Multiple sequence alignment - TraesCS1A01G134700

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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 TraesCS1A01G134700 chr1A 100.000 3459 0 0 1 3459 204317642 204321100 0.000000e+00 6388.0
1 TraesCS1A01G134700 chr1A 89.028 1832 169 21 1 1805 204302387 204304213 0.000000e+00 2241.0
2 TraesCS1A01G134700 chr1A 97.433 1013 25 1 2447 3459 39745024 39744013 0.000000e+00 1725.0
3 TraesCS1A01G134700 chr1A 89.267 969 67 14 1330 2271 177433221 177434179 0.000000e+00 1179.0
4 TraesCS1A01G134700 chr1A 88.786 972 67 17 1330 2271 177425364 177426323 0.000000e+00 1153.0
5 TraesCS1A01G134700 chr1A 93.644 472 30 0 1800 2271 204311797 204312268 0.000000e+00 706.0
6 TraesCS1A01G134700 chr1A 88.889 459 48 2 149 607 226903365 226902910 2.330000e-156 562.0
7 TraesCS1A01G134700 chr1A 91.566 83 7 0 1330 1412 111697939 111697857 7.840000e-22 115.0
8 TraesCS1A01G134700 chr7A 97.532 1013 25 0 2447 3459 233123305 233124317 0.000000e+00 1733.0
9 TraesCS1A01G134700 chr7A 97.255 1020 27 1 2441 3459 233130076 233131095 0.000000e+00 1727.0
10 TraesCS1A01G134700 chr7A 97.157 1020 28 1 2441 3459 657495248 657496267 0.000000e+00 1722.0
11 TraesCS1A01G134700 chr7A 89.017 519 46 11 1690 2203 444480117 444480629 1.750000e-177 632.0
12 TraesCS1A01G134700 chr7A 88.031 518 52 10 1690 2203 444498100 444498611 3.820000e-169 604.0
13 TraesCS1A01G134700 chr7A 91.713 181 9 1 2272 2446 341597263 341597083 2.670000e-61 246.0
14 TraesCS1A01G134700 chr7A 92.025 163 11 2 1 162 529848581 529848420 9.660000e-56 228.0
15 TraesCS1A01G134700 chr5A 97.433 1013 25 1 2447 3459 391419019 391418008 0.000000e+00 1725.0
16 TraesCS1A01G134700 chr5A 97.157 1020 28 1 2441 3459 349572389 349573408 0.000000e+00 1722.0
17 TraesCS1A01G134700 chr5A 91.525 590 44 5 1686 2271 505862707 505863294 0.000000e+00 808.0
18 TraesCS1A01G134700 chr5A 91.652 575 45 3 1699 2271 505970032 505970605 0.000000e+00 793.0
19 TraesCS1A01G134700 chr5A 78.040 551 94 21 153 699 275863246 275862719 4.310000e-84 322.0
20 TraesCS1A01G134700 chr5A 93.168 161 9 2 2272 2431 375878810 375878969 5.770000e-58 235.0
21 TraesCS1A01G134700 chr5A 94.000 50 0 2 676 722 107983463 107983512 4.790000e-09 73.1
22 TraesCS1A01G134700 chr2A 97.255 1020 25 3 2441 3459 81849293 81848276 0.000000e+00 1725.0
23 TraesCS1A01G134700 chr2A 92.611 812 48 5 1461 2271 429459257 429460057 0.000000e+00 1157.0
24 TraesCS1A01G134700 chr2A 88.525 915 70 15 1369 2271 429467269 429468160 0.000000e+00 1075.0
25 TraesCS1A01G134700 chr2A 90.948 464 39 2 144 607 467791085 467790625 3.790000e-174 621.0
26 TraesCS1A01G134700 chr2A 90.265 452 38 6 152 600 105075188 105075636 1.380000e-163 586.0
27 TraesCS1A01G134700 chr2A 92.727 55 0 3 676 727 372380848 372380795 3.700000e-10 76.8
28 TraesCS1A01G134700 chr6A 97.340 1015 26 1 2446 3459 86478224 86477210 0.000000e+00 1724.0
29 TraesCS1A01G134700 chr6A 86.559 558 53 14 149 687 305860684 305860130 2.300000e-166 595.0
30 TraesCS1A01G134700 chr6A 86.559 558 52 15 149 687 305871555 305871002 8.270000e-166 593.0
31 TraesCS1A01G134700 chr6A 89.890 455 39 7 156 606 363013869 363013418 2.310000e-161 579.0
32 TraesCS1A01G134700 chr6A 92.727 55 0 2 676 727 422633141 422633088 3.700000e-10 76.8
33 TraesCS1A01G134700 chr6A 90.909 55 1 3 676 727 254091308 254091361 1.720000e-08 71.3
34 TraesCS1A01G134700 chr6A 85.915 71 3 5 678 744 368631586 368631519 6.190000e-08 69.4
35 TraesCS1A01G134700 chr3A 97.157 1020 28 1 2441 3459 608907857 608908876 0.000000e+00 1722.0
36 TraesCS1A01G134700 chr3A 85.192 547 62 14 149 687 446986408 446986943 8.440000e-151 544.0
37 TraesCS1A01G134700 chr3A 92.727 55 0 3 676 727 437028559 437028506 3.700000e-10 76.8
38 TraesCS1A01G134700 chr4A 88.803 518 49 9 1690 2203 215532505 215533017 8.150000e-176 627.0
39 TraesCS1A01G134700 chr4A 84.909 497 52 13 809 1303 259673765 259673290 6.710000e-132 481.0
40 TraesCS1A01G134700 chr4A 91.975 162 13 0 1 162 287682233 287682394 9.660000e-56 228.0
41 TraesCS1A01G134700 chr4A 91.925 161 13 0 2 162 366946767 366946927 3.470000e-55 226.0
42 TraesCS1A01G134700 chr4A 90.741 162 15 0 1 162 122851357 122851196 2.090000e-52 217.0
43 TraesCS1A01G134700 chr4A 92.771 83 6 0 1330 1412 72108753 72108671 1.690000e-23 121.0
44 TraesCS1A01G134700 chr4A 92.453 53 0 3 678 727 347530626 347530575 4.790000e-09 73.1
45 TraesCS1A01G134700 chr4A 86.885 61 6 2 676 734 66085931 66085991 2.230000e-07 67.6
46 TraesCS1A01G134700 chr7B 83.900 559 66 21 149 697 411944138 411944682 2.380000e-141 512.0
47 TraesCS1A01G134700 chr7B 81.228 570 71 26 152 695 483582058 483581499 8.870000e-116 427.0
48 TraesCS1A01G134700 chr1D 91.553 367 31 0 801 1167 82117743 82117377 1.110000e-139 507.0
49 TraesCS1A01G134700 chr1D 88.011 367 44 0 801 1167 438009694 438010060 5.300000e-118 435.0
50 TraesCS1A01G134700 chr1D 90.055 181 12 1 2272 2446 269841169 269840989 2.690000e-56 230.0
