Multiple sequence alignment - TraesCS5B01G305900

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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 TraesCS5B01G305900 chr5B 100.000 5509 0 0 1 5509 489814665 489809157 0.000000e+00 10174.0
1 TraesCS5B01G305900 chr5D 92.800 4833 172 62 756 5509 408322511 408317776 0.000000e+00 6835.0
2 TraesCS5B01G305900 chr5A 93.173 4043 172 46 756 4740 514157539 514153543 0.000000e+00 5842.0
3 TraesCS5B01G305900 chr5A 94.865 740 29 4 4775 5509 514153547 514152812 0.000000e+00 1147.0
4 TraesCS5B01G305900 chr5A 94.595 37 1 1 493 529 470025277 470025242 7.710000e-04 56.5
5 TraesCS5B01G305900 chr3B 96.360 522 11 2 1 521 820473545 820474059 0.000000e+00 852.0
6 TraesCS5B01G305900 chr3B 93.913 115 6 1 529 643 22077459 22077572 7.340000e-39 172.0
7 TraesCS5B01G305900 chr3B 86.145 166 15 5 525 687 670548365 670548205 7.340000e-39 172.0
8 TraesCS5B01G305900 chr3D 95.393 521 17 2 1 521 93033177 93032664 0.000000e+00 822.0
9 TraesCS5B01G305900 chr3D 83.529 425 59 7 1 420 34709730 34709312 2.410000e-103 387.0
10 TraesCS5B01G305900 chr3D 81.647 425 67 9 1 420 68836383 68836801 5.280000e-90 342.0
11 TraesCS5B01G305900 chr3D 100.000 29 0 0 493 521 16249193 16249165 3.000000e-03 54.7
12 TraesCS5B01G305900 chr7B 89.937 477 37 7 1 470 128297558 128297086 6.100000e-169 604.0
13 TraesCS5B01G305900 chr7B 92.308 39 3 0 483 521 154545715 154545753 7.710000e-04 56.5
14 TraesCS5B01G305900 chr4B 89.727 477 38 6 1 470 385962112 385962584 2.840000e-167 599.0
15 TraesCS5B01G305900 chr4B 93.793 145 9 0 521 665 458318800 458318656 9.290000e-53 219.0
16 TraesCS5B01G305900 chr6B 89.518 477 39 6 1 470 41903764 41903292 1.320000e-165 593.0
17 TraesCS5B01G305900 chr6B 86.508 126 11 3 525 649 299045334 299045214 3.460000e-27 134.0
18 TraesCS5B01G305900 chr6B 92.308 39 3 0 483 521 238142922 238142960 7.710000e-04 56.5
19 TraesCS5B01G305900 chr6B 92.308 39 3 0 483 521 330059178 330059140 7.710000e-04 56.5
20 TraesCS5B01G305900 chr2B 91.304 322 25 2 151 470 103891414 103891734 2.360000e-118 436.0
21 TraesCS5B01G305900 chr2B 93.636 110 5 2 541 649 518447836 518447944 4.420000e-36 163.0
22 TraesCS5B01G305900 chr2B 91.954 87 6 1 1 87 103891322 103891407 2.700000e-23 121.0
23 TraesCS5B01G305900 chr2B 100.000 34 0 0 488 521 103891736 103891769 4.610000e-06 63.9
24 TraesCS5B01G305900 chr1B 82.046 518 52 19 3770 4284 427067260 427066781 2.390000e-108 403.0
25 TraesCS5B01G305900 chr1B 86.562 320 35 6 3371 3688 427067819 427067506 4.090000e-91 346.0
26 TraesCS5B01G305900 chr1B 91.250 80 6 1 5253 5332 427066773 427066695 2.100000e-19 108.0
27 TraesCS5B01G305900 chr1B 100.000 32 0 0 491 522 670304593 670304562 5.960000e-05 60.2
28 TraesCS5B01G305900 chr1D 82.506 423 43 20 1 420 298543883 298543489 5.280000e-90 342.0
29 TraesCS5B01G305900 chr1D 88.596 114 9 2 537 650 287169517 287169408 9.630000e-28 135.0
30 TraesCS5B01G305900 chr1A 91.228 114 6 2 537 650 403020830 403020721 9.560000e-33 152.0
31 TraesCS5B01G305900 chr4A 89.286 112 8 2 542 653 45383707 45383600 2.680000e-28 137.0
32 TraesCS5B01G305900 chr4A 88.496 113 8 2 542 653 45360648 45360540 1.250000e-26 132.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G305900 chr5B 489809157 489814665 5508 True 10174.000000 10174 100.000000 1 5509 1 chr5B.!!$R1 5508
1 TraesCS5B01G305900 chr5D 408317776 408322511 4735 True 6835.000000 6835 92.800000 756 5509 1 chr5D.!!$R1 4753
2 TraesCS5B01G305900 chr5A 514152812 514157539 4727 True 3494.500000 5842 94.019000 756 5509 2 chr5A.!!$R2 4753
3 TraesCS5B01G305900 chr3B 820473545 820474059 514 False 852.000000 852 96.360000 1 521 1 chr3B.!!$F2 520
4 TraesCS5B01G305900 chr3D 93032664 93033177 513 True 822.000000 822 95.393000 1 521 1 chr3D.!!$R3 520
5 TraesCS5B01G305900 chr1B 427066695 427067819 1124 True 285.666667 403 86.619333 3371 5332 3 chr1B.!!$R2 1961

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
713 715 0.031857 TGTTGAAATGCCCGCAACTG 59.968 50.000 0.00 0.0 41.71 3.16 F
714 716 0.031994 GTTGAAATGCCCGCAACTGT 59.968 50.000 0.00 0.0 38.96 3.55 F
