Multiple sequence alignment - TraesCS2A01G569700

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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 TraesCS2A01G569700 chr2A 100.000 3606 0 0 1 3606 767327126 767330731 0.000000e+00 6660.0
1 TraesCS2A01G569700 chr2A 79.051 864 129 25 277 1137 437206999 437206185 2.450000e-151 545.0
2 TraesCS2A01G569700 chr2A 77.104 297 48 15 1939 2222 2464138 2463849 1.730000e-33 154.0
3 TraesCS2A01G569700 chr2A 75.350 357 49 29 2542 2886 767028429 767028100 6.280000e-28 135.0
4 TraesCS2A01G569700 chr2A 100.000 31 0 0 1391 1421 748207551 748207581 1.400000e-04 58.4
5 TraesCS2A01G569700 chr2D 88.232 1589 98 33 1365 2900 642333593 642335145 0.000000e+00 1816.0
6 TraesCS2A01G569700 chr2D 88.713 1329 89 27 44 1326 642332277 642333590 0.000000e+00 1567.0
7 TraesCS2A01G569700 chr2D 89.073 1208 85 29 1293 2478 642221490 642220308 0.000000e+00 1456.0
8 TraesCS2A01G569700 chr2D 84.615 676 68 13 2945 3597 642222707 642222045 1.090000e-179 640.0
9 TraesCS2A01G569700 chr2D 88.923 325 24 7 3078 3397 642335308 642335625 1.210000e-104 390.0
10 TraesCS2A01G569700 chr2D 92.857 154 7 2 2471 2624 642220282 642220133 1.690000e-53 220.0
11 TraesCS2A01G569700 chr2D 84.615 169 20 4 1939 2104 2494995 2495160 2.880000e-36 163.0
12 TraesCS2A01G569700 chr2D 100.000 31 0 0 1391 1421 1518274 1518304 1.400000e-04 58.4
13 TraesCS2A01G569700 chr2D 100.000 31 0 0 1391 1421 10253464 10253494 1.400000e-04 58.4
14 TraesCS2A01G569700 chr2B 92.626 1112 56 7 44 1137 799531827 799532930 0.000000e+00 1576.0
15 TraesCS2A01G569700 chr2B 83.730 1512 119 67 1359 2830 799533119 799534543 0.000000e+00 1312.0
16 TraesCS2A01G569700 chr2B 84.729 406 27 14 2225 2609 799556444 799556835 1.220000e-99 374.0
17 TraesCS2A01G569700 chr2B 79.167 480 71 13 277 752 398553585 398553131 4.520000e-79 305.0
18 TraesCS2A01G569700 chr2B 92.361 144 11 0 3333 3476 799535027 799535170 4.720000e-49 206.0
19 TraesCS2A01G569700 chr2B 91.549 142 12 0 3165 3306 799563494 799563635 2.840000e-46 196.0
20 TraesCS2A01G569700 chr2B 89.565 115 4 5 2076 2188 799556333 799556441 4.850000e-29 139.0
21 TraesCS2A01G569700 chr2B 92.941 85 3 2 2810 2892 799562042 799562125 1.760000e-23 121.0
22 TraesCS2A01G569700 chr2B 82.014 139 11 6 2540 2664 799555939 799556077 4.920000e-19 106.0
23 TraesCS2A01G569700 chr2B 89.091 55 4 1 3009 3063 799534703 799534755 2.320000e-07 67.6
24 TraesCS2A01G569700 chrUn 85.694 692 66 10 304 987 94078906 94078240 0.000000e+00 699.0
25 TraesCS2A01G569700 chrUn 83.432 169 22 4 1939 2104 15885807 15885642 6.240000e-33 152.0
26 TraesCS2A01G569700 chr7A 83.694 693 78 13 304 988 387170489 387169824 3.950000e-174 621.0
27 TraesCS2A01G569700 chr7B 82.207 725 106 12 272 988 166057040 166057749 1.430000e-168 603.0
28 TraesCS2A01G569700 chr3B 78.035 346 49 9 511 856 254462471 254462153 3.670000e-45 193.0
29 TraesCS2A01G569700 chr6D 100.000 31 0 0 1391 1421 426571869 426571839 1.400000e-04 58.4
30 TraesCS2A01G569700 chr6D 100.000 28 0 0 882 909 469123028 469123055 7.000000e-03 52.8
31 TraesCS2A01G569700 chr5D 100.000 31 0 0 1391 1421 59789876 59789846 1.400000e-04 58.4
32 TraesCS2A01G569700 chr4B 100.000 31 0 0 1391 1421 238956903 238956873 1.400000e-04 58.4
33 TraesCS2A01G569700 chr3D 100.000 31 0 0 1391 1421 31450203 31450233 1.400000e-04 58.4
34 TraesCS2A01G569700 chr1A 100.000 31 0 0 1391 1421 50695815 50695845 1.400000e-04 58.4
35 TraesCS2A01G569700 chr6B 100.000 28 0 0 882 909 715347707 715347734 7.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G569700 chr2A 767327126 767330731 3605 False 6660.000000 6660 100.000000 1 3606 1 chr2A.!!$F2 3605
1 TraesCS2A01G569700 chr2A 437206185 437206999 814 True 545.000000 545 79.051000 277 1137 1 chr2A.!!$R2 860
2 TraesCS2A01G569700 chr2D 642332277 642335625 3348 False 1257.666667 1816 88.622667 44 3397 3 chr2D.!!$F4 3353
3 TraesCS2A01G569700 chr2D 642220133 642222707 2574 True 772.000000 1456 88.848333 1293 3597 3 chr2D.!!$R1 2304
4 TraesCS2A01G569700 chr2B 799531827 799535170 3343 False 790.400000 1576 89.452000 44 3476 4 chr2B.!!$F1 3432
5 TraesCS2A01G569700 chr2B 799555939 799556835 896 False 206.333333 374 85.436000 2076 2664 3 chr2B.!!$F2 588
6 TraesCS2A01G569700 chrUn 94078240 94078906 666 True 699.000000 699 85.694000 304 987 1 chrUn.!!$R2 683
7 TraesCS2A01G569700 chr7A 387169824 387170489 665 True 621.000000 621 83.694000 304 988 1 chr7A.!!$R1 684
8 TraesCS2A01G569700 chr7B 166057040 166057749 709 False 603.000000 603 82.207000 272 988 1 chr7B.!!$F1 716

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
196 221 0.312102 TCACTCTGCTCACACTCACG 59.688 55.0 0.0 0.0 0.0 4.35 F
1178 1274 0.035630 CCACTCTTGCTTCTCCCCTG 60.036 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1237 1338 0.032678 ACAGGAGACGCTGTGTTCTG 59.967 55.0 10.98 10.98 31.95 3.02 R
