Multiple sequence alignment - TraesCS2B01G332400

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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 TraesCS2B01G332400 chr2B 100.000 5071 0 0 1 5071 475603888 475608958 0.000000e+00 9365.0
1 TraesCS2B01G332400 chr2D 95.296 3614 97 29 677 4233 401535376 401538973 0.000000e+00 5664.0
2 TraesCS2B01G332400 chr2D 86.439 848 76 21 4229 5071 401539210 401540023 0.000000e+00 893.0
3 TraesCS2B01G332400 chr2D 87.906 678 67 6 1 677 401529789 401530452 0.000000e+00 784.0
4 TraesCS2B01G332400 chr2D 75.912 137 26 7 4238 4370 525077939 525078072 4.240000e-06 63.9
5 TraesCS2B01G332400 chr2D 75.969 129 24 7 4238 4362 14590148 14590273 5.480000e-05 60.2
6 TraesCS2B01G332400 chr2A 96.621 799 20 4 3438 4231 538347531 538348327 0.000000e+00 1319.0
7 TraesCS2B01G332400 chr2A 84.907 1186 106 34 631 1798 538344752 538345882 0.000000e+00 1131.0
8 TraesCS2B01G332400 chr2A 89.588 874 51 25 2541 3390 538346671 538347528 0.000000e+00 1074.0
9 TraesCS2B01G332400 chr2A 80.972 741 92 26 1827 2540 538345879 538346597 4.470000e-150 542.0
10 TraesCS2B01G332400 chr2A 88.329 377 27 7 4229 4605 538348408 538348767 2.170000e-118 436.0
11 TraesCS2B01G332400 chr2A 90.244 246 14 8 4705 4941 538362809 538363053 3.810000e-81 313.0
12 TraesCS2B01G332400 chr2A 88.194 144 9 3 4934 5071 538365757 538365898 1.130000e-36 165.0
13 TraesCS2B01G332400 chr1A 77.989 368 72 6 1 361 58713537 58713172 6.610000e-54 222.0
14 TraesCS2B01G332400 chr1A 78.059 237 39 9 4373 4605 21713218 21712991 2.460000e-28 137.0
15 TraesCS2B01G332400 chr5A 80.252 238 35 8 4373 4605 130535258 130535488 8.730000e-38 169.0
16 TraesCS2B01G332400 chr7D 79.747 237 38 6 4373 4605 388720262 388720032 4.060000e-36 163.0
17 TraesCS2B01G332400 chr1B 79.832 238 37 9 4373 4605 597080078 597079847 4.060000e-36 163.0
18 TraesCS2B01G332400 chr1B 80.729 192 34 2 169 360 95664990 95664802 4.090000e-31 147.0
19 TraesCS2B01G332400 chr6B 79.498 239 36 9 4373 4605 715838667 715838436 1.890000e-34 158.0
20 TraesCS2B01G332400 chr6B 75.969 129 25 5 4238 4362 456766144 456766018 1.520000e-05 62.1
21 TraesCS2B01G332400 chr6B 76.786 112 21 5 4238 4346 313897461 313897570 1.970000e-04 58.4
22 TraesCS2B01G332400 chr3D 81.967 183 26 7 4429 4605 71503517 71503336 1.140000e-31 148.0
23 TraesCS2B01G332400 chr3D 78.448 232 35 13 4380 4605 427084563 427084341 2.460000e-28 137.0
24 TraesCS2B01G332400 chr3D 77.064 109 18 7 4242 4346 284276514 284276619 7.090000e-04 56.5
25 TraesCS2B01G332400 chr7A 76.763 241 40 14 4373 4605 635079078 635078846 2.480000e-23 121.0
26 TraesCS2B01G332400 chr5D 78.824 85 16 2 4242 4325 221020842 221020925 7.090000e-04 56.5
27 TraesCS2B01G332400 chr5D 100.000 28 0 0 4242 4269 137722248 137722275 9.000000e-03 52.8
28 TraesCS2B01G332400 chr4A 76.636 107 21 4 4238 4341 737493325 737493430 7.090000e-04 56.5


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 TraesCS2B01G332400 chr2B 475603888 475608958 5070 False 9365.0 9365 100.0000 1 5071 1 chr2B.!!$F1 5070
1 TraesCS2B01G332400 chr2D 401535376 401540023 4647 False 3278.5 5664 90.8675 677 5071 2 chr2D.!!$F4 4394
2 TraesCS2B01G332400 chr2D 401529789 401530452 663 False 784.0 784 87.9060 1 677 1 chr2D.!!$F2 676
3 TraesCS2B01G332400 chr2A 538344752 538348767 4015 False 900.4 1319 88.0834 631 4605 5 chr2A.!!$F1 3974
4 TraesCS2B01G332400 chr2A 538362809 538365898 3089 False 239.0 313 89.2190 4705 5071 2 chr2A.!!$F2 366

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
770 772 0.107214 TCCCTCCAATCATGAACGCC 60.107 55.000 0.00 0.0 0.00 5.68 F
1108 1129 0.036010 AACCACAGAGCTCCAATCGG 60.036 55.000 10.93 6.9 0.00 4.18 F
1741 1773 0.819259 ACGAAACACATGCTGCTGGT 60.819 50.000 0.00 0.0 0.00 4.00 F
2161 2220 1.202818 ACAGAAGTCAACCCCTTCAGC 60.203 52.381 0.00 0.0 40.62 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 2718 1.084370 GTGTAGCCCTGTAGCTTGCG 61.084 60.000 0.00 0.00 41.41 4.85 R
2857 2993 1.751924 GCCAAACAAACAGGGTGTGTA 59.248 47.619 0.00 0.00 39.03 2.90 R
