Multiple sequence alignment - TraesCS5D01G452600

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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 TraesCS5D01G452600 chr5D 100.000 4723 0 0 1 4723 500488056 500492778 0.000000e+00 8722.0
1 TraesCS5D01G452600 chr5D 80.865 601 101 10 71 663 6910435 6911029 1.200000e-125 460.0
2 TraesCS5D01G452600 chr5D 78.539 438 49 25 1094 1519 26288840 26288436 3.650000e-61 246.0
3 TraesCS5D01G452600 chr5D 81.176 255 43 4 3277 3527 26286458 26286205 2.880000e-47 200.0
4 TraesCS5D01G452600 chr5B 91.525 1770 68 24 838 2559 622037470 622039205 0.000000e+00 2362.0
5 TraesCS5D01G452600 chr5B 92.670 1528 77 18 2558 4079 622039367 622040865 0.000000e+00 2169.0
6 TraesCS5D01G452600 chr5B 93.379 589 29 7 4138 4723 622041011 622041592 0.000000e+00 863.0
7 TraesCS5D01G452600 chr5B 81.463 588 96 7 73 649 54507687 54508272 1.990000e-128 470.0
8 TraesCS5D01G452600 chr5B 86.340 388 25 4 1120 1496 89692532 89692902 9.520000e-107 398.0
9 TraesCS5D01G452600 chr5B 85.049 408 34 20 1704 2107 89741634 89742018 1.590000e-104 390.0
10 TraesCS5D01G452600 chr5B 86.239 109 11 2 666 774 440259648 440259544 1.070000e-21 115.0
11 TraesCS5D01G452600 chr5B 84.956 113 12 3 666 778 122835845 122835738 5.000000e-20 110.0
12 TraesCS5D01G452600 chr5B 85.321 109 12 1 666 774 276913641 276913745 5.000000e-20 110.0
13 TraesCS5D01G452600 chr5A 84.611 1709 150 55 1084 2730 626989314 626990971 0.000000e+00 1594.0
14 TraesCS5D01G452600 chr5A 92.503 867 49 11 3217 4081 626991781 626992633 0.000000e+00 1227.0
15 TraesCS5D01G452600 chr5A 93.729 590 31 5 4138 4723 626992787 626993374 0.000000e+00 880.0
16 TraesCS5D01G452600 chr5A 89.661 590 51 6 80 660 626988432 626989020 0.000000e+00 743.0
17 TraesCS5D01G452600 chr5A 100.000 32 0 0 36 67 626988260 626988291 5.100000e-05 60.2
18 TraesCS5D01G452600 chr7D 90.207 531 31 9 1148 1661 635931374 635930848 0.000000e+00 673.0
19 TraesCS5D01G452600 chr7D 82.237 608 90 16 65 660 118868359 118868960 4.220000e-140 508.0
20 TraesCS5D01G452600 chr7D 89.311 421 23 9 1704 2107 635930853 635930438 4.220000e-140 508.0
21 TraesCS5D01G452600 chr1B 88.730 559 41 9 1120 1661 578101533 578102086 0.000000e+00 664.0
22 TraesCS5D01G452600 chr1B 87.886 421 29 9 1704 2107 578102081 578102496 4.280000e-130 475.0
23 TraesCS5D01G452600 chr1B 90.099 101 6 1 675 775 432802912 432803008 1.380000e-25 128.0
24 TraesCS5D01G452600 chr2A 87.657 559 35 10 1120 1661 441108046 441108587 1.870000e-173 619.0
25 TraesCS5D01G452600 chr2A 89.762 420 22 8 1704 2107 441108582 441108996 7.010000e-143 518.0
26 TraesCS5D01G452600 chr2A 79.089 593 106 14 79 659 471249608 471250194 4.430000e-105 392.0
27 TraesCS5D01G452600 chr4A 85.210 595 55 10 1084 1661 281594549 281593971 8.810000e-162 580.0
28 TraesCS5D01G452600 chr4A 92.105 152 9 2 1704 1855 281593976 281593828 1.330000e-50 211.0
29 TraesCS5D01G452600 chr4D 83.220 590 84 13 79 659 455753143 455753726 1.160000e-145 527.0
30 TraesCS5D01G452600 chr4D 82.888 561 85 7 83 633 344128847 344128288 1.180000e-135 494.0
31 TraesCS5D01G452600 chr4D 87.500 96 11 1 544 639 11466201 11466107 5.000000e-20 110.0
32 TraesCS5D01G452600 chr2D 82.558 602 89 14 72 660 604075044 604074446 2.520000e-142 516.0
33 TraesCS5D01G452600 chr2D 81.387 591 98 7 79 660 429082279 429081692 5.530000e-129 472.0
34 TraesCS5D01G452600 chr6D 81.748 515 87 6 149 660 354836345 354835835 1.570000e-114 424.0
35 TraesCS5D01G452600 chr6D 85.321 109 10 4 667 775 435969183 435969285 1.800000e-19 108.0
36 TraesCS5D01G452600 chr1D 76.638 351 61 11 328 658 452189746 452189397 1.750000e-39 174.0
37 TraesCS5D01G452600 chr1D 83.898 118 15 2 665 782 356219183 356219070 5.000000e-20 110.0
38 TraesCS5D01G452600 chr3D 76.471 255 53 5 406 660 473480196 473480443 1.070000e-26 132.0
39 TraesCS5D01G452600 chr2B 84.483 116 14 1 666 781 424318739 424318850 1.390000e-20 111.0
40 TraesCS5D01G452600 chr6B 85.321 109 13 1 666 774 455896013 455895908 5.000000e-20 110.0
41 TraesCS5D01G452600 chr3B 84.071 113 14 2 666 778 575165763 575165655 6.460000e-19 106.0
42 TraesCS5D01G452600 chr7A 76.471 170 34 6 494 660 265933176 265933342 2.340000e-13 87.9
43 TraesCS5D01G452600 chr7A 100.000 28 0 0 2365 2392 632527963 632527936 9.000000e-03 52.8


