Multiple sequence alignment - TraesCS1A01G223700

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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 TraesCS1A01G223700 chr1A 100.000 9162 0 0 1 9162 394261286 394252125 0.000000e+00 16920.0
1 TraesCS1A01G223700 chr1A 93.600 125 8 0 5756 5880 208884129 208884005 4.370000e-43 187.0
2 TraesCS1A01G223700 chr1A 97.059 34 0 1 4260 4293 77286129 77286097 1.000000e-03 56.5
3 TraesCS1A01G223700 chr1B 96.570 6968 163 30 32 6958 423969077 423962145 0.000000e+00 11474.0
4 TraesCS1A01G223700 chr1B 96.351 1151 36 5 7389 8536 423961540 423960393 0.000000e+00 1888.0
5 TraesCS1A01G223700 chr1B 98.614 433 5 1 6957 7389 423962063 423961632 0.000000e+00 765.0
6 TraesCS1A01G223700 chr1B 91.971 137 9 2 8566 8701 423960394 423960259 3.380000e-44 191.0
7 TraesCS1A01G223700 chr1B 92.188 64 5 0 4267 4330 68382431 68382368 3.520000e-14 91.6
8 TraesCS1A01G223700 chr1B 97.368 38 1 0 8798 8835 423946598 423946561 2.140000e-06 65.8
9 TraesCS1A01G223700 chr1D 96.938 3103 77 11 2782 5879 313857888 313854799 0.000000e+00 5188.0
10 TraesCS1A01G223700 chr1D 96.160 2995 80 25 5878 8864 313854707 313851740 0.000000e+00 4861.0
11 TraesCS1A01G223700 chr1D 95.477 2786 85 16 1 2774 313860692 313857936 0.000000e+00 4409.0
12 TraesCS1A01G223700 chr1D 84.615 273 27 12 8905 9162 313851751 313851479 3.280000e-64 257.0
13 TraesCS1A01G223700 chr1D 93.600 125 8 0 5756 5880 150941768 150941644 4.370000e-43 187.0
14 TraesCS1A01G223700 chr6D 81.081 296 35 13 8856 9133 20128037 20128329 5.570000e-52 217.0
15 TraesCS1A01G223700 chr4D 89.655 174 13 5 8863 9033 85686205 85686034 5.570000e-52 217.0
16 TraesCS1A01G223700 chr4D 93.701 127 6 2 5755 5880 408335239 408335364 1.210000e-43 189.0
17 TraesCS1A01G223700 chr6B 88.636 176 14 5 8863 9034 127391499 127391326 9.320000e-50 209.0
18 TraesCS1A01G223700 chr6B 88.372 172 15 5 8863 9031 256302235 256302404 1.560000e-47 202.0
19 TraesCS1A01G223700 chr6B 84.746 59 9 0 4281 4339 41422734 41422676 9.930000e-05 60.2
20 TraesCS1A01G223700 chr3B 88.571 175 16 4 8863 9034 31702934 31702761 9.320000e-50 209.0
21 TraesCS1A01G223700 chr3B 87.805 123 11 3 4293 4414 194071679 194071798 3.450000e-29 141.0
22 TraesCS1A01G223700 chr5A 88.824 170 8 8 8863 9028 523630377 523630539 2.020000e-46 198.0
23 TraesCS1A01G223700 chr7D 94.400 125 7 0 5756 5880 428731822 428731946 9.390000e-45 193.0
24 TraesCS1A01G223700 chrUn 93.651 126 7 1 5755 5880 253162497 253162621 4.370000e-43 187.0
25 TraesCS1A01G223700 chr7A 86.034 179 20 5 8859 9034 211733769 211733945 4.370000e-43 187.0
26 TraesCS1A01G223700 chr6A 86.364 176 18 6 8863 9034 2792365 2792538 4.370000e-43 187.0
27 TraesCS1A01G223700 chr2D 86.441 177 16 7 8863 9033 56116422 56116596 4.370000e-43 187.0
28 TraesCS1A01G223700 chr2D 93.600 125 8 0 5756 5880 298287806 298287682 4.370000e-43 187.0
29 TraesCS1A01G223700 chr2A 88.966 145 13 3 5736 5880 384888702 384888843 9.450000e-40 176.0
30 TraesCS1A01G223700 chr3A 85.714 154 15 4 4293 4446 151641827 151641973 1.230000e-33 156.0
31 TraesCS1A01G223700 chr3A 87.500 64 8 0 9068 9131 700951369 700951306 3.550000e-09 75.0


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 TraesCS1A01G223700 chr1A 394252125 394261286 9161 True 16920.00 16920 100.0000 1 9162 1 chr1A.!!$R3 9161
1 TraesCS1A01G223700 chr1B 423960259 423969077 8818 True 3579.50 11474 95.8765 32 8701 4 chr1B.!!$R3 8669
2 TraesCS1A01G223700 chr1D 313851479 313860692 9213 True 3678.75 5188 93.2975 1 9162 4 chr1D.!!$R2 9161

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
71 73 0.610232 ATGGCTGAGTTTGCTGGACC 60.610 55.000 0.00 0.00 0.00 4.46 F
483 513 0.610687 AGGAGTAGAGCTGGTTGCAC 59.389 55.000 0.00 0.00 45.94 4.57 F
1798 1841 0.986019 TATGTCCAGGATTGGCCCGT 60.986 55.000 0.00 0.00 44.63 5.28 F
2354 2397 0.105039 CACGAGTATCTCAAGGGGGC 59.895 60.000 0.00 0.00 0.00 5.80 F
2784 2827 0.454600 CATGACCATGCAGCACCTTC 59.545 55.000 0.00 0.00 31.39 3.46 F
3079 3161 1.131126 CACTTGCCACATCGAATGGAC 59.869 52.381 20.34 12.73 39.87 4.02 F
