Multiple sequence alignment - TraesCS7A01G379000

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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 TraesCS7A01G379000 chr7A 100.000 3306 0 0 402 3707 554492141 554488836 0.000000e+00 6106.0
1 TraesCS7A01G379000 chr7A 100.000 179 0 0 1 179 554492542 554492364 7.670000e-87 331.0
2 TraesCS7A01G379000 chr7A 77.823 496 100 8 2272 2762 554501563 554501073 7.780000e-77 298.0
3 TraesCS7A01G379000 chr7A 97.561 41 1 0 572 612 171417942 171417902 1.850000e-08 71.3
4 TraesCS7A01G379000 chr7B 90.884 2918 178 42 842 3707 513771728 513768847 0.000000e+00 3834.0
5 TraesCS7A01G379000 chr7B 76.185 886 178 22 996 1857 516445677 516444801 1.580000e-118 436.0
6 TraesCS7A01G379000 chr7B 78.895 507 96 11 2246 2748 513956853 513956354 2.130000e-87 333.0
7 TraesCS7A01G379000 chr7B 91.579 95 5 1 3269 3360 222691770 222691676 1.080000e-25 128.0
8 TraesCS7A01G379000 chr7D 90.265 1356 89 16 842 2173 486108099 486106763 0.000000e+00 1733.0
9 TraesCS7A01G379000 chr7D 88.861 1185 75 23 2254 3390 486106768 486105593 0.000000e+00 1404.0
10 TraesCS7A01G379000 chr7D 76.962 790 136 29 1092 1857 486242830 486242063 3.450000e-110 409.0
11 TraesCS7A01G379000 chr7D 78.107 507 100 10 2246 2748 486167747 486167248 1.000000e-80 311.0
12 TraesCS7A01G379000 chr7D 91.667 216 17 1 407 621 486108894 486108679 7.780000e-77 298.0
13 TraesCS7A01G379000 chr7D 89.412 170 13 1 3404 3573 486105609 486105445 3.750000e-50 209.0
14 TraesCS7A01G379000 chr7D 88.554 166 11 5 678 840 486108687 486108527 1.050000e-45 195.0
15 TraesCS7A01G379000 chr7D 83.851 161 19 2 9 168 486109400 486109246 2.980000e-31 147.0
16 TraesCS7A01G379000 chr7D 92.771 83 1 1 3630 3707 486105448 486105366 8.410000e-22 115.0
17 TraesCS7A01G379000 chr2A 79.859 427 82 4 2272 2696 137564458 137564034 3.600000e-80 309.0
18 TraesCS7A01G379000 chr6A 73.233 863 174 31 1013 1838 522044504 522045346 1.020000e-65 261.0
19 TraesCS7A01G379000 chr6A 84.028 144 20 3 1018 1158 610509692 610509835 6.460000e-28 135.0
20 TraesCS7A01G379000 chr6A 100.000 42 0 0 571 612 2149903 2149862 1.100000e-10 78.7
21 TraesCS7A01G379000 chr6A 97.619 42 1 0 571 612 448060451 448060492 5.140000e-09 73.1
22 TraesCS7A01G379000 chr6A 92.857 42 3 0 571 612 470895691 470895650 1.110000e-05 62.1
23 TraesCS7A01G379000 chr6B 80.571 350 52 9 1013 1360 567844228 567844563 4.750000e-64 255.0
24 TraesCS7A01G379000 chr6B 77.551 343 59 10 1029 1359 707315875 707316211 1.360000e-44 191.0
25 TraesCS7A01G379000 chr6D 79.943 349 56 8 1013 1360 380565585 380565920 1.030000e-60 244.0
26 TraesCS7A01G379000 chr6D 79.083 349 58 11 1015 1360 380495590 380495926 3.730000e-55 226.0
27 TraesCS7A01G379000 chr6D 80.172 232 34 10 1045 1272 470301975 470301752 2.960000e-36 163.0
28 TraesCS7A01G379000 chr3D 78.698 338 63 8 1039 1367 44203447 44203784 2.240000e-52 217.0
29 TraesCS7A01G379000 chr3D 95.294 85 4 0 3262 3346 548393400 548393316 6.460000e-28 135.0
30 TraesCS7A01G379000 chr3A 96.703 91 2 1 3248 3337 685288972 685288882 2.310000e-32 150.0
31 TraesCS7A01G379000 chr1D 96.250 80 3 0 3257 3336 68453727 68453806 8.350000e-27 132.0
32 TraesCS7A01G379000 chr1B 96.250 80 3 0 3257 3336 109738086 109738165 8.350000e-27 132.0
33 TraesCS7A01G379000 chr1B 91.304 69 4 1 620 686 142039722 142039654 3.940000e-15 93.5
34 TraesCS7A01G379000 chr2B 91.579 95 5 2 3269 3360 166858069 166858163 1.080000e-25 128.0
35 TraesCS7A01G379000 chr2B 91.579 95 5 2 3269 3360 166863508 166863602 1.080000e-25 128.0
36 TraesCS7A01G379000 chr2B 87.671 73 8 1 620 691 766079470 766079398 2.370000e-12 84.2
37 TraesCS7A01G379000 chr3B 87.500 80 8 1 613 690 822831586 822831665 1.420000e-14 91.6
38 TraesCS7A01G379000 chr5A 86.905 84 6 5 605 685 598636634 598636553 5.100000e-14 89.8
39 TraesCS7A01G379000 chr5B 89.706 68 5 1 620 687 532310422 532310487 6.600000e-13 86.1
40 TraesCS7A01G379000 chr5B 89.130 46 4 1 572 617 472063417 472063373 5.170000e-04 56.5
41 TraesCS7A01G379000 chr4A 88.000 75 5 1 620 690 666015311 666015237 6.600000e-13 86.1
42 TraesCS7A01G379000 chr2D 84.211 95 7 6 620 710 349603125 349603035 6.600000e-13 86.1
43 TraesCS7A01G379000 chr2D 87.671 73 7 1 616 688 58839271 58839201 2.370000e-12 84.2
