Multiple sequence alignment - TraesCS1D01G157000

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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 TraesCS1D01G157000 chr1D 100.000 5488 0 0 1 5488 221119571 221125058 0.000000e+00 10135.0
1 TraesCS1D01G157000 chr1B 95.708 4730 135 38 169 4853 317438768 317443474 0.000000e+00 7548.0
2 TraesCS1D01G157000 chr1B 87.234 564 44 10 4926 5486 317444456 317444994 7.810000e-173 617.0
3 TraesCS1D01G157000 chr1B 97.000 100 3 0 4836 4935 317443535 317443634 9.450000e-38 169.0
4 TraesCS1D01G157000 chr1A 96.859 1560 37 9 2562 4114 286008393 286009947 0.000000e+00 2599.0
5 TraesCS1D01G157000 chr1A 96.943 1374 31 4 838 2205 286006369 286007737 0.000000e+00 2294.0
6 TraesCS1D01G157000 chr1A 95.573 1378 56 5 4113 5488 286010017 286011391 0.000000e+00 2202.0
7 TraesCS1D01G157000 chr1A 90.909 704 26 18 169 845 286005381 286006073 0.000000e+00 911.0
8 TraesCS1D01G157000 chr1A 100.000 307 0 0 2254 2560 286008002 286008308 7.980000e-158 568.0
9 TraesCS1D01G157000 chr6B 81.407 398 66 8 5092 5484 482469397 482469791 8.870000e-83 318.0
10 TraesCS1D01G157000 chr6A 81.201 383 69 3 5108 5487 478311696 478311314 6.910000e-79 305.0
11 TraesCS1D01G157000 chr5B 82.571 350 57 4 5095 5440 36611884 36612233 6.910000e-79 305.0
12 TraesCS1D01G157000 chr5D 81.111 360 62 6 5098 5452 42067967 42067609 3.240000e-72 283.0
13 TraesCS1D01G157000 chr5D 79.293 396 78 4 5095 5486 328439859 328440254 1.950000e-69 274.0
14 TraesCS1D01G157000 chr5D 91.813 171 13 1 1 171 406390017 406389848 2.560000e-58 237.0
15 TraesCS1D01G157000 chr5D 95.283 106 5 0 65 170 553483227 553483332 9.450000e-38 169.0
16 TraesCS1D01G157000 chr5D 96.250 80 3 0 1 80 553481746 553481825 1.240000e-26 132.0
17 TraesCS1D01G157000 chr5D 84.328 134 17 3 38 170 565314282 565314152 1.600000e-25 128.0
18 TraesCS1D01G157000 chr7D 80.108 372 68 3 5118 5488 459077885 459077519 7.000000e-69 272.0
19 TraesCS1D01G157000 chr2D 79.146 398 76 7 5096 5487 552530511 552530115 9.060000e-68 268.0
20 TraesCS1D01G157000 chr2D 96.591 88 3 0 88 175 635747784 635747697 4.430000e-31 147.0
21 TraesCS1D01G157000 chr5A 92.398 171 12 1 1 171 670578937 670578768 5.490000e-60 243.0
22 TraesCS1D01G157000 chr3D 92.357 157 12 0 14 170 460120805 460120649 1.990000e-54 224.0
23 TraesCS1D01G157000 chr3D 84.328 134 16 4 38 170 326425029 326425158 5.770000e-25 126.0
24 TraesCS1D01G157000 chr4A 90.000 170 15 1 1 170 734407774 734407607 9.260000e-53 219.0
25 TraesCS1D01G157000 chr2A 92.466 146 11 0 1 146 5312643 5312498 5.570000e-50 209.0
26 TraesCS1D01G157000 chr2B 96.721 61 2 0 956 1016 705883054 705883114 9.730000e-18 102.0
27 TraesCS1D01G157000 chr6D 97.917 48 0 1 907 954 410203173 410203127 1.270000e-11 82.4
28 TraesCS1D01G157000 chr6D 97.917 48 0 1 907 954 410204157 410204111 1.270000e-11 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G157000 chr1D 221119571 221125058 5487 False 10135.0 10135 100.0000 1 5488 1 chr1D.!!$F1 5487
1 TraesCS1D01G157000 chr1B 317438768 317444994 6226 False 2778.0 7548 93.3140 169 5486 3 chr1B.!!$F1 5317
2 TraesCS1D01G157000 chr1A 286005381 286011391 6010 False 1714.8 2599 96.0568 169 5488 5 chr1A.!!$F1 5319

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
96 97 0.036765 TAACAGGGATGACGTGGCAC 60.037 55.000 7.79 7.79 39.23 5.01 F
901 1236 0.177604 CGCTGCTGATCCCTTCTTCT 59.822 55.000 0.00 0.00 0.00 2.85 F
1395 1744 0.105593 CCTATGCTGATGTGAGCGGT 59.894 55.000 0.00 0.00 42.32 5.68 F
1530 1879 1.503542 CGGGCAGACATTCAAGCAC 59.496 57.895 0.00 0.00 0.00 4.40 F
3254 3903 1.135803 GGACACAACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1744 0.761187 GCTCTATCCACATGGCTCCA 59.239 55.000 0.00 0.0 34.44 3.86 R
1704 2053 1.066071 GTCTCTCCCCTGCCTGTTAAC 60.066 57.143 0.00 0.0 0.00 2.01 R
2876 3525 1.625818 GGCCTGTACTGCCTGCTATAT 59.374 52.381 16.77 0.0 45.70 0.86 R
3364 4015 2.223688 TGCAACAATCGACCAACAAAGG 60.224 45.455 0.00 0.0 0.00 3.11 R
5186 6829 0.319297 GTAGCGGTCGTTCAGTGGTT 60.319 55.000 0.00 0.0 0.00 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
