Multiple sequence alignment - TraesCS5A01G219300

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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 TraesCS5A01G219300 chr5A 100.000 2608 0 0 1 2608 436336201 436338808 0.000000e+00 4817.0
1 TraesCS5A01G219300 chr5A 84.825 1028 114 27 708 1720 436352921 436353921 0.000000e+00 996.0
2 TraesCS5A01G219300 chr5A 81.165 1030 129 33 691 1705 436374226 436375205 0.000000e+00 767.0
3 TraesCS5A01G219300 chr5A 90.529 454 40 1 1253 1706 436328994 436328544 4.800000e-167 597.0
4 TraesCS5A01G219300 chr5D 88.546 1004 84 18 694 1687 335060579 335061561 0.000000e+00 1188.0
5 TraesCS5A01G219300 chr5D 81.250 1040 108 39 691 1705 335083800 335084777 0.000000e+00 760.0
6 TraesCS5A01G219300 chr5D 88.110 656 45 10 1966 2607 335062207 335062843 0.000000e+00 749.0
7 TraesCS5A01G219300 chr5D 90.744 497 39 3 1253 1749 335087486 335087975 0.000000e+00 656.0
8 TraesCS5A01G219300 chr5D 89.934 457 42 2 1258 1714 334990597 334990145 1.040000e-163 586.0
9 TraesCS5A01G219300 chr5D 89.407 472 39 6 1253 1717 335121615 335122082 3.740000e-163 584.0
10 TraesCS5A01G219300 chr5D 87.821 468 40 10 2149 2608 335089377 335089835 1.370000e-147 532.0
11 TraesCS5A01G219300 chr5D 82.988 482 55 15 691 1172 335121163 335121617 6.720000e-111 411.0
12 TraesCS5A01G219300 chr5D 92.982 228 13 3 1746 1970 335062046 335062273 1.930000e-86 329.0
13 TraesCS5A01G219300 chr5D 90.435 230 16 4 1746 1970 335088001 335088229 5.460000e-77 298.0
14 TraesCS5A01G219300 chr5D 90.909 198 14 2 1966 2163 335088163 335088356 1.990000e-66 263.0
15 TraesCS5A01G219300 chr7A 84.293 1025 112 18 707 1708 177344750 177343752 0.000000e+00 955.0
16 TraesCS5A01G219300 chr7D 83.616 1062 106 27 669 1704 175662224 175661205 0.000000e+00 935.0
17 TraesCS5A01G219300 chr7D 86.667 60 6 1 325 382 546240478 546240537 6.020000e-07 65.8
18 TraesCS5A01G219300 chr7D 100.000 28 0 0 80 107 43248081 43248108 5.000000e-03 52.8
19 TraesCS5A01G219300 chr7B 84.044 1009 93 26 694 1665 141009049 141008072 0.000000e+00 909.0
20 TraesCS5A01G219300 chr5B 79.918 488 52 23 691 1173 391866546 391866992 1.510000e-82 316.0
21 TraesCS5A01G219300 chr5B 82.965 317 49 5 2286 2601 391903110 391903422 5.500000e-72 281.0
22 TraesCS5A01G219300 chr5B 93.023 43 3 0 2072 2114 522620682 522620640 2.170000e-06 63.9
23 TraesCS5A01G219300 chr3B 80.180 111 18 4 2 109 630914123 630914232 2.150000e-11 80.5
24 TraesCS5A01G219300 chr6D 77.698 139 18 12 82 213 469821784 469821652 3.600000e-09 73.1
25 TraesCS5A01G219300 chr2B 82.500 80 9 5 318 393 142592176 142592098 6.020000e-07 65.8
26 TraesCS5A01G219300 chr3A 79.545 88 15 3 82 166 75389950 75389863 2.800000e-05 60.2
27 TraesCS5A01G219300 chr3D 100.000 29 0 0 78 106 404561741 404561769 1.000000e-03 54.7


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 TraesCS5A01G219300 chr5A 436336201 436338808 2607 False 4817.000000 4817 100.000000 1 2608 1 chr5A.!!$F1 2607
1 TraesCS5A01G219300 chr5A 436352921 436353921 1000 False 996.000000 996 84.825000 708 1720 1 chr5A.!!$F2 1012
2 TraesCS5A01G219300 chr5A 436374226 436375205 979 False 767.000000 767 81.165000 691 1705 1 chr5A.!!$F3 1014
3 TraesCS5A01G219300 chr5D 335060579 335062843 2264 False 755.333333 1188 89.879333 694 2607 3 chr5D.!!$F1 1913
4 TraesCS5A01G219300 chr5D 335083800 335089835 6035 False 501.800000 760 88.231800 691 2608 5 chr5D.!!$F2 1917
5 TraesCS5A01G219300 chr5D 335121163 335122082 919 False 497.500000 584 86.197500 691 1717 2 chr5D.!!$F3 1026
6 TraesCS5A01G219300 chr7A 177343752 177344750 998 True 955.000000 955 84.293000 707 1708 1 chr7A.!!$R1 1001
7 TraesCS5A01G219300 chr7D 175661205 175662224 1019 True 935.000000 935 83.616000 669 1704 1 chr7D.!!$R1 1035
8 TraesCS5A01G219300 chr7B 141008072 141009049 977 True 909.000000 909 84.044000 694 1665 1 chr7B.!!$R1 971

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
982 4283 0.033504 TTCTGTCCTTCGTGCACCTC 59.966 55.0 12.15 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 7386 0.391597 GCCATATTCGTCTTCCGGGA 59.608 55.0 0.0 0.0 37.11 5.14 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
141 142 2.853731 AAAATGTTCACGCGTTTGGA 57.146 40.000 10.22 0.00 0.00 3.53
142 143 2.853731 AAATGTTCACGCGTTTGGAA 57.146 40.000 10.22 7.87 0.00 3.53