44 TraesCS7A01G379000 chr4D 87.838 74 6 2 617 689 73330324 73330395 2.370000e-12 84.2


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 TraesCS7A01G379000 chr7A 554488836 554492542 3706 True 3218.500000 6106 100.000000 1 3707 2 chr7A.!!$R3 3706
1 TraesCS7A01G379000 chr7B 513768847 513771728 2881 True 3834.000000 3834 90.884000 842 3707 1 chr7B.!!$R2 2865
2 TraesCS7A01G379000 chr7B 516444801 516445677 876 True 436.000000 436 76.185000 996 1857 1 chr7B.!!$R4 861
3 TraesCS7A01G379000 chr7D 486105366 486109400 4034 True 585.857143 1733 89.340143 9 3707 7 chr7D.!!$R3 3698
4 TraesCS7A01G379000 chr7D 486242063 486242830 767 True 409.000000 409 76.962000 1092 1857 1 chr7D.!!$R2 765
5 TraesCS7A01G379000 chr6A 522044504 522045346 842 False 261.000000 261 73.233000 1013 1838 1 chr6A.!!$F2 825

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
137 139 0.167251 GTTCGGGTTGTAACATGCCG 59.833 55.0 0.0 0.0 34.10 5.69 F
149 151 0.596082 ACATGCCGGTACAAAAGCAC 59.404 50.0 1.9 0.0 38.21 4.40 F
1440 2008 0.612174 AGTGCCTCTCGCTGTCCTTA 60.612 55.0 0.0 0.0 38.78 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2300 0.746659 GCAATAGGCGGCTCCAAAAT 59.253 50.0 17.67 0.00 37.29 1.82 R
2010 2613 0.839946 AAGGCCAATATCCTGACGCT 59.160 50.0 5.01 0.00 33.43 5.07 R
3052 3691 0.459934 CCTAGCTCTGTGCAGTCTGC 60.460 60.0 18.32 18.32 45.94 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.813724 GGTCTTTTAGGCCGGCTTTATAG 59.186 47.826 28.56 17.19 25.77 1.31
51 52 4.162698 TCTTTTAGGCCGGCTTTATAGTGA 59.837 41.667 28.56 12.38 0.00 3.41
55 56 3.898482 AGGCCGGCTTTATAGTGAAATT 58.102 40.909 28.56 0.00 0.00 1.82
60 61 5.374071 CCGGCTTTATAGTGAAATTAGGGT 58.626 41.667 0.00 0.00 0.00 4.34
61 62 5.826208 CCGGCTTTATAGTGAAATTAGGGTT 59.174 40.000 0.00 0.00 0.00 4.11
64 65 6.831868 GGCTTTATAGTGAAATTAGGGTTGGA 59.168 38.462 0.00 0.00 0.00 3.53
65 66 7.013369 GGCTTTATAGTGAAATTAGGGTTGGAG 59.987 40.741 0.00 0.00 0.00 3.86
66 67 7.773690 GCTTTATAGTGAAATTAGGGTTGGAGA 59.226 37.037 0.00 0.00 0.00 3.71
67 68 9.853177 CTTTATAGTGAAATTAGGGTTGGAGAT 57.147 33.333 0.00 0.00 0.00 2.75
76 77 2.823959 AGGGTTGGAGATACGGTTACA 58.176 47.619 0.00 0.00 0.00 2.41
84 85 3.382546 GGAGATACGGTTACAACTAGCCA 59.617 47.826 0.00 0.00 0.00 4.75
87 88 4.708421 AGATACGGTTACAACTAGCCAAGA 59.292 41.667 0.00 0.00 0.00 3.02
88 89 3.756933 ACGGTTACAACTAGCCAAGAA 57.243 42.857 0.00 0.00 0.00 2.52
93 95 5.209977 GGTTACAACTAGCCAAGAAAAACG 58.790 41.667 0.00 0.00 0.00 3.60
108 110 0.256464 AAACGGGAGGGTCAACACAA 59.744 50.000 0.00 0.00 0.00 3.33
109 111 0.476771 AACGGGAGGGTCAACACAAT 59.523 50.000 0.00 0.00 0.00 2.71
137 139 0.167251 GTTCGGGTTGTAACATGCCG 59.833 55.000 0.00 0.00 34.10 5.69
149 151 0.596082 ACATGCCGGTACAAAAGCAC 59.404 50.000 1.90 0.00 38.21 4.40
153 155 0.732538 GCCGGTACAAAAGCACATGC 60.733 55.000 1.90 0.00 42.49 4.06
170 172 3.879912 GCTCTTGCAATGTTGTGCT 57.120 47.368 0.00 0.00 45.17 4.40
171 173 2.144482 GCTCTTGCAATGTTGTGCTT 57.856 45.000 0.00 0.00 45.17 3.91
172 174 3.287312 GCTCTTGCAATGTTGTGCTTA 57.713 42.857 0.00 0.00 45.17 3.09
173 175 2.982470 GCTCTTGCAATGTTGTGCTTAC 59.018 45.455 0.00 0.00 45.17 2.34
174 176 3.550639 GCTCTTGCAATGTTGTGCTTACA 60.551 43.478 0.00 0.00 45.17 2.41
176 178 3.882288 TCTTGCAATGTTGTGCTTACAGA 59.118 39.130 0.00 0.00 45.17 3.41
178 180 4.227512 TGCAATGTTGTGCTTACAGAAG 57.772 40.909 0.00 0.00 45.17 2.85
431 546 7.568199 ACCATAGGTACAAATTAGTCAATGC 57.432 36.000 0.00 0.00 32.11 3.56
442 557 8.227791 ACAAATTAGTCAATGCTAGTGTTTACG 58.772 33.333 0.00 0.00 0.00 3.18
467 583 6.092807 GGTTGAGATGAACCTAGCTAAAAGTG 59.907 42.308 0.00 0.00 42.03 3.16
481 597 6.543735 AGCTAAAAGTGTACTCCCTTCATTT 58.456 36.000 0.00 0.00 0.00 2.32
626 742 9.213777 TGACATGTATCTAGAAAAATACTCCCT 57.786 33.333 0.00 0.00 31.11 4.20
627 743 9.699703 GACATGTATCTAGAAAAATACTCCCTC 57.300 37.037 0.00 0.00 31.11 4.30
628 744 8.652290 ACATGTATCTAGAAAAATACTCCCTCC 58.348 37.037 0.00 0.00 31.11 4.30
629 745 8.651389 CATGTATCTAGAAAAATACTCCCTCCA 58.349 37.037 0.00 0.00 31.11 3.86
630 746 8.798975 TGTATCTAGAAAAATACTCCCTCCAT 57.201 34.615 0.00 0.00 31.11 3.41
631 747 8.871125 TGTATCTAGAAAAATACTCCCTCCATC 58.129 37.037 0.00 0.00 31.11 3.51
