Multiple sequence alignment - TraesCS2B01G555000

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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 TraesCS2B01G555000 chr2B 100.000 3456 0 0 1 3456 749921263 749924718 0.000000e+00 6383.0
1 TraesCS2B01G555000 chr2B 79.622 1428 248 26 992 2402 749985802 749987203 0.000000e+00 985.0
2 TraesCS2B01G555000 chr2B 85.942 626 81 5 998 1618 749888232 749888855 0.000000e+00 662.0
3 TraesCS2B01G555000 chr2B 85.645 620 89 0 999 1618 749892616 749893235 0.000000e+00 652.0
4 TraesCS2B01G555000 chr2B 95.636 275 9 2 2648 2921 749924889 749924617 4.090000e-119 438.0
5 TraesCS2B01G555000 chr2B 96.591 264 8 1 2653 2915 573128864 573128601 1.470000e-118 436.0
6 TraesCS2B01G555000 chr2B 95.865 266 10 1 2651 2915 23003043 23002778 2.460000e-116 429.0
7 TraesCS2B01G555000 chr2B 88.837 215 23 1 3058 3271 749924176 749924390 2.650000e-66 263.0
8 TraesCS2B01G555000 chr2B 88.837 215 23 1 2914 3128 749924320 749924533 2.650000e-66 263.0
9 TraesCS2B01G555000 chr2B 95.192 104 3 1 3355 3456 749924183 749924080 2.760000e-36 163.0
10 TraesCS2B01G555000 chr2B 95.789 95 3 1 3363 3456 23001904 23001810 5.970000e-33 152.0
11 TraesCS2B01G555000 chr6B 98.628 802 10 1 2655 3456 185103360 185102560 0.000000e+00 1419.0
12 TraesCS2B01G555000 chr6B 97.378 267 5 1 2655 2921 185102397 185102661 1.460000e-123 453.0
13 TraesCS2B01G555000 chr6B 90.698 215 19 1 3058 3271 185103101 185102887 5.650000e-73 285.0
14 TraesCS2B01G555000 chr6B 89.767 215 20 2 2914 3128 185102957 185102745 1.220000e-69 274.0
15 TraesCS2B01G555000 chr6B 95.192 104 3 1 3355 3456 185103094 185103197 2.760000e-36 163.0
16 TraesCS2B01G555000 chr6B 88.889 72 8 0 2535 2606 638239475 638239546 4.750000e-14 89.8
17 TraesCS2B01G555000 chr2A 92.072 782 53 4 1762 2537 745529472 745530250 0.000000e+00 1092.0
18 TraesCS2B01G555000 chr2A 87.097 713 73 13 1 704 584139895 584139193 0.000000e+00 789.0
19 TraesCS2B01G555000 chr2A 87.500 616 74 2 999 1611 745428092 745428707 0.000000e+00 708.0
20 TraesCS2B01G555000 chr2A 97.826 92 1 1 3366 3456 770129102 770129011 1.280000e-34 158.0
21 TraesCS2B01G555000 chr2D 88.390 913 80 12 771 1666 615503022 615503925 0.000000e+00 1075.0
22 TraesCS2B01G555000 chr2D 79.435 1415 258 15 992 2402 615510220 615511605 0.000000e+00 970.0
23 TraesCS2B01G555000 chr2D 87.368 855 81 13 1698 2537 615504067 615504909 0.000000e+00 955.0
24 TraesCS2B01G555000 chr2D 87.291 716 71 12 1 703 578999680 579000388 0.000000e+00 800.0
25 TraesCS2B01G555000 chr2D 86.989 661 83 3 994 1653 615567834 615568492 0.000000e+00 741.0
26 TraesCS2B01G555000 chr2D 88.169 617 70 2 1001 1614 615469217 615469833 0.000000e+00 732.0
27 TraesCS2B01G555000 chr2D 87.719 627 70 5 997 1618 615466577 615467201 0.000000e+00 725.0
28 TraesCS2B01G555000 chr2D 81.667 540 72 15 1875 2408 621996568 621997086 1.150000e-114 424.0
29 TraesCS2B01G555000 chr2D 94.595 74 4 0 2533 2606 590220856 590220783 7.840000e-22 115.0
30 TraesCS2B01G555000 chr7B 90.550 709 57 7 1 703 1041921 1042625 0.000000e+00 929.0
31 TraesCS2B01G555000 chr7B 92.537 67 4 1 3391 3456 481844980 481844914 1.020000e-15 95.3
32 TraesCS2B01G555000 chr7A 88.408 716 69 10 1 708 444977500 444978209 0.000000e+00 850.0
33 TraesCS2B01G555000 chr7A 96.578 263 8 1 2654 2915 237507363 237507625 5.300000e-118 435.0
34 TraesCS2B01G555000 chr7A 96.000 75 3 0 2532 2606 50815000 50814926 4.680000e-24 122.0
35 TraesCS2B01G555000 chr3D 88.488 721 60 13 1 706 391241426 391240714 0.000000e+00 850.0
36 TraesCS2B01G555000 chr3D 88.872 674 58 12 1 662 31959692 31959024 0.000000e+00 813.0
37 TraesCS2B01G555000 chr5D 88.154 726 67 12 1 715 473067050 473066333 0.000000e+00 846.0
38 TraesCS2B01G555000 chr5D 94.937 79 3 1 2529 2606 330595226 330595304 4.680000e-24 122.0
39 TraesCS2B01G555000 chr5D 94.937 79 3 1 2529 2606 330628905 330628983 4.680000e-24 122.0
40 TraesCS2B01G555000 chr5D 95.652 69 3 0 2538 2606 209498923 209498991 1.010000e-20 111.0
41 TraesCS2B01G555000 chr5B 87.832 715 71 12 1 706 604913220 604912513 0.000000e+00 824.0
42 TraesCS2B01G555000 chr5A 87.377 713 74 12 1 703 12585348 12586054 0.000000e+00 804.0
43 TraesCS2B01G555000 chr5A 96.739 92 2 1 3366 3456 11310367 11310276 5.970000e-33 152.0
44 TraesCS2B01G555000 chr1A 97.821 459 9 1 2914 3372 561770758 561770301 0.000000e+00 791.0
45 TraesCS2B01G555000 chr1A 88.406 276 29 3 2998 3271 561770818 561770544 2.570000e-86 329.0
46 TraesCS2B01G555000 chr1A 88.837 215 23 1 2914 3128 561770614 561770401 2.650000e-66 263.0
47 TraesCS2B01G555000 chr7D 85.825 776 65 18 1 750 365505434 365506190 0.000000e+00 782.0
48 TraesCS2B01G555000 chr7D 94.366 71 4 0 2536 2606 618423382 618423452 3.650000e-20 110.0
49 TraesCS2B01G555000 chr1B 96.255 267 8 1 2655 2921 7622422 7622686 1.470000e-118 436.0
50 TraesCS2B01G555000 chr1B 98.039 153 3 0 3304 3456 7622737 7622585 2.040000e-67 267.0
51 TraesCS2B01G555000 chr1B 90.400 125 11 1 3248 3372 648143969 648143846 2.760000e-36 163.0
52 TraesCS2B01G555000 chr1B 96.703 91 2 1 3367 3456 123986243 123986153 2.150000e-32 150.0
53 TraesCS2B01G555000 chr4B 96.578 263 8 1 2652 2913 612329088 612329350 5.300000e-118 435.0
54 TraesCS2B01G555000 chr6A 95.539 269 10 2 2648 2915 120121122 120121389 2.460000e-116 429.0