143 144 2.853731 AATGTTCACGCGTTTGGAAA 57.146 40.000 10.22 2.32 0.00 3.13
144 145 2.853731 ATGTTCACGCGTTTGGAAAA 57.146 40.000 10.22 6.01 0.00 2.29
145 146 2.853731 TGTTCACGCGTTTGGAAAAT 57.146 40.000 10.22 0.00 0.00 1.82
146 147 3.965292 TGTTCACGCGTTTGGAAAATA 57.035 38.095 10.22 0.00 0.00 1.40
147 148 4.491234 TGTTCACGCGTTTGGAAAATAT 57.509 36.364 10.22 0.00 0.00 1.28
148 149 4.222886 TGTTCACGCGTTTGGAAAATATG 58.777 39.130 10.22 0.00 0.00 1.78
149 150 4.223659 GTTCACGCGTTTGGAAAATATGT 58.776 39.130 10.22 0.00 0.00 2.29
150 151 4.491234 TCACGCGTTTGGAAAATATGTT 57.509 36.364 10.22 0.00 0.00 2.71
151 152 4.861210 TCACGCGTTTGGAAAATATGTTT 58.139 34.783 10.22 0.00 0.00 2.83
152 153 4.912766 TCACGCGTTTGGAAAATATGTTTC 59.087 37.500 10.22 0.00 0.00 2.78
153 154 4.915085 CACGCGTTTGGAAAATATGTTTCT 59.085 37.500 10.22 0.00 0.00 2.52
154 155 4.915085 ACGCGTTTGGAAAATATGTTTCTG 59.085 37.500 5.58 0.00 0.00 3.02
155 156 5.150683 CGCGTTTGGAAAATATGTTTCTGA 58.849 37.500 0.00 0.00 0.00 3.27
156 157 5.627367 CGCGTTTGGAAAATATGTTTCTGAA 59.373 36.000 0.00 0.00 0.00 3.02
157 158 6.143118 CGCGTTTGGAAAATATGTTTCTGAAA 59.857 34.615 0.00 0.00 0.00 2.69
158 159 7.148820 CGCGTTTGGAAAATATGTTTCTGAAAT 60.149 33.333 6.06 0.00 0.00 2.17
159 160 8.495148 GCGTTTGGAAAATATGTTTCTGAAATT 58.505 29.630 6.06 0.44 0.00 1.82
257 258 8.891671 ATGTTTCAGCTTGTATTGAAAAATGT 57.108 26.923 2.70 0.00 42.86 2.71
258 259 8.715191 TGTTTCAGCTTGTATTGAAAAATGTT 57.285 26.923 1.66 0.00 42.86 2.71
259 260 9.160496 TGTTTCAGCTTGTATTGAAAAATGTTT 57.840 25.926 1.66 0.00 42.86 2.83
263 264 9.809096 TCAGCTTGTATTGAAAAATGTTTAACA 57.191 25.926 0.00 0.00 0.00 2.41
264 265 9.848172 CAGCTTGTATTGAAAAATGTTTAACAC 57.152 29.630 0.00 0.00 0.00 3.32
265 266 9.816354 AGCTTGTATTGAAAAATGTTTAACACT 57.184 25.926 0.00 0.00 0.00 3.55
381 382 9.499479 ACCAAAAATGCATAATGTGTATGAAAA 57.501 25.926 0.00 0.00 33.12 2.29
382 383 9.757859 CCAAAAATGCATAATGTGTATGAAAAC 57.242 29.630 0.00 0.00 33.12 2.43
385 386 9.709495 AAAATGCATAATGTGTATGAAAACAGT 57.291 25.926 0.00 0.00 33.12 3.55
386 387 9.709495 AAATGCATAATGTGTATGAAAACAGTT 57.291 25.926 0.00 0.00 33.12 3.16
389 390 9.225436 TGCATAATGTGTATGAAAACAGTTAGA 57.775 29.630 0.00 0.00 0.00 2.10
390 391 9.490663 GCATAATGTGTATGAAAACAGTTAGAC 57.509 33.333 0.00 0.00 0.00 2.59
394 395 8.846943 ATGTGTATGAAAACAGTTAGACATCA 57.153 30.769 0.00 0.00 0.00 3.07
395 396 8.669946 TGTGTATGAAAACAGTTAGACATCAA 57.330 30.769 0.00 0.00 0.00 2.57
396 397 9.114952 TGTGTATGAAAACAGTTAGACATCAAA 57.885 29.630 0.00 0.00 0.00 2.69
441 442 9.747898 ACCATGTAGTATTTGGAAAATGTTAGA 57.252 29.630 8.01 0.00 34.52 2.10
515 516 9.936759 AGAAATGTGTTTTGTTTAGAAAAAGGA 57.063 25.926 0.00 0.00 0.00 3.36
520 521 9.765795 TGTGTTTTGTTTAGAAAAAGGAAAAGA 57.234 25.926 0.00 0.00 0.00 2.52
566 567 9.990360 AAAGAAAACCAAAGTAAGAAACAAAGA 57.010 25.926 0.00 0.00 0.00 2.52
567 568 9.990360 AAGAAAACCAAAGTAAGAAACAAAGAA 57.010 25.926 0.00 0.00 0.00 2.52
568 569 9.990360 AGAAAACCAAAGTAAGAAACAAAGAAA 57.010 25.926 0.00 0.00 0.00 2.52
573 574 8.664798 ACCAAAGTAAGAAACAAAGAAAAATGC 58.335 29.630 0.00 0.00 0.00 3.56
574 575 8.122330 CCAAAGTAAGAAACAAAGAAAAATGCC 58.878 33.333 0.00 0.00 0.00 4.40
575 576 8.663911 CAAAGTAAGAAACAAAGAAAAATGCCA 58.336 29.630 0.00 0.00 0.00 4.92
576 577 8.785329 AAGTAAGAAACAAAGAAAAATGCCAA 57.215 26.923 0.00 0.00 0.00 4.52
577 578 8.785329 AGTAAGAAACAAAGAAAAATGCCAAA 57.215 26.923 0.00 0.00 0.00 3.28
578 579 8.882736 AGTAAGAAACAAAGAAAAATGCCAAAG 58.117 29.630 0.00 0.00 0.00 2.77
579 580 7.686438 AAGAAACAAAGAAAAATGCCAAAGT 57.314 28.000 0.00 0.00 0.00 2.66
580 581 7.686438 AGAAACAAAGAAAAATGCCAAAGTT 57.314 28.000 0.00 0.00 0.00 2.66
581 582 7.751732 AGAAACAAAGAAAAATGCCAAAGTTC 58.248 30.769 0.00 0.00 0.00 3.01
582 583 7.390162 AGAAACAAAGAAAAATGCCAAAGTTCA 59.610 29.630 0.00 0.00 0.00 3.18
583 584 6.667007 ACAAAGAAAAATGCCAAAGTTCAG 57.333 33.333 0.00 0.00 0.00 3.02
584 585 5.065090 ACAAAGAAAAATGCCAAAGTTCAGC 59.935 36.000 0.00 0.00 0.00 4.26
585 586 4.677673 AGAAAAATGCCAAAGTTCAGCT 57.322 36.364 0.00 0.00 0.00 4.24
586 587 5.027293 AGAAAAATGCCAAAGTTCAGCTT 57.973 34.783 0.00 0.00 39.52 3.74
587 588 5.052481 AGAAAAATGCCAAAGTTCAGCTTC 58.948 37.500 0.00 0.00 36.17 3.86
588 589 4.677673 AAAATGCCAAAGTTCAGCTTCT 57.322 36.364 0.00 0.00 36.17 2.85
589 590 3.655276 AATGCCAAAGTTCAGCTTCTG 57.345 42.857 0.00 0.00 36.17 3.02
