Multiple sequence alignment - TraesCS4D01G098200

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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 TraesCS4D01G098200 chr4D 100.000 8357 0 0 1 8357 75043497 75051853 0.000000e+00 15433.0
1 TraesCS4D01G098200 chr4D 87.850 321 39 0 2795 3115 211388337 211388017 2.200000e-100 377.0
2 TraesCS4D01G098200 chr4A 95.918 4777 136 32 535 5286 512545741 512540999 0.000000e+00 7686.0
3 TraesCS4D01G098200 chr4A 94.704 2058 61 26 6306 8357 512540981 512538966 0.000000e+00 3153.0
4 TraesCS4D01G098200 chr4A 89.636 550 46 4 1 539 512550886 512550337 0.000000e+00 689.0
5 TraesCS4D01G098200 chr4A 82.609 92 9 1 2101 2192 528736136 528736052 3.240000e-09 75.0
6 TraesCS4D01G098200 chr4B 95.247 4629 158 31 688 5286 107450911 107455507 0.000000e+00 7273.0
7 TraesCS4D01G098200 chr4B 95.556 2070 56 17 6303 8357 107455522 107457570 0.000000e+00 3280.0
8 TraesCS4D01G098200 chr4B 83.380 710 85 18 8 699 107450036 107450730 1.980000e-175 627.0
9 TraesCS4D01G098200 chr4B 88.438 320 37 0 2796 3115 282886669 282886350 3.660000e-103 387.0
10 TraesCS4D01G098200 chr3B 84.182 550 63 9 5756 6302 473185514 473184986 5.790000e-141 512.0
11 TraesCS4D01G098200 chr3B 88.281 256 17 5 5300 5542 473186240 473185985 2.280000e-75 294.0
12 TraesCS4D01G098200 chr3B 79.137 417 66 16 5657 6063 810969574 810969979 1.380000e-67 268.0
13 TraesCS4D01G098200 chr3B 79.268 246 16 16 5314 5524 810969298 810969543 1.130000e-28 139.0
14 TraesCS4D01G098200 chr3B 94.231 52 2 1 5623 5674 5891806 5891756 2.500000e-10 78.7
15 TraesCS4D01G098200 chr1A 88.235 323 34 3 2798 3120 412467082 412466764 4.730000e-102 383.0
16 TraesCS4D01G098200 chr1A 85.759 323 26 12 5285 5589 189717546 189717866 2.910000e-84 324.0
17 TraesCS4D01G098200 chr5A 88.636 308 20 11 5286 5582 170096302 170095999 2.220000e-95 361.0
18 TraesCS4D01G098200 chr1D 86.997 323 35 5 2798 3120 326292316 326292001 2.870000e-94 357.0
19 TraesCS4D01G098200 chr7D 86.280 328 42 2 2795 3122 104883720 104883396 3.710000e-93 353.0
20 TraesCS4D01G098200 chr3A 86.604 321 35 5 2796 3116 164407965 164407653 1.730000e-91 348.0
21 TraesCS4D01G098200 chr3A 89.513 267 15 4 5286 5539 484107538 484107272 8.090000e-85 326.0
22 TraesCS4D01G098200 chr3A 91.480 223 19 0 5756 5978 484106676 484106454 2.930000e-79 307.0
23 TraesCS4D01G098200 chr3A 78.821 458 69 16 5657 6104 733410693 733411132 4.940000e-72 283.0
24 TraesCS4D01G098200 chr3A 78.821 458 69 17 5657 6104 733435488 733435927 4.940000e-72 283.0
25 TraesCS4D01G098200 chr1B 85.933 327 40 4 2795 3120 589068396 589068075 2.230000e-90 344.0
26 TraesCS4D01G098200 chr1B 90.000 60 3 2 5650 5709 608038018 608038074 3.240000e-09 75.0
27 TraesCS4D01G098200 chr5B 88.809 277 24 5 5319 5589 146810622 146810897 4.830000e-87 333.0
28 TraesCS4D01G098200 chr3D 82.274 299 42 8 5657 5948 602782362 602782068 1.800000e-61 248.0
29 TraesCS4D01G098200 chr3D 80.913 241 11 15 5318 5524 602782632 602782393 3.120000e-34 158.0
30 TraesCS4D01G098200 chr3D 95.833 48 2 0 5627 5674 619558 619511 2.500000e-10 78.7
31 TraesCS4D01G098200 chr7A 88.732 71 5 1 5649 5719 258415184 258415117 5.380000e-12 84.2


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 TraesCS4D01G098200 chr4D 75043497 75051853 8356 False 15433.000000 15433 100.000000 1 8357 1 chr4D.!!$F1 8356
1 TraesCS4D01G098200 chr4A 512538966 512545741 6775 True 5419.500000 7686 95.311000 535 8357 2 chr4A.!!$R3 7822
2 TraesCS4D01G098200 chr4A 512550337 512550886 549 True 689.000000 689 89.636000 1 539 1 chr4A.!!$R1 538
3 TraesCS4D01G098200 chr4B 107450036 107457570 7534 False 3726.666667 7273 91.394333 8 8357 3 chr4B.!!$F1 8349
4 TraesCS4D01G098200 chr3B 473184986 473186240 1254 True 403.000000 512 86.231500 5300 6302 2 chr3B.!!$R2 1002
5 TraesCS4D01G098200 chr3B 810969298 810969979 681 False 203.500000 268 79.202500 5314 6063 2 chr3B.!!$F1 749
6 TraesCS4D01G098200 chr3A 484106454 484107538 1084 True 316.500000 326 90.496500 5286 5978 2 chr3A.!!$R2 692
7 TraesCS4D01G098200 chr3D 602782068 602782632 564 True 203.000000 248 81.593500 5318 5948 2 chr3D.!!$R2 630

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
