Multiple sequence alignment - TraesCS5A01G102400

Loading Multiple Alignment...

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 TraesCS5A01G102400 chr5A 100.000 2967 0 0 1 2967 156142279 156145245 0.000000e+00 5480.0
1 TraesCS5A01G102400 chr5A 84.636 371 53 4 1399 1768 171334724 171334357 1.680000e-97 366.0
2 TraesCS5A01G102400 chr5A 89.270 233 25 0 2161 2393 140731226 140731458 2.890000e-75 292.0
3 TraesCS5A01G102400 chr5A 92.935 184 13 0 1 184 156090516 156090699 4.870000e-68 268.0
4 TraesCS5A01G102400 chr6D 93.015 2305 148 11 666 2967 419053726 419056020 0.000000e+00 3352.0
5 TraesCS5A01G102400 chr6D 91.329 519 42 3 178 694 419053267 419053784 0.000000e+00 706.0
6 TraesCS5A01G102400 chr3B 90.691 2041 162 20 784 2821 352657346 352659361 0.000000e+00 2691.0
7 TraesCS5A01G102400 chr3B 91.592 333 26 2 1593 1925 381285807 381285477 2.700000e-125 459.0
8 TraesCS5A01G102400 chr3B 86.667 315 27 9 2283 2596 58722745 58722445 4.740000e-88 335.0
9 TraesCS5A01G102400 chr6B 89.572 1870 170 12 357 2211 466770768 466768909 0.000000e+00 2350.0
10 TraesCS5A01G102400 chr6B 87.871 371 41 4 1399 1768 267068461 267068828 1.630000e-117 433.0
11 TraesCS5A01G102400 chr6B 87.601 371 42 4 1399 1768 264296613 264296980 7.600000e-116 427.0
12 TraesCS5A01G102400 chr6B 87.168 226 28 1 2168 2393 217772800 217772576 3.800000e-64 255.0
13 TraesCS5A01G102400 chr6B 94.231 52 3 0 670 721 466770484 466770433 2.450000e-11 80.5
14 TraesCS5A01G102400 chr7B 91.971 685 51 4 2283 2967 248338330 248339010 0.000000e+00 957.0
15 TraesCS5A01G102400 chr7B 89.101 367 37 3 178 542 660056671 660056306 1.250000e-123 453.0
16 TraesCS5A01G102400 chr7B 87.459 303 32 5 1846 2144 90409258 90408958 7.870000e-91 344.0
17 TraesCS5A01G102400 chr7B 83.924 367 30 14 2200 2539 708716552 708716188 1.030000e-84 324.0
18 TraesCS5A01G102400 chr2B 91.545 686 51 6 2283 2967 576583250 576582571 0.000000e+00 939.0
19 TraesCS5A01G102400 chr2B 88.456 719 74 5 598 1311 751877660 751876946 0.000000e+00 859.0
20 TraesCS5A01G102400 chr2B 93.636 330 21 0 1596 1925 751876936 751876607 7.390000e-136 494.0
21 TraesCS5A01G102400 chr2B 92.063 63 4 1 666 728 751877622 751877561 1.470000e-13 87.9
22 TraesCS5A01G102400 chr1B 91.228 684 51 9 2283 2966 580014861 580015535 0.000000e+00 922.0
23 TraesCS5A01G102400 chr1B 89.315 365 36 3 180 542 551914590 551914227 3.490000e-124 455.0
24 TraesCS5A01G102400 chr1B 87.162 296 32 6 1846 2137 492090185 492090478 6.130000e-87 331.0
25 TraesCS5A01G102400 chr1B 83.651 367 31 12 2200 2539 380832769 380833133 4.770000e-83 318.0
26 TraesCS5A01G102400 chr1B 87.168 226 28 1 2168 2393 350660222 350660446 3.800000e-64 255.0
27 TraesCS5A01G102400 chr3A 93.981 432 24 2 2537 2967 290378875 290378445 0.000000e+00 652.0
28 TraesCS5A01G102400 chr1A 93.981 432 24 2 2537 2967 144765046 144765476 0.000000e+00 652.0
29 TraesCS5A01G102400 chr1A 86.505 289 36 2 1859 2144 435224450 435224738 6.170000e-82 315.0
30 TraesCS5A01G102400 chr1A 85.911 291 36 2 1859 2144 435222174 435221884 3.720000e-79 305.0
31 TraesCS5A01G102400 chr1A 91.758 182 13 2 1 180 205578400 205578219 4.910000e-63 252.0
32 TraesCS5A01G102400 chr1A 89.785 186 17 2 1 184 157400031 157400216 1.370000e-58 237.0
33 TraesCS5A01G102400 chr1A 90.110 182 16 1 1 180 40132867 40133048 4.940000e-58 235.0
34 TraesCS5A01G102400 chr4A 93.911 427 26 0 2538 2964 22144976 22145402 0.000000e+00 645.0
35 TraesCS5A01G102400 chr4A 93.503 431 28 0 2537 2967 127393563 127393993 2.490000e-180 641.0
36 TraesCS5A01G102400 chr4A 91.713 181 13 2 1 180 106124756 106124935 1.770000e-62 250.0
37 TraesCS5A01G102400 chr4B 88.347 369 38 5 1399 1766 470633147 470632783 3.510000e-119 438.0
38 TraesCS5A01G102400 chr4B 85.714 371 49 4 1399 1768 47141506 47141873 3.590000e-104 388.0
39 TraesCS5A01G102400 chr4B 83.924 367 30 13 2200 2539 621162639 621162275 1.030000e-84 324.0
40 TraesCS5A01G102400 chr4B 87.687 268 31 1 1663 1928 129390929 129390662 7.990000e-81 311.0
41 TraesCS5A01G102400 chr5D 90.190 316 26 5 2139 2452 67807716 67807404 9.900000e-110 407.0
42 TraesCS5A01G102400 chr2D 88.462 286 30 1 1857 2139 274711662 274711377 2.830000e-90 342.0
43 TraesCS5A01G102400 chr4D 86.349 315 36 5 1831 2145 453200394 453200701 1.320000e-88 337.0
44 TraesCS5A01G102400 chr2A 91.398 186 14 1 1 184 520329324 520329139 1.360000e-63 254.0
45 TraesCS5A01G102400 chr2A 91.398 186 14 2 1 184 520337142 520336957 1.360000e-63 254.0
46 TraesCS5A01G102400 chr6A 90.710 183 14 3 1 180 343854938 343854756 1.060000e-59 241.0
47 TraesCS5A01G102400 chr1D 85.841 226 29 1 2168 2393 213947042 213947264 1.370000e-58 237.0
48 TraesCS5A01G102400 chr7A 90.164 183 13 5 1 180 345852897 345853077 1.780000e-57 233.0
49 TraesCS5A01G102400 chr5B 85.514 214 30 1 2160 2373 381324879 381325091 3.850000e-54 222.0
