Multiple sequence alignment - TraesCS5D01G259200

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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 TraesCS5D01G259200 chr5D 100.000 2609 0 0 1 2609 365442431 365439823 0.000000e+00 4819.0
1 TraesCS5D01G259200 chr5D 98.079 781 15 0 1829 2609 445494759 445495539 0.000000e+00 1360.0
2 TraesCS5D01G259200 chr5D 98.079 781 15 0 1829 2609 482740607 482739827 0.000000e+00 1360.0
3 TraesCS5D01G259200 chr5A 89.455 1138 91 19 674 1798 467059991 467058870 0.000000e+00 1410.0
4 TraesCS5D01G259200 chr3D 98.207 781 14 0 1829 2609 547907707 547906927 0.000000e+00 1365.0
5 TraesCS5D01G259200 chr3D 98.079 781 15 0 1829 2609 577171442 577170662 0.000000e+00 1360.0
6 TraesCS5D01G259200 chr3D 98.079 781 15 0 1829 2609 612683718 612684498 0.000000e+00 1360.0
7 TraesCS5D01G259200 chr3D 78.261 230 33 12 320 548 393649418 393649205 5.860000e-27 132.0
8 TraesCS5D01G259200 chr3D 100.000 32 0 0 321 352 548677337 548677368 2.800000e-05 60.2
9 TraesCS5D01G259200 chr1D 98.207 781 14 0 1829 2609 462712497 462711717 0.000000e+00 1365.0
10 TraesCS5D01G259200 chr1D 98.082 782 15 0 1828 2609 467953348 467952567 0.000000e+00 1362.0
11 TraesCS5D01G259200 chr1D 98.079 781 15 0 1829 2609 8446839 8447619 0.000000e+00 1360.0
12 TraesCS5D01G259200 chr4D 98.079 781 15 0 1829 2609 488791285 488790505 0.000000e+00 1360.0
13 TraesCS5D01G259200 chr5B 90.231 952 64 11 681 1615 431879191 431878252 0.000000e+00 1216.0
14 TraesCS5D01G259200 chr3A 80.952 147 22 6 383 528 513585059 513584918 7.630000e-21 111.0
15 TraesCS5D01G259200 chr6D 75.862 203 44 5 39 239 2814460 2814659 5.940000e-17 99.0
16 TraesCS5D01G259200 chr6B 97.917 48 1 0 417 464 712146678 712146631 1.660000e-12 84.2
17 TraesCS5D01G259200 chr6B 89.583 48 5 0 320 367 489836696 489836649 7.800000e-06 62.1
18 TraesCS5D01G259200 chr2B 97.222 36 1 0 322 357 9837611 9837646 7.800000e-06 62.1
19 TraesCS5D01G259200 chr1B 94.872 39 1 1 320 357 544946821 544946859 2.800000e-05 60.2


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 TraesCS5D01G259200 chr5D 365439823 365442431 2608 True 4819 4819 100.000 1 2609 1 chr5D.!!$R1 2608
1 TraesCS5D01G259200 chr5D 445494759 445495539 780 False 1360 1360 98.079 1829 2609 1 chr5D.!!$F1 780
2 TraesCS5D01G259200 chr5D 482739827 482740607 780 True 1360 1360 98.079 1829 2609 1 chr5D.!!$R2 780
3 TraesCS5D01G259200 chr5A 467058870 467059991 1121 True 1410 1410 89.455 674 1798 1 chr5A.!!$R1 1124
4 TraesCS5D01G259200 chr3D 547906927 547907707 780 True 1365 1365 98.207 1829 2609 1 chr3D.!!$R2 780
5 TraesCS5D01G259200 chr3D 577170662 577171442 780 True 1360 1360 98.079 1829 2609 1 chr3D.!!$R3 780
6 TraesCS5D01G259200 chr3D 612683718 612684498 780 False 1360 1360 98.079 1829 2609 1 chr3D.!!$F2 780
7 TraesCS5D01G259200 chr1D 462711717 462712497 780 True 1365 1365 98.207 1829 2609 1 chr1D.!!$R1 780
8 TraesCS5D01G259200 chr1D 467952567 467953348 781 True 1362 1362 98.082 1828 2609 1 chr1D.!!$R2 781
9 TraesCS5D01G259200 chr1D 8446839 8447619 780 False 1360 1360 98.079 1829 2609 1 chr1D.!!$F1 780
10 TraesCS5D01G259200 chr4D 488790505 488791285 780 True 1360 1360 98.079 1829 2609 1 chr4D.!!$R1 780
11 TraesCS5D01G259200 chr5B 431878252 431879191 939 True 1216 1216 90.231 681 1615 1 chr5B.!!$R1 934

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
655 656 0.249699 TGTGCACACGAGTTGGTAGG 60.25 55.0 17.42 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1824 0.037419 GACCGGGCCGTACACTAAAA 60.037 55.0 26.32 0.0 0.0 1.52 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
120 121 8.810652 TTTTTCAAATACTTGTGTTAGATGCC 57.189 30.769 0.00 0.00 33.94 4.40
121 122 7.759489 TTTCAAATACTTGTGTTAGATGCCT 57.241 32.000 0.00 0.00 33.94 4.75
122 123 8.856153 TTTCAAATACTTGTGTTAGATGCCTA 57.144 30.769 0.00 0.00 33.94 3.93
123 124 7.843490 TCAAATACTTGTGTTAGATGCCTAC 57.157 36.000 0.00 0.00 33.94 3.18
124 125 7.620880 TCAAATACTTGTGTTAGATGCCTACT 58.379 34.615 0.00 0.00 33.94 2.57
125 126 8.100791 TCAAATACTTGTGTTAGATGCCTACTT 58.899 33.333 0.00 0.00 33.94 2.24
126 127 8.730680 CAAATACTTGTGTTAGATGCCTACTTT 58.269 33.333 0.00 0.00 0.00 2.66
127 128 8.863872 AATACTTGTGTTAGATGCCTACTTTT 57.136 30.769 0.00 0.00 0.00 2.27
128 129 6.803154 ACTTGTGTTAGATGCCTACTTTTC 57.197 37.500 0.00 0.00 0.00 2.29
129 130 6.534634 ACTTGTGTTAGATGCCTACTTTTCT 58.465 36.000 0.00 0.00 0.00 2.52
130 131 6.651225 ACTTGTGTTAGATGCCTACTTTTCTC 59.349 38.462 0.00 0.00 0.00 2.87
131 132 6.109156 TGTGTTAGATGCCTACTTTTCTCA 57.891 37.500 0.00 0.00 0.00 3.27
132 133 6.711277 TGTGTTAGATGCCTACTTTTCTCAT 58.289 36.000 0.00 0.00 0.00 2.90
133 134 7.847096 TGTGTTAGATGCCTACTTTTCTCATA 58.153 34.615 0.00 0.00 0.00 2.15
134 135 7.764443 TGTGTTAGATGCCTACTTTTCTCATAC 59.236 37.037 0.00 0.00 0.00 2.39
135 136 7.764443 GTGTTAGATGCCTACTTTTCTCATACA 59.236 37.037 0.00 0.00 0.00 2.29
136 137 7.764443 TGTTAGATGCCTACTTTTCTCATACAC 59.236 37.037 0.00 0.00 0.00 2.90
137 138 6.299805 AGATGCCTACTTTTCTCATACACA 57.700 37.500 0.00 0.00 0.00 3.72
138 139 6.893583 AGATGCCTACTTTTCTCATACACAT 58.106 36.000 0.00 0.00 0.00 3.21
