Multiple sequence alignment - TraesCS2D01G241100

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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 TraesCS2D01G241100 chr2D 100.000 2771 0 0 1 2771 260867694 260864924 0.000000e+00 5118.0
1 TraesCS2D01G241100 chr2D 95.286 2270 60 15 503 2771 241269964 241272187 0.000000e+00 3555.0
2 TraesCS2D01G241100 chr2D 95.557 1913 56 4 512 2424 451467953 451469836 0.000000e+00 3035.0
3 TraesCS2D01G241100 chr2D 89.854 2326 134 37 501 2771 520043077 520045355 0.000000e+00 2894.0
4 TraesCS2D01G241100 chr2D 96.235 1514 48 1 501 2014 613419776 613421280 0.000000e+00 2471.0
5 TraesCS2D01G241100 chr2D 91.489 1645 96 12 508 2152 35331899 35330299 0.000000e+00 2222.0
6 TraesCS2D01G241100 chr2D 93.037 675 23 9 2097 2771 613421282 613421932 0.000000e+00 965.0
7 TraesCS2D01G241100 chr2D 93.849 504 31 0 4 507 248368684 248369187 0.000000e+00 760.0
8 TraesCS2D01G241100 chr2D 93.439 503 33 0 2 504 262679911 262680413 0.000000e+00 747.0
9 TraesCS2D01G241100 chr2D 93.083 506 34 1 2 507 402202902 402202398 0.000000e+00 739.0
10 TraesCS2D01G241100 chr2D 97.759 357 7 1 2416 2771 451487533 451487889 5.070000e-172 614.0
11 TraesCS2D01G241100 chr2D 89.773 264 15 4 499 761 241274316 241274064 7.400000e-86 327.0
12 TraesCS2D01G241100 chr2D 89.575 259 14 5 504 761 260861768 260862014 1.600000e-82 316.0
13 TraesCS2D01G241100 chr2D 87.692 260 20 4 503 762 35326531 35326778 2.700000e-75 292.0
14 TraesCS2D01G241100 chr5D 96.670 2132 68 2 640 2771 26959808 26957680 0.000000e+00 3541.0
15 TraesCS2D01G241100 chr5D 94.340 53 3 0 2107 2159 26958297 26958245 6.360000e-12 82.4
16 TraesCS2D01G241100 chr7D 90.596 2297 136 26 512 2771 151511976 151514229 0.000000e+00 2972.0
17 TraesCS2D01G241100 chr7D 94.071 506 30 0 2 507 291211403 291211908 0.000000e+00 769.0
18 TraesCS2D01G241100 chr7D 93.384 393 16 2 507 899 564928011 564928393 8.610000e-160 573.0
19 TraesCS2D01G241100 chr7D 87.410 278 18 8 488 761 564929099 564928835 1.250000e-78 303.0
20 TraesCS2D01G241100 chr6B 88.518 2308 168 30 496 2770 494076423 494078666 0.000000e+00 2704.0
21 TraesCS2D01G241100 chr6B 89.137 672 38 18 2135 2771 28119041 28119712 0.000000e+00 804.0
22 TraesCS2D01G241100 chr6B 76.281 527 69 30 2280 2771 260208318 260207813 2.150000e-56 230.0
23 TraesCS2D01G241100 chr6B 93.333 60 3 1 2107 2165 28119057 28119116 1.370000e-13 87.9
24 TraesCS2D01G241100 chr6A 88.042 2308 173 50 508 2771 144491473 144493721 0.000000e+00 2638.0
25 TraesCS2D01G241100 chr6A 94.103 390 13 4 2382 2771 596357344 596357723 3.980000e-163 584.0
26 TraesCS2D01G241100 chr6A 85.282 496 41 15 1952 2447 596356913 596357376 1.490000e-132 483.0
27 TraesCS2D01G241100 chr6D 95.599 1545 58 2 508 2052 114017560 114016026 0.000000e+00 2468.0
28 TraesCS2D01G241100 chr6D 90.310 258 13 4 505 761 114015080 114015326 7.400000e-86 327.0
29 TraesCS2D01G241100 chr7A 89.185 1951 158 25 506 2447 471263892 471261986 0.000000e+00 2385.0
30 TraesCS2D01G241100 chr5B 93.281 1533 90 3 507 2037 260234931 260236452 0.000000e+00 2248.0
31 TraesCS2D01G241100 chr5B 94.311 334 18 1 2390 2722 260236756 260237089 6.850000e-141 510.0
32 TraesCS2D01G241100 chr5B 91.855 221 18 0 2227 2447 260236560 260236780 2.680000e-80 309.0
33 TraesCS2D01G241100 chr5B 100.000 29 0 0 2173 2201 260236534 260236562 1.000000e-03 54.7
34 TraesCS2D01G241100 chr3A 91.590 1415 96 11 491 1897 478913578 478914977 0.000000e+00 1932.0
35 TraesCS2D01G241100 chr3A 90.040 251 21 2 1952 2201 478914993 478915240 3.440000e-84 322.0
36 TraesCS2D01G241100 chr1D 93.676 506 31 1 2 507 292938323 292938827 0.000000e+00 756.0
37 TraesCS2D01G241100 chr1D 93.083 506 35 0 2 507 230501889 230502394 0.000000e+00 741.0
38 TraesCS2D01G241100 chr4D 93.110 508 31 4 2 507 230427572 230427067 0.000000e+00 741.0
39 TraesCS2D01G241100 chr4D 93.056 504 35 0 4 507 275315065 275314562 0.000000e+00 737.0
40 TraesCS2D01G241100 chr1A 93.083 506 33 2 2 507 236573411 236573914 0.000000e+00 739.0
41 TraesCS2D01G241100 chr2A 88.845 251 24 2 1952 2201 673358973 673359220 3.470000e-79 305.0


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 TraesCS2D01G241100 chr2D 260864924 260867694 2770 True 5118.000 5118 100.00000 1 2771 1 chr2D.!!$R3 2770
1 TraesCS2D01G241100 chr2D 241269964 241272187 2223 False 3555.000 3555 95.28600 503 2771 1 chr2D.!!$F2 2268
2 TraesCS2D01G241100 chr2D 451467953 451469836 1883 False 3035.000 3035 95.55700 512 2424 1 chr2D.!!$F6 1912
3 TraesCS2D01G241100 chr2D 520043077 520045355 2278 False 2894.000 2894 89.85400 501 2771 1 chr2D.!!$F8 2270
4 TraesCS2D01G241100 chr2D 35330299 35331899 1600 True 2222.000 2222 91.48900 508 2152 1 chr2D.!!$R1 1644
5 TraesCS2D01G241100 chr2D 613419776 613421932 2156 False 1718.000 2471 94.63600 501 2771 2 chr2D.!!$F9 2270
6 TraesCS2D01G241100 chr2D 248368684 248369187 503 False 760.000 760 93.84900 4 507 1 chr2D.!!$F3 503
7 TraesCS2D01G241100 chr2D 262679911 262680413 502 False 747.000 747 93.43900 2 504 1 chr2D.!!$F5 502
8 TraesCS2D01G241100 chr2D 402202398 402202902 504 True 739.000 739 93.08300 2 507 1 chr2D.!!$R4 505
9 TraesCS2D01G241100 chr5D 26957680 26959808 2128 True 1811.700 3541 95.50500 640 2771 2 chr5D.!!$R1 2131
10 TraesCS2D01G241100 chr7D 151511976 151514229 2253 False 2972.000 2972 90.59600 512 2771 1 chr7D.!!$F1 2259
11 TraesCS2D01G241100 chr7D 291211403 291211908 505 False 769.000 769 94.07100 2 507 1 chr7D.!!$F2 505