50 TraesCS5A01G102400 chr5B 92.857 42 3 0 178 219 169200111 169200070 8.880000e-06 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 TraesCS5A01G102400 chr5A 156142279 156145245 2966 False 5480.00 5480 100.0000 1 2967 1 chr5A.!!$F3 2966
1 TraesCS5A01G102400 chr6D 419053267 419056020 2753 False 2029.00 3352 92.1720 178 2967 2 chr6D.!!$F1 2789
2 TraesCS5A01G102400 chr3B 352657346 352659361 2015 False 2691.00 2691 90.6910 784 2821 1 chr3B.!!$F1 2037
3 TraesCS5A01G102400 chr6B 466768909 466770768 1859 True 1215.25 2350 91.9015 357 2211 2 chr6B.!!$R2 1854
4 TraesCS5A01G102400 chr7B 248338330 248339010 680 False 957.00 957 91.9710 2283 2967 1 chr7B.!!$F1 684
5 TraesCS5A01G102400 chr2B 576582571 576583250 679 True 939.00 939 91.5450 2283 2967 1 chr2B.!!$R1 684
6 TraesCS5A01G102400 chr2B 751876607 751877660 1053 True 480.30 859 91.3850 598 1925 3 chr2B.!!$R2 1327
7 TraesCS5A01G102400 chr1B 580014861 580015535 674 False 922.00 922 91.2280 2283 2966 1 chr1B.!!$F4 683

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
20 21 0.039180 TAACCTCTCTCGTCAGCCCA 59.961 55.0 0.0 0.0 0.00 5.36 F
636 638 0.115547 TGGCACCTACCACCACTAGA 59.884 55.0 0.0 0.0 33.75 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1471 0.035458 CCAAAACAGCGGAGGAGAGT 59.965 55.0 0.0 0.0 0.0 3.24 R
2589 2671 0.036388 ATCACACGACCATCCACACC 60.036 55.0 0.0 0.0 0.0 4.16 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 0.741915 CTAACCTCTCTCGTCAGCCC 59.258 60.000 0.00 0.00 0.00 5.19
20 21 0.039180 TAACCTCTCTCGTCAGCCCA 59.961 55.000 0.00 0.00 0.00 5.36
21 22 1.536943 AACCTCTCTCGTCAGCCCAC 61.537 60.000 0.00 0.00 0.00 4.61
22 23 2.487428 CTCTCTCGTCAGCCCACG 59.513 66.667 0.00 0.00 41.36 4.94
23 24 3.057547 CTCTCTCGTCAGCCCACGG 62.058 68.421 5.29 0.00 40.35 4.94
46 47 3.838795 CTCGCGCCCGTTCGAAAG 61.839 66.667 0.00 0.51 34.07 2.62
47 48 4.651008 TCGCGCCCGTTCGAAAGT 62.651 61.111 10.21 0.00 35.54 2.66
48 49 3.708734 CGCGCCCGTTCGAAAGTT 61.709 61.111 10.21 0.00 0.00 2.66
49 50 2.127383 GCGCCCGTTCGAAAGTTG 60.127 61.111 10.21 2.37 0.00 3.16
50 51 2.888998 GCGCCCGTTCGAAAGTTGT 61.889 57.895 10.21 0.00 0.00 3.32
51 52 1.203313 CGCCCGTTCGAAAGTTGTC 59.797 57.895 10.21 0.00 0.00 3.18
52 53 1.572941 GCCCGTTCGAAAGTTGTCC 59.427 57.895 10.21 0.00 0.00 4.02
53 54 1.848932 GCCCGTTCGAAAGTTGTCCC 61.849 60.000 10.21 0.00 0.00 4.46
54 55 1.562575 CCCGTTCGAAAGTTGTCCCG 61.563 60.000 10.21 2.21 0.00 5.14
55 56 0.598158 CCGTTCGAAAGTTGTCCCGA 60.598 55.000 10.21 0.00 0.00 5.14
56 57 1.210870 CGTTCGAAAGTTGTCCCGAA 58.789 50.000 0.00 0.00 38.49 4.30
58 59 1.585297 TTCGAAAGTTGTCCCGAACC 58.415 50.000 0.00 0.00 36.31 3.62
59 60 0.249996 TCGAAAGTTGTCCCGAACCC 60.250 55.000 0.00 0.00 0.00 4.11
60 61 1.562575 CGAAAGTTGTCCCGAACCCG 61.563 60.000 0.00 0.00 0.00 5.28
61 62 0.249996 GAAAGTTGTCCCGAACCCGA 60.250 55.000 0.00 0.00 38.22 5.14
62 63 0.533531 AAAGTTGTCCCGAACCCGAC 60.534 55.000 0.00 0.00 38.22 4.79
63 64 2.357881 GTTGTCCCGAACCCGACC 60.358 66.667 0.00 0.00 38.22 4.79
64 65 3.628982 TTGTCCCGAACCCGACCC 61.629 66.667 0.00 0.00 38.22 4.46
75 76 4.530857 CCGACCCGGGCAGTCATC 62.531 72.222 24.08 8.67 44.15 2.92
76 77 3.770040 CGACCCGGGCAGTCATCA 61.770 66.667 24.08 0.00 33.70 3.07
77 78 2.125106 GACCCGGGCAGTCATCAC 60.125 66.667 24.08 0.00 34.27 3.06
78 79 3.682292 GACCCGGGCAGTCATCACC 62.682 68.421 24.08 0.00 34.27 4.02
79 80 4.838152 CCCGGGCAGTCATCACCG 62.838 72.222 8.08 0.00 45.57 4.94
80 81 4.082523 CCGGGCAGTCATCACCGT 62.083 66.667 0.00 0.00 44.57 4.83
81 82 2.047274 CGGGCAGTCATCACCGTT 60.047 61.111 0.00 0.00 41.34 4.44
82 83 2.390599 CGGGCAGTCATCACCGTTG 61.391 63.158 0.00 0.00 41.34 4.10
83 84 2.040544 GGGCAGTCATCACCGTTGG 61.041 63.158 0.00 0.00 0.00 3.77
84 85 2.040544 GGCAGTCATCACCGTTGGG 61.041 63.158 0.00 0.00 40.11 4.12
86 87 1.298859 GCAGTCATCACCGTTGGGTC 61.299 60.000 0.00 0.00 46.01 4.46
87 88 0.673644 CAGTCATCACCGTTGGGTCC 60.674 60.000 0.00 0.00 46.01 4.46
88 89 1.740296 GTCATCACCGTTGGGTCCG 60.740 63.158 0.00 0.00 46.01 4.79
89 90 2.435938 CATCACCGTTGGGTCCGG 60.436 66.667 0.00 0.00 46.01 5.14
90 91 2.605295 ATCACCGTTGGGTCCGGA 60.605 61.111 0.00 0.00 46.01 5.14
91 92 1.993391 ATCACCGTTGGGTCCGGAT 60.993 57.895 7.81 0.00 46.01 4.18
92 93 1.968050 ATCACCGTTGGGTCCGGATC 61.968 60.000 7.81 6.88 46.01 3.36
93 94 2.605295 ACCGTTGGGTCCGGATCA 60.605 61.111 18.43 11.70 46.01 2.92
94 95 1.993391 ACCGTTGGGTCCGGATCAT 60.993 57.895 18.43 0.00 46.01 2.45
95 96 1.968050 ACCGTTGGGTCCGGATCATC 61.968 60.000 18.43 12.01 46.01 2.92
96 97 1.227556 CGTTGGGTCCGGATCATCC 60.228 63.158 18.43 8.83 0.00 3.51
97 98 1.148498 GTTGGGTCCGGATCATCCC 59.852 63.158 18.43 18.70 40.26 3.85
98 99 2.076184 TTGGGTCCGGATCATCCCC 61.076 63.158 21.94 20.12 39.20 4.81
99 100 2.122369 GGGTCCGGATCATCCCCT 60.122 66.667 18.43 0.00 34.32 4.79