139 140 7.341805 AGATGCCTACTTTTCTCATACACATT 58.658 34.615 0.00 0.00 0.00 2.71
140 141 8.486210 AGATGCCTACTTTTCTCATACACATTA 58.514 33.333 0.00 0.00 0.00 1.90
141 142 9.277783 GATGCCTACTTTTCTCATACACATTAT 57.722 33.333 0.00 0.00 0.00 1.28
143 144 9.542462 TGCCTACTTTTCTCATACACATTATAC 57.458 33.333 0.00 0.00 0.00 1.47
144 145 9.542462 GCCTACTTTTCTCATACACATTATACA 57.458 33.333 0.00 0.00 0.00 2.29
152 153 9.607988 TTCTCATACACATTATACATTTTCGGT 57.392 29.630 0.00 0.00 0.00 4.69
159 160 9.826574 ACACATTATACATTTTCGGTATACACT 57.173 29.630 5.01 0.00 34.39 3.55
166 167 6.938507 ACATTTTCGGTATACACTAGGAACA 58.061 36.000 5.01 0.00 0.00 3.18
167 168 7.388437 ACATTTTCGGTATACACTAGGAACAA 58.612 34.615 5.01 0.01 0.00 2.83
168 169 7.332678 ACATTTTCGGTATACACTAGGAACAAC 59.667 37.037 5.01 0.00 0.00 3.32
169 170 6.594788 TTTCGGTATACACTAGGAACAACT 57.405 37.500 5.01 0.00 0.00 3.16
170 171 6.594788 TTCGGTATACACTAGGAACAACTT 57.405 37.500 5.01 0.00 0.00 2.66
171 172 6.594788 TCGGTATACACTAGGAACAACTTT 57.405 37.500 5.01 0.00 0.00 2.66
172 173 6.996509 TCGGTATACACTAGGAACAACTTTT 58.003 36.000 5.01 0.00 0.00 2.27
173 174 7.444299 TCGGTATACACTAGGAACAACTTTTT 58.556 34.615 5.01 0.00 0.00 1.94
174 175 8.584157 TCGGTATACACTAGGAACAACTTTTTA 58.416 33.333 5.01 0.00 0.00 1.52
175 176 9.374838 CGGTATACACTAGGAACAACTTTTTAT 57.625 33.333 5.01 0.00 0.00 1.40
181 182 9.010029 ACACTAGGAACAACTTTTTATACATGG 57.990 33.333 0.00 0.00 0.00 3.66
182 183 9.010029 CACTAGGAACAACTTTTTATACATGGT 57.990 33.333 0.00 0.00 0.00 3.55
183 184 9.582648 ACTAGGAACAACTTTTTATACATGGTT 57.417 29.630 0.00 0.00 0.00 3.67
262 263 7.756395 ATACATGATTAGCTGATTCCTTTGG 57.244 36.000 0.00 0.00 0.00 3.28
263 264 5.759059 ACATGATTAGCTGATTCCTTTGGA 58.241 37.500 0.00 0.00 0.00 3.53
264 265 6.189859 ACATGATTAGCTGATTCCTTTGGAA 58.810 36.000 0.00 1.24 46.39 3.53
277 278 6.834168 TTCCTTTGGAATCATGACCTTTAC 57.166 37.500 0.00 0.00 36.71 2.01
278 279 5.261216 TCCTTTGGAATCATGACCTTTACC 58.739 41.667 0.00 0.00 0.00 2.85
279 280 5.016173 CCTTTGGAATCATGACCTTTACCA 58.984 41.667 0.00 0.00 0.00 3.25
280 281 5.105756 CCTTTGGAATCATGACCTTTACCAC 60.106 44.000 0.00 0.00 0.00 4.16
281 282 4.649267 TGGAATCATGACCTTTACCACA 57.351 40.909 0.00 0.00 0.00 4.17
282 283 4.991776 TGGAATCATGACCTTTACCACAA 58.008 39.130 0.00 0.00 0.00 3.33
283 284 4.764823 TGGAATCATGACCTTTACCACAAC 59.235 41.667 0.00 0.00 0.00 3.32
284 285 4.142687 GGAATCATGACCTTTACCACAACG 60.143 45.833 0.00 0.00 0.00 4.10
285 286 2.773487 TCATGACCTTTACCACAACGG 58.227 47.619 0.00 0.00 42.50 4.44
301 302 3.434258 CGGTGTCGTTCATGGATCA 57.566 52.632 0.00 0.00 0.00 2.92
302 303 1.720805 CGGTGTCGTTCATGGATCAA 58.279 50.000 0.00 0.00 0.00 2.57
303 304 2.073056 CGGTGTCGTTCATGGATCAAA 58.927 47.619 0.00 0.00 0.00 2.69
304 305 2.677836 CGGTGTCGTTCATGGATCAAAT 59.322 45.455 0.00 0.00 0.00 2.32
305 306 3.126858 CGGTGTCGTTCATGGATCAAATT 59.873 43.478 0.00 0.00 0.00 1.82
306 307 4.331443 CGGTGTCGTTCATGGATCAAATTA 59.669 41.667 0.00 0.00 0.00 1.40
307 308 5.007626 CGGTGTCGTTCATGGATCAAATTAT 59.992 40.000 0.00 0.00 0.00 1.28
308 309 6.458206 CGGTGTCGTTCATGGATCAAATTATT 60.458 38.462 0.00 0.00 0.00 1.40
309 310 7.257722 GGTGTCGTTCATGGATCAAATTATTT 58.742 34.615 0.00 0.00 0.00 1.40
310 311 7.432252 GGTGTCGTTCATGGATCAAATTATTTC 59.568 37.037 0.00 0.00 0.00 2.17
311 312 7.967854 GTGTCGTTCATGGATCAAATTATTTCA 59.032 33.333 0.00 0.00 0.00 2.69
312 313 8.685427 TGTCGTTCATGGATCAAATTATTTCAT 58.315 29.630 0.00 0.00 0.00 2.57
313 314 8.961092 GTCGTTCATGGATCAAATTATTTCATG 58.039 33.333 9.44 9.44 33.83 3.07
314 315 8.136800 TCGTTCATGGATCAAATTATTTCATGG 58.863 33.333 13.45 3.23 33.49 3.66
315 316 8.136800 CGTTCATGGATCAAATTATTTCATGGA 58.863 33.333 13.45 5.90 33.49 3.41
316 317 9.991906 GTTCATGGATCAAATTATTTCATGGAT 57.008 29.630 13.45 3.61 33.49 3.41
318 319 9.990360 TCATGGATCAAATTATTTCATGGATTG 57.010 29.630 13.45 0.00 33.49 2.67
319 320 9.772973 CATGGATCAAATTATTTCATGGATTGT 57.227 29.630 8.37 0.00 0.00 2.71
330 331 9.558396 TTATTTCATGGATTGTTTTCAAAAGCT 57.442 25.926 0.00 0.00 43.39 3.74
331 332 7.862512 TTTCATGGATTGTTTTCAAAAGCTT 57.137 28.000 0.00 0.00 43.39 3.74
332 333 6.847956 TCATGGATTGTTTTCAAAAGCTTG 57.152 33.333 0.00 0.00 43.39 4.01
333 334 6.580788 TCATGGATTGTTTTCAAAAGCTTGA 58.419 32.000 0.00 0.00 43.39 3.02
334 335 7.218614 TCATGGATTGTTTTCAAAAGCTTGAT 58.781 30.769 0.00 0.00 41.22 2.57
335 336 7.716123 TCATGGATTGTTTTCAAAAGCTTGATT 59.284 29.630 0.00 0.00 41.22 2.57
336 337 8.991026 CATGGATTGTTTTCAAAAGCTTGATTA 58.009 29.630 0.00 0.00 41.22 1.75
337 338 8.954950 TGGATTGTTTTCAAAAGCTTGATTAA 57.045 26.923 0.00 0.00 41.22 1.40
338 339 9.558396 TGGATTGTTTTCAAAAGCTTGATTAAT 57.442 25.926 0.00 0.00 41.22 1.40
417 418 9.715121 ACATTTTTCATATGCATGAGAGTTTTT 57.285 25.926 10.16 0.00 42.11 1.94
450 451 8.940768 AACACACTTAACATTTTACAAATGCT 57.059 26.923 8.77 0.59 0.00 3.79
452 453 9.677567 ACACACTTAACATTTTACAAATGCTAG 57.322 29.630 8.77 6.67 0.00 3.42
453 454 9.891828 CACACTTAACATTTTACAAATGCTAGA 57.108 29.630 8.77 0.00 0.00 2.43
563 564 9.516314 AAAAACAAAAACCGAAAATGTGAAAAA 57.484 22.222 0.00 0.00 0.00 1.94
586 587 9.710900 AAAAACAGAAAAGAAATTTGACTCTGT 57.289 25.926 12.61 12.61 35.20 3.41
