Multiple sequence alignment - TraesCS2A01G405900

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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 TraesCS2A01G405900 chr2A 100.000 3835 0 0 1 3835 661590207 661594041 0.000000e+00 7083
1 TraesCS2A01G405900 chr2A 93.066 2120 136 11 715 2828 154830262 154832376 0.000000e+00 3090
2 TraesCS2A01G405900 chr2A 95.052 1819 89 1 1011 2828 5519278 5521096 0.000000e+00 2859
3 TraesCS2A01G405900 chr2A 97.892 996 21 0 2829 3824 189487720 189488715 0.000000e+00 1724
4 TraesCS2A01G405900 chr7A 95.452 2111 95 1 718 2828 89627230 89625121 0.000000e+00 3365
5 TraesCS2A01G405900 chr7A 97.219 1007 28 0 2829 3835 652575551 652574545 0.000000e+00 1705
6 TraesCS2A01G405900 chr1D 94.539 2051 94 8 796 2828 348028774 348026724 0.000000e+00 3151
7 TraesCS2A01G405900 chr4A 92.857 1918 129 8 718 2631 616571099 616573012 0.000000e+00 2776
8 TraesCS2A01G405900 chr4A 97.894 997 21 0 2828 3824 221723533 221722537 0.000000e+00 1725
9 TraesCS2A01G405900 chr4A 96.949 1016 29 2 2809 3824 638270560 638269547 0.000000e+00 1703
10 TraesCS2A01G405900 chr4A 91.195 1113 79 7 719 1829 734115302 734114207 0.000000e+00 1495
11 TraesCS2A01G405900 chr2D 90.298 2082 175 14 763 2828 615872233 615870163 0.000000e+00 2700
12 TraesCS2A01G405900 chr2D 95.124 1251 57 1 1582 2828 158254989 158256239 0.000000e+00 1969
13 TraesCS2A01G405900 chr2D 86.154 325 32 9 405 718 517267642 517267964 4.750000e-89 339
14 TraesCS2A01G405900 chr2D 84.921 252 25 5 94 332 517267302 517267553 3.830000e-60 243
15 TraesCS2A01G405900 chr3D 94.044 1511 85 5 719 2226 590695286 590693778 0.000000e+00 2287
16 TraesCS2A01G405900 chr3D 92.253 1123 74 9 719 1829 30785663 30786784 0.000000e+00 1580
17 TraesCS2A01G405900 chr5A 96.003 1276 51 0 1553 2828 683595562 683594287 0.000000e+00 2074
18 TraesCS2A01G405900 chr5A 95.690 1276 55 0 1553 2828 681946098 681947373 0.000000e+00 2052
19 TraesCS2A01G405900 chr5A 97.691 996 23 0 2829 3824 454851121 454850126 0.000000e+00 1712
20 TraesCS2A01G405900 chr5A 97.225 1009 26 2 2816 3824 436698883 436699889 0.000000e+00 1707
21 TraesCS2A01G405900 chr5A 97.225 1009 27 1 2828 3835 454304734 454305742 0.000000e+00 1707
22 TraesCS2A01G405900 chr6A 97.421 1008 25 1 2829 3835 554756678 554755671 0.000000e+00 1716
23 TraesCS2A01G405900 chr6A 97.038 1013 28 2 2824 3835 157487036 157488047 0.000000e+00 1703
24 TraesCS2A01G405900 chr5B 91.911 1125 75 7 719 1829 544518570 544517448 0.000000e+00 1559
25 TraesCS2A01G405900 chr4B 91.808 1123 78 8 719 1829 125423505 125422385 0.000000e+00 1552
26 TraesCS2A01G405900 chr3B 82.214 1147 141 46 718 1816 681202910 681201779 0.000000e+00 929
27 TraesCS2A01G405900 chr3B 84.958 944 108 24 718 1635 546831382 546830447 0.000000e+00 926
28 TraesCS2A01G405900 chr2B 88.288 222 24 2 1 221 609207891 609208111 8.170000e-67 265


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 TraesCS2A01G405900 chr2A 661590207 661594041 3834 False 7083 7083 100.0000 1 3835 1 chr2A.!!$F4 3834
1 TraesCS2A01G405900 chr2A 154830262 154832376 2114 False 3090 3090 93.0660 715 2828 1 chr2A.!!$F2 2113
2 TraesCS2A01G405900 chr2A 5519278 5521096 1818 False 2859 2859 95.0520 1011 2828 1 chr2A.!!$F1 1817
3 TraesCS2A01G405900 chr2A 189487720 189488715 995 False 1724 1724 97.8920 2829 3824 1 chr2A.!!$F3 995
4 TraesCS2A01G405900 chr7A 89625121 89627230 2109 True 3365 3365 95.4520 718 2828 1 chr7A.!!$R1 2110
5 TraesCS2A01G405900 chr7A 652574545 652575551 1006 True 1705 1705 97.2190 2829 3835 1 chr7A.!!$R2 1006
6 TraesCS2A01G405900 chr1D 348026724 348028774 2050 True 3151 3151 94.5390 796 2828 1 chr1D.!!$R1 2032
7 TraesCS2A01G405900 chr4A 616571099 616573012 1913 False 2776 2776 92.8570 718 2631 1 chr4A.!!$F1 1913
8 TraesCS2A01G405900 chr4A 221722537 221723533 996 True 1725 1725 97.8940 2828 3824 1 chr4A.!!$R1 996
9 TraesCS2A01G405900 chr4A 638269547 638270560 1013 True 1703 1703 96.9490 2809 3824 1 chr4A.!!$R2 1015
10 TraesCS2A01G405900 chr4A 734114207 734115302 1095 True 1495 1495 91.1950 719 1829 1 chr4A.!!$R3 1110
11 TraesCS2A01G405900 chr2D 615870163 615872233 2070 True 2700 2700 90.2980 763 2828 1 chr2D.!!$R1 2065
12 TraesCS2A01G405900 chr2D 158254989 158256239 1250 False 1969 1969 95.1240 1582 2828 1 chr2D.!!$F1 1246
13 TraesCS2A01G405900 chr2D 517267302 517267964 662 False 291 339 85.5375 94 718 2 chr2D.!!$F2 624
14 TraesCS2A01G405900 chr3D 590693778 590695286 1508 True 2287 2287 94.0440 719 2226 1 chr3D.!!$R1 1507
15 TraesCS2A01G405900 chr3D 30785663 30786784 1121 False 1580 1580 92.2530 719 1829 1 chr3D.!!$F1 1110
16 TraesCS2A01G405900 chr5A 683594287 683595562 1275 True 2074 2074 96.0030 1553 2828 1 chr5A.!!$R2 1275
17 TraesCS2A01G405900 chr5A 681946098 681947373 1275 False 2052 2052 95.6900 1553 2828 1 chr5A.!!$F3 1275
18 TraesCS2A01G405900 chr5A 454850126 454851121 995 True 1712 1712 97.6910 2829 3824 1 chr5A.!!$R1 995
