Multiple sequence alignment - TraesCS6D01G148700

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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 TraesCS6D01G148700 chr6D 100.000 4866 0 0 1 4866 122252755 122257620 0.000000e+00 8986
1 TraesCS6D01G148700 chr6B 92.699 1986 76 23 2894 4866 214027695 214029624 0.000000e+00 2800
2 TraesCS6D01G148700 chr6B 91.280 1227 48 20 366 1576 214025200 214026383 0.000000e+00 1618
3 TraesCS6D01G148700 chr6B 89.247 1302 95 22 1582 2869 214026431 214027701 0.000000e+00 1587
4 TraesCS6D01G148700 chr6B 91.321 530 37 7 2308 2829 68960614 68961142 0.000000e+00 715
5 TraesCS6D01G148700 chr6B 90.943 530 39 7 2308 2829 68982459 68982987 0.000000e+00 704
6 TraesCS6D01G148700 chr6B 90.941 287 11 3 1302 1576 23483466 23483183 5.950000e-99 372
7 TraesCS6D01G148700 chr6B 88.152 211 20 3 1582 1790 23483135 23482928 3.760000e-61 246
8 TraesCS6D01G148700 chr6B 82.673 202 35 0 1001 1202 502721672 502721873 3.870000e-41 180
9 TraesCS6D01G148700 chr6B 82.178 202 36 0 1001 1202 705836689 705836488 1.800000e-39 174
10 TraesCS6D01G148700 chr6B 89.796 98 5 1 2014 2111 23482925 23482833 2.380000e-23 121
11 TraesCS6D01G148700 chr6A 93.353 1324 70 11 2875 4193 149926120 149924810 0.000000e+00 1941
12 TraesCS6D01G148700 chr6A 91.762 959 52 12 652 1588 149928455 149927502 0.000000e+00 1308
13 TraesCS6D01G148700 chr6A 87.514 921 84 19 3277 4188 206039434 206040332 0.000000e+00 1035
14 TraesCS6D01G148700 chr6A 91.697 554 24 10 4319 4866 149924514 149923977 0.000000e+00 749
15 TraesCS6D01G148700 chr6A 90.485 557 39 11 2288 2833 149926801 149926248 0.000000e+00 723
16 TraesCS6D01G148700 chr6A 79.560 636 73 30 1587 2190 149927454 149926844 7.590000e-108 401
17 TraesCS6D01G148700 chr6A 95.259 232 6 4 386 612 149929044 149928813 3.580000e-96 363
18 TraesCS6D01G148700 chr1B 90.577 849 56 9 3353 4188 114687004 114687841 0.000000e+00 1103
19 TraesCS6D01G148700 chr1B 91.930 285 12 6 1302 1576 562670545 562670828 5.910000e-104 388
20 TraesCS6D01G148700 chr1B 88.152 211 20 3 1582 1790 562670876 562671083 3.760000e-61 246
21 TraesCS6D01G148700 chr5A 87.885 941 81 17 3258 4188 150629138 150630055 0.000000e+00 1075
22 TraesCS6D01G148700 chr3B 90.755 530 39 8 2308 2829 134460975 134461502 0.000000e+00 699
23 TraesCS6D01G148700 chr3B 90.566 530 38 6 2308 2829 42580403 42580928 0.000000e+00 691
24 TraesCS6D01G148700 chr3B 91.579 285 13 6 1302 1576 627446857 627446574 2.750000e-102 383
25 TraesCS6D01G148700 chr3B 86.256 211 24 3 1582 1790 627446526 627446319 1.760000e-54 224
26 TraesCS6D01G148700 chr3B 90.291 103 5 1 2014 2116 627446316 627446219 3.950000e-26 130
27 TraesCS6D01G148700 chr2B 91.901 284 8 3 1302 1573 750538038 750538318 2.750000e-102 383
28 TraesCS6D01G148700 chr2B 90.291 103 5 1 2014 2116 750538579 750538676 3.950000e-26 130
29 TraesCS6D01G148700 chr7B 84.290 331 52 0 2954 3284 640715971 640716301 1.690000e-84 324
30 TraesCS6D01G148700 chr7B 87.129 202 26 0 1001 1202 640714530 640714731 3.790000e-56 230
31 TraesCS6D01G148700 chr7B 77.465 213 35 7 1001 1202 647011918 647011708 1.110000e-21 115
32 TraesCS6D01G148700 chr4B 93.902 164 10 0 1413 1576 635373782 635373945 1.050000e-61 248
33 TraesCS6D01G148700 chr4B 86.792 212 22 4 1582 1791 635373993 635374200 1.050000e-56 231
34 TraesCS6D01G148700 chr1A 83.168 202 34 0 1001 1202 563755365 563755566 8.320000e-43 185
35 TraesCS6D01G148700 chr3D 82.178 202 36 0 1001 1202 513939350 513939551 1.800000e-39 174
36 TraesCS6D01G148700 chr7A 81.188 202 38 0 1001 1202 612703179 612703380 3.900000e-36 163
37 TraesCS6D01G148700 chr3A 87.500 104 13 0 1 104 203634598 203634495 2.380000e-23 121


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 TraesCS6D01G148700 chr6D 122252755 122257620 4865 False 8986.000000 8986 100.000000 1 4866 1 chr6D.!!$F1 4865
1 TraesCS6D01G148700 chr6B 214025200 214029624 4424 False 2001.666667 2800 91.075333 366 4866 3 chr6B.!!$F4 4500
2 TraesCS6D01G148700 chr6B 68960614 68961142 528 False 715.000000 715 91.321000 2308 2829 1 chr6B.!!$F1 521
3 TraesCS6D01G148700 chr6B 68982459 68982987 528 False 704.000000 704 90.943000 2308 2829 1 chr6B.!!$F2 521
4 TraesCS6D01G148700 chr6B 23482833 23483466 633 True 246.333333 372 89.629667 1302 2111 3 chr6B.!!$R2 809
5 TraesCS6D01G148700 chr6A 206039434 206040332 898 False 1035.000000 1035 87.514000 3277 4188 1 chr6A.!!$F1 911
6 TraesCS6D01G148700 chr6A 149923977 149929044 5067 True 914.166667 1941 90.352667 386 4866 6 chr6A.!!$R1 4480
7 TraesCS6D01G148700 chr1B 114687004 114687841 837 False 1103.000000 1103 90.577000 3353 4188 1 chr1B.!!$F1 835
8 TraesCS6D01G148700 chr1B 562670545 562671083 538 False 317.000000 388 90.041000 1302 1790 2 chr1B.!!$F2 488
9 TraesCS6D01G148700 chr5A 150629138 150630055 917 False 1075.000000 1075 87.885000 3258 4188 1 chr5A.!!$F1 930
10 TraesCS6D01G148700 chr3B 134460975 134461502 527 False 699.000000 699 90.755000 2308 2829 1 chr3B.!!$F2 521
11 TraesCS6D01G148700 chr3B 42580403 42580928 525 False 691.000000 691 90.566000 2308 2829 1 chr3B.!!$F1 521
12 TraesCS6D01G148700 chr3B 627446219 627446857 638 True 245.666667 383 89.375333 1302 2116 3 chr3B.!!$R1 814
13 TraesCS6D01G148700 chr2B 750538038 750538676 638 False 256.500000 383 91.096000 1302 2116 2 chr2B.!!$F1 814
14 TraesCS6D01G148700 chr7B 640714530 640716301 1771 False 277.000000 324 85.709500 1001 3284 2 chr7B.!!$F1 2283

