Multiple sequence alignment - TraesCS2D01G562500

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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 TraesCS2D01G562500 chr2D 100.000 4224 0 0 1 4224 634281228 634285451 0.000000e+00 7801.0
1 TraesCS2D01G562500 chr2D 86.256 1266 107 27 1109 2328 65810926 65812170 0.000000e+00 1312.0
2 TraesCS2D01G562500 chr2D 89.845 906 65 11 3322 4224 512374739 512375620 0.000000e+00 1138.0
3 TraesCS2D01G562500 chr2D 87.427 684 62 14 1109 1784 72814862 72815529 0.000000e+00 765.0
4 TraesCS2D01G562500 chr2D 97.727 44 1 0 3049 3092 634297511 634297554 4.530000e-10 76.8
5 TraesCS2D01G562500 chr2A 86.201 2261 146 58 147 2276 779272522 779270297 0.000000e+00 2294.0
6 TraesCS2D01G562500 chr2A 89.331 628 25 10 2724 3330 779270061 779269455 0.000000e+00 750.0
7 TraesCS2D01G562500 chr2A 82.857 315 32 11 1800 2106 598338198 598337898 3.240000e-66 263.0
8 TraesCS2D01G562500 chr2A 81.587 315 37 11 1800 2106 221983028 221983329 1.520000e-59 241.0
9 TraesCS2D01G562500 chr2A 100.000 56 0 0 2313 2368 779270289 779270234 2.080000e-18 104.0
10 TraesCS2D01G562500 chr2B 85.594 1659 135 58 297 1899 777302994 777304604 0.000000e+00 1644.0
11 TraesCS2D01G562500 chr2B 88.406 966 46 26 2406 3330 777304951 777305891 0.000000e+00 1103.0
12 TraesCS2D01G562500 chr2B 93.798 258 16 0 1 258 777302739 777302996 5.120000e-104 388.0
13 TraesCS2D01G562500 chr2B 89.333 225 16 7 2161 2379 777304671 777304893 4.160000e-70 276.0
14 TraesCS2D01G562500 chr2B 88.660 97 9 1 45 139 74047456 74047360 2.670000e-22 117.0
15 TraesCS2D01G562500 chr6B 86.514 1268 106 29 1109 2331 49617884 49616637 0.000000e+00 1334.0
16 TraesCS2D01G562500 chr6B 85.619 904 86 18 3328 4224 353877550 353878416 0.000000e+00 909.0
17 TraesCS2D01G562500 chr6B 82.540 315 34 11 1800 2106 14049208 14049509 1.510000e-64 257.0
18 TraesCS2D01G562500 chr1B 89.678 901 78 7 3325 4224 376037925 376037039 0.000000e+00 1134.0
19 TraesCS2D01G562500 chr1B 82.540 315 33 12 1800 2106 650784577 650784877 1.510000e-64 257.0
20 TraesCS2D01G562500 chr1B 90.769 65 3 2 2367 2431 668960748 668960687 2.710000e-12 84.2
21 TraesCS2D01G562500 chr1D 88.605 860 69 11 3330 4179 374638695 374639535 0.000000e+00 1018.0
22 TraesCS2D01G562500 chr1D 89.231 65 3 4 2369 2431 404066379 404066317 1.260000e-10 78.7
23 TraesCS2D01G562500 chr3D 87.612 896 59 11 3330 4224 499842956 499842112 0.000000e+00 992.0
24 TraesCS2D01G562500 chr3D 89.527 697 49 9 3521 4215 594158587 594159261 0.000000e+00 861.0
25 TraesCS2D01G562500 chr3B 86.404 787 77 8 3329 4115 633290671 633289915 0.000000e+00 833.0
26 TraesCS2D01G562500 chr3B 84.116 894 105 18 3335 4218 708369384 708370250 0.000000e+00 830.0
27 TraesCS2D01G562500 chr7B 82.942 979 104 24 1311 2245 574904571 574903612 0.000000e+00 824.0
28 TraesCS2D01G562500 chr7B 87.268 699 59 11 3326 4020 593294695 593295367 0.000000e+00 771.0
29 TraesCS2D01G562500 chr7B 83.159 671 99 10 3335 4001 533328219 533328879 6.040000e-168 601.0
30 TraesCS2D01G562500 chr7B 82.429 700 78 20 3331 4020 395457978 395457314 1.700000e-158 569.0
31 TraesCS2D01G562500 chr7B 93.491 169 8 2 4057 4224 593295363 593295529 9.070000e-62 248.0
32 TraesCS2D01G562500 chr7B 92.308 169 10 2 4057 4224 593361639 593361805 1.960000e-58 237.0
33 TraesCS2D01G562500 chr7B 89.744 156 14 2 1109 1263 574904721 574904567 9.260000e-47 198.0
34 TraesCS2D01G562500 chr7D 84.339 779 87 16 3330 4104 537032878 537033625 0.000000e+00 730.0
35 TraesCS2D01G562500 chr7D 92.537 67 1 2 2365 2431 13311068 13311006 4.500000e-15 93.5
36 TraesCS2D01G562500 chr7D 87.838 74 2 4 2366 2433 186794867 186794795 3.500000e-11 80.5
37 TraesCS2D01G562500 chr6D 88.686 548 45 10 3325 3867 118320312 118319777 0.000000e+00 652.0
38 TraesCS2D01G562500 chr6D 89.394 66 2 2 2370 2431 406205748 406205684 1.260000e-10 78.7
39 TraesCS2D01G562500 chr6D 87.324 71 3 3 2367 2432 406205681 406205750 4.530000e-10 76.8
40 TraesCS2D01G562500 chr5D 84.977 659 74 13 3327 3980 334831535 334830897 0.000000e+00 645.0
41 TraesCS2D01G562500 chr5D 85.941 441 39 8 1358 1784 107313788 107313357 2.320000e-122 449.0
