Multiple sequence alignment - TraesCS7A01G212400

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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 TraesCS7A01G212400 chr7A 100.000 3408 0 0 1 3408 175867237 175870644 0.000000e+00 6294.0
1 TraesCS7A01G212400 chr7A 79.699 133 21 5 587 716 261793172 261793301 1.300000e-14 91.6
2 TraesCS7A01G212400 chr7D 89.898 1663 99 24 849 2480 173899083 173900707 0.000000e+00 2076.0
3 TraesCS7A01G212400 chr7D 96.471 85 3 0 708 792 173898943 173899027 1.280000e-29 141.0
4 TraesCS7A01G212400 chr2B 94.805 924 38 6 2485 3408 544980379 544979466 0.000000e+00 1432.0
5 TraesCS7A01G212400 chr2B 75.623 562 86 17 185 711 190057214 190057759 7.350000e-57 231.0
6 TraesCS7A01G212400 chr7B 94.124 936 42 5 2481 3408 652303459 652304389 0.000000e+00 1411.0
7 TraesCS7A01G212400 chr7B 93.096 927 51 3 1563 2479 138667308 138668231 0.000000e+00 1345.0
8 TraesCS7A01G212400 chr7B 91.351 925 53 12 2485 3408 630143647 630142749 0.000000e+00 1240.0
9 TraesCS7A01G212400 chr7B 84.488 361 38 7 2475 2821 162086420 162086776 1.170000e-89 340.0
10 TraesCS7A01G212400 chr7B 90.196 102 7 3 849 948 138666853 138666953 2.760000e-26 130.0
11 TraesCS7A01G212400 chr7B 82.759 87 13 2 1938 2023 742071873 742071958 3.650000e-10 76.8
12 TraesCS7A01G212400 chr2A 93.743 943 43 7 2475 3408 644844665 644845600 0.000000e+00 1400.0
13 TraesCS7A01G212400 chr2A 82.275 378 42 13 187 542 627515907 627516281 1.540000e-78 303.0
14 TraesCS7A01G212400 chr5B 93.757 929 45 7 2480 3408 280607619 280608534 0.000000e+00 1382.0
15 TraesCS7A01G212400 chr3A 93.140 933 53 4 2480 3408 725155508 725156433 0.000000e+00 1358.0
16 TraesCS7A01G212400 chr3A 85.673 349 38 8 185 526 631859359 631859016 1.160000e-94 357.0
17 TraesCS7A01G212400 chr5A 92.880 941 43 10 2468 3408 502052713 502053629 0.000000e+00 1345.0
18 TraesCS7A01G212400 chr5A 89.206 315 29 4 305 618 621442412 621442722 4.120000e-104 388.0
19 TraesCS7A01G212400 chr1D 92.569 942 50 5 2480 3408 450043463 450042529 0.000000e+00 1334.0
20 TraesCS7A01G212400 chr1D 85.329 334 40 6 185 515 204801457 204801130 1.520000e-88 337.0
21 TraesCS7A01G212400 chr1D 87.179 156 8 2 2480 2623 450043889 450043734 2.100000e-37 167.0
22 TraesCS7A01G212400 chr6B 88.718 585 59 7 2822 3401 489507524 489508106 0.000000e+00 708.0
23 TraesCS7A01G212400 chr6B 78.027 446 74 12 185 615 142222824 142223260 3.370000e-65 259.0
24 TraesCS7A01G212400 chr2D 82.649 536 72 10 185 711 638151603 638151080 4.010000e-124 455.0
25 TraesCS7A01G212400 chr2D 81.588 554 63 19 185 711 112554060 112554601 4.070000e-114 422.0
26 TraesCS7A01G212400 chr4B 82.927 533 56 20 185 711 291849574 291850077 6.710000e-122 448.0
27 TraesCS7A01G212400 chr4B 82.707 133 22 1 587 718 37315092 37314960 2.150000e-22 117.0
28 TraesCS7A01G212400 chr3D 78.621 580 66 28 185 713 548820699 548821271 7.050000e-87 331.0
29 TraesCS7A01G212400 chr1B 79.646 452 64 13 186 618 17348861 17349303 1.990000e-77 300.0
30 TraesCS7A01G212400 chr4D 85.824 261 37 0 2565 2825 485486247 485486507 9.310000e-71 278.0
31 TraesCS7A01G212400 chr4D 86.822 129 9 5 587 711 44186120 44185996 1.650000e-28 137.0
32 TraesCS7A01G212400 chrUn 76.858 471 62 26 187 618 7155932 7156394 4.430000e-54 222.0
33 TraesCS7A01G212400 chrUn 83.200 125 17 4 587 709 34160941 34161063 1.000000e-20 111.0
34 TraesCS7A01G212400 chr3B 74.823 564 89 20 205 716 795811173 795810611 4.460000e-49 206.0
35 TraesCS7A01G212400 chr3B 81.860 215 14 11 415 621 771167893 771167696 1.270000e-34 158.0
36 TraesCS7A01G212400 chr6D 84.103 195 18 9 430 618 468260031 468260218 3.500000e-40 176.0
37 TraesCS7A01G212400 chr1A 74.675 308 52 19 416 713 579577272 579576981 2.780000e-21 113.0
38 TraesCS7A01G212400 chr1A 86.667 60 8 0 654 713 500924984 500925043 2.190000e-07 67.6
39 TraesCS7A01G212400 chr1A 87.097 62 5 3 657 716 529324480 529324540 2.190000e-07 67.6
40 TraesCS7A01G212400 chr1A 86.207 58 6 2 657 713 592558186 592558130 1.020000e-05 62.1


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 TraesCS7A01G212400 chr7A 175867237 175870644 3407 False 6294.0 6294 100.0000 1 3408 1 chr7A.!!$F1 3407
1 TraesCS7A01G212400 chr7D 173898943 173900707 1764 False 1108.5 2076 93.1845 708 2480 2 chr7D.!!$F1 1772
2 TraesCS7A01G212400 chr2B 544979466 544980379 913 True 1432.0 1432 94.8050 2485 3408 1 chr2B.!!$R1 923
3 TraesCS7A01G212400 chr2B 190057214 190057759 545 False 231.0 231 75.6230 185 711 1 chr2B.!!$F1 526
4 TraesCS7A01G212400 chr7B 652303459 652304389 930 False 1411.0 1411 94.1240 2481 3408 1 chr7B.!!$F2 927
5 TraesCS7A01G212400 chr7B 630142749 630143647 898 True 1240.0 1240 91.3510 2485 3408 1 chr7B.!!$R1 923
6 TraesCS7A01G212400 chr7B 138666853 138668231 1378 False 737.5 1345 91.6460 849 2479 2 chr7B.!!$F4 1630
7 TraesCS7A01G212400 chr2A 644844665 644845600 935 False 1400.0 1400 93.7430 2475 3408 1 chr2A.!!$F2 933
8 TraesCS7A01G212400 chr5B 280607619 280608534 915 False 1382.0 1382 93.7570 2480 3408 1 chr5B.!!$F1 928
9 TraesCS7A01G212400 chr3A 725155508 725156433 925 False 1358.0 1358 93.1400 2480 3408 1 chr3A.!!$F1 928
10 TraesCS7A01G212400 chr5A 502052713 502053629 916 False 1345.0 1345 92.8800 2468 3408 1 chr5A.!!$F1 940
11 TraesCS7A01G212400 chr1D 450042529 450043889 1360 True 750.5 1334 89.8740 2480 3408 2 chr1D.!!$R2 928
12 TraesCS7A01G212400 chr6B 489507524 489508106 582 False 708.0 708 88.7180 2822 3401 1 chr6B.!!$F2 579
