 57.559 33.333 12.97 1.43 46.80 2.59
683 1056 7.094463 GCTGCTTATATTGATTGCAATAGGAGT 60.094 37.037 12.97 1.77 46.80 3.85
687 1060 6.834876 TCGCTGCTTATATTGATTGCAATAG 58.165 36.000 12.97 5.33 46.80 1.73
695 1068 3.070018 GGTGCTCGCTGCTTATATTGAT 58.930 45.455 0.00 0.00 43.37 2.57
710 1083 1.000506 TGTTTACAGACGAGGGTGCTC 59.999 52.381 0.00 0.00 0.00 4.26
711 1084 1.045407 TGTTTACAGACGAGGGTGCT 58.955 50.000 0.00 0.00 0.00 4.40
712 1085 1.145803 GTGTTTACAGACGAGGGTGC 58.854 55.000 0.00 0.00 0.00 5.01
728 2583 3.375922 CACGTACAAAGGTTTTCTGGTGT 59.624 43.478 0.00 0.00 0.00 4.16
742 2597 4.055360 CTGAATCAGGAACACACGTACAA 58.945 43.478 1.53 0.00 0.00 2.41
771 2643 4.023193 CGCATCCTGTTTTGAAAACCTACT 60.023 41.667 17.21 0.00 0.00 2.57
794 2706 2.531206 CGAGAGTCTCCACGAAAATCC 58.469 52.381 14.61 0.00 0.00 3.01
826 2738 1.302271 GGTTGACCTTGACGGGGAC 60.302 63.158 0.00 0.00 36.97 4.46
829 2741 0.676782 GATGGGTTGACCTTGACGGG 60.677 60.000 0.00 0.00 41.11 5.28
832 2744 2.224523 TGTCTGATGGGTTGACCTTGAC 60.225 50.000 0.00 3.28 41.11 3.18
841 2753 3.181329 TGTAGATGGTGTCTGATGGGTT 58.819 45.455 0.00 0.00 37.83 4.11
1189 3913 1.454847 GGAGGGTGGTGTTGTTGCA 60.455 57.895 0.00 0.00 0.00 4.08
1232 4964 1.577729 AGATGGTCATCCTCCCTCTCA 59.422 52.381 7.28 0.00 38.58 3.27
1267 5002 9.829507 CACCTCAAGATTATAGAATTTGTCTCT 57.170 33.333 0.00 0.00 37.84 3.10
1296 5031 7.480810 TGACATTATATATCGTATCTGCGCTT 58.519 34.615 9.73 0.00 0.00 4.68
1311 5046 7.528543 GCCCAGATCTTCTCCTTGACATTATAT 60.529 40.741 0.00 0.00 0.00 0.86
1381 5117 2.614057 GGTCATCCTCCATTAACTTGCG 59.386 50.000 0.00 0.00 0.00 4.85
1449 5185 3.388841 CCACGTAGGTTGAGCCCT 58.611 61.111 0.00 0.00 38.26 5.19
1512 5248 1.001406 ACTCCAGTTTCCTGAAGAGCG 59.999 52.381 0.00 0.00 41.50 5.03
1521 5257 2.973945 ACGAGCAATACTCCAGTTTCC 58.026 47.619 0.00 0.00 43.01 3.13
1522 5258 6.092259 ACATTAACGAGCAATACTCCAGTTTC 59.908 38.462 0.00 0.00 43.01 2.78
1523 5259 5.938125 ACATTAACGAGCAATACTCCAGTTT 59.062 36.000 0.00 0.00 43.01 2.66
1524 5260 5.351465 CACATTAACGAGCAATACTCCAGTT 59.649 40.000 0.00 0.00 43.01 3.16
1525 5261 4.870426 CACATTAACGAGCAATACTCCAGT 59.130 41.667 0.00 0.00 43.01 4.00
1526 5262 4.870426 ACACATTAACGAGCAATACTCCAG 59.130 41.667 0.00 0.00 43.01 3.86
1527 5263 4.827692 ACACATTAACGAGCAATACTCCA 58.172 39.130 0.00 0.00 43.01 3.86
1528 5264 5.447279 CCAACACATTAACGAGCAATACTCC 60.447 44.000 0.00 0.00 43.01 3.85
1530 5266 4.394920 CCCAACACATTAACGAGCAATACT 59.605 41.667 0.00 0.00 0.00 2.12