19 TraesCS2A01G405900 chr5A 436698883 436699889 1006 False 1707 1707 97.2250 2816 3824 1 chr5A.!!$F1 1008
20 TraesCS2A01G405900 chr5A 454304734 454305742 1008 False 1707 1707 97.2250 2828 3835 1 chr5A.!!$F2 1007
21 TraesCS2A01G405900 chr6A 554755671 554756678 1007 True 1716 1716 97.4210 2829 3835 1 chr6A.!!$R1 1006
22 TraesCS2A01G405900 chr6A 157487036 157488047 1011 False 1703 1703 97.0380 2824 3835 1 chr6A.!!$F1 1011
23 TraesCS2A01G405900 chr5B 544517448 544518570 1122 True 1559 1559 91.9110 719 1829 1 chr5B.!!$R1 1110
24 TraesCS2A01G405900 chr4B 125422385 125423505 1120 True 1552 1552 91.8080 719 1829 1 chr4B.!!$R1 1110
25 TraesCS2A01G405900 chr3B 681201779 681202910 1131 True 929 929 82.2140 718 1816 1 chr3B.!!$R2 1098
26 TraesCS2A01G405900 chr3B 546830447 546831382 935 True 926 926 84.9580 718 1635 1 chr3B.!!$R1 917

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
680 714 0.252479 AGTCCAGCATCTGAGCAAGG 59.748 55.000 0.0 0.0 36.85 3.61 F
682 716 1.077644 CCAGCATCTGAGCAAGGCT 60.078 57.895 0.0 0.0 43.88 4.58 F
1143 1199 1.226974 CCCGTACATGCACTCCGAG 60.227 63.158 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2292 1.002017 CTCCATTGTTGGGGGCCAT 59.998 57.895 4.39 0.0 43.81 4.40 R
2513 2645 2.887152 AGGTTTTGGATGACAGTTGCTC 59.113 45.455 0.00 0.0 0.00 4.26 R
2879 3011 0.388649 CTCCTCGTTGGGTTCGACAG 60.389 60.000 0.00 0.0 36.20 3.51 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
17 18 4.469883 CAGCAACTGGAGCAGTGT 57.530 55.556 0.00 0.00 44.62 3.55
18 19 3.612517 CAGCAACTGGAGCAGTGTA 57.387 52.632 0.00 0.00 44.62 2.90
19 20 1.436600 CAGCAACTGGAGCAGTGTAG 58.563 55.000 0.00 0.00 44.62 2.74
20 21 1.051812 AGCAACTGGAGCAGTGTAGT 58.948 50.000 0.00 0.00 44.62 2.73
21 22 1.151668 GCAACTGGAGCAGTGTAGTG 58.848 55.000 0.00 0.00 44.62 2.74
22 23 1.800805 CAACTGGAGCAGTGTAGTGG 58.199 55.000 0.00 0.00 44.62 4.00
23 24 1.070758 CAACTGGAGCAGTGTAGTGGT 59.929 52.381 0.00 0.00 44.62 4.16
24 25 0.681733 ACTGGAGCAGTGTAGTGGTG 59.318 55.000 0.00 0.00 43.63 4.17
25 26 0.969149 CTGGAGCAGTGTAGTGGTGA 59.031 55.000 0.00 0.00 0.00 4.02
26 27 1.552337 CTGGAGCAGTGTAGTGGTGAT 59.448 52.381 0.00 0.00 0.00 3.06
27 28 2.760650 CTGGAGCAGTGTAGTGGTGATA 59.239 50.000 0.00 0.00 0.00 2.15
28 29 2.760650 TGGAGCAGTGTAGTGGTGATAG 59.239 50.000 0.00 0.00 0.00 2.08
29 30 2.761208 GGAGCAGTGTAGTGGTGATAGT 59.239 50.000 0.00 0.00 0.00 2.12
30 31 3.952323 GGAGCAGTGTAGTGGTGATAGTA 59.048 47.826 0.00 0.00 0.00 1.82
31 32 4.585162 GGAGCAGTGTAGTGGTGATAGTAT 59.415 45.833 0.00 0.00 0.00 2.12
32 33 5.278561 GGAGCAGTGTAGTGGTGATAGTATC 60.279 48.000 2.97 2.97 0.00 2.24
33 34 4.585162 AGCAGTGTAGTGGTGATAGTATCC 59.415 45.833 7.69 0.00 0.00 2.59
34 35 4.262079 GCAGTGTAGTGGTGATAGTATCCC 60.262 50.000 7.69 8.78 0.00 3.85
35 36 4.281182 CAGTGTAGTGGTGATAGTATCCCC 59.719 50.000 7.69 6.21 0.00 4.81
36 37 4.170251 AGTGTAGTGGTGATAGTATCCCCT 59.830 45.833 12.27 11.21 0.00 4.79
37 38 5.374753 AGTGTAGTGGTGATAGTATCCCCTA 59.625 44.000 12.27 10.48 0.00 3.53
38 39 5.711036 GTGTAGTGGTGATAGTATCCCCTAG 59.289 48.000 12.27 0.00 0.00 3.02
39 40 5.374753 TGTAGTGGTGATAGTATCCCCTAGT 59.625 44.000 12.27 5.00 0.00 2.57
40 41 4.742012 AGTGGTGATAGTATCCCCTAGTG 58.258 47.826 12.27 0.00 0.00 2.74
41 42 4.170251 AGTGGTGATAGTATCCCCTAGTGT 59.830 45.833 12.27 0.00 0.00 3.55
42 43 4.900054 GTGGTGATAGTATCCCCTAGTGTT 59.100 45.833 12.27 0.00 0.00 3.32
43 44 5.365895 GTGGTGATAGTATCCCCTAGTGTTT 59.634 44.000 12.27 0.00 0.00 2.83
44 45 5.968167 TGGTGATAGTATCCCCTAGTGTTTT 59.032 40.000 12.27 0.00 0.00 2.43
45 46 6.126883 TGGTGATAGTATCCCCTAGTGTTTTG 60.127 42.308 12.27 0.00 0.00 2.44
46 47 6.126854 GGTGATAGTATCCCCTAGTGTTTTGT 60.127 42.308 7.69 0.00 0.00 2.83
47 48 7.336396 GTGATAGTATCCCCTAGTGTTTTGTT 58.664 38.462 7.69 0.00 0.00 2.83
48 49 8.480501 GTGATAGTATCCCCTAGTGTTTTGTTA 58.519 37.037 7.69 0.00 0.00 2.41
49 50 8.701895 TGATAGTATCCCCTAGTGTTTTGTTAG 58.298 37.037 7.69 0.00 0.00 2.34
50 51 8.849543 ATAGTATCCCCTAGTGTTTTGTTAGA 57.150 34.615 0.00 0.00 0.00 2.10
51 52 7.750947 AGTATCCCCTAGTGTTTTGTTAGAT 57.249 36.000 0.00 0.00 0.00 1.98
52 53 8.159229 AGTATCCCCTAGTGTTTTGTTAGATT 57.841 34.615 0.00 0.00 0.00 2.40
53 54 9.275572 AGTATCCCCTAGTGTTTTGTTAGATTA 57.724 33.333 0.00 0.00 0.00 1.75
56 57 9.990868 ATCCCCTAGTGTTTTGTTAGATTATTT 57.009 29.630 0.00 0.00 0.00 1.40
57 58 9.816787 TCCCCTAGTGTTTTGTTAGATTATTTT 57.183 29.630 0.00 0.00 0.00 1.82
81 82 9.680315 TTTACATGAAAAATTACGGTTGTTAGG 57.320 29.630 0.00 0.00 0.00 2.69
82 83 6.683715 ACATGAAAAATTACGGTTGTTAGGG 58.316 36.000 0.00 0.00 0.00 3.53
83 84 6.265876 ACATGAAAAATTACGGTTGTTAGGGT 59.734 34.615 0.00 0.00 0.00 4.34
84 85 6.316440 TGAAAAATTACGGTTGTTAGGGTC 57.684 37.500 0.00 0.00 0.00 4.46
85 86 5.049543 TGAAAAATTACGGTTGTTAGGGTCG 60.050 40.000 0.00 0.00 0.00 4.79
86 87 3.959535 AATTACGGTTGTTAGGGTCGA 57.040 42.857 0.00 0.00 0.00 4.20
87 88 2.723124 TTACGGTTGTTAGGGTCGAC 57.277 50.000 7.13 7.13 0.00 4.20
