Multiple sequence alignment - TraesCS1D01G110300

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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 TraesCS1D01G110300 chr1D 100.000 2337 0 0 409 2745 104097036 104099372 0.000000e+00 4316.0
1 TraesCS1D01G110300 chr1D 100.000 167 0 0 1 167 104096628 104096794 2.650000e-80 309.0
2 TraesCS1D01G110300 chr1D 94.915 59 3 0 721 779 185936326 185936384 2.910000e-15 93.5
3 TraesCS1D01G110300 chr3B 91.839 2034 142 9 720 2745 724384958 724386975 0.000000e+00 2815.0
4 TraesCS1D01G110300 chr2B 91.864 2028 143 14 723 2745 367165830 367167840 0.000000e+00 2811.0
5 TraesCS1D01G110300 chr2B 84.966 439 59 5 2311 2744 137219109 137219545 3.250000e-119 438.0
6 TraesCS1D01G110300 chr5B 90.335 2028 163 16 725 2745 194914244 194916245 0.000000e+00 2628.0
7 TraesCS1D01G110300 chr5B 89.019 428 36 9 411 832 505099809 505099387 1.130000e-143 520.0
8 TraesCS1D01G110300 chr5B 82.500 160 28 0 1022 1181 467377385 467377226 1.020000e-29 141.0
9 TraesCS1D01G110300 chr5A 86.513 1950 181 38 725 2644 375706413 375708310 0.000000e+00 2069.0
10 TraesCS1D01G110300 chr5A 85.263 665 60 16 952 1603 678623681 678624320 0.000000e+00 651.0
11 TraesCS1D01G110300 chr5A 86.345 249 27 4 1672 1913 678624247 678624495 5.830000e-67 265.0
12 TraesCS1D01G110300 chr7B 90.332 1417 115 8 1329 2743 459361690 459360294 0.000000e+00 1838.0
13 TraesCS1D01G110300 chr7B 91.475 610 51 1 725 1333 459372297 459371688 0.000000e+00 837.0
14 TraesCS1D01G110300 chr7B 94.654 318 15 2 411 726 235124118 235124435 2.460000e-135 492.0
15 TraesCS1D01G110300 chr1B 91.327 1153 75 8 1599 2743 672176314 672177449 0.000000e+00 1552.0
16 TraesCS1D01G110300 chr1B 92.947 950 59 5 725 1667 672175514 672176462 0.000000e+00 1376.0
17 TraesCS1D01G110300 chr1B 94.637 317 16 1 411 726 235373323 235373007 8.830000e-135 490.0
18 TraesCS1D01G110300 chr3A 89.615 1040 94 6 1608 2644 291166564 291167592 0.000000e+00 1310.0
19 TraesCS1D01G110300 chr3A 84.978 912 74 26 725 1612 291153806 291154678 0.000000e+00 867.0
20 TraesCS1D01G110300 chr3A 93.491 169 9 2 1 167 124403640 124403472 1.630000e-62 250.0
21 TraesCS1D01G110300 chr3A 97.059 34 1 0 1632 1665 291154629 291154662 1.060000e-04 58.4
22 TraesCS1D01G110300 chr4D 87.086 937 66 13 954 1873 498127515 498128413 0.000000e+00 1009.0
23 TraesCS1D01G110300 chr4D 83.910 665 75 19 952 1603 498100238 498100883 8.410000e-170 606.0
24 TraesCS1D01G110300 chr4D 94.969 318 14 2 411 726 173996212 173996529 5.280000e-137 497.0
25 TraesCS1D01G110300 chr4D 95.238 315 10 3 411 720 132147603 132147289 6.830000e-136 494.0
26 TraesCS1D01G110300 chr4D 94.671 319 16 1 409 726 216309419 216309737 6.830000e-136 494.0
27 TraesCS1D01G110300 chr4D 93.491 169 9 2 1 167 285201178 285201010 1.630000e-62 250.0
28 TraesCS1D01G110300 chr4D 93.491 169 9 2 1 167 444534975 444535143 1.630000e-62 250.0
29 TraesCS1D01G110300 chr4D 92.899 169 10 2 1 167 251147702 251147534 7.590000e-61 244.0
30 TraesCS1D01G110300 chr4D 92.899 169 10 2 1 167 307612820 307612652 7.590000e-61 244.0
31 TraesCS1D01G110300 chr4D 90.714 140 9 4 2050 2186 498128494 498128632 1.680000e-42 183.0
32 TraesCS1D01G110300 chr4D 90.123 81 2 3 1955 2031 498128420 498128498 1.740000e-17 100.0
33 TraesCS1D01G110300 chr4D 83.178 107 16 2 725 831 423168435 423168331 2.250000e-16 97.1
34 TraesCS1D01G110300 chr4D 93.333 60 4 0 723 782 380699760 380699701 3.770000e-14 89.8
35 TraesCS1D01G110300 chr4D 94.545 55 3 0 2214 2268 266741874 266741928 4.870000e-13 86.1
36 TraesCS1D01G110300 chr4D 95.349 43 2 0 2214 2256 130087119 130087077 4.910000e-08 69.4
37 TraesCS1D01G110300 chr3D 95.584 317 13 1 411 726 400455200 400455516 8.770000e-140 507.0
38 TraesCS1D01G110300 chr3D 93.976 166 8 2 1 164 329104846 329105011 1.630000e-62 250.0
39 TraesCS1D01G110300 chr3D 96.364 55 2 0 725 779 145290631 145290685 1.050000e-14 91.6
40 TraesCS1D01G110300 chr7D 95.527 313 12 2 411 721 199918600 199918288 1.470000e-137 499.0
41 TraesCS1D01G110300 chr7D 82.839 472 57 20 2290 2745 415379163 415378700 4.260000e-108 401.0
42 TraesCS1D01G110300 chr7D 96.364 55 2 0 725 779 291379586 291379640 1.050000e-14 91.6
43 TraesCS1D01G110300 chr5D 94.654 318 15 2 411 726 115282151 115281834 2.460000e-135 492.0
44 TraesCS1D01G110300 chr5D 84.173 139 22 0 1043 1181 389030862 389030724 4.770000e-28 135.0
45 TraesCS1D01G110300 chr5D 81.356 118 17 5 725 840 108642518 108642632 1.050000e-14 91.6
46 TraesCS1D01G110300 chr6D 83.585 463 56 14 2295 2745 131849270 131848816 1.520000e-112 416.0
47 TraesCS1D01G110300 chr6D 94.083 169 8 2 1 167 99885349 99885517 3.510000e-64 255.0
48 TraesCS1D01G110300 chr6D 96.552 58 2 0 725 782 77332653 77332596 2.250000e-16 97.1
49 TraesCS1D01G110300 chr6D 93.220 59 4 0 721 779 152834153 152834211 1.350000e-13 87.9
50 TraesCS1D01G110300 chrUn 80.508 472 69 20 2290 2745 87464045 87463581 9.410000e-90 340.0
51 TraesCS1D01G110300 chr4B 85.766 274 29 3 952 1222 640103268 640103534 5.790000e-72 281.0
