Multiple sequence alignment - TraesCS2B01G309000

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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 TraesCS2B01G309000 chr2B 100.000 2894 0 0 1 2894 442309170 442306277 0.000000e+00 5345
1 TraesCS2B01G309000 chr2B 92.381 105 8 0 2568 2672 751263678 751263574 1.800000e-32 150
2 TraesCS2B01G309000 chr2B 93.069 101 6 1 2573 2672 13713005 13713105 2.320000e-31 147
3 TraesCS2B01G309000 chr2B 90.090 111 7 4 129 238 801152258 801152365 1.080000e-29 141
4 TraesCS2B01G309000 chr2D 93.433 1203 42 17 1411 2587 372696057 372694866 0.000000e+00 1749
5 TraesCS2B01G309000 chr2D 87.512 1017 50 32 280 1261 372697104 372696130 0.000000e+00 1103
6 TraesCS2B01G309000 chr2D 88.462 156 2 2 1 145 372697327 372697177 1.070000e-39 174
7 TraesCS2B01G309000 chr2D 82.915 199 6 6 2669 2867 372694868 372694698 1.390000e-33 154
8 TraesCS2B01G309000 chr2D 92.784 97 5 2 150 245 567672301 567672206 3.890000e-29 139
9 TraesCS2B01G309000 chr2A 87.443 876 56 22 1763 2587 504071596 504070724 0.000000e+00 959
10 TraesCS2B01G309000 chr2A 82.336 1019 55 42 280 1252 504073157 504072218 0.000000e+00 769
11 TraesCS2B01G309000 chr2A 91.860 344 20 5 1403 1741 504072024 504071684 9.390000e-130 473
12 TraesCS2B01G309000 chr2A 86.740 181 8 8 2687 2867 504070713 504070549 1.370000e-43 187
13 TraesCS2B01G309000 chr2A 95.789 95 4 0 2586 2680 153361939 153361845 1.390000e-33 154
14 TraesCS2B01G309000 chr2A 87.681 138 2 3 1 127 504073380 504073247 2.320000e-31 147
15 TraesCS2B01G309000 chr6B 96.809 94 3 0 2586 2679 120317858 120317765 1.070000e-34 158
16 TraesCS2B01G309000 chrUn 95.000 100 4 1 2586 2684 48472309 48472408 3.860000e-34 156
17 TraesCS2B01G309000 chrUn 95.000 100 4 1 2586 2684 235114410 235114509 3.860000e-34 156
18 TraesCS2B01G309000 chrUn 95.000 100 4 1 2586 2684 433967194 433967095 3.860000e-34 156
19 TraesCS2B01G309000 chr1D 95.833 96 2 2 153 247 348120773 348120867 1.390000e-33 154
20 TraesCS2B01G309000 chr3B 93.204 103 5 2 2586 2687 827868255 827868154 1.800000e-32 150
21 TraesCS2B01G309000 chr3B 91.346 104 7 2 149 251 447014541 447014643 1.080000e-29 141
22 TraesCS2B01G309000 chr7D 95.652 92 4 0 147 238 220083644 220083735 6.460000e-32 148
23 TraesCS2B01G309000 chr7D 95.652 92 4 0 147 238 220096423 220096514 6.460000e-32 148
24 TraesCS2B01G309000 chr1A 93.814 97 5 1 150 245 548772383 548772287 8.360000e-31 145
25 TraesCS2B01G309000 chr1A 90.741 108 8 2 2582 2689 287303250 287303355 3.010000e-30 143
26 TraesCS2B01G309000 chr6D 91.429 105 8 1 152 256 58042759 58042862 3.010000e-30 143
27 TraesCS2B01G309000 chr4D 91.429 105 6 3 135 239 47533167 47533268 1.080000e-29 141


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 TraesCS2B01G309000 chr2B 442306277 442309170 2893 True 5345 5345 100.0000 1 2894 1 chr2B.!!$R1 2893
1 TraesCS2B01G309000 chr2D 372694698 372697327 2629 True 795 1749 88.0805 1 2867 4 chr2D.!!$R2 2866
2 TraesCS2B01G309000 chr2A 504070549 504073380 2831 True 507 959 87.2120 1 2867 5 chr2A.!!$R2 2866

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
989 1116 0.253207 GGGAGGAAGGAAGGGAGGAA 60.253 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2872 3218 0.179089 CTCATCAGTCCTTGCTCCGG 60.179 60.0 0.0 0.0 0.0 5.14 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
145 168 4.369182 CAACCCAAAGCTACCTATCTACG 58.631 47.826 0.00 0.00 0.00 3.51
146 169 3.639952 ACCCAAAGCTACCTATCTACGT 58.360 45.455 0.00 0.00 0.00 3.57
147 170 4.796606 ACCCAAAGCTACCTATCTACGTA 58.203 43.478 0.00 0.00 0.00 3.57
149 172 5.476254 ACCCAAAGCTACCTATCTACGTATC 59.524 44.000 0.00 0.00 0.00 2.24
150 173 5.711036 CCCAAAGCTACCTATCTACGTATCT 59.289 44.000 0.00 0.00 0.00 1.98
151 174 6.883217 CCCAAAGCTACCTATCTACGTATCTA 59.117 42.308 0.00 0.00 0.00 1.98
152 175 7.066043 CCCAAAGCTACCTATCTACGTATCTAG 59.934 44.444 0.00 0.27 0.00 2.43
153 176 7.607223 CCAAAGCTACCTATCTACGTATCTAGT 59.393 40.741 0.00 0.00 0.00 2.57
154 177 9.650539 CAAAGCTACCTATCTACGTATCTAGTA 57.349 37.037 0.00 0.00 0.00 1.82
155 178 9.651913 AAAGCTACCTATCTACGTATCTAGTAC 57.348 37.037 0.00 0.00 0.00 2.73
156 179 8.593945 AGCTACCTATCTACGTATCTAGTACT 57.406 38.462 0.00 0.00 0.00 2.73
157 180 8.686334 AGCTACCTATCTACGTATCTAGTACTC 58.314 40.741 0.00 0.00 0.00 2.59
158 181 7.920682 GCTACCTATCTACGTATCTAGTACTCC 59.079 44.444 0.00 0.00 0.00 3.85
159 182 7.181569 ACCTATCTACGTATCTAGTACTCCC 57.818 44.000 0.00 0.00 0.00 4.30
160 183 6.959366 ACCTATCTACGTATCTAGTACTCCCT 59.041 42.308 0.00 0.00 0.00 4.20
161 184 7.124147 ACCTATCTACGTATCTAGTACTCCCTC 59.876 44.444 0.00 0.00 0.00 4.30
162 185 6.931790 ATCTACGTATCTAGTACTCCCTCA 57.068 41.667 0.00 0.00 0.00 3.86
163 186 6.343716 TCTACGTATCTAGTACTCCCTCAG 57.656 45.833 0.00 0.00 0.00 3.35
164 187 5.837979 TCTACGTATCTAGTACTCCCTCAGT 59.162 44.000 0.00 0.00 39.41 3.41
165 188 7.007116 TCTACGTATCTAGTACTCCCTCAGTA 58.993 42.308 0.00 0.00 36.43 2.74
166 189 6.491714 ACGTATCTAGTACTCCCTCAGTAA 57.508 41.667 0.00 0.00 39.44 2.24
167 190 6.893583 ACGTATCTAGTACTCCCTCAGTAAA 58.106 40.000 0.00 0.00 39.44 2.01
