Multiple sequence alignment - TraesCS4A01G131200

Loading Multiple Alignment...

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 TraesCS4A01G131200 chr4A 100.000 5042 0 0 1 5042 175003932 174998891 0.000000e+00 9311.0
1 TraesCS4A01G131200 chr4A 86.321 212 22 5 3447 3654 647922484 647922276 1.830000e-54 224.0
2 TraesCS4A01G131200 chr4B 94.985 4207 143 39 876 5042 379416224 379420402 0.000000e+00 6538.0
3 TraesCS4A01G131200 chr4D 94.845 3938 123 26 745 4647 304263210 304267102 0.000000e+00 6074.0
4 TraesCS4A01G131200 chr4D 84.453 521 69 8 166 681 39259826 39259313 2.100000e-138 503.0
5 TraesCS4A01G131200 chr4D 84.436 514 69 8 163 673 309623487 309622982 3.510000e-136 496.0
6 TraesCS4A01G131200 chr4D 87.500 408 15 13 4647 5042 304296041 304296424 5.990000e-119 438.0
7 TraesCS4A01G131200 chr4D 85.714 252 21 8 38 276 148683885 148684134 8.380000e-63 252.0
8 TraesCS4A01G131200 chr3B 86.248 509 57 5 166 672 535697534 535698031 1.600000e-149 540.0
9 TraesCS4A01G131200 chr3B 87.879 132 11 3 47 177 822840339 822840466 3.140000e-32 150.0
10 TraesCS4A01G131200 chr3B 89.706 68 6 1 2493 2560 76483865 76483799 8.990000e-13 86.1
11 TraesCS4A01G131200 chr7A 85.150 532 71 5 165 694 553237732 553237207 5.740000e-149 538.0
12 TraesCS4A01G131200 chr1D 84.746 531 72 6 166 694 205085819 205085296 1.610000e-144 523.0
13 TraesCS4A01G131200 chr1D 85.347 505 66 5 167 669 361801098 361800600 2.690000e-142 516.0
14 TraesCS4A01G131200 chr2A 84.701 536 67 10 163 694 673128035 673128559 5.780000e-144 521.0
15 TraesCS4A01G131200 chr2A 83.962 530 74 8 168 694 673025916 673026437 9.750000e-137 497.0
16 TraesCS4A01G131200 chr2A 83.302 533 79 7 166 695 673174725 673175250 2.730000e-132 483.0
17 TraesCS4A01G131200 chrUn 86.404 228 28 2 3430 3654 46078885 46078658 3.900000e-61 246.0
18 TraesCS4A01G131200 chr6A 84.615 234 32 4 3425 3654 39065839 39066072 3.930000e-56 230.0
19 TraesCS4A01G131200 chr6A 83.916 143 23 0 8 150 197044198 197044056 2.450000e-28 137.0
20 TraesCS4A01G131200 chr2D 86.301 146 18 1 3 148 560324657 560324514 1.880000e-34 158.0
21 TraesCS4A01G131200 chr5B 86.957 138 15 2 3464 3599 181476399 181476263 8.740000e-33 152.0
22 TraesCS4A01G131200 chr2B 81.818 176 27 3 3 177 79047434 79047263 5.260000e-30 143.0
23 TraesCS4A01G131200 chr6B 84.211 152 16 5 1 148 632432180 632432033 1.890000e-29 141.0
24 TraesCS4A01G131200 chr1B 82.022 178 21 9 3 177 632660955 632661124 1.890000e-29 141.0
25 TraesCS4A01G131200 chr1B 84.615 117 18 0 35 151 448920971 448921087 3.190000e-22 117.0
26 TraesCS4A01G131200 chr3D 87.500 112 11 1 61 172 429522369 429522477 5.300000e-25 126.0
27 TraesCS4A01G131200 chr3D 79.235 183 31 6 567 746 299556360 299556538 2.470000e-23 121.0
28 TraesCS4A01G131200 chr3D 86.957 69 7 2 2493 2560 48425258 48425191 5.410000e-10 76.8
29 TraesCS4A01G131200 chr3A 89.706 68 6 1 2493 2560 60631656 60631590 8.990000e-13 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 TraesCS4A01G131200 chr4A 174998891 175003932 5041 True 9311 9311 100.000 1 5042 1 chr4A.!!$R1 5041
1 TraesCS4A01G131200 chr4B 379416224 379420402 4178 False 6538 6538 94.985 876 5042 1 chr4B.!!$F1 4166
2 TraesCS4A01G131200 chr4D 304263210 304267102 3892 False 6074 6074 94.845 745 4647 1 chr4D.!!$F2 3902
3 TraesCS4A01G131200 chr4D 39259313 39259826 513 True 503 503 84.453 166 681 1 chr4D.!!$R1 515
4 TraesCS4A01G131200 chr4D 309622982 309623487 505 True 496 496 84.436 163 673 1 chr4D.!!$R2 510
5 TraesCS4A01G131200 chr7A 553237207 553237732 525 True 538 538 85.150 165 694 1 chr7A.!!$R1 529
6 TraesCS4A01G131200 chr1D 205085296 205085819 523 True 523 523 84.746 166 694 1 chr1D.!!$R1 528
7 TraesCS4A01G131200 chr2A 673128035 673128559 524 False 521 521 84.701 163 694 1 chr2A.!!$F2 531
8 TraesCS4A01G131200 chr2A 673025916 673026437 521 False 497 497 83.962 168 694 1 chr2A.!!$F1 526
9 TraesCS4A01G131200 chr2A 673174725 673175250 525 False 483 483 83.302 166 695 1 chr2A.!!$F3 529

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
124 125 0.032117 ACCCACCATCATCGAGGAGA 60.032 55.000 5.80 0.00 0.00 3.71 F
144 145 0.107654 AGTAGAACATGGAAGGCCGC 60.108 55.000 0.00 0.00 36.79 6.53 F
329 330 0.322816 GCATCCTCTTTGCCACTCCA 60.323 55.000 0.00 0.00 33.95 3.86 F
734 740 0.398696 ACTTATGGGTTGCCGTGTGA 59.601 50.000 0.00 0.00 0.00 3.58 F
1398 1413 0.665972 GCTATCTCAGTAGCGGCAGC 60.666 60.000 0.00 0.00 45.58 5.25 F
1524 1540 1.203162 TCTGGTGCCATTGGGATGTTT 60.203 47.619 4.53 0.00 35.59 2.83 F
3192 3236 0.035915 AGAAGAAAAGGCTCGAGGGC 60.036 55.000 15.58 7.43 41.20 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1319 0.811281 CCCAGAACAAAGAATCGCCC 59.189 55.000 0.0 0.0 0.00 6.13 R
