Multiple sequence alignment - TraesCS6D01G144700

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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 TraesCS6D01G144700 chr6D 100.000 5538 0 0 1 5538 115083036 115088573 0.000000e+00 10227
1 TraesCS6D01G144700 chr6B 94.943 4093 153 20 1479 5538 204543630 204547701 0.000000e+00 6362
2 TraesCS6D01G144700 chr6B 87.080 1130 72 28 151 1233 204542259 204543361 0.000000e+00 1210
3 TraesCS6D01G144700 chr6B 94.872 117 5 1 1262 1378 204543359 204543474 1.230000e-41 182
4 TraesCS6D01G144700 chr6A 92.128 3773 187 62 1479 5187 143493679 143497405 0.000000e+00 5221
5 TraesCS6D01G144700 chr6A 88.345 961 79 21 287 1233 143492480 143493421 0.000000e+00 1123
6 TraesCS6D01G144700 chr6A 93.624 298 18 1 5242 5538 143497851 143498148 1.420000e-120 444
7 TraesCS6D01G144700 chr6A 89.474 152 6 3 1266 1409 143493424 143493573 3.410000e-42 183


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 TraesCS6D01G144700 chr6D 115083036 115088573 5537 False 10227.000000 10227 100.000000 1 5538 1 chr6D.!!$F1 5537
1 TraesCS6D01G144700 chr6B 204542259 204547701 5442 False 2584.666667 6362 92.298333 151 5538 3 chr6B.!!$F1 5387
2 TraesCS6D01G144700 chr6A 143492480 143498148 5668 False 1742.750000 5221 90.892750 287 5538 4 chr6A.!!$F1 5251

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
73 74 0.037975 CACTGGATTTTGGCTGCCAC 60.038 55.000 23.30 9.86 30.78 5.01 F
87 88 0.039180 TGCCACTAAGAGGAGGTCGA 59.961 55.000 0.00 0.00 0.00 4.20 F
274 276 0.103208 CGTAGGCCAGGAGTCATCAC 59.897 60.000 5.01 0.00 0.00 3.06 F
1508 1623 0.179113 AACTTTGCGTTGCAGTTGGG 60.179 50.000 0.00 0.00 40.61 4.12 F
1544 1659 1.302033 CCACCAAACGAGAGCTGCT 60.302 57.895 0.00 0.00 0.00 4.24 F
2689 2837 0.472471 TTGGGGATATCCTTGACCGC 59.528 55.000 21.18 3.97 35.95 5.68 F
3376 3526 1.643868 TAGCTTGCGAATTGGCACGG 61.644 55.000 15.22 11.67 43.82 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1844 1.004394 GGCAAGTAGGTTACCAAGGCT 59.996 52.381 3.51 0.0 0.00 4.58 R
1896 2026 2.327325 AAGTGGGCTAGAGTTCAGGA 57.673 50.000 0.00 0.0 0.00 3.86 R
2182 2322 0.033503 AGGCCCCAAAACCTTATCCG 60.034 55.000 0.00 0.0 29.74 4.18 R
2482 2630 0.038892 GCCTGACTACGAAACCGTCA 60.039 55.000 0.00 0.0 41.06 4.35 R
3433 3583 1.185315 TGAGCGACTCACCATGATGA 58.815 50.000 5.59 0.0 35.39 2.92 R
3671 3821 1.777272 GGTAGCCATGAAGGGGAGATT 59.223 52.381 0.00 0.0 38.09 2.40 R
5287 5883 1.202568 CCTCATGAGCAAGCCGATACA 60.203 52.381 17.76 0.0 0.00 2.29 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
26 27 9.469807 TTGTTTTCGTATGCTATCAACATTTTT 57.530 25.926 0.00 0.00 0.00 1.94
58 59 9.691362 AATTACAATAGCAAAAAGGTTACACTG 57.309 29.630 0.00 0.00 0.00 3.66
59 60 6.084326 ACAATAGCAAAAAGGTTACACTGG 57.916 37.500 0.00 0.00 0.00 4.00
60 61 5.830991 ACAATAGCAAAAAGGTTACACTGGA 59.169 36.000 0.00 0.00 0.00 3.86
61 62 6.493458 ACAATAGCAAAAAGGTTACACTGGAT 59.507 34.615 0.00 0.00 0.00 3.41
62 63 7.015195 ACAATAGCAAAAAGGTTACACTGGATT 59.985 33.333 0.00 0.00 0.00 3.01
63 64 5.869649 AGCAAAAAGGTTACACTGGATTT 57.130 34.783 0.00 0.00 0.00 2.17
64 65 6.233905 AGCAAAAAGGTTACACTGGATTTT 57.766 33.333 0.00 0.00 0.00 1.82
65 66 6.048509 AGCAAAAAGGTTACACTGGATTTTG 58.951 36.000 0.00 0.00 38.59 2.44
66 67 5.236263 GCAAAAAGGTTACACTGGATTTTGG 59.764 40.000 9.32 0.00 36.99 3.28
67 68 4.600692 AAAGGTTACACTGGATTTTGGC 57.399 40.909 0.00 0.00 0.00 4.52
68 69 3.525800 AGGTTACACTGGATTTTGGCT 57.474 42.857 0.00 0.00 0.00 4.75
69 70 3.157087 AGGTTACACTGGATTTTGGCTG 58.843 45.455 0.00 0.00 0.00 4.85
70 71 2.352715 GGTTACACTGGATTTTGGCTGC 60.353 50.000 0.00 0.00 0.00 5.25
71 72 1.544724 TACACTGGATTTTGGCTGCC 58.455 50.000 12.87 12.87 0.00 4.85
72 73 0.469705 ACACTGGATTTTGGCTGCCA 60.470 50.000 19.30 19.30 0.00 4.92
73 74 0.037975 CACTGGATTTTGGCTGCCAC 60.038 55.000 23.30 9.86 30.78 5.01
74 75 0.178953 ACTGGATTTTGGCTGCCACT 60.179 50.000 23.30 9.22 30.78 4.00
75 76 1.075374 ACTGGATTTTGGCTGCCACTA 59.925 47.619 23.30 12.77 30.78 2.74
76 77 2.170166 CTGGATTTTGGCTGCCACTAA 58.830 47.619 23.30 18.51 30.78 2.24
77 78 2.165030 CTGGATTTTGGCTGCCACTAAG 59.835 50.000 23.30 9.49 30.78 2.18
78 79 2.224992 TGGATTTTGGCTGCCACTAAGA 60.225 45.455 23.30 2.76 30.78 2.10
79 80 2.424956 GGATTTTGGCTGCCACTAAGAG 59.575 50.000 23.30 0.00 30.78 2.85
80 81 1.909700 TTTTGGCTGCCACTAAGAGG 58.090 50.000 23.30 0.00 30.78 3.69
81 82 1.064003 TTTGGCTGCCACTAAGAGGA 58.936 50.000 23.30 0.09 30.78 3.71
82 83 0.615331 TTGGCTGCCACTAAGAGGAG 59.385 55.000 23.30 0.00 30.78 3.69
83 84 1.267574 TGGCTGCCACTAAGAGGAGG 61.268 60.000 19.30 0.00 0.00 4.30
84 85 1.268283 GGCTGCCACTAAGAGGAGGT 61.268 60.000 15.17 0.00 0.00 3.85
85 86 0.176910 GCTGCCACTAAGAGGAGGTC 59.823 60.000 0.00 0.00 0.00 3.85
86 87 0.457851 CTGCCACTAAGAGGAGGTCG 59.542 60.000 0.00 0.00 0.00 4.79
87 88 0.039180 TGCCACTAAGAGGAGGTCGA 59.961 55.000 0.00 0.00 0.00 4.20
88 89 0.741915 GCCACTAAGAGGAGGTCGAG 59.258 60.000 0.00 0.00 0.00 4.04
89 90 0.741915 CCACTAAGAGGAGGTCGAGC 59.258 60.000 6.48 6.48 0.00 5.03
