Multiple sequence alignment - TraesCS3B01G385400

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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 TraesCS3B01G385400 chr3B 100.000 3433 0 0 1 3433 605488471 605485039 0.000000e+00 6340
1 TraesCS3B01G385400 chr3B 100.000 268 0 0 3846 4113 605484626 605484359 2.860000e-136 496
2 TraesCS3B01G385400 chr3B 88.581 289 29 3 586 871 605504903 605504616 8.460000e-92 348
3 TraesCS3B01G385400 chr3B 86.458 192 22 4 1730 1918 605496044 605495854 1.500000e-49 207
4 TraesCS3B01G385400 chr3A 92.078 2752 165 28 703 3431 600747343 600744622 0.000000e+00 3825
5 TraesCS3B01G385400 chr3A 78.770 504 76 19 2375 2869 600750136 600749655 3.990000e-80 309
6 TraesCS3B01G385400 chr3A 82.011 378 44 6 203 568 600748073 600747708 2.400000e-77 300
7 TraesCS3B01G385400 chr3A 85.938 192 21 6 1731 1918 600751286 600751097 2.510000e-47 200
8 TraesCS3B01G385400 chr3A 87.333 150 13 5 2203 2350 600818867 600818722 2.540000e-37 167
9 TraesCS3B01G385400 chr3A 86.093 151 14 5 2203 2350 600782761 600782615 5.500000e-34 156
10 TraesCS3B01G385400 chr3D 94.947 2078 90 12 603 2675 458306354 458304287 0.000000e+00 3241
11 TraesCS3B01G385400 chr3D 90.958 741 57 8 2668 3401 458304080 458303343 0.000000e+00 989
12 TraesCS3B01G385400 chr3D 82.904 544 66 11 4 535 458307097 458306569 8.050000e-127 464
13 TraesCS3B01G385400 chr3D 82.126 414 60 4 2321 2733 458310478 458310078 3.940000e-90 342
14 TraesCS3B01G385400 chr3D 90.698 86 8 0 1077 1162 458311346 458311261 9.340000e-22 115
15 TraesCS3B01G385400 chr3D 93.151 73 5 0 546 618 458306442 458306370 1.560000e-19 108


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 TraesCS3B01G385400 chr3B 605484359 605488471 4112 True 3418.0 6340 100.000000 1 4113 2 chr3B.!!$R3 4112
1 TraesCS3B01G385400 chr3A 600744622 600751286 6664 True 1158.5 3825 84.699250 203 3431 4 chr3A.!!$R3 3228
2 TraesCS3B01G385400 chr3D 458303343 458311346 8003 True 876.5 3241 89.130667 4 3401 6 chr3D.!!$R1 3397

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
63 4310 0.312102 GAAAAGAAGGCGTGCTTGCT 59.688 50.000 0.00 0.00 34.52 3.91 F
64 4311 0.312102 AAAAGAAGGCGTGCTTGCTC 59.688 50.000 0.00 0.00 34.52 4.26 F
272 4519 0.322322 CATGGTGCAATTTGCTGGGT 59.678 50.000 21.19 3.91 45.31 4.51 F
1153 5797 1.079819 GCGAGCAAGTACCTGCAGA 60.080 57.895 17.39 0.00 45.18 4.26 F
2441 7097 0.037046 CAGCAATTGCCACCTTTCCC 60.037 55.000 26.45 0.00 43.38 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 5946 0.459585 TGAAAGTGCCGCCGTAGATC 60.460 55.0 0.00 0.00 0.00 2.75 R
1974 6628 2.027100 TGCTCGACAGACTAGAGGAGAA 60.027 50.0 0.00 0.00 32.96 2.87 R
2149 6803 0.940519 CGTCGCTGTAAACGGGAACA 60.941 55.0 0.00 0.00 35.32 3.18 R
2908 7779 0.104304 GTGTTCGGAGCGGGATGTAT 59.896 55.0 0.00 0.00 0.00 2.29 R
3884 8764 0.322187 TAAAGAAGGCGGCCTGAACC 60.322 55.0 24.63 12.19 32.13 3.62 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
21 4268 0.378962 TTCAACCCAAAGACGTTGCG 59.621 50.000 0.00 0.00 39.36 4.85
22 4269 1.657181 CAACCCAAAGACGTTGCGC 60.657 57.895 0.00 0.00 35.74 6.09
24 4271 2.978010 CCCAAAGACGTTGCGCCT 60.978 61.111 4.18 0.00 35.74 5.52
30 4277 2.927477 CAAAGACGTTGCGCCTAAGATA 59.073 45.455 4.18 0.00 0.00 1.98
41 4288 5.822278 TGCGCCTAAGATATTCGAGATATC 58.178 41.667 4.18 14.59 0.00 1.63
44 4291 6.416455 GCGCCTAAGATATTCGAGATATCAAG 59.584 42.308 20.16 17.13 34.36 3.02
47 4294 9.862371 GCCTAAGATATTCGAGATATCAAGAAA 57.138 33.333 20.16 7.03 34.36 2.52
54 4301 6.910536 TTCGAGATATCAAGAAAAGAAGGC 57.089 37.500 5.32 0.00 0.00 4.35
55 4302 5.043903 TCGAGATATCAAGAAAAGAAGGCG 58.956 41.667 5.32 0.00 0.00 5.52
56 4303 4.806247 CGAGATATCAAGAAAAGAAGGCGT 59.194 41.667 5.32 0.00 0.00 5.68
57 4304 5.276584 CGAGATATCAAGAAAAGAAGGCGTG 60.277 44.000 5.32 0.00 0.00 5.34
58 4305 2.997485 ATCAAGAAAAGAAGGCGTGC 57.003 45.000 0.00 0.00 0.00 5.34
60 4307 2.297701 TCAAGAAAAGAAGGCGTGCTT 58.702 42.857 0.00 0.00 0.00 3.91
63 4310 0.312102 GAAAAGAAGGCGTGCTTGCT 59.688 50.000 0.00 0.00 34.52 3.91
64 4311 0.312102 AAAAGAAGGCGTGCTTGCTC 59.688 50.000 0.00 0.00 34.52 4.26
65 4312 0.819259 AAAGAAGGCGTGCTTGCTCA 60.819 50.000 0.00 0.00 34.52 4.26
66 4313 0.819259 AAGAAGGCGTGCTTGCTCAA 60.819 50.000 0.00 0.00 34.52 3.02
67 4314 1.081840 GAAGGCGTGCTTGCTCAAC 60.082 57.895 0.92 0.00 34.52 3.18
69 4316 1.383456 AAGGCGTGCTTGCTCAACAA 61.383 50.000 0.92 0.00 36.62 2.83
108 4355 5.567037 TTTTGGGTCCATCAGATCGATAT 57.433 39.130 0.00 0.00 31.20 1.63
137 4384 2.553247 GGGCTAACCTTGGCTCATATCC 60.553 54.545 0.00 0.00 34.94 2.59
146 4393 2.763039 TGGCTCATATCCAGGAGTTCA 58.237 47.619 0.00 0.00 35.00 3.18
147 4394 3.321039 TGGCTCATATCCAGGAGTTCAT 58.679 45.455 0.00 0.00 35.00 2.57
150 4397 5.188555 TGGCTCATATCCAGGAGTTCATATC 59.811 44.000 0.00 0.00 35.00 1.63
151 4398 5.396213 GGCTCATATCCAGGAGTTCATATCC 60.396 48.000 0.00 0.00 35.00 2.59
152 4399 5.396213 GCTCATATCCAGGAGTTCATATCCC 60.396 48.000 0.00 0.00 37.57 3.85
