Multiple sequence alignment - TraesCS3A01G416200

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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 TraesCS3A01G416200 chr3A 100.000 3937 0 0 1 3937 658908061 658904125 0.000000e+00 7271.0
1 TraesCS3A01G416200 chr3A 85.795 887 74 33 1366 2238 658984605 658983757 0.000000e+00 893.0
2 TraesCS3A01G416200 chr3A 86.248 509 32 16 837 1334 658985073 658984592 5.830000e-143 518.0
3 TraesCS3A01G416200 chr3A 86.486 259 25 5 2686 2938 658983399 658983145 3.880000e-70 276.0
4 TraesCS3A01G416200 chr3A 87.387 222 19 6 598 814 658985941 658985724 3.040000e-61 246.0
5 TraesCS3A01G416200 chr3A 88.298 188 15 5 641 824 658985712 658985528 6.620000e-53 219.0
6 TraesCS3A01G416200 chr3A 95.763 118 3 2 2152 2268 658905835 658905719 5.190000e-44 189.0
7 TraesCS3A01G416200 chr3A 95.763 118 3 2 2227 2343 658905910 658905794 5.190000e-44 189.0
8 TraesCS3A01G416200 chr3A 74.662 517 66 35 1703 2173 658984223 658983726 6.770000e-38 169.0
9 TraesCS3A01G416200 chr3A 75.184 407 42 27 1938 2313 658984135 658983757 1.910000e-28 137.0
10 TraesCS3A01G416200 chr3D 86.630 1653 139 46 592 2207 524648575 524646968 0.000000e+00 1753.0
11 TraesCS3A01G416200 chr3D 85.910 1604 127 66 769 2312 524311516 524309952 0.000000e+00 1618.0
12 TraesCS3A01G416200 chr3D 89.468 978 74 11 2946 3908 524309117 524308154 0.000000e+00 1208.0
13 TraesCS3A01G416200 chr3D 82.462 918 80 46 1353 2237 524310821 524309952 0.000000e+00 728.0
14 TraesCS3A01G416200 chr3D 86.565 588 69 5 5 587 2778323 2778905 1.190000e-179 640.0
15 TraesCS3A01G416200 chr3D 85.520 587 37 20 2401 2944 524309782 524309201 1.590000e-158 569.0
16 TraesCS3A01G416200 chr3D 97.647 170 2 2 665 833 524311670 524311502 1.380000e-74 291.0
17 TraesCS3A01G416200 chr3D 86.038 265 21 7 2686 2938 524646672 524646412 1.800000e-68 270.0
18 TraesCS3A01G416200 chr3D 75.379 264 45 11 1985 2238 524310114 524309861 4.160000e-20 110.0
19 TraesCS3A01G416200 chr3D 95.588 68 3 0 1820 1887 524647394 524647327 4.160000e-20 110.0
20 TraesCS3A01G416200 chr3D 100.000 35 0 0 2337 2371 524309888 524309854 9.130000e-07 65.8
21 TraesCS3A01G416200 chr3D 93.548 31 2 0 1655 1685 524310444 524310414 3.300000e-01 47.3
22 TraesCS3A01G416200 chr3B 85.314 1784 148 71 653 2371 691752559 691750825 0.000000e+00 1738.0
23 TraesCS3A01G416200 chr3B 87.835 970 78 19 2946 3895 691750104 691749155 0.000000e+00 1101.0
24 TraesCS3A01G416200 chr3B 85.892 964 79 29 1308 2238 691923782 691922843 0.000000e+00 974.0
25 TraesCS3A01G416200 chr3B 87.092 612 33 9 2368 2940 691750795 691750191 0.000000e+00 651.0
26 TraesCS3A01G416200 chr3B 86.837 547 30 16 1747 2272 691751374 691750849 1.230000e-159 573.0
27 TraesCS3A01G416200 chr3B 82.753 574 88 9 18 587 160038601 160038035 5.870000e-138 501.0
28 TraesCS3A01G416200 chr3B 89.770 391 17 12 857 1224 691924169 691923779 2.750000e-131 479.0
29 TraesCS3A01G416200 chr3B 90.785 293 18 6 592 879 691924503 691924215 2.220000e-102 383.0
30 TraesCS3A01G416200 chr3B 89.494 257 20 4 2686 2939 691922458 691922206 6.350000e-83 318.0
31 TraesCS3A01G416200 chr3B 77.745 337 42 23 1525 1858 691751614 691751308 4.040000e-40 176.0
32 TraesCS3A01G416200 chr3B 79.817 218 32 8 3018 3233 691775647 691775440 8.810000e-32 148.0
33 TraesCS3A01G416200 chr3B 76.761 284 29 16 2053 2313 691923112 691922843 1.490000e-24 124.0
34 TraesCS3A01G416200 chr3B 100.000 33 0 0 763 795 691924208 691924176 1.180000e-05 62.1
35 TraesCS3A01G416200 chr3B 77.143 105 16 4 1588 1685 691751506 691751403 2.000000e-03 54.7
36 TraesCS3A01G416200 chr2D 86.655 592 67 8 1 587 640278997 640278413 0.000000e+00 645.0
37 TraesCS3A01G416200 chr2D 83.502 594 82 10 2 587 339369290 339369875 1.240000e-149 540.0
38 TraesCS3A01G416200 chr2D 81.619 593 98 6 1 587 479171495 479172082 7.650000e-132 481.0
39 TraesCS3A01G416200 chr1D 88.803 518 45 8 1 512 448373906 448374416 1.200000e-174 623.0
40 TraesCS3A01G416200 chr2A 86.038 573 71 7 19 587 648528273 648528840 1.210000e-169 606.0
41 TraesCS3A01G416200 chr2A 83.670 594 77 13 1 587 491575325 491575905 3.460000e-150 542.0
42 TraesCS3A01G416200 chr2A 83.649 581 84 7 18 595 451539479 451540051 1.610000e-148 536.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G416200 chr3A 658904125 658908061 3936 True 2549.666667 7271 97.175333 1 3937 3 chr3A.!!$R1 3936
1 TraesCS3A01G416200 chr3A 658983145 658985941 2796 True 351.142857 893 83.437143 598 2938 7 chr3A.!!$R2 2340
2 TraesCS3A01G416200 chr3D 524646412 524648575 2163 True 711.000000 1753 89.418667 592 2938 3 chr3D.!!$R2 2346
3 TraesCS3A01G416200 chr3D 2778323 2778905 582 False 640.000000 640 86.565000 5 587 1 chr3D.!!$F1 582
4 TraesCS3A01G416200 chr3D 524308154 524311670 3516 True 579.637500 1618 88.741750 665 3908 8 chr3D.!!$R1 3243
5 TraesCS3A01G416200 chr3B 691749155 691752559 3404 True 715.616667 1738 83.661000 653 3895 6 chr3B.!!$R3 3242