1404 1447 0.264657 TGGGGGCTATACAGAGCAGA 59.735 55.000 0.00 0.0 44.76 4.26 F
1614 1684 0.604578 TGCGCTAATATCCGTACCCC 59.395 55.000 9.73 0.0 0.00 4.95 F
1624 1694 1.535687 CCGTACCCCTCCCCTATGG 60.536 68.421 0.00 0.0 0.00 2.74 F
3062 3172 3.430042 AACACTCCTGTCTTCATGCAT 57.570 42.857 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1882 0.036010 CCAGTTGGAGCAGGTAGTGG 60.036 60.000 0.0 0.0 37.39 4.00 R
1856 1927 3.951775 ACTTGTTCTGCTCCACTCTAG 57.048 47.619 0.0 0.0 0.00 2.43 R
2852 2962 2.051334 TCCAGCAACGGGGAAATATG 57.949 50.000 0.0 0.0 0.00 1.78 R
2901 3011 3.225104 TCAGAGCCAAGTTCTTGCAATT 58.775 40.909 0.0 0.0 0.00 2.32 R
3140 3250 4.159135 ACCTGCATTGGAAAATAGCAAGAG 59.841 41.667 0.0 0.0 34.45 2.85 R
4696 4992 0.034337 TAACCCCACAGTTGAGCGTC 59.966 55.000 0.0 0.0 0.00 5.19 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
17 18 4.798585 TTAGAGGGATGACCGGCA 57.201 55.556 0.00 0.00 46.96 5.69
107 108 0.393673 GCCTGGAGGAAGAAGAAGGC 60.394 60.000 0.00 0.00 43.05 4.35
202 203 7.097192 TGAAATAGTCGCTCTCAATTGTAACT 58.903 34.615 5.13 4.33 0.00 2.24
293 295 7.983307 TGCAAATTTAAGTCATTTGTTTGCTT 58.017 26.923 17.31 0.00 45.92 3.91
448 450 4.431661 AGCTACGTAGGTTAAGTGTCAC 57.568 45.455 21.15 0.00 0.00 3.67
458 460 4.591498 AGGTTAAGTGTCACTACATGGACA 59.409 41.667 5.77 0.00 41.44 4.02
498 500 2.672188 TTAATTGGTCAACACGTGCG 57.328 45.000 17.22 7.42 0.00 5.34
521 523 3.369835 GCACGTGCACATTTACTAGTC 57.630 47.619 34.52 0.00 41.59 2.59
522 524 2.222508 GCACGTGCACATTTACTAGTCG 60.223 50.000 34.52 0.02 41.59 4.18
523 525 2.344441 CACGTGCACATTTACTAGTCGG 59.656 50.000 18.64 0.00 0.00 4.79
524 526 1.924524 CGTGCACATTTACTAGTCGGG 59.075 52.381 18.64 0.00 0.00 5.14
525 527 2.416296 CGTGCACATTTACTAGTCGGGA 60.416 50.000 18.64 0.00 0.00 5.14
526 528 3.592059 GTGCACATTTACTAGTCGGGAA 58.408 45.455 13.17 0.00 0.00 3.97
527 529 3.998341 GTGCACATTTACTAGTCGGGAAA 59.002 43.478 13.17 0.00 0.00 3.13
528 530 4.453136 GTGCACATTTACTAGTCGGGAAAA 59.547 41.667 13.17 0.00 0.00 2.29
529 531 4.453136 TGCACATTTACTAGTCGGGAAAAC 59.547 41.667 0.00 0.00 0.00 2.43
530 532 4.435121 GCACATTTACTAGTCGGGAAAACG 60.435 45.833 0.00 0.00 0.00 3.60
531 533 3.681417 ACATTTACTAGTCGGGAAAACGC 59.319 43.478 0.00 0.00 0.00 4.84
532 534 2.368655 TTACTAGTCGGGAAAACGCC 57.631 50.000 0.00 0.00 0.00 5.68
533 535 0.532115 TACTAGTCGGGAAAACGCCC 59.468 55.000 0.00 0.00 45.10 6.13
540 542 4.084888 GGAAAACGCCCGCACGAG 62.085 66.667 2.15 0.00 36.70 4.18
541 543 4.084888 GAAAACGCCCGCACGAGG 62.085 66.667 2.15 0.00 36.70 4.63
542 544 4.612412 AAAACGCCCGCACGAGGA 62.612 61.111 2.15 0.00 36.70 3.71
543 545 4.612412 AAACGCCCGCACGAGGAA 62.612 61.111 2.15 0.00 36.70 3.36
544 546 4.612412 AACGCCCGCACGAGGAAA 62.612 61.111 2.15 0.00 36.70 3.13
557 559 2.431260 GGAAACGCCTGCGACGTA 60.431 61.111 19.52 0.00 44.30 3.57
558 560 2.723719 GGAAACGCCTGCGACGTAC 61.724 63.158 19.52 0.00 44.30 3.67
559 561 3.051171 GAAACGCCTGCGACGTACG 62.051 63.158 19.52 15.01 44.30 3.67
560 562 3.541093 AAACGCCTGCGACGTACGA 62.541 57.895 24.41 0.00 44.30 3.43
561 563 3.541093 AACGCCTGCGACGTACGAA 62.541 57.895 24.41 3.43 44.30 3.85
562 564 3.530104 CGCCTGCGACGTACGAAC 61.530 66.667 24.41 14.09 45.77 3.95
572 574 4.180496 GTACGAACGAAGCCTGGG 57.820 61.111 0.14 0.00 0.00 4.45
573 575 1.588082 GTACGAACGAAGCCTGGGA 59.412 57.895 0.14 0.00 0.00 4.37
574 576 0.735287 GTACGAACGAAGCCTGGGAC 60.735 60.000 0.14 0.00 0.00 4.46
575 577 2.203972 TACGAACGAAGCCTGGGACG 62.204 60.000 0.14 0.00 0.00 4.79
576 578 2.342648 GAACGAAGCCTGGGACGT 59.657 61.111 0.00 0.00 40.64 4.34
577 579 1.588082 GAACGAAGCCTGGGACGTA 59.412 57.895 0.00 0.00 38.00 3.57
578 580 0.735287 GAACGAAGCCTGGGACGTAC 60.735 60.000 0.00 0.00 38.00 3.67
579 581 2.202570 CGAAGCCTGGGACGTACG 60.203 66.667 15.01 15.01 0.00 3.67
580 582 2.693762 CGAAGCCTGGGACGTACGA 61.694 63.158 24.41 0.00 0.00 3.43
581 583 1.588082 GAAGCCTGGGACGTACGAA 59.412 57.895 24.41 3.43 0.00 3.85
582 584 0.037975 GAAGCCTGGGACGTACGAAA 60.038 55.000 24.41 3.05 0.00 3.46