4156 4243 5.050363 GTGTTCTTTCATTCTGCTGACGTTA 60.050 40.000 0.00 0.00 0.00 3.18 F
5580 5667 3.796178 GTGCATTTTGAACACGAACATGT 59.204 39.130 0.00 0.00 0.00 3.21 F
5931 6111 1.332375 GAAGCTTAACACGTTGCACCA 59.668 47.619 0.00 0.00 0.00 4.17 F
6722 6940 2.223803 TTTACATGGTTCGGCCCAAT 57.776 45.000 0.00 0.00 38.20 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 1350 2.237392 AGTTCCTTCCTGTACATGGAGC 59.763 50.000 12.07 11.38 34.76 4.70 R
2336 2379 0.032017 AGCCCCCTTGAGATACTCGT 60.032 55.000 0.00 0.00 32.35 4.18 R
2883 2965 2.754472 GCCCAACAAGACCATTTTGTC 58.246 47.619 0.00 0.00 37.77 3.18 R
4050 4137 4.037089 TGCAGATTGCTAATTGTATGCCTG 59.963 41.667 2.48 0.00 45.31 4.85 R
4365 4452 4.157656 CCAGTTCAGAGTTGGTTTTTGTCA 59.842 41.667 0.00 0.00 0.00 3.58 R
4886 4973 8.992073 GGAAAAATTTCAGCATAAATTGACTGT 58.008 29.630 8.06 0.00 38.68 3.55 R
5658 5745 1.067495 GTCAACCTCTTACTGCTCGCT 60.067 52.381 0.00 0.00 0.00 4.93 R
6722 6940 1.455248 CCGCGAAAATTCCCTGGTAA 58.545 50.000 8.23 0.00 0.00 2.85 R
7600 7993 3.634397 TCCTCCTTAGCAAATGACAGG 57.366 47.619 0.00 0.00 0.00 4.00 R
8465 8862 0.167251 ACCGACGCCGCTTTATTTTG 59.833 50.000 0.00 0.00 0.00 2.44 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
22 23 2.500509 GCAGCTAGCACGAGACTTAT 57.499 50.000 18.83 0.00 44.79 1.73
23 24 2.389998 GCAGCTAGCACGAGACTTATC 58.610 52.381 18.83 0.00 44.79 1.75
42 43 2.311463 TCAATTTTCTGCGGGGTTTGA 58.689 42.857 0.00 0.00 0.00 2.69
57 58 1.880027 GTTTGACAACCGAGAATGGCT 59.120 47.619 0.00 0.00 0.00 4.75
71 73 0.610232 ATGGCTGAGTTTGCTGGACC 60.610 55.000 0.00 0.00 0.00 4.46
145 147 6.537566 CAACTTCTACATTTCGGTCATTGAG 58.462 40.000 0.00 0.00 0.00 3.02
208 210 6.354794 TGTTAGCTAGCTCCAAGAACTTTA 57.645 37.500 23.26 1.20 0.00 1.85
215 217 6.314152 GCTAGCTCCAAGAACTTTAGGTAAAG 59.686 42.308 7.70 7.77 46.12 1.85
264 267 3.760738 TGGTGCATTTCTGTTGGTGATA 58.239 40.909 0.00 0.00 0.00 2.15
278 281 6.061441 TGTTGGTGATACTGATTGTCAAGTT 58.939 36.000 0.00 0.00 0.00 2.66
301 304 4.280174 TGTCTTCGGTTTGTACTAGAGCTT 59.720 41.667 0.00 0.00 0.00 3.74
306 309 4.951715 TCGGTTTGTACTAGAGCTTATCCA 59.048 41.667 0.00 0.00 0.00 3.41
351 354 3.423539 AGCTTTGCTCTGTCCAATACA 57.576 42.857 0.00 0.00 30.62 2.29
352 355 3.960571 AGCTTTGCTCTGTCCAATACAT 58.039 40.909 0.00 0.00 37.50 2.29
353 356 4.338879 AGCTTTGCTCTGTCCAATACATT 58.661 39.130 0.00 0.00 37.50 2.71
354 357 4.157289 AGCTTTGCTCTGTCCAATACATTG 59.843 41.667 0.00 0.00 37.50 2.82
355 358 4.418392 CTTTGCTCTGTCCAATACATTGC 58.582 43.478 0.00 0.00 37.50 3.56
356 359 2.368439 TGCTCTGTCCAATACATTGCC 58.632 47.619 0.00 0.00 37.50 4.52
357 360 2.290832 TGCTCTGTCCAATACATTGCCA 60.291 45.455 0.00 0.00 37.50 4.92
358 361 2.098117 GCTCTGTCCAATACATTGCCAC 59.902 50.000 0.00 0.00 37.50 5.01
359 362 3.614092 CTCTGTCCAATACATTGCCACT 58.386 45.455 0.00 0.00 37.50 4.00
360 363 4.769688 CTCTGTCCAATACATTGCCACTA 58.230 43.478 0.00 0.00 37.50 2.74
361 364 5.371526 CTCTGTCCAATACATTGCCACTAT 58.628 41.667 0.00 0.00 37.50 2.12
362 365 5.125356 TCTGTCCAATACATTGCCACTATG 58.875 41.667 0.00 0.00 37.50 2.23
390 412 5.717178 TGATTAACCGGATTTGGGATTTGAA 59.283 36.000 9.46 0.00 0.00 2.69
483 513 0.610687 AGGAGTAGAGCTGGTTGCAC 59.389 55.000 0.00 0.00 45.94 4.57
488 518 4.116238 GAGTAGAGCTGGTTGCACTTATC 58.884 47.826 0.00 0.00 45.94 1.75
518 549 1.129624 GTTGCATTAATGGACGCGTCA 59.870 47.619 37.26 24.47 0.00 4.35
695 726 2.238942 AGAACAAGATGTCACACGCA 57.761 45.000 0.00 0.00 0.00 5.24
739 770 3.711863 AGTGGTGGCACAATCCATTAAT 58.288 40.909 20.82 0.00 44.16 1.40
890 921 6.825721 ACAGGTATTTCTGTGATTTGAGATCC 59.174 38.462 0.00 0.00 45.27 3.36
984 1016 4.749099 TGAACTTTTTAGCGGCGTAAACTA 59.251 37.500 9.37 0.00 0.00 2.24
1009 1041 4.385199 CCAGAACCAGGTTAATGGCATCTA 60.385 45.833 18.90 0.00 44.80 1.98
1309 1350 4.226427 TCCCCAGAAGAATCAACATCAG 57.774 45.455 0.00 0.00 0.00 2.90
1558 1599 7.970614 GGCCTTTCTTCTACAATACTGATTTTG 59.029 37.037 0.00 0.00 0.00 2.44
1798 1841 0.986019 TATGTCCAGGATTGGCCCGT 60.986 55.000 0.00 0.00 44.63 5.28
1927 1970 4.053295 AGCTTGCAGTGCTAAATTTTGTG 58.947 39.130 17.60 0.00 39.21 3.33
