Multiple sequence alignment - TraesCS7D01G136600

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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 TraesCS7D01G136600 chr7D 100.000 2096 0 0 1 2096 87755233 87757328 0.000000e+00 3871.0
1 TraesCS7D01G136600 chr7D 96.296 945 27 8 1156 2096 122527010 122526070 0.000000e+00 1544.0
2 TraesCS7D01G136600 chr7D 94.188 499 18 8 369 862 122527504 122527012 0.000000e+00 750.0
3 TraesCS7D01G136600 chr7D 91.456 316 18 4 3 318 95360130 95360436 1.920000e-115 425.0
4 TraesCS7D01G136600 chr2D 96.565 1805 32 11 318 2096 37533219 37531419 0.000000e+00 2963.0
5 TraesCS7D01G136600 chr2D 94.932 888 30 11 1176 2053 651641880 651640998 0.000000e+00 1376.0
6 TraesCS7D01G136600 chr2D 91.489 564 25 9 317 862 651642452 651641894 0.000000e+00 754.0
7 TraesCS7D01G136600 chr7A 94.853 952 35 10 1153 2096 704840652 704841597 0.000000e+00 1474.0
8 TraesCS7D01G136600 chr7A 90.948 939 70 11 1153 2083 630551292 630552223 0.000000e+00 1249.0
9 TraesCS7D01G136600 chr7A 90.147 954 76 14 1153 2096 411539079 411540024 0.000000e+00 1225.0
10 TraesCS7D01G136600 chr7A 89.617 549 41 12 321 862 411538541 411539080 0.000000e+00 684.0
11 TraesCS7D01G136600 chr6B 92.977 954 48 14 1156 2096 345630811 345629864 0.000000e+00 1373.0
12 TraesCS7D01G136600 chr6B 87.634 558 35 13 321 862 636976133 636975594 2.950000e-173 617.0
13 TraesCS7D01G136600 chr6B 87.143 70 8 1 304 372 616426366 616426297 6.200000e-11 78.7
14 TraesCS7D01G136600 chr5B 94.966 874 28 11 1158 2020 507996095 507995227 0.000000e+00 1356.0
15 TraesCS7D01G136600 chr5B 88.768 552 43 17 324 862 571508710 571508165 0.000000e+00 658.0
16 TraesCS7D01G136600 chr5B 83.533 583 28 17 306 869 507996624 507996091 1.120000e-132 483.0
17 TraesCS7D01G136600 chr5B 82.953 569 52 24 324 854 488217872 488217311 2.430000e-129 472.0
18 TraesCS7D01G136600 chr5B 93.151 292 17 1 4 295 663376697 663376985 1.920000e-115 425.0
19 TraesCS7D01G136600 chr4D 91.909 927 56 19 1153 2073 368504806 368505719 0.000000e+00 1279.0
20 TraesCS7D01G136600 chr4D 90.220 501 33 10 370 862 368504315 368504807 6.310000e-180 640.0
21 TraesCS7D01G136600 chr3D 89.655 551 37 12 317 862 93971885 93972420 0.000000e+00 684.0
22 TraesCS7D01G136600 chr2B 88.406 552 46 13 317 862 723051663 723051124 0.000000e+00 649.0
23 TraesCS7D01G136600 chr6A 86.429 560 42 21 321 862 188001857 188002400 1.080000e-162 582.0
24 TraesCS7D01G136600 chrUn 99.351 308 1 1 846 1152 404958511 404958818 6.530000e-155 556.0
25 TraesCS7D01G136600 chrUn 98.697 307 3 1 846 1152 317472913 317472608 5.090000e-151 544.0
26 TraesCS7D01G136600 chr3B 99.349 307 2 0 846 1152 201506852 201507158 6.530000e-155 556.0
27 TraesCS7D01G136600 chr3B 91.746 315 23 3 4 318 809978925 809979236 3.190000e-118 435.0
28 TraesCS7D01G136600 chr3B 90.411 292 25 3 3 294 809974018 809974306 4.220000e-102 381.0
29 TraesCS7D01G136600 chr1D 98.382 309 3 1 846 1152 394179187 394179495 1.830000e-150 542.0
30 TraesCS7D01G136600 chr1D 98.371 307 3 1 846 1152 254489976 254490280 2.370000e-149 538.0
31 TraesCS7D01G136600 chr6D 98.371 307 4 1 846 1152 431400301 431400606 2.370000e-149 538.0
32 TraesCS7D01G136600 chr5D 98.371 307 3 2 846 1152 6207546 6207242 2.370000e-149 538.0
33 TraesCS7D01G136600 chr5D 97.764 313 1 1 846 1152 554200613 554200925 3.060000e-148 534.0
34 TraesCS7D01G136600 chr7B 81.834 567 40 15 319 854 705733530 705732996 3.220000e-113 418.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G136600 chr7D 87755233 87757328 2095 False 3871.0 3871 100.0000 1 2096 1 chr7D.!!$F1 2095
1 TraesCS7D01G136600 chr7D 122526070 122527504 1434 True 1147.0 1544 95.2420 369 2096 2 chr7D.!!$R1 1727
2 TraesCS7D01G136600 chr2D 37531419 37533219 1800 True 2963.0 2963 96.5650 318 2096 1 chr2D.!!$R1 1778
3 TraesCS7D01G136600 chr2D 651640998 651642452 1454 True 1065.0 1376 93.2105 317 2053 2 chr2D.!!$R2 1736
4 TraesCS7D01G136600 chr7A 704840652 704841597 945 False 1474.0 1474 94.8530 1153 2096 1 chr7A.!!$F2 943
5 TraesCS7D01G136600 chr7A 630551292 630552223 931 False 1249.0 1249 90.9480 1153 2083 1 chr7A.!!$F1 930
6 TraesCS7D01G136600 chr7A 411538541 411540024 1483 False 954.5 1225 89.8820 321 2096 2 chr7A.!!$F3 1775
7 TraesCS7D01G136600 chr6B 345629864 345630811 947 True 1373.0 1373 92.9770 1156 2096 1 chr6B.!!$R1 940
8 TraesCS7D01G136600 chr6B 636975594 636976133 539 True 617.0 617 87.6340 321 862 1 chr6B.!!$R3 541
9 TraesCS7D01G136600 chr5B 507995227 507996624 1397 True 919.5 1356 89.2495 306 2020 2 chr5B.!!$R3 1714
10 TraesCS7D01G136600 chr5B 571508165 571508710 545 True 658.0 658 88.7680 324 862 1 chr5B.!!$R2 538
11 TraesCS7D01G136600 chr5B 488217311 488217872 561 True 472.0 472 82.9530 324 854 1 chr5B.!!$R1 530