1975 1998 2.106511 TCTGCAAAGGGAGCTACAAACT 59.893 45.455 0.0 0.0 31.59 2.66 R
2197 2220 0.527565 AGACCGCCATTGCATGAAAC 59.472 50.000 0.0 0.0 37.32 2.78 R
2312 2356 2.138320 TCTGCACAAGAGAAGCTTTCG 58.862 47.619 0.0 0.0 33.60 3.46 R
3192 3236 2.125106 GGTGTAAGCGGGCAGAGG 60.125 66.667 0.0 0.0 0.00 3.69 R
3312 3356 3.075148 GTTAGGGAACTCTGCCTTCAAC 58.925 50.000 0.0 0.0 41.49 3.18 R
4312 4361 0.253044 GTGGCATAGGCTCCTTCACA 59.747 55.000 0.0 0.0 40.87 3.58 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 3.940640 CAACCGCGCCATCCATCG 61.941 66.667 0.00 0.00 0.00 3.84
18 19 4.467084 AACCGCGCCATCCATCGT 62.467 61.111 0.00 0.00 0.00 3.73
19 20 3.969250 AACCGCGCCATCCATCGTT 62.969 57.895 0.00 0.00 0.00 3.85
20 21 3.940640 CCGCGCCATCCATCGTTG 61.941 66.667 0.00 0.00 0.00 4.10
21 22 2.889988 CGCGCCATCCATCGTTGA 60.890 61.111 0.00 0.00 0.00 3.18
22 23 2.246739 CGCGCCATCCATCGTTGAT 61.247 57.895 0.00 0.00 0.00 2.57
23 24 1.280746 GCGCCATCCATCGTTGATG 59.719 57.895 0.00 0.00 39.52 3.07
24 25 1.280746 CGCCATCCATCGTTGATGC 59.719 57.895 1.24 0.00 38.59 3.91
25 26 1.280746 GCCATCCATCGTTGATGCG 59.719 57.895 1.24 0.00 38.59 4.73
26 27 1.280746 CCATCCATCGTTGATGCGC 59.719 57.895 0.00 0.00 38.59 6.09
27 28 1.083209 CATCCATCGTTGATGCGCG 60.083 57.895 0.00 0.00 38.59 6.86
28 29 2.885676 ATCCATCGTTGATGCGCGC 61.886 57.895 27.26 27.26 38.59 6.86
29 30 4.925307 CCATCGTTGATGCGCGCG 62.925 66.667 28.44 28.44 38.59 6.86
30 31 4.208948 CATCGTTGATGCGCGCGT 62.209 61.111 32.35 28.54 33.17 6.01
31 32 2.581138 ATCGTTGATGCGCGCGTA 60.581 55.556 32.35 29.07 0.00 4.42
32 33 2.576893 ATCGTTGATGCGCGCGTAG 61.577 57.895 32.35 17.43 0.00 3.51
33 34 3.541831 CGTTGATGCGCGCGTAGT 61.542 61.111 32.35 17.48 0.00 2.73
34 35 2.316687 GTTGATGCGCGCGTAGTC 59.683 61.111 32.35 24.65 0.00 2.59
35 36 3.244603 TTGATGCGCGCGTAGTCG 61.245 61.111 32.35 3.26 40.37 4.18
36 37 3.957027 TTGATGCGCGCGTAGTCGT 62.957 57.895 32.35 15.89 39.49 4.34
43 44 3.913573 CGCGTAGTCGTGCCATGC 61.914 66.667 0.00 0.00 40.56 4.06
44 45 2.813474 GCGTAGTCGTGCCATGCA 60.813 61.111 0.00 0.00 39.49 3.96
45 46 2.173669 GCGTAGTCGTGCCATGCAT 61.174 57.895 0.00 0.00 41.91 3.96
46 47 1.637934 CGTAGTCGTGCCATGCATG 59.362 57.895 20.19 20.19 45.79 4.06
47 48 1.353103 GTAGTCGTGCCATGCATGC 59.647 57.895 21.69 11.82 44.29 4.06
48 49 1.078567 TAGTCGTGCCATGCATGCA 60.079 52.632 25.04 25.04 44.29 3.96
49 50 1.091197 TAGTCGTGCCATGCATGCAG 61.091 55.000 26.69 14.50 44.29 4.41
50 51 2.046120 TCGTGCCATGCATGCAGA 60.046 55.556 26.69 13.59 44.29 4.26
51 52 2.110352 TCGTGCCATGCATGCAGAG 61.110 57.895 26.69 19.71 44.29 3.35
52 53 2.110352 CGTGCCATGCATGCAGAGA 61.110 57.895 26.69 6.95 41.91 3.10
53 54 1.650314 CGTGCCATGCATGCAGAGAA 61.650 55.000 26.69 11.51 41.91 2.87
54 55 0.528924 GTGCCATGCATGCAGAGAAA 59.471 50.000 26.69 7.62 41.91 2.52
55 56 1.136305 GTGCCATGCATGCAGAGAAAT 59.864 47.619 26.69 4.78 41.91 2.17
56 57 2.359848 GTGCCATGCATGCAGAGAAATA 59.640 45.455 26.69 5.64 41.91 1.40
57 58 3.025262 TGCCATGCATGCAGAGAAATAA 58.975 40.909 26.69 0.00 31.71 1.40
58 59 3.067601 TGCCATGCATGCAGAGAAATAAG 59.932 43.478 26.69 8.13 31.71 1.73
59 60 3.067742 GCCATGCATGCAGAGAAATAAGT 59.932 43.478 26.69 1.43 0.00 2.24
60 61 4.792057 GCCATGCATGCAGAGAAATAAGTC 60.792 45.833 26.69 0.79 0.00 3.01
61 62 4.524749 CATGCATGCAGAGAAATAAGTCG 58.475 43.478 26.69 0.00 0.00 4.18
62 63 2.938451 TGCATGCAGAGAAATAAGTCGG 59.062 45.455 18.46 0.00 0.00 4.79
63 64 2.286654 GCATGCAGAGAAATAAGTCGGC 60.287 50.000 14.21 0.00 34.82 5.54
64 65 3.201290 CATGCAGAGAAATAAGTCGGCT 58.799 45.455 0.00 0.00 35.23 5.52
65 66 2.621338 TGCAGAGAAATAAGTCGGCTG 58.379 47.619 0.00 0.00 35.23 4.85
66 67 1.328986 GCAGAGAAATAAGTCGGCTGC 59.671 52.381 0.00 0.00 40.76 5.25
67 68 1.590238 CAGAGAAATAAGTCGGCTGCG 59.410 52.381 0.00 0.00 0.00 5.18
68 69 0.301987 GAGAAATAAGTCGGCTGCGC 59.698 55.000 0.00 0.00 0.00 6.09
69 70 1.012234 GAAATAAGTCGGCTGCGCG 60.012 57.895 0.00 0.00 0.00 6.86
70 71 2.361427 GAAATAAGTCGGCTGCGCGG 62.361 60.000 13.18 13.18 0.00 6.46
71 72 2.845752 AAATAAGTCGGCTGCGCGGA 62.846 55.000 23.20 3.19 35.61 5.54
72 73 2.644555 AATAAGTCGGCTGCGCGGAT 62.645 55.000 23.20 0.00 39.83 4.18
80 81 4.829518 CTGCGCGGATGTCGACGA 62.830 66.667 11.90 0.00 42.43 4.20
81 82 4.829518 TGCGCGGATGTCGACGAG 62.830 66.667 8.83 1.53 42.43 4.18
83 84 4.175489 CGCGGATGTCGACGAGGT 62.175 66.667 11.62 0.00 42.43 3.85
84 85 2.579787 GCGGATGTCGACGAGGTG 60.580 66.667 11.62 0.64 42.43 4.00
85 86 2.102357 CGGATGTCGACGAGGTGG 59.898 66.667 11.62 0.00 42.43 4.61
86 87 2.202756 GGATGTCGACGAGGTGGC 60.203 66.667 11.62 0.00 0.00 5.01
