Multiple sequence alignment - TraesCS3B01G425200

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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 TraesCS3B01G425200 chr3B 100.000 3014 0 0 1 3014 663073228 663070215 0.000000e+00 5566.0
1 TraesCS3B01G425200 chr3B 88.325 788 57 16 1307 2063 663061998 663061215 0.000000e+00 913.0
2 TraesCS3B01G425200 chr3B 83.236 853 80 29 1278 2074 412596273 412597118 0.000000e+00 725.0
3 TraesCS3B01G425200 chr3B 95.808 334 12 2 6 338 816786202 816785870 3.420000e-149 538.0
4 TraesCS3B01G425200 chr3B 96.584 322 10 1 1 322 737756675 737756995 1.590000e-147 532.0
5 TraesCS3B01G425200 chr3B 89.333 300 16 9 968 1252 412595871 412596169 2.210000e-96 363.0
6 TraesCS3B01G425200 chr3B 95.767 189 8 0 1058 1246 663062316 663062128 3.770000e-79 305.0
7 TraesCS3B01G425200 chr3B 82.105 285 25 16 495 768 663063246 663062977 1.410000e-53 220.0
8 TraesCS3B01G425200 chr3D 91.051 1855 95 22 335 2144 501330916 501332744 0.000000e+00 2440.0
9 TraesCS3B01G425200 chr3D 87.966 831 65 8 1307 2105 501413643 501414470 0.000000e+00 948.0
10 TraesCS3B01G425200 chr3D 84.828 903 90 21 2140 3008 501332818 501333707 0.000000e+00 865.0
11 TraesCS3B01G425200 chr3D 82.892 906 118 21 2141 3014 418368467 418369367 0.000000e+00 780.0
12 TraesCS3B01G425200 chr3D 83.847 811 59 36 495 1244 501412712 501413511 0.000000e+00 706.0
13 TraesCS3B01G425200 chr3D 81.050 876 87 31 1255 2074 308985502 308984650 2.550000e-175 625.0
14 TraesCS3B01G425200 chr3D 83.521 443 31 19 829 1252 308986004 308985585 2.840000e-100 375.0
15 TraesCS3B01G425200 chr3A 91.638 1734 90 30 443 2138 640879044 640880760 0.000000e+00 2348.0
16 TraesCS3B01G425200 chr3A 89.080 815 51 11 1307 2083 641012498 641013312 0.000000e+00 977.0
17 TraesCS3B01G425200 chr3A 88.957 815 52 11 1307 2083 640952204 640953018 0.000000e+00 972.0
18 TraesCS3B01G425200 chr3A 84.181 904 100 18 2141 3014 640891508 640892398 0.000000e+00 837.0
19 TraesCS3B01G425200 chr3A 83.642 917 115 10 2129 3014 432861488 432862400 0.000000e+00 830.0
20 TraesCS3B01G425200 chr3A 83.333 876 79 37 1255 2074 428569928 428569064 0.000000e+00 747.0
21 TraesCS3B01G425200 chr3A 81.917 918 132 19 2129 3014 26125786 26126701 0.000000e+00 745.0
22 TraesCS3B01G425200 chr3A 95.865 266 10 1 981 1246 640951828 640952092 2.150000e-116 429.0
23 TraesCS3B01G425200 chr3A 95.865 266 10 1 981 1246 641012122 641012386 2.150000e-116 429.0
24 TraesCS3B01G425200 chr3A 79.518 664 70 40 365 979 640951142 640951788 2.160000e-111 412.0
25 TraesCS3B01G425200 chr3A 79.518 664 70 40 365 979 641011436 641012082 2.160000e-111 412.0
26 TraesCS3B01G425200 chr3A 92.989 271 15 4 65 333 286834123 286834391 2.820000e-105 392.0
27 TraesCS3B01G425200 chr3A 83.784 444 29 21 829 1252 428570445 428570025 6.100000e-102 381.0
28 TraesCS3B01G425200 chr3A 100.000 46 0 0 16 61 32969845 32969800 5.350000e-13 86.1
29 TraesCS3B01G425200 chr3A 100.000 46 0 0 16 61 66274222 66274267 5.350000e-13 86.1
30 TraesCS3B01G425200 chr6D 84.048 909 103 19 2141 3014 471066269 471065368 0.000000e+00 837.0
31 TraesCS3B01G425200 chr6D 78.930 916 138 27 2130 3014 424630196 424631087 3.370000e-159 571.0
32 TraesCS3B01G425200 chr6D 90.286 175 17 0 159 333 245268723 245268897 2.340000e-56 230.0
33 TraesCS3B01G425200 chr5B 83.739 904 115 12 2141 3014 423923796 423922895 0.000000e+00 826.0
34 TraesCS3B01G425200 chr5B 92.222 270 18 2 65 333 483955102 483954835 2.190000e-101 379.0
35 TraesCS3B01G425200 chr5B 96.000 50 2 0 1 50 483955325 483955276 6.930000e-12 82.4
36 TraesCS3B01G425200 chr4D 83.572 907 111 15 2141 3014 49166155 49165254 0.000000e+00 815.0
37 TraesCS3B01G425200 chr4D 82.552 917 127 13 2129 3014 76565088 76566002 0.000000e+00 776.0
38 TraesCS3B01G425200 chr4D 91.882 271 19 3 65 333 482763134 482762865 2.840000e-100 375.0
39 TraesCS3B01G425200 chr7D 83.187 910 112 23 2141 3014 424089810 424088906 0.000000e+00 795.0
40 TraesCS3B01G425200 chr7D 81.153 902 124 21 2141 3006 11452773 11451882 0.000000e+00 682.0
41 TraesCS3B01G425200 chr6B 82.552 917 126 14 2129 3014 550790966 550790053 0.000000e+00 776.0
42 TraesCS3B01G425200 chr6B 82.594 902 118 15 2141 3007 17095448 17094551 0.000000e+00 760.0
43 TraesCS3B01G425200 chr6B 91.882 271 20 2 65 333 142798562 142798832 7.890000e-101 377.0
44 TraesCS3B01G425200 chr7B 82.585 913 124 11 2129 3009 586006480 586005571 0.000000e+00 773.0
45 TraesCS3B01G425200 chr7B 92.780 277 17 3 65 338 622525119 622525395 6.050000e-107 398.0
46 TraesCS3B01G425200 chr7A 81.878 916 134 19 2129 3014 616242098 616241185 0.000000e+00 743.0
47 TraesCS3B01G425200 chr7A 81.828 919 129 13 2129 3014 644466044 644466957 0.000000e+00 737.0
48 TraesCS3B01G425200 chr7A 81.481 918 135 17 2129 3014 642532921 642533835 0.000000e+00 721.0
49 TraesCS3B01G425200 chr7A 94.074 270 15 1 65 333 224179140 224179409 2.800000e-110 409.0
50 TraesCS3B01G425200 chr7A 98.000 50 1 0 1 50 224178917 224178966 1.490000e-13 87.9
51 TraesCS3B01G425200 chr7A 100.000 46 0 0 16 61 474521909 474521864 5.350000e-13 86.1
52 TraesCS3B01G425200 chr7A 100.000 46 0 0 16 61 535518241 535518196 5.350000e-13 86.1
53 TraesCS3B01G425200 chr5D 80.723 913 127 25 2141 3008 106932422 106933330 0.000000e+00 665.0
54 TraesCS3B01G425200 chr5D 90.909 275 22 2 62 333 559053814 559054088 1.710000e-97 366.0
