Multiple sequence alignment - TraesCS5D01G386200

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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 TraesCS5D01G386200 chr5D 100.000 7051 0 0 1 7051 455826342 455833392 0.000000e+00 13021.0
1 TraesCS5D01G386200 chr5D 79.789 757 91 26 6275 7006 505213675 505212956 1.770000e-135 494.0
2 TraesCS5D01G386200 chr5D 87.949 390 44 3 3986 4373 70388632 70388244 2.320000e-124 457.0
3 TraesCS5D01G386200 chr5D 100.000 35 0 0 6183 6217 455832474 455832508 1.640000e-06 65.8
4 TraesCS5D01G386200 chr5D 100.000 35 0 0 6133 6167 455832524 455832558 1.640000e-06 65.8
5 TraesCS5D01G386200 chr5B 89.995 3868 233 57 972 4780 557902060 557905832 0.000000e+00 4857.0
6 TraesCS5D01G386200 chr5B 95.093 1243 27 6 4993 6214 557906132 557907361 0.000000e+00 1927.0
7 TraesCS5D01G386200 chr5B 93.987 898 41 7 1 895 557899863 557900750 0.000000e+00 1347.0
8 TraesCS5D01G386200 chr5B 94.037 872 38 6 1452 2323 346851355 346852212 0.000000e+00 1310.0
9 TraesCS5D01G386200 chr5B 76.165 751 137 33 6275 6997 136033681 136032945 2.420000e-94 357.0
10 TraesCS5D01G386200 chr5B 97.500 40 1 0 6178 6217 557907275 557907314 1.270000e-07 69.4
11 TraesCS5D01G386200 chr5A 91.779 2591 122 34 989 3558 573950853 573953373 0.000000e+00 3520.0
12 TraesCS5D01G386200 chr5A 93.574 2350 89 25 3858 6181 573954110 573956423 0.000000e+00 3446.0
13 TraesCS5D01G386200 chr5A 96.923 65 2 0 88 152 573946884 573946948 7.480000e-20 110.0
14 TraesCS5D01G386200 chr5A 97.727 44 1 0 2599 2642 452111832 452111875 7.580000e-10 76.8
15 TraesCS5D01G386200 chr3A 94.700 868 40 4 1455 2322 176234189 176233328 0.000000e+00 1343.0
16 TraesCS5D01G386200 chr3A 94.266 872 45 3 1452 2323 413471234 413472100 0.000000e+00 1328.0
17 TraesCS5D01G386200 chr3A 78.273 718 116 27 6302 6997 615710438 615709739 6.540000e-115 425.0
18 TraesCS5D01G386200 chr3A 77.241 290 46 18 626 901 696284736 696284453 1.230000e-32 152.0
19 TraesCS5D01G386200 chr3A 81.452 124 10 11 2535 2645 309082872 309082749 9.740000e-14 89.8
20 TraesCS5D01G386200 chr3A 93.750 48 3 0 2598 2645 157443552 157443505 9.810000e-09 73.1
21 TraesCS5D01G386200 chr1A 94.049 857 45 4 1452 2308 198058778 198059628 0.000000e+00 1295.0
22 TraesCS5D01G386200 chr1A 93.349 872 51 5 1452 2323 198036855 198037719 0.000000e+00 1282.0
23 TraesCS5D01G386200 chr1A 80.590 881 118 32 3521 4389 83831309 83830470 1.290000e-176 630.0
24 TraesCS5D01G386200 chr1A 80.335 895 112 33 3521 4388 576607640 576606783 2.790000e-173 619.0
25 TraesCS5D01G386200 chr7A 93.448 870 51 4 1454 2322 92050127 92049263 0.000000e+00 1286.0
26 TraesCS5D01G386200 chr7A 85.938 384 33 5 3986 4368 27958241 27958604 2.380000e-104 390.0
27 TraesCS5D01G386200 chr7A 82.135 431 55 9 3517 3944 27957823 27958234 4.050000e-92 350.0
28 TraesCS5D01G386200 chr7A 76.210 744 127 35 6275 6989 699017647 699018369 1.460000e-91 348.0
29 TraesCS5D01G386200 chr7A 81.452 124 10 10 2535 2645 159930817 159930694 9.740000e-14 89.8
30 TraesCS5D01G386200 chr4B 94.723 758 38 2 1566 2323 585760358 585759603 0.000000e+00 1177.0
31 TraesCS5D01G386200 chr4B 75.746 268 36 22 626 875 653438748 653438492 2.690000e-19 108.0
32 TraesCS5D01G386200 chr4B 75.889 253 30 19 661 895 419994813 419994574 4.500000e-17 100.0
33 TraesCS5D01G386200 chr4B 94.000 50 3 0 2596 2645 488263804 488263755 7.580000e-10 76.8
34 TraesCS5D01G386200 chr2A 80.272 882 120 25 3523 4379 642435832 642436684 3.610000e-172 616.0
35 TraesCS5D01G386200 chr2A 80.369 759 105 22 6275 7006 20796104 20796845 2.890000e-148 536.0
36 TraesCS5D01G386200 chr2A 78.162 751 124 28 6275 6999 59357931 59357195 6.490000e-120 442.0
37 TraesCS5D01G386200 chr2A 77.987 745 130 26 6275 6993 634613320 634612584 3.020000e-118 436.0
38 TraesCS5D01G386200 chr2A 84.988 413 45 9 3965 4375 710764393 710763996 3.060000e-108 403.0
39 TraesCS5D01G386200 chr2A 89.175 194 20 1 3520 3712 710764851 710764658 2.540000e-59 241.0
40 TraesCS5D01G386200 chr2A 84.279 229 35 1 3540 3767 18858102 18857874 9.210000e-54 222.0
41 TraesCS5D01G386200 chr2A 79.612 206 27 10 2455 2645 119341790 119341995 4.440000e-27 134.0
42 TraesCS5D01G386200 chr2A 85.965 114 11 5 611 720 27494320 27494208 4.470000e-22 117.0
43 TraesCS5D01G386200 chr6D 82.306 746 91 23 6275 6996 156435790 156436518 6.050000e-170 608.0
44 TraesCS5D01G386200 chr6D 80.865 763 98 28 6275 7006 314515468 314514723 2.220000e-154 556.0
45 TraesCS5D01G386200 chr3D 81.989 744 102 18 6270 6994 113353162 113353892 2.810000e-168 603.0
46 TraesCS5D01G386200 chr3D 84.158 101 13 3 622 720 104212810 104212909 2.090000e-15 95.3
47 TraesCS5D01G386200 chr3D 100.000 39 0 0 2601 2639 422477180 422477218 9.810000e-09 73.1
48 TraesCS5D01G386200 chr2B 80.322 869 109 24 3521 4378 453032778 453031961 1.010000e-167 601.0
49 TraesCS5D01G386200 chr2B 86.869 99 10 2 2508 2603 515262213 515262311 2.690000e-19 108.0
50 TraesCS5D01G386200 chr2B 81.148 122 19 3 775 895 144022754 144022636 2.090000e-15 95.3
51 TraesCS5D01G386200 chr7B 80.046 872 106 33 3521 4378 677873542 677872725 1.020000e-162 584.0
52 TraesCS5D01G386200 chr7B 78.100 621 97 30 6407 6997 612832763 612833374 2.420000e-94 357.0
53 TraesCS5D01G386200 chr6A 78.826 869 133 24 3521 4378 484555103 484554275 8.050000e-149 538.0
54 TraesCS5D01G386200 chr2D 79.947 753 109 32 6275 6997 107706125 107705385 3.770000e-142 516.0
55 TraesCS5D01G386200 chr2D 78.748 767 111 32 6275 7006 106644836 106645585 3.850000e-127 466.0