87 88 2.579787 GATGTCGACGAGGTGGCG 60.580 66.667 11.62 0.00 37.29 5.69
88 89 4.129737 ATGTCGACGAGGTGGCGG 62.130 66.667 11.62 0.00 35.12 6.13
110 111 3.434319 CATGTCTGCGCCACCCAC 61.434 66.667 4.18 0.00 0.00 4.61
111 112 4.722700 ATGTCTGCGCCACCCACC 62.723 66.667 4.18 0.00 0.00 4.61
113 114 4.722700 GTCTGCGCCACCCACCAT 62.723 66.667 4.18 0.00 0.00 3.55
114 115 4.408821 TCTGCGCCACCCACCATC 62.409 66.667 4.18 0.00 0.00 3.51
115 116 4.720902 CTGCGCCACCCACCATCA 62.721 66.667 4.18 0.00 0.00 3.07
116 117 4.045781 TGCGCCACCCACCATCAT 62.046 61.111 4.18 0.00 0.00 2.45
117 118 3.211963 GCGCCACCCACCATCATC 61.212 66.667 0.00 0.00 0.00 2.92
118 119 2.896854 CGCCACCCACCATCATCG 60.897 66.667 0.00 0.00 0.00 3.84
119 120 2.589540 GCCACCCACCATCATCGA 59.410 61.111 0.00 0.00 0.00 3.59
120 121 1.524621 GCCACCCACCATCATCGAG 60.525 63.158 0.00 0.00 0.00 4.04
121 122 1.146930 CCACCCACCATCATCGAGG 59.853 63.158 0.00 0.00 0.00 4.63
122 123 1.337384 CCACCCACCATCATCGAGGA 61.337 60.000 0.65 0.65 0.00 3.71
123 124 0.105593 CACCCACCATCATCGAGGAG 59.894 60.000 5.80 0.00 0.00 3.69
124 125 0.032117 ACCCACCATCATCGAGGAGA 60.032 55.000 5.80 0.00 0.00 3.71
125 126 1.123077 CCCACCATCATCGAGGAGAA 58.877 55.000 5.80 0.00 0.00 2.87
126 127 1.069823 CCCACCATCATCGAGGAGAAG 59.930 57.143 5.80 0.00 0.00 2.85
127 128 1.759445 CCACCATCATCGAGGAGAAGT 59.241 52.381 5.80 0.00 0.00 3.01
128 129 2.959030 CCACCATCATCGAGGAGAAGTA 59.041 50.000 5.80 0.00 0.00 2.24
129 130 3.005261 CCACCATCATCGAGGAGAAGTAG 59.995 52.174 5.80 0.00 0.00 2.57
130 131 3.885901 CACCATCATCGAGGAGAAGTAGA 59.114 47.826 5.80 0.00 0.00 2.59
131 132 4.339530 CACCATCATCGAGGAGAAGTAGAA 59.660 45.833 5.80 0.00 0.00 2.10
132 133 4.339814 ACCATCATCGAGGAGAAGTAGAAC 59.660 45.833 5.80 0.00 0.00 3.01
133 134 4.339530 CCATCATCGAGGAGAAGTAGAACA 59.660 45.833 5.80 0.00 0.00 3.18
134 135 5.010516 CCATCATCGAGGAGAAGTAGAACAT 59.989 44.000 5.80 0.00 0.00 2.71
135 136 5.506686 TCATCGAGGAGAAGTAGAACATG 57.493 43.478 0.00 0.00 0.00 3.21
136 137 4.339530 TCATCGAGGAGAAGTAGAACATGG 59.660 45.833 0.00 0.00 0.00 3.66
137 138 3.964411 TCGAGGAGAAGTAGAACATGGA 58.036 45.455 0.00 0.00 0.00 3.41
138 139 4.341487 TCGAGGAGAAGTAGAACATGGAA 58.659 43.478 0.00 0.00 0.00 3.53
139 140 4.399618 TCGAGGAGAAGTAGAACATGGAAG 59.600 45.833 0.00 0.00 0.00 3.46
140 141 4.440802 CGAGGAGAAGTAGAACATGGAAGG 60.441 50.000 0.00 0.00 0.00 3.46
141 142 3.198853 AGGAGAAGTAGAACATGGAAGGC 59.801 47.826 0.00 0.00 0.00 4.35
142 143 3.536570 GAGAAGTAGAACATGGAAGGCC 58.463 50.000 0.00 0.00 0.00 5.19
143 144 2.093447 AGAAGTAGAACATGGAAGGCCG 60.093 50.000 0.00 0.00 36.79 6.13
144 145 0.107654 AGTAGAACATGGAAGGCCGC 60.108 55.000 0.00 0.00 36.79 6.53
145 146 1.095807 GTAGAACATGGAAGGCCGCC 61.096 60.000 10.45 10.45 36.79 6.13
146 147 2.587322 TAGAACATGGAAGGCCGCCG 62.587 60.000 12.28 2.79 36.79 6.46
237 238 1.204941 CCTGTACAGCCAGTGACCTAC 59.795 57.143 17.86 0.00 0.00 3.18
329 330 0.322816 GCATCCTCTTTGCCACTCCA 60.323 55.000 0.00 0.00 33.95 3.86
372 374 4.408182 AGGGAAGATACGTGGAAGAATG 57.592 45.455 0.00 0.00 0.00 2.67
430 434 1.780309 TGGACATGGGGAAGACAAAGT 59.220 47.619 0.00 0.00 0.00 2.66
460 464 0.459759 GGCCAACCGTAGACTAGTGC 60.460 60.000 0.00 0.00 0.00 4.40
463 467 1.630148 CAACCGTAGACTAGTGCAGC 58.370 55.000 0.00 0.00 0.00 5.25
591 597 7.483691 GGTTTGTATGAAATCCGTCATGTTTAC 59.516 37.037 0.00 0.00 38.69 2.01
627 633 4.685165 CGTGTTTGCATGAATTTCATCCAA 59.315 37.500 10.95 10.95 33.09 3.53
632 638 5.804692 TGCATGAATTTCATCCAATTTGC 57.195 34.783 8.95 9.84 34.28 3.68
673 679 2.202878 GCGGCTAGCGTTGGATGA 60.203 61.111 9.00 0.00 35.41 2.92
677 683 1.668419 GGCTAGCGTTGGATGATGTT 58.332 50.000 9.00 0.00 0.00 2.71
695 701 4.639135 TGTTCTCTCATATCCGTGTCTG 57.361 45.455 0.00 0.00 0.00 3.51
696 702 4.017126 TGTTCTCTCATATCCGTGTCTGT 58.983 43.478 0.00 0.00 0.00 3.41
697 703 4.462834 TGTTCTCTCATATCCGTGTCTGTT 59.537 41.667 0.00 0.00 0.00 3.16
698 704 4.639135 TCTCTCATATCCGTGTCTGTTG 57.361 45.455 0.00 0.00 0.00 3.33
699 705 4.270008 TCTCTCATATCCGTGTCTGTTGA 58.730 43.478 0.00 0.00 0.00 3.18
700 706 4.096532 TCTCTCATATCCGTGTCTGTTGAC 59.903 45.833 0.00 0.00 43.20 3.18
712 718 2.084610 CTGTTGACAGATGCGGAAGA 57.915 50.000 5.19 0.00 46.59 2.87
713 719 2.416747 CTGTTGACAGATGCGGAAGAA 58.583 47.619 5.19 0.00 46.59 2.52
714 720 2.807967 CTGTTGACAGATGCGGAAGAAA 59.192 45.455 5.19 0.00 46.59 2.52
715 721 3.210227 TGTTGACAGATGCGGAAGAAAA 58.790 40.909 0.00 0.00 0.00 2.29
716 722 3.003275 TGTTGACAGATGCGGAAGAAAAC 59.997 43.478 0.00 0.00 0.00 2.43
717 723 3.126001 TGACAGATGCGGAAGAAAACT 57.874 42.857 0.00 0.00 0.00 2.66
718 724 3.476552 TGACAGATGCGGAAGAAAACTT 58.523 40.909 0.00 0.00 0.00 2.66
