Multiple sequence alignment - TraesCS3A01G179400

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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 TraesCS3A01G179400 chr3A 100.000 3140 0 0 1 3140 207829063 207832202 0.000000e+00 5799.0
1 TraesCS3A01G179400 chr3A 77.233 347 53 18 1485 1818 207844396 207844729 2.490000e-41 180.0
2 TraesCS3A01G179400 chr3A 88.421 95 11 0 2016 2110 207844824 207844918 7.120000e-22 115.0
3 TraesCS3A01G179400 chr3B 90.499 1484 69 29 1650 3088 245359033 245360489 0.000000e+00 1893.0
4 TraesCS3A01G179400 chr3B 93.398 1030 24 15 640 1648 245357723 245358729 0.000000e+00 1485.0
5 TraesCS3A01G179400 chr3B 93.548 217 14 0 440 656 245357494 245357710 1.090000e-84 324.0
6 TraesCS3A01G179400 chr3B 88.889 144 16 0 1342 1485 245508719 245508862 8.950000e-41 178.0
7 TraesCS3A01G179400 chr3B 92.000 125 10 0 1485 1609 245508987 245509111 3.220000e-40 176.0
8 TraesCS3A01G179400 chr3D 90.607 1416 55 34 547 1918 170202440 170203821 0.000000e+00 1807.0
9 TraesCS3A01G179400 chr3D 92.958 710 31 12 1975 2673 170203967 170204668 0.000000e+00 1016.0
10 TraesCS3A01G179400 chr3D 90.323 217 16 3 2876 3087 170205948 170206164 2.380000e-71 279.0
11 TraesCS3A01G179400 chr3D 85.425 247 31 3 171 414 170201903 170202147 5.200000e-63 252.0
12 TraesCS3A01G179400 chr3D 94.771 153 8 0 2672 2824 170204779 170204931 4.050000e-59 239.0
13 TraesCS3A01G179400 chr3D 88.194 144 17 0 1342 1485 170237163 170237306 4.160000e-39 172.0
14 TraesCS3A01G179400 chr3D 77.083 336 54 17 1485 1818 170237424 170237738 4.160000e-39 172.0
15 TraesCS3A01G179400 chr3D 85.600 125 16 1 440 562 170202300 170202424 2.540000e-26 130.0
16 TraesCS3A01G179400 chr3D 100.000 67 0 0 2811 2877 170205800 170205866 1.180000e-24 124.0
17 TraesCS3A01G179400 chr3D 87.368 95 12 0 2016 2110 170237832 170237926 3.310000e-20 110.0
18 TraesCS3A01G179400 chr3D 100.000 28 0 0 1952 1979 170203878 170203905 6.000000e-03 52.8
19 TraesCS3A01G179400 chr2B 93.822 259 13 3 1406 1662 776315394 776315137 1.370000e-103 387.0
20 TraesCS3A01G179400 chr2B 95.122 41 1 1 620 659 303818738 303818698 2.610000e-06 63.9


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 TraesCS3A01G179400 chr3A 207829063 207832202 3139 False 5799.000 5799 100.000000 1 3140 1 chr3A.!!$F1 3139
1 TraesCS3A01G179400 chr3B 245357494 245360489 2995 False 1234.000 1893 92.481667 440 3088 3 chr3B.!!$F1 2648
2 TraesCS3A01G179400 chr3D 170201903 170206164 4261 False 487.475 1807 92.460500 171 3087 8 chr3D.!!$F1 2916

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
386 387 0.036306 AGTGGCTAGGGTTTTGTCCG 59.964 55.0 0.0 0.0 0.00 4.79 F
431 435 0.252239 TGAGGCTGAAGTGGCTAGGA 60.252 55.0 0.0 0.0 43.09 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1574 0.036010 CGCCAGGGACTTCATCTGTT 60.036 55.0 0.0 0.0 34.6 3.16 R
2368 3033 0.171903 GCGGTAGTGCTCGGAAAGTA 59.828 55.0 0.0 0.0 0.0 2.24 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
19 20 0.101399 CTCTGACTTGGATCCCGACG 59.899 60.000 9.90 0.00 0.00 5.12
20 21 1.519455 CTGACTTGGATCCCGACGC 60.519 63.158 9.90 0.00 0.00 5.19
21 22 2.202892 GACTTGGATCCCGACGCC 60.203 66.667 9.90 0.00 0.00 5.68
22 23 4.143333 ACTTGGATCCCGACGCCG 62.143 66.667 9.90 0.00 0.00 6.46
39 40 4.512914 GCAGGGATGAGGGGCCAC 62.513 72.222 4.39 0.00 0.00 5.01
40 41 3.813724 CAGGGATGAGGGGCCACC 61.814 72.222 0.00 0.57 40.67 4.61
43 44 3.407967 GGATGAGGGGCCACCGAA 61.408 66.667 0.00 0.00 46.96 4.30
44 45 2.190578 GATGAGGGGCCACCGAAG 59.809 66.667 0.00 0.00 46.96 3.79
57 58 3.353836 CGAAGGGGTTGCACCGTG 61.354 66.667 0.00 0.00 39.83 4.94
58 59 2.112297 GAAGGGGTTGCACCGTGA 59.888 61.111 1.65 0.00 39.83 4.35
59 60 2.203294 AAGGGGTTGCACCGTGAC 60.203 61.111 1.65 0.00 39.83 3.67
60 61 3.785122 AAGGGGTTGCACCGTGACC 62.785 63.158 1.65 1.55 39.83 4.02
92 93 2.357517 CCAGACGGTGGTCACTGC 60.358 66.667 9.61 3.65 45.92 4.40
93 94 2.734723 CAGACGGTGGTCACTGCG 60.735 66.667 9.61 4.36 45.92 5.18
94 95 3.224324 AGACGGTGGTCACTGCGT 61.224 61.111 9.61 7.36 45.92 5.24
95 96 2.733593 GACGGTGGTCACTGCGTC 60.734 66.667 13.79 13.79 42.91 5.19
96 97 4.295119 ACGGTGGTCACTGCGTCC 62.295 66.667 9.61 0.00 41.31 4.79
99 100 4.295119 GTGGTCACTGCGTCCGGT 62.295 66.667 0.00 0.00 0.00 5.28
