Multiple sequence alignment - TraesCS5D01G235700

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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 TraesCS5D01G235700 chr5D 100.000 5634 0 0 1 5634 344533317 344538950 0.000000e+00 10405.0
1 TraesCS5D01G235700 chr5D 82.145 1361 190 35 961 2298 432781755 432783085 0.000000e+00 1118.0
2 TraesCS5D01G235700 chr5D 83.515 734 116 4 3553 4286 118011671 118012399 0.000000e+00 680.0
3 TraesCS5D01G235700 chr5D 85.259 502 71 1 996 1497 432787109 432787607 1.080000e-141 514.0
4 TraesCS5D01G235700 chr5D 74.483 1015 162 60 2 952 67872804 67871823 3.230000e-92 350.0
5 TraesCS5D01G235700 chr5D 98.039 102 2 0 5086 5187 344538362 344538463 1.610000e-40 178.0
6 TraesCS5D01G235700 chr5D 98.039 102 2 0 5046 5147 344538402 344538503 1.610000e-40 178.0
7 TraesCS5D01G235700 chr5D 100.000 62 0 0 5126 5187 344538362 344538423 1.280000e-21 115.0
8 TraesCS5D01G235700 chr5D 100.000 62 0 0 5046 5107 344538442 344538503 1.280000e-21 115.0
9 TraesCS5D01G235700 chr5B 95.198 1999 65 10 894 2870 407241919 407239930 0.000000e+00 3131.0
10 TraesCS5D01G235700 chr5B 91.499 2188 139 22 2981 5147 407239917 407237756 0.000000e+00 2966.0
11 TraesCS5D01G235700 chr5B 81.961 1336 192 33 983 2298 525447597 525448903 0.000000e+00 1086.0
12 TraesCS5D01G235700 chr5B 77.422 1249 205 47 1000 2211 526574725 526575933 0.000000e+00 673.0
13 TraesCS5D01G235700 chr5B 82.016 734 125 6 3552 4284 663969287 663968560 8.020000e-173 617.0
14 TraesCS5D01G235700 chr5B 82.489 691 112 5 3601 4286 128850960 128850274 1.040000e-166 597.0
15 TraesCS5D01G235700 chr5B 85.515 573 41 21 5087 5634 407237856 407237301 1.370000e-155 560.0
16 TraesCS5D01G235700 chr5B 83.429 525 74 5 982 1497 525452628 525453148 5.110000e-130 475.0
17 TraesCS5D01G235700 chr5B 77.135 691 114 32 1000 1665 526248267 526248938 1.490000e-95 361.0
18 TraesCS5D01G235700 chr5B 96.721 61 2 0 5127 5187 407237856 407237796 9.990000e-18 102.0
19 TraesCS5D01G235700 chr5B 93.443 61 4 0 5047 5107 407237816 407237756 2.160000e-14 91.6
20 TraesCS5D01G235700 chr5B 96.154 52 2 0 2162 2213 525833441 525833492 1.010000e-12 86.1
21 TraesCS5D01G235700 chr5B 96.154 52 2 0 2162 2213 525882547 525882598 1.010000e-12 86.1
22 TraesCS5D01G235700 chr5B 96.154 52 2 0 2162 2213 525936700 525936751 1.010000e-12 86.1
23 TraesCS5D01G235700 chr5A 95.013 1945 63 8 730 2644 447547314 447545374 0.000000e+00 3024.0
24 TraesCS5D01G235700 chr5A 91.525 826 61 7 4287 5107 447544122 447543301 0.000000e+00 1129.0
25 TraesCS5D01G235700 chr5A 77.982 1249 201 39 1000 2211 547612855 547614066 0.000000e+00 715.0
26 TraesCS5D01G235700 chr5A 86.216 399 26 14 3162 3552 447544495 447544118 6.800000e-109 405.0
27 TraesCS5D01G235700 chr5A 93.496 246 8 3 2639 2880 447545054 447544813 5.370000e-95 359.0
28 TraesCS5D01G235700 chr5A 91.200 125 7 4 5127 5249 447543362 447543240 3.490000e-37 167.0
29 TraesCS5D01G235700 chr5A 95.238 63 3 0 5303 5365 447543215 447543153 3.590000e-17 100.0
30 TraesCS5D01G235700 chrUn 82.257 1347 186 33 983 2309 63282959 63281646 0.000000e+00 1114.0
31 TraesCS5D01G235700 chrUn 82.257 1347 186 33 983 2309 327299195 327297882 0.000000e+00 1114.0
32 TraesCS5D01G235700 chrUn 78.710 155 17 13 691 837 22439237 22439091 7.770000e-14 89.8
33 TraesCS5D01G235700 chrUn 92.453 53 3 1 2163 2214 296014007 296013955 2.180000e-09 75.0
34 TraesCS5D01G235700 chr6D 80.135 1329 215 30 1000 2298 31479699 31481008 0.000000e+00 946.0
35 TraesCS5D01G235700 chr6A 79.614 1295 215 33 1000 2262 31745504 31744227 0.000000e+00 883.0
36 TraesCS5D01G235700 chr6A 83.206 131 8 10 718 837 26826157 26826284 2.150000e-19 108.0
37 TraesCS5D01G235700 chr7D 82.874 689 106 8 3553 4237 267998659 267999339 4.830000e-170 608.0
38 TraesCS5D01G235700 chr7A 82.378 698 106 12 3553 4245 649034678 649035363 4.860000e-165 592.0
39 TraesCS5D01G235700 chr7A 81.107 741 118 15 3553 4287 608645105 608645829 1.760000e-159 573.0
40 TraesCS5D01G235700 chr2D 82.378 698 106 11 3553 4245 217867247 217866562 4.860000e-165 592.0
41 TraesCS5D01G235700 chr2D 81.203 133 10 12 718 837 359664761 359664631 6.010000e-15 93.5
42 TraesCS5D01G235700 chr1A 81.132 742 120 12 3552 4287 519032996 519033723 1.360000e-160 577.0
43 TraesCS5D01G235700 chr1A 78.977 176 25 9 4738 4909 208887596 208887763 5.970000e-20 110.0
44 TraesCS5D01G235700 chr2A 76.954 998 148 54 2 952 765958261 765957299 1.410000e-135 494.0
45 TraesCS5D01G235700 chr6B 79.762 252 29 16 681 929 250674886 250674654 4.520000e-36 163.0
46 TraesCS5D01G235700 chr6B 78.814 236 37 6 2066 2298 56315980 56315755 4.550000e-31 147.0
47 TraesCS5D01G235700 chr1D 78.531 177 24 11 4738 4909 150947931 150947764 2.780000e-18 104.0
48 TraesCS5D01G235700 chr1D 81.395 129 8 13 722 837 457789208 457789333 2.160000e-14 91.6
49 TraesCS5D01G235700 chr1D 77.778 162 16 17 689 837 52289828 52289982 1.300000e-11 82.4
