Multiple sequence alignment - TraesCS1D01G256100

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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 TraesCS1D01G256100 chr1D 100.000 3503 0 0 1 3503 348673613 348670111 0.000000e+00 6469.0
1 TraesCS1D01G256100 chr1D 76.000 375 69 18 1772 2143 405402892 405403248 1.290000e-39 174.0
2 TraesCS1D01G256100 chr1B 94.326 2873 75 35 667 3503 470308413 470305593 0.000000e+00 4322.0
3 TraesCS1D01G256100 chr1B 86.559 558 65 5 114 663 470310628 470310073 1.080000e-169 606.0
4 TraesCS1D01G256100 chr1B 76.871 147 26 7 515 657 16551666 16551524 3.750000e-10 76.8
5 TraesCS1D01G256100 chr1B 76.190 147 27 7 515 657 16536101 16535959 1.740000e-08 71.3
6 TraesCS1D01G256100 chr1A 93.224 2804 100 36 739 3503 449189084 449191836 0.000000e+00 4043.0
7 TraesCS1D01G256100 chr1A 76.142 394 75 15 1752 2143 500961376 500961752 4.620000e-44 189.0
8 TraesCS1D01G256100 chr3B 79.188 394 63 19 1762 2146 573619880 573619497 4.490000e-64 255.0
9 TraesCS1D01G256100 chr3A 78.894 398 59 20 1765 2146 576604626 576604238 2.700000e-61 246.0
10 TraesCS1D01G256100 chr3D 78.772 391 57 23 1762 2147 438265092 438264723 4.520000e-59 239.0
11 TraesCS1D01G256100 chr7B 73.440 625 121 30 59 663 443334849 443334250 3.570000e-45 193.0
12 TraesCS1D01G256100 chr4D 83.846 130 17 4 521 648 495628745 495628618 1.710000e-23 121.0
13 TraesCS1D01G256100 chr2A 76.733 202 42 5 431 629 108250112 108249913 1.330000e-19 108.0
14 TraesCS1D01G256100 chr6B 75.500 200 42 7 453 648 158128540 158128344 1.340000e-14 91.6
15 TraesCS1D01G256100 chr7A 74.500 200 44 7 453 648 156869081 156868885 2.900000e-11 80.5
16 TraesCS1D01G256100 chr7D 94.737 38 2 0 589 626 263953823 263953786 3.780000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G256100 chr1D 348670111 348673613 3502 True 6469 6469 100.0000 1 3503 1 chr1D.!!$R1 3502
1 TraesCS1D01G256100 chr1B 470305593 470310628 5035 True 2464 4322 90.4425 114 3503 2 chr1B.!!$R3 3389
2 TraesCS1D01G256100 chr1A 449189084 449191836 2752 False 4043 4043 93.2240 739 3503 1 chr1A.!!$F1 2764

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
121 122 0.106918 AGGTAGTGAGGGAGCTCTCG 60.107 60.000 14.64 0.0 36.61 4.04 F
665 674 0.168788 CCATGCACATCACGACAACC 59.831 55.000 0.00 0.0 0.00 3.77 F
956 2632 0.542938 CCACTCCTCCACTCCACTCA 60.543 60.000 0.00 0.0 0.00 3.41 F
963 2639 1.001406 CTCCACTCCACTCAACTCCAC 59.999 57.143 0.00 0.0 0.00 4.02 F
2012 3703 0.310232 GGGTATCGTGACGTCTAGCC 59.690 60.000 17.92 15.1 31.45 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 3405 0.030504 CTGCATGCACGAAACACCAA 59.969 50.0 18.46 0.00 0.00 3.67 R
1838 3526 0.250858 TCTTCCAGACGTCGGTGGTA 60.251 55.0 19.92 11.99 35.14 3.25 R
2008 3699 0.458669 GCACGTAGTAGGCAAGGCTA 59.541 55.0 0.00 0.00 41.61 3.93 R
2113 3804 0.606096 TGTTCTCGGCGAGGATGAAA 59.394 50.0 33.93 19.13 0.00 2.69 R
3222 4928 0.252197 GGCTCCCGTCACCAGTTAAT 59.748 55.0 0.00 0.00 0.00 1.40 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 3.801114 CATCGAGTACAGATGAACCCA 57.199 47.619 20.18 0.00 46.09 4.51
25 26 4.123497 CATCGAGTACAGATGAACCCAA 57.877 45.455 20.18 0.00 46.09 4.12
26 27 3.868757 TCGAGTACAGATGAACCCAAG 57.131 47.619 0.00 0.00 0.00 3.61
27 28 2.094182 TCGAGTACAGATGAACCCAAGC 60.094 50.000 0.00 0.00 0.00 4.01
28 29 2.093973 CGAGTACAGATGAACCCAAGCT 60.094 50.000 0.00 0.00 0.00 3.74
29 30 3.526534 GAGTACAGATGAACCCAAGCTC 58.473 50.000 0.00 0.00 0.00 4.09
30 31 2.906389 AGTACAGATGAACCCAAGCTCA 59.094 45.455 0.00 0.00 0.00 4.26
31 32 2.957402 ACAGATGAACCCAAGCTCAA 57.043 45.000 0.00 0.00 0.00 3.02
32 33 3.228188 ACAGATGAACCCAAGCTCAAA 57.772 42.857 0.00 0.00 0.00 2.69
33 34 2.887152 ACAGATGAACCCAAGCTCAAAC 59.113 45.455 0.00 0.00 0.00 2.93
34 35 3.152341 CAGATGAACCCAAGCTCAAACT 58.848 45.455 0.00 0.00 0.00 2.66
35 36 3.571401 CAGATGAACCCAAGCTCAAACTT 59.429 43.478 0.00 0.00 0.00 2.66
36 37 3.571401 AGATGAACCCAAGCTCAAACTTG 59.429 43.478 0.00 0.00 45.42 3.16
46 47 4.622701 AGCTCAAACTTGAATTATCGGC 57.377 40.909 0.00 0.00 36.64 5.54
47 48 4.265073 AGCTCAAACTTGAATTATCGGCT 58.735 39.130 0.00 0.00 36.64 5.52
48 49 4.333926 AGCTCAAACTTGAATTATCGGCTC 59.666 41.667 0.00 0.00 36.64 4.70
49 50 4.333926 GCTCAAACTTGAATTATCGGCTCT 59.666 41.667 0.00 0.00 36.64 4.09
50 51 5.503194 GCTCAAACTTGAATTATCGGCTCTC 60.503 44.000 0.00 0.00 36.64 3.20
51 52 5.487433 TCAAACTTGAATTATCGGCTCTCA 58.513 37.500 0.00 0.00 33.55 3.27
52 53 5.351465 TCAAACTTGAATTATCGGCTCTCAC 59.649 40.000 0.00 0.00 33.55 3.51