156 4403 4.778213 TCCAGGAGTTCATATCCCTTTG 57.222 45.455 0.00 0.00 37.57 2.77
180 4427 6.386927 TGGGAGATGATTTCTGGTATTACACT 59.613 38.462 0.00 0.00 33.74 3.55
183 4430 7.655328 GGAGATGATTTCTGGTATTACACTCAG 59.345 40.741 0.00 0.00 33.74 3.35
184 4431 6.989169 AGATGATTTCTGGTATTACACTCAGC 59.011 38.462 0.00 0.00 31.79 4.26
185 4432 6.299805 TGATTTCTGGTATTACACTCAGCT 57.700 37.500 0.00 0.00 0.00 4.24
226 4473 1.416401 ACTTGAAAACTCGCCTCCAGA 59.584 47.619 0.00 0.00 0.00 3.86
239 4486 3.584406 CCTCCAGAGGCGAATATACAG 57.416 52.381 0.00 0.00 42.44 2.74
240 4487 2.353208 CCTCCAGAGGCGAATATACAGC 60.353 54.545 0.00 0.00 42.44 4.40
249 4496 3.057736 GGCGAATATACAGCGTCCTTAGA 60.058 47.826 0.00 0.00 0.00 2.10
272 4519 0.322322 CATGGTGCAATTTGCTGGGT 59.678 50.000 21.19 3.91 45.31 4.51
285 4532 2.054799 TGCTGGGTTCACCTTTAGTCT 58.945 47.619 0.00 0.00 41.11 3.24
286 4533 2.441750 TGCTGGGTTCACCTTTAGTCTT 59.558 45.455 0.00 0.00 41.11 3.01
287 4534 3.649023 TGCTGGGTTCACCTTTAGTCTTA 59.351 43.478 0.00 0.00 41.11 2.10
288 4535 4.288626 TGCTGGGTTCACCTTTAGTCTTAT 59.711 41.667 0.00 0.00 41.11 1.73
289 4536 5.486063 TGCTGGGTTCACCTTTAGTCTTATA 59.514 40.000 0.00 0.00 41.11 0.98
290 4537 6.013206 TGCTGGGTTCACCTTTAGTCTTATAA 60.013 38.462 0.00 0.00 41.11 0.98
291 4538 6.539103 GCTGGGTTCACCTTTAGTCTTATAAG 59.461 42.308 6.11 6.11 41.11 1.73
292 4539 6.954232 TGGGTTCACCTTTAGTCTTATAAGG 58.046 40.000 12.54 0.00 43.25 2.69
306 4553 6.072397 AGTCTTATAAGGCTATGACTGCTACG 60.072 42.308 18.00 0.00 39.65 3.51
426 4685 1.381463 TTGCCCTCTCTGCAAGCAT 59.619 52.632 0.00 0.00 43.36 3.79
439 4698 6.825213 TCTCTGCAAGCATGTGTAAGAATATT 59.175 34.615 0.00 0.00 0.00 1.28
450 4709 7.496346 TGTGTAAGAATATTCTCCTCACCTT 57.504 36.000 26.33 12.84 36.28 3.50
460 4719 5.422214 TTCTCCTCACCTTCTATTCCAAC 57.578 43.478 0.00 0.00 0.00 3.77
506 4765 2.289694 ACGAGATTTGCACTTGGCTAGT 60.290 45.455 0.00 0.00 45.15 2.57
513 4772 1.561076 TGCACTTGGCTAGTCATCCAT 59.439 47.619 0.00 0.00 45.15 3.41
553 5165 1.543871 GGTGGCCCGAAGACTTGTAAA 60.544 52.381 0.00 0.00 0.00 2.01
583 5195 3.878778 AGGCTCGGGAAATATATCATGC 58.121 45.455 0.00 0.00 0.00 4.06
591 5203 6.714356 TCGGGAAATATATCATGCACATCAAA 59.286 34.615 0.00 0.00 0.00 2.69
629 5272 5.804944 ACACCAGATTATCCTCTGATGAG 57.195 43.478 2.52 0.00 44.48 2.90
652 5295 2.044123 CCCAAAGGGCTATGAGTGAC 57.956 55.000 0.00 0.00 35.35 3.67
653 5296 1.281867 CCCAAAGGGCTATGAGTGACA 59.718 52.381 0.00 0.00 35.35 3.58
661 5304 2.102252 GGCTATGAGTGACAAGGAGGAG 59.898 54.545 0.00 0.00 0.00 3.69
735 5378 5.748152 CCAATCACAAACCACTAACACTTTG 59.252 40.000 0.00 0.00 0.00 2.77
738 5381 5.197451 TCACAAACCACTAACACTTTGGAT 58.803 37.500 0.00 0.00 34.24 3.41
742 5385 5.767816 AACCACTAACACTTTGGATTCAC 57.232 39.130 0.00 0.00 34.24 3.18
743 5386 4.142038 ACCACTAACACTTTGGATTCACC 58.858 43.478 0.00 0.00 39.54 4.02
755 5398 4.637387 TGGATTCACCAAAATGCCAAAT 57.363 36.364 0.00 0.00 46.75 2.32
757 5400 4.286549 TGGATTCACCAAAATGCCAAATCT 59.713 37.500 0.00 0.00 46.75 2.40
774 5417 7.147689 TGCCAAATCTATGAGCCATTACATTTT 60.148 33.333 0.00 0.00 0.00 1.82
982 5626 2.906389 TCCATCTAGCCGCCATTATTCT 59.094 45.455 0.00 0.00 0.00 2.40
1153 5797 1.079819 GCGAGCAAGTACCTGCAGA 60.080 57.895 17.39 0.00 45.18 4.26
1604 6256 8.697292 ACTATGGAAGACTCTAAGAAACCATAC 58.303 37.037 0.00 0.00 37.86 2.39
1695 6348 6.687081 AAAGTGAATGGTGAAAACGAGTAA 57.313 33.333 0.00 0.00 0.00 2.24
1974 6628 2.476199 CAGAAAGGGACTCCTCTCCAT 58.524 52.381 0.00 0.00 44.07 3.41
1990 6644 4.787551 TCTCCATTCTCCTCTAGTCTGTC 58.212 47.826 0.00 0.00 0.00 3.51
2007 6661 5.934625 AGTCTGTCGAGCAAACTAAATTCAT 59.065 36.000 0.00 0.00 0.00 2.57
2010 6664 4.092821 TGTCGAGCAAACTAAATTCATCCG 59.907 41.667 0.00 0.00 0.00 4.18
2012 6666 3.374058 CGAGCAAACTAAATTCATCCGGT 59.626 43.478 0.00 0.00 0.00 5.28
2149 6803 2.656069 CCACGACGAATCCTGGGGT 61.656 63.158 0.00 0.00 29.77 4.95
2173 6827 1.202222 CCCGTTTACAGCGACGAGTAT 60.202 52.381 0.00 0.00 41.53 2.12
2197 6851 3.582208 ACTCTGCCACATTTCTTCTCTCT 59.418 43.478 0.00 0.00 0.00 3.10
2198 6852 4.183101 CTCTGCCACATTTCTTCTCTCTC 58.817 47.826 0.00 0.00 0.00 3.20
2199 6853 3.837146 TCTGCCACATTTCTTCTCTCTCT 59.163 43.478 0.00 0.00 0.00 3.10
2200 6854 4.081752 TCTGCCACATTTCTTCTCTCTCTC 60.082 45.833 0.00 0.00 0.00 3.20
2241 6895 6.347079 CGCATGCAAAAGTTCATCTTGAAAAT 60.347 34.615 19.57 0.00 38.22 1.82
2251 6907 9.801873 AAGTTCATCTTGAAAATTCGAAAAAGA 57.198 25.926 0.00 7.41 38.22 2.52
2301 6957 0.525761 TAATTTGCAGCCGCCTGTTC 59.474 50.000 0.00 0.00 41.26 3.18
2314 6970 1.291588 CTGTTCGAGCTGCTCACCT 59.708 57.895 27.46 0.00 0.00 4.00
2413 7069 3.556999 TCCGAACATTTGGGTTTCTCAA 58.443 40.909 0.00 0.00 32.26 3.02
2427 7083 5.067674 GGGTTTCTCAATACATATGCAGCAA 59.932 40.000 0.00 0.00 0.00 3.91
2441 7097 0.037046 CAGCAATTGCCACCTTTCCC 60.037 55.000 26.45 0.00 43.38 3.97
2460 7116 4.535781 TCCCGTGAATCATGAATGGATTT 58.464 39.130 3.65 0.00 35.23 2.17