55 TraesCS2B01G555000 chr6A 80.159 126 12 3 2538 2650 70958433 70958558 7.950000e-12 82.4
56 TraesCS2B01G555000 chr6D 92.500 80 4 1 2529 2606 445855781 445855860 2.820000e-21 113.0
57 TraesCS2B01G555000 chr6D 91.379 58 4 1 2604 2661 445855876 445855932 1.030000e-10 78.7
58 TraesCS2B01G555000 chrUn 94.286 70 4 0 2537 2606 295537969 295538038 1.310000e-19 108.0
59 TraesCS2B01G555000 chrUn 94.286 70 4 0 2537 2606 329605383 329605452 1.310000e-19 108.0


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 TraesCS2B01G555000 chr2B 749921263 749924718 3455 False 2303.000000 6383 92.5580 1 3456 3 chr2B.!!$F3 3455
1 TraesCS2B01G555000 chr2B 749985802 749987203 1401 False 985.000000 985 79.6220 992 2402 1 chr2B.!!$F1 1410
2 TraesCS2B01G555000 chr2B 749888232 749893235 5003 False 657.000000 662 85.7935 998 1618 2 chr2B.!!$F2 620
3 TraesCS2B01G555000 chr2B 749924080 749924889 809 True 300.500000 438 95.4140 2648 3456 2 chr2B.!!$R3 808
4 TraesCS2B01G555000 chr2B 23001810 23003043 1233 True 290.500000 429 95.8270 2651 3456 2 chr2B.!!$R2 805
5 TraesCS2B01G555000 chr6B 185102560 185103360 800 True 659.333333 1419 93.0310 2655 3456 3 chr6B.!!$R1 801
6 TraesCS2B01G555000 chr6B 185102397 185103197 800 False 308.000000 453 96.2850 2655 3456 2 chr6B.!!$F2 801
7 TraesCS2B01G555000 chr2A 745529472 745530250 778 False 1092.000000 1092 92.0720 1762 2537 1 chr2A.!!$F2 775
8 TraesCS2B01G555000 chr2A 584139193 584139895 702 True 789.000000 789 87.0970 1 704 1 chr2A.!!$R1 703
9 TraesCS2B01G555000 chr2A 745428092 745428707 615 False 708.000000 708 87.5000 999 1611 1 chr2A.!!$F1 612
10 TraesCS2B01G555000 chr2D 615503022 615504909 1887 False 1015.000000 1075 87.8790 771 2537 2 chr2D.!!$F6 1766
11 TraesCS2B01G555000 chr2D 615510220 615511605 1385 False 970.000000 970 79.4350 992 2402 1 chr2D.!!$F2 1410
12 TraesCS2B01G555000 chr2D 578999680 579000388 708 False 800.000000 800 87.2910 1 703 1 chr2D.!!$F1 702
13 TraesCS2B01G555000 chr2D 615567834 615568492 658 False 741.000000 741 86.9890 994 1653 1 chr2D.!!$F3 659
14 TraesCS2B01G555000 chr2D 615466577 615469833 3256 False 728.500000 732 87.9440 997 1618 2 chr2D.!!$F5 621
15 TraesCS2B01G555000 chr2D 621996568 621997086 518 False 424.000000 424 81.6670 1875 2408 1 chr2D.!!$F4 533
16 TraesCS2B01G555000 chr7B 1041921 1042625 704 False 929.000000 929 90.5500 1 703 1 chr7B.!!$F1 702
17 TraesCS2B01G555000 chr7A 444977500 444978209 709 False 850.000000 850 88.4080 1 708 1 chr7A.!!$F2 707
18 TraesCS2B01G555000 chr3D 391240714 391241426 712 True 850.000000 850 88.4880 1 706 1 chr3D.!!$R2 705
19 TraesCS2B01G555000 chr3D 31959024 31959692 668 True 813.000000 813 88.8720 1 662 1 chr3D.!!$R1 661
20 TraesCS2B01G555000 chr5D 473066333 473067050 717 True 846.000000 846 88.1540 1 715 1 chr5D.!!$R1 714
21 TraesCS2B01G555000 chr5B 604912513 604913220 707 True 824.000000 824 87.8320 1 706 1 chr5B.!!$R1 705
22 TraesCS2B01G555000 chr5A 12585348 12586054 706 False 804.000000 804 87.3770 1 703 1 chr5A.!!$F1 702
23 TraesCS2B01G555000 chr1A 561770301 561770818 517 True 461.000000 791 91.6880 2914 3372 3 chr1A.!!$R1 458
24 TraesCS2B01G555000 chr7D 365505434 365506190 756 False 782.000000 782 85.8250 1 750 1 chr7D.!!$F1 749

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
661 706 0.388649 ATTGAGCCGATATCGACGCC 60.389 55.0 26.32 14.84 43.02 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 5176 0.099436 CATCGCTGGCAAGTTTAGGC 59.901 55.0 0.0 0.0 0.0 3.93 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
37 38 6.558771 TGGTCAACATTTGTGAAGACTATG 57.441 37.500 9.55 0.00 0.00 2.23
76 77 3.225104 AGGCAAGAACTCTCATTTTGCA 58.775 40.909 9.36 0.00 44.33 4.08
194 195 4.025396 CGAAAGATCAAATGTGGGAGATCG 60.025 45.833 0.00 0.00 41.24 3.69
250 258 4.140599 AGCGAGCAGGAAGAGCCG 62.141 66.667 0.00 0.00 43.43 5.52
282 290 3.780294 ACTGAACCATATTACAGGCAGGA 59.220 43.478 0.00 0.00 35.08 3.86
285 293 4.660303 TGAACCATATTACAGGCAGGATCT 59.340 41.667 0.00 0.00 0.00 2.75
392 412 2.551032 CAACAACTGCAGCAAGATCTGA 59.449 45.455 15.27 0.00 36.19 3.27
441 461 0.661552 GCCTAGCTCGACGTGTGATA 59.338 55.000 0.00 0.00 0.00 2.15
590 635 1.228657 GGGCCGATTTGCTCCGATAC 61.229 60.000 0.00 0.00 0.00 2.24
603 648 1.938861 CGATACCGGGCCGATTTTG 59.061 57.895 30.79 13.10 0.00 2.44
604 649 1.652563 GATACCGGGCCGATTTTGC 59.347 57.895 30.79 7.64 0.00 3.68
605 650 1.077357 ATACCGGGCCGATTTTGCA 60.077 52.632 30.79 0.00 0.00 4.08
606 651 1.381165 ATACCGGGCCGATTTTGCAC 61.381 55.000 30.79 0.00 0.00 4.57
607 652 4.128388 CCGGGCCGATTTTGCACC 62.128 66.667 30.79 0.00 0.00 5.01
608 653 4.474846 CGGGCCGATTTTGCACCG 62.475 66.667 24.41 0.00 36.64 4.94
609 654 3.370231 GGGCCGATTTTGCACCGT 61.370 61.111 0.00 0.00 0.00 4.83
610 655 2.041686 GGGCCGATTTTGCACCGTA 61.042 57.895 0.00 0.00 0.00 4.02
611 656 1.427819 GGCCGATTTTGCACCGTAG 59.572 57.895 0.00 0.00 0.00 3.51
612 657 1.303091 GGCCGATTTTGCACCGTAGT 61.303 55.000 0.00 0.00 0.00 2.73
613 658 1.361793 GCCGATTTTGCACCGTAGTA 58.638 50.000 0.00 0.00 0.00 1.82
614 659 1.326548 GCCGATTTTGCACCGTAGTAG 59.673 52.381 0.00 0.00 0.00 2.57
615 660 2.883574 CCGATTTTGCACCGTAGTAGA 58.116 47.619 0.00 0.00 0.00 2.59
616 661 2.601763 CCGATTTTGCACCGTAGTAGAC 59.398 50.000 0.00 0.00 0.00 2.59
617 662 2.601763 CGATTTTGCACCGTAGTAGACC 59.398 50.000 0.00 0.00 0.00 3.85
618 663 3.592059 GATTTTGCACCGTAGTAGACCA 58.408 45.455 0.00 0.00 0.00 4.02