3151 3424 0.110056 GACAGCACACGAGCCAATTG 60.110 55.0 0.00 0.00 34.23 2.32 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
26 27 9.162764 ACACGCATGTAAGAAAGAATAGTTAAT 57.837 29.630 0.00 0.00 37.26 1.40
27 28 9.988350 CACGCATGTAAGAAAGAATAGTTAATT 57.012 29.630 0.00 0.00 0.00 1.40
28 29 9.988350 ACGCATGTAAGAAAGAATAGTTAATTG 57.012 29.630 0.00 0.00 0.00 2.32
29 30 9.438291 CGCATGTAAGAAAGAATAGTTAATTGG 57.562 33.333 0.00 0.00 0.00 3.16
30 31 9.237846 GCATGTAAGAAAGAATAGTTAATTGGC 57.762 33.333 0.00 0.00 0.00 4.52
33 34 9.733556 TGTAAGAAAGAATAGTTAATTGGCTCA 57.266 29.630 0.00 0.00 0.00 4.26
36 37 6.316390 AGAAAGAATAGTTAATTGGCTCACCG 59.684 38.462 0.00 0.00 39.70 4.94
40 41 0.725117 GTTAATTGGCTCACCGTCCG 59.275 55.000 0.00 0.00 39.70 4.79
41 42 0.391927 TTAATTGGCTCACCGTCCGG 60.392 55.000 3.76 3.76 39.70 5.14
71 72 0.800239 TTCTTCCTCCTCCCTCCCTT 59.200 55.000 0.00 0.00 0.00 3.95
196 221 0.312102 TCACTCTGCTCACACTCACG 59.688 55.000 0.00 0.00 0.00 4.35
248 273 2.558359 ACACAACAAATCCAAGCTAGCC 59.442 45.455 12.13 0.00 0.00 3.93
250 275 2.821969 ACAACAAATCCAAGCTAGCCAG 59.178 45.455 12.13 3.84 0.00 4.85
292 317 4.993584 TCTCAAAGAGCTCACTTCATTCAC 59.006 41.667 17.77 0.00 0.00 3.18
357 387 3.883744 GAGCTCCACCACCACCACG 62.884 68.421 0.87 0.00 0.00 4.94
432 462 2.279784 GAGAAGCCGGCGGATCAG 60.280 66.667 33.44 2.12 0.00 2.90
912 964 4.316823 TCGAGGCACTGGGGGTCT 62.317 66.667 0.00 0.00 41.55 3.85
1176 1272 0.035915 GACCACTCTTGCTTCTCCCC 60.036 60.000 0.00 0.00 0.00 4.81
1178 1274 0.035630 CCACTCTTGCTTCTCCCCTG 60.036 60.000 0.00 0.00 0.00 4.45
1207 1308 4.808767 TCTTCTGCTATCCTACCTACCA 57.191 45.455 0.00 0.00 0.00 3.25
1209 1310 4.894114 TCTTCTGCTATCCTACCTACCAAC 59.106 45.833 0.00 0.00 0.00 3.77
1235 1336 8.790718 CCTACTGTTACTCTGTTAGTAGAACAA 58.209 37.037 10.38 0.00 41.70 2.83
1237 1338 8.868635 ACTGTTACTCTGTTAGTAGAACAAAC 57.131 34.615 0.00 0.00 41.70 2.93
1320 1422 5.726397 TGGCACAACGATTAGTTACATAGT 58.274 37.500 0.00 0.00 42.02 2.12
1321 1423 6.865411 TGGCACAACGATTAGTTACATAGTA 58.135 36.000 0.00 0.00 42.02 1.82
1326 1428 8.679385 CACAACGATTAGTTACATAGTACATCG 58.321 37.037 0.00 0.00 42.02 3.84
1353 1455 2.122783 TGTTTATGGGTGCACCTAGC 57.877 50.000 33.91 18.96 45.96 3.42
1380 1482 3.072944 CTGCTCTGCTTAGCTGAAACTT 58.927 45.455 14.35 0.00 42.27 2.66
1421 1523 5.701290 GCTTAGCTGAAACTTTAGGAGTGAA 59.299 40.000 0.00 0.00 39.00 3.18
1440 1542 3.070159 TGAAGAGACTGGTGAAAGTGAGG 59.930 47.826 0.00 0.00 0.00 3.86
1443 1545 1.771255 AGACTGGTGAAAGTGAGGCTT 59.229 47.619 0.00 0.00 39.52 4.35
1446 1548 0.106769 TGGTGAAAGTGAGGCTTGCA 60.107 50.000 0.00 0.00 40.36 4.08
1516 1625 1.836166 CATGATGGTGGTCTGGTCTCT 59.164 52.381 0.00 0.00 0.00 3.10
1517 1626 2.919772 TGATGGTGGTCTGGTCTCTA 57.080 50.000 0.00 0.00 0.00 2.43
1518 1627 3.184382 TGATGGTGGTCTGGTCTCTAA 57.816 47.619 0.00 0.00 0.00 2.10
1559 1672 2.432146 CCCTGCAACAGTCATCTAGCTA 59.568 50.000 0.00 0.00 0.00 3.32
1560 1673 3.492309 CCCTGCAACAGTCATCTAGCTAG 60.492 52.174 15.01 15.01 0.00 3.42
1561 1674 3.122297 CTGCAACAGTCATCTAGCTAGC 58.878 50.000 16.35 6.62 0.00 3.42
1562 1675 2.762887 TGCAACAGTCATCTAGCTAGCT 59.237 45.455 23.12 23.12 0.00 3.32
1655 1774 1.742761 GTCACCATGACATGACCAGG 58.257 55.000 17.24 2.04 46.22 4.45
1666 1785 2.224992 ACATGACCAGGGCACAACATTA 60.225 45.455 0.00 0.00 0.00 1.90
1707 1830 2.348998 CCAGCCACAGGACCAGAC 59.651 66.667 0.00 0.00 0.00 3.51
1722 1845 3.935828 GACCAGACCAGTTAGAAGATTGC 59.064 47.826 0.00 0.00 0.00 3.56
1723 1846 3.327757 ACCAGACCAGTTAGAAGATTGCA 59.672 43.478 0.00 0.00 0.00 4.08
1913 2066 7.801104 TGATTGGTTTAGTGGAGCTGATATAA 58.199 34.615 0.00 0.00 0.00 0.98
1918 2071 6.926272 GGTTTAGTGGAGCTGATATAAGTGAG 59.074 42.308 0.00 0.00 0.00 3.51
2557 2755 1.374758 GGACGAGCTGGAGGTGTTG 60.375 63.158 1.44 0.00 0.00 3.33
2609 2814 1.199327 TCGTCTACAAGGCTTGACTCG 59.801 52.381 32.50 25.77 0.00 4.18
2610 2815 1.351153 GTCTACAAGGCTTGACTCGC 58.649 55.000 32.50 14.36 0.00 5.03
2611 2816 0.966179 TCTACAAGGCTTGACTCGCA 59.034 50.000 32.50 7.93 0.00 5.10
2612 2817 1.067565 TCTACAAGGCTTGACTCGCAG 60.068 52.381 32.50 17.35 0.00 5.18
2624 2829 3.781770 CTCGCAGATCACCTCGGCC 62.782 68.421 0.00 0.00 41.47 6.13
2635 2840 0.618968 ACCTCGGCCATCCTTCTTCT 60.619 55.000 2.24 0.00 0.00 2.85
2636 2841 0.179062 CCTCGGCCATCCTTCTTCTG 60.179 60.000 2.24 0.00 0.00 3.02
2637 2842 0.826715 CTCGGCCATCCTTCTTCTGA 59.173 55.000 2.24 0.00 0.00 3.27
2638 2843 0.537188 TCGGCCATCCTTCTTCTGAC 59.463 55.000 2.24 0.00 0.00 3.51
2644 2849 4.268359 GCCATCCTTCTTCTGACTGATTT 58.732 43.478 0.00 0.00 0.00 2.17
2705 2918 8.236586 TCAATTCCTTTCATGTCAACTTAATCG 58.763 33.333 0.00 0.00 0.00 3.34
2708 2921 6.403049 TCCTTTCATGTCAACTTAATCGCTA 58.597 36.000 0.00 0.00 0.00 4.26
