Multiple sequence alignment - TraesCS3B01G140700

Loading Multiple Alignment...

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 TraesCS3B01G140700 chr3B 100.000 2887 0 0 1490 4376 126920830 126923716 0.000000e+00 5332.0
1 TraesCS3B01G140700 chr3B 100.000 1192 0 0 1 1192 126919341 126920532 0.000000e+00 2202.0
2 TraesCS3B01G140700 chr3D 90.891 2953 153 59 1491 4376 81207001 81209904 0.000000e+00 3856.0
3 TraesCS3B01G140700 chr3D 88.305 1009 55 24 212 1192 81205954 81206927 0.000000e+00 1151.0
4 TraesCS3B01G140700 chr3A 89.019 2987 169 63 1490 4376 95477424 95480351 0.000000e+00 3552.0
5 TraesCS3B01G140700 chr3A 85.248 705 39 15 205 872 95476393 95477069 0.000000e+00 665.0
6 TraesCS3B01G140700 chr3A 97.854 233 2 3 963 1192 95477108 95477340 2.450000e-107 399.0
7 TraesCS3B01G140700 chr7B 88.933 253 16 7 2585 2830 77863575 77863822 7.110000e-78 302.0
8 TraesCS3B01G140700 chr7B 80.479 292 25 13 2210 2471 77863289 77863578 1.240000e-45 195.0
9 TraesCS3B01G140700 chrUn 88.142 253 18 7 2585 2830 275342134 275342381 1.540000e-74 291.0
10 TraesCS3B01G140700 chrUn 87.747 253 19 7 2585 2830 275341214 275341461 7.160000e-73 285.0
11 TraesCS3B01G140700 chrUn 89.640 222 13 6 2613 2830 309341312 309341527 1.550000e-69 274.0
12 TraesCS3B01G140700 chrUn 87.755 245 17 10 2593 2830 379041226 379040988 1.550000e-69 274.0
13 TraesCS3B01G140700 chrUn 89.640 222 13 6 2613 2830 412286028 412285813 1.550000e-69 274.0
14 TraesCS3B01G140700 chr2B 87.755 245 17 10 2593 2830 758941106 758940868 1.550000e-69 274.0
15 TraesCS3B01G140700 chr1A 76.022 367 53 21 1647 1989 127077178 127076823 1.630000e-34 158.0
16 TraesCS3B01G140700 chr1D 90.000 120 12 0 1882 2001 116004705 116004586 5.860000e-34 156.0
17 TraesCS3B01G140700 chr1B 89.167 120 13 0 1882 2001 177837658 177837539 2.730000e-32 150.0
18 TraesCS3B01G140700 chr5D 88.235 102 12 0 1886 1987 457777219 457777320 5.940000e-24 122.0
19 TraesCS3B01G140700 chr5B 88.235 102 12 0 1886 1987 559992272 559992373 5.940000e-24 122.0
20 TraesCS3B01G140700 chr5B 91.429 70 6 0 1921 1990 64265122 64265053 3.600000e-16 97.1
21 TraesCS3B01G140700 chr5A 87.255 102 13 0 1886 1987 575658613 575658714 2.770000e-22 117.0


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 TraesCS3B01G140700 chr3B 126919341 126923716 4375 False 3767.000000 5332 100.0000 1 4376 2 chr3B.!!$F1 4375
1 TraesCS3B01G140700 chr3D 81205954 81209904 3950 False 2503.500000 3856 89.5980 212 4376 2 chr3D.!!$F1 4164
2 TraesCS3B01G140700 chr3A 95476393 95480351 3958 False 1538.666667 3552 90.7070 205 4376 3 chr3A.!!$F1 4171
3 TraesCS3B01G140700 chr7B 77863289 77863822 533 False 248.500000 302 84.7060 2210 2830 2 chr7B.!!$F1 620
4 TraesCS3B01G140700 chrUn 275341214 275342381 1167 False 288.000000 291 87.9445 2585 2830 2 chrUn.!!$F2 245

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
190 191 0.038166 ACATTGGATGGTTGGCTCGT 59.962 50.0 0.00 0.0 33.60 4.18 F
422 445 0.038251 ACGTGCGCCGATGATATGAT 60.038 50.0 22.10 0.0 40.70 2.45 F
874 944 0.179020 CACAAAGCTGGACCAGACCA 60.179 55.0 26.25 0.0 38.33 4.02 F
1545 1620 0.383949 TTCCGCTGTTTGTTTGGCTC 59.616 50.0 0.00 0.0 0.00 4.70 F
2563 2683 0.112412 GCTGTCCTTTTTCCCCCTGA 59.888 55.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1603 0.459489 TGGTGAGCCAAACAAACAGC 59.541 50.0 0.00 0.0 42.83 4.40 R
2002 2091 0.926220 AAGGGGAAATCAGGGGAGGG 60.926 60.0 0.00 0.0 0.00 4.30 R
2544 2664 0.112412 TCAGGGGGAAAAAGGACAGC 59.888 55.0 0.00 0.0 0.00 4.40 R
2579 2699 0.345502 TTATCCAGGCCCCACTAGGT 59.654 55.0 0.00 0.0 0.00 3.08 R
4106 4311 0.664761 GAACAACAGCAGCAGCAGAA 59.335 50.0 3.17 0.0 45.49 3.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.593318 TGCGTGCATGCATGTGAT 58.407 50.000 34.08 0.00 40.62 3.06
26 27 1.298863 GCGTGCATGCATGTGATCC 60.299 57.895 34.08 17.85 35.52 3.36
30 31 2.480587 CGTGCATGCATGTGATCCAATT 60.481 45.455 28.25 0.00 0.00 2.32
32 33 3.936453 GTGCATGCATGTGATCCAATTTT 59.064 39.130 25.64 0.00 0.00 1.82
52 53 3.667087 GCACAGATTGCCGGACAA 58.333 55.556 5.05 10.03 46.63 3.18
123 124 4.647424 TTTTATTGCGATTGGGGATGTC 57.353 40.909 0.00 0.00 0.00 3.06
124 125 3.289407 TTATTGCGATTGGGGATGTCA 57.711 42.857 0.00 0.00 0.00 3.58
126 127 1.679139 TTGCGATTGGGGATGTCATC 58.321 50.000 4.06 4.06 0.00 2.92
138 139 4.266070 GTCATCCGGCGCGCTCTA 62.266 66.667 32.29 16.52 0.00 2.43