3408 3562 2.167281 GAGAGAGCTAGATTGTGCACCA 59.833 50.000 15.69 2.96 0.00 4.17 R
4106 4313 2.152830 GCAGAAAATTGCATGGCCAAA 58.847 42.857 10.96 0.00 43.53 3.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.222433 CACATTTATTATTTTGTGGCAACTGTG 58.778 33.333 0.00 0.00 36.64 3.66
37 38 4.953940 ATTATTTTGTGGCAACTGTGGT 57.046 36.364 0.00 0.00 37.61 4.16
42 43 0.466555 TGTGGCAACTGTGGTAACCC 60.467 55.000 0.00 0.00 37.61 4.11
46 47 0.958822 GCAACTGTGGTAACCCCTTG 59.041 55.000 0.00 0.00 0.00 3.61
62 63 5.098663 ACCCCTTGTGACTATAAAAGGAGA 58.901 41.667 1.88 0.00 41.49 3.71
66 67 6.480320 CCCTTGTGACTATAAAAGGAGATTCG 59.520 42.308 1.88 0.00 41.49 3.34
86 87 6.519679 TTCGTGCTACTTAGATAAAGGTCA 57.480 37.500 0.00 0.00 39.73 4.02
113 114 8.086143 ACCCTAGCAAATCATACACTAGTTAA 57.914 34.615 0.00 0.00 30.56 2.01
126 127 9.764363 CATACACTAGTTAATCCATACACACAT 57.236 33.333 0.00 0.00 0.00 3.21
127 128 9.982651 ATACACTAGTTAATCCATACACACATC 57.017 33.333 0.00 0.00 0.00 3.06
129 130 5.983720 ACTAGTTAATCCATACACACATCGC 59.016 40.000 0.00 0.00 0.00 4.58
138 139 0.908910 ACACACATCGCCCATTCCTA 59.091 50.000 0.00 0.00 0.00 2.94
139 140 1.134401 ACACACATCGCCCATTCCTAG 60.134 52.381 0.00 0.00 0.00 3.02
140 141 0.179045 ACACATCGCCCATTCCTAGC 60.179 55.000 0.00 0.00 0.00 3.42
141 142 0.886490 CACATCGCCCATTCCTAGCC 60.886 60.000 0.00 0.00 0.00 3.93
142 143 1.302832 CATCGCCCATTCCTAGCCC 60.303 63.158 0.00 0.00 0.00 5.19
143 144 2.529744 ATCGCCCATTCCTAGCCCC 61.530 63.158 0.00 0.00 0.00 5.80
144 145 4.626081 CGCCCATTCCTAGCCCCG 62.626 72.222 0.00 0.00 0.00 5.73
145 146 4.271016 GCCCATTCCTAGCCCCGG 62.271 72.222 0.00 0.00 0.00 5.73
146 147 4.271016 CCCATTCCTAGCCCCGGC 62.271 72.222 0.00 0.00 42.33 6.13
147 148 3.488569 CCATTCCTAGCCCCGGCA 61.489 66.667 8.74 0.00 44.88 5.69
167 168 3.320826 GCAAGCCCCGGAAATATAATTGT 59.679 43.478 0.73 0.00 0.00 2.71
187 188 1.377333 GCACTTGTAGCCCTGGTCC 60.377 63.158 0.00 0.00 0.00 4.46
213 214 4.141756 ACATCCATCAAAACAACCAAGCAA 60.142 37.500 0.00 0.00 0.00 3.91
216 217 3.803778 CCATCAAAACAACCAAGCAAGAC 59.196 43.478 0.00 0.00 0.00 3.01
218 219 1.587946 CAAAACAACCAAGCAAGACGC 59.412 47.619 0.00 0.00 42.91 5.19
225 226 0.947244 CCAAGCAAGACGCAGACTTT 59.053 50.000 0.00 0.00 39.90 2.66
228 229 3.545633 CAAGCAAGACGCAGACTTTTAC 58.454 45.455 0.00 0.00 39.90 2.01
231 232 1.136336 CAAGACGCAGACTTTTACGCC 60.136 52.381 0.00 0.00 39.90 5.68
247 248 4.473520 CCTCACAGCGGCCCGAAT 62.474 66.667 7.68 0.00 0.00 3.34
263 264 4.970003 GCCCGAATTTGAGTAAAATCATCG 59.030 41.667 0.00 1.45 37.51 3.84
269 270 7.460120 CGAATTTGAGTAAAATCATCGTGCAAC 60.460 37.037 0.00 0.00 37.51 4.17
272 273 4.754618 TGAGTAAAATCATCGTGCAACAGT 59.245 37.500 0.00 0.00 35.74 3.55
273 274 5.929415 TGAGTAAAATCATCGTGCAACAGTA 59.071 36.000 0.00 0.00 35.74 2.74
277 278 9.109393 AGTAAAATCATCGTGCAACAGTAATAT 57.891 29.630 0.00 0.00 35.74 1.28
281 282 6.769608 TCATCGTGCAACAGTAATATGATC 57.230 37.500 0.00 0.00 35.74 2.92
294 295 8.424918 ACAGTAATATGATCCATTCGTCTCTTT 58.575 33.333 0.00 0.00 0.00 2.52
295 296 8.706936 CAGTAATATGATCCATTCGTCTCTTTG 58.293 37.037 0.00 0.00 0.00 2.77
298 299 2.237143 TGATCCATTCGTCTCTTTGCCT 59.763 45.455 0.00 0.00 0.00 4.75
305 306 0.734253 CGTCTCTTTGCCTCTCACCG 60.734 60.000 0.00 0.00 0.00 4.94
313 314 0.181587 TGCCTCTCACCGAACCAAAA 59.818 50.000 0.00 0.00 0.00 2.44
314 315 1.314730 GCCTCTCACCGAACCAAAAA 58.685 50.000 0.00 0.00 0.00 1.94
334 335 3.334054 GGAGGCACCCAAGCTCCT 61.334 66.667 0.00 0.00 32.55 3.69
341 342 0.250513 CACCCAAGCTCCTAGGTGTC 59.749 60.000 9.08 3.05 43.91 3.67
366 367 1.520564 GCACACGTGACAGTCACCA 60.521 57.895 25.11 0.00 44.20 4.17
368 369 1.143183 ACACGTGACAGTCACCACC 59.857 57.895 25.11 3.62 44.20 4.61
379 380 1.460497 TCACCACCACTGCCACCTA 60.460 57.895 0.00 0.00 0.00 3.08
380 381 1.057275 TCACCACCACTGCCACCTAA 61.057 55.000 0.00 0.00 0.00 2.69
401 402 3.199442 TGGAGACCCATCCACTAAAGA 57.801 47.619 0.00 0.00 44.56 2.52
410 411 4.383118 CCCATCCACTAAAGACACTAGGTG 60.383 50.000 0.00 0.00 39.75 4.00
418 419 0.911525 AGACACTAGGTGCCATGGCT 60.912 55.000 35.53 19.66 42.51 4.75