2709 2922 6.312918 TCCTTTCATGTCAACTTAATCGCTAC 59.687 38.462 0.00 0.00 0.00 3.58
2711 2924 6.887376 TTCATGTCAACTTAATCGCTACTC 57.113 37.500 0.00 0.00 0.00 2.59
2712 2925 5.034797 TCATGTCAACTTAATCGCTACTCG 58.965 41.667 0.00 0.00 40.15 4.18
2713 2926 4.430137 TGTCAACTTAATCGCTACTCGT 57.570 40.909 0.00 0.00 39.67 4.18
2730 2943 2.490115 CTCGTCCTCTGCTTCAGTTAGT 59.510 50.000 0.00 0.00 32.61 2.24
2736 2949 1.071605 CTGCTTCAGTTAGTGGCGAC 58.928 55.000 0.00 0.00 0.00 5.19
2755 2968 4.148348 GCGACCGATGATGTAACATAGAAC 59.852 45.833 0.00 0.00 0.00 3.01
2780 2997 9.420118 ACCTTAATTATTTTGTATGATCAGGCA 57.580 29.630 0.09 0.00 0.00 4.75
2781 2998 9.903682 CCTTAATTATTTTGTATGATCAGGCAG 57.096 33.333 0.09 0.00 0.00 4.85
2833 3050 3.608796 TCAGTGGCAATGATCGATTGAA 58.391 40.909 14.40 0.00 43.87 2.69
2834 3051 4.009002 TCAGTGGCAATGATCGATTGAAA 58.991 39.130 14.40 0.00 43.87 2.69
2840 3057 5.357596 TGGCAATGATCGATTGAAAAGATGA 59.642 36.000 16.98 0.00 43.87 2.92
2853 3070 6.688637 TGAAAAGATGATACTTGAGCATGG 57.311 37.500 0.00 0.00 33.16 3.66
2873 3093 3.096092 GGATTACTCCCAACATTTGCCA 58.904 45.455 0.00 0.00 35.28 4.92
2900 3120 0.846427 AGGATGCTCCCAAGTCCCAA 60.846 55.000 0.00 0.00 37.19 4.12
2901 3121 0.039618 GGATGCTCCCAAGTCCCAAA 59.960 55.000 0.00 0.00 0.00 3.28
2904 3124 1.703411 TGCTCCCAAGTCCCAAAAAG 58.297 50.000 0.00 0.00 0.00 2.27
2909 3129 2.512056 TCCCAAGTCCCAAAAAGAGACA 59.488 45.455 0.00 0.00 32.82 3.41
2911 3131 3.256631 CCCAAGTCCCAAAAAGAGACATG 59.743 47.826 0.00 0.00 32.82 3.21
2912 3132 3.305608 CCAAGTCCCAAAAAGAGACATGC 60.306 47.826 0.00 0.00 32.82 4.06
2913 3133 3.228188 AGTCCCAAAAAGAGACATGCA 57.772 42.857 0.00 0.00 32.82 3.96
2915 3135 4.922206 AGTCCCAAAAAGAGACATGCATA 58.078 39.130 0.00 0.00 32.82 3.14
2916 3136 4.702131 AGTCCCAAAAAGAGACATGCATAC 59.298 41.667 0.00 0.00 32.82 2.39
2917 3137 4.016444 TCCCAAAAAGAGACATGCATACC 58.984 43.478 0.00 0.00 0.00 2.73
2918 3138 3.131046 CCCAAAAAGAGACATGCATACCC 59.869 47.826 0.00 0.00 0.00 3.69
2919 3139 3.763360 CCAAAAAGAGACATGCATACCCA 59.237 43.478 0.00 0.00 0.00 4.51
2930 3203 1.072489 TGCATACCCAGGTCGAAAACA 59.928 47.619 0.00 0.00 0.00 2.83
2942 3215 3.243855 GAAAACAGTTTTCGGCGCA 57.756 47.368 20.44 0.00 39.56 6.09
2963 3236 4.324402 GCACCGACAAACAATTCATGAATC 59.676 41.667 20.95 7.10 0.00 2.52
2966 3239 3.543494 CGACAAACAATTCATGAATCGCC 59.457 43.478 20.95 6.22 0.00 5.54
2994 3267 5.474825 ACTTCTCGGATCTCTTTCTGAAAC 58.525 41.667 0.00 0.00 30.77 2.78
3000 3273 5.639506 TCGGATCTCTTTCTGAAACAACATC 59.360 40.000 0.00 0.00 0.00 3.06
3002 3275 6.073058 CGGATCTCTTTCTGAAACAACATCAA 60.073 38.462 0.00 0.00 0.00 2.57
3005 3278 7.630242 TCTCTTTCTGAAACAACATCAAAGT 57.370 32.000 0.00 0.00 0.00 2.66
3009 3282 8.087750 TCTTTCTGAAACAACATCAAAGTTTGT 58.912 29.630 15.08 0.61 35.77 2.83
3010 3283 9.352784 CTTTCTGAAACAACATCAAAGTTTGTA 57.647 29.630 15.08 3.20 35.77 2.41
3013 3286 7.757624 TCTGAAACAACATCAAAGTTTGTAACC 59.242 33.333 15.08 0.00 35.77 2.85
3014 3287 6.528423 TGAAACAACATCAAAGTTTGTAACCG 59.472 34.615 15.08 5.70 35.77 4.44
3015 3288 4.927422 ACAACATCAAAGTTTGTAACCGG 58.073 39.130 15.08 0.00 0.00 5.28
3016 3289 4.202070 ACAACATCAAAGTTTGTAACCGGG 60.202 41.667 15.08 0.00 0.00 5.73
3017 3290 2.888414 ACATCAAAGTTTGTAACCGGGG 59.112 45.455 15.08 1.11 0.00 5.73
3018 3291 3.150767 CATCAAAGTTTGTAACCGGGGA 58.849 45.455 15.08 0.00 0.00 4.81
3019 3292 2.853705 TCAAAGTTTGTAACCGGGGAG 58.146 47.619 15.08 0.00 0.00 4.30
3020 3293 2.438763 TCAAAGTTTGTAACCGGGGAGA 59.561 45.455 15.08 0.00 0.00 3.71
3021 3294 2.812011 CAAAGTTTGTAACCGGGGAGAG 59.188 50.000 6.32 0.00 0.00 3.20
3022 3295 0.981943 AGTTTGTAACCGGGGAGAGG 59.018 55.000 6.32 0.00 0.00 3.69
3023 3296 0.675837 GTTTGTAACCGGGGAGAGGC 60.676 60.000 6.32 0.00 0.00 4.70
3024 3297 1.128809 TTTGTAACCGGGGAGAGGCA 61.129 55.000 6.32 0.00 0.00 4.75
3025 3298 1.550130 TTGTAACCGGGGAGAGGCAG 61.550 60.000 6.32 0.00 0.00 4.85
3026 3299 1.684734 GTAACCGGGGAGAGGCAGA 60.685 63.158 6.32 0.00 0.00 4.26
3027 3300 1.381327 TAACCGGGGAGAGGCAGAG 60.381 63.158 6.32 0.00 0.00 3.35
3028 3301 2.873557 TAACCGGGGAGAGGCAGAGG 62.874 65.000 6.32 0.00 0.00 3.69
3063 3336 4.640201 AGAACTTTGTGAGTGCAGCTTAAA 59.360 37.500 0.00 0.00 39.00 1.52
3064 3337 4.292977 ACTTTGTGAGTGCAGCTTAAAC 57.707 40.909 0.00 0.00 37.17 2.01
3065 3338 3.694072 ACTTTGTGAGTGCAGCTTAAACA 59.306 39.130 0.00 0.00 37.17 2.83
3066 3339 3.969117 TTGTGAGTGCAGCTTAAACAG 57.031 42.857 0.00 0.00 0.00 3.16
3094 3367 2.045926 GCCTGGAACTCGCCACAT 60.046 61.111 0.00 0.00 33.52 3.21
3117 3390 1.221466 CTCGTGTGCCGCTTCAAGAA 61.221 55.000 0.00 0.00 36.19 2.52
3141 3414 8.614469 AATTACTTCCTTTCTCAAGTTCAGAG 57.386 34.615 0.00 0.00 34.60 3.35
3143 3416 3.409026 TCCTTTCTCAAGTTCAGAGCC 57.591 47.619 0.00 0.00 33.15 4.70
