Multiple sequence alignment - TraesCS1D01G365000

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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 TraesCS1D01G365000 chr1D 100.000 2632 0 0 1 2632 445551661 445554292 0.000000e+00 4861.0
1 TraesCS1D01G365000 chr1D 82.301 226 36 2 1096 1320 445570271 445570493 2.670000e-45 193.0
2 TraesCS1D01G365000 chr1D 96.970 33 1 0 75 107 5283749 5283717 3.660000e-04 56.5
3 TraesCS1D01G365000 chr1A 87.796 1393 96 31 522 1873 541655683 541657042 0.000000e+00 1563.0
4 TraesCS1D01G365000 chr1A 80.146 685 90 26 844 1504 541718434 541719096 1.100000e-128 470.0
5 TraesCS1D01G365000 chr1A 76.524 443 38 31 101 506 541654999 541655412 5.790000e-42 182.0
6 TraesCS1D01G365000 chr1B 87.086 1146 92 31 711 1821 608838034 608839158 0.000000e+00 1245.0
7 TraesCS1D01G365000 chr1B 88.282 751 59 17 1880 2622 608839187 608839916 0.000000e+00 872.0
8 TraesCS1D01G365000 chr1B 93.258 89 6 0 104 192 608541551 608541639 5.910000e-27 132.0
9 TraesCS1D01G365000 chr1B 78.505 107 19 3 1 107 48276221 48276323 1.690000e-07 67.6
10 TraesCS1D01G365000 chr7D 96.552 87 3 0 106 192 334878068 334878154 7.590000e-31 145.0
11 TraesCS1D01G365000 chr2A 95.402 87 4 0 106 192 427584571 427584657 3.530000e-29 139.0
12 TraesCS1D01G365000 chr2A 94.253 87 5 0 106 192 360443358 360443444 1.640000e-27 134.0
13 TraesCS1D01G365000 chr3B 88.571 105 12 0 1 105 270871178 270871282 7.650000e-26 128.0
14 TraesCS1D01G365000 chr3B 96.970 33 1 0 72 104 43319224 43319256 3.660000e-04 56.5
15 TraesCS1D01G365000 chr5A 88.462 104 12 0 1 104 569541018 569541121 2.750000e-25 126.0
16 TraesCS1D01G365000 chr4A 88.298 94 11 0 11 104 140311538 140311631 2.140000e-21 113.0
17 TraesCS1D01G365000 chr4A 89.189 74 8 0 2 75 371747852 371747779 2.790000e-15 93.5
18 TraesCS1D01G365000 chr6B 90.789 76 7 0 1 76 14340180 14340255 4.630000e-18 102.0
19 TraesCS1D01G365000 chr5D 87.302 63 8 0 1 63 457778910 457778848 3.630000e-09 73.1


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 TraesCS1D01G365000 chr1D 445551661 445554292 2631 False 4861.0 4861 100.000 1 2632 1 chr1D.!!$F1 2631
1 TraesCS1D01G365000 chr1A 541654999 541657042 2043 False 872.5 1563 82.160 101 1873 2 chr1A.!!$F2 1772
2 TraesCS1D01G365000 chr1A 541718434 541719096 662 False 470.0 470 80.146 844 1504 1 chr1A.!!$F1 660
3 TraesCS1D01G365000 chr1B 608838034 608839916 1882 False 1058.5 1245 87.684 711 2622 2 chr1B.!!$F3 1911

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
319 347 0.036388 GACAGGCTCACCGAAATGGA 60.036 55.0 0.0 0.0 42.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2269 0.253327 GTGAAGGGAAGTAGGGGCTG 59.747 60.0 0.0 0.0 0.0 4.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.167831 GCTTAATTAGGCGTCTCTCTTTTAG 57.832 40.000 3.59 0.00 0.00 1.85
25 26 6.979238 GCTTAATTAGGCGTCTCTCTTTTAGA 59.021 38.462 3.59 0.00 0.00 2.10
26 27 7.491696 GCTTAATTAGGCGTCTCTCTTTTAGAA 59.508 37.037 3.59 0.00 32.46 2.10
27 28 9.367444 CTTAATTAGGCGTCTCTCTTTTAGAAA 57.633 33.333 0.00 0.00 32.46 2.52
28 29 9.886132 TTAATTAGGCGTCTCTCTTTTAGAAAT 57.114 29.630 0.00 0.00 32.46 2.17
30 31 9.535878 AATTAGGCGTCTCTCTTTTAGAAATAG 57.464 33.333 0.00 0.00 32.46 1.73
31 32 5.908341 AGGCGTCTCTCTTTTAGAAATAGG 58.092 41.667 0.00 0.00 32.46 2.57
32 33 4.508492 GGCGTCTCTCTTTTAGAAATAGGC 59.492 45.833 0.00 0.00 32.46 3.93
33 34 5.109903 GCGTCTCTCTTTTAGAAATAGGCA 58.890 41.667 0.00 0.00 32.46 4.75
34 35 5.755861 GCGTCTCTCTTTTAGAAATAGGCAT 59.244 40.000 0.00 0.00 32.46 4.40
35 36 6.258947 GCGTCTCTCTTTTAGAAATAGGCATT 59.741 38.462 0.00 0.00 32.46 3.56
36 37 7.625553 CGTCTCTCTTTTAGAAATAGGCATTG 58.374 38.462 0.00 0.00 32.46 2.82
37 38 7.254590 CGTCTCTCTTTTAGAAATAGGCATTGG 60.255 40.741 0.00 0.00 32.46 3.16
38 39 7.554476 GTCTCTCTTTTAGAAATAGGCATTGGT 59.446 37.037 0.00 0.00 32.46 3.67
39 40 7.554118 TCTCTCTTTTAGAAATAGGCATTGGTG 59.446 37.037 0.00 0.00 32.46 4.17
40 41 7.680588 CTCTCTTTTAGAAATAGGCATTGGTGC 60.681 40.741 0.00 0.00 41.46 5.01
54 55 4.954875 CATTGGTGCTTTAGAAAAACCCA 58.045 39.130 4.78 0.00 0.00 4.51
55 56 5.363939 CATTGGTGCTTTAGAAAAACCCAA 58.636 37.500 0.00 0.00 35.40 4.12
56 57 5.622346 TTGGTGCTTTAGAAAAACCCAAT 57.378 34.783 0.00 0.00 0.00 3.16
57 58 5.622346 TGGTGCTTTAGAAAAACCCAATT 57.378 34.783 4.78 0.00 0.00 2.32
58 59 5.995446 TGGTGCTTTAGAAAAACCCAATTT 58.005 33.333 4.78 0.00 0.00 1.82
