Multiple sequence alignment - TraesCS3D01G508700

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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 TraesCS3D01G508700 chr3D 100.000 2222 0 0 1 2222 594768919 594771140 0.000000e+00 4104.0
1 TraesCS3D01G508700 chr3D 80.112 895 92 48 628 1473 594748608 594749465 2.460000e-164 588.0
2 TraesCS3D01G508700 chr3D 84.685 555 56 10 1155 1682 594634854 594635406 5.430000e-146 527.0
3 TraesCS3D01G508700 chr3D 77.033 418 53 27 820 1223 594643281 594643669 1.350000e-47 200.0
4 TraesCS3D01G508700 chr3D 81.513 238 39 3 996 1229 594802691 594802927 8.100000e-45 191.0
5 TraesCS3D01G508700 chr3B 90.518 1930 125 27 130 2037 798229100 798230993 0.000000e+00 2497.0
6 TraesCS3D01G508700 chr3B 89.855 138 12 2 2086 2222 798231007 798231143 2.270000e-40 176.0
7 TraesCS3D01G508700 chr3B 79.447 253 34 13 995 1229 798236623 798236875 1.770000e-36 163.0
8 TraesCS3D01G508700 chr3B 85.321 109 15 1 7 114 706530684 706530576 6.490000e-21 111.0
9 TraesCS3D01G508700 chr3A 92.265 1435 71 15 821 2222 725553768 725555195 0.000000e+00 1999.0
10 TraesCS3D01G508700 chr3A 92.259 1434 72 14 821 2222 725596317 725597743 0.000000e+00 1997.0
11 TraesCS3D01G508700 chr3A 89.876 484 29 5 313 776 725552942 725553425 2.440000e-169 604.0
12 TraesCS3D01G508700 chr3A 89.876 484 29 5 313 776 725595491 725595974 2.440000e-169 604.0
13 TraesCS3D01G508700 chr3A 79.553 313 44 13 927 1223 725556492 725556800 2.890000e-49 206.0
14 TraesCS3D01G508700 chr3A 79.553 313 44 13 927 1223 725599040 725599348 2.890000e-49 206.0
15 TraesCS3D01G508700 chr3A 81.328 241 39 4 995 1229 725470654 725470894 8.100000e-45 191.0
16 TraesCS3D01G508700 chr3A 82.569 218 23 4 1960 2176 749487521 749487318 6.300000e-41 178.0
17 TraesCS3D01G508700 chr3A 79.668 241 41 6 996 1229 725524309 725524548 1.360000e-37 167.0
18 TraesCS3D01G508700 chr7A 86.992 246 17 4 1966 2207 75073007 75073241 1.690000e-66 263.0
19 TraesCS3D01G508700 chr7A 83.203 256 33 3 1966 2219 698129546 698129299 2.220000e-55 226.0
20 TraesCS3D01G508700 chr7D 86.777 242 21 6 1963 2204 553381062 553381292 2.190000e-65 259.0
21 TraesCS3D01G508700 chr4B 85.830 247 23 5 1963 2207 665569765 665570001 3.660000e-63 252.0
22 TraesCS3D01G508700 chr5A 84.677 248 25 5 1963 2207 705572803 705573040 3.690000e-58 235.0
23 TraesCS3D01G508700 chr5A 92.913 127 9 0 1 127 416165538 416165412 3.770000e-43 185.0
24 TraesCS3D01G508700 chr7B 83.857 223 28 3 1959 2180 124005712 124005497 2.890000e-49 206.0
25 TraesCS3D01G508700 chr7B 92.500 120 9 0 7 126 153578103 153577984 2.930000e-39 172.0
26 TraesCS3D01G508700 chr1A 93.701 127 8 0 1 127 56863623 56863497 8.100000e-45 191.0
27 TraesCS3D01G508700 chr2A 90.083 121 12 0 1966 2086 729496275 729496155 8.210000e-35 158.0
28 TraesCS3D01G508700 chr5B 93.478 92 6 0 35 126 543866282 543866191 1.070000e-28 137.0
29 TraesCS3D01G508700 chrUn 86.885 122 15 1 1965 2085 226038241 226038120 3.850000e-28 135.0
30 TraesCS3D01G508700 chrUn 86.885 122 15 1 1965 2085 250213551 250213430 3.850000e-28 135.0
31 TraesCS3D01G508700 chr5D 81.600 125 19 3 1966 2086 206507423 206507299 1.400000e-17 100.0
32 TraesCS3D01G508700 chr5D 90.476 42 4 0 127 168 142905075 142905034 3.080000e-04 56.5


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 TraesCS3D01G508700 chr3D 594768919 594771140 2221 False 4104.000000 4104 100.000000 1 2222 1 chr3D.!!$F4 2221
1 TraesCS3D01G508700 chr3D 594748608 594749465 857 False 588.000000 588 80.112000 628 1473 1 chr3D.!!$F3 845
2 TraesCS3D01G508700 chr3D 594634854 594635406 552 False 527.000000 527 84.685000 1155 1682 1 chr3D.!!$F1 527
3 TraesCS3D01G508700 chr3B 798229100 798231143 2043 False 1336.500000 2497 90.186500 130 2222 2 chr3B.!!$F2 2092