112 113 3.697747 CCGGTGAGGCCACGGTTA 61.698 66.667 16.89 0.00 44.09 2.85
113 114 2.433664 CGGTGAGGCCACGGTTAC 60.434 66.667 5.01 0.00 44.09 2.50
114 115 2.745037 GGTGAGGCCACGGTTACA 59.255 61.111 5.01 0.00 44.09 2.41
115 116 1.298667 GGTGAGGCCACGGTTACAT 59.701 57.895 5.01 0.00 44.09 2.29
116 117 1.024579 GGTGAGGCCACGGTTACATG 61.025 60.000 5.01 0.00 44.09 3.21
117 118 1.376683 TGAGGCCACGGTTACATGC 60.377 57.895 5.01 0.00 0.00 4.06
118 119 1.078426 GAGGCCACGGTTACATGCT 60.078 57.895 5.01 0.00 0.00 3.79
119 120 0.676782 GAGGCCACGGTTACATGCTT 60.677 55.000 5.01 0.00 0.00 3.91
120 121 0.960364 AGGCCACGGTTACATGCTTG 60.960 55.000 5.01 0.00 0.00 4.01
121 122 1.506262 GCCACGGTTACATGCTTGG 59.494 57.895 4.44 0.00 0.00 3.61
122 123 0.958382 GCCACGGTTACATGCTTGGA 60.958 55.000 4.44 0.00 0.00 3.53
123 124 1.086696 CCACGGTTACATGCTTGGAG 58.913 55.000 4.44 0.00 0.00 3.86
124 125 0.447801 CACGGTTACATGCTTGGAGC 59.552 55.000 4.44 0.00 42.82 4.70
125 126 0.676782 ACGGTTACATGCTTGGAGCC 60.677 55.000 7.57 7.57 41.51 4.70
126 127 0.676466 CGGTTACATGCTTGGAGCCA 60.676 55.000 16.51 0.00 41.51 4.75
127 128 0.811281 GGTTACATGCTTGGAGCCAC 59.189 55.000 12.25 0.00 41.51 5.01
128 129 1.614317 GGTTACATGCTTGGAGCCACT 60.614 52.381 12.25 0.00 41.51 4.00
129 130 2.355716 GGTTACATGCTTGGAGCCACTA 60.356 50.000 12.25 0.00 41.51 2.74
130 131 2.939103 GTTACATGCTTGGAGCCACTAG 59.061 50.000 4.44 0.00 41.51 2.57
131 132 0.254178 ACATGCTTGGAGCCACTAGG 59.746 55.000 4.44 0.00 41.51 3.02
149 150 3.201494 CTCGGCCGATCTGAGTGT 58.799 61.111 31.19 0.00 42.11 3.55
150 151 1.064946 CTCGGCCGATCTGAGTGTC 59.935 63.158 31.19 0.00 42.11 3.67
151 152 1.657751 CTCGGCCGATCTGAGTGTCA 61.658 60.000 31.19 0.52 42.11 3.58
152 153 1.037579 TCGGCCGATCTGAGTGTCAT 61.038 55.000 27.28 0.00 0.00 3.06
153 154 0.179100 CGGCCGATCTGAGTGTCATT 60.179 55.000 24.07 0.00 0.00 2.57
154 155 1.740380 CGGCCGATCTGAGTGTCATTT 60.740 52.381 24.07 0.00 0.00 2.32
155 156 1.936547 GGCCGATCTGAGTGTCATTTC 59.063 52.381 0.00 0.00 0.00 2.17
156 157 2.419297 GGCCGATCTGAGTGTCATTTCT 60.419 50.000 0.00 0.00 0.00 2.52
157 158 2.606725 GCCGATCTGAGTGTCATTTCTG 59.393 50.000 0.00 0.00 0.00 3.02
158 159 2.606725 CCGATCTGAGTGTCATTTCTGC 59.393 50.000 0.00 0.00 0.00 4.26
159 160 2.606725 CGATCTGAGTGTCATTTCTGCC 59.393 50.000 0.00 0.00 0.00 4.85
160 161 2.084610 TCTGAGTGTCATTTCTGCCG 57.915 50.000 0.00 0.00 0.00 5.69
161 162 1.618343 TCTGAGTGTCATTTCTGCCGA 59.382 47.619 0.00 0.00 0.00 5.54
162 163 1.728971 CTGAGTGTCATTTCTGCCGAC 59.271 52.381 0.00 0.00 0.00 4.79
163 164 0.716108 GAGTGTCATTTCTGCCGACG 59.284 55.000 0.00 0.00 32.17 5.12
164 165 1.132640 GTGTCATTTCTGCCGACGC 59.867 57.895 0.00 0.00 33.50 5.19
165 166 1.301322 TGTCATTTCTGCCGACGCA 60.301 52.632 0.00 0.00 44.78 5.24
166 167 0.882484 TGTCATTTCTGCCGACGCAA 60.882 50.000 0.00 0.00 46.66 4.85
167 168 0.447801 GTCATTTCTGCCGACGCAAT 59.552 50.000 0.00 0.00 46.66 3.56
168 169 0.447406 TCATTTCTGCCGACGCAATG 59.553 50.000 0.00 0.00 46.66 2.82
169 170 0.523968 CATTTCTGCCGACGCAATGG 60.524 55.000 0.00 0.00 46.66 3.16
175 176 0.676466 TGCCGACGCAATGGATTTCT 60.676 50.000 0.00 0.00 43.74 2.52
178 179 2.276201 CCGACGCAATGGATTTCTGTA 58.724 47.619 0.00 0.00 0.00 2.74
184 185 2.614057 GCAATGGATTTCTGTAGGGTCG 59.386 50.000 0.00 0.00 0.00 4.79
190 191 2.297698 TTTCTGTAGGGTCGACTCCA 57.702 50.000 12.98 2.66 0.00 3.86
192 193 2.526888 TCTGTAGGGTCGACTCCAAT 57.473 50.000 12.98 0.00 0.00 3.16
196 197 0.681887 TAGGGTCGACTCCAATCGCA 60.682 55.000 12.98 0.00 41.97 5.10
213 214 1.893786 CAGTTAGGCGCACTCCTCT 59.106 57.895 10.83 0.00 37.66 3.69
216 217 2.415608 TTAGGCGCACTCCTCTCGG 61.416 63.158 10.83 0.00 37.66 4.63
313 314 3.365565 GGAGATCTCTAAGTCGAATCCGC 60.366 52.174 21.81 0.00 35.37 5.54
315 316 3.252215 AGATCTCTAAGTCGAATCCGCTG 59.748 47.826 0.00 0.00 35.37 5.18
316 317 2.366533 TCTCTAAGTCGAATCCGCTGT 58.633 47.619 0.00 0.00 35.37 4.40
333 334 0.904649 TGTCCGCCATGTCAGAGAAT 59.095 50.000 0.00 0.00 0.00 2.40
338 339 1.442526 GCCATGTCAGAGAATGCCGG 61.443 60.000 0.00 0.00 0.00 6.13
340 341 1.202734 CCATGTCAGAGAATGCCGGAT 60.203 52.381 5.05 0.00 0.00 4.18
345 346 2.029828 GTCAGAGAATGCCGGATATCGT 60.030 50.000 5.05 0.00 37.11 3.73