139 140 3.295273 TCATCCGGCGCGCTCTAT 61.295 61.111 32.29 18.10 0.00 1.98
142 143 3.848347 ATCCGGCGCGCTCTATGTG 62.848 63.158 32.29 11.42 0.00 3.21
145 146 2.368105 CGGCGCGCTCTATGTGATC 61.368 63.158 32.29 8.93 0.00 2.92
146 147 1.300156 GGCGCGCTCTATGTGATCA 60.300 57.895 32.29 0.00 0.00 2.92
148 149 1.402852 GGCGCGCTCTATGTGATCATA 60.403 52.381 32.29 0.00 35.70 2.15
169 170 9.778993 ATCATAGACTTTGAATTCAAATTGACG 57.221 29.630 28.86 20.32 43.92 4.35
170 171 8.236586 TCATAGACTTTGAATTCAAATTGACGG 58.763 33.333 28.86 19.72 43.92 4.79
171 172 6.633500 AGACTTTGAATTCAAATTGACGGA 57.367 33.333 28.86 9.02 43.92 4.69
172 173 6.438763 AGACTTTGAATTCAAATTGACGGAC 58.561 36.000 28.86 17.72 43.92 4.79
173 174 6.039270 AGACTTTGAATTCAAATTGACGGACA 59.961 34.615 28.86 7.70 43.92 4.02
176 177 7.169645 ACTTTGAATTCAAATTGACGGACATTG 59.830 33.333 28.86 16.75 43.92 2.82
177 178 5.468592 TGAATTCAAATTGACGGACATTGG 58.531 37.500 5.45 0.00 0.00 3.16
181 182 3.443329 TCAAATTGACGGACATTGGATGG 59.557 43.478 0.00 0.00 33.60 3.51
183 184 2.577606 TTGACGGACATTGGATGGTT 57.422 45.000 0.00 0.00 33.60 3.67
184 185 1.819928 TGACGGACATTGGATGGTTG 58.180 50.000 0.00 0.00 33.60 3.77
185 186 1.094785 GACGGACATTGGATGGTTGG 58.905 55.000 0.00 0.00 33.60 3.77
187 188 0.680921 CGGACATTGGATGGTTGGCT 60.681 55.000 0.00 0.00 33.60 4.75
188 189 1.106285 GGACATTGGATGGTTGGCTC 58.894 55.000 0.00 0.00 33.60 4.70
189 190 0.734889 GACATTGGATGGTTGGCTCG 59.265 55.000 0.00 0.00 33.60 5.03
190 191 0.038166 ACATTGGATGGTTGGCTCGT 59.962 50.000 0.00 0.00 33.60 4.18
191 192 0.452987 CATTGGATGGTTGGCTCGTG 59.547 55.000 0.00 0.00 0.00 4.35
192 193 0.680921 ATTGGATGGTTGGCTCGTGG 60.681 55.000 0.00 0.00 0.00 4.94
193 194 2.438434 GGATGGTTGGCTCGTGGG 60.438 66.667 0.00 0.00 0.00 4.61
194 195 2.351276 GATGGTTGGCTCGTGGGT 59.649 61.111 0.00 0.00 0.00 4.51
195 196 2.034066 ATGGTTGGCTCGTGGGTG 59.966 61.111 0.00 0.00 0.00 4.61
196 197 4.947147 TGGTTGGCTCGTGGGTGC 62.947 66.667 0.00 0.00 0.00 5.01
199 200 2.672651 TTGGCTCGTGGGTGCATG 60.673 61.111 0.00 0.00 34.40 4.06
203 204 3.129502 CTCGTGGGTGCATGCCTG 61.130 66.667 16.68 0.00 0.00 4.85
216 217 4.427394 GCCTGTGATCGGCTACAG 57.573 61.111 3.09 3.75 44.17 2.74
305 313 0.454196 AAAACAAGGTGGCGTGTCAC 59.546 50.000 0.00 0.00 36.95 3.67
345 368 1.818674 GCAAGATTTGGTTCCATCGGT 59.181 47.619 0.00 0.00 0.00 4.69
413 436 4.792502 CGTACGTACGTGCGCCGA 62.793 66.667 37.87 13.79 45.72 5.54
415 438 2.277437 TACGTACGTGCGCCGATG 60.277 61.111 30.25 13.72 40.70 3.84
418 441 1.369568 CGTACGTGCGCCGATGATA 60.370 57.895 22.10 4.23 40.70 2.15
420 443 0.708370 GTACGTGCGCCGATGATATG 59.292 55.000 22.10 2.47 40.70 1.78
421 444 0.594110 TACGTGCGCCGATGATATGA 59.406 50.000 22.10 0.00 40.70 2.15
422 445 0.038251 ACGTGCGCCGATGATATGAT 60.038 50.000 22.10 0.00 40.70 2.45
681 743 2.917656 CGCGCTTCTCCGTTATCGC 61.918 63.158 5.56 0.00 39.26 4.58
692 754 3.908081 TTATCGCGGCTCCGTCCC 61.908 66.667 6.13 0.00 42.09 4.46
728 790 2.357154 GCAGGGGTGTGAGTGGAAATAT 60.357 50.000 0.00 0.00 0.00 1.28
872 942 1.845809 CGCACAAAGCTGGACCAGAC 61.846 60.000 26.25 15.84 42.61 3.51
873 943 1.518903 GCACAAAGCTGGACCAGACC 61.519 60.000 26.25 8.38 41.15 3.85
874 944 0.179020 CACAAAGCTGGACCAGACCA 60.179 55.000 26.25 0.00 38.33 4.02
880 950 2.204034 TGGACCAGACCAGAGGCA 59.796 61.111 0.00 0.00 34.77 4.75
881 951 1.915266 TGGACCAGACCAGAGGCAG 60.915 63.158 0.00 0.00 34.77 4.85
900 970 2.100410 CAGCATTCGCAGCAGCAG 59.900 61.111 0.82 0.00 42.27 4.24
913 983 1.950098 GCAGCAGAAGAAGACGACGC 61.950 60.000 0.00 0.00 0.00 5.19
914 984 0.664466 CAGCAGAAGAAGACGACGCA 60.664 55.000 0.00 0.00 0.00 5.24
980 1050 4.210307 TCGAGAGAGGCTGACGAG 57.790 61.111 0.00 0.00 34.84 4.18
982 1052 2.477176 CGAGAGAGGCTGACGAGGG 61.477 68.421 0.00 0.00 0.00 4.30
983 1053 2.757917 AGAGAGGCTGACGAGGGC 60.758 66.667 0.00 0.00 0.00 5.19
1545 1620 0.383949 TTCCGCTGTTTGTTTGGCTC 59.616 50.000 0.00 0.00 0.00 4.70
1546 1621 0.749818 TCCGCTGTTTGTTTGGCTCA 60.750 50.000 0.00 0.00 0.00 4.26
1548 1623 0.594796 CGCTGTTTGTTTGGCTCACC 60.595 55.000 0.00 0.00 0.00 4.02
1671 1747 2.264794 GTCAAGGTGGCCGTCGAT 59.735 61.111 0.00 0.00 0.00 3.59
1796 1875 2.246849 AGTACCTTAATCGACCCCTCCT 59.753 50.000 0.00 0.00 0.00 3.69
2002 2091 3.378206 GAAGTGAGCTTCTTGCGCCAC 62.378 57.143 4.18 2.56 45.68 5.01
2008 2097 4.344865 TTCTTGCGCCACCCTCCC 62.345 66.667 4.18 0.00 0.00 4.30
2016 2105 1.076705 GCCACCCTCCCCTGATTTC 60.077 63.158 0.00 0.00 0.00 2.17