50 TraesCS5D01G235700 chr4D 76.000 200 25 18 650 837 356310922 356311110 1.300000e-11 82.4
51 TraesCS5D01G235700 chr2B 76.510 149 23 9 696 835 701508361 701508216 2.820000e-08 71.3
52 TraesCS5D01G235700 chr1B 87.302 63 5 2 4850 4909 231655110 231655048 1.010000e-07 69.4
53 TraesCS5D01G235700 chr4A 100.000 29 0 0 910 938 164407739 164407767 3.000000e-03 54.7


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 TraesCS5D01G235700 chr5D 344533317 344538950 5633 False 2198.20 10405 99.215600 1 5634 5 chr5D.!!$F4 5633
1 TraesCS5D01G235700 chr5D 432781755 432783085 1330 False 1118.00 1118 82.145000 961 2298 1 chr5D.!!$F2 1337
2 TraesCS5D01G235700 chr5D 118011671 118012399 728 False 680.00 680 83.515000 3553 4286 1 chr5D.!!$F1 733
3 TraesCS5D01G235700 chr5D 67871823 67872804 981 True 350.00 350 74.483000 2 952 1 chr5D.!!$R1 950
4 TraesCS5D01G235700 chr5B 407237301 407241919 4618 True 1370.12 3131 92.475200 894 5634 5 chr5B.!!$R3 4740
5 TraesCS5D01G235700 chr5B 525447597 525453148 5551 False 780.50 1086 82.695000 982 2298 2 chr5B.!!$F6 1316
6 TraesCS5D01G235700 chr5B 526574725 526575933 1208 False 673.00 673 77.422000 1000 2211 1 chr5B.!!$F5 1211
7 TraesCS5D01G235700 chr5B 663968560 663969287 727 True 617.00 617 82.016000 3552 4284 1 chr5B.!!$R2 732
8 TraesCS5D01G235700 chr5B 128850274 128850960 686 True 597.00 597 82.489000 3601 4286 1 chr5B.!!$R1 685
9 TraesCS5D01G235700 chr5B 526248267 526248938 671 False 361.00 361 77.135000 1000 1665 1 chr5B.!!$F4 665
10 TraesCS5D01G235700 chr5A 447543153 447547314 4161 True 864.00 3024 92.114667 730 5365 6 chr5A.!!$R1 4635
11 TraesCS5D01G235700 chr5A 547612855 547614066 1211 False 715.00 715 77.982000 1000 2211 1 chr5A.!!$F1 1211
12 TraesCS5D01G235700 chrUn 63281646 63282959 1313 True 1114.00 1114 82.257000 983 2309 1 chrUn.!!$R2 1326
13 TraesCS5D01G235700 chrUn 327297882 327299195 1313 True 1114.00 1114 82.257000 983 2309 1 chrUn.!!$R4 1326
14 TraesCS5D01G235700 chr6D 31479699 31481008 1309 False 946.00 946 80.135000 1000 2298 1 chr6D.!!$F1 1298
15 TraesCS5D01G235700 chr6A 31744227 31745504 1277 True 883.00 883 79.614000 1000 2262 1 chr6A.!!$R1 1262
16 TraesCS5D01G235700 chr7D 267998659 267999339 680 False 608.00 608 82.874000 3553 4237 1 chr7D.!!$F1 684
17 TraesCS5D01G235700 chr7A 649034678 649035363 685 False 592.00 592 82.378000 3553 4245 1 chr7A.!!$F2 692
18 TraesCS5D01G235700 chr7A 608645105 608645829 724 False 573.00 573 81.107000 3553 4287 1 chr7A.!!$F1 734
19 TraesCS5D01G235700 chr2D 217866562 217867247 685 True 592.00 592 82.378000 3553 4245 1 chr2D.!!$R1 692
20 TraesCS5D01G235700 chr1A 519032996 519033723 727 False 577.00 577 81.132000 3552 4287 1 chr1A.!!$F2 735
21 TraesCS5D01G235700 chr2A 765957299 765958261 962 True 494.00 494 76.954000 2 952 1 chr2A.!!$R1 950

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
905 1051 0.959553 TTCTCCTCGCTCGAAGTGTT 59.040 50.0 0.00 0.0 0.00 3.32 F
1416 1583 0.520827 GCTACGTCGTCCTCGTCAAG 60.521 60.0 0.00 0.0 41.72 3.02 F
2112 2339 0.830648 TATCCCTCTGCCTGGAAACG 59.169 55.0 0.00 0.0 33.54 3.60 F
2900 3497 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.00 0.0 0.00 3.82 F
4189 4884 0.459899 TGCGCACGAGTGAGGATAAT 59.540 50.0 5.66 0.0 0.00 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2893 3490 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.00 3.72 R
2899 3496 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.00 3.72 R
3728 4409 0.969894 AGCACTAGTCTTTCCTGCGT 59.030 50.0 0.0 0.0 32.92 5.24 R
4192 4887 0.247736 AGCACTAGTCTTTCCTGCGG 59.752 55.0 0.0 0.0 32.92 5.69 R
5200 7600 1.176619 AAACGCAACCTTACCTGGCC 61.177 55.0 0.0 0.0 0.00 5.36 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
148 162 7.598493 CCCAATAAAAATTGAAGACACGAACAT 59.402 33.333 0.00 0.00 33.55 2.71
184 198 6.745794 TTCCAAACAATTTCTGAAAGGGAT 57.254 33.333 8.95 0.00 0.00 3.85
185 199 6.745794 TCCAAACAATTTCTGAAAGGGATT 57.254 33.333 8.95 2.05 0.00 3.01
186 200 7.135591 TCCAAACAATTTCTGAAAGGGATTT 57.864 32.000 8.95 4.33 0.00 2.17
302 317 4.734854 GCACGATATTTGAAACATGCGAAT 59.265 37.500 0.00 0.00 0.00 3.34
377 453 7.622893 TTTCTGAACAATTTTTGGAAAAGGG 57.377 32.000 0.00 0.00 34.12 3.95
397 474 1.270826 GCAACTTTTCTCAAGCTCCCC 59.729 52.381 0.00 0.00 0.00 4.81
398 475 1.889170 CAACTTTTCTCAAGCTCCCCC 59.111 52.381 0.00 0.00 0.00 5.40
425 502 5.806089 AATTGAAGACGCGAACATTTTTC 57.194 34.783 15.93 0.99 0.00 2.29
472 551 9.410556 ACAATAGAAACATTTTCGAAATCTTGG 57.589 29.630 12.12 6.75 0.00 3.61
478 557 9.420966 GAAACATTTTCGAAATCTTGGAAAAAC 57.579 29.630 12.12 0.00 45.78 2.43
480 559 8.485976 ACATTTTCGAAATCTTGGAAAAACAA 57.514 26.923 12.12 0.00 45.78 2.83
484 563 7.518731 TTCGAAATCTTGGAAAAACAAGTTG 57.481 32.000 0.00 0.00 46.11 3.16
485 564 6.626302 TCGAAATCTTGGAAAAACAAGTTGT 58.374 32.000 1.64 1.64 46.11 3.32
