Multiple sequence alignment - TraesCS4A01G120700

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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 TraesCS4A01G120700 chr4A 100.000 5239 0 0 1 5239 148763269 148758031 0.000000e+00 9675.0
1 TraesCS4A01G120700 chr4A 98.918 1386 14 1 1986 3371 686938993 686937609 0.000000e+00 2475.0
2 TraesCS4A01G120700 chr5B 99.062 1386 12 1 1986 3371 334291072 334289688 0.000000e+00 2486.0
3 TraesCS4A01G120700 chr5B 89.925 268 27 0 1989 2256 523671096 523670829 3.880000e-91 346.0
4 TraesCS4A01G120700 chr4D 90.436 1882 114 26 3369 5239 323352828 323354654 0.000000e+00 2418.0
5 TraesCS4A01G120700 chr4D 93.474 521 24 5 1217 1727 323352063 323352583 0.000000e+00 765.0
6 TraesCS4A01G120700 chr4D 88.454 485 32 7 675 1154 323351598 323352063 9.850000e-157 564.0
7 TraesCS4A01G120700 chr4D 91.176 408 36 0 270 677 323350496 323350903 5.930000e-154 555.0
8 TraesCS4A01G120700 chr4D 90.950 221 18 2 1752 1971 323352580 323352799 3.970000e-76 296.0
9 TraesCS4A01G120700 chr4D 85.366 82 11 1 188 269 445577289 445577209 3.360000e-12 84.2
10 TraesCS4A01G120700 chr4D 85.000 80 12 0 189 268 221624592 221624671 1.210000e-11 82.4
11 TraesCS4A01G120700 chr6B 90.984 1087 88 2 2295 3371 279031934 279030848 0.000000e+00 1456.0
12 TraesCS4A01G120700 chr6B 88.146 329 34 5 1987 2314 279032275 279031951 2.290000e-103 387.0
13 TraesCS4A01G120700 chr6B 95.604 91 2 2 4804 4893 32295730 32295641 1.520000e-30 145.0
14 TraesCS4A01G120700 chr2D 84.379 1402 189 18 1989 3371 617220289 617218899 0.000000e+00 1349.0
15 TraesCS4A01G120700 chr2D 88.034 117 7 7 4772 4882 617538392 617538277 1.180000e-26 132.0
16 TraesCS4A01G120700 chr2D 87.342 79 7 3 5146 5223 13229046 13228970 2.600000e-13 87.9
17 TraesCS4A01G120700 chr7B 88.316 1087 117 5 2295 3371 657549860 657550946 0.000000e+00 1295.0
18 TraesCS4A01G120700 chr7B 89.809 314 26 5 1985 2296 657549519 657549828 1.060000e-106 398.0
19 TraesCS4A01G120700 chr6D 82.621 1404 213 20 1988 3371 19501269 19502661 0.000000e+00 1212.0
20 TraesCS4A01G120700 chr6D 93.684 95 2 4 4804 4897 17998808 17998717 7.070000e-29 139.0
21 TraesCS4A01G120700 chr6D 97.368 76 1 1 1 76 79196968 79196894 1.530000e-25 128.0
22 TraesCS4A01G120700 chr6D 93.023 86 5 1 1 85 199748429 199748344 1.980000e-24 124.0
23 TraesCS4A01G120700 chr6D 87.879 66 8 0 204 269 11929088 11929023 1.560000e-10 78.7
24 TraesCS4A01G120700 chr1B 86.753 1087 110 10 2295 3371 407249284 407248222 0.000000e+00 1179.0
25 TraesCS4A01G120700 chr1B 89.457 313 29 3 1986 2296 407249626 407249316 4.920000e-105 392.0
26 TraesCS4A01G120700 chr4B 92.560 793 40 9 3821 4599 403623017 403623804 0.000000e+00 1120.0
27 TraesCS4A01G120700 chr4B 96.569 583 16 4 891 1471 403621544 403622124 0.000000e+00 963.0