346 347 2.628178 TCAGAGAATGCCGGATATCGTT 59.372 45.455 5.05 0.00 37.11 3.85
351 352 1.878953 ATGCCGGATATCGTTGGAAC 58.121 50.000 5.05 0.00 37.11 3.62
372 373 4.858680 GCTTAGGGGCGGAGTGGC 62.859 72.222 0.00 0.00 43.88 5.01
381 382 1.002502 GCGGAGTGGCTAGGGTTTT 60.003 57.895 0.00 0.00 0.00 2.43
386 387 0.036306 AGTGGCTAGGGTTTTGTCCG 59.964 55.000 0.00 0.00 0.00 4.79
391 392 1.487558 GCTAGGGTTTTGTCCGGGATA 59.512 52.381 0.00 0.00 0.00 2.59
402 406 3.170717 TGTCCGGGATATGAATAGGGAC 58.829 50.000 0.00 0.53 42.10 4.46
417 421 3.963428 AGGGACGAATATATGTGAGGC 57.037 47.619 0.00 0.00 0.00 4.70
418 422 3.511477 AGGGACGAATATATGTGAGGCT 58.489 45.455 0.00 0.00 0.00 4.58
420 424 3.258372 GGGACGAATATATGTGAGGCTGA 59.742 47.826 0.00 0.00 0.00 4.26
422 426 4.926238 GGACGAATATATGTGAGGCTGAAG 59.074 45.833 0.00 0.00 0.00 3.02
426 430 2.338577 ATATGTGAGGCTGAAGTGGC 57.661 50.000 0.00 0.00 0.00 5.01
427 431 1.279496 TATGTGAGGCTGAAGTGGCT 58.721 50.000 0.00 0.00 45.80 4.75
428 432 1.279496 ATGTGAGGCTGAAGTGGCTA 58.721 50.000 0.00 0.00 43.09 3.93
429 433 0.610174 TGTGAGGCTGAAGTGGCTAG 59.390 55.000 0.00 0.00 43.09 3.42
431 435 0.252239 TGAGGCTGAAGTGGCTAGGA 60.252 55.000 0.00 0.00 43.09 2.94
432 436 1.127343 GAGGCTGAAGTGGCTAGGAT 58.873 55.000 0.00 0.00 43.09 3.24
434 438 1.918957 AGGCTGAAGTGGCTAGGATTT 59.081 47.619 0.00 0.00 41.20 2.17
437 441 3.084786 GCTGAAGTGGCTAGGATTTTGT 58.915 45.455 0.00 0.00 0.00 2.83
438 442 3.127721 GCTGAAGTGGCTAGGATTTTGTC 59.872 47.826 0.00 0.00 0.00 3.18
481 612 3.461773 CGGACCGTCTGCCCAGAT 61.462 66.667 5.48 0.00 39.97 2.90
482 613 2.125326 CGGACCGTCTGCCCAGATA 61.125 63.158 5.48 0.00 39.97 1.98
520 653 1.595466 AGTCCGGCTGTAGATACTCG 58.405 55.000 0.00 0.00 0.00 4.18
521 654 1.134159 AGTCCGGCTGTAGATACTCGT 60.134 52.381 0.00 0.00 0.00 4.18
552 685 2.751259 CCTGATGACACCTCCAACAATG 59.249 50.000 0.00 0.00 0.00 2.82
585 747 3.555547 GGAAACATGTCAAAACTGGTTGC 59.444 43.478 0.00 0.00 0.00 4.17
693 901 7.009540 GCTTTAAGTGCGCATCAAATTATTTCT 59.990 33.333 15.91 0.00 0.00 2.52
694 902 7.969387 TTAAGTGCGCATCAAATTATTTCTC 57.031 32.000 15.91 0.00 0.00 2.87
695 903 5.565592 AGTGCGCATCAAATTATTTCTCA 57.434 34.783 15.91 0.00 0.00 3.27
696 904 5.335127 AGTGCGCATCAAATTATTTCTCAC 58.665 37.500 15.91 0.00 0.00 3.51
697 905 5.094812 GTGCGCATCAAATTATTTCTCACA 58.905 37.500 15.91 0.00 0.00 3.58
698 906 5.003778 GTGCGCATCAAATTATTTCTCACAC 59.996 40.000 15.91 0.00 0.00 3.82
699 907 4.202959 GCGCATCAAATTATTTCTCACACG 59.797 41.667 0.30 0.00 0.00 4.49
700 908 4.730042 CGCATCAAATTATTTCTCACACGG 59.270 41.667 0.00 0.00 0.00 4.94
701 909 5.640732 GCATCAAATTATTTCTCACACGGT 58.359 37.500 0.00 0.00 0.00 4.83
702 910 6.456315 CGCATCAAATTATTTCTCACACGGTA 60.456 38.462 0.00 0.00 0.00 4.02
703 911 6.687105 GCATCAAATTATTTCTCACACGGTAC 59.313 38.462 0.00 0.00 0.00 3.34
704 912 7.625395 GCATCAAATTATTTCTCACACGGTACA 60.625 37.037 0.00 0.00 0.00 2.90
705 913 7.915293 TCAAATTATTTCTCACACGGTACAT 57.085 32.000 0.00 0.00 0.00 2.29
706 914 9.607988 ATCAAATTATTTCTCACACGGTACATA 57.392 29.630 0.00 0.00 0.00 2.29
707 915 9.607988 TCAAATTATTTCTCACACGGTACATAT 57.392 29.630 0.00 0.00 0.00 1.78
708 916 9.650371 CAAATTATTTCTCACACGGTACATATG 57.350 33.333 0.00 0.00 0.00 1.78
709 917 6.838198 TTATTTCTCACACGGTACATATGC 57.162 37.500 1.58 0.00 0.00 3.14
768 976 1.852633 CCCCCATTGAAACCTCTTCC 58.147 55.000 0.00 0.00 0.00 3.46
847 1068 4.459089 GCTGCCTCCGTGACCTCC 62.459 72.222 0.00 0.00 0.00 4.30
848 1069 2.681778 CTGCCTCCGTGACCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
849 1070 2.680352 TGCCTCCGTGACCTCCTC 60.680 66.667 0.00 0.00 0.00 3.71
1306 1534 0.613292 ATGCACTGACTCCGTCCTCT 60.613 55.000 0.00 0.00 0.00 3.69
1313 1541 0.452585 GACTCCGTCCTCTTTCCTCG 59.547 60.000 0.00 0.00 0.00 4.63
1314 1542 1.139947 CTCCGTCCTCTTTCCTCGC 59.860 63.158 0.00 0.00 0.00 5.03
1316 1544 1.153745 CCGTCCTCTTTCCTCGCTG 60.154 63.158 0.00 0.00 0.00 5.18
1317 1545 1.587054 CGTCCTCTTTCCTCGCTGT 59.413 57.895 0.00 0.00 0.00 4.40
1322 1557 1.741706 CCTCTTTCCTCGCTGTACGTA 59.258 52.381 0.00 0.00 44.19 3.57
1337 1572 0.806868 ACGTACGTGTGTCCATCGAT 59.193 50.000 22.14 0.00 0.00 3.59
1338 1573 2.009051 ACGTACGTGTGTCCATCGATA 58.991 47.619 22.14 0.00 0.00 2.92