38 39 0.240945 CCATTTGGCGGTGTCAAGAC 59.759 55.000 0.00 0.00 0.00 3.01 F
217 222 0.449786 TGGAGCACACAACGTTGTTG 59.550 50.000 30.49 27.59 39.91 3.33 F
326 337 0.696501 ACGGGTTTCTACATGCCCTT 59.303 50.000 0.00 0.00 38.97 3.95 F
818 1051 1.064758 GCAGTCTGAGGGAGAGAGAGA 60.065 57.143 3.32 0.00 0.00 3.10 F
1310 1543 1.531149 CGGTGTTCTTGTTGCTTCGAT 59.469 47.619 0.00 0.00 0.00 3.59 F
1339 1572 2.239654 AGTGTCAGAGAGAGGAGAGAGG 59.760 54.545 0.00 0.00 0.00 3.69 F
2864 3098 2.360350 AAGCATGCCACCTCACCG 60.360 61.111 15.66 0.00 0.00 4.94 F
3383 3618 2.627699 TGAACAAAAACCAGCTGGATCC 59.372 45.455 39.19 17.24 38.94 3.36 F
4490 4734 1.202290 GCTCAACACACACTGGTTTGG 60.202 52.381 0.00 0.00 0.00 3.28 F
6169 6967 0.035458 CCCAGCCGTGTCTTCTCTTT 59.965 55.000 0.00 0.00 0.00 2.52 F
6267 7065 0.392706 CCTACCGTATCAGCATGGCA 59.607 55.000 0.00 0.00 36.16 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 2191 0.688487 ACCAAGCTTACTACCGGCAA 59.312 50.000 0.00 0.00 0.00 4.52 R
2015 2248 1.699083 TCATGTGTCTCTCCAAGGCAA 59.301 47.619 0.00 0.00 42.45 4.52 R
2038 2271 2.026822 CACTAATCCTTCCACCTGCTGT 60.027 50.000 0.00 0.00 0.00 4.40 R
2152 2385 3.633361 GGGAGAACAACTCACCAGG 57.367 57.895 0.00 0.00 46.54 4.45 R
2879 3113 0.179015 TGTTGAGGCGGGCTTTAACA 60.179 50.000 22.31 22.31 0.00 2.41 R
2881 3115 1.173043 CATGTTGAGGCGGGCTTTAA 58.827 50.000 5.24 1.73 0.00 1.52 R
4003 4238 2.335316 TGTTAAGTTTGGAGCGTGGT 57.665 45.000 0.00 0.00 0.00 4.16 R
5080 5338 0.248094 TGCGTATTCGAGACAGCGAG 60.248 55.000 0.00 0.00 41.79 5.03 R
6263 7061 0.033228 CCAAACTTGCCGAATTGCCA 59.967 50.000 0.00 0.00 0.00 4.92 R
7097 7906 1.154016 ACGAGGTGTGAAGCGATCG 60.154 57.895 11.69 11.69 36.32 3.69 R
8040 8852 2.156051 GACAGTGTCCCGGGACTGAC 62.156 65.000 44.64 36.40 44.80 3.51 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
24 25 7.222000 GTCGATCTTAGATAGGTCTCCATTT 57.778 40.000 0.00 0.00 35.87 2.32
38 39 0.240945 CCATTTGGCGGTGTCAAGAC 59.759 55.000 0.00 0.00 0.00 3.01
129 133 7.067737 TCGTATCACTAGGTGTGTGAAATATGA 59.932 37.037 0.66 0.00 45.82 2.15
145 149 8.363390 GTGAAATATGATGTGTCCTCAGATCTA 58.637 37.037 0.00 0.00 42.49 1.98
150 154 5.076182 TGATGTGTCCTCAGATCTATCTCC 58.924 45.833 0.00 0.00 42.49 3.71
217 222 0.449786 TGGAGCACACAACGTTGTTG 59.550 50.000 30.49 27.59 39.91 3.33
221 226 3.495377 GGAGCACACAACGTTGTTGTATA 59.505 43.478 30.49 0.00 39.91 1.47
270 275 1.677217 GGCGAAGATTGGCTTGTCTCT 60.677 52.381 0.00 0.00 36.83 3.10
308 319 3.013921 TGTGAGGTTTGTGTTCTCCAAC 58.986 45.455 0.00 0.00 0.00 3.77
319 330 2.435069 TGTTCTCCAACGGGTTTCTACA 59.565 45.455 0.00 0.00 34.95 2.74
326 337 0.696501 ACGGGTTTCTACATGCCCTT 59.303 50.000 0.00 0.00 38.97 3.95
332 343 4.222810 GGGTTTCTACATGCCCTTTTCATT 59.777 41.667 0.00 0.00 38.12 2.57
362 373 1.594293 CGGCGTGGCGATTTCCTAT 60.594 57.895 10.58 0.00 0.00 2.57
371 382 4.686554 GTGGCGATTTCCTATGTAGATCAC 59.313 45.833 0.00 0.00 0.00 3.06
430 441 9.252962 CTTTTCAATTGTTGCTTCTACAATCTT 57.747 29.630 5.13 0.00 43.44 2.40
455 466 5.570234 AGGTTTAAACAAGTTTGCTTCGA 57.430 34.783 19.57 0.00 34.23 3.71
458 469 5.174943 GGTTTAAACAAGTTTGCTTCGATGG 59.825 40.000 19.57 0.00 34.23 3.51
590 608 4.479993 GCCGCTGGATGCAGGAGT 62.480 66.667 16.65 0.00 43.06 3.85
591 609 2.270205 CCGCTGGATGCAGGAGTT 59.730 61.111 16.65 0.00 43.06 3.01
684 706 8.353423 AGGATTTGTCATTTGTGCTAGTTAAT 57.647 30.769 0.00 0.00 0.00 1.40
685 707 9.461312 AGGATTTGTCATTTGTGCTAGTTAATA 57.539 29.630 0.00 0.00 0.00 0.98
686 708 9.503427 GGATTTGTCATTTGTGCTAGTTAATAC 57.497 33.333 0.00 0.00 0.00 1.89
817 1050 1.392589 GCAGTCTGAGGGAGAGAGAG 58.607 60.000 3.32 0.00 0.00 3.20
818 1051 1.064758 GCAGTCTGAGGGAGAGAGAGA 60.065 57.143 3.32 0.00 0.00 3.10
819 1052 2.923121 CAGTCTGAGGGAGAGAGAGAG 58.077 57.143 0.00 0.00 0.00 3.20
820 1053 2.505407 CAGTCTGAGGGAGAGAGAGAGA 59.495 54.545 0.00 0.00 0.00 3.10
906 1139 4.157656 CCGATCAAATTACAGAAAAGCCCA 59.842 41.667 0.00 0.00 0.00 5.36
972 1205 4.028490 TCCATGGTGGTGGCCGAC 62.028 66.667 12.58 0.00 39.03 4.79
989 1222 2.111999 GACCACCAGCAGTAGCACCA 62.112 60.000 0.00 0.00 45.49 4.17
1282 1515 2.204291 TGGGGATGGGTTGAGGCT 60.204 61.111 0.00 0.00 0.00 4.58
1310 1543 1.531149 CGGTGTTCTTGTTGCTTCGAT 59.469 47.619 0.00 0.00 0.00 3.59
