Multiple sequence alignment - TraesCS4B01G350400

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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 TraesCS4B01G350400 chr4B 100.000 3485 0 0 832 4316 643281803 643285287 0.000000e+00 6436.0
1 TraesCS4B01G350400 chr4B 100.000 474 0 0 1 474 643280972 643281445 0.000000e+00 876.0
2 TraesCS4B01G350400 chr4B 95.312 64 0 1 2965 3028 613326776 613326836 9.880000e-17 99.0
3 TraesCS4B01G350400 chr4D 93.130 2096 98 26 832 2895 500013417 500015498 0.000000e+00 3031.0
4 TraesCS4B01G350400 chr4D 96.025 629 25 0 3027 3655 500015548 500016176 0.000000e+00 1024.0
5 TraesCS4B01G350400 chr4D 92.714 549 25 6 3783 4316 500016545 500017093 0.000000e+00 778.0
6 TraesCS4B01G350400 chr4D 82.213 253 21 12 232 474 500012732 500012970 3.400000e-46 196.0
7 TraesCS4B01G350400 chr5A 95.130 965 38 4 2011 2966 680833651 680834615 0.000000e+00 1513.0
8 TraesCS4B01G350400 chr5A 88.889 1170 88 24 832 1979 680832507 680833656 0.000000e+00 1402.0
9 TraesCS4B01G350400 chr5A 95.390 629 29 0 3027 3655 680834614 680835242 0.000000e+00 1002.0
10 TraesCS4B01G350400 chr5A 91.971 548 18 8 3783 4316 680835611 680836146 0.000000e+00 745.0
11 TraesCS4B01G350400 chr5A 89.391 575 53 7 1922 2493 675447589 675448158 0.000000e+00 717.0
12 TraesCS4B01G350400 chr5A 81.395 215 19 14 269 474 680831750 680831952 5.780000e-34 156.0
13 TraesCS4B01G350400 chr5B 89.043 575 55 7 1922 2493 691741090 691741659 0.000000e+00 706.0
14 TraesCS4B01G350400 chr5B 92.537 67 5 0 2962 3028 620679720 620679654 3.550000e-16 97.1
15 TraesCS4B01G350400 chr5B 86.301 73 4 2 2961 3027 446357729 446357801 1.660000e-09 75.0
16 TraesCS4B01G350400 chr1B 89.062 576 54 7 1922 2493 593780906 593781476 0.000000e+00 706.0
17 TraesCS4B01G350400 chr1A 90.128 547 29 5 3783 4316 564614872 564614338 0.000000e+00 688.0
18 TraesCS4B01G350400 chr1A 89.945 547 27 10 3783 4316 252835495 252836026 0.000000e+00 680.0
19 TraesCS4B01G350400 chr1A 94.898 98 5 0 2143 2240 252835274 252835371 2.080000e-33 154.0
20 TraesCS4B01G350400 chr1A 94.898 98 5 0 2143 2240 564615093 564614996 2.080000e-33 154.0
21 TraesCS4B01G350400 chr3B 92.754 69 1 2 2963 3031 22477638 22477702 3.550000e-16 97.1
22 TraesCS4B01G350400 chr3B 89.706 68 0 4 2962 3028 263799936 263799875 3.580000e-11 80.5
23 TraesCS4B01G350400 chr3B 100.000 28 0 0 3004 3031 730155330 730155357 8.000000e-03 52.8
24 TraesCS4B01G350400 chr6B 91.304 69 2 2 2963 3031 673622134 673622198 1.650000e-14 91.6
25 TraesCS4B01G350400 chr1D 91.045 67 4 1 2965 3029 30517879 30517813 5.940000e-14 89.8
26 TraesCS4B01G350400 chr7B 96.078 51 1 1 2957 3006 704093803 704093853 9.950000e-12 82.4
27 TraesCS4B01G350400 chr7B 100.000 29 0 0 3006 3034 711721514 711721486 2.000000e-03 54.7
28 TraesCS4B01G350400 chr2D 95.918 49 2 0 2958 3006 566134769 566134721 3.580000e-11 80.5
29 TraesCS4B01G350400 chr6A 90.741 54 5 0 1196 1249 144518140 144518193 5.990000e-09 73.1
30 TraesCS4B01G350400 chr6D 88.889 54 6 0 1196 1249 116335191 116335244 2.790000e-07 67.6
31 TraesCS4B01G350400 chr5D 95.238 42 2 0 3783 3824 434067981 434068022 2.790000e-07 67.6
32 TraesCS4B01G350400 chr2A 97.436 39 1 0 3783 3821 293893366 293893404 2.790000e-07 67.6


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 TraesCS4B01G350400 chr4B 643280972 643285287 4315 False 3656.00 6436 100.0000 1 4316 2 chr4B.!!$F2 4315
1 TraesCS4B01G350400 chr4D 500012732 500017093 4361 False 1257.25 3031 91.0205 232 4316 4 chr4D.!!$F1 4084
2 TraesCS4B01G350400 chr5A 680831750 680836146 4396 False 963.60 1513 90.5550 269 4316 5 chr5A.!!$F2 4047
3 TraesCS4B01G350400 chr5A 675447589 675448158 569 False 717.00 717 89.3910 1922 2493 1 chr5A.!!$F1 571
4 TraesCS4B01G350400 chr5B 691741090 691741659 569 False 706.00 706 89.0430 1922 2493 1 chr5B.!!$F2 571
5 TraesCS4B01G350400 chr1B 593780906 593781476 570 False 706.00 706 89.0620 1922 2493 1 chr1B.!!$F1 571
6 TraesCS4B01G350400 chr1A 564614338 564615093 755 True 421.00 688 92.5130 2143 4316 2 chr1A.!!$R1 2173
7 TraesCS4B01G350400 chr1A 252835274 252836026 752 False 417.00 680 92.4215 2143 4316 2 chr1A.!!$F1 2173

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
854 1092 0.951040 GGTCTCGGTGGCTTTGACTG 60.951 60.0 0.00 0.00 0.00 3.51 F
1708 1979 0.174845 TGATGGCTGCACGTAGTACC 59.825 55.0 0.50 0.00 41.61 3.34 F