587 588 8.693542 AAACAGAAAAGAAATTTGACTCTGTG 57.306 30.769 16.51 4.62 34.44 3.66
588 589 6.799512 ACAGAAAAGAAATTTGACTCTGTGG 58.200 36.000 15.65 0.00 33.52 4.17
589 590 6.183360 ACAGAAAAGAAATTTGACTCTGTGGG 60.183 38.462 15.65 0.00 33.52 4.61
590 591 4.590850 AAAGAAATTTGACTCTGTGGGC 57.409 40.909 0.00 0.00 0.00 5.36
591 592 3.515602 AGAAATTTGACTCTGTGGGCT 57.484 42.857 0.00 0.00 0.00 5.19
592 593 3.416156 AGAAATTTGACTCTGTGGGCTC 58.584 45.455 0.00 0.00 0.00 4.70
593 594 2.206576 AATTTGACTCTGTGGGCTCC 57.793 50.000 0.00 0.00 0.00 4.70
594 595 1.366319 ATTTGACTCTGTGGGCTCCT 58.634 50.000 0.00 0.00 0.00 3.69
595 596 0.397941 TTTGACTCTGTGGGCTCCTG 59.602 55.000 0.00 0.00 0.00 3.86
596 597 2.116983 TTGACTCTGTGGGCTCCTGC 62.117 60.000 0.00 0.00 38.76 4.85
597 598 3.655810 GACTCTGTGGGCTCCTGCG 62.656 68.421 0.00 0.00 40.82 5.18
598 599 3.385384 CTCTGTGGGCTCCTGCGA 61.385 66.667 0.00 0.00 40.82 5.10
599 600 3.655810 CTCTGTGGGCTCCTGCGAC 62.656 68.421 0.00 0.00 40.82 5.19
600 601 4.767255 CTGTGGGCTCCTGCGACC 62.767 72.222 0.00 0.00 40.82 4.79
602 603 4.767255 GTGGGCTCCTGCGACCTG 62.767 72.222 0.00 0.00 40.82 4.00
607 608 4.463879 CTCCTGCGACCTGGGCTG 62.464 72.222 0.00 0.00 0.00 4.85
622 623 4.379243 CTGGCCCAGTCTCGCGTT 62.379 66.667 5.77 0.00 0.00 4.84
623 624 4.373116 TGGCCCAGTCTCGCGTTC 62.373 66.667 5.77 0.00 0.00 3.95
626 627 3.382832 CCCAGTCTCGCGTTCCCT 61.383 66.667 5.77 0.00 0.00 4.20
627 628 2.125912 CCAGTCTCGCGTTCCCTG 60.126 66.667 5.77 8.33 0.00 4.45
628 629 2.811317 CAGTCTCGCGTTCCCTGC 60.811 66.667 5.77 0.00 0.00 4.85
629 630 2.992114 AGTCTCGCGTTCCCTGCT 60.992 61.111 5.77 0.00 0.00 4.24
630 631 2.048127 GTCTCGCGTTCCCTGCTT 60.048 61.111 5.77 0.00 0.00 3.91
631 632 1.668151 GTCTCGCGTTCCCTGCTTT 60.668 57.895 5.77 0.00 0.00 3.51
632 633 0.389426 GTCTCGCGTTCCCTGCTTTA 60.389 55.000 5.77 0.00 0.00 1.85
633 634 0.535335 TCTCGCGTTCCCTGCTTTAT 59.465 50.000 5.77 0.00 0.00 1.40
634 635 0.652592 CTCGCGTTCCCTGCTTTATG 59.347 55.000 5.77 0.00 0.00 1.90
635 636 0.742990 TCGCGTTCCCTGCTTTATGG 60.743 55.000 5.77 0.00 0.00 2.74
636 637 1.024579 CGCGTTCCCTGCTTTATGGT 61.025 55.000 0.00 0.00 0.00 3.55
637 638 0.451783 GCGTTCCCTGCTTTATGGTG 59.548 55.000 0.00 0.00 0.00 4.17
638 639 1.821216 CGTTCCCTGCTTTATGGTGT 58.179 50.000 0.00 0.00 0.00 4.16
639 640 1.468520 CGTTCCCTGCTTTATGGTGTG 59.531 52.381 0.00 0.00 0.00 3.82
640 641 1.202348 GTTCCCTGCTTTATGGTGTGC 59.798 52.381 0.00 0.00 0.00 4.57
641 642 0.403655 TCCCTGCTTTATGGTGTGCA 59.596 50.000 0.00 0.00 0.00 4.57
642 643 0.527565 CCCTGCTTTATGGTGTGCAC 59.472 55.000 10.75 10.75 0.00 4.57
643 644 1.246649 CCTGCTTTATGGTGTGCACA 58.753 50.000 17.42 17.42 0.00 4.57
644 645 1.068333 CCTGCTTTATGGTGTGCACAC 60.068 52.381 36.56 36.56 45.72 3.82
652 653 3.808036 GTGTGCACACGAGTTGGT 58.192 55.556 32.41 0.00 37.10 3.67
653 654 2.980562 GTGTGCACACGAGTTGGTA 58.019 52.632 32.41 0.00 37.10 3.25
654 655 0.859232 GTGTGCACACGAGTTGGTAG 59.141 55.000 32.41 0.00 37.10 3.18
655 656 0.249699 TGTGCACACGAGTTGGTAGG 60.250 55.000 17.42 0.00 0.00 3.18
656 657 1.301401 TGCACACGAGTTGGTAGGC 60.301 57.895 0.00 0.00 0.00 3.93
657 658 1.004918 GCACACGAGTTGGTAGGCT 60.005 57.895 0.00 0.00 0.00 4.58
658 659 1.291877 GCACACGAGTTGGTAGGCTG 61.292 60.000 0.00 0.00 0.00 4.85
659 660 0.670546 CACACGAGTTGGTAGGCTGG 60.671 60.000 0.00 0.00 0.00 4.85
660 661 1.741770 CACGAGTTGGTAGGCTGGC 60.742 63.158 0.00 0.00 0.00 4.85
661 662 2.125106 CGAGTTGGTAGGCTGGCC 60.125 66.667 3.00 3.00 0.00 5.36
662 663 2.272471 GAGTTGGTAGGCTGGCCC 59.728 66.667 8.11 0.00 36.58 5.80
663 664 3.682292 GAGTTGGTAGGCTGGCCCG 62.682 68.421 8.11 0.00 39.21 6.13
664 665 4.029809 GTTGGTAGGCTGGCCCGT 62.030 66.667 8.11 0.00 39.21 5.28
665 666 2.284773 TTGGTAGGCTGGCCCGTA 60.285 61.111 8.11 0.00 39.21 4.02
666 667 1.919308 TTGGTAGGCTGGCCCGTAA 60.919 57.895 8.11 0.00 39.21 3.18
667 668 2.187896 TTGGTAGGCTGGCCCGTAAC 62.188 60.000 8.11 0.00 39.21 2.50
668 669 2.364780 GGTAGGCTGGCCCGTAACT 61.365 63.158 8.11 0.00 39.21 2.24
669 670 1.044790 GGTAGGCTGGCCCGTAACTA 61.045 60.000 8.11 0.00 39.21 2.24
670 671 1.046204 GTAGGCTGGCCCGTAACTAT 58.954 55.000 8.11 0.00 39.21 2.12
671 672 2.242043 GTAGGCTGGCCCGTAACTATA 58.758 52.381 8.11 0.00 39.21 1.31
672 673 1.797320 AGGCTGGCCCGTAACTATAA 58.203 50.000 8.11 0.00 39.21 0.98
673 674 1.415289 AGGCTGGCCCGTAACTATAAC 59.585 52.381 8.11 0.00 39.21 1.89
674 675 1.139455 GGCTGGCCCGTAACTATAACA 59.861 52.381 0.00 0.00 0.00 2.41
675 676 2.420408 GGCTGGCCCGTAACTATAACAA 60.420 50.000 0.00 0.00 0.00 2.83
676 677 3.272581 GCTGGCCCGTAACTATAACAAA 58.727 45.455 0.00 0.00 0.00 2.83
677 678 3.064408 GCTGGCCCGTAACTATAACAAAC 59.936 47.826 0.00 0.00 0.00 2.93
678 679 4.510571 CTGGCCCGTAACTATAACAAACT 58.489 43.478 0.00 0.00 0.00 2.66
679 680 4.255301 TGGCCCGTAACTATAACAAACTG 58.745 43.478 0.00 0.00 0.00 3.16
690 691 1.058284 AACAAACTGCATGGCCCAAT 58.942 45.000 0.00 0.00 0.00 3.16
694 695 2.831742 CTGCATGGCCCAATCGCT 60.832 61.111 0.00 0.00 0.00 4.93
721 722 2.677228 CCAAGAAGTCCCGCCCAT 59.323 61.111 0.00 0.00 0.00 4.00
722 723 1.750399 CCAAGAAGTCCCGCCCATG 60.750 63.158 0.00 0.00 0.00 3.66
723 724 1.299648 CAAGAAGTCCCGCCCATGA 59.700 57.895 0.00 0.00 0.00 3.07