1339 1572 2.239654 AGTGTCAGAGAGAGGAGAGAGG 59.760 54.545 0.00 0.00 0.00 3.69
1953 2186 4.062991 CCGATGATTCTCAGATGCATTCA 58.937 43.478 0.00 0.00 0.00 2.57
1954 2187 4.695928 CCGATGATTCTCAGATGCATTCAT 59.304 41.667 0.00 3.88 35.17 2.57
1968 2201 2.632377 CATTCATCTGTTGCCGGTAGT 58.368 47.619 1.90 0.00 0.00 2.73
2015 2248 5.728741 AGAACATAGGGAAGGAAGAGAATGT 59.271 40.000 0.00 0.00 0.00 2.71
2038 2271 3.149196 GCCTTGGAGAGACACATGAAAA 58.851 45.455 0.00 0.00 0.00 2.29
2152 2385 2.821546 AGAAACCAAAGCGGAAAAAGC 58.178 42.857 0.00 0.00 38.63 3.51
2207 2440 2.669391 GCAAGAGTCGGCCAATTTGAAG 60.669 50.000 2.24 0.00 0.00 3.02
2250 2483 5.547276 TCCCTGAATTGGTGGAATTTTGATT 59.453 36.000 0.00 0.00 34.18 2.57
2373 2606 8.654230 TTTTCTGCTGTAGTGAGATCATTATC 57.346 34.615 0.00 0.00 0.00 1.75
2828 3062 4.586841 CCTAAGAGAGTCATCCCCACTAAG 59.413 50.000 0.00 0.00 0.00 2.18
2864 3098 2.360350 AAGCATGCCACCTCACCG 60.360 61.111 15.66 0.00 0.00 4.94
2879 3113 5.584649 CACCTCACCGTACAATTATGAATGT 59.415 40.000 0.00 0.00 0.00 2.71
2881 3115 5.584649 CCTCACCGTACAATTATGAATGTGT 59.415 40.000 0.00 0.00 0.00 3.72
3074 3308 9.330063 TCTCATGTGATCAACCTAAATATTCAC 57.670 33.333 0.00 0.00 34.16 3.18
3226 3461 9.771534 ACTCATAAAATATTTAGCCTCTGTCTC 57.228 33.333 0.01 0.00 0.00 3.36
3269 3504 5.712917 TGGAACATATTAACCAGGTTCAACC 59.287 40.000 8.57 0.00 39.57 3.77
3383 3618 2.627699 TGAACAAAAACCAGCTGGATCC 59.372 45.455 39.19 17.24 38.94 3.36
3533 3768 7.473735 TGATATATCTGAGGATGACAGGAAC 57.526 40.000 13.79 0.00 33.71 3.62
3657 3892 9.180678 CACATAACTCTTTGACAAATTTACACC 57.819 33.333 0.05 0.00 0.00 4.16
3778 4013 6.814954 AAGTTTAGGATCTCATTAGCCTCA 57.185 37.500 0.00 0.00 32.04 3.86
3826 4061 9.595357 GTACTTGTCAAAGTTAAAGCAGTATTC 57.405 33.333 0.00 0.00 44.47 1.75
3959 4194 9.618890 AGTGCTTTAATGTTGATATGTGATACT 57.381 29.630 0.00 0.00 0.00 2.12
4008 4243 8.804688 TTTTTCTAAAATCACCATAAACCACG 57.195 30.769 0.00 0.00 0.00 4.94
4168 4411 5.599732 TGTTTTTGGATGAAGTCACATTGG 58.400 37.500 0.00 0.00 0.00 3.16
4314 4557 1.368641 CGCATCGACTTTTCCCATCA 58.631 50.000 0.00 0.00 0.00 3.07
4379 4622 3.354467 TGCCATGCATGTATTTCAGTGA 58.646 40.909 24.58 0.00 31.71 3.41
4384 4627 5.345702 CATGCATGTATTTCAGTGAAAGGG 58.654 41.667 22.03 11.08 34.92 3.95
4490 4734 1.202290 GCTCAACACACACTGGTTTGG 60.202 52.381 0.00 0.00 0.00 3.28
4563 4807 1.553248 CAGTTGTCCCGGTCCTTATCA 59.447 52.381 0.00 0.00 0.00 2.15
4801 5045 3.173965 ACTGTGGCTACTTATCTGTGGT 58.826 45.455 0.64 0.00 0.00 4.16
4931 5179 8.885494 TCAATACAGAATTTTGAACCCTTTTG 57.115 30.769 2.48 0.00 0.00 2.44
4956 5204 1.763770 CCCTGCATATCCTGGGACC 59.236 63.158 2.31 0.00 44.35 4.46
5034 5291 6.092670 GTGTGCTTGTCTGCTTATATCTTTGA 59.907 38.462 0.00 0.00 0.00 2.69
5080 5338 7.062022 GGTTTCTAAAACTCGATAGTGTCAGTC 59.938 40.741 2.90 0.00 42.83 3.51
5163 5421 4.041567 TGTTCTCTTCCTGTCCAATAGCAA 59.958 41.667 0.00 0.00 0.00 3.91
5266 5525 2.105477 AGATTGTGTGTGGTCTGCTCTT 59.895 45.455 0.00 0.00 0.00 2.85
5294 5553 7.961827 GGTATCTTTCTTATACTCACGGATACG 59.038 40.741 0.00 0.00 46.09 3.06
5330 5589 4.769063 CACGCATACGGGGGCACA 62.769 66.667 0.00 0.00 46.04 4.57
5361 5620 4.578105 GCATTTTCCAAAAACAACCCATCA 59.422 37.500 0.00 0.00 0.00 3.07
5383 5642 5.955959 TCAGGGACACGGCAAGTATATATAT 59.044 40.000 0.00 0.00 0.00 0.86
5384 5643 6.439375 TCAGGGACACGGCAAGTATATATATT 59.561 38.462 0.00 0.00 0.00 1.28
5550 6267 8.343168 ACAATAGTCTAGTATCAGTATCAGCC 57.657 38.462 0.00 0.00 0.00 4.85
5551 6268 8.167392 ACAATAGTCTAGTATCAGTATCAGCCT 58.833 37.037 0.00 0.00 0.00 4.58
5552 6269 9.674068 CAATAGTCTAGTATCAGTATCAGCCTA 57.326 37.037 0.00 0.00 0.00 3.93
5556 6273 9.899661 AGTCTAGTATCAGTATCAGCCTATTAG 57.100 37.037 0.00 0.00 0.00 1.73
5557 6274 9.893634 GTCTAGTATCAGTATCAGCCTATTAGA 57.106 37.037 0.00 0.00 0.00 2.10
5560 6277 8.801882 AGTATCAGTATCAGCCTATTAGAGAC 57.198 38.462 0.00 0.00 0.00 3.36
5561 6278 8.387039 AGTATCAGTATCAGCCTATTAGAGACA 58.613 37.037 0.00 0.00 0.00 3.41
5562 6279 9.184523 GTATCAGTATCAGCCTATTAGAGACAT 57.815 37.037 0.00 0.00 0.00 3.06
5564 6281 9.760926 ATCAGTATCAGCCTATTAGAGACATAA 57.239 33.333 0.00 0.00 0.00 1.90
5565 6282 9.588096 TCAGTATCAGCCTATTAGAGACATAAA 57.412 33.333 0.00 0.00 0.00 1.40