2462 7118 6.125719 TCCCGTGAATCATGAATGGATTTAA 58.874 36.000 3.65 0.00 35.23 1.52
2643 7299 1.398390 CATAAGAAAGGCGAGTGCACC 59.602 52.381 14.63 4.10 45.35 5.01
2647 7303 1.152963 AAAGGCGAGTGCACCAAGT 60.153 52.632 14.63 0.00 45.35 3.16
2651 7307 0.594796 GGCGAGTGCACCAAGTTTTG 60.595 55.000 14.63 0.00 45.35 2.44
2666 7322 4.935352 AGTTTTGTGCTTATTTCTGGCA 57.065 36.364 0.00 0.00 0.00 4.92
2672 7328 6.542574 TTGTGCTTATTTCTGGCAAAATTG 57.457 33.333 11.13 7.60 37.73 2.32
2697 7567 7.065324 TGTTCTAACAAAGATATTACAAGGGCG 59.935 37.037 0.00 0.00 35.67 6.13
2698 7568 6.880484 TCTAACAAAGATATTACAAGGGCGA 58.120 36.000 0.00 0.00 0.00 5.54
2710 7580 1.338020 CAAGGGCGAGAAAAGTTTGCT 59.662 47.619 0.00 0.00 0.00 3.91
2755 7625 1.674441 CAGATGCCATGGATGTGTCAC 59.326 52.381 18.40 0.00 0.00 3.67
2758 7629 3.136992 AGATGCCATGGATGTGTCACATA 59.863 43.478 18.40 4.66 39.27 2.29
2851 7722 2.158667 GGAGTTTGGGTCTTTCAGTGGA 60.159 50.000 0.00 0.00 0.00 4.02
2908 7779 4.038162 GTGGGTAAATACAAGCACCACAAA 59.962 41.667 0.00 0.00 44.63 2.83
2977 7848 2.667199 CGACGGGGTTTTCGGCTT 60.667 61.111 0.00 0.00 32.71 4.35
3069 7940 0.673985 CGGTTCTCTGAGTGTGTCCA 59.326 55.000 4.32 0.00 0.00 4.02
3149 8020 3.121944 CAGTCTCGAACTTTGACATTCCG 59.878 47.826 4.78 0.00 35.45 4.30
3162 8033 2.228822 GACATTCCGGTGTTTGCTTCAT 59.771 45.455 0.00 0.00 31.16 2.57
3166 8037 5.047377 ACATTCCGGTGTTTGCTTCATAATT 60.047 36.000 0.00 0.00 0.00 1.40
3169 8040 5.250200 TCCGGTGTTTGCTTCATAATTACT 58.750 37.500 0.00 0.00 0.00 2.24
3196 8068 5.389859 TCACCAAAATATGCAAGAGTTGG 57.610 39.130 16.68 16.68 41.06 3.77
3200 8072 5.185056 ACCAAAATATGCAAGAGTTGGGTAC 59.815 40.000 20.31 0.00 39.87 3.34
3251 8123 9.200817 AGAGTAATGCATGGGTTGTAAATTATT 57.799 29.630 0.00 0.00 0.00 1.40
3256 8128 5.641209 TGCATGGGTTGTAAATTATTTGTGC 59.359 36.000 0.00 0.00 0.00 4.57
3316 8188 3.122948 GTGTGACTGGTATGTAAGTTGCG 59.877 47.826 0.00 0.00 0.00 4.85
3320 8192 4.081917 TGACTGGTATGTAAGTTGCGATGA 60.082 41.667 0.00 0.00 0.00 2.92
3366 8246 3.195396 GCATATCTCTTTTGTTTGGGCCA 59.805 43.478 0.00 0.00 0.00 5.36
3369 8249 4.769345 ATCTCTTTTGTTTGGGCCAAAA 57.231 36.364 31.94 19.19 38.95 2.44
3374 8254 5.995446 TCTTTTGTTTGGGCCAAAATAAGT 58.005 33.333 31.94 0.00 40.06 2.24
3381 8261 2.830923 TGGGCCAAAATAAGTCCATGTG 59.169 45.455 2.13 0.00 0.00 3.21
3404 8284 2.638480 TTAAGGAGCCCATGAATCCG 57.362 50.000 0.00 0.00 38.20 4.18
3405 8285 0.108585 TAAGGAGCCCATGAATCCGC 59.891 55.000 0.00 0.00 38.20 5.54
3409 8289 3.279875 GCCCATGAATCCGCCGTC 61.280 66.667 0.00 0.00 0.00 4.79
3415 8295 0.806102 ATGAATCCGCCGTCGAACAG 60.806 55.000 0.00 0.00 38.10 3.16
3417 8297 0.734942 GAATCCGCCGTCGAACAGAA 60.735 55.000 0.00 0.00 38.10 3.02
3866 8746 2.114411 GGCCGACCCACCTCAAAA 59.886 61.111 0.00 0.00 0.00 2.44
3867 8747 1.529713 GGCCGACCCACCTCAAAAA 60.530 57.895 0.00 0.00 0.00 1.94
3868 8748 0.898326 GGCCGACCCACCTCAAAAAT 60.898 55.000 0.00 0.00 0.00 1.82
3869 8749 0.966179 GCCGACCCACCTCAAAAATT 59.034 50.000 0.00 0.00 0.00 1.82
3870 8750 1.343142 GCCGACCCACCTCAAAAATTT 59.657 47.619 0.00 0.00 0.00 1.82
3871 8751 2.609491 GCCGACCCACCTCAAAAATTTC 60.609 50.000 0.00 0.00 0.00 2.17
3872 8752 2.890945 CCGACCCACCTCAAAAATTTCT 59.109 45.455 0.00 0.00 0.00 2.52
3873 8753 3.305335 CCGACCCACCTCAAAAATTTCTG 60.305 47.826 0.00 0.00 0.00 3.02
3874 8754 3.305335 CGACCCACCTCAAAAATTTCTGG 60.305 47.826 0.00 0.00 0.00 3.86
3875 8755 3.641436 GACCCACCTCAAAAATTTCTGGT 59.359 43.478 0.00 0.00 0.00 4.00
3876 8756 4.037222 ACCCACCTCAAAAATTTCTGGTT 58.963 39.130 0.00 0.00 0.00 3.67
3877 8757 4.473196 ACCCACCTCAAAAATTTCTGGTTT 59.527 37.500 0.00 0.00 0.00 3.27
3878 8758 5.045213 ACCCACCTCAAAAATTTCTGGTTTT 60.045 36.000 0.00 0.00 0.00 2.43
3879 8759 5.296531 CCCACCTCAAAAATTTCTGGTTTTG 59.703 40.000 0.00 3.11 43.15 2.44
3880 8760 5.296531 CCACCTCAAAAATTTCTGGTTTTGG 59.703 40.000 8.53 0.00 42.42 3.28
3881 8761 5.296531 CACCTCAAAAATTTCTGGTTTTGGG 59.703 40.000 8.53 5.61 42.41 4.12
3882 8762 5.190726 ACCTCAAAAATTTCTGGTTTTGGGA 59.809 36.000 9.70 0.00 44.50 4.37
3883 8763 6.118852 CCTCAAAAATTTCTGGTTTTGGGAA 58.881 36.000 9.70 0.00 44.50 3.97
3884 8764 6.260714 CCTCAAAAATTTCTGGTTTTGGGAAG 59.739 38.462 9.70 1.28 44.50 3.46
3885 8765 6.118852 TCAAAAATTTCTGGTTTTGGGAAGG 58.881 36.000 8.53 0.00 42.42 3.46
3886 8766 5.708736 AAAATTTCTGGTTTTGGGAAGGT 57.291 34.783 0.00 0.00 0.00 3.50
3887 8767 5.708736 AAATTTCTGGTTTTGGGAAGGTT 57.291 34.783 0.00 0.00 0.00 3.50
3888 8768 4.955811 ATTTCTGGTTTTGGGAAGGTTC 57.044 40.909 0.00 0.00 0.00 3.62
3889 8769 3.390175 TTCTGGTTTTGGGAAGGTTCA 57.610 42.857 0.00 0.00 0.00 3.18
3890 8770 2.944129 TCTGGTTTTGGGAAGGTTCAG 58.056 47.619 0.00 0.00 0.00 3.02
3891 8771 1.963515 CTGGTTTTGGGAAGGTTCAGG 59.036 52.381 0.00 0.00 0.00 3.86
3892 8772 0.679505 GGTTTTGGGAAGGTTCAGGC 59.320 55.000 0.00 0.00 0.00 4.85
3893 8773 0.679505 GTTTTGGGAAGGTTCAGGCC 59.320 55.000 0.00 0.00 0.00 5.19
