Multiple sequence alignment - TraesCS3B01G450000

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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 TraesCS3B01G450000 chr3B 100.000 3614 0 0 1 3614 690459521 690463134 0.000000e+00 6674
1 TraesCS3B01G450000 chr3B 82.573 2651 391 48 136 2752 689352320 689349707 0.000000e+00 2270
2 TraesCS3B01G450000 chr3B 84.222 2269 328 26 363 2617 690446905 690449157 0.000000e+00 2180
3 TraesCS3B01G450000 chr3B 82.872 2382 357 41 225 2587 690430366 690432715 0.000000e+00 2091
4 TraesCS3B01G450000 chr3B 83.238 2273 346 28 359 2617 690442808 690445059 0.000000e+00 2054
5 TraesCS3B01G450000 chr3B 84.172 2028 287 26 621 2629 689007188 689005176 0.000000e+00 1936
6 TraesCS3B01G450000 chr3B 78.004 2264 434 49 363 2586 43527673 43525434 0.000000e+00 1363
7 TraesCS3B01G450000 chr3B 93.636 220 10 2 3066 3282 689349564 689349346 3.480000e-85 326
8 TraesCS3B01G450000 chr3B 87.793 213 17 6 2880 3084 689337316 689337105 1.300000e-59 241
9 TraesCS3B01G450000 chr3B 94.702 151 3 3 2874 3019 689349703 689349553 2.810000e-56 230
10 TraesCS3B01G450000 chr3B 95.968 124 5 0 2754 2877 162089409 162089532 6.120000e-48 202
11 TraesCS3B01G450000 chr3B 95.000 120 6 0 2758 2877 457968679 457968798 4.760000e-44 189
12 TraesCS3B01G450000 chr3A 83.887 2557 345 42 66 2593 658288765 658291283 0.000000e+00 2377
13 TraesCS3B01G450000 chr3A 83.850 2260 340 21 336 2583 658303535 658305781 0.000000e+00 2128
14 TraesCS3B01G450000 chr3A 94.313 211 9 1 3037 3244 658314905 658315115 1.620000e-83 320
15 TraesCS3B01G450000 chr3A 96.491 114 4 0 2932 3045 658314640 658314753 4.760000e-44 189
16 TraesCS3B01G450000 chr3A 86.806 144 8 6 3460 3592 658315175 658315318 2.250000e-32 150
17 TraesCS3B01G450000 chr3D 80.578 2595 430 48 74 2648 523555060 523557600 0.000000e+00 1932
18 TraesCS3B01G450000 chr3D 83.117 2162 298 40 66 2202 523379165 523381284 0.000000e+00 1908
19 TraesCS3B01G450000 chr3D 81.846 2319 367 40 451 2752 523569669 523571950 0.000000e+00 1901
20 TraesCS3B01G450000 chr3D 79.842 2272 429 19 363 2617 523334576 523336835 0.000000e+00 1631
21 TraesCS3B01G450000 chr3D 77.756 2513 485 53 220 2699 523407732 523410203 0.000000e+00 1476
22 TraesCS3B01G450000 chr3D 79.685 1777 321 33 152 1912 523559963 523561715 0.000000e+00 1245
23 TraesCS3B01G450000 chr3D 92.401 579 24 8 2876 3449 523571956 523572519 0.000000e+00 808
24 TraesCS3B01G450000 chrUn 80.022 1807 328 22 833 2617 342677752 342679547 0.000000e+00 1306
25 TraesCS3B01G450000 chrUn 83.718 780 120 5 1842 2617 405666953 405667729 0.000000e+00 730
26 TraesCS3B01G450000 chr1D 93.893 131 7 1 2751 2881 367774471 367774600 2.850000e-46 196
27 TraesCS3B01G450000 chr7B 95.833 120 5 0 2760 2879 517095072 517095191 1.020000e-45 195
28 TraesCS3B01G450000 chr6B 95.798 119 5 0 2761 2879 470914946 470914828 3.680000e-45 193
29 TraesCS3B01G450000 chr6B 94.309 123 6 1 2758 2880 457400608 457400729 1.710000e-43 187
30 TraesCS3B01G450000 chr6B 92.188 128 10 0 2761 2888 46512109 46511982 7.970000e-42 182
31 TraesCS3B01G450000 chr1B 96.581 117 3 1 2761 2877 583149522 583149637 3.680000e-45 193
32 TraesCS3B01G450000 chr1B 95.041 121 6 0 2761 2881 156585598 156585478 1.320000e-44 191


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 TraesCS3B01G450000 chr3B 690459521 690463134 3613 False 6674.000000 6674 100.000000 1 3614 1 chr3B.!!$F4 3613
1 TraesCS3B01G450000 chr3B 690442808 690449157 6349 False 2117.000000 2180 83.730000 359 2617 2 chr3B.!!$F5 2258
2 TraesCS3B01G450000 chr3B 690430366 690432715 2349 False 2091.000000 2091 82.872000 225 2587 1 chr3B.!!$F3 2362
3 TraesCS3B01G450000 chr3B 689005176 689007188 2012 True 1936.000000 1936 84.172000 621 2629 1 chr3B.!!$R2 2008
4 TraesCS3B01G450000 chr3B 43525434 43527673 2239 True 1363.000000 1363 78.004000 363 2586 1 chr3B.!!$R1 2223
5 TraesCS3B01G450000 chr3B 689349346 689352320 2974 True 942.000000 2270 90.303667 136 3282 3 chr3B.!!$R4 3146
6 TraesCS3B01G450000 chr3A 658288765 658291283 2518 False 2377.000000 2377 83.887000 66 2593 1 chr3A.!!$F1 2527
7 TraesCS3B01G450000 chr3A 658303535 658305781 2246 False 2128.000000 2128 83.850000 336 2583 1 chr3A.!!$F2 2247
8 TraesCS3B01G450000 chr3A 658314640 658315318 678 False 219.666667 320 92.536667 2932 3592 3 chr3A.!!$F3 660
9 TraesCS3B01G450000 chr3D 523379165 523381284 2119 False 1908.000000 1908 83.117000 66 2202 1 chr3D.!!$F2 2136
10 TraesCS3B01G450000 chr3D 523334576 523336835 2259 False 1631.000000 1631 79.842000 363 2617 1 chr3D.!!$F1 2254