12 TraesCS7D01G136600 chr4D 368504315 368505719 1404 False 959.5 1279 91.0645 370 2073 2 chr4D.!!$F1 1703
13 TraesCS7D01G136600 chr3D 93971885 93972420 535 False 684.0 684 89.6550 317 862 1 chr3D.!!$F1 545
14 TraesCS7D01G136600 chr2B 723051124 723051663 539 True 649.0 649 88.4060 317 862 1 chr2B.!!$R1 545
15 TraesCS7D01G136600 chr6A 188001857 188002400 543 False 582.0 582 86.4290 321 862 1 chr6A.!!$F1 541
16 TraesCS7D01G136600 chr7B 705732996 705733530 534 True 418.0 418 81.8340 319 854 1 chr7B.!!$R1 535

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
274 275 0.174845 TGGTATGTTTCGCCTCCGAG 59.825 55.0 0.0 0.0 45.35 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2112 0.396435 TGTCCGAGTTGCAAGTCCAT 59.604 50.0 25.03 0.0 0.0 3.41 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 9.769093 CTGTCTAGGATTAAAATGGTTTTTACG 57.231 33.333 0.00 0.00 37.10 3.18
27 28 9.287373 TGTCTAGGATTAAAATGGTTTTTACGT 57.713 29.630 0.00 0.00 37.10 3.57
28 29 9.550811 GTCTAGGATTAAAATGGTTTTTACGTG 57.449 33.333 0.00 0.00 37.10 4.49
29 30 8.238631 TCTAGGATTAAAATGGTTTTTACGTGC 58.761 33.333 0.00 0.00 37.10 5.34
30 31 5.859648 AGGATTAAAATGGTTTTTACGTGCG 59.140 36.000 0.00 0.00 37.10 5.34
31 32 5.061187 GGATTAAAATGGTTTTTACGTGCGG 59.939 40.000 0.00 0.00 37.10 5.69
32 33 2.425578 AAATGGTTTTTACGTGCGGG 57.574 45.000 0.00 0.00 0.00 6.13
33 34 1.606903 AATGGTTTTTACGTGCGGGA 58.393 45.000 0.00 0.00 0.00 5.14
34 35 1.828979 ATGGTTTTTACGTGCGGGAT 58.171 45.000 0.00 0.00 0.00 3.85
35 36 0.875728 TGGTTTTTACGTGCGGGATG 59.124 50.000 0.00 0.00 0.00 3.51
36 37 0.876399 GGTTTTTACGTGCGGGATGT 59.124 50.000 0.00 0.00 0.00 3.06
37 38 1.400500 GGTTTTTACGTGCGGGATGTG 60.400 52.381 4.47 0.00 0.00 3.21
38 39 1.264826 GTTTTTACGTGCGGGATGTGT 59.735 47.619 4.47 0.00 0.00 3.72
39 40 2.452295 TTTTACGTGCGGGATGTGTA 57.548 45.000 4.47 0.00 0.00 2.90
40 41 1.712401 TTTACGTGCGGGATGTGTAC 58.288 50.000 4.47 0.00 0.00 2.90
41 42 0.456482 TTACGTGCGGGATGTGTACG 60.456 55.000 4.47 2.19 40.30 3.67
42 43 1.304509 TACGTGCGGGATGTGTACGA 61.305 55.000 10.37 0.00 38.08 3.43
43 44 1.872234 CGTGCGGGATGTGTACGAG 60.872 63.158 0.00 0.00 36.94 4.18
44 45 2.165301 GTGCGGGATGTGTACGAGC 61.165 63.158 0.00 0.00 0.00 5.03
45 46 2.183300 GCGGGATGTGTACGAGCA 59.817 61.111 0.00 0.00 0.00 4.26
46 47 1.447140 GCGGGATGTGTACGAGCAA 60.447 57.895 0.00 0.00 0.00 3.91
47 48 1.017177 GCGGGATGTGTACGAGCAAA 61.017 55.000 0.00 0.00 0.00 3.68
48 49 1.651987 CGGGATGTGTACGAGCAAAT 58.348 50.000 0.00 0.00 0.00 2.32
49 50 2.006888 CGGGATGTGTACGAGCAAATT 58.993 47.619 0.00 0.00 0.00 1.82
50 51 2.223021 CGGGATGTGTACGAGCAAATTG 60.223 50.000 0.00 0.00 0.00 2.32
51 52 3.006940 GGGATGTGTACGAGCAAATTGA 58.993 45.455 0.00 0.00 0.00 2.57
52 53 3.181510 GGGATGTGTACGAGCAAATTGAC 60.182 47.826 0.00 0.00 0.00 3.18
53 54 3.181510 GGATGTGTACGAGCAAATTGACC 60.182 47.826 0.00 0.00 0.00 4.02
54 55 3.120321 TGTGTACGAGCAAATTGACCT 57.880 42.857 0.00 0.00 0.00 3.85
55 56 2.805671 TGTGTACGAGCAAATTGACCTG 59.194 45.455 0.00 0.00 0.00 4.00
56 57 2.806244 GTGTACGAGCAAATTGACCTGT 59.194 45.455 0.00 0.00 0.00 4.00
57 58 3.064207 TGTACGAGCAAATTGACCTGTC 58.936 45.455 0.00 0.00 0.00 3.51
58 59 2.254546 ACGAGCAAATTGACCTGTCA 57.745 45.000 0.00 0.00 37.91 3.58
59 60 1.873591 ACGAGCAAATTGACCTGTCAC 59.126 47.619 0.00 0.00 39.66 3.67
60 61 1.136252 CGAGCAAATTGACCTGTCACG 60.136 52.381 0.00 0.00 39.66 4.35
61 62 1.873591 GAGCAAATTGACCTGTCACGT 59.126 47.619 0.00 0.00 39.66 4.49
62 63 1.603802 AGCAAATTGACCTGTCACGTG 59.396 47.619 9.94 9.94 39.66 4.49
63 64 1.333619 GCAAATTGACCTGTCACGTGT 59.666 47.619 16.51 0.00 39.66 4.49
64 65 2.546368 GCAAATTGACCTGTCACGTGTA 59.454 45.455 16.51 5.27 39.66 2.90
65 66 3.606153 GCAAATTGACCTGTCACGTGTAC 60.606 47.826 16.51 12.72 39.66 2.90
66 67 3.462483 AATTGACCTGTCACGTGTACA 57.538 42.857 16.51 16.43 39.66 2.90
67 68 3.678056 ATTGACCTGTCACGTGTACAT 57.322 42.857 16.51 4.87 39.66 2.29
68 69 4.794278 ATTGACCTGTCACGTGTACATA 57.206 40.909 16.51 0.00 39.66 2.29
69 70 4.794278 TTGACCTGTCACGTGTACATAT 57.206 40.909 16.51 9.17 39.66 1.78
70 71 4.794278 TGACCTGTCACGTGTACATATT 57.206 40.909 16.51 5.87 34.14 1.28
71 72 5.142061 TGACCTGTCACGTGTACATATTT 57.858 39.130 16.51 3.69 34.14 1.40
72 73 6.270156 TGACCTGTCACGTGTACATATTTA 57.730 37.500 16.51 2.77 34.14 1.40
73 74 6.689554 TGACCTGTCACGTGTACATATTTAA 58.310 36.000 16.51 1.16 34.14 1.52
74 75 6.809689 TGACCTGTCACGTGTACATATTTAAG 59.190 38.462 16.51 5.19 34.14 1.85
75 76 6.103997 ACCTGTCACGTGTACATATTTAAGG 58.896 40.000 16.51 14.55 0.00 2.69
76 77 5.006358 CCTGTCACGTGTACATATTTAAGGC 59.994 44.000 16.51 0.00 0.00 4.35
77 78 5.480205 TGTCACGTGTACATATTTAAGGCA 58.520 37.500 16.51 0.00 0.00 4.75
