Multiple sequence alignment - TraesCS7D01G197000

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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 TraesCS7D01G197000 chr7D 100.000 4806 0 0 1 4806 153640502 153635697 0.000000e+00 8876.0
1 TraesCS7D01G197000 chr7B 96.619 1952 45 9 1 1949 115410497 115408564 0.000000e+00 3219.0
2 TraesCS7D01G197000 chr7B 93.207 1266 44 13 2782 4012 115405544 115404286 0.000000e+00 1823.0
3 TraesCS7D01G197000 chr7B 81.051 818 119 26 3129 3934 547344499 547345292 1.900000e-173 619.0
4 TraesCS7D01G197000 chr7B 95.870 339 8 2 2293 2631 115407270 115406938 1.180000e-150 544.0
5 TraesCS7D01G197000 chr7B 77.814 933 111 41 1313 2152 547342559 547343488 5.590000e-134 488.0
6 TraesCS7D01G197000 chr7B 96.233 292 11 0 4515 4806 115403904 115403613 3.360000e-131 479.0
7 TraesCS7D01G197000 chr7B 95.714 210 9 0 1945 2154 115407476 115407267 5.960000e-89 339.0
8 TraesCS7D01G197000 chr7B 92.818 181 10 2 4288 4465 115404100 115403920 4.770000e-65 259.0
9 TraesCS7D01G197000 chr7B 93.678 174 10 1 4070 4243 115404270 115404098 4.770000e-65 259.0
10 TraesCS7D01G197000 chr7B 92.517 147 11 0 2149 2295 644555478 644555624 1.360000e-50 211.0
11 TraesCS7D01G197000 chr7B 94.872 78 4 0 2710 2787 115406942 115406865 6.530000e-24 122.0
12 TraesCS7D01G197000 chr7B 88.571 70 7 1 3951 4020 115355695 115355627 3.080000e-12 84.2
13 TraesCS7D01G197000 chr7B 97.436 39 1 0 2012 2050 442079459 442079497 3.100000e-07 67.6
14 TraesCS7D01G197000 chr2D 88.112 1388 142 12 46 1414 21825281 21826664 0.000000e+00 1628.0
15 TraesCS7D01G197000 chr2D 82.767 1207 165 25 94 1283 30478971 30480151 0.000000e+00 1037.0
16 TraesCS7D01G197000 chr2D 81.118 1181 187 23 134 1296 46389672 46388510 0.000000e+00 913.0
17 TraesCS7D01G197000 chr2D 85.073 891 75 25 3078 3934 21828207 21829073 0.000000e+00 856.0
18 TraesCS7D01G197000 chr2D 83.333 654 81 20 1480 2113 21826981 21827626 3.220000e-161 579.0
19 TraesCS7D01G197000 chr2D 74.281 556 94 30 3082 3614 46368445 46368974 6.350000e-44 189.0
20 TraesCS7D01G197000 chr2D 93.023 43 3 0 2715 2757 46374816 46374774 4.020000e-06 63.9
21 TraesCS7D01G197000 chr2B 90.000 940 88 5 98 1034 34798913 34797977 0.000000e+00 1210.0
22 TraesCS7D01G197000 chr2B 84.597 1227 165 19 100 1314 49981438 49980224 0.000000e+00 1197.0
23 TraesCS7D01G197000 chr2B 82.192 1168 179 17 145 1296 73390049 73388895 0.000000e+00 977.0
24 TraesCS7D01G197000 chr2B 81.401 828 114 25 3129 3933 34795761 34794951 1.460000e-179 640.0
25 TraesCS7D01G197000 chr2B 77.860 1215 125 72 1026 2154 34797945 34796789 5.280000e-174 621.0
26 TraesCS7D01G197000 chr2B 81.219 804 116 22 3129 3912 35066923 35067711 2.460000e-172 616.0
27 TraesCS7D01G197000 chr2B 80.794 781 105 25 507 1266 49987900 49987144 1.940000e-158 569.0
28 TraesCS7D01G197000 chr2B 85.623 313 31 6 1677 1986 35066065 35066366 2.790000e-82 316.0
29 TraesCS7D01G197000 chr2B 89.933 149 13 2 2151 2298 628398840 628398693 1.770000e-44 191.0
30 TraesCS7D01G197000 chr2A 84.113 1240 167 22 94 1314 32503466 32504694 0.000000e+00 1171.0
31 TraesCS7D01G197000 chr2A 82.750 1171 168 20 145 1296 49927417 49926262 0.000000e+00 1013.0
32 TraesCS7D01G197000 chr2A 82.237 1216 160 35 91 1266 32497267 32498466 0.000000e+00 998.0
33 TraesCS7D01G197000 chr7A 94.624 465 18 4 4342 4806 155513631 155513174 0.000000e+00 713.0
34 TraesCS7D01G197000 chr7A 86.290 248 31 3 1751 1997 2147842 2147597 2.850000e-67 267.0
35 TraesCS7D01G197000 chr7A 86.290 248 31 3 1751 1997 2167768 2167523 2.850000e-67 267.0
36 TraesCS7D01G197000 chr7A 96.552 58 2 0 3958 4015 155515078 155515021 3.960000e-16 97.1
37 TraesCS7D01G197000 chr7A 93.750 48 2 1 4265 4311 155514807 155514760 2.400000e-08 71.3
38 TraesCS7D01G197000 chrUn 81.499 827 114 25 3129 3933 318350525 318349716 1.130000e-180 643.0
39 TraesCS7D01G197000 chrUn 85.662 544 67 10 3395 3933 323067743 323067206 3.250000e-156 562.0
40 TraesCS7D01G197000 chrUn 86.290 248 31 3 1751 1997 340824382 340824627 2.850000e-67 267.0
41 TraesCS7D01G197000 chrUn 94.366 71 4 0 914 984 12660616 12660686 5.090000e-20 110.0
42 TraesCS7D01G197000 chr4B 86.957 322 38 4 1680 1997 75833527 75833848 4.570000e-95 359.0
43 TraesCS7D01G197000 chr4B 86.025 322 41 4 1680 1997 6976485 6976164 4.610000e-90 342.0
44 TraesCS7D01G197000 chr4B 97.778 45 1 0 2008 2052 6976129 6976085 1.430000e-10 78.7
45 TraesCS7D01G197000 chr4B 97.778 45 1 0 2008 2052 75833883 75833927 1.430000e-10 78.7
46 TraesCS7D01G197000 chr5D 81.545 466 42 15 1426 1854 76035592 76035134 1.280000e-90 344.0
47 TraesCS7D01G197000 chr5B 85.093 322 44 4 1680 1997 84142002 84141681 4.640000e-85 326.0
48 TraesCS7D01G197000 chr5B 89.655 145 15 0 2153 2297 273886571 273886427 8.210000e-43 185.0
