Multiple sequence alignment - TraesCS3D01G448100

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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 TraesCS3D01G448100 chr3D 100.000 7362 0 0 1 7362 556162822 556170183 0.000000e+00 13596.0
1 TraesCS3D01G448100 chr3D 79.167 264 41 7 5116 5375 556609356 556609609 3.530000e-38 171.0
2 TraesCS3D01G448100 chr3D 79.297 256 35 9 532 772 20751610 20751862 5.910000e-36 163.0
3 TraesCS3D01G448100 chr3D 92.784 97 5 2 2830 2926 112712670 112712764 9.960000e-29 139.0
4 TraesCS3D01G448100 chr3D 91.753 97 4 4 2829 2923 84113322 84113416 1.670000e-26 132.0
5 TraesCS3D01G448100 chr3B 92.999 3328 160 29 3485 6792 739167983 739171257 0.000000e+00 4787.0
6 TraesCS3D01G448100 chr3B 95.864 2152 72 10 693 2837 739165141 739167282 0.000000e+00 3465.0
7 TraesCS3D01G448100 chr3B 88.903 775 65 16 1 774 739164300 739165054 0.000000e+00 935.0
8 TraesCS3D01G448100 chr3B 93.610 579 21 10 2917 3484 739167279 739167852 0.000000e+00 850.0
9 TraesCS3D01G448100 chr3B 89.899 297 21 8 1949 2239 739828263 739828556 2.510000e-99 374.0
10 TraesCS3D01G448100 chr3B 90.717 237 22 0 1717 1953 739715662 739715898 4.290000e-82 316.0
11 TraesCS3D01G448100 chr3B 94.624 186 10 0 2238 2423 739828713 739828898 9.350000e-74 289.0
12 TraesCS3D01G448100 chr3B 94.340 53 2 1 693 744 540966617 540966565 6.120000e-11 80.5
13 TraesCS3D01G448100 chr3A 95.060 2753 80 19 4578 7316 693179119 693181829 0.000000e+00 4279.0
14 TraesCS3D01G448100 chr3A 97.363 2124 47 5 724 2839 693175487 693177609 0.000000e+00 3603.0
15 TraesCS3D01G448100 chr3A 98.479 1512 23 0 2923 4434 693177609 693179120 0.000000e+00 2665.0
16 TraesCS3D01G448100 chr3A 92.652 313 23 0 1 313 693175177 693175489 1.130000e-122 451.0
17 TraesCS3D01G448100 chr3A 85.470 117 15 2 513 629 625536721 625536835 3.610000e-23 121.0
18 TraesCS3D01G448100 chr4A 92.320 638 49 0 954 1591 598223605 598224242 0.000000e+00 907.0
19 TraesCS3D01G448100 chr4A 88.871 638 69 1 954 1591 590152044 590152679 0.000000e+00 784.0
20 TraesCS3D01G448100 chr5A 91.223 638 55 1 954 1591 619179183 619179819 0.000000e+00 867.0
21 TraesCS3D01G448100 chr5A 90.909 638 58 0 954 1591 474913395 474914032 0.000000e+00 857.0
22 TraesCS3D01G448100 chr5A 90.767 639 56 3 954 1591 356477203 356477839 0.000000e+00 850.0
23 TraesCS3D01G448100 chr7A 90.125 638 61 2 954 1591 115498440 115499075 0.000000e+00 828.0
24 TraesCS3D01G448100 chr7A 87.234 94 10 2 671 764 202000760 202000669 1.010000e-18 106.0
25 TraesCS3D01G448100 chr7A 87.234 94 10 2 671 764 454049065 454049156 1.010000e-18 106.0
26 TraesCS3D01G448100 chr4B 86.834 638 53 12 954 1591 44660714 44661320 0.000000e+00 684.0
27 TraesCS3D01G448100 chr4B 86.677 638 52 7 954 1591 44471477 44472081 0.000000e+00 676.0
28 TraesCS3D01G448100 chr4B 92.553 94 3 4 2836 2927 106975942 106975851 1.670000e-26 132.0
29 TraesCS3D01G448100 chr5B 85.552 616 70 9 1387 2002 692329180 692329776 1.740000e-175 627.0
30 TraesCS3D01G448100 chr5B 85.174 634 42 13 958 1591 338957299 338956718 2.940000e-168 603.0
31 TraesCS3D01G448100 chr5B 91.667 96 6 2 535 629 261989391 261989485 1.670000e-26 132.0
32 TraesCS3D01G448100 chr5B 90.196 102 6 4 2829 2927 461134481 461134381 5.990000e-26 130.0
33 TraesCS3D01G448100 chr5B 92.405 79 4 2 687 765 352378691 352378767 2.170000e-20 111.0
34 TraesCS3D01G448100 chr5D 89.041 511 30 9 954 1462 217658115 217658601 1.760000e-170 610.0
35 TraesCS3D01G448100 chr5D 93.388 242 16 0 954 1195 442758165 442757924 7.020000e-95 359.0
36 TraesCS3D01G448100 chr5D 95.604 182 8 0 954 1135 296930203 296930384 7.220000e-75 292.0
37 TraesCS3D01G448100 chr5D 93.548 93 4 2 2828 2920 438690585 438690495 3.580000e-28 137.0
38 TraesCS3D01G448100 chr1D 88.063 511 35 9 954 1462 18948616 18948130 3.830000e-162 582.0
39 TraesCS3D01G448100 chr1D 88.770 187 6 6 954 1138 221919387 221919214 1.610000e-51 215.0
40 TraesCS3D01G448100 chr1D 82.524 206 28 4 557 762 20027521 20027324 2.730000e-39 174.0
41 TraesCS3D01G448100 chr1D 97.561 41 1 0 631 671 251295252 251295212 3.690000e-08 71.3
42 TraesCS3D01G448100 chr1D 92.157 51 2 2 622 671 450582889 450582938 3.690000e-08 71.3
43 TraesCS3D01G448100 chr7D 88.557 402 22 4 1320 1718 34136336 34136716 4.020000e-127 466.0
44 TraesCS3D01G448100 chr7D 94.118 289 16 1 1714 2002 34137336 34137623 8.770000e-119 438.0
45 TraesCS3D01G448100 chr7D 89.899 99 10 0 535 633 416234063 416234161 2.160000e-25 128.0
46 TraesCS3D01G448100 chr7D 89.320 103 9 2 532 633 520308505 520308606 2.160000e-25 128.0
47 TraesCS3D01G448100 chr7D 86.400 125 4 12 2836 2956 448337046 448336931 2.790000e-24 124.0