490 572 8.791327 AATCTTGGAAAAACAAGTTGTGATTT 57.209 26.923 9.79 13.65 46.11 2.17
491 573 8.791327 ATCTTGGAAAAACAAGTTGTGATTTT 57.209 26.923 15.12 15.12 46.11 1.82
492 574 8.614469 TCTTGGAAAAACAAGTTGTGATTTTT 57.386 26.923 9.79 12.37 46.11 1.94
539 629 7.710475 ACACGAACAATTTTTGAAATTCCTGAT 59.290 29.630 0.00 0.00 0.00 2.90
540 630 8.550376 CACGAACAATTTTTGAAATTCCTGATT 58.450 29.630 0.00 0.00 0.00 2.57
541 631 9.108284 ACGAACAATTTTTGAAATTCCTGATTT 57.892 25.926 0.00 0.00 40.61 2.17
646 740 7.872163 TGAAAACTTGATCATTTTTCATCCG 57.128 32.000 26.70 2.13 41.85 4.18
736 834 8.519799 AATAGGAAACAGAAACAGAACAGAAA 57.480 30.769 0.00 0.00 0.00 2.52
737 835 6.834168 AGGAAACAGAAACAGAACAGAAAA 57.166 33.333 0.00 0.00 0.00 2.29
738 836 7.410120 AGGAAACAGAAACAGAACAGAAAAT 57.590 32.000 0.00 0.00 0.00 1.82
739 837 7.484140 AGGAAACAGAAACAGAACAGAAAATC 58.516 34.615 0.00 0.00 0.00 2.17
741 839 7.433425 GGAAACAGAAACAGAACAGAAAATCAG 59.567 37.037 0.00 0.00 0.00 2.90
780 926 8.846943 AAAAACAAGAAAGTGAAAAACCAGAT 57.153 26.923 0.00 0.00 0.00 2.90
781 927 8.846943 AAAACAAGAAAGTGAAAAACCAGATT 57.153 26.923 0.00 0.00 0.00 2.40
840 986 2.103432 GGTTCCCAAAACCGGTTGAAAT 59.897 45.455 23.08 0.95 0.00 2.17
847 993 2.279935 AACCGGTTGAAATAGGTGCA 57.720 45.000 21.56 0.00 37.03 4.57
848 994 2.507407 ACCGGTTGAAATAGGTGCAT 57.493 45.000 0.00 0.00 35.36 3.96
849 995 3.637911 ACCGGTTGAAATAGGTGCATA 57.362 42.857 0.00 0.00 35.36 3.14
850 996 3.275999 ACCGGTTGAAATAGGTGCATAC 58.724 45.455 0.00 0.00 35.36 2.39
851 997 3.054655 ACCGGTTGAAATAGGTGCATACT 60.055 43.478 0.00 0.00 35.36 2.12
852 998 3.560068 CCGGTTGAAATAGGTGCATACTC 59.440 47.826 0.00 0.00 0.00 2.59
853 999 3.245284 CGGTTGAAATAGGTGCATACTCG 59.755 47.826 0.00 0.00 0.00 4.18
905 1051 0.959553 TTCTCCTCGCTCGAAGTGTT 59.040 50.000 0.00 0.00 0.00 3.32
998 1147 2.355193 GCCTCTCTTCTCCAGGCGT 61.355 63.158 0.00 0.00 43.35 5.68
1066 1230 2.118076 CACCCACCACCATTGCCT 59.882 61.111 0.00 0.00 0.00 4.75
1068 1232 2.440147 CCCACCACCATTGCCTCA 59.560 61.111 0.00 0.00 0.00 3.86
1416 1583 0.520827 GCTACGTCGTCCTCGTCAAG 60.521 60.000 0.00 0.00 41.72 3.02
1927 2118 3.049912 GGAACGCTTCATGTTTGGTTTC 58.950 45.455 0.00 0.00 0.00 2.78
2112 2339 0.830648 TATCCCTCTGCCTGGAAACG 59.169 55.000 0.00 0.00 33.54 3.60
2299 2532 5.645056 TGAGGGCATTGGATTATTGTAGA 57.355 39.130 0.00 0.00 0.00 2.59
2301 2534 7.328404 TGAGGGCATTGGATTATTGTAGATA 57.672 36.000 0.00 0.00 0.00 1.98
2302 2535 7.754624 TGAGGGCATTGGATTATTGTAGATAA 58.245 34.615 0.00 0.00 0.00 1.75
2303 2536 8.393259 TGAGGGCATTGGATTATTGTAGATAAT 58.607 33.333 0.00 0.00 0.00 1.28
2304 2537 8.814038 AGGGCATTGGATTATTGTAGATAATC 57.186 34.615 9.28 9.28 39.21 1.75
2306 2539 8.680903 GGGCATTGGATTATTGTAGATAATCTG 58.319 37.037 14.79 9.08 39.62 2.90
2307 2540 9.236006 GGCATTGGATTATTGTAGATAATCTGT 57.764 33.333 14.79 3.58 39.62 3.41
2450 2718 1.195448 CTGACAACCGTGAGTGATTGC 59.805 52.381 0.00 0.00 0.00 3.56
2498 2766 7.094933 TGACTTCGATAGTTTTAGGGAAAAAGC 60.095 37.037 0.00 0.00 37.74 3.51
2499 2767 6.940867 ACTTCGATAGTTTTAGGGAAAAAGCT 59.059 34.615 0.00 0.00 37.74 3.74
2524 2792 3.350833 AGAGAGTTGATGGGAAATGCAC 58.649 45.455 0.00 0.00 0.00 4.57
2614 2882 8.532186 ACTGATCATACTGTACTTCTTCTCAT 57.468 34.615 0.00 0.00 0.00 2.90
2863 3460 9.155975 TCTTTTATTCTCAGCTTGAATAGTCAC 57.844 33.333 14.72 0.00 37.59 3.67
2884 3481 1.141657 CCATCCTGGGTCCACTATGTG 59.858 57.143 0.00 0.00 32.67 3.21
2886 3483 1.275666 TCCTGGGTCCACTATGTGTG 58.724 55.000 0.00 0.00 45.80 3.82
2888 3485 1.339055 CCTGGGTCCACTATGTGTGTG 60.339 57.143 0.00 0.00 44.81 3.82
2890 3487 1.071542 TGGGTCCACTATGTGTGTGTG 59.928 52.381 0.00 0.00 44.81 3.82
2892 3489 2.143122 GGTCCACTATGTGTGTGTGTG 58.857 52.381 0.00 0.00 44.81 3.82
2893 3490 2.484770 GGTCCACTATGTGTGTGTGTGT 60.485 50.000 0.00 0.00 44.81 3.72
2894 3491 2.543848 GTCCACTATGTGTGTGTGTGTG 59.456 50.000 0.00 0.00 44.81 3.82
2895 3492 2.169561 TCCACTATGTGTGTGTGTGTGT 59.830 45.455 0.00 0.00 44.81 3.72
2896 3493 2.287644 CCACTATGTGTGTGTGTGTGTG 59.712 50.000 0.00 0.00 44.81 3.82
2897 3494 2.935849 CACTATGTGTGTGTGTGTGTGT 59.064 45.455 0.00 0.00 41.53 3.72
2898 3495 2.935849 ACTATGTGTGTGTGTGTGTGTG 59.064 45.455 0.00 0.00 0.00 3.82
