Multiple sequence alignment - TraesCS6D01G149300

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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 TraesCS6D01G149300 chr6D 100.000 4637 0 0 1 4637 123055501 123060137 0.000000e+00 8564.0
1 TraesCS6D01G149300 chr6D 88.432 778 89 1 3816 4593 119109143 119108367 0.000000e+00 937.0
2 TraesCS6D01G149300 chr6D 83.911 808 123 5 3815 4621 296755818 296756619 0.000000e+00 765.0
3 TraesCS6D01G149300 chr6D 86.861 274 31 5 3809 4081 57017302 57017571 7.540000e-78 302.0
4 TraesCS6D01G149300 chr6D 91.257 183 12 3 1512 1690 164817761 164817579 3.580000e-61 246.0
5 TraesCS6D01G149300 chr6D 82.993 294 24 16 178 449 35465628 35465917 4.640000e-60 243.0
6 TraesCS6D01G149300 chr6D 92.667 150 10 1 1512 1661 56666083 56666231 1.010000e-51 215.0
7 TraesCS6D01G149300 chr6D 88.506 174 16 3 1513 1682 164815586 164815413 1.690000e-49 207.0
8 TraesCS6D01G149300 chr6D 87.356 174 16 5 1523 1690 164821023 164820850 1.320000e-45 195.0
9 TraesCS6D01G149300 chr6D 82.301 226 22 8 241 449 27767577 27767801 3.690000e-41 180.0
10 TraesCS6D01G149300 chr6D 91.346 104 8 1 1587 1690 327202005 327202107 1.740000e-29 141.0
11 TraesCS6D01G149300 chr6D 89.899 99 6 3 1587 1681 327204403 327204501 1.750000e-24 124.0
12 TraesCS6D01G149300 chr6D 78.698 169 25 10 3810 3973 174403825 174403663 8.210000e-18 102.0
13 TraesCS6D01G149300 chr6B 96.457 1383 43 2 2433 3814 216691654 216693031 0.000000e+00 2278.0
14 TraesCS6D01G149300 chr6B 96.071 789 23 4 729 1512 216690042 216690827 0.000000e+00 1279.0
15 TraesCS6D01G149300 chr6B 89.080 815 89 0 3816 4630 348825468 348826282 0.000000e+00 1013.0
16 TraesCS6D01G149300 chr6B 97.468 395 6 1 1965 2355 216691100 216691494 0.000000e+00 671.0
17 TraesCS6D01G149300 chr6B 94.361 266 6 4 1718 1982 216690823 216691080 2.600000e-107 399.0
18 TraesCS6D01G149300 chr6B 84.896 384 34 10 176 537 216688473 216688854 2.640000e-97 366.0
19 TraesCS6D01G149300 chr6B 94.737 209 7 3 534 741 216689795 216690000 5.790000e-84 322.0
20 TraesCS6D01G149300 chr6B 91.011 178 14 1 1513 1690 556071698 556071873 6.000000e-59 239.0
21 TraesCS6D01G149300 chr6B 97.115 104 3 0 2339 2442 216691507 216691610 4.770000e-40 176.0
22 TraesCS6D01G149300 chr6A 96.286 1077 27 2 2757 3820 158073690 158072614 0.000000e+00 1755.0
23 TraesCS6D01G149300 chr6A 92.149 1210 52 19 329 1512 158076131 158074939 0.000000e+00 1668.0
24 TraesCS6D01G149300 chr6A 95.101 694 18 5 1718 2409 158074943 158074264 0.000000e+00 1079.0
25 TraesCS6D01G149300 chr6A 87.015 824 103 4 3815 4637 602622836 602622016 0.000000e+00 926.0
26 TraesCS6D01G149300 chr6A 91.250 640 56 0 3816 4455 507662272 507662911 0.000000e+00 872.0
27 TraesCS6D01G149300 chr6A 83.333 300 27 9 176 453 591230835 591231133 5.950000e-64 255.0
28 TraesCS6D01G149300 chr6A 97.115 104 3 0 2423 2526 158074130 158074027 4.770000e-40 176.0
29 TraesCS6D01G149300 chr6A 81.714 175 27 5 1512 1681 48709230 48709056 1.740000e-29 141.0
30 TraesCS6D01G149300 chr6A 98.000 50 1 0 2704 2753 158074030 158073981 2.300000e-13 87.9
31 TraesCS6D01G149300 chr1A 93.260 816 55 0 3815 4630 220714679 220715494 0.000000e+00 1203.0
32 TraesCS6D01G149300 chr1A 86.893 824 98 5 3814 4637 306104845 306104032 0.000000e+00 915.0
33 TraesCS6D01G149300 chr1A 78.855 454 57 22 16 453 425066531 425066961 2.130000e-68 270.0
34 TraesCS6D01G149300 chr1A 81.852 270 28 8 204 453 575250488 575250756 1.690000e-49 207.0
35 TraesCS6D01G149300 chr1A 81.481 270 29 8 204 453 575253793 575254061 7.870000e-48 202.0
36 TraesCS6D01G149300 chr1A 90.400 125 6 5 1572 1690 499791373 499791249 4.800000e-35 159.0
37 TraesCS6D01G149300 chr3B 93.267 802 51 3 3815 4614 776543929 776543129 0.000000e+00 1179.0
38 TraesCS6D01G149300 chr3B 89.117 827 89 1 3810 4636 694266993 694266168 0.000000e+00 1027.0
39 TraesCS6D01G149300 chr1D 91.839 821 67 0 3817 4637 50915303 50914483 0.000000e+00 1146.0
40 TraesCS6D01G149300 chr1D 92.135 178 14 0 1 178 5696060 5695883 7.700000e-63 252.0
41 TraesCS6D01G149300 chr1D 91.573 178 15 0 1 178 50951904 50951727 3.580000e-61 246.0
42 TraesCS6D01G149300 chr1D 91.573 178 15 0 1 178 50957424 50957247 3.580000e-61 246.0
43 TraesCS6D01G149300 chr1D 90.058 171 15 2 1513 1681 65093113 65092943 2.170000e-53 220.0
44 TraesCS6D01G149300 chr1D 88.953 172 18 1 1512 1682 24942516 24942687 1.310000e-50 211.0
45 TraesCS6D01G149300 chr1D 94.030 134 8 0 1522 1655 89042792 89042925 2.190000e-48 204.0
46 TraesCS6D01G149300 chr1D 92.857 140 9 1 1522 1661 89065017 89065155 7.870000e-48 202.0
47 TraesCS6D01G149300 chr1D 83.260 227 24 4 241 453 444199139 444199365 3.660000e-46 196.0
48 TraesCS6D01G149300 chr1D 82.328 232 24 11 238 453 372674022 372674252 7.920000e-43 185.0
49 TraesCS6D01G149300 chr1D 82.251 231 22 10 241 453 490407221 490407450 1.020000e-41 182.0
50 TraesCS6D01G149300 chr1D 82.143 224 23 7 246 453 346604537 346604315 4.770000e-40 176.0
51 TraesCS6D01G149300 chr1D 87.970 133 10 5 1568 1694 80835931 80836063 8.040000e-33 152.0
