Multiple sequence alignment - TraesCS6D01G349500

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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 TraesCS6D01G349500 chr6D 100.000 2864 0 0 1 2864 447279902 447277039 0.000000e+00 5289.0
1 TraesCS6D01G349500 chr6D 83.547 936 76 30 1804 2680 447738370 447739286 0.000000e+00 804.0
2 TraesCS6D01G349500 chr6D 86.220 537 56 13 894 1423 447213931 447213406 1.490000e-157 566.0
3 TraesCS6D01G349500 chr6D 90.090 111 6 5 1665 1773 447278122 447278015 3.850000e-29 139.0
4 TraesCS6D01G349500 chr6D 90.090 111 6 5 1781 1888 447278238 447278130 3.850000e-29 139.0
5 TraesCS6D01G349500 chr6D 78.539 219 26 14 273 478 447737198 447737408 1.080000e-24 124.0
6 TraesCS6D01G349500 chr6D 80.435 184 14 13 649 822 447214204 447214033 1.390000e-23 121.0
7 TraesCS6D01G349500 chr6D 85.227 88 11 2 96 183 446901095 446901180 3.930000e-14 89.8
8 TraesCS6D01G349500 chr6D 87.671 73 4 2 83 150 446880707 446880779 2.370000e-11 80.5
9 TraesCS6D01G349500 chr6D 97.727 44 1 0 895 938 447445129 447445086 3.060000e-10 76.8
10 TraesCS6D01G349500 chr6D 100.000 30 0 0 841 870 447445246 447445217 3.990000e-04 56.5
11 TraesCS6D01G349500 chr6B 84.657 1473 136 52 328 1777 677046308 677044903 0.000000e+00 1386.0
12 TraesCS6D01G349500 chr6B 88.539 890 63 22 890 1777 678092878 678092026 0.000000e+00 1042.0
13 TraesCS6D01G349500 chr6B 87.968 881 72 11 1800 2657 678175340 678176209 0.000000e+00 1009.0
14 TraesCS6D01G349500 chr6B 87.058 904 66 24 890 1781 678356831 678357695 0.000000e+00 974.0
15 TraesCS6D01G349500 chr6B 87.925 853 54 21 937 1777 678174617 678175432 0.000000e+00 959.0
16 TraesCS6D01G349500 chr6B 88.674 777 63 11 882 1650 677088468 677087709 0.000000e+00 924.0
17 TraesCS6D01G349500 chr6B 88.860 763 40 20 1015 1768 678542622 678543348 0.000000e+00 896.0
18 TraesCS6D01G349500 chr6B 84.624 904 65 37 890 1777 676865982 676865137 0.000000e+00 832.0
19 TraesCS6D01G349500 chr6B 84.894 801 78 19 2056 2839 678091815 678091041 0.000000e+00 769.0
20 TraesCS6D01G349500 chr6B 83.077 845 83 20 1781 2603 678357580 678358386 0.000000e+00 713.0
21 TraesCS6D01G349500 chr6B 87.606 589 54 9 1889 2459 677087688 677087101 0.000000e+00 665.0
22 TraesCS6D01G349500 chr6B 87.365 554 50 11 1924 2459 677777854 677777303 4.050000e-173 617.0
23 TraesCS6D01G349500 chr6B 87.365 554 51 9 1924 2459 677910135 677909583 4.050000e-173 617.0
24 TraesCS6D01G349500 chr6B 88.559 472 39 9 2000 2459 676865054 676864586 2.490000e-155 558.0
25 TraesCS6D01G349500 chr6B 88.430 363 35 6 2504 2863 677044534 677044176 5.670000e-117 431.0
26 TraesCS6D01G349500 chr6B 83.529 510 33 21 1781 2266 677336358 677335876 2.040000e-116 429.0
27 TraesCS6D01G349500 chr6B 82.745 510 36 23 1781 2266 677045017 677044536 9.550000e-110 407.0
28 TraesCS6D01G349500 chr6B 78.014 705 88 39 1781 2437 678543249 678543934 5.790000e-102 381.0
29 TraesCS6D01G349500 chr6B 80.360 555 48 26 326 870 678174004 678174507 5.830000e-97 364.0
30 TraesCS6D01G349500 chr6B 82.927 369 32 10 2499 2863 677335876 677335535 1.290000e-78 303.0
31 TraesCS6D01G349500 chr6B 81.744 367 45 13 2026 2384 676124198 676124550 1.300000e-73 287.0
32 TraesCS6D01G349500 chr6B 81.851 281 35 11 1781 2051 678092137 678091863 3.710000e-54 222.0
33 TraesCS6D01G349500 chr6B 82.197 264 29 8 2516 2774 676859423 676859173 8.040000e-51 211.0
34 TraesCS6D01G349500 chr6B 79.456 331 42 13 2516 2839 677079706 677079395 8.040000e-51 211.0
35 TraesCS6D01G349500 chr6B 81.164 292 30 12 2519 2803 677774639 677774366 8.040000e-51 211.0
36 TraesCS6D01G349500 chr6B 81.017 295 31 13 2516 2803 677906750 677906474 8.040000e-51 211.0
37 TraesCS6D01G349500 chr6B 83.333 144 12 7 737 880 677337162 677337031 3.880000e-24 122.0
38 TraesCS6D01G349500 chr6B 83.333 144 12 6 737 880 678093058 678092927 3.880000e-24 122.0
39 TraesCS6D01G349500 chr6B 89.888 89 9 0 326 414 677090556 677090468 6.480000e-22 115.0
40 TraesCS6D01G349500 chr6B 91.781 73 3 2 751 822 676730945 676730875 6.530000e-17 99.0
41 TraesCS6D01G349500 chr6B 84.404 109 7 4 82 180 678093473 678093365 6.530000e-17 99.0
42 TraesCS6D01G349500 chr6B 96.296 54 1 1 272 325 677046388 677046336 1.410000e-13 87.9
43 TraesCS6D01G349500 chr6B 95.745 47 2 0 751 797 678356673 678356719 3.060000e-10 76.8
44 TraesCS6D01G349500 chr6B 85.714 77 4 3 794 870 677129704 677129635 1.100000e-09 75.0
45 TraesCS6D01G349500 chr6B 97.619 42 1 0 215 256 677585322 677585281 3.960000e-09 73.1
46 TraesCS6D01G349500 chr6B 92.308 39 3 0 107 145 678540384 678540422 3.990000e-04 56.5
47 TraesCS6D01G349500 chr6A 88.670 812 63 16 1781 2569 593991788 593990983 0.000000e+00 963.0
48 TraesCS6D01G349500 chr6A 86.946 858 66 21 932 1777 594365592 594366415 0.000000e+00 922.0
