Multiple sequence alignment - TraesCS7D01G098700

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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 TraesCS7D01G098700 chr7D 100.000 3676 0 0 1396 5071 59094712 59098387 0.000000e+00 6789
1 TraesCS7D01G098700 chr7D 100.000 1044 0 0 1 1044 59093317 59094360 0.000000e+00 1929
2 TraesCS7D01G098700 chr4A 91.917 2796 131 39 1396 4140 676531653 676534404 0.000000e+00 3823
3 TraesCS7D01G098700 chr4A 88.025 977 58 30 17 969 676530361 676531302 0.000000e+00 1101
4 TraesCS7D01G098700 chr4A 87.906 769 71 16 4182 4941 676534406 676535161 0.000000e+00 885
5 TraesCS7D01G098700 chr7A 91.226 1835 83 23 3263 5071 63704824 63703042 0.000000e+00 2425
6 TraesCS7D01G098700 chr7A 89.942 1720 123 23 1396 3096 63707583 63705895 0.000000e+00 2172
7 TraesCS7D01G098700 chr7A 85.975 1041 87 38 22 1044 63708657 63707658 0.000000e+00 1059
8 TraesCS7D01G098700 chr7A 95.082 122 5 1 3135 3256 63705670 63705550 1.860000e-44 191


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 TraesCS7D01G098700 chr7D 59093317 59098387 5070 False 4359.000000 6789 100.000000 1 5071 2 chr7D.!!$F1 5070
1 TraesCS7D01G098700 chr4A 676530361 676535161 4800 False 1936.333333 3823 89.282667 17 4941 3 chr4A.!!$F1 4924
2 TraesCS7D01G098700 chr7A 63703042 63708657 5615 True 1461.750000 2425 90.556250 22 5071 4 chr7A.!!$R1 5049

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
972 1009 0.390866 CGACTCCACTGCATCTGCTT 60.391 55.0 3.53 0.0 42.66 3.91 F
1598 1844 0.181350 CTCCTCCCAATACCTGTGCC 59.819 60.0 0.00 0.0 0.00 5.01 F
1725 1975 0.313987 TGTCTCACCGCTACAGTGTG 59.686 55.0 5.88 0.0 36.58 3.82 F
2994 3263 0.685785 TGGTGGAACTGGCAAAGCAA 60.686 50.0 0.00 0.0 36.74 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2139 0.108898 CCTTGTCTGTGAGAGCTCCG 60.109 60.000 10.93 0.00 0.00 4.63 R
2460 2713 1.202698 ACTGAACTCTTGTCCCACTGC 60.203 52.381 0.00 0.00 0.00 4.40 R
3693 4868 1.154205 CGATCTTGGACGATGGCCAC 61.154 60.000 8.16 0.47 34.56 5.01 R
4776 5971 0.173481 TTCGGATCAAGGCTCAGTCG 59.827 55.000 0.00 0.00 0.00 4.18 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
47 48 0.611340 TAGCATTGCACATGGTGGCA 60.611 50.000 11.91 0.73 38.46 4.92
72 74 8.084073 CAGTGAAGCAGATTTAAATCTTTTGGA 58.916 33.333 24.94 9.27 42.96 3.53
73 75 8.302438 AGTGAAGCAGATTTAAATCTTTTGGAG 58.698 33.333 24.94 15.01 42.96 3.86
74 76 8.299570 GTGAAGCAGATTTAAATCTTTTGGAGA 58.700 33.333 24.94 6.51 42.96 3.71
75 77 8.299570 TGAAGCAGATTTAAATCTTTTGGAGAC 58.700 33.333 24.94 11.98 42.96 3.36
76 78 8.414629 AAGCAGATTTAAATCTTTTGGAGACT 57.585 30.769 24.94 12.48 42.96 3.24
77 79 8.049655 AGCAGATTTAAATCTTTTGGAGACTC 57.950 34.615 24.94 4.93 42.96 3.36
78 80 7.121907 AGCAGATTTAAATCTTTTGGAGACTCC 59.878 37.037 24.94 15.13 42.96 3.85
79 81 7.094205 GCAGATTTAAATCTTTTGGAGACTCCA 60.094 37.037 24.94 20.74 43.13 3.86
101 103 2.251600 CTGGAGACAAACCAGCAGC 58.748 57.895 0.00 0.00 46.30 5.25
119 121 2.943690 CAGCAAGCAGTTCATAGCTCAT 59.056 45.455 0.00 0.00 40.90 2.90
144 155 2.816087 GAGCAATTTCCTGTCAGCAGAA 59.184 45.455 0.00 0.00 45.28 3.02
299 310 0.818445 TCTCGATCTCCGGCACCTAC 60.818 60.000 0.00 0.00 39.14 3.18
300 311 2.119147 CTCGATCTCCGGCACCTACG 62.119 65.000 0.00 0.00 39.14 3.51
301 312 2.027751 GATCTCCGGCACCTACGC 59.972 66.667 0.00 0.00 0.00 4.42
318 329 3.591835 CCCCCGCACACACACAAC 61.592 66.667 0.00 0.00 0.00 3.32
319 330 2.515991 CCCCGCACACACACAACT 60.516 61.111 0.00 0.00 0.00 3.16
320 331 2.542907 CCCCGCACACACACAACTC 61.543 63.158 0.00 0.00 0.00 3.01
321 332 1.523711 CCCGCACACACACAACTCT 60.524 57.895 0.00 0.00 0.00 3.24
322 333 1.498865 CCCGCACACACACAACTCTC 61.499 60.000 0.00 0.00 0.00 3.20
323 334 1.559814 CGCACACACACAACTCTCG 59.440 57.895 0.00 0.00 0.00 4.04
324 335 0.869880 CGCACACACACAACTCTCGA 60.870 55.000 0.00 0.00 0.00 4.04