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
311 312 0.241481 GAAAATTTGGCCGGCGTGTA 59.759 50.000 22.54 5.94 0.00 2.90 F
312 313 0.242555 AAAATTTGGCCGGCGTGTAG 59.757 50.000 22.54 0.00 0.00 2.74 F
314 315 0.393808 AATTTGGCCGGCGTGTAGAT 60.394 50.000 22.54 5.44 0.00 1.98 F
323 324 1.094785 GGCGTGTAGATGGCAAACAT 58.905 50.000 0.22 0.00 44.18 2.71 F
2005 2686 1.202855 ACATCTGATGGGCTGGTATGC 60.203 52.381 20.83 0.00 33.60 3.14 F
2010 2691 1.276138 TGATGGGCTGGTATGCTATCG 59.724 52.381 0.00 0.00 33.03 2.92 F
2159 2849 2.366266 ACTTGCATTGCCAACAGACAAT 59.634 40.909 6.12 0.00 36.96 2.71 F
3512 4365 0.519077 CAAGACTTTCGCAGAAGCCC 59.481 55.000 0.00 0.00 45.90 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2737 0.188342 AAAGGGGCACATGGTCTGTT 59.812 50.000 0.00 0.0 35.29 3.16 R
2048 2738 1.072266 TAAAGGGGCACATGGTCTGT 58.928 50.000 0.00 0.0 39.20 3.41 R
2050 2740 1.427368 TGTTAAAGGGGCACATGGTCT 59.573 47.619 0.00 0.0 0.00 3.85 R
2107 2797 1.537202 GCAACACAGTTTAGCCTGGAG 59.463 52.381 0.00 0.0 36.75 3.86 R
3185 4034 0.040425 CCTTGGACTTTGCCGTTTCG 60.040 55.000 0.00 0.0 0.00 3.46 R
3512 4365 0.469917 ACAGTCTTGGTGGTGTCCAG 59.530 55.000 0.00 0.0 38.80 3.86 R
3664 4523 1.361668 GCTTCGCGATTGCCTGAGAA 61.362 55.000 10.88 0.0 38.08 2.87 R
4603 5645 0.095245 CACAATAGCAGGCACGTTCG 59.905 55.000 0.00 0.0 0.00 3.95 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
25 26 3.925238 CGCGCGACCATGGCTTAC 61.925 66.667 28.94 0.00 0.00 2.34
26 27 3.925238 GCGCGACCATGGCTTACG 61.925 66.667 12.10 13.67 0.00 3.18
27 28 2.202690 CGCGACCATGGCTTACGA 60.203 61.111 13.04 0.00 0.00 3.43
28 29 2.230940 CGCGACCATGGCTTACGAG 61.231 63.158 13.04 10.75 0.00 4.18
44 45 2.726887 GAGCTCGTCGACTCAAACC 58.273 57.895 14.70 0.00 32.98 3.27
45 46 1.066114 GAGCTCGTCGACTCAAACCG 61.066 60.000 14.70 0.00 32.98 4.44
46 47 2.717809 GCTCGTCGACTCAAACCGC 61.718 63.158 14.70 1.80 0.00 5.68
47 48 2.049802 TCGTCGACTCAAACCGCC 60.050 61.111 14.70 0.00 0.00 6.13
48 49 3.110178 CGTCGACTCAAACCGCCC 61.110 66.667 14.70 0.00 0.00 6.13
49 50 2.741211 GTCGACTCAAACCGCCCC 60.741 66.667 8.70 0.00 0.00 5.80
50 51 4.011517 TCGACTCAAACCGCCCCC 62.012 66.667 0.00 0.00 0.00 5.40
63 64 4.489771 CCCCCGGCCATCACACTC 62.490 72.222 2.24 0.00 0.00 3.51
64 65 4.838152 CCCCGGCCATCACACTCG 62.838 72.222 2.24 0.00 0.00 4.18
65 66 4.082523 CCCGGCCATCACACTCGT 62.083 66.667 2.24 0.00 0.00 4.18
66 67 2.509336 CCGGCCATCACACTCGTC 60.509 66.667 2.24 0.00 0.00 4.20
67 68 2.880879 CGGCCATCACACTCGTCG 60.881 66.667 2.24 0.00 0.00 5.12
68 69 2.261671 GGCCATCACACTCGTCGT 59.738 61.111 0.00 0.00 0.00 4.34
69 70 1.805945 GGCCATCACACTCGTCGTC 60.806 63.158 0.00 0.00 0.00 4.20
70 71 1.805945 GCCATCACACTCGTCGTCC 60.806 63.158 0.00 0.00 0.00 4.79
71 72 1.883732 CCATCACACTCGTCGTCCT 59.116 57.895 0.00 0.00 0.00 3.85
72 73 0.243907 CCATCACACTCGTCGTCCTT 59.756 55.000 0.00 0.00 0.00 3.36
73 74 1.336887 CCATCACACTCGTCGTCCTTT 60.337 52.381 0.00 0.00 0.00 3.11
74 75 1.721389 CATCACACTCGTCGTCCTTTG 59.279 52.381 0.00 0.00 0.00 2.77
75 76 0.742505 TCACACTCGTCGTCCTTTGT 59.257 50.000 0.00 0.00 0.00 2.83
76 77 1.135527 TCACACTCGTCGTCCTTTGTT 59.864 47.619 0.00 0.00 0.00 2.83
77 78 2.358582 TCACACTCGTCGTCCTTTGTTA 59.641 45.455 0.00 0.00 0.00 2.41
78 79 2.724690 CACACTCGTCGTCCTTTGTTAG 59.275 50.000 0.00 0.00 0.00 2.34
79 80 2.288030 ACACTCGTCGTCCTTTGTTAGG 60.288 50.000 0.00 0.00 46.27 2.69
89 90 1.156736 CTTTGTTAGGAGCACCACCG 58.843 55.000 2.07 0.00 38.94 4.94
90 91 0.887387 TTTGTTAGGAGCACCACCGC 60.887 55.000 2.07 0.00 38.94 5.68
91 92 2.436115 GTTAGGAGCACCACCGCC 60.436 66.667 2.07 0.00 38.94 6.13
92 93 3.712907 TTAGGAGCACCACCGCCC 61.713 66.667 2.07 0.00 38.94 6.13
114 115 3.741476 CTTGCCGGGCTTGCAGAC 61.741 66.667 21.46 0.00 40.35 3.51
118 119 3.136123 CCGGGCTTGCAGACCATG 61.136 66.667 9.10 1.48 46.60 3.66
119 120 3.136123 CGGGCTTGCAGACCATGG 61.136 66.667 11.19 11.19 46.60 3.66
120 121 2.036256 GGGCTTGCAGACCATGGT 59.964 61.111 19.89 19.89 45.15 3.55
121 122 2.345760 GGGCTTGCAGACCATGGTG 61.346 63.158 25.52 10.43 45.15 4.17
122 123 2.570181 GCTTGCAGACCATGGTGC 59.430 61.111 25.52 21.16 40.29 5.01
125 126 2.674033 TGCAGACCATGGTGCAGC 60.674 61.111 25.52 22.26 44.70 5.25
126 127 3.446570 GCAGACCATGGTGCAGCC 61.447 66.667 25.52 7.35 39.62 4.85
127 128 2.753043 CAGACCATGGTGCAGCCC 60.753 66.667 25.52 6.49 36.04 5.19
128 129 4.415150 AGACCATGGTGCAGCCCG 62.415 66.667 25.52 3.94 36.04 6.13
146 147 4.436998 CGCTCGTCACCCCAGACC 62.437 72.222 0.00 0.00 35.07 3.85
147 148 3.311110 GCTCGTCACCCCAGACCA 61.311 66.667 0.00 0.00 35.07 4.02
148 149 2.657237 CTCGTCACCCCAGACCAC 59.343 66.667 0.00 0.00 35.07 4.16
149 150 2.920912 TCGTCACCCCAGACCACC 60.921 66.667 0.00 0.00 35.07 4.61
150 151 4.016706 CGTCACCCCAGACCACCC 62.017 72.222 0.00 0.00 35.07 4.61
151 152 4.016706 GTCACCCCAGACCACCCG 62.017 72.222 0.00 0.00 32.36 5.28
209 210 4.435436 TCCGCGCTCGCAAGTCAT 62.435 61.111 14.80 0.00 42.06 3.06
210 211 3.918220 CCGCGCTCGCAAGTCATC 61.918 66.667 14.80 0.00 42.06 2.92
211 212 3.918220 CGCGCTCGCAAGTCATCC 61.918 66.667 14.80 0.00 42.06 3.51
212 213 3.918220 GCGCTCGCAAGTCATCCG 61.918 66.667 9.59 0.00 41.49 4.18
213 214 3.918220 CGCTCGCAAGTCATCCGC 61.918 66.667 0.00 0.00 39.48 5.54
217 218 4.505217 CGCAAGTCATCCGCGTGC 62.505 66.667 4.92 5.33 43.86 5.34
218 219 3.422303 GCAAGTCATCCGCGTGCA 61.422 61.111 4.92 0.00 40.21 4.57
219 220 2.780643 CAAGTCATCCGCGTGCAG 59.219 61.111 4.92 0.00 0.00 4.41