449 450 0.179097 CCACTAAAGAGGAGCGAGCC 60.179 60.000 0.00 0.00 0.00 4.70
450 451 0.820871 CACTAAAGAGGAGCGAGCCT 59.179 55.000 0.00 0.00 42.17 4.58
463 464 3.249189 AGCCTCCCTTCACCGCAA 61.249 61.111 0.00 0.00 0.00 4.85
473 474 0.394488 TTCACCGCAAGAACCCAACA 60.394 50.000 0.00 0.00 43.02 3.33
474 475 1.098712 TCACCGCAAGAACCCAACAC 61.099 55.000 0.00 0.00 43.02 3.32
485 486 2.348411 ACCCAACACAGAACAAGAGG 57.652 50.000 0.00 0.00 0.00 3.69
507 508 2.182284 CCATGTCGTCCGCCGTTA 59.818 61.111 0.00 0.00 37.94 3.18
515 516 1.227147 GTCCGCCGTTAGCTATGCA 60.227 57.895 0.00 0.00 40.39 3.96
516 517 1.067416 TCCGCCGTTAGCTATGCAG 59.933 57.895 0.00 0.00 40.39 4.41
526 527 4.202020 CGTTAGCTATGCAGACTTAGTCCA 60.202 45.833 8.96 1.18 32.18 4.02
542 543 1.126846 GTCCAGCGACTTCATTTGACG 59.873 52.381 0.00 0.00 35.99 4.35
560 561 0.179026 CGACGATGAGGGGAGGTAGA 60.179 60.000 0.00 0.00 0.00 2.59
564 565 0.834261 GATGAGGGGAGGTAGAGGCC 60.834 65.000 0.00 0.00 0.00 5.19
565 566 1.603633 ATGAGGGGAGGTAGAGGCCA 61.604 60.000 5.01 0.00 0.00 5.36
566 567 1.762858 GAGGGGAGGTAGAGGCCAC 60.763 68.421 5.01 0.00 0.00 5.01
605 606 1.833049 CCGATCTAGGGTTCCGCCT 60.833 63.158 0.00 0.00 37.43 5.52
633 634 3.998672 GAAGGCGACACGGGGACA 61.999 66.667 0.00 0.00 0.00 4.02
646 647 2.500504 ACGGGGACAGGAGAAAGTAATC 59.499 50.000 0.00 0.00 0.00 1.75
665 667 6.916387 AGTAATCGTTATGATACCACTTCGTG 59.084 38.462 0.00 0.00 35.84 4.35
770 772 0.107214 TCCCTCCAATCATGAACGCC 60.107 55.000 0.00 0.00 0.00 5.68
864 867 3.383185 ACAGATTGAGAATCGAGGAGTCC 59.617 47.826 0.00 0.00 42.75 3.85
884 904 4.846551 TCCACACAAGGACACACG 57.153 55.556 0.00 0.00 31.23 4.49
886 906 0.179094 TCCACACAAGGACACACGAC 60.179 55.000 0.00 0.00 31.23 4.34
956 977 0.249322 CACGCCCCTTATCGTTCGAT 60.249 55.000 12.22 12.22 36.73 3.59
972 993 4.381079 CGTTCGATCTCCTTTTCTTCCTCT 60.381 45.833 0.00 0.00 0.00 3.69
993 1014 0.534203 GGCGTCAACCTCACTCCAAA 60.534 55.000 0.00 0.00 0.00 3.28
1000 1021 1.371183 CCTCACTCCAAACGCTCCA 59.629 57.895 0.00 0.00 0.00 3.86
1001 1022 0.250295 CCTCACTCCAAACGCTCCAA 60.250 55.000 0.00 0.00 0.00 3.53
1002 1023 1.611673 CCTCACTCCAAACGCTCCAAT 60.612 52.381 0.00 0.00 0.00 3.16
1003 1024 1.734465 CTCACTCCAAACGCTCCAATC 59.266 52.381 0.00 0.00 0.00 2.67
1004 1025 0.443869 CACTCCAAACGCTCCAATCG 59.556 55.000 0.00 0.00 0.00 3.34
1034 1055 2.711922 CCAGTACTCCTCGCCGCTT 61.712 63.158 0.00 0.00 0.00 4.68
1041 1062 4.207281 CCTCGCCGCTTCGATCCA 62.207 66.667 0.00 0.00 37.87 3.41
1054 1075 2.985896 TCGATCCACCAAATTCTCCAC 58.014 47.619 0.00 0.00 0.00 4.02
1083 1104 0.980423 CCCTAGAAGCTATCCCCTGC 59.020 60.000 0.00 0.00 0.00 4.85
1108 1129 0.036010 AACCACAGAGCTCCAATCGG 60.036 55.000 10.93 6.90 0.00 4.18
1328 1349 3.518634 TTGTGGCAAGAGTTGGTTTTC 57.481 42.857 0.00 0.00 0.00 2.29
1426 1447 5.343058 CGCTGATATTTGGTTTCAACACTTG 59.657 40.000 0.00 0.00 31.78 3.16
1479 1500 1.138247 GAGCGCTTTTGATGGCCTG 59.862 57.895 13.26 0.00 0.00 4.85
1490 1511 5.435686 TTTGATGGCCTGTGTAGTCTAAT 57.564 39.130 3.32 0.00 0.00 1.73
1521 1549 5.778161 TCATGTTTCTGTGTGTATTAGCG 57.222 39.130 0.00 0.00 0.00 4.26
1689 1717 6.484540 CATGAAACTGCTCATGTCTATCAAC 58.515 40.000 10.61 0.00 45.12 3.18
1741 1773 0.819259 ACGAAACACATGCTGCTGGT 60.819 50.000 0.00 0.00 0.00 4.00
1762 1794 4.765339 GGTTTATCTTAACAGTGGGCAGTT 59.235 41.667 0.00 0.00 0.00 3.16
1823 1855 7.996644 AGTAAGGTTCTTGGTCAAATGAACTTA 59.003 33.333 12.40 5.51 38.86 2.24
1938 1972 4.670896 ATGGCATTTAAATGTGGTAGGC 57.329 40.909 25.15 13.47 38.65 3.93
1998 2049 4.656575 TGATGGGGGTCGAAACATAAGATA 59.343 41.667 0.00 0.00 0.00 1.98
2079 2137 9.498176 TTGGAAGTATTAGTACTGAAAGAAACC 57.502 33.333 5.39 1.46 40.24 3.27
2161 2220 1.202818 ACAGAAGTCAACCCCTTCAGC 60.203 52.381 0.00 0.00 40.62 4.26
2204 2263 9.696917 AAACCTTAGTGCATTCTTTAATTTCTG 57.303 29.630 0.00 0.00 0.00 3.02
2301 2360 8.828644 AGATTACAGAGTATGTACGTTCACTAG 58.171 37.037 0.00 0.00 44.14 2.57
2387 2446 4.300189 TGATGTTCGTTGTTCAAAAGGG 57.700 40.909 0.00 0.00 0.00 3.95