88 89 1.909700 TACGGTTGTTAGGGTCGACT 58.090 50.000 16.46 0.00 0.00 4.18
89 90 1.909700 ACGGTTGTTAGGGTCGACTA 58.090 50.000 16.46 0.00 0.00 2.59
90 91 2.450476 ACGGTTGTTAGGGTCGACTAT 58.550 47.619 16.46 6.90 0.00 2.12
91 92 2.827921 ACGGTTGTTAGGGTCGACTATT 59.172 45.455 16.46 3.95 0.00 1.73
92 93 3.259123 ACGGTTGTTAGGGTCGACTATTT 59.741 43.478 16.46 1.39 0.00 1.40
95 96 4.999311 GGTTGTTAGGGTCGACTATTTGTT 59.001 41.667 16.46 0.00 0.00 2.83
98 99 5.475719 TGTTAGGGTCGACTATTTGTTCAG 58.524 41.667 16.46 0.00 0.00 3.02
109 110 7.328493 TCGACTATTTGTTCAGTGTGTTAGATG 59.672 37.037 0.00 0.00 0.00 2.90
127 128 7.445707 TGTTAGATGGCAATACAACTTTGTGTA 59.554 33.333 4.82 0.00 42.31 2.90
131 132 4.226761 GGCAATACAACTTTGTGTAGCAC 58.773 43.478 4.82 0.00 42.31 4.40
149 150 1.655597 CACGTGACATGTCTGAATCCG 59.344 52.381 25.55 18.12 0.00 4.18
161 162 3.375299 GTCTGAATCCGGGAATTTCACTG 59.625 47.826 8.63 2.27 0.00 3.66
172 173 5.448632 CGGGAATTTCACTGTTTACTATGGC 60.449 44.000 0.00 0.00 0.00 4.40
174 175 5.652452 GGAATTTCACTGTTTACTATGGCCT 59.348 40.000 3.32 0.00 0.00 5.19
175 176 6.183360 GGAATTTCACTGTTTACTATGGCCTC 60.183 42.308 3.32 0.00 0.00 4.70
181 182 3.305720 TGTTTACTATGGCCTCGGAGAT 58.694 45.455 6.58 0.00 33.89 2.75
214 215 0.539051 AAGAGTGAGATGGCGGGAAG 59.461 55.000 0.00 0.00 0.00 3.46
218 219 1.351017 AGTGAGATGGCGGGAAGAAAA 59.649 47.619 0.00 0.00 0.00 2.29
229 230 1.813178 GGGAAGAAAAAGAGCGGGAAG 59.187 52.381 0.00 0.00 0.00 3.46
231 232 2.552373 GGAAGAAAAAGAGCGGGAAGGA 60.552 50.000 0.00 0.00 0.00 3.36
232 233 2.951229 AGAAAAAGAGCGGGAAGGAA 57.049 45.000 0.00 0.00 0.00 3.36
262 276 4.358851 CGTGAGAGAGAATGATGAAGGAC 58.641 47.826 0.00 0.00 0.00 3.85
263 277 4.097741 CGTGAGAGAGAATGATGAAGGACT 59.902 45.833 0.00 0.00 0.00 3.85
268 282 3.131933 AGAGAATGATGAAGGACTGTCGG 59.868 47.826 1.07 0.00 0.00 4.79
332 346 5.938322 ACTAATAACAACATGCAACTTCGG 58.062 37.500 0.00 0.00 0.00 4.30
334 348 4.846779 ATAACAACATGCAACTTCGGTT 57.153 36.364 0.00 0.00 38.94 4.44
346 360 3.354089 ACTTCGGTTGTTCATGCAAAG 57.646 42.857 0.00 0.00 0.00 2.77
347 361 2.948979 ACTTCGGTTGTTCATGCAAAGA 59.051 40.909 0.00 0.00 0.00 2.52
348 362 3.003689 ACTTCGGTTGTTCATGCAAAGAG 59.996 43.478 0.00 0.00 0.00 2.85
349 363 1.879380 TCGGTTGTTCATGCAAAGAGG 59.121 47.619 0.00 0.00 0.00 3.69
350 364 1.608590 CGGTTGTTCATGCAAAGAGGT 59.391 47.619 0.00 0.00 0.00 3.85
352 366 2.288395 GGTTGTTCATGCAAAGAGGTGG 60.288 50.000 0.00 0.00 0.00 4.61
353 367 1.619654 TGTTCATGCAAAGAGGTGGG 58.380 50.000 0.00 0.00 0.00 4.61
355 369 0.899717 TTCATGCAAAGAGGTGGGCC 60.900 55.000 0.00 0.00 0.00 5.80
365 379 1.791230 AGGTGGGCCTAGAAGTCCT 59.209 57.895 4.53 0.00 44.90 3.85
368 382 1.574263 GTGGGCCTAGAAGTCCTCTT 58.426 55.000 4.53 0.00 35.41 2.85
379 393 4.722361 GAAGTCCTCTTCGACCTAACAT 57.278 45.455 0.00 0.00 40.24 2.71
380 394 4.425520 GAAGTCCTCTTCGACCTAACATG 58.574 47.826 0.00 0.00 40.24 3.21
382 396 3.444388 AGTCCTCTTCGACCTAACATGAC 59.556 47.826 0.00 0.00 32.91 3.06
383 397 2.758979 TCCTCTTCGACCTAACATGACC 59.241 50.000 0.00 0.00 0.00 4.02
384 398 2.479730 CCTCTTCGACCTAACATGACCG 60.480 54.545 0.00 0.00 0.00 4.79
386 400 2.821378 TCTTCGACCTAACATGACCGAA 59.179 45.455 0.00 4.36 35.24 4.30
387 401 2.933495 TCGACCTAACATGACCGAAG 57.067 50.000 0.00 0.00 0.00 3.79
388 402 2.439409 TCGACCTAACATGACCGAAGA 58.561 47.619 0.00 0.00 0.00 2.87
389 403 2.422479 TCGACCTAACATGACCGAAGAG 59.578 50.000 0.00 0.00 0.00 2.85
390 404 2.422479 CGACCTAACATGACCGAAGAGA 59.578 50.000 0.00 0.00 0.00 3.10
391 405 3.066900 CGACCTAACATGACCGAAGAGAT 59.933 47.826 0.00 0.00 0.00 2.75
392 406 4.363999 GACCTAACATGACCGAAGAGATG 58.636 47.826 0.00 0.00 0.00 2.90
393 407 4.023980 ACCTAACATGACCGAAGAGATGA 58.976 43.478 0.00 0.00 0.00 2.92
394 408 4.651503 ACCTAACATGACCGAAGAGATGAT 59.348 41.667 0.00 0.00 0.00 2.45
399 413 3.165058 TGACCGAAGAGATGATTTCCG 57.835 47.619 0.00 0.00 0.00 4.30
400 414 2.159099 TGACCGAAGAGATGATTTCCGG 60.159 50.000 0.00 0.00 0.00 5.14
401 415 1.221414 CCGAAGAGATGATTTCCGGC 58.779 55.000 0.00 0.00 0.00 6.13
402 416 1.202580 CCGAAGAGATGATTTCCGGCT 60.203 52.381 0.00 0.00 0.00 5.52
403 417 1.863454 CGAAGAGATGATTTCCGGCTG 59.137 52.381 0.00 0.00 0.00 4.85
425 455 4.631377 TGGAGCTAAAACGAAGATCACATG 59.369 41.667 0.00 0.00 30.94 3.21
428 458 6.348540 GGAGCTAAAACGAAGATCACATGTTT 60.349 38.462 0.00 0.00 34.46 2.83
429 459 7.148474 GGAGCTAAAACGAAGATCACATGTTTA 60.148 37.037 0.00 0.00 32.84 2.01
431 461 6.466097 GCTAAAACGAAGATCACATGTTTAGC 59.534 38.462 18.89 18.89 32.84 3.09
448 479 0.314935 AGCCCATGCGTGAACAAAAG 59.685 50.000 7.72 0.00 44.33 2.27
449 480 0.313672 GCCCATGCGTGAACAAAAGA 59.686 50.000 7.72 0.00 0.00 2.52
461 492 2.115343 ACAAAAGATCCTCTTCGGCC 57.885 50.000 0.00 0.00 35.27 6.13
484 515 1.370414 CGCGGACAAAAACTGGCTG 60.370 57.895 0.00 0.00 43.22 4.85
485 516 1.781025 CGCGGACAAAAACTGGCTGA 61.781 55.000 0.00 0.00 42.97 4.26
488 522 1.032014 GGACAAAAACTGGCTGAGCA 58.968 50.000 6.82 0.00 31.36 4.26