619 664 3.472283 TTTTGCACCGTAGTAGACCAA 57.528 42.857 0.00 0.00 0.00 3.67
620 665 3.472283 TTTGCACCGTAGTAGACCAAA 57.528 42.857 0.00 0.00 0.00 3.28
621 666 3.472283 TTGCACCGTAGTAGACCAAAA 57.528 42.857 0.00 0.00 0.00 2.44
622 667 3.472283 TGCACCGTAGTAGACCAAAAA 57.528 42.857 0.00 0.00 0.00 1.94
623 668 3.132925 TGCACCGTAGTAGACCAAAAAC 58.867 45.455 0.00 0.00 0.00 2.43
624 669 3.132925 GCACCGTAGTAGACCAAAAACA 58.867 45.455 0.00 0.00 0.00 2.83
625 670 3.560896 GCACCGTAGTAGACCAAAAACAA 59.439 43.478 0.00 0.00 0.00 2.83
626 671 4.035441 GCACCGTAGTAGACCAAAAACAAA 59.965 41.667 0.00 0.00 0.00 2.83
627 672 5.504392 CACCGTAGTAGACCAAAAACAAAC 58.496 41.667 0.00 0.00 0.00 2.93
628 673 5.064962 CACCGTAGTAGACCAAAAACAAACA 59.935 40.000 0.00 0.00 0.00 2.83
629 674 5.647225 ACCGTAGTAGACCAAAAACAAACAA 59.353 36.000 0.00 0.00 0.00 2.83
630 675 6.150809 ACCGTAGTAGACCAAAAACAAACAAA 59.849 34.615 0.00 0.00 0.00 2.83
631 676 7.148035 ACCGTAGTAGACCAAAAACAAACAAAT 60.148 33.333 0.00 0.00 0.00 2.32
632 677 7.703197 CCGTAGTAGACCAAAAACAAACAAATT 59.297 33.333 0.00 0.00 0.00 1.82
633 678 9.078753 CGTAGTAGACCAAAAACAAACAAATTT 57.921 29.630 0.00 0.00 0.00 1.82
636 681 9.078753 AGTAGACCAAAAACAAACAAATTTACG 57.921 29.630 0.00 0.00 0.00 3.18
637 682 6.767080 AGACCAAAAACAAACAAATTTACGC 58.233 32.000 0.00 0.00 0.00 4.42
638 683 5.870444 ACCAAAAACAAACAAATTTACGCC 58.130 33.333 0.00 0.00 0.00 5.68
639 684 5.411669 ACCAAAAACAAACAAATTTACGCCA 59.588 32.000 0.00 0.00 0.00 5.69
640 685 6.072673 ACCAAAAACAAACAAATTTACGCCAA 60.073 30.769 0.00 0.00 0.00 4.52
641 686 6.801862 CCAAAAACAAACAAATTTACGCCAAA 59.198 30.769 0.00 0.00 0.00 3.28
642 687 7.326063 CCAAAAACAAACAAATTTACGCCAAAA 59.674 29.630 0.00 0.00 0.00 2.44
643 688 8.854312 CAAAAACAAACAAATTTACGCCAAAAT 58.146 25.926 0.00 0.00 0.00 1.82
644 689 8.972262 AAAACAAACAAATTTACGCCAAAATT 57.028 23.077 0.00 0.00 40.02 1.82
645 690 7.961325 AACAAACAAATTTACGCCAAAATTG 57.039 28.000 8.55 8.55 41.08 2.32
646 691 7.308782 ACAAACAAATTTACGCCAAAATTGA 57.691 28.000 14.44 0.00 38.70 2.57
647 692 7.405769 ACAAACAAATTTACGCCAAAATTGAG 58.594 30.769 14.44 8.87 38.70 3.02
648 693 5.590104 ACAAATTTACGCCAAAATTGAGC 57.410 34.783 14.44 0.00 38.70 4.26
649 694 4.450757 ACAAATTTACGCCAAAATTGAGCC 59.549 37.500 14.44 0.00 38.70 4.70
650 695 2.339728 TTTACGCCAAAATTGAGCCG 57.660 45.000 0.00 0.00 0.00 5.52
651 696 1.524848 TTACGCCAAAATTGAGCCGA 58.475 45.000 0.00 0.00 0.00 5.54
652 697 1.745232 TACGCCAAAATTGAGCCGAT 58.255 45.000 0.00 0.00 0.00 4.18
653 698 1.745232 ACGCCAAAATTGAGCCGATA 58.255 45.000 0.00 0.00 0.00 2.92
654 699 2.297701 ACGCCAAAATTGAGCCGATAT 58.702 42.857 0.00 0.00 0.00 1.63
655 700 2.290641 ACGCCAAAATTGAGCCGATATC 59.709 45.455 0.00 0.00 0.00 1.63
656 701 2.662791 CGCCAAAATTGAGCCGATATCG 60.663 50.000 18.31 18.31 39.44 2.92
657 702 2.548057 GCCAAAATTGAGCCGATATCGA 59.452 45.455 26.32 6.29 43.02 3.59
658 703 3.607078 GCCAAAATTGAGCCGATATCGAC 60.607 47.826 26.32 15.45 43.02 4.20
659 704 3.362986 CCAAAATTGAGCCGATATCGACG 60.363 47.826 26.32 11.60 43.02 5.12
660 705 1.419374 AATTGAGCCGATATCGACGC 58.581 50.000 26.32 20.53 43.02 5.19
661 706 0.388649 ATTGAGCCGATATCGACGCC 60.389 55.000 26.32 14.84 43.02 5.68
662 707 1.452953 TTGAGCCGATATCGACGCCT 61.453 55.000 26.32 15.31 43.02 5.52
663 708 1.442857 GAGCCGATATCGACGCCTG 60.443 63.158 26.32 9.40 43.02 4.85
664 709 2.430921 GCCGATATCGACGCCTGG 60.431 66.667 26.32 8.68 43.02 4.45
665 710 2.258591 CCGATATCGACGCCTGGG 59.741 66.667 26.32 3.04 43.02 4.45
666 711 2.258591 CGATATCGACGCCTGGGG 59.741 66.667 20.50 9.49 43.02 4.96
667 712 2.657237 GATATCGACGCCTGGGGG 59.343 66.667 15.73 5.80 0.00 5.40
668 713 1.906824 GATATCGACGCCTGGGGGA 60.907 63.158 15.73 3.99 33.58 4.81
669 714 2.156051 GATATCGACGCCTGGGGGAC 62.156 65.000 15.73 7.78 33.58 4.46
702 747 3.083386 GGAACCCAATCGACCCCA 58.917 61.111 0.00 0.00 0.00 4.96
703 748 1.077716 GGAACCCAATCGACCCCAG 60.078 63.158 0.00 0.00 0.00 4.45
704 749 1.077716 GAACCCAATCGACCCCAGG 60.078 63.158 0.00 0.00 0.00 4.45
705 750 3.282374 AACCCAATCGACCCCAGGC 62.282 63.158 0.00 0.00 0.00 4.85
706 751 4.856801 CCCAATCGACCCCAGGCG 62.857 72.222 0.00 0.00 0.00 5.52
707 752 4.856801 CCAATCGACCCCAGGCGG 62.857 72.222 0.00 0.00 0.00 6.13
708 753 4.096003 CAATCGACCCCAGGCGGT 62.096 66.667 0.00 0.00 39.49 5.68
709 754 4.096003 AATCGACCCCAGGCGGTG 62.096 66.667 4.41 0.00 35.79 4.94
712 757 4.096003 CGACCCCAGGCGGTGATT 62.096 66.667 4.41 0.00 35.79 2.57
713 758 2.355115 GACCCCAGGCGGTGATTT 59.645 61.111 4.41 0.00 35.79 2.17
714 759 1.304134 GACCCCAGGCGGTGATTTT 60.304 57.895 4.41 0.00 35.79 1.82
715 760 0.898326 GACCCCAGGCGGTGATTTTT 60.898 55.000 4.41 0.00 35.79 1.94
732 777 1.314730 TTTTGAAACCCCTCGAGTGC 58.685 50.000 12.31 0.00 0.00 4.40
733 778 0.536460 TTTGAAACCCCTCGAGTGCC 60.536 55.000 12.31 0.00 0.00 5.01
734 779 1.701031 TTGAAACCCCTCGAGTGCCA 61.701 55.000 12.31 0.00 0.00 4.92
735 780 1.072505 GAAACCCCTCGAGTGCCAA 59.927 57.895 12.31 0.00 0.00 4.52
736 781 1.228154 AAACCCCTCGAGTGCCAAC 60.228 57.895 12.31 0.00 0.00 3.77
737 782 3.530910 AACCCCTCGAGTGCCAACG 62.531 63.158 12.31 0.00 0.00 4.10
738 783 3.691342 CCCCTCGAGTGCCAACGA 61.691 66.667 12.31 0.00 37.03 3.85
739 784 2.432628 CCCTCGAGTGCCAACGAC 60.433 66.667 12.31 0.00 34.82 4.34
740 785 2.651361 CCTCGAGTGCCAACGACT 59.349 61.111 12.31 0.00 34.82 4.18