53 54 3.798202 ACTTGAATTATCGGCTCTCACC 58.202 45.455 0.00 0.00 0.00 4.02
54 55 2.910688 TGAATTATCGGCTCTCACCC 57.089 50.000 0.00 0.00 0.00 4.61
55 56 1.068588 TGAATTATCGGCTCTCACCCG 59.931 52.381 0.00 0.00 46.88 5.28
65 66 4.602340 GGCTCTCACCCGATTTTATAGA 57.398 45.455 0.00 0.00 0.00 1.98
66 67 5.153950 GGCTCTCACCCGATTTTATAGAT 57.846 43.478 0.00 0.00 0.00 1.98
67 68 6.282199 GGCTCTCACCCGATTTTATAGATA 57.718 41.667 0.00 0.00 0.00 1.98
68 69 6.698380 GGCTCTCACCCGATTTTATAGATAA 58.302 40.000 0.00 0.00 0.00 1.75
69 70 7.159372 GGCTCTCACCCGATTTTATAGATAAA 58.841 38.462 0.00 0.00 0.00 1.40
70 71 7.332182 GGCTCTCACCCGATTTTATAGATAAAG 59.668 40.741 0.00 0.00 34.13 1.85
71 72 7.148557 GCTCTCACCCGATTTTATAGATAAAGC 60.149 40.741 0.00 0.00 34.13 3.51
72 73 7.732025 TCTCACCCGATTTTATAGATAAAGCA 58.268 34.615 0.00 0.00 34.13 3.91
73 74 7.656137 TCTCACCCGATTTTATAGATAAAGCAC 59.344 37.037 0.00 0.00 34.13 4.40
74 75 7.276658 TCACCCGATTTTATAGATAAAGCACA 58.723 34.615 0.00 0.00 34.13 4.57
75 76 7.936847 TCACCCGATTTTATAGATAAAGCACAT 59.063 33.333 0.00 0.00 34.13 3.21
76 77 9.214957 CACCCGATTTTATAGATAAAGCACATA 57.785 33.333 0.00 0.00 34.13 2.29
77 78 9.787435 ACCCGATTTTATAGATAAAGCACATAA 57.213 29.630 0.00 0.00 34.13 1.90
88 89 8.487313 AGATAAAGCACATAAACAATACACGA 57.513 30.769 0.00 0.00 0.00 4.35
89 90 8.388103 AGATAAAGCACATAAACAATACACGAC 58.612 33.333 0.00 0.00 0.00 4.34
90 91 4.577687 AGCACATAAACAATACACGACG 57.422 40.909 0.00 0.00 0.00 5.12
91 92 4.239304 AGCACATAAACAATACACGACGA 58.761 39.130 0.00 0.00 0.00 4.20
92 93 4.326278 AGCACATAAACAATACACGACGAG 59.674 41.667 0.00 0.00 0.00 4.18
93 94 4.325204 GCACATAAACAATACACGACGAGA 59.675 41.667 0.00 0.00 0.00 4.04
94 95 5.164031 GCACATAAACAATACACGACGAGAA 60.164 40.000 0.00 0.00 0.00 2.87
95 96 6.458503 CACATAAACAATACACGACGAGAAG 58.541 40.000 0.00 0.00 0.00 2.85
96 97 6.307077 CACATAAACAATACACGACGAGAAGA 59.693 38.462 0.00 0.00 0.00 2.87
97 98 6.864685 ACATAAACAATACACGACGAGAAGAA 59.135 34.615 0.00 0.00 0.00 2.52
98 99 7.544566 ACATAAACAATACACGACGAGAAGAAT 59.455 33.333 0.00 0.00 0.00 2.40
99 100 9.016623 CATAAACAATACACGACGAGAAGAATA 57.983 33.333 0.00 0.00 0.00 1.75
100 101 6.866179 AACAATACACGACGAGAAGAATAC 57.134 37.500 0.00 0.00 0.00 1.89
101 102 5.946298 ACAATACACGACGAGAAGAATACA 58.054 37.500 0.00 0.00 0.00 2.29
102 103 6.384224 ACAATACACGACGAGAAGAATACAA 58.616 36.000 0.00 0.00 0.00 2.41
103 104 6.527023 ACAATACACGACGAGAAGAATACAAG 59.473 38.462 0.00 0.00 0.00 3.16
104 105 3.834610 ACACGACGAGAAGAATACAAGG 58.165 45.455 0.00 0.00 0.00 3.61
105 106 3.255149 ACACGACGAGAAGAATACAAGGT 59.745 43.478 0.00 0.00 0.00 3.50
106 107 4.456911 ACACGACGAGAAGAATACAAGGTA 59.543 41.667 0.00 0.00 0.00 3.08
107 108 5.029014 CACGACGAGAAGAATACAAGGTAG 58.971 45.833 0.00 0.00 0.00 3.18
108 109 4.699257 ACGACGAGAAGAATACAAGGTAGT 59.301 41.667 0.00 0.00 0.00 2.73
109 110 5.029014 CGACGAGAAGAATACAAGGTAGTG 58.971 45.833 0.00 0.00 0.00 2.74
110 111 5.163784 CGACGAGAAGAATACAAGGTAGTGA 60.164 44.000 0.00 0.00 0.00 3.41
111 112 6.197364 ACGAGAAGAATACAAGGTAGTGAG 57.803 41.667 0.00 0.00 0.00 3.51
112 113 5.125739 ACGAGAAGAATACAAGGTAGTGAGG 59.874 44.000 0.00 0.00 0.00 3.86
117 118 2.921834 TACAAGGTAGTGAGGGAGCT 57.078 50.000 0.00 0.00 0.00 4.09
121 122 0.106918 AGGTAGTGAGGGAGCTCTCG 60.107 60.000 14.64 0.00 36.61 4.04
126 127 0.452585 GTGAGGGAGCTCTCGTACAC 59.547 60.000 19.60 19.60 36.61 2.90
131 132 1.544691 GGGAGCTCTCGTACACAGAAA 59.455 52.381 14.64 0.00 0.00 2.52
137 138 3.616560 GCTCTCGTACACAGAAAATCCCA 60.617 47.826 0.00 0.00 0.00 4.37
164 165 7.712639 GGATAACTGATCAAGACATACACACAT 59.287 37.037 0.00 0.00 36.12 3.21
166 167 6.041423 ACTGATCAAGACATACACACATGA 57.959 37.500 0.00 0.00 0.00 3.07
171 172 9.617523 TGATCAAGACATACACACATGATTATT 57.382 29.630 0.00 0.00 0.00 1.40
172 173 9.874215 GATCAAGACATACACACATGATTATTG 57.126 33.333 0.00 0.00 0.00 1.90
173 174 7.696755 TCAAGACATACACACATGATTATTGC 58.303 34.615 0.00 0.00 0.00 3.56
174 175 6.624352 AGACATACACACATGATTATTGCC 57.376 37.500 0.00 0.00 0.00 4.52
175 176 5.237127 AGACATACACACATGATTATTGCCG 59.763 40.000 0.00 0.00 0.00 5.69
176 177 4.275689 ACATACACACATGATTATTGCCGG 59.724 41.667 0.00 0.00 0.00 6.13
216 224 2.240162 CTGAAGACTACGCCACCCCC 62.240 65.000 0.00 0.00 0.00 5.40
219 227 3.001406 GACTACGCCACCCCCACT 61.001 66.667 0.00 0.00 0.00 4.00
225 233 2.368329 GCCACCCCCACTCCCTAT 60.368 66.667 0.00 0.00 0.00 2.57
235 243 1.341531 CCACTCCCTATGACGCCTAAG 59.658 57.143 0.00 0.00 0.00 2.18