78 79 5.932883 TGTCACGTGTACATATTTAAGGCAA 59.067 36.000 16.51 0.00 0.00 4.52
79 80 6.128499 TGTCACGTGTACATATTTAAGGCAAC 60.128 38.462 16.51 0.20 0.00 4.17
80 81 5.352016 TCACGTGTACATATTTAAGGCAACC 59.648 40.000 16.51 0.00 37.17 3.77
81 82 5.353123 CACGTGTACATATTTAAGGCAACCT 59.647 40.000 7.58 0.00 33.87 3.50
82 83 6.535865 CACGTGTACATATTTAAGGCAACCTA 59.464 38.462 7.58 0.00 31.13 3.08
83 84 7.225931 CACGTGTACATATTTAAGGCAACCTAT 59.774 37.037 7.58 0.00 31.13 2.57
84 85 7.225931 ACGTGTACATATTTAAGGCAACCTATG 59.774 37.037 0.00 0.00 31.13 2.23
103 104 2.849880 GCATATGCACGTTCACCAAT 57.150 45.000 22.84 0.00 41.59 3.16
104 105 3.149436 GCATATGCACGTTCACCAATT 57.851 42.857 22.84 0.00 41.59 2.32
105 106 2.853594 GCATATGCACGTTCACCAATTG 59.146 45.455 22.84 0.00 41.59 2.32
106 107 3.427368 GCATATGCACGTTCACCAATTGA 60.427 43.478 22.84 0.00 41.59 2.57
107 108 4.734402 GCATATGCACGTTCACCAATTGAT 60.734 41.667 22.84 0.00 41.59 2.57
108 109 5.505489 GCATATGCACGTTCACCAATTGATA 60.505 40.000 22.84 0.00 41.59 2.15
109 110 3.822594 TGCACGTTCACCAATTGATAC 57.177 42.857 7.12 0.00 32.84 2.24
110 111 2.158645 TGCACGTTCACCAATTGATACG 59.841 45.455 7.12 12.46 41.03 3.06
111 112 2.769376 CACGTTCACCAATTGATACGC 58.231 47.619 7.12 0.00 39.93 4.42
112 113 2.158645 CACGTTCACCAATTGATACGCA 59.841 45.455 7.12 0.00 39.93 5.24
113 114 3.006940 ACGTTCACCAATTGATACGCAT 58.993 40.909 7.12 0.00 39.93 4.73
114 115 3.063452 ACGTTCACCAATTGATACGCATC 59.937 43.478 7.12 0.00 39.93 3.91
115 116 3.607439 GTTCACCAATTGATACGCATCG 58.393 45.455 7.12 0.00 32.84 3.84
116 117 2.899976 TCACCAATTGATACGCATCGT 58.100 42.857 7.12 0.00 44.35 3.73
117 118 2.607180 TCACCAATTGATACGCATCGTG 59.393 45.455 7.12 3.28 41.39 4.35
118 119 1.939934 ACCAATTGATACGCATCGTGG 59.060 47.619 7.12 9.96 41.39 4.94
119 120 1.264020 CCAATTGATACGCATCGTGGG 59.736 52.381 7.12 1.58 41.39 4.61
120 121 2.209273 CAATTGATACGCATCGTGGGA 58.791 47.619 0.00 0.00 41.39 4.37
121 122 1.865865 ATTGATACGCATCGTGGGAC 58.134 50.000 1.77 2.36 41.39 4.46
122 123 0.533032 TTGATACGCATCGTGGGACA 59.467 50.000 1.77 4.27 41.39 4.02
134 135 3.390003 TGGGACACGTTTTGGACTC 57.610 52.632 0.00 0.00 0.00 3.36
135 136 0.834612 TGGGACACGTTTTGGACTCT 59.165 50.000 0.00 0.00 0.00 3.24
136 137 1.210967 TGGGACACGTTTTGGACTCTT 59.789 47.619 0.00 0.00 0.00 2.85
137 138 2.435069 TGGGACACGTTTTGGACTCTTA 59.565 45.455 0.00 0.00 0.00 2.10
138 139 3.118334 TGGGACACGTTTTGGACTCTTAA 60.118 43.478 0.00 0.00 0.00 1.85
139 140 4.070009 GGGACACGTTTTGGACTCTTAAT 58.930 43.478 0.00 0.00 0.00 1.40
140 141 4.083484 GGGACACGTTTTGGACTCTTAATG 60.083 45.833 0.00 0.00 0.00 1.90
141 142 4.464112 GACACGTTTTGGACTCTTAATGC 58.536 43.478 0.00 0.00 0.00 3.56
142 143 3.880490 ACACGTTTTGGACTCTTAATGCA 59.120 39.130 0.00 0.00 0.00 3.96
143 144 4.219033 CACGTTTTGGACTCTTAATGCAC 58.781 43.478 0.00 0.00 0.00 4.57
144 145 3.880490 ACGTTTTGGACTCTTAATGCACA 59.120 39.130 0.00 0.00 0.00 4.57
145 146 4.219033 CGTTTTGGACTCTTAATGCACAC 58.781 43.478 0.00 0.00 0.00 3.82
146 147 4.219033 GTTTTGGACTCTTAATGCACACG 58.781 43.478 0.00 0.00 0.00 4.49
147 148 2.093306 TGGACTCTTAATGCACACGG 57.907 50.000 0.00 0.00 0.00 4.94
148 149 1.621317 TGGACTCTTAATGCACACGGA 59.379 47.619 0.00 0.00 0.00 4.69
149 150 2.236146 TGGACTCTTAATGCACACGGAT 59.764 45.455 0.00 0.00 0.00 4.18
150 151 3.270877 GGACTCTTAATGCACACGGATT 58.729 45.455 0.00 0.00 36.99 3.01
151 152 3.309954 GGACTCTTAATGCACACGGATTC 59.690 47.826 0.00 0.00 34.62 2.52
152 153 4.184629 GACTCTTAATGCACACGGATTCT 58.815 43.478 0.00 0.00 34.62 2.40
153 154 5.339008 ACTCTTAATGCACACGGATTCTA 57.661 39.130 0.00 0.00 34.62 2.10
154 155 5.109903 ACTCTTAATGCACACGGATTCTAC 58.890 41.667 0.00 0.00 34.62 2.59
155 156 4.439057 TCTTAATGCACACGGATTCTACC 58.561 43.478 0.00 0.00 34.62 3.18
166 167 4.842139 CGGATTCTACCGTCAAAAAGAG 57.158 45.455 0.00 0.00 46.70 2.85
167 168 3.617263 CGGATTCTACCGTCAAAAAGAGG 59.383 47.826 0.00 0.00 46.70 3.69
171 172 4.058797 CCGTCAAAAAGAGGGCGT 57.941 55.556 0.00 0.00 44.55 5.68
172 173 3.220447 CCGTCAAAAAGAGGGCGTA 57.780 52.632 0.00 0.00 44.55 4.42
173 174 0.794473 CCGTCAAAAAGAGGGCGTAC 59.206 55.000 0.00 0.00 44.55 3.67
174 175 1.607251 CCGTCAAAAAGAGGGCGTACT 60.607 52.381 0.00 0.00 44.55 2.73
175 176 2.353011 CCGTCAAAAAGAGGGCGTACTA 60.353 50.000 0.00 0.00 44.55 1.82
176 177 3.518590 CGTCAAAAAGAGGGCGTACTAT 58.481 45.455 0.00 0.00 0.00 2.12
177 178 4.440525 CCGTCAAAAAGAGGGCGTACTATA 60.441 45.833 0.00 0.00 44.55 1.31
178 179 4.738740 CGTCAAAAAGAGGGCGTACTATAG 59.261 45.833 0.00 0.00 0.00 1.31
179 180 5.449588 CGTCAAAAAGAGGGCGTACTATAGA 60.450 44.000 6.78 0.00 0.00 1.98
180 181 6.335777 GTCAAAAAGAGGGCGTACTATAGAA 58.664 40.000 6.78 0.00 0.00 2.10
181 182 6.815142 GTCAAAAAGAGGGCGTACTATAGAAA 59.185 38.462 6.78 0.00 0.00 2.52