220 221 2.434884 AAGTCATCCGCGTGCAGG 60.435 61.111 4.92 1.01 0.00 4.85
221 222 2.942796 AAGTCATCCGCGTGCAGGA 61.943 57.895 11.29 2.58 42.69 3.86
222 223 2.842394 AAGTCATCCGCGTGCAGGAG 62.842 60.000 11.29 6.91 41.66 3.69
223 224 4.819761 TCATCCGCGTGCAGGAGC 62.820 66.667 11.29 4.54 41.66 4.70
229 230 4.077188 GCGTGCAGGAGCGTGTTC 62.077 66.667 11.29 0.00 46.23 3.18
230 231 3.767230 CGTGCAGGAGCGTGTTCG 61.767 66.667 0.00 0.00 46.23 3.95
240 241 3.517974 CGTGTTCGCGTCGAAGAA 58.482 55.556 5.77 0.00 46.54 2.52
241 242 1.407329 CGTGTTCGCGTCGAAGAAG 59.593 57.895 5.77 11.31 46.54 2.85
249 250 2.270091 CGTCGAAGAAGCTGCTACG 58.730 57.895 0.90 4.08 39.69 3.51
250 251 1.134530 CGTCGAAGAAGCTGCTACGG 61.135 60.000 0.90 0.00 39.69 4.02
251 252 0.802607 GTCGAAGAAGCTGCTACGGG 60.803 60.000 0.90 0.00 39.69 5.28
252 253 0.963856 TCGAAGAAGCTGCTACGGGA 60.964 55.000 0.90 0.00 0.00 5.14
253 254 0.526524 CGAAGAAGCTGCTACGGGAG 60.527 60.000 0.90 0.00 0.00 4.30
261 262 4.814294 GCTACGGGAGCCCACACG 62.814 72.222 0.00 0.00 46.41 4.49
262 263 4.814294 CTACGGGAGCCCACACGC 62.814 72.222 6.34 0.00 40.59 5.34
284 285 2.182030 GCCTCACGAGACGAAGGG 59.818 66.667 14.71 7.58 35.28 3.95
285 286 2.341101 GCCTCACGAGACGAAGGGA 61.341 63.158 14.71 0.00 35.28 4.20
286 287 1.507174 CCTCACGAGACGAAGGGAC 59.493 63.158 0.00 0.00 32.77 4.46
287 288 1.507174 CTCACGAGACGAAGGGACC 59.493 63.158 0.00 0.00 0.00 4.46
288 289 2.178521 CACGAGACGAAGGGACCG 59.821 66.667 0.00 0.00 0.00 4.79
289 290 3.060615 ACGAGACGAAGGGACCGG 61.061 66.667 0.00 0.00 0.00 5.28
290 291 4.493747 CGAGACGAAGGGACCGGC 62.494 72.222 0.00 0.00 34.76 6.13
291 292 4.144703 GAGACGAAGGGACCGGCC 62.145 72.222 0.00 3.33 35.21 6.13
295 296 4.382320 CGAAGGGACCGGCCGAAA 62.382 66.667 30.73 0.00 37.63 3.46
296 297 2.032987 GAAGGGACCGGCCGAAAA 59.967 61.111 30.73 0.00 37.63 2.29
297 298 1.378119 GAAGGGACCGGCCGAAAAT 60.378 57.895 30.73 9.08 37.63 1.82
298 299 0.963856 GAAGGGACCGGCCGAAAATT 60.964 55.000 30.73 14.54 37.63 1.82
299 300 0.541063 AAGGGACCGGCCGAAAATTT 60.541 50.000 30.73 12.55 37.63 1.82
300 301 1.214325 GGGACCGGCCGAAAATTTG 59.786 57.895 30.73 10.69 37.63 2.32
301 302 1.214325 GGACCGGCCGAAAATTTGG 59.786 57.895 30.73 9.82 34.66 3.28
307 308 2.505997 CCGAAAATTTGGCCGGCG 60.506 61.111 22.54 0.00 35.29 6.46
308 309 2.257067 CGAAAATTTGGCCGGCGT 59.743 55.556 22.54 3.01 0.00 5.68
309 310 2.085844 CGAAAATTTGGCCGGCGTG 61.086 57.895 22.54 0.00 0.00 5.34
310 311 1.006688 GAAAATTTGGCCGGCGTGT 60.007 52.632 22.54 3.00 0.00 4.49
311 312 0.241481 GAAAATTTGGCCGGCGTGTA 59.759 50.000 22.54 5.94 0.00 2.90
312 313 0.242555 AAAATTTGGCCGGCGTGTAG 59.757 50.000 22.54 0.00 0.00 2.74
313 314 0.606944 AAATTTGGCCGGCGTGTAGA 60.607 50.000 22.54 2.96 0.00 2.59
314 315 0.393808 AATTTGGCCGGCGTGTAGAT 60.394 50.000 22.54 5.44 0.00 1.98
315 316 1.095228 ATTTGGCCGGCGTGTAGATG 61.095 55.000 22.54 0.00 0.00 2.90
316 317 3.673956 TTGGCCGGCGTGTAGATGG 62.674 63.158 22.54 0.00 0.00 3.51
318 319 4.830765 GCCGGCGTGTAGATGGCA 62.831 66.667 12.58 0.00 45.06 4.92
319 320 2.125310 CCGGCGTGTAGATGGCAA 60.125 61.111 6.01 0.00 33.12 4.52
320 321 1.743623 CCGGCGTGTAGATGGCAAA 60.744 57.895 6.01 0.00 33.12 3.68
321 322 1.423845 CGGCGTGTAGATGGCAAAC 59.576 57.895 6.46 0.00 33.12 2.93
322 323 1.295357 CGGCGTGTAGATGGCAAACA 61.295 55.000 6.46 0.00 33.12 2.83
323 324 1.094785 GGCGTGTAGATGGCAAACAT 58.905 50.000 0.22 0.00 44.18 2.71
324 325 1.472480 GGCGTGTAGATGGCAAACATT 59.528 47.619 0.22 0.00 40.72 2.71
325 326 2.094752 GGCGTGTAGATGGCAAACATTT 60.095 45.455 0.22 0.00 40.72 2.32
326 327 3.127895 GGCGTGTAGATGGCAAACATTTA 59.872 43.478 0.22 0.00 40.72 1.40
327 328 4.095610 GCGTGTAGATGGCAAACATTTAC 58.904 43.478 0.00 0.00 43.73 2.01
328 329 4.331137 CGTGTAGATGGCAAACATTTACG 58.669 43.478 0.00 0.00 45.40 3.18
329 330 4.142988 CGTGTAGATGGCAAACATTTACGT 60.143 41.667 0.00 0.00 45.40 3.57
330 331 5.615984 CGTGTAGATGGCAAACATTTACGTT 60.616 40.000 0.00 0.00 45.40 3.99
331 332 6.401260 CGTGTAGATGGCAAACATTTACGTTA 60.401 38.462 0.00 0.00 45.40 3.18
332 333 6.959311 GTGTAGATGGCAAACATTTACGTTAG 59.041 38.462 0.00 0.00 45.40 2.34
333 334 5.560966 AGATGGCAAACATTTACGTTAGG 57.439 39.130 0.00 0.00 40.72 2.69
334 335 5.007682 AGATGGCAAACATTTACGTTAGGT 58.992 37.500 0.00 0.00 40.72 3.08
335 336 5.475564 AGATGGCAAACATTTACGTTAGGTT 59.524 36.000 0.00 0.00 40.72 3.50
336 337 5.517322 TGGCAAACATTTACGTTAGGTTT 57.483 34.783 0.00 0.00 32.33 3.27
337 338 5.903810 TGGCAAACATTTACGTTAGGTTTT 58.096 33.333 9.48 0.00 29.89 2.43
338 339 5.978322 TGGCAAACATTTACGTTAGGTTTTC 59.022 36.000 9.48 6.21 29.89 2.29
339 340 5.115923 GGCAAACATTTACGTTAGGTTTTCG 59.884 40.000 9.48 3.36 29.89 3.46
340 341 5.908499 GCAAACATTTACGTTAGGTTTTCGA 59.092 36.000 9.48 0.00 29.89 3.71
341 342 6.579666 GCAAACATTTACGTTAGGTTTTCGAT 59.420 34.615 9.48 0.00 29.89 3.59
342 343 7.113825 GCAAACATTTACGTTAGGTTTTCGATT 59.886 33.333 9.48 0.00 29.89 3.34
343 344 8.960075 CAAACATTTACGTTAGGTTTTCGATTT 58.040 29.630 9.48 0.00 29.89 2.17
345 346 9.815936 AACATTTACGTTAGGTTTTCGATTTAG 57.184 29.630 0.00 0.00 0.00 1.85
346 347 9.206870 ACATTTACGTTAGGTTTTCGATTTAGA 57.793 29.630 0.00 0.00 0.00 2.10
347 348 9.469239 CATTTACGTTAGGTTTTCGATTTAGAC 57.531 33.333 0.00 0.00 0.00 2.59
348 349 8.816640 TTTACGTTAGGTTTTCGATTTAGACT 57.183 30.769 0.00 0.00 0.00 3.24
349 350 8.816640 TTACGTTAGGTTTTCGATTTAGACTT 57.183 30.769 0.00 0.00 0.00 3.01
350 351 7.343614 ACGTTAGGTTTTCGATTTAGACTTC 57.656 36.000 0.00 0.00 0.00 3.01