741 786 1.734477 CCTCGAGTGCCAACGACTG 60.734 63.158 12.31 0.00 34.82 3.51
752 797 2.084610 CAACGACTGGAGATGCTTCA 57.915 50.000 2.07 0.00 0.00 3.02
753 798 1.728971 CAACGACTGGAGATGCTTCAC 59.271 52.381 2.07 0.00 0.00 3.18
754 799 1.261480 ACGACTGGAGATGCTTCACT 58.739 50.000 2.07 0.00 0.00 3.41
755 800 1.203523 ACGACTGGAGATGCTTCACTC 59.796 52.381 2.07 0.00 0.00 3.51
756 801 1.476085 CGACTGGAGATGCTTCACTCT 59.524 52.381 2.07 0.00 34.11 3.24
757 802 2.479389 CGACTGGAGATGCTTCACTCTC 60.479 54.545 2.07 0.00 37.72 3.20
758 803 2.760092 GACTGGAGATGCTTCACTCTCT 59.240 50.000 2.07 0.00 38.36 3.10
759 804 2.496871 ACTGGAGATGCTTCACTCTCTG 59.503 50.000 2.07 0.00 38.36 3.35
760 805 2.496871 CTGGAGATGCTTCACTCTCTGT 59.503 50.000 2.07 0.00 38.36 3.41
761 806 2.902486 TGGAGATGCTTCACTCTCTGTT 59.098 45.455 2.07 0.00 38.36 3.16
762 807 3.326006 TGGAGATGCTTCACTCTCTGTTT 59.674 43.478 2.07 0.00 38.36 2.83
763 808 4.202398 TGGAGATGCTTCACTCTCTGTTTT 60.202 41.667 2.07 0.00 38.36 2.43
764 809 4.391523 GGAGATGCTTCACTCTCTGTTTTC 59.608 45.833 2.07 0.00 38.36 2.29
765 810 4.322567 AGATGCTTCACTCTCTGTTTTCC 58.677 43.478 2.07 0.00 0.00 3.13
766 811 3.558931 TGCTTCACTCTCTGTTTTCCA 57.441 42.857 0.00 0.00 0.00 3.53
767 812 4.090761 TGCTTCACTCTCTGTTTTCCAT 57.909 40.909 0.00 0.00 0.00 3.41
768 813 5.227569 TGCTTCACTCTCTGTTTTCCATA 57.772 39.130 0.00 0.00 0.00 2.74
769 814 4.997395 TGCTTCACTCTCTGTTTTCCATAC 59.003 41.667 0.00 0.00 0.00 2.39
805 850 1.756538 GGGGTGGTGGATAAATTGCTG 59.243 52.381 0.00 0.00 0.00 4.41
806 851 2.456577 GGGTGGTGGATAAATTGCTGT 58.543 47.619 0.00 0.00 0.00 4.40
807 852 3.626222 GGGGTGGTGGATAAATTGCTGTA 60.626 47.826 0.00 0.00 0.00 2.74
808 853 3.380320 GGGTGGTGGATAAATTGCTGTAC 59.620 47.826 0.00 0.00 0.00 2.90
809 854 4.013728 GGTGGTGGATAAATTGCTGTACA 58.986 43.478 0.00 0.00 0.00 2.90
810 855 4.096382 GGTGGTGGATAAATTGCTGTACAG 59.904 45.833 18.93 18.93 0.00 2.74
817 862 7.012704 GTGGATAAATTGCTGTACAGTCATCAT 59.987 37.037 23.44 10.63 0.00 2.45
823 868 6.469782 TTGCTGTACAGTCATCATAGATCA 57.530 37.500 23.44 6.07 0.00 2.92
824 869 6.469782 TGCTGTACAGTCATCATAGATCAA 57.530 37.500 23.44 0.00 0.00 2.57
861 906 5.254901 TGTACCCCATAATTAAGTTGCGTT 58.745 37.500 0.00 0.00 0.00 4.84
886 943 1.737029 CGATCGACTGTGCATCCTGTT 60.737 52.381 10.26 0.00 0.00 3.16
892 949 3.425359 CGACTGTGCATCCTGTTCATTTC 60.425 47.826 0.00 0.00 0.00 2.17
913 974 0.672711 GTTCACCGGCTTGGGAGTAC 60.673 60.000 0.00 0.00 44.64 2.73
914 975 2.125673 CACCGGCTTGGGAGTACG 60.126 66.667 0.00 0.00 44.64 3.67
915 976 3.387947 ACCGGCTTGGGAGTACGG 61.388 66.667 0.00 0.00 45.10 4.02
920 981 2.494918 CTTGGGAGTACGGGAGCG 59.505 66.667 0.00 0.00 0.00 5.03
944 1026 0.894835 TAAGAGACGCCATGCACTCA 59.105 50.000 0.00 0.00 35.37 3.41
963 1045 2.560105 TCATCAGCTCCTATCATCCACG 59.440 50.000 0.00 0.00 0.00 4.94
971 1053 2.434336 TCCTATCATCCACGGGAACAAG 59.566 50.000 0.00 0.00 34.34 3.16
972 1054 2.213499 CTATCATCCACGGGAACAAGC 58.787 52.381 0.00 0.00 34.34 4.01
973 1055 0.744414 ATCATCCACGGGAACAAGCG 60.744 55.000 0.00 0.00 34.34 4.68
974 1056 2.746277 ATCCACGGGAACAAGCGC 60.746 61.111 0.00 0.00 34.34 5.92
1026 1108 2.737359 GCCGGTGACAATTATCGACTCA 60.737 50.000 1.90 0.00 0.00 3.41
1302 1390 3.103911 GACGGCGTCAGGTTCGTG 61.104 66.667 33.07 0.00 35.91 4.35
1584 1711 2.430244 GACCGCTCGCTCGTCAAA 60.430 61.111 2.37 0.00 0.00 2.69
1587 1714 2.022129 CCGCTCGCTCGTCAAACTT 61.022 57.895 0.00 0.00 0.00 2.66
1591 1718 0.038159 CTCGCTCGTCAAACTTCCCT 60.038 55.000 0.00 0.00 0.00 4.20
1602 1729 0.693049 AACTTCCCTGTGGCGAAGAT 59.307 50.000 16.18 6.74 38.18 2.40
1627 1754 1.074752 CAGGAGCGTCTTGAGAAAGC 58.925 55.000 2.64 2.64 0.00 3.51
1667 1794 2.224281 TGGTATGCTGAGCCCTTAATCG 60.224 50.000 0.23 0.00 0.00 3.34
1671 2000 2.356135 TGCTGAGCCCTTAATCGTTTC 58.644 47.619 0.23 0.00 0.00 2.78
1676 2005 5.309323 TGAGCCCTTAATCGTTTCAAATG 57.691 39.130 0.00 0.00 0.00 2.32
1680 2009 6.156519 AGCCCTTAATCGTTTCAAATGTTTC 58.843 36.000 0.00 0.00 0.00 2.78
1683 2012 6.639279 CCCTTAATCGTTTCAAATGTTTCGTT 59.361 34.615 0.00 0.00 0.00 3.85
1685 2014 5.881637 AATCGTTTCAAATGTTTCGTTGG 57.118 34.783 0.00 0.00 0.00 3.77
1724 3679 0.387494 TCATGCGTACGCGTTTCAGA 60.387 50.000 31.22 21.88 45.51 3.27
1752 3707 2.434359 GGCGTGGTTCGAAGAGGG 60.434 66.667 0.00 0.00 42.86 4.30
1826 4178 1.690283 CCTCAAGCAGCACATCGTCG 61.690 60.000 0.00 0.00 0.00 5.12
1855 4216 4.776647 GCCAACGGCGCATTGTCC 62.777 66.667 18.83 8.62 39.62 4.02
1856 4217 3.361158 CCAACGGCGCATTGTCCA 61.361 61.111 18.83 0.00 0.00 4.02
1857 4218 2.642129 CAACGGCGCATTGTCCAA 59.358 55.556 10.83 0.00 0.00 3.53
1858 4219 1.729131 CAACGGCGCATTGTCCAAC 60.729 57.895 10.83 0.00 0.00 3.77
1859 4220 1.896660 AACGGCGCATTGTCCAACT 60.897 52.632 10.83 0.00 0.00 3.16
1926 4287 1.718757 GCATGGACGTGCTTCATCCC 61.719 60.000 8.99 0.00 41.82 3.85
1930 4291 1.374252 GACGTGCTTCATCCCGTGT 60.374 57.895 0.00 0.00 33.03 4.49
1943 4304 2.872925 CGTGTAGGCCGTTCGTCG 60.873 66.667 0.00 0.00 39.52 5.12
1969 4333 0.390866 ACGAGGAAGTGCTGCTCATG 60.391 55.000 0.00 0.00 42.49 3.07
2146 4527 0.326048 ATGAGAGAGGTCCCAGTGGG 60.326 60.000 23.57 23.57 46.11 4.61
2149 4530 1.997874 GAGAGGTCCCAGTGGGCAT 60.998 63.158 24.75 16.17 43.94 4.40
2243 4624 2.758327 AGGGCATACGAGGACGCA 60.758 61.111 0.00 0.00 43.96 5.24
2261 4642 2.231380 AGACTTCGGGTGGGGCAAT 61.231 57.895 0.00 0.00 0.00 3.56