182 183 7.010275 GTCAAAAAGAGGGCGTACTATAGAAAG 59.990 40.741 6.78 0.00 0.00 2.62
183 184 6.786967 AAAAGAGGGCGTACTATAGAAAGA 57.213 37.500 6.78 0.00 0.00 2.52
184 185 6.980416 AAAGAGGGCGTACTATAGAAAGAT 57.020 37.500 6.78 0.00 0.00 2.40
185 186 5.968528 AGAGGGCGTACTATAGAAAGATG 57.031 43.478 6.78 0.00 0.00 2.90
186 187 5.632118 AGAGGGCGTACTATAGAAAGATGA 58.368 41.667 6.78 0.00 0.00 2.92
187 188 6.069331 AGAGGGCGTACTATAGAAAGATGAA 58.931 40.000 6.78 0.00 0.00 2.57
188 189 6.016108 AGAGGGCGTACTATAGAAAGATGAAC 60.016 42.308 6.78 0.00 0.00 3.18
189 190 5.597182 AGGGCGTACTATAGAAAGATGAACA 59.403 40.000 6.78 0.00 0.00 3.18
190 191 6.267928 AGGGCGTACTATAGAAAGATGAACAT 59.732 38.462 6.78 0.00 0.00 2.71
191 192 7.450634 AGGGCGTACTATAGAAAGATGAACATA 59.549 37.037 6.78 0.00 0.00 2.29
192 193 8.251721 GGGCGTACTATAGAAAGATGAACATAT 58.748 37.037 6.78 0.00 0.00 1.78
193 194 9.077674 GGCGTACTATAGAAAGATGAACATATG 57.922 37.037 6.78 0.00 0.00 1.78
194 195 9.841880 GCGTACTATAGAAAGATGAACATATGA 57.158 33.333 10.38 0.00 0.00 2.15
201 202 6.054295 AGAAAGATGAACATATGACCTCTGC 58.946 40.000 10.38 7.14 0.00 4.26
202 203 5.363562 AAGATGAACATATGACCTCTGCA 57.636 39.130 10.38 0.00 0.00 4.41
203 204 5.563876 AGATGAACATATGACCTCTGCAT 57.436 39.130 10.38 0.00 0.00 3.96
204 205 5.938279 AGATGAACATATGACCTCTGCATT 58.062 37.500 10.38 0.00 0.00 3.56
205 206 5.763698 AGATGAACATATGACCTCTGCATTG 59.236 40.000 10.38 0.00 0.00 2.82
206 207 5.101648 TGAACATATGACCTCTGCATTGA 57.898 39.130 10.38 0.00 0.00 2.57
207 208 5.499313 TGAACATATGACCTCTGCATTGAA 58.501 37.500 10.38 0.00 0.00 2.69
208 209 6.124340 TGAACATATGACCTCTGCATTGAAT 58.876 36.000 10.38 0.00 0.00 2.57
209 210 6.604396 TGAACATATGACCTCTGCATTGAATT 59.396 34.615 10.38 0.00 0.00 2.17
210 211 6.387041 ACATATGACCTCTGCATTGAATTG 57.613 37.500 10.38 0.00 0.00 2.32
211 212 5.301045 ACATATGACCTCTGCATTGAATTGG 59.699 40.000 10.38 0.00 0.00 3.16
212 213 3.438216 TGACCTCTGCATTGAATTGGA 57.562 42.857 0.00 0.00 0.00 3.53
213 214 3.349927 TGACCTCTGCATTGAATTGGAG 58.650 45.455 0.00 0.00 36.49 3.86
214 215 3.009363 TGACCTCTGCATTGAATTGGAGA 59.991 43.478 0.00 0.00 41.15 3.71
215 216 3.350833 ACCTCTGCATTGAATTGGAGAC 58.649 45.455 0.00 0.00 38.91 3.36
216 217 2.353889 CCTCTGCATTGAATTGGAGACG 59.646 50.000 0.00 0.00 38.91 4.18
217 218 3.005554 CTCTGCATTGAATTGGAGACGT 58.994 45.455 0.00 0.00 38.91 4.34
218 219 4.183865 CTCTGCATTGAATTGGAGACGTA 58.816 43.478 0.00 0.00 38.91 3.57
219 220 4.574892 TCTGCATTGAATTGGAGACGTAA 58.425 39.130 0.00 0.00 38.91 3.18
220 221 5.185454 TCTGCATTGAATTGGAGACGTAAT 58.815 37.500 0.00 0.00 38.91 1.89
221 222 6.345298 TCTGCATTGAATTGGAGACGTAATA 58.655 36.000 0.00 0.00 38.91 0.98
222 223 6.992123 TCTGCATTGAATTGGAGACGTAATAT 59.008 34.615 0.00 0.00 38.91 1.28
223 224 8.147704 TCTGCATTGAATTGGAGACGTAATATA 58.852 33.333 0.00 0.00 38.91 0.86
224 225 8.669946 TGCATTGAATTGGAGACGTAATATAA 57.330 30.769 0.00 0.00 0.00 0.98
225 226 9.114952 TGCATTGAATTGGAGACGTAATATAAA 57.885 29.630 0.00 0.00 0.00 1.40
226 227 9.944663 GCATTGAATTGGAGACGTAATATAAAA 57.055 29.630 0.00 0.00 0.00 1.52
229 230 9.893634 TTGAATTGGAGACGTAATATAAAAGGA 57.106 29.630 0.00 0.00 0.00 3.36
263 264 9.736414 ACTCTATCTATACGTGTATGGTATGTT 57.264 33.333 0.00 0.00 33.00 2.71
266 267 9.486857 CTATCTATACGTGTATGGTATGTTTCG 57.513 37.037 0.00 0.00 33.00 3.46
267 268 6.144854 TCTATACGTGTATGGTATGTTTCGC 58.855 40.000 0.00 0.00 33.00 4.70
268 269 2.273557 ACGTGTATGGTATGTTTCGCC 58.726 47.619 0.00 0.00 0.00 5.54
269 270 2.093869 ACGTGTATGGTATGTTTCGCCT 60.094 45.455 0.00 0.00 0.00 5.52
270 271 2.538449 CGTGTATGGTATGTTTCGCCTC 59.462 50.000 0.00 0.00 0.00 4.70
271 272 2.870411 GTGTATGGTATGTTTCGCCTCC 59.130 50.000 0.00 0.00 0.00 4.30
272 273 2.132762 GTATGGTATGTTTCGCCTCCG 58.867 52.381 0.00 0.00 0.00 4.63
273 274 0.828022 ATGGTATGTTTCGCCTCCGA 59.172 50.000 0.00 0.00 42.66 4.55
274 275 0.174845 TGGTATGTTTCGCCTCCGAG 59.825 55.000 0.00 0.00 45.35 4.63
275 276 1.152383 GGTATGTTTCGCCTCCGAGC 61.152 60.000 0.00 0.00 45.35 5.03
276 277 0.179108 GTATGTTTCGCCTCCGAGCT 60.179 55.000 0.00 0.00 45.35 4.09
277 278 0.179111 TATGTTTCGCCTCCGAGCTG 60.179 55.000 0.00 0.00 45.35 4.24
278 279 2.048127 GTTTCGCCTCCGAGCTGT 60.048 61.111 0.00 0.00 45.35 4.40
279 280 2.095252 GTTTCGCCTCCGAGCTGTC 61.095 63.158 0.00 0.00 45.35 3.51
280 281 3.626680 TTTCGCCTCCGAGCTGTCG 62.627 63.158 0.00 0.00 45.35 4.35
289 290 4.647654 GAGCTGTCGGTCGTTGAA 57.352 55.556 0.00 0.00 0.00 2.69
290 291 2.895039 GAGCTGTCGGTCGTTGAAA 58.105 52.632 0.00 0.00 0.00 2.69
291 292 0.784778 GAGCTGTCGGTCGTTGAAAG 59.215 55.000 0.00 0.00 0.00 2.62
292 293 1.204312 GCTGTCGGTCGTTGAAAGC 59.796 57.895 1.81 1.81 39.36 3.51
293 294 1.222115 GCTGTCGGTCGTTGAAAGCT 61.222 55.000 8.54 0.00 42.32 3.74
