Multiple sequence alignment - TraesCS7B01G428800

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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 TraesCS7B01G428800 chr7B 100.000 4296 0 0 1 4296 697544178 697548473 0.000000e+00 7934.0
1 TraesCS7B01G428800 chr7B 88.798 1830 123 35 395 2172 695358329 695360128 0.000000e+00 2169.0
2 TraesCS7B01G428800 chr7B 94.032 620 28 5 1 614 685053342 685053958 0.000000e+00 931.0
3 TraesCS7B01G428800 chr7B 78.404 1153 206 27 990 2118 685048465 685049598 0.000000e+00 710.0
4 TraesCS7B01G428800 chr7B 78.133 1157 217 22 991 2118 697422716 697423865 0.000000e+00 702.0
5 TraesCS7B01G428800 chr7B 78.639 1058 185 21 1080 2118 697033998 697035033 0.000000e+00 664.0
6 TraesCS7B01G428800 chr7B 93.734 399 23 2 1 399 695357822 695358218 7.950000e-167 597.0
7 TraesCS7B01G428800 chr7B 76.294 1063 201 38 1081 2125 698871361 698872390 1.770000e-143 520.0
8 TraesCS7B01G428800 chr7B 75.646 1084 213 36 1071 2126 695955495 695954435 3.860000e-135 492.0
9 TraesCS7B01G428800 chr7B 76.864 778 139 29 986 1734 685013118 685013883 6.690000e-108 401.0
10 TraesCS7B01G428800 chr7B 82.479 468 43 10 2738 3184 713552457 713552008 1.460000e-99 374.0
11 TraesCS7B01G428800 chr7B 82.073 463 38 20 2759 3199 710309667 710310106 1.900000e-93 353.0
12 TraesCS7B01G428800 chr7B 80.041 486 79 14 1076 1555 695286015 695286488 1.140000e-90 344.0
13 TraesCS7B01G428800 chr7B 90.234 256 16 6 583 830 685057678 685057932 4.140000e-85 326.0
14 TraesCS7B01G428800 chr7B 79.834 362 64 7 1070 1425 733045934 733046292 5.510000e-64 255.0
15 TraesCS7B01G428800 chr7B 84.232 241 36 2 15 254 695495887 695495648 2.580000e-57 233.0
16 TraesCS7B01G428800 chr7B 94.203 69 4 0 107 175 698211142 698211074 5.880000e-19 106.0
17 TraesCS7B01G428800 chr7B 92.754 69 5 0 107 175 695488841 695488773 2.730000e-17 100.0
18 TraesCS7B01G428800 chr7B 78.344 157 18 10 984 1126 697401877 697402031 2.130000e-13 87.9
19 TraesCS7B01G428800 chr3B 95.976 820 29 4 3377 4195 773031963 773032779 0.000000e+00 1328.0
20 TraesCS7B01G428800 chr3B 86.413 184 22 3 2177 2360 686124676 686124496 9.420000e-47 198.0
21 TraesCS7B01G428800 chr3B 82.482 137 18 4 2170 2302 131513165 131513031 9.760000e-22 115.0
22 TraesCS7B01G428800 chr3B 97.368 38 1 0 3201 3238 479302487 479302450 9.970000e-07 65.8
23 TraesCS7B01G428800 chr3B 95.000 40 1 1 4157 4196 51121992 51122030 1.290000e-05 62.1
24 TraesCS7B01G428800 chr3B 94.872 39 1 1 4157 4195 650052443 650052406 4.640000e-05 60.2
25 TraesCS7B01G428800 chr7A 86.587 999 70 27 465 1422 700045001 700045976 0.000000e+00 1044.0
26 TraesCS7B01G428800 chr7A 87.959 789 64 11 1401 2172 700046434 700047208 0.000000e+00 902.0
27 TraesCS7B01G428800 chr7A 78.516 1038 193 21 1096 2118 130383458 130384480 0.000000e+00 654.0
28 TraesCS7B01G428800 chr7A 77.613 1081 198 35 1065 2117 700091929 700090865 2.200000e-172 616.0
29 TraesCS7B01G428800 chr7A 75.210 1073 234 27 1070 2129 726416973 726418026 3.010000e-131 479.0
30 TraesCS7B01G428800 chr7A 80.901 466 87 2 1654 2118 700941133 700940669 2.440000e-97 366.0
31 TraesCS7B01G428800 chr7A 85.139 323 46 2 1792 2113 699925423 699925744 3.200000e-86 329.0
32 TraesCS7B01G428800 chr7A 77.618 487 103 6 1124 1607 700421780 700422263 1.510000e-74 291.0
33 TraesCS7B01G428800 chr7A 93.333 105 7 0 7 111 700044829 700044933 5.750000e-34 156.0
34 TraesCS7B01G428800 chr7A 78.307 189 31 9 2177 2358 726910031 726909846 3.510000e-21 113.0
35 TraesCS7B01G428800 chr7D 78.460 1221 196 35 1002 2178 609947372 609946175 0.000000e+00 736.0
36 TraesCS7B01G428800 chr7D 79.357 1027 159 25 1134 2126 607931256 607932263 0.000000e+00 673.0
37 TraesCS7B01G428800 chr7D 76.670 1063 201 31 1093 2118 600282120 600283172 2.920000e-151 545.0
38 TraesCS7B01G428800 chr7D 82.596 339 57 2 1787 2124 608104498 608104161 9.030000e-77 298.0
39 TraesCS7B01G428800 chr7D 85.586 111 12 4 2170 2278 49821618 49821510 3.510000e-21 113.0
40 TraesCS7B01G428800 chr7D 94.203 69 4 0 107 175 610657954 610658022 5.880000e-19 106.0
41 TraesCS7B01G428800 chrUn 91.152 486 34 8 3623 4104 23192549 23192069 0.000000e+00 651.0
42 TraesCS7B01G428800 chrUn 82.934 334 55 2 1792 2124 77780531 77780863 2.510000e-77 300.0
43 TraesCS7B01G428800 chrUn 77.824 478 100 6 1133 1607 83447732 83447258 1.510000e-74 291.0
44 TraesCS7B01G428800 chrUn 85.020 247 37 0 1 247 77778648 77778894 7.130000e-63 252.0
45 TraesCS7B01G428800 chr5B 86.275 612 44 13 2620 3200 644450684 644451286 2.820000e-176 628.0
46 TraesCS7B01G428800 chr5B 85.161 465 29 21 2169 2608 644450180 644450629 1.420000e-119 440.0
47 TraesCS7B01G428800 chr5B 82.237 304 42 10 3742 4041 1165350 1165055 7.130000e-63 252.0
48 TraesCS7B01G428800 chr5B 95.098 102 4 1 4195 4296 644451279 644451379 4.450000e-35 159.0
49 TraesCS7B01G428800 chr5B 100.000 35 0 0 4161 4195 468733033 468733067 9.970000e-07 65.8
50 TraesCS7B01G428800 chr5B 94.737 38 1 1 3204 3240 540479417 540479380 1.670000e-04 58.4