49 TraesCS6D01G349500 chr6A 84.151 978 86 29 1804 2739 594319897 594320847 0.000000e+00 883.0
50 TraesCS6D01G349500 chr6A 84.972 885 79 29 894 1773 593992517 593991682 0.000000e+00 848.0
51 TraesCS6D01G349500 chr6A 85.240 874 66 22 903 1773 594254350 594253537 0.000000e+00 841.0
52 TraesCS6D01G349500 chr6A 87.783 442 30 15 1781 2208 594253643 594253212 1.980000e-136 496.0
53 TraesCS6D01G349500 chr6A 79.079 760 99 37 704 1423 593930293 593929554 4.320000e-128 468.0
54 TraesCS6D01G349500 chr6A 85.294 374 41 10 326 696 594217479 594217117 9.690000e-100 374.0
55 TraesCS6D01G349500 chr6A 84.519 239 29 4 347 584 594255159 594254928 2.220000e-56 230.0
56 TraesCS6D01G349500 chr6A 89.167 120 12 1 752 870 594318905 594319024 6.390000e-32 148.0
57 TraesCS6D01G349500 chr6A 78.235 170 15 15 650 797 594364882 594365051 3.930000e-14 89.8
58 TraesCS6D01G349500 chr6A 92.157 51 4 0 272 322 593776446 593776496 3.960000e-09 73.1
59 TraesCS6D01G349500 chr7A 80.090 221 21 9 1804 2011 19012840 19013050 2.970000e-30 143.0
60 TraesCS6D01G349500 chr7A 93.023 43 3 0 6 48 33648436 33648478 2.380000e-06 63.9
61 TraesCS6D01G349500 chrUn 93.023 43 3 0 6 48 82039407 82039449 2.380000e-06 63.9
62 TraesCS6D01G349500 chrUn 93.023 43 3 0 6 48 318725255 318725213 2.380000e-06 63.9


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 TraesCS6D01G349500 chr6D 447277039 447279902 2863 True 1855.666667 5289 93.393333 1 2864 3 chr6D.!!$R2 2863
1 TraesCS6D01G349500 chr6D 447737198 447739286 2088 False 464.000000 804 81.043000 273 2680 2 chr6D.!!$F3 2407
2 TraesCS6D01G349500 chr6D 447213406 447214204 798 True 343.500000 566 83.327500 649 1423 2 chr6D.!!$R1 774
3 TraesCS6D01G349500 chr6B 678174004 678176209 2205 False 777.333333 1009 85.417667 326 2657 3 chr6B.!!$F2 2331
4 TraesCS6D01G349500 chr6B 676864586 676865982 1396 True 695.000000 832 86.591500 890 2459 2 chr6B.!!$R6 1569
5 TraesCS6D01G349500 chr6B 678356673 678358386 1713 False 587.933333 974 88.626667 751 2603 3 chr6B.!!$F3 1852
6 TraesCS6D01G349500 chr6B 677044176 677046388 2212 True 577.975000 1386 88.032000 272 2863 4 chr6B.!!$R7 2591
7 TraesCS6D01G349500 chr6B 677087101 677090556 3455 True 568.000000 924 88.722667 326 2459 3 chr6B.!!$R8 2133
8 TraesCS6D01G349500 chr6B 678091041 678093473 2432 True 450.800000 1042 84.604200 82 2839 5 chr6B.!!$R12 2757
9 TraesCS6D01G349500 chr6B 678540384 678543934 3550 False 444.500000 896 86.394000 107 2437 3 chr6B.!!$F4 2330
10 TraesCS6D01G349500 chr6B 677774366 677777854 3488 True 414.000000 617 84.264500 1924 2803 2 chr6B.!!$R10 879
11 TraesCS6D01G349500 chr6B 677906474 677910135 3661 True 414.000000 617 84.191000 1924 2803 2 chr6B.!!$R11 879
12 TraesCS6D01G349500 chr6B 677335535 677337162 1627 True 284.666667 429 83.263000 737 2863 3 chr6B.!!$R9 2126
13 TraesCS6D01G349500 chr6A 593990983 593992517 1534 True 905.500000 963 86.821000 894 2569 2 chr6A.!!$R3 1675
14 TraesCS6D01G349500 chr6A 594253212 594255159 1947 True 522.333333 841 85.847333 347 2208 3 chr6A.!!$R4 1861
15 TraesCS6D01G349500 chr6A 594318905 594320847 1942 False 515.500000 883 86.659000 752 2739 2 chr6A.!!$F2 1987
16 TraesCS6D01G349500 chr6A 594364882 594366415 1533 False 505.900000 922 82.590500 650 1777 2 chr6A.!!$F3 1127
17 TraesCS6D01G349500 chr6A 593929554 593930293 739 True 468.000000 468 79.079000 704 1423 1 chr6A.!!$R1 719

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
39 40 0.107165 CGGGGTTCCTCCTCCATTTC 60.107 60.0 0.00 0.00 36.25 2.17 F
1123 4903 0.101219 CTCTCATCATGTCGACGGCA 59.899 55.0 3.85 3.85 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 5602 0.249741 AGCGAACGGGATTATTCGGG 60.250 55.0 8.29 0.0 46.07 5.14 R
2493 6713 0.613853 TCGGGGGATTTCTCTCGTGT 60.614 55.0 0.00 0.0 0.00 4.49 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
19 20 0.379669 CATCGTCCAAATGCAGAGGC 59.620 55.000 0.00 0.00 41.68 4.70
20 21 0.749454 ATCGTCCAAATGCAGAGGCC 60.749 55.000 0.00 0.00 40.13 5.19
21 22 2.753966 CGTCCAAATGCAGAGGCCG 61.754 63.158 0.00 0.00 40.13 6.13
22 23 2.045045 TCCAAATGCAGAGGCCGG 60.045 61.111 0.00 0.00 40.13 6.13
23 24 3.142838 CCAAATGCAGAGGCCGGG 61.143 66.667 2.18 0.00 40.13 5.73
24 25 3.142838 CAAATGCAGAGGCCGGGG 61.143 66.667 2.18 0.00 40.13 5.73
25 26 3.661648 AAATGCAGAGGCCGGGGT 61.662 61.111 2.18 0.00 40.13 4.95
26 27 3.224007 AAATGCAGAGGCCGGGGTT 62.224 57.895 2.18 0.00 40.13 4.11
27 28 3.645268 AATGCAGAGGCCGGGGTTC 62.645 63.158 2.18 0.00 40.13 3.62
36 37 2.366972 CCGGGGTTCCTCCTCCAT 60.367 66.667 0.00 0.00 36.25 3.41
37 38 2.001269 CCGGGGTTCCTCCTCCATT 61.001 63.158 0.00 0.00 36.25 3.16
38 39 1.571773 CCGGGGTTCCTCCTCCATTT 61.572 60.000 0.00 0.00 36.25 2.32
39 40 0.107165 CGGGGTTCCTCCTCCATTTC 60.107 60.000 0.00 0.00 36.25 2.17
40 41 1.299939 GGGGTTCCTCCTCCATTTCT 58.700 55.000 0.00 0.00 36.25 2.52
