Multiple sequence alignment - TraesCS3A01G364600

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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 TraesCS3A01G364600 chr3A 100.000 3553 0 0 1 3553 613390157 613393709 0.000000e+00 6562
1 TraesCS3A01G364600 chr3D 89.340 2805 169 66 786 3553 471265476 471268187 0.000000e+00 3404
2 TraesCS3A01G364600 chr3D 83.925 479 20 21 336 783 471264985 471265437 4.270000e-109 405
3 TraesCS3A01G364600 chr3D 88.546 227 15 9 73 293 471264658 471264879 7.560000e-67 265
4 TraesCS3A01G364600 chr3B 86.368 3301 163 106 339 3553 625893511 625896610 0.000000e+00 3338
5 TraesCS3A01G364600 chr3B 91.864 295 16 6 1 293 625893117 625893405 4.270000e-109 405
6 TraesCS3A01G364600 chr6D 74.514 875 109 62 1883 2720 424931410 424930613 3.490000e-70 276
7 TraesCS3A01G364600 chr4A 81.746 252 40 4 1335 1580 701978353 701978604 4.650000e-49 206


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 TraesCS3A01G364600 chr3A 613390157 613393709 3552 False 6562.0 6562 100.000000 1 3553 1 chr3A.!!$F1 3552
1 TraesCS3A01G364600 chr3D 471264658 471268187 3529 False 1358.0 3404 87.270333 73 3553 3 chr3D.!!$F1 3480
2 TraesCS3A01G364600 chr3B 625893117 625896610 3493 False 1871.5 3338 89.116000 1 3553 2 chr3B.!!$F1 3552
3 TraesCS3A01G364600 chr6D 424930613 424931410 797 True 276.0 276 74.514000 1883 2720 1 chr6D.!!$R1 837

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
64 65 0.111089 GTGACGCACAAGCTTCTTCG 60.111 55.0 0.00 2.4 39.56 3.79 F
294 296 0.306533 ATGTTGTTTCGTCGCACACC 59.693 50.0 0.00 0.0 0.00 4.16 F
1755 1934 0.092014 CTCTTGCGCTTCGTTTCTCG 59.908 55.0 9.73 0.0 41.41 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1732 0.689745 CGTGGATGGGAGGAGGGTTA 60.690 60.0 0.00 0.0 0.00 2.85 R
2118 2300 0.114168 TTTTGGGGGACATGACAGGG 59.886 55.0 0.00 0.0 0.00 4.45 R
2881 3142 0.108756 CTTCTTCCTTCGTCGGACCC 60.109 60.0 1.91 0.0 31.44 4.46 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
64 65 0.111089 GTGACGCACAAGCTTCTTCG 60.111 55.000 0.00 2.40 39.56 3.79
95 96 3.359654 CCAACGCGGCAGTAATTTAATC 58.640 45.455 12.47 0.00 0.00 1.75
98 99 2.353579 ACGCGGCAGTAATTTAATCACC 59.646 45.455 12.47 0.00 0.00 4.02
118 119 4.398044 CACCACCACAAATAAGTATCACCC 59.602 45.833 0.00 0.00 0.00 4.61
182 183 0.324943 CCACTTCCGTGAATGGTCCT 59.675 55.000 0.00 0.00 43.97 3.85
183 184 1.676014 CCACTTCCGTGAATGGTCCTC 60.676 57.143 0.00 0.00 43.97 3.71
184 185 1.276421 CACTTCCGTGAATGGTCCTCT 59.724 52.381 0.00 0.00 43.97 3.69
229 231 1.138047 ATCGCACGTTCGATTCGGTC 61.138 55.000 17.33 0.00 45.81 4.79
231 233 2.785105 GCACGTTCGATTCGGTCCG 61.785 63.158 4.39 4.39 0.00 4.79
254 256 1.535204 CCTTGGTGTGAACCCCATGC 61.535 60.000 0.00 0.00 0.00 4.06
293 295 1.658968 GATGTTGTTTCGTCGCACAC 58.341 50.000 0.00 0.00 0.00 3.82
294 296 0.306533 ATGTTGTTTCGTCGCACACC 59.693 50.000 0.00 0.00 0.00 4.16
295 297 1.010462 GTTGTTTCGTCGCACACCC 60.010 57.895 0.00 0.00 0.00 4.61
296 298 1.449778 TTGTTTCGTCGCACACCCA 60.450 52.632 0.00 0.00 0.00 4.51
297 299 1.025113 TTGTTTCGTCGCACACCCAA 61.025 50.000 0.00 0.00 0.00 4.12
298 300 1.010462 GTTTCGTCGCACACCCAAC 60.010 57.895 0.00 0.00 0.00 3.77
299 301 1.449778 TTTCGTCGCACACCCAACA 60.450 52.632 0.00 0.00 0.00 3.33
300 302 1.707239 TTTCGTCGCACACCCAACAC 61.707 55.000 0.00 0.00 0.00 3.32
301 303 2.581208 TTCGTCGCACACCCAACACT 62.581 55.000 0.00 0.00 0.00 3.55
302 304 2.881266 CGTCGCACACCCAACACTG 61.881 63.158 0.00 0.00 0.00 3.66
303 305 2.899838 TCGCACACCCAACACTGC 60.900 61.111 0.00 0.00 0.00 4.40
322 371 3.379240 TGCAACCAAAATCACGACATTG 58.621 40.909 0.00 0.00 0.00 2.82
343 392 1.897398 GAACGCGACGCCAGACAATT 61.897 55.000 15.93 0.00 0.00 2.32
344 393 0.668096 AACGCGACGCCAGACAATTA 60.668 50.000 15.93 0.00 0.00 1.40
345 394 0.459585 ACGCGACGCCAGACAATTAT 60.460 50.000 15.93 0.00 0.00 1.28
384 456 3.303406 GCAAAAGTCACATGAGTTGAGC 58.697 45.455 0.00 6.66 37.72 4.26
386 458 4.534168 CAAAAGTCACATGAGTTGAGCTG 58.466 43.478 0.00 0.00 37.72 4.24
387 459 3.758755 AAGTCACATGAGTTGAGCTGA 57.241 42.857 0.00 0.00 36.43 4.26
388 460 3.316071 AGTCACATGAGTTGAGCTGAG 57.684 47.619 0.00 0.00 0.00 3.35
389 461 2.028294 AGTCACATGAGTTGAGCTGAGG 60.028 50.000 0.00 0.00 0.00 3.86
390 462 1.085091 CACATGAGTTGAGCTGAGGC 58.915 55.000 0.00 0.00 39.06 4.70
411 483 3.483587 GCCAGAAGGGGTGACAGA 58.516 61.111 0.00 0.00 37.04 3.41
412 484 1.003233 GCCAGAAGGGGTGACAGAC 60.003 63.158 0.00 0.00 37.04 3.51
413 485 1.768684 GCCAGAAGGGGTGACAGACA 61.769 60.000 0.00 0.00 37.04 3.41
414 486 3.916605 GCCAGAAGGGGTGACAGACAC 62.917 61.905 0.00 0.00 41.10 3.67
421 493 3.097728 GTGACAGACACGACGCGG 61.098 66.667 12.47 0.00 39.78 6.46
422 494 4.994201 TGACAGACACGACGCGGC 62.994 66.667 12.47 6.41 0.00 6.53