6 TraesCS3A01G416200 chr3B 160038035 160038601 566 True 501.000000 501 82.753000 18 587 1 chr3B.!!$R1 569
7 TraesCS3A01G416200 chr3B 691922206 691924503 2297 True 390.016667 974 88.783667 592 2939 6 chr3B.!!$R4 2347
8 TraesCS3A01G416200 chr2D 640278413 640278997 584 True 645.000000 645 86.655000 1 587 1 chr2D.!!$R1 586
9 TraesCS3A01G416200 chr2D 339369290 339369875 585 False 540.000000 540 83.502000 2 587 1 chr2D.!!$F1 585
10 TraesCS3A01G416200 chr2D 479171495 479172082 587 False 481.000000 481 81.619000 1 587 1 chr2D.!!$F2 586
11 TraesCS3A01G416200 chr1D 448373906 448374416 510 False 623.000000 623 88.803000 1 512 1 chr1D.!!$F1 511
12 TraesCS3A01G416200 chr2A 648528273 648528840 567 False 606.000000 606 86.038000 19 587 1 chr2A.!!$F3 568
13 TraesCS3A01G416200 chr2A 491575325 491575905 580 False 542.000000 542 83.670000 1 587 1 chr2A.!!$F2 586
14 TraesCS3A01G416200 chr2A 451539479 451540051 572 False 536.000000 536 83.649000 18 595 1 chr2A.!!$F1 577

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
974 1741 0.463116 ACGGCGCCTATAAAACCCTG 60.463 55.000 26.68 6.43 0.00 4.45 F
1413 2226 1.142748 GTACCAGCATGAGAGCGCT 59.857 57.895 11.27 11.27 39.69 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2816 0.034059 CTTCTGGACCTTGCTGTCGT 59.966 55.0 0.0 0.0 36.07 4.34 R
3011 4338 0.034380 GAGGAAACCTGGCCCTTACC 60.034 60.0 0.0 0.0 31.76 2.85 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
61 65 6.401047 TCTTGACTATCTTTATACCCACCG 57.599 41.667 0.00 0.00 0.00 4.94
101 105 2.562296 TGCCTCCTTCTTTAGGTCCAT 58.438 47.619 0.00 0.00 45.03 3.41
103 107 2.483889 GCCTCCTTCTTTAGGTCCATCG 60.484 54.545 0.00 0.00 45.03 3.84
194 201 3.003480 GGCTTGTCAAGAGTGATACCAC 58.997 50.000 16.99 0.00 43.50 4.16
208 215 4.021368 GTGATACCACTATACAAGCCGGAT 60.021 45.833 5.05 0.00 40.10 4.18
231 238 1.672145 GGTCGCTCTTAGTTCCGCTTT 60.672 52.381 0.00 0.00 0.00 3.51
234 241 2.751259 TCGCTCTTAGTTCCGCTTTCTA 59.249 45.455 0.00 0.00 0.00 2.10
361 369 4.242475 ACTTGCGTCGACATTAATCTTGA 58.758 39.130 17.16 0.00 0.00 3.02
400 408 4.348168 GGAGGCTTCCAGGAGATAACATTA 59.652 45.833 10.56 0.00 43.45 1.90
401 409 5.163195 GGAGGCTTCCAGGAGATAACATTAA 60.163 44.000 10.56 0.00 43.45 1.40
405 413 7.514127 AGGCTTCCAGGAGATAACATTAATCTA 59.486 37.037 0.00 0.00 0.00 1.98
463 472 4.605640 ATTGCTTACCTTTGTTGCACAT 57.394 36.364 0.00 0.00 34.18 3.21
474 484 1.171308 GTTGCACATCATCACCTGCT 58.829 50.000 0.00 0.00 0.00 4.24
483 493 1.337703 TCATCACCTGCTTGTTTGCAC 59.662 47.619 0.00 0.00 38.12 4.57
556 567 4.200092 GCGATGGATTCCTTTCCTTTACT 58.800 43.478 3.95 0.00 36.68 2.24
561 572 8.903820 CGATGGATTCCTTTCCTTTACTAAAAT 58.096 33.333 3.95 0.00 36.68 1.82
587 598 5.664294 AATTATTCATCAAGTGCCAAGCA 57.336 34.783 0.00 0.00 35.60 3.91
588 599 4.707030 TTATTCATCAAGTGCCAAGCAG 57.293 40.909 0.00 0.00 40.08 4.24
611 622 5.047872 AGTCTCTACCCTCTTTTCGAAAGAC 60.048 44.000 10.98 10.41 41.84 3.01
689 702 7.490657 AATATACGATAAGTAAGCATCCCCA 57.509 36.000 0.00 0.00 39.04 4.96
879 1640 5.854010 AGGTTCGAATCACTAGATGCTTA 57.146 39.130 11.72 0.00 33.90 3.09
974 1741 0.463116 ACGGCGCCTATAAAACCCTG 60.463 55.000 26.68 6.43 0.00 4.45
982 1749 2.447047 CCTATAAAACCCTGCCTCCCAT 59.553 50.000 0.00 0.00 0.00 4.00
1007 1792 4.679654 GCCACATACAACTAGCAAAACAAC 59.320 41.667 0.00 0.00 0.00 3.32
1008 1797 5.507315 GCCACATACAACTAGCAAAACAACT 60.507 40.000 0.00 0.00 0.00 3.16
1013 1802 5.828299 ACAACTAGCAAAACAACTAAGCA 57.172 34.783 0.00 0.00 0.00 3.91
1014 1803 6.202516 ACAACTAGCAAAACAACTAAGCAA 57.797 33.333 0.00 0.00 0.00 3.91
1015 1804 6.265577 ACAACTAGCAAAACAACTAAGCAAG 58.734 36.000 0.00 0.00 0.00 4.01
1016 1805 4.860072 ACTAGCAAAACAACTAAGCAAGC 58.140 39.130 0.00 0.00 0.00 4.01
1017 1806 3.097877 AGCAAAACAACTAAGCAAGCC 57.902 42.857 0.00 0.00 0.00 4.35
1018 1807 2.430332 AGCAAAACAACTAAGCAAGCCA 59.570 40.909 0.00 0.00 0.00 4.75
1275 2079 1.520342 GTGCTCTGAGGATGCCGAC 60.520 63.158 6.83 0.00 0.00 4.79
1374 2178 2.202932 CAGAAGCACGGCGGCTAT 60.203 61.111 20.24 11.33 45.07 2.97
1377 2181 4.096003 AAGCACGGCGGCTATGGT 62.096 61.111 20.24 8.24 45.07 3.55
1412 2225 2.233654 CGTACCAGCATGAGAGCGC 61.234 63.158 0.00 0.00 39.69 5.92
1413 2226 1.142748 GTACCAGCATGAGAGCGCT 59.857 57.895 11.27 11.27 39.69 5.92
1486 2299 1.714899 CTATGGCGGACAAAAGGCGG 61.715 60.000 0.00 0.00 35.52 6.13
1812 2811 2.886124 GGCTACGGCGAGCAGAAC 60.886 66.667 24.88 10.16 44.76 3.01
1823 2822 3.061674 GCAGAACGCGTACGACAG 58.938 61.111 21.65 11.75 43.93 3.51
1824 2823 3.055905 GCAGAACGCGTACGACAGC 62.056 63.158 21.65 9.59 43.93 4.40
1825 2824 1.728074 CAGAACGCGTACGACAGCA 60.728 57.895 21.65 0.00 43.93 4.41
1826 2825 1.008194 AGAACGCGTACGACAGCAA 60.008 52.632 21.65 0.00 43.93 3.91
1827 2826 1.002250 AGAACGCGTACGACAGCAAG 61.002 55.000 21.65 2.90 43.93 4.01
1828 2827 1.941476 GAACGCGTACGACAGCAAGG 61.941 60.000 21.65 0.00 43.93 3.61
1829 2828 2.430244 CGCGTACGACAGCAAGGT 60.430 61.111 21.65 0.00 43.93 3.50
1830 2829 2.434134 CGCGTACGACAGCAAGGTC 61.434 63.158 21.65 0.00 43.93 3.85