41 42 1.641192 GGGGTTCCTCCTCCATTTCTT 59.359 52.381 0.00 0.00 36.25 2.52
42 43 2.850568 GGGGTTCCTCCTCCATTTCTTA 59.149 50.000 0.00 0.00 36.25 2.10
43 44 3.268595 GGGGTTCCTCCTCCATTTCTTAA 59.731 47.826 0.00 0.00 36.25 1.85
44 45 4.264217 GGGGTTCCTCCTCCATTTCTTAAA 60.264 45.833 0.00 0.00 36.25 1.52
45 46 5.330233 GGGTTCCTCCTCCATTTCTTAAAA 58.670 41.667 0.00 0.00 36.25 1.52
46 47 5.778241 GGGTTCCTCCTCCATTTCTTAAAAA 59.222 40.000 0.00 0.00 36.25 1.94
71 72 5.893512 AAAAATAAAAACCTTTCGACCGC 57.106 34.783 0.00 0.00 0.00 5.68
72 73 3.564235 AATAAAAACCTTTCGACCGCC 57.436 42.857 0.00 0.00 0.00 6.13
73 74 1.237533 TAAAAACCTTTCGACCGCCC 58.762 50.000 0.00 0.00 0.00 6.13
74 75 0.466739 AAAAACCTTTCGACCGCCCT 60.467 50.000 0.00 0.00 0.00 5.19
75 76 0.397564 AAAACCTTTCGACCGCCCTA 59.602 50.000 0.00 0.00 0.00 3.53
76 77 0.616891 AAACCTTTCGACCGCCCTAT 59.383 50.000 0.00 0.00 0.00 2.57
77 78 0.177373 AACCTTTCGACCGCCCTATC 59.823 55.000 0.00 0.00 0.00 2.08
78 79 1.299926 CCTTTCGACCGCCCTATCG 60.300 63.158 0.00 0.00 39.72 2.92
79 80 1.731433 CCTTTCGACCGCCCTATCGA 61.731 60.000 0.00 0.00 45.17 3.59
80 81 0.594284 CTTTCGACCGCCCTATCGAC 60.594 60.000 0.00 0.00 46.41 4.20
81 82 2.008268 TTTCGACCGCCCTATCGACC 62.008 60.000 0.00 0.00 46.41 4.79
82 83 4.323843 CGACCGCCCTATCGACCG 62.324 72.222 0.00 0.00 40.86 4.79
83 84 4.642542 GACCGCCCTATCGACCGC 62.643 72.222 0.00 0.00 0.00 5.68
85 86 4.944372 CCGCCCTATCGACCGCAC 62.944 72.222 0.00 0.00 0.00 5.34
93 94 2.055310 TATCGACCGCACCGCAGTAG 62.055 60.000 0.00 0.00 0.00 2.57
94 95 4.111016 CGACCGCACCGCAGTAGA 62.111 66.667 0.00 0.00 0.00 2.59
112 118 3.176552 AGAAACAGCGATCAGATCAGG 57.823 47.619 11.12 1.80 0.00 3.86
182 192 3.071837 TGCCTCGCATACACCGGA 61.072 61.111 9.46 0.00 31.71 5.14
183 193 2.585247 GCCTCGCATACACCGGAC 60.585 66.667 9.46 0.00 0.00 4.79
184 194 2.278596 CCTCGCATACACCGGACG 60.279 66.667 9.46 0.00 0.00 4.79
185 195 2.767445 CCTCGCATACACCGGACGA 61.767 63.158 9.46 6.37 0.00 4.20
186 196 1.138036 CTCGCATACACCGGACGAA 59.862 57.895 9.46 0.00 31.60 3.85
187 197 1.138047 CTCGCATACACCGGACGAAC 61.138 60.000 9.46 0.00 31.60 3.95
188 198 2.502123 CGCATACACCGGACGAACG 61.502 63.158 9.46 0.00 0.00 3.95
189 199 1.153978 GCATACACCGGACGAACGA 60.154 57.895 9.46 0.00 35.47 3.85
190 200 1.138047 GCATACACCGGACGAACGAG 61.138 60.000 9.46 0.00 35.47 4.18
191 201 0.448990 CATACACCGGACGAACGAGA 59.551 55.000 9.46 0.00 35.47 4.04
192 202 0.731417 ATACACCGGACGAACGAGAG 59.269 55.000 9.46 0.00 35.47 3.20
193 203 1.915614 TACACCGGACGAACGAGAGC 61.916 60.000 9.46 0.00 35.47 4.09
194 204 4.099170 ACCGGACGAACGAGAGCG 62.099 66.667 9.46 0.00 44.79 5.03
195 205 3.796443 CCGGACGAACGAGAGCGA 61.796 66.667 0.00 0.00 41.64 4.93
196 206 2.403987 CGGACGAACGAGAGCGAT 59.596 61.111 0.14 0.00 41.64 4.58
197 207 1.934956 CGGACGAACGAGAGCGATG 60.935 63.158 0.14 0.00 41.64 3.84
198 208 1.586564 GGACGAACGAGAGCGATGG 60.587 63.158 0.14 0.00 41.64 3.51
199 209 2.202623 ACGAACGAGAGCGATGGC 60.203 61.111 0.14 0.00 41.64 4.40
200 210 3.315521 CGAACGAGAGCGATGGCG 61.316 66.667 0.00 0.00 46.35 5.69
234 255 3.785859 GCCGGCTCCACTCCATGA 61.786 66.667 22.15 0.00 0.00 3.07
235 256 3.112205 GCCGGCTCCACTCCATGAT 62.112 63.158 22.15 0.00 0.00 2.45
236 257 1.070445 CCGGCTCCACTCCATGATC 59.930 63.158 0.00 0.00 0.00 2.92
237 258 1.070445 CGGCTCCACTCCATGATCC 59.930 63.158 0.00 0.00 0.00 3.36
238 259 1.453669 GGCTCCACTCCATGATCCC 59.546 63.158 0.00 0.00 0.00 3.85
239 260 1.059006 GGCTCCACTCCATGATCCCT 61.059 60.000 0.00 0.00 0.00 4.20
240 261 0.842635 GCTCCACTCCATGATCCCTT 59.157 55.000 0.00 0.00 0.00 3.95
241 262 1.202746 GCTCCACTCCATGATCCCTTC 60.203 57.143 0.00 0.00 0.00 3.46
242 263 1.419387 CTCCACTCCATGATCCCTTCC 59.581 57.143 0.00 0.00 0.00 3.46
256 277 2.602267 TTCCTTCCCGCGGACTCA 60.602 61.111 30.73 3.99 0.00 3.41
257 278 2.564553 CTTCCTTCCCGCGGACTCAG 62.565 65.000 30.73 15.89 0.00 3.35
402 540 1.674764 ATCACCTGCCTCGCTCTGAG 61.675 60.000 0.00 0.00 44.83 3.35
426 1908 4.329256 CGTTCGGAGATAAGTTCCCTTTTC 59.671 45.833 0.00 0.00 35.04 2.29
480 1963 5.010617 ACCGGTTTAATGAAAGCAACATCTT 59.989 36.000 0.00 0.00 42.10 2.40
506 1989 0.539438 GTGATGGGTCCAGGCACAAA 60.539 55.000 16.05 0.00 36.14 2.83
507 1990 0.409092 TGATGGGTCCAGGCACAAAT 59.591 50.000 0.00 0.00 0.00 2.32
555 3140 2.228822 GTCGACATTGCCAAATTCCAGT 59.771 45.455 11.55 0.00 0.00 4.00
556 3141 2.228582 TCGACATTGCCAAATTCCAGTG 59.771 45.455 0.00 0.00 0.00 3.66
632 3288 4.154918 GCTCCTCCTGTATGACACTTTTTG 59.845 45.833 0.00 0.00 0.00 2.44
700 3462 6.808008 ACCATATGTTCCGATTCATTGATC 57.192 37.500 1.24 0.00 0.00 2.92
701 3463 6.537355 ACCATATGTTCCGATTCATTGATCT 58.463 36.000 1.24 0.00 0.00 2.75
747 3809 7.615403 ACTTCTTTCACATGACTAGCAAGATA 58.385 34.615 0.00 0.00 0.00 1.98