325 336 0.577269 GCACACACACAACTCTCGAC 59.423 55.000 0.00 0.00 0.00 4.20
326 337 1.802880 GCACACACACAACTCTCGACT 60.803 52.381 0.00 0.00 0.00 4.18
327 338 2.120232 CACACACACAACTCTCGACTC 58.880 52.381 0.00 0.00 0.00 3.36
328 339 1.749063 ACACACACAACTCTCGACTCA 59.251 47.619 0.00 0.00 0.00 3.41
345 367 1.819208 CATCAGAATTCGCCCGCCA 60.819 57.895 0.00 0.00 0.00 5.69
358 380 3.726517 CGCCAAACCAGACGCCAG 61.727 66.667 0.00 0.00 0.00 4.85
359 381 4.043200 GCCAAACCAGACGCCAGC 62.043 66.667 0.00 0.00 0.00 4.85
360 382 2.594303 CCAAACCAGACGCCAGCA 60.594 61.111 0.00 0.00 0.00 4.41
361 383 1.973281 CCAAACCAGACGCCAGCAT 60.973 57.895 0.00 0.00 0.00 3.79
362 384 1.503542 CAAACCAGACGCCAGCATC 59.496 57.895 0.00 0.00 0.00 3.91
363 385 1.073025 AAACCAGACGCCAGCATCA 59.927 52.632 0.00 0.00 0.00 3.07
364 386 0.957395 AAACCAGACGCCAGCATCAG 60.957 55.000 0.00 0.00 0.00 2.90
365 387 3.200593 CCAGACGCCAGCATCAGC 61.201 66.667 0.00 0.00 42.56 4.26
366 388 2.435410 CAGACGCCAGCATCAGCA 60.435 61.111 0.00 0.00 45.49 4.41
367 389 2.125229 AGACGCCAGCATCAGCAG 60.125 61.111 0.00 0.00 45.49 4.24
368 390 3.873883 GACGCCAGCATCAGCAGC 61.874 66.667 0.00 0.00 45.49 5.25
369 391 4.710167 ACGCCAGCATCAGCAGCA 62.710 61.111 0.00 0.00 45.49 4.41
370 392 3.209812 CGCCAGCATCAGCAGCAT 61.210 61.111 0.00 0.00 45.49 3.79
371 393 1.890510 CGCCAGCATCAGCAGCATA 60.891 57.895 0.00 0.00 45.49 3.14
379 401 3.878103 AGCATCAGCAGCATAAGAAGAAG 59.122 43.478 0.00 0.00 45.49 2.85
385 407 2.477525 GCAGCATAAGAAGAAGCACAGC 60.478 50.000 0.00 0.00 0.00 4.40
403 425 3.330720 ACCTTCTTGGAGGGCGGG 61.331 66.667 0.00 0.00 41.31 6.13
629 654 1.610522 CCATCTCCGATGGAAATTGCC 59.389 52.381 16.03 0.00 41.64 4.52
633 664 0.623194 TCCGATGGAAATTGCCTCCA 59.377 50.000 3.49 1.50 46.86 3.86
642 673 2.222227 AATTGCCTCCACTTCTTCCC 57.778 50.000 0.00 0.00 0.00 3.97
738 773 3.234730 GATCGGAGGGCACGGGAT 61.235 66.667 0.00 0.00 0.00 3.85
782 817 2.276740 CAATGGGAGGGAGGCACC 59.723 66.667 0.00 0.00 38.08 5.01
842 877 2.791927 CGTGACTCGGATGCTCGA 59.208 61.111 0.00 0.00 37.60 4.04
934 971 4.245054 GCTCAGTGCGTTCTTCGA 57.755 55.556 0.00 0.00 42.86 3.71
935 972 2.517598 GCTCAGTGCGTTCTTCGAA 58.482 52.632 0.00 0.00 42.86 3.71
936 973 0.436531 GCTCAGTGCGTTCTTCGAAG 59.563 55.000 19.35 19.35 42.86 3.79
937 974 1.063806 CTCAGTGCGTTCTTCGAAGG 58.936 55.000 24.37 10.20 42.86 3.46
938 975 0.671796 TCAGTGCGTTCTTCGAAGGA 59.328 50.000 24.37 14.37 42.86 3.36
939 976 1.067974 TCAGTGCGTTCTTCGAAGGAA 59.932 47.619 24.37 14.27 42.86 3.36
969 1006 0.738762 CACCGACTCCACTGCATCTG 60.739 60.000 0.00 0.00 0.00 2.90
972 1009 0.390866 CGACTCCACTGCATCTGCTT 60.391 55.000 3.53 0.00 42.66 3.91
1572 1818 3.851845 TACGCACGCTCCACACCAC 62.852 63.158 0.00 0.00 0.00 4.16
1590 1836 2.039418 CACACGGATCTCCTCCCAATA 58.961 52.381 0.00 0.00 41.49 1.90
1598 1844 0.181350 CTCCTCCCAATACCTGTGCC 59.819 60.000 0.00 0.00 0.00 5.01
1611 1857 2.038952 ACCTGTGCCGCACATGATATAT 59.961 45.455 28.73 8.90 43.71 0.86
1612 1858 3.260632 ACCTGTGCCGCACATGATATATA 59.739 43.478 28.73 5.20 43.71 0.86
1613 1859 3.618594 CCTGTGCCGCACATGATATATAC 59.381 47.826 25.89 0.00 43.71 1.47
1614 1860 4.498241 CTGTGCCGCACATGATATATACT 58.502 43.478 25.89 0.00 43.71 2.12
1615 1861 4.494484 TGTGCCGCACATGATATATACTC 58.506 43.478 22.32 0.00 39.62 2.59
1637 1883 4.103153 TCCCTAATTGCTGCTGCTTACTAT 59.897 41.667 17.00 0.38 40.48 2.12
1646 1892 4.041740 TGCTGCTTACTATACAACGGAG 57.958 45.455 0.00 0.00 0.00 4.63
1687 1937 1.778017 TAGCTGCAAACCTGGCCTCA 61.778 55.000 3.32 0.00 0.00 3.86
1714 1964 2.163010 CAGTTGCCATGAATGTCTCACC 59.837 50.000 0.00 0.00 36.69 4.02
1721 1971 2.654749 TGAATGTCTCACCGCTACAG 57.345 50.000 0.00 0.00 0.00 2.74
1722 1972 1.893137 TGAATGTCTCACCGCTACAGT 59.107 47.619 0.00 0.00 0.00 3.55
1723 1973 2.263077 GAATGTCTCACCGCTACAGTG 58.737 52.381 0.00 0.00 36.54 3.66
