Multiple sequence alignment - TraesCS3A01G412300

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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 TraesCS3A01G412300 chr3A 100.000 3576 0 0 1 3576 655919262 655922837 0.000000e+00 6604.0
1 TraesCS3A01G412300 chr3A 98.705 1467 12 2 2116 3576 658200356 658198891 0.000000e+00 2597.0
2 TraesCS3A01G412300 chr3A 91.605 810 54 4 1877 2675 655538823 655538017 0.000000e+00 1107.0
3 TraesCS3A01G412300 chr3A 92.771 415 19 5 2707 3110 655538018 655537604 1.110000e-164 590.0
4 TraesCS3A01G412300 chr3A 75.443 1128 210 41 1069 2141 700352273 700351158 1.490000e-133 486.0
5 TraesCS3A01G412300 chr3A 81.765 510 76 9 1022 1515 702407895 702407387 9.240000e-111 411.0
6 TraesCS3A01G412300 chr3A 89.041 219 23 1 1018 1236 699533365 699533582 1.640000e-68 270.0
7 TraesCS3A01G412300 chr3A 88.106 227 24 3 1026 1252 699975130 699975353 2.120000e-67 267.0
8 TraesCS3A01G412300 chr3A 97.902 143 3 0 1 143 424165323 424165181 7.670000e-62 248.0
9 TraesCS3A01G412300 chr3A 82.292 96 17 0 1409 1504 697591704 697591609 2.290000e-12 84.2
10 TraesCS3A01G412300 chr3A 83.333 84 8 1 2300 2377 700250456 700250539 4.950000e-09 73.1
11 TraesCS3A01G412300 chr3B 93.043 2645 112 24 971 3576 685659086 685661697 0.000000e+00 3799.0
12 TraesCS3A01G412300 chr3B 92.935 2647 113 26 971 3576 685630591 685633204 0.000000e+00 3784.0
13 TraesCS3A01G412300 chr3B 93.000 2200 103 25 860 3013 685471395 685473589 0.000000e+00 3162.0
14 TraesCS3A01G412300 chr3B 90.290 690 52 5 140 814 685470706 685471395 0.000000e+00 889.0
15 TraesCS3A01G412300 chr3B 92.333 613 25 9 2730 3334 684502741 684502143 0.000000e+00 852.0
16 TraesCS3A01G412300 chr3B 82.522 904 79 32 2715 3576 685477393 685478259 0.000000e+00 721.0
17 TraesCS3A01G412300 chr3B 83.333 504 48 14 2651 3124 601375159 601375656 1.970000e-117 433.0
18 TraesCS3A01G412300 chr3B 90.288 278 19 4 2405 2675 684503046 684502770 1.220000e-94 357.0
19 TraesCS3A01G412300 chr3B 86.486 259 27 6 976 1232 752973307 752973055 9.780000e-71 278.0
20 TraesCS3A01G412300 chr3B 88.158 228 22 4 1026 1252 753867300 753867523 2.120000e-67 267.0
21 TraesCS3A01G412300 chr3B 90.860 186 12 3 3334 3519 684502089 684501909 9.920000e-61 244.0
22 TraesCS3A01G412300 chr3B 80.345 290 33 8 1069 1334 754850205 754849916 7.830000e-47 198.0
23 TraesCS3A01G412300 chr3B 71.715 548 103 40 1357 1860 754302639 754303178 4.880000e-19 106.0
24 TraesCS3A01G412300 chr3D 94.038 2080 83 13 1064 3107 520595040 520597114 0.000000e+00 3116.0
25 TraesCS3A01G412300 chr3D 95.843 433 17 1 3144 3576 520601304 520601735 0.000000e+00 699.0
26 TraesCS3A01G412300 chr3D 91.700 494 35 3 2185 2675 520040103 520039613 0.000000e+00 680.0
27 TraesCS3A01G412300 chr3D 94.159 428 16 2 3098 3525 520600476 520600894 0.000000e+00 643.0
28 TraesCS3A01G412300 chr3D 95.812 382 15 1 3144 3525 520600909 520601289 1.820000e-172 616.0
29 TraesCS3A01G412300 chr3D 79.014 953 129 38 1642 2544 520440591 520441522 1.430000e-163 586.0
30 TraesCS3A01G412300 chr3D 74.732 1120 230 38 1063 2145 567902748 567903851 5.440000e-123 451.0
31 TraesCS3A01G412300 chr3D 74.205 1163 241 35 1017 2146 520426578 520427714 7.090000e-117 431.0
32 TraesCS3A01G412300 chr3D 93.493 292 12 5 3040 3328 519961674 519961387 9.170000e-116 427.0
33 TraesCS3A01G412300 chr3D 90.411 292 26 2 1877 2166 520075536 520075245 2.010000e-102 383.0
34 TraesCS3A01G412300 chr3D 73.951 810 192 16 1344 2145 568034167 568034965 3.470000e-80 309.0
35 TraesCS3A01G412300 chr3D 89.300 243 24 2 3334 3576 519961328 519961088 1.610000e-78 303.0
36 TraesCS3A01G412300 chr3D 78.982 452 62 20 1026 1450 565641909 565642354 9.780000e-71 278.0
37 TraesCS3A01G412300 chr3D 81.793 368 30 13 388 742 520457086 520457429 1.260000e-69 274.0
38 TraesCS3A01G412300 chr3D 85.433 254 22 5 497 741 520443640 520443887 2.130000e-62 250.0
39 TraesCS3A01G412300 chr3D 81.724 290 29 7 1069 1334 569132423 569132712 1.670000e-53 220.0
40 TraesCS3A01G412300 chr3D 91.304 115 9 1 2651 2764 520442138 520442252 4.780000e-34 156.0
41 TraesCS3A01G412300 chr3D 87.786 131 3 6 917 1036 520594914 520595042 1.340000e-29 141.0
42 TraesCS3A01G412300 chr3D 78.392 199 24 6 1155 1334 566628631 566628829 1.050000e-20 111.0
43 TraesCS3A01G412300 chr3D 90.909 66 6 0 761 826 520443882 520443947 4.920000e-14 89.8
44 TraesCS3A01G412300 chrUn 100.000 409 0 0 2845 3253 477791309 477791717 0.000000e+00 756.0
45 TraesCS3A01G412300 chrUn 74.892 1159 231 39 1029 2145 340249284 340248144 1.160000e-129 473.0
46 TraesCS3A01G412300 chrUn 75.492 457 100 4 1689 2145 41197008 41196564 2.800000e-51 213.0
47 TraesCS3A01G412300 chr1A 97.902 143 3 0 1 143 384910604 384910462 7.670000e-62 248.0
48 TraesCS3A01G412300 chr6D 97.203 143 4 0 1 143 109695877 109695735 3.570000e-60 243.0
