Multiple sequence alignment - TraesCS3D01G512100

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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 TraesCS3D01G512100 chr3D 100.000 4514 0 0 1 4514 596847704 596852217 0.000000e+00 8336.0
1 TraesCS3D01G512100 chr3D 83.752 3188 384 64 612 3748 595942816 595939712 0.000000e+00 2894.0
2 TraesCS3D01G512100 chr3D 90.014 711 65 5 3117 3825 595931010 595930304 0.000000e+00 915.0
3 TraesCS3D01G512100 chr3D 76.689 888 204 3 2492 3378 32301087 32301972 1.460000e-134 490.0
4 TraesCS3D01G512100 chr3D 89.850 266 22 2 2 266 172608587 172608848 2.010000e-88 337.0
5 TraesCS3D01G512100 chr3D 89.513 267 26 2 1 266 357428965 357428700 2.010000e-88 337.0
6 TraesCS3D01G512100 chr3B 94.225 3740 206 6 266 3996 801196493 801192755 0.000000e+00 5701.0
7 TraesCS3D01G512100 chr3B 92.214 3763 233 16 266 3996 803049814 803046080 0.000000e+00 5271.0
8 TraesCS3D01G512100 chr3B 97.645 2166 51 0 1831 3996 802610469 802608304 0.000000e+00 3718.0
9 TraesCS3D01G512100 chr3B 84.025 3180 390 65 612 3736 799104618 799101502 0.000000e+00 2950.0
10 TraesCS3D01G512100 chr3B 93.333 1035 53 7 266 1293 802616794 802615769 0.000000e+00 1515.0
11 TraesCS3D01G512100 chr3B 93.878 539 11 7 3997 4514 803046047 803045510 0.000000e+00 793.0
12 TraesCS3D01G512100 chr3B 97.399 346 9 0 4169 4514 801192358 801192013 1.400000e-164 590.0
13 TraesCS3D01G512100 chr3B 89.888 267 26 1 1 266 224931772 224931506 4.320000e-90 342.0
14 TraesCS3D01G512100 chr3B 93.299 194 5 1 3997 4182 801192722 801192529 3.440000e-71 279.0
15 TraesCS3D01G512100 chr3B 98.529 68 1 0 1768 1835 802615769 802615702 2.210000e-23 121.0
16 TraesCS3D01G512100 chr3B 80.597 134 22 4 1454 1585 54794762 54794893 2.870000e-17 100.0
17 TraesCS3D01G512100 chr3B 97.368 38 1 0 3997 4034 802608271 802608234 1.050000e-06 65.8
18 TraesCS3D01G512100 chr3B 100.000 31 0 0 3950 3980 802608234 802608204 1.750000e-04 58.4
19 TraesCS3D01G512100 chr3A 82.694 1826 251 24 925 2710 726742938 726741138 0.000000e+00 1561.0
20 TraesCS3D01G512100 chr3A 87.918 687 66 9 3152 3828 726726465 726725786 0.000000e+00 793.0
21 TraesCS3D01G512100 chr3A 91.241 411 34 2 2704 3113 726726871 726726462 3.940000e-155 558.0
22 TraesCS3D01G512100 chr3A 89.888 267 26 1 1 266 536625129 536624863 4.320000e-90 342.0
23 TraesCS3D01G512100 chr3A 75.126 398 79 19 1200 1587 44710042 44710429 7.770000e-38 169.0
24 TraesCS3D01G512100 chr3A 80.597 134 22 4 1454 1585 44639964 44640095 2.870000e-17 100.0
25 TraesCS3D01G512100 chr3A 79.114 158 23 7 4231 4385 726725553 726725403 2.870000e-17 100.0
26 TraesCS3D01G512100 chr5D 96.617 266 9 0 1 266 347017385 347017650 4.140000e-120 442.0
27 TraesCS3D01G512100 chr7A 94.382 267 14 1 1 266 256886747 256887013 4.200000e-110 409.0
28 TraesCS3D01G512100 chr6B 91.120 259 22 1 1 258 134681988 134681730 2.580000e-92 350.0
29 TraesCS3D01G512100 chr5A 89.925 268 24 3 1 266 28762046 28761780 4.320000e-90 342.0
30 TraesCS3D01G512100 chr1A 89.179 268 27 2 1 266 222370887 222370620 2.600000e-87 333.0


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 TraesCS3D01G512100 chr3D 596847704 596852217 4513 False 8336.000000 8336 100.000000 1 4514 1 chr3D.!!$F3 4513
1 TraesCS3D01G512100 chr3D 595939712 595942816 3104 True 2894.000000 2894 83.752000 612 3748 1 chr3D.!!$R3 3136
2 TraesCS3D01G512100 chr3D 595930304 595931010 706 True 915.000000 915 90.014000 3117 3825 1 chr3D.!!$R2 708
3 TraesCS3D01G512100 chr3D 32301087 32301972 885 False 490.000000 490 76.689000 2492 3378 1 chr3D.!!$F1 886
4 TraesCS3D01G512100 chr3B 803045510 803049814 4304 True 3032.000000 5271 93.046000 266 4514 2 chr3B.!!$R6 4248
5 TraesCS3D01G512100 chr3B 799101502 799104618 3116 True 2950.000000 2950 84.025000 612 3736 1 chr3B.!!$R2 3124
6 TraesCS3D01G512100 chr3B 801192013 801196493 4480 True 2190.000000 5701 94.974333 266 4514 3 chr3B.!!$R3 4248
7 TraesCS3D01G512100 chr3B 802608204 802610469 2265 True 1280.733333 3718 98.337667 1831 4034 3 chr3B.!!$R4 2203
8 TraesCS3D01G512100 chr3B 802615702 802616794 1092 True 818.000000 1515 95.931000 266 1835 2 chr3B.!!$R5 1569
9 TraesCS3D01G512100 chr3A 726741138 726742938 1800 True 1561.000000 1561 82.694000 925 2710 1 chr3A.!!$R2 1785
10 TraesCS3D01G512100 chr3A 726725403 726726871 1468 True 483.666667 793 86.091000 2704 4385 3 chr3A.!!$R3 1681

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
144 145 0.035458 CCGAGCACCCCCATCTATTC 59.965 60.0 0.0 0.0 0.00 1.75 F
215 216 0.037605 CCCGTGTAACCCTGTCACTC 60.038 60.0 0.0 0.0 0.00 3.51 F
1694 1729 0.183971 AATGTTGGGGGTTCGACACA 59.816 50.0 0.0 0.0 34.24 3.72 F
1702 1740 0.320771 GGGTTCGACACACTCTGCAT 60.321 55.0 0.0 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1753 1.139058 CTTCCCATGAACGGTAGGAGG 59.861 57.143 0.00 0.0 0.00 4.30 R
1718 1756 2.434336 TCATCTTCCCATGAACGGTAGG 59.566 50.000 0.00 0.0 29.41 3.18 R
3207 3299 0.032117 AGGGGTCGATGATCTCACCA 60.032 55.000 11.25 0.0 30.81 4.17 R
3519 3614 0.169894 GTCCCGAACGTACAGGAGTC 59.830 60.000 5.56 0.0 0.00 3.36 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
18 19 2.387309 CATGCAACCCTCTGCTACG 58.613 57.895 0.00 0.00 43.07 3.51
19 20 1.450312 ATGCAACCCTCTGCTACGC 60.450 57.895 0.00 0.00 43.07 4.42
