Multiple sequence alignment - TraesCS1A01G390500

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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 TraesCS1A01G390500 chr1A 100.000 2663 0 0 1 2663 557988219 557990881 0.000000e+00 4918.0
1 TraesCS1A01G390500 chr1A 90.168 417 22 9 249 664 557981156 557981554 2.350000e-145 525.0
2 TraesCS1A01G390500 chr1A 92.400 250 8 2 698 947 557983339 557983577 1.960000e-91 346.0
3 TraesCS1A01G390500 chr1D 94.977 1095 31 14 793 1877 465583059 465584139 0.000000e+00 1696.0
4 TraesCS1A01G390500 chr1D 88.564 822 52 15 1862 2663 465584155 465584954 0.000000e+00 959.0
5 TraesCS1A01G390500 chr1D 90.728 302 16 9 399 699 465582650 465582940 2.490000e-105 392.0
6 TraesCS1A01G390500 chr1D 82.353 119 19 1 1904 2020 400012942 400012824 4.690000e-18 102.0
7 TraesCS1A01G390500 chr1D 94.828 58 1 1 357 414 465582018 465582073 3.650000e-14 89.8
8 TraesCS1A01G390500 chr1D 100.000 32 0 0 208 239 47309056 47309025 2.860000e-05 60.2
9 TraesCS1A01G390500 chr1D 100.000 28 0 0 302 329 465581981 465582008 5.000000e-03 52.8
10 TraesCS1A01G390500 chr1B 84.302 1548 106 73 247 1719 642495028 642496513 0.000000e+00 1386.0
11 TraesCS1A01G390500 chr1B 80.961 562 94 8 2104 2656 585324497 585323940 1.460000e-117 433.0
12 TraesCS1A01G390500 chr1B 97.222 36 1 0 208 243 598473636 598473601 7.960000e-06 62.1
13 TraesCS1A01G390500 chr1B 100.000 31 0 0 209 239 535690989 535690959 1.030000e-04 58.4
14 TraesCS1A01G390500 chr5D 83.302 533 82 4 2128 2654 416589355 416589886 3.990000e-133 484.0
15 TraesCS1A01G390500 chr5D 84.277 159 25 0 1328 1486 490870384 490870542 3.550000e-34 156.0
16 TraesCS1A01G390500 chr5D 80.311 193 23 10 2105 2287 563333735 563333548 5.980000e-27 132.0
17 TraesCS1A01G390500 chr5D 94.872 39 2 0 205 243 339355852 339355890 7.960000e-06 62.1
18 TraesCS1A01G390500 chr5D 94.444 36 2 0 209 244 64744660 64744695 3.700000e-04 56.5
19 TraesCS1A01G390500 chr6D 81.195 569 81 11 2104 2663 333001632 333001081 4.070000e-118 435.0
20 TraesCS1A01G390500 chr6D 82.883 444 71 4 2223 2663 346270733 346270292 6.910000e-106 394.0
21 TraesCS1A01G390500 chr6D 97.143 35 1 0 209 243 414268877 414268843 2.860000e-05 60.2
22 TraesCS1A01G390500 chr3D 79.930 568 95 10 2104 2663 41227330 41227886 1.490000e-107 399.0
23 TraesCS1A01G390500 chr3D 79.682 566 92 15 2105 2660 98644384 98644936 1.160000e-103 387.0
24 TraesCS1A01G390500 chr3D 74.839 310 57 14 1906 2210 420308636 420308343 1.290000e-23 121.0
25 TraesCS1A01G390500 chr3D 81.208 149 23 4 1908 2054 382944620 382944765 6.020000e-22 115.0
26 TraesCS1A01G390500 chr3D 94.286 35 2 0 210 244 380048779 380048745 1.000000e-03 54.7
27 TraesCS1A01G390500 chr5A 82.327 447 75 3 2217 2660 556690437 556690882 4.160000e-103 385.0
28 TraesCS1A01G390500 chr5A 84.768 151 23 0 1328 1478 7453746 7453896 4.590000e-33 152.0
29 TraesCS1A01G390500 chr2D 81.573 483 70 14 2194 2662 134805749 134806226 5.380000e-102 381.0
30 TraesCS1A01G390500 chr2D 83.108 148 21 4 1332 1477 8338685 8338830 5.980000e-27 132.0
31 TraesCS1A01G390500 chr2D 83.333 114 18 1 1908 2020 94553188 94553075 1.300000e-18 104.0
32 TraesCS1A01G390500 chr2D 95.833 48 2 0 2058 2105 33936206 33936253 7.900000e-11 78.7
33 TraesCS1A01G390500 chr2D 95.833 48 2 0 2058 2105 630272680 630272727 7.900000e-11 78.7
34 TraesCS1A01G390500 chr2D 97.222 36 1 0 209 244 36111343 36111378 7.960000e-06 62.1
35 TraesCS1A01G390500 chr2D 97.143 35 1 0 209 243 234151685 234151651 2.860000e-05 60.2
36 TraesCS1A01G390500 chr2D 97.222 36 0 1 208 243 476692818 476692784 2.860000e-05 60.2
37 TraesCS1A01G390500 chr2D 94.444 36 2 0 208 243 491441767 491441732 3.700000e-04 56.5
38 TraesCS1A01G390500 chr4B 78.957 556 87 15 2117 2663 600883809 600883275 4.220000e-93 351.0
39 TraesCS1A01G390500 chr3A 81.567 434 68 10 2234 2663 59438272 59437847 5.460000e-92 348.0
40 TraesCS1A01G390500 chr3A 82.759 116 19 1 1906 2020 71591668 71591553 4.690000e-18 102.0
41 TraesCS1A01G390500 chr7A 80.866 439 72 7 2231 2663 550049662 550049230 4.250000e-88 335.0
42 TraesCS1A01G390500 chr7A 77.750 400 78 6 1104 1496 700822789 700823184 4.430000e-58 235.0
43 TraesCS1A01G390500 chr2B 77.680 569 99 11 2104 2663 158638305 158638854 3.310000e-84 322.0
44 TraesCS1A01G390500 chr2B 82.517 143 19 5 1332 1471 4727963 4728102 1.290000e-23 121.0
45 TraesCS1A01G390500 chr2B 83.621 116 17 2 1907 2020 763861097 763860982 1.010000e-19 108.0
46 TraesCS1A01G390500 chr7B 84.568 162 25 0 1328 1489 714049998 714050159 7.630000e-36 161.0
47 TraesCS1A01G390500 chr7B 95.833 48 2 0 2058 2105 295520645 295520692 7.900000e-11 78.7
48 TraesCS1A01G390500 chr7B 100.000 29 0 0 1575 1603 699954175 699954203 1.000000e-03 54.7
