Multiple sequence alignment - TraesCS2A01G249600

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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 TraesCS2A01G249600 chr2A 100.000 5193 0 0 1 5193 376075850 376081042 0.000000e+00 9590
1 TraesCS2A01G249600 chr2A 82.616 558 86 10 4643 5193 95286460 95287013 2.810000e-132 483
2 TraesCS2A01G249600 chr2A 96.457 254 7 2 4942 5193 721670591 721670338 8.040000e-113 418
3 TraesCS2A01G249600 chr2A 92.996 257 17 1 4938 5193 730137842 730138098 1.770000e-99 374
4 TraesCS2A01G249600 chr2D 96.017 2134 61 13 84 2201 299887253 299889378 0.000000e+00 3448
5 TraesCS2A01G249600 chr2D 90.954 1404 80 19 2557 3913 647737719 647736316 0.000000e+00 1845
6 TraesCS2A01G249600 chr2D 92.330 678 34 12 3912 4589 299889524 299890183 0.000000e+00 948
7 TraesCS2A01G249600 chr2D 96.491 171 6 0 2200 2370 196347328 196347498 3.060000e-72 283
8 TraesCS2A01G249600 chr2D 97.561 164 1 2 2363 2526 299889377 299889537 1.420000e-70 278
9 TraesCS2A01G249600 chr2D 94.886 176 9 0 2199 2374 426427966 426427791 5.120000e-70 276
10 TraesCS2A01G249600 chr2B 97.371 1179 29 1 917 2095 371167499 371166323 0.000000e+00 2004
11 TraesCS2A01G249600 chr2B 94.365 905 33 5 1 897 371168380 371167486 0.000000e+00 1373
12 TraesCS2A01G249600 chr2B 94.970 676 18 9 3915 4589 371165847 371165187 0.000000e+00 1046
13 TraesCS2A01G249600 chr2B 91.977 349 25 3 4589 4934 61288449 61288101 2.170000e-133 486
14 TraesCS2A01G249600 chr2B 94.771 153 6 1 2374 2526 371165987 371165837 2.420000e-58 237
15 TraesCS2A01G249600 chr2B 95.370 108 4 1 2095 2201 371166205 371166098 2.490000e-38 171
16 TraesCS2A01G249600 chr7D 92.641 1386 73 15 2557 3913 73130869 73132254 0.000000e+00 1967
17 TraesCS2A01G249600 chr7D 92.652 1320 73 10 2615 3913 491255240 491256556 0.000000e+00 1879
18 TraesCS2A01G249600 chr7D 95.376 173 7 1 2197 2369 376090487 376090658 1.840000e-69 274
19 TraesCS2A01G249600 chr1D 93.293 1312 71 10 2615 3911 17121730 17123039 0.000000e+00 1919
20 TraesCS2A01G249600 chr1D 91.410 1397 86 11 2557 3927 475209267 475207879 0.000000e+00 1884
21 TraesCS2A01G249600 chr1D 94.100 1017 59 1 2897 3912 99684847 99685863 0.000000e+00 1544
22 TraesCS2A01G249600 chr1D 95.930 172 7 0 2198 2369 178466472 178466301 3.960000e-71 279
23 TraesCS2A01G249600 chr1D 96.429 168 6 0 2197 2364 238940383 238940216 1.420000e-70 278
24 TraesCS2A01G249600 chr1D 93.407 182 11 1 2191 2371 80656713 80656532 8.570000e-68 268
25 TraesCS2A01G249600 chr3D 91.482 1397 80 13 2559 3916 610135225 610136621 0.000000e+00 1884
26 TraesCS2A01G249600 chr3D 90.300 1402 89 10 2557 3911 602106066 602107467 0.000000e+00 1792
27 TraesCS2A01G249600 chr3D 90.796 1369 80 22 2590 3912 570045229 570046597 0.000000e+00 1788
28 TraesCS2A01G249600 chr3D 93.023 258 16 2 4938 5193 600705247 600704990 4.910000e-100 375
29 TraesCS2A01G249600 chr3D 93.923 181 10 1 2200 2380 547518990 547518811 6.630000e-69 272
30 TraesCS2A01G249600 chr5D 92.683 1312 81 8 2616 3912 30615225 30613914 0.000000e+00 1877
31 TraesCS2A01G249600 chr5D 91.791 1340 83 8 2558 3871 364248535 364249873 0.000000e+00 1840
32 TraesCS2A01G249600 chr5D 91.238 1381 69 16 2557 3911 393901151 393902505 0.000000e+00 1832
33 TraesCS2A01G249600 chr5D 88.105 992 72 22 1 982 546366493 546365538 0.000000e+00 1136
34 TraesCS2A01G249600 chr5D 92.435 423 29 3 1031 1451 546359035 546358614 7.440000e-168 601
35 TraesCS2A01G249600 chr5D 96.429 168 6 0 2197 2364 274578179 274578012 1.420000e-70 278
36 TraesCS2A01G249600 chr5D 94.444 180 9 1 2197 2375 92111716 92111537 5.120000e-70 276
37 TraesCS2A01G249600 chr5D 96.923 65 2 0 969 1033 546361565 546361501 5.500000e-20 110
38 TraesCS2A01G249600 chr7A 91.045 1340 97 8 2589 3909 470793932 470792597 0.000000e+00 1788
39 TraesCS2A01G249600 chr7A 87.148 1385 144 19 2557 3911 29483774 29485154 0.000000e+00 1541
40 TraesCS2A01G249600 chr7A 92.308 351 22 3 4589 4934 589074161 589074511 1.300000e-135 494
41 TraesCS2A01G249600 chr7A 92.000 350 26 2 4588 4935 731605945 731606294 1.680000e-134 490
42 TraesCS2A01G249600 chr7A 94.961 258 10 3 4938 5193 22330837 22331093 8.100000e-108 401
43 TraesCS2A01G249600 chr5B 91.201 1307 109 4 2610 3910 239281867 239283173 0.000000e+00 1772
44 TraesCS2A01G249600 chr5B 87.597 903 58 17 1 897 689487756 689486902 0.000000e+00 998
45 TraesCS2A01G249600 chr5B 87.661 778 66 15 915 1683 689486917 689486161 0.000000e+00 878
46 TraesCS2A01G249600 chr6A 92.316 924 55 7 2554 3461 22062885 22063808 0.000000e+00 1299
47 TraesCS2A01G249600 chr6A 88.525 427 35 9 4582 5000 243024107 243023687 6.000000e-139 505
48 TraesCS2A01G249600 chr6A 92.996 257 15 3 4939 5193 222896898 222896643 6.350000e-99 372
49 TraesCS2A01G249600 chr6A 92.664 259 16 2 4938 5193 31887193 31887451 2.280000e-98 370
50 TraesCS2A01G249600 chr1B 89.651 831 62 3 2592 3407 533860751 533859930 0.000000e+00 1037
51 TraesCS2A01G249600 chr1B 89.140 221 23 1 2590 2810 526250842 526251061 1.840000e-69 274
52 TraesCS2A01G249600 chr4A 86.910 848 78 15 2560 3382 607287251 607286412 0.000000e+00 920
53 TraesCS2A01G249600 chr4A 92.023 351 23 3 4589 4934 527166544 527166894 6.040000e-134 488