13 TraesCS7A01G212400 chr2D 638151080 638151603 523 True 455.0 455 82.6490 185 711 1 chr2D.!!$R1 526
14 TraesCS7A01G212400 chr2D 112554060 112554601 541 False 422.0 422 81.5880 185 711 1 chr2D.!!$F1 526
15 TraesCS7A01G212400 chr4B 291849574 291850077 503 False 448.0 448 82.9270 185 711 1 chr4B.!!$F1 526
16 TraesCS7A01G212400 chr3D 548820699 548821271 572 False 331.0 331 78.6210 185 713 1 chr3D.!!$F1 528
17 TraesCS7A01G212400 chr3B 795810611 795811173 562 True 206.0 206 74.8230 205 716 1 chr3B.!!$R2 511

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
90 91 0.111832 AGGACACGTAGACAGGGTCA 59.888 55.0 0.96 0.0 34.60 4.02 F
93 94 0.111832 ACACGTAGACAGGGTCAGGA 59.888 55.0 0.00 0.0 34.60 3.86 F
1557 1908 0.093705 GAAGTTGATCGTGTGCTCGC 59.906 55.0 0.00 0.0 0.00 5.03 F
1731 2082 0.325110 CAGGAGAGGGGAGCTCTTCA 60.325 60.0 14.64 0.0 32.98 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1889 0.093705 GCGAGCACACGATCAACTTC 59.906 55.000 0.0 0.0 35.09 3.01 R
1849 2210 0.677731 GCACCATCAGTAGCTTGCCA 60.678 55.000 0.0 0.0 0.00 4.92 R
2368 2747 1.134521 TGTCCACCATACAGATTCGCC 60.135 52.381 0.0 0.0 0.00 5.54 R
2624 3443 1.186200 GGGTTCAATTCCCCTTCAGC 58.814 55.000 0.0 0.0 39.08 4.26 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
19 20 1.156736 ACGAGCAGGTTACACAATGC 58.843 50.000 0.00 0.00 38.97 3.56
20 21 1.155889 CGAGCAGGTTACACAATGCA 58.844 50.000 0.00 0.00 41.14 3.96
21 22 1.535028 CGAGCAGGTTACACAATGCAA 59.465 47.619 0.00 0.00 41.14 4.08
22 23 2.665519 CGAGCAGGTTACACAATGCAAC 60.666 50.000 0.00 0.00 41.14 4.17
23 24 2.293122 GAGCAGGTTACACAATGCAACA 59.707 45.455 0.00 0.00 41.14 3.33
24 25 2.034558 AGCAGGTTACACAATGCAACAC 59.965 45.455 0.00 0.00 41.14 3.32
25 26 2.649516 CAGGTTACACAATGCAACACG 58.350 47.619 0.00 0.00 0.00 4.49
26 27 1.001815 AGGTTACACAATGCAACACGC 60.002 47.619 0.00 0.00 42.89 5.34
47 48 4.814900 CCGTTGAGGTCGATCAGG 57.185 61.111 0.00 0.00 34.51 3.86
48 49 2.189833 CCGTTGAGGTCGATCAGGA 58.810 57.895 0.00 0.00 34.51 3.86
49 50 0.179134 CCGTTGAGGTCGATCAGGAC 60.179 60.000 0.00 0.00 36.18 3.85
50 51 0.811915 CGTTGAGGTCGATCAGGACT 59.188 55.000 0.00 0.00 37.12 3.85
51 52 1.202200 CGTTGAGGTCGATCAGGACTC 60.202 57.143 0.00 0.00 37.12 3.36
52 53 2.096248 GTTGAGGTCGATCAGGACTCT 58.904 52.381 0.00 0.00 37.12 3.24
53 54 3.280295 GTTGAGGTCGATCAGGACTCTA 58.720 50.000 0.00 0.00 37.12 2.43
54 55 3.646736 TGAGGTCGATCAGGACTCTAA 57.353 47.619 0.00 0.00 37.12 2.10
55 56 3.964411 TGAGGTCGATCAGGACTCTAAA 58.036 45.455 0.00 0.00 37.12 1.85
56 57 4.537751 TGAGGTCGATCAGGACTCTAAAT 58.462 43.478 0.00 0.00 37.12 1.40
57 58 4.339530 TGAGGTCGATCAGGACTCTAAATG 59.660 45.833 0.00 0.00 37.12 2.32
58 59 3.639094 AGGTCGATCAGGACTCTAAATGG 59.361 47.826 0.00 0.00 37.12 3.16
59 60 3.243907 GGTCGATCAGGACTCTAAATGGG 60.244 52.174 0.00 0.00 37.12 4.00
60 61 2.365617 TCGATCAGGACTCTAAATGGGC 59.634 50.000 0.00 0.00 0.00 5.36
61 62 2.760374 GATCAGGACTCTAAATGGGCG 58.240 52.381 0.00 0.00 0.00 6.13
62 63 0.830648 TCAGGACTCTAAATGGGCGG 59.169 55.000 0.00 0.00 0.00 6.13
63 64 0.815615 CAGGACTCTAAATGGGCGGC 60.816 60.000 0.00 0.00 0.00 6.53
64 65 0.983378 AGGACTCTAAATGGGCGGCT 60.983 55.000 9.56 0.00 0.00 5.52
65 66 0.756903 GGACTCTAAATGGGCGGCTA 59.243 55.000 9.56 1.93 0.00 3.93
66 67 1.140252 GGACTCTAAATGGGCGGCTAA 59.860 52.381 9.56 0.00 0.00 3.09
67 68 2.210961 GACTCTAAATGGGCGGCTAAC 58.789 52.381 9.56 0.00 0.00 2.34
68 69 1.557832 ACTCTAAATGGGCGGCTAACA 59.442 47.619 9.56 0.00 0.00 2.41
69 70 2.026636 ACTCTAAATGGGCGGCTAACAA 60.027 45.455 9.56 0.00 0.00 2.83
70 71 3.214328 CTCTAAATGGGCGGCTAACAAT 58.786 45.455 9.56 0.00 0.00 2.71
71 72 4.141574 ACTCTAAATGGGCGGCTAACAATA 60.142 41.667 9.56 0.00 0.00 1.90
72 73 4.385825 TCTAAATGGGCGGCTAACAATAG 58.614 43.478 9.56 4.98 0.00 1.73
73 74 1.981256 AATGGGCGGCTAACAATAGG 58.019 50.000 9.56 0.00 0.00 2.57
74 75 1.136828 ATGGGCGGCTAACAATAGGA 58.863 50.000 9.56 0.00 0.00 2.94
75 76 0.179468 TGGGCGGCTAACAATAGGAC 59.821 55.000 9.56 0.00 0.00 3.85
76 77 0.179468 GGGCGGCTAACAATAGGACA 59.821 55.000 9.56 0.00 0.00 4.02
77 78 1.296727 GGCGGCTAACAATAGGACAC 58.703 55.000 0.00 0.00 0.00 3.67
78 79 0.928229 GCGGCTAACAATAGGACACG 59.072 55.000 0.00 0.00 0.00 4.49
79 80 1.738030 GCGGCTAACAATAGGACACGT 60.738 52.381 0.00 0.00 0.00 4.49
80 81 2.480073 GCGGCTAACAATAGGACACGTA 60.480 50.000 0.00 0.00 0.00 3.57
81 82 3.369385 CGGCTAACAATAGGACACGTAG 58.631 50.000 0.00 0.00 0.00 3.51
82 83 3.065786 CGGCTAACAATAGGACACGTAGA 59.934 47.826 0.00 0.00 0.00 2.59
83 84 4.357996 GGCTAACAATAGGACACGTAGAC 58.642 47.826 0.00 0.00 0.00 2.59
84 85 4.142315 GGCTAACAATAGGACACGTAGACA 60.142 45.833 0.00 0.00 0.00 3.41
85 86 5.035443 GCTAACAATAGGACACGTAGACAG 58.965 45.833 0.00 0.00 0.00 3.51
86 87 4.451629 AACAATAGGACACGTAGACAGG 57.548 45.455 0.00 0.00 0.00 4.00
87 88 2.758979 ACAATAGGACACGTAGACAGGG 59.241 50.000 0.00 0.00 0.00 4.45
88 89 2.758979 CAATAGGACACGTAGACAGGGT 59.241 50.000 0.00 0.00 0.00 4.34
89 90 2.119801 TAGGACACGTAGACAGGGTC 57.880 55.000 0.00 0.00 0.00 4.46
90 91 0.111832 AGGACACGTAGACAGGGTCA 59.888 55.000 0.96 0.00 34.60 4.02
91 92 0.526662 GGACACGTAGACAGGGTCAG 59.473 60.000 0.96 0.00 34.60 3.51
92 93 0.526662 GACACGTAGACAGGGTCAGG 59.473 60.000 0.00 0.00 34.60 3.86
93 94 0.111832 ACACGTAGACAGGGTCAGGA 59.888 55.000 0.00 0.00 34.60 3.86
94 95 0.526662 CACGTAGACAGGGTCAGGAC 59.473 60.000 0.00 0.00 34.60 3.85