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 TraesCS5D01G452600 chr5D 500488056 500492778 4722 False 8722.00 8722 100.000000 1 4723 1 chr5D.!!$F2 4722
1 TraesCS5D01G452600 chr5D 6910435 6911029 594 False 460.00 460 80.865000 71 663 1 chr5D.!!$F1 592
2 TraesCS5D01G452600 chr5D 26286205 26288840 2635 True 223.00 246 79.857500 1094 3527 2 chr5D.!!$R1 2433
3 TraesCS5D01G452600 chr5B 622037470 622041592 4122 False 1798.00 2362 92.524667 838 4723 3 chr5B.!!$F5 3885
4 TraesCS5D01G452600 chr5B 54507687 54508272 585 False 470.00 470 81.463000 73 649 1 chr5B.!!$F1 576
5 TraesCS5D01G452600 chr5A 626988260 626993374 5114 False 900.84 1594 92.100800 36 4723 5 chr5A.!!$F1 4687
6 TraesCS5D01G452600 chr7D 635930438 635931374 936 True 590.50 673 89.759000 1148 2107 2 chr7D.!!$R1 959
7 TraesCS5D01G452600 chr7D 118868359 118868960 601 False 508.00 508 82.237000 65 660 1 chr7D.!!$F1 595
8 TraesCS5D01G452600 chr1B 578101533 578102496 963 False 569.50 664 88.308000 1120 2107 2 chr1B.!!$F2 987
9 TraesCS5D01G452600 chr2A 441108046 441108996 950 False 568.50 619 88.709500 1120 2107 2 chr2A.!!$F2 987
10 TraesCS5D01G452600 chr2A 471249608 471250194 586 False 392.00 392 79.089000 79 659 1 chr2A.!!$F1 580
11 TraesCS5D01G452600 chr4A 281593828 281594549 721 True 395.50 580 88.657500 1084 1855 2 chr4A.!!$R1 771
12 TraesCS5D01G452600 chr4D 455753143 455753726 583 False 527.00 527 83.220000 79 659 1 chr4D.!!$F1 580
13 TraesCS5D01G452600 chr4D 344128288 344128847 559 True 494.00 494 82.888000 83 633 1 chr4D.!!$R2 550
14 TraesCS5D01G452600 chr2D 604074446 604075044 598 True 516.00 516 82.558000 72 660 1 chr2D.!!$R2 588
15 TraesCS5D01G452600 chr2D 429081692 429082279 587 True 472.00 472 81.387000 79 660 1 chr2D.!!$R1 581
16 TraesCS5D01G452600 chr6D 354835835 354836345 510 True 424.00 424 81.748000 149 660 1 chr6D.!!$R1 511

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
27 28 0.312416 TGAACGCGGGTTTGAAATGG 59.688 50.000 19.59 0.0 36.24 3.16 F
28 29 0.388006 GAACGCGGGTTTGAAATGGG 60.388 55.000 19.59 0.0 36.24 4.00 F
381 516 0.461339 GCGGCGAGGTTAGGATTTCA 60.461 55.000 12.98 0.0 0.00 2.69 F
1088 1251 1.157513 GATCCCTCTCCCTCTCCCC 59.842 68.421 0.00 0.0 0.00 4.81 F
2252 3603 0.958382 GGCGCCCACACATTTCAGTA 60.958 55.000 18.11 0.0 0.00 2.74 F
2714 4252 1.279496 TATGACAGTCCCTTGCTGCT 58.721 50.000 0.00 0.0 37.47 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1734 0.402126 AAAGAGGGGAGGGATAGGGC 60.402 60.000 0.00 0.0 0.00 5.19 R
1744 2014 2.094752 CCAATTTAACTGGGTCAAGCGG 60.095 50.000 0.00 0.0 0.00 5.52 R
2144 3492 0.907704 AGGACAGATACCGCACCCAA 60.908 55.000 0.00 0.0 0.00 4.12 R
2761 4301 0.892755 TGGACGAATCTAACACCGCT 59.107 50.000 0.00 0.0 0.00 5.52 R
3371 5580 1.067495 AGAGTTTACAGTCTCTGGCGC 60.067 52.381 0.00 0.0 39.23 6.53 R
4649 6967 0.034863 GTCCCGGGTAAGATTTGCCA 60.035 55.000 22.86 0.0 37.12 4.92 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
20 21 3.378911 AATTTCATTGAACGCGGGTTT 57.621 38.095 19.59 0.27 36.24 3.27
21 22 2.126914 TTTCATTGAACGCGGGTTTG 57.873 45.000 19.59 13.56 36.24 2.93
22 23 1.309950 TTCATTGAACGCGGGTTTGA 58.690 45.000 19.59 15.64 36.24 2.69
23 24 1.309950 TCATTGAACGCGGGTTTGAA 58.690 45.000 19.59 14.86 36.24 2.69
24 25 1.676529 TCATTGAACGCGGGTTTGAAA 59.323 42.857 19.59 14.00 36.24 2.69
25 26 2.294791 TCATTGAACGCGGGTTTGAAAT 59.705 40.909 19.59 15.47 36.24 2.17
26 27 2.126914 TTGAACGCGGGTTTGAAATG 57.873 45.000 19.59 0.00 36.24 2.32
27 28 0.312416 TGAACGCGGGTTTGAAATGG 59.688 50.000 19.59 0.00 36.24 3.16
28 29 0.388006 GAACGCGGGTTTGAAATGGG 60.388 55.000 19.59 0.00 36.24 4.00
29 30 1.811645 AACGCGGGTTTGAAATGGGG 61.812 55.000 12.67 0.00 30.42 4.96
30 31 2.264480 GCGGGTTTGAAATGGGGC 59.736 61.111 0.00 0.00 0.00 5.80
31 32 2.578714 GCGGGTTTGAAATGGGGCA 61.579 57.895 0.00 0.00 0.00 5.36
32 33 1.591183 CGGGTTTGAAATGGGGCAG 59.409 57.895 0.00 0.00 0.00 4.85
33 34 0.897863 CGGGTTTGAAATGGGGCAGA 60.898 55.000 0.00 0.00 0.00 4.26
34 35 0.608130 GGGTTTGAAATGGGGCAGAC 59.392 55.000 0.00 0.00 0.00 3.51
68 69 2.506472 GGATGACCGGCTTCTCCC 59.494 66.667 0.00 0.00 0.00 4.30
205 335 2.707849 GGTGCCTCGTCTCCGCTAA 61.708 63.158 0.00 0.00 0.00 3.09
214 344 3.008330 TCGTCTCCGCTAATAGATAGGC 58.992 50.000 0.00 0.00 31.83 3.93
224 356 6.228258 CGCTAATAGATAGGCAGGGTTTTAA 58.772 40.000 0.00 0.00 31.83 1.52
275 407 1.321743 CGGTGCTTCTTCTTCGAATCG 59.678 52.381 0.00 0.00 0.00 3.34