51 TraesCS7B01G428800 chr5B 100.000 29 0 0 3201 3229 592365836 592365808 2.000000e-03 54.7
52 TraesCS7B01G428800 chr4D 89.877 326 32 1 3512 3837 448165446 448165122 6.640000e-113 418.0
53 TraesCS7B01G428800 chr4D 90.943 265 18 6 3836 4097 448157063 448156802 6.830000e-93 351.0
54 TraesCS7B01G428800 chr4B 87.978 183 19 3 2177 2358 508979368 508979548 3.370000e-51 213.0
55 TraesCS7B01G428800 chr1D 83.158 190 29 3 2170 2357 411733344 411733156 2.050000e-38 171.0
56 TraesCS7B01G428800 chr1D 85.455 110 11 5 2170 2277 385091376 385091270 4.540000e-20 110.0
57 TraesCS7B01G428800 chr5D 83.721 129 18 3 2179 2307 66298456 66298331 7.550000e-23 119.0
58 TraesCS7B01G428800 chr5D 95.000 40 1 1 3201 3239 4304365 4304326 1.290000e-05 62.1
59 TraesCS7B01G428800 chr1A 93.878 49 1 2 3201 3247 513367647 513367599 5.960000e-09 73.1
60 TraesCS7B01G428800 chr3D 100.000 36 0 0 4161 4196 200608034 200607999 2.770000e-07 67.6
61 TraesCS7B01G428800 chr3D 100.000 36 0 0 4161 4196 200608578 200608543 2.770000e-07 67.6
62 TraesCS7B01G428800 chr2A 97.500 40 0 1 4157 4195 398705769 398705730 2.770000e-07 67.6
63 TraesCS7B01G428800 chr2A 100.000 31 0 0 3201 3231 45155299 45155269 1.670000e-04 58.4
64 TraesCS7B01G428800 chr1B 97.297 37 1 0 4160 4196 686738736 686738700 3.590000e-06 63.9
65 TraesCS7B01G428800 chr1B 97.297 37 0 1 4161 4196 25432326 25432290 1.290000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G428800 chr7B 697544178 697548473 4295 False 7934.000000 7934 100.000000 1 4296 1 chr7B.!!$F6 4295
1 TraesCS7B01G428800 chr7B 695357822 695360128 2306 False 1383.000000 2169 91.266000 1 2172 2 chr7B.!!$F11 2171
2 TraesCS7B01G428800 chr7B 697422716 697423865 1149 False 702.000000 702 78.133000 991 2118 1 chr7B.!!$F5 1127
3 TraesCS7B01G428800 chr7B 697033998 697035033 1035 False 664.000000 664 78.639000 1080 2118 1 chr7B.!!$F3 1038
4 TraesCS7B01G428800 chr7B 685048465 685057932 9467 False 655.666667 931 87.556667 1 2118 3 chr7B.!!$F10 2117
5 TraesCS7B01G428800 chr7B 698871361 698872390 1029 False 520.000000 520 76.294000 1081 2125 1 chr7B.!!$F7 1044
6 TraesCS7B01G428800 chr7B 695954435 695955495 1060 True 492.000000 492 75.646000 1071 2126 1 chr7B.!!$R3 1055
7 TraesCS7B01G428800 chr7B 685013118 685013883 765 False 401.000000 401 76.864000 986 1734 1 chr7B.!!$F1 748
8 TraesCS7B01G428800 chr3B 773031963 773032779 816 False 1328.000000 1328 95.976000 3377 4195 1 chr3B.!!$F2 818
9 TraesCS7B01G428800 chr7A 700044829 700047208 2379 False 700.666667 1044 89.293000 7 2172 3 chr7A.!!$F5 2165
10 TraesCS7B01G428800 chr7A 130383458 130384480 1022 False 654.000000 654 78.516000 1096 2118 1 chr7A.!!$F1 1022
11 TraesCS7B01G428800 chr7A 700090865 700091929 1064 True 616.000000 616 77.613000 1065 2117 1 chr7A.!!$R1 1052
12 TraesCS7B01G428800 chr7A 726416973 726418026 1053 False 479.000000 479 75.210000 1070 2129 1 chr7A.!!$F4 1059
13 TraesCS7B01G428800 chr7D 609946175 609947372 1197 True 736.000000 736 78.460000 1002 2178 1 chr7D.!!$R3 1176
14 TraesCS7B01G428800 chr7D 607931256 607932263 1007 False 673.000000 673 79.357000 1134 2126 1 chr7D.!!$F2 992
15 TraesCS7B01G428800 chr7D 600282120 600283172 1052 False 545.000000 545 76.670000 1093 2118 1 chr7D.!!$F1 1025
16 TraesCS7B01G428800 chrUn 77778648 77780863 2215 False 276.000000 300 83.977000 1 2124 2 chrUn.!!$F1 2123
17 TraesCS7B01G428800 chr5B 644450180 644451379 1199 False 409.000000 628 88.844667 2169 4296 3 chr5B.!!$F2 2127

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
225 226 0.251916 CGGGGGAGTGTCAATAAGCA 59.748 55.0 0.0 0.0 0.00 3.91 F
1010 1335 0.042731 TCCTCCCTTTCCCATCTCGT 59.957 55.0 0.0 0.0 0.00 4.18 F
2297 3398 0.319555 CCTGGCGTGGTACATATCCG 60.320 60.0 0.0 0.0 44.52 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 2827 0.323360 CCTTGCTCCATTTTCCGGGA 60.323 55.0 0.00 0.00 0.00 5.14 R
2495 7248 0.036105 CAGACACACTGCAGGCCATA 60.036 55.0 19.93 0.00 39.86 2.74 R
3607 9192 0.250209 CTGATCTGAATCTGCCCGGG 60.250 60.0 19.09 19.09 32.75 5.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 4.634184 TGTACTCCTAAAGCGACATCTC 57.366 45.455 0.00 0.00 0.00 2.75
225 226 0.251916 CGGGGGAGTGTCAATAAGCA 59.748 55.000 0.00 0.00 0.00 3.91
226 227 1.134098 CGGGGGAGTGTCAATAAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
248 292 1.002544 GGTTGGGTTCTCACTGAGGAG 59.997 57.143 6.20 0.00 36.21 3.69
249 293 1.002544 GTTGGGTTCTCACTGAGGAGG 59.997 57.143 6.20 0.00 35.58 4.30
327 371 0.255890 ACACCTATGGGGCATGTGTC 59.744 55.000 0.00 0.00 39.10 3.67
368 412 1.881973 CCCAAAGTGATCCATATGGCG 59.118 52.381 17.58 0.00 34.44 5.69
591 762 7.925993 TCAGAACATATGACGTTTGAGTTTTT 58.074 30.769 10.38 0.00 0.00 1.94
693 868 7.317842 ACAGAGAAGATGCAGTATGAAATTG 57.682 36.000 0.00 0.00 39.69 2.32
725 904 5.369404 TGGATATGGAACCTTGAGCTAATCA 59.631 40.000 0.00 0.00 35.62 2.57
741 924 8.642432 TGAGCTAATCACAGTACTTAGCATAAT 58.358 33.333 20.33 5.01 46.20 1.28
752 935 9.459640 CAGTACTTAGCATAATAAGCTTTCGTA 57.540 33.333 3.20 0.00 43.25 3.43