95 96 0.111832 ACGTAGACAGGGTCAGGACA 59.888 55.000 1.41 0.00 34.60 4.02
96 97 0.526662 CGTAGACAGGGTCAGGACAC 59.473 60.000 1.41 0.00 34.60 3.67
108 109 3.997672 AGGACACTGAGAAGCACAC 57.002 52.632 0.00 0.00 0.00 3.82
109 110 1.123077 AGGACACTGAGAAGCACACA 58.877 50.000 0.00 0.00 0.00 3.72
110 111 1.696336 AGGACACTGAGAAGCACACAT 59.304 47.619 0.00 0.00 0.00 3.21
111 112 2.105477 AGGACACTGAGAAGCACACATT 59.895 45.455 0.00 0.00 0.00 2.71
112 113 3.324846 AGGACACTGAGAAGCACACATTA 59.675 43.478 0.00 0.00 0.00 1.90
113 114 4.019860 AGGACACTGAGAAGCACACATTAT 60.020 41.667 0.00 0.00 0.00 1.28
114 115 4.331168 GGACACTGAGAAGCACACATTATC 59.669 45.833 0.00 0.00 0.00 1.75
115 116 4.898320 ACACTGAGAAGCACACATTATCA 58.102 39.130 0.00 0.00 0.00 2.15
116 117 4.934001 ACACTGAGAAGCACACATTATCAG 59.066 41.667 8.36 8.36 46.47 2.90
117 118 4.331992 CACTGAGAAGCACACATTATCAGG 59.668 45.833 13.11 1.61 45.74 3.86
118 119 4.019860 ACTGAGAAGCACACATTATCAGGT 60.020 41.667 13.11 0.00 45.74 4.00
119 120 4.256110 TGAGAAGCACACATTATCAGGTG 58.744 43.478 0.00 0.00 40.78 4.00
130 131 4.311700 TCAGGTGCCTGAGAACCA 57.688 55.556 16.28 0.00 46.80 3.67
131 132 2.538790 TCAGGTGCCTGAGAACCAA 58.461 52.632 16.28 0.00 46.80 3.67
132 133 0.843309 TCAGGTGCCTGAGAACCAAA 59.157 50.000 16.28 0.00 46.80 3.28
133 134 1.425066 TCAGGTGCCTGAGAACCAAAT 59.575 47.619 16.28 0.00 46.80 2.32
134 135 2.158475 TCAGGTGCCTGAGAACCAAATT 60.158 45.455 16.28 0.00 46.80 1.82
135 136 2.029649 CAGGTGCCTGAGAACCAAATTG 60.030 50.000 12.66 0.00 46.30 2.32
136 137 1.963515 GGTGCCTGAGAACCAAATTGT 59.036 47.619 0.12 0.00 36.41 2.71
137 138 2.288395 GGTGCCTGAGAACCAAATTGTG 60.288 50.000 0.12 0.00 36.41 3.33
138 139 2.622942 GTGCCTGAGAACCAAATTGTGA 59.377 45.455 0.00 0.00 0.00 3.58
139 140 3.068024 GTGCCTGAGAACCAAATTGTGAA 59.932 43.478 0.00 0.00 0.00 3.18
140 141 3.896888 TGCCTGAGAACCAAATTGTGAAT 59.103 39.130 0.00 0.00 0.00 2.57
141 142 4.022068 TGCCTGAGAACCAAATTGTGAATC 60.022 41.667 0.00 0.00 0.00 2.52
142 143 4.022068 GCCTGAGAACCAAATTGTGAATCA 60.022 41.667 0.00 0.00 0.00 2.57
143 144 5.509501 GCCTGAGAACCAAATTGTGAATCAA 60.510 40.000 0.00 0.00 40.53 2.57
144 145 6.514947 CCTGAGAACCAAATTGTGAATCAAA 58.485 36.000 0.00 0.00 39.62 2.69
145 146 6.643770 CCTGAGAACCAAATTGTGAATCAAAG 59.356 38.462 0.00 0.00 39.62 2.77
146 147 7.111247 TGAGAACCAAATTGTGAATCAAAGT 57.889 32.000 0.00 0.00 39.62 2.66
147 148 7.202526 TGAGAACCAAATTGTGAATCAAAGTC 58.797 34.615 0.00 0.00 39.62 3.01
148 149 6.208644 AGAACCAAATTGTGAATCAAAGTCG 58.791 36.000 0.00 0.00 39.62 4.18
149 150 4.870363 ACCAAATTGTGAATCAAAGTCGG 58.130 39.130 0.00 0.00 39.62 4.79
150 151 4.582656 ACCAAATTGTGAATCAAAGTCGGA 59.417 37.500 0.00 0.00 39.62 4.55
151 152 5.243730 ACCAAATTGTGAATCAAAGTCGGAT 59.756 36.000 0.00 0.00 39.62 4.18
152 153 5.801947 CCAAATTGTGAATCAAAGTCGGATC 59.198 40.000 0.00 0.00 39.62 3.36
153 154 6.349611 CCAAATTGTGAATCAAAGTCGGATCT 60.350 38.462 0.00 0.00 39.62 2.75
154 155 5.808042 ATTGTGAATCAAAGTCGGATCTG 57.192 39.130 0.00 0.00 39.62 2.90
155 156 3.002791 TGTGAATCAAAGTCGGATCTGC 58.997 45.455 0.00 0.00 0.00 4.26
156 157 2.352960 GTGAATCAAAGTCGGATCTGCC 59.647 50.000 0.00 0.00 0.00 4.85
157 158 2.027285 TGAATCAAAGTCGGATCTGCCA 60.027 45.455 0.00 0.00 35.94 4.92
158 159 3.209410 GAATCAAAGTCGGATCTGCCAT 58.791 45.455 0.00 0.00 35.94 4.40
159 160 2.028420 TCAAAGTCGGATCTGCCATG 57.972 50.000 0.00 0.00 35.94 3.66
160 161 1.554617 TCAAAGTCGGATCTGCCATGA 59.445 47.619 0.00 0.00 35.94 3.07
161 162 2.027285 TCAAAGTCGGATCTGCCATGAA 60.027 45.455 0.00 0.00 35.94 2.57
162 163 2.029838 AAGTCGGATCTGCCATGAAC 57.970 50.000 0.00 0.00 35.94 3.18
163 164 0.904649 AGTCGGATCTGCCATGAACA 59.095 50.000 0.00 0.00 35.94 3.18
164 165 1.278985 AGTCGGATCTGCCATGAACAA 59.721 47.619 0.00 0.00 35.94 2.83
165 166 2.083774 GTCGGATCTGCCATGAACAAA 58.916 47.619 0.00 0.00 35.94 2.83
166 167 2.487762 GTCGGATCTGCCATGAACAAAA 59.512 45.455 0.00 0.00 35.94 2.44
167 168 2.749076 TCGGATCTGCCATGAACAAAAG 59.251 45.455 0.00 0.00 35.94 2.27
168 169 2.159338 CGGATCTGCCATGAACAAAAGG 60.159 50.000 0.00 0.00 35.94 3.11
169 170 2.827921 GGATCTGCCATGAACAAAAGGT 59.172 45.455 0.00 0.00 36.34 3.50
170 171 4.016444 GGATCTGCCATGAACAAAAGGTA 58.984 43.478 0.00 0.00 36.34 3.08
171 172 4.462483 GGATCTGCCATGAACAAAAGGTAA 59.538 41.667 0.00 0.00 36.34 2.85
172 173 5.127682 GGATCTGCCATGAACAAAAGGTAAT 59.872 40.000 0.00 0.00 36.34 1.89
173 174 5.643379 TCTGCCATGAACAAAAGGTAATC 57.357 39.130 0.00 0.00 0.00 1.75
174 175 5.324409 TCTGCCATGAACAAAAGGTAATCT 58.676 37.500 0.00 0.00 0.00 2.40
175 176 6.480763 TCTGCCATGAACAAAAGGTAATCTA 58.519 36.000 0.00 0.00 0.00 1.98
176 177 6.599244 TCTGCCATGAACAAAAGGTAATCTAG 59.401 38.462 0.00 0.00 0.00 2.43
177 178 5.125417 TGCCATGAACAAAAGGTAATCTAGC 59.875 40.000 0.00 0.00 0.00 3.42
178 179 5.358160 GCCATGAACAAAAGGTAATCTAGCT 59.642 40.000 0.00 0.00 38.32 3.32
179 180 6.678900 GCCATGAACAAAAGGTAATCTAGCTG 60.679 42.308 0.00 0.00 36.50 4.24
180 181 6.599244 CCATGAACAAAAGGTAATCTAGCTGA 59.401 38.462 0.00 0.00 36.50 4.26
181 182 7.414540 CCATGAACAAAAGGTAATCTAGCTGAC 60.415 40.741 0.00 0.00 36.50 3.51
182 183 6.530120 TGAACAAAAGGTAATCTAGCTGACA 58.470 36.000 0.00 0.00 36.50 3.58
183 184 6.995686 TGAACAAAAGGTAATCTAGCTGACAA 59.004 34.615 0.00 0.00 36.50 3.18
211 212 1.226831 CGCCAACAAACACGCCTTT 60.227 52.632 0.00 0.00 0.00 3.11