632 748 9.095700 GTATCTAGAAAAATACTCCCTCCATCT 57.904 37.037 0.00 0.00 0.00 2.90
633 749 7.996758 TCTAGAAAAATACTCCCTCCATCTT 57.003 36.000 0.00 0.00 0.00 2.40
634 750 9.676129 ATCTAGAAAAATACTCCCTCCATCTTA 57.324 33.333 0.00 0.00 0.00 2.10
635 751 9.676129 TCTAGAAAAATACTCCCTCCATCTTAT 57.324 33.333 0.00 0.00 0.00 1.73
645 761 8.196378 ACTCCCTCCATCTTATAATGTAAGAC 57.804 38.462 1.55 0.00 36.51 3.01
646 762 7.039644 ACTCCCTCCATCTTATAATGTAAGACG 60.040 40.741 1.55 0.00 36.51 4.18
647 763 6.781014 TCCCTCCATCTTATAATGTAAGACGT 59.219 38.462 1.55 0.00 36.51 4.34
648 764 7.289317 TCCCTCCATCTTATAATGTAAGACGTT 59.711 37.037 1.55 0.00 36.51 3.99
649 765 7.931948 CCCTCCATCTTATAATGTAAGACGTTT 59.068 37.037 1.55 0.00 36.51 3.60
650 766 9.326413 CCTCCATCTTATAATGTAAGACGTTTT 57.674 33.333 1.55 0.00 36.51 2.43
673 789 8.642935 TTTTTGACATGTCTTACATTATGGGA 57.357 30.769 25.55 0.00 36.53 4.37
674 790 7.624360 TTTGACATGTCTTACATTATGGGAC 57.376 36.000 25.55 3.17 36.53 4.46
675 791 5.356426 TGACATGTCTTACATTATGGGACG 58.644 41.667 25.55 0.00 36.53 4.79
676 792 4.703897 ACATGTCTTACATTATGGGACGG 58.296 43.478 0.00 2.33 36.53 4.79
677 793 4.407621 ACATGTCTTACATTATGGGACGGA 59.592 41.667 0.00 0.00 36.53 4.69
679 795 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
682 798 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
696 812 5.148502 ACGGAGGGAGTAGATGTCAATAAT 58.851 41.667 0.00 0.00 0.00 1.28
698 814 6.781014 ACGGAGGGAGTAGATGTCAATAATAA 59.219 38.462 0.00 0.00 0.00 1.40
699 815 7.039644 ACGGAGGGAGTAGATGTCAATAATAAG 60.040 40.741 0.00 0.00 0.00 1.73
701 817 9.041354 GGAGGGAGTAGATGTCAATAATAAGAT 57.959 37.037 0.00 0.00 0.00 2.40
729 845 4.868314 ATCCATTAGGTCGTAGCTAACC 57.132 45.455 6.50 6.50 40.47 2.85
734 850 5.878669 CCATTAGGTCGTAGCTAACCTTTTT 59.121 40.000 19.83 5.45 43.45 1.94
807 923 8.810041 TCCTTTACTGTAAACTAGAGGGTTTAG 58.190 37.037 8.84 0.00 40.75 1.85
813 929 8.121185 ACTGTAAACTAGAGGGTTTAGATACCT 58.879 37.037 0.00 0.00 40.75 3.08
815 931 5.873146 AACTAGAGGGTTTAGATACCTGC 57.127 43.478 0.00 0.00 38.30 4.85
817 933 5.278061 ACTAGAGGGTTTAGATACCTGCAA 58.722 41.667 0.00 0.00 38.30 4.08
897 1439 7.939784 AATTCCTAAAAACGAGCTTATTCCT 57.060 32.000 0.00 0.00 0.00 3.36
1098 1640 1.175347 TCCTCCGCCAGATCATCTCG 61.175 60.000 0.00 0.00 0.00 4.04
1237 1785 0.961358 CTCCGTTGTCCGAGTCCTCT 60.961 60.000 0.00 0.00 39.56 3.69
1287 1835 4.007644 CTCACCGACTGCAGGCCA 62.008 66.667 19.93 0.00 0.00 5.36
1292 1840 3.774528 CGACTGCAGGCCAGCCTA 61.775 66.667 18.54 0.00 46.28 3.93
1369 1917 3.400255 GAACTCGCCCTCTTTAACAAGT 58.600 45.455 0.00 0.00 0.00 3.16
1370 1918 4.562143 GGAACTCGCCCTCTTTAACAAGTA 60.562 45.833 0.00 0.00 0.00 2.24
1371 1919 3.922910 ACTCGCCCTCTTTAACAAGTAC 58.077 45.455 0.00 0.00 0.00 2.73
1372 1920 3.577415 ACTCGCCCTCTTTAACAAGTACT 59.423 43.478 0.00 0.00 0.00 2.73
1409 1977 4.933064 CGCCGACATCCTCCGCTC 62.933 72.222 0.00 0.00 0.00 5.03
1440 2008 0.612174 AGTGCCTCTCGCTGTCCTTA 60.612 55.000 0.00 0.00 38.78 2.69
1511 2085 1.630148 CTCCGGAAACTCGACATGAC 58.370 55.000 5.23 0.00 0.00 3.06
1648 2225 2.844451 CGGTGTGTGCTTGTTGGGG 61.844 63.158 0.00 0.00 0.00 4.96
1705 2300 1.260538 ACTCTTGGAGCGCCTCATCA 61.261 55.000 8.34 0.00 32.04 3.07
1815 2416 3.137446 AGAGTTCACAAGCTGCAGATT 57.863 42.857 20.43 16.35 0.00 2.40
1861 2463 3.073062 GCTACCTCTCCATCTCTCTCTCT 59.927 52.174 0.00 0.00 0.00 3.10
1862 2464 3.864789 ACCTCTCCATCTCTCTCTCTC 57.135 52.381 0.00 0.00 0.00 3.20
1885 2487 7.330946 TCTCAACCTGTGAAATTATTCAGTACG 59.669 37.037 0.00 0.00 45.88 3.67
1887 2489 5.488341 ACCTGTGAAATTATTCAGTACGCT 58.512 37.500 0.00 0.00 45.88 5.07
1913 2515 7.198306 TGATCCATCAATCATGATTTTCTCG 57.802 36.000 18.41 7.24 43.89 4.04
1937 2539 7.638295 TCGATGATTATTGAACATTTAACGTGC 59.362 33.333 0.00 0.00 0.00 5.34
1938 2540 7.355593 CGATGATTATTGAACATTTAACGTGCG 60.356 37.037 0.00 0.00 0.00 5.34
1939 2541 5.509972 TGATTATTGAACATTTAACGTGCGC 59.490 36.000 0.00 0.00 0.00 6.09
1940 2542 3.552604 ATTGAACATTTAACGTGCGCT 57.447 38.095 9.73 0.00 0.00 5.92
1941 2543 4.671880 ATTGAACATTTAACGTGCGCTA 57.328 36.364 9.73 0.00 0.00 4.26
1943 2545 4.253352 TGAACATTTAACGTGCGCTATC 57.747 40.909 9.73 0.00 0.00 2.08