42 TraesCS2D01G562500 chr5D 91.391 151 11 2 1109 1258 107313936 107313787 5.540000e-49 206.0
43 TraesCS2D01G562500 chr4B 83.707 491 56 7 3720 4209 587113724 587114191 3.880000e-120 442.0
44 TraesCS2D01G562500 chr5B 83.492 315 30 11 1800 2106 505281610 505281910 1.500000e-69 274.0
45 TraesCS2D01G562500 chr5B 81.587 315 36 11 1800 2106 598233615 598233915 1.520000e-59 241.0
46 TraesCS2D01G562500 chr4A 83.121 314 33 11 1800 2106 332923114 332922814 6.960000e-68 268.0
47 TraesCS2D01G562500 chr4A 82.222 315 34 11 1800 2106 332964470 332964170 7.010000e-63 252.0
48 TraesCS2D01G562500 chr4A 82.222 315 34 11 1800 2106 704409690 704409990 7.010000e-63 252.0
49 TraesCS2D01G562500 chr6A 82.540 315 33 11 1800 2106 47994110 47994410 1.510000e-64 257.0
50 TraesCS2D01G562500 chr6A 91.935 62 2 3 2370 2430 456599256 456599197 2.710000e-12 84.2
51 TraesCS2D01G562500 chr7A 82.540 315 32 12 1800 2106 621160349 621160648 5.420000e-64 255.0
52 TraesCS2D01G562500 chr5A 82.736 307 31 11 1808 2106 516903629 516903337 1.950000e-63 254.0
53 TraesCS2D01G562500 chr5A 87.500 72 1 6 2370 2435 422040423 422040354 4.530000e-10 76.8
54 TraesCS2D01G562500 chr1A 81.270 315 37 12 1800 2106 139355115 139354815 7.060000e-58 235.0
55 TraesCS2D01G562500 chr1A 87.324 71 6 3 2363 2431 550888519 550888588 1.260000e-10 78.7
56 TraesCS2D01G562500 chr3A 87.050 139 11 3 1975 2106 241731538 241731400 2.630000e-32 150.0
57 TraesCS2D01G562500 chr3A 80.986 142 19 6 1377 1514 658703061 658702924 5.780000e-19 106.0


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 TraesCS2D01G562500 chr2D 634281228 634285451 4223 False 7801.000000 7801 100.00000 1 4224 1 chr2D.!!$F4 4223
1 TraesCS2D01G562500 chr2D 65810926 65812170 1244 False 1312.000000 1312 86.25600 1109 2328 1 chr2D.!!$F1 1219
2 TraesCS2D01G562500 chr2D 512374739 512375620 881 False 1138.000000 1138 89.84500 3322 4224 1 chr2D.!!$F3 902
3 TraesCS2D01G562500 chr2D 72814862 72815529 667 False 765.000000 765 87.42700 1109 1784 1 chr2D.!!$F2 675
4 TraesCS2D01G562500 chr2A 779269455 779272522 3067 True 1049.333333 2294 91.84400 147 3330 3 chr2A.!!$R2 3183
5 TraesCS2D01G562500 chr2B 777302739 777305891 3152 False 852.750000 1644 89.28275 1 3330 4 chr2B.!!$F1 3329
6 TraesCS2D01G562500 chr6B 49616637 49617884 1247 True 1334.000000 1334 86.51400 1109 2331 1 chr6B.!!$R1 1222
7 TraesCS2D01G562500 chr6B 353877550 353878416 866 False 909.000000 909 85.61900 3328 4224 1 chr6B.!!$F2 896
8 TraesCS2D01G562500 chr1B 376037039 376037925 886 True 1134.000000 1134 89.67800 3325 4224 1 chr1B.!!$R1 899
9 TraesCS2D01G562500 chr1D 374638695 374639535 840 False 1018.000000 1018 88.60500 3330 4179 1 chr1D.!!$F1 849
10 TraesCS2D01G562500 chr3D 499842112 499842956 844 True 992.000000 992 87.61200 3330 4224 1 chr3D.!!$R1 894
11 TraesCS2D01G562500 chr3D 594158587 594159261 674 False 861.000000 861 89.52700 3521 4215 1 chr3D.!!$F1 694
12 TraesCS2D01G562500 chr3B 633289915 633290671 756 True 833.000000 833 86.40400 3329 4115 1 chr3B.!!$R1 786
13 TraesCS2D01G562500 chr3B 708369384 708370250 866 False 830.000000 830 84.11600 3335 4218 1 chr3B.!!$F1 883
14 TraesCS2D01G562500 chr7B 533328219 533328879 660 False 601.000000 601 83.15900 3335 4001 1 chr7B.!!$F1 666
15 TraesCS2D01G562500 chr7B 395457314 395457978 664 True 569.000000 569 82.42900 3331 4020 1 chr7B.!!$R1 689
16 TraesCS2D01G562500 chr7B 574903612 574904721 1109 True 511.000000 824 86.34300 1109 2245 2 chr7B.!!$R2 1136
17 TraesCS2D01G562500 chr7B 593294695 593295529 834 False 509.500000 771 90.37950 3326 4224 2 chr7B.!!$F3 898
18 TraesCS2D01G562500 chr7D 537032878 537033625 747 False 730.000000 730 84.33900 3330 4104 1 chr7D.!!$F1 774
19 TraesCS2D01G562500 chr6D 118319777 118320312 535 True 652.000000 652 88.68600 3325 3867 1 chr6D.!!$R1 542
20 TraesCS2D01G562500 chr5D 334830897 334831535 638 True 645.000000 645 84.97700 3327 3980 1 chr5D.!!$R1 653
21 TraesCS2D01G562500 chr5D 107313357 107313936 579 True 327.500000 449 88.66600 1109 1784 2 chr5D.!!$R2 675

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