51 TraesCS1A01G134700 chr3D 89.189 370 39 1 798 1167 461807629 461807997 8.750000e-126 460.0
52 TraesCS1A01G134700 chr3D 89.373 367 38 1 801 1167 461828073 461828438 8.750000e-126 460.0
53 TraesCS1A01G134700 chr3D 89.101 367 39 1 801 1167 461835761 461836126 4.070000e-124 455.0
54 TraesCS1A01G134700 chr3D 91.160 181 10 1 2272 2446 533249416 533249236 1.240000e-59 241.0
55 TraesCS1A01G134700 chr7D 89.474 361 38 0 807 1167 289093560 289093200 1.130000e-124 457.0
56 TraesCS1A01G134700 chr7D 88.611 360 39 2 807 1166 289101207 289100850 1.470000e-118 436.0
57 TraesCS1A01G134700 chr7D 93.125 160 11 0 2272 2431 442050248 442050407 5.770000e-58 235.0
58 TraesCS1A01G134700 chr7D 93.125 160 11 0 2272 2431 509175589 509175430 5.770000e-58 235.0
59 TraesCS1A01G134700 chr6B 88.366 361 34 2 807 1167 312008553 312008201 8.870000e-116 427.0
60 TraesCS1A01G134700 chr4B 79.588 583 72 35 149 699 393576188 393576755 1.170000e-99 374.0
61 TraesCS1A01G134700 chr4B 78.840 586 75 36 149 699 392777449 392778020 1.980000e-92 350.0
62 TraesCS1A01G134700 chr6D 90.659 182 9 3 2272 2446 60580758 60580578 5.770000e-58 235.0
63 TraesCS1A01G134700 chr6D 93.168 161 9 2 2272 2431 244060951 244061110 5.770000e-58 235.0
64 TraesCS1A01G134700 chr6D 91.358 162 14 0 1 162 236128229 236128068 4.490000e-54 222.0
65 TraesCS1A01G134700 chr2D 93.125 160 11 0 2272 2431 217454309 217454150 5.770000e-58 235.0
66 TraesCS1A01G134700 chr2D 91.358 162 14 0 1 162 532725468 532725629 4.490000e-54 222.0
67 TraesCS1A01G134700 chr2D 91.720 157 13 0 6 162 532717880 532718036 5.810000e-53 219.0
68 TraesCS1A01G134700 chrUn 90.741 162 14 1 1 162 64345170 64345010 7.520000e-52 215.0


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 TraesCS1A01G134700 chr1A 204317642 204321100 3458 False 6388 6388 100.000 1 3459 1 chr1A.!!$F5 3458
1 TraesCS1A01G134700 chr1A 204302387 204304213 1826 False 2241 2241 89.028 1 1805 1 chr1A.!!$F3 1804
2 TraesCS1A01G134700 chr1A 39744013 39745024 1011 True 1725 1725 97.433 2447 3459 1 chr1A.!!$R1 1012
3 TraesCS1A01G134700 chr1A 177433221 177434179 958 False 1179 1179 89.267 1330 2271 1 chr1A.!!$F2 941
4 TraesCS1A01G134700 chr1A 177425364 177426323 959 False 1153 1153 88.786 1330 2271 1 chr1A.!!$F1 941
5 TraesCS1A01G134700 chr7A 233123305 233124317 1012 False 1733 1733 97.532 2447 3459 1 chr7A.!!$F1 1012
6 TraesCS1A01G134700 chr7A 233130076 233131095 1019 False 1727 1727 97.255 2441 3459 1 chr7A.!!$F2 1018
7 TraesCS1A01G134700 chr7A 657495248 657496267 1019 False 1722 1722 97.157 2441 3459 1 chr7A.!!$F5 1018
8 TraesCS1A01G134700 chr7A 444480117 444480629 512 False 632 632 89.017 1690 2203 1 chr7A.!!$F3 513
9 TraesCS1A01G134700 chr7A 444498100 444498611 511 False 604 604 88.031 1690 2203 1 chr7A.!!$F4 513
10 TraesCS1A01G134700 chr5A 391418008 391419019 1011 True 1725 1725 97.433 2447 3459 1 chr5A.!!$R2 1012
11 TraesCS1A01G134700 chr5A 349572389 349573408 1019 False 1722 1722 97.157 2441 3459 1 chr5A.!!$F2 1018
12 TraesCS1A01G134700 chr5A 505862707 505863294 587 False 808 808 91.525 1686 2271 1 chr5A.!!$F4 585
13 TraesCS1A01G134700 chr5A 505970032 505970605 573 False 793 793 91.652 1699 2271 1 chr5A.!!$F5 572
14 TraesCS1A01G134700 chr5A 275862719 275863246 527 True 322 322 78.040 153 699 1 chr5A.!!$R1 546
15 TraesCS1A01G134700 chr2A 81848276 81849293 1017 True 1725 1725 97.255 2441 3459 1 chr2A.!!$R1 1018
16 TraesCS1A01G134700 chr2A 429459257 429460057 800 False 1157 1157 92.611 1461 2271 1 chr2A.!!$F2 810
17 TraesCS1A01G134700 chr2A 429467269 429468160 891 False 1075 1075 88.525 1369 2271 1 chr2A.!!$F3 902
18 TraesCS1A01G134700 chr6A 86477210 86478224 1014 True 1724 1724 97.340 2446 3459 1 chr6A.!!$R1 1013
19 TraesCS1A01G134700 chr6A 305860130 305860684 554 True 595 595 86.559 149 687 1 chr6A.!!$R2 538
20 TraesCS1A01G134700 chr6A 305871002 305871555 553 True 593 593 86.559 149 687 1 chr6A.!!$R3 538
21 TraesCS1A01G134700 chr3A 608907857 608908876 1019 False 1722 1722 97.157 2441 3459 1 chr3A.!!$F2 1018
22 TraesCS1A01G134700 chr3A 446986408 446986943 535 False 544 544 85.192 149 687 1 chr3A.!!$F1 538
23 TraesCS1A01G134700 chr4A 215532505 215533017 512 False 627 627 88.803 1690 2203 1 chr4A.!!$F2 513
24 TraesCS1A01G134700 chr7B 411944138 411944682 544 False 512 512 83.900 149 697 1 chr7B.!!$F1 548
25 TraesCS1A01G134700 chr7B 483581499 483582058 559 True 427 427 81.228 152 695 1 chr7B.!!$R1 543
26 TraesCS1A01G134700 chr4B 393576188 393576755 567 False 374 374 79.588 149 699 1 chr4B.!!$F2 550
27 TraesCS1A01G134700 chr4B 392777449 392778020 571 False 350 350 78.840 149 699 1 chr4B.!!$F1 550

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
865 898 0.040204 AAGGGTCTTGGCATCCTTGG 59.960 55.0 9.93 0.0 38.11 3.61 F
2276 2766 0.462047 CTTGGGGCGTCACAGATACC 60.462 60.0 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2825 0.033208 CAGCTAGGGGCCAAATTGGA 60.033 55.000 17.47 0.0 40.96 3.53 R