11 TraesCS3B01G450000 chr3D 523555060 523561715 6655 False 1588.500000 1932 80.131500 74 2648 2 chr3D.!!$F4 2574
12 TraesCS3B01G450000 chr3D 523407732 523410203 2471 False 1476.000000 1476 77.756000 220 2699 1 chr3D.!!$F3 2479
13 TraesCS3B01G450000 chr3D 523569669 523572519 2850 False 1354.500000 1901 87.123500 451 3449 2 chr3D.!!$F5 2998
14 TraesCS3B01G450000 chrUn 342677752 342679547 1795 False 1306.000000 1306 80.022000 833 2617 1 chrUn.!!$F1 1784
15 TraesCS3B01G450000 chrUn 405666953 405667729 776 False 730.000000 730 83.718000 1842 2617 1 chrUn.!!$F2 775

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
656 4808 0.038159 ACTCGACTTCTCCGCCTTTG 60.038 55.0 0.00 0.0 0.0 2.77 F
1170 5329 0.255890 TTGGGAATAGCAGCCTCCAC 59.744 55.0 7.83 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 6659 1.078143 GCCCCAGTACAGCCAGAAG 60.078 63.158 0.00 0.0 0.00 2.85 R
2757 6960 0.324091 ACCGAACGGAGGGAGTACAT 60.324 55.000 20.14 0.0 38.96 2.29 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
20 21 3.737559 ATTGGCAGGGTATTGTCTTCA 57.262 42.857 0.00 0.00 0.00 3.02
21 22 2.787473 TGGCAGGGTATTGTCTTCAG 57.213 50.000 0.00 0.00 0.00 3.02
22 23 1.340017 TGGCAGGGTATTGTCTTCAGC 60.340 52.381 0.00 0.00 0.00 4.26
23 24 1.340017 GGCAGGGTATTGTCTTCAGCA 60.340 52.381 0.00 0.00 0.00 4.41
24 25 2.648059 GCAGGGTATTGTCTTCAGCAT 58.352 47.619 0.00 0.00 0.00 3.79
25 26 3.433598 GGCAGGGTATTGTCTTCAGCATA 60.434 47.826 0.00 0.00 0.00 3.14
26 27 3.561725 GCAGGGTATTGTCTTCAGCATAC 59.438 47.826 0.00 0.00 0.00 2.39
27 28 4.684485 GCAGGGTATTGTCTTCAGCATACT 60.684 45.833 0.00 0.00 0.00 2.12
28 29 4.813161 CAGGGTATTGTCTTCAGCATACTG 59.187 45.833 0.00 0.00 45.95 2.74
44 45 7.875316 AGCATACTGATATCAACAACGTATC 57.125 36.000 6.90 5.53 0.00 2.24
45 46 6.582672 AGCATACTGATATCAACAACGTATCG 59.417 38.462 6.90 6.89 0.00 2.92
46 47 6.183359 GCATACTGATATCAACAACGTATCGG 60.183 42.308 6.90 0.00 37.28 4.18
47 48 4.617959 ACTGATATCAACAACGTATCGGG 58.382 43.478 6.90 0.00 36.16 5.14
48 49 4.098960 ACTGATATCAACAACGTATCGGGT 59.901 41.667 6.90 0.00 36.16 5.28
49 50 4.364860 TGATATCAACAACGTATCGGGTG 58.635 43.478 1.98 0.00 0.00 4.61
50 51 4.098196 TGATATCAACAACGTATCGGGTGA 59.902 41.667 1.98 0.00 0.00 4.02
51 52 3.536956 ATCAACAACGTATCGGGTGAT 57.463 42.857 4.68 4.68 38.67 3.06
52 53 4.659111 ATCAACAACGTATCGGGTGATA 57.341 40.909 7.84 0.00 35.99 2.15
59 60 1.321474 GTATCGGGTGATACGGTCCA 58.679 55.000 0.16 0.00 45.41 4.02
60 61 1.682854 GTATCGGGTGATACGGTCCAA 59.317 52.381 0.16 0.00 45.41 3.53
61 62 1.420430 ATCGGGTGATACGGTCCAAT 58.580 50.000 0.00 0.00 31.44 3.16
62 63 2.070305 TCGGGTGATACGGTCCAATA 57.930 50.000 0.00 0.00 0.00 1.90
63 64 2.600790 TCGGGTGATACGGTCCAATAT 58.399 47.619 0.00 0.00 0.00 1.28
64 65 2.559668 TCGGGTGATACGGTCCAATATC 59.440 50.000 3.95 3.95 0.00 1.63
69 70 4.281182 GGTGATACGGTCCAATATCAGAGT 59.719 45.833 11.49 0.00 38.24 3.24
78 79 6.073548 CGGTCCAATATCAGAGTTGATTAAGC 60.074 42.308 0.00 0.00 41.24 3.09
95 96 3.072486 GCATCTGTGTGCCATGGCC 62.072 63.158 33.44 23.83 39.18 5.36
117 118 4.408921 CCTCCAAGTGTCACCCTGATAATA 59.591 45.833 0.00 0.00 0.00 0.98
122 123 7.126573 TCCAAGTGTCACCCTGATAATAACATA 59.873 37.037 0.00 0.00 0.00 2.29
215 235 7.064728 GTGTAGCTTCTCCTTAATGTAAACTGG 59.935 40.741 0.00 0.00 0.00 4.00
232 252 5.847111 AACTGGCATTACGTCATCTACTA 57.153 39.130 0.00 0.00 0.00 1.82
258 287 2.363680 TGTGCCATTTGTAAACCACCAG 59.636 45.455 0.00 0.00 0.00 4.00
259 288 1.967066 TGCCATTTGTAAACCACCAGG 59.033 47.619 0.00 0.00 42.21 4.45
354 392 1.376812 GAACCACCACCCATCCGAC 60.377 63.158 0.00 0.00 0.00 4.79
361 399 1.680522 CCACCCATCCGACCTCTGAG 61.681 65.000 0.00 0.00 0.00 3.35
378 416 0.394762 GAGGCCACCATGAAGCATCA 60.395 55.000 5.01 0.00 37.28 3.07
403 450 0.463620 CTGTAGGCCTCTTGCTCTCC 59.536 60.000 9.68 0.00 40.92 3.71
428 475 2.959030 TCTTGTCTCCTACTATGCGCAT 59.041 45.455 28.23 28.23 0.00 4.73
473 526 0.110464 GCGTGAAGCTGAAGCACTTC 60.110 55.000 4.90 3.37 45.16 3.01
543 4695 1.826054 CGTTGGCCAACTCCACCAA 60.826 57.895 38.38 5.39 41.08 3.67
620 4772 2.203280 TTGTCGGCACAACCCTGG 60.203 61.111 0.00 0.00 37.61 4.45
622 4774 2.358737 GTCGGCACAACCCTGGAG 60.359 66.667 0.00 0.00 33.26 3.86
656 4808 0.038159 ACTCGACTTCTCCGCCTTTG 60.038 55.000 0.00 0.00 0.00 2.77
684 4836 1.821088 AGGGAACTCAACCTGAACCT 58.179 50.000 0.00 0.00 32.90 3.50
711 4863 3.056322 GGTCTGTACGGTACAATTCCAGT 60.056 47.826 20.43 0.00 38.38 4.00
756 4908 1.131883 GACCATGTTGCAGATCAGCAC 59.868 52.381 12.90 8.72 45.61 4.40
764 4916 1.310933 GCAGATCAGCACCAACCAGG 61.311 60.000 5.05 0.00 45.67 4.45
776 4928 1.229951 AACCAGGATCTGAGGGGCA 60.230 57.895 0.00 0.00 32.44 5.36