590 591 1.321474 TGCCAAAGTTCAGCTTCTGG 58.679 50.000 0.00 0.00 36.17 3.86
591 592 1.322442 GCCAAAGTTCAGCTTCTGGT 58.678 50.000 0.00 0.00 36.17 4.00
592 593 1.268079 GCCAAAGTTCAGCTTCTGGTC 59.732 52.381 0.00 0.00 36.17 4.02
593 594 1.882623 CCAAAGTTCAGCTTCTGGTCC 59.117 52.381 0.00 0.00 36.17 4.46
594 595 2.575532 CAAAGTTCAGCTTCTGGTCCA 58.424 47.619 0.00 0.00 36.17 4.02
595 596 2.262423 AAGTTCAGCTTCTGGTCCAC 57.738 50.000 0.00 0.00 30.06 4.02
596 597 1.131638 AGTTCAGCTTCTGGTCCACA 58.868 50.000 0.00 0.00 31.51 4.17
597 598 1.202698 AGTTCAGCTTCTGGTCCACAC 60.203 52.381 0.00 0.00 31.51 3.82
598 599 0.249868 TTCAGCTTCTGGTCCACACG 60.250 55.000 0.00 0.00 31.51 4.49
599 600 1.112916 TCAGCTTCTGGTCCACACGA 61.113 55.000 0.00 0.00 31.51 4.35
600 601 0.668706 CAGCTTCTGGTCCACACGAG 60.669 60.000 0.00 0.00 0.00 4.18
601 602 2.029844 GCTTCTGGTCCACACGAGC 61.030 63.158 0.00 0.00 39.57 5.03
602 603 1.668294 CTTCTGGTCCACACGAGCT 59.332 57.895 0.00 0.00 39.84 4.09
603 604 0.034059 CTTCTGGTCCACACGAGCTT 59.966 55.000 0.00 0.00 39.84 3.74
604 605 1.272490 CTTCTGGTCCACACGAGCTTA 59.728 52.381 0.00 0.00 39.84 3.09
605 606 1.334160 TCTGGTCCACACGAGCTTAA 58.666 50.000 0.00 0.00 39.84 1.85
606 607 1.689813 TCTGGTCCACACGAGCTTAAA 59.310 47.619 0.00 0.00 39.84 1.52
607 608 2.103432 TCTGGTCCACACGAGCTTAAAA 59.897 45.455 0.00 0.00 39.84 1.52
608 609 2.875933 CTGGTCCACACGAGCTTAAAAA 59.124 45.455 0.00 0.00 39.84 1.94
627 628 1.308998 AAAAGCTTCTGGTCCACACG 58.691 50.000 0.00 0.00 0.00 4.49
628 629 0.180406 AAAGCTTCTGGTCCACACGT 59.820 50.000 0.00 0.00 0.00 4.49
629 630 0.532862 AAGCTTCTGGTCCACACGTG 60.533 55.000 15.48 15.48 0.00 4.49
630 631 2.607892 GCTTCTGGTCCACACGTGC 61.608 63.158 17.22 0.00 0.00 5.34
631 632 1.961277 CTTCTGGTCCACACGTGCC 60.961 63.158 17.22 9.35 0.00 5.01
632 633 2.383245 CTTCTGGTCCACACGTGCCT 62.383 60.000 17.22 0.00 0.00 4.75
633 634 2.357517 CTGGTCCACACGTGCCTC 60.358 66.667 17.22 3.76 0.00 4.70
634 635 2.842462 TGGTCCACACGTGCCTCT 60.842 61.111 17.22 0.00 0.00 3.69
635 636 2.383245 CTGGTCCACACGTGCCTCTT 62.383 60.000 17.22 0.00 0.00 2.85
636 637 1.227853 GGTCCACACGTGCCTCTTT 60.228 57.895 17.22 0.00 0.00 2.52
637 638 0.034337 GGTCCACACGTGCCTCTTTA 59.966 55.000 17.22 0.00 0.00 1.85
638 639 1.541670 GGTCCACACGTGCCTCTTTAA 60.542 52.381 17.22 0.00 0.00 1.52
639 640 1.798813 GTCCACACGTGCCTCTTTAAG 59.201 52.381 17.22 0.00 0.00 1.85
640 641 1.689813 TCCACACGTGCCTCTTTAAGA 59.310 47.619 17.22 0.00 0.00 2.10
641 642 2.301870 TCCACACGTGCCTCTTTAAGAT 59.698 45.455 17.22 0.00 0.00 2.40
642 643 2.673368 CCACACGTGCCTCTTTAAGATC 59.327 50.000 17.22 0.00 0.00 2.75
643 644 3.589988 CACACGTGCCTCTTTAAGATCT 58.410 45.455 17.22 0.00 0.00 2.75
644 645 3.369147 CACACGTGCCTCTTTAAGATCTG 59.631 47.826 17.22 0.00 0.00 2.90
645 646 3.006967 ACACGTGCCTCTTTAAGATCTGT 59.993 43.478 17.22 0.00 0.00 3.41
646 647 3.369147 CACGTGCCTCTTTAAGATCTGTG 59.631 47.826 0.82 0.00 0.00 3.66
647 648 2.349886 CGTGCCTCTTTAAGATCTGTGC 59.650 50.000 0.00 0.00 0.00 4.57
648 649 2.349886 GTGCCTCTTTAAGATCTGTGCG 59.650 50.000 0.00 0.00 0.00 5.34
649 650 2.028112 TGCCTCTTTAAGATCTGTGCGT 60.028 45.455 0.00 0.00 0.00 5.24
650 651 2.605366 GCCTCTTTAAGATCTGTGCGTC 59.395 50.000 0.00 0.00 0.00 5.19
651 652 2.854777 CCTCTTTAAGATCTGTGCGTCG 59.145 50.000 0.00 0.00 0.00 5.12
652 653 3.427638 CCTCTTTAAGATCTGTGCGTCGA 60.428 47.826 0.00 0.00 0.00 4.20
653 654 3.499048 TCTTTAAGATCTGTGCGTCGAC 58.501 45.455 5.18 5.18 0.00 4.20
654 655 3.057806 TCTTTAAGATCTGTGCGTCGACA 60.058 43.478 17.16 0.00 0.00 4.35
655 656 2.257974 TAAGATCTGTGCGTCGACAC 57.742 50.000 17.16 6.48 41.10 3.67
661 662 3.319904 GTGCGTCGACACAAGCTT 58.680 55.556 17.16 0.00 40.40 3.74
662 663 1.201825 GTGCGTCGACACAAGCTTC 59.798 57.895 17.16 5.04 40.40 3.86
663 664 1.954146 TGCGTCGACACAAGCTTCC 60.954 57.895 17.16 0.00 0.00 3.46
664 665 1.954146 GCGTCGACACAAGCTTCCA 60.954 57.895 17.16 0.00 0.00 3.53
665 666 1.495584 GCGTCGACACAAGCTTCCAA 61.496 55.000 17.16 0.00 0.00 3.53
666 667 0.232303 CGTCGACACAAGCTTCCAAC 59.768 55.000 17.16 0.00 0.00 3.77
667 668 1.583054 GTCGACACAAGCTTCCAACT 58.417 50.000 11.55 0.00 0.00 3.16
668 669 1.940613 GTCGACACAAGCTTCCAACTT 59.059 47.619 11.55 0.00 0.00 2.66
675 676 3.615849 CAAGCTTCCAACTTGTCTGTC 57.384 47.619 0.00 0.00 39.73 3.51