4 TraesCS3D01G508700 chr3A 725552942 725556800 3858 False 936.333333 1999 87.231333 313 2222 3 chr3A.!!$F3 1909
5 TraesCS3D01G508700 chr3A 725595491 725599348 3857 False 935.666667 1997 87.229333 313 2222 3 chr3A.!!$F4 1909

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
19 20 0.179029 AAACCGAGACCAGGGTTGTG 60.179 55.0 0.0 0.0 45.48 3.33 F
22 23 0.179029 CCGAGACCAGGGTTGTGTTT 60.179 55.0 0.0 0.0 0.00 2.83 F
74 75 0.251073 ACCGGTTTCATAGTTCGGGG 59.749 55.0 0.0 0.0 44.36 5.73 F
449 485 0.472471 AGCTTCGACCCACTTTCCAA 59.528 50.0 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1493 0.744771 CCTCCTTCTTTACGCCCTGC 60.745 60.000 0.0 0.0 0.0 4.85 R
1119 1496 1.223763 CCCCTCCTTCTTTACGCCC 59.776 63.158 0.0 0.0 0.0 6.13 R
1134 1526 1.562008 CCCCTCTTCTTCTCTTTCCCC 59.438 57.143 0.0 0.0 0.0 4.81 R
1302 1698 2.270352 AATCTTCAGCGGAACAACCA 57.730 45.000 0.0 0.0 38.9 3.67 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 2.227737 AAACCGAGACCAGGGTTGT 58.772 52.632 0.00 0.00 45.48 3.32
19 20 0.179029 AAACCGAGACCAGGGTTGTG 60.179 55.000 0.00 0.00 45.48 3.33
20 21 1.342672 AACCGAGACCAGGGTTGTGT 61.343 55.000 0.00 0.00 44.56 3.72
21 22 1.342672 ACCGAGACCAGGGTTGTGTT 61.343 55.000 0.00 0.00 30.73 3.32
22 23 0.179029 CCGAGACCAGGGTTGTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
23 24 1.675552 CGAGACCAGGGTTGTGTTTT 58.324 50.000 0.00 0.00 0.00 2.43
24 25 1.333619 CGAGACCAGGGTTGTGTTTTG 59.666 52.381 0.00 0.00 0.00 2.44
25 26 1.681264 GAGACCAGGGTTGTGTTTTGG 59.319 52.381 0.00 0.00 35.07 3.28
26 27 1.286553 AGACCAGGGTTGTGTTTTGGA 59.713 47.619 0.00 0.00 33.19 3.53
27 28 1.407618 GACCAGGGTTGTGTTTTGGAC 59.592 52.381 0.00 0.00 33.19 4.02
28 29 0.750249 CCAGGGTTGTGTTTTGGACC 59.250 55.000 0.00 0.00 0.00 4.46
29 30 1.687996 CCAGGGTTGTGTTTTGGACCT 60.688 52.381 0.00 0.00 32.73 3.85
30 31 1.681264 CAGGGTTGTGTTTTGGACCTC 59.319 52.381 0.00 0.00 32.73 3.85
31 32 0.666374 GGGTTGTGTTTTGGACCTCG 59.334 55.000 0.00 0.00 32.73 4.63
32 33 1.385528 GGTTGTGTTTTGGACCTCGT 58.614 50.000 0.00 0.00 0.00 4.18
33 34 1.064952 GGTTGTGTTTTGGACCTCGTG 59.935 52.381 0.00 0.00 0.00 4.35
34 35 1.064952 GTTGTGTTTTGGACCTCGTGG 59.935 52.381 0.99 0.99 39.83 4.94
45 46 1.426751 ACCTCGTGGTTAGTTTGGGA 58.573 50.000 2.61 0.00 46.05 4.37
46 47 1.982958 ACCTCGTGGTTAGTTTGGGAT 59.017 47.619 2.61 0.00 46.05 3.85
47 48 2.290071 ACCTCGTGGTTAGTTTGGGATG 60.290 50.000 2.61 0.00 46.05 3.51
48 49 2.290071 CCTCGTGGTTAGTTTGGGATGT 60.290 50.000 0.00 0.00 0.00 3.06
49 50 3.055675 CCTCGTGGTTAGTTTGGGATGTA 60.056 47.826 0.00 0.00 0.00 2.29
50 51 4.383770 CCTCGTGGTTAGTTTGGGATGTAT 60.384 45.833 0.00 0.00 0.00 2.29
51 52 5.168647 TCGTGGTTAGTTTGGGATGTATT 57.831 39.130 0.00 0.00 0.00 1.89
52 53 5.562635 TCGTGGTTAGTTTGGGATGTATTT 58.437 37.500 0.00 0.00 0.00 1.40
53 54 5.644636 TCGTGGTTAGTTTGGGATGTATTTC 59.355 40.000 0.00 0.00 0.00 2.17
54 55 5.446741 CGTGGTTAGTTTGGGATGTATTTCG 60.447 44.000 0.00 0.00 0.00 3.46
55 56 5.644636 GTGGTTAGTTTGGGATGTATTTCGA 59.355 40.000 0.00 0.00 0.00 3.71
56 57 5.644636 TGGTTAGTTTGGGATGTATTTCGAC 59.355 40.000 0.00 0.00 0.00 4.20
57 58 5.065602 GGTTAGTTTGGGATGTATTTCGACC 59.934 44.000 0.00 0.00 0.00 4.79
58 59 3.267483 AGTTTGGGATGTATTTCGACCG 58.733 45.455 0.00 0.00 0.00 4.79
59 60 2.319136 TTGGGATGTATTTCGACCGG 57.681 50.000 0.00 0.00 0.00 5.28
60 61 1.196911 TGGGATGTATTTCGACCGGT 58.803 50.000 6.92 6.92 0.00 5.28
61 62 1.555992 TGGGATGTATTTCGACCGGTT 59.444 47.619 9.42 0.00 0.00 4.44
62 63 2.027007 TGGGATGTATTTCGACCGGTTT 60.027 45.455 9.42 0.00 0.00 3.27
63 64 2.610833 GGGATGTATTTCGACCGGTTTC 59.389 50.000 9.42 0.00 0.00 2.78
64 65 3.264104 GGATGTATTTCGACCGGTTTCA 58.736 45.455 9.42 0.00 0.00 2.69
65 66 3.875134 GGATGTATTTCGACCGGTTTCAT 59.125 43.478 9.42 1.12 0.00 2.57
66 67 5.051816 GGATGTATTTCGACCGGTTTCATA 58.948 41.667 9.42 0.25 0.00 2.15
67 68 5.176958 GGATGTATTTCGACCGGTTTCATAG 59.823 44.000 9.42 0.00 0.00 2.23