26 27 9.226606 AGAGAATAGACTTCCTGAGATTATACG 57.773 37.037 0.00 0.00 0.00 3.06
27 28 8.927675 AGAATAGACTTCCTGAGATTATACGT 57.072 34.615 0.00 0.00 0.00 3.57
30 31 9.570468 AATAGACTTCCTGAGATTATACGTACA 57.430 33.333 0.00 0.00 0.00 2.90
31 32 9.742144 ATAGACTTCCTGAGATTATACGTACAT 57.258 33.333 0.00 0.00 0.00 2.29
32 33 7.877003 AGACTTCCTGAGATTATACGTACATG 58.123 38.462 0.00 0.00 0.00 3.21
33 34 6.448006 ACTTCCTGAGATTATACGTACATGC 58.552 40.000 0.00 0.00 0.00 4.06
34 35 6.040504 ACTTCCTGAGATTATACGTACATGCA 59.959 38.462 0.00 0.00 0.00 3.96
35 36 6.590234 TCCTGAGATTATACGTACATGCAT 57.410 37.500 0.00 0.00 0.00 3.96
36 37 6.389906 TCCTGAGATTATACGTACATGCATG 58.610 40.000 25.09 25.09 0.00 4.06
37 38 5.578336 CCTGAGATTATACGTACATGCATGG 59.422 44.000 29.41 14.96 0.00 3.66
38 39 5.478407 TGAGATTATACGTACATGCATGGG 58.522 41.667 29.41 19.76 0.00 4.00
39 40 4.253685 AGATTATACGTACATGCATGGGC 58.746 43.478 29.41 19.61 41.68 5.36
40 41 3.762407 TTATACGTACATGCATGGGCT 57.238 42.857 29.41 12.30 41.91 5.19
41 42 1.882912 ATACGTACATGCATGGGCTG 58.117 50.000 29.41 17.95 41.91 4.85
50 51 3.521605 CATGGGCTGCTGATGTGG 58.478 61.111 0.00 0.00 0.00 4.17
51 52 1.077285 CATGGGCTGCTGATGTGGA 60.077 57.895 0.00 0.00 0.00 4.02
52 53 0.467474 CATGGGCTGCTGATGTGGAT 60.467 55.000 0.00 0.00 0.00 3.41
53 54 1.142936 ATGGGCTGCTGATGTGGATA 58.857 50.000 0.00 0.00 0.00 2.59
54 55 0.918258 TGGGCTGCTGATGTGGATAA 59.082 50.000 0.00 0.00 0.00 1.75
55 56 1.496001 TGGGCTGCTGATGTGGATAAT 59.504 47.619 0.00 0.00 0.00 1.28
56 57 1.884579 GGGCTGCTGATGTGGATAATG 59.115 52.381 0.00 0.00 0.00 1.90
57 58 2.579873 GGCTGCTGATGTGGATAATGT 58.420 47.619 0.00 0.00 0.00 2.71
58 59 2.292569 GGCTGCTGATGTGGATAATGTG 59.707 50.000 0.00 0.00 0.00 3.21
59 60 2.287427 GCTGCTGATGTGGATAATGTGC 60.287 50.000 0.00 0.00 0.00 4.57
60 61 2.946990 CTGCTGATGTGGATAATGTGCA 59.053 45.455 0.00 0.00 0.00 4.57
61 62 3.558033 TGCTGATGTGGATAATGTGCAT 58.442 40.909 0.00 0.00 0.00 3.96
62 63 3.316868 TGCTGATGTGGATAATGTGCATG 59.683 43.478 0.00 0.00 0.00 4.06
63 64 3.317149 GCTGATGTGGATAATGTGCATGT 59.683 43.478 0.00 0.00 0.00 3.21
64 65 4.516321 GCTGATGTGGATAATGTGCATGTA 59.484 41.667 0.00 0.00 0.00 2.29
65 66 5.008911 GCTGATGTGGATAATGTGCATGTAA 59.991 40.000 0.00 0.00 0.00 2.41
66 67 6.622833 TGATGTGGATAATGTGCATGTAAG 57.377 37.500 0.00 0.00 0.00 2.34
67 68 6.355747 TGATGTGGATAATGTGCATGTAAGA 58.644 36.000 0.00 0.00 0.00 2.10
68 69 6.484308 TGATGTGGATAATGTGCATGTAAGAG 59.516 38.462 0.00 0.00 0.00 2.85
69 70 5.988287 TGTGGATAATGTGCATGTAAGAGA 58.012 37.500 0.00 0.00 0.00 3.10
70 71 6.413892 TGTGGATAATGTGCATGTAAGAGAA 58.586 36.000 0.00 0.00 0.00 2.87
71 72 6.883756 TGTGGATAATGTGCATGTAAGAGAAA 59.116 34.615 0.00 0.00 0.00 2.52
72 73 7.557358 TGTGGATAATGTGCATGTAAGAGAAAT 59.443 33.333 0.00 0.00 0.00 2.17
73 74 9.056005 GTGGATAATGTGCATGTAAGAGAAATA 57.944 33.333 0.00 0.00 0.00 1.40
74 75 9.056005 TGGATAATGTGCATGTAAGAGAAATAC 57.944 33.333 0.00 0.00 0.00 1.89
75 76 9.277783 GGATAATGTGCATGTAAGAGAAATACT 57.722 33.333 0.00 0.00 0.00 2.12
83 84 9.764363 TGCATGTAAGAGAAATACTATAACAGG 57.236 33.333 0.00 0.00 0.00 4.00
84 85 9.209175 GCATGTAAGAGAAATACTATAACAGGG 57.791 37.037 0.00 0.00 0.00 4.45
90 91 7.887381 AGAGAAATACTATAACAGGGATGACG 58.113 38.462 0.00 0.00 0.00 4.35
91 92 7.506261 AGAGAAATACTATAACAGGGATGACGT 59.494 37.037 0.00 0.00 0.00 4.34
92 93 7.434492 AGAAATACTATAACAGGGATGACGTG 58.566 38.462 0.00 0.00 40.69 4.49
93 94 5.723672 ATACTATAACAGGGATGACGTGG 57.276 43.478 0.00 0.00 39.23 4.94
94 95 2.102588 ACTATAACAGGGATGACGTGGC 59.897 50.000 0.00 0.00 39.23 5.01
95 96 0.908910 ATAACAGGGATGACGTGGCA 59.091 50.000 0.00 0.00 39.23 4.92
96 97 0.036765 TAACAGGGATGACGTGGCAC 60.037 55.000 7.79 7.79 39.23 5.01
97 98 2.050836 AACAGGGATGACGTGGCACA 62.051 55.000 19.09 0.00 39.23 4.57
98 99 1.078214 CAGGGATGACGTGGCACAT 60.078 57.895 19.09 0.54 44.52 3.21
99 100 1.091771 CAGGGATGACGTGGCACATC 61.092 60.000 19.09 13.20 44.52 3.06
100 101 2.173669 GGGATGACGTGGCACATCG 61.174 63.158 19.09 6.43 44.52 3.84