1593 5413 2.381911 TGTGGAACGGAGGGAGTATAC 58.618 52.381 0.00 0.00 42.39 1.47
1598 5418 0.324943 ACATTGTGGAACGGAGGGAG 59.675 55.000 0.00 0.00 42.39 4.30
1599 5419 1.553248 CTACATTGTGGAACGGAGGGA 59.447 52.381 0.00 0.00 42.39 4.20
1600 5420 2.012051 GCTACATTGTGGAACGGAGGG 61.012 57.143 4.11 0.00 42.39 4.30
1601 5421 1.369625 GCTACATTGTGGAACGGAGG 58.630 55.000 4.11 0.00 42.39 4.30
1602 5422 0.999406 CGCTACATTGTGGAACGGAG 59.001 55.000 4.11 0.00 42.39 4.63
1603 5423 1.017177 GCGCTACATTGTGGAACGGA 61.017 55.000 0.00 0.00 42.39 4.69
1604 5424 1.295357 TGCGCTACATTGTGGAACGG 61.295 55.000 9.73 0.00 42.39 4.44
1605 5425 0.726827 ATGCGCTACATTGTGGAACG 59.273 50.000 9.73 0.38 42.39 3.95
1606 5426 4.988540 TCTATATGCGCTACATTGTGGAAC 59.011 41.667 9.73 0.00 40.38 3.62
1607 5427 5.208463 TCTATATGCGCTACATTGTGGAA 57.792 39.130 9.73 0.00 40.38 3.53
1608 5428 4.864704 TCTATATGCGCTACATTGTGGA 57.135 40.909 9.73 0.00 40.38 4.02
1609 5429 5.414360 AGATCTATATGCGCTACATTGTGG 58.586 41.667 9.73 0.00 40.38 4.17
1610 5430 6.957984 AAGATCTATATGCGCTACATTGTG 57.042 37.500 9.73 0.00 40.38 3.33
1611 5431 7.969536 AAAAGATCTATATGCGCTACATTGT 57.030 32.000 9.73 0.00 40.38 2.71
1612 5432 9.964253 CTAAAAAGATCTATATGCGCTACATTG 57.036 33.333 9.73 0.26 40.38 2.82
1613 5433 9.929180 TCTAAAAAGATCTATATGCGCTACATT 57.071 29.630 9.73 0.00 40.38 2.71
1614 5434 9.929180 TTCTAAAAAGATCTATATGCGCTACAT 57.071 29.630 9.73 1.21 43.18 2.29
1615 5435 9.411801 CTTCTAAAAAGATCTATATGCGCTACA 57.588 33.333 9.73 0.00 0.00 2.74
1616 5436 9.413048 ACTTCTAAAAAGATCTATATGCGCTAC 57.587 33.333 9.73 0.00 0.00 3.58
1617 5437 9.627395 GACTTCTAAAAAGATCTATATGCGCTA 57.373 33.333 9.73 0.00 0.00 4.26
1618 5438 8.144478 TGACTTCTAAAAAGATCTATATGCGCT 58.856 33.333 9.73 0.00 0.00 5.92
1619 5439 8.299262 TGACTTCTAAAAAGATCTATATGCGC 57.701 34.615 0.00 0.00 0.00 6.09
1656 5476 8.405531 TGATTTTCTCTACAAACTTGGTCAAAG 58.594 33.333 0.00 0.00 42.07 2.77
1657 5477 8.287439 TGATTTTCTCTACAAACTTGGTCAAA 57.713 30.769 0.00 0.00 0.00 2.69
1658 5478 7.873719 TGATTTTCTCTACAAACTTGGTCAA 57.126 32.000 0.00 0.00 0.00 3.18
1659 5479 9.739276 ATATGATTTTCTCTACAAACTTGGTCA 57.261 29.630 0.00 0.00 0.00 4.02
1684 5504 9.692749 CACACGTATTTGGTATTCTAGATGTAT 57.307 33.333 0.00 0.00 0.00 2.29
1685 5505 7.650504 GCACACGTATTTGGTATTCTAGATGTA 59.349 37.037 0.00 0.00 0.00 2.29
1686 5506 6.479001 GCACACGTATTTGGTATTCTAGATGT 59.521 38.462 0.00 0.00 0.00 3.06
1687 5507 6.701841 AGCACACGTATTTGGTATTCTAGATG 59.298 38.462 0.00 0.00 0.00 2.90
