Multiple sequence alignment - TraesCS5A01G369000

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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 TraesCS5A01G369000 chr5A 100.000 5036 0 0 727 5762 569289607 569284572 0.000000e+00 9300.0
1 TraesCS5A01G369000 chr5A 100.000 346 0 0 1 346 569290333 569289988 1.750000e-179 640.0
2 TraesCS5A01G369000 chr5A 84.459 148 18 3 2543 2686 648815475 648815329 2.160000e-29 141.0
3 TraesCS5A01G369000 chr5A 91.667 48 3 1 3123 3170 451462839 451462793 1.340000e-06 65.8
4 TraesCS5A01G369000 chr5A 86.207 58 5 1 3074 3128 678550088 678550145 6.240000e-05 60.2
5 TraesCS5A01G369000 chr5D 94.980 3048 129 17 982 4011 449997248 449994207 0.000000e+00 4759.0
6 TraesCS5A01G369000 chr5D 90.655 1466 92 23 4309 5762 449993627 449992195 0.000000e+00 1906.0
7 TraesCS5A01G369000 chr5D 90.152 264 22 3 4009 4272 449993884 449993625 1.990000e-89 340.0
8 TraesCS5A01G369000 chr5D 90.984 122 2 2 225 346 449997948 449997836 7.730000e-34 156.0
9 TraesCS5A01G369000 chr5D 80.000 175 29 2 2515 2683 120933971 120934145 2.180000e-24 124.0
10 TraesCS5A01G369000 chr5B 95.062 2106 81 13 727 2817 549976490 549974393 0.000000e+00 3291.0
11 TraesCS5A01G369000 chr5B 92.178 2250 127 26 3528 5762 549973715 549971500 0.000000e+00 3134.0
12 TraesCS5A01G369000 chr5B 92.374 577 30 3 2944 3506 549974284 549973708 0.000000e+00 809.0
13 TraesCS5A01G369000 chr5B 87.121 132 15 2 187 316 549976995 549976864 1.290000e-31 148.0
14 TraesCS5A01G369000 chr2D 88.927 289 12 8 5347 5624 543053883 543054162 7.150000e-89 339.0
15 TraesCS5A01G369000 chr3A 83.436 163 22 4 2528 2686 557107885 557107724 4.650000e-31 147.0
16 TraesCS5A01G369000 chr3A 95.745 47 2 0 3119 3165 599863758 599863804 6.190000e-10 76.8
17 TraesCS5A01G369000 chr4B 81.714 175 26 3 2515 2683 351010280 351010454 2.160000e-29 141.0
18 TraesCS5A01G369000 chr4B 82.955 88 8 5 3044 3126 584120612 584120697 8.010000e-09 73.1
19 TraesCS5A01G369000 chr7D 80.925 173 23 5 2515 2679 77500669 77500499 1.690000e-25 128.0
20 TraesCS5A01G369000 chr7D 80.347 173 24 5 2515 2679 147584413 147584583 7.840000e-24 122.0
21 TraesCS5A01G369000 chr7D 89.655 58 2 3 3119 3172 161481041 161480984 2.880000e-08 71.3
22 TraesCS5A01G369000 chr7D 87.931 58 4 2 3075 3129 503038897 503038954 1.340000e-06 65.8
23 TraesCS5A01G369000 chr7A 83.000 100 9 4 3073 3165 34788140 34788238 3.700000e-12 84.2
24 TraesCS5A01G369000 chr7B 92.727 55 3 1 3119 3172 123782910 123782856 1.720000e-10 78.7
25 TraesCS5A01G369000 chr1A 95.745 47 2 0 3119 3165 442476531 442476485 6.190000e-10 76.8
26 TraesCS5A01G369000 chr6A 90.909 55 5 0 2231 2285 570929755 570929701 2.230000e-09 75.0
27 TraesCS5A01G369000 chr3D 90.909 55 2 1 3078 3129 7102347 7102401 2.880000e-08 71.3
28 TraesCS5A01G369000 chr3B 93.478 46 3 0 3119 3164 637088537 637088492 1.040000e-07 69.4
29 TraesCS5A01G369000 chr2A 93.617 47 0 2 3087 3130 85295832 85295786 3.730000e-07 67.6
30 TraesCS5A01G369000 chr2A 97.143 35 1 0 3078 3112 768471300 768471334 6.240000e-05 60.2
31 TraesCS5A01G369000 chr1D 100.000 28 0 0 849 876 332260869 332260896 1.000000e-02 52.8


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 TraesCS5A01G369000 chr5A 569284572 569290333 5761 True 4970.00 9300 100.00000 1 5762 2 chr5A.!!$R3 5761
1 TraesCS5A01G369000 chr5D 449992195 449997948 5753 True 1790.25 4759 91.69275 225 5762 4 chr5D.!!$R1 5537
2 TraesCS5A01G369000 chr5B 549971500 549976995 5495 True 1845.50 3291 91.68375 187 5762 4 chr5B.!!$R1 5575

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
53 54 1.067565 ACGTCAGTCGAGAATGCATGT 60.068 47.619 0.00 0.0 42.86 3.21 F
1302 1716 0.540830 CCCTCTCCAGGTCCCTATCG 60.541 65.000 0.00 0.0 38.30 2.92 F
1758 2172 0.112606 AGGCCGGAATCGAGATAGGA 59.887 55.000 5.05 0.0 39.00 2.94 F
2683 3113 0.249868 TCCAGACTCAGGTGCGTTTG 60.250 55.000 0.00 0.0 0.00 2.93 F
4235 5010 1.270571 TGTAATGCCGCTGTGTGAAGA 60.271 47.619 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 2073 1.303561 GAGCAGCACCCCAATGTGA 60.304 57.895 0.00 0.0 38.55 3.58 R
2275 2702 0.909610 TTCCAGCCCGAGGTCTGAAT 60.910 55.000 1.22 0.0 31.74 2.57 R