214 215 1.737363 GCCAACAAACACGCCTTTTGA 60.737 47.619 10.09 0.00 37.39 2.69
272 273 3.423154 GGCGTCAACGGAAGGCAG 61.423 66.667 4.54 0.00 45.22 4.85
306 307 2.099638 CGATCTCGTCAACGCCGA 59.900 61.111 0.00 0.00 39.60 5.54
310 311 1.663379 ATCTCGTCAACGCCGATGGA 61.663 55.000 0.00 0.00 39.60 3.41
325 326 3.057019 CGATGGAAAGTCGTTCTTCACA 58.943 45.455 0.00 0.00 36.40 3.58
326 327 3.121944 CGATGGAAAGTCGTTCTTCACAG 59.878 47.826 0.00 0.00 36.40 3.66
329 330 2.612212 GGAAAGTCGTTCTTCACAGCAA 59.388 45.455 0.00 0.00 36.40 3.91
338 339 4.214437 GTTCTTCACAGCAAACGATGAAG 58.786 43.478 6.51 6.51 46.18 3.02
360 361 0.544357 TGGGAGGACGTGTGGATCTT 60.544 55.000 0.00 0.00 0.00 2.40
403 413 2.301296 GGGTGATGATGATGAGGACGAT 59.699 50.000 0.00 0.00 0.00 3.73
407 417 3.569701 TGATGATGATGAGGACGATTCGA 59.430 43.478 13.95 0.00 0.00 3.71
448 465 6.029607 CGTAGTTTATCTAGTTGCACCGTAA 58.970 40.000 0.00 0.00 0.00 3.18
452 470 8.331730 AGTTTATCTAGTTGCACCGTAATTTT 57.668 30.769 0.00 0.00 0.00 1.82
567 678 7.859325 ACAAAATATTTATGCACCGTAGTCT 57.141 32.000 0.01 0.00 0.00 3.24
585 719 6.346279 CGTAGTCTAAAATGTTTGTGCGAGAA 60.346 38.462 0.00 0.00 0.00 2.87
601 735 3.046460 GAACGCGCGCTGCATTTTG 62.046 57.895 32.58 13.34 46.97 2.44
652 786 1.491670 CGGCAAATCAGACGATCGAT 58.508 50.000 24.34 6.97 44.57 3.59
655 789 1.594397 GCAAATCAGACGATCGATGCA 59.406 47.619 24.34 10.16 36.44 3.96
741 875 4.845177 CATCGCATGCAACGTGTT 57.155 50.000 19.57 0.00 0.00 3.32
746 880 2.338500 TCGCATGCAACGTGTTACATA 58.662 42.857 19.57 0.00 0.00 2.29
792 926 2.789893 CGAATAGAGTAGCGGACAAAGC 59.210 50.000 0.00 0.00 0.00 3.51
793 927 2.493713 ATAGAGTAGCGGACAAAGCG 57.506 50.000 0.00 0.00 40.04 4.68
794 928 1.456296 TAGAGTAGCGGACAAAGCGA 58.544 50.000 0.00 0.00 40.04 4.93
795 929 0.171455 AGAGTAGCGGACAAAGCGAG 59.829 55.000 0.00 0.00 40.04 5.03
796 930 1.414527 GAGTAGCGGACAAAGCGAGC 61.415 60.000 0.00 0.00 40.04 5.03
797 931 1.736645 GTAGCGGACAAAGCGAGCA 60.737 57.895 0.00 0.00 40.04 4.26
808 942 2.487428 GCGAGCAGCGAGAGAAGA 59.513 61.111 3.02 0.00 44.57 2.87
809 943 1.586042 GCGAGCAGCGAGAGAAGAG 60.586 63.158 3.02 0.00 44.57 2.85
810 944 1.586042 CGAGCAGCGAGAGAAGAGC 60.586 63.158 0.00 0.00 44.57 4.09
811 945 1.510383 GAGCAGCGAGAGAAGAGCA 59.490 57.895 0.00 0.00 0.00 4.26
812 946 0.526096 GAGCAGCGAGAGAAGAGCAG 60.526 60.000 0.00 0.00 0.00 4.24
813 947 1.519013 GCAGCGAGAGAAGAGCAGG 60.519 63.158 0.00 0.00 0.00 4.85
814 948 1.889454 CAGCGAGAGAAGAGCAGGT 59.111 57.895 0.00 0.00 0.00 4.00
815 949 0.246086 CAGCGAGAGAAGAGCAGGTT 59.754 55.000 0.00 0.00 0.00 3.50
817 951 2.100584 CAGCGAGAGAAGAGCAGGTTAT 59.899 50.000 0.00 0.00 0.00 1.89
820 954 2.801342 CGAGAGAAGAGCAGGTTATGGC 60.801 54.545 0.00 0.00 0.00 4.40
822 956 2.093235 AGAGAAGAGCAGGTTATGGCAC 60.093 50.000 0.00 0.00 0.00 5.01
823 957 1.065126 AGAAGAGCAGGTTATGGCACC 60.065 52.381 0.00 0.00 37.04 5.01
824 958 0.392998 AAGAGCAGGTTATGGCACCG 60.393 55.000 0.00 0.00 42.33 4.94
842 976 4.452733 CCGGACCGGCTTCCTGTC 62.453 72.222 22.37 0.00 41.17 3.51
843 977 4.796231 CGGACCGGCTTCCTGTCG 62.796 72.222 5.81 0.00 44.42 4.35
847 981 4.379243 CCGGCTTCCTGTCGCAGT 62.379 66.667 0.00 0.00 43.31 4.40
951 1269 4.987912 GCCGAAACAAATTCCAAGAATCAA 59.012 37.500 0.00 0.00 34.34 2.57
1000 1318 7.364522 TCATCAGGAGAAAACAACGATAAAG 57.635 36.000 0.00 0.00 0.00 1.85
1026 1344 5.699915 CAGTAGTAGTAGGCGCTATCAGTAA 59.300 44.000 7.64 0.00 0.00 2.24
1034 1352 4.262617 AGGCGCTATCAGTAAGATCGATA 58.737 43.478 7.64 0.00 38.19 2.92
1035 1353 4.700692 AGGCGCTATCAGTAAGATCGATAA 59.299 41.667 7.64 0.00 38.19 1.75
1036 1354 5.358442 AGGCGCTATCAGTAAGATCGATAAT 59.642 40.000 7.64 0.00 38.19 1.28
1037 1355 6.037098 GGCGCTATCAGTAAGATCGATAATT 58.963 40.000 7.64 0.00 38.19 1.40
1099 1450 1.299089 GTTTCACCAAGGCACGCAC 60.299 57.895 0.00 0.00 0.00 5.34
1118 1469 3.121030 CGCAGCCCTTCTTCACCG 61.121 66.667 0.00 0.00 0.00 4.94
1122 1473 2.359975 GCCCTTCTTCACCGTGGG 60.360 66.667 0.00 0.00 40.74 4.61
1167 1518 1.227205 CTCATCCTCTGCCGACTGC 60.227 63.158 0.00 0.00 41.77 4.40
1187 1538 3.434319 TCGTACACCGACCGGCTC 61.434 66.667 8.55 0.00 41.60 4.70
1379 1730 1.586564 CGACTTCGACGGGATGCTC 60.587 63.158 0.00 0.00 43.02 4.26
1380 1731 1.227002 GACTTCGACGGGATGCTCC 60.227 63.158 0.00 0.00 35.23 4.70
1403 1754 3.965539 CTTCGGCAGCTGGGTCCTG 62.966 68.421 17.12 3.55 0.00 3.86
1424 1775 2.733593 GAGCACCACCACGACGAC 60.734 66.667 0.00 0.00 0.00 4.34
1425 1776 3.208884 GAGCACCACCACGACGACT 62.209 63.158 0.00 0.00 0.00 4.18
1428 1779 1.655885 CACCACCACGACGACTACA 59.344 57.895 0.00 0.00 0.00 2.74
1430 1781 0.313043 ACCACCACGACGACTACAAG 59.687 55.000 0.00 0.00 0.00 3.16
1432 1783 1.401148 CCACCACGACGACTACAAGAG 60.401 57.143 0.00 0.00 0.00 2.85
1463 1814 1.303309 GATGCTTGCTGCGTAATCCT 58.697 50.000 0.00 0.00 46.63 3.24
1472 1823 0.461339 TGCGTAATCCTTTCTCCGGC 60.461 55.000 0.00 0.00 0.00 6.13
1502 1853 1.523711 CATACCGTGGCGCTCCATT 60.524 57.895 7.64 0.00 45.62 3.16
1538 1889 3.438360 GCCGCTCATGGAGTTTATTTTG 58.562 45.455 0.00 0.00 31.39 2.44
1557 1908 0.093705 GAAGTTGATCGTGTGCTCGC 59.906 55.000 0.00 0.00 0.00 5.03
1640 1991 1.006571 TGGCTTCTCGTGGTCGTTC 60.007 57.895 0.00 0.00 38.33 3.95
1663 2014 4.033709 AGCCCGGCTGATGATAGTTATAT 58.966 43.478 12.38 0.00 37.57 0.86
1690 2041 2.035832 ACAAGGACATTGCCTTTTTCCG 59.964 45.455 0.00 2.72 45.85 4.30
1731 2082 0.325110 CAGGAGAGGGGAGCTCTTCA 60.325 60.000 14.64 0.00 32.98 3.02