676 677 3.209410 CAAGCTTCCAACTTGTCTGTCT 58.791 45.455 0.00 0.00 39.73 3.41
677 678 2.843701 AGCTTCCAACTTGTCTGTCTG 58.156 47.619 0.00 0.00 0.00 3.51
678 679 1.265365 GCTTCCAACTTGTCTGTCTGC 59.735 52.381 0.00 0.00 0.00 4.26
679 680 2.564771 CTTCCAACTTGTCTGTCTGCA 58.435 47.619 0.00 0.00 0.00 4.41
729 737 2.202440 CGTCCGCGTACTCACTGG 60.202 66.667 4.92 0.00 0.00 4.00
730 738 2.960170 GTCCGCGTACTCACTGGT 59.040 61.111 4.92 0.00 0.00 4.00
766 4022 0.753262 ATAATTCACGGCCGAGAGCT 59.247 50.000 35.90 21.41 43.05 4.09
822 4082 1.675641 GCTCGTCATGGGTTGGCTT 60.676 57.895 0.00 0.00 0.00 4.35
852 4112 1.214424 ACGGCCTATAAATTGTGCCCT 59.786 47.619 0.00 0.00 38.92 5.19
858 4118 4.780815 CCTATAAATTGTGCCCTCTCACA 58.219 43.478 0.00 0.00 44.39 3.58
881 4158 6.483974 ACACGGAACAATACATCAGTAAACAA 59.516 34.615 0.00 0.00 33.13 2.83
882 4159 6.795114 CACGGAACAATACATCAGTAAACAAC 59.205 38.462 0.00 0.00 33.13 3.32
883 4160 6.483974 ACGGAACAATACATCAGTAAACAACA 59.516 34.615 0.00 0.00 33.13 3.33
899 4178 3.108289 CACTCGGCGACACAGCAG 61.108 66.667 4.99 0.00 39.27 4.24
904 4192 2.974698 GGCGACACAGCAGCAAGT 60.975 61.111 0.00 0.00 39.27 3.16
930 4221 3.963374 ACTCCACTAGCAATCATCTAGCA 59.037 43.478 0.00 0.00 37.60 3.49
932 4223 3.963374 TCCACTAGCAATCATCTAGCAGT 59.037 43.478 0.00 0.00 37.60 4.40
935 4226 5.587844 CCACTAGCAATCATCTAGCAGTTTT 59.412 40.000 0.00 0.00 37.60 2.43
936 4227 6.238320 CCACTAGCAATCATCTAGCAGTTTTC 60.238 42.308 0.00 0.00 37.60 2.29
965 4256 2.625737 TGCAGCATCTGTAGCTTCTTC 58.374 47.619 0.00 0.00 41.14 2.87
967 4258 2.608546 GCAGCATCTGTAGCTTCTTCTG 59.391 50.000 0.00 0.00 41.14 3.02
968 4259 3.859443 CAGCATCTGTAGCTTCTTCTGT 58.141 45.455 0.00 0.00 41.14 3.41
970 4261 3.118811 AGCATCTGTAGCTTCTTCTGTCC 60.119 47.826 0.00 0.00 39.87 4.02
982 4283 0.033504 TTCTGTCCTTCGTGCACCTC 59.966 55.000 12.15 0.00 0.00 3.85
984 4285 1.821061 CTGTCCTTCGTGCACCTCCT 61.821 60.000 12.15 0.00 0.00 3.69
991 4292 4.314440 GTGCACCTCCTGTCCGCA 62.314 66.667 5.22 0.00 0.00 5.69
1007 4318 0.870393 CGCAGCTGATTAATGGCGAT 59.130 50.000 20.43 0.00 46.65 4.58
1029 4340 0.627451 TGATGGCCATGAGCTCCTTT 59.373 50.000 26.56 0.00 43.05 3.11
1136 4450 4.742201 CGTCAGGGCACAGACCGG 62.742 72.222 5.85 0.00 34.63 5.28
1265 4615 4.385405 GCACAGGCGAGCACCTCT 62.385 66.667 0.00 0.00 38.26 3.69
1614 4973 6.349033 GCCCTTCATCAACGTGTAAAACTAAT 60.349 38.462 0.00 0.00 0.00 1.73
1634 4995 0.878961 AGCTTTGTTGTCGACCGGAC 60.879 55.000 9.46 9.78 46.27 4.79
1642 5003 2.680429 GTCGACCGGACAACACAAA 58.320 52.632 9.46 0.00 45.36 2.83
1653 5016 4.807304 CGGACAACACAAACTGTACTTAGT 59.193 41.667 0.00 0.00 30.51 2.24
1700 5067 8.239038 AGAACTGATCATCCTCGTATTCTTTA 57.761 34.615 0.00 0.00 0.00 1.85
1737 5503 7.539436 ACAGATACATAGTTCATATGCTACCG 58.461 38.462 0.00 0.00 44.50 4.02
1757 5552 2.630098 CGGGAGCTGAATTAGAGATGGA 59.370 50.000 0.00 0.00 0.00 3.41
1800 5595 6.471233 TGAAGGTACCTTGTCTCAGATATG 57.529 41.667 31.81 0.00 36.26 1.78
1866 5661 1.911357 CAGATAGGGGATGCATGGCTA 59.089 52.381 2.46 0.00 0.00 3.93
1895 5692 5.360591 GCATCCTAAATTTCGGAGAGAGAA 58.639 41.667 15.83 0.00 38.43 2.87
1896 5693 5.994668 GCATCCTAAATTTCGGAGAGAGAAT 59.005 40.000 15.83 0.00 38.43 2.40
1897 5694 6.147000 GCATCCTAAATTTCGGAGAGAGAATC 59.853 42.308 15.83 0.00 38.43 2.52
1934 5734 4.425577 CTCTTGTAGCATTCACCCAAAC 57.574 45.455 0.00 0.00 0.00 2.93
1939 5739 3.568007 TGTAGCATTCACCCAAACTTGAC 59.432 43.478 0.00 0.00 0.00 3.18
1944 5744 4.982295 GCATTCACCCAAACTTGACTTTAC 59.018 41.667 0.00 0.00 0.00 2.01
1945 5745 5.451242 GCATTCACCCAAACTTGACTTTACA 60.451 40.000 0.00 0.00 0.00 2.41
1946 5746 6.568869 CATTCACCCAAACTTGACTTTACAA 58.431 36.000 0.00 0.00 0.00 2.41
1947 5747 6.783708 TTCACCCAAACTTGACTTTACAAT 57.216 33.333 0.00 0.00 0.00 2.71
1948 5748 6.783708 TCACCCAAACTTGACTTTACAATT 57.216 33.333 0.00 0.00 0.00 2.32
1949 5749 7.883391 TCACCCAAACTTGACTTTACAATTA 57.117 32.000 0.00 0.00 0.00 1.40
1950 5750 8.294954 TCACCCAAACTTGACTTTACAATTAA 57.705 30.769 0.00 0.00 0.00 1.40
1951 5751 8.192110 TCACCCAAACTTGACTTTACAATTAAC 58.808 33.333 0.00 0.00 0.00 2.01
1952 5752 8.194769 CACCCAAACTTGACTTTACAATTAACT 58.805 33.333 0.00 0.00 0.00 2.24
1953 5753 9.411189 ACCCAAACTTGACTTTACAATTAACTA 57.589 29.630 0.00 0.00 0.00 2.24
1954 5754 9.893305 CCCAAACTTGACTTTACAATTAACTAG 57.107 33.333 0.00 0.00 0.00 2.57
