Multiple sequence alignment - TraesCS1A01G108600

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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 TraesCS1A01G108600 chr1A 100.000 3608 0 0 1 3608 107779839 107776232 0.000000e+00 6663.0
1 TraesCS1A01G108600 chr1A 88.843 242 26 1 622 863 297126522 297126282 2.720000e-76 296.0
2 TraesCS1A01G108600 chr1A 87.347 245 31 0 619 863 546321124 546321368 7.630000e-72 281.0
3 TraesCS1A01G108600 chr1B 96.084 2094 57 7 1516 3607 120061421 120059351 0.000000e+00 3389.0
4 TraesCS1A01G108600 chr1B 95.577 633 16 3 898 1518 120062125 120061493 0.000000e+00 1003.0
5 TraesCS1A01G108600 chrUn 92.525 495 34 2 1 494 26918565 26918073 0.000000e+00 706.0
6 TraesCS1A01G108600 chrUn 91.515 495 40 2 1 494 18791940 18792433 0.000000e+00 680.0
7 TraesCS1A01G108600 chr5B 87.542 594 62 10 1 583 623015026 623015618 0.000000e+00 676.0
8 TraesCS1A01G108600 chr2D 91.331 496 41 1 1 494 578999842 579000337 0.000000e+00 676.0
9 TraesCS1A01G108600 chr2D 100.000 30 0 0 501 530 423608553 423608524 5.030000e-04 56.5
10 TraesCS1A01G108600 chr6B 86.504 615 73 7 1 606 683982260 683981647 0.000000e+00 667.0
11 TraesCS1A01G108600 chr5D 87.437 597 53 9 1 576 473066888 473066293 0.000000e+00 667.0
12 TraesCS1A01G108600 chr7A 90.909 495 44 1 1 494 444977662 444978156 0.000000e+00 664.0
13 TraesCS1A01G108600 chr7A 88.259 247 24 3 993 1238 467418579 467418821 1.270000e-74 291.0
14 TraesCS1A01G108600 chr7A 87.190 242 31 0 622 863 284788024 284787783 3.550000e-70 276.0
15 TraesCS1A01G108600 chr7A 81.016 374 42 13 993 1359 467848952 467849303 1.650000e-68 270.0
16 TraesCS1A01G108600 chr7D 86.252 611 70 12 1 601 91741956 91742562 0.000000e+00 651.0
17 TraesCS1A01G108600 chr7D 85.599 618 74 8 1 605 569041526 569042141 5.080000e-178 634.0
18 TraesCS1A01G108600 chr2A 89.669 242 25 0 622 863 1507274 1507033 3.500000e-80 309.0
19 TraesCS1A01G108600 chr7B 87.454 271 29 3 993 1262 421072912 421072646 1.260000e-79 307.0
20 TraesCS1A01G108600 chr7B 87.085 271 30 3 993 1262 422894243 422894509 5.850000e-78 302.0
21 TraesCS1A01G108600 chr4A 88.462 234 27 0 630 863 541323103 541322870 2.120000e-72 283.0
22 TraesCS1A01G108600 chr4A 86.939 245 32 0 619 863 470875167 470875411 3.550000e-70 276.0
23 TraesCS1A01G108600 chr4A 86.885 244 28 3 622 863 685780529 685780288 1.650000e-68 270.0
24 TraesCS1A01G108600 chr5A 87.398 246 29 2 618 863 549412795 549413038 7.630000e-72 281.0
25 TraesCS1A01G108600 chr3D 86.992 246 31 1 619 863 162709627 162709872 3.550000e-70 276.0


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 TraesCS1A01G108600 chr1A 107776232 107779839 3607 True 6663 6663 100.0000 1 3608 1 chr1A.!!$R1 3607
1 TraesCS1A01G108600 chr1B 120059351 120062125 2774 True 2196 3389 95.8305 898 3607 2 chr1B.!!$R1 2709
2 TraesCS1A01G108600 chr5B 623015026 623015618 592 False 676 676 87.5420 1 583 1 chr5B.!!$F1 582
3 TraesCS1A01G108600 chr6B 683981647 683982260 613 True 667 667 86.5040 1 606 1 chr6B.!!$R1 605
4 TraesCS1A01G108600 chr5D 473066293 473066888 595 True 667 667 87.4370 1 576 1 chr5D.!!$R1 575
5 TraesCS1A01G108600 chr7D 91741956 91742562 606 False 651 651 86.2520 1 601 1 chr7D.!!$F1 600
6 TraesCS1A01G108600 chr7D 569041526 569042141 615 False 634 634 85.5990 1 605 1 chr7D.!!$F2 604

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
868 894 0.249489 CACTATGACTAGCCCGGCAC 60.249 60.0 13.15 0.63 0.00 5.01 F
1878 1990 0.040425 GCGTTTGCAGGTCGTCATTT 60.040 50.0 8.51 0.00 42.15 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 2684 0.035152 TACAGCATGGTGGCCTTCTG 60.035 55.0 27.32 10.11 43.62 3.02 R
2800 2912 2.926778 ACCTTAGGATGCTCATCTGC 57.073 50.0 4.77 0.00 37.92 4.26 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
40 41 6.950842 TCAAATGTAGGAGATCATGACTTGT 58.049 36.000 0.00 0.00 0.00 3.16
68 69 6.374894 TGTCATCTTGCACAACATGATCATTA 59.625 34.615 5.16 0.00 40.26 1.90
139 140 0.944386 GTCCTCTTGCGCAAGTTGAA 59.056 50.000 40.37 25.30 39.38 2.69
261 262 2.347490 GAGGCTCAAGGGCAACGA 59.653 61.111 10.25 0.00 43.56 3.85
397 403 2.053627 GTTGAATTTGCGCTGAACCAG 58.946 47.619 9.73 0.00 34.12 4.00
411 417 1.645402 AACCAGGGCGAATATGGGCT 61.645 55.000 0.00 0.00 38.48 5.19
426 432 2.331265 GGCTGATTTGCCCCGATAC 58.669 57.895 0.00 0.00 46.82 2.24
442 448 2.199236 GATACCGAGCCGATTTTTCGT 58.801 47.619 0.00 0.00 32.73 3.85
443 449 2.083167 TACCGAGCCGATTTTTCGTT 57.917 45.000 0.00 0.00 32.73 3.85
460 466 2.100916 TCGTTGAAAATGGGCCGAAAAA 59.899 40.909 0.00 0.00 32.44 1.94
462 468 3.198872 GTTGAAAATGGGCCGAAAAACA 58.801 40.909 0.00 0.00 0.00 2.83
464 470 2.695666 TGAAAATGGGCCGAAAAACAGA 59.304 40.909 0.00 0.00 0.00 3.41
474 480 3.443037 CCGAAAAACAGACACATTTGCA 58.557 40.909 0.00 0.00 0.00 4.08
494 500 3.005684 GCATCAAAAATGGGCCGATATCA 59.994 43.478 0.00 0.00 0.00 2.15