90 91 0.378962 CACTAAGAGGAGGTCGAGCG 59.621 60.000 9.28 0.00 0.00 5.03
91 92 1.357334 CTAAGAGGAGGTCGAGCGC 59.643 63.158 10.06 10.06 0.00 5.92
92 93 2.065906 CTAAGAGGAGGTCGAGCGCC 62.066 65.000 27.33 27.33 0.00 6.53
93 94 2.553765 TAAGAGGAGGTCGAGCGCCT 62.554 60.000 35.35 35.35 39.42 5.52
94 95 3.453679 GAGGAGGTCGAGCGCCTT 61.454 66.667 35.15 21.64 36.29 4.35
95 96 3.418744 GAGGAGGTCGAGCGCCTTC 62.419 68.421 35.15 24.75 36.29 3.46
96 97 3.453679 GGAGGTCGAGCGCCTTCT 61.454 66.667 27.31 0.33 36.29 2.85
97 98 2.103340 GAGGTCGAGCGCCTTCTC 59.897 66.667 9.28 0.57 36.29 2.87
98 99 2.676822 AGGTCGAGCGCCTTCTCA 60.677 61.111 9.28 0.00 31.04 3.27
99 100 2.507324 GGTCGAGCGCCTTCTCAC 60.507 66.667 2.29 0.00 33.41 3.51
100 101 2.507324 GTCGAGCGCCTTCTCACC 60.507 66.667 2.29 0.00 33.41 4.02
101 102 2.989253 TCGAGCGCCTTCTCACCA 60.989 61.111 2.29 0.00 33.41 4.17
102 103 2.811317 CGAGCGCCTTCTCACCAC 60.811 66.667 2.29 0.00 33.41 4.16
103 104 2.811317 GAGCGCCTTCTCACCACG 60.811 66.667 2.29 0.00 33.41 4.94
108 109 2.357517 CCTTCTCACCACGCGCTT 60.358 61.111 5.73 0.00 0.00 4.68
109 110 2.383527 CCTTCTCACCACGCGCTTC 61.384 63.158 5.73 0.00 0.00 3.86
110 111 1.664649 CTTCTCACCACGCGCTTCA 60.665 57.895 5.73 0.00 0.00 3.02
111 112 1.891060 CTTCTCACCACGCGCTTCAC 61.891 60.000 5.73 0.00 0.00 3.18
112 113 3.414700 CTCACCACGCGCTTCACC 61.415 66.667 5.73 0.00 0.00 4.02
113 114 4.980805 TCACCACGCGCTTCACCC 62.981 66.667 5.73 0.00 0.00 4.61
114 115 4.988598 CACCACGCGCTTCACCCT 62.989 66.667 5.73 0.00 0.00 4.34
115 116 4.988598 ACCACGCGCTTCACCCTG 62.989 66.667 5.73 0.00 0.00 4.45
116 117 4.988598 CCACGCGCTTCACCCTGT 62.989 66.667 5.73 0.00 0.00 4.00
117 118 3.716006 CACGCGCTTCACCCTGTG 61.716 66.667 5.73 0.00 34.45 3.66
118 119 4.988598 ACGCGCTTCACCCTGTGG 62.989 66.667 5.73 0.00 33.87 4.17
127 128 3.995597 ACCCTGTGGTGGTTGCTA 58.004 55.556 0.00 0.00 45.58 3.49
128 129 2.236555 ACCCTGTGGTGGTTGCTAA 58.763 52.632 0.00 0.00 45.58 3.09
129 130 0.110486 ACCCTGTGGTGGTTGCTAAG 59.890 55.000 0.00 0.00 45.58 2.18
130 131 0.400213 CCCTGTGGTGGTTGCTAAGA 59.600 55.000 0.00 0.00 0.00 2.10
131 132 1.611673 CCCTGTGGTGGTTGCTAAGAG 60.612 57.143 0.00 0.00 0.00 2.85
132 133 1.611673 CCTGTGGTGGTTGCTAAGAGG 60.612 57.143 0.00 0.00 0.00 3.69
133 134 1.072331 CTGTGGTGGTTGCTAAGAGGT 59.928 52.381 0.00 0.00 0.00 3.85
134 135 1.493022 TGTGGTGGTTGCTAAGAGGTT 59.507 47.619 0.00 0.00 0.00 3.50
135 136 2.092103 TGTGGTGGTTGCTAAGAGGTTT 60.092 45.455 0.00 0.00 0.00 3.27
136 137 2.293399 GTGGTGGTTGCTAAGAGGTTTG 59.707 50.000 0.00 0.00 0.00 2.93
137 138 1.886542 GGTGGTTGCTAAGAGGTTTGG 59.113 52.381 0.00 0.00 0.00 3.28
138 139 1.886542 GTGGTTGCTAAGAGGTTTGGG 59.113 52.381 0.00 0.00 0.00 4.12
139 140 1.497286 TGGTTGCTAAGAGGTTTGGGT 59.503 47.619 0.00 0.00 0.00 4.51
140 141 1.886542 GGTTGCTAAGAGGTTTGGGTG 59.113 52.381 0.00 0.00 0.00 4.61
141 142 1.886542 GTTGCTAAGAGGTTTGGGTGG 59.113 52.381 0.00 0.00 0.00 4.61
142 143 0.404040 TGCTAAGAGGTTTGGGTGGG 59.596 55.000 0.00 0.00 0.00 4.61
143 144 0.323451 GCTAAGAGGTTTGGGTGGGG 60.323 60.000 0.00 0.00 0.00 4.96
144 145 0.323451 CTAAGAGGTTTGGGTGGGGC 60.323 60.000 0.00 0.00 0.00 5.80
145 146 2.132089 TAAGAGGTTTGGGTGGGGCG 62.132 60.000 0.00 0.00 0.00 6.13
146 147 4.280019 GAGGTTTGGGTGGGGCGT 62.280 66.667 0.00 0.00 0.00 5.68
147 148 4.596585 AGGTTTGGGTGGGGCGTG 62.597 66.667 0.00 0.00 0.00 5.34
148 149 4.906537 GGTTTGGGTGGGGCGTGT 62.907 66.667 0.00 0.00 0.00 4.49
149 150 3.601685 GTTTGGGTGGGGCGTGTG 61.602 66.667 0.00 0.00 0.00 3.82
150 151 4.130554 TTTGGGTGGGGCGTGTGT 62.131 61.111 0.00 0.00 0.00 3.72
151 152 4.885270 TTGGGTGGGGCGTGTGTG 62.885 66.667 0.00 0.00 0.00 3.82
194 195 4.782156 AGATTCAGGTCATGAGAGGAAAGT 59.218 41.667 0.00 0.00 39.68 2.66
209 210 4.646572 AGGAAAGTGCTAGAGGTTTTGAG 58.353 43.478 0.00 0.00 0.00 3.02
210 211 4.103311 AGGAAAGTGCTAGAGGTTTTGAGT 59.897 41.667 0.00 0.00 0.00 3.41
222 223 1.701031 TTTTGAGTGGTGGGGCGAGA 61.701 55.000 0.00 0.00 0.00 4.04
223 224 1.701031 TTTGAGTGGTGGGGCGAGAA 61.701 55.000 0.00 0.00 0.00 2.87
231 232 1.615124 TGGGGCGAGAAGGATCCAA 60.615 57.895 15.82 0.00 0.00 3.53
236 237 1.674817 GGCGAGAAGGATCCAAAACGA 60.675 52.381 15.82 0.00 0.00 3.85
237 238 2.073816 GCGAGAAGGATCCAAAACGAA 58.926 47.619 15.82 0.00 0.00 3.85
242 243 5.334879 CGAGAAGGATCCAAAACGAAAACAT 60.335 40.000 15.82 0.00 0.00 2.71
250 251 3.296628 CAAAACGAAAACATGTCTCGGG 58.703 45.455 25.40 13.38 36.90 5.14
252 253 0.682852 ACGAAAACATGTCTCGGGGA 59.317 50.000 25.40 0.00 36.90 4.81
253 254 1.071071 ACGAAAACATGTCTCGGGGAA 59.929 47.619 25.40 0.00 36.90 3.97
274 276 0.103208 CGTAGGCCAGGAGTCATCAC 59.897 60.000 5.01 0.00 0.00 3.06
294 296 4.873827 TCACGACTAAACCTCATTTATGCC 59.126 41.667 0.00 0.00 32.23 4.40
300 302 7.441157 CGACTAAACCTCATTTATGCCTTATGA 59.559 37.037 0.00 0.00 32.23 2.15
338 341 1.515954 GAGGGCGGACGAAATCAGA 59.484 57.895 0.00 0.00 0.00 3.27
354 357 1.152963 AGACGCAAAAGGCTGGTGT 60.153 52.632 0.00 0.00 41.67 4.16
