Multiple sequence alignment - TraesCS4D01G165300

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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 TraesCS4D01G165300 chr4D 100.000 5243 0 0 1001 6243 274218232 274223474 0.000000e+00 9683.0
1 TraesCS4D01G165300 chr4D 100.000 618 0 0 1 618 274217232 274217849 0.000000e+00 1142.0
2 TraesCS4D01G165300 chr4D 80.934 514 75 16 5354 5854 495967479 495966976 9.820000e-103 385.0
3 TraesCS4D01G165300 chr4B 95.314 4545 149 18 1009 5531 240823912 240828414 0.000000e+00 7155.0
4 TraesCS4D01G165300 chr4B 91.899 358 23 4 5890 6243 240828761 240829116 4.350000e-136 496.0
5 TraesCS4D01G165300 chr4B 80.452 619 94 16 5351 5952 657158981 657158373 1.230000e-121 448.0
6 TraesCS4D01G165300 chr4B 91.250 320 23 2 5709 6023 240828459 240828778 1.240000e-116 431.0
7 TraesCS4D01G165300 chr4B 91.216 148 13 0 6096 6243 240847562 240847709 1.060000e-47 202.0
8 TraesCS4D01G165300 chr4B 87.943 141 8 7 350 488 240823298 240823431 2.330000e-34 158.0
9 TraesCS4D01G165300 chr4B 93.478 92 1 2 519 605 240823430 240823521 1.410000e-26 132.0
10 TraesCS4D01G165300 chr4A 95.353 2453 102 7 1001 3446 255594574 255592127 0.000000e+00 3888.0
11 TraesCS4D01G165300 chr4A 94.563 1876 61 17 3445 5291 255592003 255590140 0.000000e+00 2861.0
12 TraesCS4D01G165300 chr4A 88.718 195 12 7 419 608 255595166 255594977 4.870000e-56 230.0
13 TraesCS4D01G165300 chr4A 88.496 113 9 1 313 421 255601907 255601795 3.930000e-27 134.0
14 TraesCS4D01G165300 chr5B 84.020 607 63 19 5354 5952 705521724 705522304 2.540000e-153 553.0
15 TraesCS4D01G165300 chr5B 79.084 502 77 17 5356 5843 274470104 274469617 2.810000e-83 320.0
16 TraesCS4D01G165300 chr7A 81.099 619 85 21 5352 5952 129069648 129070252 3.410000e-127 466.0
17 TraesCS4D01G165300 chr7A 79.576 519 72 25 5354 5854 588741003 588741505 2.160000e-89 340.0
18 TraesCS4D01G165300 chr7A 95.890 146 6 0 6096 6241 129072539 129072684 2.910000e-58 237.0
19 TraesCS4D01G165300 chr7A 95.652 69 3 0 5226 5294 338989382 338989314 1.840000e-20 111.0
20 TraesCS4D01G165300 chr2A 81.068 618 87 19 5352 5952 719353168 719352564 3.410000e-127 466.0
21 TraesCS4D01G165300 chr2A 79.457 516 79 20 5354 5854 520425710 520425207 2.160000e-89 340.0
22 TraesCS4D01G165300 chr2A 96.575 146 5 0 6096 6241 719350277 719350132 6.250000e-60 243.0
23 TraesCS4D01G165300 chr2A 90.683 161 15 0 3875 4035 111422142 111421982 1.360000e-51 215.0
24 TraesCS4D01G165300 chr1B 80.937 619 88 19 5352 5952 403407039 403406433 4.410000e-126 462.0
25 TraesCS4D01G165300 chr1B 80.614 619 88 19 5352 5952 49436355 49435751 3.430000e-122 449.0
26 TraesCS4D01G165300 chr1B 96.575 146 5 0 6096 6241 403404146 403404001 6.250000e-60 243.0
27 TraesCS4D01G165300 chr1B 95.890 146 5 1 6096 6241 49433464 49433320 1.050000e-57 235.0
28 TraesCS4D01G165300 chr3A 81.643 572 75 19 5399 5952 184636582 184636023 1.230000e-121 448.0
29 TraesCS4D01G165300 chr3A 95.890 146 6 0 6096 6241 184633745 184633600 2.910000e-58 237.0
30 TraesCS4D01G165300 chr7D 96.899 258 8 0 1 258 34178983 34178726 3.460000e-117 433.0
31 TraesCS4D01G165300 chr7D 95.367 259 9 3 1 258 54987996 54988252 5.830000e-110 409.0
32 TraesCS4D01G165300 chr3D 96.512 258 9 0 1 258 500603434 500603177 1.610000e-115 427.0
33 TraesCS4D01G165300 chr3D 92.174 230 15 2 5052 5281 19853632 19853406 7.810000e-84 322.0
34 TraesCS4D01G165300 chr5D 95.167 269 12 1 1 269 526658755 526659022 2.080000e-114 424.0
35 TraesCS4D01G165300 chr5D 96.471 255 9 0 1 255 424150547 424150801 7.480000e-114 422.0
36 TraesCS4D01G165300 chr5D 93.436 259 14 3 1 258 65978504 65978760 1.270000e-101 381.0
37 TraesCS4D01G165300 chr5D 95.522 67 3 0 5225 5291 6249134 6249200 2.380000e-19 108.0
38 TraesCS4D01G165300 chr1D 96.471 255 9 0 1 255 218970434 218970688 7.480000e-114 422.0
39 TraesCS4D01G165300 chr1D 95.775 71 3 0 5224 5294 254463547 254463477 1.420000e-21 115.0
40 TraesCS4D01G165300 chr1D 95.522 67 3 0 5225 5291 180382090 180382156 2.380000e-19 108.0
41 TraesCS4D01G165300 chr1D 95.522 67 3 0 5225 5291 318562872 318562938 2.380000e-19 108.0
42 TraesCS4D01G165300 chr2D 95.753 259 10 1 1 259 594596864 594596607 3.480000e-112 416.0
43 TraesCS4D01G165300 chr2D 94.595 259 12 2 1 258 498766377 498766634 3.510000e-107 399.0
44 TraesCS4D01G165300 chr2D 89.441 161 17 0 3875 4035 111332675 111332515 2.950000e-48 204.0
45 TraesCS4D01G165300 chr2D 86.842 76 10 0 3699 3774 111332830 111332755 1.120000e-12 86.1
46 TraesCS4D01G165300 chr7B 81.048 496 67 17 5356 5837 322658474 322658956 2.750000e-98 370.0
47 TraesCS4D01G165300 chr1A 80.716 503 69 18 5356 5843 510309968 510309479 3.560000e-97 366.0
48 TraesCS4D01G165300 chr1A 88.294 299 31 3 5948 6243 101097406 101097703 7.700000e-94 355.0
49 TraesCS4D01G165300 chr6D 80.357 504 71 18 5356 5843 283466591 283466100 2.140000e-94 357.0
50 TraesCS4D01G165300 chr6D 94.286 70 4 0 5225 5294 378301904 378301835 2.380000e-19 108.0
51 TraesCS4D01G165300 chr6A 80.483 497 69 17 5356 5837 90094325 90094808 7.700000e-94 355.0