748 3810 7.547370 ACTTCTTTCACATGACTAGCAAGATAC 59.453 37.037 0.00 0.00 0.00 2.24
749 3811 6.036470 TCTTTCACATGACTAGCAAGATACG 58.964 40.000 0.00 0.00 0.00 3.06
792 3854 8.463930 AGAAATTGACCAGAATTTTGACACTA 57.536 30.769 0.00 0.00 36.00 2.74
816 3892 9.846248 CTAAAATTAGTATTCAAAGCAAGCTGT 57.154 29.630 0.00 0.00 0.00 4.40
828 3904 0.816825 CAAGCTGTCATGCGCCCTAT 60.817 55.000 4.18 0.00 38.13 2.57
871 4131 1.675641 GATTCCGGTGTGCTGCCTT 60.676 57.895 0.00 0.00 0.00 4.35
879 4158 3.431725 GTGCTGCCTTACGCCCAC 61.432 66.667 0.00 0.00 36.24 4.61
947 4678 2.160205 GAAGTTACCAAACTGCCCCTC 58.840 52.381 0.00 0.00 45.37 4.30
953 4684 1.204113 CCAAACTGCCCCTCCTCTCT 61.204 60.000 0.00 0.00 0.00 3.10
1004 4749 1.473434 GGCTCCCATCTCAGTTTACCG 60.473 57.143 0.00 0.00 0.00 4.02
1055 4823 4.012374 CTCAACTGACATACCAAAGCCAT 58.988 43.478 0.00 0.00 0.00 4.40
1087 4862 1.302832 GTCCCAACTGCTCCACCTG 60.303 63.158 0.00 0.00 0.00 4.00
1088 4863 1.461268 TCCCAACTGCTCCACCTGA 60.461 57.895 0.00 0.00 0.00 3.86
1089 4864 1.302832 CCCAACTGCTCCACCTGAC 60.303 63.158 0.00 0.00 0.00 3.51
1090 4865 1.302832 CCAACTGCTCCACCTGACC 60.303 63.158 0.00 0.00 0.00 4.02
1091 4866 1.757306 CAACTGCTCCACCTGACCT 59.243 57.895 0.00 0.00 0.00 3.85
1123 4903 0.101219 CTCTCATCATGTCGACGGCA 59.899 55.000 3.85 3.85 0.00 5.69
1248 5043 0.736672 TCCGTCAGAGTCTCGTCTCG 60.737 60.000 0.00 0.00 39.21 4.04
1288 5092 2.278857 CCCAAGATCCGTCGCTCG 60.279 66.667 0.00 0.00 39.52 5.03
1688 5563 2.212652 TGCCATAGCAGCAAAGATACG 58.787 47.619 0.00 0.00 46.52 3.06
1689 5564 2.213499 GCCATAGCAGCAAAGATACGT 58.787 47.619 0.00 0.00 39.53 3.57
1690 5565 3.181470 TGCCATAGCAGCAAAGATACGTA 60.181 43.478 0.00 0.00 46.52 3.57
1691 5566 3.184581 GCCATAGCAGCAAAGATACGTAC 59.815 47.826 0.00 0.00 39.53 3.67
1692 5567 4.368315 CCATAGCAGCAAAGATACGTACA 58.632 43.478 0.00 0.00 0.00 2.90
1693 5568 4.991056 CCATAGCAGCAAAGATACGTACAT 59.009 41.667 0.00 0.00 0.00 2.29
1694 5569 6.156519 CCATAGCAGCAAAGATACGTACATA 58.843 40.000 0.00 0.00 0.00 2.29
1695 5570 6.089551 CCATAGCAGCAAAGATACGTACATAC 59.910 42.308 0.00 0.00 0.00 2.39
1696 5571 5.263968 AGCAGCAAAGATACGTACATACT 57.736 39.130 0.00 0.00 0.00 2.12
1697 5572 5.043903 AGCAGCAAAGATACGTACATACTG 58.956 41.667 0.00 2.75 0.00 2.74
1698 5573 4.318121 GCAGCAAAGATACGTACATACTGC 60.318 45.833 16.34 16.34 39.85 4.40
1699 5574 4.803613 CAGCAAAGATACGTACATACTGCA 59.196 41.667 16.21 0.00 0.00 4.41
1700 5575 4.804139 AGCAAAGATACGTACATACTGCAC 59.196 41.667 16.21 2.45 0.00 4.57
1701 5576 4.565166 GCAAAGATACGTACATACTGCACA 59.435 41.667 0.00 0.00 0.00 4.57
1702 5577 5.062934 GCAAAGATACGTACATACTGCACAA 59.937 40.000 0.00 0.00 0.00 3.33
1703 5578 6.401688 GCAAAGATACGTACATACTGCACAAA 60.402 38.462 0.00 0.00 0.00 2.83
1704 5579 7.514805 CAAAGATACGTACATACTGCACAAAA 58.485 34.615 0.00 0.00 0.00 2.44
1705 5580 7.661127 AAGATACGTACATACTGCACAAAAA 57.339 32.000 0.00 0.00 0.00 1.94
1706 5581 7.057149 AGATACGTACATACTGCACAAAAAC 57.943 36.000 0.00 0.00 0.00 2.43
1707 5582 6.872020 AGATACGTACATACTGCACAAAAACT 59.128 34.615 0.00 0.00 0.00 2.66
1708 5583 5.090652 ACGTACATACTGCACAAAAACTG 57.909 39.130 0.00 0.00 0.00 3.16
1709 5584 4.573201 ACGTACATACTGCACAAAAACTGT 59.427 37.500 0.00 0.00 39.56 3.55
1710 5585 5.754406 ACGTACATACTGCACAAAAACTGTA 59.246 36.000 0.00 0.00 36.10 2.74
1711 5586 6.068931 CGTACATACTGCACAAAAACTGTAC 58.931 40.000 0.00 0.00 36.10 2.90
1712 5587 6.292435 CGTACATACTGCACAAAAACTGTACA 60.292 38.462 0.00 0.00 38.25 2.90
1713 5588 6.633500 ACATACTGCACAAAAACTGTACAT 57.367 33.333 0.00 0.00 36.10 2.29
1714 5589 7.737972 ACATACTGCACAAAAACTGTACATA 57.262 32.000 0.00 0.00 36.10 2.29
1715 5590 7.806690 ACATACTGCACAAAAACTGTACATAG 58.193 34.615 0.00 0.00 36.10 2.23
1716 5591 5.689383 ACTGCACAAAAACTGTACATAGG 57.311 39.130 0.00 0.00 36.10 2.57
1717 5592 5.373222 ACTGCACAAAAACTGTACATAGGA 58.627 37.500 0.00 0.00 36.10 2.94
1718 5593 5.825679 ACTGCACAAAAACTGTACATAGGAA 59.174 36.000 0.00 0.00 36.10 3.36
1719 5594 6.320164 ACTGCACAAAAACTGTACATAGGAAA 59.680 34.615 0.00 0.00 36.10 3.13
1720 5595 6.734137 TGCACAAAAACTGTACATAGGAAAG 58.266 36.000 0.00 0.00 36.10 2.62
1721 5596 6.544197 TGCACAAAAACTGTACATAGGAAAGA 59.456 34.615 0.00 0.00 36.10 2.52
1722 5597 7.067615 TGCACAAAAACTGTACATAGGAAAGAA 59.932 33.333 0.00 0.00 36.10 2.52
1723 5598 7.591426 GCACAAAAACTGTACATAGGAAAGAAG 59.409 37.037 0.00 0.00 36.10 2.85
1724 5599 8.621286 CACAAAAACTGTACATAGGAAAGAAGT 58.379 33.333 0.00 0.00 36.10 3.01
1725 5600 9.185680 ACAAAAACTGTACATAGGAAAGAAGTT 57.814 29.630 0.00 0.00 36.10 2.66
1726 5601 9.665264 CAAAAACTGTACATAGGAAAGAAGTTC 57.335 33.333 0.00 0.00 35.28 3.01
1738 5613 5.752892 GAAAGAAGTTCCCCGAATAATCC 57.247 43.478 0.00 0.00 0.00 3.01
1739 5614 3.859061 AGAAGTTCCCCGAATAATCCC 57.141 47.619 0.00 0.00 0.00 3.85
1740 5615 2.104281 AGAAGTTCCCCGAATAATCCCG 59.896 50.000 0.00 0.00 0.00 5.14