1732 2083 0.325203 AGGAGAGGGGAGCTCTTCAC 60.325 60.000 14.64 7.81 32.98 3.18
1831 2192 1.809271 CGATCCTTCATCCAGCACCTG 60.809 57.143 0.00 0.00 0.00 4.00
1840 2201 3.955145 CCAGCACCTGGTTGTATCA 57.045 52.632 0.00 0.00 45.82 2.15
1849 2210 5.618236 CACCTGGTTGTATCATCATCATCT 58.382 41.667 0.00 0.00 0.00 2.90
1870 2231 1.709147 GCAAGCTACTGATGGTGCGG 61.709 60.000 0.00 0.00 0.00 5.69
1879 2240 1.379843 GATGGTGCGGTGGGGAATT 60.380 57.895 0.00 0.00 0.00 2.17
1882 2243 1.605165 GGTGCGGTGGGGAATTGAA 60.605 57.895 0.00 0.00 0.00 2.69
1896 2257 5.243954 GGGGAATTGAACCTCCTAATTATGC 59.756 44.000 0.00 0.00 31.88 3.14
1931 2292 3.323243 GCAATTGATCATGGCATTAGGC 58.677 45.455 10.34 0.00 43.74 3.93
1963 2324 5.108385 TCGAGGCAGATTTTGAGAAAAAC 57.892 39.130 0.00 0.00 33.47 2.43
1972 2333 4.729227 TTTTGAGAAAAACCAGTGGTCC 57.271 40.909 17.06 5.59 33.12 4.46
2025 2386 2.305635 TCATTGGCAGAACAGGCTCTAA 59.694 45.455 0.00 0.00 34.73 2.10
2163 2524 8.627208 ATTAATCATGTTACTCCCAGCTATTG 57.373 34.615 0.00 0.00 0.00 1.90
2176 2537 3.932710 CCAGCTATTGTGTGTATGACGTT 59.067 43.478 0.00 0.00 0.00 3.99
2185 2546 2.229543 TGTGTATGACGTTAAGAGCGGT 59.770 45.455 0.00 0.00 0.00 5.68
2209 2570 4.067896 CAGTTACTGCAGTTTCACTGGAT 58.932 43.478 29.06 8.08 45.46 3.41
2275 2636 5.128499 CCCTTGTGACTGAGAGATTCACTAT 59.872 44.000 3.17 0.00 40.34 2.12
2371 2750 8.883731 CAATTTAGATATATACTTCCCTTGGCG 58.116 37.037 0.00 0.00 0.00 5.69
2555 3360 0.257039 CCCTTTGATCCCACCTCCTG 59.743 60.000 0.00 0.00 0.00 3.86
2580 3396 1.032794 CGACGATCCCATCTTCTCCA 58.967 55.000 0.00 0.00 0.00 3.86
2624 3443 7.170828 ACTTTAAAATAGGCAAAAAGAAAGGCG 59.829 33.333 0.00 0.00 32.72 5.52
2625 3444 2.654749 ATAGGCAAAAAGAAAGGCGC 57.345 45.000 0.00 0.00 0.00 6.53
2668 3487 2.582052 CCTCCCACACAAAACTAAGCA 58.418 47.619 0.00 0.00 0.00 3.91
2761 3580 6.470877 GTGACGAGAATAAACAAAACAAGCAA 59.529 34.615 0.00 0.00 0.00 3.91
2810 3629 1.275573 AGCCTCACTTCTACGGGTTTC 59.724 52.381 0.00 0.00 0.00 2.78
3149 3977 8.691661 ATTTACACAATGGTTATCAGGGATAC 57.308 34.615 0.00 0.00 0.00 2.24
3301 4131 4.050553 CCGAGTCAAAAGTTAACACGGTA 58.949 43.478 8.61 0.00 40.69 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.155889 TGCATTGTGTAACCTGCTCG 58.844 50.000 0.00 0.00 42.76 5.03
2 3 2.293122 TGTTGCATTGTGTAACCTGCTC 59.707 45.455 8.13 0.00 41.35 4.26
3 4 2.034558 GTGTTGCATTGTGTAACCTGCT 59.965 45.455 8.13 0.00 41.35 4.24
4 5 2.393764 GTGTTGCATTGTGTAACCTGC 58.606 47.619 8.13 0.00 41.35 4.85
5 6 2.649516 CGTGTTGCATTGTGTAACCTG 58.350 47.619 8.13 0.00 41.35 4.00
7 8 1.404477 GCGTGTTGCATTGTGTAACC 58.596 50.000 8.13 0.73 41.35 2.85
18 19 1.199852 CTCAACGGTTTGCGTGTTGC 61.200 55.000 0.00 0.00 42.00 4.17
19 20 0.591236 CCTCAACGGTTTGCGTGTTG 60.591 55.000 0.00 0.00 43.26 3.33
20 21 1.027792 ACCTCAACGGTTTGCGTGTT 61.028 50.000 0.00 0.00 46.37 3.32
21 22 1.450669 ACCTCAACGGTTTGCGTGT 60.451 52.632 0.00 0.00 46.37 4.49
22 23 3.416490 ACCTCAACGGTTTGCGTG 58.584 55.556 0.00 0.00 46.37 5.34
30 31 0.179134 GTCCTGATCGACCTCAACGG 60.179 60.000 0.00 0.00 39.35 4.44
31 32 0.811915 AGTCCTGATCGACCTCAACG 59.188 55.000 0.00 0.00 32.91 4.10
32 33 2.096248 AGAGTCCTGATCGACCTCAAC 58.904 52.381 0.00 0.00 32.91 3.18
33 34 2.516227 AGAGTCCTGATCGACCTCAA 57.484 50.000 0.00 0.00 32.91 3.02
34 35 3.646736 TTAGAGTCCTGATCGACCTCA 57.353 47.619 0.00 0.00 32.91 3.86
35 36 4.261825 CCATTTAGAGTCCTGATCGACCTC 60.262 50.000 0.00 0.00 32.91 3.85
36 37 3.639094 CCATTTAGAGTCCTGATCGACCT 59.361 47.826 0.00 0.00 32.91 3.85
37 38 3.243907 CCCATTTAGAGTCCTGATCGACC 60.244 52.174 0.00 0.00 32.91 4.79
38 39 3.800604 GCCCATTTAGAGTCCTGATCGAC 60.801 52.174 0.00 0.00 0.00 4.20
39 40 2.365617 GCCCATTTAGAGTCCTGATCGA 59.634 50.000 0.00 0.00 0.00 3.59
40 41 2.760374 GCCCATTTAGAGTCCTGATCG 58.240 52.381 0.00 0.00 0.00 3.69
41 42 2.548920 CCGCCCATTTAGAGTCCTGATC 60.549 54.545 0.00 0.00 0.00 2.92
42 43 1.417890 CCGCCCATTTAGAGTCCTGAT 59.582 52.381 0.00 0.00 0.00 2.90
43 44 0.830648 CCGCCCATTTAGAGTCCTGA 59.169 55.000 0.00 0.00 0.00 3.86
44 45 0.815615 GCCGCCCATTTAGAGTCCTG 60.816 60.000 0.00 0.00 0.00 3.86
45 46 0.983378 AGCCGCCCATTTAGAGTCCT 60.983 55.000 0.00 0.00 0.00 3.85
46 47 0.756903 TAGCCGCCCATTTAGAGTCC 59.243 55.000 0.00 0.00 0.00 3.85
47 48 2.210961 GTTAGCCGCCCATTTAGAGTC 58.789 52.381 0.00 0.00 0.00 3.36
48 49 1.557832 TGTTAGCCGCCCATTTAGAGT 59.442 47.619 0.00 0.00 0.00 3.24
49 50 2.325583 TGTTAGCCGCCCATTTAGAG 57.674 50.000 0.00 0.00 0.00 2.43
50 51 2.791347 TTGTTAGCCGCCCATTTAGA 57.209 45.000 0.00 0.00 0.00 2.10
51 52 3.502211 CCTATTGTTAGCCGCCCATTTAG 59.498 47.826 0.00 0.00 0.00 1.85
52 53 3.136809 TCCTATTGTTAGCCGCCCATTTA 59.863 43.478 0.00 0.00 0.00 1.40
53 54 2.092103 TCCTATTGTTAGCCGCCCATTT 60.092 45.455 0.00 0.00 0.00 2.32
54 55 1.493022 TCCTATTGTTAGCCGCCCATT 59.507 47.619 0.00 0.00 0.00 3.16
55 56 1.136828 TCCTATTGTTAGCCGCCCAT 58.863 50.000 0.00 0.00 0.00 4.00
56 57 0.179468 GTCCTATTGTTAGCCGCCCA 59.821 55.000 0.00 0.00 0.00 5.36
57 58 0.179468 TGTCCTATTGTTAGCCGCCC 59.821 55.000 0.00 0.00 0.00 6.13
58 59 1.296727 GTGTCCTATTGTTAGCCGCC 58.703 55.000 0.00 0.00 0.00 6.13
59 60 0.928229 CGTGTCCTATTGTTAGCCGC 59.072 55.000 0.00 0.00 0.00 6.53
60 61 2.288961 ACGTGTCCTATTGTTAGCCG 57.711 50.000 0.00 0.00 0.00 5.52
61 62 4.142315 TGTCTACGTGTCCTATTGTTAGCC 60.142 45.833 0.00 0.00 0.00 3.93
62 63 4.990257 TGTCTACGTGTCCTATTGTTAGC 58.010 43.478 0.00 0.00 0.00 3.09
63 64 5.450137 CCCTGTCTACGTGTCCTATTGTTAG 60.450 48.000 0.00 0.00 0.00 2.34