3111 3602 1.228245 GAAGGGGCAGCAAGACACA 60.228 57.895 0.00 0.0 0.00 3.72 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
42 43 5.560966 AAACACCGCATGACTTATTTAGG 57.439 39.130 0.00 0.00 0.00 2.69
44 45 4.585879 ACACCGCATGACTTATTTAGGTT 58.414 39.130 0.00 0.00 0.00 3.50
103 104 2.435372 ACAAGGCAAGAGGTGAAACA 57.565 45.000 0.00 0.00 39.98 2.83
139 140 6.995091 AGCTATTTAGGCAAGTTTAGATGAGG 59.005 38.462 0.00 0.00 0.00 3.86
143 144 1.406887 GGCAAGTTTAGATGAGGCCGA 60.407 52.381 0.00 0.00 0.00 5.54
150 151 4.455877 AGTTTAGATGAGGCCGAAAACAAG 59.544 41.667 15.13 0.00 31.02 3.16
269 271 6.377712 TGTTATGAAGCATTTGTCATCATGGA 59.622 34.615 0.00 0.00 36.00 3.41
292 294 4.323477 CGAAAGGGGTGCCACGGA 62.323 66.667 0.00 0.00 0.00 4.69
516 530 5.576774 TCTCATACATCACACAACATTCGTC 59.423 40.000 0.00 0.00 0.00 4.20
519 533 3.411446 ACATCACACAACATTCGTCCAT 58.589 40.909 0.00 0.00 0.00 3.41
526 541 0.608035 AACATTCGTCCATGGCGGTT 60.608 50.000 22.59 17.07 35.57 4.44
531 546 2.351276 GTCCATGGCGGTTGTCCT 59.649 61.111 6.96 0.00 35.57 3.85
534 563 2.040544 CCATGGCGGTTGTCCTGAC 61.041 63.158 0.00 0.00 0.00 3.51
561 590 1.000385 CCTTTGAAGCGTGCATTTCCA 60.000 47.619 0.00 0.00 0.00 3.53
562 591 2.353011 CCTTTGAAGCGTGCATTTCCAT 60.353 45.455 0.00 0.00 0.00 3.41
614 647 3.042842 TAGTCGTACACGGGCGCAG 62.043 63.158 10.83 4.90 40.29 5.18
629 662 0.108804 CGCAGTGGGTAGTAGTGGTG 60.109 60.000 0.00 0.00 0.00 4.17
635 668 0.319405 GGGTAGTAGTGGTGCACGTT 59.681 55.000 11.45 0.96 39.64 3.99
637 670 1.000060 GGTAGTAGTGGTGCACGTTCA 60.000 52.381 11.45 0.00 39.64 3.18
642 675 2.774439 AGTGGTGCACGTTCATTTTC 57.226 45.000 11.45 0.00 39.64 2.29
646 679 1.199097 GGTGCACGTTCATTTTCGGAT 59.801 47.619 11.45 0.00 0.00 4.18
680 713 2.106683 CCAATGTCTTCGGGGCGAC 61.107 63.158 0.00 0.00 34.89 5.19
696 729 0.454957 CGACGGTAGTTGTACACGGG 60.455 60.000 0.00 0.00 31.12 5.28
754 787 1.395635 ACTCGGCGTATCCATGTACA 58.604 50.000 6.85 0.00 34.01 2.90
779 812 3.671433 GCGTTCCAGTGTGATAGTCGTTA 60.671 47.826 0.00 0.00 0.00 3.18
786 819 4.737279 CAGTGTGATAGTCGTTAGAGCATG 59.263 45.833 0.00 0.00 0.00 4.06
797 830 2.736721 GTTAGAGCATGTGACAAAGCGA 59.263 45.455 7.56 0.00 0.00 4.93
805 838 3.120321 TGTGACAAAGCGATACTTGGT 57.880 42.857 0.00 0.00 45.78 3.67
812 845 4.142902 ACAAAGCGATACTTGGTGATTTCG 60.143 41.667 0.00 0.00 41.27 3.46
821 854 0.457166 TGGTGATTTCGTAGACGCGG 60.457 55.000 12.47 0.00 39.60 6.46
824 857 0.800683 TGATTTCGTAGACGCGGCAG 60.801 55.000 17.71 4.98 39.60 4.85
835 868 2.436115 GCGGCAGGGGTACTTGAC 60.436 66.667 0.00 0.00 0.00 3.18
845 878 0.108992 GGTACTTGACGCATCCACGA 60.109 55.000 0.00 0.00 36.70 4.35
852 885 1.359459 GACGCATCCACGAAAGGGTC 61.359 60.000 0.00 0.00 36.91 4.46
857 890 0.322546 ATCCACGAAAGGGTCTTGGC 60.323 55.000 0.00 0.00 43.82 4.52
858 891 1.228124 CCACGAAAGGGTCTTGGCA 60.228 57.895 0.00 0.00 38.71 4.92
865 898 0.040204 AAGGGTCTTGGCATCCTTGG 59.960 55.000 9.93 0.00 38.11 3.61
866 899 1.142688 AGGGTCTTGGCATCCTTGGT 61.143 55.000 0.00 0.00 0.00 3.67
878 911 0.613260 TCCTTGGTGGATGAAGACCG 59.387 55.000 0.00 0.00 40.56 4.79
908 941 3.047877 GTGGCTTGGGGTCGAACG 61.048 66.667 0.00 0.00 0.00 3.95
934 967 2.985847 AAGGTGGCGCAAGAAGGC 60.986 61.111 10.83 0.00 43.02 4.35
943 976 1.219393 GCAAGAAGGCGAGGCTAGT 59.781 57.895 0.00 0.00 0.00 2.57
945 978 1.086634 CAAGAAGGCGAGGCTAGTGC 61.087 60.000 0.00 0.00 38.76 4.40
946 979 1.544825 AAGAAGGCGAGGCTAGTGCA 61.545 55.000 0.00 0.00 41.91 4.57
947 980 1.079127 GAAGGCGAGGCTAGTGCAA 60.079 57.895 0.00 0.00 41.91 4.08
960 993 2.359107 TGCAAGAGCTTGAGGGCG 60.359 61.111 14.04 0.00 42.93 6.13
1020 1053 2.633509 GCAAACAGAGGCAGCCAGG 61.634 63.158 15.80 4.71 0.00 4.45
1025 1058 4.664267 AGAGGCAGCCAGGGGACA 62.664 66.667 15.80 0.00 0.00 4.02
1080 1113 1.156095 TGCAGAGGTCAGGAGGTCA 59.844 57.895 0.00 0.00 0.00 4.02
1095 1128 4.081185 TCATCGGAGCTTGGCGCA 62.081 61.111 10.83 0.00 42.61 6.09
1100 1133 2.188994 GGAGCTTGGCGCAGATCT 59.811 61.111 10.83 0.00 42.61 2.75
1106 1139 0.652592 CTTGGCGCAGATCTAAACGG 59.347 55.000 10.83 0.00 0.00 4.44
1127 1160 2.983592 GGCCAACGTGGGACTTGG 60.984 66.667 15.02 5.05 38.19 3.61
1130 1163 1.586154 GCCAACGTGGGACTTGGATG 61.586 60.000 15.02 0.00 39.58 3.51
1132 1165 1.671054 AACGTGGGACTTGGATGCG 60.671 57.895 0.00 0.00 0.00 4.73
1135 1168 4.776322 TGGGACTTGGATGCGCCG 62.776 66.667 4.18 0.00 40.66 6.46
1200 1233 1.304547 CACTGGACGAGGAGGAGGT 60.305 63.158 0.00 0.00 0.00 3.85
1222 1255 2.038269 GGCCTCACGATTTTCGGCA 61.038 57.895 0.00 0.00 45.59 5.69
1288 1321 1.153086 GCAGGACAATGGCGAGGAT 60.153 57.895 0.00 0.00 0.00 3.24
1303 1336 2.444895 GATGCGAGGGAGAGGGGT 60.445 66.667 0.00 0.00 0.00 4.95
1304 1337 2.444895 ATGCGAGGGAGAGGGGTC 60.445 66.667 0.00 0.00 0.00 4.46
1308 1341 2.444895 GAGGGAGAGGGGTCGCAT 60.445 66.667 0.00 0.00 31.87 4.73
1313 1346 1.049289 GGAGAGGGGTCGCATAAGGT 61.049 60.000 0.00 0.00 0.00 3.50
1324 1357 1.078497 CATAAGGTGGCGGTGCTCA 60.078 57.895 0.00 0.00 0.00 4.26
1338 1371 1.672356 GCTCATTGGTGCTGGTCGT 60.672 57.895 0.00 0.00 0.00 4.34