49 TraesCS7D01G197000 chr5B 95.556 45 2 0 2008 2052 84141646 84141602 6.670000e-09 73.1
50 TraesCS7D01G197000 chr1A 92.715 151 10 1 2145 2295 333508932 333508783 2.910000e-52 217.0
51 TraesCS7D01G197000 chr1A 75.931 403 83 8 3375 3772 555126103 555126496 1.360000e-45 195.0
52 TraesCS7D01G197000 chr1A 84.354 147 23 0 2153 2299 26987946 26987800 1.390000e-30 145.0
53 TraesCS7D01G197000 chr6A 91.837 147 12 0 2149 2295 121738884 121738738 6.300000e-49 206.0
54 TraesCS7D01G197000 chr4A 88.667 150 17 0 2149 2298 619313969 619314118 2.950000e-42 183.0
55 TraesCS7D01G197000 chr6B 87.821 156 18 1 2149 2303 720675950 720676105 1.060000e-41 182.0
56 TraesCS7D01G197000 chr3D 88.966 145 16 0 2149 2293 461635291 461635147 3.820000e-41 180.0
57 TraesCS7D01G197000 chr1B 94.643 56 3 0 1997 2052 44625186 44625241 2.380000e-13 87.9
58 TraesCS7D01G197000 chr1B 97.561 41 1 0 2012 2052 40975270 40975310 2.400000e-08 71.3
59 TraesCS7D01G197000 chr3B 95.122 41 2 0 2012 2052 815730243 815730203 1.120000e-06 65.8


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 TraesCS7D01G197000 chr7D 153635697 153640502 4805 True 8876.000000 8876 100.000000 1 4806 1 chr7D.!!$R1 4805
1 TraesCS7D01G197000 chr7B 115403613 115410497 6884 True 880.500000 3219 94.876375 1 4806 8 chr7B.!!$R2 4805
2 TraesCS7D01G197000 chr7B 547342559 547345292 2733 False 553.500000 619 79.432500 1313 3934 2 chr7B.!!$F3 2621
3 TraesCS7D01G197000 chr2D 30478971 30480151 1180 False 1037.000000 1037 82.767000 94 1283 1 chr2D.!!$F1 1189
4 TraesCS7D01G197000 chr2D 21825281 21829073 3792 False 1021.000000 1628 85.506000 46 3934 3 chr2D.!!$F3 3888
5 TraesCS7D01G197000 chr2D 46388510 46389672 1162 True 913.000000 913 81.118000 134 1296 1 chr2D.!!$R2 1162
6 TraesCS7D01G197000 chr2B 49980224 49981438 1214 True 1197.000000 1197 84.597000 100 1314 1 chr2B.!!$R1 1214
7 TraesCS7D01G197000 chr2B 73388895 73390049 1154 True 977.000000 977 82.192000 145 1296 1 chr2B.!!$R3 1151
8 TraesCS7D01G197000 chr2B 34794951 34798913 3962 True 823.666667 1210 83.087000 98 3933 3 chr2B.!!$R5 3835
9 TraesCS7D01G197000 chr2B 49987144 49987900 756 True 569.000000 569 80.794000 507 1266 1 chr2B.!!$R2 759
10 TraesCS7D01G197000 chr2B 35066065 35067711 1646 False 466.000000 616 83.421000 1677 3912 2 chr2B.!!$F1 2235
11 TraesCS7D01G197000 chr2A 32503466 32504694 1228 False 1171.000000 1171 84.113000 94 1314 1 chr2A.!!$F2 1220
12 TraesCS7D01G197000 chr2A 49926262 49927417 1155 True 1013.000000 1013 82.750000 145 1296 1 chr2A.!!$R1 1151
13 TraesCS7D01G197000 chr2A 32497267 32498466 1199 False 998.000000 998 82.237000 91 1266 1 chr2A.!!$F1 1175
14 TraesCS7D01G197000 chr7A 155513174 155515078 1904 True 293.800000 713 94.975333 3958 4806 3 chr7A.!!$R3 848
15 TraesCS7D01G197000 chrUn 318349716 318350525 809 True 643.000000 643 81.499000 3129 3933 1 chrUn.!!$R1 804
16 TraesCS7D01G197000 chrUn 323067206 323067743 537 True 562.000000 562 85.662000 3395 3933 1 chrUn.!!$R2 538

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
46 47 0.648441 TTCAACAACGTCGACACAGC 59.352 50.0 17.16 0.0 0.0 4.40 F
529 549 0.898789 GACCTCCTCCTCGTGAACCA 60.899 60.0 0.00 0.0 0.0 3.67 F
2221 3779 0.240945 CGGAGCCGCAGTTCAAATTT 59.759 50.0 0.00 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1165 2.135139 TCGAGCAGAACATCACACAAC 58.865 47.619 0.0 0.0 0.00 3.32 R
2260 3818 0.110486 GAAACCTCCAGCTCCACCAA 59.890 55.000 0.0 0.0 0.00 3.67 R
3943 7247 0.108585 ACAGCCACACAACCTACAGG 59.891 55.000 0.0 0.0 42.17 4.00 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
46 47 0.648441 TTCAACAACGTCGACACAGC 59.352 50.000 17.16 0.00 0.00 4.40
529 549 0.898789 GACCTCCTCCTCGTGAACCA 60.899 60.000 0.00 0.00 0.00 3.67
736 762 3.462678 GAGCCCCGTCCTGGAGAC 61.463 72.222 0.00 0.00 42.00 3.36
784 810 1.208614 GGTTGCGTCTACGTCTCGT 59.791 57.895 4.24 0.00 44.35 4.18
1250 1374 6.359804 ACTGCATATCATGGTATTTGTCACT 58.640 36.000 0.00 0.00 0.00 3.41
1487 1885 4.785346 ATTCTCAGCCACCATCTACATT 57.215 40.909 0.00 0.00 0.00 2.71
1548 1946 5.490159 TCATGCTGATCAGTTGTTGATACA 58.510 37.500 23.38 10.06 46.51 2.29
1550 1948 4.898320 TGCTGATCAGTTGTTGATACAGT 58.102 39.130 23.38 0.00 46.51 3.55
1567 1974 8.597662 TGATACAGTACTTGGTAAGTGTTTTC 57.402 34.615 4.56 0.00 42.84 2.29
1675 2083 3.217599 TCTCACTGTGTTCATACGAGC 57.782 47.619 7.79 0.00 0.00 5.03
1790 2228 7.968956 CCAGTATTAGTACTACCATAATCGCTG 59.031 40.741 0.91 7.28 39.12 5.18
1791 2229 7.485277 CAGTATTAGTACTACCATAATCGCTGC 59.515 40.741 0.91 0.00 39.12 5.25
1830 2268 8.643324 ACACTAGTTTAACCATATCAGGATCTC 58.357 37.037 0.00 0.00 0.00 2.75
2122 3680 7.121168 TGTCCTACAAATCTGATCCAACATTTC 59.879 37.037 0.00 0.00 0.00 2.17
2127 3685 7.305474 ACAAATCTGATCCAACATTTCGTTAC 58.695 34.615 0.00 0.00 35.52 2.50
2135 3693 3.181514 CCAACATTTCGTTACGGACCATC 60.182 47.826 4.53 0.00 35.52 3.51