357 360 2.489275 CGCAAAAGGCTGGTGTGGT 61.489 57.895 0.00 0.00 41.67 4.16
564 572 2.834638 AATGGTGAAGAATGGGAGGG 57.165 50.000 0.00 0.00 0.00 4.30
589 597 4.818005 GGACGAAAAGGTGGTAGAAAGAAA 59.182 41.667 0.00 0.00 0.00 2.52
680 688 1.661341 CGAATCAAAGAGGCCCTCAG 58.339 55.000 14.46 2.38 32.06 3.35
728 764 1.410517 GAGAAGCCCATGAGACATCGA 59.589 52.381 0.00 0.00 0.00 3.59
808 844 4.872485 CGAGACTCCGAGACGCGC 62.872 72.222 5.73 0.00 39.11 6.86
811 847 4.104417 GACTCCGAGACGCGCTGT 62.104 66.667 5.73 5.01 39.11 4.40
1161 1211 1.244697 CGATCATCGTCTCCGGGGAT 61.245 60.000 7.65 0.00 34.72 3.85
1207 1257 4.465512 GCCGCATTGTCGCTGGTG 62.466 66.667 0.00 0.00 0.00 4.17
1233 1283 6.129769 CGTATACTATCGTCTGTTCGCTTTTC 60.130 42.308 0.56 0.00 0.00 2.29
1235 1285 4.167268 ACTATCGTCTGTTCGCTTTTCTC 58.833 43.478 0.00 0.00 0.00 2.87
1238 1288 2.293677 TCGTCTGTTCGCTTTTCTCTCT 59.706 45.455 0.00 0.00 0.00 3.10
1239 1289 2.659279 CGTCTGTTCGCTTTTCTCTCTC 59.341 50.000 0.00 0.00 0.00 3.20
1240 1290 3.610585 CGTCTGTTCGCTTTTCTCTCTCT 60.611 47.826 0.00 0.00 0.00 3.10
1241 1291 3.917985 GTCTGTTCGCTTTTCTCTCTCTC 59.082 47.826 0.00 0.00 0.00 3.20
1242 1292 3.823873 TCTGTTCGCTTTTCTCTCTCTCT 59.176 43.478 0.00 0.00 0.00 3.10
1243 1293 4.083003 TCTGTTCGCTTTTCTCTCTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
1244 1294 3.823873 TGTTCGCTTTTCTCTCTCTCTCT 59.176 43.478 0.00 0.00 0.00 3.10
1245 1295 4.083003 TGTTCGCTTTTCTCTCTCTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
1246 1296 3.950397 TCGCTTTTCTCTCTCTCTCTCT 58.050 45.455 0.00 0.00 0.00 3.10
1247 1297 3.938963 TCGCTTTTCTCTCTCTCTCTCTC 59.061 47.826 0.00 0.00 0.00 3.20
1248 1298 3.941483 CGCTTTTCTCTCTCTCTCTCTCT 59.059 47.826 0.00 0.00 0.00 3.10
1249 1299 4.034510 CGCTTTTCTCTCTCTCTCTCTCTC 59.965 50.000 0.00 0.00 0.00 3.20
1250 1300 5.189180 GCTTTTCTCTCTCTCTCTCTCTCT 58.811 45.833 0.00 0.00 0.00 3.10
1251 1301 5.295540 GCTTTTCTCTCTCTCTCTCTCTCTC 59.704 48.000 0.00 0.00 0.00 3.20
1252 1302 6.627087 TTTTCTCTCTCTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
1253 1303 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
1254 1304 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1255 1305 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
1256 1306 5.960811 TCTCTCTCTCTCTCTCTCTCTCTTT 59.039 44.000 0.00 0.00 0.00 2.52
1257 1307 6.441924 TCTCTCTCTCTCTCTCTCTCTCTTTT 59.558 42.308 0.00 0.00 0.00 2.27
1258 1308 7.020827 TCTCTCTCTCTCTCTCTCTCTTTTT 57.979 40.000 0.00 0.00 0.00 1.94
1295 1345 4.753233 TCTGAAGAAATAGACAGCTCTGC 58.247 43.478 0.00 0.00 0.00 4.26
1300 1350 4.865776 AGAAATAGACAGCTCTGCGTATC 58.134 43.478 0.00 0.00 0.00 2.24
1402 1468 8.064814 GCTCGATCATCTCTTTGGTTAATTAAC 58.935 37.037 18.30 18.30 35.50 2.01
1409 1475 7.519032 TCTCTTTGGTTAATTAACTTGGTGG 57.481 36.000 23.89 12.79 36.47 4.61
1410 1476 6.492087 TCTCTTTGGTTAATTAACTTGGTGGG 59.508 38.462 23.89 12.83 36.47 4.61
1411 1477 6.374588 TCTTTGGTTAATTAACTTGGTGGGA 58.625 36.000 23.89 12.40 36.47 4.37
1412 1478 6.839657 TCTTTGGTTAATTAACTTGGTGGGAA 59.160 34.615 23.89 9.36 36.47 3.97
1413 1479 7.344871 TCTTTGGTTAATTAACTTGGTGGGAAA 59.655 33.333 23.89 11.19 36.47 3.13
1414 1480 7.619512 TTGGTTAATTAACTTGGTGGGAAAT 57.380 32.000 23.89 0.00 36.47 2.17
1415 1481 7.619512 TGGTTAATTAACTTGGTGGGAAATT 57.380 32.000 23.89 0.00 36.47 1.82
1416 1482 8.035448 TGGTTAATTAACTTGGTGGGAAATTT 57.965 30.769 23.89 0.00 36.47 1.82
1417 1483 8.495260 TGGTTAATTAACTTGGTGGGAAATTTT 58.505 29.630 23.89 0.00 36.47 1.82
1418 1484 8.779303 GGTTAATTAACTTGGTGGGAAATTTTG 58.221 33.333 23.89 0.00 36.47 2.44
1440 1506 6.808008 TGCCAATAGAAAAGAAGAAGAGTG 57.192 37.500 0.00 0.00 0.00 3.51
1444 1510 7.572168 GCCAATAGAAAAGAAGAAGAGTGACAC 60.572 40.741 0.00 0.00 0.00 3.67
1445 1511 7.359598 CCAATAGAAAAGAAGAAGAGTGACACG 60.360 40.741 0.00 0.00 0.00 4.49
1446 1512 4.372656 AGAAAAGAAGAAGAGTGACACGG 58.627 43.478 0.00 0.00 0.00 4.94
1447 1513 3.821421 AAAGAAGAAGAGTGACACGGT 57.179 42.857 0.00 0.00 0.00 4.83
1448 1514 3.372660 AAGAAGAAGAGTGACACGGTC 57.627 47.619 0.00 0.00 0.00 4.79
1450 1516 2.894126 AGAAGAAGAGTGACACGGTCAT 59.106 45.455 9.47 0.00 44.63 3.06
1451 1517 2.732412 AGAAGAGTGACACGGTCATG 57.268 50.000 9.47 0.00 44.63 3.07
1452 1518 2.239400 AGAAGAGTGACACGGTCATGA 58.761 47.619 9.47 0.00 44.63 3.07
1453 1519 2.230025 AGAAGAGTGACACGGTCATGAG 59.770 50.000 9.47 0.00 44.63 2.90
1455 1521 0.888619 GAGTGACACGGTCATGAGGA 59.111 55.000 9.47 0.00 44.63 3.71
1456 1522 1.272490 GAGTGACACGGTCATGAGGAA 59.728 52.381 9.47 0.00 44.63 3.36
1457 1523 1.902508 AGTGACACGGTCATGAGGAAT 59.097 47.619 9.47 0.00 44.63 3.01
1458 1524 2.303022 AGTGACACGGTCATGAGGAATT 59.697 45.455 9.47 0.00 44.63 2.17
1459 1525 3.074412 GTGACACGGTCATGAGGAATTT 58.926 45.455 9.47 0.00 44.63 1.82
1460 1526 4.020573 AGTGACACGGTCATGAGGAATTTA 60.021 41.667 9.47 0.00 44.63 1.40
1461 1527 4.876107 GTGACACGGTCATGAGGAATTTAT 59.124 41.667 9.47 0.00 44.63 1.40
1463 1529 5.104941 TGACACGGTCATGAGGAATTTATCT 60.105 40.000 0.00 0.00 37.67 1.98