1725 1975 0.313987 TGTCTCACCGCTACAGTGTG 59.686 55.000 5.88 0.00 36.58 3.82
1745 1995 9.528018 CAGTGTGTAAACCAATTTTAACTGATT 57.472 29.630 0.00 0.00 37.82 2.57
1770 2020 9.541143 TTATTGACATTCAGTTTTCCTTTTTCC 57.459 29.630 0.00 0.00 0.00 3.13
1774 2024 5.425217 ACATTCAGTTTTCCTTTTTCCTGGT 59.575 36.000 0.00 0.00 0.00 4.00
1868 2118 4.273148 TCTCTTCTTTGTTCCCAGCTAC 57.727 45.455 0.00 0.00 0.00 3.58
1889 2139 2.584791 GTCAAATGTGTTCGCATGACC 58.415 47.619 0.00 0.00 0.00 4.02
1894 2144 2.434185 TGTTCGCATGACCGGAGC 60.434 61.111 9.46 5.59 0.00 4.70
1901 2151 1.893062 CATGACCGGAGCTCTCACA 59.107 57.895 9.46 9.45 0.00 3.58
1971 2221 5.765182 CCCAGTAGAACTTGTTGATCACTTT 59.235 40.000 0.00 0.00 0.00 2.66
1995 2246 6.920569 ACTCAGGTGTGTTTAAGTTTACTG 57.079 37.500 0.00 0.00 0.00 2.74
2047 2298 1.118965 TCGTTCCCTGCAGGTTCTGA 61.119 55.000 30.63 17.96 36.75 3.27
2056 2307 1.973515 TGCAGGTTCTGAGTCAGATGT 59.026 47.619 23.23 8.45 40.39 3.06
2155 2406 6.127647 GCACCCAAAATCAAATCAGACAGATA 60.128 38.462 0.00 0.00 35.39 1.98
2158 2409 7.671398 ACCCAAAATCAAATCAGACAGATAGTT 59.329 33.333 0.00 0.00 35.39 2.24
2189 2440 4.703093 TCTTTTGGTTGAAGAAACGTTCCT 59.297 37.500 0.00 0.00 39.91 3.36
2192 2443 4.625972 TGGTTGAAGAAACGTTCCTTTC 57.374 40.909 0.00 6.81 39.91 2.62
2197 2448 6.017357 GGTTGAAGAAACGTTCCTTTCTACAT 60.017 38.462 22.17 4.24 39.18 2.29
2227 2478 5.894807 AGAACATTGTTCTTTTGTGGAGTG 58.105 37.500 23.27 0.00 0.00 3.51
2230 2481 3.502191 TTGTTCTTTTGTGGAGTGTGC 57.498 42.857 0.00 0.00 0.00 4.57
2341 2592 5.018809 TGCTGCTCTTCATATTTTCCCTTT 58.981 37.500 0.00 0.00 0.00 3.11
2342 2593 5.126061 TGCTGCTCTTCATATTTTCCCTTTC 59.874 40.000 0.00 0.00 0.00 2.62
2351 2604 9.798994 CTTCATATTTTCCCTTTCTCATTTCTG 57.201 33.333 0.00 0.00 0.00 3.02
2367 2620 8.687242 TCTCATTTCTGATAATCGTGTCTAGTT 58.313 33.333 0.00 0.00 0.00 2.24
2411 2664 0.877743 GCTTCCAGGACTGTCTTTGC 59.122 55.000 7.85 0.00 0.00 3.68
2487 2740 3.288092 GGACAAGAGTTCAGTTTGGGTT 58.712 45.455 0.00 0.00 0.00 4.11
2488 2741 3.699538 GGACAAGAGTTCAGTTTGGGTTT 59.300 43.478 0.00 0.00 0.00 3.27
2489 2742 4.440112 GGACAAGAGTTCAGTTTGGGTTTG 60.440 45.833 0.00 0.00 0.00 2.93
2491 2744 5.258051 ACAAGAGTTCAGTTTGGGTTTGTA 58.742 37.500 0.00 0.00 0.00 2.41
2493 2746 7.057894 ACAAGAGTTCAGTTTGGGTTTGTATA 58.942 34.615 0.00 0.00 0.00 1.47
2529 2797 7.885297 ACATGTTGTATTTGTTCTTGCTATGT 58.115 30.769 0.00 0.00 0.00 2.29
2549 2817 3.066760 TGTCATCTGATGTACACCTAGCG 59.933 47.826 16.66 0.00 0.00 4.26
2561 2829 7.237209 TGTACACCTAGCGTATCTAGATCTA 57.763 40.000 8.95 1.69 46.12 1.98
2565 2833 7.045416 ACACCTAGCGTATCTAGATCTATCTG 58.955 42.308 8.95 5.72 46.12 2.90
2623 2891 4.118410 CAACATAAAAACTGGCAGTTGCA 58.882 39.130 31.75 19.89 44.36 4.08
2664 2933 4.828829 TGTATATCATGAGATGCCTGCAG 58.171 43.478 13.11 6.78 35.67 4.41
2758 3027 5.220710 ACTTGCAGTCTACTTCTGACATT 57.779 39.130 0.00 0.00 36.94 2.71
2907 3176 1.327303 GTGCTGTCCAACCAATTCCA 58.673 50.000 0.00 0.00 0.00 3.53
2928 3197 6.908825 TCCATTGACGAAAAGGAAGTATTTG 58.091 36.000 0.00 0.00 0.00 2.32
2994 3263 0.685785 TGGTGGAACTGGCAAAGCAA 60.686 50.000 0.00 0.00 36.74 3.91
3080 3373 1.154197 GCTTCTGTGGGTCCGTTAAC 58.846 55.000 0.00 0.00 0.00 2.01
3082 3375 2.413837 CTTCTGTGGGTCCGTTAACAG 58.586 52.381 6.39 0.00 41.11 3.16
3108 3401 5.125417 AGTTATTATGGCAATGTTCGCAACT 59.875 36.000 0.00 0.00 0.00 3.16
3132 3425 9.113838 ACTACATGATTCTGAATGAATTGGTAC 57.886 33.333 7.78 0.00 44.70 3.34
3175 3629 8.009622 TGATTTGCATTCTTATTGCTATTCCA 57.990 30.769 0.00 0.00 40.77 3.53
3181 3635 6.239120 GCATTCTTATTGCTATTCCACCATGT 60.239 38.462 0.00 0.00 37.14 3.21
3209 3663 4.873817 TGTCAGAAATTCACATTGCAAGG 58.126 39.130 10.01 10.01 0.00 3.61
3256 3710 8.532819 GGTGCTAGCCAGAGTATTTACTTATAT 58.467 37.037 13.29 0.00 36.50 0.86
3533 4707 2.041265 TGAGCTCTCCCTTCCCCC 59.959 66.667 16.19 0.00 0.00 5.40