1339 1574 2.419673 ACGTACGTGTGTCCATCGATAA 59.580 45.455 22.14 0.00 0.00 1.75
1352 1588 5.463724 GTCCATCGATAAACAGATGAAGTCC 59.536 44.000 0.00 0.00 45.08 3.85
1505 1741 2.592861 GGCACGGAGATGATGGCC 60.593 66.667 0.00 0.00 33.01 5.36
1615 1857 1.467342 CCTCGTCGATGTACACAGACA 59.533 52.381 23.74 14.22 33.56 3.41
1616 1858 2.476352 CCTCGTCGATGTACACAGACAG 60.476 54.545 23.74 19.59 33.56 3.51
1617 1859 2.415512 CTCGTCGATGTACACAGACAGA 59.584 50.000 23.74 20.16 33.56 3.41
1618 1860 2.159037 TCGTCGATGTACACAGACAGAC 59.841 50.000 23.74 14.57 33.56 3.51
1619 1861 2.728225 CGTCGATGTACACAGACAGACC 60.728 54.545 23.74 5.56 33.56 3.85
1620 1862 2.488545 GTCGATGTACACAGACAGACCT 59.511 50.000 21.03 0.00 34.09 3.85
1622 1864 2.488153 CGATGTACACAGACAGACCTCA 59.512 50.000 0.00 0.00 31.51 3.86
1623 1865 3.057526 CGATGTACACAGACAGACCTCAA 60.058 47.826 0.00 0.00 31.51 3.02
1624 1866 3.728076 TGTACACAGACAGACCTCAAC 57.272 47.619 0.00 0.00 0.00 3.18
1625 1867 2.364324 TGTACACAGACAGACCTCAACC 59.636 50.000 0.00 0.00 0.00 3.77
1626 1868 1.794714 ACACAGACAGACCTCAACCT 58.205 50.000 0.00 0.00 0.00 3.50
1627 1869 1.689273 ACACAGACAGACCTCAACCTC 59.311 52.381 0.00 0.00 0.00 3.85
1628 1870 1.967066 CACAGACAGACCTCAACCTCT 59.033 52.381 0.00 0.00 0.00 3.69
1635 1877 3.576550 ACAGACCTCAACCTCTTCTTCTC 59.423 47.826 0.00 0.00 0.00 2.87
1674 2220 1.135046 CTCGTCTGCTGTGAACAGTG 58.865 55.000 11.87 5.93 45.45 3.66
1781 2332 0.449388 GACCGTACCTCACCTACGTG 59.551 60.000 0.00 0.00 41.72 4.49
1808 2359 2.572104 GACAACAGACTACCCCATCCTT 59.428 50.000 0.00 0.00 0.00 3.36
1855 2408 4.479158 AGCCCAGAAGAACCAAACAAATA 58.521 39.130 0.00 0.00 0.00 1.40
1879 2432 1.299926 CCGTTCCGCTCCTTATCGG 60.300 63.158 0.00 0.00 46.52 4.18
1907 2460 4.184649 ACCCAAATCTCAACTTCACCTT 57.815 40.909 0.00 0.00 0.00 3.50
1954 2520 2.743126 CCGTACCTATTTCAAACGCCAA 59.257 45.455 0.00 0.00 32.43 4.52
2067 2716 2.693591 CGCCTACTGGTTCTTGAGGATA 59.306 50.000 0.00 0.00 35.27 2.59
2141 2793 3.355378 CCAAGGTCAATGCCAAGTGATA 58.645 45.455 0.00 0.00 32.15 2.15
2158 2810 7.171508 CCAAGTGATACATCCATGTACATACAC 59.828 40.741 8.32 8.66 45.11 2.90
2316 2972 1.651240 CCACAGGCAAGCATCTTCCG 61.651 60.000 0.00 0.00 0.00 4.30
2338 2994 6.649141 TCCGAACAAAGGATGCATATATACAC 59.351 38.462 0.00 0.00 31.86 2.90
2368 3033 4.986659 GCAATTCAACTCTTGTGCAGAAAT 59.013 37.500 0.00 0.00 32.38 2.17
2378 3043 4.690748 TCTTGTGCAGAAATACTTTCCGAG 59.309 41.667 0.00 0.00 40.54 4.63
2397 3062 1.296715 CACTACCGCTTGCCTCCTT 59.703 57.895 0.00 0.00 0.00 3.36
2401 3066 0.535335 TACCGCTTGCCTCCTTACTG 59.465 55.000 0.00 0.00 0.00 2.74
2402 3067 1.296715 CCGCTTGCCTCCTTACTGT 59.703 57.895 0.00 0.00 0.00 3.55
2403 3068 0.321653 CCGCTTGCCTCCTTACTGTT 60.322 55.000 0.00 0.00 0.00 3.16
2404 3069 1.523758 CGCTTGCCTCCTTACTGTTT 58.476 50.000 0.00 0.00 0.00 2.83
2405 3070 1.197721 CGCTTGCCTCCTTACTGTTTG 59.802 52.381 0.00 0.00 0.00 2.93
2445 3110 3.333804 AGCTTCTCTTCTTGCTGCTTAC 58.666 45.455 0.00 0.00 34.19 2.34
2464 3129 6.714810 TGCTTACACAGTTGTTAGATTGGATT 59.285 34.615 0.00 0.00 34.83 3.01
2661 3328 3.369576 GCCAGAACGAACTCCCTTCTATT 60.370 47.826 0.00 0.00 0.00 1.73
2712 3492 3.706086 GGGATGGGATGCTTTGTTATGTT 59.294 43.478 0.00 0.00 0.00 2.71
2785 3565 9.667107 TCGTATGATAAAGAAAGTTCCTCAATT 57.333 29.630 0.00 0.00 0.00 2.32
2996 4756 4.340950 AGTGGGTGAACAGGTTAAACAATG 59.659 41.667 0.00 0.00 0.00 2.82
3016 4776 9.768662 AACAATGAAACAAGAAGATTTGCTAAT 57.231 25.926 0.00 0.00 0.00 1.73
3088 4851 7.247728 TCGCAAAGCTTTATTTAAATCGTCAT 58.752 30.769 12.25 0.00 0.00 3.06
3089 4852 7.218014 TCGCAAAGCTTTATTTAAATCGTCATG 59.782 33.333 12.25 0.00 0.00 3.07
3090 4853 7.218014 CGCAAAGCTTTATTTAAATCGTCATGA 59.782 33.333 12.25 0.00 0.00 3.07
3091 4854 9.023967 GCAAAGCTTTATTTAAATCGTCATGAT 57.976 29.630 12.25 0.00 39.67 2.45
3111 4874 9.745018 TCATGATATTCCAAGATAAAAGATCCC 57.255 33.333 0.00 0.00 0.00 3.85
3112 4875 9.750783 CATGATATTCCAAGATAAAAGATCCCT 57.249 33.333 0.00 0.00 0.00 4.20
3113 4876 9.972106 ATGATATTCCAAGATAAAAGATCCCTC 57.028 33.333 0.00 0.00 0.00 4.30
3114 4877 8.097038 TGATATTCCAAGATAAAAGATCCCTCG 58.903 37.037 0.00 0.00 0.00 4.63
3115 4878 4.689612 TCCAAGATAAAAGATCCCTCGG 57.310 45.455 0.00 0.00 0.00 4.63