2048 2091 1.816835 CAGTGTACGGGTTGCTCTCTA 59.183 52.381 0.00 0.00 0.00 2.43
2049 2092 2.427453 CAGTGTACGGGTTGCTCTCTAT 59.573 50.000 0.00 0.00 0.00 1.98
2050 2093 2.688958 AGTGTACGGGTTGCTCTCTATC 59.311 50.000 0.00 0.00 0.00 2.08
2051 2094 2.688958 GTGTACGGGTTGCTCTCTATCT 59.311 50.000 0.00 0.00 0.00 1.98
2052 2095 2.950309 TGTACGGGTTGCTCTCTATCTC 59.050 50.000 0.00 0.00 0.00 2.75
2053 2096 2.445682 ACGGGTTGCTCTCTATCTCT 57.554 50.000 0.00 0.00 0.00 3.10
2070 2113 9.743057 CTCTATCTCTATTAGTTTTCCACACTG 57.257 37.037 0.00 0.00 0.00 3.66
2182 2225 6.257411 TGTTTTGTCATTGTTAACTTGCATGG 59.743 34.615 7.22 0.00 0.00 3.66
2336 2379 6.295688 GGTTTACTAGATTGACTCAAGGACCA 60.296 42.308 0.00 0.00 0.00 4.02
2354 2397 0.105039 CACGAGTATCTCAAGGGGGC 59.895 60.000 0.00 0.00 0.00 5.80
2359 2402 2.443394 TATCTCAAGGGGGCTGGCG 61.443 63.158 0.00 0.00 0.00 5.69
2529 2572 6.531948 GCTTCATCTGTTAGTACTTCACGAAT 59.468 38.462 0.00 0.00 0.00 3.34
2639 2682 3.681897 CAGGTGAAAGACTCATTCTTCGG 59.318 47.826 0.00 0.00 44.41 4.30
2652 2695 2.930826 TCTTCGGTCCTTGCTTTTCT 57.069 45.000 0.00 0.00 0.00 2.52
2784 2827 0.454600 CATGACCATGCAGCACCTTC 59.545 55.000 0.00 0.00 31.39 3.46
2909 2991 2.106683 GGTCTTGTTGGGCGATCCG 61.107 63.158 0.00 0.00 38.76 4.18
2968 3050 4.995487 ACTAACAAAAGGGATCGACAACTC 59.005 41.667 0.00 0.00 0.00 3.01
3079 3161 1.131126 CACTTGCCACATCGAATGGAC 59.869 52.381 20.34 12.73 39.87 4.02
4156 4243 5.050363 GTGTTCTTTCATTCTGCTGACGTTA 60.050 40.000 0.00 0.00 0.00 3.18
4363 4450 6.833933 ACTTTACAACCTCAGACTTCCAAAAT 59.166 34.615 0.00 0.00 0.00 1.82
4365 4452 5.053978 ACAACCTCAGACTTCCAAAATCT 57.946 39.130 0.00 0.00 0.00 2.40
4886 4973 5.789574 ATCCCTACCATTTGTTTCTGGTA 57.210 39.130 1.82 1.82 43.91 3.25
5146 5233 8.668510 TTATTCAAGCTTGGATAGATGAAGAC 57.331 34.615 23.46 0.00 35.81 3.01
5490 5577 5.278364 CCGTGGTAGGTATCTTGTCACTATC 60.278 48.000 0.00 0.00 0.00 2.08
5568 5655 6.380560 TGATTATCTTCCCATGTGCATTTTGA 59.619 34.615 0.00 0.00 0.00 2.69
5580 5667 3.796178 GTGCATTTTGAACACGAACATGT 59.204 39.130 0.00 0.00 0.00 3.21
5601 5688 7.396339 ACATGTATGGTCTACTCTCAGTAACAA 59.604 37.037 0.00 0.00 29.00 2.83
5658 5745 9.342308 CAGATAATAACTTTGGAGATTGCCTTA 57.658 33.333 0.00 0.00 0.00 2.69
5659 5746 9.566432 AGATAATAACTTTGGAGATTGCCTTAG 57.434 33.333 0.00 0.00 0.00 2.18
5660 5747 6.456795 AATAACTTTGGAGATTGCCTTAGC 57.543 37.500 0.00 0.00 40.48 3.09
5661 5748 2.359900 ACTTTGGAGATTGCCTTAGCG 58.640 47.619 0.00 0.00 44.31 4.26
5681 5768 3.589988 CGAGCAGTAAGAGGTTGACAAT 58.410 45.455 0.00 0.00 0.00 2.71
5695 5782 7.389053 AGAGGTTGACAATCATTGAAGTTAGAC 59.611 37.037 3.79 0.00 0.00 2.59
5739 5826 1.339291 TCTGCCGAGACTGCTCATATG 59.661 52.381 0.00 0.00 41.36 1.78
5746 5833 3.474600 GAGACTGCTCATATGCCAACAT 58.525 45.455 0.00 0.00 40.96 2.71
5752 5839 2.288030 GCTCATATGCCAACATCTTGCC 60.288 50.000 0.00 0.00 37.74 4.52
5764 5851 1.608590 CATCTTGCCCGTGTTGAAGTT 59.391 47.619 0.00 0.00 0.00 2.66
5798 5885 2.621668 GCCTAGCCCTTTCCATCAGTTT 60.622 50.000 0.00 0.00 0.00 2.66
5931 6111 1.332375 GAAGCTTAACACGTTGCACCA 59.668 47.619 0.00 0.00 0.00 4.17
6094 6276 6.969366 TGTTGGACATGTGAAGAGTATTTTG 58.031 36.000 1.15 0.00 0.00 2.44
6137 6319 8.297470 ACCTGCAGCCCAATAATAATAATATG 57.703 34.615 8.66 0.00 0.00 1.78
6139 6321 9.139734 CCTGCAGCCCAATAATAATAATATGAT 57.860 33.333 8.66 0.00 0.00 2.45
6140 6322 9.961265 CTGCAGCCCAATAATAATAATATGATG 57.039 33.333 0.00 0.00 0.00 3.07
6141 6323 9.697990 TGCAGCCCAATAATAATAATATGATGA 57.302 29.630 0.00 0.00 0.00 2.92
6580 6777 6.133356 TCCTTTTATGGTGTTGAAGGTTCTT 58.867 36.000 0.00 0.00 38.38 2.52
6661 6879 5.874810 TCAGCAGAGGTATTGTACATTGTTC 59.125 40.000 0.00 0.00 0.00 3.18
6722 6940 2.223803 TTTACATGGTTCGGCCCAAT 57.776 45.000 0.00 0.00 38.20 3.16
6827 7045 9.685005 CTAAAAATCTCGAAAATACAACTACGG 57.315 33.333 0.00 0.00 0.00 4.02
6828 7046 7.894376 AAAATCTCGAAAATACAACTACGGA 57.106 32.000 0.00 0.00 0.00 4.69
6829 7047 7.894376 AAATCTCGAAAATACAACTACGGAA 57.106 32.000 0.00 0.00 0.00 4.30
6830 7048 7.521509 AATCTCGAAAATACAACTACGGAAG 57.478 36.000 0.00 0.00 0.00 3.46
6832 7050 7.144722 TCTCGAAAATACAACTACGGAAGTA 57.855 36.000 0.00 0.00 46.88 2.24