2534 5153 8.942338 TCATTAGTATCAGCGTATGTTTTTCT 57.058 30.769 0.00 0.00 0.00 2.52
2537 5156 9.988350 ATTAGTATCAGCGTATGTTTTTCTTTG 57.012 29.630 0.00 0.00 0.00 2.77
2538 5157 7.667043 AGTATCAGCGTATGTTTTTCTTTGA 57.333 32.000 0.00 0.00 0.00 2.69
2539 5158 7.743104 AGTATCAGCGTATGTTTTTCTTTGAG 58.257 34.615 0.00 0.00 0.00 3.02
2540 5159 5.356882 TCAGCGTATGTTTTTCTTTGAGG 57.643 39.130 0.00 0.00 0.00 3.86
2541 5160 4.819630 TCAGCGTATGTTTTTCTTTGAGGT 59.180 37.500 0.00 0.00 0.00 3.85
2542 5161 5.992829 TCAGCGTATGTTTTTCTTTGAGGTA 59.007 36.000 0.00 0.00 0.00 3.08
2543 5162 6.483974 TCAGCGTATGTTTTTCTTTGAGGTAA 59.516 34.615 0.00 0.00 0.00 2.85
2544 5163 7.174253 TCAGCGTATGTTTTTCTTTGAGGTAAT 59.826 33.333 0.00 0.00 0.00 1.89
2545 5164 8.447833 CAGCGTATGTTTTTCTTTGAGGTAATA 58.552 33.333 0.00 0.00 0.00 0.98
2546 5165 9.005777 AGCGTATGTTTTTCTTTGAGGTAATAA 57.994 29.630 0.00 0.00 0.00 1.40
2547 5166 9.058424 GCGTATGTTTTTCTTTGAGGTAATAAC 57.942 33.333 0.00 0.00 0.00 1.89
2555 5174 8.842358 TTTCTTTGAGGTAATAACACTAGTGG 57.158 34.615 26.12 9.07 34.19 4.00
2556 5175 7.549147 TCTTTGAGGTAATAACACTAGTGGT 57.451 36.000 26.12 22.89 34.19 4.16
2568 5187 2.484264 CACTAGTGGTGCCTAAACTTGC 59.516 50.000 15.49 0.00 39.22 4.01
2569 5188 2.084546 CTAGTGGTGCCTAAACTTGCC 58.915 52.381 0.00 0.00 0.00 4.52
2570 5189 0.184933 AGTGGTGCCTAAACTTGCCA 59.815 50.000 0.00 0.00 0.00 4.92
2571 5190 0.598065 GTGGTGCCTAAACTTGCCAG 59.402 55.000 0.00 0.00 0.00 4.85
2572 5191 1.178534 TGGTGCCTAAACTTGCCAGC 61.179 55.000 0.00 0.00 0.00 4.85
2573 5192 1.210155 GTGCCTAAACTTGCCAGCG 59.790 57.895 0.00 0.00 0.00 5.18
2574 5193 1.072332 TGCCTAAACTTGCCAGCGA 59.928 52.632 0.00 0.00 0.00 4.93
2575 5194 0.322456 TGCCTAAACTTGCCAGCGAT 60.322 50.000 0.00 0.00 0.00 4.58
2576 5195 0.099436 GCCTAAACTTGCCAGCGATG 59.901 55.000 0.00 0.00 0.00 3.84
2577 5196 1.453155 CCTAAACTTGCCAGCGATGT 58.547 50.000 0.00 0.00 0.00 3.06
2578 5197 1.812571 CCTAAACTTGCCAGCGATGTT 59.187 47.619 0.00 0.00 0.00 2.71
2579 5198 2.228822 CCTAAACTTGCCAGCGATGTTT 59.771 45.455 0.00 10.59 35.43 2.83
2580 5199 3.438781 CCTAAACTTGCCAGCGATGTTTA 59.561 43.478 0.00 11.37 33.63 2.01
2581 5200 2.989422 AACTTGCCAGCGATGTTTAC 57.011 45.000 0.00 0.00 0.00 2.01
2582 5201 2.185004 ACTTGCCAGCGATGTTTACT 57.815 45.000 0.00 0.00 0.00 2.24
2583 5202 2.504367 ACTTGCCAGCGATGTTTACTT 58.496 42.857 0.00 0.00 0.00 2.24
2584 5203 2.884639 ACTTGCCAGCGATGTTTACTTT 59.115 40.909 0.00 0.00 0.00 2.66
2585 5204 2.987413 TGCCAGCGATGTTTACTTTG 57.013 45.000 0.00 0.00 0.00 2.77
2586 5205 1.539388 TGCCAGCGATGTTTACTTTGG 59.461 47.619 0.00 0.00 0.00 3.28
2587 5206 1.539827 GCCAGCGATGTTTACTTTGGT 59.460 47.619 0.00 0.00 0.00 3.67
2588 5207 2.668279 GCCAGCGATGTTTACTTTGGTG 60.668 50.000 0.00 7.76 34.54 4.17
2589 5208 2.584791 CAGCGATGTTTACTTTGGTGC 58.415 47.619 0.00 0.00 0.00 5.01
2590 5209 2.031245 CAGCGATGTTTACTTTGGTGCA 60.031 45.455 0.00 0.00 0.00 4.57
2591 5210 2.819608 AGCGATGTTTACTTTGGTGCAT 59.180 40.909 0.00 0.00 0.00 3.96
2592 5211 2.916716 GCGATGTTTACTTTGGTGCATG 59.083 45.455 0.00 0.00 0.00 4.06
2593 5212 3.365868 GCGATGTTTACTTTGGTGCATGA 60.366 43.478 0.00 0.00 0.00 3.07
2594 5213 4.793071 CGATGTTTACTTTGGTGCATGAA 58.207 39.130 0.00 0.00 0.00 2.57
2595 5214 4.616802 CGATGTTTACTTTGGTGCATGAAC 59.383 41.667 0.00 0.00 0.00 3.18
2596 5215 5.562696 CGATGTTTACTTTGGTGCATGAACT 60.563 40.000 3.21 0.00 0.00 3.01
2597 5216 5.590530 TGTTTACTTTGGTGCATGAACTT 57.409 34.783 3.21 0.00 0.00 2.66
2598 5217 5.347342 TGTTTACTTTGGTGCATGAACTTG 58.653 37.500 3.21 0.00 0.00 3.16
2602 5221 5.083533 ACTTTGGTGCATGAACTTGAAAA 57.916 34.783 3.21 0.00 0.00 2.29
2604 5223 6.114767 ACTTTGGTGCATGAACTTGAAAAAT 58.885 32.000 3.21 0.00 0.00 1.82
2606 5225 7.768120 ACTTTGGTGCATGAACTTGAAAAATAA 59.232 29.630 3.21 0.00 0.00 1.40
2607 5226 7.475771 TTGGTGCATGAACTTGAAAAATAAC 57.524 32.000 3.21 0.00 0.00 1.89
2608 5227 6.815089 TGGTGCATGAACTTGAAAAATAACT 58.185 32.000 3.21 0.00 0.00 2.24
2612 5231 6.202570 TGCATGAACTTGAAAAATAACTTGGC 59.797 34.615 0.00 0.00 0.00 4.52
2617 5236 8.637986 TGAACTTGAAAAATAACTTGGCAGTAT 58.362 29.630 0.00 0.00 30.68 2.12
2618 5237 8.816640 AACTTGAAAAATAACTTGGCAGTATG 57.183 30.769 0.00 0.00 40.87 2.39
2619 5238 7.378181 ACTTGAAAAATAACTTGGCAGTATGG 58.622 34.615 0.00 0.00 35.86 2.74
2620 5239 6.909550 TGAAAAATAACTTGGCAGTATGGT 57.090 33.333 0.00 0.00 35.86 3.55
2623 5242 6.909550 AAAATAACTTGGCAGTATGGTTCA 57.090 33.333 0.00 0.00 35.86 3.18
2624 5243 6.909550 AAATAACTTGGCAGTATGGTTCAA 57.090 33.333 0.00 0.00 35.86 2.69
2625 5244 6.909550 AATAACTTGGCAGTATGGTTCAAA 57.090 33.333 0.00 0.00 35.86 2.69
2626 5245 7.480760 AATAACTTGGCAGTATGGTTCAAAT 57.519 32.000 0.00 0.00 35.86 2.32
2627 5246 8.588290 AATAACTTGGCAGTATGGTTCAAATA 57.412 30.769 0.00 0.00 35.86 1.40
2630 5249 5.415701 ACTTGGCAGTATGGTTCAAATACAG 59.584 40.000 0.00 0.00 35.86 2.74
2638 5257 9.559958 CAGTATGGTTCAAATACAGTTCAAATC 57.440 33.333 0.00 0.00 33.70 2.17
2640 5259 9.341899 GTATGGTTCAAATACAGTTCAAATCAC 57.658 33.333 0.00 0.00 31.94 3.06
2641 5260 6.434596 TGGTTCAAATACAGTTCAAATCACG 58.565 36.000 0.00 0.00 0.00 4.35
2642 5261 6.038825 TGGTTCAAATACAGTTCAAATCACGT 59.961 34.615 0.00 0.00 0.00 4.49
2643 5262 6.577427 GGTTCAAATACAGTTCAAATCACGTC 59.423 38.462 0.00 0.00 0.00 4.34
2644 5263 7.352739 GTTCAAATACAGTTCAAATCACGTCT 58.647 34.615 0.00 0.00 0.00 4.18