28 TraesCS4A01G120700 chr4B 93.304 448 23 3 4793 5239 403624059 403624500 0.000000e+00 654.0
29 TraesCS4A01G120700 chr4B 96.748 369 11 1 3455 3822 403622566 403622934 9.640000e-172 614.0
30 TraesCS4A01G120700 chr4B 89.877 405 37 1 270 674 403619595 403619995 7.780000e-143 518.0
31 TraesCS4A01G120700 chr4B 91.228 285 24 1 1699 1982 403622138 403622422 2.290000e-103 387.0
32 TraesCS4A01G120700 chr4B 85.410 329 39 7 1989 2314 481521338 481521016 3.020000e-87 333.0
33 TraesCS4A01G120700 chr4B 86.161 224 28 3 675 897 403620482 403620703 6.780000e-59 239.0
34 TraesCS4A01G120700 chr4B 89.444 180 6 8 4583 4759 403623894 403624063 1.140000e-51 215.0
35 TraesCS4A01G120700 chr4B 95.745 94 2 1 3369 3460 403622424 403622517 3.270000e-32 150.0
36 TraesCS4A01G120700 chr7D 83.939 1046 158 2 2335 3371 13887230 13888274 0.000000e+00 992.0
37 TraesCS4A01G120700 chr7D 84.749 977 140 1 2404 3371 48268640 48269616 0.000000e+00 970.0
38 TraesCS4A01G120700 chr7D 83.399 253 30 1 17 269 600927774 600927534 1.900000e-54 224.0
39 TraesCS4A01G120700 chr7D 98.649 74 1 0 1 74 229103786 229103859 1.180000e-26 132.0
40 TraesCS4A01G120700 chr7D 97.297 74 2 0 1 74 130016011 130015938 5.510000e-25 126.0
41 TraesCS4A01G120700 chr1D 83.779 1048 159 3 2334 3371 77841811 77842857 0.000000e+00 983.0
42 TraesCS4A01G120700 chr1D 86.047 301 38 4 1987 2285 77841435 77841733 2.350000e-83 320.0
43 TraesCS4A01G120700 chr1A 98.366 306 5 0 1986 2291 589369586 589369281 5.970000e-149 538.0
44 TraesCS4A01G120700 chr1A 97.297 74 2 0 1 74 149051305 149051378 5.510000e-25 126.0
45 TraesCS4A01G120700 chr6A 93.000 100 4 3 4794 4890 18580880 18580781 5.470000e-30 143.0
46 TraesCS4A01G120700 chr6A 92.157 102 4 4 4793 4893 520853755 520853853 1.970000e-29 141.0
47 TraesCS4A01G120700 chr6A 88.333 60 5 2 224 282 237124462 237124404 2.620000e-08 71.3
48 TraesCS4A01G120700 chr3A 94.624 93 4 1 4792 4884 25367995 25368086 5.470000e-30 143.0
49 TraesCS4A01G120700 chr3B 90.566 106 5 4 4777 4881 5587444 5587343 9.150000e-28 135.0
50 TraesCS4A01G120700 chr3B 75.648 193 42 5 78 269 322730779 322730591 2.010000e-14 91.6
51 TraesCS4A01G120700 chr5D 97.297 74 2 0 1 74 179554945 179555018 5.510000e-25 126.0
52 TraesCS4A01G120700 chr5D 92.222 90 2 5 1 88 257453983 257454069 7.120000e-24 122.0
53 TraesCS4A01G120700 chr5D 75.773 194 41 6 77 267 104281228 104281418 5.590000e-15 93.5
54 TraesCS4A01G120700 chr3D 96.104 77 2 1 1 76 151117692 151117616 1.980000e-24 124.0
55 TraesCS4A01G120700 chr2A 95.000 80 3 1 1 79 87917719 87917640 1.980000e-24 124.0
56 TraesCS4A01G120700 chr2A 88.750 80 6 3 5146 5224 15270379 15270302 1.550000e-15 95.3
57 TraesCS4A01G120700 chr2B 87.500 80 7 3 5146 5224 23878496 23878419 7.230000e-14 89.8
58 TraesCS4A01G120700 chr2B 83.908 87 10 3 186 269 247515144 247515229 4.350000e-11 80.5