54 TraesCS2A01G249600 chr4A 91.977 349 24 4 4589 4934 249007675 249008022 2.170000e-133 486
55 TraesCS2A01G249600 chr3A 85.434 611 62 20 272 871 724300903 724300309 1.240000e-170 610
56 TraesCS2A01G249600 chr3A 85.517 145 19 1 1 145 724301193 724301051 3.240000e-32 150
57 TraesCS2A01G249600 chr1A 92.550 349 23 3 4589 4934 100100972 100101320 1.000000e-136 497
58 TraesCS2A01G249600 chr1A 93.023 258 16 2 4938 5193 449955083 449954826 4.910000e-100 375
59 TraesCS2A01G249600 chr5A 92.023 351 22 4 4589 4934 621966201 621965852 6.040000e-134 488
60 TraesCS2A01G249600 chr5A 95.455 176 7 1 2192 2367 382566809 382566635 3.960000e-71 279
61 TraesCS2A01G249600 chr4D 93.385 257 16 1 4938 5193 505435262 505435518 3.800000e-101 379
62 TraesCS2A01G249600 chr4D 96.429 168 6 0 2197 2364 404108575 404108742 1.420000e-70 278
63 TraesCS2A01G249600 chr4D 95.882 170 7 0 2198 2367 75782219 75782050 5.120000e-70 276
64 TraesCS2A01G249600 chr4D 96.407 167 6 0 2198 2364 93338040 93338206 5.120000e-70 276
65 TraesCS2A01G249600 chr4D 94.413 179 8 2 2196 2373 403412906 403413083 1.840000e-69 274
66 TraesCS2A01G249600 chr4D 95.376 173 7 1 2197 2368 477898792 477898964 1.840000e-69 274
67 TraesCS2A01G249600 chr4D 94.350 177 9 1 2189 2364 452926123 452926299 2.380000e-68 270
68 TraesCS2A01G249600 chr6D 95.930 172 7 0 2200 2371 389700541 389700712 3.960000e-71 279
69 TraesCS2A01G249600 chr6D 95.906 171 6 1 2200 2369 32865334 32865164 5.120000e-70 276
70 TraesCS2A01G249600 chr6D 95.858 169 7 0 2199 2367 206560273 206560441 1.840000e-69 274
71 TraesCS2A01G249600 chr6D 94.886 176 8 1 2196 2370 392896971 392897146 1.840000e-69 274
72 TraesCS2A01G249600 chr6D 95.808 167 7 0 2200 2366 406391359 406391525 2.380000e-68 270
73 TraesCS2A01G249600 chr6D 95.758 165 7 0 2200 2364 315624010 315624174 3.080000e-67 267
74 TraesCS2A01G249600 chr6D 95.238 168 8 0 2200 2367 352878326 352878493 3.080000e-67 267
75 TraesCS2A01G249600 chr6D 95.266 169 7 1 2197 2364 387100809 387100977 3.080000e-67 267
76 TraesCS2A01G249600 chr6D 93.785 177 10 1 2189 2364 419319544 419319368 1.110000e-66 265
77 TraesCS2A01G249600 chr6B 94.915 177 8 1 2200 2376 423196051 423195876 5.120000e-70 276


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 TraesCS2A01G249600 chr2A 376075850 376081042 5192 False 9590.000000 9590 100.000000 1 5193 1 chr2A.!!$F2 5192
1 TraesCS2A01G249600 chr2A 95286460 95287013 553 False 483.000000 483 82.616000 4643 5193 1 chr2A.!!$F1 550
2 TraesCS2A01G249600 chr2D 647736316 647737719 1403 True 1845.000000 1845 90.954000 2557 3913 1 chr2D.!!$R2 1356
3 TraesCS2A01G249600 chr2D 299887253 299890183 2930 False 1558.000000 3448 95.302667 84 4589 3 chr2D.!!$F2 4505
4 TraesCS2A01G249600 chr2B 371165187 371168380 3193 True 966.200000 2004 95.369400 1 4589 5 chr2B.!!$R2 4588
5 TraesCS2A01G249600 chr7D 73130869 73132254 1385 False 1967.000000 1967 92.641000 2557 3913 1 chr7D.!!$F1 1356
6 TraesCS2A01G249600 chr7D 491255240 491256556 1316 False 1879.000000 1879 92.652000 2615 3913 1 chr7D.!!$F3 1298
7 TraesCS2A01G249600 chr1D 17121730 17123039 1309 False 1919.000000 1919 93.293000 2615 3911 1 chr1D.!!$F1 1296
8 TraesCS2A01G249600 chr1D 475207879 475209267 1388 True 1884.000000 1884 91.410000 2557 3927 1 chr1D.!!$R4 1370
9 TraesCS2A01G249600 chr1D 99684847 99685863 1016 False 1544.000000 1544 94.100000 2897 3912 1 chr1D.!!$F2 1015
10 TraesCS2A01G249600 chr3D 610135225 610136621 1396 False 1884.000000 1884 91.482000 2559 3916 1 chr3D.!!$F3 1357
11 TraesCS2A01G249600 chr3D 602106066 602107467 1401 False 1792.000000 1792 90.300000 2557 3911 1 chr3D.!!$F2 1354
12 TraesCS2A01G249600 chr3D 570045229 570046597 1368 False 1788.000000 1788 90.796000 2590 3912 1 chr3D.!!$F1 1322
13 TraesCS2A01G249600 chr5D 30613914 30615225 1311 True 1877.000000 1877 92.683000 2616 3912 1 chr5D.!!$R1 1296
14 TraesCS2A01G249600 chr5D 364248535 364249873 1338 False 1840.000000 1840 91.791000 2558 3871 1 chr5D.!!$F1 1313
15 TraesCS2A01G249600 chr5D 393901151 393902505 1354 False 1832.000000 1832 91.238000 2557 3911 1 chr5D.!!$F2 1354
16 TraesCS2A01G249600 chr5D 546358614 546366493 7879 True 615.666667 1136 92.487667 1 1451 3 chr5D.!!$R4 1450
17 TraesCS2A01G249600 chr7A 470792597 470793932 1335 True 1788.000000 1788 91.045000 2589 3909 1 chr7A.!!$R1 1320
18 TraesCS2A01G249600 chr7A 29483774 29485154 1380 False 1541.000000 1541 87.148000 2557 3911 1 chr7A.!!$F2 1354
19 TraesCS2A01G249600 chr5B 239281867 239283173 1306 False 1772.000000 1772 91.201000 2610 3910 1 chr5B.!!$F1 1300
20 TraesCS2A01G249600 chr5B 689486161 689487756 1595 True 938.000000 998 87.629000 1 1683 2 chr5B.!!$R1 1682
21 TraesCS2A01G249600 chr6A 22062885 22063808 923 False 1299.000000 1299 92.316000 2554 3461 1 chr6A.!!$F1 907
22 TraesCS2A01G249600 chr1B 533859930 533860751 821 True 1037.000000 1037 89.651000 2592 3407 1 chr1B.!!$R1 815
23 TraesCS2A01G249600 chr4A 607286412 607287251 839 True 920.000000 920 86.910000 2560 3382 1 chr4A.!!$R1 822
24 TraesCS2A01G249600 chr3A 724300309 724301193 884 True 380.000000 610 85.475500 1 871 2 chr3A.!!$R1 870

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
824 916 0.243907 TCTCGCGTTTCTCAAGAGGG 59.756 55.000 5.77 0.0 0.00 4.30 F