861 1090 1.581934 CAGCTCGAGTTTGAACCACA 58.418 50.000 15.13 0.00 0.00 4.17
896 1141 0.676736 CTTTTTGGTTAAGCCGGGCA 59.323 50.000 23.09 0.00 41.21 5.36
906 1151 1.244019 AAGCCGGGCATGACAAACTC 61.244 55.000 23.09 0.00 0.00 3.01
907 1152 2.700773 GCCGGGCATGACAAACTCC 61.701 63.158 15.62 0.00 0.00 3.85
912 1157 2.700773 GCATGACAAACTCCGGGCC 61.701 63.158 0.00 0.00 0.00 5.80
917 1162 2.391724 GACAAACTCCGGGCCTGACA 62.392 60.000 15.09 0.00 0.00 3.58
919 1164 0.821711 CAAACTCCGGGCCTGACAAA 60.822 55.000 15.09 0.00 0.00 2.83
921 1166 1.705997 AACTCCGGGCCTGACAAACT 61.706 55.000 15.09 0.00 0.00 2.66
923 1168 2.672996 CCGGGCCTGACAAACTGG 60.673 66.667 15.09 0.00 40.02 4.00
924 1169 2.672996 CGGGCCTGACAAACTGGG 60.673 66.667 5.28 0.00 37.94 4.45
927 1172 4.181051 GCCTGACAAACTGGGCTT 57.819 55.556 0.00 0.00 41.20 4.35
928 1173 1.662044 GCCTGACAAACTGGGCTTG 59.338 57.895 0.00 0.00 41.20 4.01
929 1174 1.662044 CCTGACAAACTGGGCTTGC 59.338 57.895 0.00 0.00 34.55 4.01
930 1175 1.662044 CTGACAAACTGGGCTTGCC 59.338 57.895 2.49 2.49 0.00 4.52
931 1176 1.076412 TGACAAACTGGGCTTGCCA 60.076 52.632 14.04 0.00 0.00 4.92
960 1205 6.127647 CCGAGGAAGGAAAATCAATCAATCAA 60.128 38.462 0.00 0.00 0.00 2.57
963 1208 8.370266 AGGAAGGAAAATCAATCAATCAATCA 57.630 30.769 0.00 0.00 0.00 2.57
964 1209 8.255905 AGGAAGGAAAATCAATCAATCAATCAC 58.744 33.333 0.00 0.00 0.00 3.06
965 1210 8.255905 GGAAGGAAAATCAATCAATCAATCACT 58.744 33.333 0.00 0.00 0.00 3.41
966 1211 9.298774 GAAGGAAAATCAATCAATCAATCACTC 57.701 33.333 0.00 0.00 0.00 3.51
968 1213 7.337689 AGGAAAATCAATCAATCAATCACTCGA 59.662 33.333 0.00 0.00 0.00 4.04
969 1214 7.430502 GGAAAATCAATCAATCAATCACTCGAC 59.569 37.037 0.00 0.00 0.00 4.20
970 1215 5.998454 ATCAATCAATCAATCACTCGACC 57.002 39.130 0.00 0.00 0.00 4.79
1010 1335 0.042731 TCCTCCCTTTCCCATCTCGT 59.957 55.000 0.00 0.00 0.00 4.18
1011 1336 0.466124 CCTCCCTTTCCCATCTCGTC 59.534 60.000 0.00 0.00 0.00 4.20
1115 1461 2.278206 CGCCTCTGACGGACATCG 60.278 66.667 0.00 0.00 45.88 3.84
1129 1475 2.683933 ATCGCCGACCACCTCCTT 60.684 61.111 0.00 0.00 0.00 3.36
1259 1605 4.511246 CCCTCCATGCGCCACCAT 62.511 66.667 4.18 0.00 0.00 3.55
1262 1608 1.750018 CTCCATGCGCCACCATTCA 60.750 57.895 4.18 0.00 0.00 2.57
1505 2370 1.148157 CTTGCACCAGCGGTATCTCG 61.148 60.000 0.00 0.00 46.23 4.04
1525 2390 2.070650 GCTTCCCCCGGTACCTGAT 61.071 63.158 10.90 0.00 0.00 2.90
1543 2408 2.231529 GATGACCTAGCCGCTTCTCTA 58.768 52.381 0.00 0.00 0.00 2.43
1658 2573 1.331447 GGTTGGCGTGTTACGAAACTT 59.669 47.619 5.44 0.00 46.05 2.66
1717 2640 2.527497 TGGAGAATTGCTGCATCCAAA 58.473 42.857 17.80 0.00 40.31 3.28
1760 2687 1.918609 GCACGGACGAGTCTTTCATAC 59.081 52.381 0.00 0.00 0.00 2.39
1897 2827 2.040412 GTTCTCCATTGTTGACCTCCCT 59.960 50.000 0.00 0.00 0.00 4.20
1976 2906 3.181417 TGGGATGTTTGGTTTCCATGGTA 60.181 43.478 12.58 0.00 31.53 3.25
2002 2938 3.570540 TGCATCTGACCTCAGCTATACT 58.429 45.455 0.00 0.00 43.46 2.12
2028 2964 2.910688 TCGAACAAAGGCAAGAGTCT 57.089 45.000 0.00 0.00 0.00 3.24
2145 3081 5.451242 GGACAAAAACACTGCCAAACTCATA 60.451 40.000 0.00 0.00 0.00 2.15
2251 3351 1.879380 CAGTGAAAATCGAGCCAACCA 59.121 47.619 0.00 0.00 0.00 3.67
2254 3354 2.552315 GTGAAAATCGAGCCAACCAGAA 59.448 45.455 0.00 0.00 0.00 3.02
2292 3393 2.666098 GGGACCTGGCGTGGTACAT 61.666 63.158 12.76 0.00 42.69 2.29
2297 3398 0.319555 CCTGGCGTGGTACATATCCG 60.320 60.000 0.00 0.00 44.52 4.18
2375 6930 3.792047 CGGCATGCGTGGTGTCAG 61.792 66.667 12.44 0.00 0.00 3.51
2377 6932 2.260869 GGCATGCGTGGTGTCAGTT 61.261 57.895 12.44 0.00 0.00 3.16
2420 6980 1.109323 GGCTCTTTGTGGTTGGCTGT 61.109 55.000 0.00 0.00 0.00 4.40
2424 6984 3.149196 CTCTTTGTGGTTGGCTGTGTAT 58.851 45.455 0.00 0.00 0.00 2.29
2425 6985 2.884012 TCTTTGTGGTTGGCTGTGTATG 59.116 45.455 0.00 0.00 0.00 2.39
2426 6986 2.647683 TTGTGGTTGGCTGTGTATGA 57.352 45.000 0.00 0.00 0.00 2.15
2427 6987 2.877097 TGTGGTTGGCTGTGTATGAT 57.123 45.000 0.00 0.00 0.00 2.45
2428 6988 3.153369 TGTGGTTGGCTGTGTATGATT 57.847 42.857 0.00 0.00 0.00 2.57
2429 6989 2.819019 TGTGGTTGGCTGTGTATGATTG 59.181 45.455 0.00 0.00 0.00 2.67
2430 6990 2.819608 GTGGTTGGCTGTGTATGATTGT 59.180 45.455 0.00 0.00 0.00 2.71
2431 6991 3.081061 TGGTTGGCTGTGTATGATTGTC 58.919 45.455 0.00 0.00 0.00 3.18
2432 6992 3.244875 TGGTTGGCTGTGTATGATTGTCT 60.245 43.478 0.00 0.00 0.00 3.41
2433 6993 4.019771 TGGTTGGCTGTGTATGATTGTCTA 60.020 41.667 0.00 0.00 0.00 2.59
2434 6994 5.126067 GGTTGGCTGTGTATGATTGTCTAT 58.874 41.667 0.00 0.00 0.00 1.98
2437 7189 5.988287 TGGCTGTGTATGATTGTCTATTGA 58.012 37.500 0.00 0.00 0.00 2.57
2444 7196 6.017934 GTGTATGATTGTCTATTGATTGCCGT 60.018 38.462 0.00 0.00 0.00 5.68
2448 7200 6.092092 TGATTGTCTATTGATTGCCGTTTTG 58.908 36.000 0.00 0.00 0.00 2.44
2456 7208 3.367607 TGATTGCCGTTTTGTTTTCTCG 58.632 40.909 0.00 0.00 0.00 4.04
2457 7209 1.551145 TTGCCGTTTTGTTTTCTCGC 58.449 45.000 0.00 0.00 0.00 5.03
2461 7213 2.601314 GCCGTTTTGTTTTCTCGCTTTT 59.399 40.909 0.00 0.00 0.00 2.27
2463 7215 4.564281 CCGTTTTGTTTTCTCGCTTTTTG 58.436 39.130 0.00 0.00 0.00 2.44