450 527 2.143925 GGTGAAACTGAAACCTCTCCG 58.856 52.381 0.00 0.00 36.74 4.63
466 543 4.799473 CGCCAGACGTTGCGCATG 62.799 66.667 12.75 10.15 44.64 4.06
467 544 3.422303 GCCAGACGTTGCGCATGA 61.422 61.111 12.75 0.00 0.00 3.07
468 545 2.780643 CCAGACGTTGCGCATGAG 59.219 61.111 12.75 8.45 0.00 2.90
469 546 2.743752 CCAGACGTTGCGCATGAGG 61.744 63.158 12.75 5.42 0.00 3.86
470 547 2.434884 AGACGTTGCGCATGAGGG 60.435 61.111 12.75 1.10 0.00 4.30
471 548 3.499737 GACGTTGCGCATGAGGGG 61.500 66.667 12.75 0.00 0.00 4.79
534 611 3.800531 CCAGGTTACCATACTTAACCCG 58.199 50.000 3.51 0.00 46.81 5.28
612 713 0.731174 CCGCAAACGCAATGGTAACC 60.731 55.000 0.00 0.00 38.22 2.85
620 727 4.492791 ACGCAATGGTAACCTTTTACAC 57.507 40.909 0.00 0.00 39.64 2.90
631 738 8.365647 TGGTAACCTTTTACACTTTTGAACAAA 58.634 29.630 0.00 0.00 39.64 2.83
640 747 1.000717 CTTTTGAACAAATCGCCCGGT 60.001 47.619 0.00 0.00 0.00 5.28
641 748 1.893544 TTTGAACAAATCGCCCGGTA 58.106 45.000 0.00 0.00 0.00 4.02
642 749 1.893544 TTGAACAAATCGCCCGGTAA 58.106 45.000 0.00 0.00 0.00 2.85
643 750 1.893544 TGAACAAATCGCCCGGTAAA 58.106 45.000 0.00 0.00 0.00 2.01
644 751 2.438411 TGAACAAATCGCCCGGTAAAT 58.562 42.857 0.00 0.00 0.00 1.40
645 752 2.820787 TGAACAAATCGCCCGGTAAATT 59.179 40.909 0.00 0.00 0.00 1.82
646 753 3.256136 TGAACAAATCGCCCGGTAAATTT 59.744 39.130 0.00 0.00 0.00 1.82
648 755 3.580731 ACAAATCGCCCGGTAAATTTTG 58.419 40.909 0.00 6.64 0.00 2.44
649 756 2.287393 AATCGCCCGGTAAATTTTGC 57.713 45.000 0.00 0.00 0.00 3.68
690 811 0.746563 ATAAACCACCCGCACATCCG 60.747 55.000 0.00 0.00 0.00 4.18
736 857 0.739813 CGTCCGTCCTTGACATTCCC 60.740 60.000 0.00 0.00 32.91 3.97
789 931 3.138798 CCGTCCGTCCGGTGAGAT 61.139 66.667 0.00 0.00 43.07 2.75
791 933 1.378882 CCGTCCGTCCGGTGAGATAA 61.379 60.000 0.00 0.00 43.07 1.75
793 935 1.066605 CGTCCGTCCGGTGAGATAAAT 59.933 52.381 0.00 0.00 36.47 1.40
795 937 3.636381 GTCCGTCCGGTGAGATAAATAC 58.364 50.000 0.00 0.00 36.47 1.89
797 939 2.049228 CGTCCGGTGAGATAAATACGC 58.951 52.381 0.00 0.00 0.00 4.42
837 1001 3.662117 TAGCGGCAGGAGAGGCAGA 62.662 63.158 1.45 0.00 0.00 4.26
838 1002 4.527583 GCGGCAGGAGAGGCAGAG 62.528 72.222 0.00 0.00 0.00 3.35
839 1003 3.847602 CGGCAGGAGAGGCAGAGG 61.848 72.222 0.00 0.00 0.00 3.69
840 1004 3.478274 GGCAGGAGAGGCAGAGGG 61.478 72.222 0.00 0.00 0.00 4.30
841 1005 2.364842 GCAGGAGAGGCAGAGGGA 60.365 66.667 0.00 0.00 0.00 4.20
842 1006 2.433994 GCAGGAGAGGCAGAGGGAG 61.434 68.421 0.00 0.00 0.00 4.30
909 1077 2.610532 GATTTCTGGCCTCCGTCCCC 62.611 65.000 3.32 0.00 0.00 4.81
1146 1325 3.437795 GACGAGGACGGGCTCGAA 61.438 66.667 15.95 0.00 44.85 3.71
1221 1400 2.217429 CCAAGGTTGGTTTTCGGTTG 57.783 50.000 0.09 0.00 43.43 3.77
1235 1414 2.637383 GGTTGCCGGACTCTCGTCT 61.637 63.158 5.05 0.00 40.10 4.18
1236 1415 1.153997 GTTGCCGGACTCTCGTCTC 60.154 63.158 5.05 0.00 40.10 3.36
1258 1437 2.095252 GTCTCGTCGCTTCTTGGCC 61.095 63.158 0.00 0.00 0.00 5.36
1287 1466 1.412343 GTTGGCATCCCTGTTTGTTGT 59.588 47.619 0.00 0.00 0.00 3.32
1304 1483 4.401022 TGTTGTCTTTGGAAGCATCTGAT 58.599 39.130 0.00 0.00 0.00 2.90
1305 1484 4.828939 TGTTGTCTTTGGAAGCATCTGATT 59.171 37.500 0.00 0.00 0.00 2.57
1306 1485 5.159209 GTTGTCTTTGGAAGCATCTGATTG 58.841 41.667 0.00 0.00 0.00 2.67
1307 1486 3.760151 TGTCTTTGGAAGCATCTGATTGG 59.240 43.478 0.00 0.00 0.00 3.16
1329 1508 4.509600 GGTTGTTGTTTCTCTCTGTCTCTG 59.490 45.833 0.00 0.00 0.00 3.35
1490 1669 4.176752 GCCGACCCATGGGACCTC 62.177 72.222 38.07 22.74 38.96 3.85
1550 1729 3.650950 AGCATCCCCGTGCCTGTT 61.651 61.111 0.00 0.00 46.19 3.16
1551 1730 3.443045 GCATCCCCGTGCCTGTTG 61.443 66.667 0.00 0.00 39.18 3.33
1552 1731 2.034066 CATCCCCGTGCCTGTTGT 59.966 61.111 0.00 0.00 0.00 3.32
1553 1732 1.603455 CATCCCCGTGCCTGTTGTT 60.603 57.895 0.00 0.00 0.00 2.83
1571 1750 1.212195 GTTAACCCTCCTCCCATCCAC 59.788 57.143 0.00 0.00 0.00 4.02
1673 1852 2.733218 CCGAACAACTCGCTCGCA 60.733 61.111 0.00 0.00 46.71 5.10
1713 1892 1.883275 CTCGTGTGAGTTCCTCTGTCT 59.117 52.381 0.00 0.00 37.46 3.41
1715 1894 2.293677 TCGTGTGAGTTCCTCTGTCTTC 59.706 50.000 0.00 0.00 0.00 2.87
1716 1895 2.294791 CGTGTGAGTTCCTCTGTCTTCT 59.705 50.000 0.00 0.00 0.00 2.85
1717 1896 3.610585 CGTGTGAGTTCCTCTGTCTTCTC 60.611 52.174 0.00 0.00 0.00 2.87
1718 1897 3.319405 GTGTGAGTTCCTCTGTCTTCTCA 59.681 47.826 0.00 0.00 0.00 3.27
1719 1898 4.021544 GTGTGAGTTCCTCTGTCTTCTCAT 60.022 45.833 0.00 0.00 35.07 2.90
1722 1901 2.902486 AGTTCCTCTGTCTTCTCATGCA 59.098 45.455 0.00 0.00 0.00 3.96
1723 1902 2.999355 GTTCCTCTGTCTTCTCATGCAC 59.001 50.000 0.00 0.00 0.00 4.57
1724 1903 1.552337 TCCTCTGTCTTCTCATGCACC 59.448 52.381 0.00 0.00 0.00 5.01
1726 1905 0.969149 TCTGTCTTCTCATGCACCGT 59.031 50.000 0.00 0.00 0.00 4.83
1727 1906 1.073964 CTGTCTTCTCATGCACCGTG 58.926 55.000 0.00 0.00 0.00 4.94