967 5053 0.600255 GACCGAACCCACTGACACAG 60.600 60.000 0.00 0.0 37.52 3.66 F
2549 9347 0.466124 ATCTCTAACGAAGCCCCTGC 59.534 55.000 0.00 0.0 37.95 4.85 F
3232 10128 1.152419 TGGAGTTCCAGGTCGGACA 60.152 57.895 10.76 0.0 46.36 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 9328 0.466124 GCAGGGGCTTCGTTAGAGAT 59.534 55.000 0.00 0.00 36.96 2.75 R
2950 9835 1.144936 GATGAAGTAGGGCGCTGCT 59.855 57.895 15.69 15.69 0.00 4.24 R
3436 10334 0.036388 CAAGTACCACCAGCCGACAT 60.036 55.000 0.00 0.00 0.00 3.06 R
4598 11514 0.172578 CAGGGTGACGAATAGCACGA 59.827 55.000 0.00 0.00 35.91 4.35 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
51 52 3.279434 CTGAAAAATCTAACCCTCCCCG 58.721 50.000 0.00 0.00 0.00 5.73
52 53 2.025699 TGAAAAATCTAACCCTCCCCGG 60.026 50.000 0.00 0.00 0.00 5.73
92 93 0.827925 AGGACTCTGCCTTGTCGACA 60.828 55.000 15.76 15.76 33.46 4.35
104 105 3.473367 CTTGTCGACAATTGCTTCTTCG 58.527 45.455 29.79 11.44 35.02 3.79
112 113 5.615544 CGACAATTGCTTCTTCGTTCTTCAT 60.616 40.000 5.05 0.00 0.00 2.57
150 151 1.079658 AGGAAGTAGCCTCCTCAACCT 59.920 52.381 0.00 0.00 30.76 3.50
209 270 5.361427 TCTCCGTTGTTCTTGTTTGTATCA 58.639 37.500 0.00 0.00 0.00 2.15
405 469 3.292936 ACGACACGAACGCCTCCT 61.293 61.111 0.00 0.00 0.00 3.69
420 484 3.373565 CCTTTGCAACCTCCGGCC 61.374 66.667 0.00 0.00 0.00 6.13
534 604 4.382541 TCCTCTCGGCTGCCTCCA 62.383 66.667 17.92 0.00 0.00 3.86
594 676 2.772691 GGGATCGACTTCGGACGCT 61.773 63.158 0.00 0.00 40.29 5.07
595 677 1.442526 GGGATCGACTTCGGACGCTA 61.443 60.000 0.00 0.00 40.29 4.26
596 678 0.316854 GGATCGACTTCGGACGCTAC 60.317 60.000 0.00 0.00 40.29 3.58
597 679 0.316854 GATCGACTTCGGACGCTACC 60.317 60.000 0.00 0.00 40.29 3.18
824 916 0.243907 TCTCGCGTTTCTCAAGAGGG 59.756 55.000 5.77 0.00 0.00 4.30
956 1048 2.027625 CCACAAGAGCGACCGAACC 61.028 63.158 0.00 0.00 0.00 3.62
957 1049 2.027625 CACAAGAGCGACCGAACCC 61.028 63.158 0.00 0.00 0.00 4.11
967 5053 0.600255 GACCGAACCCACTGACACAG 60.600 60.000 0.00 0.00 37.52 3.66
1254 7815 2.041350 AGAGGAGTACGTGGAGGAAGAA 59.959 50.000 0.00 0.00 0.00 2.52
1257 7818 1.477295 GAGTACGTGGAGGAAGAAGGG 59.523 57.143 0.00 0.00 0.00 3.95
1287 7848 3.775654 CCCGAGGTCCAGGCAGTC 61.776 72.222 0.00 0.00 0.00 3.51
1493 8055 2.292521 TGCCTATCTCTGGTCTTCCTGT 60.293 50.000 0.00 0.00 34.80 4.00
1502 8077 3.064931 CTGGTCTTCCTGTAACGGTTTC 58.935 50.000 0.00 0.00 34.23 2.78
1704 8280 5.449588 CCTGTTCTTGGTCATGAATGCATAC 60.450 44.000 0.00 0.00 32.27 2.39
1782 8358 0.755327 GAGGAGGAGAGAGGGCAGTC 60.755 65.000 0.00 0.00 0.00 3.51
1971 8547 1.155155 TTCCAGGGGGTTTGGCTTC 59.845 57.895 0.00 0.00 35.62 3.86
2006 8582 4.338879 ACAATAGAAGATGCAAAGGCTGT 58.661 39.130 0.00 0.00 41.91 4.40
2053 8629 5.695851 ATGTCTTTGTTGCAACCTTAGAG 57.304 39.130 26.14 15.53 0.00 2.43
2137 8832 3.382227 CCAAGCCATGCATGATAAGAACA 59.618 43.478 28.31 0.00 27.85 3.18
2201 8897 6.938596 AGGTTACCAGGTGTTTCTTGTTATAC 59.061 38.462 0.76 0.00 0.00 1.47
2203 8899 7.118825 GGTTACCAGGTGTTTCTTGTTATACTC 59.881 40.741 0.76 0.00 0.00 2.59
2204 8900 5.557866 ACCAGGTGTTTCTTGTTATACTCC 58.442 41.667 0.00 0.00 0.00 3.85
2205 8901 4.941873 CCAGGTGTTTCTTGTTATACTCCC 59.058 45.833 0.00 0.00 0.00 4.30
2206 8902 5.280521 CCAGGTGTTTCTTGTTATACTCCCT 60.281 44.000 0.00 0.00 0.00 4.20
2207 8903 5.875359 CAGGTGTTTCTTGTTATACTCCCTC 59.125 44.000 0.00 0.00 0.00 4.30
2208 8904 5.045797 AGGTGTTTCTTGTTATACTCCCTCC 60.046 44.000 0.00 0.00 0.00 4.30
2209 8905 4.868734 GTGTTTCTTGTTATACTCCCTCCG 59.131 45.833 0.00 0.00 0.00 4.63
2210 8906 4.529377 TGTTTCTTGTTATACTCCCTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
2211 8907 5.012354 TGTTTCTTGTTATACTCCCTCCGTT 59.988 40.000 0.00 0.00 0.00 4.44
2212 8908 4.996788 TCTTGTTATACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
2213 8909 3.703052 TCTTGTTATACTCCCTCCGTTCC 59.297 47.826 0.00 0.00 0.00 3.62
2214 8910 3.393426 TGTTATACTCCCTCCGTTCCT 57.607 47.619 0.00 0.00 0.00 3.36
2215 8911 4.524802 TGTTATACTCCCTCCGTTCCTA 57.475 45.455 0.00 0.00 0.00 2.94
2216 8912 4.870636 TGTTATACTCCCTCCGTTCCTAA 58.129 43.478 0.00 0.00 0.00 2.69
2217 8913 5.271598 TGTTATACTCCCTCCGTTCCTAAA 58.728 41.667 0.00 0.00 0.00 1.85
2218 8914 5.901276 TGTTATACTCCCTCCGTTCCTAAAT 59.099 40.000 0.00 0.00 0.00 1.40
2219 8915 7.068702 TGTTATACTCCCTCCGTTCCTAAATA 58.931 38.462 0.00 0.00 0.00 1.40
2220 8916 7.731688 TGTTATACTCCCTCCGTTCCTAAATAT 59.268 37.037 0.00 0.00 0.00 1.28
2221 8917 8.591940 GTTATACTCCCTCCGTTCCTAAATATT 58.408 37.037 0.00 0.00 0.00 1.28
2222 8918 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2223 8919 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2224 8920 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2225 8921 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2226 8922 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2227 8923 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2228 8924 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2229 8925 7.771826 CCCTCCGTTCCTAAATATTTGTCTTTA 59.228 37.037 11.05 0.00 0.00 1.85
2230 8926 9.338622 CCTCCGTTCCTAAATATTTGTCTTTAT 57.661 33.333 11.05 0.00 0.00 1.40
2258 8954 9.702726 CAGATTTCAACAAATAACTACATACGG 57.297 33.333 0.00 0.00 31.94 4.02