2402 2680 0.391597 GGCTTATAGGTGGCGCTACA 59.608 55.0 25.79 6.29 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2744 0.531532 CCAGCACGCAGATCCCTTAG 60.532 60.0 0.0 0.0 0.00 2.18 R
3011 3296 0.038744 AACTACTCCCTCCGTTCCGA 59.961 55.0 0.0 0.0 0.00 4.55 R
4029 4580 1.008875 TTCAAGCTACAGTGCTCGCG 61.009 55.0 0.0 0.0 43.24 5.87 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
24 25 5.721876 TCGTTTTAACACACGATGAACTT 57.278 34.783 0.00 0.00 40.43 2.66
25 26 6.109320 TCGTTTTAACACACGATGAACTTT 57.891 33.333 0.00 0.00 40.43 2.66
26 27 6.544622 TCGTTTTAACACACGATGAACTTTT 58.455 32.000 0.00 0.00 40.43 2.27
27 28 7.022384 TCGTTTTAACACACGATGAACTTTTT 58.978 30.769 0.00 0.00 40.43 1.94
107 108 2.899303 GGGGGAGAAAGAACCATCAA 57.101 50.000 0.00 0.00 0.00 2.57
108 109 2.728007 GGGGGAGAAAGAACCATCAAG 58.272 52.381 0.00 0.00 0.00 3.02
109 110 2.308866 GGGGGAGAAAGAACCATCAAGA 59.691 50.000 0.00 0.00 0.00 3.02
110 111 3.245264 GGGGGAGAAAGAACCATCAAGAA 60.245 47.826 0.00 0.00 0.00 2.52
111 112 4.407365 GGGGAGAAAGAACCATCAAGAAA 58.593 43.478 0.00 0.00 0.00 2.52
112 113 4.832823 GGGGAGAAAGAACCATCAAGAAAA 59.167 41.667 0.00 0.00 0.00 2.29
113 114 5.279006 GGGGAGAAAGAACCATCAAGAAAAC 60.279 44.000 0.00 0.00 0.00 2.43
114 115 5.279006 GGGAGAAAGAACCATCAAGAAAACC 60.279 44.000 0.00 0.00 0.00 3.27
115 116 5.301805 GGAGAAAGAACCATCAAGAAAACCA 59.698 40.000 0.00 0.00 0.00 3.67
116 117 6.396829 AGAAAGAACCATCAAGAAAACCAG 57.603 37.500 0.00 0.00 0.00 4.00
117 118 6.129179 AGAAAGAACCATCAAGAAAACCAGA 58.871 36.000 0.00 0.00 0.00 3.86
118 119 6.264067 AGAAAGAACCATCAAGAAAACCAGAG 59.736 38.462 0.00 0.00 0.00 3.35
119 120 5.310409 AGAACCATCAAGAAAACCAGAGA 57.690 39.130 0.00 0.00 0.00 3.10
120 121 5.694995 AGAACCATCAAGAAAACCAGAGAA 58.305 37.500 0.00 0.00 0.00 2.87
121 122 6.129179 AGAACCATCAAGAAAACCAGAGAAA 58.871 36.000 0.00 0.00 0.00 2.52
122 123 6.607198 AGAACCATCAAGAAAACCAGAGAAAA 59.393 34.615 0.00 0.00 0.00 2.29
123 124 6.149129 ACCATCAAGAAAACCAGAGAAAAC 57.851 37.500 0.00 0.00 0.00 2.43
124 125 5.656416 ACCATCAAGAAAACCAGAGAAAACA 59.344 36.000 0.00 0.00 0.00 2.83
125 126 6.154363 ACCATCAAGAAAACCAGAGAAAACAA 59.846 34.615 0.00 0.00 0.00 2.83
126 127 7.041107 CCATCAAGAAAACCAGAGAAAACAAA 58.959 34.615 0.00 0.00 0.00 2.83
127 128 7.548780 CCATCAAGAAAACCAGAGAAAACAAAA 59.451 33.333 0.00 0.00 0.00 2.44
128 129 8.934825 CATCAAGAAAACCAGAGAAAACAAAAA 58.065 29.630 0.00 0.00 0.00 1.94
209 210 4.437772 AAAAACCGAACAGAAAACCGAA 57.562 36.364 0.00 0.00 0.00 4.30
210 211 3.409851 AAACCGAACAGAAAACCGAAC 57.590 42.857 0.00 0.00 0.00 3.95
211 212 2.027003 ACCGAACAGAAAACCGAACA 57.973 45.000 0.00 0.00 0.00 3.18
212 213 1.937899 ACCGAACAGAAAACCGAACAG 59.062 47.619 0.00 0.00 0.00 3.16
213 214 2.206750 CCGAACAGAAAACCGAACAGA 58.793 47.619 0.00 0.00 0.00 3.41
214 215 2.033151 CCGAACAGAAAACCGAACAGAC 60.033 50.000 0.00 0.00 0.00 3.51
215 216 2.347292 CGAACAGAAAACCGAACAGACG 60.347 50.000 0.00 0.00 0.00 4.18
223 224 2.579201 CGAACAGACGGATGGGCT 59.421 61.111 0.00 0.00 0.00 5.19
224 225 1.519455 CGAACAGACGGATGGGCTC 60.519 63.158 0.00 0.00 0.00 4.70
225 226 1.519455 GAACAGACGGATGGGCTCG 60.519 63.158 0.00 0.00 0.00 5.03
226 227 3.665675 AACAGACGGATGGGCTCGC 62.666 63.158 0.00 0.00 0.00 5.03
227 228 3.842923 CAGACGGATGGGCTCGCT 61.843 66.667 0.00 0.00 0.00 4.93
228 229 3.077556 AGACGGATGGGCTCGCTT 61.078 61.111 0.00 0.00 0.00 4.68
229 230 2.586357 GACGGATGGGCTCGCTTC 60.586 66.667 0.00 0.00 0.00 3.86
230 231 3.371097 GACGGATGGGCTCGCTTCA 62.371 63.158 0.00 0.00 0.00 3.02
265 266 1.964373 GAGCAAAAGCCCGTCGGAA 60.964 57.895 14.39 0.00 0.00 4.30
334 335 2.835895 GAGCTCGTCCTCCCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
335 336 4.467107 AGCTCGTCCTCCCCTCCC 62.467 72.222 0.00 0.00 0.00 4.30
337 338 3.756783 CTCGTCCTCCCCTCCCCT 61.757 72.222 0.00 0.00 0.00 4.79
338 339 3.742248 CTCGTCCTCCCCTCCCCTC 62.742 73.684 0.00 0.00 0.00 4.30
339 340 4.862823 CGTCCTCCCCTCCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
340 341 4.500826 GTCCTCCCCTCCCCTCCC 62.501 77.778 0.00 0.00 0.00 4.30
452 481 4.675303 CCCCCTCCTCCACCACCA 62.675 72.222 0.00 0.00 0.00 4.17
455 484 2.529136 CCTCCTCCACCACCACCA 60.529 66.667 0.00 0.00 0.00 4.17
854 1092 0.951040 GGTCTCGGTGGCTTTGACTG 60.951 60.000 0.00 0.00 0.00 3.51
861 1099 2.147150 GGTGGCTTTGACTGTTCTCTC 58.853 52.381 0.00 0.00 0.00 3.20
863 1101 2.805099 GTGGCTTTGACTGTTCTCTCTG 59.195 50.000 0.00 0.00 0.00 3.35