56 TraesCS5D01G386200 chr2D 86.607 112 12 3 611 720 596574753 596574643 3.450000e-23 121.0
57 TraesCS5D01G386200 chr2D 75.329 304 39 25 613 895 7139849 7140137 5.780000e-21 113.0
58 TraesCS5D01G386200 chr2D 87.500 96 10 2 626 719 25013475 25013380 7.480000e-20 110.0
59 TraesCS5D01G386200 chr2D 80.597 134 19 5 769 898 586806377 586806507 5.820000e-16 97.1
60 TraesCS5D01G386200 chr1D 81.222 671 92 22 6275 6932 465169317 465168668 1.750000e-140 510.0
61 TraesCS5D01G386200 chr7D 78.968 756 118 26 6275 7006 134829715 134828977 1.780000e-130 477.0
62 TraesCS5D01G386200 chr7D 78.382 754 124 29 6275 6997 187249988 187250733 3.000000e-123 453.0
63 TraesCS5D01G386200 chr7D 77.403 770 120 39 6275 7006 533011654 533012407 6.580000e-110 409.0
64 TraesCS5D01G386200 chr7D 77.206 680 114 28 6342 6989 596905914 596906584 6.720000e-95 359.0
65 TraesCS5D01G386200 chr7D 82.540 126 17 4 777 900 623508603 623508481 9.670000e-19 106.0
66 TraesCS5D01G386200 chr7D 84.314 102 13 3 617 715 88367871 88367770 5.820000e-16 97.1
67 TraesCS5D01G386200 chr7D 81.356 118 17 5 766 881 607124318 607124204 2.710000e-14 91.6
68 TraesCS5D01G386200 chr7D 80.159 126 20 4 775 899 98629508 98629629 9.740000e-14 89.8
69 TraesCS5D01G386200 chr7D 73.778 225 32 24 6835 7051 576655402 576655607 5.900000e-06 63.9
70 TraesCS5D01G386200 chr3B 78.418 746 127 27 6275 6997 661208331 661207597 8.340000e-124 455.0
71 TraesCS5D01G386200 chr3B 77.384 734 126 28 6275 6997 749724448 749723744 3.960000e-107 399.0
72 TraesCS5D01G386200 chr3B 86.316 95 9 4 629 720 679508963 679508870 4.500000e-17 100.0
73 TraesCS5D01G386200 chr3B 100.000 39 0 0 2601 2639 550318737 550318775 9.810000e-09 73.1
74 TraesCS5D01G386200 chr6B 78.457 752 119 22 6275 7006 49770370 49769642 1.080000e-122 451.0
75 TraesCS5D01G386200 chr6B 84.252 127 12 7 2484 2602 49990093 49989967 4.470000e-22 117.0
76 TraesCS5D01G386200 chr1B 81.567 434 61 17 3949 4375 70309021 70308600 2.440000e-89 340.0
77 TraesCS5D01G386200 chr1B 90.650 246 22 1 4134 4378 233947879 233947634 6.820000e-85 326.0
78 TraesCS5D01G386200 chr1B 85.600 250 35 1 3521 3770 233948431 233948183 1.950000e-65 261.0
79 TraesCS5D01G386200 chr1B 88.732 71 6 1 2535 2603 276162395 276162325 1.260000e-12 86.1
80 TraesCS5D01G386200 chr4D 83.471 242 31 7 6690 6924 12296008 12295769 4.280000e-52 217.0
81 TraesCS5D01G386200 chr4A 83.333 114 10 7 2535 2645 244231598 244231705 5.820000e-16 97.1
82 TraesCS5D01G386200 chr4A 80.909 110 19 1 766 875 699889591 699889698 1.260000e-12 86.1


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 TraesCS5D01G386200 chr5D 455826342 455833392 7050 False 4384.200000 13021 100.00000 1 7051 3 chr5D.!!$F1 7050
1 TraesCS5D01G386200 chr5D 505212956 505213675 719 True 494.000000 494 79.78900 6275 7006 1 chr5D.!!$R2 731
2 TraesCS5D01G386200 chr5B 557899863 557907361 7498 False 2050.100000 4857 94.14375 1 6217 4 chr5B.!!$F2 6216
3 TraesCS5D01G386200 chr5B 346851355 346852212 857 False 1310.000000 1310 94.03700 1452 2323 1 chr5B.!!$F1 871
4 TraesCS5D01G386200 chr5B 136032945 136033681 736 True 357.000000 357 76.16500 6275 6997 1 chr5B.!!$R1 722
5 TraesCS5D01G386200 chr5A 573946884 573956423 9539 False 2358.666667 3520 94.09200 88 6181 3 chr5A.!!$F2 6093
6 TraesCS5D01G386200 chr3A 176233328 176234189 861 True 1343.000000 1343 94.70000 1455 2322 1 chr3A.!!$R2 867
7 TraesCS5D01G386200 chr3A 413471234 413472100 866 False 1328.000000 1328 94.26600 1452 2323 1 chr3A.!!$F1 871
8 TraesCS5D01G386200 chr3A 615709739 615710438 699 True 425.000000 425 78.27300 6302 6997 1 chr3A.!!$R4 695
9 TraesCS5D01G386200 chr1A 198058778 198059628 850 False 1295.000000 1295 94.04900 1452 2308 1 chr1A.!!$F2 856
10 TraesCS5D01G386200 chr1A 198036855 198037719 864 False 1282.000000 1282 93.34900 1452 2323 1 chr1A.!!$F1 871
11 TraesCS5D01G386200 chr1A 83830470 83831309 839 True 630.000000 630 80.59000 3521 4389 1 chr1A.!!$R1 868
12 TraesCS5D01G386200 chr1A 576606783 576607640 857 True 619.000000 619 80.33500 3521 4388 1 chr1A.!!$R2 867
13 TraesCS5D01G386200 chr7A 92049263 92050127 864 True 1286.000000 1286 93.44800 1454 2322 1 chr7A.!!$R1 868
14 TraesCS5D01G386200 chr7A 27957823 27958604 781 False 370.000000 390 84.03650 3517 4368 2 chr7A.!!$F2 851
15 TraesCS5D01G386200 chr7A 699017647 699018369 722 False 348.000000 348 76.21000 6275 6989 1 chr7A.!!$F1 714
16 TraesCS5D01G386200 chr4B 585759603 585760358 755 True 1177.000000 1177 94.72300 1566 2323 1 chr4B.!!$R3 757
17 TraesCS5D01G386200 chr2A 642435832 642436684 852 False 616.000000 616 80.27200 3523 4379 1 chr2A.!!$F3 856
18 TraesCS5D01G386200 chr2A 20796104 20796845 741 False 536.000000 536 80.36900 6275 7006 1 chr2A.!!$F1 731
19 TraesCS5D01G386200 chr2A 59357195 59357931 736 True 442.000000 442 78.16200 6275 6999 1 chr2A.!!$R3 724
20 TraesCS5D01G386200 chr2A 634612584 634613320 736 True 436.000000 436 77.98700 6275 6993 1 chr2A.!!$R4 718
21 TraesCS5D01G386200 chr2A 710763996 710764851 855 True 322.000000 403 87.08150 3520 4375 2 chr2A.!!$R5 855
22 TraesCS5D01G386200 chr6D 156435790 156436518 728 False 608.000000 608 82.30600 6275 6996 1 chr6D.!!$F1 721
23 TraesCS5D01G386200 chr6D 314514723 314515468 745 True 556.000000 556 80.86500 6275 7006 1 chr6D.!!$R1 731
24 TraesCS5D01G386200 chr3D 113353162 113353892 730 False 603.000000 603 81.98900 6270 6994 1 chr3D.!!$F2 724
25 TraesCS5D01G386200 chr2B 453031961 453032778 817 True 601.000000 601 80.32200 3521 4378 1 chr2B.!!$R2 857