1729 1908 1.375908 TCTTCTCATGCACCGTGCC 60.376 57.895 20.67 3.67 44.23 5.01
1730 1909 2.741985 TTCTCATGCACCGTGCCG 60.742 61.111 20.67 11.88 44.23 5.69
1741 1920 3.726517 CGTGCCGGCCAACTCTTG 61.727 66.667 26.77 0.00 0.00 3.02
1755 1934 0.092014 CTCTTGCGCTTCGTTTCTCG 59.908 55.000 9.73 0.00 41.41 4.04
1757 1936 2.818296 CTTGCGCTTCGTTTCTCGCC 62.818 60.000 9.73 0.00 46.14 5.54
1759 1938 3.838795 CGCTTCGTTTCTCGCCGG 61.839 66.667 0.00 0.00 39.67 6.13
1760 1939 2.431942 GCTTCGTTTCTCGCCGGA 60.432 61.111 5.05 0.00 39.67 5.14
1761 1940 2.445438 GCTTCGTTTCTCGCCGGAG 61.445 63.158 5.05 0.00 41.89 4.63
1762 1941 1.080705 CTTCGTTTCTCGCCGGAGT 60.081 57.895 5.05 0.00 41.26 3.85
1787 1966 8.116753 GTGATTATTCTCTGACGTTTTGTATGG 58.883 37.037 0.00 0.00 0.00 2.74
1998 2180 2.663196 GTGTTCCTCACCCCTCCG 59.337 66.667 0.00 0.00 40.84 4.63
2118 2300 2.278330 CCCACTTCCTTTGCCTGCC 61.278 63.158 0.00 0.00 0.00 4.85
2143 2326 4.340617 TGTCATGTCCCCCAAAAGTATTC 58.659 43.478 0.00 0.00 0.00 1.75
2163 2346 5.897377 TTCTTAGCTAAAAATCCTGTGGC 57.103 39.130 7.74 0.00 0.00 5.01
2170 2353 1.831580 AAAATCCTGTGGCTCTGCTC 58.168 50.000 0.00 0.00 0.00 4.26
2192 2375 3.655810 CTCAGGCTGCTCCACGGTC 62.656 68.421 10.34 0.00 37.29 4.79
2237 2427 0.937699 CGCTCAACCTCAACGTCGAA 60.938 55.000 0.00 0.00 0.00 3.71
2289 2487 1.726791 CCTTCGTTCTTGATCACGGTG 59.273 52.381 0.56 0.56 37.02 4.94
2307 2505 2.686915 GGTGAGCAATCAATCCCTTCTG 59.313 50.000 0.00 0.00 0.00 3.02
2353 2551 7.326789 CGCCAATGATAATCGCATCTTTATTTT 59.673 33.333 0.00 0.00 0.00 1.82
2369 2567 8.220755 TCTTTATTTTGGGTTATGAAGATCCG 57.779 34.615 0.00 0.00 0.00 4.18
2378 2576 5.360591 GGTTATGAAGATCCGTCAATGACT 58.639 41.667 11.92 0.00 0.00 3.41
2379 2577 5.235186 GGTTATGAAGATCCGTCAATGACTG 59.765 44.000 11.92 5.08 0.00 3.51
2380 2578 4.743057 ATGAAGATCCGTCAATGACTGA 57.257 40.909 11.92 10.83 31.08 3.41
2393 2591 4.385748 TCAATGACTGACATTTCGAACTCG 59.614 41.667 0.00 0.00 45.60 4.18
2397 2602 4.208460 TGACTGACATTTCGAACTCGTTTC 59.792 41.667 0.00 0.00 40.80 2.78
2398 2603 4.369182 ACTGACATTTCGAACTCGTTTCT 58.631 39.130 0.00 0.00 40.80 2.52
2400 2605 5.293569 ACTGACATTTCGAACTCGTTTCTTT 59.706 36.000 0.00 0.00 40.80 2.52
2401 2606 5.498159 TGACATTTCGAACTCGTTTCTTTG 58.502 37.500 0.00 0.00 40.80 2.77
2402 2607 5.064198 TGACATTTCGAACTCGTTTCTTTGT 59.936 36.000 0.00 0.00 40.80 2.83
2403 2608 5.263185 ACATTTCGAACTCGTTTCTTTGTG 58.737 37.500 0.00 0.00 40.80 3.33
2404 2609 4.932268 TTTCGAACTCGTTTCTTTGTGT 57.068 36.364 0.00 0.00 40.80 3.72
2405 2610 4.509915 TTCGAACTCGTTTCTTTGTGTC 57.490 40.909 0.00 0.00 40.80 3.67
2570 2797 2.104331 GATGCATCGTCCGTCCGT 59.896 61.111 11.68 0.00 0.00 4.69
2571 2798 1.944676 GATGCATCGTCCGTCCGTC 60.945 63.158 11.68 0.00 0.00 4.79
2622 2849 9.687210 TCACTGCCATATTTAAGTATTACTACG 57.313 33.333 0.00 0.00 32.82 3.51
2760 3012 7.288852 TGTGGGTGATATATTGGTTATTTTGGG 59.711 37.037 0.00 0.00 0.00 4.12
2773 3025 4.589675 TTGGGGGACGGTTGGTGC 62.590 66.667 0.00 0.00 36.02 5.01
2781 3037 2.350895 CGGTTGGTGCTGGATGGA 59.649 61.111 0.00 0.00 0.00 3.41
2782 3038 1.077501 CGGTTGGTGCTGGATGGAT 60.078 57.895 0.00 0.00 0.00 3.41
2784 3040 1.039233 GGTTGGTGCTGGATGGATGG 61.039 60.000 0.00 0.00 0.00 3.51
2785 3041 0.034186 GTTGGTGCTGGATGGATGGA 60.034 55.000 0.00 0.00 0.00 3.41
2786 3042 0.928505 TTGGTGCTGGATGGATGGAT 59.071 50.000 0.00 0.00 0.00 3.41
2787 3043 0.184211 TGGTGCTGGATGGATGGATG 59.816 55.000 0.00 0.00 0.00 3.51
2788 3044 0.538977 GGTGCTGGATGGATGGATGG 60.539 60.000 0.00 0.00 0.00 3.51
2789 3045 0.475475 GTGCTGGATGGATGGATGGA 59.525 55.000 0.00 0.00 0.00 3.41
2790 3046 1.075050 GTGCTGGATGGATGGATGGAT 59.925 52.381 0.00 0.00 0.00 3.41
2791 3047 1.074889 TGCTGGATGGATGGATGGATG 59.925 52.381 0.00 0.00 0.00 3.51
2792 3048 1.616187 GCTGGATGGATGGATGGATGG 60.616 57.143 0.00 0.00 0.00 3.51
2793 3049 1.990327 CTGGATGGATGGATGGATGGA 59.010 52.381 0.00 0.00 0.00 3.41
2794 3050 1.706866 TGGATGGATGGATGGATGGAC 59.293 52.381 0.00 0.00 0.00 4.02
2795 3051 1.339438 GGATGGATGGATGGATGGACG 60.339 57.143 0.00 0.00 0.00 4.79
2796 3052 0.037303 ATGGATGGATGGATGGACGC 59.963 55.000 0.00 0.00 0.00 5.19
2797 3053 1.302832 GGATGGATGGATGGACGCC 60.303 63.158 0.00 0.00 0.00 5.68
2798 3054 1.669115 GATGGATGGATGGACGCCG 60.669 63.158 0.00 0.00 0.00 6.46
2799 3055 2.099652 GATGGATGGATGGACGCCGA 62.100 60.000 0.00 0.00 0.00 5.54
2800 3056 2.280186 GGATGGATGGACGCCGAC 60.280 66.667 0.00 0.00 0.00 4.79
2802 3058 3.133767 GATGGATGGACGCCGACGA 62.134 63.158 0.00 0.00 43.93 4.20
2803 3059 3.138930 ATGGATGGACGCCGACGAG 62.139 63.158 0.00 0.00 43.93 4.18
2805 3061 4.492160 GATGGACGCCGACGAGCA 62.492 66.667 0.00 0.00 43.93 4.26
2835 3096 3.509442 AGGAGAAACAAAATCCATGGCA 58.491 40.909 6.96 0.00 35.45 4.92