349 482 1.482593 AGCTCCAACGTAGATTCCTGG 59.517 52.381 0.00 0.00 0.00 4.45
381 516 0.461339 GCGGCGAGGTTAGGATTTCA 60.461 55.000 12.98 0.00 0.00 2.69
424 559 5.780751 GCGATATTCGATGTCAAATTCTTCG 59.219 40.000 0.32 0.00 43.74 3.79
684 829 9.463902 AGTAGTAGATGTGTACAGACATACTTT 57.536 33.333 18.44 9.27 36.67 2.66
687 832 9.682465 AGTAGATGTGTACAGACATACTTTAGA 57.318 33.333 11.24 0.00 36.67 2.10
688 833 9.938670 GTAGATGTGTACAGACATACTTTAGAG 57.061 37.037 0.00 0.00 36.67 2.43
689 834 7.484975 AGATGTGTACAGACATACTTTAGAGC 58.515 38.462 0.00 0.00 36.67 4.09
690 835 5.637809 TGTGTACAGACATACTTTAGAGCG 58.362 41.667 0.00 0.00 38.04 5.03
691 836 5.182570 TGTGTACAGACATACTTTAGAGCGT 59.817 40.000 0.00 0.00 38.04 5.07
692 837 6.372381 TGTGTACAGACATACTTTAGAGCGTA 59.628 38.462 0.00 0.00 38.04 4.42
693 838 6.906143 GTGTACAGACATACTTTAGAGCGTAG 59.094 42.308 0.00 0.00 38.04 3.51
694 839 6.820152 TGTACAGACATACTTTAGAGCGTAGA 59.180 38.462 0.00 0.00 0.00 2.59
695 840 6.945938 ACAGACATACTTTAGAGCGTAGAT 57.054 37.500 0.00 0.00 0.00 1.98
696 841 7.336161 ACAGACATACTTTAGAGCGTAGATT 57.664 36.000 0.00 0.00 0.00 2.40
697 842 7.419204 ACAGACATACTTTAGAGCGTAGATTC 58.581 38.462 0.00 0.00 0.00 2.52
698 843 7.067129 ACAGACATACTTTAGAGCGTAGATTCA 59.933 37.037 0.00 0.00 0.00 2.57
699 844 7.377397 CAGACATACTTTAGAGCGTAGATTCAC 59.623 40.741 0.00 0.00 0.00 3.18
700 845 7.283580 AGACATACTTTAGAGCGTAGATTCACT 59.716 37.037 0.00 0.00 0.00 3.41
701 846 7.419204 ACATACTTTAGAGCGTAGATTCACTC 58.581 38.462 0.00 0.00 0.00 3.51
702 847 5.899120 ACTTTAGAGCGTAGATTCACTCA 57.101 39.130 0.00 0.00 0.00 3.41
703 848 6.458232 ACTTTAGAGCGTAGATTCACTCAT 57.542 37.500 0.00 0.00 0.00 2.90
704 849 6.868622 ACTTTAGAGCGTAGATTCACTCATT 58.131 36.000 0.00 0.00 0.00 2.57
705 850 7.324178 ACTTTAGAGCGTAGATTCACTCATTT 58.676 34.615 0.00 0.00 0.00 2.32
706 851 7.819900 ACTTTAGAGCGTAGATTCACTCATTTT 59.180 33.333 0.00 0.00 0.00 1.82
707 852 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
708 853 4.331168 AGAGCGTAGATTCACTCATTTTGC 59.669 41.667 0.00 0.00 0.00 3.68
709 854 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
710 855 4.697352 AGCGTAGATTCACTCATTTTGCTT 59.303 37.500 0.00 0.00 0.00 3.91
711 856 5.024555 GCGTAGATTCACTCATTTTGCTTC 58.975 41.667 0.00 0.00 0.00 3.86
712 857 5.390885 GCGTAGATTCACTCATTTTGCTTCA 60.391 40.000 0.00 0.00 0.00 3.02
713 858 6.676456 GCGTAGATTCACTCATTTTGCTTCAT 60.676 38.462 0.00 0.00 0.00 2.57
714 859 7.465916 GCGTAGATTCACTCATTTTGCTTCATA 60.466 37.037 0.00 0.00 0.00 2.15
715 860 8.554528 CGTAGATTCACTCATTTTGCTTCATAT 58.445 33.333 0.00 0.00 0.00 1.78
808 953 1.734477 CTAATCCTCGATGCCGCGG 60.734 63.158 24.05 24.05 41.73 6.46
1023 1186 3.862124 CGACTTGTGAAGAGGCGG 58.138 61.111 0.00 0.00 41.86 6.13
1081 1244 3.299190 CTCCGCGATCCCTCTCCC 61.299 72.222 8.23 0.00 0.00 4.30
1082 1245 3.801068 CTCCGCGATCCCTCTCCCT 62.801 68.421 8.23 0.00 0.00 4.20
1083 1246 3.299190 CCGCGATCCCTCTCCCTC 61.299 72.222 8.23 0.00 0.00 4.30
1084 1247 2.203422 CGCGATCCCTCTCCCTCT 60.203 66.667 0.00 0.00 0.00 3.69
1085 1248 2.265182 CGCGATCCCTCTCCCTCTC 61.265 68.421 0.00 0.00 0.00 3.20
1086 1249 1.906333 GCGATCCCTCTCCCTCTCC 60.906 68.421 0.00 0.00 0.00 3.71
1087 1250 1.228737 CGATCCCTCTCCCTCTCCC 60.229 68.421 0.00 0.00 0.00 4.30
1088 1251 1.157513 GATCCCTCTCCCTCTCCCC 59.842 68.421 0.00 0.00 0.00 4.81
1089 1252 1.311371 ATCCCTCTCCCTCTCCCCT 60.311 63.158 0.00 0.00 0.00 4.79
1091 1254 2.612251 CCTCTCCCTCTCCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1097 1260 3.039526 CCTCTCCCCTCCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1358 1528 2.996153 TGGGCCGCCAAGTACGTA 60.996 61.111 12.58 0.00 0.00 3.57
1611 1821 7.284716 TCTGTCTTACGATGGTATCTGTAACAT 59.715 37.037 0.00 0.00 40.91 2.71
1612 1822 8.454570 TGTCTTACGATGGTATCTGTAACATA 57.545 34.615 0.00 0.00 38.34 2.29
1613 1823 8.347771 TGTCTTACGATGGTATCTGTAACATAC 58.652 37.037 0.00 0.00 38.34 2.39
1614 1824 8.566260 GTCTTACGATGGTATCTGTAACATACT 58.434 37.037 0.00 0.00 38.34 2.12
1655 1875 3.072944 CAGCTAGCAGGGATATTCTTGC 58.927 50.000 18.83 10.09 0.00 4.01
1679 1899 8.489489 TGCTTTCTGAATAATCTCTATCCAGTT 58.511 33.333 0.00 0.00 0.00 3.16
1744 2014 3.206150 TCACTTCAGCCTGTTTCTGTTC 58.794 45.455 0.00 0.00 33.48 3.18
2066 3414 4.796606 CCATGTTAGATTTGTCCATCCCT 58.203 43.478 0.00 0.00 0.00 4.20
2067 3415 5.203528 CCATGTTAGATTTGTCCATCCCTT 58.796 41.667 0.00 0.00 0.00 3.95