49 TraesCS1A01G390500 chr5B 76.369 347 54 14 2105 2442 466703053 466702726 7.630000e-36 161.0
50 TraesCS1A01G390500 chr5B 83.648 159 26 0 1328 1486 605336464 605336622 1.650000e-32 150.0
51 TraesCS1A01G390500 chr5B 83.444 151 25 0 1328 1478 9284876 9285026 9.940000e-30 141.0
52 TraesCS1A01G390500 chr5B 85.185 81 12 0 1981 2061 515581933 515581853 1.700000e-12 84.2
53 TraesCS1A01G390500 chr5B 95.833 48 2 0 2058 2105 413609812 413609859 7.900000e-11 78.7
54 TraesCS1A01G390500 chr7D 85.430 151 22 0 1336 1486 619113052 619113202 9.870000e-35 158.0
55 TraesCS1A01G390500 chr6A 79.439 214 36 4 2114 2319 56935889 56936102 7.680000e-31 145.0
56 TraesCS1A01G390500 chr6A 97.222 36 1 0 208 243 16617892 16617927 7.960000e-06 62.1
57 TraesCS1A01G390500 chr6A 94.444 36 2 0 209 244 504942464 504942429 3.700000e-04 56.5
58 TraesCS1A01G390500 chr4A 83.439 157 24 2 1908 2063 589728824 589728669 7.680000e-31 145.0
59 TraesCS1A01G390500 chr6B 87.387 111 12 2 2104 2213 260102237 260102128 2.780000e-25 126.0
60 TraesCS1A01G390500 chr3B 81.203 133 24 1 1931 2063 425463108 425462977 3.630000e-19 106.0
61 TraesCS1A01G390500 chr3B 95.918 49 2 0 2057 2105 260377575 260377623 2.200000e-11 80.5
62 TraesCS1A01G390500 chrUn 95.833 48 2 0 2058 2105 371050843 371050890 7.900000e-11 78.7
63 TraesCS1A01G390500 chrUn 95.833 48 2 0 2058 2105 451363053 451363100 7.900000e-11 78.7
64 TraesCS1A01G390500 chrUn 95.833 48 2 0 2058 2105 452650905 452650952 7.900000e-11 78.7


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 TraesCS1A01G390500 chr1A 557988219 557990881 2662 False 4918.00 4918 100.0000 1 2663 1 chr1A.!!$F1 2662
1 TraesCS1A01G390500 chr1A 557981156 557983577 2421 False 435.50 525 91.2840 249 947 2 chr1A.!!$F2 698
2 TraesCS1A01G390500 chr1D 465581981 465584954 2973 False 637.92 1696 93.8194 302 2663 5 chr1D.!!$F1 2361
3 TraesCS1A01G390500 chr1B 642495028 642496513 1485 False 1386.00 1386 84.3020 247 1719 1 chr1B.!!$F1 1472
4 TraesCS1A01G390500 chr1B 585323940 585324497 557 True 433.00 433 80.9610 2104 2656 1 chr1B.!!$R2 552
5 TraesCS1A01G390500 chr5D 416589355 416589886 531 False 484.00 484 83.3020 2128 2654 1 chr5D.!!$F3 526
6 TraesCS1A01G390500 chr6D 333001081 333001632 551 True 435.00 435 81.1950 2104 2663 1 chr6D.!!$R1 559
7 TraesCS1A01G390500 chr3D 41227330 41227886 556 False 399.00 399 79.9300 2104 2663 1 chr3D.!!$F1 559
8 TraesCS1A01G390500 chr3D 98644384 98644936 552 False 387.00 387 79.6820 2105 2660 1 chr3D.!!$F2 555
9 TraesCS1A01G390500 chr4B 600883275 600883809 534 True 351.00 351 78.9570 2117 2663 1 chr4B.!!$R1 546
10 TraesCS1A01G390500 chr2B 158638305 158638854 549 False 322.00 322 77.6800 2104 2663 1 chr2B.!!$F2 559

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
352 354 0.030101 TCTTTTTGCGGGCTGTTTCG 59.97 50.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 4346 0.252197 GTCGTTGGAGGTGCCCTTAT 59.748 55.0 0.0 0.0 31.76 1.73 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
23 24 6.662414 ATGTTACATACATCCGTTTGTGAG 57.338 37.500 0.00 0.00 44.15 3.51
24 25 5.785243 TGTTACATACATCCGTTTGTGAGA 58.215 37.500 0.00 0.00 37.77 3.27
25 26 5.867174 TGTTACATACATCCGTTTGTGAGAG 59.133 40.000 0.00 0.00 37.77 3.20
26 27 4.801330 ACATACATCCGTTTGTGAGAGA 57.199 40.909 0.00 0.00 36.16 3.10
27 28 5.147330 ACATACATCCGTTTGTGAGAGAA 57.853 39.130 0.00 0.00 36.16 2.87
28 29 5.171476 ACATACATCCGTTTGTGAGAGAAG 58.829 41.667 0.00 0.00 36.16 2.85
29 30 3.753294 ACATCCGTTTGTGAGAGAAGT 57.247 42.857 0.00 0.00 0.00 3.01
30 31 4.073293 ACATCCGTTTGTGAGAGAAGTT 57.927 40.909 0.00 0.00 0.00 2.66
31 32 4.451900 ACATCCGTTTGTGAGAGAAGTTT 58.548 39.130 0.00 0.00 0.00 2.66
32 33 4.881850 ACATCCGTTTGTGAGAGAAGTTTT 59.118 37.500 0.00 0.00 0.00 2.43
33 34 5.357032 ACATCCGTTTGTGAGAGAAGTTTTT 59.643 36.000 0.00 0.00 0.00 1.94
64 65 9.590451 ACGAATGGAGTATTATTTTTAACTCGA 57.410 29.630 0.00 0.00 39.39 4.04
68 69 8.205131 TGGAGTATTATTTTTAACTCGAAGGC 57.795 34.615 0.00 0.00 39.39 4.35
69 70 7.010738 TGGAGTATTATTTTTAACTCGAAGGCG 59.989 37.037 0.00 0.00 39.39 5.52
70 71 7.242914 AGTATTATTTTTAACTCGAAGGCGG 57.757 36.000 0.00 0.00 38.28 6.13
71 72 2.913777 ATTTTTAACTCGAAGGCGGC 57.086 45.000 0.00 0.00 38.28 6.53
72 73 0.876399 TTTTTAACTCGAAGGCGGCC 59.124 50.000 12.11 12.11 38.28 6.13
73 74 1.293267 TTTTAACTCGAAGGCGGCCG 61.293 55.000 24.05 24.05 38.28 6.13
74 75 2.438951 TTTAACTCGAAGGCGGCCGT 62.439 55.000 28.70 11.02 38.28 5.68
75 76 3.636313 TAACTCGAAGGCGGCCGTG 62.636 63.158 28.70 11.86 38.28 4.94
80 81 2.981350 GAAGGCGGCCGTGGAAAA 60.981 61.111 28.70 0.00 0.00 2.29
81 82 2.519780 AAGGCGGCCGTGGAAAAA 60.520 55.556 28.70 0.00 0.00 1.94
82 83 2.742710 GAAGGCGGCCGTGGAAAAAC 62.743 60.000 28.70 6.82 0.00 2.43
83 84 3.597728 GGCGGCCGTGGAAAAACA 61.598 61.111 28.70 0.00 0.00 2.83
