Multiple sequence alignment - TraesCS7A01G017500

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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 TraesCS7A01G017500 chr7A 100.000 7569 0 0 1 7569 7593459 7585891 0.000000e+00 13978
1 TraesCS7A01G017500 chr7D 91.839 7695 344 127 1 7569 6478746 6471210 0.000000e+00 10469
2 TraesCS7A01G017500 chr4A 92.904 6440 276 85 801 7135 733705622 733711985 0.000000e+00 9193
3 TraesCS7A01G017500 chr4A 85.177 452 30 13 7132 7569 733712096 733712524 5.430000e-116 429
4 TraesCS7A01G017500 chr4A 83.465 127 9 8 1 127 733699966 733700080 2.890000e-19 108
5 TraesCS7A01G017500 chr1B 85.362 690 90 8 3645 4331 683126101 683126782 0.000000e+00 704
6 TraesCS7A01G017500 chr1B 84.571 350 38 3 5219 5565 683132882 683133218 4.380000e-87 333
7 TraesCS7A01G017500 chr1D 83.838 594 58 19 4427 5018 490421990 490422547 1.450000e-146 531
8 TraesCS7A01G017500 chr1D 86.091 417 44 9 3654 4059 490420865 490421278 3.240000e-118 436
9 TraesCS7A01G017500 chr1D 80.769 546 43 23 5124 5653 490422545 490423044 3.340000e-98 370
10 TraesCS7A01G017500 chr1D 87.552 241 27 2 4093 4333 490421279 490421516 7.480000e-70 276
11 TraesCS7A01G017500 chr1A 89.873 158 13 3 2546 2701 8628974 8628818 4.630000e-47 200
12 TraesCS7A01G017500 chr4B 88.618 123 6 6 1 123 44859380 44859266 7.920000e-30 143


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 TraesCS7A01G017500 chr7A 7585891 7593459 7568 True 13978.00 13978 100.0000 1 7569 1 chr7A.!!$R1 7568
1 TraesCS7A01G017500 chr7D 6471210 6478746 7536 True 10469.00 10469 91.8390 1 7569 1 chr7D.!!$R1 7568
2 TraesCS7A01G017500 chr4A 733705622 733712524 6902 False 4811.00 9193 89.0405 801 7569 2 chr4A.!!$F2 6768
3 TraesCS7A01G017500 chr1B 683126101 683126782 681 False 704.00 704 85.3620 3645 4331 1 chr1B.!!$F1 686
4 TraesCS7A01G017500 chr1D 490420865 490423044 2179 False 403.25 531 84.5625 3654 5653 4 chr1D.!!$F1 1999

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
152 156 0.188342 GCCTCAGATCCTCTCTCCCT 59.812 60.000 0.00 0.0 29.16 4.20 F
1049 1107 0.105593 CTCATCACTATGCCCTGCGT 59.894 55.000 0.00 0.0 32.76 5.24 F
1207 1269 0.322975 AGTCTGACCGCTGCAAGAAT 59.677 50.000 3.76 0.0 34.07 2.40 F
2123 2210 0.034059 CAAGGTCTGAGCTTCCACGT 59.966 55.000 18.45 0.0 32.99 4.49 F
2137 2224 0.108615 CCACGTGTGTCTCTCCATCC 60.109 60.000 15.65 0.0 0.00 3.51 F
3296 3418 0.250513 ACTTCCATCTGGAGGCGTTC 59.749 55.000 8.17 0.0 46.36 3.95 F
4696 5215 1.082019 TGGTATCCCAGAGCCACCA 59.918 57.895 0.00 0.0 35.17 4.17 F
6047 6591 0.250727 GGCCTGCTGTTGGTGACTAA 60.251 55.000 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1146 0.029035 GCAGCGGATCAGCAAATCAG 59.971 55.000 20.15 3.78 40.15 2.90 R
2110 2197 0.032678 AGACACACGTGGAAGCTCAG 59.967 55.000 21.57 1.60 34.19 3.35 R
3028 3146 3.055094 GGCAACTAGAATCCCAAGAGTGA 60.055 47.826 0.00 0.00 0.00 3.41 R
3649 3771 2.717639 AGGTTGGTCCATGTCATAGC 57.282 50.000 0.00 0.00 39.02 2.97 R
3652 3774 5.192522 AGAGAATAAGGTTGGTCCATGTCAT 59.807 40.000 0.00 0.00 39.02 3.06 R
5098 5619 1.590932 CATCCTTGGAATGGAGCTCG 58.409 55.000 7.83 0.00 44.09 5.03 R
6398 6963 0.396695 TCTGGACCCGATGGACCTAC 60.397 60.000 2.02 0.00 45.57 3.18 R
7044 7634 0.178767 TCCAAGGCTGACATCCATCG 59.821 55.000 0.00 0.00 0.00 3.84 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
36 37 1.359848 GCGACTTGGTGATGGTGTAG 58.640 55.000 0.00 0.00 0.00 2.74
144 148 2.039624 ACCCACGCCTCAGATCCT 59.960 61.111 0.00 0.00 0.00 3.24
146 150 1.760086 CCCACGCCTCAGATCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
147 151 1.739049 CCACGCCTCAGATCCTCTC 59.261 63.158 0.00 0.00 0.00 3.20
148 152 0.754957 CCACGCCTCAGATCCTCTCT 60.755 60.000 0.00 0.00 33.14 3.10
149 153 0.667993 CACGCCTCAGATCCTCTCTC 59.332 60.000 0.00 0.00 29.16 3.20
150 154 0.467290 ACGCCTCAGATCCTCTCTCC 60.467 60.000 0.00 0.00 29.16 3.71
151 155 1.178534 CGCCTCAGATCCTCTCTCCC 61.179 65.000 0.00 0.00 29.16 4.30
152 156 0.188342 GCCTCAGATCCTCTCTCCCT 59.812 60.000 0.00 0.00 29.16 4.20
153 157 1.823250 GCCTCAGATCCTCTCTCCCTC 60.823 61.905 0.00 0.00 29.16 4.30
154 158 1.782752 CCTCAGATCCTCTCTCCCTCT 59.217 57.143 0.00 0.00 29.16 3.69
155 159 2.224867 CCTCAGATCCTCTCTCCCTCTC 60.225 59.091 0.00 0.00 29.16 3.20
156 160 2.713167 CTCAGATCCTCTCTCCCTCTCT 59.287 54.545 0.00 0.00 29.16 3.10
157 161 2.442878 TCAGATCCTCTCTCCCTCTCTG 59.557 54.545 0.00 0.00 29.16 3.35
158 162 2.442878 CAGATCCTCTCTCCCTCTCTGA 59.557 54.545 0.00 0.00 32.36 3.27
159 163 3.074985 CAGATCCTCTCTCCCTCTCTGAT 59.925 52.174 0.00 0.00 32.36 2.90
160 164 3.331889 AGATCCTCTCTCCCTCTCTGATC 59.668 52.174 0.00 0.00 0.00 2.92
161 165 1.780309 TCCTCTCTCCCTCTCTGATCC 59.220 57.143 0.00 0.00 0.00 3.36
162 166 1.545428 CCTCTCTCCCTCTCTGATCCG 60.545 61.905 0.00 0.00 0.00 4.18
163 167 1.419762 CTCTCTCCCTCTCTGATCCGA 59.580 57.143 0.00 0.00 0.00 4.55
164 168 2.040278 CTCTCTCCCTCTCTGATCCGAT 59.960 54.545 0.00 0.00 0.00 4.18
165 169 2.039746 TCTCTCCCTCTCTGATCCGATC 59.960 54.545 1.01 1.01 0.00 3.69