2899 3496 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2900 3497 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2901 3498 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2902 3499 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2903 3500 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2904 3501 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2905 3502 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2906 3503 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2907 3504 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2908 3505 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2909 3506 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2910 3507 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2911 3508 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2912 3509 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2913 3510 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2914 3511 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2915 3512 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2916 3513 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2917 3514 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2918 3515 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2919 3516 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2920 3517 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2921 3518 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2922 3519 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2930 3527 4.142795 TGTGTGTGTGTGTGTGTTATTGAC 60.143 41.667 0.00 0.00 0.00 3.18
2945 3542 7.667635 TGTGTTATTGACCCAGTCATTTTATCA 59.332 33.333 0.00 0.00 42.40 2.15
2946 3543 7.968405 GTGTTATTGACCCAGTCATTTTATCAC 59.032 37.037 0.00 4.18 42.40 3.06
2951 3548 5.705441 TGACCCAGTCATTTTATCACTTGTC 59.295 40.000 0.00 0.00 37.67 3.18
2963 3560 4.724279 ATCACTTGTCCCTAACCTTGTT 57.276 40.909 0.00 0.00 0.00 2.83
2967 3564 5.358725 TCACTTGTCCCTAACCTTGTTTTTC 59.641 40.000 0.00 0.00 0.00 2.29
2974 3571 6.439375 GTCCCTAACCTTGTTTTTCCCATTAT 59.561 38.462 0.00 0.00 0.00 1.28
2983 3580 8.466798 CCTTGTTTTTCCCATTATGGTACTTAG 58.533 37.037 10.65 0.00 35.17 2.18
2995 3592 9.840427 CATTATGGTACTTAGTTTCCTTTTGTG 57.160 33.333 0.00 0.00 0.00 3.33
3043 3640 1.134128 TGGCACTGAAGTTGCAGAGAA 60.134 47.619 0.00 0.00 39.20 2.87
3045 3642 2.161211 GGCACTGAAGTTGCAGAGAATC 59.839 50.000 0.00 0.00 39.20 2.52
3116 3713 6.092748 AGTTATTTGCATAGTTTTGCTTCGG 58.907 36.000 0.00 0.00 43.18 4.30
3255 3927 7.755591 TGCAGCTAACTTAAGAATTGAGATTG 58.244 34.615 10.09 3.07 34.95 2.67
3508 4183 4.307443 TCTTAGCTGGTATGTGATGTCG 57.693 45.455 0.00 0.00 0.00 4.35
3572 4253 4.568072 TTGTGAGAGCCTGGCTTAATAA 57.432 40.909 24.26 12.64 39.88 1.40
3585 4266 7.118971 GCCTGGCTTAATAAGAATGATAGACTG 59.881 40.741 12.43 0.00 0.00 3.51
3589 4270 7.062839 GGCTTAATAAGAATGATAGACTGCTCG 59.937 40.741 3.88 0.00 0.00 5.03
3619 4300 3.431415 AGGAATTCCTTCTTTTTCGGGG 58.569 45.455 21.89 0.00 46.09 5.73
3643 4324 5.122519 GCCCATTTGAAAAGAACTCCAAAA 58.877 37.500 0.00 0.00 33.05 2.44
3715 4396 2.110213 GTCCCAGGTGTGCACGAA 59.890 61.111 13.13 0.00 0.00 3.85
3728 4409 3.064207 GTGCACGAATGAGGACAAAGTA 58.936 45.455 0.00 0.00 0.00 2.24
3746 4427 2.094649 AGTACGCAGGAAAGACTAGTGC 60.095 50.000 0.00 0.00 0.00 4.40
3817 4503 2.895372 GCTATGACCGGGGCGTTG 60.895 66.667 6.32 0.00 0.00 4.10
3950 4640 1.298413 CGGACTGGACGCAGATACG 60.298 63.158 0.00 0.00 39.50 3.06
4022 4713 1.906574 GAGTGGGGGTGTATGTGAGAA 59.093 52.381 0.00 0.00 0.00 2.87
4121 4816 2.548057 CTCCAAAGTTAAGCGTGCTTGA 59.452 45.455 16.98 6.15 37.47 3.02
4186 4881 2.125912 GTGCGCACGAGTGAGGAT 60.126 61.111 26.77 0.00 33.11 3.24
4189 4884 0.459899 TGCGCACGAGTGAGGATAAT 59.540 50.000 5.66 0.00 0.00 1.28
4192 4887 2.120232 CGCACGAGTGAGGATAATGTC 58.880 52.381 7.50 0.00 0.00 3.06
4225 4920 0.115349 AGTGCTAGTCTGTGGGGTCT 59.885 55.000 0.00 0.00 0.00 3.85
4230 4925 2.530701 CTAGTCTGTGGGGTCTGTCTT 58.469 52.381 0.00 0.00 0.00 3.01
4238 4933 1.915983 GGGTCTGTCTTGATCCCCC 59.084 63.158 0.00 0.00 31.19 5.40
4250 4949 2.142292 GATCCCCCGCCAGGCATAAT 62.142 60.000 13.30 0.00 35.76 1.28
4333 5032 2.436417 TGTACTCCAAGCTTGATTGCC 58.564 47.619 28.05 12.38 0.00 4.52
4392 5091 3.060602 GTGAGTCCAAGCTGTTCACTAC 58.939 50.000 0.00 0.00 36.21 2.73
4420 5119 6.152932 AGATGGCATTGATGTAACAAATCC 57.847 37.500 0.00 0.00 33.44 3.01
4481 5219 5.051907 GCGATTTGTCTATACAAGTACGTGG 60.052 44.000 13.47 0.00 45.99 4.94
4510 5248 7.760340 CCTGTACTTACACTGAACTATCCTTTC 59.240 40.741 0.00 0.00 31.93 2.62
4581 5322 1.970114 CTGCTCCTGTGGGCACAAG 60.970 63.158 0.00 0.00 41.33 3.16
4613 5354 0.388520 TGTTCATGTCTCAGCGTCGG 60.389 55.000 0.00 0.00 0.00 4.79
4754 5501 1.620822 ACCCAACCTCTTTGTCATGC 58.379 50.000 0.00 0.00 32.71 4.06
4951 7164 2.641815 AGCCTTCTGAATCACTTGTCCT 59.358 45.455 0.00 0.00 0.00 3.85
4967 7180 5.527582 ACTTGTCCTATCAACCGATTATTGC 59.472 40.000 0.00 0.00 32.73 3.56
5068 7335 6.297080 ACATTCATATTTGTTCATGGGCAA 57.703 33.333 0.00 0.00 0.00 4.52
5069 7336 6.342906 ACATTCATATTTGTTCATGGGCAAG 58.657 36.000 0.00 0.00 0.00 4.01
5070 7337 5.999205 TTCATATTTGTTCATGGGCAAGT 57.001 34.783 0.00 0.00 0.00 3.16
5071 7338 5.581126 TCATATTTGTTCATGGGCAAGTC 57.419 39.130 0.00 0.00 0.00 3.01
5072 7339 5.015515 TCATATTTGTTCATGGGCAAGTCA 58.984 37.500 0.00 0.00 0.00 3.41
5073 7340 5.657745 TCATATTTGTTCATGGGCAAGTCAT 59.342 36.000 0.00 0.00 0.00 3.06
5076 7343 3.719268 TGTTCATGGGCAAGTCATACT 57.281 42.857 0.00 0.00 0.00 2.12
5104 7371 9.507280 GTCAGTAACATTCATATTTGTTCATGG 57.493 33.333 0.00 0.00 37.29 3.66