3135 3579 3.558321 CCTCCGTCCCAAATTACTTGTCA 60.558 47.826 0.00 0.0 32.65 3.58 R
4587 5373 0.835941 CCACCTGCCTATTGAGCTCT 59.164 55.000 16.19 0.0 0.00 4.09 R
5337 6131 0.043183 TCCTCCTCCATCCTGAGCAA 59.957 55.000 0.00 0.0 0.00 3.91 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
38 39 9.594478 AAACTATGAACATATATGACAACGTCA 57.406 29.630 19.63 11.52 46.90 4.35
39 40 8.803201 ACTATGAACATATATGACAACGTCAG 57.197 34.615 19.63 12.56 46.04 3.51
40 41 8.414003 ACTATGAACATATATGACAACGTCAGT 58.586 33.333 19.63 13.01 46.04 3.41
41 42 7.700322 ATGAACATATATGACAACGTCAGTC 57.300 36.000 19.63 12.65 46.04 3.51
42 43 5.741982 TGAACATATATGACAACGTCAGTCG 59.258 40.000 19.63 4.13 46.04 4.18
43 44 5.494632 ACATATATGACAACGTCAGTCGA 57.505 39.130 19.63 7.12 46.04 4.20
44 45 5.511571 ACATATATGACAACGTCAGTCGAG 58.488 41.667 19.63 5.29 46.04 4.04
45 46 5.296035 ACATATATGACAACGTCAGTCGAGA 59.704 40.000 19.63 5.13 46.04 4.04
46 47 4.696899 ATATGACAACGTCAGTCGAGAA 57.303 40.909 14.10 0.51 46.04 2.87
47 48 3.577649 ATGACAACGTCAGTCGAGAAT 57.422 42.857 14.10 2.50 46.04 2.40
48 49 2.661594 TGACAACGTCAGTCGAGAATG 58.338 47.619 14.10 0.00 37.67 2.67
49 50 1.387084 GACAACGTCAGTCGAGAATGC 59.613 52.381 5.49 0.00 42.86 3.56
50 51 1.269569 ACAACGTCAGTCGAGAATGCA 60.270 47.619 0.00 0.00 42.86 3.96
51 52 1.995484 CAACGTCAGTCGAGAATGCAT 59.005 47.619 0.00 0.00 42.86 3.96
52 53 1.633561 ACGTCAGTCGAGAATGCATG 58.366 50.000 0.00 0.00 42.86 4.06
53 54 1.067565 ACGTCAGTCGAGAATGCATGT 60.068 47.619 0.00 0.00 42.86 3.21
54 55 2.163613 ACGTCAGTCGAGAATGCATGTA 59.836 45.455 0.00 0.00 42.86 2.29
55 56 2.531912 CGTCAGTCGAGAATGCATGTAC 59.468 50.000 0.00 0.00 42.86 2.90
56 57 3.511699 GTCAGTCGAGAATGCATGTACA 58.488 45.455 0.00 0.00 0.00 2.90
57 58 3.549471 GTCAGTCGAGAATGCATGTACAG 59.451 47.826 0.00 0.00 0.00 2.74
58 59 3.443681 TCAGTCGAGAATGCATGTACAGA 59.556 43.478 0.00 0.00 0.00 3.41
59 60 3.795639 CAGTCGAGAATGCATGTACAGAG 59.204 47.826 0.00 0.00 0.00 3.35
60 61 3.696548 AGTCGAGAATGCATGTACAGAGA 59.303 43.478 0.00 0.00 0.00 3.10
61 62 4.340666 AGTCGAGAATGCATGTACAGAGAT 59.659 41.667 0.00 0.00 0.00 2.75
62 63 5.046529 GTCGAGAATGCATGTACAGAGATT 58.953 41.667 0.00 0.00 0.00 2.40
63 64 5.045872 TCGAGAATGCATGTACAGAGATTG 58.954 41.667 0.00 0.00 0.00 2.67
64 65 5.045872 CGAGAATGCATGTACAGAGATTGA 58.954 41.667 0.00 0.00 0.00 2.57
65 66 5.521372 CGAGAATGCATGTACAGAGATTGAA 59.479 40.000 0.00 0.00 0.00 2.69
66 67 6.202379 CGAGAATGCATGTACAGAGATTGAAT 59.798 38.462 0.00 0.00 0.00 2.57
67 68 7.383300 CGAGAATGCATGTACAGAGATTGAATA 59.617 37.037 0.00 0.00 0.00 1.75
68 69 8.969260 AGAATGCATGTACAGAGATTGAATAA 57.031 30.769 0.00 0.00 0.00 1.40
69 70 8.834465 AGAATGCATGTACAGAGATTGAATAAC 58.166 33.333 0.00 0.00 0.00 1.89
70 71 8.510243 AATGCATGTACAGAGATTGAATAACA 57.490 30.769 0.00 0.00 0.00 2.41
71 72 8.687292 ATGCATGTACAGAGATTGAATAACAT 57.313 30.769 0.00 0.00 0.00 2.71
72 73 7.922837 TGCATGTACAGAGATTGAATAACATG 58.077 34.615 0.33 7.55 43.54 3.21
74 75 6.925610 TGTACAGAGATTGAATAACATGCC 57.074 37.500 0.00 0.00 0.00 4.40
75 76 6.653020 TGTACAGAGATTGAATAACATGCCT 58.347 36.000 0.00 0.00 0.00 4.75
76 77 7.791029 TGTACAGAGATTGAATAACATGCCTA 58.209 34.615 0.00 0.00 0.00 3.93
77 78 8.432013 TGTACAGAGATTGAATAACATGCCTAT 58.568 33.333 0.00 0.00 0.00 2.57
78 79 9.277783 GTACAGAGATTGAATAACATGCCTATT 57.722 33.333 0.00 0.00 0.00 1.73
79 80 8.757982 ACAGAGATTGAATAACATGCCTATTT 57.242 30.769 0.00 0.00 0.00 1.40
80 81 8.627403 ACAGAGATTGAATAACATGCCTATTTG 58.373 33.333 0.00 0.00 0.00 2.32
81 82 8.843262 CAGAGATTGAATAACATGCCTATTTGA 58.157 33.333 0.00 0.00 0.00 2.69
82 83 9.412460 AGAGATTGAATAACATGCCTATTTGAA 57.588 29.630 0.00 0.00 0.00 2.69
90 91 6.913873 AACATGCCTATTTGAAATTCATGC 57.086 33.333 18.52 9.17 34.77 4.06
91 92 6.229936 ACATGCCTATTTGAAATTCATGCT 57.770 33.333 18.52 9.65 34.77 3.79
92 93 6.278363 ACATGCCTATTTGAAATTCATGCTC 58.722 36.000 18.52 0.00 34.77 4.26
93 94 5.918426 TGCCTATTTGAAATTCATGCTCA 57.082 34.783 0.00 0.00 0.00 4.26
94 95 6.474140 TGCCTATTTGAAATTCATGCTCAT 57.526 33.333 0.00 0.00 0.00 2.90
95 96 7.585579 TGCCTATTTGAAATTCATGCTCATA 57.414 32.000 0.00 0.00 0.00 2.15
96 97 8.185506 TGCCTATTTGAAATTCATGCTCATAT 57.814 30.769 0.00 0.00 0.00 1.78