3116 4879 4.037927 TCCAAGATAAAAGATCCCTCGGT 58.962 43.478 0.00 0.00 0.00 4.69
3117 4880 4.473559 TCCAAGATAAAAGATCCCTCGGTT 59.526 41.667 0.00 0.00 0.00 4.44
3118 4881 4.576463 CCAAGATAAAAGATCCCTCGGTTG 59.424 45.833 0.00 0.00 0.00 3.77
3119 4882 5.428253 CAAGATAAAAGATCCCTCGGTTGA 58.572 41.667 0.00 0.00 0.00 3.18
3120 4883 5.024785 AGATAAAAGATCCCTCGGTTGAC 57.975 43.478 0.00 0.00 0.00 3.18
3121 4884 2.491675 AAAAGATCCCTCGGTTGACC 57.508 50.000 0.00 0.00 0.00 4.02
3122 4885 1.657804 AAAGATCCCTCGGTTGACCT 58.342 50.000 0.00 0.00 0.00 3.85
3123 4886 2.544844 AAGATCCCTCGGTTGACCTA 57.455 50.000 0.00 0.00 0.00 3.08
3124 4887 2.544844 AGATCCCTCGGTTGACCTAA 57.455 50.000 0.00 0.00 0.00 2.69
3125 4888 2.108970 AGATCCCTCGGTTGACCTAAC 58.891 52.381 0.00 0.00 38.60 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.101399 CGTCGGGATCCAAGTCAGAG 59.899 60.000 15.23 0.00 0.00 3.35
1 2 1.945354 GCGTCGGGATCCAAGTCAGA 61.945 60.000 15.23 0.00 0.00 3.27
2 3 1.519455 GCGTCGGGATCCAAGTCAG 60.519 63.158 15.23 0.41 0.00 3.51
3 4 2.577059 GCGTCGGGATCCAAGTCA 59.423 61.111 15.23 0.00 0.00 3.41
4 5 2.202892 GGCGTCGGGATCCAAGTC 60.203 66.667 15.23 3.94 0.00 3.01
5 6 4.143333 CGGCGTCGGGATCCAAGT 62.143 66.667 15.23 0.00 0.00 3.16
16 17 4.899239 CCTCATCCCTGCGGCGTC 62.899 72.222 9.37 0.91 0.00 5.19
22 23 4.512914 GTGGCCCCTCATCCCTGC 62.513 72.222 0.00 0.00 0.00 4.85
23 24 3.813724 GGTGGCCCCTCATCCCTG 61.814 72.222 0.00 0.00 0.00 4.45
26 27 3.406595 CTTCGGTGGCCCCTCATCC 62.407 68.421 0.00 0.00 0.00 3.51
27 28 2.190578 CTTCGGTGGCCCCTCATC 59.809 66.667 0.00 0.00 0.00 2.92
28 29 3.411517 CCTTCGGTGGCCCCTCAT 61.412 66.667 0.00 0.00 0.00 2.90
54 55 4.388499 CCCAACTCCGGGGTCACG 62.388 72.222 7.88 0.00 43.21 4.35
73 74 3.991051 AGTGACCACCGTCTGGCG 61.991 66.667 0.00 0.00 45.32 5.69
74 75 2.357517 CAGTGACCACCGTCTGGC 60.358 66.667 0.00 0.00 45.32 4.85
76 77 2.734723 CGCAGTGACCACCGTCTG 60.735 66.667 0.00 0.00 39.94 3.51
77 78 3.224324 ACGCAGTGACCACCGTCT 61.224 61.111 0.00 0.00 42.51 4.18
95 96 3.697747 TAACCGTGGCCTCACCGG 61.698 66.667 18.04 18.04 43.94 5.28
96 97 2.433664 GTAACCGTGGCCTCACCG 60.434 66.667 3.32 0.56 43.94 4.94
97 98 1.024579 CATGTAACCGTGGCCTCACC 61.025 60.000 3.32 0.00 40.65 4.02
98 99 1.644786 GCATGTAACCGTGGCCTCAC 61.645 60.000 3.32 0.00 40.36 3.51
99 100 1.376683 GCATGTAACCGTGGCCTCA 60.377 57.895 3.32 0.00 0.00 3.86
100 101 0.676782 AAGCATGTAACCGTGGCCTC 60.677 55.000 3.32 0.00 0.00 4.70
101 102 0.960364 CAAGCATGTAACCGTGGCCT 60.960 55.000 3.32 0.00 0.00 5.19
102 103 1.506262 CAAGCATGTAACCGTGGCC 59.494 57.895 0.00 0.00 0.00 5.36
103 104 0.958382 TCCAAGCATGTAACCGTGGC 60.958 55.000 0.00 0.00 31.77 5.01
104 105 1.086696 CTCCAAGCATGTAACCGTGG 58.913 55.000 0.00 0.00 32.79 4.94
105 106 0.447801 GCTCCAAGCATGTAACCGTG 59.552 55.000 0.00 0.00 41.89 4.94
106 107 0.676782 GGCTCCAAGCATGTAACCGT 60.677 55.000 0.86 0.00 44.75 4.83
107 108 0.676466 TGGCTCCAAGCATGTAACCG 60.676 55.000 0.86 0.00 44.75 4.44
108 109 0.811281 GTGGCTCCAAGCATGTAACC 59.189 55.000 0.86 0.00 44.75 2.85
109 110 1.826385 AGTGGCTCCAAGCATGTAAC 58.174 50.000 0.86 0.00 44.75 2.50
110 111 2.092968 CCTAGTGGCTCCAAGCATGTAA 60.093 50.000 0.86 0.00 44.75 2.41
111 112 1.486310 CCTAGTGGCTCCAAGCATGTA 59.514 52.381 0.86 0.00 44.75 2.29
112 113 0.254178 CCTAGTGGCTCCAAGCATGT 59.746 55.000 0.86 0.00 44.75 3.21
113 114 3.091318 CCTAGTGGCTCCAAGCATG 57.909 57.895 0.86 0.00 44.75 4.06
130 131 3.532155 ACTCAGATCGGCCGAGCC 61.532 66.667 37.65 27.73 46.75 4.70
131 132 2.279120 CACTCAGATCGGCCGAGC 60.279 66.667 35.12 35.12 0.00 5.03
132 133 1.064946 GACACTCAGATCGGCCGAG 59.935 63.158 33.87 21.34 0.00 4.63
133 134 1.037579 ATGACACTCAGATCGGCCGA 61.038 55.000 33.12 33.12 0.00 5.54
134 135 0.179100 AATGACACTCAGATCGGCCG 60.179 55.000 22.12 22.12 0.00 6.13
135 136 1.936547 GAAATGACACTCAGATCGGCC 59.063 52.381 0.00 0.00 0.00 6.13
136 137 2.606725 CAGAAATGACACTCAGATCGGC 59.393 50.000 0.00 0.00 0.00 5.54
137 138 2.606725 GCAGAAATGACACTCAGATCGG 59.393 50.000 0.00 0.00 0.00 4.18
138 139 2.606725 GGCAGAAATGACACTCAGATCG 59.393 50.000 0.00 0.00 0.00 3.69
139 140 2.606725 CGGCAGAAATGACACTCAGATC 59.393 50.000 0.00 0.00 0.00 2.75
140 141 2.234661 TCGGCAGAAATGACACTCAGAT 59.765 45.455 0.00 0.00 0.00 2.90