239 247 0.318762 CCCTATGACGCCTAAGCTCC 59.681 60.000 0.00 0.00 36.60 4.70
240 248 1.040646 CCTATGACGCCTAAGCTCCA 58.959 55.000 0.00 0.00 36.60 3.86
241 249 1.620819 CCTATGACGCCTAAGCTCCAT 59.379 52.381 0.00 0.00 36.60 3.41
250 258 2.359900 CCTAAGCTCCATGACAACACC 58.640 52.381 0.00 0.00 0.00 4.16
253 261 0.326264 AGCTCCATGACAACACCCTC 59.674 55.000 0.00 0.00 0.00 4.30
275 283 2.028385 AGAAGGGATAACGACGCAAAGT 60.028 45.455 0.00 0.00 0.00 2.66
279 287 2.063266 GGATAACGACGCAAAGTGTCA 58.937 47.619 10.80 0.00 42.42 3.58
280 288 2.671396 GGATAACGACGCAAAGTGTCAT 59.329 45.455 10.80 2.30 42.42 3.06
289 297 2.320805 CAAAGTGTCATTGCTGTCGG 57.679 50.000 0.00 0.00 0.00 4.79
301 309 1.837439 TGCTGTCGGGTCCAAATAGAT 59.163 47.619 0.00 0.00 0.00 1.98
304 313 3.555168 GCTGTCGGGTCCAAATAGATAGG 60.555 52.174 0.00 0.00 0.00 2.57
308 317 3.116862 TCGGGTCCAAATAGATAGGGTCT 60.117 47.826 0.00 0.00 41.11 3.85
328 337 3.728373 ACCCCGGAATCCTGGCAC 61.728 66.667 0.73 0.00 37.51 5.01
330 339 3.781307 CCCGGAATCCTGGCACGA 61.781 66.667 0.73 0.00 37.51 4.35
341 350 0.390472 CTGGCACGAAGAGGAGAACC 60.390 60.000 0.00 0.00 0.00 3.62
382 391 1.083806 CCATCGCTAGCGTTGAAGCA 61.084 55.000 37.24 19.89 40.37 3.91
412 421 2.672908 CCAGCAGCTCACCCATGA 59.327 61.111 0.00 0.00 0.00 3.07
413 422 1.748122 CCAGCAGCTCACCCATGAC 60.748 63.158 0.00 0.00 0.00 3.06
421 430 1.735386 CTCACCCATGACAGCAAGAG 58.265 55.000 0.00 0.00 0.00 2.85
426 435 1.302285 CATGACAGCAAGAGGCCCT 59.698 57.895 0.00 0.00 46.50 5.19
440 449 2.975536 CCCTTAGGACAACCGCGA 59.024 61.111 8.23 0.00 41.83 5.87
441 450 1.520666 CCCTTAGGACAACCGCGAT 59.479 57.895 8.23 0.00 41.83 4.58
442 451 0.810031 CCCTTAGGACAACCGCGATG 60.810 60.000 8.23 9.26 41.83 3.84
472 481 1.827969 CTCCATATCCGGATCTGGACC 59.172 57.143 35.75 0.00 41.85 4.46
485 494 3.948719 GGACCCCGTCACTGCCAA 61.949 66.667 0.00 0.00 33.68 4.52
487 496 4.619227 ACCCCGTCACTGCCAACG 62.619 66.667 0.00 0.00 38.58 4.10
499 508 2.146342 CTGCCAACGACAGAGAACATT 58.854 47.619 0.00 0.00 37.32 2.71
506 515 3.079578 ACGACAGAGAACATTACCGAGA 58.920 45.455 0.00 0.00 0.00 4.04
512 521 1.203994 AGAACATTACCGAGACACCCG 59.796 52.381 0.00 0.00 0.00 5.28
513 522 0.971386 AACATTACCGAGACACCCGT 59.029 50.000 0.00 0.00 0.00 5.28
556 565 0.537188 ACCAAGAGGCATAGTCACCG 59.463 55.000 0.00 0.00 39.06 4.94
650 659 1.746615 CGAGACCCTGCCAACCATG 60.747 63.158 0.00 0.00 0.00 3.66
659 668 1.153978 GCCAACCATGCACATCACG 60.154 57.895 0.00 0.00 0.00 4.35
663 672 1.266446 CAACCATGCACATCACGACAA 59.734 47.619 0.00 0.00 0.00 3.18
664 673 0.874390 ACCATGCACATCACGACAAC 59.126 50.000 0.00 0.00 0.00 3.32
665 674 0.168788 CCATGCACATCACGACAACC 59.831 55.000 0.00 0.00 0.00 3.77
679 2344 4.000988 ACGACAACCATGGATAAGTTCAC 58.999 43.478 21.47 0.00 0.00 3.18
680 2345 3.374058 CGACAACCATGGATAAGTTCACC 59.626 47.826 21.47 0.00 0.00 4.02
681 2346 3.343617 ACAACCATGGATAAGTTCACCG 58.656 45.455 21.47 0.00 0.00 4.94
682 2347 2.682856 CAACCATGGATAAGTTCACCGG 59.317 50.000 21.47 0.00 0.00 5.28
683 2348 1.308998 CCATGGATAAGTTCACCGGC 58.691 55.000 5.56 0.00 0.00 6.13
693 2358 3.943479 TTCACCGGCCCGATCAACG 62.943 63.158 3.71 0.00 42.18 4.10
708 2373 4.500545 CGATCAACGGATCCATCTTCTTCT 60.501 45.833 13.41 0.00 45.89 2.85
728 2393 6.369890 TCTTCTATTCAAGCACAGTAGCAAAG 59.630 38.462 0.00 0.00 36.85 2.77
745 2410 5.799213 AGCAAAGAACTAGCTACTCACAAT 58.201 37.500 0.00 0.00 36.73 2.71
791 2460 1.985159 ACCAGTGTGGGAATAAGAGCA 59.015 47.619 0.00 0.00 43.37 4.26
792 2461 2.578021 ACCAGTGTGGGAATAAGAGCAT 59.422 45.455 0.00 0.00 43.37 3.79
848 2522 1.226888 CGCCACCTACGTAAGCTCC 60.227 63.158 0.00 0.00 45.62 4.70
903 2579 3.937062 CCCGCGCCGCTTGTATTC 61.937 66.667 7.78 0.00 0.00 1.75
956 2632 0.542938 CCACTCCTCCACTCCACTCA 60.543 60.000 0.00 0.00 0.00 3.41
962 2638 1.342074 CTCCACTCCACTCAACTCCA 58.658 55.000 0.00 0.00 0.00 3.86
963 2639 1.001406 CTCCACTCCACTCAACTCCAC 59.999 57.143 0.00 0.00 0.00 4.02
964 2640 1.051812 CCACTCCACTCAACTCCACT 58.948 55.000 0.00 0.00 0.00 4.00
965 2641 1.001406 CCACTCCACTCAACTCCACTC 59.999 57.143 0.00 0.00 0.00 3.51
966 2642 1.001406 CACTCCACTCAACTCCACTCC 59.999 57.143 0.00 0.00 0.00 3.85
970 2646 1.913762 ACTCAACTCCACTCCCCGG 60.914 63.158 0.00 0.00 0.00 5.73
1017 2697 3.348554 AATGGCGATGCAGCAGGGA 62.349 57.895 1.53 0.00 39.27 4.20
1317 2997 2.783333 GACCAGAACTTCTACTACGCG 58.217 52.381 3.53 3.53 0.00 6.01
1320 3000 1.101331 AGAACTTCTACTACGCGGGG 58.899 55.000 12.47 4.86 0.00 5.73
1332 3012 2.345991 GCGGGGCTCAAGTACACA 59.654 61.111 0.00 0.00 0.00 3.72