724 725 1.026718 CAAGAAGTCCCGCCCATGAC 61.027 60.000 0.00 0.00 0.00 3.06
836 838 8.007716 ACACGTATTTCAGTTGTCTTTAATTCG 58.992 33.333 0.00 0.00 0.00 3.34
843 845 4.840772 CAGTTGTCTTTAATTCGAACTGCG 59.159 41.667 0.00 0.00 35.36 5.18
925 927 1.841663 CTCCACGCAACCAAAGTCCG 61.842 60.000 0.00 0.00 0.00 4.79
975 977 2.401766 GGCAGTCGCATCAACTGGG 61.402 63.158 5.51 0.00 43.50 4.45
1086 1098 1.065764 CGCTCTAGCATGGCACGTA 59.934 57.895 2.44 0.00 42.21 3.57
1093 1105 2.885676 GCATGGCACGTATGGAGCG 61.886 63.158 0.00 0.00 0.00 5.03
1264 1279 2.359850 TGGATTGGACGGCACAGC 60.360 61.111 0.00 0.00 0.00 4.40
1265 1280 2.359850 GGATTGGACGGCACAGCA 60.360 61.111 0.00 0.00 0.00 4.41
1301 1319 0.456312 GCGTACTCGTGTGAAGAGGG 60.456 60.000 0.00 0.00 39.90 4.30
1311 1329 1.160870 TGAAGAGGGGGAGGAGCAA 59.839 57.895 0.00 0.00 0.00 3.91
1377 1395 1.871080 CTTACATCGATGGAGCCCAC 58.129 55.000 28.09 0.00 35.80 4.61
1420 1438 1.710013 TGAGCAAGATCGTCGGTTTC 58.290 50.000 0.00 0.00 0.00 2.78
1427 1445 1.343465 AGATCGTCGGTTTCTGTTGGT 59.657 47.619 0.00 0.00 0.00 3.67
1431 1449 0.942252 GTCGGTTTCTGTTGGTGGAC 59.058 55.000 0.00 0.00 0.00 4.02
1458 1476 6.228258 TGGGAACTACTACTACTGCAAAAAG 58.772 40.000 0.00 0.00 0.00 2.27
1464 1482 4.065789 ACTACTACTGCAAAAAGGTGAGC 58.934 43.478 0.00 0.00 0.00 4.26
1476 1494 3.334583 AAGGTGAGCGAGCATTTCTTA 57.665 42.857 0.00 0.00 0.00 2.10
1479 1497 2.219674 GGTGAGCGAGCATTTCTTATCG 59.780 50.000 0.00 0.00 38.19 2.92
1489 1507 3.565482 GCATTTCTTATCGATCCCTGCAA 59.435 43.478 0.00 0.00 0.00 4.08
1512 1530 2.277969 TGTTTTCGGCTGTTGTTCGTA 58.722 42.857 0.00 0.00 0.00 3.43
1513 1531 2.285756 TGTTTTCGGCTGTTGTTCGTAG 59.714 45.455 0.00 0.00 0.00 3.51
1514 1532 2.228138 TTTCGGCTGTTGTTCGTAGT 57.772 45.000 0.00 0.00 0.00 2.73
1515 1533 3.367992 TTTCGGCTGTTGTTCGTAGTA 57.632 42.857 0.00 0.00 0.00 1.82
1520 1538 4.156556 TCGGCTGTTGTTCGTAGTACTATT 59.843 41.667 5.75 0.00 0.00 1.73
1618 1640 2.035449 TGGAGAAGGTGAACAGTACACG 59.965 50.000 0.00 0.00 38.90 4.49
1644 1666 1.078426 ACATACAGGTTCAGGCGCC 60.078 57.895 21.89 21.89 0.00 6.53
1674 1696 5.907207 AGTGTGATTACGATGTGCTTATCT 58.093 37.500 0.00 0.00 0.00 1.98
1701 1723 2.575461 GCAATGGGCTGCAAGGTC 59.425 61.111 0.50 0.00 42.17 3.85
1714 1736 1.882352 GCAAGGTCCGATTGTTCTGGT 60.882 52.381 0.00 0.00 0.00 4.00
1715 1737 1.806542 CAAGGTCCGATTGTTCTGGTG 59.193 52.381 0.00 0.00 0.00 4.17
1718 1740 0.798776 GTCCGATTGTTCTGGTGCAG 59.201 55.000 0.00 0.00 0.00 4.41
1721 1743 1.609061 CCGATTGTTCTGGTGCAGACT 60.609 52.381 0.00 0.00 40.46 3.24
1722 1744 1.462283 CGATTGTTCTGGTGCAGACTG 59.538 52.381 0.00 0.00 40.46 3.51
1723 1745 1.198637 GATTGTTCTGGTGCAGACTGC 59.801 52.381 20.86 20.86 40.46 4.40
1732 1754 3.755434 GCAGACTGCAAGCAAGGT 58.245 55.556 22.62 0.00 44.26 3.50
1733 1755 1.578423 GCAGACTGCAAGCAAGGTC 59.422 57.895 22.62 6.38 44.26 3.85
1734 1756 1.860484 GCAGACTGCAAGCAAGGTCC 61.860 60.000 22.62 0.00 44.26 4.46
1735 1757 1.302033 AGACTGCAAGCAAGGTCCG 60.302 57.895 9.86 0.00 37.60 4.79
1737 1759 2.281761 CTGCAAGCAAGGTCCGGT 60.282 61.111 0.00 0.00 0.00 5.28
1738 1760 1.898574 CTGCAAGCAAGGTCCGGTT 60.899 57.895 0.00 0.00 0.00 4.44
1741 1763 1.654220 CAAGCAAGGTCCGGTTGTG 59.346 57.895 0.00 0.00 37.15 3.33
1742 1764 1.528309 AAGCAAGGTCCGGTTGTGG 60.528 57.895 0.00 0.00 0.00 4.17
1748 1770 3.284449 GTCCGGTTGTGGGTGTGC 61.284 66.667 0.00 0.00 0.00 4.57
1757 1779 4.641645 TGGGTGTGCTTCTGCCCG 62.642 66.667 0.00 0.00 43.89 6.13
1794 1816 2.303175 GGAACCGCTCTGATCTCTAGT 58.697 52.381 0.00 0.00 0.00 2.57
1798 1820 4.116747 ACCGCTCTGATCTCTAGTTTTG 57.883 45.455 0.00 0.00 0.00 2.44
1799 1821 3.511934 ACCGCTCTGATCTCTAGTTTTGT 59.488 43.478 0.00 0.00 0.00 2.83
1800 1822 4.021016 ACCGCTCTGATCTCTAGTTTTGTT 60.021 41.667 0.00 0.00 0.00 2.83
1801 1823 4.932200 CCGCTCTGATCTCTAGTTTTGTTT 59.068 41.667 0.00 0.00 0.00 2.83
1802 1824 5.409826 CCGCTCTGATCTCTAGTTTTGTTTT 59.590 40.000 0.00 0.00 0.00 2.43
1803 1825 6.073003 CCGCTCTGATCTCTAGTTTTGTTTTT 60.073 38.462 0.00 0.00 0.00 1.94
1819 1841 3.230115 TTTTTAGTGTACGGCCCGG 57.770 52.632 8.57 0.00 0.00 5.73
1820 1842 0.396060 TTTTTAGTGTACGGCCCGGT 59.604 50.000 8.57 0.00 0.00 5.28
1821 1843 0.037419 TTTTAGTGTACGGCCCGGTC 60.037 55.000 8.57 0.00 0.00 4.79
1822 1844 0.899717 TTTAGTGTACGGCCCGGTCT 60.900 55.000 8.57 2.45 0.00 3.85
1823 1845 1.315257 TTAGTGTACGGCCCGGTCTC 61.315 60.000 8.57 0.78 0.00 3.36
1824 1846 2.202236 TAGTGTACGGCCCGGTCTCT 62.202 60.000 8.57 8.70 0.00 3.10
1825 1847 1.750399 GTGTACGGCCCGGTCTCTA 60.750 63.158 8.57 0.00 0.00 2.43
1826 1848 1.452651 TGTACGGCCCGGTCTCTAG 60.453 63.158 8.57 0.00 0.00 2.43
1927 1949 1.302993 GGTTCCAACGGCTAGCCAA 60.303 57.895 32.47 16.50 35.37 4.52
2129 2151 1.420138 TCGCTCTGTTCTTCCCCTTTT 59.580 47.619 0.00 0.00 0.00 2.27
2139 2161 2.389267 TCTTCCCCTTTTCCCTCTCCTA 59.611 50.000 0.00 0.00 0.00 2.94
2173 2195 2.886523 CTCTTCCTCTCGAGCTCATCAT 59.113 50.000 15.40 0.00 0.00 2.45
2234 2256 6.127281 CCCATCCATTCAAATGATCACAAAGA 60.127 38.462 0.00 0.00 38.70 2.52
2274 2296 8.149647 CCTTTCATCTCTCATTGCTAGATTAGT 58.850 37.037 0.00 0.00 0.00 2.24