168 191 6.765512 ACGTATCTAGTACTCCCTCAGTAAAC 59.234 42.308 0.00 0.00 39.44 2.01
169 192 6.991531 CGTATCTAGTACTCCCTCAGTAAACT 59.008 42.308 0.00 0.00 39.44 2.66
170 193 8.147058 CGTATCTAGTACTCCCTCAGTAAACTA 58.853 40.741 0.00 0.00 39.44 2.24
171 194 9.844257 GTATCTAGTACTCCCTCAGTAAACTAA 57.156 37.037 0.00 0.00 39.44 2.24
180 203 8.862085 ACTCCCTCAGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 31.37 4.09
181 204 7.883217 TCCCTCAGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
182 205 7.504911 TCCCTCAGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
183 206 8.142551 CCCTCAGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
184 207 9.530633 CCTCAGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
212 235 9.413048 GATAACTAAAATAGTGATCTAAGCGCT 57.587 33.333 2.64 2.64 41.55 5.92
213 236 7.701809 AACTAAAATAGTGATCTAAGCGCTC 57.298 36.000 12.06 0.00 39.39 5.03
214 237 7.045126 ACTAAAATAGTGATCTAAGCGCTCT 57.955 36.000 12.06 3.67 37.69 4.09
215 238 7.493367 ACTAAAATAGTGATCTAAGCGCTCTT 58.507 34.615 12.06 0.00 37.69 2.85
216 239 8.630917 ACTAAAATAGTGATCTAAGCGCTCTTA 58.369 33.333 12.06 0.00 37.69 2.10
217 240 9.632807 CTAAAATAGTGATCTAAGCGCTCTTAT 57.367 33.333 12.06 3.87 34.54 1.73
223 246 8.343168 AGTGATCTAAGCGCTCTTATATTAGT 57.657 34.615 12.06 0.00 34.54 2.24
224 247 8.798402 AGTGATCTAAGCGCTCTTATATTAGTT 58.202 33.333 12.06 1.51 34.54 2.24
225 248 9.413048 GTGATCTAAGCGCTCTTATATTAGTTT 57.587 33.333 12.06 0.00 34.54 2.66
229 252 9.894783 TCTAAGCGCTCTTATATTAGTTTACAG 57.105 33.333 12.06 0.00 34.54 2.74
230 253 9.894783 CTAAGCGCTCTTATATTAGTTTACAGA 57.105 33.333 12.06 0.00 34.54 3.41
231 254 8.804688 AAGCGCTCTTATATTAGTTTACAGAG 57.195 34.615 12.06 0.00 0.00 3.35
232 255 7.371936 AGCGCTCTTATATTAGTTTACAGAGG 58.628 38.462 2.64 0.00 0.00 3.69
233 256 6.586844 GCGCTCTTATATTAGTTTACAGAGGG 59.413 42.308 0.00 0.00 40.81 4.30
249 272 4.093011 CAGAGGGAGTATAGCTTAGCCAT 58.907 47.826 0.00 0.00 0.00 4.40
257 288 6.205658 GGAGTATAGCTTAGCCATTCAAAAGG 59.794 42.308 0.00 0.00 0.00 3.11
267 298 3.313690 CCATTCAAAAGGTACGCCAAAC 58.686 45.455 0.00 0.00 37.19 2.93
278 309 2.661537 GCCAAACGGCCAAAGTGC 60.662 61.111 2.24 0.00 44.46 4.40
292 348 5.473039 GCCAAAGTGCAAAGAAAGACATAT 58.527 37.500 0.00 0.00 0.00 1.78
376 436 0.464013 GTCCGATCCCTGTCGAGAGA 60.464 60.000 11.84 0.00 44.06 3.10
457 521 1.005037 CGGCAGCTCACCTAACACA 60.005 57.895 0.00 0.00 0.00 3.72
515 590 4.566759 ACAATACGATCGACATGGTTTCTG 59.433 41.667 24.34 10.30 0.00 3.02
516 591 2.010145 ACGATCGACATGGTTTCTGG 57.990 50.000 24.34 0.00 0.00 3.86
517 592 0.652592 CGATCGACATGGTTTCTGGC 59.347 55.000 10.26 0.00 0.00 4.85
518 593 1.740380 CGATCGACATGGTTTCTGGCT 60.740 52.381 10.26 0.00 0.00 4.75
519 594 1.667724 GATCGACATGGTTTCTGGCTG 59.332 52.381 0.00 0.00 0.00 4.85
551 631 3.786901 TTGGTTCGGCGCACGTACA 62.787 57.895 22.00 14.77 43.59 2.90
552 632 2.812178 GGTTCGGCGCACGTACAT 60.812 61.111 22.00 0.00 43.59 2.29
553 633 1.516821 GGTTCGGCGCACGTACATA 60.517 57.895 22.00 2.56 43.59 2.29
554 634 1.627424 GTTCGGCGCACGTACATAC 59.373 57.895 10.83 2.82 41.73 2.39
563 643 4.207203 CGTACATACGCTCCTCGC 57.793 61.111 0.00 0.00 43.14 5.03
616 700 3.009723 TGAAATGATGCTTCCGTCCTTC 58.990 45.455 0.00 0.00 0.00 3.46
624 708 2.280628 GCTTCCGTCCTTCGATTTGAT 58.719 47.619 0.00 0.00 42.86 2.57
635 719 2.557317 TCGATTTGATTTACCTCCGCC 58.443 47.619 0.00 0.00 0.00 6.13
666 758 2.958365 TTTCCTACCCGGGCCCCTA 61.958 63.158 24.08 4.00 0.00 3.53
695 792 3.423154 CGCAGCCGTTTCACCTCC 61.423 66.667 0.00 0.00 0.00 4.30
696 793 2.281484 GCAGCCGTTTCACCTCCA 60.281 61.111 0.00 0.00 0.00 3.86
699 801 1.247567 CAGCCGTTTCACCTCCATTT 58.752 50.000 0.00 0.00 0.00 2.32
700 802 1.068333 CAGCCGTTTCACCTCCATTTG 60.068 52.381 0.00 0.00 0.00 2.32
716 818 6.238374 CCTCCATTTGCCTTTTATACTGTACG 60.238 42.308 0.00 0.00 0.00 3.67
717 819 6.174760 TCCATTTGCCTTTTATACTGTACGT 58.825 36.000 0.00 0.00 0.00 3.57
718 820 7.329499 TCCATTTGCCTTTTATACTGTACGTA 58.671 34.615 0.00 0.00 0.00 3.57
719 821 7.278424 TCCATTTGCCTTTTATACTGTACGTAC 59.722 37.037 18.90 18.90 0.00 3.67
720 822 7.064847 CCATTTGCCTTTTATACTGTACGTACA 59.935 37.037 25.88 25.88 34.56 2.90
763 866 3.361977 GTTCCGCGGCCATGTTGT 61.362 61.111 23.51 0.00 0.00 3.32
787 897 2.134201 TGCGTAGACGATAAGCATGG 57.866 50.000 6.19 0.00 43.02 3.66
790 900 2.922758 GCGTAGACGATAAGCATGGGAG 60.923 54.545 6.19 0.00 43.02 4.30
870 980 2.342279 CCGGCCGTGAAGACAAGA 59.658 61.111 26.12 0.00 0.00 3.02
942 1052 4.790140 AGTCGATTGATTACGTTACGTGAC 59.210 41.667 21.22 15.30 41.39 3.67
959 1086 2.024163 CGTGCGTCGATCGATCCA 59.976 61.111 22.50 17.64 42.86 3.41
972 1099 2.609747 TCGATCCATAGGAAGGAAGGG 58.390 52.381 0.00 0.00 38.93 3.95
979 1106 2.570386 TAGGAAGGAAGGGAGGAAGG 57.430 55.000 0.00 0.00 0.00 3.46
983 1110 1.562008 GAAGGAAGGGAGGAAGGAAGG 59.438 57.143 0.00 0.00 0.00 3.46
984 1111 0.253394 AGGAAGGGAGGAAGGAAGGG 60.253 60.000 0.00 0.00 0.00 3.95
989 1116 0.253207 GGGAGGAAGGAAGGGAGGAA 60.253 60.000 0.00 0.00 0.00 3.36
990 1117 1.208706 GGAGGAAGGAAGGGAGGAAG 58.791 60.000 0.00 0.00 0.00 3.46
992 1119 0.800239 AGGAAGGAAGGGAGGAAGGA 59.200 55.000 0.00 0.00 0.00 3.36