495 501 4.501229 GCATCAAAAATGGGCCGATATCAA 60.501 41.667 0.00 0.00 0.00 2.57
496 502 5.599732 CATCAAAAATGGGCCGATATCAAA 58.400 37.500 0.00 0.00 0.00 2.69
498 504 6.042638 TCAAAAATGGGCCGATATCAAAAA 57.957 33.333 0.00 0.00 0.00 1.94
499 505 6.648192 TCAAAAATGGGCCGATATCAAAAAT 58.352 32.000 0.00 0.00 0.00 1.82
530 549 1.077716 GGGAACTCAATCACCCCCG 60.078 63.158 0.00 0.00 36.65 5.73
531 550 1.683441 GGAACTCAATCACCCCCGT 59.317 57.895 0.00 0.00 0.00 5.28
546 566 1.082117 CCCGTGTCGATTTTAGCGCT 61.082 55.000 17.26 17.26 0.00 5.92
601 627 3.434319 CAACGGCCAGCGATGCTT 61.434 61.111 2.24 0.00 36.40 3.91
602 628 2.672996 AACGGCCAGCGATGCTTT 60.673 55.556 2.24 0.00 36.40 3.51
603 629 2.268076 AACGGCCAGCGATGCTTTT 61.268 52.632 2.24 0.00 36.40 2.27
604 630 0.958382 AACGGCCAGCGATGCTTTTA 60.958 50.000 2.24 0.00 36.40 1.52
605 631 1.353103 CGGCCAGCGATGCTTTTAG 59.647 57.895 2.24 0.00 36.40 1.85
606 632 1.089481 CGGCCAGCGATGCTTTTAGA 61.089 55.000 2.24 0.00 36.40 2.10
607 633 1.312815 GGCCAGCGATGCTTTTAGAT 58.687 50.000 0.00 0.00 36.40 1.98
608 634 1.678101 GGCCAGCGATGCTTTTAGATT 59.322 47.619 0.00 0.00 36.40 2.40
609 635 2.542411 GGCCAGCGATGCTTTTAGATTG 60.542 50.000 0.00 0.00 36.40 2.67
610 636 2.542411 GCCAGCGATGCTTTTAGATTGG 60.542 50.000 0.00 0.00 36.40 3.16
611 637 2.684881 CCAGCGATGCTTTTAGATTGGT 59.315 45.455 0.00 0.00 36.40 3.67
612 638 3.242870 CCAGCGATGCTTTTAGATTGGTC 60.243 47.826 0.00 0.00 36.40 4.02
613 639 3.374988 CAGCGATGCTTTTAGATTGGTCA 59.625 43.478 0.00 0.00 36.40 4.02
614 640 4.036027 CAGCGATGCTTTTAGATTGGTCAT 59.964 41.667 0.00 0.00 36.40 3.06
615 641 5.237127 CAGCGATGCTTTTAGATTGGTCATA 59.763 40.000 0.00 0.00 36.40 2.15
616 642 5.468072 AGCGATGCTTTTAGATTGGTCATAG 59.532 40.000 0.00 0.00 33.89 2.23
617 643 5.466728 GCGATGCTTTTAGATTGGTCATAGA 59.533 40.000 0.00 0.00 0.00 1.98
618 644 6.017934 GCGATGCTTTTAGATTGGTCATAGAA 60.018 38.462 0.00 0.00 0.00 2.10
619 645 7.571026 CGATGCTTTTAGATTGGTCATAGAAG 58.429 38.462 0.00 0.00 0.00 2.85
620 646 7.439356 CGATGCTTTTAGATTGGTCATAGAAGA 59.561 37.037 0.00 0.00 0.00 2.87
621 647 9.113838 GATGCTTTTAGATTGGTCATAGAAGAA 57.886 33.333 0.00 0.00 0.00 2.52
622 648 8.862325 TGCTTTTAGATTGGTCATAGAAGAAA 57.138 30.769 0.00 0.00 0.00 2.52
623 649 8.730680 TGCTTTTAGATTGGTCATAGAAGAAAC 58.269 33.333 0.00 0.00 0.00 2.78
624 650 8.951243 GCTTTTAGATTGGTCATAGAAGAAACT 58.049 33.333 0.00 0.00 0.00 2.66
676 702 7.493367 ACTCTAAGTTACCATTCTCATAGTGC 58.507 38.462 0.00 0.00 0.00 4.40
677 703 7.124298 ACTCTAAGTTACCATTCTCATAGTGCA 59.876 37.037 0.00 0.00 0.00 4.57
678 704 7.847096 TCTAAGTTACCATTCTCATAGTGCAA 58.153 34.615 0.00 0.00 0.00 4.08
679 705 8.318412 TCTAAGTTACCATTCTCATAGTGCAAA 58.682 33.333 0.00 0.00 0.00 3.68
680 706 6.992063 AGTTACCATTCTCATAGTGCAAAG 57.008 37.500 0.00 0.00 0.00 2.77
681 707 6.476378 AGTTACCATTCTCATAGTGCAAAGT 58.524 36.000 0.00 0.00 0.00 2.66
682 708 7.620880 AGTTACCATTCTCATAGTGCAAAGTA 58.379 34.615 0.00 0.00 0.00 2.24
683 709 8.100791 AGTTACCATTCTCATAGTGCAAAGTAA 58.899 33.333 0.00 0.00 0.00 2.24
684 710 8.893727 GTTACCATTCTCATAGTGCAAAGTAAT 58.106 33.333 0.00 0.00 0.00 1.89
708 734 9.535170 AATATAGTAGTAGTGTCATATGTGGCT 57.465 33.333 1.90 2.27 0.00 4.75
709 735 7.841282 ATAGTAGTAGTGTCATATGTGGCTT 57.159 36.000 1.90 0.00 0.00 4.35
710 736 6.150396 AGTAGTAGTGTCATATGTGGCTTC 57.850 41.667 1.90 0.00 0.00 3.86
711 737 5.656859 AGTAGTAGTGTCATATGTGGCTTCA 59.343 40.000 1.90 0.00 0.00 3.02
712 738 5.620738 AGTAGTGTCATATGTGGCTTCAT 57.379 39.130 1.90 0.00 0.00 2.57
713 739 5.994250 AGTAGTGTCATATGTGGCTTCATT 58.006 37.500 1.90 0.00 0.00 2.57
714 740 6.418101 AGTAGTGTCATATGTGGCTTCATTT 58.582 36.000 1.90 0.00 0.00 2.32
715 741 7.564793 AGTAGTGTCATATGTGGCTTCATTTA 58.435 34.615 1.90 0.00 0.00 1.40
716 742 8.046708 AGTAGTGTCATATGTGGCTTCATTTAA 58.953 33.333 1.90 0.00 0.00 1.52
717 743 7.886629 AGTGTCATATGTGGCTTCATTTAAT 57.113 32.000 1.90 0.00 0.00 1.40
718 744 8.978874 AGTGTCATATGTGGCTTCATTTAATA 57.021 30.769 1.90 0.00 0.00 0.98
719 745 9.060347 AGTGTCATATGTGGCTTCATTTAATAG 57.940 33.333 1.90 0.00 0.00 1.73
720 746 7.805071 GTGTCATATGTGGCTTCATTTAATAGC 59.195 37.037 1.90 0.00 0.00 2.97
721 747 7.720957 TGTCATATGTGGCTTCATTTAATAGCT 59.279 33.333 1.90 0.00 35.30 3.32
722 748 8.571336 GTCATATGTGGCTTCATTTAATAGCTT 58.429 33.333 1.90 0.00 35.30 3.74
723 749 8.570488 TCATATGTGGCTTCATTTAATAGCTTG 58.430 33.333 1.90 0.00 35.30 4.01
724 750 6.780457 ATGTGGCTTCATTTAATAGCTTGT 57.220 33.333 0.00 0.00 35.30 3.16
725 751 7.880160 ATGTGGCTTCATTTAATAGCTTGTA 57.120 32.000 0.00 0.00 35.30 2.41
726 752 7.880160 TGTGGCTTCATTTAATAGCTTGTAT 57.120 32.000 0.00 0.00 35.30 2.29
727 753 8.972458 TGTGGCTTCATTTAATAGCTTGTATA 57.028 30.769 0.00 0.00 35.30 1.47
728 754 8.836413 TGTGGCTTCATTTAATAGCTTGTATAC 58.164 33.333 0.00 0.00 35.30 1.47
729 755 9.057089 GTGGCTTCATTTAATAGCTTGTATACT 57.943 33.333 4.17 0.00 35.30 2.12