2389 2448 4.882427 TGATGTTCGTTGTTCAAAAGGGTA 59.118 37.500 0.00 0.00 0.00 3.69
2445 2504 3.576078 TCCACCTGAGCTTTTCTGAAA 57.424 42.857 0.00 0.00 0.00 2.69
2755 2891 8.558700 GCTGTTGACCAAATAATTGAAAATGTT 58.441 29.630 0.00 0.00 38.94 2.71
2775 2911 6.647334 TGTTGAGACTTGCAAAATAATGGA 57.353 33.333 0.00 0.00 0.00 3.41
2781 2917 9.806203 TGAGACTTGCAAAATAATGGAAATATG 57.194 29.630 0.00 0.00 29.89 1.78
2855 2991 3.530535 TGCATAAGTAGCTTCGCATCAA 58.469 40.909 0.00 0.00 30.59 2.57
2856 2992 3.938334 TGCATAAGTAGCTTCGCATCAAA 59.062 39.130 0.00 0.00 30.59 2.69
2857 2993 4.576053 TGCATAAGTAGCTTCGCATCAAAT 59.424 37.500 0.00 0.00 30.59 2.32
3015 3167 6.756074 CACTTTCTACATCTCTCCTTCACATC 59.244 42.308 0.00 0.00 0.00 3.06
3236 3388 5.790593 TCCGTTCTCCCATATTAATGCTAC 58.209 41.667 0.00 0.00 0.00 3.58
3381 3535 8.153550 AGCTCTAGTTTTTCTCTTCTGATTTGA 58.846 33.333 0.00 0.00 0.00 2.69
3382 3536 8.442384 GCTCTAGTTTTTCTCTTCTGATTTGAG 58.558 37.037 0.00 0.00 0.00 3.02
3383 3537 8.316640 TCTAGTTTTTCTCTTCTGATTTGAGC 57.683 34.615 0.00 0.00 0.00 4.26
3384 3538 8.153550 TCTAGTTTTTCTCTTCTGATTTGAGCT 58.846 33.333 0.00 0.00 0.00 4.09
3385 3539 9.429359 CTAGTTTTTCTCTTCTGATTTGAGCTA 57.571 33.333 0.00 0.00 0.00 3.32
3388 3542 9.392021 GTTTTTCTCTTCTGATTTGAGCTAAAG 57.608 33.333 0.00 0.00 0.00 1.85
3389 3543 8.908786 TTTTCTCTTCTGATTTGAGCTAAAGA 57.091 30.769 0.00 0.00 0.00 2.52
3391 3545 8.545229 TTCTCTTCTGATTTGAGCTAAAGAAG 57.455 34.615 4.41 4.41 33.07 2.85
3407 3561 7.964604 CTAAAGAAGCAGTAAGTACACCTTT 57.035 36.000 0.00 0.00 34.46 3.11
3408 3562 8.379457 CTAAAGAAGCAGTAAGTACACCTTTT 57.621 34.615 0.00 0.00 34.46 2.27
3409 3563 6.619801 AAGAAGCAGTAAGTACACCTTTTG 57.380 37.500 0.00 0.00 34.46 2.44
3423 3577 3.221964 CCTTTTGGTGCACAATCTAGC 57.778 47.619 20.43 0.00 39.21 3.42
3424 3578 2.821969 CCTTTTGGTGCACAATCTAGCT 59.178 45.455 20.43 0.00 39.21 3.32
3425 3579 3.119708 CCTTTTGGTGCACAATCTAGCTC 60.120 47.826 20.43 0.00 39.21 4.09
3426 3580 3.423539 TTTGGTGCACAATCTAGCTCT 57.576 42.857 20.43 0.00 39.21 4.09
3427 3581 2.680312 TGGTGCACAATCTAGCTCTC 57.320 50.000 20.43 0.00 0.00 3.20
3428 3582 2.182827 TGGTGCACAATCTAGCTCTCT 58.817 47.619 20.43 0.00 0.00 3.10
3429 3583 2.167281 TGGTGCACAATCTAGCTCTCTC 59.833 50.000 20.43 0.00 0.00 3.20
3430 3584 2.430332 GGTGCACAATCTAGCTCTCTCT 59.570 50.000 20.43 0.00 0.00 3.10
3431 3585 3.118811 GGTGCACAATCTAGCTCTCTCTT 60.119 47.826 20.43 0.00 0.00 2.85
3432 3586 4.502962 GTGCACAATCTAGCTCTCTCTTT 58.497 43.478 13.17 0.00 0.00 2.52
3433 3587 4.934602 GTGCACAATCTAGCTCTCTCTTTT 59.065 41.667 13.17 0.00 0.00 2.27
3434 3588 5.063312 GTGCACAATCTAGCTCTCTCTTTTC 59.937 44.000 13.17 0.00 0.00 2.29
3435 3589 5.174395 GCACAATCTAGCTCTCTCTTTTCA 58.826 41.667 0.00 0.00 0.00 2.69
3436 3590 5.816777 GCACAATCTAGCTCTCTCTTTTCAT 59.183 40.000 0.00 0.00 0.00 2.57
3802 4005 3.721706 CCCCAGGCCGAGAAAGCT 61.722 66.667 0.00 0.00 0.00 3.74
4051 4257 4.093743 TCTTCCTCAGTAGCAATGTACCA 58.906 43.478 0.00 0.00 0.00 3.25
4106 4313 7.220030 TGTTTCTCTTTCTTGAGAGCTGTTAT 58.780 34.615 0.00 0.00 43.05 1.89
4129 4336 1.206371 GGCCATGCAATTTTCTGCTCT 59.794 47.619 0.00 0.00 43.07 4.09
4141 4348 2.865119 TCTGCTCTGATTCTTGGCAA 57.135 45.000 0.00 0.00 32.43 4.52
4142 4349 3.361281 TCTGCTCTGATTCTTGGCAAT 57.639 42.857 0.00 0.00 32.43 3.56
4171 4378 2.095768 CGTCTTTGGTGAATCGCATTGT 60.096 45.455 0.00 0.00 0.00 2.71
4215 4423 3.131755 CGTTCCCTATTACTTCCTCGGTT 59.868 47.826 0.00 0.00 0.00 4.44
4220 4428 0.988832 ATTACTTCCTCGGTTGGGCA 59.011 50.000 0.00 0.00 0.00 5.36
4246 4695 7.919621 AGGTTTATTAGACTCCTTTCGAATACG 59.080 37.037 0.00 0.00 41.26 3.06
4311 4760 6.649155 TGCTAGACAAATCTATGGCTAAACA 58.351 36.000 0.00 0.00 40.35 2.83
4322 4771 7.701539 TCTATGGCTAAACATTGACACAATT 57.298 32.000 0.00 0.00 29.81 2.32
4394 4843 7.146648 TCTCTCTCTCCGTTTCTTTTTACTTC 58.853 38.462 0.00 0.00 0.00 3.01
4417 4866 6.040247 TCGCATATACGAATTGTCTGAAGTT 58.960 36.000 0.00 0.00 39.54 2.66
4422 4871 9.916397 CATATACGAATTGTCTGAAGTTAAACC 57.084 33.333 0.00 0.00 0.00 3.27
4423 4872 7.972832 ATACGAATTGTCTGAAGTTAAACCA 57.027 32.000 0.00 0.00 0.00 3.67
