Multiple sequence alignment - TraesCS7A01G209100

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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 TraesCS7A01G209100 chr7A 100.000 3633 0 0 1 3633 171440568 171436936 0.000000e+00 6709.0
1 TraesCS7A01G209100 chr7A 89.465 1177 70 18 677 1799 171536813 171535637 0.000000e+00 1437.0
2 TraesCS7A01G209100 chr7A 89.465 1177 70 18 677 1799 171950431 171949255 0.000000e+00 1437.0
3 TraesCS7A01G209100 chr7A 88.283 1246 68 36 2385 3571 171547286 171546060 0.000000e+00 1421.0
4 TraesCS7A01G209100 chr7A 95.422 830 34 2 2385 3211 171875846 171875018 0.000000e+00 1319.0
5 TraesCS7A01G209100 chr7A 89.771 1046 61 14 811 1826 172235397 172234368 0.000000e+00 1297.0
6 TraesCS7A01G209100 chr7A 91.005 856 61 12 885 1736 171577194 171576351 0.000000e+00 1140.0
7 TraesCS7A01G209100 chr7A 94.465 271 8 2 1 270 541240141 541240405 9.390000e-111 411.0
8 TraesCS7A01G209100 chr7A 88.418 354 18 9 3275 3608 171945752 171945402 1.210000e-109 407.0
9 TraesCS7A01G209100 chr7A 94.096 271 9 4 1 270 407795085 407795349 4.370000e-109 405.0
10 TraesCS7A01G209100 chr7A 85.489 317 22 17 3278 3571 171554415 171554100 3.520000e-80 309.0
11 TraesCS7A01G209100 chr7A 93.567 171 8 3 3275 3444 172232907 172232739 6.020000e-63 252.0
12 TraesCS7A01G209100 chr7A 90.566 159 13 2 309 467 389548170 389548014 3.680000e-50 209.0
13 TraesCS7A01G209100 chr6A 94.606 1372 61 9 2272 3633 124424170 124425538 0.000000e+00 2111.0
14 TraesCS7A01G209100 chr6A 90.347 1067 77 18 925 1971 124422812 124423872 0.000000e+00 1376.0
15 TraesCS7A01G209100 chr6A 90.347 1067 77 19 925 1971 124917059 124915999 0.000000e+00 1376.0
16 TraesCS7A01G209100 chr6A 94.973 736 30 5 2902 3633 124915865 124915133 0.000000e+00 1147.0
17 TraesCS7A01G209100 chr6A 94.776 268 8 3 1 267 109354128 109353866 2.610000e-111 412.0
18 TraesCS7A01G209100 chr7D 89.757 1689 99 26 1871 3521 169498304 169496652 0.000000e+00 2093.0
19 TraesCS7A01G209100 chr7D 91.973 1495 82 9 809 2270 169422924 169421435 0.000000e+00 2061.0
20 TraesCS7A01G209100 chr7D 93.328 1274 68 4 1019 2276 169024396 169025668 0.000000e+00 1866.0
21 TraesCS7A01G209100 chr7D 88.750 1360 78 35 2272 3571 169439761 169438417 0.000000e+00 1594.0
22 TraesCS7A01G209100 chr7D 90.669 1211 80 16 809 1995 168990629 168991830 0.000000e+00 1580.0
23 TraesCS7A01G209100 chr7D 87.426 1352 90 34 2274 3571 169025708 169027033 0.000000e+00 1482.0
24 TraesCS7A01G209100 chr7D 89.559 1111 74 11 677 1774 169457285 169456204 0.000000e+00 1371.0
25 TraesCS7A01G209100 chr7D 90.372 914 72 12 925 1826 169499206 169498297 0.000000e+00 1186.0
26 TraesCS7A01G209100 chr7D 92.947 794 42 10 1031 1824 169441030 169440251 0.000000e+00 1144.0
27 TraesCS7A01G209100 chr7D 95.502 667 29 1 2013 2678 168991807 168992473 0.000000e+00 1064.0
28 TraesCS7A01G209100 chr7D 91.266 687 45 12 2958 3633 169419713 169419031 0.000000e+00 922.0
29 TraesCS7A01G209100 chr7D 89.140 663 47 10 2272 2927 165119355 165119999 0.000000e+00 802.0
30 TraesCS7A01G209100 chr7D 94.541 403 22 0 580 982 169023782 169024184 1.110000e-174 623.0
31 TraesCS7A01G209100 chr7D 87.981 416 33 10 1874 2276 164751977 164751566 3.280000e-130 475.0
32 TraesCS7A01G209100 chr7D 94.096 271 10 3 1 270 151564569 151564834 1.210000e-109 407.0
33 TraesCS7A01G209100 chr7D 95.259 232 10 1 289 519 169023061 169023292 2.060000e-97 366.0
34 TraesCS7A01G209100 chr7D 86.667 180 21 3 288 466 288025449 288025626 2.860000e-46 196.0
35 TraesCS7A01G209100 chrUn 89.465 1177 70 17 677 1799 262504939 262506115 0.000000e+00 1437.0
36 TraesCS7A01G209100 chrUn 88.508 1166 89 26 831 1970 244606725 244607871 0.000000e+00 1369.0
37 TraesCS7A01G209100 chrUn 95.663 830 32 2 2385 3211 374568661 374567833 0.000000e+00 1330.0
38 TraesCS7A01G209100 chrUn 87.836 1192 67 36 2439 3571 309086295 309085123 0.000000e+00 1327.0
39 TraesCS7A01G209100 chrUn 91.077 919 66 12 885 1799 248282140 248283046 0.000000e+00 1229.0
40 TraesCS7A01G209100 chrUn 96.582 673 20 1 2272 2944 218480563 218481232 0.000000e+00 1112.0
41 TraesCS7A01G209100 chrUn 85.489 317 22 17 3278 3571 82712358 82712043 3.520000e-80 309.0
42 TraesCS7A01G209100 chrUn 98.830 171 2 0 1801 1971 262506256 262506426 4.560000e-79 305.0
43 TraesCS7A01G209100 chrUn 92.523 214 12 4 3397 3608 293553707 293553918 1.640000e-78 303.0
44 TraesCS7A01G209100 chrUn 92.523 214 12 4 3397 3608 314486469 314486680 1.640000e-78 303.0
45 TraesCS7A01G209100 chrUn 92.523 214 12 4 3397 3608 325383265 325383054 1.640000e-78 303.0
46 TraesCS7A01G209100 chrUn 84.286 280 15 14 3320 3571 233053275 233053553 2.800000e-61 246.0