730 756 9.273016 TGGCTTCATTTAATAGCTTGTATACTC 57.727 33.333 4.17 0.00 35.30 2.59
731 757 9.273016 GGCTTCATTTAATAGCTTGTATACTCA 57.727 33.333 4.17 0.00 35.30 3.41
741 767 6.974932 AGCTTGTATACTCATGTTGTCTTG 57.025 37.500 4.17 0.00 0.00 3.02
742 768 6.701340 AGCTTGTATACTCATGTTGTCTTGA 58.299 36.000 4.17 0.00 0.00 3.02
743 769 7.161404 AGCTTGTATACTCATGTTGTCTTGAA 58.839 34.615 4.17 0.00 0.00 2.69
744 770 7.661437 AGCTTGTATACTCATGTTGTCTTGAAA 59.339 33.333 4.17 0.00 0.00 2.69
745 771 8.289618 GCTTGTATACTCATGTTGTCTTGAAAA 58.710 33.333 4.17 0.00 0.00 2.29
747 773 9.944663 TTGTATACTCATGTTGTCTTGAAAAAC 57.055 29.630 4.17 0.00 0.00 2.43
748 774 9.114952 TGTATACTCATGTTGTCTTGAAAAACA 57.885 29.630 4.17 0.00 38.13 2.83
749 775 9.382244 GTATACTCATGTTGTCTTGAAAAACAC 57.618 33.333 0.00 0.00 36.69 3.32
750 776 6.515272 ACTCATGTTGTCTTGAAAAACACT 57.485 33.333 0.00 0.00 36.69 3.55
751 777 7.624360 ACTCATGTTGTCTTGAAAAACACTA 57.376 32.000 0.00 0.00 36.69 2.74
752 778 8.225603 ACTCATGTTGTCTTGAAAAACACTAT 57.774 30.769 0.00 0.00 36.69 2.12
753 779 8.131100 ACTCATGTTGTCTTGAAAAACACTATG 58.869 33.333 0.00 0.00 36.69 2.23
754 780 7.995289 TCATGTTGTCTTGAAAAACACTATGT 58.005 30.769 0.00 0.00 36.69 2.29
755 781 8.465999 TCATGTTGTCTTGAAAAACACTATGTT 58.534 29.630 0.00 0.00 43.41 2.71
756 782 9.729023 CATGTTGTCTTGAAAAACACTATGTTA 57.271 29.630 0.00 0.00 40.14 2.41
757 783 9.730420 ATGTTGTCTTGAAAAACACTATGTTAC 57.270 29.630 0.00 0.00 40.14 2.50
758 784 8.731605 TGTTGTCTTGAAAAACACTATGTTACA 58.268 29.630 0.00 0.00 40.14 2.41
759 785 9.221775 GTTGTCTTGAAAAACACTATGTTACAG 57.778 33.333 0.00 0.00 40.14 2.74
760 786 8.500753 TGTCTTGAAAAACACTATGTTACAGT 57.499 30.769 0.00 0.00 40.14 3.55
761 787 9.602568 TGTCTTGAAAAACACTATGTTACAGTA 57.397 29.630 0.00 0.00 40.14 2.74
786 812 7.886629 ACATATTATGTTGCCACTTCTCATT 57.113 32.000 3.40 0.00 41.63 2.57
787 813 8.978874 ACATATTATGTTGCCACTTCTCATTA 57.021 30.769 3.40 0.00 41.63 1.90
788 814 9.407380 ACATATTATGTTGCCACTTCTCATTAA 57.593 29.630 3.40 0.00 41.63 1.40
789 815 9.669353 CATATTATGTTGCCACTTCTCATTAAC 57.331 33.333 0.00 0.00 0.00 2.01
790 816 7.944729 ATTATGTTGCCACTTCTCATTAACT 57.055 32.000 0.00 0.00 0.00 2.24
792 818 6.743575 ATGTTGCCACTTCTCATTAACTAC 57.256 37.500 0.00 0.00 0.00 2.73
793 819 5.865085 TGTTGCCACTTCTCATTAACTACT 58.135 37.500 0.00 0.00 0.00 2.57
794 820 6.296026 TGTTGCCACTTCTCATTAACTACTT 58.704 36.000 0.00 0.00 0.00 2.24
795 821 6.204688 TGTTGCCACTTCTCATTAACTACTTG 59.795 38.462 0.00 0.00 0.00 3.16
796 822 4.695455 TGCCACTTCTCATTAACTACTTGC 59.305 41.667 0.00 0.00 0.00 4.01
797 823 4.938226 GCCACTTCTCATTAACTACTTGCT 59.062 41.667 0.00 0.00 0.00 3.91
798 824 6.106673 GCCACTTCTCATTAACTACTTGCTA 58.893 40.000 0.00 0.00 0.00 3.49
799 825 6.036191 GCCACTTCTCATTAACTACTTGCTAC 59.964 42.308 0.00 0.00 0.00 3.58
800 826 7.097192 CCACTTCTCATTAACTACTTGCTACA 58.903 38.462 0.00 0.00 0.00 2.74
801 827 7.766278 CCACTTCTCATTAACTACTTGCTACAT 59.234 37.037 0.00 0.00 0.00 2.29
802 828 9.803315 CACTTCTCATTAACTACTTGCTACATA 57.197 33.333 0.00 0.00 0.00 2.29
823 849 8.693542 ACATAAGCAAAAATATCTCAAAGTGC 57.306 30.769 0.00 0.00 0.00 4.40
824 850 7.485913 ACATAAGCAAAAATATCTCAAAGTGCG 59.514 33.333 0.00 0.00 35.92 5.34
825 851 5.376854 AGCAAAAATATCTCAAAGTGCGT 57.623 34.783 0.00 0.00 35.92 5.24
826 852 5.772521 AGCAAAAATATCTCAAAGTGCGTT 58.227 33.333 0.00 0.00 35.92 4.84
827 853 6.908825 AGCAAAAATATCTCAAAGTGCGTTA 58.091 32.000 0.00 0.00 35.92 3.18
828 854 7.538575 AGCAAAAATATCTCAAAGTGCGTTAT 58.461 30.769 0.00 0.00 35.92 1.89
829 855 7.485913 AGCAAAAATATCTCAAAGTGCGTTATG 59.514 33.333 0.00 0.00 35.92 1.90
830 856 7.273381 GCAAAAATATCTCAAAGTGCGTTATGT 59.727 33.333 0.00 0.00 0.00 2.29
831 857 9.128107 CAAAAATATCTCAAAGTGCGTTATGTT 57.872 29.630 0.00 0.00 0.00 2.71
835 861 9.935682 AATATCTCAAAGTGCGTTATGTTATTG 57.064 29.630 0.00 0.00 0.00 1.90
836 862 6.795098 TCTCAAAGTGCGTTATGTTATTGT 57.205 33.333 0.00 0.00 0.00 2.71
837 863 7.197071 TCTCAAAGTGCGTTATGTTATTGTT 57.803 32.000 0.00 0.00 0.00 2.83
838 864 7.644490 TCTCAAAGTGCGTTATGTTATTGTTT 58.356 30.769 0.00 0.00 0.00 2.83
839 865 8.775527 TCTCAAAGTGCGTTATGTTATTGTTTA 58.224 29.630 0.00 0.00 0.00 2.01
840 866 9.388346 CTCAAAGTGCGTTATGTTATTGTTTAA 57.612 29.630 0.00 0.00 0.00 1.52
841 867 9.388346 TCAAAGTGCGTTATGTTATTGTTTAAG 57.612 29.630 0.00 0.00 0.00 1.85
842 868 9.176181 CAAAGTGCGTTATGTTATTGTTTAAGT 57.824 29.630 0.00 0.00 0.00 2.24
843 869 9.738832 AAAGTGCGTTATGTTATTGTTTAAGTT 57.261 25.926 0.00 0.00 0.00 2.66
845 871 9.815936 AGTGCGTTATGTTATTGTTTAAGTTAC 57.184 29.630 0.00 0.00 0.00 2.50
846 872 9.815936 GTGCGTTATGTTATTGTTTAAGTTACT 57.184 29.630 0.00 0.00 0.00 2.24
861 887 9.505995 GTTTAAGTTACTCTCACTATGACTAGC 57.494 37.037 0.00 0.00 0.00 3.42
862 888 6.702716 AAGTTACTCTCACTATGACTAGCC 57.297 41.667 0.00 0.00 0.00 3.93