12 TraesCS2D01G241100 chr6B 494076423 494078666 2243 False 2704.000 2704 88.51800 496 2770 1 chr6B.!!$F1 2274
13 TraesCS2D01G241100 chr6B 28119041 28119712 671 False 445.950 804 91.23500 2107 2771 2 chr6B.!!$F2 664
14 TraesCS2D01G241100 chr6B 260207813 260208318 505 True 230.000 230 76.28100 2280 2771 1 chr6B.!!$R1 491
15 TraesCS2D01G241100 chr6A 144491473 144493721 2248 False 2638.000 2638 88.04200 508 2771 1 chr6A.!!$F1 2263
16 TraesCS2D01G241100 chr6A 596356913 596357723 810 False 533.500 584 89.69250 1952 2771 2 chr6A.!!$F2 819
17 TraesCS2D01G241100 chr6D 114016026 114017560 1534 True 2468.000 2468 95.59900 508 2052 1 chr6D.!!$R1 1544
18 TraesCS2D01G241100 chr7A 471261986 471263892 1906 True 2385.000 2385 89.18500 506 2447 1 chr7A.!!$R1 1941
19 TraesCS2D01G241100 chr5B 260234931 260237089 2158 False 780.425 2248 94.86175 507 2722 4 chr5B.!!$F1 2215
20 TraesCS2D01G241100 chr3A 478913578 478915240 1662 False 1127.000 1932 90.81500 491 2201 2 chr3A.!!$F1 1710
21 TraesCS2D01G241100 chr1D 292938323 292938827 504 False 756.000 756 93.67600 2 507 1 chr1D.!!$F2 505
22 TraesCS2D01G241100 chr1D 230501889 230502394 505 False 741.000 741 93.08300 2 507 1 chr1D.!!$F1 505
23 TraesCS2D01G241100 chr4D 230427067 230427572 505 True 741.000 741 93.11000 2 507 1 chr4D.!!$R1 505
24 TraesCS2D01G241100 chr4D 275314562 275315065 503 True 737.000 737 93.05600 4 507 1 chr4D.!!$R2 503
25 TraesCS2D01G241100 chr1A 236573411 236573914 503 False 739.000 739 93.08300 2 507 1 chr1A.!!$F1 505

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
988 994 0.033228 GAGCCATGTCCTGATCTCCG 59.967 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 2605 1.965754 GAGGGACAGCACAGCCTAGG 61.966 65.0 3.67 3.67 0.0 3.02 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
33 34 1.860906 AGGTCCTCCTCTACCTAAGGG 59.139 57.143 0.00 0.00 44.40 3.95
34 35 2.843693 AGGTCCTCCTCTACCTAAGGGT 60.844 54.545 0.00 0.00 44.40 4.34
35 36 2.668625 GTCCTCCTCTACCTAAGGGTG 58.331 57.143 0.00 0.00 46.75 4.61
36 37 2.244252 GTCCTCCTCTACCTAAGGGTGA 59.756 54.545 0.00 0.00 46.75 4.02
37 38 3.117054 GTCCTCCTCTACCTAAGGGTGAT 60.117 52.174 0.00 0.00 46.75 3.06
38 39 3.140519 TCCTCCTCTACCTAAGGGTGATC 59.859 52.174 0.00 0.00 46.75 2.92
39 40 3.117093 CCTCCTCTACCTAAGGGTGATCA 60.117 52.174 0.00 0.00 46.75 2.92
40 41 4.449968 CCTCCTCTACCTAAGGGTGATCAT 60.450 50.000 0.00 0.00 46.75 2.45
41 42 4.483950 TCCTCTACCTAAGGGTGATCATG 58.516 47.826 0.00 0.00 46.75 3.07
42 43 4.078571 TCCTCTACCTAAGGGTGATCATGT 60.079 45.833 0.00 0.00 46.75 3.21
43 44 4.039730 CCTCTACCTAAGGGTGATCATGTG 59.960 50.000 0.00 0.00 46.75 3.21
44 45 4.620723 TCTACCTAAGGGTGATCATGTGT 58.379 43.478 0.00 0.00 46.75 3.72
45 46 5.030147 TCTACCTAAGGGTGATCATGTGTT 58.970 41.667 0.00 0.00 46.75 3.32
46 47 4.657814 ACCTAAGGGTGATCATGTGTTT 57.342 40.909 0.00 0.00 45.43 2.83
47 48 4.335416 ACCTAAGGGTGATCATGTGTTTG 58.665 43.478 0.00 0.00 45.43 2.93
48 49 4.042809 ACCTAAGGGTGATCATGTGTTTGA 59.957 41.667 0.00 0.00 45.43 2.69
49 50 5.009631 CCTAAGGGTGATCATGTGTTTGAA 58.990 41.667 0.00 0.00 0.00 2.69
50 51 5.653769 CCTAAGGGTGATCATGTGTTTGAAT 59.346 40.000 0.00 0.00 0.00 2.57
51 52 6.153340 CCTAAGGGTGATCATGTGTTTGAATT 59.847 38.462 0.00 0.00 0.00 2.17
52 53 7.339212 CCTAAGGGTGATCATGTGTTTGAATTA 59.661 37.037 0.00 0.00 0.00 1.40
53 54 7.537596 AAGGGTGATCATGTGTTTGAATTAA 57.462 32.000 0.00 0.00 0.00 1.40
54 55 7.537596 AGGGTGATCATGTGTTTGAATTAAA 57.462 32.000 0.00 0.00 0.00 1.52
55 56 7.961351 AGGGTGATCATGTGTTTGAATTAAAA 58.039 30.769 0.00 0.00 0.00 1.52
56 57 7.872483 AGGGTGATCATGTGTTTGAATTAAAAC 59.128 33.333 11.04 11.04 39.90 2.43
57 58 7.655328 GGGTGATCATGTGTTTGAATTAAAACA 59.345 33.333 15.90 15.90 45.38 2.83
68 69 9.658799 TGTTTGAATTAAAACAATTTCCAGACA 57.341 25.926 17.26 0.00 44.79 3.41
69 70 9.914923 GTTTGAATTAAAACAATTTCCAGACAC 57.085 29.630 12.80 0.00 39.39 3.67
70 71 9.883142 TTTGAATTAAAACAATTTCCAGACACT 57.117 25.926 0.00 0.00 0.00 3.55
71 72 9.883142 TTGAATTAAAACAATTTCCAGACACTT 57.117 25.926 0.00 0.00 0.00 3.16
72 73 9.883142 TGAATTAAAACAATTTCCAGACACTTT 57.117 25.926 0.00 0.00 0.00 2.66
74 75 9.883142 AATTAAAACAATTTCCAGACACTTTGA 57.117 25.926 0.00 0.00 0.00 2.69
75 76 9.883142 ATTAAAACAATTTCCAGACACTTTGAA 57.117 25.926 0.00 0.00 0.00 2.69
76 77 9.712305 TTAAAACAATTTCCAGACACTTTGAAA 57.288 25.926 0.00 0.00 0.00 2.69
77 78 8.791327 AAAACAATTTCCAGACACTTTGAAAT 57.209 26.923 0.00 0.00 38.66 2.17
78 79 9.883142 AAAACAATTTCCAGACACTTTGAAATA 57.117 25.926 0.00 0.00 36.65 1.40
80 81 9.480053 AACAATTTCCAGACACTTTGAAATATG 57.520 29.630 0.00 0.00 36.65 1.78
81 82 7.599998 ACAATTTCCAGACACTTTGAAATATGC 59.400 33.333 0.00 0.00 36.65 3.14
82 83 6.899393 TTTCCAGACACTTTGAAATATGCT 57.101 33.333 0.00 0.00 0.00 3.79
83 84 6.899393 TTCCAGACACTTTGAAATATGCTT 57.101 33.333 0.00 0.00 0.00 3.91
84 85 7.994425 TTCCAGACACTTTGAAATATGCTTA 57.006 32.000 0.00 0.00 0.00 3.09
85 86 8.579850 TTCCAGACACTTTGAAATATGCTTAT 57.420 30.769 0.00 0.00 0.00 1.73
86 87 8.213518 TCCAGACACTTTGAAATATGCTTATC 57.786 34.615 0.00 0.00 0.00 1.75
87 88 8.049117 TCCAGACACTTTGAAATATGCTTATCT 58.951 33.333 0.00 0.00 0.00 1.98
88 89 8.680903 CCAGACACTTTGAAATATGCTTATCTT 58.319 33.333 0.00 0.00 0.00 2.40
89 90 9.499585 CAGACACTTTGAAATATGCTTATCTTG 57.500 33.333 0.00 0.00 0.00 3.02
90 91 9.453572 AGACACTTTGAAATATGCTTATCTTGA 57.546 29.630 0.00 0.00 0.00 3.02
132 133 9.982651 TCATGTTATTATTAGTGCTAACCTCTC 57.017 33.333 0.00 0.00 0.00 3.20
133 134 9.764363 CATGTTATTATTAGTGCTAACCTCTCA 57.236 33.333 0.00 0.00 0.00 3.27