2259 8955 9.661563 AGATTTCAACAAATAACTACATACGGA 57.338 29.630 0.00 0.00 31.94 4.69
2260 8956 9.916397 GATTTCAACAAATAACTACATACGGAG 57.084 33.333 0.00 0.00 31.94 4.63
2261 8957 6.897259 TCAACAAATAACTACATACGGAGC 57.103 37.500 0.00 0.00 0.00 4.70
2262 8958 6.399743 TCAACAAATAACTACATACGGAGCA 58.600 36.000 0.00 0.00 0.00 4.26
2263 8959 6.874664 TCAACAAATAACTACATACGGAGCAA 59.125 34.615 0.00 0.00 0.00 3.91
2264 8960 7.388224 TCAACAAATAACTACATACGGAGCAAA 59.612 33.333 0.00 0.00 0.00 3.68
2265 8961 7.675962 ACAAATAACTACATACGGAGCAAAA 57.324 32.000 0.00 0.00 0.00 2.44
2266 8962 8.276252 ACAAATAACTACATACGGAGCAAAAT 57.724 30.769 0.00 0.00 0.00 1.82
2267 8963 8.181573 ACAAATAACTACATACGGAGCAAAATG 58.818 33.333 0.00 0.00 0.00 2.32
2268 8964 8.394877 CAAATAACTACATACGGAGCAAAATGA 58.605 33.333 0.00 0.00 0.00 2.57
2269 8965 7.715265 ATAACTACATACGGAGCAAAATGAG 57.285 36.000 0.00 0.00 0.00 2.90
2270 8966 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2271 8967 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2272 8968 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2273 8969 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2274 8970 4.154195 ACATACGGAGCAAAATGAGTGAAC 59.846 41.667 0.00 0.00 0.00 3.18
2275 8971 1.880027 ACGGAGCAAAATGAGTGAACC 59.120 47.619 0.00 0.00 0.00 3.62
2276 8972 2.154462 CGGAGCAAAATGAGTGAACCT 58.846 47.619 0.00 0.00 0.00 3.50
2277 8973 3.244422 ACGGAGCAAAATGAGTGAACCTA 60.244 43.478 0.00 0.00 0.00 3.08
2278 8974 3.125316 CGGAGCAAAATGAGTGAACCTAC 59.875 47.826 0.00 0.00 0.00 3.18
2279 8975 4.072131 GGAGCAAAATGAGTGAACCTACA 58.928 43.478 0.00 0.00 0.00 2.74
2280 8976 4.083271 GGAGCAAAATGAGTGAACCTACAC 60.083 45.833 0.00 0.00 40.60 2.90
2294 8990 9.036980 AGTGAACCTACACTCTAAAATATGTCT 57.963 33.333 0.00 0.00 46.36 3.41
2319 9015 9.788889 CTATATACATCCGTATATGGTAGTCCA 57.211 37.037 10.85 3.57 46.31 4.02
2336 9032 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2340 9036 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2341 9037 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2358 9054 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2359 9055 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2360 9056 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2361 9057 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2362 9058 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2363 9059 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2364 9060 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
2365 9061 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
2366 9062 3.463048 TTAGGAACGGAGGGAGTAGTT 57.537 47.619 0.00 0.00 0.00 2.24
2367 9063 1.558233 AGGAACGGAGGGAGTAGTTG 58.442 55.000 0.00 0.00 0.00 3.16
2368 9064 1.203149 AGGAACGGAGGGAGTAGTTGT 60.203 52.381 0.00 0.00 0.00 3.32
2525 9323 4.403585 GGTACCCTAAGATCTCACCAAC 57.596 50.000 0.00 0.00 0.00 3.77
2526 9324 3.181478 GGTACCCTAAGATCTCACCAACG 60.181 52.174 0.00 0.00 0.00 4.10
2527 9325 1.831736 ACCCTAAGATCTCACCAACGG 59.168 52.381 0.00 0.00 0.00 4.44
2528 9326 1.831736 CCCTAAGATCTCACCAACGGT 59.168 52.381 0.00 0.00 35.62 4.83
2529 9327 2.159085 CCCTAAGATCTCACCAACGGTC 60.159 54.545 0.00 0.00 31.02 4.79
2530 9328 2.496070 CCTAAGATCTCACCAACGGTCA 59.504 50.000 0.00 0.00 31.02 4.02
2531 9329 3.133003 CCTAAGATCTCACCAACGGTCAT 59.867 47.826 0.00 0.00 31.02 3.06
2532 9330 2.969628 AGATCTCACCAACGGTCATC 57.030 50.000 0.00 0.00 31.02 2.92
2533 9331 2.461695 AGATCTCACCAACGGTCATCT 58.538 47.619 0.00 0.00 31.02 2.90
2534 9332 2.428890 AGATCTCACCAACGGTCATCTC 59.571 50.000 0.00 0.00 31.02 2.75
2535 9333 1.924731 TCTCACCAACGGTCATCTCT 58.075 50.000 0.00 0.00 31.02 3.10
2536 9334 3.081710 TCTCACCAACGGTCATCTCTA 57.918 47.619 0.00 0.00 31.02 2.43
2537 9335 3.427573 TCTCACCAACGGTCATCTCTAA 58.572 45.455 0.00 0.00 31.02 2.10
2538 9336 3.192844 TCTCACCAACGGTCATCTCTAAC 59.807 47.826 0.00 0.00 31.02 2.34
2539 9337 2.094906 TCACCAACGGTCATCTCTAACG 60.095 50.000 0.00 0.00 31.02 3.18
2540 9338 2.094906 CACCAACGGTCATCTCTAACGA 60.095 50.000 0.00 0.00 31.02 3.85
2541 9339 2.559668 ACCAACGGTCATCTCTAACGAA 59.440 45.455 0.00 0.00 0.00 3.85
2542 9340 3.179830 CCAACGGTCATCTCTAACGAAG 58.820 50.000 0.00 0.00 0.00 3.79
2543 9341 2.563471 ACGGTCATCTCTAACGAAGC 57.437 50.000 0.00 0.00 0.00 3.86
2544 9342 1.134560 ACGGTCATCTCTAACGAAGCC 59.865 52.381 0.00 0.00 0.00 4.35
2545 9343 1.536284 CGGTCATCTCTAACGAAGCCC 60.536 57.143 0.00 0.00 0.00 5.19
2546 9344 1.202545 GGTCATCTCTAACGAAGCCCC 60.203 57.143 0.00 0.00 0.00 5.80
2547 9345 1.757699 GTCATCTCTAACGAAGCCCCT 59.242 52.381 0.00 0.00 0.00 4.79
2548 9346 1.757118 TCATCTCTAACGAAGCCCCTG 59.243 52.381 0.00 0.00 0.00 4.45
2549 9347 0.466124 ATCTCTAACGAAGCCCCTGC 59.534 55.000 0.00 0.00 37.95 4.85
2550 9348 1.519455 CTCTAACGAAGCCCCTGCG 60.519 63.158 0.00 0.00 44.33 5.18
2551 9349 3.195698 CTAACGAAGCCCCTGCGC 61.196 66.667 0.00 0.00 44.33 6.09
2884 9755 3.733960 CTGCGTCCTCGTCGTGGA 61.734 66.667 11.90 11.90 39.49 4.02
2909 9794 3.770040 CCATGAGGCGTGGTCCGA 61.770 66.667 0.00 0.00 39.56 4.55
2974 9859 1.951631 GCCCTACTTCATCTCGCGC 60.952 63.158 0.00 0.00 0.00 6.86
3173 10065 2.034305 GGAGGCATCGTCGTGTAACTAT 59.966 50.000 0.00 0.00 31.75 2.12