20 21 2.047274 GCAACCCTCTGCTACGCA 60.047 61.111 0.00 0.00 39.34 5.24
21 22 2.391389 GCAACCCTCTGCTACGCAC 61.391 63.158 0.00 0.00 39.34 5.34
22 23 1.741770 CAACCCTCTGCTACGCACC 60.742 63.158 0.00 0.00 33.79 5.01
23 24 1.913762 AACCCTCTGCTACGCACCT 60.914 57.895 0.00 0.00 33.79 4.00
24 25 1.481056 AACCCTCTGCTACGCACCTT 61.481 55.000 0.00 0.00 33.79 3.50
25 26 1.153549 CCCTCTGCTACGCACCTTC 60.154 63.158 0.00 0.00 33.79 3.46
26 27 1.608717 CCCTCTGCTACGCACCTTCT 61.609 60.000 0.00 0.00 33.79 2.85
27 28 0.247736 CCTCTGCTACGCACCTTCTT 59.752 55.000 0.00 0.00 33.79 2.52
28 29 1.634702 CTCTGCTACGCACCTTCTTC 58.365 55.000 0.00 0.00 33.79 2.87
29 30 0.966179 TCTGCTACGCACCTTCTTCA 59.034 50.000 0.00 0.00 33.79 3.02
30 31 1.067565 TCTGCTACGCACCTTCTTCAG 60.068 52.381 0.00 0.00 33.79 3.02
41 42 3.988976 CCTTCTTCAGGTCATCAAGGA 57.011 47.619 0.00 0.00 37.99 3.36
42 43 3.604582 CCTTCTTCAGGTCATCAAGGAC 58.395 50.000 0.00 0.00 37.99 3.85
43 44 3.257393 CTTCTTCAGGTCATCAAGGACG 58.743 50.000 0.00 0.00 38.70 4.79
44 45 2.525368 TCTTCAGGTCATCAAGGACGA 58.475 47.619 0.00 0.00 38.70 4.20
45 46 2.231478 TCTTCAGGTCATCAAGGACGAC 59.769 50.000 0.00 0.00 38.70 4.34
46 47 0.526211 TCAGGTCATCAAGGACGACG 59.474 55.000 0.00 0.00 38.70 5.12
47 48 1.078759 CAGGTCATCAAGGACGACGC 61.079 60.000 0.00 0.00 38.70 5.19
48 49 1.215647 GGTCATCAAGGACGACGCT 59.784 57.895 0.00 0.00 38.70 5.07
49 50 0.802607 GGTCATCAAGGACGACGCTC 60.803 60.000 0.00 0.00 38.70 5.03
50 51 1.134530 GTCATCAAGGACGACGCTCG 61.135 60.000 0.00 5.97 46.93 5.03
51 52 1.874019 CATCAAGGACGACGCTCGG 60.874 63.158 11.13 0.00 45.59 4.63
52 53 3.064987 ATCAAGGACGACGCTCGGG 62.065 63.158 11.13 0.00 45.59 5.14
63 64 4.575973 GCTCGGGCATGGGCATCT 62.576 66.667 0.00 0.00 43.71 2.90
64 65 2.593725 CTCGGGCATGGGCATCTG 60.594 66.667 0.00 0.00 43.71 2.90
65 66 4.881440 TCGGGCATGGGCATCTGC 62.881 66.667 0.00 0.00 43.71 4.26
82 83 4.856801 CCGGGGCCAAGGACATCG 62.857 72.222 11.39 0.00 0.00 3.84
84 85 4.424711 GGGGCCAAGGACATCGCA 62.425 66.667 4.39 0.00 0.00 5.10
85 86 2.361104 GGGCCAAGGACATCGCAA 60.361 61.111 4.39 0.00 0.00 4.85
86 87 1.976474 GGGCCAAGGACATCGCAAA 60.976 57.895 4.39 0.00 0.00 3.68
87 88 1.212751 GGCCAAGGACATCGCAAAC 59.787 57.895 0.00 0.00 0.00 2.93
88 89 1.244019 GGCCAAGGACATCGCAAACT 61.244 55.000 0.00 0.00 0.00 2.66
89 90 0.598065 GCCAAGGACATCGCAAACTT 59.402 50.000 0.00 0.00 0.00 2.66
90 91 1.000274 GCCAAGGACATCGCAAACTTT 60.000 47.619 0.00 0.00 0.00 2.66
91 92 2.227865 GCCAAGGACATCGCAAACTTTA 59.772 45.455 0.00 0.00 0.00 1.85
92 93 3.670627 GCCAAGGACATCGCAAACTTTAG 60.671 47.826 0.00 0.00 0.00 1.85
93 94 3.119849 CCAAGGACATCGCAAACTTTAGG 60.120 47.826 0.00 0.00 0.00 2.69
94 95 2.084546 AGGACATCGCAAACTTTAGGC 58.915 47.619 0.00 0.00 0.00 3.93
95 96 1.132453 GGACATCGCAAACTTTAGGCC 59.868 52.381 0.00 0.00 0.00 5.19
96 97 2.084546 GACATCGCAAACTTTAGGCCT 58.915 47.619 11.78 11.78 0.00 5.19
97 98 2.084546 ACATCGCAAACTTTAGGCCTC 58.915 47.619 9.68 0.00 0.00 4.70
98 99 1.401905 CATCGCAAACTTTAGGCCTCC 59.598 52.381 9.68 0.00 0.00 4.30
99 100 0.322187 TCGCAAACTTTAGGCCTCCC 60.322 55.000 9.68 0.00 0.00 4.30
100 101 0.322546 CGCAAACTTTAGGCCTCCCT 60.323 55.000 9.68 0.00 45.61 4.20
101 102 1.177401 GCAAACTTTAGGCCTCCCTG 58.823 55.000 9.68 0.17 42.90 4.45
102 103 1.271926 GCAAACTTTAGGCCTCCCTGA 60.272 52.381 9.68 0.00 42.90 3.86
103 104 2.621668 GCAAACTTTAGGCCTCCCTGAT 60.622 50.000 9.68 0.00 42.90 2.90
104 105 3.701664 CAAACTTTAGGCCTCCCTGATT 58.298 45.455 9.68 0.00 42.90 2.57
105 106 4.089361 CAAACTTTAGGCCTCCCTGATTT 58.911 43.478 9.68 0.69 42.90 2.17
106 107 3.372440 ACTTTAGGCCTCCCTGATTTG 57.628 47.619 9.68 0.00 42.90 2.32
107 108 2.649816 ACTTTAGGCCTCCCTGATTTGT 59.350 45.455 9.68 0.00 42.90 2.83
108 109 3.850173 ACTTTAGGCCTCCCTGATTTGTA 59.150 43.478 9.68 0.00 42.90 2.41
109 110 4.080299 ACTTTAGGCCTCCCTGATTTGTAG 60.080 45.833 9.68 0.00 42.90 2.74
110 111 1.216990 AGGCCTCCCTGATTTGTAGG 58.783 55.000 0.00 0.00 40.94 3.18
111 112 0.919710 GGCCTCCCTGATTTGTAGGT 59.080 55.000 0.00 0.00 33.31 3.08
112 113 2.124411 GGCCTCCCTGATTTGTAGGTA 58.876 52.381 0.00 0.00 33.31 3.08
113 114 2.104963 GGCCTCCCTGATTTGTAGGTAG 59.895 54.545 0.00 0.00 33.31 3.18
114 115 2.772515 GCCTCCCTGATTTGTAGGTAGT 59.227 50.000 0.00 0.00 33.31 2.73
115 116 3.200165 GCCTCCCTGATTTGTAGGTAGTT 59.800 47.826 0.00 0.00 33.31 2.24
116 117 4.407945 GCCTCCCTGATTTGTAGGTAGTTA 59.592 45.833 0.00 0.00 33.31 2.24
117 118 5.453480 GCCTCCCTGATTTGTAGGTAGTTAG 60.453 48.000 0.00 0.00 33.31 2.34
118 119 5.661759 CCTCCCTGATTTGTAGGTAGTTAGT 59.338 44.000 0.00 0.00 33.31 2.24
119 120 6.156429 CCTCCCTGATTTGTAGGTAGTTAGTT 59.844 42.308 0.00 0.00 33.31 2.24
120 121 7.311109 CCTCCCTGATTTGTAGGTAGTTAGTTT 60.311 40.741 0.00 0.00 33.31 2.66
121 122 7.391620 TCCCTGATTTGTAGGTAGTTAGTTTG 58.608 38.462 0.00 0.00 33.31 2.93
122 123 6.598064 CCCTGATTTGTAGGTAGTTAGTTTGG 59.402 42.308 0.00 0.00 33.31 3.28
123 124 6.598064 CCTGATTTGTAGGTAGTTAGTTTGGG 59.402 42.308 0.00 0.00 0.00 4.12
124 125 6.478129 TGATTTGTAGGTAGTTAGTTTGGGG 58.522 40.000 0.00 0.00 0.00 4.96
125 126 3.986996 TGTAGGTAGTTAGTTTGGGGC 57.013 47.619 0.00 0.00 0.00 5.80
126 127 2.573009 TGTAGGTAGTTAGTTTGGGGCC 59.427 50.000 0.00 0.00 0.00 5.80
127 128 0.616891 AGGTAGTTAGTTTGGGGCCG 59.383 55.000 0.00 0.00 0.00 6.13