101 102 2.173669 GGATGACGTGGCACATCGG 61.174 63.158 19.09 3.40 44.52 4.18
102 103 1.447838 GATGACGTGGCACATCGGT 60.448 57.895 19.09 7.04 44.52 4.69
114 115 3.840831 CATCGGTGATGTGGACAGT 57.159 52.632 0.00 0.00 35.54 3.55
115 116 2.959507 CATCGGTGATGTGGACAGTA 57.040 50.000 0.00 0.00 35.54 2.74
116 117 3.459232 CATCGGTGATGTGGACAGTAT 57.541 47.619 0.00 0.00 35.54 2.12
117 118 2.959507 TCGGTGATGTGGACAGTATG 57.040 50.000 0.00 0.00 46.00 2.39
118 119 1.134818 TCGGTGATGTGGACAGTATGC 60.135 52.381 0.00 0.00 42.53 3.14
119 120 1.405391 CGGTGATGTGGACAGTATGCA 60.405 52.381 0.00 0.00 42.53 3.96
120 121 2.742856 CGGTGATGTGGACAGTATGCAT 60.743 50.000 3.79 3.79 42.53 3.96
121 122 2.615447 GGTGATGTGGACAGTATGCATG 59.385 50.000 10.16 0.00 42.53 4.06
122 123 2.615447 GTGATGTGGACAGTATGCATGG 59.385 50.000 10.16 1.09 42.53 3.66
123 124 2.239402 TGATGTGGACAGTATGCATGGT 59.761 45.455 10.16 4.73 42.53 3.55
124 125 2.112380 TGTGGACAGTATGCATGGTG 57.888 50.000 10.16 8.99 42.53 4.17
125 126 1.627834 TGTGGACAGTATGCATGGTGA 59.372 47.619 10.16 0.00 42.53 4.02
126 127 2.039613 TGTGGACAGTATGCATGGTGAA 59.960 45.455 10.16 0.00 42.53 3.18
127 128 3.081061 GTGGACAGTATGCATGGTGAAA 58.919 45.455 10.16 0.00 42.53 2.69
128 129 3.127548 GTGGACAGTATGCATGGTGAAAG 59.872 47.826 10.16 0.00 42.53 2.62
129 130 3.008923 TGGACAGTATGCATGGTGAAAGA 59.991 43.478 10.16 0.00 42.53 2.52
130 131 4.009675 GGACAGTATGCATGGTGAAAGAA 58.990 43.478 10.16 0.00 42.53 2.52
131 132 4.641989 GGACAGTATGCATGGTGAAAGAAT 59.358 41.667 10.16 0.00 42.53 2.40
132 133 5.822519 GGACAGTATGCATGGTGAAAGAATA 59.177 40.000 10.16 0.00 42.53 1.75
133 134 6.017605 GGACAGTATGCATGGTGAAAGAATAG 60.018 42.308 10.16 0.00 42.53 1.73
134 135 5.824624 ACAGTATGCATGGTGAAAGAATAGG 59.175 40.000 10.16 0.00 42.53 2.57
135 136 5.240183 CAGTATGCATGGTGAAAGAATAGGG 59.760 44.000 10.16 0.00 0.00 3.53
136 137 4.524802 ATGCATGGTGAAAGAATAGGGA 57.475 40.909 0.00 0.00 0.00 4.20
137 138 3.889815 TGCATGGTGAAAGAATAGGGAG 58.110 45.455 0.00 0.00 0.00 4.30
138 139 3.266772 TGCATGGTGAAAGAATAGGGAGT 59.733 43.478 0.00 0.00 0.00 3.85
139 140 4.473196 TGCATGGTGAAAGAATAGGGAGTA 59.527 41.667 0.00 0.00 0.00 2.59
140 141 5.059833 GCATGGTGAAAGAATAGGGAGTAG 58.940 45.833 0.00 0.00 0.00 2.57
141 142 5.396884 GCATGGTGAAAGAATAGGGAGTAGT 60.397 44.000 0.00 0.00 0.00 2.73
142 143 5.677319 TGGTGAAAGAATAGGGAGTAGTG 57.323 43.478 0.00 0.00 0.00 2.74
143 144 4.469945 TGGTGAAAGAATAGGGAGTAGTGG 59.530 45.833 0.00 0.00 0.00 4.00
144 145 4.141688 GGTGAAAGAATAGGGAGTAGTGGG 60.142 50.000 0.00 0.00 0.00 4.61
145 146 4.037927 TGAAAGAATAGGGAGTAGTGGGG 58.962 47.826 0.00 0.00 0.00 4.96
146 147 4.265124 TGAAAGAATAGGGAGTAGTGGGGA 60.265 45.833 0.00 0.00 0.00 4.81
147 148 3.621682 AGAATAGGGAGTAGTGGGGAG 57.378 52.381 0.00 0.00 0.00 4.30
148 149 1.972075 GAATAGGGAGTAGTGGGGAGC 59.028 57.143 0.00 0.00 0.00 4.70
149 150 0.941963 ATAGGGAGTAGTGGGGAGCA 59.058 55.000 0.00 0.00 0.00 4.26
150 151 0.714180 TAGGGAGTAGTGGGGAGCAA 59.286 55.000 0.00 0.00 0.00 3.91
151 152 0.910088 AGGGAGTAGTGGGGAGCAAC 60.910 60.000 0.00 0.00 0.00 4.17
152 153 0.910088 GGGAGTAGTGGGGAGCAACT 60.910 60.000 0.00 0.00 0.00 3.16
153 154 0.984995 GGAGTAGTGGGGAGCAACTT 59.015 55.000 0.00 0.00 0.00 2.66
154 155 1.066071 GGAGTAGTGGGGAGCAACTTC 60.066 57.143 0.00 0.00 0.00 3.01
155 156 1.903183 GAGTAGTGGGGAGCAACTTCT 59.097 52.381 0.00 0.00 0.00 2.85
156 157 2.303311 GAGTAGTGGGGAGCAACTTCTT 59.697 50.000 0.00 0.00 0.00 2.52
157 158 3.514309 GAGTAGTGGGGAGCAACTTCTTA 59.486 47.826 0.00 0.00 0.00 2.10
158 159 3.908103 AGTAGTGGGGAGCAACTTCTTAA 59.092 43.478 0.00 0.00 0.00 1.85
159 160 3.425162 AGTGGGGAGCAACTTCTTAAG 57.575 47.619 0.00 0.00 0.00 1.85
160 161 2.979678 AGTGGGGAGCAACTTCTTAAGA 59.020 45.455 0.00 0.00 0.00 2.10
161 162 3.394606 AGTGGGGAGCAACTTCTTAAGAA 59.605 43.478 16.85 16.85 0.00 2.52
162 163 4.043435 AGTGGGGAGCAACTTCTTAAGAAT 59.957 41.667 18.02 3.17 33.01 2.40
163 164 4.156739 GTGGGGAGCAACTTCTTAAGAATG 59.843 45.833 18.02 14.95 33.01 2.67
164 165 3.696548 GGGGAGCAACTTCTTAAGAATGG 59.303 47.826 18.02 10.22 33.01 3.16