48 TraesCS3D01G448100 chr7B 85.207 169 7 3 1441 1591 89778672 89778840 2.750000e-34 158.0
49 TraesCS3D01G448100 chr7B 83.099 71 4 5 631 699 336723900 336723836 2.870000e-04 58.4
50 TraesCS3D01G448100 chr6D 91.837 98 4 3 2834 2929 363038076 363038171 4.630000e-27 134.0
51 TraesCS3D01G448100 chr2B 91.753 97 7 1 537 632 361574999 361574903 4.630000e-27 134.0
52 TraesCS3D01G448100 chr2D 91.753 97 4 3 2836 2930 622355887 622355981 1.670000e-26 132.0
53 TraesCS3D01G448100 chr2D 88.679 106 10 2 532 636 411647097 411646993 2.160000e-25 128.0
54 TraesCS3D01G448100 chr2D 92.500 80 4 2 687 766 571079033 571078956 6.040000e-21 113.0
55 TraesCS3D01G448100 chr2D 97.561 41 1 0 631 671 591362874 591362834 3.690000e-08 71.3
56 TraesCS3D01G448100 chr2D 95.238 42 2 0 630 671 314344368 314344409 4.770000e-07 67.6
57 TraesCS3D01G448100 chr2A 88.679 106 8 3 2829 2932 102692165 102692062 7.750000e-25 126.0
58 TraesCS3D01G448100 chr2A 92.500 80 4 2 687 766 709835017 709834940 6.040000e-21 113.0
59 TraesCS3D01G448100 chr6B 88.043 92 9 2 677 767 684977959 684977869 2.810000e-19 108.0
60 TraesCS3D01G448100 chr1A 91.489 47 3 1 630 675 390097781 390097735 6.170000e-06 63.9


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 TraesCS3D01G448100 chr3D 556162822 556170183 7361 False 13596.00 13596 100.0000 1 7362 1 chr3D.!!$F4 7361
1 TraesCS3D01G448100 chr3B 739164300 739171257 6957 False 2509.25 4787 92.8440 1 6792 4 chr3B.!!$F2 6791
2 TraesCS3D01G448100 chr3B 739828263 739828898 635 False 331.50 374 92.2615 1949 2423 2 chr3B.!!$F3 474
3 TraesCS3D01G448100 chr3A 693175177 693181829 6652 False 2749.50 4279 95.8885 1 7316 4 chr3A.!!$F2 7315
4 TraesCS3D01G448100 chr4A 598223605 598224242 637 False 907.00 907 92.3200 954 1591 1 chr4A.!!$F2 637
5 TraesCS3D01G448100 chr4A 590152044 590152679 635 False 784.00 784 88.8710 954 1591 1 chr4A.!!$F1 637
6 TraesCS3D01G448100 chr5A 619179183 619179819 636 False 867.00 867 91.2230 954 1591 1 chr5A.!!$F3 637
7 TraesCS3D01G448100 chr5A 474913395 474914032 637 False 857.00 857 90.9090 954 1591 1 chr5A.!!$F2 637
8 TraesCS3D01G448100 chr5A 356477203 356477839 636 False 850.00 850 90.7670 954 1591 1 chr5A.!!$F1 637
9 TraesCS3D01G448100 chr7A 115498440 115499075 635 False 828.00 828 90.1250 954 1591 1 chr7A.!!$F1 637
10 TraesCS3D01G448100 chr4B 44660714 44661320 606 False 684.00 684 86.8340 954 1591 1 chr4B.!!$F2 637
11 TraesCS3D01G448100 chr4B 44471477 44472081 604 False 676.00 676 86.6770 954 1591 1 chr4B.!!$F1 637
12 TraesCS3D01G448100 chr5B 692329180 692329776 596 False 627.00 627 85.5520 1387 2002 1 chr5B.!!$F3 615
13 TraesCS3D01G448100 chr5B 338956718 338957299 581 True 603.00 603 85.1740 958 1591 1 chr5B.!!$R1 633
14 TraesCS3D01G448100 chr7D 34136336 34137623 1287 False 452.00 466 91.3375 1320 2002 2 chr7D.!!$F3 682

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
558 575 0.032217 AATACCCCCTCCGGTCGTAA 60.032 55.000 0.00 0.00 37.34 3.18 F
1792 2608 2.044946 CTGCAACCCAGCCTACCC 60.045 66.667 0.00 0.00 34.21 3.69 F
2202 3024 0.036010 ATGTCAAGCCTGAACTCGGG 60.036 55.000 0.00 0.00 45.30 5.14 F
2850 3832 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37 F
2851 3833 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00 F
2852 3834 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74 F
2853 3835 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90 F
3845 4969 1.827344 TCCTGATGACTCACGAGCATT 59.173 47.619 0.00 0.00 0.00 3.56 F
5002 6132 0.035739 GTGTTTTCCCCTAGGCGACA 59.964 55.000 2.05 0.13 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2721 0.795085 GCAGCTCGATGATGGCATAC 59.205 55.000 0.00 0.00 34.11 2.39 R
2904 3886 1.151413 ACAACTACTCCCTCCTTCCCA 59.849 52.381 0.00 0.00 0.00 4.37 R
3010 3992 1.160137 CACAGCAACTAGTTGGAGCC 58.840 55.000 31.42 17.67 40.74 4.70 R
4470 5594 2.614057 GCATGGTGGCAGTAGTGTTATC 59.386 50.000 0.00 0.00 0.00 1.75 R
4523 5647 4.014273 AGATCTAGGGACCTCCATTGTT 57.986 45.455 0.00 0.00 38.24 2.83 R
4660 5784 7.327214 TCCTTGCAGTTTGTAAATCTTTTTGT 58.673 30.769 0.00 0.00 0.00 2.83 R
4661 5785 7.706179 TCTCCTTGCAGTTTGTAAATCTTTTTG 59.294 33.333 0.00 0.00 0.00 2.44 R
5619 6760 2.037121 TGCTTCACACAAGATCGAGGAA 59.963 45.455 0.00 0.00 0.00 3.36 R
6934 8086 0.388134 CTCGGTCACCACGGTAACTG 60.388 60.000 0.00 0.00 0.00 3.16 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
82 83 2.632512 TGAAAAGGGGCAAATCCAAGAC 59.367 45.455 0.00 0.00 36.21 3.01
192 193 8.181904 TGGAAGAGAAACTGCAAGAAATATTT 57.818 30.769 0.00 0.00 37.43 1.40
214 215 5.651387 TGACAGATAAGAAGACACTCCAG 57.349 43.478 0.00 0.00 0.00 3.86