134 135 9.988815 ATGTTATTATTAGTGCTAACCTCTCAG 57.011 33.333 0.00 0.00 0.00 3.35
135 136 9.197306 TGTTATTATTAGTGCTAACCTCTCAGA 57.803 33.333 0.00 0.00 0.00 3.27
138 139 7.476540 TTATTAGTGCTAACCTCTCAGAACA 57.523 36.000 0.00 0.00 0.00 3.18
139 140 6.552445 ATTAGTGCTAACCTCTCAGAACAT 57.448 37.500 0.00 0.00 0.00 2.71
140 141 4.199432 AGTGCTAACCTCTCAGAACATG 57.801 45.455 0.00 0.00 0.00 3.21
141 142 3.834813 AGTGCTAACCTCTCAGAACATGA 59.165 43.478 0.00 0.00 36.21 3.07
142 143 4.284490 AGTGCTAACCTCTCAGAACATGAA 59.716 41.667 0.00 0.00 37.52 2.57
143 144 4.629200 GTGCTAACCTCTCAGAACATGAAG 59.371 45.833 0.00 0.00 37.52 3.02
144 145 4.528206 TGCTAACCTCTCAGAACATGAAGA 59.472 41.667 0.00 0.00 37.52 2.87
145 146 5.012046 TGCTAACCTCTCAGAACATGAAGAA 59.988 40.000 0.00 0.00 37.52 2.52
146 147 5.580297 GCTAACCTCTCAGAACATGAAGAAG 59.420 44.000 0.00 0.00 37.52 2.85
147 148 5.815233 AACCTCTCAGAACATGAAGAAGA 57.185 39.130 0.00 0.00 37.52 2.87
148 149 5.815233 ACCTCTCAGAACATGAAGAAGAA 57.185 39.130 0.00 0.00 37.52 2.52
149 150 6.179906 ACCTCTCAGAACATGAAGAAGAAA 57.820 37.500 0.00 0.00 37.52 2.52
150 151 6.229733 ACCTCTCAGAACATGAAGAAGAAAG 58.770 40.000 0.00 0.00 37.52 2.62
151 152 6.042552 ACCTCTCAGAACATGAAGAAGAAAGA 59.957 38.462 0.00 0.00 37.52 2.52
152 153 7.104939 CCTCTCAGAACATGAAGAAGAAAGAT 58.895 38.462 0.00 0.00 37.52 2.40
153 154 7.607223 CCTCTCAGAACATGAAGAAGAAAGATT 59.393 37.037 0.00 0.00 37.52 2.40
154 155 9.650539 CTCTCAGAACATGAAGAAGAAAGATTA 57.349 33.333 0.00 0.00 37.52 1.75
177 178 8.900511 TTATTGAAAATTCTGAAGAAGCATCG 57.099 30.769 0.00 0.00 37.48 3.84
178 179 6.558771 TTGAAAATTCTGAAGAAGCATCGA 57.441 33.333 0.00 0.00 37.48 3.59
179 180 6.174451 TGAAAATTCTGAAGAAGCATCGAG 57.826 37.500 0.00 0.00 37.48 4.04
180 181 4.612932 AAATTCTGAAGAAGCATCGAGC 57.387 40.909 0.00 0.00 46.19 5.03
196 197 7.079182 GCATCGAGCTACTATTGAGTATACT 57.921 40.000 4.68 4.68 37.53 2.12
197 198 7.184106 GCATCGAGCTACTATTGAGTATACTC 58.816 42.308 23.53 23.53 37.53 2.59
198 199 7.065324 GCATCGAGCTACTATTGAGTATACTCT 59.935 40.741 28.53 15.28 41.00 3.24
199 200 8.941977 CATCGAGCTACTATTGAGTATACTCTT 58.058 37.037 28.53 19.68 43.25 2.85
201 202 9.993454 TCGAGCTACTATTGAGTATACTCTTAA 57.007 33.333 28.53 18.24 43.25 1.85
222 223 9.561069 TCTTAATGATCTTAAAGGCATTAGTCC 57.439 33.333 0.00 0.00 35.42 3.85
223 224 8.691661 TTAATGATCTTAAAGGCATTAGTCCC 57.308 34.615 0.00 0.00 35.42 4.46
224 225 5.708736 TGATCTTAAAGGCATTAGTCCCA 57.291 39.130 0.00 0.00 0.00 4.37
225 226 5.437060 TGATCTTAAAGGCATTAGTCCCAC 58.563 41.667 0.00 0.00 0.00 4.61
226 227 5.191722 TGATCTTAAAGGCATTAGTCCCACT 59.808 40.000 0.00 0.00 0.00 4.00
227 228 5.099042 TCTTAAAGGCATTAGTCCCACTC 57.901 43.478 0.00 0.00 0.00 3.51
228 229 4.783227 TCTTAAAGGCATTAGTCCCACTCT 59.217 41.667 0.00 0.00 0.00 3.24
229 230 3.636153 AAAGGCATTAGTCCCACTCTC 57.364 47.619 0.00 0.00 0.00 3.20
230 231 2.559381 AGGCATTAGTCCCACTCTCT 57.441 50.000 0.00 0.00 0.00 3.10
231 232 2.114616 AGGCATTAGTCCCACTCTCTG 58.885 52.381 0.00 0.00 0.00 3.35
232 233 1.834263 GGCATTAGTCCCACTCTCTGT 59.166 52.381 0.00 0.00 0.00 3.41
233 234 2.159028 GGCATTAGTCCCACTCTCTGTC 60.159 54.545 0.00 0.00 0.00 3.51
234 235 2.497675 GCATTAGTCCCACTCTCTGTCA 59.502 50.000 0.00 0.00 0.00 3.58
235 236 3.430098 GCATTAGTCCCACTCTCTGTCAG 60.430 52.174 0.00 0.00 0.00 3.51
236 237 1.840737 TAGTCCCACTCTCTGTCAGC 58.159 55.000 0.00 0.00 0.00 4.26
237 238 0.178950 AGTCCCACTCTCTGTCAGCA 60.179 55.000 0.00 0.00 0.00 4.41
238 239 0.037790 GTCCCACTCTCTGTCAGCAC 60.038 60.000 0.00 0.00 0.00 4.40
239 240 0.469892 TCCCACTCTCTGTCAGCACA 60.470 55.000 0.00 0.00 0.00 4.57
240 241 0.612229 CCCACTCTCTGTCAGCACAT 59.388 55.000 0.00 0.00 0.00 3.21
241 242 1.675116 CCCACTCTCTGTCAGCACATG 60.675 57.143 0.00 0.00 0.00 3.21
242 243 1.274447 CCACTCTCTGTCAGCACATGA 59.726 52.381 0.00 0.00 34.79 3.07
243 244 2.093606 CCACTCTCTGTCAGCACATGAT 60.094 50.000 0.00 0.00 40.92 2.45
244 245 3.597255 CACTCTCTGTCAGCACATGATT 58.403 45.455 0.00 0.00 40.92 2.57
245 246 4.382362 CCACTCTCTGTCAGCACATGATTA 60.382 45.833 0.00 0.00 40.92 1.75
246 247 5.173664 CACTCTCTGTCAGCACATGATTAA 58.826 41.667 0.00 0.00 40.92 1.40
247 248 5.816258 CACTCTCTGTCAGCACATGATTAAT 59.184 40.000 0.00 0.00 40.92 1.40
248 249 6.982724 CACTCTCTGTCAGCACATGATTAATA 59.017 38.462 0.00 0.00 40.92 0.98
249 250 7.656542 CACTCTCTGTCAGCACATGATTAATAT 59.343 37.037 0.00 0.00 40.92 1.28
250 251 7.656542 ACTCTCTGTCAGCACATGATTAATATG 59.343 37.037 0.00 0.00 40.92 1.78
251 252 6.932960 TCTCTGTCAGCACATGATTAATATGG 59.067 38.462 0.00 0.00 40.92 2.74
252 253 6.829849 TCTGTCAGCACATGATTAATATGGA 58.170 36.000 0.00 0.00 40.92 3.41
253 254 7.281841 TCTGTCAGCACATGATTAATATGGAA 58.718 34.615 0.00 0.00 40.92 3.53
254 255 7.227314 TCTGTCAGCACATGATTAATATGGAAC 59.773 37.037 0.00 0.00 40.92 3.62
255 256 6.262944 TGTCAGCACATGATTAATATGGAACC 59.737 38.462 0.00 0.00 40.92 3.62
256 257 6.488006 GTCAGCACATGATTAATATGGAACCT 59.512 38.462 0.00 0.00 40.92 3.50
257 258 6.487668 TCAGCACATGATTAATATGGAACCTG 59.512 38.462 0.00 0.00 31.12 4.00
258 259 5.771666 AGCACATGATTAATATGGAACCTGG 59.228 40.000 0.00 0.00 0.00 4.45
259 260 5.536161 GCACATGATTAATATGGAACCTGGT 59.464 40.000 0.00 0.00 0.00 4.00
260 261 6.515531 GCACATGATTAATATGGAACCTGGTG 60.516 42.308 0.00 0.00 0.00 4.17
261 262 5.536161 ACATGATTAATATGGAACCTGGTGC 59.464 40.000 0.00 0.00 0.00 5.01
262 263 5.387113 TGATTAATATGGAACCTGGTGCT 57.613 39.130 4.46 0.00 0.00 4.40
263 264 6.508030 TGATTAATATGGAACCTGGTGCTA 57.492 37.500 4.46 0.00 0.00 3.49