2017 2106 1.615262 CCACCCTCCCCTGATTTCC 59.385 63.158 0.00 0.00 0.00 3.13
2027 2116 2.767960 CCCCTGATTTCCCCTTGATTTG 59.232 50.000 0.00 0.00 0.00 2.32
2028 2117 3.444029 CCCTGATTTCCCCTTGATTTGT 58.556 45.455 0.00 0.00 0.00 2.83
2030 2119 5.022787 CCCTGATTTCCCCTTGATTTGTTA 58.977 41.667 0.00 0.00 0.00 2.41
2038 2127 7.712204 TTCCCCTTGATTTGTTATCTTTACC 57.288 36.000 0.00 0.00 0.00 2.85
2039 2128 6.795590 TCCCCTTGATTTGTTATCTTTACCA 58.204 36.000 0.00 0.00 0.00 3.25
2040 2129 6.889722 TCCCCTTGATTTGTTATCTTTACCAG 59.110 38.462 0.00 0.00 0.00 4.00
2041 2130 6.405842 CCCCTTGATTTGTTATCTTTACCAGC 60.406 42.308 0.00 0.00 0.00 4.85
2042 2131 6.378280 CCCTTGATTTGTTATCTTTACCAGCT 59.622 38.462 0.00 0.00 0.00 4.24
2043 2132 7.093771 CCCTTGATTTGTTATCTTTACCAGCTT 60.094 37.037 0.00 0.00 0.00 3.74
2044 2133 8.306761 CCTTGATTTGTTATCTTTACCAGCTTT 58.693 33.333 0.00 0.00 0.00 3.51
2045 2134 9.696917 CTTGATTTGTTATCTTTACCAGCTTTT 57.303 29.630 0.00 0.00 0.00 2.27
2046 2135 9.474920 TTGATTTGTTATCTTTACCAGCTTTTG 57.525 29.630 0.00 0.00 0.00 2.44
2060 2149 3.515330 GCTTTTGCTATGTGCTTGGAT 57.485 42.857 0.00 0.00 43.35 3.41
2061 2150 3.184541 GCTTTTGCTATGTGCTTGGATG 58.815 45.455 0.00 0.00 43.35 3.51
2062 2151 3.119388 GCTTTTGCTATGTGCTTGGATGA 60.119 43.478 0.00 0.00 43.35 2.92
2118 2218 5.523438 TGTTTGGACTGGGTTAATTTGTC 57.477 39.130 0.00 0.00 0.00 3.18
2152 2252 7.576403 TCTTGGACTGATCAAATTGGATATCA 58.424 34.615 4.83 0.00 0.00 2.15
2180 2280 3.430453 TGGGTGAATTGACCAAATCCTC 58.570 45.455 16.35 0.00 37.80 3.71
2251 2367 0.464554 TGCAACGGACATGGTTGTGA 60.465 50.000 12.86 1.10 45.01 3.58
2254 2370 2.150390 CAACGGACATGGTTGTGATGA 58.850 47.619 0.00 0.00 39.83 2.92
2278 2394 6.178239 ACTGATGCTTTACGATTTGGTTAC 57.822 37.500 0.00 0.00 0.00 2.50
2303 2419 1.134729 CACCAAGGTTGCTTTGCTTGT 60.135 47.619 0.00 0.00 0.00 3.16
2399 2519 0.953471 TGCATTGCGTGGGTCTGTAC 60.953 55.000 3.84 0.00 0.00 2.90
2428 2548 7.964559 TGAGATTTGAACAGATTAATTGCTTCG 59.035 33.333 0.00 0.00 0.00 3.79
2429 2549 6.749118 AGATTTGAACAGATTAATTGCTTCGC 59.251 34.615 0.00 0.00 0.00 4.70
2442 2562 0.737715 GCTTCGCTGATTCCGTCTGT 60.738 55.000 0.00 0.00 0.00 3.41
2453 2573 7.148950 CGCTGATTCCGTCTGTATTTATCTAAC 60.149 40.741 0.00 0.00 0.00 2.34
2454 2574 7.868415 GCTGATTCCGTCTGTATTTATCTAACT 59.132 37.037 0.00 0.00 0.00 2.24
2455 2575 9.186323 CTGATTCCGTCTGTATTTATCTAACTG 57.814 37.037 0.00 0.00 0.00 3.16
2456 2576 7.652105 TGATTCCGTCTGTATTTATCTAACTGC 59.348 37.037 0.00 0.00 0.00 4.40
2459 2579 6.016527 TCCGTCTGTATTTATCTAACTGCGAT 60.017 38.462 0.00 0.00 0.00 4.58
2503 2623 1.239968 GGCAGACCTGAGCAAAGTGG 61.240 60.000 0.47 0.00 0.00 4.00
2531 2651 6.339587 GGAACCAACTGAATACCATTTCAA 57.660 37.500 0.00 0.00 35.31 2.69
2535 2655 9.271828 GAACCAACTGAATACCATTTCAAAAAT 57.728 29.630 0.00 0.00 35.31 1.82
2536 2656 8.606040 ACCAACTGAATACCATTTCAAAAATG 57.394 30.769 5.60 5.60 35.31 2.32
2538 2658 9.270640 CCAACTGAATACCATTTCAAAAATGAA 57.729 29.630 12.73 2.93 35.31 2.57
2540 2660 9.829507 AACTGAATACCATTTCAAAAATGAACA 57.170 25.926 12.73 5.78 35.31 3.18
2547 2667 8.314143 ACCATTTCAAAAATGAACATAAGCTG 57.686 30.769 12.73 0.00 0.00 4.24
2549 2669 8.437742 CCATTTCAAAAATGAACATAAGCTGTC 58.562 33.333 12.73 0.00 36.98 3.51
2550 2670 7.945033 TTTCAAAAATGAACATAAGCTGTCC 57.055 32.000 0.00 0.00 36.98 4.02
2551 2671 6.899393 TCAAAAATGAACATAAGCTGTCCT 57.101 33.333 0.00 0.00 36.98 3.85
2552 2672 7.288810 TCAAAAATGAACATAAGCTGTCCTT 57.711 32.000 0.00 0.00 36.98 3.36
2553 2673 7.725251 TCAAAAATGAACATAAGCTGTCCTTT 58.275 30.769 0.00 0.00 36.98 3.11
2554 2674 8.203485 TCAAAAATGAACATAAGCTGTCCTTTT 58.797 29.630 0.00 0.00 36.98 2.27
2555 2675 8.829612 CAAAAATGAACATAAGCTGTCCTTTTT 58.170 29.630 0.00 0.00 36.98 1.94
2556 2676 8.593492 AAAATGAACATAAGCTGTCCTTTTTC 57.407 30.769 0.00 0.00 36.98 2.29
2557 2677 5.705609 TGAACATAAGCTGTCCTTTTTCC 57.294 39.130 0.00 0.00 36.98 3.13
2558 2678 4.522789 TGAACATAAGCTGTCCTTTTTCCC 59.477 41.667 0.00 0.00 36.98 3.97
2559 2679 3.431415 ACATAAGCTGTCCTTTTTCCCC 58.569 45.455 0.00 0.00 34.95 4.81
2560 2680 2.597578 TAAGCTGTCCTTTTTCCCCC 57.402 50.000 0.00 0.00 34.95 5.40
2561 2681 0.860457 AAGCTGTCCTTTTTCCCCCT 59.140 50.000 0.00 0.00 0.00 4.79
2562 2682 0.113190 AGCTGTCCTTTTTCCCCCTG 59.887 55.000 0.00 0.00 0.00 4.45
2563 2683 0.112412 GCTGTCCTTTTTCCCCCTGA 59.888 55.000 0.00 0.00 0.00 3.86