52 TraesCS6D01G149300 chr1D 77.922 231 22 14 251 453 72629055 72629284 2.930000e-22 117.0
53 TraesCS6D01G149300 chr4D 90.036 823 70 2 3815 4637 103256354 103257164 0.000000e+00 1055.0
54 TraesCS6D01G149300 chr4D 84.561 285 30 7 183 453 506009582 506009298 2.130000e-68 270.0
55 TraesCS6D01G149300 chr4D 91.860 86 5 1 1592 1675 323602204 323602289 8.150000e-23 119.0
56 TraesCS6D01G149300 chr3D 83.887 813 130 1 3815 4627 345519481 345520292 0.000000e+00 774.0
57 TraesCS6D01G149300 chr3D 84.175 297 24 11 175 449 157433369 157433074 2.750000e-67 267.0
58 TraesCS6D01G149300 chr3D 92.697 178 13 0 1 178 143297810 143297987 1.660000e-64 257.0
59 TraesCS6D01G149300 chr3D 89.595 173 15 2 1512 1681 537634169 537634341 2.810000e-52 217.0
60 TraesCS6D01G149300 chr7D 80.443 813 156 3 3816 4627 467763810 467763000 6.590000e-173 617.0
61 TraesCS6D01G149300 chr7D 85.374 294 26 7 176 453 602687870 602687578 5.870000e-74 289.0
62 TraesCS6D01G149300 chr7D 89.617 183 12 5 1513 1690 28384263 28384083 4.670000e-55 226.0
63 TraesCS6D01G149300 chr7D 87.791 172 21 0 3105 3276 163358005 163357834 7.870000e-48 202.0
64 TraesCS6D01G149300 chr7D 87.097 124 14 2 1202 1324 163359309 163359187 6.260000e-29 139.0
65 TraesCS6D01G149300 chr7D 80.220 182 30 5 275 453 21835508 21835686 1.050000e-26 132.0
66 TraesCS6D01G149300 chr4B 89.896 386 36 2 3816 4201 561170966 561171348 1.160000e-135 494.0
67 TraesCS6D01G149300 chr4B 92.135 178 14 0 1 178 38635065 38635242 7.700000e-63 252.0
68 TraesCS6D01G149300 chr4B 83.219 292 32 7 178 453 614265388 614265098 7.700000e-63 252.0
69 TraesCS6D01G149300 chr5B 85.121 289 25 9 181 453 663080910 663080624 3.530000e-71 279.0
70 TraesCS6D01G149300 chr5B 82.313 294 36 7 175 453 522583763 522584055 1.670000e-59 241.0
71 TraesCS6D01G149300 chr5B 84.305 223 19 7 246 453 550753397 550753618 2.190000e-48 204.0
72 TraesCS6D01G149300 chr5D 85.401 274 24 6 195 453 545126881 545126609 2.130000e-68 270.0
73 TraesCS6D01G149300 chr5D 84.083 289 31 7 175 449 554486779 554486492 9.890000e-67 265.0
74 TraesCS6D01G149300 chr5D 90.860 186 13 3 1513 1694 486815083 486815268 3.580000e-61 246.0
75 TraesCS6D01G149300 chr5D 91.515 165 11 2 1512 1673 486817506 486817670 1.680000e-54 224.0
76 TraesCS6D01G149300 chr2D 93.143 175 11 1 4 178 325320213 325320040 5.950000e-64 255.0
77 TraesCS6D01G149300 chr2D 92.135 178 13 1 1 178 608866791 608866967 2.770000e-62 250.0
78 TraesCS6D01G149300 chr2D 90.110 182 15 2 1510 1688 189371351 189371532 2.790000e-57 233.0
79 TraesCS6D01G149300 chr2D 89.714 175 13 3 1512 1682 189373812 189373985 7.810000e-53 219.0
80 TraesCS6D01G149300 chr2A 83.221 298 29 9 176 453 14766375 14766671 2.140000e-63 254.0
81 TraesCS6D01G149300 chr5A 92.090 177 14 0 2 178 333451041 333451217 2.770000e-62 250.0
82 TraesCS6D01G149300 chrUn 91.573 178 15 0 1 178 89715698 89715875 3.580000e-61 246.0
83 TraesCS6D01G149300 chrUn 87.069 116 9 5 1572 1681 38444289 38444404 4.870000e-25 126.0
84 TraesCS6D01G149300 chrUn 86.207 116 10 5 1572 1681 41912428 41912313 2.270000e-23 121.0
85 TraesCS6D01G149300 chrUn 86.869 99 8 4 1587 1681 307325442 307325539 6.350000e-19 106.0
86 TraesCS6D01G149300 chr7A 90.698 172 14 1 1512 1681 566986209 566986380 1.300000e-55 228.0
87 TraesCS6D01G149300 chr7A 79.805 307 32 19 176 453 46960456 46960761 3.660000e-46 196.0
88 TraesCS6D01G149300 chr7A 82.203 236 23 10 241 458 47496945 47496711 7.920000e-43 185.0
89 TraesCS6D01G149300 chr7A 89.600 125 11 2 1202 1325 164652602 164652479 1.730000e-34 158.0
90 TraesCS6D01G149300 chr3A 84.513 226 18 8 244 453 59477548 59477324 1.690000e-49 207.0
91 TraesCS6D01G149300 chr7B 80.786 229 27 12 241 453 647788653 647788426 3.710000e-36 163.0
92 TraesCS6D01G149300 chr7B 89.516 124 11 2 1202 1324 125598690 125598568 6.210000e-34 156.0


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 TraesCS6D01G149300 chr6D 123055501 123060137 4636 False 8564.000000 8564 100.000000 1 4637 1 chr6D.!!$F5 4636
1 TraesCS6D01G149300 chr6D 119108367 119109143 776 True 937.000000 937 88.432000 3816 4593 1 chr6D.!!$R1 777
2 TraesCS6D01G149300 chr6D 296755818 296756619 801 False 765.000000 765 83.911000 3815 4621 1 chr6D.!!$F6 806
3 TraesCS6D01G149300 chr6D 164815413 164821023 5610 True 216.000000 246 89.039667 1512 1690 3 chr6D.!!$R3 178
4 TraesCS6D01G149300 chr6B 348825468 348826282 814 False 1013.000000 1013 89.080000 3816 4630 1 chr6B.!!$F1 814
5 TraesCS6D01G149300 chr6B 216688473 216693031 4558 False 784.428571 2278 94.443571 176 3814 7 chr6B.!!$F3 3638
6 TraesCS6D01G149300 chr6A 158072614 158076131 3517 True 953.180000 1755 95.730200 329 3820 5 chr6A.!!$R3 3491
7 TraesCS6D01G149300 chr6A 602622016 602622836 820 True 926.000000 926 87.015000 3815 4637 1 chr6A.!!$R2 822
8 TraesCS6D01G149300 chr6A 507662272 507662911 639 False 872.000000 872 91.250000 3816 4455 1 chr6A.!!$F1 639
9 TraesCS6D01G149300 chr1A 220714679 220715494 815 False 1203.000000 1203 93.260000 3815 4630 1 chr1A.!!$F1 815
10 TraesCS6D01G149300 chr1A 306104032 306104845 813 True 915.000000 915 86.893000 3814 4637 1 chr1A.!!$R1 823