55 TraesCS3B01G425200 chr5D 89.888 178 18 0 159 336 559053180 559053003 2.340000e-56 230.0
56 TraesCS3B01G425200 chr1B 94.848 330 16 1 13 341 5691464 5691135 5.760000e-142 514.0
57 TraesCS3B01G425200 chrUn 82.421 603 76 7 2352 2926 265471160 265471760 1.610000e-137 499.0
58 TraesCS3B01G425200 chr6A 76.072 886 166 28 2141 3007 24277422 24278280 1.290000e-113 420.0
59 TraesCS3B01G425200 chr6A 93.333 270 17 1 65 333 504391027 504390758 6.050000e-107 398.0
60 TraesCS3B01G425200 chr6A 92.058 277 20 2 61 335 81128792 81129068 3.640000e-104 388.0
61 TraesCS3B01G425200 chr6A 91.892 185 10 4 159 340 89292927 89292745 1.390000e-63 254.0
62 TraesCS3B01G425200 chr6A 100.000 46 0 0 16 61 89293535 89293490 5.350000e-13 86.1
63 TraesCS3B01G425200 chr6A 100.000 46 0 0 16 61 132610874 132610829 5.350000e-13 86.1
64 TraesCS3B01G425200 chr5A 92.580 283 19 2 65 345 602443824 602443542 3.620000e-109 405.0
65 TraesCS3B01G425200 chr5A 94.000 50 3 0 1 50 602444047 602443998 3.220000e-10 76.8
66 TraesCS3B01G425200 chr2A 93.455 275 15 3 65 337 258804005 258803732 3.620000e-109 405.0
67 TraesCS3B01G425200 chr2A 100.000 46 0 0 16 61 681242502 681242457 5.350000e-13 86.1
68 TraesCS3B01G425200 chr1A 92.419 277 18 3 65 339 455942301 455942576 2.820000e-105 392.0
69 TraesCS3B01G425200 chr1A 92.593 270 19 1 65 333 91111467 91111736 1.310000e-103 387.0
70 TraesCS3B01G425200 chr1A 91.912 272 20 2 65 334 456038913 456039184 2.190000e-101 379.0
71 TraesCS3B01G425200 chr1A 90.710 183 17 0 159 341 455941661 455941479 8.350000e-61 244.0
72 TraesCS3B01G425200 chr1A 90.710 183 17 0 159 341 456038273 456038091 8.350000e-61 244.0
73 TraesCS3B01G425200 chr4A 92.308 273 20 1 65 336 173431363 173431635 1.310000e-103 387.0
74 TraesCS3B01G425200 chr1D 91.941 273 19 2 65 334 10731079 10730807 2.190000e-101 379.0
75 TraesCS3B01G425200 chr4B 90.775 271 22 3 67 335 91725658 91725927 2.860000e-95 359.0


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 TraesCS3B01G425200 chr3B 663070215 663073228 3013 True 5566.000000 5566 100.000000 1 3014 1 chr3B.!!$R1 3013
1 TraesCS3B01G425200 chr3B 412595871 412597118 1247 False 544.000000 725 86.284500 968 2074 2 chr3B.!!$F2 1106
2 TraesCS3B01G425200 chr3B 663061215 663063246 2031 True 479.333333 913 88.732333 495 2063 3 chr3B.!!$R3 1568
3 TraesCS3B01G425200 chr3D 501330916 501333707 2791 False 1652.500000 2440 87.939500 335 3008 2 chr3D.!!$F2 2673
4 TraesCS3B01G425200 chr3D 501412712 501414470 1758 False 827.000000 948 85.906500 495 2105 2 chr3D.!!$F3 1610
5 TraesCS3B01G425200 chr3D 418368467 418369367 900 False 780.000000 780 82.892000 2141 3014 1 chr3D.!!$F1 873
6 TraesCS3B01G425200 chr3D 308984650 308986004 1354 True 500.000000 625 82.285500 829 2074 2 chr3D.!!$R1 1245
7 TraesCS3B01G425200 chr3A 640879044 640880760 1716 False 2348.000000 2348 91.638000 443 2138 1 chr3A.!!$F5 1695
8 TraesCS3B01G425200 chr3A 640891508 640892398 890 False 837.000000 837 84.181000 2141 3014 1 chr3A.!!$F6 873
9 TraesCS3B01G425200 chr3A 432861488 432862400 912 False 830.000000 830 83.642000 2129 3014 1 chr3A.!!$F4 885
10 TraesCS3B01G425200 chr3A 26125786 26126701 915 False 745.000000 745 81.917000 2129 3014 1 chr3A.!!$F1 885
11 TraesCS3B01G425200 chr3A 641011436 641013312 1876 False 606.000000 977 88.154333 365 2083 3 chr3A.!!$F8 1718
12 TraesCS3B01G425200 chr3A 640951142 640953018 1876 False 604.333333 972 88.113333 365 2083 3 chr3A.!!$F7 1718
13 TraesCS3B01G425200 chr3A 428569064 428570445 1381 True 564.000000 747 83.558500 829 2074 2 chr3A.!!$R2 1245
14 TraesCS3B01G425200 chr6D 471065368 471066269 901 True 837.000000 837 84.048000 2141 3014 1 chr6D.!!$R1 873
15 TraesCS3B01G425200 chr6D 424630196 424631087 891 False 571.000000 571 78.930000 2130 3014 1 chr6D.!!$F2 884
16 TraesCS3B01G425200 chr5B 423922895 423923796 901 True 826.000000 826 83.739000 2141 3014 1 chr5B.!!$R1 873
17 TraesCS3B01G425200 chr4D 49165254 49166155 901 True 815.000000 815 83.572000 2141 3014 1 chr4D.!!$R1 873
18 TraesCS3B01G425200 chr4D 76565088 76566002 914 False 776.000000 776 82.552000 2129 3014 1 chr4D.!!$F1 885
19 TraesCS3B01G425200 chr7D 424088906 424089810 904 True 795.000000 795 83.187000 2141 3014 1 chr7D.!!$R2 873
20 TraesCS3B01G425200 chr7D 11451882 11452773 891 True 682.000000 682 81.153000 2141 3006 1 chr7D.!!$R1 865
21 TraesCS3B01G425200 chr6B 550790053 550790966 913 True 776.000000 776 82.552000 2129 3014 1 chr6B.!!$R2 885
22 TraesCS3B01G425200 chr6B 17094551 17095448 897 True 760.000000 760 82.594000 2141 3007 1 chr6B.!!$R1 866
23 TraesCS3B01G425200 chr7B 586005571 586006480 909 True 773.000000 773 82.585000 2129 3009 1 chr7B.!!$R1 880
24 TraesCS3B01G425200 chr7A 616241185 616242098 913 True 743.000000 743 81.878000 2129 3014 1 chr7A.!!$R3 885
25 TraesCS3B01G425200 chr7A 644466044 644466957 913 False 737.000000 737 81.828000 2129 3014 1 chr7A.!!$F2 885
26 TraesCS3B01G425200 chr7A 642532921 642533835 914 False 721.000000 721 81.481000 2129 3014 1 chr7A.!!$F1 885
27 TraesCS3B01G425200 chr5D 106932422 106933330 908 False 665.000000 665 80.723000 2141 3008 1 chr5D.!!$F1 867
28 TraesCS3B01G425200 chrUn 265471160 265471760 600 False 499.000000 499 82.421000 2352 2926 1 chrUn.!!$F1 574
29 TraesCS3B01G425200 chr6A 24277422 24278280 858 False 420.000000 420 76.072000 2141 3007 1 chr6A.!!$F1 866