2141 3699 6.202188 ACATTTCGTTACGGACCATCATAATC 59.798 38.462 4.53 0.00 0.00 1.75
2151 3709 5.702670 CGGACCATCATAATCTGCAGTATTT 59.297 40.000 14.67 8.86 0.00 1.40
2154 3712 7.335422 GGACCATCATAATCTGCAGTATTTAGG 59.665 40.741 14.67 11.82 0.00 2.69
2155 3713 7.170965 ACCATCATAATCTGCAGTATTTAGGG 58.829 38.462 14.67 9.79 0.00 3.53
2156 3714 6.094603 CCATCATAATCTGCAGTATTTAGGGC 59.905 42.308 14.67 0.00 0.00 5.19
2157 3715 5.560724 TCATAATCTGCAGTATTTAGGGCC 58.439 41.667 14.67 0.00 0.00 5.80
2158 3716 5.310594 TCATAATCTGCAGTATTTAGGGCCT 59.689 40.000 12.58 12.58 0.00 5.19
2159 3717 3.498774 ATCTGCAGTATTTAGGGCCTG 57.501 47.619 18.53 0.00 0.00 4.85
2160 3718 2.196595 TCTGCAGTATTTAGGGCCTGT 58.803 47.619 18.53 4.61 0.00 4.00
2161 3719 2.576191 TCTGCAGTATTTAGGGCCTGTT 59.424 45.455 18.53 2.87 0.00 3.16
2162 3720 2.945668 CTGCAGTATTTAGGGCCTGTTC 59.054 50.000 18.53 2.10 0.00 3.18
2163 3721 1.940613 GCAGTATTTAGGGCCTGTTCG 59.059 52.381 18.53 0.00 0.00 3.95
2164 3722 2.561569 CAGTATTTAGGGCCTGTTCGG 58.438 52.381 18.53 0.00 0.00 4.30
2165 3723 2.169769 CAGTATTTAGGGCCTGTTCGGA 59.830 50.000 18.53 0.00 33.16 4.55
2166 3724 2.434702 AGTATTTAGGGCCTGTTCGGAG 59.565 50.000 18.53 0.00 33.16 4.63
2167 3725 1.286248 ATTTAGGGCCTGTTCGGAGT 58.714 50.000 18.53 0.00 33.16 3.85
2168 3726 0.611714 TTTAGGGCCTGTTCGGAGTC 59.388 55.000 18.53 0.00 33.16 3.36
2169 3727 1.262640 TTAGGGCCTGTTCGGAGTCC 61.263 60.000 18.53 0.00 33.16 3.85
2170 3728 4.097361 GGGCCTGTTCGGAGTCCC 62.097 72.222 0.84 0.00 33.16 4.46
2171 3729 3.003763 GGCCTGTTCGGAGTCCCT 61.004 66.667 2.80 0.00 33.16 4.20
2172 3730 2.579738 GCCTGTTCGGAGTCCCTC 59.420 66.667 2.80 0.00 33.16 4.30
2173 3731 3.020237 GCCTGTTCGGAGTCCCTCC 62.020 68.421 2.80 0.00 46.44 4.30
2186 3744 3.827898 CCTCCCGCTCCGTGACTC 61.828 72.222 0.00 0.00 0.00 3.36
2187 3745 3.827898 CTCCCGCTCCGTGACTCC 61.828 72.222 0.00 0.00 0.00 3.85
2191 3749 4.838486 CGCTCCGTGACTCCGCTC 62.838 72.222 0.00 0.00 0.00 5.03
2192 3750 4.500116 GCTCCGTGACTCCGCTCC 62.500 72.222 0.00 0.00 0.00 4.70
2193 3751 3.827898 CTCCGTGACTCCGCTCCC 61.828 72.222 0.00 0.00 0.00 4.30
2218 3776 2.668212 CCGGAGCCGCAGTTCAAA 60.668 61.111 0.00 0.00 38.24 2.69
2219 3777 2.040544 CCGGAGCCGCAGTTCAAAT 61.041 57.895 0.00 0.00 38.24 2.32
2220 3778 1.586154 CCGGAGCCGCAGTTCAAATT 61.586 55.000 0.00 0.00 38.24 1.82
2221 3779 0.240945 CGGAGCCGCAGTTCAAATTT 59.759 50.000 0.00 0.00 0.00 1.82
2222 3780 1.466950 CGGAGCCGCAGTTCAAATTTA 59.533 47.619 0.00 0.00 0.00 1.40
2223 3781 2.097466 CGGAGCCGCAGTTCAAATTTAT 59.903 45.455 0.00 0.00 0.00 1.40
2224 3782 3.438360 GGAGCCGCAGTTCAAATTTATG 58.562 45.455 0.00 0.00 0.00 1.90
2225 3783 3.438360 GAGCCGCAGTTCAAATTTATGG 58.562 45.455 0.00 0.00 0.00 2.74
2226 3784 3.088532 AGCCGCAGTTCAAATTTATGGA 58.911 40.909 0.00 0.00 0.00 3.41
2227 3785 3.129287 AGCCGCAGTTCAAATTTATGGAG 59.871 43.478 0.00 0.00 0.00 3.86
2228 3786 3.438360 CCGCAGTTCAAATTTATGGAGC 58.562 45.455 0.00 0.00 0.00 4.70
2229 3787 3.100817 CGCAGTTCAAATTTATGGAGCG 58.899 45.455 10.58 10.58 35.42 5.03
2230 3788 3.438360 GCAGTTCAAATTTATGGAGCGG 58.562 45.455 0.00 0.00 0.00 5.52
2231 3789 3.734902 GCAGTTCAAATTTATGGAGCGGG 60.735 47.826 0.00 0.00 0.00 6.13
2232 3790 3.023832 AGTTCAAATTTATGGAGCGGGG 58.976 45.455 0.00 0.00 0.00 5.73
2233 3791 2.065899 TCAAATTTATGGAGCGGGGG 57.934 50.000 0.00 0.00 0.00 5.40
2234 3792 1.566703 TCAAATTTATGGAGCGGGGGA 59.433 47.619 0.00 0.00 0.00 4.81
2235 3793 2.024846 TCAAATTTATGGAGCGGGGGAA 60.025 45.455 0.00 0.00 0.00 3.97
2236 3794 2.067365 AATTTATGGAGCGGGGGAAC 57.933 50.000 0.00 0.00 0.00 3.62
2237 3795 0.923358 ATTTATGGAGCGGGGGAACA 59.077 50.000 0.00 0.00 0.00 3.18
2238 3796 0.254747 TTTATGGAGCGGGGGAACAG 59.745 55.000 0.00 0.00 0.00 3.16
2239 3797 1.632018 TTATGGAGCGGGGGAACAGG 61.632 60.000 0.00 0.00 0.00 4.00
2240 3798 2.833151 TATGGAGCGGGGGAACAGGT 62.833 60.000 0.00 0.00 0.00 4.00
2241 3799 2.686106 GGAGCGGGGGAACAGGTA 60.686 66.667 0.00 0.00 0.00 3.08
2242 3800 2.582978 GAGCGGGGGAACAGGTAC 59.417 66.667 0.00 0.00 0.00 3.34
2243 3801 1.988406 GAGCGGGGGAACAGGTACT 60.988 63.158 0.00 0.00 43.88 2.73
2244 3802 1.957765 GAGCGGGGGAACAGGTACTC 61.958 65.000 0.00 0.00 34.60 2.59
2245 3803 3.027675 GCGGGGGAACAGGTACTCC 62.028 68.421 0.00 0.00 34.60 3.85
2246 3804 2.718073 CGGGGGAACAGGTACTCCG 61.718 68.421 0.00 0.00 34.60 4.63
2247 3805 1.611556 GGGGGAACAGGTACTCCGT 60.612 63.158 0.00 0.00 34.60 4.69
2248 3806 1.595357 GGGGAACAGGTACTCCGTG 59.405 63.158 0.00 0.00 34.60 4.94
2249 3807 1.595357 GGGAACAGGTACTCCGTGG 59.405 63.158 0.00 0.00 34.60 4.94
2250 3808 0.901580 GGGAACAGGTACTCCGTGGA 60.902 60.000 0.00 0.00 34.60 4.02
2251 3809 1.192428 GGAACAGGTACTCCGTGGAT 58.808 55.000 0.00 0.00 34.60 3.41