5105 7372 8.685427 TCAGTAACATTCATATTTGTTCATGGG 58.315 33.333 0.00 0.00 37.29 4.00
5106 7373 7.436080 CAGTAACATTCATATTTGTTCATGGGC 59.564 37.037 0.00 0.00 37.29 5.36
5108 7375 6.297080 ACATTCATATTTGTTCATGGGCAA 57.703 33.333 0.00 0.00 0.00 4.52
5109 7376 6.342906 ACATTCATATTTGTTCATGGGCAAG 58.657 36.000 0.00 0.00 0.00 4.01
5110 7377 5.999205 TTCATATTTGTTCATGGGCAAGT 57.001 34.783 0.00 0.00 0.00 3.16
5111 7378 5.581126 TCATATTTGTTCATGGGCAAGTC 57.419 39.130 0.00 0.00 0.00 3.01
5112 7379 4.096231 TCATATTTGTTCATGGGCAAGTCG 59.904 41.667 0.00 0.00 0.00 4.18
5114 7381 2.552599 TTGTTCATGGGCAAGTCGTA 57.447 45.000 0.00 0.00 0.00 3.43
5131 7398 6.080648 AGTCGTACTTGTCAGTAACATTCA 57.919 37.500 0.00 0.00 37.24 2.57
5132 7399 6.688578 AGTCGTACTTGTCAGTAACATTCAT 58.311 36.000 0.00 0.00 37.24 2.57
5133 7400 7.823665 AGTCGTACTTGTCAGTAACATTCATA 58.176 34.615 0.00 0.00 37.24 2.15
5136 7403 9.647797 TCGTACTTGTCAGTAACATTCATATTT 57.352 29.630 0.00 0.00 37.24 1.40
5144 7411 9.507280 GTCAGTAACATTCATATTTGTTCATGG 57.493 33.333 0.00 0.00 37.29 3.66
5146 7413 7.436080 CAGTAACATTCATATTTGTTCATGGGC 59.564 37.037 0.00 0.00 37.29 5.36
5197 7597 0.895100 TTCATGGGCTGCTTCGCTTT 60.895 50.000 0.00 0.00 0.00 3.51
5198 7598 1.153901 CATGGGCTGCTTCGCTTTG 60.154 57.895 0.00 0.00 0.00 2.77
5200 7600 1.310933 ATGGGCTGCTTCGCTTTGAG 61.311 55.000 0.00 0.00 0.00 3.02
5236 7920 5.218885 TGCGTTTTGTCAATAACATTCAGG 58.781 37.500 9.67 0.00 37.82 3.86
5292 7976 7.299246 TCCTAGGAGGAATTTTATTCTACCG 57.701 40.000 7.62 0.00 42.51 4.02
5295 7979 7.819900 CCTAGGAGGAATTTTATTCTACCGATG 59.180 40.741 1.05 0.00 37.67 3.84
5296 7980 7.138054 AGGAGGAATTTTATTCTACCGATGT 57.862 36.000 0.00 0.00 0.00 3.06
5297 7981 7.574607 AGGAGGAATTTTATTCTACCGATGTT 58.425 34.615 0.00 0.00 0.00 2.71
5298 7982 8.053355 AGGAGGAATTTTATTCTACCGATGTTT 58.947 33.333 0.00 0.00 0.00 2.83
5299 7983 8.129211 GGAGGAATTTTATTCTACCGATGTTTG 58.871 37.037 0.00 0.00 0.00 2.93
5300 7984 8.801882 AGGAATTTTATTCTACCGATGTTTGA 57.198 30.769 0.00 0.00 0.00 2.69
5301 7985 9.238368 AGGAATTTTATTCTACCGATGTTTGAA 57.762 29.630 0.00 0.00 0.00 2.69
5352 8036 3.065233 TGAAATCGAACATGCATACTGGC 59.935 43.478 0.00 0.00 0.00 4.85
5359 8043 1.031571 CATGCATACTGGCGGTGGTT 61.032 55.000 9.79 0.00 36.28 3.67
5365 8049 2.191786 TACTGGCGGTGGTTCCCATG 62.192 60.000 9.79 0.00 35.28 3.66
5374 8058 0.395586 TGGTTCCCATGCATACTGGC 60.396 55.000 0.00 0.00 32.08 4.85
5406 8131 0.911769 CCTGGGTGAGATAGTGGCAA 59.088 55.000 0.00 0.00 0.00 4.52
5408 8133 1.556911 CTGGGTGAGATAGTGGCAACT 59.443 52.381 0.00 0.00 40.67 3.16
5432 8157 0.674581 TGGCGGTTCAAGATGAGCTG 60.675 55.000 0.00 0.00 37.09 4.24
5449 8175 2.626743 AGCTGCTCATTTGCTTTCTTGT 59.373 40.909 0.00 0.00 32.61 3.16
5500 8226 3.243367 TGGCAAACATTTCCGTTTCTCTG 60.243 43.478 0.00 0.00 36.98 3.35
5501 8227 2.726241 GCAAACATTTCCGTTTCTCTGC 59.274 45.455 0.00 0.00 36.98 4.26
5503 8229 3.904136 AACATTTCCGTTTCTCTGCTG 57.096 42.857 0.00 0.00 0.00 4.41
5610 8341 6.085573 TGTCGATCAATGTATGCTGTTTTTG 58.914 36.000 0.00 0.00 0.00 2.44
5612 8343 7.095017 TGTCGATCAATGTATGCTGTTTTTGTA 60.095 33.333 0.00 0.00 0.00 2.41
5618 8349 4.465886 TGTATGCTGTTTTTGTACCCTGT 58.534 39.130 0.00 0.00 0.00 4.00
5622 8353 3.132925 GCTGTTTTTGTACCCTGTCGTA 58.867 45.455 0.00 0.00 0.00 3.43
5626 8357 6.073112 GCTGTTTTTGTACCCTGTCGTAATTA 60.073 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 173 6.951971 TCCCTTTCAGAAATTGTTTGGAAAA 58.048 32.000 0.00 0.00 0.00 2.29
276 291 4.661125 GCATGTTTCAAATATCGTGCAGA 58.339 39.130 0.00 0.00 40.93 4.26
277 292 3.479590 CGCATGTTTCAAATATCGTGCAG 59.520 43.478 0.00 0.00 41.19 4.41
279 294 3.679725 TCGCATGTTTCAAATATCGTGC 58.320 40.909 0.00 0.00 38.81 5.34
280 295 8.492920 AATATTCGCATGTTTCAAATATCGTG 57.507 30.769 0.00 0.00 0.00 4.35
377 453 1.270826 GGGGAGCTTGAGAAAAGTTGC 59.729 52.381 0.00 0.00 0.00 4.17
397 474 2.697431 TCGCGTCTTCAATTTTTGGG 57.303 45.000 5.77 0.00 0.00 4.12
398 475 3.367607 TGTTCGCGTCTTCAATTTTTGG 58.632 40.909 5.77 0.00 0.00 3.28
399 476 5.559694 AATGTTCGCGTCTTCAATTTTTG 57.440 34.783 5.77 0.00 0.00 2.44
402 479 5.174943 GGAAAAATGTTCGCGTCTTCAATTT 59.825 36.000 5.77 4.65 0.00 1.82
451 529 8.940768 TTTTCCAAGATTTCGAAAATGTTTCT 57.059 26.923 15.66 9.80 32.14 2.52
455 533 8.485976 TTGTTTTTCCAAGATTTCGAAAATGT 57.514 26.923 15.66 0.00 35.90 2.71
457 535 8.716646 ACTTGTTTTTCCAAGATTTCGAAAAT 57.283 26.923 15.66 3.82 43.65 1.82
494 576 9.743937 GTTCGTGTTACAAATCGTTCATATTAA 57.256 29.630 0.00 0.00 0.00 1.40
495 577 8.923683 TGTTCGTGTTACAAATCGTTCATATTA 58.076 29.630 0.00 0.00 0.00 0.98
498 580 6.766452 TGTTCGTGTTACAAATCGTTCATA 57.234 33.333 0.00 0.00 0.00 2.15
501 583 6.963017 AATTGTTCGTGTTACAAATCGTTC 57.037 33.333 0.00 0.00 38.82 3.95
502 584 7.743520 AAAATTGTTCGTGTTACAAATCGTT 57.256 28.000 0.00 0.00 38.82 3.85
503 585 7.485277 TCAAAAATTGTTCGTGTTACAAATCGT 59.515 29.630 0.00 0.00 38.82 3.73