5609 6326 7.172703 GGTACTAGTACTTGACAAACAGCAAAT 59.827 37.037 27.71 0.00 36.36 2.32
5610 6327 6.959361 ACTAGTACTTGACAAACAGCAAATG 58.041 36.000 11.43 0.00 0.00 2.32
5611 6328 5.835113 AGTACTTGACAAACAGCAAATGT 57.165 34.783 0.00 0.00 46.97 2.71
5620 6337 1.821216 ACAGCAAATGTTCCCTACGG 58.179 50.000 0.00 0.00 39.96 4.02
5621 6338 1.349688 ACAGCAAATGTTCCCTACGGA 59.650 47.619 0.00 0.00 39.96 4.69
5622 6339 2.026262 ACAGCAAATGTTCCCTACGGAT 60.026 45.455 0.00 0.00 39.96 4.18
5624 6341 1.947456 GCAAATGTTCCCTACGGATCC 59.053 52.381 0.00 0.00 38.24 3.36
5626 6343 2.943033 CAAATGTTCCCTACGGATCCAC 59.057 50.000 13.41 0.47 38.24 4.02
5627 6344 1.874129 ATGTTCCCTACGGATCCACA 58.126 50.000 13.41 6.93 38.24 4.17
5628 6345 1.191535 TGTTCCCTACGGATCCACAG 58.808 55.000 13.41 7.59 38.24 3.66
5629 6346 0.179081 GTTCCCTACGGATCCACAGC 60.179 60.000 13.41 0.00 38.24 4.40
5630 6347 0.616395 TTCCCTACGGATCCACAGCA 60.616 55.000 13.41 0.00 38.24 4.41
5631 6348 1.144057 CCCTACGGATCCACAGCAC 59.856 63.158 13.41 0.00 0.00 4.40
5633 6350 1.613317 CCTACGGATCCACAGCACCA 61.613 60.000 13.41 0.00 0.00 4.17
5635 6352 0.613572 TACGGATCCACAGCACCAGA 60.614 55.000 13.41 0.00 0.00 3.86
5637 6354 0.531532 CGGATCCACAGCACCAGATC 60.532 60.000 13.41 0.00 35.45 2.75
5638 6355 0.179034 GGATCCACAGCACCAGATCC 60.179 60.000 6.95 9.29 45.84 3.36
5639 6356 0.543277 GATCCACAGCACCAGATCCA 59.457 55.000 0.00 0.00 30.97 3.41
5663 6380 0.899019 GTCCTCCTTCACTCTCACCC 59.101 60.000 0.00 0.00 0.00 4.61
5665 6382 1.079490 TCCTCCTTCACTCTCACCCAT 59.921 52.381 0.00 0.00 0.00 4.00
5666 6383 1.209019 CCTCCTTCACTCTCACCCATG 59.791 57.143 0.00 0.00 0.00 3.66
5681 6406 1.145531 CCCATGGATGATTGGCTACCA 59.854 52.381 15.22 0.00 35.09 3.25
5684 6409 0.918258 TGGATGATTGGCTACCAGCA 59.082 50.000 0.00 0.00 44.75 4.41
5704 6429 2.439156 GGTGCCACTCCCAGATGC 60.439 66.667 0.00 0.00 0.00 3.91
5705 6430 2.352422 GTGCCACTCCCAGATGCA 59.648 61.111 0.00 0.00 0.00 3.96
5706 6431 1.303561 GTGCCACTCCCAGATGCAA 60.304 57.895 0.00 0.00 33.11 4.08
5730 6455 3.517296 TCCCTAACATGAAGCACCAAA 57.483 42.857 0.00 0.00 0.00 3.28
5739 6464 5.613329 ACATGAAGCACCAAACATTCAATT 58.387 33.333 0.00 0.00 35.47 2.32
5751 6476 7.710475 ACCAAACATTCAATTAACAGTTCAAGG 59.290 33.333 0.00 0.00 0.00 3.61
5752 6477 7.307337 CCAAACATTCAATTAACAGTTCAAGGC 60.307 37.037 0.00 0.00 0.00 4.35
5753 6478 6.655078 ACATTCAATTAACAGTTCAAGGCT 57.345 33.333 0.00 0.00 0.00 4.58
5754 6479 7.054491 ACATTCAATTAACAGTTCAAGGCTT 57.946 32.000 0.00 0.00 0.00 4.35
5778 6555 0.526211 CAGCAGCAGCACATGAACAT 59.474 50.000 3.17 0.00 45.49 2.71
5788 6565 4.036027 CAGCACATGAACATCATAGGGAAC 59.964 45.833 0.00 0.00 34.28 3.62
5808 6585 0.890542 CTACTGGCCAGCAGCAACAA 60.891 55.000 33.06 7.03 46.50 2.83
5813 6590 1.735360 GCCAGCAGCAACAACAAGA 59.265 52.632 0.00 0.00 42.97 3.02
5907 6684 0.771127 TACCTGCTCCAGCTTGGTTT 59.229 50.000 17.57 2.41 42.46 3.27
5913 6690 1.318576 CTCCAGCTTGGTTTCCGTTT 58.681 50.000 0.00 0.00 39.03 3.60
5932 6709 2.187424 GAGGAGAGGCTGCTGCAG 59.813 66.667 24.80 24.80 41.91 4.41
5983 6765 2.718073 GGCGGTGACTCCATACGGT 61.718 63.158 0.00 0.00 35.57 4.83
5984 6766 1.518572 GCGGTGACTCCATACGGTG 60.519 63.158 0.00 0.00 35.57 4.94
5992 6774 2.515991 CCATACGGTGGCGGCATT 60.516 61.111 17.19 5.37 42.12 3.56
5993 6775 2.715005 CATACGGTGGCGGCATTG 59.285 61.111 17.19 13.55 0.00 2.82
5994 6776 2.515991 ATACGGTGGCGGCATTGG 60.516 61.111 17.19 10.17 0.00 3.16
6043 6827 3.454375 CCTATTTTGTGGCGTCGACTAT 58.546 45.455 14.70 0.00 0.00 2.12
6119 6903 1.316617 AAAAAGGGTGGGCCAAGGT 59.683 52.632 8.40 0.00 36.17 3.50
6162 6960 3.991051 CGTGTCCCAGCCGTGTCT 61.991 66.667 0.00 0.00 0.00 3.41
6165 6963 1.837051 TGTCCCAGCCGTGTCTTCT 60.837 57.895 0.00 0.00 0.00 2.85
6166 6964 1.079750 GTCCCAGCCGTGTCTTCTC 60.080 63.158 0.00 0.00 0.00 2.87
6167 6965 1.228894 TCCCAGCCGTGTCTTCTCT 60.229 57.895 0.00 0.00 0.00 3.10
6168 6966 0.832135 TCCCAGCCGTGTCTTCTCTT 60.832 55.000 0.00 0.00 0.00 2.85
6169 6967 0.035458 CCCAGCCGTGTCTTCTCTTT 59.965 55.000 0.00 0.00 0.00 2.52
6170 6968 1.433534 CCAGCCGTGTCTTCTCTTTC 58.566 55.000 0.00 0.00 0.00 2.62
6171 6969 1.001406 CCAGCCGTGTCTTCTCTTTCT 59.999 52.381 0.00 0.00 0.00 2.52
6172 6970 2.548920 CCAGCCGTGTCTTCTCTTTCTT 60.549 50.000 0.00 0.00 0.00 2.52