4424 4873 6.687081 ACGAATTGTCTGAAGTTAAACCAA 57.313 33.333 0.00 0.00 0.00 3.67
4425 4874 7.090953 ACGAATTGTCTGAAGTTAAACCAAA 57.909 32.000 0.00 0.00 0.00 3.28
4426 4875 6.970613 ACGAATTGTCTGAAGTTAAACCAAAC 59.029 34.615 0.00 0.00 0.00 2.93
4427 4876 6.416750 CGAATTGTCTGAAGTTAAACCAAACC 59.583 38.462 0.00 0.00 0.00 3.27
4488 4937 9.251792 CAACGCCTACAATACTATGTTGTATAA 57.748 33.333 0.00 0.00 40.22 0.98
4626 5077 3.400439 TTTTTGCGGGGTAACGAGT 57.600 47.368 0.00 0.00 35.47 4.18
4627 5078 2.540265 TTTTTGCGGGGTAACGAGTA 57.460 45.000 0.00 0.00 35.47 2.59
4628 5079 1.794512 TTTTGCGGGGTAACGAGTAC 58.205 50.000 0.00 0.00 35.47 2.73
4686 5137 0.529378 GCTGCTGGATTGGTGAAAGG 59.471 55.000 0.00 0.00 0.00 3.11
4737 5188 3.001514 GCCTGGCCCATTCTCTGA 58.998 61.111 7.66 0.00 0.00 3.27
4830 5282 2.348998 GGGGCTGACAGACAGGTG 59.651 66.667 11.27 0.00 45.82 4.00
4854 5306 8.196802 TGAAGGTCGTTCACATTATATCTTTG 57.803 34.615 3.85 0.00 40.45 2.77
4855 5307 7.822334 TGAAGGTCGTTCACATTATATCTTTGT 59.178 33.333 3.85 0.00 40.45 2.83
4856 5308 7.539712 AGGTCGTTCACATTATATCTTTGTG 57.460 36.000 6.35 6.35 41.60 3.33
4858 5310 7.606456 AGGTCGTTCACATTATATCTTTGTGTT 59.394 33.333 10.60 0.00 41.14 3.32
4863 5322 8.647226 GTTCACATTATATCTTTGTGTTTTGCC 58.353 33.333 10.60 0.00 41.14 4.52
4899 5358 1.103398 GTTGCTGTTGCTGTCTGGGT 61.103 55.000 0.00 0.00 40.48 4.51
4936 5395 3.484229 CCGCTTTCTTTTCGCTGTATCAG 60.484 47.826 0.00 0.00 34.12 2.90
4942 5401 2.561733 TTTCGCTGTATCAGTCCGAG 57.438 50.000 0.00 0.00 30.57 4.63
4944 5403 1.968704 TCGCTGTATCAGTCCGAGAT 58.031 50.000 0.00 0.00 33.43 2.75
4970 8141 5.612688 ACCCACCCATCAATCATTATCTACT 59.387 40.000 0.00 0.00 0.00 2.57
5009 8180 1.321743 CGCAGTAAGATCTTGCACGAC 59.678 52.381 24.50 13.25 32.18 4.34
5011 8182 1.321743 CAGTAAGATCTTGCACGACGC 59.678 52.381 23.22 0.00 42.89 5.19
5047 8222 2.034879 CAGATCCACGGCAGCGTTT 61.035 57.895 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.371936 GTTACCACAGTTGCCACAAAATAATA 58.628 34.615 0.00 0.00 0.00 0.98
20 21 2.166664 GGTTACCACAGTTGCCACAAAA 59.833 45.455 0.00 0.00 0.00 2.44
35 36 5.884232 CCTTTTATAGTCACAAGGGGTTACC 59.116 44.000 0.00 0.00 40.67 2.85
37 38 6.731919 TCTCCTTTTATAGTCACAAGGGGTTA 59.268 38.462 0.00 0.00 38.01 2.85
42 43 7.010552 CACGAATCTCCTTTTATAGTCACAAGG 59.989 40.741 0.00 0.00 37.70 3.61
46 47 6.043411 AGCACGAATCTCCTTTTATAGTCAC 58.957 40.000 0.00 0.00 0.00 3.67
62 63 7.068348 TCTGACCTTTATCTAAGTAGCACGAAT 59.932 37.037 0.00 0.00 31.56 3.34
66 67 6.274579 GGTCTGACCTTTATCTAAGTAGCAC 58.725 44.000 19.53 0.00 34.73 4.40
86 87 5.900123 ACTAGTGTATGATTTGCTAGGGTCT 59.100 40.000 0.00 0.00 34.94 3.85
113 114 0.836606 TGGGCGATGTGTGTATGGAT 59.163 50.000 0.00 0.00 0.00 3.41
126 127 3.168528 GGGGCTAGGAATGGGCGA 61.169 66.667 0.00 0.00 0.00 5.54
127 128 4.626081 CGGGGCTAGGAATGGGCG 62.626 72.222 0.00 0.00 0.00 6.13
129 130 4.271016 GCCGGGGCTAGGAATGGG 62.271 72.222 2.18 0.00 38.26 4.00
143 144 0.250553 TATATTTCCGGGGCTTGCCG 60.251 55.000 0.00 0.00 0.00 5.69
144 145 1.989706 TTATATTTCCGGGGCTTGCC 58.010 50.000 0.00 2.49 0.00 4.52
145 146 3.320826 ACAATTATATTTCCGGGGCTTGC 59.679 43.478 0.00 0.00 0.00 4.01
146 147 5.288804 CAACAATTATATTTCCGGGGCTTG 58.711 41.667 0.00 0.00 0.00 4.01
147 148 4.202212 GCAACAATTATATTTCCGGGGCTT 60.202 41.667 0.00 0.00 0.00 4.35
158 159 6.039717 CAGGGCTACAAGTGCAACAATTATAT 59.960 38.462 0.00 0.00 41.43 0.86
159 160 5.356751 CAGGGCTACAAGTGCAACAATTATA 59.643 40.000 0.00 0.00 41.43 0.98
167 168 0.250727 GACCAGGGCTACAAGTGCAA 60.251 55.000 0.00 0.00 0.00 4.08
187 188 4.319139 TGGTTGTTTTGATGGATGTGTG 57.681 40.909 0.00 0.00 0.00 3.82
213 214 0.317479 AGGCGTAAAAGTCTGCGTCT 59.683 50.000 0.00 0.00 34.29 4.18
216 217 0.438830 GTGAGGCGTAAAAGTCTGCG 59.561 55.000 0.00 0.00 0.00 5.18
218 219 1.461127 GCTGTGAGGCGTAAAAGTCTG 59.539 52.381 0.00 0.00 0.00 3.51
231 232 2.040544 AAATTCGGGCCGCTGTGAG 61.041 57.895 23.83 0.00 0.00 3.51
247 248 6.066054 TGTTGCACGATGATTTTACTCAAA 57.934 33.333 0.00 0.00 0.00 2.69