166 170 2.040278 CTCTCCCTCTCTGATCCGATCT 59.960 54.545 9.78 0.00 0.00 2.75
167 171 2.039746 TCTCCCTCTCTGATCCGATCTC 59.960 54.545 9.78 0.00 0.00 2.75
168 172 1.777272 TCCCTCTCTGATCCGATCTCA 59.223 52.381 9.78 0.00 0.00 3.27
169 173 2.161855 CCCTCTCTGATCCGATCTCAG 58.838 57.143 9.78 4.46 41.23 3.35
174 178 3.390967 TCTCTGATCCGATCTCAGTCTCT 59.609 47.826 9.78 0.00 40.79 3.10
191 195 5.596361 CAGTCTCTCTCTCTCTCTCTCTAGT 59.404 48.000 0.00 0.00 0.00 2.57
195 199 5.766590 TCTCTCTCTCTCTCTCTAGTCTGA 58.233 45.833 0.00 0.00 0.00 3.27
196 200 5.830457 TCTCTCTCTCTCTCTCTAGTCTGAG 59.170 48.000 0.00 0.00 35.52 3.35
197 201 5.519808 TCTCTCTCTCTCTCTAGTCTGAGT 58.480 45.833 8.94 0.00 35.68 3.41
198 202 5.594725 TCTCTCTCTCTCTCTAGTCTGAGTC 59.405 48.000 8.94 0.00 35.68 3.36
199 203 5.519808 TCTCTCTCTCTCTAGTCTGAGTCT 58.480 45.833 0.00 0.00 35.68 3.24
200 204 5.360999 TCTCTCTCTCTCTAGTCTGAGTCTG 59.639 48.000 0.00 0.00 35.68 3.51
201 205 4.122776 CTCTCTCTCTAGTCTGAGTCTGC 58.877 52.174 0.00 0.00 35.68 4.26
227 231 5.146868 TGAGGAATGGAATGGAATGGAAT 57.853 39.130 0.00 0.00 0.00 3.01
228 232 4.897076 TGAGGAATGGAATGGAATGGAATG 59.103 41.667 0.00 0.00 0.00 2.67
230 234 3.388676 GGAATGGAATGGAATGGAATGCA 59.611 43.478 0.00 0.00 0.00 3.96
231 235 4.141665 GGAATGGAATGGAATGGAATGCAA 60.142 41.667 0.00 0.00 0.00 4.08
232 236 3.891422 TGGAATGGAATGGAATGCAAC 57.109 42.857 0.00 0.00 0.00 4.17
258 262 4.486503 CAGCAGCAGAGCCCTCCC 62.487 72.222 0.00 0.00 34.23 4.30
418 434 2.332654 GGGGCTGAACGCGAAATGT 61.333 57.895 15.93 0.00 40.44 2.71
419 435 1.154225 GGGCTGAACGCGAAATGTG 60.154 57.895 15.93 0.00 40.44 3.21
420 436 1.797537 GGCTGAACGCGAAATGTGC 60.798 57.895 15.93 9.06 40.44 4.57
454 470 6.234177 TCTCCAAAATGTTTTCTCTCTCCTC 58.766 40.000 0.00 0.00 0.00 3.71
455 471 5.316987 TCCAAAATGTTTTCTCTCTCCTCC 58.683 41.667 0.00 0.00 0.00 4.30
456 472 4.460731 CCAAAATGTTTTCTCTCTCCTCCC 59.539 45.833 0.00 0.00 0.00 4.30
457 473 4.308526 AAATGTTTTCTCTCTCCTCCCC 57.691 45.455 0.00 0.00 0.00 4.81
458 474 2.723530 TGTTTTCTCTCTCCTCCCCT 57.276 50.000 0.00 0.00 0.00 4.79
459 475 2.541466 TGTTTTCTCTCTCCTCCCCTC 58.459 52.381 0.00 0.00 0.00 4.30
460 476 1.834896 GTTTTCTCTCTCCTCCCCTCC 59.165 57.143 0.00 0.00 0.00 4.30
461 477 1.398799 TTTCTCTCTCCTCCCCTCCT 58.601 55.000 0.00 0.00 0.00 3.69
462 478 0.930726 TTCTCTCTCCTCCCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
463 479 0.996762 TCTCTCTCCTCCCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
464 480 0.998945 CTCTCTCCTCCCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
476 492 1.760029 CCTCCTCCTGTTAGCTTCCTC 59.240 57.143 0.00 0.00 0.00 3.71
518 546 0.900647 ATCATCCCCGTCCGATCTCC 60.901 60.000 0.00 0.00 0.00 3.71
520 548 2.780185 ATCCCCGTCCGATCTCCCT 61.780 63.158 0.00 0.00 0.00 4.20
522 550 2.913060 CCCGTCCGATCTCCCTCC 60.913 72.222 0.00 0.00 0.00 4.30
526 554 2.704198 TCCGATCTCCCTCCCCCT 60.704 66.667 0.00 0.00 0.00 4.79
528 556 2.203714 CGATCTCCCTCCCCCTCC 60.204 72.222 0.00 0.00 0.00 4.30
624 663 4.038080 CGGAAAACCCAGGTGCGC 62.038 66.667 0.00 0.00 34.14 6.09
625 664 2.909965 GGAAAACCCAGGTGCGCA 60.910 61.111 5.66 5.66 34.14 6.09
626 665 2.644992 GAAAACCCAGGTGCGCAG 59.355 61.111 12.22 0.00 0.00 5.18
673 712 3.854669 CCGCCCAGATTCGCCTCT 61.855 66.667 0.00 0.00 0.00 3.69
687 735 1.521681 CCTCTGAATCGCGGTTCCC 60.522 63.158 28.05 6.76 0.00 3.97
703 751 0.759812 TCCCCGTTTGTTTTTCCCCC 60.760 55.000 0.00 0.00 0.00 5.40
704 752 1.364536 CCCGTTTGTTTTTCCCCCG 59.635 57.895 0.00 0.00 0.00 5.73
705 753 1.364536 CCGTTTGTTTTTCCCCCGG 59.635 57.895 0.00 0.00 0.00 5.73
706 754 1.300311 CGTTTGTTTTTCCCCCGGC 60.300 57.895 0.00 0.00 0.00 6.13
707 755 1.740332 CGTTTGTTTTTCCCCCGGCT 61.740 55.000 0.00 0.00 0.00 5.52
709 757 1.271379 GTTTGTTTTTCCCCCGGCTAG 59.729 52.381 0.00 0.00 0.00 3.42
710 758 0.896479 TTGTTTTTCCCCCGGCTAGC 60.896 55.000 6.04 6.04 0.00 3.42
711 759 1.001269 GTTTTTCCCCCGGCTAGCT 60.001 57.895 15.72 0.00 0.00 3.32
712 760 1.030488 GTTTTTCCCCCGGCTAGCTC 61.030 60.000 15.72 3.82 0.00 4.09
713 761 2.206182 TTTTTCCCCCGGCTAGCTCC 62.206 60.000 15.72 0.00 0.00 4.70
761 809 1.148048 GCTGCAGGAGGAGGATTCC 59.852 63.158 17.12 0.00 44.39 3.01
764 812 2.812619 GCAGGAGGAGGATTCCCGG 61.813 68.421 0.00 0.00 45.24 5.73
907 965 4.787280 CACCGCCTCCCTCCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
923 981 1.346722 CCTCTCGCCCCGGTTAATTAT 59.653 52.381 0.00 0.00 0.00 1.28
924 982 2.224450 CCTCTCGCCCCGGTTAATTATT 60.224 50.000 0.00 0.00 0.00 1.40
925 983 3.473625 CTCTCGCCCCGGTTAATTATTT 58.526 45.455 0.00 0.00 0.00 1.40
926 984 3.207778 TCTCGCCCCGGTTAATTATTTG 58.792 45.455 0.00 0.00 0.00 2.32
927 985 1.677052 TCGCCCCGGTTAATTATTTGC 59.323 47.619 0.00 0.00 0.00 3.68
928 986 1.679153 CGCCCCGGTTAATTATTTGCT 59.321 47.619 0.00 0.00 0.00 3.91
929 987 2.879646 CGCCCCGGTTAATTATTTGCTA 59.120 45.455 0.00 0.00 0.00 3.49
965 1023 4.769050 AGATTTTAGCCTAGCCCCTAGAT 58.231 43.478 0.00 0.00 36.26 1.98
1025 1083 4.785453 CGAGGCCCCCAAGTGAGC 62.785 72.222 0.00 0.00 0.00 4.26