52 TraesCS4D01G165300 chrUn 81.622 370 43 19 5391 5746 77427860 77427502 3.680000e-72 283.0
53 TraesCS4D01G165300 chr6B 96.575 146 5 0 6096 6241 636785 636930 6.250000e-60 243.0
54 TraesCS4D01G165300 chr2B 90.062 161 16 0 3875 4035 161415633 161415473 6.340000e-50 209.0
55 TraesCS4D01G165300 chr2B 86.842 76 10 0 3699 3774 161415791 161415716 1.120000e-12 86.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G165300 chr4D 274217232 274223474 6242 False 5412.500000 9683 100.0000 1 6243 2 chr4D.!!$F1 6242
1 TraesCS4D01G165300 chr4D 495966976 495967479 503 True 385.000000 385 80.9340 5354 5854 1 chr4D.!!$R1 500
2 TraesCS4D01G165300 chr4B 240823298 240829116 5818 False 1674.400000 7155 91.9768 350 6243 5 chr4B.!!$F2 5893
3 TraesCS4D01G165300 chr4B 657158373 657158981 608 True 448.000000 448 80.4520 5351 5952 1 chr4B.!!$R1 601
4 TraesCS4D01G165300 chr4A 255590140 255595166 5026 True 2326.333333 3888 92.8780 419 5291 3 chr4A.!!$R2 4872
5 TraesCS4D01G165300 chr5B 705521724 705522304 580 False 553.000000 553 84.0200 5354 5952 1 chr5B.!!$F1 598
6 TraesCS4D01G165300 chr7A 129069648 129072684 3036 False 351.500000 466 88.4945 5352 6241 2 chr7A.!!$F2 889
7 TraesCS4D01G165300 chr7A 588741003 588741505 502 False 340.000000 340 79.5760 5354 5854 1 chr7A.!!$F1 500
8 TraesCS4D01G165300 chr2A 719350132 719353168 3036 True 354.500000 466 88.8215 5352 6241 2 chr2A.!!$R3 889
9 TraesCS4D01G165300 chr2A 520425207 520425710 503 True 340.000000 340 79.4570 5354 5854 1 chr2A.!!$R2 500
10 TraesCS4D01G165300 chr1B 403404001 403407039 3038 True 352.500000 462 88.7560 5352 6241 2 chr1B.!!$R2 889
11 TraesCS4D01G165300 chr1B 49433320 49436355 3035 True 342.000000 449 88.2520 5352 6241 2 chr1B.!!$R1 889
12 TraesCS4D01G165300 chr3A 184633600 184636582 2982 True 342.500000 448 88.7665 5399 6241 2 chr3A.!!$R1 842

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
30 31 0.034337 ACGGCTAAAACGCTGGAGAA 59.966 50.0 0.00 0.0 40.59 2.87 F
235 236 0.091344 CGTTCTGTCTGTTTAGCGCG 59.909 55.0 0.00 0.0 0.00 6.86 F
394 395 0.107410 TTTTGGCTCGGCATATCGGT 60.107 50.0 0.00 0.0 0.00 4.69 F
1908 1934 0.036022 GGAAACTGCAGTGCCTCTCT 59.964 55.0 22.49 0.0 0.00 3.10 F
3035 3062 1.664873 GCTCCCGGAGTAAATTCCAC 58.335 55.0 16.09 0.0 37.05 4.02 F
4508 4674 1.888436 CGGTGGAGGAAGCTACAGCA 61.888 60.0 3.70 0.0 45.16 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1778 1.805428 GCGTCTTTGCCAATGGGTGT 61.805 55.000 0.00 0.0 36.17 4.16 R
1901 1927 3.130340 CCTGAGTAACTTCTGAGAGAGGC 59.870 52.174 0.00 0.0 0.00 4.70 R
2343 2369 0.464373 ATCGAAGCATTGTCGCCCAT 60.464 50.000 0.00 0.0 38.39 4.00 R
3863 4020 0.249031 GTGGCACTGCAAGACCAAAC 60.249 55.000 11.13 0.0 43.31 2.93 R
4802 4968 1.725169 CCTTCTTTGGGGTGGGTGGA 61.725 60.000 0.00 0.0 0.00 4.02 R
5540 5757 0.169672 CCGAAGAAGCAGCCAACATG 59.830 55.000 0.00 0.0 0.00 3.21 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
22 23 4.643675 CGCATGACGGCTAAAACG 57.356 55.556 0.00 0.00 38.44 3.60
23 24 1.580132 CGCATGACGGCTAAAACGC 60.580 57.895 0.00 0.00 38.44 4.84
24 25 1.794222 GCATGACGGCTAAAACGCT 59.206 52.632 0.00 0.00 34.00 5.07
25 26 0.521242 GCATGACGGCTAAAACGCTG 60.521 55.000 0.00 0.00 42.00 5.18
26 27 0.096976 CATGACGGCTAAAACGCTGG 59.903 55.000 0.00 0.00 40.59 4.85
27 28 0.036765 ATGACGGCTAAAACGCTGGA 60.037 50.000 0.00 0.00 40.59 3.86
28 29 0.669318 TGACGGCTAAAACGCTGGAG 60.669 55.000 0.00 0.00 40.59 3.86
29 30 0.389426 GACGGCTAAAACGCTGGAGA 60.389 55.000 0.00 0.00 40.59 3.71
30 31 0.034337 ACGGCTAAAACGCTGGAGAA 59.966 50.000 0.00 0.00 40.59 2.87
31 32 0.442699 CGGCTAAAACGCTGGAGAAC 59.557 55.000 0.00 0.00 32.64 3.01
32 33 1.809684 GGCTAAAACGCTGGAGAACT 58.190 50.000 0.00 0.00 0.00 3.01
33 34 1.464997 GGCTAAAACGCTGGAGAACTG 59.535 52.381 0.00 0.00 0.00 3.16
34 35 1.135944 GCTAAAACGCTGGAGAACTGC 60.136 52.381 0.00 0.00 40.30 4.40
35 36 1.464997 CTAAAACGCTGGAGAACTGCC 59.535 52.381 0.00 0.00 40.57 4.85
36 37 0.179018 AAAACGCTGGAGAACTGCCT 60.179 50.000 0.00 0.00 40.57 4.75
37 38 0.685097 AAACGCTGGAGAACTGCCTA 59.315 50.000 0.00 0.00 40.57 3.93
38 39 0.685097 AACGCTGGAGAACTGCCTAA 59.315 50.000 0.00 0.00 40.57 2.69
39 40 0.905357 ACGCTGGAGAACTGCCTAAT 59.095 50.000 0.00 0.00 40.57 1.73
40 41 1.134670 ACGCTGGAGAACTGCCTAATC 60.135 52.381 0.00 0.00 40.57 1.75
41 42 1.808133 CGCTGGAGAACTGCCTAATCC 60.808 57.143 0.00 0.00 40.57 3.01
42 43 1.488393 GCTGGAGAACTGCCTAATCCT 59.512 52.381 0.00 0.00 38.01 3.24
43 44 2.484594 GCTGGAGAACTGCCTAATCCTC 60.485 54.545 0.00 0.00 38.01 3.71
44 45 2.768527 CTGGAGAACTGCCTAATCCTCA 59.231 50.000 0.00 0.00 0.00 3.86
45 46 3.181329 TGGAGAACTGCCTAATCCTCAA 58.819 45.455 0.00 0.00 0.00 3.02
46 47 3.782523 TGGAGAACTGCCTAATCCTCAAT 59.217 43.478 0.00 0.00 0.00 2.57
47 48 4.133078 GGAGAACTGCCTAATCCTCAATG 58.867 47.826 0.00 0.00 0.00 2.82
48 49 4.141620 GGAGAACTGCCTAATCCTCAATGA 60.142 45.833 0.00 0.00 0.00 2.57
49 50 4.775236 AGAACTGCCTAATCCTCAATGAC 58.225 43.478 0.00 0.00 0.00 3.06
50 51 4.225942 AGAACTGCCTAATCCTCAATGACA 59.774 41.667 0.00 0.00 0.00 3.58
51 52 4.785346 ACTGCCTAATCCTCAATGACAT 57.215 40.909 0.00 0.00 0.00 3.06