68 69 5.075858 TGTATTTCGACCGGTTTCATAGT 57.924 39.130 9.42 0.00 0.00 2.12
69 70 5.481105 TGTATTTCGACCGGTTTCATAGTT 58.519 37.500 9.42 0.00 0.00 2.24
70 71 5.577945 TGTATTTCGACCGGTTTCATAGTTC 59.422 40.000 9.42 0.00 0.00 3.01
71 72 2.267188 TCGACCGGTTTCATAGTTCG 57.733 50.000 9.42 4.04 0.00 3.95
72 73 1.135315 TCGACCGGTTTCATAGTTCGG 60.135 52.381 9.42 0.00 45.42 4.30
73 74 1.648504 GACCGGTTTCATAGTTCGGG 58.351 55.000 9.42 0.00 44.36 5.14
74 75 0.251073 ACCGGTTTCATAGTTCGGGG 59.749 55.000 0.00 0.00 44.36 5.73
75 76 0.251073 CCGGTTTCATAGTTCGGGGT 59.749 55.000 0.00 0.00 37.35 4.95
76 77 1.339342 CCGGTTTCATAGTTCGGGGTT 60.339 52.381 0.00 0.00 37.35 4.11
77 78 1.735571 CGGTTTCATAGTTCGGGGTTG 59.264 52.381 0.00 0.00 0.00 3.77
78 79 2.786777 GGTTTCATAGTTCGGGGTTGT 58.213 47.619 0.00 0.00 0.00 3.32
79 80 3.617045 CGGTTTCATAGTTCGGGGTTGTA 60.617 47.826 0.00 0.00 0.00 2.41
80 81 4.325972 GGTTTCATAGTTCGGGGTTGTAA 58.674 43.478 0.00 0.00 0.00 2.41
81 82 4.761227 GGTTTCATAGTTCGGGGTTGTAAA 59.239 41.667 0.00 0.00 0.00 2.01
82 83 5.416639 GGTTTCATAGTTCGGGGTTGTAAAT 59.583 40.000 0.00 0.00 0.00 1.40
83 84 6.403964 GGTTTCATAGTTCGGGGTTGTAAATC 60.404 42.308 0.00 0.00 0.00 2.17
84 85 5.423704 TCATAGTTCGGGGTTGTAAATCA 57.576 39.130 0.00 0.00 0.00 2.57
85 86 5.806818 TCATAGTTCGGGGTTGTAAATCAA 58.193 37.500 0.00 0.00 0.00 2.57
86 87 6.239396 TCATAGTTCGGGGTTGTAAATCAAA 58.761 36.000 0.00 0.00 37.81 2.69
87 88 4.841443 AGTTCGGGGTTGTAAATCAAAC 57.159 40.909 0.00 0.00 42.50 2.93
88 89 4.466827 AGTTCGGGGTTGTAAATCAAACT 58.533 39.130 0.00 0.00 42.79 2.66
89 90 4.277423 AGTTCGGGGTTGTAAATCAAACTG 59.723 41.667 0.00 0.00 42.79 3.16
90 91 4.088056 TCGGGGTTGTAAATCAAACTGA 57.912 40.909 0.00 0.00 42.79 3.41
91 92 4.069304 TCGGGGTTGTAAATCAAACTGAG 58.931 43.478 0.00 0.00 42.79 3.35
92 93 3.818773 CGGGGTTGTAAATCAAACTGAGT 59.181 43.478 0.00 0.00 42.79 3.41
93 94 4.320202 CGGGGTTGTAAATCAAACTGAGTG 60.320 45.833 0.00 0.00 42.79 3.51
94 95 4.022329 GGGGTTGTAAATCAAACTGAGTGG 60.022 45.833 0.00 0.00 42.79 4.00
95 96 4.583073 GGGTTGTAAATCAAACTGAGTGGT 59.417 41.667 0.00 0.00 42.79 4.16
96 97 5.068591 GGGTTGTAAATCAAACTGAGTGGTT 59.931 40.000 0.00 0.00 42.79 3.67
97 98 6.263617 GGGTTGTAAATCAAACTGAGTGGTTA 59.736 38.462 0.00 0.00 42.79 2.85
98 99 7.360361 GGTTGTAAATCAAACTGAGTGGTTAG 58.640 38.462 0.00 0.00 40.30 2.34
99 100 7.012989 GGTTGTAAATCAAACTGAGTGGTTAGT 59.987 37.037 0.00 0.00 40.30 2.24
100 101 8.403236 GTTGTAAATCAAACTGAGTGGTTAGTT 58.597 33.333 0.00 0.00 38.70 2.24
101 102 8.149973 TGTAAATCAAACTGAGTGGTTAGTTC 57.850 34.615 0.00 0.00 36.19 3.01
102 103 5.924475 AATCAAACTGAGTGGTTAGTTCG 57.076 39.130 0.00 0.00 36.19 3.95
103 104 4.659111 TCAAACTGAGTGGTTAGTTCGA 57.341 40.909 0.00 0.00 36.19 3.71
104 105 4.617959 TCAAACTGAGTGGTTAGTTCGAG 58.382 43.478 0.00 0.00 36.19 4.04
105 106 3.662247 AACTGAGTGGTTAGTTCGAGG 57.338 47.619 0.00 0.00 31.88 4.63
106 107 2.595238 ACTGAGTGGTTAGTTCGAGGT 58.405 47.619 0.00 0.00 0.00 3.85
107 108 2.963782 ACTGAGTGGTTAGTTCGAGGTT 59.036 45.455 0.00 0.00 0.00 3.50
108 109 3.243771 ACTGAGTGGTTAGTTCGAGGTTG 60.244 47.826 0.00 0.00 0.00 3.77
109 110 2.960384 TGAGTGGTTAGTTCGAGGTTGA 59.040 45.455 0.00 0.00 0.00 3.18
110 111 3.385433 TGAGTGGTTAGTTCGAGGTTGAA 59.615 43.478 0.00 0.00 0.00 2.69
111 112 4.141892 TGAGTGGTTAGTTCGAGGTTGAAA 60.142 41.667 0.00 0.00 0.00 2.69
112 113 4.969484 AGTGGTTAGTTCGAGGTTGAAAT 58.031 39.130 0.00 0.00 0.00 2.17
113 114 6.105397 AGTGGTTAGTTCGAGGTTGAAATA 57.895 37.500 0.00 0.00 0.00 1.40
114 115 6.708285 AGTGGTTAGTTCGAGGTTGAAATAT 58.292 36.000 0.00 0.00 29.65 1.28
115 116 6.594159 AGTGGTTAGTTCGAGGTTGAAATATG 59.406 38.462 0.00 0.00 29.65 1.78
116 117 5.878116 TGGTTAGTTCGAGGTTGAAATATGG 59.122 40.000 0.00 0.00 29.65 2.74
117 118 6.110707 GGTTAGTTCGAGGTTGAAATATGGA 58.889 40.000 0.00 0.00 29.65 3.41