6173 6971 3.134458 CAGCCGTGTCTTCTCTTTCTTT 58.866 45.455 0.00 0.00 0.00 2.52
6174 6972 3.561725 CAGCCGTGTCTTCTCTTTCTTTT 59.438 43.478 0.00 0.00 0.00 2.27
6175 6973 4.035675 CAGCCGTGTCTTCTCTTTCTTTTT 59.964 41.667 0.00 0.00 0.00 1.94
6211 7009 3.644966 TTTCAGGAAATACAGCGGGAT 57.355 42.857 0.00 0.00 0.00 3.85
6214 7012 3.035363 TCAGGAAATACAGCGGGATACA 58.965 45.455 0.00 0.00 39.74 2.29
6225 7023 2.202837 GGATACACGTGTCCGGCC 60.203 66.667 27.16 17.68 38.78 6.13
6233 7031 3.376078 GTGTCCGGCCGTGTCCTA 61.376 66.667 26.12 0.63 0.00 2.94
6250 7048 3.873679 TAGCGTGTCCCCGTGTCCT 62.874 63.158 0.00 0.00 0.00 3.85
6251 7049 2.482796 TAGCGTGTCCCCGTGTCCTA 62.483 60.000 0.00 0.00 0.00 2.94
6263 7061 1.337071 CGTGTCCTACCGTATCAGCAT 59.663 52.381 0.00 0.00 0.00 3.79
6266 7064 0.679505 TCCTACCGTATCAGCATGGC 59.320 55.000 0.00 0.00 36.16 4.40
6267 7065 0.392706 CCTACCGTATCAGCATGGCA 59.607 55.000 0.00 0.00 36.16 4.92
6291 7089 2.048601 GCAAGTTTGGCCATGTCCA 58.951 52.632 6.09 0.00 0.00 4.02
6298 7096 0.609151 TTGGCCATGTCCATGCTTTG 59.391 50.000 6.09 0.00 37.49 2.77
6302 7100 1.406539 GCCATGTCCATGCTTTGTAGG 59.593 52.381 1.64 0.00 37.49 3.18
6303 7101 2.026641 CCATGTCCATGCTTTGTAGGG 58.973 52.381 1.64 0.00 37.49 3.53
6304 7102 1.406539 CATGTCCATGCTTTGTAGGGC 59.593 52.381 0.00 0.00 31.39 5.19
6353 7151 1.302752 AGCTGTCCGATTTGCTGCA 60.303 52.632 0.00 0.00 34.19 4.41
6444 7249 1.670087 CCGATCAGCACTTCAGTTCGT 60.670 52.381 0.00 0.00 0.00 3.85
6565 7371 7.189693 TGCTTTTTGTAAGTCACAGTATGAG 57.810 36.000 0.00 0.00 39.69 2.90
6656 7462 6.000246 TGAACCATCCTGTTCTGCAATATA 58.000 37.500 5.61 0.00 43.96 0.86
7082 7891 7.824289 CCAATGTCCAACTTATTCTCTTGTCTA 59.176 37.037 0.00 0.00 0.00 2.59
7097 7906 5.734720 TCTTGTCTATGGTTCAATGAGGTC 58.265 41.667 0.00 0.00 0.00 3.85
7410 8220 3.988976 AAGCAGAGATAGCACAAGGAA 57.011 42.857 0.00 0.00 0.00 3.36
7411 8221 3.988976 AGCAGAGATAGCACAAGGAAA 57.011 42.857 0.00 0.00 0.00 3.13
7412 8222 3.871485 AGCAGAGATAGCACAAGGAAAG 58.129 45.455 0.00 0.00 0.00 2.62
7413 8223 2.941720 GCAGAGATAGCACAAGGAAAGG 59.058 50.000 0.00 0.00 0.00 3.11
7414 8224 3.369892 GCAGAGATAGCACAAGGAAAGGA 60.370 47.826 0.00 0.00 0.00 3.36
7574 8384 2.434702 ACTCTACAAAGGCGGATTAGGG 59.565 50.000 0.00 0.00 0.00 3.53
7576 8386 2.698797 TCTACAAAGGCGGATTAGGGAG 59.301 50.000 0.00 0.00 0.00 4.30
7696 8506 1.376037 GCCAGGCTCTGTGTACCAC 60.376 63.158 3.29 0.00 34.56 4.16
7701 8511 1.831736 AGGCTCTGTGTACCACCATAC 59.168 52.381 0.00 0.00 32.73 2.39
7719 8529 6.278363 ACCATACGGTGTATTCTCATGTAAC 58.722 40.000 0.00 0.00 46.79 2.50
7833 8644 7.446001 ACTTTTGGAATCTTCAGACTTGATC 57.554 36.000 0.00 0.00 32.27 2.92
7852 8663 4.881273 TGATCTGTTATGTTTGATTCCGGG 59.119 41.667 0.00 0.00 0.00 5.73
7863 8674 3.712016 TGATTCCGGGAACTCATTTCA 57.288 42.857 12.53 7.98 35.70 2.69
7904 8715 8.687824 ATTTTGTCTGATATTTTTAAGTGGCG 57.312 30.769 0.00 0.00 0.00 5.69
7909 8720 7.066404 TGTCTGATATTTTTAAGTGGCGCATTA 59.934 33.333 10.83 1.87 0.00 1.90
7950 8762 9.630098 ACAATAAACAATATGTTGCTTCAAGAG 57.370 29.630 1.57 0.00 40.14 2.85
8010 8822 6.348213 GCTTGAAGCTATTTAACTCGTGGAAA 60.348 38.462 10.44 0.00 38.45 3.13
8292 9106 3.118775 CCGATTCAGTTATGTGAGGACCA 60.119 47.826 0.00 0.00 0.00 4.02
8294 9108 5.221441 CCGATTCAGTTATGTGAGGACCATA 60.221 44.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.374125 CATCGTCTTGACACCGCCA 60.374 57.895 1.59 0.00 0.00 5.69
87 88 1.227089 CGAGGAAGCATCACCGGAG 60.227 63.158 9.46 0.00 0.00 4.63
129 133 5.324409 GAGGAGATAGATCTGAGGACACAT 58.676 45.833 5.18 0.00 37.25 3.21
145 149 3.864789 AAAATGCCATACCGAGGAGAT 57.135 42.857 0.00 0.00 0.00 2.75
270 275 1.664649 CACGCTCTTCAACGAGGCA 60.665 57.895 0.00 0.00 0.00 4.75
319 330 7.105588 GGAGAATAAAACAATGAAAAGGGCAT 58.894 34.615 0.00 0.00 0.00 4.40
326 337 4.216687 ACGCCGGAGAATAAAACAATGAAA 59.783 37.500 13.83 0.00 0.00 2.69
332 343 1.444836 CCACGCCGGAGAATAAAACA 58.555 50.000 13.83 0.00 36.56 2.83
362 373 1.136891 CATCAGTGGCCGTGATCTACA 59.863 52.381 15.82 0.00 32.06 2.74
371 382 1.478510 ACTAGAAGACATCAGTGGCCG 59.521 52.381 0.00 0.00 31.93 6.13
410 421 7.885399 ACCTAGAAGATTGTAGAAGCAACAATT 59.115 33.333 3.23 0.00 45.24 2.32