504 586 7.822713 TCAAAAATTGTTCGTGTTACAAATCG 58.177 30.769 0.00 0.00 38.82 3.34
505 587 9.959775 TTTCAAAAATTGTTCGTGTTACAAATC 57.040 25.926 0.00 0.00 38.82 2.17
508 590 9.959775 GAATTTCAAAAATTGTTCGTGTTACAA 57.040 25.926 2.56 0.00 39.58 2.41
509 591 8.596380 GGAATTTCAAAAATTGTTCGTGTTACA 58.404 29.630 2.56 0.00 0.00 2.41
510 592 8.813282 AGGAATTTCAAAAATTGTTCGTGTTAC 58.187 29.630 2.56 0.00 0.00 2.50
511 593 8.812329 CAGGAATTTCAAAAATTGTTCGTGTTA 58.188 29.630 2.56 0.00 30.94 2.41
512 594 7.547370 TCAGGAATTTCAAAAATTGTTCGTGTT 59.453 29.630 2.56 0.00 34.74 3.32
513 595 7.038659 TCAGGAATTTCAAAAATTGTTCGTGT 58.961 30.769 2.56 0.00 34.74 4.49
514 596 7.462109 TCAGGAATTTCAAAAATTGTTCGTG 57.538 32.000 2.56 0.65 34.56 4.35
515 597 8.661352 AATCAGGAATTTCAAAAATTGTTCGT 57.339 26.923 2.56 0.00 0.00 3.85
516 598 9.934190 AAAATCAGGAATTTCAAAAATTGTTCG 57.066 25.926 2.56 0.00 36.54 3.95
675 769 5.235831 TGTTTGTTTTTCCGTTTTTCCGTTT 59.764 32.000 0.00 0.00 0.00 3.60
679 773 5.849357 ACTGTTTGTTTTTCCGTTTTTCC 57.151 34.783 0.00 0.00 0.00 3.13
708 802 9.621629 TCTGTTCTGTTTCTGTTTCCTATTTAA 57.378 29.630 0.00 0.00 0.00 1.52
709 803 9.621629 TTCTGTTCTGTTTCTGTTTCCTATTTA 57.378 29.630 0.00 0.00 0.00 1.40
711 805 8.519799 TTTCTGTTCTGTTTCTGTTTCCTATT 57.480 30.769 0.00 0.00 0.00 1.73
712 806 8.519799 TTTTCTGTTCTGTTTCTGTTTCCTAT 57.480 30.769 0.00 0.00 0.00 2.57
713 807 7.931578 TTTTCTGTTCTGTTTCTGTTTCCTA 57.068 32.000 0.00 0.00 0.00 2.94
776 921 8.953313 ACCGGTTTTCCTTTATAGTTTAATCTG 58.047 33.333 0.00 0.00 37.95 2.90
780 926 8.688747 TGAACCGGTTTTCCTTTATAGTTTAA 57.311 30.769 23.22 0.00 37.95 1.52
781 927 7.391275 CCTGAACCGGTTTTCCTTTATAGTTTA 59.609 37.037 23.22 0.00 37.95 2.01
840 986 1.100510 AAGCGTCGAGTATGCACCTA 58.899 50.000 0.00 0.00 43.05 3.08
847 993 4.304939 GGCCTATTTTAAGCGTCGAGTAT 58.695 43.478 0.00 0.00 0.00 2.12
848 994 3.709987 GGCCTATTTTAAGCGTCGAGTA 58.290 45.455 0.00 0.00 0.00 2.59
849 995 2.547826 GGCCTATTTTAAGCGTCGAGT 58.452 47.619 0.00 0.00 0.00 4.18
850 996 1.521423 CGGCCTATTTTAAGCGTCGAG 59.479 52.381 0.00 0.00 0.00 4.04
851 997 1.563111 CGGCCTATTTTAAGCGTCGA 58.437 50.000 0.00 0.00 0.00 4.20
852 998 0.580104 CCGGCCTATTTTAAGCGTCG 59.420 55.000 0.00 0.00 0.00 5.12
853 999 0.306840 GCCGGCCTATTTTAAGCGTC 59.693 55.000 18.11 0.00 0.00 5.19
905 1051 0.653636 GCAAACTGTCGACCAAACGA 59.346 50.000 14.12 0.00 40.00 3.85
977 1124 1.608717 GCCTGGAGAAGAGAGGCGAA 61.609 60.000 0.00 0.00 42.84 4.70
998 1147 1.834378 CCTAGCTCGGAGGCCATGA 60.834 63.158 5.01 0.00 0.00 3.07
1066 1230 0.965866 AGGAGGTCGTCGCTGATTGA 60.966 55.000 0.00 0.00 0.00 2.57
1068 1232 0.681564 AGAGGAGGTCGTCGCTGATT 60.682 55.000 0.00 0.00 36.02 2.57
1416 1583 0.393077 CGATCTGGTGGGTGGTATCC 59.607 60.000 0.00 0.00 0.00 2.59
1497 1664 1.135228 GCCTCAAGAGAGTCGGAGAAC 60.135 57.143 0.00 0.00 39.69 3.01
1927 2118 1.343789 ACCATCATCATCAGCTCTCCG 59.656 52.381 0.00 0.00 0.00 4.63
2299 2532 6.000219 ACAGTTGACTCAAAGCACAGATTAT 59.000 36.000 0.00 0.00 0.00 1.28
2301 2534 4.202441 ACAGTTGACTCAAAGCACAGATT 58.798 39.130 0.00 0.00 0.00 2.40
2302 2535 3.813443 ACAGTTGACTCAAAGCACAGAT 58.187 40.909 0.00 0.00 0.00 2.90
2303 2536 3.266510 ACAGTTGACTCAAAGCACAGA 57.733 42.857 0.00 0.00 0.00 3.41
2304 2537 4.361451 AAACAGTTGACTCAAAGCACAG 57.639 40.909 0.00 0.00 0.00 3.66
2471 2739 8.680039 TTTTTCCCTAAAACTATCGAAGTCAA 57.320 30.769 0.00 0.00 37.50 3.18
2498 2766 5.392811 GCATTTCCCATCAACTCTCTTTCAG 60.393 44.000 0.00 0.00 0.00 3.02
2499 2767 4.460382 GCATTTCCCATCAACTCTCTTTCA 59.540 41.667 0.00 0.00 0.00 2.69
2524 2792 1.746220 AGATCTCGACAACTTCCCTCG 59.254 52.381 0.00 0.00 0.00 4.63
2614 2882 6.712095 ACACATTTGTAAGAAAGCTCATCTCA 59.288 34.615 2.73 0.00 32.60 3.27
2882 3479 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2884 3481 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2886 3483 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2888 3485 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2890 3487 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2892 3489 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2893 3490 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2894 3491 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2895 3492 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2896 3493 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2897 3494 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2898 3495 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2899 3496 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2900 3497 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2901 3498 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2902 3499 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2903 3500 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2904 3501 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2905 3502 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