118 119 6.766467 GGTTAGTTCGAGGTTGAAATATGGAT 59.234 38.462 0.00 0.00 29.65 3.41
119 120 7.282450 GGTTAGTTCGAGGTTGAAATATGGATT 59.718 37.037 0.00 0.00 29.65 3.01
120 121 8.674607 GTTAGTTCGAGGTTGAAATATGGATTT 58.325 33.333 0.00 0.00 38.00 2.17
133 134 8.744568 GAAATATGGATTTCTCTCTCCAAAGT 57.255 34.615 3.66 0.00 45.15 2.66
134 135 9.183368 GAAATATGGATTTCTCTCTCCAAAGTT 57.817 33.333 3.66 0.00 45.15 2.66
149 150 4.819630 TCCAAAGTTAAGTGTCGCTGATTT 59.180 37.500 0.00 0.00 0.00 2.17
150 151 5.992829 TCCAAAGTTAAGTGTCGCTGATTTA 59.007 36.000 0.00 0.00 0.00 1.40
151 152 6.147164 TCCAAAGTTAAGTGTCGCTGATTTAG 59.853 38.462 0.00 0.00 0.00 1.85
154 155 8.656849 CAAAGTTAAGTGTCGCTGATTTAGTAT 58.343 33.333 0.00 0.00 0.00 2.12
157 158 9.298774 AGTTAAGTGTCGCTGATTTAGTATAAC 57.701 33.333 0.00 0.00 0.00 1.89
192 193 3.928727 ACGACACTTATTTGGAGACGA 57.071 42.857 0.00 0.00 0.00 4.20
195 196 3.367087 CGACACTTATTTGGAGACGAGGT 60.367 47.826 0.00 0.00 0.00 3.85
196 197 3.926616 ACACTTATTTGGAGACGAGGTG 58.073 45.455 0.00 0.00 0.00 4.00
213 214 4.634883 CGAGGTGAGTAGTAAGCAGAACTA 59.365 45.833 0.00 0.00 0.00 2.24
216 217 6.719301 AGGTGAGTAGTAAGCAGAACTAGTA 58.281 40.000 0.00 0.00 34.08 1.82
232 233 9.227490 CAGAACTAGTACTCATGAAATAACTCG 57.773 37.037 0.00 0.00 0.00 4.18
243 244 6.429692 TCATGAAATAACTCGTGGTTTGTGAT 59.570 34.615 0.00 0.00 39.17 3.06
247 248 6.490566 AATAACTCGTGGTTTGTGATTACC 57.509 37.500 2.46 0.00 39.17 2.85
254 255 2.550606 TGGTTTGTGATTACCGCAGAAC 59.449 45.455 0.00 0.00 37.23 3.01
255 256 2.550606 GGTTTGTGATTACCGCAGAACA 59.449 45.455 0.00 0.00 36.53 3.18
259 260 2.161410 TGTGATTACCGCAGAACAATGC 59.839 45.455 0.00 0.00 42.95 3.56
267 268 1.689959 GCAGAACAATGCGAAAGTGG 58.310 50.000 0.00 0.00 36.28 4.00
270 271 3.795150 GCAGAACAATGCGAAAGTGGAAA 60.795 43.478 0.00 0.00 36.28 3.13
272 273 3.380004 AGAACAATGCGAAAGTGGAAACA 59.620 39.130 0.00 0.00 38.70 2.83
341 342 5.928264 AGCCAAAATAACAGCTTGATGAAAC 59.072 36.000 0.00 0.00 29.27 2.78
361 362 5.850557 AACATGTGTGGTGAAATTCTTCA 57.149 34.783 0.00 0.00 39.30 3.02
364 365 5.009010 ACATGTGTGGTGAAATTCTTCAGTC 59.991 40.000 0.00 0.00 42.27 3.51
449 485 0.472471 AGCTTCGACCCACTTTCCAA 59.528 50.000 0.00 0.00 0.00 3.53
451 487 1.814248 GCTTCGACCCACTTTCCAACT 60.814 52.381 0.00 0.00 0.00 3.16
454 490 1.697432 TCGACCCACTTTCCAACTCAT 59.303 47.619 0.00 0.00 0.00 2.90
515 553 2.898705 CTGCCAAGGAAGCTAGTAGTG 58.101 52.381 0.00 0.00 0.00 2.74
521 559 2.104170 AGGAAGCTAGTAGTGGCTCAC 58.896 52.381 9.08 5.40 40.18 3.51
525 563 1.286553 AGCTAGTAGTGGCTCACTCCT 59.713 52.381 10.60 8.06 41.21 3.69
532 570 0.536006 GTGGCTCACTCCTTTGCTGT 60.536 55.000 0.00 0.00 0.00 4.40
670 708 2.670251 CGCAAGCCCACCCGTTAA 60.670 61.111 0.00 0.00 0.00 2.01
725 763 3.106407 GCGCGAGTGTCACTGTCC 61.106 66.667 12.10 0.00 0.00 4.02
726 764 2.335011 CGCGAGTGTCACTGTCCA 59.665 61.111 11.04 0.00 0.00 4.02
727 765 1.080501 CGCGAGTGTCACTGTCCAT 60.081 57.895 11.04 0.00 0.00 3.41
742 780 1.191489 TCCATGGAAGGCTCGTGTGA 61.191 55.000 13.46 0.00 0.00 3.58
749 787 0.542232 AAGGCTCGTGTGAGGGTACT 60.542 55.000 0.00 0.00 42.79 2.73
803 842 4.752101 AGAGAGTTTTGACATTTGACTCCG 59.248 41.667 0.00 0.00 37.93 4.63
804 843 4.703897 AGAGTTTTGACATTTGACTCCGA 58.296 39.130 0.00 0.00 37.93 4.55
807 846 6.369065 AGAGTTTTGACATTTGACTCCGATAC 59.631 38.462 0.00 0.00 37.93 2.24
811 850 3.767131 TGACATTTGACTCCGATACCAGA 59.233 43.478 0.00 0.00 0.00 3.86
874 1228 3.843999 TGCTTTTCCAACAGAAACACAC 58.156 40.909 0.00 0.00 44.20 3.82
956 1327 5.550290 AGAGCAGAGGAAAGAAAGAAAGAG 58.450 41.667 0.00 0.00 0.00 2.85
961 1338 6.520272 CAGAGGAAAGAAAGAAAGAGAGACA 58.480 40.000 0.00 0.00 0.00 3.41
998 1375 1.482593 GTAGAAGCTTAGCAGGGCAGA 59.517 52.381 7.07 0.00 0.00 4.26
1018 1395 2.216331 ATGGGGTTTTGCTGTGGGC 61.216 57.895 0.00 0.00 42.22 5.36