351 352 6.925165 ACGTTAGGTTTTCGATTTAGACTTCA 59.075 34.615 0.00 0.00 0.00 3.02
352 353 7.601508 ACGTTAGGTTTTCGATTTAGACTTCAT 59.398 33.333 0.00 0.00 0.00 2.57
353 354 7.898309 CGTTAGGTTTTCGATTTAGACTTCATG 59.102 37.037 0.00 0.00 0.00 3.07
354 355 8.718734 GTTAGGTTTTCGATTTAGACTTCATGT 58.281 33.333 0.00 0.00 0.00 3.21
355 356 9.932207 TTAGGTTTTCGATTTAGACTTCATGTA 57.068 29.630 0.00 0.00 0.00 2.29
357 358 8.883731 AGGTTTTCGATTTAGACTTCATGTATG 58.116 33.333 0.00 0.00 0.00 2.39
358 359 8.879759 GGTTTTCGATTTAGACTTCATGTATGA 58.120 33.333 0.00 0.00 34.44 2.15
363 364 9.816354 TCGATTTAGACTTCATGTATGAATTGA 57.184 29.630 7.67 0.00 44.92 2.57
368 369 7.798596 AGACTTCATGTATGAATTGATGGTC 57.201 36.000 7.67 9.91 44.92 4.02
634 914 2.674380 GCTCCAAGCCACACCCAG 60.674 66.667 0.00 0.00 34.48 4.45
644 924 1.531748 CACACCCAGACAACACCCT 59.468 57.895 0.00 0.00 0.00 4.34
781 1104 3.192466 TCGCCTCTATAAAGAAAACCGC 58.808 45.455 0.00 0.00 0.00 5.68
852 1175 1.811266 CACTCCAATCCAGCGACCG 60.811 63.158 0.00 0.00 0.00 4.79
898 1221 2.646719 CGGTTCCTCGACGGTGAA 59.353 61.111 0.00 0.00 0.00 3.18
973 1301 2.752238 CGGCGTCTGACCTCCTCT 60.752 66.667 0.00 0.00 0.00 3.69
1211 1539 2.141011 CTGGTGAGCATCCCAACCCA 62.141 60.000 0.00 0.00 35.50 4.51
1264 1592 7.451877 AGCATGCTAGTAGCCTATAAGAAGTTA 59.548 37.037 21.21 0.00 41.51 2.24
1286 1614 3.903714 AGGCCTTGGATTTATTTATGGGC 59.096 43.478 0.00 0.00 38.87 5.36
1291 1619 5.243730 CCTTGGATTTATTTATGGGCATCGT 59.756 40.000 0.00 0.00 0.00 3.73
1365 1797 4.377839 TTTGAGCTCCAGACTAAGATCG 57.622 45.455 12.15 0.00 30.59 3.69
1537 1988 6.735678 TTTGCTCTCAGTTAATTTCGCATA 57.264 33.333 0.00 0.00 0.00 3.14
1576 2027 1.490490 AGTCAGTCTTGCAACCCTTGA 59.510 47.619 0.00 0.00 0.00 3.02
1578 2030 2.687935 GTCAGTCTTGCAACCCTTGAAA 59.312 45.455 0.00 0.00 0.00 2.69
1617 2120 5.475564 TCAGTTAATGCCCCTTCAACTTAAC 59.524 40.000 0.00 0.00 32.11 2.01
1618 2121 4.770531 AGTTAATGCCCCTTCAACTTAACC 59.229 41.667 0.00 0.00 32.26 2.85
1651 2154 4.035675 GCCATACTATCTGAACCAGTTTGC 59.964 45.833 0.00 0.00 32.61 3.68
1657 2160 2.210116 TCTGAACCAGTTTGCGTCTTC 58.790 47.619 0.00 0.00 32.61 2.87
1671 2174 1.394917 CGTCTTCTGCACAGTTATGGC 59.605 52.381 0.00 0.00 0.00 4.40
1791 2466 6.635755 CCCAACTTGTTCCTTTTTCACTTTA 58.364 36.000 0.00 0.00 0.00 1.85
1842 2517 3.963665 TGCCAAAAATGAACGTCTTCAG 58.036 40.909 0.00 0.00 39.83 3.02
1844 2519 3.975035 GCCAAAAATGAACGTCTTCAGTC 59.025 43.478 0.00 0.00 39.83 3.51
1887 2562 3.639094 TCTGATTCTTAGTAGGAGGCAGC 59.361 47.826 7.95 0.00 0.00 5.25
1892 2567 3.288964 TCTTAGTAGGAGGCAGCTACAC 58.711 50.000 0.00 0.00 0.00 2.90
1927 2602 2.964464 TGTTTGCACCTCCACATTTCAT 59.036 40.909 0.00 0.00 0.00 2.57
1942 2617 6.404954 CCACATTTCATGCATGACATTCAGTA 60.405 38.462 28.72 9.12 36.64 2.74
1997 2678 6.998802 AGTAGTATTAGAACATCTGATGGGC 58.001 40.000 20.83 12.17 33.60 5.36
2005 2686 1.202855 ACATCTGATGGGCTGGTATGC 60.203 52.381 20.83 0.00 33.60 3.14
2010 2691 1.276138 TGATGGGCTGGTATGCTATCG 59.724 52.381 0.00 0.00 33.03 2.92
2034 2715 3.721087 ATCTGGTTCCTGGTAACTTGG 57.279 47.619 0.00 0.00 37.61 3.61
2046 2736 6.386927 TCCTGGTAACTTGGAGATGTATTGAT 59.613 38.462 0.00 0.00 35.56 2.57
2047 2737 7.567250 TCCTGGTAACTTGGAGATGTATTGATA 59.433 37.037 0.00 0.00 35.56 2.15
2048 2738 8.210946 CCTGGTAACTTGGAGATGTATTGATAA 58.789 37.037 0.00 0.00 33.67 1.75
2049 2739 8.958119 TGGTAACTTGGAGATGTATTGATAAC 57.042 34.615 0.00 0.00 37.61 1.89
2050 2740 8.544622 TGGTAACTTGGAGATGTATTGATAACA 58.455 33.333 0.00 0.00 37.61 2.41
2053 2743 8.723942 AACTTGGAGATGTATTGATAACAGAC 57.276 34.615 0.00 0.00 0.00 3.51
2142 2832 4.992688 TGTGTTGCTTTCACCTAAACTTG 58.007 39.130 0.00 0.00 35.25 3.16
2154 2844 3.243839 ACCTAAACTTGCATTGCCAACAG 60.244 43.478 6.12 0.00 0.00 3.16
2159 2849 2.366266 ACTTGCATTGCCAACAGACAAT 59.634 40.909 6.12 0.00 36.96 2.71
2164 2854 4.749099 TGCATTGCCAACAGACAATTTTAC 59.251 37.500 6.12 0.00 34.32 2.01
2211 2903 6.152661 GTGTCAACCAATCCAATCCAGATTTA 59.847 38.462 0.00 0.00 31.56 1.40
2267 2959 3.960755 TCACCTGATATGACGAGGAACAT 59.039 43.478 0.00 0.00 0.00 2.71
2268 2960 4.053983 CACCTGATATGACGAGGAACATG 58.946 47.826 0.00 0.00 0.00 3.21
2314 3007 7.595311 AAGTGTGATTGTTGTTTTTCCTTTC 57.405 32.000 0.00 0.00 0.00 2.62
2428 3122 3.935828 GCTCCTTGGACTTGAAGTATGTC 59.064 47.826 0.00 0.00 33.82 3.06
2435 3129 4.192317 GGACTTGAAGTATGTCATGGGAC 58.808 47.826 0.00 0.00 44.57 4.46
2497 3197 8.425577 AAGAGCACTTATATGTGTACATTGTC 57.574 34.615 17.33 1.98 39.89 3.18
2781 3483 4.636249 CTTCCTCATGCAGAAGGTATACC 58.364 47.826 14.54 14.54 36.63 2.73
2873 3676 3.201290 GCAAGTCAGTACATGGATCCTG 58.799 50.000 14.23 11.14 0.00 3.86
2879 3728 5.837437 GTCAGTACATGGATCCTGACTTAG 58.163 45.833 17.50 3.81 46.46 2.18
2885 3734 8.207545 AGTACATGGATCCTGACTTAGATTTTC 58.792 37.037 14.23 0.00 0.00 2.29
2888 3737 5.994250 TGGATCCTGACTTAGATTTTCCAG 58.006 41.667 14.23 0.00 0.00 3.86
2892 3741 7.777440 GGATCCTGACTTAGATTTTCCAGAAAT 59.223 37.037 3.84 0.00 0.00 2.17
3185 4034 3.141398 TGAACTGGCAACTTCACTGATC 58.859 45.455 3.69 0.00 37.61 2.92
3329 4178 8.946085 TGTGATAGCACTTTATACTCCAAAAAG 58.054 33.333 13.05 0.00 45.36 2.27
3512 4365 0.519077 CAAGACTTTCGCAGAAGCCC 59.481 55.000 0.00 0.00 45.90 5.19
3664 4523 5.359576 TGTTGCTAATGACAACTGTCCTTTT 59.640 36.000 7.37 2.16 46.03 2.27
3936 4796 0.457853 TCATCTCGGTGTAACGCTGC 60.458 55.000 0.00 0.00 38.12 5.25
3955 4815 3.938963 CTGCAACGTTATATGTCCCAAGT 59.061 43.478 0.00 0.00 0.00 3.16