2565 2685 2.519013 CTGTCCTTTTTCCCCCTGAAG 58.481 52.381 0.00 0.00 33.63 3.02
2566 2686 2.108250 CTGTCCTTTTTCCCCCTGAAGA 59.892 50.000 0.00 0.00 33.63 2.87
2567 2687 2.721906 TGTCCTTTTTCCCCCTGAAGAT 59.278 45.455 0.00 0.00 33.63 2.40
2568 2688 3.920197 TGTCCTTTTTCCCCCTGAAGATA 59.080 43.478 0.00 0.00 33.63 1.98
2569 2689 4.355588 TGTCCTTTTTCCCCCTGAAGATAA 59.644 41.667 0.00 0.00 33.63 1.75
2572 2692 5.496168 TCCTTTTTCCCCCTGAAGATAATCT 59.504 40.000 0.00 0.00 33.63 2.40
2573 2693 5.595952 CCTTTTTCCCCCTGAAGATAATCTG 59.404 44.000 0.00 0.00 33.63 2.90
2574 2694 6.401537 TTTTTCCCCCTGAAGATAATCTGA 57.598 37.500 0.00 0.00 33.63 3.27
2575 2695 6.401537 TTTTCCCCCTGAAGATAATCTGAA 57.598 37.500 0.00 0.00 33.63 3.02
2577 2697 6.596869 TTCCCCCTGAAGATAATCTGAATT 57.403 37.500 0.00 0.00 0.00 2.17
2578 2698 6.192970 TCCCCCTGAAGATAATCTGAATTC 57.807 41.667 0.00 0.00 0.00 2.17
2579 2699 5.671735 TCCCCCTGAAGATAATCTGAATTCA 59.328 40.000 8.12 8.12 0.00 2.57
2582 2702 6.410157 CCCCTGAAGATAATCTGAATTCACCT 60.410 42.308 3.38 0.00 0.00 4.00
2583 2703 7.202130 CCCCTGAAGATAATCTGAATTCACCTA 60.202 40.741 3.38 0.00 0.00 3.08
2585 2705 8.428063 CCTGAAGATAATCTGAATTCACCTAGT 58.572 37.037 3.38 0.00 0.00 2.57
2586 2706 9.258826 CTGAAGATAATCTGAATTCACCTAGTG 57.741 37.037 3.38 0.00 34.45 2.74
2588 2708 7.072263 AGATAATCTGAATTCACCTAGTGGG 57.928 40.000 3.38 0.00 41.89 4.61
2591 2734 0.623723 TGAATTCACCTAGTGGGGCC 59.376 55.000 3.38 0.00 40.03 5.80
2600 2743 2.065799 CCTAGTGGGGCCTGGATAATT 58.934 52.381 0.84 0.00 0.00 1.40
2604 2747 2.519691 AGTGGGGCCTGGATAATTGAAT 59.480 45.455 0.84 0.00 0.00 2.57
2701 2850 6.414732 CCTGTGGGTCAGTTATAAGAATTGA 58.585 40.000 0.00 0.00 42.19 2.57
2704 2853 8.506168 TGTGGGTCAGTTATAAGAATTGAATC 57.494 34.615 0.00 0.00 0.00 2.52
2725 2875 9.581289 TGAATCTTTGGTTCTTCTTGGTTATTA 57.419 29.630 0.00 0.00 0.00 0.98
2905 3057 7.211966 TGTTAAGATATAGGCTACTTCGGAC 57.788 40.000 0.00 0.38 0.00 4.79
2937 3089 7.215085 TCCTTTCTAGTTTTGTTCTCCACTAC 58.785 38.462 0.00 0.00 0.00 2.73
3071 3223 6.700081 TCGTTATCTTTTATCTCGGTTGGATG 59.300 38.462 0.00 0.00 0.00 3.51
3133 3287 2.631062 TCACCAGACTTGTTACACCGAT 59.369 45.455 0.00 0.00 0.00 4.18
3134 3288 2.736721 CACCAGACTTGTTACACCGATG 59.263 50.000 0.00 0.00 0.00 3.84
3230 3384 3.569049 AACTCCGAGGCCGTGAACG 62.569 63.158 0.00 0.00 39.44 3.95
3296 3450 4.796231 GCGCCCGTCATCTCACGT 62.796 66.667 0.00 0.00 38.14 4.49
3297 3451 2.579787 CGCCCGTCATCTCACGTC 60.580 66.667 0.00 0.00 38.14 4.34
3298 3452 2.579787 GCCCGTCATCTCACGTCG 60.580 66.667 0.00 0.00 38.14 5.12
3299 3453 2.875485 CCCGTCATCTCACGTCGT 59.125 61.111 0.00 0.00 38.14 4.34
3300 3454 1.514228 CCCGTCATCTCACGTCGTG 60.514 63.158 19.38 19.38 38.14 4.35
3320 3474 1.419922 GTACGTGCACAATCAGCCG 59.580 57.895 18.64 2.23 33.79 5.52
3331 3485 1.086696 AATCAGCCGTGTTGATTCGG 58.913 50.000 9.16 0.00 38.71 4.30
3423 3577 1.990060 CTGCCGGAAAGGAGGAGGA 60.990 63.158 5.05 0.00 45.00 3.71
3471 3625 3.788333 TGTGTACAGCTATCGGTTACC 57.212 47.619 0.00 0.00 0.00 2.85
3608 3776 5.844004 AGTACTGGGAGCTTGAAATATACG 58.156 41.667 0.00 0.00 0.00 3.06
3685 3863 0.946221 CTCGGCGTTCTCTGCTGTTT 60.946 55.000 6.85 0.00 39.73 2.83
3781 3975 4.630894 TGTGTCAAGTGATGGTTTTGTC 57.369 40.909 0.00 0.00 0.00 3.18
3837 4031 5.473504 AGAAATGTGTCCACCTTGTTCATAC 59.526 40.000 0.00 0.00 0.00 2.39
3838 4032 4.640771 ATGTGTCCACCTTGTTCATACT 57.359 40.909 0.00 0.00 0.00 2.12
3839 4033 5.755409 ATGTGTCCACCTTGTTCATACTA 57.245 39.130 0.00 0.00 0.00 1.82
3868 4064 5.619132 TGGATGTATGATGCATATCCGAT 57.381 39.130 16.92 1.34 31.62 4.18
3885 4081 5.914898 TCCGATCTTTATCAGTGAAGTGA 57.085 39.130 0.00 0.00 31.93 3.41
3888 4084 7.331026 TCCGATCTTTATCAGTGAAGTGAAAT 58.669 34.615 0.00 0.00 31.93 2.17
3926 4122 1.135199 CACTGTGCTGCCAAATGGATC 60.135 52.381 2.98 0.00 37.39 3.36
4044 4247 9.463443 GGTGACTGGTATTATCAAAATAATTGC 57.537 33.333 0.00 0.00 38.66 3.56
4096 4301 2.328099 GGTGCTGAACTGAAGGCCG 61.328 63.158 0.00 0.00 0.00 6.13
4103 4308 1.202758 TGAACTGAAGGCCGTGTTGAT 60.203 47.619 0.00 0.00 0.00 2.57
4104 4309 1.197721 GAACTGAAGGCCGTGTTGATG 59.802 52.381 0.00 0.00 0.00 3.07
4105 4310 1.237285 ACTGAAGGCCGTGTTGATGC 61.237 55.000 0.00 0.00 0.00 3.91
4106 4311 0.957395 CTGAAGGCCGTGTTGATGCT 60.957 55.000 0.00 0.00 0.00 3.79
4107 4312 0.537143 TGAAGGCCGTGTTGATGCTT 60.537 50.000 0.00 0.00 0.00 3.91
4108 4313 0.169009 GAAGGCCGTGTTGATGCTTC 59.831 55.000 0.00 0.00 0.00 3.86