3894 8774 0.825840 TTTTGGGAAGGTTCAGGCCG 60.826 55.000 0.00 0.00 0.00 6.13
3895 8775 3.860930 TTGGGAAGGTTCAGGCCGC 62.861 63.158 0.00 0.00 0.00 6.53
3897 8777 4.035102 GGAAGGTTCAGGCCGCCT 62.035 66.667 5.94 5.94 0.00 5.52
3898 8778 2.034221 GAAGGTTCAGGCCGCCTT 59.966 61.111 9.99 19.03 44.46 4.35
3899 8779 2.034221 AAGGTTCAGGCCGCCTTC 59.966 61.111 9.99 3.29 38.09 3.46
3900 8780 2.529744 AAGGTTCAGGCCGCCTTCT 61.530 57.895 9.99 2.32 38.09 2.85
3901 8781 2.034221 GGTTCAGGCCGCCTTCTT 59.966 61.111 9.99 0.00 0.00 2.52
3902 8782 1.603739 GGTTCAGGCCGCCTTCTTT 60.604 57.895 9.99 0.00 0.00 2.52
3903 8783 0.322187 GGTTCAGGCCGCCTTCTTTA 60.322 55.000 9.99 0.00 0.00 1.85
3904 8784 1.530323 GTTCAGGCCGCCTTCTTTAA 58.470 50.000 9.99 0.00 0.00 1.52
3905 8785 2.092323 GTTCAGGCCGCCTTCTTTAAT 58.908 47.619 9.99 0.00 0.00 1.40
3906 8786 2.492088 GTTCAGGCCGCCTTCTTTAATT 59.508 45.455 9.99 0.00 0.00 1.40
3907 8787 2.802719 TCAGGCCGCCTTCTTTAATTT 58.197 42.857 9.99 0.00 0.00 1.82
3908 8788 3.161866 TCAGGCCGCCTTCTTTAATTTT 58.838 40.909 9.99 0.00 0.00 1.82
3909 8789 3.576550 TCAGGCCGCCTTCTTTAATTTTT 59.423 39.130 9.99 0.00 0.00 1.94
3934 8814 9.863845 TTTTATGTTTTTCTTTCGGTTTTCTCT 57.136 25.926 0.00 0.00 0.00 3.10
3935 8815 8.850454 TTATGTTTTTCTTTCGGTTTTCTCTG 57.150 30.769 0.00 0.00 0.00 3.35
3936 8816 5.099575 TGTTTTTCTTTCGGTTTTCTCTGC 58.900 37.500 0.00 0.00 0.00 4.26
3937 8817 5.105917 TGTTTTTCTTTCGGTTTTCTCTGCT 60.106 36.000 0.00 0.00 0.00 4.24
3938 8818 5.576447 TTTTCTTTCGGTTTTCTCTGCTT 57.424 34.783 0.00 0.00 0.00 3.91
3939 8819 5.576447 TTTCTTTCGGTTTTCTCTGCTTT 57.424 34.783 0.00 0.00 0.00 3.51
3940 8820 5.576447 TTCTTTCGGTTTTCTCTGCTTTT 57.424 34.783 0.00 0.00 0.00 2.27
3941 8821 5.169836 TCTTTCGGTTTTCTCTGCTTTTC 57.830 39.130 0.00 0.00 0.00 2.29
3942 8822 4.881850 TCTTTCGGTTTTCTCTGCTTTTCT 59.118 37.500 0.00 0.00 0.00 2.52
3943 8823 6.053005 TCTTTCGGTTTTCTCTGCTTTTCTA 58.947 36.000 0.00 0.00 0.00 2.10
3944 8824 5.668558 TTCGGTTTTCTCTGCTTTTCTAC 57.331 39.130 0.00 0.00 0.00 2.59
3945 8825 4.699637 TCGGTTTTCTCTGCTTTTCTACA 58.300 39.130 0.00 0.00 0.00 2.74
3946 8826 5.305585 TCGGTTTTCTCTGCTTTTCTACAT 58.694 37.500 0.00 0.00 0.00 2.29
3947 8827 5.763204 TCGGTTTTCTCTGCTTTTCTACATT 59.237 36.000 0.00 0.00 0.00 2.71
3948 8828 6.262273 TCGGTTTTCTCTGCTTTTCTACATTT 59.738 34.615 0.00 0.00 0.00 2.32
3949 8829 6.918022 CGGTTTTCTCTGCTTTTCTACATTTT 59.082 34.615 0.00 0.00 0.00 1.82
3950 8830 7.435192 CGGTTTTCTCTGCTTTTCTACATTTTT 59.565 33.333 0.00 0.00 0.00 1.94
3951 8831 8.542953 GGTTTTCTCTGCTTTTCTACATTTTTG 58.457 33.333 0.00 0.00 0.00 2.44
3952 8832 9.087424 GTTTTCTCTGCTTTTCTACATTTTTGT 57.913 29.630 0.00 0.00 0.00 2.83
3953 8833 9.651913 TTTTCTCTGCTTTTCTACATTTTTGTT 57.348 25.926 0.00 0.00 0.00 2.83
3954 8834 8.856490 TTCTCTGCTTTTCTACATTTTTGTTC 57.144 30.769 0.00 0.00 0.00 3.18
3955 8835 8.225603 TCTCTGCTTTTCTACATTTTTGTTCT 57.774 30.769 0.00 0.00 0.00 3.01
3956 8836 8.686334 TCTCTGCTTTTCTACATTTTTGTTCTT 58.314 29.630 0.00 0.00 0.00 2.52
3957 8837 9.305925 CTCTGCTTTTCTACATTTTTGTTCTTT 57.694 29.630 0.00 0.00 0.00 2.52
3958 8838 9.301153 TCTGCTTTTCTACATTTTTGTTCTTTC 57.699 29.630 0.00 0.00 0.00 2.62
3959 8839 8.419076 TGCTTTTCTACATTTTTGTTCTTTCC 57.581 30.769 0.00 0.00 0.00 3.13
3960 8840 8.037758 TGCTTTTCTACATTTTTGTTCTTTCCA 58.962 29.630 0.00 0.00 0.00 3.53
3961 8841 8.878769 GCTTTTCTACATTTTTGTTCTTTCCAA 58.121 29.630 0.00 0.00 0.00 3.53
3965 8845 8.795786 TCTACATTTTTGTTCTTTCCAATTCG 57.204 30.769 0.00 0.00 0.00 3.34
3966 8846 8.410141 TCTACATTTTTGTTCTTTCCAATTCGT 58.590 29.630 0.00 0.00 0.00 3.85
3967 8847 7.841915 ACATTTTTGTTCTTTCCAATTCGTT 57.158 28.000 0.00 0.00 0.00 3.85
3968 8848 8.262715 ACATTTTTGTTCTTTCCAATTCGTTT 57.737 26.923 0.00 0.00 0.00 3.60
3969 8849 8.726068 ACATTTTTGTTCTTTCCAATTCGTTTT 58.274 25.926 0.00 0.00 0.00 2.43
3970 8850 9.553418 CATTTTTGTTCTTTCCAATTCGTTTTT 57.447 25.926 0.00 0.00 0.00 1.94
3971 8851 9.767684 ATTTTTGTTCTTTCCAATTCGTTTTTC 57.232 25.926 0.00 0.00 0.00 2.29
3972 8852 7.891183 TTTGTTCTTTCCAATTCGTTTTTCA 57.109 28.000 0.00 0.00 0.00 2.69
3973 8853 8.485976 TTTGTTCTTTCCAATTCGTTTTTCAT 57.514 26.923 0.00 0.00 0.00 2.57
3974 8854 8.485976 TTGTTCTTTCCAATTCGTTTTTCATT 57.514 26.923 0.00 0.00 0.00 2.57
3975 8855 8.485976 TGTTCTTTCCAATTCGTTTTTCATTT 57.514 26.923 0.00 0.00 0.00 2.32
3976 8856 8.940952 TGTTCTTTCCAATTCGTTTTTCATTTT 58.059 25.926 0.00 0.00 0.00 1.82
3977 8857 9.420966 GTTCTTTCCAATTCGTTTTTCATTTTC 57.579 29.630 0.00 0.00 0.00 2.29
3978 8858 8.940768 TCTTTCCAATTCGTTTTTCATTTTCT 57.059 26.923 0.00 0.00 0.00 2.52
3979 8859 9.377312 TCTTTCCAATTCGTTTTTCATTTTCTT 57.623 25.926 0.00 0.00 0.00 2.52
3980 8860 9.986833 CTTTCCAATTCGTTTTTCATTTTCTTT 57.013 25.926 0.00 0.00 0.00 2.52
3989 8869 9.849166 TCGTTTTTCATTTTCTTTTACTTCACT 57.151 25.926 0.00 0.00 0.00 3.41
4032 8912 5.828299 TTTTGAACATCTTTCAAGTCCGT 57.172 34.783 0.16 0.00 39.30 4.69