264 265 6.905736 TGATTAATATGGAACCTGGTGCTAA 58.094 36.000 4.46 0.00 0.00 3.09
265 266 7.350382 TGATTAATATGGAACCTGGTGCTAAA 58.650 34.615 4.46 0.00 0.00 1.85
266 267 7.284489 TGATTAATATGGAACCTGGTGCTAAAC 59.716 37.037 4.46 0.00 0.00 2.01
275 276 3.857638 GGTGCTAAACCCGTTGTTG 57.142 52.632 0.00 0.00 44.02 3.33
276 277 1.310904 GGTGCTAAACCCGTTGTTGA 58.689 50.000 0.00 0.00 44.02 3.18
277 278 1.883926 GGTGCTAAACCCGTTGTTGAT 59.116 47.619 0.00 0.00 44.02 2.57
278 279 2.095415 GGTGCTAAACCCGTTGTTGATC 60.095 50.000 0.00 0.00 44.02 2.92
279 280 2.550606 GTGCTAAACCCGTTGTTGATCA 59.449 45.455 0.00 0.00 37.23 2.92
280 281 2.550606 TGCTAAACCCGTTGTTGATCAC 59.449 45.455 0.00 0.00 37.23 3.06
281 282 2.095415 GCTAAACCCGTTGTTGATCACC 60.095 50.000 0.00 0.00 37.23 4.02
282 283 2.060050 AAACCCGTTGTTGATCACCA 57.940 45.000 0.00 0.00 37.23 4.17
283 284 2.060050 AACCCGTTGTTGATCACCAA 57.940 45.000 0.91 0.91 35.31 3.67
292 293 2.635444 GTTGATCACCAACGACGTTTG 58.365 47.619 11.24 10.55 44.76 2.93
293 294 2.226602 TGATCACCAACGACGTTTGA 57.773 45.000 17.66 16.43 0.00 2.69
294 295 2.552031 TGATCACCAACGACGTTTGAA 58.448 42.857 17.66 6.48 0.00 2.69
295 296 3.135225 TGATCACCAACGACGTTTGAAT 58.865 40.909 17.66 10.48 0.00 2.57
296 297 3.185594 TGATCACCAACGACGTTTGAATC 59.814 43.478 17.66 17.26 0.00 2.52
297 298 1.868498 TCACCAACGACGTTTGAATCC 59.132 47.619 17.66 0.00 0.00 3.01
298 299 1.871039 CACCAACGACGTTTGAATCCT 59.129 47.619 17.66 0.00 0.00 3.24
299 300 3.061322 CACCAACGACGTTTGAATCCTA 58.939 45.455 17.66 0.00 0.00 2.94
300 301 3.495377 CACCAACGACGTTTGAATCCTAA 59.505 43.478 17.66 0.00 0.00 2.69
301 302 3.744426 ACCAACGACGTTTGAATCCTAAG 59.256 43.478 17.66 0.13 0.00 2.18
302 303 3.991773 CCAACGACGTTTGAATCCTAAGA 59.008 43.478 11.24 0.00 0.00 2.10
303 304 4.630069 CCAACGACGTTTGAATCCTAAGAT 59.370 41.667 11.24 0.00 0.00 2.40
304 305 5.445939 CCAACGACGTTTGAATCCTAAGATG 60.446 44.000 11.24 0.00 31.29 2.90
305 306 5.068234 ACGACGTTTGAATCCTAAGATGA 57.932 39.130 0.00 0.00 31.29 2.92
306 307 5.475719 ACGACGTTTGAATCCTAAGATGAA 58.524 37.500 0.00 0.00 31.29 2.57
307 308 5.929992 ACGACGTTTGAATCCTAAGATGAAA 59.070 36.000 0.00 0.00 31.29 2.69
308 309 6.594159 ACGACGTTTGAATCCTAAGATGAAAT 59.406 34.615 0.00 0.00 31.29 2.17
309 310 7.762615 ACGACGTTTGAATCCTAAGATGAAATA 59.237 33.333 0.00 0.00 31.29 1.40
310 311 8.600625 CGACGTTTGAATCCTAAGATGAAATAA 58.399 33.333 0.00 0.00 31.29 1.40
311 312 9.922305 GACGTTTGAATCCTAAGATGAAATAAG 57.078 33.333 0.00 0.00 31.29 1.73
312 313 9.449719 ACGTTTGAATCCTAAGATGAAATAAGT 57.550 29.630 0.00 0.00 31.29 2.24
313 314 9.708222 CGTTTGAATCCTAAGATGAAATAAGTG 57.292 33.333 0.00 0.00 31.29 3.16
315 316 9.753674 TTTGAATCCTAAGATGAAATAAGTGGT 57.246 29.630 0.00 0.00 31.29 4.16
321 322 9.886132 TCCTAAGATGAAATAAGTGGTAAGAAC 57.114 33.333 0.00 0.00 0.00 3.01
322 323 9.892130 CCTAAGATGAAATAAGTGGTAAGAACT 57.108 33.333 0.00 0.00 0.00 3.01
325 326 9.793259 AAGATGAAATAAGTGGTAAGAACTGAA 57.207 29.630 0.00 0.00 0.00 3.02
326 327 9.793259 AGATGAAATAAGTGGTAAGAACTGAAA 57.207 29.630 0.00 0.00 0.00 2.69
336 337 9.740710 AGTGGTAAGAACTGAAATATTAAAGCT 57.259 29.630 0.00 0.00 0.00 3.74
345 346 9.631452 AACTGAAATATTAAAGCTTCTTGAAGC 57.369 29.630 23.24 23.24 45.81 3.86
360 361 9.061435 GCTTCTTGAAGCAGGTATAATTTATCT 57.939 33.333 25.03 0.00 44.85 1.98
366 367 9.658799 TGAAGCAGGTATAATTTATCTCATAGC 57.341 33.333 0.00 0.00 0.00 2.97
367 368 9.883142 GAAGCAGGTATAATTTATCTCATAGCT 57.117 33.333 0.00 0.00 33.24 3.32
368 369 9.664332 AAGCAGGTATAATTTATCTCATAGCTG 57.336 33.333 14.38 14.38 45.57 4.24
369 370 9.040259 AGCAGGTATAATTTATCTCATAGCTGA 57.960 33.333 19.69 0.00 45.62 4.26
370 371 9.829507 GCAGGTATAATTTATCTCATAGCTGAT 57.170 33.333 19.69 0.00 45.62 2.90
380 381 8.759481 TTATCTCATAGCTGATAGTAGATGGG 57.241 38.462 0.00 0.00 0.00 4.00
381 382 6.146140 TCTCATAGCTGATAGTAGATGGGT 57.854 41.667 0.00 0.00 0.00 4.51
382 383 7.272144 TCTCATAGCTGATAGTAGATGGGTA 57.728 40.000 0.00 0.00 0.00 3.69
383 384 7.699878 TCTCATAGCTGATAGTAGATGGGTAA 58.300 38.462 0.00 0.00 0.00 2.85
384 385 7.831690 TCTCATAGCTGATAGTAGATGGGTAAG 59.168 40.741 0.00 0.00 0.00 2.34
385 386 7.471041 TCATAGCTGATAGTAGATGGGTAAGT 58.529 38.462 0.00 0.00 0.00 2.24
386 387 7.612244 TCATAGCTGATAGTAGATGGGTAAGTC 59.388 40.741 0.00 0.00 0.00 3.01
387 388 5.081032 AGCTGATAGTAGATGGGTAAGTCC 58.919 45.833 0.00 0.00 0.00 3.85
399 400 2.774687 GGTAAGTCCCGTTCATTGTGT 58.225 47.619 0.00 0.00 0.00 3.72
400 401 2.740447 GGTAAGTCCCGTTCATTGTGTC 59.260 50.000 0.00 0.00 0.00 3.67
401 402 1.892209 AAGTCCCGTTCATTGTGTCC 58.108 50.000 0.00 0.00 0.00 4.02
402 403 0.036306 AGTCCCGTTCATTGTGTCCC 59.964 55.000 0.00 0.00 0.00 4.46
403 404 0.036306 GTCCCGTTCATTGTGTCCCT 59.964 55.000 0.00 0.00 0.00 4.20
404 405 1.276989 GTCCCGTTCATTGTGTCCCTA 59.723 52.381 0.00 0.00 0.00 3.53
405 406 1.979308 TCCCGTTCATTGTGTCCCTAA 59.021 47.619 0.00 0.00 0.00 2.69
406 407 2.027561 TCCCGTTCATTGTGTCCCTAAG 60.028 50.000 0.00 0.00 0.00 2.18
407 408 2.027561 CCCGTTCATTGTGTCCCTAAGA 60.028 50.000 0.00 0.00 0.00 2.10
408 409 3.558321 CCCGTTCATTGTGTCCCTAAGAA 60.558 47.826 0.00 0.00 0.00 2.52
409 410 3.684788 CCGTTCATTGTGTCCCTAAGAAG 59.315 47.826 0.00 0.00 0.00 2.85
410 411 3.684788 CGTTCATTGTGTCCCTAAGAAGG 59.315 47.826 0.00 0.00 43.25 3.46
424 425 6.809976 CCTAAGAAGGGAGGTATTACTGTT 57.190 41.667 0.00 0.00 39.48 3.16
425 426 6.583562 CCTAAGAAGGGAGGTATTACTGTTG 58.416 44.000 0.00 0.00 39.48 3.33
426 427 6.156429 CCTAAGAAGGGAGGTATTACTGTTGT 59.844 42.308 0.00 0.00 39.48 3.32