2836 3097 4.098894 AGGAGAAACAAAATCCATGGCAT 58.901 39.130 6.96 0.00 35.45 4.40
2837 3098 4.081309 AGGAGAAACAAAATCCATGGCATG 60.081 41.667 20.56 20.56 35.45 4.06
2878 3139 4.296690 CGGGAGGAATAATAAGTGTCGTC 58.703 47.826 0.00 0.00 0.00 4.20
2881 3142 4.738740 GGAGGAATAATAAGTGTCGTCGTG 59.261 45.833 0.00 0.00 0.00 4.35
2882 3143 4.679662 AGGAATAATAAGTGTCGTCGTGG 58.320 43.478 0.00 0.00 0.00 4.94
2883 3144 3.800506 GGAATAATAAGTGTCGTCGTGGG 59.199 47.826 0.00 0.00 0.00 4.61
2884 3145 4.427312 GAATAATAAGTGTCGTCGTGGGT 58.573 43.478 0.00 0.00 0.00 4.51
2885 3146 2.358939 AATAAGTGTCGTCGTGGGTC 57.641 50.000 0.00 0.00 0.00 4.46
2887 3148 1.855213 TAAGTGTCGTCGTGGGTCCG 61.855 60.000 0.00 0.00 0.00 4.79
2888 3149 3.663176 GTGTCGTCGTGGGTCCGA 61.663 66.667 0.00 0.00 33.79 4.55
2893 3154 2.126580 GTCGTGGGTCCGACGAAG 60.127 66.667 27.84 1.00 46.71 3.79
2900 3165 0.108756 GGGTCCGACGAAGGAAGAAG 60.109 60.000 0.00 0.00 42.77 2.85
2909 3174 1.727335 CGAAGGAAGAAGTTTCGGAGC 59.273 52.381 0.00 0.00 39.82 4.70
2915 3180 2.317530 AGAAGTTTCGGAGCTATGGC 57.682 50.000 0.00 0.00 39.06 4.40
2947 3212 5.542779 CCAAGTAGTTCTTCTAGCTGTGTT 58.457 41.667 0.00 0.00 33.63 3.32
2966 3231 4.748102 GTGTTAAGGTGATGAACTGACGAA 59.252 41.667 0.00 0.00 0.00 3.85
3019 3284 2.662156 GGCGTCGCTGTAAGATATAAGC 59.338 50.000 18.11 0.00 34.07 3.09
3025 3290 5.631512 GTCGCTGTAAGATATAAGCAAGGAG 59.368 44.000 0.00 0.00 34.07 3.69
3055 3320 7.398332 AGAAATAAGAGCTCCATGTTTCCATTT 59.602 33.333 23.76 11.68 0.00 2.32
3057 3322 3.771216 AGAGCTCCATGTTTCCATTTGT 58.229 40.909 10.93 0.00 0.00 2.83
3058 3323 3.508793 AGAGCTCCATGTTTCCATTTGTG 59.491 43.478 10.93 0.00 0.00 3.33
3059 3324 2.028748 AGCTCCATGTTTCCATTTGTGC 60.029 45.455 0.00 0.00 0.00 4.57
3060 3325 2.028748 GCTCCATGTTTCCATTTGTGCT 60.029 45.455 0.00 0.00 0.00 4.40
3061 3326 3.555586 GCTCCATGTTTCCATTTGTGCTT 60.556 43.478 0.00 0.00 0.00 3.91
3062 3327 4.321899 GCTCCATGTTTCCATTTGTGCTTA 60.322 41.667 0.00 0.00 0.00 3.09
3063 3328 5.782047 CTCCATGTTTCCATTTGTGCTTAA 58.218 37.500 0.00 0.00 0.00 1.85
3064 3329 5.782047 TCCATGTTTCCATTTGTGCTTAAG 58.218 37.500 0.00 0.00 0.00 1.85
3065 3330 4.931002 CCATGTTTCCATTTGTGCTTAAGG 59.069 41.667 4.29 0.00 0.00 2.69
3066 3331 3.988819 TGTTTCCATTTGTGCTTAAGGC 58.011 40.909 4.29 0.00 42.22 4.35
3067 3332 3.640967 TGTTTCCATTTGTGCTTAAGGCT 59.359 39.130 4.29 0.00 42.39 4.58
3068 3333 4.100808 TGTTTCCATTTGTGCTTAAGGCTT 59.899 37.500 4.58 4.58 42.39 4.35
3069 3334 3.940209 TCCATTTGTGCTTAAGGCTTG 57.060 42.857 10.69 0.00 42.39 4.01
3070 3335 2.562298 TCCATTTGTGCTTAAGGCTTGG 59.438 45.455 10.69 3.83 42.39 3.61
3071 3336 2.562298 CCATTTGTGCTTAAGGCTTGGA 59.438 45.455 10.69 0.00 42.39 3.53
3082 3361 0.819582 AGGCTTGGATTGGATTTGCG 59.180 50.000 0.00 0.00 0.00 4.85
3106 3385 1.522668 TGCAATTCCACTTCGGTCAG 58.477 50.000 0.00 0.00 35.57 3.51
3107 3386 1.202758 TGCAATTCCACTTCGGTCAGT 60.203 47.619 0.00 0.00 35.57 3.41
3108 3387 1.464997 GCAATTCCACTTCGGTCAGTC 59.535 52.381 0.00 0.00 35.57 3.51
3109 3388 2.766313 CAATTCCACTTCGGTCAGTCA 58.234 47.619 0.00 0.00 35.57 3.41
3111 3390 2.455674 TTCCACTTCGGTCAGTCATG 57.544 50.000 0.00 0.00 35.57 3.07
3112 3391 1.338107 TCCACTTCGGTCAGTCATGT 58.662 50.000 0.00 0.00 35.57 3.21
3113 3392 1.000843 TCCACTTCGGTCAGTCATGTG 59.999 52.381 0.00 0.00 35.57 3.21
3114 3393 1.270305 CCACTTCGGTCAGTCATGTGT 60.270 52.381 0.00 0.00 0.00 3.72
3115 3394 2.029380 CCACTTCGGTCAGTCATGTGTA 60.029 50.000 0.00 0.00 0.00 2.90
3117 3396 2.251040 CTTCGGTCAGTCATGTGTACG 58.749 52.381 0.00 0.00 0.00 3.67
3118 3397 0.109458 TCGGTCAGTCATGTGTACGC 60.109 55.000 0.00 0.00 0.00 4.42
3119 3398 0.388006 CGGTCAGTCATGTGTACGCA 60.388 55.000 12.26 12.26 0.00 5.24
3120 3399 1.068474 GGTCAGTCATGTGTACGCAC 58.932 55.000 12.10 0.00 45.44 5.34
3148 3427 1.035139 ATCATCCCTTTTGGCATCGC 58.965 50.000 0.00 0.00 38.58 4.58
3160 3439 2.697425 CATCGCTCGGTTGCTTCG 59.303 61.111 0.00 0.00 0.00 3.79
3176 3455 2.640184 CTTCGTGAATAAGGAACCCCC 58.360 52.381 0.00 0.00 0.00 5.40
3177 3456 1.659022 TCGTGAATAAGGAACCCCCA 58.341 50.000 0.00 0.00 37.41 4.96
3243 3530 3.496331 CTTGGGCTTTTCCTCCTTGTTA 58.504 45.455 0.00 0.00 34.39 2.41
3249 3536 5.470368 GGCTTTTCCTCCTTGTTACATTTC 58.530 41.667 0.00 0.00 0.00 2.17
3256 3547 7.038154 TCCTCCTTGTTACATTTCTGTTTTG 57.962 36.000 0.00 0.00 36.79 2.44
3281 3572 9.281371 TGGAATTATTTTTGCATGTGAAATTGA 57.719 25.926 0.00 0.00 0.00 2.57
3291 3582 4.728882 GCATGTGAAATTGATCGAGTGTCC 60.729 45.833 0.00 0.00 0.00 4.02
3308 3609 6.453791 CGAGTGTCCGTGATTAATTACACTTG 60.454 42.308 10.60 13.20 45.46 3.16
3309 3610 5.642063 AGTGTCCGTGATTAATTACACTTGG 59.358 40.000 10.60 3.97 43.63 3.61
3310 3611 4.938832 TGTCCGTGATTAATTACACTTGGG 59.061 41.667 10.60 3.65 35.23 4.12