1976 5776 9.367444 ACTAGTACAGTACATTTCATACTTTGC 57.633 33.333 13.37 0.00 34.98 3.68
1977 5777 9.587772 CTAGTACAGTACATTTCATACTTTGCT 57.412 33.333 13.37 0.00 32.35 3.91
1978 5778 8.480643 AGTACAGTACATTTCATACTTTGCTC 57.519 34.615 13.37 0.00 30.22 4.26
1979 5779 8.314751 AGTACAGTACATTTCATACTTTGCTCT 58.685 33.333 13.37 0.00 30.22 4.09
1980 5780 7.986085 ACAGTACATTTCATACTTTGCTCTT 57.014 32.000 0.00 0.00 30.22 2.85
1981 5781 7.810658 ACAGTACATTTCATACTTTGCTCTTG 58.189 34.615 0.00 0.00 30.22 3.02
1982 5782 7.445402 ACAGTACATTTCATACTTTGCTCTTGT 59.555 33.333 0.00 0.00 30.22 3.16
1983 5783 8.935844 CAGTACATTTCATACTTTGCTCTTGTA 58.064 33.333 0.00 0.00 30.22 2.41
1984 5784 9.155975 AGTACATTTCATACTTTGCTCTTGTAG 57.844 33.333 0.00 0.00 28.03 2.74
1996 5796 3.811722 CTCTTGTAGCATTCGCACAAA 57.188 42.857 0.00 0.00 42.27 2.83
1997 5797 3.482786 CTCTTGTAGCATTCGCACAAAC 58.517 45.455 0.00 0.00 42.27 2.93
1998 5798 3.138304 TCTTGTAGCATTCGCACAAACT 58.862 40.909 0.00 0.00 42.27 2.66
1999 5799 3.563808 TCTTGTAGCATTCGCACAAACTT 59.436 39.130 0.00 0.00 42.27 2.66
2000 5800 3.980646 TGTAGCATTCGCACAAACTTT 57.019 38.095 0.00 0.00 42.27 2.66
2001 5801 5.237561 TCTTGTAGCATTCGCACAAACTTTA 59.762 36.000 0.00 0.00 42.27 1.85
2009 5809 7.114811 AGCATTCGCACAAACTTTATTTTACAG 59.885 33.333 0.00 0.00 42.27 2.74
2038 5838 7.331026 ACTAGTACAGTACATTTCATGCACAT 58.669 34.615 13.37 0.00 34.98 3.21
2046 5846 7.329962 CAGTACATTTCATGCACATTGTGATTT 59.670 33.333 20.77 1.11 35.23 2.17
2047 5847 8.522003 AGTACATTTCATGCACATTGTGATTTA 58.478 29.630 20.77 3.75 35.23 1.40
2048 5848 7.821595 ACATTTCATGCACATTGTGATTTAG 57.178 32.000 20.77 5.13 35.23 1.85
2123 5923 9.299963 TGATAATTCAGATTTTTACGCCAAATG 57.700 29.630 0.00 0.00 0.00 2.32
2212 7053 0.249573 TCGGGATTACGAAATCGCCC 60.250 55.000 2.15 4.59 46.87 6.13
2341 7193 5.209818 ACGAATACAAGACTCAACAGGAA 57.790 39.130 0.00 0.00 0.00 3.36
2347 7199 9.436957 GAATACAAGACTCAACAGGAAGAATAA 57.563 33.333 0.00 0.00 0.00 1.40
2391 7243 8.585189 AAATATACGGAATCCTAAAAGACGAC 57.415 34.615 0.00 0.00 0.00 4.34
2427 7279 6.848562 ACCCTAGAAGACAAATATGGGATT 57.151 37.500 0.00 0.00 37.25 3.01
2428 7280 7.226059 ACCCTAGAAGACAAATATGGGATTT 57.774 36.000 0.00 0.00 37.25 2.17
2431 7283 7.779798 CCCTAGAAGACAAATATGGGATTTCAA 59.220 37.037 0.00 0.00 35.64 2.69
2485 7337 5.485353 TCGGAAGATGAATATAAGAGCCCAT 59.515 40.000 0.00 0.00 33.31 4.00
2519 7371 5.551305 ATGACCCAAGATGACGAATATGA 57.449 39.130 0.00 0.00 0.00 2.15
2534 7386 7.339721 TGACGAATATGAAACTCTAGAGGAAGT 59.660 37.037 23.50 5.64 0.00 3.01
2565 7417 0.923358 AATATGGCAACCCCGAGGAA 59.077 50.000 0.00 0.00 36.73 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 3.152261 TCCAAACGCGTGAACATTTTT 57.848 38.095 14.98 0.00 0.00 1.94
122 123 2.853731 TCCAAACGCGTGAACATTTT 57.146 40.000 14.98 0.00 0.00 1.82
123 124 2.853731 TTCCAAACGCGTGAACATTT 57.146 40.000 14.98 0.00 0.00 2.32
124 125 2.853731 TTTCCAAACGCGTGAACATT 57.146 40.000 14.98 0.00 0.00 2.71
125 126 2.853731 TTTTCCAAACGCGTGAACAT 57.146 40.000 14.98 0.00 0.00 2.71
126 127 2.853731 ATTTTCCAAACGCGTGAACA 57.146 40.000 14.98 5.75 0.00 3.18
127 128 4.223659 ACATATTTTCCAAACGCGTGAAC 58.776 39.130 14.98 0.00 0.00 3.18
128 129 4.491234 ACATATTTTCCAAACGCGTGAA 57.509 36.364 14.98 9.81 0.00 3.18
129 130 4.491234 AACATATTTTCCAAACGCGTGA 57.509 36.364 14.98 2.18 0.00 4.35
130 131 4.915085 AGAAACATATTTTCCAAACGCGTG 59.085 37.500 14.98 0.00 0.00 5.34
131 132 4.915085 CAGAAACATATTTTCCAAACGCGT 59.085 37.500 5.58 5.58 0.00 6.01
132 133 5.150683 TCAGAAACATATTTTCCAAACGCG 58.849 37.500 3.53 3.53 0.00 6.01
133 134 7.401484 TTTCAGAAACATATTTTCCAAACGC 57.599 32.000 0.00 0.00 0.00 4.84
231 232 9.328845 ACATTTTTCAATACAAGCTGAAACATT 57.671 25.926 0.00 0.00 40.36 2.71
232 233 8.891671 ACATTTTTCAATACAAGCTGAAACAT 57.108 26.923 0.00 0.00 40.36 2.71
233 234 8.715191 AACATTTTTCAATACAAGCTGAAACA 57.285 26.923 0.00 0.00 40.36 2.83
237 238 9.809096 TGTTAAACATTTTTCAATACAAGCTGA 57.191 25.926 0.00 0.00 0.00 4.26
238 239 9.848172 GTGTTAAACATTTTTCAATACAAGCTG 57.152 29.630 0.00 0.00 0.00 4.24
239 240 9.816354 AGTGTTAAACATTTTTCAATACAAGCT 57.184 25.926 0.00 0.00 0.00 3.74
355 356 9.499479 TTTTCATACACATTATGCATTTTTGGT 57.501 25.926 3.54 1.23 0.00 3.67
356 357 9.757859 GTTTTCATACACATTATGCATTTTTGG 57.242 29.630 3.54 0.00 0.00 3.28