1831 2830 2.092882 GCGTACGACAGCAAGGTCC 61.093 63.158 21.65 0.00 34.24 4.46
1832 2831 1.287815 CGTACGACAGCAAGGTCCA 59.712 57.895 10.44 0.00 34.24 4.02
1833 2832 0.732880 CGTACGACAGCAAGGTCCAG 60.733 60.000 10.44 0.00 34.24 3.86
1834 2833 0.601558 GTACGACAGCAAGGTCCAGA 59.398 55.000 0.00 0.00 34.24 3.86
1835 2834 1.000506 GTACGACAGCAAGGTCCAGAA 59.999 52.381 0.00 0.00 34.24 3.02
1836 2835 0.034059 ACGACAGCAAGGTCCAGAAG 59.966 55.000 0.00 0.00 34.24 2.85
1837 2836 1.294659 CGACAGCAAGGTCCAGAAGC 61.295 60.000 0.00 0.00 34.24 3.86
1838 2837 0.250467 GACAGCAAGGTCCAGAAGCA 60.250 55.000 0.00 0.00 0.00 3.91
1839 2838 0.403271 ACAGCAAGGTCCAGAAGCAT 59.597 50.000 0.00 0.00 0.00 3.79
1840 2839 0.809385 CAGCAAGGTCCAGAAGCATG 59.191 55.000 0.00 0.00 0.00 4.06
1841 2840 0.323178 AGCAAGGTCCAGAAGCATGG 60.323 55.000 0.00 0.00 42.11 3.66
1842 2841 1.941999 GCAAGGTCCAGAAGCATGGC 61.942 60.000 0.00 0.00 40.41 4.40
1843 2842 0.323178 CAAGGTCCAGAAGCATGGCT 60.323 55.000 0.00 0.00 42.56 4.75
1844 2843 1.065199 CAAGGTCCAGAAGCATGGCTA 60.065 52.381 0.00 0.00 38.25 3.93
1845 2844 1.516110 AGGTCCAGAAGCATGGCTAT 58.484 50.000 0.00 0.00 38.25 2.97
1846 2845 1.142465 AGGTCCAGAAGCATGGCTATG 59.858 52.381 5.55 5.55 38.25 2.23
1847 2846 1.602311 GTCCAGAAGCATGGCTATGG 58.398 55.000 12.41 13.42 43.02 2.74
1848 2847 0.179009 TCCAGAAGCATGGCTATGGC 60.179 55.000 12.41 4.41 42.07 4.40
1849 2848 1.512996 CCAGAAGCATGGCTATGGCG 61.513 60.000 12.41 0.00 38.25 5.69
1850 2849 0.533531 CAGAAGCATGGCTATGGCGA 60.534 55.000 12.41 0.00 38.25 5.54
1851 2850 0.250209 AGAAGCATGGCTATGGCGAG 60.250 55.000 12.41 0.00 38.25 5.03
1852 2851 0.250038 GAAGCATGGCTATGGCGAGA 60.250 55.000 12.41 0.00 38.25 4.04
1853 2852 0.181114 AAGCATGGCTATGGCGAGAA 59.819 50.000 12.41 0.00 38.25 2.87
1854 2853 0.250209 AGCATGGCTATGGCGAGAAG 60.250 55.000 12.41 0.00 36.99 2.85
1855 2854 1.233285 GCATGGCTATGGCGAGAAGG 61.233 60.000 12.41 0.00 39.81 3.46
1856 2855 1.072159 ATGGCTATGGCGAGAAGGC 59.928 57.895 0.00 1.35 46.95 4.35
1878 2877 4.040068 GGCTATGGCGAGCAGAAG 57.960 61.111 12.59 0.00 44.76 2.85
1879 2878 1.596477 GGCTATGGCGAGCAGAAGG 60.596 63.158 12.59 0.00 44.76 3.46
1880 2879 2.250237 GCTATGGCGAGCAGAAGGC 61.250 63.158 6.35 0.00 42.36 4.35
2193 3243 2.594592 GCTGCTTTCCACCACGGT 60.595 61.111 0.00 0.00 35.57 4.83
2268 3354 1.071471 CTCTGCTTTCCACCACGGT 59.929 57.895 0.00 0.00 35.57 4.83
2330 3446 2.799371 CGGAGGGTACGACTCTGC 59.201 66.667 13.73 0.00 33.24 4.26
2331 3447 1.749638 CGGAGGGTACGACTCTGCT 60.750 63.158 13.73 0.00 34.57 4.24
2332 3448 1.313812 CGGAGGGTACGACTCTGCTT 61.314 60.000 13.73 0.00 34.57 3.91
2333 3449 0.896226 GGAGGGTACGACTCTGCTTT 59.104 55.000 13.73 0.00 33.86 3.51
2334 3450 1.135053 GGAGGGTACGACTCTGCTTTC 60.135 57.143 13.73 0.00 33.86 2.62
2335 3451 0.896226 AGGGTACGACTCTGCTTTCC 59.104 55.000 0.00 0.00 0.00 3.13
2336 3452 0.606604 GGGTACGACTCTGCTTTCCA 59.393 55.000 0.00 0.00 0.00 3.53
2337 3453 1.404315 GGGTACGACTCTGCTTTCCAG 60.404 57.143 0.00 0.00 43.17 3.86
2348 3464 3.950794 CTTTCCAGCACGGCGCCTA 62.951 63.158 26.68 0.00 44.04 3.93
2349 3465 3.323758 TTTCCAGCACGGCGCCTAT 62.324 57.895 26.68 9.97 44.04 2.57
2350 3466 4.529219 TCCAGCACGGCGCCTATG 62.529 66.667 26.68 22.96 44.04 2.23
2362 3478 2.111878 CCTATGGCGGGCAGAAGG 59.888 66.667 17.57 17.57 0.00 3.46
2363 3479 2.592861 CTATGGCGGGCAGAAGGC 60.593 66.667 10.83 0.00 43.74 4.35
2364 3480 4.545706 TATGGCGGGCAGAAGGCG 62.546 66.667 10.83 0.00 46.16 5.52
2398 3514 2.750350 CCCAGAAGAAGCACGGGT 59.250 61.111 0.00 0.00 31.80 5.28
2417 3551 0.321387 TACGGGCAAAATGCGTACCA 60.321 50.000 0.00 0.00 46.21 3.25
2457 3591 1.585521 CGACGTCGCAGGGTATGAC 60.586 63.158 26.59 0.00 0.00 3.06
2506 3640 0.883833 GCAGCTGCAATACAACCAGT 59.116 50.000 33.36 0.00 41.59 4.00
2507 3641 1.270550 GCAGCTGCAATACAACCAGTT 59.729 47.619 33.36 0.00 41.59 3.16
2523 3669 3.379445 TTCGGGTGGGAGAGCGAC 61.379 66.667 0.00 0.00 0.00 5.19
2526 3672 3.379445 GGGTGGGAGAGCGACGAA 61.379 66.667 0.00 0.00 0.00 3.85
2657 3827 3.511595 CCACTACGAGGCGGCGTA 61.512 66.667 9.37 13.39 43.61 4.42
2658 3828 2.277756 CACTACGAGGCGGCGTAC 60.278 66.667 9.37 1.56 43.61 3.67
2659 3829 3.512516 ACTACGAGGCGGCGTACC 61.513 66.667 9.37 1.22 43.61 3.34
2660 3830 3.511595 CTACGAGGCGGCGTACCA 61.512 66.667 9.37 0.00 43.61 3.25
2661 3831 3.465296 CTACGAGGCGGCGTACCAG 62.465 68.421 9.37 3.23 43.61 4.00
2662 3832 3.974835 TACGAGGCGGCGTACCAGA 62.975 63.158 9.37 0.00 43.61 3.86
2663 3833 4.554363 CGAGGCGGCGTACCAGAG 62.554 72.222 9.37 0.00 34.57 3.35
2664 3834 4.874977 GAGGCGGCGTACCAGAGC 62.875 72.222 9.37 0.00 34.57 4.09
2666 3836 4.874977 GGCGGCGTACCAGAGCTC 62.875 72.222 9.37 5.27 34.57 4.09
2667 3837 4.874977 GCGGCGTACCAGAGCTCC 62.875 72.222 10.93 0.00 34.57 4.70
2668 3838 3.449227 CGGCGTACCAGAGCTCCA 61.449 66.667 10.93 0.00 34.57 3.86
2669 3839 2.184579 GGCGTACCAGAGCTCCAC 59.815 66.667 10.93 2.71 35.26 4.02
2670 3840 2.184579 GCGTACCAGAGCTCCACC 59.815 66.667 10.93 0.00 0.00 4.61