1945 2547 4.390603 TGAACATTTAACGTGCGCTATCTT 59.609 37.500 9.73 0.00 0.00 2.40
1957 2560 5.172591 CGTGCGCTATCTTATCTTTTTCGTA 59.827 40.000 9.73 0.00 0.00 3.43
1963 2566 7.096023 CGCTATCTTATCTTTTTCGTAGTGCAT 60.096 37.037 0.00 0.00 0.00 3.96
1964 2567 8.006590 GCTATCTTATCTTTTTCGTAGTGCATG 58.993 37.037 0.00 0.00 0.00 4.06
1965 2568 9.249457 CTATCTTATCTTTTTCGTAGTGCATGA 57.751 33.333 0.00 0.00 0.00 3.07
2010 2613 1.073025 AGATGCGCTGTGGTTCCAA 59.927 52.632 9.73 0.00 0.00 3.53
2055 2658 4.832248 AGTGAATTTCCGTATCTTCAGCA 58.168 39.130 0.00 0.00 0.00 4.41
2082 2685 4.432685 AAGATGCTAGCCAGCTTCCTCG 62.433 54.545 13.29 0.00 46.61 4.63
2107 2710 2.659428 CTTCCCCAACATCTCAATCCC 58.341 52.381 0.00 0.00 0.00 3.85
2108 2711 1.679981 TCCCCAACATCTCAATCCCA 58.320 50.000 0.00 0.00 0.00 4.37
2132 2737 6.875726 CACACATTGAGGTATATATCACCCAG 59.124 42.308 0.00 0.00 36.67 4.45
2156 2761 4.887748 TCCTTCAGTCAGTCAGTCATTTC 58.112 43.478 0.00 0.00 0.00 2.17
2158 2763 4.302455 CTTCAGTCAGTCAGTCATTTCGT 58.698 43.478 0.00 0.00 0.00 3.85
2256 2862 3.065371 GGCACCAGACACAATGCTATAAC 59.935 47.826 0.00 0.00 38.18 1.89
2263 2869 6.036083 CCAGACACAATGCTATAACACTGTAC 59.964 42.308 0.00 0.00 0.00 2.90
2270 2876 7.442364 ACAATGCTATAACACTGTACATCATCC 59.558 37.037 0.00 0.00 0.00 3.51
2292 2898 7.024345 TCCTGATCCATATATGCAACTGAAT 57.976 36.000 7.24 0.00 0.00 2.57
2337 2944 1.227380 GTCTGCCCTACATGCTCCG 60.227 63.158 0.00 0.00 0.00 4.63
2341 2948 2.731571 GCCCTACATGCTCCGTCCA 61.732 63.158 0.00 0.00 0.00 4.02
2392 2999 0.473694 TGCCAAGTTCTGGGAGGAGA 60.474 55.000 0.00 0.00 46.54 3.71
2405 3012 2.102252 GGGAGGAGATCAGTGCAGTTAG 59.898 54.545 0.00 0.00 0.00 2.34
2421 3028 3.935203 CAGTTAGATGCTGGAAATCACGT 59.065 43.478 0.00 0.00 0.00 4.49
2530 3137 1.823470 TCTTTGCTGCTTGTGCCGT 60.823 52.632 0.00 0.00 38.71 5.68
2535 3142 2.551270 CTGCTTGTGCCGTTCGAC 59.449 61.111 0.00 0.00 38.71 4.20
2541 3148 0.725686 TTGTGCCGTTCGACGAAAAA 59.274 45.000 12.67 0.00 46.05 1.94
2556 3163 4.533222 ACGAAAAATTTACTTCAGCGGTG 58.467 39.130 8.67 8.67 0.00 4.94
2571 3178 1.407437 GCGGTGGAGGTGAATGAGATT 60.407 52.381 0.00 0.00 0.00 2.40
2582 3189 8.034215 GGAGGTGAATGAGATTATAGACAGATG 58.966 40.741 0.00 0.00 0.00 2.90
2584 3191 7.015974 AGGTGAATGAGATTATAGACAGATGCA 59.984 37.037 0.00 0.00 0.00 3.96
2600 3207 0.836606 TGCAGGTGTCCTCAGTTTCA 59.163 50.000 0.00 0.00 0.00 2.69
2634 3241 3.660111 GTGTTGCTGGTGTCGCCC 61.660 66.667 0.00 0.00 36.04 6.13
2719 3326 2.230892 TGCTGAACGCACGGTTTAG 58.769 52.632 0.00 0.00 45.47 1.85
2756 3363 4.019174 ACATGATTGATCCGAGCCTTTTT 58.981 39.130 0.00 0.00 0.00 1.94
2797 3404 7.849804 AGTTATGCATTTTCTTGAGATACGT 57.150 32.000 3.54 0.00 0.00 3.57
2800 3407 6.741992 ATGCATTTTCTTGAGATACGTCAA 57.258 33.333 0.00 0.00 35.16 3.18
2833 3440 8.893727 AGTTTTCAACTACCATTAGCATACATC 58.106 33.333 0.00 0.00 40.69 3.06
2850 3457 8.454106 AGCATACATCTATGTTTCAACTTTCAC 58.546 33.333 0.12 0.00 41.97 3.18
2856 3463 7.074653 TCTATGTTTCAACTTTCACCTACCT 57.925 36.000 0.00 0.00 0.00 3.08
2857 3464 7.514721 TCTATGTTTCAACTTTCACCTACCTT 58.485 34.615 0.00 0.00 0.00 3.50
2858 3465 5.828299 TGTTTCAACTTTCACCTACCTTG 57.172 39.130 0.00 0.00 0.00 3.61
2859 3466 5.258051 TGTTTCAACTTTCACCTACCTTGT 58.742 37.500 0.00 0.00 0.00 3.16
2860 3467 5.355910 TGTTTCAACTTTCACCTACCTTGTC 59.644 40.000 0.00 0.00 0.00 3.18
2861 3468 4.081322 TCAACTTTCACCTACCTTGTCC 57.919 45.455 0.00 0.00 0.00 4.02
2880 3490 7.228706 CCTTGTCCTTGAGTACATTTTAGTGTT 59.771 37.037 0.00 0.00 33.62 3.32
2903 3513 9.179909 TGTTCTGAAAAGACCAGTGTTATTTAA 57.820 29.630 0.00 0.00 33.57 1.52
2910 3520 8.983702 AAAGACCAGTGTTATTTAACCTGTTA 57.016 30.769 13.26 0.00 35.03 2.41
2929 3539 7.455638 ACCTGTTACCTAAAGACCAGTATTACA 59.544 37.037 0.00 0.00 0.00 2.41
2960 3570 6.649557 GTGATATAACCTACAACTATGTGGCC 59.350 42.308 0.00 0.00 40.84 5.36
2984 3621 1.050204 AGCATGTTGTTGGTTGCCAT 58.950 45.000 0.00 0.00 35.71 4.40
3010 3647 5.312895 TCTTTGCTATGCTCTGGTTTTGTA 58.687 37.500 0.00 0.00 0.00 2.41
3011 3648 5.412594 TCTTTGCTATGCTCTGGTTTTGTAG 59.587 40.000 0.00 0.00 0.00 2.74
3034 3673 1.754803 TGTCACCTCTGTCTGTTTCGT 59.245 47.619 0.00 0.00 0.00 3.85
3040 3679 2.218759 CCTCTGTCTGTTTCGTTCGTTG 59.781 50.000 0.00 0.00 0.00 4.10
3041 3680 1.591158 TCTGTCTGTTTCGTTCGTTGC 59.409 47.619 0.00 0.00 0.00 4.17