3991 4857 3.253230 GCTTGTCGCCAATTTTTGCTAT 58.747 40.909 0.00 0.00 0.00 2.97
3995 4861 4.992688 TGTCGCCAATTTTTGCTATTAGG 58.007 39.130 0.00 0.00 0.00 2.69
4040 4906 1.668337 CCTCTGTGCGAGTGAAGTGAG 60.668 57.143 0.00 0.00 38.11 3.51
4159 5027 5.996219 TGAAATGAAACCTTGTCATGTACG 58.004 37.500 0.00 0.00 35.87 3.67
4166 5034 1.406751 CCTTGTCATGTACGGCCATGA 60.407 52.381 13.34 13.34 46.74 3.07
4233 5131 1.447140 GCATTAGGCGTCGTGGTGA 60.447 57.895 0.00 0.00 0.00 4.02
4234 5132 1.421410 GCATTAGGCGTCGTGGTGAG 61.421 60.000 0.00 0.00 0.00 3.51
4235 5133 0.806102 CATTAGGCGTCGTGGTGAGG 60.806 60.000 0.00 0.00 35.56 3.86
4236 5134 1.255667 ATTAGGCGTCGTGGTGAGGT 61.256 55.000 0.00 0.00 34.92 3.85
4239 5137 2.604174 GGCGTCGTGGTGAGGTTTG 61.604 63.158 0.00 0.00 34.92 2.93
4243 5141 0.883370 GTCGTGGTGAGGTTTGTCCC 60.883 60.000 0.00 0.00 36.75 4.46
4246 5144 1.749286 CGTGGTGAGGTTTGTCCCTTT 60.749 52.381 0.00 0.00 34.03 3.11
4247 5145 1.954382 GTGGTGAGGTTTGTCCCTTTC 59.046 52.381 0.00 0.00 34.03 2.62
4248 5146 1.850345 TGGTGAGGTTTGTCCCTTTCT 59.150 47.619 0.00 0.00 34.03 2.52
4252 5150 2.372172 TGAGGTTTGTCCCTTTCTCCTC 59.628 50.000 0.00 0.00 39.97 3.71
4255 5153 2.372172 GGTTTGTCCCTTTCTCCTCTCA 59.628 50.000 0.00 0.00 0.00 3.27
4258 5156 2.191400 TGTCCCTTTCTCCTCTCATGG 58.809 52.381 0.00 0.00 0.00 3.66
4259 5157 1.488393 GTCCCTTTCTCCTCTCATGGG 59.512 57.143 0.00 0.00 34.76 4.00
4261 5159 1.211457 CCCTTTCTCCTCTCATGGGTG 59.789 57.143 0.00 0.00 0.00 4.61
4264 5162 1.573108 TTCTCCTCTCATGGGTGTCC 58.427 55.000 0.00 0.00 0.00 4.02
4274 5172 2.606826 GGGTGTCCCCCGTTCTCT 60.607 66.667 0.00 0.00 45.80 3.10
4277 5175 1.265454 GGTGTCCCCCGTTCTCTCAT 61.265 60.000 0.00 0.00 0.00 2.90
4286 5184 2.005451 CCGTTCTCTCATTGCTGGAAG 58.995 52.381 0.00 0.00 0.00 3.46
4287 5185 2.354103 CCGTTCTCTCATTGCTGGAAGA 60.354 50.000 0.00 0.00 34.07 2.87
4289 5187 3.309138 CGTTCTCTCATTGCTGGAAGATG 59.691 47.826 0.00 0.00 34.07 2.90
4290 5188 4.260170 GTTCTCTCATTGCTGGAAGATGT 58.740 43.478 0.00 0.00 34.07 3.06
4291 5189 4.134379 TCTCTCATTGCTGGAAGATGTC 57.866 45.455 0.00 0.00 34.07 3.06
4292 5190 3.773667 TCTCTCATTGCTGGAAGATGTCT 59.226 43.478 0.00 0.00 34.07 3.41
4293 5191 4.224594 TCTCTCATTGCTGGAAGATGTCTT 59.775 41.667 0.00 0.00 39.23 3.01
4370 5407 0.592637 CCACTTTCTGAATGCACGCA 59.407 50.000 0.00 0.00 0.00 5.24
4371 5408 1.664016 CCACTTTCTGAATGCACGCAC 60.664 52.381 0.00 0.00 0.00 5.34
4404 5441 9.970395 ACAAATACATGGCTGAAATAATACATG 57.030 29.630 0.00 0.00 40.94 3.21
4405 5442 9.414295 CAAATACATGGCTGAAATAATACATGG 57.586 33.333 0.00 0.00 39.83 3.66
4407 5444 9.806448 AATACATGGCTGAAATAATACATGGTA 57.194 29.630 0.00 0.00 39.83 3.25
4432 5469 1.301423 AAAGGCGCGAACTACACAAA 58.699 45.000 12.10 0.00 0.00 2.83
4511 5553 6.945435 TGGCCATTATTTTTCAGAGACAACTA 59.055 34.615 0.00 0.00 0.00 2.24
4535 5577 7.757097 AGACAAAGTATCGCTGTAGTATTTG 57.243 36.000 0.00 0.00 33.70 2.32
4540 5582 5.282510 AGTATCGCTGTAGTATTTGCAGAC 58.717 41.667 0.00 0.00 41.55 3.51
4700 5742 3.135348 AGCACAAGCATCAGAGCCTTATA 59.865 43.478 0.00 0.00 45.49 0.98
4706 5748 6.373774 ACAAGCATCAGAGCCTTATAATATGC 59.626 38.462 0.00 0.00 38.95 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.925238 GTAAGCCATGGTCGCGCG 61.925 66.667 26.76 26.76 0.00 6.86
9 10 3.925238 CGTAAGCCATGGTCGCGC 61.925 66.667 14.67 0.00 0.00 6.86
10 11 2.202690 TCGTAAGCCATGGTCGCG 60.203 61.111 14.67 12.92 37.18 5.87
11 12 2.526120 GCTCGTAAGCCATGGTCGC 61.526 63.158 14.67 0.00 43.10 5.19
12 13 3.706140 GCTCGTAAGCCATGGTCG 58.294 61.111 14.67 13.08 43.10 4.79
25 26 1.066114 GGTTTGAGTCGACGAGCTCG 61.066 60.000 33.45 33.45 44.44 5.03
26 27 1.066114 CGGTTTGAGTCGACGAGCTC 61.066 60.000 10.46 2.73 0.00 4.09
27 28 1.081376 CGGTTTGAGTCGACGAGCT 60.081 57.895 10.46 0.00 0.00 4.09
28 29 2.717809 GCGGTTTGAGTCGACGAGC 61.718 63.158 10.46 4.54 0.00 5.03
29 30 2.087009 GGCGGTTTGAGTCGACGAG 61.087 63.158 10.46 0.00 0.00 4.18
30 31 2.049802 GGCGGTTTGAGTCGACGA 60.050 61.111 10.46 0.00 0.00 4.20
31 32 3.110178 GGGCGGTTTGAGTCGACG 61.110 66.667 10.46 0.00 34.82 5.12
32 33 2.741211 GGGGCGGTTTGAGTCGAC 60.741 66.667 7.70 7.70 0.00 4.20
33 34 4.011517 GGGGGCGGTTTGAGTCGA 62.012 66.667 0.00 0.00 0.00 4.20
46 47 4.489771 GAGTGTGATGGCCGGGGG 62.490 72.222 2.18 0.00 0.00 5.40
47 48 4.838152 CGAGTGTGATGGCCGGGG 62.838 72.222 2.18 0.00 0.00 5.73
48 49 4.082523 ACGAGTGTGATGGCCGGG 62.083 66.667 2.18 0.00 0.00 5.73
49 50 2.509336 GACGAGTGTGATGGCCGG 60.509 66.667 0.00 0.00 0.00 6.13
50 51 2.880879 CGACGAGTGTGATGGCCG 60.881 66.667 0.00 0.00 0.00 6.13
51 52 1.805945 GACGACGAGTGTGATGGCC 60.806 63.158 0.00 0.00 0.00 5.36
52 53 1.805945 GGACGACGAGTGTGATGGC 60.806 63.158 0.00 0.00 0.00 4.40
53 54 0.243907 AAGGACGACGAGTGTGATGG 59.756 55.000 0.00 0.00 0.00 3.51
54 55 1.721389 CAAAGGACGACGAGTGTGATG 59.279 52.381 0.00 0.00 0.00 3.07
55 56 1.340248 ACAAAGGACGACGAGTGTGAT 59.660 47.619 0.00 0.00 0.00 3.06
56 57 0.742505 ACAAAGGACGACGAGTGTGA 59.257 50.000 0.00 0.00 0.00 3.58
57 58 1.567504 AACAAAGGACGACGAGTGTG 58.432 50.000 0.00 0.00 0.00 3.82
58 59 3.009301 CTAACAAAGGACGACGAGTGT 57.991 47.619 0.00 0.00 0.00 3.55
70 71 1.156736 CGGTGGTGCTCCTAACAAAG 58.843 55.000 6.34 0.00 34.23 2.77
71 72 0.887387 GCGGTGGTGCTCCTAACAAA 60.887 55.000 6.34 0.00 34.23 2.83
72 73 1.302192 GCGGTGGTGCTCCTAACAA 60.302 57.895 6.34 0.00 34.23 2.83
73 74 2.345991 GCGGTGGTGCTCCTAACA 59.654 61.111 6.34 0.00 34.23 2.41
74 75 2.436115 GGCGGTGGTGCTCCTAAC 60.436 66.667 6.34 0.00 34.52 2.34