2072 3420 8.893563 TGTTAGATTTGTCCATCCCTTTTATT 57.106 30.769 0.00 0.00 0.00 1.40
2142 3490 8.543774 GCTAGTTGCTACACAAAATATCTAGTG 58.456 37.037 0.13 0.00 40.82 2.74
2144 3492 8.848474 AGTTGCTACACAAAATATCTAGTGTT 57.152 30.769 10.89 0.00 42.06 3.32
2145 3493 9.284968 AGTTGCTACACAAAATATCTAGTGTTT 57.715 29.630 10.89 0.00 42.06 2.83
2146 3494 9.329913 GTTGCTACACAAAATATCTAGTGTTTG 57.670 33.333 10.89 3.76 42.06 2.93
2252 3603 0.958382 GGCGCCCACACATTTCAGTA 60.958 55.000 18.11 0.00 0.00 2.74
2300 3665 7.859325 AGATTACGTGCCACAAAAATATACT 57.141 32.000 0.00 0.00 0.00 2.12
2428 3794 1.966295 GCCATGTGAATTGGGGTGGAT 60.966 52.381 0.00 0.00 34.66 3.41
2444 3810 4.770010 GGGTGGATGAAGTACCAATTTCAA 59.230 41.667 0.03 0.00 35.29 2.69
2465 3831 6.764379 TCAACCCCCATCAAGTTTTATTTTC 58.236 36.000 0.00 0.00 0.00 2.29
2466 3832 5.400066 ACCCCCATCAAGTTTTATTTTCG 57.600 39.130 0.00 0.00 0.00 3.46
2493 3859 8.200792 AGACCAAGTTTTTGCATTGTATTGTTA 58.799 29.630 0.00 0.00 32.79 2.41
2683 4221 5.700832 TGTTACCAGTTGATCTTTAGTGCTG 59.299 40.000 0.00 0.00 0.00 4.41
2714 4252 1.279496 TATGACAGTCCCTTGCTGCT 58.721 50.000 0.00 0.00 37.47 4.24
2741 4281 7.147689 TGCTGCTTTAATAATTCATGAACCCAT 60.148 33.333 11.07 1.37 0.00 4.00
2761 4301 3.510531 TGTAAACCACTGCATAACCCA 57.489 42.857 0.00 0.00 0.00 4.51
2773 4313 2.745152 GCATAACCCAGCGGTGTTAGAT 60.745 50.000 14.40 0.00 43.71 1.98
2775 4315 2.109425 AACCCAGCGGTGTTAGATTC 57.891 50.000 14.40 0.00 43.71 2.52
2790 4330 6.978659 GTGTTAGATTCGTCCATCACTTATGA 59.021 38.462 0.00 0.00 37.86 2.15
2792 4332 8.856103 TGTTAGATTCGTCCATCACTTATGATA 58.144 33.333 0.00 0.00 44.13 2.15
2793 4333 9.692749 GTTAGATTCGTCCATCACTTATGATAA 57.307 33.333 0.00 0.00 44.13 1.75
2794 4334 9.692749 TTAGATTCGTCCATCACTTATGATAAC 57.307 33.333 0.00 0.00 44.13 1.89
2795 4335 7.726216 AGATTCGTCCATCACTTATGATAACA 58.274 34.615 0.00 0.00 44.13 2.41
2796 4336 8.204160 AGATTCGTCCATCACTTATGATAACAA 58.796 33.333 0.00 0.00 44.13 2.83
2797 4337 8.908786 ATTCGTCCATCACTTATGATAACAAT 57.091 30.769 0.00 0.00 44.13 2.71
2798 4338 9.996554 ATTCGTCCATCACTTATGATAACAATA 57.003 29.630 0.00 0.00 44.13 1.90
2799 4339 9.996554 TTCGTCCATCACTTATGATAACAATAT 57.003 29.630 0.00 0.00 44.13 1.28
2800 4340 9.423061 TCGTCCATCACTTATGATAACAATATG 57.577 33.333 0.00 0.00 44.13 1.78
2815 4355 5.762825 ACAATATGTTGAATAGCCAGCTG 57.237 39.130 6.78 6.78 38.71 4.24
2837 4377 3.407424 AAGTGAACTGAGCATGCTACA 57.593 42.857 22.74 18.42 0.00 2.74
2857 4397 9.158233 TGCTACACAAAATATCTAGTTTGGTAC 57.842 33.333 12.94 0.00 43.28 3.34
2870 4410 5.479124 AGTTTGGTACGGTAGAATCAAGT 57.521 39.130 0.00 0.00 0.00 3.16
2872 4412 6.293698 AGTTTGGTACGGTAGAATCAAGTTT 58.706 36.000 0.00 0.00 0.00 2.66
2873 4413 6.769341 AGTTTGGTACGGTAGAATCAAGTTTT 59.231 34.615 0.00 0.00 0.00 2.43
2962 4503 5.124457 CCAGTGTTGACATTAGAATCTTGGG 59.876 44.000 0.00 0.00 0.00 4.12
2983 4524 3.366985 GGGCAATTACAGTTTGTAGCACC 60.367 47.826 0.00 0.00 33.92 5.01
2984 4525 3.366985 GGCAATTACAGTTTGTAGCACCC 60.367 47.826 0.00 0.00 33.92 4.61
2995 4536 7.092846 ACAGTTTGTAGCACCCTAAGATATTCT 60.093 37.037 0.00 0.00 0.00 2.40
3007 4548 6.957020 CCCTAAGATATTCTCCTAGATGTGGT 59.043 42.308 0.00 0.00 0.00 4.16
3055 4596 4.602340 TTTGGGAACTCTCTAGTGTGTC 57.398 45.455 0.42 0.00 35.62 3.67
3061 4602 5.448904 GGGAACTCTCTAGTGTGTCGATTAC 60.449 48.000 0.00 0.00 35.62 1.89
3076 4617 6.582295 GTGTCGATTACGTTTCTTACCAGTTA 59.418 38.462 0.00 0.00 40.69 2.24
3114 4655 7.806180 ACTTCTATACATTATGACAGCCCTTT 58.194 34.615 0.00 0.00 0.00 3.11
3140 5348 5.977171 TGGAAAATACATTATGACGGTCG 57.023 39.130 0.00 0.00 0.00 4.79
3167 5375 4.672801 GCATCAAAACCGGAAGAGATGTTC 60.673 45.833 22.59 10.92 36.24 3.18
3179 5388 8.768955 CCGGAAGAGATGTTCTTAATTTCTATG 58.231 37.037 0.00 0.00 46.12 2.23
3254 5463 4.039730 ACTCTCATGGTCATTAAGGGATCG 59.960 45.833 0.00 0.00 0.00 3.69
3259 5468 2.158813 TGGTCATTAAGGGATCGCTTCC 60.159 50.000 26.48 20.59 44.62 3.46
3317 5526 6.028146 TGCAGTTTCTAATCTACAACCGTA 57.972 37.500 0.00 0.00 0.00 4.02
3371 5580 2.079925 GGCTTACTGGTCAAGAGCAAG 58.920 52.381 3.39 0.00 38.46 4.01
3414 5626 7.726216 TCTAATCCTGTATGTCATACCACAAG 58.274 38.462 18.31 9.93 34.86 3.16
3656 5868 2.159393 TGCTTGAAACCATTATCGCAGC 60.159 45.455 0.00 0.00 0.00 5.25
3662 5874 4.335315 TGAAACCATTATCGCAGCCTTAAG 59.665 41.667 0.00 0.00 0.00 1.85
3670 5882 0.108424 CGCAGCCTTAAGACTCAGCT 60.108 55.000 3.36 0.29 0.00 4.24