583 585 0.393820 AAGCCTGGGACGTACGAAAA 59.606 50.000 24.41 3.42 0.00 2.29
584 586 0.611714 AGCCTGGGACGTACGAAAAT 59.388 50.000 24.41 0.00 0.00 1.82
585 587 1.002773 AGCCTGGGACGTACGAAAATT 59.997 47.619 24.41 0.00 0.00 1.82
586 588 2.234414 AGCCTGGGACGTACGAAAATTA 59.766 45.455 24.41 2.06 0.00 1.40
587 589 3.118519 AGCCTGGGACGTACGAAAATTAT 60.119 43.478 24.41 0.00 0.00 1.28
588 590 3.001939 GCCTGGGACGTACGAAAATTATG 59.998 47.826 24.41 4.32 0.00 1.90
589 591 4.186159 CCTGGGACGTACGAAAATTATGT 58.814 43.478 24.41 0.00 0.00 2.29
590 592 4.033587 CCTGGGACGTACGAAAATTATGTG 59.966 45.833 24.41 1.35 0.00 3.21
591 593 3.933955 TGGGACGTACGAAAATTATGTGG 59.066 43.478 24.41 0.00 0.00 4.17
592 594 3.310501 GGGACGTACGAAAATTATGTGGG 59.689 47.826 24.41 0.00 0.00 4.61
593 595 3.934579 GGACGTACGAAAATTATGTGGGT 59.065 43.478 24.41 0.00 0.00 4.51
594 596 4.033243 GGACGTACGAAAATTATGTGGGTC 59.967 45.833 24.41 3.13 0.00 4.46
595 597 3.934579 ACGTACGAAAATTATGTGGGTCC 59.065 43.478 24.41 0.00 0.00 4.46
596 598 3.310501 CGTACGAAAATTATGTGGGTCCC 59.689 47.826 10.44 0.00 0.00 4.46
597 599 3.443145 ACGAAAATTATGTGGGTCCCA 57.557 42.857 6.47 6.47 0.00 4.37
606 608 2.753701 TGGGTCCCACCATGAACG 59.246 61.111 6.47 0.00 41.02 3.95
607 609 1.843832 TGGGTCCCACCATGAACGA 60.844 57.895 6.47 0.00 41.02 3.85
608 610 1.377229 GGGTCCCACCATGAACGAA 59.623 57.895 1.78 0.00 41.02 3.85
609 611 0.250989 GGGTCCCACCATGAACGAAA 60.251 55.000 1.78 0.00 41.02 3.46
610 612 1.611519 GGTCCCACCATGAACGAAAA 58.388 50.000 0.00 0.00 38.42 2.29
611 613 1.957877 GGTCCCACCATGAACGAAAAA 59.042 47.619 0.00 0.00 38.42 1.94
632 634 5.459536 AAAGCTGAAGAAACAATCCTTCC 57.540 39.130 0.00 0.00 38.33 3.46
633 635 4.379302 AGCTGAAGAAACAATCCTTCCT 57.621 40.909 0.00 0.00 38.33 3.36
634 636 4.734266 AGCTGAAGAAACAATCCTTCCTT 58.266 39.130 0.00 0.00 38.33 3.36
635 637 5.143369 AGCTGAAGAAACAATCCTTCCTTT 58.857 37.500 0.00 0.00 38.33 3.11
636 638 6.306987 AGCTGAAGAAACAATCCTTCCTTTA 58.693 36.000 0.00 0.00 38.33 1.85
637 639 6.777580 AGCTGAAGAAACAATCCTTCCTTTAA 59.222 34.615 0.00 0.00 38.33 1.52
638 640 7.452813 AGCTGAAGAAACAATCCTTCCTTTAAT 59.547 33.333 0.00 0.00 38.33 1.40
639 641 8.739972 GCTGAAGAAACAATCCTTCCTTTAATA 58.260 33.333 0.00 0.00 38.33 0.98
706 708 9.468532 GATAAAGATAAAGATGTTGAAATGCCC 57.531 33.333 0.00 0.00 0.00 5.36
707 709 5.505173 AGATAAAGATGTTGAAATGCCCG 57.495 39.130 0.00 0.00 0.00 6.13
708 710 2.368655 AAAGATGTTGAAATGCCCGC 57.631 45.000 0.00 0.00 0.00 6.13
709 711 1.255882 AAGATGTTGAAATGCCCGCA 58.744 45.000 0.00 0.00 0.00 5.69
710 712 1.255882 AGATGTTGAAATGCCCGCAA 58.744 45.000 0.00 0.00 0.00 4.85
711 713 1.067635 AGATGTTGAAATGCCCGCAAC 60.068 47.619 0.00 0.00 41.57 4.17
712 714 0.968405 ATGTTGAAATGCCCGCAACT 59.032 45.000 0.00 0.00 41.71 3.16
713 715 0.031857 TGTTGAAATGCCCGCAACTG 59.968 50.000 0.00 0.00 41.71 3.16
714 716 0.031994 GTTGAAATGCCCGCAACTGT 59.968 50.000 0.00 0.00 38.96 3.55
715 717 0.749649 TTGAAATGCCCGCAACTGTT 59.250 45.000 0.00 0.00 0.00 3.16
716 718 0.749649 TGAAATGCCCGCAACTGTTT 59.250 45.000 0.00 0.00 0.00 2.83
717 719 1.957177 TGAAATGCCCGCAACTGTTTA 59.043 42.857 0.00 0.00 0.00 2.01
718 720 2.560542 TGAAATGCCCGCAACTGTTTAT 59.439 40.909 0.00 0.00 0.00 1.40
719 721 3.006323 TGAAATGCCCGCAACTGTTTATT 59.994 39.130 0.00 0.00 0.00 1.40
720 722 3.676291 AATGCCCGCAACTGTTTATTT 57.324 38.095 0.00 0.00 0.00 1.40
721 723 4.792521 AATGCCCGCAACTGTTTATTTA 57.207 36.364 0.00 0.00 0.00 1.40
722 724 4.792521 ATGCCCGCAACTGTTTATTTAA 57.207 36.364 0.00 0.00 0.00 1.52
723 725 4.792521 TGCCCGCAACTGTTTATTTAAT 57.207 36.364 0.00 0.00 0.00 1.40
724 726 5.140747 TGCCCGCAACTGTTTATTTAATT 57.859 34.783 0.00 0.00 0.00 1.40
725 727 5.542779 TGCCCGCAACTGTTTATTTAATTT 58.457 33.333 0.00 0.00 0.00 1.82
726 728 6.688578 TGCCCGCAACTGTTTATTTAATTTA 58.311 32.000 0.00 0.00 0.00 1.40
727 729 7.152645 TGCCCGCAACTGTTTATTTAATTTAA 58.847 30.769 0.00 0.00 0.00 1.52
728 730 7.819900 TGCCCGCAACTGTTTATTTAATTTAAT 59.180 29.630 0.00 0.00 0.00 1.40
729 731 8.661257 GCCCGCAACTGTTTATTTAATTTAATT 58.339 29.630 0.00 0.00 0.00 1.40