1464 1530 5.745227 ACACGGTCATGAGGAATTTATCTT 58.255 37.500 0.00 0.00 0.00 2.40
1465 1531 6.180472 ACACGGTCATGAGGAATTTATCTTT 58.820 36.000 0.00 0.00 0.00 2.52
1466 1532 6.316390 ACACGGTCATGAGGAATTTATCTTTC 59.684 38.462 0.00 0.00 0.00 2.62
1467 1533 6.316140 CACGGTCATGAGGAATTTATCTTTCA 59.684 38.462 0.00 0.00 0.00 2.69
1468 1534 6.316390 ACGGTCATGAGGAATTTATCTTTCAC 59.684 38.462 0.00 0.00 0.00 3.18
1470 1536 7.466455 CGGTCATGAGGAATTTATCTTTCACAG 60.466 40.741 0.00 0.00 0.00 3.66
1471 1537 7.192232 GTCATGAGGAATTTATCTTTCACAGC 58.808 38.462 0.00 0.00 0.00 4.40
1472 1538 5.801350 TGAGGAATTTATCTTTCACAGCG 57.199 39.130 0.00 0.00 0.00 5.18
1474 1540 5.351465 TGAGGAATTTATCTTTCACAGCGTC 59.649 40.000 0.00 0.00 0.00 5.19
1475 1541 5.245531 AGGAATTTATCTTTCACAGCGTCA 58.754 37.500 0.00 0.00 0.00 4.35
1476 1542 5.882557 AGGAATTTATCTTTCACAGCGTCAT 59.117 36.000 0.00 0.00 0.00 3.06
1487 1602 2.934553 CACAGCGTCATCATCTGAACAT 59.065 45.455 0.00 0.00 35.07 2.71
1508 1623 0.179113 AACTTTGCGTTGCAGTTGGG 60.179 50.000 0.00 0.00 40.61 4.12
1538 1653 2.743636 GTGATCTCCACCAAACGAGA 57.256 50.000 0.00 0.00 39.86 4.04
1544 1659 1.302033 CCACCAAACGAGAGCTGCT 60.302 57.895 0.00 0.00 0.00 4.24
1630 1745 4.681483 GGTACTTCTACGTTTACACCACAC 59.319 45.833 0.00 0.00 0.00 3.82
1631 1746 4.389890 ACTTCTACGTTTACACCACACA 57.610 40.909 0.00 0.00 0.00 3.72
1633 1748 5.362263 ACTTCTACGTTTACACCACACATT 58.638 37.500 0.00 0.00 0.00 2.71
1634 1749 5.818857 ACTTCTACGTTTACACCACACATTT 59.181 36.000 0.00 0.00 0.00 2.32
1635 1750 5.910637 TCTACGTTTACACCACACATTTC 57.089 39.130 0.00 0.00 0.00 2.17
1636 1751 5.358090 TCTACGTTTACACCACACATTTCA 58.642 37.500 0.00 0.00 0.00 2.69
1637 1752 4.966965 ACGTTTACACCACACATTTCAA 57.033 36.364 0.00 0.00 0.00 2.69
1638 1753 4.915704 ACGTTTACACCACACATTTCAAG 58.084 39.130 0.00 0.00 0.00 3.02
1639 1754 4.396790 ACGTTTACACCACACATTTCAAGT 59.603 37.500 0.00 0.00 0.00 3.16
1640 1755 5.106078 ACGTTTACACCACACATTTCAAGTT 60.106 36.000 0.00 0.00 0.00 2.66
1641 1756 5.802956 CGTTTACACCACACATTTCAAGTTT 59.197 36.000 0.00 0.00 0.00 2.66
1642 1757 6.309251 CGTTTACACCACACATTTCAAGTTTT 59.691 34.615 0.00 0.00 0.00 2.43
1643 1758 7.485277 CGTTTACACCACACATTTCAAGTTTTA 59.515 33.333 0.00 0.00 0.00 1.52
1688 1804 9.981114 TTTGAAATTTCCATTTCTAGGTTCTTC 57.019 29.630 15.48 0.00 46.06 2.87
1699 1816 7.808279 TTTCTAGGTTCTTCTTAGGGATTGA 57.192 36.000 0.00 0.00 0.00 2.57
1725 1842 8.630917 ACTAGATAGCGCTTTCTTGTAGAATAA 58.369 33.333 31.41 14.36 33.67 1.40
1726 1843 9.632807 CTAGATAGCGCTTTCTTGTAGAATAAT 57.367 33.333 30.82 7.45 33.67 1.28
1733 1850 7.348201 CGCTTTCTTGTAGAATAATAGCCTTG 58.652 38.462 0.00 0.00 33.18 3.61
1765 1882 3.893326 GCCAAAATGTAGGGCATCTTT 57.107 42.857 0.00 0.00 46.92 2.52
1767 1884 3.679639 GCCAAAATGTAGGGCATCTTTGG 60.680 47.826 18.41 18.41 46.92 3.28
1776 1893 4.337264 AGGGCATCTTTGGATTTTACCT 57.663 40.909 0.00 0.00 0.00 3.08
1818 1948 4.761739 GTCTTGTTGGTCCATTCTGAATCA 59.238 41.667 0.00 0.00 0.00 2.57
1896 2026 7.972832 TTCTGAATGTTCTACAACCGTTTAT 57.027 32.000 0.00 0.00 0.00 1.40
1946 2076 2.368548 GGTTCTGCATTTTGGGGTTTCT 59.631 45.455 0.00 0.00 0.00 2.52
1948 2078 1.885887 TCTGCATTTTGGGGTTTCTCG 59.114 47.619 0.00 0.00 0.00 4.04
1967 2097 9.925268 GTTTCTCGAAACTGTAAGAAAACATAA 57.075 29.630 13.70 0.00 45.26 1.90
1988 2118 9.512588 ACATAAATATAGGGAATGCTCTGAAAG 57.487 33.333 0.00 0.00 0.00 2.62
2013 2150 3.963428 ACCCACAGACACTATGACTTC 57.037 47.619 0.00 0.00 0.00 3.01
2019 2156 4.876125 ACAGACACTATGACTTCTGTGTG 58.124 43.478 2.37 0.00 45.49 3.82
2025 2162 2.916702 ATGACTTCTGTGTGTGCAGA 57.083 45.000 0.00 0.00 43.03 4.26
2113 2253 6.017400 TGAATCTTTGCAAGTTCTCATTCC 57.983 37.500 16.89 0.00 0.00 3.01
2200 2340 1.672854 GCGGATAAGGTTTTGGGGCC 61.673 60.000 0.00 0.00 0.00 5.80
2475 2623 3.252458 AGCGGTTTTGGAAAGTGTATGAC 59.748 43.478 0.00 0.00 0.00 3.06
2482 2630 8.311109 GGTTTTGGAAAGTGTATGACCAATATT 58.689 33.333 0.00 0.00 39.75 1.28
2487 2635 6.238374 GGAAAGTGTATGACCAATATTGACGG 60.238 42.308 17.23 2.84 0.00 4.79
2504 2652 2.642139 CGGTTTCGTAGTCAGGCTTA 57.358 50.000 0.00 0.00 0.00 3.09
2507 2655 3.742369 CGGTTTCGTAGTCAGGCTTAAAA 59.258 43.478 0.00 0.00 0.00 1.52
2689 2837 0.472471 TTGGGGATATCCTTGACCGC 59.528 55.000 21.18 3.97 35.95 5.68
3182 3332 5.130477 ACATCGGTAAGTACATCCCAAATCT 59.870 40.000 0.00 0.00 0.00 2.40
3227 3377 5.664294 AATAACCAGCAGCATTTCATTCA 57.336 34.783 0.00 0.00 0.00 2.57
3300 3450 2.459555 ATTTCCCTCCAAATGCCGAT 57.540 45.000 0.00 0.00 0.00 4.18
3376 3526 1.643868 TAGCTTGCGAATTGGCACGG 61.644 55.000 15.22 11.67 43.82 4.94
3403 3553 4.703575 CCTGTTGTCCTGAATGTCAATGAT 59.296 41.667 0.00 0.00 0.00 2.45
3433 3583 1.693640 CCATGGTGGCCTTCTTCCT 59.306 57.895 3.32 0.00 0.00 3.36
3463 3613 1.658095 GAGTCGCTCAAGAGATTGTGC 59.342 52.381 0.32 5.25 37.88 4.57
3475 3625 2.221169 AGATTGTGCGTTTTGAGCTCA 58.779 42.857 13.74 13.74 36.49 4.26
3526 3676 3.611766 ACTGCACCTAGTATGTTCCAC 57.388 47.619 0.00 0.00 0.00 4.02