3742 5954 1.133598 AGTGATGCGCCATGATTTGTG 59.866 47.619 4.18 0.00 0.00 3.33
3817 6030 2.490903 ACATGTCGTCTGTAGTGGTACC 59.509 50.000 4.43 4.43 0.00 3.34
3850 6063 6.566079 AATGTATCTCCTTGTTCCAGATCA 57.434 37.500 0.00 0.00 0.00 2.92
3862 6075 8.043710 CCTTGTTCCAGATCAGAGTTAACTATT 58.956 37.037 8.42 0.00 0.00 1.73
3863 6076 9.442047 CTTGTTCCAGATCAGAGTTAACTATTT 57.558 33.333 8.42 0.00 0.00 1.40
3956 6171 2.041216 AGGTACTTTTAGGCCCCAAGTG 59.959 50.000 18.01 5.23 27.25 3.16
3985 6200 7.566760 TTGGTATTGATGACGAGCAATTAAT 57.433 32.000 0.00 0.00 39.02 1.40
3988 6203 7.931407 TGGTATTGATGACGAGCAATTAATAGT 59.069 33.333 0.00 0.00 39.02 2.12
4043 6258 2.335712 CCCAAGAGCGAAGGTTGCC 61.336 63.158 0.00 0.00 39.88 4.52
4113 6357 5.188359 ACTTGATGCATCCCTAAATTTGCTT 59.812 36.000 23.67 0.00 36.10 3.91
4411 6727 2.231478 TGTCTCTCTGGATTCACGGAAC 59.769 50.000 0.00 0.00 0.00 3.62
4443 6759 6.727824 GAAATTCTTCGGAGAAGATGTCAA 57.272 37.500 12.62 0.00 44.65 3.18
4459 6777 2.169789 CAATCTCTGCCACTCCGCG 61.170 63.158 0.00 0.00 0.00 6.46
4517 6835 1.452110 CACGCATCACCATTTCCTCA 58.548 50.000 0.00 0.00 0.00 3.86
4595 6913 3.948473 CGATTGAGTCCTGGTAGAGAAGA 59.052 47.826 0.00 0.00 0.00 2.87
4644 6962 7.710766 AACTTTGAAGTTTCCGTAGAGTAAG 57.289 36.000 3.37 0.00 46.52 2.34
4645 6963 5.695363 ACTTTGAAGTTTCCGTAGAGTAAGC 59.305 40.000 0.00 0.00 35.21 3.09
4649 6967 6.285990 TGAAGTTTCCGTAGAGTAAGCTTTT 58.714 36.000 3.20 0.00 0.00 2.27
4651 6969 4.995487 AGTTTCCGTAGAGTAAGCTTTTGG 59.005 41.667 3.20 0.00 0.00 3.28
4652 6970 2.968675 TCCGTAGAGTAAGCTTTTGGC 58.031 47.619 3.20 0.00 42.19 4.52
4653 6971 2.300723 TCCGTAGAGTAAGCTTTTGGCA 59.699 45.455 3.20 0.00 44.79 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.056304 CAAACCCGCGTTCAATGAAATT 58.944 40.909 4.92 0.00 36.63 1.82
1 2 2.294791 TCAAACCCGCGTTCAATGAAAT 59.705 40.909 4.92 0.00 0.00 2.17
3 4 1.309950 TCAAACCCGCGTTCAATGAA 58.690 45.000 4.92 0.00 0.00 2.57
6 7 2.609244 CCATTTCAAACCCGCGTTCAAT 60.609 45.455 4.92 0.00 0.00 2.57
10 11 1.663173 CCCATTTCAAACCCGCGTT 59.337 52.632 4.92 0.00 0.00 4.84
11 12 2.272447 CCCCATTTCAAACCCGCGT 61.272 57.895 4.92 0.00 0.00 6.01
12 13 2.571231 CCCCATTTCAAACCCGCG 59.429 61.111 0.00 0.00 0.00 6.46
13 14 2.264480 GCCCCATTTCAAACCCGC 59.736 61.111 0.00 0.00 0.00 6.13
14 15 0.897863 TCTGCCCCATTTCAAACCCG 60.898 55.000 0.00 0.00 0.00 5.28
15 16 0.608130 GTCTGCCCCATTTCAAACCC 59.392 55.000 0.00 0.00 0.00 4.11
16 17 1.273327 CTGTCTGCCCCATTTCAAACC 59.727 52.381 0.00 0.00 0.00 3.27
17 18 1.963515 ACTGTCTGCCCCATTTCAAAC 59.036 47.619 0.00 0.00 0.00 2.93
18 19 2.364970 CAACTGTCTGCCCCATTTCAAA 59.635 45.455 0.00 0.00 0.00 2.69
19 20 1.962807 CAACTGTCTGCCCCATTTCAA 59.037 47.619 0.00 0.00 0.00 2.69
20 21 1.619654 CAACTGTCTGCCCCATTTCA 58.380 50.000 0.00 0.00 0.00 2.69
21 22 0.244721 GCAACTGTCTGCCCCATTTC 59.755 55.000 4.34 0.00 36.25 2.17
22 23 1.526575 CGCAACTGTCTGCCCCATTT 61.527 55.000 8.61 0.00 39.26 2.32
23 24 1.973281 CGCAACTGTCTGCCCCATT 60.973 57.895 8.61 0.00 39.26 3.16
24 25 2.360350 CGCAACTGTCTGCCCCAT 60.360 61.111 8.61 0.00 39.26 4.00
27 28 3.058160 ATGCGCAACTGTCTGCCC 61.058 61.111 17.11 2.50 39.26 5.36
28 29 2.177531 CATGCGCAACTGTCTGCC 59.822 61.111 17.11 4.17 39.26 4.85
29 30 2.503375 GCATGCGCAACTGTCTGC 60.503 61.111 17.11 15.73 38.36 4.26
30 31 1.974249 ATCGCATGCGCAACTGTCTG 61.974 55.000 34.45 8.36 38.40 3.51
31 32 1.699656 GATCGCATGCGCAACTGTCT 61.700 55.000 34.45 11.01 38.40 3.41
32 33 1.297158 GATCGCATGCGCAACTGTC 60.297 57.895 34.45 19.27 38.40 3.51
33 34 2.787249 GATCGCATGCGCAACTGT 59.213 55.556 34.45 15.29 38.40 3.55
34 35 2.350425 CGATCGCATGCGCAACTG 60.350 61.111 34.45 17.66 38.40 3.16
92 221 2.023307 AGATCGAGGGGAGGAAGGTTTA 60.023 50.000 0.00 0.00 0.00 2.01
205 335 7.162082 CGAGAATTAAAACCCTGCCTATCTAT 58.838 38.462 0.00 0.00 0.00 1.98
214 344 2.423538 CCCTGCGAGAATTAAAACCCTG 59.576 50.000 0.00 0.00 0.00 4.45
247 379 1.372087 GAAGAAGCACCGCCATCCAG 61.372 60.000 0.00 0.00 0.00 3.86
275 407 1.153147 GATTGGAGCCCGGAAGACC 60.153 63.158 0.73 0.99 0.00 3.85
325 457 0.460311 AATCTACGTTGGAGCTCCGG 59.540 55.000 27.43 20.44 39.43 5.14
395 530 3.629438 TGACATCGAATATCGCCGTTA 57.371 42.857 0.00 0.00 40.21 3.18
408 543 5.469373 TCAATCCGAAGAATTTGACATCG 57.531 39.130 0.00 0.00 0.00 3.84
424 559 7.930217 TCATCGTTGAATCCTTAAATCAATCC 58.070 34.615 0.00 0.00 35.70 3.01