836 934 0.818296 GGTGGCATCGACAGACTACT 59.182 55.0 0.00 0.00 0.0 2.57 F
1969 2173 0.652592 GCACATGGCATGTCTCGTAC 59.347 55.0 29.32 11.45 42.7 3.67 F
2922 3260 0.169672 GTGAGCGGCTACTACAACGA 59.830 55.0 0.60 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2356 0.531200 CCGAACAGAGGGTGTACTCC 59.469 60.000 5.35 5.35 39.03 3.85 R
3106 3453 0.590732 ACGACACGAACAGACACGAC 60.591 55.000 0.00 0.00 0.00 4.34 R
4035 4437 2.477375 GCCGACTAATTTCACACAACGA 59.523 45.455 0.00 0.00 0.00 3.85 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
27 28 4.838959 GACACATTTGGCGGTTCG 57.161 55.556 0.00 0.00 0.00 3.95
42 43 2.288886 CGGTTCGGAAAGAAGAAGAGGT 60.289 50.000 0.00 0.00 39.95 3.85
89 90 1.825474 ACGATCTTCATCCAACCGTCT 59.175 47.619 0.00 0.00 0.00 4.18
96 97 7.062371 CGATCTTCATCCAACCGTCTATAAATC 59.938 40.741 0.00 0.00 0.00 2.17
99 100 5.526115 TCATCCAACCGTCTATAAATCGAC 58.474 41.667 0.00 0.00 0.00 4.20
102 103 4.641541 TCCAACCGTCTATAAATCGACTGA 59.358 41.667 0.00 0.00 0.00 3.41
118 119 7.703058 ATCGACTGACCCTAATTGAAAAATT 57.297 32.000 0.00 0.00 0.00 1.82
124 125 7.505585 ACTGACCCTAATTGAAAAATTCAGTCA 59.494 33.333 9.04 9.04 41.38 3.41
142 143 3.056250 AGTCAAGTGATGTGTAGCCTCTG 60.056 47.826 0.00 0.00 0.00 3.35
296 297 2.598394 GACCAGCAAGCTGCCCAA 60.598 61.111 16.33 0.00 46.52 4.12
377 378 4.147449 TGGCTGCTGACCGATCCG 62.147 66.667 0.00 0.00 0.00 4.18
464 474 2.667470 CACCTCCTCCTTCGATTCCTA 58.333 52.381 0.00 0.00 0.00 2.94
477 494 1.414550 GATTCCTAGGTGCCCACTCTC 59.585 57.143 9.08 0.00 0.00 3.20
487 504 1.596934 CCCACTCTCCGCTTTGCTA 59.403 57.895 0.00 0.00 0.00 3.49
579 623 2.106938 GGACATCTGGCGCATCGA 59.893 61.111 10.83 1.73 0.00 3.59
681 725 5.815740 GGAAGCCGTGATCTAAACAAGATAA 59.184 40.000 0.00 0.00 45.35 1.75
682 726 6.018669 GGAAGCCGTGATCTAAACAAGATAAG 60.019 42.308 0.00 0.00 45.35 1.73
768 845 4.021456 TGGCTGGAATCGTATAGGTGTATG 60.021 45.833 0.00 0.00 0.00 2.39
769 846 4.021368 GGCTGGAATCGTATAGGTGTATGT 60.021 45.833 0.00 0.00 0.00 2.29
770 847 5.184479 GGCTGGAATCGTATAGGTGTATGTA 59.816 44.000 0.00 0.00 0.00 2.29
771 848 6.127423 GGCTGGAATCGTATAGGTGTATGTAT 60.127 42.308 0.00 0.00 0.00 2.29
819 917 3.775654 GCCAGCAGAGTAGGCGGT 61.776 66.667 0.00 0.00 38.86 5.68
828 926 2.585247 GTAGGCGGTGGCATCGAC 60.585 66.667 26.58 23.72 42.47 4.20
836 934 0.818296 GGTGGCATCGACAGACTACT 59.182 55.000 0.00 0.00 0.00 2.57
837 935 2.022195 GGTGGCATCGACAGACTACTA 58.978 52.381 0.00 0.00 0.00 1.82
838 936 2.223525 GGTGGCATCGACAGACTACTAC 60.224 54.545 0.00 0.00 0.00 2.73
886 988 1.675415 GCAGAGTGGCAAGAGGAAGAG 60.675 57.143 0.00 0.00 0.00 2.85
1023 1129 3.775654 AGAGGAAAGCCGGCGAGG 61.776 66.667 23.20 0.00 44.97 4.63
1024 1130 3.771160 GAGGAAAGCCGGCGAGGA 61.771 66.667 23.20 0.00 45.00 3.71
1025 1131 3.724914 GAGGAAAGCCGGCGAGGAG 62.725 68.421 23.20 0.00 45.00 3.69
1058 1169 1.134699 TGCTTAGCAGGTTCGATCCAG 60.135 52.381 14.83 7.87 33.32 3.86
1065 1176 2.106683 GGTTCGATCCAGCAACCCG 61.107 63.158 7.68 0.00 34.55 5.28
1068 1179 2.829043 TTCGATCCAGCAACCCGTCG 62.829 60.000 0.00 0.00 0.00 5.12
1084 1195 4.923710 CGATCGATCGCCGGTGCA 62.924 66.667 32.34 0.00 43.84 4.57
1271 1387 4.036027 AGCCAATTCGTTCAAGCATCTATG 59.964 41.667 0.00 0.00 0.00 2.23
1276 1392 3.113322 TCGTTCAAGCATCTATGTACGC 58.887 45.455 0.00 0.00 39.29 4.42
1279 1395 4.679654 CGTTCAAGCATCTATGTACGCATA 59.320 41.667 0.00 0.00 34.48 3.14
1280 1396 5.174943 CGTTCAAGCATCTATGTACGCATAA 59.825 40.000 0.00 0.00 37.16 1.90
1549 1682 1.174783 TCTTCGTCCTCTGCTGGTAC 58.825 55.000 0.00 0.00 0.00 3.34
1575 1724 4.159377 GATGACCTGATCTCATCTCGTC 57.841 50.000 13.53 1.39 40.60 4.20
1622 1774 1.270305 GCCTGCCGATTAGCATCTACA 60.270 52.381 0.00 0.00 43.09 2.74
1687 1842 3.490759 GCGGTCGCACACCTGATG 61.491 66.667 10.67 0.00 44.21 3.07
1699 1857 2.414994 ACCTGATGGTGCTGATTGAG 57.585 50.000 0.00 0.00 46.51 3.02
1721 1885 1.080366 CGGTGCGCTGGTGTTAGTA 60.080 57.895 9.73 0.00 0.00 1.82
1731 1895 4.961551 CGCTGGTGTTAGTAAATTATTGCG 59.038 41.667 0.00 0.00 0.00 4.85
1742 1906 4.558538 AAATTATTGCGAGCACCATCTC 57.441 40.909 0.00 0.00 0.00 2.75
1825 1994 3.284617 CATTTGGATGTGGCAGAGATGA 58.715 45.455 0.00 0.00 0.00 2.92