128 129 0.614812 GGTAGTTAGTTTGGGGCCGA 59.385 55.000 0.00 0.00 0.00 5.54
129 130 1.406477 GGTAGTTAGTTTGGGGCCGAG 60.406 57.143 0.00 0.00 0.00 4.63
130 131 0.251073 TAGTTAGTTTGGGGCCGAGC 59.749 55.000 0.00 0.00 0.00 5.03
131 132 1.302993 GTTAGTTTGGGGCCGAGCA 60.303 57.895 0.00 0.00 0.00 4.26
132 133 1.302993 TTAGTTTGGGGCCGAGCAC 60.303 57.895 0.00 0.00 0.00 4.40
141 142 3.161450 GCCGAGCACCCCCATCTA 61.161 66.667 0.00 0.00 0.00 1.98
142 143 2.520536 GCCGAGCACCCCCATCTAT 61.521 63.158 0.00 0.00 0.00 1.98
143 144 2.056906 GCCGAGCACCCCCATCTATT 62.057 60.000 0.00 0.00 0.00 1.73
144 145 0.035458 CCGAGCACCCCCATCTATTC 59.965 60.000 0.00 0.00 0.00 1.75
145 146 1.051812 CGAGCACCCCCATCTATTCT 58.948 55.000 0.00 0.00 0.00 2.40
146 147 1.270518 CGAGCACCCCCATCTATTCTG 60.271 57.143 0.00 0.00 0.00 3.02
147 148 1.771255 GAGCACCCCCATCTATTCTGT 59.229 52.381 0.00 0.00 0.00 3.41
148 149 2.173569 GAGCACCCCCATCTATTCTGTT 59.826 50.000 0.00 0.00 0.00 3.16
149 150 2.173569 AGCACCCCCATCTATTCTGTTC 59.826 50.000 0.00 0.00 0.00 3.18
150 151 2.092429 GCACCCCCATCTATTCTGTTCA 60.092 50.000 0.00 0.00 0.00 3.18
151 152 3.435601 GCACCCCCATCTATTCTGTTCAT 60.436 47.826 0.00 0.00 0.00 2.57
152 153 4.139786 CACCCCCATCTATTCTGTTCATG 58.860 47.826 0.00 0.00 0.00 3.07
153 154 3.788142 ACCCCCATCTATTCTGTTCATGT 59.212 43.478 0.00 0.00 0.00 3.21
154 155 4.975147 ACCCCCATCTATTCTGTTCATGTA 59.025 41.667 0.00 0.00 0.00 2.29
155 156 5.163195 ACCCCCATCTATTCTGTTCATGTAC 60.163 44.000 0.00 0.00 0.00 2.90
156 157 5.308825 CCCCATCTATTCTGTTCATGTACC 58.691 45.833 0.00 0.00 0.00 3.34
157 158 5.163205 CCCCATCTATTCTGTTCATGTACCA 60.163 44.000 0.00 0.00 0.00 3.25
158 159 5.760253 CCCATCTATTCTGTTCATGTACCAC 59.240 44.000 0.00 0.00 0.00 4.16
159 160 6.408548 CCCATCTATTCTGTTCATGTACCACT 60.409 42.308 0.00 0.00 0.00 4.00
160 161 7.050377 CCATCTATTCTGTTCATGTACCACTT 58.950 38.462 0.00 0.00 0.00 3.16
161 162 7.225538 CCATCTATTCTGTTCATGTACCACTTC 59.774 40.741 0.00 0.00 0.00 3.01
162 163 7.482169 TCTATTCTGTTCATGTACCACTTCT 57.518 36.000 0.00 0.00 0.00 2.85
163 164 7.548097 TCTATTCTGTTCATGTACCACTTCTC 58.452 38.462 0.00 0.00 0.00 2.87
164 165 4.537135 TCTGTTCATGTACCACTTCTCC 57.463 45.455 0.00 0.00 0.00 3.71
165 166 3.901222 TCTGTTCATGTACCACTTCTCCA 59.099 43.478 0.00 0.00 0.00 3.86
166 167 3.997021 CTGTTCATGTACCACTTCTCCAC 59.003 47.826 0.00 0.00 0.00 4.02
167 168 2.993899 GTTCATGTACCACTTCTCCACG 59.006 50.000 0.00 0.00 0.00 4.94
168 169 1.067142 TCATGTACCACTTCTCCACGC 60.067 52.381 0.00 0.00 0.00 5.34
169 170 1.066858 CATGTACCACTTCTCCACGCT 60.067 52.381 0.00 0.00 0.00 5.07
170 171 1.913778 TGTACCACTTCTCCACGCTA 58.086 50.000 0.00 0.00 0.00 4.26
171 172 1.816835 TGTACCACTTCTCCACGCTAG 59.183 52.381 0.00 0.00 0.00 3.42
172 173 0.815734 TACCACTTCTCCACGCTAGC 59.184 55.000 4.06 4.06 0.00 3.42
173 174 0.900647 ACCACTTCTCCACGCTAGCT 60.901 55.000 13.93 0.00 0.00 3.32
174 175 0.179124 CCACTTCTCCACGCTAGCTC 60.179 60.000 13.93 0.00 0.00 4.09
175 176 0.814457 CACTTCTCCACGCTAGCTCT 59.186 55.000 13.93 0.00 0.00 4.09
176 177 0.814457 ACTTCTCCACGCTAGCTCTG 59.186 55.000 13.93 7.69 0.00 3.35
177 178 0.814457 CTTCTCCACGCTAGCTCTGT 59.186 55.000 13.93 0.00 0.00 3.41
178 179 0.528017 TTCTCCACGCTAGCTCTGTG 59.472 55.000 13.93 13.21 0.00 3.66
179 180 0.609406 TCTCCACGCTAGCTCTGTGT 60.609 55.000 13.93 0.00 31.75 3.72
180 181 1.095600 CTCCACGCTAGCTCTGTGTA 58.904 55.000 13.93 0.00 31.75 2.90
181 182 0.809385 TCCACGCTAGCTCTGTGTAC 59.191 55.000 13.93 0.00 31.75 2.90
182 183 0.523546 CCACGCTAGCTCTGTGTACG 60.524 60.000 13.93 0.00 31.75 3.67
183 184 0.168348 CACGCTAGCTCTGTGTACGT 59.832 55.000 13.93 0.00 0.00 3.57
184 185 0.168348 ACGCTAGCTCTGTGTACGTG 59.832 55.000 13.93 0.00 0.00 4.49
185 186 0.523546 CGCTAGCTCTGTGTACGTGG 60.524 60.000 13.93 0.00 0.00 4.94
186 187 0.526662 GCTAGCTCTGTGTACGTGGT 59.473 55.000 7.70 0.00 0.00 4.16
187 188 1.067776 GCTAGCTCTGTGTACGTGGTT 60.068 52.381 7.70 0.00 0.00 3.67
188 189 2.163010 GCTAGCTCTGTGTACGTGGTTA 59.837 50.000 7.70 0.00 0.00 2.85
189 190 3.731264 GCTAGCTCTGTGTACGTGGTTAG 60.731 52.174 7.70 0.00 0.00 2.34
190 191 1.544691 AGCTCTGTGTACGTGGTTAGG 59.455 52.381 0.00 0.00 0.00 2.69
191 192 1.271656 GCTCTGTGTACGTGGTTAGGT 59.728 52.381 0.00 0.00 0.00 3.08
192 193 2.925306 GCTCTGTGTACGTGGTTAGGTG 60.925 54.545 0.00 0.00 0.00 4.00
193 194 2.555325 CTCTGTGTACGTGGTTAGGTGA 59.445 50.000 0.00 0.00 0.00 4.02
194 195 3.159472 TCTGTGTACGTGGTTAGGTGAT 58.841 45.455 0.00 0.00 0.00 3.06
195 196 4.334552 TCTGTGTACGTGGTTAGGTGATA 58.665 43.478 0.00 0.00 0.00 2.15
196 197 4.156556 TCTGTGTACGTGGTTAGGTGATAC 59.843 45.833 0.00 0.00 0.00 2.24
197 198 3.193267 TGTGTACGTGGTTAGGTGATACC 59.807 47.826 0.00 0.00 38.99 2.73
198 199 2.760092 TGTACGTGGTTAGGTGATACCC 59.240 50.000 0.00 0.00 39.75 3.69
199 200 0.819582 ACGTGGTTAGGTGATACCCG 59.180 55.000 0.00 0.00 39.75 5.28
200 201 0.819582 CGTGGTTAGGTGATACCCGT 59.180 55.000 0.00 0.00 39.75 5.28
201 202 1.470285 CGTGGTTAGGTGATACCCGTG 60.470 57.143 0.00 0.00 39.75 4.94
202 203 1.551883 GTGGTTAGGTGATACCCGTGT 59.448 52.381 0.00 0.00 39.75 4.49
203 204 2.760092 GTGGTTAGGTGATACCCGTGTA 59.240 50.000 0.00 0.00 39.75 2.90
204 205 3.195396 GTGGTTAGGTGATACCCGTGTAA 59.805 47.826 0.00 0.00 39.75 2.41
205 206 3.195396 TGGTTAGGTGATACCCGTGTAAC 59.805 47.826 0.00 0.00 39.75 2.50