480 616 4.059459 GTCTTCGTGCACGTGCCG 62.059 66.667 35.72 33.57 41.18 5.69
563 708 3.667087 GACCATTGTCGCTGCCAA 58.333 55.556 0.00 0.00 0.00 4.52
661 806 9.682465 TCTAAAGTATGTCTGTACACATCTACT 57.318 33.333 2.45 0.41 38.78 2.57
664 809 7.484975 GCTCTAAAGTATGTCTGTACACATCT 58.515 38.462 2.45 0.00 38.78 2.90
665 810 6.415280 CGCTCTAAAGTATGTCTGTACACATC 59.585 42.308 2.45 0.00 38.78 3.06
666 811 6.127703 ACGCTCTAAAGTATGTCTGTACACAT 60.128 38.462 4.56 4.56 38.78 3.21
667 812 5.182570 ACGCTCTAAAGTATGTCTGTACACA 59.817 40.000 0.00 0.00 38.78 3.72
668 813 5.638783 ACGCTCTAAAGTATGTCTGTACAC 58.361 41.667 0.00 0.00 38.78 2.90
669 814 5.892160 ACGCTCTAAAGTATGTCTGTACA 57.108 39.130 0.00 0.00 40.69 2.90
670 815 7.244166 TCTACGCTCTAAAGTATGTCTGTAC 57.756 40.000 0.00 0.00 0.00 2.90
672 817 6.945938 ATCTACGCTCTAAAGTATGTCTGT 57.054 37.500 0.00 0.00 0.00 3.41
673 818 7.377397 GTGAATCTACGCTCTAAAGTATGTCTG 59.623 40.741 0.00 0.00 0.00 3.51
675 820 7.419204 AGTGAATCTACGCTCTAAAGTATGTC 58.581 38.462 0.00 0.00 0.00 3.06
677 822 7.418408 TGAGTGAATCTACGCTCTAAAGTATG 58.582 38.462 0.00 0.00 44.58 2.39
679 824 6.997239 TGAGTGAATCTACGCTCTAAAGTA 57.003 37.500 0.00 0.00 44.58 2.24
681 826 7.763172 AAATGAGTGAATCTACGCTCTAAAG 57.237 36.000 0.00 0.00 44.58 1.85
682 827 7.413000 GCAAAATGAGTGAATCTACGCTCTAAA 60.413 37.037 0.00 0.00 44.58 1.85
683 828 6.036083 GCAAAATGAGTGAATCTACGCTCTAA 59.964 38.462 0.00 0.00 44.58 2.10
684 829 5.520288 GCAAAATGAGTGAATCTACGCTCTA 59.480 40.000 0.00 0.00 44.58 2.43
685 830 4.331168 GCAAAATGAGTGAATCTACGCTCT 59.669 41.667 0.00 0.00 44.58 4.09
686 831 4.331168 AGCAAAATGAGTGAATCTACGCTC 59.669 41.667 0.00 0.00 44.55 5.03
687 832 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
688 833 4.606457 AGCAAAATGAGTGAATCTACGC 57.394 40.909 0.00 0.00 0.00 4.42
689 834 6.169419 TGAAGCAAAATGAGTGAATCTACG 57.831 37.500 0.00 0.00 0.00 3.51
745 890 9.883142 CTCTCTCAGTTCCTAAATATTTGTCTT 57.117 33.333 11.05 0.00 0.00 3.01
746 891 9.041354 ACTCTCTCAGTTCCTAAATATTTGTCT 57.959 33.333 11.05 0.00 26.56 3.41
749 894 9.239002 CGTACTCTCTCAGTTCCTAAATATTTG 57.761 37.037 11.05 1.40 36.43 2.32
750 895 9.186837 TCGTACTCTCTCAGTTCCTAAATATTT 57.813 33.333 5.89 5.89 36.43 1.40
751 896 8.749026 TCGTACTCTCTCAGTTCCTAAATATT 57.251 34.615 0.00 0.00 36.43 1.28
752 897 8.788806 CATCGTACTCTCTCAGTTCCTAAATAT 58.211 37.037 0.00 0.00 36.43 1.28
753 898 7.774157 ACATCGTACTCTCTCAGTTCCTAAATA 59.226 37.037 0.00 0.00 36.43 1.40
754 899 6.603997 ACATCGTACTCTCTCAGTTCCTAAAT 59.396 38.462 0.00 0.00 36.43 1.40
755 900 5.944599 ACATCGTACTCTCTCAGTTCCTAAA 59.055 40.000 0.00 0.00 36.43 1.85
756 901 5.498393 ACATCGTACTCTCTCAGTTCCTAA 58.502 41.667 0.00 0.00 36.43 2.69
757 902 5.100344 ACATCGTACTCTCTCAGTTCCTA 57.900 43.478 0.00 0.00 36.43 2.94
758 903 3.958018 ACATCGTACTCTCTCAGTTCCT 58.042 45.455 0.00 0.00 36.43 3.36
759 904 4.416620 CAACATCGTACTCTCTCAGTTCC 58.583 47.826 0.00 0.00 36.43 3.62
760 905 4.416620 CCAACATCGTACTCTCTCAGTTC 58.583 47.826 0.00 0.00 36.43 3.01
761 906 3.367498 GCCAACATCGTACTCTCTCAGTT 60.367 47.826 0.00 0.00 36.43 3.16
762 907 2.164624 GCCAACATCGTACTCTCTCAGT 59.835 50.000 0.00 0.00 39.41 3.41
763 908 2.792890 CGCCAACATCGTACTCTCTCAG 60.793 54.545 0.00 0.00 0.00 3.35
764 909 1.132453 CGCCAACATCGTACTCTCTCA 59.868 52.381 0.00 0.00 0.00 3.27
765 910 1.400846 TCGCCAACATCGTACTCTCTC 59.599 52.381 0.00 0.00 0.00 3.20
766 911 1.460504 TCGCCAACATCGTACTCTCT 58.539 50.000 0.00 0.00 0.00 3.10
767 912 2.120232 CATCGCCAACATCGTACTCTC 58.880 52.381 0.00 0.00 0.00 3.20
768 913 1.802880 GCATCGCCAACATCGTACTCT 60.803 52.381 0.00 0.00 0.00 3.24
769 914 0.577269 GCATCGCCAACATCGTACTC 59.423 55.000 0.00 0.00 0.00 2.59
770 915 2.677971 GCATCGCCAACATCGTACT 58.322 52.632 0.00 0.00 0.00 2.73
1066 1229 3.299190 GAGGGAGAGGGATCGCGG 61.299 72.222 6.13 0.00 37.24 6.46
1076 1239 3.036959 GGGGAGGGGAGAGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
1077 1240 3.039526 AGGGGAGGGGAGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1078 1241 3.036959 GAGGGGAGGGGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1081 1244 2.612251 GAGGAGGGGAGGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
1082 1245 3.036959 GGAGGAGGGGAGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