59 TraesCS4A01G120700 chr2B 83.333 84 14 0 186 269 449466586 449466669 1.560000e-10 78.7


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 TraesCS4A01G120700 chr4A 148758031 148763269 5238 True 9675.0 9675 100.0000 1 5239 1 chr4A.!!$R1 5238
1 TraesCS4A01G120700 chr4A 686937609 686938993 1384 True 2475.0 2475 98.9180 1986 3371 1 chr4A.!!$R2 1385
2 TraesCS4A01G120700 chr5B 334289688 334291072 1384 True 2486.0 2486 99.0620 1986 3371 1 chr5B.!!$R1 1385
3 TraesCS4A01G120700 chr4D 323350496 323354654 4158 False 919.6 2418 90.8980 270 5239 5 chr4D.!!$F2 4969
4 TraesCS4A01G120700 chr6B 279030848 279032275 1427 True 921.5 1456 89.5650 1987 3371 2 chr6B.!!$R2 1384
5 TraesCS4A01G120700 chr2D 617218899 617220289 1390 True 1349.0 1349 84.3790 1989 3371 1 chr2D.!!$R2 1382
6 TraesCS4A01G120700 chr7B 657549519 657550946 1427 False 846.5 1295 89.0625 1985 3371 2 chr7B.!!$F1 1386
7 TraesCS4A01G120700 chr6D 19501269 19502661 1392 False 1212.0 1212 82.6210 1988 3371 1 chr6D.!!$F1 1383
8 TraesCS4A01G120700 chr1B 407248222 407249626 1404 True 785.5 1179 88.1050 1986 3371 2 chr1B.!!$R1 1385
9 TraesCS4A01G120700 chr4B 403619595 403624500 4905 False 540.0 1120 92.4040 270 5239 9 chr4B.!!$F1 4969
10 TraesCS4A01G120700 chr7D 13887230 13888274 1044 False 992.0 992 83.9390 2335 3371 1 chr7D.!!$F1 1036
11 TraesCS4A01G120700 chr7D 48268640 48269616 976 False 970.0 970 84.7490 2404 3371 1 chr7D.!!$F2 967
12 TraesCS4A01G120700 chr1D 77841435 77842857 1422 False 651.5 983 84.9130 1987 3371 2 chr1D.!!$F1 1384

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
237 238 0.103572 GGGAACCGCGCTACTGATAA 59.896 55.0 5.56 0.00 40.86 1.75 F
244 245 0.389391 GCGCTACTGATAAGCCTCCA 59.611 55.0 0.00 0.00 36.60 3.86 F
643 644 0.392706 TGAGCTCTTGAAACTGCGGA 59.607 50.0 16.19 0.00 0.00 5.54 F
684 1382 0.535335 TCATGGGCACGAACTAGTCC 59.465 55.0 0.00 0.00 0.00 3.85 F
1574 3128 0.675522 AGAAACGGCATGGTTACGGG 60.676 55.0 0.00 0.00 0.00 5.28 F
1844 3406 0.681243 GTCAGGGGCACATTTCTCCC 60.681 60.0 0.00 0.00 39.67 4.30 F
3563 5252 0.322187 AATCCCACAGTGGTTACCGC 60.322 55.0 18.82 6.88 35.17 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 3391 0.251787 AACAGGGAGAAATGTGCCCC 60.252 55.000 0.00 0.0 43.08 5.80 R
1871 3433 4.900684 TCCGTAAACATGACAGGAAATCA 58.099 39.130 0.00 0.0 0.00 2.57 R
2152 3732 5.415221 GTTTTGGGTGACATCAAGTTTTCA 58.585 37.500 0.00 0.0 0.00 2.69 R
2621 4255 6.098982 TGGGATGGACAAAATTTACACTGTTT 59.901 34.615 0.00 0.0 0.00 2.83 R
3562 5251 2.675348 GAGCATCAACAACAGGAGTAGC 59.325 50.000 0.00 0.0 33.17 3.58 R
3781 5474 1.021390 CGGCCAGATCAACACTCCAC 61.021 60.000 2.24 0.0 0.00 4.02 R
4919 6819 0.745845 CAAGGCAAGCTGCGAGGTAT 60.746 55.000 0.00 0.0 46.21 2.73 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