59 60 7.125792 TGGTGCTTTAGAAAAACCCAATTTA 57.874 32.000 4.78 0.00 0.00 1.40
60 61 7.740805 TGGTGCTTTAGAAAAACCCAATTTAT 58.259 30.769 4.78 0.00 0.00 1.40
61 62 8.214364 TGGTGCTTTAGAAAAACCCAATTTATT 58.786 29.630 4.78 0.00 0.00 1.40
62 63 9.062524 GGTGCTTTAGAAAAACCCAATTTATTT 57.937 29.630 0.00 0.00 0.00 1.40
75 76 9.875691 AACCCAATTTATTTTTCTAAGCATCTC 57.124 29.630 0.00 0.00 0.00 2.75
76 77 9.259832 ACCCAATTTATTTTTCTAAGCATCTCT 57.740 29.630 0.00 0.00 0.00 3.10
77 78 9.741647 CCCAATTTATTTTTCTAAGCATCTCTC 57.258 33.333 0.00 0.00 0.00 3.20
82 83 9.846248 TTTATTTTTCTAAGCATCTCTCAAAGC 57.154 29.630 0.00 0.00 0.00 3.51
83 84 6.882610 TTTTTCTAAGCATCTCTCAAAGCA 57.117 33.333 0.00 0.00 0.00 3.91
84 85 5.869753 TTTCTAAGCATCTCTCAAAGCAC 57.130 39.130 0.00 0.00 0.00 4.40
85 86 3.866651 TCTAAGCATCTCTCAAAGCACC 58.133 45.455 0.00 0.00 0.00 5.01
86 87 2.875094 AAGCATCTCTCAAAGCACCT 57.125 45.000 0.00 0.00 0.00 4.00
87 88 2.875094 AGCATCTCTCAAAGCACCTT 57.125 45.000 0.00 0.00 0.00 3.50
88 89 2.434428 AGCATCTCTCAAAGCACCTTG 58.566 47.619 0.00 0.00 0.00 3.61
89 90 1.135460 GCATCTCTCAAAGCACCTTGC 60.135 52.381 0.00 0.00 45.46 4.01
107 108 0.453390 GCATTGTACAAGGCCTGAGC 59.547 55.000 29.85 13.26 41.71 4.26
127 128 1.881973 CCAACAACATCCTGTCCACAG 59.118 52.381 0.00 0.00 43.40 3.66
144 145 4.787999 GCTGCAAGAAGCTCATGC 57.212 55.556 10.45 10.45 45.94 4.06
149 150 1.810755 TGCAAGAAGCTCATGCAGAAG 59.189 47.619 14.77 0.00 44.77 2.85
157 158 2.818432 AGCTCATGCAGAAGGAACAAAG 59.182 45.455 0.00 0.00 42.74 2.77
195 207 5.644636 TGAACCCAAACTTATTAGTAAGGCG 59.355 40.000 9.54 0.00 41.33 5.52
200 212 5.329493 CAAACTTATTAGTAAGGCGCCAAC 58.671 41.667 31.54 25.45 41.33 3.77
202 214 2.228138 TATTAGTAAGGCGCCAACGG 57.772 50.000 31.54 0.00 40.57 4.44
203 215 0.251073 ATTAGTAAGGCGCCAACGGT 59.749 50.000 31.54 13.50 40.57 4.83
223 235 3.119779 GGTTGAGACTCGAGTTCACCTAG 60.120 52.174 21.08 0.00 0.00 3.02
230 258 1.448013 GAGTTCACCTAGGCGGCAC 60.448 63.158 13.08 1.92 35.61 5.01
250 278 3.559655 CACACTTGAACTCATCGACCAAA 59.440 43.478 0.00 0.00 0.00 3.28
251 279 3.560068 ACACTTGAACTCATCGACCAAAC 59.440 43.478 0.00 0.00 0.00 2.93
252 280 3.809832 CACTTGAACTCATCGACCAAACT 59.190 43.478 0.00 0.00 0.00 2.66
253 281 4.988540 CACTTGAACTCATCGACCAAACTA 59.011 41.667 0.00 0.00 0.00 2.24
260 288 3.571571 TCATCGACCAAACTAGTGAACG 58.428 45.455 0.00 0.00 0.00 3.95
278 306 1.587613 GCACGACGAGAGAGCCATC 60.588 63.158 0.00 0.00 0.00 3.51
281 309 0.816018 ACGACGAGAGAGCCATCGAT 60.816 55.000 0.00 0.00 41.40 3.59
282 310 0.110419 CGACGAGAGAGCCATCGATC 60.110 60.000 0.00 0.00 41.40 3.69
283 311 0.110419 GACGAGAGAGCCATCGATCG 60.110 60.000 9.36 9.36 41.40 3.69
284 312 1.208870 CGAGAGAGCCATCGATCGG 59.791 63.158 16.41 1.97 41.40 4.18
292 320 2.029073 CATCGATCGGGGGAACGG 59.971 66.667 16.41 0.00 0.00 4.44
314 342 4.373116 GGCGACAGGCTCACCGAA 62.373 66.667 4.22 0.00 42.76 4.30
315 343 2.357034 GCGACAGGCTCACCGAAA 60.357 61.111 4.22 0.00 42.76 3.46
316 344 1.741770 GCGACAGGCTCACCGAAAT 60.742 57.895 4.22 0.00 42.76 2.17
317 345 1.970917 GCGACAGGCTCACCGAAATG 61.971 60.000 4.22 0.00 42.76 2.32
319 347 0.036388 GACAGGCTCACCGAAATGGA 60.036 55.000 0.00 0.00 42.00 3.41
321 349 1.079127 AGGCTCACCGAAATGGACG 60.079 57.895 0.00 0.00 42.00 4.79
386 418 2.579787 GACATCGTCGTGGCCTCG 60.580 66.667 20.92 20.92 0.00 4.63
387 419 3.338126 GACATCGTCGTGGCCTCGT 62.338 63.158 25.10 6.28 0.00 4.18
388 420 2.880879 CATCGTCGTGGCCTCGTG 60.881 66.667 25.10 18.70 0.00 4.35
389 421 4.129737 ATCGTCGTGGCCTCGTGG 62.130 66.667 25.10 17.87 0.00 4.94
392 424 4.736896 GTCGTGGCCTCGTGGGTC 62.737 72.222 25.10 9.47 40.85 4.46
400 432 2.574018 CCTCGTGGGTCAGCTGTCA 61.574 63.158 14.67 8.25 0.00 3.58
436 468 1.852067 GCAGTTGGCCACGTACAAGG 61.852 60.000 3.88 0.00 36.11 3.61
476 508 2.048127 GGCGGTGTCCTCTGTGAC 60.048 66.667 0.00 0.00 35.77 3.67
481 513 3.680786 TGTCCTCTGTGACGGGCG 61.681 66.667 0.00 0.00 38.11 6.13
499 531 4.367023 GCGGGTGCGTGTACCAGA 62.367 66.667 11.06 0.00 42.69 3.86
500 532 2.431942 CGGGTGCGTGTACCAGAC 60.432 66.667 9.37 0.00 42.69 3.51
501 533 2.927580 CGGGTGCGTGTACCAGACT 61.928 63.158 9.37 0.00 42.69 3.24
502 534 1.374252 GGGTGCGTGTACCAGACTG 60.374 63.158 9.37 0.00 42.69 3.51
504 536 2.027625 GTGCGTGTACCAGACTGGC 61.028 63.158 21.95 6.79 42.67 4.85
506 538 3.056458 CGTGTACCAGACTGGCCA 58.944 61.111 21.95 15.23 42.67 5.36