26 TraesCS5D01G386200 chr7B 677872725 677873542 817 True 584.000000 584 80.04600 3521 4378 1 chr7B.!!$R1 857
27 TraesCS5D01G386200 chr7B 612832763 612833374 611 False 357.000000 357 78.10000 6407 6997 1 chr7B.!!$F1 590
28 TraesCS5D01G386200 chr6A 484554275 484555103 828 True 538.000000 538 78.82600 3521 4378 1 chr6A.!!$R1 857
29 TraesCS5D01G386200 chr2D 107705385 107706125 740 True 516.000000 516 79.94700 6275 6997 1 chr2D.!!$R2 722
30 TraesCS5D01G386200 chr2D 106644836 106645585 749 False 466.000000 466 78.74800 6275 7006 1 chr2D.!!$F2 731
31 TraesCS5D01G386200 chr1D 465168668 465169317 649 True 510.000000 510 81.22200 6275 6932 1 chr1D.!!$R1 657
32 TraesCS5D01G386200 chr7D 134828977 134829715 738 True 477.000000 477 78.96800 6275 7006 1 chr7D.!!$R2 731
33 TraesCS5D01G386200 chr7D 187249988 187250733 745 False 453.000000 453 78.38200 6275 6997 1 chr7D.!!$F2 722
34 TraesCS5D01G386200 chr7D 533011654 533012407 753 False 409.000000 409 77.40300 6275 7006 1 chr7D.!!$F3 731
35 TraesCS5D01G386200 chr7D 596905914 596906584 670 False 359.000000 359 77.20600 6342 6989 1 chr7D.!!$F5 647
36 TraesCS5D01G386200 chr3B 661207597 661208331 734 True 455.000000 455 78.41800 6275 6997 1 chr3B.!!$R1 722
37 TraesCS5D01G386200 chr3B 749723744 749724448 704 True 399.000000 399 77.38400 6275 6997 1 chr3B.!!$R3 722
38 TraesCS5D01G386200 chr6B 49769642 49770370 728 True 451.000000 451 78.45700 6275 7006 1 chr6B.!!$R1 731
39 TraesCS5D01G386200 chr1B 233947634 233948431 797 True 293.500000 326 88.12500 3521 4378 2 chr1B.!!$R3 857

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
915 1190 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.0 0.00 0.00 0.00 4.30 F
963 3293 0.034337 TTTGTTTCGGACGGAGGGAG 59.966 55.0 0.00 0.00 0.00 4.30 F
965 3295 0.251297 TGTTTCGGACGGAGGGAGTA 60.251 55.0 0.00 0.00 0.00 2.59 F
1007 4661 0.738389 AAATAAGAATGCCACCGCGG 59.262 50.0 26.86 26.86 38.08 6.46 F
1801 5472 1.064825 ACCATCCCGAGGTTCAACTT 58.935 50.0 0.00 0.00 35.33 2.66 F
3438 7127 0.849094 TCCCACCATACCTTGCCCTT 60.849 55.0 0.00 0.00 0.00 3.95 F
4903 9166 0.394565 AGAATGATAGCGGCCTCACC 59.605 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 6369 1.903183 GGAGGTAGCAGAGGTTTGACT 59.097 52.381 0.00 0.00 0.00 3.41 R
2857 6542 5.721000 TCAGGTTTGAGCCCATATTGATTTT 59.279 36.000 0.00 0.00 0.00 1.82 R
2983 6668 6.822667 TTATAGATGGCGCATTTGAATGAT 57.177 33.333 10.83 0.00 38.70 2.45 R
2988 6673 7.920160 TGAATATTATAGATGGCGCATTTGA 57.080 32.000 10.83 0.00 0.00 2.69 R
3603 7310 1.530013 GCCACAGCTGAATGCCAAGT 61.530 55.000 23.35 0.00 44.23 3.16 R
4916 9179 0.526662 AACTCGACCTGGCTAGAACG 59.473 55.000 0.00 4.08 0.00 3.95 R
6225 10676 0.035056 CCCCGTCTCTGCCTTGAATT 60.035 55.000 0.00 0.00 0.00 2.17 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
74 75 7.391148 ACAAATATAGCAAAGTGTAACCTGG 57.609 36.000 0.00 0.00 37.80 4.45
573 684 0.547712 TGCAGGAGTAGGCCCTTCTT 60.548 55.000 0.00 0.00 0.00 2.52
574 685 0.621082 GCAGGAGTAGGCCCTTCTTT 59.379 55.000 0.00 0.00 0.00 2.52
585 696 1.546548 GCCCTTCTTTCACTGGCTTCT 60.547 52.381 0.00 0.00 39.05 2.85
605 716 1.840737 TGGGAGAACCGAGAGAGAAG 58.159 55.000 0.00 0.00 44.64 2.85
680 792 2.026262 GCCATCAGGGTTCAAGTCCTAA 60.026 50.000 0.00 0.00 39.65 2.69
698 810 6.428159 AGTCCTAAACTTGACACTAATGCTTG 59.572 38.462 0.00 0.00 33.03 4.01
699 811 5.181245 TCCTAAACTTGACACTAATGCTTGC 59.819 40.000 0.00 0.00 0.00 4.01
700 812 4.916983 AAACTTGACACTAATGCTTGCA 57.083 36.364 0.00 0.00 0.00 4.08
733 845 7.438622 GAATTTAATTCCAGCCTCGAGTGGC 62.439 48.000 15.54 11.93 41.97 5.01
827 1102 2.167281 GCTCAGTCTCTGGAATGTGCTA 59.833 50.000 11.39 0.00 46.50 3.49
895 1170 5.763444 ATATGTGTATTTATGCGCGTCTC 57.237 39.130 4.79 0.00 0.00 3.36
901 1176 4.443063 TGTATTTATGCGCGTCTCATGTAC 59.557 41.667 4.79 8.60 0.00 2.90
902 1177 2.863401 TTATGCGCGTCTCATGTACT 57.137 45.000 4.79 0.00 0.00 2.73
903 1178 2.401017 TATGCGCGTCTCATGTACTC 57.599 50.000 4.79 0.00 0.00 2.59
904 1179 0.249073 ATGCGCGTCTCATGTACTCC 60.249 55.000 8.43 0.00 0.00 3.85
909 1184 0.663688 CGTCTCATGTACTCCCTCCG 59.336 60.000 0.00 0.00 0.00 4.63
910 1185 1.765230 GTCTCATGTACTCCCTCCGT 58.235 55.000 0.00 0.00 0.00 4.69
911 1186 1.677052 GTCTCATGTACTCCCTCCGTC 59.323 57.143 0.00 0.00 0.00 4.79
912 1187 1.033574 CTCATGTACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
913 1188 0.750546 TCATGTACTCCCTCCGTCCG 60.751 60.000 0.00 0.00 0.00 4.79
915 1190 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
917 1192 1.109609 GTACTCCCTCCGTCCGAATT 58.890 55.000 0.00 0.00 0.00 2.17
943 1218 6.537453 TTTGTCCCAATCTTGTTTCTCAAA 57.463 33.333 0.00 0.00 35.48 2.69
944 1219 6.729690 TTGTCCCAATCTTGTTTCTCAAAT 57.270 33.333 0.00 0.00 35.48 2.32
946 1221 7.123355 TGTCCCAATCTTGTTTCTCAAATTT 57.877 32.000 0.00 0.00 35.48 1.82
947 1222 6.985645 TGTCCCAATCTTGTTTCTCAAATTTG 59.014 34.615 12.15 12.15 35.48 2.32
951 3281 8.337532 CCCAATCTTGTTTCTCAAATTTGTTTC 58.662 33.333 17.47 6.42 35.48 2.78
957 3287 3.889196 TCTCAAATTTGTTTCGGACGG 57.111 42.857 17.47 0.08 0.00 4.79
963 3293 0.034337 TTTGTTTCGGACGGAGGGAG 59.966 55.000 0.00 0.00 0.00 4.30
965 3295 0.251297 TGTTTCGGACGGAGGGAGTA 60.251 55.000 0.00 0.00 0.00 2.59
967 3297 2.301346 GTTTCGGACGGAGGGAGTATA 58.699 52.381 0.00 0.00 0.00 1.47
972 3302 2.664015 GGACGGAGGGAGTATAGTGTT 58.336 52.381 0.00 0.00 0.00 3.32
973 3303 3.029570 GGACGGAGGGAGTATAGTGTTT 58.970 50.000 0.00 0.00 0.00 2.83
974 3304 4.210331 GGACGGAGGGAGTATAGTGTTTA 58.790 47.826 0.00 0.00 0.00 2.01