68 69 9.734984 TTATAGATACATTGGAGACGTATCAGA 57.265 33.333 12.92 0.00 42.52 3.27
69 70 6.961360 AGATACATTGGAGACGTATCAGAA 57.039 37.500 12.92 4.48 42.52 3.02
70 71 7.348080 AGATACATTGGAGACGTATCAGAAA 57.652 36.000 12.92 3.72 42.52 2.52
71 72 7.429633 AGATACATTGGAGACGTATCAGAAAG 58.570 38.462 12.92 3.97 42.52 2.62
72 73 4.184629 ACATTGGAGACGTATCAGAAAGC 58.815 43.478 12.92 0.00 0.00 3.51
73 74 3.953712 TTGGAGACGTATCAGAAAGCA 57.046 42.857 12.92 0.00 0.00 3.91
74 75 3.232213 TGGAGACGTATCAGAAAGCAC 57.768 47.619 12.92 0.00 0.00 4.40
75 76 2.560981 TGGAGACGTATCAGAAAGCACA 59.439 45.455 12.92 0.00 0.00 4.57
76 77 3.195610 TGGAGACGTATCAGAAAGCACAT 59.804 43.478 12.92 0.00 0.00 3.21
77 78 4.184629 GGAGACGTATCAGAAAGCACATT 58.815 43.478 12.92 0.00 0.00 2.71
78 79 4.033358 GGAGACGTATCAGAAAGCACATTG 59.967 45.833 12.92 0.00 0.00 2.82
79 80 3.372206 AGACGTATCAGAAAGCACATTGC 59.628 43.478 0.00 0.00 45.46 3.56
93 94 4.246458 GCACATTGCTACTATACCTAGCC 58.754 47.826 0.00 0.00 40.96 3.93
94 95 4.822026 CACATTGCTACTATACCTAGCCC 58.178 47.826 0.00 0.00 36.54 5.19
95 96 3.510360 ACATTGCTACTATACCTAGCCCG 59.490 47.826 0.00 0.00 36.54 6.13
96 97 2.211250 TGCTACTATACCTAGCCCGG 57.789 55.000 0.00 0.00 36.54 5.73
97 98 1.426598 TGCTACTATACCTAGCCCGGT 59.573 52.381 0.00 0.00 41.10 5.28
98 99 1.817447 GCTACTATACCTAGCCCGGTG 59.183 57.143 0.00 0.00 37.93 4.94
99 100 2.444421 CTACTATACCTAGCCCGGTGG 58.556 57.143 0.00 0.00 37.93 4.61
100 101 0.559699 ACTATACCTAGCCCGGTGGT 59.440 55.000 0.00 5.80 37.93 4.16
101 102 1.062658 ACTATACCTAGCCCGGTGGTT 60.063 52.381 0.00 0.00 37.93 3.67
102 103 2.177669 ACTATACCTAGCCCGGTGGTTA 59.822 50.000 0.00 0.00 37.93 2.85
103 104 1.417288 ATACCTAGCCCGGTGGTTAC 58.583 55.000 0.00 0.00 37.93 2.50
104 105 1.037030 TACCTAGCCCGGTGGTTACG 61.037 60.000 0.00 0.00 37.93 3.18
111 112 4.317444 CGGTGGTTACGGTGGCCA 62.317 66.667 0.00 0.00 0.00 5.36
113 114 2.670592 GTGGTTACGGTGGCCACC 60.671 66.667 40.56 40.56 44.95 4.61
123 124 2.034066 TGGCCACCACTTAGCAGC 59.966 61.111 0.00 0.00 0.00 5.25
124 125 2.034066 GGCCACCACTTAGCAGCA 59.966 61.111 0.00 0.00 0.00 4.41
125 126 1.603455 GGCCACCACTTAGCAGCAA 60.603 57.895 0.00 0.00 0.00 3.91
126 127 1.581447 GCCACCACTTAGCAGCAAC 59.419 57.895 0.00 0.00 0.00 4.17
127 128 1.868997 CCACCACTTAGCAGCAACG 59.131 57.895 0.00 0.00 0.00 4.10
128 129 0.884704 CCACCACTTAGCAGCAACGT 60.885 55.000 0.00 0.00 0.00 3.99
129 130 0.512952 CACCACTTAGCAGCAACGTC 59.487 55.000 0.00 0.00 0.00 4.34
130 131 0.944311 ACCACTTAGCAGCAACGTCG 60.944 55.000 0.00 0.00 0.00 5.12
131 132 0.944311 CCACTTAGCAGCAACGTCGT 60.944 55.000 0.00 0.00 0.00 4.34
132 133 0.859232 CACTTAGCAGCAACGTCGTT 59.141 50.000 4.40 4.40 0.00 3.85
133 134 1.260561 CACTTAGCAGCAACGTCGTTT 59.739 47.619 8.15 0.00 0.00 3.60
134 135 1.260561 ACTTAGCAGCAACGTCGTTTG 59.739 47.619 8.15 6.66 0.00 2.93