206 207 3.430790 GGTTAGGTGATACCCGTGTAACC 60.431 52.174 9.67 9.67 39.75 2.85
207 208 1.197812 AGGTGATACCCGTGTAACCC 58.802 55.000 0.00 0.00 39.75 4.11
208 209 1.197812 GGTGATACCCGTGTAACCCT 58.802 55.000 0.00 0.00 30.04 4.34
209 210 1.134610 GGTGATACCCGTGTAACCCTG 60.135 57.143 0.00 0.00 30.04 4.45
210 211 1.551883 GTGATACCCGTGTAACCCTGT 59.448 52.381 0.00 0.00 0.00 4.00
211 212 1.826720 TGATACCCGTGTAACCCTGTC 59.173 52.381 0.00 0.00 0.00 3.51
212 213 1.826720 GATACCCGTGTAACCCTGTCA 59.173 52.381 0.00 0.00 0.00 3.58
213 214 0.968405 TACCCGTGTAACCCTGTCAC 59.032 55.000 0.00 0.00 0.00 3.67
214 215 0.761702 ACCCGTGTAACCCTGTCACT 60.762 55.000 0.00 0.00 0.00 3.41
215 216 0.037605 CCCGTGTAACCCTGTCACTC 60.038 60.000 0.00 0.00 0.00 3.51
216 217 0.966920 CCGTGTAACCCTGTCACTCT 59.033 55.000 0.00 0.00 0.00 3.24
217 218 1.343465 CCGTGTAACCCTGTCACTCTT 59.657 52.381 0.00 0.00 0.00 2.85
218 219 2.404215 CGTGTAACCCTGTCACTCTTG 58.596 52.381 0.00 0.00 0.00 3.02
219 220 2.223971 CGTGTAACCCTGTCACTCTTGT 60.224 50.000 0.00 0.00 0.00 3.16
220 221 3.740141 CGTGTAACCCTGTCACTCTTGTT 60.740 47.826 0.00 0.00 0.00 2.83
221 222 4.196971 GTGTAACCCTGTCACTCTTGTTT 58.803 43.478 0.00 0.00 0.00 2.83
222 223 4.272748 GTGTAACCCTGTCACTCTTGTTTC 59.727 45.833 0.00 0.00 0.00 2.78
223 224 3.933861 AACCCTGTCACTCTTGTTTCT 57.066 42.857 0.00 0.00 0.00 2.52
224 225 5.364446 TGTAACCCTGTCACTCTTGTTTCTA 59.636 40.000 0.00 0.00 0.00 2.10
225 226 4.338379 ACCCTGTCACTCTTGTTTCTAC 57.662 45.455 0.00 0.00 0.00 2.59
226 227 3.071167 ACCCTGTCACTCTTGTTTCTACC 59.929 47.826 0.00 0.00 0.00 3.18
227 228 3.325135 CCCTGTCACTCTTGTTTCTACCT 59.675 47.826 0.00 0.00 0.00 3.08
228 229 4.527038 CCCTGTCACTCTTGTTTCTACCTA 59.473 45.833 0.00 0.00 0.00 3.08
229 230 5.187967 CCCTGTCACTCTTGTTTCTACCTAT 59.812 44.000 0.00 0.00 0.00 2.57
230 231 6.334202 CCTGTCACTCTTGTTTCTACCTATC 58.666 44.000 0.00 0.00 0.00 2.08
231 232 6.071334 CCTGTCACTCTTGTTTCTACCTATCA 60.071 42.308 0.00 0.00 0.00 2.15
232 233 7.297936 TGTCACTCTTGTTTCTACCTATCAA 57.702 36.000 0.00 0.00 0.00 2.57
233 234 7.907389 TGTCACTCTTGTTTCTACCTATCAAT 58.093 34.615 0.00 0.00 0.00 2.57
234 235 7.819415 TGTCACTCTTGTTTCTACCTATCAATG 59.181 37.037 0.00 0.00 0.00 2.82
235 236 7.278868 GTCACTCTTGTTTCTACCTATCAATGG 59.721 40.741 0.00 0.00 0.00 3.16
236 237 7.180229 TCACTCTTGTTTCTACCTATCAATGGA 59.820 37.037 0.00 0.00 0.00 3.41
237 238 7.824289 CACTCTTGTTTCTACCTATCAATGGAA 59.176 37.037 0.00 0.00 0.00 3.53
238 239 8.552296 ACTCTTGTTTCTACCTATCAATGGAAT 58.448 33.333 0.00 0.00 0.00 3.01
239 240 8.737168 TCTTGTTTCTACCTATCAATGGAATG 57.263 34.615 0.00 0.00 0.00 2.67
240 241 8.548025 TCTTGTTTCTACCTATCAATGGAATGA 58.452 33.333 0.00 0.00 0.00 2.57
241 242 9.347240 CTTGTTTCTACCTATCAATGGAATGAT 57.653 33.333 0.00 0.00 42.52 2.45
243 244 9.778741 TGTTTCTACCTATCAATGGAATGATAC 57.221 33.333 0.00 0.00 40.44 2.24
244 245 8.926710 GTTTCTACCTATCAATGGAATGATACG 58.073 37.037 0.00 0.00 40.44 3.06
245 246 6.631016 TCTACCTATCAATGGAATGATACGC 58.369 40.000 0.00 0.00 40.44 4.42
246 247 5.227569 ACCTATCAATGGAATGATACGCA 57.772 39.130 0.00 0.00 40.44 5.24
247 248 5.809001 ACCTATCAATGGAATGATACGCAT 58.191 37.500 0.00 0.00 40.44 4.73
248 249 5.877012 ACCTATCAATGGAATGATACGCATC 59.123 40.000 0.00 0.00 40.44 3.91
249 250 6.111382 CCTATCAATGGAATGATACGCATCT 58.889 40.000 0.00 0.00 40.44 2.90
250 251 6.596888 CCTATCAATGGAATGATACGCATCTT 59.403 38.462 0.00 0.00 40.44 2.40
251 252 5.678132 TCAATGGAATGATACGCATCTTG 57.322 39.130 0.00 0.00 35.78 3.02
252 253 4.023792 TCAATGGAATGATACGCATCTTGC 60.024 41.667 0.00 0.00 40.69 4.01
358 359 0.601558 ATTGTTTGGCTGCAGCAGAG 59.398 50.000 37.63 2.80 44.36 3.35
374 375 3.118408 AGCAGAGACCGGTATTTGCATAA 60.118 43.478 36.63 0.00 34.17 1.90
424 425 8.193438 CAGATCCTTTGAATTTAATGGTTCCTC 58.807 37.037 16.23 9.70 30.03 3.71
426 427 7.227049 TCCTTTGAATTTAATGGTTCCTCAC 57.773 36.000 12.76 0.00 0.00 3.51
429 430 8.096414 CCTTTGAATTTAATGGTTCCTCACAAT 58.904 33.333 6.70 0.00 0.00 2.71
539 547 1.760029 ACAATTTCCCGTTGGCAACTT 59.240 42.857 26.26 11.16 37.61 2.66
663 677 6.315393 TCGCTCTTGTAGGGATTGTTAATTTC 59.685 38.462 0.00 0.00 41.89 2.17
689 705 5.539955 AGTTACTGGCCACATGATTTTCTTT 59.460 36.000 0.00 0.00 0.00 2.52
702 718 7.881232 ACATGATTTTCTTTCTAACCGTCCTAA 59.119 33.333 0.00 0.00 0.00 2.69
715 731 3.257624 ACCGTCCTAATCTCTTCAAACGT 59.742 43.478 0.00 0.00 0.00 3.99
724 743 5.808042 ATCTCTTCAAACGTTGATGGATG 57.192 39.130 0.00 0.00 39.84 3.51
757 776 1.540363 CGAATACCCCGTATTGCTGCT 60.540 52.381 0.00 0.00 38.62 4.24
854 877 2.852449 TCGCCACACCAATAAGACAAA 58.148 42.857 0.00 0.00 0.00 2.83
855 878 2.811431 TCGCCACACCAATAAGACAAAG 59.189 45.455 0.00 0.00 0.00 2.77
860 883 4.539870 CACACCAATAAGACAAAGCAGTG 58.460 43.478 0.00 0.00 0.00 3.66
928 952 4.014406 TGTCTTAGTCCGATACTCTTGCA 58.986 43.478 0.00 0.00 39.80 4.08
951 975 5.766150 TGGTACAATTGTTCTTGGAACAG 57.234 39.130 17.78 5.29 31.63 3.16
1298 1333 7.703328 TCGAATTTCACATATTTTCTTAGGGC 58.297 34.615 0.00 0.00 0.00 5.19
1329 1364 1.202698 GGCATGTTCCTTCGGCTCTAT 60.203 52.381 0.00 0.00 0.00 1.98
1359 1394 8.877864 ATCCAACTTCTTATGGTAAACATTCA 57.122 30.769 0.00 0.00 41.03 2.57
1401 1436 0.900182 TCACTGCAGGACTCCATCGT 60.900 55.000 19.93 0.00 0.00 3.73