52 TraesCS1D01G110300 chr4B 88.889 63 7 0 721 783 213765667 213765729 8.150000e-11 78.7
53 TraesCS1D01G110300 chr2D 93.491 169 9 2 1 167 132891876 132891708 1.630000e-62 250.0
54 TraesCS1D01G110300 chr2D 93.413 167 9 2 3 167 364845470 364845636 2.110000e-61 246.0
55 TraesCS1D01G110300 chr2D 94.828 58 3 0 725 782 52459257 52459200 1.050000e-14 91.6
56 TraesCS1D01G110300 chr4A 80.909 110 18 3 732 840 554031679 554031572 1.750000e-12 84.2
57 TraesCS1D01G110300 chr1A 91.667 60 3 1 720 779 537039820 537039877 6.300000e-12 82.4


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 TraesCS1D01G110300 chr1D 104096628 104099372 2744 False 2312.500000 4316 100.000000 1 2745 2 chr1D.!!$F2 2744
1 TraesCS1D01G110300 chr3B 724384958 724386975 2017 False 2815.000000 2815 91.839000 720 2745 1 chr3B.!!$F1 2025
2 TraesCS1D01G110300 chr2B 367165830 367167840 2010 False 2811.000000 2811 91.864000 723 2745 1 chr2B.!!$F2 2022
3 TraesCS1D01G110300 chr5B 194914244 194916245 2001 False 2628.000000 2628 90.335000 725 2745 1 chr5B.!!$F1 2020
4 TraesCS1D01G110300 chr5A 375706413 375708310 1897 False 2069.000000 2069 86.513000 725 2644 1 chr5A.!!$F1 1919
5 TraesCS1D01G110300 chr5A 678623681 678624495 814 False 458.000000 651 85.804000 952 1913 2 chr5A.!!$F2 961
6 TraesCS1D01G110300 chr7B 459360294 459361690 1396 True 1838.000000 1838 90.332000 1329 2743 1 chr7B.!!$R1 1414
7 TraesCS1D01G110300 chr7B 459371688 459372297 609 True 837.000000 837 91.475000 725 1333 1 chr7B.!!$R2 608
8 TraesCS1D01G110300 chr1B 672175514 672177449 1935 False 1464.000000 1552 92.137000 725 2743 2 chr1B.!!$F1 2018
9 TraesCS1D01G110300 chr3A 291166564 291167592 1028 False 1310.000000 1310 89.615000 1608 2644 1 chr3A.!!$F1 1036
10 TraesCS1D01G110300 chr3A 291153806 291154678 872 False 462.700000 867 91.018500 725 1665 2 chr3A.!!$F2 940
11 TraesCS1D01G110300 chr4D 498100238 498100883 645 False 606.000000 606 83.910000 952 1603 1 chr4D.!!$F5 651
12 TraesCS1D01G110300 chr4D 498127515 498128632 1117 False 430.666667 1009 89.307667 954 2186 3 chr4D.!!$F6 1232

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
967 990 0.103208 CGACACCAGGATCTAGCACC 59.897 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2825 0.109781 CGGGAAAAGCAACATGACGG 60.11 55.0 0.0 0.0 0.0 4.79 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
17 18 2.742372 ACGGCATGCGGTTCACTC 60.742 61.111 23.72 0.57 0.00 3.51
18 19 3.853330 CGGCATGCGGTTCACTCG 61.853 66.667 16.56 5.74 0.00 4.18
19 20 3.499737 GGCATGCGGTTCACTCGG 61.500 66.667 12.44 0.00 0.00 4.63
20 21 2.434185 GCATGCGGTTCACTCGGA 60.434 61.111 0.00 0.00 0.00 4.55
21 22 1.815421 GCATGCGGTTCACTCGGAT 60.815 57.895 0.00 0.00 39.15 4.18
22 23 0.529773 GCATGCGGTTCACTCGGATA 60.530 55.000 0.00 0.00 36.59 2.59
23 24 1.934589 CATGCGGTTCACTCGGATAA 58.065 50.000 0.00 0.00 36.59 1.75
24 25 2.276201 CATGCGGTTCACTCGGATAAA 58.724 47.619 0.00 0.00 36.59 1.40
25 26 1.717194 TGCGGTTCACTCGGATAAAC 58.283 50.000 0.00 0.00 0.00 2.01
26 27 1.274167 TGCGGTTCACTCGGATAAACT 59.726 47.619 0.00 0.00 0.00 2.66
27 28 1.659098 GCGGTTCACTCGGATAAACTG 59.341 52.381 0.00 0.00 0.00 3.16
28 29 2.929592 GCGGTTCACTCGGATAAACTGT 60.930 50.000 0.00 0.00 31.95 3.55
29 30 3.323243 CGGTTCACTCGGATAAACTGTT 58.677 45.455 0.00 0.00 0.00 3.16
30 31 3.744426 CGGTTCACTCGGATAAACTGTTT 59.256 43.478 10.98 10.98 0.00 2.83
31 32 4.377022 CGGTTCACTCGGATAAACTGTTTG 60.377 45.833 15.69 0.63 0.00 2.93
32 33 4.464112 GTTCACTCGGATAAACTGTTTGC 58.536 43.478 15.69 7.58 0.00 3.68
33 34 2.734606 TCACTCGGATAAACTGTTTGCG 59.265 45.455 15.69 7.83 0.00 4.85
34 35 2.478894 CACTCGGATAAACTGTTTGCGT 59.521 45.455 15.69 2.10 0.00 5.24
35 36 3.059188 CACTCGGATAAACTGTTTGCGTT 60.059 43.478 15.69 0.00 0.00 4.84
36 37 3.059188 ACTCGGATAAACTGTTTGCGTTG 60.059 43.478 15.69 7.82 0.00 4.10
37 38 3.132160 TCGGATAAACTGTTTGCGTTGA 58.868 40.909 15.69 4.83 0.00 3.18
38 39 3.185594 TCGGATAAACTGTTTGCGTTGAG 59.814 43.478 15.69 1.79 0.00 3.02
39 40 3.185594 CGGATAAACTGTTTGCGTTGAGA 59.814 43.478 15.69 0.00 0.00 3.27
40 41 4.464112 GGATAAACTGTTTGCGTTGAGAC 58.536 43.478 15.69 0.00 0.00 3.36
41 42 4.024387 GGATAAACTGTTTGCGTTGAGACA 60.024 41.667 15.69 0.00 0.00 3.41
42 43 5.334879 GGATAAACTGTTTGCGTTGAGACAT 60.335 40.000 15.69 0.00 0.00 3.06
43 44 3.338818 AACTGTTTGCGTTGAGACATG 57.661 42.857 0.00 0.00 0.00 3.21
44 45 2.560504 ACTGTTTGCGTTGAGACATGA 58.439 42.857 0.00 0.00 0.00 3.07
45 46 2.545526 ACTGTTTGCGTTGAGACATGAG 59.454 45.455 0.00 0.00 0.00 2.90
46 47 2.802247 CTGTTTGCGTTGAGACATGAGA 59.198 45.455 0.00 0.00 0.00 3.27
47 48 3.202097 TGTTTGCGTTGAGACATGAGAA 58.798 40.909 0.00 0.00 0.00 2.87
48 49 3.002246 TGTTTGCGTTGAGACATGAGAAC 59.998 43.478 0.00 0.00 0.00 3.01
49 50 2.524569 TGCGTTGAGACATGAGAACA 57.475 45.000 0.00 0.00 0.00 3.18
50 51 2.407090 TGCGTTGAGACATGAGAACAG 58.593 47.619 0.00 0.00 0.00 3.16
51 52 2.035832 TGCGTTGAGACATGAGAACAGA 59.964 45.455 0.00 0.00 0.00 3.41
52 53 3.059884 GCGTTGAGACATGAGAACAGAA 58.940 45.455 0.00 0.00 0.00 3.02