507 541 0.460284 ATGGCTACGAACCAAGAGCG 60.460 55.000 0.00 0.00 41.49 5.03
510 544 1.810030 CTACGAACCAAGAGCGCCC 60.810 63.158 2.29 0.00 0.00 6.13
514 548 2.034221 AACCAAGAGCGCCCCTTC 59.966 61.111 2.29 0.00 0.00 3.46
539 573 3.873883 ACGCGACCGACGAGATCC 61.874 66.667 15.93 0.00 44.01 3.36
543 577 0.879400 GCGACCGACGAGATCCTAGA 60.879 60.000 0.00 0.00 45.77 2.43
627 661 5.964958 AAAAAGAATCAAAGCTGATCCGA 57.035 34.783 0.00 0.00 41.66 4.55
628 662 4.954092 AAAGAATCAAAGCTGATCCGAC 57.046 40.909 0.00 0.00 41.66 4.79
629 663 3.616956 AGAATCAAAGCTGATCCGACA 57.383 42.857 0.00 0.00 41.66 4.35
630 664 4.148128 AGAATCAAAGCTGATCCGACAT 57.852 40.909 0.00 0.00 41.66 3.06
631 665 3.875727 AGAATCAAAGCTGATCCGACATG 59.124 43.478 0.00 0.00 41.66 3.21
632 666 2.768253 TCAAAGCTGATCCGACATGT 57.232 45.000 0.00 0.00 0.00 3.21
633 667 3.885724 TCAAAGCTGATCCGACATGTA 57.114 42.857 0.00 0.00 0.00 2.29
634 668 4.200838 TCAAAGCTGATCCGACATGTAA 57.799 40.909 0.00 0.00 0.00 2.41
635 669 4.574892 TCAAAGCTGATCCGACATGTAAA 58.425 39.130 0.00 0.00 0.00 2.01
636 670 4.631377 TCAAAGCTGATCCGACATGTAAAG 59.369 41.667 0.00 0.00 0.00 1.85
637 671 2.555199 AGCTGATCCGACATGTAAAGC 58.445 47.619 0.00 2.15 0.00 3.51
638 672 1.599542 GCTGATCCGACATGTAAAGCC 59.400 52.381 0.00 0.00 0.00 4.35
639 673 1.860950 CTGATCCGACATGTAAAGCCG 59.139 52.381 0.00 0.00 0.00 5.52
640 674 1.478916 TGATCCGACATGTAAAGCCGA 59.521 47.619 0.00 0.00 0.00 5.54
641 675 2.093921 TGATCCGACATGTAAAGCCGAA 60.094 45.455 0.00 0.00 0.00 4.30
642 676 2.004583 TCCGACATGTAAAGCCGAAG 57.995 50.000 0.00 0.00 0.00 3.79
656 690 1.949257 CGAAGGGCATTAATCCGGC 59.051 57.895 0.00 0.00 0.00 6.13
657 691 0.817634 CGAAGGGCATTAATCCGGCA 60.818 55.000 0.00 0.00 0.00 5.69
658 692 1.620822 GAAGGGCATTAATCCGGCAT 58.379 50.000 0.00 0.00 0.00 4.40
659 693 1.541588 GAAGGGCATTAATCCGGCATC 59.458 52.381 0.00 0.00 0.00 3.91
660 694 0.478072 AGGGCATTAATCCGGCATCA 59.522 50.000 0.00 0.00 0.00 3.07
661 695 1.133513 AGGGCATTAATCCGGCATCAA 60.134 47.619 0.00 0.00 0.00 2.57
662 696 1.270550 GGGCATTAATCCGGCATCAAG 59.729 52.381 0.00 0.00 0.00 3.02
663 697 1.956477 GGCATTAATCCGGCATCAAGT 59.044 47.619 0.00 0.00 0.00 3.16
664 698 2.030805 GGCATTAATCCGGCATCAAGTC 60.031 50.000 0.00 0.00 0.00 3.01
665 699 2.030805 GCATTAATCCGGCATCAAGTCC 60.031 50.000 0.00 0.00 0.00 3.85
666 700 3.213506 CATTAATCCGGCATCAAGTCCA 58.786 45.455 0.00 0.00 0.00 4.02
667 701 2.620251 TAATCCGGCATCAAGTCCAG 57.380 50.000 0.00 0.00 0.00 3.86
668 702 0.749454 AATCCGGCATCAAGTCCAGC 60.749 55.000 0.00 0.00 0.00 4.85
669 703 1.913951 ATCCGGCATCAAGTCCAGCA 61.914 55.000 0.00 0.00 0.00 4.41
670 704 1.452651 CCGGCATCAAGTCCAGCAT 60.453 57.895 0.00 0.00 0.00 3.79
671 705 1.442526 CCGGCATCAAGTCCAGCATC 61.443 60.000 0.00 0.00 0.00 3.91
672 706 0.463295 CGGCATCAAGTCCAGCATCT 60.463 55.000 0.00 0.00 0.00 2.90
673 707 1.022735 GGCATCAAGTCCAGCATCTG 58.977 55.000 0.00 0.00 0.00 2.90
674 708 1.407851 GGCATCAAGTCCAGCATCTGA 60.408 52.381 0.00 0.00 32.44 3.27
675 709 1.941294 GCATCAAGTCCAGCATCTGAG 59.059 52.381 0.00 0.00 32.44 3.35
676 710 1.941294 CATCAAGTCCAGCATCTGAGC 59.059 52.381 0.00 0.00 32.44 4.26
677 711 0.978907 TCAAGTCCAGCATCTGAGCA 59.021 50.000 0.00 0.00 36.85 4.26
678 712 1.348696 TCAAGTCCAGCATCTGAGCAA 59.651 47.619 0.00 0.00 36.85 3.91
679 713 1.738350 CAAGTCCAGCATCTGAGCAAG 59.262 52.381 0.00 0.00 36.85 4.01
680 714 0.252479 AGTCCAGCATCTGAGCAAGG 59.748 55.000 0.00 0.00 36.85 3.61
681 715 1.077930 TCCAGCATCTGAGCAAGGC 60.078 57.895 0.00 0.00 36.85 4.35
682 716 1.077644 CCAGCATCTGAGCAAGGCT 60.078 57.895 0.00 0.00 43.88 4.58
774 808 2.290896 TGGAAGCAGATTGGTACCAAGG 60.291 50.000 30.00 22.15 39.47 3.61
943 990 3.148279 CTAGGACGAGGCCGGCTT 61.148 66.667 28.56 21.53 44.92 4.35
1021 1077 4.322801 CGCCTTCTTCTTCCTTTCTTCCTA 60.323 45.833 0.00 0.00 0.00 2.94
1143 1199 1.226974 CCCGTACATGCACTCCGAG 60.227 63.158 0.00 0.00 0.00 4.63
1277 1345 4.641396 TCGTTTGATTTGATGTGTCCTCT 58.359 39.130 0.00 0.00 0.00 3.69
1294 1382 4.336713 GTCCTCTTGTTCTGCTTTTGACTT 59.663 41.667 0.00 0.00 0.00 3.01
1297 1385 5.163622 CCTCTTGTTCTGCTTTTGACTTTGA 60.164 40.000 0.00 0.00 0.00 2.69
1361 1449 5.449553 TGAGCTAGATCTGATGGTGTTCTA 58.550 41.667 9.79 0.00 0.00 2.10
1415 1503 6.219417 TGTTGTGTTTGAAGGAACAATCAT 57.781 33.333 0.00 0.00 40.86 2.45
1474 1564 3.370840 TCTTGCCTTGGTGATTAGCAT 57.629 42.857 0.00 0.00 33.73 3.79
1601 1691 7.716799 TGTGGGAATGCTCATTATTAAGTTT 57.283 32.000 0.00 0.00 0.00 2.66
1666 1764 7.754475 TGTGCACATGCTATTTATTTACACTTG 59.246 33.333 17.42 0.00 42.66 3.16
1790 1904 6.942976 TGCAGGCTAGTTTAGTGTATTTAGT 58.057 36.000 0.00 0.00 0.00 2.24
1795 1909 7.181485 AGGCTAGTTTAGTGTATTTAGTTGGGA 59.819 37.037 0.00 0.00 0.00 4.37
1906 2034 4.935808 GGCTGCTTAGCAACTTCTAAGTTA 59.064 41.667 8.68 0.00 46.89 2.24
1997 2129 2.554032 ACAATGTGCTCCTGTTGCTTAC 59.446 45.455 0.00 0.00 0.00 2.34
2005 2137 3.420893 CTCCTGTTGCTTACCAAATGGA 58.579 45.455 6.42 0.00 38.94 3.41