2495 7248 1.201647 CTTCCGGACGTGTATGTCTGT 59.798 52.381 1.83 0.00 42.52 3.41
2498 7251 2.356695 TCCGGACGTGTATGTCTGTATG 59.643 50.000 0.00 0.00 42.52 2.39
2528 7281 1.279271 GTGTCTGCCAAGTGGGTCTAT 59.721 52.381 0.00 0.00 39.65 1.98
2535 7288 3.181423 TGCCAAGTGGGTCTATTTTTCCT 60.181 43.478 0.00 0.00 39.65 3.36
2554 7307 2.639286 CCGGTCTTGCTGTTGTGC 59.361 61.111 0.00 0.00 0.00 4.57
2558 7311 0.819259 GGTCTTGCTGTTGTGCTGGA 60.819 55.000 0.00 0.00 0.00 3.86
2590 7343 5.008811 ACGTTGGTGGTTATTTCGATTTTGA 59.991 36.000 0.00 0.00 0.00 2.69
2592 7345 6.087555 CGTTGGTGGTTATTTCGATTTTGAAG 59.912 38.462 0.00 0.00 0.00 3.02
2601 7355 5.432885 TTTCGATTTTGAAGTCCTTCCAC 57.567 39.130 4.67 0.00 38.77 4.02
2608 7362 2.710724 GAAGTCCTTCCACGCCGTGT 62.711 60.000 16.99 0.00 33.64 4.49
2658 7455 2.543653 CCTTCCAGCCGTTTCTTTGTTG 60.544 50.000 0.00 0.00 0.00 3.33
2666 7463 1.477105 GTTTCTTTGTTGCACCGCTC 58.523 50.000 0.00 0.00 0.00 5.03
2690 7487 5.574830 CGGTTGTGTTCAATTTGTTCTTTGA 59.425 36.000 0.00 0.00 35.92 2.69
2714 7511 6.693315 TTTGTCCCTGCTTGCTATAAATAC 57.307 37.500 0.00 0.00 0.00 1.89
2735 7532 0.387565 GAGAGGCTCTTCCATCCGTC 59.612 60.000 19.80 0.00 37.29 4.79
2736 7533 0.032615 AGAGGCTCTTCCATCCGTCT 60.033 55.000 12.24 0.00 37.29 4.18
2738 7535 1.208293 GAGGCTCTTCCATCCGTCTTT 59.792 52.381 7.40 0.00 37.29 2.52
2767 7587 4.486125 TGTGGCTGCATTTAGTGATAGA 57.514 40.909 0.50 0.00 0.00 1.98
2832 7652 2.840102 CTGGGGCGTCCTCCTAGG 60.840 72.222 5.77 0.82 36.46 3.02
2841 7661 1.073373 TCCTCCTAGGATCCGAGCG 59.927 63.158 13.12 9.66 40.06 5.03
2845 7665 2.912542 CTAGGATCCGAGCGGCCA 60.913 66.667 9.11 0.00 34.68 5.36
2866 7686 0.041576 CGCTGTTCATGCCATCATCG 60.042 55.000 0.00 0.00 0.00 3.84
2910 7730 4.011517 GCCTTTGGTCGACCGGGA 62.012 66.667 31.70 19.23 39.43 5.14
2929 7749 3.695606 GTCCAGCAGGCGAGGTGA 61.696 66.667 12.59 0.00 39.26 4.02
2938 7758 2.035442 GGCGAGGTGAGTTTCAGCC 61.035 63.158 4.78 0.00 45.34 4.85
2947 7767 0.398318 GAGTTTCAGCCACCTCCTGT 59.602 55.000 0.00 0.00 0.00 4.00
2971 7791 2.434359 CCGACGAGGCCTTTGGTC 60.434 66.667 6.77 14.28 0.00 4.02
3002 7822 3.380637 GTCCAGGCTACGTAGATTTCTCA 59.619 47.826 26.53 0.15 0.00 3.27
3005 7825 3.381908 CAGGCTACGTAGATTTCTCAGGT 59.618 47.826 26.53 0.00 0.00 4.00
3024 7850 0.178861 TGAGGCCCTCTTTCCTCCTT 60.179 55.000 12.94 0.00 46.39 3.36
3039 7865 8.055790 TCTTTCCTCCTTCTTCTTCTTCTTTTT 58.944 33.333 0.00 0.00 0.00 1.94
3040 7866 7.809546 TTCCTCCTTCTTCTTCTTCTTTTTC 57.190 36.000 0.00 0.00 0.00 2.29
3041 7867 7.142995 TCCTCCTTCTTCTTCTTCTTTTTCT 57.857 36.000 0.00 0.00 0.00 2.52
3043 7869 7.717436 TCCTCCTTCTTCTTCTTCTTTTTCTTC 59.283 37.037 0.00 0.00 0.00 2.87
3046 7872 9.114952 TCCTTCTTCTTCTTCTTTTTCTTCTTC 57.885 33.333 0.00 0.00 0.00 2.87
3074 7900 2.070028 GAGTGTTTTCTTCTCCGCCTC 58.930 52.381 0.00 0.00 0.00 4.70
3142 7968 4.789075 GCCAGTGCTGCGCCAATG 62.789 66.667 9.97 5.98 33.53 2.82
3201 8035 4.994201 GTGACGACCAGCGCGACA 62.994 66.667 12.10 0.00 46.04 4.35
3202 8036 4.700365 TGACGACCAGCGCGACAG 62.700 66.667 12.10 0.00 46.04 3.51
3203 8037 4.702081 GACGACCAGCGCGACAGT 62.702 66.667 12.10 1.72 46.04 3.55
3271 8105 5.890424 TTTTTGCGGGGAACTTTATAGAG 57.110 39.130 0.00 0.00 0.00 2.43
3272 8106 2.614829 TGCGGGGAACTTTATAGAGC 57.385 50.000 0.00 0.00 0.00 4.09
3273 8107 2.116238 TGCGGGGAACTTTATAGAGCT 58.884 47.619 0.00 0.00 0.00 4.09
3274 8108 2.504175 TGCGGGGAACTTTATAGAGCTT 59.496 45.455 0.00 0.00 0.00 3.74
3275 8109 3.054655 TGCGGGGAACTTTATAGAGCTTT 60.055 43.478 0.00 0.00 0.00 3.51
3276 8110 4.162698 TGCGGGGAACTTTATAGAGCTTTA 59.837 41.667 0.00 0.00 0.00 1.85
3277 8111 5.163237 TGCGGGGAACTTTATAGAGCTTTAT 60.163 40.000 1.94 1.94 0.00 1.40
3278 8112 5.763698 GCGGGGAACTTTATAGAGCTTTATT 59.236 40.000 1.57 0.00 0.00 1.40
3279 8113 6.932960 GCGGGGAACTTTATAGAGCTTTATTA 59.067 38.462 1.57 0.00 0.00 0.98
3280 8114 7.443272 GCGGGGAACTTTATAGAGCTTTATTAA 59.557 37.037 1.57 0.00 0.00 1.40
3281 8115 9.333724 CGGGGAACTTTATAGAGCTTTATTAAA 57.666 33.333 1.57 1.66 0.00 1.52
3302 8136 3.102052 CAAAGGCATTTGCTGAACAGT 57.898 42.857 11.30 0.00 39.43 3.55
3303 8137 3.054878 CAAAGGCATTTGCTGAACAGTC 58.945 45.455 11.30 0.00 39.43 3.51
3304 8138 1.985473 AGGCATTTGCTGAACAGTCA 58.015 45.000 2.12 0.20 41.70 3.41
3312 8146 3.529252 CTGAACAGTCAGCCAGGAG 57.471 57.895 0.00 0.00 44.74 3.69
3313 8147 0.036577 CTGAACAGTCAGCCAGGAGG 60.037 60.000 0.00 0.00 44.74 4.30
3323 8157 3.385384 CCAGGAGGCTGCTGTCGA 61.385 66.667 30.38 0.00 33.66 4.20
3324 8158 2.729479 CCAGGAGGCTGCTGTCGAT 61.729 63.158 30.38 0.00 33.66 3.59
3325 8159 1.227205 CAGGAGGCTGCTGTCGATC 60.227 63.158 25.94 0.00 30.66 3.69
3326 8160 2.279120 GGAGGCTGCTGTCGATCG 60.279 66.667 9.36 9.36 0.00 3.69
3327 8161 2.775856 GGAGGCTGCTGTCGATCGA 61.776 63.158 15.15 15.15 0.00 3.59
3328 8162 1.299014 GAGGCTGCTGTCGATCGAG 60.299 63.158 20.09 9.18 0.00 4.04
3329 8163 2.959071 GGCTGCTGTCGATCGAGC 60.959 66.667 20.09 19.61 35.65 5.03
3330 8164 3.318555 GCTGCTGTCGATCGAGCG 61.319 66.667 20.09 18.51 38.09 5.03