2252 3810 1.136500 GGAACAGGTACTCCGTGGATC 59.864 57.143 0.00 0.00 34.60 3.36
2253 3811 1.136500 GAACAGGTACTCCGTGGATCC 59.864 57.143 4.20 4.20 34.60 3.36
2254 3812 0.335361 ACAGGTACTCCGTGGATCCT 59.665 55.000 14.23 0.00 34.60 3.24
2255 3813 1.273098 ACAGGTACTCCGTGGATCCTT 60.273 52.381 14.23 0.00 34.60 3.36
2256 3814 1.137086 CAGGTACTCCGTGGATCCTTG 59.863 57.143 14.23 5.02 34.60 3.61
2257 3815 0.464452 GGTACTCCGTGGATCCTTGG 59.536 60.000 14.23 14.50 0.00 3.61
2258 3816 1.481871 GTACTCCGTGGATCCTTGGA 58.518 55.000 20.22 20.22 0.00 3.53
2259 3817 2.040178 GTACTCCGTGGATCCTTGGAT 58.960 52.381 21.28 15.08 0.00 3.41
2260 3818 1.584724 ACTCCGTGGATCCTTGGATT 58.415 50.000 21.28 15.17 0.00 3.01
2261 3819 1.916181 ACTCCGTGGATCCTTGGATTT 59.084 47.619 21.28 11.71 0.00 2.17
2262 3820 2.292267 CTCCGTGGATCCTTGGATTTG 58.708 52.381 21.28 9.95 0.00 2.32
2263 3821 1.064758 TCCGTGGATCCTTGGATTTGG 60.065 52.381 18.31 7.01 0.00 3.28
2264 3822 1.340991 CCGTGGATCCTTGGATTTGGT 60.341 52.381 14.23 0.00 0.00 3.67
2265 3823 1.745087 CGTGGATCCTTGGATTTGGTG 59.255 52.381 14.23 0.00 0.00 4.17
2266 3824 2.102578 GTGGATCCTTGGATTTGGTGG 58.897 52.381 14.23 0.00 0.00 4.61
2267 3825 1.999295 TGGATCCTTGGATTTGGTGGA 59.001 47.619 14.23 0.00 0.00 4.02
2268 3826 2.025037 TGGATCCTTGGATTTGGTGGAG 60.025 50.000 14.23 0.00 0.00 3.86
2269 3827 2.027385 GATCCTTGGATTTGGTGGAGC 58.973 52.381 3.43 0.00 0.00 4.70
2270 3828 1.075601 TCCTTGGATTTGGTGGAGCT 58.924 50.000 0.00 0.00 0.00 4.09
2271 3829 1.180029 CCTTGGATTTGGTGGAGCTG 58.820 55.000 0.00 0.00 0.00 4.24
2272 3830 1.180029 CTTGGATTTGGTGGAGCTGG 58.820 55.000 0.00 0.00 0.00 4.85
2273 3831 0.776810 TTGGATTTGGTGGAGCTGGA 59.223 50.000 0.00 0.00 0.00 3.86
2274 3832 0.329261 TGGATTTGGTGGAGCTGGAG 59.671 55.000 0.00 0.00 0.00 3.86
2275 3833 0.394899 GGATTTGGTGGAGCTGGAGG 60.395 60.000 0.00 0.00 0.00 4.30
2276 3834 0.329596 GATTTGGTGGAGCTGGAGGT 59.670 55.000 0.00 0.00 0.00 3.85
2277 3835 0.779997 ATTTGGTGGAGCTGGAGGTT 59.220 50.000 0.00 0.00 0.00 3.50
2278 3836 0.555769 TTTGGTGGAGCTGGAGGTTT 59.444 50.000 0.00 0.00 0.00 3.27
2279 3837 0.110486 TTGGTGGAGCTGGAGGTTTC 59.890 55.000 0.00 0.00 0.00 2.78
2280 3838 1.002011 GGTGGAGCTGGAGGTTTCC 60.002 63.158 0.00 0.00 44.31 3.13
2281 3839 1.002011 GTGGAGCTGGAGGTTTCCC 60.002 63.158 0.00 0.00 43.33 3.97
2282 3840 2.269241 GGAGCTGGAGGTTTCCCG 59.731 66.667 0.00 0.00 43.33 5.14
2283 3841 2.291043 GGAGCTGGAGGTTTCCCGA 61.291 63.158 0.00 0.00 43.33 5.14
2284 3842 1.677552 GAGCTGGAGGTTTCCCGAA 59.322 57.895 0.00 0.00 43.33 4.30
2285 3843 0.673956 GAGCTGGAGGTTTCCCGAAC 60.674 60.000 0.00 0.00 43.33 3.95
2286 3844 1.072505 GCTGGAGGTTTCCCGAACA 59.927 57.895 0.00 0.00 43.33 3.18
2287 3845 0.955919 GCTGGAGGTTTCCCGAACAG 60.956 60.000 0.00 0.00 43.33 3.16
2288 3846 0.955919 CTGGAGGTTTCCCGAACAGC 60.956 60.000 0.00 0.00 43.33 4.40
2289 3847 1.375326 GGAGGTTTCCCGAACAGCT 59.625 57.895 0.00 0.00 40.13 4.24
2290 3848 0.673956 GGAGGTTTCCCGAACAGCTC 60.674 60.000 0.00 8.83 40.13 4.09
2291 3849 0.673956 GAGGTTTCCCGAACAGCTCC 60.674 60.000 0.00 0.00 40.13 4.70
2380 3939 6.096423 AGTCAACACAAGTCTACTCAACACTA 59.904 38.462 0.00 0.00 0.00 2.74
2473 4032 4.215109 CCTTTTCCAACCTTCTCTTTCCA 58.785 43.478 0.00 0.00 0.00 3.53
2564 4130 7.548075 ACAATGTTAGTAATTTCCTCTACACGG 59.452 37.037 0.00 0.00 0.00 4.94
2633 4203 5.647658 TGGTGTTCTCACTTATTTGCATAGG 59.352 40.000 0.00 0.00 43.41 2.57
2638 4208 5.118990 TCTCACTTATTTGCATAGGTCTGC 58.881 41.667 0.00 0.00 42.62 4.26
2657 4232 6.398918 GTCTGCCAAGTCTCATTAGAGTTTA 58.601 40.000 0.00 0.00 41.70 2.01
2694 4269 6.884280 ATTTTCTTCTACTGTGAAAGGTGG 57.116 37.500 0.00 0.00 32.36 4.61
2696 4271 3.583228 TCTTCTACTGTGAAAGGTGGGA 58.417 45.455 0.00 0.00 0.00 4.37
2704 4279 4.534500 ACTGTGAAAGGTGGGACATGTATA 59.466 41.667 0.00 0.00 44.52 1.47
2705 4280 4.839121 TGTGAAAGGTGGGACATGTATAC 58.161 43.478 0.00 0.00 44.52 1.47
2706 4281 4.534500 TGTGAAAGGTGGGACATGTATACT 59.466 41.667 0.00 0.00 44.52 2.12
2707 4282 5.013704 TGTGAAAGGTGGGACATGTATACTT 59.986 40.000 0.00 0.00 44.52 2.24
2708 4283 6.213802 TGTGAAAGGTGGGACATGTATACTTA 59.786 38.462 0.00 0.00 44.52 2.24
2710 4285 7.226720 GTGAAAGGTGGGACATGTATACTTATG 59.773 40.741 0.00 3.19 44.52 1.90
2711 4286 5.228945 AGGTGGGACATGTATACTTATGC 57.771 43.478 0.00 0.00 44.52 3.14
2713 4288 4.502604 GGTGGGACATGTATACTTATGCGT 60.503 45.833 0.00 0.00 44.52 5.24
2827 5739 7.722728 AGCCAATCATTGCTATTTATTCTCAGA 59.277 33.333 0.00 0.00 35.69 3.27
2970 6082 6.199937 TCTGCTATTTCTGGATTTTCTTGC 57.800 37.500 0.00 0.00 0.00 4.01
3064 6176 1.703513 GGGGAAGTTCTGGTTGTACCT 59.296 52.381 2.25 0.00 39.58 3.08
3178 6434 5.071788 ACCTCCACAGTAAACTGAAATCTGA 59.928 40.000 16.74 3.39 46.59 3.27
3246 6503 2.931325 GTGACAACACCGACACAGTTTA 59.069 45.455 0.00 0.00 40.74 2.01
3250 6507 5.816258 TGACAACACCGACACAGTTTATTTA 59.184 36.000 0.00 0.00 0.00 1.40