993 1120 1.371415 AGGAAGGAAGGGAGGAAGGAT 59.629 52.381 0.00 0.00 0.00 3.24
994 1121 2.597304 AGGAAGGAAGGGAGGAAGGATA 59.403 50.000 0.00 0.00 0.00 2.59
995 1122 2.976185 GGAAGGAAGGGAGGAAGGATAG 59.024 54.545 0.00 0.00 0.00 2.08
998 1125 4.920781 AGGAAGGGAGGAAGGATAGTAA 57.079 45.455 0.00 0.00 0.00 2.24
1016 1143 2.692368 GATGCAGGGGGAGGTGGA 60.692 66.667 0.00 0.00 0.00 4.02
1017 1144 2.693864 ATGCAGGGGGAGGTGGAG 60.694 66.667 0.00 0.00 0.00 3.86
1020 1147 2.935481 CAGGGGGAGGTGGAGCAA 60.935 66.667 0.00 0.00 0.00 3.91
1021 1148 2.936032 AGGGGGAGGTGGAGCAAC 60.936 66.667 0.00 0.00 0.00 4.17
1071 1198 2.028484 GTGAAGCACCCGTCGTCA 59.972 61.111 0.00 0.00 0.00 4.35
1191 1318 1.127567 TGGAGGTCAGGGACAAGGTG 61.128 60.000 0.00 0.00 33.68 4.00
1252 1379 4.799678 CCTAGCATTCATACGACAGGTAG 58.200 47.826 0.00 0.00 33.84 3.18
1253 1380 3.735237 AGCATTCATACGACAGGTAGG 57.265 47.619 0.00 0.00 33.84 3.18
1256 1396 4.037684 AGCATTCATACGACAGGTAGGTAC 59.962 45.833 0.00 0.00 34.59 3.34
1274 1414 8.664992 GGTAGGTACCTAGGAGTAGTAATACTT 58.335 40.741 22.37 3.84 43.10 2.24
1278 1418 9.413734 GGTACCTAGGAGTAGTAATACTTTTCA 57.586 37.037 17.98 0.00 0.00 2.69
1282 1422 9.804758 CCTAGGAGTAGTAATACTTTTCAGTTG 57.195 37.037 1.05 0.00 34.06 3.16
1285 1425 9.091220 AGGAGTAGTAATACTTTTCAGTTGAGT 57.909 33.333 4.06 0.00 34.06 3.41
1287 1427 9.909644 GAGTAGTAATACTTTTCAGTTGAGTCA 57.090 33.333 4.06 0.00 34.06 3.41
1315 1502 3.048337 TGGAGACCCAAAATGACGTAC 57.952 47.619 0.00 0.00 40.09 3.67
1316 1503 2.635915 TGGAGACCCAAAATGACGTACT 59.364 45.455 0.00 0.00 40.09 2.73
1321 1523 4.039973 AGACCCAAAATGACGTACTCTTGA 59.960 41.667 0.00 0.00 0.00 3.02
1323 1525 4.514066 ACCCAAAATGACGTACTCTTGAAC 59.486 41.667 0.00 0.00 0.00 3.18
1336 1538 6.292168 CGTACTCTTGAACGATCAGTTTGTTT 60.292 38.462 0.00 0.00 44.35 2.83
1337 1539 6.049263 ACTCTTGAACGATCAGTTTGTTTC 57.951 37.500 0.00 0.00 44.35 2.78
1338 1540 5.584649 ACTCTTGAACGATCAGTTTGTTTCA 59.415 36.000 0.00 0.00 44.35 2.69
1339 1541 6.048073 TCTTGAACGATCAGTTTGTTTCAG 57.952 37.500 0.00 0.00 44.35 3.02
1341 1543 3.876914 TGAACGATCAGTTTGTTTCAGCT 59.123 39.130 0.00 0.00 44.35 4.24
1342 1544 3.885484 ACGATCAGTTTGTTTCAGCTG 57.115 42.857 7.63 7.63 0.00 4.24
1343 1545 3.466836 ACGATCAGTTTGTTTCAGCTGA 58.533 40.909 13.74 13.74 41.43 4.26
1344 1546 3.496130 ACGATCAGTTTGTTTCAGCTGAG 59.504 43.478 17.43 2.60 40.67 3.35
1346 1548 1.949525 TCAGTTTGTTTCAGCTGAGCC 59.050 47.619 17.43 11.78 33.62 4.70
1347 1549 1.677576 CAGTTTGTTTCAGCTGAGCCA 59.322 47.619 17.43 14.30 0.00 4.75
1348 1550 1.678101 AGTTTGTTTCAGCTGAGCCAC 59.322 47.619 17.43 14.95 0.00 5.01
1349 1551 1.678101 GTTTGTTTCAGCTGAGCCACT 59.322 47.619 17.43 0.00 0.00 4.00
1350 1552 1.311859 TTGTTTCAGCTGAGCCACTG 58.688 50.000 17.43 0.00 35.15 3.66
1353 1561 3.620061 TTCAGCTGAGCCACTGAAG 57.380 52.632 17.43 0.00 45.48 3.02
1355 1563 0.761187 TCAGCTGAGCCACTGAAGTT 59.239 50.000 13.74 0.00 39.89 2.66
1364 1572 4.095782 TGAGCCACTGAAGTTTGTAACAAC 59.904 41.667 0.00 0.00 0.00 3.32
1396 1604 4.775236 ACTGAGATTGAGCCTAAACCATC 58.225 43.478 0.00 0.00 0.00 3.51
1397 1605 4.225942 ACTGAGATTGAGCCTAAACCATCA 59.774 41.667 0.00 0.00 0.00 3.07
1398 1606 5.104193 ACTGAGATTGAGCCTAAACCATCAT 60.104 40.000 0.00 0.00 0.00 2.45
1399 1607 6.100279 ACTGAGATTGAGCCTAAACCATCATA 59.900 38.462 0.00 0.00 0.00 2.15
1400 1608 6.528321 TGAGATTGAGCCTAAACCATCATAG 58.472 40.000 0.00 0.00 0.00 2.23
1401 1609 5.312079 AGATTGAGCCTAAACCATCATAGC 58.688 41.667 0.00 0.00 0.00 2.97
1430 1642 3.126001 TGTGTTTTGTAGGAGCTGGAG 57.874 47.619 0.00 0.00 0.00 3.86
1540 1752 1.939934 CTGCGTCAAGAAGGTGACAAA 59.060 47.619 6.19 0.00 46.90 2.83
1584 1806 8.725148 AGAAATTCTACTTACTTTCACTGCATG 58.275 33.333 0.00 0.00 31.55 4.06
1589 1811 5.051891 ACTTACTTTCACTGCATGCATTC 57.948 39.130 22.97 0.00 0.00 2.67
1590 1812 2.624316 ACTTTCACTGCATGCATTCG 57.376 45.000 22.97 12.59 0.00 3.34
1591 1813 1.881973 ACTTTCACTGCATGCATTCGT 59.118 42.857 22.97 13.33 0.00 3.85
1592 1814 3.073678 ACTTTCACTGCATGCATTCGTA 58.926 40.909 22.97 6.32 0.00 3.43
1593 1815 3.120199 ACTTTCACTGCATGCATTCGTAC 60.120 43.478 22.97 0.00 0.00 3.67
1594 1816 0.998669 TCACTGCATGCATTCGTACG 59.001 50.000 22.97 9.53 0.00 3.67
1595 1817 0.721154 CACTGCATGCATTCGTACGT 59.279 50.000 22.97 10.90 0.00 3.57
1596 1818 1.923864 CACTGCATGCATTCGTACGTA 59.076 47.619 22.97 6.02 0.00 3.57
1597 1819 2.347150 CACTGCATGCATTCGTACGTAA 59.653 45.455 22.97 8.76 0.00 3.18
1602 1824 3.723764 GCATGCATTCGTACGTAAATTGG 59.276 43.478 14.21 3.21 0.00 3.16
1611 1833 3.484557 CGTACGTAAATTGGCATGTGGAC 60.485 47.826 7.22 0.00 0.00 4.02
1614 1836 4.328536 ACGTAAATTGGCATGTGGACTTA 58.671 39.130 0.00 0.00 0.00 2.24
1630 1852 8.231692 TGTGGACTTAATTGTTCTTGAATTGA 57.768 30.769 0.00 0.00 0.00 2.57
1752 1997 2.670414 GCATCACCTCGTCTTCTTCTTG 59.330 50.000 0.00 0.00 0.00 3.02
1753 1998 3.862642 GCATCACCTCGTCTTCTTCTTGT 60.863 47.826 0.00 0.00 0.00 3.16
1754 1999 3.644884 TCACCTCGTCTTCTTCTTGTC 57.355 47.619 0.00 0.00 0.00 3.18
1756 2001 3.637229 TCACCTCGTCTTCTTCTTGTCTT 59.363 43.478 0.00 0.00 0.00 3.01
1757 2002 4.825634 TCACCTCGTCTTCTTCTTGTCTTA 59.174 41.667 0.00 0.00 0.00 2.10