11 TraesCS6D01G149300 chr1A 575250488 575254061 3573 False 204.500000 207 81.666500 204 453 2 chr1A.!!$F3 249
12 TraesCS6D01G149300 chr3B 776543129 776543929 800 True 1179.000000 1179 93.267000 3815 4614 1 chr3B.!!$R2 799
13 TraesCS6D01G149300 chr3B 694266168 694266993 825 True 1027.000000 1027 89.117000 3810 4636 1 chr3B.!!$R1 826
14 TraesCS6D01G149300 chr1D 50914483 50915303 820 True 1146.000000 1146 91.839000 3817 4637 1 chr1D.!!$R2 820
15 TraesCS6D01G149300 chr4D 103256354 103257164 810 False 1055.000000 1055 90.036000 3815 4637 1 chr4D.!!$F1 822
16 TraesCS6D01G149300 chr3D 345519481 345520292 811 False 774.000000 774 83.887000 3815 4627 1 chr3D.!!$F2 812
17 TraesCS6D01G149300 chr7D 467763000 467763810 810 True 617.000000 617 80.443000 3816 4627 1 chr7D.!!$R2 811
18 TraesCS6D01G149300 chr5D 486815083 486817670 2587 False 235.000000 246 91.187500 1512 1694 2 chr5D.!!$F1 182
19 TraesCS6D01G149300 chr2D 189371351 189373985 2634 False 226.000000 233 89.912000 1510 1688 2 chr2D.!!$F2 178

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
127 128 0.034896 AAGCGTACTGTCCCAACCTG 59.965 55.000 0.00 0.0 0.00 4.00 F
390 403 0.323302 TCCACTGCCTTGCACGAATA 59.677 50.000 0.00 0.0 33.79 1.75 F
1514 2546 0.034574 TTGGCCACATCCGCTAATGT 60.035 50.000 3.88 0.0 40.49 2.71 F
1515 2547 0.034574 TGGCCACATCCGCTAATGTT 60.035 50.000 0.00 0.0 37.78 2.71 F
1516 2548 1.210722 TGGCCACATCCGCTAATGTTA 59.789 47.619 0.00 0.0 37.78 2.41 F
1599 2631 1.360393 AAGGTGTCCTGCCCTCCAAA 61.360 55.000 0.00 0.0 32.13 3.28 F
1711 2922 1.611936 GCACCAAACCTCTCTCCCTTC 60.612 57.143 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 2510 0.524862 CCAATCAACTCTGCTGGCAC 59.475 55.000 0.00 0.00 0.00 5.01 R
2284 4118 1.487976 TCACTCCCATGCATTCCTCTC 59.512 52.381 0.00 0.00 0.00 3.20 R
2342 4176 1.772063 CGCCCCTAAATAGCACGTGC 61.772 60.000 32.79 32.79 42.49 5.34 R
2958 5281 3.423539 AGTCCTCTGCATTGCTTTACA 57.576 42.857 10.49 0.00 0.00 2.41 R
3444 5768 3.813724 AGAAACGGAAAACTTAGCAGGAC 59.186 43.478 0.00 0.00 0.00 3.85 R
3576 5900 3.380004 CCAGCTTTACAAACACACTTCCA 59.620 43.478 0.00 0.00 0.00 3.53 R
3655 5979 4.341235 GTGTTCCCCTAATTATTTCAGCCC 59.659 45.833 0.00 0.00 0.00 5.19 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
27 28 2.511600 GGGGCGTCCGTGATGAAG 60.512 66.667 0.00 0.00 0.00 3.02
28 29 2.577059 GGGCGTCCGTGATGAAGA 59.423 61.111 0.00 0.00 0.00 2.87
29 30 1.079405 GGGCGTCCGTGATGAAGAA 60.079 57.895 0.00 0.00 0.00 2.52
30 31 1.084370 GGGCGTCCGTGATGAAGAAG 61.084 60.000 0.00 0.00 0.00 2.85
31 32 0.389948 GGCGTCCGTGATGAAGAAGT 60.390 55.000 0.00 0.00 0.00 3.01
32 33 0.992802 GCGTCCGTGATGAAGAAGTC 59.007 55.000 0.00 0.00 0.00 3.01
33 34 1.668919 GCGTCCGTGATGAAGAAGTCA 60.669 52.381 0.00 0.00 41.67 3.41
34 35 2.254459 CGTCCGTGATGAAGAAGTCAG 58.746 52.381 0.00 0.00 40.43 3.51
35 36 2.351835 CGTCCGTGATGAAGAAGTCAGT 60.352 50.000 0.00 0.00 40.43 3.41
36 37 3.119955 CGTCCGTGATGAAGAAGTCAGTA 60.120 47.826 0.00 0.00 40.43 2.74
37 38 4.416620 GTCCGTGATGAAGAAGTCAGTAG 58.583 47.826 0.00 0.00 40.43 2.57
38 39 4.079970 TCCGTGATGAAGAAGTCAGTAGT 58.920 43.478 0.00 0.00 40.43 2.73
39 40 4.156190 TCCGTGATGAAGAAGTCAGTAGTC 59.844 45.833 0.00 0.00 40.43 2.59
40 41 4.092120 CGTGATGAAGAAGTCAGTAGTCG 58.908 47.826 0.00 0.00 40.43 4.18
41 42 3.854809 GTGATGAAGAAGTCAGTAGTCGC 59.145 47.826 0.00 0.00 40.43 5.19
42 43 2.613730 TGAAGAAGTCAGTAGTCGCG 57.386 50.000 0.00 0.00 0.00 5.87
43 44 1.878088 TGAAGAAGTCAGTAGTCGCGT 59.122 47.619 5.77 0.00 0.00 6.01
44 45 2.243407 GAAGAAGTCAGTAGTCGCGTG 58.757 52.381 5.77 0.00 0.00 5.34
45 46 0.522180 AGAAGTCAGTAGTCGCGTGG 59.478 55.000 5.77 0.00 0.00 4.94
46 47 0.520404 GAAGTCAGTAGTCGCGTGGA 59.480 55.000 5.77 0.00 0.00 4.02
47 48 0.522180 AAGTCAGTAGTCGCGTGGAG 59.478 55.000 5.77 0.00 0.00 3.86
48 49 1.514443 GTCAGTAGTCGCGTGGAGC 60.514 63.158 5.77 0.00 43.95 4.70
58 59 4.323477 CGTGGAGCGGTCCCCAAA 62.323 66.667 29.73 9.36 43.15 3.28
59 60 2.114411 GTGGAGCGGTCCCCAAAA 59.886 61.111 29.73 8.95 43.15 2.44
60 61 1.529713 GTGGAGCGGTCCCCAAAAA 60.530 57.895 29.73 8.15 43.15 1.94
61 62 1.529713 TGGAGCGGTCCCCAAAAAC 60.530 57.895 29.73 3.74 43.15 2.43
62 63 2.273179 GGAGCGGTCCCCAAAAACC 61.273 63.158 23.28 0.00 36.76 3.27
63 64 1.228459 GAGCGGTCCCCAAAAACCT 60.228 57.895 2.39 0.00 33.14 3.50
64 65 0.826256 GAGCGGTCCCCAAAAACCTT 60.826 55.000 2.39 0.00 33.14 3.50
65 66 0.479378 AGCGGTCCCCAAAAACCTTA 59.521 50.000 0.00 0.00 33.14 2.69
66 67 1.076513 AGCGGTCCCCAAAAACCTTAT 59.923 47.619 0.00 0.00 33.14 1.73
67 68 1.475280 GCGGTCCCCAAAAACCTTATC 59.525 52.381 0.00 0.00 33.14 1.75
68 69 2.797786 CGGTCCCCAAAAACCTTATCA 58.202 47.619 0.00 0.00 33.14 2.15
69 70 2.490509 CGGTCCCCAAAAACCTTATCAC 59.509 50.000 0.00 0.00 33.14 3.06
70 71 2.829720 GGTCCCCAAAAACCTTATCACC 59.170 50.000 0.00 0.00 32.54 4.02
71 72 2.829720 GTCCCCAAAAACCTTATCACCC 59.170 50.000 0.00 0.00 0.00 4.61
72 73 2.725227 TCCCCAAAAACCTTATCACCCT 59.275 45.455 0.00 0.00 0.00 4.34
73 74 3.143168 TCCCCAAAAACCTTATCACCCTT 59.857 43.478 0.00 0.00 0.00 3.95