3147 3420 3.393089 TTCTCAAGTTCAGAGCCTGAC 57.607 47.619 4.59 1.99 40.46 3.51
3150 3423 3.065655 CTCAAGTTCAGAGCCTGACAAG 58.934 50.000 4.59 0.00 40.46 3.16
3151 3424 1.534595 CAAGTTCAGAGCCTGACAAGC 59.465 52.381 4.59 0.00 40.46 4.01
3154 3427 2.157738 GTTCAGAGCCTGACAAGCAAT 58.842 47.619 4.59 0.00 40.46 3.56
3155 3428 2.555757 GTTCAGAGCCTGACAAGCAATT 59.444 45.455 4.59 0.00 40.46 2.32
3158 3431 0.108945 GAGCCTGACAAGCAATTGGC 60.109 55.000 7.72 0.00 45.30 4.52
3193 3466 1.379642 GCAGGCATGACAAGCTACCC 61.380 60.000 0.62 0.00 0.00 3.69
3223 3496 7.451501 TTCTGACATGATAAACAGCAATGAA 57.548 32.000 0.00 0.00 0.00 2.57
3257 3530 5.640189 ATCTTCAGAAAGACAGGCATTTG 57.360 39.130 0.00 0.00 44.13 2.32
3258 3531 3.254166 TCTTCAGAAAGACAGGCATTTGC 59.746 43.478 0.00 0.00 36.59 3.68
3290 3563 6.032094 GTGATGCAATTTATCTTGGTCACTG 58.968 40.000 0.00 0.00 32.82 3.66
3398 3678 6.270815 CCATGTTCTTCAGCTTAATTCATGG 58.729 40.000 16.77 16.77 41.97 3.66
3399 3679 5.314923 TGTTCTTCAGCTTAATTCATGGC 57.685 39.130 0.00 0.00 0.00 4.40
3407 3687 3.840078 AGCTTAATTCATGGCAAGGGTTT 59.160 39.130 0.00 0.00 0.00 3.27
3408 3688 3.934579 GCTTAATTCATGGCAAGGGTTTG 59.065 43.478 0.00 0.00 37.36 2.93
3439 3719 3.262842 TCCTCCCCTGCATATCATCATT 58.737 45.455 0.00 0.00 0.00 2.57
3471 3751 4.142600 GGTTAGGCATCAGTTTTGTGCTAG 60.143 45.833 0.00 0.00 38.83 3.42
3476 3756 3.999663 GCATCAGTTTTGTGCTAGTCTCT 59.000 43.478 0.00 0.00 36.02 3.10
3477 3757 4.092675 GCATCAGTTTTGTGCTAGTCTCTC 59.907 45.833 0.00 0.00 36.02 3.20
3478 3758 5.477510 CATCAGTTTTGTGCTAGTCTCTCT 58.522 41.667 0.00 0.00 0.00 3.10
3479 3759 5.127693 TCAGTTTTGTGCTAGTCTCTCTC 57.872 43.478 0.00 0.00 0.00 3.20
3480 3760 4.584743 TCAGTTTTGTGCTAGTCTCTCTCA 59.415 41.667 0.00 0.00 0.00 3.27
3481 3761 5.244851 TCAGTTTTGTGCTAGTCTCTCTCAT 59.755 40.000 0.00 0.00 0.00 2.90
3482 3762 5.348179 CAGTTTTGTGCTAGTCTCTCTCATG 59.652 44.000 0.00 0.00 0.00 3.07
3483 3763 5.011533 AGTTTTGTGCTAGTCTCTCTCATGT 59.988 40.000 0.00 0.00 0.00 3.21
3484 3764 4.710423 TTGTGCTAGTCTCTCTCATGTC 57.290 45.455 0.00 0.00 0.00 3.06
3485 3765 3.690460 TGTGCTAGTCTCTCTCATGTCA 58.310 45.455 0.00 0.00 0.00 3.58
3486 3766 4.082125 TGTGCTAGTCTCTCTCATGTCAA 58.918 43.478 0.00 0.00 0.00 3.18
3487 3767 4.708909 TGTGCTAGTCTCTCTCATGTCAAT 59.291 41.667 0.00 0.00 0.00 2.57
3488 3768 5.042593 GTGCTAGTCTCTCTCATGTCAATG 58.957 45.833 0.00 0.00 34.88 2.82
3489 3769 4.099113 TGCTAGTCTCTCTCATGTCAATGG 59.901 45.833 0.00 0.00 34.30 3.16
3490 3770 4.340666 GCTAGTCTCTCTCATGTCAATGGA 59.659 45.833 0.00 0.00 34.30 3.41
3491 3771 4.734398 AGTCTCTCTCATGTCAATGGAC 57.266 45.455 0.00 0.00 44.57 4.02
3502 3782 3.791973 GTCAATGGACAACACAAACCA 57.208 42.857 0.00 0.00 43.73 3.67
3503 3783 4.320608 GTCAATGGACAACACAAACCAT 57.679 40.909 0.00 0.00 43.73 3.55
3504 3784 4.298332 GTCAATGGACAACACAAACCATC 58.702 43.478 0.00 0.00 43.73 3.51
3505 3785 4.037923 GTCAATGGACAACACAAACCATCT 59.962 41.667 0.00 0.00 43.73 2.90
3506 3786 4.037803 TCAATGGACAACACAAACCATCTG 59.962 41.667 0.00 0.00 41.47 2.90
3507 3787 1.680735 TGGACAACACAAACCATCTGC 59.319 47.619 0.00 0.00 0.00 4.26
3508 3788 1.680735 GGACAACACAAACCATCTGCA 59.319 47.619 0.00 0.00 0.00 4.41
3509 3789 2.297033 GGACAACACAAACCATCTGCAT 59.703 45.455 0.00 0.00 0.00 3.96
3510 3790 3.243839 GGACAACACAAACCATCTGCATT 60.244 43.478 0.00 0.00 0.00 3.56
3511 3791 4.370917 GACAACACAAACCATCTGCATTT 58.629 39.130 0.00 0.00 0.00 2.32
3512 3792 4.768583 ACAACACAAACCATCTGCATTTT 58.231 34.783 0.00 0.00 0.00 1.82
3513 3793 5.911752 ACAACACAAACCATCTGCATTTTA 58.088 33.333 0.00 0.00 0.00 1.52
3514 3794 5.752955 ACAACACAAACCATCTGCATTTTAC 59.247 36.000 0.00 0.00 0.00 2.01
3515 3795 5.789643 ACACAAACCATCTGCATTTTACT 57.210 34.783 0.00 0.00 0.00 2.24
3516 3796 6.160576 ACACAAACCATCTGCATTTTACTT 57.839 33.333 0.00 0.00 0.00 2.24
3517 3797 7.283625 ACACAAACCATCTGCATTTTACTTA 57.716 32.000 0.00 0.00 0.00 2.24
3518 3798 7.370383 ACACAAACCATCTGCATTTTACTTAG 58.630 34.615 0.00 0.00 0.00 2.18
3519 3799 7.230510 ACACAAACCATCTGCATTTTACTTAGA 59.769 33.333 0.00 0.00 0.00 2.10
3520 3800 8.081633 CACAAACCATCTGCATTTTACTTAGAA 58.918 33.333 0.00 0.00 0.00 2.10
3521 3801 8.637986 ACAAACCATCTGCATTTTACTTAGAAA 58.362 29.630 0.00 0.00 0.00 2.52
3522 3802 9.474920 CAAACCATCTGCATTTTACTTAGAAAA 57.525 29.630 0.00 0.00 33.04 2.29
3523 3803 9.476202 AAACCATCTGCATTTTACTTAGAAAAC 57.524 29.630 0.00 0.00 31.35 2.43
3524 3804 8.177119 ACCATCTGCATTTTACTTAGAAAACA 57.823 30.769 0.00 0.00 31.35 2.83
3525 3805 8.806146 ACCATCTGCATTTTACTTAGAAAACAT 58.194 29.630 0.00 0.00 31.35 2.71
3526 3806 9.294030 CCATCTGCATTTTACTTAGAAAACATC 57.706 33.333 0.00 0.00 31.35 3.06
3527 3807 9.003112 CATCTGCATTTTACTTAGAAAACATCG 57.997 33.333 0.00 0.00 31.35 3.84
3528 3808 8.317891 TCTGCATTTTACTTAGAAAACATCGA 57.682 30.769 0.00 0.00 31.35 3.59