47 TraesCS7A01G209100 chr7B 92.004 1013 58 10 2289 3280 135018252 135017242 0.000000e+00 1400.0
48 TraesCS7A01G209100 chr7B 89.753 1054 66 12 809 1821 134636932 134635880 0.000000e+00 1310.0
49 TraesCS7A01G209100 chr7B 91.253 926 65 11 885 1799 134492101 134493021 0.000000e+00 1247.0
50 TraesCS7A01G209100 chr7B 96.065 432 16 1 1849 2279 135035747 135035316 0.000000e+00 702.0
51 TraesCS7A01G209100 chr7B 87.740 416 34 9 1874 2276 128070279 128069868 1.530000e-128 470.0
52 TraesCS7A01G209100 chr7B 87.740 416 34 10 1874 2276 128437446 128437857 1.530000e-128 470.0
53 TraesCS7A01G209100 chr7B 87.260 416 36 10 1874 2276 127652515 127652104 3.310000e-125 459.0
54 TraesCS7A01G209100 chr7B 85.802 324 17 16 3275 3571 135034310 135033989 2.110000e-82 316.0
55 TraesCS7A01G209100 chr7B 85.804 317 20 14 3278 3571 134494915 134495229 2.720000e-81 313.0
56 TraesCS7A01G209100 chr7B 88.889 126 11 2 558 682 134638556 134638433 6.280000e-33 152.0
57 TraesCS7A01G209100 chr7B 90.196 51 2 1 758 808 134637022 134636975 3.030000e-06 63.9
58 TraesCS7A01G209100 chr6D 88.165 1166 93 26 831 1970 103051553 103052699 0.000000e+00 1347.0
59 TraesCS7A01G209100 chr6D 87.993 1166 95 26 831 1970 103082860 103084006 0.000000e+00 1336.0
60 TraesCS7A01G209100 chr6D 96.285 673 22 1 2272 2944 103084305 103084974 0.000000e+00 1101.0
61 TraesCS7A01G209100 chr1D 95.941 271 7 1 1 271 444473152 444473418 1.550000e-118 436.0
62 TraesCS7A01G209100 chr4A 95.203 271 8 2 1 270 30566402 30566136 1.210000e-114 424.0
63 TraesCS7A01G209100 chr5D 94.853 272 11 3 1 270 556267974 556268244 4.340000e-114 422.0
64 TraesCS7A01G209100 chr3A 94.776 268 9 2 1 267 88580739 88580476 2.610000e-111 412.0
65 TraesCS7A01G209100 chr3A 81.982 222 29 11 309 526 130465275 130465061 1.040000e-40 178.0
66 TraesCS7A01G209100 chr5A 94.096 271 8 6 1 270 520121440 520121177 4.370000e-109 405.0
67 TraesCS7A01G209100 chr5A 85.052 194 26 3 288 479 149090130 149090322 1.030000e-45 195.0
68 TraesCS7A01G209100 chr3D 88.398 181 20 1 288 468 430906200 430906379 2.200000e-52 217.0
69 TraesCS7A01G209100 chr3D 87.293 181 22 1 288 468 430914167 430914346 4.760000e-49 206.0
70 TraesCS7A01G209100 chr3D 86.813 182 21 3 289 468 460678718 460678538 2.210000e-47 200.0
71 TraesCS7A01G209100 chr3D 86.111 180 25 0 289 468 273974034 273974213 1.030000e-45 195.0


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 TraesCS7A01G209100 chr7A 171436936 171440568 3632 True 6709.000000 6709 100.000000 1 3633 1 chr7A.!!$R1 3632
1 TraesCS7A01G209100 chr7A 171535637 171536813 1176 True 1437.000000 1437 89.465000 677 1799 1 chr7A.!!$R2 1122
2 TraesCS7A01G209100 chr7A 171546060 171547286 1226 True 1421.000000 1421 88.283000 2385 3571 1 chr7A.!!$R3 1186
3 TraesCS7A01G209100 chr7A 171875018 171875846 828 True 1319.000000 1319 95.422000 2385 3211 1 chr7A.!!$R6 826
4 TraesCS7A01G209100 chr7A 171576351 171577194 843 True 1140.000000 1140 91.005000 885 1736 1 chr7A.!!$R5 851
5 TraesCS7A01G209100 chr7A 171945402 171950431 5029 True 922.000000 1437 88.941500 677 3608 2 chr7A.!!$R8 2931
6 TraesCS7A01G209100 chr7A 172232739 172235397 2658 True 774.500000 1297 91.669000 811 3444 2 chr7A.!!$R9 2633
7 TraesCS7A01G209100 chr6A 124422812 124425538 2726 False 1743.500000 2111 92.476500 925 3633 2 chr6A.!!$F1 2708
8 TraesCS7A01G209100 chr6A 124915133 124917059 1926 True 1261.500000 1376 92.660000 925 3633 2 chr6A.!!$R2 2708
9 TraesCS7A01G209100 chr7D 169496652 169499206 2554 True 1639.500000 2093 90.064500 925 3521 2 chr7D.!!$R5 2596
10 TraesCS7A01G209100 chr7D 169419031 169422924 3893 True 1491.500000 2061 91.619500 809 3633 2 chr7D.!!$R3 2824
11 TraesCS7A01G209100 chr7D 169456204 169457285 1081 True 1371.000000 1371 89.559000 677 1774 1 chr7D.!!$R2 1097
12 TraesCS7A01G209100 chr7D 169438417 169441030 2613 True 1369.000000 1594 90.848500 1031 3571 2 chr7D.!!$R4 2540
13 TraesCS7A01G209100 chr7D 168990629 168992473 1844 False 1322.000000 1580 93.085500 809 2678 2 chr7D.!!$F4 1869
14 TraesCS7A01G209100 chr7D 169023061 169027033 3972 False 1084.250000 1866 92.638500 289 3571 4 chr7D.!!$F5 3282
15 TraesCS7A01G209100 chr7D 165119355 165119999 644 False 802.000000 802 89.140000 2272 2927 1 chr7D.!!$F2 655
16 TraesCS7A01G209100 chrUn 244606725 244607871 1146 False 1369.000000 1369 88.508000 831 1970 1 chrUn.!!$F3 1139
17 TraesCS7A01G209100 chrUn 374567833 374568661 828 True 1330.000000 1330 95.663000 2385 3211 1 chrUn.!!$R4 826
18 TraesCS7A01G209100 chrUn 309085123 309086295 1172 True 1327.000000 1327 87.836000 2439 3571 1 chrUn.!!$R2 1132