2671 3841 2.646175 GCGTACCAGAGCTCCACCA 61.646 63.158 10.93 0.00 0.00 4.17
2672 3842 1.215647 CGTACCAGAGCTCCACCAC 59.784 63.158 10.93 3.09 0.00 4.16
2673 3843 1.597461 GTACCAGAGCTCCACCACC 59.403 63.158 10.93 0.00 0.00 4.61
2674 3844 1.612442 TACCAGAGCTCCACCACCC 60.612 63.158 10.93 0.00 0.00 4.61
2675 3845 2.395180 TACCAGAGCTCCACCACCCA 62.395 60.000 10.93 0.00 0.00 4.51
2676 3846 2.667418 CAGAGCTCCACCACCCAG 59.333 66.667 10.93 0.00 0.00 4.45
2677 3847 2.608988 AGAGCTCCACCACCCAGG 60.609 66.667 10.93 0.00 45.67 4.45
2678 3848 3.721706 GAGCTCCACCACCCAGGG 61.722 72.222 2.85 2.85 43.89 4.45
2760 3995 4.641645 CCTGCGTCCTGCCCACAA 62.642 66.667 0.00 0.00 45.60 3.33
2773 4008 1.800315 CCACAAGCGACGACTACCG 60.800 63.158 0.00 0.00 45.44 4.02
2809 4050 6.136857 TCCTACCTGCAGTGATACTTATCTT 58.863 40.000 13.81 0.00 33.88 2.40
2811 4052 5.283457 ACCTGCAGTGATACTTATCTTCC 57.717 43.478 13.81 0.00 33.88 3.46
2812 4053 4.716784 ACCTGCAGTGATACTTATCTTCCA 59.283 41.667 13.81 0.00 33.88 3.53
2934 4180 5.921976 CGTAAGTGGCATCGGTACAATAATA 59.078 40.000 0.00 0.00 0.00 0.98
2940 4186 8.248945 AGTGGCATCGGTACAATAATATACTAC 58.751 37.037 0.00 0.00 0.00 2.73
2941 4187 7.219535 GTGGCATCGGTACAATAATATACTACG 59.780 40.741 0.00 0.00 0.00 3.51
2942 4188 7.094248 TGGCATCGGTACAATAATATACTACGT 60.094 37.037 0.00 0.00 0.00 3.57
2943 4189 7.219535 GGCATCGGTACAATAATATACTACGTG 59.780 40.741 0.00 0.00 0.00 4.49
2944 4190 7.219535 GCATCGGTACAATAATATACTACGTGG 59.780 40.741 0.00 0.00 0.00 4.94
2989 4316 4.762289 ACTAGTAGGCAGCTGCTATTTT 57.238 40.909 35.82 20.38 41.70 1.82
2990 4317 4.698575 ACTAGTAGGCAGCTGCTATTTTC 58.301 43.478 35.82 19.44 41.70 2.29
2991 4318 3.634397 AGTAGGCAGCTGCTATTTTCA 57.366 42.857 35.82 12.13 41.70 2.69
3011 4338 4.614946 TCATCATGAACGATACTGAGCAG 58.385 43.478 0.00 0.00 0.00 4.24
3178 4505 1.439679 CCCACTCTTTTCTACACCGC 58.560 55.000 0.00 0.00 0.00 5.68
3237 4567 4.562082 TGACGGTAAGTGTAAATCCACAG 58.438 43.478 0.00 0.00 37.82 3.66
3242 4572 4.096382 GGTAAGTGTAAATCCACAGGCATG 59.904 45.833 0.00 0.00 37.82 4.06
3257 4587 4.281435 ACAGGCATGAATTGATTTGTGTCA 59.719 37.500 4.84 0.00 0.00 3.58
3258 4588 4.624024 CAGGCATGAATTGATTTGTGTCAC 59.376 41.667 0.00 0.00 0.00 3.67
3259 4589 4.281435 AGGCATGAATTGATTTGTGTCACA 59.719 37.500 0.18 0.18 0.00 3.58
3262 4592 4.915158 TGAATTGATTTGTGTCACAGCA 57.085 36.364 5.67 3.71 0.00 4.41
3269 4599 3.483808 TTTGTGTCACAGCATGGAGTA 57.516 42.857 5.67 0.00 43.62 2.59
3370 4712 0.250234 CATTCTCCGACTTGCCCTGA 59.750 55.000 0.00 0.00 0.00 3.86
3374 4716 1.533033 TCCGACTTGCCCTGACAGA 60.533 57.895 3.32 0.00 0.00 3.41
3450 4793 4.771577 TGAAACGGTGACTATACCTGGTTA 59.228 41.667 3.84 0.00 38.62 2.85
3489 4832 2.349590 TGATGAACAATCCACTGAGCG 58.650 47.619 0.00 0.00 34.00 5.03
3516 4859 5.075493 ACAACTCCAATTTTCTCATGAGCT 58.925 37.500 18.36 0.00 0.00 4.09
3529 4873 5.012239 TCTCATGAGCTGGCTGTTTAATTT 58.988 37.500 18.36 0.00 0.00 1.82
3532 4876 6.855836 TCATGAGCTGGCTGTTTAATTTAAG 58.144 36.000 0.00 0.00 0.00 1.85
3534 4878 7.340232 TCATGAGCTGGCTGTTTAATTTAAGAT 59.660 33.333 0.00 0.00 0.00 2.40
3535 4879 7.088589 TGAGCTGGCTGTTTAATTTAAGATC 57.911 36.000 0.00 0.00 0.00 2.75
3541 4885 8.420374 TGGCTGTTTAATTTAAGATCGAGTAG 57.580 34.615 0.00 0.00 0.00 2.57
3544 4888 9.903185 GCTGTTTAATTTAAGATCGAGTAGAAC 57.097 33.333 0.00 0.00 0.00 3.01
3552 4896 5.723672 AAGATCGAGTAGAACAGTTCCAA 57.276 39.130 9.85 0.00 0.00 3.53
3560 4905 6.866770 CGAGTAGAACAGTTCCAATCAGTAAA 59.133 38.462 9.85 0.00 0.00 2.01
3566 4911 6.331369 ACAGTTCCAATCAGTAAAACATGG 57.669 37.500 0.00 0.00 0.00 3.66
3568 4913 6.721208 ACAGTTCCAATCAGTAAAACATGGAT 59.279 34.615 0.00 0.00 36.87 3.41
3570 4915 6.721208 AGTTCCAATCAGTAAAACATGGATGT 59.279 34.615 0.00 0.00 44.20 3.06
3596 4941 4.706962 GGGGAAAGCATGTAAAGTGAAGAT 59.293 41.667 0.00 0.00 0.00 2.40
3611 4957 5.975410 GTGAAGATCACATAACTACAGCC 57.025 43.478 5.65 0.00 46.22 4.85
3614 4960 2.706190 AGATCACATAACTACAGCCCCC 59.294 50.000 0.00 0.00 0.00 5.40
3735 5081 6.260271 GGTTTTGTAGGATTACAGTCCATAGC 59.740 42.308 0.00 0.00 40.68 2.97
3784 5130 5.652994 TTTGGATCAAAGGAATAAACCCG 57.347 39.130 0.00 0.00 0.00 5.28
3806 5152 3.381272 GCCAAACTTCCTATGCATTGCTA 59.619 43.478 3.54 0.00 0.00 3.49
3822 5168 2.047061 TGCTATCTACGCCCCAATTCT 58.953 47.619 0.00 0.00 0.00 2.40
3836 5182 2.104963 CCAATTCTACAGGGTCCCTAGC 59.895 54.545 11.12 0.00 29.64 3.42
3837 5183 2.771943 CAATTCTACAGGGTCCCTAGCA 59.228 50.000 11.12 0.00 29.64 3.49
3838 5184 2.634639 TTCTACAGGGTCCCTAGCAA 57.365 50.000 11.12 0.00 29.64 3.91
3839 5185 2.868964 TCTACAGGGTCCCTAGCAAT 57.131 50.000 11.12 0.00 29.64 3.56
3852 5198 6.717084 GGTCCCTAGCAATCAATTTAAGCTAT 59.283 38.462 0.00 0.00 37.20 2.97
3889 5235 7.166167 AGGAGGTTAACTTAAATGTACAGTGG 58.834 38.462 5.42 0.00 0.00 4.00
3901 5247 4.746535 TGTACAGTGGTCACTTTCAAGA 57.253 40.909 0.20 0.00 40.20 3.02
3902 5248 4.693283 TGTACAGTGGTCACTTTCAAGAG 58.307 43.478 0.20 0.00 40.20 2.85
3903 5249 4.404394 TGTACAGTGGTCACTTTCAAGAGA 59.596 41.667 0.20 0.00 40.20 3.10