100 101 1.157751 GGGTCCGGATCATCCCCTA 59.842 63.158 18.43 0.00 34.32 3.53
101 102 0.473117 GGGTCCGGATCATCCCCTAA 60.473 60.000 18.43 0.00 34.32 2.69
102 103 0.685660 GGTCCGGATCATCCCCTAAC 59.314 60.000 10.69 0.00 31.13 2.34
103 104 1.420430 GTCCGGATCATCCCCTAACA 58.580 55.000 7.81 0.00 31.13 2.41
104 105 1.978580 GTCCGGATCATCCCCTAACAT 59.021 52.381 7.81 0.00 31.13 2.71
105 106 2.028020 GTCCGGATCATCCCCTAACATC 60.028 54.545 7.81 0.00 31.13 3.06
106 107 2.158158 TCCGGATCATCCCCTAACATCT 60.158 50.000 0.00 0.00 31.13 2.90
107 108 3.076937 TCCGGATCATCCCCTAACATCTA 59.923 47.826 0.00 0.00 31.13 1.98
108 109 3.195825 CCGGATCATCCCCTAACATCTAC 59.804 52.174 0.00 0.00 31.13 2.59
109 110 3.832490 CGGATCATCCCCTAACATCTACA 59.168 47.826 0.00 0.00 31.13 2.74
110 111 4.283467 CGGATCATCCCCTAACATCTACAA 59.717 45.833 0.00 0.00 31.13 2.41
111 112 5.221641 CGGATCATCCCCTAACATCTACAAA 60.222 44.000 0.00 0.00 31.13 2.83
112 113 6.601332 GGATCATCCCCTAACATCTACAAAA 58.399 40.000 0.00 0.00 0.00 2.44
113 114 6.486993 GGATCATCCCCTAACATCTACAAAAC 59.513 42.308 0.00 0.00 0.00 2.43
114 115 6.381498 TCATCCCCTAACATCTACAAAACA 57.619 37.500 0.00 0.00 0.00 2.83
115 116 6.969043 TCATCCCCTAACATCTACAAAACAT 58.031 36.000 0.00 0.00 0.00 2.71
116 117 7.054124 TCATCCCCTAACATCTACAAAACATC 58.946 38.462 0.00 0.00 0.00 3.06
117 118 6.636454 TCCCCTAACATCTACAAAACATCT 57.364 37.500 0.00 0.00 0.00 2.90
118 119 6.650120 TCCCCTAACATCTACAAAACATCTC 58.350 40.000 0.00 0.00 0.00 2.75
119 120 5.823045 CCCCTAACATCTACAAAACATCTCC 59.177 44.000 0.00 0.00 0.00 3.71
120 121 6.414732 CCCTAACATCTACAAAACATCTCCA 58.585 40.000 0.00 0.00 0.00 3.86
121 122 7.056635 CCCTAACATCTACAAAACATCTCCAT 58.943 38.462 0.00 0.00 0.00 3.41
122 123 7.557719 CCCTAACATCTACAAAACATCTCCATT 59.442 37.037 0.00 0.00 0.00 3.16
123 124 8.960591 CCTAACATCTACAAAACATCTCCATTT 58.039 33.333 0.00 0.00 0.00 2.32
126 127 9.696917 AACATCTACAAAACATCTCCATTTTTC 57.303 29.630 0.00 0.00 0.00 2.29
127 128 9.082313 ACATCTACAAAACATCTCCATTTTTCT 57.918 29.630 0.00 0.00 0.00 2.52
128 129 9.918630 CATCTACAAAACATCTCCATTTTTCTT 57.081 29.630 0.00 0.00 0.00 2.52
133 134 8.676401 ACAAAACATCTCCATTTTTCTTTTTGG 58.324 29.630 0.00 0.00 36.29 3.28
134 135 8.891720 CAAAACATCTCCATTTTTCTTTTTGGA 58.108 29.630 0.00 0.00 36.81 3.53
135 136 8.437360 AAACATCTCCATTTTTCTTTTTGGAC 57.563 30.769 0.00 0.00 34.62 4.02
136 137 7.365497 ACATCTCCATTTTTCTTTTTGGACT 57.635 32.000 0.00 0.00 34.62 3.85
137 138 7.436933 ACATCTCCATTTTTCTTTTTGGACTC 58.563 34.615 0.00 0.00 34.62 3.36
138 139 6.405278 TCTCCATTTTTCTTTTTGGACTCC 57.595 37.500 0.00 0.00 34.62 3.85
139 140 5.304357 TCTCCATTTTTCTTTTTGGACTCCC 59.696 40.000 0.00 0.00 34.62 4.30
140 141 5.215845 TCCATTTTTCTTTTTGGACTCCCT 58.784 37.500 0.00 0.00 33.40 4.20
141 142 6.377912 TCCATTTTTCTTTTTGGACTCCCTA 58.622 36.000 0.00 0.00 33.40 3.53
142 143 6.266786 TCCATTTTTCTTTTTGGACTCCCTAC 59.733 38.462 0.00 0.00 33.40 3.18
143 144 6.455647 CATTTTTCTTTTTGGACTCCCTACC 58.544 40.000 0.00 0.00 0.00 3.18
144 145 5.397553 TTTTCTTTTTGGACTCCCTACCT 57.602 39.130 0.00 0.00 0.00 3.08
145 146 6.518516 TTTTCTTTTTGGACTCCCTACCTA 57.481 37.500 0.00 0.00 0.00 3.08
146 147 6.713731 TTTCTTTTTGGACTCCCTACCTAT 57.286 37.500 0.00 0.00 0.00 2.57
147 148 6.713731 TTCTTTTTGGACTCCCTACCTATT 57.286 37.500 0.00 0.00 0.00 1.73
148 149 6.713731 TCTTTTTGGACTCCCTACCTATTT 57.286 37.500 0.00 0.00 0.00 1.40
149 150 6.481643 TCTTTTTGGACTCCCTACCTATTTG 58.518 40.000 0.00 0.00 0.00 2.32
150 151 5.853572 TTTTGGACTCCCTACCTATTTGT 57.146 39.130 0.00 0.00 0.00 2.83
151 152 5.853572 TTTGGACTCCCTACCTATTTGTT 57.146 39.130 0.00 0.00 0.00 2.83
152 153 5.853572 TTGGACTCCCTACCTATTTGTTT 57.146 39.130 0.00 0.00 0.00 2.83
153 154 5.431179 TGGACTCCCTACCTATTTGTTTC 57.569 43.478 0.00 0.00 0.00 2.78
154 155 5.098663 TGGACTCCCTACCTATTTGTTTCT 58.901 41.667 0.00 0.00 0.00 2.52
155 156 5.045869 TGGACTCCCTACCTATTTGTTTCTG 60.046 44.000 0.00 0.00 0.00 3.02
156 157 5.429130 GACTCCCTACCTATTTGTTTCTGG 58.571 45.833 0.00 0.00 0.00 3.86
157 158 5.098663 ACTCCCTACCTATTTGTTTCTGGA 58.901 41.667 0.00 0.00 0.00 3.86
158 159 5.045797 ACTCCCTACCTATTTGTTTCTGGAC 60.046 44.000 0.00 0.00 0.00 4.02
159 160 4.226620 TCCCTACCTATTTGTTTCTGGACC 59.773 45.833 0.00 0.00 0.00 4.46
160 161 4.189231 CCTACCTATTTGTTTCTGGACCG 58.811 47.826 0.00 0.00 0.00 4.79
161 162 3.782656 ACCTATTTGTTTCTGGACCGT 57.217 42.857 0.00 0.00 0.00 4.83
162 163 3.671716 ACCTATTTGTTTCTGGACCGTC 58.328 45.455 0.00 0.00 0.00 4.79
163 164 3.007635 CCTATTTGTTTCTGGACCGTCC 58.992 50.000 10.96 10.96 36.96 4.79
164 165 1.519408 ATTTGTTTCTGGACCGTCCG 58.481 50.000 13.02 7.91 40.17 4.79
165 166 0.464870 TTTGTTTCTGGACCGTCCGA 59.535 50.000 13.02 10.04 40.17 4.55
166 167 0.682852 TTGTTTCTGGACCGTCCGAT 59.317 50.000 13.02 0.00 40.17 4.18
167 168 0.682852 TGTTTCTGGACCGTCCGATT 59.317 50.000 13.02 0.00 40.17 3.34