30 TraesCS3B01G425200 chr5A 602443542 602444047 505 True 240.900000 405 93.290000 1 345 2 chr5A.!!$R1 344

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
56 57 0.179073 CGAAGGCCTCGGTCATGATT 60.179 55.0 5.23 0.0 44.2 2.57 F
1338 2154 0.615331 ATGAGATCGTTGTGCAGGGT 59.385 50.0 0.00 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 2311 0.105224 CCGATATTGGCCACCACGTA 59.895 55.000 3.88 0.0 30.78 3.57 R
2378 3348 1.152355 CCCTTGGGCTTGTGGGAAA 60.152 57.895 0.00 0.0 42.11 3.13 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
35 36 4.009675 GAGGTCAATTAGCACATGAACCA 58.990 43.478 0.00 0.00 31.03 3.67
37 38 4.641989 AGGTCAATTAGCACATGAACCATC 59.358 41.667 0.00 0.00 31.03 3.51
44 45 0.734889 CACATGAACCATCGAAGGCC 59.265 55.000 6.60 0.00 0.00 5.19
45 46 0.620556 ACATGAACCATCGAAGGCCT 59.379 50.000 6.60 0.00 0.00 5.19
46 47 1.303309 CATGAACCATCGAAGGCCTC 58.697 55.000 5.23 4.55 0.00 4.70
54 55 2.892640 CGAAGGCCTCGGTCATGA 59.107 61.111 5.23 0.00 44.20 3.07
55 56 1.443407 CGAAGGCCTCGGTCATGAT 59.557 57.895 5.23 0.00 44.20 2.45
56 57 0.179073 CGAAGGCCTCGGTCATGATT 60.179 55.000 5.23 0.00 44.20 2.57
57 58 1.743772 CGAAGGCCTCGGTCATGATTT 60.744 52.381 5.23 0.00 44.20 2.17
58 59 1.943340 GAAGGCCTCGGTCATGATTTC 59.057 52.381 5.23 0.00 0.00 2.17
59 60 1.207791 AGGCCTCGGTCATGATTTCT 58.792 50.000 0.00 0.00 0.00 2.52
60 61 1.561542 AGGCCTCGGTCATGATTTCTT 59.438 47.619 0.00 0.00 0.00 2.52
61 62 2.771943 AGGCCTCGGTCATGATTTCTTA 59.228 45.455 0.00 0.00 0.00 2.10
62 63 3.134458 GGCCTCGGTCATGATTTCTTAG 58.866 50.000 0.00 0.00 0.00 2.18
63 64 2.545946 GCCTCGGTCATGATTTCTTAGC 59.454 50.000 0.00 0.00 0.00 3.09
64 65 3.797039 CCTCGGTCATGATTTCTTAGCA 58.203 45.455 0.00 0.00 0.00 3.49
65 66 3.557595 CCTCGGTCATGATTTCTTAGCAC 59.442 47.826 0.00 0.00 0.00 4.40
66 67 4.183865 CTCGGTCATGATTTCTTAGCACA 58.816 43.478 0.00 0.00 0.00 4.57
67 68 4.183865 TCGGTCATGATTTCTTAGCACAG 58.816 43.478 0.00 0.00 0.00 3.66
68 69 3.935203 CGGTCATGATTTCTTAGCACAGT 59.065 43.478 0.00 0.00 0.00 3.55
69 70 5.105513 TCGGTCATGATTTCTTAGCACAGTA 60.106 40.000 0.00 0.00 0.00 2.74
70 71 5.233050 CGGTCATGATTTCTTAGCACAGTAG 59.767 44.000 0.00 0.00 0.00 2.57
71 72 6.109359 GGTCATGATTTCTTAGCACAGTAGT 58.891 40.000 0.00 0.00 0.00 2.73
72 73 7.265673 GGTCATGATTTCTTAGCACAGTAGTA 58.734 38.462 0.00 0.00 0.00 1.82
73 74 7.764443 GGTCATGATTTCTTAGCACAGTAGTAA 59.236 37.037 0.00 0.00 0.00 2.24
74 75 9.151471 GTCATGATTTCTTAGCACAGTAGTAAA 57.849 33.333 0.00 0.00 0.00 2.01
75 76 9.890629 TCATGATTTCTTAGCACAGTAGTAAAT 57.109 29.630 0.00 0.00 0.00 1.40
78 79 9.719355 TGATTTCTTAGCACAGTAGTAAATTGA 57.281 29.630 0.00 0.00 0.00 2.57
79 80 9.974750 GATTTCTTAGCACAGTAGTAAATTGAC 57.025 33.333 0.00 0.00 0.00 3.18
80 81 9.726438 ATTTCTTAGCACAGTAGTAAATTGACT 57.274 29.630 0.00 0.00 0.00 3.41
81 82 8.534333 TTCTTAGCACAGTAGTAAATTGACTG 57.466 34.615 5.64 7.04 44.98 3.51
82 83 7.097192 TCTTAGCACAGTAGTAAATTGACTGG 58.903 38.462 5.64 0.00 43.98 4.00
83 84 4.003648 AGCACAGTAGTAAATTGACTGGC 58.996 43.478 5.64 9.47 43.98 4.85
84 85 3.751175 GCACAGTAGTAAATTGACTGGCA 59.249 43.478 5.64 0.00 43.98 4.92
85 86 4.396166 GCACAGTAGTAAATTGACTGGCAT 59.604 41.667 5.64 0.00 43.98 4.40
86 87 5.674569 GCACAGTAGTAAATTGACTGGCATG 60.675 44.000 5.64 2.07 43.98 4.06
87 88 5.643348 CACAGTAGTAAATTGACTGGCATGA 59.357 40.000 5.64 0.00 43.98 3.07
88 89 5.643777 ACAGTAGTAAATTGACTGGCATGAC 59.356 40.000 5.64 0.00 43.98 3.06
89 90 5.643348 CAGTAGTAAATTGACTGGCATGACA 59.357 40.000 0.00 0.00 37.52 3.58
90 91 6.149308 CAGTAGTAAATTGACTGGCATGACAA 59.851 38.462 1.11 0.00 37.52 3.18
91 92 6.886459 AGTAGTAAATTGACTGGCATGACAAT 59.114 34.615 1.11 0.00 34.79 2.71
92 93 8.046708 AGTAGTAAATTGACTGGCATGACAATA 58.953 33.333 1.11 0.00 33.48 1.90
93 94 7.088589 AGTAAATTGACTGGCATGACAATAC 57.911 36.000 1.11 0.00 33.48 1.89
94 95 4.989279 AATTGACTGGCATGACAATACC 57.011 40.909 1.11 0.00 33.48 2.73
95 96 3.431673 TTGACTGGCATGACAATACCA 57.568 42.857 1.11 0.00 0.00 3.25
98 99 1.753930 CTGGCATGACAATACCAGCA 58.246 50.000 1.11 0.00 39.88 4.41
99 100 2.304092 CTGGCATGACAATACCAGCAT 58.696 47.619 1.11 0.00 39.88 3.79
100 101 3.479489 CTGGCATGACAATACCAGCATA 58.521 45.455 1.11 0.00 39.88 3.14
101 102 4.077108 CTGGCATGACAATACCAGCATAT 58.923 43.478 1.11 0.00 39.88 1.78
102 103 5.240013 TGGCATGACAATACCAGCATATA 57.760 39.130 0.00 0.00 0.00 0.86
103 104 5.818887 TGGCATGACAATACCAGCATATAT 58.181 37.500 0.00 0.00 0.00 0.86
104 105 5.648960 TGGCATGACAATACCAGCATATATG 59.351 40.000 0.00 8.45 0.00 1.78
105 106 5.882000 GGCATGACAATACCAGCATATATGA 59.118 40.000 17.10 0.00 0.00 2.15
106 107 6.544931 GGCATGACAATACCAGCATATATGAT 59.455 38.462 17.10 7.36 0.00 2.45
107 108 7.415229 GCATGACAATACCAGCATATATGATG 58.585 38.462 21.50 21.50 43.38 3.07
108 109 7.066645 GCATGACAATACCAGCATATATGATGT 59.933 37.037 25.08 16.88 42.28 3.06
109 110 8.610035 CATGACAATACCAGCATATATGATGTC 58.390 37.037 25.08 16.66 42.28 3.06
110 111 7.678837 TGACAATACCAGCATATATGATGTCA 58.321 34.615 25.08 18.62 42.28 3.58
111 112 7.603784 TGACAATACCAGCATATATGATGTCAC 59.396 37.037 25.08 12.01 42.28 3.67
112 113 7.452562 ACAATACCAGCATATATGATGTCACA 58.547 34.615 25.08 10.64 42.28 3.58
113 114 8.105197 ACAATACCAGCATATATGATGTCACAT 58.895 33.333 25.08 12.14 42.28 3.21
114 115 9.603921 CAATACCAGCATATATGATGTCACATA 57.396 33.333 25.08 12.20 42.28 2.29