1411 1446 3.414549 GACTCCATCGTCTTCTGAGTC 57.585 52.381 0.00 0.00 43.42 3.36
1671 1706 1.402325 GGCCTTGAAACAATGTACCGC 60.402 52.381 0.00 0.00 0.00 5.68
1687 1722 2.970205 CGCCTTAATGTTGGGGGTT 58.030 52.632 0.00 0.00 33.35 4.11
1694 1729 0.183971 AATGTTGGGGGTTCGACACA 59.816 50.000 0.00 0.00 34.24 3.72
1702 1740 0.320771 GGGTTCGACACACTCTGCAT 60.321 55.000 0.00 0.00 0.00 3.96
1710 1748 5.281727 TCGACACACTCTGCATATTATGAC 58.718 41.667 7.87 0.32 0.00 3.06
1715 1753 3.750130 CACTCTGCATATTATGACCCTGC 59.250 47.826 7.87 0.00 0.00 4.85
1718 1756 3.008375 TCTGCATATTATGACCCTGCCTC 59.992 47.826 7.87 0.00 31.89 4.70
1719 1757 2.040278 TGCATATTATGACCCTGCCTCC 59.960 50.000 7.87 0.00 31.89 4.30
1745 1783 1.511613 TCATGGGAAGATGACTCCCC 58.488 55.000 5.45 0.00 42.91 4.81
1895 1936 7.086376 GGGATAAATGCACATATCAACATGAC 58.914 38.462 17.67 3.83 31.51 3.06
2159 2203 1.343478 CCACCCTGATCTCAGTACCCT 60.343 57.143 6.46 0.00 42.27 4.34
2570 2662 1.471829 GGCAAAGGTGGGTTTGGGAG 61.472 60.000 0.00 0.00 37.80 4.30
3174 3266 3.672293 CAAGTGGGCTTGCGTGAT 58.328 55.556 0.00 0.00 44.54 3.06
3207 3299 0.538287 GCCAGAGGAAAGGTGTGCTT 60.538 55.000 0.00 0.00 0.00 3.91
3246 3338 3.313526 CCTATCTGAAGGGCAAAATCACG 59.686 47.826 0.00 0.00 32.55 4.35
3423 3518 1.660167 ACATGTCATCACTCATGGCG 58.340 50.000 0.00 0.00 40.38 5.69
3429 3524 0.176449 CATCACTCATGGCGACCAGA 59.824 55.000 4.90 0.00 36.75 3.86
3519 3614 1.336332 CCAGATGGCCGATAAGACGAG 60.336 57.143 0.00 0.00 35.09 4.18
3542 3645 0.599558 CCTGTACGTTCGGGACTTCA 59.400 55.000 14.51 0.00 36.02 3.02
3652 3762 3.806521 CAGTTCCATAAATCTCTCTGCGG 59.193 47.826 0.00 0.00 0.00 5.69
3777 3889 5.981088 TTTGTGCCAAGACATACATCAAT 57.019 34.783 0.00 0.00 0.00 2.57
3853 3965 5.946942 ATTATCTCCAGAAGAGCTCAACA 57.053 39.130 17.77 0.00 42.90 3.33
3889 4001 9.515020 GTTCAGTGAACATGTTCTTAAAATCAA 57.485 29.630 32.57 11.86 41.62 2.57
3901 4013 9.730420 TGTTCTTAAAATCAAAAGCTAAGACAC 57.270 29.630 0.00 0.00 30.37 3.67
3922 4034 5.222337 ACACCAGGGAACTCATTTAAAGGAT 60.222 40.000 2.58 0.00 40.21 3.24
3924 4036 5.015178 ACCAGGGAACTCATTTAAAGGATCA 59.985 40.000 2.58 0.00 40.21 2.92
3982 4094 1.896660 GGAGCAGCACACGGGAAAA 60.897 57.895 0.00 0.00 0.00 2.29
3983 4095 1.452145 GGAGCAGCACACGGGAAAAA 61.452 55.000 0.00 0.00 0.00 1.94
4025 4169 5.238006 TCAAACCGTAAAAAGACAACTGG 57.762 39.130 0.00 0.00 0.00 4.00
4049 4193 9.970395 TGGATTGCACATTTTGAAAGATATATC 57.030 29.630 4.42 4.42 0.00 1.63
4203 4539 5.811100 GTGAAAGACTATACCCACTAAGCAC 59.189 44.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.387309 CGTAGCAGAGGGTTGCATG 58.613 57.895 0.52 0.00 46.47 4.06
1 2 4.941609 CGTAGCAGAGGGTTGCAT 57.058 55.556 0.52 0.00 46.47 3.96
22 23 3.056536 TCGTCCTTGATGACCTGAAGAAG 60.057 47.826 0.00 0.00 31.35 2.85
23 24 2.897326 TCGTCCTTGATGACCTGAAGAA 59.103 45.455 0.00 0.00 31.35 2.52
24 25 2.231478 GTCGTCCTTGATGACCTGAAGA 59.769 50.000 5.34 0.00 41.25 2.87
25 26 2.611518 GTCGTCCTTGATGACCTGAAG 58.388 52.381 5.34 0.00 41.25 3.02
26 27 1.067846 CGTCGTCCTTGATGACCTGAA 60.068 52.381 10.07 0.00 43.36 3.02
27 28 0.526211 CGTCGTCCTTGATGACCTGA 59.474 55.000 10.07 0.00 43.36 3.86
28 29 1.078759 GCGTCGTCCTTGATGACCTG 61.079 60.000 10.07 0.46 43.36 4.00
29 30 1.215647 GCGTCGTCCTTGATGACCT 59.784 57.895 10.07 0.00 43.36 3.85
30 31 0.802607 GAGCGTCGTCCTTGATGACC 60.803 60.000 10.07 4.53 43.36 4.02
31 32 1.134530 CGAGCGTCGTCCTTGATGAC 61.135 60.000 6.41 6.41 42.99 3.06
32 33 1.136774 CGAGCGTCGTCCTTGATGA 59.863 57.895 0.00 0.00 34.72 2.92
33 34 1.874019 CCGAGCGTCGTCCTTGATG 60.874 63.158 0.00 0.00 38.40 3.07
34 35 2.490217 CCGAGCGTCGTCCTTGAT 59.510 61.111 0.00 0.00 38.40 2.57
35 36 3.744719 CCCGAGCGTCGTCCTTGA 61.745 66.667 0.00 0.00 38.40 3.02
46 47 4.575973 AGATGCCCATGCCCGAGC 62.576 66.667 0.00 0.00 40.48 5.03
47 48 2.593725 CAGATGCCCATGCCCGAG 60.594 66.667 0.00 0.00 36.33 4.63
48 49 4.881440 GCAGATGCCCATGCCCGA 62.881 66.667 0.00 0.00 36.41 5.14
65 66 4.856801 CGATGTCCTTGGCCCCGG 62.857 72.222 0.00 0.00 0.00 5.73
67 68 3.936772 TTGCGATGTCCTTGGCCCC 62.937 63.158 0.00 0.00 0.00 5.80
68 69 1.976474 TTTGCGATGTCCTTGGCCC 60.976 57.895 0.00 0.00 0.00 5.80
69 70 1.212751 GTTTGCGATGTCCTTGGCC 59.787 57.895 0.00 0.00 0.00 5.36
70 71 0.598065 AAGTTTGCGATGTCCTTGGC 59.402 50.000 0.00 0.00 0.00 4.52
71 72 3.119849 CCTAAAGTTTGCGATGTCCTTGG 60.120 47.826 0.00 0.00 0.00 3.61
72 73 3.670627 GCCTAAAGTTTGCGATGTCCTTG 60.671 47.826 0.00 0.00 0.00 3.61
73 74 2.488153 GCCTAAAGTTTGCGATGTCCTT 59.512 45.455 0.00 0.00 0.00 3.36
74 75 2.084546 GCCTAAAGTTTGCGATGTCCT 58.915 47.619 0.00 0.00 0.00 3.85
75 76 1.132453 GGCCTAAAGTTTGCGATGTCC 59.868 52.381 0.00 0.00 0.00 4.02
76 77 2.084546 AGGCCTAAAGTTTGCGATGTC 58.915 47.619 1.29 0.00 0.00 3.06
77 78 2.084546 GAGGCCTAAAGTTTGCGATGT 58.915 47.619 4.42 0.00 0.00 3.06
78 79 1.401905 GGAGGCCTAAAGTTTGCGATG 59.598 52.381 4.42 0.00 0.00 3.84
79 80 1.682087 GGGAGGCCTAAAGTTTGCGAT 60.682 52.381 4.42 0.00 0.00 4.58
80 81 0.322187 GGGAGGCCTAAAGTTTGCGA 60.322 55.000 4.42 0.00 0.00 5.10
81 82 0.322546 AGGGAGGCCTAAAGTTTGCG 60.323 55.000 4.42 0.00 0.00 4.85
82 83 1.177401 CAGGGAGGCCTAAAGTTTGC 58.823 55.000 4.42 0.00 0.00 3.68
83 84 2.879103 TCAGGGAGGCCTAAAGTTTG 57.121 50.000 4.42 0.00 0.00 2.93
84 85 4.089361 CAAATCAGGGAGGCCTAAAGTTT 58.911 43.478 4.42 0.00 0.00 2.66