4033 8913 4.811555 TTGAACATCTTTCAAGTCCGTG 57.188 40.909 0.00 0.00 33.90 4.94
4034 8914 4.066646 TGAACATCTTTCAAGTCCGTGA 57.933 40.909 0.00 0.00 0.00 4.35
4035 8915 4.447290 TGAACATCTTTCAAGTCCGTGAA 58.553 39.130 0.00 0.00 35.72 3.18
4036 8916 4.272504 TGAACATCTTTCAAGTCCGTGAAC 59.727 41.667 0.00 0.00 37.24 3.18
4037 8917 4.073293 ACATCTTTCAAGTCCGTGAACT 57.927 40.909 0.00 0.00 37.24 3.01
4038 8918 4.451900 ACATCTTTCAAGTCCGTGAACTT 58.548 39.130 0.00 0.00 40.08 2.66
4039 8919 4.881850 ACATCTTTCAAGTCCGTGAACTTT 59.118 37.500 0.00 0.00 37.38 2.66
4040 8920 5.357032 ACATCTTTCAAGTCCGTGAACTTTT 59.643 36.000 0.00 0.00 37.38 2.27
4041 8921 5.890424 TCTTTCAAGTCCGTGAACTTTTT 57.110 34.783 0.00 0.00 37.38 1.94
4095 8975 8.417780 TGAAAAGAGAAAATTCAATTTTGCGA 57.582 26.923 12.95 0.00 42.15 5.10
4096 8976 8.877779 TGAAAAGAGAAAATTCAATTTTGCGAA 58.122 25.926 12.95 0.00 42.15 4.70
4097 8977 9.147364 GAAAAGAGAAAATTCAATTTTGCGAAC 57.853 29.630 12.95 0.00 42.15 3.95
4098 8978 7.769272 AAGAGAAAATTCAATTTTGCGAACA 57.231 28.000 12.95 0.00 42.15 3.18
4099 8979 7.951530 AGAGAAAATTCAATTTTGCGAACAT 57.048 28.000 12.95 0.00 42.15 2.71
4100 8980 8.369218 AGAGAAAATTCAATTTTGCGAACATT 57.631 26.923 12.95 0.00 42.15 2.71
4101 8981 8.829612 AGAGAAAATTCAATTTTGCGAACATTT 58.170 25.926 12.95 0.00 42.15 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.269051 GCAACGTCTTTGGGTTGAAGG 60.269 52.381 7.98 0.00 44.80 3.46
3 4 2.018544 CGCAACGTCTTTGGGTTGA 58.981 52.632 7.98 0.00 44.80 3.18
4 5 4.607024 CGCAACGTCTTTGGGTTG 57.393 55.556 0.00 0.00 44.80 3.77
5 6 3.849840 TAGGCGCAACGTCTTTGGGTT 62.850 52.381 10.83 0.92 39.37 4.11
14 4261 2.124903 CGAATATCTTAGGCGCAACGT 58.875 47.619 10.83 0.00 0.00 3.99
15 4262 2.390938 TCGAATATCTTAGGCGCAACG 58.609 47.619 10.83 0.00 0.00 4.10
18 4265 5.357032 TGATATCTCGAATATCTTAGGCGCA 59.643 40.000 10.83 0.00 33.39 6.09
21 4268 9.862371 TTTCTTGATATCTCGAATATCTTAGGC 57.138 33.333 19.33 0.00 33.39 3.93
30 4277 6.201806 CGCCTTCTTTTCTTGATATCTCGAAT 59.798 38.462 3.98 0.00 0.00 3.34
41 4288 2.388121 CAAGCACGCCTTCTTTTCTTG 58.612 47.619 0.00 0.00 0.00 3.02
44 4291 0.312102 AGCAAGCACGCCTTCTTTTC 59.688 50.000 0.00 0.00 0.00 2.29
47 4294 0.819259 TTGAGCAAGCACGCCTTCTT 60.819 50.000 0.00 0.00 0.00 2.52
48 4295 1.227943 TTGAGCAAGCACGCCTTCT 60.228 52.632 0.00 0.00 0.00 2.85
49 4296 1.081840 GTTGAGCAAGCACGCCTTC 60.082 57.895 0.00 0.00 0.00 3.46
50 4297 1.383456 TTGTTGAGCAAGCACGCCTT 61.383 50.000 0.00 0.00 32.52 4.35
51 4298 1.789078 CTTGTTGAGCAAGCACGCCT 61.789 55.000 0.00 0.00 46.68 5.52
52 4299 1.370900 CTTGTTGAGCAAGCACGCC 60.371 57.895 0.00 0.00 46.68 5.68
53 4300 4.216963 CTTGTTGAGCAAGCACGC 57.783 55.556 0.00 0.00 46.68 5.34
60 4307 1.134128 TGTCAAGAGCCTTGTTGAGCA 60.134 47.619 12.71 1.36 37.28 4.26
63 4310 2.997980 TGTTGTCAAGAGCCTTGTTGA 58.002 42.857 12.71 0.00 34.54 3.18
64 4311 3.781079 TTGTTGTCAAGAGCCTTGTTG 57.219 42.857 12.71 0.00 0.00 3.33
65 4312 5.343307 AAATTGTTGTCAAGAGCCTTGTT 57.657 34.783 12.71 0.00 36.97 2.83
66 4313 5.343307 AAAATTGTTGTCAAGAGCCTTGT 57.657 34.783 12.71 0.00 36.97 3.16
67 4314 5.006941 CCAAAAATTGTTGTCAAGAGCCTTG 59.993 40.000 7.58 8.22 36.97 3.61
69 4316 4.443315 CCCAAAAATTGTTGTCAAGAGCCT 60.443 41.667 7.58 0.00 36.97 4.58
70 4317 3.809279 CCCAAAAATTGTTGTCAAGAGCC 59.191 43.478 7.58 0.00 36.97 4.70
128 4375 5.396213 GGGATATGAACTCCTGGATATGAGC 60.396 48.000 0.00 0.00 33.05 4.26
150 4397 3.294214 CCAGAAATCATCTCCCAAAGGG 58.706 50.000 0.00 0.00 46.11 3.95
151 4398 3.973425 ACCAGAAATCATCTCCCAAAGG 58.027 45.455 0.00 0.00 35.73 3.11
152 4399 7.775093 TGTAATACCAGAAATCATCTCCCAAAG 59.225 37.037 0.00 0.00 35.73 2.77
156 4403 6.831976 AGTGTAATACCAGAAATCATCTCCC 58.168 40.000 0.00 0.00 35.73 4.30
164 4411 8.079211 TCTTAGCTGAGTGTAATACCAGAAAT 57.921 34.615 5.29 0.00 32.55 2.17
165 4412 7.476540 TCTTAGCTGAGTGTAATACCAGAAA 57.523 36.000 5.29 0.00 32.55 2.52
167 4414 8.218488 TCTATCTTAGCTGAGTGTAATACCAGA 58.782 37.037 5.29 0.00 32.55 3.86
180 4427 6.670695 TTGTGGCATATCTATCTTAGCTGA 57.329 37.500 0.00 0.00 0.00 4.26
183 4430 9.442047 AAGTTATTGTGGCATATCTATCTTAGC 57.558 33.333 0.00 0.00 0.00 3.09
226 4473 1.329256 AGGACGCTGTATATTCGCCT 58.671 50.000 0.00 0.00 0.00 5.52
228 4475 4.156664 TCTAAGGACGCTGTATATTCGC 57.843 45.455 0.00 0.00 0.00 4.70
258 4505 2.033738 AGGTGAACCCAGCAAATTGCA 61.034 47.619 20.82 0.00 40.93 4.08
272 4519 9.209048 TCATAGCCTTATAAGACTAAAGGTGAA 57.791 33.333 14.28 0.00 41.57 3.18
285 4532 6.835819 ATCGTAGCAGTCATAGCCTTATAA 57.164 37.500 0.00 0.00 0.00 0.98
286 4533 6.835819 AATCGTAGCAGTCATAGCCTTATA 57.164 37.500 0.00 0.00 0.00 0.98
287 4534 5.730296 AATCGTAGCAGTCATAGCCTTAT 57.270 39.130 0.00 0.00 0.00 1.73
288 4535 5.289595 CAAATCGTAGCAGTCATAGCCTTA 58.710 41.667 0.00 0.00 0.00 2.69
289 4536 4.122776 CAAATCGTAGCAGTCATAGCCTT 58.877 43.478 0.00 0.00 0.00 4.35
290 4537 3.493350 CCAAATCGTAGCAGTCATAGCCT 60.493 47.826 0.00 0.00 0.00 4.58