975 3305 4.646492 GGACGGAGGGAGTATAGTGTTTAA 59.354 45.833 0.00 0.00 0.00 1.52
977 3307 6.218108 ACGGAGGGAGTATAGTGTTTAAAG 57.782 41.667 0.00 0.00 0.00 1.85
1007 4661 0.738389 AAATAAGAATGCCACCGCGG 59.262 50.000 26.86 26.86 38.08 6.46
1021 4675 1.566018 CCGCGGGAATAATCGGAAGC 61.566 60.000 20.10 0.00 44.23 3.86
1415 5077 2.904131 GCAGGGCAGAGTAGGGTC 59.096 66.667 0.00 0.00 0.00 4.46
1436 5098 1.449601 TCGCGCTTTCCCCAATCTC 60.450 57.895 5.56 0.00 0.00 2.75
1441 5103 1.098129 GCTTTCCCCAATCTCGCTCC 61.098 60.000 0.00 0.00 0.00 4.70
1506 5168 9.840427 ATTTAGTTTTGGTAGATTTCGTTGATG 57.160 29.630 0.00 0.00 0.00 3.07
1507 5169 8.610248 TTAGTTTTGGTAGATTTCGTTGATGA 57.390 30.769 0.00 0.00 0.00 2.92
1508 5170 7.687941 AGTTTTGGTAGATTTCGTTGATGAT 57.312 32.000 0.00 0.00 0.00 2.45
1564 5226 2.818274 CCTTACGCCGTTGCTCCC 60.818 66.667 0.00 0.00 34.43 4.30
1801 5472 1.064825 ACCATCCCGAGGTTCAACTT 58.935 50.000 0.00 0.00 35.33 2.66
1915 5586 1.959989 GCCAAAGAGTTACCATGGGGG 60.960 57.143 18.09 4.23 44.81 5.40
2067 5744 9.463443 CGATAATATCAGCGTGATGGATAAATA 57.537 33.333 9.77 0.00 37.70 1.40
2185 5862 6.514063 TCGTTTAAAGTTTATTTGGGTTGGG 58.486 36.000 0.00 0.00 0.00 4.12
2242 5919 5.521735 CCTGTACATTCACAGCTGAATAGAC 59.478 44.000 23.35 11.85 44.04 2.59
2308 5990 7.463431 TGGATTGGTGGTTAGTTTTATGTACT 58.537 34.615 0.00 0.00 0.00 2.73
2314 5996 6.128472 GGTGGTTAGTTTTATGTACTGTTCGG 60.128 42.308 0.00 0.00 0.00 4.30
2479 6161 5.104693 TGCTCCCTCCGATTCAATTTACTTA 60.105 40.000 0.00 0.00 0.00 2.24
2654 6338 4.214545 TGGTCAAAGTTTACTTGTATGCGG 59.785 41.667 0.00 0.00 36.12 5.69
2718 6402 2.565841 CTACCTCCTGCTTACCAATGC 58.434 52.381 0.00 0.00 0.00 3.56
2742 6426 4.887071 ACCAAAGTGCTGTTTAGATTGTCA 59.113 37.500 0.00 0.00 0.00 3.58
2857 6542 1.380785 ATCTCCGTGCCCCTTACGA 60.381 57.895 0.00 0.00 43.82 3.43
2936 6621 4.119136 GCATTCTCTCTTTCTCTACTGCC 58.881 47.826 0.00 0.00 0.00 4.85
2941 6626 1.760029 CTCTTTCTCTACTGCCCCTCC 59.240 57.143 0.00 0.00 0.00 4.30
2943 6628 2.192263 CTTTCTCTACTGCCCCTCCTT 58.808 52.381 0.00 0.00 0.00 3.36
3034 6721 7.591421 TCATATGTCTTGAAATACTACGGGA 57.409 36.000 1.90 0.00 0.00 5.14
3035 6722 8.190326 TCATATGTCTTGAAATACTACGGGAT 57.810 34.615 1.90 0.00 0.00 3.85
3036 6723 8.647796 TCATATGTCTTGAAATACTACGGGATT 58.352 33.333 1.90 0.00 0.00 3.01
3037 6724 8.926710 CATATGTCTTGAAATACTACGGGATTC 58.073 37.037 0.00 0.00 0.00 2.52
3038 6725 6.288941 TGTCTTGAAATACTACGGGATTCA 57.711 37.500 0.00 0.00 0.00 2.57
3039 6726 6.884832 TGTCTTGAAATACTACGGGATTCAT 58.115 36.000 0.00 0.00 30.81 2.57
3063 6751 3.624861 AGTTCGATGGCATTCATTGTCTC 59.375 43.478 0.00 0.00 38.22 3.36
3344 7033 2.498644 AAAGCTTCAGGGAAGTAGGC 57.501 50.000 0.00 0.00 41.27 3.93
3363 7052 2.290577 GGCCTTCATCTTCTTCACAGGT 60.291 50.000 0.00 0.00 0.00 4.00
3364 7053 3.006247 GCCTTCATCTTCTTCACAGGTC 58.994 50.000 0.00 0.00 0.00 3.85
3365 7054 3.557898 GCCTTCATCTTCTTCACAGGTCA 60.558 47.826 0.00 0.00 0.00 4.02
3366 7055 3.999663 CCTTCATCTTCTTCACAGGTCAC 59.000 47.826 0.00 0.00 0.00 3.67
3367 7056 3.685139 TCATCTTCTTCACAGGTCACC 57.315 47.619 0.00 0.00 0.00 4.02
3368 7057 2.972021 TCATCTTCTTCACAGGTCACCA 59.028 45.455 0.00 0.00 0.00 4.17
3369 7058 2.910688 TCTTCTTCACAGGTCACCAC 57.089 50.000 0.00 0.00 0.00 4.16
3392 7081 4.180817 TCACCAGTTGTGTATTCTATGCG 58.819 43.478 0.00 0.00 45.61 4.73
3435 7124 1.037579 GCTTCCCACCATACCTTGCC 61.038 60.000 0.00 0.00 0.00 4.52
3438 7127 0.849094 TCCCACCATACCTTGCCCTT 60.849 55.000 0.00 0.00 0.00 3.95
3475 7164 2.417243 CCACATGTATCTCGTGCAGTGA 60.417 50.000 0.00 0.00 36.60 3.41
3494 7183 9.491675 TGCAGTGATGATTTTATTGATTGTTTT 57.508 25.926 0.00 0.00 0.00 2.43
3673 7429 0.755327 AACGCAAAAACTCCTGGCCT 60.755 50.000 3.32 0.00 0.00 5.19
3801 7913 1.536907 TGCCCTAAGGAACGGTGGA 60.537 57.895 0.00 0.00 33.47 4.02
3902 8096 2.606519 CACCCTTCCTCCCCGTCA 60.607 66.667 0.00 0.00 0.00 4.35
3916 8110 2.279069 CGTCACCACCCTGAGCTCT 61.279 63.158 16.19 0.00 0.00 4.09
4134 8385 1.719378 TCCAACCTTCTCTCCTCTCCT 59.281 52.381 0.00 0.00 0.00 3.69
4142 8395 4.280819 CTTCTCTCCTCTCCTCTGTCAAT 58.719 47.826 0.00 0.00 0.00 2.57
4208 8461 0.439985 CTCAATGCCTCACGTTGACG 59.560 55.000 1.41 1.41 46.92 4.35
4257 8511 5.518128 CCTCAATATCAAGTCTGTGTTCGAG 59.482 44.000 0.00 0.00 0.00 4.04
4265 8519 6.204359 TCAAGTCTGTGTTCGAGTACTTAAC 58.796 40.000 12.70 12.70 0.00 2.01
4298 8552 7.713750 ACAGAAATATTGGCATTCAATCTCAG 58.286 34.615 1.81 0.00 44.32 3.35
4502 8756 7.979115 TGTAACAAAAATGCTTACACAAGTC 57.021 32.000 0.00 0.00 34.00 3.01
4640 8896 2.906389 TCTTGTCAGACCAGGTAATGCT 59.094 45.455 0.00 0.00 0.00 3.79
4773 9036 4.922471 TGGCAAATATGTGTCATCCATG 57.078 40.909 0.00 0.00 0.00 3.66
4774 9037 3.637694 TGGCAAATATGTGTCATCCATGG 59.362 43.478 4.97 4.97 0.00 3.66
4775 9038 3.890756 GGCAAATATGTGTCATCCATGGA 59.109 43.478 18.88 18.88 0.00 3.41
4776 9039 4.341806 GGCAAATATGTGTCATCCATGGAA 59.658 41.667 20.67 0.00 0.00 3.53
4777 9040 5.284079 GCAAATATGTGTCATCCATGGAAC 58.716 41.667 20.67 14.23 0.00 3.62
4778 9041 5.068198 GCAAATATGTGTCATCCATGGAACT 59.932 40.000 20.67 0.00 0.00 3.01
4779 9042 6.406177 GCAAATATGTGTCATCCATGGAACTT 60.406 38.462 20.67 12.64 0.00 2.66
4780 9043 7.549839 CAAATATGTGTCATCCATGGAACTTT 58.450 34.615 20.67 6.72 0.00 2.66
4781 9044 7.722949 AATATGTGTCATCCATGGAACTTTT 57.277 32.000 20.67 0.00 0.00 2.27
4782 9045 7.722949 ATATGTGTCATCCATGGAACTTTTT 57.277 32.000 20.67 0.00 0.00 1.94
4834 9097 5.957842 TGTGGTCAATTGTCTTCCATAAC 57.042 39.130 5.13 0.00 0.00 1.89
4870 9133 1.980765 TGATTCAAGACCTGAGTGGCT 59.019 47.619 0.00 0.00 40.22 4.75