263 264 6.017934 ACGAATGGATCATATTACTGTTGCAC 60.018 38.462 0.00 0.00 0.00 4.57
269 270 8.706936 CAAAGAGACGAATGGATCATATTACTG 58.293 37.037 0.00 0.00 0.00 2.74
272 273 6.650807 GGCAAAGAGACGAATGGATCATATTA 59.349 38.462 0.00 0.00 0.00 0.98
273 274 5.471456 GGCAAAGAGACGAATGGATCATATT 59.529 40.000 0.00 0.00 0.00 1.28
277 278 2.237143 AGGCAAAGAGACGAATGGATCA 59.763 45.455 0.00 0.00 0.00 2.92
281 282 2.275318 GAGAGGCAAAGAGACGAATGG 58.725 52.381 0.00 0.00 0.00 3.16
294 295 0.181587 TTTTGGTTCGGTGAGAGGCA 59.818 50.000 0.00 0.00 0.00 4.75
295 296 1.314730 TTTTTGGTTCGGTGAGAGGC 58.685 50.000 0.00 0.00 0.00 4.70
313 314 0.540597 GAGCTTGGGTGCCTCCTTTT 60.541 55.000 0.00 0.00 36.25 2.27
314 315 1.075659 GAGCTTGGGTGCCTCCTTT 59.924 57.895 0.00 0.00 36.25 3.11
315 316 2.759795 GAGCTTGGGTGCCTCCTT 59.240 61.111 0.00 0.00 36.25 3.36
316 317 2.477190 TAGGAGCTTGGGTGCCTCCT 62.477 60.000 12.51 12.51 40.73 3.69
319 320 1.997874 CCTAGGAGCTTGGGTGCCT 60.998 63.158 1.05 0.00 34.56 4.75
334 335 2.646719 GTGCGGACACGACACCTA 59.353 61.111 0.63 0.00 44.60 3.08
355 356 1.146041 GCAGTGGTGGTGACTGTCA 59.854 57.895 6.36 6.36 42.47 3.58
357 358 2.374525 TGGCAGTGGTGGTGACTGT 61.375 57.895 0.00 0.00 42.47 3.55
397 398 1.614317 GCCATGGCACCTAGTGTCTTT 60.614 52.381 32.08 0.00 39.12 2.52
401 402 1.300963 CAGCCATGGCACCTAGTGT 59.699 57.895 37.18 12.49 44.88 3.55
449 450 0.955919 GGTTCTTGCGGTGAAGGGAG 60.956 60.000 0.00 0.00 0.00 4.30
450 451 1.072505 GGTTCTTGCGGTGAAGGGA 59.927 57.895 0.00 0.00 0.00 4.20
463 464 3.545703 CTCTTGTTCTGTGTTGGGTTCT 58.454 45.455 0.00 0.00 0.00 3.01
473 474 3.152341 CATGGCTTTCCTCTTGTTCTGT 58.848 45.455 0.00 0.00 0.00 3.41
474 475 3.152341 ACATGGCTTTCCTCTTGTTCTG 58.848 45.455 0.00 0.00 0.00 3.02
485 486 2.750888 GGCGGACGACATGGCTTTC 61.751 63.158 0.00 0.00 0.00 2.62
507 508 2.102252 GCTGGACTAAGTCTGCATAGCT 59.898 50.000 0.00 0.00 34.40 3.32
526 527 1.060713 CGTCGTCAAATGAAGTCGCT 58.939 50.000 3.67 0.00 30.85 4.93
537 538 1.320344 CCTCCCCTCATCGTCGTCAA 61.320 60.000 0.00 0.00 0.00 3.18
538 539 1.753078 CCTCCCCTCATCGTCGTCA 60.753 63.158 0.00 0.00 0.00 4.35
539 540 0.465097 TACCTCCCCTCATCGTCGTC 60.465 60.000 0.00 0.00 0.00 4.20
542 543 1.611519 CTCTACCTCCCCTCATCGTC 58.388 60.000 0.00 0.00 0.00 4.20
564 565 3.775654 GCCAGGTCTCTCCCCGTG 61.776 72.222 0.00 0.00 36.75 4.94
633 634 8.142551 GTGGTATCATAACGATTACTTTCTCCT 58.857 37.037 0.00 0.00 35.39 3.69
797 799 5.105997 CCCTTTGTTTTGCCAAATTTCACAA 60.106 36.000 1.96 1.96 34.07 3.33
845 848 2.287909 CCGGACTCCTCGATTCTCAATC 60.288 54.545 0.00 0.00 34.52 2.67
850 853 0.752376 GGACCGGACTCCTCGATTCT 60.752 60.000 9.46 0.00 0.00 2.40
851 854 1.035932 TGGACCGGACTCCTCGATTC 61.036 60.000 9.46 0.00 0.00 2.52
884 904 2.125106 GGACCACCATGGCTCGTC 60.125 66.667 13.04 14.27 42.67 4.20
931 952 1.067582 GATAAGGGGCGTGACGAGG 59.932 63.158 10.10 0.00 0.00 4.63
972 993 2.649034 GAGTGAGGTTGACGCCGA 59.351 61.111 0.00 0.00 0.00 5.54
993 1014 2.980568 TGGTAAATTCGATTGGAGCGT 58.019 42.857 0.00 0.00 0.00 5.07
1000 1021 6.373495 GGAGTACTGGTTTGGTAAATTCGATT 59.627 38.462 0.00 0.00 0.00 3.34
1001 1022 5.878669 GGAGTACTGGTTTGGTAAATTCGAT 59.121 40.000 0.00 0.00 0.00 3.59
1002 1023 5.012354 AGGAGTACTGGTTTGGTAAATTCGA 59.988 40.000 0.00 0.00 0.00 3.71
1003 1024 5.243207 AGGAGTACTGGTTTGGTAAATTCG 58.757 41.667 0.00 0.00 0.00 3.34
1004 1025 5.350640 CGAGGAGTACTGGTTTGGTAAATTC 59.649 44.000 0.00 0.00 0.00 2.17
1034 1055 2.571653 AGTGGAGAATTTGGTGGATCGA 59.428 45.455 0.00 0.00 0.00 3.59
1041 1062 1.347707 TGAGCGAGTGGAGAATTTGGT 59.652 47.619 0.00 0.00 0.00 3.67
1054 1075 1.205893 AGCTTCTAGGGTTTGAGCGAG 59.794 52.381 0.00 0.00 0.00 5.03
1083 1104 4.379243 AGCTCTGTGGTTCGCCGG 62.379 66.667 0.00 0.00 41.18 6.13
1108 1129 2.279784 CCTGATCGGCCGCTTCTC 60.280 66.667 23.51 14.60 0.00 2.87
1328 1349 1.194781 ATCGGATCCAAGATCCCCGG 61.195 60.000 13.41 0.00 40.48 5.73
1479 1500 6.752351 ACATGATGTTCGTCATTAGACTACAC 59.248 38.462 0.00 0.00 42.73 2.90
1490 1511 4.024977 CACACAGAAACATGATGTTCGTCA 60.025 41.667 11.70 0.00 40.14 4.35
1521 1549 1.068333 ACACATCTGCAACGATTTGGC 60.068 47.619 6.94 0.00 32.81 4.52