3568 4742 2.693591 TGAGTGCATACCTACACCTAGC 59.306 50.000 0.00 0.00 37.51 3.42
3569 4743 2.959707 GAGTGCATACCTACACCTAGCT 59.040 50.000 0.00 0.00 37.51 3.32
3570 4744 4.142790 GAGTGCATACCTACACCTAGCTA 58.857 47.826 0.00 0.00 37.51 3.32
3571 4745 4.145807 AGTGCATACCTACACCTAGCTAG 58.854 47.826 14.20 14.20 37.51 3.42
3693 4868 7.130303 TGACTACACCGAGATATCGATAAAG 57.870 40.000 12.11 6.01 34.64 1.85
3753 4928 3.637229 ACCTTGAGTCGATACCAGGTATG 59.363 47.826 17.54 9.38 0.00 2.39
3762 4937 0.328061 TACCAGGTATGCCCCCACAT 60.328 55.000 0.00 0.00 34.57 3.21
3777 4952 4.013050 CCCCACATTTTTCTTCTCTCCTC 58.987 47.826 0.00 0.00 0.00 3.71
3794 4969 6.499699 TCTCTCCTCTGCAATTATACCATCAT 59.500 38.462 0.00 0.00 0.00 2.45
3807 4982 8.924511 ATTATACCATCATTTAGTCCTGTTGG 57.075 34.615 0.00 0.00 37.94 3.77
3875 5050 3.426117 GATGATCGCCCGTGGACGT 62.426 63.158 0.00 0.00 37.74 4.34
4083 5258 0.318441 ACCATGACTCTCCGTGTGTG 59.682 55.000 0.00 0.00 0.00 3.82
4097 5272 1.169661 TGTGTGTCGGGTTGATTGGC 61.170 55.000 0.00 0.00 0.00 4.52
4145 5320 0.824759 ATGTTCGAGGTAGGGTGAGC 59.175 55.000 0.00 0.00 0.00 4.26
4151 5326 0.896226 GAGGTAGGGTGAGCGACTTT 59.104 55.000 0.00 0.00 0.00 2.66
4170 5345 7.905493 GCGACTTTTCTTTCGATCTATTCATTT 59.095 33.333 0.00 0.00 37.43 2.32
4171 5346 9.760660 CGACTTTTCTTTCGATCTATTCATTTT 57.239 29.630 0.00 0.00 37.43 1.82
4291 5471 9.239002 TGTAACATTTTTGTCCATTTACTTTCG 57.761 29.630 0.00 0.00 0.00 3.46
4403 5583 2.742372 CAAGGAACCGTCGCCTGG 60.742 66.667 0.00 0.00 34.00 4.45
4411 5591 1.815421 CCGTCGCCTGGGAGAATTG 60.815 63.158 0.00 0.00 0.00 2.32
4424 5604 3.305608 GGGAGAATTGGTTTGCTCTGTTG 60.306 47.826 0.00 0.00 0.00 3.33
4440 5620 1.346395 TGTTGGCAGTTCATACCTCGT 59.654 47.619 0.00 0.00 0.00 4.18
4451 5631 2.242965 TCATACCTCGTTCTCCCTACCA 59.757 50.000 0.00 0.00 0.00 3.25
4462 5642 3.955471 TCTCCCTACCAAAGAAATGCAG 58.045 45.455 0.00 0.00 0.00 4.41
4463 5643 3.330701 TCTCCCTACCAAAGAAATGCAGT 59.669 43.478 0.00 0.00 0.00 4.40
4464 5644 4.082125 CTCCCTACCAAAGAAATGCAGTT 58.918 43.478 0.00 0.00 0.00 3.16
4539 5725 5.579511 GCAAGCAAAAGATGAAGCAATATGT 59.420 36.000 0.00 0.00 0.00 2.29
4554 5740 5.926542 AGCAATATGTAGTTATGTACGCCAG 59.073 40.000 0.00 0.00 0.00 4.85
4563 5749 1.182667 ATGTACGCCAGCTGAGTGTA 58.817 50.000 17.39 18.24 0.00 2.90
4564 5750 0.526211 TGTACGCCAGCTGAGTGTAG 59.474 55.000 17.39 0.00 31.22 2.74
4565 5751 0.802607 GTACGCCAGCTGAGTGTAGC 60.803 60.000 17.39 7.87 44.01 3.58
4575 5764 2.478134 GCTGAGTGTAGCTGTGTGAAAG 59.522 50.000 0.00 0.00 40.52 2.62
4628 5818 2.896044 TGCTGGCACATTACCAAAATCA 59.104 40.909 0.00 0.00 38.20 2.57
4629 5819 3.056678 TGCTGGCACATTACCAAAATCAG 60.057 43.478 0.00 0.00 38.20 2.90
4694 5889 0.250252 TGGCACGCAGAAGATTGTCA 60.250 50.000 0.00 0.00 0.00 3.58
4730 5925 2.992543 GGCGCATGAGATCTTAGATGAC 59.007 50.000 10.83 0.00 0.00 3.06
4783 5978 2.957491 AGGATTTCTGAGCGACTGAG 57.043 50.000 0.00 0.00 0.00 3.35
4787 5982 0.681733 TTTCTGAGCGACTGAGCCTT 59.318 50.000 0.00 0.00 38.01 4.35
4788 5983 0.037882 TTCTGAGCGACTGAGCCTTG 60.038 55.000 0.00 0.00 38.01 3.61
4867 6062 0.907230 AAGGAGAGGTGGAGGTCAGC 60.907 60.000 0.00 0.00 43.73 4.26
4996 6191 7.575414 TTTGTTTGCTAGTCCTGTAATTGAA 57.425 32.000 0.00 0.00 0.00 2.69
5002 6197 8.635765 TTGCTAGTCCTGTAATTGAAAAGAAT 57.364 30.769 0.00 0.00 0.00 2.40
5007 6202 8.924511 AGTCCTGTAATTGAAAAGAATCTGAA 57.075 30.769 0.00 0.00 0.00 3.02
5022 6217 9.455847 AAAGAATCTGAAATCTCTTTTTGAACG 57.544 29.630 0.00 0.00 35.15 3.95
5023 6218 8.159344 AGAATCTGAAATCTCTTTTTGAACGT 57.841 30.769 0.00 0.00 0.00 3.99
5024 6219 8.072567 AGAATCTGAAATCTCTTTTTGAACGTG 58.927 33.333 0.00 0.00 0.00 4.49
5046 6256 6.428771 CGTGAAAGGTTGGGATAAAAGAAGTA 59.571 38.462 0.00 0.00 0.00 2.24
5054 6264 6.945636 TGGGATAAAAGAAGTAGAACAGGA 57.054 37.500 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.095691 GCTAAATGCTATGCAAACAGTTCAAAA 60.096 33.333 0.00 0.00 43.62 2.44