797 4949 1.978080 ATTCCACGCAGCATTGGCA 60.978 52.632 5.27 0.00 44.61 4.92
814 4966 1.238439 GCAAGCTGAAGCACCTTGTA 58.762 50.000 4.90 0.00 45.16 2.41
816 4968 2.159462 GCAAGCTGAAGCACCTTGTATC 60.159 50.000 4.90 0.00 45.16 2.24
823 4975 4.566004 TGAAGCACCTTGTATCACTGTAC 58.434 43.478 0.00 0.00 0.00 2.90
889 5041 2.218953 ACTTGACGAGCTTGAACGAA 57.781 45.000 8.31 0.00 0.00 3.85
925 5077 3.126831 GGCTACTTTGACTGGATCGATG 58.873 50.000 0.54 0.00 0.00 3.84
929 5081 2.290260 ACTTTGACTGGATCGATGCCAA 60.290 45.455 14.82 8.57 34.44 4.52
930 5082 2.488204 TTGACTGGATCGATGCCAAA 57.512 45.000 14.82 5.21 34.44 3.28
961 5113 2.348998 CTCGGGAAGCTTGGCAGT 59.651 61.111 2.10 0.00 0.00 4.40
967 5119 0.957888 GGAAGCTTGGCAGTCTGGAC 60.958 60.000 2.10 0.00 0.00 4.02
968 5120 0.957888 GAAGCTTGGCAGTCTGGACC 60.958 60.000 2.10 0.00 0.00 4.46
969 5121 1.422161 AAGCTTGGCAGTCTGGACCT 61.422 55.000 0.00 0.00 0.00 3.85
982 5140 2.365617 TCTGGACCTCAGAGACAACAAC 59.634 50.000 0.00 0.00 46.71 3.32
1029 5188 4.371624 TGGAAACATGACAGAACTGGAT 57.628 40.909 0.00 0.00 33.40 3.41
1032 5191 3.430042 AACATGACAGAACTGGATGCT 57.570 42.857 0.00 0.00 31.56 3.79
1060 5219 7.847711 TTCCTTCAGAATAACCATTTGGAAA 57.152 32.000 3.01 0.00 38.94 3.13
1169 5328 0.998928 TTTGGGAATAGCAGCCTCCA 59.001 50.000 7.83 0.00 0.00 3.86
1170 5329 0.255890 TTGGGAATAGCAGCCTCCAC 59.744 55.000 7.83 0.00 0.00 4.02
1203 5377 2.159254 TGCAAACAACAACTTCTCTGGC 60.159 45.455 0.00 0.00 0.00 4.85
1386 5566 0.826715 GTGAGCATCCAGGACAGCTA 59.173 55.000 16.41 5.01 37.48 3.32
1402 5582 2.289002 CAGCTAATCACGATGGCTTTCC 59.711 50.000 0.00 0.00 31.58 3.13
1471 5651 2.783135 TCCTTTGCAACTCCACTGATC 58.217 47.619 0.00 0.00 0.00 2.92
1475 5655 4.564406 CCTTTGCAACTCCACTGATCTAGT 60.564 45.833 0.00 0.00 41.36 2.57
1497 5677 6.786122 AGTCCTCCTAGACCTATCAGATAAC 58.214 44.000 0.00 0.00 37.49 1.89
1585 5765 4.067896 CAGCAACTCTTTCAGTGGTGTAT 58.932 43.478 0.00 0.00 34.56 2.29
1644 5824 9.381038 AGATATCTACTCCTAGGCAATAACAAA 57.619 33.333 2.53 0.00 0.00 2.83
1716 5896 6.814954 ACTCTAGATCTTGGAGGCAATAAA 57.185 37.500 21.48 0.00 0.00 1.40
1942 6126 3.375299 GCAAAACACTGACTTCACAGACT 59.625 43.478 0.00 0.00 40.63 3.24
2274 6461 5.140747 ACTTCTCGAGCAATAGTTTGTCT 57.859 39.130 7.81 0.00 35.17 3.41
2469 6659 1.372087 CTGCTGGGTTCATCTTCGGC 61.372 60.000 0.00 0.00 0.00 5.54
2593 6786 2.889503 GCTGCATCTCGCGCTTCT 60.890 61.111 5.56 0.00 46.97 2.85
2714 6917 5.774690 TCCTTGGTTTGTAGAAGAATTGCAT 59.225 36.000 0.00 0.00 0.00 3.96
2732 6935 3.300009 GCATTGAGCAAGTTGTGTGTAC 58.700 45.455 4.48 0.00 44.79 2.90
2736 6939 2.169561 TGAGCAAGTTGTGTGTACCTGA 59.830 45.455 4.48 0.00 0.00 3.86
2750 6953 1.901591 ACCTGATGGTGCTTTGACTG 58.098 50.000 0.00 0.00 46.51 3.51
2751 6954 1.143684 ACCTGATGGTGCTTTGACTGT 59.856 47.619 0.00 0.00 46.51 3.55
2753 6956 2.624838 CCTGATGGTGCTTTGACTGTTT 59.375 45.455 0.00 0.00 0.00 2.83
2754 6957 3.551454 CCTGATGGTGCTTTGACTGTTTG 60.551 47.826 0.00 0.00 0.00 2.93
2757 6960 2.441410 TGGTGCTTTGACTGTTTGACA 58.559 42.857 0.00 0.00 0.00 3.58
2759 6962 3.181488 TGGTGCTTTGACTGTTTGACATG 60.181 43.478 0.00 0.00 0.00 3.21
2760 6963 3.181487 GGTGCTTTGACTGTTTGACATGT 60.181 43.478 0.00 0.00 0.00 3.21
2762 6965 4.970003 GTGCTTTGACTGTTTGACATGTAC 59.030 41.667 0.00 0.00 0.00 2.90
2763 6966 4.881273 TGCTTTGACTGTTTGACATGTACT 59.119 37.500 0.00 0.00 0.00 2.73
2764 6967 5.007626 TGCTTTGACTGTTTGACATGTACTC 59.992 40.000 0.00 0.00 0.00 2.59
2765 6968 5.560953 GCTTTGACTGTTTGACATGTACTCC 60.561 44.000 0.00 0.00 0.00 3.85
2766 6969 4.002906 TGACTGTTTGACATGTACTCCC 57.997 45.455 0.00 0.00 0.00 4.30
2767 6970 3.646162 TGACTGTTTGACATGTACTCCCT 59.354 43.478 0.00 0.00 0.00 4.20
2768 6971 4.246458 GACTGTTTGACATGTACTCCCTC 58.754 47.826 0.00 0.00 0.00 4.30
2769 6972 3.008049 ACTGTTTGACATGTACTCCCTCC 59.992 47.826 0.00 0.00 0.00 4.30
2770 6973 2.028476 TGTTTGACATGTACTCCCTCCG 60.028 50.000 0.00 0.00 0.00 4.63
2771 6974 1.933021 TTGACATGTACTCCCTCCGT 58.067 50.000 0.00 0.00 0.00 4.69
2772 6975 1.933021 TGACATGTACTCCCTCCGTT 58.067 50.000 0.00 0.00 0.00 4.44
2773 6976 1.822990 TGACATGTACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
2774 6977 0.815734 ACATGTACTCCCTCCGTTCG 59.184 55.000 0.00 0.00 0.00 3.95
2775 6978 0.102481 CATGTACTCCCTCCGTTCGG 59.898 60.000 4.74 4.74 0.00 4.30
2776 6979 0.324091 ATGTACTCCCTCCGTTCGGT 60.324 55.000 11.04 0.00 0.00 4.69
2777 6980 0.327924 TGTACTCCCTCCGTTCGGTA 59.672 55.000 11.04 0.00 0.00 4.02
2778 6981 1.064463 TGTACTCCCTCCGTTCGGTAT 60.064 52.381 11.04 0.00 0.00 2.73
2779 6982 2.027385 GTACTCCCTCCGTTCGGTATT 58.973 52.381 11.04 0.00 0.00 1.89