509 541 0.905357 GTGTACCAGACTGGCCATCT 59.095 55.000 21.95 8.99 42.67 2.90
510 542 0.904649 TGTACCAGACTGGCCATCTG 59.095 55.000 26.05 26.05 42.67 2.90
512 544 1.960040 TACCAGACTGGCCATCTGCG 61.960 60.000 26.93 23.00 42.67 5.18
513 545 2.513204 CAGACTGGCCATCTGCGG 60.513 66.667 23.48 8.68 42.61 5.69
515 547 2.045926 GACTGGCCATCTGCGGTT 60.046 61.111 5.51 0.00 42.61 4.44
517 549 1.648467 GACTGGCCATCTGCGGTTTC 61.648 60.000 5.51 0.00 42.61 2.78
537 825 1.360551 CGACAGCCGGAGATCGAAT 59.639 57.895 5.05 0.00 42.43 3.34
546 834 1.409064 CGGAGATCGAATTGGAGGTGA 59.591 52.381 0.00 0.00 42.43 4.02
547 835 2.544694 CGGAGATCGAATTGGAGGTGAG 60.545 54.545 0.00 0.00 42.43 3.51
548 836 2.224161 GGAGATCGAATTGGAGGTGAGG 60.224 54.545 0.00 0.00 0.00 3.86
562 850 3.462678 GAGGGTGGACGGAGGAGC 61.463 72.222 0.00 0.00 0.00 4.70
655 943 4.200283 CGCGCTCCCCTGTCTCTC 62.200 72.222 5.56 0.00 0.00 3.20
690 985 1.378119 GGACGGGATGGGTTGGAAC 60.378 63.158 0.00 0.00 0.00 3.62
691 986 1.743995 GACGGGATGGGTTGGAACG 60.744 63.158 0.00 0.00 0.00 3.95
697 992 2.478335 GATGGGTTGGAACGGAGGCA 62.478 60.000 0.00 0.00 0.00 4.75
721 1016 5.705397 ATCCCTTGTCAAGATTCAGATCA 57.295 39.130 14.42 0.00 34.60 2.92
724 1019 3.626670 CCTTGTCAAGATTCAGATCAGGC 59.373 47.826 14.42 0.00 34.60 4.85
726 1021 2.208431 GTCAAGATTCAGATCAGGCGG 58.792 52.381 0.00 0.00 34.60 6.13
739 1034 2.440247 GGCGGGGATCAGGTTTGG 60.440 66.667 0.00 0.00 0.00 3.28
768 1063 5.059404 TGGAAAGAAAAATCAGAATCGGC 57.941 39.130 0.00 0.00 0.00 5.54
778 1073 0.940126 CAGAATCGGCGAGGATTTGG 59.060 55.000 17.22 0.00 36.79 3.28
807 1102 3.561241 GGGCCGGGAAGGAGATCC 61.561 72.222 2.18 0.00 45.00 3.36
822 1117 3.309582 TCCGTCTGGAATGGAGCC 58.690 61.111 0.00 0.00 42.85 4.70
830 1125 3.321111 GTCTGGAATGGAGCCGATTACTA 59.679 47.826 0.00 0.00 0.00 1.82
842 1137 3.372954 CCGATTACTAGCAGTGTAGCAC 58.627 50.000 0.00 0.00 36.85 4.40
853 1170 5.111989 AGCAGTGTAGCACATGTATGTAAG 58.888 41.667 0.00 0.00 39.39 2.34
928 1254 5.989168 TCTCACCGAACGCATATTGATTTAT 59.011 36.000 0.00 0.00 0.00 1.40
929 1255 7.149307 TCTCACCGAACGCATATTGATTTATA 58.851 34.615 0.00 0.00 0.00 0.98
931 1257 6.926826 TCACCGAACGCATATTGATTTATAGT 59.073 34.615 0.00 0.00 0.00 2.12
933 1259 8.160342 CACCGAACGCATATTGATTTATAGTAC 58.840 37.037 0.00 0.00 0.00 2.73
934 1260 8.086522 ACCGAACGCATATTGATTTATAGTACT 58.913 33.333 0.00 0.00 0.00 2.73
935 1261 9.563898 CCGAACGCATATTGATTTATAGTACTA 57.436 33.333 4.77 4.77 0.00 1.82
967 1299 5.437946 ACGCGATCATCTCTCCCTATATAA 58.562 41.667 15.93 0.00 0.00 0.98
1054 1402 6.998074 TCATATCACACATTTTCCCCATCTAC 59.002 38.462 0.00 0.00 0.00 2.59
1056 1404 4.331968 TCACACATTTTCCCCATCTACAC 58.668 43.478 0.00 0.00 0.00 2.90
1173 1532 2.185608 GACGCCTTGCTCCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
1196 1555 0.388006 CCATTGTTTTTCCGGTCGCC 60.388 55.000 0.00 0.00 0.00 5.54
1212 1575 1.866925 GCCGTCTAACTTGTGGTGC 59.133 57.895 0.00 0.00 0.00 5.01
1253 1616 2.501610 GCCGGGAGAAGCTACAGG 59.498 66.667 2.18 0.00 32.70 4.00
1310 1681 2.167861 GGTGAAGATCTGCGTCCGC 61.168 63.158 4.42 4.42 42.35 5.54
1504 1882 2.440627 AGCAGATGGATGGCAACTGATA 59.559 45.455 0.00 0.00 37.61 2.15
1514 1897 1.359848 GCAACTGATACGGTGAGGTG 58.640 55.000 0.00 0.00 0.00 4.00
1515 1898 1.337823 GCAACTGATACGGTGAGGTGT 60.338 52.381 0.00 0.00 0.00 4.16
1516 1899 2.094390 GCAACTGATACGGTGAGGTGTA 60.094 50.000 0.00 0.00 0.00 2.90
1552 1935 2.267426 TGCGTGATCGTAAAGGTGATG 58.733 47.619 0.00 0.00 39.49 3.07
1570 1953 0.033601 TGGTGGTTGACAAGTTGGCT 60.034 50.000 10.75 0.00 0.00 4.75
1634 2017 3.645687 GCTTGGGGGCATGGAATAAATTA 59.354 43.478 0.00 0.00 0.00 1.40
1635 2018 4.286808 GCTTGGGGGCATGGAATAAATTAT 59.713 41.667 0.00 0.00 0.00 1.28
1636 2019 5.483583 GCTTGGGGGCATGGAATAAATTATA 59.516 40.000 0.00 0.00 0.00 0.98
1637 2020 6.574269 GCTTGGGGGCATGGAATAAATTATAC 60.574 42.308 0.00 0.00 0.00 1.47
1638 2021 6.226272 TGGGGGCATGGAATAAATTATACT 57.774 37.500 0.00 0.00 0.00 2.12
1641 2024 8.235230 TGGGGGCATGGAATAAATTATACTTTA 58.765 33.333 0.00 0.00 0.00 1.85
1680 2074 2.682856 AGTTGAATGTTCGTGTGTTGCT 59.317 40.909 0.00 0.00 0.00 3.91
1764 2160 9.599322 GTCGAATAATGATGATATGTGGTTTTC 57.401 33.333 0.00 0.00 0.00 2.29
1765 2161 8.495148 TCGAATAATGATGATATGTGGTTTTCG 58.505 33.333 0.00 0.00 0.00 3.46
1816 2212 6.482308 TCTTTTCCCTACTTGTTTTCTTCTCG 59.518 38.462 0.00 0.00 0.00 4.04
1821 2217 5.048713 CCCTACTTGTTTTCTTCTCGCAATT 60.049 40.000 0.00 0.00 0.00 2.32