53 54 3.494626 GCGTTGAGACATGAGAACAGAAA 59.505 43.478 0.00 0.00 0.00 2.52
54 55 4.609336 GCGTTGAGACATGAGAACAGAAAC 60.609 45.833 0.00 0.00 0.00 2.78
55 56 4.507756 CGTTGAGACATGAGAACAGAAACA 59.492 41.667 0.00 0.00 0.00 2.83
56 57 5.332883 CGTTGAGACATGAGAACAGAAACAG 60.333 44.000 0.00 0.00 0.00 3.16
57 58 5.282055 TGAGACATGAGAACAGAAACAGT 57.718 39.130 0.00 0.00 0.00 3.55
58 59 5.674525 TGAGACATGAGAACAGAAACAGTT 58.325 37.500 0.00 0.00 0.00 3.16
59 60 5.755375 TGAGACATGAGAACAGAAACAGTTC 59.245 40.000 0.00 0.00 44.32 3.01
60 61 5.674525 AGACATGAGAACAGAAACAGTTCA 58.325 37.500 0.00 0.00 45.93 3.18
61 62 6.115446 AGACATGAGAACAGAAACAGTTCAA 58.885 36.000 0.00 0.00 45.93 2.69
62 63 6.599244 AGACATGAGAACAGAAACAGTTCAAA 59.401 34.615 0.00 0.00 45.93 2.69
63 64 7.284034 AGACATGAGAACAGAAACAGTTCAAAT 59.716 33.333 0.00 0.00 45.93 2.32
64 65 7.198390 ACATGAGAACAGAAACAGTTCAAATG 58.802 34.615 0.00 11.90 45.93 2.32
65 66 7.067372 ACATGAGAACAGAAACAGTTCAAATGA 59.933 33.333 19.00 0.00 45.93 2.57
66 67 7.389803 TGAGAACAGAAACAGTTCAAATGAA 57.610 32.000 8.54 0.00 45.93 2.57
78 79 4.955925 TTCAAATGAACAAGACGTGTGT 57.044 36.364 0.00 0.00 40.60 3.72
79 80 4.271590 TCAAATGAACAAGACGTGTGTG 57.728 40.909 0.00 0.00 40.60 3.82
80 81 3.935828 TCAAATGAACAAGACGTGTGTGA 59.064 39.130 0.00 0.00 40.60 3.58
81 82 4.574421 TCAAATGAACAAGACGTGTGTGAT 59.426 37.500 0.00 0.00 40.60 3.06
82 83 5.755861 TCAAATGAACAAGACGTGTGTGATA 59.244 36.000 0.00 0.00 40.60 2.15
83 84 5.591643 AATGAACAAGACGTGTGTGATAC 57.408 39.130 0.00 0.00 40.60 2.24
84 85 3.047093 TGAACAAGACGTGTGTGATACG 58.953 45.455 0.00 0.00 40.60 3.06
85 86 1.415374 ACAAGACGTGTGTGATACGC 58.585 50.000 0.00 0.00 44.87 4.42
90 91 3.556625 GTGTGTGATACGCGGCAA 58.443 55.556 12.47 0.00 0.00 4.52
91 92 1.863491 GTGTGTGATACGCGGCAAA 59.137 52.632 12.47 0.00 0.00 3.68
92 93 0.452122 GTGTGTGATACGCGGCAAAC 60.452 55.000 12.47 11.50 0.00 2.93
93 94 0.880718 TGTGTGATACGCGGCAAACA 60.881 50.000 12.47 14.11 30.15 2.83
94 95 0.179225 GTGTGATACGCGGCAAACAG 60.179 55.000 12.47 0.00 0.00 3.16
95 96 1.295357 TGTGATACGCGGCAAACAGG 61.295 55.000 12.47 0.00 0.00 4.00
96 97 1.004320 TGATACGCGGCAAACAGGT 60.004 52.632 12.47 0.00 0.00 4.00
97 98 1.017177 TGATACGCGGCAAACAGGTC 61.017 55.000 12.47 0.00 0.00 3.85
98 99 0.739813 GATACGCGGCAAACAGGTCT 60.740 55.000 12.47 0.00 0.00 3.85
99 100 1.019278 ATACGCGGCAAACAGGTCTG 61.019 55.000 12.47 0.00 0.00 3.51
101 102 1.666553 CGCGGCAAACAGGTCTGTA 60.667 57.895 0.00 0.00 44.13 2.74
102 103 1.225376 CGCGGCAAACAGGTCTGTAA 61.225 55.000 0.00 0.00 44.13 2.41
103 104 1.165270 GCGGCAAACAGGTCTGTAAT 58.835 50.000 3.87 0.00 44.13 1.89
104 105 2.352388 GCGGCAAACAGGTCTGTAATA 58.648 47.619 3.87 0.00 44.13 0.98
105 106 2.745281 GCGGCAAACAGGTCTGTAATAA 59.255 45.455 3.87 0.00 44.13 1.40
106 107 3.189702 GCGGCAAACAGGTCTGTAATAAA 59.810 43.478 3.87 0.00 44.13 1.40
107 108 4.320641 GCGGCAAACAGGTCTGTAATAAAA 60.321 41.667 3.87 0.00 44.13 1.52
108 109 5.764131 CGGCAAACAGGTCTGTAATAAAAA 58.236 37.500 3.87 0.00 44.13 1.94
127 128 5.643379 AAAAATGTGTGTGAGCCGATAAT 57.357 34.783 0.00 0.00 0.00 1.28
128 129 6.751514 AAAAATGTGTGTGAGCCGATAATA 57.248 33.333 0.00 0.00 0.00 0.98
129 130 6.751514 AAAATGTGTGTGAGCCGATAATAA 57.248 33.333 0.00 0.00 0.00 1.40
130 131 5.734855 AATGTGTGTGAGCCGATAATAAC 57.265 39.130 0.00 0.00 0.00 1.89
131 132 4.195225 TGTGTGTGAGCCGATAATAACA 57.805 40.909 0.00 0.00 0.00 2.41
132 133 4.765273 TGTGTGTGAGCCGATAATAACAT 58.235 39.130 0.00 0.00 0.00 2.71
133 134 5.908341 TGTGTGTGAGCCGATAATAACATA 58.092 37.500 0.00 0.00 0.00 2.29
134 135 5.983118 TGTGTGTGAGCCGATAATAACATAG 59.017 40.000 0.00 0.00 0.00 2.23
135 136 6.183360 TGTGTGTGAGCCGATAATAACATAGA 60.183 38.462 0.00 0.00 0.00 1.98
136 137 6.144080 GTGTGTGAGCCGATAATAACATAGAC 59.856 42.308 0.00 0.00 0.00 2.59
137 138 5.342525 GTGTGAGCCGATAATAACATAGACG 59.657 44.000 0.00 0.00 0.00 4.18
138 139 4.857588 GTGAGCCGATAATAACATAGACGG 59.142 45.833 0.00 0.00 41.44 4.79
139 140 4.521639 TGAGCCGATAATAACATAGACGGT 59.478 41.667 0.00 0.00 40.76 4.83
140 141 5.010314 TGAGCCGATAATAACATAGACGGTT 59.990 40.000 0.00 0.00 40.76 4.44
141 142 5.227908 AGCCGATAATAACATAGACGGTTG 58.772 41.667 0.00 0.00 40.76 3.77
142 143 4.143179 GCCGATAATAACATAGACGGTTGC 60.143 45.833 0.00 0.00 40.76 4.17
143 144 5.227908 CCGATAATAACATAGACGGTTGCT 58.772 41.667 0.00 0.00 35.21 3.91
144 145 5.118664 CCGATAATAACATAGACGGTTGCTG 59.881 44.000 0.00 0.00 35.21 4.41
145 146 5.388475 CGATAATAACATAGACGGTTGCTGC 60.388 44.000 0.00 0.00 0.00 5.25
146 147 3.543680 ATAACATAGACGGTTGCTGCT 57.456 42.857 0.00 0.00 0.00 4.24
147 148 4.665833 ATAACATAGACGGTTGCTGCTA 57.334 40.909 0.00 0.00 0.00 3.49
148 149 3.328382 AACATAGACGGTTGCTGCTAA 57.672 42.857 0.00 0.00 0.00 3.09
149 150 3.543680 ACATAGACGGTTGCTGCTAAT 57.456 42.857 0.00 0.00 0.00 1.73
150 151 4.665833 ACATAGACGGTTGCTGCTAATA 57.334 40.909 0.00 0.00 0.00 0.98
151 152 5.018539 ACATAGACGGTTGCTGCTAATAA 57.981 39.130 0.00 0.00 0.00 1.40