719 725 4.637276 TGACAGATGCGGAAGAAAACTTA 58.363 39.130 0.00 0.00 0.00 2.24
720 726 5.245531 TGACAGATGCGGAAGAAAACTTAT 58.754 37.500 0.00 0.00 0.00 1.73
721 727 5.122239 TGACAGATGCGGAAGAAAACTTATG 59.878 40.000 0.00 0.00 0.00 1.90
722 728 4.396166 ACAGATGCGGAAGAAAACTTATGG 59.604 41.667 0.00 0.00 0.00 2.74
723 729 3.947834 AGATGCGGAAGAAAACTTATGGG 59.052 43.478 0.00 0.00 0.00 4.00
724 730 3.149005 TGCGGAAGAAAACTTATGGGT 57.851 42.857 0.00 0.00 0.00 4.51
725 731 3.492337 TGCGGAAGAAAACTTATGGGTT 58.508 40.909 0.00 0.00 0.00 4.11
726 732 3.254657 TGCGGAAGAAAACTTATGGGTTG 59.745 43.478 0.00 0.00 0.00 3.77
727 733 3.833442 CGGAAGAAAACTTATGGGTTGC 58.167 45.455 0.00 0.00 0.00 4.17
728 734 3.366985 CGGAAGAAAACTTATGGGTTGCC 60.367 47.826 0.00 0.00 0.00 4.52
729 735 3.366985 GGAAGAAAACTTATGGGTTGCCG 60.367 47.826 0.00 0.00 0.00 5.69
730 736 2.871453 AGAAAACTTATGGGTTGCCGT 58.129 42.857 0.00 0.00 0.00 5.68
731 737 2.556622 AGAAAACTTATGGGTTGCCGTG 59.443 45.455 0.00 0.00 0.00 4.94
732 738 1.989706 AAACTTATGGGTTGCCGTGT 58.010 45.000 0.00 0.00 0.00 4.49
733 739 1.243902 AACTTATGGGTTGCCGTGTG 58.756 50.000 0.00 0.00 0.00 3.82
734 740 0.398696 ACTTATGGGTTGCCGTGTGA 59.601 50.000 0.00 0.00 0.00 3.58
735 741 1.086696 CTTATGGGTTGCCGTGTGAG 58.913 55.000 0.00 0.00 0.00 3.51
736 742 0.687920 TTATGGGTTGCCGTGTGAGA 59.312 50.000 0.00 0.00 0.00 3.27
737 743 0.908910 TATGGGTTGCCGTGTGAGAT 59.091 50.000 0.00 0.00 0.00 2.75
738 744 0.677731 ATGGGTTGCCGTGTGAGATG 60.678 55.000 0.00 0.00 0.00 2.90
739 745 2.690778 GGGTTGCCGTGTGAGATGC 61.691 63.158 0.00 0.00 0.00 3.91
740 746 2.690778 GGTTGCCGTGTGAGATGCC 61.691 63.158 0.00 0.00 0.00 4.40
741 747 2.359850 TTGCCGTGTGAGATGCCC 60.360 61.111 0.00 0.00 0.00 5.36
742 748 2.894257 TTGCCGTGTGAGATGCCCT 61.894 57.895 0.00 0.00 0.00 5.19
743 749 1.549243 TTGCCGTGTGAGATGCCCTA 61.549 55.000 0.00 0.00 0.00 3.53
765 771 8.151596 CCCTAAAATAGTGGGCTTTGTTTTAAA 58.848 33.333 0.00 0.00 33.88 1.52
766 772 9.203421 CCTAAAATAGTGGGCTTTGTTTTAAAG 57.797 33.333 0.00 0.00 0.00 1.85
770 776 5.784578 AGTGGGCTTTGTTTTAAAGTAGG 57.215 39.130 0.00 0.00 0.00 3.18
772 778 4.038763 GTGGGCTTTGTTTTAAAGTAGGCT 59.961 41.667 0.00 0.00 0.00 4.58
777 783 7.306213 GGCTTTGTTTTAAAGTAGGCTTAGAG 58.694 38.462 0.00 0.00 33.95 2.43
802 808 1.435408 GCTCTTGCCGGAGATGCTTC 61.435 60.000 5.05 0.00 35.52 3.86
819 829 7.527796 AGATGCTTCTAATCCCTACAGTAGTA 58.472 38.462 6.84 0.00 0.00 1.82
921 931 1.072331 CAGTTAAGCCCAGTCTGTGGT 59.928 52.381 0.00 0.00 46.37 4.16
944 954 3.936203 AACGAACGCTCCTGGCCA 61.936 61.111 4.71 4.71 37.74 5.36
1137 1152 2.724454 CTCTCCACCTTCTTCGGTCTA 58.276 52.381 0.00 0.00 34.29 2.59
1304 1319 1.656095 GTCTTCTTGATCTCGCCGTTG 59.344 52.381 0.00 0.00 0.00 4.10
1356 1371 4.146564 GGAATCTGGTCCTACCTACTCTC 58.853 52.174 0.00 0.00 39.58 3.20
1376 1391 2.269241 CCTCCTTCGTTGAGGGGC 59.731 66.667 9.00 0.00 44.73 5.80
1398 1413 0.665972 GCTATCTCAGTAGCGGCAGC 60.666 60.000 0.00 0.00 45.58 5.25
1411 1426 1.247419 CGGCAGCCCAAATGTGGTTA 61.247 55.000 5.63 0.00 44.30 2.85
1524 1540 1.203162 TCTGGTGCCATTGGGATGTTT 60.203 47.619 4.53 0.00 35.59 2.83
1603 1619 4.022849 AGTGCATGTCTTGGTTCTTTTAGC 60.023 41.667 0.00 0.00 0.00 3.09
1713 1730 4.037446 GGTGTTGTCTTATGCTGTTTCCAA 59.963 41.667 0.00 0.00 0.00 3.53
1757 1774 1.517257 GGTCCTGTGATGCGAGTCG 60.517 63.158 8.54 8.54 0.00 4.18
1827 1845 2.034675 GTGCATTTGTGTCGTTTGCTTG 60.035 45.455 0.00 0.00 34.47 4.01
1872 1890 6.957631 TGTTGTAGACATGGAGATAATTGGT 58.042 36.000 0.00 0.00 32.00 3.67
1873 1891 8.084985 TGTTGTAGACATGGAGATAATTGGTA 57.915 34.615 0.00 0.00 32.00 3.25
1874 1892 8.713971 TGTTGTAGACATGGAGATAATTGGTAT 58.286 33.333 0.00 0.00 32.00 2.73
1875 1893 9.561069 GTTGTAGACATGGAGATAATTGGTATT 57.439 33.333 0.00 0.00 0.00 1.89
1931 1954 4.219143 GGAAGTTTTTCCCTGTTACACG 57.781 45.455 0.00 0.00 46.03 4.49
1936 1959 3.495434 TTTTCCCTGTTACACGGTGAT 57.505 42.857 16.29 1.80 0.00 3.06
1975 1998 4.979335 TGGTGATACATCCAACAGAAACA 58.021 39.130 0.00 0.00 0.00 2.83
1996 2019 2.106511 AGTTTGTAGCTCCCTTTGCAGA 59.893 45.455 0.00 0.00 0.00 4.26
2041 2064 5.308237 ACAGTTTCCTCATCTTTACCTGAGT 59.692 40.000 0.00 0.00 37.73 3.41
2197 2220 8.752766 TTACAGAAGTAACGGTTATCTTCTTG 57.247 34.615 25.81 23.13 42.80 3.02
2291 2335 5.703592 TGTTACTGAAATGTTAGCGTCCAAT 59.296 36.000 0.00 0.00 0.00 3.16
2312 2356 1.964552 ATGCTCTGCTAATGCTCCAC 58.035 50.000 0.00 0.00 40.48 4.02
3073 3117 6.036735 GCGATACAGCTTTTCAGTTAACCATA 59.963 38.462 0.88 0.00 0.00 2.74
3089 3133 3.736094 ACCATACTTTCTCCTCCCATCA 58.264 45.455 0.00 0.00 0.00 3.07
3192 3236 0.035915 AGAAGAAAAGGCTCGAGGGC 60.036 55.000 15.58 7.43 41.20 5.19