1823 2219 5.248870 ACTTGTTTTCTTCTCGCAATTGT 57.751 34.783 7.40 0.00 0.00 2.71
1839 2235 4.496673 GCAATTGTCGTGTCTTGTTAACCA 60.497 41.667 7.40 0.00 0.00 3.67
1841 2237 5.607119 ATTGTCGTGTCTTGTTAACCATC 57.393 39.130 2.48 0.00 0.00 3.51
1854 2250 2.503895 AACCATCCTCTCCTTGCAAG 57.496 50.000 19.93 19.93 0.00 4.01
1876 2272 3.064900 AGACAACATCTTTCTCCCAGC 57.935 47.619 0.00 0.00 31.62 4.85
1877 2273 2.087646 GACAACATCTTTCTCCCAGCC 58.912 52.381 0.00 0.00 0.00 4.85
1878 2274 1.272147 ACAACATCTTTCTCCCAGCCC 60.272 52.381 0.00 0.00 0.00 5.19
1939 2335 2.938451 TCTAACATTGCCATCGCTTCAG 59.062 45.455 0.00 0.00 35.36 3.02
1948 2344 2.418746 GCCATCGCTTCAGAAGTCCTTA 60.419 50.000 11.94 0.00 0.00 2.69
1953 2349 5.000012 TCGCTTCAGAAGTCCTTAATCTC 58.000 43.478 11.94 0.00 0.00 2.75
1956 2352 3.422417 TCAGAAGTCCTTAATCTCGCG 57.578 47.619 0.00 0.00 0.00 5.87
1963 2359 1.344438 TCCTTAATCTCGCGATGCCAT 59.656 47.619 10.36 0.00 0.00 4.40
1964 2360 1.728971 CCTTAATCTCGCGATGCCATC 59.271 52.381 10.36 0.00 0.00 3.51
1971 2367 1.008194 CGCGATGCCATCATTTGGG 60.008 57.895 0.00 0.00 46.55 4.12
1979 2375 2.299582 TGCCATCATTTGGGAAACTGTG 59.700 45.455 0.00 0.00 43.86 3.66
1983 2379 5.367302 CCATCATTTGGGAAACTGTGTTTT 58.633 37.500 0.00 0.00 42.33 2.43
1990 2386 8.672815 CATTTGGGAAACTGTGTTTTGTTTTAT 58.327 29.630 0.00 0.00 36.64 1.40
1993 2389 7.038659 TGGGAAACTGTGTTTTGTTTTATCAG 58.961 34.615 0.00 0.00 36.64 2.90
2008 2404 8.070034 TGTTTTATCAGATCAATGAAATGCCT 57.930 30.769 0.00 0.00 31.76 4.75
2043 2442 2.418197 GCGATGGTGGTGTACTGTATGT 60.418 50.000 0.00 0.00 0.00 2.29
2066 2465 9.965824 ATGTCCGATTTATAAATGAAATGGTTC 57.034 29.630 15.39 0.00 0.00 3.62
2067 2466 9.184523 TGTCCGATTTATAAATGAAATGGTTCT 57.815 29.630 15.39 0.00 34.60 3.01
2087 2486 6.216569 GTTCTTCAAAACCCCAAAGAATCTC 58.783 40.000 0.00 0.00 39.26 2.75
2088 2487 5.705400 TCTTCAAAACCCCAAAGAATCTCT 58.295 37.500 0.00 0.00 0.00 3.10
2090 2489 7.470192 TCTTCAAAACCCCAAAGAATCTCTAT 58.530 34.615 0.00 0.00 0.00 1.98
2095 2494 3.775316 ACCCCAAAGAATCTCTATCGTGT 59.225 43.478 0.00 0.00 0.00 4.49
2103 2502 5.605534 AGAATCTCTATCGTGTTTCATGGG 58.394 41.667 0.00 0.00 0.00 4.00
2123 2522 2.359900 GTCTCTTCCACGGATGCATTT 58.640 47.619 0.00 0.00 0.00 2.32
2129 2528 2.234143 TCCACGGATGCATTTGACAAA 58.766 42.857 0.00 2.48 0.00 2.83
2130 2529 2.030363 TCCACGGATGCATTTGACAAAC 60.030 45.455 0.00 0.00 0.00 2.93
2163 2563 6.622896 GCTTAGCCACTTACACAATACAAAGG 60.623 42.308 0.00 0.00 0.00 3.11
2217 2618 6.126390 TGTTACTCCAATGGATCCTTCATCAT 60.126 38.462 14.23 0.00 32.33 2.45
2225 2626 8.867097 CCAATGGATCCTTCATCATTCTATTTT 58.133 33.333 14.23 0.00 32.33 1.82
2278 2679 5.883661 AGAGAACGCCATTGAAACAATATG 58.116 37.500 0.00 0.00 0.00 1.78
2284 2685 3.450457 GCCATTGAAACAATATGTGGGGA 59.550 43.478 0.00 0.00 0.00 4.81
2288 2689 4.380843 TGAAACAATATGTGGGGAGTGT 57.619 40.909 0.00 0.00 0.00 3.55
2290 2691 2.806945 ACAATATGTGGGGAGTGTGG 57.193 50.000 0.00 0.00 0.00 4.17
2291 2692 1.340991 ACAATATGTGGGGAGTGTGGC 60.341 52.381 0.00 0.00 0.00 5.01
2346 2747 5.772825 TCTAAGTGCCATGCAATATTTCC 57.227 39.130 0.00 0.00 41.47 3.13
2353 2754 3.798337 GCCATGCAATATTTCCTTTCACG 59.202 43.478 0.00 0.00 0.00 4.35
2367 2768 8.475331 TTTCCTTTCACGAGATAACTCAATAC 57.525 34.615 0.59 0.00 42.72 1.89
2368 2769 6.570692 TCCTTTCACGAGATAACTCAATACC 58.429 40.000 0.59 0.00 42.72 2.73
2379 2781 9.091220 GAGATAACTCAATACCCCTTGTATACT 57.909 37.037 4.17 0.00 42.21 2.12
2380 2782 9.448587 AGATAACTCAATACCCCTTGTATACTT 57.551 33.333 4.17 0.00 39.28 2.24
2381 2783 9.490379 GATAACTCAATACCCCTTGTATACTTG 57.510 37.037 4.17 0.00 39.28 3.16
2382 2784 6.248569 ACTCAATACCCCTTGTATACTTGG 57.751 41.667 4.17 6.14 39.28 3.61
2383 2785 5.968167 ACTCAATACCCCTTGTATACTTGGA 59.032 40.000 13.77 0.00 39.28 3.53
2414 2816 5.474532 TCATAAATGCATACCTCATTCAGCC 59.525 40.000 0.00 0.00 33.41 4.85
2422 2824 2.747460 TCATTCAGCCGCACCTGC 60.747 61.111 0.00 0.00 32.87 4.85
2428 2830 1.005867 CAGCCGCACCTGCAAAAAT 60.006 52.632 0.00 0.00 42.21 1.82
2460 2862 2.988010 TAGCAAGTGATTCGATGGCT 57.012 45.000 0.00 0.00 0.00 4.75
2520 2922 6.823689 TGTTCTTGGATGAAATTCTAGTAGGC 59.176 38.462 0.00 0.00 0.00 3.93
2535 2937 4.487714 AGTAGGCAAAGTAGCATAAGCA 57.512 40.909 0.00 0.00 45.49 3.91
2550 2952 5.826737 AGCATAAGCAGCAGAATATCAGTTT 59.173 36.000 0.00 0.00 45.49 2.66
2566 2968 5.186996 TCAGTTTCAAGAATGTTGGCTTC 57.813 39.130 0.00 0.00 0.00 3.86