2645 5264 8.492748 GTTCAAATACAGTTCAAATCACGTCTA 58.507 33.333 0.00 0.00 0.00 2.59
2646 5265 8.239681 TCAAATACAGTTCAAATCACGTCTAG 57.760 34.615 0.00 0.00 0.00 2.43
2647 5266 8.085909 TCAAATACAGTTCAAATCACGTCTAGA 58.914 33.333 0.00 0.00 0.00 2.43
2648 5267 8.873830 CAAATACAGTTCAAATCACGTCTAGAT 58.126 33.333 0.00 0.00 0.00 1.98
2795 5878 2.359107 CTGCTCGCTTTGCCTGGA 60.359 61.111 0.00 0.00 0.00 3.86
3383 8139 1.002274 GGAGGAGGAGAAGGAGGCA 59.998 63.158 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.239306 GTCTTCACAAATGTTGACCATCTCA 59.761 40.000 0.00 0.00 31.75 3.27
76 77 0.185901 TGCAAGCCTCCTGAACCTTT 59.814 50.000 0.00 0.00 0.00 3.11
282 290 3.760684 GTGATCAACTTGGGCAAGAAGAT 59.239 43.478 0.00 0.00 40.79 2.40
285 293 2.238521 GGTGATCAACTTGGGCAAGAA 58.761 47.619 2.64 0.00 40.79 2.52
319 327 3.830755 GCATATTGAGGAAGGCAATCCAT 59.169 43.478 11.34 0.34 42.27 3.41
324 332 2.288666 GACGCATATTGAGGAAGGCAA 58.711 47.619 0.00 0.00 0.00 4.52
392 412 1.419387 GAGCCTTCATAGGTGCTCCAT 59.581 52.381 7.70 0.00 43.40 3.41
562 607 1.956477 GCAAATCGGCCCATATTCACT 59.044 47.619 0.00 0.00 0.00 3.41
590 635 4.128388 GGTGCAAAATCGGCCCGG 62.128 66.667 1.90 0.00 0.00 5.73
603 648 3.132925 TGTTTTTGGTCTACTACGGTGC 58.867 45.455 0.00 0.00 0.00 5.01
604 649 5.064962 TGTTTGTTTTTGGTCTACTACGGTG 59.935 40.000 0.00 0.00 0.00 4.94
605 650 5.184711 TGTTTGTTTTTGGTCTACTACGGT 58.815 37.500 0.00 0.00 0.00 4.83
606 651 5.738118 TGTTTGTTTTTGGTCTACTACGG 57.262 39.130 0.00 0.00 0.00 4.02
607 652 8.623310 AATTTGTTTGTTTTTGGTCTACTACG 57.377 30.769 0.00 0.00 0.00 3.51
610 655 9.078753 CGTAAATTTGTTTGTTTTTGGTCTACT 57.921 29.630 0.00 0.00 0.00 2.57
611 656 7.842239 GCGTAAATTTGTTTGTTTTTGGTCTAC 59.158 33.333 0.00 0.00 0.00 2.59
612 657 7.010275 GGCGTAAATTTGTTTGTTTTTGGTCTA 59.990 33.333 0.00 0.00 0.00 2.59
613 658 6.183360 GGCGTAAATTTGTTTGTTTTTGGTCT 60.183 34.615 0.00 0.00 0.00 3.85
614 659 5.960683 GGCGTAAATTTGTTTGTTTTTGGTC 59.039 36.000 0.00 0.00 0.00 4.02
615 660 5.411669 TGGCGTAAATTTGTTTGTTTTTGGT 59.588 32.000 0.00 0.00 0.00 3.67
616 661 5.869350 TGGCGTAAATTTGTTTGTTTTTGG 58.131 33.333 0.00 0.00 0.00 3.28
617 662 7.781763 TTTGGCGTAAATTTGTTTGTTTTTG 57.218 28.000 0.00 0.00 0.00 2.44
618 663 8.972262 ATTTTGGCGTAAATTTGTTTGTTTTT 57.028 23.077 0.00 0.00 0.00 1.94
619 664 8.854312 CAATTTTGGCGTAAATTTGTTTGTTTT 58.146 25.926 0.00 0.00 35.98 2.43
620 665 8.237267 TCAATTTTGGCGTAAATTTGTTTGTTT 58.763 25.926 0.00 0.00 39.17 2.83
621 666 7.752695 TCAATTTTGGCGTAAATTTGTTTGTT 58.247 26.923 0.00 0.00 39.17 2.83
622 667 7.308782 TCAATTTTGGCGTAAATTTGTTTGT 57.691 28.000 0.00 0.00 39.17 2.83
623 668 6.356714 GCTCAATTTTGGCGTAAATTTGTTTG 59.643 34.615 0.00 0.31 39.17 2.93
624 669 6.426327 GCTCAATTTTGGCGTAAATTTGTTT 58.574 32.000 0.00 0.00 39.17 2.83
625 670 5.049749 GGCTCAATTTTGGCGTAAATTTGTT 60.050 36.000 0.00 0.00 39.17 2.83
626 671 4.450757 GGCTCAATTTTGGCGTAAATTTGT 59.549 37.500 0.00 0.00 39.17 2.83
627 672 4.434067 CGGCTCAATTTTGGCGTAAATTTG 60.434 41.667 13.06 8.28 45.15 2.32
628 673 3.677596 CGGCTCAATTTTGGCGTAAATTT 59.322 39.130 13.06 0.00 45.15 1.82
629 674 3.249917 CGGCTCAATTTTGGCGTAAATT 58.750 40.909 13.06 4.80 45.15 1.82
630 675 2.874849 CGGCTCAATTTTGGCGTAAAT 58.125 42.857 13.06 0.00 45.15 1.40
631 676 2.339728 CGGCTCAATTTTGGCGTAAA 57.660 45.000 13.06 0.00 45.15 2.01
636 681 2.548057 TCGATATCGGCTCAATTTTGGC 59.452 45.455 24.12 0.00 40.29 4.52
637 682 3.362986 CGTCGATATCGGCTCAATTTTGG 60.363 47.826 25.70 4.75 42.59 3.28
638 683 3.787826 CGTCGATATCGGCTCAATTTTG 58.212 45.455 25.70 5.45 42.59 2.44
639 684 2.221055 GCGTCGATATCGGCTCAATTTT 59.779 45.455 25.70 0.00 42.59 1.82
640 685 1.792949 GCGTCGATATCGGCTCAATTT 59.207 47.619 25.70 0.00 42.59 1.82
641 686 1.419374 GCGTCGATATCGGCTCAATT 58.581 50.000 25.70 0.00 42.59 2.32
642 687 3.108521 GCGTCGATATCGGCTCAAT 57.891 52.632 25.70 0.00 42.59 2.57
643 688 4.628160 GCGTCGATATCGGCTCAA 57.372 55.556 25.70 3.74 42.59 3.02
648 693 2.258591 CCCAGGCGTCGATATCGG 59.741 66.667 24.12 10.83 40.29 4.18
649 694 2.258591 CCCCAGGCGTCGATATCG 59.741 66.667 19.14 19.14 41.45 2.92
650 695 1.906824 TCCCCCAGGCGTCGATATC 60.907 63.158 0.00 0.00 0.00 1.63
651 696 2.200370 TCCCCCAGGCGTCGATAT 59.800 61.111 0.00 0.00 0.00 1.63
652 697 2.836360 GTCCCCCAGGCGTCGATA 60.836 66.667 0.00 0.00 0.00 2.92
677 722 4.759205 ATTGGGTTCCCAGCCGCC 62.759 66.667 10.62 0.00 44.44 6.13
678 723 3.140814 GATTGGGTTCCCAGCCGC 61.141 66.667 10.62 0.00 44.44 6.53
679 724 2.824041 CGATTGGGTTCCCAGCCG 60.824 66.667 10.62 13.43 44.44 5.52
680 725 1.749258 GTCGATTGGGTTCCCAGCC 60.749 63.158 10.62 6.17 41.49 4.85
681 726 1.749258 GGTCGATTGGGTTCCCAGC 60.749 63.158 10.62 6.70 37.42 4.85
682 727 1.077716 GGGTCGATTGGGTTCCCAG 60.078 63.158 10.62 0.27 37.42 4.45
683 728 2.608550 GGGGTCGATTGGGTTCCCA 61.609 63.158 6.46 6.46 39.85 4.37
684 729 2.274432 GGGGTCGATTGGGTTCCC 59.726 66.667 0.12 0.12 37.59 3.97
685 730 1.077716 CTGGGGTCGATTGGGTTCC 60.078 63.158 0.00 0.00 0.00 3.62
686 731 1.077716 CCTGGGGTCGATTGGGTTC 60.078 63.158 0.00 0.00 0.00 3.62
687 732 3.087065 CCTGGGGTCGATTGGGTT 58.913 61.111 0.00 0.00 0.00 4.11
688 733 3.728373 GCCTGGGGTCGATTGGGT 61.728 66.667 0.00 0.00 0.00 4.51
689 734 4.856801 CGCCTGGGGTCGATTGGG 62.857 72.222 1.98 0.00 0.00 4.12
690 735 4.856801 CCGCCTGGGGTCGATTGG 62.857 72.222 10.09 0.00 0.00 3.16