1758 2003 4.918583 CACCTCGTCTTCTTCTTGTCTTAC 59.081 45.833 0.00 0.00 0.00 2.34
1759 2004 4.828387 ACCTCGTCTTCTTCTTGTCTTACT 59.172 41.667 0.00 0.00 0.00 2.24
1760 2005 5.302313 ACCTCGTCTTCTTCTTGTCTTACTT 59.698 40.000 0.00 0.00 0.00 2.24
1761 2006 6.489361 ACCTCGTCTTCTTCTTGTCTTACTTA 59.511 38.462 0.00 0.00 0.00 2.24
1813 2105 4.111375 TCACTTTACTCGGCTCTTCATC 57.889 45.455 0.00 0.00 0.00 2.92
1954 2250 4.437930 GCTTAATTTCGCTGTGCAATCTCT 60.438 41.667 0.00 0.00 0.00 3.10
2101 2416 2.880268 TGTTGAGTCCATCTTGTTGCAG 59.120 45.455 0.00 0.00 0.00 4.41
2154 2479 4.340617 ACCAAGGAACAAGACTGACAAAA 58.659 39.130 0.00 0.00 0.00 2.44
2271 2607 3.428316 GCTAATATGCTAGAGAGGCCGAC 60.428 52.174 0.00 0.00 0.00 4.79
2299 2636 3.442273 GTGCCCATTGATTCTTCCGTTAA 59.558 43.478 0.00 0.00 0.00 2.01
2301 2638 5.298276 GTGCCCATTGATTCTTCCGTTAATA 59.702 40.000 0.00 0.00 0.00 0.98
2313 2652 6.498304 TCTTCCGTTAATACTTAAGTAGCCG 58.502 40.000 19.58 16.45 33.52 5.52
2405 2745 0.038892 CTTGCAACACCATCAGCACC 60.039 55.000 0.00 0.00 36.62 5.01
2517 2863 3.482110 GTCACGTTTAGCTGCAAAACTTG 59.518 43.478 10.97 10.97 37.40 3.16
2588 2934 2.544726 GCGCTTGCTTCTTGGTACT 58.455 52.632 0.00 0.00 35.07 2.73
2589 2935 0.444260 GCGCTTGCTTCTTGGTACTC 59.556 55.000 0.00 0.00 35.07 2.59
2590 2936 1.079503 CGCTTGCTTCTTGGTACTCC 58.920 55.000 0.00 0.00 0.00 3.85
2591 2937 1.454201 GCTTGCTTCTTGGTACTCCC 58.546 55.000 0.00 0.00 0.00 4.30
2592 2938 1.003696 GCTTGCTTCTTGGTACTCCCT 59.996 52.381 0.00 0.00 0.00 4.20
2593 2939 2.937433 GCTTGCTTCTTGGTACTCCCTC 60.937 54.545 0.00 0.00 0.00 4.30
2594 2940 1.276622 TGCTTCTTGGTACTCCCTCC 58.723 55.000 0.00 0.00 0.00 4.30
2595 2941 0.175989 GCTTCTTGGTACTCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
2596 2942 1.558233 CTTCTTGGTACTCCCTCCGT 58.442 55.000 0.00 0.00 0.00 4.69
2597 2943 1.900486 CTTCTTGGTACTCCCTCCGTT 59.100 52.381 0.00 0.00 0.00 4.44
2598 2944 1.553706 TCTTGGTACTCCCTCCGTTC 58.446 55.000 0.00 0.00 0.00 3.95
2599 2945 0.535797 CTTGGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
2600 2946 0.178926 TTGGTACTCCCTCCGTTCCA 60.179 55.000 0.00 0.00 31.17 3.53
2601 2947 0.178926 TGGTACTCCCTCCGTTCCAA 60.179 55.000 0.00 0.00 30.28 3.53
2602 2948 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2603 2949 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
2604 2950 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
2605 2951 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
2606 2952 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2607 2953 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2608 2954 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2609 2955 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2610 2956 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2611 2957 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2612 2958 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2613 2959 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2614 2960 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2615 2961 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2616 2962 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2617 2963 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2618 2964 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2619 2965 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2620 2966 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
2621 2967 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
2622 2968 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
2623 2969 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
2624 2970 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
2661 3007 9.746711 CAAAGTTGAGTCATCTATTTTAGAACG 57.253 33.333 4.14 0.00 38.50 3.95
2662 3008 8.480643 AAGTTGAGTCATCTATTTTAGAACGG 57.519 34.615 4.14 0.00 38.50 4.44
2663 3009 7.837863 AGTTGAGTCATCTATTTTAGAACGGA 58.162 34.615 1.70 0.00 38.50 4.69
2664 3010 7.976734 AGTTGAGTCATCTATTTTAGAACGGAG 59.023 37.037 1.70 0.00 38.50 4.63
2665 3011 6.806751 TGAGTCATCTATTTTAGAACGGAGG 58.193 40.000 0.00 0.00 38.50 4.30
2666 3012 6.163135 AGTCATCTATTTTAGAACGGAGGG 57.837 41.667 0.00 0.00 38.50 4.30
2667 3013 5.897824 AGTCATCTATTTTAGAACGGAGGGA 59.102 40.000 0.00 0.00 38.50 4.20
2668 3014 6.041069 AGTCATCTATTTTAGAACGGAGGGAG 59.959 42.308 0.00 0.00 38.50 4.30
2669 3015 5.897824 TCATCTATTTTAGAACGGAGGGAGT 59.102 40.000 0.00 0.00 38.50 3.85
2670 3016 7.014038 GTCATCTATTTTAGAACGGAGGGAGTA 59.986 40.741 0.00 0.00 38.50 2.59
2671 3017 6.956202 TCTATTTTAGAACGGAGGGAGTAG 57.044 41.667 0.00 0.00 0.00 2.57
2672 3018 6.666678 TCTATTTTAGAACGGAGGGAGTAGA 58.333 40.000 0.00 0.00 0.00 2.59
2673 3019 7.296098 TCTATTTTAGAACGGAGGGAGTAGAT 58.704 38.462 0.00 0.00 0.00 1.98
2714 3060 1.519719 CTAGCTGGTCCCTGAGTGC 59.480 63.158 0.00 0.00 0.00 4.40
2715 3061 0.975040 CTAGCTGGTCCCTGAGTGCT 60.975 60.000 0.00 0.00 34.92 4.40
2716 3062 1.260538 TAGCTGGTCCCTGAGTGCTG 61.261 60.000 0.00 0.00 32.72 4.41
2717 3063 2.587247 GCTGGTCCCTGAGTGCTGA 61.587 63.158 0.00 0.00 0.00 4.26
2718 3064 1.595882 CTGGTCCCTGAGTGCTGAG 59.404 63.158 0.00 0.00 0.00 3.35