1741 5616 1.503800 AGTTCCCCGAATAATCCCGT 58.496 50.000 0.00 0.00 0.00 5.28
1742 5617 1.841919 AGTTCCCCGAATAATCCCGTT 59.158 47.619 0.00 0.00 0.00 4.44
1743 5618 2.158856 AGTTCCCCGAATAATCCCGTTC 60.159 50.000 0.00 0.00 0.00 3.95
1744 5619 0.390124 TCCCCGAATAATCCCGTTCG 59.610 55.000 0.91 0.91 44.89 3.95
1745 5620 1.226030 CCCCGAATAATCCCGTTCGC 61.226 60.000 2.28 0.00 44.19 4.70
1746 5621 0.249741 CCCGAATAATCCCGTTCGCT 60.250 55.000 2.28 0.00 44.19 4.93
1747 5622 0.859232 CCGAATAATCCCGTTCGCTG 59.141 55.000 2.28 0.00 44.19 5.18
1748 5623 1.567504 CGAATAATCCCGTTCGCTGT 58.432 50.000 0.00 0.00 40.39 4.40
1749 5624 2.544277 CCGAATAATCCCGTTCGCTGTA 60.544 50.000 2.28 0.00 44.19 2.74
1750 5625 3.314553 CGAATAATCCCGTTCGCTGTAT 58.685 45.455 0.00 0.00 40.39 2.29
1751 5626 3.121279 CGAATAATCCCGTTCGCTGTATG 59.879 47.826 0.00 0.00 40.39 2.39
1752 5627 1.860676 TAATCCCGTTCGCTGTATGC 58.139 50.000 0.00 0.00 38.57 3.14
1753 5628 0.107897 AATCCCGTTCGCTGTATGCA 60.108 50.000 0.00 0.00 43.06 3.96
1754 5629 0.530650 ATCCCGTTCGCTGTATGCAG 60.531 55.000 6.42 6.42 45.23 4.41
1755 5630 1.153647 CCCGTTCGCTGTATGCAGA 60.154 57.895 15.68 0.00 45.28 4.26
1756 5631 0.739462 CCCGTTCGCTGTATGCAGAA 60.739 55.000 15.68 0.00 45.28 3.02
1757 5632 0.647410 CCGTTCGCTGTATGCAGAAG 59.353 55.000 15.68 7.63 45.28 2.85
1758 5633 1.629013 CGTTCGCTGTATGCAGAAGA 58.371 50.000 15.68 9.89 45.28 2.87
1759 5634 2.196749 CGTTCGCTGTATGCAGAAGAT 58.803 47.619 15.68 0.00 45.28 2.40
1760 5635 2.217393 CGTTCGCTGTATGCAGAAGATC 59.783 50.000 15.68 10.43 45.28 2.75
1761 5636 2.125461 TCGCTGTATGCAGAAGATCG 57.875 50.000 15.68 8.12 45.28 3.69
1762 5637 1.135046 CGCTGTATGCAGAAGATCGG 58.865 55.000 15.68 0.00 45.28 4.18
1763 5638 1.536922 CGCTGTATGCAGAAGATCGGT 60.537 52.381 15.68 0.00 45.28 4.69
1764 5639 1.863454 GCTGTATGCAGAAGATCGGTG 59.137 52.381 15.68 0.00 45.28 4.94
1765 5640 2.477825 CTGTATGCAGAAGATCGGTGG 58.522 52.381 4.57 0.00 45.28 4.61
1766 5641 1.138859 TGTATGCAGAAGATCGGTGGG 59.861 52.381 0.00 0.00 0.00 4.61
1767 5642 0.758734 TATGCAGAAGATCGGTGGGG 59.241 55.000 0.00 0.00 0.00 4.96
1768 5643 0.982852 ATGCAGAAGATCGGTGGGGA 60.983 55.000 0.00 0.00 0.00 4.81
1769 5644 0.982852 TGCAGAAGATCGGTGGGGAT 60.983 55.000 0.00 0.00 0.00 3.85
1770 5645 0.250081 GCAGAAGATCGGTGGGGATC 60.250 60.000 0.00 0.00 42.52 3.36
1771 5646 1.123077 CAGAAGATCGGTGGGGATCA 58.877 55.000 5.46 0.00 44.21 2.92
1772 5647 1.069823 CAGAAGATCGGTGGGGATCAG 59.930 57.143 5.46 0.00 44.21 2.90
1773 5648 0.394565 GAAGATCGGTGGGGATCAGG 59.605 60.000 5.46 0.00 44.21 3.86
1774 5649 1.700042 AAGATCGGTGGGGATCAGGC 61.700 60.000 5.46 0.00 44.21 4.85
1775 5650 3.171388 ATCGGTGGGGATCAGGCC 61.171 66.667 0.00 0.00 0.00 5.19
1784 5659 4.241555 GATCAGGCCGCCGGACAT 62.242 66.667 13.69 0.00 29.21 3.06
1785 5660 4.552365 ATCAGGCCGCCGGACATG 62.552 66.667 13.69 8.94 29.21 3.21
1790 5665 4.927782 GCCGCCGGACATGCCATA 62.928 66.667 7.68 0.00 35.94 2.74
1791 5666 2.666190 CCGCCGGACATGCCATAG 60.666 66.667 5.05 0.00 35.94 2.23
1792 5667 2.666190 CGCCGGACATGCCATAGG 60.666 66.667 5.05 0.00 35.94 2.57
1793 5668 2.828868 GCCGGACATGCCATAGGA 59.171 61.111 5.05 0.00 35.94 2.94
1794 5669 1.302033 GCCGGACATGCCATAGGAG 60.302 63.158 5.05 0.00 35.94 3.69
1795 5670 1.302033 CCGGACATGCCATAGGAGC 60.302 63.158 0.00 0.00 35.94 4.70
1796 5671 1.665916 CGGACATGCCATAGGAGCG 60.666 63.158 0.00 0.00 35.94 5.03
1797 5672 1.748403 GGACATGCCATAGGAGCGA 59.252 57.895 0.00 0.00 36.34 4.93
1806 5694 2.683867 GCCATAGGAGCGAGATACGTAT 59.316 50.000 8.05 8.05 44.60 3.06
1974 5923 1.829849 CAGTGAGCCTCATCTTCCTCA 59.170 52.381 0.00 0.00 32.35 3.86
2023 5995 2.030185 GTCGTCTCTGCTCCACTTGTAA 60.030 50.000 0.00 0.00 0.00 2.41
2024 5996 2.826128 TCGTCTCTGCTCCACTTGTAAT 59.174 45.455 0.00 0.00 0.00 1.89
2054 6069 2.752238 CTCGTCCTCTCTGCCCGT 60.752 66.667 0.00 0.00 0.00 5.28
2099 6127 9.725019 TTGGTTCTGGATATACATCAATACATC 57.275 33.333 0.00 0.00 32.32 3.06
2196 6300 2.200067 TGATTTGCCGCAACAACTTTG 58.800 42.857 4.98 0.00 0.00 2.77
2386 6509 1.071228 TCCTCCGATTCCGACGAGATA 59.929 52.381 0.00 0.00 38.22 1.98
2447 6570 6.879458 CGAGGATTTTTCTTCTTCTTTCCCTA 59.121 38.462 0.00 0.00 0.00 3.53
2717 9634 4.364470 TCCCCCTCCGAGTCTTAAATTAA 58.636 43.478 0.00 0.00 0.00 1.40
2718 9635 4.407945 TCCCCCTCCGAGTCTTAAATTAAG 59.592 45.833 6.42 6.42 37.13 1.85
2732 9651 7.486232 GTCTTAAATTAAGCAAGAAGATGGTGC 59.514 37.037 7.83 0.00 38.59 5.01
2752 9672 2.922335 GCTGAAAATTCGGTGGCACTTC 60.922 50.000 18.45 12.32 35.96 3.01
2795 9721 1.282157 GAGGGCAGTTGGTTCCTACAT 59.718 52.381 6.26 0.00 0.00 2.29
2799 9725 3.153919 GGCAGTTGGTTCCTACATTTCA 58.846 45.455 6.26 0.00 0.00 2.69
2807 9733 7.174946 AGTTGGTTCCTACATTTCATTACACTG 59.825 37.037 6.26 0.00 0.00 3.66