1023 1400 1.398958 GGTTTTGCTGTGGGCCTTCA 61.399 55.000 4.53 3.28 40.92 3.02
1086 1463 1.153901 CTCGCCGTCCGCTAAAGAA 60.154 57.895 0.00 0.00 36.73 2.52
1116 1493 1.003355 TGGGAAGAAGAAGCAGCCG 60.003 57.895 0.00 0.00 0.00 5.52
1119 1496 1.642952 GGAAGAAGAAGCAGCCGCAG 61.643 60.000 0.00 0.00 42.27 5.18
1134 1526 2.768834 GCAGGGCGTAAAGAAGGAG 58.231 57.895 0.00 0.00 0.00 3.69
1170 1562 4.660938 GGCAACCTTGACCGGGCT 62.661 66.667 9.82 0.00 0.00 5.19
1231 1623 6.442564 ACCCGGCCTAATGTAATAGATTATGA 59.557 38.462 0.00 0.00 0.00 2.15
1302 1698 0.893727 CTTACGCCTGGGTTTGCCTT 60.894 55.000 0.00 0.00 34.45 4.35
1341 1737 6.061441 AGATTTCATTTGTACTGTGTCCACA 58.939 36.000 0.00 0.00 39.32 4.17
1374 1771 0.108377 TCATGGACGGTCGGTTGATG 60.108 55.000 1.43 0.21 0.00 3.07
1386 1783 1.472082 CGGTTGATGCAATTGCTGGTA 59.528 47.619 29.37 11.25 42.66 3.25
1434 1831 9.060347 ACATTACATTCATTGTCATCAGGATAC 57.940 33.333 0.00 0.00 39.87 2.24
1696 2120 2.493035 CAAACCCAACAAAGGATTGGC 58.507 47.619 0.00 0.00 44.57 4.52
1708 2132 5.482878 ACAAAGGATTGGCTCATGATTTTCT 59.517 36.000 0.00 0.00 41.01 2.52
1716 2140 5.713025 TGGCTCATGATTTTCTTTAACTGC 58.287 37.500 0.00 0.00 0.00 4.40
1724 2148 5.401972 TGATTTTCTTTAACTGCATTGCACG 59.598 36.000 7.38 6.88 33.79 5.34
1810 2234 6.870971 TTACCTTGGAGTTGTTACATTGTC 57.129 37.500 0.00 0.00 0.00 3.18
1923 2347 2.294449 AGATAGCATAGACCAGCGGA 57.706 50.000 1.50 0.00 35.48 5.54
2078 2503 2.649190 TGCACTCAGCCAAAACTAACA 58.351 42.857 0.00 0.00 44.83 2.41
2080 2505 2.357637 GCACTCAGCCAAAACTAACACA 59.642 45.455 0.00 0.00 37.23 3.72
2134 2590 6.385033 GCAAATAGCAAAGTCATTCAAGACT 58.615 36.000 0.00 0.00 46.40 3.24
2158 2614 0.969894 CTATGCCTAGTCGAAGGGGG 59.030 60.000 5.32 0.00 37.11 5.40
2161 2617 1.262640 TGCCTAGTCGAAGGGGGAAC 61.263 60.000 5.32 0.00 37.11 3.62
2164 2620 0.824759 CTAGTCGAAGGGGGAACAGG 59.175 60.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.179029 AAACACAACCCTGGTCTCGG 60.179 55.000 0.00 0.00 0.00 4.63
4 5 1.333619 CAAAACACAACCCTGGTCTCG 59.666 52.381 0.00 0.00 0.00 4.04
5 6 1.681264 CCAAAACACAACCCTGGTCTC 59.319 52.381 0.00 0.00 0.00 3.36
6 7 1.286553 TCCAAAACACAACCCTGGTCT 59.713 47.619 0.00 0.00 0.00 3.85
7 8 1.407618 GTCCAAAACACAACCCTGGTC 59.592 52.381 0.00 0.00 0.00 4.02
8 9 1.480789 GTCCAAAACACAACCCTGGT 58.519 50.000 0.00 0.00 0.00 4.00
9 10 0.750249 GGTCCAAAACACAACCCTGG 59.250 55.000 0.00 0.00 0.00 4.45
10 11 1.681264 GAGGTCCAAAACACAACCCTG 59.319 52.381 0.00 0.00 31.91 4.45
11 12 1.749286 CGAGGTCCAAAACACAACCCT 60.749 52.381 0.00 0.00 31.91 4.34
12 13 0.666374 CGAGGTCCAAAACACAACCC 59.334 55.000 0.00 0.00 31.91 4.11
13 14 1.064952 CACGAGGTCCAAAACACAACC 59.935 52.381 0.00 0.00 0.00 3.77
14 15 1.064952 CCACGAGGTCCAAAACACAAC 59.935 52.381 0.00 0.00 0.00 3.32
15 16 1.384525 CCACGAGGTCCAAAACACAA 58.615 50.000 0.00 0.00 0.00 3.33
16 17 3.088259 CCACGAGGTCCAAAACACA 57.912 52.632 0.00 0.00 0.00 3.72
27 28 2.290071 ACATCCCAAACTAACCACGAGG 60.290 50.000 0.00 0.00 42.21 4.63
28 29 3.053831 ACATCCCAAACTAACCACGAG 57.946 47.619 0.00 0.00 0.00 4.18
29 30 4.829872 ATACATCCCAAACTAACCACGA 57.170 40.909 0.00 0.00 0.00 4.35
30 31 5.446741 CGAAATACATCCCAAACTAACCACG 60.447 44.000 0.00 0.00 0.00 4.94
31 32 5.644636 TCGAAATACATCCCAAACTAACCAC 59.355 40.000 0.00 0.00 0.00 4.16
32 33 5.644636 GTCGAAATACATCCCAAACTAACCA 59.355 40.000 0.00 0.00 0.00 3.67
33 34 5.065602 GGTCGAAATACATCCCAAACTAACC 59.934 44.000 0.00 0.00 0.00 2.85
34 35 5.220529 CGGTCGAAATACATCCCAAACTAAC 60.221 44.000 0.00 0.00 0.00 2.34
35 36 4.871557 CGGTCGAAATACATCCCAAACTAA 59.128 41.667 0.00 0.00 0.00 2.24
36 37 4.435425 CGGTCGAAATACATCCCAAACTA 58.565 43.478 0.00 0.00 0.00 2.24
37 38 3.267483 CGGTCGAAATACATCCCAAACT 58.733 45.455 0.00 0.00 0.00 2.66
38 39 2.353579 CCGGTCGAAATACATCCCAAAC 59.646 50.000 0.00 0.00 0.00 2.93