116 117 9.774413 ATACCAGCATATATGATGTCACATATG 57.226 33.333 25.08 14.11 43.19 1.78
117 118 7.052248 ACCAGCATATATGATGTCACATATGG 58.948 38.462 25.08 12.03 41.57 2.74
118 119 7.092757 ACCAGCATATATGATGTCACATATGGA 60.093 37.037 25.08 0.00 41.57 3.41
119 120 7.937394 CCAGCATATATGATGTCACATATGGAT 59.063 37.037 25.08 1.58 41.57 3.41
120 121 9.991906 CAGCATATATGATGTCACATATGGATA 57.008 33.333 20.43 0.70 41.57 2.59
127 128 8.613060 ATGATGTCACATATGGATAACTTGAC 57.387 34.615 7.80 10.05 33.91 3.18
128 129 7.795047 TGATGTCACATATGGATAACTTGACT 58.205 34.615 16.64 6.85 34.33 3.41
129 130 7.712205 TGATGTCACATATGGATAACTTGACTG 59.288 37.037 16.64 0.25 34.33 3.51
130 131 7.181569 TGTCACATATGGATAACTTGACTGA 57.818 36.000 16.64 2.28 34.33 3.41
131 132 7.795047 TGTCACATATGGATAACTTGACTGAT 58.205 34.615 16.64 0.00 34.33 2.90
132 133 8.267183 TGTCACATATGGATAACTTGACTGATT 58.733 33.333 16.64 0.00 34.33 2.57
133 134 9.113838 GTCACATATGGATAACTTGACTGATTT 57.886 33.333 7.80 0.00 31.25 2.17
134 135 9.685276 TCACATATGGATAACTTGACTGATTTT 57.315 29.630 7.80 0.00 0.00 1.82
173 174 9.679661 ATTATCTTGTACATATTTGTGGTCACA 57.320 29.630 0.00 0.00 39.98 3.58
174 175 9.679661 TTATCTTGTACATATTTGTGGTCACAT 57.320 29.630 4.53 0.00 41.52 3.21
175 176 7.994425 TCTTGTACATATTTGTGGTCACATT 57.006 32.000 4.53 0.00 41.52 2.71
176 177 9.679661 ATCTTGTACATATTTGTGGTCACATTA 57.320 29.630 4.53 1.48 41.52 1.90
177 178 9.679661 TCTTGTACATATTTGTGGTCACATTAT 57.320 29.630 4.53 4.91 41.52 1.28
180 181 9.892130 TGTACATATTTGTGGTCACATTATACA 57.108 29.630 4.53 6.04 41.52 2.29
186 187 7.815840 TTTGTGGTCACATTATACATATGGG 57.184 36.000 7.80 0.00 41.52 4.00
187 188 6.508030 TGTGGTCACATTATACATATGGGT 57.492 37.500 7.80 0.00 36.21 4.51
188 189 7.619512 TGTGGTCACATTATACATATGGGTA 57.380 36.000 7.80 0.00 36.21 3.69
189 190 8.035448 TGTGGTCACATTATACATATGGGTAA 57.965 34.615 7.80 6.14 36.21 2.85
190 191 8.495260 TGTGGTCACATTATACATATGGGTAAA 58.505 33.333 7.80 0.00 36.21 2.01
191 192 9.344772 GTGGTCACATTATACATATGGGTAAAA 57.655 33.333 7.80 0.00 0.00 1.52
202 203 9.707957 ATACATATGGGTAAAATGGTCTTTTCA 57.292 29.630 7.80 0.00 0.00 2.69
203 204 7.836842 ACATATGGGTAAAATGGTCTTTTCAC 58.163 34.615 7.80 0.00 0.00 3.18
204 205 4.839668 TGGGTAAAATGGTCTTTTCACG 57.160 40.909 0.00 0.00 0.00 4.35
205 206 4.208746 TGGGTAAAATGGTCTTTTCACGT 58.791 39.130 0.00 0.00 0.00 4.49
206 207 4.036971 TGGGTAAAATGGTCTTTTCACGTG 59.963 41.667 9.94 9.94 0.00 4.49
207 208 4.276431 GGGTAAAATGGTCTTTTCACGTGA 59.724 41.667 15.76 15.76 0.00 4.35
208 209 5.221087 GGGTAAAATGGTCTTTTCACGTGAA 60.221 40.000 26.53 26.53 0.00 3.18
209 210 5.684184 GGTAAAATGGTCTTTTCACGTGAAC 59.316 40.000 29.74 18.92 33.13 3.18
210 211 4.974368 AAATGGTCTTTTCACGTGAACA 57.026 36.364 29.74 22.47 33.13 3.18
211 212 4.974368 AATGGTCTTTTCACGTGAACAA 57.026 36.364 29.74 22.79 33.13 2.83
212 213 4.974368 ATGGTCTTTTCACGTGAACAAA 57.026 36.364 29.74 20.61 33.13 2.83
213 214 4.768130 TGGTCTTTTCACGTGAACAAAA 57.232 36.364 29.74 19.92 33.13 2.44
214 215 5.317733 TGGTCTTTTCACGTGAACAAAAT 57.682 34.783 29.74 0.00 33.13 1.82
215 216 5.098893 TGGTCTTTTCACGTGAACAAAATG 58.901 37.500 29.74 16.79 33.13 2.32
216 217 4.026886 GGTCTTTTCACGTGAACAAAATGC 60.027 41.667 29.74 15.57 33.13 3.56
217 218 4.560819 GTCTTTTCACGTGAACAAAATGCA 59.439 37.500 29.74 10.62 33.13 3.96
218 219 4.560819 TCTTTTCACGTGAACAAAATGCAC 59.439 37.500 29.74 0.00 33.13 4.57
219 220 3.773860 TTCACGTGAACAAAATGCACT 57.226 38.095 26.53 0.00 0.00 4.40
220 221 4.884458 TTCACGTGAACAAAATGCACTA 57.116 36.364 26.53 0.00 0.00 2.74
221 222 4.466567 TCACGTGAACAAAATGCACTAG 57.533 40.909 17.62 0.00 0.00 2.57
222 223 4.123506 TCACGTGAACAAAATGCACTAGA 58.876 39.130 17.62 0.00 0.00 2.43
223 224 4.211164 TCACGTGAACAAAATGCACTAGAG 59.789 41.667 17.62 0.00 0.00 2.43
224 225 4.024893 CACGTGAACAAAATGCACTAGAGT 60.025 41.667 10.90 0.00 0.00 3.24
238 239 5.661056 CACTAGAGTGTCACATAGGGAAA 57.339 43.478 15.69 0.00 40.96 3.13
239 240 5.655488 CACTAGAGTGTCACATAGGGAAAG 58.345 45.833 15.69 2.14 40.96 2.62
240 241 5.419155 CACTAGAGTGTCACATAGGGAAAGA 59.581 44.000 15.69 0.00 40.96 2.52
241 242 6.017192 ACTAGAGTGTCACATAGGGAAAGAA 58.983 40.000 15.69 0.00 0.00 2.52
242 243 5.825593 AGAGTGTCACATAGGGAAAGAAA 57.174 39.130 5.62 0.00 0.00 2.52
243 244 6.380079 AGAGTGTCACATAGGGAAAGAAAT 57.620 37.500 5.62 0.00 0.00 2.17
244 245 6.784031 AGAGTGTCACATAGGGAAAGAAATT 58.216 36.000 5.62 0.00 0.00 1.82
245 246 7.918076 AGAGTGTCACATAGGGAAAGAAATTA 58.082 34.615 5.62 0.00 0.00 1.40
246 247 8.383175 AGAGTGTCACATAGGGAAAGAAATTAA 58.617 33.333 5.62 0.00 0.00 1.40
247 248 8.567285 AGTGTCACATAGGGAAAGAAATTAAG 57.433 34.615 5.62 0.00 0.00 1.85
248 249 8.383175 AGTGTCACATAGGGAAAGAAATTAAGA 58.617 33.333 5.62 0.00 0.00 2.10
249 250 8.451748 GTGTCACATAGGGAAAGAAATTAAGAC 58.548 37.037 0.00 0.00 0.00 3.01
250 251 8.383175 TGTCACATAGGGAAAGAAATTAAGACT 58.617 33.333 0.00 0.00 0.00 3.24
251 252 9.886132 GTCACATAGGGAAAGAAATTAAGACTA 57.114 33.333 0.00 0.00 0.00 2.59
258 259 9.280456 AGGGAAAGAAATTAAGACTATAGGTCA 57.720 33.333 4.43 0.00 46.72 4.02
279 280 9.201989 AGGTCATATAGGGAAGAAAAATTTTCC 57.798 33.333 14.17 0.81 41.71 3.13
280 281 8.977412 GGTCATATAGGGAAGAAAAATTTTCCA 58.023 33.333 14.17 0.00 43.74 3.53
282 283 8.695456 TCATATAGGGAAGAAAAATTTTCCAGC 58.305 33.333 14.17 4.89 43.74 4.85