430 441 6.539464 TCGAAGCAAACTTGTTTAAACCTAGA 59.461 34.615 15.59 4.75 35.82 2.43
521 538 1.549950 GGGTCATGGCCTCCTTTTCAA 60.550 52.381 17.62 0.00 0.00 2.69
590 608 2.232399 GGGGTTGCCGAAGTCTTTTAA 58.768 47.619 0.00 0.00 0.00 1.52
591 609 1.143277 TGGGGTTGCCGAAGTCTTTTA 59.857 47.619 0.00 0.00 0.00 1.52
684 706 5.950758 AAAACGTCAAATGCCATGTAGTA 57.049 34.783 0.00 0.00 0.00 1.82
685 707 4.846779 AAAACGTCAAATGCCATGTAGT 57.153 36.364 0.00 0.00 0.00 2.73
686 708 5.218885 TGAAAAACGTCAAATGCCATGTAG 58.781 37.500 0.00 0.00 0.00 2.74
819 1052 4.154176 GGGGTTAGGAGAAGAGGTATCTC 58.846 52.174 0.00 0.00 42.09 2.75
820 1053 3.536434 TGGGGTTAGGAGAAGAGGTATCT 59.464 47.826 0.00 0.00 37.39 1.98
972 1205 1.672356 GTGGTGCTACTGCTGGTGG 60.672 63.158 0.00 0.00 40.48 4.61
989 1222 2.437359 GCGCCATCAAGCAGAGGT 60.437 61.111 0.00 0.00 0.00 3.85
1188 1421 1.435515 GCGCGAGAGGATGAAGACT 59.564 57.895 12.10 0.00 0.00 3.24
1236 1469 2.317609 CGTGCCGGGAGTGTGAAAG 61.318 63.158 2.18 0.00 0.00 2.62
1282 1515 1.300620 CAAGAACACCGAGCGGACA 60.301 57.895 16.83 0.00 38.96 4.02
1310 1543 3.454447 CCTCTCTCTGACACTCTCTCCTA 59.546 52.174 0.00 0.00 0.00 2.94
1322 1555 4.535781 CATTTCCTCTCTCCTCTCTCTGA 58.464 47.826 0.00 0.00 0.00 3.27
1323 1556 3.638160 CCATTTCCTCTCTCCTCTCTCTG 59.362 52.174 0.00 0.00 0.00 3.35
1339 1572 2.421424 AGAGCGTCAAAGATGCCATTTC 59.579 45.455 7.54 0.00 44.75 2.17
1656 1889 1.152756 AGTGTTTCCACCTGCACCC 60.153 57.895 0.00 0.00 42.88 4.61
1883 2116 1.069823 CATCTGGATCAACCTCCCTCG 59.930 57.143 0.00 0.00 39.86 4.63
1953 2186 1.831736 AGCTTACTACCGGCAACAGAT 59.168 47.619 0.00 0.00 0.00 2.90
1954 2187 1.263356 AGCTTACTACCGGCAACAGA 58.737 50.000 0.00 0.00 0.00 3.41
1955 2188 1.732259 CAAGCTTACTACCGGCAACAG 59.268 52.381 0.00 0.00 0.00 3.16
1956 2189 1.609580 CCAAGCTTACTACCGGCAACA 60.610 52.381 0.00 0.00 0.00 3.33
1957 2190 1.084289 CCAAGCTTACTACCGGCAAC 58.916 55.000 0.00 0.00 0.00 4.17
1958 2191 0.688487 ACCAAGCTTACTACCGGCAA 59.312 50.000 0.00 0.00 0.00 4.52
1968 2201 6.000246 TCATGAATACCATCACCAAGCTTA 58.000 37.500 0.00 0.00 31.94 3.09
2015 2248 1.699083 TCATGTGTCTCTCCAAGGCAA 59.301 47.619 0.00 0.00 42.45 4.52
2038 2271 2.026822 CACTAATCCTTCCACCTGCTGT 60.027 50.000 0.00 0.00 0.00 4.40
2152 2385 3.633361 GGGAGAACAACTCACCAGG 57.367 57.895 0.00 0.00 46.54 4.45
2207 2440 5.358160 CAGGGAAGAAAACCATGATCCTAAC 59.642 44.000 0.00 0.00 40.97 2.34
2250 2483 8.786826 ATCTTATGTTATTTCAAGTGAACGGA 57.213 30.769 0.00 0.00 33.13 4.69
2302 2535 6.520272 ACTTAGCTAGCTGAATTACCTCATG 58.480 40.000 27.68 7.70 0.00 3.07
2662 2896 5.841810 TCAGTTAATTCACCAGGCAAAAAG 58.158 37.500 0.00 0.00 0.00 2.27
2771 3005 4.744795 AGCAAAGGTACTGATAGACCTG 57.255 45.455 0.00 0.00 45.64 4.00
2828 3062 8.057812 CATGCTTGCATGTTGAGATAAATAAC 57.942 34.615 23.00 0.00 0.00 1.89
2864 3098 7.431084 CGGGCTTTAACACATTCATAATTGTAC 59.569 37.037 0.00 0.00 0.00 2.90
2879 3113 0.179015 TGTTGAGGCGGGCTTTAACA 60.179 50.000 22.31 22.31 0.00 2.41
2881 3115 1.173043 CATGTTGAGGCGGGCTTTAA 58.827 50.000 5.24 1.73 0.00 1.52
3074 3308 1.467678 TTGCCGTGGGAATTGGTTGG 61.468 55.000 0.00 0.00 0.00 3.77
3226 3461 6.819649 TGTTCCAACTAATTAGGTAACCATCG 59.180 38.462 16.73 0.00 37.17 3.84
3383 3618 3.874392 AATCTTGGCTCCCAATTTTCG 57.126 42.857 0.00 0.00 43.07 3.46
3533 3768 0.734309 TGCGGCATTTGCTCATGTAG 59.266 50.000 0.00 0.00 41.70 2.74
3657 3892 7.072263 ACAGGATGGAGGAATCATAGTAAAG 57.928 40.000 0.00 0.00 43.62 1.85
3778 4013 8.280807 AGTACCTAGAGGCTATAACAGTAAAGT 58.719 37.037 0.00 0.00 39.32 2.66
3826 4061 8.479313 TGTATGTGAAACTAATCAGCAGTAAG 57.521 34.615 0.00 0.00 38.04 2.34
4003 4238 2.335316 TGTTAAGTTTGGAGCGTGGT 57.665 45.000 0.00 0.00 0.00 4.16
4008 4243 5.461526 GTCAGGAATTGTTAAGTTTGGAGC 58.538 41.667 0.00 0.00 0.00 4.70
4083 4326 8.654230 TCTGCAAAGATATCATAGAAAGACAC 57.346 34.615 5.32 0.00 0.00 3.67
4114 4357 4.806247 ACAAACTGTCTTCTTTGAGAGACG 59.194 41.667 0.00 0.00 33.02 4.18
4168 4411 3.758554 TGGCCTTCAGATAGCAAAGTTTC 59.241 43.478 3.32 0.00 0.00 2.78
4314 4557 4.499183 CAGAAACTCGCTCTTACCTTGAT 58.501 43.478 0.00 0.00 0.00 2.57
4379 4622 6.039382 CACTTAAAACTACAGTTGAGCCCTTT 59.961 38.462 0.00 0.00 38.44 3.11
4384 4627 7.534239 GCATAACACTTAAAACTACAGTTGAGC 59.466 37.037 0.00 0.00 38.44 4.26