6833 7051 7.023575 TCTCGAAAATACAACTACGGAAGTAC 58.976 38.462 0.00 0.00 46.88 2.73
7083 7384 5.606348 TGGTTGCTTTGTTTACCTCAATT 57.394 34.783 0.00 0.00 0.00 2.32
7085 7386 6.045955 TGGTTGCTTTGTTTACCTCAATTTC 58.954 36.000 0.00 0.00 0.00 2.17
7414 7807 7.500720 TTAAGCATCCATACACAGATTCATG 57.499 36.000 0.00 0.00 0.00 3.07
7600 7993 1.073216 CGAGCAGTCACATGTCGGAC 61.073 60.000 7.99 7.99 0.00 4.79
7701 8094 1.650528 ACTGGAGGAACCCTGAAGAG 58.349 55.000 0.00 0.00 38.00 2.85
7733 8126 1.478105 GGGCTTCCCTTGTTAGCAATG 59.522 52.381 0.00 0.00 41.34 2.82
7949 8342 2.289002 GACAACAAGAGCAAGGACAGTG 59.711 50.000 0.00 0.00 0.00 3.66
8026 8419 7.654116 GCTGAAATACCAGACTTATCTAACCTC 59.346 40.741 0.00 0.00 36.29 3.85
8041 8434 1.222936 CCTCGAGCTGCCAGGAATT 59.777 57.895 6.99 0.00 0.00 2.17
8045 8438 0.674581 CGAGCTGCCAGGAATTGACA 60.675 55.000 0.00 0.00 0.00 3.58
8225 8618 5.313712 GGTTCTCTCAAGATAACCACCAAA 58.686 41.667 17.75 0.00 45.34 3.28
8268 8661 1.202952 CCGGATAGTCTCCAGGTAGCT 60.203 57.143 0.00 0.00 45.24 3.32
8360 8757 0.460311 CGCCTCCCTACCTTGTACAG 59.540 60.000 0.00 0.00 0.00 2.74
8369 8766 0.249741 ACCTTGTACAGCACGTCACC 60.250 55.000 0.00 0.00 0.00 4.02
8370 8767 0.033504 CCTTGTACAGCACGTCACCT 59.966 55.000 0.00 0.00 0.00 4.00
8379 8776 0.859232 GCACGTCACCTTGTACTGTG 59.141 55.000 0.00 0.00 0.00 3.66
8465 8862 2.108250 ACATATGGTATCCCCTTGTGCC 59.892 50.000 7.80 0.00 34.11 5.01
8497 8894 2.793232 GGCGTCGGTTATAGCTTTACTG 59.207 50.000 0.00 0.00 0.00 2.74
8503 8900 5.350640 GTCGGTTATAGCTTTACTGCTGTTT 59.649 40.000 0.09 0.00 43.87 2.83
8597 8995 3.243201 GCATTTCCCTTGCTATTTCGGAG 60.243 47.826 0.00 0.00 37.14 4.63
8640 9038 2.945008 TGCTTTCTGTCACCTGTTTCAG 59.055 45.455 0.00 0.00 0.00 3.02
8654 9052 2.092699 TGTTTCAGTGGACCATGTGACA 60.093 45.455 8.63 8.87 0.00 3.58
8675 9074 1.148157 CGTCTCGTTATGCCAGCCAG 61.148 60.000 0.00 0.00 0.00 4.85
8707 9106 7.094377 GGACCAAGTGCTATGAACTTCAAATTA 60.094 37.037 0.00 0.00 35.70 1.40
8710 9109 8.299570 CCAAGTGCTATGAACTTCAAATTAAGT 58.700 33.333 0.00 0.00 41.46 2.24
8787 9186 6.013639 ACCAACTAGTCTTGCTATAACAAGGT 60.014 38.462 14.37 6.50 45.77 3.50
8847 9246 6.691754 TGCCGCTTTGATTATAAAAGATCA 57.308 33.333 6.24 0.00 36.88 2.92
8848 9247 7.094508 TGCCGCTTTGATTATAAAAGATCAA 57.905 32.000 6.24 0.00 39.71 2.57
8851 9250 9.677567 GCCGCTTTGATTATAAAAGATCAAATA 57.322 29.630 6.24 0.00 45.76 1.40
8865 9264 8.658499 AAAGATCAAATACCGAGTAACATACC 57.342 34.615 0.00 0.00 0.00 2.73
8866 9265 6.444633 AGATCAAATACCGAGTAACATACCG 58.555 40.000 0.00 0.00 0.00 4.02
8867 9266 5.833406 TCAAATACCGAGTAACATACCGA 57.167 39.130 0.00 0.00 0.00 4.69
8868 9267 6.206395 TCAAATACCGAGTAACATACCGAA 57.794 37.500 0.00 0.00 0.00 4.30
8869 9268 6.629128 TCAAATACCGAGTAACATACCGAAA 58.371 36.000 0.00 0.00 0.00 3.46
8870 9269 7.095910 TCAAATACCGAGTAACATACCGAAAA 58.904 34.615 0.00 0.00 0.00 2.29
8871 9270 7.601886 TCAAATACCGAGTAACATACCGAAAAA 59.398 33.333 0.00 0.00 0.00 1.94
8872 9271 7.529880 AATACCGAGTAACATACCGAAAAAG 57.470 36.000 0.00 0.00 0.00 2.27
8873 9272 4.248058 ACCGAGTAACATACCGAAAAAGG 58.752 43.478 0.00 0.00 37.30 3.11
8875 9274 4.692155 CCGAGTAACATACCGAAAAAGGTT 59.308 41.667 0.00 0.00 43.00 3.50
8876 9275 5.163923 CCGAGTAACATACCGAAAAAGGTTC 60.164 44.000 0.00 0.00 43.00 3.62
8877 9276 5.163923 CGAGTAACATACCGAAAAAGGTTCC 60.164 44.000 0.00 0.00 43.00 3.62
8878 9277 5.005740 AGTAACATACCGAAAAAGGTTCCC 58.994 41.667 0.00 0.00 43.00 3.97
8879 9278 2.799017 ACATACCGAAAAAGGTTCCCC 58.201 47.619 0.00 0.00 43.00 4.81
8880 9279 2.377531 ACATACCGAAAAAGGTTCCCCT 59.622 45.455 0.00 0.00 43.00 4.79
8881 9280 2.572209 TACCGAAAAAGGTTCCCCTG 57.428 50.000 0.00 0.00 43.00 4.45
8882 9281 0.826256 ACCGAAAAAGGTTCCCCTGC 60.826 55.000 0.00 0.00 43.00 4.85
8883 9282 0.539669 CCGAAAAAGGTTCCCCTGCT 60.540 55.000 0.00 0.00 41.56 4.24
8884 9283 1.328279 CGAAAAAGGTTCCCCTGCTT 58.672 50.000 0.00 0.00 41.56 3.91
8885 9284 1.686587 CGAAAAAGGTTCCCCTGCTTT 59.313 47.619 0.00 0.00 41.56 3.51
8886 9285 2.545742 CGAAAAAGGTTCCCCTGCTTTG 60.546 50.000 0.00 0.00 41.56 2.77