237 238 5.779260 AGCTCAGATATGAGTGTCATATGGT 59.221 40.000 18.17 3.41 46.75 3.55
241 242 6.153510 TCAGATATGAGTGTCATATGGTAGGC 59.846 42.308 13.01 0.15 46.75 3.93
317 318 1.202498 TCTCTGCCATCGCAATGAGAG 60.202 52.381 0.98 0.00 46.66 3.20
329 330 4.096231 TCGCAATGAGAGAGAGAGAGAAAG 59.904 45.833 0.00 0.00 0.00 2.62
330 331 4.685924 GCAATGAGAGAGAGAGAGAAAGG 58.314 47.826 0.00 0.00 0.00 3.11
333 334 4.235079 TGAGAGAGAGAGAGAAAGGGAG 57.765 50.000 0.00 0.00 0.00 4.30
336 337 3.203040 AGAGAGAGAGAGAAAGGGAGAGG 59.797 52.174 0.00 0.00 0.00 3.69
337 338 2.244769 AGAGAGAGAGAAAGGGAGAGGG 59.755 54.545 0.00 0.00 0.00 4.30
341 342 2.244769 AGAGAGAAAGGGAGAGGGAGAG 59.755 54.545 0.00 0.00 0.00 3.20
358 374 2.226149 GAGGGACGAGGAGGAAGGGA 62.226 65.000 0.00 0.00 0.00 4.20
359 375 1.305887 GGGACGAGGAGGAAGGGAA 60.306 63.158 0.00 0.00 0.00 3.97
360 376 1.331399 GGGACGAGGAGGAAGGGAAG 61.331 65.000 0.00 0.00 0.00 3.46
361 377 0.324460 GGACGAGGAGGAAGGGAAGA 60.324 60.000 0.00 0.00 0.00 2.87
362 378 1.689892 GGACGAGGAGGAAGGGAAGAT 60.690 57.143 0.00 0.00 0.00 2.40
363 379 1.410882 GACGAGGAGGAAGGGAAGATG 59.589 57.143 0.00 0.00 0.00 2.90
364 380 1.273324 ACGAGGAGGAAGGGAAGATGT 60.273 52.381 0.00 0.00 0.00 3.06
365 381 1.137872 CGAGGAGGAAGGGAAGATGTG 59.862 57.143 0.00 0.00 0.00 3.21
366 382 1.488393 GAGGAGGAAGGGAAGATGTGG 59.512 57.143 0.00 0.00 0.00 4.17
367 383 0.548510 GGAGGAAGGGAAGATGTGGG 59.451 60.000 0.00 0.00 0.00 4.61
368 384 1.584724 GAGGAAGGGAAGATGTGGGA 58.415 55.000 0.00 0.00 0.00 4.37
369 385 1.916181 GAGGAAGGGAAGATGTGGGAA 59.084 52.381 0.00 0.00 0.00 3.97
370 386 2.308866 GAGGAAGGGAAGATGTGGGAAA 59.691 50.000 0.00 0.00 0.00 3.13
371 387 2.721906 AGGAAGGGAAGATGTGGGAAAA 59.278 45.455 0.00 0.00 0.00 2.29
372 388 3.142028 AGGAAGGGAAGATGTGGGAAAAA 59.858 43.478 0.00 0.00 0.00 1.94
425 441 5.705441 GTGAAATAGGTGGAACATGTGAAGA 59.295 40.000 0.00 0.00 44.52 2.87
461 477 1.070134 ACCAGTCTGTTACATGTGCGT 59.930 47.619 9.11 0.00 0.00 5.24
506 522 4.717233 ATTCAATATTCCGCAGTTGCAA 57.283 36.364 0.00 0.00 42.21 4.08
507 523 3.485947 TCAATATTCCGCAGTTGCAAC 57.514 42.857 22.17 22.17 42.21 4.17
514 530 3.717400 TCCGCAGTTGCAACAATAAAA 57.283 38.095 30.11 9.15 42.21 1.52
550 567 4.741928 AATCATACCAAATACCCCCTCC 57.258 45.455 0.00 0.00 0.00 4.30
554 571 1.276859 ACCAAATACCCCCTCCGGTC 61.277 60.000 0.00 0.00 37.34 4.79
558 575 0.032217 AATACCCCCTCCGGTCGTAA 60.032 55.000 0.00 0.00 37.34 3.18
656 673 5.769484 TCCTCCGTCTCATAATGTAAGAC 57.231 43.478 0.00 0.00 36.82 3.01
687 704 4.664392 ACTCTATTATGGGACGGAGGTAG 58.336 47.826 0.00 0.00 0.00 3.18
700 717 6.765512 GGGACGGAGGTAGTATGTCTATATAC 59.234 46.154 0.00 0.00 34.48 1.47
703 720 8.961294 ACGGAGGTAGTATGTCTATATACATC 57.039 38.462 7.00 0.00 40.52 3.06
726 743 8.799091 CATCCGTATGTAGTTCATATCGAAATC 58.201 37.037 0.00 0.00 40.54 2.17
729 746 8.021396 CCGTATGTAGTTCATATCGAAATCTCA 58.979 37.037 0.00 0.00 40.54 3.27
806 982 6.094048 GCTATGCAAAAGTGAAGTCAAGGATA 59.906 38.462 0.00 0.00 0.00 2.59
1584 1776 3.869272 GACATCAAGCGCCGCCTG 61.869 66.667 4.98 2.39 0.00 4.85
1758 2574 2.882777 CGCGCAGACTTCGAGCAT 60.883 61.111 8.75 0.00 0.00 3.79
1792 2608 2.044946 CTGCAACCCAGCCTACCC 60.045 66.667 0.00 0.00 34.21 3.69
1830 2646 4.767255 GGCTGCCTCACCCGTCTG 62.767 72.222 12.43 0.00 0.00 3.51
1905 2721 3.499737 GGCGAGGATGGTGTTGCG 61.500 66.667 0.00 0.00 0.00 4.85
1941 2757 1.219124 GCAGGAGGAATGCGACTCA 59.781 57.895 0.00 0.00 35.45 3.41
2202 3024 0.036010 ATGTCAAGCCTGAACTCGGG 60.036 55.000 0.00 0.00 45.30 5.14
2839 3821 7.159322 TGGTGACATTCTCTAGAAAGTACTC 57.841 40.000 0.00 0.00 36.28 2.59
2840 3822 6.153000 TGGTGACATTCTCTAGAAAGTACTCC 59.847 42.308 0.00 5.20 36.28 3.85
2841 3823 6.406065 GGTGACATTCTCTAGAAAGTACTCCC 60.406 46.154 0.00 0.00 36.28 4.30
2842 3824 6.378848 GTGACATTCTCTAGAAAGTACTCCCT 59.621 42.308 0.00 0.00 36.28 4.20
2843 3825 6.603997 TGACATTCTCTAGAAAGTACTCCCTC 59.396 42.308 0.00 0.00 36.28 4.30
2844 3826 5.894964 ACATTCTCTAGAAAGTACTCCCTCC 59.105 44.000 0.00 0.00 34.65 4.30
2845 3827 4.153673 TCTCTAGAAAGTACTCCCTCCG 57.846 50.000 0.00 0.00 0.00 4.63
2846 3828 3.522750 TCTCTAGAAAGTACTCCCTCCGT 59.477 47.826 0.00 0.00 0.00 4.69
2847 3829 3.878699 CTCTAGAAAGTACTCCCTCCGTC 59.121 52.174 0.00 0.00 0.00 4.79
2848 3830 1.849977 AGAAAGTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
2849 3831 0.822811 GAAAGTACTCCCTCCGTCCC 59.177 60.000 0.00 0.00 0.00 4.46
2850 3832 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