3311 3612 5.180271 GTCCGTGATTAATTACACTTGGGA 58.820 41.667 10.60 5.71 35.23 4.37
3312 3613 5.293569 GTCCGTGATTAATTACACTTGGGAG 59.706 44.000 10.60 0.00 35.23 4.30
3323 3624 1.555533 CACTTGGGAGGGAGTAGGTTC 59.444 57.143 0.00 0.00 0.00 3.62
3324 3625 0.824759 CTTGGGAGGGAGTAGGTTCG 59.175 60.000 0.00 0.00 0.00 3.95
3329 3630 1.340795 GGAGGGAGTAGGTTCGACAGA 60.341 57.143 0.00 0.00 0.00 3.41
3332 3633 1.616456 GGGAGTAGGTTCGACAGAGGT 60.616 57.143 0.00 0.00 0.00 3.85
3335 3636 2.161030 AGTAGGTTCGACAGAGGTGAC 58.839 52.381 0.00 0.00 0.00 3.67
3344 3645 1.689273 GACAGAGGTGACTTGAGGTGT 59.311 52.381 0.00 0.00 44.43 4.16
3362 3663 1.152777 TTGGGTGCACTCCACTTGG 60.153 57.895 22.09 0.00 44.08 3.61
3389 3702 6.237835 CGCAAAAGTCTAATCATGTGACGTAT 60.238 38.462 0.00 0.00 36.01 3.06
3404 3717 5.636121 TGTGACGTATAGTTGCTTAACAAGG 59.364 40.000 0.00 0.00 39.50 3.61
3405 3718 5.063060 GTGACGTATAGTTGCTTAACAAGGG 59.937 44.000 0.00 0.00 39.50 3.95
3411 3724 1.339929 GTTGCTTAACAAGGGGGTGTG 59.660 52.381 0.00 0.00 39.50 3.82
3415 3728 0.250553 TTAACAAGGGGGTGTGCTCG 60.251 55.000 0.00 0.00 0.00 5.03
3423 3736 1.515521 GGGGTGTGCTCGGTTCTTTG 61.516 60.000 0.00 0.00 0.00 2.77
3449 3762 3.728076 TGTATAGCTGATGGTTCCGAC 57.272 47.619 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.598787 CGGGCCCCAGGAGTTTGTA 61.599 63.158 18.66 0.00 0.00 2.41
16 17 3.966543 CGGGCCCCAGGAGTTTGT 61.967 66.667 18.66 0.00 0.00 2.83
39 40 2.658707 GCTTGTGCGTCACGAGACC 61.659 63.158 23.20 9.10 45.84 3.85
52 53 2.658707 GCGCGACGAAGAAGCTTGT 61.659 57.895 12.10 0.00 0.00 3.16
95 96 4.398044 GGGTGATACTTATTTGTGGTGGTG 59.602 45.833 0.00 0.00 0.00 4.17
98 99 4.509616 TCGGGTGATACTTATTTGTGGTG 58.490 43.478 0.00 0.00 0.00 4.17
118 119 0.179166 CACCGAAATGCCACCATTCG 60.179 55.000 0.00 0.00 40.69 3.34
182 183 2.794910 GCAGATCAGCGCGTTATTAAGA 59.205 45.455 8.43 0.00 0.00 2.10
183 184 2.096713 GGCAGATCAGCGCGTTATTAAG 60.097 50.000 8.43 0.00 34.64 1.85
184 185 1.864711 GGCAGATCAGCGCGTTATTAA 59.135 47.619 8.43 0.00 34.64 1.40
229 231 2.203280 TTCACACCAAGGCACCGG 60.203 61.111 0.00 0.00 0.00 5.28
231 233 2.200337 GGGTTCACACCAAGGCACC 61.200 63.158 0.00 0.00 46.43 5.01
254 256 2.734606 TCGTATGAACAGCGGAAAGTTG 59.265 45.455 0.00 0.00 37.08 3.16
293 295 2.158986 TGATTTTGGTTGCAGTGTTGGG 60.159 45.455 0.00 0.00 0.00 4.12
294 296 2.865551 GTGATTTTGGTTGCAGTGTTGG 59.134 45.455 0.00 0.00 0.00 3.77
295 297 2.535166 CGTGATTTTGGTTGCAGTGTTG 59.465 45.455 0.00 0.00 0.00 3.33
296 298 2.425312 TCGTGATTTTGGTTGCAGTGTT 59.575 40.909 0.00 0.00 0.00 3.32
297 299 2.020720 TCGTGATTTTGGTTGCAGTGT 58.979 42.857 0.00 0.00 0.00 3.55
298 300 2.223456 TGTCGTGATTTTGGTTGCAGTG 60.223 45.455 0.00 0.00 0.00 3.66
299 301 2.020720 TGTCGTGATTTTGGTTGCAGT 58.979 42.857 0.00 0.00 0.00 4.40
300 302 2.772568 TGTCGTGATTTTGGTTGCAG 57.227 45.000 0.00 0.00 0.00 4.41
301 303 3.379240 CAATGTCGTGATTTTGGTTGCA 58.621 40.909 0.00 0.00 0.00 4.08
302 304 2.155539 GCAATGTCGTGATTTTGGTTGC 59.844 45.455 0.00 0.00 34.71 4.17
303 305 2.404693 CGCAATGTCGTGATTTTGGTTG 59.595 45.455 0.00 0.00 0.00 3.77
337 386 5.083533 TGGAAATGGCACCAATAATTGTC 57.916 39.130 0.00 0.00 32.93 3.18
339 388 5.341872 TCTGGAAATGGCACCAATAATTG 57.658 39.130 0.00 0.00 35.67 2.32
343 392 2.949963 GCCTCTGGAAATGGCACCAATA 60.950 50.000 0.00 0.00 45.46 1.90
344 393 1.856629 CCTCTGGAAATGGCACCAAT 58.143 50.000 0.00 0.00 35.67 3.16
345 394 0.899717 GCCTCTGGAAATGGCACCAA 60.900 55.000 0.00 0.00 45.46 3.67
389 461 2.045536 CACCCCTTCTGGCTGAGC 60.046 66.667 0.00 0.00 0.00 4.26
390 462 1.298014 GTCACCCCTTCTGGCTGAG 59.702 63.158 0.00 0.00 0.00 3.35
404 476 3.097728 CCGCGTCGTGTCTGTCAC 61.098 66.667 4.92 0.00 43.03 3.67
418 490 3.876589 TTTCACCTCACCTCGCCGC 62.877 63.158 0.00 0.00 0.00 6.53
419 491 2.027625 GTTTCACCTCACCTCGCCG 61.028 63.158 0.00 0.00 0.00 6.46
420 492 0.951040 CAGTTTCACCTCACCTCGCC 60.951 60.000 0.00 0.00 0.00 5.54
421 493 0.033504 TCAGTTTCACCTCACCTCGC 59.966 55.000 0.00 0.00 0.00 5.03
422 494 2.526304 TTCAGTTTCACCTCACCTCG 57.474 50.000 0.00 0.00 0.00 4.63
423 495 2.879026 GGTTTCAGTTTCACCTCACCTC 59.121 50.000 0.00 0.00 0.00 3.85
424 496 2.509964 AGGTTTCAGTTTCACCTCACCT 59.490 45.455 0.00 0.00 35.99 4.00
450 527 3.372676 CTCATGCGCAACGTCTGGC 62.373 63.158 17.11 0.00 0.00 4.85
470 547 4.770874 TGCGCTTTACGGCTCCCC 62.771 66.667 9.73 0.00 43.93 4.81
471 548 3.195698 CTGCGCTTTACGGCTCCC 61.196 66.667 9.73 0.00 43.93 4.30
472 549 3.865830 GCTGCGCTTTACGGCTCC 61.866 66.667 9.73 0.00 43.93 4.70
516 593 2.564771 GCCGGGTTAAGTATGGTAACC 58.435 52.381 2.18 5.02 46.65 2.85
534 611 3.493440 CCGCGTTTCTAACCGGCC 61.493 66.667 4.92 0.00 38.01 6.13
563 645 3.016203 CGGCGTGTTTGTTGTGCG 61.016 61.111 0.00 0.00 0.00 5.34