39 40 2.027007 ACCGGTCGAAATACATCCCAAA 60.027 45.455 0.00 0.00 0.00 3.28
40 41 1.555992 ACCGGTCGAAATACATCCCAA 59.444 47.619 0.00 0.00 0.00 4.12
41 42 1.196911 ACCGGTCGAAATACATCCCA 58.803 50.000 0.00 0.00 0.00 4.37
42 43 2.320745 AACCGGTCGAAATACATCCC 57.679 50.000 8.04 0.00 0.00 3.85
43 44 3.264104 TGAAACCGGTCGAAATACATCC 58.736 45.455 8.04 0.00 0.00 3.51
44 45 5.751990 ACTATGAAACCGGTCGAAATACATC 59.248 40.000 8.04 0.00 0.00 3.06
45 46 5.667466 ACTATGAAACCGGTCGAAATACAT 58.333 37.500 8.04 8.67 0.00 2.29
46 47 5.075858 ACTATGAAACCGGTCGAAATACA 57.924 39.130 8.04 1.05 0.00 2.29
47 48 5.276067 CGAACTATGAAACCGGTCGAAATAC 60.276 44.000 8.04 0.00 0.00 1.89
48 49 4.799949 CGAACTATGAAACCGGTCGAAATA 59.200 41.667 8.04 3.30 0.00 1.40
49 50 3.615496 CGAACTATGAAACCGGTCGAAAT 59.385 43.478 8.04 2.11 0.00 2.17
50 51 2.988493 CGAACTATGAAACCGGTCGAAA 59.012 45.455 8.04 0.00 0.00 3.46
51 52 2.598589 CGAACTATGAAACCGGTCGAA 58.401 47.619 8.04 0.00 0.00 3.71
52 53 1.135315 CCGAACTATGAAACCGGTCGA 60.135 52.381 8.04 0.00 35.83 4.20
53 54 1.274596 CCGAACTATGAAACCGGTCG 58.725 55.000 8.04 3.09 35.83 4.79
54 55 1.648504 CCCGAACTATGAAACCGGTC 58.351 55.000 8.04 0.00 38.61 4.79
55 56 0.251073 CCCCGAACTATGAAACCGGT 59.749 55.000 0.00 0.00 38.61 5.28
56 57 0.251073 ACCCCGAACTATGAAACCGG 59.749 55.000 0.00 0.00 39.85 5.28
57 58 1.735571 CAACCCCGAACTATGAAACCG 59.264 52.381 0.00 0.00 0.00 4.44
58 59 2.786777 ACAACCCCGAACTATGAAACC 58.213 47.619 0.00 0.00 0.00 3.27
59 60 5.945466 TTTACAACCCCGAACTATGAAAC 57.055 39.130 0.00 0.00 0.00 2.78
60 61 6.239396 TGATTTACAACCCCGAACTATGAAA 58.761 36.000 0.00 0.00 0.00 2.69
61 62 5.806818 TGATTTACAACCCCGAACTATGAA 58.193 37.500 0.00 0.00 0.00 2.57
62 63 5.423704 TGATTTACAACCCCGAACTATGA 57.576 39.130 0.00 0.00 0.00 2.15
63 64 6.150474 AGTTTGATTTACAACCCCGAACTATG 59.850 38.462 0.00 0.00 38.29 2.23
64 65 6.150474 CAGTTTGATTTACAACCCCGAACTAT 59.850 38.462 0.00 0.00 38.29 2.12
65 66 5.470777 CAGTTTGATTTACAACCCCGAACTA 59.529 40.000 0.00 0.00 38.29 2.24
66 67 4.277423 CAGTTTGATTTACAACCCCGAACT 59.723 41.667 0.00 0.00 38.29 3.01
67 68 4.276431 TCAGTTTGATTTACAACCCCGAAC 59.724 41.667 0.00 0.00 38.29 3.95
68 69 4.462133 TCAGTTTGATTTACAACCCCGAA 58.538 39.130 0.00 0.00 38.29 4.30
69 70 4.069304 CTCAGTTTGATTTACAACCCCGA 58.931 43.478 0.00 0.00 38.29 5.14
70 71 3.818773 ACTCAGTTTGATTTACAACCCCG 59.181 43.478 0.00 0.00 38.29 5.73
71 72 4.022329 CCACTCAGTTTGATTTACAACCCC 60.022 45.833 0.00 0.00 38.29 4.95
72 73 4.583073 ACCACTCAGTTTGATTTACAACCC 59.417 41.667 0.00 0.00 38.29 4.11
73 74 5.767816 ACCACTCAGTTTGATTTACAACC 57.232 39.130 0.00 0.00 38.29 3.77
74 75 7.927048 ACTAACCACTCAGTTTGATTTACAAC 58.073 34.615 0.00 0.00 38.29 3.32
75 76 8.514330 AACTAACCACTCAGTTTGATTTACAA 57.486 30.769 0.00 0.00 30.89 2.41
76 77 7.042321 CGAACTAACCACTCAGTTTGATTTACA 60.042 37.037 0.00 0.00 38.08 2.41
77 78 7.170320 TCGAACTAACCACTCAGTTTGATTTAC 59.830 37.037 1.20 0.00 39.28 2.01
78 79 7.211573 TCGAACTAACCACTCAGTTTGATTTA 58.788 34.615 1.20 0.00 39.28 1.40
79 80 6.053005 TCGAACTAACCACTCAGTTTGATTT 58.947 36.000 1.20 0.00 39.28 2.17
80 81 5.607477 TCGAACTAACCACTCAGTTTGATT 58.393 37.500 1.20 0.00 39.28 2.57
81 82 5.209818 TCGAACTAACCACTCAGTTTGAT 57.790 39.130 1.20 0.00 39.28 2.57
82 83 4.500887 CCTCGAACTAACCACTCAGTTTGA 60.501 45.833 4.74 4.74 41.01 2.69
83 84 3.741344 CCTCGAACTAACCACTCAGTTTG 59.259 47.826 0.00 0.00 37.46 2.93
84 85 3.387050 ACCTCGAACTAACCACTCAGTTT 59.613 43.478 0.00 0.00 35.17 2.66
85 86 2.963782 ACCTCGAACTAACCACTCAGTT 59.036 45.455 0.00 0.00 37.69 3.16
86 87 2.595238 ACCTCGAACTAACCACTCAGT 58.405 47.619 0.00 0.00 0.00 3.41
87 88 3.005472 TCAACCTCGAACTAACCACTCAG 59.995 47.826 0.00 0.00 0.00 3.35
88 89 2.960384 TCAACCTCGAACTAACCACTCA 59.040 45.455 0.00 0.00 0.00 3.41
89 90 3.655276 TCAACCTCGAACTAACCACTC 57.345 47.619 0.00 0.00 0.00 3.51