691 736 4.096003 ACCGCCTGGGGTCGATTG 62.096 66.667 10.09 0.00 41.60 2.67
692 737 4.096003 CACCGCCTGGGGTCGATT 62.096 66.667 10.09 0.00 38.56 3.34
695 740 3.622060 AAATCACCGCCTGGGGTCG 62.622 63.158 10.09 0.30 40.71 4.79
696 741 0.898326 AAAAATCACCGCCTGGGGTC 60.898 55.000 10.09 0.00 40.71 4.46
697 742 1.155155 AAAAATCACCGCCTGGGGT 59.845 52.632 10.09 5.55 40.71 4.95
698 743 4.111967 AAAAATCACCGCCTGGGG 57.888 55.556 3.33 3.33 41.53 4.96
712 757 1.679153 GCACTCGAGGGGTTTCAAAAA 59.321 47.619 18.15 0.00 0.00 1.94
713 758 1.314730 GCACTCGAGGGGTTTCAAAA 58.685 50.000 18.15 0.00 0.00 2.44
714 759 0.536460 GGCACTCGAGGGGTTTCAAA 60.536 55.000 18.15 0.00 0.00 2.69
715 760 1.072505 GGCACTCGAGGGGTTTCAA 59.927 57.895 18.15 0.00 0.00 2.69
716 761 1.701031 TTGGCACTCGAGGGGTTTCA 61.701 55.000 18.15 3.10 0.00 2.69
717 762 1.072505 TTGGCACTCGAGGGGTTTC 59.927 57.895 18.15 0.00 0.00 2.78
718 763 1.228154 GTTGGCACTCGAGGGGTTT 60.228 57.895 18.15 0.00 0.00 3.27
719 764 2.430367 GTTGGCACTCGAGGGGTT 59.570 61.111 18.15 0.00 0.00 4.11
720 765 4.003788 CGTTGGCACTCGAGGGGT 62.004 66.667 18.15 0.00 0.00 4.95
721 766 3.691342 TCGTTGGCACTCGAGGGG 61.691 66.667 18.15 9.47 32.97 4.79
722 767 2.432628 GTCGTTGGCACTCGAGGG 60.433 66.667 18.41 15.12 36.39 4.30
723 768 1.734477 CAGTCGTTGGCACTCGAGG 60.734 63.158 18.41 6.97 36.39 4.63
724 769 1.734477 CCAGTCGTTGGCACTCGAG 60.734 63.158 11.84 11.84 40.87 4.04
725 770 2.338620 CCAGTCGTTGGCACTCGA 59.661 61.111 9.37 9.37 40.87 4.04
733 778 1.728971 GTGAAGCATCTCCAGTCGTTG 59.271 52.381 0.00 0.00 0.00 4.10
734 779 1.620819 AGTGAAGCATCTCCAGTCGTT 59.379 47.619 0.00 0.00 0.00 3.85
735 780 1.203523 GAGTGAAGCATCTCCAGTCGT 59.796 52.381 0.00 0.00 0.00 4.34
736 781 1.476085 AGAGTGAAGCATCTCCAGTCG 59.524 52.381 0.00 0.00 35.88 4.18
737 782 2.760092 AGAGAGTGAAGCATCTCCAGTC 59.240 50.000 0.00 0.00 42.45 3.51
738 783 2.496871 CAGAGAGTGAAGCATCTCCAGT 59.503 50.000 0.00 0.00 42.45 4.00
739 784 2.496871 ACAGAGAGTGAAGCATCTCCAG 59.503 50.000 0.00 0.00 42.45 3.86
740 785 2.533916 ACAGAGAGTGAAGCATCTCCA 58.466 47.619 0.00 0.00 42.45 3.86
741 786 3.608316 AACAGAGAGTGAAGCATCTCC 57.392 47.619 0.00 0.00 42.45 3.71
742 787 4.391523 GGAAAACAGAGAGTGAAGCATCTC 59.608 45.833 0.00 0.00 41.90 2.75
743 788 4.202398 TGGAAAACAGAGAGTGAAGCATCT 60.202 41.667 0.00 0.00 0.00 2.90
744 789 4.067896 TGGAAAACAGAGAGTGAAGCATC 58.932 43.478 0.00 0.00 0.00 3.91
745 790 4.090761 TGGAAAACAGAGAGTGAAGCAT 57.909 40.909 0.00 0.00 0.00 3.79
746 791 3.558931 TGGAAAACAGAGAGTGAAGCA 57.441 42.857 0.00 0.00 0.00 3.91
747 792 5.121454 CAGTATGGAAAACAGAGAGTGAAGC 59.879 44.000 0.00 0.00 0.00 3.86
748 793 6.718454 CAGTATGGAAAACAGAGAGTGAAG 57.282 41.667 0.00 0.00 0.00 3.02
765 810 1.745115 CGGTGGGTGTGCCAGTATG 60.745 63.158 0.00 0.00 36.17 2.39
766 811 2.668632 CGGTGGGTGTGCCAGTAT 59.331 61.111 0.00 0.00 36.17 2.12
767 812 4.323477 GCGGTGGGTGTGCCAGTA 62.323 66.667 0.00 0.00 36.17 2.74
786 831 2.456577 ACAGCAATTTATCCACCACCC 58.543 47.619 0.00 0.00 0.00 4.61
823 868 6.865834 TGGGGTACATGCAATTAATTCTTT 57.134 33.333 0.00 0.00 0.00 2.52
824 869 8.546083 TTATGGGGTACATGCAATTAATTCTT 57.454 30.769 0.00 0.00 40.82 2.52
841 886 5.889289 ACATAACGCAACTTAATTATGGGGT 59.111 36.000 8.39 2.94 38.69 4.95
861 906 2.287608 GGATGCACAGTCGATCGACATA 60.288 50.000 40.51 24.95 46.76 2.29
913 974 2.852748 CGTCTCTTATATTCGCTCCCG 58.147 52.381 0.00 0.00 0.00 5.14
914 975 2.597520 GCGTCTCTTATATTCGCTCCC 58.402 52.381 0.00 0.00 42.88 4.30
915 976 2.030185 TGGCGTCTCTTATATTCGCTCC 60.030 50.000 7.69 0.00 45.01 4.70
920 981 4.310769 AGTGCATGGCGTCTCTTATATTC 58.689 43.478 0.00 0.00 0.00 1.75
936 997 2.970640 TGATAGGAGCTGATGAGTGCAT 59.029 45.455 0.00 0.00 37.47 3.96
944 1026 1.898472 CCGTGGATGATAGGAGCTGAT 59.102 52.381 0.00 0.00 0.00 2.90
1013 1095 8.323854 CACTGACATAGTTTGAGTCGATAATTG 58.676 37.037 0.00 0.00 37.60 2.32
1026 1108 1.346395 TCCGGCACACTGACATAGTTT 59.654 47.619 0.00 0.00 37.60 2.66
1551 1678 4.228567 TCGAAGCACGGTGTGGCA 62.229 61.111 10.24 0.00 42.82 4.92
1587 1714 1.617018 CCAGATCTTCGCCACAGGGA 61.617 60.000 0.00 0.00 35.59 4.20
1591 1718 2.268920 GGCCAGATCTTCGCCACA 59.731 61.111 21.03 0.00 42.52 4.17
1602 1729 2.604686 AAGACGCTCCTGGCCAGA 60.605 61.111 34.91 18.49 37.74 3.86
1627 1754 1.151777 AATGGTAGATTCGGCGCGTG 61.152 55.000 8.43 0.00 0.00 5.34
1667 1794 5.369947 GTCACCAACGAAACATTTGAAAC 57.630 39.130 0.00 0.00 0.00 2.78
1708 3190 2.359040 CGTCTGAAACGCGTACGCA 61.359 57.895 36.44 18.14 45.76 5.24
1709 3191 2.385361 CGTCTGAAACGCGTACGC 59.615 61.111 29.83 29.83 45.76 4.42
1742 3697 3.621805 TGTGCGCCCCTCTTCGAA 61.622 61.111 4.18 0.00 0.00 3.71
1851 4212 4.329545 GCAGGGGCGAGTTGGACA 62.330 66.667 0.00 0.00 0.00 4.02
1926 4287 2.872925 CGACGAACGGCCTACACG 60.873 66.667 0.00 3.99 38.46 4.49
1943 4304 2.504244 CACTTCCTCGTCGTCCGC 60.504 66.667 0.00 0.00 36.19 5.54
1954 4318 1.818642 AGAACATGAGCAGCACTTCC 58.181 50.000 0.00 0.00 0.00 3.46
1969 4333 1.129326 CACGGATATCGGCGAAGAAC 58.871 55.000 15.93 3.60 44.45 3.01
2146 4527 3.488047 CGATGTCTGAAAATCCCACATGC 60.488 47.826 0.00 0.00 0.00 4.06
2149 4530 2.039746 ACCGATGTCTGAAAATCCCACA 59.960 45.455 0.00 0.00 0.00 4.17
2243 4624 2.198304 GATTGCCCCACCCGAAGTCT 62.198 60.000 0.00 0.00 0.00 3.24
2291 4672 3.248171 GCGATCTGACCGTCGTGC 61.248 66.667 0.00 0.00 39.87 5.34