4109 4314 0.250901 AAGGCCGTGTTGATGCTTCT 60.251 50.000 0.00 0.00 0.00 2.85
4110 4315 0.957395 AGGCCGTGTTGATGCTTCTG 60.957 55.000 0.00 0.00 0.00 3.02
4111 4316 1.154150 GCCGTGTTGATGCTTCTGC 60.154 57.895 0.88 0.00 40.20 4.26
4129 4334 1.727511 GCTGCTGCTGTTGTTCCACA 61.728 55.000 8.53 0.00 36.03 4.17
4135 4340 1.327303 GCTGTTGTTCCACAATCCCA 58.673 50.000 0.00 0.00 40.59 4.37
4271 4476 2.501610 GATCAGACCAGACCGGCC 59.498 66.667 0.00 0.00 39.03 6.13
4306 4516 0.037232 CTCCTTTCCCTTTCGCTCGT 60.037 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.864377 GATCACATGCATGCACGCAC 60.864 55.000 25.37 8.98 46.56 5.34
8 9 1.298863 GGATCACATGCATGCACGC 60.299 57.895 25.37 13.31 0.00 5.34
9 10 0.452585 TTGGATCACATGCATGCACG 59.547 50.000 25.37 19.13 0.00 5.34
11 12 3.897141 AAATTGGATCACATGCATGCA 57.103 38.095 26.53 25.04 0.00 3.96
36 37 1.167851 ACATTGTCCGGCAATCTGTG 58.832 50.000 17.66 12.40 45.33 3.66
37 38 1.909700 AACATTGTCCGGCAATCTGT 58.090 45.000 17.66 13.74 45.33 3.41
38 39 3.302365 AAAACATTGTCCGGCAATCTG 57.698 42.857 17.66 13.23 45.33 2.90
102 103 4.019858 TGACATCCCCAATCGCAATAAAA 58.980 39.130 0.00 0.00 0.00 1.52
103 104 3.625853 TGACATCCCCAATCGCAATAAA 58.374 40.909 0.00 0.00 0.00 1.40
104 105 3.289407 TGACATCCCCAATCGCAATAA 57.711 42.857 0.00 0.00 0.00 1.40
106 107 2.233271 GATGACATCCCCAATCGCAAT 58.767 47.619 3.89 0.00 0.00 3.56
107 108 1.679139 GATGACATCCCCAATCGCAA 58.321 50.000 3.89 0.00 0.00 4.85
108 109 0.179020 GGATGACATCCCCAATCGCA 60.179 55.000 22.12 0.00 43.88 5.10
109 110 2.633860 GGATGACATCCCCAATCGC 58.366 57.895 22.12 0.00 43.88 4.58
122 123 3.295273 ATAGAGCGCGCCGGATGA 61.295 61.111 30.33 7.91 0.00 2.92
123 124 3.108289 CATAGAGCGCGCCGGATG 61.108 66.667 30.33 23.20 0.00 3.51
124 125 3.606662 ACATAGAGCGCGCCGGAT 61.607 61.111 30.33 15.67 0.00 4.18
126 127 3.848347 ATCACATAGAGCGCGCCGG 62.848 63.158 30.33 15.30 0.00 6.13
127 128 2.355126 ATCACATAGAGCGCGCCG 60.355 61.111 30.33 13.94 0.00 6.46
153 154 5.925397 CCAATGTCCGTCAATTTGAATTCAA 59.075 36.000 16.91 16.91 0.00 2.69
155 156 5.708948 TCCAATGTCCGTCAATTTGAATTC 58.291 37.500 0.00 0.00 0.00 2.17
156 157 5.720371 TCCAATGTCCGTCAATTTGAATT 57.280 34.783 0.00 0.00 0.00 2.17
157 158 5.394443 CCATCCAATGTCCGTCAATTTGAAT 60.394 40.000 0.00 0.00 0.00 2.57
158 159 4.082300 CCATCCAATGTCCGTCAATTTGAA 60.082 41.667 0.00 0.00 0.00 2.69
159 160 3.443329 CCATCCAATGTCCGTCAATTTGA 59.557 43.478 0.00 0.00 0.00 2.69
160 161 3.193267 ACCATCCAATGTCCGTCAATTTG 59.807 43.478 0.00 0.00 0.00 2.32
161 162 3.430453 ACCATCCAATGTCCGTCAATTT 58.570 40.909 0.00 0.00 0.00 1.82
162 163 3.085952 ACCATCCAATGTCCGTCAATT 57.914 42.857 0.00 0.00 0.00 2.32
166 167 1.094785 CCAACCATCCAATGTCCGTC 58.905 55.000 0.00 0.00 0.00 4.79
167 168 0.965363 GCCAACCATCCAATGTCCGT 60.965 55.000 0.00 0.00 0.00 4.69
168 169 0.680921 AGCCAACCATCCAATGTCCG 60.681 55.000 0.00 0.00 0.00 4.79
169 170 1.106285 GAGCCAACCATCCAATGTCC 58.894 55.000 0.00 0.00 0.00 4.02
170 171 0.734889 CGAGCCAACCATCCAATGTC 59.265 55.000 0.00 0.00 0.00 3.06
171 172 0.038166 ACGAGCCAACCATCCAATGT 59.962 50.000 0.00 0.00 0.00 2.71
172 173 0.452987 CACGAGCCAACCATCCAATG 59.547 55.000 0.00 0.00 0.00 2.82
173 174 0.680921 CCACGAGCCAACCATCCAAT 60.681 55.000 0.00 0.00 0.00 3.16
176 177 2.438434 CCCACGAGCCAACCATCC 60.438 66.667 0.00 0.00 0.00 3.51
177 178 2.040544 CACCCACGAGCCAACCATC 61.041 63.158 0.00 0.00 0.00 3.51
181 182 2.672996 ATGCACCCACGAGCCAAC 60.673 61.111 0.00 0.00 0.00 3.77
187 188 3.952508 ACAGGCATGCACCCACGA 61.953 61.111 21.36 0.00 0.00 4.35
188 189 3.740397 CACAGGCATGCACCCACG 61.740 66.667 21.36 2.92 0.00 4.94
189 190 1.660560 GATCACAGGCATGCACCCAC 61.661 60.000 21.36 0.72 0.00 4.61
190 191 1.378911 GATCACAGGCATGCACCCA 60.379 57.895 21.36 0.00 0.00 4.51
191 192 2.475466 CGATCACAGGCATGCACCC 61.475 63.158 21.36 1.57 0.00 4.61
192 193 2.475466 CCGATCACAGGCATGCACC 61.475 63.158 21.36 2.42 0.00 5.01
193 194 3.104766 CCGATCACAGGCATGCAC 58.895 61.111 21.36 9.10 0.00 4.57
200 201 1.589993 CGCTGTAGCCGATCACAGG 60.590 63.158 11.62 0.00 42.00 4.00
201 202 2.233654 GCGCTGTAGCCGATCACAG 61.234 63.158 0.00 6.56 44.07 3.66
202 203 2.202743 GCGCTGTAGCCGATCACA 60.203 61.111 0.00 0.00 37.91 3.58
203 204 1.592669 ATGCGCTGTAGCCGATCAC 60.593 57.895 9.73 0.00 37.91 3.06
214 215 2.480037 TCTAGAAACACAACATGCGCTG 59.520 45.455 9.73 7.16 0.00 5.18