1688 5508 6.817184 AGCACACGTATTTGGTATTCTAGAT 58.183 36.000 0.00 0.00 0.00 1.98
1689 5509 6.216801 AGCACACGTATTTGGTATTCTAGA 57.783 37.500 0.00 0.00 0.00 2.43
1690 5510 6.903883 AAGCACACGTATTTGGTATTCTAG 57.096 37.500 0.00 0.00 0.00 2.43
1691 5511 7.774134 TCTAAGCACACGTATTTGGTATTCTA 58.226 34.615 0.00 0.00 0.00 2.10
1692 5512 6.636705 TCTAAGCACACGTATTTGGTATTCT 58.363 36.000 0.00 0.00 0.00 2.40
1693 5513 6.897259 TCTAAGCACACGTATTTGGTATTC 57.103 37.500 0.00 0.00 0.00 1.75
1694 5514 7.982919 TGTATCTAAGCACACGTATTTGGTATT 59.017 33.333 0.00 0.00 0.00 1.89
1695 5515 7.494211 TGTATCTAAGCACACGTATTTGGTAT 58.506 34.615 0.00 0.00 0.00 2.73
1696 5516 6.865411 TGTATCTAAGCACACGTATTTGGTA 58.135 36.000 0.00 0.00 0.00 3.25
1697 5517 5.726397 TGTATCTAAGCACACGTATTTGGT 58.274 37.500 0.00 0.00 0.00 3.67
1698 5518 6.478673 TGATGTATCTAAGCACACGTATTTGG 59.521 38.462 0.00 0.00 0.00 3.28
1699 5519 7.010091 TGTGATGTATCTAAGCACACGTATTTG 59.990 37.037 0.00 0.00 34.85 2.32
1700 5520 7.039270 TGTGATGTATCTAAGCACACGTATTT 58.961 34.615 0.00 0.00 34.85 1.40
1701 5521 6.569780 TGTGATGTATCTAAGCACACGTATT 58.430 36.000 0.00 0.00 34.85 1.89
1702 5522 6.144078 TGTGATGTATCTAAGCACACGTAT 57.856 37.500 0.00 0.00 34.85 3.06
1703 5523 5.570234 TGTGATGTATCTAAGCACACGTA 57.430 39.130 0.00 0.00 34.85 3.57
1704 5524 4.450082 TGTGATGTATCTAAGCACACGT 57.550 40.909 0.00 0.00 34.85 4.49
1705 5525 4.625311 TGTTGTGATGTATCTAAGCACACG 59.375 41.667 0.00 0.00 38.98 4.49
1706 5526 5.408299 TGTGTTGTGATGTATCTAAGCACAC 59.592 40.000 0.00 0.00 38.98 3.82
1707 5527 5.546526 TGTGTTGTGATGTATCTAAGCACA 58.453 37.500 10.51 10.51 37.66 4.57
1708 5528 6.668541 ATGTGTTGTGATGTATCTAAGCAC 57.331 37.500 0.00 0.00 0.00 4.40
1709 5529 7.555965 AGTATGTGTTGTGATGTATCTAAGCA 58.444 34.615 0.00 0.00 0.00 3.91
1710 5530 8.425577 AAGTATGTGTTGTGATGTATCTAAGC 57.574 34.615 0.00 0.00 0.00 3.09
1712 5532 9.936759 TGAAAGTATGTGTTGTGATGTATCTAA 57.063 29.630 0.00 0.00 0.00 2.10
1771 5591 9.628500 ACTTTGACCAAGTTTATAGAGAAAACT 57.372 29.630 0.00 0.00 43.89 2.66
1807 5627 8.335356 GCGCATATAGATTTTCTACAAAGTCAA 58.665 33.333 0.30 0.00 32.03 3.18
1808 5628 7.710907 AGCGCATATAGATTTTCTACAAAGTCA 59.289 33.333 11.47 0.00 32.03 3.41
1809 5629 8.077836 AGCGCATATAGATTTTCTACAAAGTC 57.922 34.615 11.47 0.00 30.79 3.01
1810 5630 8.979574 GTAGCGCATATAGATTTTCTACAAAGT 58.020 33.333 11.47 0.00 30.79 2.66
1811 5631 8.978539 TGTAGCGCATATAGATTTTCTACAAAG 58.021 33.333 11.47 0.00 34.20 2.77