97 98 8.644216 TGCCTATTTGAAATTCATGCTCATATT 58.356 29.630 0.00 0.00 0.00 1.28
98 99 9.485206 GCCTATTTGAAATTCATGCTCATATTT 57.515 29.630 0.00 0.00 0.00 1.40
103 104 9.947433 TTTGAAATTCATGCTCATATTTTTCCT 57.053 25.926 0.00 0.00 0.00 3.36
104 105 9.590451 TTGAAATTCATGCTCATATTTTTCCTC 57.410 29.630 0.00 0.00 0.00 3.71
105 106 8.751242 TGAAATTCATGCTCATATTTTTCCTCA 58.249 29.630 0.00 0.00 0.00 3.86
106 107 9.590451 GAAATTCATGCTCATATTTTTCCTCAA 57.410 29.630 0.00 0.00 0.00 3.02
107 108 8.937634 AATTCATGCTCATATTTTTCCTCAAC 57.062 30.769 0.00 0.00 0.00 3.18
108 109 7.707624 TTCATGCTCATATTTTTCCTCAACT 57.292 32.000 0.00 0.00 0.00 3.16
109 110 8.806429 TTCATGCTCATATTTTTCCTCAACTA 57.194 30.769 0.00 0.00 0.00 2.24
110 111 8.985315 TCATGCTCATATTTTTCCTCAACTAT 57.015 30.769 0.00 0.00 0.00 2.12
111 112 9.412460 TCATGCTCATATTTTTCCTCAACTATT 57.588 29.630 0.00 0.00 0.00 1.73
137 138 9.748708 TTTTCTAGGAATCAAAATCAAGTGTTG 57.251 29.630 0.00 0.00 0.00 3.33
138 139 8.690203 TTCTAGGAATCAAAATCAAGTGTTGA 57.310 30.769 0.00 0.00 45.01 3.18
165 166 5.629079 AAAGAATCGAAATCAAGTGACCC 57.371 39.130 0.00 0.00 0.00 4.46
166 167 4.286297 AGAATCGAAATCAAGTGACCCA 57.714 40.909 0.00 0.00 0.00 4.51
167 168 4.848357 AGAATCGAAATCAAGTGACCCAT 58.152 39.130 0.00 0.00 0.00 4.00
168 169 4.878397 AGAATCGAAATCAAGTGACCCATC 59.122 41.667 0.00 0.00 0.00 3.51
169 170 3.981071 TCGAAATCAAGTGACCCATCT 57.019 42.857 0.00 0.00 0.00 2.90
170 171 4.286297 TCGAAATCAAGTGACCCATCTT 57.714 40.909 0.00 0.00 0.00 2.40
171 172 4.651778 TCGAAATCAAGTGACCCATCTTT 58.348 39.130 0.00 0.00 0.00 2.52
172 173 5.070001 TCGAAATCAAGTGACCCATCTTTT 58.930 37.500 0.00 0.00 0.00 2.27
173 174 6.234920 TCGAAATCAAGTGACCCATCTTTTA 58.765 36.000 0.00 0.00 0.00 1.52
174 175 6.884295 TCGAAATCAAGTGACCCATCTTTTAT 59.116 34.615 0.00 0.00 0.00 1.40
175 176 7.065803 TCGAAATCAAGTGACCCATCTTTTATC 59.934 37.037 0.00 0.00 0.00 1.75
176 177 7.066284 CGAAATCAAGTGACCCATCTTTTATCT 59.934 37.037 0.00 0.00 0.00 1.98
177 178 8.655935 AAATCAAGTGACCCATCTTTTATCTT 57.344 30.769 0.00 0.00 0.00 2.40
178 179 8.655935 AATCAAGTGACCCATCTTTTATCTTT 57.344 30.769 0.00 0.00 0.00 2.52
179 180 8.655935 ATCAAGTGACCCATCTTTTATCTTTT 57.344 30.769 0.00 0.00 0.00 2.27
180 181 9.753674 ATCAAGTGACCCATCTTTTATCTTTTA 57.246 29.630 0.00 0.00 0.00 1.52
181 182 9.581289 TCAAGTGACCCATCTTTTATCTTTTAA 57.419 29.630 0.00 0.00 0.00 1.52
186 187 9.685828 TGACCCATCTTTTATCTTTTAAAAACG 57.314 29.630 1.66 0.00 0.00 3.60
187 188 9.902196 GACCCATCTTTTATCTTTTAAAAACGA 57.098 29.630 1.66 0.00 0.00 3.85
316 325 4.487219 ACCCTACCGGCCTACCCC 62.487 72.222 0.00 0.00 33.26 4.95
1299 1713 0.555369 AGTCCCTCTCCAGGTCCCTA 60.555 60.000 0.00 0.00 38.30 3.53
1302 1716 0.540830 CCCTCTCCAGGTCCCTATCG 60.541 65.000 0.00 0.00 38.30 2.92
1331 1745 3.219928 GGAGATCTCCGCGCTCCA 61.220 66.667 25.78 0.00 45.89 3.86
1336 1750 1.228583 ATCTCCGCGCTCCAGGATA 60.229 57.895 5.56 0.00 35.75 2.59
1451 1865 1.479323 GGTAGTTATGCTGGTGGACGA 59.521 52.381 0.00 0.00 0.00 4.20
1452 1866 2.537401 GTAGTTATGCTGGTGGACGAC 58.463 52.381 0.00 0.00 0.00 4.34
1454 1868 1.447140 TTATGCTGGTGGACGACGC 60.447 57.895 0.00 0.00 0.00 5.19
1659 2073 2.066999 GCTGACCCGGGAGAAGGAT 61.067 63.158 32.02 0.82 0.00 3.24
1722 2136 0.537371 CCGAGGTTTTGAAGGTGGCT 60.537 55.000 0.00 0.00 0.00 4.75
1758 2172 0.112606 AGGCCGGAATCGAGATAGGA 59.887 55.000 5.05 0.00 39.00 2.94
1836 2250 2.183478 TGGTAGGTGCACTGTGAATG 57.817 50.000 17.98 0.00 0.00 2.67
1839 2253 2.679837 GGTAGGTGCACTGTGAATGATG 59.320 50.000 17.98 0.00 0.00 3.07
1871 2285 3.256383 TGCAAGTTCATTGACTTCCCATG 59.744 43.478 0.00 0.00 41.83 3.66
1895 2309 8.662781 TGTATCTAGCCATACTGAATTGTTTC 57.337 34.615 3.91 0.00 31.42 2.78
2007 2421 4.456535 TGTTGAAGCACAAAGGTAGCTAA 58.543 39.130 0.00 0.00 40.36 3.09
2028 2446 9.180678 AGCTAACTTGATTCATTTTTGTTTACG 57.819 29.630 0.00 0.00 0.00 3.18
2031 2449 8.696410 AACTTGATTCATTTTTGTTTACGTGT 57.304 26.923 0.00 0.00 0.00 4.49
2070 2488 1.166531 ACTGCCGGTTGAACTTGAGC 61.167 55.000 1.90 0.00 0.00 4.26
2080 2498 6.348950 CCGGTTGAACTTGAGCAACATTAATA 60.349 38.462 0.00 0.00 44.59 0.98
2131 2551 2.042464 TGGCCATGTGGTTTAAAGCAA 58.958 42.857 20.88 12.01 38.25 3.91