2443 2465 0.594602 CTCCGTCGTAACCACAGTCA 59.405 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 9.423061 GGCATCTAACACAAGTATTTGAAAAAT 57.577 29.630 4.81 0.00 37.73 1.82
95 96 8.637986 AGGCATCTAACACAAGTATTTGAAAAA 58.362 29.630 4.81 0.00 37.73 1.94
96 97 8.177119 AGGCATCTAACACAAGTATTTGAAAA 57.823 30.769 4.81 0.00 37.73 2.29
97 98 7.759489 AGGCATCTAACACAAGTATTTGAAA 57.241 32.000 4.81 0.00 37.73 2.69
98 99 8.100791 AGTAGGCATCTAACACAAGTATTTGAA 58.899 33.333 4.81 0.00 37.73 2.69
99 100 7.620880 AGTAGGCATCTAACACAAGTATTTGA 58.379 34.615 4.81 0.00 37.73 2.69
100 101 7.849804 AGTAGGCATCTAACACAAGTATTTG 57.150 36.000 0.00 0.00 40.24 2.32
101 102 8.863872 AAAGTAGGCATCTAACACAAGTATTT 57.136 30.769 0.00 0.00 0.00 1.40
102 103 8.863872 AAAAGTAGGCATCTAACACAAGTATT 57.136 30.769 0.00 0.00 0.00 1.89
103 104 8.322091 AGAAAAGTAGGCATCTAACACAAGTAT 58.678 33.333 0.00 0.00 0.00 2.12
104 105 7.676947 AGAAAAGTAGGCATCTAACACAAGTA 58.323 34.615 0.00 0.00 0.00 2.24
105 106 6.534634 AGAAAAGTAGGCATCTAACACAAGT 58.465 36.000 0.00 0.00 0.00 3.16
106 107 6.650807 TGAGAAAAGTAGGCATCTAACACAAG 59.349 38.462 0.00 0.00 0.00 3.16
107 108 6.530120 TGAGAAAAGTAGGCATCTAACACAA 58.470 36.000 0.00 0.00 0.00 3.33
108 109 6.109156 TGAGAAAAGTAGGCATCTAACACA 57.891 37.500 0.00 0.00 0.00 3.72
109 110 7.764443 TGTATGAGAAAAGTAGGCATCTAACAC 59.236 37.037 0.00 0.00 0.00 3.32
110 111 7.764443 GTGTATGAGAAAAGTAGGCATCTAACA 59.236 37.037 0.00 0.00 0.00 2.41
111 112 7.764443 TGTGTATGAGAAAAGTAGGCATCTAAC 59.236 37.037 0.00 0.00 0.00 2.34
112 113 7.847096 TGTGTATGAGAAAAGTAGGCATCTAA 58.153 34.615 0.00 0.00 0.00 2.10
113 114 7.418337 TGTGTATGAGAAAAGTAGGCATCTA 57.582 36.000 0.00 0.00 0.00 1.98
114 115 6.299805 TGTGTATGAGAAAAGTAGGCATCT 57.700 37.500 0.00 0.00 0.00 2.90
115 116 7.559590 AATGTGTATGAGAAAAGTAGGCATC 57.440 36.000 0.00 0.00 0.00 3.91
117 118 9.542462 GTATAATGTGTATGAGAAAAGTAGGCA 57.458 33.333 0.00 0.00 0.00 4.75
118 119 9.542462 TGTATAATGTGTATGAGAAAAGTAGGC 57.458 33.333 0.00 0.00 0.00 3.93
126 127 9.607988 ACCGAAAATGTATAATGTGTATGAGAA 57.392 29.630 0.00 0.00 0.00 2.87
133 134 9.826574 AGTGTATACCGAAAATGTATAATGTGT 57.173 29.630 0.00 0.00 34.03 3.72
140 141 8.698210 TGTTCCTAGTGTATACCGAAAATGTAT 58.302 33.333 0.00 0.00 33.63 2.29
141 142 8.065473 TGTTCCTAGTGTATACCGAAAATGTA 57.935 34.615 0.00 0.00 0.00 2.29
142 143 6.938507 TGTTCCTAGTGTATACCGAAAATGT 58.061 36.000 0.00 0.00 0.00 2.71
143 144 7.548075 AGTTGTTCCTAGTGTATACCGAAAATG 59.452 37.037 0.00 0.00 0.00 2.32
144 145 7.618137 AGTTGTTCCTAGTGTATACCGAAAAT 58.382 34.615 0.00 0.00 0.00 1.82
145 146 6.996509 AGTTGTTCCTAGTGTATACCGAAAA 58.003 36.000 0.00 0.00 0.00 2.29
146 147 6.594788 AGTTGTTCCTAGTGTATACCGAAA 57.405 37.500 0.00 0.00 0.00 3.46
147 148 6.594788 AAGTTGTTCCTAGTGTATACCGAA 57.405 37.500 0.00 0.00 0.00 4.30
148 149 6.594788 AAAGTTGTTCCTAGTGTATACCGA 57.405 37.500 0.00 0.00 0.00 4.69
149 150 7.662604 AAAAAGTTGTTCCTAGTGTATACCG 57.337 36.000 0.00 0.00 0.00 4.02
155 156 9.010029 CCATGTATAAAAAGTTGTTCCTAGTGT 57.990 33.333 0.00 0.00 0.00 3.55
156 157 9.010029 ACCATGTATAAAAAGTTGTTCCTAGTG 57.990 33.333 0.00 0.00 0.00 2.74
157 158 9.582648 AACCATGTATAAAAAGTTGTTCCTAGT 57.417 29.630 0.00 0.00 0.00 2.57
236 237 8.636213 CCAAAGGAATCAGCTAATCATGTATTT 58.364 33.333 0.00 0.00 0.00 1.40
237 238 8.000709 TCCAAAGGAATCAGCTAATCATGTATT 58.999 33.333 0.00 0.00 0.00 1.89
238 239 7.520798 TCCAAAGGAATCAGCTAATCATGTAT 58.479 34.615 0.00 0.00 0.00 2.29
239 240 6.899089 TCCAAAGGAATCAGCTAATCATGTA 58.101 36.000 0.00 0.00 0.00 2.29
240 241 5.759059 TCCAAAGGAATCAGCTAATCATGT 58.241 37.500 0.00 0.00 0.00 3.21
241 242 6.704289 TTCCAAAGGAATCAGCTAATCATG 57.296 37.500 0.00 0.00 36.71 3.07
254 255 5.714806 GGTAAAGGTCATGATTCCAAAGGAA 59.285 40.000 0.00 0.30 46.39 3.36
255 256 5.222233 TGGTAAAGGTCATGATTCCAAAGGA 60.222 40.000 0.00 0.00 0.00 3.36
256 257 5.016173 TGGTAAAGGTCATGATTCCAAAGG 58.984 41.667 0.00 0.00 0.00 3.11
257 258 5.476599 TGTGGTAAAGGTCATGATTCCAAAG 59.523 40.000 0.00 0.00 0.00 2.77
258 259 5.389520 TGTGGTAAAGGTCATGATTCCAAA 58.610 37.500 0.00 0.00 0.00 3.28
259 260 4.991776 TGTGGTAAAGGTCATGATTCCAA 58.008 39.130 0.00 0.00 0.00 3.53
260 261 4.649267 TGTGGTAAAGGTCATGATTCCA 57.351 40.909 0.00 0.00 0.00 3.53
261 262 4.142687 CGTTGTGGTAAAGGTCATGATTCC 60.143 45.833 0.00 0.00 0.00 3.01
262 263 4.142687 CCGTTGTGGTAAAGGTCATGATTC 60.143 45.833 0.00 0.00 0.00 2.52
263 264 3.756434 CCGTTGTGGTAAAGGTCATGATT 59.244 43.478 0.00 0.00 0.00 2.57
264 265 3.343617 CCGTTGTGGTAAAGGTCATGAT 58.656 45.455 0.00 0.00 0.00 2.45
265 266 2.773487 CCGTTGTGGTAAAGGTCATGA 58.227 47.619 0.00 0.00 0.00 3.07
283 284 1.720805 TTGATCCATGAACGACACCG 58.279 50.000 0.00 0.00 42.50 4.94
284 285 4.701956 AATTTGATCCATGAACGACACC 57.298 40.909 0.00 0.00 0.00 4.16
285 286 7.967854 TGAAATAATTTGATCCATGAACGACAC 59.032 33.333 0.00 0.00 0.00 3.67
286 287 8.049655 TGAAATAATTTGATCCATGAACGACA 57.950 30.769 0.00 0.00 0.00 4.35
287 288 8.961092 CATGAAATAATTTGATCCATGAACGAC 58.039 33.333 0.00 0.00 33.72 4.34
288 289 8.136800 CCATGAAATAATTTGATCCATGAACGA 58.863 33.333 0.00 0.00 33.72 3.85
289 290 8.136800 TCCATGAAATAATTTGATCCATGAACG 58.863 33.333 0.00 0.00 33.72 3.95
290 291 9.991906 ATCCATGAAATAATTTGATCCATGAAC 57.008 29.630 0.00 0.00 33.72 3.18