1826 1995 3.438216 TTTGGATGTGGCAGAGATGAA 57.562 42.857 0.00 0.00 0.00 2.57
1827 1996 2.704464 TGGATGTGGCAGAGATGAAG 57.296 50.000 0.00 0.00 0.00 3.02
1865 2041 9.262358 GGAGTAGTTGATTCCTAAACATGATAC 57.738 37.037 0.00 0.00 31.11 2.24
1907 2090 4.081972 AGGCACACTGTCAGTTACTATGAG 60.082 45.833 1.67 0.00 0.00 2.90
1917 2100 8.310406 TGTCAGTTACTATGAGTGACATTTTG 57.690 34.615 9.91 0.00 46.80 2.44
1937 2120 3.202829 GGTCAACAGACCCTACAAACA 57.797 47.619 3.27 0.00 44.97 2.83
1941 2124 4.272748 GTCAACAGACCCTACAAACAAGTC 59.727 45.833 0.00 0.00 0.00 3.01
1969 2173 0.652592 GCACATGGCATGTCTCGTAC 59.347 55.000 29.32 11.45 42.70 3.67
1996 2207 2.005971 AGCTACCAACCGAACGAATC 57.994 50.000 0.00 0.00 0.00 2.52
2003 2214 2.031157 CCAACCGAACGAATCTTTTGCT 60.031 45.455 0.00 0.00 0.00 3.91
2007 2218 4.312443 ACCGAACGAATCTTTTGCTTCTA 58.688 39.130 0.00 0.00 0.00 2.10
2010 2221 5.073478 CGAACGAATCTTTTGCTTCTACAC 58.927 41.667 0.00 0.00 0.00 2.90
2045 2259 3.192422 ACGCTATAGAATGCAGCCTAGAG 59.808 47.826 3.21 12.72 31.43 2.43
2100 2356 4.795970 ACTCTGTTCAGCAAAAACTACG 57.204 40.909 0.00 0.00 0.00 3.51
2104 2360 8.794036 ACTCTGTTCAGCAAAAACTACGGAGT 62.794 42.308 0.00 0.00 43.62 3.85
2106 2362 4.508861 TGTTCAGCAAAAACTACGGAGTAC 59.491 41.667 0.00 0.00 45.11 2.73
2107 2363 4.325028 TCAGCAAAAACTACGGAGTACA 57.675 40.909 0.00 0.00 45.11 2.90
2108 2364 4.053295 TCAGCAAAAACTACGGAGTACAC 58.947 43.478 0.00 0.00 45.11 2.90
2109 2365 3.185797 CAGCAAAAACTACGGAGTACACC 59.814 47.826 0.00 0.00 45.11 4.16
2128 2384 4.529377 ACACCCTCTGTTCGGAATAAACTA 59.471 41.667 0.00 0.00 0.00 2.24
2134 2390 5.279384 TCTGTTCGGAATAAACTATCGCTC 58.721 41.667 0.00 0.00 0.00 5.03
2154 2410 4.697352 GCTCAAATGAGTGAACCTACACAT 59.303 41.667 11.77 0.00 43.85 3.21
2155 2411 5.874810 GCTCAAATGAGTGAACCTACACATA 59.125 40.000 11.77 0.00 43.85 2.29
2156 2412 6.036517 GCTCAAATGAGTGAACCTACACATAG 59.963 42.308 11.77 0.00 43.85 2.23
2169 2425 6.351711 ACCTACACATAGTGATACACGTCTA 58.648 40.000 3.88 0.00 39.64 2.59
2170 2426 6.482641 ACCTACACATAGTGATACACGTCTAG 59.517 42.308 3.88 0.00 39.64 2.43
2171 2427 6.704937 CCTACACATAGTGATACACGTCTAGA 59.295 42.308 3.88 0.00 39.64 2.43
2172 2428 7.388224 CCTACACATAGTGATACACGTCTAGAT 59.612 40.741 3.88 0.00 39.64 1.98
2173 2429 9.420551 CTACACATAGTGATACACGTCTAGATA 57.579 37.037 3.88 0.00 39.64 1.98
2174 2430 8.085720 ACACATAGTGATACACGTCTAGATAC 57.914 38.462 3.88 0.00 39.64 2.24
2175 2431 7.713942 ACACATAGTGATACACGTCTAGATACA 59.286 37.037 3.88 0.00 39.64 2.29
2176 2432 8.010540 CACATAGTGATACACGTCTAGATACAC 58.989 40.741 0.00 0.00 39.64 2.90
2177 2433 7.932491 ACATAGTGATACACGTCTAGATACACT 59.068 37.037 0.00 0.00 39.64 3.55
2178 2434 6.847956 AGTGATACACGTCTAGATACACTC 57.152 41.667 0.00 0.00 39.64 3.51
2187 2453 7.067615 ACACGTCTAGATACACTCATTTCATCT 59.932 37.037 0.00 0.00 0.00 2.90
2216 2482 3.380479 TTCTGAACGGAGGTTGTACAG 57.620 47.619 0.00 0.00 36.24 2.74
2297 2564 7.707464 TGGGTATTATTGACTGTAATGTACACG 59.293 37.037 0.00 0.00 34.46 4.49
2379 2646 6.097915 TGCTCTTAAATATTACTCCCTCCG 57.902 41.667 0.00 0.00 0.00 4.63
2380 2647 5.601313 TGCTCTTAAATATTACTCCCTCCGT 59.399 40.000 0.00 0.00 0.00 4.69
2381 2648 6.779049 TGCTCTTAAATATTACTCCCTCCGTA 59.221 38.462 0.00 0.00 0.00 4.02
2383 2650 8.146412 GCTCTTAAATATTACTCCCTCCGTAAA 58.854 37.037 0.00 0.00 31.36 2.01
2384 2651 9.694137 CTCTTAAATATTACTCCCTCCGTAAAG 57.306 37.037 0.00 0.00 31.36 1.85
2386 2653 5.881923 AATATTACTCCCTCCGTAAAGCA 57.118 39.130 0.00 0.00 31.36 3.91
2389 2656 4.563140 TTACTCCCTCCGTAAAGCAAAT 57.437 40.909 0.00 0.00 0.00 2.32
2394 2661 6.289064 ACTCCCTCCGTAAAGCAAATATAAG 58.711 40.000 0.00 0.00 0.00 1.73
2395 2662 6.099269 ACTCCCTCCGTAAAGCAAATATAAGA 59.901 38.462 0.00 0.00 0.00 2.10
2396 2663 6.522054 TCCCTCCGTAAAGCAAATATAAGAG 58.478 40.000 0.00 0.00 0.00 2.85
2397 2664 5.179555 CCCTCCGTAAAGCAAATATAAGAGC 59.820 44.000 0.00 0.00 0.00 4.09
2398 2665 5.758296 CCTCCGTAAAGCAAATATAAGAGCA 59.242 40.000 0.00 0.00 0.00 4.26
2399 2666 6.260050 CCTCCGTAAAGCAAATATAAGAGCAA 59.740 38.462 0.00 0.00 0.00 3.91
2400 2667 7.201696 CCTCCGTAAAGCAAATATAAGAGCAAA 60.202 37.037 0.00 0.00 0.00 3.68
2401 2668 7.469260 TCCGTAAAGCAAATATAAGAGCAAAC 58.531 34.615 0.00 0.00 0.00 2.93