3256 6513 8.568732 ACACCGACACAGTTTATTTATTTTTG 57.431 30.769 0.00 0.00 0.00 2.44
3346 6618 8.980143 ACATAATTAATTTGAGGTTTGGTTCG 57.020 30.769 5.91 0.00 0.00 3.95
3363 6642 0.323302 TCGTTTGCCATGTCAGCCTA 59.677 50.000 0.00 0.00 0.00 3.93
3488 6781 2.572290 CCAAACAAAACCTCCTCTCGT 58.428 47.619 0.00 0.00 0.00 4.18
3777 7070 0.613853 TCCTTCGAGGACCCGTTCAT 60.614 55.000 0.00 0.00 40.06 2.57
3804 7100 2.442272 GGCGAGGGAGGACAGCTA 60.442 66.667 0.00 0.00 0.00 3.32
3870 7166 6.751888 GCAAACTATGAATTGTGGTGGTATTC 59.248 38.462 0.00 0.00 0.00 1.75
3942 7246 2.758979 GCCTGGTAAGCAGACTACACTA 59.241 50.000 0.00 0.00 0.00 2.74
3943 7247 3.429135 GCCTGGTAAGCAGACTACACTAC 60.429 52.174 0.00 0.00 0.00 2.73
3944 7248 3.130693 CCTGGTAAGCAGACTACACTACC 59.869 52.174 0.00 0.00 0.00 3.18
3946 7250 3.762288 TGGTAAGCAGACTACACTACCTG 59.238 47.826 5.88 0.00 0.00 4.00
4005 7328 0.823769 TGCCGAGTGAGACTGTCAGT 60.824 55.000 4.81 4.81 41.97 3.41
4015 7338 4.570772 GTGAGACTGTCAGTTAAAGCAACA 59.429 41.667 7.00 0.00 39.81 3.33
4016 7339 5.064707 GTGAGACTGTCAGTTAAAGCAACAA 59.935 40.000 7.00 0.00 39.81 2.83
4017 7340 5.064707 TGAGACTGTCAGTTAAAGCAACAAC 59.935 40.000 7.00 0.00 39.81 3.32
4018 7341 4.941263 AGACTGTCAGTTAAAGCAACAACA 59.059 37.500 7.00 0.00 39.81 3.33
4020 7343 4.096382 ACTGTCAGTTAAAGCAACAACAGG 59.904 41.667 18.59 8.03 46.76 4.00
4027 7379 5.889289 AGTTAAAGCAACAACAGGAGGTTTA 59.111 36.000 0.00 0.00 39.81 2.01
4065 7417 7.979444 AAGTTTACTTTCGATTGAATCCTCA 57.021 32.000 0.00 0.00 33.20 3.86
4066 7418 8.567285 AAGTTTACTTTCGATTGAATCCTCAT 57.433 30.769 0.00 0.00 33.20 2.90
4067 7419 7.978982 AGTTTACTTTCGATTGAATCCTCATG 58.021 34.615 0.00 0.00 33.20 3.07
4158 7522 0.681733 ACGACACACTGATGAGGCTT 59.318 50.000 0.00 0.00 0.00 4.35
4195 7559 1.339631 TGCCTGGTGTGTTACATAGCC 60.340 52.381 8.68 2.89 0.00 3.93
4196 7560 1.339631 GCCTGGTGTGTTACATAGCCA 60.340 52.381 8.68 7.00 0.00 4.75
4198 7562 3.433031 GCCTGGTGTGTTACATAGCCATA 60.433 47.826 8.68 0.00 0.00 2.74
4218 7582 1.556591 CGTTTCTACGCAGCACAGCA 61.557 55.000 0.00 0.00 41.41 4.41
4245 7609 9.533253 AAAAATGGTACTTTGAGATTTTGACTG 57.467 29.630 0.00 0.00 0.00 3.51
4246 7610 5.689383 TGGTACTTTGAGATTTTGACTGC 57.311 39.130 0.00 0.00 0.00 4.40
4247 7611 5.129634 TGGTACTTTGAGATTTTGACTGCA 58.870 37.500 0.00 0.00 0.00 4.41
4248 7612 5.769662 TGGTACTTTGAGATTTTGACTGCAT 59.230 36.000 0.00 0.00 0.00 3.96
4249 7613 6.088824 GGTACTTTGAGATTTTGACTGCATG 58.911 40.000 0.00 0.00 0.00 4.06
4250 7614 4.553323 ACTTTGAGATTTTGACTGCATGC 58.447 39.130 11.82 11.82 0.00 4.06
4251 7615 4.038282 ACTTTGAGATTTTGACTGCATGCA 59.962 37.500 21.29 21.29 0.00 3.96
4252 7616 4.794278 TTGAGATTTTGACTGCATGCAT 57.206 36.364 22.97 11.62 0.00 3.96
4253 7617 4.794278 TGAGATTTTGACTGCATGCATT 57.206 36.364 22.97 16.79 0.00 3.56
4254 7618 4.740268 TGAGATTTTGACTGCATGCATTC 58.260 39.130 26.32 26.32 0.00 2.67
4255 7619 4.461431 TGAGATTTTGACTGCATGCATTCT 59.539 37.500 30.70 19.04 0.00 2.40
4256 7620 5.047590 TGAGATTTTGACTGCATGCATTCTT 60.048 36.000 30.70 17.17 0.00 2.52
4257 7621 5.168569 AGATTTTGACTGCATGCATTCTTG 58.831 37.500 30.70 18.44 0.00 3.02
4258 7622 4.587584 TTTTGACTGCATGCATTCTTGA 57.412 36.364 30.70 17.97 0.00 3.02
4259 7623 3.564235 TTGACTGCATGCATTCTTGAC 57.436 42.857 30.70 16.64 0.00 3.18
4260 7624 2.506444 TGACTGCATGCATTCTTGACA 58.494 42.857 30.70 18.69 0.00 3.58
4261 7625 2.227149 TGACTGCATGCATTCTTGACAC 59.773 45.455 30.70 10.69 0.00 3.67
4262 7626 2.486982 GACTGCATGCATTCTTGACACT 59.513 45.455 25.92 0.00 0.00 3.55
4263 7627 2.228103 ACTGCATGCATTCTTGACACTG 59.772 45.455 22.97 7.24 0.00 3.66
4264 7628 2.486592 CTGCATGCATTCTTGACACTGA 59.513 45.455 22.97 0.00 0.00 3.41
4265 7629 2.227149 TGCATGCATTCTTGACACTGAC 59.773 45.455 18.46 0.00 0.00 3.51
4266 7630 2.726989 GCATGCATTCTTGACACTGACG 60.727 50.000 14.21 0.00 0.00 4.35
4267 7631 2.238942 TGCATTCTTGACACTGACGT 57.761 45.000 0.00 0.00 0.00 4.34
4268 7632 1.866601 TGCATTCTTGACACTGACGTG 59.133 47.619 0.00 0.00 46.63 4.49
4326 8768 9.697250 CATTTTTCAGCATTATAAAACTGCATG 57.303 29.630 11.15 7.22 38.37 4.06
4340 8782 2.375174 ACTGCATGTTCCCCTACTTGAA 59.625 45.455 0.00 0.00 0.00 2.69
4410 8873 9.065798 TCTGAAACACATCAATCACAAGATAAA 57.934 29.630 0.00 0.00 33.08 1.40
4412 8875 9.681692 TGAAACACATCAATCACAAGATAAAAG 57.318 29.630 0.00 0.00 33.08 2.27
4423 8886 7.364522 TCACAAGATAAAAGGAATCAGTTCG 57.635 36.000 0.00 0.00 35.10 3.95
4442 8905 4.811969 TCGGTCCACTTGCTTAAGAATA 57.188 40.909 6.67 0.00 0.00 1.75
4469 8932 9.993454 TTCAATTCCATGATTCATGTGTTTTAA 57.007 25.926 21.95 9.30 39.94 1.52
4482 8945 3.061322 GTGTTTTAAAAATGGGGACGCC 58.939 45.455 1.31 0.53 0.00 5.68
4489 8952 1.241315 AAATGGGGACGCCAGTTTCG 61.241 55.000 17.49 0.00 0.00 3.46
4607 9070 6.518493 TGTCTACATTCTTCAAAACGTAGGT 58.482 36.000 0.00 0.00 0.00 3.08
