Multiple sequence alignment - TraesCS3D01G329500

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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 TraesCS3D01G329500 chr3D 100.000 8519 0 0 1 8519 442360767 442369285 0.000000e+00 15732
1 TraesCS3D01G329500 chr3D 86.492 459 48 6 6376 6833 442366686 442367131 7.680000e-135 492
2 TraesCS3D01G329500 chr3D 86.492 459 48 6 5920 6365 442367142 442367599 7.680000e-135 492
3 TraesCS3D01G329500 chr3D 84.466 206 20 6 7728 7921 582243403 582243608 8.730000e-45 193
4 TraesCS3D01G329500 chr3D 83.981 206 21 6 7728 7921 285171071 285171276 4.060000e-43 187
5 TraesCS3D01G329500 chr7B 97.489 5376 104 14 2114 7480 32050557 32045204 0.000000e+00 9151
6 TraesCS3D01G329500 chr7B 91.371 1379 65 33 610 1968 32051938 32050594 0.000000e+00 1838
7 TraesCS3D01G329500 chr7B 85.900 461 53 3 5920 6368 32046295 32045835 1.660000e-131 481
8 TraesCS3D01G329500 chr7B 85.714 462 52 6 6376 6836 32046751 32046303 7.740000e-130 475
9 TraesCS3D01G329500 chr7B 97.701 261 6 0 1 261 32067829 32067569 4.690000e-122 449
10 TraesCS3D01G329500 chr7B 94.141 256 10 1 289 544 32067571 32067321 1.340000e-102 385
11 TraesCS3D01G329500 chr7B 85.000 180 15 6 7556 7729 32045049 32044876 1.140000e-38 172
12 TraesCS3D01G329500 chr7B 98.529 68 1 0 530 597 32051995 32051928 4.180000e-23 121
13 TraesCS3D01G329500 chr2A 98.090 4921 89 3 2111 7030 337664705 337669621 0.000000e+00 8562
14 TraesCS3D01G329500 chr2A 92.868 1374 58 19 610 1968 337663324 337664672 0.000000e+00 1958
15 TraesCS3D01G329500 chr2A 92.235 631 20 7 6858 7480 337669621 337670230 0.000000e+00 867
16 TraesCS3D01G329500 chr2A 86.026 458 52 3 5920 6365 337668967 337669424 1.660000e-131 481
17 TraesCS3D01G329500 chr2A 85.839 459 51 6 6376 6833 337668511 337668956 7.740000e-130 475
18 TraesCS3D01G329500 chr2A 98.851 261 3 0 1 261 337652016 337652276 4.660000e-127 466
19 TraesCS3D01G329500 chr2A 93.750 256 10 5 289 544 337652274 337652523 6.240000e-101 379
20 TraesCS3D01G329500 chr2A 83.333 180 18 8 7556 7729 337670440 337670613 1.140000e-33 156
21 TraesCS3D01G329500 chr2A 96.429 84 2 1 2029 2111 667018368 667018451 4.150000e-28 137
22 TraesCS3D01G329500 chr2A 95.238 84 2 2 2033 2115 667018451 667018369 1.930000e-26 132
23 TraesCS3D01G329500 chr2A 98.529 68 1 0 530 597 337663267 337663334 4.180000e-23 121
24 TraesCS3D01G329500 chr3B 95.711 2285 87 4 2108 4388 579885758 579888035 0.000000e+00 3666
25 TraesCS3D01G329500 chr3B 94.297 1473 61 3 6126 7597 579889880 579891330 0.000000e+00 2233
26 TraesCS3D01G329500 chr3B 97.887 1183 25 0 4917 6099 579888698 579889880 0.000000e+00 2047
27 TraesCS3D01G329500 chr3B 90.657 1445 62 26 618 2033 579884360 579885760 0.000000e+00 1853
28 TraesCS3D01G329500 chr3B 85.433 762 72 17 7732 8469 534171593 534170847 0.000000e+00 756
29 TraesCS3D01G329500 chr3B 83.573 627 52 24 1 594 579883181 579883789 2.710000e-149 540
30 TraesCS3D01G329500 chr3B 86.900 458 48 3 5920 6365 579890130 579890587 3.550000e-138 503
31 TraesCS3D01G329500 chr3B 90.556 180 17 0 6376 6555 579889701 579889880 1.110000e-58 239
32 TraesCS3D01G329500 chr3A 90.909 957 49 10 1102 2034 583694873 583695815 0.000000e+00 1251
33 TraesCS3D01G329500 chr3A 83.683 1048 71 28 1 1008 583693510 583694497 0.000000e+00 896
34 TraesCS3D01G329500 chr3A 83.051 236 39 1 7732 7966 330740942 330741177 6.700000e-51 213
35 TraesCS3D01G329500 chr2D 87.401 754 65 11 7732 8469 171050592 171049853 0.000000e+00 839
36 TraesCS3D01G329500 chr2D 90.426 94 3 3 2031 2123 642198715 642198803 1.500000e-22 119
37 TraesCS3D01G329500 chr7D 86.737 754 65 11 7732 8469 180068652 180069386 0.000000e+00 806
38 TraesCS3D01G329500 chr7D 82.517 755 103 15 7735 8468 630470956 630470210 3.350000e-178 636
39 TraesCS3D01G329500 chr5D 86.166 759 84 13 7728 8468 502540088 502540843 0.000000e+00 800
40 TraesCS3D01G329500 chr2B 88.235 680 63 10 7791 8468 50567539 50568203 0.000000e+00 797
41 TraesCS3D01G329500 chr2B 91.291 333 25 3 8137 8467 50568817 50569147 1.300000e-122 451
42 TraesCS3D01G329500 chr6A 83.926 759 94 15 7731 8472 615169919 615169172 0.000000e+00 701
43 TraesCS3D01G329500 chr1D 87.824 386 35 6 7734 8107 433506004 433506389 7.850000e-120 442
44 TraesCS3D01G329500 chr1D 93.103 87 5 1 2026 2111 433187998 433188084 8.980000e-25 126
45 TraesCS3D01G329500 chr4D 82.546 487 76 7 7987 8468 99218670 99218188 3.680000e-113 420
46 TraesCS3D01G329500 chr4A 84.615 390 45 8 7732 8108 744011876 744012263 2.900000e-99 374
47 TraesCS3D01G329500 chr4B 76.699 515 96 17 7974 8475 269287015 269287518 1.820000e-66 265
48 TraesCS3D01G329500 chr4B 84.416 231 32 4 7730 7958 16501214 16500986 3.090000e-54 224
49 TraesCS3D01G329500 chr4B 95.349 86 3 1 2033 2117 25847391 25847306 1.490000e-27 135
50 TraesCS3D01G329500 chr4B 96.296 81 2 1 2033 2112 25847312 25847392 1.930000e-26 132
51 TraesCS3D01G329500 chr5B 94.382 89 3 2 2029 2116 466779761 466779848 1.490000e-27 135
52 TraesCS3D01G329500 chr5B 95.294 85 3 1 2029 2112 466779847 466779763 5.360000e-27 134
53 TraesCS3D01G329500 chr5A 95.062 81 2 1 2032 2112 638032981 638032903 8.980000e-25 126


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 TraesCS3D01G329500 chr3D 442360767 442369285 8518 False 5572.000000 15732 90.994667 1 8519 3 chr3D.!!$F3 8518