2719 3065 1.152247 TGGTCCCTGAGTGCTGAGT 60.152 57.895 0.00 0.00 0.00 3.41
2720 3066 1.294780 GGTCCCTGAGTGCTGAGTG 59.705 63.158 0.00 0.00 0.00 3.51
2721 3067 1.188219 GGTCCCTGAGTGCTGAGTGA 61.188 60.000 0.00 0.00 0.00 3.41
2722 3068 0.246086 GTCCCTGAGTGCTGAGTGAG 59.754 60.000 0.00 0.00 0.00 3.51
2723 3069 0.178950 TCCCTGAGTGCTGAGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
2724 3070 0.037512 CCCTGAGTGCTGAGTGAGTG 60.038 60.000 0.00 0.00 0.00 3.51
2781 3127 7.295322 TGATGCTGATACATATAGATAGGCC 57.705 40.000 0.00 0.00 0.00 5.19
2819 3165 2.301346 CATGAACCCCAGGTGATTAGC 58.699 52.381 0.00 0.00 35.34 3.09
2828 3174 0.953471 AGGTGATTAGCGCACGCAAA 60.953 50.000 18.24 1.62 44.88 3.68
2829 3175 0.098728 GGTGATTAGCGCACGCAAAT 59.901 50.000 18.24 0.52 44.88 2.32
2830 3176 1.467374 GGTGATTAGCGCACGCAAATT 60.467 47.619 18.24 0.00 44.88 1.82
2831 3177 2.223157 GGTGATTAGCGCACGCAAATTA 60.223 45.455 18.24 0.00 44.88 1.40
2832 3178 3.421741 GTGATTAGCGCACGCAAATTAA 58.578 40.909 18.24 7.32 44.88 1.40
2842 3188 2.029470 CACGCAAATTAAAGGCCCAAGA 60.029 45.455 0.00 0.00 0.00 3.02
2845 3191 3.325870 GCAAATTAAAGGCCCAAGACAC 58.674 45.455 0.00 0.00 0.00 3.67
2851 3197 2.032681 GGCCCAAGACACGAAGCT 59.967 61.111 0.00 0.00 0.00 3.74
2852 3198 1.192146 AGGCCCAAGACACGAAGCTA 61.192 55.000 0.00 0.00 0.00 3.32
2853 3199 0.741221 GGCCCAAGACACGAAGCTAG 60.741 60.000 0.00 0.00 0.00 3.42
2854 3200 1.362406 GCCCAAGACACGAAGCTAGC 61.362 60.000 6.62 6.62 0.00 3.42
2855 3201 0.247736 CCCAAGACACGAAGCTAGCT 59.752 55.000 12.68 12.68 0.00 3.32
2867 3213 3.492756 CGAAGCTAGCTATCTTTTGGCTC 59.507 47.826 19.70 6.66 37.50 4.70
2868 3214 3.483808 AGCTAGCTATCTTTTGGCTCC 57.516 47.619 17.69 0.00 37.50 4.70
2869 3215 2.774234 AGCTAGCTATCTTTTGGCTCCA 59.226 45.455 17.69 0.00 37.50 3.86
2870 3216 3.393941 AGCTAGCTATCTTTTGGCTCCAT 59.606 43.478 17.69 0.00 37.50 3.41
2871 3217 3.501445 GCTAGCTATCTTTTGGCTCCATG 59.499 47.826 7.70 0.00 37.50 3.66
2872 3218 2.305009 AGCTATCTTTTGGCTCCATGC 58.695 47.619 0.00 0.00 41.94 4.06
2888 3234 2.586792 GCCGGAGCAAGGACTGAT 59.413 61.111 5.05 0.00 39.53 2.90
2889 3235 1.817099 GCCGGAGCAAGGACTGATG 60.817 63.158 5.05 0.00 39.53 3.07
2890 3236 1.900351 CCGGAGCAAGGACTGATGA 59.100 57.895 0.00 0.00 0.00 2.92
2891 3237 0.179089 CCGGAGCAAGGACTGATGAG 60.179 60.000 0.00 0.00 0.00 2.90
2892 3238 0.534412 CGGAGCAAGGACTGATGAGT 59.466 55.000 0.00 0.00 33.98 3.41
2893 3239 1.751351 CGGAGCAAGGACTGATGAGTA 59.249 52.381 0.00 0.00 30.16 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 109 1.814634 GCTAGGAAGACGATCGAGGGA 60.815 57.143 24.34 0.00 0.00 4.20
145 168 9.844257 TTAGTTTACTGAGGGAGTACTAGATAC 57.156 37.037 0.00 0.00 36.86 2.24
154 177 8.862085 GCTCTTATATTAGTTTACTGAGGGAGT 58.138 37.037 0.00 0.00 38.88 3.85
155 178 8.024285 CGCTCTTATATTAGTTTACTGAGGGAG 58.976 40.741 0.00 0.00 35.10 4.30
156 179 7.504911 ACGCTCTTATATTAGTTTACTGAGGGA 59.495 37.037 0.00 0.00 36.36 4.20
157 180 7.659186 ACGCTCTTATATTAGTTTACTGAGGG 58.341 38.462 0.00 0.00 37.76 4.30
158 181 9.530633 AAACGCTCTTATATTAGTTTACTGAGG 57.469 33.333 0.00 0.00 31.14 3.86
185 208 9.413048 GCGCTTAGATCACTATTTTAGTTATCT 57.587 33.333 13.18 13.18 46.18 1.98
186 209 9.413048 AGCGCTTAGATCACTATTTTAGTTATC 57.587 33.333 2.64 2.14 38.88 1.75
187 210 9.413048 GAGCGCTTAGATCACTATTTTAGTTAT 57.587 33.333 13.26 0.00 36.76 1.89
188 211 8.630917 AGAGCGCTTAGATCACTATTTTAGTTA 58.369 33.333 13.26 0.00 37.82 2.24
189 212 7.493367 AGAGCGCTTAGATCACTATTTTAGTT 58.507 34.615 13.26 0.00 37.82 2.24
190 213 7.045126 AGAGCGCTTAGATCACTATTTTAGT 57.955 36.000 13.26 0.00 37.82 2.24
191 214 7.938563 AAGAGCGCTTAGATCACTATTTTAG 57.061 36.000 13.26 0.00 37.82 1.85
197 220 9.451002 ACTAATATAAGAGCGCTTAGATCACTA 57.549 33.333 13.26 6.27 37.50 2.74
198 221 8.343168 ACTAATATAAGAGCGCTTAGATCACT 57.657 34.615 13.26 0.00 37.50 3.41
199 222 8.973835 AACTAATATAAGAGCGCTTAGATCAC 57.026 34.615 13.26 0.00 37.50 3.06
203 226 9.894783 CTGTAAACTAATATAAGAGCGCTTAGA 57.105 33.333 13.26 11.33 39.79 2.10
204 227 9.894783 TCTGTAAACTAATATAAGAGCGCTTAG 57.105 33.333 13.26 10.09 39.79 2.18
205 228 9.894783 CTCTGTAAACTAATATAAGAGCGCTTA 57.105 33.333 13.26 12.50 40.65 3.09
206 229 7.868415 CCTCTGTAAACTAATATAAGAGCGCTT 59.132 37.037 13.26 8.09 38.15 4.68
207 230 7.371936 CCTCTGTAAACTAATATAAGAGCGCT 58.628 38.462 11.27 11.27 0.00 5.92
208 231 6.586844 CCCTCTGTAAACTAATATAAGAGCGC 59.413 42.308 0.00 0.00 0.00 5.92
209 232 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
210 233 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
217 240 9.878737 AAGCTATACTCCCTCTGTAAACTAATA 57.121 33.333 0.00 0.00 0.00 0.98
218 241 8.785184 AAGCTATACTCCCTCTGTAAACTAAT 57.215 34.615 0.00 0.00 0.00 1.73
219 242 9.352191 CTAAGCTATACTCCCTCTGTAAACTAA 57.648 37.037 0.00 0.00 0.00 2.24
220 243 7.447853 GCTAAGCTATACTCCCTCTGTAAACTA 59.552 40.741 0.00 0.00 0.00 2.24
221 244 6.265876 GCTAAGCTATACTCCCTCTGTAAACT 59.734 42.308 0.00 0.00 0.00 2.66
222 245 6.448852 GCTAAGCTATACTCCCTCTGTAAAC 58.551 44.000 0.00 0.00 0.00 2.01
223 246 5.539193 GGCTAAGCTATACTCCCTCTGTAAA 59.461 44.000 0.00 0.00 0.00 2.01