1386 1422 2.496817 GGGCGCTCAAGATCGAGT 59.503 61.111 7.64 0.00 35.33 4.18
1452 1488 1.323412 CGAGGATGGGTCGAGAGAAT 58.677 55.000 0.00 0.00 45.01 2.40
1453 1489 1.683917 CGAGGATGGGTCGAGAGAATT 59.316 52.381 0.00 0.00 45.01 2.17
1545 1611 1.632965 GGGTGTGGGCTAGGGTTAGG 61.633 65.000 0.00 0.00 0.00 2.69
1560 1626 1.286849 GTTAGGGTGGTTGGGCCTTAT 59.713 52.381 4.53 0.00 38.35 1.73
1575 1641 1.348036 CCTTATAGGCAGGCCCAGTAC 59.652 57.143 6.70 0.00 36.58 2.73
1581 1647 1.990060 GCAGGCCCAGTACAGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
1586 1656 1.383248 CCCAGTACAGAGGAGGGGG 60.383 68.421 0.00 0.00 35.83 5.40
1657 1727 4.278669 GCCTTATCACCGATCTCTCACTAA 59.721 45.833 0.00 0.00 0.00 2.24
1805 1879 5.397142 AGAAATGGCCAAGATTGAAAGAC 57.603 39.130 10.96 0.00 0.00 3.01
2097 2173 5.949354 TGTGAATTCCCTCGATTTAAATGGT 59.051 36.000 5.17 0.00 0.00 3.55
2098 2174 7.113437 TGTGAATTCCCTCGATTTAAATGGTA 58.887 34.615 5.17 0.00 0.00 3.25
2118 2194 6.709281 TGGTACAAAGATCCATACGGTTTAA 58.291 36.000 0.00 0.00 31.92 1.52
2177 2297 4.580995 TGATGACATGATGCAATGCACATA 59.419 37.500 11.23 0.00 43.04 2.29
2231 2720 5.808042 ATCACACAATGAATCTCGGAAAG 57.192 39.130 0.00 0.00 41.93 2.62
2251 2741 0.749091 CATGGAAGGCATTCGGAGCA 60.749 55.000 4.84 0.00 36.19 4.26
2271 2761 2.358737 GGTCTTGGGGCGTCACAG 60.359 66.667 0.00 0.00 0.00 3.66
2272 2762 2.741092 GTCTTGGGGCGTCACAGA 59.259 61.111 0.00 0.00 0.00 3.41
2273 2763 1.296715 GTCTTGGGGCGTCACAGAT 59.703 57.895 0.00 0.00 0.00 2.90
2274 2764 0.535335 GTCTTGGGGCGTCACAGATA 59.465 55.000 0.00 0.00 0.00 1.98
2275 2765 0.535335 TCTTGGGGCGTCACAGATAC 59.465 55.000 0.00 0.00 0.00 2.24
2276 2766 0.462047 CTTGGGGCGTCACAGATACC 60.462 60.000 0.00 0.00 0.00 2.73
2277 2767 0.907704 TTGGGGCGTCACAGATACCT 60.908 55.000 0.00 0.00 0.00 3.08
2278 2768 1.327690 TGGGGCGTCACAGATACCTC 61.328 60.000 0.00 0.00 0.00 3.85
2279 2769 1.065928 GGGCGTCACAGATACCTCG 59.934 63.158 0.00 0.00 0.00 4.63
2280 2770 1.065928 GGCGTCACAGATACCTCGG 59.934 63.158 0.00 0.00 0.00 4.63
2281 2771 1.589196 GCGTCACAGATACCTCGGC 60.589 63.158 0.00 0.00 0.00 5.54
2282 2772 1.065928 CGTCACAGATACCTCGGCC 59.934 63.158 0.00 0.00 0.00 6.13
2283 2773 1.065928 GTCACAGATACCTCGGCCG 59.934 63.158 22.12 22.12 0.00 6.13
2284 2774 2.279517 CACAGATACCTCGGCCGC 60.280 66.667 23.51 4.91 0.00 6.53
2285 2775 3.537874 ACAGATACCTCGGCCGCC 61.538 66.667 23.51 0.00 0.00 6.13
2298 2788 4.838152 CCGCCGGACACATGGAGG 62.838 72.222 5.05 0.00 38.91 4.30
2299 2789 3.770040 CGCCGGACACATGGAGGA 61.770 66.667 5.05 0.00 0.00 3.71
2300 2790 2.187946 GCCGGACACATGGAGGAG 59.812 66.667 5.05 0.00 0.00 3.69
2301 2791 2.359169 GCCGGACACATGGAGGAGA 61.359 63.158 5.05 0.00 0.00 3.71
2302 2792 1.899437 GCCGGACACATGGAGGAGAA 61.899 60.000 5.05 0.00 0.00 2.87
2303 2793 0.613260 CCGGACACATGGAGGAGAAA 59.387 55.000 0.00 0.00 0.00 2.52
2304 2794 1.003118 CCGGACACATGGAGGAGAAAA 59.997 52.381 0.00 0.00 0.00 2.29
2305 2795 2.356125 CCGGACACATGGAGGAGAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2306 2796 2.939103 CGGACACATGGAGGAGAAAATC 59.061 50.000 0.00 0.00 0.00 2.17
2316 2806 1.596496 GGAGAAAATCCCCCTGGAGA 58.404 55.000 0.00 0.00 46.08 3.71
2317 2807 1.213182 GGAGAAAATCCCCCTGGAGAC 59.787 57.143 0.00 0.00 46.08 3.36
2318 2808 2.200955 GAGAAAATCCCCCTGGAGACT 58.799 52.381 0.00 0.00 46.08 3.24
2319 2809 1.918957 AGAAAATCCCCCTGGAGACTG 59.081 52.381 0.00 0.00 46.08 3.51
2320 2810 1.002857 AAAATCCCCCTGGAGACTGG 58.997 55.000 0.00 0.00 46.08 4.00
2321 2811 1.575447 AAATCCCCCTGGAGACTGGC 61.575 60.000 0.00 0.00 46.08 4.85
2326 2816 2.503061 CCTGGAGACTGGCGATGG 59.497 66.667 0.00 0.00 42.94 3.51
2327 2817 2.503061 CTGGAGACTGGCGATGGG 59.497 66.667 0.00 0.00 0.00 4.00
2328 2818 3.083349 TGGAGACTGGCGATGGGG 61.083 66.667 0.00 0.00 0.00 4.96
2329 2819 3.866582 GGAGACTGGCGATGGGGG 61.867 72.222 0.00 0.00 0.00 5.40
2330 2820 4.554036 GAGACTGGCGATGGGGGC 62.554 72.222 0.00 0.00 0.00 5.80
2338 2828 3.807839 CGATGGGGGCCATGTCCA 61.808 66.667 4.39 6.97 45.26 4.02
2339 2829 2.689175 GATGGGGGCCATGTCCAA 59.311 61.111 4.39 0.00 45.26 3.53
2340 2830 1.233949 GATGGGGGCCATGTCCAAT 59.766 57.895 4.39 0.00 45.26 3.16
2341 2831 0.398948 GATGGGGGCCATGTCCAATT 60.399 55.000 4.39 0.00 45.26 2.32
2342 2832 0.044549 ATGGGGGCCATGTCCAATTT 59.955 50.000 4.39 0.00 43.39 1.82
2343 2833 0.908656 TGGGGGCCATGTCCAATTTG 60.909 55.000 4.39 0.00 0.00 2.32
2344 2834 1.625417 GGGGGCCATGTCCAATTTGG 61.625 60.000 9.28 9.28 39.43 3.28
2348 2838 1.906995 CCATGTCCAATTTGGCCCC 59.093 57.895 10.76 2.07 37.47 5.80
2349 2839 0.618393 CCATGTCCAATTTGGCCCCT 60.618 55.000 10.76 0.00 37.47 4.79
2350 2840 1.342874 CCATGTCCAATTTGGCCCCTA 60.343 52.381 10.76 0.00 37.47 3.53
2351 2841 2.034124 CATGTCCAATTTGGCCCCTAG 58.966 52.381 10.76 0.00 37.47 3.02
2352 2842 0.324275 TGTCCAATTTGGCCCCTAGC 60.324 55.000 10.76 0.00 37.47 3.42
2353 2843 0.033109 GTCCAATTTGGCCCCTAGCT 60.033 55.000 10.76 0.00 43.05 3.32