1 TraesCS3D01G329500 chr7B 32044876 32050557 5681 True 4661.500000 9151 91.244500 2114 7729 2 chr7B.!!$R1 5615
2 TraesCS3D01G329500 chr7B 32045835 32051995 6160 True 728.750000 1838 90.378500 530 6836 4 chr7B.!!$R2 6306
3 TraesCS3D01G329500 chr7B 32067321 32067829 508 True 417.000000 449 95.921000 1 544 2 chr7B.!!$R3 543
4 TraesCS3D01G329500 chr2A 337663267 337670613 7346 False 1802.857143 8562 90.988571 530 7729 7 chr2A.!!$F3 7199
5 TraesCS3D01G329500 chr2A 337652016 337652523 507 False 422.500000 466 96.300500 1 544 2 chr2A.!!$F2 543
6 TraesCS3D01G329500 chr3B 579883181 579891330 8149 False 1583.000000 3666 91.368714 1 7597 7 chr3B.!!$F1 7596
7 TraesCS3D01G329500 chr3B 534170847 534171593 746 True 756.000000 756 85.433000 7732 8469 1 chr3B.!!$R1 737
8 TraesCS3D01G329500 chr3A 583693510 583695815 2305 False 1073.500000 1251 87.296000 1 2034 2 chr3A.!!$F2 2033
9 TraesCS3D01G329500 chr2D 171049853 171050592 739 True 839.000000 839 87.401000 7732 8469 1 chr2D.!!$R1 737
10 TraesCS3D01G329500 chr7D 180068652 180069386 734 False 806.000000 806 86.737000 7732 8469 1 chr7D.!!$F1 737
11 TraesCS3D01G329500 chr7D 630470210 630470956 746 True 636.000000 636 82.517000 7735 8468 1 chr7D.!!$R1 733
12 TraesCS3D01G329500 chr5D 502540088 502540843 755 False 800.000000 800 86.166000 7728 8468 1 chr5D.!!$F1 740
13 TraesCS3D01G329500 chr2B 50567539 50569147 1608 False 624.000000 797 89.763000 7791 8468 2 chr2B.!!$F1 677
14 TraesCS3D01G329500 chr6A 615169172 615169919 747 True 701.000000 701 83.926000 7731 8472 1 chr6A.!!$R1 741
15 TraesCS3D01G329500 chr4B 269287015 269287518 503 False 265.000000 265 76.699000 7974 8475 1 chr4B.!!$F2 501

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
864 1503 0.179116 CCTCCACGCAGACATCTCAG 60.179 60.000 0.0 0.0 0.00 3.35 F
2047 3015 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.0 0.0 0.00 4.37 F
2050 3018 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.0 0.0 0.00 2.44 F
2051 3019 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.0 0.0 0.00 1.82 F
2052 3020 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.0 0.0 0.00 1.40 F
3875 4848 1.000827 CTACAGATGCTACGCAGGAGG 60.001 57.143 0.0 0.0 43.65 4.30 F
4037 5010 2.103153 TCAGGAGGAACACAAGGACT 57.897 50.000 0.0 0.0 0.00 3.85 F
5677 6796 0.833287 GTGCCTGATCTTAGCTCCCA 59.167 55.000 0.0 0.0 0.00 4.37 F
6425 7544 0.251297 CACCTTCAGTCAATGCCCCA 60.251 55.000 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 3175 0.757188 ATGTACCCTCTCAGGCTCCG 60.757 60.000 0.00 0.00 32.73 4.63 R
3520 4493 0.826715 TCTTCCTGGATCTTCGCCTG 59.173 55.000 0.00 0.00 0.00 4.85 R
3673 4646 2.100631 AGGAATTGCCGCTTCGTCG 61.101 57.895 0.00 0.00 43.43 5.12 R
3875 4848 2.930682 GCCTCAATCTAGACAAACGTCC 59.069 50.000 0.00 0.00 33.60 4.79 R
4037 5010 3.145286 TGTGCACATCCTTTTCATCGAA 58.855 40.909 17.42 0.00 0.00 3.71 R
4725 5736 0.373716 CTTCATCACCGCGCCTAAAC 59.626 55.000 0.00 0.00 0.00 2.01 R
6012 7131 0.738975 GTCCCGGGCTCATTTTTAGC 59.261 55.000 18.49 0.00 39.33 3.09 R
7093 8384 0.317479 AGTACCGTGGAGTGCTTCAC 59.683 55.000 0.59 0.59 34.10 3.18 R
8343 10501 0.106708 AGAAAGTGGCTCGTGCTCAA 59.893 50.000 9.61 0.00 39.59 3.02 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
115 116 7.658167 TCACACCGTATCACAAGATTCTTTTTA 59.342 33.333 0.00 0.00 35.67 1.52
168 180 2.881513 TCAATAAAAAGGTGTGCGAGCA 59.118 40.909 0.00 0.00 0.00 4.26
189 201 7.448748 AGCACGGTAAAATTTTGACTAATCT 57.551 32.000 13.76 0.57 0.00 2.40
270 322 5.224888 TGATTGTGTACGTCCTAAAGACAC 58.775 41.667 8.25 8.25 46.69 3.67
290 342 5.340803 ACACGATGTGTACTCATATGTGTC 58.659 41.667 26.59 11.10 45.56 3.67
352 404 7.532884 CACACTTTATAAAAAGCTAACGACACC 59.467 37.037 0.00 0.00 45.06 4.16
416 468 7.524717 AAAGACAGTATAACCACAAATGCTT 57.475 32.000 0.00 0.00 0.00 3.91
495 556 3.775202 CTTCGGAAACATCTCGTCTCAT 58.225 45.455 0.00 0.00 0.00 2.90
496 557 3.422417 TCGGAAACATCTCGTCTCATC 57.578 47.619 0.00 0.00 0.00 2.92
497 558 3.017442 TCGGAAACATCTCGTCTCATCT 58.983 45.455 0.00 0.00 0.00 2.90
498 559 3.065510 TCGGAAACATCTCGTCTCATCTC 59.934 47.826 0.00 0.00 0.00 2.75
499 560 3.181496 CGGAAACATCTCGTCTCATCTCA 60.181 47.826 0.00 0.00 0.00 3.27
506 567 5.416013 ACATCTCGTCTCATCTCACTAAACA 59.584 40.000 0.00 0.00 0.00 2.83
860 1499 0.460987 CCTTCCTCCACGCAGACATC 60.461 60.000 0.00 0.00 0.00 3.06
861 1500 0.534412 CTTCCTCCACGCAGACATCT 59.466 55.000 0.00 0.00 0.00 2.90
862 1501 0.532573 TTCCTCCACGCAGACATCTC 59.467 55.000 0.00 0.00 0.00 2.75
863 1502 0.611896 TCCTCCACGCAGACATCTCA 60.612 55.000 0.00 0.00 0.00 3.27
864 1503 0.179116 CCTCCACGCAGACATCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
865 1504 0.805322 CTCCACGCAGACATCTCAGC 60.805 60.000 0.00 0.00 0.00 4.26
866 1505 1.812922 CCACGCAGACATCTCAGCC 60.813 63.158 0.00 0.00 0.00 4.85
867 1506 1.812922 CACGCAGACATCTCAGCCC 60.813 63.158 0.00 0.00 0.00 5.19
868 1507 2.285773 ACGCAGACATCTCAGCCCA 61.286 57.895 0.00 0.00 0.00 5.36
869 1508 1.812922 CGCAGACATCTCAGCCCAC 60.813 63.158 0.00 0.00 0.00 4.61
875 1514 3.092511 ATCTCAGCCCACGCCCAT 61.093 61.111 0.00 0.00 34.57 4.00
892 1531 0.401105 CATCCCTCTCCCCCTGACAT 60.401 60.000 0.00 0.00 0.00 3.06
894 1533 1.231751 TCCCTCTCCCCCTGACATCT 61.232 60.000 0.00 0.00 0.00 2.90
896 1535 1.112315 CCTCTCCCCCTGACATCTCG 61.112 65.000 0.00 0.00 0.00 4.04
898 1537 2.764128 TCCCCCTGACATCTCGGC 60.764 66.667 0.00 0.00 0.00 5.54