1027 1085 3.927481 GAGGCCCCCAAGTGAGCAC 62.927 68.421 0.00 0.00 0.00 4.40
1049 1107 0.105593 CTCATCACTATGCCCTGCGT 59.894 55.000 0.00 0.00 32.76 5.24
1066 1124 1.656441 GTTGTCTGTTGCTGCCAGG 59.344 57.895 0.00 0.00 0.00 4.45
1071 1129 4.208403 TGTTGCTGCCAGGGTGCT 62.208 61.111 0.00 0.00 0.00 4.40
1072 1130 2.034066 GTTGCTGCCAGGGTGCTA 59.966 61.111 0.00 0.00 0.00 3.49
1074 1132 2.223443 TTGCTGCCAGGGTGCTAGA 61.223 57.895 0.00 0.00 0.00 2.43
1075 1133 2.188994 GCTGCCAGGGTGCTAGAG 59.811 66.667 0.00 0.00 0.00 2.43
1076 1134 2.362369 GCTGCCAGGGTGCTAGAGA 61.362 63.158 0.00 0.00 0.00 3.10
1077 1135 1.519719 CTGCCAGGGTGCTAGAGAC 59.480 63.158 0.00 0.00 0.00 3.36
1078 1136 0.975040 CTGCCAGGGTGCTAGAGACT 60.975 60.000 0.00 0.00 0.00 3.24
1080 1138 1.681486 GCCAGGGTGCTAGAGACTCC 61.681 65.000 0.00 0.00 0.00 3.85
1081 1139 1.045911 CCAGGGTGCTAGAGACTCCC 61.046 65.000 0.00 0.00 38.50 4.30
1083 1141 1.225403 AGGGTGCTAGAGACTCCCCT 61.225 60.000 9.77 9.77 38.97 4.79
1084 1142 0.325765 GGGTGCTAGAGACTCCCCTT 60.326 60.000 6.51 0.00 32.66 3.95
1088 1146 2.364002 GTGCTAGAGACTCCCCTTCATC 59.636 54.545 0.00 0.00 0.00 2.92
1089 1147 2.246067 TGCTAGAGACTCCCCTTCATCT 59.754 50.000 0.00 0.00 0.00 2.90
1090 1148 2.627699 GCTAGAGACTCCCCTTCATCTG 59.372 54.545 0.00 0.00 0.00 2.90
1091 1149 3.689858 GCTAGAGACTCCCCTTCATCTGA 60.690 52.174 0.00 0.00 0.00 3.27
1092 1150 3.704545 AGAGACTCCCCTTCATCTGAT 57.295 47.619 0.00 0.00 0.00 2.90
1093 1151 4.006247 AGAGACTCCCCTTCATCTGATT 57.994 45.455 0.00 0.00 0.00 2.57
1095 1153 4.163839 AGAGACTCCCCTTCATCTGATTTG 59.836 45.833 0.00 0.00 0.00 2.32
1101 1163 3.568853 CCCCTTCATCTGATTTGCTGATC 59.431 47.826 0.00 0.00 33.45 2.92
1136 1198 1.378531 GTGTTTGTCTGTCTGTGCCA 58.621 50.000 0.00 0.00 0.00 4.92
1207 1269 0.322975 AGTCTGACCGCTGCAAGAAT 59.677 50.000 3.76 0.00 34.07 2.40
1264 1327 1.302832 CTGTCGCTTTGCCCTCCTT 60.303 57.895 0.00 0.00 0.00 3.36
1267 1333 1.150536 TCGCTTTGCCCTCCTTGTT 59.849 52.632 0.00 0.00 0.00 2.83
1271 1337 1.538849 GCTTTGCCCTCCTTGTTTGTG 60.539 52.381 0.00 0.00 0.00 3.33
1277 1343 2.956333 GCCCTCCTTGTTTGTGTAACTT 59.044 45.455 0.00 0.00 38.04 2.66
1283 1349 6.094881 CCTCCTTGTTTGTGTAACTTCTTTCA 59.905 38.462 0.00 0.00 38.04 2.69
1328 1395 4.381079 GCGACAACCTTCTATCTCTGTCTT 60.381 45.833 0.00 0.00 32.80 3.01
1329 1396 5.715070 CGACAACCTTCTATCTCTGTCTTT 58.285 41.667 0.00 0.00 32.80 2.52
1336 1403 5.105392 CCTTCTATCTCTGTCTTTGAGCAGT 60.105 44.000 0.00 0.00 34.57 4.40
1417 1484 2.995574 CTGGGAAGGTCCGACGGT 60.996 66.667 14.79 0.00 37.43 4.83
1610 1677 2.957402 AGCTCTGGGAACATGTGAAA 57.043 45.000 0.00 0.00 41.51 2.69
1613 1680 3.149196 GCTCTGGGAACATGTGAAAGAA 58.851 45.455 0.00 0.00 41.51 2.52
1614 1681 3.190118 GCTCTGGGAACATGTGAAAGAAG 59.810 47.826 0.00 0.00 41.51 2.85
1616 1683 5.047566 TCTGGGAACATGTGAAAGAAGAA 57.952 39.130 0.00 0.00 41.51 2.52
1617 1684 5.634118 TCTGGGAACATGTGAAAGAAGAAT 58.366 37.500 0.00 0.00 41.51 2.40
1620 1687 7.391554 TCTGGGAACATGTGAAAGAAGAATTAG 59.608 37.037 0.00 0.00 41.51 1.73
1621 1688 6.071952 TGGGAACATGTGAAAGAAGAATTAGC 60.072 38.462 0.00 0.00 33.40 3.09
1622 1689 6.151817 GGGAACATGTGAAAGAAGAATTAGCT 59.848 38.462 0.00 0.00 0.00 3.32
1660 1732 3.118371 ACCCTTTTCGATATGACCACTCC 60.118 47.826 0.00 0.00 0.00 3.85
1663 1735 3.880047 TTTCGATATGACCACTCCGTT 57.120 42.857 0.00 0.00 0.00 4.44
1664 1736 2.863401 TCGATATGACCACTCCGTTG 57.137 50.000 0.00 0.00 0.00 4.10
1665 1737 1.407618 TCGATATGACCACTCCGTTGG 59.592 52.381 0.00 0.00 43.04 3.77
1676 1748 4.732784 CCACTCCGTTGGTGAAATAAATG 58.267 43.478 0.00 0.00 36.89 2.32
1679 1751 6.317642 CCACTCCGTTGGTGAAATAAATGATA 59.682 38.462 0.00 0.00 36.89 2.15
1711 1783 5.411781 CGTATCAGGAGCTTTTTACTCTGT 58.588 41.667 0.00 0.00 34.46 3.41
1722 1796 7.475840 AGCTTTTTACTCTGTGTCTCAAAAAG 58.524 34.615 16.83 16.83 40.78 2.27
1738 1812 5.136828 TCAAAAAGGAAACCTGATGTGCTA 58.863 37.500 0.00 0.00 32.13 3.49
1771 1847 0.885879 TGTCTGTCGGTGTCGCTAAT 59.114 50.000 0.00 0.00 36.13 1.73
1848 1935 5.705609 TTTTCTTTCCTGTGCATCCTAAC 57.294 39.130 0.00 0.00 0.00 2.34
1853 1940 4.901197 TTCCTGTGCATCCTAACTTACA 57.099 40.909 0.00 0.00 0.00 2.41
1863 1950 8.601476 GTGCATCCTAACTTACACACTTATTAC 58.399 37.037 0.00 0.00 0.00 1.89
1864 1951 8.537016 TGCATCCTAACTTACACACTTATTACT 58.463 33.333 0.00 0.00 0.00 2.24
1865 1952 9.379791 GCATCCTAACTTACACACTTATTACTT 57.620 33.333 0.00 0.00 0.00 2.24
1906 1993 3.944015 GCATTCTTCTTATCTGCTGTGGT 59.056 43.478 0.00 0.00 0.00 4.16
1923 2010 6.030228 GCTGTGGTATTCTTTTTATGTCTGC 58.970 40.000 0.00 0.00 0.00 4.26
1931 2018 6.683974 TTCTTTTTATGTCTGCAGATAGGC 57.316 37.500 21.47 7.44 0.00 3.93
1951 2038 4.895297 AGGCATAATGGAACCCAATACAAG 59.105 41.667 0.00 0.00 36.95 3.16
2110 2197 0.953960 CACCACGCCCTTACAAGGTC 60.954 60.000 7.23 0.00 44.98 3.85
2123 2210 0.034059 CAAGGTCTGAGCTTCCACGT 59.966 55.000 18.45 0.00 32.99 4.49
2131 2218 0.315568 GAGCTTCCACGTGTGTCTCT 59.684 55.000 15.65 4.61 0.00 3.10
2132 2219 0.315568 AGCTTCCACGTGTGTCTCTC 59.684 55.000 15.65 0.00 0.00 3.20