2402 2669 6.691388 CCGTAAAGCAAATATAAGAGCAAACC 59.309 38.462 0.00 0.00 0.00 3.27
2403 2670 6.691388 CGTAAAGCAAATATAAGAGCAAACCC 59.309 38.462 0.00 0.00 0.00 4.11
2404 2671 6.857437 AAAGCAAATATAAGAGCAAACCCT 57.143 33.333 0.00 0.00 0.00 4.34
2405 2672 6.456795 AAGCAAATATAAGAGCAAACCCTC 57.543 37.500 0.00 0.00 0.00 4.30
2431 2730 9.984190 CTTATATTTCTTTACAGAGGGAGTACC 57.016 37.037 0.00 0.00 40.67 3.34
2451 2750 1.066303 CTCCTGACACGCTAGGATCAC 59.934 57.143 0.00 0.00 41.96 3.06
2452 2751 1.107114 CCTGACACGCTAGGATCACT 58.893 55.000 0.00 0.00 36.11 3.41
2454 2753 1.745653 CTGACACGCTAGGATCACTCA 59.254 52.381 0.00 0.00 0.00 3.41
2492 2793 4.883585 GGCTCATCTCACATTGGTTTATGA 59.116 41.667 0.00 0.00 0.00 2.15
2496 2797 7.250445 TCATCTCACATTGGTTTATGATTCG 57.750 36.000 0.00 0.00 0.00 3.34
2528 2835 3.950397 TGTGTCCTTTGATCATACCACC 58.050 45.455 0.00 0.00 0.00 4.61
2535 2842 5.251932 TCCTTTGATCATACCACCCTAAACA 59.748 40.000 0.00 0.00 0.00 2.83
2538 2845 7.039363 CCTTTGATCATACCACCCTAAACAAAA 60.039 37.037 0.00 0.00 0.00 2.44
2702 3023 6.647067 AGAGTACAGTTTTGAATAGTCTGCAC 59.353 38.462 0.00 0.00 0.00 4.57
2732 3053 3.005897 TCCTAACTCTGTTCAGCACACTC 59.994 47.826 0.00 0.00 0.00 3.51
2740 3061 4.570772 TCTGTTCAGCACACTCTAAAACAC 59.429 41.667 0.00 0.00 0.00 3.32
2770 3091 2.612212 CAGTTTACACCAGCAACGACTT 59.388 45.455 0.00 0.00 0.00 3.01
2771 3092 3.064820 CAGTTTACACCAGCAACGACTTT 59.935 43.478 0.00 0.00 0.00 2.66
2772 3093 3.064820 AGTTTACACCAGCAACGACTTTG 59.935 43.478 0.00 0.00 38.37 2.77
2773 3094 2.319136 TACACCAGCAACGACTTTGT 57.681 45.000 0.00 0.00 37.54 2.83
2793 3116 2.476997 GTCTGTCGGCAGTTTCTTTCTC 59.523 50.000 18.04 0.00 43.05 2.87
2794 3117 2.365617 TCTGTCGGCAGTTTCTTTCTCT 59.634 45.455 18.04 0.00 43.05 3.10
2795 3118 2.478134 CTGTCGGCAGTTTCTTTCTCTG 59.522 50.000 9.39 0.00 37.92 3.35
2796 3119 2.102420 TGTCGGCAGTTTCTTTCTCTGA 59.898 45.455 0.00 0.00 0.00 3.27
2801 3124 5.299279 TCGGCAGTTTCTTTCTCTGAAAATT 59.701 36.000 0.00 0.00 35.54 1.82
2818 3141 6.454795 TGAAAATTTATCTGAACTTGTGGGC 58.545 36.000 0.00 0.00 0.00 5.36
2921 3259 1.132199 CGTGAGCGGCTACTACAACG 61.132 60.000 0.60 3.10 0.00 4.10
2922 3260 0.169672 GTGAGCGGCTACTACAACGA 59.830 55.000 0.60 0.00 0.00 3.85
2923 3261 0.450583 TGAGCGGCTACTACAACGAG 59.549 55.000 0.60 0.00 0.00 4.18
2924 3262 0.248539 GAGCGGCTACTACAACGAGG 60.249 60.000 0.60 0.00 0.00 4.63
2925 3263 1.226888 GCGGCTACTACAACGAGGG 60.227 63.158 0.00 0.00 0.00 4.30
2926 3264 1.436336 CGGCTACTACAACGAGGGG 59.564 63.158 0.00 0.00 0.00 4.79
2927 3265 1.821258 GGCTACTACAACGAGGGGG 59.179 63.158 0.00 0.00 0.00 5.40
2928 3266 1.143401 GCTACTACAACGAGGGGGC 59.857 63.158 0.00 0.00 0.00 5.80
2929 3267 1.436336 CTACTACAACGAGGGGGCG 59.564 63.158 0.00 0.00 37.29 6.13
2930 3268 2.624437 CTACTACAACGAGGGGGCGC 62.624 65.000 0.00 0.00 33.86 6.53
2931 3269 3.771160 CTACAACGAGGGGGCGCT 61.771 66.667 7.64 0.00 33.86 5.92
2932 3270 4.077184 TACAACGAGGGGGCGCTG 62.077 66.667 7.64 0.00 33.88 5.18
3106 3453 1.004080 CTGATCCCTGCGGCTATGG 60.004 63.158 0.00 0.83 0.00 2.74
3112 3459 2.184322 CTGCGGCTATGGTCGTGT 59.816 61.111 4.63 0.00 43.14 4.49
3154 3509 2.242196 AGGATAAGTGTGGGGTGAATGG 59.758 50.000 0.00 0.00 0.00 3.16
3165 3525 0.678048 GGTGAATGGGTGGCTCTGTC 60.678 60.000 0.00 0.00 0.00 3.51
3235 3603 1.298859 GGGATTGTGGAGTGTGCGTC 61.299 60.000 0.00 0.00 0.00 5.19
3236 3604 1.298859 GGATTGTGGAGTGTGCGTCC 61.299 60.000 0.00 0.00 34.31 4.79
3255 3623 3.434984 GTCCAAGAGATCAGTCTGTTTGC 59.565 47.826 0.00 0.00 35.94 3.68
3318 3686 6.660887 TTTCATTTGTGAAAAGGCAAAGAC 57.339 33.333 1.41 0.00 37.89 3.01
3320 3688 2.861462 TTGTGAAAAGGCAAAGACCG 57.139 45.000 0.00 0.00 33.69 4.79
3324 3692 4.643463 TGTGAAAAGGCAAAGACCGTATA 58.357 39.130 0.00 0.00 33.69 1.47
3515 3883 4.473520 CCCGTCTCGCCCAATGCT 62.474 66.667 0.00 0.00 38.05 3.79
3680 4065 3.567797 GGCGTCTGATTCTGCGGC 61.568 66.667 13.98 13.98 42.13 6.53
3706 4095 2.659063 GCATTCCCCACCCCTTTGC 61.659 63.158 0.00 0.00 0.00 3.68
4027 4429 4.152223 GGCTCGGAAATTTGGTTCAATTTG 59.848 41.667 0.00 0.00 0.00 2.32
4028 4430 4.749598 GCTCGGAAATTTGGTTCAATTTGT 59.250 37.500 0.00 0.00 0.00 2.83