905 1544 4.176752 GACATCTCGGCCCCCACC 62.177 72.222 0.00 0.00 0.00 4.61
1025 1664 2.035783 GCCGCCCTTCCTTTTCCT 59.964 61.111 0.00 0.00 0.00 3.36
1059 1705 5.870706 TCTTTTCTTTCCCTTCTCTTCTCC 58.129 41.667 0.00 0.00 0.00 3.71
1584 2534 4.910458 AAGCAGTAGTAAAGGTGATGGT 57.090 40.909 0.00 0.00 0.00 3.55
1617 2574 4.471904 TCGTGCTATGATTCACCTTCTT 57.528 40.909 0.00 0.00 0.00 2.52
1684 2641 2.024369 TGCTAGATAGTGTCCCACCAGA 60.024 50.000 0.00 0.00 34.49 3.86
1772 2739 5.590259 TGCTGGGTAATTTCTGAATAAGAGC 59.410 40.000 0.00 0.00 35.91 4.09
1898 2866 4.634012 AATTGGTGCAGTTGGTCTACTA 57.366 40.909 0.00 0.00 0.00 1.82
1923 2891 4.559704 GCTGTGGCTATTCGTATTAGCTCT 60.560 45.833 0.00 0.00 37.05 4.09
1933 2901 5.933187 TCGTATTAGCTCTGCTCTCTTAG 57.067 43.478 0.00 0.00 40.44 2.18
1939 2907 9.541143 GTATTAGCTCTGCTCTCTTAGAAAATT 57.459 33.333 0.00 0.00 40.44 1.82
2034 3002 8.515414 AGCATAACAGATTTTTCTGGAAAGTAC 58.485 33.333 7.80 0.00 41.76 2.73
2035 3003 8.515414 GCATAACAGATTTTTCTGGAAAGTACT 58.485 33.333 7.80 0.00 41.76 2.73
2037 3005 7.511959 AACAGATTTTTCTGGAAAGTACTCC 57.488 36.000 0.00 0.00 41.76 3.85
2038 3006 6.004574 ACAGATTTTTCTGGAAAGTACTCCC 58.995 40.000 0.00 1.23 41.76 4.30
2039 3007 6.183361 ACAGATTTTTCTGGAAAGTACTCCCT 60.183 38.462 13.46 0.00 41.76 4.20
2040 3008 6.372937 CAGATTTTTCTGGAAAGTACTCCCTC 59.627 42.308 13.46 4.06 34.22 4.30
2041 3009 4.635699 TTTTCTGGAAAGTACTCCCTCC 57.364 45.455 13.46 11.91 34.22 4.30
2042 3010 1.848652 TCTGGAAAGTACTCCCTCCG 58.151 55.000 13.46 8.84 34.22 4.63
2043 3011 1.076677 TCTGGAAAGTACTCCCTCCGT 59.923 52.381 13.46 0.00 34.22 4.69
2044 3012 1.477295 CTGGAAAGTACTCCCTCCGTC 59.523 57.143 13.46 0.00 34.22 4.79
2045 3013 0.822811 GGAAAGTACTCCCTCCGTCC 59.177 60.000 0.00 0.00 0.00 4.79
2046 3014 0.822811 GAAAGTACTCCCTCCGTCCC 59.177 60.000 0.00 0.00 0.00 4.46
2047 3015 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
2048 3016 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
2049 3017 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2050 3018 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2051 3019 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2052 3020 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2053 3021 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2054 3022 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2055 3023 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2056 3024 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2057 3025 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
2058 3026 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
2059 3027 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
2060 3028 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
2061 3029 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2062 3030 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2063 3031 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2064 3032 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2065 3033 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2066 3034 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2067 3035 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2068 3036 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2069 3037 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2070 3038 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2071 3039 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2072 3040 9.438291 CAAAATAAGTGACTCAACTTTGTACTG 57.562 33.333 0.00 0.00 40.77 2.74
2073 3041 8.732746 AAATAAGTGACTCAACTTTGTACTGT 57.267 30.769 0.00 0.00 40.77 3.55
2074 3042 9.826574 AAATAAGTGACTCAACTTTGTACTGTA 57.173 29.630 0.00 0.00 40.77 2.74
2075 3043 8.813643 ATAAGTGACTCAACTTTGTACTGTAC 57.186 34.615 10.98 10.98 40.77 2.90
2076 3044 6.216801 AGTGACTCAACTTTGTACTGTACA 57.783 37.500 16.26 16.26 36.79 2.90
2077 3045 6.636705 AGTGACTCAACTTTGTACTGTACAA 58.363 36.000 25.14 25.14 46.13 2.41
2088 3056 6.897259 TTGTACTGTACAAAGTTGAGTCAC 57.103 37.500 26.32 0.00 44.95 3.67
2089 3057 6.216801 TGTACTGTACAAAGTTGAGTCACT 57.783 37.500 17.74 0.00 35.38 3.41
2090 3058 6.636705 TGTACTGTACAAAGTTGAGTCACTT 58.363 36.000 17.74 0.00 38.74 3.16
2091 3059 7.774134 TGTACTGTACAAAGTTGAGTCACTTA 58.226 34.615 17.74 0.00 35.87 2.24
2092 3060 8.252417 TGTACTGTACAAAGTTGAGTCACTTAA 58.748 33.333 17.74 0.00 35.87 1.85
2093 3061 9.257651 GTACTGTACAAAGTTGAGTCACTTAAT 57.742 33.333 12.89 0.00 35.87 1.40
2094 3062 8.732746 ACTGTACAAAGTTGAGTCACTTAATT 57.267 30.769 0.00 0.00 35.87 1.40
2095 3063 9.174166 ACTGTACAAAGTTGAGTCACTTAATTT 57.826 29.630 0.00 0.00 35.87 1.82
2096 3064 9.438291 CTGTACAAAGTTGAGTCACTTAATTTG 57.562 33.333 12.37 12.37 35.87 2.32
2097 3065 8.402472 TGTACAAAGTTGAGTCACTTAATTTGG 58.598 33.333 16.35 5.04 35.87 3.28
2098 3066 6.805713 ACAAAGTTGAGTCACTTAATTTGGG 58.194 36.000 16.35 4.33 35.87 4.12
2099 3067 6.605594 ACAAAGTTGAGTCACTTAATTTGGGA 59.394 34.615 16.35 0.00 35.87 4.37
2100 3068 6.635030 AAGTTGAGTCACTTAATTTGGGAC 57.365 37.500 0.00 5.66 35.10 4.46
2101 3069 5.690865 AGTTGAGTCACTTAATTTGGGACA 58.309 37.500 13.57 0.00 0.00 4.02
2102 3070 5.765182 AGTTGAGTCACTTAATTTGGGACAG 59.235 40.000 13.57 0.00 42.39 3.51
2103 3071 5.560722 TGAGTCACTTAATTTGGGACAGA 57.439 39.130 13.57 0.54 42.39 3.41
2104 3072 5.551233 TGAGTCACTTAATTTGGGACAGAG 58.449 41.667 13.57 0.00 42.39 3.35