283 284 4.257267 AGGGAAGAAAAATTTTCCAGCG 57.743 40.909 14.17 0.00 43.74 5.18
284 285 3.641436 AGGGAAGAAAAATTTTCCAGCGT 59.359 39.130 14.17 0.00 43.74 5.07
285 286 3.987868 GGGAAGAAAAATTTTCCAGCGTC 59.012 43.478 14.17 5.35 43.74 5.19
286 287 4.500716 GGGAAGAAAAATTTTCCAGCGTCA 60.501 41.667 14.17 0.00 43.74 4.35
287 288 5.047188 GGAAGAAAAATTTTCCAGCGTCAA 58.953 37.500 14.17 0.00 41.97 3.18
288 289 5.522097 GGAAGAAAAATTTTCCAGCGTCAAA 59.478 36.000 14.17 0.00 41.97 2.69
289 290 6.202762 GGAAGAAAAATTTTCCAGCGTCAAAT 59.797 34.615 14.17 0.00 41.97 2.32
290 291 7.383843 GGAAGAAAAATTTTCCAGCGTCAAATA 59.616 33.333 14.17 0.00 41.97 1.40
291 292 8.655651 AAGAAAAATTTTCCAGCGTCAAATAA 57.344 26.923 14.17 0.00 0.00 1.40
292 293 8.298030 AGAAAAATTTTCCAGCGTCAAATAAG 57.702 30.769 14.17 0.00 0.00 1.73
293 294 8.141268 AGAAAAATTTTCCAGCGTCAAATAAGA 58.859 29.630 14.17 0.00 0.00 2.10
294 295 8.655651 AAAAATTTTCCAGCGTCAAATAAGAA 57.344 26.923 3.41 0.00 0.00 2.52
295 296 8.655651 AAAATTTTCCAGCGTCAAATAAGAAA 57.344 26.923 0.00 0.00 0.00 2.52
296 297 7.637709 AATTTTCCAGCGTCAAATAAGAAAC 57.362 32.000 0.00 0.00 0.00 2.78
297 298 5.759506 TTTCCAGCGTCAAATAAGAAACA 57.240 34.783 0.00 0.00 0.00 2.83
298 299 5.957842 TTCCAGCGTCAAATAAGAAACAT 57.042 34.783 0.00 0.00 0.00 2.71
299 300 5.295431 TCCAGCGTCAAATAAGAAACATG 57.705 39.130 0.00 0.00 0.00 3.21
300 301 5.000591 TCCAGCGTCAAATAAGAAACATGA 58.999 37.500 0.00 0.00 0.00 3.07
301 302 5.647658 TCCAGCGTCAAATAAGAAACATGAT 59.352 36.000 0.00 0.00 0.00 2.45
302 303 6.150976 TCCAGCGTCAAATAAGAAACATGATT 59.849 34.615 0.00 0.00 0.00 2.57
303 304 6.808212 CCAGCGTCAAATAAGAAACATGATTT 59.192 34.615 0.00 0.00 0.00 2.17
304 305 7.329226 CCAGCGTCAAATAAGAAACATGATTTT 59.671 33.333 0.00 0.00 0.00 1.82
305 306 9.340695 CAGCGTCAAATAAGAAACATGATTTTA 57.659 29.630 0.00 0.00 0.00 1.52
306 307 9.906660 AGCGTCAAATAAGAAACATGATTTTAA 57.093 25.926 0.00 0.00 0.00 1.52
316 317 8.908786 AGAAACATGATTTTAAGAGAGTGTCA 57.091 30.769 0.00 0.00 0.00 3.58
317 318 9.342308 AGAAACATGATTTTAAGAGAGTGTCAA 57.658 29.630 0.00 0.00 0.00 3.18
318 319 9.950680 GAAACATGATTTTAAGAGAGTGTCAAA 57.049 29.630 0.00 0.00 0.00 2.69
328 329 9.490379 TTTAAGAGAGTGTCAAATAAGGAACTC 57.510 33.333 0.00 0.00 38.49 3.01
329 330 6.926630 AGAGAGTGTCAAATAAGGAACTCT 57.073 37.500 2.94 2.94 45.24 3.24
331 332 6.926630 AGAGTGTCAAATAAGGAACTCTCT 57.073 37.500 0.00 0.00 40.11 3.10
332 333 6.930731 AGAGTGTCAAATAAGGAACTCTCTC 58.069 40.000 0.00 0.00 40.11 3.20
333 334 6.723977 AGAGTGTCAAATAAGGAACTCTCTCT 59.276 38.462 0.00 0.00 40.11 3.10
357 358 9.938280 TCTATATTTTGTTACTACAAGCACAGT 57.062 29.630 0.00 0.00 44.56 3.55
360 361 9.720769 ATATTTTGTTACTACAAGCACAGTACT 57.279 29.630 0.00 0.00 44.56 2.73
361 362 7.852971 TTTTGTTACTACAAGCACAGTACTT 57.147 32.000 0.00 0.00 44.56 2.24
362 363 8.945481 TTTTGTTACTACAAGCACAGTACTTA 57.055 30.769 0.00 0.00 44.56 2.24
363 364 7.935338 TTGTTACTACAAGCACAGTACTTAC 57.065 36.000 0.00 0.00 39.29 2.34
390 391 5.578336 CCATATCTGTCGCGTTATCATCATT 59.422 40.000 5.77 0.00 0.00 2.57
407 408 6.631016 TCATCATTTGAGACTGTAGTGTACC 58.369 40.000 0.00 0.00 0.00 3.34
431 432 5.122396 CAGTACAAGGGAAGCATAGTGTTTC 59.878 44.000 0.00 0.00 36.95 2.78
484 497 1.214062 CACAGTGCGAGGAGAGGAC 59.786 63.158 0.00 0.00 0.00 3.85
491 506 2.684735 GAGGAGAGGACCGAGGGT 59.315 66.667 0.00 0.00 39.44 4.34
517 532 3.604582 GTCCAGATCAAGAGGAACAAGG 58.395 50.000 0.00 0.00 32.30 3.61
578 607 4.083565 GTTGGGTTAGCTGGGTTTTGATA 58.916 43.478 0.00 0.00 0.00 2.15
605 639 8.856153 TTAGGTTATCATTTTCTGCACTGTTA 57.144 30.769 0.00 0.00 0.00 2.41
658 697 6.128035 CGGTTTCAATGATAATCACCAGAACA 60.128 38.462 0.00 0.00 0.00 3.18
659 698 7.029563 GGTTTCAATGATAATCACCAGAACAC 58.970 38.462 0.00 0.00 0.00 3.32
660 699 6.757897 TTCAATGATAATCACCAGAACACC 57.242 37.500 0.00 0.00 0.00 4.16
821 893 1.711206 GTTTAGCGTCCTCCTGTCAC 58.289 55.000 0.00 0.00 0.00 3.67
971 1594 1.004918 GTCGTGGTGGGGAGAAGTG 60.005 63.158 0.00 0.00 0.00 3.16
977 1642 3.650950 TGGGGAGAAGTGGGCAGC 61.651 66.667 0.00 0.00 0.00 5.25
1206 1888 0.662619 TCTTCAAGCACGGCAACTTG 59.337 50.000 5.12 5.12 43.73 3.16
1295 2106 4.913924 GCATACACTTGCTTGAAAGAACTG 59.086 41.667 0.00 0.00 39.57 3.16
1305 2116 4.314121 CTTGAAAGAACTGTCTGCTAGCT 58.686 43.478 17.23 0.00 33.05 3.32
1338 2154 0.615331 ATGAGATCGTTGTGCAGGGT 59.385 50.000 0.00 0.00 0.00 4.34
1395 2211 2.125512 GAGTCATTCCTGCGCGGT 60.126 61.111 16.49 0.00 0.00 5.68
1497 2334 2.210116 CAGTACGTGGTGGCCAATATC 58.790 52.381 7.24 0.00 34.18 1.63
1500 2337 1.891919 CGTGGTGGCCAATATCGGG 60.892 63.158 7.24 0.00 34.18 5.14
1748 2585 3.585020 CCAGCACACGCAGTTGCA 61.585 61.111 4.84 0.00 41.61 4.08
1876 2743 3.278574 CCACTGAAACTCACAACCTTCA 58.721 45.455 0.00 0.00 0.00 3.02
1967 2846 2.523168 TGACAGTGGGACCGCAGA 60.523 61.111 4.54 0.00 0.00 4.26
2091 2982 6.150738 TGCAATCATTTGTACGCATTTTTC 57.849 33.333 0.00 0.00 35.17 2.29
2094 2985 7.042187 TGCAATCATTTGTACGCATTTTTCTTT 60.042 29.630 0.00 0.00 35.17 2.52
2131 3022 1.960250 GATGCTGGGAGCGAGATGC 60.960 63.158 0.00 0.00 46.26 3.91
2286 3256 1.895798 GAGGATGTCATCGGCCATCTA 59.104 52.381 2.24 0.00 38.02 1.98
2330 3300 4.816385 AGAAAATGACTCGCACAGAAAAGA 59.184 37.500 0.00 0.00 0.00 2.52
2463 3435 7.418408 GGTAAGAAGACCTTCAAGAAAAACAG 58.582 38.462 11.80 0.00 41.84 3.16
2513 3489 1.427368 AGGAACATTGGCCCACAAGTA 59.573 47.619 0.00 0.00 43.48 2.24