863 889 5.134661 AGTTACTCTCACTATGACTAGCCC 58.865 45.833 0.00 0.00 0.00 5.19
864 890 2.577700 ACTCTCACTATGACTAGCCCG 58.422 52.381 0.00 0.00 0.00 6.13
865 891 1.883275 CTCTCACTATGACTAGCCCGG 59.117 57.143 0.00 0.00 0.00 5.73
866 892 0.315568 CTCACTATGACTAGCCCGGC 59.684 60.000 0.00 0.00 0.00 6.13
867 893 0.396556 TCACTATGACTAGCCCGGCA 60.397 55.000 13.15 0.00 0.00 5.69
868 894 0.249489 CACTATGACTAGCCCGGCAC 60.249 60.000 13.15 0.63 0.00 5.01
869 895 0.686441 ACTATGACTAGCCCGGCACA 60.686 55.000 13.15 6.63 0.00 4.57
870 896 0.681733 CTATGACTAGCCCGGCACAT 59.318 55.000 13.15 13.14 0.00 3.21
871 897 0.679505 TATGACTAGCCCGGCACATC 59.320 55.000 13.15 6.03 0.00 3.06
872 898 1.050988 ATGACTAGCCCGGCACATCT 61.051 55.000 13.15 0.00 0.00 2.90
873 899 0.396556 TGACTAGCCCGGCACATCTA 60.397 55.000 13.15 0.00 0.00 1.98
874 900 0.750850 GACTAGCCCGGCACATCTAA 59.249 55.000 13.15 0.00 0.00 2.10
875 901 1.138266 GACTAGCCCGGCACATCTAAA 59.862 52.381 13.15 0.00 0.00 1.85
876 902 1.768870 ACTAGCCCGGCACATCTAAAT 59.231 47.619 13.15 0.00 0.00 1.40
877 903 2.969950 ACTAGCCCGGCACATCTAAATA 59.030 45.455 13.15 0.00 0.00 1.40
878 904 3.583086 ACTAGCCCGGCACATCTAAATAT 59.417 43.478 13.15 0.00 0.00 1.28
879 905 2.783135 AGCCCGGCACATCTAAATATG 58.217 47.619 13.15 0.00 0.00 1.78
880 906 1.200020 GCCCGGCACATCTAAATATGC 59.800 52.381 3.91 0.00 37.35 3.14
881 907 2.783135 CCCGGCACATCTAAATATGCT 58.217 47.619 0.00 0.00 38.18 3.79
882 908 2.485426 CCCGGCACATCTAAATATGCTG 59.515 50.000 0.00 0.00 42.87 4.41
883 909 3.141398 CCGGCACATCTAAATATGCTGT 58.859 45.455 0.00 0.00 41.89 4.40
884 910 4.314961 CCGGCACATCTAAATATGCTGTA 58.685 43.478 0.00 0.00 41.89 2.74
885 911 4.389992 CCGGCACATCTAAATATGCTGTAG 59.610 45.833 0.00 0.00 41.89 2.74
886 912 4.143030 CGGCACATCTAAATATGCTGTAGC 60.143 45.833 0.00 0.00 39.20 3.58
904 930 6.692249 GCTGTAGCAAAACGGTAAAGTAAAAA 59.308 34.615 0.00 0.00 41.59 1.94
916 942 7.015389 ACGGTAAAGTAAAAATCAATTCCCCAA 59.985 33.333 0.00 0.00 0.00 4.12
918 944 7.604927 GGTAAAGTAAAAATCAATTCCCCAACC 59.395 37.037 0.00 0.00 0.00 3.77
920 946 3.694043 AAAAATCAATTCCCCAACCCG 57.306 42.857 0.00 0.00 0.00 5.28
949 975 2.202837 GCGATCGTAAAGGCCCGT 60.203 61.111 17.81 0.00 0.00 5.28
951 977 2.522638 CGATCGTAAAGGCCCGTGC 61.523 63.158 7.03 0.00 0.00 5.34
980 1006 2.507992 CTCTCTTGCTGACCGCGG 60.508 66.667 26.86 26.86 43.27 6.46
1055 1087 4.754667 GTCCGGACCAACCCTCGC 62.755 72.222 24.75 0.00 34.64 5.03
1092 1124 1.734477 CTCCACCGTCTCAGCAACG 60.734 63.158 0.00 0.00 39.78 4.10
1329 1367 2.412089 GCAGATTCCGGATGCGTTATAC 59.588 50.000 12.49 0.00 0.00 1.47
1347 1385 6.689241 CGTTATACGAAGATCTGGATATGCTC 59.311 42.308 0.00 0.00 46.05 4.26
1363 1401 2.097036 TGCTCAAGGCCATTCAAGATG 58.903 47.619 5.01 0.00 40.92 2.90
1440 1478 5.008217 CCTTTTAATGTTTCACGTCCTGTCA 59.992 40.000 0.00 0.00 0.00 3.58
1484 1522 2.369860 TGCCTGTGAGAGACAAGAACAT 59.630 45.455 0.00 0.00 32.80 2.71
1598 1710 7.970061 GCTGAAATCAAATGACAGTTTAGCATA 59.030 33.333 11.76 0.00 31.52 3.14
1635 1747 1.171308 TTGCTGATCTTCTTGCAGGC 58.829 50.000 0.00 0.00 36.75 4.85
1722 1834 1.067776 CCTAAGCTTCTTCGTGTCCGT 60.068 52.381 0.00 0.00 35.01 4.69
1779 1891 6.122277 TCCATCAGTTATTGGACTTTCATCC 58.878 40.000 0.00 0.00 37.10 3.51
1793 1905 5.491982 ACTTTCATCCTCTGTTGGTATGAC 58.508 41.667 0.00 0.00 0.00 3.06
1818 1930 9.383519 ACAACTATGTCATGTCTATTTGTTAGG 57.616 33.333 0.00 0.00 33.41 2.69
1852 1964 7.201530 CGAGAATAGGTTGTTCCTTGTTCATAC 60.202 40.741 11.37 0.00 45.67 2.39
1878 1990 0.040425 GCGTTTGCAGGTCGTCATTT 60.040 50.000 8.51 0.00 42.15 2.32
1921 2033 1.999295 TGGGTTGATTGGGATGAGGAA 59.001 47.619 0.00 0.00 0.00 3.36
1955 2067 4.818534 ACTGTTTTGACTACTGCACATG 57.181 40.909 0.00 0.00 0.00 3.21
2048 2160 7.611855 AGGTGAGTTGTTAAGGATAGGAAAATG 59.388 37.037 0.00 0.00 0.00 2.32
2066 2178 7.232534 AGGAAAATGGCAGTTTGTATTCACTTA 59.767 33.333 18.48 0.00 0.00 2.24
2097 2209 6.377146 TGTGCATGTAGTCTCATACTAGTTCA 59.623 38.462 0.00 0.00 41.42 3.18
2131 2243 6.811253 ACTCATTTTATTTGTGGCGTAAGA 57.189 33.333 0.00 0.00 43.02 2.10
2168 2280 5.820423 TCCACATTTAACATAACTCCATCCG 59.180 40.000 0.00 0.00 0.00 4.18
2178 2290 0.249398 ACTCCATCCGCAGTTACACC 59.751 55.000 0.00 0.00 0.00 4.16
2180 2292 0.249120 TCCATCCGCAGTTACACCTG 59.751 55.000 0.00 0.00 35.49 4.00
2206 2318 9.405587 GCATATTCTATCTTCTGACACTAGAAC 57.594 37.037 0.00 0.00 32.82 3.01
2213 2325 5.502079 TCTTCTGACACTAGAACTAGGGAG 58.498 45.833 16.62 5.94 38.86 4.30
2264 2376 6.260936 ACACAATGATACAATTAGCTAGCACC 59.739 38.462 18.83 0.00 0.00 5.01
2308 2420 4.648307 TGGTAAACCATGCATGCATAATGA 59.352 37.500 31.73 14.08 42.01 2.57
2309 2421 5.128335 TGGTAAACCATGCATGCATAATGAA 59.872 36.000 31.73 15.26 42.01 2.57
2310 2422 6.183360 TGGTAAACCATGCATGCATAATGAAT 60.183 34.615 31.73 17.79 42.01 2.57
2311 2423 6.366877 GGTAAACCATGCATGCATAATGAATC 59.633 38.462 31.73 18.21 31.38 2.52