2105 3073 4.911390 AGTCACTTAATTTGGGACAGAGG 58.089 43.478 13.57 0.00 42.39 3.69
2106 3074 4.010349 GTCACTTAATTTGGGACAGAGGG 58.990 47.826 8.18 0.00 42.39 4.30
2107 3075 3.913799 TCACTTAATTTGGGACAGAGGGA 59.086 43.478 0.00 0.00 42.39 4.20
2108 3076 4.019321 TCACTTAATTTGGGACAGAGGGAG 60.019 45.833 0.00 0.00 42.39 4.30
2109 3077 3.916989 ACTTAATTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
2112 3080 4.779993 AATTTGGGACAGAGGGAGTATC 57.220 45.455 0.00 0.00 42.39 2.24
2202 3175 4.513198 TTTGCAATGCTAGGTTTGTACC 57.487 40.909 6.82 0.00 45.39 3.34
2267 3240 6.772716 ACAAGTTGGTCTGTGTATCAAGAAAT 59.227 34.615 7.96 0.00 0.00 2.17
2348 3321 4.518970 TCAGTTTGGGTGTTTTGCTCTATC 59.481 41.667 0.00 0.00 0.00 2.08
2713 3686 6.302269 AGAAGATGAGAAGTTTGAACATGGT 58.698 36.000 0.00 0.00 0.00 3.55
3520 4493 5.237344 CCGTAGATTGGAGATTTTGATGGTC 59.763 44.000 0.00 0.00 0.00 4.02
3673 4646 4.275936 CCGTTTGACCTTCCATATGATTCC 59.724 45.833 3.65 0.00 0.00 3.01
3875 4848 1.000827 CTACAGATGCTACGCAGGAGG 60.001 57.143 0.00 0.00 43.65 4.30
4037 5010 2.103153 TCAGGAGGAACACAAGGACT 57.897 50.000 0.00 0.00 0.00 3.85
4541 5552 6.765989 CGACTAATGGGTATTCTCCAAAATCA 59.234 38.462 0.00 0.00 37.87 2.57
4725 5736 2.305928 TGGTCCATTGGTTGTGAACTG 58.694 47.619 1.86 0.00 0.00 3.16
5677 6796 0.833287 GTGCCTGATCTTAGCTCCCA 59.167 55.000 0.00 0.00 0.00 4.37
5765 6884 1.381928 CCACATCAGATGCCAGTGCC 61.382 60.000 10.59 0.00 36.33 5.01
6137 7256 2.158623 TGGTGTTGATGAGGCTGAAACT 60.159 45.455 0.00 0.00 0.00 2.66
6142 7261 0.445436 GATGAGGCTGAAACTGCACG 59.555 55.000 0.00 0.00 0.00 5.34
6405 7524 1.000283 ACGAGCCAGAAGTCACAGAAG 60.000 52.381 0.00 0.00 0.00 2.85
6420 7539 3.058432 CACAGAAGCACCTTCAGTCAATG 60.058 47.826 7.62 0.00 42.37 2.82
6422 7541 1.200948 GAAGCACCTTCAGTCAATGCC 59.799 52.381 0.35 0.00 39.95 4.40
6425 7544 0.251297 CACCTTCAGTCAATGCCCCA 60.251 55.000 0.00 0.00 0.00 4.96
6487 7606 3.386932 TGCTAAAAATGAGGCTGGGAT 57.613 42.857 0.00 0.00 0.00 3.85
6589 7708 3.341270 TGGGTATGATGGGCCCAC 58.659 61.111 31.51 21.60 46.59 4.61
6603 7722 3.047877 CCACCCTTGACGCCGAAC 61.048 66.667 0.00 0.00 0.00 3.95
6868 7987 1.487976 TGATAGGGAGCCTGAAAGCAG 59.512 52.381 0.00 0.00 41.93 4.24
6924 8043 4.823442 ACATGAATGCAGTGTTCAAGAAGA 59.177 37.500 9.94 0.00 38.89 2.87
6981 8100 1.287503 GAGTCCGAGGATGATCGCC 59.712 63.158 0.00 0.00 41.37 5.54
6983 8102 0.829602 AGTCCGAGGATGATCGCCAT 60.830 55.000 7.13 0.00 41.37 4.40
7024 8315 5.234752 ACAACACTGAATTACTATCGCACA 58.765 37.500 0.00 0.00 0.00 4.57
7051 8342 5.129485 TGGTAAAAGGGAATGCAAGTTGAAA 59.871 36.000 7.16 0.00 0.00 2.69
7052 8343 6.183361 TGGTAAAAGGGAATGCAAGTTGAAAT 60.183 34.615 7.16 0.00 0.00 2.17
7053 8344 6.147656 GGTAAAAGGGAATGCAAGTTGAAATG 59.852 38.462 7.16 0.00 0.00 2.32
7054 8345 3.967332 AGGGAATGCAAGTTGAAATGG 57.033 42.857 7.16 0.00 0.00 3.16
7055 8346 3.509442 AGGGAATGCAAGTTGAAATGGA 58.491 40.909 7.16 0.00 0.00 3.41
7056 8347 4.098894 AGGGAATGCAAGTTGAAATGGAT 58.901 39.130 7.16 0.00 0.00 3.41
7057 8348 4.161001 AGGGAATGCAAGTTGAAATGGATC 59.839 41.667 7.16 0.00 0.00 3.36
7058 8349 4.436332 GGAATGCAAGTTGAAATGGATCC 58.564 43.478 7.16 4.20 0.00 3.36
7059 8350 4.161001 GGAATGCAAGTTGAAATGGATCCT 59.839 41.667 14.23 0.00 0.00 3.24
7060 8351 5.337813 GGAATGCAAGTTGAAATGGATCCTT 60.338 40.000 14.23 3.29 0.00 3.36
7061 8352 6.127366 GGAATGCAAGTTGAAATGGATCCTTA 60.127 38.462 14.23 0.00 0.00 2.69
7062 8353 7.418254 GGAATGCAAGTTGAAATGGATCCTTAT 60.418 37.037 14.23 0.00 0.00 1.73
7063 8354 6.855763 TGCAAGTTGAAATGGATCCTTATT 57.144 33.333 14.23 2.07 0.00 1.40
7064 8355 6.632909 TGCAAGTTGAAATGGATCCTTATTG 58.367 36.000 14.23 7.74 0.00 1.90
7065 8356 6.436847 TGCAAGTTGAAATGGATCCTTATTGA 59.563 34.615 14.23 0.00 0.00 2.57
7066 8357 7.124599 TGCAAGTTGAAATGGATCCTTATTGAT 59.875 33.333 14.23 0.00 0.00 2.57
7067 8358 7.983484 GCAAGTTGAAATGGATCCTTATTGATT 59.017 33.333 14.23 0.00 0.00 2.57
7068 8359 9.309516 CAAGTTGAAATGGATCCTTATTGATTG 57.690 33.333 14.23 5.88 0.00 2.67
7069 8360 8.827832 AGTTGAAATGGATCCTTATTGATTGA 57.172 30.769 14.23 0.00 0.00 2.57
7070 8361 9.258629 AGTTGAAATGGATCCTTATTGATTGAA 57.741 29.630 14.23 0.00 0.00 2.69
7093 8384 7.174946 TGAAGAAGCTTATTCTTGGTTACCTTG 59.825 37.037 28.54 0.00 38.73 3.61
7263 8555 1.045911 ATTCTCTCCCTCCGCTGTCC 61.046 60.000 0.00 0.00 0.00 4.02
7278 8570 3.483574 CGCTGTCCGTAATTTGTTAGCTG 60.484 47.826 0.00 0.00 0.00 4.24
7449 8747 4.819769 TGCTTGCAATCTATTTTTCCACC 58.180 39.130 0.00 0.00 0.00 4.61
7453 8751 3.768757 TGCAATCTATTTTTCCACCTGGG 59.231 43.478 0.00 0.00 35.41 4.45
7460 8758 0.854218 TTTTCCACCTGGGCTGGTAA 59.146 50.000 0.00 0.00 38.45 2.85
7461 8759 0.111639 TTTCCACCTGGGCTGGTAAC 59.888 55.000 0.00 0.00 38.45 2.50
7466 8764 0.539669 ACCTGGGCTGGTAACTTTGC 60.540 55.000 0.00 0.00 38.79 3.68
7483 8781 2.848858 GCAACTGCAGGTGTGGGTG 61.849 63.158 31.37 7.88 41.59 4.61
7488 8786 0.540365 CTGCAGGTGTGGGTGGAAAT 60.540 55.000 5.57 0.00 0.00 2.17
7551 8849 5.876651 ATATCACTACATGCCTGTCAGAA 57.123 39.130 0.00 0.00 36.79 3.02
7561 9043 6.066690 ACATGCCTGTCAGAATTATAGCATT 58.933 36.000 0.00 0.00 37.60 3.56
7614 9096 9.722184 ATTTCTTTACCAAGGTTCTACTAGTTC 57.278 33.333 0.00 0.00 0.00 3.01
7616 9098 8.120140 TCTTTACCAAGGTTCTACTAGTTCTC 57.880 38.462 0.00 0.00 0.00 2.87
7617 9099 7.949006 TCTTTACCAAGGTTCTACTAGTTCTCT 59.051 37.037 0.00 0.00 0.00 3.10