141 142 1.618343 TCGGCAGAAATGACACTCAGA 59.382 47.619 0.00 0.00 0.00 3.27
142 143 1.728971 GTCGGCAGAAATGACACTCAG 59.271 52.381 0.00 0.00 32.91 3.35
143 144 1.795768 GTCGGCAGAAATGACACTCA 58.204 50.000 0.00 0.00 32.91 3.41
144 145 0.716108 CGTCGGCAGAAATGACACTC 59.284 55.000 0.00 0.00 32.91 3.51
145 146 1.291877 GCGTCGGCAGAAATGACACT 61.292 55.000 0.00 0.00 39.62 3.55
146 147 1.132640 GCGTCGGCAGAAATGACAC 59.867 57.895 0.00 0.00 39.62 3.67
147 148 1.301322 TGCGTCGGCAGAAATGACA 60.301 52.632 0.00 0.00 46.21 3.58
148 149 3.561429 TGCGTCGGCAGAAATGAC 58.439 55.556 0.00 0.00 46.21 3.06
157 158 0.248215 CAGAAATCCATTGCGTCGGC 60.248 55.000 0.00 0.00 40.52 5.54
158 159 1.086696 ACAGAAATCCATTGCGTCGG 58.913 50.000 0.00 0.00 0.00 4.79
159 160 2.285220 CCTACAGAAATCCATTGCGTCG 59.715 50.000 0.00 0.00 0.00 5.12
160 161 2.614057 CCCTACAGAAATCCATTGCGTC 59.386 50.000 0.00 0.00 0.00 5.19
161 162 2.026262 ACCCTACAGAAATCCATTGCGT 60.026 45.455 0.00 0.00 0.00 5.24
162 163 2.614057 GACCCTACAGAAATCCATTGCG 59.386 50.000 0.00 0.00 0.00 4.85
163 164 2.614057 CGACCCTACAGAAATCCATTGC 59.386 50.000 0.00 0.00 0.00 3.56
164 165 3.871594 GTCGACCCTACAGAAATCCATTG 59.128 47.826 3.51 0.00 0.00 2.82
165 166 3.775316 AGTCGACCCTACAGAAATCCATT 59.225 43.478 13.01 0.00 0.00 3.16
166 167 3.375699 AGTCGACCCTACAGAAATCCAT 58.624 45.455 13.01 0.00 0.00 3.41
167 168 2.758979 GAGTCGACCCTACAGAAATCCA 59.241 50.000 13.01 0.00 0.00 3.41
168 169 2.101082 GGAGTCGACCCTACAGAAATCC 59.899 54.545 13.01 4.62 0.00 3.01
169 170 2.758979 TGGAGTCGACCCTACAGAAATC 59.241 50.000 13.01 0.00 0.00 2.17
175 176 1.100510 CGATTGGAGTCGACCCTACA 58.899 55.000 13.01 0.00 44.06 2.74
178 179 1.949847 CTGCGATTGGAGTCGACCCT 61.950 60.000 13.01 0.00 44.06 4.34
196 197 1.658686 CGAGAGGAGTGCGCCTAACT 61.659 60.000 4.18 0.40 38.73 2.24
216 217 3.474570 ATGGCTCTCCACCGCTCC 61.475 66.667 0.00 0.00 46.92 4.70
238 239 1.207791 GAAGAGGAGGAGATGGCCAA 58.792 55.000 10.96 0.00 0.00 4.52
239 240 0.692419 GGAAGAGGAGGAGATGGCCA 60.692 60.000 8.56 8.56 0.00 5.36
268 269 3.147595 CGCCATCTGGGACCTCGA 61.148 66.667 0.00 0.00 40.01 4.04
269 270 4.227134 CCGCCATCTGGGACCTCG 62.227 72.222 0.00 0.00 40.01 4.63
279 280 3.830679 GATCTCCTGATCCGCCATC 57.169 57.895 0.00 0.00 42.35 3.51
301 302 1.153823 CGGACAGCGGATTCGACTT 60.154 57.895 0.00 0.00 39.00 3.01
313 314 0.247460 TTCTCTGACATGGCGGACAG 59.753 55.000 5.79 0.00 0.00 3.51
315 316 1.293924 CATTCTCTGACATGGCGGAC 58.706 55.000 5.79 0.00 0.00 4.79
316 317 0.462581 GCATTCTCTGACATGGCGGA 60.463 55.000 10.40 10.40 0.00 5.54
333 334 3.372795 GTTCCAACGATATCCGGCA 57.627 52.632 0.00 0.00 43.93 5.69
345 346 1.988015 CCCCTAAGCTCCGTTCCAA 59.012 57.895 0.00 0.00 0.00 3.53
346 347 2.666098 GCCCCTAAGCTCCGTTCCA 61.666 63.158 0.00 0.00 0.00 3.53
351 352 3.917760 CTCCGCCCCTAAGCTCCG 61.918 72.222 0.00 0.00 0.00 4.63
352 353 2.764547 ACTCCGCCCCTAAGCTCC 60.765 66.667 0.00 0.00 0.00 4.70
372 373 3.389983 TCATATCCCGGACAAAACCCTAG 59.610 47.826 0.73 0.00 0.00 3.02
381 382 3.170717 GTCCCTATTCATATCCCGGACA 58.829 50.000 0.73 0.00 38.52 4.02
386 387 8.871125 ACATATATTCGTCCCTATTCATATCCC 58.129 37.037 0.00 0.00 0.00 3.85
391 392 7.633772 GCCTCACATATATTCGTCCCTATTCAT 60.634 40.741 0.00 0.00 0.00 2.57
402 406 4.687948 CCACTTCAGCCTCACATATATTCG 59.312 45.833 0.00 0.00 0.00 3.34
414 418 1.589414 AATCCTAGCCACTTCAGCCT 58.411 50.000 0.00 0.00 0.00 4.58
417 421 3.691609 GGACAAAATCCTAGCCACTTCAG 59.308 47.826 0.00 0.00 45.22 3.02
418 422 3.686016 GGACAAAATCCTAGCCACTTCA 58.314 45.455 0.00 0.00 45.22 3.02
420 424 2.711542 CGGACAAAATCCTAGCCACTT 58.288 47.619 0.00 0.00 46.69 3.16
422 426 0.733150 GCGGACAAAATCCTAGCCAC 59.267 55.000 0.00 0.00 46.69 5.01
426 430 4.616181 AAAATCGCGGACAAAATCCTAG 57.384 40.909 6.13 0.00 46.69 3.02
427 431 5.818336 TCATAAAATCGCGGACAAAATCCTA 59.182 36.000 6.13 0.00 46.69 2.94
428 432 4.638421 TCATAAAATCGCGGACAAAATCCT 59.362 37.500 6.13 0.00 46.69 3.24
429 433 4.733405 GTCATAAAATCGCGGACAAAATCC 59.267 41.667 6.13 0.00 45.20 3.01
431 435 5.303747 TGTCATAAAATCGCGGACAAAAT 57.696 34.783 6.13 0.00 35.72 1.82
432 436 4.750952 TGTCATAAAATCGCGGACAAAA 57.249 36.364 6.13 0.00 35.72 2.44