3052 3691 1.325640 CGTTCGTTGCCATCAGATGAG 59.674 52.381 12.41 3.43 0.00 2.90
3106 3745 4.424566 GCTGTGCGCCATGTTGGG 62.425 66.667 4.18 0.00 38.19 4.12
3156 3798 9.603189 ACTAATTAGCTAGTAATACCCAGTGAT 57.397 33.333 12.54 0.00 30.55 3.06
3196 3838 7.000472 TGAAATTGAGAGACAGGTTCAGAAAT 59.000 34.615 0.00 0.00 32.89 2.17
3203 3845 6.799512 AGAGACAGGTTCAGAAATTGTTTTG 58.200 36.000 3.08 0.00 0.00 2.44
3204 3846 5.351458 AGACAGGTTCAGAAATTGTTTTGC 58.649 37.500 3.08 0.00 0.00 3.68
3230 3888 3.197766 AGGATGATGGTAGAAAGCGTTCA 59.802 43.478 14.88 0.00 36.09 3.18
3241 3899 1.284657 AAGCGTTCATGATCTCTGCG 58.715 50.000 0.00 0.00 0.00 5.18
3343 4001 6.055368 GGGTTCAAATCCCACTGTCAACAG 62.055 50.000 8.59 8.59 44.05 3.16
3379 4038 7.739498 TCTTCCAGGCGTATAAAAATATTCC 57.261 36.000 0.00 0.00 0.00 3.01
3414 4073 6.431198 TTTTGGCGAGGTATATTCTGAAAC 57.569 37.500 0.00 0.00 0.00 2.78
3416 4075 5.353394 TGGCGAGGTATATTCTGAAACTT 57.647 39.130 0.00 0.00 0.00 2.66
3417 4076 5.741011 TGGCGAGGTATATTCTGAAACTTT 58.259 37.500 0.00 0.00 0.00 2.66
3418 4077 6.177610 TGGCGAGGTATATTCTGAAACTTTT 58.822 36.000 0.00 0.00 0.00 2.27
3419 4078 6.657541 TGGCGAGGTATATTCTGAAACTTTTT 59.342 34.615 0.00 0.00 0.00 1.94
3420 4079 6.967199 GGCGAGGTATATTCTGAAACTTTTTG 59.033 38.462 0.00 0.00 0.00 2.44
3421 4080 7.148306 GGCGAGGTATATTCTGAAACTTTTTGA 60.148 37.037 0.00 0.00 0.00 2.69
3422 4081 8.398665 GCGAGGTATATTCTGAAACTTTTTGAT 58.601 33.333 0.00 0.00 0.00 2.57
3423 4082 9.922305 CGAGGTATATTCTGAAACTTTTTGATC 57.078 33.333 0.00 0.00 0.00 2.92
3434 4093 8.539770 TGAAACTTTTTGATCTACTAGAGCTG 57.460 34.615 0.00 0.00 30.68 4.24
3448 4107 0.179119 GAGCTGTGCAATTGCCCATC 60.179 55.000 26.94 17.51 41.18 3.51
3449 4108 1.153509 GCTGTGCAATTGCCCATCC 60.154 57.895 26.94 12.15 41.18 3.51
3494 4153 8.436778 ACACTTTGTTATATATACAGATGGCCA 58.563 33.333 8.56 8.56 0.00 5.36
3495 4154 9.453572 CACTTTGTTATATATACAGATGGCCAT 57.546 33.333 20.96 20.96 0.00 4.40
3496 4155 9.453572 ACTTTGTTATATATACAGATGGCCATG 57.546 33.333 26.56 14.75 0.00 3.66
3575 4234 2.030958 GTTCCCCGTCGACGCAAAT 61.031 57.895 31.73 0.00 38.18 2.32
3603 4262 6.718912 AGGATCCAAAAAGAAGGAGAGAAAAG 59.281 38.462 15.82 0.00 37.34 2.27
3607 4266 8.361169 TCCAAAAAGAAGGAGAGAAAAGAAAA 57.639 30.769 0.00 0.00 0.00 2.29
3608 4267 8.251026 TCCAAAAAGAAGGAGAGAAAAGAAAAC 58.749 33.333 0.00 0.00 0.00 2.43
3609 4268 8.034804 CCAAAAAGAAGGAGAGAAAAGAAAACA 58.965 33.333 0.00 0.00 0.00 2.83
3610 4269 8.864024 CAAAAAGAAGGAGAGAAAAGAAAACAC 58.136 33.333 0.00 0.00 0.00 3.32
3651 4310 0.105760 ACACCACCCATCCAGCAAAA 60.106 50.000 0.00 0.00 0.00 2.44
3652 4311 0.604578 CACCACCCATCCAGCAAAAG 59.395 55.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.789643 TGCTATGGAATTTTAGGCCATTC 57.210 39.130 5.01 5.13 42.19 2.67
1 2 6.527423 CATTGCTATGGAATTTTAGGCCATT 58.473 36.000 5.01 0.00 42.19 3.16
2 3 6.105397 CATTGCTATGGAATTTTAGGCCAT 57.895 37.500 5.01 0.00 44.23 4.40
3 4 5.534207 CATTGCTATGGAATTTTAGGCCA 57.466 39.130 5.01 0.00 35.91 5.36
18 19 2.682563 CGGCCTAAAAGACCCATTGCTA 60.683 50.000 0.00 0.00 0.00 3.49
48 49 4.814771 CCGTATCTCCAACCCTAATTTCAC 59.185 45.833 0.00 0.00 0.00 3.18
51 52 5.446260 AACCGTATCTCCAACCCTAATTT 57.554 39.130 0.00 0.00 0.00 1.82
55 56 3.979911 TGTAACCGTATCTCCAACCCTA 58.020 45.455 0.00 0.00 0.00 3.53
60 61 4.142093 GGCTAGTTGTAACCGTATCTCCAA 60.142 45.833 0.00 0.00 0.00 3.53
61 62 3.382546 GGCTAGTTGTAACCGTATCTCCA 59.617 47.826 0.00 0.00 0.00 3.86
64 65 4.708421 TCTTGGCTAGTTGTAACCGTATCT 59.292 41.667 0.00 0.00 0.00 1.98
65 66 5.002464 TCTTGGCTAGTTGTAACCGTATC 57.998 43.478 0.00 0.00 0.00 2.24
66 67 5.410355 TTCTTGGCTAGTTGTAACCGTAT 57.590 39.130 0.00 0.00 0.00 3.06
67 68 4.870123 TTCTTGGCTAGTTGTAACCGTA 57.130 40.909 0.00 0.00 0.00 4.02
68 69 3.756933 TTCTTGGCTAGTTGTAACCGT 57.243 42.857 0.00 0.00 0.00 4.83
69 70 5.209977 GTTTTTCTTGGCTAGTTGTAACCG 58.790 41.667 0.00 0.00 0.00 4.44
76 77 3.146847 CTCCCGTTTTTCTTGGCTAGTT 58.853 45.455 0.00 0.00 0.00 2.24
84 85 2.304092 GTTGACCCTCCCGTTTTTCTT 58.696 47.619 0.00 0.00 0.00 2.52
87 88 1.341187 TGTGTTGACCCTCCCGTTTTT 60.341 47.619 0.00 0.00 0.00 1.94
88 89 0.256464 TGTGTTGACCCTCCCGTTTT 59.744 50.000 0.00 0.00 0.00 2.43