3560 3710 8.177663 CACATATTTCTGTAATTGGTCTGTGTC 58.822 37.037 0.00 0.00 0.00 3.67
3631 3781 3.937814 ACGCATCAACAAGGAAGTATCA 58.062 40.909 0.00 0.00 0.00 2.15
3651 3801 8.095792 AGTATCAAATTGGATGCAATGTTCAAA 58.904 29.630 13.66 0.00 32.99 2.69
3671 3821 4.406648 AATGAAGACAGCGATGATACCA 57.593 40.909 8.12 0.00 0.00 3.25
3685 3835 4.712051 TGATACCAATCTCCCCTTCATG 57.288 45.455 0.00 0.00 32.93 3.07
4354 4553 6.442513 AGCCTGCATGACTAGTAAAATTTC 57.557 37.500 0.00 0.00 0.00 2.17
4375 4574 7.967771 TTTCATATGTTGATGCACATAAACG 57.032 32.000 1.90 0.00 41.83 3.60
4588 4790 8.846423 TTAAATTCATCTCTCCTCTTAGTCCT 57.154 34.615 0.00 0.00 0.00 3.85
4622 4825 6.909357 GGTAAATCATCTTTGAAGAATCTGCG 59.091 38.462 0.00 0.00 38.77 5.18
4982 5187 9.284131 TCATTCTATGCCCCTACTGAAATATAT 57.716 33.333 0.00 0.00 0.00 0.86
5059 5264 6.708949 ACCTGTGTGTGTAAGTTACAATTAGG 59.291 38.462 17.16 19.19 40.93 2.69
5214 5419 3.417779 GTGGGGGTAAGGGAGGGC 61.418 72.222 0.00 0.00 0.00 5.19
5221 5426 2.120940 TAAGGGAGGGCGTGGACA 59.879 61.111 0.00 0.00 0.00 4.02
5225 5430 2.112297 GGAGGGCGTGGACAACAA 59.888 61.111 0.00 0.00 0.00 2.83
5287 5883 4.456280 TCACTCAGTCTTACATCGCAAT 57.544 40.909 0.00 0.00 0.00 3.56
5523 6120 9.149225 CCTAGAATGTTAATGTCTATGATGCTC 57.851 37.037 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.691362 CAGTGTAACCTTTTTGCTATTGTAATT 57.309 29.630 0.00 0.00 37.80 1.40
33 34 8.303876 CCAGTGTAACCTTTTTGCTATTGTAAT 58.696 33.333 0.00 0.00 37.80 1.89
34 35 7.502895 TCCAGTGTAACCTTTTTGCTATTGTAA 59.497 33.333 0.00 0.00 37.80 2.41
35 36 6.999272 TCCAGTGTAACCTTTTTGCTATTGTA 59.001 34.615 0.00 0.00 37.80 2.41
36 37 5.830991 TCCAGTGTAACCTTTTTGCTATTGT 59.169 36.000 0.00 0.00 37.80 2.71
37 38 6.325919 TCCAGTGTAACCTTTTTGCTATTG 57.674 37.500 0.00 0.00 37.80 1.90
38 39 7.539034 AATCCAGTGTAACCTTTTTGCTATT 57.461 32.000 0.00 0.00 37.80 1.73
39 40 7.539034 AAATCCAGTGTAACCTTTTTGCTAT 57.461 32.000 0.00 0.00 37.80 2.97
40 41 6.969993 AAATCCAGTGTAACCTTTTTGCTA 57.030 33.333 0.00 0.00 37.80 3.49
41 42 5.869649 AAATCCAGTGTAACCTTTTTGCT 57.130 34.783 0.00 0.00 37.80 3.91
42 43 5.236263 CCAAAATCCAGTGTAACCTTTTTGC 59.764 40.000 0.00 0.00 37.80 3.68
43 44 5.236263 GCCAAAATCCAGTGTAACCTTTTTG 59.764 40.000 0.00 0.00 37.80 2.44
44 45 5.130311 AGCCAAAATCCAGTGTAACCTTTTT 59.870 36.000 0.00 0.00 37.80 1.94
45 46 4.653801 AGCCAAAATCCAGTGTAACCTTTT 59.346 37.500 0.00 0.00 37.80 2.27
46 47 4.039124 CAGCCAAAATCCAGTGTAACCTTT 59.961 41.667 0.00 0.00 37.80 3.11
47 48 3.573967 CAGCCAAAATCCAGTGTAACCTT 59.426 43.478 0.00 0.00 37.80 3.50
48 49 3.157087 CAGCCAAAATCCAGTGTAACCT 58.843 45.455 0.00 0.00 37.80 3.50
49 50 2.352715 GCAGCCAAAATCCAGTGTAACC 60.353 50.000 0.00 0.00 37.80 2.85
50 51 2.352715 GGCAGCCAAAATCCAGTGTAAC 60.353 50.000 6.55 0.00 0.00 2.50
51 52 1.892474 GGCAGCCAAAATCCAGTGTAA 59.108 47.619 6.55 0.00 0.00 2.41
52 53 1.202989 TGGCAGCCAAAATCCAGTGTA 60.203 47.619 13.33 0.00 0.00 2.90
53 54 0.469705 TGGCAGCCAAAATCCAGTGT 60.470 50.000 13.33 0.00 0.00 3.55
54 55 0.037975 GTGGCAGCCAAAATCCAGTG 60.038 55.000 18.28 0.00 34.18 3.66
55 56 0.178953 AGTGGCAGCCAAAATCCAGT 60.179 50.000 18.28 0.00 34.18 4.00
56 57 1.838112 TAGTGGCAGCCAAAATCCAG 58.162 50.000 18.28 0.00 34.18 3.86
57 58 2.170166 CTTAGTGGCAGCCAAAATCCA 58.830 47.619 18.28 0.00 34.18 3.41
58 59 2.424956 CTCTTAGTGGCAGCCAAAATCC 59.575 50.000 18.28 2.71 34.18 3.01
59 60 2.424956 CCTCTTAGTGGCAGCCAAAATC 59.575 50.000 18.28 3.16 34.18 2.17
60 61 2.041620 TCCTCTTAGTGGCAGCCAAAAT 59.958 45.455 18.28 8.07 34.18 1.82
61 62 1.423541 TCCTCTTAGTGGCAGCCAAAA 59.576 47.619 18.28 12.95 34.18 2.44
62 63 1.003580 CTCCTCTTAGTGGCAGCCAAA 59.996 52.381 18.28 7.09 34.18 3.28
63 64 0.615331 CTCCTCTTAGTGGCAGCCAA 59.385 55.000 18.28 0.00 34.18 4.52
64 65 1.267574 CCTCCTCTTAGTGGCAGCCA 61.268 60.000 11.22 11.22 0.00 4.75
65 66 1.268283 ACCTCCTCTTAGTGGCAGCC 61.268 60.000 3.66 3.66 0.00 4.85
66 67 0.176910 GACCTCCTCTTAGTGGCAGC 59.823 60.000 0.00 0.00 0.00 5.25
67 68 0.457851 CGACCTCCTCTTAGTGGCAG 59.542 60.000 0.00 0.00 0.00 4.85
68 69 0.039180 TCGACCTCCTCTTAGTGGCA 59.961 55.000 0.00 0.00 0.00 4.92
69 70 0.741915 CTCGACCTCCTCTTAGTGGC 59.258 60.000 0.00 0.00 0.00 5.01
70 71 0.741915 GCTCGACCTCCTCTTAGTGG 59.258 60.000 0.00 0.00 0.00 4.00
71 72 0.378962 CGCTCGACCTCCTCTTAGTG 59.621 60.000 0.00 0.00 0.00 2.74
72 73 1.378124 GCGCTCGACCTCCTCTTAGT 61.378 60.000 0.00 0.00 0.00 2.24
73 74 1.357334 GCGCTCGACCTCCTCTTAG 59.643 63.158 0.00 0.00 0.00 2.18
74 75 2.119655 GGCGCTCGACCTCCTCTTA 61.120 63.158 7.64 0.00 0.00 2.10
75 76 3.453679 GGCGCTCGACCTCCTCTT 61.454 66.667 7.64 0.00 0.00 2.85
76 77 3.948004 AAGGCGCTCGACCTCCTCT 62.948 63.158 7.64 0.00 36.14 3.69
77 78 3.418744 GAAGGCGCTCGACCTCCTC 62.419 68.421 7.64 0.00 36.14 3.71
78 79 3.453679 GAAGGCGCTCGACCTCCT 61.454 66.667 7.64 0.00 36.14 3.69
79 80 3.418744 GAGAAGGCGCTCGACCTCC 62.419 68.421 7.64 0.00 36.14 4.30
80 81 2.103340 GAGAAGGCGCTCGACCTC 59.897 66.667 7.64 3.77 36.14 3.85