2582 2984 1.673033 GCTTCTAGAGCCTCGTGCAAA 60.673 52.381 0.00 0.00 46.01 3.68
2609 3011 3.223674 TGGAGAAAAAGGGAAGTCCAC 57.776 47.619 0.00 0.00 38.24 4.02
2610 3012 2.512056 TGGAGAAAAAGGGAAGTCCACA 59.488 45.455 0.00 0.00 38.24 4.17
2617 3019 2.034221 GGAAGTCCACACAGGGGC 59.966 66.667 0.00 0.00 38.24 5.80
2622 3024 0.341961 AGTCCACACAGGGGCCTATA 59.658 55.000 0.84 0.00 38.24 1.31
2623 3025 1.061346 AGTCCACACAGGGGCCTATAT 60.061 52.381 0.84 0.00 38.24 0.86
2624 3026 1.774856 GTCCACACAGGGGCCTATATT 59.225 52.381 0.84 0.00 38.24 1.28
2625 3027 1.774254 TCCACACAGGGGCCTATATTG 59.226 52.381 0.84 0.00 38.24 1.90
2626 3028 1.202927 CCACACAGGGGCCTATATTGG 60.203 57.143 0.84 1.24 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.979238 TCTAAAAGAGAGACGCCTAATTAAGC 59.021 38.462 0.00 0.00 0.00 3.09
1 2 8.928270 TTCTAAAAGAGAGACGCCTAATTAAG 57.072 34.615 0.00 0.00 34.93 1.85
2 3 9.886132 ATTTCTAAAAGAGAGACGCCTAATTAA 57.114 29.630 0.00 0.00 34.93 1.40
5 6 8.145122 CCTATTTCTAAAAGAGAGACGCCTAAT 58.855 37.037 0.00 0.00 34.93 1.73
6 7 7.490000 CCTATTTCTAAAAGAGAGACGCCTAA 58.510 38.462 0.00 0.00 34.93 2.69
7 8 6.461231 GCCTATTTCTAAAAGAGAGACGCCTA 60.461 42.308 0.00 0.00 34.93 3.93
8 9 5.682730 GCCTATTTCTAAAAGAGAGACGCCT 60.683 44.000 0.00 0.00 34.93 5.52
9 10 4.508492 GCCTATTTCTAAAAGAGAGACGCC 59.492 45.833 0.00 0.00 34.93 5.68
10 11 5.109903 TGCCTATTTCTAAAAGAGAGACGC 58.890 41.667 0.00 0.00 34.93 5.19
11 12 7.254590 CCAATGCCTATTTCTAAAAGAGAGACG 60.255 40.741 0.00 0.00 34.93 4.18
12 13 7.554476 ACCAATGCCTATTTCTAAAAGAGAGAC 59.446 37.037 0.00 0.00 34.93 3.36
13 14 7.554118 CACCAATGCCTATTTCTAAAAGAGAGA 59.446 37.037 0.00 0.00 34.93 3.10
14 15 7.680588 GCACCAATGCCTATTTCTAAAAGAGAG 60.681 40.741 0.00 0.00 46.97 3.20
15 16 6.095440 GCACCAATGCCTATTTCTAAAAGAGA 59.905 38.462 0.00 0.00 46.97 3.10
16 17 6.268566 GCACCAATGCCTATTTCTAAAAGAG 58.731 40.000 0.00 0.00 46.97 2.85
17 18 6.207691 GCACCAATGCCTATTTCTAAAAGA 57.792 37.500 0.00 0.00 46.97 2.52
32 33 4.954875 TGGGTTTTTCTAAAGCACCAATG 58.045 39.130 0.00 0.00 42.19 2.82
33 34 5.622346 TTGGGTTTTTCTAAAGCACCAAT 57.378 34.783 0.00 0.00 42.19 3.16
34 35 5.622346 ATTGGGTTTTTCTAAAGCACCAA 57.378 34.783 0.00 0.00 42.19 3.67
35 36 5.622346 AATTGGGTTTTTCTAAAGCACCA 57.378 34.783 0.00 0.00 42.19 4.17
36 37 8.615878 AATAAATTGGGTTTTTCTAAAGCACC 57.384 30.769 0.00 0.00 42.19 5.01
49 50 9.875691 GAGATGCTTAGAAAAATAAATTGGGTT 57.124 29.630 0.00 0.00 0.00 4.11
50 51 9.259832 AGAGATGCTTAGAAAAATAAATTGGGT 57.740 29.630 0.00 0.00 0.00 4.51
51 52 9.741647 GAGAGATGCTTAGAAAAATAAATTGGG 57.258 33.333 0.00 0.00 0.00 4.12
56 57 9.846248 GCTTTGAGAGATGCTTAGAAAAATAAA 57.154 29.630 0.00 0.00 0.00 1.40
57 58 9.013229 TGCTTTGAGAGATGCTTAGAAAAATAA 57.987 29.630 0.00 0.00 0.00 1.40
58 59 8.454106 GTGCTTTGAGAGATGCTTAGAAAAATA 58.546 33.333 0.00 0.00 0.00 1.40
59 60 7.311408 GTGCTTTGAGAGATGCTTAGAAAAAT 58.689 34.615 0.00 0.00 0.00 1.82
60 61 6.294176 GGTGCTTTGAGAGATGCTTAGAAAAA 60.294 38.462 0.00 0.00 0.00 1.94
61 62 5.182001 GGTGCTTTGAGAGATGCTTAGAAAA 59.818 40.000 0.00 0.00 0.00 2.29
62 63 4.697352 GGTGCTTTGAGAGATGCTTAGAAA 59.303 41.667 0.00 0.00 0.00 2.52
63 64 4.019860 AGGTGCTTTGAGAGATGCTTAGAA 60.020 41.667 0.00 0.00 0.00 2.10
64 65 3.517100 AGGTGCTTTGAGAGATGCTTAGA 59.483 43.478 0.00 0.00 0.00 2.10
65 66 3.871485 AGGTGCTTTGAGAGATGCTTAG 58.129 45.455 0.00 0.00 0.00 2.18
66 67 3.988976 AGGTGCTTTGAGAGATGCTTA 57.011 42.857 0.00 0.00 0.00 3.09
67 68 2.818432 CAAGGTGCTTTGAGAGATGCTT 59.182 45.455 0.00 0.00 0.00 3.91
68 69 2.434428 CAAGGTGCTTTGAGAGATGCT 58.566 47.619 0.00 0.00 0.00 3.79
69 70 1.135460 GCAAGGTGCTTTGAGAGATGC 60.135 52.381 0.00 0.00 40.96 3.91
70 71 2.156917 TGCAAGGTGCTTTGAGAGATG 58.843 47.619 1.43 0.00 45.31 2.90
71 72 2.574006 TGCAAGGTGCTTTGAGAGAT 57.426 45.000 1.43 0.00 45.31 2.75
72 73 2.574006 ATGCAAGGTGCTTTGAGAGA 57.426 45.000 0.00 0.00 45.31 3.10
78 79 3.981211 CTTGTACAATGCAAGGTGCTTT 58.019 40.909 9.13 0.00 45.31 3.51
79 80 3.648339 CTTGTACAATGCAAGGTGCTT 57.352 42.857 9.13 0.00 45.31 3.91
85 86 2.161855 TCAGGCCTTGTACAATGCAAG 58.838 47.619 29.20 22.10 42.00 4.01
86 87 2.161855 CTCAGGCCTTGTACAATGCAA 58.838 47.619 29.20 16.91 34.30 4.08
87 88 1.825090 CTCAGGCCTTGTACAATGCA 58.175 50.000 29.20 13.85 34.30 3.96
88 89 0.453390 GCTCAGGCCTTGTACAATGC 59.547 55.000 23.06 23.06 0.00 3.56