4507 4751 7.768120 TGCAGAACAACCTTTGATTAAATTGTT 59.232 29.630 12.07 12.07 39.68 2.83
4529 4773 3.201707 AACTGGCTCCCTGGTGCAG 62.202 63.158 11.90 9.43 36.47 4.41
4563 4807 7.837689 TGGATAGTATGTACTGTTACTTGTCCT 59.162 37.037 20.26 0.00 37.10 3.85
4664 4908 5.806654 TTATGCTAGCATACTGACCATCA 57.193 39.130 32.19 14.92 38.48 3.07
4931 5179 1.073897 GGATATGCAGGGGGAGTGC 59.926 63.158 0.00 0.00 41.59 4.40
4956 5204 2.214376 TGCCTGGAACAAATACCCAG 57.786 50.000 0.00 0.00 45.28 4.45
5034 5291 8.986991 AGAAACCAAGATGATTACTACTCTGAT 58.013 33.333 0.00 0.00 0.00 2.90
5080 5338 0.248094 TGCGTATTCGAGACAGCGAG 60.248 55.000 0.00 0.00 41.79 5.03
5163 5421 0.743688 TTTTGTGCCAGTGTTCGCAT 59.256 45.000 0.00 0.00 37.33 4.73
5244 5503 2.899900 AGAGCAGACCACACACAATCTA 59.100 45.455 0.00 0.00 0.00 1.98
5266 5525 6.057533 TCCGTGAGTATAAGAAAGATACCGA 58.942 40.000 0.00 0.00 31.27 4.69
5326 5585 1.065551 GGAAAATGCCGTATCCTGTGC 59.934 52.381 0.00 0.00 0.00 4.57
5330 5589 4.282195 TGTTTTTGGAAAATGCCGTATCCT 59.718 37.500 0.00 0.00 33.02 3.24
5361 5620 6.869206 AATATATATACTTGCCGTGTCCCT 57.131 37.500 0.00 0.00 0.00 4.20
5429 5690 9.861138 GACATCAAATTCATTATCTCTTTCTCG 57.139 33.333 0.00 0.00 0.00 4.04
5445 5722 7.395489 AGCACTTGAAATAGGAGACATCAAATT 59.605 33.333 0.00 0.00 30.37 1.82
5451 5738 5.809001 TCAAGCACTTGAAATAGGAGACAT 58.191 37.500 10.58 0.00 45.56 3.06
5589 6306 5.835113 ACATTTGCTGTTTGTCAAGTACT 57.165 34.783 0.00 0.00 32.90 2.73
5615 6332 0.179100 CTGGTGCTGTGGATCCGTAG 60.179 60.000 7.39 8.93 0.00 3.51
5616 6333 0.613572 TCTGGTGCTGTGGATCCGTA 60.614 55.000 7.39 0.00 0.00 4.02
5617 6334 1.267574 ATCTGGTGCTGTGGATCCGT 61.268 55.000 7.39 0.00 0.00 4.69
5618 6335 0.531532 GATCTGGTGCTGTGGATCCG 60.532 60.000 7.39 0.00 31.32 4.18
5619 6336 0.179034 GGATCTGGTGCTGTGGATCC 60.179 60.000 4.20 4.20 44.58 3.36
5620 6337 0.543277 TGGATCTGGTGCTGTGGATC 59.457 55.000 0.00 0.00 35.28 3.36
5621 6338 0.545171 CTGGATCTGGTGCTGTGGAT 59.455 55.000 0.00 0.00 0.00 3.41
5622 6339 1.556373 CCTGGATCTGGTGCTGTGGA 61.556 60.000 0.00 0.00 0.00 4.02
5624 6341 0.037303 AACCTGGATCTGGTGCTGTG 59.963 55.000 0.00 0.00 35.88 3.66
5626 6343 0.037303 ACAACCTGGATCTGGTGCTG 59.963 55.000 0.00 9.16 35.88 4.41
5627 6344 0.326264 GACAACCTGGATCTGGTGCT 59.674 55.000 0.00 1.28 35.88 4.40
5628 6345 0.678048 GGACAACCTGGATCTGGTGC 60.678 60.000 0.00 5.24 35.88 5.01
5629 6346 0.987294 AGGACAACCTGGATCTGGTG 59.013 55.000 0.00 3.41 45.92 4.17
5630 6347 3.502086 AGGACAACCTGGATCTGGT 57.498 52.632 0.00 5.34 45.92 4.00
5663 6380 1.884579 GCTGGTAGCCAATCATCCATG 59.115 52.381 0.00 0.00 34.48 3.66
5665 6382 0.918258 TGCTGGTAGCCAATCATCCA 59.082 50.000 0.00 0.00 41.51 3.41
5666 6383 1.133976 ACTGCTGGTAGCCAATCATCC 60.134 52.381 0.00 0.00 41.51 3.51
5689 6414 0.681887 CATTGCATCTGGGAGTGGCA 60.682 55.000 0.00 0.00 0.00 4.92
5730 6455 6.655078 AGCCTTGAACTGTTAATTGAATGT 57.345 33.333 0.00 0.00 0.00 2.71
5739 6464 3.550820 TGCTTGAAGCCTTGAACTGTTA 58.449 40.909 15.43 0.00 41.51 2.41
5752 6477 1.081376 GTGCTGCTGCTGCTTGAAG 60.081 57.895 27.67 6.70 40.48 3.02
5753 6478 1.176619 ATGTGCTGCTGCTGCTTGAA 61.177 50.000 27.67 13.63 40.48 2.69
5754 6479 1.602605 ATGTGCTGCTGCTGCTTGA 60.603 52.632 27.67 14.41 40.48 3.02
5778 6555 1.009060 TGGCCAGTAGGTTCCCTATGA 59.991 52.381 0.00 0.00 38.48 2.15
5788 6565 2.042831 GTTGCTGCTGGCCAGTAGG 61.043 63.158 40.69 26.97 43.71 3.18
5797 6574 0.382873 TGCTCTTGTTGTTGCTGCTG 59.617 50.000 0.00 0.00 0.00 4.41
5808 6585 0.957395 CCTGTTCGCCATGCTCTTGT 60.957 55.000 0.00 0.00 0.00 3.16
5813 6590 2.826777 CTTCCCCTGTTCGCCATGCT 62.827 60.000 0.00 0.00 0.00 3.79
5907 6684 1.229209 AGCCTCTCCTCCAAACGGA 60.229 57.895 0.00 0.00 0.00 4.69
5913 6690 3.397439 GCAGCAGCCTCTCCTCCA 61.397 66.667 0.00 0.00 33.58 3.86
6066 6850 3.591835 CACGGGCGCCACAAAAGT 61.592 61.111 30.85 14.46 0.00 2.66
6101 6885 1.053835 CACCTTGGCCCACCCTTTTT 61.054 55.000 0.00 0.00 33.59 1.94
6102 6886 1.459348 CACCTTGGCCCACCCTTTT 60.459 57.895 0.00 0.00 33.59 2.27
6103 6887 1.365105 TACACCTTGGCCCACCCTTT 61.365 55.000 0.00 0.00 33.59 3.11
6115 6899 1.498176 GGGAGGCCCAACTACACCTT 61.498 60.000 0.00 0.00 44.65 3.50
6119 6903 1.987855 CTCGGGAGGCCCAACTACA 60.988 63.158 0.00 0.00 45.83 2.74