294 295 1.933500 GCTGTCGGTCGTTGAAAGCTA 60.934 52.381 8.54 0.00 42.32 3.32
295 296 1.986378 CTGTCGGTCGTTGAAAGCTAG 59.014 52.381 0.00 0.00 0.00 3.42
296 297 1.610038 TGTCGGTCGTTGAAAGCTAGA 59.390 47.619 0.00 0.00 0.00 2.43
297 298 2.034939 TGTCGGTCGTTGAAAGCTAGAA 59.965 45.455 0.00 0.00 0.00 2.10
298 299 2.662156 GTCGGTCGTTGAAAGCTAGAAG 59.338 50.000 0.00 0.00 0.00 2.85
299 300 1.390463 CGGTCGTTGAAAGCTAGAAGC 59.610 52.381 0.00 0.00 42.84 3.86
300 301 1.732809 GGTCGTTGAAAGCTAGAAGCC 59.267 52.381 0.00 0.00 43.77 4.35
301 302 1.390463 GTCGTTGAAAGCTAGAAGCCG 59.610 52.381 0.00 0.00 43.77 5.52
302 303 0.721718 CGTTGAAAGCTAGAAGCCGG 59.278 55.000 0.00 0.00 43.77 6.13
303 304 1.809684 GTTGAAAGCTAGAAGCCGGT 58.190 50.000 1.90 0.00 43.77 5.28
304 305 2.673043 CGTTGAAAGCTAGAAGCCGGTA 60.673 50.000 1.90 0.00 43.77 4.02
311 312 7.502696 TGAAAGCTAGAAGCCGGTAATAATTA 58.497 34.615 1.90 0.00 43.77 1.40
453 478 4.335647 CCGCCTTGGTCACCAGCT 62.336 66.667 6.50 0.00 33.81 4.24
659 745 7.754625 TCTAGGCAACCAACGATTTATTTTAC 58.245 34.615 0.00 0.00 37.17 2.01
844 936 7.643569 ATGGTGAACAATGCTTTATATGACA 57.356 32.000 0.00 0.00 0.00 3.58
1612 1743 2.738846 CTGCAGTTTGTTCGCTGACTAT 59.261 45.455 5.25 0.00 34.87 2.12
1972 2112 0.803117 CTGTAGTTGCGAGTCGAGGA 59.197 55.000 18.61 0.00 0.00 3.71
1992 2132 0.249868 TGGACTTGCAACTCGGACAG 60.250 55.000 0.00 0.00 0.00 3.51
2074 2216 1.506718 CCTAGTTGCGAGTCGAGCA 59.493 57.895 18.61 2.06 43.59 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.769093 CGTAAAAACCATTTTAATCCTAGACAG 57.231 33.333 0.00 0.00 41.38 3.51
1 2 9.287373 ACGTAAAAACCATTTTAATCCTAGACA 57.713 29.630 0.00 0.00 41.38 3.41
2 3 9.550811 CACGTAAAAACCATTTTAATCCTAGAC 57.449 33.333 0.00 0.00 41.38 2.59
3 4 8.238631 GCACGTAAAAACCATTTTAATCCTAGA 58.761 33.333 0.00 0.00 41.38 2.43
4 5 7.217447 CGCACGTAAAAACCATTTTAATCCTAG 59.783 37.037 0.00 0.00 41.38 3.02
5 6 7.022384 CGCACGTAAAAACCATTTTAATCCTA 58.978 34.615 0.00 0.00 41.38 2.94
6 7 5.859648 CGCACGTAAAAACCATTTTAATCCT 59.140 36.000 0.00 0.00 41.38 3.24
7 8 5.061187 CCGCACGTAAAAACCATTTTAATCC 59.939 40.000 0.00 0.00 41.38 3.01
8 9 5.061187 CCCGCACGTAAAAACCATTTTAATC 59.939 40.000 0.00 0.00 41.38 1.75
9 10 4.924462 CCCGCACGTAAAAACCATTTTAAT 59.076 37.500 0.00 0.00 41.38 1.40
10 11 4.037208 TCCCGCACGTAAAAACCATTTTAA 59.963 37.500 0.00 0.00 41.38 1.52
11 12 3.567164 TCCCGCACGTAAAAACCATTTTA 59.433 39.130 0.00 0.00 39.42 1.52
12 13 2.361438 TCCCGCACGTAAAAACCATTTT 59.639 40.909 0.00 0.00 41.50 1.82
13 14 1.955080 TCCCGCACGTAAAAACCATTT 59.045 42.857 0.00 0.00 0.00 2.32
14 15 1.606903 TCCCGCACGTAAAAACCATT 58.393 45.000 0.00 0.00 0.00 3.16
15 16 1.470890 CATCCCGCACGTAAAAACCAT 59.529 47.619 0.00 0.00 0.00 3.55
16 17 0.875728 CATCCCGCACGTAAAAACCA 59.124 50.000 0.00 0.00 0.00 3.67
17 18 0.876399 ACATCCCGCACGTAAAAACC 59.124 50.000 0.00 0.00 0.00 3.27
18 19 1.264826 ACACATCCCGCACGTAAAAAC 59.735 47.619 0.00 0.00 0.00 2.43
19 20 1.595466 ACACATCCCGCACGTAAAAA 58.405 45.000 0.00 0.00 0.00 1.94
20 21 2.067766 GTACACATCCCGCACGTAAAA 58.932 47.619 0.00 0.00 0.00 1.52
21 22 1.712401 GTACACATCCCGCACGTAAA 58.288 50.000 0.00 0.00 0.00 2.01
22 23 0.456482 CGTACACATCCCGCACGTAA 60.456 55.000 0.00 0.00 0.00 3.18
23 24 1.137194 CGTACACATCCCGCACGTA 59.863 57.895 0.00 0.00 0.00 3.57
24 25 2.126228 CGTACACATCCCGCACGT 60.126 61.111 0.00 0.00 0.00 4.49
25 26 1.872234 CTCGTACACATCCCGCACG 60.872 63.158 0.00 0.00 0.00 5.34
26 27 2.165301 GCTCGTACACATCCCGCAC 61.165 63.158 0.00 0.00 0.00 5.34
27 28 2.161078 TTGCTCGTACACATCCCGCA 62.161 55.000 0.00 0.00 0.00 5.69
28 29 1.017177 TTTGCTCGTACACATCCCGC 61.017 55.000 0.00 0.00 0.00 6.13
29 30 1.651987 ATTTGCTCGTACACATCCCG 58.348 50.000 0.00 0.00 0.00 5.14
30 31 3.006940 TCAATTTGCTCGTACACATCCC 58.993 45.455 0.00 0.00 0.00 3.85
31 32 3.181510 GGTCAATTTGCTCGTACACATCC 60.182 47.826 0.00 0.00 0.00 3.51
32 33 3.684788 AGGTCAATTTGCTCGTACACATC 59.315 43.478 0.00 0.00 0.00 3.06
33 34 3.436704 CAGGTCAATTTGCTCGTACACAT 59.563 43.478 0.00 0.00 0.00 3.21
34 35 2.805671 CAGGTCAATTTGCTCGTACACA 59.194 45.455 0.00 0.00 0.00 3.72
35 36 2.806244 ACAGGTCAATTTGCTCGTACAC 59.194 45.455 0.00 0.00 0.00 2.90
36 37 3.064207 GACAGGTCAATTTGCTCGTACA 58.936 45.455 0.00 0.00 0.00 2.90
37 38 3.064207 TGACAGGTCAATTTGCTCGTAC 58.936 45.455 0.00 0.00 36.53 3.67
38 39 3.064207 GTGACAGGTCAATTTGCTCGTA 58.936 45.455 3.28 0.00 41.85 3.43
39 40 1.873591 GTGACAGGTCAATTTGCTCGT 59.126 47.619 3.28 0.00 41.85 4.18
40 41 1.136252 CGTGACAGGTCAATTTGCTCG 60.136 52.381 3.28 0.00 41.85 5.03
41 42 1.873591 ACGTGACAGGTCAATTTGCTC 59.126 47.619 3.28 0.00 41.85 4.26
42 43 1.603802 CACGTGACAGGTCAATTTGCT 59.396 47.619 10.90 0.00 41.85 3.91
43 44 1.333619 ACACGTGACAGGTCAATTTGC 59.666 47.619 25.01 0.00 41.85 3.68