3904 5250 4.065321 ACAGTGGTCACTTTCAAGAGAG 57.935 45.455 0.20 0.00 40.20 3.20
3905 5251 2.805099 CAGTGGTCACTTTCAAGAGAGC 59.195 50.000 8.68 8.68 42.10 4.09
3907 5253 3.558931 TGGTCACTTTCAAGAGAGCAA 57.441 42.857 14.13 1.96 46.04 3.91
3908 5254 3.884895 TGGTCACTTTCAAGAGAGCAAA 58.115 40.909 14.13 0.00 46.04 3.68
3909 5255 3.879295 TGGTCACTTTCAAGAGAGCAAAG 59.121 43.478 14.13 0.00 46.04 2.77
3910 5256 4.130118 GGTCACTTTCAAGAGAGCAAAGA 58.870 43.478 10.24 0.00 41.62 2.52
3911 5257 4.576463 GGTCACTTTCAAGAGAGCAAAGAA 59.424 41.667 10.24 0.00 41.62 2.52
3912 5258 5.066505 GGTCACTTTCAAGAGAGCAAAGAAA 59.933 40.000 10.24 0.00 41.62 2.52
3913 5259 6.404734 GGTCACTTTCAAGAGAGCAAAGAAAA 60.405 38.462 10.24 0.00 41.62 2.29
3914 5260 7.199078 GTCACTTTCAAGAGAGCAAAGAAAAT 58.801 34.615 0.00 0.00 32.44 1.82
3915 5261 8.345565 GTCACTTTCAAGAGAGCAAAGAAAATA 58.654 33.333 0.00 0.00 32.44 1.40
3916 5262 8.345565 TCACTTTCAAGAGAGCAAAGAAAATAC 58.654 33.333 0.00 0.00 32.44 1.89
3917 5263 7.592903 CACTTTCAAGAGAGCAAAGAAAATACC 59.407 37.037 0.00 0.00 32.44 2.73
3918 5264 7.503902 ACTTTCAAGAGAGCAAAGAAAATACCT 59.496 33.333 0.00 0.00 32.44 3.08
3919 5265 7.440523 TTCAAGAGAGCAAAGAAAATACCTC 57.559 36.000 0.00 0.00 0.00 3.85
3920 5266 5.940470 TCAAGAGAGCAAAGAAAATACCTCC 59.060 40.000 0.00 0.00 0.00 4.30
3921 5267 5.505181 AGAGAGCAAAGAAAATACCTCCA 57.495 39.130 0.00 0.00 0.00 3.86
3922 5268 5.249420 AGAGAGCAAAGAAAATACCTCCAC 58.751 41.667 0.00 0.00 0.00 4.02
3923 5269 4.985538 AGAGCAAAGAAAATACCTCCACA 58.014 39.130 0.00 0.00 0.00 4.17
3924 5270 4.762251 AGAGCAAAGAAAATACCTCCACAC 59.238 41.667 0.00 0.00 0.00 3.82
3925 5271 4.469657 AGCAAAGAAAATACCTCCACACA 58.530 39.130 0.00 0.00 0.00 3.72
3926 5272 5.079643 AGCAAAGAAAATACCTCCACACAT 58.920 37.500 0.00 0.00 0.00 3.21
3927 5273 5.539955 AGCAAAGAAAATACCTCCACACATT 59.460 36.000 0.00 0.00 0.00 2.71
3928 5274 6.041979 AGCAAAGAAAATACCTCCACACATTT 59.958 34.615 0.00 0.00 0.00 2.32
3929 5275 6.366061 GCAAAGAAAATACCTCCACACATTTC 59.634 38.462 0.00 0.00 0.00 2.17
3930 5276 6.590234 AAGAAAATACCTCCACACATTTCC 57.410 37.500 0.00 0.00 0.00 3.13
3931 5277 5.892348 AGAAAATACCTCCACACATTTCCT 58.108 37.500 0.00 0.00 0.00 3.36
3932 5278 7.027874 AGAAAATACCTCCACACATTTCCTA 57.972 36.000 0.00 0.00 0.00 2.94
3933 5279 7.466804 AGAAAATACCTCCACACATTTCCTAA 58.533 34.615 0.00 0.00 0.00 2.69
3934 5280 7.611855 AGAAAATACCTCCACACATTTCCTAAG 59.388 37.037 0.00 0.00 0.00 2.18
3935 5281 6.636454 AATACCTCCACACATTTCCTAAGA 57.364 37.500 0.00 0.00 0.00 2.10
3936 5282 4.559862 ACCTCCACACATTTCCTAAGAG 57.440 45.455 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 36 9.976511 TGGGTATAAAGATAGTCAAGATTAACG 57.023 33.333 0.00 0.00 0.00 3.18
61 65 4.034975 GGCATTGAATGTCTCTAAGCTGAC 59.965 45.833 7.05 0.00 30.66 3.51
194 201 2.163815 CGACCCTATCCGGCTTGTATAG 59.836 54.545 0.00 0.00 0.00 1.31
208 215 1.386533 CGGAACTAAGAGCGACCCTA 58.613 55.000 0.00 0.00 0.00 3.53
231 238 1.338337 GAGCTTGCCATAGCGTCTAGA 59.662 52.381 0.00 0.00 45.82 2.43
234 241 1.144936 GGAGCTTGCCATAGCGTCT 59.855 57.895 0.00 0.00 45.82 4.18
368 376 0.840288 TGGAAGCCTCCTACCTTGCA 60.840 55.000 2.35 0.00 42.94 4.08
369 377 0.107459 CTGGAAGCCTCCTACCTTGC 60.107 60.000 2.35 0.00 42.94 4.01
376 384 2.293184 TGTTATCTCCTGGAAGCCTCCT 60.293 50.000 2.35 0.00 42.94 3.69
463 472 1.337703 GTGCAAACAAGCAGGTGATGA 59.662 47.619 0.00 0.00 46.69 2.92
474 484 1.326245 CTCGTCTTGTCGTGCAAACAA 59.674 47.619 13.54 13.54 36.53 2.83
483 493 1.721926 GGCTTCTTTCTCGTCTTGTCG 59.278 52.381 0.00 0.00 0.00 4.35
561 572 6.591062 GCTTGGCACTTGATGAATAATTTGAA 59.409 34.615 0.00 0.00 0.00 2.69
568 579 3.689347 ACTGCTTGGCACTTGATGAATA 58.311 40.909 0.00 0.00 33.79 1.75
573 584 1.350351 AGAGACTGCTTGGCACTTGAT 59.650 47.619 0.00 0.00 33.79 2.57
587 598 5.047872 GTCTTTCGAAAAGAGGGTAGAGACT 60.048 44.000 12.41 0.00 0.00 3.24
588 599 5.162794 GTCTTTCGAAAAGAGGGTAGAGAC 58.837 45.833 12.41 7.69 0.00 3.36
619 630 6.795098 TGTGCTAACGTCACAAAAATAGAT 57.205 33.333 6.13 0.00 41.01 1.98
667 680 5.186409 GGTGGGGATGCTTACTTATCGTATA 59.814 44.000 0.00 0.00 0.00 1.47
689 702 0.822121 GTTTTCTTCCCACGCCTGGT 60.822 55.000 0.86 0.00 35.46 4.00
700 714 6.753744 GCCATATTTGATGTCCTGTTTTCTTC 59.246 38.462 0.00 0.00 0.00 2.87
982 1749 2.869101 TTGCTAGTTGTATGTGGCCA 57.131 45.000 0.00 0.00 0.00 5.36
1007 1792 1.009829 CTACGGCTTGGCTTGCTTAG 58.990 55.000 2.77 1.46 0.00 2.18
1008 1797 0.323629 ACTACGGCTTGGCTTGCTTA 59.676 50.000 2.77 0.00 0.00 3.09
1013 1802 3.094572 TCTTACTACTACGGCTTGGCTT 58.905 45.455 0.00 0.00 0.00 4.35
1014 1803 2.688958 CTCTTACTACTACGGCTTGGCT 59.311 50.000 0.00 0.00 0.00 4.75
1015 1804 2.798853 GCTCTTACTACTACGGCTTGGC 60.799 54.545 0.00 0.00 0.00 4.52
1016 1805 2.426024 TGCTCTTACTACTACGGCTTGG 59.574 50.000 0.00 0.00 0.00 3.61
1017 1806 3.777465 TGCTCTTACTACTACGGCTTG 57.223 47.619 0.00 0.00 0.00 4.01
1018 1807 3.762823 ACTTGCTCTTACTACTACGGCTT 59.237 43.478 0.00 0.00 0.00 4.35