168 169 1.894466 TGTTTCTGGACCGTCCGATTA 59.106 47.619 13.02 0.00 40.17 1.75
169 170 2.265683 GTTTCTGGACCGTCCGATTAC 58.734 52.381 13.02 9.95 40.17 1.89
170 171 0.452987 TTCTGGACCGTCCGATTACG 59.547 55.000 13.02 0.00 40.17 3.18
171 172 0.392863 TCTGGACCGTCCGATTACGA 60.393 55.000 13.02 0.16 45.68 3.43
172 173 0.666913 CTGGACCGTCCGATTACGAT 59.333 55.000 13.02 0.00 45.68 3.73
173 174 0.664761 TGGACCGTCCGATTACGATC 59.335 55.000 13.02 0.00 45.68 3.69
204 205 7.392418 GTCTATTCTAACAACACCCCTTAAGT 58.608 38.462 0.97 0.00 0.00 2.24
226 227 3.009723 CCTTATTCTGCACATCAACCGT 58.990 45.455 0.00 0.00 0.00 4.83
228 229 1.453155 ATTCTGCACATCAACCGTCC 58.547 50.000 0.00 0.00 0.00 4.79
233 234 3.009723 CTGCACATCAACCGTCCTATTT 58.990 45.455 0.00 0.00 0.00 1.40
307 308 0.916358 CTTCACCCCACCTCCCTCAT 60.916 60.000 0.00 0.00 0.00 2.90
352 353 1.356398 GATTCCAAACCCCACCTACCA 59.644 52.381 0.00 0.00 0.00 3.25
405 406 4.686437 CACCCCACCCCACCCCTA 62.686 72.222 0.00 0.00 0.00 3.53
409 410 2.376842 CCACCCCACCCCTATCCT 59.623 66.667 0.00 0.00 0.00 3.24
494 495 3.390521 CTCCTACCAGTGCCGCCA 61.391 66.667 0.00 0.00 0.00 5.69
577 579 3.883744 AACTGGCCGCGACCTTCAG 62.884 63.158 14.09 11.97 0.00 3.02
590 592 3.573772 CTTCAGCACCTCGTCGGCA 62.574 63.158 0.00 0.00 35.61 5.69
608 610 1.133976 GCAAGCTATGGTGGTCCTCAT 60.134 52.381 0.00 0.00 34.23 2.90
629 631 1.378514 CCCACATGGCACCTACCAC 60.379 63.158 0.00 0.00 44.17 4.16
633 635 1.133809 ACATGGCACCTACCACCACT 61.134 55.000 0.00 0.00 44.17 4.00
635 637 1.134401 CATGGCACCTACCACCACTAG 60.134 57.143 0.00 0.00 44.17 2.57
636 638 0.115547 TGGCACCTACCACCACTAGA 59.884 55.000 0.00 0.00 33.75 2.43
637 639 0.535797 GGCACCTACCACCACTAGAC 59.464 60.000 0.00 0.00 0.00 2.59
638 640 1.263356 GCACCTACCACCACTAGACA 58.737 55.000 0.00 0.00 0.00 3.41
639 641 1.204941 GCACCTACCACCACTAGACAG 59.795 57.143 0.00 0.00 0.00 3.51
640 642 2.803956 CACCTACCACCACTAGACAGA 58.196 52.381 0.00 0.00 0.00 3.41
641 643 3.366396 CACCTACCACCACTAGACAGAT 58.634 50.000 0.00 0.00 0.00 2.90
642 644 3.381908 CACCTACCACCACTAGACAGATC 59.618 52.174 0.00 0.00 0.00 2.75
643 645 2.959707 CCTACCACCACTAGACAGATCC 59.040 54.545 0.00 0.00 0.00 3.36
644 646 2.623418 ACCACCACTAGACAGATCCA 57.377 50.000 0.00 0.00 0.00 3.41
645 647 2.461695 ACCACCACTAGACAGATCCAG 58.538 52.381 0.00 0.00 0.00 3.86
646 648 1.759445 CCACCACTAGACAGATCCAGG 59.241 57.143 0.00 0.00 0.00 4.45
647 649 1.137872 CACCACTAGACAGATCCAGGC 59.862 57.143 0.00 0.00 0.00 4.85
648 650 0.755686 CCACTAGACAGATCCAGGCC 59.244 60.000 0.00 0.00 0.00 5.19
649 651 1.489481 CACTAGACAGATCCAGGCCA 58.511 55.000 5.01 0.00 0.00 5.36
650 652 1.137872 CACTAGACAGATCCAGGCCAC 59.862 57.143 5.01 0.00 0.00 5.01
651 653 0.387202 CTAGACAGATCCAGGCCACG 59.613 60.000 5.01 0.00 0.00 4.94
652 654 1.043116 TAGACAGATCCAGGCCACGG 61.043 60.000 5.01 4.90 0.00 4.94
653 655 4.101448 ACAGATCCAGGCCACGGC 62.101 66.667 5.01 0.00 41.06 5.68
654 656 4.100084 CAGATCCAGGCCACGGCA 62.100 66.667 10.83 0.00 44.11 5.69
655 657 3.790437 AGATCCAGGCCACGGCAG 61.790 66.667 10.83 1.44 44.11 4.85
755 817 2.760799 CGGATCCGGTACCCCACA 60.761 66.667 26.95 0.00 35.56 4.17
843 906 1.843851 CACTTTGGGCCTCCTATGGTA 59.156 52.381 4.53 0.00 0.00 3.25
915 978 3.285215 CAGCATGCCCATCTCGCC 61.285 66.667 15.66 0.00 0.00 5.54
917 980 2.596631 GCATGCCCATCTCGCCAT 60.597 61.111 6.36 0.00 0.00 4.40
937 1000 1.352622 TGGGAGGGCAAGTGTTGAGT 61.353 55.000 0.00 0.00 0.00 3.41
942 1005 1.111277 GGGCAAGTGTTGAGTGGTTT 58.889 50.000 0.00 0.00 0.00 3.27
947 1010 3.283751 CAAGTGTTGAGTGGTTTGGGTA 58.716 45.455 0.00 0.00 0.00 3.69
962 1025 1.078848 GGTAGTGCTCCACTGCAGG 60.079 63.158 19.93 6.95 46.22 4.85
979 1042 2.047179 GTCGGTTGCTGGAGGGAC 60.047 66.667 0.00 0.00 0.00 4.46
1005 1068 1.335132 GGTAACCTGCGGAGATGGGA 61.335 60.000 5.10 0.00 0.00 4.37
1009 1072 1.144936 CCTGCGGAGATGGGAGTTC 59.855 63.158 5.10 0.00 0.00 3.01
1029 1092 1.976132 GATGCCTGGTGCTGCTCCTA 61.976 60.000 20.19 7.35 42.00 2.94
1040 1103 2.123640 GCTCCTACGCCCTCCTCT 60.124 66.667 0.00 0.00 0.00 3.69
1116 1179 1.746220 CTCGACTCCCAACTCTACAGG 59.254 57.143 0.00 0.00 0.00 4.00
1151 1214 2.288457 CGTGTGACCTTCTCTGATGTGT 60.288 50.000 0.00 0.00 0.00 3.72
1163 1226 1.376466 GATGTGTGCCTCACCCACT 59.624 57.895 6.66 0.00 45.61 4.00
1245 1313 4.659172 CCCAGCCGGCAACTTCCA 62.659 66.667 31.54 0.00 0.00 3.53
1247 1315 2.199652 CCAGCCGGCAACTTCCAAA 61.200 57.895 31.54 0.00 0.00 3.28
1257 1325 1.138069 CAACTTCCAAAACGCCCCTTT 59.862 47.619 0.00 0.00 0.00 3.11
1272 1340 2.192263 CCCTTTCCTCTCTAAGCAGGT 58.808 52.381 0.00 0.00 0.00 4.00
1327 1395 0.734889 GTATCCATGCTTTGCGTGCT 59.265 50.000 6.27 0.00 43.41 4.40
1355 1425 1.377725 CCCTCCACCATGTGCAGTC 60.378 63.158 0.00 0.00 31.34 3.51
1369 1439 1.314730 GCAGTCCGGTTTTCTTCCAA 58.685 50.000 0.00 0.00 0.00 3.53
1375 1445 5.122396 CAGTCCGGTTTTCTTCCAATAAGAG 59.878 44.000 0.00 0.00 0.00 2.85