2064 2196 7.110155 AGGTACTACCATGAACTAATTGTTGG 58.890 38.462 8.01 0.00 41.95 3.77
2086 2218 9.833182 GTTGGTTAGTACTCTTAGTAGTTGTAC 57.167 37.037 0.00 0.00 35.97 2.90
2160 2292 2.229792 GTTCAGTGGGTTGATGAGCAA 58.770 47.619 0.00 0.00 0.00 3.91
2212 2344 4.344679 TGAAGCTTTGGTCAATGGTTGAAT 59.655 37.500 15.37 0.00 42.15 2.57
2275 2407 9.624697 GTGCTTTAACTATTCATCATTTGACAA 57.375 29.630 0.00 0.00 32.84 3.18
2439 2571 1.672881 GTGGCTGGTATGAATGCAGAC 59.327 52.381 0.00 0.00 35.54 3.51
2513 2645 1.159713 TGCAACCTGACAAGTGCTCG 61.160 55.000 6.31 0.00 0.00 5.03
2595 2727 4.786425 AGGCTAGGATGAATTTGGAGTTC 58.214 43.478 0.00 0.00 0.00 3.01
2667 2799 1.609072 GAGTTGAAGTTCCAGGTTGCC 59.391 52.381 0.00 0.00 0.00 4.52
2680 2812 0.391661 GGTTGCCGATCTGCTGAAGA 60.392 55.000 10.62 0.00 39.94 2.87
2771 2903 4.432712 GAGAAGCTGAAGGAGAAGATCAC 58.567 47.826 0.00 0.00 0.00 3.06
2822 2954 9.159364 CTGAACAAGATGAATTGAGATTAGTGA 57.841 33.333 0.00 0.00 34.20 3.41
2846 2978 6.186957 AGCATTTGATGACCCACAAGTATAA 58.813 36.000 0.00 0.00 0.00 0.98
2879 3011 7.009568 TCGTAGTCCTTTCGATAAGTAAGAC 57.990 40.000 0.00 0.00 29.89 3.01
2918 3051 4.122776 GAGCAGAAGGAAATGATAAGCGA 58.877 43.478 0.00 0.00 0.00 4.93
2943 3076 5.880054 TTTAGCAAGGTATTCTCTGCAAC 57.120 39.130 0.00 0.00 34.34 4.17
3055 3190 3.006859 GCCCAATCCTTTTGTAGCAAAGT 59.993 43.478 0.00 0.00 0.00 2.66
3319 3454 2.291735 ACATGTGGATCCAAATCAGCCA 60.292 45.455 18.20 8.83 33.21 4.75
3480 3615 4.946478 AGAGGCTAGACAACATACATCC 57.054 45.455 0.00 0.00 0.00 3.51
3572 3707 8.286800 CAGGAACGAACATAATTACTCACAAAA 58.713 33.333 0.00 0.00 0.00 2.44
3691 3826 6.210784 AGGAGTAATCAACACTACTAGCAACA 59.789 38.462 0.00 0.00 35.34 3.33
3787 3922 3.285484 GCTGGTGAAGATGTTGATGGAT 58.715 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.051812 ACTACACTGCTCCAGTTGCT 58.948 50.000 0.00 0.00 42.59 3.91
2 3 1.151668 CACTACACTGCTCCAGTTGC 58.848 55.000 0.00 0.00 42.59 4.17
3 4 1.070758 ACCACTACACTGCTCCAGTTG 59.929 52.381 0.00 0.00 42.59 3.16
4 5 1.070758 CACCACTACACTGCTCCAGTT 59.929 52.381 0.00 0.00 42.59 3.16
5 6 0.681733 CACCACTACACTGCTCCAGT 59.318 55.000 0.00 0.00 46.51 4.00
6 7 0.969149 TCACCACTACACTGCTCCAG 59.031 55.000 0.00 0.00 37.52 3.86
7 8 1.644509 ATCACCACTACACTGCTCCA 58.355 50.000 0.00 0.00 0.00 3.86
8 9 2.761208 ACTATCACCACTACACTGCTCC 59.239 50.000 0.00 0.00 0.00 4.70
9 10 5.278561 GGATACTATCACCACTACACTGCTC 60.279 48.000 0.00 0.00 0.00 4.26
10 11 4.585162 GGATACTATCACCACTACACTGCT 59.415 45.833 0.00 0.00 0.00 4.24
11 12 4.262079 GGGATACTATCACCACTACACTGC 60.262 50.000 0.00 0.00 0.00 4.40
12 13 5.455056 GGGATACTATCACCACTACACTG 57.545 47.826 0.00 0.00 0.00 3.66
22 23 6.885922 ACAAAACACTAGGGGATACTATCAC 58.114 40.000 0.00 0.00 0.00 3.06
23 24 7.504926 AACAAAACACTAGGGGATACTATCA 57.495 36.000 0.00 0.00 0.00 2.15
24 25 8.921205 TCTAACAAAACACTAGGGGATACTATC 58.079 37.037 0.00 0.00 0.00 2.08
25 26 8.849543 TCTAACAAAACACTAGGGGATACTAT 57.150 34.615 0.00 0.00 0.00 2.12
26 27 8.849543 ATCTAACAAAACACTAGGGGATACTA 57.150 34.615 0.00 0.00 0.00 1.82
27 28 7.750947 ATCTAACAAAACACTAGGGGATACT 57.249 36.000 0.00 0.00 0.00 2.12
30 31 9.990868 AAATAATCTAACAAAACACTAGGGGAT 57.009 29.630 0.00 0.00 0.00 3.85
31 32 9.816787 AAAATAATCTAACAAAACACTAGGGGA 57.183 29.630 0.00 0.00 0.00 4.81
55 56 9.680315 CCTAACAACCGTAATTTTTCATGTAAA 57.320 29.630 0.00 0.00 0.00 2.01
56 57 8.298140 CCCTAACAACCGTAATTTTTCATGTAA 58.702 33.333 0.00 0.00 0.00 2.41
57 58 7.447853 ACCCTAACAACCGTAATTTTTCATGTA 59.552 33.333 0.00 0.00 0.00 2.29
58 59 6.265876 ACCCTAACAACCGTAATTTTTCATGT 59.734 34.615 0.00 0.00 0.00 3.21
59 60 6.683715 ACCCTAACAACCGTAATTTTTCATG 58.316 36.000 0.00 0.00 0.00 3.07
60 61 6.348704 CGACCCTAACAACCGTAATTTTTCAT 60.349 38.462 0.00 0.00 0.00 2.57
61 62 5.049543 CGACCCTAACAACCGTAATTTTTCA 60.050 40.000 0.00 0.00 0.00 2.69
62 63 5.179182 TCGACCCTAACAACCGTAATTTTTC 59.821 40.000 0.00 0.00 0.00 2.29
63 64 5.049474 GTCGACCCTAACAACCGTAATTTTT 60.049 40.000 3.51 0.00 0.00 1.94
64 65 4.452114 GTCGACCCTAACAACCGTAATTTT 59.548 41.667 3.51 0.00 0.00 1.82
65 66 3.996363 GTCGACCCTAACAACCGTAATTT 59.004 43.478 3.51 0.00 0.00 1.82
66 67 3.259123 AGTCGACCCTAACAACCGTAATT 59.741 43.478 13.01 0.00 0.00 1.40
67 68 2.827921 AGTCGACCCTAACAACCGTAAT 59.172 45.455 13.01 0.00 0.00 1.89
68 69 2.238521 AGTCGACCCTAACAACCGTAA 58.761 47.619 13.01 0.00 0.00 3.18
69 70 1.909700 AGTCGACCCTAACAACCGTA 58.090 50.000 13.01 0.00 0.00 4.02
70 71 1.909700 TAGTCGACCCTAACAACCGT 58.090 50.000 13.01 0.00 0.00 4.83
71 72 3.515330 AATAGTCGACCCTAACAACCG 57.485 47.619 13.01 0.00 0.00 4.44
72 73 4.572909 ACAAATAGTCGACCCTAACAACC 58.427 43.478 13.01 0.00 0.00 3.77
73 74 5.697633 TGAACAAATAGTCGACCCTAACAAC 59.302 40.000 13.01 0.00 0.00 3.32
74 75 5.856156 TGAACAAATAGTCGACCCTAACAA 58.144 37.500 13.01 0.00 0.00 2.83
75 76 5.011329 ACTGAACAAATAGTCGACCCTAACA 59.989 40.000 13.01 2.39 0.00 2.41
76 77 5.347907 CACTGAACAAATAGTCGACCCTAAC 59.652 44.000 13.01 0.00 0.00 2.34