1635 1663 5.506686 TGTAGCAACAACACAAAGCATTA 57.493 34.783 0.00 0.00 30.91 1.90
1689 1717 8.616942 CATCTATCATACTATCAGAACCCTACG 58.383 40.741 0.00 0.00 0.00 3.51
1741 1773 6.177610 CCTAACTGCCCACTGTTAAGATAAA 58.822 40.000 0.00 0.00 39.02 1.40
1938 1972 1.358152 TCCCTACCCAACCAACTGAG 58.642 55.000 0.00 0.00 0.00 3.35
2161 2220 8.483758 ACTAAGGTTTCCATACATAACCAGTAG 58.516 37.037 0.00 0.00 42.96 2.57
2312 2371 8.848474 ACAAACAGACTAACAGCATATACTTT 57.152 30.769 0.00 0.00 0.00 2.66
2586 2718 1.084370 GTGTAGCCCTGTAGCTTGCG 61.084 60.000 0.00 0.00 41.41 4.85
2755 2891 9.806203 CATATTTCCATTATTTTGCAAGTCTCA 57.194 29.630 0.00 0.00 0.00 3.27
2775 2911 9.654663 GTAGGTGTTTCTGTTCTACTCATATTT 57.345 33.333 0.00 0.00 0.00 1.40
2781 2917 5.010820 AGGTGTAGGTGTTTCTGTTCTACTC 59.989 44.000 0.00 0.00 33.51 2.59
2855 2991 3.181470 GCCAAACAAACAGGGTGTGTATT 60.181 43.478 0.00 0.00 39.03 1.89
2856 2992 2.364002 GCCAAACAAACAGGGTGTGTAT 59.636 45.455 0.00 0.00 39.03 2.29
2857 2993 1.751924 GCCAAACAAACAGGGTGTGTA 59.248 47.619 0.00 0.00 39.03 2.90
2922 3071 5.110940 GTCCATCTCGTAGTAGGACAATC 57.889 47.826 0.00 0.00 46.15 2.67
3216 3368 8.317679 AGATCTGTAGCATTAATATGGGAGAAC 58.682 37.037 0.00 0.00 32.15 3.01
3236 3388 4.485024 GCTCAATGCAATACCAGATCTG 57.515 45.455 16.24 16.24 42.31 2.90
3381 3535 6.239629 AAGGTGTACTTACTGCTTCTTTAGCT 60.240 38.462 0.00 0.00 43.53 3.32
3382 3536 5.932883 AAGGTGTACTTACTGCTTCTTTAGC 59.067 40.000 0.00 0.00 43.48 3.09
3383 3537 7.964604 AAAGGTGTACTTACTGCTTCTTTAG 57.035 36.000 0.00 0.00 38.85 1.85
3384 3538 7.227910 CCAAAAGGTGTACTTACTGCTTCTTTA 59.772 37.037 0.00 0.00 38.85 1.85
3385 3539 6.039382 CCAAAAGGTGTACTTACTGCTTCTTT 59.961 38.462 0.00 0.00 38.85 2.52
3388 3542 4.820173 ACCAAAAGGTGTACTTACTGCTTC 59.180 41.667 0.00 0.00 38.85 3.86
3389 3543 4.578928 CACCAAAAGGTGTACTTACTGCTT 59.421 41.667 6.49 0.00 38.85 3.91
3391 3545 3.304458 GCACCAAAAGGTGTACTTACTGC 60.304 47.826 15.35 0.00 38.85 4.40
3392 3546 3.880490 TGCACCAAAAGGTGTACTTACTG 59.120 43.478 15.35 0.00 38.85 2.74
3393 3547 3.881089 GTGCACCAAAAGGTGTACTTACT 59.119 43.478 22.91 0.00 46.60 2.24
3394 3548 4.219143 GTGCACCAAAAGGTGTACTTAC 57.781 45.455 22.91 9.36 46.60 2.34
3399 3553 3.561143 AGATTGTGCACCAAAAGGTGTA 58.439 40.909 15.69 8.82 41.46 2.90
3400 3554 2.387757 AGATTGTGCACCAAAAGGTGT 58.612 42.857 15.69 0.00 41.46 4.16
3401 3555 3.612479 GCTAGATTGTGCACCAAAAGGTG 60.612 47.826 15.69 10.21 42.22 4.00
3402 3556 2.558359 GCTAGATTGTGCACCAAAAGGT 59.442 45.455 15.69 0.00 36.44 3.50
3403 3557 2.821969 AGCTAGATTGTGCACCAAAAGG 59.178 45.455 15.69 2.03 36.44 3.11
3404 3558 3.755378 AGAGCTAGATTGTGCACCAAAAG 59.245 43.478 15.69 6.66 36.44 2.27
3405 3559 3.753272 GAGAGCTAGATTGTGCACCAAAA 59.247 43.478 15.69 1.92 36.44 2.44
3406 3560 3.008375 AGAGAGCTAGATTGTGCACCAAA 59.992 43.478 15.69 2.77 36.44 3.28
3407 3561 2.568956 AGAGAGCTAGATTGTGCACCAA 59.431 45.455 15.69 9.23 37.49 3.67
3408 3562 2.167281 GAGAGAGCTAGATTGTGCACCA 59.833 50.000 15.69 2.96 0.00 4.17
3409 3563 2.430332 AGAGAGAGCTAGATTGTGCACC 59.570 50.000 15.69 0.00 0.00 5.01
3410 3564 3.799281 AGAGAGAGCTAGATTGTGCAC 57.201 47.619 10.75 10.75 0.00 4.57
3411 3565 4.815533 AAAGAGAGAGCTAGATTGTGCA 57.184 40.909 0.00 0.00 0.00 4.57
3412 3566 5.174395 TGAAAAGAGAGAGCTAGATTGTGC 58.826 41.667 0.00 0.00 0.00 4.57
3413 3567 7.846644 AATGAAAAGAGAGAGCTAGATTGTG 57.153 36.000 0.00 0.00 0.00 3.33
3414 3568 9.598517 CTTAATGAAAAGAGAGAGCTAGATTGT 57.401 33.333 0.00 0.00 0.00 2.71
3415 3569 9.044150 CCTTAATGAAAAGAGAGAGCTAGATTG 57.956 37.037 0.00 0.00 0.00 2.67
3416 3570 7.714813 GCCTTAATGAAAAGAGAGAGCTAGATT 59.285 37.037 0.00 0.00 0.00 2.40
3417 3571 7.071071 AGCCTTAATGAAAAGAGAGAGCTAGAT 59.929 37.037 0.00 0.00 0.00 1.98
3418 3572 6.382570 AGCCTTAATGAAAAGAGAGAGCTAGA 59.617 38.462 0.00 0.00 0.00 2.43
3419 3573 6.581712 AGCCTTAATGAAAAGAGAGAGCTAG 58.418 40.000 0.00 0.00 0.00 3.42
3420 3574 6.552445 AGCCTTAATGAAAAGAGAGAGCTA 57.448 37.500 0.00 0.00 0.00 3.32
3421 3575 5.434182 AGCCTTAATGAAAAGAGAGAGCT 57.566 39.130 0.00 0.00 0.00 4.09