2906 3503 4.094911 CAATAACACACACACACACACAC 58.905 43.478 0.00 0.00 0.00 3.82
2907 3504 4.003648 TCAATAACACACACACACACACA 58.996 39.130 0.00 0.00 0.00 3.72
2908 3505 4.339429 GTCAATAACACACACACACACAC 58.661 43.478 0.00 0.00 0.00 3.82
2909 3506 3.375610 GGTCAATAACACACACACACACA 59.624 43.478 0.00 0.00 0.00 3.72
2910 3507 3.242936 GGGTCAATAACACACACACACAC 60.243 47.826 0.00 0.00 0.00 3.82
2911 3508 2.946329 GGGTCAATAACACACACACACA 59.054 45.455 0.00 0.00 0.00 3.72
2912 3509 2.946329 TGGGTCAATAACACACACACAC 59.054 45.455 0.00 0.00 35.96 3.82
2913 3510 3.210227 CTGGGTCAATAACACACACACA 58.790 45.455 0.00 0.00 35.96 3.72
2914 3511 3.211045 ACTGGGTCAATAACACACACAC 58.789 45.455 0.00 0.00 35.96 3.82
2915 3512 3.118223 TGACTGGGTCAATAACACACACA 60.118 43.478 0.00 0.00 39.78 3.72
2916 3513 3.472652 TGACTGGGTCAATAACACACAC 58.527 45.455 0.00 0.00 39.78 3.82
2917 3514 3.847671 TGACTGGGTCAATAACACACA 57.152 42.857 0.00 0.00 39.78 3.72
2918 3515 5.705609 AAATGACTGGGTCAATAACACAC 57.294 39.130 4.46 0.00 45.96 3.82
2919 3516 7.667635 TGATAAAATGACTGGGTCAATAACACA 59.332 33.333 4.46 0.71 45.96 3.72
2920 3517 7.968405 GTGATAAAATGACTGGGTCAATAACAC 59.032 37.037 4.46 9.16 45.96 3.32
2921 3518 7.888021 AGTGATAAAATGACTGGGTCAATAACA 59.112 33.333 4.46 2.29 45.96 2.41
2922 3519 8.281212 AGTGATAAAATGACTGGGTCAATAAC 57.719 34.615 4.46 0.00 45.96 1.89
2930 3527 4.399303 GGGACAAGTGATAAAATGACTGGG 59.601 45.833 0.00 0.00 0.00 4.45
2945 3542 4.647853 GGAAAAACAAGGTTAGGGACAAGT 59.352 41.667 0.00 0.00 0.00 3.16
2946 3543 4.038763 GGGAAAAACAAGGTTAGGGACAAG 59.961 45.833 0.00 0.00 0.00 3.16
2951 3548 6.351796 CCATAATGGGAAAAACAAGGTTAGGG 60.352 42.308 0.00 0.00 32.67 3.53
2963 3560 8.395605 AGGAAACTAAGTACCATAATGGGAAAA 58.604 33.333 0.00 0.00 40.17 2.29
2967 3564 8.466798 CAAAAGGAAACTAAGTACCATAATGGG 58.533 37.037 0.00 0.00 40.91 4.00
2974 3571 7.567458 ACTACACAAAAGGAAACTAAGTACCA 58.433 34.615 0.00 0.00 42.68 3.25
2983 3580 8.440059 CAAAAGGAAAACTACACAAAAGGAAAC 58.560 33.333 0.00 0.00 0.00 2.78
2995 3592 7.592533 GGTAATCCGTTTCAAAAGGAAAACTAC 59.407 37.037 9.01 8.21 46.53 2.73
3043 3640 5.799213 ACAGTTGCTGCTAAACTAGAAGAT 58.201 37.500 5.21 0.00 35.70 2.40
3045 3642 6.036517 CCATACAGTTGCTGCTAAACTAGAAG 59.963 42.308 5.21 0.00 35.70 2.85
3048 3645 4.572389 CCCATACAGTTGCTGCTAAACTAG 59.428 45.833 5.21 0.00 35.70 2.57
3116 3713 1.021390 AGGTATGCAAGCAGACACGC 61.021 55.000 19.81 4.60 39.64 5.34
3229 3901 6.974932 TCTCAATTCTTAAGTTAGCTGCAG 57.025 37.500 10.11 10.11 0.00 4.41
3282 3955 6.997655 TCATGTATCTCCACATCAATAGGTC 58.002 40.000 0.00 0.00 37.02 3.85
3468 4142 2.307098 AGAAATACCTGCCACTGAAGCT 59.693 45.455 0.00 0.00 0.00 3.74
3544 4225 3.455910 AGCCAGGCTCTCACAATATACAA 59.544 43.478 8.70 0.00 30.62 2.41
3545 4226 3.041211 AGCCAGGCTCTCACAATATACA 58.959 45.455 8.70 0.00 30.62 2.29
3572 4253 6.039829 TGTTGATACGAGCAGTCTATCATTCT 59.960 38.462 0.00 0.00 29.99 2.40
3585 4266 4.192317 AGGAATTCCTTGTTGATACGAGC 58.808 43.478 21.89 0.00 46.09 5.03
3619 4300 2.632512 TGGAGTTCTTTTCAAATGGGCC 59.367 45.455 0.00 0.00 0.00 5.80
3643 4324 3.368739 GCTCCAAACCAAGCATGCTTAAT 60.369 43.478 31.48 19.72 38.42 1.40
3715 4396 1.899814 TCCTGCGTACTTTGTCCTCAT 59.100 47.619 0.00 0.00 0.00 2.90
3728 4409 0.969894 AGCACTAGTCTTTCCTGCGT 59.030 50.000 0.00 0.00 32.92 5.24
3746 4427 7.450074 AGATCTAGACTGACCACATAGACTAG 58.550 42.308 0.00 0.00 39.21 2.57
3756 4438 1.064685 TGGCGAGATCTAGACTGACCA 60.065 52.381 10.29 2.92 0.00 4.02
3790 4476 1.600107 GGTCATAGCCACCGGTTCA 59.400 57.895 2.97 0.00 0.00 3.18
3825 4512 2.415010 CGAGGGTCGGCTCTGATG 59.585 66.667 0.00 0.00 36.00 3.07
3950 4640 2.353505 GGAACGTTCCCTCTTGGTAGAC 60.354 54.545 33.02 6.34 41.62 2.59
3952 4642 2.381725 GGAACGTTCCCTCTTGGTAG 57.618 55.000 33.02 0.00 41.62 3.18
4022 4713 6.789959 AGTCTATCATTCCTATTAAGCCAGGT 59.210 38.462 0.00 0.00 33.37 4.00
4078 4773 6.110411 AGTTCTTTTCGAATGGACTCCTAA 57.890 37.500 0.00 0.00 33.45 2.69
4079 4774 5.721232 GAGTTCTTTTCGAATGGACTCCTA 58.279 41.667 20.68 0.00 35.95 2.94
4085 4780 5.130350 ACTTTGGAGTTCTTTTCGAATGGA 58.870 37.500 0.00 0.00 33.45 3.41
4121 4816 3.117738 CCCATCCTAGAATTGCTCCAAGT 60.118 47.826 0.00 0.00 0.00 3.16
4186 4881 3.767673 ACTAGTCTTTCCTGCGGACATTA 59.232 43.478 0.00 0.00 32.98 1.90
4189 4884 1.272490 CACTAGTCTTTCCTGCGGACA 59.728 52.381 0.00 0.00 32.98 4.02
4192 4887 0.247736 AGCACTAGTCTTTCCTGCGG 59.752 55.000 0.00 0.00 32.92 5.69
4210 4905 2.223803 AGACAGACCCCACAGACTAG 57.776 55.000 0.00 0.00 0.00 2.57
4225 4920 2.609299 TGGCGGGGGATCAAGACA 60.609 61.111 0.00 0.00 0.00 3.41
4306 5005 1.945387 AGCTTGGAGTACATGATGCG 58.055 50.000 0.00 0.00 0.00 4.73
4333 5032 2.280389 ACACTGCACTGTGAGGCG 60.280 61.111 12.86 5.04 40.12 5.52
4392 5091 4.571984 TGTTACATCAATGCCATCTTCTCG 59.428 41.667 0.00 0.00 0.00 4.04