3529 3809 8.227791 TCTGCATTTTACTTAGAAAACATCGAC 58.772 33.333 0.00 0.00 31.35 4.20
3530 3810 7.866729 TGCATTTTACTTAGAAAACATCGACA 58.133 30.769 0.00 0.00 31.35 4.35
3531 3811 8.511321 TGCATTTTACTTAGAAAACATCGACAT 58.489 29.630 0.00 0.00 31.35 3.06
3532 3812 9.000018 GCATTTTACTTAGAAAACATCGACATC 58.000 33.333 0.00 0.00 31.35 3.06
3535 3815 8.827177 TTTACTTAGAAAACATCGACATCACT 57.173 30.769 0.00 0.00 0.00 3.41
3536 3816 9.917129 TTTACTTAGAAAACATCGACATCACTA 57.083 29.630 0.00 0.00 0.00 2.74
3537 3817 9.917129 TTACTTAGAAAACATCGACATCACTAA 57.083 29.630 0.00 0.00 0.00 2.24
3539 3819 9.436957 ACTTAGAAAACATCGACATCACTAATT 57.563 29.630 0.00 0.00 0.00 1.40
3546 3826 9.599866 AAACATCGACATCACTAATTTATCAGA 57.400 29.630 0.00 0.00 0.00 3.27
3547 3827 8.581057 ACATCGACATCACTAATTTATCAGAC 57.419 34.615 0.00 0.00 0.00 3.51
3548 3828 8.417106 ACATCGACATCACTAATTTATCAGACT 58.583 33.333 0.00 0.00 0.00 3.24
3549 3829 8.910666 CATCGACATCACTAATTTATCAGACTC 58.089 37.037 0.00 0.00 0.00 3.36
3550 3830 7.132863 TCGACATCACTAATTTATCAGACTCG 58.867 38.462 0.00 0.00 0.00 4.18
3551 3831 6.360947 CGACATCACTAATTTATCAGACTCGG 59.639 42.308 0.00 0.00 0.00 4.63
3552 3832 7.348080 ACATCACTAATTTATCAGACTCGGA 57.652 36.000 0.00 0.00 0.00 4.55
3553 3833 7.782049 ACATCACTAATTTATCAGACTCGGAA 58.218 34.615 0.00 0.00 0.00 4.30
3554 3834 7.707035 ACATCACTAATTTATCAGACTCGGAAC 59.293 37.037 0.00 0.00 0.00 3.62
3555 3835 7.165460 TCACTAATTTATCAGACTCGGAACA 57.835 36.000 0.00 0.00 0.00 3.18
3556 3836 7.033791 TCACTAATTTATCAGACTCGGAACAC 58.966 38.462 0.00 0.00 0.00 3.32
3557 3837 6.255887 CACTAATTTATCAGACTCGGAACACC 59.744 42.308 0.00 0.00 0.00 4.16
3558 3838 5.422214 AATTTATCAGACTCGGAACACCT 57.578 39.130 0.00 0.00 0.00 4.00
3559 3839 3.868757 TTATCAGACTCGGAACACCTG 57.131 47.619 0.00 0.00 0.00 4.00
3560 3840 1.633774 ATCAGACTCGGAACACCTGT 58.366 50.000 0.00 0.00 0.00 4.00
3561 3841 0.673985 TCAGACTCGGAACACCTGTG 59.326 55.000 0.00 0.00 0.00 3.66
3573 3853 3.676291 ACACCTGTGTTTTGCTTTGTT 57.324 38.095 0.00 0.00 41.83 2.83
3574 3854 3.584834 ACACCTGTGTTTTGCTTTGTTC 58.415 40.909 0.00 0.00 41.83 3.18
3575 3855 3.006323 ACACCTGTGTTTTGCTTTGTTCA 59.994 39.130 0.00 0.00 41.83 3.18
3576 3856 3.993081 CACCTGTGTTTTGCTTTGTTCAA 59.007 39.130 0.00 0.00 0.00 2.69
3577 3857 4.450419 CACCTGTGTTTTGCTTTGTTCAAA 59.550 37.500 0.00 0.00 0.00 2.69
3578 3858 4.690280 ACCTGTGTTTTGCTTTGTTCAAAG 59.310 37.500 17.65 17.65 35.21 2.77
3588 3868 4.233123 CTTTGTTCAAAGCAGAGCATGA 57.767 40.909 11.48 0.00 0.00 3.07
3589 3869 4.806330 CTTTGTTCAAAGCAGAGCATGAT 58.194 39.130 11.48 0.00 0.00 2.45
3590 3870 5.946298 CTTTGTTCAAAGCAGAGCATGATA 58.054 37.500 11.48 0.00 0.00 2.15
3591 3871 6.519679 TTTGTTCAAAGCAGAGCATGATAT 57.480 33.333 0.00 0.00 0.00 1.63
3592 3872 7.628769 TTTGTTCAAAGCAGAGCATGATATA 57.371 32.000 0.00 0.00 0.00 0.86
3593 3873 7.812690 TTGTTCAAAGCAGAGCATGATATAT 57.187 32.000 0.00 0.00 0.00 0.86
3594 3874 8.907222 TTGTTCAAAGCAGAGCATGATATATA 57.093 30.769 0.00 0.00 0.00 0.86
3595 3875 9.511272 TTGTTCAAAGCAGAGCATGATATATAT 57.489 29.630 0.00 0.00 0.00 0.86
3603 3883 9.874195 AGCAGAGCATGATATATATAACTAGGA 57.126 33.333 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.542497 TTAACTATTCTTTCTTACATGCGTGT 57.458 30.769 17.19 17.19 42.39 4.49
7 8 9.733556 TGAGCCAATTAACTATTCTTTCTTACA 57.266 29.630 0.00 0.00 0.00 2.41
8 9 9.989869 GTGAGCCAATTAACTATTCTTTCTTAC 57.010 33.333 0.00 0.00 0.00 2.34
10 11 7.148239 CGGTGAGCCAATTAACTATTCTTTCTT 60.148 37.037 0.00 0.00 34.09 2.52
11 12 6.316390 CGGTGAGCCAATTAACTATTCTTTCT 59.684 38.462 0.00 0.00 34.09 2.52
12 13 6.093633 ACGGTGAGCCAATTAACTATTCTTTC 59.906 38.462 0.00 0.00 34.09 2.62
14 15 5.497474 ACGGTGAGCCAATTAACTATTCTT 58.503 37.500 0.00 0.00 34.09 2.52
15 16 5.099042 ACGGTGAGCCAATTAACTATTCT 57.901 39.130 0.00 0.00 34.09 2.40
18 19 3.740141 CGGACGGTGAGCCAATTAACTAT 60.740 47.826 0.00 0.00 34.09 2.12
19 20 2.417651 CGGACGGTGAGCCAATTAACTA 60.418 50.000 0.00 0.00 34.09 2.24
21 22 0.725117 CGGACGGTGAGCCAATTAAC 59.275 55.000 0.00 0.00 34.09 2.01
40 41 2.045242 GAAGAAAGGGGCCGGACC 60.045 66.667 22.07 22.07 37.93 4.46
41 42 2.045242 GGAAGAAAGGGGCCGGAC 60.045 66.667 5.05 0.00 0.00 4.79
48 49 1.208706 GAGGGAGGAGGAAGAAAGGG 58.791 60.000 0.00 0.00 0.00 3.95
71 72 2.170166 CTGCTTTATGCTTTGTGGGGA 58.830 47.619 0.00 0.00 43.37 4.81
139 149 1.612726 GGGATGGATGATGGCTGCTAC 60.613 57.143 0.00 0.00 0.00 3.58
248 273 2.880890 ACAGAAGCTGGTAAACTTGCTG 59.119 45.455 0.00 0.00 35.51 4.41
250 275 3.142174 AGACAGAAGCTGGTAAACTTGC 58.858 45.455 0.00 0.00 35.51 4.01
292 317 4.137872 CATTGCCTTGCCGCCCTG 62.138 66.667 0.00 0.00 0.00 4.45
357 387 1.811679 CTTCTTCTTCCTCGCGGGC 60.812 63.158 6.13 0.00 34.39 6.13
358 388 1.811679 GCTTCTTCTTCCTCGCGGG 60.812 63.158 6.13 0.59 0.00 6.13