2851 3833 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2852 3834 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2853 3835 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2854 3836 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2855 3837 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2856 3838 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2857 3839 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2858 3840 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2859 3841 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2860 3842 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2861 3843 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2862 3844 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2863 3845 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2864 3846 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2865 3847 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2866 3848 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2867 3849 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2868 3850 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2911 3893 7.745620 AAAACGCTCTTATATTATGGGAAGG 57.254 36.000 0.00 0.00 0.00 3.46
2912 3894 6.681729 AACGCTCTTATATTATGGGAAGGA 57.318 37.500 0.00 0.00 0.00 3.36
2913 3895 6.287589 ACGCTCTTATATTATGGGAAGGAG 57.712 41.667 0.00 0.00 0.00 3.69
2914 3896 5.187967 ACGCTCTTATATTATGGGAAGGAGG 59.812 44.000 0.00 0.00 0.00 4.30
2915 3897 5.395768 CGCTCTTATATTATGGGAAGGAGGG 60.396 48.000 0.00 0.00 0.00 4.30
2916 3898 5.726793 GCTCTTATATTATGGGAAGGAGGGA 59.273 44.000 0.00 0.00 0.00 4.20
2917 3899 6.126911 GCTCTTATATTATGGGAAGGAGGGAG 60.127 46.154 0.00 0.00 0.00 4.30
2918 3900 6.886637 TCTTATATTATGGGAAGGAGGGAGT 58.113 40.000 0.00 0.00 0.00 3.85
2919 3901 8.019537 TCTTATATTATGGGAAGGAGGGAGTA 57.980 38.462 0.00 0.00 0.00 2.59
2920 3902 8.123130 TCTTATATTATGGGAAGGAGGGAGTAG 58.877 40.741 0.00 0.00 0.00 2.57
2921 3903 4.578149 ATTATGGGAAGGAGGGAGTAGT 57.422 45.455 0.00 0.00 0.00 2.73
2922 3904 2.972153 ATGGGAAGGAGGGAGTAGTT 57.028 50.000 0.00 0.00 0.00 2.24
3010 3992 5.173774 TCTTTGAACTGCAAGCTTAGTTG 57.826 39.130 17.34 5.40 37.27 3.16
3094 4076 3.850273 ACTTGTTTACTCGACGCTAATCG 59.150 43.478 0.00 0.00 43.63 3.34
3241 4229 8.106462 TCTCAACCATTCACTTTATTCCATGTA 58.894 33.333 0.00 0.00 0.00 2.29
3845 4969 1.827344 TCCTGATGACTCACGAGCATT 59.173 47.619 0.00 0.00 0.00 3.56
3854 4978 2.037772 ACTCACGAGCATTTCCTTCTGT 59.962 45.455 0.00 0.00 0.00 3.41
4158 5282 3.134458 GTGCTTCAGTGTCAGCTAAACT 58.866 45.455 15.26 0.00 36.92 2.66
4307 5431 9.462174 CAACAAAACAGCTTAAATGATTCAGTA 57.538 29.630 0.00 0.00 0.00 2.74
4470 5594 6.245115 TCAAGATAAACAAGTGTCATGCAG 57.755 37.500 0.00 0.00 0.00 4.41
4505 5629 7.669304 ACTGCCACCATGCATTATTACATTATA 59.331 33.333 0.00 0.00 41.16 0.98
4534 5658 6.824958 ATATACAGGTACAACAATGGAGGT 57.175 37.500 0.00 0.00 0.00 3.85
4576 5700 3.073274 AGGTGGCTTGAAATGTAGGAC 57.927 47.619 0.00 0.00 0.00 3.85
4585 5709 6.458342 GGCTTGAAATGTAGGACCTAAAATCG 60.458 42.308 1.75 0.00 0.00 3.34
4877 6007 5.049267 CCATTCTGGCAAATTGAAAACCTTG 60.049 40.000 0.00 0.00 0.00 3.61
4957 6087 7.712639 TGAAATAAGACTAGGAGCATTGATCAC 59.287 37.037 4.07 0.00 0.00 3.06
4964 6094 2.433604 AGGAGCATTGATCACGAGATGT 59.566 45.455 0.00 0.00 33.72 3.06
5002 6132 0.035739 GTGTTTTCCCCTAGGCGACA 59.964 55.000 2.05 0.13 0.00 4.35
5030 6160 6.959639 ATATTTGGGTGTTAGCTATTGTGG 57.040 37.500 0.00 0.00 0.00 4.17
5123 6259 8.713971 ACCCATCAATGTGATTACAGAAGTATA 58.286 33.333 0.00 0.00 40.79 1.47
5181 6317 7.701924 ACACATTAATGGAATATCTTGTTTGCG 59.298 33.333 19.37 0.00 0.00 4.85
5492 6631 6.441088 AAGAAGAGGAACTAATGGTCAAGT 57.559 37.500 0.00 0.00 41.55 3.16
5542 6681 7.175641 CCAAAGTGACAAGTAAAGAGATTGGAT 59.824 37.037 0.00 0.00 35.58 3.41
5617 6758 2.673368 GGCTCTTATGTGTTGTTCCTCG 59.327 50.000 0.00 0.00 0.00 4.63
5619 6760 4.184629 GCTCTTATGTGTTGTTCCTCGAT 58.815 43.478 0.00 0.00 0.00 3.59
5980 7122 4.623932 TCTCCTTGCAGTTGACACTAAT 57.376 40.909 0.00 0.00 0.00 1.73
6025 7167 5.055642 TGACATCGAACAACTACGATTCT 57.944 39.130 0.00 0.00 44.93 2.40
6136 7278 0.252103 ACAAGGAGGTTCGCTCCCTA 60.252 55.000 4.16 0.00 41.76 3.53
6464 7607 5.070446 TGTCCTCTTGCTATCGTGGATAATT 59.930 40.000 0.00 0.00 0.00 1.40
6531 7674 1.022735 TTTGCCGCGTTAACTTTGGA 58.977 45.000 4.92 0.00 0.00 3.53
6532 7675 0.589223 TTGCCGCGTTAACTTTGGAG 59.411 50.000 4.92 0.00 0.00 3.86
6533 7676 0.249953 TGCCGCGTTAACTTTGGAGA 60.250 50.000 4.92 0.00 0.00 3.71
6704 7854 9.463443 AATTTAAGAAGTTGAAATTTGACGAGG 57.537 29.630 0.00 0.00 30.47 4.63
6735 7885 9.947433 TTCTTGATGAAAATGATAATTTTGGCT 57.053 25.926 5.44 0.00 34.24 4.75
6738 7888 7.332557 TGATGAAAATGATAATTTTGGCTGCT 58.667 30.769 5.44 0.00 34.24 4.24
6751 7901 1.106285 GGCTGCTTGGAGTATTTGGG 58.894 55.000 0.00 0.00 0.00 4.12