2133 2553 2.805671 GGCCATGTGGTTTAAAGCAAAC 59.194 45.455 20.88 10.79 44.94 2.93
2168 2590 9.309224 ACCTCTTTTAACCAACAATAAGCTATT 57.691 29.630 0.00 0.00 0.00 1.73
2205 2632 1.071385 CTTCAGTCTGCCACTCTTGGT 59.929 52.381 0.00 0.00 45.98 3.67
2246 2673 4.706476 AGCTGCAATTCATTACTAAAGCCA 59.294 37.500 1.02 0.00 0.00 4.75
2291 2718 0.539051 AAGATTCAGACCTCGGGCTG 59.461 55.000 12.75 12.75 0.00 4.85
2459 2886 5.590530 TGGCCAATGAAAGCGTAATATTT 57.409 34.783 0.61 0.00 0.00 1.40
2460 2887 5.971763 TGGCCAATGAAAGCGTAATATTTT 58.028 33.333 0.61 0.00 0.00 1.82
2461 2888 6.039616 TGGCCAATGAAAGCGTAATATTTTC 58.960 36.000 0.61 0.00 0.00 2.29
2525 2955 4.923415 TCTTATGGTCAGAGTCAGTGAGA 58.077 43.478 0.00 0.00 0.00 3.27
2683 3113 0.249868 TCCAGACTCAGGTGCGTTTG 60.250 55.000 0.00 0.00 0.00 2.93
2744 3176 8.750298 TCCTTTATGTTTTTGGTGTCTTGTTTA 58.250 29.630 0.00 0.00 0.00 2.01
2799 3231 5.105752 GCTCGACTCAATTGATCACTTAGT 58.894 41.667 8.96 0.99 0.00 2.24
2846 3280 3.648339 TTTTGGAGCATTCAAGACAGC 57.352 42.857 0.00 0.00 33.25 4.40
2888 3322 9.367160 TGACATATATTTCTCATAGTCACCAGA 57.633 33.333 0.82 0.00 30.64 3.86
2959 3393 7.202139 CCCTCTAGCCTAGATATTTCTTTTGGT 60.202 40.741 1.05 0.00 33.66 3.67
2964 3398 6.603599 AGCCTAGATATTTCTTTTGGTGAACC 59.396 38.462 0.00 0.00 33.17 3.62
3018 3452 6.904626 AGCAAACTAGGACTCCATGAATTAT 58.095 36.000 0.00 0.00 0.00 1.28
3098 3532 4.105697 TCCCTCTGTCCCAAATTACTTGTT 59.894 41.667 0.00 0.00 32.65 2.83
3202 3646 7.768240 TCGAGAACAGAGTAATATTAAGCACA 58.232 34.615 0.00 0.00 0.00 4.57
3249 3693 6.516739 TGACTCCATGAGTTAACTAGACAG 57.483 41.667 8.42 4.06 43.53 3.51
3256 3700 7.047891 CCATGAGTTAACTAGACAGGCAAATA 58.952 38.462 8.42 0.00 0.00 1.40
3380 3828 5.163622 GCATACTACCATGTGCACTTTTGAT 60.164 40.000 19.41 2.73 36.75 2.57
3435 3883 9.309516 CACTACAGAAAGTGTAAGAAAGTACAA 57.690 33.333 0.00 0.00 41.28 2.41
3455 3903 4.341235 ACAAGATCGTAGTAGGCATGCTTA 59.659 41.667 18.92 12.19 0.00 3.09
3460 3908 5.018539 TCGTAGTAGGCATGCTTAAACAT 57.981 39.130 18.92 4.19 0.00 2.71
3464 3912 7.010738 TCGTAGTAGGCATGCTTAAACATTTAC 59.989 37.037 18.92 2.12 0.00 2.01
3621 4069 2.243994 AGGGTAGCAGGGGTTTTATTCC 59.756 50.000 0.00 0.00 0.00 3.01
3724 4172 5.041951 TCCATTGTTGTATTCAGTTTCGC 57.958 39.130 0.00 0.00 0.00 4.70
3810 4259 8.304596 TGTTAGAGTATCCTTCAGTTGTTACTG 58.695 37.037 0.00 0.00 44.77 2.74
3853 4302 6.357579 TGCCACATTGTCCATAGAAAAATT 57.642 33.333 0.00 0.00 0.00 1.82
3880 4329 9.243637 CTTCGGTTGAGAAACAATAATTTTGAA 57.756 29.630 7.18 0.00 40.76 2.69
3913 4362 3.954904 ACTATGCCCGCCAGTATAGATAG 59.045 47.826 11.22 0.00 0.00 2.08
3931 4380 5.665459 AGATAGGTTGTGTCTAAGTGATGC 58.335 41.667 0.00 0.00 0.00 3.91
4007 4781 2.767505 CTGAGTCCCACAACTTGGTAC 58.232 52.381 0.00 0.00 45.25 3.34
4052 4826 4.556592 ATTGTGCAAGGTGGCATAAATT 57.443 36.364 1.63 0.00 45.78 1.82
4110 4885 9.429359 AGATAACTTGTAATCAACAGTCTTGAG 57.571 33.333 0.00 0.00 39.87 3.02
4111 4886 9.209175 GATAACTTGTAATCAACAGTCTTGAGT 57.791 33.333 0.00 0.00 39.87 3.41
4112 4887 6.851222 ACTTGTAATCAACAGTCTTGAGTG 57.149 37.500 4.10 4.10 39.87 3.51
4113 4888 6.349300 ACTTGTAATCAACAGTCTTGAGTGT 58.651 36.000 5.36 5.36 39.87 3.55
4114 4889 6.823689 ACTTGTAATCAACAGTCTTGAGTGTT 59.176 34.615 15.65 15.65 39.87 3.32
4183 4958 4.539726 TGTAGGGCGAAGTATCCTTTCTA 58.460 43.478 0.00 0.00 32.46 2.10
4235 5010 1.270571 TGTAATGCCGCTGTGTGAAGA 60.271 47.619 0.00 0.00 0.00 2.87
4246 5021 6.368791 GCCGCTGTGTGAAGAATATATGAATA 59.631 38.462 0.00 0.00 0.00 1.75
4325 5106 7.615365 TGTAAGGAAATGGCTTGTTCTCATATT 59.385 33.333 0.00 0.00 0.00 1.28
4354 5135 1.666888 GCGTCCTTTCTGGTTGCAATG 60.667 52.381 0.59 0.00 37.13 2.82
4366 5147 3.565482 TGGTTGCAATGAACAGTCTTCTC 59.435 43.478 0.59 0.00 0.00 2.87
4394 5175 7.114754 TCCATGAGAAGCTGAACTGAATTATT 58.885 34.615 0.00 0.00 0.00 1.40
4596 5382 1.908340 AGCGGCTGGAAGAGCTCAAT 61.908 55.000 17.77 3.78 44.10 2.57
4604 5390 1.488393 GGAAGAGCTCAATAGGCAGGT 59.512 52.381 17.77 0.00 0.00 4.00
4614 5400 0.399233 ATAGGCAGGTGGAGGAGTCC 60.399 60.000 0.00 0.00 44.24 3.85
4746 5532 3.476552 CTCTAACGAGATGGAGCTCTCT 58.523 50.000 14.64 9.59 39.65 3.10
4801 5587 2.030958 GATCGAAACACGGGCCGTT 61.031 57.895 32.12 16.54 38.32 4.44