434 438 3.687212 ACATGTCATAAAATCGCGGACAA 59.313 39.130 14.41 0.00 41.30 3.18
437 441 3.526534 TGACATGTCATAAAATCGCGGA 58.473 40.909 24.56 0.00 34.14 5.54
438 442 3.942539 TGACATGTCATAAAATCGCGG 57.057 42.857 24.56 0.00 34.14 6.46
534 667 2.489329 CACCATTGTTGGAGGTGTCATC 59.511 50.000 0.00 0.00 46.92 2.92
552 685 4.323417 TGACATGTTTCCTATGACACACC 58.677 43.478 0.00 0.00 34.21 4.16
585 747 2.833794 TGTGTTCTCCTTCTCCAAACG 58.166 47.619 0.00 0.00 0.00 3.60
693 901 1.138069 CTGGGCATATGTACCGTGTGA 59.862 52.381 4.29 0.00 0.00 3.58
694 902 1.581934 CTGGGCATATGTACCGTGTG 58.418 55.000 4.29 0.00 0.00 3.82
695 903 0.179056 GCTGGGCATATGTACCGTGT 60.179 55.000 4.29 0.00 0.00 4.49
696 904 1.221466 CGCTGGGCATATGTACCGTG 61.221 60.000 4.29 6.98 0.00 4.94
697 905 1.069090 CGCTGGGCATATGTACCGT 59.931 57.895 4.29 0.00 0.00 4.83
698 906 1.667830 CCGCTGGGCATATGTACCG 60.668 63.158 4.29 5.58 0.00 4.02
699 907 0.324943 ATCCGCTGGGCATATGTACC 59.675 55.000 4.29 8.00 0.00 3.34
700 908 1.806542 CAATCCGCTGGGCATATGTAC 59.193 52.381 4.29 0.00 0.00 2.90
701 909 1.271325 CCAATCCGCTGGGCATATGTA 60.271 52.381 4.29 0.00 32.32 2.29
702 910 0.538057 CCAATCCGCTGGGCATATGT 60.538 55.000 4.29 0.00 32.32 2.29
703 911 0.250858 TCCAATCCGCTGGGCATATG 60.251 55.000 0.00 0.00 37.06 1.78
704 912 0.037303 CTCCAATCCGCTGGGCATAT 59.963 55.000 0.00 0.00 37.06 1.78
705 913 1.344953 ACTCCAATCCGCTGGGCATA 61.345 55.000 0.00 0.00 37.06 3.14
706 914 2.194056 CTCCAATCCGCTGGGCAT 59.806 61.111 0.00 0.00 37.06 4.40
707 915 1.558167 TAACTCCAATCCGCTGGGCA 61.558 55.000 0.00 0.00 37.06 5.36
708 916 0.815615 CTAACTCCAATCCGCTGGGC 60.816 60.000 0.00 0.00 37.06 5.36
709 917 0.830648 TCTAACTCCAATCCGCTGGG 59.169 55.000 0.00 0.00 37.06 4.45
768 976 5.281609 GCGATTGAGCTTTTTCGTTTAAGAG 59.718 40.000 12.64 0.00 34.24 2.85
847 1068 3.628618 TATAGGGGCAGAGGGAGCGAG 62.629 61.905 0.00 0.00 0.00 5.03
848 1069 1.726192 TATAGGGGCAGAGGGAGCGA 61.726 60.000 0.00 0.00 0.00 4.93
849 1070 0.616111 ATATAGGGGCAGAGGGAGCG 60.616 60.000 0.00 0.00 0.00 5.03
893 1114 4.021981 GGAAGGAGGAAGAAACAACAATGG 60.022 45.833 0.00 0.00 0.00 3.16
1089 1317 1.732732 CGGTTGCAGAACTCGTAGGAG 60.733 57.143 10.86 10.86 46.13 3.69
1306 1534 0.874390 ACGTACGTACAGCGAGGAAA 59.126 50.000 21.41 0.00 44.77 3.13
1313 1541 0.040157 TGGACACACGTACGTACAGC 60.040 55.000 22.34 10.93 0.00 4.40
1314 1542 2.512885 GATGGACACACGTACGTACAG 58.487 52.381 22.34 17.96 27.06 2.74
1316 1544 1.128507 TCGATGGACACACGTACGTAC 59.871 52.381 22.34 15.90 0.00 3.67
1317 1545 1.437625 TCGATGGACACACGTACGTA 58.562 50.000 22.34 4.43 0.00 3.57
1322 1557 3.057104 TCTGTTTATCGATGGACACACGT 60.057 43.478 8.54 0.00 0.00 4.49
1337 1572 2.354704 CGCCAGGGACTTCATCTGTTTA 60.355 50.000 0.00 0.00 34.60 2.01
1338 1573 1.611673 CGCCAGGGACTTCATCTGTTT 60.612 52.381 0.00 0.00 34.60 2.83
1339 1574 0.036010 CGCCAGGGACTTCATCTGTT 60.036 55.000 0.00 0.00 34.60 3.16
1505 1741 2.014335 TCTCCGTGATGAACATGCAG 57.986 50.000 0.00 0.00 34.47 4.41
1615 1857 3.169908 GGAGAAGAAGAGGTTGAGGTCT 58.830 50.000 0.00 0.00 0.00 3.85
1616 1858 2.235155 GGGAGAAGAAGAGGTTGAGGTC 59.765 54.545 0.00 0.00 0.00 3.85
1617 1859 2.158081 AGGGAGAAGAAGAGGTTGAGGT 60.158 50.000 0.00 0.00 0.00 3.85
1618 1860 2.499693 GAGGGAGAAGAAGAGGTTGAGG 59.500 54.545 0.00 0.00 0.00 3.86
1619 1861 3.440127 AGAGGGAGAAGAAGAGGTTGAG 58.560 50.000 0.00 0.00 0.00 3.02
1620 1862 3.076785 AGAGAGGGAGAAGAAGAGGTTGA 59.923 47.826 0.00 0.00 0.00 3.18
1622 1864 3.336694 AGAGAGAGGGAGAAGAAGAGGTT 59.663 47.826 0.00 0.00 0.00 3.50
1623 1865 2.926329 AGAGAGAGGGAGAAGAAGAGGT 59.074 50.000 0.00 0.00 0.00 3.85
1624 1866 3.203040 AGAGAGAGAGGGAGAAGAAGAGG 59.797 52.174 0.00 0.00 0.00 3.69
1625 1867 4.164988 AGAGAGAGAGAGGGAGAAGAAGAG 59.835 50.000 0.00 0.00 0.00 2.85
1626 1868 4.111577 AGAGAGAGAGAGGGAGAAGAAGA 58.888 47.826 0.00 0.00 0.00 2.87
1627 1869 4.164988 AGAGAGAGAGAGAGGGAGAAGAAG 59.835 50.000 0.00 0.00 0.00 2.85
1628 1870 4.111577 AGAGAGAGAGAGAGGGAGAAGAA 58.888 47.826 0.00 0.00 0.00 2.52
1635 1877 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
1781 2332 2.289506 GGGGTAGTCTGTTGTCAAGGTC 60.290 54.545 0.00 0.00 0.00 3.85
1831 2384 3.586470 TGTTTGGTTCTTCTGGGCTTA 57.414 42.857 0.00 0.00 0.00 3.09