6773 7923 5.396324 GGGTCATCAATGATACAGGTGTGTA 60.396 44.000 0.00 0.00 43.43 2.90
6803 7954 4.262617 GGAAAGGGTTGGAAGTGAGATAC 58.737 47.826 0.00 0.00 0.00 2.24
6826 7977 0.675522 TTTACAGCTAGCCAACCCGC 60.676 55.000 12.13 0.00 0.00 6.13
6896 8048 2.557924 TGTGTTCATTTGCTTGCCCTAG 59.442 45.455 0.00 0.00 0.00 3.02
6903 8055 0.680921 TTGCTTGCCCTAGGATGTGC 60.681 55.000 11.48 5.47 0.00 4.57
6914 8066 2.768253 AGGATGTGCGACTTGATTCA 57.232 45.000 0.00 0.00 0.00 2.57
6933 8085 8.924511 TGATTCAAACTCTCCAACTCTTTATT 57.075 30.769 0.00 0.00 0.00 1.40
6934 8086 9.003658 TGATTCAAACTCTCCAACTCTTTATTC 57.996 33.333 0.00 0.00 0.00 1.75
6971 8123 2.190578 GGAAGGAGATGGTGGCGG 59.809 66.667 0.00 0.00 0.00 6.13
6972 8124 2.190578 GAAGGAGATGGTGGCGGG 59.809 66.667 0.00 0.00 0.00 6.13
6973 8125 2.285368 AAGGAGATGGTGGCGGGA 60.285 61.111 0.00 0.00 0.00 5.14
6975 8127 3.866582 GGAGATGGTGGCGGGAGG 61.867 72.222 0.00 0.00 0.00 4.30
6977 8129 2.285368 AGATGGTGGCGGGAGGAA 60.285 61.111 0.00 0.00 0.00 3.36
6979 8131 1.227383 GATGGTGGCGGGAGGAATT 59.773 57.895 0.00 0.00 0.00 2.17
6980 8132 0.472471 GATGGTGGCGGGAGGAATTA 59.528 55.000 0.00 0.00 0.00 1.40
6982 8134 1.148498 GGTGGCGGGAGGAATTAGG 59.852 63.158 0.00 0.00 0.00 2.69
7054 8206 3.725740 CGATCCAAAATAATTGACGCAGC 59.274 43.478 0.00 0.00 0.00 5.25
7055 8207 4.496341 CGATCCAAAATAATTGACGCAGCT 60.496 41.667 0.00 0.00 0.00 4.24
7056 8208 4.355543 TCCAAAATAATTGACGCAGCTC 57.644 40.909 0.00 0.00 0.00 4.09
7057 8209 4.009675 TCCAAAATAATTGACGCAGCTCT 58.990 39.130 0.00 0.00 0.00 4.09
7058 8210 5.182487 TCCAAAATAATTGACGCAGCTCTA 58.818 37.500 0.00 0.00 0.00 2.43
7059 8211 5.294306 TCCAAAATAATTGACGCAGCTCTAG 59.706 40.000 0.00 0.00 0.00 2.43
7060 8212 5.065218 CCAAAATAATTGACGCAGCTCTAGT 59.935 40.000 0.00 0.00 0.00 2.57
7061 8213 6.257849 CCAAAATAATTGACGCAGCTCTAGTA 59.742 38.462 0.00 0.00 0.00 1.82
7112 8264 5.591067 ACTCTTACTTTCCTAGATCCTCACG 59.409 44.000 0.00 0.00 0.00 4.35
7129 8281 4.142665 CCTCACGGATACATCCTACATACG 60.143 50.000 6.68 0.00 44.93 3.06
7152 8304 6.381994 ACGGGAGACATGAATAAAAGGTACTA 59.618 38.462 0.00 0.00 38.49 1.82
7156 8308 9.046296 GGAGACATGAATAAAAGGTACTATGTG 57.954 37.037 0.00 0.00 38.49 3.21
7157 8309 9.817809 GAGACATGAATAAAAGGTACTATGTGA 57.182 33.333 0.00 0.00 38.49 3.58
7170 8322 9.959721 AAGGTACTATGTGAAATAATGACTTGT 57.040 29.630 0.00 0.00 38.49 3.16
7171 8323 9.383519 AGGTACTATGTGAAATAATGACTTGTG 57.616 33.333 0.00 0.00 36.02 3.33
7172 8324 8.612619 GGTACTATGTGAAATAATGACTTGTGG 58.387 37.037 0.00 0.00 0.00 4.17
7173 8325 7.630242 ACTATGTGAAATAATGACTTGTGGG 57.370 36.000 0.00 0.00 0.00 4.61
7174 8326 7.175104 ACTATGTGAAATAATGACTTGTGGGT 58.825 34.615 0.00 0.00 0.00 4.51
7175 8327 6.916360 ATGTGAAATAATGACTTGTGGGTT 57.084 33.333 0.00 0.00 0.00 4.11
7176 8328 6.723298 TGTGAAATAATGACTTGTGGGTTT 57.277 33.333 0.00 0.00 0.00 3.27
7177 8329 7.825331 TGTGAAATAATGACTTGTGGGTTTA 57.175 32.000 0.00 0.00 0.00 2.01
7178 8330 8.415950 TGTGAAATAATGACTTGTGGGTTTAT 57.584 30.769 0.00 0.00 0.00 1.40
7179 8331 9.521841 TGTGAAATAATGACTTGTGGGTTTATA 57.478 29.630 0.00 0.00 0.00 0.98
7183 8335 8.533569 AATAATGACTTGTGGGTTTATAAGGG 57.466 34.615 0.00 0.00 0.00 3.95
7184 8336 5.530176 ATGACTTGTGGGTTTATAAGGGT 57.470 39.130 0.00 0.00 0.00 4.34
7185 8337 6.645884 ATGACTTGTGGGTTTATAAGGGTA 57.354 37.500 0.00 0.00 0.00 3.69
7186 8338 6.057321 TGACTTGTGGGTTTATAAGGGTAG 57.943 41.667 0.00 0.00 0.00 3.18
7187 8339 5.786457 TGACTTGTGGGTTTATAAGGGTAGA 59.214 40.000 0.00 0.00 0.00 2.59
7188 8340 6.272792 TGACTTGTGGGTTTATAAGGGTAGAA 59.727 38.462 0.00 0.00 0.00 2.10
7207 8359 7.015584 GGGTAGAAATATACTCCCTTCGGTTAA 59.984 40.741 0.00 0.00 32.89 2.01
7316 8468 6.013085 GCATTAACTACAACACATACACACG 58.987 40.000 0.00 0.00 0.00 4.49
7317 8469 6.347079 GCATTAACTACAACACATACACACGT 60.347 38.462 0.00 0.00 0.00 4.49
7318 8470 6.513609 TTAACTACAACACATACACACGTG 57.486 37.500 15.48 15.48 39.10 4.49
7319 8471 4.310357 ACTACAACACATACACACGTGA 57.690 40.909 25.01 0.00 36.91 4.35
7320 8472 4.046462 ACTACAACACATACACACGTGAC 58.954 43.478 25.01 0.00 36.91 3.67
7321 8473 2.206750 ACAACACATACACACGTGACC 58.793 47.619 25.01 0.00 36.91 4.02
7322 8474 2.205911 CAACACATACACACGTGACCA 58.794 47.619 25.01 6.37 36.91 4.02
7323 8475 1.860676 ACACATACACACGTGACCAC 58.139 50.000 25.01 0.00 36.91 4.16
7324 8476 1.411246 ACACATACACACGTGACCACT 59.589 47.619 25.01 0.00 36.91 4.00
7325 8477 2.624364 ACACATACACACGTGACCACTA 59.376 45.455 25.01 3.85 36.91 2.74
7326 8478 3.068448 ACACATACACACGTGACCACTAA 59.932 43.478 25.01 0.18 36.91 2.24
7327 8479 4.052608 CACATACACACGTGACCACTAAA 58.947 43.478 25.01 0.00 35.02 1.85