4871 9134 2.027745 TGATTCAAGACCTGAGTGGCTC 60.028 50.000 0.00 0.00 40.22 4.70
4882 9145 1.409064 TGAGTGGCTCGTGATATGGTC 59.591 52.381 0.00 0.00 32.35 4.02
4895 9158 5.968261 CGTGATATGGTCTAGAATGATAGCG 59.032 44.000 0.00 0.00 0.00 4.26
4903 9166 0.394565 AGAATGATAGCGGCCTCACC 59.605 55.000 0.00 0.00 0.00 4.02
5040 9462 0.811281 GTGCTTTGCGCTTTCCCTAT 59.189 50.000 9.73 0.00 40.11 2.57
5067 9489 6.959954 AGGATATGTTATACTGCCTCCATACA 59.040 38.462 0.00 0.00 0.00 2.29
5106 9528 8.790718 CCAATTATGTATGGATCTCCTTTCTTG 58.209 37.037 0.00 0.00 39.12 3.02
5107 9529 9.347240 CAATTATGTATGGATCTCCTTTCTTGT 57.653 33.333 0.00 0.00 36.82 3.16
5619 10059 8.408043 TTTATGTCTCAACAATCCATTGAACT 57.592 30.769 6.29 0.00 40.14 3.01
5788 10228 7.613551 TCTATATAAGAACCTGGAAAGACCC 57.386 40.000 0.00 0.00 38.00 4.46
5853 10293 3.885297 ACCTGGAAGAACAAAGACACATG 59.115 43.478 0.00 0.00 34.07 3.21
6099 10543 9.522804 ACGTTAATGTCAAAGCAGAAAAATAAA 57.477 25.926 0.00 0.00 0.00 1.40
6186 10637 6.279882 CACAAAGGTTGTTGGACAAATACAT 58.720 36.000 0.00 0.00 43.23 2.29
6221 10672 9.337396 TGATATGATAGATTAACCACAACAACC 57.663 33.333 0.00 0.00 0.00 3.77
6222 10673 6.677781 ATGATAGATTAACCACAACAACCG 57.322 37.500 0.00 0.00 0.00 4.44
6223 10674 5.795972 TGATAGATTAACCACAACAACCGA 58.204 37.500 0.00 0.00 0.00 4.69
6224 10675 6.411376 TGATAGATTAACCACAACAACCGAT 58.589 36.000 0.00 0.00 0.00 4.18
6225 10676 7.557724 TGATAGATTAACCACAACAACCGATA 58.442 34.615 0.00 0.00 0.00 2.92
6226 10677 8.041919 TGATAGATTAACCACAACAACCGATAA 58.958 33.333 0.00 0.00 0.00 1.75
6227 10678 8.974060 ATAGATTAACCACAACAACCGATAAT 57.026 30.769 0.00 0.00 0.00 1.28
6228 10679 7.696992 AGATTAACCACAACAACCGATAATT 57.303 32.000 0.00 0.00 0.00 1.40
6229 10680 7.758495 AGATTAACCACAACAACCGATAATTC 58.242 34.615 0.00 0.00 0.00 2.17
6230 10681 6.879276 TTAACCACAACAACCGATAATTCA 57.121 33.333 0.00 0.00 0.00 2.57
6231 10682 5.776173 AACCACAACAACCGATAATTCAA 57.224 34.783 0.00 0.00 0.00 2.69
6232 10683 5.371115 ACCACAACAACCGATAATTCAAG 57.629 39.130 0.00 0.00 0.00 3.02
6233 10684 4.217550 ACCACAACAACCGATAATTCAAGG 59.782 41.667 0.00 0.00 0.00 3.61
6234 10685 4.165779 CACAACAACCGATAATTCAAGGC 58.834 43.478 0.00 0.00 0.00 4.35
6235 10686 3.823873 ACAACAACCGATAATTCAAGGCA 59.176 39.130 0.00 0.00 0.00 4.75
6236 10687 4.082787 ACAACAACCGATAATTCAAGGCAG 60.083 41.667 0.00 0.00 0.00 4.85
6237 10688 3.950397 ACAACCGATAATTCAAGGCAGA 58.050 40.909 0.00 0.00 0.00 4.26
6238 10689 3.941483 ACAACCGATAATTCAAGGCAGAG 59.059 43.478 0.00 0.00 0.00 3.35
6239 10690 4.191544 CAACCGATAATTCAAGGCAGAGA 58.808 43.478 0.00 0.00 0.00 3.10
6240 10691 3.798202 ACCGATAATTCAAGGCAGAGAC 58.202 45.455 0.00 0.00 0.00 3.36
6241 10692 2.797156 CCGATAATTCAAGGCAGAGACG 59.203 50.000 0.00 0.00 0.00 4.18
6242 10693 2.797156 CGATAATTCAAGGCAGAGACGG 59.203 50.000 0.00 0.00 0.00 4.79
6243 10694 2.691409 TAATTCAAGGCAGAGACGGG 57.309 50.000 0.00 0.00 0.00 5.28
6244 10695 0.035056 AATTCAAGGCAGAGACGGGG 60.035 55.000 0.00 0.00 0.00 5.73
6245 10696 2.543067 ATTCAAGGCAGAGACGGGGC 62.543 60.000 0.00 0.00 0.00 5.80
6246 10697 3.710722 CAAGGCAGAGACGGGGCT 61.711 66.667 0.00 0.00 42.29 5.19
6247 10698 3.394836 AAGGCAGAGACGGGGCTC 61.395 66.667 0.00 0.00 39.21 4.70
6248 10699 4.704103 AGGCAGAGACGGGGCTCA 62.704 66.667 4.05 0.00 37.37 4.26
6249 10700 4.154347 GGCAGAGACGGGGCTCAG 62.154 72.222 4.05 0.00 37.37 3.35
6250 10701 3.071206 GCAGAGACGGGGCTCAGA 61.071 66.667 4.05 0.00 37.37 3.27
6251 10702 2.430610 GCAGAGACGGGGCTCAGAT 61.431 63.158 4.05 0.00 37.37 2.90
6252 10703 1.440893 CAGAGACGGGGCTCAGATG 59.559 63.158 4.05 0.00 37.37 2.90
6253 10704 1.039785 CAGAGACGGGGCTCAGATGA 61.040 60.000 4.05 0.00 37.37 2.92
6254 10705 0.754957 AGAGACGGGGCTCAGATGAG 60.755 60.000 4.05 5.45 44.75 2.90
6262 10713 3.621225 CTCAGATGAGCCCCGTGA 58.379 61.111 0.00 0.00 35.13 4.35
6263 10714 1.900351 CTCAGATGAGCCCCGTGAA 59.100 57.895 0.00 0.00 35.13 3.18
6264 10715 0.460987 CTCAGATGAGCCCCGTGAAC 60.461 60.000 0.00 0.00 35.13 3.18
6265 10716 1.191489 TCAGATGAGCCCCGTGAACA 61.191 55.000 0.00 0.00 0.00 3.18
6266 10717 0.107508 CAGATGAGCCCCGTGAACAT 60.108 55.000 0.00 0.00 0.00 2.71
6267 10718 0.107508 AGATGAGCCCCGTGAACATG 60.108 55.000 0.00 0.00 0.00 3.21
6268 10719 1.077501 ATGAGCCCCGTGAACATGG 60.078 57.895 6.12 6.12 37.23 3.66
6296 10747 1.246056 ACTCTAGCCGCGGTGTGTTA 61.246 55.000 28.70 10.69 0.00 2.41
6298 10749 1.214589 CTAGCCGCGGTGTGTTACT 59.785 57.895 28.70 15.63 0.00 2.24
6460 10914 2.186826 GCTCCCACAACGTGCTGTT 61.187 57.895 0.00 0.00 43.09 3.16
6568 11056 1.070786 GAACCCTGCCGACACTCAA 59.929 57.895 0.00 0.00 0.00 3.02
6578 11066 1.001974 CCGACACTCAACCTCCATGAA 59.998 52.381 0.00 0.00 0.00 2.57
6625 11113 0.749454 GGGTACTCGGCCTCGTAGAA 60.749 60.000 0.00 0.00 34.09 2.10
6715 11205 2.040442 TCGGCCATGGGAGGAGAA 59.960 61.111 15.13 0.00 0.00 2.87
6740 11246 1.444119 CGGCGAGAAGAGAGGAGAGG 61.444 65.000 0.00 0.00 0.00 3.69
6741 11258 0.395173 GGCGAGAAGAGAGGAGAGGT 60.395 60.000 0.00 0.00 0.00 3.85
6766 11306 4.649705 TCGGCTGTGGAGGGGGAA 62.650 66.667 0.00 0.00 0.00 3.97
6976 11565 1.138883 CGAGAACCGAGGCGATGAA 59.861 57.895 0.00 0.00 41.76 2.57
7006 11595 1.210413 GACGAGAAGCGCTGAGTCA 59.790 57.895 12.58 0.00 46.04 3.41
7007 11596 0.387367 GACGAGAAGCGCTGAGTCAA 60.387 55.000 12.58 0.00 46.04 3.18
7008 11597 0.244994 ACGAGAAGCGCTGAGTCAAT 59.755 50.000 12.58 0.00 46.04 2.57
7009 11598 1.337260 ACGAGAAGCGCTGAGTCAATT 60.337 47.619 12.58 0.00 46.04 2.32
7010 11599 1.728971 CGAGAAGCGCTGAGTCAATTT 59.271 47.619 12.58 0.00 0.00 1.82