1374 2178 2.343758 GACGCCTTCTGCTCACCA 59.656 61.111 0.00 0.00 38.05 4.17
1377 2181 2.258591 GACGACGCCTTCTGCTCA 59.741 61.111 0.00 0.00 38.05 4.26
1412 2225 4.609018 CGCCATACCCTCCGGCAG 62.609 72.222 0.00 0.00 46.60 4.85
1426 2239 4.980805 TTCGTGGTGGTGAGCGCC 62.981 66.667 7.39 7.39 0.00 6.53
1476 2289 4.992511 TACGCCGCCGCCTTTTGT 62.993 61.111 0.00 0.00 38.22 2.83
1486 2299 4.830765 TCCATGCTGGTACGCCGC 62.831 66.667 2.68 0.00 39.03 6.53
1489 2302 2.028125 TAGCCTCCATGCTGGTACGC 62.028 60.000 0.00 3.57 42.77 4.42
1692 2514 1.518572 GTCCTGGTGATACGCCGTG 60.519 63.158 0.00 0.00 36.72 4.94
1812 2811 2.430244 ACCTTGCTGTCGTACGCG 60.430 61.111 11.24 3.53 39.92 6.01
1817 2816 0.034059 CTTCTGGACCTTGCTGTCGT 59.966 55.000 0.00 0.00 36.07 4.34
1818 2817 1.294659 GCTTCTGGACCTTGCTGTCG 61.295 60.000 0.00 0.00 36.07 4.35
1819 2818 0.250467 TGCTTCTGGACCTTGCTGTC 60.250 55.000 0.00 0.00 34.42 3.51
1820 2819 0.403271 ATGCTTCTGGACCTTGCTGT 59.597 50.000 0.00 0.00 0.00 4.40
1821 2820 0.809385 CATGCTTCTGGACCTTGCTG 59.191 55.000 0.00 0.00 0.00 4.41
1822 2821 0.323178 CCATGCTTCTGGACCTTGCT 60.323 55.000 0.00 0.00 38.69 3.91
1823 2822 1.941999 GCCATGCTTCTGGACCTTGC 61.942 60.000 4.93 0.00 38.69 4.01
1824 2823 0.323178 AGCCATGCTTCTGGACCTTG 60.323 55.000 4.93 0.00 38.69 3.61
1825 2824 1.289160 TAGCCATGCTTCTGGACCTT 58.711 50.000 4.93 0.00 40.44 3.50
1826 2825 1.142465 CATAGCCATGCTTCTGGACCT 59.858 52.381 4.93 0.00 40.44 3.85
1827 2826 1.602311 CATAGCCATGCTTCTGGACC 58.398 55.000 4.93 0.00 40.44 4.46
1828 2827 1.602311 CCATAGCCATGCTTCTGGAC 58.398 55.000 10.29 0.00 40.42 4.02
1829 2828 0.179009 GCCATAGCCATGCTTCTGGA 60.179 55.000 16.87 0.00 40.42 3.86
1830 2829 1.512996 CGCCATAGCCATGCTTCTGG 61.513 60.000 11.10 11.10 40.71 3.86
1831 2830 0.533531 TCGCCATAGCCATGCTTCTG 60.534 55.000 0.00 0.00 40.44 3.02
1832 2831 0.250209 CTCGCCATAGCCATGCTTCT 60.250 55.000 0.00 0.00 40.44 2.85
1833 2832 0.250038 TCTCGCCATAGCCATGCTTC 60.250 55.000 0.00 0.00 40.44 3.86
1834 2833 0.181114 TTCTCGCCATAGCCATGCTT 59.819 50.000 0.00 0.00 40.44 3.91
1835 2834 0.250209 CTTCTCGCCATAGCCATGCT 60.250 55.000 0.00 0.00 43.41 3.79
1836 2835 1.233285 CCTTCTCGCCATAGCCATGC 61.233 60.000 0.00 0.00 34.57 4.06
1837 2836 1.233285 GCCTTCTCGCCATAGCCATG 61.233 60.000 0.00 0.00 34.57 3.66
1838 2837 1.072159 GCCTTCTCGCCATAGCCAT 59.928 57.895 0.00 0.00 34.57 4.40
1839 2838 2.505982 GCCTTCTCGCCATAGCCA 59.494 61.111 0.00 0.00 34.57 4.75
1840 2839 2.663188 CGCCTTCTCGCCATAGCC 60.663 66.667 0.00 0.00 34.57 3.93
1848 2847 3.774959 ATAGCCGTGCGCCTTCTCG 62.775 63.158 4.18 1.87 38.78 4.04
1849 2848 2.107141 ATAGCCGTGCGCCTTCTC 59.893 61.111 4.18 0.00 38.78 2.87
1850 2849 2.202932 CATAGCCGTGCGCCTTCT 60.203 61.111 4.18 0.00 38.78 2.85
1851 2850 3.272334 CCATAGCCGTGCGCCTTC 61.272 66.667 4.18 0.00 38.78 3.46
1858 2857 2.906182 TTCTGCTCGCCATAGCCGTG 62.906 60.000 0.00 0.00 42.05 4.94
1859 2858 2.635229 CTTCTGCTCGCCATAGCCGT 62.635 60.000 0.00 0.00 42.05 5.68
1860 2859 1.953138 CTTCTGCTCGCCATAGCCG 60.953 63.158 0.00 0.00 42.05 5.52
1861 2860 1.596477 CCTTCTGCTCGCCATAGCC 60.596 63.158 0.00 0.00 42.05 3.93
1862 2861 2.250237 GCCTTCTGCTCGCCATAGC 61.250 63.158 0.00 0.00 43.08 2.97
1863 2862 1.953138 CGCCTTCTGCTCGCCATAG 60.953 63.158 0.00 0.00 38.05 2.23
1864 2863 1.388837 TACGCCTTCTGCTCGCCATA 61.389 55.000 0.00 0.00 38.05 2.74
1865 2864 2.721167 TACGCCTTCTGCTCGCCAT 61.721 57.895 0.00 0.00 38.05 4.40
1866 2865 3.378602 TACGCCTTCTGCTCGCCA 61.379 61.111 0.00 0.00 38.05 5.69
1867 2866 2.886124 GTACGCCTTCTGCTCGCC 60.886 66.667 0.00 0.00 38.05 5.54
1868 2867 3.248171 CGTACGCCTTCTGCTCGC 61.248 66.667 0.52 0.00 38.05 5.03
1869 2868 1.583967 CTCGTACGCCTTCTGCTCG 60.584 63.158 11.24 0.00 38.05 5.03
1870 2869 1.874466 GCTCGTACGCCTTCTGCTC 60.874 63.158 11.24 0.00 38.05 4.26
1871 2870 1.949847 ATGCTCGTACGCCTTCTGCT 61.950 55.000 11.24 0.00 38.05 4.24
1872 2871 1.519455 ATGCTCGTACGCCTTCTGC 60.519 57.895 11.24 8.11 0.00 4.26
1873 2872 1.148157 CCATGCTCGTACGCCTTCTG 61.148 60.000 11.24 4.21 0.00 3.02
1874 2873 1.141881 CCATGCTCGTACGCCTTCT 59.858 57.895 11.24 0.00 0.00 2.85
1875 2874 1.883084 CCCATGCTCGTACGCCTTC 60.883 63.158 11.24 0.00 0.00 3.46
1876 2875 2.186903 CCCATGCTCGTACGCCTT 59.813 61.111 11.24 0.00 0.00 4.35
1877 2876 2.758327 TCCCATGCTCGTACGCCT 60.758 61.111 11.24 0.00 0.00 5.52
1878 2877 2.279517 CTCCCATGCTCGTACGCC 60.280 66.667 11.24 4.54 0.00 5.68
1879 2878 2.962253 GCTCCCATGCTCGTACGC 60.962 66.667 11.24 0.00 0.00 4.42
1880 2879 2.655364 CGCTCCCATGCTCGTACG 60.655 66.667 9.53 9.53 0.00 3.67
1881 2880 2.962253 GCGCTCCCATGCTCGTAC 60.962 66.667 0.00 0.00 0.00 3.67
1882 2881 4.221422 GGCGCTCCCATGCTCGTA 62.221 66.667 7.64 0.00 0.00 3.43
1933 2968 1.959042 CCATAGCCGTGCTTCTTCAT 58.041 50.000 3.71 0.00 40.44 2.57
2105 3155 2.636412 TAGCCGTGCTTCTGCGTCT 61.636 57.895 3.71 0.00 43.34 4.18
2193 3243 4.656117 TTCGTCTGCTTCGCGCCA 62.656 61.111 0.00 0.00 38.05 5.69
2248 3328 0.951040 CCGTGGTGGAAAGCAGAGTC 60.951 60.000 0.00 0.00 42.00 3.36