4818 5604 2.031157 CCGTTTGCTCCTTTGTTTCGAT 60.031 45.455 0.00 0.00 0.00 3.59
4828 5614 7.647715 TGCTCCTTTGTTTCGATAAAAGAAAAG 59.352 33.333 13.58 6.54 38.99 2.27
4846 5632 7.823745 AGAAAAGGCAAAGAGAACATTAGAA 57.176 32.000 0.00 0.00 0.00 2.10
4965 5751 6.453396 GCGTGTAATTGTAGAGAAAGTTACCG 60.453 42.308 0.00 0.00 0.00 4.02
5013 5799 6.648879 TCATTCTTTTGGGAAAATCGTCTT 57.351 33.333 0.00 0.00 0.00 3.01
5039 5825 5.110814 TCAACATATCACTTTACCCTGGG 57.889 43.478 12.28 12.28 0.00 4.45
5061 5847 5.357032 GGGTTTCTTTATATGACCACCACAG 59.643 44.000 0.00 0.00 32.00 3.66
5138 5926 3.996150 AACATGTGAAGACTTGCCAAG 57.004 42.857 2.11 2.11 31.78 3.61
5176 5964 8.376270 AGATGTAGTTTTACCTAGAAGCTGTTT 58.624 33.333 0.00 0.00 0.00 2.83
5177 5965 9.649167 GATGTAGTTTTACCTAGAAGCTGTTTA 57.351 33.333 0.00 0.00 0.00 2.01
5282 6076 6.113411 ACTAAAATGGTAACTTCATCCTCCG 58.887 40.000 0.00 0.00 37.61 4.63
5285 6079 2.816411 TGGTAACTTCATCCTCCGACT 58.184 47.619 0.00 0.00 37.61 4.18
5318 6112 0.109153 ATGAACCTGACTGTGCAGCA 59.891 50.000 0.00 0.00 34.56 4.41
5325 6119 1.029408 TGACTGTGCAGCAAAACCGT 61.029 50.000 0.00 0.00 0.00 4.83
5363 6157 1.414866 GGATGGAGGAGGAAGAGGCC 61.415 65.000 0.00 0.00 0.00 5.19
5411 6205 7.886970 CCAGATCACTGAAAATGGACCATATAT 59.113 37.037 7.59 0.00 46.03 0.86
5466 6261 7.309133 CCAATAAATCAACCTTCAGTGCTACAA 60.309 37.037 0.00 0.00 0.00 2.41
5478 6273 4.991056 TCAGTGCTACAACATTTCTCTGAC 59.009 41.667 0.00 0.00 0.00 3.51
5485 6282 4.454678 ACAACATTTCTCTGACTTGCTGA 58.545 39.130 0.00 0.00 0.00 4.26
5486 6283 5.068636 ACAACATTTCTCTGACTTGCTGAT 58.931 37.500 0.00 0.00 0.00 2.90
5498 6295 6.833933 TCTGACTTGCTGATTAGTACCTGATA 59.166 38.462 0.00 0.00 0.00 2.15
5549 6346 1.680522 GGATCTTCTCCAGCGCCTCA 61.681 60.000 2.29 0.00 44.26 3.86
5612 6409 4.096984 GTGGACATGATCTTGGTGAAATCC 59.903 45.833 12.76 9.38 0.00 3.01
5650 6447 1.059098 AGGCAACATGAGTGAGGTGA 58.941 50.000 0.00 0.00 41.41 4.02
5663 6460 2.094442 GTGAGGTGAGGACTGAGTTAGC 60.094 54.545 0.00 0.00 0.00 3.09
5674 6471 4.402793 GGACTGAGTTAGCTTAGGACATGA 59.597 45.833 0.00 0.00 33.16 3.07
5711 6508 3.571401 CCCTCTTGCAGAAACAAAGTGAT 59.429 43.478 0.00 0.00 0.00 3.06
5712 6509 4.761739 CCCTCTTGCAGAAACAAAGTGATA 59.238 41.667 0.00 0.00 0.00 2.15
5740 6537 4.819105 TCTACCACATACCTGGAAGTTG 57.181 45.455 0.00 0.00 35.04 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.594478 TGACGTTGTCATATATGTTCATAGTTT 57.406 29.630 12.42 0.00 37.67 2.66
13 14 9.249457 CTGACGTTGTCATATATGTTCATAGTT 57.751 33.333 12.42 0.53 41.94 2.24
14 15 8.414003 ACTGACGTTGTCATATATGTTCATAGT 58.586 33.333 12.42 13.58 41.94 2.12
15 16 8.803201 ACTGACGTTGTCATATATGTTCATAG 57.197 34.615 12.42 11.26 41.94 2.23
16 17 7.589954 CGACTGACGTTGTCATATATGTTCATA 59.410 37.037 12.42 0.00 41.94 2.15
17 18 6.417930 CGACTGACGTTGTCATATATGTTCAT 59.582 38.462 12.42 0.22 41.94 2.57
18 19 5.741982 CGACTGACGTTGTCATATATGTTCA 59.258 40.000 12.42 10.13 41.94 3.18
19 20 5.969435 TCGACTGACGTTGTCATATATGTTC 59.031 40.000 12.42 7.88 41.94 3.18
20 21 5.886992 TCGACTGACGTTGTCATATATGTT 58.113 37.500 12.42 0.00 41.94 2.71
21 22 5.296035 TCTCGACTGACGTTGTCATATATGT 59.704 40.000 12.42 0.00 41.94 2.29
22 23 5.748592 TCTCGACTGACGTTGTCATATATG 58.251 41.667 18.24 6.36 41.94 1.78
23 24 6.373186 TTCTCGACTGACGTTGTCATATAT 57.627 37.500 18.24 0.00 41.94 0.86
24 25 5.806366 TTCTCGACTGACGTTGTCATATA 57.194 39.130 18.24 4.59 41.94 0.86
25 26 4.696899 TTCTCGACTGACGTTGTCATAT 57.303 40.909 18.24 0.00 41.94 1.78
26 27 4.412207 CATTCTCGACTGACGTTGTCATA 58.588 43.478 18.24 8.24 41.94 2.15
27 28 3.245797 CATTCTCGACTGACGTTGTCAT 58.754 45.455 18.24 5.76 41.94 3.06
28 29 2.661594 CATTCTCGACTGACGTTGTCA 58.338 47.619 18.24 0.00 40.50 3.58
29 30 1.387084 GCATTCTCGACTGACGTTGTC 59.613 52.381 11.17 11.17 43.13 3.18
30 31 1.269569 TGCATTCTCGACTGACGTTGT 60.270 47.619 0.00 0.00 43.13 3.32
31 32 1.418373 TGCATTCTCGACTGACGTTG 58.582 50.000 0.00 0.00 43.13 4.10
32 33 1.995484 CATGCATTCTCGACTGACGTT 59.005 47.619 0.00 0.00 43.13 3.99
33 34 1.067565 ACATGCATTCTCGACTGACGT 60.068 47.619 0.00 0.00 43.13 4.34
34 35 1.633561 ACATGCATTCTCGACTGACG 58.366 50.000 0.00 0.00 44.09 4.35
35 36 3.511699 TGTACATGCATTCTCGACTGAC 58.488 45.455 0.00 0.00 0.00 3.51