2847 9773 9.753674 TGGTCCAGTTTATAAGAAAAATCAGAT 57.246 29.630 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.749454 GGCCTCTGCATTTGGACGAT 60.749 55.000 0.00 0.00 40.13 3.73
2 3 1.377202 GGCCTCTGCATTTGGACGA 60.377 57.895 0.00 0.00 40.13 4.20
3 4 2.753966 CGGCCTCTGCATTTGGACG 61.754 63.158 12.46 12.46 46.31 4.79
5 6 2.045045 CCGGCCTCTGCATTTGGA 60.045 61.111 0.00 0.00 40.13 3.53
6 7 3.142838 CCCGGCCTCTGCATTTGG 61.143 66.667 0.00 0.00 40.13 3.28
7 8 3.142838 CCCCGGCCTCTGCATTTG 61.143 66.667 0.00 0.00 40.13 2.32
8 9 3.224007 AACCCCGGCCTCTGCATTT 62.224 57.895 0.00 0.00 40.13 2.32
9 10 3.645268 GAACCCCGGCCTCTGCATT 62.645 63.158 0.00 0.00 40.13 3.56
10 11 4.115199 GAACCCCGGCCTCTGCAT 62.115 66.667 0.00 0.00 40.13 3.96
13 14 3.787001 GAGGAACCCCGGCCTCTG 61.787 72.222 16.27 0.00 45.72 3.35
19 20 1.571773 AAATGGAGGAGGAACCCCGG 61.572 60.000 0.00 0.00 40.05 5.73
20 21 0.107165 GAAATGGAGGAGGAACCCCG 60.107 60.000 0.00 0.00 40.05 5.73
21 22 1.299939 AGAAATGGAGGAGGAACCCC 58.700 55.000 0.00 0.00 40.05 4.95
22 23 4.586306 TTAAGAAATGGAGGAGGAACCC 57.414 45.455 0.00 0.00 40.05 4.11
23 24 6.911250 TTTTTAAGAAATGGAGGAGGAACC 57.089 37.500 0.00 0.00 39.35 3.62
45 46 8.489559 GCGGTCGAAAGGTTTTTATTTTTATTT 58.510 29.630 0.00 0.00 0.00 1.40
46 47 7.116662 GGCGGTCGAAAGGTTTTTATTTTTATT 59.883 33.333 0.00 0.00 0.00 1.40
47 48 6.587226 GGCGGTCGAAAGGTTTTTATTTTTAT 59.413 34.615 0.00 0.00 0.00 1.40
48 49 5.919707 GGCGGTCGAAAGGTTTTTATTTTTA 59.080 36.000 0.00 0.00 0.00 1.52
49 50 4.746115 GGCGGTCGAAAGGTTTTTATTTTT 59.254 37.500 0.00 0.00 0.00 1.94
50 51 4.300803 GGCGGTCGAAAGGTTTTTATTTT 58.699 39.130 0.00 0.00 0.00 1.82
51 52 3.305539 GGGCGGTCGAAAGGTTTTTATTT 60.306 43.478 0.00 0.00 0.00 1.40
52 53 2.229543 GGGCGGTCGAAAGGTTTTTATT 59.770 45.455 0.00 0.00 0.00 1.40
53 54 1.814394 GGGCGGTCGAAAGGTTTTTAT 59.186 47.619 0.00 0.00 0.00 1.40
54 55 1.202794 AGGGCGGTCGAAAGGTTTTTA 60.203 47.619 0.00 0.00 0.00 1.52
55 56 0.466739 AGGGCGGTCGAAAGGTTTTT 60.467 50.000 0.00 0.00 0.00 1.94
56 57 0.397564 TAGGGCGGTCGAAAGGTTTT 59.602 50.000 0.00 0.00 0.00 2.43
57 58 0.616891 ATAGGGCGGTCGAAAGGTTT 59.383 50.000 0.00 0.00 0.00 3.27
58 59 0.177373 GATAGGGCGGTCGAAAGGTT 59.823 55.000 0.00 0.00 0.00 3.50
59 60 1.821258 GATAGGGCGGTCGAAAGGT 59.179 57.895 0.00 0.00 0.00 3.50
60 61 1.299926 CGATAGGGCGGTCGAAAGG 60.300 63.158 0.00 0.00 40.11 3.11
61 62 0.594284 GTCGATAGGGCGGTCGAAAG 60.594 60.000 8.66 0.00 46.91 2.62
62 63 1.434696 GTCGATAGGGCGGTCGAAA 59.565 57.895 8.66 0.00 46.91 3.46
63 64 2.484062 GGTCGATAGGGCGGTCGAA 61.484 63.158 8.66 0.00 46.91 3.71
64 65 2.903855 GGTCGATAGGGCGGTCGA 60.904 66.667 3.85 3.85 43.79 4.20
65 66 4.323843 CGGTCGATAGGGCGGTCG 62.324 72.222 0.00 0.00 39.11 4.79
66 67 4.642542 GCGGTCGATAGGGCGGTC 62.643 72.222 0.00 0.00 0.00 4.79
68 69 4.944372 GTGCGGTCGATAGGGCGG 62.944 72.222 0.00 0.00 0.00 6.13
69 70 4.944372 GGTGCGGTCGATAGGGCG 62.944 72.222 0.00 0.00 0.00 6.13
70 71 4.944372 CGGTGCGGTCGATAGGGC 62.944 72.222 0.00 0.00 0.00 5.19
71 72 4.944372 GCGGTGCGGTCGATAGGG 62.944 72.222 0.00 0.00 0.00 3.53
72 73 4.201679 TGCGGTGCGGTCGATAGG 62.202 66.667 0.00 0.00 0.00 2.57
73 74 2.055310 TACTGCGGTGCGGTCGATAG 62.055 60.000 8.92 0.00 45.94 2.08
74 75 2.055310 CTACTGCGGTGCGGTCGATA 62.055 60.000 8.92 0.00 45.94 2.92
75 76 3.411418 CTACTGCGGTGCGGTCGAT 62.411 63.158 8.92 0.00 45.94 3.59
76 77 4.111016 CTACTGCGGTGCGGTCGA 62.111 66.667 8.92 0.00 45.94 4.20
77 78 3.620300 TTCTACTGCGGTGCGGTCG 62.620 63.158 8.92 1.02 45.94 4.79
78 79 1.373748 TTTCTACTGCGGTGCGGTC 60.374 57.895 8.92 0.00 45.94 4.79
80 81 1.626654 CTGTTTCTACTGCGGTGCGG 61.627 60.000 8.92 0.00 41.29 5.69
81 82 1.781555 CTGTTTCTACTGCGGTGCG 59.218 57.895 8.92 0.00 0.00 5.34
82 83 1.497722 GCTGTTTCTACTGCGGTGC 59.502 57.895 8.92 0.00 39.05 5.01
93 94 2.208431 CCCTGATCTGATCGCTGTTTC 58.792 52.381 12.65 0.00 0.00 2.78
94 95 1.745141 GCCCTGATCTGATCGCTGTTT 60.745 52.381 12.65 0.00 0.00 2.83
112 118 3.414700 CCGCCGCGATAAGATGCC 61.415 66.667 15.93 0.00 0.00 4.40
174 184 1.915614 GCTCTCGTTCGTCCGGTGTA 61.916 60.000 0.00 0.00 0.00 2.90
180 190 1.586564 CCATCGCTCTCGTTCGTCC 60.587 63.158 0.00 0.00 36.96 4.79
181 191 2.224885 GCCATCGCTCTCGTTCGTC 61.225 63.158 0.00 0.00 36.96 4.20
182 192 2.202623 GCCATCGCTCTCGTTCGT 60.203 61.111 0.00 0.00 36.96 3.85
183 193 3.315521 CGCCATCGCTCTCGTTCG 61.316 66.667 0.00 0.00 36.96 3.95
209 219 2.022129 GTGGAGCCGGCGATAATCG 61.022 63.158 23.20 0.00 43.89 3.34
210 220 0.667792 GAGTGGAGCCGGCGATAATC 60.668 60.000 23.20 15.63 0.00 1.75
211 221 1.367840 GAGTGGAGCCGGCGATAAT 59.632 57.895 23.20 10.38 0.00 1.28
212 222 2.792947 GGAGTGGAGCCGGCGATAA 61.793 63.158 23.20 5.29 0.00 1.75
213 223 3.224324 GGAGTGGAGCCGGCGATA 61.224 66.667 23.20 8.27 0.00 2.92
231 252 1.839894 GCGGGAAGGAAGGGATCAT 59.160 57.895 0.00 0.00 0.00 2.45