44 45 3.558006 TGTACACGTGACAGGTCAATTTG 59.442 43.478 25.01 4.47 41.85 2.32
45 46 3.799366 TGTACACGTGACAGGTCAATTT 58.201 40.909 25.01 0.00 41.85 1.82
46 47 3.462483 TGTACACGTGACAGGTCAATT 57.538 42.857 25.01 0.00 41.85 2.32
47 48 3.678056 ATGTACACGTGACAGGTCAAT 57.322 42.857 25.01 3.48 41.85 2.57
48 49 4.794278 ATATGTACACGTGACAGGTCAA 57.206 40.909 25.01 7.29 41.85 3.18
49 50 4.794278 AATATGTACACGTGACAGGTCA 57.206 40.909 25.01 11.34 37.24 4.02
50 51 6.255020 CCTTAAATATGTACACGTGACAGGTC 59.745 42.308 25.01 6.06 0.00 3.85
51 52 6.103997 CCTTAAATATGTACACGTGACAGGT 58.896 40.000 25.01 10.39 0.00 4.00
52 53 5.006358 GCCTTAAATATGTACACGTGACAGG 59.994 44.000 25.01 16.37 0.00 4.00
53 54 5.579119 TGCCTTAAATATGTACACGTGACAG 59.421 40.000 25.01 8.56 0.00 3.51
54 55 5.480205 TGCCTTAAATATGTACACGTGACA 58.520 37.500 25.01 21.06 0.00 3.58
55 56 6.245724 GTTGCCTTAAATATGTACACGTGAC 58.754 40.000 25.01 16.06 0.00 3.67
56 57 5.352016 GGTTGCCTTAAATATGTACACGTGA 59.648 40.000 25.01 0.00 0.00 4.35
57 58 5.353123 AGGTTGCCTTAAATATGTACACGTG 59.647 40.000 15.48 15.48 0.00 4.49
58 59 5.493809 AGGTTGCCTTAAATATGTACACGT 58.506 37.500 0.00 0.00 0.00 4.49
59 60 7.572759 CATAGGTTGCCTTAAATATGTACACG 58.427 38.462 0.00 0.00 34.61 4.49
60 61 7.360361 GCATAGGTTGCCTTAAATATGTACAC 58.640 38.462 0.00 0.00 46.15 2.90
61 62 7.504924 GCATAGGTTGCCTTAAATATGTACA 57.495 36.000 0.00 0.00 46.15 2.90
80 81 9.528211 TCAATTGGTGAACGTGCATATGCATAG 62.528 40.741 31.70 27.83 42.96 2.23
81 82 7.845042 TCAATTGGTGAACGTGCATATGCATA 61.845 38.462 31.70 9.27 42.96 3.14
82 83 7.118200 TCAATTGGTGAACGTGCATATGCAT 62.118 40.000 31.70 17.48 42.96 3.96
83 84 5.872383 TCAATTGGTGAACGTGCATATGCA 61.872 41.667 26.32 26.32 40.40 3.96
84 85 2.849880 ATTGGTGAACGTGCATATGC 57.150 45.000 21.09 21.09 42.50 3.14
85 86 4.354071 TCAATTGGTGAACGTGCATATG 57.646 40.909 0.00 0.00 31.51 1.78
86 87 5.277297 CGTATCAATTGGTGAACGTGCATAT 60.277 40.000 0.00 0.00 40.50 1.78
87 88 4.033472 CGTATCAATTGGTGAACGTGCATA 59.967 41.667 0.00 0.00 40.50 3.14
88 89 3.181511 CGTATCAATTGGTGAACGTGCAT 60.182 43.478 0.00 0.00 40.50 3.96
89 90 2.158645 CGTATCAATTGGTGAACGTGCA 59.841 45.455 5.42 0.00 40.50 4.57
90 91 2.769376 CGTATCAATTGGTGAACGTGC 58.231 47.619 5.42 0.00 40.50 5.34
91 92 2.158645 TGCGTATCAATTGGTGAACGTG 59.841 45.455 13.88 0.00 40.50 4.49
92 93 2.418692 TGCGTATCAATTGGTGAACGT 58.581 42.857 13.88 0.00 40.50 3.99
93 94 3.607439 GATGCGTATCAATTGGTGAACG 58.393 45.455 8.77 9.22 40.50 3.95
94 95 3.063452 ACGATGCGTATCAATTGGTGAAC 59.937 43.478 14.06 0.00 38.73 3.18
95 96 3.063316 CACGATGCGTATCAATTGGTGAA 59.937 43.478 14.06 0.00 37.69 3.18
96 97 2.607180 CACGATGCGTATCAATTGGTGA 59.393 45.455 14.06 0.00 38.32 4.02
97 98 2.286359 CCACGATGCGTATCAATTGGTG 60.286 50.000 14.06 11.81 38.32 4.17
98 99 1.939934 CCACGATGCGTATCAATTGGT 59.060 47.619 14.06 0.00 38.32 3.67
99 100 1.264020 CCCACGATGCGTATCAATTGG 59.736 52.381 14.06 14.60 38.32 3.16
100 101 2.032894 GTCCCACGATGCGTATCAATTG 60.033 50.000 14.06 0.00 38.32 2.32
101 102 2.210116 GTCCCACGATGCGTATCAATT 58.790 47.619 14.06 0.00 38.32 2.32
102 103 1.138069 TGTCCCACGATGCGTATCAAT 59.862 47.619 14.06 0.00 38.32 2.57
103 104 0.533032 TGTCCCACGATGCGTATCAA 59.467 50.000 14.06 0.00 38.32 2.57
104 105 0.179121 GTGTCCCACGATGCGTATCA 60.179 55.000 14.06 0.00 38.32 2.15
105 106 2.589890 GTGTCCCACGATGCGTATC 58.410 57.895 3.04 3.04 38.32 2.24
106 107 4.827481 GTGTCCCACGATGCGTAT 57.173 55.556 0.00 0.00 38.32 3.06
115 116 0.942252 GAGTCCAAAACGTGTCCCAC 59.058 55.000 0.00 0.00 0.00 4.61
116 117 0.834612 AGAGTCCAAAACGTGTCCCA 59.165 50.000 0.00 0.00 0.00 4.37
117 118 1.963172 AAGAGTCCAAAACGTGTCCC 58.037 50.000 0.00 0.00 0.00 4.46
118 119 4.612939 GCATTAAGAGTCCAAAACGTGTCC 60.613 45.833 0.00 0.00 0.00 4.02
119 120 4.024387 TGCATTAAGAGTCCAAAACGTGTC 60.024 41.667 0.00 0.00 0.00 3.67
120 121 3.880490 TGCATTAAGAGTCCAAAACGTGT 59.120 39.130 0.00 0.00 0.00 4.49
121 122 4.219033 GTGCATTAAGAGTCCAAAACGTG 58.781 43.478 0.00 0.00 0.00 4.49
122 123 3.880490 TGTGCATTAAGAGTCCAAAACGT 59.120 39.130 0.00 0.00 0.00 3.99
123 124 4.219033 GTGTGCATTAAGAGTCCAAAACG 58.781 43.478 0.00 0.00 0.00 3.60
124 125 4.219033 CGTGTGCATTAAGAGTCCAAAAC 58.781 43.478 0.00 0.00 0.00 2.43
125 126 3.252215 CCGTGTGCATTAAGAGTCCAAAA 59.748 43.478 0.00 0.00 0.00 2.44
126 127 2.811431 CCGTGTGCATTAAGAGTCCAAA 59.189 45.455 0.00 0.00 0.00 3.28
127 128 2.037902 TCCGTGTGCATTAAGAGTCCAA 59.962 45.455 0.00 0.00 0.00 3.53
128 129 1.621317 TCCGTGTGCATTAAGAGTCCA 59.379 47.619 0.00 0.00 0.00 4.02
129 130 2.380084 TCCGTGTGCATTAAGAGTCC 57.620 50.000 0.00 0.00 0.00 3.85
130 131 4.184629 AGAATCCGTGTGCATTAAGAGTC 58.815 43.478 0.00 0.00 0.00 3.36