359 360 9.709495 ACTGTTTTCATACACATTATGCATTTT 57.291 25.926 3.54 0.00 0.00 1.82
360 361 9.709495 AACTGTTTTCATACACATTATGCATTT 57.291 25.926 3.54 0.00 0.00 2.32
363 364 9.225436 TCTAACTGTTTTCATACACATTATGCA 57.775 29.630 0.00 0.00 0.00 3.96
364 365 9.490663 GTCTAACTGTTTTCATACACATTATGC 57.509 33.333 0.00 0.00 0.00 3.14
368 369 9.283768 TGATGTCTAACTGTTTTCATACACATT 57.716 29.630 0.00 0.00 0.00 2.71
369 370 8.846943 TGATGTCTAACTGTTTTCATACACAT 57.153 30.769 0.00 0.00 0.00 3.21
370 371 8.669946 TTGATGTCTAACTGTTTTCATACACA 57.330 30.769 0.00 0.00 0.00 3.72
415 416 9.747898 TCTAACATTTTCCAAATACTACATGGT 57.252 29.630 0.00 0.00 35.66 3.55
489 490 9.936759 TCCTTTTTCTAAACAAAACACATTTCT 57.063 25.926 0.00 0.00 0.00 2.52
494 495 9.765795 TCTTTTCCTTTTTCTAAACAAAACACA 57.234 25.926 0.00 0.00 0.00 3.72
540 541 9.990360 TCTTTGTTTCTTACTTTGGTTTTCTTT 57.010 25.926 0.00 0.00 0.00 2.52
541 542 9.990360 TTCTTTGTTTCTTACTTTGGTTTTCTT 57.010 25.926 0.00 0.00 0.00 2.52
542 543 9.990360 TTTCTTTGTTTCTTACTTTGGTTTTCT 57.010 25.926 0.00 0.00 0.00 2.52
547 548 8.664798 GCATTTTTCTTTGTTTCTTACTTTGGT 58.335 29.630 0.00 0.00 0.00 3.67
548 549 8.122330 GGCATTTTTCTTTGTTTCTTACTTTGG 58.878 33.333 0.00 0.00 0.00 3.28
549 550 8.663911 TGGCATTTTTCTTTGTTTCTTACTTTG 58.336 29.630 0.00 0.00 0.00 2.77
550 551 8.785329 TGGCATTTTTCTTTGTTTCTTACTTT 57.215 26.923 0.00 0.00 0.00 2.66
551 552 8.785329 TTGGCATTTTTCTTTGTTTCTTACTT 57.215 26.923 0.00 0.00 0.00 2.24
552 553 8.785329 TTTGGCATTTTTCTTTGTTTCTTACT 57.215 26.923 0.00 0.00 0.00 2.24
553 554 8.664798 ACTTTGGCATTTTTCTTTGTTTCTTAC 58.335 29.630 0.00 0.00 0.00 2.34
554 555 8.785329 ACTTTGGCATTTTTCTTTGTTTCTTA 57.215 26.923 0.00 0.00 0.00 2.10
555 556 7.686438 ACTTTGGCATTTTTCTTTGTTTCTT 57.314 28.000 0.00 0.00 0.00 2.52
556 557 7.390162 TGAACTTTGGCATTTTTCTTTGTTTCT 59.610 29.630 0.00 0.00 0.00 2.52
557 558 7.525759 TGAACTTTGGCATTTTTCTTTGTTTC 58.474 30.769 0.00 0.00 0.00 2.78
558 559 7.446001 TGAACTTTGGCATTTTTCTTTGTTT 57.554 28.000 0.00 0.00 0.00 2.83
559 560 6.403527 GCTGAACTTTGGCATTTTTCTTTGTT 60.404 34.615 0.00 0.00 0.00 2.83
560 561 5.065090 GCTGAACTTTGGCATTTTTCTTTGT 59.935 36.000 0.00 0.00 0.00 2.83
561 562 5.295045 AGCTGAACTTTGGCATTTTTCTTTG 59.705 36.000 0.00 0.00 0.00 2.77
562 563 5.430886 AGCTGAACTTTGGCATTTTTCTTT 58.569 33.333 0.00 0.00 0.00 2.52
563 564 5.027293 AGCTGAACTTTGGCATTTTTCTT 57.973 34.783 0.00 0.00 0.00 2.52
564 565 4.677673 AGCTGAACTTTGGCATTTTTCT 57.322 36.364 0.00 0.00 0.00 2.52
565 566 5.050567 CAGAAGCTGAACTTTGGCATTTTTC 60.051 40.000 0.00 0.00 39.29 2.29
566 567 4.812626 CAGAAGCTGAACTTTGGCATTTTT 59.187 37.500 0.00 0.00 39.29 1.94
567 568 4.374399 CAGAAGCTGAACTTTGGCATTTT 58.626 39.130 0.00 0.00 39.29 1.82
568 569 3.243975 CCAGAAGCTGAACTTTGGCATTT 60.244 43.478 0.00 0.00 39.29 2.32
569 570 2.298163 CCAGAAGCTGAACTTTGGCATT 59.702 45.455 0.00 0.00 39.29 3.56
570 571 1.891150 CCAGAAGCTGAACTTTGGCAT 59.109 47.619 0.00 0.00 39.29 4.40
571 572 1.321474 CCAGAAGCTGAACTTTGGCA 58.679 50.000 0.00 0.00 39.29 4.92
572 573 1.268079 GACCAGAAGCTGAACTTTGGC 59.732 52.381 0.00 0.00 39.29 4.52
573 574 1.882623 GGACCAGAAGCTGAACTTTGG 59.117 52.381 0.00 0.00 39.29 3.28
574 575 2.291741 GTGGACCAGAAGCTGAACTTTG 59.708 50.000 0.00 0.00 39.29 2.77
575 576 2.092429 TGTGGACCAGAAGCTGAACTTT 60.092 45.455 0.00 0.00 39.29 2.66
576 577 1.490490 TGTGGACCAGAAGCTGAACTT 59.510 47.619 0.00 0.00 42.98 2.66
577 578 1.131638 TGTGGACCAGAAGCTGAACT 58.868 50.000 0.00 0.00 32.44 3.01
578 579 1.230324 GTGTGGACCAGAAGCTGAAC 58.770 55.000 0.00 0.00 32.44 3.18
579 580 0.249868 CGTGTGGACCAGAAGCTGAA 60.250 55.000 0.00 0.00 32.44 3.02
580 581 1.112916 TCGTGTGGACCAGAAGCTGA 61.113 55.000 0.00 0.00 32.44 4.26
581 582 0.668706 CTCGTGTGGACCAGAAGCTG 60.669 60.000 0.00 0.00 0.00 4.24
582 583 1.668294 CTCGTGTGGACCAGAAGCT 59.332 57.895 0.00 0.00 0.00 3.74
583 584 2.029844 GCTCGTGTGGACCAGAAGC 61.030 63.158 0.00 0.00 0.00 3.86
584 585 0.034059 AAGCTCGTGTGGACCAGAAG 59.966 55.000 0.00 0.00 0.00 2.85
585 586 1.334160 TAAGCTCGTGTGGACCAGAA 58.666 50.000 0.00 0.00 0.00 3.02
586 587 1.334160 TTAAGCTCGTGTGGACCAGA 58.666 50.000 0.00 0.00 0.00 3.86
587 588 2.163818 TTTAAGCTCGTGTGGACCAG 57.836 50.000 0.00 0.00 0.00 4.00
588 589 2.623878 TTTTAAGCTCGTGTGGACCA 57.376 45.000 0.00 0.00 0.00 4.02