2516 3492 0.480690 ACATTGGCCCACAAGTACCA 59.519 50.000 0.00 0.00 43.48 3.25
2520 3496 2.160721 TGGCCCACAAGTACCAAAAA 57.839 45.000 0.00 0.00 0.00 1.94
2645 3644 3.248446 ATCGGTTGGTGGGTGGACG 62.248 63.158 0.00 0.00 0.00 4.79
2657 3659 2.036006 GTGGACGCGGGTGCAAATA 61.036 57.895 27.43 2.88 46.53 1.40
2734 3738 4.401925 GGTCCCTATTGATGAAGAATGGG 58.598 47.826 0.00 0.00 32.57 4.00
2753 3757 2.139118 GGGCGAGTGCTTCTATTCATC 58.861 52.381 0.00 0.00 42.25 2.92
2809 3828 1.450134 GATCGTGCAGCATGTCCCA 60.450 57.895 14.47 0.00 39.31 4.37
2816 3835 2.184830 CAGCATGTCCCAGCCATCG 61.185 63.158 0.00 0.00 0.00 3.84
2855 3874 2.769095 GGCTCCCTTCTGTGTAGAGAAT 59.231 50.000 0.00 0.00 33.70 2.40
2857 3876 3.791245 CTCCCTTCTGTGTAGAGAATGC 58.209 50.000 0.00 0.00 33.70 3.56
2941 3966 2.028385 AGGTTACGAATGTGGAGGTGTC 60.028 50.000 0.00 0.00 0.00 3.67
2942 3967 2.289195 GGTTACGAATGTGGAGGTGTCA 60.289 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.183865 TGTGCTAAGAAATCATGACCGAG 58.816 43.478 0.00 0.00 0.00 4.63
45 46 4.183865 CTGTGCTAAGAAATCATGACCGA 58.816 43.478 0.00 0.00 0.00 4.69
46 47 3.935203 ACTGTGCTAAGAAATCATGACCG 59.065 43.478 0.00 0.00 0.00 4.79
47 48 6.109359 ACTACTGTGCTAAGAAATCATGACC 58.891 40.000 0.00 0.00 0.00 4.02
48 49 8.703604 TTACTACTGTGCTAAGAAATCATGAC 57.296 34.615 0.00 0.00 0.00 3.06
49 50 9.890629 ATTTACTACTGTGCTAAGAAATCATGA 57.109 29.630 0.00 0.00 0.00 3.07
52 53 9.719355 TCAATTTACTACTGTGCTAAGAAATCA 57.281 29.630 0.00 0.00 0.00 2.57
53 54 9.974750 GTCAATTTACTACTGTGCTAAGAAATC 57.025 33.333 0.00 0.00 0.00 2.17
54 55 9.726438 AGTCAATTTACTACTGTGCTAAGAAAT 57.274 29.630 0.00 0.00 0.00 2.17
55 56 8.988934 CAGTCAATTTACTACTGTGCTAAGAAA 58.011 33.333 0.00 0.00 36.66 2.52
56 57 7.602644 CCAGTCAATTTACTACTGTGCTAAGAA 59.397 37.037 0.00 0.00 39.17 2.52
57 58 7.097192 CCAGTCAATTTACTACTGTGCTAAGA 58.903 38.462 0.00 0.00 39.17 2.10
58 59 6.183360 GCCAGTCAATTTACTACTGTGCTAAG 60.183 42.308 0.00 0.00 39.17 2.18
59 60 5.642063 GCCAGTCAATTTACTACTGTGCTAA 59.358 40.000 0.00 0.00 39.17 3.09
60 61 5.175859 GCCAGTCAATTTACTACTGTGCTA 58.824 41.667 0.00 0.00 39.17 3.49
61 62 4.003648 GCCAGTCAATTTACTACTGTGCT 58.996 43.478 0.00 0.00 39.17 4.40
62 63 3.751175 TGCCAGTCAATTTACTACTGTGC 59.249 43.478 0.00 0.00 39.17 4.57
63 64 5.643348 TCATGCCAGTCAATTTACTACTGTG 59.357 40.000 0.00 0.00 39.17 3.66
64 65 5.643777 GTCATGCCAGTCAATTTACTACTGT 59.356 40.000 0.00 0.00 39.17 3.55
65 66 5.643348 TGTCATGCCAGTCAATTTACTACTG 59.357 40.000 0.00 0.00 40.24 2.74
66 67 5.804639 TGTCATGCCAGTCAATTTACTACT 58.195 37.500 0.00 0.00 0.00 2.57
67 68 6.494893 TTGTCATGCCAGTCAATTTACTAC 57.505 37.500 0.00 0.00 0.00 2.73
68 69 7.282224 GGTATTGTCATGCCAGTCAATTTACTA 59.718 37.037 0.00 0.00 35.26 1.82
69 70 6.095440 GGTATTGTCATGCCAGTCAATTTACT 59.905 38.462 4.02 0.00 35.26 2.24
70 71 6.127758 TGGTATTGTCATGCCAGTCAATTTAC 60.128 38.462 4.02 0.00 40.07 2.01
71 72 5.948758 TGGTATTGTCATGCCAGTCAATTTA 59.051 36.000 4.02 0.00 40.07 1.40
72 73 4.771577 TGGTATTGTCATGCCAGTCAATTT 59.228 37.500 4.02 0.00 40.07 1.82
73 74 4.343231 TGGTATTGTCATGCCAGTCAATT 58.657 39.130 4.02 0.00 40.07 2.32
74 75 3.966979 TGGTATTGTCATGCCAGTCAAT 58.033 40.909 0.00 0.00 40.07 2.57
75 76 3.431673 TGGTATTGTCATGCCAGTCAA 57.568 42.857 0.00 0.00 40.07 3.18
80 81 2.440517 ATGCTGGTATTGTCATGCCA 57.559 45.000 0.00 0.00 42.54 4.92
81 82 5.882000 TCATATATGCTGGTATTGTCATGCC 59.118 40.000 7.92 0.00 35.72 4.40
82 83 6.990341 TCATATATGCTGGTATTGTCATGC 57.010 37.500 7.92 0.00 0.00 4.06
83 84 8.502105 ACATCATATATGCTGGTATTGTCATG 57.498 34.615 18.26 10.08 0.00 3.07
84 85 8.323567 TGACATCATATATGCTGGTATTGTCAT 58.676 33.333 18.26 0.00 35.97 3.06
85 86 7.603784 GTGACATCATATATGCTGGTATTGTCA 59.396 37.037 18.26 16.58 37.86 3.58
86 87 7.603784 TGTGACATCATATATGCTGGTATTGTC 59.396 37.037 18.26 14.90 0.00 3.18
87 88 7.452562 TGTGACATCATATATGCTGGTATTGT 58.547 34.615 18.26 8.54 0.00 2.71
88 89 7.910441 TGTGACATCATATATGCTGGTATTG 57.090 36.000 18.26 6.09 0.00 1.90
90 91 9.774413 CATATGTGACATCATATATGCTGGTAT 57.226 33.333 19.45 10.23 45.03 2.73
101 102 9.710900 GTCAAGTTATCCATATGTGACATCATA 57.289 33.333 0.00 0.00 35.20 2.15
102 103 8.435187 AGTCAAGTTATCCATATGTGACATCAT 58.565 33.333 17.58 0.00 37.07 2.45
103 104 7.712205 CAGTCAAGTTATCCATATGTGACATCA 59.288 37.037 17.58 0.00 37.07 3.07
104 105 7.928167 TCAGTCAAGTTATCCATATGTGACATC 59.072 37.037 17.58 0.07 37.07 3.06
105 106 7.795047 TCAGTCAAGTTATCCATATGTGACAT 58.205 34.615 17.58 2.65 37.07 3.06
106 107 7.181569 TCAGTCAAGTTATCCATATGTGACA 57.818 36.000 17.58 0.00 37.07 3.58
107 108 8.668510 AATCAGTCAAGTTATCCATATGTGAC 57.331 34.615 10.74 10.74 35.30 3.67
108 109 9.685276 AAAATCAGTCAAGTTATCCATATGTGA 57.315 29.630 1.24 0.00 0.00 3.58
147 148 9.679661 TGTGACCACAAATATGTACAAGATAAT 57.320 29.630 0.00 0.00 37.82 1.28
148 149 9.679661 ATGTGACCACAAATATGTACAAGATAA 57.320 29.630 6.95 0.00 45.41 1.75
149 150 9.679661 AATGTGACCACAAATATGTACAAGATA 57.320 29.630 6.95 0.00 45.41 1.98
150 151 8.579850 AATGTGACCACAAATATGTACAAGAT 57.420 30.769 6.95 0.00 45.41 2.40
151 152 7.994425 AATGTGACCACAAATATGTACAAGA 57.006 32.000 6.95 0.00 45.41 3.02
154 155 9.892130 TGTATAATGTGACCACAAATATGTACA 57.108 29.630 6.95 0.00 45.41 2.90
160 161 9.513906 CCCATATGTATAATGTGACCACAAATA 57.486 33.333 6.95 5.86 45.41 1.40
161 162 8.004215 ACCCATATGTATAATGTGACCACAAAT 58.996 33.333 6.95 6.74 45.41 2.32