3244 3288 4.617253 TTAGTGCTCAAAGCTCTTGGTA 57.383 40.909 8.61 0.00 41.75 3.25
3517 3561 1.792949 GTTTCTGTCGCGAGTGATGTT 59.207 47.619 10.24 0.00 0.00 2.71
3624 3670 6.351286 GCATATTTTCTTCTTCCCACCATGTT 60.351 38.462 0.00 0.00 0.00 2.71
3628 3674 8.893563 ATTTTCTTCTTCCCACCATGTTTATA 57.106 30.769 0.00 0.00 0.00 0.98
3960 4009 0.179936 CAGGGCAGCCTAAGGAAGAG 59.820 60.000 12.43 0.00 0.00 2.85
4069 4118 0.394216 CTTGGGTGCCCGATTGATCA 60.394 55.000 2.44 0.00 39.42 2.92
4134 4183 4.467795 GCTACATCTAGATGCCCATCCTAA 59.532 45.833 28.86 6.05 42.39 2.69
4195 4244 1.815421 GCAGCCACCTCATGTACCG 60.815 63.158 0.00 0.00 0.00 4.02
4202 4251 2.417379 CCACCTCATGTACCGAAGACAG 60.417 54.545 0.00 0.00 0.00 3.51
4254 4303 7.888812 ACTCATGAAGTTGTAACACTGCTGTG 61.889 42.308 20.83 20.83 41.95 3.66
4273 4322 0.449388 GCATGTGCAACCTGTAGCTC 59.551 55.000 0.00 0.00 41.59 4.09
4312 4361 3.041561 TGGATGATCCACATGGGGT 57.958 52.632 15.27 0.54 42.67 4.95
4369 4418 3.500471 GGGTTTCCCAGTTCTTCAGGATT 60.500 47.826 0.00 0.00 44.65 3.01
4438 4487 9.011407 GTGAACTGTAATGTAGATCTAACTTCG 57.989 37.037 3.40 0.00 0.00 3.79
4597 4646 0.940126 GGCATTGAGCTGGTATGACG 59.060 55.000 0.00 0.00 44.79 4.35
4677 4730 7.772332 AACTTGAGATTTTTATCGTATCGCT 57.228 32.000 0.00 0.00 0.00 4.93
4689 4742 0.874607 GTATCGCTTGGTAGCCACGG 60.875 60.000 0.00 0.00 44.86 4.94
4717 4770 9.276590 CTTAATATCTGATACCACAAGCATTCA 57.723 33.333 0.00 0.00 0.00 2.57
4737 4790 7.410407 GCATTCAACTTGTTTCGTAAATAAGGC 60.410 37.037 15.57 8.43 41.98 4.35
4740 4793 6.207810 TCAACTTGTTTCGTAAATAAGGCCAT 59.792 34.615 5.01 0.00 41.98 4.40
4741 4794 7.390996 TCAACTTGTTTCGTAAATAAGGCCATA 59.609 33.333 5.01 0.00 41.98 2.74
4744 4797 6.687081 TGTTTCGTAAATAAGGCCATAAGG 57.313 37.500 5.01 0.00 38.23 2.69
4745 4798 5.591067 TGTTTCGTAAATAAGGCCATAAGGG 59.409 40.000 5.01 0.00 40.85 3.95
4770 4823 2.113860 GCACAAGGCAAGACCATCTA 57.886 50.000 0.00 0.00 43.14 1.98
4773 4826 3.369471 GCACAAGGCAAGACCATCTAGTA 60.369 47.826 0.00 0.00 43.14 1.82
4782 4841 7.125811 AGGCAAGACCATCTAGTATACTGAAAA 59.874 37.037 15.90 0.00 43.14 2.29
4801 4860 8.762426 ACTGAAAACGTACTTCTCTAAATGAAC 58.238 33.333 10.62 0.00 0.00 3.18
4850 4909 1.003118 ACACTTTCATTCCAGCGGCTA 59.997 47.619 0.26 0.00 0.00 3.93
4890 4951 7.873719 TCACACCCGATAATGACAATAAAAT 57.126 32.000 0.00 0.00 0.00 1.82
5001 5064 3.006323 ACTGTCAGCAAACCACAAACAAA 59.994 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.467084 AACGATGGATGGCGCGGT 62.467 61.111 8.83 0.00 0.00 5.68
3 4 3.940640 CAACGATGGATGGCGCGG 61.941 66.667 8.83 0.00 0.00 6.46
4 5 2.246739 ATCAACGATGGATGGCGCG 61.247 57.895 0.00 0.00 0.00 6.86
6 7 1.280746 GCATCAACGATGGATGGCG 59.719 57.895 14.23 0.00 41.87 5.69
7 8 1.280746 CGCATCAACGATGGATGGC 59.719 57.895 14.23 4.16 41.87 4.40
8 9 1.280746 GCGCATCAACGATGGATGG 59.719 57.895 0.30 8.03 41.87 3.51
9 10 1.083209 CGCGCATCAACGATGGATG 60.083 57.895 8.75 10.05 43.89 3.51
10 11 2.885676 GCGCGCATCAACGATGGAT 61.886 57.895 29.10 0.00 40.10 3.41
11 12 3.563088 GCGCGCATCAACGATGGA 61.563 61.111 29.10 0.00 40.10 3.41
12 13 4.925307 CGCGCGCATCAACGATGG 62.925 66.667 32.61 6.38 40.10 3.51
13 14 2.717702 CTACGCGCGCATCAACGATG 62.718 60.000 32.58 13.71 42.37 3.84
14 15 2.576893 CTACGCGCGCATCAACGAT 61.577 57.895 32.58 9.66 34.06 3.73
15 16 3.244603 CTACGCGCGCATCAACGA 61.245 61.111 32.58 0.00 34.06 3.85
16 17 3.458164 GACTACGCGCGCATCAACG 62.458 63.158 32.58 16.12 0.00 4.10
17 18 2.316687 GACTACGCGCGCATCAAC 59.683 61.111 32.58 15.01 0.00 3.18
18 19 3.244603 CGACTACGCGCGCATCAA 61.245 61.111 32.58 11.69 0.00 2.57
19 20 4.470170 ACGACTACGCGCGCATCA 62.470 61.111 32.58 14.08 43.96 3.07
20 21 3.960998 CACGACTACGCGCGCATC 61.961 66.667 32.58 22.92 43.96 3.91
25 26 3.913573 CATGGCACGACTACGCGC 61.914 66.667 5.73 0.00 45.13 6.86
26 27 3.913573 GCATGGCACGACTACGCG 61.914 66.667 3.53 3.53 43.96 6.01
27 28 2.173669 ATGCATGGCACGACTACGC 61.174 57.895 0.00 0.00 43.04 4.42
28 29 1.637934 CATGCATGGCACGACTACG 59.362 57.895 19.40 0.00 43.04 3.51
29 30 1.353103 GCATGCATGGCACGACTAC 59.647 57.895 27.34 4.17 43.04 2.73
30 31 1.078567 TGCATGCATGGCACGACTA 60.079 52.632 27.34 1.28 43.04 2.59
31 32 2.360225 TGCATGCATGGCACGACT 60.360 55.556 27.34 0.00 43.04 4.18
32 33 2.101575 CTGCATGCATGGCACGAC 59.898 61.111 27.34 10.52 43.04 4.34
33 34 2.046120 TCTGCATGCATGGCACGA 60.046 55.556 27.34 18.69 43.04 4.35
34 35 1.650314 TTCTCTGCATGCATGGCACG 61.650 55.000 27.34 17.14 43.04 5.34
35 36 0.528924 TTTCTCTGCATGCATGGCAC 59.471 50.000 27.34 11.97 43.04 5.01
36 37 1.480789 ATTTCTCTGCATGCATGGCA 58.519 45.000 27.34 22.30 44.86 4.92