77 78 5.011329 ACACTGAACAAATAGTCGACCCTAA 59.989 40.000 13.01 0.00 0.00 2.69
78 79 4.525487 ACACTGAACAAATAGTCGACCCTA 59.475 41.667 13.01 0.00 0.00 3.53
79 80 3.323979 ACACTGAACAAATAGTCGACCCT 59.676 43.478 13.01 0.00 0.00 4.34
80 81 3.432252 CACACTGAACAAATAGTCGACCC 59.568 47.826 13.01 0.00 0.00 4.46
81 82 4.056050 ACACACTGAACAAATAGTCGACC 58.944 43.478 13.01 0.00 0.00 4.79
82 83 5.652744 AACACACTGAACAAATAGTCGAC 57.347 39.130 7.70 7.70 0.00 4.20
83 84 6.741109 TCTAACACACTGAACAAATAGTCGA 58.259 36.000 0.00 0.00 0.00 4.20
84 85 7.411912 CCATCTAACACACTGAACAAATAGTCG 60.412 40.741 0.00 0.00 0.00 4.18
85 86 7.624344 GCCATCTAACACACTGAACAAATAGTC 60.624 40.741 0.00 0.00 0.00 2.59
86 87 6.149474 GCCATCTAACACACTGAACAAATAGT 59.851 38.462 0.00 0.00 0.00 2.12
87 88 6.149308 TGCCATCTAACACACTGAACAAATAG 59.851 38.462 0.00 0.00 0.00 1.73
88 89 6.000840 TGCCATCTAACACACTGAACAAATA 58.999 36.000 0.00 0.00 0.00 1.40
89 90 4.826733 TGCCATCTAACACACTGAACAAAT 59.173 37.500 0.00 0.00 0.00 2.32
90 91 4.203226 TGCCATCTAACACACTGAACAAA 58.797 39.130 0.00 0.00 0.00 2.83
91 92 3.814625 TGCCATCTAACACACTGAACAA 58.185 40.909 0.00 0.00 0.00 2.83
92 93 3.483808 TGCCATCTAACACACTGAACA 57.516 42.857 0.00 0.00 0.00 3.18
95 96 5.159273 TGTATTGCCATCTAACACACTGA 57.841 39.130 0.00 0.00 0.00 3.41
98 99 5.880054 AGTTGTATTGCCATCTAACACAC 57.120 39.130 0.00 0.00 0.00 3.82
109 110 4.226761 GTGCTACACAAAGTTGTATTGCC 58.773 43.478 6.46 0.00 39.91 4.52
127 128 2.341257 GATTCAGACATGTCACGTGCT 58.659 47.619 27.02 8.11 0.00 4.40
131 132 1.280982 CCGGATTCAGACATGTCACG 58.719 55.000 27.02 17.36 0.00 4.35
149 150 5.163550 GGCCATAGTAAACAGTGAAATTCCC 60.164 44.000 0.00 0.00 0.00 3.97
161 162 3.555168 CCATCTCCGAGGCCATAGTAAAC 60.555 52.174 5.01 0.00 0.00 2.01
172 173 2.959030 TCATACAACTCCATCTCCGAGG 59.041 50.000 0.00 0.00 0.00 4.63
174 175 3.361786 TGTCATACAACTCCATCTCCGA 58.638 45.455 0.00 0.00 0.00 4.55
175 176 3.801114 TGTCATACAACTCCATCTCCG 57.199 47.619 0.00 0.00 0.00 4.63
181 182 4.832823 TCTCACTCTTGTCATACAACTCCA 59.167 41.667 0.00 0.00 33.96 3.86
214 215 4.316205 TTTTTCCTTCCCGCTCTTTTTC 57.684 40.909 0.00 0.00 0.00 2.29
232 233 4.326826 TCATTCTCTCTCACGCCATTTTT 58.673 39.130 0.00 0.00 0.00 1.94
237 251 2.102578 TCATCATTCTCTCTCACGCCA 58.897 47.619 0.00 0.00 0.00 5.69
242 256 5.022122 ACAGTCCTTCATCATTCTCTCTCA 58.978 41.667 0.00 0.00 0.00 3.27
299 313 6.017109 GCATGTTGTTATTAGTCCGGATGATT 60.017 38.462 7.81 0.00 0.00 2.57
303 317 4.776349 TGCATGTTGTTATTAGTCCGGAT 58.224 39.130 7.81 0.00 0.00 4.18
314 328 3.958704 CAACCGAAGTTGCATGTTGTTA 58.041 40.909 0.00 0.00 46.43 2.41
332 346 2.288395 CCCACCTCTTTGCATGAACAAC 60.288 50.000 0.00 0.00 0.00 3.32
334 348 1.619654 CCCACCTCTTTGCATGAACA 58.380 50.000 0.00 0.00 0.00 3.18
335 349 0.244721 GCCCACCTCTTTGCATGAAC 59.755 55.000 0.00 0.00 0.00 3.18
336 350 0.899717 GGCCCACCTCTTTGCATGAA 60.900 55.000 0.00 0.00 0.00 2.57
338 352 0.034186 TAGGCCCACCTCTTTGCATG 60.034 55.000 0.00 0.00 46.34 4.06
339 353 0.257039 CTAGGCCCACCTCTTTGCAT 59.743 55.000 0.00 0.00 46.34 3.96
341 355 0.328258 TTCTAGGCCCACCTCTTTGC 59.672 55.000 0.00 0.00 46.34 3.68
342 356 1.630878 ACTTCTAGGCCCACCTCTTTG 59.369 52.381 0.00 0.00 46.34 2.77
343 357 1.909986 GACTTCTAGGCCCACCTCTTT 59.090 52.381 0.00 0.00 46.34 2.52
346 360 2.213280 GGACTTCTAGGCCCACCTC 58.787 63.158 0.00 0.00 46.34 3.85
352 366 1.406180 GTCGAAGAGGACTTCTAGGCC 59.594 57.143 0.00 0.00 46.64 5.19
358 372 4.158025 TCATGTTAGGTCGAAGAGGACTTC 59.842 45.833 0.00 0.00 46.21 3.01
360 374 3.444388 GTCATGTTAGGTCGAAGAGGACT 59.556 47.826 0.00 0.00 36.95 3.85
361 375 3.429135 GGTCATGTTAGGTCGAAGAGGAC 60.429 52.174 0.00 0.00 36.95 3.85
362 376 2.758979 GGTCATGTTAGGTCGAAGAGGA 59.241 50.000 0.00 0.00 36.95 3.71
363 377 2.479730 CGGTCATGTTAGGTCGAAGAGG 60.480 54.545 0.00 0.00 36.95 3.69
365 379 2.439409 TCGGTCATGTTAGGTCGAAGA 58.561 47.619 0.00 0.00 0.00 2.87
368 382 2.422479 CTCTTCGGTCATGTTAGGTCGA 59.578 50.000 0.00 0.00 0.00 4.20
369 383 2.422479 TCTCTTCGGTCATGTTAGGTCG 59.578 50.000 0.00 0.00 0.00 4.79
370 384 4.098044 TCATCTCTTCGGTCATGTTAGGTC 59.902 45.833 0.00 0.00 0.00 3.85
372 386 4.655762 TCATCTCTTCGGTCATGTTAGG 57.344 45.455 0.00 0.00 0.00 2.69
373 387 6.201806 GGAAATCATCTCTTCGGTCATGTTAG 59.798 42.308 0.00 0.00 0.00 2.34
374 388 6.049149 GGAAATCATCTCTTCGGTCATGTTA 58.951 40.000 0.00 0.00 0.00 2.41
376 390 4.446371 GGAAATCATCTCTTCGGTCATGT 58.554 43.478 0.00 0.00 0.00 3.21
377 391 3.492383 CGGAAATCATCTCTTCGGTCATG 59.508 47.826 0.00 0.00 0.00 3.07
379 393 2.159099 CCGGAAATCATCTCTTCGGTCA 60.159 50.000 0.00 0.00 0.00 4.02
380 394 2.474816 CCGGAAATCATCTCTTCGGTC 58.525 52.381 0.00 0.00 0.00 4.79
382 396 1.202580 AGCCGGAAATCATCTCTTCGG 60.203 52.381 5.05 0.00 0.00 4.30
383 397 1.863454 CAGCCGGAAATCATCTCTTCG 59.137 52.381 5.05 0.00 0.00 3.79
384 398 2.158900 TCCAGCCGGAAATCATCTCTTC 60.159 50.000 5.05 0.00 38.83 2.87
386 400 1.415659 CTCCAGCCGGAAATCATCTCT 59.584 52.381 5.05 0.00 42.21 3.10