49 TraesCS3A01G412300 chr6D 97.203 143 4 0 1 143 264932624 264932482 3.570000e-60 243.0
50 TraesCS3A01G412300 chr6D 97.203 143 4 0 1 143 430619034 430619176 3.570000e-60 243.0
51 TraesCS3A01G412300 chr4D 97.203 143 4 0 1 143 181513585 181513443 3.570000e-60 243.0
52 TraesCS3A01G412300 chr1D 97.203 143 4 0 1 143 57842566 57842708 3.570000e-60 243.0
53 TraesCS3A01G412300 chr1D 97.203 143 4 0 1 143 271384149 271384291 3.570000e-60 243.0
54 TraesCS3A01G412300 chr1D 97.203 143 4 0 1 143 291445208 291445350 3.570000e-60 243.0


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 TraesCS3A01G412300 chr3A 655919262 655922837 3575 False 6604.000000 6604 100.000000 1 3576 1 chr3A.!!$F1 3575
1 TraesCS3A01G412300 chr3A 658198891 658200356 1465 True 2597.000000 2597 98.705000 2116 3576 1 chr3A.!!$R2 1460
2 TraesCS3A01G412300 chr3A 655537604 655538823 1219 True 848.500000 1107 92.188000 1877 3110 2 chr3A.!!$R6 1233
3 TraesCS3A01G412300 chr3A 700351158 700352273 1115 True 486.000000 486 75.443000 1069 2141 1 chr3A.!!$R4 1072
4 TraesCS3A01G412300 chr3A 702407387 702407895 508 True 411.000000 411 81.765000 1022 1515 1 chr3A.!!$R5 493
5 TraesCS3A01G412300 chr3B 685659086 685661697 2611 False 3799.000000 3799 93.043000 971 3576 1 chr3B.!!$F3 2605
6 TraesCS3A01G412300 chr3B 685630591 685633204 2613 False 3784.000000 3784 92.935000 971 3576 1 chr3B.!!$F2 2605
7 TraesCS3A01G412300 chr3B 685470706 685478259 7553 False 1590.666667 3162 88.604000 140 3576 3 chr3B.!!$F6 3436
8 TraesCS3A01G412300 chr3B 684501909 684503046 1137 True 484.333333 852 91.160333 2405 3519 3 chr3B.!!$R3 1114
9 TraesCS3A01G412300 chr3D 520594914 520601735 6821 False 1043.000000 3116 93.527600 917 3576 5 chr3D.!!$F9 2659
10 TraesCS3A01G412300 chr3D 567902748 567903851 1103 False 451.000000 451 74.732000 1063 2145 1 chr3D.!!$F5 1082
11 TraesCS3A01G412300 chr3D 520426578 520427714 1136 False 431.000000 431 74.205000 1017 2146 1 chr3D.!!$F1 1129
12 TraesCS3A01G412300 chr3D 519961088 519961674 586 True 365.000000 427 91.396500 3040 3576 2 chr3D.!!$R3 536
13 TraesCS3A01G412300 chr3D 568034167 568034965 798 False 309.000000 309 73.951000 1344 2145 1 chr3D.!!$F6 801
14 TraesCS3A01G412300 chr3D 520440591 520443947 3356 False 270.450000 586 86.665000 497 2764 4 chr3D.!!$F8 2267
15 TraesCS3A01G412300 chrUn 340248144 340249284 1140 True 473.000000 473 74.892000 1029 2145 1 chrUn.!!$R2 1116

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
82 83 0.032403 GCAAGCAAGTTGGATGCACA 59.968 50.0 4.75 0.0 46.22 4.57 F
836 852 0.034089 GCATGGGCTTAACCTGGACT 60.034 55.0 0.00 0.0 39.10 3.85 F
840 856 0.035343 GGGCTTAACCTGGACTGGAC 60.035 60.0 0.00 0.0 39.10 4.02 F
849 865 0.035458 CTGGACTGGACCACCTTCAC 59.965 60.0 2.98 0.0 35.91 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1759 2.046314 CCACCGCGGAACAGGAAT 60.046 61.111 35.90 2.6 36.56 3.01 R
1861 2010 4.290155 CAACTCAATGTGGTACTTGTTGC 58.710 43.478 0.00 0.0 0.00 4.17 R
2297 2462 6.337356 ACAAAATGACTTGGTAGTTTTGGTG 58.663 36.000 16.59 0.0 35.43 4.17 R
3360 12480 5.262804 AGATTATACTCCCTACGTCCCATC 58.737 45.833 0.00 0.0 0.00 3.51 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
28 29 6.759497 AGAACTTGGCTTGTATATTCCAAC 57.241 37.500 0.00 0.00 35.07 3.77
29 30 5.354234 AGAACTTGGCTTGTATATTCCAACG 59.646 40.000 0.00 0.00 35.07 4.10
30 31 4.839121 ACTTGGCTTGTATATTCCAACGA 58.161 39.130 0.00 0.00 35.07 3.85
31 32 5.437060 ACTTGGCTTGTATATTCCAACGAT 58.563 37.500 0.00 0.00 35.07 3.73
32 33 5.296780 ACTTGGCTTGTATATTCCAACGATG 59.703 40.000 0.00 0.00 35.07 3.84
41 42 4.225497 CCAACGATGGGCTTCCTC 57.775 61.111 3.28 0.00 43.51 3.71
42 43 1.299648 CCAACGATGGGCTTCCTCA 59.700 57.895 3.28 0.00 43.51 3.86
43 44 0.322456 CCAACGATGGGCTTCCTCAA 60.322 55.000 3.28 0.00 43.51 3.02
44 45 1.089920 CAACGATGGGCTTCCTCAAG 58.910 55.000 0.00 0.00 0.00 3.02
45 46 0.693049 AACGATGGGCTTCCTCAAGT 59.307 50.000 0.00 0.00 31.45 3.16
46 47 0.036010 ACGATGGGCTTCCTCAAGTG 60.036 55.000 0.00 0.00 31.45 3.16
47 48 1.372087 CGATGGGCTTCCTCAAGTGC 61.372 60.000 0.00 0.00 31.45 4.40
48 49 1.000396 ATGGGCTTCCTCAAGTGCC 60.000 57.895 0.00 0.00 44.22 5.01
50 51 2.759795 GGCTTCCTCAAGTGCCCT 59.240 61.111 0.00 0.00 39.49 5.19
51 52 1.991230 GGCTTCCTCAAGTGCCCTA 59.009 57.895 0.00 0.00 39.49 3.53
52 53 0.107459 GGCTTCCTCAAGTGCCCTAG 60.107 60.000 0.00 0.00 39.49 3.02
53 54 0.107459 GCTTCCTCAAGTGCCCTAGG 60.107 60.000 0.06 0.06 31.45 3.02
54 55 1.280457 CTTCCTCAAGTGCCCTAGGT 58.720 55.000 8.29 0.00 0.00 3.08
55 56 1.208293 CTTCCTCAAGTGCCCTAGGTC 59.792 57.143 8.29 0.00 0.00 3.85
56 57 0.413832 TCCTCAAGTGCCCTAGGTCT 59.586 55.000 8.29 0.18 0.00 3.85
57 58 1.203313 TCCTCAAGTGCCCTAGGTCTT 60.203 52.381 8.29 6.65 0.00 3.01
58 59 1.208293 CCTCAAGTGCCCTAGGTCTTC 59.792 57.143 8.29 0.00 0.00 2.87