2137 2224 0.108615 CCACGTGTGTCTCTCCATCC 60.109 60.000 15.65 0.00 0.00 3.51
2746 2839 7.754851 ATGCATGCAATCATCATCTAAGTAA 57.245 32.000 26.68 0.00 0.00 2.24
2870 2969 8.896320 TTACTATTGCTGACAGTTTTTACTCA 57.104 30.769 3.99 0.00 0.00 3.41
2986 3102 9.270640 GCACTATGAGATATTGTTCTGATTTCT 57.729 33.333 0.00 0.00 0.00 2.52
3063 3181 2.687700 AGTTGCCATCTCTGTAGCAG 57.312 50.000 0.00 0.00 36.44 4.24
3296 3418 0.250513 ACTTCCATCTGGAGGCGTTC 59.749 55.000 8.17 0.00 46.36 3.95
3370 3492 5.010314 GGAAGCTGATGCAATGGATGATAAA 59.990 40.000 0.00 0.00 42.74 1.40
3506 3628 7.627340 CAATTTACCGACATATGTTGAGGTAC 58.373 38.462 25.38 7.91 39.75 3.34
3546 3668 4.530094 TTTTGTTGTGCTCACTCTTACG 57.470 40.909 1.47 0.00 0.00 3.18
3591 3713 2.429971 TGTGGATCTCTGTCATCTCTGC 59.570 50.000 0.00 0.00 0.00 4.26
3649 3771 6.737254 AAGACCATTTTGTACGGTTATGAG 57.263 37.500 0.00 0.00 31.63 2.90
3652 3774 5.736813 ACCATTTTGTACGGTTATGAGCTA 58.263 37.500 0.00 0.00 0.00 3.32
3672 3794 5.103940 AGCTATGACATGGACCAACCTTATT 60.104 40.000 0.00 0.00 39.86 1.40
3696 3818 5.997129 TCTCTGAATGTAAATGTGCTGTTGA 59.003 36.000 0.00 0.00 0.00 3.18
3768 3891 5.868257 TGCTGTTCATGTCGTCATAAAATC 58.132 37.500 0.00 0.00 32.47 2.17
3794 3917 7.175641 CCCAATGGGTCTTACTCAAATATGATC 59.824 40.741 10.91 0.00 38.25 2.92
3852 3975 1.202903 GGGATGAATGGCTGCTGAGAT 60.203 52.381 0.00 0.00 0.00 2.75
3867 3991 8.235905 GGCTGCTGAGATATTTTCTATCAAATC 58.764 37.037 0.00 0.00 33.74 2.17
3929 4053 7.659390 AGCTGATGGTGATATAAACTTCTTAGC 59.341 37.037 0.00 0.00 0.00 3.09
4100 4232 3.499338 ACAGATTTGTTGGGCATTCAGA 58.501 40.909 0.00 0.00 32.28 3.27
4101 4233 4.091549 ACAGATTTGTTGGGCATTCAGAT 58.908 39.130 0.00 0.00 32.28 2.90
4303 4435 3.786635 AGAAGTAGAATCGTCATGCCAC 58.213 45.455 0.00 0.00 0.00 5.01
4305 4437 1.202417 AGTAGAATCGTCATGCCACGG 60.202 52.381 7.05 0.00 40.35 4.94
4415 4918 9.642343 ACTTCTCCTTTTATTTTACAAGGTTCT 57.358 29.630 0.00 0.00 38.62 3.01
4471 4990 7.079451 AGATTCAAAACCTTCAGAGGACTTA 57.921 36.000 0.00 0.00 46.74 2.24
4521 5040 1.686052 GAACAATGACAAACCAGGCCA 59.314 47.619 5.01 0.00 0.00 5.36
4533 5052 2.957474 ACCAGGCCAACAAAACATAGT 58.043 42.857 5.01 0.00 0.00 2.12
4555 5074 2.158813 TCCTGGTCCAACTTTGTCTGAC 60.159 50.000 0.00 0.00 0.00 3.51
4695 5214 4.066614 TGGTATCCCAGAGCCACC 57.933 61.111 0.00 0.00 35.17 4.61
4696 5215 1.082019 TGGTATCCCAGAGCCACCA 59.918 57.895 0.00 0.00 35.17 4.17
5098 5619 1.388547 TCGGGGCTGCATTTATGAAC 58.611 50.000 0.50 0.00 0.00 3.18
5680 6217 2.591715 CATGATCCCCGCCGTTCC 60.592 66.667 0.00 0.00 0.00 3.62
5782 6319 3.506096 CTGCAGCGCATGAGTGGG 61.506 66.667 11.47 0.00 38.13 4.61
5993 6535 4.219033 GCAGTTTATTCCGTCACTGTTTG 58.781 43.478 0.00 0.00 39.14 2.93
6047 6591 0.250727 GGCCTGCTGTTGGTGACTAA 60.251 55.000 0.00 0.00 0.00 2.24
6060 6604 4.806330 TGGTGACTAAGACAAGAACGATC 58.194 43.478 0.00 0.00 0.00 3.69
6067 6611 7.808381 TGACTAAGACAAGAACGATCTGTTTAG 59.192 37.037 0.00 5.38 42.09 1.85
6082 6626 7.118390 CGATCTGTTTAGTTCCAAAATCTGACT 59.882 37.037 0.00 0.00 0.00 3.41
6088 6632 8.841300 GTTTAGTTCCAAAATCTGACTTCTCTT 58.159 33.333 0.00 0.00 0.00 2.85
6090 6634 9.712305 TTAGTTCCAAAATCTGACTTCTCTTAG 57.288 33.333 0.00 0.00 0.00 2.18
6132 6681 2.880890 ACTCATTCAAGTTGTGCCTGAC 59.119 45.455 2.11 0.00 0.00 3.51
6172 6721 8.421249 AATTGGTTGATTGGAGTTGAATTCTA 57.579 30.769 7.05 0.00 0.00 2.10
6174 6723 6.303054 TGGTTGATTGGAGTTGAATTCTACA 58.697 36.000 19.82 0.00 0.00 2.74
6177 6726 7.415653 GGTTGATTGGAGTTGAATTCTACATCC 60.416 40.741 19.82 20.30 0.00 3.51
6225 6777 8.211116 TCGGAACTTCATTTACTGTTAAAACA 57.789 30.769 0.00 0.00 37.37 2.83
6355 6914 1.194547 CGTGACATCCAAACCGTTCAG 59.805 52.381 0.00 0.00 0.00 3.02
6445 7010 1.528309 CAACCACCCAGACGCCTTT 60.528 57.895 0.00 0.00 0.00 3.11
6475 7040 1.078637 GCAGATGGAGCTCACAGCA 60.079 57.895 17.19 4.28 45.56 4.41
6493 7058 5.066117 CACAGCAAGATCAAAGCAGATACAT 59.934 40.000 0.00 0.00 0.00 2.29
6538 7103 4.489771 GGCAGCATGTACGGGCCT 62.490 66.667 0.84 0.00 41.39 5.19
6544 7109 1.522355 CATGTACGGGCCTGAGCTG 60.522 63.158 21.41 6.19 39.73 4.24
6600 7166 2.742372 GTGCCTGTCGTCGCCATT 60.742 61.111 0.00 0.00 0.00 3.16
6605 7171 1.811266 CTGTCGTCGCCATTCCCTG 60.811 63.158 0.00 0.00 0.00 4.45
6607 7173 1.375523 GTCGTCGCCATTCCCTGTT 60.376 57.895 0.00 0.00 0.00 3.16
6697 7267 2.885861 CTCGTCGGGGAGGAAGTG 59.114 66.667 0.00 0.00 0.00 3.16
6787 7368 1.383803 ATCTGGTGAGGGAGGGAGC 60.384 63.158 0.00 0.00 0.00 4.70
6939 7524 0.324645 GCATTTGGTCCCCCTGATGT 60.325 55.000 0.00 0.00 0.00 3.06
6944 7529 2.302587 TGGTCCCCCTGATGTTTTTC 57.697 50.000 0.00 0.00 0.00 2.29
6948 7535 3.258372 GGTCCCCCTGATGTTTTTCTTTC 59.742 47.826 0.00 0.00 0.00 2.62
6982 7572 6.645003 GGAAAAACTAACCATTCACATCAACC 59.355 38.462 0.00 0.00 0.00 3.77
7012 7602 5.652994 AAGGCTGTGACACAAAGTTAAAA 57.347 34.783 10.02 0.00 0.00 1.52
7014 7604 5.831997 AGGCTGTGACACAAAGTTAAAATC 58.168 37.500 10.02 0.00 0.00 2.17
7018 7608 6.533367 GCTGTGACACAAAGTTAAAATCCAAA 59.467 34.615 10.02 0.00 0.00 3.28