84 85 2.413765 GCGGCCGTGGAAAAACAA 59.586 55.556 28.70 0.00 0.00 2.83
85 86 1.006688 GCGGCCGTGGAAAAACAAT 60.007 52.632 28.70 0.00 0.00 2.71
86 87 1.006825 GCGGCCGTGGAAAAACAATC 61.007 55.000 28.70 0.08 0.00 2.67
87 88 0.388006 CGGCCGTGGAAAAACAATCC 60.388 55.000 19.50 0.00 37.48 3.01
88 89 0.037697 GGCCGTGGAAAAACAATCCC 60.038 55.000 0.00 0.00 36.04 3.85
89 90 0.966179 GCCGTGGAAAAACAATCCCT 59.034 50.000 0.00 0.00 36.04 4.20
90 91 1.336795 GCCGTGGAAAAACAATCCCTG 60.337 52.381 0.00 0.00 36.04 4.45
91 92 1.960689 CCGTGGAAAAACAATCCCTGT 59.039 47.619 0.00 0.00 41.27 4.00
92 93 2.030274 CCGTGGAAAAACAATCCCTGTC 60.030 50.000 0.00 0.00 37.23 3.51
93 94 2.621055 CGTGGAAAAACAATCCCTGTCA 59.379 45.455 0.00 0.00 37.23 3.58
94 95 3.067461 CGTGGAAAAACAATCCCTGTCAA 59.933 43.478 0.00 0.00 37.23 3.18
95 96 4.261994 CGTGGAAAAACAATCCCTGTCAAT 60.262 41.667 0.00 0.00 37.23 2.57
96 97 4.990426 GTGGAAAAACAATCCCTGTCAATG 59.010 41.667 0.00 0.00 37.23 2.82
97 98 4.898265 TGGAAAAACAATCCCTGTCAATGA 59.102 37.500 0.00 0.00 37.23 2.57
98 99 5.010922 TGGAAAAACAATCCCTGTCAATGAG 59.989 40.000 0.00 0.00 37.23 2.90
99 100 5.473039 GAAAAACAATCCCTGTCAATGAGG 58.527 41.667 0.00 0.00 37.23 3.86
100 101 3.814504 AACAATCCCTGTCAATGAGGT 57.185 42.857 0.00 0.00 37.23 3.85
101 102 3.356529 ACAATCCCTGTCAATGAGGTC 57.643 47.619 0.00 0.00 29.87 3.85
102 103 2.644299 ACAATCCCTGTCAATGAGGTCA 59.356 45.455 0.00 0.00 29.87 4.02
103 104 3.012518 CAATCCCTGTCAATGAGGTCAC 58.987 50.000 0.00 0.00 0.00 3.67
104 105 0.984230 TCCCTGTCAATGAGGTCACC 59.016 55.000 0.00 0.00 0.00 4.02
105 106 0.391661 CCCTGTCAATGAGGTCACCG 60.392 60.000 0.00 0.00 0.00 4.94
106 107 0.391661 CCTGTCAATGAGGTCACCGG 60.392 60.000 0.00 0.00 0.00 5.28
107 108 0.608130 CTGTCAATGAGGTCACCGGA 59.392 55.000 9.46 0.00 0.00 5.14
108 109 0.608130 TGTCAATGAGGTCACCGGAG 59.392 55.000 9.46 0.00 0.00 4.63
109 110 0.895530 GTCAATGAGGTCACCGGAGA 59.104 55.000 9.46 1.33 0.00 3.71
110 111 0.895530 TCAATGAGGTCACCGGAGAC 59.104 55.000 22.30 22.30 37.80 3.36
128 129 6.721571 GGAGACGAAGACAAAATAACATCA 57.278 37.500 0.00 0.00 0.00 3.07
129 130 7.129109 GGAGACGAAGACAAAATAACATCAA 57.871 36.000 0.00 0.00 0.00 2.57
130 131 7.752695 GGAGACGAAGACAAAATAACATCAAT 58.247 34.615 0.00 0.00 0.00 2.57
131 132 8.879759 GGAGACGAAGACAAAATAACATCAATA 58.120 33.333 0.00 0.00 0.00 1.90
132 133 9.907576 GAGACGAAGACAAAATAACATCAATAG 57.092 33.333 0.00 0.00 0.00 1.73
133 134 9.436957 AGACGAAGACAAAATAACATCAATAGT 57.563 29.630 0.00 0.00 0.00 2.12
150 151 9.650539 CATCAATAGTATGAATACTGGAAGAGG 57.349 37.037 12.30 4.54 43.10 3.69
151 152 9.607333 ATCAATAGTATGAATACTGGAAGAGGA 57.393 33.333 12.30 2.67 43.10 3.71
152 153 9.434275 TCAATAGTATGAATACTGGAAGAGGAA 57.566 33.333 12.30 0.00 43.10 3.36
155 156 7.072263 AGTATGAATACTGGAAGAGGAATGG 57.928 40.000 2.15 0.00 41.77 3.16
156 157 6.846505 AGTATGAATACTGGAAGAGGAATGGA 59.153 38.462 2.15 0.00 41.77 3.41
157 158 5.359194 TGAATACTGGAAGAGGAATGGAC 57.641 43.478 0.00 0.00 37.43 4.02
158 159 4.782691 TGAATACTGGAAGAGGAATGGACA 59.217 41.667 0.00 0.00 37.43 4.02
159 160 4.762289 ATACTGGAAGAGGAATGGACAC 57.238 45.455 0.00 0.00 37.43 3.67
160 161 2.338809 ACTGGAAGAGGAATGGACACA 58.661 47.619 0.00 0.00 37.43 3.72
161 162 2.711009 ACTGGAAGAGGAATGGACACAA 59.289 45.455 0.00 0.00 37.43 3.33
162 163 3.331889 ACTGGAAGAGGAATGGACACAAT 59.668 43.478 0.00 0.00 37.43 2.71
163 164 3.944015 CTGGAAGAGGAATGGACACAATC 59.056 47.826 0.00 0.00 34.07 2.67
164 165 3.330405 TGGAAGAGGAATGGACACAATCA 59.670 43.478 0.00 0.00 0.00 2.57
165 166 4.202556 TGGAAGAGGAATGGACACAATCAA 60.203 41.667 0.00 0.00 0.00 2.57
166 167 4.952335 GGAAGAGGAATGGACACAATCAAT 59.048 41.667 0.00 0.00 0.00 2.57
167 168 5.067023 GGAAGAGGAATGGACACAATCAATC 59.933 44.000 0.00 0.00 0.00 2.67
168 169 4.194640 AGAGGAATGGACACAATCAATCG 58.805 43.478 0.00 0.00 0.00 3.34
169 170 4.080919 AGAGGAATGGACACAATCAATCGA 60.081 41.667 0.00 0.00 0.00 3.59
170 171 4.588899 AGGAATGGACACAATCAATCGAA 58.411 39.130 0.00 0.00 0.00 3.71
171 172 4.637534 AGGAATGGACACAATCAATCGAAG 59.362 41.667 0.00 0.00 0.00 3.79
172 173 4.635765 GGAATGGACACAATCAATCGAAGA 59.364 41.667 0.00 0.00 45.75 2.87
173 174 5.123820 GGAATGGACACAATCAATCGAAGAA 59.876 40.000 0.00 0.00 43.58 2.52
174 175 5.808042 ATGGACACAATCAATCGAAGAAG 57.192 39.130 0.00 0.00 43.58 2.85
175 176 4.893608 TGGACACAATCAATCGAAGAAGA 58.106 39.130 0.00 0.00 43.58 2.87
176 177 5.304778 TGGACACAATCAATCGAAGAAGAA 58.695 37.500 0.00 0.00 43.58 2.52
177 178 5.762711 TGGACACAATCAATCGAAGAAGAAA 59.237 36.000 0.00 0.00 43.58 2.52
178 179 6.080406 GGACACAATCAATCGAAGAAGAAAC 58.920 40.000 0.00 0.00 43.58 2.78
179 180 6.002062 ACACAATCAATCGAAGAAGAAACC 57.998 37.500 0.00 0.00 43.58 3.27
180 181 5.765182 ACACAATCAATCGAAGAAGAAACCT 59.235 36.000 0.00 0.00 43.58 3.50