224 247 5.078256 GGCTAAGCTATACTCCCTCTGTAA 58.922 45.833 0.00 0.00 0.00 2.41
225 248 4.105858 TGGCTAAGCTATACTCCCTCTGTA 59.894 45.833 0.00 0.00 0.00 2.74
226 249 3.117093 TGGCTAAGCTATACTCCCTCTGT 60.117 47.826 0.00 0.00 0.00 3.41
227 250 3.501349 TGGCTAAGCTATACTCCCTCTG 58.499 50.000 0.00 0.00 0.00 3.35
228 251 3.905493 TGGCTAAGCTATACTCCCTCT 57.095 47.619 0.00 0.00 0.00 3.69
229 252 4.528596 TGAATGGCTAAGCTATACTCCCTC 59.471 45.833 0.00 0.00 0.00 4.30
230 253 4.493618 TGAATGGCTAAGCTATACTCCCT 58.506 43.478 0.00 0.00 0.00 4.20
231 254 4.891992 TGAATGGCTAAGCTATACTCCC 57.108 45.455 0.00 0.00 0.00 4.30
232 255 6.205658 CCTTTTGAATGGCTAAGCTATACTCC 59.794 42.308 0.00 0.00 0.00 3.85
233 256 6.768381 ACCTTTTGAATGGCTAAGCTATACTC 59.232 38.462 0.00 0.00 0.00 2.59
249 272 1.334243 CCGTTTGGCGTACCTTTTGAA 59.666 47.619 0.00 0.00 39.32 2.69
267 298 1.066908 TCTTTCTTTGCACTTTGGCCG 59.933 47.619 0.00 0.00 0.00 6.13
268 299 2.159114 TGTCTTTCTTTGCACTTTGGCC 60.159 45.455 0.00 0.00 0.00 5.36
271 302 9.121517 CTTGTATATGTCTTTCTTTGCACTTTG 57.878 33.333 0.00 0.00 0.00 2.77
273 304 7.665559 TCCTTGTATATGTCTTTCTTTGCACTT 59.334 33.333 0.00 0.00 0.00 3.16
274 305 7.168219 TCCTTGTATATGTCTTTCTTTGCACT 58.832 34.615 0.00 0.00 0.00 4.40
276 307 7.334421 GTCTCCTTGTATATGTCTTTCTTTGCA 59.666 37.037 0.00 0.00 0.00 4.08
277 308 7.334421 TGTCTCCTTGTATATGTCTTTCTTTGC 59.666 37.037 0.00 0.00 0.00 3.68
278 309 8.777865 TGTCTCCTTGTATATGTCTTTCTTTG 57.222 34.615 0.00 0.00 0.00 2.77
292 348 1.655484 CGCATGCATGTCTCCTTGTA 58.345 50.000 26.79 0.00 0.00 2.41
324 380 1.450312 CAGTGCGGGGGAAGTGATC 60.450 63.158 0.00 0.00 0.00 2.92
376 436 2.797786 AGTAACTCTTCCTCTCGCTGT 58.202 47.619 0.00 0.00 0.00 4.40
377 437 3.506810 CAAGTAACTCTTCCTCTCGCTG 58.493 50.000 0.00 0.00 33.63 5.18
418 482 4.711949 CGTCTTGGCTGGCAGGCT 62.712 66.667 36.29 0.00 41.96 4.58
439 503 1.005037 TGTGTTAGGTGAGCTGCCG 60.005 57.895 0.00 0.00 0.00 5.69
457 521 1.376466 CTGCACCTGTAGTTGGCCT 59.624 57.895 3.32 0.00 0.00 5.19
515 590 1.298859 AACCAACGATCGCTTCAGCC 61.299 55.000 16.60 0.00 37.91 4.85
516 591 0.179215 CAACCAACGATCGCTTCAGC 60.179 55.000 16.60 0.00 37.78 4.26
517 592 0.443869 CCAACCAACGATCGCTTCAG 59.556 55.000 16.60 2.23 0.00 3.02
518 593 0.250124 ACCAACCAACGATCGCTTCA 60.250 50.000 16.60 0.00 0.00 3.02
519 594 0.872388 AACCAACCAACGATCGCTTC 59.128 50.000 16.60 0.00 0.00 3.86
556 636 4.933064 GGGTGATCGCGCGAGGAG 62.933 72.222 36.99 5.65 0.00 3.69
564 644 4.856801 ATGTGGCCGGGTGATCGC 62.857 66.667 2.18 0.00 0.00 4.58
616 700 2.561569 AGGCGGAGGTAAATCAAATCG 58.438 47.619 0.00 0.00 0.00 3.34
653 739 3.724733 AATGCTAGGGGCCCGGGTA 62.725 63.158 24.63 13.92 40.92 3.69
695 792 7.966111 TGTACGTACAGTATAAAAGGCAAATG 58.034 34.615 24.10 0.00 37.69 2.32
696 793 8.193250 CTGTACGTACAGTATAAAAGGCAAAT 57.807 34.615 36.61 0.00 46.51 2.32
716 818 2.857618 GATCGATCGATCCTGCTGTAC 58.142 52.381 36.97 17.01 43.71 2.90
744 846 2.746277 AACATGGCCGCGGAACTC 60.746 61.111 33.48 15.20 0.00 3.01
763 866 4.295857 TGCTTATCGTCTACGCAACATA 57.704 40.909 0.00 0.00 39.60 2.29
787 897 1.912371 CTTGTCGCTTTTCGCCCTCC 61.912 60.000 0.00 0.00 38.27 4.30
790 900 1.964373 TCCTTGTCGCTTTTCGCCC 60.964 57.895 0.00 0.00 38.27 6.13
830 940 3.233355 GCTCCCCGCCACTTATATG 57.767 57.895 0.00 0.00 0.00 1.78
896 1006 1.616865 TGAGTTGCTACTAGTTGGCGT 59.383 47.619 0.00 0.00 33.84 5.68
942 1052 0.110373 TATGGATCGATCGACGCACG 60.110 55.000 22.06 7.06 42.26 5.34
959 1086 2.597304 TCCTTCCTCCCTTCCTTCCTAT 59.403 50.000 0.00 0.00 0.00 2.57
972 1099 1.208706 CCTTCCTCCCTTCCTTCCTC 58.791 60.000 0.00 0.00 0.00 3.71
979 1106 5.279758 GCATCTTACTATCCTTCCTCCCTTC 60.280 48.000 0.00 0.00 0.00 3.46
983 1110 4.020662 CCTGCATCTTACTATCCTTCCTCC 60.021 50.000 0.00 0.00 0.00 4.30
984 1111 4.020662 CCCTGCATCTTACTATCCTTCCTC 60.021 50.000 0.00 0.00 0.00 3.71
989 1116 2.182312 TCCCCCTGCATCTTACTATCCT 59.818 50.000 0.00 0.00 0.00 3.24
990 1117 2.569404 CTCCCCCTGCATCTTACTATCC 59.431 54.545 0.00 0.00 0.00 2.59
992 1119 2.089925 ACCTCCCCCTGCATCTTACTAT 60.090 50.000 0.00 0.00 0.00 2.12
993 1120 1.294068 ACCTCCCCCTGCATCTTACTA 59.706 52.381 0.00 0.00 0.00 1.82
994 1121 0.044855 ACCTCCCCCTGCATCTTACT 59.955 55.000 0.00 0.00 0.00 2.24
995 1122 0.181350 CACCTCCCCCTGCATCTTAC 59.819 60.000 0.00 0.00 0.00 2.34
998 1125 2.693864 CCACCTCCCCCTGCATCT 60.694 66.667 0.00 0.00 0.00 2.90
1098 1225 4.077180 GACGACCCCTCCCCCTCT 62.077 72.222 0.00 0.00 0.00 3.69
1252 1379 9.413734 TGAAAAGTATTACTACTCCTAGGTACC 57.586 37.037 9.08 2.73 37.20 3.34
1256 1396 9.804758 CAACTGAAAAGTATTACTACTCCTAGG 57.195 37.037 0.82 0.82 37.20 3.02
1260 1400 9.356433 GACTCAACTGAAAAGTATTACTACTCC 57.644 37.037 0.00 0.00 37.20 3.85
1261 1401 9.909644 TGACTCAACTGAAAAGTATTACTACTC 57.090 33.333 0.00 0.00 37.20 2.59
1274 1414 9.958180 TCTCCAATATTAATGACTCAACTGAAA 57.042 29.630 0.00 0.00 0.00 2.69
1278 1418 7.092444 TGGGTCTCCAATATTAATGACTCAACT 60.092 37.037 11.58 0.00 40.73 3.16
1295 1435 2.635915 AGTACGTCATTTTGGGTCTCCA 59.364 45.455 0.00 0.00 42.25 3.86
1315 1502 6.048073 TGAAACAAACTGATCGTTCAAGAG 57.952 37.500 0.00 0.00 33.90 2.85