6188 6986 4.703897 TCCCGCTGTATTTCCTGAAATAG 58.296 43.478 11.57 5.58 42.09 1.73
6190 6988 3.644966 TCCCGCTGTATTTCCTGAAAT 57.355 42.857 9.81 9.81 42.95 2.17
6193 6991 3.035363 TGTATCCCGCTGTATTTCCTGA 58.965 45.455 0.00 0.00 0.00 3.86
6204 7002 2.890371 GGACACGTGTATCCCGCT 59.110 61.111 23.44 0.00 0.00 5.52
6225 7023 2.181021 GGGACACGCTAGGACACG 59.819 66.667 0.00 0.00 0.00 4.49
6231 7029 2.181021 GACACGGGGACACGCTAG 59.819 66.667 0.00 0.00 37.37 3.42
6233 7031 3.873679 TAGGACACGGGGACACGCT 62.874 63.158 0.00 0.00 37.37 5.07
6250 7048 2.928801 ATTGCCATGCTGATACGGTA 57.071 45.000 0.00 0.00 0.00 4.02
6251 7049 1.949525 GAATTGCCATGCTGATACGGT 59.050 47.619 0.00 0.00 0.00 4.83
6263 7061 0.033228 CCAAACTTGCCGAATTGCCA 59.967 50.000 0.00 0.00 0.00 4.92
6266 7064 2.826277 GGCCAAACTTGCCGAATTG 58.174 52.632 0.00 0.00 39.48 2.32
6285 7083 1.767759 GCCCTACAAAGCATGGACAT 58.232 50.000 0.00 0.00 0.00 3.06
6291 7089 0.676782 GTCACCGCCCTACAAAGCAT 60.677 55.000 0.00 0.00 0.00 3.79
6298 7096 0.179108 GATGACTGTCACCGCCCTAC 60.179 60.000 13.50 0.00 0.00 3.18
6302 7100 1.741770 GTGGATGACTGTCACCGCC 60.742 63.158 21.80 18.81 0.00 6.13
6303 7101 0.320771 AAGTGGATGACTGTCACCGC 60.321 55.000 23.49 23.49 34.02 5.68
6304 7102 1.800586 CAAAGTGGATGACTGTCACCG 59.199 52.381 13.50 0.77 34.02 4.94
6422 7227 0.035317 AACTGAAGTGCTGATCGGCA 59.965 50.000 25.40 25.40 40.15 5.69
6533 7339 9.683069 CTGTGACTTACAAAAAGCAAGATAATT 57.317 29.630 0.00 0.00 39.20 1.40
6540 7346 7.497579 TCTCATACTGTGACTTACAAAAAGCAA 59.502 33.333 0.00 0.00 39.20 3.91
6565 7371 5.689383 TCTGACAAAGCACATTTACCTTC 57.311 39.130 0.00 0.00 0.00 3.46
6656 7462 6.759497 ACAAGCAAAGTTCTTAGACAAACT 57.241 33.333 0.00 0.00 37.32 2.66
6892 7698 2.503765 TGAGTTGAACCTTGTCAGTCCA 59.496 45.455 0.00 0.00 0.00 4.02
7058 7867 9.388506 CATAGACAAGAGAATAAGTTGGACATT 57.611 33.333 0.00 0.00 0.00 2.71
7082 7891 2.826428 CGATCGACCTCATTGAACCAT 58.174 47.619 10.26 0.00 0.00 3.55
7097 7906 1.154016 ACGAGGTGTGAAGCGATCG 60.154 57.895 11.69 11.69 36.32 3.69
7411 8221 5.665812 TGAGCTGTACCAAAGGTATAATCCT 59.334 40.000 0.00 0.00 40.54 3.24
7412 8222 5.758784 GTGAGCTGTACCAAAGGTATAATCC 59.241 44.000 0.00 0.00 40.54 3.01
7413 8223 5.462398 CGTGAGCTGTACCAAAGGTATAATC 59.538 44.000 0.00 0.00 40.54 1.75
7414 8224 5.128171 TCGTGAGCTGTACCAAAGGTATAAT 59.872 40.000 0.00 0.00 40.54 1.28
7574 8384 2.878406 TGAAACCAAACAGCTAGCACTC 59.122 45.455 18.83 0.36 0.00 3.51
7576 8386 3.923017 ATGAAACCAAACAGCTAGCAC 57.077 42.857 18.83 0.00 0.00 4.40
7696 8506 5.694910 GGTTACATGAGAATACACCGTATGG 59.305 44.000 0.00 0.00 42.84 2.74
7701 8511 4.131649 TGGGTTACATGAGAATACACCG 57.868 45.455 0.00 0.00 0.00 4.94
7833 8644 4.700213 AGTTCCCGGAATCAAACATAACAG 59.300 41.667 0.73 0.00 0.00 3.16
7852 8663 6.038714 AGGTCAAGTTTGAGTGAAATGAGTTC 59.961 38.462 0.00 0.00 37.98 3.01
7901 8712 3.242059 GCATTCAACACAAATAATGCGCC 60.242 43.478 4.18 0.00 43.17 6.53
7924 8736 9.630098 CTCTTGAAGCAACATATTGTTTATTGT 57.370 29.630 0.00 0.00 38.77 2.71
8029 8841 2.432444 CGGGACTGACCAATAAAGCAA 58.568 47.619 0.00 0.00 41.20 3.91
8040 8852 2.156051 GACAGTGTCCCGGGACTGAC 62.156 65.000 44.64 36.40 44.80 3.51
8149 8961 9.787532 GATCAGCTGAAATCTCTACAGTATATC 57.212 37.037 22.50 3.30 34.60 1.63
8151 8963 7.661847 TCGATCAGCTGAAATCTCTACAGTATA 59.338 37.037 22.50 0.00 34.60 1.47
8152 8964 6.488344 TCGATCAGCTGAAATCTCTACAGTAT 59.512 38.462 22.50 0.00 34.60 2.12
8153 8965 5.823045 TCGATCAGCTGAAATCTCTACAGTA 59.177 40.000 22.50 0.00 34.60 2.74
8154 8966 4.642437 TCGATCAGCTGAAATCTCTACAGT 59.358 41.667 22.50 0.00 34.60 3.55
8155 8967 5.180367 TCGATCAGCTGAAATCTCTACAG 57.820 43.478 22.50 1.16 35.14 2.74
8156 8968 5.300286 TCATCGATCAGCTGAAATCTCTACA 59.700 40.000 22.50 0.96 0.00 2.74
8157 8969 5.767269 TCATCGATCAGCTGAAATCTCTAC 58.233 41.667 22.50 4.31 0.00 2.59
8162 8974 6.073385 TGCTAATTCATCGATCAGCTGAAATC 60.073 38.462 22.50 13.90 38.32 2.17
8213 9027 6.477033 CCGTGTAAAAATTTGGTGATGTTTGA 59.523 34.615 0.00 0.00 0.00 2.69
8292 9106 3.866816 TGCTGGGGATCTTCAGAGATAT 58.133 45.455 16.26 0.00 42.66 1.63
8294 9108 2.187239 TGCTGGGGATCTTCAGAGAT 57.813 50.000 16.26 0.00 45.27 2.75


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

AutoCloner maintained by Alex Coulton.