232 253 2.731571 CGCGGGAAGGAAGGGATCA 61.732 63.158 0.00 0.00 0.00 2.92
233 254 2.109181 CGCGGGAAGGAAGGGATC 59.891 66.667 0.00 0.00 0.00 3.36
234 255 3.480133 CCGCGGGAAGGAAGGGAT 61.480 66.667 20.10 0.00 0.00 3.85
235 256 4.707768 TCCGCGGGAAGGAAGGGA 62.708 66.667 27.83 0.00 34.33 4.20
236 257 4.468689 GTCCGCGGGAAGGAAGGG 62.469 72.222 27.83 0.00 39.84 3.95
237 258 3.372554 GAGTCCGCGGGAAGGAAGG 62.373 68.421 27.83 0.00 39.84 3.46
238 259 2.184579 GAGTCCGCGGGAAGGAAG 59.815 66.667 27.83 0.00 39.84 3.46
239 260 2.602267 TGAGTCCGCGGGAAGGAA 60.602 61.111 27.83 0.17 39.84 3.36
240 261 3.068691 CTGAGTCCGCGGGAAGGA 61.069 66.667 27.83 1.12 31.38 3.36
241 262 4.821589 GCTGAGTCCGCGGGAAGG 62.822 72.222 27.83 13.06 31.38 3.46
242 263 3.589654 TTGCTGAGTCCGCGGGAAG 62.590 63.158 27.83 17.96 31.38 3.46
256 277 1.820519 CACAGCCCATGTATGTTTGCT 59.179 47.619 0.00 0.00 41.41 3.91
257 278 1.545582 ACACAGCCCATGTATGTTTGC 59.454 47.619 0.00 0.00 41.41 3.68
343 479 1.592400 GACCTGATCGACGTGACCCA 61.592 60.000 0.00 0.00 0.00 4.51
345 481 0.456221 ATGACCTGATCGACGTGACC 59.544 55.000 0.00 0.00 0.00 4.02
402 540 1.136500 AGGGAACTTATCTCCGAACGC 59.864 52.381 0.00 0.00 37.44 4.84
426 1908 0.685097 TGAAAGGACGGTCCCAGAAG 59.315 55.000 23.21 0.00 37.19 2.85
465 1948 9.715121 ATCACATTTTTAAGATGTTGCTTTCAT 57.285 25.926 0.00 0.00 35.64 2.57
480 1963 3.096092 GCCTGGACCCATCACATTTTTA 58.904 45.455 0.00 0.00 0.00 1.52
555 3140 3.364441 GCGCATGTGCCAGTTCCA 61.364 61.111 20.70 0.00 37.91 3.53
556 3141 4.465512 CGCGCATGTGCCAGTTCC 62.466 66.667 24.76 0.00 37.91 3.62
632 3288 7.382759 ACTGATTCGTAAGTTTCTCTTCTTGAC 59.617 37.037 0.00 0.00 37.56 3.18
634 3290 7.148722 GGACTGATTCGTAAGTTTCTCTTCTTG 60.149 40.741 0.00 0.00 37.56 3.02
720 3483 6.868864 TCTTGCTAGTCATGTGAAAGAAGTAC 59.131 38.462 0.00 0.00 0.00 2.73
727 3490 5.720202 ACGTATCTTGCTAGTCATGTGAAA 58.280 37.500 0.00 0.00 0.00 2.69
732 3495 5.215903 CCAGTACGTATCTTGCTAGTCATG 58.784 45.833 0.00 0.00 0.00 3.07
733 3496 4.888239 ACCAGTACGTATCTTGCTAGTCAT 59.112 41.667 0.00 0.00 0.00 3.06
734 3497 4.267536 ACCAGTACGTATCTTGCTAGTCA 58.732 43.478 0.00 0.00 0.00 3.41
747 3809 4.382291 TCTTGCATTACAAACCAGTACGT 58.618 39.130 0.00 0.00 37.96 3.57
748 3810 5.351233 TTCTTGCATTACAAACCAGTACG 57.649 39.130 0.00 0.00 37.96 3.67
749 3811 7.865385 TCAATTTCTTGCATTACAAACCAGTAC 59.135 33.333 0.00 0.00 37.96 2.73
792 3854 8.359642 TGACAGCTTGCTTTGAATACTAATTTT 58.640 29.630 0.00 0.00 0.00 1.82
816 3892 2.571212 CAGGTAAAATAGGGCGCATGA 58.429 47.619 10.83 0.00 0.00 3.07
828 3904 2.509569 TGCGATTCAAGGCAGGTAAAA 58.490 42.857 0.00 0.00 33.52 1.52
871 4131 2.042404 AAACTCGGGTTGTGGGCGTA 62.042 55.000 0.00 0.00 35.63 4.42
1055 4823 4.779733 GGACTCAGGAGGGGGCGA 62.780 72.222 0.83 0.00 0.00 5.54
1087 4862 3.139397 TGAGAGATTAGAGGAGGGAGGTC 59.861 52.174 0.00 0.00 0.00 3.85
1088 4863 3.135279 TGAGAGATTAGAGGAGGGAGGT 58.865 50.000 0.00 0.00 0.00 3.85
1089 4864 3.893753 TGAGAGATTAGAGGAGGGAGG 57.106 52.381 0.00 0.00 0.00 4.30
1090 4865 4.996793 TGATGAGAGATTAGAGGAGGGAG 58.003 47.826 0.00 0.00 0.00 4.30
1091 4866 5.162892 ACATGATGAGAGATTAGAGGAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
1237 5032 2.438795 GAGGGGCGAGACGAGACT 60.439 66.667 0.00 0.00 0.00 3.24
1267 5071 3.781307 CGACGGATCTTGGGGGCA 61.781 66.667 0.00 0.00 0.00 5.36
1285 5089 2.821366 GGGGAGCACATGCACGAG 60.821 66.667 6.64 0.00 45.16 4.18
1288 5092 3.127533 GTCGGGGAGCACATGCAC 61.128 66.667 6.64 0.00 45.16 4.57
1697 5572 6.966021 TCTTTCCTATGTACAGTTTTTGTGC 58.034 36.000 0.33 0.00 41.10 4.57
1698 5573 8.621286 ACTTCTTTCCTATGTACAGTTTTTGTG 58.379 33.333 0.33 0.00 41.10 3.33
1699 5574 8.747538 ACTTCTTTCCTATGTACAGTTTTTGT 57.252 30.769 0.33 0.00 43.96 2.83
1700 5575 9.665264 GAACTTCTTTCCTATGTACAGTTTTTG 57.335 33.333 0.33 0.00 0.00 2.44
1716 5591 4.579340 GGGATTATTCGGGGAACTTCTTTC 59.421 45.833 0.00 0.00 0.00 2.62
1717 5592 4.533815 GGGATTATTCGGGGAACTTCTTT 58.466 43.478 0.00 0.00 0.00 2.52
1718 5593 3.433173 CGGGATTATTCGGGGAACTTCTT 60.433 47.826 0.00 0.00 0.00 2.52
1719 5594 2.104281 CGGGATTATTCGGGGAACTTCT 59.896 50.000 0.00 0.00 0.00 2.85
1720 5595 2.158856 ACGGGATTATTCGGGGAACTTC 60.159 50.000 0.00 0.00 0.00 3.01
1721 5596 1.841919 ACGGGATTATTCGGGGAACTT 59.158 47.619 0.00 0.00 0.00 2.66
1722 5597 1.503800 ACGGGATTATTCGGGGAACT 58.496 50.000 0.00 0.00 0.00 3.01
1723 5598 2.216046 GAACGGGATTATTCGGGGAAC 58.784 52.381 0.00 0.00 0.00 3.62
1724 5599 1.202557 CGAACGGGATTATTCGGGGAA 60.203 52.381 0.00 0.00 43.08 3.97
1725 5600 0.390124 CGAACGGGATTATTCGGGGA 59.610 55.000 0.00 0.00 43.08 4.81
1726 5601 1.226030 GCGAACGGGATTATTCGGGG 61.226 60.000 8.29 0.00 46.07 5.73
1727 5602 0.249741 AGCGAACGGGATTATTCGGG 60.250 55.000 8.29 0.00 46.07 5.14
1728 5603 0.859232 CAGCGAACGGGATTATTCGG 59.141 55.000 8.29 0.00 46.07 4.30