75 76 3.712907 GGGCGGTGGTGCTCCTAA 61.713 66.667 6.34 0.00 34.52 2.69
97 98 3.741476 GTCTGCAAGCCCGGCAAG 61.741 66.667 13.15 4.33 41.39 4.01
101 102 3.136123 CATGGTCTGCAAGCCCGG 61.136 66.667 0.00 0.00 30.41 5.73
102 103 3.136123 CCATGGTCTGCAAGCCCG 61.136 66.667 2.57 0.00 30.41 6.13
103 104 2.036256 ACCATGGTCTGCAAGCCC 59.964 61.111 13.00 0.00 30.41 5.19
104 105 2.998279 GCACCATGGTCTGCAAGCC 61.998 63.158 16.53 0.00 0.00 4.35
105 106 2.209064 CTGCACCATGGTCTGCAAGC 62.209 60.000 25.25 19.97 36.81 4.01
106 107 1.880894 CTGCACCATGGTCTGCAAG 59.119 57.895 25.25 17.18 36.81 4.01
107 108 2.270257 GCTGCACCATGGTCTGCAA 61.270 57.895 25.25 12.95 36.81 4.08
108 109 2.674033 GCTGCACCATGGTCTGCA 60.674 61.111 24.15 24.15 35.83 4.41
109 110 3.446570 GGCTGCACCATGGTCTGC 61.447 66.667 24.70 24.70 38.86 4.26
110 111 2.753043 GGGCTGCACCATGGTCTG 60.753 66.667 16.53 14.40 42.05 3.51
111 112 4.415150 CGGGCTGCACCATGGTCT 62.415 66.667 16.53 0.00 42.05 3.85
129 130 4.436998 GGTCTGGGGTGACGAGCG 62.437 72.222 0.00 0.00 37.81 5.03
130 131 3.311110 TGGTCTGGGGTGACGAGC 61.311 66.667 0.00 0.00 37.81 5.03
131 132 2.657237 GTGGTCTGGGGTGACGAG 59.343 66.667 0.00 0.00 37.81 4.18
132 133 2.920912 GGTGGTCTGGGGTGACGA 60.921 66.667 0.00 0.00 37.81 4.20
133 134 4.016706 GGGTGGTCTGGGGTGACG 62.017 72.222 0.00 0.00 37.81 4.35
134 135 4.016706 CGGGTGGTCTGGGGTGAC 62.017 72.222 0.00 0.00 36.31 3.67
192 193 4.435436 ATGACTTGCGAGCGCGGA 62.435 61.111 12.86 5.78 45.51 5.54
193 194 3.918220 GATGACTTGCGAGCGCGG 61.918 66.667 12.86 8.08 45.51 6.46
194 195 3.918220 GGATGACTTGCGAGCGCG 61.918 66.667 5.14 5.14 45.51 6.86
195 196 3.918220 CGGATGACTTGCGAGCGC 61.918 66.667 8.08 8.08 42.53 5.92
196 197 3.918220 GCGGATGACTTGCGAGCG 61.918 66.667 6.43 0.00 42.53 5.03
201 202 3.372676 CTGCACGCGGATGACTTGC 62.373 63.158 12.47 10.12 0.00 4.01
202 203 2.743752 CCTGCACGCGGATGACTTG 61.744 63.158 12.47 0.00 0.00 3.16
203 204 2.434884 CCTGCACGCGGATGACTT 60.435 61.111 12.47 0.00 0.00 3.01
204 205 3.362399 CTCCTGCACGCGGATGACT 62.362 63.158 12.47 0.00 0.00 3.41
205 206 2.887568 CTCCTGCACGCGGATGAC 60.888 66.667 12.47 0.00 0.00 3.06
206 207 4.819761 GCTCCTGCACGCGGATGA 62.820 66.667 12.47 0.00 39.41 2.92
212 213 4.077188 GAACACGCTCCTGCACGC 62.077 66.667 0.00 0.00 39.64 5.34
213 214 3.767230 CGAACACGCTCCTGCACG 61.767 66.667 0.00 0.00 39.64 5.34
223 224 1.407329 CTTCTTCGACGCGAACACG 59.593 57.895 15.93 13.05 41.05 4.49
224 225 1.128015 GCTTCTTCGACGCGAACAC 59.872 57.895 15.93 0.00 41.05 3.32
225 226 1.007734 AGCTTCTTCGACGCGAACA 60.008 52.632 15.93 0.00 41.05 3.18
226 227 1.412606 CAGCTTCTTCGACGCGAAC 59.587 57.895 15.93 5.44 41.05 3.95
227 228 2.372690 GCAGCTTCTTCGACGCGAA 61.373 57.895 15.93 12.72 43.75 4.70
228 229 1.918868 TAGCAGCTTCTTCGACGCGA 61.919 55.000 15.93 0.00 31.98 5.87
229 230 1.514228 TAGCAGCTTCTTCGACGCG 60.514 57.895 3.53 3.53 31.98 6.01
230 231 1.734359 CGTAGCAGCTTCTTCGACGC 61.734 60.000 6.55 0.00 0.00 5.19
231 232 1.134530 CCGTAGCAGCTTCTTCGACG 61.135 60.000 13.49 7.04 0.00 5.12
232 233 0.802607 CCCGTAGCAGCTTCTTCGAC 60.803 60.000 13.49 0.00 0.00 4.20
233 234 0.963856 TCCCGTAGCAGCTTCTTCGA 60.964 55.000 13.49 0.00 0.00 3.71
234 235 0.526524 CTCCCGTAGCAGCTTCTTCG 60.527 60.000 0.00 5.46 0.00 3.79
235 236 3.354131 CTCCCGTAGCAGCTTCTTC 57.646 57.895 0.00 0.00 0.00 2.87
245 246 4.814294 GCGTGTGGGCTCCCGTAG 62.814 72.222 0.00 0.00 39.42 3.51
267 268 2.182030 CCCTTCGTCTCGTGAGGC 59.818 66.667 2.43 0.00 32.96 4.70
268 269 1.507174 GTCCCTTCGTCTCGTGAGG 59.493 63.158 0.89 0.89 33.63 3.86
269 270 1.507174 GGTCCCTTCGTCTCGTGAG 59.493 63.158 0.00 0.00 0.00 3.51
270 271 2.330372 CGGTCCCTTCGTCTCGTGA 61.330 63.158 0.00 0.00 0.00 4.35
271 272 2.178521 CGGTCCCTTCGTCTCGTG 59.821 66.667 0.00 0.00 0.00 4.35
272 273 3.060615 CCGGTCCCTTCGTCTCGT 61.061 66.667 0.00 0.00 0.00 4.18
273 274 4.493747 GCCGGTCCCTTCGTCTCG 62.494 72.222 1.90 0.00 0.00 4.04
274 275 4.144703 GGCCGGTCCCTTCGTCTC 62.145 72.222 1.90 0.00 0.00 3.36
278 279 3.887335 TTTTCGGCCGGTCCCTTCG 62.887 63.158 27.83 0.00 0.00 3.79
279 280 0.963856 AATTTTCGGCCGGTCCCTTC 60.964 55.000 27.83 0.00 0.00 3.46
280 281 0.541063 AAATTTTCGGCCGGTCCCTT 60.541 50.000 27.83 11.05 0.00 3.95
281 282 1.076014 AAATTTTCGGCCGGTCCCT 59.924 52.632 27.83 4.54 0.00 4.20
282 283 1.214325 CAAATTTTCGGCCGGTCCC 59.786 57.895 27.83 0.00 0.00 4.46
283 284 1.214325 CCAAATTTTCGGCCGGTCC 59.786 57.895 27.83 2.02 0.00 4.46
284 285 1.445410 GCCAAATTTTCGGCCGGTC 60.445 57.895 27.83 0.00 42.82 4.79
285 286 2.654289 GCCAAATTTTCGGCCGGT 59.346 55.556 27.83 6.35 42.82 5.28
290 291 2.505997 CGCCGGCCAAATTTTCGG 60.506 61.111 23.46 15.86 44.70 4.30
291 292 2.085844 CACGCCGGCCAAATTTTCG 61.086 57.895 23.46 5.65 0.00 3.46
292 293 0.241481 TACACGCCGGCCAAATTTTC 59.759 50.000 23.46 0.00 0.00 2.29
293 294 0.242555 CTACACGCCGGCCAAATTTT 59.757 50.000 23.46 0.30 0.00 1.82
294 295 0.606944 TCTACACGCCGGCCAAATTT 60.607 50.000 23.46 1.51 0.00 1.82
295 296 0.393808 ATCTACACGCCGGCCAAATT 60.394 50.000 23.46 3.13 0.00 1.82
296 297 1.095228 CATCTACACGCCGGCCAAAT 61.095 55.000 23.46 6.62 0.00 2.32
297 298 1.743623 CATCTACACGCCGGCCAAA 60.744 57.895 23.46 2.69 0.00 3.28
298 299 2.125310 CATCTACACGCCGGCCAA 60.125 61.111 23.46 2.28 0.00 4.52
299 300 4.155733 CCATCTACACGCCGGCCA 62.156 66.667 23.46 2.28 0.00 5.36
301 302 4.830765 TGCCATCTACACGCCGGC 62.831 66.667 19.07 19.07 43.28 6.13
302 303 1.743623 TTTGCCATCTACACGCCGG 60.744 57.895 0.00 0.00 0.00 6.13