607 608 1.676006 CGTGTGGACCAGAAGCTTTTT 59.324 47.619 0.00 0.00 0.00 1.94
608 609 1.308998 CGTGTGGACCAGAAGCTTTT 58.691 50.000 0.00 0.00 0.00 2.27
609 610 0.180406 ACGTGTGGACCAGAAGCTTT 59.820 50.000 0.00 0.00 0.00 3.51
610 611 0.532862 CACGTGTGGACCAGAAGCTT 60.533 55.000 7.58 0.00 0.00 3.74
611 612 1.069765 CACGTGTGGACCAGAAGCT 59.930 57.895 7.58 0.00 0.00 3.74
612 613 2.607892 GCACGTGTGGACCAGAAGC 61.608 63.158 18.38 0.72 0.00 3.86
613 614 1.961277 GGCACGTGTGGACCAGAAG 60.961 63.158 18.38 2.92 0.00 2.85
614 615 2.110213 GGCACGTGTGGACCAGAA 59.890 61.111 18.38 0.00 0.00 3.02
615 616 2.842462 AGGCACGTGTGGACCAGA 60.842 61.111 18.38 0.00 0.00 3.86
616 617 2.357517 GAGGCACGTGTGGACCAG 60.358 66.667 18.38 0.00 0.00 4.00
617 618 1.978455 AAAGAGGCACGTGTGGACCA 61.978 55.000 18.38 0.00 0.00 4.02
618 619 0.034337 TAAAGAGGCACGTGTGGACC 59.966 55.000 18.38 9.68 0.00 4.46
619 620 1.798813 CTTAAAGAGGCACGTGTGGAC 59.201 52.381 18.38 5.53 0.00 4.02
620 621 1.689813 TCTTAAAGAGGCACGTGTGGA 59.310 47.619 18.38 0.18 0.00 4.02
621 622 2.163818 TCTTAAAGAGGCACGTGTGG 57.836 50.000 18.38 0.00 0.00 4.17
622 623 3.369147 CAGATCTTAAAGAGGCACGTGTG 59.631 47.826 18.38 0.00 0.00 3.82
623 624 3.006967 ACAGATCTTAAAGAGGCACGTGT 59.993 43.478 18.38 0.00 0.00 4.49
624 625 3.369147 CACAGATCTTAAAGAGGCACGTG 59.631 47.826 12.28 12.28 0.00 4.49
625 626 3.589988 CACAGATCTTAAAGAGGCACGT 58.410 45.455 0.00 0.00 0.00 4.49
626 627 2.349886 GCACAGATCTTAAAGAGGCACG 59.650 50.000 0.00 0.00 0.00 5.34
627 628 2.349886 CGCACAGATCTTAAAGAGGCAC 59.650 50.000 0.00 0.00 0.00 5.01
628 629 2.028112 ACGCACAGATCTTAAAGAGGCA 60.028 45.455 0.00 0.00 0.00 4.75
629 630 2.605366 GACGCACAGATCTTAAAGAGGC 59.395 50.000 0.00 0.00 0.00 4.70
630 631 2.854777 CGACGCACAGATCTTAAAGAGG 59.145 50.000 0.00 0.00 0.00 3.69
631 632 3.544285 GTCGACGCACAGATCTTAAAGAG 59.456 47.826 0.00 0.00 0.00 2.85
632 633 3.057806 TGTCGACGCACAGATCTTAAAGA 60.058 43.478 11.62 0.00 0.00 2.52
633 634 3.059570 GTGTCGACGCACAGATCTTAAAG 59.940 47.826 23.67 0.00 39.07 1.85
634 635 2.984471 GTGTCGACGCACAGATCTTAAA 59.016 45.455 23.67 0.00 39.07 1.52
635 636 2.030628 TGTGTCGACGCACAGATCTTAA 60.031 45.455 27.03 0.84 43.54 1.85
636 637 1.538075 TGTGTCGACGCACAGATCTTA 59.462 47.619 27.03 1.62 43.54 2.10
637 638 0.313987 TGTGTCGACGCACAGATCTT 59.686 50.000 27.03 0.00 43.54 2.40
638 639 1.956802 TGTGTCGACGCACAGATCT 59.043 52.632 27.03 0.00 43.54 2.75
639 640 4.552278 TGTGTCGACGCACAGATC 57.448 55.556 27.03 2.83 43.54 2.75
643 644 1.487452 GAAGCTTGTGTCGACGCACA 61.487 55.000 30.18 17.51 46.30 4.57
644 645 1.201825 GAAGCTTGTGTCGACGCAC 59.798 57.895 30.18 19.81 39.65 5.34
645 646 1.954146 GGAAGCTTGTGTCGACGCA 60.954 57.895 27.03 27.03 34.11 5.24
646 647 1.495584 TTGGAAGCTTGTGTCGACGC 61.496 55.000 22.00 22.00 0.00 5.19
647 648 0.232303 GTTGGAAGCTTGTGTCGACG 59.768 55.000 2.10 0.00 0.00 5.12
648 649 1.583054 AGTTGGAAGCTTGTGTCGAC 58.417 50.000 9.11 9.11 0.00 4.20
649 650 1.939934 CAAGTTGGAAGCTTGTGTCGA 59.060 47.619 2.10 0.00 38.68 4.20
650 651 2.389713 CAAGTTGGAAGCTTGTGTCG 57.610 50.000 2.10 0.00 38.68 4.35
655 656 3.003068 CAGACAGACAAGTTGGAAGCTTG 59.997 47.826 2.10 2.73 46.23 4.01
656 657 3.209410 CAGACAGACAAGTTGGAAGCTT 58.791 45.455 7.96 0.00 0.00 3.74
657 658 2.843701 CAGACAGACAAGTTGGAAGCT 58.156 47.619 7.96 0.00 0.00 3.74
658 659 1.265365 GCAGACAGACAAGTTGGAAGC 59.735 52.381 7.96 0.00 0.00 3.86
659 660 2.564771 TGCAGACAGACAAGTTGGAAG 58.435 47.619 7.96 0.00 0.00 3.46
660 661 2.708216 TGCAGACAGACAAGTTGGAA 57.292 45.000 7.96 0.00 0.00 3.53
672 673 1.726865 CAACGCCAAACTGCAGACA 59.273 52.632 23.35 0.00 0.00 3.41
673 674 1.658409 GCAACGCCAAACTGCAGAC 60.658 57.895 23.35 3.08 36.09 3.51
674 675 2.721231 GCAACGCCAAACTGCAGA 59.279 55.556 23.35 0.00 36.09 4.26
729 737 0.739561 ATCCTCTACGTGGAGCGAAC 59.260 55.000 22.41 0.00 44.77 3.95
730 738 2.336945 TATCCTCTACGTGGAGCGAA 57.663 50.000 22.41 10.77 44.77 4.70
852 4112 4.021456 ACTGATGTATTGTTCCGTGTGAGA 60.021 41.667 0.00 0.00 0.00 3.27
858 4118 6.483974 TGTTGTTTACTGATGTATTGTTCCGT 59.516 34.615 0.00 0.00 0.00 4.69
881 4158 3.848347 CTGCTGTGTCGCCGAGTGT 62.848 63.158 0.00 0.00 0.00 3.55
882 4159 3.108289 CTGCTGTGTCGCCGAGTG 61.108 66.667 0.00 0.00 0.00 3.51
899 4178 1.646189 GCTAGTGGAGTGCTACTTGC 58.354 55.000 0.00 0.00 43.93 4.01
904 4192 3.963374 AGATGATTGCTAGTGGAGTGCTA 59.037 43.478 0.00 0.00 0.00 3.49