6 7 6.365789 GCTAAATGCTATGCAAACAGTTCAAA 59.634 34.615 0.00 0.00 43.62 2.69
7 8 5.863397 GCTAAATGCTATGCAAACAGTTCAA 59.137 36.000 0.00 0.00 43.62 2.69
8 9 5.048154 TGCTAAATGCTATGCAAACAGTTCA 60.048 36.000 0.00 0.00 43.62 3.18
9 10 5.401550 TGCTAAATGCTATGCAAACAGTTC 58.598 37.500 0.00 0.00 43.62 3.01
10 11 5.389859 TGCTAAATGCTATGCAAACAGTT 57.610 34.783 0.00 0.00 43.62 3.16
11 12 5.587388 ATGCTAAATGCTATGCAAACAGT 57.413 34.783 0.00 0.00 43.62 3.55
12 13 5.276678 GCAATGCTAAATGCTATGCAAACAG 60.277 40.000 0.00 0.00 45.94 3.16
13 14 4.567558 GCAATGCTAAATGCTATGCAAACA 59.432 37.500 0.00 0.00 45.94 2.83
14 15 5.074430 GCAATGCTAAATGCTATGCAAAC 57.926 39.130 0.00 0.00 45.94 2.93
18 19 3.708890 TGTGCAATGCTAAATGCTATGC 58.291 40.909 6.82 9.84 46.43 3.14
19 20 4.684242 CCATGTGCAATGCTAAATGCTATG 59.316 41.667 6.82 0.00 42.97 2.23
20 21 4.342951 ACCATGTGCAATGCTAAATGCTAT 59.657 37.500 6.82 0.00 42.97 2.97
39 40 0.330604 ATCTGCTTCACTGCCACCAT 59.669 50.000 0.00 0.00 0.00 3.55
47 48 8.181904 TCCAAAAGATTTAAATCTGCTTCACT 57.818 30.769 27.25 10.33 44.67 3.41
77 79 0.178992 TGGTTTGTCTCCAGGCTTGG 60.179 55.000 8.96 8.96 46.49 3.61
78 80 1.242076 CTGGTTTGTCTCCAGGCTTG 58.758 55.000 4.27 0.00 46.03 4.01
79 81 3.733709 CTGGTTTGTCTCCAGGCTT 57.266 52.632 4.27 0.00 46.03 4.35
89 91 1.039233 ACTGCTTGCTGCTGGTTTGT 61.039 50.000 0.00 0.00 43.66 2.83
91 93 0.386838 GAACTGCTTGCTGCTGGTTT 59.613 50.000 0.00 1.34 40.70 3.27
92 94 0.752743 TGAACTGCTTGCTGCTGGTT 60.753 50.000 0.00 11.50 40.70 3.67
101 103 3.538591 TGGATGAGCTATGAACTGCTTG 58.461 45.455 0.00 0.00 39.91 4.01
119 121 2.877300 GCTGACAGGAAATTGCTCTGGA 60.877 50.000 4.26 0.00 33.19 3.86
134 143 4.286910 GTGCGTTTTTAATTCTGCTGACA 58.713 39.130 0.00 0.00 0.00 3.58
144 155 2.511879 GCGGATTCGTGCGTTTTTAAT 58.488 42.857 0.00 0.00 38.89 1.40
301 312 3.591835 GTTGTGTGTGTGCGGGGG 61.592 66.667 0.00 0.00 0.00 5.40
302 313 2.515991 AGTTGTGTGTGTGCGGGG 60.516 61.111 0.00 0.00 0.00 5.73
306 317 0.577269 GTCGAGAGTTGTGTGTGTGC 59.423 55.000 0.00 0.00 0.00 4.57
313 324 3.839051 TCTGATGAGTCGAGAGTTGTG 57.161 47.619 0.00 0.00 0.00 3.33
315 326 4.498681 CGAATTCTGATGAGTCGAGAGTTG 59.501 45.833 3.52 0.00 35.14 3.16
318 329 3.042189 GCGAATTCTGATGAGTCGAGAG 58.958 50.000 3.52 0.00 35.14 3.20
319 330 2.223595 GGCGAATTCTGATGAGTCGAGA 60.224 50.000 3.52 0.00 35.14 4.04
320 331 2.123342 GGCGAATTCTGATGAGTCGAG 58.877 52.381 3.52 0.00 35.14 4.04
321 332 1.202417 GGGCGAATTCTGATGAGTCGA 60.202 52.381 3.52 0.00 35.14 4.20
322 333 1.212616 GGGCGAATTCTGATGAGTCG 58.787 55.000 3.52 0.00 35.80 4.18
323 334 1.212616 CGGGCGAATTCTGATGAGTC 58.787 55.000 3.52 0.00 0.00 3.36
324 335 0.811616 GCGGGCGAATTCTGATGAGT 60.812 55.000 3.52 0.00 0.00 3.41
325 336 1.502163 GGCGGGCGAATTCTGATGAG 61.502 60.000 3.52 0.00 0.00 2.90
326 337 1.523711 GGCGGGCGAATTCTGATGA 60.524 57.895 3.52 0.00 0.00 2.92
327 338 1.375853 TTGGCGGGCGAATTCTGATG 61.376 55.000 3.52 0.00 0.00 3.07
328 339 0.679640 TTTGGCGGGCGAATTCTGAT 60.680 50.000 3.52 0.00 0.00 2.90
345 367 0.957395 CTGATGCTGGCGTCTGGTTT 60.957 55.000 14.64 0.00 33.41 3.27
353 375 1.441732 TTATGCTGCTGATGCTGGCG 61.442 55.000 0.00 0.00 39.78 5.69
355 377 1.963172 TCTTATGCTGCTGATGCTGG 58.037 50.000 0.00 0.00 40.48 4.85
356 378 3.203716 TCTTCTTATGCTGCTGATGCTG 58.796 45.455 0.00 0.00 40.48 4.41
357 379 3.555527 TCTTCTTATGCTGCTGATGCT 57.444 42.857 0.00 0.00 40.48 3.79
358 380 3.548415 GCTTCTTCTTATGCTGCTGATGC 60.548 47.826 0.00 0.00 40.20 3.91
359 381 3.626217 TGCTTCTTCTTATGCTGCTGATG 59.374 43.478 0.00 0.00 0.00 3.07
360 382 3.626670 GTGCTTCTTCTTATGCTGCTGAT 59.373 43.478 0.00 0.00 0.00 2.90
361 383 3.005554 GTGCTTCTTCTTATGCTGCTGA 58.994 45.455 0.00 0.00 0.00 4.26
362 384 2.745821 TGTGCTTCTTCTTATGCTGCTG 59.254 45.455 0.00 0.00 0.00 4.41