52 53 4.458397 ACTGCCTAATCCTCAATGACATG 58.542 43.478 0.00 0.00 0.00 3.21
53 54 4.080129 ACTGCCTAATCCTCAATGACATGT 60.080 41.667 0.00 0.00 0.00 3.21
54 55 4.201657 TGCCTAATCCTCAATGACATGTG 58.798 43.478 1.15 0.00 0.00 3.21
55 56 3.567164 GCCTAATCCTCAATGACATGTGG 59.433 47.826 1.15 0.00 35.71 4.17
56 57 4.139786 CCTAATCCTCAATGACATGTGGG 58.860 47.826 1.15 0.00 35.24 4.61
57 58 3.744940 AATCCTCAATGACATGTGGGT 57.255 42.857 1.15 0.00 35.24 4.51
58 59 2.787473 TCCTCAATGACATGTGGGTC 57.213 50.000 1.15 0.00 35.24 4.46
59 60 1.281867 TCCTCAATGACATGTGGGTCC 59.718 52.381 1.15 0.00 36.97 4.46
60 61 1.683011 CCTCAATGACATGTGGGTCCC 60.683 57.143 1.15 0.00 36.97 4.46
61 62 1.004628 CTCAATGACATGTGGGTCCCA 59.995 52.381 6.47 6.47 36.97 4.37
72 73 4.019312 GGTCCCACGGGCGGTTTA 62.019 66.667 0.00 0.00 34.68 2.01
73 74 2.269883 GTCCCACGGGCGGTTTAT 59.730 61.111 0.00 0.00 34.68 1.40
74 75 1.816679 GTCCCACGGGCGGTTTATC 60.817 63.158 0.00 0.00 34.68 1.75
75 76 1.991167 TCCCACGGGCGGTTTATCT 60.991 57.895 0.00 0.00 34.68 1.98
76 77 1.523032 CCCACGGGCGGTTTATCTC 60.523 63.158 0.00 0.00 0.00 2.75
77 78 1.881252 CCACGGGCGGTTTATCTCG 60.881 63.158 0.00 0.00 0.00 4.04
82 83 3.984765 GCGGTTTATCTCGCGCGG 61.985 66.667 31.69 20.60 42.48 6.46
83 84 3.984765 CGGTTTATCTCGCGCGGC 61.985 66.667 31.69 11.01 0.00 6.53
101 102 3.330853 GCGGCGCAATCGGACTAG 61.331 66.667 29.21 0.00 35.95 2.57
102 103 2.658593 CGGCGCAATCGGACTAGG 60.659 66.667 10.83 0.00 35.95 3.02
103 104 2.967615 GGCGCAATCGGACTAGGC 60.968 66.667 10.83 0.00 35.95 3.93
106 107 4.014065 GCAATCGGACTAGGCGAC 57.986 61.111 0.00 0.00 0.00 5.19
107 108 1.591863 GCAATCGGACTAGGCGACC 60.592 63.158 0.00 0.00 0.00 4.79
111 112 3.885521 CGGACTAGGCGACCGGTC 61.886 72.222 25.28 25.28 45.23 4.79
112 113 3.525545 GGACTAGGCGACCGGTCC 61.526 72.222 28.52 20.04 41.13 4.46
113 114 2.753043 GACTAGGCGACCGGTCCA 60.753 66.667 28.52 10.52 0.00 4.02
114 115 3.061260 GACTAGGCGACCGGTCCAC 62.061 68.421 28.52 20.58 0.00 4.02
115 116 4.189188 CTAGGCGACCGGTCCACG 62.189 72.222 28.52 18.95 43.80 4.94
169 170 4.016706 GGGGACACCTGGACACGG 62.017 72.222 0.00 0.00 36.80 4.94
170 171 4.699522 GGGACACCTGGACACGGC 62.700 72.222 0.00 0.00 0.00 5.68
172 173 4.295119 GACACCTGGACACGGCGT 62.295 66.667 6.77 6.77 0.00 5.68
173 174 4.602259 ACACCTGGACACGGCGTG 62.602 66.667 35.89 35.89 39.75 5.34
200 201 2.586357 GGGACGAGATCAAGCGGC 60.586 66.667 0.00 0.00 34.04 6.53
201 202 2.496817 GGACGAGATCAAGCGGCT 59.503 61.111 0.00 0.00 35.46 5.52
202 203 1.590259 GGACGAGATCAAGCGGCTC 60.590 63.158 1.45 0.00 35.46 4.70
203 204 1.435515 GACGAGATCAAGCGGCTCT 59.564 57.895 1.45 0.00 31.57 4.09
204 205 0.593773 GACGAGATCAAGCGGCTCTC 60.594 60.000 1.45 4.87 31.57 3.20
205 206 4.317529 GAGATCAAGCGGCTCTCG 57.682 61.111 1.45 0.00 42.76 4.04
206 207 1.435515 GAGATCAAGCGGCTCTCGT 59.564 57.895 1.45 0.00 41.72 4.18
207 208 0.179124 GAGATCAAGCGGCTCTCGTT 60.179 55.000 1.45 0.00 41.72 3.85
208 209 0.179124 AGATCAAGCGGCTCTCGTTC 60.179 55.000 1.45 0.25 41.72 3.95
209 210 1.475441 GATCAAGCGGCTCTCGTTCG 61.475 60.000 1.45 0.00 41.72 3.95
210 211 2.890847 ATCAAGCGGCTCTCGTTCGG 62.891 60.000 1.45 0.00 41.72 4.30
222 223 3.479269 GTTCGGCCGCTCGTTCTG 61.479 66.667 23.51 0.00 0.00 3.02
223 224 3.986006 TTCGGCCGCTCGTTCTGT 61.986 61.111 23.51 0.00 0.00 3.41
224 225 3.909258 TTCGGCCGCTCGTTCTGTC 62.909 63.158 23.51 0.00 0.00 3.51
225 226 4.421479 CGGCCGCTCGTTCTGTCT 62.421 66.667 14.67 0.00 0.00 3.41
226 227 2.811317 GGCCGCTCGTTCTGTCTG 60.811 66.667 0.00 0.00 0.00 3.51
227 228 2.049063 GCCGCTCGTTCTGTCTGT 60.049 61.111 0.00 0.00 0.00 3.41
228 229 1.664965 GCCGCTCGTTCTGTCTGTT 60.665 57.895 0.00 0.00 0.00 3.16
229 230 1.222115 GCCGCTCGTTCTGTCTGTTT 61.222 55.000 0.00 0.00 0.00 2.83
230 231 1.933500 GCCGCTCGTTCTGTCTGTTTA 60.934 52.381 0.00 0.00 0.00 2.01
231 232 1.986378 CCGCTCGTTCTGTCTGTTTAG 59.014 52.381 0.00 0.00 0.00 1.85
232 233 1.387084 CGCTCGTTCTGTCTGTTTAGC 59.613 52.381 0.00 0.00 0.00 3.09
233 234 1.387084 GCTCGTTCTGTCTGTTTAGCG 59.613 52.381 0.00 0.00 0.00 4.26
234 235 1.387084 CTCGTTCTGTCTGTTTAGCGC 59.613 52.381 0.00 0.00 0.00 5.92
235 236 0.091344 CGTTCTGTCTGTTTAGCGCG 59.909 55.000 0.00 0.00 0.00 6.86
236 237 0.179248 GTTCTGTCTGTTTAGCGCGC 60.179 55.000 26.66 26.66 0.00 6.86
237 238 1.614227 TTCTGTCTGTTTAGCGCGCG 61.614 55.000 28.44 28.44 0.00 6.86
238 239 3.071459 CTGTCTGTTTAGCGCGCGG 62.071 63.158 33.06 13.10 0.00 6.46
239 240 4.500568 GTCTGTTTAGCGCGCGGC 62.501 66.667 33.06 23.14 44.05 6.53
248 249 4.392576 GCGCGCGGCCACTTTTTA 62.393 61.111 33.06 0.00 34.80 1.52
249 250 2.202298 CGCGCGGCCACTTTTTAG 60.202 61.111 24.84 0.00 0.00 1.85
250 251 2.673114 CGCGCGGCCACTTTTTAGA 61.673 57.895 24.84 0.00 0.00 2.10
251 252 1.800681 GCGCGGCCACTTTTTAGAT 59.199 52.632 8.83 0.00 0.00 1.98
252 253 0.170339 GCGCGGCCACTTTTTAGATT 59.830 50.000 8.83 0.00 0.00 2.40
253 254 1.402325 GCGCGGCCACTTTTTAGATTT 60.402 47.619 8.83 0.00 0.00 2.17
254 255 2.924880 GCGCGGCCACTTTTTAGATTTT 60.925 45.455 8.83 0.00 0.00 1.82
255 256 3.671164 GCGCGGCCACTTTTTAGATTTTA 60.671 43.478 8.83 0.00 0.00 1.52