2780 6983 2.442236 ACTCCCTCCGTTCGGTATTA 57.558 50.000 11.04 0.00 0.00 0.98
2781 6984 2.027385 ACTCCCTCCGTTCGGTATTAC 58.973 52.381 11.04 0.00 0.00 1.89
2782 6985 2.305009 CTCCCTCCGTTCGGTATTACT 58.695 52.381 11.04 0.00 0.00 2.24
2783 6986 2.692041 CTCCCTCCGTTCGGTATTACTT 59.308 50.000 11.04 0.00 0.00 2.24
2784 6987 2.428171 TCCCTCCGTTCGGTATTACTTG 59.572 50.000 11.04 0.00 0.00 3.16
2785 6988 2.167075 CCCTCCGTTCGGTATTACTTGT 59.833 50.000 11.04 0.00 0.00 3.16
2786 6989 3.442100 CCTCCGTTCGGTATTACTTGTC 58.558 50.000 11.04 0.00 0.00 3.18
2787 6990 3.119388 CCTCCGTTCGGTATTACTTGTCA 60.119 47.826 11.04 0.00 0.00 3.58
2788 6991 3.836949 TCCGTTCGGTATTACTTGTCAC 58.163 45.455 11.04 0.00 0.00 3.67
2789 6992 3.255395 TCCGTTCGGTATTACTTGTCACA 59.745 43.478 11.04 0.00 0.00 3.58
2790 6993 3.989167 CCGTTCGGTATTACTTGTCACAA 59.011 43.478 2.82 0.00 0.00 3.33
2791 6994 4.448395 CCGTTCGGTATTACTTGTCACAAA 59.552 41.667 2.82 0.00 0.00 2.83
2792 6995 5.050227 CCGTTCGGTATTACTTGTCACAAAA 60.050 40.000 2.82 0.00 0.00 2.44
2793 6996 6.420588 CGTTCGGTATTACTTGTCACAAAAA 58.579 36.000 0.00 0.00 0.00 1.94
2794 6997 7.073265 CGTTCGGTATTACTTGTCACAAAAAT 58.927 34.615 0.00 0.00 0.00 1.82
2795 6998 7.059033 CGTTCGGTATTACTTGTCACAAAAATG 59.941 37.037 7.68 0.00 0.00 2.32
2796 6999 6.904498 TCGGTATTACTTGTCACAAAAATGG 58.096 36.000 7.68 0.00 0.00 3.16
2797 7000 6.711194 TCGGTATTACTTGTCACAAAAATGGA 59.289 34.615 7.68 1.93 0.00 3.41
2798 7001 7.392113 TCGGTATTACTTGTCACAAAAATGGAT 59.608 33.333 7.68 0.00 0.00 3.41
2799 7002 8.670135 CGGTATTACTTGTCACAAAAATGGATA 58.330 33.333 7.68 0.00 0.00 2.59
2853 7056 8.824159 ATCTAGATACATTCATTTCTTGGACG 57.176 34.615 2.53 0.00 0.00 4.79
2854 7057 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
2855 7058 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
2856 7059 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
2857 7060 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
2858 7061 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2859 7062 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2860 7063 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2861 7064 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2862 7065 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2863 7066 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
2864 7067 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2865 7068 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
2866 7069 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2867 7070 3.256383 TCTTGGACGAGTAATTCCGAACA 59.744 43.478 0.00 0.00 0.00 3.18
2868 7071 3.226346 TGGACGAGTAATTCCGAACAG 57.774 47.619 0.00 0.00 0.00 3.16
2869 7072 2.821378 TGGACGAGTAATTCCGAACAGA 59.179 45.455 0.00 0.00 0.00 3.41
2870 7073 3.119602 TGGACGAGTAATTCCGAACAGAG 60.120 47.826 0.00 0.00 0.00 3.35
2871 7074 3.436496 GACGAGTAATTCCGAACAGAGG 58.564 50.000 0.00 0.00 0.00 3.69
2872 7075 2.165845 ACGAGTAATTCCGAACAGAGGG 59.834 50.000 0.00 0.00 0.00 4.30
2873 7076 2.426024 CGAGTAATTCCGAACAGAGGGA 59.574 50.000 0.00 0.00 0.00 4.20
2874 7077 3.489398 CGAGTAATTCCGAACAGAGGGAG 60.489 52.174 0.00 0.00 33.01 4.30
3030 7638 6.038825 TCGTTTTGTCACATCAAGTACCAATT 59.961 34.615 0.00 0.00 0.00 2.32
3065 7834 8.044060 TGTTATCACCAGCTTGAAAATCTTAG 57.956 34.615 0.00 0.00 0.00 2.18
3130 8556 7.994425 TCTTTATTTGCACATTTCTGGACTA 57.006 32.000 0.00 0.00 0.00 2.59
3186 8612 0.249398 ATTTCGTTGGACGGGAGGAG 59.751 55.000 0.27 0.00 42.81 3.69
3246 8977 0.732571 ATGCAATTGGTACGAAGGCG 59.267 50.000 7.72 0.00 44.79 5.52
3248 8979 5.507364 AATGCAATTGGTACGAAGGCGTG 62.507 47.826 7.72 2.26 43.36 5.34
3277 9008 4.451096 ACAATTAATTGACAGCGAACGACT 59.549 37.500 30.18 4.50 40.14 4.18
3314 10530 0.445436 GTGTGATCAAGCGGCAAGAG 59.555 55.000 1.45 0.00 0.00 2.85
3315 10531 0.674581 TGTGATCAAGCGGCAAGAGG 60.675 55.000 1.45 0.00 0.00 3.69
3319 10535 3.494336 CAAGCGGCAAGAGGAGCG 61.494 66.667 1.45 0.00 34.34 5.03
3364 10580 6.651755 GCCATATGGTGAAACAGAAAAATG 57.348 37.500 22.79 0.00 39.98 2.32
3365 10581 5.581874 GCCATATGGTGAAACAGAAAAATGG 59.418 40.000 22.79 0.00 39.98 3.16
3371 10587 2.061028 GAAACAGAAAAATGGGCAGCG 58.939 47.619 0.00 0.00 0.00 5.18
3391 10607 0.467384 CCTGATGGCCGAACTGATCT 59.533 55.000 0.00 0.00 0.00 2.75
3393 10609 0.178767 TGATGGCCGAACTGATCTGG 59.821 55.000 0.00 0.00 0.00 3.86
3431 11111 0.178964 TGCCTTGGTTTCCTGGGAAG 60.179 55.000 2.19 0.00 35.38 3.46
3434 11114 0.900182 CTTGGTTTCCTGGGAAGGCC 60.900 60.000 0.00 0.00 35.38 5.19
3449 11129 1.007038 GGCCGGACGCGTATGATAA 60.007 57.895 13.97 0.00 38.94 1.75