59 60 1.902508 CTCAAGTGCCCTAGGTCTTCA 59.097 52.381 8.29 0.00 0.00 3.02
60 61 2.503356 CTCAAGTGCCCTAGGTCTTCAT 59.497 50.000 8.29 0.00 0.00 2.57
61 62 2.237143 TCAAGTGCCCTAGGTCTTCATG 59.763 50.000 8.29 0.00 0.00 3.07
62 63 2.237143 CAAGTGCCCTAGGTCTTCATGA 59.763 50.000 8.29 0.00 0.00 3.07
63 64 2.114616 AGTGCCCTAGGTCTTCATGAG 58.885 52.381 8.29 0.00 0.00 2.90
64 65 0.833287 TGCCCTAGGTCTTCATGAGC 59.167 55.000 8.29 0.74 43.05 4.26
65 66 0.833287 GCCCTAGGTCTTCATGAGCA 59.167 55.000 8.29 0.00 44.98 4.26
66 67 1.210478 GCCCTAGGTCTTCATGAGCAA 59.790 52.381 8.29 0.00 44.98 3.91
67 68 2.744494 GCCCTAGGTCTTCATGAGCAAG 60.744 54.545 8.29 0.00 44.98 4.01
68 69 2.559440 CCTAGGTCTTCATGAGCAAGC 58.441 52.381 0.00 0.00 44.98 4.01
69 70 2.093288 CCTAGGTCTTCATGAGCAAGCA 60.093 50.000 0.00 0.00 44.98 3.91
70 71 2.574006 AGGTCTTCATGAGCAAGCAA 57.426 45.000 0.00 0.00 44.98 3.91
71 72 2.434428 AGGTCTTCATGAGCAAGCAAG 58.566 47.619 0.00 0.00 44.98 4.01
72 73 2.157738 GGTCTTCATGAGCAAGCAAGT 58.842 47.619 0.00 0.00 42.34 3.16
73 74 2.555757 GGTCTTCATGAGCAAGCAAGTT 59.444 45.455 0.00 0.00 42.34 2.66
74 75 3.562505 GTCTTCATGAGCAAGCAAGTTG 58.437 45.455 0.00 0.00 39.41 3.16
75 76 2.555325 TCTTCATGAGCAAGCAAGTTGG 59.445 45.455 4.75 0.00 36.56 3.77
76 77 2.275134 TCATGAGCAAGCAAGTTGGA 57.725 45.000 4.75 0.00 36.56 3.53
77 78 2.799017 TCATGAGCAAGCAAGTTGGAT 58.201 42.857 4.75 0.00 36.56 3.41
78 79 2.490509 TCATGAGCAAGCAAGTTGGATG 59.509 45.455 4.75 0.00 36.56 3.51
79 80 0.599558 TGAGCAAGCAAGTTGGATGC 59.400 50.000 4.75 0.00 44.15 3.91
80 81 0.599558 GAGCAAGCAAGTTGGATGCA 59.400 50.000 4.75 0.00 46.22 3.96
81 82 0.316204 AGCAAGCAAGTTGGATGCAC 59.684 50.000 4.75 0.00 46.22 4.57
82 83 0.032403 GCAAGCAAGTTGGATGCACA 59.968 50.000 4.75 0.00 46.22 4.57
83 84 1.774639 CAAGCAAGTTGGATGCACAC 58.225 50.000 4.75 0.00 46.22 3.82
84 85 0.675633 AAGCAAGTTGGATGCACACC 59.324 50.000 4.75 4.98 46.22 4.16
85 86 1.181098 AGCAAGTTGGATGCACACCC 61.181 55.000 4.75 2.41 46.22 4.61
86 87 1.462731 GCAAGTTGGATGCACACCCA 61.463 55.000 4.75 4.95 43.29 4.51
87 88 0.314935 CAAGTTGGATGCACACCCAC 59.685 55.000 8.94 8.22 31.11 4.61
88 89 0.185901 AAGTTGGATGCACACCCACT 59.814 50.000 11.14 11.14 35.39 4.00
89 90 0.185901 AGTTGGATGCACACCCACTT 59.814 50.000 11.14 0.00 30.80 3.16
90 91 1.423541 AGTTGGATGCACACCCACTTA 59.576 47.619 11.14 0.00 30.80 2.24
91 92 1.812571 GTTGGATGCACACCCACTTAG 59.187 52.381 8.94 0.00 31.11 2.18
92 93 1.064003 TGGATGCACACCCACTTAGT 58.936 50.000 8.94 0.00 0.00 2.24
93 94 1.423541 TGGATGCACACCCACTTAGTT 59.576 47.619 8.94 0.00 0.00 2.24
94 95 2.158534 TGGATGCACACCCACTTAGTTT 60.159 45.455 8.94 0.00 0.00 2.66
95 96 2.488153 GGATGCACACCCACTTAGTTTC 59.512 50.000 0.00 0.00 0.00 2.78
96 97 2.719531 TGCACACCCACTTAGTTTCA 57.280 45.000 0.00 0.00 0.00 2.69
97 98 2.571212 TGCACACCCACTTAGTTTCAG 58.429 47.619 0.00 0.00 0.00 3.02
98 99 2.092646 TGCACACCCACTTAGTTTCAGT 60.093 45.455 0.00 0.00 0.00 3.41
99 100 2.949644 GCACACCCACTTAGTTTCAGTT 59.050 45.455 0.00 0.00 0.00 3.16
100 101 3.380320 GCACACCCACTTAGTTTCAGTTT 59.620 43.478 0.00 0.00 0.00 2.66
101 102 4.733523 GCACACCCACTTAGTTTCAGTTTG 60.734 45.833 0.00 0.00 0.00 2.93
102 103 4.638421 CACACCCACTTAGTTTCAGTTTGA 59.362 41.667 0.00 0.00 0.00 2.69
103 104 4.881850 ACACCCACTTAGTTTCAGTTTGAG 59.118 41.667 0.00 0.00 0.00 3.02
104 105 3.883489 ACCCACTTAGTTTCAGTTTGAGC 59.117 43.478 0.00 0.00 0.00 4.26
105 106 4.137543 CCCACTTAGTTTCAGTTTGAGCT 58.862 43.478 0.00 0.00 0.00 4.09
106 107 4.580580 CCCACTTAGTTTCAGTTTGAGCTT 59.419 41.667 0.00 0.00 0.00 3.74
107 108 5.278022 CCCACTTAGTTTCAGTTTGAGCTTC 60.278 44.000 0.00 0.00 0.00 3.86
108 109 5.278022 CCACTTAGTTTCAGTTTGAGCTTCC 60.278 44.000 0.00 0.00 0.00 3.46
109 110 5.296780 CACTTAGTTTCAGTTTGAGCTTCCA 59.703 40.000 0.00 0.00 0.00 3.53
110 111 6.016777 CACTTAGTTTCAGTTTGAGCTTCCAT 60.017 38.462 0.00 0.00 0.00 3.41
111 112 7.173218 CACTTAGTTTCAGTTTGAGCTTCCATA 59.827 37.037 0.00 0.00 0.00 2.74
112 113 5.948992 AGTTTCAGTTTGAGCTTCCATAC 57.051 39.130 0.00 0.00 0.00 2.39
113 114 5.376625 AGTTTCAGTTTGAGCTTCCATACA 58.623 37.500 0.00 0.00 0.00 2.29
114 115 5.239525 AGTTTCAGTTTGAGCTTCCATACAC 59.760 40.000 0.00 0.00 0.00 2.90
115 116 4.623932 TCAGTTTGAGCTTCCATACACT 57.376 40.909 0.00 0.00 0.00 3.55
116 117 4.973168 TCAGTTTGAGCTTCCATACACTT 58.027 39.130 0.00 0.00 0.00 3.16
117 118 4.756642 TCAGTTTGAGCTTCCATACACTTG 59.243 41.667 0.00 0.00 0.00 3.16
118 119 4.516698 CAGTTTGAGCTTCCATACACTTGT 59.483 41.667 0.00 0.00 0.00 3.16
119 120 5.700832 CAGTTTGAGCTTCCATACACTTGTA 59.299 40.000 0.00 0.00 34.67 2.41
120 121 5.934625 AGTTTGAGCTTCCATACACTTGTAG 59.065 40.000 0.00 0.00 33.52 2.74
121 122 3.861840 TGAGCTTCCATACACTTGTAGC 58.138 45.455 0.00 0.00 33.52 3.58