362 392 1.623359 CGTCAGCTTCTTCTTCCTCG 58.377 55.000 0.00 0.00 0.00 4.63
606 642 4.803426 CTGCTGGAGGCGTCGTCC 62.803 72.222 10.42 10.42 45.43 4.79
819 855 2.032528 TGCAGGGGCTTCTTCACG 59.967 61.111 0.00 0.00 41.91 4.35
912 964 4.047059 GACGAGGACGCCGTGGAA 62.047 66.667 0.00 0.00 43.96 3.53
1127 1183 1.878775 GGGAGCAACAGTGATGTGC 59.121 57.895 0.00 3.52 0.00 4.57
1176 1272 0.465705 TAGCAGAAGAATCGGGGCAG 59.534 55.000 0.00 0.00 0.00 4.85
1178 1274 1.609320 GGATAGCAGAAGAATCGGGGC 60.609 57.143 0.00 0.00 0.00 5.80
1207 1308 8.791675 GTTCTACTAACAGAGTAACAGTAGGTT 58.208 37.037 7.10 0.00 40.23 3.50
1209 1310 8.332996 TGTTCTACTAACAGAGTAACAGTAGG 57.667 38.462 7.10 0.00 40.23 3.18
1235 1336 0.753262 AGGAGACGCTGTGTTCTGTT 59.247 50.000 0.00 0.00 0.00 3.16
1237 1338 0.032678 ACAGGAGACGCTGTGTTCTG 59.967 55.000 10.98 10.98 31.95 3.02
1319 1421 6.262273 ACCCATAAACATTGGATTCGATGTAC 59.738 38.462 7.34 0.00 44.86 2.90
1320 1422 6.262049 CACCCATAAACATTGGATTCGATGTA 59.738 38.462 7.34 0.00 44.86 2.29
1321 1423 5.067674 CACCCATAAACATTGGATTCGATGT 59.932 40.000 0.37 0.37 46.92 3.06
1326 1428 4.432712 GTGCACCCATAAACATTGGATTC 58.567 43.478 5.22 0.00 36.26 2.52
1353 1455 3.629855 TCAGCTAAGCAGAGCAGTACTAG 59.370 47.826 11.90 0.00 45.43 2.57
1380 1482 9.448438 TCAGCTAAGCACATCTAGAAAAATAAA 57.552 29.630 0.00 0.00 0.00 1.40
1421 1523 1.346068 GCCTCACTTTCACCAGTCTCT 59.654 52.381 0.00 0.00 0.00 3.10
1516 1625 5.414454 GGGACACTTTGCACAGTGATTATTA 59.586 40.000 33.66 0.00 46.29 0.98
1517 1626 4.218417 GGGACACTTTGCACAGTGATTATT 59.782 41.667 33.66 15.17 46.29 1.40
1518 1627 3.758554 GGGACACTTTGCACAGTGATTAT 59.241 43.478 33.66 15.53 46.29 1.28
1559 1672 8.049721 GGGTTAATGCATAAGATAATCCTAGCT 58.950 37.037 9.91 0.00 0.00 3.32
1560 1673 7.829211 TGGGTTAATGCATAAGATAATCCTAGC 59.171 37.037 15.83 0.00 31.22 3.42
1561 1674 9.167311 GTGGGTTAATGCATAAGATAATCCTAG 57.833 37.037 15.83 0.00 31.22 3.02
1562 1675 8.890472 AGTGGGTTAATGCATAAGATAATCCTA 58.110 33.333 15.83 5.23 31.22 2.94
1655 1774 6.705825 ACTTGGAAGAAAAATAATGTTGTGCC 59.294 34.615 0.00 0.00 0.00 5.01
1666 1785 8.482128 TGGTCAAATTGTACTTGGAAGAAAAAT 58.518 29.630 0.00 0.00 0.00 1.82
1707 1830 3.350833 AGCCTTGCAATCTTCTAACTGG 58.649 45.455 0.00 0.00 0.00 4.00
1722 1845 8.025445 GTGGATTAATGCATAAGATAAGCCTTG 58.975 37.037 18.94 0.00 35.41 3.61
1723 1846 7.946776 AGTGGATTAATGCATAAGATAAGCCTT 59.053 33.333 18.94 8.78 35.41 4.35
1805 1928 6.503524 TGAAAATAAACTGTTGAGAACTGGC 58.496 36.000 0.00 0.00 34.98 4.85
1883 2011 5.757320 CAGCTCCACTAAACCAATCATCTAG 59.243 44.000 0.00 0.00 0.00 2.43
1924 2077 3.315191 CCGACACTGTCAAAAGAACCAAT 59.685 43.478 9.84 0.00 32.09 3.16
2275 2433 0.949105 CCCTGAACTTGAACCCGTCG 60.949 60.000 0.00 0.00 0.00 5.12
2557 2755 3.699134 GAGGATGGCGGTGGGGTTC 62.699 68.421 0.00 0.00 0.00 3.62
2609 2814 1.596477 GATGGCCGAGGTGATCTGC 60.596 63.158 0.00 0.00 37.42 4.26
2610 2815 1.070445 GGATGGCCGAGGTGATCTG 59.930 63.158 0.00 0.00 0.00 2.90
2611 2816 0.692419 AAGGATGGCCGAGGTGATCT 60.692 55.000 0.00 0.00 39.96 2.75
2612 2817 0.250081 GAAGGATGGCCGAGGTGATC 60.250 60.000 0.00 0.00 39.96 2.92
2624 2829 7.992033 AGGAATAAATCAGTCAGAAGAAGGATG 59.008 37.037 0.00 0.00 0.00 3.51
2635 2840 6.408548 CCAGGAAGCTAGGAATAAATCAGTCA 60.409 42.308 0.00 0.00 0.00 3.41
2636 2841 5.994668 CCAGGAAGCTAGGAATAAATCAGTC 59.005 44.000 0.00 0.00 0.00 3.51
2637 2842 5.163152 CCCAGGAAGCTAGGAATAAATCAGT 60.163 44.000 0.00 0.00 0.00 3.41
2638 2843 5.312079 CCCAGGAAGCTAGGAATAAATCAG 58.688 45.833 0.00 0.00 0.00 2.90
2644 2849 2.330216 GAGCCCAGGAAGCTAGGAATA 58.670 52.381 0.00 0.00 41.75 1.75
2670 2883 9.166173 TGACATGAAAGGAATTGATTAGTACAG 57.834 33.333 0.00 0.00 0.00 2.74
2672 2885 9.774742 GTTGACATGAAAGGAATTGATTAGTAC 57.225 33.333 0.00 0.00 0.00 2.73
2673 2886 9.739276 AGTTGACATGAAAGGAATTGATTAGTA 57.261 29.630 0.00 0.00 0.00 1.82
2704 2917 4.688169 CTGAAGCAGAGGACGAGTAGCG 62.688 59.091 0.00 0.00 38.87 4.26
2705 2918 0.811915 TGAAGCAGAGGACGAGTAGC 59.188 55.000 0.00 0.00 0.00 3.58
2708 2921 1.333177 AACTGAAGCAGAGGACGAGT 58.667 50.000 0.82 0.00 35.18 4.18
2709 2922 2.490115 ACTAACTGAAGCAGAGGACGAG 59.510 50.000 0.82 0.00 35.18 4.18
2711 2924 2.600731 CACTAACTGAAGCAGAGGACG 58.399 52.381 0.82 0.00 35.18 4.79
2712 2925 2.933056 GCCACTAACTGAAGCAGAGGAC 60.933 54.545 0.82 0.00 35.18 3.85
2713 2926 1.276421 GCCACTAACTGAAGCAGAGGA 59.724 52.381 0.82 0.00 35.18 3.71
2730 2943 0.533032 TGTTACATCATCGGTCGCCA 59.467 50.000 0.00 0.00 0.00 5.69
2736 2949 8.833231 ATTAAGGTTCTATGTTACATCATCGG 57.167 34.615 0.00 0.00 0.00 4.18
2755 2968 9.903682 CTGCCTGATCATACAAAATAATTAAGG 57.096 33.333 0.00 0.00 0.00 2.69
2764 2981 2.424601 GCTGCTGCCTGATCATACAAAA 59.575 45.455 3.85 0.00 0.00 2.44
2804 3021 4.151867 CGATCATTGCCACTGATCATACAG 59.848 45.833 20.72 4.72 46.08 2.74