81 82 2.676822 TGAGAAGGCGCTCGACCT 60.677 61.111 7.64 0.00 40.02 3.85
82 83 2.507324 GTGAGAAGGCGCTCGACC 60.507 66.667 7.64 0.00 37.73 4.79
83 84 2.507324 GGTGAGAAGGCGCTCGAC 60.507 66.667 7.64 0.33 37.73 4.20
84 85 2.989253 TGGTGAGAAGGCGCTCGA 60.989 61.111 7.64 0.00 37.73 4.04
85 86 2.811317 GTGGTGAGAAGGCGCTCG 60.811 66.667 7.64 0.00 37.73 5.03
86 87 2.811317 CGTGGTGAGAAGGCGCTC 60.811 66.667 7.64 0.00 35.46 5.03
91 92 2.357517 AAGCGCGTGGTGAGAAGG 60.358 61.111 8.43 0.00 0.00 3.46
92 93 1.664649 TGAAGCGCGTGGTGAGAAG 60.665 57.895 8.43 0.00 0.00 2.85
93 94 1.954146 GTGAAGCGCGTGGTGAGAA 60.954 57.895 8.43 0.00 0.00 2.87
94 95 2.355837 GTGAAGCGCGTGGTGAGA 60.356 61.111 8.43 0.00 0.00 3.27
95 96 3.414700 GGTGAAGCGCGTGGTGAG 61.415 66.667 8.43 0.00 0.00 3.51
96 97 4.980805 GGGTGAAGCGCGTGGTGA 62.981 66.667 8.43 0.00 0.00 4.02
97 98 4.988598 AGGGTGAAGCGCGTGGTG 62.989 66.667 8.43 0.00 34.93 4.17
98 99 4.988598 CAGGGTGAAGCGCGTGGT 62.989 66.667 8.43 0.00 34.93 4.16
99 100 4.988598 ACAGGGTGAAGCGCGTGG 62.989 66.667 8.43 0.00 34.93 4.94
100 101 3.716006 CACAGGGTGAAGCGCGTG 61.716 66.667 8.43 0.00 35.23 5.34
101 102 4.988598 CCACAGGGTGAAGCGCGT 62.989 66.667 8.43 0.00 35.23 6.01
111 112 0.400213 TCTTAGCAACCACCACAGGG 59.600 55.000 0.00 0.00 41.29 4.45
112 113 1.611673 CCTCTTAGCAACCACCACAGG 60.612 57.143 0.00 0.00 0.00 4.00
113 114 1.072331 ACCTCTTAGCAACCACCACAG 59.928 52.381 0.00 0.00 0.00 3.66
114 115 1.136828 ACCTCTTAGCAACCACCACA 58.863 50.000 0.00 0.00 0.00 4.17
115 116 2.271944 AACCTCTTAGCAACCACCAC 57.728 50.000 0.00 0.00 0.00 4.16
116 117 2.582052 CAAACCTCTTAGCAACCACCA 58.418 47.619 0.00 0.00 0.00 4.17
117 118 1.886542 CCAAACCTCTTAGCAACCACC 59.113 52.381 0.00 0.00 0.00 4.61
118 119 1.886542 CCCAAACCTCTTAGCAACCAC 59.113 52.381 0.00 0.00 0.00 4.16
119 120 1.497286 ACCCAAACCTCTTAGCAACCA 59.503 47.619 0.00 0.00 0.00 3.67
120 121 1.886542 CACCCAAACCTCTTAGCAACC 59.113 52.381 0.00 0.00 0.00 3.77
121 122 1.886542 CCACCCAAACCTCTTAGCAAC 59.113 52.381 0.00 0.00 0.00 4.17
122 123 1.203001 CCCACCCAAACCTCTTAGCAA 60.203 52.381 0.00 0.00 0.00 3.91
123 124 0.404040 CCCACCCAAACCTCTTAGCA 59.596 55.000 0.00 0.00 0.00 3.49
124 125 0.323451 CCCCACCCAAACCTCTTAGC 60.323 60.000 0.00 0.00 0.00 3.09
125 126 0.323451 GCCCCACCCAAACCTCTTAG 60.323 60.000 0.00 0.00 0.00 2.18
126 127 1.771646 GCCCCACCCAAACCTCTTA 59.228 57.895 0.00 0.00 0.00 2.10
127 128 2.526110 GCCCCACCCAAACCTCTT 59.474 61.111 0.00 0.00 0.00 2.85
128 129 3.966543 CGCCCCACCCAAACCTCT 61.967 66.667 0.00 0.00 0.00 3.69
129 130 4.280019 ACGCCCCACCCAAACCTC 62.280 66.667 0.00 0.00 0.00 3.85
130 131 4.596585 CACGCCCCACCCAAACCT 62.597 66.667 0.00 0.00 0.00 3.50
131 132 4.906537 ACACGCCCCACCCAAACC 62.907 66.667 0.00 0.00 0.00 3.27
132 133 3.601685 CACACGCCCCACCCAAAC 61.602 66.667 0.00 0.00 0.00 2.93
133 134 4.130554 ACACACGCCCCACCCAAA 62.131 61.111 0.00 0.00 0.00 3.28
134 135 4.885270 CACACACGCCCCACCCAA 62.885 66.667 0.00 0.00 0.00 4.12
143 144 3.976701 ATAGCCCTGCCACACACGC 62.977 63.158 0.00 0.00 0.00 5.34
144 145 2.108514 CATAGCCCTGCCACACACG 61.109 63.158 0.00 0.00 0.00 4.49
145 146 1.750399 CCATAGCCCTGCCACACAC 60.750 63.158 0.00 0.00 0.00 3.82
146 147 2.230653 ACCATAGCCCTGCCACACA 61.231 57.895 0.00 0.00 0.00 3.72
147 148 1.750399 CACCATAGCCCTGCCACAC 60.750 63.158 0.00 0.00 0.00 3.82
148 149 2.196997 GACACCATAGCCCTGCCACA 62.197 60.000 0.00 0.00 0.00 4.17
149 150 1.452108 GACACCATAGCCCTGCCAC 60.452 63.158 0.00 0.00 0.00 5.01
150 151 2.998097 GACACCATAGCCCTGCCA 59.002 61.111 0.00 0.00 0.00 4.92
151 152 2.203070 CGACACCATAGCCCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
152 153 2.028125 TAGCGACACCATAGCCCTGC 62.028 60.000 0.00 0.00 0.00 4.85
153 154 0.032678 CTAGCGACACCATAGCCCTG 59.967 60.000 0.00 0.00 0.00 4.45
154 155 0.106167 TCTAGCGACACCATAGCCCT 60.106 55.000 0.00 0.00 0.00 5.19
155 156 0.969894 ATCTAGCGACACCATAGCCC 59.030 55.000 0.00 0.00 0.00 5.19
194 195 2.224523 CCACCACTCAAAACCTCTAGCA 60.225 50.000 0.00 0.00 0.00 3.49
209 210 2.595009 GATCCTTCTCGCCCCACCAC 62.595 65.000 0.00 0.00 0.00 4.16
210 211 2.285368 ATCCTTCTCGCCCCACCA 60.285 61.111 0.00 0.00 0.00 4.17
222 223 5.301805 AGACATGTTTTCGTTTTGGATCCTT 59.698 36.000 14.23 0.00 0.00 3.36
223 224 4.827284 AGACATGTTTTCGTTTTGGATCCT 59.173 37.500 14.23 0.00 0.00 3.24
231 232 1.877443 CCCCGAGACATGTTTTCGTTT 59.123 47.619 23.44 0.00 32.73 3.60
236 237 1.905637 GGTTCCCCGAGACATGTTTT 58.094 50.000 0.00 0.00 0.00 2.43
237 238 3.644861 GGTTCCCCGAGACATGTTT 57.355 52.632 0.00 0.00 0.00 2.83
250 251 1.957765 GACTCCTGGCCTACGGTTCC 61.958 65.000 3.32 0.00 0.00 3.62
252 253 0.617820 ATGACTCCTGGCCTACGGTT 60.618 55.000 3.32 0.00 0.00 4.44
253 254 1.001760 ATGACTCCTGGCCTACGGT 59.998 57.895 3.32 0.00 0.00 4.83
274 276 7.441157 TCATAAGGCATAAATGAGGTTTAGTCG 59.559 37.037 0.00 0.00 35.83 4.18
307 310 3.077907 CCCTCCTTTCTCCGCCAA 58.922 61.111 0.00 0.00 0.00 4.52
309 312 4.840005 CGCCCTCCTTTCTCCGCC 62.840 72.222 0.00 0.00 0.00 6.13