181 182 6.073003 ACACAATCAATCGAAGAAGAAACCTC 60.073 38.462 0.00 0.00 43.58 3.85
182 183 5.997746 ACAATCAATCGAAGAAGAAACCTCA 59.002 36.000 0.00 0.00 43.58 3.86
183 184 6.486657 ACAATCAATCGAAGAAGAAACCTCAA 59.513 34.615 0.00 0.00 43.58 3.02
184 185 6.734104 ATCAATCGAAGAAGAAACCTCAAG 57.266 37.500 0.00 0.00 43.58 3.02
185 186 5.853936 TCAATCGAAGAAGAAACCTCAAGA 58.146 37.500 0.00 0.00 43.58 3.02
186 187 5.928839 TCAATCGAAGAAGAAACCTCAAGAG 59.071 40.000 0.00 0.00 43.58 2.85
187 188 5.730296 ATCGAAGAAGAAACCTCAAGAGA 57.270 39.130 0.00 0.00 43.58 3.10
188 189 4.872664 TCGAAGAAGAAACCTCAAGAGAC 58.127 43.478 0.00 0.00 0.00 3.36
189 190 4.585162 TCGAAGAAGAAACCTCAAGAGACT 59.415 41.667 0.00 0.00 0.00 3.24
190 191 4.683781 CGAAGAAGAAACCTCAAGAGACTG 59.316 45.833 0.00 0.00 0.00 3.51
191 192 5.508153 CGAAGAAGAAACCTCAAGAGACTGA 60.508 44.000 0.00 0.00 0.00 3.41
192 193 6.432403 AAGAAGAAACCTCAAGAGACTGAT 57.568 37.500 0.00 0.00 0.00 2.90
193 194 6.036577 AGAAGAAACCTCAAGAGACTGATC 57.963 41.667 0.00 0.00 0.00 2.92
194 195 5.541868 AGAAGAAACCTCAAGAGACTGATCA 59.458 40.000 0.00 0.00 0.00 2.92
195 196 5.146010 AGAAACCTCAAGAGACTGATCAC 57.854 43.478 0.00 0.00 0.00 3.06
196 197 3.584406 AACCTCAAGAGACTGATCACG 57.416 47.619 0.00 0.00 0.00 4.35
197 198 1.821753 ACCTCAAGAGACTGATCACGG 59.178 52.381 0.00 0.00 0.00 4.94
198 199 2.095461 CCTCAAGAGACTGATCACGGA 58.905 52.381 0.00 0.00 0.00 4.69
199 200 2.692557 CCTCAAGAGACTGATCACGGAT 59.307 50.000 0.00 0.00 0.00 4.18
200 201 3.885901 CCTCAAGAGACTGATCACGGATA 59.114 47.826 0.00 0.00 0.00 2.59
201 202 4.522405 CCTCAAGAGACTGATCACGGATAT 59.478 45.833 0.00 0.00 0.00 1.63
202 203 5.707764 CCTCAAGAGACTGATCACGGATATA 59.292 44.000 0.00 0.00 0.00 0.86
203 204 6.128035 CCTCAAGAGACTGATCACGGATATAG 60.128 46.154 0.00 0.00 0.00 1.31
204 205 6.534634 TCAAGAGACTGATCACGGATATAGA 58.465 40.000 0.00 0.00 0.00 1.98
205 206 7.171653 TCAAGAGACTGATCACGGATATAGAT 58.828 38.462 0.00 0.00 0.00 1.98
206 207 8.322091 TCAAGAGACTGATCACGGATATAGATA 58.678 37.037 0.00 0.00 0.00 1.98
207 208 8.951243 CAAGAGACTGATCACGGATATAGATAA 58.049 37.037 0.00 0.00 0.00 1.75
208 209 9.693739 AAGAGACTGATCACGGATATAGATAAT 57.306 33.333 0.00 0.00 0.00 1.28
215 216 9.922477 TGATCACGGATATAGATAATACTTCCT 57.078 33.333 0.00 0.00 0.00 3.36
218 219 8.890718 TCACGGATATAGATAATACTTCCTTCG 58.109 37.037 0.00 0.00 0.00 3.79
219 220 8.675504 CACGGATATAGATAATACTTCCTTCGT 58.324 37.037 0.00 0.00 0.00 3.85
220 221 9.896645 ACGGATATAGATAATACTTCCTTCGTA 57.103 33.333 0.00 0.00 0.00 3.43
235 236 9.315525 ACTTCCTTCGTAAAGAAATATAAGAGC 57.684 33.333 0.00 0.00 38.57 4.09
236 237 7.925703 TCCTTCGTAAAGAAATATAAGAGCG 57.074 36.000 0.00 0.00 38.57 5.03
237 238 7.486647 TCCTTCGTAAAGAAATATAAGAGCGT 58.513 34.615 0.00 0.00 38.57 5.07
238 239 7.977853 TCCTTCGTAAAGAAATATAAGAGCGTT 59.022 33.333 0.00 0.00 38.57 4.84
239 240 8.267367 CCTTCGTAAAGAAATATAAGAGCGTTC 58.733 37.037 0.00 0.00 38.57 3.95
240 241 8.692110 TTCGTAAAGAAATATAAGAGCGTTCA 57.308 30.769 1.01 0.00 35.61 3.18
241 242 8.336498 TCGTAAAGAAATATAAGAGCGTTCAG 57.664 34.615 1.01 0.00 0.00 3.02
242 243 8.186163 TCGTAAAGAAATATAAGAGCGTTCAGA 58.814 33.333 1.01 0.00 0.00 3.27
243 244 8.260550 CGTAAAGAAATATAAGAGCGTTCAGAC 58.739 37.037 1.01 0.00 0.00 3.51
244 245 9.084164 GTAAAGAAATATAAGAGCGTTCAGACA 57.916 33.333 1.01 0.00 0.00 3.41
245 246 7.763172 AAGAAATATAAGAGCGTTCAGACAG 57.237 36.000 1.01 0.00 0.00 3.51
270 271 4.415846 GGGGGTAATAAAGAAGAGGGTCAT 59.584 45.833 0.00 0.00 0.00 3.06
298 300 3.187227 GCATGGTTCTATGCCAGATAACG 59.813 47.826 9.45 0.00 45.93 3.18
329 331 2.905996 ATGCTGTTTCGGCCCCTCA 61.906 57.895 0.00 0.00 34.37 3.86
331 333 1.678970 GCTGTTTCGGCCCCTCATT 60.679 57.895 0.00 0.00 0.00 2.57
332 334 1.250840 GCTGTTTCGGCCCCTCATTT 61.251 55.000 0.00 0.00 0.00 2.32
333 335 1.256812 CTGTTTCGGCCCCTCATTTT 58.743 50.000 0.00 0.00 0.00 1.82
335 337 1.203001 TGTTTCGGCCCCTCATTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
336 338 1.893137 GTTTCGGCCCCTCATTTTCTT 59.107 47.619 0.00 0.00 0.00 2.52
337 339 2.299013 GTTTCGGCCCCTCATTTTCTTT 59.701 45.455 0.00 0.00 0.00 2.52
338 340 2.302587 TCGGCCCCTCATTTTCTTTT 57.697 45.000 0.00 0.00 0.00 2.27
339 341 2.604139 TCGGCCCCTCATTTTCTTTTT 58.396 42.857 0.00 0.00 0.00 1.94
340 342 2.298729 TCGGCCCCTCATTTTCTTTTTG 59.701 45.455 0.00 0.00 0.00 2.44
341 343 2.426522 GGCCCCTCATTTTCTTTTTGC 58.573 47.619 0.00 0.00 0.00 3.68
342 344 2.068519 GCCCCTCATTTTCTTTTTGCG 58.931 47.619 0.00 0.00 0.00 4.85
343 345 2.687370 CCCCTCATTTTCTTTTTGCGG 58.313 47.619 0.00 0.00 0.00 5.69
344 346 2.612721 CCCCTCATTTTCTTTTTGCGGG 60.613 50.000 0.00 0.00 35.56 6.13
345 347 2.068519 CCTCATTTTCTTTTTGCGGGC 58.931 47.619 0.00 0.00 0.00 6.13
346 348 2.289010 CCTCATTTTCTTTTTGCGGGCT 60.289 45.455 0.00 0.00 0.00 5.19