2354 2844 0.033208 TCCAATTTGGCCCCTAGCTG 60.033 55.000 10.76 0.00 43.05 4.24
2355 2845 0.033208 CCAATTTGGCCCCTAGCTGA 60.033 55.000 0.00 0.00 43.05 4.26
2356 2846 1.619432 CCAATTTGGCCCCTAGCTGAA 60.619 52.381 0.00 0.00 43.05 3.02
2357 2847 2.391678 CAATTTGGCCCCTAGCTGAAT 58.608 47.619 0.00 0.00 43.05 2.57
2358 2848 3.565307 CAATTTGGCCCCTAGCTGAATA 58.435 45.455 0.00 0.00 43.05 1.75
2359 2849 2.729028 TTTGGCCCCTAGCTGAATAC 57.271 50.000 0.00 0.00 43.05 1.89
2360 2850 1.893315 TTGGCCCCTAGCTGAATACT 58.107 50.000 0.00 0.00 43.05 2.12
2361 2851 2.787339 TGGCCCCTAGCTGAATACTA 57.213 50.000 0.00 0.00 43.05 1.82
2362 2852 3.275848 TGGCCCCTAGCTGAATACTAT 57.724 47.619 0.00 0.00 43.05 2.12
2363 2853 3.598264 TGGCCCCTAGCTGAATACTATT 58.402 45.455 0.00 0.00 43.05 1.73
2364 2854 3.980698 TGGCCCCTAGCTGAATACTATTT 59.019 43.478 0.00 0.00 43.05 1.40
2365 2855 4.041691 TGGCCCCTAGCTGAATACTATTTC 59.958 45.833 0.00 0.00 43.05 2.17
2366 2856 4.041691 GGCCCCTAGCTGAATACTATTTCA 59.958 45.833 0.00 0.00 43.05 2.69
2375 2865 5.912149 TGAATACTATTTCAGAGGCCCAT 57.088 39.130 0.00 0.00 32.07 4.00
2377 2867 7.574021 TGAATACTATTTCAGAGGCCCATAT 57.426 36.000 0.00 0.00 32.07 1.78
2378 2868 7.397221 TGAATACTATTTCAGAGGCCCATATG 58.603 38.462 0.00 0.00 32.07 1.78
2379 2869 4.647564 ACTATTTCAGAGGCCCATATGG 57.352 45.455 15.41 15.41 37.09 2.74
2388 2878 3.891817 CCCATATGGCTCCGGAGT 58.108 61.111 31.43 15.52 0.00 3.85
2389 2879 1.674057 CCCATATGGCTCCGGAGTC 59.326 63.158 29.45 29.45 0.00 3.36
2395 2885 3.706373 GGCTCCGGAGTCAGGCAA 61.706 66.667 30.98 0.00 35.29 4.52
2396 2886 2.125350 GCTCCGGAGTCAGGCAAG 60.125 66.667 31.43 5.20 0.00 4.01
2397 2887 2.125350 CTCCGGAGTCAGGCAAGC 60.125 66.667 24.04 0.00 0.00 4.01
2398 2888 2.922503 TCCGGAGTCAGGCAAGCA 60.923 61.111 0.00 0.00 0.00 3.91
2399 2889 2.435586 CCGGAGTCAGGCAAGCAG 60.436 66.667 0.00 0.00 0.00 4.24
2400 2890 3.123620 CGGAGTCAGGCAAGCAGC 61.124 66.667 0.00 0.00 44.65 5.25
2409 2899 2.046892 GCAAGCAGCCTCCTTCGA 60.047 61.111 0.00 0.00 37.23 3.71
2410 2900 1.672356 GCAAGCAGCCTCCTTCGAA 60.672 57.895 0.00 0.00 37.23 3.71
2411 2901 1.237285 GCAAGCAGCCTCCTTCGAAA 61.237 55.000 0.00 0.00 37.23 3.46
2412 2902 0.801251 CAAGCAGCCTCCTTCGAAAG 59.199 55.000 0.00 0.00 0.00 2.62
2413 2903 0.687354 AAGCAGCCTCCTTCGAAAGA 59.313 50.000 0.00 0.00 39.20 2.52
2424 2914 1.878953 TTCGAAAGAAGGAGGTGCAC 58.121 50.000 8.80 8.80 46.92 4.57
2425 2915 0.034896 TCGAAAGAAGGAGGTGCACC 59.965 55.000 29.22 29.22 37.03 5.01
2426 2916 2.378162 TCGAAAGAAGGAGGTGCACCT 61.378 52.381 38.42 38.42 43.98 4.00
2427 2917 3.084331 TCGAAAGAAGGAGGTGCACCTA 61.084 50.000 37.87 15.98 42.04 3.08
2428 2918 4.387326 TCGAAAGAAGGAGGTGCACCTAT 61.387 47.826 37.87 26.04 42.04 2.57
2429 2919 5.844539 TCGAAAGAAGGAGGTGCACCTATT 61.845 45.833 37.87 31.99 42.04 1.73
2430 2920 7.586390 TCGAAAGAAGGAGGTGCACCTATTC 62.586 48.000 35.23 35.23 42.04 1.75
2436 2926 1.958288 AGGTGCACCTATTCTGACCT 58.042 50.000 37.12 9.06 46.48 3.85
2437 2927 1.834263 AGGTGCACCTATTCTGACCTC 59.166 52.381 37.12 4.57 46.48 3.85
2438 2928 1.834263 GGTGCACCTATTCTGACCTCT 59.166 52.381 29.12 0.00 0.00 3.69
2439 2929 2.419297 GGTGCACCTATTCTGACCTCTG 60.419 54.545 29.12 0.00 0.00 3.35
2440 2930 2.234908 GTGCACCTATTCTGACCTCTGT 59.765 50.000 5.22 0.00 0.00 3.41
2441 2931 2.497675 TGCACCTATTCTGACCTCTGTC 59.502 50.000 0.00 0.00 42.12 3.51
2442 2932 2.159028 GCACCTATTCTGACCTCTGTCC 60.159 54.545 0.00 0.00 41.01 4.02
2443 2933 3.099905 CACCTATTCTGACCTCTGTCCA 58.900 50.000 0.00 0.00 41.01 4.02
2444 2934 3.708631 CACCTATTCTGACCTCTGTCCAT 59.291 47.826 0.00 0.00 41.01 3.41
2464 2954 1.886542 TCTGCTACGTCTTGAGCTTGA 59.113 47.619 9.31 5.25 39.54 3.02
2473 2963 3.303395 CGTCTTGAGCTTGAGTTGGTTTC 60.303 47.826 0.00 0.00 0.00 2.78
2525 3015 3.821421 AGCGTAAGTATTTCCCTCAGG 57.179 47.619 0.00 0.00 41.68 3.86
2549 3039 6.314784 GTTTTGAGAACCAAGGTATCAATCG 58.685 40.000 16.11 0.00 35.41 3.34
2564 3054 1.688735 CAATCGAGTAGGAGGCCATGA 59.311 52.381 5.01 0.00 0.00 3.07
2587 3077 2.758979 CAAGTCCCTCGTACCTACACAT 59.241 50.000 0.00 0.00 0.00 3.21
2794 3285 1.694856 GGGGGCCATAGGTTTCACA 59.305 57.895 4.39 0.00 0.00 3.58
3103 3594 0.582005 GTTATCCTCGATGGCAACGC 59.418 55.000 12.67 0.00 42.51 4.84
3111 3602 3.059884 CTCGATGGCAACGCTACAATAT 58.940 45.455 12.67 0.00 42.51 1.28
3351 3842 3.119316 TCTCAACAAACACACCGCAAAAT 60.119 39.130 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.018669 CCGAGAGAAACCTAAATAAGTCATGC 60.019 42.308 0.00 0.00 0.00 4.06
37 38 4.933400 GTGCATAACCGAGAGAAACCTAAA 59.067 41.667 0.00 0.00 0.00 1.85
42 43 3.585862 TGAGTGCATAACCGAGAGAAAC 58.414 45.455 0.00 0.00 0.00 2.78
44 45 3.447229 TGATGAGTGCATAACCGAGAGAA 59.553 43.478 0.00 0.00 34.11 2.87
76 77 4.892934 TCACCTCTTGCCTTGTTTAACAAT 59.107 37.500 11.12 0.00 37.48 2.71
133 134 3.004315 TGTTTCTTGTTTTCGGCCTCATC 59.996 43.478 0.00 0.00 0.00 2.92
139 140 5.463499 AATTGTTGTTTCTTGTTTTCGGC 57.537 34.783 0.00 0.00 0.00 5.54
188 189 1.612950 ACTTGCAAATGTCATCCGCAA 59.387 42.857 16.68 16.68 40.08 4.85