865 1103 2.805099 GGCTTTGACTGTTCTCTCTGTG 59.195 50.000 0.00 0.00 0.00 3.66
867 1105 3.247173 GCTTTGACTGTTCTCTCTGTGTG 59.753 47.826 0.00 0.00 0.00 3.82
869 1107 4.471904 TTGACTGTTCTCTCTGTGTGTT 57.528 40.909 0.00 0.00 0.00 3.32
871 1109 4.832248 TGACTGTTCTCTCTGTGTGTTTT 58.168 39.130 0.00 0.00 0.00 2.43
872 1110 5.245531 TGACTGTTCTCTCTGTGTGTTTTT 58.754 37.500 0.00 0.00 0.00 1.94
941 1179 3.997021 ACTGTTTGCTTATTCTCGGAGTG 59.003 43.478 4.69 0.00 0.00 3.51
949 1187 7.055667 TGCTTATTCTCGGAGTGAATCTATT 57.944 36.000 4.69 0.00 46.04 1.73
952 1190 9.646427 GCTTATTCTCGGAGTGAATCTATTAAT 57.354 33.333 4.69 0.00 46.04 1.40
978 1227 6.973474 TCTTTTTCTTTTAATTTCGCGTCCAA 59.027 30.769 5.77 0.00 0.00 3.53
995 1244 4.467378 TCCAATTTGGTTGCTCACGCAC 62.467 50.000 14.98 0.00 40.48 5.34
1074 1323 4.938226 CCCAAGTGTATTCACCTCTTTCTC 59.062 45.833 0.00 0.00 44.83 2.87
1098 1355 3.117131 CCCCCTGCCACCTTATTTATTCT 60.117 47.826 0.00 0.00 0.00 2.40
1099 1356 4.105697 CCCCCTGCCACCTTATTTATTCTA 59.894 45.833 0.00 0.00 0.00 2.10
1145 1405 5.739161 CGTGCTATTTGTTAGGATCTTTTGC 59.261 40.000 0.00 0.00 30.25 3.68
1179 1439 4.027458 CAGTGCTGTTTCAACAAATTGACG 60.027 41.667 0.00 0.00 44.66 4.35
1180 1440 4.101942 GTGCTGTTTCAACAAATTGACGA 58.898 39.130 0.00 0.00 44.66 4.20
1184 1444 5.395486 GCTGTTTCAACAAATTGACGAGTAC 59.605 40.000 0.00 0.00 44.66 2.73
1185 1445 5.812652 TGTTTCAACAAATTGACGAGTACC 58.187 37.500 0.00 0.00 44.66 3.34
1218 1478 3.152341 CCTGTCTGCAGATTCCAAGTTT 58.848 45.455 21.47 0.00 45.28 2.66
1221 1481 3.745975 TGTCTGCAGATTCCAAGTTTACG 59.254 43.478 21.47 0.00 0.00 3.18
1318 1578 5.562506 ATCATCTTCATTCAGTTGCTGTG 57.437 39.130 0.00 0.00 32.61 3.66
1466 1726 1.202110 CGACAGGTCAAATGCAGATGC 60.202 52.381 0.00 0.00 42.50 3.91
1474 1734 2.613691 CAAATGCAGATGCCTTTGGTC 58.386 47.619 20.97 0.00 46.05 4.02
1484 1755 1.494721 TGCCTTTGGTCTTTCTCTGGT 59.505 47.619 0.00 0.00 0.00 4.00
1485 1756 2.091885 TGCCTTTGGTCTTTCTCTGGTT 60.092 45.455 0.00 0.00 0.00 3.67
1631 1902 3.023119 AGGACTGACAAAACATGCACAA 58.977 40.909 0.00 0.00 0.00 3.33
1649 1920 4.201628 GCACAATAACGATGACTGTGAGTC 60.202 45.833 4.76 0.00 45.26 3.36
1652 1923 2.620779 AACGATGACTGTGAGTCTCG 57.379 50.000 16.85 16.85 45.27 4.04
1662 1933 5.240844 TGACTGTGAGTCTCGAGTGAAAATA 59.759 40.000 13.13 0.00 45.27 1.40
1664 1935 6.326375 ACTGTGAGTCTCGAGTGAAAATATC 58.674 40.000 13.13 1.39 0.00 1.63
1680 1951 9.533983 GTGAAAATATCATCGCAGTTATACATG 57.466 33.333 0.00 0.00 40.97 3.21
1695 1966 7.910162 CAGTTATACATGTTTACTTGTGATGGC 59.090 37.037 2.30 0.00 36.02 4.40
1699 1970 2.580962 TGTTTACTTGTGATGGCTGCA 58.419 42.857 0.50 0.00 0.00 4.41
1708 1979 0.174845 TGATGGCTGCACGTAGTACC 59.825 55.000 0.50 0.00 41.61 3.34
1730 2001 6.357367 ACCACTGTTGTTGAGATAGTCTTTT 58.643 36.000 0.00 0.00 0.00 2.27
1816 2087 1.064463 TGAAGAGCCCAATCCATGTCC 60.064 52.381 0.00 0.00 0.00 4.02
1868 2139 9.503399 AAACCATCGAAGGTATATTTTCCTATC 57.497 33.333 13.59 0.00 42.25 2.08
2104 2379 5.408604 GTCGACATACTCAGACCAATTGTTT 59.591 40.000 11.55 0.00 0.00 2.83
2153 2428 1.062002 CGAAGTGACAAACAACTGCGT 59.938 47.619 0.00 0.00 30.15 5.24
2402 2680 0.391597 GGCTTATAGGTGGCGCTACA 59.608 55.000 25.79 6.29 0.00 2.74
2588 2873 5.177326 AGTGAGCAAGAAGATCTCATTGTC 58.823 41.667 16.83 13.79 38.85 3.18
2840 3125 7.039644 GCTATGGGCTTCTTAGTTCTCTACATA 60.040 40.741 0.00 0.00 38.06 2.29
2873 3158 7.754924 CGAAGGTATGTTTAACAATTTGCTCAT 59.245 33.333 0.66 0.00 0.00 2.90
2909 3194 7.288810 ACTGGACATCTCATTTCTCTATCTC 57.711 40.000 0.00 0.00 0.00 2.75
2910 3195 6.016360 ACTGGACATCTCATTTCTCTATCTCG 60.016 42.308 0.00 0.00 0.00 4.04
2958 3243 2.099098 CACTTGCTTTTCACGAACCCTT 59.901 45.455 0.00 0.00 0.00 3.95
2959 3244 2.099098 ACTTGCTTTTCACGAACCCTTG 59.901 45.455 0.00 0.00 0.00 3.61
2961 3246 2.096248 TGCTTTTCACGAACCCTTGTT 58.904 42.857 0.00 0.00 37.42 2.83
2962 3247 3.280295 TGCTTTTCACGAACCCTTGTTA 58.720 40.909 0.00 0.00 33.97 2.41
2964 3249 4.339814 TGCTTTTCACGAACCCTTGTTATT 59.660 37.500 0.00 0.00 33.97 1.40
2965 3250 5.531659 TGCTTTTCACGAACCCTTGTTATTA 59.468 36.000 0.00 0.00 33.97 0.98
2966 3251 5.854866 GCTTTTCACGAACCCTTGTTATTAC 59.145 40.000 0.00 0.00 33.97 1.89
2967 3252 6.293790 GCTTTTCACGAACCCTTGTTATTACT 60.294 38.462 0.00 0.00 33.97 2.24
2968 3253 6.790285 TTTCACGAACCCTTGTTATTACTC 57.210 37.500 0.00 0.00 33.97 2.59