303 304 1.295357 TGTTTGCCATCTACACGCCG 61.295 55.000 0.00 0.00 0.00 6.46
304 305 1.094785 ATGTTTGCCATCTACACGCC 58.905 50.000 0.00 0.00 0.00 5.68
305 306 2.919666 AATGTTTGCCATCTACACGC 57.080 45.000 0.00 0.00 31.75 5.34
306 307 4.142988 ACGTAAATGTTTGCCATCTACACG 60.143 41.667 0.00 0.00 27.96 4.49
307 308 5.291293 ACGTAAATGTTTGCCATCTACAC 57.709 39.130 0.00 0.00 27.96 2.90
308 309 5.950758 AACGTAAATGTTTGCCATCTACA 57.049 34.783 0.00 0.00 27.96 2.74
309 310 6.093082 ACCTAACGTAAATGTTTGCCATCTAC 59.907 38.462 0.00 0.00 33.32 2.59
310 311 6.174760 ACCTAACGTAAATGTTTGCCATCTA 58.825 36.000 0.00 0.00 33.32 1.98
311 312 5.007682 ACCTAACGTAAATGTTTGCCATCT 58.992 37.500 0.00 0.00 33.32 2.90
312 313 5.305139 ACCTAACGTAAATGTTTGCCATC 57.695 39.130 0.00 0.00 33.32 3.51
313 314 5.715434 AACCTAACGTAAATGTTTGCCAT 57.285 34.783 0.00 0.00 33.32 4.40
314 315 5.517322 AAACCTAACGTAAATGTTTGCCA 57.483 34.783 0.00 0.00 33.32 4.92
315 316 5.115923 CGAAAACCTAACGTAAATGTTTGCC 59.884 40.000 0.00 0.00 33.32 4.52
316 317 5.908499 TCGAAAACCTAACGTAAATGTTTGC 59.092 36.000 0.00 0.00 33.32 3.68
317 318 8.496872 AATCGAAAACCTAACGTAAATGTTTG 57.503 30.769 0.00 0.00 33.32 2.93
319 320 9.815936 CTAAATCGAAAACCTAACGTAAATGTT 57.184 29.630 0.00 0.00 35.86 2.71
320 321 9.206870 TCTAAATCGAAAACCTAACGTAAATGT 57.793 29.630 0.00 0.00 0.00 2.71
321 322 9.469239 GTCTAAATCGAAAACCTAACGTAAATG 57.531 33.333 0.00 0.00 0.00 2.32
322 323 9.428097 AGTCTAAATCGAAAACCTAACGTAAAT 57.572 29.630 0.00 0.00 0.00 1.40
323 324 8.816640 AGTCTAAATCGAAAACCTAACGTAAA 57.183 30.769 0.00 0.00 0.00 2.01
324 325 8.816640 AAGTCTAAATCGAAAACCTAACGTAA 57.183 30.769 0.00 0.00 0.00 3.18
325 326 8.081633 TGAAGTCTAAATCGAAAACCTAACGTA 58.918 33.333 0.00 0.00 0.00 3.57
326 327 6.925165 TGAAGTCTAAATCGAAAACCTAACGT 59.075 34.615 0.00 0.00 0.00 3.99
327 328 7.342318 TGAAGTCTAAATCGAAAACCTAACG 57.658 36.000 0.00 0.00 0.00 3.18
328 329 8.718734 ACATGAAGTCTAAATCGAAAACCTAAC 58.281 33.333 0.00 0.00 0.00 2.34
329 330 8.842358 ACATGAAGTCTAAATCGAAAACCTAA 57.158 30.769 0.00 0.00 0.00 2.69
331 332 8.883731 CATACATGAAGTCTAAATCGAAAACCT 58.116 33.333 0.00 0.00 0.00 3.50
332 333 8.879759 TCATACATGAAGTCTAAATCGAAAACC 58.120 33.333 0.00 0.00 33.08 3.27
349 350 9.850198 TGAAATAGACCATCAATTCATACATGA 57.150 29.630 0.00 0.00 34.44 3.07
351 352 9.857656 ACTGAAATAGACCATCAATTCATACAT 57.142 29.630 0.00 0.00 0.00 2.29
352 353 9.685276 AACTGAAATAGACCATCAATTCATACA 57.315 29.630 0.00 0.00 0.00 2.29
440 442 3.827898 CTCCGACAGCCTCCGACC 61.828 72.222 0.00 0.00 0.00 4.79
634 914 3.694566 GGATGGATTTGTAGGGTGTTGTC 59.305 47.826 0.00 0.00 0.00 3.18
644 924 1.136828 CGGGAGGGGATGGATTTGTA 58.863 55.000 0.00 0.00 0.00 2.41
761 1084 2.933906 TGCGGTTTTCTTTATAGAGGCG 59.066 45.455 0.00 0.00 0.00 5.52
935 1259 4.924187 CGCGAGGGAGGGAGGGAT 62.924 72.222 0.00 0.00 0.00 3.85
958 1286 1.137825 CGAAGAGGAGGTCAGACGC 59.862 63.158 0.00 0.00 0.00 5.19
973 1301 2.629210 CAAAACAGACGCCGCGAA 59.371 55.556 21.79 0.00 0.00 4.70
1211 1539 2.264794 GGATCAACGAGCGTGGGT 59.735 61.111 0.00 0.00 0.00 4.51
1238 1566 5.777732 ACTTCTTATAGGCTACTAGCATGCT 59.222 40.000 25.99 25.99 44.75 3.79
1264 1592 3.903714 GCCCATAAATAAATCCAAGGCCT 59.096 43.478 0.00 0.00 31.59 5.19
1286 1614 3.133691 CCCAGGAATCACACATACGATG 58.866 50.000 0.00 0.00 0.00 3.84
1291 1619 2.195727 TGCTCCCAGGAATCACACATA 58.804 47.619 0.00 0.00 0.00 2.29
1365 1797 6.365520 ACAGTTCCCAATATTTATCTCCACC 58.634 40.000 0.00 0.00 0.00 4.61
1537 1988 8.396272 ACTGACTTTAAATTACAGACTTGCAT 57.604 30.769 17.23 0.00 33.53 3.96
1578 2030 7.499232 GGCATTAACTGAACCTCACTGTAATAT 59.501 37.037 0.00 0.00 0.00 1.28
1617 2120 9.035607 GTTCAGATAGTATGGCAATATTATCGG 57.964 37.037 14.67 14.32 40.41 4.18
1618 2121 9.035607 GGTTCAGATAGTATGGCAATATTATCG 57.964 37.037 14.67 11.11 40.41 2.92
1651 2154 1.394917 GCCATAACTGTGCAGAAGACG 59.605 52.381 6.17 0.00 0.00 4.18
1812 2487 5.418840 ACGTTCATTTTTGGCAGAGGAATAT 59.581 36.000 0.00 0.00 0.00 1.28
1814 2489 3.573967 ACGTTCATTTTTGGCAGAGGAAT 59.426 39.130 0.00 0.00 0.00 3.01
1842 2517 3.105203 CACAACAATGAACAACCACGAC 58.895 45.455 0.00 0.00 0.00 4.34
1844 2519 3.143807 ACACAACAATGAACAACCACG 57.856 42.857 0.00 0.00 0.00 4.94
1887 2562 7.095857 TGCAAACAACTTGAAAGTTTTGTGTAG 60.096 33.333 16.16 7.46 46.52 2.74
1892 2567 5.179182 AGGTGCAAACAACTTGAAAGTTTTG 59.821 36.000 5.70 9.97 42.91 2.44
1959 2634 2.586258 ACTACTTGGCTATGCGACAG 57.414 50.000 0.00 0.00 0.00 3.51
1964 2639 8.091449 AGATGTTCTAATACTACTTGGCTATGC 58.909 37.037 0.00 0.00 0.00 3.14
1997 2678 4.220821 ACCAGATAACCGATAGCATACCAG 59.779 45.833 0.00 0.00 0.00 4.00
2005 2686 3.641906 ACCAGGAACCAGATAACCGATAG 59.358 47.826 0.00 0.00 0.00 2.08
2010 2691 4.838904 AGTTACCAGGAACCAGATAACC 57.161 45.455 0.00 0.00 0.00 2.85
2034 2715 7.307632 GCACATGGTCTGTTATCAATACATCTC 60.308 40.741 0.00 0.00 35.29 2.75
2046 2736 1.072266 AAGGGGCACATGGTCTGTTA 58.928 50.000 0.00 0.00 35.29 2.41
2047 2737 0.188342 AAAGGGGCACATGGTCTGTT 59.812 50.000 0.00 0.00 35.29 3.16
2048 2738 1.072266 TAAAGGGGCACATGGTCTGT 58.928 50.000 0.00 0.00 39.20 3.41
2049 2739 1.818674 GTTAAAGGGGCACATGGTCTG 59.181 52.381 0.00 0.00 0.00 3.51
2050 2740 1.427368 TGTTAAAGGGGCACATGGTCT 59.573 47.619 0.00 0.00 0.00 3.85
2053 2743 3.675775 CGAAATGTTAAAGGGGCACATGG 60.676 47.826 0.00 0.00 31.37 3.66
2107 2797 1.537202 GCAACACAGTTTAGCCTGGAG 59.463 52.381 0.00 0.00 36.75 3.86
2142 2832 4.143347 CGTAAAATTGTCTGTTGGCAATGC 60.143 41.667 1.92 0.00 35.72 3.56