7618 9100 8.488308 TTTACCAAGGTTCTACTAGTTCTCTT 57.512 34.615 0.00 0.00 0.00 2.85
7619 9101 6.593268 ACCAAGGTTCTACTAGTTCTCTTC 57.407 41.667 0.00 0.00 0.00 2.87
7620 9102 6.075984 ACCAAGGTTCTACTAGTTCTCTTCA 58.924 40.000 0.00 0.00 0.00 3.02
7636 9119 1.197721 CTTCACTTGCTAAACCCTGCG 59.802 52.381 0.00 0.00 0.00 5.18
7645 9128 0.320374 TAAACCCTGCGACCAGACAG 59.680 55.000 0.00 0.00 41.77 3.51
7650 9133 0.318441 CCTGCGACCAGACAGAAGAA 59.682 55.000 0.00 0.00 41.77 2.52
7651 9134 1.423395 CTGCGACCAGACAGAAGAAC 58.577 55.000 0.00 0.00 41.77 3.01
7663 9146 3.356290 ACAGAAGAACAGCAAAACACCT 58.644 40.909 0.00 0.00 0.00 4.00
7693 9176 5.304614 GCCACTGAACTAATCCTGGTAGATA 59.695 44.000 0.00 0.00 30.68 1.98
7712 9195 3.758715 AAAAACAGCCTTGGTGTGC 57.241 47.368 0.00 0.00 43.73 4.57
7719 9202 2.034687 CCTTGGTGTGCTGGGAGG 59.965 66.667 0.00 0.00 0.00 4.30
7729 9212 0.329261 TGCTGGGAGGAGATTTGTGG 59.671 55.000 0.00 0.00 0.00 4.17
7809 9305 3.181529 GGCTCGACTCGAAAAGAAATGAC 60.182 47.826 2.16 0.00 34.74 3.06
7823 9319 8.463930 AAAAGAAATGACCTGAGTATGAACAA 57.536 30.769 0.00 0.00 0.00 2.83
7878 9397 1.594293 CCAACACTGGCTCGTTCGT 60.594 57.895 0.00 0.00 35.39 3.85
7881 9400 1.063469 CAACACTGGCTCGTTCGTTTT 59.937 47.619 0.00 0.00 0.00 2.43
7886 9405 1.798813 CTGGCTCGTTCGTTTTTAGCT 59.201 47.619 0.00 0.00 33.67 3.32
7888 9407 1.201780 GGCTCGTTCGTTTTTAGCTCG 60.202 52.381 0.00 0.00 33.67 5.03
7913 9443 9.995957 CGATAGCCCGAGATCATATAATTATAG 57.004 37.037 10.79 4.12 0.00 1.31
8036 9573 6.943718 CCTCCATTTTACCTACTACCAAACAA 59.056 38.462 0.00 0.00 0.00 2.83
8042 9579 8.454570 TTTTACCTACTACCAAACAAGGAAAG 57.545 34.615 0.00 0.00 0.00 2.62
8046 9583 7.222161 ACCTACTACCAAACAAGGAAAGTTAG 58.778 38.462 0.00 0.00 33.02 2.34
8071 9608 4.039603 ACTGCAGAGAAAATTTAGCCCT 57.960 40.909 23.35 0.00 0.00 5.19
8076 9613 6.717289 TGCAGAGAAAATTTAGCCCTACTAA 58.283 36.000 0.00 0.00 39.14 2.24
8095 9633 7.232737 CCTACTAAGGTATGTGATCACCATGTA 59.767 40.741 22.85 4.25 38.19 2.29
8129 9670 8.034215 TCATGTTATTTTGGCAATAGTTTGAGG 58.966 33.333 0.00 0.00 34.60 3.86
8130 9671 7.531857 TGTTATTTTGGCAATAGTTTGAGGA 57.468 32.000 0.00 0.00 34.60 3.71
8133 9674 4.846779 TTTGGCAATAGTTTGAGGACAC 57.153 40.909 0.00 0.00 34.60 3.67
8336 10494 3.650183 GAGATCGACTCGAGATCGC 57.350 57.895 21.68 10.17 46.60 4.58
8343 10501 1.328069 CGACTCGAGATCGCTACAAGT 59.672 52.381 21.68 0.00 39.60 3.16
8394 10553 1.896220 TGAGCTTCGCTTGGTTTGAT 58.104 45.000 0.00 0.00 39.88 2.57
8406 10565 3.793797 TGGTTTGATCTCGCTCGAATA 57.206 42.857 0.00 0.00 0.00 1.75
8423 10582 7.291567 GCTCGAATATTTGTATAAGTTGAGCC 58.708 38.462 2.57 0.00 36.71 4.70
8469 10628 0.320421 GACTCGTTTGCAGCCCTACA 60.320 55.000 0.00 0.00 0.00 2.74
8475 10634 0.970640 TTTGCAGCCCTACACGTAGA 59.029 50.000 5.77 0.00 35.21 2.59
8476 10635 1.191535 TTGCAGCCCTACACGTAGAT 58.808 50.000 5.77 0.00 35.21 1.98
8477 10636 1.191535 TGCAGCCCTACACGTAGATT 58.808 50.000 5.77 0.00 35.21 2.40
8478 10637 1.134818 TGCAGCCCTACACGTAGATTG 60.135 52.381 5.77 2.86 35.21 2.67
8481 10640 1.480954 AGCCCTACACGTAGATTGTGG 59.519 52.381 5.77 0.00 41.64 4.17
8482 10641 1.479323 GCCCTACACGTAGATTGTGGA 59.521 52.381 5.77 0.00 41.64 4.02
8483 10642 2.102588 GCCCTACACGTAGATTGTGGAT 59.897 50.000 5.77 0.00 41.64 3.41
8484 10643 3.799232 GCCCTACACGTAGATTGTGGATC 60.799 52.174 5.77 0.00 41.64 3.36
8485 10644 3.550233 CCCTACACGTAGATTGTGGATCG 60.550 52.174 5.77 0.00 41.64 3.69
8486 10645 1.922570 ACACGTAGATTGTGGATCGC 58.077 50.000 0.00 0.00 41.64 4.58
8487 10646 1.476891 ACACGTAGATTGTGGATCGCT 59.523 47.619 0.00 0.00 41.64 4.93
8488 10647 1.854743 CACGTAGATTGTGGATCGCTG 59.145 52.381 0.00 0.00 39.85 5.18
8489 10648 1.749063 ACGTAGATTGTGGATCGCTGA 59.251 47.619 0.00 0.00 39.85 4.26
8490 10649 2.362397 ACGTAGATTGTGGATCGCTGAT 59.638 45.455 0.00 0.00 39.85 2.90
8491 10650 3.181475 ACGTAGATTGTGGATCGCTGATT 60.181 43.478 0.00 0.00 39.85 2.57
8492 10651 3.804325 CGTAGATTGTGGATCGCTGATTT 59.196 43.478 0.00 0.00 39.85 2.17
8493 10652 4.318333 CGTAGATTGTGGATCGCTGATTTG 60.318 45.833 0.00 0.00 39.85 2.32
8506 10665 4.997905 GCTGATTTGCGCTATGATTCTA 57.002 40.909 9.73 0.00 0.00 2.10
8507 10666 5.348418 GCTGATTTGCGCTATGATTCTAA 57.652 39.130 9.73 0.00 0.00 2.10
8508 10667 5.751680 GCTGATTTGCGCTATGATTCTAAA 58.248 37.500 9.73 0.00 0.00 1.85
8509 10668 5.622856 GCTGATTTGCGCTATGATTCTAAAC 59.377 40.000 9.73 0.00 0.00 2.01
8510 10669 6.512415 GCTGATTTGCGCTATGATTCTAAACT 60.512 38.462 9.73 0.00 0.00 2.66
8511 10670 7.320443 TGATTTGCGCTATGATTCTAAACTT 57.680 32.000 9.73 0.00 0.00 2.66
8512 10671 7.188834 TGATTTGCGCTATGATTCTAAACTTG 58.811 34.615 9.73 0.00 0.00 3.16
8513 10672 6.494893 TTTGCGCTATGATTCTAAACTTGT 57.505 33.333 9.73 0.00 0.00 3.16
8514 10673 6.494893 TTGCGCTATGATTCTAAACTTGTT 57.505 33.333 9.73 0.00 0.00 2.83
8517 10676 8.208718 TGCGCTATGATTCTAAACTTGTTTAT 57.791 30.769 9.73 0.00 0.00 1.40
8518 10677 8.122330 TGCGCTATGATTCTAAACTTGTTTATG 58.878 33.333 9.73 2.69 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 2.627945 TCCTTAACGCGAGATGCAAAT 58.372 42.857 15.93 0.00 46.97 2.32
168 180 9.226606 TCATGAGATTAGTCAAAATTTTACCGT 57.773 29.630 2.44 0.00 0.00 4.83
270 322 5.582550 ACAGACACATATGAGTACACATCG 58.417 41.667 10.38 5.25 0.00 3.84
290 342 9.282247 GATCAAAACAAAGCATCAAGTATACAG 57.718 33.333 5.50 0.00 0.00 2.74
343 395 6.627395 ACAAAATTGATCTTGGTGTCGTTA 57.373 33.333 0.00 0.00 0.00 3.18