1378 1448 5.001232 CCGGTTTTCTTCCAATAAGAGTCA 58.999 41.667 0.00 0.00 0.00 3.41
1411 1481 0.882927 CGAGCTCCTACTCTCCTCCG 60.883 65.000 8.47 0.00 34.35 4.63
1414 1484 1.452145 GCTCCTACTCTCCTCCGCTG 61.452 65.000 0.00 0.00 0.00 5.18
1480 1550 1.599606 CCGGCTCTGCTGTGTAGTCT 61.600 60.000 0.00 0.00 32.22 3.24
1481 1551 0.457509 CGGCTCTGCTGTGTAGTCTG 60.458 60.000 0.00 0.00 0.00 3.51
1522 1592 1.373812 CCCCGTTCCTTTTCTCCGT 59.626 57.895 0.00 0.00 0.00 4.69
1556 1626 1.433879 GTCGTCGCTGGAGCAGTAT 59.566 57.895 0.00 0.00 42.21 2.12
1575 1645 1.143620 GCTTGCCTCATCTCTCGCT 59.856 57.895 0.00 0.00 0.00 4.93
1824 1899 3.438087 CAGTGGATGGATGTTTCAGTGTC 59.562 47.826 0.00 0.00 0.00 3.67
1980 2055 7.715657 ACACTTTGCTGATTTTGTGATTTCTA 58.284 30.769 0.00 0.00 0.00 2.10
2072 2151 5.624344 AAAGATGAAGTGATGCAGTTCTG 57.376 39.130 14.08 0.00 42.39 3.02
2076 2155 3.807553 TGAAGTGATGCAGTTCTGTTGA 58.192 40.909 14.08 0.00 42.39 3.18
2079 2158 5.300034 TGAAGTGATGCAGTTCTGTTGAATT 59.700 36.000 14.08 0.00 42.39 2.17
2080 2159 5.779529 AGTGATGCAGTTCTGTTGAATTT 57.220 34.783 0.00 0.00 34.40 1.82
2149 2228 4.817464 TCATTGTAAAAACTACAGCCGTGT 59.183 37.500 0.00 0.00 41.06 4.49
2157 2236 3.039452 TACAGCCGTGTAGTCCACA 57.961 52.632 0.00 0.00 44.78 4.17
2162 2241 0.533308 GCCGTGTAGTCCACAAACCA 60.533 55.000 0.00 0.00 44.78 3.67
2196 2275 1.000385 CAAACAAGCCCGCAATGAAGA 60.000 47.619 0.26 0.00 0.00 2.87
2197 2276 0.883833 AACAAGCCCGCAATGAAGAG 59.116 50.000 0.26 0.00 0.00 2.85
2206 2285 1.992667 CGCAATGAAGAGTCGTGCTTA 59.007 47.619 0.00 0.00 35.99 3.09
2249 2328 2.281345 GTGCACTGCAGCTCCTGT 60.281 61.111 15.27 0.00 40.08 4.00
2260 2339 2.388735 CAGCTCCTGTATGGTGGACTA 58.611 52.381 0.00 0.00 37.07 2.59
2270 2349 0.470456 TGGTGGACTACGGAAGGTGT 60.470 55.000 0.00 0.00 0.00 4.16
2372 2452 8.621286 GTTGATTTTTCAGGTTTTCAGAGACTA 58.379 33.333 0.00 0.00 0.00 2.59
2376 2456 6.920569 TTTCAGGTTTTCAGAGACTACAAC 57.079 37.500 0.00 0.00 0.00 3.32
2449 2531 3.509575 TGGCACCCATTTACTTTGCTAAG 59.490 43.478 6.35 6.35 37.40 2.18
2458 2540 7.078228 CCATTTACTTTGCTAAGTTGTCTGAC 58.922 38.462 18.49 0.00 41.85 3.51
2460 2542 3.793559 ACTTTGCTAAGTTGTCTGACGT 58.206 40.909 7.78 0.00 41.85 4.34
2461 2543 4.189231 ACTTTGCTAAGTTGTCTGACGTT 58.811 39.130 7.78 0.00 41.85 3.99
2466 2548 3.554324 GCTAAGTTGTCTGACGTTGTTCA 59.446 43.478 2.98 0.00 0.00 3.18
2589 2671 3.003689 AGTGTGGTTTTCATTCTGAAGCG 59.996 43.478 0.00 0.00 37.70 4.68
2593 2675 2.293399 GGTTTTCATTCTGAAGCGGTGT 59.707 45.455 0.00 0.00 37.70 4.16
2697 2780 8.684386 TCTTGATAGTGTTGTGGTTCATTTAA 57.316 30.769 0.00 0.00 0.00 1.52
2699 2782 9.743057 CTTGATAGTGTTGTGGTTCATTTAAAA 57.257 29.630 0.00 0.00 0.00 1.52
2782 2866 1.334160 TGCAGTTCTCTTACCCGTCA 58.666 50.000 0.00 0.00 0.00 4.35
2828 2913 1.145377 AGTGCGGTTTTCAGTCGGT 59.855 52.632 0.00 0.00 0.00 4.69
2841 2926 1.069513 CAGTCGGTTGAAGTACCCACA 59.930 52.381 0.00 0.00 32.41 4.17
2880 2966 4.359706 GAAAAACAGAGTGTCCGCATTTT 58.640 39.130 0.00 0.00 0.00 1.82
2894 2980 7.794810 GTGTCCGCATTTTGGTAAATTTAAAAC 59.205 33.333 0.00 0.00 31.63 2.43
2896 2982 8.007152 GTCCGCATTTTGGTAAATTTAAAACTG 58.993 33.333 0.00 4.35 31.63 3.16
2911 2997 9.673454 AATTTAAAACTGCTCTTAAACCGTAAG 57.327 29.630 0.00 0.00 31.63 2.34
2932 3018 8.842280 CGTAAGGAATTAGAGAGAGTGTTCTAT 58.158 37.037 0.00 0.00 32.53 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.741915 GGGCTGACGAGAGAGGTTAG 59.258 60.000 0.00 0.00 0.00 2.34
1 2 0.039180 TGGGCTGACGAGAGAGGTTA 59.961 55.000 0.00 0.00 0.00 2.85
2 3 1.228894 TGGGCTGACGAGAGAGGTT 60.229 57.895 0.00 0.00 0.00 3.50
3 4 1.979693 GTGGGCTGACGAGAGAGGT 60.980 63.158 0.00 0.00 0.00 3.85
4 5 2.888863 GTGGGCTGACGAGAGAGG 59.111 66.667 0.00 0.00 0.00 3.69
5 6 2.487428 CGTGGGCTGACGAGAGAG 59.513 66.667 3.92 0.00 42.10 3.20
6 7 3.062466 CCGTGGGCTGACGAGAGA 61.062 66.667 10.52 0.00 42.10 3.10
7 8 4.803426 GCCGTGGGCTGACGAGAG 62.803 72.222 10.52 0.00 46.69 3.20
29 30 3.838795 CTTTCGAACGGGCGCGAG 61.839 66.667 30.98 19.13 37.85 5.03
30 31 4.651008 ACTTTCGAACGGGCGCGA 62.651 61.111 30.98 3.80 34.32 5.87
31 32 3.708734 AACTTTCGAACGGGCGCG 61.709 61.111 22.69 22.69 0.00 6.86
32 33 2.127383 CAACTTTCGAACGGGCGC 60.127 61.111 0.00 0.00 0.00 6.53
33 34 1.203313 GACAACTTTCGAACGGGCG 59.797 57.895 6.60 0.00 0.00 6.13
34 35 1.572941 GGACAACTTTCGAACGGGC 59.427 57.895 6.60 0.00 0.00 6.13
35 36 1.562575 CGGGACAACTTTCGAACGGG 61.563 60.000 6.60 0.73 0.00 5.28
36 37 0.598158 TCGGGACAACTTTCGAACGG 60.598 55.000 6.60 1.39 0.00 4.44
37 38 1.071041 GTTCGGGACAACTTTCGAACG 60.071 52.381 10.80 0.00 36.86 3.95
38 39 1.262417 GGTTCGGGACAACTTTCGAAC 59.738 52.381 16.02 16.02 36.86 3.95
39 40 1.585297 GGTTCGGGACAACTTTCGAA 58.415 50.000 0.00 0.00 36.86 3.71
40 41 0.249996 GGGTTCGGGACAACTTTCGA 60.250 55.000 0.00 0.00 0.00 3.71