19 TraesCS7A01G209100 chrUn 248282140 248283046 906 False 1229.000000 1229 91.077000 885 1799 1 chrUn.!!$F4 914
20 TraesCS7A01G209100 chrUn 218480563 218481232 669 False 1112.000000 1112 96.582000 2272 2944 1 chrUn.!!$F1 672
21 TraesCS7A01G209100 chrUn 262504939 262506426 1487 False 871.000000 1437 94.147500 677 1971 2 chrUn.!!$F7 1294
22 TraesCS7A01G209100 chr7B 135017242 135018252 1010 True 1400.000000 1400 92.004000 2289 3280 1 chr7B.!!$R3 991
23 TraesCS7A01G209100 chr7B 134492101 134495229 3128 False 780.000000 1247 88.528500 885 3571 2 chr7B.!!$F2 2686
24 TraesCS7A01G209100 chr7B 135033989 135035747 1758 True 509.000000 702 90.933500 1849 3571 2 chr7B.!!$R5 1722
25 TraesCS7A01G209100 chr7B 134635880 134638556 2676 True 508.633333 1310 89.612667 558 1821 3 chr7B.!!$R4 1263
26 TraesCS7A01G209100 chr6D 103051553 103052699 1146 False 1347.000000 1347 88.165000 831 1970 1 chr6D.!!$F1 1139
27 TraesCS7A01G209100 chr6D 103082860 103084974 2114 False 1218.500000 1336 92.139000 831 2944 2 chr6D.!!$F2 2113

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
178 179 0.045778 CCCTTCCTTTCCCCCTCCTA 59.954 60.0 0.00 0.0 0.0 2.94 F
530 532 0.108585 GTCCCACAAAGTCAGCTGGA 59.891 55.0 15.13 0.0 0.0 3.86 F
1648 3764 0.178068 AGGAATCGGCTGCGTACAAT 59.822 50.0 0.00 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 6064 0.745486 TGGACTCGCATGATGCTTGG 60.745 55.0 16.17 7.61 42.25 3.61 R
2255 6525 0.179045 GGGTAATCGGACTGCAGCAT 60.179 55.0 15.27 0.00 0.00 3.79 R
3598 9111 0.820074 CGCCTCTCCAGTAGACCGAT 60.820 60.0 0.00 0.00 0.00 4.18 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
29 30 2.194868 CCCTCGGGGTTAATGGGC 59.805 66.667 0.00 0.00 38.25 5.36
30 31 2.194868 CCTCGGGGTTAATGGGCC 59.805 66.667 0.00 0.00 0.00 5.80
31 32 2.383601 CCTCGGGGTTAATGGGCCT 61.384 63.158 4.53 0.00 0.00 5.19
32 33 1.613061 CTCGGGGTTAATGGGCCTT 59.387 57.895 4.53 0.00 0.00 4.35
33 34 0.841289 CTCGGGGTTAATGGGCCTTA 59.159 55.000 4.53 0.00 0.00 2.69
34 35 1.423921 CTCGGGGTTAATGGGCCTTAT 59.576 52.381 4.53 0.00 0.00 1.73
35 36 1.854280 TCGGGGTTAATGGGCCTTATT 59.146 47.619 4.53 6.86 0.00 1.40
36 37 1.960689 CGGGGTTAATGGGCCTTATTG 59.039 52.381 4.53 0.00 0.00 1.90
37 38 2.325484 GGGGTTAATGGGCCTTATTGG 58.675 52.381 4.53 0.00 39.35 3.16
38 39 2.325484 GGGTTAATGGGCCTTATTGGG 58.675 52.381 4.53 0.00 36.00 4.12
46 47 3.421567 GCCTTATTGGGCCCTAGTG 57.578 57.895 25.70 9.51 45.92 2.74
47 48 0.178990 GCCTTATTGGGCCCTAGTGG 60.179 60.000 25.70 18.81 45.92 4.00
48 49 1.518367 CCTTATTGGGCCCTAGTGGA 58.482 55.000 25.70 0.00 35.39 4.02
49 50 1.421646 CCTTATTGGGCCCTAGTGGAG 59.578 57.143 25.70 12.85 35.39 3.86
50 51 2.408565 CTTATTGGGCCCTAGTGGAGA 58.591 52.381 25.70 0.00 35.39 3.71
51 52 2.103153 TATTGGGCCCTAGTGGAGAG 57.897 55.000 25.70 0.00 35.39 3.20
52 53 0.343372 ATTGGGCCCTAGTGGAGAGA 59.657 55.000 25.70 0.00 35.39 3.10
53 54 0.325671 TTGGGCCCTAGTGGAGAGAG 60.326 60.000 25.70 0.00 35.39 3.20
54 55 1.221909 TGGGCCCTAGTGGAGAGAGA 61.222 60.000 25.70 0.00 35.39 3.10
55 56 0.469144 GGGCCCTAGTGGAGAGAGAG 60.469 65.000 17.04 0.00 35.39 3.20
56 57 0.553819 GGCCCTAGTGGAGAGAGAGA 59.446 60.000 0.00 0.00 35.39 3.10
57 58 1.478654 GGCCCTAGTGGAGAGAGAGAG 60.479 61.905 0.00 0.00 35.39 3.20
58 59 1.493022 GCCCTAGTGGAGAGAGAGAGA 59.507 57.143 1.75 0.00 35.39 3.10
59 60 2.487265 GCCCTAGTGGAGAGAGAGAGAG 60.487 59.091 1.75 0.00 35.39 3.20
60 61 3.045634 CCCTAGTGGAGAGAGAGAGAGA 58.954 54.545 0.00 0.00 35.39 3.10
61 62 3.071602 CCCTAGTGGAGAGAGAGAGAGAG 59.928 56.522 0.00 0.00 35.39 3.20
62 63 3.967326 CCTAGTGGAGAGAGAGAGAGAGA 59.033 52.174 0.00 0.00 34.57 3.10
63 64 4.039730 CCTAGTGGAGAGAGAGAGAGAGAG 59.960 54.167 0.00 0.00 34.57 3.20
64 65 3.724478 AGTGGAGAGAGAGAGAGAGAGA 58.276 50.000 0.00 0.00 0.00 3.10
65 66 3.708631 AGTGGAGAGAGAGAGAGAGAGAG 59.291 52.174 0.00 0.00 0.00 3.20
66 67 3.041211 TGGAGAGAGAGAGAGAGAGAGG 58.959 54.545 0.00 0.00 0.00 3.69
67 68 2.370189 GGAGAGAGAGAGAGAGAGAGGG 59.630 59.091 0.00 0.00 0.00 4.30
68 69 2.370189 GAGAGAGAGAGAGAGAGAGGGG 59.630 59.091 0.00 0.00 0.00 4.79
69 70 0.846693 AGAGAGAGAGAGAGAGGGGC 59.153 60.000 0.00 0.00 0.00 5.80
70 71 0.178990 GAGAGAGAGAGAGAGGGGCC 60.179 65.000 0.00 0.00 0.00 5.80
71 72 1.528309 GAGAGAGAGAGAGGGGCCG 60.528 68.421 0.00 0.00 0.00 6.13
72 73 2.520741 GAGAGAGAGAGGGGCCGG 60.521 72.222 0.00 0.00 0.00 6.13
73 74 4.851214 AGAGAGAGAGGGGCCGGC 62.851 72.222 21.18 21.18 0.00 6.13
107 108 4.825679 CCCCCTCCCCCTCTGGTC 62.826 77.778 0.00 0.00 0.00 4.02
108 109 4.825679 CCCCTCCCCCTCTGGTCC 62.826 77.778 0.00 0.00 0.00 4.46
110 111 4.075793 CCTCCCCCTCTGGTCCGA 62.076 72.222 0.00 0.00 0.00 4.55
111 112 2.038975 CTCCCCCTCTGGTCCGAA 59.961 66.667 0.00 0.00 0.00 4.30