363 385 3.008330 CTGTGCTTCTTCTTATGCTGCT 58.992 45.455 0.00 0.00 0.00 4.24
364 386 2.477525 GCTGTGCTTCTTCTTATGCTGC 60.478 50.000 0.00 0.00 0.00 5.25
365 387 2.745821 TGCTGTGCTTCTTCTTATGCTG 59.254 45.455 0.00 0.00 0.00 4.41
366 388 2.746362 GTGCTGTGCTTCTTCTTATGCT 59.254 45.455 0.00 0.00 0.00 3.79
367 389 2.159462 GGTGCTGTGCTTCTTCTTATGC 60.159 50.000 0.00 0.00 0.00 3.14
368 390 3.341823 AGGTGCTGTGCTTCTTCTTATG 58.658 45.455 0.00 0.00 0.00 1.90
369 391 3.710209 AGGTGCTGTGCTTCTTCTTAT 57.290 42.857 0.00 0.00 0.00 1.73
370 392 3.071602 AGAAGGTGCTGTGCTTCTTCTTA 59.928 43.478 15.89 0.00 41.52 2.10
371 393 2.158696 AGAAGGTGCTGTGCTTCTTCTT 60.159 45.455 15.89 0.00 41.52 2.52
379 401 1.239968 CCTCCAAGAAGGTGCTGTGC 61.240 60.000 0.00 0.00 39.02 4.57
385 407 2.045926 CCGCCCTCCAAGAAGGTG 60.046 66.667 0.00 0.00 39.02 4.00
541 563 2.363018 CTCCTCCTCCTGGTCGCA 60.363 66.667 0.00 0.00 34.23 5.10
590 615 4.847444 GAGAGGAAGCGCTGCCCC 62.847 72.222 31.70 21.08 0.00 5.80
629 654 0.035630 CTGCAGGGGAAGAAGTGGAG 60.036 60.000 5.57 0.00 0.00 3.86
633 664 1.682257 GAGCTGCAGGGGAAGAAGT 59.318 57.895 17.12 0.00 0.00 3.01
642 673 2.433838 CACTGACCGAGCTGCAGG 60.434 66.667 17.12 11.76 34.05 4.85
823 858 2.951745 GAGCATCCGAGTCACGCG 60.952 66.667 3.53 3.53 41.07 6.01
868 903 3.020237 GCCACCTCGGTTCTCCTCC 62.020 68.421 0.00 0.00 36.97 4.30
869 904 2.579738 GCCACCTCGGTTCTCCTC 59.420 66.667 0.00 0.00 36.97 3.71
901 936 4.811761 GCGCCGATTTGCCGTCAC 62.812 66.667 0.00 0.00 0.00 3.67
905 940 4.228097 CTGAGCGCCGATTTGCCG 62.228 66.667 2.29 0.00 0.00 5.69
908 943 2.099062 GCACTGAGCGCCGATTTG 59.901 61.111 2.29 0.00 0.00 2.32
948 985 1.004560 ATGCAGTGGAGTCGGTGTG 60.005 57.895 0.00 0.00 0.00 3.82
1598 1844 7.042456 GCAATTAGGGAGTATATATCATGTGCG 60.042 40.741 0.00 0.00 0.00 5.34
1611 1857 1.839994 AGCAGCAGCAATTAGGGAGTA 59.160 47.619 3.17 0.00 45.49 2.59
1612 1858 0.622665 AGCAGCAGCAATTAGGGAGT 59.377 50.000 3.17 0.00 45.49 3.85
1613 1859 1.760192 AAGCAGCAGCAATTAGGGAG 58.240 50.000 3.17 0.00 45.49 4.30
1614 1860 2.239654 AGTAAGCAGCAGCAATTAGGGA 59.760 45.455 3.17 0.00 45.49 4.20
1615 1861 2.648059 AGTAAGCAGCAGCAATTAGGG 58.352 47.619 3.17 0.00 45.49 3.53
1687 1937 2.040813 ACATTCATGGCAACTGAGGTCT 59.959 45.455 0.00 0.00 37.61 3.85
1714 1964 4.742438 AATTGGTTTACACACTGTAGCG 57.258 40.909 0.00 0.00 33.92 4.26
1745 1995 8.923270 AGGAAAAAGGAAAACTGAATGTCAATA 58.077 29.630 0.00 0.00 0.00 1.90
1746 1996 7.712205 CAGGAAAAAGGAAAACTGAATGTCAAT 59.288 33.333 0.00 0.00 0.00 2.57
1747 1997 7.041107 CAGGAAAAAGGAAAACTGAATGTCAA 58.959 34.615 0.00 0.00 0.00 3.18
1748 1998 6.406849 CCAGGAAAAAGGAAAACTGAATGTCA 60.407 38.462 0.00 0.00 0.00 3.58
1750 2000 5.425217 ACCAGGAAAAAGGAAAACTGAATGT 59.575 36.000 0.00 0.00 0.00 2.71
1753 2003 5.066764 CGTACCAGGAAAAAGGAAAACTGAA 59.933 40.000 0.00 0.00 0.00 3.02
1763 2013 4.189231 CCTATCACCGTACCAGGAAAAAG 58.811 47.826 0.00 0.00 34.73 2.27
1770 2020 3.021695 TCTTCACCTATCACCGTACCAG 58.978 50.000 0.00 0.00 0.00 4.00
1774 2024 3.635373 GTGGATCTTCACCTATCACCGTA 59.365 47.826 0.00 0.00 0.00 4.02
1868 2118 2.233355 GTCATGCGAACACATTTGACG 58.767 47.619 0.00 0.00 0.00 4.35
1889 2139 0.108898 CCTTGTCTGTGAGAGCTCCG 60.109 60.000 10.93 0.00 0.00 4.63
1894 2144 5.936372 TGATTGATTTCCTTGTCTGTGAGAG 59.064 40.000 0.00 0.00 0.00 3.20
1901 2151 8.051535 ACATATGTCTGATTGATTTCCTTGTCT 58.948 33.333 1.41 0.00 0.00 3.41
1971 2221 7.707893 GTCAGTAAACTTAAACACACCTGAGTA 59.292 37.037 0.00 0.00 0.00 2.59
1995 2246 3.432592 GGTTAAGAAGAGAACTTGCGGTC 59.567 47.826 0.00 0.00 36.39 4.79
2047 2298 4.100035 TCTGCGGAAATATGACATCTGACT 59.900 41.667 0.00 0.00 0.00 3.41
2155 2406 6.321181 TCTTCAACCAAAAGACAATGCTAACT 59.679 34.615 0.00 0.00 0.00 2.24
2158 2409 6.707440 TTCTTCAACCAAAAGACAATGCTA 57.293 33.333 0.00 0.00 32.64 3.49
2197 2448 7.920151 CCACAAAAGAACAATGTTCTTACATGA 59.080 33.333 33.29 0.00 44.14 3.07