292 293 9.990360 CAATCCATGAAATAATTTGATCCATGA 57.010 29.630 0.00 0.00 33.72 3.07
293 294 9.772973 ACAATCCATGAAATAATTTGATCCATG 57.227 29.630 0.00 0.00 0.00 3.66
304 305 9.558396 AGCTTTTGAAAACAATCCATGAAATAA 57.442 25.926 0.00 0.00 0.00 1.40
305 306 9.558396 AAGCTTTTGAAAACAATCCATGAAATA 57.442 25.926 0.00 0.00 0.00 1.40
306 307 8.347035 CAAGCTTTTGAAAACAATCCATGAAAT 58.653 29.630 0.00 0.00 0.00 2.17
307 308 7.551974 TCAAGCTTTTGAAAACAATCCATGAAA 59.448 29.630 0.00 0.00 0.00 2.69
308 309 7.046652 TCAAGCTTTTGAAAACAATCCATGAA 58.953 30.769 0.00 0.00 0.00 2.57
309 310 6.580788 TCAAGCTTTTGAAAACAATCCATGA 58.419 32.000 0.00 0.00 0.00 3.07
310 311 6.847956 TCAAGCTTTTGAAAACAATCCATG 57.152 33.333 0.00 0.00 0.00 3.66
311 312 9.558396 TTAATCAAGCTTTTGAAAACAATCCAT 57.442 25.926 0.00 0.00 34.24 3.41
312 313 8.954950 TTAATCAAGCTTTTGAAAACAATCCA 57.045 26.923 0.00 0.00 34.24 3.41
391 392 9.715121 AAAAACTCTCATGCATATGAAAAATGT 57.285 25.926 6.97 0.00 42.48 2.71
424 425 9.377312 AGCATTTGTAAAATGTTAAGTGTGTTT 57.623 25.926 12.82 0.00 0.00 2.83
425 426 8.940768 AGCATTTGTAAAATGTTAAGTGTGTT 57.059 26.923 12.82 0.00 0.00 3.32
426 427 9.677567 CTAGCATTTGTAAAATGTTAAGTGTGT 57.322 29.630 12.82 0.00 0.00 3.72
427 428 9.891828 TCTAGCATTTGTAAAATGTTAAGTGTG 57.108 29.630 12.82 2.18 0.00 3.82
537 538 9.516314 TTTTTCACATTTTCGGTTTTTGTTTTT 57.484 22.222 0.00 0.00 0.00 1.94
560 561 9.710900 ACAGAGTCAAATTTCTTTTCTGTTTTT 57.289 25.926 13.98 0.00 36.95 1.94
561 562 9.143631 CACAGAGTCAAATTTCTTTTCTGTTTT 57.856 29.630 15.86 0.83 37.64 2.43
562 563 7.761249 CCACAGAGTCAAATTTCTTTTCTGTTT 59.239 33.333 15.86 1.32 37.64 2.83
563 564 7.260603 CCACAGAGTCAAATTTCTTTTCTGTT 58.739 34.615 15.86 5.39 37.64 3.16
564 565 6.183360 CCCACAGAGTCAAATTTCTTTTCTGT 60.183 38.462 13.98 13.98 39.12 3.41
565 566 6.211515 CCCACAGAGTCAAATTTCTTTTCTG 58.788 40.000 13.09 13.09 34.81 3.02
566 567 5.221322 GCCCACAGAGTCAAATTTCTTTTCT 60.221 40.000 0.00 0.00 0.00 2.52
567 568 4.984785 GCCCACAGAGTCAAATTTCTTTTC 59.015 41.667 0.00 0.00 0.00 2.29
568 569 4.651045 AGCCCACAGAGTCAAATTTCTTTT 59.349 37.500 0.00 0.00 0.00 2.27
569 570 4.218312 AGCCCACAGAGTCAAATTTCTTT 58.782 39.130 0.00 0.00 0.00 2.52
570 571 3.823304 GAGCCCACAGAGTCAAATTTCTT 59.177 43.478 0.00 0.00 0.00 2.52
571 572 3.416156 GAGCCCACAGAGTCAAATTTCT 58.584 45.455 0.00 0.00 0.00 2.52
572 573 2.489722 GGAGCCCACAGAGTCAAATTTC 59.510 50.000 0.00 0.00 0.00 2.17
573 574 2.108952 AGGAGCCCACAGAGTCAAATTT 59.891 45.455 0.00 0.00 0.00 1.82
574 575 1.707427 AGGAGCCCACAGAGTCAAATT 59.293 47.619 0.00 0.00 0.00 1.82
575 576 1.004044 CAGGAGCCCACAGAGTCAAAT 59.996 52.381 0.00 0.00 0.00 2.32
576 577 0.397941 CAGGAGCCCACAGAGTCAAA 59.602 55.000 0.00 0.00 0.00 2.69
577 578 2.061220 CAGGAGCCCACAGAGTCAA 58.939 57.895 0.00 0.00 0.00 3.18
578 579 2.587247 GCAGGAGCCCACAGAGTCA 61.587 63.158 0.00 0.00 33.58 3.41
579 580 2.267324 GCAGGAGCCCACAGAGTC 59.733 66.667 0.00 0.00 33.58 3.36
580 581 3.699894 CGCAGGAGCCCACAGAGT 61.700 66.667 0.00 0.00 37.52 3.24
581 582 3.385384 TCGCAGGAGCCCACAGAG 61.385 66.667 0.00 0.00 37.52 3.35
582 583 3.695606 GTCGCAGGAGCCCACAGA 61.696 66.667 0.00 0.00 37.52 3.41
583 584 4.767255 GGTCGCAGGAGCCCACAG 62.767 72.222 0.00 0.00 37.52 3.66
585 586 4.767255 CAGGTCGCAGGAGCCCAC 62.767 72.222 0.00 0.00 41.62 4.61
590 591 4.463879 CAGCCCAGGTCGCAGGAG 62.464 72.222 0.00 0.00 0.00 3.69
605 606 4.379243 AACGCGAGACTGGGCCAG 62.379 66.667 31.62 31.62 37.52 4.85
606 607 4.373116 GAACGCGAGACTGGGCCA 62.373 66.667 15.93 5.85 0.00 5.36
609 610 3.382832 AGGGAACGCGAGACTGGG 61.383 66.667 15.93 0.00 0.00 4.45
610 611 2.125912 CAGGGAACGCGAGACTGG 60.126 66.667 15.93 0.00 0.00 4.00
611 612 2.771763 AAGCAGGGAACGCGAGACTG 62.772 60.000 15.93 16.12 35.50 3.51
612 613 2.100879 AAAGCAGGGAACGCGAGACT 62.101 55.000 15.93 1.77 35.50 3.24
613 614 0.389426 TAAAGCAGGGAACGCGAGAC 60.389 55.000 15.93 2.91 35.50 3.36
614 615 0.535335 ATAAAGCAGGGAACGCGAGA 59.465 50.000 15.93 0.00 35.50 4.04
615 616 0.652592 CATAAAGCAGGGAACGCGAG 59.347 55.000 15.93 0.00 35.50 5.03
616 617 0.742990 CCATAAAGCAGGGAACGCGA 60.743 55.000 15.93 0.00 35.50 5.87
617 618 1.024579 ACCATAAAGCAGGGAACGCG 61.025 55.000 3.53 3.53 35.50 6.01
618 619 0.451783 CACCATAAAGCAGGGAACGC 59.548 55.000 0.00 0.00 0.00 4.84
619 620 1.468520 CACACCATAAAGCAGGGAACG 59.531 52.381 0.00 0.00 0.00 3.95
620 621 1.202348 GCACACCATAAAGCAGGGAAC 59.798 52.381 0.00 0.00 0.00 3.62
621 622 1.202989 TGCACACCATAAAGCAGGGAA 60.203 47.619 0.00 0.00 32.48 3.97
622 623 0.403655 TGCACACCATAAAGCAGGGA 59.596 50.000 0.00 0.00 32.48 4.20
623 624 0.527565 GTGCACACCATAAAGCAGGG 59.472 55.000 13.17 0.00 37.72 4.45
624 625 1.068333 GTGTGCACACCATAAAGCAGG 60.068 52.381 34.94 0.00 40.85 4.85
625 626 1.400113 CGTGTGCACACCATAAAGCAG 60.400 52.381 37.23 20.03 43.66 4.24
626 627 0.590682 CGTGTGCACACCATAAAGCA 59.409 50.000 37.23 3.17 43.66 3.91
627 628 0.871722 TCGTGTGCACACCATAAAGC 59.128 50.000 37.23 15.86 43.66 3.51
628 629 2.143122 ACTCGTGTGCACACCATAAAG 58.857 47.619 37.23 27.55 43.66 1.85
629 630 2.248280 ACTCGTGTGCACACCATAAA 57.752 45.000 37.23 19.86 43.66 1.40