112 113 1.383248 CTCCCCCTCTGGTCCGAAT 60.383 63.158 0.00 0.00 0.00 3.34
113 114 0.983378 CTCCCCCTCTGGTCCGAATT 60.983 60.000 0.00 0.00 0.00 2.17
114 115 1.224592 CCCCCTCTGGTCCGAATTG 59.775 63.158 0.00 0.00 0.00 2.32
115 116 1.224592 CCCCTCTGGTCCGAATTGG 59.775 63.158 0.00 0.00 40.09 3.16
126 127 2.667470 TCCGAATTGGACTAGGAGAGG 58.333 52.381 0.00 0.00 43.74 3.69
127 128 1.689273 CCGAATTGGACTAGGAGAGGG 59.311 57.143 0.00 0.00 42.00 4.30
128 129 1.689273 CGAATTGGACTAGGAGAGGGG 59.311 57.143 0.00 0.00 0.00 4.79
129 130 2.050918 GAATTGGACTAGGAGAGGGGG 58.949 57.143 0.00 0.00 0.00 5.40
156 157 1.675007 CCCCCTTTCCTTCTCCTTCT 58.325 55.000 0.00 0.00 0.00 2.85
157 158 1.562008 CCCCCTTTCCTTCTCCTTCTC 59.438 57.143 0.00 0.00 0.00 2.87
158 159 1.562008 CCCCTTTCCTTCTCCTTCTCC 59.438 57.143 0.00 0.00 0.00 3.71
159 160 1.562008 CCCTTTCCTTCTCCTTCTCCC 59.438 57.143 0.00 0.00 0.00 4.30
160 161 1.562008 CCTTTCCTTCTCCTTCTCCCC 59.438 57.143 0.00 0.00 0.00 4.81
161 162 1.562008 CTTTCCTTCTCCTTCTCCCCC 59.438 57.143 0.00 0.00 0.00 5.40
162 163 0.800239 TTCCTTCTCCTTCTCCCCCT 59.200 55.000 0.00 0.00 0.00 4.79
163 164 0.800239 TCCTTCTCCTTCTCCCCCTT 59.200 55.000 0.00 0.00 0.00 3.95
164 165 1.208706 CCTTCTCCTTCTCCCCCTTC 58.791 60.000 0.00 0.00 0.00 3.46
165 166 1.208706 CTTCTCCTTCTCCCCCTTCC 58.791 60.000 0.00 0.00 0.00 3.46
166 167 0.800239 TTCTCCTTCTCCCCCTTCCT 59.200 55.000 0.00 0.00 0.00 3.36
167 168 0.800239 TCTCCTTCTCCCCCTTCCTT 59.200 55.000 0.00 0.00 0.00 3.36
168 169 1.154434 TCTCCTTCTCCCCCTTCCTTT 59.846 52.381 0.00 0.00 0.00 3.11
169 170 1.562008 CTCCTTCTCCCCCTTCCTTTC 59.438 57.143 0.00 0.00 0.00 2.62
170 171 0.626382 CCTTCTCCCCCTTCCTTTCC 59.374 60.000 0.00 0.00 0.00 3.13
171 172 0.626382 CTTCTCCCCCTTCCTTTCCC 59.374 60.000 0.00 0.00 0.00 3.97
172 173 0.849540 TTCTCCCCCTTCCTTTCCCC 60.850 60.000 0.00 0.00 0.00 4.81
173 174 2.204401 TCCCCCTTCCTTTCCCCC 60.204 66.667 0.00 0.00 0.00 5.40
174 175 2.204464 CCCCCTTCCTTTCCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
175 176 2.317378 CCCCCTTCCTTTCCCCCTC 61.317 68.421 0.00 0.00 0.00 4.30
176 177 2.317378 CCCCTTCCTTTCCCCCTCC 61.317 68.421 0.00 0.00 0.00 4.30
177 178 1.230314 CCCTTCCTTTCCCCCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
178 179 0.045778 CCCTTCCTTTCCCCCTCCTA 59.954 60.000 0.00 0.00 0.00 2.94
179 180 1.512735 CCTTCCTTTCCCCCTCCTAG 58.487 60.000 0.00 0.00 0.00 3.02
180 181 1.274475 CCTTCCTTTCCCCCTCCTAGT 60.274 57.143 0.00 0.00 0.00 2.57
181 182 2.022330 CCTTCCTTTCCCCCTCCTAGTA 60.022 54.545 0.00 0.00 0.00 1.82
182 183 3.310193 CTTCCTTTCCCCCTCCTAGTAG 58.690 54.545 0.00 0.00 0.00 2.57
183 184 1.579191 TCCTTTCCCCCTCCTAGTAGG 59.421 57.143 10.24 10.24 36.46 3.18
184 185 1.579191 CCTTTCCCCCTCCTAGTAGGA 59.421 57.143 18.15 18.15 43.43 2.94
196 197 5.649970 TCCTAGTAGGAGTAGGAAAGAGG 57.350 47.826 15.33 0.00 44.96 3.69
197 198 4.416179 TCCTAGTAGGAGTAGGAAAGAGGG 59.584 50.000 15.33 0.00 44.96 4.30
198 199 3.691698 AGTAGGAGTAGGAAAGAGGGG 57.308 52.381 0.00 0.00 0.00 4.79
199 200 3.208173 AGTAGGAGTAGGAAAGAGGGGA 58.792 50.000 0.00 0.00 0.00 4.81
200 201 3.601537 AGTAGGAGTAGGAAAGAGGGGAA 59.398 47.826 0.00 0.00 0.00 3.97
201 202 3.805360 AGGAGTAGGAAAGAGGGGAAT 57.195 47.619 0.00 0.00 0.00 3.01
202 203 3.659841 AGGAGTAGGAAAGAGGGGAATC 58.340 50.000 0.00 0.00 0.00 2.52
203 204 2.706723 GGAGTAGGAAAGAGGGGAATCC 59.293 54.545 0.00 0.00 0.00 3.01
216 217 3.663632 AGGGGAATCCTACTCCTACTAGG 59.336 52.174 0.00 0.00 45.98 3.02
217 218 3.661654 GGGGAATCCTACTCCTACTAGGA 59.338 52.174 4.65 4.65 43.43 2.94
238 239 2.825264 GGATTCCTCCTCCTGGCG 59.175 66.667 0.00 0.00 38.65 5.69
239 240 2.110006 GATTCCTCCTCCTGGCGC 59.890 66.667 0.00 0.00 0.00 6.53
240 241 3.798954 GATTCCTCCTCCTGGCGCG 62.799 68.421 0.00 0.00 0.00 6.86
284 285 2.165641 CCCCCTTTGGAAAAATCGTAGC 59.834 50.000 0.00 0.00 35.39 3.58
285 286 3.089284 CCCCTTTGGAAAAATCGTAGCT 58.911 45.455 0.00 0.00 35.39 3.32
286 287 3.128764 CCCCTTTGGAAAAATCGTAGCTC 59.871 47.826 0.00 0.00 35.39 4.09
287 288 3.756434 CCCTTTGGAAAAATCGTAGCTCA 59.244 43.478 0.00 0.00 0.00 4.26
457 459 3.754850 CCAGAGATGATTTGCTGTGTCAA 59.245 43.478 0.00 0.00 0.00 3.18
526 528 1.230324 GTGAGTCCCACAAAGTCAGC 58.770 55.000 0.00 0.00 45.03 4.26
527 529 1.131638 TGAGTCCCACAAAGTCAGCT 58.868 50.000 0.00 0.00 0.00 4.24
528 530 1.202687 TGAGTCCCACAAAGTCAGCTG 60.203 52.381 7.63 7.63 0.00 4.24
529 531 0.109342 AGTCCCACAAAGTCAGCTGG 59.891 55.000 15.13 0.00 0.00 4.85
530 532 0.108585 GTCCCACAAAGTCAGCTGGA 59.891 55.000 15.13 0.00 0.00 3.86
542 544 4.935885 GTCAGCTGGACTAGTTTTGATG 57.064 45.455 15.13 0.00 43.46 3.07