162 163 7.350382 ACCCATATGTATAATGTGACCACAAA 58.650 34.615 6.95 0.00 45.41 2.83
163 164 6.905736 ACCCATATGTATAATGTGACCACAA 58.094 36.000 6.95 0.00 45.41 3.33
164 165 6.508030 ACCCATATGTATAATGTGACCACA 57.492 37.500 5.22 5.22 46.44 4.17
165 166 8.911918 TTTACCCATATGTATAATGTGACCAC 57.088 34.615 1.24 0.00 0.00 4.16
176 177 9.707957 TGAAAAGACCATTTTACCCATATGTAT 57.292 29.630 1.24 0.00 0.00 2.29
177 178 8.962679 GTGAAAAGACCATTTTACCCATATGTA 58.037 33.333 1.24 0.00 0.00 2.29
178 179 7.362574 CGTGAAAAGACCATTTTACCCATATGT 60.363 37.037 1.24 0.00 0.00 2.29
179 180 6.972328 CGTGAAAAGACCATTTTACCCATATG 59.028 38.462 0.00 0.00 0.00 1.78
180 181 6.661805 ACGTGAAAAGACCATTTTACCCATAT 59.338 34.615 0.00 0.00 0.00 1.78
181 182 6.005198 ACGTGAAAAGACCATTTTACCCATA 58.995 36.000 0.00 0.00 0.00 2.74
182 183 4.830600 ACGTGAAAAGACCATTTTACCCAT 59.169 37.500 0.00 0.00 0.00 4.00
183 184 4.036971 CACGTGAAAAGACCATTTTACCCA 59.963 41.667 10.90 0.00 0.00 4.51
184 185 4.276431 TCACGTGAAAAGACCATTTTACCC 59.724 41.667 17.62 0.00 0.00 3.69
185 186 5.427036 TCACGTGAAAAGACCATTTTACC 57.573 39.130 17.62 0.00 0.00 2.85
186 187 6.259638 TGTTCACGTGAAAAGACCATTTTAC 58.740 36.000 31.20 15.70 35.58 2.01
187 188 6.438259 TGTTCACGTGAAAAGACCATTTTA 57.562 33.333 31.20 2.89 35.58 1.52
188 189 5.317733 TGTTCACGTGAAAAGACCATTTT 57.682 34.783 31.20 0.00 35.58 1.82
189 190 4.974368 TGTTCACGTGAAAAGACCATTT 57.026 36.364 31.20 0.00 35.58 2.32
190 191 4.974368 TTGTTCACGTGAAAAGACCATT 57.026 36.364 31.20 0.00 35.58 3.16
191 192 4.974368 TTTGTTCACGTGAAAAGACCAT 57.026 36.364 31.20 0.00 35.58 3.55
192 193 4.768130 TTTTGTTCACGTGAAAAGACCA 57.232 36.364 31.20 21.24 35.58 4.02
193 194 4.026886 GCATTTTGTTCACGTGAAAAGACC 60.027 41.667 31.20 18.96 35.58 3.85
194 195 4.560819 TGCATTTTGTTCACGTGAAAAGAC 59.439 37.500 31.20 20.31 35.58 3.01
195 196 4.560819 GTGCATTTTGTTCACGTGAAAAGA 59.439 37.500 31.20 19.57 35.58 2.52
196 197 4.562394 AGTGCATTTTGTTCACGTGAAAAG 59.438 37.500 31.20 15.69 35.58 2.27
197 198 4.489810 AGTGCATTTTGTTCACGTGAAAA 58.510 34.783 31.20 24.50 35.58 2.29
198 199 4.103365 AGTGCATTTTGTTCACGTGAAA 57.897 36.364 31.20 17.11 35.58 2.69
199 200 3.773860 AGTGCATTTTGTTCACGTGAA 57.226 38.095 26.53 26.53 35.97 3.18
200 201 4.123506 TCTAGTGCATTTTGTTCACGTGA 58.876 39.130 15.76 15.76 35.97 4.35
201 202 4.024893 ACTCTAGTGCATTTTGTTCACGTG 60.025 41.667 9.94 9.94 35.97 4.49
202 203 4.024893 CACTCTAGTGCATTTTGTTCACGT 60.025 41.667 0.00 0.00 39.39 4.49
203 204 4.457810 CACTCTAGTGCATTTTGTTCACG 58.542 43.478 0.00 0.00 39.39 4.35
217 218 5.580998 TCTTTCCCTATGTGACACTCTAGT 58.419 41.667 7.20 0.00 0.00 2.57
218 219 6.531503 TTCTTTCCCTATGTGACACTCTAG 57.468 41.667 7.20 7.77 0.00 2.43
219 220 6.928348 TTTCTTTCCCTATGTGACACTCTA 57.072 37.500 7.20 0.00 0.00 2.43
220 221 5.825593 TTTCTTTCCCTATGTGACACTCT 57.174 39.130 7.20 0.00 0.00 3.24
221 222 8.561738 TTAATTTCTTTCCCTATGTGACACTC 57.438 34.615 7.20 0.00 0.00 3.51
222 223 8.383175 TCTTAATTTCTTTCCCTATGTGACACT 58.617 33.333 7.20 0.00 0.00 3.55
223 224 8.451748 GTCTTAATTTCTTTCCCTATGTGACAC 58.548 37.037 0.00 0.00 0.00 3.67
224 225 8.383175 AGTCTTAATTTCTTTCCCTATGTGACA 58.617 33.333 0.00 0.00 0.00 3.58
225 226 8.794335 AGTCTTAATTTCTTTCCCTATGTGAC 57.206 34.615 0.00 0.00 0.00 3.67
232 233 9.280456 TGACCTATAGTCTTAATTTCTTTCCCT 57.720 33.333 0.00 0.00 46.46 4.20
253 254 9.201989 GGAAAATTTTTCTTCCCTATATGACCT 57.798 33.333 18.63 0.00 35.95 3.85
254 255 8.977412 TGGAAAATTTTTCTTCCCTATATGACC 58.023 33.333 18.63 0.00 40.45 4.02
256 257 8.695456 GCTGGAAAATTTTTCTTCCCTATATGA 58.305 33.333 18.63 0.00 40.45 2.15
257 258 7.649306 CGCTGGAAAATTTTTCTTCCCTATATG 59.351 37.037 18.63 2.65 40.45 1.78
258 259 7.342026 ACGCTGGAAAATTTTTCTTCCCTATAT 59.658 33.333 18.63 0.00 40.45 0.86
259 260 6.661805 ACGCTGGAAAATTTTTCTTCCCTATA 59.338 34.615 18.63 0.00 40.45 1.31
260 261 5.480422 ACGCTGGAAAATTTTTCTTCCCTAT 59.520 36.000 18.63 0.63 40.45 2.57
261 262 4.830600 ACGCTGGAAAATTTTTCTTCCCTA 59.169 37.500 18.63 0.00 40.45 3.53
262 263 3.641436 ACGCTGGAAAATTTTTCTTCCCT 59.359 39.130 18.63 0.62 40.45 4.20
263 264 3.987868 GACGCTGGAAAATTTTTCTTCCC 59.012 43.478 18.63 4.90 40.45 3.97
264 265 4.616953 TGACGCTGGAAAATTTTTCTTCC 58.383 39.130 18.63 5.33 41.37 3.46
265 266 6.582437 TTTGACGCTGGAAAATTTTTCTTC 57.418 33.333 18.63 6.53 0.00 2.87
266 267 8.655651 TTATTTGACGCTGGAAAATTTTTCTT 57.344 26.923 18.63 2.30 0.00 2.52
267 268 8.141268 TCTTATTTGACGCTGGAAAATTTTTCT 58.859 29.630 18.63 1.79 0.00 2.52
268 269 8.293114 TCTTATTTGACGCTGGAAAATTTTTC 57.707 30.769 12.51 12.51 0.00 2.29
269 270 8.655651 TTCTTATTTGACGCTGGAAAATTTTT 57.344 26.923 4.63 0.00 0.00 1.94
270 271 8.547894 GTTTCTTATTTGACGCTGGAAAATTTT 58.452 29.630 2.28 2.28 0.00 1.82
271 272 7.708752 TGTTTCTTATTTGACGCTGGAAAATTT 59.291 29.630 0.00 0.00 0.00 1.82
272 273 7.206687 TGTTTCTTATTTGACGCTGGAAAATT 58.793 30.769 0.00 0.00 0.00 1.82
273 274 6.744112 TGTTTCTTATTTGACGCTGGAAAAT 58.256 32.000 0.00 0.00 0.00 1.82
274 275 6.137794 TGTTTCTTATTTGACGCTGGAAAA 57.862 33.333 0.00 0.00 0.00 2.29
275 276 5.759506 TGTTTCTTATTTGACGCTGGAAA 57.240 34.783 0.00 0.00 0.00 3.13
276 277 5.471797 TCATGTTTCTTATTTGACGCTGGAA 59.528 36.000 0.00 0.00 0.00 3.53
277 278 5.000591 TCATGTTTCTTATTTGACGCTGGA 58.999 37.500 0.00 0.00 0.00 3.86
278 279 5.295431 TCATGTTTCTTATTTGACGCTGG 57.705 39.130 0.00 0.00 0.00 4.85