131 132 4.207891 AGAATCCGTGTGCATTAAGAGT 57.792 40.909 0.00 0.00 0.00 3.24
132 133 4.508124 GGTAGAATCCGTGTGCATTAAGAG 59.492 45.833 0.00 0.00 0.00 2.85
133 134 4.439057 GGTAGAATCCGTGTGCATTAAGA 58.561 43.478 0.00 0.00 0.00 2.10
134 135 3.245284 CGGTAGAATCCGTGTGCATTAAG 59.755 47.826 0.00 0.00 44.77 1.85
135 136 3.191669 CGGTAGAATCCGTGTGCATTAA 58.808 45.455 0.00 0.00 44.77 1.40
136 137 2.816689 CGGTAGAATCCGTGTGCATTA 58.183 47.619 0.00 0.00 44.77 1.90
137 138 1.651987 CGGTAGAATCCGTGTGCATT 58.348 50.000 0.00 0.00 44.77 3.56
138 139 3.362581 CGGTAGAATCCGTGTGCAT 57.637 52.632 0.00 0.00 44.77 3.96
139 140 4.902308 CGGTAGAATCCGTGTGCA 57.098 55.556 0.00 0.00 44.77 4.57
146 147 3.939592 CCCTCTTTTTGACGGTAGAATCC 59.060 47.826 0.00 0.00 0.00 3.01
147 148 3.374367 GCCCTCTTTTTGACGGTAGAATC 59.626 47.826 0.00 0.00 0.00 2.52
148 149 3.344515 GCCCTCTTTTTGACGGTAGAAT 58.655 45.455 0.00 0.00 0.00 2.40
149 150 2.774687 GCCCTCTTTTTGACGGTAGAA 58.225 47.619 0.00 0.00 0.00 2.10
150 151 1.337447 CGCCCTCTTTTTGACGGTAGA 60.337 52.381 0.00 0.00 0.00 2.59
151 152 1.076332 CGCCCTCTTTTTGACGGTAG 58.924 55.000 0.00 0.00 0.00 3.18
152 153 0.393820 ACGCCCTCTTTTTGACGGTA 59.606 50.000 0.00 0.00 0.00 4.02
153 154 0.393820 TACGCCCTCTTTTTGACGGT 59.606 50.000 0.00 0.00 0.00 4.83
154 155 0.794473 GTACGCCCTCTTTTTGACGG 59.206 55.000 0.00 0.00 0.00 4.79
155 156 1.792006 AGTACGCCCTCTTTTTGACG 58.208 50.000 0.00 0.00 0.00 4.35
156 157 5.899299 TCTATAGTACGCCCTCTTTTTGAC 58.101 41.667 0.00 0.00 0.00 3.18
157 158 6.534475 TTCTATAGTACGCCCTCTTTTTGA 57.466 37.500 0.00 0.00 0.00 2.69
158 159 7.039882 TCTTTCTATAGTACGCCCTCTTTTTG 58.960 38.462 0.00 0.00 0.00 2.44
159 160 7.179076 TCTTTCTATAGTACGCCCTCTTTTT 57.821 36.000 0.00 0.00 0.00 1.94
160 161 6.786967 TCTTTCTATAGTACGCCCTCTTTT 57.213 37.500 0.00 0.00 0.00 2.27
161 162 6.550108 TCATCTTTCTATAGTACGCCCTCTTT 59.450 38.462 0.00 0.00 0.00 2.52
162 163 6.069331 TCATCTTTCTATAGTACGCCCTCTT 58.931 40.000 0.00 0.00 0.00 2.85
163 164 5.632118 TCATCTTTCTATAGTACGCCCTCT 58.368 41.667 0.00 0.00 0.00 3.69
164 165 5.961396 TCATCTTTCTATAGTACGCCCTC 57.039 43.478 0.00 0.00 0.00 4.30
165 166 5.597182 TGTTCATCTTTCTATAGTACGCCCT 59.403 40.000 0.00 0.00 0.00 5.19
166 167 5.839621 TGTTCATCTTTCTATAGTACGCCC 58.160 41.667 0.00 0.00 0.00 6.13
167 168 9.077674 CATATGTTCATCTTTCTATAGTACGCC 57.922 37.037 0.00 0.00 0.00 5.68
168 169 9.841880 TCATATGTTCATCTTTCTATAGTACGC 57.158 33.333 1.90 0.00 0.00 4.42
175 176 7.877097 GCAGAGGTCATATGTTCATCTTTCTAT 59.123 37.037 12.34 0.00 0.00 1.98
176 177 7.147672 TGCAGAGGTCATATGTTCATCTTTCTA 60.148 37.037 12.34 2.03 0.00 2.10
177 178 6.054295 GCAGAGGTCATATGTTCATCTTTCT 58.946 40.000 12.34 1.51 0.00 2.52
178 179 5.819379 TGCAGAGGTCATATGTTCATCTTTC 59.181 40.000 12.34 9.38 0.00 2.62
179 180 5.748402 TGCAGAGGTCATATGTTCATCTTT 58.252 37.500 12.34 0.00 0.00 2.52
180 181 5.363562 TGCAGAGGTCATATGTTCATCTT 57.636 39.130 12.34 1.17 0.00 2.40
181 182 5.563876 ATGCAGAGGTCATATGTTCATCT 57.436 39.130 1.90 7.21 0.00 2.90
182 183 5.761726 TCAATGCAGAGGTCATATGTTCATC 59.238 40.000 1.90 5.12 0.00 2.92
183 184 5.687780 TCAATGCAGAGGTCATATGTTCAT 58.312 37.500 1.90 0.00 0.00 2.57
184 185 5.101648 TCAATGCAGAGGTCATATGTTCA 57.898 39.130 1.90 0.00 0.00 3.18
185 186 6.630444 ATTCAATGCAGAGGTCATATGTTC 57.370 37.500 1.90 0.05 0.00 3.18
186 187 6.183360 CCAATTCAATGCAGAGGTCATATGTT 60.183 38.462 1.90 0.00 0.00 2.71
187 188 5.301045 CCAATTCAATGCAGAGGTCATATGT 59.699 40.000 1.90 0.00 0.00 2.29
188 189 5.533528 TCCAATTCAATGCAGAGGTCATATG 59.466 40.000 0.00 0.00 0.00 1.78
189 190 5.698104 TCCAATTCAATGCAGAGGTCATAT 58.302 37.500 0.00 0.00 0.00 1.78
190 191 5.104402 TCTCCAATTCAATGCAGAGGTCATA 60.104 40.000 0.00 0.00 0.00 2.15
191 192 3.952323 CTCCAATTCAATGCAGAGGTCAT 59.048 43.478 0.00 0.00 0.00 3.06
192 193 3.009363 TCTCCAATTCAATGCAGAGGTCA 59.991 43.478 0.00 0.00 0.00 4.02
193 194 3.376546 GTCTCCAATTCAATGCAGAGGTC 59.623 47.826 0.00 0.00 0.00 3.85
194 195 3.350833 GTCTCCAATTCAATGCAGAGGT 58.649 45.455 0.00 0.00 0.00 3.85
195 196 2.353889 CGTCTCCAATTCAATGCAGAGG 59.646 50.000 0.00 0.00 0.00 3.69
196 197 3.005554 ACGTCTCCAATTCAATGCAGAG 58.994 45.455 0.00 0.00 0.00 3.35
197 198 3.057969 ACGTCTCCAATTCAATGCAGA 57.942 42.857 0.00 0.00 0.00 4.26
198 199 4.944962 TTACGTCTCCAATTCAATGCAG 57.055 40.909 0.00 0.00 0.00 4.41
199 200 8.669946 TTATATTACGTCTCCAATTCAATGCA 57.330 30.769 0.00 0.00 0.00 3.96
200 201 9.944663 TTTTATATTACGTCTCCAATTCAATGC 57.055 29.630 0.00 0.00 0.00 3.56
203 204 9.893634 TCCTTTTATATTACGTCTCCAATTCAA 57.106 29.630 0.00 0.00 0.00 2.69
237 238 9.736414 AACATACCATACACGTATAGATAGAGT 57.264 33.333 0.00 0.00 0.00 3.24
240 241 9.486857 CGAAACATACCATACACGTATAGATAG 57.513 37.037 0.00 0.00 0.00 2.08
241 242 7.964559 GCGAAACATACCATACACGTATAGATA 59.035 37.037 0.00 0.00 0.00 1.98