165 166 4.336280 GGGAGCAACTTCTTAAGAATGGT 58.664 43.478 18.02 18.40 34.27 3.55
166 167 5.497474 GGGAGCAACTTCTTAAGAATGGTA 58.503 41.667 18.02 0.00 32.73 3.25
167 168 5.586643 GGGAGCAACTTCTTAAGAATGGTAG 59.413 44.000 18.02 8.78 32.73 3.18
208 209 2.380064 TTTTTGGTCCTGAGCCATGT 57.620 45.000 0.00 0.00 35.71 3.21
209 210 1.619654 TTTTGGTCCTGAGCCATGTG 58.380 50.000 0.00 0.00 35.71 3.21
364 371 7.649370 ACTTGCATGTCATCGATCTTATTAG 57.351 36.000 0.00 0.00 0.00 1.73
371 378 8.639428 CATGTCATCGATCTTATTAGTTAACGG 58.361 37.037 0.00 0.00 0.00 4.44
442 449 1.000771 GGGGAGAAAAGTGGGAGCC 60.001 63.158 0.00 0.00 0.00 4.70
484 497 4.985409 GGAGCTGACTTAAGTATGATTCCG 59.015 45.833 8.42 0.00 0.00 4.30
528 541 6.425114 GTCAGTGTGATCTACATTGTCTTTGT 59.575 38.462 15.24 0.00 44.65 2.83
585 598 8.363390 TCATTTATATTGTGCTGGTTTGTTTCA 58.637 29.630 0.00 0.00 0.00 2.69
638 651 2.487762 GTGTGTGAGAGAGAGAGACTGG 59.512 54.545 0.00 0.00 0.00 4.00
768 800 2.432146 TCAGCTGTTGAGTGAGTGAGTT 59.568 45.455 14.67 0.00 0.00 3.01
769 801 2.799412 CAGCTGTTGAGTGAGTGAGTTC 59.201 50.000 5.25 0.00 0.00 3.01
770 802 2.139118 GCTGTTGAGTGAGTGAGTTCC 58.861 52.381 0.00 0.00 0.00 3.62
834 866 5.163673 GCTCATCCCTTTCTTCTTCATTCAC 60.164 44.000 0.00 0.00 0.00 3.18
901 1236 0.177604 CGCTGCTGATCCCTTCTTCT 59.822 55.000 0.00 0.00 0.00 2.85
971 1320 2.412847 CGCCTTTCTTCTTTTACCAGCG 60.413 50.000 0.00 0.00 0.00 5.18
983 1332 2.672961 TACCAGCGTCCAAGAATCAG 57.327 50.000 0.00 0.00 0.00 2.90
1395 1744 0.105593 CCTATGCTGATGTGAGCGGT 59.894 55.000 0.00 0.00 42.32 5.68
1530 1879 1.503542 CGGGCAGACATTCAAGCAC 59.496 57.895 0.00 0.00 0.00 4.40
1704 2053 5.006386 AGTAGATTTTGTGCTCCTCTTTGG 58.994 41.667 0.00 0.00 37.10 3.28
1882 2231 5.187186 ACCCGTCTTGTTCTCATTAGTGTAT 59.813 40.000 0.00 0.00 0.00 2.29
1886 2235 7.201444 CCGTCTTGTTCTCATTAGTGTATTGTC 60.201 40.741 0.00 0.00 0.00 3.18
1915 2264 5.122711 TGTGCCATGCATAGATGATTAATCG 59.877 40.000 10.80 0.00 41.91 3.34
1922 2271 6.969366 TGCATAGATGATTAATCGGGTTTTG 58.031 36.000 10.80 5.60 40.54 2.44
1923 2272 6.016360 TGCATAGATGATTAATCGGGTTTTGG 60.016 38.462 10.80 0.00 40.54 3.28
1924 2273 6.206634 GCATAGATGATTAATCGGGTTTTGGA 59.793 38.462 10.80 0.00 40.54 3.53
1925 2274 7.094205 GCATAGATGATTAATCGGGTTTTGGAT 60.094 37.037 10.80 0.00 40.54 3.41
2172 2521 4.946784 AGAGTTTGCGGTTCATGATTAC 57.053 40.909 0.00 0.00 0.00 1.89
2196 2545 2.163412 GCGCAAGAATACCAATGTGGAA 59.837 45.455 0.30 0.00 39.21 3.53
2560 3125 2.213499 ACAAGTAAGCTGTGTGTGCTC 58.787 47.619 0.00 0.00 40.22 4.26
2755 3403 3.485877 CCTTTCTCCGCATCATTTTCGTC 60.486 47.826 0.00 0.00 0.00 4.20
2775 3424 6.369005 TCGTCTAGTAACGAGTTCTTTTCTG 58.631 40.000 2.76 0.00 46.02 3.02
2777 3426 7.171508 TCGTCTAGTAACGAGTTCTTTTCTGTA 59.828 37.037 2.76 0.00 46.02 2.74
2795 3444 6.109156 TCTGTATAACCAAAGTGCTGAGAA 57.891 37.500 0.00 0.00 0.00 2.87
2876 3525 6.239887 GCCCCATTTTCTACCATCTATACTGA 60.240 42.308 0.00 0.00 0.00 3.41
2955 3604 3.152341 CACCATTCTGCTCTTCTTTGGT 58.848 45.455 0.00 0.00 36.46 3.67
3253 3902 1.160989 GGACACAACACACACACACA 58.839 50.000 0.00 0.00 0.00 3.72
3254 3903 1.135803 GGACACAACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
3510 4161 7.325660 TGAGTGGCATCTTCTTTATTTGATC 57.674 36.000 0.00 0.00 0.00 2.92
3593 4244 7.056635 AGAAAAGAAACTGAGATTTGTCCTGA 58.943 34.615 0.00 0.00 0.00 3.86
4163 4894 0.679960 GGTGGGGCACTAACACATCC 60.680 60.000 0.00 0.00 36.87 3.51
4166 4897 0.322187 GGGGCACTAACACATCCGTT 60.322 55.000 0.00 0.00 0.00 4.44
4262 4993 3.278072 ATGCTCCCACCACTGCCTG 62.278 63.158 0.00 0.00 0.00 4.85
4634 5365 4.191804 TGGGTTGGATTATTATGGTGGG 57.808 45.455 0.00 0.00 0.00 4.61
4649 5380 2.286885 GGGGGTGGATCCTGGGAA 60.287 66.667 14.23 0.00 36.25 3.97
4821 5552 1.913451 AACTCTCCGCACTCGACTCG 61.913 60.000 0.00 0.00 38.10 4.18
4924 5733 6.893958 ATGCTTACGAATTTACAGAGTGAG 57.106 37.500 0.00 0.00 0.00 3.51
4967 6607 6.639632 ATCATTGCTGTGAATTATACACCC 57.360 37.500 0.00 0.00 37.45 4.61
4990 6630 7.460402 ACCCTGTCCATCTGATATTCTTATCAT 59.540 37.037 0.00 0.00 42.51 2.45
5013 6653 8.154203 TCATTACTTTTGTCTGATGTTGGTCTA 58.846 33.333 0.00 0.00 0.00 2.59