427 428 6.449830 AAGAAGGGAGGTATTACTGTTGTT 57.550 37.500 0.00 0.00 0.00 2.83
428 429 6.051179 AGAAGGGAGGTATTACTGTTGTTC 57.949 41.667 0.00 0.00 0.00 3.18
429 430 4.838904 AGGGAGGTATTACTGTTGTTCC 57.161 45.455 0.00 0.00 0.00 3.62
430 431 4.436079 AGGGAGGTATTACTGTTGTTCCT 58.564 43.478 0.00 0.00 0.00 3.36
431 432 5.596763 AGGGAGGTATTACTGTTGTTCCTA 58.403 41.667 0.00 0.00 0.00 2.94
432 433 6.027482 AGGGAGGTATTACTGTTGTTCCTAA 58.973 40.000 0.00 0.00 0.00 2.69
433 434 6.677076 AGGGAGGTATTACTGTTGTTCCTAAT 59.323 38.462 0.00 0.00 0.00 1.73
434 435 6.766467 GGGAGGTATTACTGTTGTTCCTAATG 59.234 42.308 0.00 0.00 0.00 1.90
435 436 7.365295 GGGAGGTATTACTGTTGTTCCTAATGA 60.365 40.741 0.00 0.00 0.00 2.57
436 437 8.211629 GGAGGTATTACTGTTGTTCCTAATGAT 58.788 37.037 0.00 0.00 0.00 2.45
466 467 9.696917 AATGAACTTATTCCACAAAGAATTGTC 57.303 29.630 0.00 0.00 38.49 3.18
467 468 8.231692 TGAACTTATTCCACAAAGAATTGTCA 57.768 30.769 0.00 0.00 38.49 3.58
468 469 8.859090 TGAACTTATTCCACAAAGAATTGTCAT 58.141 29.630 0.00 0.00 38.49 3.06
469 470 9.696917 GAACTTATTCCACAAAGAATTGTCATT 57.303 29.630 0.00 0.00 46.78 2.57
470 471 9.480053 AACTTATTCCACAAAGAATTGTCATTG 57.520 29.630 0.00 0.00 46.78 2.82
471 472 8.090214 ACTTATTCCACAAAGAATTGTCATTGG 58.910 33.333 0.00 0.00 46.78 3.16
472 473 5.867903 TTCCACAAAGAATTGTCATTGGT 57.132 34.783 0.00 0.00 46.78 3.67
473 474 5.867903 TCCACAAAGAATTGTCATTGGTT 57.132 34.783 0.00 0.00 46.78 3.67
474 475 6.968263 TCCACAAAGAATTGTCATTGGTTA 57.032 33.333 0.00 0.00 46.78 2.85
475 476 6.744112 TCCACAAAGAATTGTCATTGGTTAC 58.256 36.000 0.00 0.00 46.78 2.50
476 477 6.322456 TCCACAAAGAATTGTCATTGGTTACA 59.678 34.615 0.00 0.00 46.78 2.41
477 478 6.642131 CCACAAAGAATTGTCATTGGTTACAG 59.358 38.462 0.00 0.00 46.78 2.74
478 479 7.424803 CACAAAGAATTGTCATTGGTTACAGA 58.575 34.615 0.00 0.00 46.78 3.41
479 480 7.920151 CACAAAGAATTGTCATTGGTTACAGAA 59.080 33.333 0.00 0.00 46.78 3.02
480 481 8.641541 ACAAAGAATTGTCATTGGTTACAGAAT 58.358 29.630 0.00 0.00 46.78 2.40
481 482 8.918658 CAAAGAATTGTCATTGGTTACAGAATG 58.081 33.333 0.00 0.00 33.82 2.67
482 483 7.161773 AGAATTGTCATTGGTTACAGAATGG 57.838 36.000 6.53 0.00 43.62 3.16
483 484 6.721208 AGAATTGTCATTGGTTACAGAATGGT 59.279 34.615 6.53 0.00 43.62 3.55
484 485 7.888021 AGAATTGTCATTGGTTACAGAATGGTA 59.112 33.333 6.53 0.00 43.62 3.25
485 486 8.415950 AATTGTCATTGGTTACAGAATGGTAA 57.584 30.769 6.53 0.00 43.62 2.85
486 487 8.593945 ATTGTCATTGGTTACAGAATGGTAAT 57.406 30.769 6.53 5.48 43.62 1.89
487 488 8.415950 TTGTCATTGGTTACAGAATGGTAATT 57.584 30.769 6.53 0.00 43.62 1.40
488 489 7.825681 TGTCATTGGTTACAGAATGGTAATTG 58.174 34.615 6.53 0.00 43.62 2.32
489 490 7.667635 TGTCATTGGTTACAGAATGGTAATTGA 59.332 33.333 6.53 0.00 43.62 2.57
786 792 5.045869 CACTTCCTAGTCCAAATCCCTAACA 60.046 44.000 0.00 0.00 30.26 2.41
988 994 0.033228 GAGCCATGTCCTGATCTCCG 59.967 60.000 0.00 0.00 0.00 4.63
994 1000 0.904865 TGTCCTGATCTCCGGCACTT 60.905 55.000 0.00 0.00 0.00 3.16
1316 1322 2.296190 TGAAGTACAAGAGCAAGCTCGA 59.704 45.455 15.67 1.31 46.90 4.04
1657 1663 1.739562 CGTGGTCCTCTGCTTGCTC 60.740 63.158 0.00 0.00 0.00 4.26
1858 1874 4.868171 GTGTTGTACTGTGTCTTCAGTTCA 59.132 41.667 4.72 3.74 44.92 3.18
1969 2004 7.816945 AATTTCTATTTGTGTAATGTGCTGC 57.183 32.000 0.00 0.00 0.00 5.25
2171 2281 5.067674 TGAAACACAAGTTCTGCAGCTTAAT 59.932 36.000 9.47 0.00 36.84 1.40
2218 2328 7.703195 AACACAAGTTCATGCAAGTAGCACG 62.703 44.000 0.00 0.00 45.94 5.34
2239 2349 3.064931 GTCACCAGCAACCTACTAACAC 58.935 50.000 0.00 0.00 0.00 3.32
2248 2358 4.820173 GCAACCTACTAACACTTTGAAGGT 59.180 41.667 0.00 0.00 37.47 3.50
2271 2381 9.143155 AGGTTCTAAACAACATAAATTGTCCTT 57.857 29.630 0.00 0.00 42.01 3.36
2310 2537 2.107378 TCAAACATGCTAACCCTGGTGA 59.893 45.455 0.00 0.00 0.00 4.02
2571 2940 9.019656 ACAATTGTTAGGTATTTCACATTGCTA 57.980 29.630 4.92 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.588899 TCAAACACATGATCACCCTTAGG 58.411 43.478 0.00 0.00 40.04 2.69
27 28 6.764308 ATTCAAACACATGATCACCCTTAG 57.236 37.500 0.00 0.00 0.00 2.18
28 29 8.642935 TTAATTCAAACACATGATCACCCTTA 57.357 30.769 0.00 0.00 0.00 2.69
29 30 7.537596 TTAATTCAAACACATGATCACCCTT 57.462 32.000 0.00 0.00 0.00 3.95
30 31 7.537596 TTTAATTCAAACACATGATCACCCT 57.462 32.000 0.00 0.00 0.00 4.34
31 32 7.655328 TGTTTTAATTCAAACACATGATCACCC 59.345 33.333 12.75 0.00 40.88 4.61
32 33 8.586570 TGTTTTAATTCAAACACATGATCACC 57.413 30.769 12.75 0.00 40.88 4.02
40 41 9.658799 TCTGGAAATTGTTTTAATTCAAACACA 57.341 25.926 15.70 10.12 44.51 3.72
41 42 9.914923 GTCTGGAAATTGTTTTAATTCAAACAC 57.085 29.630 15.70 6.31 44.51 3.32
42 43 9.658799 TGTCTGGAAATTGTTTTAATTCAAACA 57.341 25.926 12.75 12.75 43.42 2.83
43 44 9.914923 GTGTCTGGAAATTGTTTTAATTCAAAC 57.085 29.630 8.07 8.07 37.20 2.93
44 45 9.883142 AGTGTCTGGAAATTGTTTTAATTCAAA 57.117 25.926 0.00 0.00 0.00 2.69
45 46 9.883142 AAGTGTCTGGAAATTGTTTTAATTCAA 57.117 25.926 0.00 0.00 0.00 2.69
46 47 9.883142 AAAGTGTCTGGAAATTGTTTTAATTCA 57.117 25.926 0.00 0.00 0.00 2.57
48 49 9.883142 TCAAAGTGTCTGGAAATTGTTTTAATT 57.117 25.926 0.00 0.00 0.00 1.40
49 50 9.883142 TTCAAAGTGTCTGGAAATTGTTTTAAT 57.117 25.926 0.00 0.00 0.00 1.40
50 51 9.712305 TTTCAAAGTGTCTGGAAATTGTTTTAA 57.288 25.926 0.00 0.00 0.00 1.52
51 52 9.883142 ATTTCAAAGTGTCTGGAAATTGTTTTA 57.117 25.926 0.00 0.00 36.79 1.52
52 53 8.791327 ATTTCAAAGTGTCTGGAAATTGTTTT 57.209 26.923 0.00 0.00 36.79 2.43
54 55 9.480053 CATATTTCAAAGTGTCTGGAAATTGTT 57.520 29.630 0.00 0.00 39.76 2.83
55 56 7.599998 GCATATTTCAAAGTGTCTGGAAATTGT 59.400 33.333 0.00 0.00 39.76 2.71