3331 8165 2.405191 CTGCTGTCGATCGAGCGA 59.595 61.111 23.46 23.46 38.09 4.93
3332 8166 1.226407 CTGCTGTCGATCGAGCGAA 60.226 57.895 28.87 16.39 42.55 4.70
3333 8167 1.467556 CTGCTGTCGATCGAGCGAAC 61.468 60.000 28.87 20.85 42.55 3.95
3334 8168 1.514228 GCTGTCGATCGAGCGAACA 60.514 57.895 28.87 23.96 42.55 3.18
3335 8169 1.734359 GCTGTCGATCGAGCGAACAC 61.734 60.000 28.87 16.72 42.55 3.32
3336 8170 1.456678 CTGTCGATCGAGCGAACACG 61.457 60.000 28.87 15.88 42.55 4.49
3345 8179 2.942879 GCGAACACGCCACATTGA 59.057 55.556 3.16 0.00 45.62 2.57
3346 8180 1.501741 GCGAACACGCCACATTGAT 59.498 52.632 3.16 0.00 45.62 2.57
3347 8181 0.724549 GCGAACACGCCACATTGATA 59.275 50.000 3.16 0.00 45.62 2.15
3348 8182 1.330521 GCGAACACGCCACATTGATAT 59.669 47.619 3.16 0.00 45.62 1.63
3349 8183 2.850631 GCGAACACGCCACATTGATATG 60.851 50.000 3.16 0.00 45.62 1.78
3350 8184 2.286359 CGAACACGCCACATTGATATGG 60.286 50.000 0.00 0.00 39.16 2.74
3351 8185 2.418368 ACACGCCACATTGATATGGT 57.582 45.000 0.00 0.00 38.34 3.55
3352 8186 3.552132 ACACGCCACATTGATATGGTA 57.448 42.857 0.00 0.00 38.34 3.25
3353 8187 4.085357 ACACGCCACATTGATATGGTAT 57.915 40.909 0.00 0.00 38.34 2.73
3354 8188 4.460263 ACACGCCACATTGATATGGTATT 58.540 39.130 0.00 0.00 38.34 1.89
3355 8189 5.616270 ACACGCCACATTGATATGGTATTA 58.384 37.500 0.00 0.00 38.34 0.98
3356 8190 5.700832 ACACGCCACATTGATATGGTATTAG 59.299 40.000 0.00 0.00 38.34 1.73
3357 8191 4.695455 ACGCCACATTGATATGGTATTAGC 59.305 41.667 0.00 0.00 38.34 3.09
3358 8192 4.201714 CGCCACATTGATATGGTATTAGCG 60.202 45.833 0.00 0.00 38.34 4.26
3359 8193 4.935205 GCCACATTGATATGGTATTAGCGA 59.065 41.667 0.00 0.00 38.34 4.93
3360 8194 5.586243 GCCACATTGATATGGTATTAGCGAT 59.414 40.000 0.00 0.00 38.34 4.58
3361 8195 6.761242 GCCACATTGATATGGTATTAGCGATA 59.239 38.462 0.00 0.00 38.34 2.92
3362 8196 7.042456 GCCACATTGATATGGTATTAGCGATAG 60.042 40.741 0.00 0.00 38.34 2.08
3363 8197 8.197439 CCACATTGATATGGTATTAGCGATAGA 58.803 37.037 0.00 0.00 36.01 1.98
3364 8198 9.586435 CACATTGATATGGTATTAGCGATAGAA 57.414 33.333 0.00 0.00 36.01 2.10
3367 8201 8.683550 TTGATATGGTATTAGCGATAGAAACG 57.316 34.615 0.00 0.00 39.76 3.60
3368 8202 7.823665 TGATATGGTATTAGCGATAGAAACGT 58.176 34.615 0.00 0.00 39.76 3.99
3369 8203 8.949177 TGATATGGTATTAGCGATAGAAACGTA 58.051 33.333 0.00 0.00 39.76 3.57
3370 8204 9.219497 GATATGGTATTAGCGATAGAAACGTAC 57.781 37.037 0.00 0.00 39.76 3.67
3371 8205 5.443261 TGGTATTAGCGATAGAAACGTACG 58.557 41.667 15.01 15.01 39.76 3.67
3372 8206 5.007626 TGGTATTAGCGATAGAAACGTACGT 59.992 40.000 16.72 16.72 39.76 3.57
3373 8207 6.201997 TGGTATTAGCGATAGAAACGTACGTA 59.798 38.462 23.12 6.15 39.76 3.57
3374 8208 7.095229 TGGTATTAGCGATAGAAACGTACGTAT 60.095 37.037 23.12 11.46 39.76 3.06
3375 8209 8.380644 GGTATTAGCGATAGAAACGTACGTATA 58.619 37.037 23.12 14.99 39.76 1.47
3386 8220 7.409697 AGAAACGTACGTATACATGTATTCGT 58.590 34.615 36.28 36.28 46.23 3.85
3415 8250 2.507484 TCTGGCTGTCTTTCATTGTGG 58.493 47.619 0.00 0.00 0.00 4.17
3419 8254 1.915141 CTGTCTTTCATTGTGGGGCT 58.085 50.000 0.00 0.00 0.00 5.19
3509 8462 1.816074 ACGTTCTACCCGTAACCGTA 58.184 50.000 0.00 0.00 36.65 4.02
3526 8479 3.730715 ACCGTAAATTAGCGTATACGTGC 59.269 43.478 25.04 10.60 39.45 5.34
3588 9173 0.397816 GCCTCTTCTCTCCCTGCCTA 60.398 60.000 0.00 0.00 0.00 3.93
3599 9184 0.958091 CCCTGCCTACTCTCGATCTG 59.042 60.000 0.00 0.00 0.00 2.90
3607 9192 5.219633 GCCTACTCTCGATCTGAATTTCTC 58.780 45.833 0.00 0.00 0.00 2.87
3680 9265 2.771372 ACTTGTTTCAACCTGGCCATTT 59.229 40.909 5.51 0.00 0.00 2.32
3693 9278 1.144057 CCATTTAGCGACGGCCTCT 59.856 57.895 0.00 0.00 41.24 3.69
3696 9281 1.961180 ATTTAGCGACGGCCTCTGCT 61.961 55.000 15.44 15.44 41.24 4.24
3766 9351 3.489785 CGCTAACGATTACCATTCTGGAC 59.510 47.826 0.00 0.00 40.37 4.02
3865 9783 7.935520 TGTTTGATGTGTTCATGCTTTAGTAA 58.064 30.769 0.00 0.00 33.34 2.24
3869 11289 8.969121 TGATGTGTTCATGCTTTAGTAAATTG 57.031 30.769 0.00 0.00 34.06 2.32
4005 11425 5.716228 TCAATCTTTAACCCATGCACTGAAT 59.284 36.000 0.00 0.00 0.00 2.57
4104 11524 9.030301 TCGAACATGTATCTATTACAATGTGTG 57.970 33.333 0.00 0.00 43.84 3.82
4235 11655 2.875786 GCAGCAGCGAATACGAGGC 61.876 63.158 0.00 0.00 42.66 4.70
4236 11656 2.278857 AGCAGCGAATACGAGGCG 60.279 61.111 0.00 0.00 41.99 5.52
4237 11657 2.278596 GCAGCGAATACGAGGCGA 60.279 61.111 0.00 0.00 42.66 5.54
4244 11694 2.403671 GAATACGAGGCGACGGAGGG 62.404 65.000 11.12 0.00 37.61 4.30
4281 11731 3.488090 GCGGTGTTGGTAGCTCGC 61.488 66.667 0.00 0.00 36.51 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 212 3.063997 CCAACCGATGCTTATTGACACTC 59.936 47.826 0.00 0.00 0.00 3.51
219 220 2.238646 TGAGAACCCAACCGATGCTTAT 59.761 45.455 0.00 0.00 0.00 1.73
225 226 1.276421 CTCAGTGAGAACCCAACCGAT 59.724 52.381 15.46 0.00 0.00 4.18
226 227 0.679505 CTCAGTGAGAACCCAACCGA 59.320 55.000 15.46 0.00 0.00 4.69
278 322 9.270640 GTGCCCAATTATTTTTAATATCATGCA 57.729 29.630 0.00 0.00 0.00 3.96
327 371 4.095610 GGCGAAAAAGAATAACATGTCCG 58.904 43.478 0.00 0.00 0.00 4.79
335 379 5.776173 TCACTTTGGGCGAAAAAGAATAA 57.224 34.783 11.44 0.00 37.91 1.40