1657 3337 7.361438 CCTCTTCATCCTCCAGGTCTATATAT 58.639 42.308 0.00 0.00 36.34 0.86
1658 3338 8.506921 CCTCTTCATCCTCCAGGTCTATATATA 58.493 40.741 0.00 0.00 36.34 0.86
1688 3372 2.609299 TTCCCTCCCGTCCATGCA 60.609 61.111 0.00 0.00 0.00 3.96
1717 3405 5.769662 TGCATGAACTGAAAATCCTAACAGT 59.230 36.000 0.00 0.00 43.92 3.55
1838 3526 1.380785 CACCTTGGCCATGGAGCAT 60.381 57.895 37.33 17.21 0.00 3.79
1962 3653 8.710749 ATAATTAAACATGGCATGGTACTGAT 57.289 30.769 29.49 11.88 33.60 2.90
2008 3699 0.963856 TGCAGGGTATCGTGACGTCT 60.964 55.000 17.92 0.00 0.00 4.18
2012 3703 0.310232 GGGTATCGTGACGTCTAGCC 59.690 60.000 17.92 15.10 31.45 3.93
2164 3857 1.209128 GGTACGTGCATCAATCCTCG 58.791 55.000 5.86 0.00 0.00 4.63
2173 3866 2.224137 GCATCAATCCTCGTCTCCATGA 60.224 50.000 0.00 0.00 0.00 3.07
2174 3867 3.556633 GCATCAATCCTCGTCTCCATGAT 60.557 47.826 0.00 0.00 0.00 2.45
2175 3868 4.322273 GCATCAATCCTCGTCTCCATGATA 60.322 45.833 0.00 0.00 0.00 2.15
2176 3869 5.626347 GCATCAATCCTCGTCTCCATGATAT 60.626 44.000 0.00 0.00 0.00 1.63
2177 3870 5.397142 TCAATCCTCGTCTCCATGATATG 57.603 43.478 0.00 0.00 0.00 1.78
2178 3871 5.079643 TCAATCCTCGTCTCCATGATATGA 58.920 41.667 0.00 0.00 0.00 2.15
2179 3872 5.539955 TCAATCCTCGTCTCCATGATATGAA 59.460 40.000 0.00 0.00 0.00 2.57
2180 3873 6.212187 TCAATCCTCGTCTCCATGATATGAAT 59.788 38.462 0.00 0.00 0.00 2.57
2181 3874 5.651387 TCCTCGTCTCCATGATATGAATC 57.349 43.478 0.00 0.00 0.00 2.52
2182 3875 5.079643 TCCTCGTCTCCATGATATGAATCA 58.920 41.667 0.00 0.00 46.01 2.57
2183 3876 5.047731 TCCTCGTCTCCATGATATGAATCAC 60.048 44.000 0.00 0.00 44.79 3.06
2199 3892 5.668471 TGAATCACCATGAGAGACAAGATC 58.332 41.667 0.00 0.00 0.00 2.75
2206 3899 3.942130 TGAGAGACAAGATCGAGCAAA 57.058 42.857 2.38 0.00 0.00 3.68
2207 3900 4.462508 TGAGAGACAAGATCGAGCAAAT 57.537 40.909 2.38 0.00 0.00 2.32
2208 3901 5.582689 TGAGAGACAAGATCGAGCAAATA 57.417 39.130 2.38 0.00 0.00 1.40
2209 3902 5.586339 TGAGAGACAAGATCGAGCAAATAG 58.414 41.667 2.38 0.00 0.00 1.73
2210 3903 5.126222 TGAGAGACAAGATCGAGCAAATAGT 59.874 40.000 2.38 0.00 0.00 2.12
2211 3904 5.587289 AGAGACAAGATCGAGCAAATAGTC 58.413 41.667 2.38 3.29 0.00 2.59
2212 3905 5.126222 AGAGACAAGATCGAGCAAATAGTCA 59.874 40.000 2.38 0.00 0.00 3.41
2213 3906 5.347342 AGACAAGATCGAGCAAATAGTCAG 58.653 41.667 2.38 0.00 0.00 3.51
2230 3926 5.679734 AGTCAGTACATTCTTGCTGTTTG 57.320 39.130 0.00 0.00 0.00 2.93
2231 3927 5.368145 AGTCAGTACATTCTTGCTGTTTGA 58.632 37.500 0.00 0.00 0.00 2.69
2232 3928 6.000219 AGTCAGTACATTCTTGCTGTTTGAT 59.000 36.000 0.00 0.00 0.00 2.57
2233 3929 7.161404 AGTCAGTACATTCTTGCTGTTTGATA 58.839 34.615 0.00 0.00 0.00 2.15
2236 3932 9.013229 TCAGTACATTCTTGCTGTTTGATATTT 57.987 29.630 0.00 0.00 0.00 1.40
2237 3933 9.630098 CAGTACATTCTTGCTGTTTGATATTTT 57.370 29.630 0.00 0.00 0.00 1.82
2391 4087 1.602311 GCAGGATCATGGACATGGTC 58.398 55.000 15.47 15.47 45.76 4.02
2418 4114 0.832135 ACGAGGTGGAGCTGGAGAAA 60.832 55.000 0.00 0.00 0.00 2.52
2506 4205 0.369248 CGACGACGAGAACTGATCGA 59.631 55.000 0.00 0.00 42.76 3.59
2735 4434 2.771943 TCTTGTATCAGCTACCCCCTTG 59.228 50.000 0.00 0.00 0.00 3.61
2736 4435 1.507140 TGTATCAGCTACCCCCTTGG 58.493 55.000 0.00 0.00 41.37 3.61
2771 4470 9.517868 TTATGACATATGAACCATGATTATGCA 57.482 29.630 10.38 0.00 32.79 3.96
2772 4471 8.589701 ATGACATATGAACCATGATTATGCAT 57.410 30.769 10.38 3.79 32.79 3.96
2773 4472 7.822658 TGACATATGAACCATGATTATGCATG 58.177 34.615 10.16 0.00 44.05 4.06
2774 4473 6.627243 ACATATGAACCATGATTATGCATGC 58.373 36.000 11.82 11.82 43.30 4.06
2775 4474 4.530710 ATGAACCATGATTATGCATGCC 57.469 40.909 16.68 0.00 43.30 4.40
2895 4597 2.191128 AGTCTTTGGGCTCACATGAC 57.809 50.000 0.00 0.00 0.00 3.06
3002 4704 9.468532 GCATTTCCCATATCTTTTCAATTCTAC 57.531 33.333 0.00 0.00 0.00 2.59
3218 4924 3.850173 ACTATGGCCTTAAAGAACCAGGA 59.150 43.478 3.32 0.00 35.20 3.86
3221 4927 3.430453 TGGCCTTAAAGAACCAGGATTG 58.570 45.455 3.32 0.00 0.00 2.67
3222 4928 3.075283 TGGCCTTAAAGAACCAGGATTGA 59.925 43.478 3.32 0.00 0.00 2.57
3224 4930 4.711846 GGCCTTAAAGAACCAGGATTGATT 59.288 41.667 0.00 0.00 0.00 2.57
3226 4932 6.379988 GGCCTTAAAGAACCAGGATTGATTAA 59.620 38.462 0.00 0.00 0.00 1.40
3227 4933 7.258441 GCCTTAAAGAACCAGGATTGATTAAC 58.742 38.462 0.00 0.00 0.00 2.01
3228 4934 7.122799 GCCTTAAAGAACCAGGATTGATTAACT 59.877 37.037 0.00 0.00 0.00 2.24
3235 4941 3.623060 CCAGGATTGATTAACTGGTGACG 59.377 47.826 0.00 0.00 44.21 4.35
3241 4956 0.252197 ATTAACTGGTGACGGGAGCC 59.748 55.000 0.00 0.00 42.76 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.361786 TGGGTTCATCTGTACTCGATGA 58.638 45.455 18.38 18.38 43.90 2.92