965 4256 1.374758 GGAGGTGCACGAAGGACAG 60.375 63.158 11.45 0.00 40.89 3.51
967 4258 1.374758 CAGGAGGTGCACGAAGGAC 60.375 63.158 11.45 0.00 37.94 3.85
968 4259 1.816863 GACAGGAGGTGCACGAAGGA 61.817 60.000 11.45 0.00 0.00 3.36
970 4261 1.374758 GGACAGGAGGTGCACGAAG 60.375 63.158 11.45 1.31 37.84 3.79
982 4283 1.600957 CATTAATCAGCTGCGGACAGG 59.399 52.381 9.47 0.00 44.63 4.00
984 4285 1.667236 CCATTAATCAGCTGCGGACA 58.333 50.000 9.47 0.00 0.00 4.02
991 4292 4.011966 TCATGATCGCCATTAATCAGCT 57.988 40.909 0.00 0.00 35.49 4.24
1224 4571 6.668323 CCGTGAACAAATATCAGAAAACTGT 58.332 36.000 0.00 0.00 0.00 3.55
1265 4615 4.221422 GCCAGCGCGTCCCAGATA 62.221 66.667 8.43 0.00 0.00 1.98
1446 4796 2.659016 CAGCGGCACCAGAGAAGA 59.341 61.111 1.45 0.00 0.00 2.87
1498 4848 1.793581 GCGTTGGCGTTCATGATGA 59.206 52.632 0.00 0.00 40.81 2.92
1614 4973 0.675083 TCCGGTCGACAACAAAGCTA 59.325 50.000 18.91 0.00 0.00 3.32
1634 4995 8.975439 CCTACTAACTAAGTACAGTTTGTGTTG 58.025 37.037 17.43 10.52 42.07 3.33
1642 5003 9.745018 TTACATGTCCTACTAACTAAGTACAGT 57.255 33.333 0.00 0.00 39.80 3.55
1653 5016 9.817809 GTTCTCATCATTTACATGTCCTACTAA 57.182 33.333 0.00 0.00 0.00 2.24
1713 5479 6.975197 CCGGTAGCATATGAACTATGTATCTG 59.025 42.308 6.97 0.00 39.61 2.90
1737 5503 4.906747 ATCCATCTCTAATTCAGCTCCC 57.093 45.455 0.00 0.00 0.00 4.30
1817 5612 4.081697 CGGCCATTTTTAAGGAATCCAACT 60.082 41.667 2.24 0.00 0.00 3.16
1837 5632 2.217510 TCCCCTATCTGACTATCGGC 57.782 55.000 0.00 0.00 0.00 5.54
1866 5661 2.884639 CCGAAATTTAGGATGCGGGATT 59.115 45.455 11.63 0.00 35.42 3.01
1895 5692 7.573968 ACAAGAGCAAAGTTGAGTTTAAGAT 57.426 32.000 0.00 0.00 0.00 2.40
1896 5693 8.142994 CTACAAGAGCAAAGTTGAGTTTAAGA 57.857 34.615 0.00 0.00 0.00 2.10
1950 5750 9.367444 GCAAAGTATGAAATGTACTGTACTAGT 57.633 33.333 17.98 0.00 43.56 2.57
1951 5751 9.587772 AGCAAAGTATGAAATGTACTGTACTAG 57.412 33.333 17.98 0.00 32.94 2.57
1952 5752 9.582431 GAGCAAAGTATGAAATGTACTGTACTA 57.418 33.333 17.98 6.12 32.94 1.82
1953 5753 8.314751 AGAGCAAAGTATGAAATGTACTGTACT 58.685 33.333 17.98 0.00 32.94 2.73
1954 5754 8.480643 AGAGCAAAGTATGAAATGTACTGTAC 57.519 34.615 10.98 10.98 32.94 2.90
1955 5755 8.935844 CAAGAGCAAAGTATGAAATGTACTGTA 58.064 33.333 0.00 0.00 32.94 2.74
1956 5756 7.445402 ACAAGAGCAAAGTATGAAATGTACTGT 59.555 33.333 0.00 0.00 32.94 3.55
1957 5757 7.810658 ACAAGAGCAAAGTATGAAATGTACTG 58.189 34.615 0.00 0.00 32.94 2.74
1958 5758 7.986085 ACAAGAGCAAAGTATGAAATGTACT 57.014 32.000 0.00 0.00 33.98 2.73
1976 5776 3.187227 AGTTTGTGCGAATGCTACAAGAG 59.813 43.478 0.00 0.00 40.54 2.85
1977 5777 3.138304 AGTTTGTGCGAATGCTACAAGA 58.862 40.909 0.00 0.00 40.54 3.02
1978 5778 3.542712 AGTTTGTGCGAATGCTACAAG 57.457 42.857 0.00 0.00 40.54 3.16
1979 5779 3.980646 AAGTTTGTGCGAATGCTACAA 57.019 38.095 0.00 0.00 43.34 2.41
1980 5780 3.980646 AAAGTTTGTGCGAATGCTACA 57.019 38.095 0.00 0.00 43.34 2.74
1981 5781 6.927933 AAATAAAGTTTGTGCGAATGCTAC 57.072 33.333 0.00 0.00 43.34 3.58
1982 5782 8.076781 TGTAAAATAAAGTTTGTGCGAATGCTA 58.923 29.630 0.00 0.00 43.34 3.49
1983 5783 6.920758 TGTAAAATAAAGTTTGTGCGAATGCT 59.079 30.769 0.00 0.00 43.34 3.79
1984 5784 7.096230 ACTGTAAAATAAAGTTTGTGCGAATGC 60.096 33.333 0.00 0.00 43.20 3.56
1985 5785 8.280909 ACTGTAAAATAAAGTTTGTGCGAATG 57.719 30.769 0.00 0.00 0.00 2.67
1986 5786 8.865590 AACTGTAAAATAAAGTTTGTGCGAAT 57.134 26.923 0.00 0.00 29.98 3.34
1987 5787 9.784680 TTAACTGTAAAATAAAGTTTGTGCGAA 57.215 25.926 0.00 0.00 35.77 4.70
1988 5788 9.224058 GTTAACTGTAAAATAAAGTTTGTGCGA 57.776 29.630 0.00 0.00 35.77 5.10
1989 5789 9.228636 AGTTAACTGTAAAATAAAGTTTGTGCG 57.771 29.630 7.48 0.00 35.77 5.34
2122 5922 8.958119 AGAATACTGAAATAATTTCTACGCCA 57.042 30.769 0.00 0.00 40.32 5.69
2181 7018 8.528917 TTTCGTAATCCCGAACATGATAATAG 57.471 34.615 0.00 0.00 45.64 1.73
2388 7240 5.902681 TCTAGGGTTTCATATTCACAGTCG 58.097 41.667 0.00 0.00 0.00 4.18
2391 7243 7.331026 TGTCTTCTAGGGTTTCATATTCACAG 58.669 38.462 0.00 0.00 0.00 3.66
2519 7371 2.042706 TCCGGGACTTCCTCTAGAGTTT 59.957 50.000 18.42 0.00 35.95 2.66
2534 7386 0.391597 GCCATATTCGTCTTCCGGGA 59.608 55.000 0.00 0.00 37.11 5.14
2549 7401 1.076777 CATTCCTCGGGGTTGCCAT 60.077 57.895 0.00 0.00 0.00 4.40
2565 7417 5.366186 AGTCATCTATTTGTCCTCTGAGCAT 59.634 40.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.