352 404 7.236674 TGTTGCAGAAACAAAATTGATCTTG 57.763 32.000 0.00 0.00 45.85 3.02
495 556 4.350368 TGGCAATGTCTGTTTAGTGAGA 57.650 40.909 0.00 0.00 0.00 3.27
496 557 5.437289 TTTGGCAATGTCTGTTTAGTGAG 57.563 39.130 0.00 0.00 0.00 3.51
497 558 5.843673 TTTTGGCAATGTCTGTTTAGTGA 57.156 34.783 0.00 0.00 0.00 3.41
612 676 6.183360 CGTAGCTCATATTGTTACGGGTTTTT 60.183 38.462 11.47 0.00 34.94 1.94
613 677 5.292589 CGTAGCTCATATTGTTACGGGTTTT 59.707 40.000 11.47 0.00 34.94 2.43
614 678 4.807304 CGTAGCTCATATTGTTACGGGTTT 59.193 41.667 11.47 0.00 34.94 3.27
615 679 4.365723 CGTAGCTCATATTGTTACGGGTT 58.634 43.478 11.47 0.00 34.94 4.11
616 680 3.973657 CGTAGCTCATATTGTTACGGGT 58.026 45.455 11.47 0.00 34.94 5.28
860 1499 4.864334 GGATGGGCGTGGGCTGAG 62.864 72.222 0.00 0.00 39.81 3.35
865 1504 3.866582 GAGAGGGATGGGCGTGGG 61.867 72.222 0.00 0.00 0.00 4.61
866 1505 3.866582 GGAGAGGGATGGGCGTGG 61.867 72.222 0.00 0.00 0.00 4.94
867 1506 3.866582 GGGAGAGGGATGGGCGTG 61.867 72.222 0.00 0.00 0.00 5.34
875 1514 1.231751 AGATGTCAGGGGGAGAGGGA 61.232 60.000 0.00 0.00 0.00 4.20
1037 1677 5.875224 AGGAGAAGAGAAGGGAAAGAAAAG 58.125 41.667 0.00 0.00 0.00 2.27
1136 2057 2.668212 CTTGGACCGCCGCTTTCA 60.668 61.111 0.00 0.00 36.79 2.69
1617 2574 3.953612 TCGATAAGCTAAACCCCGACTAA 59.046 43.478 0.00 0.00 0.00 2.24
1684 2641 3.218453 CCGGTCACTAGTCAGATCATCT 58.782 50.000 0.00 0.00 0.00 2.90
1694 2651 2.663196 GGCAAGCCGGTCACTAGT 59.337 61.111 1.90 0.00 0.00 2.57
1809 2776 7.229581 ACTAGCTAGTAAAATTAGATCGGGG 57.770 40.000 24.97 0.00 34.13 5.73
1923 2891 7.425606 GTTTGTTCCAATTTTCTAAGAGAGCA 58.574 34.615 0.00 0.00 0.00 4.26
1933 2901 6.456853 GCAAGTCTTGGTTTGTTCCAATTTTC 60.457 38.462 14.40 0.00 44.94 2.29
1939 2907 1.754226 GGCAAGTCTTGGTTTGTTCCA 59.246 47.619 14.40 0.00 35.49 3.53
1951 2919 2.108952 AGTCCCAAATCAAGGCAAGTCT 59.891 45.455 0.00 0.00 0.00 3.24
1952 2920 2.519013 AGTCCCAAATCAAGGCAAGTC 58.481 47.619 0.00 0.00 0.00 3.01
2034 3002 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2035 3003 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2036 3004 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2037 3005 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2038 3006 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
2039 3007 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
2040 3008 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
2041 3009 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
2042 3010 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2043 3011 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
2044 3012 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
2045 3013 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
2046 3014 9.438291 CAGTACAAAGTTGAGTCACTTATTTTG 57.562 33.333 8.80 8.80 35.87 2.44
2047 3015 9.174166 ACAGTACAAAGTTGAGTCACTTATTTT 57.826 29.630 0.00 0.00 35.87 1.82
2048 3016 8.732746 ACAGTACAAAGTTGAGTCACTTATTT 57.267 30.769 0.00 0.00 35.87 1.40
2049 3017 9.257651 GTACAGTACAAAGTTGAGTCACTTATT 57.742 33.333 5.79 0.00 35.87 1.40
2050 3018 8.418662 TGTACAGTACAAAGTTGAGTCACTTAT 58.581 33.333 11.21 0.00 35.87 1.73
2051 3019 7.774134 TGTACAGTACAAAGTTGAGTCACTTA 58.226 34.615 11.21 0.00 35.87 2.24
2052 3020 6.636705 TGTACAGTACAAAGTTGAGTCACTT 58.363 36.000 11.21 0.00 38.74 3.16
2053 3021 6.216801 TGTACAGTACAAAGTTGAGTCACT 57.783 37.500 11.21 0.00 35.38 3.41
2054 3022 6.897259 TTGTACAGTACAAAGTTGAGTCAC 57.103 37.500 21.64 0.00 44.95 3.67
2065 3033 6.636705 AGTGACTCAACTTTGTACAGTACAA 58.363 36.000 20.32 20.32 46.13 2.41
2066 3034 6.216801 AGTGACTCAACTTTGTACAGTACA 57.783 37.500 9.51 9.51 36.79 2.90
2067 3035 8.638685 TTAAGTGACTCAACTTTGTACAGTAC 57.361 34.615 3.49 3.49 40.77 2.73
2068 3036 9.826574 AATTAAGTGACTCAACTTTGTACAGTA 57.173 29.630 0.00 0.00 40.77 2.74
2069 3037 8.732746 AATTAAGTGACTCAACTTTGTACAGT 57.267 30.769 0.00 0.00 40.77 3.55
2070 3038 9.438291 CAAATTAAGTGACTCAACTTTGTACAG 57.562 33.333 0.00 0.00 40.77 2.74
2071 3039 8.402472 CCAAATTAAGTGACTCAACTTTGTACA 58.598 33.333 0.00 0.00 40.77 2.90
2072 3040 7.860872 CCCAAATTAAGTGACTCAACTTTGTAC 59.139 37.037 8.71 0.00 40.77 2.90
2073 3041 7.776030 TCCCAAATTAAGTGACTCAACTTTGTA 59.224 33.333 8.71 0.00 40.77 2.41
2074 3042 6.605594 TCCCAAATTAAGTGACTCAACTTTGT 59.394 34.615 8.71 0.00 40.77 2.83
2075 3043 6.918022 GTCCCAAATTAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2076 3044 6.605594 TGTCCCAAATTAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
2077 3045 6.126409 TGTCCCAAATTAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
2078 3046 5.690865 TGTCCCAAATTAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
2079 3047 5.763204 TCTGTCCCAAATTAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
2080 3048 5.935945 TCTGTCCCAAATTAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
2081 3049 5.513094 CCTCTGTCCCAAATTAAGTGACTCA 60.513 44.000 0.00 0.00 0.00 3.41
2082 3050 4.938226 CCTCTGTCCCAAATTAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
2083 3051 4.263506 CCCTCTGTCCCAAATTAAGTGACT 60.264 45.833 0.00 0.00 0.00 3.41
2084 3052 4.010349 CCCTCTGTCCCAAATTAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
2085 3053 3.913799 TCCCTCTGTCCCAAATTAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
2086 3054 4.263506 ACTCCCTCTGTCCCAAATTAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