36 37 3.443681 TCTGTACATGCATTCTCGACTGA 59.556 43.478 0.00 0.00 0.00 3.41
37 38 3.774066 TCTGTACATGCATTCTCGACTG 58.226 45.455 0.00 0.00 0.00 3.51
38 39 3.696548 TCTCTGTACATGCATTCTCGACT 59.303 43.478 0.00 0.00 0.00 4.18
39 40 4.033990 TCTCTGTACATGCATTCTCGAC 57.966 45.455 0.00 0.00 0.00 4.20
40 41 4.926140 ATCTCTGTACATGCATTCTCGA 57.074 40.909 0.00 0.00 0.00 4.04
41 42 5.045872 TCAATCTCTGTACATGCATTCTCG 58.954 41.667 0.00 0.00 0.00 4.04
42 43 6.915544 TTCAATCTCTGTACATGCATTCTC 57.084 37.500 0.00 0.00 0.00 2.87
43 44 8.834465 GTTATTCAATCTCTGTACATGCATTCT 58.166 33.333 0.00 0.00 0.00 2.40
44 45 8.615211 TGTTATTCAATCTCTGTACATGCATTC 58.385 33.333 0.00 0.00 0.00 2.67
45 46 8.510243 TGTTATTCAATCTCTGTACATGCATT 57.490 30.769 0.00 0.00 0.00 3.56
46 47 8.565416 CATGTTATTCAATCTCTGTACATGCAT 58.435 33.333 0.00 0.00 36.39 3.96
47 48 7.922837 CATGTTATTCAATCTCTGTACATGCA 58.077 34.615 0.00 0.00 36.39 3.96
49 50 7.228108 AGGCATGTTATTCAATCTCTGTACATG 59.772 37.037 0.00 0.00 42.59 3.21
50 51 7.285566 AGGCATGTTATTCAATCTCTGTACAT 58.714 34.615 0.00 0.00 0.00 2.29
51 52 6.653020 AGGCATGTTATTCAATCTCTGTACA 58.347 36.000 0.00 0.00 0.00 2.90
52 53 8.839310 ATAGGCATGTTATTCAATCTCTGTAC 57.161 34.615 0.00 0.00 0.00 2.90
53 54 9.851686 AAATAGGCATGTTATTCAATCTCTGTA 57.148 29.630 0.00 0.00 0.00 2.74
54 55 8.627403 CAAATAGGCATGTTATTCAATCTCTGT 58.373 33.333 0.00 0.00 0.00 3.41
55 56 8.843262 TCAAATAGGCATGTTATTCAATCTCTG 58.157 33.333 0.00 0.00 0.00 3.35
56 57 8.985315 TCAAATAGGCATGTTATTCAATCTCT 57.015 30.769 0.00 0.00 0.00 3.10
64 65 9.048446 GCATGAATTTCAAATAGGCATGTTATT 57.952 29.630 16.01 0.00 35.38 1.40
65 66 8.426489 AGCATGAATTTCAAATAGGCATGTTAT 58.574 29.630 16.01 0.00 35.38 1.89
66 67 7.784037 AGCATGAATTTCAAATAGGCATGTTA 58.216 30.769 16.01 0.00 35.38 2.41
67 68 6.646267 AGCATGAATTTCAAATAGGCATGTT 58.354 32.000 16.01 10.78 35.38 2.71
68 69 6.127281 TGAGCATGAATTTCAAATAGGCATGT 60.127 34.615 16.01 7.94 35.38 3.21
69 70 6.277605 TGAGCATGAATTTCAAATAGGCATG 58.722 36.000 2.68 12.71 35.87 4.06
70 71 6.474140 TGAGCATGAATTTCAAATAGGCAT 57.526 33.333 2.68 0.00 0.00 4.40
71 72 5.918426 TGAGCATGAATTTCAAATAGGCA 57.082 34.783 2.68 0.00 0.00 4.75
72 73 9.485206 AAATATGAGCATGAATTTCAAATAGGC 57.515 29.630 2.68 3.27 0.00 3.93
77 78 9.947433 AGGAAAAATATGAGCATGAATTTCAAA 57.053 25.926 2.68 0.00 0.00 2.69
78 79 9.590451 GAGGAAAAATATGAGCATGAATTTCAA 57.410 29.630 2.68 0.00 0.00 2.69
79 80 8.751242 TGAGGAAAAATATGAGCATGAATTTCA 58.249 29.630 0.75 0.75 0.00 2.69
80 81 9.590451 TTGAGGAAAAATATGAGCATGAATTTC 57.410 29.630 0.00 0.00 0.00 2.17
81 82 9.374838 GTTGAGGAAAAATATGAGCATGAATTT 57.625 29.630 0.00 0.00 0.00 1.82
82 83 8.755977 AGTTGAGGAAAAATATGAGCATGAATT 58.244 29.630 0.00 0.00 0.00 2.17
83 84 8.302515 AGTTGAGGAAAAATATGAGCATGAAT 57.697 30.769 0.00 0.00 0.00 2.57
84 85 7.707624 AGTTGAGGAAAAATATGAGCATGAA 57.292 32.000 0.00 0.00 0.00 2.57
85 86 8.985315 ATAGTTGAGGAAAAATATGAGCATGA 57.015 30.769 0.00 0.00 0.00 3.07
111 112 9.748708 CAACACTTGATTTTGATTCCTAGAAAA 57.251 29.630 0.00 0.00 0.00 2.29
112 113 9.130661 TCAACACTTGATTTTGATTCCTAGAAA 57.869 29.630 0.00 0.00 34.08 2.52
113 114 8.690203 TCAACACTTGATTTTGATTCCTAGAA 57.310 30.769 0.00 0.00 34.08 2.10
141 142 6.040391 TGGGTCACTTGATTTCGATTCTTTTT 59.960 34.615 0.00 0.00 0.00 1.94
142 143 5.534654 TGGGTCACTTGATTTCGATTCTTTT 59.465 36.000 0.00 0.00 0.00 2.27
143 144 5.070001 TGGGTCACTTGATTTCGATTCTTT 58.930 37.500 0.00 0.00 0.00 2.52
144 145 4.651778 TGGGTCACTTGATTTCGATTCTT 58.348 39.130 0.00 0.00 0.00 2.52
145 146 4.286297 TGGGTCACTTGATTTCGATTCT 57.714 40.909 0.00 0.00 0.00 2.40
146 147 4.878397 AGATGGGTCACTTGATTTCGATTC 59.122 41.667 0.00 0.00 0.00 2.52
147 148 4.848357 AGATGGGTCACTTGATTTCGATT 58.152 39.130 0.00 0.00 0.00 3.34
148 149 4.494091 AGATGGGTCACTTGATTTCGAT 57.506 40.909 0.00 0.00 0.00 3.59
149 150 3.981071 AGATGGGTCACTTGATTTCGA 57.019 42.857 0.00 0.00 0.00 3.71
150 151 5.376854 AAAAGATGGGTCACTTGATTTCG 57.623 39.130 0.00 0.00 0.00 3.46
151 152 8.286191 AGATAAAAGATGGGTCACTTGATTTC 57.714 34.615 0.00 0.00 0.00 2.17
152 153 8.655935 AAGATAAAAGATGGGTCACTTGATTT 57.344 30.769 0.00 0.00 0.00 2.17