85 86 3.076032 ACAAATCAGGGAGGCCTAAAGTT 59.924 43.478 4.42 0.00 0.00 2.66
86 87 2.649816 ACAAATCAGGGAGGCCTAAAGT 59.350 45.455 4.42 0.00 0.00 2.66
87 88 3.372440 ACAAATCAGGGAGGCCTAAAG 57.628 47.619 4.42 0.00 0.00 1.85
88 89 3.202151 CCTACAAATCAGGGAGGCCTAAA 59.798 47.826 4.42 0.00 0.00 1.85
89 90 2.777692 CCTACAAATCAGGGAGGCCTAA 59.222 50.000 4.42 0.00 0.00 2.69
90 91 2.293586 ACCTACAAATCAGGGAGGCCTA 60.294 50.000 4.42 0.00 37.51 3.93
91 92 1.216990 CCTACAAATCAGGGAGGCCT 58.783 55.000 3.86 3.86 0.00 5.19
92 93 0.919710 ACCTACAAATCAGGGAGGCC 59.080 55.000 0.00 0.00 37.51 5.19
93 94 3.477210 CTACCTACAAATCAGGGAGGC 57.523 52.381 0.00 0.00 40.09 4.70
96 97 7.391620 CAAACTAACTACCTACAAATCAGGGA 58.608 38.462 0.00 0.00 37.51 4.20
97 98 6.598064 CCAAACTAACTACCTACAAATCAGGG 59.402 42.308 0.00 0.00 37.51 4.45
98 99 6.598064 CCCAAACTAACTACCTACAAATCAGG 59.402 42.308 0.00 0.00 39.25 3.86
99 100 6.598064 CCCCAAACTAACTACCTACAAATCAG 59.402 42.308 0.00 0.00 0.00 2.90
100 101 6.478129 CCCCAAACTAACTACCTACAAATCA 58.522 40.000 0.00 0.00 0.00 2.57
101 102 5.356190 GCCCCAAACTAACTACCTACAAATC 59.644 44.000 0.00 0.00 0.00 2.17
102 103 5.258841 GCCCCAAACTAACTACCTACAAAT 58.741 41.667 0.00 0.00 0.00 2.32
103 104 4.507157 GGCCCCAAACTAACTACCTACAAA 60.507 45.833 0.00 0.00 0.00 2.83
104 105 3.009363 GGCCCCAAACTAACTACCTACAA 59.991 47.826 0.00 0.00 0.00 2.41
105 106 2.573009 GGCCCCAAACTAACTACCTACA 59.427 50.000 0.00 0.00 0.00 2.74
106 107 2.419159 CGGCCCCAAACTAACTACCTAC 60.419 54.545 0.00 0.00 0.00 3.18
107 108 1.832998 CGGCCCCAAACTAACTACCTA 59.167 52.381 0.00 0.00 0.00 3.08
108 109 0.616891 CGGCCCCAAACTAACTACCT 59.383 55.000 0.00 0.00 0.00 3.08
109 110 0.614812 TCGGCCCCAAACTAACTACC 59.385 55.000 0.00 0.00 0.00 3.18
110 111 2.010544 GCTCGGCCCCAAACTAACTAC 61.011 57.143 0.00 0.00 0.00 2.73
111 112 0.251073 GCTCGGCCCCAAACTAACTA 59.749 55.000 0.00 0.00 0.00 2.24
112 113 1.002502 GCTCGGCCCCAAACTAACT 60.003 57.895 0.00 0.00 0.00 2.24
113 114 1.302993 TGCTCGGCCCCAAACTAAC 60.303 57.895 0.00 0.00 0.00 2.34
114 115 1.302993 GTGCTCGGCCCCAAACTAA 60.303 57.895 0.00 0.00 0.00 2.24
115 116 2.349755 GTGCTCGGCCCCAAACTA 59.650 61.111 0.00 0.00 0.00 2.24
116 117 4.660938 GGTGCTCGGCCCCAAACT 62.661 66.667 0.00 0.00 0.00 2.66
124 125 2.056906 AATAGATGGGGGTGCTCGGC 62.057 60.000 0.00 0.00 0.00 5.54
125 126 0.035458 GAATAGATGGGGGTGCTCGG 59.965 60.000 0.00 0.00 0.00 4.63
126 127 1.051812 AGAATAGATGGGGGTGCTCG 58.948 55.000 0.00 0.00 0.00 5.03
127 128 1.771255 ACAGAATAGATGGGGGTGCTC 59.229 52.381 0.00 0.00 0.00 4.26
128 129 1.898863 ACAGAATAGATGGGGGTGCT 58.101 50.000 0.00 0.00 0.00 4.40
129 130 2.092429 TGAACAGAATAGATGGGGGTGC 60.092 50.000 0.00 0.00 0.00 5.01
130 131 3.931907 TGAACAGAATAGATGGGGGTG 57.068 47.619 0.00 0.00 0.00 4.61
131 132 3.788142 ACATGAACAGAATAGATGGGGGT 59.212 43.478 0.00 0.00 0.00 4.95
132 133 4.443978 ACATGAACAGAATAGATGGGGG 57.556 45.455 0.00 0.00 0.00 5.40
133 134 5.163205 TGGTACATGAACAGAATAGATGGGG 60.163 44.000 0.00 0.00 0.00 4.96
134 135 5.760253 GTGGTACATGAACAGAATAGATGGG 59.240 44.000 0.00 0.00 44.52 4.00
135 136 6.586344 AGTGGTACATGAACAGAATAGATGG 58.414 40.000 0.00 0.00 44.52 3.51
136 137 7.984050 AGAAGTGGTACATGAACAGAATAGATG 59.016 37.037 0.00 0.00 44.52 2.90
137 138 8.083828 AGAAGTGGTACATGAACAGAATAGAT 57.916 34.615 0.00 0.00 44.52 1.98
138 139 7.363880 GGAGAAGTGGTACATGAACAGAATAGA 60.364 40.741 0.00 0.00 44.52 1.98
139 140 6.758886 GGAGAAGTGGTACATGAACAGAATAG 59.241 42.308 0.00 0.00 44.52 1.73
140 141 6.212589 TGGAGAAGTGGTACATGAACAGAATA 59.787 38.462 0.00 0.00 44.52 1.75
141 142 5.013079 TGGAGAAGTGGTACATGAACAGAAT 59.987 40.000 0.00 0.00 44.52 2.40
142 143 4.346709 TGGAGAAGTGGTACATGAACAGAA 59.653 41.667 0.00 0.00 44.52 3.02
143 144 3.901222 TGGAGAAGTGGTACATGAACAGA 59.099 43.478 0.00 0.00 44.52 3.41
144 145 3.997021 GTGGAGAAGTGGTACATGAACAG 59.003 47.826 0.00 0.00 44.52 3.16
145 146 3.554129 CGTGGAGAAGTGGTACATGAACA 60.554 47.826 0.00 0.00 44.52 3.18
146 147 2.993899 CGTGGAGAAGTGGTACATGAAC 59.006 50.000 0.00 0.00 44.52 3.18
147 148 2.611971 GCGTGGAGAAGTGGTACATGAA 60.612 50.000 0.00 0.00 44.52 2.57
148 149 1.067142 GCGTGGAGAAGTGGTACATGA 60.067 52.381 0.00 0.00 44.52 3.07
149 150 1.066858 AGCGTGGAGAAGTGGTACATG 60.067 52.381 0.00 0.00 44.52 3.21
150 151 1.267121 AGCGTGGAGAAGTGGTACAT 58.733 50.000 0.00 0.00 44.52 2.29
151 152 1.816835 CTAGCGTGGAGAAGTGGTACA 59.183 52.381 0.00 0.00 0.00 2.90
152 153 1.469423 GCTAGCGTGGAGAAGTGGTAC 60.469 57.143 0.00 0.00 0.00 3.34
153 154 0.815734 GCTAGCGTGGAGAAGTGGTA 59.184 55.000 0.00 0.00 0.00 3.25
154 155 0.900647 AGCTAGCGTGGAGAAGTGGT 60.901 55.000 9.55 0.00 0.00 4.16
155 156 0.179124 GAGCTAGCGTGGAGAAGTGG 60.179 60.000 9.55 0.00 0.00 4.00
156 157 0.814457 AGAGCTAGCGTGGAGAAGTG 59.186 55.000 9.55 0.00 0.00 3.16
157 158 0.814457 CAGAGCTAGCGTGGAGAAGT 59.186 55.000 9.55 0.00 0.00 3.01
158 159 0.814457 ACAGAGCTAGCGTGGAGAAG 59.186 55.000 20.24 5.54 0.00 2.85
159 160 0.528017 CACAGAGCTAGCGTGGAGAA 59.472 55.000 20.24 0.00 0.00 2.87
160 161 0.609406 ACACAGAGCTAGCGTGGAGA 60.609 55.000 20.69 0.00 34.91 3.71
161 162 1.095600 TACACAGAGCTAGCGTGGAG 58.904 55.000 20.69 15.55 34.91 3.86
162 163 0.809385 GTACACAGAGCTAGCGTGGA 59.191 55.000 20.69 12.73 34.91 4.02