291 4538 2.802816 CCAAATCGTAGCAGTCATAGCC 59.197 50.000 0.00 0.00 0.00 3.93
292 4539 3.717707 TCCAAATCGTAGCAGTCATAGC 58.282 45.455 0.00 0.00 0.00 2.97
306 4553 2.027385 GGAGCCCACATCTTCCAAATC 58.973 52.381 0.00 0.00 0.00 2.17
355 4602 2.158740 TCCACACACGATTTTGGAGGAA 60.159 45.455 0.00 0.00 33.02 3.36
426 4685 7.400339 AGAAGGTGAGGAGAATATTCTTACACA 59.600 37.037 29.30 22.38 37.73 3.72
439 4698 3.447586 CGTTGGAATAGAAGGTGAGGAGA 59.552 47.826 0.00 0.00 0.00 3.71
450 4709 3.833650 TGGTGAACCTACGTTGGAATAGA 59.166 43.478 23.12 0.00 36.82 1.98
475 4734 2.161410 TGCAAATCTCGTTCCAAATCCG 59.839 45.455 0.00 0.00 0.00 4.18
506 4765 0.687427 TGGCGAGGAGTCATGGATGA 60.687 55.000 0.00 0.00 0.00 2.92
513 4772 2.268920 GCCATTGGCGAGGAGTCA 59.731 61.111 12.82 0.00 39.62 3.41
535 4794 2.432444 CATTTACAAGTCTTCGGGCCA 58.568 47.619 4.39 0.00 0.00 5.36
539 4798 6.534079 CCTACTAACCATTTACAAGTCTTCGG 59.466 42.308 0.00 0.00 0.00 4.30
540 4799 6.035758 GCCTACTAACCATTTACAAGTCTTCG 59.964 42.308 0.00 0.00 0.00 3.79
553 5165 2.170012 TTCCCGAGCCTACTAACCAT 57.830 50.000 0.00 0.00 0.00 3.55
652 5295 2.431454 GTTTTCTCCTGCTCCTCCTTG 58.569 52.381 0.00 0.00 0.00 3.61
653 5296 1.352687 GGTTTTCTCCTGCTCCTCCTT 59.647 52.381 0.00 0.00 0.00 3.36
661 5304 1.228552 TGGGCTGGTTTTCTCCTGC 60.229 57.895 6.14 6.14 46.76 4.85
735 5378 4.835678 AGATTTGGCATTTTGGTGAATCC 58.164 39.130 0.00 0.00 0.00 3.01
738 5381 6.602410 TCATAGATTTGGCATTTTGGTGAA 57.398 33.333 0.00 0.00 0.00 3.18
742 5385 4.141892 TGGCTCATAGATTTGGCATTTTGG 60.142 41.667 0.00 0.00 0.00 3.28
743 5386 5.013568 TGGCTCATAGATTTGGCATTTTG 57.986 39.130 0.00 0.00 0.00 2.44
908 5551 2.432510 GTTTTGAAATGTGTGTGGGGGA 59.567 45.455 0.00 0.00 0.00 4.81
912 5555 3.533606 TGGGTTTTGAAATGTGTGTGG 57.466 42.857 0.00 0.00 0.00 4.17
982 5626 2.291465 GCATTGTGAGAACTGCAGTCAA 59.709 45.455 21.95 19.12 34.77 3.18
1017 5661 4.193893 TGCCTGCTGCTGTGGTGT 62.194 61.111 0.00 0.00 42.00 4.16
1153 5797 1.526917 GCGGGCATACAAGCATCCT 60.527 57.895 0.00 0.00 35.83 3.24
1302 5946 0.459585 TGAAAGTGCCGCCGTAGATC 60.460 55.000 0.00 0.00 0.00 2.75
1617 6269 2.222931 CGTTGTTCTTGCACGTGAAAGA 60.223 45.455 31.13 31.13 37.91 2.52
1695 6348 9.771534 TTGGTGCAAAGCTAATTAACTAAATTT 57.228 25.926 0.00 0.00 38.71 1.82
1764 6418 9.415544 CTTGATTTGATTTTTCCTCTAACCTTG 57.584 33.333 0.00 0.00 0.00 3.61
1868 6522 9.965824 TCTTAATTTGGTCAAATCAAGAGTTTC 57.034 29.630 14.65 0.00 39.11 2.78
1974 6628 2.027100 TGCTCGACAGACTAGAGGAGAA 60.027 50.000 0.00 0.00 32.96 2.87
1990 6644 3.374058 ACCGGATGAATTTAGTTTGCTCG 59.626 43.478 9.46 0.00 0.00 5.03
2045 6699 4.993029 TTTGTCCTTCGTTTGGTCAAAT 57.007 36.364 0.00 0.00 37.56 2.32
2149 6803 0.940519 CGTCGCTGTAAACGGGAACA 60.941 55.000 0.00 0.00 35.32 3.18
2155 6809 2.525096 GTCATACTCGTCGCTGTAAACG 59.475 50.000 2.92 0.00 40.17 3.60
2158 6812 3.670311 GAGTCATACTCGTCGCTGTAA 57.330 47.619 2.92 0.00 35.28 2.41
2173 6827 3.326006 AGAGAAGAAATGTGGCAGAGTCA 59.674 43.478 0.00 0.00 0.00 3.41
2301 6957 1.005748 TGACAAGGTGAGCAGCTCG 60.006 57.895 17.81 5.35 38.35 5.03
2314 6970 2.435805 GGTCTATGAGCATCCCTGACAA 59.564 50.000 0.00 0.00 31.28 3.18
2427 7083 0.178975 TTCACGGGAAAGGTGGCAAT 60.179 50.000 0.00 0.00 36.09 3.56
2431 7087 1.745087 CATGATTCACGGGAAAGGTGG 59.255 52.381 3.14 0.00 36.43 4.61
2435 7091 3.947196 TCCATTCATGATTCACGGGAAAG 59.053 43.478 3.14 0.00 36.43 2.62
2438 7094 3.862877 ATCCATTCATGATTCACGGGA 57.137 42.857 0.00 0.00 0.00 5.14
2462 7118 7.064490 GGAATCGACAATATTGCCACAATTTTT 59.936 33.333 15.48 0.00 0.00 1.94
2476 7132 2.503765 TGCTTCCCTGGAATCGACAATA 59.496 45.455 0.00 0.00 33.28 1.90
2551 7207 1.209261 TCCTTATTGGCGCTGATCACA 59.791 47.619 7.64 0.00 35.26 3.58
2643 7299 5.049167 TGCCAGAAATAAGCACAAAACTTG 58.951 37.500 0.00 0.00 0.00 3.16
2647 7303 7.066766 ACAATTTTGCCAGAAATAAGCACAAAA 59.933 29.630 0.00 0.00 39.14 2.44
2651 7307 6.424812 AGAACAATTTTGCCAGAAATAAGCAC 59.575 34.615 0.00 0.00 35.96 4.40
2672 7328 7.279313 TCGCCCTTGTAATATCTTTGTTAGAAC 59.721 37.037 0.00 0.00 36.22 3.01
2695 7565 6.086222 TCATTTCATAGCAAACTTTTCTCGC 58.914 36.000 0.00 0.00 0.00 5.03
2697 7567 7.031975 CCCTCATTTCATAGCAAACTTTTCTC 58.968 38.462 0.00 0.00 0.00 2.87
2698 7568 6.721208 TCCCTCATTTCATAGCAAACTTTTCT 59.279 34.615 0.00 0.00 0.00 2.52
2710 7580 6.263842 GCATGTCATTCTTCCCTCATTTCATA 59.736 38.462 0.00 0.00 0.00 2.15
2851 7722 1.521764 TCATGTGCCCCCAGATGTAT 58.478 50.000 0.00 0.00 41.90 2.29
2908 7779 0.104304 GTGTTCGGAGCGGGATGTAT 59.896 55.000 0.00 0.00 0.00 2.29
2977 7848 3.646162 AGTAGACAATGACAGGACCAACA 59.354 43.478 0.00 0.00 0.00 3.33
3043 7914 2.158957 ACACTCAGAGAACCGAAAGCAA 60.159 45.455 3.79 0.00 0.00 3.91
3069 7940 1.302033 CAAGACCGCTCAGCAAGGT 60.302 57.895 0.00 0.00 41.63 3.50
3176 8047 4.159557 ACCCAACTCTTGCATATTTTGGT 58.840 39.130 13.61 4.18 33.07 3.67
3179 8050 5.914898 GGTACCCAACTCTTGCATATTTT 57.085 39.130 0.00 0.00 0.00 1.82
3227 8099 9.598517 CAAATAATTTACAACCCATGCATTACT 57.401 29.630 0.00 0.00 0.00 2.24