127 128 4.787999 GCATGAGCTTCTTGCAGC 57.212 55.556 14.70 0.00 44.16 5.25
139 140 5.129634 TGTAACTTTGTTCCTTCTGCATGA 58.870 37.500 0.00 0.00 0.00 3.07
141 142 7.944729 ATATGTAACTTTGTTCCTTCTGCAT 57.055 32.000 0.00 0.00 0.00 3.96
157 158 8.788325 AGTTTGGGTTCAGTAGAATATGTAAC 57.212 34.615 0.00 0.00 35.92 2.50
189 190 1.669760 CTCAACCGTTGGCGCCTTA 60.670 57.895 29.70 13.30 36.67 2.69
195 207 1.006571 TCGAGTCTCAACCGTTGGC 60.007 57.895 11.35 2.94 0.00 4.52
200 212 1.666311 GGTGAACTCGAGTCTCAACCG 60.666 57.143 23.80 0.00 0.00 4.44
202 214 3.119779 CCTAGGTGAACTCGAGTCTCAAC 60.120 52.174 25.49 25.49 0.00 3.18
203 215 3.082548 CCTAGGTGAACTCGAGTCTCAA 58.917 50.000 20.33 8.95 0.00 3.02
223 235 1.237285 ATGAGTTCAAGTGTGCCGCC 61.237 55.000 0.00 0.00 0.00 6.13
230 258 3.809832 AGTTTGGTCGATGAGTTCAAGTG 59.190 43.478 0.00 0.00 0.00 3.16
250 278 0.110328 CTCGTCGTGCGTTCACTAGT 60.110 55.000 0.00 0.00 40.99 2.57
251 279 0.165295 TCTCGTCGTGCGTTCACTAG 59.835 55.000 0.00 0.00 40.99 2.57
252 280 0.165295 CTCTCGTCGTGCGTTCACTA 59.835 55.000 0.00 0.00 40.99 2.74
253 281 1.082038 CTCTCGTCGTGCGTTCACT 60.082 57.895 0.00 0.00 40.99 3.41
260 288 1.587613 GATGGCTCTCTCGTCGTGC 60.588 63.158 0.00 0.00 0.00 5.34
269 297 2.653702 CCCCGATCGATGGCTCTC 59.346 66.667 18.66 0.00 0.00 3.20
278 306 2.201022 ATCTCCGTTCCCCCGATCG 61.201 63.158 8.51 8.51 0.00 3.69
281 309 2.762459 CCATCTCCGTTCCCCCGA 60.762 66.667 0.00 0.00 0.00 5.14
282 310 4.547367 GCCATCTCCGTTCCCCCG 62.547 72.222 0.00 0.00 0.00 5.73
283 311 4.547367 CGCCATCTCCGTTCCCCC 62.547 72.222 0.00 0.00 0.00 5.40
284 312 3.467226 TCGCCATCTCCGTTCCCC 61.467 66.667 0.00 0.00 0.00 4.81
292 320 1.520342 GTGAGCCTGTCGCCATCTC 60.520 63.158 0.00 0.00 38.78 2.75
303 331 1.079127 CGTCCATTTCGGTGAGCCT 60.079 57.895 0.00 0.00 35.57 4.58
311 339 2.776072 GCGTCACCGTCCATTTCG 59.224 61.111 0.00 0.00 36.15 3.46
313 341 3.419759 GCGCGTCACCGTCCATTT 61.420 61.111 8.43 0.00 36.15 2.32
369 401 2.579787 CGAGGCCACGACGATGTC 60.580 66.667 18.51 0.00 35.09 3.06
370 402 3.371063 ACGAGGCCACGACGATGT 61.371 61.111 29.67 1.97 37.03 3.06
382 414 2.262915 GACAGCTGACCCACGAGG 59.737 66.667 23.35 0.00 43.78 4.63
383 415 1.080230 CTGACAGCTGACCCACGAG 60.080 63.158 23.35 3.23 0.00 4.18
384 416 3.051210 CTGACAGCTGACCCACGA 58.949 61.111 23.35 0.00 0.00 4.35
385 417 2.740055 GCTGACAGCTGACCCACG 60.740 66.667 23.35 9.79 38.45 4.94
386 418 1.963338 GTGCTGACAGCTGACCCAC 60.963 63.158 26.94 18.97 42.97 4.61
387 419 2.427320 GTGCTGACAGCTGACCCA 59.573 61.111 26.94 13.72 42.97 4.51
388 420 2.359230 GGTGCTGACAGCTGACCC 60.359 66.667 26.94 17.11 42.97 4.46
389 421 1.963338 GTGGTGCTGACAGCTGACC 60.963 63.158 26.94 25.13 44.77 4.02
390 422 1.963338 GGTGGTGCTGACAGCTGAC 60.963 63.158 26.94 15.92 44.77 3.51
391 423 2.427320 GGTGGTGCTGACAGCTGA 59.573 61.111 26.94 6.17 44.77 4.26
392 424 3.046087 CGGTGGTGCTGACAGCTG 61.046 66.667 26.94 13.48 44.77 4.24
393 425 4.996434 GCGGTGGTGCTGACAGCT 62.996 66.667 26.94 0.00 44.77 4.24
395 427 3.046087 CTGCGGTGGTGCTGACAG 61.046 66.667 0.00 0.00 36.04 3.51
396 428 4.624364 CCTGCGGTGGTGCTGACA 62.624 66.667 0.00 0.00 36.04 3.58
463 495 2.048127 GCCCGTCACAGAGGACAC 60.048 66.667 0.00 0.00 37.66 3.67
484 516 1.374252 CAGTCTGGTACACGCACCC 60.374 63.158 0.00 0.00 37.84 4.61
494 526 2.673523 GCAGATGGCCAGTCTGGT 59.326 61.111 30.11 10.08 42.58 4.00
497 529 2.129555 AAACCGCAGATGGCCAGTCT 62.130 55.000 13.05 11.64 40.31 3.24
498 530 1.648467 GAAACCGCAGATGGCCAGTC 61.648 60.000 13.05 9.33 40.31 3.51
499 531 1.675641 GAAACCGCAGATGGCCAGT 60.676 57.895 13.05 0.00 40.31 4.00
500 532 2.753966 CGAAACCGCAGATGGCCAG 61.754 63.158 13.05 0.00 40.31 4.85
501 533 2.745884 CGAAACCGCAGATGGCCA 60.746 61.111 8.56 8.56 40.31 5.36
513 545 3.479269 CTCCGGCTGTCGCGAAAC 61.479 66.667 12.06 0.00 37.59 2.78
515 547 3.411418 GATCTCCGGCTGTCGCGAA 62.411 63.158 12.06 0.00 37.59 4.70
519 551 0.249073 AATTCGATCTCCGGCTGTCG 60.249 55.000 13.66 13.66 39.14 4.35
520 552 1.212616 CAATTCGATCTCCGGCTGTC 58.787 55.000 0.00 0.00 39.14 3.51
537 825 2.214216 CGTCCACCCTCACCTCCAA 61.214 63.158 0.00 0.00 0.00 3.53
546 834 4.316823 TGCTCCTCCGTCCACCCT 62.317 66.667 0.00 0.00 0.00 4.34
547 835 4.083862 GTGCTCCTCCGTCCACCC 62.084 72.222 0.00 0.00 0.00 4.61
548 836 4.436998 CGTGCTCCTCCGTCCACC 62.437 72.222 0.00 0.00 0.00 4.61
649 937 1.028868 GTGCAAGCCATGGGAGAGAC 61.029 60.000 15.13 0.00 0.00 3.36