122 123 3.515502 TGAGCTTCCATACACTTGTAGCT 59.484 43.478 3.73 3.73 36.20 3.32
123 124 4.116238 GAGCTTCCATACACTTGTAGCTC 58.884 47.826 12.89 12.89 39.82 4.09
124 125 3.772025 AGCTTCCATACACTTGTAGCTCT 59.228 43.478 0.00 0.00 31.10 4.09
125 126 4.956700 AGCTTCCATACACTTGTAGCTCTA 59.043 41.667 0.00 0.00 31.10 2.43
126 127 5.068460 AGCTTCCATACACTTGTAGCTCTAG 59.932 44.000 0.00 0.00 31.10 2.43
127 128 5.163499 GCTTCCATACACTTGTAGCTCTAGT 60.163 44.000 0.00 0.00 33.52 2.57
133 134 4.383850 CACTTGTAGCTCTAGTGCATCT 57.616 45.455 18.36 1.24 41.25 2.90
134 135 4.111198 CACTTGTAGCTCTAGTGCATCTG 58.889 47.826 18.36 7.25 41.25 2.90
135 136 3.766591 ACTTGTAGCTCTAGTGCATCTGT 59.233 43.478 18.36 7.80 31.55 3.41
136 137 4.221703 ACTTGTAGCTCTAGTGCATCTGTT 59.778 41.667 18.36 0.00 31.55 3.16
137 138 4.115401 TGTAGCTCTAGTGCATCTGTTG 57.885 45.455 18.36 0.00 34.99 3.33
138 139 2.687700 AGCTCTAGTGCATCTGTTGG 57.312 50.000 18.36 0.00 34.99 3.77
166 167 1.920835 GTGCAACCCTCCTCCTCCT 60.921 63.158 0.00 0.00 0.00 3.69
170 171 0.689412 CAACCCTCCTCCTCCTCCTC 60.689 65.000 0.00 0.00 0.00 3.71
182 183 2.108168 CTCCTCCTCGTGGTAAATCCA 58.892 52.381 2.99 0.00 45.01 3.41
208 209 1.961277 GTCAGGGAGCACCAACACG 60.961 63.158 1.58 0.00 43.89 4.49
228 229 2.744166 CGACATCCCATCATGTTGCTCT 60.744 50.000 0.00 0.00 37.11 4.09
231 232 2.118313 TCCCATCATGTTGCTCTGTG 57.882 50.000 0.00 0.00 0.00 3.66
235 236 1.400846 CATCATGTTGCTCTGTGCTCC 59.599 52.381 3.20 0.00 43.37 4.70
237 238 1.085091 CATGTTGCTCTGTGCTCCTC 58.915 55.000 3.20 0.00 43.37 3.71
249 250 0.399091 TGCTCCTCCGATCTCCCAAT 60.399 55.000 0.00 0.00 0.00 3.16
259 260 2.580962 GATCTCCCAATTTCCAGCCTC 58.419 52.381 0.00 0.00 0.00 4.70
276 277 1.412217 CCTCCCTCTCTGGCTATGTCA 60.412 57.143 0.00 0.00 0.00 3.58
285 286 5.086621 TCTCTGGCTATGTCATTGGCTATA 58.913 41.667 18.77 6.36 0.00 1.31
286 287 5.723405 TCTCTGGCTATGTCATTGGCTATAT 59.277 40.000 18.77 0.00 0.00 0.86
354 355 7.041372 TGAGTGTAGATGGCTTTTAAACAACTC 60.041 37.037 0.00 0.00 0.00 3.01
355 356 6.073222 AGTGTAGATGGCTTTTAAACAACTCG 60.073 38.462 0.00 0.00 0.00 4.18
414 415 2.163613 CCTTAGTTCGTTTTGGGCCATC 59.836 50.000 7.26 0.00 0.00 3.51
442 443 4.255301 GGCAATGGCTTCAATTTGATTCA 58.745 39.130 0.00 0.33 40.87 2.57
460 461 1.447838 AGCGCACTACGTGATTGGG 60.448 57.895 11.47 1.79 46.11 4.12
473 474 0.984230 GATTGGGCCCGATCTATCCA 59.016 55.000 36.39 6.67 34.75 3.41
475 476 0.399949 TTGGGCCCGATCTATCCAGT 60.400 55.000 19.37 0.00 0.00 4.00
476 477 0.399949 TGGGCCCGATCTATCCAGTT 60.400 55.000 19.37 0.00 0.00 3.16
497 510 2.196295 TTTGTTTTTGCGAGGAACGG 57.804 45.000 0.00 0.00 42.83 4.44
547 560 3.233578 GTTGCCATACATTCGTGTGTTG 58.766 45.455 1.17 1.37 32.66 3.33
555 568 4.530094 ACATTCGTGTGTTGTGTGTTAG 57.470 40.909 0.00 0.00 0.00 2.34
572 585 6.092807 GTGTGTTAGGATCATTTCTTGGAGAC 59.907 42.308 0.00 0.00 0.00 3.36
576 589 8.772250 TGTTAGGATCATTTCTTGGAGACTATT 58.228 33.333 0.00 0.00 0.00 1.73
639 655 5.914085 GGATCTCTTCCAATTATGTGTCG 57.086 43.478 0.00 0.00 44.74 4.35
640 656 4.752101 GGATCTCTTCCAATTATGTGTCGG 59.248 45.833 0.00 0.00 44.74 4.79
645 661 2.088423 TCCAATTATGTGTCGGGTTGC 58.912 47.619 0.00 0.00 0.00 4.17
657 673 0.313987 CGGGTTGCCTGAAGGAAAAC 59.686 55.000 0.00 0.00 39.86 2.43
659 675 1.068588 GGGTTGCCTGAAGGAAAACAC 59.931 52.381 7.44 4.89 42.53 3.32
661 677 2.167487 GGTTGCCTGAAGGAAAACACAA 59.833 45.455 0.00 0.00 40.34 3.33
674 690 4.379652 GAAAACACAATGACCCATGCTTT 58.620 39.130 0.00 0.00 0.00 3.51
677 693 2.679450 CACAATGACCCATGCTTTGTG 58.321 47.619 12.70 12.70 41.65 3.33
742 758 7.772757 ACAAAATCAATAGGACTTCCAGATCTC 59.227 37.037 0.00 0.00 38.89 2.75
796 812 3.173668 TCAAATAATCAGTACGCGGCT 57.826 42.857 12.47 5.16 0.00 5.52
801 817 5.399604 AATAATCAGTACGCGGCTAAAAC 57.600 39.130 12.47 0.00 0.00 2.43
802 818 2.667473 ATCAGTACGCGGCTAAAACT 57.333 45.000 12.47 0.63 0.00 2.66
813 829 4.295051 GCGGCTAAAACTCAAACATGAAA 58.705 39.130 0.00 0.00 0.00 2.69
814 830 4.148174 GCGGCTAAAACTCAAACATGAAAC 59.852 41.667 0.00 0.00 0.00 2.78
815 831 5.277825 CGGCTAAAACTCAAACATGAAACA 58.722 37.500 0.00 0.00 0.00 2.83
816 832 5.173131 CGGCTAAAACTCAAACATGAAACAC 59.827 40.000 0.00 0.00 0.00 3.32
817 833 5.173131 GGCTAAAACTCAAACATGAAACACG 59.827 40.000 0.00 0.00 0.00 4.49
818 834 5.331532 GCTAAAACTCAAACATGAAACACGC 60.332 40.000 0.00 0.00 0.00 5.34
819 835 3.773860 AACTCAAACATGAAACACGCA 57.226 38.095 0.00 0.00 0.00 5.24
820 836 3.988379 ACTCAAACATGAAACACGCAT 57.012 38.095 0.00 0.00 0.00 4.73
821 837 3.631144 ACTCAAACATGAAACACGCATG 58.369 40.909 0.00 0.00 46.49 4.06
822 838 2.981805 CTCAAACATGAAACACGCATGG 59.018 45.455 0.00 0.00 45.62 3.66
823 839 2.060284 CAAACATGAAACACGCATGGG 58.940 47.619 8.44 8.44 45.62 4.00
824 840 0.038343 AACATGAAACACGCATGGGC 60.038 50.000 10.10 0.00 45.62 5.36
825 841 0.895100 ACATGAAACACGCATGGGCT 60.895 50.000 10.10 0.00 45.62 5.19