387 401 1.876322 CTCCAGCCGGAAATCATCTC 58.124 55.000 5.05 0.00 42.21 2.75
388 402 0.179034 GCTCCAGCCGGAAATCATCT 60.179 55.000 5.05 0.00 42.21 2.90
389 403 0.179034 AGCTCCAGCCGGAAATCATC 60.179 55.000 5.05 0.00 42.21 2.92
390 404 1.131638 TAGCTCCAGCCGGAAATCAT 58.868 50.000 5.05 0.00 42.21 2.45
391 405 0.908910 TTAGCTCCAGCCGGAAATCA 59.091 50.000 5.05 0.00 42.21 2.57
392 406 2.038387 TTTAGCTCCAGCCGGAAATC 57.962 50.000 5.05 0.00 42.21 2.17
393 407 2.092323 GTTTTAGCTCCAGCCGGAAAT 58.908 47.619 5.05 0.00 42.21 2.17
394 408 1.530323 GTTTTAGCTCCAGCCGGAAA 58.470 50.000 5.05 0.00 42.21 3.13
399 413 2.094762 TCTTCGTTTTAGCTCCAGCC 57.905 50.000 0.00 0.00 43.38 4.85
400 414 3.062774 GTGATCTTCGTTTTAGCTCCAGC 59.937 47.826 0.00 0.00 42.49 4.85
401 415 4.245660 TGTGATCTTCGTTTTAGCTCCAG 58.754 43.478 0.00 0.00 0.00 3.86
402 416 4.265904 TGTGATCTTCGTTTTAGCTCCA 57.734 40.909 0.00 0.00 0.00 3.86
403 417 4.631813 ACATGTGATCTTCGTTTTAGCTCC 59.368 41.667 0.00 0.00 0.00 4.70
409 439 5.335661 GGGCTAAACATGTGATCTTCGTTTT 60.336 40.000 0.00 0.00 32.42 2.43
425 455 0.878416 TGTTCACGCATGGGCTAAAC 59.122 50.000 10.10 11.70 38.10 2.01
428 458 1.539388 CTTTTGTTCACGCATGGGCTA 59.461 47.619 10.10 0.00 38.10 3.93
429 459 0.314935 CTTTTGTTCACGCATGGGCT 59.685 50.000 10.10 0.00 38.10 5.19
431 461 2.415893 GGATCTTTTGTTCACGCATGGG 60.416 50.000 8.44 8.44 0.00 4.00
461 492 2.127383 GTTTTTGTCCGCGCCTCG 60.127 61.111 0.00 0.00 38.08 4.63
467 498 0.040067 CTCAGCCAGTTTTTGTCCGC 60.040 55.000 0.00 0.00 0.00 5.54
484 515 1.009829 CTTGGTTCGTAGCCATGCTC 58.990 55.000 0.00 0.00 40.44 4.26
485 516 0.613260 TCTTGGTTCGTAGCCATGCT 59.387 50.000 0.00 0.00 43.41 3.79
488 522 0.460284 CGCTCTTGGTTCGTAGCCAT 60.460 55.000 0.00 0.00 35.71 4.40
526 560 3.854045 GCATTTCTAGGATCTCGTCGGTC 60.854 52.174 0.00 0.00 0.00 4.79
530 564 6.610741 AAATTGCATTTCTAGGATCTCGTC 57.389 37.500 0.00 0.00 0.00 4.20
605 639 5.241506 TGTCGGATCAGCTTTGATTCTTTTT 59.758 36.000 0.00 0.00 0.00 1.94
606 640 4.761739 TGTCGGATCAGCTTTGATTCTTTT 59.238 37.500 0.00 0.00 0.00 2.27
607 641 4.326826 TGTCGGATCAGCTTTGATTCTTT 58.673 39.130 0.00 0.00 0.00 2.52
608 642 3.942829 TGTCGGATCAGCTTTGATTCTT 58.057 40.909 0.00 0.00 0.00 2.52
609 643 3.616956 TGTCGGATCAGCTTTGATTCT 57.383 42.857 0.00 0.00 0.00 2.40
610 644 3.624861 ACATGTCGGATCAGCTTTGATTC 59.375 43.478 0.00 0.00 0.00 2.52
611 645 3.614092 ACATGTCGGATCAGCTTTGATT 58.386 40.909 0.00 0.00 0.00 2.57
612 646 3.272574 ACATGTCGGATCAGCTTTGAT 57.727 42.857 0.00 0.00 0.00 2.57
613 647 2.768253 ACATGTCGGATCAGCTTTGA 57.232 45.000 0.00 0.00 0.00 2.69
614 648 4.728882 GCTTTACATGTCGGATCAGCTTTG 60.729 45.833 0.00 0.00 0.00 2.77
615 649 3.375299 GCTTTACATGTCGGATCAGCTTT 59.625 43.478 0.00 0.00 0.00 3.51
616 650 2.939103 GCTTTACATGTCGGATCAGCTT 59.061 45.455 0.00 0.00 0.00 3.74
617 651 2.555199 GCTTTACATGTCGGATCAGCT 58.445 47.619 0.00 0.00 0.00 4.24
618 652 1.599542 GGCTTTACATGTCGGATCAGC 59.400 52.381 0.00 2.02 0.00 4.26
619 653 1.860950 CGGCTTTACATGTCGGATCAG 59.139 52.381 0.00 0.00 0.00 2.90
620 654 1.478916 TCGGCTTTACATGTCGGATCA 59.521 47.619 0.00 0.00 32.95 2.92
621 655 2.218953 TCGGCTTTACATGTCGGATC 57.781 50.000 0.00 0.00 32.95 3.36
622 656 2.550978 CTTCGGCTTTACATGTCGGAT 58.449 47.619 0.00 0.00 32.95 4.18
623 657 1.404986 CCTTCGGCTTTACATGTCGGA 60.405 52.381 0.00 0.00 32.95 4.55
624 658 1.006832 CCTTCGGCTTTACATGTCGG 58.993 55.000 0.00 0.00 32.95 4.79
625 659 1.006832 CCCTTCGGCTTTACATGTCG 58.993 55.000 0.00 0.00 0.00 4.35
637 671 1.515521 GCCGGATTAATGCCCTTCGG 61.516 60.000 5.05 0.00 39.07 4.30
638 672 0.817634 TGCCGGATTAATGCCCTTCG 60.818 55.000 5.05 0.00 0.00 3.79
639 673 1.541588 GATGCCGGATTAATGCCCTTC 59.458 52.381 5.05 0.00 0.00 3.46
640 674 1.133513 TGATGCCGGATTAATGCCCTT 60.134 47.619 5.05 0.00 0.00 3.95
641 675 0.478072 TGATGCCGGATTAATGCCCT 59.522 50.000 5.05 0.00 0.00 5.19
642 676 1.270550 CTTGATGCCGGATTAATGCCC 59.729 52.381 5.05 0.00 0.00 5.36
643 677 1.956477 ACTTGATGCCGGATTAATGCC 59.044 47.619 5.05 0.00 0.00 4.40
644 678 2.030805 GGACTTGATGCCGGATTAATGC 60.031 50.000 5.05 0.00 0.00 3.56
645 679 3.213506 TGGACTTGATGCCGGATTAATG 58.786 45.455 5.05 0.00 0.00 1.90
646 680 3.480470 CTGGACTTGATGCCGGATTAAT 58.520 45.455 5.05 0.00 32.05 1.40
647 681 2.917933 CTGGACTTGATGCCGGATTAA 58.082 47.619 5.05 0.00 32.05 1.40
648 682 1.475034 GCTGGACTTGATGCCGGATTA 60.475 52.381 5.05 0.00 32.05 1.75
649 683 0.749454 GCTGGACTTGATGCCGGATT 60.749 55.000 5.05 0.00 32.05 3.01
650 684 1.153086 GCTGGACTTGATGCCGGAT 60.153 57.895 5.05 0.00 32.05 4.18
651 685 1.913951 ATGCTGGACTTGATGCCGGA 61.914 55.000 5.05 0.00 32.05 5.14
652 686 1.442526 GATGCTGGACTTGATGCCGG 61.443 60.000 0.00 0.00 0.00 6.13
653 687 0.463295 AGATGCTGGACTTGATGCCG 60.463 55.000 0.00 0.00 0.00 5.69
654 688 1.022735 CAGATGCTGGACTTGATGCC 58.977 55.000 0.00 0.00 0.00 4.40
655 689 1.941294 CTCAGATGCTGGACTTGATGC 59.059 52.381 0.00 0.00 31.51 3.91