4481 5219 7.285858 AGGATAGTTCAGTGTAAGTACAGGATC 59.714 40.741 0.00 0.00 36.78 3.36
4510 5248 5.355350 GGTTTGTGAATCCTCCTAAGACATG 59.645 44.000 0.00 0.00 0.00 3.21
4581 5322 5.546526 AGACATGAACAGAGGAAGTTTCTC 58.453 41.667 2.58 2.58 0.00 2.87
4638 5379 6.639632 ACACTATGTGACTTTTGCTTCATT 57.360 33.333 4.61 0.00 36.96 2.57
4925 6432 4.999950 ACAAGTGATTCAGAAGGCTAACTG 59.000 41.667 13.20 13.20 35.72 3.16
4951 7164 4.193090 ACCAACGCAATAATCGGTTGATA 58.807 39.130 4.47 0.00 33.40 2.15
4967 7180 4.353737 CATATGGAATGCAGAAACCAACG 58.646 43.478 7.75 0.00 36.00 4.10
5078 7345 9.507280 CCATGAACAAATATGAATGTTACTGAC 57.493 33.333 0.00 0.00 39.73 3.51
5080 7347 7.436080 GCCCATGAACAAATATGAATGTTACTG 59.564 37.037 0.00 4.02 39.73 2.74
5081 7348 7.123997 TGCCCATGAACAAATATGAATGTTACT 59.876 33.333 0.00 0.00 39.73 2.24
5083 7350 7.415592 TGCCCATGAACAAATATGAATGTTA 57.584 32.000 0.00 0.00 39.73 2.41
5086 7353 6.342906 ACTTGCCCATGAACAAATATGAATG 58.657 36.000 0.00 0.00 0.00 2.67
5087 7354 6.549433 ACTTGCCCATGAACAAATATGAAT 57.451 33.333 0.00 0.00 0.00 2.57
5088 7355 5.392919 CGACTTGCCCATGAACAAATATGAA 60.393 40.000 0.00 0.00 0.00 2.57
5089 7356 4.096231 CGACTTGCCCATGAACAAATATGA 59.904 41.667 0.00 0.00 0.00 2.15
5090 7357 4.142403 ACGACTTGCCCATGAACAAATATG 60.142 41.667 0.00 0.00 0.00 1.78
5091 7358 4.016444 ACGACTTGCCCATGAACAAATAT 58.984 39.130 0.00 0.00 0.00 1.28
5093 7360 2.238521 ACGACTTGCCCATGAACAAAT 58.761 42.857 0.00 0.00 0.00 2.32
5095 7362 2.147958 GTACGACTTGCCCATGAACAA 58.852 47.619 0.00 0.00 0.00 2.83
5097 7364 2.094762 AGTACGACTTGCCCATGAAC 57.905 50.000 0.00 0.00 0.00 3.18
5098 7365 2.851263 AAGTACGACTTGCCCATGAA 57.149 45.000 0.00 0.00 37.00 2.57
5108 7375 6.080648 TGAATGTTACTGACAAGTACGACT 57.919 37.500 0.00 0.00 42.62 4.18
5109 7376 6.946229 ATGAATGTTACTGACAAGTACGAC 57.054 37.500 0.00 0.00 42.62 4.34
5110 7377 9.647797 AAATATGAATGTTACTGACAAGTACGA 57.352 29.630 0.00 0.00 42.62 3.43
5111 7378 9.689075 CAAATATGAATGTTACTGACAAGTACG 57.311 33.333 0.00 0.00 42.62 3.67
5118 7385 9.507280 CCATGAACAAATATGAATGTTACTGAC 57.493 33.333 0.00 0.00 39.73 3.51
5119 7386 8.685427 CCCATGAACAAATATGAATGTTACTGA 58.315 33.333 0.00 0.00 39.73 3.41
5121 7388 7.123997 TGCCCATGAACAAATATGAATGTTACT 59.876 33.333 0.00 0.00 39.73 2.24
5123 7390 7.415592 TGCCCATGAACAAATATGAATGTTA 57.584 32.000 0.00 0.00 39.73 2.41
5126 7393 6.342906 ACTTGCCCATGAACAAATATGAATG 58.657 36.000 0.00 0.00 0.00 2.67
5129 7396 5.015515 TGACTTGCCCATGAACAAATATGA 58.984 37.500 0.00 0.00 0.00 2.15
5130 7397 5.327616 TGACTTGCCCATGAACAAATATG 57.672 39.130 0.00 0.00 0.00 1.78
5131 7398 6.835488 AGTATGACTTGCCCATGAACAAATAT 59.165 34.615 0.00 0.00 0.00 1.28
5132 7399 6.186957 AGTATGACTTGCCCATGAACAAATA 58.813 36.000 0.00 0.00 0.00 1.40
5133 7400 5.018809 AGTATGACTTGCCCATGAACAAAT 58.981 37.500 0.00 0.00 0.00 2.32
5136 7403 3.719268 AGTATGACTTGCCCATGAACA 57.281 42.857 0.00 0.00 0.00 3.18
5197 7597 1.378762 GCAACCTTACCTGGCCTCA 59.621 57.895 3.32 0.00 0.00 3.86
5198 7598 1.745489 CGCAACCTTACCTGGCCTC 60.745 63.158 3.32 0.00 0.00 4.70
5200 7600 1.176619 AAACGCAACCTTACCTGGCC 61.177 55.000 0.00 0.00 0.00 5.36
5285 7969 6.653320 ACATTAAGCTTCAAACATCGGTAGAA 59.347 34.615 0.00 0.00 0.00 2.10
5292 7976 3.853671 CGCCACATTAAGCTTCAAACATC 59.146 43.478 0.00 0.00 0.00 3.06
5295 7979 3.188460 TCTCGCCACATTAAGCTTCAAAC 59.812 43.478 0.00 0.00 0.00 2.93
5296 7980 3.407698 TCTCGCCACATTAAGCTTCAAA 58.592 40.909 0.00 0.00 0.00 2.69
5297 7981 3.002791 CTCTCGCCACATTAAGCTTCAA 58.997 45.455 0.00 0.00 0.00 2.69
5298 7982 2.233676 TCTCTCGCCACATTAAGCTTCA 59.766 45.455 0.00 0.00 0.00 3.02
5299 7983 2.893637 TCTCTCGCCACATTAAGCTTC 58.106 47.619 0.00 0.00 0.00 3.86
5300 7984 3.334583 TTCTCTCGCCACATTAAGCTT 57.665 42.857 3.48 3.48 0.00 3.74
5301 7985 3.550437 ATTCTCTCGCCACATTAAGCT 57.450 42.857 0.00 0.00 0.00 3.74
5359 8043 2.374525 ACCGCCAGTATGCATGGGA 61.375 57.895 10.16 0.00 38.33 4.37
5365 8049 2.112815 GGAACCACCGCCAGTATGC 61.113 63.158 0.00 0.00 31.97 3.14
5366 8050 4.218722 GGAACCACCGCCAGTATG 57.781 61.111 0.00 0.00 0.00 2.39
5396 8080 3.243068 CCGCCAAATAAGTTGCCACTATC 60.243 47.826 0.00 0.00 35.74 2.08
5397 8081 2.687935 CCGCCAAATAAGTTGCCACTAT 59.312 45.455 0.00 0.00 35.74 2.12
5398 8082 2.088423 CCGCCAAATAAGTTGCCACTA 58.912 47.619 0.00 0.00 35.74 2.74
5406 8131 4.331968 TCATCTTGAACCGCCAAATAAGT 58.668 39.130 0.00 0.00 0.00 2.24
5408 8133 3.128589 GCTCATCTTGAACCGCCAAATAA 59.871 43.478 0.00 0.00 0.00 1.40
5432 8157 4.082354 AGGATCACAAGAAAGCAAATGAGC 60.082 41.667 0.00 0.00 0.00 4.26
5449 8175 4.223556 ACTCTAGACAGAACGAGGATCA 57.776 45.455 0.00 0.00 33.17 2.92
5500 8226 4.692625 TCAGAAGTTCAGAATAGCAACAGC 59.307 41.667 5.50 0.00 0.00 4.40
5501 8227 6.675002 GCATCAGAAGTTCAGAATAGCAACAG 60.675 42.308 5.50 0.00 0.00 3.16
5503 8229 5.567552 GCATCAGAAGTTCAGAATAGCAAC 58.432 41.667 5.50 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.