655 943 2.259204 CGTTGTGCAAGCCATGGG 59.741 61.111 15.13 0.00 0.00 4.00
690 985 0.322456 TGACAAGGGATTTGCCTCCG 60.322 55.000 0.00 0.00 40.59 4.63
691 986 1.821136 CTTGACAAGGGATTTGCCTCC 59.179 52.381 7.35 0.00 40.59 4.30
697 992 6.487828 TGATCTGAATCTTGACAAGGGATTT 58.512 36.000 15.13 4.66 32.75 2.17
721 1016 2.677228 CAAACCTGATCCCCGCCT 59.323 61.111 0.00 0.00 0.00 5.52
724 1019 1.004277 TCTTTCCAAACCTGATCCCCG 59.996 52.381 0.00 0.00 0.00 5.73
726 1021 3.448660 CCATTCTTTCCAAACCTGATCCC 59.551 47.826 0.00 0.00 0.00 3.85
768 1063 1.199097 CCACCGAAAACCAAATCCTCG 59.801 52.381 0.00 0.00 0.00 4.63
793 1088 1.455959 AGACGGATCTCCTTCCCGG 60.456 63.158 0.00 0.00 46.83 5.73
807 1102 0.179073 AATCGGCTCCATTCCAGACG 60.179 55.000 0.00 0.00 44.35 4.18
822 1117 4.028852 TGTGCTACACTGCTAGTAATCG 57.971 45.455 0.00 0.00 35.11 3.34
830 1125 3.616956 ACATACATGTGCTACACTGCT 57.383 42.857 9.11 0.00 40.03 4.24
842 1137 4.160736 TCCGCGAGATCTTACATACATG 57.839 45.455 8.23 0.00 0.00 3.21
929 1255 9.381033 AGATGATCGCGTAGTTATTATAGTACT 57.619 33.333 5.77 0.00 0.00 2.73
931 1257 9.597170 AGAGATGATCGCGTAGTTATTATAGTA 57.403 33.333 5.77 0.00 0.00 1.82
933 1259 8.065407 GGAGAGATGATCGCGTAGTTATTATAG 58.935 40.741 5.77 0.00 0.00 1.31
934 1260 7.012138 GGGAGAGATGATCGCGTAGTTATTATA 59.988 40.741 5.77 0.00 0.00 0.98
935 1261 6.183360 GGGAGAGATGATCGCGTAGTTATTAT 60.183 42.308 5.77 0.00 0.00 1.28
936 1262 5.123502 GGGAGAGATGATCGCGTAGTTATTA 59.876 44.000 5.77 0.00 0.00 0.98
1054 1402 5.773575 TGTTTCTTGCAGTCTAGTCTAGTG 58.226 41.667 6.77 0.43 0.00 2.74
1056 1404 6.625362 TCATGTTTCTTGCAGTCTAGTCTAG 58.375 40.000 0.00 0.00 0.00 2.43
1173 1532 2.350388 CGACCGGAAAAACAATGGTCTG 60.350 50.000 9.46 0.00 45.43 3.51
1196 1555 0.512952 GCAGCACCACAAGTTAGACG 59.487 55.000 0.00 0.00 0.00 4.18
1310 1681 3.649277 CTTGGTCTCGCAGTCCCGG 62.649 68.421 0.00 0.00 0.00 5.73
1504 1882 2.350522 CGTACTACTACACCTCACCGT 58.649 52.381 0.00 0.00 0.00 4.83
1514 1897 2.452105 GCAGCTCTTGCGTACTACTAC 58.548 52.381 0.00 0.00 44.09 2.73
1515 1898 2.846039 GCAGCTCTTGCGTACTACTA 57.154 50.000 0.00 0.00 44.09 1.82
1516 1899 3.723554 GCAGCTCTTGCGTACTACT 57.276 52.632 0.00 0.00 44.09 2.57
1552 1935 1.111277 AAGCCAACTTGTCAACCACC 58.889 50.000 0.00 0.00 33.84 4.61
1643 2026 9.739276 AACATTCAACTATCTGACATAAAAGGA 57.261 29.630 0.00 0.00 0.00 3.36
1644 2027 9.994432 GAACATTCAACTATCTGACATAAAAGG 57.006 33.333 0.00 0.00 0.00 3.11
1645 2028 9.694520 CGAACATTCAACTATCTGACATAAAAG 57.305 33.333 0.00 0.00 0.00 2.27
1646 2029 9.214957 ACGAACATTCAACTATCTGACATAAAA 57.785 29.630 0.00 0.00 0.00 1.52
1647 2030 8.655970 CACGAACATTCAACTATCTGACATAAA 58.344 33.333 0.00 0.00 0.00 1.40
1650 2033 6.091305 CACACGAACATTCAACTATCTGACAT 59.909 38.462 0.00 0.00 0.00 3.06
1652 2035 5.405571 ACACACGAACATTCAACTATCTGAC 59.594 40.000 0.00 0.00 0.00 3.51
1654 2037 5.845985 ACACACGAACATTCAACTATCTG 57.154 39.130 0.00 0.00 0.00 2.90
1655 2038 5.334105 GCAACACACGAACATTCAACTATCT 60.334 40.000 0.00 0.00 0.00 1.98
1774 2170 6.801862 GGGAAAAGAATCAGTATTTGTCGTTG 59.198 38.462 0.00 0.00 0.00 4.10
1776 2172 6.238648 AGGGAAAAGAATCAGTATTTGTCGT 58.761 36.000 0.00 0.00 0.00 4.34
1787 2183 8.533569 AAGAAAACAAGTAGGGAAAAGAATCA 57.466 30.769 0.00 0.00 0.00 2.57
1794 2190 4.514066 GCGAGAAGAAAACAAGTAGGGAAA 59.486 41.667 0.00 0.00 0.00 3.13
1816 2212 3.972502 GGTTAACAAGACACGACAATTGC 59.027 43.478 5.05 0.00 0.00 3.56
1821 2217 3.070446 AGGATGGTTAACAAGACACGACA 59.930 43.478 8.10 0.00 0.00 4.35
1823 2219 3.576982 AGAGGATGGTTAACAAGACACGA 59.423 43.478 8.10 0.00 0.00 4.35
1839 2235 2.909006 TGTCTTCTTGCAAGGAGAGGAT 59.091 45.455 33.46 0.00 41.25 3.24
1841 2237 2.810852 GTTGTCTTCTTGCAAGGAGAGG 59.189 50.000 33.46 13.20 41.25 3.69
1854 2250 3.438434 GCTGGGAGAAAGATGTTGTCTTC 59.562 47.826 0.00 0.00 46.39 2.87
1873 2269 0.253327 GTGAAGGGAAGTAGGGGCTG 59.747 60.000 0.00 0.00 0.00 4.85
1874 2270 0.914902 GGTGAAGGGAAGTAGGGGCT 60.915 60.000 0.00 0.00 0.00 5.19
1875 2271 0.914902 AGGTGAAGGGAAGTAGGGGC 60.915 60.000 0.00 0.00 0.00 5.80
1876 2272 1.560146 GAAGGTGAAGGGAAGTAGGGG 59.440 57.143 0.00 0.00 0.00 4.79
1877 2273 2.266279 TGAAGGTGAAGGGAAGTAGGG 58.734 52.381 0.00 0.00 0.00 3.53
1878 2274 4.226168 AGAATGAAGGTGAAGGGAAGTAGG 59.774 45.833 0.00 0.00 0.00 3.18
1948 2344 5.152053 CCAAATGATGGCATCGCGAGATT 62.152 47.826 21.65 12.61 46.03 2.40
1953 2349 4.620437 CCAAATGATGGCATCGCG 57.380 55.556 21.65 0.00 43.80 5.87