3232 10128 1.152419 TGGAGTTCCAGGTCGGACA 60.152 57.895 10.76 0.00 46.36 4.02
3264 10160 1.868519 GCGGTGTCGTTTCTCTCTTGT 60.869 52.381 0.00 0.00 38.89 3.16
3304 10202 1.881903 CGCTGGAAGTCAGAGGCAGA 61.882 60.000 0.00 0.00 46.18 4.26
3315 10213 2.604686 AGGCAGAAGGTGGAGCGA 60.605 61.111 0.00 0.00 0.00 4.93
3361 10259 3.209410 GGAGATGTTAAGTCATGCCTGG 58.791 50.000 0.00 0.00 0.00 4.45
3387 10285 2.674852 CAGATGCTACGCTTTGTCATGT 59.325 45.455 0.00 0.00 0.00 3.21
3436 10334 9.436957 GACATATCTTCCAAAGACTTCAAGTTA 57.563 33.333 0.00 0.00 41.01 2.24
3478 10376 1.755179 GCATGGTGCTGAGGTGTATT 58.245 50.000 0.00 0.00 40.96 1.89
3567 10471 1.068281 TCGACGATAGCTAGACCGAGT 59.932 52.381 16.48 3.42 42.67 4.18
3694 10600 1.007963 AGATGGGTCCTCGGGTCTTAA 59.992 52.381 0.00 0.00 0.00 1.85
3781 10695 4.519730 ACTGGATAGGTGTAGCGATAGTTC 59.480 45.833 0.00 0.00 39.35 3.01
3820 10735 7.985752 GTGGCTTTAGTCTTACTGTGGTATTAT 59.014 37.037 0.00 0.00 0.00 1.28
4130 11046 6.488006 AGAGGTCGACAAAAACAGTACTACTA 59.512 38.462 18.91 0.00 0.00 1.82
4131 11047 6.442112 AGGTCGACAAAAACAGTACTACTAC 58.558 40.000 18.91 0.00 0.00 2.73
4132 11048 6.264067 AGGTCGACAAAAACAGTACTACTACT 59.736 38.462 18.91 0.00 33.01 2.57
4175 11091 4.457257 AGATGGAAAAGAGCAACTTACAGC 59.543 41.667 0.00 0.00 37.93 4.40
4293 11209 4.573900 AGATGTACTGGTCTGAGCAAAAG 58.426 43.478 11.07 2.22 0.00 2.27
4348 11264 7.858382 CGGACACTAGATTATTAGACTCTTGTG 59.142 40.741 0.00 7.09 43.62 3.33
4387 11303 6.705863 AGAAATATCTGGATCCAAAAGTGC 57.294 37.500 17.00 1.97 33.59 4.40
4388 11304 5.595952 AGAAATATCTGGATCCAAAAGTGCC 59.404 40.000 17.00 3.70 33.59 5.01
4389 11305 4.803329 ATATCTGGATCCAAAAGTGCCT 57.197 40.909 17.00 0.00 0.00 4.75
4390 11306 2.496899 TCTGGATCCAAAAGTGCCTC 57.503 50.000 17.00 0.00 0.00 4.70
4391 11307 1.704628 TCTGGATCCAAAAGTGCCTCA 59.295 47.619 17.00 0.00 0.00 3.86
4392 11308 2.309755 TCTGGATCCAAAAGTGCCTCAT 59.690 45.455 17.00 0.00 0.00 2.90
4394 11310 1.753073 GGATCCAAAAGTGCCTCATGG 59.247 52.381 6.95 0.00 0.00 3.66
4471 11387 3.181445 TGGATTGACTAAGTGGTTGTGCT 60.181 43.478 0.00 0.00 0.00 4.40
4472 11388 3.189287 GGATTGACTAAGTGGTTGTGCTG 59.811 47.826 0.00 0.00 0.00 4.41
4473 11389 1.593196 TGACTAAGTGGTTGTGCTGC 58.407 50.000 0.00 0.00 0.00 5.25
4479 11395 1.109323 AGTGGTTGTGCTGCCCTTTC 61.109 55.000 0.00 0.00 0.00 2.62
4492 11408 7.041107 GTGCTGCCCTTTCATGAAATAAATTA 58.959 34.615 20.76 5.76 0.00 1.40
4527 11443 3.303132 GGTTGTTCGCTACTGTCAGTTTG 60.303 47.826 11.54 6.09 0.00 2.93
4554 11470 2.115427 AGGCTCTTAGCTCCTTTCTCC 58.885 52.381 0.00 0.00 41.99 3.71
4577 11493 4.322349 CCTGGACTTGTTTCCACACAAAAA 60.322 41.667 0.00 0.00 41.00 1.94
4589 11505 4.576873 TCCACACAAAAAGCGATTTGAGTA 59.423 37.500 19.70 5.60 40.53 2.59
4590 11506 5.240623 TCCACACAAAAAGCGATTTGAGTAT 59.759 36.000 19.70 0.00 40.53 2.12
4591 11507 6.428465 TCCACACAAAAAGCGATTTGAGTATA 59.572 34.615 19.70 9.36 40.53 1.47
4592 11508 7.120579 TCCACACAAAAAGCGATTTGAGTATAT 59.879 33.333 19.70 0.00 40.53 0.86
4593 11509 8.394877 CCACACAAAAAGCGATTTGAGTATATA 58.605 33.333 19.70 0.00 40.53 0.86
4594 11510 9.935682 CACACAAAAAGCGATTTGAGTATATAT 57.064 29.630 19.70 0.00 40.53 0.86
4603 11519 9.613957 AGCGATTTGAGTATATATATATCGTGC 57.386 33.333 17.96 10.16 0.00 5.34
4604 11520 9.613957 GCGATTTGAGTATATATATATCGTGCT 57.386 33.333 17.96 7.14 0.00 4.40
4615 11531 2.787601 TATCGTGCTATTCGTCACCC 57.212 50.000 0.00 0.00 0.00 4.61
4616 11532 1.112113 ATCGTGCTATTCGTCACCCT 58.888 50.000 0.00 0.00 0.00 4.34
4617 11533 0.172578 TCGTGCTATTCGTCACCCTG 59.827 55.000 0.00 0.00 0.00 4.45
4618 11534 1.421410 CGTGCTATTCGTCACCCTGC 61.421 60.000 0.00 0.00 0.00 4.85
4619 11535 1.153647 TGCTATTCGTCACCCTGCG 60.154 57.895 0.00 0.00 0.00 5.18
4620 11536 1.153628 GCTATTCGTCACCCTGCGT 60.154 57.895 0.00 0.00 0.00 5.24
4621 11537 1.421410 GCTATTCGTCACCCTGCGTG 61.421 60.000 0.00 0.00 44.50 5.34
4627 11543 3.805928 TCACCCTGCGTGAGGAAT 58.194 55.556 4.32 0.00 46.80 3.01
4628 11544 2.985001 TCACCCTGCGTGAGGAATA 58.015 52.632 4.32 0.00 46.80 1.75
4629 11545 0.824109 TCACCCTGCGTGAGGAATAG 59.176 55.000 4.32 0.00 46.80 1.73
4630 11546 0.537188 CACCCTGCGTGAGGAATAGT 59.463 55.000 4.32 0.00 46.33 2.12
4631 11547 1.066143 CACCCTGCGTGAGGAATAGTT 60.066 52.381 4.32 0.00 46.33 2.24
4632 11548 2.167693 CACCCTGCGTGAGGAATAGTTA 59.832 50.000 4.32 0.00 46.33 2.24
4633 11549 3.039011 ACCCTGCGTGAGGAATAGTTAT 58.961 45.455 4.32 0.00 46.33 1.89
4634 11550 3.454812 ACCCTGCGTGAGGAATAGTTATT 59.545 43.478 4.32 0.00 46.33 1.40
4635 11551 4.058817 CCCTGCGTGAGGAATAGTTATTC 58.941 47.826 4.32 3.75 46.33 1.75
4636 11552 4.202264 CCCTGCGTGAGGAATAGTTATTCT 60.202 45.833 10.71 0.00 46.33 2.40
4637 11553 5.360591 CCTGCGTGAGGAATAGTTATTCTT 58.639 41.667 10.71 4.41 46.33 2.52
4638 11554 5.463724 CCTGCGTGAGGAATAGTTATTCTTC 59.536 44.000 13.90 13.90 46.33 2.87
4668 11584 8.388853 CCTCTCTATTTTATCATCAATGCATCG 58.611 37.037 0.00 0.00 0.00 3.84
4707 11623 8.227791 TCATAAGTTTTGTCTTATTTCTGACGC 58.772 33.333 0.00 0.00 38.19 5.19
4715 11631 7.202016 TGTCTTATTTCTGACGCAAAAAGAT 57.798 32.000 0.00 0.00 36.10 2.40
4717 11633 8.227791 TGTCTTATTTCTGACGCAAAAAGATAC 58.772 33.333 0.00 0.00 36.10 2.24
4719 11635 5.957842 ATTTCTGACGCAAAAAGATACCA 57.042 34.783 0.00 0.00 0.00 3.25