826 842 0.244450 CATGAAACACGCATGGGCTT 59.756 50.000 10.10 0.80 39.48 4.35
827 843 1.472082 CATGAAACACGCATGGGCTTA 59.528 47.619 10.10 0.00 39.48 3.09
828 844 1.610363 TGAAACACGCATGGGCTTAA 58.390 45.000 10.10 0.00 38.10 1.85
829 845 1.268352 TGAAACACGCATGGGCTTAAC 59.732 47.619 10.10 0.18 38.10 2.01
830 846 0.601057 AAACACGCATGGGCTTAACC 59.399 50.000 10.10 0.00 38.10 2.85
831 847 0.251165 AACACGCATGGGCTTAACCT 60.251 50.000 10.10 0.00 39.10 3.50
832 848 0.960364 ACACGCATGGGCTTAACCTG 60.960 55.000 10.10 1.22 39.10 4.00
833 849 1.378514 ACGCATGGGCTTAACCTGG 60.379 57.895 10.10 0.00 39.10 4.45
834 850 1.077787 CGCATGGGCTTAACCTGGA 60.078 57.895 0.00 0.00 39.10 3.86
835 851 1.376609 CGCATGGGCTTAACCTGGAC 61.377 60.000 0.00 0.00 39.10 4.02
836 852 0.034089 GCATGGGCTTAACCTGGACT 60.034 55.000 0.00 0.00 39.10 3.85
837 853 1.755179 CATGGGCTTAACCTGGACTG 58.245 55.000 0.00 0.00 39.10 3.51
838 854 0.625849 ATGGGCTTAACCTGGACTGG 59.374 55.000 0.00 0.00 39.10 4.00
839 855 0.474854 TGGGCTTAACCTGGACTGGA 60.475 55.000 0.00 0.00 39.10 3.86
840 856 0.035343 GGGCTTAACCTGGACTGGAC 60.035 60.000 0.00 0.00 39.10 4.02
841 857 0.035343 GGCTTAACCTGGACTGGACC 60.035 60.000 0.00 0.00 34.51 4.46
842 858 0.690762 GCTTAACCTGGACTGGACCA 59.309 55.000 0.00 0.00 38.33 4.02
843 859 1.610886 GCTTAACCTGGACTGGACCAC 60.611 57.143 0.00 0.00 35.91 4.16
844 860 1.003233 CTTAACCTGGACTGGACCACC 59.997 57.143 0.00 0.00 35.91 4.61
845 861 0.192566 TAACCTGGACTGGACCACCT 59.807 55.000 0.00 0.00 35.91 4.00
846 862 0.697854 AACCTGGACTGGACCACCTT 60.698 55.000 0.00 0.00 35.91 3.50
847 863 1.128188 ACCTGGACTGGACCACCTTC 61.128 60.000 0.00 0.00 35.91 3.46
848 864 1.127567 CCTGGACTGGACCACCTTCA 61.128 60.000 2.98 0.00 35.91 3.02
849 865 0.035458 CTGGACTGGACCACCTTCAC 59.965 60.000 2.98 0.00 35.91 3.18
850 866 0.692756 TGGACTGGACCACCTTCACA 60.693 55.000 2.98 0.00 34.77 3.58
851 867 0.472471 GGACTGGACCACCTTCACAA 59.528 55.000 0.00 0.00 37.04 3.33
852 868 1.133915 GGACTGGACCACCTTCACAAA 60.134 52.381 0.00 0.00 37.04 2.83
853 869 2.650322 GACTGGACCACCTTCACAAAA 58.350 47.619 0.00 0.00 37.04 2.44
854 870 3.020984 GACTGGACCACCTTCACAAAAA 58.979 45.455 0.00 0.00 37.04 1.94
855 871 3.023832 ACTGGACCACCTTCACAAAAAG 58.976 45.455 0.00 0.00 37.04 2.27
856 872 3.023832 CTGGACCACCTTCACAAAAAGT 58.976 45.455 0.00 0.00 37.04 2.66
857 873 4.204012 CTGGACCACCTTCACAAAAAGTA 58.796 43.478 0.00 0.00 37.04 2.24
858 874 4.204012 TGGACCACCTTCACAAAAAGTAG 58.796 43.478 0.00 0.00 37.04 2.57
877 893 9.574516 AAAAGTAGAGGAAAGCTCTATCAAAAA 57.425 29.630 0.00 0.00 36.06 1.94
1383 1466 3.441290 ACGGCCTCCTCGTCTTCG 61.441 66.667 0.00 0.00 35.87 3.79
1483 1572 1.227263 CCTTGGGGATGTACTCGCG 60.227 63.158 0.00 0.00 37.69 5.87
1861 2010 1.583495 TACACGAGCGAGGTCTGGTG 61.583 60.000 0.00 4.73 44.81 4.17
2297 2462 8.647226 GTTGTATGGAATTTATGCTTGTTTGAC 58.353 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.226720 CGTTGGAATATACAAGCCAAGTTCTAT 59.773 37.037 0.00 0.00 40.75 1.98
5 6 5.354234 CGTTGGAATATACAAGCCAAGTTCT 59.646 40.000 0.00 0.00 40.75 3.01
6 7 5.353123 TCGTTGGAATATACAAGCCAAGTTC 59.647 40.000 0.00 0.00 40.75 3.01
7 8 5.250200 TCGTTGGAATATACAAGCCAAGTT 58.750 37.500 0.00 0.00 40.75 2.66
8 9 4.839121 TCGTTGGAATATACAAGCCAAGT 58.161 39.130 0.00 0.00 40.75 3.16
9 10 5.277974 CCATCGTTGGAATATACAAGCCAAG 60.278 44.000 6.68 0.00 46.92 3.61
10 11 4.578516 CCATCGTTGGAATATACAAGCCAA 59.421 41.667 6.68 0.00 46.92 4.52
11 12 4.133820 CCATCGTTGGAATATACAAGCCA 58.866 43.478 6.68 0.00 46.92 4.75
12 13 3.502211 CCCATCGTTGGAATATACAAGCC 59.498 47.826 14.27 0.00 46.92 4.35
13 14 3.058224 GCCCATCGTTGGAATATACAAGC 60.058 47.826 14.27 1.81 46.92 4.01
14 15 4.389374 AGCCCATCGTTGGAATATACAAG 58.611 43.478 14.27 0.00 46.92 3.16
15 16 4.431416 AGCCCATCGTTGGAATATACAA 57.569 40.909 14.27 0.00 46.92 2.41
16 17 4.385825 GAAGCCCATCGTTGGAATATACA 58.614 43.478 14.27 0.00 46.92 2.29
17 18 3.751698 GGAAGCCCATCGTTGGAATATAC 59.248 47.826 14.27 1.00 46.92 1.47
18 19 3.650942 AGGAAGCCCATCGTTGGAATATA 59.349 43.478 14.27 0.00 46.92 0.86
19 20 2.443255 AGGAAGCCCATCGTTGGAATAT 59.557 45.455 14.27 0.00 46.92 1.28
20 21 1.843851 AGGAAGCCCATCGTTGGAATA 59.156 47.619 14.27 0.00 46.92 1.75
21 22 0.625849 AGGAAGCCCATCGTTGGAAT 59.374 50.000 14.27 0.00 46.92 3.01
22 23 0.035439 GAGGAAGCCCATCGTTGGAA 60.035 55.000 14.27 0.00 46.92 3.53
23 24 1.198094 TGAGGAAGCCCATCGTTGGA 61.198 55.000 14.27 0.00 46.92 3.53
24 25 0.322456 TTGAGGAAGCCCATCGTTGG 60.322 55.000 5.47 5.47 43.23 3.77
25 26 1.089920 CTTGAGGAAGCCCATCGTTG 58.910 55.000 0.00 0.00 33.88 4.10
26 27 0.693049 ACTTGAGGAAGCCCATCGTT 59.307 50.000 0.00 0.00 31.68 3.85
27 28 0.036010 CACTTGAGGAAGCCCATCGT 60.036 55.000 0.00 0.00 31.68 3.73
28 29 1.372087 GCACTTGAGGAAGCCCATCG 61.372 60.000 0.00 0.00 31.68 3.84