7328 8480 4.149922 CACATACACACGTGACCACTAAAG 59.850 45.833 25.01 5.15 35.02 1.85
7329 8481 1.578583 ACACACGTGACCACTAAAGC 58.421 50.000 25.01 0.00 0.00 3.51
7330 8482 1.134640 ACACACGTGACCACTAAAGCA 60.135 47.619 25.01 0.00 0.00 3.91
7331 8483 2.143122 CACACGTGACCACTAAAGCAT 58.857 47.619 25.01 0.00 0.00 3.79
7332 8484 2.096268 CACACGTGACCACTAAAGCATG 60.096 50.000 25.01 0.52 0.00 4.06
7333 8485 1.464608 CACGTGACCACTAAAGCATGG 59.535 52.381 10.90 0.00 42.13 3.66
7346 8498 9.561069 CCACTAAAGCATGGTTAATAATACTCT 57.439 33.333 11.15 0.00 0.00 3.24
7351 8503 7.730364 AGCATGGTTAATAATACTCTTTCCG 57.270 36.000 0.00 0.00 0.00 4.30
7352 8504 7.280356 AGCATGGTTAATAATACTCTTTCCGT 58.720 34.615 0.00 0.00 0.00 4.69
7353 8505 7.773690 AGCATGGTTAATAATACTCTTTCCGTT 59.226 33.333 0.00 0.00 0.00 4.44
7354 8506 8.068380 GCATGGTTAATAATACTCTTTCCGTTC 58.932 37.037 0.00 0.00 0.00 3.95
7355 8507 8.557029 CATGGTTAATAATACTCTTTCCGTTCC 58.443 37.037 0.00 0.00 0.00 3.62
7356 8508 7.622713 TGGTTAATAATACTCTTTCCGTTCCA 58.377 34.615 0.00 0.00 0.00 3.53
7357 8509 8.269317 TGGTTAATAATACTCTTTCCGTTCCAT 58.731 33.333 0.00 0.00 0.00 3.41
7358 8510 9.768662 GGTTAATAATACTCTTTCCGTTCCATA 57.231 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 193 4.081972 GCTGGAGTGTCTTCTTATCTGTCA 60.082 45.833 0.00 0.00 0.00 3.58
237 238 2.510064 ATTGCGTTCGTTCCGGCCTA 62.510 55.000 0.00 0.00 0.00 3.93
241 242 0.738412 ACCTATTGCGTTCGTTCCGG 60.738 55.000 0.00 0.00 0.00 5.14
317 318 2.243736 TCCCTCTCCCTTTCTCTCTCTC 59.756 54.545 0.00 0.00 0.00 3.20
329 330 2.123640 CGTCCCTCTCCCTCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
330 331 1.152839 CTCGTCCCTCTCCCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
333 334 1.152839 CTCCTCGTCCCTCTCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
336 337 0.753848 CTTCCTCCTCGTCCCTCTCC 60.754 65.000 0.00 0.00 0.00 3.71
337 338 0.753848 CCTTCCTCCTCGTCCCTCTC 60.754 65.000 0.00 0.00 0.00 3.20
341 342 1.305887 TTCCCTTCCTCCTCGTCCC 60.306 63.158 0.00 0.00 0.00 4.46
369 385 7.768120 TGCACTTTCACACATAAAATCCTTTTT 59.232 29.630 0.00 0.00 38.56 1.94
370 386 7.271511 TGCACTTTCACACATAAAATCCTTTT 58.728 30.769 0.00 0.00 36.67 2.27
371 387 6.815089 TGCACTTTCACACATAAAATCCTTT 58.185 32.000 0.00 0.00 0.00 3.11
372 388 6.403866 TGCACTTTCACACATAAAATCCTT 57.596 33.333 0.00 0.00 0.00 3.36
373 389 6.403866 TTGCACTTTCACACATAAAATCCT 57.596 33.333 0.00 0.00 0.00 3.24
374 390 7.360269 CCATTTGCACTTTCACACATAAAATCC 60.360 37.037 0.00 0.00 0.00 3.01
375 391 7.360269 CCCATTTGCACTTTCACACATAAAATC 60.360 37.037 0.00 0.00 0.00 2.17
376 392 6.427547 CCCATTTGCACTTTCACACATAAAAT 59.572 34.615 0.00 0.00 0.00 1.82
377 393 5.757320 CCCATTTGCACTTTCACACATAAAA 59.243 36.000 0.00 0.00 0.00 1.52
378 394 5.163364 ACCCATTTGCACTTTCACACATAAA 60.163 36.000 0.00 0.00 0.00 1.40
379 395 4.343526 ACCCATTTGCACTTTCACACATAA 59.656 37.500 0.00 0.00 0.00 1.90
380 396 3.894427 ACCCATTTGCACTTTCACACATA 59.106 39.130 0.00 0.00 0.00 2.29
381 397 2.699846 ACCCATTTGCACTTTCACACAT 59.300 40.909 0.00 0.00 0.00 3.21
382 398 2.106566 ACCCATTTGCACTTTCACACA 58.893 42.857 0.00 0.00 0.00 3.72
383 399 2.100584 TCACCCATTTGCACTTTCACAC 59.899 45.455 0.00 0.00 0.00 3.82
384 400 2.382882 TCACCCATTTGCACTTTCACA 58.617 42.857 0.00 0.00 0.00 3.58
385 401 3.451141 TTCACCCATTTGCACTTTCAC 57.549 42.857 0.00 0.00 0.00 3.18
386 402 4.686191 ATTTCACCCATTTGCACTTTCA 57.314 36.364 0.00 0.00 0.00 2.69
387 403 5.170748 CCTATTTCACCCATTTGCACTTTC 58.829 41.667 0.00 0.00 0.00 2.62
388 404 4.592778 ACCTATTTCACCCATTTGCACTTT 59.407 37.500 0.00 0.00 0.00 2.66
389 405 4.021192 CACCTATTTCACCCATTTGCACTT 60.021 41.667 0.00 0.00 0.00 3.16
390 406 3.511146 CACCTATTTCACCCATTTGCACT 59.489 43.478 0.00 0.00 0.00 4.40
461 477 3.688673 TCATTCGTGTGATATGCTTTGCA 59.311 39.130 0.00 0.00 44.86 4.08
492 508 3.932545 TTATTGTTGCAACTGCGGAAT 57.067 38.095 28.61 20.67 45.83 3.01
496 512 8.759260 TTTTAATTTTTATTGTTGCAACTGCG 57.241 26.923 28.61 0.00 45.83 5.18
632 649 6.210078 GTCTTACATTATGAGACGGAGGAAG 58.790 44.000 0.00 0.00 34.53 3.46
664 681 4.736611 ACCTCCGTCCCATAATAGAGTA 57.263 45.455 0.00 0.00 0.00 2.59
681 698 8.961294 ACGGATGTATATAGACATACTACCTC 57.039 38.462 18.29 4.26 40.18 3.85
700 717 8.689251 ATTTCGATATGAACTACATACGGATG 57.311 34.615 5.94 5.94 43.12 3.51
703 720 8.021396 TGAGATTTCGATATGAACTACATACGG 58.979 37.037 0.00 0.00 43.12 4.02
864 1046 2.073816 CGTGTATGAAAACGCCCTCTT 58.926 47.619 0.00 0.00 32.40 2.85
1758 2574 2.025155 GCAGAGATTAGGTCGGTGAGA 58.975 52.381 0.00 0.00 0.00 3.27
1792 2608 2.897350 GAAATCAGGGCGCTCCGG 60.897 66.667 2.00 6.15 41.52 5.14
1830 2646 2.939103 AGCGAGCACAATATCCTTGAAC 59.061 45.455 0.00 0.00 0.00 3.18