2215 2466 1.066002 CCACTGCACACTCCACAAAAG 59.934 52.381 0.00 0.00 0.00 2.27
2227 2478 3.360340 GCTCCAGCACCACTGCAC 61.360 66.667 0.00 0.00 46.97 4.57
2230 2481 1.670406 GTGAGCTCCAGCACCACTG 60.670 63.158 12.15 0.00 46.77 3.66
2341 2592 8.226819 ACTAGACACGATTATCAGAAATGAGA 57.773 34.615 0.00 0.00 0.00 3.27
2342 2593 8.864069 AACTAGACACGATTATCAGAAATGAG 57.136 34.615 0.00 0.00 0.00 2.90
2387 2640 3.064900 AGACAGTCCTGGAAGCAATTC 57.935 47.619 0.00 0.00 34.19 2.17
2390 2643 2.575532 CAAAGACAGTCCTGGAAGCAA 58.424 47.619 0.00 0.00 34.19 3.91
2427 2680 9.435570 AGGAAGCCTTCTTCTAATACAGTATTA 57.564 33.333 11.78 11.78 46.12 0.98
2428 2681 8.325477 AGGAAGCCTTCTTCTAATACAGTATT 57.675 34.615 10.71 10.71 46.12 1.89
2429 2682 7.922699 AGGAAGCCTTCTTCTAATACAGTAT 57.077 36.000 4.15 0.00 46.12 2.12
2430 2683 8.834004 TTAGGAAGCCTTCTTCTAATACAGTA 57.166 34.615 4.15 0.00 46.12 2.74
2431 2684 7.735326 TTAGGAAGCCTTCTTCTAATACAGT 57.265 36.000 4.15 0.00 46.12 3.55
2432 2685 9.620259 AAATTAGGAAGCCTTCTTCTAATACAG 57.380 33.333 13.15 0.00 46.12 2.74
2450 2703 4.534500 TCTTGTCCCACTGCTAAATTAGGA 59.466 41.667 1.88 0.00 0.00 2.94
2454 2707 4.373156 ACTCTTGTCCCACTGCTAAATT 57.627 40.909 0.00 0.00 0.00 1.82
2458 2711 2.300152 CTGAACTCTTGTCCCACTGCTA 59.700 50.000 0.00 0.00 0.00 3.49
2460 2713 1.202698 ACTGAACTCTTGTCCCACTGC 60.203 52.381 0.00 0.00 0.00 4.40
2529 2797 3.288092 ACGCTAGGTGTACATCAGATGA 58.712 45.455 17.81 0.00 0.00 2.92
2580 2848 4.861196 TGGGATTTGGGAAAACATCGATA 58.139 39.130 0.00 0.00 0.00 2.92
2584 2852 4.615588 TGTTGGGATTTGGGAAAACATC 57.384 40.909 0.00 0.00 0.00 3.06
2657 2926 2.340809 TGCAAACATGCTGCAGGC 59.659 55.556 17.12 8.91 44.67 4.85
2664 2933 2.270047 ACACAAACACTGCAAACATGC 58.730 42.857 0.00 0.00 0.00 4.06
2676 2945 4.202101 CCAAGTCAATTGCCTACACAAACA 60.202 41.667 0.00 0.00 37.60 2.83
2758 3027 5.411361 ACAAGAATGCAAGTCGCTATGTAAA 59.589 36.000 0.00 0.00 43.06 2.01
2780 3049 2.964464 TCAGTACGGTCACCCTAAAACA 59.036 45.455 0.00 0.00 0.00 2.83
2907 3176 5.242838 TGCCAAATACTTCCTTTTCGTCAAT 59.757 36.000 0.00 0.00 0.00 2.57
2928 3197 1.864029 GCACGACCAAGAAAGTTTGCC 60.864 52.381 0.00 0.00 0.00 4.52
3080 3373 5.682862 GCGAACATTGCCATAATAACTTCTG 59.317 40.000 0.00 0.00 0.00 3.02
3082 3375 5.577835 TGCGAACATTGCCATAATAACTTC 58.422 37.500 0.00 0.00 0.00 3.01
3102 3395 5.723492 TCATTCAGAATCATGTAGTTGCG 57.277 39.130 0.00 0.00 0.00 4.85
3108 3401 9.631257 ATGTACCAATTCATTCAGAATCATGTA 57.369 29.630 0.00 0.00 46.09 2.29
3132 3425 8.896744 TGCAAATCAAGGTTCTAATCTTCTATG 58.103 33.333 0.00 0.00 0.00 2.23
3144 3598 6.815142 AGCAATAAGAATGCAAATCAAGGTTC 59.185 34.615 0.00 0.00 46.22 3.62
3175 3629 7.448161 TGTGAATTTCTGACAATAGAACATGGT 59.552 33.333 0.00 0.00 36.48 3.55
3181 3635 7.884257 TGCAATGTGAATTTCTGACAATAGAA 58.116 30.769 0.00 0.00 35.02 2.10
3209 3663 5.527582 CACCCTAGAATACCAACTTGTATGC 59.472 44.000 0.00 0.00 31.90 3.14
3260 3714 9.602568 TGAAAGCACGATTAACCTTGTATATTA 57.397 29.630 0.00 0.00 0.00 0.98
3540 4714 7.346471 AGGTGTAGGTATGCACTCAATATTTT 58.654 34.615 0.00 0.00 41.36 1.82
3542 4716 6.500589 AGGTGTAGGTATGCACTCAATATT 57.499 37.500 0.00 0.00 41.36 1.28
3568 4742 4.036262 GTGGACAGCTGAGTCAGATACTAG 59.964 50.000 24.55 8.09 39.07 2.57
3569 4743 3.948473 GTGGACAGCTGAGTCAGATACTA 59.052 47.826 24.55 10.12 39.07 1.82
3570 4744 2.757868 GTGGACAGCTGAGTCAGATACT 59.242 50.000 24.55 8.60 42.80 2.12
3571 4745 2.493675 TGTGGACAGCTGAGTCAGATAC 59.506 50.000 24.55 12.76 40.29 2.24
3693 4868 1.154205 CGATCTTGGACGATGGCCAC 61.154 60.000 8.16 0.47 34.56 5.01
3753 4928 2.493675 GAGAGAAGAAAAATGTGGGGGC 59.506 50.000 0.00 0.00 0.00 5.80
3762 4937 9.167311 GTATAATTGCAGAGGAGAGAAGAAAAA 57.833 33.333 0.00 0.00 0.00 1.94
3777 4952 8.509690 CAGGACTAAATGATGGTATAATTGCAG 58.490 37.037 0.00 0.00 0.00 4.41
3794 4969 0.323629 CTCGCCCCAACAGGACTAAA 59.676 55.000 0.00 0.00 38.24 1.85