29 30 1.034292 GGCACTTGAGGAAGCCCATC 61.034 60.000 0.00 0.00 41.25 3.51
30 31 1.000396 GGCACTTGAGGAAGCCCAT 60.000 57.895 0.00 0.00 41.25 4.00
31 32 2.436109 GGCACTTGAGGAAGCCCA 59.564 61.111 0.00 0.00 41.25 5.36
33 34 0.107459 CTAGGGCACTTGAGGAAGCC 60.107 60.000 0.00 0.00 46.28 4.35
34 35 0.107459 CCTAGGGCACTTGAGGAAGC 60.107 60.000 0.00 0.00 31.68 3.86
35 36 1.208293 GACCTAGGGCACTTGAGGAAG 59.792 57.143 10.77 0.00 33.04 3.46
36 37 1.203313 AGACCTAGGGCACTTGAGGAA 60.203 52.381 19.45 0.00 33.04 3.36
37 38 0.413832 AGACCTAGGGCACTTGAGGA 59.586 55.000 19.45 0.00 33.04 3.71
38 39 1.208293 GAAGACCTAGGGCACTTGAGG 59.792 57.143 19.45 3.01 35.05 3.86
39 40 1.902508 TGAAGACCTAGGGCACTTGAG 59.097 52.381 19.45 0.00 0.00 3.02
40 41 2.024176 TGAAGACCTAGGGCACTTGA 57.976 50.000 19.45 8.88 0.00 3.02
41 42 2.237143 TCATGAAGACCTAGGGCACTTG 59.763 50.000 19.45 17.44 0.00 3.16
42 43 2.503356 CTCATGAAGACCTAGGGCACTT 59.497 50.000 19.45 16.58 0.00 3.16
43 44 2.114616 CTCATGAAGACCTAGGGCACT 58.885 52.381 19.45 2.41 0.00 4.40
44 45 1.474143 GCTCATGAAGACCTAGGGCAC 60.474 57.143 19.45 11.25 0.00 5.01
45 46 0.833287 GCTCATGAAGACCTAGGGCA 59.167 55.000 19.45 7.87 0.00 5.36
46 47 0.833287 TGCTCATGAAGACCTAGGGC 59.167 55.000 14.81 11.09 0.00 5.19
47 48 2.744494 GCTTGCTCATGAAGACCTAGGG 60.744 54.545 14.81 0.00 0.00 3.53
48 49 2.093288 TGCTTGCTCATGAAGACCTAGG 60.093 50.000 7.41 7.41 0.00 3.02
49 50 3.257469 TGCTTGCTCATGAAGACCTAG 57.743 47.619 0.00 0.00 0.00 3.02
50 51 3.008375 ACTTGCTTGCTCATGAAGACCTA 59.992 43.478 0.00 0.00 0.00 3.08
51 52 2.224719 ACTTGCTTGCTCATGAAGACCT 60.225 45.455 0.00 0.00 0.00 3.85
52 53 2.157738 ACTTGCTTGCTCATGAAGACC 58.842 47.619 0.00 0.00 0.00 3.85
53 54 3.562505 CAACTTGCTTGCTCATGAAGAC 58.437 45.455 0.00 0.00 0.00 3.01
54 55 2.555325 CCAACTTGCTTGCTCATGAAGA 59.445 45.455 0.00 0.00 0.00 2.87
55 56 2.555325 TCCAACTTGCTTGCTCATGAAG 59.445 45.455 0.00 0.00 0.00 3.02
56 57 2.585330 TCCAACTTGCTTGCTCATGAA 58.415 42.857 0.00 0.00 0.00 2.57
57 58 2.275134 TCCAACTTGCTTGCTCATGA 57.725 45.000 0.00 0.00 0.00 3.07
58 59 2.876091 CATCCAACTTGCTTGCTCATG 58.124 47.619 0.00 0.00 0.00 3.07
59 60 1.203994 GCATCCAACTTGCTTGCTCAT 59.796 47.619 6.83 0.00 37.14 2.90
60 61 0.599558 GCATCCAACTTGCTTGCTCA 59.400 50.000 6.83 0.00 37.14 4.26
61 62 0.599558 TGCATCCAACTTGCTTGCTC 59.400 50.000 12.63 0.00 40.77 4.26
62 63 0.316204 GTGCATCCAACTTGCTTGCT 59.684 50.000 12.63 0.00 40.77 3.91
63 64 0.032403 TGTGCATCCAACTTGCTTGC 59.968 50.000 0.00 7.05 40.77 4.01
64 65 1.603678 GGTGTGCATCCAACTTGCTTG 60.604 52.381 0.00 0.00 40.77 4.01
65 66 0.675633 GGTGTGCATCCAACTTGCTT 59.324 50.000 0.00 0.00 40.77 3.91
66 67 1.181098 GGGTGTGCATCCAACTTGCT 61.181 55.000 11.91 0.00 40.77 3.91
67 68 1.290009 GGGTGTGCATCCAACTTGC 59.710 57.895 11.91 0.00 40.55 4.01
68 69 0.314935 GTGGGTGTGCATCCAACTTG 59.685 55.000 5.65 0.00 44.47 3.16
69 70 0.185901 AGTGGGTGTGCATCCAACTT 59.814 50.000 13.15 0.00 44.47 2.66
70 71 0.185901 AAGTGGGTGTGCATCCAACT 59.814 50.000 13.15 13.15 44.47 3.16
71 72 1.812571 CTAAGTGGGTGTGCATCCAAC 59.187 52.381 5.65 9.55 44.47 3.77
72 73 1.423541 ACTAAGTGGGTGTGCATCCAA 59.576 47.619 5.65 0.00 44.47 3.53
73 74 1.064003 ACTAAGTGGGTGTGCATCCA 58.936 50.000 0.00 0.00 39.79 3.41
74 75 2.200373 AACTAAGTGGGTGTGCATCC 57.800 50.000 0.00 0.00 0.00 3.51
75 76 3.146066 TGAAACTAAGTGGGTGTGCATC 58.854 45.455 0.00 0.00 0.00 3.91
76 77 3.149196 CTGAAACTAAGTGGGTGTGCAT 58.851 45.455 0.00 0.00 0.00 3.96
77 78 2.092646 ACTGAAACTAAGTGGGTGTGCA 60.093 45.455 0.00 0.00 0.00 4.57
78 79 2.572290 ACTGAAACTAAGTGGGTGTGC 58.428 47.619 0.00 0.00 0.00 4.57
79 80 4.638421 TCAAACTGAAACTAAGTGGGTGTG 59.362 41.667 0.00 0.00 0.00 3.82
80 81 4.850680 TCAAACTGAAACTAAGTGGGTGT 58.149 39.130 0.00 0.00 0.00 4.16
81 82 4.261197 GCTCAAACTGAAACTAAGTGGGTG 60.261 45.833 0.00 0.00 0.00 4.61
82 83 3.883489 GCTCAAACTGAAACTAAGTGGGT 59.117 43.478 0.00 0.00 0.00 4.51
83 84 4.137543 AGCTCAAACTGAAACTAAGTGGG 58.862 43.478 0.00 0.00 0.00 4.61
84 85 5.278022 GGAAGCTCAAACTGAAACTAAGTGG 60.278 44.000 0.00 0.00 0.00 4.00
85 86 5.296780 TGGAAGCTCAAACTGAAACTAAGTG 59.703 40.000 0.00 0.00 0.00 3.16
86 87 5.437060 TGGAAGCTCAAACTGAAACTAAGT 58.563 37.500 0.00 0.00 0.00 2.24
87 88 6.566197 ATGGAAGCTCAAACTGAAACTAAG 57.434 37.500 0.00 0.00 0.00 2.18
88 89 6.995686 TGTATGGAAGCTCAAACTGAAACTAA 59.004 34.615 0.00 0.00 0.00 2.24
89 90 6.426937 GTGTATGGAAGCTCAAACTGAAACTA 59.573 38.462 0.00 0.00 0.00 2.24
90 91 5.239525 GTGTATGGAAGCTCAAACTGAAACT 59.760 40.000 0.00 0.00 0.00 2.66
91 92 5.239525 AGTGTATGGAAGCTCAAACTGAAAC 59.760 40.000 0.00 0.00 0.00 2.78
92 93 5.376625 AGTGTATGGAAGCTCAAACTGAAA 58.623 37.500 0.00 0.00 0.00 2.69
93 94 4.973168 AGTGTATGGAAGCTCAAACTGAA 58.027 39.130 0.00 0.00 0.00 3.02
94 95 4.623932 AGTGTATGGAAGCTCAAACTGA 57.376 40.909 0.00 0.00 0.00 3.41