163 164 0.523546 CGTACACAGAGCTAGCGTGG 60.524 60.000 20.69 12.11 34.91 4.94
164 165 0.168348 ACGTACACAGAGCTAGCGTG 59.832 55.000 16.71 16.71 36.70 5.34
165 166 0.168348 CACGTACACAGAGCTAGCGT 59.832 55.000 9.55 3.10 0.00 5.07
166 167 0.523546 CCACGTACACAGAGCTAGCG 60.524 60.000 9.55 0.00 0.00 4.26
167 168 0.526662 ACCACGTACACAGAGCTAGC 59.473 55.000 6.62 6.62 0.00 3.42
168 169 3.181499 CCTAACCACGTACACAGAGCTAG 60.181 52.174 0.00 0.00 0.00 3.42
169 170 2.751259 CCTAACCACGTACACAGAGCTA 59.249 50.000 0.00 0.00 0.00 3.32
170 171 1.544691 CCTAACCACGTACACAGAGCT 59.455 52.381 0.00 0.00 0.00 4.09
171 172 1.271656 ACCTAACCACGTACACAGAGC 59.728 52.381 0.00 0.00 0.00 4.09
172 173 2.555325 TCACCTAACCACGTACACAGAG 59.445 50.000 0.00 0.00 0.00 3.35
173 174 2.585330 TCACCTAACCACGTACACAGA 58.415 47.619 0.00 0.00 0.00 3.41
174 175 3.587797 ATCACCTAACCACGTACACAG 57.412 47.619 0.00 0.00 0.00 3.66
175 176 3.193267 GGTATCACCTAACCACGTACACA 59.807 47.826 0.00 0.00 34.73 3.72
176 177 3.429410 GGGTATCACCTAACCACGTACAC 60.429 52.174 0.00 0.00 37.13 2.90
177 178 2.760092 GGGTATCACCTAACCACGTACA 59.240 50.000 0.00 0.00 37.13 2.90
178 179 2.223572 CGGGTATCACCTAACCACGTAC 60.224 54.545 0.00 0.00 36.97 3.67
179 180 2.023673 CGGGTATCACCTAACCACGTA 58.976 52.381 0.00 0.00 36.97 3.57
180 181 0.819582 CGGGTATCACCTAACCACGT 59.180 55.000 0.00 0.00 36.97 4.49
181 182 0.819582 ACGGGTATCACCTAACCACG 59.180 55.000 0.00 0.00 36.97 4.94
182 183 1.551883 ACACGGGTATCACCTAACCAC 59.448 52.381 0.00 0.00 36.97 4.16
183 184 1.941377 ACACGGGTATCACCTAACCA 58.059 50.000 0.00 0.00 36.97 3.67
184 185 3.430790 GGTTACACGGGTATCACCTAACC 60.431 52.174 10.85 6.09 37.82 2.85
185 186 3.430790 GGGTTACACGGGTATCACCTAAC 60.431 52.174 16.38 3.98 38.64 2.34
186 187 2.765699 GGGTTACACGGGTATCACCTAA 59.234 50.000 16.38 0.00 38.64 2.69
187 188 2.024080 AGGGTTACACGGGTATCACCTA 60.024 50.000 16.38 0.00 38.64 3.08
188 189 1.197812 GGGTTACACGGGTATCACCT 58.802 55.000 16.38 0.00 38.64 4.00
189 190 1.134610 CAGGGTTACACGGGTATCACC 60.135 57.143 9.81 9.81 37.60 4.02
190 191 1.551883 ACAGGGTTACACGGGTATCAC 59.448 52.381 0.00 0.00 0.00 3.06
191 192 1.826720 GACAGGGTTACACGGGTATCA 59.173 52.381 0.00 0.00 0.00 2.15
192 193 1.826720 TGACAGGGTTACACGGGTATC 59.173 52.381 0.00 0.00 0.00 2.24
193 194 1.551883 GTGACAGGGTTACACGGGTAT 59.448 52.381 0.00 0.00 0.00 2.73
194 195 0.968405 GTGACAGGGTTACACGGGTA 59.032 55.000 0.00 0.00 0.00 3.69
195 196 0.761702 AGTGACAGGGTTACACGGGT 60.762 55.000 0.00 0.00 39.19 5.28
196 197 0.037605 GAGTGACAGGGTTACACGGG 60.038 60.000 0.00 0.00 39.19 5.28
197 198 0.966920 AGAGTGACAGGGTTACACGG 59.033 55.000 0.00 0.00 39.19 4.94
198 199 2.223971 ACAAGAGTGACAGGGTTACACG 60.224 50.000 0.00 0.00 39.19 4.49
199 200 3.470645 ACAAGAGTGACAGGGTTACAC 57.529 47.619 0.00 0.00 35.15 2.90
200 201 4.163458 AGAAACAAGAGTGACAGGGTTACA 59.837 41.667 0.00 0.00 0.00 2.41
201 202 4.704965 AGAAACAAGAGTGACAGGGTTAC 58.295 43.478 0.00 0.00 0.00 2.50
202 203 5.221581 GGTAGAAACAAGAGTGACAGGGTTA 60.222 44.000 0.00 0.00 0.00 2.85
203 204 3.933861 AGAAACAAGAGTGACAGGGTT 57.066 42.857 0.00 0.00 0.00 4.11
204 205 3.071167 GGTAGAAACAAGAGTGACAGGGT 59.929 47.826 0.00 0.00 0.00 4.34
205 206 3.325135 AGGTAGAAACAAGAGTGACAGGG 59.675 47.826 0.00 0.00 0.00 4.45
206 207 4.608948 AGGTAGAAACAAGAGTGACAGG 57.391 45.455 0.00 0.00 0.00 4.00
207 208 6.925211 TGATAGGTAGAAACAAGAGTGACAG 58.075 40.000 0.00 0.00 0.00 3.51
208 209 6.911250 TGATAGGTAGAAACAAGAGTGACA 57.089 37.500 0.00 0.00 0.00 3.58
209 210 7.278868 CCATTGATAGGTAGAAACAAGAGTGAC 59.721 40.741 0.00 0.00 0.00 3.67
210 211 7.180229 TCCATTGATAGGTAGAAACAAGAGTGA 59.820 37.037 0.00 0.00 0.00 3.41
211 212 7.331026 TCCATTGATAGGTAGAAACAAGAGTG 58.669 38.462 0.00 0.00 0.00 3.51
212 213 7.496346 TCCATTGATAGGTAGAAACAAGAGT 57.504 36.000 0.00 0.00 0.00 3.24
213 214 8.834465 CATTCCATTGATAGGTAGAAACAAGAG 58.166 37.037 0.00 0.00 0.00 2.85
214 215 8.548025 TCATTCCATTGATAGGTAGAAACAAGA 58.452 33.333 0.00 0.00 0.00 3.02
215 216 8.737168 TCATTCCATTGATAGGTAGAAACAAG 57.263 34.615 0.00 0.00 0.00 3.16
217 218 9.778741 GTATCATTCCATTGATAGGTAGAAACA 57.221 33.333 0.00 0.00 38.83 2.83
218 219 8.926710 CGTATCATTCCATTGATAGGTAGAAAC 58.073 37.037 6.17 0.00 38.83 2.78
219 220 7.602644 GCGTATCATTCCATTGATAGGTAGAAA 59.397 37.037 12.85 0.00 42.39 2.52
220 221 7.097192 GCGTATCATTCCATTGATAGGTAGAA 58.903 38.462 12.85 0.00 42.39 2.10
221 222 6.210584 TGCGTATCATTCCATTGATAGGTAGA 59.789 38.462 12.85 0.00 42.39 2.59
222 223 6.398095 TGCGTATCATTCCATTGATAGGTAG 58.602 40.000 12.85 1.44 42.39 3.18
223 224 6.353404 TGCGTATCATTCCATTGATAGGTA 57.647 37.500 12.85 7.89 42.39 3.08
224 225 5.227569 TGCGTATCATTCCATTGATAGGT 57.772 39.130 12.85 0.00 42.39 3.08
225 226 6.111382 AGATGCGTATCATTCCATTGATAGG 58.889 40.000 16.11 8.89 42.88 2.57
226 227 7.461918 CAAGATGCGTATCATTCCATTGATAG 58.538 38.462 16.11 0.00 38.83 2.08
227 228 6.128200 GCAAGATGCGTATCATTCCATTGATA 60.128 38.462 16.11 0.00 34.16 2.15
228 229 5.335426 GCAAGATGCGTATCATTCCATTGAT 60.335 40.000 16.11 0.00 35.50 2.57
229 230 4.023792 GCAAGATGCGTATCATTCCATTGA 60.024 41.667 16.11 0.00 35.05 2.57
230 231 4.224433 GCAAGATGCGTATCATTCCATTG 58.776 43.478 16.11 10.67 35.05 2.82
231 232 4.494350 GCAAGATGCGTATCATTCCATT 57.506 40.909 16.11 0.00 35.05 3.16