1812 5632 8.880878 TGTAGCGCATATAGATTTTCTACAAA 57.119 30.769 11.47 0.00 34.20 2.83
1813 5633 9.489084 AATGTAGCGCATATAGATTTTCTACAA 57.511 29.630 11.47 0.00 38.67 2.41
1814 5634 9.489084 AAATGTAGCGCATATAGATTTTCTACA 57.511 29.630 11.47 4.87 39.25 2.74
1815 5635 9.746711 CAAATGTAGCGCATATAGATTTTCTAC 57.253 33.333 11.47 0.00 36.67 2.59
1816 5636 8.935844 CCAAATGTAGCGCATATAGATTTTCTA 58.064 33.333 11.47 0.00 36.67 2.10
1817 5637 7.445402 ACCAAATGTAGCGCATATAGATTTTCT 59.555 33.333 11.47 0.00 36.67 2.52
1818 5638 7.584987 ACCAAATGTAGCGCATATAGATTTTC 58.415 34.615 11.47 0.00 36.67 2.29
1819 5639 7.510549 ACCAAATGTAGCGCATATAGATTTT 57.489 32.000 11.47 0.00 36.67 1.82
1820 5640 8.792830 ATACCAAATGTAGCGCATATAGATTT 57.207 30.769 11.47 7.30 36.67 2.17
1821 5641 8.792830 AATACCAAATGTAGCGCATATAGATT 57.207 30.769 11.47 0.41 36.67 2.40
1822 5642 8.792830 AAATACCAAATGTAGCGCATATAGAT 57.207 30.769 11.47 0.00 36.67 1.98
1823 5643 8.503196 CAAAATACCAAATGTAGCGCATATAGA 58.497 33.333 11.47 0.00 36.67 1.98
1824 5644 8.503196 TCAAAATACCAAATGTAGCGCATATAG 58.497 33.333 11.47 0.00 36.67 1.31
1825 5645 8.384607 TCAAAATACCAAATGTAGCGCATATA 57.615 30.769 11.47 0.00 36.67 0.86
1826 5646 7.270757 TCAAAATACCAAATGTAGCGCATAT 57.729 32.000 11.47 0.00 36.67 1.78
1827 5647 6.685527 TCAAAATACCAAATGTAGCGCATA 57.314 33.333 11.47 0.00 36.67 3.14
1828 5648 5.574891 TCAAAATACCAAATGTAGCGCAT 57.425 34.783 11.47 0.00 40.03 4.73
1829 5649 5.378292 TTCAAAATACCAAATGTAGCGCA 57.622 34.783 11.47 0.00 31.61 6.09
1830 5650 6.310224 ACAATTCAAAATACCAAATGTAGCGC 59.690 34.615 0.00 0.00 31.61 5.92
1831 5651 7.810766 ACAATTCAAAATACCAAATGTAGCG 57.189 32.000 0.00 0.00 31.61 4.26
1832 5652 8.442384 CCAACAATTCAAAATACCAAATGTAGC 58.558 33.333 0.00 0.00 31.61 3.58
1833 5653 8.442384 GCCAACAATTCAAAATACCAAATGTAG 58.558 33.333 0.00 0.00 31.61 2.74
1834 5654 7.116948 CGCCAACAATTCAAAATACCAAATGTA 59.883 33.333 0.00 0.00 0.00 2.29
1835 5655 6.073331 CGCCAACAATTCAAAATACCAAATGT 60.073 34.615 0.00 0.00 0.00 2.71
1836 5656 6.073331 ACGCCAACAATTCAAAATACCAAATG 60.073 34.615 0.00 0.00 0.00 2.32
1837 5657 5.994668 ACGCCAACAATTCAAAATACCAAAT 59.005 32.000 0.00 0.00 0.00 2.32
1838 5658 5.360591 ACGCCAACAATTCAAAATACCAAA 58.639 33.333 0.00 0.00 0.00 3.28
1839 5659 4.950050 ACGCCAACAATTCAAAATACCAA 58.050 34.783 0.00 0.00 0.00 3.67
1840 5660 4.592485 ACGCCAACAATTCAAAATACCA 57.408 36.364 0.00 0.00 0.00 3.25
1841 5661 7.329717 TCATTAACGCCAACAATTCAAAATACC 59.670 33.333 0.00 0.00 0.00 2.73