612 713 6.292114 GGGCGATTTGTTCAAAAGTGTAAAAG 60.292 38.462 2.11 0.00 0.00 2.27
620 727 1.000717 ACCGGGCGATTTGTTCAAAAG 60.001 47.619 6.32 1.90 0.00 2.27
631 738 0.458260 GGCAAAATTTACCGGGCGAT 59.542 50.000 6.32 0.00 0.00 4.58
654 775 4.350225 GGTTTATAAAGAGAGGGTAGGGGG 59.650 50.000 0.00 0.00 0.00 5.40
660 781 3.199289 CGGGTGGTTTATAAAGAGAGGGT 59.801 47.826 0.00 0.00 0.00 4.34
665 786 3.340034 TGTGCGGGTGGTTTATAAAGAG 58.660 45.455 0.00 0.00 0.00 2.85
690 811 0.681243 GATGTGGAGGTCAAAGGGGC 60.681 60.000 0.00 0.00 0.00 5.80
722 843 0.256177 GGAGGGGGAATGTCAAGGAC 59.744 60.000 0.00 0.00 0.00 3.85
723 844 0.919289 GGGAGGGGGAATGTCAAGGA 60.919 60.000 0.00 0.00 0.00 3.36
724 845 1.615262 GGGAGGGGGAATGTCAAGG 59.385 63.158 0.00 0.00 0.00 3.61
725 846 1.615262 GGGGAGGGGGAATGTCAAG 59.385 63.158 0.00 0.00 0.00 3.02
789 931 5.047590 TCTCACTCCTCACAAAGCGTATTTA 60.048 40.000 0.00 0.00 0.00 1.40
791 933 3.258372 TCTCACTCCTCACAAAGCGTATT 59.742 43.478 0.00 0.00 0.00 1.89
793 935 2.235891 TCTCACTCCTCACAAAGCGTA 58.764 47.619 0.00 0.00 0.00 4.42
795 937 2.064762 CTTCTCACTCCTCACAAAGCG 58.935 52.381 0.00 0.00 0.00 4.68
797 939 3.117491 TGCTTCTCACTCCTCACAAAG 57.883 47.619 0.00 0.00 0.00 2.77
837 1001 3.326385 TACCGGGTGATGGCTCCCT 62.326 63.158 10.66 0.00 44.10 4.20
838 1002 2.766651 TACCGGGTGATGGCTCCC 60.767 66.667 10.66 0.00 43.08 4.30
839 1003 2.504519 GTACCGGGTGATGGCTCC 59.495 66.667 10.66 0.00 0.00 4.70
840 1004 2.106332 CGTACCGGGTGATGGCTC 59.894 66.667 10.66 0.00 0.00 4.70
841 1005 2.682494 ACGTACCGGGTGATGGCT 60.682 61.111 10.66 0.00 0.00 4.75
842 1006 2.510691 CACGTACCGGGTGATGGC 60.511 66.667 10.66 0.00 37.60 4.40
852 1016 1.441738 AATTACGCCCAACACGTACC 58.558 50.000 0.00 0.00 44.95 3.34
919 1087 0.928229 CCCGAATATTATAGGCGCGC 59.072 55.000 25.94 25.94 0.00 6.86
988 1164 3.825611 CGCCATTTCCGCCCAAGG 61.826 66.667 0.00 0.00 0.00 3.61
1235 1414 0.954449 AAGAAGCGACGAGACGAGGA 60.954 55.000 0.00 0.00 35.09 3.71
1236 1415 0.794981 CAAGAAGCGACGAGACGAGG 60.795 60.000 0.00 0.00 35.09 4.63
1258 1437 1.543944 GGGATGCCAACCCAAACCAG 61.544 60.000 4.94 0.00 46.05 4.00
1287 1466 4.038271 ACCAATCAGATGCTTCCAAAGA 57.962 40.909 0.00 0.00 0.00 2.52
1304 1483 4.843728 AGACAGAGAGAAACAACAACCAA 58.156 39.130 0.00 0.00 0.00 3.67
1305 1484 4.162320 AGAGACAGAGAGAAACAACAACCA 59.838 41.667 0.00 0.00 0.00 3.67
1306 1485 4.509600 CAGAGACAGAGAGAAACAACAACC 59.490 45.833 0.00 0.00 0.00 3.77
1307 1486 4.025313 GCAGAGACAGAGAGAAACAACAAC 60.025 45.833 0.00 0.00 0.00 3.32
1550 1729 1.203505 TGGATGGGAGGAGGGTTAACA 60.204 52.381 8.10 0.00 0.00 2.41
1551 1730 1.212195 GTGGATGGGAGGAGGGTTAAC 59.788 57.143 0.00 0.00 0.00 2.01
1552 1731 1.591768 GTGGATGGGAGGAGGGTTAA 58.408 55.000 0.00 0.00 0.00 2.01
1553 1732 0.689745 CGTGGATGGGAGGAGGGTTA 60.690 60.000 0.00 0.00 0.00 2.85
1622 1801 4.778143 CCGACGGGCTTTGGGGAG 62.778 72.222 5.81 0.00 0.00 4.30
1729 1908 3.314388 GAAGCGCAAGAGTTGGCCG 62.314 63.158 11.47 0.00 43.02 6.13
1730 1909 2.563427 GAAGCGCAAGAGTTGGCC 59.437 61.111 11.47 0.00 43.02 5.36
1731 1910 2.117941 AACGAAGCGCAAGAGTTGGC 62.118 55.000 11.47 0.00 43.02 4.52
1733 1912 1.261619 AGAAACGAAGCGCAAGAGTTG 59.738 47.619 11.47 0.00 43.02 3.16
1735 1914 1.140816 GAGAAACGAAGCGCAAGAGT 58.859 50.000 11.47 0.26 43.02 3.24
1738 1917 4.706233 CGAGAAACGAAGCGCAAG 57.294 55.556 11.47 2.09 45.77 4.01
1755 1934 3.385577 GTCAGAGAATAATCACTCCGGC 58.614 50.000 0.00 0.00 34.13 6.13
1757 1936 4.294416 ACGTCAGAGAATAATCACTCCG 57.706 45.455 0.00 0.00 34.13 4.63
1759 1938 7.352719 ACAAAACGTCAGAGAATAATCACTC 57.647 36.000 0.00 0.00 0.00 3.51
1760 1939 8.873830 CATACAAAACGTCAGAGAATAATCACT 58.126 33.333 0.00 0.00 0.00 3.41
1761 1940 8.116753 CCATACAAAACGTCAGAGAATAATCAC 58.883 37.037 0.00 0.00 0.00 3.06
1762 1941 7.822334 ACCATACAAAACGTCAGAGAATAATCA 59.178 33.333 0.00 0.00 0.00 2.57
1787 1966 3.146847 AGATGGAACTGAAACCCGAAAC 58.853 45.455 0.00 0.00 0.00 2.78
2118 2300 0.114168 TTTTGGGGGACATGACAGGG 59.886 55.000 0.00 0.00 0.00 4.45
2143 2326 5.065731 CAGAGCCACAGGATTTTTAGCTAAG 59.934 44.000 6.24 0.00 0.00 2.18
2163 2346 4.527583 GCCTGAGGCCGAGCAGAG 62.528 72.222 13.77 13.16 44.06 3.35
2289 2487 5.049818 CGTAATCAGAAGGGATTGATTGCTC 60.050 44.000 9.33 1.49 42.35 4.26
2307 2505 0.996462 TTGCTAGTGCGTGCGTAATC 59.004 50.000 0.00 0.00 43.34 1.75
2353 2551 4.163268 TCATTGACGGATCTTCATAACCCA 59.837 41.667 0.00 0.00 0.00 4.51
2378 2576 5.064198 ACAAAGAAACGAGTTCGAAATGTCA 59.936 36.000 1.32 0.00 41.52 3.58
2379 2577 5.392585 CACAAAGAAACGAGTTCGAAATGTC 59.607 40.000 1.32 0.00 41.52 3.06
2380 2578 5.163794 ACACAAAGAAACGAGTTCGAAATGT 60.164 36.000 1.32 0.00 41.52 2.71
2381 2579 5.263185 ACACAAAGAAACGAGTTCGAAATG 58.737 37.500 1.32 0.00 41.52 2.32
2401 2606 3.106407 GCGCGTCTGTGAGGACAC 61.106 66.667 8.43 0.00 46.09 3.67