4612 9075 7.272037 ACATTCTTCAAAACGTAGGTGAATT 57.728 32.000 8.42 0.00 31.21 2.17
4644 9107 8.389586 AGTTGAAAATTACACGTTTCAGAAAC 57.610 30.769 15.16 15.16 42.86 2.78
4683 9146 2.091555 AGAACCCAACTAGCAAAACCCA 60.092 45.455 0.00 0.00 0.00 4.51
4702 9165 0.171903 AAGAATGCGCTCAACATGCC 59.828 50.000 9.73 0.00 0.00 4.40
4791 9254 1.153289 CTCAGTTCCAGATGGCCGG 60.153 63.158 0.00 0.00 34.44 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.426621 CATCAGCTTTGCGCATCGT 59.573 52.632 12.75 0.00 42.61 3.73
736 762 1.097547 GCATCCCACGATGTTGAGGG 61.098 60.000 0.00 0.00 46.56 4.30
1058 1165 2.135139 TCGAGCAGAACATCACACAAC 58.865 47.619 0.00 0.00 0.00 3.32
1098 1211 2.673368 CACTTTCGCTCGCCTTTATTCT 59.327 45.455 0.00 0.00 0.00 2.40
1250 1374 8.462589 TGCAAATGTAAGCAGAATATGGATTA 57.537 30.769 0.00 0.00 35.51 1.75
1548 1946 8.241367 CACAAAAGAAAACACTTACCAAGTACT 58.759 33.333 0.00 0.00 40.46 2.73
1550 1948 7.540299 CCACAAAAGAAAACACTTACCAAGTA 58.460 34.615 0.00 0.00 40.46 2.24
1567 1974 9.590451 AGAATAATAATCATTGTGCCACAAAAG 57.410 29.630 15.17 10.42 41.96 2.27
1790 2228 6.910536 AAACTAGTGTAGTAGCATCAATGC 57.089 37.500 6.88 6.88 45.61 3.56
1791 2229 8.818057 GGTTAAACTAGTGTAGTAGCATCAATG 58.182 37.037 0.00 0.00 38.26 2.82
2122 3680 3.428870 GCAGATTATGATGGTCCGTAACG 59.571 47.826 0.00 0.00 0.00 3.18
2127 3685 3.117491 ACTGCAGATTATGATGGTCCG 57.883 47.619 23.35 0.00 0.00 4.79
2135 3693 5.413833 CAGGCCCTAAATACTGCAGATTATG 59.586 44.000 23.35 12.48 0.00 1.90
2141 3699 2.717639 ACAGGCCCTAAATACTGCAG 57.282 50.000 13.48 13.48 34.40 4.41
2151 3709 1.684734 GGACTCCGAACAGGCCCTA 60.685 63.158 0.00 0.00 35.10 3.53
2154 3712 3.003763 AGGGACTCCGAACAGGCC 61.004 66.667 0.00 0.00 41.65 5.19
2169 3727 3.827898 GAGTCACGGAGCGGGAGG 61.828 72.222 0.00 0.00 41.01 4.30
2170 3728 3.827898 GGAGTCACGGAGCGGGAG 61.828 72.222 0.00 0.00 41.01 4.30
2174 3732 4.838486 GAGCGGAGTCACGGAGCG 62.838 72.222 0.00 0.00 0.00 5.03
2175 3733 4.500116 GGAGCGGAGTCACGGAGC 62.500 72.222 0.00 0.00 0.00 4.70
2176 3734 3.827898 GGGAGCGGAGTCACGGAG 61.828 72.222 0.00 0.00 0.00 4.63
2201 3759 1.586154 AATTTGAACTGCGGCTCCGG 61.586 55.000 10.57 0.00 40.19 5.14
2202 3760 0.240945 AAATTTGAACTGCGGCTCCG 59.759 50.000 3.56 3.56 43.09 4.63
2203 3761 3.438360 CATAAATTTGAACTGCGGCTCC 58.562 45.455 0.00 0.00 0.00 4.70
2204 3762 3.128589 TCCATAAATTTGAACTGCGGCTC 59.871 43.478 0.00 0.00 0.00 4.70
2205 3763 3.088532 TCCATAAATTTGAACTGCGGCT 58.911 40.909 0.00 0.00 0.00 5.52
2206 3764 3.438360 CTCCATAAATTTGAACTGCGGC 58.562 45.455 0.00 0.00 0.00 6.53
2207 3765 3.438360 GCTCCATAAATTTGAACTGCGG 58.562 45.455 0.00 0.00 0.00 5.69
2208 3766 3.100817 CGCTCCATAAATTTGAACTGCG 58.899 45.455 0.00 7.95 0.00 5.18
2209 3767 3.438360 CCGCTCCATAAATTTGAACTGC 58.562 45.455 0.00 0.00 0.00 4.40
2210 3768 3.181487 CCCCGCTCCATAAATTTGAACTG 60.181 47.826 0.00 0.00 0.00 3.16
2211 3769 3.023832 CCCCGCTCCATAAATTTGAACT 58.976 45.455 0.00 0.00 0.00 3.01
2212 3770 2.100749 CCCCCGCTCCATAAATTTGAAC 59.899 50.000 0.00 0.00 0.00 3.18
2213 3771 2.024846 TCCCCCGCTCCATAAATTTGAA 60.025 45.455 0.00 0.00 0.00 2.69
2214 3772 1.566703 TCCCCCGCTCCATAAATTTGA 59.433 47.619 0.00 0.00 0.00 2.69
2215 3773 2.065899 TCCCCCGCTCCATAAATTTG 57.934 50.000 0.00 0.00 0.00 2.32
2216 3774 2.291930 TGTTCCCCCGCTCCATAAATTT 60.292 45.455 0.00 0.00 0.00 1.82
2217 3775 1.286553 TGTTCCCCCGCTCCATAAATT 59.713 47.619 0.00 0.00 0.00 1.82
2218 3776 0.923358 TGTTCCCCCGCTCCATAAAT 59.077 50.000 0.00 0.00 0.00 1.40
2219 3777 0.254747 CTGTTCCCCCGCTCCATAAA 59.745 55.000 0.00 0.00 0.00 1.40
2220 3778 1.632018 CCTGTTCCCCCGCTCCATAA 61.632 60.000 0.00 0.00 0.00 1.90
2221 3779 2.070039 CCTGTTCCCCCGCTCCATA 61.070 63.158 0.00 0.00 0.00 2.74
2222 3780 2.833151 TACCTGTTCCCCCGCTCCAT 62.833 60.000 0.00 0.00 0.00 3.41
2223 3781 3.549433 TACCTGTTCCCCCGCTCCA 62.549 63.158 0.00 0.00 0.00 3.86
2224 3782 2.686106 TACCTGTTCCCCCGCTCC 60.686 66.667 0.00 0.00 0.00 4.70
2225 3783 1.957765 GAGTACCTGTTCCCCCGCTC 61.958 65.000 0.00 0.00 0.00 5.03
2226 3784 1.988406 GAGTACCTGTTCCCCCGCT 60.988 63.158 0.00 0.00 0.00 5.52
2227 3785 2.582978 GAGTACCTGTTCCCCCGC 59.417 66.667 0.00 0.00 0.00 6.13
2228 3786 2.718073 CGGAGTACCTGTTCCCCCG 61.718 68.421 0.00 0.00 0.00 5.73
2229 3787 1.611556 ACGGAGTACCTGTTCCCCC 60.612 63.158 0.00 0.00 41.94 5.40
2230 3788 1.595357 CACGGAGTACCTGTTCCCC 59.405 63.158 0.00 0.00 41.61 4.81
2231 3789 0.901580 TCCACGGAGTACCTGTTCCC 60.902 60.000 0.00 0.00 41.61 3.97
2232 3790 1.136500 GATCCACGGAGTACCTGTTCC 59.864 57.143 0.00 0.00 41.61 3.62
2233 3791 1.136500 GGATCCACGGAGTACCTGTTC 59.864 57.143 6.95 0.00 41.61 3.18
2234 3792 1.192428 GGATCCACGGAGTACCTGTT 58.808 55.000 6.95 0.00 41.61 3.16
2235 3793 0.335361 AGGATCCACGGAGTACCTGT 59.665 55.000 15.82 0.00 41.61 4.00