4029 4431 5.333263 GCTCGGAAATTTGGTTCAATTTGTG 60.333 40.000 0.00 0.00 0.00 3.33
4030 4432 5.665459 TCGGAAATTTGGTTCAATTTGTGT 58.335 33.333 0.00 0.00 0.00 3.72
4031 4433 5.521735 TCGGAAATTTGGTTCAATTTGTGTG 59.478 36.000 0.00 0.00 0.00 3.82
4032 4434 5.521735 CGGAAATTTGGTTCAATTTGTGTGA 59.478 36.000 0.00 0.00 0.00 3.58
4033 4435 6.036517 CGGAAATTTGGTTCAATTTGTGTGAA 59.963 34.615 0.00 0.00 32.62 3.18
4034 4436 7.408910 GGAAATTTGGTTCAATTTGTGTGAAG 58.591 34.615 0.00 0.00 35.71 3.02
4035 4437 7.065683 GGAAATTTGGTTCAATTTGTGTGAAGT 59.934 33.333 0.00 0.00 35.71 3.01
4036 4438 7.538303 AATTTGGTTCAATTTGTGTGAAGTC 57.462 32.000 0.00 0.00 35.71 3.01
4037 4439 4.285807 TGGTTCAATTTGTGTGAAGTCG 57.714 40.909 0.00 0.00 35.71 4.18
4038 4440 3.692101 TGGTTCAATTTGTGTGAAGTCGT 59.308 39.130 0.00 0.00 35.71 4.34
4115 4517 5.107824 GTGGTCGGTTCTACTAAGGATTTC 58.892 45.833 0.00 0.00 0.00 2.17
4185 4590 3.507233 AGGACATGCAATAGTGTTTGGTG 59.493 43.478 0.00 0.00 0.00 4.17
4186 4591 3.255642 GGACATGCAATAGTGTTTGGTGT 59.744 43.478 0.00 0.00 0.00 4.16
4190 4595 6.810911 ACATGCAATAGTGTTTGGTGTTTAA 58.189 32.000 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.820074 TTCCGAACCGCCAAATGTGT 60.820 50.000 0.00 0.00 0.00 3.72
14 15 0.878416 TCTTTCCGAACCGCCAAATG 59.122 50.000 0.00 0.00 0.00 2.32
15 16 1.539827 CTTCTTTCCGAACCGCCAAAT 59.460 47.619 0.00 0.00 0.00 2.32
27 28 3.615351 CGTCCTCACCTCTTCTTCTTTCC 60.615 52.174 0.00 0.00 0.00 3.13
42 43 1.248785 CCGGACCTTCTTCGTCCTCA 61.249 60.000 0.00 0.00 46.48 3.86
71 72 7.062371 CGATTTATAGACGGTTGGATGAAGATC 59.938 40.741 0.00 0.00 0.00 2.75
89 90 9.893634 TTTTCAATTAGGGTCAGTCGATTTATA 57.106 29.630 0.00 0.00 0.00 0.98
96 97 6.908825 TGAATTTTTCAATTAGGGTCAGTCG 58.091 36.000 0.00 0.00 36.59 4.18
99 100 7.885297 TGACTGAATTTTTCAATTAGGGTCAG 58.115 34.615 0.00 0.00 39.58 3.51
102 103 8.143835 CACTTGACTGAATTTTTCAATTAGGGT 58.856 33.333 0.00 0.00 39.58 4.34
118 119 2.899900 AGGCTACACATCACTTGACTGA 59.100 45.455 0.00 0.00 0.00 3.41
124 125 1.065854 GGCAGAGGCTACACATCACTT 60.066 52.381 0.00 0.00 40.87 3.16
184 185 1.546476 CTCTGTTTCCGTCTGCTACCT 59.454 52.381 0.00 0.00 0.00 3.08
281 282 3.688159 GGTTGGGCAGCTTGCTGG 61.688 66.667 21.98 6.28 44.28 4.85
283 284 3.875510 GAGGGTTGGGCAGCTTGCT 62.876 63.158 7.85 0.00 44.28 3.91
296 297 2.447429 TGCTAGTAGATGCCTAGAGGGT 59.553 50.000 0.00 0.00 35.01 4.34
358 359 2.581354 GATCGGTCAGCAGCCAGT 59.419 61.111 0.00 0.00 0.00 4.00
371 372 2.795389 GAAAACGACGGCCGGATCG 61.795 63.158 29.78 29.78 43.93 3.69
377 378 3.116531 CGGAGGAAAACGACGGCC 61.117 66.667 0.00 0.00 0.00 6.13
413 414 1.228459 GAGGTGGGCGGTCCTTTTT 60.228 57.895 0.00 0.00 33.83 1.94
435 436 3.151022 GAGGAGGTGGAGCCGGAG 61.151 72.222 5.05 0.00 43.70 4.63
436 437 4.779733 GGAGGAGGTGGAGCCGGA 62.780 72.222 5.05 0.00 43.70 5.14
437 438 4.787280 AGGAGGAGGTGGAGCCGG 62.787 72.222 0.00 0.00 43.70 6.13
438 439 2.685380 AAGGAGGAGGTGGAGCCG 60.685 66.667 0.00 0.00 43.70 5.52
439 440 2.726351 CGAAGGAGGAGGTGGAGCC 61.726 68.421 0.00 0.00 37.58 4.70
440 441 1.045911 ATCGAAGGAGGAGGTGGAGC 61.046 60.000 0.00 0.00 0.00 4.70
579 623 1.061570 GTAGCGACGACGAACCGAT 59.938 57.895 12.29 3.43 42.66 4.18
623 667 1.600663 CGAAGGATCCGATCGGTTGAG 60.601 57.143 32.15 14.91 36.47 3.02
681 725 7.660030 TTTCCCTTTCACTTTCTCATTTTCT 57.340 32.000 0.00 0.00 0.00 2.52
682 726 8.768019 CAATTTCCCTTTCACTTTCTCATTTTC 58.232 33.333 0.00 0.00 0.00 2.29
745 822 2.394632 ACACCTATACGATTCCAGCCA 58.605 47.619 0.00 0.00 0.00 4.75
819 917 2.422479 GTGTAGTAGTCTGTCGATGCCA 59.578 50.000 0.00 0.00 0.00 4.92
836 934 2.557056 GTGCTGGTCTGTAGACTGTGTA 59.443 50.000 11.45 0.00 44.20 2.90
837 935 1.341531 GTGCTGGTCTGTAGACTGTGT 59.658 52.381 11.45 0.00 44.20 3.72
838 936 1.667177 CGTGCTGGTCTGTAGACTGTG 60.667 57.143 11.45 4.20 44.20 3.66
886 988 1.078637 GTCCCCTCCCGCTTTGTAC 60.079 63.158 0.00 0.00 0.00 2.90
908 1010 1.134438 GGGTGGGTCTTCCTGAGGTT 61.134 60.000 0.00 0.00 36.20 3.50
1025 1131 0.527385 CTAAGCAGAGCACGGAGAGC 60.527 60.000 0.00 0.00 46.67 4.09
1058 1169 3.614143 GATCGATCGACGGGTTGC 58.386 61.111 22.06 0.37 42.82 4.17