8887 9286 2.174685 AAAAGGTTCCCCTGCTTTGT 57.825 45.000 0.00 0.00 41.56 2.83
8888 9287 3.322191 AAAAGGTTCCCCTGCTTTGTA 57.678 42.857 0.00 0.00 41.56 2.41
8889 9288 3.542969 AAAGGTTCCCCTGCTTTGTAT 57.457 42.857 0.00 0.00 41.56 2.29
8890 9289 4.668138 AAAGGTTCCCCTGCTTTGTATA 57.332 40.909 0.00 0.00 41.56 1.47
8891 9290 3.646736 AGGTTCCCCTGCTTTGTATAC 57.353 47.619 0.00 0.00 40.58 1.47
8892 9291 2.916934 AGGTTCCCCTGCTTTGTATACA 59.083 45.455 0.08 0.08 40.58 2.29
8893 9292 3.332485 AGGTTCCCCTGCTTTGTATACAA 59.668 43.478 14.35 14.35 40.58 2.41
8894 9293 4.083565 GGTTCCCCTGCTTTGTATACAAA 58.916 43.478 25.48 25.48 42.90 2.83
8923 9322 2.355756 ACACCGATCACATAGCAATTGC 59.644 45.455 23.05 23.05 42.49 3.56
8966 9365 6.985188 AGCCCAAAAGAAAAGAAAAAGAAC 57.015 33.333 0.00 0.00 0.00 3.01
8970 9370 8.079203 GCCCAAAAGAAAAGAAAAAGAACAAAA 58.921 29.630 0.00 0.00 0.00 2.44
9020 9420 0.865111 CGACAAAAGCACGGATGACA 59.135 50.000 0.00 0.00 0.00 3.58
9035 9435 4.386951 ACATGCCACCGCTGCGTA 62.387 61.111 21.59 2.11 35.36 4.42
9040 9440 3.118454 CCACCGCTGCGTACCAAG 61.118 66.667 21.59 6.74 0.00 3.61
9041 9441 3.788766 CACCGCTGCGTACCAAGC 61.789 66.667 21.59 4.68 0.00 4.01
9044 9444 2.173382 CGCTGCGTACCAAGCAAC 59.827 61.111 14.93 0.94 44.67 4.17
9045 9445 2.603247 CGCTGCGTACCAAGCAACA 61.603 57.895 14.93 0.00 44.67 3.33
9046 9446 1.082104 GCTGCGTACCAAGCAACAC 60.082 57.895 9.08 0.00 44.67 3.32
9047 9447 1.574428 CTGCGTACCAAGCAACACC 59.426 57.895 0.00 0.00 44.67 4.16
9048 9448 0.884704 CTGCGTACCAAGCAACACCT 60.885 55.000 0.00 0.00 44.67 4.00
9051 9451 1.289109 CGTACCAAGCAACACCTCCG 61.289 60.000 0.00 0.00 0.00 4.63
9052 9452 0.034337 GTACCAAGCAACACCTCCGA 59.966 55.000 0.00 0.00 0.00 4.55
9054 9454 1.966451 CCAAGCAACACCTCCGACC 60.966 63.158 0.00 0.00 0.00 4.79
9056 9456 2.147387 AAGCAACACCTCCGACCCT 61.147 57.895 0.00 0.00 0.00 4.34
9057 9457 2.047179 GCAACACCTCCGACCCTC 60.047 66.667 0.00 0.00 0.00 4.30
9059 9459 1.752198 CAACACCTCCGACCCTCAA 59.248 57.895 0.00 0.00 0.00 3.02
9060 9460 0.107831 CAACACCTCCGACCCTCAAA 59.892 55.000 0.00 0.00 0.00 2.69
9088 9502 2.031120 CCAAGCAACACCTCCAAGAAA 58.969 47.619 0.00 0.00 0.00 2.52
9108 9522 1.692148 GAATGCAACGCCGACGATGA 61.692 55.000 5.42 0.00 44.07 2.92
9111 9525 2.452813 GCAACGCCGACGATGATGT 61.453 57.895 5.42 0.00 44.07 3.06
9153 9567 7.460071 AGGATACCGAGTAACATATACTCACT 58.540 38.462 14.09 3.02 42.94 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.699779 TGATAAGTCTCGTGCTAGCTG 57.300 47.619 17.23 8.75 0.00 4.24
10 11 5.024555 GCAGAAAATTGATAAGTCTCGTGC 58.975 41.667 0.00 0.00 0.00 5.34
22 23 2.035321 GTCAAACCCCGCAGAAAATTGA 59.965 45.455 0.00 0.00 0.00 2.57
23 24 2.223923 TGTCAAACCCCGCAGAAAATTG 60.224 45.455 0.00 0.00 0.00 2.32
42 43 0.687354 ACTCAGCCATTCTCGGTTGT 59.313 50.000 0.00 0.00 38.35 3.32
57 58 2.727123 TCAAAGGTCCAGCAAACTCA 57.273 45.000 0.00 0.00 0.00 3.41
145 147 3.134127 GGCTCCATGCAACGTCCC 61.134 66.667 0.00 0.00 45.15 4.46
208 210 3.387050 AGGACGACTGAACAACTTTACCT 59.613 43.478 0.00 0.00 0.00 3.08
215 217 3.203716 AGGAAAAGGACGACTGAACAAC 58.796 45.455 0.00 0.00 0.00 3.32
216 218 3.553828 AGGAAAAGGACGACTGAACAA 57.446 42.857 0.00 0.00 0.00 2.83
218 220 3.203716 ACAAGGAAAAGGACGACTGAAC 58.796 45.455 0.00 0.00 0.00 3.18
219 221 3.553828 ACAAGGAAAAGGACGACTGAA 57.446 42.857 0.00 0.00 0.00 3.02
220 222 3.893200 TCTACAAGGAAAAGGACGACTGA 59.107 43.478 0.00 0.00 0.00 3.41
221 223 4.252971 TCTACAAGGAAAAGGACGACTG 57.747 45.455 0.00 0.00 0.00 3.51
264 267 3.809832 CCGAAGACAACTTGACAATCAGT 59.190 43.478 0.00 0.00 36.39 3.41
278 281 3.825014 AGCTCTAGTACAAACCGAAGACA 59.175 43.478 0.00 0.00 0.00 3.41
301 304 2.461300 ACTAGCAGCTCCTGTGGATA 57.539 50.000 0.00 0.00 33.43 2.59
306 309 3.221771 CAGAGATACTAGCAGCTCCTGT 58.778 50.000 0.00 0.00 31.13 4.00
355 358 2.813754 CCGGTTAATCATGCCATAGTGG 59.186 50.000 0.00 0.00 41.55 4.00
356 359 3.738982 TCCGGTTAATCATGCCATAGTG 58.261 45.455 0.00 0.00 0.00 2.74
357 360 4.640771 ATCCGGTTAATCATGCCATAGT 57.359 40.909 0.00 0.00 0.00 2.12
358 361 5.335897 CCAAATCCGGTTAATCATGCCATAG 60.336 44.000 0.00 0.00 0.00 2.23