2833 3050 8.216423 AGTAATCCATGCTCAAGTATCATCTTT 58.784 33.333 0.00 0.00 0.00 2.52
2834 3051 7.743749 AGTAATCCATGCTCAAGTATCATCTT 58.256 34.615 0.00 0.00 0.00 2.40
2840 3057 4.660303 TGGGAGTAATCCATGCTCAAGTAT 59.340 41.667 12.01 0.00 42.08 2.12
2853 3070 4.021544 TGTTGGCAAATGTTGGGAGTAATC 60.022 41.667 0.00 0.00 0.00 1.75
2900 3120 3.010584 ACCTGGGTATGCATGTCTCTTTT 59.989 43.478 10.16 0.00 0.00 2.27
2901 3121 2.578021 ACCTGGGTATGCATGTCTCTTT 59.422 45.455 10.16 0.00 0.00 2.52
2904 3124 1.539065 CGACCTGGGTATGCATGTCTC 60.539 57.143 10.16 2.92 0.00 3.36
2909 3129 2.290641 TGTTTTCGACCTGGGTATGCAT 60.291 45.455 3.79 3.79 0.00 3.96
2911 3131 1.737793 CTGTTTTCGACCTGGGTATGC 59.262 52.381 0.00 0.00 0.00 3.14
2912 3132 3.053831 ACTGTTTTCGACCTGGGTATG 57.946 47.619 0.00 0.00 0.00 2.39
2913 3133 3.782656 AACTGTTTTCGACCTGGGTAT 57.217 42.857 0.00 0.00 0.00 2.73
2915 3135 2.430248 AAACTGTTTTCGACCTGGGT 57.570 45.000 0.00 0.00 0.00 4.51
2916 3136 3.349488 GAAAACTGTTTTCGACCTGGG 57.651 47.619 25.02 0.00 39.56 4.45
2938 3211 0.317436 TGAATTGTTTGTCGGTGCGC 60.317 50.000 0.00 0.00 0.00 6.09
2942 3215 4.722194 CGATTCATGAATTGTTTGTCGGT 58.278 39.130 21.57 0.00 0.00 4.69
2948 3221 5.389859 TTCAGGCGATTCATGAATTGTTT 57.610 34.783 28.55 18.05 40.16 2.83
2953 3226 4.946157 AGAAGTTTCAGGCGATTCATGAAT 59.054 37.500 20.85 20.85 43.86 2.57
2963 3236 1.134965 AGATCCGAGAAGTTTCAGGCG 60.135 52.381 0.00 0.00 0.00 5.52
2966 3239 5.576384 CAGAAAGAGATCCGAGAAGTTTCAG 59.424 44.000 0.00 0.00 0.00 3.02
2994 3267 4.295051 CCCGGTTACAAACTTTGATGTTG 58.705 43.478 8.55 0.00 0.00 3.33
3000 3273 2.812011 CTCTCCCCGGTTACAAACTTTG 59.188 50.000 0.00 0.00 0.00 2.77
3002 3275 1.350019 CCTCTCCCCGGTTACAAACTT 59.650 52.381 0.00 0.00 0.00 2.66
3005 3278 1.128809 TGCCTCTCCCCGGTTACAAA 61.129 55.000 0.00 0.00 0.00 2.83
3009 3282 1.381327 CTCTGCCTCTCCCCGGTTA 60.381 63.158 0.00 0.00 0.00 2.85
3010 3283 2.685380 CTCTGCCTCTCCCCGGTT 60.685 66.667 0.00 0.00 0.00 4.44
3022 3295 3.329542 TTCATGTCCCGGCCTCTGC 62.330 63.158 0.00 0.00 0.00 4.26
3023 3296 1.153289 CTTCATGTCCCGGCCTCTG 60.153 63.158 0.00 0.00 0.00 3.35
3024 3297 0.909610 TTCTTCATGTCCCGGCCTCT 60.910 55.000 0.00 0.00 0.00 3.69
3025 3298 0.744771 GTTCTTCATGTCCCGGCCTC 60.745 60.000 0.00 0.00 0.00 4.70
3026 3299 1.201429 AGTTCTTCATGTCCCGGCCT 61.201 55.000 0.00 0.00 0.00 5.19
3027 3300 0.322546 AAGTTCTTCATGTCCCGGCC 60.323 55.000 0.00 0.00 0.00 6.13
3028 3301 1.200020 CAAAGTTCTTCATGTCCCGGC 59.800 52.381 0.00 0.00 0.00 6.13
3029 3302 2.226437 CACAAAGTTCTTCATGTCCCGG 59.774 50.000 0.00 0.00 0.00 5.73
3030 3303 3.138304 TCACAAAGTTCTTCATGTCCCG 58.862 45.455 0.00 0.00 0.00 5.14
3068 3341 2.282180 GTTCCAGGCGCTTGGGAA 60.282 61.111 34.94 26.30 38.81 3.97
3069 3342 3.249189 AGTTCCAGGCGCTTGGGA 61.249 61.111 34.94 27.25 38.81 4.37
3071 3344 3.121030 CGAGTTCCAGGCGCTTGG 61.121 66.667 31.27 31.27 39.70 3.61
3072 3345 3.793144 GCGAGTTCCAGGCGCTTG 61.793 66.667 13.36 13.36 46.53 4.01
3076 3349 3.958147 ATGTGGCGAGTTCCAGGCG 62.958 63.158 0.00 0.00 36.67 5.52
3117 3390 6.652900 GCTCTGAACTTGAGAAAGGAAGTAAT 59.347 38.462 0.00 0.00 32.03 1.89
3141 3414 4.584688 GCCAATTGCTTGTCAGGC 57.415 55.556 0.00 0.00 36.87 4.85
3150 3423 1.443194 CAGCACACGAGCCAATTGC 60.443 57.895 0.00 0.00 41.71 3.56
3151 3424 0.110056 GACAGCACACGAGCCAATTG 60.110 55.000 0.00 0.00 34.23 2.32
3154 3427 2.280797 GGACAGCACACGAGCCAA 60.281 61.111 0.00 0.00 34.23 4.52
3155 3428 4.314440 GGGACAGCACACGAGCCA 62.314 66.667 0.00 0.00 34.23 4.75
3173 3446 1.709147 GGTAGCTTGTCATGCCTGCG 61.709 60.000 7.07 0.00 0.00 5.18
3193 3466 7.532571 TGCTGTTTATCATGTCAGAAATCTTG 58.467 34.615 0.00 0.00 0.00 3.02
3223 3496 7.884877 TGTCTTTCTGAAGATAAATGACACCAT 59.115 33.333 0.00 0.00 43.41 3.55
3235 3508 4.082354 GCAAATGCCTGTCTTTCTGAAGAT 60.082 41.667 0.00 0.00 38.43 2.40
3257 3530 8.492748 CAAGATAAATTGCATCACATTATTGGC 58.507 33.333 0.00 0.00 0.00 4.52
3258 3531 8.984764 CCAAGATAAATTGCATCACATTATTGG 58.015 33.333 0.00 0.00 0.00 3.16
3262 3535 8.190122 GTGACCAAGATAAATTGCATCACATTA 58.810 33.333 13.06 0.00 40.69 1.90
3327 3600 1.006998 TGCATGGAACCCCTTAATGCT 59.993 47.619 12.10 0.00 39.08 3.79
3363 3643 4.129380 TGAAGAACATGGTGTTGTCAGAG 58.871 43.478 0.00 0.00 41.28 3.35
3415 3695 3.181440 TGATGATATGCAGGGGAGGAAAC 60.181 47.826 0.00 0.00 0.00 2.78
3439 3719 5.950544 ACTGATGCCTAACCTTGTGTATA 57.049 39.130 0.00 0.00 0.00 1.47
3454 3734 3.999663 AGAGACTAGCACAAAACTGATGC 59.000 43.478 0.00 0.00 39.74 3.91
3471 3751 4.462508 TGTCCATTGACATGAGAGAGAC 57.537 45.455 0.00 0.00 46.40 3.36
3482 3762 3.791973 TGGTTTGTGTTGTCCATTGAC 57.208 42.857 0.00 0.00 42.12 3.18
3483 3763 4.037803 CAGATGGTTTGTGTTGTCCATTGA 59.962 41.667 0.00 0.00 40.24 2.57
3484 3764 4.300803 CAGATGGTTTGTGTTGTCCATTG 58.699 43.478 0.00 0.00 40.24 2.82