74 75 3.513912 CCCCAAAAACCTTATCACCCTTC 59.486 47.826 0.00 0.00 0.00 3.46
75 76 4.416516 CCCAAAAACCTTATCACCCTTCT 58.583 43.478 0.00 0.00 0.00 2.85
76 77 4.462834 CCCAAAAACCTTATCACCCTTCTC 59.537 45.833 0.00 0.00 0.00 2.87
77 78 4.462834 CCAAAAACCTTATCACCCTTCTCC 59.537 45.833 0.00 0.00 0.00 3.71
78 79 4.317530 AAAACCTTATCACCCTTCTCCC 57.682 45.455 0.00 0.00 0.00 4.30
79 80 1.497161 ACCTTATCACCCTTCTCCCG 58.503 55.000 0.00 0.00 0.00 5.14
80 81 1.273666 ACCTTATCACCCTTCTCCCGT 60.274 52.381 0.00 0.00 0.00 5.28
81 82 2.023695 ACCTTATCACCCTTCTCCCGTA 60.024 50.000 0.00 0.00 0.00 4.02
82 83 2.364647 CCTTATCACCCTTCTCCCGTAC 59.635 54.545 0.00 0.00 0.00 3.67
83 84 2.832643 TATCACCCTTCTCCCGTACA 57.167 50.000 0.00 0.00 0.00 2.90
84 85 1.486211 ATCACCCTTCTCCCGTACAG 58.514 55.000 0.00 0.00 0.00 2.74
85 86 0.613853 TCACCCTTCTCCCGTACAGG 60.614 60.000 0.00 0.00 40.63 4.00
86 87 0.613853 CACCCTTCTCCCGTACAGGA 60.614 60.000 0.00 0.00 45.00 3.86
87 88 0.614134 ACCCTTCTCCCGTACAGGAC 60.614 60.000 0.00 0.00 45.00 3.85
88 89 0.324460 CCCTTCTCCCGTACAGGACT 60.324 60.000 0.00 0.00 45.00 3.85
89 90 1.104630 CCTTCTCCCGTACAGGACTC 58.895 60.000 0.00 0.00 45.00 3.36
90 91 1.616187 CCTTCTCCCGTACAGGACTCA 60.616 57.143 0.00 0.00 45.00 3.41
91 92 2.168496 CTTCTCCCGTACAGGACTCAA 58.832 52.381 0.00 0.00 45.00 3.02
92 93 2.297698 TCTCCCGTACAGGACTCAAA 57.702 50.000 0.00 0.00 45.00 2.69
93 94 2.168496 TCTCCCGTACAGGACTCAAAG 58.832 52.381 0.00 0.00 45.00 2.77
94 95 1.893801 CTCCCGTACAGGACTCAAAGT 59.106 52.381 0.00 0.00 45.00 2.66
95 96 1.616865 TCCCGTACAGGACTCAAAGTG 59.383 52.381 0.00 0.00 45.00 3.16
96 97 1.337823 CCCGTACAGGACTCAAAGTGG 60.338 57.143 5.46 0.00 45.00 4.00
97 98 1.343465 CCGTACAGGACTCAAAGTGGT 59.657 52.381 0.00 0.00 45.00 4.16
98 99 2.404215 CGTACAGGACTCAAAGTGGTG 58.596 52.381 0.00 0.00 0.00 4.17
99 100 2.767505 GTACAGGACTCAAAGTGGTGG 58.232 52.381 0.00 0.00 0.00 4.61
100 101 0.474184 ACAGGACTCAAAGTGGTGGG 59.526 55.000 0.00 0.00 0.00 4.61
101 102 0.250901 CAGGACTCAAAGTGGTGGGG 60.251 60.000 0.00 0.00 0.00 4.96
102 103 0.697854 AGGACTCAAAGTGGTGGGGT 60.698 55.000 0.00 0.00 0.00 4.95
103 104 0.185175 GGACTCAAAGTGGTGGGGTT 59.815 55.000 0.00 0.00 0.00 4.11
104 105 1.411074 GGACTCAAAGTGGTGGGGTTT 60.411 52.381 0.00 0.00 0.00 3.27
105 106 1.954382 GACTCAAAGTGGTGGGGTTTC 59.046 52.381 0.00 0.00 0.00 2.78
106 107 0.951558 CTCAAAGTGGTGGGGTTTCG 59.048 55.000 0.00 0.00 0.00 3.46
107 108 0.466555 TCAAAGTGGTGGGGTTTCGG 60.467 55.000 0.00 0.00 0.00 4.30
108 109 0.466555 CAAAGTGGTGGGGTTTCGGA 60.467 55.000 0.00 0.00 0.00 4.55
109 110 0.259356 AAAGTGGTGGGGTTTCGGAA 59.741 50.000 0.00 0.00 0.00 4.30
110 111 0.179001 AAGTGGTGGGGTTTCGGAAG 60.179 55.000 0.00 0.00 0.00 3.46
111 112 2.114411 TGGTGGGGTTTCGGAAGC 59.886 61.111 0.00 0.00 0.00 3.86
112 113 3.053896 GGTGGGGTTTCGGAAGCG 61.054 66.667 0.00 0.00 34.11 4.68
113 114 2.281276 GTGGGGTTTCGGAAGCGT 60.281 61.111 0.00 0.00 34.11 5.07
114 115 1.004679 GTGGGGTTTCGGAAGCGTA 60.005 57.895 0.00 0.00 34.11 4.42
115 116 1.004679 TGGGGTTTCGGAAGCGTAC 60.005 57.895 0.00 0.00 34.11 3.67
116 117 1.294459 GGGGTTTCGGAAGCGTACT 59.706 57.895 0.00 0.00 34.11 2.73
117 118 1.017701 GGGGTTTCGGAAGCGTACTG 61.018 60.000 0.00 0.00 34.11 2.74
118 119 0.320160 GGGTTTCGGAAGCGTACTGT 60.320 55.000 0.00 0.00 34.11 3.55
119 120 1.066136 GGTTTCGGAAGCGTACTGTC 58.934 55.000 0.00 0.00 0.00 3.51
120 121 1.066136 GTTTCGGAAGCGTACTGTCC 58.934 55.000 0.00 0.00 0.00 4.02
121 122 0.037975 TTTCGGAAGCGTACTGTCCC 60.038 55.000 0.00 0.00 0.00 4.46
122 123 1.180456 TTCGGAAGCGTACTGTCCCA 61.180 55.000 0.00 0.00 0.00 4.37
123 124 1.180456 TCGGAAGCGTACTGTCCCAA 61.180 55.000 0.00 0.00 0.00 4.12
124 125 1.012486 CGGAAGCGTACTGTCCCAAC 61.012 60.000 0.00 0.00 0.00 3.77
125 126 0.672711 GGAAGCGTACTGTCCCAACC 60.673 60.000 0.00 0.00 0.00 3.77
126 127 0.320697 GAAGCGTACTGTCCCAACCT 59.679 55.000 0.00 0.00 0.00 3.50
127 128 0.034896 AAGCGTACTGTCCCAACCTG 59.965 55.000 0.00 0.00 0.00 4.00
128 129 2.033194 GCGTACTGTCCCAACCTGC 61.033 63.158 0.00 0.00 0.00 4.85
129 130 1.736645 CGTACTGTCCCAACCTGCG 60.737 63.158 0.00 0.00 0.00 5.18
130 131 1.375523 GTACTGTCCCAACCTGCGG 60.376 63.158 0.00 0.00 0.00 5.69
131 132 1.839747 TACTGTCCCAACCTGCGGT 60.840 57.895 0.00 0.00 37.65 5.68
132 133 2.107041 TACTGTCCCAACCTGCGGTG 62.107 60.000 0.94 0.00 35.34 4.94
133 134 4.947147 TGTCCCAACCTGCGGTGC 62.947 66.667 0.94 0.00 35.34 5.01
134 135 4.947147 GTCCCAACCTGCGGTGCA 62.947 66.667 0.94 0.00 35.34 4.57
135 136 4.947147 TCCCAACCTGCGGTGCAC 62.947 66.667 8.80 8.80 35.34 4.57
137 138 3.964875 CCAACCTGCGGTGCACAC 61.965 66.667 20.43 10.78 35.34 3.82
147 148 2.723746 GTGCACACCACAAGCCAG 59.276 61.111 13.17 0.00 44.06 4.85
148 149 2.519063 TGCACACCACAAGCCAGG 60.519 61.111 0.00 0.00 0.00 4.45
149 150 2.203337 GCACACCACAAGCCAGGA 60.203 61.111 0.00 0.00 0.00 3.86
150 151 1.604593 GCACACCACAAGCCAGGAT 60.605 57.895 0.00 0.00 0.00 3.24
151 152 1.870055 GCACACCACAAGCCAGGATG 61.870 60.000 0.00 0.00 0.00 3.51
165 166 3.296322 CAGGATGGAGAAGATCGTAGC 57.704 52.381 0.00 0.00 0.00 3.58