2312 2424 5.538849 AACCATGCATGCATAATGAATCA 57.461 34.783 31.73 0.55 38.72 2.57
2313 2425 5.538849 ACCATGCATGCATAATGAATCAA 57.461 34.783 31.73 0.00 38.72 2.57
2314 2426 6.109156 ACCATGCATGCATAATGAATCAAT 57.891 33.333 31.73 4.38 38.72 2.57
2315 2427 6.530120 ACCATGCATGCATAATGAATCAATT 58.470 32.000 31.73 4.16 38.72 2.32
2316 2428 6.649141 ACCATGCATGCATAATGAATCAATTC 59.351 34.615 31.73 0.00 38.72 2.17
2317 2429 6.648725 CCATGCATGCATAATGAATCAATTCA 59.351 34.615 31.73 7.82 41.63 2.57
2318 2430 7.172361 CCATGCATGCATAATGAATCAATTCAA 59.828 33.333 31.73 0.00 41.20 2.69
2319 2431 8.720562 CATGCATGCATAATGAATCAATTCAAT 58.279 29.630 31.73 2.14 41.20 2.57
2436 2548 8.553153 TGACCAATTTAAGAAGACATGGGTATA 58.447 33.333 0.00 0.00 0.00 1.47
2490 2602 9.793259 TTCTAACTTCTAAGACATCATTGGTTT 57.207 29.630 0.00 0.00 0.00 3.27
2500 2612 6.748132 AGACATCATTGGTTTTCGAACAAAT 58.252 32.000 0.00 0.00 0.00 2.32
2556 2668 6.155827 TCTGTTTCAGGTTTTTGTTCACTTG 58.844 36.000 0.00 0.00 31.51 3.16
2572 2684 0.811616 CTTGCGGGATGCCACTACTC 60.812 60.000 3.39 0.00 45.60 2.59
2607 2719 3.374367 TGCTGTACTACGAGAAGCACTAG 59.626 47.826 0.00 0.00 38.88 2.57
2620 2732 5.055812 AGAAGCACTAGAATCTTGCTATGC 58.944 41.667 9.58 4.17 45.93 3.14
2637 2749 5.656859 TGCTATGCTTGAGGTTAGAGTAGAA 59.343 40.000 0.00 0.00 0.00 2.10
2800 2912 4.620982 TCACTATCTGTATGTTCATGGCG 58.379 43.478 0.00 0.00 0.00 5.69
2819 2931 1.069823 CGCAGATGAGCATCCTAAGGT 59.930 52.381 6.84 0.00 38.58 3.50
2832 2944 7.445945 AGCATCCTAAGGTACAGATTGTAATC 58.554 38.462 0.00 0.00 34.21 1.75
3018 3130 1.374758 CAACAGCACGAGAGGGTCC 60.375 63.158 0.00 0.00 36.38 4.46
3024 3136 1.689273 AGCACGAGAGGGTCCATTATC 59.311 52.381 0.00 0.00 36.38 1.75
3060 3172 2.800629 GCTCAAGTGCTTGCATTTGTGT 60.801 45.455 23.29 0.00 40.24 3.72
3095 3207 8.846211 TGGGTATTGTCTTTTCTTTTAGTTCTG 58.154 33.333 0.00 0.00 0.00 3.02
3201 3313 4.811555 TGAGTTGTTCCACTTCGATTTG 57.188 40.909 0.00 0.00 0.00 2.32
3202 3314 4.196193 TGAGTTGTTCCACTTCGATTTGT 58.804 39.130 0.00 0.00 0.00 2.83
3203 3315 4.272504 TGAGTTGTTCCACTTCGATTTGTC 59.727 41.667 0.00 0.00 0.00 3.18
3204 3316 4.451900 AGTTGTTCCACTTCGATTTGTCT 58.548 39.130 0.00 0.00 0.00 3.41
3250 3363 6.620678 TCTTTCAAATATAGTTTGCTGCCAC 58.379 36.000 0.00 0.00 0.00 5.01
3263 3376 3.480133 GCCACGGGGGATAGCTGT 61.480 66.667 5.47 0.00 40.01 4.40
3294 3407 4.776647 GCCATTGGACGCGTTGCC 62.777 66.667 15.53 12.26 0.00 4.52
3295 3408 3.055719 CCATTGGACGCGTTGCCT 61.056 61.111 15.53 0.00 0.00 4.75
3296 3409 2.625823 CCATTGGACGCGTTGCCTT 61.626 57.895 15.53 0.00 0.00 4.35
3297 3410 1.442520 CATTGGACGCGTTGCCTTG 60.443 57.895 15.53 9.44 0.00 3.61
3298 3411 2.625823 ATTGGACGCGTTGCCTTGG 61.626 57.895 15.53 0.00 0.00 3.61
3301 3414 2.746277 GACGCGTTGCCTTGGGAT 60.746 61.111 15.53 0.00 0.00 3.85
3327 3440 5.542635 TGTGTCCTCAACTTGGTAGTAATCT 59.457 40.000 0.00 0.00 33.17 2.40
3392 3505 5.221641 ACAAATGAGTGCTACTTACACCTGA 60.222 40.000 0.00 0.00 38.87 3.86
3404 3517 0.394938 ACACCTGACATTGCGTACCA 59.605 50.000 0.00 0.00 0.00 3.25
3412 3525 5.758296 CCTGACATTGCGTACCATACTTATT 59.242 40.000 0.00 0.00 0.00 1.40
3418 3531 7.982919 ACATTGCGTACCATACTTATTACTTGA 59.017 33.333 0.00 0.00 0.00 3.02
3462 3575 1.039068 TGGTGAACATGTTGCTTGGG 58.961 50.000 17.58 0.00 0.00 4.12
3479 3592 5.658634 TGCTTGGGTTTATGTGCCATATTTA 59.341 36.000 0.00 0.00 0.00 1.40
3576 3690 6.486657 TGAGAACAAGCAAATACTGTAAGCTT 59.513 34.615 15.31 15.31 45.54 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.040829 TGACACAACAAGTCATGATCTCCT 59.959 41.667 0.00 0.00 40.80 3.69
68 69 1.217779 GCTCTTCCTGCTCGCTCTT 59.782 57.895 0.00 0.00 0.00 2.85
139 140 1.119574 AGGTTGTCGGTAGCTGGTGT 61.120 55.000 0.00 0.00 0.00 4.16
220 221 1.986413 GTGCTCCACCAGATCCTGT 59.014 57.895 0.00 0.00 0.00 4.00
261 262 1.450025 TCATCACACGTCGAGCTAGT 58.550 50.000 0.00 0.00 0.00 2.57
374 380 2.472488 GGTTCAGCGCAAATTCAACAAG 59.528 45.455 11.47 0.00 0.00 3.16
397 403 1.270550 CAAATCAGCCCATATTCGCCC 59.729 52.381 0.00 0.00 0.00 6.13
411 417 0.105964 CTCGGTATCGGGGCAAATCA 59.894 55.000 0.00 0.00 36.95 2.57
419 425 0.249741 AAAATCGGCTCGGTATCGGG 60.250 55.000 0.00 0.00 40.45 5.14
426 432 0.793861 TCAACGAAAAATCGGCTCGG 59.206 50.000 3.12 0.00 36.90 4.63
442 448 3.133003 TCTGTTTTTCGGCCCATTTTCAA 59.867 39.130 0.00 0.00 0.00 2.69
443 449 2.695666 TCTGTTTTTCGGCCCATTTTCA 59.304 40.909 0.00 0.00 0.00 2.69
460 466 5.467399 CCATTTTTGATGCAAATGTGTCTGT 59.533 36.000 7.17 0.00 39.18 3.41
462 468 4.998672 CCCATTTTTGATGCAAATGTGTCT 59.001 37.500 7.17 0.00 39.18 3.41
464 470 3.502979 GCCCATTTTTGATGCAAATGTGT 59.497 39.130 7.17 0.00 39.18 3.72
474 480 5.867903 TTTGATATCGGCCCATTTTTGAT 57.132 34.783 0.00 0.00 0.00 2.57
530 549 0.247695 GCCAGCGCTAAAATCGACAC 60.248 55.000 10.99 0.00 0.00 3.67
531 550 0.391130 AGCCAGCGCTAAAATCGACA 60.391 50.000 10.99 0.00 46.08 4.35
546 566 2.803155 AAAATCGCCTCTCGCAGCCA 62.803 55.000 0.00 0.00 37.30 4.75