95 96 4.516698 ACAAGTGTATGGAAGCTCAAACTG 59.483 41.667 0.00 0.00 0.00 3.16
96 97 4.718961 ACAAGTGTATGGAAGCTCAAACT 58.281 39.130 0.00 0.00 0.00 2.66
97 98 5.390991 GCTACAAGTGTATGGAAGCTCAAAC 60.391 44.000 0.00 0.00 33.28 2.93
98 99 4.695455 GCTACAAGTGTATGGAAGCTCAAA 59.305 41.667 0.00 0.00 33.28 2.69
99 100 4.020218 AGCTACAAGTGTATGGAAGCTCAA 60.020 41.667 0.78 0.00 38.58 3.02
100 101 3.515502 AGCTACAAGTGTATGGAAGCTCA 59.484 43.478 0.78 0.00 38.58 4.26
101 102 4.116238 GAGCTACAAGTGTATGGAAGCTC 58.884 47.826 14.26 14.26 45.18 4.09
102 103 3.772025 AGAGCTACAAGTGTATGGAAGCT 59.228 43.478 5.55 5.55 42.72 3.74
103 104 4.130286 AGAGCTACAAGTGTATGGAAGC 57.870 45.455 0.00 0.00 35.10 3.86
104 105 6.269315 CACTAGAGCTACAAGTGTATGGAAG 58.731 44.000 12.30 0.00 36.66 3.46
105 106 5.394224 GCACTAGAGCTACAAGTGTATGGAA 60.394 44.000 18.58 0.00 42.10 3.53
106 107 4.098044 GCACTAGAGCTACAAGTGTATGGA 59.902 45.833 18.58 0.00 42.10 3.41
107 108 4.142160 TGCACTAGAGCTACAAGTGTATGG 60.142 45.833 18.58 0.60 42.10 2.74
108 109 4.998788 TGCACTAGAGCTACAAGTGTATG 58.001 43.478 18.58 0.93 42.10 2.39
109 110 5.596361 AGATGCACTAGAGCTACAAGTGTAT 59.404 40.000 19.29 19.29 45.40 2.29
110 111 4.950475 AGATGCACTAGAGCTACAAGTGTA 59.050 41.667 18.58 16.00 42.10 2.90
111 112 3.766591 AGATGCACTAGAGCTACAAGTGT 59.233 43.478 18.58 5.37 42.10 3.55
112 113 4.111198 CAGATGCACTAGAGCTACAAGTG 58.889 47.826 13.47 15.02 42.80 3.16
113 114 3.766591 ACAGATGCACTAGAGCTACAAGT 59.233 43.478 13.47 7.33 34.99 3.16
114 115 4.383850 ACAGATGCACTAGAGCTACAAG 57.616 45.455 13.47 6.82 34.99 3.16
115 116 4.498241 CAACAGATGCACTAGAGCTACAA 58.502 43.478 13.47 0.00 34.99 2.41
116 117 3.118992 CCAACAGATGCACTAGAGCTACA 60.119 47.826 13.47 0.00 34.99 2.74
117 118 3.131223 TCCAACAGATGCACTAGAGCTAC 59.869 47.826 13.47 7.27 34.99 3.58
118 119 3.365472 TCCAACAGATGCACTAGAGCTA 58.635 45.455 13.47 0.65 34.99 3.32
119 120 2.182827 TCCAACAGATGCACTAGAGCT 58.817 47.619 13.47 0.00 34.99 4.09
120 121 2.680312 TCCAACAGATGCACTAGAGC 57.320 50.000 5.07 5.07 0.00 4.09
129 130 5.761184 GCACAAGCACCATCCAACAGATG 62.761 52.174 0.00 0.00 45.44 2.90
130 131 2.165167 CACAAGCACCATCCAACAGAT 58.835 47.619 0.00 0.00 34.66 2.90
131 132 1.608055 CACAAGCACCATCCAACAGA 58.392 50.000 0.00 0.00 0.00 3.41
132 133 0.038892 GCACAAGCACCATCCAACAG 60.039 55.000 0.00 0.00 41.58 3.16
133 134 2.040330 GCACAAGCACCATCCAACA 58.960 52.632 0.00 0.00 41.58 3.33
134 135 4.972591 GCACAAGCACCATCCAAC 57.027 55.556 0.00 0.00 41.58 3.77
145 146 0.322008 GAGGAGGAGGGTTGCACAAG 60.322 60.000 0.00 0.00 0.00 3.16
153 154 2.695970 CGAGGAGGAGGAGGAGGGT 61.696 68.421 0.00 0.00 0.00 4.34
159 160 1.848652 TTTACCACGAGGAGGAGGAG 58.151 55.000 5.68 0.00 38.69 3.69
166 167 1.066430 GTGCTGGATTTACCACGAGGA 60.066 52.381 5.68 0.00 44.64 3.71
170 171 3.531538 ACATAGTGCTGGATTTACCACG 58.468 45.455 0.00 0.00 44.64 4.94
182 183 0.539051 GTGCTCCCTGACATAGTGCT 59.461 55.000 0.00 0.00 0.00 4.40
183 184 0.462759 GGTGCTCCCTGACATAGTGC 60.463 60.000 0.00 0.00 0.00 4.40
188 189 0.250901 GTGTTGGTGCTCCCTGACAT 60.251 55.000 1.59 0.00 34.17 3.06
190 191 1.961277 CGTGTTGGTGCTCCCTGAC 60.961 63.158 1.59 0.00 0.00 3.51
208 209 2.617308 CAGAGCAACATGATGGGATGTC 59.383 50.000 0.00 0.00 35.43 3.06
228 229 1.758514 GGGAGATCGGAGGAGCACA 60.759 63.158 0.00 0.00 0.00 4.57
231 232 0.761802 AATTGGGAGATCGGAGGAGC 59.238 55.000 0.00 0.00 0.00 4.70
235 236 2.843701 CTGGAAATTGGGAGATCGGAG 58.156 52.381 0.00 0.00 0.00 4.63
237 238 1.312815 GCTGGAAATTGGGAGATCGG 58.687 55.000 0.00 0.00 0.00 4.18
249 250 2.689073 CAGAGAGGGAGGCTGGAAA 58.311 57.895 0.00 0.00 0.00 3.13
259 260 2.224475 CCAATGACATAGCCAGAGAGGG 60.224 54.545 0.00 0.00 38.09 4.30
276 277 3.848377 TGGAGGAGCATCATATAGCCAAT 59.152 43.478 0.00 0.00 36.25 3.16
285 286 0.400975 GGCTGATGGAGGAGCATCAT 59.599 55.000 0.00 0.00 37.23 2.45
286 287 0.693430 AGGCTGATGGAGGAGCATCA 60.693 55.000 0.00 0.00 36.90 3.07
354 355 0.543749 ATTTGGCTTCTCCTCCTCCG 59.456 55.000 0.00 0.00 35.26 4.63
355 356 1.409381 CCATTTGGCTTCTCCTCCTCC 60.409 57.143 0.00 0.00 35.26 4.30
402 403 2.125952 GCTGCGATGGCCCAAAAC 60.126 61.111 0.00 0.00 38.85 2.43
414 415 4.842091 GAAGCCATTGCCGCTGCG 62.842 66.667 16.34 16.34 41.78 5.18
476 477 2.924290 CCGTTCCTCGCAAAAACAAAAA 59.076 40.909 0.00 0.00 38.35 1.94
481 494 1.284715 CCCCGTTCCTCGCAAAAAC 59.715 57.895 0.00 0.00 38.35 2.43
492 505 1.227853 AACACACTGAGCCCCGTTC 60.228 57.895 0.00 0.00 0.00 3.95
497 510 1.823470 TGCACAACACACTGAGCCC 60.823 57.895 0.00 0.00 32.58 5.19
525 538 2.499197 ACACACGAATGTATGGCAACA 58.501 42.857 0.00 0.00 46.05 3.33
536 549 3.799366 TCCTAACACACAACACACGAAT 58.201 40.909 0.00 0.00 0.00 3.34
547 560 6.092807 GTCTCCAAGAAATGATCCTAACACAC 59.907 42.308 0.00 0.00 0.00 3.82
555 568 9.213799 GATGTAATAGTCTCCAAGAAATGATCC 57.786 37.037 0.00 0.00 0.00 3.36