256 257 4.095610 CGCGGCCACTTTTTAGATTTTAG 58.904 43.478 2.24 0.00 0.00 1.85
257 258 4.421058 GCGGCCACTTTTTAGATTTTAGG 58.579 43.478 2.24 0.00 0.00 2.69
258 259 4.421058 CGGCCACTTTTTAGATTTTAGGC 58.579 43.478 2.24 0.00 38.84 3.93
259 260 4.157840 CGGCCACTTTTTAGATTTTAGGCT 59.842 41.667 2.24 0.00 39.48 4.58
260 261 5.651530 GGCCACTTTTTAGATTTTAGGCTC 58.348 41.667 0.00 0.00 39.48 4.70
261 262 5.419155 GGCCACTTTTTAGATTTTAGGCTCT 59.581 40.000 0.00 0.00 39.48 4.09
262 263 6.071334 GGCCACTTTTTAGATTTTAGGCTCTT 60.071 38.462 0.00 0.00 39.48 2.85
263 264 7.378966 GCCACTTTTTAGATTTTAGGCTCTTT 58.621 34.615 0.00 0.00 36.72 2.52
264 265 7.872993 GCCACTTTTTAGATTTTAGGCTCTTTT 59.127 33.333 0.00 0.00 36.72 2.27
334 335 3.297830 AAAAGATAACCCAGCGCAAAC 57.702 42.857 11.47 0.00 0.00 2.93
335 336 1.904287 AAGATAACCCAGCGCAAACA 58.096 45.000 11.47 0.00 0.00 2.83
336 337 1.165270 AGATAACCCAGCGCAAACAC 58.835 50.000 11.47 0.00 0.00 3.32
337 338 0.170339 GATAACCCAGCGCAAACACC 59.830 55.000 11.47 0.00 0.00 4.16
338 339 1.582610 ATAACCCAGCGCAAACACCG 61.583 55.000 11.47 0.00 0.00 4.94
339 340 2.661840 TAACCCAGCGCAAACACCGA 62.662 55.000 11.47 0.00 0.00 4.69
340 341 3.283684 CCCAGCGCAAACACCGAA 61.284 61.111 11.47 0.00 0.00 4.30
341 342 2.718731 CCAGCGCAAACACCGAAA 59.281 55.556 11.47 0.00 0.00 3.46
342 343 1.285641 CCAGCGCAAACACCGAAAT 59.714 52.632 11.47 0.00 0.00 2.17
343 344 0.318614 CCAGCGCAAACACCGAAATT 60.319 50.000 11.47 0.00 0.00 1.82
344 345 1.068885 CCAGCGCAAACACCGAAATTA 60.069 47.619 11.47 0.00 0.00 1.40
345 346 1.976045 CAGCGCAAACACCGAAATTAC 59.024 47.619 11.47 0.00 0.00 1.89
346 347 1.877443 AGCGCAAACACCGAAATTACT 59.123 42.857 11.47 0.00 0.00 2.24
347 348 3.068560 AGCGCAAACACCGAAATTACTA 58.931 40.909 11.47 0.00 0.00 1.82
348 349 3.499157 AGCGCAAACACCGAAATTACTAA 59.501 39.130 11.47 0.00 0.00 2.24
352 353 6.523893 GCGCAAACACCGAAATTACTAAATAA 59.476 34.615 0.30 0.00 0.00 1.40
370 371 5.400066 AATAAATTTTGGTTCGGTCCTGG 57.600 39.130 0.00 0.00 0.00 4.45
394 395 0.107410 TTTTGGCTCGGCATATCGGT 60.107 50.000 0.00 0.00 0.00 4.69
608 615 3.564511 CAAATCCACACCTTTTACGCAG 58.435 45.455 0.00 0.00 0.00 5.18
609 616 2.851263 ATCCACACCTTTTACGCAGA 57.149 45.000 0.00 0.00 0.00 4.26
610 617 2.851263 TCCACACCTTTTACGCAGAT 57.149 45.000 0.00 0.00 0.00 2.90
611 618 3.134574 TCCACACCTTTTACGCAGATT 57.865 42.857 0.00 0.00 0.00 2.40
612 619 3.071479 TCCACACCTTTTACGCAGATTC 58.929 45.455 0.00 0.00 0.00 2.52
613 620 2.161609 CCACACCTTTTACGCAGATTCC 59.838 50.000 0.00 0.00 0.00 3.01
614 621 2.161609 CACACCTTTTACGCAGATTCCC 59.838 50.000 0.00 0.00 0.00 3.97
615 622 1.743394 CACCTTTTACGCAGATTCCCC 59.257 52.381 0.00 0.00 0.00 4.81
616 623 1.633945 ACCTTTTACGCAGATTCCCCT 59.366 47.619 0.00 0.00 0.00 4.79
617 624 2.017049 CCTTTTACGCAGATTCCCCTG 58.983 52.381 0.00 0.00 37.23 4.45
1212 1234 0.741221 GCATCTCCGTCAAGGGTGTC 60.741 60.000 0.00 0.00 41.52 3.67
1306 1328 4.435917 GCTTGCTTCCTTTTTGTTTGTGTG 60.436 41.667 0.00 0.00 0.00 3.82
1384 1406 5.798934 GCATGCTGCTATTATATCTTGTTGC 59.201 40.000 11.37 0.00 40.96 4.17
1422 1444 2.483188 GGCCATCCTGTTAACTCGTAGG 60.483 54.545 7.22 5.30 0.00 3.18
1545 1571 8.476925 GGCGACTTTAGTTTTTATTTGTTTCTG 58.523 33.333 0.00 0.00 0.00 3.02
1592 1618 1.066573 CCTGTGCTGAAGAATCGACCT 60.067 52.381 0.00 0.00 0.00 3.85
1682 1708 1.884235 AAGAAGAACTTGTGAGGCGG 58.116 50.000 0.00 0.00 37.45 6.13
1769 1795 0.319813 GCACACCCATTGGCAAAGAC 60.320 55.000 3.01 0.00 33.59 3.01
1807 1833 3.461773 CGGACCGGCTGATCAGGT 61.462 66.667 23.89 14.56 46.20 4.00
1908 1934 0.036022 GGAAACTGCAGTGCCTCTCT 59.964 55.000 22.49 0.00 0.00 3.10
1982 2008 2.425143 ATGTAGTGGCAACCCATGAG 57.575 50.000 0.00 0.00 44.51 2.90
2020 2046 6.543792 AAGCTCCAACAGAAAAAGGAGATCG 61.544 44.000 11.25 0.00 45.38 3.69
2189 2215 3.367806 CGGACTTGATCTCTTCTGAAGCA 60.368 47.826 12.54 2.20 0.00 3.91
2278 2304 4.999950 CCAAATACCAGATGCTGATCCTAC 59.000 45.833 0.00 0.00 32.44 3.18
2343 2369 7.365652 GGGAGAGGTTTGTTCCTAAGAATGATA 60.366 40.741 0.00 0.00 38.02 2.15
2355 2381 5.122869 CCTAAGAATGATATGGGCGACAATG 59.877 44.000 0.00 0.00 0.00 2.82
2359 2385 2.221169 TGATATGGGCGACAATGCTTC 58.779 47.619 0.00 0.00 34.52 3.86
2451 2477 2.921834 TCAGGTACCTGAGGTTAGCT 57.078 50.000 35.91 8.17 46.80 3.32
2769 2795 4.520179 TGAGTCAATGGAGGATGATGTTG 58.480 43.478 0.00 0.00 0.00 3.33
2794 2820 7.014134 TGTGGAGATTAAGCAACTTGATTTCAA 59.986 33.333 0.00 0.00 27.49 2.69
2860 2886 4.129380 TCAGAACATGTGAAAGAGGTGTG 58.871 43.478 0.00 0.00 0.00 3.82
3035 3062 1.664873 GCTCCCGGAGTAAATTCCAC 58.335 55.000 16.09 0.00 37.05 4.02
3050 3077 5.909621 AATTCCACCTTGAATGATGAGTG 57.090 39.130 0.00 0.00 35.21 3.51
3057 3084 5.297776 CACCTTGAATGATGAGTGGGATTAC 59.702 44.000 0.00 0.00 0.00 1.89
3077 3104 7.201652 GGATTACCTTTGTAGTTCTGATTGCTC 60.202 40.741 0.00 0.00 0.00 4.26
3127 3154 2.031157 GTGTACTGCATTGGGTGTGTTC 60.031 50.000 0.00 0.00 0.00 3.18
3305 3333 6.384258 TTGTGAGTGCAAGTTAATTTAGCA 57.616 33.333 0.00 4.53 0.00 3.49
3313 3341 5.106157 TGCAAGTTAATTTAGCAGAGGAAGC 60.106 40.000 0.00 0.00 0.00 3.86
3497 3652 7.655328 AGAATGCTAGTGAAGTAATGAGCATAC 59.345 37.037 7.53 0.00 46.94 2.39