630 631 1.870402 CAACTCGTGTGCACACCATAA 59.130 47.619 37.23 22.01 43.66 1.90
631 632 1.507562 CAACTCGTGTGCACACCATA 58.492 50.000 37.23 24.23 43.66 2.74
632 633 1.165907 CCAACTCGTGTGCACACCAT 61.166 55.000 37.23 23.24 43.66 3.55
633 634 1.817520 CCAACTCGTGTGCACACCA 60.818 57.895 37.23 27.76 43.66 4.17
634 635 0.531090 TACCAACTCGTGTGCACACC 60.531 55.000 37.23 22.73 43.66 4.16
635 636 0.859232 CTACCAACTCGTGTGCACAC 59.141 55.000 35.04 35.04 43.15 3.82
636 637 0.249699 CCTACCAACTCGTGTGCACA 60.250 55.000 17.42 17.42 0.00 4.57
637 638 1.566018 GCCTACCAACTCGTGTGCAC 61.566 60.000 10.75 10.75 0.00 4.57
638 639 1.301401 GCCTACCAACTCGTGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
639 640 1.004918 AGCCTACCAACTCGTGTGC 60.005 57.895 0.00 0.00 0.00 4.57
640 641 0.670546 CCAGCCTACCAACTCGTGTG 60.671 60.000 0.00 0.00 0.00 3.82
641 642 1.671742 CCAGCCTACCAACTCGTGT 59.328 57.895 0.00 0.00 0.00 4.49
642 643 1.741770 GCCAGCCTACCAACTCGTG 60.742 63.158 0.00 0.00 0.00 4.35
643 644 2.663196 GCCAGCCTACCAACTCGT 59.337 61.111 0.00 0.00 0.00 4.18
644 645 2.125106 GGCCAGCCTACCAACTCG 60.125 66.667 0.00 0.00 0.00 4.18
645 646 2.272471 GGGCCAGCCTACCAACTC 59.728 66.667 4.39 0.00 36.10 3.01
646 647 3.717294 CGGGCCAGCCTACCAACT 61.717 66.667 4.39 0.00 36.10 3.16
647 648 2.187896 TTACGGGCCAGCCTACCAAC 62.188 60.000 4.39 0.00 36.10 3.77
648 649 1.919308 TTACGGGCCAGCCTACCAA 60.919 57.895 4.39 0.00 36.10 3.67
649 650 2.284773 TTACGGGCCAGCCTACCA 60.285 61.111 4.39 0.00 36.10 3.25
650 651 1.044790 TAGTTACGGGCCAGCCTACC 61.045 60.000 4.39 0.00 36.10 3.18
651 652 1.046204 ATAGTTACGGGCCAGCCTAC 58.954 55.000 4.39 0.00 36.10 3.18
652 653 2.629617 GTTATAGTTACGGGCCAGCCTA 59.370 50.000 4.39 2.34 36.10 3.93
653 654 1.415289 GTTATAGTTACGGGCCAGCCT 59.585 52.381 4.39 0.00 36.10 4.58
654 655 1.139455 TGTTATAGTTACGGGCCAGCC 59.861 52.381 4.39 0.00 0.00 4.85
655 656 2.607631 TGTTATAGTTACGGGCCAGC 57.392 50.000 4.39 0.00 0.00 4.85
656 657 4.331717 CAGTTTGTTATAGTTACGGGCCAG 59.668 45.833 4.39 1.85 0.00 4.85
657 658 4.255301 CAGTTTGTTATAGTTACGGGCCA 58.745 43.478 4.39 0.00 0.00 5.36
658 659 3.064408 GCAGTTTGTTATAGTTACGGGCC 59.936 47.826 0.00 0.00 0.00 5.80
659 660 3.685756 TGCAGTTTGTTATAGTTACGGGC 59.314 43.478 0.00 0.00 0.00 6.13
660 661 5.220777 CCATGCAGTTTGTTATAGTTACGGG 60.221 44.000 0.00 0.00 0.00 5.28
661 662 5.729454 GCCATGCAGTTTGTTATAGTTACGG 60.729 44.000 0.00 0.00 0.00 4.02
662 663 5.263185 GCCATGCAGTTTGTTATAGTTACG 58.737 41.667 0.00 0.00 0.00 3.18
663 664 5.449999 GGGCCATGCAGTTTGTTATAGTTAC 60.450 44.000 4.39 0.00 0.00 2.50
664 665 4.642885 GGGCCATGCAGTTTGTTATAGTTA 59.357 41.667 4.39 0.00 0.00 2.24
665 666 3.447229 GGGCCATGCAGTTTGTTATAGTT 59.553 43.478 4.39 0.00 0.00 2.24
666 667 3.023832 GGGCCATGCAGTTTGTTATAGT 58.976 45.455 4.39 0.00 0.00 2.12
667 668 3.023119 TGGGCCATGCAGTTTGTTATAG 58.977 45.455 0.00 0.00 0.00 1.31
668 669 3.093057 TGGGCCATGCAGTTTGTTATA 57.907 42.857 0.00 0.00 0.00 0.98
669 670 1.935799 TGGGCCATGCAGTTTGTTAT 58.064 45.000 0.00 0.00 0.00 1.89
670 671 1.709578 TTGGGCCATGCAGTTTGTTA 58.290 45.000 7.26 0.00 0.00 2.41
671 672 1.002315 GATTGGGCCATGCAGTTTGTT 59.998 47.619 7.26 0.00 0.00 2.83
672 673 0.609662 GATTGGGCCATGCAGTTTGT 59.390 50.000 7.26 0.00 0.00 2.83
673 674 0.458889 CGATTGGGCCATGCAGTTTG 60.459 55.000 7.26 0.00 0.00 2.93
674 675 1.892338 CGATTGGGCCATGCAGTTT 59.108 52.632 7.26 0.00 0.00 2.66
675 676 2.713967 GCGATTGGGCCATGCAGTT 61.714 57.895 7.26 0.00 0.00 3.16
676 677 2.269520 TAGCGATTGGGCCATGCAGT 62.270 55.000 22.67 9.76 0.00 4.40
677 678 0.892358 ATAGCGATTGGGCCATGCAG 60.892 55.000 22.67 10.57 0.00 4.41
678 679 0.890542 GATAGCGATTGGGCCATGCA 60.891 55.000 22.67 12.24 0.00 3.96
679 680 0.607489 AGATAGCGATTGGGCCATGC 60.607 55.000 7.26 12.68 0.00 4.06
690 691 1.485124 TCTTGGCAGGAAGATAGCGA 58.515 50.000 0.00 0.00 0.00 4.93
694 695 2.505819 GGGACTTCTTGGCAGGAAGATA 59.494 50.000 36.57 7.41 41.71 1.98
721 722 2.416244 GAACTGTCGGCCGTCAGTCA 62.416 60.000 43.16 25.64 41.97 3.41
722 723 1.733399 GAACTGTCGGCCGTCAGTC 60.733 63.158 43.16 33.51 41.97 3.51
723 724 1.745320 AAGAACTGTCGGCCGTCAGT 61.745 55.000 40.13 40.13 43.95 3.41
724 725 0.242825 TAAGAACTGTCGGCCGTCAG 59.757 55.000 38.94 38.94 37.32 3.51
799 801 2.303163 AATACGTGTATTGCTCCGCA 57.697 45.000 0.00 0.00 34.71 5.69
843 845 2.593257 GGTACGTAGAACTGCAGTGAC 58.407 52.381 22.49 17.42 0.00 3.67
925 927 7.142680 CCTATGGACGAGTAAGATTTCTCTTC 58.857 42.308 0.00 0.00 40.92 2.87
1093 1105 3.617538 GACGTGGAGCGCGCATAC 61.618 66.667 35.10 25.39 46.11 2.39
1113 1125 2.438795 ACGGAGGAGAGGACGAGC 60.439 66.667 0.00 0.00 0.00 5.03
1323 1341 3.423154 CCGCGTGTTTCCAGCTCC 61.423 66.667 4.92 0.00 0.00 4.70
1396 1414 2.159043 ACCGACGATCTTGCTCATCAAT 60.159 45.455 0.00 0.00 33.57 2.57
1397 1415 1.204704 ACCGACGATCTTGCTCATCAA 59.795 47.619 0.00 0.00 0.00 2.57
1420 1438 0.182537 TTCCCAGTGTCCACCAACAG 59.817 55.000 0.00 0.00 0.00 3.16
1427 1445 3.537795 AGTAGTAGTTCCCAGTGTCCA 57.462 47.619 0.00 0.00 0.00 4.02
1431 1449 3.762288 TGCAGTAGTAGTAGTTCCCAGTG 59.238 47.826 0.00 0.00 0.00 3.66
1458 1476 2.219674 CGATAAGAAATGCTCGCTCACC 59.780 50.000 0.00 0.00 0.00 4.02