1068 1179 2.584970 TTGCACCGGCGATCGATC 60.585 61.111 21.57 15.68 45.35 3.69
1137 1253 2.896854 CCACGATGGACGCCATGG 60.897 66.667 14.84 7.63 45.26 3.66
1276 1392 2.079158 CCGGCCTGAGCACATATTATG 58.921 52.381 0.00 2.03 42.56 1.90
1279 1395 0.107456 CTCCGGCCTGAGCACATATT 59.893 55.000 11.59 0.00 42.56 1.28
1280 1396 1.750930 CTCCGGCCTGAGCACATAT 59.249 57.895 11.59 0.00 42.56 1.78
1622 1774 1.135972 CGCACGAACAAATAAGCAGCT 60.136 47.619 0.00 0.00 0.00 4.24
1687 1842 1.817099 CCGCTCCTCAATCAGCACC 60.817 63.158 0.00 0.00 35.15 5.01
1721 1885 4.558538 GAGATGGTGCTCGCAATAATTT 57.441 40.909 0.00 0.00 0.00 1.82
1731 1895 3.119673 ACATATCGATCGAGATGGTGCTC 60.120 47.826 40.08 0.00 45.11 4.26
1742 1906 8.212372 ACACGTTAGATTAAACATATCGATCG 57.788 34.615 9.36 9.36 0.00 3.69
1786 1954 6.372937 TCCAAATGTGATTAAACATACGCTCA 59.627 34.615 0.00 0.00 39.89 4.26
1838 2007 7.252612 TCATGTTTAGGAATCAACTACTCCA 57.747 36.000 0.00 0.00 0.00 3.86
1865 2041 7.962918 GTGTGCCTTGACATGTTTATAAGTTAG 59.037 37.037 0.00 0.00 0.00 2.34
1870 2053 5.767665 ACAGTGTGCCTTGACATGTTTATAA 59.232 36.000 0.00 0.00 0.00 0.98
1928 2111 7.119116 TGTGCTAATATGTGACTTGTTTGTAGG 59.881 37.037 0.00 0.00 0.00 3.18
1937 2120 4.525996 TGCCATGTGCTAATATGTGACTT 58.474 39.130 7.54 0.00 42.00 3.01
1941 2124 4.517832 AGACATGCCATGTGCTAATATGTG 59.482 41.667 16.43 0.00 45.03 3.21
1965 2159 0.806868 TGGTAGCTTCAGGTCGTACG 59.193 55.000 9.53 9.53 0.00 3.67
1966 2160 2.603953 GTTGGTAGCTTCAGGTCGTAC 58.396 52.381 0.00 0.00 0.00 3.67
1969 2173 0.736325 CGGTTGGTAGCTTCAGGTCG 60.736 60.000 0.00 0.00 0.00 4.79
1996 2207 5.991328 TGAACAGAGTGTAGAAGCAAAAG 57.009 39.130 0.00 0.00 0.00 2.27
2003 2214 4.546570 CGTGTGATGAACAGAGTGTAGAA 58.453 43.478 0.00 0.00 40.26 2.10
2007 2218 1.069204 AGCGTGTGATGAACAGAGTGT 59.931 47.619 0.00 0.00 40.26 3.55
2010 2221 5.175090 TCTATAGCGTGTGATGAACAGAG 57.825 43.478 0.00 0.00 40.26 3.35
2045 2259 0.947180 TAGTTTGTGCCGAACGGAGC 60.947 55.000 17.63 8.71 37.50 4.70
2049 2263 1.455786 CTCTGTAGTTTGTGCCGAACG 59.544 52.381 0.00 0.00 33.34 3.95
2100 2356 0.531200 CCGAACAGAGGGTGTACTCC 59.469 60.000 5.35 5.35 39.03 3.85
2104 2360 4.529377 AGTTTATTCCGAACAGAGGGTGTA 59.471 41.667 0.00 0.00 39.03 2.90
2106 2362 3.939066 AGTTTATTCCGAACAGAGGGTG 58.061 45.455 0.00 0.00 0.00 4.61
2107 2363 5.451520 CGATAGTTTATTCCGAACAGAGGGT 60.452 44.000 0.00 0.00 0.00 4.34
2108 2364 4.982916 CGATAGTTTATTCCGAACAGAGGG 59.017 45.833 0.00 0.00 0.00 4.30
2109 2365 4.444720 GCGATAGTTTATTCCGAACAGAGG 59.555 45.833 0.00 0.00 39.35 3.69
2128 2384 3.340814 AGGTTCACTCATTTGAGCGAT 57.659 42.857 7.48 0.00 45.79 4.58
2134 2390 6.873605 TCACTATGTGTAGGTTCACTCATTTG 59.126 38.462 0.00 0.00 38.90 2.32
2146 2402 5.752892 AGACGTGTATCACTATGTGTAGG 57.247 43.478 0.00 0.00 34.79 3.18
2154 2410 7.495055 TGAGTGTATCTAGACGTGTATCACTA 58.505 38.462 14.65 1.26 34.49 2.74
2155 2411 6.346896 TGAGTGTATCTAGACGTGTATCACT 58.653 40.000 14.61 14.61 36.54 3.41
2156 2412 6.600246 TGAGTGTATCTAGACGTGTATCAC 57.400 41.667 0.00 1.25 0.00 3.06
2173 2429 9.950496 AGAATTAACTGTAGATGAAATGAGTGT 57.050 29.630 0.00 0.00 0.00 3.55
2178 2434 9.694520 CGTTCAGAATTAACTGTAGATGAAATG 57.305 33.333 0.00 0.00 38.79 2.32
2187 2453 5.733620 ACCTCCGTTCAGAATTAACTGTA 57.266 39.130 0.00 0.00 38.79 2.74
2216 2482 2.398803 GGTCGGTACCGGTCTAGAC 58.601 63.158 32.80 21.70 40.25 2.59
2245 2512 3.674528 TCAGAGTTTCAGAGCAAGGAG 57.325 47.619 0.00 0.00 0.00 3.69
2368 2635 4.563140 ATTTGCTTTACGGAGGGAGTAA 57.437 40.909 0.00 0.00 32.84 2.24
2371 2638 6.522054 TCTTATATTTGCTTTACGGAGGGAG 58.478 40.000 0.00 0.00 0.00 4.30
2373 2640 5.179555 GCTCTTATATTTGCTTTACGGAGGG 59.820 44.000 0.00 0.00 0.00 4.30
2375 2642 6.844696 TGCTCTTATATTTGCTTTACGGAG 57.155 37.500 0.00 0.00 0.00 4.63
2379 2646 7.772166 AGGGTTTGCTCTTATATTTGCTTTAC 58.228 34.615 0.00 0.00 0.00 2.01
2380 2647 7.834181 AGAGGGTTTGCTCTTATATTTGCTTTA 59.166 33.333 0.00 0.00 0.00 1.85
2381 2648 6.665248 AGAGGGTTTGCTCTTATATTTGCTTT 59.335 34.615 0.00 0.00 0.00 3.51
2383 2650 5.760131 AGAGGGTTTGCTCTTATATTTGCT 58.240 37.500 0.00 0.00 0.00 3.91
2384 2651 6.456795 AAGAGGGTTTGCTCTTATATTTGC 57.543 37.500 0.00 0.00 38.06 3.68