544 546 5.181748 GTCAGCTGGACTAGTTTTGATGAT 58.818 41.667 15.13 0.00 43.46 2.45
546 548 6.256757 GTCAGCTGGACTAGTTTTGATGATAC 59.743 42.308 15.13 0.00 43.46 2.24
547 549 6.070824 TCAGCTGGACTAGTTTTGATGATACA 60.071 38.462 15.13 0.00 0.00 2.29
548 550 6.765036 CAGCTGGACTAGTTTTGATGATACAT 59.235 38.462 5.57 0.00 0.00 2.29
549 551 7.281774 CAGCTGGACTAGTTTTGATGATACATT 59.718 37.037 5.57 0.00 0.00 2.71
551 553 8.552034 GCTGGACTAGTTTTGATGATACATTAC 58.448 37.037 0.00 0.00 0.00 1.89
552 554 8.958119 TGGACTAGTTTTGATGATACATTACC 57.042 34.615 0.00 0.00 0.00 2.85
556 558 9.396022 ACTAGTTTTGATGATACATTACCAAGG 57.604 33.333 0.00 0.00 0.00 3.61
572 574 2.154462 CAAGGCAAGTACCAGTTCCAG 58.846 52.381 0.00 0.00 0.00 3.86
619 1050 1.288419 ACATTGCGTGAATCGTGCGA 61.288 50.000 0.00 0.00 42.13 5.10
620 1051 0.584785 CATTGCGTGAATCGTGCGAG 60.585 55.000 0.00 0.00 42.13 5.03
622 1053 2.809601 GCGTGAATCGTGCGAGGT 60.810 61.111 0.00 0.00 42.13 3.85
623 1054 1.515519 GCGTGAATCGTGCGAGGTA 60.516 57.895 0.00 0.00 42.13 3.08
656 1088 4.820744 GGTGGTGCCATGGCCGAT 62.821 66.667 33.44 0.00 41.09 4.18
669 1101 2.098614 TGGCCGATGTTAATTGCACAT 58.901 42.857 0.00 5.08 37.58 3.21
799 2582 5.741093 GCCATGGATGAAAAGAAATGGATCC 60.741 44.000 18.40 4.20 37.36 3.36
844 2685 2.485426 CACAATCAGCACGGAATCTGTT 59.515 45.455 0.00 0.00 0.00 3.16
959 2813 2.546795 GGGCACATAGTCGGATTCAGAG 60.547 54.545 0.00 0.00 0.00 3.35
1058 3112 1.203492 ACAGACCTCTCCCAAATCCCT 60.203 52.381 0.00 0.00 0.00 4.20
1059 3113 1.488393 CAGACCTCTCCCAAATCCCTC 59.512 57.143 0.00 0.00 0.00 4.30
1060 3114 0.466124 GACCTCTCCCAAATCCCTCG 59.534 60.000 0.00 0.00 0.00 4.63
1065 3119 4.109675 CCCAAATCCCTCGCCCGT 62.110 66.667 0.00 0.00 0.00 5.28
1078 3134 2.716244 CCCGTCCTCGATCGACAG 59.284 66.667 15.15 8.92 39.71 3.51
1216 3329 0.253044 ACGCCGTCACCTACTACCTA 59.747 55.000 0.00 0.00 0.00 3.08
1282 3395 2.444624 CCACCGCGTCAACATCTCG 61.445 63.158 4.92 0.00 0.00 4.04
1366 3481 1.070289 GACCGGTTCTTCTTCACCACT 59.930 52.381 9.42 0.00 31.84 4.00
1452 3567 2.637872 TCCAGAAGACCACGGAGATTTT 59.362 45.455 0.00 0.00 0.00 1.82
1648 3764 0.178068 AGGAATCGGCTGCGTACAAT 59.822 50.000 0.00 0.00 0.00 2.71
1650 3766 0.229753 GAATCGGCTGCGTACAATCG 59.770 55.000 0.00 0.00 0.00 3.34
1870 6064 2.749621 CAACTTCCCTGTTCAGTATGCC 59.250 50.000 0.00 0.00 34.76 4.40
2247 6517 4.907457 CTTGGACCAAGGTGTGCT 57.093 55.556 24.42 0.00 37.77 4.40
2248 6518 2.334307 CTTGGACCAAGGTGTGCTG 58.666 57.895 24.42 0.00 37.77 4.41
2249 6519 1.152777 TTGGACCAAGGTGTGCTGG 60.153 57.895 1.69 0.00 38.77 4.85
2250 6520 1.640593 TTGGACCAAGGTGTGCTGGA 61.641 55.000 1.69 0.00 36.49 3.86
2251 6521 1.302832 GGACCAAGGTGTGCTGGAG 60.303 63.158 0.00 0.00 36.49 3.86
2252 6522 1.302832 GACCAAGGTGTGCTGGAGG 60.303 63.158 0.00 0.00 36.49 4.30
2253 6523 1.768684 GACCAAGGTGTGCTGGAGGA 61.769 60.000 0.00 0.00 36.49 3.71
2254 6524 1.302832 CCAAGGTGTGCTGGAGGAC 60.303 63.158 0.00 0.00 34.35 3.85
2255 6525 1.451504 CAAGGTGTGCTGGAGGACA 59.548 57.895 0.00 0.00 44.12 4.02
2647 7003 6.928979 TGCAAGCTAGTAAAACTGTTGTTA 57.071 33.333 0.00 0.00 34.96 2.41
2917 7302 2.810274 GCAGAGCAGATTCAAGTTGTGA 59.190 45.455 2.11 0.00 0.00 3.58
2956 8360 6.025749 TCTGTCTATTTACAGTGTGGAGTG 57.974 41.667 5.88 0.00 45.78 3.51
2999 8420 7.230309 TCAATGTTCATGATTTACAGTGTGGAA 59.770 33.333 20.03 0.98 38.56 3.53
3036 8457 7.727331 TCCTTGAAATTTAAGTGCAATTTGG 57.273 32.000 4.05 0.00 34.61 3.28
3047 8468 3.118665 AGTGCAATTTGGCTGTCTTGTTT 60.119 39.130 0.00 0.00 34.04 2.83
3273 8707 3.071167 ACAGGAGGTACAAGAGGTTGAAC 59.929 47.826 0.00 0.00 37.10 3.18
3280 8714 5.071788 AGGTACAAGAGGTTGAACTGAATCA 59.928 40.000 0.00 0.00 37.10 2.57
3461 8973 3.469008 AATGACTGACAGTTTCGGACA 57.531 42.857 10.01 2.10 39.23 4.02
3598 9111 4.467084 GAGGTTGCGGGGCATCGA 62.467 66.667 3.72 0.00 38.76 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.580815 CCGAGGGGTTCCGGTAAC 59.419 66.667 0.00 4.72 40.78 2.50
13 14 1.933307 AAGGCCCATTAACCCCGAGG 61.933 60.000 0.00 0.00 40.04 4.63
14 15 0.841289 TAAGGCCCATTAACCCCGAG 59.159 55.000 0.00 0.00 0.00 4.63
15 16 1.525175 ATAAGGCCCATTAACCCCGA 58.475 50.000 0.00 0.00 0.00 5.14
16 17 1.960689 CAATAAGGCCCATTAACCCCG 59.039 52.381 0.00 0.00 0.00 5.73
17 18 2.325484 CCAATAAGGCCCATTAACCCC 58.675 52.381 0.00 0.00 0.00 4.95
18 19 2.325484 CCCAATAAGGCCCATTAACCC 58.675 52.381 0.00 0.00 35.39 4.11
29 30 1.421646 CTCCACTAGGGCCCAATAAGG 59.578 57.143 27.56 18.74 36.21 2.69
30 31 2.370189 CTCTCCACTAGGGCCCAATAAG 59.630 54.545 27.56 17.68 36.21 1.73
31 32 2.022428 TCTCTCCACTAGGGCCCAATAA 60.022 50.000 27.56 5.13 36.21 1.40
32 33 1.578703 TCTCTCCACTAGGGCCCAATA 59.421 52.381 27.56 7.70 36.21 1.90