572 585 4.920340 CAGCGCTGGTTAGAGATGTAATAG 59.080 45.833 29.88 0.00 35.73 1.73
576 589 1.202417 GCAGCGCTGGTTAGAGATGTA 60.202 52.381 36.47 0.00 41.37 2.29
577 590 0.460987 GCAGCGCTGGTTAGAGATGT 60.461 55.000 36.47 0.00 41.37 3.06
620 636 3.517901 ACCCGACACATAATTGGAAGAGA 59.482 43.478 0.00 0.00 0.00 3.10
636 652 0.536460 TTTCCTTCAGGCAACCCGAC 60.536 55.000 0.00 0.00 35.76 4.79
639 655 1.068588 GTGTTTTCCTTCAGGCAACCC 59.931 52.381 5.66 0.00 34.44 4.11
640 656 1.754226 TGTGTTTTCCTTCAGGCAACC 59.246 47.619 5.66 0.00 34.44 3.77
645 661 3.005791 GGGTCATTGTGTTTTCCTTCAGG 59.994 47.826 0.00 0.00 0.00 3.86
657 673 2.036217 ACACAAAGCATGGGTCATTGTG 59.964 45.455 14.38 14.38 44.33 3.33
659 675 3.255395 TGTACACAAAGCATGGGTCATTG 59.745 43.478 0.16 0.00 44.33 2.82
661 677 3.153369 TGTACACAAAGCATGGGTCAT 57.847 42.857 0.16 0.00 44.33 3.06
674 690 7.012799 TGTTATGCTGTTTTCTGAATGTACACA 59.987 33.333 0.00 0.00 0.00 3.72
677 693 7.584987 ACTGTTATGCTGTTTTCTGAATGTAC 58.415 34.615 0.00 0.00 0.00 2.90
750 766 1.815003 CACTGGATCTGGAAGTTTGCC 59.185 52.381 0.00 0.00 33.76 4.52
796 812 5.641709 TGCGTGTTTCATGTTTGAGTTTTA 58.358 33.333 0.00 0.00 32.27 1.52
801 817 2.981805 CCATGCGTGTTTCATGTTTGAG 59.018 45.455 4.96 0.00 39.60 3.02
802 818 2.288091 CCCATGCGTGTTTCATGTTTGA 60.288 45.455 4.96 0.00 39.60 2.69
813 829 0.960364 CAGGTTAAGCCCATGCGTGT 60.960 55.000 4.96 0.00 44.33 4.49
814 830 1.656818 CCAGGTTAAGCCCATGCGTG 61.657 60.000 0.00 0.00 44.33 5.34
815 831 1.378514 CCAGGTTAAGCCCATGCGT 60.379 57.895 0.00 0.00 44.33 5.24
816 832 1.077787 TCCAGGTTAAGCCCATGCG 60.078 57.895 0.00 0.00 44.33 4.73
817 833 0.034089 AGTCCAGGTTAAGCCCATGC 60.034 55.000 0.00 0.00 38.26 4.06
818 834 1.683011 CCAGTCCAGGTTAAGCCCATG 60.683 57.143 0.00 0.00 38.26 3.66
819 835 0.625849 CCAGTCCAGGTTAAGCCCAT 59.374 55.000 0.00 0.00 38.26 4.00
820 836 0.474854 TCCAGTCCAGGTTAAGCCCA 60.475 55.000 0.00 0.00 38.26 5.36
821 837 0.035343 GTCCAGTCCAGGTTAAGCCC 60.035 60.000 0.00 0.00 38.26 5.19
822 838 0.035343 GGTCCAGTCCAGGTTAAGCC 60.035 60.000 0.00 0.00 37.58 4.35
823 839 0.690762 TGGTCCAGTCCAGGTTAAGC 59.309 55.000 0.00 0.00 33.19 3.09
824 840 1.003233 GGTGGTCCAGTCCAGGTTAAG 59.997 57.143 0.00 0.00 38.23 1.85
825 841 1.061546 GGTGGTCCAGTCCAGGTTAA 58.938 55.000 0.00 0.00 38.23 2.01
826 842 0.192566 AGGTGGTCCAGTCCAGGTTA 59.807 55.000 0.00 0.00 38.23 2.85
827 843 0.697854 AAGGTGGTCCAGTCCAGGTT 60.698 55.000 0.00 0.00 38.23 3.50
828 844 1.073706 AAGGTGGTCCAGTCCAGGT 60.074 57.895 0.00 0.00 38.23 4.00
829 845 1.127567 TGAAGGTGGTCCAGTCCAGG 61.128 60.000 0.00 0.00 38.23 4.45
830 846 0.035458 GTGAAGGTGGTCCAGTCCAG 59.965 60.000 0.00 0.00 38.23 3.86
831 847 0.692756 TGTGAAGGTGGTCCAGTCCA 60.693 55.000 0.00 0.00 35.89 4.02
832 848 0.472471 TTGTGAAGGTGGTCCAGTCC 59.528 55.000 0.00 0.00 35.89 3.85
833 849 2.341846 TTTGTGAAGGTGGTCCAGTC 57.658 50.000 0.00 0.00 35.89 3.51
834 850 2.818751 TTTTGTGAAGGTGGTCCAGT 57.181 45.000 0.00 0.00 35.89 4.00
835 851 3.023832 ACTTTTTGTGAAGGTGGTCCAG 58.976 45.455 0.00 0.00 35.89 3.86
836 852 3.094484 ACTTTTTGTGAAGGTGGTCCA 57.906 42.857 0.00 0.00 35.89 4.02
837 853 4.457466 TCTACTTTTTGTGAAGGTGGTCC 58.543 43.478 0.00 0.00 0.00 4.46
838 854 4.515567 CCTCTACTTTTTGTGAAGGTGGTC 59.484 45.833 0.00 0.00 31.19 4.02
839 855 4.165372 TCCTCTACTTTTTGTGAAGGTGGT 59.835 41.667 0.00 0.00 34.91 4.16
840 856 4.714632 TCCTCTACTTTTTGTGAAGGTGG 58.285 43.478 0.00 0.00 34.91 4.61
841 857 6.693315 TTTCCTCTACTTTTTGTGAAGGTG 57.307 37.500 0.00 0.00 34.91 4.00
842 858 5.299531 GCTTTCCTCTACTTTTTGTGAAGGT 59.700 40.000 0.00 0.00 34.91 3.50
843 859 5.532779 AGCTTTCCTCTACTTTTTGTGAAGG 59.467 40.000 0.00 0.00 34.75 3.46
844 860 6.625873 AGCTTTCCTCTACTTTTTGTGAAG 57.374 37.500 0.00 0.00 0.00 3.02
845 861 6.619801 GAGCTTTCCTCTACTTTTTGTGAA 57.380 37.500 0.00 0.00 37.60 3.18
877 893 2.160205 GCTTAAACGGGCCTCTTTCTT 58.840 47.619 0.84 0.00 0.00 2.52
880 896 1.583495 GCGCTTAAACGGGCCTCTTT 61.583 55.000 0.84 2.87 36.92 2.52
881 897 2.038837 GCGCTTAAACGGGCCTCTT 61.039 57.895 0.84 0.00 36.92 2.85
883 899 1.152383 CTAGCGCTTAAACGGGCCTC 61.152 60.000 18.68 0.00 43.11 4.70
884 900 1.153429 CTAGCGCTTAAACGGGCCT 60.153 57.895 18.68 0.00 43.11 5.19
885 901 0.179103 TACTAGCGCTTAAACGGGCC 60.179 55.000 18.68 0.00 43.11 5.80
1232 1273 3.546417 CGATGTTGTAGACGTAGAGGAGC 60.546 52.174 0.00 0.00 0.00 4.70
1627 1734 2.719739 ACAGGAATGACAGGCTGAATG 58.280 47.619 23.66 10.49 0.00 2.67
1640 1759 2.046314 CCACCGCGGAACAGGAAT 60.046 61.111 35.90 2.60 36.56 3.01
1861 2010 4.290155 CAACTCAATGTGGTACTTGTTGC 58.710 43.478 0.00 0.00 0.00 4.17
2297 2462 6.337356 ACAAAATGACTTGGTAGTTTTGGTG 58.663 36.000 16.59 0.00 35.43 4.17
3360 12480 5.262804 AGATTATACTCCCTACGTCCCATC 58.737 45.833 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.