221 222 9.793252 AACATGCTCTTATCAACATTTTCATAC 57.207 29.630 0.00 0.00 0.00 2.39
269 271 1.228459 GGCACCCCTTTCGTTTCCT 60.228 57.895 0.00 0.00 0.00 3.36
292 294 5.111293 GTGGCATCATTTTCGGATTCATTT 58.889 37.500 0.00 0.00 0.00 2.32
516 530 2.040544 GTCAGGACAACCGCCATGG 61.041 63.158 7.63 7.63 46.41 3.66
519 533 1.746322 TAACGTCAGGACAACCGCCA 61.746 55.000 0.00 0.00 41.83 5.69
526 541 5.471556 TTCAAAGGTATAACGTCAGGACA 57.528 39.130 0.00 0.00 0.00 4.02
531 546 3.676172 CACGCTTCAAAGGTATAACGTCA 59.324 43.478 0.00 0.00 0.00 4.35
534 563 2.413796 TGCACGCTTCAAAGGTATAACG 59.586 45.455 0.00 0.00 0.00 3.18
583 612 3.679980 TGTACGACTACTTCCGTCTACAC 59.320 47.826 0.00 0.00 39.86 2.90
614 647 0.389426 CGTGCACCACTACTACCCAC 60.389 60.000 12.15 0.00 31.34 4.61
629 662 2.676342 ACCTATCCGAAAATGAACGTGC 59.324 45.455 0.00 0.00 0.00 5.34
635 668 5.125900 TCGTCAAGTACCTATCCGAAAATGA 59.874 40.000 0.00 0.00 0.00 2.57
637 670 5.587388 TCGTCAAGTACCTATCCGAAAAT 57.413 39.130 0.00 0.00 0.00 1.82
642 675 3.317149 TGGATTCGTCAAGTACCTATCCG 59.683 47.826 0.00 0.00 37.36 4.18
646 679 5.421056 AGACATTGGATTCGTCAAGTACCTA 59.579 40.000 0.00 0.00 31.92 3.08
680 713 0.883833 AGACCCGTGTACAACTACCG 59.116 55.000 0.00 0.00 0.00 4.02
709 742 6.827251 TCCTCTCTAAATGTGTGTACGACTAT 59.173 38.462 0.00 0.00 0.00 2.12
726 759 2.492012 GATACGCCGAGTTCCTCTCTA 58.508 52.381 0.00 0.00 40.75 2.43
727 760 1.310904 GATACGCCGAGTTCCTCTCT 58.689 55.000 0.00 0.00 40.75 3.10
728 761 0.311477 GGATACGCCGAGTTCCTCTC 59.689 60.000 0.00 0.00 39.62 3.20
754 787 1.555075 ACTATCACACTGGAACGCCAT 59.445 47.619 0.00 0.00 44.91 4.40
758 791 2.631418 ACGACTATCACACTGGAACG 57.369 50.000 0.00 0.00 0.00 3.95
764 797 4.399618 ACATGCTCTAACGACTATCACACT 59.600 41.667 0.00 0.00 0.00 3.55
779 812 2.105006 ATCGCTTTGTCACATGCTCT 57.895 45.000 0.00 0.00 0.00 4.09
786 819 3.064207 TCACCAAGTATCGCTTTGTCAC 58.936 45.455 0.00 0.00 34.69 3.67
797 830 4.110482 GCGTCTACGAAATCACCAAGTAT 58.890 43.478 6.71 0.00 43.02 2.12
805 838 0.800683 CTGCCGCGTCTACGAAATCA 60.801 55.000 4.92 0.00 43.02 2.57
812 845 3.142838 TACCCCTGCCGCGTCTAC 61.143 66.667 4.92 0.00 0.00 2.59
821 854 1.078426 ATGCGTCAAGTACCCCTGC 60.078 57.895 0.00 0.00 0.00 4.85
824 857 0.743345 GTGGATGCGTCAAGTACCCC 60.743 60.000 8.47 0.00 0.00 4.95
835 868 0.673644 AAGACCCTTTCGTGGATGCG 60.674 55.000 0.00 0.00 0.00 4.73
845 878 1.550869 CCAAGGATGCCAAGACCCTTT 60.551 52.381 0.00 0.00 36.93 3.11
865 898 2.100631 CACCGCGGTCTTCATCCAC 61.101 63.158 31.80 0.00 0.00 4.02
866 899 2.264480 CACCGCGGTCTTCATCCA 59.736 61.111 31.80 0.00 0.00 3.41
904 937 1.515521 CCACCTTGCCTTGGTCGTTC 61.516 60.000 0.00 0.00 35.28 3.95
908 941 3.365265 CGCCACCTTGCCTTGGTC 61.365 66.667 0.00 0.00 35.28 4.02
911 944 3.562779 CTTGCGCCACCTTGCCTTG 62.563 63.158 4.18 0.00 0.00 3.61
912 945 3.297620 CTTGCGCCACCTTGCCTT 61.298 61.111 4.18 0.00 0.00 4.35
928 961 1.544825 TTGCACTAGCCTCGCCTTCT 61.545 55.000 0.00 0.00 41.13 2.85
934 967 0.108424 AAGCTCTTGCACTAGCCTCG 60.108 55.000 14.33 0.00 42.74 4.63
943 976 2.359107 CGCCCTCAAGCTCTTGCA 60.359 61.111 4.81 0.00 42.74 4.08
945 978 3.494336 CGCGCCCTCAAGCTCTTG 61.494 66.667 0.00 3.32 41.71 3.02
946 979 4.767255 CCGCGCCCTCAAGCTCTT 62.767 66.667 0.00 0.00 0.00 2.85
1005 1038 3.655211 CCCCTGGCTGCCTCTGTT 61.655 66.667 21.03 0.00 0.00 3.16
1007 1040 4.106925 GTCCCCTGGCTGCCTCTG 62.107 72.222 21.03 9.83 0.00 3.35
1036 1069 2.058595 ACTCATCCCCGTCTTCCCG 61.059 63.158 0.00 0.00 0.00 5.14
1059 1092 2.664081 CCTCCTGACCTCTGCACCC 61.664 68.421 0.00 0.00 0.00 4.61
1072 1105 1.333636 CCAAGCTCCGATGACCTCCT 61.334 60.000 0.00 0.00 0.00 3.69
1089 1122 1.813753 GCCGTTTAGATCTGCGCCA 60.814 57.895 4.18 0.00 0.00 5.69
1095 1128 1.442148 GGCCTCGCCGTTTAGATCT 59.558 57.895 0.00 0.00 39.62 2.75
1118 1151 4.776322 CGGCGCATCCAAGTCCCA 62.776 66.667 10.83 0.00 34.01 4.37
1127 1160 2.650813 ATCTCTTCCACCGGCGCATC 62.651 60.000 10.83 0.00 0.00 3.91
1130 1163 2.852495 TTCATCTCTTCCACCGGCGC 62.852 60.000 0.00 0.00 0.00 6.53
1132 1165 1.084370 CGTTCATCTCTTCCACCGGC 61.084 60.000 0.00 0.00 0.00 6.13
1135 1168 1.084370 CGCCGTTCATCTCTTCCACC 61.084 60.000 0.00 0.00 0.00 4.61
1200 1233 1.873165 GAAAATCGTGAGGCCGCAA 59.127 52.632 12.05 0.00 0.00 4.85
1210 1243 3.124921 CCCGCTGCCGAAAATCGT 61.125 61.111 0.00 0.00 38.40 3.73
1277 1310 2.109799 CCTCGCATCCTCGCCATT 59.890 61.111 0.00 0.00 0.00 3.16
1307 1340 0.255890 AATGAGCACCGCCACCTTAT 59.744 50.000 0.00 0.00 0.00 1.73
1308 1341 0.676466 CAATGAGCACCGCCACCTTA 60.676 55.000 0.00 0.00 0.00 2.69
1313 1346 2.672651 CACCAATGAGCACCGCCA 60.673 61.111 0.00 0.00 0.00 5.69
1324 1357 0.606401 CTCCAACGACCAGCACCAAT 60.606 55.000 0.00 0.00 0.00 3.16
1386 1422 3.647921 ATCCCTGCAGCCCTCCTCA 62.648 63.158 8.66 0.00 0.00 3.86
1435 1471 1.139853 GCAATTCTCTCGACCCATCCT 59.860 52.381 0.00 0.00 0.00 3.24
1452 1488 0.252761 TTGCATGATCCCTCTCGCAA 59.747 50.000 0.00 0.00 37.10 4.85
1453 1489 0.179065 CTTGCATGATCCCTCTCGCA 60.179 55.000 0.00 0.00 0.00 5.10