4 5 3.801114 TGGGTTCATCTGTACTCGATG 57.199 47.619 15.35 15.35 39.62 3.84
5 6 3.430929 GCTTGGGTTCATCTGTACTCGAT 60.431 47.826 0.00 0.00 0.00 3.59
6 7 2.094182 GCTTGGGTTCATCTGTACTCGA 60.094 50.000 0.00 0.00 0.00 4.04
7 8 2.093973 AGCTTGGGTTCATCTGTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
8 9 3.055819 TGAGCTTGGGTTCATCTGTACTC 60.056 47.826 0.00 0.00 0.00 2.59
9 10 2.906389 TGAGCTTGGGTTCATCTGTACT 59.094 45.455 0.00 0.00 0.00 2.73
10 11 3.334583 TGAGCTTGGGTTCATCTGTAC 57.665 47.619 0.00 0.00 0.00 2.90
11 12 4.072131 GTTTGAGCTTGGGTTCATCTGTA 58.928 43.478 0.00 0.00 32.96 2.74
12 13 2.887152 GTTTGAGCTTGGGTTCATCTGT 59.113 45.455 0.00 0.00 32.96 3.41
13 14 3.152341 AGTTTGAGCTTGGGTTCATCTG 58.848 45.455 0.00 0.00 32.96 2.90
14 15 3.515602 AGTTTGAGCTTGGGTTCATCT 57.484 42.857 0.00 0.00 32.96 2.90
15 16 3.569701 TCAAGTTTGAGCTTGGGTTCATC 59.430 43.478 7.57 0.00 44.26 2.92
16 17 3.565307 TCAAGTTTGAGCTTGGGTTCAT 58.435 40.909 7.57 0.00 44.26 2.57
17 18 3.011566 TCAAGTTTGAGCTTGGGTTCA 57.988 42.857 7.57 0.00 44.26 3.18
18 19 4.590850 ATTCAAGTTTGAGCTTGGGTTC 57.409 40.909 7.57 0.00 44.26 3.62
19 20 6.570378 CGATAATTCAAGTTTGAGCTTGGGTT 60.570 38.462 7.57 5.94 44.26 4.11
20 21 5.106157 CGATAATTCAAGTTTGAGCTTGGGT 60.106 40.000 7.57 0.00 44.26 4.51
21 22 5.335127 CGATAATTCAAGTTTGAGCTTGGG 58.665 41.667 7.57 0.00 44.26 4.12
22 23 5.335127 CCGATAATTCAAGTTTGAGCTTGG 58.665 41.667 7.57 0.00 44.26 3.61
23 24 4.795278 GCCGATAATTCAAGTTTGAGCTTG 59.205 41.667 1.66 1.66 45.18 4.01
24 25 4.702131 AGCCGATAATTCAAGTTTGAGCTT 59.298 37.500 0.00 0.00 38.61 3.74
25 26 4.265073 AGCCGATAATTCAAGTTTGAGCT 58.735 39.130 0.00 0.00 38.61 4.09
26 27 4.333926 AGAGCCGATAATTCAAGTTTGAGC 59.666 41.667 0.00 0.00 38.61 4.26
27 28 5.582269 TGAGAGCCGATAATTCAAGTTTGAG 59.418 40.000 0.00 0.00 38.61 3.02
28 29 5.351465 GTGAGAGCCGATAATTCAAGTTTGA 59.649 40.000 0.00 0.00 34.92 2.69
29 30 5.447818 GGTGAGAGCCGATAATTCAAGTTTG 60.448 44.000 0.00 0.00 0.00 2.93
30 31 4.636206 GGTGAGAGCCGATAATTCAAGTTT 59.364 41.667 0.00 0.00 0.00 2.66
31 32 4.192317 GGTGAGAGCCGATAATTCAAGTT 58.808 43.478 0.00 0.00 0.00 2.66
32 33 3.432326 GGGTGAGAGCCGATAATTCAAGT 60.432 47.826 0.00 0.00 0.00 3.16
33 34 3.134458 GGGTGAGAGCCGATAATTCAAG 58.866 50.000 0.00 0.00 0.00 3.02
34 35 3.194005 GGGTGAGAGCCGATAATTCAA 57.806 47.619 0.00 0.00 0.00 2.69
35 36 2.910688 GGGTGAGAGCCGATAATTCA 57.089 50.000 0.00 0.00 0.00 2.57
43 44 8.003426 TTTATCTATAAAATCGGGTGAGAGCCG 61.003 40.741 7.90 7.90 43.08 5.52
44 45 4.602340 TCTATAAAATCGGGTGAGAGCC 57.398 45.455 0.00 0.00 0.00 4.70
45 46 7.148557 GCTTTATCTATAAAATCGGGTGAGAGC 60.149 40.741 0.00 0.00 32.39 4.09
46 47 7.872993 TGCTTTATCTATAAAATCGGGTGAGAG 59.127 37.037 0.00 0.00 32.39 3.20
47 48 7.656137 GTGCTTTATCTATAAAATCGGGTGAGA 59.344 37.037 0.00 0.00 32.39 3.27
48 49 7.441157 TGTGCTTTATCTATAAAATCGGGTGAG 59.559 37.037 0.00 0.00 32.39 3.51
49 50 7.276658 TGTGCTTTATCTATAAAATCGGGTGA 58.723 34.615 0.00 0.00 32.39 4.02
50 51 7.490962 TGTGCTTTATCTATAAAATCGGGTG 57.509 36.000 0.00 0.00 32.39 4.61
51 52 9.787435 TTATGTGCTTTATCTATAAAATCGGGT 57.213 29.630 0.00 0.00 32.39 5.28
62 63 9.589111 TCGTGTATTGTTTATGTGCTTTATCTA 57.411 29.630 0.00 0.00 0.00 1.98
63 64 8.388103 GTCGTGTATTGTTTATGTGCTTTATCT 58.612 33.333 0.00 0.00 0.00 1.98
64 65 7.369800 CGTCGTGTATTGTTTATGTGCTTTATC 59.630 37.037 0.00 0.00 0.00 1.75
65 66 7.063662 TCGTCGTGTATTGTTTATGTGCTTTAT 59.936 33.333 0.00 0.00 0.00 1.40
66 67 6.365518 TCGTCGTGTATTGTTTATGTGCTTTA 59.634 34.615 0.00 0.00 0.00 1.85
67 68 5.177881 TCGTCGTGTATTGTTTATGTGCTTT 59.822 36.000 0.00 0.00 0.00 3.51
68 69 4.687018 TCGTCGTGTATTGTTTATGTGCTT 59.313 37.500 0.00 0.00 0.00 3.91
69 70 4.239304 TCGTCGTGTATTGTTTATGTGCT 58.761 39.130 0.00 0.00 0.00 4.40
70 71 4.325204 TCTCGTCGTGTATTGTTTATGTGC 59.675 41.667 0.00 0.00 0.00 4.57
71 72 6.307077 TCTTCTCGTCGTGTATTGTTTATGTG 59.693 38.462 0.00 0.00 0.00 3.21
72 73 6.384224 TCTTCTCGTCGTGTATTGTTTATGT 58.616 36.000 0.00 0.00 0.00 2.29
73 74 6.864560 TCTTCTCGTCGTGTATTGTTTATG 57.135 37.500 0.00 0.00 0.00 1.90
74 75 9.017669 GTATTCTTCTCGTCGTGTATTGTTTAT 57.982 33.333 0.00 0.00 0.00 1.40
75 76 8.022550 TGTATTCTTCTCGTCGTGTATTGTTTA 58.977 33.333 0.00 0.00 0.00 2.01
76 77 6.864685 TGTATTCTTCTCGTCGTGTATTGTTT 59.135 34.615 0.00 0.00 0.00 2.83
77 78 6.384224 TGTATTCTTCTCGTCGTGTATTGTT 58.616 36.000 0.00 0.00 0.00 2.83
78 79 5.946298 TGTATTCTTCTCGTCGTGTATTGT 58.054 37.500 0.00 0.00 0.00 2.71