56 57 7.816031 AGCATATTTCAAAGTGTCTGGAAATTG 59.184 33.333 0.00 0.00 39.76 2.32
57 58 7.899973 AGCATATTTCAAAGTGTCTGGAAATT 58.100 30.769 0.00 0.00 39.76 1.82
58 59 7.472334 AGCATATTTCAAAGTGTCTGGAAAT 57.528 32.000 0.00 0.00 41.41 2.17
59 60 6.899393 AGCATATTTCAAAGTGTCTGGAAA 57.101 33.333 0.00 0.00 34.17 3.13
60 61 6.899393 AAGCATATTTCAAAGTGTCTGGAA 57.101 33.333 0.00 0.00 0.00 3.53
61 62 8.049117 AGATAAGCATATTTCAAAGTGTCTGGA 58.951 33.333 0.00 0.00 0.00 3.86
62 63 8.218338 AGATAAGCATATTTCAAAGTGTCTGG 57.782 34.615 0.00 0.00 0.00 3.86
63 64 9.499585 CAAGATAAGCATATTTCAAAGTGTCTG 57.500 33.333 0.00 0.00 0.00 3.51
64 65 9.453572 TCAAGATAAGCATATTTCAAAGTGTCT 57.546 29.630 0.00 0.00 0.00 3.41
106 107 9.982651 GAGAGGTTAGCACTAATAATAACATGA 57.017 33.333 0.00 0.00 31.25 3.07
107 108 9.764363 TGAGAGGTTAGCACTAATAATAACATG 57.236 33.333 0.00 0.00 31.25 3.21
108 109 9.988815 CTGAGAGGTTAGCACTAATAATAACAT 57.011 33.333 0.00 0.00 31.25 2.71
109 110 9.197306 TCTGAGAGGTTAGCACTAATAATAACA 57.803 33.333 0.00 0.00 31.25 2.41
112 113 9.197306 TGTTCTGAGAGGTTAGCACTAATAATA 57.803 33.333 0.00 0.00 0.00 0.98
113 114 8.079211 TGTTCTGAGAGGTTAGCACTAATAAT 57.921 34.615 0.00 0.00 0.00 1.28
114 115 7.476540 TGTTCTGAGAGGTTAGCACTAATAA 57.523 36.000 0.00 0.00 0.00 1.40
115 116 7.342026 TCATGTTCTGAGAGGTTAGCACTAATA 59.658 37.037 0.00 0.00 0.00 0.98
116 117 6.155221 TCATGTTCTGAGAGGTTAGCACTAAT 59.845 38.462 0.00 0.00 0.00 1.73
117 118 5.480422 TCATGTTCTGAGAGGTTAGCACTAA 59.520 40.000 0.00 0.00 0.00 2.24
118 119 5.016831 TCATGTTCTGAGAGGTTAGCACTA 58.983 41.667 0.00 0.00 0.00 2.74
119 120 3.834813 TCATGTTCTGAGAGGTTAGCACT 59.165 43.478 0.00 0.00 0.00 4.40
120 121 4.193826 TCATGTTCTGAGAGGTTAGCAC 57.806 45.455 0.00 0.00 0.00 4.40
121 122 4.528206 TCTTCATGTTCTGAGAGGTTAGCA 59.472 41.667 0.00 0.00 34.68 3.49
122 123 5.078411 TCTTCATGTTCTGAGAGGTTAGC 57.922 43.478 0.00 0.00 34.68 3.09
123 124 6.929625 TCTTCTTCATGTTCTGAGAGGTTAG 58.070 40.000 0.00 0.00 34.68 2.34
124 125 6.918067 TCTTCTTCATGTTCTGAGAGGTTA 57.082 37.500 0.00 0.00 34.68 2.85
125 126 5.815233 TCTTCTTCATGTTCTGAGAGGTT 57.185 39.130 0.00 0.00 34.68 3.50
126 127 5.815233 TTCTTCTTCATGTTCTGAGAGGT 57.185 39.130 0.00 0.00 34.68 3.85
127 128 6.462500 TCTTTCTTCTTCATGTTCTGAGAGG 58.538 40.000 0.00 0.00 34.68 3.69
128 129 8.550710 AATCTTTCTTCTTCATGTTCTGAGAG 57.449 34.615 0.00 0.00 34.68 3.20
151 152 9.512435 CGATGCTTCTTCAGAATTTTCAATAAT 57.488 29.630 0.00 0.00 33.01 1.28
152 153 8.729756 TCGATGCTTCTTCAGAATTTTCAATAA 58.270 29.630 0.00 0.00 33.01 1.40
153 154 8.267620 TCGATGCTTCTTCAGAATTTTCAATA 57.732 30.769 0.00 0.00 33.01 1.90
154 155 7.149569 TCGATGCTTCTTCAGAATTTTCAAT 57.850 32.000 0.00 0.00 33.01 2.57
155 156 6.558771 TCGATGCTTCTTCAGAATTTTCAA 57.441 33.333 0.00 0.00 33.01 2.69
156 157 5.391310 GCTCGATGCTTCTTCAGAATTTTCA 60.391 40.000 0.00 0.00 38.95 2.69
157 158 5.027099 GCTCGATGCTTCTTCAGAATTTTC 58.973 41.667 0.00 0.00 38.95 2.29
158 159 4.979388 GCTCGATGCTTCTTCAGAATTTT 58.021 39.130 0.00 0.00 38.95 1.82
159 160 4.612932 GCTCGATGCTTCTTCAGAATTT 57.387 40.909 0.00 0.00 38.95 1.82
172 173 7.065324 AGAGTATACTCAATAGTAGCTCGATGC 59.935 40.741 29.85 2.10 45.21 3.91
173 174 8.487313 AGAGTATACTCAATAGTAGCTCGATG 57.513 38.462 29.85 0.00 45.21 3.84
175 176 9.993454 TTAAGAGTATACTCAATAGTAGCTCGA 57.007 33.333 29.85 6.92 45.21 4.04
196 197 9.561069 GGACTAATGCCTTTAAGATCATTAAGA 57.439 33.333 15.03 3.05 32.89 2.10
197 198 8.787852 GGGACTAATGCCTTTAAGATCATTAAG 58.212 37.037 15.03 12.56 32.89 1.85
198 199 8.278639 TGGGACTAATGCCTTTAAGATCATTAA 58.721 33.333 15.03 0.00 37.19 1.40
199 200 7.719633 GTGGGACTAATGCCTTTAAGATCATTA 59.280 37.037 14.12 14.12 37.19 1.90
200 201 6.547510 GTGGGACTAATGCCTTTAAGATCATT 59.452 38.462 13.58 13.58 37.19 2.57
201 202 6.064717 GTGGGACTAATGCCTTTAAGATCAT 58.935 40.000 0.00 0.00 37.19 2.45
202 203 5.191722 AGTGGGACTAATGCCTTTAAGATCA 59.808 40.000 0.00 0.00 37.19 2.92
203 204 5.685728 AGTGGGACTAATGCCTTTAAGATC 58.314 41.667 0.00 0.00 37.19 2.75
204 205 5.430089 AGAGTGGGACTAATGCCTTTAAGAT 59.570 40.000 0.00 0.00 37.19 2.40
205 206 4.783227 AGAGTGGGACTAATGCCTTTAAGA 59.217 41.667 0.00 0.00 37.19 2.10
206 207 5.104259 AGAGTGGGACTAATGCCTTTAAG 57.896 43.478 0.00 0.00 37.19 1.85
207 208 4.783227 AGAGAGTGGGACTAATGCCTTTAA 59.217 41.667 0.00 0.00 37.19 1.52
208 209 4.162320 CAGAGAGTGGGACTAATGCCTTTA 59.838 45.833 0.00 0.00 37.19 1.85
209 210 3.054802 CAGAGAGTGGGACTAATGCCTTT 60.055 47.826 0.00 0.00 37.19 3.11
210 211 2.503356 CAGAGAGTGGGACTAATGCCTT 59.497 50.000 0.00 0.00 37.19 4.35
211 212 2.114616 CAGAGAGTGGGACTAATGCCT 58.885 52.381 0.00 0.00 37.19 4.75
212 213 1.834263 ACAGAGAGTGGGACTAATGCC 59.166 52.381 0.00 0.00 36.69 4.40
213 214 2.497675 TGACAGAGAGTGGGACTAATGC 59.502 50.000 0.00 0.00 0.00 3.56
214 215 3.430098 GCTGACAGAGAGTGGGACTAATG 60.430 52.174 6.65 0.00 0.00 1.90
215 216 2.763448 GCTGACAGAGAGTGGGACTAAT 59.237 50.000 6.65 0.00 0.00 1.73
216 217 2.171840 GCTGACAGAGAGTGGGACTAA 58.828 52.381 6.65 0.00 0.00 2.24
217 218 1.075536 TGCTGACAGAGAGTGGGACTA 59.924 52.381 6.65 0.00 0.00 2.59
218 219 0.178950 TGCTGACAGAGAGTGGGACT 60.179 55.000 6.65 0.00 0.00 3.85
219 220 0.037790 GTGCTGACAGAGAGTGGGAC 60.038 60.000 6.65 0.00 0.00 4.46
220 221 0.469892 TGTGCTGACAGAGAGTGGGA 60.470 55.000 6.65 0.00 0.00 4.37
221 222 0.612229 ATGTGCTGACAGAGAGTGGG 59.388 55.000 6.65 0.00 34.87 4.61
222 223 1.274447 TCATGTGCTGACAGAGAGTGG 59.726 52.381 6.65 0.00 34.87 4.00