152 153 5.050490 ACATAGACGGTTGCTGCTAATAAG 58.950 41.667 0.00 0.00 0.00 1.73
153 154 3.887621 AGACGGTTGCTGCTAATAAGA 57.112 42.857 0.00 0.00 0.00 2.10
154 155 3.522553 AGACGGTTGCTGCTAATAAGAC 58.477 45.455 0.00 0.00 0.00 3.01
155 156 2.268298 ACGGTTGCTGCTAATAAGACG 58.732 47.619 0.00 0.00 0.00 4.18
156 157 1.004927 CGGTTGCTGCTAATAAGACGC 60.005 52.381 0.00 0.00 0.00 5.19
157 158 1.004927 GGTTGCTGCTAATAAGACGCG 60.005 52.381 3.53 3.53 0.00 6.01
158 159 1.659098 GTTGCTGCTAATAAGACGCGT 59.341 47.619 13.85 13.85 0.00 6.01
159 160 1.277326 TGCTGCTAATAAGACGCGTG 58.723 50.000 20.70 0.00 0.00 5.34
160 161 1.278238 GCTGCTAATAAGACGCGTGT 58.722 50.000 20.70 11.10 0.00 4.49
161 162 1.005975 GCTGCTAATAAGACGCGTGTG 60.006 52.381 20.70 0.20 0.00 3.82
162 163 2.259618 CTGCTAATAAGACGCGTGTGT 58.740 47.619 20.70 0.00 0.00 3.72
163 164 2.666508 CTGCTAATAAGACGCGTGTGTT 59.333 45.455 20.70 16.16 35.49 3.32
164 165 2.410392 TGCTAATAAGACGCGTGTGTTG 59.590 45.455 20.70 4.21 33.10 3.33
165 166 2.410730 GCTAATAAGACGCGTGTGTTGT 59.589 45.455 20.70 11.90 33.10 3.32
166 167 2.941891 AATAAGACGCGTGTGTTGTG 57.058 45.000 20.70 0.00 33.10 3.33
541 542 8.833976 TTGTGAAATGCGTACATATTTGTATG 57.166 30.769 10.25 10.25 44.71 2.39
542 543 7.980062 TGTGAAATGCGTACATATTTGTATGT 58.020 30.769 14.54 6.36 44.07 2.29
543 544 9.099454 TGTGAAATGCGTACATATTTGTATGTA 57.901 29.630 14.54 11.55 44.07 2.29
544 545 9.923786 GTGAAATGCGTACATATTTGTATGTAA 57.076 29.630 14.54 6.50 44.07 2.41
642 643 9.566530 ACTACATACTACACGTATATACTCTCG 57.433 37.037 11.05 0.46 36.69 4.04
643 644 7.824704 ACATACTACACGTATATACTCTCGG 57.175 40.000 11.05 0.00 36.69 4.63
644 645 7.382110 ACATACTACACGTATATACTCTCGGT 58.618 38.462 11.05 6.99 36.69 4.69
645 646 7.875041 ACATACTACACGTATATACTCTCGGTT 59.125 37.037 11.05 0.00 36.69 4.44
646 647 8.715998 CATACTACACGTATATACTCTCGGTTT 58.284 37.037 11.05 0.00 36.69 3.27
647 648 7.559590 ACTACACGTATATACTCTCGGTTTT 57.440 36.000 11.05 0.00 0.00 2.43
648 649 7.412853 ACTACACGTATATACTCTCGGTTTTG 58.587 38.462 11.05 0.00 0.00 2.44
649 650 6.441093 ACACGTATATACTCTCGGTTTTGA 57.559 37.500 11.05 0.00 0.00 2.69
650 651 6.261118 ACACGTATATACTCTCGGTTTTGAC 58.739 40.000 11.05 0.00 0.00 3.18
651 652 6.127925 ACACGTATATACTCTCGGTTTTGACA 60.128 38.462 11.05 0.00 0.00 3.58
652 653 6.414109 CACGTATATACTCTCGGTTTTGACAG 59.586 42.308 11.05 0.00 0.00 3.51
653 654 6.317140 ACGTATATACTCTCGGTTTTGACAGA 59.683 38.462 11.05 0.00 0.00 3.41
654 655 7.013083 ACGTATATACTCTCGGTTTTGACAGAT 59.987 37.037 11.05 0.00 0.00 2.90
655 656 8.501580 CGTATATACTCTCGGTTTTGACAGATA 58.498 37.037 11.05 0.00 0.00 1.98
656 657 9.609950 GTATATACTCTCGGTTTTGACAGATAC 57.390 37.037 5.58 0.00 0.00 2.24
657 658 6.777213 ATACTCTCGGTTTTGACAGATACT 57.223 37.500 0.00 0.00 0.00 2.12
658 659 7.876936 ATACTCTCGGTTTTGACAGATACTA 57.123 36.000 0.00 0.00 0.00 1.82
659 660 5.952033 ACTCTCGGTTTTGACAGATACTAC 58.048 41.667 0.00 0.00 0.00 2.73
660 661 5.475909 ACTCTCGGTTTTGACAGATACTACA 59.524 40.000 0.00 0.00 0.00 2.74
661 662 6.153000 ACTCTCGGTTTTGACAGATACTACAT 59.847 38.462 0.00 0.00 0.00 2.29
662 663 7.338703 ACTCTCGGTTTTGACAGATACTACATA 59.661 37.037 0.00 0.00 0.00 2.29
663 664 7.478322 TCTCGGTTTTGACAGATACTACATAC 58.522 38.462 0.00 0.00 0.00 2.39
664 665 7.121611 TCTCGGTTTTGACAGATACTACATACA 59.878 37.037 0.00 0.00 0.00 2.29
665 666 7.604549 TCGGTTTTGACAGATACTACATACAA 58.395 34.615 0.00 0.00 0.00 2.41
666 667 7.543172 TCGGTTTTGACAGATACTACATACAAC 59.457 37.037 0.00 0.00 0.00 3.32
667 668 7.329962 CGGTTTTGACAGATACTACATACAACA 59.670 37.037 0.00 0.00 0.00 3.33
668 669 9.162764 GGTTTTGACAGATACTACATACAACAT 57.837 33.333 0.00 0.00 0.00 2.71
681 682 9.555727 ACTACATACAACATAGAAAACACAAGT 57.444 29.630 0.00 0.00 0.00 3.16
682 683 9.811655 CTACATACAACATAGAAAACACAAGTG 57.188 33.333 0.00 0.00 0.00 3.16
683 684 7.648142 ACATACAACATAGAAAACACAAGTGG 58.352 34.615 5.08 0.00 34.19 4.00
684 685 7.284489 ACATACAACATAGAAAACACAAGTGGT 59.716 33.333 5.08 0.00 34.19 4.16
706 707 3.858247 GGTAACTACCACTGCTTGTAGG 58.142 50.000 0.80 0.00 45.73 3.18
707 708 3.512724 GGTAACTACCACTGCTTGTAGGA 59.487 47.826 0.80 0.00 45.73 2.94
708 709 4.020839 GGTAACTACCACTGCTTGTAGGAA 60.021 45.833 0.80 0.00 45.73 3.36
709 710 4.699925 AACTACCACTGCTTGTAGGAAA 57.300 40.909 0.00 0.00 38.98 3.13
710 711 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
711 712 3.389983 ACTACCACTGCTTGTAGGAAACA 59.610 43.478 0.00 0.00 38.98 2.83
712 713 3.508845 ACCACTGCTTGTAGGAAACAT 57.491 42.857 0.00 0.00 38.10 2.71
713 714 3.832527 ACCACTGCTTGTAGGAAACATT 58.167 40.909 0.00 0.00 38.10 2.71
714 715 4.215109 ACCACTGCTTGTAGGAAACATTT 58.785 39.130 0.00 0.00 38.10 2.32
715 716 4.037923 ACCACTGCTTGTAGGAAACATTTG 59.962 41.667 0.00 0.00 38.10 2.32
716 717 4.037923 CCACTGCTTGTAGGAAACATTTGT 59.962 41.667 0.00 0.00 38.10 2.83
717 718 5.215160 CACTGCTTGTAGGAAACATTTGTC 58.785 41.667 0.00 0.00 38.10 3.18
718 719 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
719 720 4.469657 TGCTTGTAGGAAACATTTGTCCT 58.530 39.130 0.00 0.00 46.29 3.85