347 349 2.733026 CTCATTTTCTTTTTGCGGGCTG 59.267 45.455 0.00 0.00 0.00 4.85
348 350 2.102252 TCATTTTCTTTTTGCGGGCTGT 59.898 40.909 0.00 0.00 0.00 4.40
349 351 2.682155 TTTTCTTTTTGCGGGCTGTT 57.318 40.000 0.00 0.00 0.00 3.16
350 352 2.682155 TTTCTTTTTGCGGGCTGTTT 57.318 40.000 0.00 0.00 0.00 2.83
351 353 2.217429 TTCTTTTTGCGGGCTGTTTC 57.783 45.000 0.00 0.00 0.00 2.78
352 354 0.030101 TCTTTTTGCGGGCTGTTTCG 59.970 50.000 0.00 0.00 0.00 3.46
353 355 0.939106 CTTTTTGCGGGCTGTTTCGG 60.939 55.000 0.00 0.00 0.00 4.30
354 356 2.962697 TTTTTGCGGGCTGTTTCGGC 62.963 55.000 0.00 0.00 34.56 5.54
496 1087 2.540265 TTAAACTTGCCCCGTCGTAA 57.460 45.000 0.00 0.00 0.00 3.18
644 1238 0.033228 GCATCTCCATCTCCGGTCTG 59.967 60.000 0.00 0.00 0.00 3.51
656 1250 4.554036 GGTCTGCCCCGGCTCATC 62.554 72.222 7.35 0.00 42.51 2.92
657 1251 3.474570 GTCTGCCCCGGCTCATCT 61.475 66.667 7.35 0.00 42.51 2.90
757 3112 2.071540 CTCACGCTGTCATTGTCATGT 58.928 47.619 0.00 0.00 0.00 3.21
803 3176 1.144057 CAGCCTGTATCGGTGGACC 59.856 63.158 0.00 0.00 0.00 4.46
906 3280 4.324991 GCCCCGTCCGGAACAAGT 62.325 66.667 5.23 0.00 37.50 3.16
975 3355 1.203187 TGGCTCCTCCTGTCTTGTAGT 60.203 52.381 0.00 0.00 35.26 2.73
1317 3700 1.773054 CGCTCATCATGCTGCTCACC 61.773 60.000 0.00 0.00 0.00 4.02
1351 3734 1.064611 TCTACTCCTGCTTCTACCGCT 60.065 52.381 0.00 0.00 0.00 5.52
1464 3847 1.518133 CCGCGAGCTCAAGAAGAGG 60.518 63.158 15.40 4.19 44.86 3.69
1486 3869 1.350193 CTTCGACATGAACCTCGGTG 58.650 55.000 0.00 0.00 31.87 4.94
1684 4081 3.067106 TCGATCTGTGCTTTTGTTCTCC 58.933 45.455 0.00 0.00 0.00 3.71
1711 4118 2.294233 ACGTCTAAAGTGTGCGTCCTTA 59.706 45.455 0.00 0.00 0.00 2.69
1739 4147 9.069082 GTAGTAGAAGAAGTAATCTCCATGCTA 57.931 37.037 0.00 0.00 37.42 3.49
1768 4177 4.992511 TGCGGTGCCGGTGTTACC 62.993 66.667 12.82 6.29 40.19 2.85
1910 4352 8.909423 ATATTAAGAGGAGAAGAGGATAAGGG 57.091 38.462 0.00 0.00 0.00 3.95
1926 4368 2.264794 GGCACCTCCAACGACGAT 59.735 61.111 0.00 0.00 34.01 3.73
1942 4384 4.110482 CGACGATCCGTAAATTTTCTCCT 58.890 43.478 0.00 0.00 41.37 3.69
1952 4394 3.356529 AATTTTCTCCTGCATCCGTCT 57.643 42.857 0.00 0.00 0.00 4.18
2013 4455 3.272334 CCATCCAACGCTAGCCGC 61.272 66.667 9.66 0.00 41.76 6.53
2021 4463 0.600255 AACGCTAGCCGCATACATCC 60.600 55.000 9.66 0.00 41.76 3.51
2030 4472 0.659427 CGCATACATCCTGCCAACAG 59.341 55.000 0.00 0.00 44.05 3.16
2031 4473 1.755179 GCATACATCCTGCCAACAGT 58.245 50.000 0.00 0.00 42.81 3.55
2043 4485 4.693566 CCTGCCAACAGTTCGAATTAACTA 59.306 41.667 0.00 0.00 42.81 2.24
2406 4881 1.452470 AAACTTGGCGTCAACGGGT 60.452 52.632 0.00 0.00 40.23 5.28
2507 4982 2.103042 GGACATGACAGCCTCGTGC 61.103 63.158 0.00 0.00 39.29 5.34
2542 5017 1.079127 CGGCCTCGATGTTGTCCTT 60.079 57.895 0.00 0.00 39.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.785243 TCTCACAAACGGATGTATGTAACA 58.215 37.500 0.00 0.00 43.86 2.41
2 3 6.097356 TCTCTCACAAACGGATGTATGTAAC 58.903 40.000 0.00 0.00 30.84 2.50
3 4 6.275494 TCTCTCACAAACGGATGTATGTAA 57.725 37.500 0.00 0.00 30.84 2.41
4 5 5.907866 TCTCTCACAAACGGATGTATGTA 57.092 39.130 0.00 0.00 30.84 2.29
5 6 4.801330 TCTCTCACAAACGGATGTATGT 57.199 40.909 0.00 0.00 30.84 2.29
6 7 5.171476 ACTTCTCTCACAAACGGATGTATG 58.829 41.667 0.00 0.00 30.84 2.39
7 8 5.407407 ACTTCTCTCACAAACGGATGTAT 57.593 39.130 0.00 0.00 30.84 2.29
8 9 4.866508 ACTTCTCTCACAAACGGATGTA 57.133 40.909 0.00 0.00 30.84 2.29
9 10 3.753294 ACTTCTCTCACAAACGGATGT 57.247 42.857 0.00 0.00 0.00 3.06
10 11 5.424121 AAAACTTCTCTCACAAACGGATG 57.576 39.130 0.00 0.00 0.00 3.51
38 39 9.590451 TCGAGTTAAAAATAATACTCCATTCGT 57.410 29.630 0.00 0.00 34.86 3.85
42 43 8.837389 GCCTTCGAGTTAAAAATAATACTCCAT 58.163 33.333 0.00 0.00 34.86 3.41
43 44 7.010738 CGCCTTCGAGTTAAAAATAATACTCCA 59.989 37.037 0.00 0.00 38.10 3.86
44 45 7.342942 CGCCTTCGAGTTAAAAATAATACTCC 58.657 38.462 0.00 0.00 38.10 3.85
45 46 7.342942 CCGCCTTCGAGTTAAAAATAATACTC 58.657 38.462 0.00 0.00 38.10 2.59
46 47 6.238293 GCCGCCTTCGAGTTAAAAATAATACT 60.238 38.462 0.00 0.00 38.10 2.12
47 48 5.905733 GCCGCCTTCGAGTTAAAAATAATAC 59.094 40.000 0.00 0.00 38.10 1.89
48 49 5.007921 GGCCGCCTTCGAGTTAAAAATAATA 59.992 40.000 0.71 0.00 38.10 0.98
49 50 4.201980 GGCCGCCTTCGAGTTAAAAATAAT 60.202 41.667 0.71 0.00 38.10 1.28
50 51 3.127376 GGCCGCCTTCGAGTTAAAAATAA 59.873 43.478 0.71 0.00 38.10 1.40
51 52 2.679336 GGCCGCCTTCGAGTTAAAAATA 59.321 45.455 0.71 0.00 38.10 1.40
52 53 1.471287 GGCCGCCTTCGAGTTAAAAAT 59.529 47.619 0.71 0.00 38.10 1.82
53 54 0.876399 GGCCGCCTTCGAGTTAAAAA 59.124 50.000 0.71 0.00 38.10 1.94
54 55 1.293267 CGGCCGCCTTCGAGTTAAAA 61.293 55.000 14.67 0.00 38.10 1.52
55 56 1.738830 CGGCCGCCTTCGAGTTAAA 60.739 57.895 14.67 0.00 38.10 1.52
56 57 2.125832 CGGCCGCCTTCGAGTTAA 60.126 61.111 14.67 0.00 38.10 2.01