2087 3055 3.916989 ACTCCCTCTGTCCCAAATTAAGT 59.083 43.478 0.00 0.00 0.00 2.24
2088 3056 4.576330 ACTCCCTCTGTCCCAAATTAAG 57.424 45.455 0.00 0.00 0.00 1.85
2089 3057 5.970640 AGATACTCCCTCTGTCCCAAATTAA 59.029 40.000 0.00 0.00 0.00 1.40
2090 3058 5.538877 AGATACTCCCTCTGTCCCAAATTA 58.461 41.667 0.00 0.00 0.00 1.40
2091 3059 4.375313 AGATACTCCCTCTGTCCCAAATT 58.625 43.478 0.00 0.00 0.00 1.82
2092 3060 4.014273 AGATACTCCCTCTGTCCCAAAT 57.986 45.455 0.00 0.00 0.00 2.32
2093 3061 3.491766 AGATACTCCCTCTGTCCCAAA 57.508 47.619 0.00 0.00 0.00 3.28
2094 3062 3.491766 AAGATACTCCCTCTGTCCCAA 57.508 47.619 0.00 0.00 0.00 4.12
2095 3063 4.834406 ATAAGATACTCCCTCTGTCCCA 57.166 45.455 0.00 0.00 0.00 4.37
2096 3064 5.128008 GCATATAAGATACTCCCTCTGTCCC 59.872 48.000 0.00 0.00 0.00 4.46
2097 3065 5.717178 TGCATATAAGATACTCCCTCTGTCC 59.283 44.000 0.00 0.00 0.00 4.02
2098 3066 6.842437 TGCATATAAGATACTCCCTCTGTC 57.158 41.667 0.00 0.00 0.00 3.51
2099 3067 6.956435 TGATGCATATAAGATACTCCCTCTGT 59.044 38.462 0.00 0.00 0.00 3.41
2100 3068 7.415592 TGATGCATATAAGATACTCCCTCTG 57.584 40.000 0.00 0.00 0.00 3.35
2101 3069 8.621126 ATTGATGCATATAAGATACTCCCTCT 57.379 34.615 0.00 0.00 0.00 3.69
2102 3070 9.107177 CAATTGATGCATATAAGATACTCCCTC 57.893 37.037 0.00 0.00 0.00 4.30
2103 3071 8.829746 TCAATTGATGCATATAAGATACTCCCT 58.170 33.333 3.38 0.00 0.00 4.20
2104 3072 9.624373 ATCAATTGATGCATATAAGATACTCCC 57.376 33.333 20.11 0.00 32.68 4.30
2148 3116 7.984050 AGACAATATCAGTTGGTTCATCTAGTG 59.016 37.037 0.00 0.00 33.40 2.74
2200 3173 2.623450 TACCCTCTCAGGCTCCGGT 61.623 63.158 0.00 0.00 32.73 5.28
2202 3175 0.757188 ATGTACCCTCTCAGGCTCCG 60.757 60.000 0.00 0.00 32.73 4.63
2207 3180 1.135094 ATGGCATGTACCCTCTCAGG 58.865 55.000 0.00 0.00 34.30 3.86
2267 3240 4.844085 TGTTCTAATGGAGGACCTCAGAAA 59.156 41.667 23.06 10.56 31.70 2.52
2348 3321 2.998670 CTGGTGCAGATCTGTACAACAG 59.001 50.000 35.07 29.75 45.99 3.16
2368 3341 1.143073 AGAAGGAACGCAAAGAACCCT 59.857 47.619 0.00 0.00 0.00 4.34
2413 3386 3.604582 GATTCCCAGAAGAAGAGTGGTG 58.395 50.000 0.00 0.00 0.00 4.17
2713 3686 7.883391 TGGAGTTAATGTTTTAGGTTTGTCA 57.117 32.000 0.00 0.00 0.00 3.58
3075 4048 4.503296 CCTCAACGGCCTTGCTAGTATTAT 60.503 45.833 0.00 0.00 0.00 1.28
3520 4493 0.826715 TCTTCCTGGATCTTCGCCTG 59.173 55.000 0.00 0.00 0.00 4.85
3561 4534 2.878406 CCATTGGCATCCGTTAGGTTAG 59.122 50.000 0.00 0.00 39.05 2.34
3673 4646 2.100631 AGGAATTGCCGCTTCGTCG 61.101 57.895 0.00 0.00 43.43 5.12
3875 4848 2.930682 GCCTCAATCTAGACAAACGTCC 59.069 50.000 0.00 0.00 33.60 4.79
4037 5010 3.145286 TGTGCACATCCTTTTCATCGAA 58.855 40.909 17.42 0.00 0.00 3.71
4165 5138 1.913317 TCTCACGCTCATCAATGTCG 58.087 50.000 6.09 6.09 0.00 4.35
4541 5552 5.009010 GGCCGTTCATGATCAATTTAGACAT 59.991 40.000 0.00 0.00 0.00 3.06
4725 5736 0.373716 CTTCATCACCGCGCCTAAAC 59.626 55.000 0.00 0.00 0.00 2.01
5677 6796 3.523564 ACCATCAGCAGGGTTGTAAGTAT 59.476 43.478 0.00 0.00 32.12 2.12
5765 6884 2.034053 GGACAGATCGCCAGAGTCTAAG 59.966 54.545 0.00 0.00 0.00 2.18
6012 7131 0.738975 GTCCCGGGCTCATTTTTAGC 59.261 55.000 18.49 0.00 39.33 3.09
6142 7261 3.059325 GTCAATATCAACGCCTGAGATGC 60.059 47.826 0.00 0.00 36.11 3.91
6194 7313 5.416083 ACAGATTTTGCATCAATCACATGG 58.584 37.500 17.24 7.22 33.67 3.66
6405 7524 1.598701 GGGGCATTGACTGAAGGTGC 61.599 60.000 0.00 0.00 35.17 5.01
6420 7539 2.355010 AAGTATGCTTCTGATGGGGC 57.645 50.000 0.00 0.00 0.00 5.80
6422 7541 4.063689 CTGCTAAGTATGCTTCTGATGGG 58.936 47.826 0.00 0.00 36.22 4.00
6425 7544 5.104776 TCCAACTGCTAAGTATGCTTCTGAT 60.105 40.000 0.00 0.00 34.77 2.90
6457 7576 5.703876 CCTCATTTTTAGCAACTTCCAGTC 58.296 41.667 0.00 0.00 0.00 3.51
6468 7587 3.254411 GCTATCCCAGCCTCATTTTTAGC 59.746 47.826 0.00 0.00 45.23 3.09
6487 7606 6.225981 TCATCTCAGCATCAGTTTTAGCTA 57.774 37.500 0.00 0.00 35.19 3.32
6599 7718 1.354337 CTGAGATGTGTGCGGGTTCG 61.354 60.000 0.00 0.00 39.81 3.95
6603 7722 2.821366 GCCTGAGATGTGTGCGGG 60.821 66.667 0.00 0.00 0.00 6.13
6716 7835 8.902540 AGTAATTGTTCACATCAACACTAGAA 57.097 30.769 0.00 0.00 35.97 2.10
6868 7987 0.855349 CGCCTCGATACAACTCATGC 59.145 55.000 0.00 0.00 0.00 4.06
6924 8043 1.514983 TCCTCATGGCCATCAGACAT 58.485 50.000 19.69 0.00 0.00 3.06
6981 8100 2.084610 TCACTTGCGTCTCTTCCATG 57.915 50.000 0.00 0.00 0.00 3.66
6983 8102 1.138069 TGTTCACTTGCGTCTCTTCCA 59.862 47.619 0.00 0.00 0.00 3.53
7024 8315 5.823861 ACTTGCATTCCCTTTTACCAATT 57.176 34.783 0.00 0.00 0.00 2.32
7051 8342 7.296098 AGCTTCTTCAATCAATAAGGATCCAT 58.704 34.615 15.82 4.17 0.00 3.41
7052 8343 6.666678 AGCTTCTTCAATCAATAAGGATCCA 58.333 36.000 15.82 0.00 0.00 3.41
7053 8344 7.579761 AAGCTTCTTCAATCAATAAGGATCC 57.420 36.000 2.48 2.48 0.00 3.36
7056 8347 9.911788 AGAATAAGCTTCTTCAATCAATAAGGA 57.088 29.630 22.26 0.00 0.00 3.36
7060 8351 9.466497 ACCAAGAATAAGCTTCTTCAATCAATA 57.534 29.630 22.26 0.00 36.69 1.90
7061 8352 8.358582 ACCAAGAATAAGCTTCTTCAATCAAT 57.641 30.769 22.26 2.49 36.69 2.57
7062 8353 7.765695 ACCAAGAATAAGCTTCTTCAATCAA 57.234 32.000 22.26 0.00 36.69 2.57
7063 8354 7.765695 AACCAAGAATAAGCTTCTTCAATCA 57.234 32.000 22.26 0.00 36.69 2.57
7064 8355 8.184848 GGTAACCAAGAATAAGCTTCTTCAATC 58.815 37.037 22.26 1.22 36.69 2.67
7065 8356 7.890655 AGGTAACCAAGAATAAGCTTCTTCAAT 59.109 33.333 22.26 10.88 36.69 2.57
7066 8357 7.231467 AGGTAACCAAGAATAAGCTTCTTCAA 58.769 34.615 22.26 0.00 36.69 2.69