427 587 6.211384 TCTTCCTCATTCATCACTGTCTACAA 59.789 38.462 0.00 0.00 0.00 2.41
648 822 8.696043 TCTGTTTATAAGGCTCATGCATATTT 57.304 30.769 0.00 0.00 41.91 1.40
693 868 1.071228 GGTTCCATATCCACGTACCCC 59.929 57.143 0.00 0.00 0.00 4.95
725 904 7.980099 ACGAAAGCTTATTATGCTAAGTACTGT 59.020 33.333 0.00 0.00 40.22 3.55
752 935 1.831389 GCGTGCACATTCGTGTGACT 61.831 55.000 18.64 0.00 45.50 3.41
822 1044 5.801947 AGCTGCATTTTATTCTGCTAAAACG 59.198 36.000 1.02 0.00 39.16 3.60
830 1052 4.871993 ACTCGAGCTGCATTTTATTCTG 57.128 40.909 13.61 0.00 0.00 3.02
875 1107 1.336517 GCCCGGCTTAACCAAAAAGAC 60.337 52.381 0.71 0.00 39.03 3.01
896 1141 1.002134 CAGGCCCGGAGTTTGTCAT 60.002 57.895 0.73 0.00 0.00 3.06
906 1151 2.672996 CCAGTTTGTCAGGCCCGG 60.673 66.667 0.00 0.00 0.00 5.73
907 1152 2.672996 CCCAGTTTGTCAGGCCCG 60.673 66.667 0.00 0.00 0.00 6.13
912 1157 1.108727 TGGCAAGCCCAGTTTGTCAG 61.109 55.000 8.89 0.00 39.18 3.51
926 1171 2.034066 CTTCCTCGGGCTTGGCAA 59.966 61.111 0.00 0.00 0.00 4.52
927 1172 4.033776 CCTTCCTCGGGCTTGGCA 62.034 66.667 0.00 0.00 0.00 4.92
928 1173 2.764637 TTTCCTTCCTCGGGCTTGGC 62.765 60.000 0.00 0.00 0.00 4.52
929 1174 0.251165 TTTTCCTTCCTCGGGCTTGG 60.251 55.000 0.00 0.00 0.00 3.61
930 1175 1.745653 GATTTTCCTTCCTCGGGCTTG 59.254 52.381 0.00 0.00 0.00 4.01
931 1176 1.354368 TGATTTTCCTTCCTCGGGCTT 59.646 47.619 0.00 0.00 0.00 4.35
960 1205 4.796231 GCGTGCGGGTCGAGTGAT 62.796 66.667 0.00 0.00 0.00 3.06
1115 1461 1.450312 CATCAAGGAGGTGGTCGGC 60.450 63.158 0.00 0.00 0.00 5.54
1259 1605 3.436001 GGTCGAAGAAGCCGATGAA 57.564 52.632 0.00 0.00 39.69 2.57
1346 1695 2.027100 GGAAGGAGAAGGTGAAATCGGT 60.027 50.000 0.00 0.00 0.00 4.69
1505 2370 3.007323 AGGTACCGGGGGAAGCAC 61.007 66.667 6.32 0.00 0.00 4.40
1525 2390 1.212195 TCTAGAGAAGCGGCTAGGTCA 59.788 52.381 1.35 0.00 35.83 4.02
1543 2408 2.039624 ATGGAGACCCGGTGCTCT 59.960 61.111 17.25 6.95 34.29 4.09
1577 2447 1.414897 GAACGAGTAAAGGCACGCG 59.585 57.895 3.53 3.53 45.59 6.01
1614 2484 7.052873 CCAAATCACTCTGAATGAGGTATCTT 58.947 38.462 0.00 0.00 46.72 2.40
1658 2573 4.947147 GACCAAGGCGGCCACACA 62.947 66.667 23.09 0.00 39.03 3.72
1717 2640 1.002069 TGGCCAAATCACTCCATCCT 58.998 50.000 0.61 0.00 0.00 3.24
1897 2827 0.323360 CCTTGCTCCATTTTCCGGGA 60.323 55.000 0.00 0.00 0.00 5.14
1976 2906 2.157738 GCTGAGGTCAGATGCAGTTTT 58.842 47.619 11.29 0.00 46.59 2.43
2002 2938 1.028130 TGCCTTTGTTCGATGCAACA 58.972 45.000 0.00 0.00 34.36 3.33
2074 3010 7.498900 CCTGTTGCACCTCTGATACAATATTTA 59.501 37.037 0.00 0.00 0.00 1.40
2292 3393 1.065764 CGCTAGCTGCACACGGATA 59.934 57.895 13.93 0.00 43.06 2.59
2297 3398 1.005975 CGTTAATCGCTAGCTGCACAC 60.006 52.381 13.93 3.31 43.06 3.82
2371 6926 1.212751 GGGCAAATCGGCAACTGAC 59.787 57.895 0.00 0.00 43.60 3.51
2373 6928 1.080569 GTGGGCAAATCGGCAACTG 60.081 57.895 0.00 0.00 41.03 3.16
2374 6929 2.625823 CGTGGGCAAATCGGCAACT 61.626 57.895 0.00 0.00 42.09 3.16
2375 6930 1.579084 TACGTGGGCAAATCGGCAAC 61.579 55.000 0.00 0.00 43.60 4.17
2377 6932 0.678366 ATTACGTGGGCAAATCGGCA 60.678 50.000 0.00 0.00 43.60 5.69
2420 6980 6.054941 ACGGCAATCAATAGACAATCATACA 58.945 36.000 0.00 0.00 0.00 2.29
2424 6984 5.895636 AAACGGCAATCAATAGACAATCA 57.104 34.783 0.00 0.00 0.00 2.57
2425 6985 6.092748 ACAAAACGGCAATCAATAGACAATC 58.907 36.000 0.00 0.00 0.00 2.67
2426 6986 6.024552 ACAAAACGGCAATCAATAGACAAT 57.975 33.333 0.00 0.00 0.00 2.71
2427 6987 5.446143 ACAAAACGGCAATCAATAGACAA 57.554 34.783 0.00 0.00 0.00 3.18
2428 6988 5.446143 AACAAAACGGCAATCAATAGACA 57.554 34.783 0.00 0.00 0.00 3.41
2429 6989 6.640907 AGAAAACAAAACGGCAATCAATAGAC 59.359 34.615 0.00 0.00 0.00 2.59
2430 6990 6.744112 AGAAAACAAAACGGCAATCAATAGA 58.256 32.000 0.00 0.00 0.00 1.98
2431 6991 6.183359 CGAGAAAACAAAACGGCAATCAATAG 60.183 38.462 0.00 0.00 0.00 1.73
2432 6992 5.627367 CGAGAAAACAAAACGGCAATCAATA 59.373 36.000 0.00 0.00 0.00 1.90
2433 6993 4.444056 CGAGAAAACAAAACGGCAATCAAT 59.556 37.500 0.00 0.00 0.00 2.57
2434 6994 3.794028 CGAGAAAACAAAACGGCAATCAA 59.206 39.130 0.00 0.00 0.00 2.57
2437 7189 2.124122 GCGAGAAAACAAAACGGCAAT 58.876 42.857 0.00 0.00 0.00 3.56
2481 7234 2.100916 AGGCCATACAGACATACACGTC 59.899 50.000 5.01 0.00 36.08 4.34
2495 7248 0.036105 CAGACACACTGCAGGCCATA 60.036 55.000 19.93 0.00 39.86 2.74
2528 7281 0.467290 AGCAAGACCGGCAGGAAAAA 60.467 50.000 10.86 0.00 41.02 1.94
2535 7288 2.186160 CACAACAGCAAGACCGGCA 61.186 57.895 0.00 0.00 0.00 5.69
2554 7307 0.606401 ACCAACGTGGCATTCTCCAG 60.606 55.000 0.00 0.00 42.67 3.86
2578 7331 5.334879 CGTGGAAGGACTTCAAAATCGAAAT 60.335 40.000 13.51 0.00 41.20 2.17
2590 7343 2.030562 CACGGCGTGGAAGGACTT 59.969 61.111 31.19 0.00 0.00 3.01
2592 7345 3.041940 CACACGGCGTGGAAGGAC 61.042 66.667 39.03 0.00 42.34 3.85
2611 7365 3.902162 AAAGCGGCTGCATGCGTTG 62.902 57.895 21.93 7.00 46.23 4.10
2666 7463 5.574830 TCAAAGAACAAATTGAACACAACCG 59.425 36.000 0.00 0.00 32.89 4.44
2690 7487 6.017109 CGTATTTATAGCAAGCAGGGACAAAT 60.017 38.462 0.00 0.00 0.00 2.32