1842 5662 8.233692 TCATTAACGCCAACAATTCAAAATAC 57.766 30.769 0.00 0.00 0.00 1.89
1885 5705 3.246226 GCCAGTTCATTGTAGCTATCACG 59.754 47.826 0.00 0.00 0.00 4.35
1889 5709 3.931907 TGGCCAGTTCATTGTAGCTAT 57.068 42.857 0.00 0.00 0.00 2.97
1890 5710 3.244735 TGTTGGCCAGTTCATTGTAGCTA 60.245 43.478 5.11 0.00 0.00 3.32
1903 5723 2.101249 ACAATGTCAAGTTGTTGGCCAG 59.899 45.455 5.11 0.00 37.49 4.85
1932 5752 7.913297 GTCGCAACACACAACCATATATTATTT 59.087 33.333 0.00 0.00 0.00 1.40
1937 5757 3.308595 CGTCGCAACACACAACCATATAT 59.691 43.478 0.00 0.00 0.00 0.86
1951 5771 2.350760 GCACACACACGTCGCAAC 60.351 61.111 0.00 0.00 0.00 4.17
1952 5772 2.176926 ATGCACACACACGTCGCAA 61.177 52.632 0.00 0.00 35.98 4.85
1953 5773 2.587473 ATGCACACACACGTCGCA 60.587 55.556 0.00 0.00 36.95 5.10
1967 5787 1.931172 ACGTACTAATTGGCGTCATGC 59.069 47.619 0.00 0.00 45.38 4.06
2034 5873 3.127533 GGCTCGCGGCATGAAAGT 61.128 61.111 18.87 0.00 44.01 2.66
2043 5882 1.073964 CATCATAGATTGGCTCGCGG 58.926 55.000 6.13 0.00 0.00 6.46
2051 5890 4.990426 TGTATGTCCGTGCATCATAGATTG 59.010 41.667 0.00 0.00 0.00 2.67
2061 5900 0.034756 AGCAGTTGTATGTCCGTGCA 59.965 50.000 0.00 0.00 33.24 4.57
2079 5918 8.789743 CGCGCTATTATATATTATCGGATCAAG 58.210 37.037 5.56 0.00 0.00 3.02
2085 5924 7.847166 TTGTCGCGCTATTATATATTATCGG 57.153 36.000 5.56 2.38 0.00 4.18
2086 5925 9.924408 GATTTGTCGCGCTATTATATATTATCG 57.076 33.333 5.56 4.38 0.00 2.92
2102 5941 0.109827 TTGCCATGTGATTTGTCGCG 60.110 50.000 0.00 0.00 0.00 5.87
2105 5944 2.962125 TGCATTGCCATGTGATTTGTC 58.038 42.857 6.12 0.00 32.28 3.18
2110 5949 3.449377 TCTTTCATGCATTGCCATGTGAT 59.551 39.130 6.12 0.00 42.44 3.06
2111 5950 2.826725 TCTTTCATGCATTGCCATGTGA 59.173 40.909 6.12 2.91 42.44 3.58
2112 5951 3.119280 TCTCTTTCATGCATTGCCATGTG 60.119 43.478 6.12 0.51 42.44 3.21
2113 5952 3.093814 TCTCTTTCATGCATTGCCATGT 58.906 40.909 6.12 0.00 42.44 3.21
2114 5953 3.793797 TCTCTTTCATGCATTGCCATG 57.206 42.857 6.12 9.93 43.04 3.66
2199 6104 3.336509 TCCCCCTTGGAATGACAAAAA 57.663 42.857 0.00 0.00 41.40 1.94
2245 6150 6.495526 GGCTATCTTGAGGAGTAGACCTTTAT 59.504 42.308 0.00 0.00 40.73 1.40
2256 6162 2.104451 ACATGCAGGCTATCTTGAGGAG 59.896 50.000 0.00 0.00 0.00 3.69
2412 6339 7.839680 ACCTAATGAAAAGAAAAGATGTGGT 57.160 32.000 0.00 0.00 0.00 4.16
2432 6361 5.784023 TCCATGGATAGAGGTAACAACCTA 58.216 41.667 11.44 0.00 40.86 3.08


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

AutoCloner maintained by Alex Coulton.