7056 7646 6.871844 AGACCAATATATCGATGGATGTCAG 58.128 40.000 8.54 0.00 37.66 3.51
7061 7651 2.251409 ATCGATGGATGTCAGCCTTG 57.749 50.000 8.91 0.00 0.00 3.61
7062 7652 0.178767 TCGATGGATGTCAGCCTTGG 59.821 55.000 8.91 3.66 0.00 3.61
7071 7661 3.057969 TGTCAGCCTTGGACAATACTG 57.942 47.619 7.68 7.68 41.96 2.74
7073 7663 3.580895 TGTCAGCCTTGGACAATACTGTA 59.419 43.478 11.70 0.00 41.96 2.74
7075 7665 5.186198 GTCAGCCTTGGACAATACTGTATT 58.814 41.667 7.22 7.22 35.30 1.89
7076 7666 5.648092 GTCAGCCTTGGACAATACTGTATTT 59.352 40.000 10.25 3.21 35.30 1.40
7156 7861 1.671556 GGTTGGGGTAAAATGCTTGCG 60.672 52.381 0.00 0.00 0.00 4.85
7177 7882 4.391830 GCGGAAATCTGTGACATGAAGTTA 59.608 41.667 0.00 0.00 0.00 2.24
7184 7889 9.520204 AAATCTGTGACATGAAGTTAAAAGTTG 57.480 29.630 0.00 0.00 0.00 3.16
7202 7907 8.735692 AAAAGTTGATCATCACAAAACCAAAT 57.264 26.923 6.55 0.00 0.00 2.32
7204 7909 7.718272 AGTTGATCATCACAAAACCAAATTG 57.282 32.000 6.55 0.00 0.00 2.32
7305 8014 4.962995 TGTTTTTGTGAGGGTAAAATGGGA 59.037 37.500 0.00 0.00 0.00 4.37
7310 8019 5.736951 TGTGAGGGTAAAATGGGAATTTG 57.263 39.130 0.00 0.00 0.00 2.32
7314 8023 6.995686 GTGAGGGTAAAATGGGAATTTGTTTT 59.004 34.615 0.00 0.00 0.00 2.43
7356 8065 2.607892 GCGGCACTGTGTTGGAGTC 61.608 63.158 9.86 0.00 0.00 3.36
7362 8071 2.224066 GCACTGTGTTGGAGTCTAGTGT 60.224 50.000 9.86 0.00 38.17 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 148 1.512735 TCGGATCAGAGAGGGAGAGA 58.487 55.000 0.00 0.00 0.00 3.10
146 150 2.039746 GAGATCGGATCAGAGAGGGAGA 59.960 54.545 19.47 0.00 0.00 3.71
147 151 2.224744 TGAGATCGGATCAGAGAGGGAG 60.225 54.545 19.47 0.00 0.00 4.30
148 152 1.777272 TGAGATCGGATCAGAGAGGGA 59.223 52.381 19.47 0.00 0.00 4.20
149 153 2.161855 CTGAGATCGGATCAGAGAGGG 58.838 57.143 19.47 0.05 45.80 4.30
150 154 2.813754 GACTGAGATCGGATCAGAGAGG 59.186 54.545 19.47 6.37 45.80 3.69
151 155 3.743521 AGACTGAGATCGGATCAGAGAG 58.256 50.000 19.47 11.13 45.80 3.20
152 156 3.390967 AGAGACTGAGATCGGATCAGAGA 59.609 47.826 19.47 0.32 45.80 3.10
153 157 3.743521 AGAGACTGAGATCGGATCAGAG 58.256 50.000 19.47 15.44 45.80 3.35
154 158 3.390967 AGAGAGACTGAGATCGGATCAGA 59.609 47.826 19.47 0.00 45.80 3.27
156 160 3.390967 AGAGAGAGACTGAGATCGGATCA 59.609 47.826 19.47 0.99 0.00 2.92
157 161 3.997021 GAGAGAGAGACTGAGATCGGATC 59.003 52.174 10.02 10.02 0.00 3.36
158 162 3.648067 AGAGAGAGAGACTGAGATCGGAT 59.352 47.826 0.00 0.00 0.00 4.18
159 163 3.038280 AGAGAGAGAGACTGAGATCGGA 58.962 50.000 0.00 0.00 0.00 4.55
160 164 3.070159 AGAGAGAGAGAGACTGAGATCGG 59.930 52.174 0.00 0.00 0.00 4.18
161 165 4.038522 AGAGAGAGAGAGAGACTGAGATCG 59.961 50.000 0.00 0.00 0.00 3.69
162 166 5.304101 AGAGAGAGAGAGAGAGACTGAGATC 59.696 48.000 0.00 0.00 0.00 2.75
163 167 5.215069 AGAGAGAGAGAGAGAGACTGAGAT 58.785 45.833 0.00 0.00 0.00 2.75
164 168 4.614475 AGAGAGAGAGAGAGAGACTGAGA 58.386 47.826 0.00 0.00 0.00 3.27
165 169 4.648762 AGAGAGAGAGAGAGAGAGACTGAG 59.351 50.000 0.00 0.00 0.00 3.35
166 170 4.614475 AGAGAGAGAGAGAGAGAGACTGA 58.386 47.826 0.00 0.00 0.00 3.41
167 171 5.596361 ACTAGAGAGAGAGAGAGAGAGACTG 59.404 48.000 0.00 0.00 0.00 3.51
168 172 5.772004 ACTAGAGAGAGAGAGAGAGAGACT 58.228 45.833 0.00 0.00 0.00 3.24
169 173 5.830991 AGACTAGAGAGAGAGAGAGAGAGAC 59.169 48.000 0.00 0.00 0.00 3.36
174 178 5.519808 ACTCAGACTAGAGAGAGAGAGAGA 58.480 45.833 15.12 0.00 38.98 3.10
191 195 2.521547 TCCTCATCAGCAGACTCAGA 57.478 50.000 0.00 0.00 0.00 3.27
195 199 2.475155 TCCATTCCTCATCAGCAGACT 58.525 47.619 0.00 0.00 0.00 3.24
196 200 2.996249 TCCATTCCTCATCAGCAGAC 57.004 50.000 0.00 0.00 0.00 3.51
197 201 3.434596 CCATTCCATTCCTCATCAGCAGA 60.435 47.826 0.00 0.00 0.00 4.26
198 202 2.885266 CCATTCCATTCCTCATCAGCAG 59.115 50.000 0.00 0.00 0.00 4.24
199 203 2.510800 TCCATTCCATTCCTCATCAGCA 59.489 45.455 0.00 0.00 0.00 4.41
200 204 3.219176 TCCATTCCATTCCTCATCAGC 57.781 47.619 0.00 0.00 0.00 4.26
201 205 4.523173 CCATTCCATTCCATTCCTCATCAG 59.477 45.833 0.00 0.00 0.00 2.90
260 264 3.188786 CCTACCTTGAGCACGCGC 61.189 66.667 5.73 0.00 38.99 6.86
262 266 3.188786 CGCCTACCTTGAGCACGC 61.189 66.667 0.00 0.00 0.00 5.34
263 267 1.517257 CTCGCCTACCTTGAGCACG 60.517 63.158 0.00 0.00 0.00 5.34
264 268 0.458716 GTCTCGCCTACCTTGAGCAC 60.459 60.000 0.00 0.00 0.00 4.40
265 269 1.890894 GTCTCGCCTACCTTGAGCA 59.109 57.895 0.00 0.00 0.00 4.26
266 270 1.226717 CGTCTCGCCTACCTTGAGC 60.227 63.158 0.00 0.00 0.00 4.26
269 273 1.030488 TCCTCGTCTCGCCTACCTTG 61.030 60.000 0.00 0.00 0.00 3.61
270 274 1.031029 GTCCTCGTCTCGCCTACCTT 61.031 60.000 0.00 0.00 0.00 3.50
271 275 1.451747 GTCCTCGTCTCGCCTACCT 60.452 63.158 0.00 0.00 0.00 3.08
272 276 2.821688 CGTCCTCGTCTCGCCTACC 61.822 68.421 0.00 0.00 0.00 3.18
274 278 2.513204 CCGTCCTCGTCTCGCCTA 60.513 66.667 0.00 0.00 35.01 3.93
364 379 0.835543 TTGCAATTTGGTCCCTGGGG 60.836 55.000 14.00 2.42 0.00 4.96
366 381 3.675775 CGTATTTGCAATTTGGTCCCTGG 60.676 47.826 0.00 0.00 0.00 4.45
368 383 2.094234 GCGTATTTGCAATTTGGTCCCT 60.094 45.455 0.00 0.00 34.15 4.20