4727 11643 7.877003 TGACGCAAAAAGATACCATAAGAAAA 58.123 30.769 0.00 0.00 0.00 2.29
4805 11723 9.893305 AAACTGTCTAAAATACACATAAACTGC 57.107 29.630 0.00 0.00 0.00 4.40
4806 11724 8.615878 ACTGTCTAAAATACACATAAACTGCA 57.384 30.769 0.00 0.00 0.00 4.41
4808 11726 9.891828 CTGTCTAAAATACACATAAACTGCAAA 57.108 29.630 0.00 0.00 0.00 3.68
4952 11873 7.681125 ACGTCGAAAGTTACTATTCATCATC 57.319 36.000 0.00 0.00 0.00 2.92
4990 11911 5.727434 AGTTATTCTTCACCCGACGTAATT 58.273 37.500 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.066374 AGATTTTTCAGCTCGTGATAACTTC 57.934 36.000 0.00 0.00 34.17 3.01
51 52 7.120285 GTCCTTGTCTTTGGGTAACTAATAACC 59.880 40.741 0.00 0.00 42.26 2.85
52 53 7.881751 AGTCCTTGTCTTTGGGTAACTAATAAC 59.118 37.037 0.00 0.00 36.70 1.89
92 93 4.156739 GGGATGAAGAACGAAGAAGCAATT 59.843 41.667 0.00 0.00 0.00 2.32
104 105 1.521681 CGCCGAGGGGATGAAGAAC 60.522 63.158 0.00 0.00 34.06 3.01
150 151 1.676968 CGGACACTGATTGGGTGGA 59.323 57.895 0.00 0.00 38.83 4.02
235 296 4.452733 CCGTCTCCGACCAAGCCC 62.453 72.222 0.00 0.00 35.63 5.19
420 484 2.359900 GGGTTCTGCCTGTACATGAAG 58.640 52.381 0.00 0.77 37.43 3.02
534 604 3.444805 GAGGAGTCGTCCAGCGCT 61.445 66.667 2.64 2.64 46.80 5.92
594 676 1.169577 ATTTTGCAATGGCGTCGGTA 58.830 45.000 0.00 0.00 45.35 4.02
595 677 0.316841 AATTTTGCAATGGCGTCGGT 59.683 45.000 0.00 0.00 45.35 4.69
596 678 1.389784 GAAATTTTGCAATGGCGTCGG 59.610 47.619 0.00 0.00 45.35 4.79
597 679 2.327568 AGAAATTTTGCAATGGCGTCG 58.672 42.857 0.00 0.00 45.35 5.12
598 680 2.342354 CGAGAAATTTTGCAATGGCGTC 59.658 45.455 0.00 0.00 45.35 5.19
599 681 2.327568 CGAGAAATTTTGCAATGGCGT 58.672 42.857 0.00 0.00 45.35 5.68
600 682 1.059549 GCGAGAAATTTTGCAATGGCG 59.940 47.619 0.00 0.00 45.35 5.69
601 683 2.067766 TGCGAGAAATTTTGCAATGGC 58.932 42.857 0.00 0.00 34.59 4.40
602 684 2.090967 CGTGCGAGAAATTTTGCAATGG 59.909 45.455 13.16 5.10 39.10 3.16
902 994 3.587506 CCCCTACTCCTCTTTTTCCTTGA 59.412 47.826 0.00 0.00 0.00 3.02
903 995 3.587506 TCCCCTACTCCTCTTTTTCCTTG 59.412 47.826 0.00 0.00 0.00 3.61
904 996 3.883135 TCCCCTACTCCTCTTTTTCCTT 58.117 45.455 0.00 0.00 0.00 3.36
906 998 5.163184 CCTTATCCCCTACTCCTCTTTTTCC 60.163 48.000 0.00 0.00 0.00 3.13
907 999 5.666265 TCCTTATCCCCTACTCCTCTTTTTC 59.334 44.000 0.00 0.00 0.00 2.29
913 1005 6.013553 GGTAATTTCCTTATCCCCTACTCCTC 60.014 46.154 0.00 0.00 0.00 3.71
956 1048 1.524393 TGCTGTGCTGTGTCAGTGG 60.524 57.895 0.00 0.00 33.43 4.00
957 1049 1.645455 GTGCTGTGCTGTGTCAGTG 59.355 57.895 0.00 0.00 33.43 3.66
1213 7768 2.697751 CTGGACCCTCCTCAGAGTAATG 59.302 54.545 0.00 0.00 38.58 1.90
1254 7815 2.285743 GGTTCTGCCTCCTCCCCT 60.286 66.667 0.00 0.00 0.00 4.79
1257 7818 2.683933 TCGGGTTCTGCCTCCTCC 60.684 66.667 0.00 0.00 37.43 4.30
1287 7848 2.739132 GGGGGATAGTAACCGCGG 59.261 66.667 26.86 26.86 40.53 6.46
1493 8055 2.080693 AGCGCAATCATGAAACCGTTA 58.919 42.857 11.47 0.00 0.00 3.18
1502 8077 1.093496 TCTGCAGGAGCGCAATCATG 61.093 55.000 15.13 8.75 46.23 3.07
1583 8159 4.811364 GCCTTGGCAGCCTCCTCC 62.811 72.222 14.15 0.00 0.00 4.30
1704 8280 1.154282 CAGCAGCTGCATTGACACG 60.154 57.895 38.24 13.19 45.16 4.49
1971 8547 5.955488 TCTTCTATTGTCTGAAAGGAGACG 58.045 41.667 0.00 0.00 44.68 4.18
2006 8582 2.046023 CGTCCATGGCCTGCAAGA 60.046 61.111 6.96 0.00 34.07 3.02
2053 8629 3.066380 GTGATGTGGTGGGAATTTTTGC 58.934 45.455 0.00 0.00 0.00 3.68
2116 8811 4.642445 TGTTCTTATCATGCATGGCTTG 57.358 40.909 25.97 14.06 35.46 4.01
2137 8832 7.924412 TCATAGTTCAGTTTTCAAGTACTCGTT 59.076 33.333 0.00 0.00 0.00 3.85
2201 8897 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2203 8899 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2204 8900 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2232 8928 9.702726 CCGTATGTAGTTATTTGTTGAAATCTG 57.297 33.333 0.00 0.00 33.63 2.90
2233 8929 9.661563 TCCGTATGTAGTTATTTGTTGAAATCT 57.338 29.630 0.00 0.00 33.63 2.40
2234 8930 9.916397 CTCCGTATGTAGTTATTTGTTGAAATC 57.084 33.333 0.00 0.00 33.63 2.17
2235 8931 8.395633 GCTCCGTATGTAGTTATTTGTTGAAAT 58.604 33.333 0.00 0.00 35.83 2.17
2236 8932 7.388224 TGCTCCGTATGTAGTTATTTGTTGAAA 59.612 33.333 0.00 0.00 0.00 2.69
2237 8933 6.874664 TGCTCCGTATGTAGTTATTTGTTGAA 59.125 34.615 0.00 0.00 0.00 2.69
2238 8934 6.399743 TGCTCCGTATGTAGTTATTTGTTGA 58.600 36.000 0.00 0.00 0.00 3.18
2239 8935 6.656314 TGCTCCGTATGTAGTTATTTGTTG 57.344 37.500 0.00 0.00 0.00 3.33
2240 8936 7.675962 TTTGCTCCGTATGTAGTTATTTGTT 57.324 32.000 0.00 0.00 0.00 2.83
2241 8937 7.675962 TTTTGCTCCGTATGTAGTTATTTGT 57.324 32.000 0.00 0.00 0.00 2.83
2242 8938 8.394877 TCATTTTGCTCCGTATGTAGTTATTTG 58.605 33.333 0.00 0.00 0.00 2.32
2243 8939 8.500753 TCATTTTGCTCCGTATGTAGTTATTT 57.499 30.769 0.00 0.00 0.00 1.40
2244 8940 7.769044 ACTCATTTTGCTCCGTATGTAGTTATT 59.231 33.333 0.00 0.00 0.00 1.40
2245 8941 7.224753 CACTCATTTTGCTCCGTATGTAGTTAT 59.775 37.037 0.00 0.00 0.00 1.89
2246 8942 6.533723 CACTCATTTTGCTCCGTATGTAGTTA 59.466 38.462 0.00 0.00 0.00 2.24
2247 8943 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
2248 8944 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2249 8945 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2250 8946 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2251 8947 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2252 8948 4.437390 GGTTCACTCATTTTGCTCCGTATG 60.437 45.833 0.00 0.00 0.00 2.39