223 224 2.738013 TCATGTGCTGACAGAGAGTG 57.262 50.000 6.65 0.00 34.87 3.51
224 225 3.977134 AATCATGTGCTGACAGAGAGT 57.023 42.857 6.65 0.00 36.48 3.24
225 226 7.117956 CCATATTAATCATGTGCTGACAGAGAG 59.882 40.741 6.65 0.00 36.48 3.20
226 227 6.932960 CCATATTAATCATGTGCTGACAGAGA 59.067 38.462 6.65 0.00 36.48 3.10
227 228 6.932960 TCCATATTAATCATGTGCTGACAGAG 59.067 38.462 6.65 0.00 36.48 3.35
228 229 6.829849 TCCATATTAATCATGTGCTGACAGA 58.170 36.000 6.65 0.00 36.48 3.41
229 230 7.358066 GTTCCATATTAATCATGTGCTGACAG 58.642 38.462 0.00 0.00 36.48 3.51
230 231 6.262944 GGTTCCATATTAATCATGTGCTGACA 59.737 38.462 0.00 0.00 36.48 3.58
231 232 6.488006 AGGTTCCATATTAATCATGTGCTGAC 59.512 38.462 0.00 0.00 36.48 3.51
232 233 6.487668 CAGGTTCCATATTAATCATGTGCTGA 59.512 38.462 0.00 0.00 38.53 4.26
233 234 6.294342 CCAGGTTCCATATTAATCATGTGCTG 60.294 42.308 0.00 0.00 0.00 4.41
234 235 5.771666 CCAGGTTCCATATTAATCATGTGCT 59.228 40.000 0.00 0.00 0.00 4.40
235 236 5.536161 ACCAGGTTCCATATTAATCATGTGC 59.464 40.000 0.00 0.00 0.00 4.57
236 237 6.515531 GCACCAGGTTCCATATTAATCATGTG 60.516 42.308 0.00 0.00 0.00 3.21
237 238 5.536161 GCACCAGGTTCCATATTAATCATGT 59.464 40.000 0.00 0.00 0.00 3.21
238 239 5.771666 AGCACCAGGTTCCATATTAATCATG 59.228 40.000 0.00 0.00 0.00 3.07
239 240 5.957132 AGCACCAGGTTCCATATTAATCAT 58.043 37.500 0.00 0.00 0.00 2.45
240 241 5.387113 AGCACCAGGTTCCATATTAATCA 57.613 39.130 0.00 0.00 0.00 2.57
241 242 7.255486 GGTTTAGCACCAGGTTCCATATTAATC 60.255 40.741 0.00 0.00 46.42 1.75
242 243 6.549736 GGTTTAGCACCAGGTTCCATATTAAT 59.450 38.462 0.00 0.00 46.42 1.40
243 244 5.889289 GGTTTAGCACCAGGTTCCATATTAA 59.111 40.000 0.00 0.00 46.42 1.40
244 245 5.442391 GGTTTAGCACCAGGTTCCATATTA 58.558 41.667 0.00 0.00 46.42 0.98
245 246 4.278310 GGTTTAGCACCAGGTTCCATATT 58.722 43.478 0.00 0.00 46.42 1.28
246 247 3.898482 GGTTTAGCACCAGGTTCCATAT 58.102 45.455 0.00 0.00 46.42 1.78
247 248 3.359695 GGTTTAGCACCAGGTTCCATA 57.640 47.619 0.00 0.00 46.42 2.74
248 249 2.215942 GGTTTAGCACCAGGTTCCAT 57.784 50.000 0.00 0.00 46.42 3.41
249 250 3.737702 GGTTTAGCACCAGGTTCCA 57.262 52.632 0.00 0.00 46.42 3.53
257 258 1.310904 TCAACAACGGGTTTAGCACC 58.689 50.000 0.00 0.00 46.46 5.01
258 259 2.550606 TGATCAACAACGGGTTTAGCAC 59.449 45.455 0.00 0.00 37.72 4.40
259 260 2.550606 GTGATCAACAACGGGTTTAGCA 59.449 45.455 0.00 0.00 37.72 3.49
260 261 2.095415 GGTGATCAACAACGGGTTTAGC 60.095 50.000 5.69 0.00 37.72 3.09
261 262 3.142951 TGGTGATCAACAACGGGTTTAG 58.857 45.455 12.03 0.00 39.39 1.85
262 263 3.210232 TGGTGATCAACAACGGGTTTA 57.790 42.857 12.03 0.00 39.39 2.01
263 264 2.060050 TGGTGATCAACAACGGGTTT 57.940 45.000 12.03 0.00 39.39 3.27
264 265 2.060050 TTGGTGATCAACAACGGGTT 57.940 45.000 22.25 0.00 39.39 4.11
265 266 3.811031 TTGGTGATCAACAACGGGT 57.189 47.368 22.25 0.00 39.39 5.28
273 274 2.552031 TCAAACGTCGTTGGTGATCAA 58.448 42.857 12.12 0.00 0.00 2.57
274 275 2.226602 TCAAACGTCGTTGGTGATCA 57.773 45.000 12.12 0.00 0.00 2.92
275 276 3.424433 GGATTCAAACGTCGTTGGTGATC 60.424 47.826 12.12 14.99 0.00 2.92
276 277 2.482721 GGATTCAAACGTCGTTGGTGAT 59.517 45.455 12.12 7.52 0.00 3.06
277 278 1.868498 GGATTCAAACGTCGTTGGTGA 59.132 47.619 12.12 9.82 0.00 4.02
278 279 1.871039 AGGATTCAAACGTCGTTGGTG 59.129 47.619 12.12 7.42 0.00 4.17
279 280 2.249844 AGGATTCAAACGTCGTTGGT 57.750 45.000 12.12 0.00 0.00 3.67
280 281 3.991773 TCTTAGGATTCAAACGTCGTTGG 59.008 43.478 12.12 9.01 0.00 3.77
281 282 5.347635 TCATCTTAGGATTCAAACGTCGTTG 59.652 40.000 12.12 6.32 0.00 4.10
282 283 5.475719 TCATCTTAGGATTCAAACGTCGTT 58.524 37.500 4.40 4.40 0.00 3.85
283 284 5.068234 TCATCTTAGGATTCAAACGTCGT 57.932 39.130 0.00 0.00 0.00 4.34
284 285 6.403333 TTTCATCTTAGGATTCAAACGTCG 57.597 37.500 0.00 0.00 0.00 5.12
285 286 9.922305 CTTATTTCATCTTAGGATTCAAACGTC 57.078 33.333 0.00 0.00 0.00 4.34
286 287 9.449719 ACTTATTTCATCTTAGGATTCAAACGT 57.550 29.630 0.00 0.00 0.00 3.99
287 288 9.708222 CACTTATTTCATCTTAGGATTCAAACG 57.292 33.333 0.00 0.00 0.00 3.60
289 290 9.753674 ACCACTTATTTCATCTTAGGATTCAAA 57.246 29.630 0.00 0.00 0.00 2.69
295 296 9.886132 GTTCTTACCACTTATTTCATCTTAGGA 57.114 33.333 0.00 0.00 0.00 2.94
296 297 9.892130 AGTTCTTACCACTTATTTCATCTTAGG 57.108 33.333 0.00 0.00 0.00 2.69
299 300 9.793259 TTCAGTTCTTACCACTTATTTCATCTT 57.207 29.630 0.00 0.00 0.00 2.40
300 301 9.793259 TTTCAGTTCTTACCACTTATTTCATCT 57.207 29.630 0.00 0.00 0.00 2.90
310 311 9.740710 AGCTTTAATATTTCAGTTCTTACCACT 57.259 29.630 0.00 0.00 0.00 4.00
340 341 9.658799 GCTATGAGATAAATTATACCTGCTTCA 57.341 33.333 0.00 0.00 0.00 3.02
341 342 9.883142 AGCTATGAGATAAATTATACCTGCTTC 57.117 33.333 0.00 0.00 0.00 3.86
342 343 9.664332 CAGCTATGAGATAAATTATACCTGCTT 57.336 33.333 0.00 0.00 0.00 3.91
343 344 9.040259 TCAGCTATGAGATAAATTATACCTGCT 57.960 33.333 0.00 0.00 0.00 4.24
344 345 9.829507 ATCAGCTATGAGATAAATTATACCTGC 57.170 33.333 0.00 0.00 39.29 4.85
354 355 9.194972 CCCATCTACTATCAGCTATGAGATAAA 57.805 37.037 0.00 0.00 39.29 1.40
355 356 8.340002 ACCCATCTACTATCAGCTATGAGATAA 58.660 37.037 0.00 0.00 39.29 1.75
356 357 7.877433 ACCCATCTACTATCAGCTATGAGATA 58.123 38.462 0.00 0.00 39.29 1.98
357 358 6.740693 ACCCATCTACTATCAGCTATGAGAT 58.259 40.000 0.00 0.00 39.29 2.75
358 359 6.146140 ACCCATCTACTATCAGCTATGAGA 57.854 41.667 0.00 0.00 39.29 3.27
359 360 7.613801 ACTTACCCATCTACTATCAGCTATGAG 59.386 40.741 0.00 0.00 39.29 2.90
360 361 7.471041 ACTTACCCATCTACTATCAGCTATGA 58.529 38.462 0.00 0.00 40.50 2.15
361 362 7.147983 GGACTTACCCATCTACTATCAGCTATG 60.148 44.444 0.00 0.00 0.00 2.23