41 42 1.562575 CGGGTTCGGGACAACTTTCG 61.563 60.000 0.00 0.00 0.00 3.46
42 43 0.249996 TCGGGTTCGGGACAACTTTC 60.250 55.000 0.00 0.00 36.95 2.62
43 44 0.533531 GTCGGGTTCGGGACAACTTT 60.534 55.000 0.00 0.00 36.95 2.66
44 45 1.070275 GTCGGGTTCGGGACAACTT 59.930 57.895 0.00 0.00 36.95 2.66
45 46 2.739132 GTCGGGTTCGGGACAACT 59.261 61.111 0.00 0.00 36.95 3.16
46 47 2.357881 GGTCGGGTTCGGGACAAC 60.358 66.667 0.00 0.00 34.87 3.32
47 48 3.628982 GGGTCGGGTTCGGGACAA 61.629 66.667 0.00 0.00 34.87 3.18
59 60 3.770040 TGATGACTGCCCGGGTCG 61.770 66.667 24.63 16.02 36.58 4.79
60 61 2.125106 GTGATGACTGCCCGGGTC 60.125 66.667 24.63 15.35 0.00 4.46
61 62 3.717294 GGTGATGACTGCCCGGGT 61.717 66.667 24.63 0.58 0.00 5.28
62 63 4.838152 CGGTGATGACTGCCCGGG 62.838 72.222 19.09 19.09 36.84 5.73
63 64 3.605749 AACGGTGATGACTGCCCGG 62.606 63.158 0.00 0.00 44.57 5.73
64 65 2.047274 AACGGTGATGACTGCCCG 60.047 61.111 0.00 0.00 45.72 6.13
65 66 2.040544 CCAACGGTGATGACTGCCC 61.041 63.158 0.00 0.00 30.67 5.36
66 67 2.040544 CCCAACGGTGATGACTGCC 61.041 63.158 0.00 0.00 30.67 4.85
67 68 1.298859 GACCCAACGGTGATGACTGC 61.299 60.000 0.00 0.00 44.88 4.40
68 69 0.673644 GGACCCAACGGTGATGACTG 60.674 60.000 0.00 0.00 44.88 3.51
69 70 1.677552 GGACCCAACGGTGATGACT 59.322 57.895 0.00 0.00 44.88 3.41
70 71 1.740296 CGGACCCAACGGTGATGAC 60.740 63.158 0.00 0.00 44.88 3.06
71 72 2.660206 CGGACCCAACGGTGATGA 59.340 61.111 0.00 0.00 44.88 2.92
72 73 2.435938 CCGGACCCAACGGTGATG 60.436 66.667 0.00 0.00 44.88 3.07
78 79 1.227556 GGATGATCCGGACCCAACG 60.228 63.158 6.12 0.00 0.00 4.10
79 80 1.148498 GGGATGATCCGGACCCAAC 59.852 63.158 20.42 13.57 41.72 3.77
80 81 2.076184 GGGGATGATCCGGACCCAA 61.076 63.158 25.06 5.06 43.67 4.12
81 82 1.670925 TAGGGGATGATCCGGACCCA 61.671 60.000 25.06 18.22 43.96 4.51
82 83 0.473117 TTAGGGGATGATCCGGACCC 60.473 60.000 17.77 17.77 37.43 4.46
83 84 0.685660 GTTAGGGGATGATCCGGACC 59.314 60.000 6.12 2.47 37.43 4.46
84 85 1.420430 TGTTAGGGGATGATCCGGAC 58.580 55.000 6.12 0.90 37.43 4.79
85 86 2.158158 AGATGTTAGGGGATGATCCGGA 60.158 50.000 6.61 6.61 37.43 5.14
86 87 2.260822 AGATGTTAGGGGATGATCCGG 58.739 52.381 5.22 0.00 37.43 5.14
87 88 3.832490 TGTAGATGTTAGGGGATGATCCG 59.168 47.826 5.22 0.00 37.43 4.18
88 89 5.825593 TTGTAGATGTTAGGGGATGATCC 57.174 43.478 1.94 1.94 35.23 3.36
89 90 7.054124 TGTTTTGTAGATGTTAGGGGATGATC 58.946 38.462 0.00 0.00 0.00 2.92
90 91 6.969043 TGTTTTGTAGATGTTAGGGGATGAT 58.031 36.000 0.00 0.00 0.00 2.45
91 92 6.381498 TGTTTTGTAGATGTTAGGGGATGA 57.619 37.500 0.00 0.00 0.00 2.92
92 93 7.056635 AGATGTTTTGTAGATGTTAGGGGATG 58.943 38.462 0.00 0.00 0.00 3.51
93 94 7.213178 AGATGTTTTGTAGATGTTAGGGGAT 57.787 36.000 0.00 0.00 0.00 3.85
94 95 6.352737 GGAGATGTTTTGTAGATGTTAGGGGA 60.353 42.308 0.00 0.00 0.00 4.81
95 96 5.823045 GGAGATGTTTTGTAGATGTTAGGGG 59.177 44.000 0.00 0.00 0.00 4.79
96 97 6.414732 TGGAGATGTTTTGTAGATGTTAGGG 58.585 40.000 0.00 0.00 0.00 3.53
97 98 8.511604 AATGGAGATGTTTTGTAGATGTTAGG 57.488 34.615 0.00 0.00 0.00 2.69
100 101 9.696917 GAAAAATGGAGATGTTTTGTAGATGTT 57.303 29.630 0.00 0.00 0.00 2.71
101 102 9.082313 AGAAAAATGGAGATGTTTTGTAGATGT 57.918 29.630 0.00 0.00 0.00 3.06
102 103 9.918630 AAGAAAAATGGAGATGTTTTGTAGATG 57.081 29.630 0.00 0.00 0.00 2.90
107 108 8.676401 CCAAAAAGAAAAATGGAGATGTTTTGT 58.324 29.630 0.00 0.00 34.82 2.83
108 109 8.891720 TCCAAAAAGAAAAATGGAGATGTTTTG 58.108 29.630 0.00 0.00 37.05 2.44
109 110 8.892723 GTCCAAAAAGAAAAATGGAGATGTTTT 58.107 29.630 0.00 0.00 42.35 2.43
110 111 8.267183 AGTCCAAAAAGAAAAATGGAGATGTTT 58.733 29.630 0.00 0.00 42.35 2.83
111 112 7.795047 AGTCCAAAAAGAAAAATGGAGATGTT 58.205 30.769 0.00 0.00 42.35 2.71
112 113 7.365497 AGTCCAAAAAGAAAAATGGAGATGT 57.635 32.000 0.00 0.00 42.35 3.06
113 114 6.870439 GGAGTCCAAAAAGAAAAATGGAGATG 59.130 38.462 3.60 0.00 42.35 2.90
114 115 6.014242 GGGAGTCCAAAAAGAAAAATGGAGAT 60.014 38.462 12.30 0.00 42.35 2.75
115 116 5.304357 GGGAGTCCAAAAAGAAAAATGGAGA 59.696 40.000 12.30 0.00 42.35 3.71
116 117 5.305386 AGGGAGTCCAAAAAGAAAAATGGAG 59.695 40.000 12.30 0.00 42.35 3.86
117 118 5.215845 AGGGAGTCCAAAAAGAAAAATGGA 58.784 37.500 12.30 0.00 39.57 3.41
118 119 5.551305 AGGGAGTCCAAAAAGAAAAATGG 57.449 39.130 12.30 0.00 34.83 3.16
119 120 6.267699 AGGTAGGGAGTCCAAAAAGAAAAATG 59.732 38.462 12.30 0.00 34.83 2.32
120 121 6.382087 AGGTAGGGAGTCCAAAAAGAAAAAT 58.618 36.000 12.30 0.00 34.83 1.82
121 122 5.773091 AGGTAGGGAGTCCAAAAAGAAAAA 58.227 37.500 12.30 0.00 34.83 1.94
122 123 5.397553 AGGTAGGGAGTCCAAAAAGAAAA 57.602 39.130 12.30 0.00 34.83 2.29
123 124 6.713731 ATAGGTAGGGAGTCCAAAAAGAAA 57.286 37.500 12.30 0.00 34.83 2.52
124 125 6.713731 AATAGGTAGGGAGTCCAAAAAGAA 57.286 37.500 12.30 0.00 34.83 2.52
125 126 6.045106 ACAAATAGGTAGGGAGTCCAAAAAGA 59.955 38.462 12.30 0.00 34.83 2.52
126 127 6.246163 ACAAATAGGTAGGGAGTCCAAAAAG 58.754 40.000 12.30 0.00 34.83 2.27