359 362 4.522405 CCAAATCCGGTTAATCATGCCATA 59.478 41.667 0.00 0.00 0.00 2.74
360 363 3.321682 CCAAATCCGGTTAATCATGCCAT 59.678 43.478 0.00 0.00 0.00 4.40
361 364 2.692557 CCAAATCCGGTTAATCATGCCA 59.307 45.455 0.00 0.00 0.00 4.92
362 365 2.035832 CCCAAATCCGGTTAATCATGCC 59.964 50.000 0.00 0.00 0.00 4.40
488 518 7.113404 GCGTCCATTAATGCAACAATACTATTG 59.887 37.037 10.11 7.17 0.00 1.90
511 541 5.350365 ACTTGTCAAATTATATGTGACGCGT 59.650 36.000 13.85 13.85 43.73 6.01
512 542 5.795766 ACTTGTCAAATTATATGTGACGCG 58.204 37.500 3.53 3.53 43.73 6.01
624 655 8.721019 TTCTTTCCGTGTAAAGAAACTTTCTA 57.279 30.769 4.41 0.00 46.96 2.10
739 770 3.075148 TGACCAAAGAAAACACACGACA 58.925 40.909 0.00 0.00 0.00 4.35
890 921 0.323178 ATGCCCAAGAAGCAGTGAGG 60.323 55.000 0.00 0.00 44.90 3.86
984 1016 1.616994 GCCATTAACCTGGTTCTGGCT 60.617 52.381 35.67 13.32 44.19 4.75
1309 1350 2.237392 AGTTCCTTCCTGTACATGGAGC 59.763 50.000 12.07 11.38 34.76 4.70
1558 1599 5.269313 CCATAGAACGTTTCCTAGTACGAC 58.731 45.833 0.46 8.65 40.03 4.34
1798 1841 3.402110 CATCTGCATTTAGATGGCCGTA 58.598 45.455 0.00 0.00 46.55 4.02
1927 1970 2.726832 AGTGACAAGCGGAGAGTTAC 57.273 50.000 0.00 0.00 0.00 2.50
2048 2091 7.907389 TGACAGTGTGGAAAACTAATAGAGAT 58.093 34.615 0.00 0.00 25.60 2.75
2049 2092 7.297936 TGACAGTGTGGAAAACTAATAGAGA 57.702 36.000 0.00 0.00 25.60 3.10
2050 2093 7.962964 TTGACAGTGTGGAAAACTAATAGAG 57.037 36.000 0.00 0.00 25.60 2.43
2051 2094 8.918202 ATTTGACAGTGTGGAAAACTAATAGA 57.082 30.769 0.00 0.00 25.60 1.98
2070 2113 6.366061 CAGTTTAAAGCAAGGCCTAATTTGAC 59.634 38.462 5.16 10.68 0.00 3.18
2182 2225 8.882415 ATTTCCATGCACAAGAAATATCATTC 57.118 30.769 15.23 0.00 38.20 2.67
2323 2366 2.281539 TACTCGTGGTCCTTGAGTCA 57.718 50.000 16.75 0.00 41.78 3.41
2336 2379 0.032017 AGCCCCCTTGAGATACTCGT 60.032 55.000 0.00 0.00 32.35 4.18
2354 2397 1.153449 TTCTATCAACGGGCGCCAG 60.153 57.895 30.85 28.22 0.00 4.85
2359 2402 0.876342 CCGAGCTTCTATCAACGGGC 60.876 60.000 0.00 0.00 37.28 6.13
2435 2478 4.336433 CCAACCATCAATACTAGTTGCCAG 59.664 45.833 0.00 0.00 37.17 4.85
2505 2548 7.755373 TGATTCGTGAAGTACTAACAGATGAAG 59.245 37.037 0.00 0.00 0.00 3.02
2529 2572 1.704641 CTCCCGGTCTACATCCATGA 58.295 55.000 0.00 0.00 0.00 3.07
2639 2682 3.118542 CAGTGCAAAGAAAAGCAAGGAC 58.881 45.455 0.00 0.00 43.20 3.85
2652 2695 6.149973 CCTGAACAATAGAGAATCAGTGCAAA 59.850 38.462 0.00 0.00 37.82 3.68
2755 2798 3.106827 TGCATGGTCATGAGAAGGACTA 58.893 45.455 14.43 0.00 41.20 2.59
2883 2965 2.754472 GCCCAACAAGACCATTTTGTC 58.246 47.619 0.00 0.00 37.77 3.18
2909 2991 5.352569 CACTGTCTTGGTCATTCCTATTCAC 59.647 44.000 0.00 0.00 37.07 3.18
2968 3050 5.682943 TGGACATTTCCTTGTCTAAAACG 57.317 39.130 0.00 0.00 44.39 3.60
3124 3206 6.885735 TTTTTACTTGCAGAAAGAAGCAAC 57.114 33.333 0.00 0.00 44.98 4.17
3154 3238 7.039270 TCTGAAAAATTCAATGCATCAGATGG 58.961 34.615 12.54 0.00 39.58 3.51
4050 4137 4.037089 TGCAGATTGCTAATTGTATGCCTG 59.963 41.667 2.48 0.00 45.31 4.85
4363 4450 5.123820 CAGTTCAGAGTTGGTTTTTGTCAGA 59.876 40.000 0.00 0.00 0.00 3.27
4365 4452 4.157656 CCAGTTCAGAGTTGGTTTTTGTCA 59.842 41.667 0.00 0.00 0.00 3.58
4886 4973 8.992073 GGAAAAATTTCAGCATAAATTGACTGT 58.008 29.630 8.06 0.00 38.68 3.55
5146 5233 4.096231 TCGTTGGCAATATCATCAACCTTG 59.904 41.667 1.92 0.00 36.95 3.61
5568 5655 5.185249 AGAGTAGACCATACATGTTCGTGTT 59.815 40.000 2.30 0.00 33.62 3.32
5580 5667 9.696572 ATAAGTTGTTACTGAGAGTAGACCATA 57.303 33.333 0.00 0.00 34.01 2.74
5601 5688 9.558396 TGCAAAAGAAATGGATTGAAAATAAGT 57.442 25.926 0.00 0.00 0.00 2.24
5643 5730 2.632377 CTCGCTAAGGCAATCTCCAAA 58.368 47.619 0.00 0.00 38.60 3.28
5658 5745 1.067495 GTCAACCTCTTACTGCTCGCT 60.067 52.381 0.00 0.00 0.00 4.93
5659 5746 1.336887 TGTCAACCTCTTACTGCTCGC 60.337 52.381 0.00 0.00 0.00 5.03
5660 5747 2.724977 TGTCAACCTCTTACTGCTCG 57.275 50.000 0.00 0.00 0.00 5.03
5661 5748 4.569943 TGATTGTCAACCTCTTACTGCTC 58.430 43.478 0.00 0.00 0.00 4.26
5681 5768 3.953712 TGAGCGGTCTAACTTCAATGA 57.046 42.857 16.64 0.00 0.00 2.57
5695 5782 1.926511 GCAAACCCACTCATGAGCGG 61.927 60.000 22.83 21.82 0.00 5.52
5746 5833 1.757682 AAACTTCAACACGGGCAAGA 58.242 45.000 0.00 0.00 0.00 3.02