3450 11130 0.598158 GGCCGGACGCGTATGATAAA 60.598 55.000 13.97 0.00 38.94 1.40
3451 11131 1.425412 GCCGGACGCGTATGATAAAT 58.575 50.000 13.97 0.00 0.00 1.40
3453 11133 2.343544 GCCGGACGCGTATGATAAATAC 59.656 50.000 13.97 0.00 0.00 1.89
3456 11136 3.296426 CGGACGCGTATGATAAATACGTC 59.704 47.826 13.97 8.59 46.30 4.34
3458 11138 5.794650 GACGCGTATGATAAATACGTCAA 57.205 39.130 13.97 0.00 46.30 3.18
3462 11142 6.418523 ACGCGTATGATAAATACGTCAATTCA 59.581 34.615 11.67 0.00 46.30 2.57
3511 11191 2.102420 TGCAGGCGCTGTACAATAGTAT 59.898 45.455 7.64 0.00 39.64 2.12
3514 11194 4.552767 GCAGGCGCTGTACAATAGTATTTG 60.553 45.833 7.64 0.00 33.43 2.32
3515 11195 4.024893 CAGGCGCTGTACAATAGTATTTGG 60.025 45.833 7.64 0.00 31.84 3.28
3555 11245 5.362556 AGAATGCATTTACGGATATGTGC 57.637 39.130 14.33 0.00 0.00 4.57
3565 11255 2.426738 ACGGATATGTGCCCACAAATTG 59.573 45.455 5.08 0.00 45.41 2.32
3566 11256 2.687425 CGGATATGTGCCCACAAATTGA 59.313 45.455 5.08 0.00 45.41 2.57
3592 11283 7.784470 ACCCTTAATTGCCAGTGTTAATTTA 57.216 32.000 7.02 0.00 0.00 1.40
3593 11284 7.836842 ACCCTTAATTGCCAGTGTTAATTTAG 58.163 34.615 7.02 7.40 0.00 1.85
3594 11285 6.756542 CCCTTAATTGCCAGTGTTAATTTAGC 59.243 38.462 7.02 0.00 0.00 3.09
3595 11286 7.319646 CCTTAATTGCCAGTGTTAATTTAGCA 58.680 34.615 7.02 0.00 0.00 3.49
3596 11287 7.981225 CCTTAATTGCCAGTGTTAATTTAGCAT 59.019 33.333 7.02 0.00 0.00 3.79
3597 11288 9.369904 CTTAATTGCCAGTGTTAATTTAGCATT 57.630 29.630 7.02 0.00 0.00 3.56
3598 11289 7.599630 AATTGCCAGTGTTAATTTAGCATTG 57.400 32.000 8.26 8.26 0.00 2.82
3599 11290 5.973899 TGCCAGTGTTAATTTAGCATTGA 57.026 34.783 14.51 0.00 30.19 2.57
3600 11291 6.528537 TGCCAGTGTTAATTTAGCATTGAT 57.471 33.333 14.51 0.00 30.19 2.57
3601 11292 7.637631 TGCCAGTGTTAATTTAGCATTGATA 57.362 32.000 14.51 3.76 30.19 2.15
3602 11293 8.236585 TGCCAGTGTTAATTTAGCATTGATAT 57.763 30.769 14.51 0.00 30.19 1.63
3603 11294 8.136800 TGCCAGTGTTAATTTAGCATTGATATG 58.863 33.333 14.51 2.85 30.19 1.78
3604 11295 7.596248 GCCAGTGTTAATTTAGCATTGATATGG 59.404 37.037 14.51 8.98 30.19 2.74
3605 11296 8.632679 CCAGTGTTAATTTAGCATTGATATGGT 58.367 33.333 14.51 0.00 44.29 3.55
3608 11299 9.463443 GTGTTAATTTAGCATTGATATGGTTCC 57.537 33.333 0.00 0.00 42.25 3.62
3609 11300 9.420118 TGTTAATTTAGCATTGATATGGTTCCT 57.580 29.630 0.00 0.00 42.25 3.36
3610 11301 9.683069 GTTAATTTAGCATTGATATGGTTCCTG 57.317 33.333 0.00 0.00 42.25 3.86
3611 11302 9.639563 TTAATTTAGCATTGATATGGTTCCTGA 57.360 29.630 0.00 0.00 42.25 3.86
3612 11303 8.716674 AATTTAGCATTGATATGGTTCCTGAT 57.283 30.769 0.00 0.00 42.25 2.90
3613 11304 8.716674 ATTTAGCATTGATATGGTTCCTGATT 57.283 30.769 0.00 0.00 42.25 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.624777 CTGAAGACAATACCCTGCCAAT 58.375 45.455 0.00 0.00 0.00 3.16
2 3 1.340017 GCTGAAGACAATACCCTGCCA 60.340 52.381 0.00 0.00 0.00 4.92
3 4 1.340017 TGCTGAAGACAATACCCTGCC 60.340 52.381 0.00 0.00 0.00 4.85
19 20 5.973651 ACGTTGTTGATATCAGTATGCTG 57.026 39.130 5.39 4.14 43.87 4.41
20 21 6.582672 CGATACGTTGTTGATATCAGTATGCT 59.417 38.462 15.52 0.00 34.76 3.79
21 22 6.183359 CCGATACGTTGTTGATATCAGTATGC 60.183 42.308 15.52 8.91 34.76 3.14
22 23 6.308041 CCCGATACGTTGTTGATATCAGTATG 59.692 42.308 15.52 9.25 37.54 2.39
23 24 6.015688 ACCCGATACGTTGTTGATATCAGTAT 60.016 38.462 12.11 12.11 0.00 2.12
24 25 5.300034 ACCCGATACGTTGTTGATATCAGTA 59.700 40.000 5.39 5.00 0.00 2.74
25 26 4.098960 ACCCGATACGTTGTTGATATCAGT 59.901 41.667 5.39 2.80 0.00 3.41
26 27 4.444388 CACCCGATACGTTGTTGATATCAG 59.556 45.833 5.39 0.00 0.00 2.90
27 28 4.098196 TCACCCGATACGTTGTTGATATCA 59.902 41.667 0.00 0.00 0.00 2.15
28 29 4.613944 TCACCCGATACGTTGTTGATATC 58.386 43.478 0.00 0.00 0.00 1.63
29 30 4.659111 TCACCCGATACGTTGTTGATAT 57.341 40.909 0.00 0.00 0.00 1.63
30 31 4.659111 ATCACCCGATACGTTGTTGATA 57.341 40.909 0.00 0.00 0.00 2.15
31 32 3.536956 ATCACCCGATACGTTGTTGAT 57.463 42.857 0.00 0.00 0.00 2.57
32 33 3.772932 GTATCACCCGATACGTTGTTGA 58.227 45.455 0.00 0.00 43.41 3.18
41 42 2.070305 TTGGACCGTATCACCCGATA 57.930 50.000 0.00 0.00 32.73 2.92
42 43 1.420430 ATTGGACCGTATCACCCGAT 58.580 50.000 0.00 0.00 35.50 4.18
43 44 2.070305 TATTGGACCGTATCACCCGA 57.930 50.000 0.00 0.00 0.00 5.14
44 45 2.297880 TGATATTGGACCGTATCACCCG 59.702 50.000 12.85 0.00 33.60 5.28
45 46 3.576982 TCTGATATTGGACCGTATCACCC 59.423 47.826 12.85 0.00 34.55 4.61
46 47 4.281182 ACTCTGATATTGGACCGTATCACC 59.719 45.833 12.85 0.00 34.55 4.02
47 48 5.455056 ACTCTGATATTGGACCGTATCAC 57.545 43.478 12.85 0.00 34.55 3.06
48 49 5.596772 TCAACTCTGATATTGGACCGTATCA 59.403 40.000 15.00 15.00 36.28 2.15