752 754 8.944212 ATTTAAAAAGAAAATGAGGACGTACG 57.056 30.769 15.01 15.01 0.00 3.67
753 755 4.400036 AAAAGAAAATGAGGACGTACGC 57.600 40.909 16.72 8.19 0.00 4.42
754 756 2.005971 AGAAAATGAGGACGTACGCC 57.994 50.000 16.72 17.21 0.00 5.68
928 947 4.394712 GGCCCTCTCACACGTGGG 62.395 72.222 21.57 17.59 42.41 4.61
984 1003 4.191243 CCCCCAACACCCAGAAAC 57.809 61.111 0.00 0.00 0.00 2.78
985 1004 1.533033 CCCCCAACACCCAGAAACC 60.533 63.158 0.00 0.00 0.00 3.27
987 1006 1.901464 CCCAACACCCAGAAACCCG 60.901 63.158 0.00 0.00 0.00 5.28
988 1007 1.149627 CCAACACCCAGAAACCCGA 59.850 57.895 0.00 0.00 0.00 5.14
1156 1185 0.462047 CTCCAATCTGGGCGTGGTAC 60.462 60.000 0.00 0.00 38.32 3.34
1189 1218 4.476410 CCGCGTGCGCTCTGAGTA 62.476 66.667 9.73 0.00 39.32 2.59
1190 1219 2.278206 CGCGTGCGCTCTGAGTAT 60.278 61.111 9.73 0.00 39.32 2.12
1195 1224 2.154007 GCGTGCGCTCTGAGTATAATTC 59.846 50.000 9.73 0.00 38.26 2.17
1295 1324 4.018415 AGGAAATGCCAACTACTGTGGTAT 60.018 41.667 0.00 0.00 40.02 2.73
1401 1444 1.002544 GTGATGGGGGCTATACAGAGC 59.997 57.143 0.00 0.00 42.05 4.09
1402 1445 1.352083 GATGGGGGCTATACAGAGCA 58.648 55.000 0.00 0.00 44.76 4.26
1403 1446 1.277557 GATGGGGGCTATACAGAGCAG 59.722 57.143 0.00 0.00 44.76 4.24
1404 1447 0.264657 TGGGGGCTATACAGAGCAGA 59.735 55.000 0.00 0.00 44.76 4.26
1405 1448 0.972883 GGGGGCTATACAGAGCAGAG 59.027 60.000 0.00 0.00 44.76 3.35
1444 1513 3.069289 TGTGTGCATGATCACTTCAGAC 58.931 45.455 17.18 5.83 37.89 3.51
1450 1519 2.347697 TGATCACTTCAGACGAACCG 57.652 50.000 0.00 0.00 0.00 4.44
1451 1520 1.067846 TGATCACTTCAGACGAACCGG 60.068 52.381 0.00 0.00 0.00 5.28
1539 1609 3.586100 TTTCTTTTGCTAAATCCCGCC 57.414 42.857 0.00 0.00 0.00 6.13
1561 1631 3.359580 CGTGCGGTTAAAACTTGCAATAC 59.640 43.478 0.00 0.00 40.15 1.89
1607 1677 4.686554 CCTCAGTTTACTGCGCTAATATCC 59.313 45.833 9.73 0.00 43.46 2.59
1614 1684 0.604578 TGCGCTAATATCCGTACCCC 59.395 55.000 9.73 0.00 0.00 4.95
1624 1694 1.535687 CCGTACCCCTCCCCTATGG 60.536 68.421 0.00 0.00 0.00 2.74
1811 1882 7.711339 CAGACTTGAACTCCTTTGGGTATATAC 59.289 40.741 4.14 4.14 0.00 1.47
1849 1920 7.393234 CCAACTGGGAATCACTTACTAAATGAA 59.607 37.037 0.00 0.00 40.01 2.57
1856 1927 9.455847 GGAATCACTTACTAAATGAATTGATGC 57.544 33.333 0.00 0.00 28.72 3.91
1890 1961 7.547227 AGCAGAACAAGTTCTTGTTTTTATGT 58.453 30.769 25.05 7.67 46.95 2.29
2106 2179 9.732130 GAAGGAGGTGCTAATATTATCTTTGAT 57.268 33.333 0.00 0.00 0.00 2.57
2256 2343 7.149569 ACTTGGTCATATTTCTTGTGATGTG 57.850 36.000 0.00 0.00 0.00 3.21
2388 2479 7.907214 AGGCAAGTTTTCTATAGTGTGTTAG 57.093 36.000 0.00 0.00 0.00 2.34
2710 2806 9.601217 ACTTTCGTATCTTCTAGCAACAAATAT 57.399 29.630 0.00 0.00 0.00 1.28
2901 3011 9.295825 TCTGCAAATCCAAGAAATTCTAGTTAA 57.704 29.630 0.00 0.00 0.00 2.01
3027 3137 7.165485 TGGCTTTTGTACTGTATGTTACTGAT 58.835 34.615 0.00 0.00 0.00 2.90
3062 3172 3.430042 AACACTCCTGTCTTCATGCAT 57.570 42.857 0.00 0.00 0.00 3.96
3118 3228 8.710835 TGCATTGTTTTACTATCTACAATCGA 57.289 30.769 0.00 0.00 38.71 3.59
3140 3250 6.641314 TCGACTTTGTCTTGACTATTGAGTTC 59.359 38.462 2.35 0.00 35.45 3.01
3333 3443 4.462483 ACTGAATGTTCGGGTATTGCATTT 59.538 37.500 6.54 0.00 37.89 2.32
3367 3477 7.815383 TCATATCCTTTTGTCACCATTCCTAT 58.185 34.615 0.00 0.00 0.00 2.57
3415 3525 3.366781 GCTGCTTGATCCCTTTTCAGTTC 60.367 47.826 0.00 0.00 0.00 3.01
3666 3778 4.026062 GCGTGTTTTCCTTCAATTTTGACC 60.026 41.667 0.00 0.00 36.83 4.02
3957 4252 8.166422 AGGTAAAGTTTGGAAGTACTCATTTG 57.834 34.615 0.00 0.00 0.00 2.32
3958 4253 7.230712 AGGTAAAGTTTGGAAGTACTCATTTGG 59.769 37.037 0.00 0.00 0.00 3.28
3959 4254 6.405278 AAAGTTTGGAAGTACTCATTTGGG 57.595 37.500 0.00 0.00 0.00 4.12
3960 4255 5.319043 AGTTTGGAAGTACTCATTTGGGA 57.681 39.130 0.00 0.00 0.00 4.37
3961 4256 5.701224 AGTTTGGAAGTACTCATTTGGGAA 58.299 37.500 0.00 0.00 0.00 3.97
3962 4257 6.314917 AGTTTGGAAGTACTCATTTGGGAAT 58.685 36.000 0.00 0.00 0.00 3.01
3963 4258 7.466804 AGTTTGGAAGTACTCATTTGGGAATA 58.533 34.615 0.00 0.00 0.00 1.75
3990 4285 2.127271 TAGGCATGGTGTTGGATGTG 57.873 50.000 0.00 0.00 0.00 3.21
4021 4317 3.587797 TCTGCTAAAGTGTACTTCCCG 57.412 47.619 0.00 0.00 34.61 5.14