1890 2706 0.930310 CATACGCAACACCATCCTCG 59.070 55.000 0.00 0.00 0.00 4.63
1905 2721 0.795085 GCAGCTCGATGATGGCATAC 59.205 55.000 0.00 0.00 34.11 2.39
1941 2757 1.544917 AAGGATCTGGGTGCCCCTT 60.545 57.895 11.10 0.00 45.70 3.95
2202 3024 4.698056 GCTTTCATAGCTTGCGGC 57.302 55.556 0.00 0.00 46.77 6.53
2211 3033 4.497291 ACCATTACGGAAGGCTTTCATA 57.503 40.909 11.04 0.00 38.63 2.15
2839 3821 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2840 3822 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2841 3823 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2842 3824 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2843 3825 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2844 3826 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2886 3868 7.996644 TCCTTCCCATAATATAAGAGCGTTTTT 59.003 33.333 0.00 0.00 0.00 1.94
2887 3869 7.514721 TCCTTCCCATAATATAAGAGCGTTTT 58.485 34.615 0.00 0.00 0.00 2.43
2888 3870 7.074653 TCCTTCCCATAATATAAGAGCGTTT 57.925 36.000 0.00 0.00 0.00 3.60
2889 3871 6.295916 CCTCCTTCCCATAATATAAGAGCGTT 60.296 42.308 0.00 0.00 0.00 4.84
2890 3872 5.187967 CCTCCTTCCCATAATATAAGAGCGT 59.812 44.000 0.00 0.00 0.00 5.07
2891 3873 5.395768 CCCTCCTTCCCATAATATAAGAGCG 60.396 48.000 0.00 0.00 0.00 5.03
2892 3874 5.726793 TCCCTCCTTCCCATAATATAAGAGC 59.273 44.000 0.00 0.00 0.00 4.09
2893 3875 6.962902 ACTCCCTCCTTCCCATAATATAAGAG 59.037 42.308 0.00 0.00 0.00 2.85
2894 3876 6.886637 ACTCCCTCCTTCCCATAATATAAGA 58.113 40.000 0.00 0.00 0.00 2.10
2895 3877 7.901861 ACTACTCCCTCCTTCCCATAATATAAG 59.098 40.741 0.00 0.00 0.00 1.73
2896 3878 7.786968 ACTACTCCCTCCTTCCCATAATATAA 58.213 38.462 0.00 0.00 0.00 0.98
2897 3879 7.372060 ACTACTCCCTCCTTCCCATAATATA 57.628 40.000 0.00 0.00 0.00 0.86
2898 3880 6.248080 ACTACTCCCTCCTTCCCATAATAT 57.752 41.667 0.00 0.00 0.00 1.28
2899 3881 5.698369 ACTACTCCCTCCTTCCCATAATA 57.302 43.478 0.00 0.00 0.00 0.98
2900 3882 4.578149 ACTACTCCCTCCTTCCCATAAT 57.422 45.455 0.00 0.00 0.00 1.28
2901 3883 4.037927 CAACTACTCCCTCCTTCCCATAA 58.962 47.826 0.00 0.00 0.00 1.90
2902 3884 3.013648 ACAACTACTCCCTCCTTCCCATA 59.986 47.826 0.00 0.00 0.00 2.74
2903 3885 2.225908 ACAACTACTCCCTCCTTCCCAT 60.226 50.000 0.00 0.00 0.00 4.00
2904 3886 1.151413 ACAACTACTCCCTCCTTCCCA 59.849 52.381 0.00 0.00 0.00 4.37
2905 3887 1.954035 ACAACTACTCCCTCCTTCCC 58.046 55.000 0.00 0.00 0.00 3.97
2906 3888 4.095211 ACTAACAACTACTCCCTCCTTCC 58.905 47.826 0.00 0.00 0.00 3.46
2907 3889 5.951148 ACTACTAACAACTACTCCCTCCTTC 59.049 44.000 0.00 0.00 0.00 3.46
2908 3890 5.901598 ACTACTAACAACTACTCCCTCCTT 58.098 41.667 0.00 0.00 0.00 3.36
2909 3891 5.533333 ACTACTAACAACTACTCCCTCCT 57.467 43.478 0.00 0.00 0.00 3.69
2910 3892 7.059156 TGATACTACTAACAACTACTCCCTCC 58.941 42.308 0.00 0.00 0.00 4.30
2911 3893 8.694581 ATGATACTACTAACAACTACTCCCTC 57.305 38.462 0.00 0.00 0.00 4.30
2912 3894 9.134055 GAATGATACTACTAACAACTACTCCCT 57.866 37.037 0.00 0.00 0.00 4.20
2913 3895 9.134055 AGAATGATACTACTAACAACTACTCCC 57.866 37.037 0.00 0.00 0.00 4.30
2914 3896 9.953697 CAGAATGATACTACTAACAACTACTCC 57.046 37.037 0.00 0.00 39.69 3.85
2919 3901 9.244292 TCAGACAGAATGATACTACTAACAACT 57.756 33.333 0.00 0.00 39.69 3.16
2920 3902 9.856488 TTCAGACAGAATGATACTACTAACAAC 57.144 33.333 0.00 0.00 39.69 3.32
2921 3903 9.856488 GTTCAGACAGAATGATACTACTAACAA 57.144 33.333 0.00 0.00 39.69 2.83
2922 3904 9.020731 TGTTCAGACAGAATGATACTACTAACA 57.979 33.333 0.00 0.00 39.69 2.41
3010 3992 1.160137 CACAGCAACTAGTTGGAGCC 58.840 55.000 31.42 17.67 40.74 4.70
3094 4076 2.564721 GCCACTGGCCCACAACTTC 61.565 63.158 9.13 0.00 44.06 3.01
4341 5465 6.384224 TCTGACAAATGCAAAGATGATTCAC 58.616 36.000 0.00 0.00 0.00 3.18
4470 5594 2.614057 GCATGGTGGCAGTAGTGTTATC 59.386 50.000 0.00 0.00 0.00 1.75
4523 5647 4.014273 AGATCTAGGGACCTCCATTGTT 57.986 45.455 0.00 0.00 38.24 2.83
4564 5688 9.706691 GATATCGATTTTAGGTCCTACATTTCA 57.293 33.333 1.71 0.00 0.00 2.69
4565 5689 9.930693 AGATATCGATTTTAGGTCCTACATTTC 57.069 33.333 1.71 0.00 0.00 2.17
4654 5778 9.605955 GCAGTTTGTAAATCTTTTTGTTTTTGT 57.394 25.926 0.00 0.00 0.00 2.83
4655 5779 9.604626 TGCAGTTTGTAAATCTTTTTGTTTTTG 57.395 25.926 0.00 0.00 0.00 2.44
4657 5781 9.824534 CTTGCAGTTTGTAAATCTTTTTGTTTT 57.175 25.926 0.00 0.00 0.00 2.43
4658 5782 8.450180 CCTTGCAGTTTGTAAATCTTTTTGTTT 58.550 29.630 0.00 0.00 0.00 2.83
4659 5783 7.821846 TCCTTGCAGTTTGTAAATCTTTTTGTT 59.178 29.630 0.00 0.00 0.00 2.83
4660 5784 7.327214 TCCTTGCAGTTTGTAAATCTTTTTGT 58.673 30.769 0.00 0.00 0.00 2.83
4661 5785 7.706179 TCTCCTTGCAGTTTGTAAATCTTTTTG 59.294 33.333 0.00 0.00 0.00 2.44
4808 5938 9.216117 CTTTACTGGGGTATCCTATTTTATTCG 57.784 37.037 0.00 0.00 36.20 3.34