369 384 2.267426 GCGTATTTGCAATTTGGTCCC 58.733 47.619 0.00 0.00 34.15 4.46
372 387 1.542030 TCCGCGTATTTGCAATTTGGT 59.458 42.857 4.92 0.00 34.15 3.67
373 388 2.184448 CTCCGCGTATTTGCAATTTGG 58.816 47.619 4.92 0.00 34.15 3.28
375 390 1.201181 TGCTCCGCGTATTTGCAATTT 59.799 42.857 4.92 0.00 34.15 1.82
376 391 0.808125 TGCTCCGCGTATTTGCAATT 59.192 45.000 4.92 0.00 34.15 2.32
378 393 1.499949 GTGCTCCGCGTATTTGCAA 59.500 52.632 4.92 0.00 35.34 4.08
379 394 2.735677 CGTGCTCCGCGTATTTGCA 61.736 57.895 4.92 4.98 32.40 4.08
405 421 2.553770 CGGCACATTTCGCGTTCA 59.446 55.556 5.77 0.00 0.00 3.18
406 422 2.869702 GCGGCACATTTCGCGTTC 60.870 61.111 5.77 0.00 42.48 3.95
425 441 4.835056 AGAGAAAACATTTTGGAGAAGGGG 59.165 41.667 0.00 0.00 0.00 4.79
454 470 0.833949 GAAGCTAACAGGAGGAGGGG 59.166 60.000 0.00 0.00 0.00 4.79
455 471 0.833949 GGAAGCTAACAGGAGGAGGG 59.166 60.000 0.00 0.00 0.00 4.30
456 472 1.760029 GAGGAAGCTAACAGGAGGAGG 59.240 57.143 0.00 0.00 0.00 4.30
457 473 1.760029 GGAGGAAGCTAACAGGAGGAG 59.240 57.143 0.00 0.00 0.00 3.69
458 474 1.622725 GGGAGGAAGCTAACAGGAGGA 60.623 57.143 0.00 0.00 0.00 3.71
459 475 0.833949 GGGAGGAAGCTAACAGGAGG 59.166 60.000 0.00 0.00 0.00 4.30
460 476 1.760029 GAGGGAGGAAGCTAACAGGAG 59.240 57.143 0.00 0.00 0.00 3.69
461 477 1.362932 AGAGGGAGGAAGCTAACAGGA 59.637 52.381 0.00 0.00 0.00 3.86
462 478 1.760029 GAGAGGGAGGAAGCTAACAGG 59.240 57.143 0.00 0.00 0.00 4.00
463 479 2.693074 GAGAGAGGGAGGAAGCTAACAG 59.307 54.545 0.00 0.00 0.00 3.16
464 480 2.313342 AGAGAGAGGGAGGAAGCTAACA 59.687 50.000 0.00 0.00 0.00 2.41
476 492 1.106944 GGCGAGGAAGAGAGAGAGGG 61.107 65.000 0.00 0.00 0.00 4.30
687 735 1.364536 CCGGGGGAAAAACAAACGG 59.635 57.895 0.00 0.00 0.00 4.44
692 740 1.303806 GCTAGCCGGGGGAAAAACA 60.304 57.895 2.29 0.00 0.00 2.83
713 761 4.838152 CATCAGGACCCACGGGCG 62.838 72.222 0.69 0.00 39.32 6.13
715 763 4.838152 CGCATCAGGACCCACGGG 62.838 72.222 0.00 0.00 42.03 5.28
716 764 4.838152 CCGCATCAGGACCCACGG 62.838 72.222 0.00 0.00 0.00 4.94
717 765 4.838152 CCCGCATCAGGACCCACG 62.838 72.222 0.00 0.00 0.00 4.94
718 766 2.764637 AAACCCGCATCAGGACCCAC 62.765 60.000 0.00 0.00 0.00 4.61
719 767 2.478335 GAAACCCGCATCAGGACCCA 62.478 60.000 0.00 0.00 0.00 4.51
720 768 1.749258 GAAACCCGCATCAGGACCC 60.749 63.158 0.00 0.00 0.00 4.46
721 769 2.106683 CGAAACCCGCATCAGGACC 61.107 63.158 0.00 0.00 0.00 4.46
722 770 3.486263 CGAAACCCGCATCAGGAC 58.514 61.111 0.00 0.00 0.00 3.85
905 963 3.207778 CAAATAATTAACCGGGGCGAGA 58.792 45.455 6.32 0.00 0.00 4.04
907 965 1.677052 GCAAATAATTAACCGGGGCGA 59.323 47.619 6.32 0.00 0.00 5.54
923 981 1.070601 TCTGTCAGCAGCAGTAGCAAA 59.929 47.619 0.00 0.00 45.49 3.68
924 982 0.681175 TCTGTCAGCAGCAGTAGCAA 59.319 50.000 0.00 0.00 45.49 3.91
925 983 0.245813 CTCTGTCAGCAGCAGTAGCA 59.754 55.000 0.00 0.00 45.49 3.49
926 984 0.529833 TCTCTGTCAGCAGCAGTAGC 59.470 55.000 0.00 0.00 42.29 3.58
927 985 3.523606 AATCTCTGTCAGCAGCAGTAG 57.476 47.619 0.00 0.00 42.29 2.57
928 986 3.969287 AAATCTCTGTCAGCAGCAGTA 57.031 42.857 0.00 0.00 42.29 2.74
929 987 2.855209 AAATCTCTGTCAGCAGCAGT 57.145 45.000 0.00 0.00 42.29 4.40
965 1023 1.270839 GCAACAGCAACACCTCTAGGA 60.271 52.381 2.23 0.00 38.94 2.94
1025 1083 1.487976 AGGGCATAGTGATGAGTGGTG 59.512 52.381 0.00 0.00 34.73 4.17
1027 1085 1.813092 GCAGGGCATAGTGATGAGTGG 60.813 57.143 0.00 0.00 34.73 4.00
1028 1086 1.590932 GCAGGGCATAGTGATGAGTG 58.409 55.000 0.00 0.00 34.73 3.51
1033 1091 0.253044 ACAACGCAGGGCATAGTGAT 59.747 50.000 0.00 0.00 0.00 3.06
1037 1095 0.391661 ACAGACAACGCAGGGCATAG 60.392 55.000 0.00 0.00 0.00 2.23
1049 1107 1.529010 CCCTGGCAGCAACAGACAA 60.529 57.895 9.56 0.00 38.20 3.18
1066 1124 1.116308 GAAGGGGAGTCTCTAGCACC 58.884 60.000 0.00 0.00 0.00 5.01
1071 1129 4.823364 ATCAGATGAAGGGGAGTCTCTA 57.177 45.455 0.00 0.00 0.00 2.43
1072 1130 3.704545 ATCAGATGAAGGGGAGTCTCT 57.295 47.619 0.00 0.00 0.00 3.10
1074 1132 3.371380 GCAAATCAGATGAAGGGGAGTCT 60.371 47.826 0.00 0.00 0.00 3.24
1075 1133 2.948315 GCAAATCAGATGAAGGGGAGTC 59.052 50.000 0.00 0.00 0.00 3.36
1076 1134 2.579860 AGCAAATCAGATGAAGGGGAGT 59.420 45.455 0.00 0.00 0.00 3.85
1077 1135 2.950309 CAGCAAATCAGATGAAGGGGAG 59.050 50.000 0.00 0.00 0.00 4.30
1078 1136 2.577563 TCAGCAAATCAGATGAAGGGGA 59.422 45.455 0.00 0.00 29.85 4.81
1080 1138 3.568853 GGATCAGCAAATCAGATGAAGGG 59.431 47.826 0.00 0.00 37.48 3.95
1081 1139 3.250280 CGGATCAGCAAATCAGATGAAGG 59.750 47.826 0.00 0.00 37.48 3.46
1083 1141 2.615447 GCGGATCAGCAAATCAGATGAA 59.385 45.455 13.30 0.00 37.48 2.57
1084 1142 2.158856 AGCGGATCAGCAAATCAGATGA 60.159 45.455 20.15 0.00 38.41 2.92
1088 1146 0.029035 GCAGCGGATCAGCAAATCAG 59.971 55.000 20.15 3.78 40.15 2.90
1089 1147 1.708193 CGCAGCGGATCAGCAAATCA 61.708 55.000 20.15 0.00 40.15 2.57
1090 1148 1.010350 CGCAGCGGATCAGCAAATC 60.010 57.895 20.15 4.85 40.15 2.17
1091 1149 3.104766 CGCAGCGGATCAGCAAAT 58.895 55.556 20.15 0.00 40.15 2.32
1136 1198 1.194781 ACCGTCCTCATGTTCCTGCT 61.195 55.000 0.00 0.00 0.00 4.24