2236 3794 1.137086 CAAGGATCCACGGAGTACCTG 59.863 57.143 15.82 0.00 41.61 4.00
2237 3795 1.486211 CAAGGATCCACGGAGTACCT 58.514 55.000 15.82 4.18 41.61 3.08
2238 3796 0.464452 CCAAGGATCCACGGAGTACC 59.536 60.000 15.82 0.00 41.61 3.34
2239 3797 1.481871 TCCAAGGATCCACGGAGTAC 58.518 55.000 15.82 0.00 41.61 2.73
2240 3798 2.471815 ATCCAAGGATCCACGGAGTA 57.528 50.000 22.52 5.34 41.61 2.59
2241 3799 1.584724 AATCCAAGGATCCACGGAGT 58.415 50.000 22.52 18.81 35.38 3.85
2242 3800 2.292267 CAAATCCAAGGATCCACGGAG 58.708 52.381 22.52 9.60 33.08 4.63
2243 3801 1.064758 CCAAATCCAAGGATCCACGGA 60.065 52.381 20.98 20.98 33.08 4.69
2244 3802 1.340991 ACCAAATCCAAGGATCCACGG 60.341 52.381 15.82 13.81 33.08 4.94
2245 3803 1.745087 CACCAAATCCAAGGATCCACG 59.255 52.381 15.82 3.77 33.08 4.94
2246 3804 2.102578 CCACCAAATCCAAGGATCCAC 58.897 52.381 15.82 0.00 33.08 4.02
2247 3805 1.999295 TCCACCAAATCCAAGGATCCA 59.001 47.619 15.82 0.00 33.08 3.41
2248 3806 2.659428 CTCCACCAAATCCAAGGATCC 58.341 52.381 2.48 2.48 33.08 3.36
2249 3807 2.027385 GCTCCACCAAATCCAAGGATC 58.973 52.381 1.37 0.00 33.08 3.36
2250 3808 1.642762 AGCTCCACCAAATCCAAGGAT 59.357 47.619 0.00 0.00 36.23 3.24
2251 3809 1.075601 AGCTCCACCAAATCCAAGGA 58.924 50.000 0.00 0.00 0.00 3.36
2252 3810 1.180029 CAGCTCCACCAAATCCAAGG 58.820 55.000 0.00 0.00 0.00 3.61
2253 3811 1.180029 CCAGCTCCACCAAATCCAAG 58.820 55.000 0.00 0.00 0.00 3.61
2254 3812 0.776810 TCCAGCTCCACCAAATCCAA 59.223 50.000 0.00 0.00 0.00 3.53
2255 3813 0.329261 CTCCAGCTCCACCAAATCCA 59.671 55.000 0.00 0.00 0.00 3.41
2256 3814 0.394899 CCTCCAGCTCCACCAAATCC 60.395 60.000 0.00 0.00 0.00 3.01
2257 3815 0.329596 ACCTCCAGCTCCACCAAATC 59.670 55.000 0.00 0.00 0.00 2.17
2258 3816 0.779997 AACCTCCAGCTCCACCAAAT 59.220 50.000 0.00 0.00 0.00 2.32
2259 3817 0.555769 AAACCTCCAGCTCCACCAAA 59.444 50.000 0.00 0.00 0.00 3.28
2260 3818 0.110486 GAAACCTCCAGCTCCACCAA 59.890 55.000 0.00 0.00 0.00 3.67
2261 3819 1.761174 GAAACCTCCAGCTCCACCA 59.239 57.895 0.00 0.00 0.00 4.17
2262 3820 1.002011 GGAAACCTCCAGCTCCACC 60.002 63.158 0.00 0.00 41.96 4.61
2263 3821 4.724262 GGAAACCTCCAGCTCCAC 57.276 61.111 0.00 0.00 41.96 4.02
2275 3833 2.289506 ACTAAGGAGCTGTTCGGGAAAC 60.290 50.000 0.00 0.00 38.43 2.78
2276 3834 1.975680 ACTAAGGAGCTGTTCGGGAAA 59.024 47.619 0.00 0.00 0.00 3.13
2277 3835 1.275291 CACTAAGGAGCTGTTCGGGAA 59.725 52.381 0.00 0.00 0.00 3.97
2278 3836 0.895530 CACTAAGGAGCTGTTCGGGA 59.104 55.000 0.00 0.00 0.00 5.14
2279 3837 0.608640 ACACTAAGGAGCTGTTCGGG 59.391 55.000 0.00 0.00 0.00 5.14
2280 3838 2.069273 CAACACTAAGGAGCTGTTCGG 58.931 52.381 0.00 0.00 29.79 4.30
2281 3839 2.989840 CTCAACACTAAGGAGCTGTTCG 59.010 50.000 0.00 0.00 29.79 3.95
2288 3846 2.758736 AGCTGCTCAACACTAAGGAG 57.241 50.000 0.00 0.00 34.40 3.69
2289 3847 2.093973 GCTAGCTGCTCAACACTAAGGA 60.094 50.000 4.91 0.00 38.95 3.36
2290 3848 2.275318 GCTAGCTGCTCAACACTAAGG 58.725 52.381 4.91 0.00 38.95 2.69
2380 3939 4.079385 GGGGGTATCCTTAGAAACATGGTT 60.079 45.833 0.00 0.00 35.33 3.67
2442 4001 4.600692 AGGTTGGAAAAGGCAATTGTAC 57.399 40.909 7.40 0.64 0.00 2.90
2443 4002 4.898861 AGAAGGTTGGAAAAGGCAATTGTA 59.101 37.500 7.40 0.00 0.00 2.41
2444 4003 3.711190 AGAAGGTTGGAAAAGGCAATTGT 59.289 39.130 7.40 0.00 0.00 2.71
2458 4017 3.817647 CTGGAACTGGAAAGAGAAGGTTG 59.182 47.826 0.00 0.00 0.00 3.77
2473 4032 4.042187 AGTTTCCATTAGCTGTCTGGAACT 59.958 41.667 19.98 17.23 46.05 3.01
2633 4203 4.464069 ACTCTAATGAGACTTGGCAGAC 57.536 45.455 0.00 0.00 42.73 3.51
2638 4208 9.838339 ACCATAATAAACTCTAATGAGACTTGG 57.162 33.333 0.00 0.00 42.73 3.61
2667 4242 9.273016 CACCTTTCACAGTAGAAGAAAATAAGA 57.727 33.333 0.00 0.00 31.59 2.10
2668 4243 8.507249 CCACCTTTCACAGTAGAAGAAAATAAG 58.493 37.037 0.00 0.00 31.59 1.73
2690 4265 3.994392 CGCATAAGTATACATGTCCCACC 59.006 47.826 0.00 0.00 0.00 4.61
2694 4269 4.307432 AGCACGCATAAGTATACATGTCC 58.693 43.478 0.00 0.00 0.00 4.02
2696 4271 6.513180 ACTTAGCACGCATAAGTATACATGT 58.487 36.000 2.69 2.69 40.74 3.21
2704 4279 7.095774 CGGATAAATTACTTAGCACGCATAAGT 60.096 37.037 14.18 14.18 43.89 2.24
2705 4280 7.095774 ACGGATAAATTACTTAGCACGCATAAG 60.096 37.037 0.00 0.00 36.51 1.73
2706 4281 6.702723 ACGGATAAATTACTTAGCACGCATAA 59.297 34.615 0.00 0.00 0.00 1.90
2707 4282 6.144886 CACGGATAAATTACTTAGCACGCATA 59.855 38.462 0.00 0.00 0.00 3.14
2708 4283 5.050363 CACGGATAAATTACTTAGCACGCAT 60.050 40.000 0.00 0.00 0.00 4.73
2710 4285 4.505191 TCACGGATAAATTACTTAGCACGC 59.495 41.667 0.00 0.00 0.00 5.34
2711 4286 6.578020 TTCACGGATAAATTACTTAGCACG 57.422 37.500 0.00 0.00 0.00 5.34
2713 4288 9.602568 TGTTATTCACGGATAAATTACTTAGCA 57.397 29.630 0.00 0.00 0.00 3.49
2768 4350 2.632377 ACTGGTCAAGTATGCCGATTG 58.368 47.619 0.00 0.00 37.36 2.67
2813 5725 8.954950 AACACCTGATGTCTGAGAATAAATAG 57.045 34.615 0.00 0.00 42.31 1.73