5050 6690 4.750098 TCATTGTGACCGACTCTTTCTTTC 59.250 41.667 0.00 0.00 0.00 2.62
5222 6865 0.679505 TACTGCTGCCAGAACGAACT 59.320 50.000 0.00 0.00 41.77 3.01
5230 6873 1.660575 CAGAACGAACTGCCGACGT 60.661 57.895 0.00 0.00 41.97 4.34
5294 6937 3.152341 CAATGACAGGCAGGAAGTCTTT 58.848 45.455 0.00 0.00 33.56 2.52
5312 6955 2.046009 TTGTGCACGTGCCCCTAAGA 62.046 55.000 35.72 14.25 41.18 2.10
5356 7000 1.543802 CGCCTTTGAACCCTTGCATAA 59.456 47.619 0.00 0.00 0.00 1.90
5361 7005 5.127031 GCCTTTGAACCCTTGCATAAATCTA 59.873 40.000 0.00 0.00 0.00 1.98
5374 7018 7.255491 TGCATAAATCTAAAGCATCTGACAG 57.745 36.000 0.00 0.00 0.00 3.51
5441 7085 1.069823 AGATGGCAGGAATCTACGCAG 59.930 52.381 0.00 0.00 32.54 5.18
5455 7099 0.878961 ACGCAGAAGTTCCGTTGACC 60.879 55.000 0.00 0.00 0.00 4.02
5466 7110 1.227527 CGTTGACCACAGCCAGACA 60.228 57.895 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.226606 CGTATAATCTCAGGAAGTCTATTCTCT 57.773 37.037 0.00 0.00 0.00 3.10
1 2 9.005777 ACGTATAATCTCAGGAAGTCTATTCTC 57.994 37.037 0.00 0.00 0.00 2.87
2 3 8.927675 ACGTATAATCTCAGGAAGTCTATTCT 57.072 34.615 0.00 0.00 0.00 2.40
4 5 9.570468 TGTACGTATAATCTCAGGAAGTCTATT 57.430 33.333 0.00 0.00 0.00 1.73
5 6 9.742144 ATGTACGTATAATCTCAGGAAGTCTAT 57.258 33.333 0.00 0.00 0.00 1.98
6 7 9.000486 CATGTACGTATAATCTCAGGAAGTCTA 58.000 37.037 0.00 0.00 0.00 2.59
7 8 7.522399 GCATGTACGTATAATCTCAGGAAGTCT 60.522 40.741 0.00 0.00 0.00 3.24
8 9 6.583050 GCATGTACGTATAATCTCAGGAAGTC 59.417 42.308 0.00 0.00 0.00 3.01
9 10 6.040504 TGCATGTACGTATAATCTCAGGAAGT 59.959 38.462 0.00 0.00 0.00 3.01
10 11 6.447162 TGCATGTACGTATAATCTCAGGAAG 58.553 40.000 0.00 0.00 0.00 3.46
11 12 6.399639 TGCATGTACGTATAATCTCAGGAA 57.600 37.500 0.00 0.00 0.00 3.36
12 13 6.389906 CATGCATGTACGTATAATCTCAGGA 58.610 40.000 18.91 0.00 0.00 3.86
13 14 5.578336 CCATGCATGTACGTATAATCTCAGG 59.422 44.000 24.58 0.00 0.00 3.86
14 15 5.578336 CCCATGCATGTACGTATAATCTCAG 59.422 44.000 24.58 3.94 0.00 3.35
15 16 5.478407 CCCATGCATGTACGTATAATCTCA 58.522 41.667 24.58 0.00 0.00 3.27
16 17 4.330074 GCCCATGCATGTACGTATAATCTC 59.670 45.833 24.58 0.00 37.47 2.75
17 18 4.020218 AGCCCATGCATGTACGTATAATCT 60.020 41.667 24.58 4.27 41.13 2.40
18 19 4.093408 CAGCCCATGCATGTACGTATAATC 59.907 45.833 24.58 2.24 41.13 1.75
19 20 4.002982 CAGCCCATGCATGTACGTATAAT 58.997 43.478 24.58 0.00 41.13 1.28
20 21 3.398406 CAGCCCATGCATGTACGTATAA 58.602 45.455 24.58 0.00 41.13 0.98
21 22 3.038788 CAGCCCATGCATGTACGTATA 57.961 47.619 24.58 0.00 41.13 1.47
22 23 1.882912 CAGCCCATGCATGTACGTAT 58.117 50.000 24.58 2.42 41.13 3.06
23 24 3.377933 CAGCCCATGCATGTACGTA 57.622 52.632 24.58 0.00 41.13 3.57
24 25 4.223800 CAGCCCATGCATGTACGT 57.776 55.556 24.58 4.22 41.13 3.57
33 34 0.467474 ATCCACATCAGCAGCCCATG 60.467 55.000 0.00 0.00 0.00 3.66
34 35 1.142936 TATCCACATCAGCAGCCCAT 58.857 50.000 0.00 0.00 0.00 4.00
35 36 0.918258 TTATCCACATCAGCAGCCCA 59.082 50.000 0.00 0.00 0.00 5.36
36 37 1.884579 CATTATCCACATCAGCAGCCC 59.115 52.381 0.00 0.00 0.00 5.19
37 38 2.292569 CACATTATCCACATCAGCAGCC 59.707 50.000 0.00 0.00 0.00 4.85
38 39 2.287427 GCACATTATCCACATCAGCAGC 60.287 50.000 0.00 0.00 0.00 5.25
39 40 2.946990 TGCACATTATCCACATCAGCAG 59.053 45.455 0.00 0.00 0.00 4.24
40 41 3.002038 TGCACATTATCCACATCAGCA 57.998 42.857 0.00 0.00 0.00 4.41
41 42 3.317149 ACATGCACATTATCCACATCAGC 59.683 43.478 0.00 0.00 0.00 4.26
42 43 6.484308 TCTTACATGCACATTATCCACATCAG 59.516 38.462 0.00 0.00 0.00 2.90
43 44 6.355747 TCTTACATGCACATTATCCACATCA 58.644 36.000 0.00 0.00 0.00 3.07
44 45 6.707608 TCTCTTACATGCACATTATCCACATC 59.292 38.462 0.00 0.00 0.00 3.06
45 46 6.594744 TCTCTTACATGCACATTATCCACAT 58.405 36.000 0.00 0.00 0.00 3.21
46 47 5.988287 TCTCTTACATGCACATTATCCACA 58.012 37.500 0.00 0.00 0.00 4.17
47 48 6.925610 TTCTCTTACATGCACATTATCCAC 57.074 37.500 0.00 0.00 0.00 4.02
48 49 9.056005 GTATTTCTCTTACATGCACATTATCCA 57.944 33.333 0.00 0.00 0.00 3.41
49 50 9.277783 AGTATTTCTCTTACATGCACATTATCC 57.722 33.333 0.00 0.00 0.00 2.59
57 58 9.764363 CCTGTTATAGTATTTCTCTTACATGCA 57.236 33.333 0.00 0.00 0.00 3.96