4877 6007 2.297033 TCAAAAGATTCAGCCAAGGCAC 59.703 45.455 14.40 0.00 44.88 5.01
4957 6087 5.362556 AAACCTGACAATCAAACATCTCG 57.637 39.130 0.00 0.00 0.00 4.04
4964 6094 9.959749 GAAAACACTATAAACCTGACAATCAAA 57.040 29.630 0.00 0.00 0.00 2.69
5125 6261 8.143193 TGCAATGTGAACAGATTTTAAACATCT 58.857 29.630 6.92 6.92 0.00 2.90
5126 6262 8.296799 TGCAATGTGAACAGATTTTAAACATC 57.703 30.769 0.00 0.00 0.00 3.06
5181 6317 6.803642 ACATAGGAGTACCACGTAAGATTTC 58.196 40.000 0.00 0.00 43.62 2.17
5569 6708 9.975218 ATACCATTTGTAAGTGAGTTAATTCCT 57.025 29.630 0.00 0.00 31.94 3.36
5591 6732 4.335594 GGAACAACACATAAGAGCCATACC 59.664 45.833 0.00 0.00 0.00 2.73
5617 6758 3.308323 GCTTCACACAAGATCGAGGAATC 59.692 47.826 0.00 0.00 0.00 2.52
5619 6760 2.037121 TGCTTCACACAAGATCGAGGAA 59.963 45.455 0.00 0.00 0.00 3.36
5631 6772 3.253188 TCAAACCATTAGCTGCTTCACAC 59.747 43.478 7.79 0.00 0.00 3.82
5638 6779 3.129988 AGCTCAATCAAACCATTAGCTGC 59.870 43.478 0.00 0.00 37.44 5.25
6025 7167 0.950836 CGATGACCAGGTGCACAAAA 59.049 50.000 20.43 0.00 0.00 2.44
6136 7278 4.848357 ACATCTCCGAGAAATGGTTGATT 58.152 39.130 1.27 0.00 0.00 2.57
6464 7607 7.889873 TTTCAACAAGGATTAAAGAAGTGGA 57.110 32.000 0.00 0.00 0.00 4.02
6516 7659 2.073816 ACATCTCCAAAGTTAACGCGG 58.926 47.619 12.47 2.44 0.00 6.46
6556 7705 5.177511 CCACGCACATAGGTTTCACATATAG 59.822 44.000 0.00 0.00 0.00 1.31
6557 7706 5.053811 CCACGCACATAGGTTTCACATATA 58.946 41.667 0.00 0.00 0.00 0.86
6558 7707 3.876914 CCACGCACATAGGTTTCACATAT 59.123 43.478 0.00 0.00 0.00 1.78
6559 7708 3.266636 CCACGCACATAGGTTTCACATA 58.733 45.455 0.00 0.00 0.00 2.29
6560 7709 2.083774 CCACGCACATAGGTTTCACAT 58.916 47.619 0.00 0.00 0.00 3.21
6561 7710 1.202710 ACCACGCACATAGGTTTCACA 60.203 47.619 0.00 0.00 29.58 3.58
6562 7711 1.519408 ACCACGCACATAGGTTTCAC 58.481 50.000 0.00 0.00 29.58 3.18
6563 7712 3.404224 TTACCACGCACATAGGTTTCA 57.596 42.857 0.00 0.00 36.87 2.69
6564 7713 3.486875 GCATTACCACGCACATAGGTTTC 60.487 47.826 0.00 0.00 36.87 2.78
6704 7854 8.953368 AATTATCATTTTCATCAAGAAAGGGC 57.047 30.769 0.00 0.00 46.24 5.19
6735 7885 3.010027 TGATGACCCAAATACTCCAAGCA 59.990 43.478 0.00 0.00 0.00 3.91
6738 7888 5.825532 TCATTGATGACCCAAATACTCCAA 58.174 37.500 0.00 0.00 0.00 3.53
6751 7901 5.235186 GCTACACACCTGTATCATTGATGAC 59.765 44.000 9.46 4.76 40.03 3.06
6773 7923 2.688477 TCCAACCCTTTCCATTTTGCT 58.312 42.857 0.00 0.00 0.00 3.91
6803 7954 3.427503 CGGGTTGGCTAGCTGTAAAAATG 60.428 47.826 15.72 0.00 0.00 2.32
6843 7995 5.424121 AATCTGATAATACGCACAAAGGC 57.576 39.130 0.00 0.00 0.00 4.35
6896 8048 3.189287 AGTTTGAATCAAGTCGCACATCC 59.811 43.478 0.00 0.00 0.00 3.51
6903 8055 4.752101 AGTTGGAGAGTTTGAATCAAGTCG 59.248 41.667 0.00 0.00 0.00 4.18
6914 8066 9.274206 GTAACTGAATAAAGAGTTGGAGAGTTT 57.726 33.333 0.00 0.00 34.28 2.66
6933 8085 0.822944 TCGGTCACCACGGTAACTGA 60.823 55.000 0.00 0.00 29.76 3.41
6934 8086 0.388134 CTCGGTCACCACGGTAACTG 60.388 60.000 0.00 0.00 0.00 3.16
7029 8181 4.101942 GCGTCAATTATTTTGGATCGCAA 58.898 39.130 0.00 0.00 40.63 4.85
7129 8281 8.211629 ACATAGTACCTTTTATTCATGTCTCCC 58.788 37.037 0.00 0.00 0.00 4.30
7152 8304 6.916360 AACCCACAAGTCATTATTTCACAT 57.084 33.333 0.00 0.00 0.00 3.21
7157 8309 8.977412 CCCTTATAAACCCACAAGTCATTATTT 58.023 33.333 0.00 0.00 0.00 1.40
7160 8312 7.034967 ACCCTTATAAACCCACAAGTCATTA 57.965 36.000 0.00 0.00 0.00 1.90
7161 8313 5.899278 ACCCTTATAAACCCACAAGTCATT 58.101 37.500 0.00 0.00 0.00 2.57
7164 8316 6.303903 TCTACCCTTATAAACCCACAAGTC 57.696 41.667 0.00 0.00 0.00 3.01
7165 8317 6.707273 TTCTACCCTTATAAACCCACAAGT 57.293 37.500 0.00 0.00 0.00 3.16
7166 8318 9.862149 ATATTTCTACCCTTATAAACCCACAAG 57.138 33.333 0.00 0.00 0.00 3.16
7207 8359 5.920273 CAGTTTTGCATCCTACGAAATTTGT 59.080 36.000 0.00 0.00 0.00 2.83
7275 8427 8.511604 AGTTAATGCATATTAAAGCACTGACT 57.488 30.769 0.00 2.82 44.49 3.41
7320 8472 9.561069 AGAGTATTATTAACCATGCTTTAGTGG 57.439 33.333 0.00 0.00 41.35 4.00
7325 8477 8.621286 CGGAAAGAGTATTATTAACCATGCTTT 58.379 33.333 0.00 0.00 0.00 3.51
7326 8478 7.773690 ACGGAAAGAGTATTATTAACCATGCTT 59.226 33.333 0.00 0.00 0.00 3.91
7327 8479 7.280356 ACGGAAAGAGTATTATTAACCATGCT 58.720 34.615 0.00 0.00 0.00 3.79
7328 8480 7.492352 ACGGAAAGAGTATTATTAACCATGC 57.508 36.000 0.00 0.00 0.00 4.06
7329 8481 8.557029 GGAACGGAAAGAGTATTATTAACCATG 58.443 37.037 0.00 0.00 0.00 3.66
7330 8482 8.269317 TGGAACGGAAAGAGTATTATTAACCAT 58.731 33.333 0.00 0.00 0.00 3.55
7331 8483 7.622713 TGGAACGGAAAGAGTATTATTAACCA 58.377 34.615 0.00 0.00 0.00 3.67
7332 8484 8.672823 ATGGAACGGAAAGAGTATTATTAACC 57.327 34.615 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.