33 34 0.343372 TCTCTCCACTAGGGCCCAAT 59.657 55.000 27.56 6.67 36.21 3.16
34 35 0.325671 CTCTCTCCACTAGGGCCCAA 60.326 60.000 27.56 0.25 36.21 4.12
35 36 1.221909 TCTCTCTCCACTAGGGCCCA 61.222 60.000 27.56 9.36 36.21 5.36
36 37 0.469144 CTCTCTCTCCACTAGGGCCC 60.469 65.000 16.46 16.46 36.21 5.80
37 38 0.553819 TCTCTCTCTCCACTAGGGCC 59.446 60.000 0.00 0.00 36.21 5.80
38 39 1.493022 TCTCTCTCTCTCCACTAGGGC 59.507 57.143 0.00 0.00 36.21 5.19
39 40 3.045634 TCTCTCTCTCTCTCCACTAGGG 58.954 54.545 0.00 0.00 34.83 3.53
40 41 3.967326 TCTCTCTCTCTCTCTCCACTAGG 59.033 52.174 0.00 0.00 0.00 3.02
41 42 4.895889 TCTCTCTCTCTCTCTCTCCACTAG 59.104 50.000 0.00 0.00 0.00 2.57
42 43 4.878968 TCTCTCTCTCTCTCTCTCCACTA 58.121 47.826 0.00 0.00 0.00 2.74
43 44 3.708631 CTCTCTCTCTCTCTCTCTCCACT 59.291 52.174 0.00 0.00 0.00 4.00
44 45 3.181461 CCTCTCTCTCTCTCTCTCTCCAC 60.181 56.522 0.00 0.00 0.00 4.02
45 46 3.041211 CCTCTCTCTCTCTCTCTCTCCA 58.959 54.545 0.00 0.00 0.00 3.86
46 47 2.370189 CCCTCTCTCTCTCTCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
47 48 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
48 49 2.412591 CCCCTCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
49 50 1.202818 GCCCCTCTCTCTCTCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
50 51 0.846693 GCCCCTCTCTCTCTCTCTCT 59.153 60.000 0.00 0.00 0.00 3.10
51 52 0.178990 GGCCCCTCTCTCTCTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
52 53 1.930520 GGCCCCTCTCTCTCTCTCT 59.069 63.158 0.00 0.00 0.00 3.10
53 54 1.528309 CGGCCCCTCTCTCTCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
54 55 2.600731 CGGCCCCTCTCTCTCTCT 59.399 66.667 0.00 0.00 0.00 3.10
55 56 2.520741 CCGGCCCCTCTCTCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
56 57 4.851214 GCCGGCCCCTCTCTCTCT 62.851 72.222 18.11 0.00 0.00 3.10
90 91 4.825679 GACCAGAGGGGGAGGGGG 62.826 77.778 0.00 0.00 42.91 5.40
91 92 4.825679 GGACCAGAGGGGGAGGGG 62.826 77.778 0.00 0.00 42.91 4.79
93 94 2.898472 ATTCGGACCAGAGGGGGAGG 62.898 65.000 0.00 0.00 42.91 4.30
94 95 0.983378 AATTCGGACCAGAGGGGGAG 60.983 60.000 0.00 0.00 42.91 4.30
95 96 1.082206 AATTCGGACCAGAGGGGGA 59.918 57.895 0.00 0.00 42.91 4.81
96 97 1.224592 CAATTCGGACCAGAGGGGG 59.775 63.158 0.00 0.00 42.91 5.40
97 98 1.224592 CCAATTCGGACCAGAGGGG 59.775 63.158 0.00 0.00 44.81 4.79
98 99 2.296920 TCCAATTCGGACCAGAGGG 58.703 57.895 0.00 0.00 39.64 4.30
106 107 2.667470 CCTCTCCTAGTCCAATTCGGA 58.333 52.381 0.00 0.00 43.61 4.55
107 108 1.689273 CCCTCTCCTAGTCCAATTCGG 59.311 57.143 0.00 0.00 0.00 4.30
108 109 1.689273 CCCCTCTCCTAGTCCAATTCG 59.311 57.143 0.00 0.00 0.00 3.34
109 110 2.050918 CCCCCTCTCCTAGTCCAATTC 58.949 57.143 0.00 0.00 0.00 2.17
110 111 2.198334 CCCCCTCTCCTAGTCCAATT 57.802 55.000 0.00 0.00 0.00 2.32
111 112 3.979313 CCCCCTCTCCTAGTCCAAT 57.021 57.895 0.00 0.00 0.00 3.16
137 138 1.562008 GAGAAGGAGAAGGAAAGGGGG 59.438 57.143 0.00 0.00 0.00 5.40
138 139 1.562008 GGAGAAGGAGAAGGAAAGGGG 59.438 57.143 0.00 0.00 0.00 4.79
139 140 1.562008 GGGAGAAGGAGAAGGAAAGGG 59.438 57.143 0.00 0.00 0.00 3.95
140 141 1.562008 GGGGAGAAGGAGAAGGAAAGG 59.438 57.143 0.00 0.00 0.00 3.11
141 142 1.562008 GGGGGAGAAGGAGAAGGAAAG 59.438 57.143 0.00 0.00 0.00 2.62
142 143 1.154434 AGGGGGAGAAGGAGAAGGAAA 59.846 52.381 0.00 0.00 0.00 3.13
143 144 0.800239 AGGGGGAGAAGGAGAAGGAA 59.200 55.000 0.00 0.00 0.00 3.36
144 145 0.800239 AAGGGGGAGAAGGAGAAGGA 59.200 55.000 0.00 0.00 0.00 3.36
145 146 1.208706 GAAGGGGGAGAAGGAGAAGG 58.791 60.000 0.00 0.00 0.00 3.46
146 147 1.208706 GGAAGGGGGAGAAGGAGAAG 58.791 60.000 0.00 0.00 0.00 2.85
147 148 0.800239 AGGAAGGGGGAGAAGGAGAA 59.200 55.000 0.00 0.00 0.00 2.87
148 149 0.800239 AAGGAAGGGGGAGAAGGAGA 59.200 55.000 0.00 0.00 0.00 3.71
149 150 1.562008 GAAAGGAAGGGGGAGAAGGAG 59.438 57.143 0.00 0.00 0.00 3.69
150 151 1.670059 GAAAGGAAGGGGGAGAAGGA 58.330 55.000 0.00 0.00 0.00 3.36
151 152 0.626382 GGAAAGGAAGGGGGAGAAGG 59.374 60.000 0.00 0.00 0.00 3.46
152 153 0.626382 GGGAAAGGAAGGGGGAGAAG 59.374 60.000 0.00 0.00 0.00 2.85
153 154 0.849540 GGGGAAAGGAAGGGGGAGAA 60.850 60.000 0.00 0.00 0.00 2.87
154 155 1.230182 GGGGAAAGGAAGGGGGAGA 60.230 63.158 0.00 0.00 0.00 3.71
155 156 2.317378 GGGGGAAAGGAAGGGGGAG 61.317 68.421 0.00 0.00 0.00 4.30
156 157 2.204401 GGGGGAAAGGAAGGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
157 158 2.204464 AGGGGGAAAGGAAGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
158 159 2.317378 GGAGGGGGAAAGGAAGGGG 61.317 68.421 0.00 0.00 0.00 4.79
159 160 0.045778 TAGGAGGGGGAAAGGAAGGG 59.954 60.000 0.00 0.00 0.00 3.95
160 161 1.274475 ACTAGGAGGGGGAAAGGAAGG 60.274 57.143 0.00 0.00 0.00 3.46