3807 4982 2.048603 AAGGCTTTGATGCTCGCCC 61.049 57.895 0.00 0.00 43.48 6.13
3875 5050 0.253894 CCCACATGCATCTCACCTCA 59.746 55.000 0.00 0.00 0.00 3.86
4083 5258 0.394352 ATCTGGCCAATCAACCCGAC 60.394 55.000 7.01 0.00 0.00 4.79
4097 5272 4.283212 ACCATACAACAACCCAAAATCTGG 59.717 41.667 0.00 0.00 45.97 3.86
4170 5345 1.663739 CCTCAAGGGTGACGACGAA 59.336 57.895 0.00 0.00 0.00 3.85
4171 5346 3.362262 CCTCAAGGGTGACGACGA 58.638 61.111 0.00 0.00 0.00 4.20
4349 5529 7.820872 TGGTAAGCATATGTCATACAGATCATG 59.179 37.037 4.29 0.00 25.56 3.07
4403 5583 3.305608 CCAACAGAGCAAACCAATTCTCC 60.306 47.826 0.00 0.00 0.00 3.71
4424 5604 2.541556 GAGAACGAGGTATGAACTGCC 58.458 52.381 0.00 0.00 0.00 4.85
4440 5620 4.202567 ACTGCATTTCTTTGGTAGGGAGAA 60.203 41.667 0.00 0.00 0.00 2.87
4451 5631 7.264221 TCATGTGTTTACAACTGCATTTCTTT 58.736 30.769 0.00 0.00 40.84 2.52
4462 5642 7.915397 AGAGACAATTGTTCATGTGTTTACAAC 59.085 33.333 13.36 0.00 40.84 3.32
4463 5643 7.995289 AGAGACAATTGTTCATGTGTTTACAA 58.005 30.769 13.36 0.00 40.84 2.41
4464 5644 7.566760 AGAGACAATTGTTCATGTGTTTACA 57.433 32.000 13.36 0.00 41.89 2.41
4505 5691 6.672147 TCATCTTTTGCTTGCTTAGTTCTTC 58.328 36.000 0.00 0.00 0.00 2.87
4506 5692 6.639632 TCATCTTTTGCTTGCTTAGTTCTT 57.360 33.333 0.00 0.00 0.00 2.52
4507 5693 6.639632 TTCATCTTTTGCTTGCTTAGTTCT 57.360 33.333 0.00 0.00 0.00 3.01
4519 5705 9.956720 ATAACTACATATTGCTTCATCTTTTGC 57.043 29.630 0.00 0.00 0.00 3.68
4539 5725 3.021695 ACTCAGCTGGCGTACATAACTA 58.978 45.455 15.13 0.00 0.00 2.24
4554 5740 2.154854 TTCACACAGCTACACTCAGC 57.845 50.000 0.00 0.00 42.12 4.26
4563 5749 1.267806 CGGATTTGCTTTCACACAGCT 59.732 47.619 0.00 0.00 38.19 4.24
4564 5750 1.689959 CGGATTTGCTTTCACACAGC 58.310 50.000 0.00 0.00 37.82 4.40
4565 5751 1.001487 TGCGGATTTGCTTTCACACAG 60.001 47.619 0.00 0.00 35.36 3.66
4575 5764 1.202336 CCTTTGGAGATGCGGATTTGC 60.202 52.381 0.00 0.00 0.00 3.68
4628 5818 8.312564 GGTTGGTAAGATTCTTACTTAGTGACT 58.687 37.037 27.33 0.00 31.75 3.41
4629 5819 8.092687 TGGTTGGTAAGATTCTTACTTAGTGAC 58.907 37.037 27.33 18.28 31.75 3.67
4677 5872 1.127582 GTCTGACAATCTTCTGCGTGC 59.872 52.381 2.24 0.00 0.00 5.34
4680 5875 1.916651 CGAGTCTGACAATCTTCTGCG 59.083 52.381 10.88 0.00 0.00 5.18
4694 5889 3.444805 GCCGAGTGGAGCGAGTCT 61.445 66.667 0.00 0.00 37.49 3.24
4730 5925 1.370609 CAGAAGCTCTGTGCAGGATG 58.629 55.000 4.39 0.00 45.94 3.51
4772 5967 0.174389 GATCAAGGCTCAGTCGCTCA 59.826 55.000 0.00 0.00 0.00 4.26
4776 5971 0.173481 TTCGGATCAAGGCTCAGTCG 59.827 55.000 0.00 0.00 0.00 4.18
4783 5978 0.469917 TCCATCCTTCGGATCAAGGC 59.530 55.000 6.91 0.00 40.98 4.35
4787 5982 1.123077 CCAGTCCATCCTTCGGATCA 58.877 55.000 0.00 0.00 40.98 2.92
4788 5983 0.394565 CCCAGTCCATCCTTCGGATC 59.605 60.000 0.00 0.00 40.98 3.36
4833 6028 2.172082 TCTCCTTGGCCAGATCATGAAG 59.828 50.000 5.11 0.00 0.00 3.02
4867 6062 1.079543 CCGTGCACTCTTGAGGAGG 60.080 63.158 16.19 0.89 45.83 4.30
4870 6065 0.318441 TTCTCCGTGCACTCTTGAGG 59.682 55.000 16.19 7.60 0.00 3.86
4964 6159 5.763204 CAGGACTAGCAAACAAAAGGAACTA 59.237 40.000 0.00 0.00 38.49 2.24
4975 6170 7.871853 TCTTTTCAATTACAGGACTAGCAAAC 58.128 34.615 0.00 0.00 0.00 2.93
4996 6191 9.455847 CGTTCAAAAAGAGATTTCAGATTCTTT 57.544 29.630 0.00 0.00 40.53 2.52
5002 6197 6.918892 TCACGTTCAAAAAGAGATTTCAGA 57.081 33.333 0.00 0.00 0.00 3.27
5007 6202 6.451064 ACCTTTCACGTTCAAAAAGAGATT 57.549 33.333 9.76 0.00 32.89 2.40
5022 6217 6.650427 ACTTCTTTTATCCCAACCTTTCAC 57.350 37.500 0.00 0.00 0.00 3.18
5023 6218 7.751646 TCTACTTCTTTTATCCCAACCTTTCA 58.248 34.615 0.00 0.00 0.00 2.69
5024 6219 8.512956 GTTCTACTTCTTTTATCCCAACCTTTC 58.487 37.037 0.00 0.00 0.00 2.62
5046 6256 3.328931 TCCATCTTTCAGCTTCCTGTTCT 59.671 43.478 0.00 0.00 40.09 3.01


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

AutoCloner maintained by Alex Coulton.