2268 3354 4.656117 TTCGTCTGCTTCGCGCCA 62.656 61.111 0.00 0.00 38.05 5.69
2273 3377 2.720758 CCGTGCTTCGTCTGCTTCG 61.721 63.158 1.89 0.00 37.94 3.79
2275 3382 2.154798 TAGCCGTGCTTCGTCTGCTT 62.155 55.000 3.71 0.00 40.44 3.91
2276 3383 2.636412 TAGCCGTGCTTCGTCTGCT 61.636 57.895 3.71 0.00 40.44 4.24
2304 3420 3.161450 TACCCTCCGGCCATCTGC 61.161 66.667 2.24 0.00 40.16 4.26
2305 3421 2.822399 GTACCCTCCGGCCATCTG 59.178 66.667 2.24 0.00 0.00 2.90
2306 3422 2.838225 CGTACCCTCCGGCCATCT 60.838 66.667 2.24 0.00 0.00 2.90
2307 3423 2.836360 TCGTACCCTCCGGCCATC 60.836 66.667 2.24 0.00 0.00 3.51
2308 3424 3.152400 GTCGTACCCTCCGGCCAT 61.152 66.667 2.24 0.00 0.00 4.40
2309 3425 4.371417 AGTCGTACCCTCCGGCCA 62.371 66.667 2.24 0.00 0.00 5.36
2310 3426 3.525545 GAGTCGTACCCTCCGGCC 61.526 72.222 0.00 0.00 0.00 6.13
2312 3428 2.772691 GCAGAGTCGTACCCTCCGG 61.773 68.421 0.00 0.00 0.00 5.14
2313 3429 1.313812 AAGCAGAGTCGTACCCTCCG 61.314 60.000 4.09 0.00 0.00 4.63
2314 3430 0.896226 AAAGCAGAGTCGTACCCTCC 59.104 55.000 4.09 0.00 0.00 4.30
2315 3431 1.135053 GGAAAGCAGAGTCGTACCCTC 60.135 57.143 0.01 0.01 0.00 4.30
2316 3432 0.896226 GGAAAGCAGAGTCGTACCCT 59.104 55.000 0.00 0.00 0.00 4.34
2317 3433 0.606604 TGGAAAGCAGAGTCGTACCC 59.393 55.000 0.00 0.00 0.00 3.69
2318 3434 1.997669 CTGGAAAGCAGAGTCGTACC 58.002 55.000 0.00 0.00 0.00 3.34
2319 3435 1.336887 TGCTGGAAAGCAGAGTCGTAC 60.337 52.381 0.00 0.00 40.23 3.67
2320 3436 0.966179 TGCTGGAAAGCAGAGTCGTA 59.034 50.000 0.00 0.00 40.23 3.43
2321 3437 0.601311 GTGCTGGAAAGCAGAGTCGT 60.601 55.000 0.00 0.00 46.32 4.34
2322 3438 1.621301 CGTGCTGGAAAGCAGAGTCG 61.621 60.000 0.00 0.00 46.32 4.18
2323 3439 1.294659 CCGTGCTGGAAAGCAGAGTC 61.295 60.000 0.00 0.00 46.32 3.36
2324 3440 1.302033 CCGTGCTGGAAAGCAGAGT 60.302 57.895 0.00 0.00 46.32 3.24
2325 3441 2.684843 GCCGTGCTGGAAAGCAGAG 61.685 63.158 0.00 0.00 46.32 3.35
2326 3442 2.669569 GCCGTGCTGGAAAGCAGA 60.670 61.111 0.00 0.00 46.32 4.26
2327 3443 4.093952 CGCCGTGCTGGAAAGCAG 62.094 66.667 0.00 0.00 46.32 4.24
2330 3446 3.950794 TAGGCGCCGTGCTGGAAAG 62.951 63.158 23.20 0.00 45.43 2.62
2331 3447 3.323758 ATAGGCGCCGTGCTGGAAA 62.324 57.895 23.20 0.00 45.43 3.13
2332 3448 3.781307 ATAGGCGCCGTGCTGGAA 61.781 61.111 23.20 0.28 45.43 3.53
2333 3449 4.529219 CATAGGCGCCGTGCTGGA 62.529 66.667 23.20 1.57 45.43 3.86
2345 3461 2.111878 CCTTCTGCCCGCCATAGG 59.888 66.667 0.00 0.00 0.00 2.57
2346 3462 2.592861 GCCTTCTGCCCGCCATAG 60.593 66.667 0.00 0.00 0.00 2.23
2347 3463 4.545706 CGCCTTCTGCCCGCCATA 62.546 66.667 0.00 0.00 36.24 2.74
2352 3468 4.124351 TACGACGCCTTCTGCCCG 62.124 66.667 0.00 0.00 38.17 6.13
2353 3469 2.508663 GTACGACGCCTTCTGCCC 60.509 66.667 0.00 0.00 36.24 5.36
2354 3470 2.879462 CGTACGACGCCTTCTGCC 60.879 66.667 10.44 0.00 33.65 4.85
2355 3471 2.150837 GTCGTACGACGCCTTCTGC 61.151 63.158 30.48 6.81 42.21 4.26
2356 3472 4.053067 GTCGTACGACGCCTTCTG 57.947 61.111 30.48 0.00 42.21 3.02
2381 3497 0.391263 GTACCCGTGCTTCTTCTGGG 60.391 60.000 0.00 0.00 45.70 4.45
2398 3514 0.321387 TGGTACGCATTTTGCCCGTA 60.321 50.000 0.00 0.00 41.12 4.02
2457 3591 3.777925 CGGCGTTGGACAAGAGCG 61.778 66.667 0.00 0.00 0.00 5.03
2492 3626 1.202830 ACCCGAACTGGTTGTATTGCA 60.203 47.619 0.00 0.00 33.91 4.08
2496 3630 0.326927 CCCACCCGAACTGGTTGTAT 59.673 55.000 0.00 0.00 36.12 2.29
2506 3640 3.379445 GTCGCTCTCCCACCCGAA 61.379 66.667 0.00 0.00 0.00 4.30
2514 3648 1.063488 GCTCTCTTCGTCGCTCTCC 59.937 63.158 0.00 0.00 0.00 3.71
2523 3669 1.131037 CTTCGCAGTCGCTCTCTTCG 61.131 60.000 0.00 0.00 35.30 3.79
2526 3672 1.504446 GTCTTCGCAGTCGCTCTCT 59.496 57.895 0.00 0.00 35.30 3.10
2588 3758 0.179171 CGCGGAGTAGTACTGTGTGG 60.179 60.000 7.76 0.00 0.00 4.17
2592 3762 1.002366 CGTACGCGGAGTAGTACTGT 58.998 55.000 12.47 1.84 39.91 3.55
2633 3803 4.208686 CCTCGTAGTGGCTCCCGC 62.209 72.222 0.00 0.00 33.13 6.13
2640 3810 3.511595 TACGCCGCCTCGTAGTGG 61.512 66.667 1.54 3.13 45.21 4.00
2641 3811 2.277756 GTACGCCGCCTCGTAGTG 60.278 66.667 5.50 0.00 44.35 2.74
2642 3812 3.512516 GGTACGCCGCCTCGTAGT 61.513 66.667 5.50 0.00 44.35 2.73
2643 3813 3.465296 CTGGTACGCCGCCTCGTAG 62.465 68.421 5.50 0.00 44.35 3.51
2644 3814 3.511595 CTGGTACGCCGCCTCGTA 61.512 66.667 1.54 1.54 43.15 3.43
2646 3816 4.554363 CTCTGGTACGCCGCCTCG 62.554 72.222 0.00 0.00 37.67 4.63
2647 3817 4.874977 GCTCTGGTACGCCGCCTC 62.875 72.222 0.00 0.00 37.67 4.70
2649 3819 4.874977 GAGCTCTGGTACGCCGCC 62.875 72.222 6.43 0.00 37.67 6.13
2650 3820 4.874977 GGAGCTCTGGTACGCCGC 62.875 72.222 14.64 0.00 37.67 6.53
2651 3821 3.449227 TGGAGCTCTGGTACGCCG 61.449 66.667 14.64 0.00 37.67 6.46
2652 3822 2.184579 GTGGAGCTCTGGTACGCC 59.815 66.667 14.64 0.00 0.00 5.68
2653 3823 2.184579 GGTGGAGCTCTGGTACGC 59.815 66.667 14.64 2.68 0.00 4.42
2654 3824 1.215647 GTGGTGGAGCTCTGGTACG 59.784 63.158 14.64 0.00 0.00 3.67
2655 3825 1.597461 GGTGGTGGAGCTCTGGTAC 59.403 63.158 14.64 8.25 0.00 3.34
2656 3826 1.612442 GGGTGGTGGAGCTCTGGTA 60.612 63.158 14.64 0.00 0.00 3.25