3518 3673 2.159430 CGATCGTTTGGTCATTCTGCAA 59.841 45.455 7.03 0.00 0.00 4.08
3793 3950 6.458342 GGTGAGTCCTTGTTTCTTTACTTGTG 60.458 42.308 0.00 0.00 0.00 3.33
3863 4020 7.784633 TTGGAAGCTAATTGTTTTTCTTTGG 57.215 32.000 0.00 0.00 0.00 3.28
4196 4354 5.480073 TGCAGCCTTTCTTATGTAACCAAAT 59.520 36.000 0.00 0.00 0.00 2.32
4304 4470 2.086869 TCAGCAAAGCCTGATAACTGC 58.913 47.619 0.00 0.00 36.96 4.40
4378 4544 7.993183 GGAGTGGATATGGTTCTTAAAGAATGA 59.007 37.037 0.00 0.00 36.50 2.57
4379 4545 9.566432 GAGTGGATATGGTTCTTAAAGAATGAT 57.434 33.333 0.00 0.00 36.50 2.45
4380 4546 9.347240 AGTGGATATGGTTCTTAAAGAATGATG 57.653 33.333 0.00 0.00 36.50 3.07
4381 4547 8.078596 GTGGATATGGTTCTTAAAGAATGATGC 58.921 37.037 0.00 0.00 36.50 3.91
4508 4674 1.888436 CGGTGGAGGAAGCTACAGCA 61.888 60.000 3.70 0.00 45.16 4.41
4583 4749 6.240894 TCTGTTAGCTGAATTTGTTGATCCT 58.759 36.000 0.00 0.00 0.00 3.24
4802 4968 2.555664 TCTGATCCAAGGGAGAAGCTT 58.444 47.619 0.00 0.00 34.05 3.74
4949 5115 2.765122 GCACAGGGCAAAGCAAATTAA 58.235 42.857 0.00 0.00 43.97 1.40
4961 5127 5.680594 AAGCAAATTAATGAATGGCCTCA 57.319 34.783 3.32 0.00 30.26 3.86
5108 5291 5.337330 CCGGAGTACTGAGATACTGGTTTTT 60.337 44.000 0.00 0.00 35.48 1.94
5128 5311 7.447545 GGTTTTTAGTTAGAACATCCTGGAACT 59.552 37.037 0.00 0.00 0.00 3.01
5219 5411 3.052082 CTTGGGTGCTGCTGTCCG 61.052 66.667 0.00 0.00 0.00 4.79
5243 5435 8.290325 CCGTCTTATAAGAAGCAAAGTTTTTCT 58.710 33.333 16.73 0.00 36.68 2.52
5305 5503 4.837860 TGCAATCCCCACTGTAATCTTTTT 59.162 37.500 0.00 0.00 0.00 1.94
5309 5507 5.055265 TCCCCACTGTAATCTTTTTGTCA 57.945 39.130 0.00 0.00 0.00 3.58
5312 5510 6.657541 TCCCCACTGTAATCTTTTTGTCATAC 59.342 38.462 0.00 0.00 0.00 2.39
5315 5513 7.308348 CCCACTGTAATCTTTTTGTCATACGTT 60.308 37.037 0.00 0.00 0.00 3.99
5318 5516 8.617809 ACTGTAATCTTTTTGTCATACGTTGTT 58.382 29.630 0.00 0.00 0.00 2.83
5321 5519 5.821516 TCTTTTTGTCATACGTTGTTGGT 57.178 34.783 0.00 0.00 0.00 3.67
5327 5525 3.040099 GTCATACGTTGTTGGTGTTTGC 58.960 45.455 0.00 0.00 0.00 3.68
5329 5527 3.128764 TCATACGTTGTTGGTGTTTGCAA 59.871 39.130 0.00 0.00 0.00 4.08
5340 5538 2.952310 GGTGTTTGCAAGAGAAAGTCCT 59.048 45.455 0.00 0.00 0.00 3.85
5361 5560 8.993424 AGTCCTAGTGAATTACATATTCAACCT 58.007 33.333 2.06 0.30 39.43 3.50
5377 5576 7.775053 ATTCAACCTGCAGTCCTATTTTAAA 57.225 32.000 13.81 0.00 0.00 1.52
5382 5581 4.202151 CCTGCAGTCCTATTTTAAATGGCC 60.202 45.833 13.81 0.00 0.00 5.36
5414 5614 9.484326 AAGAAAATGTTTCGTTTATGCAAAAAC 57.516 25.926 0.00 0.00 36.26 2.43
5512 5729 1.271127 GCTTGCCTCCTCTCCCTCTT 61.271 60.000 0.00 0.00 0.00 2.85
5518 5735 0.693767 CTCCTCTCCCTCTTGCCCAT 60.694 60.000 0.00 0.00 0.00 4.00
5544 5761 4.659172 CACCGCCACCACCCATGT 62.659 66.667 0.00 0.00 0.00 3.21
5545 5762 3.897122 ACCGCCACCACCCATGTT 61.897 61.111 0.00 0.00 0.00 2.71
5546 5763 3.372730 CCGCCACCACCCATGTTG 61.373 66.667 0.00 0.00 0.00 3.33
5547 5764 3.372730 CGCCACCACCCATGTTGG 61.373 66.667 8.71 8.71 37.25 3.77
5548 5765 3.694538 GCCACCACCCATGTTGGC 61.695 66.667 9.96 0.00 35.79 4.52
5549 5766 2.118076 CCACCACCCATGTTGGCT 59.882 61.111 9.96 0.00 35.79 4.75
5556 5780 0.178953 ACCCATGTTGGCTGCTTCTT 60.179 50.000 0.00 0.00 35.79 2.52
5569 5794 1.691215 GCTTCTTCGGCGAGCTTCAG 61.691 60.000 10.46 4.21 33.72 3.02
5624 5849 3.066198 CTTCCGTTCCGTCCCCTT 58.934 61.111 0.00 0.00 0.00 3.95
5637 5862 0.914417 TCCCCTTCGGCCAGATTCTT 60.914 55.000 2.24 0.00 0.00 2.52
5654 5879 3.949885 TTCGCTCCCGGCCTCTACA 62.950 63.158 0.00 0.00 37.74 2.74
5656 5881 2.442272 GCTCCCGGCCTCTACAGA 60.442 66.667 0.00 0.00 34.27 3.41
5696 5927 2.556782 GCTAGGGTTTTGGGTAGGCTTT 60.557 50.000 0.00 0.00 0.00 3.51
5813 6049 0.461516 CAGATGCAGATGGAGCACGT 60.462 55.000 0.00 0.00 45.95 4.49
5969 6322 4.766373 CCTCATCTCTCTTGCTAGCTATCA 59.234 45.833 17.23 0.00 0.00 2.15
6190 8727 2.744768 GAACTGCACTGCTGCCCTCT 62.745 60.000 7.76 0.00 43.51 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.635844 TTTAGCCGTCATGCGTAGTG 58.364 50.000 8.37 0.00 39.32 2.74
1 2 1.997606 GTTTTAGCCGTCATGCGTAGT 59.002 47.619 8.37 0.00 39.32 2.73
2 3 1.006391 CGTTTTAGCCGTCATGCGTAG 60.006 52.381 8.37 0.00 39.32 3.51
3 4 0.993532 CGTTTTAGCCGTCATGCGTA 59.006 50.000 8.37 0.00 39.32 4.42
5 6 1.580132 GCGTTTTAGCCGTCATGCG 60.580 57.895 3.02 3.02 40.95 4.73
6 7 0.521242 CAGCGTTTTAGCCGTCATGC 60.521 55.000 0.00 0.00 38.01 4.06
7 8 0.096976 CCAGCGTTTTAGCCGTCATG 59.903 55.000 0.00 0.00 38.01 3.07
8 9 0.036765 TCCAGCGTTTTAGCCGTCAT 60.037 50.000 0.00 0.00 38.01 3.06
9 10 0.669318 CTCCAGCGTTTTAGCCGTCA 60.669 55.000 0.00 0.00 38.01 4.35
10 11 0.389426 TCTCCAGCGTTTTAGCCGTC 60.389 55.000 0.00 0.00 38.01 4.79
11 12 0.034337 TTCTCCAGCGTTTTAGCCGT 59.966 50.000 0.00 0.00 38.01 5.68
12 13 0.442699 GTTCTCCAGCGTTTTAGCCG 59.557 55.000 0.00 0.00 38.01 5.52
13 14 1.464997 CAGTTCTCCAGCGTTTTAGCC 59.535 52.381 0.00 0.00 38.01 3.93
14 15 1.135944 GCAGTTCTCCAGCGTTTTAGC 60.136 52.381 0.00 0.00 37.41 3.09
15 16 1.464997 GGCAGTTCTCCAGCGTTTTAG 59.535 52.381 0.00 0.00 0.00 1.85
16 17 1.071699 AGGCAGTTCTCCAGCGTTTTA 59.928 47.619 0.00 0.00 0.00 1.52