2402 2607 3.295273 AGCGCGTCTGTGAGGACA 61.295 61.111 8.43 0.00 36.12 4.02
2403 2608 2.807045 CAGCGCGTCTGTGAGGAC 60.807 66.667 18.43 0.00 38.02 3.85
2404 2609 4.056125 CCAGCGCGTCTGTGAGGA 62.056 66.667 22.70 0.00 41.25 3.71
2405 2610 4.363990 ACCAGCGCGTCTGTGAGG 62.364 66.667 22.70 13.59 41.25 3.86
2439 2644 3.123620 CTTCTGGCTCGCCTGCAC 61.124 66.667 9.65 0.00 36.94 4.57
2620 2847 7.392494 ACCATCGATGATGATAGTAATACGT 57.608 36.000 26.86 7.59 42.09 3.57
2621 2848 9.439537 CTAACCATCGATGATGATAGTAATACG 57.560 37.037 26.86 6.95 42.09 3.06
2622 2849 9.239002 GCTAACCATCGATGATGATAGTAATAC 57.761 37.037 26.86 6.34 42.09 1.89
2625 2852 6.322491 CGCTAACCATCGATGATGATAGTAA 58.678 40.000 26.86 1.04 42.09 2.24
2628 2855 3.549471 GCGCTAACCATCGATGATGATAG 59.451 47.826 26.86 20.06 42.09 2.08
2631 2858 1.341209 AGCGCTAACCATCGATGATGA 59.659 47.619 26.86 0.69 42.09 2.92
2635 2862 1.000163 ACCTAGCGCTAACCATCGATG 60.000 52.381 19.37 18.76 0.00 3.84
2728 2980 2.543777 ATATATCACCCACACGCACC 57.456 50.000 0.00 0.00 0.00 5.01
2732 2984 7.504924 AAATAACCAATATATCACCCACACG 57.495 36.000 0.00 0.00 0.00 4.49
2733 2985 8.141268 CCAAAATAACCAATATATCACCCACAC 58.859 37.037 0.00 0.00 0.00 3.82
2734 2986 7.288852 CCCAAAATAACCAATATATCACCCACA 59.711 37.037 0.00 0.00 0.00 4.17
2735 2987 7.256154 CCCCAAAATAACCAATATATCACCCAC 60.256 40.741 0.00 0.00 0.00 4.61
2736 2988 6.784969 CCCCAAAATAACCAATATATCACCCA 59.215 38.462 0.00 0.00 0.00 4.51
2737 2989 6.212589 CCCCCAAAATAACCAATATATCACCC 59.787 42.308 0.00 0.00 0.00 4.61
2760 3012 3.268103 ATCCAGCACCAACCGTCCC 62.268 63.158 0.00 0.00 0.00 4.46
2773 3025 1.990327 TCCATCCATCCATCCATCCAG 59.010 52.381 0.00 0.00 0.00 3.86
2781 3037 2.140138 TCGGCGTCCATCCATCCAT 61.140 57.895 6.85 0.00 0.00 3.41
2782 3038 2.762043 TCGGCGTCCATCCATCCA 60.762 61.111 6.85 0.00 0.00 3.41
2784 3040 2.658593 CGTCGGCGTCCATCCATC 60.659 66.667 6.85 0.00 0.00 3.51
2785 3041 3.138930 CTCGTCGGCGTCCATCCAT 62.139 63.158 10.18 0.00 39.49 3.41
2786 3042 3.822192 CTCGTCGGCGTCCATCCA 61.822 66.667 10.18 0.00 39.49 3.41
2788 3044 3.982372 TTGCTCGTCGGCGTCCATC 62.982 63.158 10.18 0.00 39.49 3.51
2789 3045 3.583276 TTTGCTCGTCGGCGTCCAT 62.583 57.895 10.18 0.00 39.49 3.41
2790 3046 4.287781 TTTGCTCGTCGGCGTCCA 62.288 61.111 10.18 4.83 39.49 4.02
2791 3047 3.774702 GTTTGCTCGTCGGCGTCC 61.775 66.667 10.18 1.73 39.49 4.79
2792 3048 2.591311 TTGTTTGCTCGTCGGCGTC 61.591 57.895 10.18 3.09 39.49 5.19
2793 3049 2.586635 TTGTTTGCTCGTCGGCGT 60.587 55.556 10.18 0.00 39.49 5.68
2794 3050 2.127758 GTTGTTTGCTCGTCGGCG 60.128 61.111 1.15 1.15 39.92 6.46
2795 3051 2.127758 CGTTGTTTGCTCGTCGGC 60.128 61.111 0.00 0.00 0.00 5.54
2796 3052 1.886861 CTCCGTTGTTTGCTCGTCGG 61.887 60.000 0.00 0.00 39.40 4.79
2797 3053 1.487231 CTCCGTTGTTTGCTCGTCG 59.513 57.895 0.00 0.00 0.00 5.12
2798 3054 0.599204 TCCTCCGTTGTTTGCTCGTC 60.599 55.000 0.00 0.00 0.00 4.20
2799 3055 0.600255 CTCCTCCGTTGTTTGCTCGT 60.600 55.000 0.00 0.00 0.00 4.18
2800 3056 0.319555 TCTCCTCCGTTGTTTGCTCG 60.320 55.000 0.00 0.00 0.00 5.03
2801 3057 1.878953 TTCTCCTCCGTTGTTTGCTC 58.121 50.000 0.00 0.00 0.00 4.26
2802 3058 1.947456 GTTTCTCCTCCGTTGTTTGCT 59.053 47.619 0.00 0.00 0.00 3.91
2803 3059 1.673920 TGTTTCTCCTCCGTTGTTTGC 59.326 47.619 0.00 0.00 0.00 3.68
2804 3060 4.364415 TTTGTTTCTCCTCCGTTGTTTG 57.636 40.909 0.00 0.00 0.00 2.93
2805 3061 5.451381 GGATTTTGTTTCTCCTCCGTTGTTT 60.451 40.000 0.00 0.00 0.00 2.83
2878 3139 2.814183 CTTCCTTCGTCGGACCCACG 62.814 65.000 5.14 5.14 38.67 4.94
2881 3142 0.108756 CTTCTTCCTTCGTCGGACCC 60.109 60.000 1.91 0.00 31.44 4.46
2882 3143 0.602060 ACTTCTTCCTTCGTCGGACC 59.398 55.000 1.91 0.00 31.44 4.46
2883 3144 2.435533 AACTTCTTCCTTCGTCGGAC 57.564 50.000 0.00 0.00 31.44 4.79
2884 3145 2.606308 CGAAACTTCTTCCTTCGTCGGA 60.606 50.000 0.00 0.00 37.70 4.55
2885 3146 1.719780 CGAAACTTCTTCCTTCGTCGG 59.280 52.381 0.00 0.00 37.70 4.79
2887 3148 2.987821 CTCCGAAACTTCTTCCTTCGTC 59.012 50.000 3.15 0.00 40.17 4.20
2888 3149 2.866855 GCTCCGAAACTTCTTCCTTCGT 60.867 50.000 3.15 0.00 40.17 3.85
2889 3150 1.727335 GCTCCGAAACTTCTTCCTTCG 59.273 52.381 0.00 0.00 41.18 3.79
2890 3151 3.046968 AGCTCCGAAACTTCTTCCTTC 57.953 47.619 0.00 0.00 0.00 3.46
2891 3152 4.508662 CATAGCTCCGAAACTTCTTCCTT 58.491 43.478 0.00 0.00 0.00 3.36
2892 3153 3.118592 CCATAGCTCCGAAACTTCTTCCT 60.119 47.826 0.00 0.00 0.00 3.36
2893 3154 3.198872 CCATAGCTCCGAAACTTCTTCC 58.801 50.000 0.00 0.00 0.00 3.46
2900 3165 1.521681 AGCGCCATAGCTCCGAAAC 60.522 57.895 2.29 0.00 45.67 2.78
2925 3190 7.329717 CCTTAACACAGCTAGAAGAACTACTTG 59.670 40.741 0.00 0.00 39.13 3.16
2947 3212 5.661056 ATCTTCGTCAGTTCATCACCTTA 57.339 39.130 0.00 0.00 0.00 2.69
2966 3231 3.139077 GCCGACGATATTTTCCCAATCT 58.861 45.455 0.00 0.00 0.00 2.40