720 721 5.626142 TGCTTGTAGGAAACATTTGTCCTA 58.374 37.500 0.00 0.00 42.68 2.94
730 731 7.054124 GGAAACATTTGTCCTACATATCTGGA 58.946 38.462 0.00 0.00 0.00 3.86
751 752 4.386652 GGACTATTCTGTTTCGCGTAACAA 59.613 41.667 27.40 16.90 37.55 2.83
809 810 3.322254 GGGAGACGTTGGACTGATATGAT 59.678 47.826 0.00 0.00 0.00 2.45
878 880 0.800012 GCCTAATTCAACGCGGACAA 59.200 50.000 12.47 0.00 0.00 3.18
892 900 4.235762 ACAACGCCACGGACTGCT 62.236 61.111 0.00 0.00 0.00 4.24
967 990 0.103208 CGACACCAGGATCTAGCACC 59.897 60.000 0.00 0.00 0.00 5.01
1065 1097 4.445545 GCGTGCAAGTACCTGCGC 62.446 66.667 18.12 18.12 45.74 6.09
1106 1139 0.910088 GTGCTCACCCCCTACTTCCT 60.910 60.000 0.00 0.00 0.00 3.36
1128 1162 3.395702 TCGCAACCCCACCGCTAT 61.396 61.111 0.00 0.00 0.00 2.97
1173 1207 1.507141 CCAGCAAAGTCGCGAGGTTT 61.507 55.000 10.24 10.06 36.85 3.27
1214 1248 5.186215 TGTGACCTCTGGTAATCAATCGTTA 59.814 40.000 0.00 0.00 35.25 3.18
1583 1646 2.597510 GGCAAGGAAAGGCGGTGT 60.598 61.111 0.00 0.00 0.00 4.16
2209 2634 9.442047 GATCATATAGGAATTTCCATCGTCTTT 57.558 33.333 17.57 0.00 39.61 2.52
2377 2811 9.932207 TGAGATACTTTTCACGGAGTAATTTTA 57.068 29.630 0.00 0.00 41.61 1.52
2384 2818 9.269415 CTTTTCACGGAGTAATTTTAAATACGG 57.731 33.333 0.00 0.00 41.61 4.02
2385 2819 7.903995 TTCACGGAGTAATTTTAAATACGGT 57.096 32.000 0.00 0.00 41.61 4.83
2386 2820 7.293402 TCACGGAGTAATTTTAAATACGGTG 57.707 36.000 0.00 0.00 41.61 4.94
2387 2821 6.873076 TCACGGAGTAATTTTAAATACGGTGT 59.127 34.615 15.63 0.00 41.61 4.16
2388 2822 6.957077 CACGGAGTAATTTTAAATACGGTGTG 59.043 38.462 0.00 0.00 41.61 3.82
2389 2823 6.873076 ACGGAGTAATTTTAAATACGGTGTGA 59.127 34.615 0.00 0.00 41.94 3.58
2390 2824 7.148590 ACGGAGTAATTTTAAATACGGTGTGAC 60.149 37.037 0.00 0.00 41.94 3.67
2391 2825 7.466805 GGAGTAATTTTAAATACGGTGTGACC 58.533 38.462 0.00 0.00 34.05 4.02
2392 2826 7.381766 AGTAATTTTAAATACGGTGTGACCC 57.618 36.000 0.00 0.00 33.75 4.46
2428 2876 2.071540 CCGTTCGGGAAAAAGAGTACC 58.928 52.381 3.04 0.00 38.47 3.34
2435 2883 4.541973 GGGAAAAAGAGTACCCGAACTA 57.458 45.455 0.00 0.00 32.73 2.24
2459 2907 1.004277 TCCCTATGGGTTTGTGCTGAC 59.996 52.381 2.25 0.00 44.74 3.51
2462 2910 0.398696 TATGGGTTTGTGCTGACCGT 59.601 50.000 0.00 0.00 36.78 4.83
2564 3013 6.406065 CCAATGATCTTGCATGGTTTACATCA 60.406 38.462 0.00 1.41 37.84 3.07
2592 3041 9.248291 TGAACTGAATGCTATTCTTTTCAAAAC 57.752 29.630 15.13 0.00 0.00 2.43
2593 3042 9.248291 GAACTGAATGCTATTCTTTTCAAAACA 57.752 29.630 9.34 0.00 0.00 2.83
2616 3065 8.672214 ACAAAAATGTTTTGCATGTTTTCTTC 57.328 26.923 12.23 0.00 41.03 2.87
2685 3136 5.695818 ACGACTTGTACATTTACCATTTGC 58.304 37.500 0.00 0.00 0.00 3.68
2691 3142 9.336171 ACTTGTACATTTACCATTTGCATTTTT 57.664 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.853330 CGAGTGAACCGCATGCCG 61.853 66.667 13.15 8.50 0.00 5.69
2 3 3.499737 CCGAGTGAACCGCATGCC 61.500 66.667 13.15 0.00 0.00 4.40
3 4 0.529773 TATCCGAGTGAACCGCATGC 60.530 55.000 7.91 7.91 0.00 4.06
4 5 1.934589 TTATCCGAGTGAACCGCATG 58.065 50.000 0.00 0.00 0.00 4.06
6 7 1.274167 AGTTTATCCGAGTGAACCGCA 59.726 47.619 0.00 0.00 0.00 5.69
7 8 1.659098 CAGTTTATCCGAGTGAACCGC 59.341 52.381 0.00 0.00 0.00 5.68
8 9 2.955614 ACAGTTTATCCGAGTGAACCG 58.044 47.619 0.00 0.00 0.00 4.44
9 10 4.612939 GCAAACAGTTTATCCGAGTGAACC 60.613 45.833 0.00 0.00 0.00 3.62
10 11 4.464112 GCAAACAGTTTATCCGAGTGAAC 58.536 43.478 0.00 0.00 0.00 3.18
11 12 3.185594 CGCAAACAGTTTATCCGAGTGAA 59.814 43.478 0.00 0.00 0.00 3.18
12 13 2.734606 CGCAAACAGTTTATCCGAGTGA 59.265 45.455 0.00 0.00 0.00 3.41
13 14 2.478894 ACGCAAACAGTTTATCCGAGTG 59.521 45.455 15.64 5.67 0.00 3.51
14 15 2.762745 ACGCAAACAGTTTATCCGAGT 58.237 42.857 15.64 3.24 0.00 4.18
15 16 3.185594 TCAACGCAAACAGTTTATCCGAG 59.814 43.478 15.64 9.84 0.00 4.63
16 17 3.132160 TCAACGCAAACAGTTTATCCGA 58.868 40.909 15.64 1.69 0.00 4.55
17 18 3.185594 TCTCAACGCAAACAGTTTATCCG 59.814 43.478 0.00 4.98 0.00 4.18
18 19 4.024387 TGTCTCAACGCAAACAGTTTATCC 60.024 41.667 0.00 0.00 0.00 2.59
19 20 5.090652 TGTCTCAACGCAAACAGTTTATC 57.909 39.130 0.00 0.00 0.00 1.75
20 21 5.238432 TCATGTCTCAACGCAAACAGTTTAT 59.762 36.000 0.00 0.00 0.00 1.40
21 22 4.572795 TCATGTCTCAACGCAAACAGTTTA 59.427 37.500 0.00 0.00 0.00 2.01
22 23 3.376859 TCATGTCTCAACGCAAACAGTTT 59.623 39.130 0.00 0.00 0.00 2.66
23 24 2.942376 TCATGTCTCAACGCAAACAGTT 59.058 40.909 0.00 0.00 0.00 3.16
24 25 2.545526 CTCATGTCTCAACGCAAACAGT 59.454 45.455 0.00 0.00 0.00 3.55
25 26 2.802247 TCTCATGTCTCAACGCAAACAG 59.198 45.455 0.00 0.00 0.00 3.16
26 27 2.832563 TCTCATGTCTCAACGCAAACA 58.167 42.857 0.00 0.00 0.00 2.83
27 28 3.002246 TGTTCTCATGTCTCAACGCAAAC 59.998 43.478 0.00 0.00 0.00 2.93
28 29 3.202097 TGTTCTCATGTCTCAACGCAAA 58.798 40.909 0.00 0.00 0.00 3.68
29 30 2.802247 CTGTTCTCATGTCTCAACGCAA 59.198 45.455 0.00 0.00 0.00 4.85
30 31 2.035832 TCTGTTCTCATGTCTCAACGCA 59.964 45.455 0.00 0.00 0.00 5.24
31 32 2.677199 TCTGTTCTCATGTCTCAACGC 58.323 47.619 0.00 0.00 0.00 4.84
32 33 4.507756 TGTTTCTGTTCTCATGTCTCAACG 59.492 41.667 0.00 0.00 0.00 4.10