90 91 4.411256 TTTCAACCTCGAACTAACCACT 57.589 40.909 0.00 0.00 0.00 4.00
91 92 6.183360 CCATATTTCAACCTCGAACTAACCAC 60.183 42.308 0.00 0.00 0.00 4.16
92 93 5.878116 CCATATTTCAACCTCGAACTAACCA 59.122 40.000 0.00 0.00 0.00 3.67
93 94 6.110707 TCCATATTTCAACCTCGAACTAACC 58.889 40.000 0.00 0.00 0.00 2.85
94 95 7.787725 ATCCATATTTCAACCTCGAACTAAC 57.212 36.000 0.00 0.00 0.00 2.34
95 96 8.801882 AAATCCATATTTCAACCTCGAACTAA 57.198 30.769 0.00 0.00 28.88 2.24
96 97 8.433421 GAAATCCATATTTCAACCTCGAACTA 57.567 34.615 6.08 0.00 46.87 2.24
97 98 7.321745 GAAATCCATATTTCAACCTCGAACT 57.678 36.000 6.08 0.00 46.87 3.01
111 112 9.844257 CTTAACTTTGGAGAGAGAAATCCATAT 57.156 33.333 0.00 0.00 44.87 1.78
112 113 8.826765 ACTTAACTTTGGAGAGAGAAATCCATA 58.173 33.333 0.00 0.00 44.87 2.74
113 114 7.609532 CACTTAACTTTGGAGAGAGAAATCCAT 59.390 37.037 0.00 0.00 44.87 3.41
114 115 6.936900 CACTTAACTTTGGAGAGAGAAATCCA 59.063 38.462 0.00 0.00 43.87 3.41
115 116 6.937465 ACACTTAACTTTGGAGAGAGAAATCC 59.063 38.462 0.00 0.00 36.05 3.01
116 117 7.148722 CGACACTTAACTTTGGAGAGAGAAATC 60.149 40.741 0.00 0.00 0.00 2.17
117 118 6.647067 CGACACTTAACTTTGGAGAGAGAAAT 59.353 38.462 0.00 0.00 0.00 2.17
118 119 5.983720 CGACACTTAACTTTGGAGAGAGAAA 59.016 40.000 0.00 0.00 0.00 2.52
119 120 5.529791 CGACACTTAACTTTGGAGAGAGAA 58.470 41.667 0.00 0.00 0.00 2.87
120 121 4.558898 GCGACACTTAACTTTGGAGAGAGA 60.559 45.833 0.00 0.00 0.00 3.10
121 122 3.675698 GCGACACTTAACTTTGGAGAGAG 59.324 47.826 0.00 0.00 0.00 3.20
122 123 3.321111 AGCGACACTTAACTTTGGAGAGA 59.679 43.478 0.00 0.00 0.00 3.10
123 124 3.430218 CAGCGACACTTAACTTTGGAGAG 59.570 47.826 0.00 0.00 0.00 3.20
124 125 3.069016 TCAGCGACACTTAACTTTGGAGA 59.931 43.478 0.00 0.00 0.00 3.71
125 126 3.390135 TCAGCGACACTTAACTTTGGAG 58.610 45.455 0.00 0.00 0.00 3.86
126 127 3.462483 TCAGCGACACTTAACTTTGGA 57.538 42.857 0.00 0.00 0.00 3.53
127 128 4.749245 AATCAGCGACACTTAACTTTGG 57.251 40.909 0.00 0.00 0.00 3.28
128 129 6.888430 ACTAAATCAGCGACACTTAACTTTG 58.112 36.000 0.00 0.00 0.00 2.77
129 130 8.773404 ATACTAAATCAGCGACACTTAACTTT 57.227 30.769 0.00 0.00 0.00 2.66
130 131 9.865321 TTATACTAAATCAGCGACACTTAACTT 57.135 29.630 0.00 0.00 0.00 2.66
131 132 9.298774 GTTATACTAAATCAGCGACACTTAACT 57.701 33.333 0.00 0.00 0.00 2.24
132 133 9.298774 AGTTATACTAAATCAGCGACACTTAAC 57.701 33.333 0.00 0.00 0.00 2.01
172 173 3.367087 CCTCGTCTCCAAATAAGTGTCGT 60.367 47.826 0.00 0.00 0.00 4.34
185 186 2.355444 GCTTACTACTCACCTCGTCTCC 59.645 54.545 0.00 0.00 0.00 3.71
192 193 5.572252 ACTAGTTCTGCTTACTACTCACCT 58.428 41.667 0.00 0.00 0.00 4.00
195 196 7.392418 TGAGTACTAGTTCTGCTTACTACTCA 58.608 38.462 6.76 9.79 35.81 3.41
196 197 7.846644 TGAGTACTAGTTCTGCTTACTACTC 57.153 40.000 6.76 7.36 32.52 2.59
213 214 6.282199 ACCACGAGTTATTTCATGAGTACT 57.718 37.500 0.00 0.00 0.00 2.73
216 217 5.763204 ACAAACCACGAGTTATTTCATGAGT 59.237 36.000 0.00 0.00 37.88 3.41
232 233 2.147958 TCTGCGGTAATCACAAACCAC 58.852 47.619 0.00 0.00 35.35 4.16
254 255 5.462034 TTTTTGTTTCCACTTTCGCATTG 57.538 34.783 0.00 0.00 0.00 2.82
292 293 5.503376 GTGTTTCAATATTGCGTACGAACTG 59.497 40.000 21.65 6.66 0.00 3.16
293 294 5.177881 TGTGTTTCAATATTGCGTACGAACT 59.822 36.000 21.65 5.16 0.00 3.01
294 295 5.375717 TGTGTTTCAATATTGCGTACGAAC 58.624 37.500 21.65 11.31 0.00 3.95
295 296 5.593183 TGTGTTTCAATATTGCGTACGAA 57.407 34.783 21.65 5.28 0.00 3.85
296 297 4.434989 GCTGTGTTTCAATATTGCGTACGA 60.435 41.667 21.65 0.00 0.00 3.43
297 298 3.778718 GCTGTGTTTCAATATTGCGTACG 59.221 43.478 11.84 11.84 0.00 3.67
302 303 5.921004 TTTTGGCTGTGTTTCAATATTGC 57.079 34.783 10.76 0.00 0.00 3.56
305 306 7.331687 GCTGTTATTTTGGCTGTGTTTCAATAT 59.668 33.333 0.00 0.00 0.00 1.28
341 342 5.443185 ACTGAAGAATTTCACCACACATG 57.557 39.130 0.00 0.00 38.37 3.21
361 362 6.464222 TGAATCCAAACTGATTTACTCGACT 58.536 36.000 0.00 0.00 35.15 4.18