7011 11600 2.222685 CGAGAAGCGCTGAGTCAATTTC 60.223 50.000 12.58 0.14 0.00 2.17
7012 11601 1.728971 AGAAGCGCTGAGTCAATTTCG 59.271 47.619 12.58 0.00 0.00 3.46
7013 11602 0.166814 AAGCGCTGAGTCAATTTCGC 59.833 50.000 12.58 16.12 42.46 4.70
7014 11603 1.578618 GCGCTGAGTCAATTTCGCG 60.579 57.895 16.74 16.74 39.09 5.87
7015 11604 1.578618 CGCTGAGTCAATTTCGCGC 60.579 57.895 10.26 0.00 33.56 6.86
7016 11605 1.226128 GCTGAGTCAATTTCGCGCC 60.226 57.895 0.00 0.00 0.00 6.53
7017 11606 1.911293 GCTGAGTCAATTTCGCGCCA 61.911 55.000 0.00 0.00 0.00 5.69
7018 11607 0.516877 CTGAGTCAATTTCGCGCCAA 59.483 50.000 0.00 0.00 0.00 4.52
7019 11608 0.947960 TGAGTCAATTTCGCGCCAAA 59.052 45.000 1.83 1.83 0.00 3.28
7020 11609 1.539388 TGAGTCAATTTCGCGCCAAAT 59.461 42.857 7.19 7.19 0.00 2.32
7021 11610 2.744741 TGAGTCAATTTCGCGCCAAATA 59.255 40.909 13.43 0.00 0.00 1.40
7022 11611 3.376859 TGAGTCAATTTCGCGCCAAATAT 59.623 39.130 13.43 1.94 0.00 1.28
7023 11612 3.694734 AGTCAATTTCGCGCCAAATATG 58.305 40.909 13.43 12.98 0.00 1.78
7024 11613 3.376859 AGTCAATTTCGCGCCAAATATGA 59.623 39.130 13.43 14.75 0.00 2.15
7025 11614 4.036734 AGTCAATTTCGCGCCAAATATGAT 59.963 37.500 13.43 0.00 0.00 2.45
7026 11615 4.739716 GTCAATTTCGCGCCAAATATGATT 59.260 37.500 13.43 0.00 0.00 2.57
7027 11616 4.975502 TCAATTTCGCGCCAAATATGATTC 59.024 37.500 13.43 0.00 0.00 2.52
7028 11617 2.661504 TTCGCGCCAAATATGATTCG 57.338 45.000 0.00 0.00 0.00 3.34
7029 11618 0.234625 TCGCGCCAAATATGATTCGC 59.765 50.000 0.00 0.00 36.75 4.70
7030 11619 0.725784 CGCGCCAAATATGATTCGCC 60.726 55.000 0.00 0.00 36.76 5.54
7031 11620 0.387239 GCGCCAAATATGATTCGCCC 60.387 55.000 0.00 0.00 35.28 6.13
7032 11621 0.110238 CGCCAAATATGATTCGCCCG 60.110 55.000 0.00 0.00 0.00 6.13
7033 11622 0.240945 GCCAAATATGATTCGCCCGG 59.759 55.000 0.00 0.00 0.00 5.73
7034 11623 0.240945 CCAAATATGATTCGCCCGGC 59.759 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.178912 TCTCCCGCGTTCTTTCAAAT 57.821 45.000 4.92 0.00 0.00 2.32
74 75 6.369340 TGATGATTTGAAATTGCATGTCAACC 59.631 34.615 6.70 4.05 37.53 3.77
244 348 6.070309 TGGCTTGCCACCAATTATCTTTTATT 60.070 34.615 10.65 0.00 33.12 1.40
296 400 7.884816 ATACATCATCCGTTCTAAATTACCG 57.115 36.000 0.00 0.00 0.00 4.02
416 522 9.573133 AGAAACATGAGAACTAACAAAAAGTTG 57.427 29.630 0.00 0.00 41.50 3.16
492 603 3.019933 CCTCTGCTACGAGGCTAATTC 57.980 52.381 4.70 0.00 43.69 2.17
573 684 1.434188 TCTCCCAAGAAGCCAGTGAA 58.566 50.000 0.00 0.00 0.00 3.18
574 685 1.072331 GTTCTCCCAAGAAGCCAGTGA 59.928 52.381 0.00 0.00 42.14 3.41
585 696 2.171840 CTTCTCTCTCGGTTCTCCCAA 58.828 52.381 0.00 0.00 0.00 4.12
623 734 2.027561 CCTTCTAACCATCCAACCACGA 60.028 50.000 0.00 0.00 0.00 4.35
680 792 5.458041 AATGCAAGCATTAGTGTCAAGTT 57.542 34.783 17.92 0.00 43.92 2.66
726 838 2.665519 CGAAAACATTTCCTGCCACTCG 60.666 50.000 0.00 0.00 0.00 4.18
733 845 4.942765 GTAGTCGACGAAAACATTTCCTG 58.057 43.478 10.46 0.00 0.00 3.86
785 897 3.441163 CCGGCACATCATTTTGAGATTG 58.559 45.455 0.00 0.00 0.00 2.67
787 899 1.406539 GCCGGCACATCATTTTGAGAT 59.593 47.619 24.80 0.00 0.00 2.75
789 901 0.813184 AGCCGGCACATCATTTTGAG 59.187 50.000 31.54 0.00 0.00 3.02
827 1102 4.382040 GCACGTATGCCCTATCACTATGAT 60.382 45.833 0.00 0.00 46.97 2.45
895 1170 0.750546 TCGGACGGAGGGAGTACATG 60.751 60.000 0.00 0.00 0.00 3.21
901 1176 2.109425 AAAAATTCGGACGGAGGGAG 57.891 50.000 0.00 0.00 0.00 4.30
921 1196 6.729690 ATTTGAGAAACAAGATTGGGACAA 57.270 33.333 0.00 0.00 41.27 3.18
923 1198 6.986231 ACAAATTTGAGAAACAAGATTGGGAC 59.014 34.615 24.64 0.00 38.73 4.46
925 1200 7.790823 AACAAATTTGAGAAACAAGATTGGG 57.209 32.000 24.64 0.00 38.73 4.12
928 1203 7.978975 TCCGAAACAAATTTGAGAAACAAGATT 59.021 29.630 24.64 1.56 39.77 2.40
932 1207 5.513495 CGTCCGAAACAAATTTGAGAAACAA 59.487 36.000 24.64 1.99 36.65 2.83
933 1208 5.031578 CGTCCGAAACAAATTTGAGAAACA 58.968 37.500 24.64 1.76 0.00 2.83
935 1210 4.335874 TCCGTCCGAAACAAATTTGAGAAA 59.664 37.500 24.64 2.40 0.00 2.52
936 1211 3.878103 TCCGTCCGAAACAAATTTGAGAA 59.122 39.130 24.64 1.39 0.00 2.87
943 1218 0.688487 TCCCTCCGTCCGAAACAAAT 59.312 50.000 0.00 0.00 0.00 2.32
944 1219 0.034337 CTCCCTCCGTCCGAAACAAA 59.966 55.000 0.00 0.00 0.00 2.83
946 1221 0.251297 TACTCCCTCCGTCCGAAACA 60.251 55.000 0.00 0.00 0.00 2.83
947 1222 1.109609 ATACTCCCTCCGTCCGAAAC 58.890 55.000 0.00 0.00 0.00 2.78
951 3281 1.236628 CACTATACTCCCTCCGTCCG 58.763 60.000 0.00 0.00 0.00 4.79
974 3304 8.925700 GGCATTCTTATTTGTCGATTTTTCTTT 58.074 29.630 0.00 0.00 0.00 2.52
975 3305 8.087750 TGGCATTCTTATTTGTCGATTTTTCTT 58.912 29.630 0.00 0.00 0.00 2.52
977 3307 7.201435 GGTGGCATTCTTATTTGTCGATTTTTC 60.201 37.037 0.00 0.00 0.00 2.29
984 3314 2.791158 GCGGTGGCATTCTTATTTGTCG 60.791 50.000 0.00 0.00 39.62 4.35
1021 4675 1.248101 AAGGGGAAAACCGCGGAATG 61.248 55.000 35.90 5.06 41.60 2.67
1027 4681 2.207229 AGCCAAAGGGGAAAACCGC 61.207 57.895 0.00 0.00 41.60 5.68
1057 4715 3.490759 GGTAGCGTCGTCGTCGGA 61.491 66.667 13.43 0.00 39.49 4.55
1328 4986 4.641645 TGAAGCAGCGGGTGGGTG 62.642 66.667 9.49 0.00 46.88 4.61
1329 4987 4.643387 GTGAAGCAGCGGGTGGGT 62.643 66.667 9.49 0.00 0.00 4.51
1331 4989 3.958147 ATCGTGAAGCAGCGGGTGG 62.958 63.158 9.49 0.00 0.00 4.61
1332 4990 2.434884 ATCGTGAAGCAGCGGGTG 60.435 61.111 2.14 2.14 0.00 4.61
1333 4991 2.125512 GATCGTGAAGCAGCGGGT 60.126 61.111 0.00 0.00 0.00 5.28
1339 4997 2.765108 GAGATCTCGATCGTGAAGCA 57.235 50.000 22.16 1.52 42.48 3.91
1404 5066 2.799371 GCGACCGACCCTACTCTG 59.201 66.667 0.00 0.00 0.00 3.35
1436 5098 3.878519 GACGAGGTCGAGGGAGCG 61.879 72.222 6.35 0.00 45.26 5.03