2714 7511 1.745264 GGATGGAAGAGCCTCTCCG 59.255 63.158 0.00 0.00 37.63 4.63
2735 7532 0.785979 GCAGCCACAAATGCGAAAAG 59.214 50.000 0.00 0.00 31.87 2.27
2736 7533 0.103755 TGCAGCCACAAATGCGAAAA 59.896 45.000 0.00 0.00 45.54 2.29
2738 7535 0.317799 AATGCAGCCACAAATGCGAA 59.682 45.000 0.00 0.00 45.54 4.70
2767 7587 4.646492 GGCATGAGGAACCATCTGTATTTT 59.354 41.667 0.00 0.00 0.00 1.82
2779 7599 0.165944 CGAACAACGGCATGAGGAAC 59.834 55.000 0.00 0.00 38.46 3.62
2816 7636 3.352748 TCCTAGGAGGACGCCCCA 61.353 66.667 7.62 0.00 40.06 4.96
2830 7650 3.620785 GATGGCCGCTCGGATCCT 61.621 66.667 13.11 0.00 37.50 3.24
2841 7661 2.410469 GCATGAACAGCGATGGCC 59.590 61.111 5.32 0.00 41.24 5.36
2845 7665 1.878088 GATGATGGCATGAACAGCGAT 59.122 47.619 3.81 0.00 34.11 4.58
2874 7694 2.125952 TCACGTGCTCCATCGCTG 60.126 61.111 11.67 0.00 0.00 5.18
2877 7697 2.887568 GCCTCACGTGCTCCATCG 60.888 66.667 11.67 0.00 0.00 3.84
2910 7730 3.005539 ACCTCGCCTGCTGGACAT 61.006 61.111 14.77 0.00 34.57 3.06
2929 7749 0.109342 CACAGGAGGTGGCTGAAACT 59.891 55.000 0.00 0.00 44.04 2.66
2947 7767 3.371063 GGCCTCGTCGGTGAGTCA 61.371 66.667 0.00 0.00 34.04 3.41
2954 7774 2.434359 GACCAAAGGCCTCGTCGG 60.434 66.667 5.23 6.97 0.00 4.79
2971 7791 3.356639 TAGCCTGGACTTGCGCTCG 62.357 63.158 9.73 1.27 32.76 5.03
2977 7797 3.802948 AATCTACGTAGCCTGGACTTG 57.197 47.619 18.00 0.00 0.00 3.16
3002 7822 1.162085 AGGAAAGAGGGCCTCACCT 59.838 57.895 33.86 30.79 45.57 4.00
3054 7880 2.070028 GAGGCGGAGAAGAAAACACTC 58.930 52.381 0.00 0.00 0.00 3.51
3055 7881 1.605712 CGAGGCGGAGAAGAAAACACT 60.606 52.381 0.00 0.00 0.00 3.55
3056 7882 0.790814 CGAGGCGGAGAAGAAAACAC 59.209 55.000 0.00 0.00 0.00 3.32
3057 7883 3.210857 CGAGGCGGAGAAGAAAACA 57.789 52.632 0.00 0.00 0.00 2.83
3074 7900 1.308069 CCTGAAGGCAATGGACACCG 61.308 60.000 0.00 0.00 0.00 4.94
3148 7974 4.778415 CACACCGTCGGGAGCTCG 62.778 72.222 17.28 0.00 36.97 5.03
3249 8083 4.157105 GCTCTATAAAGTTCCCCGCAAAAA 59.843 41.667 0.00 0.00 0.00 1.94
3250 8084 3.692593 GCTCTATAAAGTTCCCCGCAAAA 59.307 43.478 0.00 0.00 0.00 2.44
3251 8085 3.054655 AGCTCTATAAAGTTCCCCGCAAA 60.055 43.478 0.00 0.00 0.00 3.68
3252 8086 2.504175 AGCTCTATAAAGTTCCCCGCAA 59.496 45.455 0.00 0.00 0.00 4.85
3253 8087 2.116238 AGCTCTATAAAGTTCCCCGCA 58.884 47.619 0.00 0.00 0.00 5.69
3254 8088 2.912690 AGCTCTATAAAGTTCCCCGC 57.087 50.000 0.00 0.00 0.00 6.13
3255 8089 8.897872 TTAATAAAGCTCTATAAAGTTCCCCG 57.102 34.615 0.00 0.00 0.00 5.73
3267 8101 9.638239 CAAATGCCTTTGTTTAATAAAGCTCTA 57.362 29.630 8.39 0.00 37.54 2.43
3268 8102 7.118245 GCAAATGCCTTTGTTTAATAAAGCTCT 59.882 33.333 14.74 0.00 43.07 4.09
3269 8103 7.118245 AGCAAATGCCTTTGTTTAATAAAGCTC 59.882 33.333 14.74 4.01 43.07 4.09
3270 8104 6.936335 AGCAAATGCCTTTGTTTAATAAAGCT 59.064 30.769 14.74 0.15 43.07 3.74
3271 8105 7.017055 CAGCAAATGCCTTTGTTTAATAAAGC 58.983 34.615 14.74 5.52 43.07 3.51
3272 8106 8.309163 TCAGCAAATGCCTTTGTTTAATAAAG 57.691 30.769 14.74 7.13 43.07 1.85
3273 8107 8.555361 GTTCAGCAAATGCCTTTGTTTAATAAA 58.445 29.630 14.74 0.44 43.07 1.40
3274 8108 7.712639 TGTTCAGCAAATGCCTTTGTTTAATAA 59.287 29.630 14.74 0.52 43.07 1.40
3275 8109 7.212976 TGTTCAGCAAATGCCTTTGTTTAATA 58.787 30.769 14.74 4.06 43.07 0.98
3276 8110 6.054295 TGTTCAGCAAATGCCTTTGTTTAAT 58.946 32.000 14.74 0.00 43.07 1.40
3277 8111 5.423015 TGTTCAGCAAATGCCTTTGTTTAA 58.577 33.333 14.74 5.33 43.07 1.52
3278 8112 5.016051 TGTTCAGCAAATGCCTTTGTTTA 57.984 34.783 14.74 0.00 43.07 2.01
3279 8113 3.871485 TGTTCAGCAAATGCCTTTGTTT 58.129 36.364 14.74 2.84 43.07 2.83
3280 8114 3.118665 ACTGTTCAGCAAATGCCTTTGTT 60.119 39.130 14.74 7.11 43.07 2.83
3281 8115 2.431782 ACTGTTCAGCAAATGCCTTTGT 59.568 40.909 14.74 1.14 43.07 2.83
3282 8116 3.054878 GACTGTTCAGCAAATGCCTTTG 58.945 45.455 9.82 9.82 43.81 2.77
3283 8117 2.694628 TGACTGTTCAGCAAATGCCTTT 59.305 40.909 0.94 0.00 43.38 3.11
3284 8118 2.295349 CTGACTGTTCAGCAAATGCCTT 59.705 45.455 0.94 0.00 42.99 4.35
3285 8119 1.884579 CTGACTGTTCAGCAAATGCCT 59.115 47.619 0.94 0.00 42.99 4.75
3286 8120 2.342910 CTGACTGTTCAGCAAATGCC 57.657 50.000 0.94 0.00 42.99 4.40
3295 8129 2.061220 CCTCCTGGCTGACTGTTCA 58.939 57.895 0.00 0.00 0.00 3.18
3306 8140 2.641439 GATCGACAGCAGCCTCCTGG 62.641 65.000 0.00 0.00 39.54 4.45
3307 8141 1.227205 GATCGACAGCAGCCTCCTG 60.227 63.158 0.00 0.00 42.13 3.86
3308 8142 2.780094 CGATCGACAGCAGCCTCCT 61.780 63.158 10.26 0.00 0.00 3.69
3309 8143 2.279120 CGATCGACAGCAGCCTCC 60.279 66.667 10.26 0.00 0.00 4.30
3310 8144 1.299014 CTCGATCGACAGCAGCCTC 60.299 63.158 15.15 0.00 0.00 4.70
3311 8145 2.804167 CTCGATCGACAGCAGCCT 59.196 61.111 15.15 0.00 0.00 4.58
3312 8146 2.959071 GCTCGATCGACAGCAGCC 60.959 66.667 20.69 3.13 0.00 4.85
3313 8147 3.318555 CGCTCGATCGACAGCAGC 61.319 66.667 23.80 19.31 0.00 5.25
3314 8148 1.226407 TTCGCTCGATCGACAGCAG 60.226 57.895 23.80 17.44 38.30 4.24
3315 8149 1.514228 GTTCGCTCGATCGACAGCA 60.514 57.895 23.80 11.82 38.30 4.41
3316 8150 1.514228 TGTTCGCTCGATCGACAGC 60.514 57.895 15.15 16.20 38.30 4.40