58 59 9.209175 CCCTGTTATAGTATTTCTCTTACATGC 57.791 37.037 0.00 0.00 0.00 4.06
64 65 8.361139 CGTCATCCCTGTTATAGTATTTCTCTT 58.639 37.037 0.00 0.00 0.00 2.85
65 66 7.506261 ACGTCATCCCTGTTATAGTATTTCTCT 59.494 37.037 0.00 0.00 0.00 3.10
66 67 7.595502 CACGTCATCCCTGTTATAGTATTTCTC 59.404 40.741 0.00 0.00 0.00 2.87
67 68 7.434492 CACGTCATCCCTGTTATAGTATTTCT 58.566 38.462 0.00 0.00 0.00 2.52
68 69 6.645415 CCACGTCATCCCTGTTATAGTATTTC 59.355 42.308 0.00 0.00 0.00 2.17
69 70 6.522054 CCACGTCATCCCTGTTATAGTATTT 58.478 40.000 0.00 0.00 0.00 1.40
70 71 5.510861 GCCACGTCATCCCTGTTATAGTATT 60.511 44.000 0.00 0.00 0.00 1.89
71 72 4.021368 GCCACGTCATCCCTGTTATAGTAT 60.021 45.833 0.00 0.00 0.00 2.12
72 73 3.319972 GCCACGTCATCCCTGTTATAGTA 59.680 47.826 0.00 0.00 0.00 1.82
73 74 2.102588 GCCACGTCATCCCTGTTATAGT 59.897 50.000 0.00 0.00 0.00 2.12
74 75 2.102420 TGCCACGTCATCCCTGTTATAG 59.898 50.000 0.00 0.00 0.00 1.31
75 76 2.112190 TGCCACGTCATCCCTGTTATA 58.888 47.619 0.00 0.00 0.00 0.98
76 77 0.908910 TGCCACGTCATCCCTGTTAT 59.091 50.000 0.00 0.00 0.00 1.89
77 78 0.036765 GTGCCACGTCATCCCTGTTA 60.037 55.000 0.00 0.00 0.00 2.41
78 79 1.302511 GTGCCACGTCATCCCTGTT 60.303 57.895 0.00 0.00 0.00 3.16
79 80 1.841302 ATGTGCCACGTCATCCCTGT 61.841 55.000 0.00 0.00 0.00 4.00
80 81 1.078214 ATGTGCCACGTCATCCCTG 60.078 57.895 0.00 0.00 0.00 4.45
81 82 1.221840 GATGTGCCACGTCATCCCT 59.778 57.895 12.14 0.00 34.36 4.20
82 83 2.173669 CGATGTGCCACGTCATCCC 61.174 63.158 16.77 0.00 37.67 3.85
83 84 2.173669 CCGATGTGCCACGTCATCC 61.174 63.158 16.77 0.00 37.67 3.51
84 85 1.447838 ACCGATGTGCCACGTCATC 60.448 57.895 16.77 5.17 33.83 2.92
85 86 1.741401 CACCGATGTGCCACGTCAT 60.741 57.895 16.77 1.67 33.83 3.06
86 87 2.166130 ATCACCGATGTGCCACGTCA 62.166 55.000 16.77 0.00 42.46 4.35
87 88 1.447838 ATCACCGATGTGCCACGTC 60.448 57.895 7.00 7.00 42.46 4.34
88 89 1.741401 CATCACCGATGTGCCACGT 60.741 57.895 0.00 0.00 42.46 4.49
89 90 3.092403 CATCACCGATGTGCCACG 58.908 61.111 0.00 0.00 42.46 4.94
96 97 2.959507 TACTGTCCACATCACCGATG 57.040 50.000 2.45 2.45 44.71 3.84
97 98 2.483714 GCATACTGTCCACATCACCGAT 60.484 50.000 0.00 0.00 0.00 4.18
98 99 1.134818 GCATACTGTCCACATCACCGA 60.135 52.381 0.00 0.00 0.00 4.69
99 100 1.290203 GCATACTGTCCACATCACCG 58.710 55.000 0.00 0.00 0.00 4.94
100 101 2.401583 TGCATACTGTCCACATCACC 57.598 50.000 0.00 0.00 0.00 4.02
101 102 2.615447 CCATGCATACTGTCCACATCAC 59.385 50.000 0.00 0.00 0.00 3.06
102 103 2.239402 ACCATGCATACTGTCCACATCA 59.761 45.455 0.00 0.00 0.00 3.07
103 104 2.615447 CACCATGCATACTGTCCACATC 59.385 50.000 0.00 0.00 0.00 3.06
104 105 2.239402 TCACCATGCATACTGTCCACAT 59.761 45.455 0.00 0.00 0.00 3.21
105 106 1.627834 TCACCATGCATACTGTCCACA 59.372 47.619 0.00 0.00 0.00 4.17
106 107 2.401583 TCACCATGCATACTGTCCAC 57.598 50.000 0.00 0.00 0.00 4.02
107 108 3.008923 TCTTTCACCATGCATACTGTCCA 59.991 43.478 0.00 0.00 0.00 4.02
108 109 3.609853 TCTTTCACCATGCATACTGTCC 58.390 45.455 0.00 0.00 0.00 4.02
109 110 5.824904 ATTCTTTCACCATGCATACTGTC 57.175 39.130 0.00 0.00 0.00 3.51
110 111 5.824624 CCTATTCTTTCACCATGCATACTGT 59.175 40.000 0.00 0.00 0.00 3.55
111 112 5.240183 CCCTATTCTTTCACCATGCATACTG 59.760 44.000 0.00 0.00 0.00 2.74
112 113 5.132648 TCCCTATTCTTTCACCATGCATACT 59.867 40.000 0.00 0.00 0.00 2.12
113 114 5.376625 TCCCTATTCTTTCACCATGCATAC 58.623 41.667 0.00 0.00 0.00 2.39
114 115 5.132648 ACTCCCTATTCTTTCACCATGCATA 59.867 40.000 0.00 0.00 0.00 3.14
115 116 4.079558 ACTCCCTATTCTTTCACCATGCAT 60.080 41.667 0.00 0.00 0.00 3.96
116 117 3.266772 ACTCCCTATTCTTTCACCATGCA 59.733 43.478 0.00 0.00 0.00 3.96
117 118 3.891049 ACTCCCTATTCTTTCACCATGC 58.109 45.455 0.00 0.00 0.00 4.06
118 119 6.051717 CACTACTCCCTATTCTTTCACCATG 58.948 44.000 0.00 0.00 0.00 3.66
119 120 5.131142 CCACTACTCCCTATTCTTTCACCAT 59.869 44.000 0.00 0.00 0.00 3.55
120 121 4.469945 CCACTACTCCCTATTCTTTCACCA 59.530 45.833 0.00 0.00 0.00 4.17
121 122 4.141688 CCCACTACTCCCTATTCTTTCACC 60.142 50.000 0.00 0.00 0.00 4.02
122 123 4.141688 CCCCACTACTCCCTATTCTTTCAC 60.142 50.000 0.00 0.00 0.00 3.18