1832 2385 2.452600 TGTTTGGTTCTTCTGGGCTT 57.547 45.000 0.00 0.00 0.00 4.35
1833 2386 2.452600 TTGTTTGGTTCTTCTGGGCT 57.547 45.000 0.00 0.00 0.00 5.19
1879 2432 3.665190 AGTTGAGATTTGGGTTCGAGAC 58.335 45.455 0.00 0.00 0.00 3.36
1934 2500 3.434299 AGTTGGCGTTTGAAATAGGTACG 59.566 43.478 0.00 0.00 35.48 3.67
1954 2520 6.461640 AGTAAGCACTACATACGGAAAAAGT 58.538 36.000 0.00 0.00 31.45 2.66
2067 2716 2.623418 TGTACCTGACCATCCTGAGT 57.377 50.000 0.00 0.00 0.00 3.41
2141 2793 5.528690 GCAAGATGTGTATGTACATGGATGT 59.471 40.000 18.81 1.81 41.15 3.06
2158 2810 2.925306 GCTCAAGGTTGCAAGCAAGATG 60.925 50.000 28.75 20.29 36.52 2.90
2274 2930 7.645340 GTGGAACAATTGATATGCTACATGAAC 59.355 37.037 13.59 0.00 44.16 3.18
2316 2972 8.285394 CAGTGTGTATATATGCATCCTTTGTTC 58.715 37.037 0.19 0.00 0.00 3.18
2338 2994 5.446709 CACAAGAGTTGAATTGCTACAGTG 58.553 41.667 0.00 0.00 0.00 3.66
2368 3033 0.171903 GCGGTAGTGCTCGGAAAGTA 59.828 55.000 0.00 0.00 0.00 2.24
2378 3043 2.804828 AAGGAGGCAAGCGGTAGTGC 62.805 60.000 2.68 2.68 40.14 4.40
2401 3066 9.000486 AGCTTAAAATCCTCTACAACTACAAAC 58.000 33.333 0.00 0.00 0.00 2.93
2402 3067 9.569122 AAGCTTAAAATCCTCTACAACTACAAA 57.431 29.630 0.00 0.00 0.00 2.83
2403 3068 9.216117 GAAGCTTAAAATCCTCTACAACTACAA 57.784 33.333 0.00 0.00 0.00 2.41
2404 3069 8.594550 AGAAGCTTAAAATCCTCTACAACTACA 58.405 33.333 0.00 0.00 0.00 2.74
2405 3070 9.089601 GAGAAGCTTAAAATCCTCTACAACTAC 57.910 37.037 0.00 0.00 0.00 2.73
2445 3110 9.778993 CAAGAATAATCCAATCTAACAACTGTG 57.221 33.333 0.00 0.00 0.00 3.66
2464 3129 6.153067 CACCAAAACGGCATTAACAAGAATA 58.847 36.000 0.00 0.00 39.03 1.75
2563 3230 0.248866 GGACAACGCAAAACACCAGG 60.249 55.000 0.00 0.00 0.00 4.45
2661 3328 5.540337 TCCCAGTGCATATACAAACCAAAAA 59.460 36.000 0.00 0.00 0.00 1.94
2767 3547 6.239289 CCTTGCCAATTGAGGAACTTTCTTTA 60.239 38.462 7.12 0.00 41.55 1.85
2785 3565 1.892474 GCACCTATTTTGTCCTTGCCA 59.108 47.619 0.00 0.00 0.00 4.92
3064 4827 6.846870 TGACGATTTAAATAAAGCTTTGCG 57.153 33.333 22.02 13.01 29.96 4.85
3088 4851 8.097038 CGAGGGATCTTTTATCTTGGAATATCA 58.903 37.037 0.00 0.00 0.00 2.15
3089 4852 7.550906 CCGAGGGATCTTTTATCTTGGAATATC 59.449 40.741 0.00 0.00 32.16 1.63
3090 4853 7.017651 ACCGAGGGATCTTTTATCTTGGAATAT 59.982 37.037 0.00 0.00 34.10 1.28
3091 4854 6.329197 ACCGAGGGATCTTTTATCTTGGAATA 59.671 38.462 0.00 0.00 34.10 1.75
3092 4855 5.132816 ACCGAGGGATCTTTTATCTTGGAAT 59.867 40.000 0.00 0.00 34.10 3.01
3093 4856 4.473559 ACCGAGGGATCTTTTATCTTGGAA 59.526 41.667 0.00 0.00 34.10 3.53
3094 4857 4.037927 ACCGAGGGATCTTTTATCTTGGA 58.962 43.478 0.00 0.00 34.10 3.53
3095 4858 4.423625 ACCGAGGGATCTTTTATCTTGG 57.576 45.455 0.00 0.00 35.63 3.61
3096 4859 5.294552 GTCAACCGAGGGATCTTTTATCTTG 59.705 44.000 0.00 0.00 0.00 3.02
3097 4860 5.429130 GTCAACCGAGGGATCTTTTATCTT 58.571 41.667 0.00 0.00 0.00 2.40
3098 4861 4.141688 GGTCAACCGAGGGATCTTTTATCT 60.142 45.833 0.00 0.00 0.00 1.98
3099 4862 4.127907 GGTCAACCGAGGGATCTTTTATC 58.872 47.826 0.00 0.00 0.00 1.75
3100 4863 3.780850 AGGTCAACCGAGGGATCTTTTAT 59.219 43.478 0.00 0.00 42.08 1.40
3101 4864 3.178865 AGGTCAACCGAGGGATCTTTTA 58.821 45.455 0.00 0.00 42.08 1.52
3102 4865 1.985895 AGGTCAACCGAGGGATCTTTT 59.014 47.619 0.00 0.00 42.08 2.27
3103 4866 1.657804 AGGTCAACCGAGGGATCTTT 58.342 50.000 0.00 0.00 42.08 2.52
3104 4867 2.500504 GTTAGGTCAACCGAGGGATCTT 59.499 50.000 0.00 0.00 42.08 2.40
3105 4868 2.108970 GTTAGGTCAACCGAGGGATCT 58.891 52.381 0.00 0.00 42.08 2.75
3106 4869 2.598686 GTTAGGTCAACCGAGGGATC 57.401 55.000 0.00 0.00 42.08 3.36
3115 4878 1.202348 GCCATGCTTGGTTAGGTCAAC 59.798 52.381 19.05 0.00 45.57 3.18
3116 4879 1.544724 GCCATGCTTGGTTAGGTCAA 58.455 50.000 19.05 0.00 45.57 3.18
3117 4880 0.676466 CGCCATGCTTGGTTAGGTCA 60.676 55.000 19.05 0.00 45.57 4.02
3118 4881 1.376609 CCGCCATGCTTGGTTAGGTC 61.377 60.000 19.05 1.57 45.57 3.85
3119 4882 1.378514 CCGCCATGCTTGGTTAGGT 60.379 57.895 19.05 0.00 45.57 3.08
3120 4883 1.376609 GACCGCCATGCTTGGTTAGG 61.377 60.000 19.05 19.77 45.57 2.69
3121 4884 2.098293 GACCGCCATGCTTGGTTAG 58.902 57.895 19.05 10.85 45.57 2.34
3122 4885 4.312052 GACCGCCATGCTTGGTTA 57.688 55.556 19.05 0.00 45.57 2.85


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

AutoCloner maintained by Alex Coulton.