2969 3254 4.824289 TCACGAACCCTTGTTATTACTCC 58.176 43.478 0.00 0.00 33.97 3.85
2970 3255 3.937079 CACGAACCCTTGTTATTACTCCC 59.063 47.826 0.00 0.00 33.97 4.30
2971 3256 3.842436 ACGAACCCTTGTTATTACTCCCT 59.158 43.478 0.00 0.00 33.97 4.20
2972 3257 4.081254 ACGAACCCTTGTTATTACTCCCTC 60.081 45.833 0.00 0.00 33.97 4.30
2973 3258 4.682589 CGAACCCTTGTTATTACTCCCTCC 60.683 50.000 0.00 0.00 33.97 4.30
2974 3259 2.770232 ACCCTTGTTATTACTCCCTCCG 59.230 50.000 0.00 0.00 0.00 4.63
2975 3260 2.770232 CCCTTGTTATTACTCCCTCCGT 59.230 50.000 0.00 0.00 0.00 4.69
2976 3261 3.199289 CCCTTGTTATTACTCCCTCCGTT 59.801 47.826 0.00 0.00 0.00 4.44
2977 3262 4.439968 CCTTGTTATTACTCCCTCCGTTC 58.560 47.826 0.00 0.00 0.00 3.95
2978 3263 4.439968 CTTGTTATTACTCCCTCCGTTCC 58.560 47.826 0.00 0.00 0.00 3.62
2979 3264 2.428171 TGTTATTACTCCCTCCGTTCCG 59.572 50.000 0.00 0.00 0.00 4.30
2980 3265 2.689983 GTTATTACTCCCTCCGTTCCGA 59.310 50.000 0.00 0.00 0.00 4.55
2981 3266 2.083628 ATTACTCCCTCCGTTCCGAT 57.916 50.000 0.00 0.00 0.00 4.18
2982 3267 1.856629 TTACTCCCTCCGTTCCGATT 58.143 50.000 0.00 0.00 0.00 3.34
2983 3268 1.856629 TACTCCCTCCGTTCCGATTT 58.143 50.000 0.00 0.00 0.00 2.17
2984 3269 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
2985 3270 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2986 3271 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
2987 3272 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2989 3274 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
2990 3275 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
2991 3276 1.811965 TCCGTTCCGATTTACTCGTCA 59.188 47.619 0.00 0.00 46.18 4.35
2992 3277 2.424601 TCCGTTCCGATTTACTCGTCAT 59.575 45.455 0.00 0.00 46.18 3.06
2993 3278 2.534349 CCGTTCCGATTTACTCGTCATG 59.466 50.000 0.00 0.00 46.18 3.07
2994 3279 2.534349 CGTTCCGATTTACTCGTCATGG 59.466 50.000 0.00 0.00 46.18 3.66
2995 3280 3.518590 GTTCCGATTTACTCGTCATGGT 58.481 45.455 0.00 0.00 46.18 3.55
2996 3281 3.880047 TCCGATTTACTCGTCATGGTT 57.120 42.857 0.00 0.00 46.18 3.67
2997 3282 4.196626 TCCGATTTACTCGTCATGGTTT 57.803 40.909 0.00 0.00 46.18 3.27
2998 3283 4.571919 TCCGATTTACTCGTCATGGTTTT 58.428 39.130 0.00 0.00 46.18 2.43
2999 3284 5.722263 TCCGATTTACTCGTCATGGTTTTA 58.278 37.500 0.00 0.00 46.18 1.52
3000 3285 5.808540 TCCGATTTACTCGTCATGGTTTTAG 59.191 40.000 0.00 0.00 46.18 1.85
3001 3286 5.579511 CCGATTTACTCGTCATGGTTTTAGT 59.420 40.000 0.00 0.00 46.18 2.24
3002 3287 6.091713 CCGATTTACTCGTCATGGTTTTAGTT 59.908 38.462 0.00 0.00 46.18 2.24
3003 3288 7.171434 CGATTTACTCGTCATGGTTTTAGTTC 58.829 38.462 0.00 0.00 42.56 3.01
3004 3289 7.148705 CGATTTACTCGTCATGGTTTTAGTTCA 60.149 37.037 0.00 0.00 42.56 3.18
3005 3290 7.789273 TTTACTCGTCATGGTTTTAGTTCAA 57.211 32.000 0.00 0.00 0.00 2.69
3006 3291 5.924475 ACTCGTCATGGTTTTAGTTCAAG 57.076 39.130 0.00 0.00 0.00 3.02
3007 3292 5.365619 ACTCGTCATGGTTTTAGTTCAAGT 58.634 37.500 0.00 0.00 0.00 3.16
3008 3293 6.518493 ACTCGTCATGGTTTTAGTTCAAGTA 58.482 36.000 0.00 0.00 0.00 2.24
3009 3294 6.987992 ACTCGTCATGGTTTTAGTTCAAGTAA 59.012 34.615 0.00 0.00 0.00 2.24
3010 3295 7.496591 ACTCGTCATGGTTTTAGTTCAAGTAAA 59.503 33.333 0.00 0.00 0.00 2.01
3011 3296 8.385898 TCGTCATGGTTTTAGTTCAAGTAAAT 57.614 30.769 0.00 0.00 0.00 1.40
3012 3297 8.500773 TCGTCATGGTTTTAGTTCAAGTAAATC 58.499 33.333 0.00 0.00 0.00 2.17
3013 3298 7.477422 CGTCATGGTTTTAGTTCAAGTAAATCG 59.523 37.037 0.00 0.00 0.00 3.34
3014 3299 7.749126 GTCATGGTTTTAGTTCAAGTAAATCGG 59.251 37.037 0.00 0.00 0.00 4.18
3015 3300 7.662258 TCATGGTTTTAGTTCAAGTAAATCGGA 59.338 33.333 0.00 0.00 0.00 4.55
3016 3301 7.804843 TGGTTTTAGTTCAAGTAAATCGGAA 57.195 32.000 0.00 0.00 0.00 4.30
3017 3302 7.641760 TGGTTTTAGTTCAAGTAAATCGGAAC 58.358 34.615 0.00 0.00 39.83 3.62
3038 3323 3.257624 ACGGAGGGAGTAGTTTGTTACTG 59.742 47.826 0.00 0.00 37.73 2.74
3087 3372 3.127030 GCCAGTGTAGTTATTGGTTCTGC 59.873 47.826 0.00 0.00 33.21 4.26
3190 3475 7.452880 TCTAGTTTTCAGCTTGTTATGCATT 57.547 32.000 3.54 0.00 0.00 3.56
3300 3585 1.827399 TTGCAGACCCCTCGAACCTC 61.827 60.000 0.00 0.00 0.00 3.85
3386 3671 7.408756 TCATTCAATGGGTAAATTCTTCCAG 57.591 36.000 0.00 0.00 32.30 3.86
3608 3893 5.184864 TGAACCAACTAATTGTGCTTATGGG 59.815 40.000 0.00 0.00 33.60 4.00
3611 3896 4.339247 CCAACTAATTGTGCTTATGGGAGG 59.661 45.833 0.00 0.00 33.60 4.30
3618 3903 2.972713 TGTGCTTATGGGAGGAGATACC 59.027 50.000 0.00 0.00 39.35 2.73