93 95 3.133901 ACAAAAATTGTGTTGACCCTCCC 59.866 43.478 0.00 0.00 43.48 4.30
108 110 3.897141 ACAACCCGAACCAACAAAAAT 57.103 38.095 0.00 0.00 0.00 1.82
109 111 4.021719 TGTTACAACCCGAACCAACAAAAA 60.022 37.500 0.00 0.00 0.00 1.94
153 155 4.023792 TCTGTAAGCACAACATTGCAAGAG 60.024 41.667 4.94 2.40 45.62 2.85
155 157 4.227512 TCTGTAAGCACAACATTGCAAG 57.772 40.909 4.94 0.00 45.62 4.01
417 532 7.692291 CCGTAAACACTAGCATTGACTAATTTG 59.308 37.037 0.00 0.00 0.00 2.32
424 539 4.449743 TCAACCGTAAACACTAGCATTGAC 59.550 41.667 0.00 0.00 0.00 3.18
427 542 4.890088 TCTCAACCGTAAACACTAGCATT 58.110 39.130 0.00 0.00 0.00 3.56
431 546 5.347907 GGTTCATCTCAACCGTAAACACTAG 59.652 44.000 0.00 0.00 36.69 2.57
442 557 6.092807 CACTTTTAGCTAGGTTCATCTCAACC 59.907 42.308 0.00 0.00 45.66 3.77
538 654 8.765219 CGAATGATTAACTGAAGGGTAGTATTG 58.235 37.037 0.00 0.00 0.00 1.90
543 659 8.712285 TTTACGAATGATTAACTGAAGGGTAG 57.288 34.615 0.00 0.00 0.00 3.18
619 735 9.310449 GTCTTACATTATAAGATGGAGGGAGTA 57.690 37.037 0.04 0.00 36.16 2.59
620 736 7.039644 CGTCTTACATTATAAGATGGAGGGAGT 60.040 40.741 7.68 0.00 37.08 3.85
621 737 7.039644 ACGTCTTACATTATAAGATGGAGGGAG 60.040 40.741 16.42 0.00 42.10 4.30
622 738 6.781014 ACGTCTTACATTATAAGATGGAGGGA 59.219 38.462 16.42 0.00 42.10 4.20
623 739 6.994221 ACGTCTTACATTATAAGATGGAGGG 58.006 40.000 16.42 1.18 42.10 4.30
624 740 8.888579 AAACGTCTTACATTATAAGATGGAGG 57.111 34.615 16.42 0.00 42.10 4.30
648 764 8.519526 GTCCCATAATGTAAGACATGTCAAAAA 58.480 33.333 27.02 10.42 37.97 1.94
649 765 7.148323 CGTCCCATAATGTAAGACATGTCAAAA 60.148 37.037 27.02 10.78 37.97 2.44
650 766 6.315144 CGTCCCATAATGTAAGACATGTCAAA 59.685 38.462 27.02 12.01 37.97 2.69
651 767 5.815222 CGTCCCATAATGTAAGACATGTCAA 59.185 40.000 27.02 12.38 37.97 3.18
652 768 5.356426 CGTCCCATAATGTAAGACATGTCA 58.644 41.667 27.02 8.04 37.97 3.58
653 769 4.750098 CCGTCCCATAATGTAAGACATGTC 59.250 45.833 18.47 18.47 37.97 3.06
654 770 4.407621 TCCGTCCCATAATGTAAGACATGT 59.592 41.667 0.00 0.00 37.97 3.21
655 771 4.956085 TCCGTCCCATAATGTAAGACATG 58.044 43.478 0.00 0.00 37.97 3.21
656 772 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
657 773 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
658 774 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
659 775 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
660 776 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
661 777 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
662 778 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
663 779 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
664 780 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
665 781 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
666 782 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
667 783 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
668 784 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
669 785 0.106167 CATCTACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
670 786 0.106116 ACATCTACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
671 787 1.320507 GACATCTACTCCCTCCGTCC 58.679 60.000 0.00 0.00 0.00 4.79
672 788 2.054232 TGACATCTACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
673 789 2.526888 TTGACATCTACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
674 790 5.730296 ATTATTGACATCTACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
675 791 8.423906 TCTTATTATTGACATCTACTCCCTCC 57.576 38.462 0.00 0.00 0.00 4.30
705 821 6.053650 GGTTAGCTACGACCTAATGGATTTT 58.946 40.000 7.28 0.00 37.04 1.82
734 850 9.751542 TCATATTCTTTGCGTTTTAAAGGAAAA 57.248 25.926 1.30 2.73 36.16 2.29
735 851 9.751542 TTCATATTCTTTGCGTTTTAAAGGAAA 57.248 25.926 1.30 0.00 36.16 3.13
736 852 9.921637 ATTCATATTCTTTGCGTTTTAAAGGAA 57.078 25.926 1.30 0.00 36.16 3.36
779 895 7.809880 ACCCTCTAGTTTACAGTAAAGGATT 57.190 36.000 5.96 0.00 0.00 3.01
880 1422 4.394729 TGACCAGGAATAAGCTCGTTTTT 58.605 39.130 0.00 0.00 0.00 1.94
897 1439 4.590553 TCCCCTGCCCACTGACCA 62.591 66.667 0.00 0.00 0.00 4.02
1287 1835 1.889530 GCTCACGGTTCAGGTAGGCT 61.890 60.000 0.00 0.00 0.00 4.58
1292 1840 2.651361 CGAGCTCACGGTTCAGGT 59.349 61.111 15.40 0.00 0.00 4.00
1371 1919 4.233635 AGGCGCGCGTAGACGTAG 62.234 66.667 32.35 0.00 42.22 3.51