4336 4632 5.240623 TGTTGTGCATTCTACTTCGGAATTT 59.759 36.000 0.00 0.00 31.90 1.82
4353 4649 6.147000 TCGGAATTTTCAAAAATAGCCTTTGC 59.853 34.615 13.58 0.00 37.62 3.68
4358 4654 8.845413 ATTTTCAAAAATAGCCTTTGCATACA 57.155 26.923 0.00 0.00 36.88 2.29
4375 4671 1.349067 ACACAGGTTCAGGAGGGTAC 58.651 55.000 0.00 0.00 0.00 3.34
4478 4774 3.656457 TGCAATCAGGCAGTCACAT 57.344 47.368 0.00 0.00 39.25 3.21
4517 4813 2.558359 GGTGCAAACTTAGTCAATGGCT 59.442 45.455 0.00 0.00 0.00 4.75
4548 4844 6.569179 AAACCATATACAATAATGGCGACC 57.431 37.500 1.29 0.00 45.53 4.79
4613 4909 6.466812 TGAATCAACAATCTGTCTAGAAGCA 58.533 36.000 0.00 0.00 36.32 3.91
4693 4989 3.487120 AACACTAATAATCCGGGAGCC 57.513 47.619 0.00 0.00 0.00 4.70
4695 4991 2.979678 ACACTAATAATCCGGGAGCCAT 59.020 45.455 0.00 0.00 0.00 4.40
4696 4992 3.244561 ACACTAATAATCCGGGAGCCATG 60.245 47.826 0.00 0.00 0.00 3.66
4711 5007 1.300971 CCATGACGCTCAACTGTGGG 61.301 60.000 0.00 0.00 0.00 4.61
4723 5019 1.699730 ACTGTGGGGTTAAAACTGGC 58.300 50.000 0.00 0.00 0.00 4.85
4725 5021 2.316108 CTGTGGGGTTAAAACTGGCTT 58.684 47.619 0.00 0.00 0.00 4.35
4759 5055 5.665812 TGTATAACCATGCTAACCTCCTCTT 59.334 40.000 0.00 0.00 0.00 2.85
4831 5127 4.280929 AGACACTGTACTGCAATGTGAGTA 59.719 41.667 0.00 0.00 37.71 2.59
4834 5130 3.987868 ACTGTACTGCAATGTGAGTAACG 59.012 43.478 0.00 0.00 0.00 3.18
4908 5204 9.688091 TGTATCTACTCTGTTCTTTGTATCTCT 57.312 33.333 0.00 0.00 0.00 3.10
5091 5387 3.335579 CCCAAGGAGAAAGAAACGGTAG 58.664 50.000 0.00 0.00 0.00 3.18
5112 5413 7.095355 CGGTAGTGCCCAATGTAATAATACTTC 60.095 40.741 0.00 0.00 32.98 3.01
5118 5419 7.015098 TGCCCAATGTAATAATACTTCCCATTG 59.985 37.037 0.00 0.00 32.98 2.82
5181 5482 4.819761 TGCAGATCGCGTGGAGCC 62.820 66.667 5.77 0.00 46.97 4.70
5239 5540 5.596772 TGGCCTTTTATTATTCAGGTAAGCC 59.403 40.000 3.32 0.00 0.00 4.35
5285 5586 2.116238 TGTATGTTACCTGCTCTCCCC 58.884 52.381 0.00 0.00 0.00 4.81
5362 5663 6.303903 TGAAGAATGGATCACATGAAGAGA 57.696 37.500 0.00 0.00 40.44 3.10
5376 5677 1.139853 GAAGAGATTCTCCGGCATGGT 59.860 52.381 10.09 0.00 39.52 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.293498 CCGAGCTACCACTGCTGTT 59.707 57.895 0.00 0.00 41.30 3.16
107 108 3.685139 ATGCATCCAACGGACCTATAG 57.315 47.619 0.00 0.00 32.98 1.31
202 203 0.107831 AACCGTGCCAAGCTTCTACA 59.892 50.000 0.00 0.00 0.00 2.74
448 450 4.677673 TGTGATGATCCTGTCCATGTAG 57.322 45.455 0.00 0.00 0.00 2.74
458 460 9.529823 AATTAATCATAGCAATGTGATGATCCT 57.470 29.630 10.81 2.48 38.96 3.24
523 525 4.084888 CTCGTGCGGGCGTTTTCC 62.085 66.667 0.00 0.00 0.00 3.13
524 526 4.084888 CCTCGTGCGGGCGTTTTC 62.085 66.667 0.00 0.00 0.00 2.29
525 527 4.612412 TCCTCGTGCGGGCGTTTT 62.612 61.111 0.00 0.00 0.00 2.43
526 528 4.612412 TTCCTCGTGCGGGCGTTT 62.612 61.111 0.00 0.00 0.00 3.60
527 529 4.612412 TTTCCTCGTGCGGGCGTT 62.612 61.111 0.00 0.00 0.00 4.84
533 535 3.777925 CAGGCGTTTCCTCGTGCG 61.778 66.667 0.00 0.00 45.52 5.34
534 536 4.090057 GCAGGCGTTTCCTCGTGC 62.090 66.667 0.00 0.00 45.52 5.34
535 537 3.777925 CGCAGGCGTTTCCTCGTG 61.778 66.667 5.34 0.00 45.52 4.35
536 538 3.986006 TCGCAGGCGTTTCCTCGT 61.986 61.111 13.83 0.00 45.52 4.18
537 539 3.479269 GTCGCAGGCGTTTCCTCG 61.479 66.667 13.83 0.00 45.52 4.63
546 548 3.530104 CGTTCGTACGTCGCAGGC 61.530 66.667 16.05 0.00 42.72 4.85
555 557 0.735287 GTCCCAGGCTTCGTTCGTAC 60.735 60.000 0.00 0.00 0.00 3.67
556 558 1.588082 GTCCCAGGCTTCGTTCGTA 59.412 57.895 0.00 0.00 0.00 3.43
557 559 2.342648 GTCCCAGGCTTCGTTCGT 59.657 61.111 0.00 0.00 0.00 3.85
558 560 2.203972 TACGTCCCAGGCTTCGTTCG 62.204 60.000 0.00 2.69 37.66 3.95
559 561 0.735287 GTACGTCCCAGGCTTCGTTC 60.735 60.000 0.00 2.07 37.66 3.95
560 562 1.291272 GTACGTCCCAGGCTTCGTT 59.709 57.895 0.00 0.00 37.66 3.85
561 563 2.968206 GTACGTCCCAGGCTTCGT 59.032 61.111 0.00 8.38 39.74 3.85
562 564 2.202570 CGTACGTCCCAGGCTTCG 60.203 66.667 7.22 0.00 0.00 3.79
563 565 0.037975 TTTCGTACGTCCCAGGCTTC 60.038 55.000 16.05 0.00 0.00 3.86
564 566 0.393820 TTTTCGTACGTCCCAGGCTT 59.606 50.000 16.05 0.00 0.00 4.35
565 567 0.611714 ATTTTCGTACGTCCCAGGCT 59.388 50.000 16.05 0.00 0.00 4.58