64 65 4.400251 CCCTGTCTACGTGTCCTATTGTTA 59.600 45.833 0.00 0.00 0.00 2.41
65 66 3.194968 CCCTGTCTACGTGTCCTATTGTT 59.805 47.826 0.00 0.00 0.00 2.83
66 67 2.758979 CCCTGTCTACGTGTCCTATTGT 59.241 50.000 0.00 0.00 0.00 2.71
67 68 2.758979 ACCCTGTCTACGTGTCCTATTG 59.241 50.000 0.00 0.00 0.00 1.90
68 69 3.022406 GACCCTGTCTACGTGTCCTATT 58.978 50.000 0.00 0.00 0.00 1.73
69 70 2.025605 TGACCCTGTCTACGTGTCCTAT 60.026 50.000 0.00 0.00 33.15 2.57
70 71 1.352017 TGACCCTGTCTACGTGTCCTA 59.648 52.381 0.00 0.00 33.15 2.94
71 72 0.111832 TGACCCTGTCTACGTGTCCT 59.888 55.000 0.00 0.00 33.15 3.85
72 73 0.526662 CTGACCCTGTCTACGTGTCC 59.473 60.000 0.00 0.00 33.15 4.02
73 74 0.526662 CCTGACCCTGTCTACGTGTC 59.473 60.000 0.00 0.00 33.15 3.67
74 75 0.111832 TCCTGACCCTGTCTACGTGT 59.888 55.000 0.00 0.00 33.15 4.49
75 76 0.526662 GTCCTGACCCTGTCTACGTG 59.473 60.000 0.00 0.00 33.15 4.49
76 77 0.111832 TGTCCTGACCCTGTCTACGT 59.888 55.000 0.00 0.00 33.15 3.57
77 78 0.526662 GTGTCCTGACCCTGTCTACG 59.473 60.000 0.00 0.00 33.15 3.51
78 79 1.546476 CAGTGTCCTGACCCTGTCTAC 59.454 57.143 2.10 0.00 41.50 2.59
79 80 1.427753 TCAGTGTCCTGACCCTGTCTA 59.572 52.381 9.15 0.00 42.80 2.59
80 81 0.188587 TCAGTGTCCTGACCCTGTCT 59.811 55.000 9.15 0.00 42.80 3.41
81 82 0.605589 CTCAGTGTCCTGACCCTGTC 59.394 60.000 9.15 0.00 42.80 3.51
82 83 0.188587 TCTCAGTGTCCTGACCCTGT 59.811 55.000 9.15 0.00 42.80 4.00
83 84 1.274728 CTTCTCAGTGTCCTGACCCTG 59.725 57.143 3.69 3.69 42.80 4.45
84 85 1.638529 CTTCTCAGTGTCCTGACCCT 58.361 55.000 0.00 0.00 42.80 4.34
85 86 0.036858 GCTTCTCAGTGTCCTGACCC 60.037 60.000 0.00 0.00 42.80 4.46
86 87 0.681733 TGCTTCTCAGTGTCCTGACC 59.318 55.000 0.00 0.00 42.80 4.02
87 88 1.069204 TGTGCTTCTCAGTGTCCTGAC 59.931 52.381 0.00 0.00 42.80 3.51
88 89 1.069204 GTGTGCTTCTCAGTGTCCTGA 59.931 52.381 0.00 0.00 45.44 3.86
89 90 1.202568 TGTGTGCTTCTCAGTGTCCTG 60.203 52.381 0.00 0.00 40.25 3.86
90 91 1.123077 TGTGTGCTTCTCAGTGTCCT 58.877 50.000 0.00 0.00 0.00 3.85
91 92 2.175878 ATGTGTGCTTCTCAGTGTCC 57.824 50.000 0.00 0.00 0.00 4.02
92 93 4.931601 TGATAATGTGTGCTTCTCAGTGTC 59.068 41.667 0.00 0.00 0.00 3.67
93 94 4.898320 TGATAATGTGTGCTTCTCAGTGT 58.102 39.130 0.00 0.00 0.00 3.55
94 95 4.331992 CCTGATAATGTGTGCTTCTCAGTG 59.668 45.833 0.00 0.00 0.00 3.66
95 96 4.019860 ACCTGATAATGTGTGCTTCTCAGT 60.020 41.667 0.00 0.00 0.00 3.41
96 97 4.331992 CACCTGATAATGTGTGCTTCTCAG 59.668 45.833 0.00 0.00 0.00 3.35
97 98 4.256110 CACCTGATAATGTGTGCTTCTCA 58.744 43.478 0.00 0.00 0.00 3.27
98 99 4.871993 CACCTGATAATGTGTGCTTCTC 57.128 45.455 0.00 0.00 0.00 2.87
104 105 2.989909 TCAGGCACCTGATAATGTGTG 58.010 47.619 15.46 0.00 46.80 3.82
114 115 1.915141 ATTTGGTTCTCAGGCACCTG 58.085 50.000 10.60 10.60 44.86 4.00
115 116 2.242043 CAATTTGGTTCTCAGGCACCT 58.758 47.619 0.00 0.00 33.76 4.00
116 117 1.963515 ACAATTTGGTTCTCAGGCACC 59.036 47.619 0.78 0.00 0.00 5.01
117 118 2.622942 TCACAATTTGGTTCTCAGGCAC 59.377 45.455 0.78 0.00 0.00 5.01
118 119 2.942804 TCACAATTTGGTTCTCAGGCA 58.057 42.857 0.78 0.00 0.00 4.75
119 120 4.022068 TGATTCACAATTTGGTTCTCAGGC 60.022 41.667 0.78 0.00 0.00 4.85
120 121 5.710513 TGATTCACAATTTGGTTCTCAGG 57.289 39.130 0.78 0.00 0.00 3.86
121 122 7.205297 ACTTTGATTCACAATTTGGTTCTCAG 58.795 34.615 0.78 0.00 38.36 3.35
122 123 7.111247 ACTTTGATTCACAATTTGGTTCTCA 57.889 32.000 0.78 0.00 38.36 3.27
123 124 6.360681 CGACTTTGATTCACAATTTGGTTCTC 59.639 38.462 0.78 0.00 38.36 2.87
124 125 6.208644 CGACTTTGATTCACAATTTGGTTCT 58.791 36.000 0.78 0.00 38.36 3.01
125 126 5.402270 CCGACTTTGATTCACAATTTGGTTC 59.598 40.000 0.78 0.00 38.36 3.62
126 127 5.068460 TCCGACTTTGATTCACAATTTGGTT 59.932 36.000 0.78 0.00 38.36 3.67
127 128 4.582656 TCCGACTTTGATTCACAATTTGGT 59.417 37.500 0.78 0.00 38.36 3.67
128 129 5.119931 TCCGACTTTGATTCACAATTTGG 57.880 39.130 0.78 0.00 38.36 3.28
129 130 6.525628 CAGATCCGACTTTGATTCACAATTTG 59.474 38.462 0.00 0.00 38.36 2.32
130 131 6.615088 CAGATCCGACTTTGATTCACAATTT 58.385 36.000 0.00 0.00 38.36 1.82
131 132 5.392380 GCAGATCCGACTTTGATTCACAATT 60.392 40.000 0.00 0.00 38.36 2.32
132 133 4.095483 GCAGATCCGACTTTGATTCACAAT 59.905 41.667 0.00 0.00 38.36 2.71
133 134 3.436704 GCAGATCCGACTTTGATTCACAA 59.563 43.478 0.00 0.00 36.65 3.33
134 135 3.002791 GCAGATCCGACTTTGATTCACA 58.997 45.455 0.00 0.00 0.00 3.58
135 136 2.352960 GGCAGATCCGACTTTGATTCAC 59.647 50.000 0.00 0.00 0.00 3.18
136 137 2.027285 TGGCAGATCCGACTTTGATTCA 60.027 45.455 0.00 0.00 37.80 2.57
137 138 2.632377 TGGCAGATCCGACTTTGATTC 58.368 47.619 0.00 0.00 37.80 2.52
138 139 2.787473 TGGCAGATCCGACTTTGATT 57.213 45.000 0.00 0.00 37.80 2.57
139 140 2.171237 TCATGGCAGATCCGACTTTGAT 59.829 45.455 0.00 0.00 37.80 2.57
140 141 1.554617 TCATGGCAGATCCGACTTTGA 59.445 47.619 0.00 0.00 37.80 2.69
141 142 2.028420 TCATGGCAGATCCGACTTTG 57.972 50.000 0.00 0.00 37.80 2.77
142 143 2.290260 TGTTCATGGCAGATCCGACTTT 60.290 45.455 0.00 0.00 37.80 2.66
143 144 1.278985 TGTTCATGGCAGATCCGACTT 59.721 47.619 0.00 0.00 37.80 3.01
144 145 0.904649 TGTTCATGGCAGATCCGACT 59.095 50.000 0.00 0.00 37.80 4.18
145 146 1.737838 TTGTTCATGGCAGATCCGAC 58.262 50.000 0.00 0.00 37.80 4.79
146 147 2.488204 TTTGTTCATGGCAGATCCGA 57.512 45.000 0.00 0.00 37.80 4.55
147 148 2.159338 CCTTTTGTTCATGGCAGATCCG 60.159 50.000 0.00 0.00 37.80 4.18
148 149 2.827921 ACCTTTTGTTCATGGCAGATCC 59.172 45.455 0.00 0.00 0.00 3.36