57 58 3.376078 ACGGCCGCCTTCGAGTTA 61.376 61.111 28.58 0.00 38.10 2.24
63 64 2.557372 TTTTTCCACGGCCGCCTTC 61.557 57.895 28.58 0.00 0.00 3.46
64 65 2.519780 TTTTTCCACGGCCGCCTT 60.520 55.556 28.58 1.81 0.00 4.35
65 66 3.292159 GTTTTTCCACGGCCGCCT 61.292 61.111 28.58 2.80 0.00 5.52
66 67 2.428960 ATTGTTTTTCCACGGCCGCC 62.429 55.000 28.58 0.00 0.00 6.13
67 68 1.006688 ATTGTTTTTCCACGGCCGC 60.007 52.632 28.58 6.62 0.00 6.53
68 69 0.388006 GGATTGTTTTTCCACGGCCG 60.388 55.000 26.86 26.86 33.21 6.13
69 70 0.037697 GGGATTGTTTTTCCACGGCC 60.038 55.000 0.00 0.00 34.77 6.13
70 71 0.966179 AGGGATTGTTTTTCCACGGC 59.034 50.000 0.00 0.00 34.77 5.68
71 72 1.960689 ACAGGGATTGTTTTTCCACGG 59.039 47.619 0.00 0.00 36.31 4.94
72 73 2.621055 TGACAGGGATTGTTTTTCCACG 59.379 45.455 0.00 0.00 41.05 4.94
73 74 4.664150 TTGACAGGGATTGTTTTTCCAC 57.336 40.909 0.00 0.00 41.05 4.02
74 75 4.898265 TCATTGACAGGGATTGTTTTTCCA 59.102 37.500 0.00 0.00 41.05 3.53
75 76 5.467035 TCATTGACAGGGATTGTTTTTCC 57.533 39.130 0.00 0.00 41.05 3.13
76 77 5.011023 ACCTCATTGACAGGGATTGTTTTTC 59.989 40.000 0.00 0.00 41.05 2.29
77 78 4.901250 ACCTCATTGACAGGGATTGTTTTT 59.099 37.500 0.00 0.00 41.05 1.94
78 79 4.482990 ACCTCATTGACAGGGATTGTTTT 58.517 39.130 0.00 0.00 41.05 2.43
79 80 4.082125 GACCTCATTGACAGGGATTGTTT 58.918 43.478 0.00 0.00 41.05 2.83
80 81 3.074390 TGACCTCATTGACAGGGATTGTT 59.926 43.478 0.00 0.00 41.05 2.83
81 82 2.644299 TGACCTCATTGACAGGGATTGT 59.356 45.455 0.00 0.00 44.55 2.71
82 83 3.012518 GTGACCTCATTGACAGGGATTG 58.987 50.000 0.00 0.00 35.01 2.67
83 84 2.025887 GGTGACCTCATTGACAGGGATT 60.026 50.000 0.00 0.00 35.01 3.01
84 85 1.561542 GGTGACCTCATTGACAGGGAT 59.438 52.381 0.00 0.00 35.01 3.85
85 86 0.984230 GGTGACCTCATTGACAGGGA 59.016 55.000 0.00 0.00 35.01 4.20
86 87 0.391661 CGGTGACCTCATTGACAGGG 60.392 60.000 0.00 0.00 35.01 4.45
87 88 0.391661 CCGGTGACCTCATTGACAGG 60.392 60.000 0.00 0.00 37.03 4.00
88 89 0.608130 TCCGGTGACCTCATTGACAG 59.392 55.000 0.00 0.00 0.00 3.51
89 90 0.608130 CTCCGGTGACCTCATTGACA 59.392 55.000 0.00 0.00 0.00 3.58
90 91 0.895530 TCTCCGGTGACCTCATTGAC 59.104 55.000 0.00 0.00 0.00 3.18
91 92 0.895530 GTCTCCGGTGACCTCATTGA 59.104 55.000 23.20 0.00 0.00 2.57
92 93 0.458543 CGTCTCCGGTGACCTCATTG 60.459 60.000 26.45 10.95 33.70 2.82
93 94 0.611062 TCGTCTCCGGTGACCTCATT 60.611 55.000 26.45 0.00 33.70 2.57
94 95 0.611062 TTCGTCTCCGGTGACCTCAT 60.611 55.000 26.45 0.00 33.70 2.90
95 96 1.228337 TTCGTCTCCGGTGACCTCA 60.228 57.895 26.45 11.31 33.70 3.86
96 97 0.959372 TCTTCGTCTCCGGTGACCTC 60.959 60.000 26.45 6.79 33.70 3.85
97 98 1.074423 TCTTCGTCTCCGGTGACCT 59.926 57.895 26.45 0.00 33.70 3.85
98 99 1.212229 GTCTTCGTCTCCGGTGACC 59.788 63.158 26.45 11.60 33.71 4.02
99 100 0.313043 TTGTCTTCGTCTCCGGTGAC 59.687 55.000 23.68 23.68 37.29 3.67
100 101 1.034356 TTTGTCTTCGTCTCCGGTGA 58.966 50.000 0.00 0.06 33.95 4.02
101 102 1.860676 TTTTGTCTTCGTCTCCGGTG 58.139 50.000 0.00 0.00 33.95 4.94
102 103 2.833631 ATTTTGTCTTCGTCTCCGGT 57.166 45.000 0.00 0.00 33.95 5.28
103 104 3.991773 TGTTATTTTGTCTTCGTCTCCGG 59.008 43.478 0.00 0.00 33.95 5.14
104 105 5.347635 TGATGTTATTTTGTCTTCGTCTCCG 59.652 40.000 0.00 0.00 0.00 4.63
105 106 6.721571 TGATGTTATTTTGTCTTCGTCTCC 57.278 37.500 0.00 0.00 0.00 3.71
106 107 9.907576 CTATTGATGTTATTTTGTCTTCGTCTC 57.092 33.333 0.00 0.00 0.00 3.36
107 108 9.436957 ACTATTGATGTTATTTTGTCTTCGTCT 57.563 29.630 0.00 0.00 0.00 4.18
124 125 9.650539 CCTCTTCCAGTATTCATACTATTGATG 57.349 37.037 0.00 1.38 41.44 3.07
125 126 9.607333 TCCTCTTCCAGTATTCATACTATTGAT 57.393 33.333 0.00 0.00 41.44 2.57
126 127 9.434275 TTCCTCTTCCAGTATTCATACTATTGA 57.566 33.333 0.00 0.00 41.44 2.57
129 130 8.820831 CCATTCCTCTTCCAGTATTCATACTAT 58.179 37.037 0.00 0.00 41.44 2.12
130 131 8.010697 TCCATTCCTCTTCCAGTATTCATACTA 58.989 37.037 0.00 0.00 41.44 1.82
131 132 6.846505 TCCATTCCTCTTCCAGTATTCATACT 59.153 38.462 0.00 0.00 44.03 2.12
132 133 6.931840 GTCCATTCCTCTTCCAGTATTCATAC 59.068 42.308 0.00 0.00 0.00 2.39
133 134 6.615316 TGTCCATTCCTCTTCCAGTATTCATA 59.385 38.462 0.00 0.00 0.00 2.15
134 135 5.429762 TGTCCATTCCTCTTCCAGTATTCAT 59.570 40.000 0.00 0.00 0.00 2.57
135 136 4.782691 TGTCCATTCCTCTTCCAGTATTCA 59.217 41.667 0.00 0.00 0.00 2.57
136 137 5.119694 GTGTCCATTCCTCTTCCAGTATTC 58.880 45.833 0.00 0.00 0.00 1.75
137 138 4.536090 TGTGTCCATTCCTCTTCCAGTATT 59.464 41.667 0.00 0.00 0.00 1.89
138 139 4.104086 TGTGTCCATTCCTCTTCCAGTAT 58.896 43.478 0.00 0.00 0.00 2.12
139 140 3.516586 TGTGTCCATTCCTCTTCCAGTA 58.483 45.455 0.00 0.00 0.00 2.74
140 141 2.338809 TGTGTCCATTCCTCTTCCAGT 58.661 47.619 0.00 0.00 0.00 4.00
141 142 3.423539 TTGTGTCCATTCCTCTTCCAG 57.576 47.619 0.00 0.00 0.00 3.86
142 143 3.330405 TGATTGTGTCCATTCCTCTTCCA 59.670 43.478 0.00 0.00 0.00 3.53