17 18 0.179018 AGGCAGTTCTCCAGCGTTTT 60.179 50.000 0.00 0.00 0.00 2.43
18 19 0.685097 TAGGCAGTTCTCCAGCGTTT 59.315 50.000 0.00 0.00 0.00 3.60
19 20 0.685097 TTAGGCAGTTCTCCAGCGTT 59.315 50.000 0.00 0.00 0.00 4.84
20 21 0.905357 ATTAGGCAGTTCTCCAGCGT 59.095 50.000 0.00 0.00 0.00 5.07
21 22 1.576356 GATTAGGCAGTTCTCCAGCG 58.424 55.000 0.00 0.00 0.00 5.18
22 23 1.488393 AGGATTAGGCAGTTCTCCAGC 59.512 52.381 0.00 0.00 0.00 4.85
23 24 2.768527 TGAGGATTAGGCAGTTCTCCAG 59.231 50.000 0.00 0.00 0.00 3.86
24 25 2.832838 TGAGGATTAGGCAGTTCTCCA 58.167 47.619 0.00 0.00 0.00 3.86
25 26 3.914426 TTGAGGATTAGGCAGTTCTCC 57.086 47.619 0.00 0.00 0.00 3.71
26 27 4.813697 GTCATTGAGGATTAGGCAGTTCTC 59.186 45.833 0.00 0.00 0.00 2.87
27 28 4.225942 TGTCATTGAGGATTAGGCAGTTCT 59.774 41.667 0.00 0.00 0.00 3.01
28 29 4.517285 TGTCATTGAGGATTAGGCAGTTC 58.483 43.478 0.00 0.00 0.00 3.01
29 30 4.574674 TGTCATTGAGGATTAGGCAGTT 57.425 40.909 0.00 0.00 0.00 3.16
30 31 4.080129 ACATGTCATTGAGGATTAGGCAGT 60.080 41.667 0.00 0.00 0.00 4.40
31 32 4.275196 CACATGTCATTGAGGATTAGGCAG 59.725 45.833 0.00 0.00 0.00 4.85
32 33 4.201657 CACATGTCATTGAGGATTAGGCA 58.798 43.478 0.00 0.00 0.00 4.75
33 34 3.567164 CCACATGTCATTGAGGATTAGGC 59.433 47.826 0.00 0.00 29.71 3.93
34 35 4.139786 CCCACATGTCATTGAGGATTAGG 58.860 47.826 0.00 0.00 29.71 2.69
35 36 4.785301 ACCCACATGTCATTGAGGATTAG 58.215 43.478 0.00 0.00 29.71 1.73
36 37 4.385199 GGACCCACATGTCATTGAGGATTA 60.385 45.833 0.00 0.00 36.97 1.75
37 38 3.624777 GACCCACATGTCATTGAGGATT 58.375 45.455 0.00 0.00 35.29 3.01
38 39 2.092212 GGACCCACATGTCATTGAGGAT 60.092 50.000 0.00 0.00 36.97 3.24
39 40 1.281867 GGACCCACATGTCATTGAGGA 59.718 52.381 0.00 0.00 36.97 3.71
40 41 1.683011 GGGACCCACATGTCATTGAGG 60.683 57.143 5.33 0.00 36.97 3.86
41 42 1.004628 TGGGACCCACATGTCATTGAG 59.995 52.381 9.95 0.00 36.97 3.02
42 43 1.071434 TGGGACCCACATGTCATTGA 58.929 50.000 9.95 0.00 36.97 2.57
43 44 3.668147 TGGGACCCACATGTCATTG 57.332 52.632 9.95 0.00 36.97 2.82
55 56 3.333899 ATAAACCGCCCGTGGGACC 62.334 63.158 9.72 0.00 37.50 4.46
56 57 1.816679 GATAAACCGCCCGTGGGAC 60.817 63.158 9.72 0.00 37.50 4.46
57 58 1.963464 GAGATAAACCGCCCGTGGGA 61.963 60.000 9.72 0.00 37.50 4.37
58 59 1.523032 GAGATAAACCGCCCGTGGG 60.523 63.158 0.00 0.00 38.57 4.61
59 60 1.881252 CGAGATAAACCGCCCGTGG 60.881 63.158 0.00 0.00 0.00 4.94
60 61 2.522638 GCGAGATAAACCGCCCGTG 61.523 63.158 0.00 0.00 45.06 4.94
61 62 2.202837 GCGAGATAAACCGCCCGT 60.203 61.111 0.00 0.00 45.06 5.28
66 67 3.984765 GCCGCGCGAGATAAACCG 61.985 66.667 34.63 12.35 0.00 4.44
84 85 3.330853 CTAGTCCGATTGCGCCGC 61.331 66.667 4.18 0.00 35.83 6.53
85 86 2.658593 CCTAGTCCGATTGCGCCG 60.659 66.667 4.18 0.03 35.83 6.46
86 87 2.967615 GCCTAGTCCGATTGCGCC 60.968 66.667 4.18 0.00 35.83 6.53
87 88 3.330853 CGCCTAGTCCGATTGCGC 61.331 66.667 0.00 0.00 38.69 6.09
88 89 1.944676 GTCGCCTAGTCCGATTGCG 60.945 63.158 6.10 3.85 46.09 4.85
89 90 1.591863 GGTCGCCTAGTCCGATTGC 60.592 63.158 6.10 0.00 37.04 3.56
90 91 4.732106 GGTCGCCTAGTCCGATTG 57.268 61.111 6.10 0.00 37.04 2.67
95 96 3.525545 GGACCGGTCGCCTAGTCC 61.526 72.222 27.68 8.80 37.42 3.85
96 97 2.753043 TGGACCGGTCGCCTAGTC 60.753 66.667 27.68 12.78 0.00 2.59
97 98 3.066814 GTGGACCGGTCGCCTAGT 61.067 66.667 27.68 0.00 0.00 2.57
98 99 4.189188 CGTGGACCGGTCGCCTAG 62.189 72.222 27.68 13.27 0.00 3.02
152 153 4.016706 CCGTGTCCAGGTGTCCCC 62.017 72.222 0.00 0.00 0.00 4.81
153 154 4.699522 GCCGTGTCCAGGTGTCCC 62.700 72.222 0.00 0.00 0.00 4.46
175 176 0.380733 TGATCTCGTCCCGATCAACG 59.619 55.000 6.06 6.06 42.97 4.10
176 177 2.464865 CTTGATCTCGTCCCGATCAAC 58.535 52.381 10.43 0.00 46.96 3.18
178 179 0.385751 GCTTGATCTCGTCCCGATCA 59.614 55.000 0.00 0.00 43.90 2.92
179 180 0.661780 CGCTTGATCTCGTCCCGATC 60.662 60.000 0.00 0.00 38.17 3.69
180 181 1.360551 CGCTTGATCTCGTCCCGAT 59.639 57.895 0.00 0.00 34.61 4.18
181 182 2.771639 CCGCTTGATCTCGTCCCGA 61.772 63.158 0.00 0.00 0.00 5.14
182 183 2.278857 CCGCTTGATCTCGTCCCG 60.279 66.667 0.00 0.00 0.00 5.14
183 184 2.586357 GCCGCTTGATCTCGTCCC 60.586 66.667 0.00 0.00 0.00 4.46
184 185 1.590259 GAGCCGCTTGATCTCGTCC 60.590 63.158 0.00 0.00 0.00 4.79
185 186 0.593773 GAGAGCCGCTTGATCTCGTC 60.594 60.000 0.00 0.00 30.96 4.20
186 187 1.435515 GAGAGCCGCTTGATCTCGT 59.564 57.895 0.00 0.00 30.96 4.18
187 188 4.317529 GAGAGCCGCTTGATCTCG 57.682 61.111 0.00 0.00 30.96 4.04
188 189 0.179124 AACGAGAGCCGCTTGATCTC 60.179 55.000 7.97 7.97 43.32 2.75
189 190 0.179124 GAACGAGAGCCGCTTGATCT 60.179 55.000 0.00 0.00 43.32 2.75
190 191 1.475441 CGAACGAGAGCCGCTTGATC 61.475 60.000 0.00 0.00 43.32 2.92
191 192 1.517257 CGAACGAGAGCCGCTTGAT 60.517 57.895 0.00 0.00 43.32 2.57
192 193 2.126463 CGAACGAGAGCCGCTTGA 60.126 61.111 0.00 0.00 43.32 3.02
193 194 3.181967 CCGAACGAGAGCCGCTTG 61.182 66.667 0.00 0.00 43.32 4.01
205 206 3.479269 CAGAACGAGCGGCCGAAC 61.479 66.667 33.48 20.43 0.00 3.95
206 207 3.909258 GACAGAACGAGCGGCCGAA 62.909 63.158 33.48 0.00 0.00 4.30
207 208 4.415332 GACAGAACGAGCGGCCGA 62.415 66.667 33.48 0.00 0.00 5.54
208 209 4.421479 AGACAGAACGAGCGGCCG 62.421 66.667 24.05 24.05 0.00 6.13