161 162 2.272074 ACTAGGAGGGGGAAAGGAAG 57.728 55.000 0.00 0.00 0.00 3.46
162 163 2.022330 CCTACTAGGAGGGGGAAAGGAA 60.022 54.545 14.01 0.00 37.67 3.36
163 164 1.579191 CCTACTAGGAGGGGGAAAGGA 59.421 57.143 14.01 0.00 37.67 3.36
164 165 1.579191 TCCTACTAGGAGGGGGAAAGG 59.421 57.143 21.59 0.00 40.06 3.11
174 175 4.416179 CCCTCTTTCCTACTCCTACTAGGA 59.584 50.000 4.65 4.65 43.43 2.94
175 176 4.448054 CCCCTCTTTCCTACTCCTACTAGG 60.448 54.167 0.00 0.00 36.46 3.02
176 177 4.416179 TCCCCTCTTTCCTACTCCTACTAG 59.584 50.000 0.00 0.00 0.00 2.57
177 178 4.387232 TCCCCTCTTTCCTACTCCTACTA 58.613 47.826 0.00 0.00 0.00 1.82
178 179 3.208173 TCCCCTCTTTCCTACTCCTACT 58.792 50.000 0.00 0.00 0.00 2.57
179 180 3.684408 TCCCCTCTTTCCTACTCCTAC 57.316 52.381 0.00 0.00 0.00 3.18
180 181 4.388804 GGATTCCCCTCTTTCCTACTCCTA 60.389 50.000 0.00 0.00 0.00 2.94
181 182 3.633952 GGATTCCCCTCTTTCCTACTCCT 60.634 52.174 0.00 0.00 0.00 3.69
182 183 2.706723 GGATTCCCCTCTTTCCTACTCC 59.293 54.545 0.00 0.00 0.00 3.85
183 184 3.659841 AGGATTCCCCTCTTTCCTACTC 58.340 50.000 0.00 0.00 43.31 2.59
184 185 3.805360 AGGATTCCCCTCTTTCCTACT 57.195 47.619 0.00 0.00 43.31 2.57
186 187 4.388804 GGAGTAGGATTCCCCTCTTTCCTA 60.389 50.000 15.78 0.00 43.31 2.94
187 188 3.633952 GGAGTAGGATTCCCCTCTTTCCT 60.634 52.174 15.78 0.00 43.31 3.36
188 189 2.706723 GGAGTAGGATTCCCCTCTTTCC 59.293 54.545 15.78 5.61 43.31 3.13
189 190 3.659841 AGGAGTAGGATTCCCCTCTTTC 58.340 50.000 15.78 4.29 43.31 2.62
190 191 3.805360 AGGAGTAGGATTCCCCTCTTT 57.195 47.619 15.78 6.09 43.31 2.52
191 192 3.800736 AGTAGGAGTAGGATTCCCCTCTT 59.199 47.826 15.78 12.39 43.31 2.85
192 193 3.418985 AGTAGGAGTAGGATTCCCCTCT 58.581 50.000 15.78 5.96 43.31 3.69
193 194 3.907459 AGTAGGAGTAGGATTCCCCTC 57.093 52.381 10.25 10.25 43.31 4.30
194 195 3.663632 CCTAGTAGGAGTAGGATTCCCCT 59.336 52.174 11.09 1.25 42.66 4.79
195 196 3.661654 TCCTAGTAGGAGTAGGATTCCCC 59.338 52.174 15.33 0.00 43.52 4.81
221 222 2.825264 CGCCAGGAGGAGGAATCC 59.175 66.667 0.00 0.00 36.89 3.01
222 223 2.110006 GCGCCAGGAGGAGGAATC 59.890 66.667 0.00 0.00 36.89 2.52
223 224 3.854669 CGCGCCAGGAGGAGGAAT 61.855 66.667 0.00 0.00 36.89 3.01
263 264 2.165641 GCTACGATTTTTCCAAAGGGGG 59.834 50.000 0.00 0.00 37.22 5.40
264 265 3.089284 AGCTACGATTTTTCCAAAGGGG 58.911 45.455 0.00 0.00 38.37 4.79
265 266 3.756434 TGAGCTACGATTTTTCCAAAGGG 59.244 43.478 0.00 0.00 0.00 3.95
266 267 5.371115 TTGAGCTACGATTTTTCCAAAGG 57.629 39.130 0.00 0.00 0.00 3.11
267 268 7.148755 CCATTTTGAGCTACGATTTTTCCAAAG 60.149 37.037 0.00 0.00 0.00 2.77
268 269 6.644592 CCATTTTGAGCTACGATTTTTCCAAA 59.355 34.615 0.00 0.00 0.00 3.28
269 270 6.155827 CCATTTTGAGCTACGATTTTTCCAA 58.844 36.000 0.00 0.00 0.00 3.53
270 271 5.242838 ACCATTTTGAGCTACGATTTTTCCA 59.757 36.000 0.00 0.00 0.00 3.53
271 272 5.709966 ACCATTTTGAGCTACGATTTTTCC 58.290 37.500 0.00 0.00 0.00 3.13
272 273 7.302524 TGTACCATTTTGAGCTACGATTTTTC 58.697 34.615 0.00 0.00 0.00 2.29
273 274 7.209471 TGTACCATTTTGAGCTACGATTTTT 57.791 32.000 0.00 0.00 0.00 1.94
274 275 6.811253 TGTACCATTTTGAGCTACGATTTT 57.189 33.333 0.00 0.00 0.00 1.82
275 276 6.811253 TTGTACCATTTTGAGCTACGATTT 57.189 33.333 0.00 0.00 0.00 2.17
276 277 6.608610 GTTTGTACCATTTTGAGCTACGATT 58.391 36.000 0.00 0.00 0.00 3.34
277 278 5.163893 CGTTTGTACCATTTTGAGCTACGAT 60.164 40.000 0.00 0.00 0.00 3.73
278 279 4.150980 CGTTTGTACCATTTTGAGCTACGA 59.849 41.667 0.00 0.00 0.00 3.43
279 280 4.150980 TCGTTTGTACCATTTTGAGCTACG 59.849 41.667 0.00 0.00 0.00 3.51
280 281 5.600908 TCGTTTGTACCATTTTGAGCTAC 57.399 39.130 0.00 0.00 0.00 3.58
281 282 6.621316 TTTCGTTTGTACCATTTTGAGCTA 57.379 33.333 0.00 0.00 0.00 3.32
282 283 5.508200 TTTCGTTTGTACCATTTTGAGCT 57.492 34.783 0.00 0.00 0.00 4.09
283 284 5.746721 ACTTTTCGTTTGTACCATTTTGAGC 59.253 36.000 0.00 0.00 0.00 4.26
284 285 7.749539 AACTTTTCGTTTGTACCATTTTGAG 57.250 32.000 0.00 0.00 29.63 3.02
448 450 3.189080 TGCTGATGTAATGTTGACACAGC 59.811 43.478 16.47 16.47 43.94 4.40
457 459 3.005554 GCTGACTGTGCTGATGTAATGT 58.994 45.455 0.00 0.00 0.00 2.71
521 523 4.569943 TCATCAAAACTAGTCCAGCTGAC 58.430 43.478 17.39 11.61 44.82 3.51
522 524 4.890158 TCATCAAAACTAGTCCAGCTGA 57.110 40.909 17.39 0.00 0.00 4.26
523 525 6.108687 TGTATCATCAAAACTAGTCCAGCTG 58.891 40.000 6.78 6.78 0.00 4.24
524 526 6.299805 TGTATCATCAAAACTAGTCCAGCT 57.700 37.500 0.00 0.00 0.00 4.24
525 527 7.559590 AATGTATCATCAAAACTAGTCCAGC 57.440 36.000 0.00 0.00 0.00 4.85
526 528 9.046296 GGTAATGTATCATCAAAACTAGTCCAG 57.954 37.037 0.00 0.00 0.00 3.86
527 529 8.544622 TGGTAATGTATCATCAAAACTAGTCCA 58.455 33.333 0.00 0.00 0.00 4.02
528 530 8.958119 TGGTAATGTATCATCAAAACTAGTCC 57.042 34.615 0.00 0.00 0.00 3.85