1083 1246 3.039526 AGGAGGAGGGGAGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1084 1247 3.036959 GAGGAGGAGGGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
1085 1248 4.179599 GGAGGAGGAGGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
1086 1249 4.179599 GGGAGGAGGAGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1087 1250 4.179599 GGGGAGGAGGAGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1088 1251 4.179599 GGGGGAGGAGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1358 1528 3.790437 CGGCCTCCCAGTCAGCAT 61.790 66.667 0.00 0.00 0.00 3.79
1535 1733 1.613284 AAGAGGGGAGGGATAGGGCA 61.613 60.000 0.00 0.00 0.00 5.36
1536 1734 0.402126 AAAGAGGGGAGGGATAGGGC 60.402 60.000 0.00 0.00 0.00 5.19
1537 1735 2.182536 AGTAAAGAGGGGAGGGATAGGG 59.817 54.545 0.00 0.00 0.00 3.53
1538 1736 3.116707 TGAGTAAAGAGGGGAGGGATAGG 60.117 52.174 0.00 0.00 0.00 2.57
1539 1737 4.200447 TGAGTAAAGAGGGGAGGGATAG 57.800 50.000 0.00 0.00 0.00 2.08
1679 1899 5.352293 CAGTATGTTCTTAGCATTGCACTGA 59.648 40.000 11.91 2.57 34.71 3.41
1744 2014 2.094752 CCAATTTAACTGGGTCAAGCGG 60.095 50.000 0.00 0.00 0.00 5.52
2001 3349 4.815308 ACAGCAAAATCAGATAGCTAGCAG 59.185 41.667 18.83 2.99 33.59 4.24
2072 3420 8.360390 CAGCTGGTGATTCTACATACTGTTATA 58.640 37.037 5.57 0.00 0.00 0.98
2142 3490 1.084289 GACAGATACCGCACCCAAAC 58.916 55.000 0.00 0.00 0.00 2.93
2144 3492 0.907704 AGGACAGATACCGCACCCAA 60.908 55.000 0.00 0.00 0.00 4.12
2145 3493 1.305802 AGGACAGATACCGCACCCA 60.306 57.895 0.00 0.00 0.00 4.51
2146 3494 1.144057 CAGGACAGATACCGCACCC 59.856 63.158 0.00 0.00 0.00 4.61
2203 3554 5.074102 TGAATTAGGACGGAGGGACTATCTA 59.926 44.000 0.00 0.00 41.55 1.98
2269 3632 5.950758 TTGTGGCACGTAATCTATGTTTT 57.049 34.783 13.77 0.00 0.00 2.43
2282 3645 8.682128 ATTTAACAGTATATTTTTGTGGCACG 57.318 30.769 13.77 0.00 0.00 5.34
2375 3741 9.097257 ACTTTTTGTGATTTAACTTTGACCATG 57.903 29.630 0.00 0.00 0.00 3.66
2406 3772 1.076549 ACCCCAATTCACATGGCGT 59.923 52.632 0.00 0.00 36.58 5.68
2428 3794 3.117093 TGGGGGTTGAAATTGGTACTTCA 60.117 43.478 0.00 0.00 0.00 3.02
2444 3810 5.081032 TCGAAAATAAAACTTGATGGGGGT 58.919 37.500 0.00 0.00 0.00 4.95
2465 3831 3.705604 ACAATGCAAAAACTTGGTCTCG 58.294 40.909 0.00 0.00 0.00 4.04
2466 3832 6.701400 ACAATACAATGCAAAAACTTGGTCTC 59.299 34.615 0.00 0.00 0.00 3.36
2683 4221 6.998802 AGGGACTGTCATAATGTATAGAAGC 58.001 40.000 10.38 0.00 37.18 3.86
2714 4252 7.041107 GGGTTCATGAATTATTAAAGCAGCAA 58.959 34.615 12.12 0.00 0.00 3.91
2741 4281 3.417101 CTGGGTTATGCAGTGGTTTACA 58.583 45.455 0.00 0.00 0.00 2.41
2761 4301 0.892755 TGGACGAATCTAACACCGCT 59.107 50.000 0.00 0.00 0.00 5.52
2773 4313 9.996554 ATATTGTTATCATAAGTGATGGACGAA 57.003 29.630 0.00 0.43 44.62 3.85
2775 4315 9.208022 ACATATTGTTATCATAAGTGATGGACG 57.792 33.333 1.37 0.00 44.62 4.79
2790 4330 7.720957 TCAGCTGGCTATTCAACATATTGTTAT 59.279 33.333 15.13 0.00 38.77 1.89
2791 4331 7.053498 TCAGCTGGCTATTCAACATATTGTTA 58.947 34.615 15.13 0.00 38.77 2.41
2792 4332 5.887598 TCAGCTGGCTATTCAACATATTGTT 59.112 36.000 15.13 0.00 42.08 2.83
2793 4333 5.439721 TCAGCTGGCTATTCAACATATTGT 58.560 37.500 15.13 0.00 37.11 2.71
2794 4334 6.381481 TTCAGCTGGCTATTCAACATATTG 57.619 37.500 15.13 0.00 37.14 1.90
2795 4335 6.604795 ACTTTCAGCTGGCTATTCAACATATT 59.395 34.615 15.13 0.00 0.00 1.28
2796 4336 6.039047 CACTTTCAGCTGGCTATTCAACATAT 59.961 38.462 15.13 0.00 0.00 1.78
2797 4337 5.355071 CACTTTCAGCTGGCTATTCAACATA 59.645 40.000 15.13 0.00 0.00 2.29
2798 4338 4.157289 CACTTTCAGCTGGCTATTCAACAT 59.843 41.667 15.13 0.00 0.00 2.71
2799 4339 3.503363 CACTTTCAGCTGGCTATTCAACA 59.497 43.478 15.13 0.00 0.00 3.33
2800 4340 3.753272 TCACTTTCAGCTGGCTATTCAAC 59.247 43.478 15.13 0.00 0.00 3.18
2807 4347 1.141657 TCAGTTCACTTTCAGCTGGCT 59.858 47.619 15.13 0.00 0.00 4.75
2809 4349 1.534595 GCTCAGTTCACTTTCAGCTGG 59.465 52.381 15.13 0.00 0.00 4.85
2815 4355 3.748048 TGTAGCATGCTCAGTTCACTTTC 59.252 43.478 26.57 0.00 0.00 2.62
2837 4377 8.752187 TCTACCGTACCAAACTAGATATTTTGT 58.248 33.333 0.00 0.00 31.86 2.83
2884 4424 7.607250 TGAACAAGACAATACAAAAACTTGGT 58.393 30.769 0.00 0.00 38.93 3.67
2939 4480 5.124457 CCCCAAGATTCTAATGTCAACACTG 59.876 44.000 0.00 0.00 0.00 3.66
2962 4503 3.366985 GGGTGCTACAAACTGTAATTGCC 60.367 47.826 0.00 0.00 31.67 4.52
2983 4524 8.962679 GTACCACATCTAGGAGAATATCTTAGG 58.037 40.741 0.00 0.00 38.00 2.69
2984 4525 9.521841 TGTACCACATCTAGGAGAATATCTTAG 57.478 37.037 0.00 0.00 38.62 2.18