127 128 6.208840 ACAAATAGGTAGGGAGTCCAAAAA 57.791 37.500 12.30 0.00 34.83 1.94
128 129 5.853572 ACAAATAGGTAGGGAGTCCAAAA 57.146 39.130 12.30 0.00 34.83 2.44
129 130 5.853572 AACAAATAGGTAGGGAGTCCAAA 57.146 39.130 12.30 0.00 34.83 3.28
130 131 5.550403 AGAAACAAATAGGTAGGGAGTCCAA 59.450 40.000 12.30 0.00 34.83 3.53
131 132 5.045869 CAGAAACAAATAGGTAGGGAGTCCA 60.046 44.000 12.30 0.00 34.83 4.02
132 133 5.429130 CAGAAACAAATAGGTAGGGAGTCC 58.571 45.833 0.00 0.00 0.00 3.85
133 134 5.189145 TCCAGAAACAAATAGGTAGGGAGTC 59.811 44.000 0.00 0.00 0.00 3.36
134 135 5.045797 GTCCAGAAACAAATAGGTAGGGAGT 60.046 44.000 0.00 0.00 0.00 3.85
135 136 5.429130 GTCCAGAAACAAATAGGTAGGGAG 58.571 45.833 0.00 0.00 0.00 4.30
136 137 4.226620 GGTCCAGAAACAAATAGGTAGGGA 59.773 45.833 0.00 0.00 0.00 4.20
137 138 4.524053 GGTCCAGAAACAAATAGGTAGGG 58.476 47.826 0.00 0.00 0.00 3.53
138 139 4.189231 CGGTCCAGAAACAAATAGGTAGG 58.811 47.826 0.00 0.00 0.00 3.18
139 140 4.828829 ACGGTCCAGAAACAAATAGGTAG 58.171 43.478 0.00 0.00 0.00 3.18
140 141 4.322953 GGACGGTCCAGAAACAAATAGGTA 60.323 45.833 22.10 0.00 36.28 3.08
141 142 3.558533 GGACGGTCCAGAAACAAATAGGT 60.559 47.826 22.10 0.00 36.28 3.08
142 143 3.007635 GGACGGTCCAGAAACAAATAGG 58.992 50.000 22.10 0.00 36.28 2.57
143 144 2.671396 CGGACGGTCCAGAAACAAATAG 59.329 50.000 25.80 2.19 35.91 1.73
144 145 2.299582 TCGGACGGTCCAGAAACAAATA 59.700 45.455 25.80 0.00 35.91 1.40
145 146 1.071071 TCGGACGGTCCAGAAACAAAT 59.929 47.619 25.80 0.00 35.91 2.32
146 147 0.464870 TCGGACGGTCCAGAAACAAA 59.535 50.000 25.80 0.78 35.91 2.83
147 148 0.682852 ATCGGACGGTCCAGAAACAA 59.317 50.000 25.80 4.33 35.91 2.83
148 149 0.682852 AATCGGACGGTCCAGAAACA 59.317 50.000 25.80 3.53 35.91 2.83
149 150 2.265683 GTAATCGGACGGTCCAGAAAC 58.734 52.381 25.80 19.15 35.91 2.78
150 151 1.135315 CGTAATCGGACGGTCCAGAAA 60.135 52.381 25.80 13.34 39.19 2.52
151 152 0.452987 CGTAATCGGACGGTCCAGAA 59.547 55.000 25.80 11.61 39.19 3.02
152 153 0.392863 TCGTAATCGGACGGTCCAGA 60.393 55.000 25.80 21.99 43.12 3.86
153 154 0.666913 ATCGTAATCGGACGGTCCAG 59.333 55.000 25.80 17.93 43.12 3.86
154 155 0.664761 GATCGTAATCGGACGGTCCA 59.335 55.000 25.80 13.80 45.28 4.02
155 156 3.468780 GATCGTAATCGGACGGTCC 57.531 57.895 17.38 17.38 45.28 4.46
164 165 6.256912 AGAATAGACCCTTCGATCGTAATC 57.743 41.667 15.94 7.19 0.00 1.75
165 166 7.230108 TGTTAGAATAGACCCTTCGATCGTAAT 59.770 37.037 15.94 0.00 0.00 1.89
166 167 6.543465 TGTTAGAATAGACCCTTCGATCGTAA 59.457 38.462 15.94 7.36 0.00 3.18
167 168 6.057533 TGTTAGAATAGACCCTTCGATCGTA 58.942 40.000 15.94 4.34 0.00 3.43
168 169 4.885907 TGTTAGAATAGACCCTTCGATCGT 59.114 41.667 15.94 0.00 0.00 3.73
169 170 5.434352 TGTTAGAATAGACCCTTCGATCG 57.566 43.478 9.36 9.36 0.00 3.69
170 171 6.476053 GTGTTGTTAGAATAGACCCTTCGATC 59.524 42.308 0.00 0.00 0.00 3.69
171 172 6.338937 GTGTTGTTAGAATAGACCCTTCGAT 58.661 40.000 0.00 0.00 0.00 3.59
172 173 5.337009 GGTGTTGTTAGAATAGACCCTTCGA 60.337 44.000 0.00 0.00 0.00 3.71
173 174 4.868734 GGTGTTGTTAGAATAGACCCTTCG 59.131 45.833 0.00 0.00 0.00 3.79
174 175 5.183969 GGGTGTTGTTAGAATAGACCCTTC 58.816 45.833 0.00 0.00 38.85 3.46
175 176 4.018688 GGGGTGTTGTTAGAATAGACCCTT 60.019 45.833 0.00 0.00 41.26 3.95
176 177 3.522343 GGGGTGTTGTTAGAATAGACCCT 59.478 47.826 0.00 0.00 41.26 4.34
204 205 3.270027 CGGTTGATGTGCAGAATAAGGA 58.730 45.455 0.00 0.00 0.00 3.36
226 227 7.365295 GGGTAGTGAGGTGTTATCAAAATAGGA 60.365 40.741 0.00 0.00 0.00 2.94
228 229 6.479001 CGGGTAGTGAGGTGTTATCAAAATAG 59.521 42.308 0.00 0.00 0.00 1.73
233 234 2.093869 GCGGGTAGTGAGGTGTTATCAA 60.094 50.000 0.00 0.00 0.00 2.57
281 282 2.358737 GTGGGGTGAAGGTGAGCG 60.359 66.667 0.00 0.00 0.00 5.03
283 284 1.679898 GAGGTGGGGTGAAGGTGAG 59.320 63.158 0.00 0.00 0.00 3.51
287 288 2.204151 AGGGAGGTGGGGTGAAGG 60.204 66.667 0.00 0.00 0.00 3.46
307 308 3.164977 TGGGCGAGGTGGTTGTCA 61.165 61.111 0.00 0.00 0.00 3.58
331 332 1.356398 GGTAGGTGGGGTTTGGAATCA 59.644 52.381 0.00 0.00 0.00 2.57
352 353 1.542187 GCACTCCGGTAGAAGGTGGT 61.542 60.000 0.00 0.00 0.00 4.16
399 400 1.147399 CGGTAGAAGGAGGATAGGGGT 59.853 57.143 0.00 0.00 0.00 4.95
405 406 1.108132 GGCGTCGGTAGAAGGAGGAT 61.108 60.000 0.00 0.00 0.00 3.24
409 410 1.973281 AACGGCGTCGGTAGAAGGA 60.973 57.895 15.17 0.00 41.39 3.36
523 524 2.960688 GCCCCTATCCATCGGAGCC 61.961 68.421 0.00 0.00 34.05 4.70
526 527 1.229209 GGAGCCCCTATCCATCGGA 60.229 63.158 0.00 0.00 36.79 4.55
559 560 3.883744 CTGAAGGTCGCGGCCAGTT 62.884 63.158 34.17 19.30 0.00 3.16
577 579 2.907897 ATAGCTTGCCGACGAGGTGC 62.908 60.000 0.36 0.00 43.70 5.01
579 581 1.141881 CATAGCTTGCCGACGAGGT 59.858 57.895 0.00 0.00 43.70 3.85
590 592 1.133976 GCATGAGGACCACCATAGCTT 60.134 52.381 0.00 0.00 38.94 3.74
629 631 0.755686 GGCCTGGATCTGTCTAGTGG 59.244 60.000 0.00 0.00 31.49 4.00
633 635 1.043116 CCGTGGCCTGGATCTGTCTA 61.043 60.000 3.32 0.00 0.00 2.59