1506 5168 2.538449 CGTCAATACGGTACCAGCAATC 59.462 50.000 13.54 0.00 45.50 2.67
1507 5169 2.546778 CGTCAATACGGTACCAGCAAT 58.453 47.619 13.54 0.00 45.50 3.56
1508 5170 1.999048 CGTCAATACGGTACCAGCAA 58.001 50.000 13.54 0.00 45.50 3.91
1564 5226 4.333649 TGCAATCGAAGCAGATAAGAAAGG 59.666 41.667 11.34 0.00 37.02 3.11
1801 5472 3.037549 ACTTCCAAAGCAACATTCCCAA 58.962 40.909 0.00 0.00 0.00 4.12
1915 5586 7.387397 TGCATGTGGGAAGAATGAAATTTAAAC 59.613 33.333 0.00 0.00 36.07 2.01
2041 5718 7.755582 TTTATCCATCACGCTGATATTATCG 57.244 36.000 0.00 0.00 34.28 2.92
2067 5744 4.527816 ACAAATGACAGGGTGCAACATAAT 59.472 37.500 3.06 0.00 39.98 1.28
2308 5990 5.339008 ACAGAGCAGTTATAATCCGAACA 57.661 39.130 0.00 0.00 0.00 3.18
2654 6338 4.576879 ACTCCCTCCGTTTCAATTTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2685 6369 1.903183 GGAGGTAGCAGAGGTTTGACT 59.097 52.381 0.00 0.00 0.00 3.41
2742 6426 8.591114 ATGATCCAAGATTCTTGTGAAAATCT 57.409 30.769 21.75 6.64 42.56 2.40
2857 6542 5.721000 TCAGGTTTGAGCCCATATTGATTTT 59.279 36.000 0.00 0.00 0.00 1.82
2983 6668 6.822667 TTATAGATGGCGCATTTGAATGAT 57.177 33.333 10.83 0.00 38.70 2.45
2984 6669 6.822667 ATTATAGATGGCGCATTTGAATGA 57.177 33.333 10.83 0.00 38.70 2.57
2985 6670 9.229784 GAATATTATAGATGGCGCATTTGAATG 57.770 33.333 10.83 0.00 39.40 2.67
2988 6673 7.920160 TGAATATTATAGATGGCGCATTTGA 57.080 32.000 10.83 0.00 0.00 2.69
3029 6716 3.728845 CCATCGAACTAATGAATCCCGT 58.271 45.455 0.00 0.00 0.00 5.28
3030 6717 2.480419 GCCATCGAACTAATGAATCCCG 59.520 50.000 0.00 0.00 0.00 5.14
3032 6719 5.239306 TGAATGCCATCGAACTAATGAATCC 59.761 40.000 0.00 0.00 0.00 3.01
3034 6721 6.889301 ATGAATGCCATCGAACTAATGAAT 57.111 33.333 0.00 0.00 0.00 2.57
3035 6722 6.095300 ACAATGAATGCCATCGAACTAATGAA 59.905 34.615 0.00 0.00 33.53 2.57
3036 6723 5.589855 ACAATGAATGCCATCGAACTAATGA 59.410 36.000 0.00 0.00 33.53 2.57
3037 6724 5.824429 ACAATGAATGCCATCGAACTAATG 58.176 37.500 0.00 0.00 33.53 1.90
3038 6725 5.824624 AGACAATGAATGCCATCGAACTAAT 59.175 36.000 0.00 0.00 33.53 1.73
3039 6726 5.185454 AGACAATGAATGCCATCGAACTAA 58.815 37.500 0.00 0.00 33.53 2.24
3063 6751 5.551760 ACTCAGGAACAGAAAATAATGCG 57.448 39.130 0.00 0.00 0.00 4.73
3344 7033 3.999663 GTGACCTGTGAAGAAGATGAAGG 59.000 47.826 0.00 0.00 0.00 3.46
3392 7081 5.504755 CGAAAAGCAACGAAATATGTCTCAC 59.495 40.000 0.00 0.00 0.00 3.51
3603 7310 1.530013 GCCACAGCTGAATGCCAAGT 61.530 55.000 23.35 0.00 44.23 3.16
3902 8096 2.055042 CGCTAGAGCTCAGGGTGGT 61.055 63.158 17.77 0.00 39.32 4.16
3927 8121 4.640690 AGGCGGAGTGGGAGTGGT 62.641 66.667 0.00 0.00 0.00 4.16
4134 8385 1.945354 GAGGCCGGACGATTGACAGA 61.945 60.000 5.05 0.00 0.00 3.41
4142 8395 2.283676 AAAGAGGAGGCCGGACGA 60.284 61.111 5.05 0.00 0.00 4.20
4265 8519 5.341872 TGCCAATATTTCTGTTTGGATGG 57.658 39.130 5.15 0.00 42.02 3.51
4502 8756 2.600420 CACTGCTGCAATAGAGTACGTG 59.400 50.000 3.02 1.03 0.00 4.49
4782 9045 4.358494 TCCTTTGCGTTTTCTCGAAAAA 57.642 36.364 6.41 0.00 41.37 1.94
4783 9046 4.099824 GTTCCTTTGCGTTTTCTCGAAAA 58.900 39.130 0.93 0.93 36.21 2.29
4784 9047 3.375922 AGTTCCTTTGCGTTTTCTCGAAA 59.624 39.130 0.00 0.00 0.00 3.46
4785 9048 2.940410 AGTTCCTTTGCGTTTTCTCGAA 59.060 40.909 0.00 0.00 0.00 3.71
4786 9049 2.557317 AGTTCCTTTGCGTTTTCTCGA 58.443 42.857 0.00 0.00 0.00 4.04
4787 9050 3.334272 AAGTTCCTTTGCGTTTTCTCG 57.666 42.857 0.00 0.00 0.00 4.04
4788 9051 6.056428 TCTAAAGTTCCTTTGCGTTTTCTC 57.944 37.500 0.00 0.00 35.21 2.87
4789 9052 6.039382 ACATCTAAAGTTCCTTTGCGTTTTCT 59.961 34.615 0.00 0.00 35.21 2.52
4790 9053 6.142320 CACATCTAAAGTTCCTTTGCGTTTTC 59.858 38.462 0.00 0.00 35.21 2.29
4791 9054 5.977129 CACATCTAAAGTTCCTTTGCGTTTT 59.023 36.000 0.00 0.00 35.21 2.43
4792 9055 5.507315 CCACATCTAAAGTTCCTTTGCGTTT 60.507 40.000 0.00 0.00 35.21 3.60
4793 9056 4.023193 CCACATCTAAAGTTCCTTTGCGTT 60.023 41.667 0.00 0.00 35.21 4.84
4794 9057 3.502211 CCACATCTAAAGTTCCTTTGCGT 59.498 43.478 0.00 0.00 35.21 5.24
4795 9058 3.502211 ACCACATCTAAAGTTCCTTTGCG 59.498 43.478 0.00 0.00 35.21 4.85
4796 9059 4.518970 TGACCACATCTAAAGTTCCTTTGC 59.481 41.667 0.00 0.00 35.21 3.68
4797 9060 6.633500 TTGACCACATCTAAAGTTCCTTTG 57.367 37.500 0.00 0.00 35.21 2.77
4798 9061 7.287696 ACAATTGACCACATCTAAAGTTCCTTT 59.712 33.333 13.59 0.00 37.46 3.11
4799 9062 6.777580 ACAATTGACCACATCTAAAGTTCCTT 59.222 34.615 13.59 0.00 0.00 3.36
4800 9063 6.306987 ACAATTGACCACATCTAAAGTTCCT 58.693 36.000 13.59 0.00 0.00 3.36
4834 9097 9.214953 GTCTTGAATCAGTATTTGCGAAATTAG 57.785 33.333 0.00 0.00 32.38 1.73
4870 9133 6.183360 CGCTATCATTCTAGACCATATCACGA 60.183 42.308 0.00 0.00 0.00 4.35
4871 9134 5.968261 CGCTATCATTCTAGACCATATCACG 59.032 44.000 0.00 0.00 0.00 4.35
4882 9145 2.353208 GGTGAGGCCGCTATCATTCTAG 60.353 54.545 8.34 0.00 0.00 2.43
4895 9158 1.298014 CACTTCTCCAGGTGAGGCC 59.702 63.158 0.00 0.00 41.76 5.19
4903 9166 2.600731 CTAGAACGCACACTTCTCCAG 58.399 52.381 0.00 0.00 0.00 3.86
4916 9179 0.526662 AACTCGACCTGGCTAGAACG 59.473 55.000 0.00 4.08 0.00 3.95
5040 9462 8.978472 GTATGGAGGCAGTATAACATATCCTAA 58.022 37.037 0.00 0.00 0.00 2.69
5067 9489 9.985730 CCATACATAATTGGAGCATAACATTTT 57.014 29.630 0.00 0.00 34.81 1.82
5619 10059 6.735678 ATCAGCATTGTAAAATACGACACA 57.264 33.333 0.00 0.00 0.00 3.72
5944 10388 0.681733 TGCCCAGAGTGAAGTCTGAC 59.318 55.000 15.33 0.00 46.02 3.51
6214 10665 4.155826 TCTGCCTTGAATTATCGGTTGTTG 59.844 41.667 0.00 0.00 0.00 3.33
6215 10666 4.331968 TCTGCCTTGAATTATCGGTTGTT 58.668 39.130 0.00 0.00 0.00 2.83