33 34 5.525378 ACTGTTTCTGTTCTCATGTCTCAAC 59.475 40.000 0.00 0.00 0.00 3.18
34 35 5.674525 ACTGTTTCTGTTCTCATGTCTCAA 58.325 37.500 0.00 0.00 0.00 3.02
35 36 5.282055 ACTGTTTCTGTTCTCATGTCTCA 57.718 39.130 0.00 0.00 0.00 3.27
36 37 5.755375 TGAACTGTTTCTGTTCTCATGTCTC 59.245 40.000 16.12 0.00 40.99 3.36
37 38 5.674525 TGAACTGTTTCTGTTCTCATGTCT 58.325 37.500 16.12 0.00 40.99 3.41
38 39 5.991328 TGAACTGTTTCTGTTCTCATGTC 57.009 39.130 16.12 0.00 40.99 3.06
39 40 6.757897 TTTGAACTGTTTCTGTTCTCATGT 57.242 33.333 16.12 0.00 40.99 3.21
40 41 7.420002 TCATTTGAACTGTTTCTGTTCTCATG 58.580 34.615 16.12 15.98 40.99 3.07
41 42 7.572523 TCATTTGAACTGTTTCTGTTCTCAT 57.427 32.000 16.12 8.51 40.99 2.90
42 43 7.389803 TTCATTTGAACTGTTTCTGTTCTCA 57.610 32.000 16.12 7.11 40.99 3.27
57 58 4.393371 TCACACACGTCTTGTTCATTTGAA 59.607 37.500 0.00 0.00 35.67 2.69
58 59 3.935828 TCACACACGTCTTGTTCATTTGA 59.064 39.130 0.00 0.00 35.67 2.69
59 60 4.271590 TCACACACGTCTTGTTCATTTG 57.728 40.909 0.00 0.00 35.67 2.32
60 61 5.333035 CGTATCACACACGTCTTGTTCATTT 60.333 40.000 0.00 0.00 35.67 2.32
61 62 4.149922 CGTATCACACACGTCTTGTTCATT 59.850 41.667 0.00 0.00 35.67 2.57
62 63 3.673338 CGTATCACACACGTCTTGTTCAT 59.327 43.478 0.00 0.00 35.67 2.57
63 64 3.047093 CGTATCACACACGTCTTGTTCA 58.953 45.455 0.00 0.00 35.67 3.18
64 65 2.160013 GCGTATCACACACGTCTTGTTC 60.160 50.000 0.00 0.00 41.41 3.18
65 66 1.790623 GCGTATCACACACGTCTTGTT 59.209 47.619 0.00 0.00 41.41 2.83
66 67 1.415374 GCGTATCACACACGTCTTGT 58.585 50.000 0.00 0.00 41.41 3.16
67 68 0.362179 CGCGTATCACACACGTCTTG 59.638 55.000 0.00 0.00 41.41 3.02
68 69 0.731514 CCGCGTATCACACACGTCTT 60.732 55.000 4.92 0.00 41.41 3.01
69 70 1.154093 CCGCGTATCACACACGTCT 60.154 57.895 4.92 0.00 41.41 4.18
70 71 2.785105 GCCGCGTATCACACACGTC 61.785 63.158 4.92 0.00 41.41 4.34
71 72 2.807895 GCCGCGTATCACACACGT 60.808 61.111 4.92 0.00 41.41 4.49
72 73 1.892113 TTTGCCGCGTATCACACACG 61.892 55.000 4.92 0.00 42.24 4.49
73 74 0.452122 GTTTGCCGCGTATCACACAC 60.452 55.000 4.92 0.00 0.00 3.82
74 75 0.880718 TGTTTGCCGCGTATCACACA 60.881 50.000 4.92 6.74 0.00 3.72
75 76 0.179225 CTGTTTGCCGCGTATCACAC 60.179 55.000 4.92 4.06 0.00 3.82
76 77 1.295357 CCTGTTTGCCGCGTATCACA 61.295 55.000 4.92 1.60 0.00 3.58
77 78 1.296056 ACCTGTTTGCCGCGTATCAC 61.296 55.000 4.92 0.00 0.00 3.06
78 79 1.004320 ACCTGTTTGCCGCGTATCA 60.004 52.632 4.92 0.00 0.00 2.15
79 80 0.739813 AGACCTGTTTGCCGCGTATC 60.740 55.000 4.92 0.00 0.00 2.24
80 81 1.019278 CAGACCTGTTTGCCGCGTAT 61.019 55.000 4.92 0.00 0.00 3.06
81 82 1.666553 CAGACCTGTTTGCCGCGTA 60.667 57.895 4.92 0.00 0.00 4.42
82 83 2.372040 TACAGACCTGTTTGCCGCGT 62.372 55.000 4.92 0.00 41.83 6.01
83 84 1.225376 TTACAGACCTGTTTGCCGCG 61.225 55.000 8.06 0.00 41.83 6.46
84 85 1.165270 ATTACAGACCTGTTTGCCGC 58.835 50.000 8.06 0.00 41.83 6.53
85 86 5.365403 TTTTATTACAGACCTGTTTGCCG 57.635 39.130 8.06 0.00 41.83 5.69
105 106 5.643379 ATTATCGGCTCACACACATTTTT 57.357 34.783 0.00 0.00 0.00 1.94
106 107 6.150307 TGTTATTATCGGCTCACACACATTTT 59.850 34.615 0.00 0.00 0.00 1.82
107 108 5.645929 TGTTATTATCGGCTCACACACATTT 59.354 36.000 0.00 0.00 0.00 2.32
108 109 5.182487 TGTTATTATCGGCTCACACACATT 58.818 37.500 0.00 0.00 0.00 2.71
109 110 4.765273 TGTTATTATCGGCTCACACACAT 58.235 39.130 0.00 0.00 0.00 3.21
110 111 4.195225 TGTTATTATCGGCTCACACACA 57.805 40.909 0.00 0.00 0.00 3.72
111 112 6.144080 GTCTATGTTATTATCGGCTCACACAC 59.856 42.308 0.00 0.00 0.00 3.82
112 113 6.213677 GTCTATGTTATTATCGGCTCACACA 58.786 40.000 0.00 0.00 0.00 3.72
113 114 5.342525 CGTCTATGTTATTATCGGCTCACAC 59.657 44.000 0.00 0.00 0.00 3.82
114 115 5.458015 CGTCTATGTTATTATCGGCTCACA 58.542 41.667 0.00 0.00 0.00 3.58
115 116 4.857588 CCGTCTATGTTATTATCGGCTCAC 59.142 45.833 0.00 0.00 0.00 3.51
116 117 4.521639 ACCGTCTATGTTATTATCGGCTCA 59.478 41.667 0.00 0.00 40.05 4.26
117 118 5.056894 ACCGTCTATGTTATTATCGGCTC 57.943 43.478 0.00 0.00 40.05 4.70
118 119 5.227908 CAACCGTCTATGTTATTATCGGCT 58.772 41.667 0.00 0.00 40.05 5.52
119 120 4.143179 GCAACCGTCTATGTTATTATCGGC 60.143 45.833 0.00 0.00 40.05 5.54
120 121 5.118664 CAGCAACCGTCTATGTTATTATCGG 59.881 44.000 0.00 0.00 41.77 4.18
121 122 5.388475 GCAGCAACCGTCTATGTTATTATCG 60.388 44.000 0.00 0.00 0.00 2.92
122 123 5.696724 AGCAGCAACCGTCTATGTTATTATC 59.303 40.000 0.00 0.00 0.00 1.75
123 124 5.611374 AGCAGCAACCGTCTATGTTATTAT 58.389 37.500 0.00 0.00 0.00 1.28
124 125 5.018539 AGCAGCAACCGTCTATGTTATTA 57.981 39.130 0.00 0.00 0.00 0.98
125 126 3.873910 AGCAGCAACCGTCTATGTTATT 58.126 40.909 0.00 0.00 0.00 1.40
126 127 3.543680 AGCAGCAACCGTCTATGTTAT 57.456 42.857 0.00 0.00 0.00 1.89
127 128 4.459390 TTAGCAGCAACCGTCTATGTTA 57.541 40.909 0.00 0.00 0.00 2.41
128 129 3.328382 TTAGCAGCAACCGTCTATGTT 57.672 42.857 0.00 0.00 0.00 2.71
129 130 3.543680 ATTAGCAGCAACCGTCTATGT 57.456 42.857 0.00 0.00 0.00 2.29
130 131 5.175856 GTCTTATTAGCAGCAACCGTCTATG 59.824 44.000 0.00 0.00 0.00 2.23
131 132 5.290386 GTCTTATTAGCAGCAACCGTCTAT 58.710 41.667 0.00 0.00 0.00 1.98