209 210 2.811317 CAGACAGAACGAGCGGCC 60.811 66.667 0.00 0.00 0.00 6.13
210 211 1.222115 AAACAGACAGAACGAGCGGC 61.222 55.000 0.00 0.00 0.00 6.53
211 212 1.986378 CTAAACAGACAGAACGAGCGG 59.014 52.381 0.00 0.00 0.00 5.52
212 213 1.387084 GCTAAACAGACAGAACGAGCG 59.613 52.381 0.00 0.00 0.00 5.03
213 214 1.387084 CGCTAAACAGACAGAACGAGC 59.613 52.381 0.00 0.00 0.00 5.03
214 215 1.387084 GCGCTAAACAGACAGAACGAG 59.613 52.381 0.00 0.00 0.00 4.18
215 216 1.415374 GCGCTAAACAGACAGAACGA 58.585 50.000 0.00 0.00 0.00 3.85
216 217 0.091344 CGCGCTAAACAGACAGAACG 59.909 55.000 5.56 0.00 0.00 3.95
217 218 0.179248 GCGCGCTAAACAGACAGAAC 60.179 55.000 26.67 0.00 0.00 3.01
218 219 1.614227 CGCGCGCTAAACAGACAGAA 61.614 55.000 30.48 0.00 0.00 3.02
219 220 2.086426 CGCGCGCTAAACAGACAGA 61.086 57.895 30.48 0.00 0.00 3.41
220 221 2.391821 CGCGCGCTAAACAGACAG 59.608 61.111 30.48 5.07 0.00 3.51
221 222 3.109547 CCGCGCGCTAAACAGACA 61.110 61.111 30.48 0.00 0.00 3.41
222 223 4.500568 GCCGCGCGCTAAACAGAC 62.501 66.667 30.48 0.00 0.00 3.51
231 232 4.392576 TAAAAAGTGGCCGCGCGC 62.393 61.111 27.36 23.91 0.00 6.86
232 233 1.977594 ATCTAAAAAGTGGCCGCGCG 61.978 55.000 25.67 25.67 0.00 6.86
233 234 0.170339 AATCTAAAAAGTGGCCGCGC 59.830 50.000 11.42 0.00 0.00 6.86
234 235 2.629639 AAATCTAAAAAGTGGCCGCG 57.370 45.000 11.42 0.00 0.00 6.46
235 236 4.421058 CCTAAAATCTAAAAAGTGGCCGC 58.579 43.478 8.71 8.71 0.00 6.53
236 237 4.157840 AGCCTAAAATCTAAAAAGTGGCCG 59.842 41.667 0.00 0.00 38.69 6.13
237 238 5.419155 AGAGCCTAAAATCTAAAAAGTGGCC 59.581 40.000 0.00 0.00 38.69 5.36
238 239 6.516739 AGAGCCTAAAATCTAAAAAGTGGC 57.483 37.500 0.00 0.00 38.24 5.01
313 314 3.068873 TGTTTGCGCTGGGTTATCTTTTT 59.931 39.130 9.73 0.00 0.00 1.94
314 315 2.625790 TGTTTGCGCTGGGTTATCTTTT 59.374 40.909 9.73 0.00 0.00 2.27
315 316 2.030274 GTGTTTGCGCTGGGTTATCTTT 60.030 45.455 9.73 0.00 0.00 2.52
316 317 1.539827 GTGTTTGCGCTGGGTTATCTT 59.460 47.619 9.73 0.00 0.00 2.40
317 318 1.165270 GTGTTTGCGCTGGGTTATCT 58.835 50.000 9.73 0.00 0.00 1.98
318 319 0.170339 GGTGTTTGCGCTGGGTTATC 59.830 55.000 9.73 0.00 0.00 1.75
319 320 1.582610 CGGTGTTTGCGCTGGGTTAT 61.583 55.000 9.73 0.00 0.00 1.89
320 321 2.255172 CGGTGTTTGCGCTGGGTTA 61.255 57.895 9.73 0.00 0.00 2.85
321 322 3.591835 CGGTGTTTGCGCTGGGTT 61.592 61.111 9.73 0.00 0.00 4.11
322 323 4.555709 TCGGTGTTTGCGCTGGGT 62.556 61.111 9.73 0.00 32.59 4.51
323 324 2.141122 ATTTCGGTGTTTGCGCTGGG 62.141 55.000 9.73 0.00 32.59 4.45
324 325 0.318614 AATTTCGGTGTTTGCGCTGG 60.319 50.000 9.73 0.00 32.59 4.85
325 326 1.976045 GTAATTTCGGTGTTTGCGCTG 59.024 47.619 9.73 0.00 0.00 5.18
326 327 1.877443 AGTAATTTCGGTGTTTGCGCT 59.123 42.857 9.73 0.00 0.00 5.92
327 328 2.325509 AGTAATTTCGGTGTTTGCGC 57.674 45.000 0.00 0.00 0.00 6.09
328 329 8.437443 TTTATTTAGTAATTTCGGTGTTTGCG 57.563 30.769 0.00 0.00 0.00 4.85
342 343 9.299465 AGGACCGAACCAAAATTTATTTAGTAA 57.701 29.630 0.00 0.00 0.00 2.24
343 344 8.732531 CAGGACCGAACCAAAATTTATTTAGTA 58.267 33.333 0.00 0.00 0.00 1.82
344 345 7.309560 CCAGGACCGAACCAAAATTTATTTAGT 60.310 37.037 0.00 0.00 0.00 2.24
345 346 7.033185 CCAGGACCGAACCAAAATTTATTTAG 58.967 38.462 0.00 0.00 0.00 1.85
346 347 6.494146 ACCAGGACCGAACCAAAATTTATTTA 59.506 34.615 0.00 0.00 0.00 1.40
347 348 5.305902 ACCAGGACCGAACCAAAATTTATTT 59.694 36.000 0.00 0.00 0.00 1.40
348 349 4.836175 ACCAGGACCGAACCAAAATTTATT 59.164 37.500 0.00 0.00 0.00 1.40
352 353 2.375014 ACCAGGACCGAACCAAAATT 57.625 45.000 0.00 0.00 0.00 1.82
356 357 2.146920 AAAAACCAGGACCGAACCAA 57.853 45.000 0.00 0.00 0.00 3.67
378 379 1.069090 GAACCGATATGCCGAGCCA 59.931 57.895 0.00 0.00 0.00 4.75
379 380 0.667792 GAGAACCGATATGCCGAGCC 60.668 60.000 0.00 0.00 0.00 4.70
380 381 1.004277 CGAGAACCGATATGCCGAGC 61.004 60.000 0.00 0.00 41.76 5.03
394 395 3.055458 TGTGGATGCAGATTAACCGAGAA 60.055 43.478 0.00 0.00 0.00 2.87
462 464 3.119709 GAGAGGCGAGGCGACAGAG 62.120 68.421 0.00 0.00 37.34 3.35
464 466 4.200283 GGAGAGGCGAGGCGACAG 62.200 72.222 0.00 0.00 37.34 3.51
1306 1328 2.391389 CCTTCGAGGAAAGGCGCAC 61.391 63.158 10.83 0.00 39.47 5.34
1382 1404 3.822735 GGCCAGATTAATCAATAGCAGCA 59.177 43.478 17.56 0.00 0.00 4.41
1384 1406 5.125097 GGATGGCCAGATTAATCAATAGCAG 59.875 44.000 13.05 0.00 0.00 4.24
1422 1444 4.976116 GTGGCCTAATGCATCGATTTAAAC 59.024 41.667 3.32 0.00 43.89 2.01
1498 1524 4.325119 CCATCACCAGATCTCAATGGATC 58.675 47.826 13.37 4.30 41.55 3.36
1545 1571 4.395854 TGATGACATGATAACTGCCAACAC 59.604 41.667 0.00 0.00 0.00 3.32
1592 1618 7.782049 ACTCAGTAACTTTCCATTGATCGATA 58.218 34.615 0.00 0.00 0.00 2.92
1682 1708 7.763528 TCTTCACTCTGAATAGATTCAAAGAGC 59.236 37.037 11.63 0.00 45.26 4.09
1752 1778 1.805428 GCGTCTTTGCCAATGGGTGT 61.805 55.000 0.00 0.00 36.17 4.16
1769 1795 3.508840 GCCCCCACATCTTTCGCG 61.509 66.667 0.00 0.00 0.00 5.87
1807 1833 5.949952 TGACTAGCAGTATGTTCTTCAGGTA 59.050 40.000 0.00 0.00 39.31 3.08
1901 1927 3.130340 CCTGAGTAACTTCTGAGAGAGGC 59.870 52.174 0.00 0.00 0.00 4.70
1908 1934 6.823689 GCCATAATTTCCTGAGTAACTTCTGA 59.176 38.462 0.00 0.00 0.00 3.27
2000 2026 3.674997 CCGATCTCCTTTTTCTGTTGGA 58.325 45.455 0.00 0.00 0.00 3.53