566 568 1.445871 AATTTTCGTACGTCCCAGGC 58.554 50.000 16.05 0.00 0.00 4.85
567 569 4.033587 CACATAATTTTCGTACGTCCCAGG 59.966 45.833 16.05 1.75 0.00 4.45
568 570 4.033587 CCACATAATTTTCGTACGTCCCAG 59.966 45.833 16.05 2.09 0.00 4.45
569 571 3.933955 CCACATAATTTTCGTACGTCCCA 59.066 43.478 16.05 0.00 0.00 4.37
570 572 3.310501 CCCACATAATTTTCGTACGTCCC 59.689 47.826 16.05 0.00 0.00 4.46
571 573 3.934579 ACCCACATAATTTTCGTACGTCC 59.065 43.478 16.05 0.00 0.00 4.79
572 574 4.033243 GGACCCACATAATTTTCGTACGTC 59.967 45.833 16.05 0.00 0.00 4.34
573 575 3.934579 GGACCCACATAATTTTCGTACGT 59.065 43.478 16.05 0.00 0.00 3.57
574 576 3.310501 GGGACCCACATAATTTTCGTACG 59.689 47.826 9.53 9.53 0.00 3.67
575 577 4.263435 TGGGACCCACATAATTTTCGTAC 58.737 43.478 9.95 0.00 0.00 3.67
576 578 4.571369 TGGGACCCACATAATTTTCGTA 57.429 40.909 9.95 0.00 0.00 3.43
577 579 3.443145 TGGGACCCACATAATTTTCGT 57.557 42.857 9.95 0.00 0.00 3.85
589 591 1.419720 TTCGTTCATGGTGGGACCCA 61.420 55.000 9.95 9.95 37.50 4.51
590 592 0.250989 TTTCGTTCATGGTGGGACCC 60.251 55.000 2.45 2.45 37.50 4.46
591 593 1.611519 TTTTCGTTCATGGTGGGACC 58.388 50.000 0.00 0.00 39.22 4.46
608 610 6.098838 AGGAAGGATTGTTTCTTCAGCTTTTT 59.901 34.615 0.00 0.00 40.65 1.94
609 611 5.600069 AGGAAGGATTGTTTCTTCAGCTTTT 59.400 36.000 0.00 0.00 40.65 2.27
610 612 5.143369 AGGAAGGATTGTTTCTTCAGCTTT 58.857 37.500 0.00 0.00 40.65 3.51
611 613 4.734266 AGGAAGGATTGTTTCTTCAGCTT 58.266 39.130 0.00 0.00 40.65 3.74
612 614 4.379302 AGGAAGGATTGTTTCTTCAGCT 57.621 40.909 0.00 0.00 40.65 4.24
613 615 5.459536 AAAGGAAGGATTGTTTCTTCAGC 57.540 39.130 0.00 0.00 40.65 4.26
680 682 9.468532 GGGCATTTCAACATCTTTATCTTTATC 57.531 33.333 0.00 0.00 0.00 1.75
681 683 8.137437 CGGGCATTTCAACATCTTTATCTTTAT 58.863 33.333 0.00 0.00 0.00 1.40
682 684 7.479980 CGGGCATTTCAACATCTTTATCTTTA 58.520 34.615 0.00 0.00 0.00 1.85
683 685 6.332630 CGGGCATTTCAACATCTTTATCTTT 58.667 36.000 0.00 0.00 0.00 2.52
684 686 5.679638 GCGGGCATTTCAACATCTTTATCTT 60.680 40.000 0.00 0.00 0.00 2.40
685 687 4.202050 GCGGGCATTTCAACATCTTTATCT 60.202 41.667 0.00 0.00 0.00 1.98
686 688 4.044426 GCGGGCATTTCAACATCTTTATC 58.956 43.478 0.00 0.00 0.00 1.75
687 689 3.446873 TGCGGGCATTTCAACATCTTTAT 59.553 39.130 0.00 0.00 0.00 1.40
688 690 2.822561 TGCGGGCATTTCAACATCTTTA 59.177 40.909 0.00 0.00 0.00 1.85
689 691 1.617850 TGCGGGCATTTCAACATCTTT 59.382 42.857 0.00 0.00 0.00 2.52
690 692 1.255882 TGCGGGCATTTCAACATCTT 58.744 45.000 0.00 0.00 0.00 2.40
691 693 1.067635 GTTGCGGGCATTTCAACATCT 60.068 47.619 0.00 0.00 39.69 2.90
692 694 1.067635 AGTTGCGGGCATTTCAACATC 60.068 47.619 11.17 0.00 41.67 3.06
693 695 0.968405 AGTTGCGGGCATTTCAACAT 59.032 45.000 11.17 0.00 41.67 2.71
694 696 0.031857 CAGTTGCGGGCATTTCAACA 59.968 50.000 11.17 0.00 41.67 3.33
695 697 0.031994 ACAGTTGCGGGCATTTCAAC 59.968 50.000 0.00 0.00 40.08 3.18
696 698 0.749649 AACAGTTGCGGGCATTTCAA 59.250 45.000 0.00 0.00 0.00 2.69
697 699 0.749649 AAACAGTTGCGGGCATTTCA 59.250 45.000 0.00 0.00 0.00 2.69
698 700 2.715737 TAAACAGTTGCGGGCATTTC 57.284 45.000 0.00 0.00 0.00 2.17
699 701 3.676291 AATAAACAGTTGCGGGCATTT 57.324 38.095 0.00 0.00 0.00 2.32
700 702 3.676291 AAATAAACAGTTGCGGGCATT 57.324 38.095 0.00 0.00 0.00 3.56
701 703 4.792521 TTAAATAAACAGTTGCGGGCAT 57.207 36.364 0.00 0.00 0.00 4.40
702 704 4.792521 ATTAAATAAACAGTTGCGGGCA 57.207 36.364 0.00 0.00 0.00 5.36
703 705 7.583860 TTAAATTAAATAAACAGTTGCGGGC 57.416 32.000 0.00 0.00 0.00 6.13
726 728 9.389570 CGTACGTCCTCATTTTCTTTTTAAATT 57.610 29.630 7.22 0.00 0.00 1.82
727 729 7.536281 GCGTACGTCCTCATTTTCTTTTTAAAT 59.464 33.333 17.90 0.00 0.00 1.40
728 730 6.852345 GCGTACGTCCTCATTTTCTTTTTAAA 59.148 34.615 17.90 0.00 0.00 1.52
729 731 6.365050 GCGTACGTCCTCATTTTCTTTTTAA 58.635 36.000 17.90 0.00 0.00 1.52
730 732 5.106987 GGCGTACGTCCTCATTTTCTTTTTA 60.107 40.000 17.90 0.00 0.00 1.52
731 733 4.319984 GGCGTACGTCCTCATTTTCTTTTT 60.320 41.667 17.90 0.00 0.00 1.94
732 734 3.187842 GGCGTACGTCCTCATTTTCTTTT 59.812 43.478 17.90 0.00 0.00 2.27