3229 8101 9.376075 CACAAATAATTTACAACCCATGCATTA 57.624 29.630 0.00 0.00 0.00 1.90
3230 8102 7.148272 GCACAAATAATTTACAACCCATGCATT 60.148 33.333 0.00 0.00 0.00 3.56
3231 8103 6.315891 GCACAAATAATTTACAACCCATGCAT 59.684 34.615 0.00 0.00 0.00 3.96
3233 8105 5.874261 AGCACAAATAATTTACAACCCATGC 59.126 36.000 0.00 0.00 0.00 4.06
3234 8106 8.465999 TCTAGCACAAATAATTTACAACCCATG 58.534 33.333 0.00 0.00 0.00 3.66
3251 8123 9.991906 AAAACATAACTTAGTAGTCTAGCACAA 57.008 29.630 0.00 0.00 31.99 3.33
3282 8154 3.707611 ACCAGTCACACTACCACAAGTAA 59.292 43.478 0.00 0.00 0.00 2.24
3345 8223 5.404466 TTGGCCCAAACAAAAGAGATATG 57.596 39.130 0.00 0.00 0.00 1.78
3366 8246 8.877864 TCCTTAATCACACATGGACTTATTTT 57.122 30.769 0.00 0.00 0.00 1.82
3369 8249 6.058183 GCTCCTTAATCACACATGGACTTAT 58.942 40.000 0.00 0.00 0.00 1.73
3374 8254 2.092429 GGGCTCCTTAATCACACATGGA 60.092 50.000 0.00 0.00 0.00 3.41
3381 8261 3.823304 GGATTCATGGGCTCCTTAATCAC 59.177 47.826 0.00 0.00 0.00 3.06
3404 8284 0.669318 TGGACATTCTGTTCGACGGC 60.669 55.000 0.00 0.00 0.00 5.68
3405 8285 1.660607 CATGGACATTCTGTTCGACGG 59.339 52.381 0.00 0.00 0.00 4.79
3409 8289 5.941733 TGAAAATCATGGACATTCTGTTCG 58.058 37.500 0.00 0.00 0.00 3.95
3849 8729 0.898326 ATTTTTGAGGTGGGTCGGCC 60.898 55.000 0.00 0.00 0.00 6.13
3850 8730 0.966179 AATTTTTGAGGTGGGTCGGC 59.034 50.000 0.00 0.00 0.00 5.54
3851 8731 2.890945 AGAAATTTTTGAGGTGGGTCGG 59.109 45.455 0.00 0.00 0.00 4.79
3852 8732 3.305335 CCAGAAATTTTTGAGGTGGGTCG 60.305 47.826 10.16 0.00 0.00 4.79
3853 8733 3.641436 ACCAGAAATTTTTGAGGTGGGTC 59.359 43.478 10.16 0.00 0.00 4.46
3854 8734 3.653164 ACCAGAAATTTTTGAGGTGGGT 58.347 40.909 10.16 0.00 0.00 4.51
3855 8735 4.687901 AACCAGAAATTTTTGAGGTGGG 57.312 40.909 10.16 0.00 0.00 4.61
3856 8736 5.296531 CCAAAACCAGAAATTTTTGAGGTGG 59.703 40.000 10.16 7.90 36.74 4.61
3857 8737 5.296531 CCCAAAACCAGAAATTTTTGAGGTG 59.703 40.000 10.16 3.34 36.74 4.00
3858 8738 5.190726 TCCCAAAACCAGAAATTTTTGAGGT 59.809 36.000 10.16 4.90 36.74 3.85
3859 8739 5.679601 TCCCAAAACCAGAAATTTTTGAGG 58.320 37.500 10.16 4.32 36.74 3.86
3860 8740 6.260714 CCTTCCCAAAACCAGAAATTTTTGAG 59.739 38.462 10.16 3.52 36.74 3.02
3861 8741 6.118852 CCTTCCCAAAACCAGAAATTTTTGA 58.881 36.000 10.16 0.00 36.74 2.69
3862 8742 5.885352 ACCTTCCCAAAACCAGAAATTTTTG 59.115 36.000 1.75 1.75 35.00 2.44
3863 8743 6.073447 ACCTTCCCAAAACCAGAAATTTTT 57.927 33.333 0.00 0.00 0.00 1.94
3864 8744 5.708736 ACCTTCCCAAAACCAGAAATTTT 57.291 34.783 0.00 0.00 0.00 1.82
3865 8745 5.190726 TGAACCTTCCCAAAACCAGAAATTT 59.809 36.000 0.00 0.00 0.00 1.82
3866 8746 4.719273 TGAACCTTCCCAAAACCAGAAATT 59.281 37.500 0.00 0.00 0.00 1.82
3867 8747 4.294347 TGAACCTTCCCAAAACCAGAAAT 58.706 39.130 0.00 0.00 0.00 2.17
3868 8748 3.704061 CTGAACCTTCCCAAAACCAGAAA 59.296 43.478 0.00 0.00 0.00 2.52
3869 8749 3.295973 CTGAACCTTCCCAAAACCAGAA 58.704 45.455 0.00 0.00 0.00 3.02
3870 8750 2.424234 CCTGAACCTTCCCAAAACCAGA 60.424 50.000 0.00 0.00 0.00 3.86
3871 8751 1.963515 CCTGAACCTTCCCAAAACCAG 59.036 52.381 0.00 0.00 0.00 4.00
3872 8752 2.032151 GCCTGAACCTTCCCAAAACCA 61.032 52.381 0.00 0.00 0.00 3.67
3873 8753 0.679505 GCCTGAACCTTCCCAAAACC 59.320 55.000 0.00 0.00 0.00 3.27
3874 8754 0.679505 GGCCTGAACCTTCCCAAAAC 59.320 55.000 0.00 0.00 0.00 2.43
3875 8755 0.825840 CGGCCTGAACCTTCCCAAAA 60.826 55.000 0.00 0.00 0.00 2.44
3876 8756 1.228429 CGGCCTGAACCTTCCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
3877 8757 2.434331 CGGCCTGAACCTTCCCAA 59.566 61.111 0.00 0.00 0.00 4.12
3878 8758 4.344865 GCGGCCTGAACCTTCCCA 62.345 66.667 0.00 0.00 0.00 4.37
3880 8760 3.569200 AAGGCGGCCTGAACCTTCC 62.569 63.158 24.63 0.00 39.65 3.46
3881 8761 2.034221 AAGGCGGCCTGAACCTTC 59.966 61.111 24.63 0.00 39.65 3.46
3882 8762 2.034221 GAAGGCGGCCTGAACCTT 59.966 61.111 24.63 14.04 46.43 3.50
3883 8763 2.069165 AAAGAAGGCGGCCTGAACCT 62.069 55.000 24.63 14.29 32.13 3.50
3884 8764 0.322187 TAAAGAAGGCGGCCTGAACC 60.322 55.000 24.63 12.19 32.13 3.62
3885 8765 1.530323 TTAAAGAAGGCGGCCTGAAC 58.470 50.000 24.63 16.67 32.13 3.18
3886 8766 2.507407 ATTAAAGAAGGCGGCCTGAA 57.493 45.000 24.63 12.12 32.13 3.02
3887 8767 2.507407 AATTAAAGAAGGCGGCCTGA 57.493 45.000 24.63 5.16 32.13 3.86
3888 8768 3.592898 AAAATTAAAGAAGGCGGCCTG 57.407 42.857 24.63 0.00 32.13 4.85
3908 8788 9.863845 AGAGAAAACCGAAAGAAAAACATAAAA 57.136 25.926 0.00 0.00 0.00 1.52
3909 8789 9.296400 CAGAGAAAACCGAAAGAAAAACATAAA 57.704 29.630 0.00 0.00 0.00 1.40
3910 8790 7.434013 GCAGAGAAAACCGAAAGAAAAACATAA 59.566 33.333 0.00 0.00 0.00 1.90
3911 8791 6.915843 GCAGAGAAAACCGAAAGAAAAACATA 59.084 34.615 0.00 0.00 0.00 2.29
3912 8792 5.748630 GCAGAGAAAACCGAAAGAAAAACAT 59.251 36.000 0.00 0.00 0.00 2.71
3913 8793 5.099575 GCAGAGAAAACCGAAAGAAAAACA 58.900 37.500 0.00 0.00 0.00 2.83
3914 8794 5.340803 AGCAGAGAAAACCGAAAGAAAAAC 58.659 37.500 0.00 0.00 0.00 2.43