37 38 3.067742 ACTTATTTCTCTGCATGCATGGC 59.932 43.478 27.34 19.18 0.00 4.40
38 39 4.554134 CGACTTATTTCTCTGCATGCATGG 60.554 45.833 27.34 16.51 0.00 3.66
39 40 4.524749 CGACTTATTTCTCTGCATGCATG 58.475 43.478 22.97 22.70 0.00 4.06
40 41 3.562973 CCGACTTATTTCTCTGCATGCAT 59.437 43.478 22.97 7.74 0.00 3.96
41 42 2.938451 CCGACTTATTTCTCTGCATGCA 59.062 45.455 21.29 21.29 0.00 3.96
42 43 2.286654 GCCGACTTATTTCTCTGCATGC 60.287 50.000 11.82 11.82 0.00 4.06
43 44 3.002042 CAGCCGACTTATTTCTCTGCATG 59.998 47.826 0.00 0.00 0.00 4.06
44 45 3.201290 CAGCCGACTTATTTCTCTGCAT 58.799 45.455 0.00 0.00 0.00 3.96
45 46 2.621338 CAGCCGACTTATTTCTCTGCA 58.379 47.619 0.00 0.00 0.00 4.41
46 47 1.328986 GCAGCCGACTTATTTCTCTGC 59.671 52.381 0.00 0.00 38.62 4.26
47 48 1.590238 CGCAGCCGACTTATTTCTCTG 59.410 52.381 0.00 0.00 36.29 3.35
48 49 1.927895 CGCAGCCGACTTATTTCTCT 58.072 50.000 0.00 0.00 36.29 3.10
63 64 4.829518 TCGTCGACATCCGCGCAG 62.830 66.667 17.16 0.00 37.58 5.18
64 65 4.829518 CTCGTCGACATCCGCGCA 62.830 66.667 17.16 0.00 37.58 6.09
66 67 4.175489 ACCTCGTCGACATCCGCG 62.175 66.667 17.16 0.00 38.47 6.46
67 68 2.579787 CACCTCGTCGACATCCGC 60.580 66.667 17.16 0.00 38.37 5.54
68 69 2.102357 CCACCTCGTCGACATCCG 59.898 66.667 17.16 0.96 40.25 4.18
69 70 2.202756 GCCACCTCGTCGACATCC 60.203 66.667 17.16 0.00 0.00 3.51
70 71 2.579787 CGCCACCTCGTCGACATC 60.580 66.667 17.16 0.00 0.00 3.06
71 72 4.129737 CCGCCACCTCGTCGACAT 62.130 66.667 17.16 0.00 0.00 3.06
96 97 4.722700 ATGGTGGGTGGCGCAGAC 62.723 66.667 10.83 4.75 0.00 3.51
97 98 4.408821 GATGGTGGGTGGCGCAGA 62.409 66.667 10.83 0.00 0.00 4.26
98 99 4.720902 TGATGGTGGGTGGCGCAG 62.721 66.667 10.83 0.00 0.00 5.18
99 100 3.993614 GATGATGGTGGGTGGCGCA 62.994 63.158 10.83 0.00 0.00 6.09
100 101 3.211963 GATGATGGTGGGTGGCGC 61.212 66.667 0.00 0.00 0.00 6.53
101 102 2.896854 CGATGATGGTGGGTGGCG 60.897 66.667 0.00 0.00 0.00 5.69
102 103 1.524621 CTCGATGATGGTGGGTGGC 60.525 63.158 0.00 0.00 0.00 5.01
103 104 1.146930 CCTCGATGATGGTGGGTGG 59.853 63.158 0.00 0.00 0.00 4.61
104 105 0.105593 CTCCTCGATGATGGTGGGTG 59.894 60.000 0.00 0.00 0.00 4.61
105 106 0.032117 TCTCCTCGATGATGGTGGGT 60.032 55.000 0.00 0.00 0.00 4.51
106 107 1.069823 CTTCTCCTCGATGATGGTGGG 59.930 57.143 0.00 0.00 0.00 4.61
107 108 1.759445 ACTTCTCCTCGATGATGGTGG 59.241 52.381 0.00 0.00 0.00 4.61
108 109 3.885901 TCTACTTCTCCTCGATGATGGTG 59.114 47.826 0.00 0.00 0.00 4.17
109 110 4.171878 TCTACTTCTCCTCGATGATGGT 57.828 45.455 0.00 0.00 0.00 3.55
110 111 4.339530 TGTTCTACTTCTCCTCGATGATGG 59.660 45.833 0.00 0.00 0.00 3.51
111 112 5.506686 TGTTCTACTTCTCCTCGATGATG 57.493 43.478 0.00 0.00 0.00 3.07
112 113 5.010516 CCATGTTCTACTTCTCCTCGATGAT 59.989 44.000 0.00 0.00 0.00 2.45
113 114 4.339530 CCATGTTCTACTTCTCCTCGATGA 59.660 45.833 0.00 0.00 0.00 2.92
114 115 4.339530 TCCATGTTCTACTTCTCCTCGATG 59.660 45.833 0.00 0.00 0.00 3.84
115 116 4.537751 TCCATGTTCTACTTCTCCTCGAT 58.462 43.478 0.00 0.00 0.00 3.59
116 117 3.964411 TCCATGTTCTACTTCTCCTCGA 58.036 45.455 0.00 0.00 0.00 4.04
117 118 4.440802 CCTTCCATGTTCTACTTCTCCTCG 60.441 50.000 0.00 0.00 0.00 4.63
118 119 4.682050 GCCTTCCATGTTCTACTTCTCCTC 60.682 50.000 0.00 0.00 0.00 3.71
119 120 3.198853 GCCTTCCATGTTCTACTTCTCCT 59.801 47.826 0.00 0.00 0.00 3.69
120 121 3.536570 GCCTTCCATGTTCTACTTCTCC 58.463 50.000 0.00 0.00 0.00 3.71
121 122 3.536570 GGCCTTCCATGTTCTACTTCTC 58.463 50.000 0.00 0.00 0.00 2.87
122 123 2.093447 CGGCCTTCCATGTTCTACTTCT 60.093 50.000 0.00 0.00 0.00 2.85
123 124 2.280628 CGGCCTTCCATGTTCTACTTC 58.719 52.381 0.00 0.00 0.00 3.01
124 125 1.679032 GCGGCCTTCCATGTTCTACTT 60.679 52.381 0.00 0.00 0.00 2.24
125 126 0.107654 GCGGCCTTCCATGTTCTACT 60.108 55.000 0.00 0.00 0.00 2.57
126 127 1.095807 GGCGGCCTTCCATGTTCTAC 61.096 60.000 12.87 0.00 0.00 2.59
127 128 1.223487 GGCGGCCTTCCATGTTCTA 59.777 57.895 12.87 0.00 0.00 2.10
128 129 2.044946 GGCGGCCTTCCATGTTCT 60.045 61.111 12.87 0.00 0.00 3.01
129 130 3.508840 CGGCGGCCTTCCATGTTC 61.509 66.667 18.34 0.00 0.00 3.18
147 148 2.967076 ATGCGATACAAGCGGCGG 60.967 61.111 9.78 0.00 37.44 6.13
148 149 2.246397 CATGCGATACAAGCGGCG 59.754 61.111 0.51 0.51 37.44 6.46
149 150 1.835483 CTCCATGCGATACAAGCGGC 61.835 60.000 0.00 0.00 37.44 6.53
150 151 1.224069 CCTCCATGCGATACAAGCGG 61.224 60.000 0.00 0.00 37.44 5.52
151 152 1.835483 GCCTCCATGCGATACAAGCG 61.835 60.000 0.00 0.00 37.44 4.68
152 153 1.510480 GGCCTCCATGCGATACAAGC 61.510 60.000 0.00 0.00 0.00 4.01
153 154 1.224069 CGGCCTCCATGCGATACAAG 61.224 60.000 0.00 0.00 0.00 3.16
154 155 1.227527 CGGCCTCCATGCGATACAA 60.228 57.895 0.00 0.00 0.00 2.41
155 156 2.421314 CGGCCTCCATGCGATACA 59.579 61.111 0.00 0.00 0.00 2.29