551 571 1.268083 GGCTTAAAAATCGCCTCTCGC 60.268 52.381 0.00 0.00 40.62 5.03
552 572 2.739293 GGCTTAAAAATCGCCTCTCG 57.261 50.000 0.00 0.00 40.62 4.04
592 618 3.609853 TGACCAATCTAAAAGCATCGCT 58.390 40.909 0.00 0.00 42.56 4.93
593 619 4.558538 ATGACCAATCTAAAAGCATCGC 57.441 40.909 0.00 0.00 0.00 4.58
594 620 7.439356 TCTTCTATGACCAATCTAAAAGCATCG 59.561 37.037 0.00 0.00 0.00 3.84
595 621 8.668510 TCTTCTATGACCAATCTAAAAGCATC 57.331 34.615 0.00 0.00 0.00 3.91
596 622 9.466497 TTTCTTCTATGACCAATCTAAAAGCAT 57.534 29.630 0.00 0.00 0.00 3.79
597 623 8.730680 GTTTCTTCTATGACCAATCTAAAAGCA 58.269 33.333 0.00 0.00 0.00 3.91
598 624 8.951243 AGTTTCTTCTATGACCAATCTAAAAGC 58.049 33.333 0.00 0.00 0.00 3.51
650 676 8.630917 GCACTATGAGAATGGTAACTTAGAGTA 58.369 37.037 0.00 0.00 37.61 2.59
651 677 7.124298 TGCACTATGAGAATGGTAACTTAGAGT 59.876 37.037 0.00 0.00 37.61 3.24
652 678 7.492524 TGCACTATGAGAATGGTAACTTAGAG 58.507 38.462 0.00 0.00 37.61 2.43
653 679 7.418337 TGCACTATGAGAATGGTAACTTAGA 57.582 36.000 0.00 0.00 37.61 2.10
654 680 8.492673 TTTGCACTATGAGAATGGTAACTTAG 57.507 34.615 0.00 0.00 37.61 2.18
655 681 8.100791 ACTTTGCACTATGAGAATGGTAACTTA 58.899 33.333 0.00 0.00 37.61 2.24
656 682 6.942576 ACTTTGCACTATGAGAATGGTAACTT 59.057 34.615 0.00 0.00 37.61 2.66
657 683 6.476378 ACTTTGCACTATGAGAATGGTAACT 58.524 36.000 0.00 0.00 37.61 2.24
658 684 6.743575 ACTTTGCACTATGAGAATGGTAAC 57.256 37.500 0.00 0.00 0.00 2.50
682 708 9.535170 AGCCACATATGACACTACTACTATATT 57.465 33.333 10.38 0.00 0.00 1.28
683 709 9.535170 AAGCCACATATGACACTACTACTATAT 57.465 33.333 10.38 0.00 0.00 0.86
684 710 8.935614 AAGCCACATATGACACTACTACTATA 57.064 34.615 10.38 0.00 0.00 1.31
685 711 7.505923 TGAAGCCACATATGACACTACTACTAT 59.494 37.037 10.38 0.00 0.00 2.12
686 712 6.831868 TGAAGCCACATATGACACTACTACTA 59.168 38.462 10.38 0.00 0.00 1.82
687 713 5.656859 TGAAGCCACATATGACACTACTACT 59.343 40.000 10.38 0.00 0.00 2.57
688 714 5.902681 TGAAGCCACATATGACACTACTAC 58.097 41.667 10.38 0.00 0.00 2.73
689 715 6.731292 ATGAAGCCACATATGACACTACTA 57.269 37.500 10.38 0.00 0.00 1.82
690 716 5.620738 ATGAAGCCACATATGACACTACT 57.379 39.130 10.38 0.00 0.00 2.57
691 717 6.683974 AAATGAAGCCACATATGACACTAC 57.316 37.500 10.38 0.00 0.00 2.73
692 718 8.978874 ATTAAATGAAGCCACATATGACACTA 57.021 30.769 10.38 0.00 0.00 2.74
693 719 7.886629 ATTAAATGAAGCCACATATGACACT 57.113 32.000 10.38 0.00 0.00 3.55
694 720 7.805071 GCTATTAAATGAAGCCACATATGACAC 59.195 37.037 10.38 0.00 0.00 3.67
695 721 7.720957 AGCTATTAAATGAAGCCACATATGACA 59.279 33.333 10.38 0.52 36.92 3.58
696 722 8.103948 AGCTATTAAATGAAGCCACATATGAC 57.896 34.615 10.38 0.00 36.92 3.06
697 723 8.570488 CAAGCTATTAAATGAAGCCACATATGA 58.430 33.333 10.38 0.00 36.92 2.15
698 724 8.355169 ACAAGCTATTAAATGAAGCCACATATG 58.645 33.333 0.00 0.00 36.92 1.78
699 725 8.469309 ACAAGCTATTAAATGAAGCCACATAT 57.531 30.769 0.00 0.00 36.92 1.78
700 726 7.880160 ACAAGCTATTAAATGAAGCCACATA 57.120 32.000 0.00 0.00 36.92 2.29
701 727 6.780457 ACAAGCTATTAAATGAAGCCACAT 57.220 33.333 0.00 0.00 36.92 3.21
702 728 7.880160 ATACAAGCTATTAAATGAAGCCACA 57.120 32.000 0.00 0.00 36.92 4.17
703 729 9.057089 AGTATACAAGCTATTAAATGAAGCCAC 57.943 33.333 5.50 0.00 36.92 5.01
704 730 9.273016 GAGTATACAAGCTATTAAATGAAGCCA 57.727 33.333 5.50 0.00 36.92 4.75
705 731 9.273016 TGAGTATACAAGCTATTAAATGAAGCC 57.727 33.333 5.50 0.00 36.92 4.35
715 741 9.102757 CAAGACAACATGAGTATACAAGCTATT 57.897 33.333 5.50 0.00 0.00 1.73
716 742 8.478066 TCAAGACAACATGAGTATACAAGCTAT 58.522 33.333 5.50 0.00 0.00 2.97
717 743 7.836842 TCAAGACAACATGAGTATACAAGCTA 58.163 34.615 5.50 0.00 0.00 3.32
718 744 6.701340 TCAAGACAACATGAGTATACAAGCT 58.299 36.000 5.50 0.00 0.00 3.74
719 745 6.968131 TCAAGACAACATGAGTATACAAGC 57.032 37.500 5.50 0.00 0.00 4.01
721 747 9.944663 GTTTTTCAAGACAACATGAGTATACAA 57.055 29.630 5.50 0.00 0.00 2.41
722 748 9.114952 TGTTTTTCAAGACAACATGAGTATACA 57.885 29.630 5.50 0.00 0.00 2.29
723 749 9.382244 GTGTTTTTCAAGACAACATGAGTATAC 57.618 33.333 0.00 0.00 33.15 1.47
724 750 9.337396 AGTGTTTTTCAAGACAACATGAGTATA 57.663 29.630 0.00 0.00 33.15 1.47
725 751 8.225603 AGTGTTTTTCAAGACAACATGAGTAT 57.774 30.769 0.00 0.00 33.15 2.12
726 752 7.624360 AGTGTTTTTCAAGACAACATGAGTA 57.376 32.000 0.00 0.00 33.15 2.59
727 753 6.515272 AGTGTTTTTCAAGACAACATGAGT 57.485 33.333 0.00 0.00 33.15 3.41
728 754 8.131100 ACATAGTGTTTTTCAAGACAACATGAG 58.869 33.333 0.00 0.00 33.15 2.90
729 755 7.995289 ACATAGTGTTTTTCAAGACAACATGA 58.005 30.769 0.00 0.00 33.15 3.07
730 756 8.633075 AACATAGTGTTTTTCAAGACAACATG 57.367 30.769 0.00 0.00 37.26 3.21
731 757 9.730420 GTAACATAGTGTTTTTCAAGACAACAT 57.270 29.630 0.20 0.00 41.45 2.71
732 758 8.731605 TGTAACATAGTGTTTTTCAAGACAACA 58.268 29.630 0.20 0.00 41.45 3.33
733 759 9.221775 CTGTAACATAGTGTTTTTCAAGACAAC 57.778 33.333 0.20 0.00 41.45 3.32