3422 3576 7.800155 ATTAGCCTTAATGAAAAGAGAGAGC 57.200 36.000 0.00 0.00 0.00 4.09
3459 3662 4.459330 TCACATGTGACATCTTTTCCACA 58.541 39.130 24.56 0.00 42.71 4.17
3461 3664 6.653526 ATTTCACATGTGACATCTTTTCCA 57.346 33.333 27.88 6.74 39.66 3.53
3564 3767 7.340122 TGTCATGTTTATTGTTCAAGTCCAA 57.660 32.000 0.00 0.00 0.00 3.53
3802 4005 3.074390 TCAGATCCCTTGCTTCCTTTTCA 59.926 43.478 0.00 0.00 0.00 2.69
4051 4257 6.352516 CAACAGAAGATAAGAATACAGGGCT 58.647 40.000 0.00 0.00 0.00 5.19
4106 4313 2.152830 GCAGAAAATTGCATGGCCAAA 58.847 42.857 10.96 0.00 43.53 3.28
4171 4378 4.445162 CGGTCCCAGGTAATTATTTAGGCA 60.445 45.833 0.00 0.00 0.00 4.75
4215 4423 3.460825 AGGAGTCTAATAAACCTGCCCA 58.539 45.455 0.00 0.00 0.00 5.36
4220 4428 7.919621 CGTATTCGAAAGGAGTCTAATAAACCT 59.080 37.037 0.00 0.00 39.71 3.50
4278 4727 9.494271 CCATAGATTTGTCTAGCAGCTTATAAA 57.506 33.333 0.00 0.92 0.00 1.40
4284 4733 3.390639 AGCCATAGATTTGTCTAGCAGCT 59.609 43.478 0.00 0.00 0.00 4.24
4286 4735 6.763135 TGTTTAGCCATAGATTTGTCTAGCAG 59.237 38.462 0.00 0.00 0.00 4.24
4311 4760 5.144100 TGGTCACCCTTAAATTGTGTCAAT 58.856 37.500 0.00 0.00 0.00 2.57
4374 4823 4.210537 TGCGAAGTAAAAAGAAACGGAGAG 59.789 41.667 0.00 0.00 0.00 3.20
4378 4827 6.622183 CGTATATGCGAAGTAAAAAGAAACGG 59.378 38.462 7.50 0.00 0.00 4.44
4379 4828 7.385650 TCGTATATGCGAAGTAAAAAGAAACG 58.614 34.615 13.77 0.00 37.99 3.60
4394 4843 5.890110 ACTTCAGACAATTCGTATATGCG 57.110 39.130 6.90 6.90 0.00 4.73
4417 4866 3.870633 AACTTTGCGTGGTTTGGTTTA 57.129 38.095 0.00 0.00 0.00 2.01
4422 4871 3.427243 TCGTTAAACTTTGCGTGGTTTG 58.573 40.909 9.81 0.00 37.01 2.93
4423 4872 3.761311 TCGTTAAACTTTGCGTGGTTT 57.239 38.095 6.13 6.13 38.82 3.27
4424 4873 3.761311 TTCGTTAAACTTTGCGTGGTT 57.239 38.095 0.00 0.00 0.00 3.67
4425 4874 3.974871 ATTCGTTAAACTTTGCGTGGT 57.025 38.095 0.00 0.00 0.00 4.16
4426 4875 6.921332 ATAAATTCGTTAAACTTTGCGTGG 57.079 33.333 0.00 0.00 0.00 4.94
4454 4903 8.700644 CATAGTATTGTAGGCGTTGATAACTTC 58.299 37.037 0.00 0.00 0.00 3.01
4622 5073 4.790123 GCTGGCAGTCAATAGTAGTACTCG 60.790 50.000 17.16 0.00 0.00 4.18
4626 5077 5.419542 CAAAGCTGGCAGTCAATAGTAGTA 58.580 41.667 17.16 0.00 0.00 1.82
4627 5078 4.256920 CAAAGCTGGCAGTCAATAGTAGT 58.743 43.478 17.16 0.00 0.00 2.73
4628 5079 3.064545 GCAAAGCTGGCAGTCAATAGTAG 59.935 47.826 17.16 0.00 0.00 2.57
4686 5137 2.434185 TGGTCGACGCCATGCTTC 60.434 61.111 9.92 0.00 32.81 3.86
4737 5188 1.478105 GGCGCTCTGGGAATTCATTTT 59.522 47.619 7.64 0.00 0.00 1.82
4830 5282 8.116753 CACAAAGATATAATGTGAACGACCTTC 58.883 37.037 8.57 0.00 45.61 3.46
4849 5301 6.127196 GGGGATATTATGGCAAAACACAAAGA 60.127 38.462 0.00 0.00 0.00 2.52
4850 5302 6.048509 GGGGATATTATGGCAAAACACAAAG 58.951 40.000 0.00 0.00 0.00 2.77
4851 5303 5.485353 TGGGGATATTATGGCAAAACACAAA 59.515 36.000 0.00 0.00 0.00 2.83
4853 5305 4.614475 TGGGGATATTATGGCAAAACACA 58.386 39.130 0.00 0.00 0.00 3.72
4854 5306 4.649218 ACTGGGGATATTATGGCAAAACAC 59.351 41.667 0.00 0.00 0.00 3.32
4855 5307 4.877773 ACTGGGGATATTATGGCAAAACA 58.122 39.130 0.00 0.00 0.00 2.83
4856 5308 5.010012 CAGACTGGGGATATTATGGCAAAAC 59.990 44.000 0.00 0.00 0.00 2.43
4858 5310 4.167892 ACAGACTGGGGATATTATGGCAAA 59.832 41.667 7.51 0.00 0.00 3.68
4863 5322 4.758674 CAGCAACAGACTGGGGATATTATG 59.241 45.833 7.51 0.00 0.00 1.90
4905 5364 3.670627 CGAAAAGAAAGCGGGAAAGGATG 60.671 47.826 0.00 0.00 0.00 3.51
4936 5395 1.338136 ATGGGTGGGTGATCTCGGAC 61.338 60.000 0.00 0.00 0.00 4.79
4942 5401 2.734755 TGATTGATGGGTGGGTGATC 57.265 50.000 0.00 0.00 0.00 2.92
4944 5403 4.416513 AGATAATGATTGATGGGTGGGTGA 59.583 41.667 0.00 0.00 0.00 4.02
4970 8141 2.223502 GCGAGATCACCTTGTCACGATA 60.224 50.000 0.00 0.00 31.53 2.92
5009 8180 0.378257 CGGATCCAAAGGAACATGCG 59.622 55.000 13.41 0.00 34.34 4.73
5011 8182 1.402968 CTGCGGATCCAAAGGAACATG 59.597 52.381 13.41 0.00 34.34 3.21
5012 8183 1.281867 TCTGCGGATCCAAAGGAACAT 59.718 47.619 13.41 0.00 34.34 2.71
5047 8222 0.678366 GAGACAGACGGAGAGAGGCA 60.678 60.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.