79 80 6.020599 CCTTGTATTCTTCTCGTCGTGTATTG 60.021 42.308 0.00 0.00 0.00 1.90
80 81 6.034591 CCTTGTATTCTTCTCGTCGTGTATT 58.965 40.000 0.00 0.00 0.00 1.89
81 82 5.125097 ACCTTGTATTCTTCTCGTCGTGTAT 59.875 40.000 0.00 0.00 0.00 2.29
82 83 4.456911 ACCTTGTATTCTTCTCGTCGTGTA 59.543 41.667 0.00 0.00 0.00 2.90
83 84 3.255149 ACCTTGTATTCTTCTCGTCGTGT 59.745 43.478 0.00 0.00 0.00 4.49
84 85 3.834610 ACCTTGTATTCTTCTCGTCGTG 58.165 45.455 0.00 0.00 0.00 4.35
85 86 4.699257 ACTACCTTGTATTCTTCTCGTCGT 59.301 41.667 0.00 0.00 0.00 4.34
86 87 5.029014 CACTACCTTGTATTCTTCTCGTCG 58.971 45.833 0.00 0.00 0.00 5.12
87 88 6.192234 TCACTACCTTGTATTCTTCTCGTC 57.808 41.667 0.00 0.00 0.00 4.20
88 89 5.125739 CCTCACTACCTTGTATTCTTCTCGT 59.874 44.000 0.00 0.00 0.00 4.18
89 90 5.450688 CCCTCACTACCTTGTATTCTTCTCG 60.451 48.000 0.00 0.00 0.00 4.04
90 91 5.657302 TCCCTCACTACCTTGTATTCTTCTC 59.343 44.000 0.00 0.00 0.00 2.87
91 92 5.590818 TCCCTCACTACCTTGTATTCTTCT 58.409 41.667 0.00 0.00 0.00 2.85
92 93 5.682730 GCTCCCTCACTACCTTGTATTCTTC 60.683 48.000 0.00 0.00 0.00 2.87
93 94 4.162509 GCTCCCTCACTACCTTGTATTCTT 59.837 45.833 0.00 0.00 0.00 2.52
94 95 3.707102 GCTCCCTCACTACCTTGTATTCT 59.293 47.826 0.00 0.00 0.00 2.40
95 96 3.707102 AGCTCCCTCACTACCTTGTATTC 59.293 47.826 0.00 0.00 0.00 1.75
96 97 3.707102 GAGCTCCCTCACTACCTTGTATT 59.293 47.826 0.87 0.00 38.03 1.89
97 98 3.052490 AGAGCTCCCTCACTACCTTGTAT 60.052 47.826 10.93 0.00 40.68 2.29
98 99 2.312140 AGAGCTCCCTCACTACCTTGTA 59.688 50.000 10.93 0.00 40.68 2.41
99 100 1.077993 AGAGCTCCCTCACTACCTTGT 59.922 52.381 10.93 0.00 40.68 3.16
100 101 1.754226 GAGAGCTCCCTCACTACCTTG 59.246 57.143 10.93 0.00 40.68 3.61
101 102 1.683629 CGAGAGCTCCCTCACTACCTT 60.684 57.143 10.93 0.00 40.68 3.50
102 103 0.106918 CGAGAGCTCCCTCACTACCT 60.107 60.000 10.93 0.00 40.68 3.08
103 104 0.394625 ACGAGAGCTCCCTCACTACC 60.395 60.000 10.93 0.00 40.68 3.18
104 105 1.941975 GTACGAGAGCTCCCTCACTAC 59.058 57.143 10.93 1.64 40.68 2.73
105 106 1.558294 TGTACGAGAGCTCCCTCACTA 59.442 52.381 10.93 0.00 40.68 2.74
106 107 0.328592 TGTACGAGAGCTCCCTCACT 59.671 55.000 10.93 0.00 40.68 3.41
107 108 0.452585 GTGTACGAGAGCTCCCTCAC 59.547 60.000 10.93 9.39 40.68 3.51
108 109 0.037734 TGTGTACGAGAGCTCCCTCA 59.962 55.000 10.93 0.32 40.68 3.86
109 110 0.736053 CTGTGTACGAGAGCTCCCTC 59.264 60.000 10.93 0.90 38.42 4.30
110 111 0.328592 TCTGTGTACGAGAGCTCCCT 59.671 55.000 10.93 0.00 0.00 4.20
111 112 1.174783 TTCTGTGTACGAGAGCTCCC 58.825 55.000 10.93 0.00 0.00 4.30
112 113 3.299340 TTTTCTGTGTACGAGAGCTCC 57.701 47.619 10.93 0.68 0.00 4.70
117 118 3.056107 CCTGGGATTTTCTGTGTACGAGA 60.056 47.826 0.00 0.00 0.00 4.04
121 122 6.316390 CAGTTATCCTGGGATTTTCTGTGTAC 59.684 42.308 7.48 0.00 37.54 2.90
126 127 6.359804 TGATCAGTTATCCTGGGATTTTCTG 58.640 40.000 7.48 12.54 41.83 3.02
131 132 5.429762 TGTCTTGATCAGTTATCCTGGGATT 59.570 40.000 7.48 0.00 41.83 3.01
137 138 7.093333 TGTGTGTATGTCTTGATCAGTTATCCT 60.093 37.037 0.00 0.00 33.22 3.24
151 152 5.237127 CGGCAATAATCATGTGTGTATGTCT 59.763 40.000 0.00 0.00 0.00 3.41
156 157 4.143986 TCCGGCAATAATCATGTGTGTA 57.856 40.909 0.00 0.00 0.00 2.90
159 160 3.761218 TGTTTCCGGCAATAATCATGTGT 59.239 39.130 0.00 0.00 0.00 3.72
190 198 0.456628 GCGTAGTCTTCAGTCCCTCC 59.543 60.000 0.00 0.00 0.00 4.30
193 201 0.108756 GTGGCGTAGTCTTCAGTCCC 60.109 60.000 0.00 0.00 0.00 4.46
198 206 2.288025 GGGGGTGGCGTAGTCTTCA 61.288 63.158 0.00 0.00 0.00 3.02
216 224 1.269831 GCTTAGGCGTCATAGGGAGTG 60.270 57.143 0.00 0.00 0.00 3.51
219 227 1.329256 GAGCTTAGGCGTCATAGGGA 58.671 55.000 0.00 0.00 44.37 4.20
225 233 0.175760 GTCATGGAGCTTAGGCGTCA 59.824 55.000 0.00 0.00 44.37 4.35
235 243 0.036732 TGAGGGTGTTGTCATGGAGC 59.963 55.000 0.00 0.00 0.00 4.70
239 247 2.430465 CCTTCTGAGGGTGTTGTCATG 58.570 52.381 0.00 0.00 39.55 3.07
240 248 2.867109 CCTTCTGAGGGTGTTGTCAT 57.133 50.000 0.00 0.00 39.55 3.06
250 258 1.536284 GCGTCGTTATCCCTTCTGAGG 60.536 57.143 0.00 0.00 43.15 3.86
253 261 2.004583 TTGCGTCGTTATCCCTTCTG 57.995 50.000 0.00 0.00 0.00 3.02
262 270 2.349060 GCAATGACACTTTGCGTCGTTA 60.349 45.455 0.00 0.00 39.91 3.18
275 283 1.003839 GGACCCGACAGCAATGACA 60.004 57.895 0.00 0.00 0.00 3.58
279 287 2.238646 TCTATTTGGACCCGACAGCAAT 59.761 45.455 0.00 0.00 0.00 3.56
280 288 1.626321 TCTATTTGGACCCGACAGCAA 59.374 47.619 0.00 0.00 0.00 3.91
283 291 3.006967 CCCTATCTATTTGGACCCGACAG 59.993 52.174 0.00 0.00 0.00 3.51
286 294 3.116862 AGACCCTATCTATTTGGACCCGA 60.117 47.826 0.00 0.00 35.15 5.14