252 253 3.838550 CCTGAAAACTTTTCGCGAATACG 59.161 43.478 24.05 15.67 42.93 3.06
253 254 5.025986 TCCTGAAAACTTTTCGCGAATAC 57.974 39.130 24.05 6.16 0.00 1.89
254 255 5.237779 ACTTCCTGAAAACTTTTCGCGAATA 59.762 36.000 24.05 17.24 0.00 1.75
255 256 4.036380 ACTTCCTGAAAACTTTTCGCGAAT 59.964 37.500 24.05 6.18 0.00 3.34
256 257 3.375922 ACTTCCTGAAAACTTTTCGCGAA 59.624 39.130 19.38 19.38 0.00 4.70
257 258 2.940410 ACTTCCTGAAAACTTTTCGCGA 59.060 40.909 3.71 3.71 0.00 5.87
258 259 3.334272 ACTTCCTGAAAACTTTTCGCG 57.666 42.857 0.00 0.00 0.00 5.87
259 260 4.921547 AGAACTTCCTGAAAACTTTTCGC 58.078 39.130 9.25 0.00 0.00 4.70
260 261 6.037172 TGAGAGAACTTCCTGAAAACTTTTCG 59.963 38.462 9.25 4.97 0.00 3.46
261 262 7.321745 TGAGAGAACTTCCTGAAAACTTTTC 57.678 36.000 7.24 7.24 0.00 2.29
262 263 7.777440 AGATGAGAGAACTTCCTGAAAACTTTT 59.223 33.333 0.00 0.00 0.00 2.27
263 264 7.286313 AGATGAGAGAACTTCCTGAAAACTTT 58.714 34.615 0.00 0.00 0.00 2.66
264 265 6.836242 AGATGAGAGAACTTCCTGAAAACTT 58.164 36.000 0.00 0.00 0.00 2.66
358 359 3.619929 AGTCGTTTATGCAAATACCGGTC 59.380 43.478 12.40 0.00 0.00 4.79
374 375 6.429692 TGTTCATATGGTTCAATCAAGTCGTT 59.570 34.615 2.13 0.00 0.00 3.85
424 425 2.768253 TGCTAGTGACTCCCATTGTG 57.232 50.000 0.00 0.00 0.00 3.33
426 427 2.437281 AGGATGCTAGTGACTCCCATTG 59.563 50.000 0.00 0.00 0.00 2.82
429 430 1.489481 CAGGATGCTAGTGACTCCCA 58.511 55.000 0.00 0.00 0.00 4.37
499 501 5.913137 TGTGAACTTTGTCAGGTGAAAAT 57.087 34.783 0.00 0.00 0.00 1.82
539 547 8.964420 GATTCGAATCCAAATGTTAACAAGAA 57.036 30.769 24.74 7.58 0.00 2.52
631 641 4.650754 TCCCTACAAGAGCGATAGAAAC 57.349 45.455 0.00 0.00 39.76 2.78
663 677 5.882557 AGAAAATCATGTGGCCAGTAACTAG 59.117 40.000 5.11 0.00 0.00 2.57
669 683 4.154942 AGAAAGAAAATCATGTGGCCAGT 58.845 39.130 5.11 0.00 0.00 4.00
689 705 6.624423 CGTTTGAAGAGATTAGGACGGTTAGA 60.624 42.308 0.00 0.00 0.00 2.10
702 718 5.491070 TCATCCATCAACGTTTGAAGAGAT 58.509 37.500 0.00 0.00 43.95 2.75
715 731 8.504812 TTCGTCAATAAGAAATCATCCATCAA 57.495 30.769 0.00 0.00 0.00 2.57
724 743 5.756833 ACGGGGTATTCGTCAATAAGAAATC 59.243 40.000 0.00 0.00 35.87 2.17
757 776 6.381498 TCAAAGTGGGTGATGACCTAATTA 57.619 37.500 0.20 0.00 39.82 1.40
808 831 4.029809 CGGGACCCCACCTGAACC 62.030 72.222 4.46 0.00 38.49 3.62
854 877 3.806625 AAGTTGATTTTGTGCACTGCT 57.193 38.095 19.41 0.00 0.00 4.24
855 878 3.245990 GGAAAGTTGATTTTGTGCACTGC 59.754 43.478 19.41 3.39 0.00 4.40
860 883 4.122046 AGCAAGGAAAGTTGATTTTGTGC 58.878 39.130 0.00 0.00 34.73 4.57
928 952 5.833131 ACTGTTCCAAGAACAATTGTACCAT 59.167 36.000 12.39 0.00 0.00 3.55
1351 1386 2.522185 AGCATCCACAGCTGAATGTTT 58.478 42.857 23.35 10.33 41.61 2.83
1359 1394 2.289694 ACTAAACGAAGCATCCACAGCT 60.290 45.455 0.00 0.00 45.97 4.24
1401 1436 6.295916 GGGAAGGATTAAAGTGACTCAGAAGA 60.296 42.308 0.00 0.00 0.00 2.87
1411 1446 3.691609 GCAGTCTGGGAAGGATTAAAGTG 59.308 47.826 1.14 0.00 0.00 3.16
1671 1706 2.089201 GTCGAACCCCCAACATTAAGG 58.911 52.381 0.00 0.00 0.00 2.69
1687 1722 5.281727 GTCATAATATGCAGAGTGTGTCGA 58.718 41.667 5.46 0.00 0.00 4.20
1694 1729 3.244700 GGCAGGGTCATAATATGCAGAGT 60.245 47.826 0.00 0.00 38.63 3.24
1702 1740 3.517612 GGTAGGAGGCAGGGTCATAATA 58.482 50.000 0.00 0.00 0.00 0.98
1710 1748 1.338136 ATGAACGGTAGGAGGCAGGG 61.338 60.000 0.00 0.00 0.00 4.45
1715 1753 1.139058 CTTCCCATGAACGGTAGGAGG 59.861 57.143 0.00 0.00 0.00 4.30
1718 1756 2.434336 TCATCTTCCCATGAACGGTAGG 59.566 50.000 0.00 0.00 29.41 3.18
1719 1757 3.133003 AGTCATCTTCCCATGAACGGTAG 59.867 47.826 0.00 0.00 34.50 3.18
1745 1783 6.313905 GCCACGTGAAGATCCATAAATATAGG 59.686 42.308 19.30 0.00 0.00 2.57
1895 1936 5.971202 GGCAAAATCCATGTAAGATTGTACG 59.029 40.000 0.00 0.00 34.23 3.67
2159 2203 9.577222 TCAGAATTGCATCATAATATTCTGGAA 57.423 29.630 24.41 11.39 46.10 3.53
2570 2662 3.568853 AGCTATCTGACCGTGGTATACAC 59.431 47.826 5.01 0.68 46.78 2.90
3207 3299 0.032117 AGGGGTCGATGATCTCACCA 60.032 55.000 11.25 0.00 30.81 4.17
3246 3338 1.260544 ATTTTCTGAAGCACTGGGGC 58.739 50.000 0.00 0.00 0.00 5.80
3363 3455 2.433604 GGAGAGATTGCAGTCATCCTCA 59.566 50.000 19.86 0.00 0.00 3.86
3423 3518 0.247736 AAGATGGTCGCACTCTGGTC 59.752 55.000 0.00 0.00 0.00 4.02
3429 3524 0.687354 AACCTGAAGATGGTCGCACT 59.313 50.000 0.00 0.00 36.69 4.40
3519 3614 0.169894 GTCCCGAACGTACAGGAGTC 59.830 60.000 5.56 0.00 0.00 3.36
3652 3762 9.817809 TTAGGAACATAATCAGATTGTACAGTC 57.182 33.333 10.23 10.23 0.00 3.51
3777 3889 6.716628 GGAAATCTTTGATATGGCCTGATACA 59.283 38.462 3.32 0.00 0.00 2.29
3860 3972 9.736023 ATTTTAAGAACATGTTCACTGAACTTC 57.264 29.630 33.92 15.55 42.39 3.01
3889 4001 2.711547 AGTTCCCTGGTGTCTTAGCTTT 59.288 45.455 0.00 0.00 0.00 3.51
3895 4007 3.884037 AAATGAGTTCCCTGGTGTCTT 57.116 42.857 0.00 0.00 0.00 3.01
3901 4013 5.509498 TGATCCTTTAAATGAGTTCCCTGG 58.491 41.667 0.00 0.00 0.00 4.45
3982 4094 6.817765 TGATTAAAGACTGCCGAGAAATTT 57.182 33.333 0.00 0.00 0.00 1.82
3983 4095 6.817765 TTGATTAAAGACTGCCGAGAAATT 57.182 33.333 0.00 0.00 0.00 1.82
3984 4096 6.349363 GGTTTGATTAAAGACTGCCGAGAAAT 60.349 38.462 0.00 0.00 0.00 2.17
4203 4539 7.412137 TGATTGCATCTTGTATTCTGTATCG 57.588 36.000 0.00 0.00 0.00 2.92
4343 4757 2.492088 GTTCCCAACAGGCAAATACTCC 59.508 50.000 0.00 0.00 34.51 3.85


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

AutoCloner maintained by Alex Coulton.