123 124 4.037927 CCCCACTACTCCCTATTCTTTCA 58.962 47.826 0.00 0.00 0.00 2.69
124 125 4.296056 TCCCCACTACTCCCTATTCTTTC 58.704 47.826 0.00 0.00 0.00 2.62
125 126 4.299485 CTCCCCACTACTCCCTATTCTTT 58.701 47.826 0.00 0.00 0.00 2.52
126 127 3.930035 CTCCCCACTACTCCCTATTCTT 58.070 50.000 0.00 0.00 0.00 2.52
127 128 2.426561 GCTCCCCACTACTCCCTATTCT 60.427 54.545 0.00 0.00 0.00 2.40
128 129 1.972075 GCTCCCCACTACTCCCTATTC 59.028 57.143 0.00 0.00 0.00 1.75
129 130 1.294068 TGCTCCCCACTACTCCCTATT 59.706 52.381 0.00 0.00 0.00 1.73
130 131 0.941963 TGCTCCCCACTACTCCCTAT 59.058 55.000 0.00 0.00 0.00 2.57
131 132 0.714180 TTGCTCCCCACTACTCCCTA 59.286 55.000 0.00 0.00 0.00 3.53
132 133 0.910088 GTTGCTCCCCACTACTCCCT 60.910 60.000 0.00 0.00 0.00 4.20
133 134 0.910088 AGTTGCTCCCCACTACTCCC 60.910 60.000 0.00 0.00 0.00 4.30
134 135 0.984995 AAGTTGCTCCCCACTACTCC 59.015 55.000 0.00 0.00 0.00 3.85
135 136 1.903183 AGAAGTTGCTCCCCACTACTC 59.097 52.381 0.00 0.00 0.00 2.59
136 137 2.031495 AGAAGTTGCTCCCCACTACT 57.969 50.000 0.00 0.00 0.00 2.57
137 138 2.861147 AAGAAGTTGCTCCCCACTAC 57.139 50.000 0.00 0.00 0.00 2.73
138 139 4.164981 TCTTAAGAAGTTGCTCCCCACTA 58.835 43.478 1.68 0.00 0.00 2.74
139 140 2.979678 TCTTAAGAAGTTGCTCCCCACT 59.020 45.455 1.68 0.00 0.00 4.00
140 141 3.418684 TCTTAAGAAGTTGCTCCCCAC 57.581 47.619 1.68 0.00 0.00 4.61
141 142 4.335416 CATTCTTAAGAAGTTGCTCCCCA 58.665 43.478 21.75 0.00 37.48 4.96
142 143 3.696548 CCATTCTTAAGAAGTTGCTCCCC 59.303 47.826 21.75 0.00 37.48 4.81
143 144 4.336280 ACCATTCTTAAGAAGTTGCTCCC 58.664 43.478 21.75 0.00 37.48 4.30
144 145 6.407202 TCTACCATTCTTAAGAAGTTGCTCC 58.593 40.000 21.75 0.00 37.48 4.70
145 146 9.601217 TTATCTACCATTCTTAAGAAGTTGCTC 57.399 33.333 21.75 0.00 37.48 4.26
146 147 9.384764 GTTATCTACCATTCTTAAGAAGTTGCT 57.615 33.333 21.75 10.88 37.48 3.91
147 148 8.613482 GGTTATCTACCATTCTTAAGAAGTTGC 58.387 37.037 21.75 5.40 46.92 4.17
164 165 7.923414 AAATGGTTGACTTCTGGTTATCTAC 57.077 36.000 0.00 0.00 0.00 2.59
165 166 8.934023 AAAAATGGTTGACTTCTGGTTATCTA 57.066 30.769 0.00 0.00 0.00 1.98
166 167 7.839680 AAAAATGGTTGACTTCTGGTTATCT 57.160 32.000 0.00 0.00 0.00 1.98
193 194 1.376086 CACACATGGCTCAGGACCA 59.624 57.895 0.00 0.00 42.61 4.02
195 196 0.250467 ACACACACATGGCTCAGGAC 60.250 55.000 0.00 0.00 0.00 3.85
196 197 0.250424 CACACACACATGGCTCAGGA 60.250 55.000 0.00 0.00 0.00 3.86
204 205 5.743398 CACCTTTAAGAAACACACACACATG 59.257 40.000 0.00 0.00 0.00 3.21
206 207 4.762765 ACACCTTTAAGAAACACACACACA 59.237 37.500 0.00 0.00 0.00 3.72
207 208 5.305139 ACACCTTTAAGAAACACACACAC 57.695 39.130 0.00 0.00 0.00 3.82
208 209 4.396790 GGACACCTTTAAGAAACACACACA 59.603 41.667 0.00 0.00 0.00 3.72
209 210 4.638865 AGGACACCTTTAAGAAACACACAC 59.361 41.667 0.00 0.00 0.00 3.82
250 253 9.911788 CAATGGACAAGGGCTTCTAATATATAT 57.088 33.333 0.00 0.00 0.00 0.86
364 371 3.192466 AGATTACCATGCGTCCGTTAAC 58.808 45.455 0.00 0.00 0.00 2.01
442 449 5.699915 AGCTCCATGTGATTCTATTTCATCG 59.300 40.000 0.00 0.00 0.00 3.84
484 497 2.031870 ACTGCACCCCTTTTCTGTTTC 58.968 47.619 0.00 0.00 0.00 2.78
528 541 2.487265 GCACTCCTGTCAAAAGGAAGGA 60.487 50.000 0.00 0.00 45.81 3.36
604 617 0.369931 CACACACACACTCACACACG 59.630 55.000 0.00 0.00 0.00 4.49
605 618 1.660607 CTCACACACACACTCACACAC 59.339 52.381 0.00 0.00 0.00 3.82
606 619 1.548269 TCTCACACACACACTCACACA 59.452 47.619 0.00 0.00 0.00 3.72
607 620 2.159240 TCTCTCACACACACACTCACAC 60.159 50.000 0.00 0.00 0.00 3.82
608 621 2.099405 TCTCTCACACACACACTCACA 58.901 47.619 0.00 0.00 0.00 3.58
609 622 2.359214 TCTCTCTCACACACACACTCAC 59.641 50.000 0.00 0.00 0.00 3.51
610 623 2.620585 CTCTCTCTCACACACACACTCA 59.379 50.000 0.00 0.00 0.00 3.41
611 624 2.881513 TCTCTCTCTCACACACACACTC 59.118 50.000 0.00 0.00 0.00 3.51
612 625 2.884012 CTCTCTCTCTCACACACACACT 59.116 50.000 0.00 0.00 0.00 3.55
638 651 2.361610 CACCATGTGCCCCCTCAC 60.362 66.667 0.00 0.00 37.48 3.51
768 800 7.124448 GTCTTAAAGGAGTATGAGAAGGAAGGA 59.876 40.741 0.00 0.00 0.00 3.36
769 801 7.269316 GTCTTAAAGGAGTATGAGAAGGAAGG 58.731 42.308 0.00 0.00 0.00 3.46