2177 2867 6.367374 TGGATTGGTTGACACTAGTAATCA 57.633 37.500 12.18 9.03 0.00 2.57
2182 2872 4.042809 TGGATTGGATTGGTTGACACTAGT 59.957 41.667 0.00 0.00 0.00 2.57
2190 2880 7.350744 TGATAAATCTGGATTGGATTGGTTG 57.649 36.000 0.00 0.00 34.19 3.77
2191 2881 8.557304 AATGATAAATCTGGATTGGATTGGTT 57.443 30.769 0.00 0.00 34.19 3.67
2192 2882 8.557304 AAATGATAAATCTGGATTGGATTGGT 57.443 30.769 0.00 0.00 34.19 3.67
2193 2883 9.841295 AAAAATGATAAATCTGGATTGGATTGG 57.159 29.630 0.00 0.00 34.19 3.16
2231 2923 9.088987 TCATATCAGGTGACATAAGTAGCATAA 57.911 33.333 0.00 0.00 0.00 1.90
2232 2924 8.523658 GTCATATCAGGTGACATAAGTAGCATA 58.476 37.037 1.69 0.00 44.13 3.14
2323 3016 5.452636 GGCCCTGAAAGTTACAACAATGAAA 60.453 40.000 0.00 0.00 0.00 2.69
2428 3122 2.224042 TGCAAGATACTAGCGTCCCATG 60.224 50.000 0.00 0.00 0.00 3.66
2435 3129 2.476619 CCGGAATTGCAAGATACTAGCG 59.523 50.000 4.94 0.00 0.00 4.26
2437 3131 4.442706 ACACCGGAATTGCAAGATACTAG 58.557 43.478 9.46 0.00 0.00 2.57
2497 3197 7.011763 CCATCACAACCTATTGACAGACATAAG 59.988 40.741 0.00 0.00 39.30 1.73
2502 3202 3.375299 GCCATCACAACCTATTGACAGAC 59.625 47.826 0.00 0.00 39.30 3.51
2781 3483 4.333095 CAGGAATGAGAGTCATTTCAGCTG 59.667 45.833 7.63 7.63 46.20 4.24
2834 3610 5.540911 ACTTGCACACCAAAGGATAATTTG 58.459 37.500 0.00 0.00 39.41 2.32
2838 3614 3.820467 CTGACTTGCACACCAAAGGATAA 59.180 43.478 0.00 0.00 31.94 1.75
2873 3676 8.960591 TCCAATGATTTCTGGAAAATCTAAGTC 58.039 33.333 10.77 0.00 38.81 3.01
2892 3741 9.813826 TGATCTGAGATATACTAGTTCCAATGA 57.186 33.333 0.00 0.00 0.00 2.57
2910 3759 7.789273 AGACATCTTGCTATTTTGATCTGAG 57.211 36.000 0.00 0.00 0.00 3.35
2939 3788 7.234355 AGTCAAGTTCCTGGAGTAATTGAAAT 58.766 34.615 11.56 3.37 0.00 2.17
2943 3792 7.560368 AGATAGTCAAGTTCCTGGAGTAATTG 58.440 38.462 0.00 0.00 0.00 2.32
3185 4034 0.040425 CCTTGGACTTTGCCGTTTCG 60.040 55.000 0.00 0.00 0.00 3.46
3329 4178 5.635700 CACTGAGAGCCTTTGAAACTACTAC 59.364 44.000 0.00 0.00 0.00 2.73
3512 4365 0.469917 ACAGTCTTGGTGGTGTCCAG 59.530 55.000 0.00 0.00 38.80 3.86
3610 4469 8.731605 ACGAATACGAGATAGATGAATGTACAT 58.268 33.333 1.41 1.41 42.66 2.29
3611 4470 8.095937 ACGAATACGAGATAGATGAATGTACA 57.904 34.615 0.00 0.00 42.66 2.90
3664 4523 1.361668 GCTTCGCGATTGCCTGAGAA 61.362 55.000 10.88 0.00 38.08 2.87
3936 4796 7.605410 AGTTTACTTGGGACATATAACGTTG 57.395 36.000 11.99 0.00 39.30 4.10
3955 4815 4.630069 GCGACAAGCCTATCTCAAAGTTTA 59.370 41.667 0.00 0.00 40.81 2.01
3991 4857 9.309516 GTTCATAATTATTCACGACTCACCTAA 57.690 33.333 0.00 0.00 0.00 2.69
3995 4861 8.328864 GGAAGTTCATAATTATTCACGACTCAC 58.671 37.037 5.01 0.00 0.00 3.51
4040 4906 3.686241 GGGTACGTTAAATTCCAGTCACC 59.314 47.826 0.00 0.00 0.00 4.02
4201 5069 4.083110 CGCCTAATGCTATTTGGAAGATGG 60.083 45.833 11.42 0.00 38.05 3.51
4226 5124 0.179029 AAGGGACAAACCTCACCACG 60.179 55.000 0.00 0.00 40.87 4.94
4227 5125 1.954382 GAAAGGGACAAACCTCACCAC 59.046 52.381 0.00 0.00 40.87 4.16
4228 5126 1.850345 AGAAAGGGACAAACCTCACCA 59.150 47.619 0.00 0.00 40.87 4.17
4230 5128 2.106684 AGGAGAAAGGGACAAACCTCAC 59.893 50.000 0.00 0.00 40.87 3.51
4233 5131 2.640332 GAGAGGAGAAAGGGACAAACCT 59.360 50.000 0.00 0.00 44.56 3.50
4234 5132 2.372172 TGAGAGGAGAAAGGGACAAACC 59.628 50.000 0.00 0.00 38.08 3.27
4235 5133 3.771577 TGAGAGGAGAAAGGGACAAAC 57.228 47.619 0.00 0.00 0.00 2.93
4236 5134 3.009473 CCATGAGAGGAGAAAGGGACAAA 59.991 47.826 0.00 0.00 0.00 2.83
4239 5137 1.488393 CCCATGAGAGGAGAAAGGGAC 59.512 57.143 0.00 0.00 36.96 4.46
4243 5141 2.093235 GGACACCCATGAGAGGAGAAAG 60.093 54.545 0.00 0.00 0.00 2.62
4246 5144 0.325671 GGGACACCCATGAGAGGAGA 60.326 60.000 0.00 0.00 44.65 3.71
4247 5145 2.216148 GGGACACCCATGAGAGGAG 58.784 63.158 0.00 0.00 44.65 3.69
4248 5146 4.480480 GGGACACCCATGAGAGGA 57.520 61.111 0.00 0.00 44.65 3.71
4258 5156 1.265454 ATGAGAGAACGGGGGACACC 61.265 60.000 0.00 0.00 39.11 4.16
4259 5157 0.613777 AATGAGAGAACGGGGGACAC 59.386 55.000 0.00 0.00 0.00 3.67
4261 5159 0.744771 GCAATGAGAGAACGGGGGAC 60.745 60.000 0.00 0.00 0.00 4.46
4264 5162 0.745845 CCAGCAATGAGAGAACGGGG 60.746 60.000 0.00 0.00 0.00 5.73
4322 5220 5.075493 AGCATCAAAACAGACAAAGAGGAT 58.925 37.500 0.00 0.00 0.00 3.24
4370 5407 1.545582 GCCATGTATTTGTGTGCCTGT 59.454 47.619 0.00 0.00 0.00 4.00
4371 5408 1.820519 AGCCATGTATTTGTGTGCCTG 59.179 47.619 0.00 0.00 0.00 4.85
4404 5441 1.296056 TTCGCGCCTTTTCAGCTACC 61.296 55.000 0.00 0.00 0.00 3.18
4405 5442 0.179222 GTTCGCGCCTTTTCAGCTAC 60.179 55.000 0.00 0.00 0.00 3.58
4407 5444 0.320421 TAGTTCGCGCCTTTTCAGCT 60.320 50.000 0.00 0.00 0.00 4.24
4432 5469 6.268387 CCCAGATTATTTCCAGCCATGTATTT 59.732 38.462 0.00 0.00 0.00 1.40
4468 5510 2.790433 CCACAGCTGTTAGGCCTTTAA 58.210 47.619 18.94 0.00 0.00 1.52
4511 5553 6.255887 GCAAATACTACAGCGATACTTTGTCT 59.744 38.462 0.00 0.00 0.00 3.41
4535 5577 3.855689 AATTATGCAACTGTGGTCTGC 57.144 42.857 0.00 0.00 36.60 4.26
4540 5582 5.163530 TGCCATCTAAATTATGCAACTGTGG 60.164 40.000 0.00 0.00 0.00 4.17
4603 5645 0.095245 CACAATAGCAGGCACGTTCG 59.905 55.000 0.00 0.00 0.00 3.95
4685 5727 9.941325 ATATAGCATATTATAAGGCTCTGATGC 57.059 33.333 11.09 0.00 38.94 3.91
4700 5742 7.239773 ACCCTGGGTTCACTAATATAGCATATT 59.760 37.037 14.05 6.62 27.29 1.28
4706 5748 7.455008 ACTCATACCCTGGGTTCACTAATATAG 59.545 40.741 26.00 12.57 33.59 1.31
4724 5766 1.767759 AAGGGCATGCAACTCATACC 58.232 50.000 21.36 8.68 37.79 2.73


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

AutoCloner maintained by Alex Coulton.