242 243 6.805271 GCGAAACATACCATACACGTATAGAT 59.195 38.462 0.00 0.00 0.00 1.98
243 244 6.144854 GCGAAACATACCATACACGTATAGA 58.855 40.000 0.00 0.00 0.00 1.98
244 245 5.344128 GGCGAAACATACCATACACGTATAG 59.656 44.000 0.00 0.00 0.00 1.31
245 246 5.009911 AGGCGAAACATACCATACACGTATA 59.990 40.000 0.00 0.00 0.00 1.47
246 247 4.053295 GGCGAAACATACCATACACGTAT 58.947 43.478 0.00 0.00 0.00 3.06
247 248 3.130869 AGGCGAAACATACCATACACGTA 59.869 43.478 0.00 0.00 0.00 3.57
248 249 2.093869 AGGCGAAACATACCATACACGT 60.094 45.455 0.00 0.00 0.00 4.49
249 250 2.538449 GAGGCGAAACATACCATACACG 59.462 50.000 0.00 0.00 0.00 4.49
250 251 2.870411 GGAGGCGAAACATACCATACAC 59.130 50.000 0.00 0.00 0.00 2.90
251 252 2.482316 CGGAGGCGAAACATACCATACA 60.482 50.000 0.00 0.00 0.00 2.29
252 253 2.132762 CGGAGGCGAAACATACCATAC 58.867 52.381 0.00 0.00 0.00 2.39
253 254 2.033372 TCGGAGGCGAAACATACCATA 58.967 47.619 0.00 0.00 0.00 2.74
254 255 0.828022 TCGGAGGCGAAACATACCAT 59.172 50.000 0.00 0.00 0.00 3.55
255 256 0.174845 CTCGGAGGCGAAACATACCA 59.825 55.000 0.00 0.00 0.00 3.25
256 257 1.152383 GCTCGGAGGCGAAACATACC 61.152 60.000 7.20 0.00 0.00 2.73
257 258 0.179108 AGCTCGGAGGCGAAACATAC 60.179 55.000 7.20 0.00 37.29 2.39
258 259 0.179111 CAGCTCGGAGGCGAAACATA 60.179 55.000 7.20 0.00 37.29 2.29
259 260 1.448540 CAGCTCGGAGGCGAAACAT 60.449 57.895 7.20 0.00 37.29 2.71
260 261 2.048222 CAGCTCGGAGGCGAAACA 60.048 61.111 7.20 0.00 37.29 2.83
261 262 2.048127 ACAGCTCGGAGGCGAAAC 60.048 61.111 7.20 0.00 37.29 2.78
262 263 2.261671 GACAGCTCGGAGGCGAAA 59.738 61.111 7.20 0.00 37.29 3.46
263 264 4.116328 CGACAGCTCGGAGGCGAA 62.116 66.667 7.20 0.00 36.16 4.70
271 272 0.937699 TTTCAACGACCGACAGCTCG 60.938 55.000 0.00 0.00 39.83 5.03
272 273 0.784778 CTTTCAACGACCGACAGCTC 59.215 55.000 0.00 0.00 0.00 4.09
273 274 1.222115 GCTTTCAACGACCGACAGCT 61.222 55.000 0.00 0.00 34.16 4.24
274 275 1.204312 GCTTTCAACGACCGACAGC 59.796 57.895 0.00 0.00 0.00 4.40
275 276 1.986378 CTAGCTTTCAACGACCGACAG 59.014 52.381 0.00 0.00 0.00 3.51
276 277 1.610038 TCTAGCTTTCAACGACCGACA 59.390 47.619 0.00 0.00 0.00 4.35
277 278 2.342910 TCTAGCTTTCAACGACCGAC 57.657 50.000 0.00 0.00 0.00 4.79
278 279 2.925306 GCTTCTAGCTTTCAACGACCGA 60.925 50.000 0.00 0.00 38.45 4.69
279 280 1.390463 GCTTCTAGCTTTCAACGACCG 59.610 52.381 0.00 0.00 38.45 4.79
280 281 1.732809 GGCTTCTAGCTTTCAACGACC 59.267 52.381 0.00 0.00 41.99 4.79
281 282 1.390463 CGGCTTCTAGCTTTCAACGAC 59.610 52.381 0.00 0.00 41.99 4.34
282 283 1.671850 CCGGCTTCTAGCTTTCAACGA 60.672 52.381 0.00 0.00 41.99 3.85
283 284 0.721718 CCGGCTTCTAGCTTTCAACG 59.278 55.000 0.00 0.00 41.99 4.10
284 285 1.809684 ACCGGCTTCTAGCTTTCAAC 58.190 50.000 0.00 0.00 41.99 3.18
285 286 3.688694 TTACCGGCTTCTAGCTTTCAA 57.311 42.857 0.00 0.00 41.99 2.69
286 287 3.906720 ATTACCGGCTTCTAGCTTTCA 57.093 42.857 0.00 0.00 41.99 2.69
287 288 6.862711 AATTATTACCGGCTTCTAGCTTTC 57.137 37.500 0.00 0.00 41.99 2.62
289 290 9.654663 CTTATAATTATTACCGGCTTCTAGCTT 57.345 33.333 0.00 0.00 41.99 3.74
290 291 9.032624 TCTTATAATTATTACCGGCTTCTAGCT 57.967 33.333 0.00 0.00 41.99 3.32
291 292 9.649167 TTCTTATAATTATTACCGGCTTCTAGC 57.351 33.333 0.00 0.00 41.46 3.42
294 295 9.930693 CTCTTCTTATAATTATTACCGGCTTCT 57.069 33.333 0.00 0.00 0.00 2.85
295 296 9.708092 ACTCTTCTTATAATTATTACCGGCTTC 57.292 33.333 0.00 0.00 0.00 3.86
296 297 9.708092 GACTCTTCTTATAATTATTACCGGCTT 57.292 33.333 0.00 0.00 0.00 4.35
297 298 9.091220 AGACTCTTCTTATAATTATTACCGGCT 57.909 33.333 0.00 0.00 0.00 5.52
298 299 9.141400 CAGACTCTTCTTATAATTATTACCGGC 57.859 37.037 0.00 0.00 0.00 6.13
311 312 7.946381 TGTGACATAGACAGACTCTTCTTAT 57.054 36.000 0.00 0.00 0.00 1.73
314 315 6.186957 AGATGTGACATAGACAGACTCTTCT 58.813 40.000 0.00 0.00 0.00 2.85
453 478 6.830912 AGCTAGTGACCAGATTTGCATATAA 58.169 36.000 0.00 0.00 0.00 0.98
844 936 8.641498 AGTGTAAAAGAAAGTGGATTCATCAT 57.359 30.769 0.00 0.00 0.00 2.45
978 1070 9.783081 AGCATGAAAGAGTTAAATTCCATTTTT 57.217 25.926 0.00 0.00 33.82 1.94
1033 1125 4.263994 TGGGGTTATAGTTAAAGCAGCCAA 60.264 41.667 0.00 0.00 0.00 4.52
1139 1231 3.883489 GTGTATTTAGTGCCAGGAATCCC 59.117 47.826 0.00 0.00 0.00 3.85
1612 1743 4.781775 TTTCCTAGTTTCAAGTCCACCA 57.218 40.909 0.00 0.00 0.00 4.17
1691 1825 4.660938 GCAACTCGGGCCCAACCT 62.661 66.667 24.92 0.00 39.10 3.50
1702 1836 0.784778 CCAAACTCGACTCGCAACTC 59.215 55.000 0.00 0.00 0.00 3.01
1972 2112 0.396435 TGTCCGAGTTGCAAGTCCAT 59.604 50.000 25.03 0.00 0.00 3.41
1992 2132 1.055849 AACTGGGGCCCAACATTTTC 58.944 50.000 28.43 3.34 30.80 2.29
2074 2216 2.936919 TGTCTGAGTTGCAAGTCCAT 57.063 45.000 27.35 0.02 0.00 3.41


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

AutoCloner maintained by Alex Coulton.