7067 8358 6.779860 AGGTAACCAAGAATAAGCTTCTTCA 58.220 36.000 22.26 0.00 36.69 3.02
7068 8359 7.175119 ACAAGGTAACCAAGAATAAGCTTCTTC 59.825 37.037 14.93 14.93 36.69 2.87
7069 8360 7.004691 ACAAGGTAACCAAGAATAAGCTTCTT 58.995 34.615 0.00 0.00 39.16 2.52
7070 8361 6.431234 CACAAGGTAACCAAGAATAAGCTTCT 59.569 38.462 0.00 0.00 37.17 2.85
7093 8384 0.317479 AGTACCGTGGAGTGCTTCAC 59.683 55.000 0.59 0.59 34.10 3.18
7263 8555 2.088423 TGCCCCAGCTAACAAATTACG 58.912 47.619 0.00 0.00 40.80 3.18
7278 8570 4.204028 ACCACACCACACTGCCCC 62.204 66.667 0.00 0.00 0.00 5.80
7449 8747 1.000274 GTTGCAAAGTTACCAGCCCAG 60.000 52.381 0.00 0.00 0.00 4.45
7453 8751 1.770957 GCAGTTGCAAAGTTACCAGC 58.229 50.000 0.00 0.00 41.59 4.85
7466 8764 2.195567 CCACCCACACCTGCAGTTG 61.196 63.158 13.81 11.92 0.00 3.16
7480 8778 7.830739 ACAAGAAGAAATGTGATATTTCCACC 58.169 34.615 10.47 1.95 38.44 4.61
7561 9043 2.489329 GCAGGCAAAATAAGCAGACTGA 59.511 45.455 6.65 0.00 0.00 3.41
7588 9070 9.722184 GAACTAGTAGAACCTTGGTAAAGAAAT 57.278 33.333 3.59 0.00 35.19 2.17
7599 9081 7.662897 CAAGTGAAGAGAACTAGTAGAACCTT 58.337 38.462 3.59 1.89 0.00 3.50
7600 9082 6.294843 GCAAGTGAAGAGAACTAGTAGAACCT 60.295 42.308 3.59 0.00 0.00 3.50
7601 9083 5.865013 GCAAGTGAAGAGAACTAGTAGAACC 59.135 44.000 3.59 0.00 0.00 3.62
7602 9084 6.683715 AGCAAGTGAAGAGAACTAGTAGAAC 58.316 40.000 3.59 0.00 0.00 3.01
7603 9085 6.902771 AGCAAGTGAAGAGAACTAGTAGAA 57.097 37.500 3.59 0.00 0.00 2.10
7604 9086 7.997773 TTAGCAAGTGAAGAGAACTAGTAGA 57.002 36.000 3.59 0.00 0.00 2.59
7605 9087 7.542824 GGTTTAGCAAGTGAAGAGAACTAGTAG 59.457 40.741 0.00 0.00 0.00 2.57
7606 9088 7.376615 GGTTTAGCAAGTGAAGAGAACTAGTA 58.623 38.462 0.00 0.00 0.00 1.82
7608 9090 5.639931 GGGTTTAGCAAGTGAAGAGAACTAG 59.360 44.000 0.00 0.00 0.00 2.57
7609 9091 5.307196 AGGGTTTAGCAAGTGAAGAGAACTA 59.693 40.000 0.00 0.00 0.00 2.24
7611 9093 4.214332 CAGGGTTTAGCAAGTGAAGAGAAC 59.786 45.833 0.00 0.00 0.00 3.01
7613 9095 3.807209 GCAGGGTTTAGCAAGTGAAGAGA 60.807 47.826 0.00 0.00 0.00 3.10
7614 9096 2.485814 GCAGGGTTTAGCAAGTGAAGAG 59.514 50.000 0.00 0.00 0.00 2.85
7616 9098 1.197721 CGCAGGGTTTAGCAAGTGAAG 59.802 52.381 0.00 0.00 0.00 3.02
7617 9099 1.202710 TCGCAGGGTTTAGCAAGTGAA 60.203 47.619 0.00 0.00 0.00 3.18
7618 9100 0.394938 TCGCAGGGTTTAGCAAGTGA 59.605 50.000 0.00 0.00 0.00 3.41
7619 9101 0.517316 GTCGCAGGGTTTAGCAAGTG 59.483 55.000 0.00 0.00 0.00 3.16
7620 9102 0.605589 GGTCGCAGGGTTTAGCAAGT 60.606 55.000 0.00 0.00 0.00 3.16
7636 9119 2.533266 TGCTGTTCTTCTGTCTGGTC 57.467 50.000 0.00 0.00 0.00 4.02
7645 9128 5.222631 CCATAAGGTGTTTTGCTGTTCTTC 58.777 41.667 0.00 0.00 0.00 2.87
7650 9133 1.618343 GCCCATAAGGTGTTTTGCTGT 59.382 47.619 0.00 0.00 38.26 4.40
7651 9134 1.066929 GGCCCATAAGGTGTTTTGCTG 60.067 52.381 0.00 0.00 38.26 4.41
7663 9146 3.785887 AGGATTAGTTCAGTGGCCCATAA 59.214 43.478 0.00 0.00 0.00 1.90
7711 9194 1.034292 GCCACAAATCTCCTCCCAGC 61.034 60.000 0.00 0.00 0.00 4.85
7712 9195 0.622665 AGCCACAAATCTCCTCCCAG 59.377 55.000 0.00 0.00 0.00 4.45
7719 9202 1.673168 CAGCCCTAGCCACAAATCTC 58.327 55.000 0.00 0.00 41.25 2.75
7729 9212 0.172127 GCTTTTCTTGCAGCCCTAGC 59.828 55.000 0.00 0.00 40.32 3.42
7809 9305 8.668510 AGCTACATAAATTGTTCATACTCAGG 57.331 34.615 0.00 0.00 39.87 3.86
7823 9319 9.971922 GCTTATTTCCAATCAAGCTACATAAAT 57.028 29.630 0.00 0.00 40.16 1.40
7886 9405 6.961360 AATTATATGATCTCGGGCTATCGA 57.039 37.500 0.00 0.00 37.60 3.59
8036 9573 6.420913 TCTCTGCAGTTAACTAACTTTCCT 57.579 37.500 14.67 0.00 43.57 3.36
8042 9579 9.331106 GCTAAATTTTCTCTGCAGTTAACTAAC 57.669 33.333 14.67 4.34 36.46 2.34
8046 9583 6.071896 AGGGCTAAATTTTCTCTGCAGTTAAC 60.072 38.462 14.67 0.00 0.00 2.01
8071 9608 8.721133 ATACATGGTGATCACATACCTTAGTA 57.279 34.615 26.47 15.75 37.84 1.82
8120 9661 1.539496 GGTGCGTGTGTCCTCAAACTA 60.539 52.381 0.00 0.00 30.10 2.24
8129 9670 2.774439 AAAATGAAGGTGCGTGTGTC 57.226 45.000 0.00 0.00 0.00 3.67
8304 10462 3.231965 TCGATCTCGAACAAGTTTCGAC 58.768 45.455 5.04 0.00 46.30 4.20
8336 10494 1.071605 GGCTCGTGCTCAACTTGTAG 58.928 55.000 9.61 0.00 39.59 2.74
8343 10501 0.106708 AGAAAGTGGCTCGTGCTCAA 59.893 50.000 9.61 0.00 39.59 3.02
8394 10553 8.132995 TCAACTTATACAAATATTCGAGCGAGA 58.867 33.333 0.00 0.00 0.00 4.04
8406 10565 3.877508 GGCTCGGCTCAACTTATACAAAT 59.122 43.478 0.00 0.00 0.00 2.32
8423 10582 1.936547 GAGCAAGTTGGATTAGGCTCG 59.063 52.381 4.75 0.00 38.44 5.03
8469 10628 1.749063 TCAGCGATCCACAATCTACGT 59.251 47.619 0.00 0.00 31.68 3.57
8475 10634 2.857592 GCAAATCAGCGATCCACAAT 57.142 45.000 0.00 0.00 0.00 2.71
8485 10644 3.892918 AGAATCATAGCGCAAATCAGC 57.107 42.857 11.47 0.00 0.00 4.26
8486 10645 6.952743 AGTTTAGAATCATAGCGCAAATCAG 58.047 36.000 11.47 0.00 0.00 2.90
8487 10646 6.925610 AGTTTAGAATCATAGCGCAAATCA 57.074 33.333 11.47 0.00 0.00 2.57
8488 10647 7.189512 ACAAGTTTAGAATCATAGCGCAAATC 58.810 34.615 11.47 0.00 0.00 2.17
8489 10648 7.088589 ACAAGTTTAGAATCATAGCGCAAAT 57.911 32.000 11.47 0.00 0.00 2.32
8490 10649 6.494893 ACAAGTTTAGAATCATAGCGCAAA 57.505 33.333 11.47 0.00 0.00 3.68
8491 10650 6.494893 AACAAGTTTAGAATCATAGCGCAA 57.505 33.333 11.47 0.00 0.00 4.85
8492 10651 6.494893 AAACAAGTTTAGAATCATAGCGCA 57.505 33.333 11.47 0.00 0.00 6.09
8493 10652 8.481132 CATAAACAAGTTTAGAATCATAGCGC 57.519 34.615 0.00 0.00 38.30 5.92


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

AutoCloner maintained by Alex Coulton.