530 532 9.396022 CCTTGGTAATGTATCATCAAAACTAGT 57.604 33.333 0.00 0.00 0.00 2.57
531 533 8.345565 GCCTTGGTAATGTATCATCAAAACTAG 58.654 37.037 0.00 0.00 0.00 2.57
532 534 7.831690 TGCCTTGGTAATGTATCATCAAAACTA 59.168 33.333 0.00 0.00 0.00 2.24
533 535 6.663093 TGCCTTGGTAATGTATCATCAAAACT 59.337 34.615 0.00 0.00 0.00 2.66
537 539 6.186957 ACTTGCCTTGGTAATGTATCATCAA 58.813 36.000 0.00 0.00 0.00 2.57
538 540 5.754782 ACTTGCCTTGGTAATGTATCATCA 58.245 37.500 0.00 0.00 0.00 3.07
539 541 6.204882 GGTACTTGCCTTGGTAATGTATCATC 59.795 42.308 0.00 0.00 0.00 2.92
540 542 6.062095 GGTACTTGCCTTGGTAATGTATCAT 58.938 40.000 0.00 0.00 0.00 2.45
541 543 5.045505 TGGTACTTGCCTTGGTAATGTATCA 60.046 40.000 0.00 8.02 0.00 2.15
542 544 5.433526 TGGTACTTGCCTTGGTAATGTATC 58.566 41.667 0.00 0.00 0.00 2.24
544 546 4.287585 ACTGGTACTTGCCTTGGTAATGTA 59.712 41.667 0.00 0.00 0.00 2.29
546 548 3.686016 ACTGGTACTTGCCTTGGTAATG 58.314 45.455 0.00 0.00 0.00 1.90
547 549 4.332828 GAACTGGTACTTGCCTTGGTAAT 58.667 43.478 0.00 0.00 0.00 1.89
548 550 3.497227 GGAACTGGTACTTGCCTTGGTAA 60.497 47.826 0.00 0.00 0.00 2.85
549 551 2.039348 GGAACTGGTACTTGCCTTGGTA 59.961 50.000 0.00 0.00 0.00 3.25
551 553 1.202879 TGGAACTGGTACTTGCCTTGG 60.203 52.381 0.00 0.00 0.00 3.61
552 554 2.154462 CTGGAACTGGTACTTGCCTTG 58.846 52.381 0.00 0.00 0.00 3.61
555 557 3.249687 CCTGGAACTGGTACTTGCC 57.750 57.895 0.00 0.00 42.87 4.52
572 574 2.424956 GTCAGAATGGATTCAAGTGGCC 59.575 50.000 0.00 0.00 39.23 5.36
619 1050 2.485479 CCTGCGTGATGCCTATTTACCT 60.485 50.000 0.00 0.00 45.60 3.08
620 1051 1.873591 CCTGCGTGATGCCTATTTACC 59.126 52.381 0.00 0.00 45.60 2.85
622 1053 2.560504 CACCTGCGTGATGCCTATTTA 58.439 47.619 0.00 0.00 45.60 1.40
623 1054 1.382522 CACCTGCGTGATGCCTATTT 58.617 50.000 0.00 0.00 45.60 1.40
669 1101 4.284550 GGCCCCTGTCCAACTGCA 62.285 66.667 0.00 0.00 0.00 4.41
799 2582 7.430502 GTGATTCTTGATTTTGAGCCTTATTCG 59.569 37.037 0.00 0.00 0.00 3.34
959 2813 1.393883 GGACGCGTCAGATTTCCTTTC 59.606 52.381 37.26 14.11 0.00 2.62
1058 3112 4.843719 TCGATCGAGGACGGGCGA 62.844 66.667 15.15 0.00 40.57 5.54
1059 3113 4.609247 GTCGATCGAGGACGGGCG 62.609 72.222 20.09 0.00 40.21 6.13
1060 3114 3.471244 CTGTCGATCGAGGACGGGC 62.471 68.421 20.09 5.31 37.18 6.13
1065 3119 2.415608 GGGTGCTGTCGATCGAGGA 61.416 63.158 20.09 6.23 0.00 3.71
1078 3134 3.911137 GCAGCTAGGAAAGGGTGC 58.089 61.111 0.00 0.00 46.73 5.01
1192 3305 2.598099 TAGGTGACGGCGTCCACA 60.598 61.111 34.28 16.52 0.00 4.17
1452 3567 3.691342 CCTTGACTCCCGCGTGGA 61.691 66.667 18.79 14.41 42.41 4.02
1639 3755 2.729360 CTCTTGTTGACGATTGTACGCA 59.271 45.455 0.00 0.00 36.70 5.24
1648 3764 1.138069 TCTGGTTGCTCTTGTTGACGA 59.862 47.619 0.00 0.00 0.00 4.20
1650 3766 1.876156 CCTCTGGTTGCTCTTGTTGAC 59.124 52.381 0.00 0.00 0.00 3.18
1870 6064 0.745486 TGGACTCGCATGATGCTTGG 60.745 55.000 16.17 7.61 42.25 3.61
2242 6512 1.002990 CAGCATGTCCTCCAGCACA 60.003 57.895 0.00 0.00 0.00 4.57
2244 6514 2.045634 GCAGCATGTCCTCCAGCA 60.046 61.111 0.00 0.00 39.31 4.41
2245 6515 2.045634 TGCAGCATGTCCTCCAGC 60.046 61.111 0.00 0.00 39.31 4.85
2246 6516 0.743701 GACTGCAGCATGTCCTCCAG 60.744 60.000 15.27 0.00 39.31 3.86
2247 6517 1.297689 GACTGCAGCATGTCCTCCA 59.702 57.895 15.27 0.00 39.31 3.86
2248 6518 1.451028 GGACTGCAGCATGTCCTCC 60.451 63.158 25.35 7.63 46.65 4.30
2249 6519 4.215349 GGACTGCAGCATGTCCTC 57.785 61.111 25.35 1.14 46.65 3.71
2251 6521 0.745845 AATCGGACTGCAGCATGTCC 60.746 55.000 23.88 23.88 46.69 4.02
2252 6522 1.594862 GTAATCGGACTGCAGCATGTC 59.405 52.381 15.27 13.63 39.31 3.06
2253 6523 1.656652 GTAATCGGACTGCAGCATGT 58.343 50.000 15.27 0.00 39.31 3.21
2254 6524 0.940126 GGTAATCGGACTGCAGCATG 59.060 55.000 15.27 3.19 40.87 4.06
2255 6525 0.179045 GGGTAATCGGACTGCAGCAT 60.179 55.000 15.27 0.00 0.00 3.79
2316 6652 2.184322 GAGCGTCAAGATCCGGCA 59.816 61.111 0.00 0.00 0.00 5.69
2647 7003 3.265221 TCCATCACAGGAGCAAGAAGAAT 59.735 43.478 0.00 0.00 32.77 2.40
2956 8360 8.556194 TGAACATTGACACTGTAATAACTGTTC 58.444 33.333 0.00 0.00 35.79 3.18
3022 8443 4.099266 ACAAGACAGCCAAATTGCACTTAA 59.901 37.500 0.00 0.00 0.00 1.85
3036 8457 8.342634 TGTAAATTCAGTTAGAAACAAGACAGC 58.657 33.333 0.00 0.00 40.22 4.40
3273 8707 5.259632 AGGGAATTCAGAAAGGTGATTCAG 58.740 41.667 7.93 0.00 0.00 3.02
3280 8714 7.855784 ATAACAAAAGGGAATTCAGAAAGGT 57.144 32.000 7.93 0.00 0.00 3.50
3461 8973 6.488006 AGACTTAAATGATCAACAAGTGCAGT 59.512 34.615 19.02 6.58 29.89 4.40
3594 9107 2.551287 CCTCTCCAGTAGACCGATCGAT 60.551 54.545 18.66 0.00 0.00 3.59
3598 9111 0.820074 CGCCTCTCCAGTAGACCGAT 60.820 60.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.