362 363 6.893005 GGACTTACCCATCTACTATCAGCTAT 59.107 42.308 0.00 0.00 0.00 2.97
363 364 6.246919 GGACTTACCCATCTACTATCAGCTA 58.753 44.000 0.00 0.00 0.00 3.32
364 365 5.081032 GGACTTACCCATCTACTATCAGCT 58.919 45.833 0.00 0.00 0.00 4.24
365 366 5.394224 GGACTTACCCATCTACTATCAGC 57.606 47.826 0.00 0.00 0.00 4.26
379 380 2.740447 GACACAATGAACGGGACTTACC 59.260 50.000 0.00 0.00 38.08 2.85
380 381 2.740447 GGACACAATGAACGGGACTTAC 59.260 50.000 0.00 0.00 0.00 2.34
381 382 2.289819 GGGACACAATGAACGGGACTTA 60.290 50.000 0.00 0.00 0.00 2.24
382 383 1.544759 GGGACACAATGAACGGGACTT 60.545 52.381 0.00 0.00 0.00 3.01
383 384 0.036306 GGGACACAATGAACGGGACT 59.964 55.000 0.00 0.00 0.00 3.85
384 385 0.036306 AGGGACACAATGAACGGGAC 59.964 55.000 0.00 0.00 0.00 4.46
385 386 1.646912 TAGGGACACAATGAACGGGA 58.353 50.000 0.00 0.00 0.00 5.14
386 387 2.027561 TCTTAGGGACACAATGAACGGG 60.028 50.000 0.00 0.00 0.00 5.28
387 388 3.328382 TCTTAGGGACACAATGAACGG 57.672 47.619 0.00 0.00 0.00 4.44
388 389 3.684788 CCTTCTTAGGGACACAATGAACG 59.315 47.826 0.00 0.00 37.94 3.95
401 402 6.156429 ACAACAGTAATACCTCCCTTCTTAGG 59.844 42.308 0.00 0.00 41.60 2.69
402 403 7.184067 ACAACAGTAATACCTCCCTTCTTAG 57.816 40.000 0.00 0.00 0.00 2.18
403 404 7.310858 GGAACAACAGTAATACCTCCCTTCTTA 60.311 40.741 0.00 0.00 0.00 2.10
404 405 6.449830 AACAACAGTAATACCTCCCTTCTT 57.550 37.500 0.00 0.00 0.00 2.52
405 406 5.045797 GGAACAACAGTAATACCTCCCTTCT 60.046 44.000 0.00 0.00 0.00 2.85
406 407 5.045797 AGGAACAACAGTAATACCTCCCTTC 60.046 44.000 0.00 0.00 0.00 3.46
407 408 4.850386 AGGAACAACAGTAATACCTCCCTT 59.150 41.667 0.00 0.00 0.00 3.95
408 409 4.436079 AGGAACAACAGTAATACCTCCCT 58.564 43.478 0.00 0.00 0.00 4.20
409 410 4.838904 AGGAACAACAGTAATACCTCCC 57.161 45.455 0.00 0.00 0.00 4.30
410 411 7.562135 TCATTAGGAACAACAGTAATACCTCC 58.438 38.462 0.00 0.00 0.00 4.30
440 441 9.696917 GACAATTCTTTGTGGAATAAGTTCATT 57.303 29.630 0.00 0.00 46.01 2.57
441 442 8.859090 TGACAATTCTTTGTGGAATAAGTTCAT 58.141 29.630 0.00 0.00 46.01 2.57
442 443 8.231692 TGACAATTCTTTGTGGAATAAGTTCA 57.768 30.769 0.00 0.00 46.01 3.18
443 444 9.696917 AATGACAATTCTTTGTGGAATAAGTTC 57.303 29.630 0.00 0.00 46.01 3.01
444 445 9.480053 CAATGACAATTCTTTGTGGAATAAGTT 57.520 29.630 0.00 0.00 46.01 2.66
445 446 8.090214 CCAATGACAATTCTTTGTGGAATAAGT 58.910 33.333 0.00 0.00 46.01 2.24
446 447 8.090214 ACCAATGACAATTCTTTGTGGAATAAG 58.910 33.333 0.00 0.00 46.01 1.73
447 448 7.961351 ACCAATGACAATTCTTTGTGGAATAA 58.039 30.769 0.00 0.00 46.01 1.40
448 449 7.537596 ACCAATGACAATTCTTTGTGGAATA 57.462 32.000 0.00 0.00 46.01 1.75
449 450 6.423776 ACCAATGACAATTCTTTGTGGAAT 57.576 33.333 0.00 0.00 46.01 3.01
450 451 5.867903 ACCAATGACAATTCTTTGTGGAA 57.132 34.783 0.00 0.00 46.01 3.53
451 452 5.867903 AACCAATGACAATTCTTTGTGGA 57.132 34.783 0.00 0.00 46.01 4.02
452 453 6.511416 TGTAACCAATGACAATTCTTTGTGG 58.489 36.000 0.00 0.00 46.01 4.17
453 454 7.424803 TCTGTAACCAATGACAATTCTTTGTG 58.575 34.615 0.00 0.00 46.01 3.33
455 456 8.918658 CATTCTGTAACCAATGACAATTCTTTG 58.081 33.333 0.00 0.00 36.88 2.77
456 457 8.090214 CCATTCTGTAACCAATGACAATTCTTT 58.910 33.333 0.00 0.00 32.56 2.52
457 458 7.233348 ACCATTCTGTAACCAATGACAATTCTT 59.767 33.333 0.00 0.00 32.56 2.52
458 459 6.721208 ACCATTCTGTAACCAATGACAATTCT 59.279 34.615 0.00 0.00 32.56 2.40
459 460 6.924111 ACCATTCTGTAACCAATGACAATTC 58.076 36.000 0.00 0.00 32.56 2.17
460 461 6.916360 ACCATTCTGTAACCAATGACAATT 57.084 33.333 0.00 0.00 32.56 2.32
461 462 8.593945 ATTACCATTCTGTAACCAATGACAAT 57.406 30.769 0.00 0.00 33.78 2.71
462 463 8.303156 CAATTACCATTCTGTAACCAATGACAA 58.697 33.333 0.00 0.00 33.78 3.18
463 464 7.667635 TCAATTACCATTCTGTAACCAATGACA 59.332 33.333 0.00 0.00 33.78 3.58
464 465 8.050778 TCAATTACCATTCTGTAACCAATGAC 57.949 34.615 0.00 0.00 33.78 3.06
465 466 8.821686 ATCAATTACCATTCTGTAACCAATGA 57.178 30.769 0.00 0.00 33.78 2.57
466 467 9.874205 AAATCAATTACCATTCTGTAACCAATG 57.126 29.630 0.00 0.00 33.78 2.82
514 516 4.733077 TGTTCAGGGGAGTAAAATGGAA 57.267 40.909 0.00 0.00 0.00 3.53
621 627 3.128032 AAACCAGTCGGGGGTGTGG 62.128 63.158 0.00 0.00 42.91 4.17
622 628 1.896660 CAAACCAGTCGGGGGTGTG 60.897 63.158 0.00 0.00 42.91 3.82
623 629 2.333701 GACAAACCAGTCGGGGGTGT 62.334 60.000 0.46 0.46 42.91 4.16
624 630 1.599797 GACAAACCAGTCGGGGGTG 60.600 63.158 0.00 0.00 42.91 4.61
625 631 1.765597 GAGACAAACCAGTCGGGGGT 61.766 60.000 0.00 0.00 43.24 4.95
786 792 1.451936 GCCGCCCATGGAGAATAGT 59.548 57.895 15.22 0.00 0.00 2.12
951 957 2.826738 GCCTCTCGACGGAGCTCT 60.827 66.667 14.64 0.00 40.26 4.09
1316 1322 1.354705 GGTTAGGGAGGCCTTCAAAGT 59.645 52.381 14.70 0.00 0.00 2.66
1657 1663 1.678123 CCACTCATCAGGCAGTCCTTG 60.678 57.143 0.00 0.00 41.93 3.61
1858 1874 2.353605 CCACAACAACCAGCACAAAGTT 60.354 45.455 0.00 0.00 0.00 2.66
1969 2004 5.877012 ACCATTTCACAAGACAGCATAGTAG 59.123 40.000 0.00 0.00 0.00 2.57
1999 2034 2.111756 GCACAAACAAAGAAGCTCACG 58.888 47.619 0.00 0.00 0.00 4.35
2171 2281 8.731605 TGTTTGATGAACTTGTGTTTGTTACTA 58.268 29.630 0.00 0.00 39.08 1.82
2218 2328 3.064931 GTGTTAGTAGGTTGCTGGTGAC 58.935 50.000 0.00 0.00 0.00 3.67
2271 2381 5.163141 TGTTTGATGAACTGAGGGGTTAAGA 60.163 40.000 0.00 0.00 39.08 2.10
2310 2537 5.725551 TCTAGTCAGAGAAGGAGGAGATT 57.274 43.478 0.00 0.00 0.00 2.40
2351 2578 2.397597 AGGCCTCCAAAGAAAGCAAAA 58.602 42.857 0.00 0.00 0.00 2.44
2378 2605 1.965754 GAGGGACAGCACAGCCTAGG 61.966 65.000 3.67 3.67 0.00 3.02


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

AutoCloner maintained by Alex Coulton.