3637 3922 7.493367 AGATACCTATACTTGTTCTTGCAGTC 58.507 38.462 0.00 0.00 0.00 3.51
3655 3940 3.056607 CAGTCCATGTTTCATGTTTCCCC 60.057 47.826 8.57 0.00 0.00 4.81
3672 3990 1.202758 CCCCATCTTACGGCATGCTTA 60.203 52.381 18.92 6.56 0.00 3.09
3683 4001 5.151632 ACGGCATGCTTAGTTTATTTACG 57.848 39.130 18.92 9.98 0.00 3.18
3694 4180 7.163682 GCTTAGTTTATTTACGTAATGTGCTGC 59.836 37.037 9.18 0.00 0.00 5.25
3704 4190 1.376543 AATGTGCTGCGATTCTCCTG 58.623 50.000 0.00 0.00 0.00 3.86
3705 4191 0.251354 ATGTGCTGCGATTCTCCTGT 59.749 50.000 0.00 0.00 0.00 4.00
3725 4211 4.295051 TGTTATTTCTTTTGTCCGCTTGC 58.705 39.130 0.00 0.00 0.00 4.01
3747 4233 5.102313 GCAAGCCAAACTAATAATGTGACC 58.898 41.667 0.00 0.00 0.00 4.02
3748 4234 5.105756 GCAAGCCAAACTAATAATGTGACCT 60.106 40.000 0.00 0.00 0.00 3.85
3749 4235 6.572314 GCAAGCCAAACTAATAATGTGACCTT 60.572 38.462 0.00 0.00 0.00 3.50
3755 4249 8.576442 CCAAACTAATAATGTGACCTTTGACTT 58.424 33.333 0.00 0.00 0.00 3.01
3765 4259 6.116806 TGTGACCTTTGACTTAGCTTACAAA 58.883 36.000 0.00 0.00 0.00 2.83
3773 4267 7.618502 TTGACTTAGCTTACAAACAGTTCAA 57.381 32.000 0.00 0.00 0.00 2.69
3774 4268 7.246674 TGACTTAGCTTACAAACAGTTCAAG 57.753 36.000 0.00 0.00 0.00 3.02
3775 4269 7.045416 TGACTTAGCTTACAAACAGTTCAAGA 58.955 34.615 0.00 0.00 0.00 3.02
3776 4270 7.551262 TGACTTAGCTTACAAACAGTTCAAGAA 59.449 33.333 0.00 0.00 0.00 2.52
3777 4271 8.451908 ACTTAGCTTACAAACAGTTCAAGAAT 57.548 30.769 0.00 0.00 0.00 2.40
3778 4272 9.555727 ACTTAGCTTACAAACAGTTCAAGAATA 57.444 29.630 0.00 0.00 0.00 1.75
3780 4274 9.555727 TTAGCTTACAAACAGTTCAAGAATAGT 57.444 29.630 0.00 0.00 0.00 2.12
3875 4411 6.896613 CACTTTATCAAAACGATCGACAGATG 59.103 38.462 24.34 12.64 37.19 2.90
3894 4430 2.977914 TGAAGATACAACTGCTGCTCC 58.022 47.619 0.00 0.00 0.00 4.70
3935 4486 7.363431 TGACGATTGATGAGTATAGTGATGTC 58.637 38.462 0.00 0.00 0.00 3.06
3985 4536 3.258622 AGTCACCTTGTCAGTAACCTAGC 59.741 47.826 0.00 0.00 0.00 3.42
4029 4580 3.375299 CCCACTAATAAGCTTGCACTGTC 59.625 47.826 9.86 0.00 0.00 3.51
4229 4793 6.791867 AATGGTTTAGGAAAAAGATAGCCC 57.208 37.500 0.00 0.00 0.00 5.19
4310 4875 5.959618 CCGTTGGGAAGAAAACTTCTATT 57.040 39.130 9.32 0.00 39.61 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.784068 AAAAGTTCATCGTGTGTTAAAACG 57.216 33.333 0.00 0.00 41.11 3.60
88 89 2.308866 TCTTGATGGTTCTTTCTCCCCC 59.691 50.000 0.00 0.00 0.00 5.40
89 90 3.721087 TCTTGATGGTTCTTTCTCCCC 57.279 47.619 0.00 0.00 0.00 4.81
90 91 5.279006 GGTTTTCTTGATGGTTCTTTCTCCC 60.279 44.000 0.00 0.00 0.00 4.30
91 92 5.301805 TGGTTTTCTTGATGGTTCTTTCTCC 59.698 40.000 0.00 0.00 0.00 3.71
92 93 6.263168 TCTGGTTTTCTTGATGGTTCTTTCTC 59.737 38.462 0.00 0.00 0.00 2.87
93 94 6.129179 TCTGGTTTTCTTGATGGTTCTTTCT 58.871 36.000 0.00 0.00 0.00 2.52
94 95 6.263168 TCTCTGGTTTTCTTGATGGTTCTTTC 59.737 38.462 0.00 0.00 0.00 2.62
95 96 6.129179 TCTCTGGTTTTCTTGATGGTTCTTT 58.871 36.000 0.00 0.00 0.00 2.52
96 97 5.694995 TCTCTGGTTTTCTTGATGGTTCTT 58.305 37.500 0.00 0.00 0.00 2.52
97 98 5.310409 TCTCTGGTTTTCTTGATGGTTCT 57.690 39.130 0.00 0.00 0.00 3.01
98 99 6.391227 TTTCTCTGGTTTTCTTGATGGTTC 57.609 37.500 0.00 0.00 0.00 3.62
99 100 6.154363 TGTTTTCTCTGGTTTTCTTGATGGTT 59.846 34.615 0.00 0.00 0.00 3.67
100 101 5.656416 TGTTTTCTCTGGTTTTCTTGATGGT 59.344 36.000 0.00 0.00 0.00 3.55
101 102 6.147864 TGTTTTCTCTGGTTTTCTTGATGG 57.852 37.500 0.00 0.00 0.00 3.51
102 103 8.477984 TTTTGTTTTCTCTGGTTTTCTTGATG 57.522 30.769 0.00 0.00 0.00 3.07
188 189 4.168014 GTTCGGTTTTCTGTTCGGTTTTT 58.832 39.130 0.00 0.00 0.00 1.94
189 190 3.190953 TGTTCGGTTTTCTGTTCGGTTTT 59.809 39.130 0.00 0.00 0.00 2.43
190 191 2.748532 TGTTCGGTTTTCTGTTCGGTTT 59.251 40.909 0.00 0.00 0.00 3.27
191 192 2.353579 CTGTTCGGTTTTCTGTTCGGTT 59.646 45.455 0.00 0.00 0.00 4.44
192 193 1.937899 CTGTTCGGTTTTCTGTTCGGT 59.062 47.619 0.00 0.00 0.00 4.69
193 194 2.033151 GTCTGTTCGGTTTTCTGTTCGG 60.033 50.000 0.00 0.00 0.00 4.30
194 195 2.347292 CGTCTGTTCGGTTTTCTGTTCG 60.347 50.000 0.00 0.00 0.00 3.95
195 196 2.033151 CCGTCTGTTCGGTTTTCTGTTC 60.033 50.000 0.00 0.00 44.77 3.18
196 197 1.937899 CCGTCTGTTCGGTTTTCTGTT 59.062 47.619 0.00 0.00 44.77 3.16
197 198 1.578583 CCGTCTGTTCGGTTTTCTGT 58.421 50.000 0.00 0.00 44.77 3.41
206 207 1.519455 GAGCCCATCCGTCTGTTCG 60.519 63.158 0.00 0.00 0.00 3.95
207 208 1.519455 CGAGCCCATCCGTCTGTTC 60.519 63.158 0.00 0.00 0.00 3.18
208 209 2.579201 CGAGCCCATCCGTCTGTT 59.421 61.111 0.00 0.00 0.00 3.16