3038 6150 5.853572 ACAACCAGAACTTCCCCTATTTA 57.146 39.130 0.00 0.00 0.00 1.40
3039 6151 4.741928 ACAACCAGAACTTCCCCTATTT 57.258 40.909 0.00 0.00 0.00 1.40
3040 6152 4.018688 GGTACAACCAGAACTTCCCCTATT 60.019 45.833 0.00 0.00 38.42 1.73
3055 6167 2.093128 CACTGGTATGGGAGGTACAACC 60.093 54.545 0.00 0.00 38.99 3.77
3178 6434 9.041354 TCTATAACAAATTAAAAAGTGGGGCAT 57.959 29.630 0.00 0.00 0.00 4.40
3246 6503 6.723977 TCAGCCTACTGGAACCAAAAATAAAT 59.276 34.615 0.00 0.00 44.59 1.40
3250 6507 4.112634 TCAGCCTACTGGAACCAAAAAT 57.887 40.909 0.00 0.00 44.59 1.82
3256 6513 1.282157 ACCAATCAGCCTACTGGAACC 59.718 52.381 0.00 0.00 44.59 3.62
3346 6618 0.453390 GCTAGGCTGACATGGCAAAC 59.547 55.000 1.11 0.00 34.73 2.93
3804 7100 8.043710 CCACTTCTCCACAGAAACTATAAGATT 58.956 37.037 0.00 0.00 38.23 2.40
3857 7153 2.147958 GAGCAACGAATACCACCACAA 58.852 47.619 0.00 0.00 0.00 3.33
3870 7166 4.731503 GCAGCACAGCGAGCAACG 62.732 66.667 0.00 0.00 45.66 4.10
3943 7247 0.108585 ACAGCCACACAACCTACAGG 59.891 55.000 0.00 0.00 42.17 4.00
3944 7248 1.229428 CACAGCCACACAACCTACAG 58.771 55.000 0.00 0.00 0.00 2.74
3946 7250 0.944386 CACACAGCCACACAACCTAC 59.056 55.000 0.00 0.00 0.00 3.18
4005 7328 6.969993 ATAAACCTCCTGTTGTTGCTTTAA 57.030 33.333 0.00 0.00 37.23 1.52
4043 7395 6.688813 GCATGAGGATTCAATCGAAAGTAAAC 59.311 38.462 0.00 0.00 36.78 2.01
4044 7396 6.456853 CGCATGAGGATTCAATCGAAAGTAAA 60.457 38.462 0.00 0.00 36.78 2.01
4053 7405 3.879295 TCCTTTCGCATGAGGATTCAATC 59.121 43.478 0.00 0.00 37.15 2.67
4054 7406 3.889815 TCCTTTCGCATGAGGATTCAAT 58.110 40.909 0.00 0.00 37.15 2.57
4062 7414 4.052159 ACTAGTGATCCTTTCGCATGAG 57.948 45.455 0.00 0.00 37.31 2.90
4064 7416 4.437239 AGAACTAGTGATCCTTTCGCATG 58.563 43.478 0.00 0.00 37.31 4.06
4065 7417 4.404073 AGAGAACTAGTGATCCTTTCGCAT 59.596 41.667 0.00 0.00 37.31 4.73
4066 7418 3.764434 AGAGAACTAGTGATCCTTTCGCA 59.236 43.478 0.00 0.00 37.31 5.10
4067 7419 4.379339 AGAGAACTAGTGATCCTTTCGC 57.621 45.455 0.00 0.00 34.93 4.70
4078 7442 6.820656 CCAATGCAAAGATGTAGAGAACTAGT 59.179 38.462 0.00 0.00 0.00 2.57
4158 7522 4.278170 CCAGGCAAGAACAATAACTTCACA 59.722 41.667 0.00 0.00 0.00 3.58
4243 7607 2.486592 TCAGTGTCAAGAATGCATGCAG 59.513 45.455 26.69 12.05 0.00 4.41
4244 7608 2.227149 GTCAGTGTCAAGAATGCATGCA 59.773 45.455 25.04 25.04 0.00 3.96
4245 7609 2.726989 CGTCAGTGTCAAGAATGCATGC 60.727 50.000 11.82 11.82 0.00 4.06
4246 7610 2.481568 ACGTCAGTGTCAAGAATGCATG 59.518 45.455 0.00 0.00 0.00 4.06
4247 7611 2.481568 CACGTCAGTGTCAAGAATGCAT 59.518 45.455 0.00 0.00 43.15 3.96
4248 7612 1.866601 CACGTCAGTGTCAAGAATGCA 59.133 47.619 0.00 0.00 43.15 3.96
4249 7613 2.584166 CACGTCAGTGTCAAGAATGC 57.416 50.000 0.00 0.00 43.15 3.56
4260 7624 2.555325 TGATTCTCGGTAACACGTCAGT 59.445 45.455 0.00 0.00 34.94 3.41
4261 7625 3.211803 TGATTCTCGGTAACACGTCAG 57.788 47.619 0.00 0.00 34.94 3.51
4262 7626 3.057104 ACATGATTCTCGGTAACACGTCA 60.057 43.478 0.00 0.00 34.94 4.35
4263 7627 3.508762 ACATGATTCTCGGTAACACGTC 58.491 45.455 0.00 0.00 34.94 4.34
4264 7628 3.508762 GACATGATTCTCGGTAACACGT 58.491 45.455 0.00 0.00 34.94 4.49
4265 7629 2.858344 GGACATGATTCTCGGTAACACG 59.142 50.000 0.00 0.00 0.00 4.49
4266 7630 3.865745 CAGGACATGATTCTCGGTAACAC 59.134 47.826 0.00 0.00 0.00 3.32
4267 7631 3.767131 TCAGGACATGATTCTCGGTAACA 59.233 43.478 0.00 0.00 31.12 2.41
4268 7632 4.386867 TCAGGACATGATTCTCGGTAAC 57.613 45.455 0.00 0.00 31.12 2.50
4274 7638 7.062839 GCGTTAGATTATCAGGACATGATTCTC 59.937 40.741 8.06 5.82 46.97 2.87
4326 8768 5.812286 TGAAAGGTATTCAAGTAGGGGAAC 58.188 41.667 0.00 0.00 0.00 3.62
4340 8782 8.477419 TTGGAGAAAATTCAACTGAAAGGTAT 57.523 30.769 0.00 0.00 39.30 2.73
4410 8873 1.978580 AGTGGACCGAACTGATTCCTT 59.021 47.619 0.00 0.00 0.00 3.36
4412 8875 2.076863 CAAGTGGACCGAACTGATTCC 58.923 52.381 0.00 0.00 0.00 3.01
4423 8886 7.391148 TTGAATATTCTTAAGCAAGTGGACC 57.609 36.000 16.24 0.00 33.20 4.46
4457 8920 5.533482 CGTCCCCATTTTTAAAACACATGA 58.467 37.500 11.12 0.34 0.00 3.07
4469 8932 0.966179 GAAACTGGCGTCCCCATTTT 59.034 50.000 0.00 0.00 45.84 1.82
4482 8945 2.349155 GGTTTGTTACTCGCCGAAACTG 60.349 50.000 3.63 0.00 0.00 3.16
4489 8952 1.392510 GTCGATGGTTTGTTACTCGCC 59.607 52.381 0.00 0.00 0.00 5.54
4493 8956 4.345859 TCAAGGTCGATGGTTTGTTACT 57.654 40.909 0.00 0.00 0.00 2.24
4495 8958 4.710324 ACTTCAAGGTCGATGGTTTGTTA 58.290 39.130 0.00 0.00 0.00 2.41
4612 9075 9.654417 GAAACGTGTAATTTTCAACTTTAGCTA 57.346 29.630 0.00 0.00 32.84 3.32
4644 9107 8.340618 TGGGTTCTTCTTTTATCTTTCATCTG 57.659 34.615 0.00 0.00 0.00 2.90
4683 9146 0.171903 GGCATGTTGAGCGCATTCTT 59.828 50.000 11.47 0.00 0.00 2.52
4702 9165 2.855180 CCTTGCAAAATCTGTAGCACG 58.145 47.619 0.00 0.00 36.62 5.34


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

AutoCloner maintained by Alex Coulton.