3915 8795 5.576447 AGCAGAGAAAACCGAAAGAAAAA 57.424 34.783 0.00 0.00 0.00 1.94
3916 8796 5.576447 AAGCAGAGAAAACCGAAAGAAAA 57.424 34.783 0.00 0.00 0.00 2.29
3917 8797 5.576447 AAAGCAGAGAAAACCGAAAGAAA 57.424 34.783 0.00 0.00 0.00 2.52
3918 8798 5.357032 AGAAAAGCAGAGAAAACCGAAAGAA 59.643 36.000 0.00 0.00 0.00 2.52
3919 8799 4.881850 AGAAAAGCAGAGAAAACCGAAAGA 59.118 37.500 0.00 0.00 0.00 2.52
3920 8800 5.175090 AGAAAAGCAGAGAAAACCGAAAG 57.825 39.130 0.00 0.00 0.00 2.62
3921 8801 5.587043 TGTAGAAAAGCAGAGAAAACCGAAA 59.413 36.000 0.00 0.00 0.00 3.46
3922 8802 5.120399 TGTAGAAAAGCAGAGAAAACCGAA 58.880 37.500 0.00 0.00 0.00 4.30
3923 8803 4.699637 TGTAGAAAAGCAGAGAAAACCGA 58.300 39.130 0.00 0.00 0.00 4.69
3924 8804 5.613358 ATGTAGAAAAGCAGAGAAAACCG 57.387 39.130 0.00 0.00 0.00 4.44
3925 8805 8.542953 CAAAAATGTAGAAAAGCAGAGAAAACC 58.457 33.333 0.00 0.00 0.00 3.27
3926 8806 9.087424 ACAAAAATGTAGAAAAGCAGAGAAAAC 57.913 29.630 0.00 0.00 0.00 2.43
3927 8807 9.651913 AACAAAAATGTAGAAAAGCAGAGAAAA 57.348 25.926 0.00 0.00 0.00 2.29
3928 8808 9.301153 GAACAAAAATGTAGAAAAGCAGAGAAA 57.699 29.630 0.00 0.00 0.00 2.52
3929 8809 8.686334 AGAACAAAAATGTAGAAAAGCAGAGAA 58.314 29.630 0.00 0.00 0.00 2.87
3930 8810 8.225603 AGAACAAAAATGTAGAAAAGCAGAGA 57.774 30.769 0.00 0.00 0.00 3.10
3931 8811 8.862550 AAGAACAAAAATGTAGAAAAGCAGAG 57.137 30.769 0.00 0.00 0.00 3.35
3932 8812 9.301153 GAAAGAACAAAAATGTAGAAAAGCAGA 57.699 29.630 0.00 0.00 0.00 4.26
3933 8813 8.542953 GGAAAGAACAAAAATGTAGAAAAGCAG 58.457 33.333 0.00 0.00 0.00 4.24
3934 8814 8.037758 TGGAAAGAACAAAAATGTAGAAAAGCA 58.962 29.630 0.00 0.00 0.00 3.91
3935 8815 8.419076 TGGAAAGAACAAAAATGTAGAAAAGC 57.581 30.769 0.00 0.00 0.00 3.51
3939 8819 9.243637 CGAATTGGAAAGAACAAAAATGTAGAA 57.756 29.630 0.00 0.00 0.00 2.10
3940 8820 8.410141 ACGAATTGGAAAGAACAAAAATGTAGA 58.590 29.630 0.00 0.00 0.00 2.59
3941 8821 8.574196 ACGAATTGGAAAGAACAAAAATGTAG 57.426 30.769 0.00 0.00 0.00 2.74
3942 8822 8.934507 AACGAATTGGAAAGAACAAAAATGTA 57.065 26.923 0.00 0.00 0.00 2.29
3943 8823 7.841915 AACGAATTGGAAAGAACAAAAATGT 57.158 28.000 0.00 0.00 0.00 2.71
3944 8824 9.553418 AAAAACGAATTGGAAAGAACAAAAATG 57.447 25.926 0.00 0.00 0.00 2.32
3945 8825 9.767684 GAAAAACGAATTGGAAAGAACAAAAAT 57.232 25.926 0.00 0.00 0.00 1.82
3946 8826 8.774586 TGAAAAACGAATTGGAAAGAACAAAAA 58.225 25.926 0.00 0.00 0.00 1.94
3947 8827 8.311650 TGAAAAACGAATTGGAAAGAACAAAA 57.688 26.923 0.00 0.00 0.00 2.44
3948 8828 7.891183 TGAAAAACGAATTGGAAAGAACAAA 57.109 28.000 0.00 0.00 0.00 2.83
3949 8829 8.485976 AATGAAAAACGAATTGGAAAGAACAA 57.514 26.923 0.00 0.00 0.00 2.83
3950 8830 8.485976 AAATGAAAAACGAATTGGAAAGAACA 57.514 26.923 0.00 0.00 0.00 3.18
3951 8831 9.420966 GAAAATGAAAAACGAATTGGAAAGAAC 57.579 29.630 0.00 0.00 0.00 3.01
3952 8832 9.377312 AGAAAATGAAAAACGAATTGGAAAGAA 57.623 25.926 0.00 0.00 0.00 2.52
3953 8833 8.940768 AGAAAATGAAAAACGAATTGGAAAGA 57.059 26.923 0.00 0.00 0.00 2.52
3954 8834 9.986833 AAAGAAAATGAAAAACGAATTGGAAAG 57.013 25.926 0.00 0.00 0.00 2.62
3963 8843 9.849166 AGTGAAGTAAAAGAAAATGAAAAACGA 57.151 25.926 0.00 0.00 0.00 3.85
4009 8889 6.033341 CACGGACTTGAAAGATGTTCAAAAA 58.967 36.000 3.37 0.00 37.89 1.94
4010 8890 5.355630 TCACGGACTTGAAAGATGTTCAAAA 59.644 36.000 3.37 0.00 37.89 2.44
4011 8891 4.878971 TCACGGACTTGAAAGATGTTCAAA 59.121 37.500 3.37 0.00 37.89 2.69
4012 8892 4.447290 TCACGGACTTGAAAGATGTTCAA 58.553 39.130 0.00 1.88 36.98 2.69
4013 8893 4.066646 TCACGGACTTGAAAGATGTTCA 57.933 40.909 0.00 0.00 0.00 3.18
4014 8894 4.511826 AGTTCACGGACTTGAAAGATGTTC 59.488 41.667 0.00 0.00 37.24 3.18
4015 8895 4.451900 AGTTCACGGACTTGAAAGATGTT 58.548 39.130 0.00 0.00 37.24 2.71
4016 8896 4.073293 AGTTCACGGACTTGAAAGATGT 57.927 40.909 0.00 0.00 37.24 3.06
4017 8897 5.424121 AAAGTTCACGGACTTGAAAGATG 57.576 39.130 0.00 0.00 39.68 2.90
4018 8898 6.451064 AAAAAGTTCACGGACTTGAAAGAT 57.549 33.333 0.00 0.00 39.68 2.40
4019 8899 5.890424 AAAAAGTTCACGGACTTGAAAGA 57.110 34.783 0.00 0.00 39.68 2.52
4054 8934 9.874205 TTCTCTTTTCAAGATTTCAAAACATGT 57.126 25.926 0.00 0.00 36.82 3.21
4068 8948 9.150653 CGCAAAATTGAATTTTCTCTTTTCAAG 57.849 29.630 12.58 0.36 41.24 3.02
4069 8949 8.877779 TCGCAAAATTGAATTTTCTCTTTTCAA 58.122 25.926 12.58 0.00 40.27 2.69
4070 8950 8.417780 TCGCAAAATTGAATTTTCTCTTTTCA 57.582 26.923 12.58 0.00 40.27 2.69
4071 8951 9.147364 GTTCGCAAAATTGAATTTTCTCTTTTC 57.853 29.630 12.58 0.00 40.27 2.29
4072 8952 8.663911 TGTTCGCAAAATTGAATTTTCTCTTTT 58.336 25.926 12.58 0.00 40.27 2.27
4073 8953 8.195617 TGTTCGCAAAATTGAATTTTCTCTTT 57.804 26.923 12.58 0.00 40.27 2.52
4074 8954 7.769272 TGTTCGCAAAATTGAATTTTCTCTT 57.231 28.000 12.58 0.00 40.27 2.85
4075 8955 7.951530 ATGTTCGCAAAATTGAATTTTCTCT 57.048 28.000 12.58 0.00 40.27 3.10
4076 8956 8.992287 AAATGTTCGCAAAATTGAATTTTCTC 57.008 26.923 12.58 7.33 40.27 2.87


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

AutoCloner maintained by Alex Coulton.