153 154 8.655935 AAAGATAAAAGATGGGTCACTTGATT 57.344 30.769 0.00 0.00 0.00 2.57
154 155 8.655935 AAAAGATAAAAGATGGGTCACTTGAT 57.344 30.769 0.00 0.00 0.00 2.57
155 156 9.581289 TTAAAAGATAAAAGATGGGTCACTTGA 57.419 29.630 0.00 0.00 0.00 3.02
160 161 9.685828 CGTTTTTAAAAGATAAAAGATGGGTCA 57.314 29.630 0.14 0.00 0.00 4.02
161 162 9.902196 TCGTTTTTAAAAGATAAAAGATGGGTC 57.098 29.630 0.14 0.00 0.00 4.46
213 214 1.271102 GAGTCTGGACGCTCTTGAGTT 59.729 52.381 0.00 0.00 36.20 3.01
215 216 0.172352 GGAGTCTGGACGCTCTTGAG 59.828 60.000 4.67 0.00 36.20 3.02
216 217 0.539669 TGGAGTCTGGACGCTCTTGA 60.540 55.000 4.67 0.00 36.20 3.02
217 218 0.108898 CTGGAGTCTGGACGCTCTTG 60.109 60.000 4.67 0.00 36.20 3.02
220 221 0.820871 ATTCTGGAGTCTGGACGCTC 59.179 55.000 4.67 0.00 36.20 5.03
221 222 1.205893 GAATTCTGGAGTCTGGACGCT 59.794 52.381 0.00 0.00 36.20 5.07
222 223 1.205893 AGAATTCTGGAGTCTGGACGC 59.794 52.381 7.30 0.00 36.20 5.19
741 750 4.722700 GCGTGGTGGGGCTGTGAT 62.723 66.667 0.00 0.00 0.00 3.06
1299 1713 4.598319 TCCGCCTCCCGATCCGAT 62.598 66.667 0.00 0.00 40.02 4.18
1302 1716 2.601966 ATCTCCGCCTCCCGATCC 60.602 66.667 0.00 0.00 40.02 3.36
1331 1745 1.548128 CGAGGGATCGGACCTTATCCT 60.548 57.143 17.72 7.58 46.69 3.24
1336 1750 1.455959 CCTCGAGGGATCGGACCTT 60.456 63.158 24.62 0.00 38.79 3.50
1356 1770 1.880340 CCTCTGCGCGTCCATCTTC 60.880 63.158 8.43 0.00 0.00 2.87
1659 2073 1.303561 GAGCAGCACCCCAATGTGA 60.304 57.895 0.00 0.00 38.55 3.58
1722 2136 1.383664 CTCCCTCAGCCCATCCTCA 60.384 63.158 0.00 0.00 0.00 3.86
1743 2157 3.607310 CGTTGAGTCCTATCTCGATTCCG 60.607 52.174 0.00 0.00 37.28 4.30
1758 2172 2.185310 GATCCCTGTGGCCGTTGAGT 62.185 60.000 0.00 0.00 0.00 3.41
1836 2250 3.240069 GAACTTGCAACAGCATGACATC 58.760 45.455 9.85 2.89 39.69 3.06
1839 2253 2.780065 TGAACTTGCAACAGCATGAC 57.220 45.000 9.85 4.96 39.69 3.06
1860 2274 3.653164 TGGCTAGATACATGGGAAGTCA 58.347 45.455 0.00 0.00 0.00 3.41
1861 2275 4.899352 ATGGCTAGATACATGGGAAGTC 57.101 45.455 0.00 0.00 0.00 3.01
1871 2285 8.894768 AGAAACAATTCAGTATGGCTAGATAC 57.105 34.615 0.00 0.00 38.06 2.24
1895 2309 8.028354 TGCAATATTGGTTGATTGTTACAGAAG 58.972 33.333 17.02 0.00 35.80 2.85
2007 2421 7.971168 TGACACGTAAACAAAAATGAATCAAGT 59.029 29.630 0.00 0.00 0.00 3.16
2057 2475 8.810652 TTTATTAATGTTGCTCAAGTTCAACC 57.189 30.769 0.00 0.00 41.21 3.77
2131 2551 5.105675 TGGTTAAAAGAGGTCAAAAAGCGTT 60.106 36.000 0.00 0.00 0.00 4.84
2133 2553 4.927422 TGGTTAAAAGAGGTCAAAAAGCG 58.073 39.130 0.00 0.00 0.00 4.68
2173 2595 7.291182 AGTGGCAGACTGAAGGATAGTTATAAT 59.709 37.037 6.65 0.00 31.75 1.28
2175 2597 6.136857 AGTGGCAGACTGAAGGATAGTTATA 58.863 40.000 6.65 0.00 31.75 0.98
2180 2607 3.030291 AGAGTGGCAGACTGAAGGATAG 58.970 50.000 6.65 0.00 33.83 2.08
2183 2610 1.345741 CAAGAGTGGCAGACTGAAGGA 59.654 52.381 6.65 0.00 33.83 3.36
2268 2695 2.162408 GCCCGAGGTCTGAATCTTTTTG 59.838 50.000 0.00 0.00 0.00 2.44
2275 2702 0.909610 TTCCAGCCCGAGGTCTGAAT 60.910 55.000 1.22 0.00 31.74 2.57
2434 2861 2.418368 TACGCTTTCATTGGCCATCT 57.582 45.000 6.09 0.00 0.00 2.90
2459 2886 4.895889 ACATCCGATTAGACATGAGGAGAA 59.104 41.667 0.00 0.00 0.00 2.87
2460 2887 4.474394 ACATCCGATTAGACATGAGGAGA 58.526 43.478 0.00 0.00 0.00 3.71
2461 2888 4.862902 ACATCCGATTAGACATGAGGAG 57.137 45.455 0.00 0.00 0.00 3.69
2477 2907 9.224267 AGTGATATGCATATACTCAAAACATCC 57.776 33.333 19.12 3.10 0.00 3.51
2683 3113 7.553881 AATGGTGCATGTCTGTATAAAGTAC 57.446 36.000 0.00 0.00 0.00 2.73
2888 3322 6.737608 ACATGGTTGTAATACCCCTTGTAAT 58.262 36.000 12.72 0.00 37.39 1.89
2959 3393 7.011950 CACCATGCTTAATATTTACTCGGTTCA 59.988 37.037 0.00 0.00 0.00 3.18
2964 3398 6.202762 TGCTCACCATGCTTAATATTTACTCG 59.797 38.462 0.00 0.00 0.00 4.18
3130 3574 5.878116 CCGTCCCAAATTACTTGTCATAGAA 59.122 40.000 0.00 0.00 32.65 2.10
3135 3579 3.558321 CCTCCGTCCCAAATTACTTGTCA 60.558 47.826 0.00 0.00 32.65 3.58
3178 3622 7.702772 ACTGTGCTTAATATTACTCTGTTCTCG 59.297 37.037 0.00 0.00 0.00 4.04
3202 3646 4.817464 TGGTCGTTTGCTAACATGTTTACT 59.183 37.500 17.78 0.00 33.75 2.24
3249 3693 8.462016 AGTGATTAATTCAGTCAAGTATTTGCC 58.538 33.333 0.00 0.00 32.22 4.52
3380 3828 6.039829 TGCTGTCAAAACACCAAACATATGTA 59.960 34.615 9.21 0.00 0.00 2.29