5752 5839 6.677781 ATCCACATATAAACTTCAACACGG 57.322 37.500 0.00 0.00 0.00 4.94
5764 5851 3.916349 AGGGCTAGGCAATCCACATATAA 59.084 43.478 19.14 0.00 33.74 0.98
5798 5885 1.205893 GCCAACACAACCAAAAGTCCA 59.794 47.619 0.00 0.00 0.00 4.02
6094 6276 4.049186 CAGGTATATTCGGTGTGTAGCAC 58.951 47.826 0.00 0.00 46.97 4.40
6136 6318 7.913789 TCCAATACTCATCATCATCATCATCA 58.086 34.615 0.00 0.00 0.00 3.07
6137 6319 7.496263 CCTCCAATACTCATCATCATCATCATC 59.504 40.741 0.00 0.00 0.00 2.92
6139 6321 6.708285 CCTCCAATACTCATCATCATCATCA 58.292 40.000 0.00 0.00 0.00 3.07
6140 6322 5.585445 GCCTCCAATACTCATCATCATCATC 59.415 44.000 0.00 0.00 0.00 2.92
6141 6323 5.013808 TGCCTCCAATACTCATCATCATCAT 59.986 40.000 0.00 0.00 0.00 2.45
6142 6324 4.348754 TGCCTCCAATACTCATCATCATCA 59.651 41.667 0.00 0.00 0.00 3.07
6143 6325 4.903054 TGCCTCCAATACTCATCATCATC 58.097 43.478 0.00 0.00 0.00 2.92
6144 6326 4.987963 TGCCTCCAATACTCATCATCAT 57.012 40.909 0.00 0.00 0.00 2.45
6145 6327 4.776435 TTGCCTCCAATACTCATCATCA 57.224 40.909 0.00 0.00 0.00 3.07
6146 6328 6.939163 ACTATTTGCCTCCAATACTCATCATC 59.061 38.462 0.00 0.00 0.00 2.92
6580 6777 5.717078 TCGCTAGTAACTTTTCCTTCTCA 57.283 39.130 0.00 0.00 0.00 3.27
6722 6940 1.455248 CCGCGAAAATTCCCTGGTAA 58.545 50.000 8.23 0.00 0.00 2.85
6826 7044 6.946583 ACCCAAAGAAATTAAGAGGTACTTCC 59.053 38.462 0.61 0.00 41.55 3.46
6827 7045 7.664318 TGACCCAAAGAAATTAAGAGGTACTTC 59.336 37.037 0.00 0.00 41.55 3.01
6828 7046 7.523415 TGACCCAAAGAAATTAAGAGGTACTT 58.477 34.615 0.00 0.00 41.55 2.24
6830 7048 7.939784 ATGACCCAAAGAAATTAAGAGGTAC 57.060 36.000 0.00 0.00 0.00 3.34
6831 7049 7.396055 CCAATGACCCAAAGAAATTAAGAGGTA 59.604 37.037 0.00 0.00 0.00 3.08
6832 7050 6.211384 CCAATGACCCAAAGAAATTAAGAGGT 59.789 38.462 0.00 0.00 0.00 3.85
6833 7051 6.633856 CCAATGACCCAAAGAAATTAAGAGG 58.366 40.000 0.00 0.00 0.00 3.69
7083 7384 8.838365 CAATGAATTTGGGATTCACAAAAAGAA 58.162 29.630 17.47 5.27 40.74 2.52
7085 7386 8.071368 CACAATGAATTTGGGATTCACAAAAAG 58.929 33.333 17.47 7.19 41.60 2.27
7170 7471 7.042523 ACACTTTTGCTGCTTGAATTATTTGAC 60.043 33.333 0.00 0.00 0.00 3.18
7389 7690 7.940688 TCATGAATCTGTGTATGGATGCTTAAT 59.059 33.333 0.00 0.00 0.00 1.40
7397 7790 6.298441 TGTCTTCATGAATCTGTGTATGGA 57.702 37.500 8.96 0.00 0.00 3.41
7432 7825 4.092968 CACGAATGCTTACTACCAAGAACC 59.907 45.833 0.00 0.00 0.00 3.62
7434 7827 4.890088 ACACGAATGCTTACTACCAAGAA 58.110 39.130 0.00 0.00 0.00 2.52
7600 7993 3.634397 TCCTCCTTAGCAAATGACAGG 57.366 47.619 0.00 0.00 0.00 4.00
7733 8126 5.059833 TCTCTCACTTCTCTTTCCTTTTGC 58.940 41.667 0.00 0.00 0.00 3.68
8026 8419 0.674581 TGTCAATTCCTGGCAGCTCG 60.675 55.000 9.56 0.00 33.67 5.03
8041 8434 2.976840 GCCGCCAAAATCGCTGTCA 61.977 57.895 0.00 0.00 0.00 3.58
8045 8438 3.443045 CCAGCCGCCAAAATCGCT 61.443 61.111 0.00 0.00 0.00 4.93
8225 8618 0.178973 GGTGTTAAACCTGCTGGGGT 60.179 55.000 14.82 2.65 46.55 4.95
8360 8757 0.859232 CACAGTACAAGGTGACGTGC 59.141 55.000 0.00 0.00 44.26 5.34
8369 8766 8.124823 CACCAAAATAGATATGCACAGTACAAG 58.875 37.037 0.00 0.00 0.00 3.16
8370 8767 7.415095 GCACCAAAATAGATATGCACAGTACAA 60.415 37.037 0.00 0.00 33.27 2.41
8379 8776 6.618287 TGTACAGCACCAAAATAGATATGC 57.382 37.500 0.00 0.00 0.00 3.14
8465 8862 0.167251 ACCGACGCCGCTTTATTTTG 59.833 50.000 0.00 0.00 0.00 2.44
8552 8950 2.125106 CCAGGTAGCAACGGAGGC 60.125 66.667 0.00 0.00 0.00 4.70
8597 8995 1.146358 GGCCGAGATACACAAGACGC 61.146 60.000 0.00 0.00 0.00 5.19
8640 9038 0.949105 GACGGTGTCACATGGTCCAC 60.949 60.000 5.12 0.00 32.09 4.02
8654 9052 1.153628 GCTGGCATAACGAGACGGT 60.154 57.895 0.00 0.00 0.00 4.83
8675 9074 0.676782 ATAGCACTTGGTCCCGCAAC 60.677 55.000 0.00 0.00 0.00 4.17
8707 9106 3.970640 AGAGGGAGTGTCTCTTTCAACTT 59.029 43.478 0.00 0.00 38.32 2.66
8710 9109 3.309296 ACAGAGGGAGTGTCTCTTTCAA 58.691 45.455 0.00 0.00 39.36 2.69
8787 9186 6.968263 TTTGGCGATAATAAAATGGATGGA 57.032 33.333 0.00 0.00 0.00 3.41
8847 9246 7.064966 CCTTTTTCGGTATGTTACTCGGTATTT 59.935 37.037 0.00 0.00 0.00 1.40
8848 9247 6.536224 CCTTTTTCGGTATGTTACTCGGTATT 59.464 38.462 0.00 0.00 0.00 1.89