209 210 4.148825 GCGAGCCCATCCGTCTGT 62.149 66.667 0.00 0.00 0.00 3.41
210 211 3.376935 AAGCGAGCCCATCCGTCTG 62.377 63.158 0.00 0.00 0.00 3.51
211 212 3.077556 AAGCGAGCCCATCCGTCT 61.078 61.111 0.00 0.00 0.00 4.18
212 213 2.586357 GAAGCGAGCCCATCCGTC 60.586 66.667 0.00 0.00 0.00 4.79
213 214 3.376935 CTGAAGCGAGCCCATCCGT 62.377 63.158 0.00 0.00 0.00 4.69
214 215 2.587194 CTGAAGCGAGCCCATCCG 60.587 66.667 0.00 0.00 0.00 4.18
215 216 2.899339 GCTGAAGCGAGCCCATCC 60.899 66.667 0.00 0.00 32.35 3.51
225 226 3.435186 GTCTTGGGCGGCTGAAGC 61.435 66.667 9.56 4.76 41.14 3.86
226 227 1.377725 ATGTCTTGGGCGGCTGAAG 60.378 57.895 9.56 11.67 0.00 3.02
227 228 1.675310 CATGTCTTGGGCGGCTGAA 60.675 57.895 9.56 1.05 0.00 3.02
228 229 2.046023 CATGTCTTGGGCGGCTGA 60.046 61.111 9.56 2.16 0.00 4.26
229 230 3.136123 CCATGTCTTGGGCGGCTG 61.136 66.667 9.56 0.00 42.33 4.85
246 247 3.431725 CCGACGGGCTTTTGCTCC 61.432 66.667 5.81 0.00 44.81 4.70
250 251 0.170339 GGAATTCCGACGGGCTTTTG 59.830 55.000 15.25 0.00 0.00 2.44
265 266 4.740822 GCCCAGCCCACACGGAAT 62.741 66.667 0.00 0.00 0.00 3.01
323 324 4.500826 GGGAGGGGAGGGGAGGAC 62.501 77.778 0.00 0.00 0.00 3.85
336 337 4.748798 ACAGCAGGGGAGGGGGAG 62.749 72.222 0.00 0.00 0.00 4.30
337 338 4.741239 GACAGCAGGGGAGGGGGA 62.741 72.222 0.00 0.00 0.00 4.81
420 446 4.995058 GGGTGGGGTCTGGGTGGA 62.995 72.222 0.00 0.00 0.00 4.02
440 466 2.852075 GGTGGTGGTGGTGGAGGA 60.852 66.667 0.00 0.00 0.00 3.71
446 475 3.175710 GTGGGAGGTGGTGGTGGT 61.176 66.667 0.00 0.00 0.00 4.16
452 481 4.677151 GGGGAGGTGGGAGGTGGT 62.677 72.222 0.00 0.00 0.00 4.16
841 1079 2.147150 GAGAGAACAGTCAAAGCCACC 58.853 52.381 0.00 0.00 0.00 4.61
886 1124 6.672147 AGAAGTGAGAAAACAATCGGAATTG 58.328 36.000 0.00 0.00 46.42 2.32
887 1125 6.884280 AGAAGTGAGAAAACAATCGGAATT 57.116 33.333 0.00 0.00 0.00 2.17
921 1159 4.265904 TCACTCCGAGAATAAGCAAACA 57.734 40.909 1.33 0.00 0.00 2.83
952 1190 6.973474 TGGACGCGAAATTAAAAGAAAAAGAA 59.027 30.769 15.93 0.00 0.00 2.52
954 1192 6.741448 TGGACGCGAAATTAAAAGAAAAAG 57.259 33.333 15.93 0.00 0.00 2.27
960 1209 5.404066 ACCAAATTGGACGCGAAATTAAAAG 59.596 36.000 20.25 7.99 40.96 2.27
964 1213 4.230657 CAACCAAATTGGACGCGAAATTA 58.769 39.130 20.25 0.00 40.96 1.40
966 1215 2.671596 CAACCAAATTGGACGCGAAAT 58.328 42.857 20.25 6.88 40.96 2.17
967 1216 1.866063 GCAACCAAATTGGACGCGAAA 60.866 47.619 20.25 4.36 40.96 3.46
968 1217 0.318275 GCAACCAAATTGGACGCGAA 60.318 50.000 20.25 0.00 40.96 4.70
972 1221 1.662876 CGTGAGCAACCAAATTGGACG 60.663 52.381 20.25 12.79 40.96 4.79
973 1222 2.050477 CGTGAGCAACCAAATTGGAC 57.950 50.000 20.25 7.63 40.96 4.02
995 1244 4.261322 CCATTTCCAAAGGATACATCTGCG 60.261 45.833 0.00 0.00 41.41 5.18
1020 1269 0.472471 TCTTTGGGTTCGAGTTGCCT 59.528 50.000 0.00 0.00 0.00 4.75
1074 1323 2.854300 AAATAAGGTGGCAGGGGGCG 62.854 60.000 0.00 0.00 46.16 6.13
1098 1355 4.415735 GCATGCATTCGAGTCGAGATATA 58.584 43.478 15.88 0.22 37.14 0.86
1099 1356 3.249091 GCATGCATTCGAGTCGAGATAT 58.751 45.455 15.88 3.74 37.14 1.63
1152 1412 3.763097 TTGTTGAAACAGCACTGACTG 57.237 42.857 4.31 0.00 40.50 3.51
1153 1413 4.989279 ATTTGTTGAAACAGCACTGACT 57.011 36.364 4.31 0.00 40.50 3.41
1154 1414 5.004726 GTCAATTTGTTGAAACAGCACTGAC 59.995 40.000 4.31 10.97 40.50 3.51
1155 1415 5.101628 GTCAATTTGTTGAAACAGCACTGA 58.898 37.500 4.31 0.00 40.50 3.41
1179 1439 3.064931 CAGGAAGAACCAAACGGTACTC 58.935 50.000 0.00 0.00 42.04 2.59
1180 1440 2.436911 ACAGGAAGAACCAAACGGTACT 59.563 45.455 0.00 0.00 42.04 2.73
1184 1444 1.873591 CAGACAGGAAGAACCAAACGG 59.126 52.381 0.00 0.00 42.04 4.44
1185 1445 1.264288 GCAGACAGGAAGAACCAAACG 59.736 52.381 0.00 0.00 42.04 3.60
1318 1578 7.305474 AGCAACTTGTAAATTACATGTGTAGC 58.695 34.615 20.49 21.44 43.57 3.58
1372 1632 1.024579 AAAGGCGGCAATGACCTACG 61.025 55.000 13.08 0.00 32.08 3.51
1373 1633 0.451783 CAAAGGCGGCAATGACCTAC 59.548 55.000 13.08 0.00 32.08 3.18
1466 1726 4.207165 TCAAACCAGAGAAAGACCAAAGG 58.793 43.478 0.00 0.00 0.00 3.11
1472 1732 6.914757 CACAAAGAATCAAACCAGAGAAAGAC 59.085 38.462 0.00 0.00 0.00 3.01
1474 1734 6.183360 ACCACAAAGAATCAAACCAGAGAAAG 60.183 38.462 0.00 0.00 0.00 2.62
1484 1755 5.426504 ACAAATGCACCACAAAGAATCAAA 58.573 33.333 0.00 0.00 0.00 2.69
1485 1756 5.021033 ACAAATGCACCACAAAGAATCAA 57.979 34.783 0.00 0.00 0.00 2.57
1649 1920 4.742167 ACTGCGATGATATTTTCACTCGAG 59.258 41.667 11.84 11.84 37.46 4.04