1545 1611 3.821306 CCTATAAGGCCCAACCACC 57.179 57.895 0.00 0.00 43.14 4.61
1560 1626 0.687757 CTCTGTACTGGGCCTGCCTA 60.688 60.000 10.71 0.22 36.10 3.93
1565 1631 1.002274 CCTCCTCTGTACTGGGCCT 59.998 63.158 4.53 0.00 0.00 5.19
1591 1661 4.554036 CTGCGCCTAGGGGAAGCC 62.554 72.222 28.92 11.73 37.11 4.35
1592 1662 2.812619 ATCTGCGCCTAGGGGAAGC 61.813 63.158 28.92 12.08 37.95 3.86
1593 1663 1.070445 CATCTGCGCCTAGGGGAAG 59.930 63.158 28.92 26.98 35.29 3.46
1594 1664 2.443394 CCATCTGCGCCTAGGGGAA 61.443 63.158 28.92 18.48 33.58 3.97
1595 1665 2.844362 CCATCTGCGCCTAGGGGA 60.844 66.667 28.92 12.96 33.58 4.81
1596 1666 3.946201 CCCATCTGCGCCTAGGGG 61.946 72.222 21.24 21.24 35.83 4.79
1597 1667 3.164269 ACCCATCTGCGCCTAGGG 61.164 66.667 19.04 19.04 45.20 3.53
1879 1953 5.222631 CGAGGTTCCTCCAAAAATTTCAAG 58.777 41.667 12.54 0.00 39.02 3.02
2038 2114 9.847224 TTCTCTTTAAAACATACCAAAGTCTCT 57.153 29.630 0.00 0.00 31.44 3.10
2098 2174 9.457436 AACTAATTAAACCGTATGGATCTTTGT 57.543 29.630 8.33 0.00 39.21 2.83
2231 2720 2.028130 CTCCGAATGCCTTCCATGC 58.972 57.895 0.00 0.00 33.49 4.06
2281 2771 4.838152 CCTCCATGTGTCCGGCGG 62.838 72.222 22.51 22.51 0.00 6.13
2282 2772 3.723235 CTCCTCCATGTGTCCGGCG 62.723 68.421 0.00 0.00 0.00 6.46
2283 2773 1.899437 TTCTCCTCCATGTGTCCGGC 61.899 60.000 0.00 0.00 0.00 6.13
2284 2774 0.613260 TTTCTCCTCCATGTGTCCGG 59.387 55.000 0.00 0.00 0.00 5.14
2285 2775 2.472695 TTTTCTCCTCCATGTGTCCG 57.527 50.000 0.00 0.00 0.00 4.79
2286 2776 3.282885 GGATTTTCTCCTCCATGTGTCC 58.717 50.000 0.00 0.00 41.29 4.02
2287 2777 3.282885 GGGATTTTCTCCTCCATGTGTC 58.717 50.000 0.00 0.00 44.28 3.67
2288 2778 2.024941 GGGGATTTTCTCCTCCATGTGT 60.025 50.000 0.00 0.00 44.28 3.72
2289 2779 2.659428 GGGGATTTTCTCCTCCATGTG 58.341 52.381 0.00 0.00 44.28 3.21
2295 2785 1.492599 CTCCAGGGGGATTTTCTCCTC 59.507 57.143 0.00 0.00 44.83 3.71
2296 2786 1.082879 TCTCCAGGGGGATTTTCTCCT 59.917 52.381 0.00 0.00 43.91 3.69
2297 2787 1.213182 GTCTCCAGGGGGATTTTCTCC 59.787 57.143 0.00 0.00 43.91 3.71
2298 2788 2.092699 CAGTCTCCAGGGGGATTTTCTC 60.093 54.545 0.00 0.00 43.91 2.87
2299 2789 1.918957 CAGTCTCCAGGGGGATTTTCT 59.081 52.381 0.00 0.00 43.91 2.52
2300 2790 1.064389 CCAGTCTCCAGGGGGATTTTC 60.064 57.143 0.00 0.00 43.91 2.29
2301 2791 1.002857 CCAGTCTCCAGGGGGATTTT 58.997 55.000 0.00 0.00 43.91 1.82
2302 2792 1.575447 GCCAGTCTCCAGGGGGATTT 61.575 60.000 0.00 0.00 43.91 2.17
2303 2793 2.003548 GCCAGTCTCCAGGGGGATT 61.004 63.158 0.00 0.00 43.91 3.01
2304 2794 2.367512 GCCAGTCTCCAGGGGGAT 60.368 66.667 0.00 0.00 43.91 3.85
2307 2797 2.765807 ATCGCCAGTCTCCAGGGG 60.766 66.667 0.00 0.00 39.04 4.79
2308 2798 2.503061 CATCGCCAGTCTCCAGGG 59.497 66.667 0.00 0.00 0.00 4.45
2309 2799 2.503061 CCATCGCCAGTCTCCAGG 59.497 66.667 0.00 0.00 0.00 4.45
2310 2800 2.503061 CCCATCGCCAGTCTCCAG 59.497 66.667 0.00 0.00 0.00 3.86
2311 2801 3.083349 CCCCATCGCCAGTCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
2312 2802 3.866582 CCCCCATCGCCAGTCTCC 61.867 72.222 0.00 0.00 0.00 3.71
2313 2803 4.554036 GCCCCCATCGCCAGTCTC 62.554 72.222 0.00 0.00 0.00 3.36
2321 2811 2.645394 ATTGGACATGGCCCCCATCG 62.645 60.000 17.19 0.00 43.15 3.84
2322 2812 0.398948 AATTGGACATGGCCCCCATC 60.399 55.000 17.19 0.00 43.15 3.51
2323 2813 0.044549 AAATTGGACATGGCCCCCAT 59.955 50.000 17.19 0.96 46.37 4.00
2324 2814 0.908656 CAAATTGGACATGGCCCCCA 60.909 55.000 17.19 4.65 38.19 4.96
2325 2815 1.625417 CCAAATTGGACATGGCCCCC 61.625 60.000 17.19 1.73 40.96 5.40
2326 2816 1.906995 CCAAATTGGACATGGCCCC 59.093 57.895 17.19 4.51 40.96 5.80
2335 2825 0.033208 CAGCTAGGGGCCAAATTGGA 60.033 55.000 17.47 0.00 40.96 3.53
2336 2826 0.033208 TCAGCTAGGGGCCAAATTGG 60.033 55.000 7.84 7.84 43.05 3.16
2337 2827 1.851304 TTCAGCTAGGGGCCAAATTG 58.149 50.000 4.39 0.00 43.05 2.32
2338 2828 2.854736 ATTCAGCTAGGGGCCAAATT 57.145 45.000 4.39 0.00 43.05 1.82
2339 2829 2.785857 AGTATTCAGCTAGGGGCCAAAT 59.214 45.455 4.39 0.00 43.05 2.32
2340 2830 2.205342 AGTATTCAGCTAGGGGCCAAA 58.795 47.619 4.39 0.00 43.05 3.28
2341 2831 1.893315 AGTATTCAGCTAGGGGCCAA 58.107 50.000 4.39 0.00 43.05 4.52
2342 2832 2.787339 TAGTATTCAGCTAGGGGCCA 57.213 50.000 4.39 0.00 43.05 5.36
2343 2833 4.041691 TGAAATAGTATTCAGCTAGGGGCC 59.958 45.833 0.00 0.00 43.05 5.80
2344 2834 5.228945 TGAAATAGTATTCAGCTAGGGGC 57.771 43.478 0.00 0.00 42.19 5.80
2353 2843 5.912149 ATGGGCCTCTGAAATAGTATTCA 57.088 39.130 4.53 0.00 37.70 2.57
2354 2844 6.825721 CCATATGGGCCTCTGAAATAGTATTC 59.174 42.308 14.52 0.00 0.00 1.75
2355 2845 6.725364 CCATATGGGCCTCTGAAATAGTATT 58.275 40.000 14.52 0.00 0.00 1.89
2356 2846 6.319048 CCATATGGGCCTCTGAAATAGTAT 57.681 41.667 14.52 0.00 0.00 2.12
2357 2847 5.762179 CCATATGGGCCTCTGAAATAGTA 57.238 43.478 14.52 0.00 0.00 1.82
2358 2848 4.647564 CCATATGGGCCTCTGAAATAGT 57.352 45.455 14.52 0.00 0.00 2.12
2371 2861 1.121407 TGACTCCGGAGCCATATGGG 61.121 60.000 31.56 5.63 40.85 4.00
2372 2862 0.319728 CTGACTCCGGAGCCATATGG 59.680 60.000 31.56 18.07 38.53 2.74