132 133 4.679662 GTCTTATTAGCAGCAACCGTCTA 58.320 43.478 0.00 0.00 0.00 2.59
133 134 3.522553 GTCTTATTAGCAGCAACCGTCT 58.477 45.455 0.00 0.00 0.00 4.18
134 135 2.281762 CGTCTTATTAGCAGCAACCGTC 59.718 50.000 0.00 0.00 0.00 4.79
135 136 2.268298 CGTCTTATTAGCAGCAACCGT 58.732 47.619 0.00 0.00 0.00 4.83
136 137 1.004927 GCGTCTTATTAGCAGCAACCG 60.005 52.381 0.00 0.00 0.00 4.44
137 138 1.004927 CGCGTCTTATTAGCAGCAACC 60.005 52.381 0.00 0.00 0.00 3.77
138 139 1.659098 ACGCGTCTTATTAGCAGCAAC 59.341 47.619 5.58 0.00 0.00 4.17
139 140 1.658596 CACGCGTCTTATTAGCAGCAA 59.341 47.619 9.86 0.00 0.00 3.91
140 141 1.277326 CACGCGTCTTATTAGCAGCA 58.723 50.000 9.86 0.00 0.00 4.41
141 142 1.005975 CACACGCGTCTTATTAGCAGC 60.006 52.381 9.86 0.00 0.00 5.25
142 143 2.259618 ACACACGCGTCTTATTAGCAG 58.740 47.619 9.86 0.00 0.00 4.24
143 144 2.357327 ACACACGCGTCTTATTAGCA 57.643 45.000 9.86 0.00 0.00 3.49
144 145 2.410730 ACAACACACGCGTCTTATTAGC 59.589 45.455 9.86 0.00 0.00 3.09
145 146 3.973874 CACAACACACGCGTCTTATTAG 58.026 45.455 9.86 0.00 0.00 1.73
147 148 2.941891 CACAACACACGCGTCTTATT 57.058 45.000 9.86 0.00 0.00 1.40
515 516 9.449550 CATACAAATATGTACGCATTTCACAAT 57.550 29.630 2.41 0.00 44.47 2.71
516 517 8.833976 CATACAAATATGTACGCATTTCACAA 57.166 30.769 2.41 0.00 44.47 3.33
545 546 7.721402 TGTACCATGTTTTGAGTATGCTTTTT 58.279 30.769 0.00 0.00 0.00 1.94
546 547 7.283625 TGTACCATGTTTTGAGTATGCTTTT 57.716 32.000 0.00 0.00 0.00 2.27
547 548 6.892658 TGTACCATGTTTTGAGTATGCTTT 57.107 33.333 0.00 0.00 0.00 3.51
548 549 7.829211 AGTATGTACCATGTTTTGAGTATGCTT 59.171 33.333 0.00 0.00 0.00 3.91
549 550 7.338710 AGTATGTACCATGTTTTGAGTATGCT 58.661 34.615 0.00 0.00 0.00 3.79
550 551 7.553881 AGTATGTACCATGTTTTGAGTATGC 57.446 36.000 0.00 0.00 0.00 3.14
616 617 9.566530 CGAGAGTATATACGTGTAGTATGTAGT 57.433 37.037 7.23 2.44 45.10 2.73
617 618 9.018716 CCGAGAGTATATACGTGTAGTATGTAG 57.981 40.741 7.23 0.00 45.10 2.74
618 619 8.523658 ACCGAGAGTATATACGTGTAGTATGTA 58.476 37.037 7.23 0.00 45.10 2.29
619 620 7.382110 ACCGAGAGTATATACGTGTAGTATGT 58.618 38.462 7.23 0.00 45.10 2.29
620 621 7.824704 ACCGAGAGTATATACGTGTAGTATG 57.175 40.000 7.23 0.00 45.10 2.39
621 622 8.839310 AAACCGAGAGTATATACGTGTAGTAT 57.161 34.615 7.23 0.00 46.90 2.12
622 623 8.551205 CAAAACCGAGAGTATATACGTGTAGTA 58.449 37.037 7.23 0.00 40.03 1.82
623 624 7.280876 TCAAAACCGAGAGTATATACGTGTAGT 59.719 37.037 7.23 1.85 0.00 2.73
624 625 7.585573 GTCAAAACCGAGAGTATATACGTGTAG 59.414 40.741 7.23 1.27 0.00 2.74
625 626 7.065683 TGTCAAAACCGAGAGTATATACGTGTA 59.934 37.037 7.23 0.00 0.00 2.90
626 627 6.127925 TGTCAAAACCGAGAGTATATACGTGT 60.128 38.462 7.23 0.00 0.00 4.49
627 628 6.260377 TGTCAAAACCGAGAGTATATACGTG 58.740 40.000 7.23 0.00 0.00 4.49
628 629 6.317140 TCTGTCAAAACCGAGAGTATATACGT 59.683 38.462 7.23 0.00 0.00 3.57
629 630 6.722301 TCTGTCAAAACCGAGAGTATATACG 58.278 40.000 7.23 0.00 0.00 3.06
630 631 9.609950 GTATCTGTCAAAACCGAGAGTATATAC 57.390 37.037 4.60 4.60 0.00 1.47
631 632 9.570468 AGTATCTGTCAAAACCGAGAGTATATA 57.430 33.333 0.00 0.00 0.00 0.86
632 633 8.466617 AGTATCTGTCAAAACCGAGAGTATAT 57.533 34.615 0.00 0.00 0.00 0.86
633 634 7.876936 AGTATCTGTCAAAACCGAGAGTATA 57.123 36.000 0.00 0.00 0.00 1.47
634 635 6.777213 AGTATCTGTCAAAACCGAGAGTAT 57.223 37.500 0.00 0.00 0.00 2.12
635 636 6.656270 TGTAGTATCTGTCAAAACCGAGAGTA 59.344 38.462 0.00 0.00 0.00 2.59
636 637 5.475909 TGTAGTATCTGTCAAAACCGAGAGT 59.524 40.000 0.00 0.00 0.00 3.24
637 638 5.950883 TGTAGTATCTGTCAAAACCGAGAG 58.049 41.667 0.00 0.00 0.00 3.20
638 639 5.970317 TGTAGTATCTGTCAAAACCGAGA 57.030 39.130 0.00 0.00 0.00 4.04
639 640 7.255569 TGTATGTAGTATCTGTCAAAACCGAG 58.744 38.462 0.00 0.00 0.00 4.63
640 641 7.160547 TGTATGTAGTATCTGTCAAAACCGA 57.839 36.000 0.00 0.00 0.00 4.69
641 642 7.329962 TGTTGTATGTAGTATCTGTCAAAACCG 59.670 37.037 0.00 0.00 0.00 4.44
642 643 8.542497 TGTTGTATGTAGTATCTGTCAAAACC 57.458 34.615 0.00 0.00 0.00 3.27
655 656 9.555727 ACTTGTGTTTTCTATGTTGTATGTAGT 57.444 29.630 0.00 0.00 0.00 2.73
656 657 9.811655 CACTTGTGTTTTCTATGTTGTATGTAG 57.188 33.333 0.00 0.00 0.00 2.74
657 658 8.779303 CCACTTGTGTTTTCTATGTTGTATGTA 58.221 33.333 0.00 0.00 0.00 2.29
658 659 7.284489 ACCACTTGTGTTTTCTATGTTGTATGT 59.716 33.333 0.00 0.00 0.00 2.29
659 660 7.591057 CACCACTTGTGTTTTCTATGTTGTATG 59.409 37.037 0.00 0.00 40.26 2.39
660 661 7.255451 CCACCACTTGTGTTTTCTATGTTGTAT 60.255 37.037 0.00 0.00 43.85 2.29
661 662 6.038825 CCACCACTTGTGTTTTCTATGTTGTA 59.961 38.462 0.00 0.00 43.85 2.41
662 663 5.163561 CCACCACTTGTGTTTTCTATGTTGT 60.164 40.000 0.00 0.00 43.85 3.32
663 664 5.163561 ACCACCACTTGTGTTTTCTATGTTG 60.164 40.000 0.00 0.00 43.85 3.33
664 665 4.953579 ACCACCACTTGTGTTTTCTATGTT 59.046 37.500 0.00 0.00 43.85 2.71
665 666 4.532834 ACCACCACTTGTGTTTTCTATGT 58.467 39.130 0.00 0.00 43.85 2.29
666 667 6.262273 AGTTACCACCACTTGTGTTTTCTATG 59.738 38.462 0.00 0.00 43.85 2.23
667 668 6.362248 AGTTACCACCACTTGTGTTTTCTAT 58.638 36.000 0.00 0.00 43.85 1.98