289 297 5.454897 GGTGAAGACCCTATCTATTTGGACC 60.455 48.000 0.00 0.00 36.27 4.46
304 313 1.223763 GGATTCCGGGGTGAAGACC 59.776 63.158 0.00 0.00 42.27 3.85
308 317 2.978946 GCCAGGATTCCGGGGTGAA 61.979 63.158 21.55 0.00 39.29 3.18
315 324 0.807667 CTCTTCGTGCCAGGATTCCG 60.808 60.000 0.00 0.00 0.00 4.30
317 326 0.537188 TCCTCTTCGTGCCAGGATTC 59.463 55.000 0.00 0.00 30.92 2.52
320 329 0.541998 TTCTCCTCTTCGTGCCAGGA 60.542 55.000 0.00 0.00 34.97 3.86
328 337 3.201290 CATCATTGGGTTCTCCTCTTCG 58.799 50.000 0.00 0.00 36.20 3.79
330 339 2.357569 GGCATCATTGGGTTCTCCTCTT 60.358 50.000 0.00 0.00 36.20 2.85
370 379 2.047655 CCCCGTGCTTCAACGCTA 60.048 61.111 0.00 0.00 42.23 4.26
391 400 1.207488 ATGGGTGAGCTGCTGGGTAA 61.207 55.000 7.01 0.00 0.00 2.85
392 401 1.616327 ATGGGTGAGCTGCTGGGTA 60.616 57.895 7.01 0.00 0.00 3.69
412 421 0.547712 TCCTAAGGGCCTCTTGCTGT 60.548 55.000 6.46 0.00 40.92 4.40
413 422 0.107459 GTCCTAAGGGCCTCTTGCTG 60.107 60.000 6.46 6.61 40.92 4.41
421 430 2.437895 GCGGTTGTCCTAAGGGCC 60.438 66.667 0.00 0.00 0.00 5.80
426 435 0.459585 GCTCATCGCGGTTGTCCTAA 60.460 55.000 6.13 0.00 0.00 2.69
436 445 0.941463 GGAGGTATGTGCTCATCGCG 60.941 60.000 4.19 0.00 43.27 5.87
440 449 3.196469 CGGATATGGAGGTATGTGCTCAT 59.804 47.826 6.50 6.50 38.00 2.90
441 450 2.562738 CGGATATGGAGGTATGTGCTCA 59.437 50.000 0.00 0.00 0.00 4.26
442 451 2.093973 CCGGATATGGAGGTATGTGCTC 60.094 54.545 0.00 0.00 0.00 4.26
472 481 3.041940 GTCGTTGGCAGTGACGGG 61.042 66.667 10.01 0.00 39.59 5.28
485 494 3.079578 TCTCGGTAATGTTCTCTGTCGT 58.920 45.455 0.00 0.00 0.00 4.34
487 496 4.167268 GTGTCTCGGTAATGTTCTCTGTC 58.833 47.826 0.00 0.00 0.00 3.51
499 508 0.394762 ATAGCACGGGTGTCTCGGTA 60.395 55.000 0.25 0.00 0.00 4.02
506 515 1.002533 AGGGGTATAGCACGGGTGT 59.997 57.895 4.02 0.00 0.00 4.16
512 521 1.007618 GCGACGAGGGGTATAGCAC 60.008 63.158 0.00 0.00 0.00 4.40
513 522 2.198287 GGCGACGAGGGGTATAGCA 61.198 63.158 0.00 0.00 0.00 3.49
650 659 0.168788 CCATGGTTGTCGTGATGTGC 59.831 55.000 2.57 0.00 34.35 4.57
659 668 3.374058 CGGTGAACTTATCCATGGTTGTC 59.626 47.826 12.58 2.97 0.00 3.18
663 672 1.408266 GCCGGTGAACTTATCCATGGT 60.408 52.381 12.58 1.59 0.00 3.55
664 673 1.308998 GCCGGTGAACTTATCCATGG 58.691 55.000 4.97 4.97 0.00 3.66
665 674 1.308998 GGCCGGTGAACTTATCCATG 58.691 55.000 1.90 0.00 0.00 3.66
693 2358 6.204495 GTGCTTGAATAGAAGAAGATGGATCC 59.796 42.308 4.20 4.20 0.00 3.36
701 2366 5.871524 TGCTACTGTGCTTGAATAGAAGAAG 59.128 40.000 0.00 0.00 0.00 2.85
702 2367 5.793817 TGCTACTGTGCTTGAATAGAAGAA 58.206 37.500 0.00 0.00 0.00 2.52
703 2368 5.405935 TGCTACTGTGCTTGAATAGAAGA 57.594 39.130 0.00 0.00 0.00 2.87
708 2373 5.997746 AGTTCTTTGCTACTGTGCTTGAATA 59.002 36.000 0.00 0.00 0.00 1.75
728 2393 5.962433 TGGTGTATTGTGAGTAGCTAGTTC 58.038 41.667 1.78 0.39 0.00 3.01
745 2410 3.567478 CTCGCGTGCCACTGGTGTA 62.567 63.158 5.77 0.00 0.00 2.90
791 2460 1.886313 CTTCGCTCGCTGCATGGAT 60.886 57.895 0.00 0.00 43.06 3.41
792 2461 2.510012 CTTCGCTCGCTGCATGGA 60.510 61.111 0.00 0.00 43.06 3.41
900 2576 4.480480 TCCTTCGCCTGAGGGAAT 57.520 55.556 0.00 0.00 46.47 3.01
903 2579 2.959484 TTGCTCCTTCGCCTGAGGG 61.959 63.158 0.00 0.00 42.60 4.30
931 2607 1.074471 AGTGGAGGAGTGGTGTGGT 60.074 57.895 0.00 0.00 0.00 4.16
932 2608 1.674057 GAGTGGAGGAGTGGTGTGG 59.326 63.158 0.00 0.00 0.00 4.17
956 2632 3.322466 CTGCCGGGGAGTGGAGTT 61.322 66.667 7.49 0.00 0.00 3.01
962 2638 4.021925 GAAGTGCTGCCGGGGAGT 62.022 66.667 17.35 0.00 0.00 3.85
963 2639 4.020617 TGAAGTGCTGCCGGGGAG 62.021 66.667 11.72 11.72 0.00 4.30
964 2640 4.329545 GTGAAGTGCTGCCGGGGA 62.330 66.667 2.18 0.00 0.00 4.81
966 2642 3.583276 TACGTGAAGTGCTGCCGGG 62.583 63.158 2.18 0.00 0.00 5.73
970 2646 1.630148 CTAGGTACGTGAAGTGCTGC 58.370 55.000 0.00 0.00 35.67 5.25
1317 2997 1.090052 GCGATGTGTACTTGAGCCCC 61.090 60.000 0.00 0.00 0.00 5.80
1320 3000 0.391130 TGGGCGATGTGTACTTGAGC 60.391 55.000 0.00 0.00 0.00 4.26
1332 3012 3.036429 GCAGGAGAAGGTGGGCGAT 62.036 63.158 0.00 0.00 0.00 4.58
1688 3372 4.529377 AGGATTTTCAGTTCATGCATGGTT 59.471 37.500 25.97 9.51 0.00 3.67
1717 3405 0.030504 CTGCATGCACGAAACACCAA 59.969 50.000 18.46 0.00 0.00 3.67
1719 3407 1.081242 CCTGCATGCACGAAACACC 60.081 57.895 18.46 0.00 0.00 4.16
1838 3526 0.250858 TCTTCCAGACGTCGGTGGTA 60.251 55.000 19.92 11.99 35.14 3.25
1962 3653 9.485206 CACATACATATTCACAGAGATTCATGA 57.515 33.333 0.00 0.00 0.00 3.07
2008 3699 0.458669 GCACGTAGTAGGCAAGGCTA 59.541 55.000 0.00 0.00 41.61 3.93
2059 3750 2.815647 CTGAAGGCCGAGGCGAAC 60.816 66.667 8.14 2.46 43.06 3.95