734 760 8.952278 ACTGTAACATAGTGTTTTTCAAGACAA 58.048 29.630 0.20 0.00 41.45 3.18
735 761 8.500753 ACTGTAACATAGTGTTTTTCAAGACA 57.499 30.769 0.20 0.00 41.45 3.41
771 797 6.603095 CAAGTAGTTAATGAGAAGTGGCAAC 58.397 40.000 0.00 0.00 0.00 4.17
772 798 5.181245 GCAAGTAGTTAATGAGAAGTGGCAA 59.819 40.000 0.00 0.00 0.00 4.52
773 799 4.695455 GCAAGTAGTTAATGAGAAGTGGCA 59.305 41.667 0.00 0.00 0.00 4.92
774 800 4.938226 AGCAAGTAGTTAATGAGAAGTGGC 59.062 41.667 0.00 0.00 0.00 5.01
775 801 7.097192 TGTAGCAAGTAGTTAATGAGAAGTGG 58.903 38.462 0.00 0.00 0.00 4.00
776 802 8.709386 ATGTAGCAAGTAGTTAATGAGAAGTG 57.291 34.615 0.00 0.00 0.00 3.16
797 823 9.787532 GCACTTTGAGATATTTTTGCTTATGTA 57.212 29.630 0.00 0.00 0.00 2.29
798 824 7.485913 CGCACTTTGAGATATTTTTGCTTATGT 59.514 33.333 0.00 0.00 0.00 2.29
799 825 7.485913 ACGCACTTTGAGATATTTTTGCTTATG 59.514 33.333 0.00 0.00 0.00 1.90
800 826 7.538575 ACGCACTTTGAGATATTTTTGCTTAT 58.461 30.769 0.00 0.00 0.00 1.73
801 827 6.908825 ACGCACTTTGAGATATTTTTGCTTA 58.091 32.000 0.00 0.00 0.00 3.09
802 828 5.772521 ACGCACTTTGAGATATTTTTGCTT 58.227 33.333 0.00 0.00 0.00 3.91
803 829 5.376854 ACGCACTTTGAGATATTTTTGCT 57.623 34.783 0.00 0.00 0.00 3.91
804 830 7.273381 ACATAACGCACTTTGAGATATTTTTGC 59.727 33.333 0.00 0.00 0.00 3.68
805 831 8.673626 ACATAACGCACTTTGAGATATTTTTG 57.326 30.769 0.00 0.00 0.00 2.44
809 835 9.935682 CAATAACATAACGCACTTTGAGATATT 57.064 29.630 0.00 0.00 0.00 1.28
810 836 9.109393 ACAATAACATAACGCACTTTGAGATAT 57.891 29.630 0.00 0.00 0.00 1.63
811 837 8.487313 ACAATAACATAACGCACTTTGAGATA 57.513 30.769 0.00 0.00 0.00 1.98
812 838 7.377766 ACAATAACATAACGCACTTTGAGAT 57.622 32.000 0.00 0.00 0.00 2.75
813 839 6.795098 ACAATAACATAACGCACTTTGAGA 57.205 33.333 0.00 0.00 0.00 3.27
814 840 7.851822 AAACAATAACATAACGCACTTTGAG 57.148 32.000 0.00 0.00 0.00 3.02
815 841 9.388346 CTTAAACAATAACATAACGCACTTTGA 57.612 29.630 0.00 0.00 0.00 2.69
816 842 9.176181 ACTTAAACAATAACATAACGCACTTTG 57.824 29.630 0.00 0.00 0.00 2.77
817 843 9.738832 AACTTAAACAATAACATAACGCACTTT 57.261 25.926 0.00 0.00 0.00 2.66
819 845 9.815936 GTAACTTAAACAATAACATAACGCACT 57.184 29.630 0.00 0.00 0.00 4.40
820 846 9.815936 AGTAACTTAAACAATAACATAACGCAC 57.184 29.630 0.00 0.00 0.00 5.34
835 861 9.505995 GCTAGTCATAGTGAGAGTAACTTAAAC 57.494 37.037 0.00 0.00 0.00 2.01
836 862 8.684520 GGCTAGTCATAGTGAGAGTAACTTAAA 58.315 37.037 0.00 0.00 0.00 1.52
837 863 7.284944 GGGCTAGTCATAGTGAGAGTAACTTAA 59.715 40.741 0.00 0.00 0.00 1.85
838 864 6.771749 GGGCTAGTCATAGTGAGAGTAACTTA 59.228 42.308 0.00 0.00 0.00 2.24
839 865 5.595133 GGGCTAGTCATAGTGAGAGTAACTT 59.405 44.000 0.00 0.00 0.00 2.66
840 866 5.134661 GGGCTAGTCATAGTGAGAGTAACT 58.865 45.833 0.00 0.00 0.00 2.24
841 867 4.023878 CGGGCTAGTCATAGTGAGAGTAAC 60.024 50.000 0.00 0.00 0.00 2.50
842 868 4.135306 CGGGCTAGTCATAGTGAGAGTAA 58.865 47.826 0.00 0.00 0.00 2.24
843 869 3.496337 CCGGGCTAGTCATAGTGAGAGTA 60.496 52.174 0.00 0.00 0.00 2.59
844 870 2.577700 CGGGCTAGTCATAGTGAGAGT 58.422 52.381 0.00 0.00 0.00 3.24
845 871 1.883275 CCGGGCTAGTCATAGTGAGAG 59.117 57.143 0.00 0.00 0.00 3.20
846 872 1.982660 CCGGGCTAGTCATAGTGAGA 58.017 55.000 0.00 0.00 0.00 3.27
847 873 0.315568 GCCGGGCTAGTCATAGTGAG 59.684 60.000 12.87 0.00 0.00 3.51
848 874 0.396556 TGCCGGGCTAGTCATAGTGA 60.397 55.000 21.46 0.00 0.00 3.41
849 875 0.249489 GTGCCGGGCTAGTCATAGTG 60.249 60.000 21.46 0.00 0.00 2.74
850 876 0.686441 TGTGCCGGGCTAGTCATAGT 60.686 55.000 21.46 0.00 0.00 2.12
851 877 0.681733 ATGTGCCGGGCTAGTCATAG 59.318 55.000 21.46 0.00 0.00 2.23
852 878 0.679505 GATGTGCCGGGCTAGTCATA 59.320 55.000 21.46 0.00 0.00 2.15
853 879 1.050988 AGATGTGCCGGGCTAGTCAT 61.051 55.000 21.46 17.56 0.00 3.06
854 880 0.396556 TAGATGTGCCGGGCTAGTCA 60.397 55.000 21.46 13.81 0.00 3.41
855 881 0.750850 TTAGATGTGCCGGGCTAGTC 59.249 55.000 21.46 14.27 0.00 2.59
856 882 1.200519 TTTAGATGTGCCGGGCTAGT 58.799 50.000 21.46 5.41 0.00 2.57
857 883 2.550830 ATTTAGATGTGCCGGGCTAG 57.449 50.000 21.46 0.00 0.00 3.42
858 884 3.868369 GCATATTTAGATGTGCCGGGCTA 60.868 47.826 21.46 9.83 42.56 3.93
859 885 2.783135 CATATTTAGATGTGCCGGGCT 58.217 47.619 21.46 0.00 0.00 5.19
860 886 1.200020 GCATATTTAGATGTGCCGGGC 59.800 52.381 13.32 13.32 42.56 6.13
879 905 3.891056 ACTTTACCGTTTTGCTACAGC 57.109 42.857 0.00 0.00 42.50 4.40
880 906 8.791355 ATTTTTACTTTACCGTTTTGCTACAG 57.209 30.769 0.00 0.00 0.00 2.74
881 907 8.404000 TGATTTTTACTTTACCGTTTTGCTACA 58.596 29.630 0.00 0.00 0.00 2.74
882 908 8.785468 TGATTTTTACTTTACCGTTTTGCTAC 57.215 30.769 0.00 0.00 0.00 3.58
883 909 9.968870 ATTGATTTTTACTTTACCGTTTTGCTA 57.031 25.926 0.00 0.00 0.00 3.49
884 910 8.880878 ATTGATTTTTACTTTACCGTTTTGCT 57.119 26.923 0.00 0.00 0.00 3.91
885 911 9.575702 GAATTGATTTTTACTTTACCGTTTTGC 57.424 29.630 0.00 0.00 0.00 3.68
887 913 9.263538 GGGAATTGATTTTTACTTTACCGTTTT 57.736 29.630 0.00 0.00 0.00 2.43