2253 8949 3.689649 GGTTCACTCATTTTGCTCCGTAT 59.310 43.478 0.00 0.00 0.00 3.06
2254 8950 3.071479 GGTTCACTCATTTTGCTCCGTA 58.929 45.455 0.00 0.00 0.00 4.02
2255 8951 1.880027 GGTTCACTCATTTTGCTCCGT 59.120 47.619 0.00 0.00 0.00 4.69
2256 8952 2.154462 AGGTTCACTCATTTTGCTCCG 58.846 47.619 0.00 0.00 0.00 4.63
2257 8953 4.072131 TGTAGGTTCACTCATTTTGCTCC 58.928 43.478 0.00 0.00 0.00 4.70
2258 8954 4.757149 AGTGTAGGTTCACTCATTTTGCTC 59.243 41.667 0.00 0.00 44.07 4.26
2259 8955 4.718961 AGTGTAGGTTCACTCATTTTGCT 58.281 39.130 0.00 0.00 44.07 3.91
2314 9010 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2315 9011 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2332 9028 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2333 9029 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2334 9030 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2335 9031 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2336 9032 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2337 9033 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2338 9034 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2339 9035 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2340 9036 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2341 9037 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2342 9038 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2343 9039 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2344 9040 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2345 9041 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2346 9042 3.094572 CAACTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
2347 9043 2.042162 ACAACTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
2348 9044 1.203149 ACAACTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
2349 9045 1.264295 ACAACTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
2350 9046 4.021632 ACTTAACAACTACTCCCTCCGTTC 60.022 45.833 0.00 0.00 0.00 3.95
2351 9047 3.899980 ACTTAACAACTACTCCCTCCGTT 59.100 43.478 0.00 0.00 0.00 4.44
2352 9048 3.504375 ACTTAACAACTACTCCCTCCGT 58.496 45.455 0.00 0.00 0.00 4.69
2353 9049 5.848833 ATACTTAACAACTACTCCCTCCG 57.151 43.478 0.00 0.00 0.00 4.63
2354 9050 6.755607 CGAAATACTTAACAACTACTCCCTCC 59.244 42.308 0.00 0.00 0.00 4.30
2355 9051 7.318893 ACGAAATACTTAACAACTACTCCCTC 58.681 38.462 0.00 0.00 0.00 4.30
2356 9052 7.237209 ACGAAATACTTAACAACTACTCCCT 57.763 36.000 0.00 0.00 0.00 4.20
2357 9053 8.462016 TCTACGAAATACTTAACAACTACTCCC 58.538 37.037 0.00 0.00 0.00 4.30
2358 9054 9.500864 CTCTACGAAATACTTAACAACTACTCC 57.499 37.037 0.00 0.00 0.00 3.85
2391 9189 9.322773 CAGTTCATGTTATCAGTATTGACTCAT 57.677 33.333 0.00 0.00 35.83 2.90
2392 9190 8.531146 TCAGTTCATGTTATCAGTATTGACTCA 58.469 33.333 0.00 0.00 35.83 3.41
2524 9322 1.134560 GGCTTCGTTAGAGATGACCGT 59.865 52.381 0.00 0.00 0.00 4.83
2525 9323 1.536284 GGGCTTCGTTAGAGATGACCG 60.536 57.143 0.00 0.00 34.38 4.79
2526 9324 1.202545 GGGGCTTCGTTAGAGATGACC 60.203 57.143 0.00 0.00 41.36 4.02
2527 9325 1.757699 AGGGGCTTCGTTAGAGATGAC 59.242 52.381 0.00 0.00 0.00 3.06
2528 9326 1.757118 CAGGGGCTTCGTTAGAGATGA 59.243 52.381 0.00 0.00 0.00 2.92
2529 9327 1.808133 GCAGGGGCTTCGTTAGAGATG 60.808 57.143 0.00 0.00 36.96 2.90
2530 9328 0.466124 GCAGGGGCTTCGTTAGAGAT 59.534 55.000 0.00 0.00 36.96 2.75
2531 9329 1.898154 GCAGGGGCTTCGTTAGAGA 59.102 57.895 0.00 0.00 36.96 3.10
2532 9330 1.519455 CGCAGGGGCTTCGTTAGAG 60.519 63.158 0.00 0.00 38.10 2.43
2533 9331 2.577059 CGCAGGGGCTTCGTTAGA 59.423 61.111 0.00 0.00 38.10 2.10
2534 9332 3.195698 GCGCAGGGGCTTCGTTAG 61.196 66.667 0.30 0.00 38.10 2.34
2803 9674 2.551270 CACCAAGCGTCGTTCAGC 59.449 61.111 0.00 0.00 0.00 4.26
2884 9755 2.821366 CGCCTCATGGAAGCGCTT 60.821 61.111 25.35 25.35 43.72 4.68
2950 9835 1.144936 GATGAAGTAGGGCGCTGCT 59.855 57.895 15.69 15.69 0.00 4.24
2974 9859 2.930385 ATCATTGGCCAGCGAGACGG 62.930 60.000 5.11 0.00 0.00 4.79
3173 10065 0.813610 CAGCACGAGTGGGTCAACAA 60.814 55.000 5.32 0.00 0.00 2.83
3225 10121 2.406616 AATGCCGCCATTGTCCGAC 61.407 57.895 0.00 0.00 40.09 4.79
3232 10128 4.132441 CACCGCAATGCCGCCATT 62.132 61.111 0.00 0.00 42.26 3.16
3264 10160 0.250252 TGCTCCACAAACGATGCTCA 60.250 50.000 0.00 0.00 0.00 4.26
3304 10202 3.456317 ACGAAGTCGCTCCACCTT 58.544 55.556 0.00 0.00 44.43 3.50
3333 10231 3.921677 TGACTTAACATCTCCACCGAAC 58.078 45.455 0.00 0.00 0.00 3.95
3387 10285 2.283604 TAGCACCTGCCGACCAGA 60.284 61.111 4.84 0.00 44.64 3.86
3414 10312 9.436957 GACATAACTTGAAGTCTTTGGAAGATA 57.563 33.333 0.00 1.84 40.18 1.98
3436 10334 0.036388 CAAGTACCACCAGCCGACAT 60.036 55.000 0.00 0.00 0.00 3.06
3567 10471 5.420725 ACTGTACTGATGCATCAACCTTA 57.579 39.130 28.39 14.88 36.18 2.69
3694 10600 1.904287 TCGCAGCCAAACCTAACATT 58.096 45.000 0.00 0.00 0.00 2.71
3745 10655 0.259938 ATCCAGTTGATGAAGGGGCC 59.740 55.000 0.00 0.00 30.54 5.80
3781 10695 0.949105 AAGCCACCGTCTAAGCAACG 60.949 55.000 0.00 0.00 39.78 4.10
3856 10771 0.319813 CATCTGGGCGATGCATACGA 60.320 55.000 18.54 2.30 42.75 3.43
3915 10830 6.951062 TGTCAAATTAACATGTTGGTGAGA 57.049 33.333 21.42 13.19 0.00 3.27