3485 3765 3.243839 GCAGATGGTTTGTGTTGTCCATT 60.244 43.478 0.00 0.00 40.24 3.16
3486 3766 2.297033 GCAGATGGTTTGTGTTGTCCAT 59.703 45.455 0.00 0.00 42.44 3.41
3487 3767 1.680735 GCAGATGGTTTGTGTTGTCCA 59.319 47.619 0.00 0.00 0.00 4.02
3488 3768 1.680735 TGCAGATGGTTTGTGTTGTCC 59.319 47.619 0.00 0.00 0.00 4.02
3489 3769 3.648339 ATGCAGATGGTTTGTGTTGTC 57.352 42.857 0.00 0.00 0.00 3.18
3490 3770 4.405116 AAATGCAGATGGTTTGTGTTGT 57.595 36.364 0.00 0.00 0.00 3.32
3491 3771 5.984926 AGTAAAATGCAGATGGTTTGTGTTG 59.015 36.000 0.00 0.00 0.00 3.33
3492 3772 6.160576 AGTAAAATGCAGATGGTTTGTGTT 57.839 33.333 0.00 0.00 0.00 3.32
3493 3773 5.789643 AGTAAAATGCAGATGGTTTGTGT 57.210 34.783 0.00 0.00 0.00 3.72
3494 3774 7.592938 TCTAAGTAAAATGCAGATGGTTTGTG 58.407 34.615 0.00 0.00 0.00 3.33
3495 3775 7.759489 TCTAAGTAAAATGCAGATGGTTTGT 57.241 32.000 0.00 0.00 0.00 2.83
3496 3776 9.474920 TTTTCTAAGTAAAATGCAGATGGTTTG 57.525 29.630 0.00 0.00 0.00 2.93
3497 3777 9.476202 GTTTTCTAAGTAAAATGCAGATGGTTT 57.524 29.630 0.00 0.00 31.43 3.27
3498 3778 8.637986 TGTTTTCTAAGTAAAATGCAGATGGTT 58.362 29.630 0.00 0.00 31.43 3.67
3499 3779 8.177119 TGTTTTCTAAGTAAAATGCAGATGGT 57.823 30.769 0.00 0.00 31.43 3.55
3500 3780 9.294030 GATGTTTTCTAAGTAAAATGCAGATGG 57.706 33.333 0.00 0.00 31.43 3.51
3501 3781 9.003112 CGATGTTTTCTAAGTAAAATGCAGATG 57.997 33.333 0.00 0.00 31.43 2.90
3502 3782 8.946085 TCGATGTTTTCTAAGTAAAATGCAGAT 58.054 29.630 0.00 0.00 31.43 2.90
3503 3783 8.227791 GTCGATGTTTTCTAAGTAAAATGCAGA 58.772 33.333 0.00 0.00 31.43 4.26
3504 3784 8.015087 TGTCGATGTTTTCTAAGTAAAATGCAG 58.985 33.333 0.00 0.00 31.43 4.41
3505 3785 7.866729 TGTCGATGTTTTCTAAGTAAAATGCA 58.133 30.769 0.00 0.00 31.43 3.96
3506 3786 8.895932 ATGTCGATGTTTTCTAAGTAAAATGC 57.104 30.769 0.00 0.00 31.43 3.56
3509 3789 9.268268 AGTGATGTCGATGTTTTCTAAGTAAAA 57.732 29.630 0.00 0.00 0.00 1.52
3510 3790 8.827177 AGTGATGTCGATGTTTTCTAAGTAAA 57.173 30.769 0.00 0.00 0.00 2.01
3511 3791 9.917129 TTAGTGATGTCGATGTTTTCTAAGTAA 57.083 29.630 0.00 0.00 0.00 2.24
3513 3793 9.436957 AATTAGTGATGTCGATGTTTTCTAAGT 57.563 29.630 0.00 0.00 0.00 2.24
3520 3800 9.599866 TCTGATAAATTAGTGATGTCGATGTTT 57.400 29.630 0.00 0.00 0.00 2.83
3521 3801 9.035607 GTCTGATAAATTAGTGATGTCGATGTT 57.964 33.333 0.00 0.00 0.00 2.71
3522 3802 8.417106 AGTCTGATAAATTAGTGATGTCGATGT 58.583 33.333 0.00 0.00 0.00 3.06
3523 3803 8.809159 AGTCTGATAAATTAGTGATGTCGATG 57.191 34.615 0.00 0.00 0.00 3.84
3524 3804 7.805542 CGAGTCTGATAAATTAGTGATGTCGAT 59.194 37.037 0.00 0.00 0.00 3.59
3525 3805 7.132863 CGAGTCTGATAAATTAGTGATGTCGA 58.867 38.462 0.00 0.00 0.00 4.20
3526 3806 6.360947 CCGAGTCTGATAAATTAGTGATGTCG 59.639 42.308 0.00 0.00 0.00 4.35
3527 3807 7.426410 TCCGAGTCTGATAAATTAGTGATGTC 58.574 38.462 0.00 0.00 0.00 3.06
3528 3808 7.348080 TCCGAGTCTGATAAATTAGTGATGT 57.652 36.000 0.00 0.00 0.00 3.06
3529 3809 7.706607 TGTTCCGAGTCTGATAAATTAGTGATG 59.293 37.037 0.00 0.00 0.00 3.07
3530 3810 7.707035 GTGTTCCGAGTCTGATAAATTAGTGAT 59.293 37.037 0.00 0.00 0.00 3.06
3531 3811 7.033791 GTGTTCCGAGTCTGATAAATTAGTGA 58.966 38.462 0.00 0.00 0.00 3.41
3532 3812 6.255887 GGTGTTCCGAGTCTGATAAATTAGTG 59.744 42.308 0.00 0.00 0.00 2.74
3533 3813 6.154706 AGGTGTTCCGAGTCTGATAAATTAGT 59.845 38.462 0.00 0.00 39.05 2.24
3534 3814 6.477033 CAGGTGTTCCGAGTCTGATAAATTAG 59.523 42.308 0.00 0.00 39.05 1.73
3535 3815 6.070995 ACAGGTGTTCCGAGTCTGATAAATTA 60.071 38.462 0.00 0.00 39.05 1.40
3536 3816 5.178797 CAGGTGTTCCGAGTCTGATAAATT 58.821 41.667 0.00 0.00 39.05 1.82
3537 3817 4.223032 ACAGGTGTTCCGAGTCTGATAAAT 59.777 41.667 0.00 0.00 39.05 1.40
3538 3818 3.576982 ACAGGTGTTCCGAGTCTGATAAA 59.423 43.478 0.00 0.00 39.05 1.40
3539 3819 3.056821 CACAGGTGTTCCGAGTCTGATAA 60.057 47.826 0.00 0.00 39.05 1.75
3540 3820 2.492088 CACAGGTGTTCCGAGTCTGATA 59.508 50.000 0.00 0.00 39.05 2.15
3541 3821 1.273606 CACAGGTGTTCCGAGTCTGAT 59.726 52.381 0.00 0.00 39.05 2.90
3542 3822 0.673985 CACAGGTGTTCCGAGTCTGA 59.326 55.000 0.00 0.00 39.05 3.27
3543 3823 0.389391 ACACAGGTGTTCCGAGTCTG 59.611 55.000 0.00 0.00 41.83 3.51
3544 3824 2.822215 ACACAGGTGTTCCGAGTCT 58.178 52.632 0.00 0.00 41.83 3.24
3552 3832 9.107312 CTTTGAACAAAGCAAAACACAGGTGTT 62.107 37.037 11.80 11.80 46.01 3.32
3553 3833 7.721483 CTTTGAACAAAGCAAAACACAGGTGT 61.721 38.462 13.12 0.00 42.23 4.16
3554 3834 3.583806 TGAACAAAGCAAAACACAGGTG 58.416 40.909 0.00 0.00 0.00 4.00
3555 3835 3.951775 TGAACAAAGCAAAACACAGGT 57.048 38.095 0.00 0.00 0.00 4.00
3556 3836 5.207305 CTTTGAACAAAGCAAAACACAGG 57.793 39.130 13.12 0.00 40.94 4.00
3568 3848 4.859304 ATCATGCTCTGCTTTGAACAAA 57.141 36.364 0.17 0.17 0.00 2.83
3569 3849 7.812690 ATATATCATGCTCTGCTTTGAACAA 57.187 32.000 0.00 0.00 0.00 2.83
3577 3857 9.874195 TCCTAGTTATATATATCATGCTCTGCT 57.126 33.333 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.