8851 9250 4.248058 CCTTTTTCGGTATGTTACTCGGT 58.752 43.478 0.00 0.00 0.00 4.69
8852 9251 4.248058 ACCTTTTTCGGTATGTTACTCGG 58.752 43.478 0.00 0.00 34.94 4.63
8853 9252 5.163923 GGAACCTTTTTCGGTATGTTACTCG 60.164 44.000 0.00 0.00 35.89 4.18
8854 9253 6.174451 GGAACCTTTTTCGGTATGTTACTC 57.826 41.667 0.00 0.00 35.89 2.59
8867 9266 8.567417 TTGTATACAAAGCAGGGGAACCTTTTT 61.567 37.037 15.92 0.00 46.43 1.94
8868 9267 7.147900 TTGTATACAAAGCAGGGGAACCTTTT 61.148 38.462 15.92 0.00 46.43 2.27
8869 9268 5.694405 TTGTATACAAAGCAGGGGAACCTTT 60.694 40.000 15.92 0.00 46.43 3.11
8870 9269 4.202631 TTGTATACAAAGCAGGGGAACCTT 60.203 41.667 15.92 0.00 46.43 3.50
8872 9271 3.692690 TTGTATACAAAGCAGGGGAACC 58.307 45.455 15.92 0.00 41.58 3.62
8883 9282 5.593010 GGTGTTGGTTGCTTTGTATACAAA 58.407 37.500 25.48 25.48 42.90 2.83
8884 9283 4.261238 CGGTGTTGGTTGCTTTGTATACAA 60.261 41.667 14.35 14.35 0.00 2.41
8885 9284 3.251245 CGGTGTTGGTTGCTTTGTATACA 59.749 43.478 0.08 0.08 0.00 2.29
8886 9285 3.499157 TCGGTGTTGGTTGCTTTGTATAC 59.501 43.478 0.00 0.00 0.00 1.47
8887 9286 3.741249 TCGGTGTTGGTTGCTTTGTATA 58.259 40.909 0.00 0.00 0.00 1.47
8888 9287 2.577700 TCGGTGTTGGTTGCTTTGTAT 58.422 42.857 0.00 0.00 0.00 2.29
8889 9288 2.039818 TCGGTGTTGGTTGCTTTGTA 57.960 45.000 0.00 0.00 0.00 2.41
8890 9289 1.336755 GATCGGTGTTGGTTGCTTTGT 59.663 47.619 0.00 0.00 0.00 2.83
8891 9290 1.336440 TGATCGGTGTTGGTTGCTTTG 59.664 47.619 0.00 0.00 0.00 2.77
8892 9291 1.336755 GTGATCGGTGTTGGTTGCTTT 59.663 47.619 0.00 0.00 0.00 3.51
8893 9292 0.951558 GTGATCGGTGTTGGTTGCTT 59.048 50.000 0.00 0.00 0.00 3.91
8894 9293 0.179032 TGTGATCGGTGTTGGTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
8895 9294 0.881118 ATGTGATCGGTGTTGGTTGC 59.119 50.000 0.00 0.00 0.00 4.17
8896 9295 2.095853 GCTATGTGATCGGTGTTGGTTG 59.904 50.000 0.00 0.00 0.00 3.77
8897 9296 2.290008 TGCTATGTGATCGGTGTTGGTT 60.290 45.455 0.00 0.00 0.00 3.67
8898 9297 1.277842 TGCTATGTGATCGGTGTTGGT 59.722 47.619 0.00 0.00 0.00 3.67
8899 9298 2.022764 TGCTATGTGATCGGTGTTGG 57.977 50.000 0.00 0.00 0.00 3.77
8900 9299 4.345288 CAATTGCTATGTGATCGGTGTTG 58.655 43.478 0.00 0.00 0.00 3.33
8901 9300 3.181497 GCAATTGCTATGTGATCGGTGTT 60.181 43.478 23.21 0.00 38.21 3.32
8902 9301 2.355756 GCAATTGCTATGTGATCGGTGT 59.644 45.455 23.21 0.00 38.21 4.16
8903 9302 2.990941 GCAATTGCTATGTGATCGGTG 58.009 47.619 23.21 0.00 38.21 4.94
8923 9322 3.502920 CTTGTTGTGCTACTCGTCCTAG 58.497 50.000 0.00 0.00 0.00 3.02
8925 9324 1.605712 GCTTGTTGTGCTACTCGTCCT 60.606 52.381 0.00 0.00 0.00 3.85
8926 9325 0.790814 GCTTGTTGTGCTACTCGTCC 59.209 55.000 0.00 0.00 0.00 4.79
8970 9370 6.038492 CCATTGTTGGCATTTGTTTCTTCTTT 59.962 34.615 0.00 0.00 35.85 2.52
8995 9395 1.439365 CGTGCTTTTGTCGAGCTGC 60.439 57.895 0.00 0.00 40.75 5.25
9001 9401 0.865111 TGTCATCCGTGCTTTTGTCG 59.135 50.000 0.00 0.00 0.00 4.35
9034 9434 0.034337 GTCGGAGGTGTTGCTTGGTA 59.966 55.000 0.00 0.00 0.00 3.25
9035 9435 1.227853 GTCGGAGGTGTTGCTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
9037 9437 1.966451 GGGTCGGAGGTGTTGCTTG 60.966 63.158 0.00 0.00 0.00 4.01
9038 9438 2.113243 GAGGGTCGGAGGTGTTGCTT 62.113 60.000 0.00 0.00 0.00 3.91
9039 9439 2.526873 AGGGTCGGAGGTGTTGCT 60.527 61.111 0.00 0.00 0.00 3.91
9040 9440 2.047179 GAGGGTCGGAGGTGTTGC 60.047 66.667 0.00 0.00 0.00 4.17
9041 9441 0.107831 TTTGAGGGTCGGAGGTGTTG 59.892 55.000 0.00 0.00 0.00 3.33
9044 9444 3.717842 TTTTTGAGGGTCGGAGGTG 57.282 52.632 0.00 0.00 0.00 4.00
9063 9463 2.183679 TGGAGGTGTTGCTTGGTTTTT 58.816 42.857 0.00 0.00 0.00 1.94
9064 9464 1.859302 TGGAGGTGTTGCTTGGTTTT 58.141 45.000 0.00 0.00 0.00 2.43
9065 9465 1.756538 CTTGGAGGTGTTGCTTGGTTT 59.243 47.619 0.00 0.00 0.00 3.27
9066 9466 1.064017 TCTTGGAGGTGTTGCTTGGTT 60.064 47.619 0.00 0.00 0.00 3.67
9075 9489 3.228188 TGCATTCTTTCTTGGAGGTGT 57.772 42.857 0.00 0.00 0.00 4.16
9088 9502 1.447838 ATCGTCGGCGTTGCATTCT 60.448 52.632 10.18 0.00 39.49 2.40
9108 9522 4.379174 GACACGTCCAGGCAACAT 57.621 55.556 0.00 0.00 41.41 2.71


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

AutoCloner maintained by Alex Coulton.