1316 1503 5.504010 GCTGAAACAAACTGATCGTTCAAGA 60.504 40.000 0.00 0.00 33.90 3.02
1321 1523 3.876914 TCAGCTGAAACAAACTGATCGTT 59.123 39.130 15.67 0.00 34.35 3.85
1323 1525 3.666374 GCTCAGCTGAAACAAACTGATCG 60.666 47.826 18.85 2.06 38.41 3.69
1336 1538 0.761187 AACTTCAGTGGCTCAGCTGA 59.239 50.000 17.19 17.19 39.66 4.26
1337 1539 1.266175 CAAACTTCAGTGGCTCAGCTG 59.734 52.381 7.63 7.63 0.00 4.24
1338 1540 1.133976 ACAAACTTCAGTGGCTCAGCT 60.134 47.619 0.00 0.00 0.00 4.24
1339 1541 1.312815 ACAAACTTCAGTGGCTCAGC 58.687 50.000 0.00 0.00 0.00 4.26
1341 1543 3.879998 TGTTACAAACTTCAGTGGCTCA 58.120 40.909 0.00 0.00 0.00 4.26
1342 1544 4.095782 TGTTGTTACAAACTTCAGTGGCTC 59.904 41.667 0.00 0.00 0.00 4.70
1343 1545 4.013728 TGTTGTTACAAACTTCAGTGGCT 58.986 39.130 0.00 0.00 0.00 4.75
1344 1546 4.364415 TGTTGTTACAAACTTCAGTGGC 57.636 40.909 0.00 0.00 0.00 5.01
1364 1572 7.330900 AGGCTCAATCTCAGTATCATTTTTG 57.669 36.000 0.00 0.00 0.00 2.44
1375 1583 4.774124 TGATGGTTTAGGCTCAATCTCAG 58.226 43.478 0.00 0.00 0.00 3.35
1376 1584 4.842531 TGATGGTTTAGGCTCAATCTCA 57.157 40.909 0.00 0.00 0.00 3.27
1378 1586 5.072872 AGCTATGATGGTTTAGGCTCAATCT 59.927 40.000 0.00 0.00 0.00 2.40
1379 1587 5.312079 AGCTATGATGGTTTAGGCTCAATC 58.688 41.667 0.00 0.00 0.00 2.67
1380 1588 5.316158 AGCTATGATGGTTTAGGCTCAAT 57.684 39.130 0.00 0.00 0.00 2.57
1382 1590 4.778213 AAGCTATGATGGTTTAGGCTCA 57.222 40.909 0.00 0.00 0.00 4.26
1383 1591 4.884164 ACAAAGCTATGATGGTTTAGGCTC 59.116 41.667 0.00 0.00 36.12 4.70
1396 1604 6.645700 ACAAAACACAAACACAAAGCTATG 57.354 33.333 0.00 0.00 0.00 2.23
1397 1605 6.978080 CCTACAAAACACAAACACAAAGCTAT 59.022 34.615 0.00 0.00 0.00 2.97
1398 1606 6.151312 TCCTACAAAACACAAACACAAAGCTA 59.849 34.615 0.00 0.00 0.00 3.32
1399 1607 5.047660 TCCTACAAAACACAAACACAAAGCT 60.048 36.000 0.00 0.00 0.00 3.74
1400 1608 5.164954 TCCTACAAAACACAAACACAAAGC 58.835 37.500 0.00 0.00 0.00 3.51
1401 1609 5.288472 GCTCCTACAAAACACAAACACAAAG 59.712 40.000 0.00 0.00 0.00 2.77
1448 1660 3.659183 ATTGATTCCACCTCCTTCCTG 57.341 47.619 0.00 0.00 0.00 3.86
1540 1752 3.367646 TCTATCACGTCCAGGAAGTCT 57.632 47.619 4.83 0.00 0.00 3.24
1584 1806 3.392769 TGCCAATTTACGTACGAATGC 57.607 42.857 24.41 12.65 0.00 3.56
1589 1811 2.673862 TCCACATGCCAATTTACGTACG 59.326 45.455 15.01 15.01 0.00 3.67
1590 1812 3.687698 AGTCCACATGCCAATTTACGTAC 59.312 43.478 0.00 0.00 0.00 3.67
1591 1813 3.945346 AGTCCACATGCCAATTTACGTA 58.055 40.909 0.00 0.00 0.00 3.57
1592 1814 2.790433 AGTCCACATGCCAATTTACGT 58.210 42.857 0.00 0.00 0.00 3.57
1593 1815 3.848272 AAGTCCACATGCCAATTTACG 57.152 42.857 0.00 0.00 0.00 3.18
1594 1816 7.096551 ACAATTAAGTCCACATGCCAATTTAC 58.903 34.615 0.00 0.00 0.00 2.01
1595 1817 7.238486 ACAATTAAGTCCACATGCCAATTTA 57.762 32.000 0.00 0.00 0.00 1.40
1596 1818 6.112927 ACAATTAAGTCCACATGCCAATTT 57.887 33.333 0.00 0.00 0.00 1.82
1597 1819 5.743636 ACAATTAAGTCCACATGCCAATT 57.256 34.783 0.00 0.00 0.00 2.32
1602 1824 6.012658 TCAAGAACAATTAAGTCCACATGC 57.987 37.500 0.00 0.00 0.00 4.06
1630 1852 8.575649 TCTTTCTCCTGTTTTGTAAGTTTTCT 57.424 30.769 0.00 0.00 0.00 2.52
1637 1859 8.846211 CCTTGTATTCTTTCTCCTGTTTTGTAA 58.154 33.333 0.00 0.00 0.00 2.41
1638 1860 8.215050 TCCTTGTATTCTTTCTCCTGTTTTGTA 58.785 33.333 0.00 0.00 0.00 2.41
1774 2066 5.939764 AGTGATCAATGCTACTAACCTGA 57.060 39.130 0.00 0.00 0.00 3.86
1777 2069 7.043325 CGAGTAAAGTGATCAATGCTACTAACC 60.043 40.741 14.67 5.86 0.00 2.85
1778 2070 7.043325 CCGAGTAAAGTGATCAATGCTACTAAC 60.043 40.741 14.67 6.36 0.00 2.34
1782 2074 4.025647 GCCGAGTAAAGTGATCAATGCTAC 60.026 45.833 0.00 2.25 0.00 3.58
1786 2078 4.437239 AGAGCCGAGTAAAGTGATCAATG 58.563 43.478 0.00 0.00 0.00 2.82
1788 2080 4.021456 TGAAGAGCCGAGTAAAGTGATCAA 60.021 41.667 0.00 0.00 0.00 2.57
1813 2105 1.909141 CTTTCGCTCACCAGCTGCAG 61.909 60.000 10.11 10.11 44.40 4.41
1954 2250 0.988063 TCAAATCCATGGGACGGACA 59.012 50.000 13.02 0.00 34.69 4.02
2154 2479 1.613437 CCAGCGATGTTCACCCTTTTT 59.387 47.619 0.00 0.00 0.00 1.94
2299 2636 6.709846 CAGTACTAGGTCGGCTACTTAAGTAT 59.290 42.308 15.57 2.18 0.00 2.12
2301 2638 4.880696 CAGTACTAGGTCGGCTACTTAAGT 59.119 45.833 13.68 13.68 0.00 2.24
2313 2652 4.576879 CCTTTTTGGGACAGTACTAGGTC 58.423 47.826 0.00 0.00 42.39 3.85
2482 2827 2.896745 ACGTGACGTTTTAACCTCCT 57.103 45.000 4.10 0.00 36.35 3.69
2587 2933 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2588 2934 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2589 2935 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2590 2936 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2591 2937 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2592 2938 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2593 2939 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2594 2940 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2595 2941 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2596 2942 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
2597 2943 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
2598 2944 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
2635 2981 9.746711 CGTTCTAAAATAGATGACTCAACTTTG 57.253 33.333 0.00 0.00 34.22 2.77