354 357 9.816787 AAATAAGTAAGGTTCATTTTCCTACCA 57.183 29.630 0.00 0.00 33.27 3.25
516 524 5.018809 TGGTAAACTCTAATACCGACCAGT 58.981 41.667 0.00 0.00 43.71 4.00
564 572 0.037975 TCTACCACCTTTTCGTCCGC 60.038 55.000 0.00 0.00 0.00 5.54
589 597 6.560253 ATGTAAAGATTCTTGCGTCAACTT 57.440 33.333 0.00 0.00 0.00 2.66
702 738 1.007600 TCTCATGGGCTTCTCCTCTCA 59.992 52.381 0.00 0.00 34.39 3.27
728 764 0.472734 AAGCCACACACCCTCTCTCT 60.473 55.000 0.00 0.00 0.00 3.10
814 850 2.049433 ACTGTCTTCGTTCGGCCG 60.049 61.111 22.12 22.12 0.00 6.13
815 851 0.389948 ATGACTGTCTTCGTTCGGCC 60.390 55.000 9.51 0.00 0.00 6.13
817 853 1.630148 GGATGACTGTCTTCGTTCGG 58.370 55.000 15.01 0.00 0.00 4.30
820 856 0.317160 TGCGGATGACTGTCTTCGTT 59.683 50.000 15.01 0.00 0.00 3.85
821 857 0.317160 TTGCGGATGACTGTCTTCGT 59.683 50.000 15.01 0.00 0.00 3.85
994 1038 3.950794 GAAGGACGGCCATGTCGCA 62.951 63.158 11.69 0.00 39.83 5.10
1065 1115 1.400142 CTGCTAGGACAGACGACAGAG 59.600 57.143 0.00 0.00 40.25 3.35
1137 1187 1.283181 GGAGACGATGATCGGTCCG 59.717 63.158 19.82 4.39 45.59 4.79
1161 1211 4.047059 GAGACGAACGTGGGCGGA 62.047 66.667 4.19 0.00 43.45 5.54
1233 1283 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
1263 1313 9.650539 CTGTCTATTTCTTCAGAATCAGAAAGA 57.349 33.333 10.20 0.00 41.26 2.52
1264 1314 8.389603 GCTGTCTATTTCTTCAGAATCAGAAAG 58.610 37.037 10.90 10.90 41.26 2.62
1265 1315 8.099537 AGCTGTCTATTTCTTCAGAATCAGAAA 58.900 33.333 0.00 0.00 41.97 2.52
1266 1316 7.619050 AGCTGTCTATTTCTTCAGAATCAGAA 58.381 34.615 0.00 0.00 33.54 3.02
1267 1317 7.123997 AGAGCTGTCTATTTCTTCAGAATCAGA 59.876 37.037 0.00 0.00 33.54 3.27
1268 1318 7.223193 CAGAGCTGTCTATTTCTTCAGAATCAG 59.777 40.741 0.00 0.00 33.54 2.90
1269 1319 7.040494 CAGAGCTGTCTATTTCTTCAGAATCA 58.960 38.462 0.00 0.00 33.54 2.57
1270 1320 6.018832 GCAGAGCTGTCTATTTCTTCAGAATC 60.019 42.308 0.00 0.00 33.54 2.52
1271 1321 5.816777 GCAGAGCTGTCTATTTCTTCAGAAT 59.183 40.000 0.00 0.00 33.54 2.40
1402 1468 2.926778 TGGCAAAATTTCCCACCAAG 57.073 45.000 6.46 0.00 0.00 3.61
1409 1475 8.831715 TCTTCTTTTCTATTGGCAAAATTTCC 57.168 30.769 3.01 0.00 0.00 3.13
1412 1478 9.702494 CTCTTCTTCTTTTCTATTGGCAAAATT 57.298 29.630 3.01 0.00 0.00 1.82
1413 1479 8.864087 ACTCTTCTTCTTTTCTATTGGCAAAAT 58.136 29.630 3.01 0.00 0.00 1.82
1414 1480 8.137437 CACTCTTCTTCTTTTCTATTGGCAAAA 58.863 33.333 3.01 0.00 0.00 2.44
1415 1481 7.502226 TCACTCTTCTTCTTTTCTATTGGCAAA 59.498 33.333 3.01 0.00 0.00 3.68
1416 1482 6.998074 TCACTCTTCTTCTTTTCTATTGGCAA 59.002 34.615 0.68 0.68 0.00 4.52
1417 1483 6.428159 GTCACTCTTCTTCTTTTCTATTGGCA 59.572 38.462 0.00 0.00 0.00 4.92
1418 1484 6.428159 TGTCACTCTTCTTCTTTTCTATTGGC 59.572 38.462 0.00 0.00 0.00 4.52
1422 1488 6.159988 CCGTGTCACTCTTCTTCTTTTCTAT 58.840 40.000 0.65 0.00 0.00 1.98
1440 1506 5.360591 AGATAAATTCCTCATGACCGTGTC 58.639 41.667 0.00 0.00 0.00 3.67
1444 1510 6.316140 TGTGAAAGATAAATTCCTCATGACCG 59.684 38.462 0.00 0.00 0.00 4.79
1445 1511 7.630242 TGTGAAAGATAAATTCCTCATGACC 57.370 36.000 0.00 0.00 0.00 4.02
1446 1512 7.192232 GCTGTGAAAGATAAATTCCTCATGAC 58.808 38.462 0.00 0.00 0.00 3.06
1447 1513 6.037500 CGCTGTGAAAGATAAATTCCTCATGA 59.962 38.462 0.00 0.00 0.00 3.07
1448 1514 6.183360 ACGCTGTGAAAGATAAATTCCTCATG 60.183 38.462 0.00 0.00 0.00 3.07
1450 1516 5.245531 ACGCTGTGAAAGATAAATTCCTCA 58.754 37.500 0.00 0.00 0.00 3.86
1451 1517 5.351465 TGACGCTGTGAAAGATAAATTCCTC 59.649 40.000 0.00 0.00 0.00 3.71
1452 1518 5.245531 TGACGCTGTGAAAGATAAATTCCT 58.754 37.500 0.00 0.00 0.00 3.36
1453 1519 5.545658 TGACGCTGTGAAAGATAAATTCC 57.454 39.130 0.00 0.00 0.00 3.01
1455 1521 6.741992 TGATGACGCTGTGAAAGATAAATT 57.258 33.333 0.00 0.00 0.00 1.82
1456 1522 6.765036 AGATGATGACGCTGTGAAAGATAAAT 59.235 34.615 0.00 0.00 0.00 1.40
1457 1523 6.036408 CAGATGATGACGCTGTGAAAGATAAA 59.964 38.462 0.00 0.00 0.00 1.40
1458 1524 5.521372 CAGATGATGACGCTGTGAAAGATAA 59.479 40.000 0.00 0.00 0.00 1.75
1459 1525 5.045872 CAGATGATGACGCTGTGAAAGATA 58.954 41.667 0.00 0.00 0.00 1.98
1460 1526 3.869832 CAGATGATGACGCTGTGAAAGAT 59.130 43.478 0.00 0.00 0.00 2.40
1461 1527 3.056607 TCAGATGATGACGCTGTGAAAGA 60.057 43.478 0.00 0.00 31.12 2.52
1463 1529 3.317603 TCAGATGATGACGCTGTGAAA 57.682 42.857 0.00 0.00 31.12 2.69
1464 1530 2.995939 GTTCAGATGATGACGCTGTGAA 59.004 45.455 0.00 0.00 37.77 3.18
1465 1531 2.029110 TGTTCAGATGATGACGCTGTGA 60.029 45.455 0.00 0.00 37.77 3.58
1466 1532 2.340337 TGTTCAGATGATGACGCTGTG 58.660 47.619 0.00 0.00 37.77 3.66
1467 1533 2.749280 TGTTCAGATGATGACGCTGT 57.251 45.000 0.00 0.00 37.77 4.40
1468 1534 3.192466 TCATGTTCAGATGATGACGCTG 58.808 45.455 0.00 0.00 37.77 5.18
1470 1536 3.620374 AGTTCATGTTCAGATGATGACGC 59.380 43.478 0.00 0.00 37.77 5.19
1471 1537 5.791367 AAGTTCATGTTCAGATGATGACG 57.209 39.130 0.00 0.00 37.77 4.35
1472 1538 5.798934 GCAAAGTTCATGTTCAGATGATGAC 59.201 40.000 0.00 0.00 37.77 3.06
1474 1540 4.791676 CGCAAAGTTCATGTTCAGATGATG 59.208 41.667 0.00 0.00 32.35 3.07
1475 1541 4.456911 ACGCAAAGTTCATGTTCAGATGAT 59.543 37.500 0.00 0.00 32.35 2.45