6216 10667 3.941483 CTCTGCCTTGAATTATCGGTTGT 59.059 43.478 0.00 0.00 0.00 3.32
6217 10668 4.034510 GTCTCTGCCTTGAATTATCGGTTG 59.965 45.833 0.00 0.00 0.00 3.77
6218 10669 4.192317 GTCTCTGCCTTGAATTATCGGTT 58.808 43.478 0.00 0.00 0.00 4.44
6219 10670 3.738281 CGTCTCTGCCTTGAATTATCGGT 60.738 47.826 0.00 0.00 0.00 4.69
6220 10671 2.797156 CGTCTCTGCCTTGAATTATCGG 59.203 50.000 0.00 0.00 0.00 4.18
6221 10672 2.797156 CCGTCTCTGCCTTGAATTATCG 59.203 50.000 0.00 0.00 0.00 2.92
6222 10673 3.134458 CCCGTCTCTGCCTTGAATTATC 58.866 50.000 0.00 0.00 0.00 1.75
6223 10674 2.158755 CCCCGTCTCTGCCTTGAATTAT 60.159 50.000 0.00 0.00 0.00 1.28
6224 10675 1.209504 CCCCGTCTCTGCCTTGAATTA 59.790 52.381 0.00 0.00 0.00 1.40
6225 10676 0.035056 CCCCGTCTCTGCCTTGAATT 60.035 55.000 0.00 0.00 0.00 2.17
6226 10677 1.604378 CCCCGTCTCTGCCTTGAAT 59.396 57.895 0.00 0.00 0.00 2.57
6227 10678 3.068881 CCCCGTCTCTGCCTTGAA 58.931 61.111 0.00 0.00 0.00 2.69
6228 10679 3.706373 GCCCCGTCTCTGCCTTGA 61.706 66.667 0.00 0.00 0.00 3.02
6229 10680 3.672295 GAGCCCCGTCTCTGCCTTG 62.672 68.421 0.00 0.00 0.00 3.61
6230 10681 3.394836 GAGCCCCGTCTCTGCCTT 61.395 66.667 0.00 0.00 0.00 4.35
6231 10682 4.704103 TGAGCCCCGTCTCTGCCT 62.704 66.667 0.00 0.00 34.29 4.75
6232 10683 4.154347 CTGAGCCCCGTCTCTGCC 62.154 72.222 0.00 0.00 34.29 4.85
6233 10684 2.430610 ATCTGAGCCCCGTCTCTGC 61.431 63.158 0.00 0.00 34.29 4.26
6234 10685 1.039785 TCATCTGAGCCCCGTCTCTG 61.040 60.000 0.00 0.00 34.29 3.35
6235 10686 0.754957 CTCATCTGAGCCCCGTCTCT 60.755 60.000 0.00 0.00 35.13 3.10
6236 10687 1.739049 CTCATCTGAGCCCCGTCTC 59.261 63.158 0.00 0.00 35.13 3.36
6237 10688 3.947173 CTCATCTGAGCCCCGTCT 58.053 61.111 0.00 0.00 35.13 4.18
6245 10696 0.460987 GTTCACGGGGCTCATCTGAG 60.461 60.000 2.75 2.75 44.75 3.35
6246 10697 1.191489 TGTTCACGGGGCTCATCTGA 61.191 55.000 0.00 0.00 0.00 3.27
6247 10698 0.107508 ATGTTCACGGGGCTCATCTG 60.108 55.000 0.00 0.00 0.00 2.90
6248 10699 0.107508 CATGTTCACGGGGCTCATCT 60.108 55.000 0.00 0.00 0.00 2.90
6249 10700 1.097547 CCATGTTCACGGGGCTCATC 61.098 60.000 0.00 0.00 0.00 2.92
6250 10701 1.077501 CCATGTTCACGGGGCTCAT 60.078 57.895 0.00 0.00 0.00 2.90
6251 10702 2.350895 CCATGTTCACGGGGCTCA 59.649 61.111 0.00 0.00 0.00 4.26
6252 10703 3.134127 GCCATGTTCACGGGGCTC 61.134 66.667 0.00 0.00 43.09 4.70
6255 10706 3.124921 GTCGCCATGTTCACGGGG 61.125 66.667 0.00 0.00 36.60 5.73
6256 10707 2.358125 TGTCGCCATGTTCACGGG 60.358 61.111 0.00 0.00 0.00 5.28
6257 10708 2.390599 CCTGTCGCCATGTTCACGG 61.391 63.158 0.00 0.00 0.00 4.94
6258 10709 0.389296 TACCTGTCGCCATGTTCACG 60.389 55.000 0.00 0.00 0.00 4.35
6259 10710 1.076332 GTACCTGTCGCCATGTTCAC 58.924 55.000 0.00 0.00 0.00 3.18
6260 10711 0.973632 AGTACCTGTCGCCATGTTCA 59.026 50.000 0.00 0.00 0.00 3.18
6261 10712 1.204941 AGAGTACCTGTCGCCATGTTC 59.795 52.381 0.00 0.00 0.00 3.18
6262 10713 1.267121 AGAGTACCTGTCGCCATGTT 58.733 50.000 0.00 0.00 0.00 2.71
6263 10714 2.025155 CTAGAGTACCTGTCGCCATGT 58.975 52.381 0.00 0.00 0.00 3.21
6264 10715 1.269309 GCTAGAGTACCTGTCGCCATG 60.269 57.143 0.00 0.00 0.00 3.66
6265 10716 1.033574 GCTAGAGTACCTGTCGCCAT 58.966 55.000 0.00 0.00 0.00 4.40
6266 10717 1.035932 GGCTAGAGTACCTGTCGCCA 61.036 60.000 0.00 0.00 35.48 5.69
6267 10718 1.734748 GGCTAGAGTACCTGTCGCC 59.265 63.158 0.00 0.00 0.00 5.54
6268 10719 1.355916 CGGCTAGAGTACCTGTCGC 59.644 63.158 0.00 0.00 0.00 5.19
6273 10724 2.119655 CACCGCGGCTAGAGTACCT 61.120 63.158 28.58 0.00 0.00 3.08
6281 10732 1.080366 CAGTAACACACCGCGGCTA 60.080 57.895 28.58 6.21 0.00 3.93
6401 10852 3.768922 GAGCAGCTCGAGGCCACT 61.769 66.667 15.58 6.74 43.05 4.00
6493 10959 2.037772 GTGGAGATCGCCTGTATCCAAT 59.962 50.000 17.00 0.00 41.52 3.16
6494 10960 1.412710 GTGGAGATCGCCTGTATCCAA 59.587 52.381 17.00 0.00 41.52 3.53
6551 11039 1.227853 GTTGAGTGTCGGCAGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
6556 11044 1.480212 ATGGAGGTTGAGTGTCGGCA 61.480 55.000 0.00 0.00 0.00 5.69
6563 11051 0.324943 CCGGTTCATGGAGGTTGAGT 59.675 55.000 0.00 0.00 0.00 3.41
6568 11056 2.933287 TGCCCGGTTCATGGAGGT 60.933 61.111 0.00 0.00 0.00 3.85
6715 11205 1.304217 TCTCTTCTCGCCGTTCCCT 60.304 57.895 0.00 0.00 0.00 4.20
6754 11289 2.829384 GCACACTTCCCCCTCCACA 61.829 63.158 0.00 0.00 0.00 4.17
6761 11301 1.668151 GTGAGACGCACACTTCCCC 60.668 63.158 4.27 0.00 46.91 4.81
6899 11483 1.105759 GTCAGCCTCCATTGATGCCC 61.106 60.000 0.00 0.00 33.08 5.36
6934 11521 2.302733 GGGGAATCAATGCCAAAGTTGT 59.697 45.455 0.00 0.00 42.44 3.32
6976 11565 1.563435 TTCTCGTCGCTTCGTCGTCT 61.563 55.000 5.88 0.00 39.12 4.18
7000 11589 0.947960 TTTGGCGCGAAATTGACTCA 59.052 45.000 13.91 0.00 0.00 3.41
7006 11595 3.974401 CGAATCATATTTGGCGCGAAATT 59.026 39.130 30.82 16.42 0.00 1.82
7007 11596 3.554524 CGAATCATATTTGGCGCGAAAT 58.445 40.909 29.10 29.10 0.00 2.17
7008 11597 2.852901 GCGAATCATATTTGGCGCGAAA 60.853 45.455 19.96 19.96 35.02 3.46
7009 11598 1.333702 GCGAATCATATTTGGCGCGAA 60.334 47.619 12.10 0.00 35.02 4.70
7010 11599 0.234625 GCGAATCATATTTGGCGCGA 59.765 50.000 12.10 0.00 35.02 5.87
7011 11600 0.725784 GGCGAATCATATTTGGCGCG 60.726 55.000 0.00 0.00 44.75 6.86
7012 11601 0.387239 GGGCGAATCATATTTGGCGC 60.387 55.000 0.00 0.00 43.27 6.53
7013 11602 0.110238 CGGGCGAATCATATTTGGCG 60.110 55.000 7.19 0.00 31.83 5.69
7014 11603 0.240945 CCGGGCGAATCATATTTGGC 59.759 55.000 0.00 5.15 0.00 4.52
7015 11604 0.240945 GCCGGGCGAATCATATTTGG 59.759 55.000 1.81 0.00 0.00 3.28
7016 11605 3.773117 GCCGGGCGAATCATATTTG 57.227 52.632 1.81 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.