49 50 6.085555 TCAACTCTGATATTGGACCGTATC 57.914 41.667 8.91 8.91 0.00 2.24
50 51 6.672266 ATCAACTCTGATATTGGACCGTAT 57.328 37.500 2.96 0.00 40.67 3.06
51 52 6.479972 AATCAACTCTGATATTGGACCGTA 57.520 37.500 2.96 0.00 41.66 4.02
52 53 5.359194 AATCAACTCTGATATTGGACCGT 57.641 39.130 2.96 0.00 41.66 4.83
53 54 6.073548 GCTTAATCAACTCTGATATTGGACCG 60.074 42.308 2.96 0.00 41.66 4.79
54 55 6.767902 TGCTTAATCAACTCTGATATTGGACC 59.232 38.462 2.96 0.00 41.66 4.46
55 56 7.792374 TGCTTAATCAACTCTGATATTGGAC 57.208 36.000 2.96 0.00 41.66 4.02
56 57 8.435187 AGATGCTTAATCAACTCTGATATTGGA 58.565 33.333 2.96 0.00 41.66 3.53
57 58 8.504815 CAGATGCTTAATCAACTCTGATATTGG 58.495 37.037 4.58 0.00 41.66 3.16
58 59 9.053840 ACAGATGCTTAATCAACTCTGATATTG 57.946 33.333 14.00 0.00 41.66 1.90
59 60 9.053840 CACAGATGCTTAATCAACTCTGATATT 57.946 33.333 14.00 0.00 41.66 1.28
60 61 8.209584 ACACAGATGCTTAATCAACTCTGATAT 58.790 33.333 14.00 0.82 41.66 1.63
61 62 7.493645 CACACAGATGCTTAATCAACTCTGATA 59.506 37.037 14.00 0.00 41.66 2.15
62 63 6.315642 CACACAGATGCTTAATCAACTCTGAT 59.684 38.462 14.00 2.90 44.54 2.90
63 64 5.640783 CACACAGATGCTTAATCAACTCTGA 59.359 40.000 14.00 0.00 37.81 3.27
64 65 5.673068 GCACACAGATGCTTAATCAACTCTG 60.673 44.000 7.90 7.90 42.62 3.35
69 70 3.419943 TGGCACACAGATGCTTAATCAA 58.580 40.909 0.00 0.00 45.38 2.57
95 96 3.981071 TTATCAGGGTGACACTTGGAG 57.019 47.619 5.39 0.00 0.00 3.86
117 118 8.783093 CAAATGGTACGATGTATGGATTATGTT 58.217 33.333 0.00 0.00 0.00 2.71
122 123 8.918202 ATTACAAATGGTACGATGTATGGATT 57.082 30.769 0.00 0.00 0.00 3.01
169 183 2.835764 ACGCTAGTTTATTGTGGAGGGA 59.164 45.455 0.00 0.00 0.00 4.20
207 227 6.040878 AGTAGATGACGTAATGCCAGTTTAC 58.959 40.000 0.00 0.00 0.00 2.01
215 235 6.415280 CACACTCTTAGTAGATGACGTAATGC 59.585 42.308 0.00 0.00 0.00 3.56
260 289 2.659946 TACAGTGGTGGTCCGGTGGA 62.660 60.000 0.00 0.00 36.30 4.02
261 290 2.167398 CTACAGTGGTGGTCCGGTGG 62.167 65.000 0.00 0.00 36.30 4.61
262 291 1.292223 CTACAGTGGTGGTCCGGTG 59.708 63.158 0.00 0.00 36.30 4.94
263 292 1.152398 ACTACAGTGGTGGTCCGGT 60.152 57.895 0.00 0.00 32.73 5.28
264 293 1.292223 CACTACAGTGGTGGTCCGG 59.708 63.158 9.19 0.00 42.10 5.14
265 294 4.988065 CACTACAGTGGTGGTCCG 57.012 61.111 9.19 0.00 42.10 4.79
294 323 3.838903 GAGTATTATCCCCCGGATGAACT 59.161 47.826 0.73 0.00 43.06 3.01
296 325 3.178865 GGAGTATTATCCCCCGGATGAA 58.821 50.000 0.73 0.00 43.06 2.57
354 392 0.107312 CTTCATGGTGGCCTCAGAGG 60.107 60.000 12.81 12.81 38.80 3.69
361 399 1.669999 GGTGATGCTTCATGGTGGCC 61.670 60.000 5.49 0.00 33.56 5.36
378 416 1.207791 CAAGAGGCCTACAGGATGGT 58.792 55.000 4.42 0.00 43.62 3.55
403 450 3.549827 CGCATAGTAGGAGACAAGAGCAG 60.550 52.174 0.00 0.00 0.00 4.24
473 526 2.354259 CAAGCTAGCCTTCCACTTCAG 58.646 52.381 12.13 0.00 0.00 3.02
543 4695 2.594592 GCGTCCACCTGCAAAGGT 60.595 61.111 0.00 0.00 44.23 3.50
620 4772 0.249911 AGTTCGTCAAGTGTGCCCTC 60.250 55.000 0.00 0.00 0.00 4.30
622 4774 1.557443 CGAGTTCGTCAAGTGTGCCC 61.557 60.000 0.00 0.00 34.11 5.36
656 4808 2.435059 GAGTTCCCTCAGGTGCGC 60.435 66.667 0.00 0.00 37.67 6.09
684 4836 4.811969 ATTGTACCGTACAGACCATTCA 57.188 40.909 11.15 0.00 40.24 2.57
711 4863 3.618997 GCTCGTCAAGTTTCCAATCCCTA 60.619 47.826 0.00 0.00 0.00 3.53
721 4873 2.325583 TGGTCAAGCTCGTCAAGTTT 57.674 45.000 0.00 0.00 0.00 2.66
725 4877 1.872952 CAACATGGTCAAGCTCGTCAA 59.127 47.619 0.00 0.00 0.00 3.18
756 4908 1.918253 CCCCTCAGATCCTGGTTGG 59.082 63.158 0.00 0.00 31.51 3.77
764 4916 0.179006 GGAATGGTGCCCCTCAGATC 60.179 60.000 0.00 0.00 0.00 2.75
776 4928 1.597797 CCAATGCTGCGTGGAATGGT 61.598 55.000 15.09 0.00 37.03 3.55
823 4975 1.019673 CGAGCCCCAAATCTGTCATG 58.980 55.000 0.00 0.00 0.00 3.07
889 5041 1.667154 TAGCCGAGCGCAGATTGAGT 61.667 55.000 11.47 0.00 41.38 3.41
925 5077 2.743664 GAGCATCCCAATTGTTTTTGGC 59.256 45.455 4.43 0.72 44.04 4.52
929 5081 1.550072 CCCGAGCATCCCAATTGTTTT 59.450 47.619 4.43 0.00 0.00 2.43
930 5082 1.185315 CCCGAGCATCCCAATTGTTT 58.815 50.000 4.43 0.00 0.00 2.83
955 5107 0.902048 CTCTGAGGTCCAGACTGCCA 60.902 60.000 0.00 0.00 46.38 4.92
956 5108 0.613292 TCTCTGAGGTCCAGACTGCC 60.613 60.000 4.59 0.00 46.38 4.85
967 5119 2.103094 TGTCAGGTTGTTGTCTCTGAGG 59.897 50.000 4.59 0.00 37.00 3.86
968 5120 3.388308 CTGTCAGGTTGTTGTCTCTGAG 58.612 50.000 0.00 0.00 37.00 3.35
969 5121 2.103094 CCTGTCAGGTTGTTGTCTCTGA 59.897 50.000 11.09 0.00 34.34 3.27
982 5140 0.549950 ATTGGATGCTCCCTGTCAGG 59.450 55.000 12.40 12.40 35.03 3.86
1006 5165 4.531854 TCCAGTTCTGTCATGTTTCCAAA 58.468 39.130 0.00 0.00 0.00 3.28
1029 5188 9.866655 AAATGGTTATTCTGAAGGAATATAGCA 57.133 29.630 0.00 0.00 43.75 3.49