149 150 5.643379 TTACCTTTTGTTCATGGCAGATC 57.357 39.130 0.00 0.00 0.00 2.75
150 151 5.954150 AGATTACCTTTTGTTCATGGCAGAT 59.046 36.000 0.00 0.00 0.00 2.90
151 152 5.324409 AGATTACCTTTTGTTCATGGCAGA 58.676 37.500 0.00 0.00 0.00 4.26
152 153 5.649782 AGATTACCTTTTGTTCATGGCAG 57.350 39.130 0.00 0.00 0.00 4.85
153 154 5.125417 GCTAGATTACCTTTTGTTCATGGCA 59.875 40.000 0.00 0.00 0.00 4.92
154 155 5.358160 AGCTAGATTACCTTTTGTTCATGGC 59.642 40.000 0.00 0.00 0.00 4.40
155 156 6.599244 TCAGCTAGATTACCTTTTGTTCATGG 59.401 38.462 0.00 0.00 0.00 3.66
156 157 7.119699 TGTCAGCTAGATTACCTTTTGTTCATG 59.880 37.037 0.00 0.00 0.00 3.07
157 158 7.168219 TGTCAGCTAGATTACCTTTTGTTCAT 58.832 34.615 0.00 0.00 0.00 2.57
158 159 6.530120 TGTCAGCTAGATTACCTTTTGTTCA 58.470 36.000 0.00 0.00 0.00 3.18
159 160 7.361286 CCTTGTCAGCTAGATTACCTTTTGTTC 60.361 40.741 0.00 0.00 0.00 3.18
160 161 6.431234 CCTTGTCAGCTAGATTACCTTTTGTT 59.569 38.462 0.00 0.00 0.00 2.83
161 162 5.940470 CCTTGTCAGCTAGATTACCTTTTGT 59.060 40.000 0.00 0.00 0.00 2.83
162 163 6.173339 TCCTTGTCAGCTAGATTACCTTTTG 58.827 40.000 0.00 0.00 0.00 2.44
163 164 6.374417 TCCTTGTCAGCTAGATTACCTTTT 57.626 37.500 0.00 0.00 0.00 2.27
164 165 5.104735 CCTCCTTGTCAGCTAGATTACCTTT 60.105 44.000 0.00 0.00 0.00 3.11
165 166 4.407296 CCTCCTTGTCAGCTAGATTACCTT 59.593 45.833 0.00 0.00 0.00 3.50
166 167 3.964031 CCTCCTTGTCAGCTAGATTACCT 59.036 47.826 0.00 0.00 0.00 3.08
167 168 3.961408 TCCTCCTTGTCAGCTAGATTACC 59.039 47.826 0.00 0.00 0.00 2.85
168 169 4.498345 CGTCCTCCTTGTCAGCTAGATTAC 60.498 50.000 0.00 0.00 0.00 1.89
169 170 3.632604 CGTCCTCCTTGTCAGCTAGATTA 59.367 47.826 0.00 0.00 0.00 1.75
170 171 2.428890 CGTCCTCCTTGTCAGCTAGATT 59.571 50.000 0.00 0.00 0.00 2.40
171 172 2.028130 CGTCCTCCTTGTCAGCTAGAT 58.972 52.381 0.00 0.00 0.00 1.98
172 173 1.271982 ACGTCCTCCTTGTCAGCTAGA 60.272 52.381 0.00 0.00 0.00 2.43
173 174 1.133407 GACGTCCTCCTTGTCAGCTAG 59.867 57.143 3.51 0.00 32.91 3.42
174 175 1.174783 GACGTCCTCCTTGTCAGCTA 58.825 55.000 3.51 0.00 32.91 3.32
175 176 1.867919 CGACGTCCTCCTTGTCAGCT 61.868 60.000 10.58 0.00 32.91 4.24
176 177 1.444553 CGACGTCCTCCTTGTCAGC 60.445 63.158 10.58 0.00 32.91 4.26
177 178 1.444553 GCGACGTCCTCCTTGTCAG 60.445 63.158 10.58 0.00 32.91 3.51
178 179 2.649034 GCGACGTCCTCCTTGTCA 59.351 61.111 10.58 0.00 32.91 3.58
179 180 2.126031 GGCGACGTCCTCCTTGTC 60.126 66.667 10.58 0.00 0.00 3.18
180 181 2.504274 TTGGCGACGTCCTCCTTGT 61.504 57.895 18.69 0.00 0.00 3.16
181 182 2.027625 GTTGGCGACGTCCTCCTTG 61.028 63.158 18.69 2.79 0.00 3.61
182 183 2.035237 TTGTTGGCGACGTCCTCCTT 62.035 55.000 18.69 0.00 0.00 3.36
183 184 2.035237 TTTGTTGGCGACGTCCTCCT 62.035 55.000 18.69 0.00 0.00 3.69
211 212 3.760035 GCCGTCCTCTCCGCTCAA 61.760 66.667 0.00 0.00 0.00 3.02
214 215 3.302347 CTTTGCCGTCCTCTCCGCT 62.302 63.158 0.00 0.00 0.00 5.52
272 273 3.025619 GCACTGCGATATGGCCAC 58.974 61.111 8.16 0.00 0.00 5.01
306 307 2.808543 GCTGTGAAGAACGACTTTCCAT 59.191 45.455 0.00 0.00 39.13 3.41
310 311 3.485216 CGTTTGCTGTGAAGAACGACTTT 60.485 43.478 1.64 0.00 45.44 2.66
325 326 1.202879 TCCCAACCTTCATCGTTTGCT 60.203 47.619 0.00 0.00 0.00 3.91
326 327 1.200020 CTCCCAACCTTCATCGTTTGC 59.800 52.381 0.00 0.00 0.00 3.68
329 330 1.003233 GTCCTCCCAACCTTCATCGTT 59.997 52.381 0.00 0.00 0.00 3.85
338 339 1.838073 ATCCACACGTCCTCCCAACC 61.838 60.000 0.00 0.00 0.00 3.77
360 361 1.812324 CGCTGGTGTTGTCCAAGGTAA 60.812 52.381 0.00 0.00 37.01 2.85
403 413 4.224433 CGTGCAACTAGAACTACTTCGAA 58.776 43.478 0.00 0.00 31.75 3.71
407 417 5.702349 ACTACGTGCAACTAGAACTACTT 57.298 39.130 0.00 0.00 31.75 2.24
552 663 7.173562 ACAAACATTTTAGACTACGGTGCATAA 59.826 33.333 0.00 0.00 0.00 1.90
629 763 0.530650 ATCGTCTGATTTGCCGCGAT 60.531 50.000 8.23 0.00 34.78 4.58
630 764 1.145759 GATCGTCTGATTTGCCGCGA 61.146 55.000 8.23 0.00 34.09 5.87
635 769 1.594397 TGCATCGATCGTCTGATTTGC 59.406 47.619 15.94 13.27 36.56 3.68
640 774 0.526310 GCAGTGCATCGATCGTCTGA 60.526 55.000 15.94 0.00 0.00 3.27
652 786 4.502282 CGTTAAAAATCAGTTTGCAGTGCA 59.498 37.500 15.37 15.37 36.47 4.57
655 789 3.728718 CGCGTTAAAAATCAGTTTGCAGT 59.271 39.130 0.00 0.00 0.00 4.40
740 874 0.862701 CGTCGAACGCGGCTATGTAA 60.863 55.000 12.47 0.00 40.67 2.41
741 875 1.297819 CGTCGAACGCGGCTATGTA 60.298 57.895 12.47 0.00 40.67 2.29
792 926 1.586042 GCTCTTCTCTCGCTGCTCG 60.586 63.158 0.00 0.00 40.15 5.03
793 927 0.526096 CTGCTCTTCTCTCGCTGCTC 60.526 60.000 0.00 0.00 0.00 4.26
794 928 1.512230 CTGCTCTTCTCTCGCTGCT 59.488 57.895 0.00 0.00 0.00 4.24
795 929 1.519013 CCTGCTCTTCTCTCGCTGC 60.519 63.158 0.00 0.00 0.00 5.25
796 930 0.246086 AACCTGCTCTTCTCTCGCTG 59.754 55.000 0.00 0.00 0.00 5.18
797 931 1.840737 TAACCTGCTCTTCTCTCGCT 58.159 50.000 0.00 0.00 0.00 4.93
799 933 2.801342 GCCATAACCTGCTCTTCTCTCG 60.801 54.545 0.00 0.00 0.00 4.04
801 935 2.093235 GTGCCATAACCTGCTCTTCTCT 60.093 50.000 0.00 0.00 0.00 3.10
803 937 1.065126 GGTGCCATAACCTGCTCTTCT 60.065 52.381 0.00 0.00 37.24 2.85
806 940 1.221840 CGGTGCCATAACCTGCTCT 59.778 57.895 0.00 0.00 38.14 4.09
808 942 2.438434 GCGGTGCCATAACCTGCT 60.438 61.111 0.00 0.00 38.14 4.24
826 960 4.796231 CGACAGGAAGCCGGTCCG 62.796 72.222 3.60 3.60 43.89 4.79
828 962 4.373116 TGCGACAGGAAGCCGGTC 62.373 66.667 1.90 6.67 43.46 4.79
829 963 4.379243 CTGCGACAGGAAGCCGGT 62.379 66.667 1.90 0.00 34.02 5.28
830 964 4.379243 ACTGCGACAGGAAGCCGG 62.379 66.667 0.00 0.00 35.51 6.13