216 217 3.536158 TTCTAGAAACACAACATGCGC 57.464 42.857 1.68 0.00 0.00 6.09
305 313 2.361230 GGGAGCTTTGTTCCCGGG 60.361 66.667 16.85 16.85 42.85 5.73
387 410 2.430582 GTACGTACGGTTGCGCCA 60.431 61.111 21.06 0.00 36.97 5.69
410 433 2.745821 CTGTTGGGCATCATATCATCGG 59.254 50.000 0.00 0.00 0.00 4.18
411 434 3.405831 ACTGTTGGGCATCATATCATCG 58.594 45.455 0.00 0.00 0.00 3.84
412 435 4.217118 GGAACTGTTGGGCATCATATCATC 59.783 45.833 0.00 0.00 0.00 2.92
413 436 4.147321 GGAACTGTTGGGCATCATATCAT 58.853 43.478 0.00 0.00 0.00 2.45
415 438 2.549754 CGGAACTGTTGGGCATCATATC 59.450 50.000 0.00 0.00 0.00 1.63
418 441 0.038166 ACGGAACTGTTGGGCATCAT 59.962 50.000 0.00 0.00 0.00 2.45
420 443 1.305930 GGACGGAACTGTTGGGCATC 61.306 60.000 0.00 0.00 0.00 3.91
421 444 1.303317 GGACGGAACTGTTGGGCAT 60.303 57.895 0.00 0.00 0.00 4.40
422 445 2.112297 GGACGGAACTGTTGGGCA 59.888 61.111 0.00 0.00 0.00 5.36
687 749 2.046892 CCTTGCTCCAGTGGGACG 60.047 66.667 9.92 0.00 38.64 4.79
692 754 1.376942 CTGCTCCCTTGCTCCAGTG 60.377 63.158 0.00 0.00 0.00 3.66
693 755 2.600729 CCTGCTCCCTTGCTCCAGT 61.601 63.158 0.00 0.00 0.00 4.00
694 756 2.271497 CCTGCTCCCTTGCTCCAG 59.729 66.667 0.00 0.00 0.00 3.86
695 757 3.333219 CCCTGCTCCCTTGCTCCA 61.333 66.667 0.00 0.00 0.00 3.86
700 762 2.034687 CACACCCCTGCTCCCTTG 59.965 66.667 0.00 0.00 0.00 3.61
706 768 1.352622 TTTCCACTCACACCCCTGCT 61.353 55.000 0.00 0.00 0.00 4.24
764 826 2.668550 GTCAACGGTCACTGCCCC 60.669 66.667 0.00 0.00 0.00 5.80
765 827 2.668550 GGTCAACGGTCACTGCCC 60.669 66.667 0.00 0.00 0.00 5.36
766 828 3.041940 CGGTCAACGGTCACTGCC 61.042 66.667 0.00 0.00 39.42 4.85
767 829 3.712881 GCGGTCAACGGTCACTGC 61.713 66.667 0.00 0.00 44.51 4.40
768 830 3.041940 GGCGGTCAACGGTCACTG 61.042 66.667 0.00 0.00 44.51 3.66
769 831 4.657824 CGGCGGTCAACGGTCACT 62.658 66.667 0.00 0.00 44.51 3.41
872 942 2.044252 AATGCTGCCTGCCTCTGG 60.044 61.111 0.00 0.00 42.00 3.86
873 943 2.470362 CGAATGCTGCCTGCCTCTG 61.470 63.158 0.00 0.00 42.00 3.35
874 944 2.124819 CGAATGCTGCCTGCCTCT 60.125 61.111 0.00 0.00 42.00 3.69
875 945 3.885521 GCGAATGCTGCCTGCCTC 61.886 66.667 0.00 0.00 42.00 4.70
876 946 4.728110 TGCGAATGCTGCCTGCCT 62.728 61.111 0.00 0.00 43.34 4.75
877 947 4.189188 CTGCGAATGCTGCCTGCC 62.189 66.667 0.00 0.00 43.34 4.85
888 958 0.033920 TCTTCTTCTGCTGCTGCGAA 59.966 50.000 11.21 14.74 43.34 4.70
889 959 0.668706 GTCTTCTTCTGCTGCTGCGA 60.669 55.000 11.21 8.36 43.34 5.10
900 970 2.437343 CGGCTGCGTCGTCTTCTTC 61.437 63.158 0.00 0.00 0.00 2.87
947 1017 2.878520 GAGTGTCGAGCTCTGCGC 60.879 66.667 12.85 10.65 39.57 6.09
960 1030 1.021920 TCGTCAGCCTCTCTCGAGTG 61.022 60.000 13.13 10.53 35.43 3.51
1530 1603 0.459489 TGGTGAGCCAAACAAACAGC 59.541 50.000 0.00 0.00 42.83 4.40
1531 1604 1.067516 CCTGGTGAGCCAAACAAACAG 59.932 52.381 0.00 0.00 45.51 3.16
1548 1623 4.722700 CCAACCACCCGCTCCCTG 62.723 72.222 0.00 0.00 0.00 4.45
1778 1854 1.790818 GAGGAGGGGTCGATTAAGGT 58.209 55.000 0.00 0.00 0.00 3.50
1782 1858 1.831286 GGCGAGGAGGGGTCGATTA 60.831 63.158 0.00 0.00 39.92 1.75
2002 2091 0.926220 AAGGGGAAATCAGGGGAGGG 60.926 60.000 0.00 0.00 0.00 4.30
2008 2097 6.608808 AGATAACAAATCAAGGGGAAATCAGG 59.391 38.462 0.00 0.00 0.00 3.86
2011 2100 9.803315 GTAAAGATAACAAATCAAGGGGAAATC 57.197 33.333 0.00 0.00 0.00 2.17
2012 2101 8.758829 GGTAAAGATAACAAATCAAGGGGAAAT 58.241 33.333 0.00 0.00 0.00 2.17
2016 2105 6.405842 GCTGGTAAAGATAACAAATCAAGGGG 60.406 42.308 0.00 0.00 0.00 4.79
2017 2106 6.378280 AGCTGGTAAAGATAACAAATCAAGGG 59.622 38.462 0.00 0.00 0.00 3.95
2027 2116 7.698130 CACATAGCAAAAGCTGGTAAAGATAAC 59.302 37.037 0.00 0.00 41.23 1.89
2028 2117 7.628366 GCACATAGCAAAAGCTGGTAAAGATAA 60.628 37.037 0.00 0.00 41.23 1.75
2030 2119 5.393461 GCACATAGCAAAAGCTGGTAAAGAT 60.393 40.000 0.00 0.00 41.23 2.40
2046 2135 3.379372 ACACAATCATCCAAGCACATAGC 59.621 43.478 0.00 0.00 46.19 2.97
2047 2136 4.036027 GGACACAATCATCCAAGCACATAG 59.964 45.833 0.00 0.00 34.87 2.23
2049 2138 2.756760 GGACACAATCATCCAAGCACAT 59.243 45.455 0.00 0.00 34.87 3.21
2050 2139 2.161855 GGACACAATCATCCAAGCACA 58.838 47.619 0.00 0.00 34.87 4.57
2051 2140 2.163010 CAGGACACAATCATCCAAGCAC 59.837 50.000 0.00 0.00 37.47 4.40
2052 2141 2.224843 ACAGGACACAATCATCCAAGCA 60.225 45.455 0.00 0.00 37.47 3.91
2053 2142 2.440409 ACAGGACACAATCATCCAAGC 58.560 47.619 0.00 0.00 37.47 4.01
2054 2143 3.366679 GCAACAGGACACAATCATCCAAG 60.367 47.826 0.00 0.00 37.47 3.61