156 157 3.044305 GCGGCCTCCATGCGATAC 61.044 66.667 0.00 0.00 0.00 2.24
157 158 4.314440 GGCGGCCTCCATGCGATA 62.314 66.667 12.87 0.00 0.00 2.92
387 389 3.407046 CTCGCTAACCGGACCGTCC 62.407 68.421 9.46 7.59 37.59 4.79
388 390 2.101770 CTCGCTAACCGGACCGTC 59.898 66.667 9.46 0.00 37.59 4.79
389 391 4.125695 GCTCGCTAACCGGACCGT 62.126 66.667 9.46 0.00 37.59 4.83
390 392 3.823330 AGCTCGCTAACCGGACCG 61.823 66.667 9.46 6.99 37.59 4.79
391 393 2.202756 CAGCTCGCTAACCGGACC 60.203 66.667 9.46 0.00 37.59 4.46
410 414 1.780309 ACTTTGTCTTCCCCATGTCCA 59.220 47.619 0.00 0.00 0.00 4.02
446 450 0.959372 ACGCTGCACTAGTCTACGGT 60.959 55.000 0.00 0.00 0.00 4.83
557 563 2.373540 TTCATACAAACCGGACGAGG 57.626 50.000 9.46 0.00 37.30 4.63
591 597 2.598589 CAAACACGGCTGGATTTCATG 58.401 47.619 0.00 0.00 0.00 3.07
601 607 2.035704 TGAAATTCATGCAAACACGGCT 59.964 40.909 0.00 0.00 0.00 5.52
641 647 4.438744 GCTAGCCGCATACATTTCAAACTT 60.439 41.667 2.29 0.00 38.92 2.66
673 679 4.646945 ACAGACACGGATATGAGAGAACAT 59.353 41.667 0.00 0.00 0.00 2.71
677 683 4.096532 GTCAACAGACACGGATATGAGAGA 59.903 45.833 0.00 0.00 32.50 3.10
695 701 3.251004 AGTTTTCTTCCGCATCTGTCAAC 59.749 43.478 0.00 0.00 0.00 3.18
696 702 3.476552 AGTTTTCTTCCGCATCTGTCAA 58.523 40.909 0.00 0.00 0.00 3.18
697 703 3.126001 AGTTTTCTTCCGCATCTGTCA 57.874 42.857 0.00 0.00 0.00 3.58
698 704 5.447818 CCATAAGTTTTCTTCCGCATCTGTC 60.448 44.000 0.00 0.00 40.91 3.51
699 705 4.396166 CCATAAGTTTTCTTCCGCATCTGT 59.604 41.667 0.00 0.00 40.91 3.41
700 706 4.201950 CCCATAAGTTTTCTTCCGCATCTG 60.202 45.833 0.00 0.00 40.91 2.90
701 707 3.947834 CCCATAAGTTTTCTTCCGCATCT 59.052 43.478 0.00 0.00 40.91 2.90
702 708 3.694566 ACCCATAAGTTTTCTTCCGCATC 59.305 43.478 0.00 0.00 40.91 3.91
703 709 3.697166 ACCCATAAGTTTTCTTCCGCAT 58.303 40.909 0.00 0.00 40.91 4.73
704 710 3.149005 ACCCATAAGTTTTCTTCCGCA 57.851 42.857 0.00 0.00 40.91 5.69
705 711 3.833442 CAACCCATAAGTTTTCTTCCGC 58.167 45.455 0.00 0.00 40.91 5.54
706 712 3.366985 GGCAACCCATAAGTTTTCTTCCG 60.367 47.826 0.00 0.00 40.91 4.30
707 713 3.366985 CGGCAACCCATAAGTTTTCTTCC 60.367 47.826 0.00 0.00 40.91 3.46
708 714 3.254903 ACGGCAACCCATAAGTTTTCTTC 59.745 43.478 0.00 0.00 40.91 2.87
709 715 3.005367 CACGGCAACCCATAAGTTTTCTT 59.995 43.478 0.00 0.00 43.24 2.52
710 716 2.556622 CACGGCAACCCATAAGTTTTCT 59.443 45.455 0.00 0.00 0.00 2.52
711 717 2.295070 ACACGGCAACCCATAAGTTTTC 59.705 45.455 0.00 0.00 0.00 2.29
712 718 2.035321 CACACGGCAACCCATAAGTTTT 59.965 45.455 0.00 0.00 0.00 2.43
713 719 1.611491 CACACGGCAACCCATAAGTTT 59.389 47.619 0.00 0.00 0.00 2.66
714 720 1.202830 TCACACGGCAACCCATAAGTT 60.203 47.619 0.00 0.00 0.00 2.66
715 721 0.398696 TCACACGGCAACCCATAAGT 59.601 50.000 0.00 0.00 0.00 2.24
716 722 1.086696 CTCACACGGCAACCCATAAG 58.913 55.000 0.00 0.00 0.00 1.73
717 723 0.687920 TCTCACACGGCAACCCATAA 59.312 50.000 0.00 0.00 0.00 1.90
718 724 0.908910 ATCTCACACGGCAACCCATA 59.091 50.000 0.00 0.00 0.00 2.74
719 725 0.677731 CATCTCACACGGCAACCCAT 60.678 55.000 0.00 0.00 0.00 4.00
720 726 1.302431 CATCTCACACGGCAACCCA 60.302 57.895 0.00 0.00 0.00 4.51
721 727 2.690778 GCATCTCACACGGCAACCC 61.691 63.158 0.00 0.00 0.00 4.11
722 728 2.690778 GGCATCTCACACGGCAACC 61.691 63.158 0.00 0.00 0.00 3.77
723 729 2.690778 GGGCATCTCACACGGCAAC 61.691 63.158 0.00 0.00 0.00 4.17
724 730 1.549243 TAGGGCATCTCACACGGCAA 61.549 55.000 0.00 0.00 0.00 4.52
725 731 1.549243 TTAGGGCATCTCACACGGCA 61.549 55.000 0.00 0.00 0.00 5.69
726 732 0.392461 TTTAGGGCATCTCACACGGC 60.392 55.000 0.00 0.00 0.00 5.68
727 733 2.107950 TTTTAGGGCATCTCACACGG 57.892 50.000 0.00 0.00 0.00 4.94
728 734 4.271049 CACTATTTTAGGGCATCTCACACG 59.729 45.833 0.00 0.00 0.00 4.49
729 735 4.576463 CCACTATTTTAGGGCATCTCACAC 59.424 45.833 0.00 0.00 0.00 3.82
730 736 4.385199 CCCACTATTTTAGGGCATCTCACA 60.385 45.833 0.00 0.00 35.44 3.58
731 737 4.137543 CCCACTATTTTAGGGCATCTCAC 58.862 47.826 0.00 0.00 35.44 3.51
732 738 4.437682 CCCACTATTTTAGGGCATCTCA 57.562 45.455 0.00 0.00 35.44 3.27
739 745 5.738619 AAACAAAGCCCACTATTTTAGGG 57.261 39.130 0.00 0.00 45.68 3.53
740 746 9.203421 CTTTAAAACAAAGCCCACTATTTTAGG 57.797 33.333 0.00 0.00 0.00 2.69
741 747 9.758651 ACTTTAAAACAAAGCCCACTATTTTAG 57.241 29.630 0.00 0.00 0.00 1.85
743 749 9.758651 CTACTTTAAAACAAAGCCCACTATTTT 57.241 29.630 0.00 0.00 0.00 1.82
765 771 3.720002 AGAGCCTCTACTCTAAGCCTACT 59.280 47.826 0.00 0.00 45.25 2.57
766 772 4.094830 AGAGCCTCTACTCTAAGCCTAC 57.905 50.000 0.00 0.00 45.25 3.18
768 774 3.295973 CAAGAGCCTCTACTCTAAGCCT 58.704 50.000 0.00 0.00 46.38 4.58
770 776 3.092334 GCAAGAGCCTCTACTCTAAGC 57.908 52.381 0.00 0.00 46.38 3.09