1464 1482 3.677121 CAGGGATCGATAAGAAATGCTCG 59.323 47.826 0.00 0.00 0.00 5.03
1476 1494 3.287867 AAACAGATTGCAGGGATCGAT 57.712 42.857 0.00 0.00 0.00 3.59
1479 1497 2.098117 CCGAAAACAGATTGCAGGGATC 59.902 50.000 0.00 0.00 0.00 3.36
1489 1507 2.032030 CGAACAACAGCCGAAAACAGAT 60.032 45.455 0.00 0.00 0.00 2.90
1512 1530 6.896307 AGTCCAGTAACTAAGCCAATAGTACT 59.104 38.462 0.00 0.00 35.09 2.73
1513 1531 6.979238 CAGTCCAGTAACTAAGCCAATAGTAC 59.021 42.308 0.00 0.00 35.09 2.73
1514 1532 6.097839 CCAGTCCAGTAACTAAGCCAATAGTA 59.902 42.308 0.00 0.00 35.09 1.82
1515 1533 5.104900 CCAGTCCAGTAACTAAGCCAATAGT 60.105 44.000 0.00 0.00 37.73 2.12
1520 1538 2.565834 GTCCAGTCCAGTAACTAAGCCA 59.434 50.000 0.00 0.00 0.00 4.75
1618 1640 0.657840 GAACCTGTATGTGCCATCGC 59.342 55.000 0.00 0.00 0.00 4.58
1644 1666 3.132289 ACATCGTAATCACACTACCCTGG 59.868 47.826 0.00 0.00 0.00 4.45
1687 1709 2.215451 AATCGGACCTTGCAGCCCAT 62.215 55.000 0.00 0.00 0.00 4.00
1701 1723 0.798776 GTCTGCACCAGAACAATCGG 59.201 55.000 0.00 0.00 42.46 4.18
1715 1737 1.578423 GACCTTGCTTGCAGTCTGC 59.422 57.895 18.32 18.32 45.29 4.26
1718 1740 2.328099 CCGGACCTTGCTTGCAGTC 61.328 63.158 0.00 6.48 0.00 3.51
1721 1743 2.192861 CAACCGGACCTTGCTTGCA 61.193 57.895 9.46 0.00 0.00 4.08
1722 1744 2.193536 ACAACCGGACCTTGCTTGC 61.194 57.895 9.46 0.00 0.00 4.01
1723 1745 1.654220 CACAACCGGACCTTGCTTG 59.346 57.895 9.46 2.14 0.00 4.01
1724 1746 1.528309 CCACAACCGGACCTTGCTT 60.528 57.895 9.46 0.00 0.00 3.91
1725 1747 2.113139 CCACAACCGGACCTTGCT 59.887 61.111 9.46 0.00 0.00 3.91
1726 1748 2.983592 CCCACAACCGGACCTTGC 60.984 66.667 9.46 0.00 0.00 4.01
1727 1749 1.896660 CACCCACAACCGGACCTTG 60.897 63.158 9.46 4.81 0.00 3.61
1729 1751 2.770904 ACACCCACAACCGGACCT 60.771 61.111 9.46 0.00 0.00 3.85
1730 1752 2.593436 CACACCCACAACCGGACC 60.593 66.667 9.46 0.00 0.00 4.46
1731 1753 3.284449 GCACACCCACAACCGGAC 61.284 66.667 9.46 0.00 0.00 4.79
1732 1754 2.951475 GAAGCACACCCACAACCGGA 62.951 60.000 9.46 0.00 0.00 5.14
1733 1755 2.518349 AAGCACACCCACAACCGG 60.518 61.111 0.00 0.00 0.00 5.28
1734 1756 1.525995 AGAAGCACACCCACAACCG 60.526 57.895 0.00 0.00 0.00 4.44
1735 1757 2.032981 CAGAAGCACACCCACAACC 58.967 57.895 0.00 0.00 0.00 3.77
1737 1759 1.827789 GGCAGAAGCACACCCACAA 60.828 57.895 0.00 0.00 44.61 3.33
1738 1760 2.203337 GGCAGAAGCACACCCACA 60.203 61.111 0.00 0.00 44.61 4.17
1748 1770 4.101448 CCTGGACCCGGGCAGAAG 62.101 72.222 25.07 15.88 35.46 2.85
1772 1794 0.324738 AGAGATCAGAGCGGTTCCCA 60.325 55.000 0.00 0.00 0.00 4.37
1801 1823 0.396060 ACCGGGCCGTACACTAAAAA 59.604 50.000 26.32 0.00 0.00 1.94
1802 1824 0.037419 GACCGGGCCGTACACTAAAA 60.037 55.000 26.32 0.00 0.00 1.52
1803 1825 0.899717 AGACCGGGCCGTACACTAAA 60.900 55.000 26.32 0.00 0.00 1.85
1804 1826 1.304381 AGACCGGGCCGTACACTAA 60.304 57.895 26.32 0.00 0.00 2.24
1805 1827 1.750399 GAGACCGGGCCGTACACTA 60.750 63.158 26.32 0.00 0.00 2.74
1806 1828 2.202236 TAGAGACCGGGCCGTACACT 62.202 60.000 26.32 21.63 0.00 3.55
1807 1829 1.722636 CTAGAGACCGGGCCGTACAC 61.723 65.000 26.32 15.95 0.00 2.90
1808 1830 1.452651 CTAGAGACCGGGCCGTACA 60.453 63.158 26.32 2.45 0.00 2.90
1809 1831 1.443322 GACTAGAGACCGGGCCGTAC 61.443 65.000 26.32 17.72 0.00 3.67
1810 1832 1.153086 GACTAGAGACCGGGCCGTA 60.153 63.158 26.32 9.18 0.00 4.02
1811 1833 2.439883 GACTAGAGACCGGGCCGT 60.440 66.667 26.32 13.20 0.00 5.68
1812 1834 2.439701 TGACTAGAGACCGGGCCG 60.440 66.667 21.46 21.46 0.00 6.13
1813 1835 0.106819 TAGTGACTAGAGACCGGGCC 60.107 60.000 1.76 0.00 0.00 5.80
1814 1836 1.310904 CTAGTGACTAGAGACCGGGC 58.689 60.000 14.31 0.52 36.26 6.13
1815 1837 2.713863 ACTAGTGACTAGAGACCGGG 57.286 55.000 25.21 0.00 37.49 5.73
1816 1838 4.669206 TCTACTAGTGACTAGAGACCGG 57.331 50.000 25.21 0.00 37.49 5.28
1817 1839 6.981762 TTTTCTACTAGTGACTAGAGACCG 57.018 41.667 25.21 8.79 37.49 4.79
1818 1840 7.148035 CCCTTTTTCTACTAGTGACTAGAGACC 60.148 44.444 25.21 0.00 37.49 3.85
1819 1841 7.394077 ACCCTTTTTCTACTAGTGACTAGAGAC 59.606 40.741 25.21 0.00 37.49 3.36
1820 1842 7.468496 ACCCTTTTTCTACTAGTGACTAGAGA 58.532 38.462 25.21 18.59 37.49 3.10
1821 1843 7.393796 TGACCCTTTTTCTACTAGTGACTAGAG 59.606 40.741 25.21 16.85 37.49 2.43
1822 1844 7.236529 TGACCCTTTTTCTACTAGTGACTAGA 58.763 38.462 25.21 2.86 37.49 2.43
1823 1845 7.463961 TGACCCTTTTTCTACTAGTGACTAG 57.536 40.000 17.61 17.61 39.72 2.57
1824 1846 7.844493 TTGACCCTTTTTCTACTAGTGACTA 57.156 36.000 5.39 0.00 0.00 2.59
1825 1847 6.742559 TTGACCCTTTTTCTACTAGTGACT 57.257 37.500 5.39 0.00 0.00 3.41
1826 1848 7.444487 ACATTTGACCCTTTTTCTACTAGTGAC 59.556 37.037 5.39 0.00 0.00 3.67
1927 1949 2.304751 CCGGTACTAATGAAAGCGGT 57.695 50.000 0.00 0.00 46.34 5.68
2129 2151 3.374318 GGGAAGAACAGATAGGAGAGGGA 60.374 52.174 0.00 0.00 0.00 4.20
2139 2161 3.111484 GAGGAAGAGGGGAAGAACAGAT 58.889 50.000 0.00 0.00 0.00 2.90
2173 2195 9.956640 ATCTTGATAAATTTTGGGCAAAATGTA 57.043 25.926 0.00 0.00 46.76 2.29
2234 2256 6.944862 AGAGATGAAAGGACAAAGTTGCTAAT 59.055 34.615 0.00 0.00 0.00 1.73
2274 2296 6.816134 TCACTATACAAAGCATTGCAAGAA 57.184 33.333 11.91 0.00 40.34 2.52
2551 2573 8.629158 ACAACGTACGGGTAAGATAATTATACA 58.371 33.333 21.06 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.