1476 1542 3.814842 ACGCAAAGTTCATGTTCAGATGA 59.185 39.130 0.00 0.00 0.00 2.92
1487 1602 1.468908 CCAACTGCAACGCAAAGTTCA 60.469 47.619 0.00 0.00 42.02 3.18
1538 1653 2.271497 GCCATCACCAGAGCAGCT 59.729 61.111 0.00 0.00 0.00 4.24
1544 1659 2.927856 ACACCGGCCATCACCAGA 60.928 61.111 0.00 0.00 0.00 3.86
1688 1804 4.461081 AGCGCTATCTAGTCAATCCCTAAG 59.539 45.833 8.99 0.00 0.00 2.18
1699 1816 6.452494 TTCTACAAGAAAGCGCTATCTAGT 57.548 37.500 12.05 10.21 29.99 2.57
1725 1842 3.118000 GGCAAGTAGGTTACCAAGGCTAT 60.118 47.826 3.51 0.00 0.00 2.97
1726 1843 2.237893 GGCAAGTAGGTTACCAAGGCTA 59.762 50.000 3.51 0.00 0.00 3.93
1727 1844 1.004394 GGCAAGTAGGTTACCAAGGCT 59.996 52.381 3.51 0.00 0.00 4.58
1733 1850 5.124936 CCTACATTTTGGCAAGTAGGTTACC 59.875 44.000 25.12 0.00 45.38 2.85
1818 1948 4.218417 GTCTAACCAAGCACCACAATTCAT 59.782 41.667 0.00 0.00 0.00 2.57
1896 2026 2.327325 AAGTGGGCTAGAGTTCAGGA 57.673 50.000 0.00 0.00 0.00 3.86
1962 2092 9.512588 CTTTCAGAGCATTCCCTATATTTATGT 57.487 33.333 0.00 0.00 0.00 2.29
1967 2097 6.904626 ACACTTTCAGAGCATTCCCTATATT 58.095 36.000 0.00 0.00 0.00 1.28
2182 2322 0.033503 AGGCCCCAAAACCTTATCCG 60.034 55.000 0.00 0.00 29.74 4.18
2230 2370 8.570038 TGGTATGGGAAATTACTATAACAGGA 57.430 34.615 0.00 0.00 0.00 3.86
2438 2580 3.695830 ACCGCTTAAATCCTTGTCTGA 57.304 42.857 0.00 0.00 0.00 3.27
2439 2581 4.766404 AAACCGCTTAAATCCTTGTCTG 57.234 40.909 0.00 0.00 0.00 3.51
2440 2582 4.022329 CCAAAACCGCTTAAATCCTTGTCT 60.022 41.667 0.00 0.00 0.00 3.41
2442 2584 3.892588 TCCAAAACCGCTTAAATCCTTGT 59.107 39.130 0.00 0.00 0.00 3.16
2448 2591 5.270893 ACACTTTCCAAAACCGCTTAAAT 57.729 34.783 0.00 0.00 0.00 1.40
2475 2623 4.865925 TGACTACGAAACCGTCAATATTGG 59.134 41.667 15.36 2.23 41.06 3.16
2482 2630 0.038892 GCCTGACTACGAAACCGTCA 60.039 55.000 0.00 0.00 41.06 4.35
2487 2635 4.376717 CGGTTTTAAGCCTGACTACGAAAC 60.377 45.833 0.00 0.00 0.00 2.78
2504 2652 2.927028 AGTAGTGCTTGGTTCGGTTTT 58.073 42.857 0.00 0.00 0.00 2.43
2507 2655 2.632987 AAAGTAGTGCTTGGTTCGGT 57.367 45.000 0.00 0.00 37.52 4.69
2689 2837 4.747108 AGTATTGCGATTTCATCTTCTCCG 59.253 41.667 0.00 0.00 0.00 4.63
2824 2972 6.470557 TTCCGTTTACCTAACATTTTCTCG 57.529 37.500 0.00 0.00 36.50 4.04
3080 3230 7.446931 TGGTTAATTGAACAAGCTCAGTCATTA 59.553 33.333 0.00 0.00 40.09 1.90
3138 3288 7.849026 CCGATGTAGTAAAATTGGAAATGTACG 59.151 37.037 0.00 0.00 29.78 3.67
3300 3450 5.335348 GCAGCGAACCCTTTATTTTTCTGTA 60.335 40.000 0.00 0.00 0.00 2.74
3376 3526 2.421424 GACATTCAGGACAACAGGATGC 59.579 50.000 0.00 0.00 42.53 3.91
3403 3553 1.347050 CCACCATGGCAAAACATCCAA 59.653 47.619 13.04 0.00 35.75 3.53
3433 3583 1.185315 TGAGCGACTCACCATGATGA 58.815 50.000 5.59 0.00 35.39 2.92
3463 3613 4.145876 TGTAAATGCTGAGCTCAAAACG 57.854 40.909 18.85 7.12 0.00 3.60
3465 3615 6.864685 CAGAATTGTAAATGCTGAGCTCAAAA 59.135 34.615 18.85 9.20 0.00 2.44
3507 3657 3.895232 AGTGGAACATACTAGGTGCAG 57.105 47.619 0.00 0.00 44.52 4.41
3508 3658 3.580895 TCAAGTGGAACATACTAGGTGCA 59.419 43.478 0.00 0.00 44.52 4.57
3509 3659 4.202245 TCAAGTGGAACATACTAGGTGC 57.798 45.455 0.00 0.00 44.52 5.01
3549 3699 6.611613 AGAATCTTAGATGACACAGACCAA 57.388 37.500 0.00 0.00 0.00 3.67
3550 3700 7.397476 ACTTAGAATCTTAGATGACACAGACCA 59.603 37.037 3.05 0.00 0.00 4.02
3551 3701 7.777095 ACTTAGAATCTTAGATGACACAGACC 58.223 38.462 3.05 0.00 0.00 3.85
3552 3702 7.918562 GGACTTAGAATCTTAGATGACACAGAC 59.081 40.741 3.05 0.00 0.00 3.51
3553 3703 7.615757 TGGACTTAGAATCTTAGATGACACAGA 59.384 37.037 3.05 0.00 0.00 3.41
3554 3704 7.776107 TGGACTTAGAATCTTAGATGACACAG 58.224 38.462 3.05 0.00 0.00 3.66
3555 3705 7.718334 TGGACTTAGAATCTTAGATGACACA 57.282 36.000 3.05 0.00 0.00 3.72
3560 3710 9.050601 GTGGAAATGGACTTAGAATCTTAGATG 57.949 37.037 3.05 0.00 0.00 2.90
3631 3781 7.662258 TCTTCATTTGAACATTGCATCCAATTT 59.338 29.630 0.00 0.00 39.60 1.82
3651 3801 4.406648 TTGGTATCATCGCTGTCTTCAT 57.593 40.909 0.00 0.00 0.00 2.57
3671 3821 1.777272 GGTAGCCATGAAGGGGAGATT 59.223 52.381 0.00 0.00 38.09 2.40
3685 3835 3.006323 CACTGTCATATCCTCTGGTAGCC 59.994 52.174 0.00 0.00 0.00 3.93
3757 3907 3.453717 TGGATCTTCTCACATCCCAAGAG 59.546 47.826 0.00 0.00 38.29 2.85
4354 4553 6.257423 ACACGTTTATGTGCATCAACATATG 58.743 36.000 0.00 0.00 43.74 1.78
4588 4790 7.831691 TCAAAGATGATTTACCCAGTTTTGA 57.168 32.000 0.00 0.00 32.47 2.69
4784 4989 2.357952 GTGTCCACCCAAAACTGTCTTC 59.642 50.000 0.00 0.00 0.00 2.87
4847 5052 1.890489 GTTATGGAAAGCCGGTTGGTT 59.110 47.619 1.90 0.00 37.67 3.67
4982 5187 6.539173 TCAAATTAGCTACTTTGGAAGACCA 58.461 36.000 26.92 10.68 45.34 4.02
5059 5264 7.672983 TTCATGTATTCTGGAGTTGTTCTTC 57.327 36.000 0.00 0.00 0.00 2.87
5214 5419 9.787532 AAAATATTCAGATATTTGTTGTCCACG 57.212 29.630 5.44 0.00 44.00 4.94
5287 5883 1.202568 CCTCATGAGCAAGCCGATACA 60.203 52.381 17.76 0.00 0.00 2.29
5491 6088 9.265901 CATAGACATTAACATTCTAGGTGAAGG 57.734 37.037 3.50 0.00 41.68 3.46


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

AutoCloner maintained by Alex Coulton.