3019 3284 5.588246 GGAGCTCTTATTTCTTTCCTCCTTG 59.412 44.000 14.64 0.00 35.80 3.61
3025 3290 6.765915 AACATGGAGCTCTTATTTCTTTCC 57.234 37.500 14.64 0.00 0.00 3.13
3058 3323 4.436332 CAAATCCAATCCAAGCCTTAAGC 58.564 43.478 0.00 0.00 44.25 3.09
3059 3324 4.436332 GCAAATCCAATCCAAGCCTTAAG 58.564 43.478 0.00 0.00 0.00 1.85
3060 3325 3.119173 CGCAAATCCAATCCAAGCCTTAA 60.119 43.478 0.00 0.00 0.00 1.85
3061 3326 2.426738 CGCAAATCCAATCCAAGCCTTA 59.573 45.455 0.00 0.00 0.00 2.69
3062 3327 1.205417 CGCAAATCCAATCCAAGCCTT 59.795 47.619 0.00 0.00 0.00 4.35
3063 3328 0.819582 CGCAAATCCAATCCAAGCCT 59.180 50.000 0.00 0.00 0.00 4.58
3064 3329 0.532115 ACGCAAATCCAATCCAAGCC 59.468 50.000 0.00 0.00 0.00 4.35
3065 3330 1.994779 CAACGCAAATCCAATCCAAGC 59.005 47.619 0.00 0.00 0.00 4.01
3066 3331 3.302365 ACAACGCAAATCCAATCCAAG 57.698 42.857 0.00 0.00 0.00 3.61
3067 3332 3.388308 CAACAACGCAAATCCAATCCAA 58.612 40.909 0.00 0.00 0.00 3.53
3068 3333 2.865670 GCAACAACGCAAATCCAATCCA 60.866 45.455 0.00 0.00 0.00 3.41
3069 3334 1.726248 GCAACAACGCAAATCCAATCC 59.274 47.619 0.00 0.00 0.00 3.01
3070 3335 2.402305 TGCAACAACGCAAATCCAATC 58.598 42.857 0.00 0.00 39.45 2.67
3071 3336 2.522836 TGCAACAACGCAAATCCAAT 57.477 40.000 0.00 0.00 39.45 3.16
3082 3361 2.223711 ACCGAAGTGGAATTGCAACAAC 60.224 45.455 0.00 0.00 42.00 3.32
3114 3393 2.287970 GGATGATGATGGTACGTGCGTA 60.288 50.000 0.00 0.00 0.00 4.42
3115 3394 1.538204 GGATGATGATGGTACGTGCGT 60.538 52.381 0.00 2.05 0.00 5.24
3117 3396 1.070758 AGGGATGATGATGGTACGTGC 59.929 52.381 0.00 0.00 0.00 5.34
3118 3397 3.475566 AAGGGATGATGATGGTACGTG 57.524 47.619 0.00 0.00 0.00 4.49
3119 3398 4.199310 CAAAAGGGATGATGATGGTACGT 58.801 43.478 0.00 0.00 0.00 3.57
3120 3399 3.565482 CCAAAAGGGATGATGATGGTACG 59.435 47.826 0.00 0.00 40.01 3.67
3121 3400 3.319122 GCCAAAAGGGATGATGATGGTAC 59.681 47.826 0.00 0.00 40.01 3.34
3122 3401 3.053019 TGCCAAAAGGGATGATGATGGTA 60.053 43.478 0.00 0.00 40.01 3.25
3123 3402 2.292389 TGCCAAAAGGGATGATGATGGT 60.292 45.455 0.00 0.00 40.01 3.55
3124 3403 2.390696 TGCCAAAAGGGATGATGATGG 58.609 47.619 0.00 0.00 40.01 3.51
3125 3404 3.305131 CGATGCCAAAAGGGATGATGATG 60.305 47.826 0.00 0.00 40.01 3.07
3126 3405 2.889045 CGATGCCAAAAGGGATGATGAT 59.111 45.455 0.00 0.00 40.01 2.45
3127 3406 2.300433 CGATGCCAAAAGGGATGATGA 58.700 47.619 0.00 0.00 40.01 2.92
3128 3407 1.269413 GCGATGCCAAAAGGGATGATG 60.269 52.381 0.00 0.00 40.01 3.07
3148 3427 2.348666 CCTTATTCACGAAGCAACCGAG 59.651 50.000 0.00 0.00 0.00 4.63
3160 3439 3.953542 AGATGGGGGTTCCTTATTCAC 57.046 47.619 0.00 0.00 36.20 3.18
3243 3530 9.949174 GCAAAAATAATTCCAAAACAGAAATGT 57.051 25.926 0.00 0.00 0.00 2.71
3249 3536 8.557864 TCACATGCAAAAATAATTCCAAAACAG 58.442 29.630 0.00 0.00 0.00 3.16
3281 3572 5.747197 GTGTAATTAATCACGGACACTCGAT 59.253 40.000 0.00 0.00 35.44 3.59
3282 3573 5.097529 GTGTAATTAATCACGGACACTCGA 58.902 41.667 0.00 0.00 35.44 4.04
3291 3582 4.574828 CCCTCCCAAGTGTAATTAATCACG 59.425 45.833 2.58 0.00 39.25 4.35
3308 3609 0.324091 TGTCGAACCTACTCCCTCCC 60.324 60.000 0.00 0.00 0.00 4.30
3309 3610 1.104630 CTGTCGAACCTACTCCCTCC 58.895 60.000 0.00 0.00 0.00 4.30
3310 3611 2.018515 CTCTGTCGAACCTACTCCCTC 58.981 57.143 0.00 0.00 0.00 4.30
3311 3612 1.341187 CCTCTGTCGAACCTACTCCCT 60.341 57.143 0.00 0.00 0.00 4.20
3312 3613 1.104630 CCTCTGTCGAACCTACTCCC 58.895 60.000 0.00 0.00 0.00 4.30
3323 3624 0.962489 ACCTCAAGTCACCTCTGTCG 59.038 55.000 0.00 0.00 0.00 4.35
3324 3625 1.689273 ACACCTCAAGTCACCTCTGTC 59.311 52.381 0.00 0.00 0.00 3.51
3329 3630 0.474184 CCCAACACCTCAAGTCACCT 59.526 55.000 0.00 0.00 0.00 4.00
3332 3633 0.465460 GCACCCAACACCTCAAGTCA 60.465 55.000 0.00 0.00 0.00 3.41
3335 3636 0.466189 AGTGCACCCAACACCTCAAG 60.466 55.000 14.63 0.00 38.87 3.02
3336 3637 0.465460 GAGTGCACCCAACACCTCAA 60.465 55.000 14.63 0.00 38.87 3.02
3344 3645 1.152777 CCAAGTGGAGTGCACCCAA 60.153 57.895 23.40 0.00 37.39 4.12
3362 3663 3.126858 TCACATGATTAGACTTTTGCGCC 59.873 43.478 4.18 0.00 0.00 6.53
3389 3702 2.444010 ACACCCCCTTGTTAAGCAACTA 59.556 45.455 0.00 0.00 35.56 2.24
3404 3717 1.228154 AAAGAACCGAGCACACCCC 60.228 57.895 0.00 0.00 0.00 4.95
3405 3718 0.818040 ACAAAGAACCGAGCACACCC 60.818 55.000 0.00 0.00 0.00 4.61
3411 3724 6.905609 GCTATACAATTAACAAAGAACCGAGC 59.094 38.462 0.00 0.00 0.00 5.03
3415 3728 9.722056 CATCAGCTATACAATTAACAAAGAACC 57.278 33.333 0.00 0.00 0.00 3.62
3423 3736 6.704493 TCGGAACCATCAGCTATACAATTAAC 59.296 38.462 0.00 0.00 0.00 2.01
3449 3762 0.463833 GGATGGCCCGTTAACTCCAG 60.464 60.000 0.00 0.00 31.36 3.86
3476 3789 1.383523 GCCGGGGAAGAAGATTCTTG 58.616 55.000 12.38 0.00 46.84 3.02


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

AutoCloner maintained by Alex Coulton.