635 637 2.187946 CCGTGGCCTGGATCTGTC 59.812 66.667 3.32 0.00 0.00 3.51
636 638 4.101448 GCCGTGGCCTGGATCTGT 62.101 66.667 17.63 0.00 34.56 3.41
637 639 4.100084 TGCCGTGGCCTGGATCTG 62.100 66.667 17.63 0.00 41.09 2.90
638 640 3.790437 CTGCCGTGGCCTGGATCT 61.790 66.667 17.63 0.00 41.09 2.75
656 658 2.273449 GGATCTGGCACTGGGTGG 59.727 66.667 0.00 0.00 33.64 4.61
657 659 1.077930 CTGGATCTGGCACTGGGTG 60.078 63.158 0.00 0.00 36.51 4.61
658 660 2.304056 CCTGGATCTGGCACTGGGT 61.304 63.158 0.00 0.00 0.00 4.51
659 661 2.593978 CCTGGATCTGGCACTGGG 59.406 66.667 0.00 0.00 0.00 4.45
660 662 2.124403 GCCTGGATCTGGCACTGG 60.124 66.667 20.14 6.47 45.75 4.00
903 966 3.719646 CCCAATGGCGAGATGGGCA 62.720 63.158 9.06 0.00 46.77 5.36
915 978 0.604578 CAACACTTGCCCTCCCAATG 59.395 55.000 0.00 0.00 0.00 2.82
917 980 0.178992 CTCAACACTTGCCCTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
937 1000 0.109723 GTGGAGCACTACCCAAACCA 59.890 55.000 0.00 0.00 33.69 3.67
942 1005 1.830587 CTGCAGTGGAGCACTACCCA 61.831 60.000 5.25 0.00 43.43 4.51
947 1010 2.746359 GACCTGCAGTGGAGCACT 59.254 61.111 13.81 0.00 46.51 4.40
962 1025 2.047179 GTCCCTCCAGCAACCGAC 60.047 66.667 0.00 0.00 0.00 4.79
1029 1092 3.394836 GGCAGAAGAGGAGGGCGT 61.395 66.667 0.00 0.00 0.00 5.68
1040 1103 2.747686 GGTGGACGAAGGGCAGAA 59.252 61.111 0.00 0.00 0.00 3.02
1097 1160 1.075050 ACCTGTAGAGTTGGGAGTCGA 59.925 52.381 0.00 0.00 0.00 4.20
1116 1179 1.601903 TCACACGCATCAAAGTTGGAC 59.398 47.619 0.00 0.00 0.00 4.02
1151 1214 3.805928 CCACTAGTGGGTGAGGCA 58.194 61.111 31.15 0.00 46.81 4.75
1245 1313 0.771755 AGAGAGGAAAGGGGCGTTTT 59.228 50.000 0.00 0.00 0.00 2.43
1247 1315 1.555533 CTTAGAGAGGAAAGGGGCGTT 59.444 52.381 0.00 0.00 0.00 4.84
1257 1325 1.288037 TGGCTACCTGCTTAGAGAGGA 59.712 52.381 4.95 0.00 42.39 3.71
1272 1340 1.064003 TTTCTCACCTGGCTTGGCTA 58.936 50.000 0.00 0.00 0.00 3.93
1346 1416 1.880027 GAAGAAAACCGGACTGCACAT 59.120 47.619 9.46 0.00 0.00 3.21
1355 1425 5.001232 TGACTCTTATTGGAAGAAAACCGG 58.999 41.667 0.00 0.00 0.00 5.28
1401 1471 0.035458 CCAAAACAGCGGAGGAGAGT 59.965 55.000 0.00 0.00 0.00 3.24
1411 1481 1.079612 GCATCCAGCCCAAAACAGC 60.080 57.895 0.00 0.00 37.23 4.40
1470 1540 0.108662 TGGCGATGCAGACTACACAG 60.109 55.000 0.00 0.00 0.00 3.66
1480 1550 3.422122 GCTTTTCATTGGCGATGCA 57.578 47.368 10.00 0.00 35.64 3.96
1514 1584 1.739466 GCATTGCTCATCACGGAGAAA 59.261 47.619 0.16 0.00 36.87 2.52
1522 1592 1.089112 CGACCTTGCATTGCTCATCA 58.911 50.000 10.49 0.00 0.00 3.07
1556 1626 1.153489 GCGAGAGATGAGGCAAGCA 60.153 57.895 0.00 0.00 0.00 3.91
1679 1749 2.083774 CGGGAGCACAGCAAAAATCTA 58.916 47.619 0.00 0.00 0.00 1.98
1746 1821 0.606944 TGGATAAACCACACCACGGC 60.607 55.000 0.00 0.00 44.64 5.68
1824 1899 5.323900 CACAGGCACGACAATAAACATAAG 58.676 41.667 0.00 0.00 0.00 1.73
1900 1975 0.747255 CGTACTGCATAGTGGAGGCT 59.253 55.000 3.57 0.00 40.38 4.58
2079 2158 9.892130 AACAACAACAAAATTAAGTTATGGGAA 57.108 25.926 0.00 0.00 0.00 3.97
2080 2159 9.319143 CAACAACAACAAAATTAAGTTATGGGA 57.681 29.630 0.00 0.00 0.00 4.37
2149 2228 1.071814 GGCCGTGGTTTGTGGACTA 59.928 57.895 0.00 0.00 0.00 2.59
2162 2241 4.927782 TTTGAGCTGCACGGCCGT 62.928 61.111 28.70 28.70 0.00 5.68
2196 2275 3.876274 ATCACAGACATAAGCACGACT 57.124 42.857 0.00 0.00 0.00 4.18
2197 2276 5.108217 CGAATATCACAGACATAAGCACGAC 60.108 44.000 0.00 0.00 0.00 4.34
2206 2285 6.340522 TGTGTTCATCGAATATCACAGACAT 58.659 36.000 10.99 0.00 33.07 3.06
2249 2328 2.104967 CACCTTCCGTAGTCCACCATA 58.895 52.381 0.00 0.00 0.00 2.74
2260 2339 4.619227 CCGCACCACACCTTCCGT 62.619 66.667 0.00 0.00 0.00 4.69
2270 2349 1.302431 CAGTCCATCAACCGCACCA 60.302 57.895 0.00 0.00 0.00 4.17
2345 2425 7.122650 AGTCTCTGAAAACCTGAAAAATCAACA 59.877 33.333 0.00 0.00 0.00 3.33
2525 2607 6.363088 CGAGCTGCATAATTTTTGTCTTTTCA 59.637 34.615 1.02 0.00 0.00 2.69
2589 2671 0.036388 ATCACACGACCATCCACACC 60.036 55.000 0.00 0.00 0.00 4.16
2593 2675 1.071542 ACAACATCACACGACCATCCA 59.928 47.619 0.00 0.00 0.00 3.41
2697 2780 2.037772 AGAGTGCACTTCAGATCGGTTT 59.962 45.455 22.65 0.00 0.00 3.27
2699 2782 1.261480 AGAGTGCACTTCAGATCGGT 58.739 50.000 22.65 0.00 0.00 4.69
2705 2788 3.917380 CGAGAAAGTAGAGTGCACTTCAG 59.083 47.826 22.65 7.80 35.19 3.02
2782 2866 0.238289 CGAAAAACCGCACTGCATCT 59.762 50.000 1.11 0.00 0.00 2.90
2828 2913 4.006989 CCAAATCGATGTGGGTACTTCAA 58.993 43.478 24.94 0.00 32.17 2.69
2841 2926 0.390603 TTCGCGACACCCAAATCGAT 60.391 50.000 9.15 0.00 40.86 3.59
2880 2966 9.752961 GGTTTAAGAGCAGTTTTAAATTTACCA 57.247 29.630 0.00 0.00 33.02 3.25
2894 2980 7.039882 TCTAATTCCTTACGGTTTAAGAGCAG 58.960 38.462 0.00 0.00 0.00 4.24
2896 2982 7.263496 TCTCTAATTCCTTACGGTTTAAGAGC 58.737 38.462 0.00 0.00 0.00 4.09
2932 3018 5.283294 TCGACGAGACACAACTTTTTCATA 58.717 37.500 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.