2636 2982 8.936864 CCGTTCTAAAATAGATGACTCAACTTT 58.063 33.333 0.00 0.00 34.22 2.66
2637 2983 8.311836 TCCGTTCTAAAATAGATGACTCAACTT 58.688 33.333 0.00 0.00 34.22 2.66
2638 2984 7.837863 TCCGTTCTAAAATAGATGACTCAACT 58.162 34.615 0.00 0.00 34.22 3.16
2639 2985 7.222999 CCTCCGTTCTAAAATAGATGACTCAAC 59.777 40.741 0.00 0.00 34.22 3.18
2640 2986 7.265673 CCTCCGTTCTAAAATAGATGACTCAA 58.734 38.462 0.00 0.00 34.22 3.02
2641 2987 6.183360 CCCTCCGTTCTAAAATAGATGACTCA 60.183 42.308 0.00 0.00 34.22 3.41
2642 2988 6.040616 TCCCTCCGTTCTAAAATAGATGACTC 59.959 42.308 0.00 0.00 34.22 3.36
2643 2989 5.897824 TCCCTCCGTTCTAAAATAGATGACT 59.102 40.000 0.00 0.00 34.22 3.41
2644 2990 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
2645 2991 5.897824 ACTCCCTCCGTTCTAAAATAGATGA 59.102 40.000 0.00 0.00 34.22 2.92
2646 2992 6.163135 ACTCCCTCCGTTCTAAAATAGATG 57.837 41.667 0.00 0.00 34.22 2.90
2647 2993 7.296098 TCTACTCCCTCCGTTCTAAAATAGAT 58.704 38.462 0.00 0.00 34.22 1.98
2648 2994 6.666678 TCTACTCCCTCCGTTCTAAAATAGA 58.333 40.000 0.00 0.00 0.00 1.98
2649 2995 6.956202 TCTACTCCCTCCGTTCTAAAATAG 57.044 41.667 0.00 0.00 0.00 1.73
2650 2996 7.014038 GTCATCTACTCCCTCCGTTCTAAAATA 59.986 40.741 0.00 0.00 0.00 1.40
2651 2997 5.897824 TCATCTACTCCCTCCGTTCTAAAAT 59.102 40.000 0.00 0.00 0.00 1.82
2652 2998 5.126707 GTCATCTACTCCCTCCGTTCTAAAA 59.873 44.000 0.00 0.00 0.00 1.52
2653 2999 4.643784 GTCATCTACTCCCTCCGTTCTAAA 59.356 45.833 0.00 0.00 0.00 1.85
2654 3000 4.079901 AGTCATCTACTCCCTCCGTTCTAA 60.080 45.833 0.00 0.00 30.33 2.10
2655 3001 3.458857 AGTCATCTACTCCCTCCGTTCTA 59.541 47.826 0.00 0.00 30.33 2.10
2656 3002 2.242708 AGTCATCTACTCCCTCCGTTCT 59.757 50.000 0.00 0.00 30.33 3.01
2657 3003 2.359531 CAGTCATCTACTCCCTCCGTTC 59.640 54.545 0.00 0.00 35.76 3.95
2658 3004 2.025226 TCAGTCATCTACTCCCTCCGTT 60.025 50.000 0.00 0.00 35.76 4.44
2659 3005 1.564818 TCAGTCATCTACTCCCTCCGT 59.435 52.381 0.00 0.00 35.76 4.69
2660 3006 1.950909 GTCAGTCATCTACTCCCTCCG 59.049 57.143 0.00 0.00 35.76 4.63
2661 3007 3.219281 GAGTCAGTCATCTACTCCCTCC 58.781 54.545 0.00 0.00 35.76 4.30
2662 3008 3.892284 TGAGTCAGTCATCTACTCCCTC 58.108 50.000 0.00 0.00 39.10 4.30
2663 3009 4.079500 TCATGAGTCAGTCATCTACTCCCT 60.080 45.833 0.00 0.00 44.73 4.20
2664 3010 4.211125 TCATGAGTCAGTCATCTACTCCC 58.789 47.826 0.00 0.00 44.73 4.30
2665 3011 5.771469 CATCATGAGTCAGTCATCTACTCC 58.229 45.833 0.09 0.00 44.73 3.85
2666 3012 5.221204 TGCATCATGAGTCAGTCATCTACTC 60.221 44.000 0.09 0.00 44.73 2.59
2667 3013 4.648307 TGCATCATGAGTCAGTCATCTACT 59.352 41.667 0.09 0.00 44.73 2.57
2668 3014 4.941657 TGCATCATGAGTCAGTCATCTAC 58.058 43.478 0.09 0.00 44.73 2.59
2669 3015 4.038883 CCTGCATCATGAGTCAGTCATCTA 59.961 45.833 19.48 0.00 44.73 1.98
2670 3016 3.181464 CCTGCATCATGAGTCAGTCATCT 60.181 47.826 19.48 0.00 44.73 2.90
2671 3017 3.132160 CCTGCATCATGAGTCAGTCATC 58.868 50.000 19.48 0.00 44.73 2.92
2673 3019 1.904537 ACCTGCATCATGAGTCAGTCA 59.095 47.619 19.48 0.00 40.38 3.41
2714 3060 3.145286 TCTCACTCACTCACTCACTCAG 58.855 50.000 0.00 0.00 0.00 3.35
2715 3061 3.214696 TCTCACTCACTCACTCACTCA 57.785 47.619 0.00 0.00 0.00 3.41
2716 3062 3.119531 CCATCTCACTCACTCACTCACTC 60.120 52.174 0.00 0.00 0.00 3.51
2717 3063 2.824936 CCATCTCACTCACTCACTCACT 59.175 50.000 0.00 0.00 0.00 3.41
2718 3064 2.822561 TCCATCTCACTCACTCACTCAC 59.177 50.000 0.00 0.00 0.00 3.51
2719 3065 3.087781 CTCCATCTCACTCACTCACTCA 58.912 50.000 0.00 0.00 0.00 3.41
2720 3066 2.426738 CCTCCATCTCACTCACTCACTC 59.573 54.545 0.00 0.00 0.00 3.51
2721 3067 2.455557 CCTCCATCTCACTCACTCACT 58.544 52.381 0.00 0.00 0.00 3.41
2722 3068 1.480137 CCCTCCATCTCACTCACTCAC 59.520 57.143 0.00 0.00 0.00 3.51
2723 3069 1.620798 CCCCTCCATCTCACTCACTCA 60.621 57.143 0.00 0.00 0.00 3.41
2724 3070 1.118838 CCCCTCCATCTCACTCACTC 58.881 60.000 0.00 0.00 0.00 3.51
2778 3124 2.105128 CCTGTCTCGTCGATGGCC 59.895 66.667 4.48 0.00 0.00 5.36
2781 3127 1.517257 GTGGCCTGTCTCGTCGATG 60.517 63.158 3.32 0.00 0.00 3.84
2819 3165 1.075979 GGGCCTTTAATTTGCGTGCG 61.076 55.000 0.84 0.00 0.00 5.34
2828 3174 2.871096 TCGTGTCTTGGGCCTTTAAT 57.129 45.000 4.53 0.00 0.00 1.40
2829 3175 2.500229 CTTCGTGTCTTGGGCCTTTAA 58.500 47.619 4.53 0.00 0.00 1.52
2830 3176 1.880646 GCTTCGTGTCTTGGGCCTTTA 60.881 52.381 4.53 0.00 0.00 1.85
2831 3177 1.172812 GCTTCGTGTCTTGGGCCTTT 61.173 55.000 4.53 0.00 0.00 3.11
2832 3178 1.600916 GCTTCGTGTCTTGGGCCTT 60.601 57.895 4.53 0.00 0.00 4.35
2842 3188 4.184629 CCAAAAGATAGCTAGCTTCGTGT 58.815 43.478 24.88 10.61 29.43 4.49
2845 3191 3.462021 AGCCAAAAGATAGCTAGCTTCG 58.538 45.455 24.88 17.09 34.38 3.79
2851 3197 3.480470 GCATGGAGCCAAAAGATAGCTA 58.520 45.455 0.00 0.00 36.87 3.32
2852 3198 2.305009 GCATGGAGCCAAAAGATAGCT 58.695 47.619 0.00 0.00 40.24 3.32
2853 3199 2.789491 GCATGGAGCCAAAAGATAGC 57.211 50.000 0.00 0.00 37.23 2.97
2871 3217 1.817099 CATCAGTCCTTGCTCCGGC 60.817 63.158 0.00 0.00 39.26 6.13
2872 3218 0.179089 CTCATCAGTCCTTGCTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
2873 3219 0.534412 ACTCATCAGTCCTTGCTCCG 59.466 55.000 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.