1652 1923 8.978539 TGTATAACTGCGATGATATTTTCACTC 58.021 33.333 0.00 0.00 37.11 3.51
1662 1933 8.551205 CAAGTAAACATGTATAACTGCGATGAT 58.449 33.333 0.00 0.00 0.00 2.45
1664 1935 7.635973 CACAAGTAAACATGTATAACTGCGATG 59.364 37.037 0.00 1.52 0.00 3.84
1680 1951 2.665519 CGTGCAGCCATCACAAGTAAAC 60.666 50.000 0.00 0.00 34.27 2.01
1695 1966 2.058798 CAACAGTGGTACTACGTGCAG 58.941 52.381 3.48 0.00 0.00 4.41
1699 1970 3.633525 TCTCAACAACAGTGGTACTACGT 59.366 43.478 3.48 0.00 0.00 3.57
1708 1979 7.171508 TGCTAAAAGACTATCTCAACAACAGTG 59.828 37.037 0.00 0.00 0.00 3.66
1816 2087 2.128035 GAAGCCGTCGATCAGGTAATG 58.872 52.381 0.00 0.00 0.00 1.90
2015 2289 5.833667 AGTGTGCCTGCTAATGTAGTAGATA 59.166 40.000 2.36 0.00 40.44 1.98
2016 2290 4.651503 AGTGTGCCTGCTAATGTAGTAGAT 59.348 41.667 2.36 0.00 40.44 1.98
2062 2337 4.387862 GTCGACATAATTTGTTCCGACAGT 59.612 41.667 11.55 0.00 46.63 3.55
2104 2379 5.258841 TCACATACCTAGGAAAAGACGAGA 58.741 41.667 17.98 0.00 0.00 4.04
2153 2428 5.704978 TGTCAAATGTGCAGCACTCTTATAA 59.295 36.000 25.83 4.45 35.11 0.98
2402 2680 5.360144 ACGTACTGGTATGCTCTCATTTAGT 59.640 40.000 0.00 0.00 34.22 2.24
2466 2744 0.531532 CCAGCACGCAGATCCCTTAG 60.532 60.000 0.00 0.00 0.00 2.18
2588 2873 0.747283 GGGCAGCAGTTCTCATCCAG 60.747 60.000 0.00 0.00 0.00 3.86
2775 3060 5.754782 ACCACCAATAGTCAGATATGCAAA 58.245 37.500 0.00 0.00 0.00 3.68
2873 3158 6.888105 TGAGATGTCCAGTATGAAATAGCAA 58.112 36.000 0.00 0.00 39.69 3.91
2909 3194 5.886715 TGAATGCTTCAAAACATGTTTCG 57.113 34.783 23.47 13.64 36.59 3.46
2910 3195 8.316046 CGATATGAATGCTTCAAAACATGTTTC 58.684 33.333 23.47 11.53 43.95 2.78
2936 3221 1.477105 GGTTCGTGAAAAGCAAGTGC 58.523 50.000 0.00 0.00 42.49 4.40
2942 3227 2.863401 AACAAGGGTTCGTGAAAAGC 57.137 45.000 0.00 0.00 29.00 3.51
2979 3264 8.025243 TGAACTAAAACCATGACGAGTAAATC 57.975 34.615 0.00 0.00 0.00 2.17
2980 3265 7.972832 TGAACTAAAACCATGACGAGTAAAT 57.027 32.000 0.00 0.00 0.00 1.40
2981 3266 7.496591 ACTTGAACTAAAACCATGACGAGTAAA 59.503 33.333 0.00 0.00 0.00 2.01
2982 3267 6.987992 ACTTGAACTAAAACCATGACGAGTAA 59.012 34.615 0.00 0.00 0.00 2.24
2983 3268 6.518493 ACTTGAACTAAAACCATGACGAGTA 58.482 36.000 0.00 0.00 0.00 2.59
2984 3269 5.365619 ACTTGAACTAAAACCATGACGAGT 58.634 37.500 0.00 0.00 0.00 4.18
2985 3270 5.924475 ACTTGAACTAAAACCATGACGAG 57.076 39.130 0.00 0.00 0.00 4.18
2986 3271 7.789273 TTTACTTGAACTAAAACCATGACGA 57.211 32.000 0.00 0.00 0.00 4.20
2987 3272 7.477422 CGATTTACTTGAACTAAAACCATGACG 59.523 37.037 0.00 0.00 0.00 4.35
2988 3273 7.749126 CCGATTTACTTGAACTAAAACCATGAC 59.251 37.037 0.00 0.00 0.00 3.06
2989 3274 7.662258 TCCGATTTACTTGAACTAAAACCATGA 59.338 33.333 0.00 0.00 0.00 3.07
2990 3275 7.812648 TCCGATTTACTTGAACTAAAACCATG 58.187 34.615 0.00 0.00 0.00 3.66
2991 3276 7.989416 TCCGATTTACTTGAACTAAAACCAT 57.011 32.000 0.00 0.00 0.00 3.55
2992 3277 7.518689 CGTTCCGATTTACTTGAACTAAAACCA 60.519 37.037 0.00 0.00 35.97 3.67
2993 3278 6.793680 CGTTCCGATTTACTTGAACTAAAACC 59.206 38.462 0.00 0.00 35.97 3.27
2994 3279 6.793680 CCGTTCCGATTTACTTGAACTAAAAC 59.206 38.462 0.00 0.00 35.97 2.43
2995 3280 6.705381 TCCGTTCCGATTTACTTGAACTAAAA 59.295 34.615 0.00 0.00 35.97 1.52
2996 3281 6.222389 TCCGTTCCGATTTACTTGAACTAAA 58.778 36.000 0.00 0.00 35.97 1.85
2997 3282 5.782047 TCCGTTCCGATTTACTTGAACTAA 58.218 37.500 0.00 0.00 35.97 2.24
2998 3283 5.389859 TCCGTTCCGATTTACTTGAACTA 57.610 39.130 0.00 0.00 35.97 2.24
2999 3284 4.243270 CTCCGTTCCGATTTACTTGAACT 58.757 43.478 0.00 0.00 35.97 3.01
3000 3285 3.370061 CCTCCGTTCCGATTTACTTGAAC 59.630 47.826 0.00 0.00 35.03 3.18
3001 3286 3.592059 CCTCCGTTCCGATTTACTTGAA 58.408 45.455 0.00 0.00 0.00 2.69
3002 3287 2.093869 CCCTCCGTTCCGATTTACTTGA 60.094 50.000 0.00 0.00 0.00 3.02
3003 3288 2.093869 TCCCTCCGTTCCGATTTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3004 3289 2.167900 CTCCCTCCGTTCCGATTTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3005 3290 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
3006 3291 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
3007 3292 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
3008 3293 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
3009 3294 1.341778 ACTACTCCCTCCGTTCCGATT 60.342 52.381 0.00 0.00 0.00 3.34
3010 3295 0.258194 ACTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18
3011 3296 0.038744 AACTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