2113 3804 0.606096 TGTTCTCGGCGAGGATGAAA 59.394 50.000 33.93 19.13 0.00 2.69
2164 3857 6.470278 TCATGGTGATTCATATCATGGAGAC 58.530 40.000 18.63 0.00 42.49 3.36
2173 3866 7.370905 TCTTGTCTCTCATGGTGATTCATAT 57.629 36.000 0.00 0.00 0.00 1.78
2174 3867 6.796785 TCTTGTCTCTCATGGTGATTCATA 57.203 37.500 0.00 0.00 0.00 2.15
2175 3868 5.688814 TCTTGTCTCTCATGGTGATTCAT 57.311 39.130 0.00 0.00 0.00 2.57
2176 3869 5.668471 GATCTTGTCTCTCATGGTGATTCA 58.332 41.667 0.00 0.00 0.00 2.57
2177 3870 4.744137 CGATCTTGTCTCTCATGGTGATTC 59.256 45.833 0.00 0.00 0.00 2.52
2178 3871 4.403752 TCGATCTTGTCTCTCATGGTGATT 59.596 41.667 0.00 0.00 0.00 2.57
2179 3872 3.956848 TCGATCTTGTCTCTCATGGTGAT 59.043 43.478 0.00 0.00 0.00 3.06
2180 3873 3.356290 TCGATCTTGTCTCTCATGGTGA 58.644 45.455 0.00 0.00 0.00 4.02
2181 3874 3.704512 CTCGATCTTGTCTCTCATGGTG 58.295 50.000 0.00 0.00 0.00 4.17
2182 3875 2.100584 GCTCGATCTTGTCTCTCATGGT 59.899 50.000 0.00 0.00 0.00 3.55
2183 3876 2.100418 TGCTCGATCTTGTCTCTCATGG 59.900 50.000 0.00 0.00 0.00 3.66
2199 3892 6.700020 CAAGAATGTACTGACTATTTGCTCG 58.300 40.000 0.00 0.00 0.00 5.03
2206 3899 7.161404 TCAAACAGCAAGAATGTACTGACTAT 58.839 34.615 0.00 0.00 34.25 2.12
2207 3900 6.521162 TCAAACAGCAAGAATGTACTGACTA 58.479 36.000 0.00 0.00 34.25 2.59
2208 3901 5.368145 TCAAACAGCAAGAATGTACTGACT 58.632 37.500 0.00 0.00 34.25 3.41
2209 3902 5.673337 TCAAACAGCAAGAATGTACTGAC 57.327 39.130 0.00 0.00 34.25 3.51
2210 3903 8.565896 AATATCAAACAGCAAGAATGTACTGA 57.434 30.769 0.00 0.00 34.25 3.41
2211 3904 9.630098 AAAATATCAAACAGCAAGAATGTACTG 57.370 29.630 0.00 0.00 36.22 2.74
2212 3905 9.846248 GAAAATATCAAACAGCAAGAATGTACT 57.154 29.630 0.00 0.00 0.00 2.73
2213 3906 9.624697 TGAAAATATCAAACAGCAAGAATGTAC 57.375 29.630 0.00 0.00 34.30 2.90
2230 3926 4.938226 GGACCCGATGATCCTGAAAATATC 59.062 45.833 0.00 0.00 31.75 1.63
2231 3927 4.563580 CGGACCCGATGATCCTGAAAATAT 60.564 45.833 1.54 0.00 42.83 1.28
2232 3928 3.244078 CGGACCCGATGATCCTGAAAATA 60.244 47.826 1.54 0.00 42.83 1.40
2233 3929 2.485479 CGGACCCGATGATCCTGAAAAT 60.485 50.000 1.54 0.00 42.83 1.82
2236 3932 0.686441 ACGGACCCGATGATCCTGAA 60.686 55.000 16.07 0.00 42.83 3.02
2237 3933 1.076265 ACGGACCCGATGATCCTGA 60.076 57.895 16.07 0.00 42.83 3.86
2391 4087 3.057547 CTCCACCTCGTCCAGCTCG 62.058 68.421 0.00 0.00 0.00 5.03
2506 4205 3.051940 TCCACCTATCTCTTGCTCCAT 57.948 47.619 0.00 0.00 0.00 3.41
2684 4383 5.772672 AGATAGATAAGACAGGCTACCACAG 59.227 44.000 0.00 0.00 0.00 3.66
2735 4434 9.349713 TGGTTCATATGTCATAATTAACTTCCC 57.650 33.333 1.90 0.00 0.00 3.97
2758 4457 3.765511 GGTATGGCATGCATAATCATGGT 59.234 43.478 21.36 0.00 42.97 3.55
2771 4470 1.622811 GAGCTAGCTGAGGTATGGCAT 59.377 52.381 24.99 4.88 35.50 4.40
2772 4471 1.043816 GAGCTAGCTGAGGTATGGCA 58.956 55.000 24.99 0.00 35.50 4.92
2773 4472 1.337118 AGAGCTAGCTGAGGTATGGC 58.663 55.000 24.99 3.83 35.50 4.40
2774 4473 2.298729 GGAAGAGCTAGCTGAGGTATGG 59.701 54.545 24.99 0.00 35.50 2.74
2775 4474 2.961741 TGGAAGAGCTAGCTGAGGTATG 59.038 50.000 24.99 0.00 35.50 2.39
2895 4597 2.162208 CACAAATCCCACGTCCAATCAG 59.838 50.000 0.00 0.00 0.00 2.90
3002 4704 6.225701 CGAAAACGCACATTTGACAAATATG 58.774 36.000 13.70 13.70 0.00 1.78
3218 4924 3.873910 CTCCCGTCACCAGTTAATCAAT 58.126 45.455 0.00 0.00 0.00 2.57
3221 4927 1.653151 GCTCCCGTCACCAGTTAATC 58.347 55.000 0.00 0.00 0.00 1.75
3222 4928 0.252197 GGCTCCCGTCACCAGTTAAT 59.748 55.000 0.00 0.00 0.00 1.40
3224 4930 1.534476 TGGCTCCCGTCACCAGTTA 60.534 57.895 0.00 0.00 0.00 2.24
3226 4932 3.314331 CTGGCTCCCGTCACCAGT 61.314 66.667 0.00 0.00 44.91 4.00
3228 4934 3.993837 TATTCCTGGCTCCCGTCACCA 62.994 57.143 0.00 0.00 0.00 4.17
3230 4936 0.539986 TTATTCCTGGCTCCCGTCAC 59.460 55.000 0.00 0.00 0.00 3.67
3231 4937 1.065709 GTTTATTCCTGGCTCCCGTCA 60.066 52.381 0.00 0.00 0.00 4.35
3232 4938 1.065709 TGTTTATTCCTGGCTCCCGTC 60.066 52.381 0.00 0.00 0.00 4.79
3233 4939 0.988832 TGTTTATTCCTGGCTCCCGT 59.011 50.000 0.00 0.00 0.00 5.28
3234 4940 2.348411 ATGTTTATTCCTGGCTCCCG 57.652 50.000 0.00 0.00 0.00 5.14
3260 4975 5.411831 AGGATTCCATGCTTTTCTTTTCC 57.588 39.130 5.29 0.00 0.00 3.13
3459 5174 2.766229 GGTGGAGGAGGAGGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
3460 5175 1.687493 GTGGTGGAGGAGGAGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
3461 5176 1.687493 GGTGGTGGAGGAGGAGGAG 60.687 68.421 0.00 0.00 0.00 3.69
3462 5177 1.751143 AAGGTGGTGGAGGAGGAGGA 61.751 60.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.