1169 5328 4.217334 TGTTGTTTGCAATATCGACATGGT 59.783 37.500 0.00 0.00 36.92 3.55
1170 5329 4.731720 TGTTGTTTGCAATATCGACATGG 58.268 39.130 0.00 0.00 36.92 3.66
1386 5566 1.338674 TGACGGAAAGCCATCGTGATT 60.339 47.619 0.00 0.00 37.25 2.57
1402 5582 1.369209 CGTGCAGCTGGTTTTGACG 60.369 57.895 17.12 0.00 0.00 4.35
1475 5655 5.803795 GCGTTATCTGATAGGTCTAGGAGGA 60.804 48.000 0.00 0.00 0.00 3.71
1585 5765 1.616865 ACAAGTCATCGAGGACGGAAA 59.383 47.619 23.00 0.00 42.62 3.13
1634 5814 8.601845 AAAGGTTCCTGTAAATTTGTTATTGC 57.398 30.769 0.00 0.00 0.00 3.56
1921 6102 6.479990 TCATAGTCTGTGAAGTCAGTGTTTTG 59.520 38.462 0.00 0.00 36.85 2.44
1942 6126 8.141298 TCCACTTGGTAAGAGTATTTGTCATA 57.859 34.615 0.00 0.00 36.34 2.15
2144 6331 3.250762 CAGTACCATATTGCCAATGTCCG 59.749 47.826 0.00 0.00 0.00 4.79
2145 6332 3.004734 GCAGTACCATATTGCCAATGTCC 59.995 47.826 0.00 0.00 35.63 4.02
2274 6461 2.510330 TCTCCTGTAGGTATCCTCCCA 58.490 52.381 0.00 0.00 34.61 4.37
2469 6659 1.078143 GCCCCAGTACAGCCAGAAG 60.078 63.158 0.00 0.00 0.00 2.85
2632 6825 2.031157 CACAAACCCCTTTACTTCAGCG 60.031 50.000 0.00 0.00 0.00 5.18
2714 6917 2.942376 CAGGTACACACAACTTGCTCAA 59.058 45.455 0.00 0.00 0.00 3.02
2732 6935 1.901591 ACAGTCAAAGCACCATCAGG 58.098 50.000 0.00 0.00 42.21 3.86
2736 6939 3.023119 TGTCAAACAGTCAAAGCACCAT 58.977 40.909 0.00 0.00 0.00 3.55
2749 6952 2.028476 CGGAGGGAGTACATGTCAAACA 60.028 50.000 0.00 0.00 0.00 2.83
2750 6953 2.028385 ACGGAGGGAGTACATGTCAAAC 60.028 50.000 0.00 0.00 0.00 2.93
2751 6954 2.253610 ACGGAGGGAGTACATGTCAAA 58.746 47.619 0.00 0.00 0.00 2.69
2753 6956 1.822990 GAACGGAGGGAGTACATGTCA 59.177 52.381 0.00 0.00 0.00 3.58
2754 6957 1.202268 CGAACGGAGGGAGTACATGTC 60.202 57.143 0.00 0.00 0.00 3.06
2757 6960 0.324091 ACCGAACGGAGGGAGTACAT 60.324 55.000 20.14 0.00 38.96 2.29
2759 6962 1.685148 ATACCGAACGGAGGGAGTAC 58.315 55.000 20.14 0.00 38.96 2.73
2760 6963 2.442236 AATACCGAACGGAGGGAGTA 57.558 50.000 20.14 1.06 38.96 2.59
2762 6965 2.305009 AGTAATACCGAACGGAGGGAG 58.695 52.381 20.14 0.00 38.96 4.30
2763 6966 2.428171 CAAGTAATACCGAACGGAGGGA 59.572 50.000 20.14 2.73 38.96 4.20
2764 6967 2.167075 ACAAGTAATACCGAACGGAGGG 59.833 50.000 20.14 3.28 38.96 4.30
2765 6968 3.119388 TGACAAGTAATACCGAACGGAGG 60.119 47.826 20.14 0.00 38.96 4.30
2766 6969 3.855950 GTGACAAGTAATACCGAACGGAG 59.144 47.826 20.14 0.00 38.96 4.63
2767 6970 3.255395 TGTGACAAGTAATACCGAACGGA 59.745 43.478 20.14 4.23 38.96 4.69
2768 6971 3.577667 TGTGACAAGTAATACCGAACGG 58.422 45.455 11.83 11.83 42.03 4.44
2769 6972 5.579384 TTTGTGACAAGTAATACCGAACG 57.421 39.130 0.00 0.00 0.00 3.95
2770 6973 7.325097 CCATTTTTGTGACAAGTAATACCGAAC 59.675 37.037 0.00 0.00 0.00 3.95
2771 6974 7.228906 TCCATTTTTGTGACAAGTAATACCGAA 59.771 33.333 0.00 0.00 0.00 4.30
2772 6975 6.711194 TCCATTTTTGTGACAAGTAATACCGA 59.289 34.615 0.00 0.00 0.00 4.69
2773 6976 6.904498 TCCATTTTTGTGACAAGTAATACCG 58.096 36.000 0.00 0.00 0.00 4.02
2827 7030 9.914131 CGTCCAAGAAATGAATGTATCTAGATA 57.086 33.333 8.44 8.44 0.00 1.98
2828 7031 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
2829 7032 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
2830 7033 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
2831 7034 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2832 7035 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
2833 7036 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2834 7037 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2835 7038 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2836 7039 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
2837 7040 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
2838 7041 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
2839 7042 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
2840 7043 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
2841 7044 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
2842 7045 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
2843 7046 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
2844 7047 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
2845 7048 3.256383 TGTTCGGAATTACTCGTCCAAGA 59.744 43.478 0.00 0.00 33.10 3.02
2846 7049 3.581755 TGTTCGGAATTACTCGTCCAAG 58.418 45.455 0.00 0.00 33.10 3.61
2847 7050 3.256383 TCTGTTCGGAATTACTCGTCCAA 59.744 43.478 0.00 0.00 33.10 3.53
2848 7051 2.821378 TCTGTTCGGAATTACTCGTCCA 59.179 45.455 0.00 0.00 33.10 4.02
2849 7052 3.436496 CTCTGTTCGGAATTACTCGTCC 58.564 50.000 0.00 0.00 0.00 4.79