831 965 3.114616 CACTGCGACAGGAAGCCG 61.115 66.667 10.80 0.00 35.51 5.52
834 968 1.864862 CTTGCACTGCGACAGGAAG 59.135 57.895 10.80 6.51 35.51 3.46
835 969 2.253758 GCTTGCACTGCGACAGGAA 61.254 57.895 10.80 1.70 35.51 3.36
836 970 2.666190 GCTTGCACTGCGACAGGA 60.666 61.111 10.80 0.00 35.51 3.86
837 971 3.730761 GGCTTGCACTGCGACAGG 61.731 66.667 10.80 2.65 35.51 4.00
838 972 4.081030 CGGCTTGCACTGCGACAG 62.081 66.667 5.47 5.47 37.52 3.51
892 1026 2.202824 CCGGACGCGGCTTGAATA 60.203 61.111 13.91 0.00 0.00 1.75
951 1269 2.835705 CGATCCGGTCACGCTAGCT 61.836 63.158 13.93 0.00 39.22 3.32
975 1293 7.414540 GCTTTATCGTTGTTTTCTCCTGATGAT 60.415 37.037 0.00 0.00 0.00 2.45
976 1294 6.128282 GCTTTATCGTTGTTTTCTCCTGATGA 60.128 38.462 0.00 0.00 0.00 2.92
977 1295 6.024049 GCTTTATCGTTGTTTTCTCCTGATG 58.976 40.000 0.00 0.00 0.00 3.07
978 1296 5.123979 GGCTTTATCGTTGTTTTCTCCTGAT 59.876 40.000 0.00 0.00 0.00 2.90
979 1297 4.454504 GGCTTTATCGTTGTTTTCTCCTGA 59.545 41.667 0.00 0.00 0.00 3.86
980 1298 4.215399 TGGCTTTATCGTTGTTTTCTCCTG 59.785 41.667 0.00 0.00 0.00 3.86
981 1299 4.394729 TGGCTTTATCGTTGTTTTCTCCT 58.605 39.130 0.00 0.00 0.00 3.69
982 1300 4.215613 ACTGGCTTTATCGTTGTTTTCTCC 59.784 41.667 0.00 0.00 0.00 3.71
1000 1318 1.602311 TAGCGCCTACTACTACTGGC 58.398 55.000 2.29 0.00 41.76 4.85
1034 1352 5.281727 GGCACGAAGAAGTTTGAAGAAATT 58.718 37.500 0.00 0.00 0.00 1.82
1035 1353 4.860072 GGCACGAAGAAGTTTGAAGAAAT 58.140 39.130 0.00 0.00 0.00 2.17
1036 1354 4.287238 GGCACGAAGAAGTTTGAAGAAA 57.713 40.909 0.00 0.00 0.00 2.52
1037 1355 3.963383 GGCACGAAGAAGTTTGAAGAA 57.037 42.857 0.00 0.00 0.00 2.52
1078 1429 1.008538 CGTGCCTTGGTGAAACAGC 60.009 57.895 0.00 0.00 39.98 4.40
1082 1433 1.750780 TGTGCGTGCCTTGGTGAAA 60.751 52.632 0.00 0.00 0.00 2.69
1099 1450 2.328099 GGTGAAGAAGGGCTGCGTG 61.328 63.158 0.00 0.00 0.00 5.34
1137 1488 2.514824 GATGAGCCCCGCAACCTC 60.515 66.667 0.00 0.00 0.00 3.85
1172 1523 2.181021 CTGAGCCGGTCGGTGTAC 59.819 66.667 11.25 0.00 37.65 2.90
1176 1527 4.070552 GAAGCTGAGCCGGTCGGT 62.071 66.667 11.25 0.00 37.65 4.69
1380 1731 4.093952 CCAGCTGCCGAAGTTGCG 62.094 66.667 8.66 0.00 35.87 4.85
1391 1742 1.513158 CTCGTACAGGACCCAGCTG 59.487 63.158 6.78 6.78 0.00 4.24
1403 1754 1.731969 GTCGTGGTGGTGCTCGTAC 60.732 63.158 0.00 0.00 0.00 3.67
1424 1775 0.528684 GCCGCCTGTAGCTCTTGTAG 60.529 60.000 0.00 0.00 40.39 2.74
1425 1776 1.515954 GCCGCCTGTAGCTCTTGTA 59.484 57.895 0.00 0.00 40.39 2.41
1428 1779 2.427245 ATCGCCGCCTGTAGCTCTT 61.427 57.895 0.00 0.00 40.39 2.85
1430 1781 2.659897 CATCGCCGCCTGTAGCTC 60.660 66.667 0.00 0.00 40.39 4.09
1432 1783 4.899239 AGCATCGCCGCCTGTAGC 62.899 66.667 0.00 0.00 38.52 3.58
1442 1793 0.655626 GATTACGCAGCAAGCATCGC 60.656 55.000 0.00 0.00 46.13 4.58
1445 1796 1.755179 AAGGATTACGCAGCAAGCAT 58.245 45.000 0.00 0.00 46.13 3.79
1472 1823 3.496131 GGTATGTGCACGGTGGCG 61.496 66.667 13.13 0.00 36.28 5.69
1538 1889 0.093705 GCGAGCACACGATCAACTTC 59.906 55.000 0.00 0.00 35.09 3.01
1621 1972 1.006102 AACGACCACGAGAAGCCAG 60.006 57.895 0.00 0.00 42.66 4.85
1622 1973 1.006571 GAACGACCACGAGAAGCCA 60.007 57.895 0.00 0.00 42.66 4.75
1623 1974 1.006571 TGAACGACCACGAGAAGCC 60.007 57.895 0.00 0.00 42.66 4.35
1640 1991 8.372600 GTTATATAACTATCATCAGCCGGGCTG 61.373 44.444 37.43 37.43 43.60 4.85
1663 2014 3.688694 AGGCAATGTCCTTGTACGTTA 57.311 42.857 0.00 0.00 37.18 3.18
1690 2041 3.795623 TGAGAGCGTATAGGTTTCCAC 57.204 47.619 0.00 0.00 31.27 4.02
1831 2192 4.392047 TGCCAGATGATGATGATACAACC 58.608 43.478 0.00 0.00 0.00 3.77
1840 2201 3.390311 TCAGTAGCTTGCCAGATGATGAT 59.610 43.478 0.00 0.00 0.00 2.45
1849 2210 0.677731 GCACCATCAGTAGCTTGCCA 60.678 55.000 0.00 0.00 0.00 4.92
1870 2231 3.732048 TTAGGAGGTTCAATTCCCCAC 57.268 47.619 0.00 0.00 33.83 4.61
1879 2240 5.617528 TTACCGCATAATTAGGAGGTTCA 57.382 39.130 26.66 13.80 40.50 3.18
1931 2292 1.734477 CTGCCTCGAACACGTCCAG 60.734 63.158 0.00 0.00 0.00 3.86
1963 2324 1.293498 CTTGACCTCGGACCACTGG 59.707 63.158 0.00 0.00 0.00 4.00
1972 2333 1.376037 GCCCAAGTCCTTGACCTCG 60.376 63.158 8.59 0.00 42.93 4.63
2055 2416 1.202722 ACACACGGTTCCCTCGAAATT 60.203 47.619 0.00 0.00 0.00 1.82
2162 2523 3.239254 CGCTCTTAACGTCATACACACA 58.761 45.455 0.00 0.00 0.00 3.72
2163 2524 2.597305 CCGCTCTTAACGTCATACACAC 59.403 50.000 0.00 0.00 0.00 3.82
2176 2537 2.821378 TGCAGTAACTGTACCGCTCTTA 59.179 45.455 0.00 0.00 35.10 2.10
2368 2747 1.134521 TGTCCACCATACAGATTCGCC 60.135 52.381 0.00 0.00 0.00 5.54
2371 2750 6.757897 TTTCATTGTCCACCATACAGATTC 57.242 37.500 0.00 0.00 0.00 2.52
2412 2791 9.308318 AGTGACCACAACAAAAATATTTACAAC 57.692 29.630 0.01 0.00 0.00 3.32
2555 3360 4.286320 ATGGGATCGTCGCTCGGC 62.286 66.667 0.00 0.00 40.32 5.54
2599 3417 7.509797 CGCCTTTCTTTTTGCCTATTTTAAAG 58.490 34.615 0.00 0.00 0.00 1.85
2624 3443 1.186200 GGGTTCAATTCCCCTTCAGC 58.814 55.000 0.00 0.00 39.08 4.26
2625 3444 2.041620 TCTGGGTTCAATTCCCCTTCAG 59.958 50.000 6.06 0.00 44.00 3.02
2761 3580 8.458843 CGGTTTGGATTTTCAGTTACTAATCAT 58.541 33.333 8.15 0.00 0.00 2.45
2880 3705 8.483307 AAATAACGTGATAATTTACTCACCGT 57.517 30.769 0.00 7.80 38.83 4.83
3134 3962 7.566569 TGATAAAAACGTATCCCTGATAACCA 58.433 34.615 0.00 0.00 30.62 3.67
3149 3977 6.277605 ACCCAGGAAAAAGTTGATAAAAACG 58.722 36.000 0.00 0.00 35.13 3.60
3325 4155 1.816074 AACGGTAATTCACGCACCAT 58.184 45.000 2.05 0.00 32.32 3.55


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

AutoCloner maintained by Alex Coulton.