1192 1254 1.300971 GCAGATTCTTGCAGCGGTCA 61.301 55.000 0.00 0.00 43.53 4.02
1260 1323 7.639113 ATGAAAGAAGTTACACAAACAAGGA 57.361 32.000 0.00 0.00 40.83 3.36
1264 1327 8.519526 AGACAAATGAAAGAAGTTACACAAACA 58.480 29.630 0.00 0.00 40.83 2.83
1267 1333 6.972328 GCAGACAAATGAAAGAAGTTACACAA 59.028 34.615 0.00 0.00 0.00 3.33
1271 1337 5.147162 CCGCAGACAAATGAAAGAAGTTAC 58.853 41.667 0.00 0.00 0.00 2.50
1277 1343 0.516877 CGCCGCAGACAAATGAAAGA 59.483 50.000 0.00 0.00 0.00 2.52
1283 1349 1.577328 CCTGAACGCCGCAGACAAAT 61.577 55.000 0.00 0.00 35.39 2.32
1306 1372 4.974368 AGACAGAGATAGAAGGTTGTCG 57.026 45.455 0.00 0.00 39.76 4.35
1316 1383 5.321959 TCACTGCTCAAAGACAGAGATAG 57.678 43.478 0.00 0.00 37.35 2.08
1336 1403 4.074526 GACGCCTCCTGCAGCTCA 62.075 66.667 8.66 0.00 41.33 4.26
1417 1484 1.901833 GAGTAAGTGTAACCCCCGGAA 59.098 52.381 0.73 0.00 37.80 4.30
1531 1598 0.324943 AGAACGCATGCTTACCCTGT 59.675 50.000 17.13 0.71 0.00 4.00
1616 1683 8.699130 AGGGTAACGTAACAACTATTAGCTAAT 58.301 33.333 22.09 22.09 37.60 1.73
1617 1684 8.066612 AGGGTAACGTAACAACTATTAGCTAA 57.933 34.615 8.99 8.99 37.60 3.09
1620 1687 7.601073 AAAGGGTAACGTAACAACTATTAGC 57.399 36.000 0.00 0.00 37.60 3.09
1621 1688 8.375465 CGAAAAGGGTAACGTAACAACTATTAG 58.625 37.037 0.00 0.00 37.60 1.73
1622 1689 8.085296 TCGAAAAGGGTAACGTAACAACTATTA 58.915 33.333 0.00 0.00 37.60 0.98
1663 1735 8.867935 CGCAACAAAATATCATTTATTTCACCA 58.132 29.630 0.00 0.00 0.00 4.17
1664 1736 8.868916 ACGCAACAAAATATCATTTATTTCACC 58.131 29.630 0.00 0.00 0.00 4.02
1671 1743 9.114952 TCCTGATACGCAACAAAATATCATTTA 57.885 29.630 0.00 0.00 34.42 1.40
1673 1745 7.566760 TCCTGATACGCAACAAAATATCATT 57.433 32.000 0.00 0.00 34.42 2.57
1674 1746 6.293626 GCTCCTGATACGCAACAAAATATCAT 60.294 38.462 0.00 0.00 34.42 2.45
1675 1747 5.007626 GCTCCTGATACGCAACAAAATATCA 59.992 40.000 0.00 0.00 33.93 2.15
1676 1748 5.237344 AGCTCCTGATACGCAACAAAATATC 59.763 40.000 0.00 0.00 0.00 1.63
1679 1751 3.347216 AGCTCCTGATACGCAACAAAAT 58.653 40.909 0.00 0.00 0.00 1.82
1711 1783 5.067674 CACATCAGGTTTCCTTTTTGAGACA 59.932 40.000 0.00 0.00 0.00 3.41
1722 1796 3.821033 ACAAACTAGCACATCAGGTTTCC 59.179 43.478 0.00 0.00 0.00 3.13
1738 1812 2.420022 GACAGACACACAAGCACAAACT 59.580 45.455 0.00 0.00 0.00 2.66
1832 1917 4.041075 TGTGTAAGTTAGGATGCACAGGAA 59.959 41.667 0.00 0.00 37.26 3.36
1863 1950 5.237815 TGCCAGTTGACATGTCTACTAAAG 58.762 41.667 32.78 25.74 42.20 1.85
1864 1951 5.222079 TGCCAGTTGACATGTCTACTAAA 57.778 39.130 32.78 21.72 42.20 1.85
1865 1952 4.882842 TGCCAGTTGACATGTCTACTAA 57.117 40.909 32.78 21.99 42.20 2.24
1866 1953 5.187772 AGAATGCCAGTTGACATGTCTACTA 59.812 40.000 32.78 22.39 42.20 1.82
1867 1954 3.988976 ATGCCAGTTGACATGTCTACT 57.011 42.857 29.61 29.61 44.26 2.57
1868 1955 4.256920 AGAATGCCAGTTGACATGTCTAC 58.743 43.478 26.60 26.60 35.96 2.59
1869 1956 4.558226 AGAATGCCAGTTGACATGTCTA 57.442 40.909 25.55 16.43 0.00 2.59
1870 1957 3.430042 AGAATGCCAGTTGACATGTCT 57.570 42.857 25.55 3.73 0.00 3.41
1871 1958 3.755378 AGAAGAATGCCAGTTGACATGTC 59.245 43.478 19.27 19.27 0.00 3.06
1872 1959 3.759581 AGAAGAATGCCAGTTGACATGT 58.240 40.909 0.00 0.00 0.00 3.21
1873 1960 4.778534 AAGAAGAATGCCAGTTGACATG 57.221 40.909 0.00 0.00 0.00 3.21
1906 1993 7.992608 TGCCTATCTGCAGACATAAAAAGAATA 59.007 33.333 20.97 1.67 36.04 1.75
1923 2010 4.371624 TGGGTTCCATTATGCCTATCTG 57.628 45.455 0.00 0.00 0.00 2.90
1931 2018 4.792704 GCGCTTGTATTGGGTTCCATTATG 60.793 45.833 0.00 0.00 31.53 1.90
1951 2038 1.001815 TCTACTTTTTGCCAAGTGCGC 60.002 47.619 0.00 0.00 45.60 6.09
2110 2197 0.032678 AGACACACGTGGAAGCTCAG 59.967 55.000 21.57 1.60 34.19 3.35
2123 2210 7.921041 ATATAAAGAAGGATGGAGAGACACA 57.079 36.000 0.00 0.00 0.00 3.72
2160 2249 9.619316 TGTGTAATGTATTCACTAAACAATTGC 57.381 29.630 5.05 0.00 33.82 3.56
2271 2362 7.116948 CGTTTCTTTTCTTCTTCTGCTCTATCA 59.883 37.037 0.00 0.00 0.00 2.15
2733 2826 6.920758 GGTACAGAGCTGTTACTTAGATGATG 59.079 42.308 8.60 0.00 41.83 3.07
2870 2969 8.497745 AGATAAACAGATGAACCCATTAGACAT 58.502 33.333 0.00 0.00 32.09 3.06
2918 3034 4.699925 AGTAACTGCTTTTCACCTGGTA 57.300 40.909 0.00 0.00 0.00 3.25
2986 3102 7.920160 TGAACACATCAATCTAGTAATTGCA 57.080 32.000 0.00 0.00 36.72 4.08
3028 3146 3.055094 GGCAACTAGAATCCCAAGAGTGA 60.055 47.826 0.00 0.00 0.00 3.41
3296 3418 4.023707 AGGAACAAATTCAGTTGAAGAGCG 60.024 41.667 0.74 0.00 37.48 5.03
3370 3492 3.266772 TGCCCTGTTTCTCAATGGAGTAT 59.733 43.478 0.00 0.00 42.05 2.12
3506 3628 9.520204 CAACAAAATAAGGATTAGTTGGCATAG 57.480 33.333 0.00 0.00 37.96 2.23
3649 3771 2.717639 AGGTTGGTCCATGTCATAGC 57.282 50.000 0.00 0.00 39.02 2.97
3652 3774 5.192522 AGAGAATAAGGTTGGTCCATGTCAT 59.807 40.000 0.00 0.00 39.02 3.06
3672 3794 5.997129 TCAACAGCACATTTACATTCAGAGA 59.003 36.000 0.00 0.00 0.00 3.10
3696 3818 6.655078 AAATTACAGAGGTGCAAATTCAGT 57.345 33.333 0.00 0.00 0.00 3.41
3768 3891 7.006509 ATCATATTTGAGTAAGACCCATTGGG 58.993 38.462 20.71 20.71 41.51 4.12
3794 3917 5.754406 TGTTGAATTGGCACAGAAAAAGATG 59.246 36.000 0.00 0.00 42.39 2.90