2394 2661 9.174166 TGTAAAGAAATATAAGAGGGTTTGCTC 57.826 33.333 0.00 0.00 0.00 4.26
2395 2662 9.178758 CTGTAAAGAAATATAAGAGGGTTTGCT 57.821 33.333 0.00 0.00 0.00 3.91
2396 2663 9.174166 TCTGTAAAGAAATATAAGAGGGTTTGC 57.826 33.333 0.00 0.00 0.00 3.68
2398 2665 9.907229 CCTCTGTAAAGAAATATAAGAGGGTTT 57.093 33.333 7.76 0.00 37.38 3.27
2402 2669 8.929487 ACTCCCTCTGTAAAGAAATATAAGAGG 58.071 37.037 8.54 8.54 39.86 3.69
2405 2672 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
2430 2729 0.671251 GATCCTAGCGTGTCAGGAGG 59.329 60.000 0.00 0.00 44.06 4.30
2431 2730 1.066303 GTGATCCTAGCGTGTCAGGAG 59.934 57.143 0.00 0.00 44.06 3.69
2432 2731 1.103803 GTGATCCTAGCGTGTCAGGA 58.896 55.000 0.00 0.00 44.90 3.86
2434 2733 1.745653 TGAGTGATCCTAGCGTGTCAG 59.254 52.381 0.00 0.00 0.00 3.51
2492 2793 6.817765 AAGGACACAATGACATTTACGAAT 57.182 33.333 0.00 0.00 0.00 3.34
2496 2797 7.592938 TGATCAAAGGACACAATGACATTTAC 58.407 34.615 0.00 0.00 26.82 2.01
2528 2835 7.141363 CAGAGAGTCATTTGGTTTTGTTTAGG 58.859 38.462 0.00 0.00 0.00 2.69
2535 2842 4.037208 CAGTGCAGAGAGTCATTTGGTTTT 59.963 41.667 0.00 0.00 0.00 2.43
2538 2845 2.775890 CAGTGCAGAGAGTCATTTGGT 58.224 47.619 0.00 0.00 0.00 3.67
2590 2906 6.203338 TGAACATACGAGTTAGGAAACCAAAC 59.797 38.462 0.00 0.00 36.15 2.93
2604 2920 2.677199 ACAGTGTGCTGAACATACGAG 58.323 47.619 0.00 0.00 44.55 4.18
2605 2921 2.812358 ACAGTGTGCTGAACATACGA 57.188 45.000 0.00 0.00 44.55 3.43
2702 3023 4.380531 TGAACAGAGTTAGGAAACTGCAG 58.619 43.478 13.48 13.48 46.09 4.41
2732 3053 8.753175 GTGTAAACTGTACTCTCTGTGTTTTAG 58.247 37.037 0.00 0.00 0.00 1.85
2740 3061 4.238514 GCTGGTGTAAACTGTACTCTCTG 58.761 47.826 0.00 0.00 0.00 3.35
2793 3116 6.587608 GCCCACAAGTTCAGATAAATTTTCAG 59.412 38.462 0.00 0.00 0.00 3.02
2794 3117 6.454795 GCCCACAAGTTCAGATAAATTTTCA 58.545 36.000 0.00 0.00 0.00 2.69
2795 3118 5.572896 CGCCCACAAGTTCAGATAAATTTTC 59.427 40.000 0.00 0.00 0.00 2.29
2796 3119 5.469479 CGCCCACAAGTTCAGATAAATTTT 58.531 37.500 0.00 0.00 0.00 1.82
2801 3124 1.349688 ACCGCCCACAAGTTCAGATAA 59.650 47.619 0.00 0.00 0.00 1.75
3046 3384 2.124736 CCGTTGATGATGGGCGGT 60.125 61.111 0.00 0.00 37.87 5.68
3106 3453 0.590732 ACGACACGAACAGACACGAC 60.591 55.000 0.00 0.00 0.00 4.34
3112 3459 1.273688 CAACACACGACACGAACAGA 58.726 50.000 0.00 0.00 0.00 3.41
3165 3525 1.294659 GCAACCTCTGTTCTCGGCAG 61.295 60.000 0.00 0.00 30.42 4.85
3235 3603 2.746362 GGCAAACAGACTGATCTCTTGG 59.254 50.000 10.08 0.00 30.42 3.61
3236 3604 3.672808 AGGCAAACAGACTGATCTCTTG 58.327 45.455 10.08 5.71 30.74 3.02
3255 3623 5.682862 GCGCATGAATGTAAAATACTCAAGG 59.317 40.000 0.30 0.00 0.00 3.61
3298 3666 3.490526 CGGTCTTTGCCTTTTCACAAATG 59.509 43.478 0.00 0.00 35.38 2.32
3305 3673 7.427318 CGTTTAATATACGGTCTTTGCCTTTTC 59.573 37.037 0.00 0.00 35.47 2.29
3318 3686 9.925268 ATTTTAGCTTTGTCGTTTAATATACGG 57.075 29.630 0.00 0.00 39.38 4.02
3324 3692 6.806739 GCAGGATTTTAGCTTTGTCGTTTAAT 59.193 34.615 0.00 0.00 0.00 1.40
3515 3883 2.365105 GGGGAGTGGGGATCGTGA 60.365 66.667 0.00 0.00 0.00 4.35
3869 4266 3.959991 GAAGACAGAGCGGGGGCAC 62.960 68.421 0.00 0.00 0.00 5.01
4027 4429 3.733024 TTTCACACAACGACTTCACAC 57.267 42.857 0.00 0.00 0.00 3.82
4028 4430 4.955925 AATTTCACACAACGACTTCACA 57.044 36.364 0.00 0.00 0.00 3.58
4029 4431 6.044512 ACTAATTTCACACAACGACTTCAC 57.955 37.500 0.00 0.00 0.00 3.18
4030 4432 5.051307 CGACTAATTTCACACAACGACTTCA 60.051 40.000 0.00 0.00 0.00 3.02
4031 4433 5.363517 CGACTAATTTCACACAACGACTTC 58.636 41.667 0.00 0.00 0.00 3.01
4032 4434 4.210537 CCGACTAATTTCACACAACGACTT 59.789 41.667 0.00 0.00 0.00 3.01
4033 4435 3.739300 CCGACTAATTTCACACAACGACT 59.261 43.478 0.00 0.00 0.00 4.18
4034 4436 3.663493 GCCGACTAATTTCACACAACGAC 60.663 47.826 0.00 0.00 0.00 4.34
4035 4437 2.477375 GCCGACTAATTTCACACAACGA 59.523 45.455 0.00 0.00 0.00 3.85
4036 4438 2.478894 AGCCGACTAATTTCACACAACG 59.521 45.455 0.00 0.00 0.00 4.10
4037 4439 3.364964 CCAGCCGACTAATTTCACACAAC 60.365 47.826 0.00 0.00 0.00 3.32
4038 4440 2.811431 CCAGCCGACTAATTTCACACAA 59.189 45.455 0.00 0.00 0.00 3.33
4190 4595 7.118723 TCCACTAATGCACATCTTAAAATCCT 58.881 34.615 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.