875 885 2.428171 GTGGGTGCGATTGGTAGTACTA 59.572 50.000 0.00 0.00 0.00 1.82
876 886 1.206371 GTGGGTGCGATTGGTAGTACT 59.794 52.381 0.00 0.00 0.00 2.73
889 899 1.228429 TTAACTGCAGGGTGGGTGC 60.228 57.895 19.93 0.00 41.59 5.01
921 931 1.336517 CCAGGAGCGTTCGTTGTTCTA 60.337 52.381 0.00 0.00 0.00 2.10
944 954 1.407618 TCGTGTATACAAGCGCAGGAT 59.592 47.619 11.47 6.48 0.00 3.24
998 1013 3.441244 GCCTTTTGCTTGGCCATAC 57.559 52.632 6.09 1.51 43.11 2.39
1248 1263 1.313822 GGTAGGTAGAGCTGGGGGT 59.686 63.158 0.00 0.00 0.00 4.95
1304 1319 0.811281 CCCAGAACAAAGAATCGCCC 59.189 55.000 0.00 0.00 0.00 6.13
1411 1426 4.645136 TCCTATCTAACGAATGCTGTCAGT 59.355 41.667 0.93 0.00 0.00 3.41
1524 1540 3.763360 ACTTCGGCAATCATGAATTTCCA 59.237 39.130 0.00 0.00 30.71 3.53
1603 1619 2.609350 CCACCAAATCGGCATTGAAAG 58.391 47.619 0.00 0.00 39.03 2.62
1713 1730 2.290071 CGACCCCAACTCACCAACTAAT 60.290 50.000 0.00 0.00 0.00 1.73
1757 1774 2.897326 AGACCCCACTTTTTGGCATAAC 59.103 45.455 0.00 0.00 45.37 1.89
1827 1845 6.613153 ACAGATATTAGACCTAGCATTCCC 57.387 41.667 0.00 0.00 0.00 3.97
1975 1998 2.106511 TCTGCAAAGGGAGCTACAAACT 59.893 45.455 0.00 0.00 31.59 2.66
2041 2064 8.902540 ATGTCAAAATCAAACTACACAGTAGA 57.097 30.769 10.87 0.00 33.48 2.59
2120 2143 4.264253 TCTGCCTGAACTTATCATTGTGG 58.736 43.478 0.00 0.00 37.44 4.17
2197 2220 0.527565 AGACCGCCATTGCATGAAAC 59.472 50.000 0.00 0.00 37.32 2.78
2238 2261 5.413833 ACCAGAGAGTTTGCATTCATTACTG 59.586 40.000 0.00 0.00 0.00 2.74
2291 2335 3.470709 GTGGAGCATTAGCAGAGCATAA 58.529 45.455 0.00 0.00 45.49 1.90
2312 2356 2.138320 TCTGCACAAGAGAAGCTTTCG 58.862 47.619 0.00 0.00 33.60 3.46
2445 2489 5.172687 TCTAACTGCATAATCAACCACCA 57.827 39.130 0.00 0.00 0.00 4.17
3073 3117 4.664688 ACAAATGATGGGAGGAGAAAGT 57.335 40.909 0.00 0.00 0.00 2.66
3110 3154 3.397482 CTGAGGTCCAAAGAACAGACAG 58.603 50.000 0.00 0.00 31.99 3.51
3192 3236 2.125106 GGTGTAAGCGGGCAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
3312 3356 3.075148 GTTAGGGAACTCTGCCTTCAAC 58.925 50.000 0.00 0.00 41.49 3.18
3315 3359 3.536570 GATGTTAGGGAACTCTGCCTTC 58.463 50.000 0.00 0.00 41.49 3.46
3517 3561 8.657387 TGTTTCCATCATTACTGGGAATAAAA 57.343 30.769 0.00 0.00 39.05 1.52
3628 3674 8.166061 ACCCAGCTAATCATGTCATAATAACAT 58.834 33.333 0.00 0.00 37.85 2.71
3960 4009 8.150945 TCATAAGGATTTGCATAGAAGTAGTCC 58.849 37.037 0.00 0.00 0.00 3.85
4069 4118 7.333672 CCGTTTTTAACTTCAGCCTTCTATACT 59.666 37.037 0.00 0.00 0.00 2.12
4134 4183 2.502947 TGCAGTCAGCTGATCAGGTTAT 59.497 45.455 24.44 10.67 45.28 1.89
4254 4303 0.449388 GAGCTACAGGTTGCACATGC 59.551 55.000 8.45 0.00 42.50 4.06
4259 4308 0.321034 CTGCTGAGCTACAGGTTGCA 60.321 55.000 5.83 8.83 45.82 4.08
4267 4316 5.514274 AGAAGAATACTCTGCTGAGCTAC 57.486 43.478 19.49 9.37 43.85 3.58
4312 4361 0.253044 GTGGCATAGGCTCCTTCACA 59.747 55.000 0.00 0.00 40.87 3.58
4369 4418 0.392461 GTAAGGCCGCACCATCAGAA 60.392 55.000 0.00 0.00 43.14 3.02
4438 4487 2.045926 ATCTGGTGCGACCCAAGC 60.046 61.111 3.33 0.00 37.50 4.01
4597 4646 1.205417 ACAAAACATGCATGCCCTAGC 59.795 47.619 26.53 0.00 40.48 3.42
4677 4730 4.652421 AGATATTAAGACCGTGGCTACCAA 59.348 41.667 0.00 0.00 34.18 3.67
4689 4742 8.839310 ATGCTTGTGGTATCAGATATTAAGAC 57.161 34.615 0.00 0.00 0.00 3.01
4717 4770 6.584185 ATGGCCTTATTTACGAAACAAGTT 57.416 33.333 3.32 0.00 0.00 2.66
4737 4790 0.676466 TTGTGCTCGTGCCCTTATGG 60.676 55.000 7.05 0.00 38.71 2.74
4740 4793 1.003839 CCTTGTGCTCGTGCCCTTA 60.004 57.895 7.05 0.00 38.71 2.69
4741 4794 2.281761 CCTTGTGCTCGTGCCCTT 60.282 61.111 7.05 0.00 38.71 3.95
4744 4797 3.259425 CTTGCCTTGTGCTCGTGCC 62.259 63.158 7.05 0.00 42.00 5.01
4745 4798 2.253452 CTTGCCTTGTGCTCGTGC 59.747 61.111 1.71 1.71 42.00 5.34
4748 4801 0.957395 ATGGTCTTGCCTTGTGCTCG 60.957 55.000 0.00 0.00 42.00 5.03
4749 4802 0.807496 GATGGTCTTGCCTTGTGCTC 59.193 55.000 0.00 0.00 42.00 4.26
4750 4803 0.403271 AGATGGTCTTGCCTTGTGCT 59.597 50.000 0.00 0.00 42.00 4.40
4751 4804 2.012673 CTAGATGGTCTTGCCTTGTGC 58.987 52.381 0.00 0.00 41.77 4.57
4752 4805 3.340814 ACTAGATGGTCTTGCCTTGTG 57.659 47.619 0.00 0.00 38.35 3.33
4753 4806 5.900123 AGTATACTAGATGGTCTTGCCTTGT 59.100 40.000 2.75 0.00 38.35 3.16
4754 4807 6.040955 TCAGTATACTAGATGGTCTTGCCTTG 59.959 42.308 4.74 0.00 38.35 3.61
4762 4815 8.619546 AGTACGTTTTCAGTATACTAGATGGTC 58.380 37.037 4.74 0.00 0.00 4.02
4940 5001 2.408333 GCTGTTGGAGCGGCATTAT 58.592 52.632 1.45 0.00 38.15 1.28
4973 5036 2.744202 GTGGTTTGCTGACAGTGATAGG 59.256 50.000 3.99 0.00 0.00 2.57
5001 5064 3.031013 TGATGTACCTGGATCATCGTGT 58.969 45.455 20.86 0.89 40.25 4.49


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

AutoCloner maintained by Alex Coulton.