3431 3879 3.889538 AGCATGCCTACTACGATCTTGTA 59.110 43.478 15.66 0.00 0.00 2.41
3435 3883 5.163447 TGTTTAAGCATGCCTACTACGATCT 60.163 40.000 15.66 0.00 0.00 2.75
3455 3903 6.569179 ACCAAGAATGCTACGTAAATGTTT 57.431 33.333 0.00 0.00 0.00 2.83
3460 3908 6.225318 ACACTAACCAAGAATGCTACGTAAA 58.775 36.000 0.00 0.00 0.00 2.01
3464 3912 6.533723 TGATAACACTAACCAAGAATGCTACG 59.466 38.462 0.00 0.00 0.00 3.51
3552 4000 9.234384 GTATAGCATAACATATGGTCGATACAC 57.766 37.037 7.80 0.00 0.00 2.90
3810 4259 4.746611 GGCAATGCAATATCTAAAACTGGC 59.253 41.667 7.79 0.00 0.00 4.85
3853 4302 8.625651 TCAAAATTATTGTTTCTCAACCGAAGA 58.374 29.630 0.00 0.00 38.97 2.87
3901 4350 8.353684 CACTTAGACACAACCTATCTATACTGG 58.646 40.741 0.00 0.00 0.00 4.00
3913 4362 1.128692 GCGCATCACTTAGACACAACC 59.871 52.381 0.30 0.00 0.00 3.77
3931 4380 2.415893 CCCTTCCTTGCACTTTATTGCG 60.416 50.000 0.00 0.00 46.20 4.85
4007 4781 4.679373 AGTATCCTTCATACAGCCACAG 57.321 45.455 0.00 0.00 40.14 3.66
4104 4879 8.122472 TCTACAGTTATCATCAACACTCAAGA 57.878 34.615 0.00 0.00 0.00 3.02
4110 4885 8.942338 TGGTTATCTACAGTTATCATCAACAC 57.058 34.615 0.00 0.00 0.00 3.32
4111 4886 8.758829 ACTGGTTATCTACAGTTATCATCAACA 58.241 33.333 0.00 0.00 45.03 3.33
4112 4887 9.035607 CACTGGTTATCTACAGTTATCATCAAC 57.964 37.037 0.00 0.00 45.03 3.18
4113 4888 7.710907 GCACTGGTTATCTACAGTTATCATCAA 59.289 37.037 0.00 0.00 45.03 2.57
4114 4889 7.147742 TGCACTGGTTATCTACAGTTATCATCA 60.148 37.037 0.00 0.00 45.03 3.07
4115 4890 7.210174 TGCACTGGTTATCTACAGTTATCATC 58.790 38.462 0.00 0.00 45.03 2.92
4116 4891 7.124573 TGCACTGGTTATCTACAGTTATCAT 57.875 36.000 0.00 0.00 45.03 2.45
4246 5021 6.239217 TGAAGACACTATGCATCCTTGTAT 57.761 37.500 0.19 0.00 32.52 2.29
4284 5059 6.721571 TTCCTTACAACTTATGCTCTTTCG 57.278 37.500 0.00 0.00 0.00 3.46
4325 5106 3.894547 GAAAGGACGCTTCGCCCCA 62.895 63.158 0.00 0.00 0.00 4.96
4354 5135 4.097135 TCTCATGGATCGAGAAGACTGTTC 59.903 45.833 0.00 0.00 36.59 3.18
4366 5147 2.864946 CAGTTCAGCTTCTCATGGATCG 59.135 50.000 0.00 0.00 0.00 3.69
4422 5208 3.827817 TCCTCTAGTTCCTTGTGGAGA 57.172 47.619 0.00 0.00 44.24 3.71
4587 5373 0.835941 CCACCTGCCTATTGAGCTCT 59.164 55.000 16.19 0.00 0.00 4.09
4596 5382 1.001760 GGACTCCTCCACCTGCCTA 59.998 63.158 0.00 0.00 36.42 3.93
4604 5390 1.688311 CCCTATTGTCGGACTCCTCCA 60.688 57.143 9.88 0.00 36.12 3.86
4710 5496 3.948702 GAGGTCTCCTCTGCCTCC 58.051 66.667 8.38 0.00 46.41 4.30
4746 5532 1.344438 CGCTGCTATATCAGGGGTTCA 59.656 52.381 11.68 0.00 41.57 3.18
4801 5587 6.627395 TCTTTTATCGAAACAAAGGAGCAA 57.373 33.333 12.06 0.00 0.00 3.91
4818 5604 9.965824 CTAATGTTCTCTTTGCCTTTTCTTTTA 57.034 29.630 0.00 0.00 0.00 1.52
4965 5751 4.767928 ACATCTTCACTATATCCCGAGTCC 59.232 45.833 0.00 0.00 0.00 3.85
4999 5785 4.399618 TGTTGAAACAAGACGATTTTCCCA 59.600 37.500 0.00 0.00 35.67 4.37
5013 5799 6.432783 CCAGGGTAAAGTGATATGTTGAAACA 59.567 38.462 0.00 0.00 44.06 2.83
5039 5825 7.174253 TGAACTGTGGTGGTCATATAAAGAAAC 59.826 37.037 0.00 0.00 0.00 2.78
5061 5847 4.687483 CCACCTGAATCAGCAAAAATGAAC 59.313 41.667 4.40 0.00 0.00 3.18
5282 6076 6.648310 CAGGTTCATGATATGGTCACATAGTC 59.352 42.308 0.00 0.00 42.48 2.59
5285 6079 6.327365 AGTCAGGTTCATGATATGGTCACATA 59.673 38.462 0.00 0.00 43.31 2.29
5337 6131 0.043183 TCCTCCTCCATCCTGAGCAA 59.957 55.000 0.00 0.00 0.00 3.91
5466 6261 6.471146 ACTAATCAGCAAGTCAGAGAAATGT 58.529 36.000 0.00 0.00 0.00 2.71
5478 6273 4.681942 GCGTATCAGGTACTAATCAGCAAG 59.318 45.833 0.00 0.00 36.02 4.01
5485 6282 3.005897 CAGCCAGCGTATCAGGTACTAAT 59.994 47.826 0.00 0.00 36.02 1.73
5486 6283 2.361119 CAGCCAGCGTATCAGGTACTAA 59.639 50.000 0.00 0.00 36.02 2.24
5519 6316 2.243810 GAGAAGATCCCGAGCCAGTAT 58.756 52.381 0.00 0.00 0.00 2.12
5590 6387 4.263860 TGGATTTCACCAAGATCATGTCCA 60.264 41.667 0.00 0.00 36.96 4.02
5591 6388 4.096984 GTGGATTTCACCAAGATCATGTCC 59.903 45.833 0.00 0.00 41.87 4.02
5650 6447 4.048970 TGTCCTAAGCTAACTCAGTCCT 57.951 45.455 0.00 0.00 0.00 3.85
5663 6460 5.121105 TGCTCATTCATGTCATGTCCTAAG 58.879 41.667 12.54 6.65 0.00 2.18
5674 6471 1.214673 AGAGGGCATGCTCATTCATGT 59.785 47.619 22.09 0.00 44.20 3.21


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

AutoCloner maintained by Alex Coulton.