2995 4536 5.586877 AGGTTTACTGTACCACATCTAGGA 58.413 41.667 2.79 0.00 38.16 2.94
3007 4548 3.517612 AGAGCTGGGAAGGTTTACTGTA 58.482 45.455 0.00 0.00 0.00 2.74
3035 4576 2.557056 CGACACACTAGAGAGTTCCCAA 59.443 50.000 0.00 0.00 31.73 4.12
3036 4577 2.160205 CGACACACTAGAGAGTTCCCA 58.840 52.381 0.00 0.00 31.73 4.37
3049 4590 4.681025 TGGTAAGAAACGTAATCGACACAC 59.319 41.667 0.00 0.00 40.62 3.82
3055 4596 7.025963 AGACTAACTGGTAAGAAACGTAATCG 58.974 38.462 0.00 0.00 43.34 3.34
3061 4602 5.756833 ACCAAAGACTAACTGGTAAGAAACG 59.243 40.000 2.68 0.00 41.72 3.60
3076 4617 6.852420 TGTATAGAAGTAGCACCAAAGACT 57.148 37.500 0.00 0.00 0.00 3.24
3114 4655 5.650266 ACCGTCATAATGTATTTTCCAAGCA 59.350 36.000 0.00 0.00 0.00 3.91
3125 5198 2.950975 TGCTACCGACCGTCATAATGTA 59.049 45.455 0.00 0.00 0.00 2.29
3140 5348 2.678336 CTCTTCCGGTTTTGATGCTACC 59.322 50.000 0.00 0.00 0.00 3.18
3185 5394 4.046286 TGGGTCATGGCAGTTATTTTCT 57.954 40.909 0.00 0.00 0.00 2.52
3265 5474 9.891828 CTGCACAAACAGTATATAACTCAAAAA 57.108 29.630 0.00 0.00 35.76 1.94
3266 5475 9.278978 TCTGCACAAACAGTATATAACTCAAAA 57.721 29.630 0.00 0.00 35.76 2.44
3267 5476 8.840833 TCTGCACAAACAGTATATAACTCAAA 57.159 30.769 0.00 0.00 35.76 2.69
3268 5477 9.448438 AATCTGCACAAACAGTATATAACTCAA 57.552 29.630 0.00 0.00 35.76 3.02
3269 5478 8.882736 CAATCTGCACAAACAGTATATAACTCA 58.117 33.333 0.00 0.00 35.76 3.41
3270 5479 7.852945 GCAATCTGCACAAACAGTATATAACTC 59.147 37.037 0.00 0.00 44.26 3.01
3271 5480 7.697691 GCAATCTGCACAAACAGTATATAACT 58.302 34.615 0.00 0.00 44.26 2.24
3272 5481 7.898725 GCAATCTGCACAAACAGTATATAAC 57.101 36.000 0.00 0.00 44.26 1.89
3317 5526 4.107072 TCTGGGTTCTCCTGAAGAATCAT 58.893 43.478 0.94 0.00 45.51 2.45
3371 5580 1.067495 AGAGTTTACAGTCTCTGGCGC 60.067 52.381 0.00 0.00 39.23 6.53
3414 5626 2.835156 AGAGGGGCAGAAGAAGAGTTAC 59.165 50.000 0.00 0.00 0.00 2.50
3656 5868 6.410540 AGGATAACAAAGCTGAGTCTTAAGG 58.589 40.000 1.85 0.00 0.00 2.69
3662 5874 3.190874 CCGAGGATAACAAAGCTGAGTC 58.809 50.000 0.00 0.00 0.00 3.36
3670 5882 5.408880 TCATACACACCGAGGATAACAAA 57.591 39.130 0.00 0.00 0.00 2.83
3742 5954 8.970691 ATTACTAGCACAAATCAAATGACAAC 57.029 30.769 0.00 0.00 0.00 3.32
3798 6010 1.741706 CGGTACCACTACAGACGACAT 59.258 52.381 13.54 0.00 0.00 3.06
3817 6030 1.331756 GGAGATACATTTGGCTGCACG 59.668 52.381 0.50 0.00 0.00 5.34
3862 6075 2.670789 GCGCCAGTGATTTGTGCATAAA 60.671 45.455 11.24 11.24 0.00 1.40
3863 6076 1.135431 GCGCCAGTGATTTGTGCATAA 60.135 47.619 0.00 0.00 0.00 1.90
3933 6146 3.918270 ACTTGGGGCCTAAAAGTACCTTA 59.082 43.478 15.14 0.00 32.48 2.69
3951 6166 6.029607 CGTCATCAATACCAAAATCCACTTG 58.970 40.000 0.00 0.00 0.00 3.16
3956 6171 4.335315 TGCTCGTCATCAATACCAAAATCC 59.665 41.667 0.00 0.00 0.00 3.01
3994 6209 8.477419 TCTGATTTTTCAAACTTAAGGGTCAT 57.523 30.769 7.53 0.00 0.00 3.06
4010 6225 5.355350 CGCTCTTGGGACTAATCTGATTTTT 59.645 40.000 8.38 0.00 0.00 1.94
4011 6226 4.878397 CGCTCTTGGGACTAATCTGATTTT 59.122 41.667 8.38 0.00 0.00 1.82
4043 6258 6.617317 GCATACAAGCAAGCAATAGATACTCG 60.617 42.308 0.00 0.00 0.00 4.18
4093 6331 8.491331 TTTTTAAGCAAATTTAGGGATGCATC 57.509 30.769 18.81 18.81 41.18 3.91
4196 6510 6.897259 ATTTGTATTGCAATGCTTGATGTC 57.103 33.333 24.99 5.23 36.89 3.06
4281 6595 9.788960 TTGTAATATATGAGTGATCGCTATGAC 57.211 33.333 9.20 2.82 0.00 3.06
4316 6630 9.961265 GCATCATCTTATTCTTTCATTTGATCA 57.039 29.630 0.00 0.00 0.00 2.92
4411 6727 1.226018 GAAGAATTTCGCGGGCACG 60.226 57.895 2.50 2.50 44.63 5.34
4422 6738 6.648192 AGATTGACATCTTCTCCGAAGAATT 58.352 36.000 10.02 1.16 40.68 2.17
4469 6787 2.124695 CCGGCTGGTTCTTAGGCC 60.125 66.667 2.29 0.00 41.02 5.19
4562 6880 3.165875 GGACTCAATCGGGAGGATCATA 58.834 50.000 0.00 0.00 39.27 2.15
4595 6913 8.792830 TCGAAGTTCCTGATTCTTTCAATAAT 57.207 30.769 0.00 0.00 32.78 1.28
4643 6961 2.231235 CGGGTAAGATTTGCCAAAAGCT 59.769 45.455 0.00 0.00 43.74 3.74
4644 6962 2.606108 CGGGTAAGATTTGCCAAAAGC 58.394 47.619 0.00 0.00 44.14 3.51
4645 6963 2.094234 CCCGGGTAAGATTTGCCAAAAG 60.094 50.000 14.18 0.00 37.12 2.27
4649 6967 0.034863 GTCCCGGGTAAGATTTGCCA 60.035 55.000 22.86 0.00 37.12 4.92
4651 6969 1.092348 GTGTCCCGGGTAAGATTTGC 58.908 55.000 22.86 1.44 0.00 3.68
4652 6970 2.483014 TGTGTCCCGGGTAAGATTTG 57.517 50.000 22.86 0.00 0.00 2.32
4653 6971 3.732048 ATTGTGTCCCGGGTAAGATTT 57.268 42.857 22.86 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.