2055 2144 2.557924 GCAACAGGACACAATCATCCAA 59.442 45.455 0.00 0.00 37.47 3.53
2056 2145 2.161855 GCAACAGGACACAATCATCCA 58.838 47.619 0.00 0.00 37.47 3.41
2057 2146 2.163010 CAGCAACAGGACACAATCATCC 59.837 50.000 0.00 0.00 34.98 3.51
2058 2147 2.415090 GCAGCAACAGGACACAATCATC 60.415 50.000 0.00 0.00 0.00 2.92
2059 2148 1.542915 GCAGCAACAGGACACAATCAT 59.457 47.619 0.00 0.00 0.00 2.45
2060 2149 0.953727 GCAGCAACAGGACACAATCA 59.046 50.000 0.00 0.00 0.00 2.57
2061 2150 1.242076 AGCAGCAACAGGACACAATC 58.758 50.000 0.00 0.00 0.00 2.67
2062 2151 2.566833 TAGCAGCAACAGGACACAAT 57.433 45.000 0.00 0.00 0.00 2.71
2118 2218 0.972134 TCAGTCCAAGAGCCTGACAG 59.028 55.000 0.00 0.00 30.58 3.51
2152 2252 4.320546 TGGTCAATTCACCCAGATCAAT 57.679 40.909 0.00 0.00 35.26 2.57
2251 2367 5.415701 ACCAAATCGTAAAGCATCAGTTCAT 59.584 36.000 0.00 0.00 0.00 2.57
2254 2370 5.705609 AACCAAATCGTAAAGCATCAGTT 57.294 34.783 0.00 0.00 0.00 3.16
2278 2394 2.192624 CAAAGCAACCTTGGTGTTTCG 58.807 47.619 0.00 0.00 39.13 3.46
2303 2419 7.765695 AAAATCAATCTCTTGCTCTAAACCA 57.234 32.000 0.00 0.00 32.11 3.67
2351 2467 4.517453 TGCTAACAACCAACAACATCTACC 59.483 41.667 0.00 0.00 0.00 3.18
2399 2519 8.195436 AGCAATTAATCTGTTCAAATCTCATGG 58.805 33.333 0.00 0.00 0.00 3.66
2428 2548 7.868415 AGTTAGATAAATACAGACGGAATCAGC 59.132 37.037 0.00 0.00 0.00 4.26
2429 2549 9.186323 CAGTTAGATAAATACAGACGGAATCAG 57.814 37.037 0.00 0.00 0.00 2.90
2453 2573 5.221891 ACAAGCTACAATAACAATCGCAG 57.778 39.130 0.00 0.00 0.00 5.18
2454 2574 6.592220 TCTTACAAGCTACAATAACAATCGCA 59.408 34.615 0.00 0.00 0.00 5.10
2455 2575 7.000575 TCTTACAAGCTACAATAACAATCGC 57.999 36.000 0.00 0.00 0.00 4.58
2503 2623 3.892588 TGGTATTCAGTTGGTTCCCAAAC 59.107 43.478 0.00 0.00 45.73 2.93
2529 2649 7.951530 AAAGGACAGCTTATGTTCATTTTTG 57.048 32.000 0.00 0.00 44.17 2.44
2531 2651 7.657354 GGAAAAAGGACAGCTTATGTTCATTTT 59.343 33.333 2.77 2.77 46.15 1.82
2535 2655 4.522789 GGGAAAAAGGACAGCTTATGTTCA 59.477 41.667 0.00 0.00 44.17 3.18
2536 2656 4.082190 GGGGAAAAAGGACAGCTTATGTTC 60.082 45.833 0.00 0.00 44.17 3.18
2539 2659 2.760650 GGGGGAAAAAGGACAGCTTATG 59.239 50.000 0.00 0.00 0.00 1.90
2540 2660 2.654896 AGGGGGAAAAAGGACAGCTTAT 59.345 45.455 0.00 0.00 0.00 1.73
2541 2661 2.070573 AGGGGGAAAAAGGACAGCTTA 58.929 47.619 0.00 0.00 0.00 3.09
2543 2663 0.113190 CAGGGGGAAAAAGGACAGCT 59.887 55.000 0.00 0.00 0.00 4.24
2544 2664 0.112412 TCAGGGGGAAAAAGGACAGC 59.888 55.000 0.00 0.00 0.00 4.40
2546 2666 2.140224 TCTTCAGGGGGAAAAAGGACA 58.860 47.619 0.00 0.00 34.44 4.02
2547 2667 2.971901 TCTTCAGGGGGAAAAAGGAC 57.028 50.000 0.00 0.00 34.44 3.85
2549 2669 5.595952 CAGATTATCTTCAGGGGGAAAAAGG 59.404 44.000 0.00 0.00 34.44 3.11
2550 2670 6.426587 TCAGATTATCTTCAGGGGGAAAAAG 58.573 40.000 0.00 0.00 34.44 2.27
2551 2671 6.401537 TCAGATTATCTTCAGGGGGAAAAA 57.598 37.500 0.00 0.00 34.44 1.94
2552 2672 6.401537 TTCAGATTATCTTCAGGGGGAAAA 57.598 37.500 0.00 0.00 34.44 2.29
2553 2673 6.596869 ATTCAGATTATCTTCAGGGGGAAA 57.403 37.500 0.00 0.00 34.44 3.13
2554 2674 6.160282 TGAATTCAGATTATCTTCAGGGGGAA 59.840 38.462 3.38 0.00 0.00 3.97
2555 2675 5.671735 TGAATTCAGATTATCTTCAGGGGGA 59.328 40.000 3.38 0.00 0.00 4.81
2556 2676 5.767168 GTGAATTCAGATTATCTTCAGGGGG 59.233 44.000 8.80 0.00 0.00 5.40
2557 2677 5.767168 GGTGAATTCAGATTATCTTCAGGGG 59.233 44.000 8.80 0.00 0.00 4.79
2558 2678 6.599445 AGGTGAATTCAGATTATCTTCAGGG 58.401 40.000 8.80 0.00 0.00 4.45
2559 2679 8.428063 ACTAGGTGAATTCAGATTATCTTCAGG 58.572 37.037 8.80 0.00 0.00 3.86
2560 2680 9.258826 CACTAGGTGAATTCAGATTATCTTCAG 57.741 37.037 8.80 0.00 35.23 3.02
2561 2681 8.206867 CCACTAGGTGAATTCAGATTATCTTCA 58.793 37.037 8.80 0.00 35.23 3.02
2562 2682 7.659390 CCCACTAGGTGAATTCAGATTATCTTC 59.341 40.741 8.80 0.00 35.23 2.87
2563 2683 7.420680 CCCCACTAGGTGAATTCAGATTATCTT 60.421 40.741 8.80 0.00 35.23 2.40
2565 2685 6.234177 CCCCACTAGGTGAATTCAGATTATC 58.766 44.000 8.80 0.00 35.23 1.75
2566 2686 5.456763 GCCCCACTAGGTGAATTCAGATTAT 60.457 44.000 8.80 0.00 35.23 1.28
2567 2687 4.141482 GCCCCACTAGGTGAATTCAGATTA 60.141 45.833 8.80 1.17 35.23 1.75
2568 2688 3.372025 GCCCCACTAGGTGAATTCAGATT 60.372 47.826 8.80 0.00 35.23 2.40
2569 2689 2.173569 GCCCCACTAGGTGAATTCAGAT 59.826 50.000 8.80 2.88 35.23 2.90
2572 2692 0.623723 GGCCCCACTAGGTGAATTCA 59.376 55.000 3.38 3.38 35.23 2.57
2573 2693 0.919710 AGGCCCCACTAGGTGAATTC 59.080 55.000 0.00 0.00 35.23 2.17