668 669 5.747342 AGTTACCACCACTTGTGTTTTCTA 58.253 37.500 0.00 0.00 43.85 2.10
669 670 4.595986 AGTTACCACCACTTGTGTTTTCT 58.404 39.130 0.00 0.00 43.85 2.52
670 671 4.976224 AGTTACCACCACTTGTGTTTTC 57.024 40.909 0.00 0.00 43.85 2.29
671 672 4.641541 GGTAGTTACCACCACTTGTGTTTT 59.358 41.667 3.45 0.00 45.73 2.43
672 673 4.201657 GGTAGTTACCACCACTTGTGTTT 58.798 43.478 3.45 0.00 45.73 2.83
673 674 3.812262 GGTAGTTACCACCACTTGTGTT 58.188 45.455 3.45 0.00 45.73 3.32
674 675 3.480505 GGTAGTTACCACCACTTGTGT 57.519 47.619 3.45 0.00 45.73 3.72
685 686 3.512724 TCCTACAAGCAGTGGTAGTTACC 59.487 47.826 0.00 1.25 46.62 2.85
686 687 4.796038 TCCTACAAGCAGTGGTAGTTAC 57.204 45.455 0.00 0.00 36.17 2.50
687 688 5.070714 TGTTTCCTACAAGCAGTGGTAGTTA 59.929 40.000 0.00 0.00 36.17 2.24
688 689 4.141574 TGTTTCCTACAAGCAGTGGTAGTT 60.142 41.667 0.00 0.00 36.17 2.24
689 690 3.389983 TGTTTCCTACAAGCAGTGGTAGT 59.610 43.478 0.00 0.00 36.17 2.73
690 691 4.002906 TGTTTCCTACAAGCAGTGGTAG 57.997 45.455 0.00 0.00 37.36 3.18
691 692 4.634012 ATGTTTCCTACAAGCAGTGGTA 57.366 40.909 0.00 0.00 40.89 3.25
692 693 3.508845 ATGTTTCCTACAAGCAGTGGT 57.491 42.857 0.00 0.00 40.89 4.16
693 694 4.037923 ACAAATGTTTCCTACAAGCAGTGG 59.962 41.667 0.00 0.00 40.89 4.00
694 695 5.186996 ACAAATGTTTCCTACAAGCAGTG 57.813 39.130 0.00 0.00 40.89 3.66
695 696 4.278419 GGACAAATGTTTCCTACAAGCAGT 59.722 41.667 0.00 0.00 40.89 4.40
696 697 4.520492 AGGACAAATGTTTCCTACAAGCAG 59.480 41.667 0.00 0.00 40.70 4.24
697 698 4.469657 AGGACAAATGTTTCCTACAAGCA 58.530 39.130 0.00 0.00 40.70 3.91
703 704 8.210946 CCAGATATGTAGGACAAATGTTTCCTA 58.789 37.037 0.00 0.00 42.56 2.94
704 705 7.056635 CCAGATATGTAGGACAAATGTTTCCT 58.943 38.462 0.00 0.00 44.82 3.36
705 706 7.054124 TCCAGATATGTAGGACAAATGTTTCC 58.946 38.462 0.00 0.00 0.00 3.13
716 717 8.783660 AAACAGAATAGTCCAGATATGTAGGA 57.216 34.615 0.00 0.00 0.00 2.94
717 718 7.810282 CGAAACAGAATAGTCCAGATATGTAGG 59.190 40.741 0.00 0.00 0.00 3.18
718 719 7.327275 GCGAAACAGAATAGTCCAGATATGTAG 59.673 40.741 0.00 0.00 0.00 2.74
719 720 7.145985 GCGAAACAGAATAGTCCAGATATGTA 58.854 38.462 0.00 0.00 0.00 2.29
720 721 5.986135 GCGAAACAGAATAGTCCAGATATGT 59.014 40.000 0.00 0.00 0.00 2.29
721 722 5.117745 CGCGAAACAGAATAGTCCAGATATG 59.882 44.000 0.00 0.00 0.00 1.78
722 723 5.221263 ACGCGAAACAGAATAGTCCAGATAT 60.221 40.000 15.93 0.00 0.00 1.63
723 724 4.097437 ACGCGAAACAGAATAGTCCAGATA 59.903 41.667 15.93 0.00 0.00 1.98
730 731 5.910637 TTTGTTACGCGAAACAGAATAGT 57.089 34.783 15.93 0.00 40.29 2.12
809 810 4.453480 AAGATCAGTTCACCTGGGAAAA 57.547 40.909 0.00 0.00 41.83 2.29
892 900 1.601663 CCCAAAAATCAAAGCGTCGCA 60.602 47.619 21.09 0.00 0.00 5.10
967 990 1.550065 GTGGTCGACGTGATGATCTG 58.450 55.000 9.92 0.00 0.00 2.90
1139 1173 3.589654 CTGGCGCCAAAGACTCGGA 62.590 63.158 32.09 2.57 0.00 4.55
1143 1177 1.799258 CTTTGCTGGCGCCAAAGACT 61.799 55.000 32.09 0.00 36.89 3.24
1190 1224 3.513912 ACGATTGATTACCAGAGGTCACA 59.486 43.478 0.00 0.00 37.09 3.58
1570 1633 1.597027 CAACGACACCGCCTTTCCT 60.597 57.895 0.00 0.00 39.95 3.36
1583 1646 2.029964 GTCCGGGTCAAGCAACGA 59.970 61.111 0.00 0.00 0.00 3.85
1700 2108 4.682714 TCTCCCTGCCCCTGCCTT 62.683 66.667 0.00 0.00 36.33 4.35
2273 2699 7.591006 AACACGATGTGTCTTTCGTATTTAT 57.409 32.000 2.68 0.00 46.79 1.40
2274 2700 7.410800 AAACACGATGTGTCTTTCGTATTTA 57.589 32.000 2.68 0.00 46.79 1.40
2358 2792 9.269415 CCGTATTTAAAATTACTCCGTGAAAAG 57.731 33.333 0.00 0.00 0.00 2.27
2384 2818 0.884704 AGCAACATGACGGGTCACAC 60.885 55.000 3.22 0.00 43.11 3.82
2385 2819 0.179032 AAGCAACATGACGGGTCACA 60.179 50.000 3.22 0.00 43.11 3.58
2386 2820 0.951558 AAAGCAACATGACGGGTCAC 59.048 50.000 3.22 0.00 43.11 3.67
2387 2821 1.606668 GAAAAGCAACATGACGGGTCA 59.393 47.619 0.00 3.69 44.59 4.02
2388 2822 1.068541 GGAAAAGCAACATGACGGGTC 60.069 52.381 0.00 0.00 0.00 4.46
2389 2823 0.958822 GGAAAAGCAACATGACGGGT 59.041 50.000 0.00 0.00 0.00 5.28
2390 2824 0.243636 GGGAAAAGCAACATGACGGG 59.756 55.000 0.00 0.00 0.00 5.28
2391 2825 0.109781 CGGGAAAAGCAACATGACGG 60.110 55.000 0.00 0.00 0.00 4.79
2392 2826 0.591170 ACGGGAAAAGCAACATGACG 59.409 50.000 0.00 0.00 0.00 4.35
2393 2827 2.661594 GAACGGGAAAAGCAACATGAC 58.338 47.619 0.00 0.00 0.00 3.06
2394 2828 1.265635 CGAACGGGAAAAGCAACATGA 59.734 47.619 0.00 0.00 0.00 3.07
2395 2829 1.665735 CCGAACGGGAAAAGCAACATG 60.666 52.381 5.25 0.00 38.47 3.21
2396 2830 0.596082 CCGAACGGGAAAAGCAACAT 59.404 50.000 5.25 0.00 38.47 2.71
2397 2831 2.026522 CCGAACGGGAAAAGCAACA 58.973 52.632 5.25 0.00 38.47 3.33
2459 2907 1.567504 AGACGAGTGTGAAAACACGG 58.432 50.000 3.52 3.14 44.71 4.94
2462 2910 6.730960 AAGTAAAAGACGAGTGTGAAAACA 57.269 33.333 0.00 0.00 0.00 2.83
2546 2995 6.209192 AGTTCAATGATGTAAACCATGCAAGA 59.791 34.615 0.00 0.00 32.56 3.02
2564 3013 9.985730 TTTGAAAAGAATAGCATTCAGTTCAAT 57.014 25.926 22.41 5.33 35.44 2.57
2592 3041 8.898983 AGAAGAAAACATGCAAAACATTTTTG 57.101 26.923 6.96 6.96 37.61 2.44


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

AutoCloner maintained by Alex Coulton.