143 144 3.955471 TGATTGTGTCCATTCCTCTTCC 58.045 45.455 0.00 0.00 0.00 3.46
144 145 5.220739 CGATTGATTGTGTCCATTCCTCTTC 60.221 44.000 0.00 0.00 0.00 2.87
145 146 4.637534 CGATTGATTGTGTCCATTCCTCTT 59.362 41.667 0.00 0.00 0.00 2.85
146 147 4.080919 TCGATTGATTGTGTCCATTCCTCT 60.081 41.667 0.00 0.00 0.00 3.69
147 148 4.191544 TCGATTGATTGTGTCCATTCCTC 58.808 43.478 0.00 0.00 0.00 3.71
148 149 4.220693 TCGATTGATTGTGTCCATTCCT 57.779 40.909 0.00 0.00 0.00 3.36
149 150 4.635765 TCTTCGATTGATTGTGTCCATTCC 59.364 41.667 0.00 0.00 0.00 3.01
150 151 5.801350 TCTTCGATTGATTGTGTCCATTC 57.199 39.130 0.00 0.00 0.00 2.67
151 152 5.939883 TCTTCTTCGATTGATTGTGTCCATT 59.060 36.000 0.00 0.00 0.00 3.16
152 153 5.491070 TCTTCTTCGATTGATTGTGTCCAT 58.509 37.500 0.00 0.00 0.00 3.41
153 154 4.893608 TCTTCTTCGATTGATTGTGTCCA 58.106 39.130 0.00 0.00 0.00 4.02
154 155 5.862924 TTCTTCTTCGATTGATTGTGTCC 57.137 39.130 0.00 0.00 0.00 4.02
155 156 6.073003 AGGTTTCTTCTTCGATTGATTGTGTC 60.073 38.462 0.00 0.00 0.00 3.67
156 157 5.765182 AGGTTTCTTCTTCGATTGATTGTGT 59.235 36.000 0.00 0.00 0.00 3.72
157 158 6.073058 TGAGGTTTCTTCTTCGATTGATTGTG 60.073 38.462 0.00 0.00 0.00 3.33
158 159 5.997746 TGAGGTTTCTTCTTCGATTGATTGT 59.002 36.000 0.00 0.00 0.00 2.71
159 160 6.486253 TGAGGTTTCTTCTTCGATTGATTG 57.514 37.500 0.00 0.00 0.00 2.67
160 161 6.936900 TCTTGAGGTTTCTTCTTCGATTGATT 59.063 34.615 0.00 0.00 0.00 2.57
161 162 6.467677 TCTTGAGGTTTCTTCTTCGATTGAT 58.532 36.000 0.00 0.00 0.00 2.57
162 163 5.853936 TCTTGAGGTTTCTTCTTCGATTGA 58.146 37.500 0.00 0.00 0.00 2.57
163 164 5.928839 TCTCTTGAGGTTTCTTCTTCGATTG 59.071 40.000 0.00 0.00 0.00 2.67
164 165 5.929415 GTCTCTTGAGGTTTCTTCTTCGATT 59.071 40.000 0.00 0.00 0.00 3.34
165 166 5.245075 AGTCTCTTGAGGTTTCTTCTTCGAT 59.755 40.000 0.00 0.00 0.00 3.59
166 167 4.585162 AGTCTCTTGAGGTTTCTTCTTCGA 59.415 41.667 0.00 0.00 0.00 3.71
167 168 4.683781 CAGTCTCTTGAGGTTTCTTCTTCG 59.316 45.833 0.00 0.00 0.00 3.79
168 169 5.848406 TCAGTCTCTTGAGGTTTCTTCTTC 58.152 41.667 0.00 0.00 0.00 2.87
169 170 5.878406 TCAGTCTCTTGAGGTTTCTTCTT 57.122 39.130 0.00 0.00 0.00 2.52
170 171 5.541868 TGATCAGTCTCTTGAGGTTTCTTCT 59.458 40.000 0.00 0.00 0.00 2.85
171 172 5.637387 GTGATCAGTCTCTTGAGGTTTCTTC 59.363 44.000 0.00 0.00 0.00 2.87
172 173 5.546526 GTGATCAGTCTCTTGAGGTTTCTT 58.453 41.667 0.00 0.00 0.00 2.52
173 174 4.321601 CGTGATCAGTCTCTTGAGGTTTCT 60.322 45.833 0.00 0.00 0.00 2.52
174 175 3.923461 CGTGATCAGTCTCTTGAGGTTTC 59.077 47.826 0.00 0.00 0.00 2.78
175 176 3.306364 CCGTGATCAGTCTCTTGAGGTTT 60.306 47.826 0.00 0.00 0.00 3.27
176 177 2.232452 CCGTGATCAGTCTCTTGAGGTT 59.768 50.000 0.00 0.00 0.00 3.50
177 178 1.821753 CCGTGATCAGTCTCTTGAGGT 59.178 52.381 0.00 0.00 0.00 3.85
178 179 2.095461 TCCGTGATCAGTCTCTTGAGG 58.905 52.381 0.00 0.00 0.00 3.86
179 180 5.703978 ATATCCGTGATCAGTCTCTTGAG 57.296 43.478 0.00 0.00 0.00 3.02
180 181 6.534634 TCTATATCCGTGATCAGTCTCTTGA 58.465 40.000 0.00 0.00 0.00 3.02
181 182 6.809630 TCTATATCCGTGATCAGTCTCTTG 57.190 41.667 0.00 0.00 0.00 3.02
182 183 9.693739 ATTATCTATATCCGTGATCAGTCTCTT 57.306 33.333 0.00 0.00 0.00 2.85
189 190 9.922477 AGGAAGTATTATCTATATCCGTGATCA 57.078 33.333 0.00 0.00 0.00 2.92
192 193 8.890718 CGAAGGAAGTATTATCTATATCCGTGA 58.109 37.037 0.00 0.00 0.00 4.35
193 194 8.675504 ACGAAGGAAGTATTATCTATATCCGTG 58.324 37.037 0.00 0.00 0.00 4.94
194 195 8.804912 ACGAAGGAAGTATTATCTATATCCGT 57.195 34.615 0.00 0.00 0.00 4.69
209 210 9.315525 GCTCTTATATTTCTTTACGAAGGAAGT 57.684 33.333 0.00 0.00 33.92 3.01
210 211 8.480853 CGCTCTTATATTTCTTTACGAAGGAAG 58.519 37.037 0.00 0.00 33.92 3.46
211 212 7.977853 ACGCTCTTATATTTCTTTACGAAGGAA 59.022 33.333 0.00 0.00 34.90 3.36
212 213 7.486647 ACGCTCTTATATTTCTTTACGAAGGA 58.513 34.615 0.00 0.00 33.56 3.36
213 214 7.695869 ACGCTCTTATATTTCTTTACGAAGG 57.304 36.000 0.00 0.00 33.56 3.46
214 215 8.804743 TGAACGCTCTTATATTTCTTTACGAAG 58.195 33.333 0.00 0.00 32.21 3.79
215 216 8.692110 TGAACGCTCTTATATTTCTTTACGAA 57.308 30.769 0.00 0.00 0.00 3.85
216 217 8.186163 TCTGAACGCTCTTATATTTCTTTACGA 58.814 33.333 0.00 0.00 0.00 3.43
217 218 8.260550 GTCTGAACGCTCTTATATTTCTTTACG 58.739 37.037 0.00 0.00 0.00 3.18
218 219 9.084164 TGTCTGAACGCTCTTATATTTCTTTAC 57.916 33.333 0.00 0.00 0.00 2.01
219 220 9.302345 CTGTCTGAACGCTCTTATATTTCTTTA 57.698 33.333 0.00 0.00 0.00 1.85
220 221 8.035394 TCTGTCTGAACGCTCTTATATTTCTTT 58.965 33.333 0.00 0.00 0.00 2.52
221 222 7.548097 TCTGTCTGAACGCTCTTATATTTCTT 58.452 34.615 0.00 0.00 0.00 2.52
222 223 7.101652 TCTGTCTGAACGCTCTTATATTTCT 57.898 36.000 0.00 0.00 0.00 2.52
223 224 6.419413 CCTCTGTCTGAACGCTCTTATATTTC 59.581 42.308 0.00 0.00 0.00 2.17
224 225 6.276847 CCTCTGTCTGAACGCTCTTATATTT 58.723 40.000 0.00 0.00 0.00 1.40
225 226 5.221342 CCCTCTGTCTGAACGCTCTTATATT 60.221 44.000 0.00 0.00 0.00 1.28