2533 5152 7.596749 CACCACTAGTGTTATTACCTCAAAG 57.403 40.000 21.18 3.58 41.93 2.77
2548 5167 2.552373 GGCAAGTTTAGGCACCACTAGT 60.552 50.000 0.00 0.00 0.00 2.57
2549 5168 2.084546 GGCAAGTTTAGGCACCACTAG 58.915 52.381 0.00 0.00 0.00 2.57
2550 5169 1.422024 TGGCAAGTTTAGGCACCACTA 59.578 47.619 0.00 0.00 36.56 2.74
2551 5170 0.184933 TGGCAAGTTTAGGCACCACT 59.815 50.000 0.00 0.00 36.56 4.00
2552 5171 0.598065 CTGGCAAGTTTAGGCACCAC 59.402 55.000 0.00 0.00 36.56 4.16
2553 5172 1.178534 GCTGGCAAGTTTAGGCACCA 61.179 55.000 0.00 0.00 36.56 4.17
2554 5173 1.586541 GCTGGCAAGTTTAGGCACC 59.413 57.895 0.00 0.00 36.56 5.01
2555 5174 1.210155 CGCTGGCAAGTTTAGGCAC 59.790 57.895 0.00 0.00 36.56 5.01
2556 5175 0.322456 ATCGCTGGCAAGTTTAGGCA 60.322 50.000 0.00 0.00 39.41 4.75
2557 5176 0.099436 CATCGCTGGCAAGTTTAGGC 59.901 55.000 0.00 0.00 0.00 3.93
2558 5177 1.453155 ACATCGCTGGCAAGTTTAGG 58.547 50.000 0.00 0.00 0.00 2.69
2559 5178 3.559238 AAACATCGCTGGCAAGTTTAG 57.441 42.857 0.00 0.00 31.29 1.85
2560 5179 4.069304 AGTAAACATCGCTGGCAAGTTTA 58.931 39.130 0.00 8.85 34.58 2.01
2561 5180 2.884639 AGTAAACATCGCTGGCAAGTTT 59.115 40.909 10.23 10.23 36.49 2.66
2562 5181 2.504367 AGTAAACATCGCTGGCAAGTT 58.496 42.857 0.00 0.00 0.00 2.66
2563 5182 2.185004 AGTAAACATCGCTGGCAAGT 57.815 45.000 0.00 0.00 0.00 3.16
2564 5183 3.236816 CAAAGTAAACATCGCTGGCAAG 58.763 45.455 0.00 0.00 0.00 4.01
2565 5184 2.030363 CCAAAGTAAACATCGCTGGCAA 60.030 45.455 0.00 0.00 0.00 4.52
2566 5185 1.539388 CCAAAGTAAACATCGCTGGCA 59.461 47.619 0.00 0.00 0.00 4.92
2567 5186 1.539827 ACCAAAGTAAACATCGCTGGC 59.460 47.619 0.00 0.00 0.00 4.85
2568 5187 2.668279 GCACCAAAGTAAACATCGCTGG 60.668 50.000 0.00 0.00 0.00 4.85
2569 5188 2.031245 TGCACCAAAGTAAACATCGCTG 60.031 45.455 0.00 0.00 0.00 5.18
2570 5189 2.226330 TGCACCAAAGTAAACATCGCT 58.774 42.857 0.00 0.00 0.00 4.93
2571 5190 2.697431 TGCACCAAAGTAAACATCGC 57.303 45.000 0.00 0.00 0.00 4.58
2572 5191 4.418013 TCATGCACCAAAGTAAACATCG 57.582 40.909 0.00 0.00 0.00 3.84
2573 5192 5.772521 AGTTCATGCACCAAAGTAAACATC 58.227 37.500 0.00 0.00 0.00 3.06
2574 5193 5.789643 AGTTCATGCACCAAAGTAAACAT 57.210 34.783 0.00 0.00 0.00 2.71
2575 5194 5.126222 TCAAGTTCATGCACCAAAGTAAACA 59.874 36.000 0.00 0.00 0.00 2.83
2576 5195 5.587289 TCAAGTTCATGCACCAAAGTAAAC 58.413 37.500 0.00 0.00 0.00 2.01
2577 5196 5.843673 TCAAGTTCATGCACCAAAGTAAA 57.156 34.783 0.00 0.00 0.00 2.01
2578 5197 5.843673 TTCAAGTTCATGCACCAAAGTAA 57.156 34.783 0.00 0.00 0.00 2.24
2579 5198 5.843673 TTTCAAGTTCATGCACCAAAGTA 57.156 34.783 0.00 0.00 0.00 2.24
2580 5199 4.734398 TTTCAAGTTCATGCACCAAAGT 57.266 36.364 0.00 0.00 0.00 2.66
2581 5200 6.607735 ATTTTTCAAGTTCATGCACCAAAG 57.392 33.333 0.00 0.00 0.00 2.77
2582 5201 7.768120 AGTTATTTTTCAAGTTCATGCACCAAA 59.232 29.630 0.00 0.00 0.00 3.28
2583 5202 7.271511 AGTTATTTTTCAAGTTCATGCACCAA 58.728 30.769 0.00 0.00 0.00 3.67
2584 5203 6.815089 AGTTATTTTTCAAGTTCATGCACCA 58.185 32.000 0.00 0.00 0.00 4.17
2585 5204 7.307337 CCAAGTTATTTTTCAAGTTCATGCACC 60.307 37.037 0.00 0.00 0.00 5.01
2586 5205 7.566709 CCAAGTTATTTTTCAAGTTCATGCAC 58.433 34.615 0.00 0.00 0.00 4.57
2587 5206 6.202570 GCCAAGTTATTTTTCAAGTTCATGCA 59.797 34.615 0.00 0.00 0.00 3.96
2588 5207 6.202570 TGCCAAGTTATTTTTCAAGTTCATGC 59.797 34.615 0.00 0.00 0.00 4.06
2589 5208 7.439056 ACTGCCAAGTTATTTTTCAAGTTCATG 59.561 33.333 0.00 0.00 30.14 3.07
2590 5209 7.500141 ACTGCCAAGTTATTTTTCAAGTTCAT 58.500 30.769 0.00 0.00 30.14 2.57
2591 5210 6.872920 ACTGCCAAGTTATTTTTCAAGTTCA 58.127 32.000 0.00 0.00 30.14 3.18
2592 5211 8.915654 CATACTGCCAAGTTATTTTTCAAGTTC 58.084 33.333 0.00 0.00 37.88 3.01
2593 5212 7.872483 CCATACTGCCAAGTTATTTTTCAAGTT 59.128 33.333 0.00 0.00 37.88 2.66
2594 5213 7.015195 ACCATACTGCCAAGTTATTTTTCAAGT 59.985 33.333 0.00 0.00 37.88 3.16
2595 5214 7.378181 ACCATACTGCCAAGTTATTTTTCAAG 58.622 34.615 0.00 0.00 37.88 3.02
2596 5215 7.296628 ACCATACTGCCAAGTTATTTTTCAA 57.703 32.000 0.00 0.00 37.88 2.69
2597 5216 6.909550 ACCATACTGCCAAGTTATTTTTCA 57.090 33.333 0.00 0.00 37.88 2.69
2598 5217 7.375053 TGAACCATACTGCCAAGTTATTTTTC 58.625 34.615 0.00 0.00 37.88 2.29
2602 5221 6.909550 TTTGAACCATACTGCCAAGTTATT 57.090 33.333 0.00 0.00 37.88 1.40
2604 5223 6.943146 TGTATTTGAACCATACTGCCAAGTTA 59.057 34.615 0.00 0.00 37.88 2.24
2606 5225 5.321102 TGTATTTGAACCATACTGCCAAGT 58.679 37.500 0.00 0.00 40.67 3.16
2607 5226 5.415701 ACTGTATTTGAACCATACTGCCAAG 59.584 40.000 0.00 0.00 32.17 3.61
2608 5227 5.321102 ACTGTATTTGAACCATACTGCCAA 58.679 37.500 0.00 0.00 32.17 4.52
2612 5231 9.559958 GATTTGAACTGTATTTGAACCATACTG 57.440 33.333 0.00 0.00 34.10 2.74
2617 5236 6.038825 ACGTGATTTGAACTGTATTTGAACCA 59.961 34.615 0.00 0.00 0.00 3.67
2618 5237 6.435428 ACGTGATTTGAACTGTATTTGAACC 58.565 36.000 0.00 0.00 0.00 3.62
2619 5238 7.352739 AGACGTGATTTGAACTGTATTTGAAC 58.647 34.615 0.00 0.00 0.00 3.18
2620 5239 7.490962 AGACGTGATTTGAACTGTATTTGAA 57.509 32.000 0.00 0.00 0.00 2.69
2653 5272 8.983702 TGTGGTAGTTTTTGGTTAAATACTCT 57.016 30.769 0.00 0.00 38.47 3.24
2696 5315 7.420002 ACAAAATCGTAAAGTGGTAGTTTTCC 58.580 34.615 0.00 0.00 0.00 3.13
2795 5878 2.351726 GGCTGTCAGATTCGCGTTTAAT 59.648 45.455 5.77 0.00 0.00 1.40
3054 6964 4.035102 GCCCTCCGCCTCACCTTT 62.035 66.667 0.00 0.00 0.00 3.11
3383 8139 2.586648 AAAAAGCAATCGGGTCCTCT 57.413 45.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.