166 167 2.625314 CAGGATGGAGAAGATCGTAGCA 59.375 50.000 0.00 0.00 0.00 3.49
167 168 2.890311 AGGATGGAGAAGATCGTAGCAG 59.110 50.000 0.00 0.00 0.00 4.24
168 169 2.625790 GGATGGAGAAGATCGTAGCAGT 59.374 50.000 0.00 0.00 0.00 4.40
169 170 3.821600 GGATGGAGAAGATCGTAGCAGTA 59.178 47.826 0.00 0.00 0.00 2.74
170 171 4.083003 GGATGGAGAAGATCGTAGCAGTAG 60.083 50.000 0.00 0.00 0.00 2.57
171 172 2.619177 TGGAGAAGATCGTAGCAGTAGC 59.381 50.000 0.00 0.00 42.56 3.58
192 193 3.692576 CTCAGTGACCTTTCGTATACCG 58.307 50.000 0.00 0.00 38.13 4.02
235 236 1.077787 ATCGGCTCATTCCCGCAAA 60.078 52.632 0.00 0.00 45.19 3.68
238 239 1.976474 GGCTCATTCCCGCAAACCA 60.976 57.895 0.00 0.00 0.00 3.67
239 240 1.531739 GGCTCATTCCCGCAAACCAA 61.532 55.000 0.00 0.00 0.00 3.67
249 255 2.668212 CAAACCAAGGCGAGGCGA 60.668 61.111 0.00 0.00 0.00 5.54
301 309 6.463472 CCCTCTTGTTCTCATGCTCATACATA 60.463 42.308 0.00 0.00 0.00 2.29
304 312 7.729116 TCTTGTTCTCATGCTCATACATATGA 58.271 34.615 10.38 1.75 40.19 2.15
353 361 3.191371 CCAACTCCCATCAAACTAGCAAC 59.809 47.826 0.00 0.00 0.00 4.17
355 363 1.398390 CTCCCATCAAACTAGCAACGC 59.602 52.381 0.00 0.00 0.00 4.84
390 403 0.323302 TCCACTGCCTTGCACGAATA 59.677 50.000 0.00 0.00 33.79 1.75
396 409 2.397751 CCTTGCACGAATAGGCTGG 58.602 57.895 0.00 0.00 0.00 4.85
439 459 3.054139 TCTGAAACTGCTATTGGGCTGAT 60.054 43.478 0.00 0.00 35.59 2.90
577 1543 5.239525 CCCGCTTAGATTATTTTTCTCCAGG 59.760 44.000 0.00 0.00 0.00 4.45
583 1549 6.956202 AGATTATTTTTCTCCAGGCTCATG 57.044 37.500 0.00 0.00 0.00 3.07
626 1593 5.359009 CACCTGCTGGTAATTCAAGATTGAT 59.641 40.000 15.70 0.00 46.60 2.57
627 1594 5.954150 ACCTGCTGGTAATTCAAGATTGATT 59.046 36.000 14.47 0.00 46.43 2.57
829 1850 2.625823 CCGCATCCGCCAACAAAGT 61.626 57.895 0.00 0.00 33.11 2.66
961 1983 0.668535 CACACTCTCAGTCACACGGA 59.331 55.000 0.00 0.00 0.00 4.69
1011 2036 4.950062 GCAGCGATGGCGATCCGA 62.950 66.667 1.46 0.00 46.35 4.55
1095 2120 1.600023 TGTTTGGCGGTAAGTCTTGG 58.400 50.000 0.00 0.00 0.00 3.61
1106 2131 1.442769 AAGTCTTGGTACATGCTGCG 58.557 50.000 0.00 0.00 39.30 5.18
1107 2132 0.608130 AGTCTTGGTACATGCTGCGA 59.392 50.000 0.00 0.00 39.30 5.10
1114 2139 1.599542 GGTACATGCTGCGATTTCCTC 59.400 52.381 0.00 0.00 0.00 3.71
1123 2148 7.661437 ACATGCTGCGATTTCCTCTATTATTTA 59.339 33.333 0.00 0.00 0.00 1.40
1166 2194 9.768662 ATTGCAAACTTTTCTGTAATTTCTCAT 57.231 25.926 1.71 0.00 0.00 2.90
1324 2354 5.782893 TCGGAAACATTTGAAGGTGATTT 57.217 34.783 0.00 0.00 0.00 2.17
1440 2471 7.798596 TCATGGATAAAAGAGAAGCTCAATC 57.201 36.000 0.00 0.00 32.06 2.67
1479 2510 6.868622 AGCTACAGAGTACAAATTAGTCCAG 58.131 40.000 0.00 0.00 0.00 3.86
1508 2540 1.139520 GTTGATTGGCCACATCCGC 59.860 57.895 3.88 4.29 0.00 5.54
1509 2541 1.001020 TTGATTGGCCACATCCGCT 60.001 52.632 3.88 0.00 0.00 5.52
1510 2542 0.254462 TTGATTGGCCACATCCGCTA 59.746 50.000 3.88 0.00 0.00 4.26
1511 2543 0.254462 TGATTGGCCACATCCGCTAA 59.746 50.000 3.88 0.00 0.00 3.09
1512 2544 1.133823 TGATTGGCCACATCCGCTAAT 60.134 47.619 3.88 0.00 39.77 1.73
1513 2545 1.267806 GATTGGCCACATCCGCTAATG 59.732 52.381 3.88 0.00 37.52 1.90
1514 2546 0.034574 TTGGCCACATCCGCTAATGT 60.035 50.000 3.88 0.00 40.49 2.71
1515 2547 0.034574 TGGCCACATCCGCTAATGTT 60.035 50.000 0.00 0.00 37.78 2.71
1516 2548 1.210722 TGGCCACATCCGCTAATGTTA 59.789 47.619 0.00 0.00 37.78 2.41
1521 2553 4.051922 CCACATCCGCTAATGTTAGAGAC 58.948 47.826 4.03 0.00 37.78 3.36
1570 2602 9.929180 CGGGATTAGATAGAGTTATTTTCATCA 57.071 33.333 0.00 0.00 0.00 3.07
1588 2620 7.531857 TTCATCATATCTCTAGAAGGTGTCC 57.468 40.000 0.00 0.00 0.00 4.02
1599 2631 1.360393 AAGGTGTCCTGCCCTCCAAA 61.360 55.000 0.00 0.00 32.13 3.28
1643 2675 4.336889 CCCTCGAGGCTCAATAATACAA 57.663 45.455 26.87 0.00 0.00 2.41
1659 2765 8.998377 CAATAATACAACCATCATATTCCGTCA 58.002 33.333 0.00 0.00 0.00 4.35
1663 2769 4.821805 ACAACCATCATATTCCGTCAATCC 59.178 41.667 0.00 0.00 0.00 3.01
1670 2776 4.901849 TCATATTCCGTCAATCCCTCTCTT 59.098 41.667 0.00 0.00 0.00 2.85
1675 2781 2.237392 CCGTCAATCCCTCTCTTCCTTT 59.763 50.000 0.00 0.00 0.00 3.11
1700 2807 2.489938 TGGTATCAGAGCACCAAACC 57.510 50.000 4.48 0.00 41.83 3.27
1701 2808 1.985159 TGGTATCAGAGCACCAAACCT 59.015 47.619 4.48 0.00 41.83 3.50
1702 2809 2.027192 TGGTATCAGAGCACCAAACCTC 60.027 50.000 4.48 0.00 41.83 3.85
1703 2810 2.237392 GGTATCAGAGCACCAAACCTCT 59.763 50.000 0.00 0.00 38.91 3.69
1704 2811 2.777832 ATCAGAGCACCAAACCTCTC 57.222 50.000 0.00 0.00 36.33 3.20
1705 2812 1.722034 TCAGAGCACCAAACCTCTCT 58.278 50.000 0.00 0.00 36.33 3.10
1706 2813 1.620819 TCAGAGCACCAAACCTCTCTC 59.379 52.381 0.00 0.00 36.33 3.20
1711 2922 1.611936 GCACCAAACCTCTCTCCCTTC 60.612 57.143 0.00 0.00 0.00 3.46
1717 2928 4.323104 CCAAACCTCTCTCCCTTCTAACAG 60.323 50.000 0.00 0.00 0.00 3.16
1734 2945 6.936279 TCTAACAGCTAAGTAATTGCACTCT 58.064 36.000 0.00 0.00 31.68 3.24
2073 3902 8.055402 GCAATTGGTTTTAATGTTACATATGCG 58.945 33.333 7.72 0.00 0.00 4.73
2418 4281 2.092323 GGTATTTGGCTGTCTGAACCC 58.908 52.381 0.00 0.00 0.00 4.11
2457 4493 2.094762 ACCCATTAACTCACGACTGC 57.905 50.000 0.00 0.00 0.00 4.40