226 227 4.279671 CCCTCTGTCTGAACGCTCTTATAT 59.720 45.833 0.00 0.00 0.00 0.86
227 228 3.632604 CCCTCTGTCTGAACGCTCTTATA 59.367 47.826 0.00 0.00 0.00 0.98
228 229 2.428890 CCCTCTGTCTGAACGCTCTTAT 59.571 50.000 0.00 0.00 0.00 1.73
229 230 1.819288 CCCTCTGTCTGAACGCTCTTA 59.181 52.381 0.00 0.00 0.00 2.10
230 231 0.605589 CCCTCTGTCTGAACGCTCTT 59.394 55.000 0.00 0.00 0.00 2.85
231 232 1.254284 CCCCTCTGTCTGAACGCTCT 61.254 60.000 0.00 0.00 0.00 4.09
232 233 1.216710 CCCCTCTGTCTGAACGCTC 59.783 63.158 0.00 0.00 0.00 5.03
233 234 2.286523 CCCCCTCTGTCTGAACGCT 61.287 63.158 0.00 0.00 0.00 5.07
234 235 1.255667 TACCCCCTCTGTCTGAACGC 61.256 60.000 0.00 0.00 0.00 4.84
235 236 1.263356 TTACCCCCTCTGTCTGAACG 58.737 55.000 0.00 0.00 0.00 3.95
236 237 5.189145 TCTTTATTACCCCCTCTGTCTGAAC 59.811 44.000 0.00 0.00 0.00 3.18
237 238 5.347124 TCTTTATTACCCCCTCTGTCTGAA 58.653 41.667 0.00 0.00 0.00 3.02
238 239 4.955335 TCTTTATTACCCCCTCTGTCTGA 58.045 43.478 0.00 0.00 0.00 3.27
239 240 5.425539 TCTTCTTTATTACCCCCTCTGTCTG 59.574 44.000 0.00 0.00 0.00 3.51
240 241 5.600749 TCTTCTTTATTACCCCCTCTGTCT 58.399 41.667 0.00 0.00 0.00 3.41
241 242 5.163290 CCTCTTCTTTATTACCCCCTCTGTC 60.163 48.000 0.00 0.00 0.00 3.51
242 243 4.722279 CCTCTTCTTTATTACCCCCTCTGT 59.278 45.833 0.00 0.00 0.00 3.41
243 244 4.103311 CCCTCTTCTTTATTACCCCCTCTG 59.897 50.000 0.00 0.00 0.00 3.35
244 245 4.265817 ACCCTCTTCTTTATTACCCCCTCT 60.266 45.833 0.00 0.00 0.00 3.69
245 246 4.045736 ACCCTCTTCTTTATTACCCCCTC 58.954 47.826 0.00 0.00 0.00 4.30
270 271 0.463654 GCATAGAACCATGCCACCGA 60.464 55.000 0.00 0.00 44.55 4.69
298 300 6.564873 GCCGAAACAGCATGATCTAGTTATTC 60.565 42.308 0.00 0.00 39.69 1.75
329 331 2.908688 ACAGCCCGCAAAAAGAAAAT 57.091 40.000 0.00 0.00 0.00 1.82
331 333 2.545731 GAAACAGCCCGCAAAAAGAAA 58.454 42.857 0.00 0.00 0.00 2.52
332 334 1.535015 CGAAACAGCCCGCAAAAAGAA 60.535 47.619 0.00 0.00 0.00 2.52
333 335 0.030101 CGAAACAGCCCGCAAAAAGA 59.970 50.000 0.00 0.00 0.00 2.52
335 337 1.066587 CCGAAACAGCCCGCAAAAA 59.933 52.632 0.00 0.00 0.00 1.94
336 338 2.725008 CCGAAACAGCCCGCAAAA 59.275 55.556 0.00 0.00 0.00 2.44
337 339 3.972276 GCCGAAACAGCCCGCAAA 61.972 61.111 0.00 0.00 0.00 3.68
344 346 3.064324 ATGCAGGGCCGAAACAGC 61.064 61.111 0.00 0.00 0.00 4.40
345 347 2.703798 CCATGCAGGGCCGAAACAG 61.704 63.158 3.55 0.00 0.00 3.16
346 348 2.676121 CCATGCAGGGCCGAAACA 60.676 61.111 3.55 0.00 0.00 2.83
550 1141 1.303799 GCACTGACTGATGGCACCAG 61.304 60.000 7.49 7.49 37.64 4.00
644 1238 3.934962 GAGGAGATGAGCCGGGGC 61.935 72.222 2.18 0.18 42.33 5.80
650 1244 2.479389 CGTGAAGACTGAGGAGATGAGC 60.479 54.545 0.00 0.00 0.00 4.26
656 1250 0.172352 GAGGCGTGAAGACTGAGGAG 59.828 60.000 0.00 0.00 39.26 3.69
657 1251 0.539669 TGAGGCGTGAAGACTGAGGA 60.540 55.000 0.00 0.00 39.26 3.71
757 3112 1.542328 CCGTTCATGTCCACTGGTTGA 60.542 52.381 0.00 0.00 0.00 3.18
803 3176 2.222574 CGCGATGATAACCATGCATACG 60.223 50.000 0.00 0.00 35.17 3.06
975 3355 0.666274 CCTCTTGTGCACGCGAACTA 60.666 55.000 15.93 4.19 0.00 2.24
1317 3700 4.435436 TAGACGCACTGGCAGCCG 62.435 66.667 21.67 21.67 41.24 5.52
1684 4081 2.097396 CGCACACTTTAGACGTGTCTTG 60.097 50.000 7.97 3.03 43.26 3.02
1711 4118 8.364142 GCATGGAGATTACTTCTTCTACTACAT 58.636 37.037 0.00 0.00 33.74 2.29
1733 4141 1.595489 GCAAAGACGCCGAATAGCATG 60.595 52.381 0.00 0.00 0.00 4.06
1739 4147 2.358247 ACCGCAAAGACGCCGAAT 60.358 55.556 0.00 0.00 0.00 3.34
1768 4177 6.560253 ATTGTACAGAAACCTGCAAAGTAG 57.440 37.500 0.00 0.00 35.09 2.57
1900 4342 1.134068 GTTGGAGGTGCCCTTATCCTC 60.134 57.143 0.00 0.00 44.78 3.71
1904 4346 0.252197 GTCGTTGGAGGTGCCCTTAT 59.748 55.000 0.00 0.00 31.76 1.73
1910 4352 1.810030 GGATCGTCGTTGGAGGTGC 60.810 63.158 0.00 0.00 0.00 5.01
1917 4359 5.199424 AGAAAATTTACGGATCGTCGTTG 57.801 39.130 2.33 0.00 43.59 4.10
1922 4364 3.621715 GCAGGAGAAAATTTACGGATCGT 59.378 43.478 0.00 0.00 44.35 3.73
1926 4368 3.945285 GGATGCAGGAGAAAATTTACGGA 59.055 43.478 0.00 0.00 0.00 4.69
1958 4400 1.561769 TATGTGGACTGGTGCCCCTG 61.562 60.000 0.00 0.00 35.86 4.45
1976 4418 1.826921 GTCCTCCCGCATCCGTCTA 60.827 63.158 0.00 0.00 0.00 2.59
1996 4438 3.272334 GCGGCTAGCGTTGGATGG 61.272 66.667 9.00 0.00 35.41 3.51
2013 4455 2.352651 CGAACTGTTGGCAGGATGTATG 59.647 50.000 0.00 0.00 46.62 2.39
2141 4584 9.113876 GCACCGCTTAATTGATATAAATGTAAC 57.886 33.333 0.00 0.00 0.00 2.50
2367 4841 0.320073 GTGGGTTGAACATCGTCGGA 60.320 55.000 0.00 0.00 0.00 4.55
2421 4896 2.291043 GCTCGGGTCCCAAGAAGGA 61.291 63.158 9.12 0.00 41.22 3.36
2456 4931 0.528470 GCAGCGAGGAAGAGTAGTGT 59.472 55.000 0.00 0.00 0.00 3.55
2522 4997 2.434185 GACAACATCGAGGCCGCA 60.434 61.111 7.44 0.00 35.37 5.69
2542 5017 0.108089 CGAGACTGACGAGGAGGAGA 60.108 60.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.