1372 1920 4.228097 GAGGCGCGCGTAGACGTA 62.228 66.667 32.35 0.00 42.22 3.57
1409 1977 4.154347 GGCACTGGAGCGAGGAGG 62.154 72.222 0.00 0.00 34.64 4.30
1648 2225 2.427506 GAACTTCTCCATGGTGGACAC 58.572 52.381 12.58 0.00 42.67 3.67
1705 2300 0.746659 GCAATAGGCGGCTCCAAAAT 59.253 50.000 17.67 0.00 37.29 1.82
1815 2416 1.623311 ACCTCGATGACATTGTCACCA 59.377 47.619 21.19 7.65 45.65 4.17
1861 2463 6.128391 GCGTACTGAATAATTTCACAGGTTGA 60.128 38.462 0.00 0.00 36.94 3.18
1862 2464 6.021596 GCGTACTGAATAATTTCACAGGTTG 58.978 40.000 0.00 0.00 36.94 3.77
1913 2515 7.563296 GCGCACGTTAAATGTTCAATAATCATC 60.563 37.037 0.30 0.00 0.00 2.92
1937 2539 6.198403 TGCACTACGAAAAAGATAAGATAGCG 59.802 38.462 0.00 0.00 0.00 4.26
1938 2540 7.464830 TGCACTACGAAAAAGATAAGATAGC 57.535 36.000 0.00 0.00 0.00 2.97
1939 2541 9.249457 TCATGCACTACGAAAAAGATAAGATAG 57.751 33.333 0.00 0.00 0.00 2.08
1940 2542 9.031360 GTCATGCACTACGAAAAAGATAAGATA 57.969 33.333 0.00 0.00 0.00 1.98
1941 2543 7.549134 TGTCATGCACTACGAAAAAGATAAGAT 59.451 33.333 0.00 0.00 0.00 2.40
1943 2545 7.060600 TGTCATGCACTACGAAAAAGATAAG 57.939 36.000 0.00 0.00 0.00 1.73
1945 2547 7.609760 AATGTCATGCACTACGAAAAAGATA 57.390 32.000 0.00 0.00 0.00 1.98
1957 2560 1.816835 CAGGCTGAAATGTCATGCACT 59.183 47.619 9.42 2.78 32.65 4.40
1963 2566 2.636647 TGTGTCAGGCTGAAATGTCA 57.363 45.000 20.62 9.82 0.00 3.58
1964 2567 3.503363 TCATTGTGTCAGGCTGAAATGTC 59.497 43.478 27.19 14.89 0.00 3.06
1965 2568 3.254166 GTCATTGTGTCAGGCTGAAATGT 59.746 43.478 27.19 10.54 0.00 2.71
2010 2613 0.839946 AAGGCCAATATCCTGACGCT 59.160 50.000 5.01 0.00 33.43 5.07
2055 2658 2.706339 CTGGCTAGCATCTTGACCTT 57.294 50.000 18.24 0.00 0.00 3.50
2082 2685 1.064463 TGAGATGTTGGGGAAGCATCC 60.064 52.381 0.00 0.00 45.77 3.51
2107 2710 6.768483 TGGGTGATATATACCTCAATGTGTG 58.232 40.000 8.17 0.00 38.30 3.82
2108 2711 6.558775 ACTGGGTGATATATACCTCAATGTGT 59.441 38.462 8.17 0.00 38.30 3.72
2132 2737 3.735237 TGACTGACTGACTGAAGGAAC 57.265 47.619 0.00 0.00 0.00 3.62
2202 2808 7.523219 TGTTGTATTTCCGTCATTCATGTAAC 58.477 34.615 0.00 0.00 0.00 2.50
2270 2876 8.107399 ACAATTCAGTTGCATATATGGATCAG 57.893 34.615 14.51 7.90 41.69 2.90
2337 2944 2.084546 GGTTGATAGGCAGTTGTGGAC 58.915 52.381 0.00 0.00 0.00 4.02
2341 2948 1.705186 AGTGGGTTGATAGGCAGTTGT 59.295 47.619 0.00 0.00 0.00 3.32
2392 2999 2.502947 TCCAGCATCTAACTGCACTGAT 59.497 45.455 0.00 0.00 44.77 2.90
2405 3012 2.076100 TGACACGTGATTTCCAGCATC 58.924 47.619 25.01 5.50 0.00 3.91
2421 3028 3.117701 TGTGGAAAACCATCCTCTTGACA 60.118 43.478 0.00 0.00 40.35 3.58
2502 3109 1.072015 AGCAGCAAAGACTCAAGCTCT 59.928 47.619 0.00 0.00 34.61 4.09
2530 3137 5.134640 CGCTGAAGTAAATTTTTCGTCGAA 58.865 37.500 2.90 2.90 0.00 3.71
2535 3142 3.911964 CCACCGCTGAAGTAAATTTTTCG 59.088 43.478 0.00 0.00 0.00 3.46
2541 3148 1.628846 ACCTCCACCGCTGAAGTAAAT 59.371 47.619 0.00 0.00 0.00 1.40
2556 3163 7.531857 TCTGTCTATAATCTCATTCACCTCC 57.468 40.000 0.00 0.00 0.00 4.30
2571 3178 3.891977 GAGGACACCTGCATCTGTCTATA 59.108 47.826 18.51 0.00 37.53 1.31
2582 3189 1.876156 CTTGAAACTGAGGACACCTGC 59.124 52.381 0.00 0.00 31.76 4.85
2584 3191 1.490490 TGCTTGAAACTGAGGACACCT 59.510 47.619 0.00 0.00 36.03 4.00
2600 3207 1.355720 ACACTTTAGAGGCCCATGCTT 59.644 47.619 0.00 0.00 37.74 3.91
2634 3241 0.817634 TCCAAGCACCGTCCACTTTG 60.818 55.000 0.00 0.00 0.00 2.77
2719 3326 7.177498 TCAATCATGTGAACATATAGCGAAC 57.823 36.000 0.00 0.00 34.26 3.95
2756 3363 6.039829 TGCATAACTACAAACATGTGTTTCCA 59.960 34.615 8.09 0.00 45.54 3.53
2775 3382 7.841915 TGACGTATCTCAAGAAAATGCATAA 57.158 32.000 0.00 0.00 0.00 1.90
2833 3440 7.228706 ACAAGGTAGGTGAAAGTTGAAACATAG 59.771 37.037 0.00 0.00 0.00 2.23
2850 3457 5.422214 AATGTACTCAAGGACAAGGTAGG 57.578 43.478 0.00 0.00 0.00 3.18
2856 3463 7.990886 AGAACACTAAAATGTACTCAAGGACAA 59.009 33.333 0.00 0.00 30.75 3.18
2857 3464 7.441157 CAGAACACTAAAATGTACTCAAGGACA 59.559 37.037 0.00 0.00 30.75 4.02
2858 3465 7.656137 TCAGAACACTAAAATGTACTCAAGGAC 59.344 37.037 0.00 0.00 30.75 3.85
2859 3466 7.732025 TCAGAACACTAAAATGTACTCAAGGA 58.268 34.615 0.00 0.00 30.75 3.36
2860 3467 7.962964 TCAGAACACTAAAATGTACTCAAGG 57.037 36.000 0.00 0.00 30.75 3.61