3916 10831 7.571089 CATGTCAAATTAACATGTTGGTGAG 57.429 36.000 21.42 8.36 45.72 3.51
3949 10865 3.192633 GTCAACCAACCACTGTTTTCACT 59.807 43.478 0.00 0.00 30.42 3.41
4130 11046 4.792068 TCACCTTCAAATTGTCCTGAAGT 58.208 39.130 13.81 3.31 44.66 3.01
4131 11047 5.065914 TCTCACCTTCAAATTGTCCTGAAG 58.934 41.667 9.67 9.67 45.37 3.02
4132 11048 5.047566 TCTCACCTTCAAATTGTCCTGAA 57.952 39.130 0.00 0.00 0.00 3.02
4150 11066 5.620206 TGTAAGTTGCTCTTTTCCATCTCA 58.380 37.500 0.68 0.00 37.56 3.27
4175 11091 4.770795 AGTTACTAATAGCTGGCAGTTGG 58.229 43.478 17.16 7.23 0.00 3.77
4212 11128 5.220548 CCAAGCTTACAACTCAATCATCTCG 60.221 44.000 0.00 0.00 0.00 4.04
4293 11209 1.305201 TCCCACTTCTGCGTCAAAAC 58.695 50.000 0.00 0.00 0.00 2.43
4351 11267 9.970553 ATCCAGATATTTCTGCAACATATGTAT 57.029 29.630 9.21 0.00 46.76 2.29
4352 11268 9.440773 GATCCAGATATTTCTGCAACATATGTA 57.559 33.333 9.21 0.00 46.76 2.29
4353 11269 7.392673 GGATCCAGATATTTCTGCAACATATGT 59.607 37.037 6.95 1.41 46.76 2.29
4354 11270 7.392393 TGGATCCAGATATTTCTGCAACATATG 59.608 37.037 11.44 0.00 46.76 1.78
4391 11307 7.884877 TCTCTACTGAATTGAACATGTTTCCAT 59.115 33.333 13.36 2.54 0.00 3.41
4392 11308 7.223584 TCTCTACTGAATTGAACATGTTTCCA 58.776 34.615 13.36 4.08 0.00 3.53
4394 11310 8.725148 ACATCTCTACTGAATTGAACATGTTTC 58.275 33.333 13.36 6.79 0.00 2.78
4461 11377 1.363807 GAAAGGGCAGCACAACCAC 59.636 57.895 0.00 0.00 0.00 4.16
4471 11387 9.820725 CATTCTAATTTATTTCATGAAAGGGCA 57.179 29.630 24.17 10.09 33.32 5.36
4492 11408 3.873910 CGAACAACCTGGGTATCATTCT 58.126 45.455 0.00 0.00 0.00 2.40
4507 11423 2.869801 CCAAACTGACAGTAGCGAACAA 59.130 45.455 8.91 0.00 0.00 2.83
4527 11443 2.171659 AGGAGCTAAGAGCCTAAAAGCC 59.828 50.000 0.00 0.00 43.77 4.35
4577 11493 9.613957 GCACGATATATATATACTCAAATCGCT 57.386 33.333 17.32 7.42 0.00 4.93
4589 11505 8.512956 GGGTGACGAATAGCACGATATATATAT 58.487 37.037 4.86 4.86 35.91 0.86
4590 11506 7.718314 AGGGTGACGAATAGCACGATATATATA 59.282 37.037 0.00 0.00 35.91 0.86
4591 11507 6.546403 AGGGTGACGAATAGCACGATATATAT 59.454 38.462 0.00 0.00 35.91 0.86
4592 11508 5.884232 AGGGTGACGAATAGCACGATATATA 59.116 40.000 0.00 0.00 35.91 0.86
4593 11509 4.705507 AGGGTGACGAATAGCACGATATAT 59.294 41.667 0.00 0.00 35.91 0.86
4594 11510 4.077108 AGGGTGACGAATAGCACGATATA 58.923 43.478 0.00 0.00 35.91 0.86
4595 11511 2.891580 AGGGTGACGAATAGCACGATAT 59.108 45.455 0.00 0.00 35.91 1.63
4596 11512 2.034179 CAGGGTGACGAATAGCACGATA 59.966 50.000 0.00 0.00 35.91 2.92
4597 11513 1.112113 AGGGTGACGAATAGCACGAT 58.888 50.000 0.00 0.00 35.91 3.73
4598 11514 0.172578 CAGGGTGACGAATAGCACGA 59.827 55.000 0.00 0.00 35.91 4.35
4599 11515 1.421410 GCAGGGTGACGAATAGCACG 61.421 60.000 0.00 0.00 35.91 5.34
4600 11516 1.421410 CGCAGGGTGACGAATAGCAC 61.421 60.000 0.00 0.00 0.00 4.40
4601 11517 1.153647 CGCAGGGTGACGAATAGCA 60.154 57.895 0.00 0.00 0.00 3.49
4602 11518 1.153628 ACGCAGGGTGACGAATAGC 60.154 57.895 0.00 0.00 0.00 2.97
4610 11526 8.572647 GAATAACTATTCCTCACGCAGGGTGA 62.573 46.154 18.65 18.65 42.96 4.02
4611 11527 6.476690 GAATAACTATTCCTCACGCAGGGTG 61.477 48.000 11.41 11.41 43.67 4.61
4612 11528 1.276622 AACTATTCCTCACGCAGGGT 58.723 50.000 1.24 0.00 43.67 4.34
4613 11529 3.753294 ATAACTATTCCTCACGCAGGG 57.247 47.619 1.24 0.00 43.67 4.45
4614 11530 4.950050 AGAATAACTATTCCTCACGCAGG 58.050 43.478 5.95 0.00 42.29 4.85
4615 11531 6.042777 TGAAGAATAACTATTCCTCACGCAG 58.957 40.000 6.65 0.00 42.29 5.18
4616 11532 5.972935 TGAAGAATAACTATTCCTCACGCA 58.027 37.500 6.65 0.00 42.29 5.24
4617 11533 7.116519 GGTATGAAGAATAACTATTCCTCACGC 59.883 40.741 11.27 8.18 42.58 5.34
4618 11534 8.361139 AGGTATGAAGAATAACTATTCCTCACG 58.639 37.037 11.27 0.00 42.58 4.35
4619 11535 9.699703 GAGGTATGAAGAATAACTATTCCTCAC 57.300 37.037 11.27 3.04 42.58 3.51
4620 11536 9.661954 AGAGGTATGAAGAATAACTATTCCTCA 57.338 33.333 11.39 11.39 43.40 3.86
4622 11538 9.890915 AGAGAGGTATGAAGAATAACTATTCCT 57.109 33.333 5.95 0.00 39.01 3.36
4641 11557 9.228949 GATGCATTGATGATAAAATAGAGAGGT 57.771 33.333 0.00 0.00 0.00 3.85
4683 11599 8.094798 TGCGTCAGAAATAAGACAAAACTTAT 57.905 30.769 0.00 0.00 42.54 1.73
4687 11603 7.444558 TTTTGCGTCAGAAATAAGACAAAAC 57.555 32.000 0.00 0.00 34.48 2.43
4693 11609 7.389330 TGGTATCTTTTTGCGTCAGAAATAAGA 59.611 33.333 0.00 0.00 0.00 2.10
4702 11618 7.441890 TTTCTTATGGTATCTTTTTGCGTCA 57.558 32.000 0.00 0.00 0.00 4.35
4703 11619 8.911247 ATTTTCTTATGGTATCTTTTTGCGTC 57.089 30.769 0.00 0.00 0.00 5.19
4872 11790 8.995906 CGTTTCGAATTCAAATAGTTACATTCC 58.004 33.333 6.22 0.00 0.00 3.01
4928 11846 6.696148 GGATGATGAATAGTAACTTTCGACGT 59.304 38.462 0.00 0.00 0.00 4.34
4930 11848 7.169982 CCTGGATGATGAATAGTAACTTTCGAC 59.830 40.741 0.00 0.00 0.00 4.20
4932 11850 6.425114 CCCTGGATGATGAATAGTAACTTTCG 59.575 42.308 0.00 0.00 0.00 3.46
4934 11852 7.056635 CACCCTGGATGATGAATAGTAACTTT 58.943 38.462 0.00 0.00 0.00 2.66
4936 11854 5.455326 GCACCCTGGATGATGAATAGTAACT 60.455 44.000 0.00 0.00 0.00 2.24
4952 11873 5.757850 GAATAACTTATTCTGCACCCTGG 57.242 43.478 12.55 0.00 41.00 4.45
5042 11963 9.730420 GCCAAATTTTACGTAGTGAATCAATAT 57.270 29.630 0.00 0.00 45.73 1.28


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

AutoCloner maintained by Alex Coulton.