770 802 7.269316 GGTCTTAAAGGAGTATGAGAAGGAAG 58.731 42.308 0.00 0.00 0.00 3.46
834 866 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
901 1236 0.469917 GCTATTGTGGAGGCTGGCTA 59.530 55.000 2.77 0.00 0.00 3.93
971 1320 4.264460 AGTGAGTGACTGATTCTTGGAC 57.736 45.455 0.00 0.00 31.75 4.02
1173 1522 1.150536 GGACTGGGGCTTCAACACA 59.849 57.895 0.00 0.00 0.00 3.72
1302 1651 0.994247 TCTCCACCACAATGCCATCT 59.006 50.000 0.00 0.00 0.00 2.90
1395 1744 0.761187 GCTCTATCCACATGGCTCCA 59.239 55.000 0.00 0.00 34.44 3.86
1530 1879 1.233019 CATTGCTAATCTGAGGCCCG 58.767 55.000 0.00 0.00 0.00 6.13
1610 1959 6.072199 AGCCAAATAAGAAGATCTTGTCCT 57.928 37.500 14.00 0.45 37.29 3.85
1676 2025 1.398390 GAGCACAAAATCTACTGCCCG 59.602 52.381 0.00 0.00 0.00 6.13
1704 2053 1.066071 GTCTCTCCCCTGCCTGTTAAC 60.066 57.143 0.00 0.00 0.00 2.01
1882 2231 4.084265 CATGGCACAGGCTGACAA 57.916 55.556 23.66 6.67 43.08 3.18
1915 2264 3.756434 TGAATGAAGTCGATCCAAAACCC 59.244 43.478 0.00 0.00 0.00 4.11
1922 2271 3.526931 TCACCTGAATGAAGTCGATCC 57.473 47.619 0.00 0.00 0.00 3.36
2172 2521 1.745087 ACATTGGTATTCTTGCGCTGG 59.255 47.619 9.73 0.68 0.00 4.85
2213 2578 5.066505 AGCCTTGACAAGTACACAGAAAAAG 59.933 40.000 14.03 0.00 0.00 2.27
2215 2580 4.523083 AGCCTTGACAAGTACACAGAAAA 58.477 39.130 14.03 0.00 0.00 2.29
2217 2582 3.838244 AGCCTTGACAAGTACACAGAA 57.162 42.857 14.03 0.00 0.00 3.02
2219 2584 2.549754 CCAAGCCTTGACAAGTACACAG 59.450 50.000 14.03 0.00 0.00 3.66
2224 2589 3.073798 TCATTCCCAAGCCTTGACAAGTA 59.926 43.478 14.03 0.00 0.00 2.24
2560 3125 7.011016 TGTCTACAATACATTGCGTTGATTAGG 59.989 37.037 1.84 0.00 41.38 2.69
2673 3321 6.196571 CGGTCACAAACAAGGTTAGTTAAAG 58.803 40.000 0.00 0.00 0.00 1.85
2777 3426 9.023962 TGATTAATTTCTCAGCACTTTGGTTAT 57.976 29.630 0.00 0.00 0.00 1.89
2795 3444 3.201290 CGGTGAGCAGAGCTGATTAATT 58.799 45.455 0.85 0.00 39.88 1.40
2876 3525 1.625818 GGCCTGTACTGCCTGCTATAT 59.374 52.381 16.77 0.00 45.70 0.86
3162 3811 3.493350 CCATAGTAAAGGCGAGTGAGCAT 60.493 47.826 0.00 0.00 39.27 3.79
3253 3902 8.765219 CGACCGATCTAATATTCTCATTTTTGT 58.235 33.333 0.00 0.00 0.00 2.83
3254 3903 8.223769 CCGACCGATCTAATATTCTCATTTTTG 58.776 37.037 0.00 0.00 0.00 2.44
3364 4015 2.223688 TGCAACAATCGACCAACAAAGG 60.224 45.455 0.00 0.00 0.00 3.11
3510 4161 7.519032 TCTCCCTGTAATTAACAAAGGTTTG 57.481 36.000 0.77 0.77 43.62 2.93
3524 4175 7.432148 TCTTTGCTTACATATCTCCCTGTAA 57.568 36.000 0.00 0.00 36.63 2.41
4140 4871 2.434331 GTTAGTGCCCCACCTGCA 59.566 61.111 0.00 0.00 34.49 4.41
4163 4894 1.418342 CGGAATCCGGTAGCACAACG 61.418 60.000 14.91 0.00 44.15 4.10
4262 4993 3.191539 CGGCGGAGAAGCTCTTGC 61.192 66.667 0.00 0.00 37.29 4.01
4319 5050 1.601903 TGAGCCAAGTACTGTTTTGCG 59.398 47.619 0.00 0.00 0.00 4.85
4396 5127 1.668101 AAACCGGTTTTTGCGCTCCA 61.668 50.000 26.87 0.00 0.00 3.86
4634 5365 0.704664 AGTTTTCCCAGGATCCACCC 59.295 55.000 15.82 0.00 40.05 4.61
4649 5380 4.787551 TGGTATTCACAACCACTGAGTTT 58.212 39.130 0.00 0.00 42.10 2.66
4821 5552 1.212751 GAACCAGCGATGCCCAAAC 59.787 57.895 0.00 0.00 0.00 2.93
4924 5733 9.719279 CAATGATTTTAGAAGAATCTCAGAAGC 57.281 33.333 0.00 0.00 37.10 3.86
4990 6630 8.783093 CATTAGACCAACATCAGACAAAAGTAA 58.217 33.333 0.00 0.00 0.00 2.24
5013 6653 6.293407 CGGTCACAATGAACTAAACAGACATT 60.293 38.462 0.00 0.00 30.24 2.71
5165 6808 9.271828 GTGGTTTTGGAATCTCAATGTAATTTT 57.728 29.630 0.00 0.00 31.22 1.82
5175 6818 3.563808 CGTTCAGTGGTTTTGGAATCTCA 59.436 43.478 0.00 0.00 0.00 3.27
5186 6829 0.319297 GTAGCGGTCGTTCAGTGGTT 60.319 55.000 0.00 0.00 0.00 3.67
5356 7000 6.602406 AGATTTGCTGTCAGATGCTTTAGATT 59.398 34.615 3.32 0.00 0.00 2.40
5361 7005 3.126514 CGAGATTTGCTGTCAGATGCTTT 59.873 43.478 3.32 0.00 0.00 3.51
5374 7018 3.611433 GTCATGTGGCGAGATTTGC 57.389 52.632 0.00 0.00 0.00 3.68
5441 7085 0.586802 GCTGTGGTCAACGGAACTTC 59.413 55.000 0.00 0.00 37.33 3.01
5455 7099 0.032678 AGTTCGTCTGTCTGGCTGTG 59.967 55.000 0.00 0.00 0.00 3.66
5466 7110 0.752376 GATCCTCCCCGAGTTCGTCT 60.752 60.000 0.48 0.00 37.74 4.18


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

AutoCloner maintained by Alex Coulton.