364 365 8.795786 TTTTTGAATCCAAACTGATTTACTCG 57.204 30.769 0.00 0.00 41.54 4.18
449 485 4.135306 GACATGCCAATCATCTCATGAGT 58.865 43.478 21.92 7.26 43.53 3.41
451 487 4.102681 AGAGACATGCCAATCATCTCATGA 59.897 41.667 7.90 0.00 44.55 3.07
454 490 4.498894 AAGAGACATGCCAATCATCTCA 57.501 40.909 9.21 0.00 31.77 3.27
515 553 0.536006 ACACAGCAAAGGAGTGAGCC 60.536 55.000 0.00 0.00 37.05 4.70
521 559 1.233019 CAGGTGACACAGCAAAGGAG 58.767 55.000 8.08 0.00 33.95 3.69
525 563 1.742831 GTTGACAGGTGACACAGCAAA 59.257 47.619 8.08 0.00 33.95 3.68
532 570 1.067142 GGATAGCGTTGACAGGTGACA 60.067 52.381 0.00 0.00 0.00 3.58
613 651 1.131693 TCAGTCGTAGTGTATGTGGCG 59.868 52.381 0.00 0.00 0.00 5.69
715 753 0.036732 GCCTTCCATGGACAGTGACA 59.963 55.000 15.91 0.00 0.00 3.58
725 763 0.742281 CCTCACACGAGCCTTCCATG 60.742 60.000 0.00 0.00 38.00 3.66
726 764 1.599047 CCTCACACGAGCCTTCCAT 59.401 57.895 0.00 0.00 38.00 3.41
727 765 2.583441 CCCTCACACGAGCCTTCCA 61.583 63.158 0.00 0.00 38.00 3.53
742 780 1.210478 GCATGTGGTCATCAGTACCCT 59.790 52.381 0.00 0.00 36.06 4.34
749 787 2.696989 ATTCGAGCATGTGGTCATCA 57.303 45.000 12.12 0.00 42.28 3.07
803 842 3.454082 GGGAGGATGGATCATCTGGTATC 59.546 52.174 7.68 0.00 40.39 2.24
804 843 3.458831 GGGAGGATGGATCATCTGGTAT 58.541 50.000 7.68 0.00 40.39 2.73
807 846 0.990374 GGGGAGGATGGATCATCTGG 59.010 60.000 7.68 0.00 40.39 3.86
811 850 4.735309 TTATAGGGGGAGGATGGATCAT 57.265 45.455 0.00 0.00 0.00 2.45
874 1228 0.026674 CGTGTGTCAGTGTGTGCTTG 59.973 55.000 0.00 0.00 0.00 4.01
956 1327 5.070685 ACACCACTAAAATTTCCCTGTCTC 58.929 41.667 0.00 0.00 0.00 3.36
961 1338 5.710567 GCTTCTACACCACTAAAATTTCCCT 59.289 40.000 0.00 0.00 0.00 4.20
998 1375 1.120795 CCCACAGCAAAACCCCATGT 61.121 55.000 0.00 0.00 0.00 3.21
1018 1395 2.354259 GAGCACCTTGACATCTGAAGG 58.646 52.381 0.00 0.00 43.90 3.46
1023 1400 0.842030 TGGGGAGCACCTTGACATCT 60.842 55.000 0.00 0.00 40.03 2.90
1048 1425 3.862124 CGAGGACGCCAAAGAGTG 58.138 61.111 0.00 0.00 0.00 3.51
1086 1463 2.933287 TTCCCACCACCGCTGGAT 60.933 61.111 3.11 0.00 40.55 3.41
1094 1471 1.528129 CTGCTTCTTCTTCCCACCAC 58.472 55.000 0.00 0.00 0.00 4.16
1100 1477 1.642952 CTGCGGCTGCTTCTTCTTCC 61.643 60.000 20.27 0.00 43.34 3.46
1101 1478 1.642952 CCTGCGGCTGCTTCTTCTTC 61.643 60.000 20.27 0.00 43.34 2.87
1116 1493 0.744771 CCTCCTTCTTTACGCCCTGC 60.745 60.000 0.00 0.00 0.00 4.85
1119 1496 1.223763 CCCCTCCTTCTTTACGCCC 59.776 63.158 0.00 0.00 0.00 6.13
1121 1498 2.027469 TCTTTCCCCTCCTTCTTTACGC 60.027 50.000 0.00 0.00 0.00 4.42
1134 1526 1.562008 CCCCTCTTCTTCTCTTTCCCC 59.438 57.143 0.00 0.00 0.00 4.81
1231 1623 5.779529 ATGCACTGTTGTTCTGAAATCTT 57.220 34.783 0.00 0.00 0.00 2.40
1246 1639 5.698089 CCTACAGGATTGTATGTATGCACTG 59.302 44.000 0.00 0.00 39.00 3.66
1302 1698 2.270352 AATCTTCAGCGGAACAACCA 57.730 45.000 0.00 0.00 38.90 3.67
1341 1737 7.384115 CGACCGTCCATGAATAAAATAGTACAT 59.616 37.037 0.00 0.00 0.00 2.29
1374 1771 4.439305 TGACAAGAATACCAGCAATTGC 57.561 40.909 23.05 23.05 42.49 3.56
1657 2081 3.361281 TGCCTTGATGAAGCAGAATCT 57.639 42.857 0.00 0.00 0.00 2.40
1696 2120 7.329962 TGCAATGCAGTTAAAGAAAATCATGAG 59.670 33.333 2.72 0.00 33.32 2.90
1708 2132 6.144724 GGATTAAAACGTGCAATGCAGTTAAA 59.855 34.615 8.73 12.64 40.08 1.52
1716 2140 7.305474 AGAAACTAGGATTAAAACGTGCAATG 58.695 34.615 0.00 0.00 0.00 2.82
1923 2347 2.352032 GCAGGTAGGGAGACGCACT 61.352 63.158 0.00 0.00 0.00 4.40
2005 2430 8.265165 ACTCACTATAATTGTATCGCTCGATA 57.735 34.615 7.80 7.80 36.17 2.92
2063 2488 3.127895 GTGTGTGTGTTAGTTTTGGCTGA 59.872 43.478 0.00 0.00 0.00 4.26
2096 2551 3.060473 GCTATTTGCCGACGTGATACTTC 60.060 47.826 0.00 0.00 35.15 3.01
2134 2590 2.362397 CCTTCGACTAGGCATAGCTTCA 59.638 50.000 5.07 0.00 31.66 3.02


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

AutoCloner maintained by Alex Coulton.