3012 3297 0.893447 AAACTACTCCCTCCGTTCCG 59.107 55.000 0.00 0.00 0.00 4.30
3013 3298 1.622312 ACAAACTACTCCCTCCGTTCC 59.378 52.381 0.00 0.00 0.00 3.62
3014 3299 3.397849 AACAAACTACTCCCTCCGTTC 57.602 47.619 0.00 0.00 0.00 3.95
3015 3300 3.899980 AGTAACAAACTACTCCCTCCGTT 59.100 43.478 0.00 0.00 36.36 4.44
3016 3301 3.257624 CAGTAACAAACTACTCCCTCCGT 59.742 47.826 0.00 0.00 35.76 4.69
3017 3302 3.368116 CCAGTAACAAACTACTCCCTCCG 60.368 52.174 0.00 0.00 35.76 4.63
3018 3303 3.836562 TCCAGTAACAAACTACTCCCTCC 59.163 47.826 0.00 0.00 35.76 4.30
3019 3304 5.479124 TTCCAGTAACAAACTACTCCCTC 57.521 43.478 0.00 0.00 35.76 4.30
3020 3305 5.803470 GCATTCCAGTAACAAACTACTCCCT 60.803 44.000 0.00 0.00 35.76 4.20
3021 3306 4.395231 GCATTCCAGTAACAAACTACTCCC 59.605 45.833 0.00 0.00 35.76 4.30
3022 3307 5.001232 TGCATTCCAGTAACAAACTACTCC 58.999 41.667 0.00 0.00 35.76 3.85
3023 3308 6.743575 ATGCATTCCAGTAACAAACTACTC 57.256 37.500 0.00 0.00 35.76 2.59
3024 3309 7.524717 AAATGCATTCCAGTAACAAACTACT 57.475 32.000 13.38 0.00 35.76 2.57
3025 3310 7.651704 ACAAAATGCATTCCAGTAACAAACTAC 59.348 33.333 13.38 0.00 35.76 2.73
3087 3372 8.445493 GCATTTTCCTAATTTCACTCAAATTGG 58.555 33.333 3.12 0.51 43.38 3.16
3386 3671 3.914426 ACAGACACCCATAGATCCAAC 57.086 47.619 0.00 0.00 0.00 3.77
3585 3870 5.417580 TCCCATAAGCACAATTAGTTGGTTC 59.582 40.000 2.81 0.00 39.70 3.62
3608 3893 7.149307 GCAAGAACAAGTATAGGTATCTCCTC 58.851 42.308 0.00 0.00 44.42 3.71
3611 3896 7.493367 ACTGCAAGAACAAGTATAGGTATCTC 58.507 38.462 0.00 0.00 37.43 2.75
3618 3903 5.877012 ACATGGACTGCAAGAACAAGTATAG 59.123 40.000 0.00 0.00 37.43 1.31
3624 3909 3.698539 TGAAACATGGACTGCAAGAACAA 59.301 39.130 0.00 0.00 37.43 2.83
3637 3922 3.770933 AGATGGGGAAACATGAAACATGG 59.229 43.478 14.70 0.00 0.00 3.66
3655 3940 4.882671 AAACTAAGCATGCCGTAAGATG 57.117 40.909 15.66 0.00 43.02 2.90
3672 3990 5.349270 TCGCAGCACATTACGTAAATAAACT 59.651 36.000 12.81 3.96 0.00 2.66
3683 4001 2.286294 CAGGAGAATCGCAGCACATTAC 59.714 50.000 0.00 0.00 34.37 1.89
3694 4180 7.244192 GGACAAAAGAAATAACAGGAGAATCG 58.756 38.462 0.00 0.00 34.37 3.34
3704 4190 4.295051 TGCAAGCGGACAAAAGAAATAAC 58.705 39.130 0.00 0.00 0.00 1.89
3705 4191 4.576216 TGCAAGCGGACAAAAGAAATAA 57.424 36.364 0.00 0.00 0.00 1.40
3725 4211 6.515272 AGGTCACATTATTAGTTTGGCTTG 57.485 37.500 0.00 0.00 0.00 4.01
3734 4220 8.723942 AGCTAAGTCAAAGGTCACATTATTAG 57.276 34.615 0.00 0.00 0.00 1.73
3747 4233 7.693952 TGAACTGTTTGTAAGCTAAGTCAAAG 58.306 34.615 0.00 0.00 31.85 2.77
3748 4234 7.618502 TGAACTGTTTGTAAGCTAAGTCAAA 57.381 32.000 0.00 0.00 0.00 2.69
3749 4235 7.551262 TCTTGAACTGTTTGTAAGCTAAGTCAA 59.449 33.333 0.00 0.00 0.00 3.18
3755 4249 9.555727 AACTATTCTTGAACTGTTTGTAAGCTA 57.444 29.630 0.00 0.00 0.00 3.32
3765 4259 8.514330 TGGTACAAAAACTATTCTTGAACTGT 57.486 30.769 0.00 0.00 31.92 3.55
3875 4411 2.935201 CAGGAGCAGCAGTTGTATCTTC 59.065 50.000 0.00 0.00 0.00 2.87
3916 4454 7.035612 GTGTGTGACATCACTATACTCATCAA 58.964 38.462 12.98 0.00 46.55 2.57
3917 4455 6.378280 AGTGTGTGACATCACTATACTCATCA 59.622 38.462 15.65 0.00 46.55 3.07
3918 4456 6.800543 AGTGTGTGACATCACTATACTCATC 58.199 40.000 15.65 0.00 46.55 2.92
3919 4457 6.782082 AGTGTGTGACATCACTATACTCAT 57.218 37.500 15.65 0.00 46.55 2.90
3920 4458 6.590234 AAGTGTGTGACATCACTATACTCA 57.410 37.500 16.92 1.50 46.55 3.41
3921 4459 8.027189 TGTTAAGTGTGTGACATCACTATACTC 58.973 37.037 16.92 4.70 46.55 2.59
3922 4460 7.892609 TGTTAAGTGTGTGACATCACTATACT 58.107 34.615 16.92 10.78 46.55 2.12
3923 4461 8.528917 TTGTTAAGTGTGTGACATCACTATAC 57.471 34.615 16.92 16.58 46.55 1.47
3924 4462 9.549078 TTTTGTTAAGTGTGTGACATCACTATA 57.451 29.630 16.92 10.93 46.55 1.31
3925 4463 8.342634 GTTTTGTTAAGTGTGTGACATCACTAT 58.657 33.333 16.92 11.60 46.55 2.12
3926 4464 7.334671 TGTTTTGTTAAGTGTGTGACATCACTA 59.665 33.333 16.92 4.69 46.55 2.74
3927 4465 6.150307 TGTTTTGTTAAGTGTGTGACATCACT 59.850 34.615 12.98 12.75 46.55 3.41
3928 4466 6.250527 GTGTTTTGTTAAGTGTGTGACATCAC 59.749 38.462 5.02 5.02 46.59 3.06
3935 4486 3.857093 GGCAGTGTTTTGTTAAGTGTGTG 59.143 43.478 0.00 0.00 0.00 3.82
3985 4536 8.190784 GTGGGAGTGTTGGAATTATTCTAATTG 58.809 37.037 7.00 0.00 32.64 2.32
4029 4580 1.008875 TTCAAGCTACAGTGCTCGCG 61.009 55.000 0.00 0.00 43.24 5.87
4229 4793 7.576236 CAAAGGTATGCACTATATTTTCTCCG 58.424 38.462 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.