2536 4572 4.142138 ACACGCAAATTTTAAGTGAACCCA 60.142 37.500 18.58 0.00 36.71 4.51
2544 4580 9.065798 CAAATTTTAAGTGAACCCAATGGAAAT 57.934 29.630 0.00 0.00 34.81 2.17
2545 4581 9.639563 AAATTTTAAGTGAACCCAATGGAAATT 57.360 25.926 0.00 0.00 32.35 1.82
2587 4623 8.290325 TCTTCGTGCTACTTATGTACATATCAG 58.710 37.037 16.16 13.51 0.00 2.90
2606 4642 6.590234 ATCAGGTGAACCAAGGAAAATAAC 57.410 37.500 1.62 0.00 38.89 1.89
2673 4709 9.177304 CTTTTTAAACTTTAGAAATCGTCCCAC 57.823 33.333 0.00 0.00 0.00 4.61
2958 5281 3.434167 GGGATGTCACATATCCAACAGCT 60.434 47.826 0.00 0.00 44.77 4.24
3011 5334 8.613482 GCTCTTCCTTTGTAACTTGGATATAAC 58.387 37.037 0.00 0.00 0.00 1.89
3219 5542 5.068198 CCAGATGGTTTGACATATTTGGAGG 59.932 44.000 0.00 0.00 32.78 4.30
3444 5768 9.788960 GCAAAAGAGTTAGTTAAGATTATTGGG 57.211 33.333 0.00 0.00 0.00 4.12
3459 5783 6.603599 AGATTATTGGGTCCTGCTAAGTTTTC 59.396 38.462 0.00 0.00 0.00 2.29
3576 5900 4.190001 ACGATGCGAGAGGTATATACGAT 58.810 43.478 6.79 0.00 0.00 3.73
3655 5979 6.239908 TGTAATAGAGTGCAACATGTTGTG 57.760 37.500 33.01 15.77 42.31 3.33
3656 5980 4.771590 AATAGAGTGCAACATGTTGTGG 57.228 40.909 33.01 14.16 42.31 4.17
3876 7427 6.531503 TGATAGGAGAAGAGTTTGTACAGG 57.468 41.667 0.00 0.00 0.00 4.00
3891 7442 6.381498 TTGTACAGGATGGGATTACAAGAA 57.619 37.500 0.00 0.00 43.62 2.52
4107 7829 2.349817 CGTCAAAGATGCAAGCGTTCTT 60.350 45.455 0.00 0.00 0.00 2.52
4128 7850 4.929807 CTTCCAAAGCCACCAGGT 57.070 55.556 0.00 0.00 37.19 4.00
4299 8023 1.919600 GAGAAGGAGCAGCCCACCAT 61.920 60.000 3.08 0.00 37.37 3.55
4326 8050 3.509967 TGTTGCATCGTCTCTTCTTCCTA 59.490 43.478 0.00 0.00 0.00 2.94
4417 8141 3.048563 TTGCAAGGCAAGCCACATA 57.951 47.368 14.40 0.00 43.99 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.511600 CTTCATCACGGACGCCCC 60.512 66.667 0.00 0.00 0.00 5.80
11 12 1.079405 TTCTTCATCACGGACGCCC 60.079 57.895 0.00 0.00 0.00 6.13
12 13 0.389948 ACTTCTTCATCACGGACGCC 60.390 55.000 0.00 0.00 0.00 5.68
13 14 0.992802 GACTTCTTCATCACGGACGC 59.007 55.000 0.00 0.00 0.00 5.19
14 15 2.254459 CTGACTTCTTCATCACGGACG 58.746 52.381 0.00 0.00 32.17 4.79
15 16 3.305398 ACTGACTTCTTCATCACGGAC 57.695 47.619 0.00 0.00 32.17 4.79
17 18 4.416620 GACTACTGACTTCTTCATCACGG 58.583 47.826 0.00 0.00 32.17 4.94
18 19 4.092120 CGACTACTGACTTCTTCATCACG 58.908 47.826 0.00 0.00 32.17 4.35
19 20 3.854809 GCGACTACTGACTTCTTCATCAC 59.145 47.826 0.00 0.00 32.17 3.06
20 21 3.426292 CGCGACTACTGACTTCTTCATCA 60.426 47.826 0.00 0.00 32.17 3.07
21 22 3.102276 CGCGACTACTGACTTCTTCATC 58.898 50.000 0.00 0.00 32.17 2.92
22 23 2.488545 ACGCGACTACTGACTTCTTCAT 59.511 45.455 15.93 0.00 32.17 2.57
23 24 1.878088 ACGCGACTACTGACTTCTTCA 59.122 47.619 15.93 0.00 0.00 3.02
24 25 2.243407 CACGCGACTACTGACTTCTTC 58.757 52.381 15.93 0.00 0.00 2.87
25 26 1.068472 CCACGCGACTACTGACTTCTT 60.068 52.381 15.93 0.00 0.00 2.52
26 27 0.522180 CCACGCGACTACTGACTTCT 59.478 55.000 15.93 0.00 0.00 2.85
27 28 0.520404 TCCACGCGACTACTGACTTC 59.480 55.000 15.93 0.00 0.00 3.01
28 29 0.522180 CTCCACGCGACTACTGACTT 59.478 55.000 15.93 0.00 0.00 3.01
29 30 1.924320 GCTCCACGCGACTACTGACT 61.924 60.000 15.93 0.00 0.00 3.41
30 31 1.514443 GCTCCACGCGACTACTGAC 60.514 63.158 15.93 0.00 0.00 3.51
31 32 2.875485 GCTCCACGCGACTACTGA 59.125 61.111 15.93 0.00 0.00 3.41
50 51 2.829720 GGGTGATAAGGTTTTTGGGGAC 59.170 50.000 0.00 0.00 0.00 4.46
51 52 2.725227 AGGGTGATAAGGTTTTTGGGGA 59.275 45.455 0.00 0.00 0.00 4.81
52 53 3.184382 AGGGTGATAAGGTTTTTGGGG 57.816 47.619 0.00 0.00 0.00 4.96
53 54 4.416516 AGAAGGGTGATAAGGTTTTTGGG 58.583 43.478 0.00 0.00 0.00 4.12
54 55 4.462834 GGAGAAGGGTGATAAGGTTTTTGG 59.537 45.833 0.00 0.00 0.00 3.28
55 56 4.462834 GGGAGAAGGGTGATAAGGTTTTTG 59.537 45.833 0.00 0.00 0.00 2.44
56 57 4.673968 GGGAGAAGGGTGATAAGGTTTTT 58.326 43.478 0.00 0.00 0.00 1.94
57 58 3.308188 CGGGAGAAGGGTGATAAGGTTTT 60.308 47.826 0.00 0.00 0.00 2.43
58 59 2.238898 CGGGAGAAGGGTGATAAGGTTT 59.761 50.000 0.00 0.00 0.00 3.27
59 60 1.838077 CGGGAGAAGGGTGATAAGGTT 59.162 52.381 0.00 0.00 0.00 3.50
60 61 1.273666 ACGGGAGAAGGGTGATAAGGT 60.274 52.381 0.00 0.00 0.00 3.50
61 62 1.497161 ACGGGAGAAGGGTGATAAGG 58.503 55.000 0.00 0.00 0.00 2.69
62 63 3.028850 TGTACGGGAGAAGGGTGATAAG 58.971 50.000 0.00 0.00 0.00 1.73
63 64 3.028850 CTGTACGGGAGAAGGGTGATAA 58.971 50.000 0.00 0.00 0.00 1.75
64 65 2.662866 CTGTACGGGAGAAGGGTGATA 58.337 52.381 0.00 0.00 0.00 2.15
65 66 1.486211 CTGTACGGGAGAAGGGTGAT 58.514 55.000 0.00 0.00 0.00 3.06
66 67 0.613853 CCTGTACGGGAGAAGGGTGA 60.614 60.000 16.40 0.00 0.00 4.02
67 68 0.613853 TCCTGTACGGGAGAAGGGTG 60.614 60.000 20.03 0.00 32.16 4.61
68 69 0.614134 GTCCTGTACGGGAGAAGGGT 60.614 60.000 24.28 0.00 35.87 4.34
69 70 0.324460 AGTCCTGTACGGGAGAAGGG 60.324 60.000 24.28 0.00 35.87 3.95
70 71 1.104630 GAGTCCTGTACGGGAGAAGG 58.895 60.000 24.28 5.98 35.87 3.46
71 72 1.835494 TGAGTCCTGTACGGGAGAAG 58.165 55.000 24.28 0.00 35.87 2.85
72 73 2.297698 TTGAGTCCTGTACGGGAGAA 57.702 50.000 24.28 13.72 35.87 2.87
73 74 2.168496 CTTTGAGTCCTGTACGGGAGA 58.832 52.381 24.28 8.24 35.87 3.71