3929 4053 6.603201 TGATGCCATCTAAAGAAGTAAAAGGG 59.397 38.462 6.21 0.00 0.00 3.95
4335 4467 4.006319 GCATACTGGAAAGAGGGATATGC 58.994 47.826 0.00 0.00 37.39 3.14
4471 4990 3.566130 GAGCAGGCTCTTTGATGGT 57.434 52.632 13.83 0.00 39.80 3.55
4521 5040 4.798882 TGGACCAGGAACTATGTTTTGTT 58.201 39.130 0.00 0.00 36.02 2.83
4533 5052 2.507886 TCAGACAAAGTTGGACCAGGAA 59.492 45.455 0.00 0.00 0.00 3.36
4555 5074 7.425577 TGATAAATTCTGATGAATAGCACCG 57.574 36.000 0.00 0.00 41.62 4.94
4594 5113 6.513884 GCCTTGATGAAGCATCGAATTTATCA 60.514 38.462 10.04 10.04 43.14 2.15
4694 5213 3.548745 TGTCATCATAACTGGAGCTGG 57.451 47.619 0.00 0.00 0.00 4.85
4695 5214 4.272748 CACATGTCATCATAACTGGAGCTG 59.727 45.833 0.00 0.00 32.47 4.24
4696 5215 4.162888 TCACATGTCATCATAACTGGAGCT 59.837 41.667 0.00 0.00 32.47 4.09
4820 5339 2.938956 ACAGCTACTTTCTGCTTGGT 57.061 45.000 0.00 0.00 37.44 3.67
5098 5619 1.590932 CATCCTTGGAATGGAGCTCG 58.409 55.000 7.83 0.00 44.09 5.03
5278 5804 3.553508 CCAACCCATTCTTGTCAAAGCTG 60.554 47.826 0.00 0.00 33.06 4.24
5680 6217 4.510167 AGGATTCATGTTAGGTGGGAAG 57.490 45.455 0.00 0.00 0.00 3.46
6047 6591 5.927115 GGAACTAAACAGATCGTTCTTGTCT 59.073 40.000 8.27 0.00 36.59 3.41
6060 6604 8.159344 AGAAGTCAGATTTTGGAACTAAACAG 57.841 34.615 0.00 0.00 0.00 3.16
6067 6611 7.971183 ACTAAGAGAAGTCAGATTTTGGAAC 57.029 36.000 0.00 0.00 0.00 3.62
6088 6632 7.463431 AGTGGGTTTTGTGGAATGTAATACTA 58.537 34.615 0.00 0.00 0.00 1.82
6089 6633 6.311735 AGTGGGTTTTGTGGAATGTAATACT 58.688 36.000 0.00 0.00 0.00 2.12
6090 6634 6.207810 TGAGTGGGTTTTGTGGAATGTAATAC 59.792 38.462 0.00 0.00 0.00 1.89
6108 6652 1.270550 GGCACAACTTGAATGAGTGGG 59.729 52.381 0.00 0.00 0.00 4.61
6172 6721 5.831103 AGATCATAACCACCAAAAGGATGT 58.169 37.500 0.00 0.00 0.00 3.06
6174 6723 6.953520 TGAAAGATCATAACCACCAAAAGGAT 59.046 34.615 0.00 0.00 0.00 3.24
6177 6726 6.968904 CGATGAAAGATCATAACCACCAAAAG 59.031 38.462 0.00 0.00 46.30 2.27
6328 6880 1.069906 GTTTGGATGTCACGTGTCTGC 60.070 52.381 16.51 7.33 0.00 4.26
6380 6939 7.660208 TGGACCTACATAAAGAAAACAGAGTTC 59.340 37.037 0.00 0.00 0.00 3.01
6398 6963 0.396695 TCTGGACCCGATGGACCTAC 60.397 60.000 2.02 0.00 45.57 3.18
6445 7010 2.169978 CTCCATCTGCATCAACCTCTCA 59.830 50.000 0.00 0.00 0.00 3.27
6452 7017 1.279846 TGTGAGCTCCATCTGCATCAA 59.720 47.619 12.15 0.00 0.00 2.57
6475 7040 4.820716 GCTGGATGTATCTGCTTTGATCTT 59.179 41.667 0.00 0.00 0.00 2.40
6517 7082 2.046411 CCGTACATGCTGCCACCA 60.046 61.111 0.00 0.00 0.00 4.17
6520 7085 4.794648 GGCCCGTACATGCTGCCA 62.795 66.667 0.00 0.00 41.76 4.92
6524 7089 2.903357 CTCAGGCCCGTACATGCT 59.097 61.111 0.00 0.00 0.00 3.79
6538 7103 1.277273 CTCAGGTTCATGTCCAGCTCA 59.723 52.381 11.03 0.00 0.00 4.26
6544 7109 5.069648 TCATCTGTATCTCAGGTTCATGTCC 59.930 44.000 0.00 0.00 43.76 4.02
6600 7166 2.024273 TGGTTTGTTTGGGTAACAGGGA 60.024 45.455 0.00 0.00 46.81 4.20
6605 7171 3.133183 ACATGGTGGTTTGTTTGGGTAAC 59.867 43.478 0.00 0.00 37.26 2.50
6607 7173 3.033659 ACATGGTGGTTTGTTTGGGTA 57.966 42.857 0.00 0.00 0.00 3.69
6787 7368 1.070758 CACCCAATGTATCCTCCCTCG 59.929 57.143 0.00 0.00 0.00 4.63
6982 7572 1.737793 GTGTCACAGCCTTTTATCCCG 59.262 52.381 0.00 0.00 0.00 5.14
7041 7631 2.037641 CCAAGGCTGACATCCATCGATA 59.962 50.000 0.00 0.00 0.00 2.92
7044 7634 0.178767 TCCAAGGCTGACATCCATCG 59.821 55.000 0.00 0.00 0.00 3.84
7083 7673 2.364970 TGCATTTCTCCCACTTTGTTGG 59.635 45.455 0.00 0.00 36.26 3.77
7156 7861 8.352942 ACTTTTAACTTCATGTCACAGATTTCC 58.647 33.333 0.00 0.00 0.00 3.13
7177 7882 8.735692 ATTTGGTTTTGTGATGATCAACTTTT 57.264 26.923 0.00 0.00 0.00 2.27
7264 7969 3.385193 ACAAGGTTAAAATGGCACTGC 57.615 42.857 0.00 0.00 0.00 4.40
7265 7970 6.093357 ACAAAAACAAGGTTAAAATGGCACTG 59.907 34.615 0.00 0.00 0.00 3.66
7266 7971 6.093357 CACAAAAACAAGGTTAAAATGGCACT 59.907 34.615 0.00 0.00 0.00 4.40
7268 7973 6.173339 TCACAAAAACAAGGTTAAAATGGCA 58.827 32.000 0.00 0.00 0.00 4.92
7269 7974 6.238347 CCTCACAAAAACAAGGTTAAAATGGC 60.238 38.462 0.00 0.00 0.00 4.40
7270 7975 6.259829 CCCTCACAAAAACAAGGTTAAAATGG 59.740 38.462 0.00 0.00 0.00 3.16
7271 7976 6.821160 ACCCTCACAAAAACAAGGTTAAAATG 59.179 34.615 0.00 0.00 0.00 2.32
7272 7977 6.953101 ACCCTCACAAAAACAAGGTTAAAAT 58.047 32.000 0.00 0.00 0.00 1.82
7277 7986 6.361768 TTTTACCCTCACAAAAACAAGGTT 57.638 33.333 0.00 0.00 0.00 3.50
7280 7989 5.757808 CCCATTTTACCCTCACAAAAACAAG 59.242 40.000 0.00 0.00 0.00 3.16
7314 8023 4.202253 TGCTTCAGAGTTCAGACTAGCAAA 60.202 41.667 0.00 0.00 39.54 3.68
7396 8105 2.835431 ATCTCACGAGGAGGCGGG 60.835 66.667 8.56 0.00 44.19 6.13
7397 8106 2.725008 GATCTCACGAGGAGGCGG 59.275 66.667 8.56 0.00 44.19 6.13
7398 8107 1.791103 GAGGATCTCACGAGGAGGCG 61.791 65.000 8.56 0.00 44.19 5.52
7399 8108 1.460273 GGAGGATCTCACGAGGAGGC 61.460 65.000 8.56 2.87 44.19 4.70
7400 8109 0.825840 GGGAGGATCTCACGAGGAGG 60.826 65.000 8.56 0.00 44.19 4.30
7401 8110 2.727103 GGGAGGATCTCACGAGGAG 58.273 63.158 0.00 0.00 45.49 3.69


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

AutoCloner maintained by Alex Coulton.