3317 8151 1.456678 CGTGTTCGCTCGATCGACAG 61.457 60.000 15.15 11.11 38.30 3.51
3318 8152 1.511254 CGTGTTCGCTCGATCGACA 60.511 57.895 15.15 8.18 38.30 4.35
3319 8153 3.276886 CGTGTTCGCTCGATCGAC 58.723 61.111 15.15 10.43 38.30 4.20
3329 8163 2.286359 CCATATCAATGTGGCGTGTTCG 60.286 50.000 0.00 0.00 40.37 3.95
3330 8164 2.682856 ACCATATCAATGTGGCGTGTTC 59.317 45.455 5.75 0.00 42.18 3.18
3331 8165 2.722094 ACCATATCAATGTGGCGTGTT 58.278 42.857 5.75 0.00 42.18 3.32
3332 8166 2.418368 ACCATATCAATGTGGCGTGT 57.582 45.000 5.75 0.00 42.18 4.49
3333 8167 5.390885 GCTAATACCATATCAATGTGGCGTG 60.391 44.000 5.75 0.00 42.18 5.34
3334 8168 4.695455 GCTAATACCATATCAATGTGGCGT 59.305 41.667 5.75 0.00 42.18 5.68
3335 8169 4.201714 CGCTAATACCATATCAATGTGGCG 60.202 45.833 5.75 0.00 42.18 5.69
3336 8170 4.935205 TCGCTAATACCATATCAATGTGGC 59.065 41.667 5.75 0.00 42.18 5.01
3337 8171 8.197439 TCTATCGCTAATACCATATCAATGTGG 58.803 37.037 4.39 4.39 43.81 4.17
3338 8172 9.586435 TTCTATCGCTAATACCATATCAATGTG 57.414 33.333 0.00 0.00 0.00 3.21
3341 8175 9.302345 CGTTTCTATCGCTAATACCATATCAAT 57.698 33.333 0.00 0.00 0.00 2.57
3342 8176 8.301720 ACGTTTCTATCGCTAATACCATATCAA 58.698 33.333 0.00 0.00 0.00 2.57
3343 8177 7.823665 ACGTTTCTATCGCTAATACCATATCA 58.176 34.615 0.00 0.00 0.00 2.15
3344 8178 9.219497 GTACGTTTCTATCGCTAATACCATATC 57.781 37.037 0.00 0.00 0.00 1.63
3345 8179 7.907045 CGTACGTTTCTATCGCTAATACCATAT 59.093 37.037 7.22 0.00 0.00 1.78
3346 8180 7.095229 ACGTACGTTTCTATCGCTAATACCATA 60.095 37.037 16.72 0.00 0.00 2.74
3347 8181 6.082338 CGTACGTTTCTATCGCTAATACCAT 58.918 40.000 7.22 0.00 0.00 3.55
3348 8182 5.007626 ACGTACGTTTCTATCGCTAATACCA 59.992 40.000 16.72 0.00 0.00 3.25
3349 8183 5.444122 ACGTACGTTTCTATCGCTAATACC 58.556 41.667 16.72 0.00 0.00 2.73
3350 8184 9.189155 GTATACGTACGTTTCTATCGCTAATAC 57.811 37.037 27.92 17.83 0.00 1.89
3351 8185 8.921670 TGTATACGTACGTTTCTATCGCTAATA 58.078 33.333 27.92 10.36 33.36 0.98
3352 8186 7.796838 TGTATACGTACGTTTCTATCGCTAAT 58.203 34.615 27.92 11.39 33.36 1.73
3353 8187 7.172654 TGTATACGTACGTTTCTATCGCTAA 57.827 36.000 27.92 3.64 33.36 3.09
3354 8188 6.763303 TGTATACGTACGTTTCTATCGCTA 57.237 37.500 27.92 4.23 33.36 4.26
3355 8189 5.657470 TGTATACGTACGTTTCTATCGCT 57.343 39.130 27.92 0.00 33.36 4.93
3356 8190 5.848036 ACATGTATACGTACGTTTCTATCGC 59.152 40.000 27.92 10.57 33.36 4.58
3357 8191 9.533983 AATACATGTATACGTACGTTTCTATCG 57.466 33.333 27.92 12.29 33.36 2.92
3359 8193 9.533983 CGAATACATGTATACGTACGTTTCTAT 57.466 33.333 27.92 16.04 33.36 1.98
3360 8194 8.547894 ACGAATACATGTATACGTACGTTTCTA 58.452 33.333 27.92 8.87 33.36 2.10
3361 8195 7.409697 ACGAATACATGTATACGTACGTTTCT 58.590 34.615 27.92 13.99 33.36 2.52
3362 8196 7.149288 GGACGAATACATGTATACGTACGTTTC 60.149 40.741 27.92 18.15 34.26 2.78
3363 8197 6.632834 GGACGAATACATGTATACGTACGTTT 59.367 38.462 27.92 21.13 34.26 3.60
3364 8198 6.136071 GGACGAATACATGTATACGTACGTT 58.864 40.000 27.92 16.17 34.26 3.99
3365 8199 5.334105 GGGACGAATACATGTATACGTACGT 60.334 44.000 25.98 25.98 35.77 3.57
3366 8200 5.082059 GGGACGAATACATGTATACGTACG 58.918 45.833 18.56 15.01 35.77 3.67
3367 8201 5.393962 GGGGACGAATACATGTATACGTAC 58.606 45.833 18.56 13.22 34.26 3.67
3368 8202 4.458989 GGGGGACGAATACATGTATACGTA 59.541 45.833 18.56 0.00 34.26 3.57
3369 8203 3.256631 GGGGGACGAATACATGTATACGT 59.743 47.826 18.56 12.96 36.71 3.57
3370 8204 3.841643 GGGGGACGAATACATGTATACG 58.158 50.000 18.56 10.55 0.00 3.06
3402 8237 1.909700 TGAGCCCCACAATGAAAGAC 58.090 50.000 0.00 0.00 0.00 3.01
3509 8462 5.916883 ACTAATCGCACGTATACGCTAATTT 59.083 36.000 24.64 14.92 44.43 1.82
3526 8479 3.670991 GCTAATCTTCTGCGGACTAATCG 59.329 47.826 0.00 0.00 0.00 3.34
3538 8491 2.109181 GGCGGCCGCTAATCTTCT 59.891 61.111 45.23 0.00 41.60 2.85
3561 9146 3.453679 GAGAAGAGGCGAGCGGGT 61.454 66.667 0.00 0.00 0.00 5.28
3563 9148 2.411290 GAGAGAAGAGGCGAGCGG 59.589 66.667 0.00 0.00 0.00 5.52
3588 9173 3.067461 CGGGAGAAATTCAGATCGAGAGT 59.933 47.826 0.00 0.00 0.00 3.24
3599 9184 1.950216 GAATCTGCCCGGGAGAAATTC 59.050 52.381 29.31 21.41 0.00 2.17
3607 9192 0.250209 CTGATCTGAATCTGCCCGGG 60.250 60.000 19.09 19.09 32.75 5.73
3680 9265 3.826754 CAGCAGAGGCCGTCGCTA 61.827 66.667 14.34 0.00 42.56 4.26
3693 9278 5.761726 CTGTAATCCAGAATAGCAATCAGCA 59.238 40.000 0.00 0.00 44.89 4.41
3766 9351 5.586339 AGATCGTGATACATGTGTGAGAAG 58.414 41.667 9.11 0.00 0.00 2.85
3865 9783 8.853077 TGTGTATTTCTCTTCTGATCACAATT 57.147 30.769 0.00 0.00 31.85 2.32
3976 11396 4.282957 TGCATGGGTTAAAGATTGAAGCAA 59.717 37.500 0.00 0.00 0.00 3.91
4005 11425 2.028839 TCATTCGAGCTAAACCCGAACA 60.029 45.455 9.09 0.00 43.66 3.18
4077 11497 9.031360 ACACATTGTAATAGATACATGTTCGAC 57.969 33.333 2.30 2.11 43.84 4.20
4134 11554 0.319083 AGACAACACCCGCGATAACA 59.681 50.000 8.23 0.00 0.00 2.41
4236 11656 2.753043 TACGTGAGCCCCTCCGTC 60.753 66.667 0.00 0.00 38.01 4.79
4237 11657 2.754658 CTACGTGAGCCCCTCCGT 60.755 66.667 0.00 11.42 39.37 4.69


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

AutoCloner maintained by Alex Coulton.