2574 2694 0.625849 CAGGCCCCACTAGGTGAATT 59.374 55.000 0.00 0.00 35.23 2.17
2575 2695 1.281925 CCAGGCCCCACTAGGTGAAT 61.282 60.000 0.00 0.00 35.23 2.57
2577 2697 2.194951 ATCCAGGCCCCACTAGGTGA 62.195 60.000 0.00 0.00 35.23 4.02
2578 2698 0.399949 TATCCAGGCCCCACTAGGTG 60.400 60.000 0.00 0.00 0.00 4.00
2579 2699 0.345502 TTATCCAGGCCCCACTAGGT 59.654 55.000 0.00 0.00 0.00 3.08
2582 2702 2.782922 TCAATTATCCAGGCCCCACTA 58.217 47.619 0.00 0.00 0.00 2.74
2583 2703 1.607225 TCAATTATCCAGGCCCCACT 58.393 50.000 0.00 0.00 0.00 4.00
2585 2705 2.517553 TGATTCAATTATCCAGGCCCCA 59.482 45.455 0.00 0.00 0.00 4.96
2586 2706 3.243359 TGATTCAATTATCCAGGCCCC 57.757 47.619 0.00 0.00 0.00 5.80
2588 2708 4.338118 TCGTTTGATTCAATTATCCAGGCC 59.662 41.667 0.00 0.00 0.00 5.19
2600 2743 6.479990 CAGGCAGAGTATATTCGTTTGATTCA 59.520 38.462 0.00 0.00 0.00 2.57
2604 2747 5.592104 TCAGGCAGAGTATATTCGTTTGA 57.408 39.130 0.00 0.00 0.00 2.69
2704 2853 7.273381 CGCAATAATAACCAAGAAGAACCAAAG 59.727 37.037 0.00 0.00 0.00 2.77
2717 2867 4.334203 CACTACAAGGCGCAATAATAACCA 59.666 41.667 10.83 0.00 0.00 3.67
2725 2875 1.176527 AATGCACTACAAGGCGCAAT 58.823 45.000 10.83 0.00 38.01 3.56
2762 2912 6.740944 TGCTTAATGTGCTAGGGTAGAATA 57.259 37.500 0.00 0.00 0.00 1.75
2900 3052 3.644738 ACTAGAAAGGAAACCTTGTCCGA 59.355 43.478 3.73 0.00 43.92 4.55
2901 3053 4.004196 ACTAGAAAGGAAACCTTGTCCG 57.996 45.455 3.73 0.00 43.92 4.79
2905 3057 7.772166 AGAACAAAACTAGAAAGGAAACCTTG 58.228 34.615 3.73 0.00 43.92 3.61
2937 3089 5.185454 TGAAGGGTGCACAGTGAATTATAG 58.815 41.667 20.43 0.00 0.00 1.31
3038 3190 9.512435 CCGAGATAAAAGATAACGAAGAACTTA 57.488 33.333 0.00 0.00 0.00 2.24
3114 3266 2.870435 GCATCGGTGTAACAAGTCTGGT 60.870 50.000 0.00 0.00 39.98 4.00
3117 3269 2.831685 TGCATCGGTGTAACAAGTCT 57.168 45.000 0.00 0.00 39.98 3.24
3133 3287 4.783227 AGAGGTTAGGAAGTTAGGAATGCA 59.217 41.667 0.00 0.00 0.00 3.96
3134 3288 5.119694 CAGAGGTTAGGAAGTTAGGAATGC 58.880 45.833 0.00 0.00 0.00 3.56
3230 3384 1.860950 CGAGCACATGCACATACCTAC 59.139 52.381 6.64 0.00 45.16 3.18
3284 3438 2.488792 CGCACGACGTGAGATGACG 61.489 63.158 31.08 18.92 45.09 4.35
3299 3453 1.896339 GCTGATTGTGCACGTACGCA 61.896 55.000 16.72 2.78 40.32 5.24
3300 3454 1.225745 GCTGATTGTGCACGTACGC 60.226 57.895 16.72 7.25 0.00 4.42
3312 3466 1.086696 CCGAATCAACACGGCTGATT 58.913 50.000 0.00 8.17 44.34 2.57
3320 3474 4.749245 AATGAGTTCACCGAATCAACAC 57.251 40.909 0.00 0.00 0.00 3.32
3331 3485 3.803555 CGAGCAACAGAAATGAGTTCAC 58.196 45.455 0.00 0.00 38.86 3.18
3383 3537 3.484547 GTTCGTAAGGGCCACGCG 61.485 66.667 6.18 3.53 39.23 6.01
3410 3564 0.995803 AAAGCCTCCTCCTCCTTTCC 59.004 55.000 0.00 0.00 0.00 3.13
3471 3625 4.520492 AGAGCATCAAGTAAACCCAAAGTG 59.480 41.667 0.00 0.00 37.82 3.16
3608 3776 9.471084 ACAAACAAACAAACTATATGTAAAGGC 57.529 29.630 0.00 0.00 0.00 4.35
3700 3881 2.887568 GCATCACAGGCGACCTCG 60.888 66.667 0.00 0.00 43.27 4.63
3856 4052 6.939622 TCACTGATAAAGATCGGATATGCAT 58.060 36.000 3.79 3.79 40.47 3.96
3868 4064 8.886719 CAGCATATTTCACTTCACTGATAAAGA 58.113 33.333 0.00 0.00 0.00 2.52
3885 4081 2.965147 GGCATGGGGTTACAGCATATTT 59.035 45.455 0.00 0.00 0.00 1.40
3888 4084 0.922626 TGGCATGGGGTTACAGCATA 59.077 50.000 0.00 0.00 0.00 3.14
3926 4122 2.164219 CCCATTTTGAATGACCAGTCCG 59.836 50.000 2.37 0.00 0.00 4.79
4044 4247 3.504906 ACAATCATTCCTTCAGCACAGTG 59.495 43.478 0.00 0.00 0.00 3.66
4096 4301 0.879765 AGCAGCAGAAGCATCAACAC 59.120 50.000 0.00 0.00 45.49 3.32
4103 4308 1.527611 AACAGCAGCAGCAGAAGCA 60.528 52.632 3.17 0.00 45.49 3.91
4104 4309 1.081376 CAACAGCAGCAGCAGAAGC 60.081 57.895 3.17 0.00 45.49 3.86
4105 4310 0.666913 AACAACAGCAGCAGCAGAAG 59.333 50.000 3.17 0.00 45.49 2.85
4106 4311 0.664761 GAACAACAGCAGCAGCAGAA 59.335 50.000 3.17 0.00 45.49 3.02
4107 4312 1.168407 GGAACAACAGCAGCAGCAGA 61.168 55.000 3.17 0.00 45.49 4.26
4108 4313 1.285023 GGAACAACAGCAGCAGCAG 59.715 57.895 3.17 0.00 45.49 4.24
4109 4314 1.453562 TGGAACAACAGCAGCAGCA 60.454 52.632 3.17 0.00 38.57 4.41
4110 4315 1.008079 GTGGAACAACAGCAGCAGC 60.008 57.895 0.00 0.00 44.16 5.25
4129 4334 4.170449 AGCAAAGGAAAGGAAATGGGATT 58.830 39.130 0.00 0.00 0.00 3.01
4135 4340 3.007290 GCCTCAAGCAAAGGAAAGGAAAT 59.993 43.478 3.44 0.00 42.97 2.17
4306 4516 2.652530 CGGGGTCGTTTTCTCCGA 59.347 61.111 0.00 0.00 42.94 4.55


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

AutoCloner maintained by Alex Coulton.