2373 2863 0.319728 CCTGACTCCGGAGCCATATG 59.680 60.000 31.56 14.58 0.00 1.78
2374 2864 1.476007 GCCTGACTCCGGAGCCATAT 61.476 60.000 31.56 11.74 0.00 1.78
2375 2865 2.134287 GCCTGACTCCGGAGCCATA 61.134 63.158 31.56 13.73 0.00 2.74
2376 2866 3.474570 GCCTGACTCCGGAGCCAT 61.475 66.667 31.56 12.59 0.00 4.40
2378 2868 3.672295 CTTGCCTGACTCCGGAGCC 62.672 68.421 31.56 22.07 0.00 4.70
2379 2869 2.125350 CTTGCCTGACTCCGGAGC 60.125 66.667 31.56 22.90 0.00 4.70
2380 2870 2.125350 GCTTGCCTGACTCCGGAG 60.125 66.667 30.11 30.11 0.00 4.63
2381 2871 2.922503 TGCTTGCCTGACTCCGGA 60.923 61.111 2.93 2.93 0.00 5.14
2382 2872 2.435586 CTGCTTGCCTGACTCCGG 60.436 66.667 0.00 0.00 0.00 5.14
2383 2873 3.123620 GCTGCTTGCCTGACTCCG 61.124 66.667 0.00 0.00 35.15 4.63
2392 2882 1.237285 TTTCGAAGGAGGCTGCTTGC 61.237 55.000 26.61 15.48 41.94 4.01
2393 2883 0.801251 CTTTCGAAGGAGGCTGCTTG 59.199 55.000 26.61 17.08 0.00 4.01
2394 2884 0.687354 TCTTTCGAAGGAGGCTGCTT 59.313 50.000 21.91 21.91 0.00 3.91
2395 2885 0.687354 TTCTTTCGAAGGAGGCTGCT 59.313 50.000 10.08 1.28 0.00 4.24
2396 2886 1.082690 CTTCTTTCGAAGGAGGCTGC 58.917 55.000 10.08 0.00 42.35 5.25
2404 2894 1.801178 GTGCACCTCCTTCTTTCGAAG 59.199 52.381 5.22 0.00 45.00 3.79
2405 2895 1.542547 GGTGCACCTCCTTCTTTCGAA 60.543 52.381 29.12 0.00 0.00 3.71
2406 2896 0.034896 GGTGCACCTCCTTCTTTCGA 59.965 55.000 29.12 0.00 0.00 3.71
2407 2897 0.035458 AGGTGCACCTCCTTCTTTCG 59.965 55.000 33.20 0.00 44.77 3.46
2408 2898 3.636153 ATAGGTGCACCTCCTTCTTTC 57.364 47.619 41.00 8.05 44.77 2.62
2409 2899 3.589288 AGAATAGGTGCACCTCCTTCTTT 59.411 43.478 35.78 24.99 44.77 2.52
2410 2900 3.054802 CAGAATAGGTGCACCTCCTTCTT 60.055 47.826 37.36 27.25 44.77 2.52
2411 2901 2.503356 CAGAATAGGTGCACCTCCTTCT 59.497 50.000 35.78 35.78 44.77 2.85
2412 2902 2.501723 TCAGAATAGGTGCACCTCCTTC 59.498 50.000 41.00 36.40 44.77 3.46
2413 2903 2.237392 GTCAGAATAGGTGCACCTCCTT 59.763 50.000 41.00 32.23 44.77 3.36
2414 2904 1.834263 GTCAGAATAGGTGCACCTCCT 59.166 52.381 41.00 30.09 44.77 3.69
2415 2905 1.134371 GGTCAGAATAGGTGCACCTCC 60.134 57.143 41.00 28.67 44.77 4.30
2416 2906 1.834263 AGGTCAGAATAGGTGCACCTC 59.166 52.381 41.00 26.76 44.77 3.85
2418 2908 1.834263 AGAGGTCAGAATAGGTGCACC 59.166 52.381 29.22 29.22 0.00 5.01
2419 2909 2.234908 ACAGAGGTCAGAATAGGTGCAC 59.765 50.000 8.80 8.80 0.00 4.57
2420 2910 2.497675 GACAGAGGTCAGAATAGGTGCA 59.502 50.000 0.00 0.00 43.73 4.57
2421 2911 2.159028 GGACAGAGGTCAGAATAGGTGC 60.159 54.545 0.00 0.00 46.17 5.01
2422 2912 3.099905 TGGACAGAGGTCAGAATAGGTG 58.900 50.000 0.00 0.00 46.17 4.00
2423 2913 3.474798 TGGACAGAGGTCAGAATAGGT 57.525 47.619 0.00 0.00 46.17 3.08
2424 2914 4.039004 CAGATGGACAGAGGTCAGAATAGG 59.961 50.000 0.00 0.00 46.17 2.57
2425 2915 4.501229 GCAGATGGACAGAGGTCAGAATAG 60.501 50.000 0.00 0.00 46.17 1.73
2426 2916 3.386078 GCAGATGGACAGAGGTCAGAATA 59.614 47.826 0.00 0.00 46.17 1.75
2427 2917 2.170187 GCAGATGGACAGAGGTCAGAAT 59.830 50.000 0.00 0.00 46.17 2.40
2428 2918 1.552337 GCAGATGGACAGAGGTCAGAA 59.448 52.381 0.00 0.00 46.17 3.02
2429 2919 1.189752 GCAGATGGACAGAGGTCAGA 58.810 55.000 0.00 0.00 46.17 3.27
2430 2920 1.193323 AGCAGATGGACAGAGGTCAG 58.807 55.000 0.00 0.00 46.17 3.51
2431 2921 2.103373 GTAGCAGATGGACAGAGGTCA 58.897 52.381 0.00 0.00 46.17 4.02
2432 2922 1.066303 CGTAGCAGATGGACAGAGGTC 59.934 57.143 0.00 0.00 43.55 3.85
2433 2923 1.107114 CGTAGCAGATGGACAGAGGT 58.893 55.000 0.00 0.00 0.00 3.85
2434 2924 1.066303 GACGTAGCAGATGGACAGAGG 59.934 57.143 0.00 0.00 0.00 3.69
2435 2925 2.020720 AGACGTAGCAGATGGACAGAG 58.979 52.381 0.00 0.00 0.00 3.35
2436 2926 2.130272 AGACGTAGCAGATGGACAGA 57.870 50.000 0.00 0.00 0.00 3.41
2437 2927 2.164422 TCAAGACGTAGCAGATGGACAG 59.836 50.000 0.00 0.00 0.00 3.51
2438 2928 2.164422 CTCAAGACGTAGCAGATGGACA 59.836 50.000 0.00 0.00 0.00 4.02
2439 2929 2.803451 CTCAAGACGTAGCAGATGGAC 58.197 52.381 0.00 0.00 0.00 4.02
2440 2930 1.135139 GCTCAAGACGTAGCAGATGGA 59.865 52.381 3.18 0.00 38.63 3.41
2441 2931 1.135915 AGCTCAAGACGTAGCAGATGG 59.864 52.381 10.48 0.00 41.32 3.51
2442 2932 2.575694 AGCTCAAGACGTAGCAGATG 57.424 50.000 10.48 0.00 41.32 2.90
2443 2933 2.493675 TCAAGCTCAAGACGTAGCAGAT 59.506 45.455 10.48 0.00 41.32 2.90
2444 2934 1.886542 TCAAGCTCAAGACGTAGCAGA 59.113 47.619 10.48 5.22 41.32 4.26
2525 3015 6.148811 TCGATTGATACCTTGGTTCTCAAAAC 59.851 38.462 16.13 13.20 34.56 2.43
2549 3039 0.833287 TTGCTCATGGCCTCCTACTC 59.167 55.000 3.32 0.00 40.92 2.59
2564 3054 1.272313 TGTAGGTACGAGGGACTTGCT 60.272 52.381 0.00 0.00 45.68 3.91
2763 3254 2.868986 GCCCCCGGGTCTATTCTCG 61.869 68.421 21.85 0.00 37.65 4.04
2794 3285 0.530288 GCTCTCGAGAGAAGCCACTT 59.470 55.000 39.91 0.00 44.74 3.16
3103 3594 3.313526 GGGCAGCAAGACACATATTGTAG 59.686 47.826 0.00 0.00 39.17 2.74
3111 3602 1.228245 GAAGGGGCAGCAAGACACA 60.228 57.895 0.00 0.00 0.00 3.72
3258 3749 9.956720 TTTGAATCTTCTCTGAATTCTTTTGTC 57.043 29.630 7.05 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.