2880 3490 7.996644 AGGTTAAATAACACTGGTCTTTTCAGA 59.003 33.333 5.74 0.00 37.92 3.27
2903 3513 6.947376 AATACTGGTCTTTAGGTAACAGGT 57.053 37.500 0.00 0.00 41.41 4.00
2944 3554 1.559682 ACAGGGCCACATAGTTGTAGG 59.440 52.381 6.18 0.00 33.76 3.18
2946 3556 2.169769 GCTACAGGGCCACATAGTTGTA 59.830 50.000 6.18 2.60 33.76 2.41
2960 3570 2.607771 GCAACCAACAACATGCTACAGG 60.608 50.000 0.00 0.00 35.93 4.00
2984 3621 5.789643 AAACCAGAGCATAGCAAAGAAAA 57.210 34.783 0.00 0.00 0.00 2.29
3011 3648 3.385577 GAAACAGACAGAGGTGACACTC 58.614 50.000 5.39 1.50 37.77 3.51
3034 3673 1.338960 TGCTCATCTGATGGCAACGAA 60.339 47.619 22.78 7.34 42.51 3.85
3040 3679 1.584175 CAGTCTGCTCATCTGATGGC 58.416 55.000 17.06 17.80 0.00 4.40
3041 3680 1.134491 TGCAGTCTGCTCATCTGATGG 60.134 52.381 24.76 9.30 45.31 3.51
3052 3691 0.459934 CCTAGCTCTGTGCAGTCTGC 60.460 60.000 18.32 18.32 45.94 4.26
3106 3745 4.782019 TGGGACAAAGCATCATGTAAAC 57.218 40.909 0.00 0.00 31.92 2.01
3196 3838 3.896888 ACCATCATCCTTCTGCAAAACAA 59.103 39.130 0.00 0.00 0.00 2.83
3203 3845 3.563390 GCTTTCTACCATCATCCTTCTGC 59.437 47.826 0.00 0.00 0.00 4.26
3204 3846 3.806521 CGCTTTCTACCATCATCCTTCTG 59.193 47.826 0.00 0.00 0.00 3.02
3230 3888 1.727062 AATCCTCCCGCAGAGATCAT 58.273 50.000 2.33 0.00 46.50 2.45
3256 3914 3.009723 ACTCGGCCATATCAACTTGTTG 58.990 45.455 2.24 7.13 0.00 3.33
3257 3915 3.350219 ACTCGGCCATATCAACTTGTT 57.650 42.857 2.24 0.00 0.00 2.83
3258 3916 3.009723 CAACTCGGCCATATCAACTTGT 58.990 45.455 2.24 0.00 0.00 3.16
3390 4049 6.657541 AGTTTCAGAATATACCTCGCCAAAAA 59.342 34.615 0.00 0.00 0.00 1.94
3395 4054 6.679327 AAAAGTTTCAGAATATACCTCGCC 57.321 37.500 0.00 0.00 0.00 5.54
3396 4055 7.748847 TCAAAAAGTTTCAGAATATACCTCGC 58.251 34.615 0.00 0.00 0.00 5.03
3397 4056 9.922305 GATCAAAAAGTTTCAGAATATACCTCG 57.078 33.333 0.00 0.00 0.00 4.63
3406 4065 9.209175 GCTCTAGTAGATCAAAAAGTTTCAGAA 57.791 33.333 0.00 0.00 0.00 3.02
3407 4066 8.589338 AGCTCTAGTAGATCAAAAAGTTTCAGA 58.411 33.333 0.00 0.00 0.00 3.27
3410 4069 8.439286 CACAGCTCTAGTAGATCAAAAAGTTTC 58.561 37.037 0.00 0.00 0.00 2.78
3411 4070 7.095017 GCACAGCTCTAGTAGATCAAAAAGTTT 60.095 37.037 0.00 0.00 0.00 2.66
3412 4071 6.370166 GCACAGCTCTAGTAGATCAAAAAGTT 59.630 38.462 0.00 0.00 0.00 2.66
3413 4072 5.872070 GCACAGCTCTAGTAGATCAAAAAGT 59.128 40.000 0.00 0.00 0.00 2.66
3414 4073 5.871524 TGCACAGCTCTAGTAGATCAAAAAG 59.128 40.000 0.00 0.00 0.00 2.27
3416 4075 5.405935 TGCACAGCTCTAGTAGATCAAAA 57.594 39.130 0.00 0.00 0.00 2.44
3417 4076 5.405935 TTGCACAGCTCTAGTAGATCAAA 57.594 39.130 0.00 0.00 0.00 2.69
3418 4077 5.604758 ATTGCACAGCTCTAGTAGATCAA 57.395 39.130 0.00 0.17 0.00 2.57
3419 4078 5.354767 CAATTGCACAGCTCTAGTAGATCA 58.645 41.667 0.00 0.00 0.00 2.92
3420 4079 4.210955 GCAATTGCACAGCTCTAGTAGATC 59.789 45.833 25.36 0.00 41.59 2.75
3421 4080 4.125703 GCAATTGCACAGCTCTAGTAGAT 58.874 43.478 25.36 0.00 41.59 1.98
3422 4081 3.525537 GCAATTGCACAGCTCTAGTAGA 58.474 45.455 25.36 0.00 41.59 2.59
3423 4082 2.611292 GGCAATTGCACAGCTCTAGTAG 59.389 50.000 30.32 0.00 44.36 2.57
3424 4083 2.632377 GGCAATTGCACAGCTCTAGTA 58.368 47.619 30.32 0.00 44.36 1.82
3425 4084 1.457346 GGCAATTGCACAGCTCTAGT 58.543 50.000 30.32 0.00 44.36 2.57
3434 4093 0.971959 TCAGGGATGGGCAATTGCAC 60.972 55.000 30.32 28.29 46.69 4.57
3448 4107 0.035439 ACATAACTGCCGGTTCAGGG 60.035 55.000 12.92 3.34 39.17 4.45
3449 4108 2.277084 GTACATAACTGCCGGTTCAGG 58.723 52.381 12.92 0.00 39.17 3.86
3496 4155 4.386867 TCGATTCTGTACCTGATGGAAC 57.613 45.455 0.00 0.00 37.04 3.62
3575 4234 6.264528 TCTCTCCTTCTTTTTGGATCCTCTA 58.735 40.000 14.23 0.00 0.00 2.43
3603 4262 4.511454 GCATGGAAAGGGAAAAGTGTTTTC 59.489 41.667 3.92 3.92 46.36 2.29
3607 4266 2.365293 GTGCATGGAAAGGGAAAAGTGT 59.635 45.455 0.00 0.00 0.00 3.55
3608 4267 2.629617 AGTGCATGGAAAGGGAAAAGTG 59.370 45.455 0.00 0.00 0.00 3.16
3609 4268 2.629617 CAGTGCATGGAAAGGGAAAAGT 59.370 45.455 0.00 0.00 0.00 2.66
3610 4269 2.611224 GCAGTGCATGGAAAGGGAAAAG 60.611 50.000 11.09 0.00 0.00 2.27
3620 4279 1.898094 GTGGTGTGCAGTGCATGGA 60.898 57.895 22.87 5.68 41.91 3.41
3651 4310 1.202486 TCCGCACGTTCTTGTTTCTCT 60.202 47.619 0.00 0.00 0.00 3.10
3652 4311 1.070776 GTCCGCACGTTCTTGTTTCTC 60.071 52.381 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.