656 690 1.941294 GCTCAGATGCTGGACTTGATG 59.059 52.381 0.00 0.00 31.51 3.07
657 691 1.558294 TGCTCAGATGCTGGACTTGAT 59.442 47.619 0.00 0.00 31.51 2.57
658 692 0.978907 TGCTCAGATGCTGGACTTGA 59.021 50.000 0.00 0.00 31.51 3.02
659 693 1.738350 CTTGCTCAGATGCTGGACTTG 59.262 52.381 0.00 0.00 31.51 3.16
660 694 1.339824 CCTTGCTCAGATGCTGGACTT 60.340 52.381 0.00 0.00 32.29 3.01
661 695 0.252479 CCTTGCTCAGATGCTGGACT 59.748 55.000 0.00 0.00 32.29 3.85
662 696 1.375098 GCCTTGCTCAGATGCTGGAC 61.375 60.000 0.00 0.00 32.29 4.02
663 697 1.077930 GCCTTGCTCAGATGCTGGA 60.078 57.895 0.00 0.00 32.29 3.86
664 698 1.077644 AGCCTTGCTCAGATGCTGG 60.078 57.895 0.00 0.00 30.62 4.85
665 699 4.639776 AGCCTTGCTCAGATGCTG 57.360 55.556 0.00 0.00 30.62 4.41
681 715 4.504916 CAGTCTGCCTCCGCCGAG 62.505 72.222 0.00 0.00 35.72 4.63
685 719 3.890936 AACTGCAGTCTGCCTCCGC 62.891 63.158 21.95 0.00 44.23 5.54
686 720 1.739562 GAACTGCAGTCTGCCTCCG 60.740 63.158 21.95 10.13 44.23 4.63
687 721 0.035630 ATGAACTGCAGTCTGCCTCC 60.036 55.000 21.95 9.12 44.23 4.30
688 722 1.066286 AGATGAACTGCAGTCTGCCTC 60.066 52.381 21.95 14.14 44.23 4.70
689 723 0.982704 AGATGAACTGCAGTCTGCCT 59.017 50.000 21.95 12.43 44.23 4.75
690 724 1.085091 CAGATGAACTGCAGTCTGCC 58.915 55.000 21.95 10.27 44.23 4.85
700 734 1.079819 CCGTCGGTGCAGATGAACT 60.080 57.895 2.08 0.00 0.00 3.01
701 735 1.078759 CTCCGTCGGTGCAGATGAAC 61.079 60.000 11.88 0.00 0.00 3.18
702 736 1.215382 CTCCGTCGGTGCAGATGAA 59.785 57.895 11.88 0.00 0.00 2.57
703 737 0.678684 TACTCCGTCGGTGCAGATGA 60.679 55.000 11.88 0.00 0.00 2.92
704 738 0.172578 TTACTCCGTCGGTGCAGATG 59.827 55.000 11.88 0.00 0.00 2.90
705 739 0.892755 TTTACTCCGTCGGTGCAGAT 59.107 50.000 11.88 0.00 0.00 2.90
706 740 0.892755 ATTTACTCCGTCGGTGCAGA 59.107 50.000 11.88 0.00 0.00 4.26
707 741 1.393539 CAATTTACTCCGTCGGTGCAG 59.606 52.381 11.88 3.89 0.00 4.41
708 742 1.434555 CAATTTACTCCGTCGGTGCA 58.565 50.000 11.88 0.00 0.00 4.57
709 743 0.096454 GCAATTTACTCCGTCGGTGC 59.904 55.000 11.88 8.10 0.00 5.01
710 744 1.127951 GTGCAATTTACTCCGTCGGTG 59.872 52.381 11.88 11.78 0.00 4.94
711 745 1.270412 TGTGCAATTTACTCCGTCGGT 60.270 47.619 11.88 0.00 0.00 4.69
712 746 1.434555 TGTGCAATTTACTCCGTCGG 58.565 50.000 4.39 4.39 0.00 4.79
713 747 3.529634 TTTGTGCAATTTACTCCGTCG 57.470 42.857 0.00 0.00 0.00 5.12
716 750 5.151389 GGTACTTTTGTGCAATTTACTCCG 58.849 41.667 0.00 0.00 36.74 4.63
774 808 7.071414 GGTACTGACACGTAAAAATTACCAAC 58.929 38.462 0.00 0.00 0.00 3.77
848 884 5.313712 ACCGGTCAGTTTTTCTGTCAATAT 58.686 37.500 0.00 0.00 43.97 1.28
943 990 0.804544 GGCGCGACTATAACAGTGCA 60.805 55.000 12.10 0.00 41.37 4.57
1021 1077 1.662608 CGATGGCGAGGCAGATAGT 59.337 57.895 5.43 0.00 40.82 2.12
1277 1345 5.047377 ACCTTCAAAGTCAAAAGCAGAACAA 60.047 36.000 0.00 0.00 0.00 2.83
1294 1382 2.951642 CAAGTGAGAAAGGCACCTTCAA 59.048 45.455 1.61 0.00 36.95 2.69
1297 1385 2.487986 CCTCAAGTGAGAAAGGCACCTT 60.488 50.000 9.95 0.00 44.74 3.50
1361 1449 0.627451 TGGCTTCCCATGCTTCTCAT 59.373 50.000 0.00 0.00 35.79 2.90
1415 1503 3.330701 ACATGCTAAGAACCTTCTCCCAA 59.669 43.478 0.00 0.00 36.28 4.12
1474 1564 3.573538 CCACTTCCAATGAACACATCCAA 59.426 43.478 0.00 0.00 0.00 3.53
1790 1904 8.356657 CAATACAATGTGAACTACTTTTCCCAA 58.643 33.333 0.00 0.00 0.00 4.12
1906 2034 4.532521 AGGTAGCAGAGTAACACTCCATTT 59.467 41.667 2.74 0.00 46.18 2.32
1997 2129 4.571919 ACTCATTTTGCACATCCATTTGG 58.428 39.130 0.00 0.00 0.00 3.28
2005 2137 6.864685 CACTGACATTAACTCATTTTGCACAT 59.135 34.615 0.00 0.00 0.00 3.21
2046 2178 8.161425 AGTACTAACCAACAATTAGTTCATGGT 58.839 33.333 0.00 0.00 41.84 3.55
2093 2225 9.219603 CCTGGAAAAATTAGAAGGGAAAAATTC 57.780 33.333 0.00 0.00 0.00 2.17
2160 2292 1.002017 CTCCATTGTTGGGGGCCAT 59.998 57.895 4.39 0.00 43.81 4.40
2275 2407 4.099881 TGCATCCAGCTTGTTCTTTTCTTT 59.900 37.500 0.00 0.00 45.94 2.52
2439 2571 4.436242 AGCTGCATCTTTCTTTGTCATG 57.564 40.909 1.02 0.00 0.00 3.07
2513 2645 2.887152 AGGTTTTGGATGACAGTTGCTC 59.113 45.455 0.00 0.00 0.00 4.26
2595 2727 5.179045 ACTTTGTGAACTCTGCATTCTTG 57.821 39.130 0.00 0.00 0.00 3.02
2680 2812 8.884124 TTCTCTTCATTATGGTTTTCCTTGAT 57.116 30.769 0.00 0.00 41.38 2.57
2771 2903 2.455565 AAGATGGCCTGGATCCCCG 61.456 63.158 9.90 0.00 34.29 5.73
2822 2954 2.880443 ACTTGTGGGTCATCAAATGCT 58.120 42.857 0.00 0.00 0.00 3.79
2846 2978 4.073549 CGAAAGGACTACGATAGATCCCT 58.926 47.826 0.00 0.00 41.38 4.20
2879 3011 0.388649 CTCCTCGTTGGGTTCGACAG 60.389 60.000 0.00 0.00 36.20 3.51
2918 3051 7.177392 AGTTGCAGAGAATACCTTGCTAAAAAT 59.823 33.333 0.00 0.00 0.00 1.82
3055 3190 2.922740 AGAGTTTGTTCCGGCTTGTA 57.077 45.000 0.00 0.00 0.00 2.41
3319 3454 5.880054 AGTTTATGCGTTGCTTCATAAGT 57.120 34.783 0.00 0.00 36.76 2.24
3691 3826 1.692519 GTCCGGGATTGGTGCTAGTAT 59.307 52.381 0.00 0.00 0.00 2.12
3787 3922 3.550692 TCATCGGGAGAGGGCAATA 57.449 52.632 0.00 0.00 45.48 1.90


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

AutoCloner maintained by Alex Coulton.