279 280 7.801547 AAATCATGTTTCTTATTTGACGCTG 57.198 32.000 0.00 0.00 0.00 5.18
280 281 9.906660 TTAAAATCATGTTTCTTATTTGACGCT 57.093 25.926 0.00 0.00 0.00 5.07
290 291 9.342308 TGACACTCTCTTAAAATCATGTTTCTT 57.658 29.630 0.00 0.00 0.00 2.52
291 292 8.908786 TGACACTCTCTTAAAATCATGTTTCT 57.091 30.769 0.00 0.00 0.00 2.52
292 293 9.950680 TTTGACACTCTCTTAAAATCATGTTTC 57.049 29.630 0.00 0.00 0.00 2.78
301 302 9.847224 AGTTCCTTATTTGACACTCTCTTAAAA 57.153 29.630 0.00 0.00 0.00 1.52
302 303 9.490379 GAGTTCCTTATTTGACACTCTCTTAAA 57.510 33.333 0.00 0.00 0.00 1.52
303 304 8.871125 AGAGTTCCTTATTTGACACTCTCTTAA 58.129 33.333 0.00 0.00 37.06 1.85
304 305 8.423906 AGAGTTCCTTATTTGACACTCTCTTA 57.576 34.615 0.00 0.00 37.06 2.10
305 306 7.309770 AGAGTTCCTTATTTGACACTCTCTT 57.690 36.000 0.00 0.00 37.06 2.85
306 307 6.926630 AGAGTTCCTTATTTGACACTCTCT 57.073 37.500 0.00 0.00 37.06 3.10
308 309 6.723977 AGAGAGAGTTCCTTATTTGACACTCT 59.276 38.462 0.00 0.00 42.90 3.24
309 310 6.930731 AGAGAGAGTTCCTTATTTGACACTC 58.069 40.000 0.00 0.00 32.29 3.51
310 311 6.926630 AGAGAGAGTTCCTTATTTGACACT 57.073 37.500 0.00 0.00 0.00 3.55
331 332 9.938280 ACTGTGCTTGTAGTAACAAAATATAGA 57.062 29.630 0.00 0.00 44.79 1.98
360 361 1.672363 ACGCGACAGATATGGACGTAA 59.328 47.619 15.93 0.00 0.00 3.18
361 362 1.302366 ACGCGACAGATATGGACGTA 58.698 50.000 15.93 0.00 0.00 3.57
362 363 0.454600 AACGCGACAGATATGGACGT 59.545 50.000 15.93 0.00 0.00 4.34
363 364 2.394545 TAACGCGACAGATATGGACG 57.605 50.000 15.93 5.16 0.00 4.79
390 391 5.379187 TGTACTGGTACACTACAGTCTCAA 58.621 41.667 9.22 0.00 44.08 3.02
407 408 4.207891 ACACTATGCTTCCCTTGTACTG 57.792 45.455 0.00 0.00 0.00 2.74
431 432 2.783828 ATCGCCTCGATCAACTGTAG 57.216 50.000 0.00 0.00 43.45 2.74
484 497 3.528370 CTGGACGCCTACCCTCGG 61.528 72.222 0.00 0.00 0.00 4.63
491 506 1.063942 TCCTCTTGATCTGGACGCCTA 60.064 52.381 0.00 0.00 0.00 3.93
517 532 2.664971 CGTACGTGTGGTCTCTCTCAAC 60.665 54.545 7.22 0.00 0.00 3.18
578 607 6.942576 ACAGTGCAGAAAATGATAACCTAAGT 59.057 34.615 0.00 0.00 0.00 2.24
739 784 0.108585 ATTGACGTCTGTGGGCTTGT 59.891 50.000 17.92 0.00 0.00 3.16
821 893 1.481819 GCGCTGGCCAATTTTATGCG 61.482 55.000 24.16 24.16 43.91 4.73
963 1586 1.553690 TACCAGCTGCCCACTTCTCC 61.554 60.000 8.66 0.00 0.00 3.71
971 1594 1.059913 ATCCTATGTACCAGCTGCCC 58.940 55.000 8.66 0.00 0.00 5.36
977 1642 7.450014 CCATCCTAGCTATATCCTATGTACCAG 59.550 44.444 0.00 0.00 0.00 4.00
1161 1843 1.140804 GAGGAGGAGCTGCGAGAAC 59.859 63.158 0.00 0.00 0.00 3.01
1206 1888 4.373116 TGGCGGACGAAGCTGGAC 62.373 66.667 0.00 0.00 34.52 4.02
1249 1942 3.730761 GCACGTGCAAGCTGGAGG 61.731 66.667 34.52 0.00 41.59 4.30
1272 2083 4.913924 CAGTTCTTTCAAGCAAGTGTATGC 59.086 41.667 0.00 0.00 46.78 3.14
1295 2106 5.291128 TCGTAGCAAATTAAAGCTAGCAGAC 59.709 40.000 18.83 0.00 43.39 3.51
1338 2154 1.672898 CGGGTGTACCTTCCGGAAA 59.327 57.895 19.39 0.00 40.07 3.13
1350 2166 4.707768 TCCCATCGGTCCGGGTGT 62.708 66.667 12.29 0.00 43.57 4.16
1451 2282 2.829003 TGCCGACTAGAGCCGAGG 60.829 66.667 0.00 0.00 0.00 4.63
1480 2311 0.105224 CCGATATTGGCCACCACGTA 59.895 55.000 3.88 0.00 30.78 3.57
1497 2334 2.038975 TCCTCCACTTCCTCCCCG 59.961 66.667 0.00 0.00 0.00 5.73
1500 2337 1.199615 CTTCCTCCTCCACTTCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
1542 2379 2.492090 CGAACCTCCTCGAGCAGG 59.508 66.667 21.35 21.35 45.15 4.85
1748 2585 2.807676 AGGAAGCAAAATCACGGGAAT 58.192 42.857 0.00 0.00 0.00 3.01
1845 2709 1.741401 TTTCAGTGGCATCGGCTCG 60.741 57.895 0.00 0.00 40.87 5.03
1876 2743 4.443266 GCTCGCGGAGGTCTGCTT 62.443 66.667 6.13 0.00 45.75 3.91
1967 2846 3.189770 AACGGGAAGGGGGTCTCCT 62.190 63.158 0.00 0.00 39.17 3.69
2111 3002 2.865598 ATCTCGCTCCCAGCATCGG 61.866 63.158 0.00 0.00 42.58 4.18
2131 3022 3.931468 AGAAGTTCAAGCTCGATGACATG 59.069 43.478 5.50 0.00 0.00 3.21
2138 3107 6.920817 TCATACTTAAGAAGTTCAAGCTCGA 58.079 36.000 10.09 0.00 42.81 4.04
2184 3153 4.629200 GGGAGCTTAGCGATAATTCATCAG 59.371 45.833 0.00 0.00 32.71 2.90
2185 3154 4.284490 AGGGAGCTTAGCGATAATTCATCA 59.716 41.667 0.00 0.00 32.71 3.07
2190 3159 6.013293 AGGAATTAGGGAGCTTAGCGATAATT 60.013 38.462 14.08 14.08 0.00 1.40
2286 3256 4.816385 TCTCTCGAGTTTTGCTCAACAATT 59.184 37.500 13.13 0.00 44.33 2.32
2313 3283 1.412710 ACCTCTTTTCTGTGCGAGTCA 59.587 47.619 0.00 0.00 0.00 3.41
2330 3300 2.557490 GTGACAGAAGTACCTTCGACCT 59.443 50.000 0.00 0.00 44.34 3.85
2378 3348 1.152355 CCCTTGGGCTTGTGGGAAA 60.152 57.895 0.00 0.00 42.11 3.13
2463 3435 2.222227 AAAGCAACCATCTCCCTTCC 57.778 50.000 0.00 0.00 0.00 3.46
2520 3496 4.291249 TCCTACCCTGGCTTCTTGTAATTT 59.709 41.667 0.00 0.00 0.00 1.82
2523 3499 2.570302 GTCCTACCCTGGCTTCTTGTAA 59.430 50.000 0.00 0.00 0.00 2.41
2645 3644 2.159254 ACACATGAATATTTGCACCCGC 60.159 45.455 0.00 0.00 39.24 6.13
2657 3659 4.278919 TGAAATGTCAGCACACACATGAAT 59.721 37.500 0.00 0.00 34.48 2.57
2706 3709 4.478317 TCTTCATCAATAGGGACCCATGTT 59.522 41.667 14.60 0.92 0.00 2.71
2734 3738 1.789464 CGATGAATAGAAGCACTCGCC 59.211 52.381 0.00 0.00 39.83 5.54
2816 3835 4.356289 GAGCCACTAACGAGATTCTTCTC 58.644 47.826 0.00 0.00 44.24 2.87
2855 3874 5.784177 AGACTCGAAGATCAACTTAAAGCA 58.216 37.500 0.00 0.00 39.13 3.91
2941 3966 1.813513 ATCTGCAAGGGAAAGACGTG 58.186 50.000 0.00 0.00 0.00 4.49
2942 3967 2.568623 AATCTGCAAGGGAAAGACGT 57.431 45.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.