1730 5605 3.120649 GCATACAGCGAACGGGATTATTC 60.121 47.826 0.00 0.00 0.00 1.75
1731 5606 2.806244 GCATACAGCGAACGGGATTATT 59.194 45.455 0.00 0.00 0.00 1.40
1732 5607 2.413837 GCATACAGCGAACGGGATTAT 58.586 47.619 0.00 0.00 0.00 1.28
1733 5608 1.860676 GCATACAGCGAACGGGATTA 58.139 50.000 0.00 0.00 0.00 1.75
1734 5609 2.690326 GCATACAGCGAACGGGATT 58.310 52.632 0.00 0.00 0.00 3.01
1735 5610 4.438346 GCATACAGCGAACGGGAT 57.562 55.556 0.00 0.00 0.00 3.85
1744 5619 1.863454 CACCGATCTTCTGCATACAGC 59.137 52.381 0.00 0.00 44.10 4.40
1745 5620 2.477825 CCACCGATCTTCTGCATACAG 58.522 52.381 0.00 0.00 45.95 2.74
1746 5621 1.138859 CCCACCGATCTTCTGCATACA 59.861 52.381 0.00 0.00 0.00 2.29
1747 5622 1.541233 CCCCACCGATCTTCTGCATAC 60.541 57.143 0.00 0.00 0.00 2.39
1748 5623 0.758734 CCCCACCGATCTTCTGCATA 59.241 55.000 0.00 0.00 0.00 3.14
1749 5624 0.982852 TCCCCACCGATCTTCTGCAT 60.983 55.000 0.00 0.00 0.00 3.96
1750 5625 0.982852 ATCCCCACCGATCTTCTGCA 60.983 55.000 0.00 0.00 0.00 4.41
1751 5626 0.250081 GATCCCCACCGATCTTCTGC 60.250 60.000 0.00 0.00 36.51 4.26
1752 5627 1.069823 CTGATCCCCACCGATCTTCTG 59.930 57.143 0.00 0.00 39.57 3.02
1753 5628 1.418334 CTGATCCCCACCGATCTTCT 58.582 55.000 0.00 0.00 39.57 2.85
1754 5629 0.394565 CCTGATCCCCACCGATCTTC 59.605 60.000 0.00 0.00 39.57 2.87
1755 5630 1.700042 GCCTGATCCCCACCGATCTT 61.700 60.000 0.00 0.00 39.57 2.40
1756 5631 2.143419 GCCTGATCCCCACCGATCT 61.143 63.158 0.00 0.00 39.57 2.75
1757 5632 2.427753 GCCTGATCCCCACCGATC 59.572 66.667 0.00 0.00 39.35 3.69
1758 5633 3.171388 GGCCTGATCCCCACCGAT 61.171 66.667 0.00 0.00 0.00 4.18
1767 5642 4.241555 ATGTCCGGCGGCCTGATC 62.242 66.667 23.83 11.03 0.00 2.92
1768 5643 4.552365 CATGTCCGGCGGCCTGAT 62.552 66.667 23.83 7.03 0.00 2.90
1773 5648 4.927782 TATGGCATGTCCGGCGGC 62.928 66.667 23.83 17.23 37.80 6.53
1774 5649 2.666190 CTATGGCATGTCCGGCGG 60.666 66.667 22.51 22.51 37.80 6.13
1775 5650 2.666190 CCTATGGCATGTCCGGCG 60.666 66.667 10.98 0.00 37.80 6.46
1776 5651 1.302033 CTCCTATGGCATGTCCGGC 60.302 63.158 10.98 0.00 37.80 6.13
1777 5652 1.302033 GCTCCTATGGCATGTCCGG 60.302 63.158 10.98 0.00 37.80 5.14
1778 5653 1.665916 CGCTCCTATGGCATGTCCG 60.666 63.158 10.98 2.05 37.80 4.79
1779 5654 0.320247 CTCGCTCCTATGGCATGTCC 60.320 60.000 10.98 0.00 0.00 4.02
1780 5655 0.676184 TCTCGCTCCTATGGCATGTC 59.324 55.000 10.98 0.00 0.00 3.06
1781 5656 1.346062 ATCTCGCTCCTATGGCATGT 58.654 50.000 10.98 0.00 0.00 3.21
1782 5657 2.733542 CGTATCTCGCTCCTATGGCATG 60.734 54.545 10.98 0.00 0.00 4.06
1783 5658 1.474478 CGTATCTCGCTCCTATGGCAT 59.526 52.381 4.88 4.88 0.00 4.40
1784 5659 0.881796 CGTATCTCGCTCCTATGGCA 59.118 55.000 0.00 0.00 0.00 4.92
1785 5660 0.882474 ACGTATCTCGCTCCTATGGC 59.118 55.000 0.00 0.00 44.19 4.40
1786 5661 6.930164 AGTATATACGTATCTCGCTCCTATGG 59.070 42.308 12.24 0.00 44.19 2.74
1787 5662 7.652507 TCAGTATATACGTATCTCGCTCCTATG 59.347 40.741 12.24 0.00 44.19 2.23
1788 5663 7.724287 TCAGTATATACGTATCTCGCTCCTAT 58.276 38.462 12.24 0.00 44.19 2.57
1789 5664 7.105241 TCAGTATATACGTATCTCGCTCCTA 57.895 40.000 12.24 0.00 44.19 2.94
1790 5665 5.975282 TCAGTATATACGTATCTCGCTCCT 58.025 41.667 12.24 0.00 44.19 3.69
1791 5666 6.091849 TGTTCAGTATATACGTATCTCGCTCC 59.908 42.308 12.24 0.00 44.19 4.70
1792 5667 7.058298 TGTTCAGTATATACGTATCTCGCTC 57.942 40.000 12.24 0.00 44.19 5.03
1793 5668 7.612668 ATGTTCAGTATATACGTATCTCGCT 57.387 36.000 12.24 3.89 44.19 4.93
1794 5669 8.602328 AGTATGTTCAGTATATACGTATCTCGC 58.398 37.037 12.24 1.57 44.19 5.03
1795 5670 9.903185 CAGTATGTTCAGTATATACGTATCTCG 57.097 37.037 12.24 0.00 46.00 4.04
2054 6069 5.329399 ACCAAAATCAAGGGCTATACACAA 58.671 37.500 0.00 0.00 0.00 3.33
2098 6126 5.240891 GTGTCTCCAATTTCTCACTCATGA 58.759 41.667 0.00 0.00 0.00 3.07
2099 6127 4.092529 CGTGTCTCCAATTTCTCACTCATG 59.907 45.833 0.00 0.00 0.00 3.07
2108 6136 4.591202 CATGTATGCGTGTCTCCAATTTC 58.409 43.478 0.00 0.00 0.00 2.17
2196 6300 3.627577 TCCAGAAACAGAAACAGAAGCAC 59.372 43.478 0.00 0.00 0.00 4.40
2333 6456 0.964358 GCAAGTTGCTGGCCTGATCT 60.964 55.000 20.71 4.94 40.96 2.75
2386 6509 2.350522 GCGTCATGAAACTCCACAGAT 58.649 47.619 0.00 0.00 0.00 2.90
2419 6542 6.348622 GGAAAGAAGAAGAAAAATCCTCGGTC 60.349 42.308 0.00 0.00 0.00 4.79
2493 6713 0.613853 TCGGGGGATTTCTCTCGTGT 60.614 55.000 0.00 0.00 0.00 4.49
2560 9474 3.126000 CAGGACGAAGAAAAATCCTCAGC 59.874 47.826 0.00 0.00 39.66 4.26
2628 9545 5.238583 ACCACTGCTCTGAAATAACAGTAC 58.761 41.667 0.00 0.00 39.48 2.73
2704 9621 8.951243 ACCATCTTCTTGCTTAATTTAAGACTC 58.049 33.333 18.25 3.49 38.02 3.36
2718 9635 3.648339 TTTTCAGCACCATCTTCTTGC 57.352 42.857 0.00 0.00 36.45 4.01
2732 9651 2.554032 AGAAGTGCCACCGAATTTTCAG 59.446 45.455 0.00 0.00 0.00 3.02
2815 9741 8.990163 TTTTCTTATAAACTGGACCAACTCTT 57.010 30.769 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.