74 75 1.893801 ACTTTGAGTCCTGTACGGGAG 59.106 52.381 24.28 13.24 35.87 4.30
75 76 1.616865 CACTTTGAGTCCTGTACGGGA 59.383 52.381 20.03 20.03 0.00 5.14
76 77 1.337823 CCACTTTGAGTCCTGTACGGG 60.338 57.143 15.21 15.21 0.00 5.28
77 78 1.343465 ACCACTTTGAGTCCTGTACGG 59.657 52.381 0.00 0.00 0.00 4.02
78 79 2.404215 CACCACTTTGAGTCCTGTACG 58.596 52.381 0.00 0.00 0.00 3.67
79 80 2.550208 CCCACCACTTTGAGTCCTGTAC 60.550 54.545 0.00 0.00 0.00 2.90
80 81 1.697432 CCCACCACTTTGAGTCCTGTA 59.303 52.381 0.00 0.00 0.00 2.74
81 82 0.474184 CCCACCACTTTGAGTCCTGT 59.526 55.000 0.00 0.00 0.00 4.00
82 83 0.250901 CCCCACCACTTTGAGTCCTG 60.251 60.000 0.00 0.00 0.00 3.86
83 84 0.697854 ACCCCACCACTTTGAGTCCT 60.698 55.000 0.00 0.00 0.00 3.85
84 85 0.185175 AACCCCACCACTTTGAGTCC 59.815 55.000 0.00 0.00 0.00 3.85
85 86 1.954382 GAAACCCCACCACTTTGAGTC 59.046 52.381 0.00 0.00 0.00 3.36
86 87 1.749286 CGAAACCCCACCACTTTGAGT 60.749 52.381 0.00 0.00 0.00 3.41
87 88 0.951558 CGAAACCCCACCACTTTGAG 59.048 55.000 0.00 0.00 0.00 3.02
88 89 0.466555 CCGAAACCCCACCACTTTGA 60.467 55.000 0.00 0.00 0.00 2.69
89 90 0.466555 TCCGAAACCCCACCACTTTG 60.467 55.000 0.00 0.00 0.00 2.77
90 91 0.259356 TTCCGAAACCCCACCACTTT 59.741 50.000 0.00 0.00 0.00 2.66
91 92 0.179001 CTTCCGAAACCCCACCACTT 60.179 55.000 0.00 0.00 0.00 3.16
92 93 1.454539 CTTCCGAAACCCCACCACT 59.545 57.895 0.00 0.00 0.00 4.00
93 94 2.265904 GCTTCCGAAACCCCACCAC 61.266 63.158 0.00 0.00 0.00 4.16
94 95 2.114411 GCTTCCGAAACCCCACCA 59.886 61.111 0.00 0.00 0.00 4.17
95 96 2.453379 TACGCTTCCGAAACCCCACC 62.453 60.000 0.00 0.00 38.29 4.61
96 97 1.004679 TACGCTTCCGAAACCCCAC 60.005 57.895 0.00 0.00 38.29 4.61
97 98 1.004679 GTACGCTTCCGAAACCCCA 60.005 57.895 0.00 0.00 38.29 4.96
98 99 1.017701 CAGTACGCTTCCGAAACCCC 61.018 60.000 0.00 0.00 38.29 4.95
99 100 0.320160 ACAGTACGCTTCCGAAACCC 60.320 55.000 0.00 0.00 38.29 4.11
100 101 1.066136 GACAGTACGCTTCCGAAACC 58.934 55.000 0.00 0.00 38.29 3.27
101 102 1.066136 GGACAGTACGCTTCCGAAAC 58.934 55.000 0.00 0.00 38.29 2.78
102 103 0.037975 GGGACAGTACGCTTCCGAAA 60.038 55.000 4.86 0.00 38.29 3.46
103 104 1.180456 TGGGACAGTACGCTTCCGAA 61.180 55.000 4.86 0.00 38.29 4.30
104 105 1.180456 TTGGGACAGTACGCTTCCGA 61.180 55.000 4.86 0.00 42.39 4.55
105 106 1.012486 GTTGGGACAGTACGCTTCCG 61.012 60.000 4.86 0.00 42.39 4.30
106 107 0.672711 GGTTGGGACAGTACGCTTCC 60.673 60.000 2.67 2.67 42.39 3.46
107 108 0.320697 AGGTTGGGACAGTACGCTTC 59.679 55.000 0.00 0.00 42.39 3.86
108 109 0.034896 CAGGTTGGGACAGTACGCTT 59.965 55.000 0.00 0.00 42.39 4.68
109 110 1.671742 CAGGTTGGGACAGTACGCT 59.328 57.895 0.00 0.00 42.39 5.07
110 111 2.033194 GCAGGTTGGGACAGTACGC 61.033 63.158 0.00 0.00 42.39 4.42
111 112 1.736645 CGCAGGTTGGGACAGTACG 60.737 63.158 0.00 0.00 42.39 3.67
112 113 4.278956 CGCAGGTTGGGACAGTAC 57.721 61.111 0.00 0.00 42.39 2.73
130 131 2.723746 CTGGCTTGTGGTGTGCAC 59.276 61.111 10.75 10.75 0.00 4.57
131 132 2.356173 ATCCTGGCTTGTGGTGTGCA 62.356 55.000 0.00 0.00 0.00 4.57
132 133 1.604593 ATCCTGGCTTGTGGTGTGC 60.605 57.895 0.00 0.00 0.00 4.57
133 134 1.246056 CCATCCTGGCTTGTGGTGTG 61.246 60.000 0.00 0.00 0.00 3.82
134 135 1.075482 CCATCCTGGCTTGTGGTGT 59.925 57.895 0.00 0.00 0.00 4.16
135 136 0.679002 CTCCATCCTGGCTTGTGGTG 60.679 60.000 0.00 0.00 37.47 4.17
136 137 0.842030 TCTCCATCCTGGCTTGTGGT 60.842 55.000 0.00 0.00 37.47 4.16
137 138 0.329261 TTCTCCATCCTGGCTTGTGG 59.671 55.000 0.00 0.00 37.47 4.17
138 139 1.280133 TCTTCTCCATCCTGGCTTGTG 59.720 52.381 0.00 0.00 37.47 3.33
139 140 1.661463 TCTTCTCCATCCTGGCTTGT 58.339 50.000 0.00 0.00 37.47 3.16
140 141 2.806019 CGATCTTCTCCATCCTGGCTTG 60.806 54.545 0.00 0.00 37.47 4.01
141 142 1.415659 CGATCTTCTCCATCCTGGCTT 59.584 52.381 0.00 0.00 37.47 4.35
142 143 1.047002 CGATCTTCTCCATCCTGGCT 58.953 55.000 0.00 0.00 37.47 4.75
143 144 0.755686 ACGATCTTCTCCATCCTGGC 59.244 55.000 0.00 0.00 37.47 4.85
144 145 2.029470 GCTACGATCTTCTCCATCCTGG 60.029 54.545 0.00 0.00 39.43 4.45
145 146 2.625314 TGCTACGATCTTCTCCATCCTG 59.375 50.000 0.00 0.00 0.00 3.86
146 147 2.890311 CTGCTACGATCTTCTCCATCCT 59.110 50.000 0.00 0.00 0.00 3.24
147 148 2.625790 ACTGCTACGATCTTCTCCATCC 59.374 50.000 0.00 0.00 0.00 3.51
148 149 4.614993 GCTACTGCTACGATCTTCTCCATC 60.615 50.000 0.00 0.00 36.03 3.51
149 150 3.254657 GCTACTGCTACGATCTTCTCCAT 59.745 47.826 0.00 0.00 36.03 3.41
150 151 2.619177 GCTACTGCTACGATCTTCTCCA 59.381 50.000 0.00 0.00 36.03 3.86
151 152 3.276882 GCTACTGCTACGATCTTCTCC 57.723 52.381 0.00 0.00 36.03 3.71
164 165 2.342179 GAAAGGTCACTGAGCTACTGC 58.658 52.381 11.14 0.00 39.62 4.40
165 166 2.029828 ACGAAAGGTCACTGAGCTACTG 60.030 50.000 11.14 6.59 39.62 2.74
166 167 2.240279 ACGAAAGGTCACTGAGCTACT 58.760 47.619 11.14 2.19 39.62 2.57
167 168 2.726832 ACGAAAGGTCACTGAGCTAC 57.273 50.000 11.14 7.93 39.62 3.58
168 169 4.337555 GGTATACGAAAGGTCACTGAGCTA 59.662 45.833 11.14 0.00 39.62 3.32
169 170 3.130693 GGTATACGAAAGGTCACTGAGCT 59.869 47.826 4.85 4.85 42.52 4.09
170 171 3.445857 GGTATACGAAAGGTCACTGAGC 58.554 50.000 0.00 0.00 0.00 4.26
192 193 2.409651 TTTTTGCCACGCACGACC 59.590 55.556 0.00 0.00 38.71 4.79