1963 2359 5.413309 ACAAAACACAGTTTCCCAAATGA 57.587 34.783 0.00 0.00 0.00 2.57
1964 2360 6.493449 AAACAAAACACAGTTTCCCAAATG 57.507 33.333 0.00 0.00 32.90 2.32
1971 2367 9.515020 TGATCTGATAAAACAAAACACAGTTTC 57.485 29.630 0.00 0.00 36.98 2.78
1983 2379 7.977293 CAGGCATTTCATTGATCTGATAAAACA 59.023 33.333 0.00 0.00 0.00 2.83
1990 2386 3.129813 GTGCAGGCATTTCATTGATCTGA 59.870 43.478 0.00 0.00 0.00 3.27
1993 2389 2.159338 ACGTGCAGGCATTTCATTGATC 60.159 45.455 6.26 0.00 0.00 2.92
2023 2419 3.444916 GACATACAGTACACCACCATCG 58.555 50.000 0.00 0.00 0.00 3.84
2062 2461 4.746535 TTCTTTGGGGTTTTGAAGAACC 57.253 40.909 0.00 0.00 46.70 3.62
2063 2462 6.040955 AGAGATTCTTTGGGGTTTTGAAGAAC 59.959 38.462 0.00 0.00 39.93 3.01
2064 2463 6.136155 AGAGATTCTTTGGGGTTTTGAAGAA 58.864 36.000 0.00 0.00 40.96 2.52
2065 2464 5.705400 AGAGATTCTTTGGGGTTTTGAAGA 58.295 37.500 0.00 0.00 0.00 2.87
2066 2465 7.414540 CGATAGAGATTCTTTGGGGTTTTGAAG 60.415 40.741 0.00 0.00 39.76 3.02
2067 2466 6.374333 CGATAGAGATTCTTTGGGGTTTTGAA 59.626 38.462 0.00 0.00 39.76 2.69
2068 2467 5.880332 CGATAGAGATTCTTTGGGGTTTTGA 59.120 40.000 0.00 0.00 39.76 2.69
2069 2468 5.648092 ACGATAGAGATTCTTTGGGGTTTTG 59.352 40.000 0.00 0.00 41.38 2.44
2087 2486 4.392921 AGAGACCCATGAAACACGATAG 57.607 45.455 0.00 0.00 46.19 2.08
2088 2487 4.382685 GGAAGAGACCCATGAAACACGATA 60.383 45.833 0.00 0.00 0.00 2.92
2090 2489 2.289444 GGAAGAGACCCATGAAACACGA 60.289 50.000 0.00 0.00 0.00 4.35
2095 2494 1.003118 CCGTGGAAGAGACCCATGAAA 59.997 52.381 0.00 0.00 41.97 2.69
2103 2502 2.029838 AATGCATCCGTGGAAGAGAC 57.970 50.000 0.00 0.00 0.00 3.36
2123 2522 1.539388 CTAAGCCATTGCCGTTTGTCA 59.461 47.619 0.00 0.00 38.69 3.58
2189 2590 5.044919 TGAAGGATCCATTGGAGTAACATGT 60.045 40.000 15.82 0.00 34.05 3.21
2191 2592 5.715439 TGAAGGATCCATTGGAGTAACAT 57.285 39.130 15.82 0.00 34.05 2.71
2193 2594 5.684704 TGATGAAGGATCCATTGGAGTAAC 58.315 41.667 15.82 1.50 34.05 2.50
2196 2597 5.133999 AGAATGATGAAGGATCCATTGGAGT 59.866 40.000 15.82 0.00 34.05 3.85
2197 2598 5.632118 AGAATGATGAAGGATCCATTGGAG 58.368 41.667 15.82 0.00 34.05 3.86
2251 2652 2.386661 TTCAATGGCGTTCTCTCTCC 57.613 50.000 0.00 0.00 0.00 3.71
2257 2658 5.401550 CACATATTGTTTCAATGGCGTTCT 58.598 37.500 5.40 0.00 0.00 3.01
2262 2663 3.450457 TCCCCACATATTGTTTCAATGGC 59.550 43.478 5.40 0.00 0.00 4.40
2278 2679 0.827507 AACATTGCCACACTCCCCAC 60.828 55.000 0.00 0.00 0.00 4.61
2284 2685 5.789643 AATGAGTAAAACATTGCCACACT 57.210 34.783 0.00 0.00 36.74 3.55
2288 2689 8.531622 CAATGTAAATGAGTAAAACATTGCCA 57.468 30.769 12.03 0.00 45.86 4.92
2346 2747 5.753921 GGGGTATTGAGTTATCTCGTGAAAG 59.246 44.000 0.00 0.00 43.09 2.62
2353 2754 9.091220 AGTATACAAGGGGTATTGAGTTATCTC 57.909 37.037 5.50 0.00 42.63 2.75
2367 2768 6.833416 TGAATTGATTCCAAGTATACAAGGGG 59.167 38.462 5.50 1.00 35.48 4.79
2368 2769 7.880160 TGAATTGATTCCAAGTATACAAGGG 57.120 36.000 5.50 3.52 35.48 3.95
2379 2781 8.926374 AGGTATGCATTTATGAATTGATTCCAA 58.074 29.630 3.54 0.00 35.97 3.53
2380 2782 8.481492 AGGTATGCATTTATGAATTGATTCCA 57.519 30.769 3.54 0.00 35.97 3.53
2381 2783 8.579006 TGAGGTATGCATTTATGAATTGATTCC 58.421 33.333 3.54 0.00 35.97 3.01
2414 2816 4.036734 AGGTATGATATTTTTGCAGGTGCG 59.963 41.667 0.00 0.00 45.83 5.34
2428 2830 7.814587 CGAATCACTTGCTAATGAGGTATGATA 59.185 37.037 0.00 0.00 0.00 2.15
2496 2898 6.823689 TGCCTACTAGAATTTCATCCAAGAAC 59.176 38.462 0.00 0.00 0.00 3.01
2498 2900 6.560003 TGCCTACTAGAATTTCATCCAAGA 57.440 37.500 0.00 0.00 0.00 3.02
2502 2904 7.041712 GCTACTTTGCCTACTAGAATTTCATCC 60.042 40.741 0.00 0.00 0.00 3.51
2505 2907 6.707290 TGCTACTTTGCCTACTAGAATTTCA 58.293 36.000 0.00 0.00 0.00 2.69
2509 2911 6.931840 GCTTATGCTACTTTGCCTACTAGAAT 59.068 38.462 0.00 0.00 36.03 2.40
2520 2922 4.952262 TTCTGCTGCTTATGCTACTTTG 57.048 40.909 0.00 0.00 40.48 2.77
2535 2937 7.934855 ACATTCTTGAAACTGATATTCTGCT 57.065 32.000 0.00 0.00 0.00 4.24
2550 2952 4.256920 GCTCTAGAAGCCAACATTCTTGA 58.743 43.478 0.00 0.00 45.92 3.02
2582 2984 6.042093 GGACTTCCCTTTTTCTCCAAGATTTT 59.958 38.462 0.00 0.00 0.00 1.82
2589 2991 2.512056 TGTGGACTTCCCTTTTTCTCCA 59.488 45.455 0.00 0.00 35.38 3.86
2590 2992 2.885266 GTGTGGACTTCCCTTTTTCTCC 59.115 50.000 0.00 0.00 35.38 3.71
2593 2995 2.623416 CCTGTGTGGACTTCCCTTTTTC 59.377 50.000 0.00 0.00 38.35 2.29


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

AutoCloner maintained by Alex Coulton.