2074 2100 6.689554 TCAATGTGCATCTTATTGCTTTCAA 58.310 32.000 0.00 0.00 43.18 2.69
2189 2215 4.550076 AGCTTCAGCAGTATCTGACTTT 57.450 40.909 0.75 0.00 42.27 2.66
2278 2304 0.877071 AGCTGCAACATCAGTTTCCG 59.123 50.000 1.02 0.00 35.28 4.30
2343 2369 0.464373 ATCGAAGCATTGTCGCCCAT 60.464 50.000 0.00 0.00 38.39 4.00
2355 2381 4.607114 GCACACTTCATTATCGATCGAAGC 60.607 45.833 23.50 12.09 38.74 3.86
2359 2385 3.798878 ACTGCACACTTCATTATCGATCG 59.201 43.478 9.36 9.36 0.00 3.69
2451 2477 5.427481 ACTTAATTGGAGACCCTAAATCCGA 59.573 40.000 0.00 0.00 35.78 4.55
2769 2795 6.913170 TGAAATCAAGTTGCTTAATCTCCAC 58.087 36.000 0.00 0.00 0.00 4.02
2860 2886 5.300752 TCTTGACAACAGAATCAGGAAGAC 58.699 41.667 0.00 0.00 28.91 3.01
2971 2997 2.155279 GAAAGTGAAAGGGCAGGAGAC 58.845 52.381 0.00 0.00 0.00 3.36
3035 3062 4.823989 GGTAATCCCACTCATCATTCAAGG 59.176 45.833 0.00 0.00 0.00 3.61
3050 3077 6.183360 GCAATCAGAACTACAAAGGTAATCCC 60.183 42.308 0.00 0.00 0.00 3.85
3057 3084 3.181516 GCGAGCAATCAGAACTACAAAGG 60.182 47.826 0.00 0.00 0.00 3.11
3305 3333 0.540923 GAGCATCTGTGGCTTCCTCT 59.459 55.000 0.00 0.00 42.78 3.69
3459 3614 6.379386 TCACTAGCATTCTAATTCCGTATCG 58.621 40.000 0.00 0.00 0.00 2.92
3497 3652 1.731709 TGCAGAATGACCAAACGATCG 59.268 47.619 14.88 14.88 39.69 3.69
3758 3915 2.836981 CAAGGACTCACCAATCCTCTCT 59.163 50.000 0.00 0.00 44.97 3.10
3793 3950 5.358160 AGCATAAAGACTTGGTAATGGAAGC 59.642 40.000 0.00 0.00 0.00 3.86
3863 4020 0.249031 GTGGCACTGCAAGACCAAAC 60.249 55.000 11.13 0.00 43.31 2.93
4196 4354 8.410141 CCGCATTTAGAATCTATGGGTTTTTAA 58.590 33.333 8.59 0.00 32.26 1.52
4304 4470 9.155975 ACACAAGTCATTAATAGAAAGTAGCAG 57.844 33.333 0.00 0.00 0.00 4.24
4378 4544 8.997323 GCTAAGAATAATCTACAACTGATGCAT 58.003 33.333 0.00 0.00 33.77 3.96
4379 4545 8.206867 AGCTAAGAATAATCTACAACTGATGCA 58.793 33.333 0.00 0.00 33.77 3.96
4380 4546 8.494347 CAGCTAAGAATAATCTACAACTGATGC 58.506 37.037 0.00 0.00 33.77 3.91
4381 4547 9.755804 TCAGCTAAGAATAATCTACAACTGATG 57.244 33.333 0.00 0.00 33.77 3.07
4508 4674 3.318017 GTTGTAGACAGCATCACGAGTT 58.682 45.455 0.00 0.00 0.00 3.01
4583 4749 3.845781 AGCTTGAGTTTCACTTCCTGA 57.154 42.857 0.00 0.00 0.00 3.86
4802 4968 1.725169 CCTTCTTTGGGGTGGGTGGA 61.725 60.000 0.00 0.00 0.00 4.02
4949 5115 2.835764 ACAAAAGCATGAGGCCATTCAT 59.164 40.909 5.01 3.01 46.50 2.57
4961 5127 3.988819 ACATACCGCAAAACAAAAGCAT 58.011 36.364 0.00 0.00 0.00 3.79
5108 5291 7.339721 CAGTAGAGTTCCAGGATGTTCTAACTA 59.660 40.741 0.00 0.00 0.00 2.24
5305 5503 3.487711 GCAAACACCAACAACGTATGACA 60.488 43.478 0.00 0.00 0.00 3.58
5309 5507 3.378742 TCTTGCAAACACCAACAACGTAT 59.621 39.130 0.00 0.00 0.00 3.06
5312 5510 2.159448 TCTCTTGCAAACACCAACAACG 60.159 45.455 0.00 0.00 0.00 4.10
5315 5513 3.509575 ACTTTCTCTTGCAAACACCAACA 59.490 39.130 0.00 0.00 0.00 3.33
5318 5516 2.687935 GGACTTTCTCTTGCAAACACCA 59.312 45.455 0.00 0.00 0.00 4.17
5321 5519 4.816385 CACTAGGACTTTCTCTTGCAAACA 59.184 41.667 0.00 0.00 0.00 2.83
5340 5538 8.046708 ACTGCAGGTTGAATATGTAATTCACTA 58.953 33.333 19.93 0.00 37.71 2.74
5361 5560 4.609301 AGGCCATTTAAAATAGGACTGCA 58.391 39.130 5.01 0.00 38.32 4.41
5382 5581 8.798153 GCATAAACGAAACATTTTCTTGGATAG 58.202 33.333 0.00 0.00 0.00 2.08
5414 5614 2.483014 TACCCCAAATCACAAGGTCG 57.517 50.000 0.00 0.00 31.89 4.79
5476 5689 2.855514 GCCCGTGCATTGTTGTGGT 61.856 57.895 0.00 0.00 37.47 4.16
5480 5693 2.023223 GCAAGCCCGTGCATTGTTG 61.023 57.895 0.00 0.00 44.29 3.33
5540 5757 0.169672 CCGAAGAAGCAGCCAACATG 59.830 55.000 0.00 0.00 0.00 3.21
5541 5758 1.589716 GCCGAAGAAGCAGCCAACAT 61.590 55.000 0.00 0.00 0.00 2.71
5543 5760 2.563427 GCCGAAGAAGCAGCCAAC 59.437 61.111 0.00 0.00 0.00 3.77
5544 5761 3.049674 CGCCGAAGAAGCAGCCAA 61.050 61.111 0.00 0.00 0.00 4.52
5545 5762 3.939837 CTCGCCGAAGAAGCAGCCA 62.940 63.158 0.00 0.00 0.00 4.75
5546 5763 3.191539 CTCGCCGAAGAAGCAGCC 61.192 66.667 0.00 0.00 0.00 4.85
5547 5764 3.858989 GCTCGCCGAAGAAGCAGC 61.859 66.667 0.00 0.00 0.00 5.25
5548 5765 1.691215 GAAGCTCGCCGAAGAAGCAG 61.691 60.000 0.00 0.00 0.00 4.24
5549 5766 1.738099 GAAGCTCGCCGAAGAAGCA 60.738 57.895 0.00 0.00 0.00 3.91
5624 5849 1.141881 GAGCGAAGAATCTGGCCGA 59.858 57.895 0.00 0.00 0.00 5.54
5637 5862 4.435970 TGTAGAGGCCGGGAGCGA 62.436 66.667 2.18 0.00 45.17 4.93
5654 5879 2.032681 GAGGGTTGCAAGCGGTCT 59.967 61.111 21.43 13.40 0.00 3.85
5656 5881 4.250305 ACGAGGGTTGCAAGCGGT 62.250 61.111 21.43 15.87 0.00 5.68
5833 6069 3.620300 CTTACGGCGGCGACTGTGA 62.620 63.158 38.93 11.34 0.00 3.58
5993 6346 0.593128 GTGGTTGTGCATCTGGTCAC 59.407 55.000 0.00 0.00 0.00 3.67
6060 6413 8.324163 ACAACCTTGAGTGAATTCTTATGTAC 57.676 34.615 7.05 0.00 0.00 2.90
6066 6419 8.062065 TGTTTTACAACCTTGAGTGAATTCTT 57.938 30.769 7.05 0.00 31.02 2.52
6179 8714 0.251354 ACACATACAGAGGGCAGCAG 59.749 55.000 0.00 0.00 0.00 4.24
6182 8717 2.079158 CAACACACATACAGAGGGCAG 58.921 52.381 0.00 0.00 0.00 4.85
6190 8727 3.066380 CAGCAGTAGCAACACACATACA 58.934 45.455 0.00 0.00 45.49 2.29


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

AutoCloner maintained by Alex Coulton.