2657 3827 2.930562 GGGTGGTGGAGCTCTGGT 60.931 66.667 14.64 0.00 0.00 4.00
2658 3828 2.930019 TGGGTGGTGGAGCTCTGG 60.930 66.667 14.64 0.00 0.00 3.86
2659 3829 2.667418 CTGGGTGGTGGAGCTCTG 59.333 66.667 14.64 0.00 0.00 3.35
2660 3830 2.608988 CCTGGGTGGTGGAGCTCT 60.609 66.667 14.64 0.00 0.00 4.09
2661 3831 3.721706 CCCTGGGTGGTGGAGCTC 61.722 72.222 4.71 4.71 0.00 4.09
2720 3947 2.094494 GCTCAGTAGTAGCTGTGCTTCA 60.094 50.000 11.36 0.00 46.38 3.02
2773 4008 2.755650 CAGGTAGGATTGTATCACGCC 58.244 52.381 0.00 0.00 0.00 5.68
2934 4180 1.389609 CGGGCCAGACCACGTAGTAT 61.390 60.000 4.39 0.00 41.61 2.12
2944 4190 4.475135 GAAGCTCCCGGGCCAGAC 62.475 72.222 18.49 5.58 0.00 3.51
2989 4316 4.500375 CCTGCTCAGTATCGTTCATGATGA 60.500 45.833 0.00 0.00 0.00 2.92
2990 4317 3.739810 CCTGCTCAGTATCGTTCATGATG 59.260 47.826 0.00 0.00 0.00 3.07
2991 4318 3.386078 ACCTGCTCAGTATCGTTCATGAT 59.614 43.478 0.00 0.00 0.00 2.45
3011 4338 0.034380 GAGGAAACCTGGCCCTTACC 60.034 60.000 0.00 0.00 31.76 2.85
3178 4505 2.125106 GCGCCACAGGTAAGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
3237 4567 4.558178 TGTGACACAAATCAATTCATGCC 58.442 39.130 5.62 0.00 0.00 4.40
3242 4572 4.624024 CCATGCTGTGACACAAATCAATTC 59.376 41.667 10.02 0.00 0.00 2.17
3257 4587 3.055819 ACGAATTCTGTACTCCATGCTGT 60.056 43.478 3.52 0.00 0.00 4.40
3258 4588 3.308053 CACGAATTCTGTACTCCATGCTG 59.692 47.826 3.52 0.00 0.00 4.41
3259 4589 3.055819 ACACGAATTCTGTACTCCATGCT 60.056 43.478 3.52 0.00 0.00 3.79
3262 4592 5.654603 TGTACACGAATTCTGTACTCCAT 57.345 39.130 28.56 7.74 43.02 3.41
3370 4712 6.497259 TCCTGACCTGTAGTATTCTTTTCTGT 59.503 38.462 0.00 0.00 0.00 3.41
3374 4716 7.514721 TGTTTCCTGACCTGTAGTATTCTTTT 58.485 34.615 0.00 0.00 0.00 2.27
3450 4793 1.149101 AGGGTGTTCCATCACTTGGT 58.851 50.000 0.00 0.00 46.52 3.67
3489 4832 6.738114 TCATGAGAAAATTGGAGTTGTTGAC 58.262 36.000 0.00 0.00 0.00 3.18
3516 4859 8.255206 TCTACTCGATCTTAAATTAAACAGCCA 58.745 33.333 0.00 0.00 0.00 4.75
3529 4873 6.829229 TTGGAACTGTTCTACTCGATCTTA 57.171 37.500 19.05 0.00 0.00 2.10
3532 4876 5.651530 TGATTGGAACTGTTCTACTCGATC 58.348 41.667 19.05 15.74 0.00 3.69
3534 4878 4.523173 ACTGATTGGAACTGTTCTACTCGA 59.477 41.667 19.05 4.04 0.00 4.04
3535 4879 4.810790 ACTGATTGGAACTGTTCTACTCG 58.189 43.478 19.05 14.29 0.00 4.18
3541 4885 6.863126 CCATGTTTTACTGATTGGAACTGTTC 59.137 38.462 12.05 12.05 0.00 3.18
3544 4888 6.573664 TCCATGTTTTACTGATTGGAACTG 57.426 37.500 0.00 0.00 30.62 3.16
3566 4911 4.799564 TTACATGCTTTCCCCAAACATC 57.200 40.909 0.00 0.00 0.00 3.06
3568 4913 3.964031 ACTTTACATGCTTTCCCCAAACA 59.036 39.130 0.00 0.00 0.00 2.83
3570 4915 4.219115 TCACTTTACATGCTTTCCCCAAA 58.781 39.130 0.00 0.00 0.00 3.28
3596 4941 2.263895 AGGGGGCTGTAGTTATGTGA 57.736 50.000 0.00 0.00 0.00 3.58
3604 4950 3.967987 ACAATAACTCTAGGGGGCTGTAG 59.032 47.826 0.00 0.00 0.00 2.74
3637 4983 1.289160 AGAAGGCTAGCACCATCCAA 58.711 50.000 18.24 0.00 0.00 3.53
3645 4991 5.744171 TGACATTTTCATAGAAGGCTAGCA 58.256 37.500 18.24 0.00 0.00 3.49
3676 5022 6.769822 CCAAAGGAGTAGTCTGCATGATTAAT 59.230 38.462 0.00 0.00 34.40 1.40
3711 5057 6.821665 TGCTATGGACTGTAATCCTACAAAAC 59.178 38.462 0.00 0.00 37.58 2.43
3781 5127 0.679640 TGCATAGGAAGTTTGGCGGG 60.680 55.000 0.00 0.00 0.00 6.13
3784 5130 2.167075 AGCAATGCATAGGAAGTTTGGC 59.833 45.455 8.35 0.00 0.00 4.52
3806 5152 2.368875 CCTGTAGAATTGGGGCGTAGAT 59.631 50.000 0.00 0.00 0.00 1.98
3822 5168 2.561209 TGATTGCTAGGGACCCTGTA 57.439 50.000 24.42 9.81 34.61 2.74
3836 5182 9.566432 AAGGTCTAGGATAGCTTAAATTGATTG 57.434 33.333 0.00 0.00 38.99 2.67
3865 5211 6.938596 ACCACTGTACATTTAAGTTAACCTCC 59.061 38.462 0.88 0.00 0.00 4.30
3878 5224 5.680619 TCTTGAAAGTGACCACTGTACATT 58.319 37.500 3.13 0.00 41.58 2.71
3889 5235 5.741388 TTCTTTGCTCTCTTGAAAGTGAC 57.259 39.130 0.00 0.00 0.00 3.67
3901 5247 4.762251 GTGTGGAGGTATTTTCTTTGCTCT 59.238 41.667 0.00 0.00 0.00 4.09
3902 5248 4.518970 TGTGTGGAGGTATTTTCTTTGCTC 59.481 41.667 0.00 0.00 0.00 4.26
3903 5249 4.469657 TGTGTGGAGGTATTTTCTTTGCT 58.530 39.130 0.00 0.00 0.00 3.91
3904 5250 4.846779 TGTGTGGAGGTATTTTCTTTGC 57.153 40.909 0.00 0.00 0.00 3.68
3905 5251 6.868339 GGAAATGTGTGGAGGTATTTTCTTTG 59.132 38.462 0.00 0.00 0.00 2.77
3907 5253 6.314917 AGGAAATGTGTGGAGGTATTTTCTT 58.685 36.000 0.00 0.00 26.66 2.52
3908 5254 5.892348 AGGAAATGTGTGGAGGTATTTTCT 58.108 37.500 0.00 0.00 0.00 2.52
3909 5255 7.610305 TCTTAGGAAATGTGTGGAGGTATTTTC 59.390 37.037 0.00 0.00 0.00 2.29
3910 5256 7.466804 TCTTAGGAAATGTGTGGAGGTATTTT 58.533 34.615 0.00 0.00 0.00 1.82
3911 5257 7.027874 TCTTAGGAAATGTGTGGAGGTATTT 57.972 36.000 0.00 0.00 0.00 1.40
3912 5258 6.636454 TCTTAGGAAATGTGTGGAGGTATT 57.364 37.500 0.00 0.00 0.00 1.89
3913 5259 6.240549 CTCTTAGGAAATGTGTGGAGGTAT 57.759 41.667 0.00 0.00 0.00 2.73
3914 5260 5.677319 CTCTTAGGAAATGTGTGGAGGTA 57.323 43.478 0.00 0.00 0.00 3.08
3915 5261 4.559862 CTCTTAGGAAATGTGTGGAGGT 57.440 45.455 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.