2850 7053 3.436496 CCTCTGTTCGGAATTACTCGTC 58.564 50.000 0.00 0.00 0.00 4.20
2851 7054 2.165845 CCCTCTGTTCGGAATTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18
2852 7055 2.426024 TCCCTCTGTTCGGAATTACTCG 59.574 50.000 0.00 0.00 0.00 4.18
2853 7056 3.447944 ACTCCCTCTGTTCGGAATTACTC 59.552 47.826 0.00 0.00 0.00 2.59
2854 7057 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2855 7058 3.889520 ACTCCCTCTGTTCGGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2856 7059 4.346730 TGTACTCCCTCTGTTCGGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
2857 7060 3.170717 TGTACTCCCTCTGTTCGGAATT 58.829 45.455 0.00 0.00 0.00 2.17
2858 7061 2.816411 TGTACTCCCTCTGTTCGGAAT 58.184 47.619 0.00 0.00 0.00 3.01
2859 7062 2.297698 TGTACTCCCTCTGTTCGGAA 57.702 50.000 0.00 0.00 0.00 4.30
2860 7063 2.168496 CTTGTACTCCCTCTGTTCGGA 58.832 52.381 0.00 0.00 0.00 4.55
2861 7064 1.893801 ACTTGTACTCCCTCTGTTCGG 59.106 52.381 0.00 0.00 0.00 4.30
2862 7065 2.820787 AGACTTGTACTCCCTCTGTTCG 59.179 50.000 0.00 0.00 0.00 3.95
2863 7066 3.574826 ACAGACTTGTACTCCCTCTGTTC 59.425 47.826 9.09 0.00 38.75 3.18
2864 7067 3.577919 ACAGACTTGTACTCCCTCTGTT 58.422 45.455 9.09 0.00 38.75 3.16
2865 7068 3.246416 ACAGACTTGTACTCCCTCTGT 57.754 47.619 9.09 9.09 37.37 3.41
2866 7069 4.608948 AAACAGACTTGTACTCCCTCTG 57.391 45.455 0.00 2.06 36.23 3.35
2867 7070 5.839606 ACTTAAACAGACTTGTACTCCCTCT 59.160 40.000 0.00 0.00 36.23 3.69
2868 7071 6.099159 ACTTAAACAGACTTGTACTCCCTC 57.901 41.667 0.00 0.00 36.23 4.30
2869 7072 7.234988 ACATACTTAAACAGACTTGTACTCCCT 59.765 37.037 0.00 0.00 36.23 4.20
2870 7073 7.331193 CACATACTTAAACAGACTTGTACTCCC 59.669 40.741 0.00 0.00 36.23 4.30
2871 7074 7.148623 GCACATACTTAAACAGACTTGTACTCC 60.149 40.741 0.00 0.00 36.23 3.85
2872 7075 7.599245 AGCACATACTTAAACAGACTTGTACTC 59.401 37.037 0.00 0.00 36.23 2.59
2873 7076 7.385205 CAGCACATACTTAAACAGACTTGTACT 59.615 37.037 0.00 0.00 36.23 2.73
2874 7077 7.510630 CAGCACATACTTAAACAGACTTGTAC 58.489 38.462 0.00 0.00 36.23 2.90
3065 7834 5.985530 TCAGCAGTGCATATATGTACAGAAC 59.014 40.000 28.53 17.27 44.40 3.01
3130 8556 8.713971 TGACTGGTACATGATAATGGAAATACT 58.286 33.333 0.00 0.00 38.20 2.12
3186 8612 2.930040 TGTTCCGAGATTTGCGAGATTC 59.070 45.455 0.00 0.00 0.00 2.52
3246 8977 4.496895 GCTGTCAATTAATTGTCGATGCAC 59.503 41.667 23.95 14.91 38.84 4.57
3248 8979 3.720818 CGCTGTCAATTAATTGTCGATGC 59.279 43.478 23.95 20.49 38.84 3.91
3277 9008 1.590792 CGCTGCTGCTGATCGATCA 60.591 57.895 25.80 25.80 36.97 2.92
3301 9032 2.046892 GCTCCTCTTGCCGCTTGA 60.047 61.111 0.00 0.00 0.00 3.02
3383 10599 6.602406 CCTCAAATCATTTCTCCAGATCAGTT 59.398 38.462 0.00 0.00 0.00 3.16
3391 10607 4.943705 GCAGTACCTCAAATCATTTCTCCA 59.056 41.667 0.00 0.00 0.00 3.86
3393 10609 5.491635 GGCAGTACCTCAAATCATTTCTC 57.508 43.478 0.00 0.00 34.51 2.87
3431 11111 0.598158 TTTATCATACGCGTCCGGCC 60.598 55.000 18.63 0.00 38.94 6.13
3434 11114 3.858282 CGTATTTATCATACGCGTCCG 57.142 47.619 18.63 8.53 40.42 4.79
3449 11129 6.765036 AGCTTGATGATCTGAATTGACGTATT 59.235 34.615 0.00 0.00 0.00 1.89
3450 11130 6.286758 AGCTTGATGATCTGAATTGACGTAT 58.713 36.000 0.00 0.00 0.00 3.06
3451 11131 5.664457 AGCTTGATGATCTGAATTGACGTA 58.336 37.500 0.00 0.00 0.00 3.57
3453 11133 5.263948 CAAGCTTGATGATCTGAATTGACG 58.736 41.667 22.31 0.00 0.00 4.35
3454 11134 5.035443 GCAAGCTTGATGATCTGAATTGAC 58.965 41.667 30.39 2.24 0.00 3.18
3456 11136 4.035684 CGCAAGCTTGATGATCTGAATTG 58.964 43.478 30.39 0.00 0.00 2.32
3457 11137 3.066342 CCGCAAGCTTGATGATCTGAATT 59.934 43.478 30.39 0.00 0.00 2.17
3458 11138 2.617308 CCGCAAGCTTGATGATCTGAAT 59.383 45.455 30.39 0.00 0.00 2.57
3462 11142 0.465097 CCCCGCAAGCTTGATGATCT 60.465 55.000 30.39 0.00 0.00 2.75
3492 11172 4.024893 CCAAATACTATTGTACAGCGCCTG 60.025 45.833 2.29 4.31 37.52 4.85
3511 11191 3.865011 ATATCAATGCACAACGCCAAA 57.135 38.095 0.00 0.00 41.33 3.28
3514 11194 4.811555 TCTAATATCAATGCACAACGCC 57.188 40.909 0.00 0.00 41.33 5.68
3515 11195 6.664978 CATTCTAATATCAATGCACAACGC 57.335 37.500 0.00 0.00 42.89 4.84
3533 11219 4.216257 GGCACATATCCGTAAATGCATTCT 59.784 41.667 13.38 5.92 34.73 2.40
3534 11220 4.475944 GGCACATATCCGTAAATGCATTC 58.524 43.478 13.38 0.00 34.73 2.67
3548 11238 4.588528 GGGTATCAATTTGTGGGCACATAT 59.411 41.667 0.00 0.00 41.52 1.78
3555 11245 6.048509 GCAATTAAGGGTATCAATTTGTGGG 58.951 40.000 0.00 0.00 0.00 4.61
3565 11255 7.582667 ATTAACACTGGCAATTAAGGGTATC 57.417 36.000 0.00 0.00 27.37 2.24
3566 11256 7.971368 AATTAACACTGGCAATTAAGGGTAT 57.029 32.000 0.00 0.00 27.37 2.73


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

AutoCloner maintained by Alex Coulton.