888 914 7.874016 GGGGAATTGATTTTTACTTTACCGTTT 59.126 33.333 0.00 0.00 0.00 3.60
889 915 7.015389 TGGGGAATTGATTTTTACTTTACCGTT 59.985 33.333 0.00 0.00 0.00 4.44
890 916 6.494146 TGGGGAATTGATTTTTACTTTACCGT 59.506 34.615 0.00 0.00 0.00 4.83
891 917 6.926313 TGGGGAATTGATTTTTACTTTACCG 58.074 36.000 0.00 0.00 0.00 4.02
892 918 7.604927 GGTTGGGGAATTGATTTTTACTTTACC 59.395 37.037 0.00 0.00 0.00 2.85
893 919 7.604927 GGGTTGGGGAATTGATTTTTACTTTAC 59.395 37.037 0.00 0.00 0.00 2.01
894 920 7.525692 CGGGTTGGGGAATTGATTTTTACTTTA 60.526 37.037 0.00 0.00 0.00 1.85
895 921 6.539173 GGGTTGGGGAATTGATTTTTACTTT 58.461 36.000 0.00 0.00 0.00 2.66
896 922 5.279758 CGGGTTGGGGAATTGATTTTTACTT 60.280 40.000 0.00 0.00 0.00 2.24
904 930 0.258774 CTCCGGGTTGGGGAATTGAT 59.741 55.000 0.00 0.00 43.10 2.57
949 975 0.251386 AGAGAGAGGACGGAACTGCA 60.251 55.000 0.00 0.00 0.00 4.41
951 977 1.403514 GCAAGAGAGAGGACGGAACTG 60.404 57.143 0.00 0.00 0.00 3.16
1222 1254 2.038033 TCCTTGTCCGTTCCTTCGATTT 59.962 45.455 0.00 0.00 0.00 2.17
1329 1367 4.244066 CCTTGAGCATATCCAGATCTTCG 58.756 47.826 0.00 0.00 0.00 3.79
1347 1385 3.181507 CGTGTACATCTTGAATGGCCTTG 60.182 47.826 3.32 0.00 0.00 3.61
1363 1401 5.383984 TTTTCATCGTATGCATCGTGTAC 57.616 39.130 0.19 0.00 0.00 2.90
1484 1522 7.926674 TTCAAGATAATCTGCAAATGTCTCA 57.073 32.000 0.00 0.00 0.00 3.27
1598 1710 8.798859 ATCAGCAATCAGAAGTTAACACTAAT 57.201 30.769 8.61 0.00 30.68 1.73
1635 1747 2.573340 GGCAGTTCCATTTGGCGG 59.427 61.111 0.00 0.00 34.44 6.13
1722 1834 3.066621 GCACTGTCTTTGTTGTGGATTCA 59.933 43.478 0.00 0.00 0.00 2.57
1793 1905 9.599866 TCCTAACAAATAGACATGACATAGTTG 57.400 33.333 0.00 7.38 33.04 3.16
1796 1908 7.115520 CGCTCCTAACAAATAGACATGACATAG 59.884 40.741 0.00 0.00 33.04 2.23
1818 1930 0.528684 AACCTATTCTCGCAGCGCTC 60.529 55.000 7.13 1.15 0.00 5.03
1878 1990 0.894835 TCCAGAGCATCGTGTTAGCA 59.105 50.000 0.00 0.00 42.67 3.49
1955 2067 1.359459 GGGGACTTCGTGCGAATCAC 61.359 60.000 7.50 8.47 42.23 3.06
2075 2187 6.697892 GGTTGAACTAGTATGAGACTACATGC 59.302 42.308 0.00 0.00 39.81 4.06
2131 2243 6.156256 TGTTAAATGTGGACAGGACTAGCTAT 59.844 38.462 0.00 0.00 0.00 2.97
2178 2290 8.791675 TCTAGTGTCAGAAGATAGAATATGCAG 58.208 37.037 0.00 0.00 0.00 4.41
2180 2292 9.405587 GTTCTAGTGTCAGAAGATAGAATATGC 57.594 37.037 0.00 0.00 35.25 3.14
2206 2318 5.485209 ACTTCACTTTAACACCTCCCTAG 57.515 43.478 0.00 0.00 0.00 3.02
2213 2325 5.240844 AGCCAACATACTTCACTTTAACACC 59.759 40.000 0.00 0.00 0.00 4.16
2462 2574 9.793259 ACCAATGATGTCTTAGAAGTTAGAAAA 57.207 29.630 0.00 0.00 0.00 2.29
2518 2630 7.651808 ACCTGAAACAGAAGTTGTGAAATATG 58.348 34.615 7.07 0.00 40.74 1.78
2526 2638 6.096673 ACAAAAACCTGAAACAGAAGTTGT 57.903 33.333 0.00 0.00 43.45 3.32
2556 2668 1.227380 CTGAGTAGTGGCATCCCGC 60.227 63.158 0.00 0.00 42.11 6.13
2572 2684 0.035152 TACAGCATGGTGGCCTTCTG 60.035 55.000 27.32 10.11 43.62 3.02
2607 2719 6.051717 TCTAACCTCAAGCATAGCAAGATTC 58.948 40.000 0.00 0.00 0.00 2.52
2620 2732 6.209788 ACAGGTTCTTCTACTCTAACCTCAAG 59.790 42.308 2.69 0.00 46.88 3.02
2637 2749 1.346068 GAGAGCAACTGGACAGGTTCT 59.654 52.381 4.14 0.00 0.00 3.01
2800 2912 2.926778 ACCTTAGGATGCTCATCTGC 57.073 50.000 4.77 0.00 37.92 4.26
2845 2957 8.788806 TCCAAATAACGAAACAATGTAGACAAT 58.211 29.630 0.00 0.00 0.00 2.71
2857 2969 9.438291 CAGATGACATTATCCAAATAACGAAAC 57.562 33.333 0.00 0.00 30.27 2.78
2861 2973 8.397906 ACAACAGATGACATTATCCAAATAACG 58.602 33.333 0.00 0.00 30.27 3.18
3018 3130 6.041182 TGAGCAAAATGGATGAAGGGATAATG 59.959 38.462 0.00 0.00 0.00 1.90
3024 3136 3.512724 ACTTGAGCAAAATGGATGAAGGG 59.487 43.478 0.00 0.00 0.00 3.95
3294 3407 4.494091 AGTTGAGGACACATATCCCAAG 57.506 45.455 0.00 0.00 39.91 3.61
3295 3408 4.567537 CCAAGTTGAGGACACATATCCCAA 60.568 45.833 3.87 0.00 39.91 4.12
3296 3409 3.054434 CCAAGTTGAGGACACATATCCCA 60.054 47.826 3.87 0.00 39.91 4.37
3297 3410 3.054361 ACCAAGTTGAGGACACATATCCC 60.054 47.826 3.87 0.00 39.91 3.85
3298 3411 4.222124 ACCAAGTTGAGGACACATATCC 57.778 45.455 3.87 0.00 39.28 2.59
3299 3412 5.978814 ACTACCAAGTTGAGGACACATATC 58.021 41.667 3.87 0.00 29.00 1.63
3300 3413 7.490657 TTACTACCAAGTTGAGGACACATAT 57.509 36.000 3.87 0.00 37.15 1.78
3301 3414 6.921486 TTACTACCAAGTTGAGGACACATA 57.079 37.500 3.87 0.00 37.15 2.29
3327 3440 9.639563 TTATCATCAGATGCTAATTGGGTTTTA 57.360 29.630 5.41 0.00 35.67 1.52
3339 3452 4.945543 TGTGCAACTTTATCATCAGATGCT 59.054 37.500 5.41 0.00 39.06 3.79
3392 3505 7.982919 TCAAGTAATAAGTATGGTACGCAATGT 59.017 33.333 0.00 0.00 0.00 2.71
3412 3525 7.663493 TGTTGGTGTGACATGATAATTCAAGTA 59.337 33.333 0.00 0.00 34.12 2.24
3418 3531 7.465353 TTGATGTTGGTGTGACATGATAATT 57.535 32.000 0.00 0.00 37.83 1.40
3479 3592 5.601662 AGCGACACATACATGTATAGCTTT 58.398 37.500 17.86 1.71 39.39 3.51
3551 3665 5.997746 AGCTTACAGTATTTGCTTGTTCTCA 59.002 36.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.