733 735 2.740447 GGCGTACGTCCTCATTTTCTTT 59.260 45.455 17.90 0.00 0.00 2.52
734 736 2.344025 GGCGTACGTCCTCATTTTCTT 58.656 47.619 17.90 0.00 0.00 2.52
735 737 1.405121 GGGCGTACGTCCTCATTTTCT 60.405 52.381 31.04 0.00 36.84 2.52
736 738 1.004595 GGGCGTACGTCCTCATTTTC 58.995 55.000 31.04 1.87 36.84 2.29
737 739 0.392060 GGGGCGTACGTCCTCATTTT 60.392 55.000 35.47 0.00 40.34 1.82
738 740 1.219935 GGGGCGTACGTCCTCATTT 59.780 57.895 35.47 0.00 40.34 2.32
739 741 1.673808 GAGGGGCGTACGTCCTCATT 61.674 60.000 35.47 19.89 44.72 2.57
740 742 2.043248 AGGGGCGTACGTCCTCAT 60.043 61.111 35.47 20.45 40.34 2.90
741 743 2.753043 GAGGGGCGTACGTCCTCA 60.753 66.667 35.47 0.00 44.72 3.86
742 744 3.885521 CGAGGGGCGTACGTCCTC 61.886 72.222 35.47 33.11 42.60 3.71
743 745 4.415150 TCGAGGGGCGTACGTCCT 62.415 66.667 35.47 29.63 40.34 3.85
744 746 4.185059 GTCGAGGGGCGTACGTCC 62.185 72.222 30.59 30.59 41.80 4.79
745 747 3.434319 TGTCGAGGGGCGTACGTC 61.434 66.667 17.90 15.33 41.80 4.34
746 748 3.741476 GTGTCGAGGGGCGTACGT 61.741 66.667 17.90 0.00 41.80 3.57
747 749 3.678717 CTGTGTCGAGGGGCGTACG 62.679 68.421 11.84 11.84 41.80 3.67
748 750 2.181021 CTGTGTCGAGGGGCGTAC 59.819 66.667 0.00 0.00 41.80 3.67
749 751 2.282674 ACTGTGTCGAGGGGCGTA 60.283 61.111 0.00 0.00 41.80 4.42
750 752 3.991051 CACTGTGTCGAGGGGCGT 61.991 66.667 0.00 0.00 41.80 5.68
752 754 4.314440 TGCACTGTGTCGAGGGGC 62.314 66.667 9.86 0.00 0.00 5.80
753 755 2.357517 GTGCACTGTGTCGAGGGG 60.358 66.667 10.32 0.00 0.00 4.79
754 756 2.357517 GGTGCACTGTGTCGAGGG 60.358 66.667 17.98 0.00 0.00 4.30
830 848 8.671028 GGAAAGCACCTTCTCGTTTTATTTATA 58.329 33.333 0.00 0.00 0.00 0.98
831 849 7.535997 GGAAAGCACCTTCTCGTTTTATTTAT 58.464 34.615 0.00 0.00 0.00 1.40
910 929 4.742201 CCACGTGTGAGAGGGCCG 62.742 72.222 15.65 0.00 0.00 6.13
915 934 3.625897 TGGGCCCACGTGTGAGAG 61.626 66.667 24.45 0.00 0.00 3.20
916 935 3.936203 GTGGGCCCACGTGTGAGA 61.936 66.667 38.35 3.30 37.19 3.27
970 989 0.466555 TTCGGGTTTCTGGGTGTTGG 60.467 55.000 0.00 0.00 0.00 3.77
971 990 0.951558 CTTCGGGTTTCTGGGTGTTG 59.048 55.000 0.00 0.00 0.00 3.33
972 991 0.822121 GCTTCGGGTTTCTGGGTGTT 60.822 55.000 0.00 0.00 0.00 3.32
975 994 2.434774 GGCTTCGGGTTTCTGGGT 59.565 61.111 0.00 0.00 0.00 4.51
977 996 2.746277 CGGGCTTCGGGTTTCTGG 60.746 66.667 0.00 0.00 34.75 3.86
978 997 3.431725 GCGGGCTTCGGGTTTCTG 61.432 66.667 2.64 0.00 39.69 3.02
1206 1235 6.310711 GCAATCAGTTGACTACAAGGTACTAC 59.689 42.308 0.00 0.00 35.60 2.73
1326 1357 5.530915 TGAATCAAACACAGTAACTTGGAGG 59.469 40.000 0.00 0.00 0.00 4.30
1329 1360 7.041167 TGAGATGAATCAAACACAGTAACTTGG 60.041 37.037 0.00 0.00 0.00 3.61
1404 1447 9.938280 TGCACACACTTCTATTTTAAGTATACT 57.062 29.630 0.00 0.00 35.44 2.12
1426 1469 2.610433 TCGTCTGAAGTGATCATGCAC 58.390 47.619 0.00 0.00 37.44 4.57
1539 1609 1.828832 TTGCAAGTTTTAACCGCACG 58.171 45.000 0.00 0.00 37.50 5.34
1572 1642 6.404403 GCAGTAAACTGAGGGTTATAAAAGGC 60.404 42.308 14.21 0.00 46.59 4.35
1607 1677 1.545211 TCCATAGGGGAGGGGTACG 59.455 63.158 0.00 0.00 42.15 3.67
1645 1716 0.740737 GAATGTAATGCCGCAAGCCT 59.259 50.000 0.00 0.00 42.71 4.58
1718 1789 3.535860 CCGTGTAAGCGTATACGTCTAC 58.464 50.000 25.04 23.16 41.68 2.59
1719 1790 2.543848 CCCGTGTAAGCGTATACGTCTA 59.456 50.000 25.04 14.23 41.68 2.59
1720 1791 1.331756 CCCGTGTAAGCGTATACGTCT 59.668 52.381 25.04 19.01 41.68 4.18
1721 1792 1.597937 CCCCGTGTAAGCGTATACGTC 60.598 57.143 25.04 17.22 41.68 4.34
1722 1793 0.381801 CCCCGTGTAAGCGTATACGT 59.618 55.000 25.04 10.14 41.68 3.57
1723 1794 0.936297 GCCCCGTGTAAGCGTATACG 60.936 60.000 20.87 20.87 42.56 3.06
1811 1882 0.036010 CCAGTTGGAGCAGGTAGTGG 60.036 60.000 0.00 0.00 37.39 4.00
1856 1927 3.951775 ACTTGTTCTGCTCCACTCTAG 57.048 47.619 0.00 0.00 0.00 2.43
2107 2180 9.722184 CACATTCACTATCTGGATCATAAGAAT 57.278 33.333 0.00 0.00 0.00 2.40
2256 2343 8.460831 AAACATAATTTCGAATTTAGTGCACC 57.539 30.769 14.63 0.00 0.00 5.01
2399 2490 5.819379 TGATGTTCCAGCAGAGATCAAATAC 59.181 40.000 0.00 0.00 0.00 1.89
2710 2806 9.851686 ATATAAAGCAAGTTATCAGATGGTTGA 57.148 29.630 0.00 0.00 34.13 3.18