314 322 5.191124 GGAGTTGGACCTTCTTATAAGGGAA 59.809 44.000 12.54 0.23 41.71 3.97
326 334 2.447047 AGTTTGATGGGAGTTGGACCTT 59.553 45.455 0.00 0.00 0.00 3.50
353 361 4.644954 GTGGAACTAAAATTTAGTCCGCG 58.355 43.478 17.56 0.00 0.00 6.46
390 403 1.318934 AATAAATCCCCACCCAGCCT 58.681 50.000 0.00 0.00 0.00 4.58
396 409 8.533569 TCAGAAATTTCTAATAAATCCCCACC 57.466 34.615 20.07 0.00 35.34 4.61
449 469 5.619757 GCACGGATGTCAATCTTGAAATTGA 60.620 40.000 0.00 0.00 42.01 2.57
577 1543 7.809331 TGTTTCACAAAATAATCTCACATGAGC 59.191 33.333 0.00 0.00 41.80 4.26
583 1549 6.363357 GCAGGTGTTTCACAAAATAATCTCAC 59.637 38.462 2.41 0.00 35.86 3.51
626 1593 2.335316 ACCACGTTTCAGTAGGCAAA 57.665 45.000 0.00 0.00 0.00 3.68
627 1594 2.335316 AACCACGTTTCAGTAGGCAA 57.665 45.000 0.00 0.00 0.00 4.52
829 1850 3.248125 CGGAAGCTAAACCACGTAAACAA 59.752 43.478 0.00 0.00 0.00 2.83
961 1983 1.900486 CGGTAACCCCTTCTTCTCTGT 59.100 52.381 0.00 0.00 0.00 3.41
1011 2036 1.366679 CTGCTGCTGATGATTGTCGT 58.633 50.000 0.00 0.00 0.00 4.34
1095 2120 2.555199 AGAGGAAATCGCAGCATGTAC 58.445 47.619 0.00 0.00 39.31 2.90
1479 2510 0.524862 CCAATCAACTCTGCTGGCAC 59.475 55.000 0.00 0.00 0.00 5.01
1512 2544 9.916360 TCTCTACTACCAAATATGTCTCTAACA 57.084 33.333 0.00 0.00 43.51 2.41
1516 2548 8.364142 GCAATCTCTACTACCAAATATGTCTCT 58.636 37.037 0.00 0.00 0.00 3.10
1521 2553 5.639506 CGGGCAATCTCTACTACCAAATATG 59.360 44.000 0.00 0.00 0.00 1.78
1570 2602 4.156477 GGCAGGACACCTTCTAGAGATAT 58.844 47.826 0.00 0.00 0.00 1.63
1588 2620 3.274288 GAGTACAAGATTTGGAGGGCAG 58.726 50.000 0.00 0.00 34.12 4.85
1599 2631 9.105844 AGGGCAAGTATATATTGAGTACAAGAT 57.894 33.333 0.00 0.00 40.38 2.40
1643 2675 3.652869 AGGGATTGACGGAATATGATGGT 59.347 43.478 0.00 0.00 0.00 3.55
1659 2765 6.190587 CCATGTTAAAAGGAAGAGAGGGATT 58.809 40.000 0.00 0.00 0.00 3.01
1663 2769 7.338710 TGATACCATGTTAAAAGGAAGAGAGG 58.661 38.462 0.00 0.00 0.00 3.69
1670 2776 5.880332 GTGCTCTGATACCATGTTAAAAGGA 59.120 40.000 0.00 0.00 0.00 3.36
1675 2781 4.835284 TGGTGCTCTGATACCATGTTAA 57.165 40.909 9.17 0.00 41.80 2.01
1696 2803 3.262151 GCTGTTAGAAGGGAGAGAGGTTT 59.738 47.826 0.00 0.00 0.00 3.27
1697 2804 2.835156 GCTGTTAGAAGGGAGAGAGGTT 59.165 50.000 0.00 0.00 0.00 3.50
1698 2805 2.043801 AGCTGTTAGAAGGGAGAGAGGT 59.956 50.000 0.00 0.00 0.00 3.85
1699 2806 2.745968 AGCTGTTAGAAGGGAGAGAGG 58.254 52.381 0.00 0.00 0.00 3.69
1700 2807 4.953579 ACTTAGCTGTTAGAAGGGAGAGAG 59.046 45.833 0.00 0.00 0.00 3.20
1701 2808 4.936802 ACTTAGCTGTTAGAAGGGAGAGA 58.063 43.478 0.00 0.00 0.00 3.10
1702 2809 6.777213 TTACTTAGCTGTTAGAAGGGAGAG 57.223 41.667 0.00 0.00 0.00 3.20
1703 2810 7.556844 CAATTACTTAGCTGTTAGAAGGGAGA 58.443 38.462 0.00 0.00 0.00 3.71
1704 2811 6.258947 GCAATTACTTAGCTGTTAGAAGGGAG 59.741 42.308 0.00 0.00 0.00 4.30
1705 2812 6.113411 GCAATTACTTAGCTGTTAGAAGGGA 58.887 40.000 0.00 0.00 0.00 4.20
1706 2813 5.880332 TGCAATTACTTAGCTGTTAGAAGGG 59.120 40.000 0.00 0.00 0.00 3.95
1711 2922 7.009999 CAGAGAGTGCAATTACTTAGCTGTTAG 59.990 40.741 0.00 0.00 0.00 2.34
1717 2928 5.462034 CACAGAGAGTGCAATTACTTAGC 57.538 43.478 0.00 0.00 42.15 3.09
1885 3115 8.487313 AGTTAAATATATGTGTTTCGCAGTGA 57.513 30.769 0.00 0.00 0.00 3.41
1931 3723 9.042008 CGCATCTATGTAAAACCAGTTACTTAT 57.958 33.333 0.00 0.00 35.41 1.73
2073 3902 2.229784 CACCAAGGTGGCAAATTCTCTC 59.770 50.000 11.43 0.00 42.67 3.20
2284 4118 1.487976 TCACTCCCATGCATTCCTCTC 59.512 52.381 0.00 0.00 0.00 3.20
2342 4176 1.772063 CGCCCCTAAATAGCACGTGC 61.772 60.000 32.79 32.79 42.49 5.34
2418 4281 6.279882 TGGGTTCAGCTTTGATTTTTAGTTG 58.720 36.000 0.00 0.00 0.00 3.16
2457 4493 7.443879 ACAACAAAACCAAAGCAATAATAAGGG 59.556 33.333 0.00 0.00 0.00 3.95
2517 4553 5.994668 TCCATTGGGTTCACTTAAAATTTGC 59.005 36.000 2.09 0.00 34.93 3.68
2587 4623 5.784578 ACTGTTATTTTCCTTGGTTCACC 57.215 39.130 0.00 0.00 0.00 4.02
2628 4664 9.660180 TTAAAAAGTTAGCAGAAACAAAACCAT 57.340 25.926 0.00 0.00 0.00 3.55
2668 4704 5.266788 TCCTAGAAATCTCGTAAAGTGGGA 58.733 41.667 0.00 0.00 0.00 4.37
2828 5151 6.625532 AGATTTTACCCCATGCAAATTTCT 57.374 33.333 0.00 0.00 0.00 2.52
2958 5281 3.423539 AGTCCTCTGCATTGCTTTACA 57.576 42.857 10.49 0.00 0.00 2.41
3011 5334 6.359804 TCTCCCAATGATCAAGGTAAATCAG 58.640 40.000 14.41 3.34 35.49 2.90
3444 5768 3.813724 AGAAACGGAAAACTTAGCAGGAC 59.186 43.478 0.00 0.00 0.00 3.85
3459 5783 9.116067 TCCCTGAATTTATAACAATAGAAACGG 57.884 33.333 0.00 0.00 0.00 4.44
3576 5900 3.380004 CCAGCTTTACAAACACACTTCCA 59.620 43.478 0.00 0.00 0.00 3.53
3655 5979 4.341235 GTGTTCCCCTAATTATTTCAGCCC 59.659 45.833 0.00 0.00 0.00 5.19
3656 5980 4.953579 TGTGTTCCCCTAATTATTTCAGCC 59.046 41.667 0.00 0.00 0.00 4.85
3876 7427 3.798202 AGCGAGTTCTTGTAATCCCATC 58.202 45.455 0.00 0.00 0.00 3.51
3891 7442 1.548719 TGTGTACATGGCTTAGCGAGT 59.451 47.619 0.00 0.00 0.00 4.18
4128 7850 2.598565 CCTCCCTTATCATCCTCACGA 58.401 52.381 0.00 0.00 0.00 4.35
4299 8023 5.268118 AGAAGAGACGATGCAACATATCA 57.732 39.130 0.00 0.00 0.00 2.15
4417 8141 4.711846 GCTCCCCTCCACATAAAATTCTTT 59.288 41.667 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.