2751 2858 9.283420 CAGTGAGTATAATACTTCAGCATATCG 57.717 37.037 0.00 0.00 39.59 2.92
2852 2962 2.051334 TCCAGCAACGGGGAAATATG 57.949 50.000 0.00 0.00 0.00 1.78
2901 3011 3.225104 TCAGAGCCAAGTTCTTGCAATT 58.775 40.909 0.00 0.00 0.00 2.32
3027 3137 8.319057 ACAGGAGTGTTTAATGATGGTAGATA 57.681 34.615 0.00 0.00 30.30 1.98
3062 3172 5.474532 ACTGCACATAAATGCTCTTCAGAAA 59.525 36.000 0.00 0.00 46.28 2.52
3118 3228 7.731054 AGAGAACTCAATAGTCAAGACAAAGT 58.269 34.615 2.72 0.00 33.75 2.66
3140 3250 4.159135 ACCTGCATTGGAAAATAGCAAGAG 59.841 41.667 0.00 0.00 34.45 2.85
3203 3313 7.919690 TGAGTGGAAATGATAAATTAGCTTCG 58.080 34.615 0.00 0.00 0.00 3.79
3333 3443 8.912988 GGTGACAAAAGGATATGATTGGAAATA 58.087 33.333 0.00 0.00 0.00 1.40
3367 3477 7.066163 CACAATAAGTCAGCATAACCATCTTCA 59.934 37.037 0.00 0.00 0.00 3.02
3415 3525 7.435192 ACTCAAAAGAAAGCAAATAAAACTCCG 59.565 33.333 0.00 0.00 0.00 4.63
3624 3736 4.268644 CACGCAAGATGTGATTAATCGTCT 59.731 41.667 10.80 10.55 39.73 4.18
3736 4031 4.436050 CCGGTTGTTTCTGAAGATGAATCG 60.436 45.833 0.00 0.00 0.00 3.34
3805 4100 3.254903 TGTATATCTTGGACCCGTGATCG 59.745 47.826 0.00 0.00 0.00 3.69
3954 4249 9.836179 ACCATGCCTAAAATATATATTCCCAAA 57.164 29.630 8.42 0.00 0.00 3.28
3955 4250 9.253832 CACCATGCCTAAAATATATATTCCCAA 57.746 33.333 8.42 0.00 0.00 4.12
3956 4251 8.397957 ACACCATGCCTAAAATATATATTCCCA 58.602 33.333 8.42 3.10 0.00 4.37
3957 4252 8.823220 ACACCATGCCTAAAATATATATTCCC 57.177 34.615 8.42 0.00 0.00 3.97
3960 4255 9.821240 TCCAACACCATGCCTAAAATATATATT 57.179 29.630 1.91 1.91 0.00 1.28
3961 4256 9.995594 ATCCAACACCATGCCTAAAATATATAT 57.004 29.630 0.00 0.00 0.00 0.86
3962 4257 9.241919 CATCCAACACCATGCCTAAAATATATA 57.758 33.333 0.00 0.00 0.00 0.86
3963 4258 7.729881 ACATCCAACACCATGCCTAAAATATAT 59.270 33.333 0.00 0.00 0.00 0.86
3972 4267 0.112995 ACACATCCAACACCATGCCT 59.887 50.000 0.00 0.00 0.00 4.75
3990 4285 8.507249 AGTACACTTTAGCAGATGAATGAAAAC 58.493 33.333 0.00 0.00 0.00 2.43
4218 4514 9.991906 TGTACTTGACTACTAATAGCAAAAACT 57.008 29.630 0.00 0.00 29.71 2.66
4223 4519 7.406031 AGCTGTACTTGACTACTAATAGCAA 57.594 36.000 0.00 0.00 30.75 3.91
4238 4534 7.052142 AGTTACTCTGTTTGTAGCTGTACTT 57.948 36.000 0.00 0.00 31.85 2.24
4336 4632 6.753180 TGTGTATGCAAAGGCTATTTTTGAA 58.247 32.000 0.00 0.00 41.91 2.69
4353 4649 1.909302 ACCCTCCTGAACCTGTGTATG 59.091 52.381 0.00 0.00 0.00 2.39
4358 4654 0.903454 CGGTACCCTCCTGAACCTGT 60.903 60.000 6.25 0.00 0.00 4.00
4375 4671 0.100682 CACTATGACGTGGTCTCCGG 59.899 60.000 0.00 0.00 33.15 5.14
4476 4772 3.265791 CCTTCCCTTTCTTCGACTCATG 58.734 50.000 0.00 0.00 0.00 3.07
4478 4774 2.037251 CACCTTCCCTTTCTTCGACTCA 59.963 50.000 0.00 0.00 0.00 3.41
4541 4837 2.031919 GTGTGGATGTGGTCGCCA 59.968 61.111 0.00 0.00 0.00 5.69
4693 4989 1.300971 CCCCACAGTTGAGCGTCATG 61.301 60.000 0.00 0.00 0.00 3.07
4695 4991 1.978455 AACCCCACAGTTGAGCGTCA 61.978 55.000 0.00 0.00 0.00 4.35
4696 4992 0.034337 TAACCCCACAGTTGAGCGTC 59.966 55.000 0.00 0.00 0.00 5.19
4711 5007 3.140623 TGTACGGAAGCCAGTTTTAACC 58.859 45.455 0.00 0.00 0.00 2.85
4723 5019 5.006358 GCATGGTTATACACTTGTACGGAAG 59.994 44.000 0.00 0.00 32.72 3.46
4725 5021 4.160814 AGCATGGTTATACACTTGTACGGA 59.839 41.667 0.00 0.00 32.72 4.69
4831 5127 3.753272 AGCAGAAACAAGCATATCACGTT 59.247 39.130 0.00 0.00 0.00 3.99
4834 5130 4.730035 GCAGAGCAGAAACAAGCATATCAC 60.730 45.833 0.00 0.00 0.00 3.06
5091 5387 5.830991 TGGGAAGTATTATTACATTGGGCAC 59.169 40.000 0.00 0.00 0.00 5.01
5112 5413 4.175953 CATCAAGATGCAGCCCAATGGG 62.176 54.545 15.45 15.45 37.72 4.00
5118 5419 1.105759 GGGACATCAAGATGCAGCCC 61.106 60.000 15.78 15.78 42.39 5.19
5181 5482 2.827921 CAATCCTGAAAGTTTCCCTGGG 59.172 50.000 13.01 6.33 0.00 4.45
5239 5540 6.638168 CATATATTGCATACAGTGACGGAG 57.362 41.667 0.00 0.00 0.00 4.63
5285 5586 0.038526 ACTAAAGGTGCCGAGACACG 60.039 55.000 0.00 0.00 41.65 4.49
5362 5663 1.528824 CCTCACCATGCCGGAGAAT 59.471 57.895 5.05 0.00 38.63 2.40
5404 5705 0.604780 TCTCGTCTTCGTCCTTCCGT 60.605 55.000 0.00 0.00 38.33 4.69


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

AutoCloner maintained by Alex Coulton.