135 136 0.584396 TTAGCAGCAACGTCGTTTGG 59.416 50.000 8.15 0.00 0.00 3.28
136 137 1.837538 TAGCAGCAACGTCGTTTGGC 61.838 55.000 8.15 10.05 0.00 4.52
137 138 2.712539 CAGCAACGTCGTTTGGCA 59.287 55.556 18.99 0.00 0.00 4.92
138 139 1.654137 CAGCAACGTCGTTTGGCAC 60.654 57.895 18.99 4.13 0.00 5.01
139 140 2.109739 AGCAACGTCGTTTGGCACA 61.110 52.632 18.99 0.00 0.00 4.57
152 153 0.958091 TGGCACAAACATGGTACTGC 59.042 50.000 4.31 4.31 31.92 4.40
153 154 1.247567 GGCACAAACATGGTACTGCT 58.752 50.000 11.32 0.00 0.00 4.24
154 155 2.224646 TGGCACAAACATGGTACTGCTA 60.225 45.455 11.32 3.95 31.92 3.49
155 156 2.817258 GGCACAAACATGGTACTGCTAA 59.183 45.455 11.32 0.00 0.00 3.09
156 157 3.254657 GGCACAAACATGGTACTGCTAAA 59.745 43.478 11.32 0.00 0.00 1.85
157 158 4.082245 GGCACAAACATGGTACTGCTAAAT 60.082 41.667 11.32 0.00 0.00 1.40
158 159 4.858692 GCACAAACATGGTACTGCTAAATG 59.141 41.667 5.49 0.00 0.00 2.32
159 160 5.564651 GCACAAACATGGTACTGCTAAATGT 60.565 40.000 5.49 0.00 32.99 2.71
160 161 6.348950 GCACAAACATGGTACTGCTAAATGTA 60.349 38.462 5.49 0.00 31.44 2.29
161 162 7.628366 GCACAAACATGGTACTGCTAAATGTAT 60.628 37.037 5.49 0.00 31.44 2.29
162 163 8.888716 CACAAACATGGTACTGCTAAATGTATA 58.111 33.333 0.00 0.00 31.44 1.47
163 164 9.109393 ACAAACATGGTACTGCTAAATGTATAG 57.891 33.333 0.00 0.00 31.44 1.31
164 165 7.730364 AACATGGTACTGCTAAATGTATAGC 57.270 36.000 0.00 0.00 46.78 2.97
174 175 5.462405 GCTAAATGTATAGCAGTAGCGAGT 58.538 41.667 1.64 0.00 46.06 4.18
175 176 5.921408 GCTAAATGTATAGCAGTAGCGAGTT 59.079 40.000 1.64 0.00 46.06 3.01
176 177 6.088350 GCTAAATGTATAGCAGTAGCGAGTTC 59.912 42.308 1.64 0.00 46.06 3.01
177 178 8.726209 GCTAAATGTATAGCAGTAGCGAGTTCC 61.726 44.444 1.64 0.00 46.06 3.62
182 183 1.565305 GCAGTAGCGAGTTCCAGATG 58.435 55.000 0.00 0.00 0.00 2.90
183 184 1.804372 GCAGTAGCGAGTTCCAGATGG 60.804 57.143 0.00 0.00 0.00 3.51
184 185 0.461961 AGTAGCGAGTTCCAGATGGC 59.538 55.000 0.00 0.00 34.44 4.40
185 186 0.530870 GTAGCGAGTTCCAGATGGCC 60.531 60.000 0.00 0.00 34.44 5.36
186 187 0.975556 TAGCGAGTTCCAGATGGCCA 60.976 55.000 8.56 8.56 34.44 5.36
187 188 2.109126 GCGAGTTCCAGATGGCCAC 61.109 63.158 8.16 1.58 34.44 5.01
188 189 1.811266 CGAGTTCCAGATGGCCACG 60.811 63.158 8.16 0.00 34.44 4.94
189 190 2.045926 AGTTCCAGATGGCCACGC 60.046 61.111 8.16 2.66 34.44 5.34
190 191 2.045926 GTTCCAGATGGCCACGCT 60.046 61.111 8.16 5.69 34.44 5.07
191 192 1.220749 GTTCCAGATGGCCACGCTA 59.779 57.895 8.16 0.00 34.44 4.26
192 193 1.090052 GTTCCAGATGGCCACGCTAC 61.090 60.000 8.16 0.00 34.44 3.58
193 194 1.264749 TTCCAGATGGCCACGCTACT 61.265 55.000 8.16 0.00 34.44 2.57
194 195 0.396556 TCCAGATGGCCACGCTACTA 60.397 55.000 8.16 0.00 34.44 1.82
195 196 0.681733 CCAGATGGCCACGCTACTAT 59.318 55.000 8.16 0.00 0.00 2.12
196 197 1.893137 CCAGATGGCCACGCTACTATA 59.107 52.381 8.16 0.00 0.00 1.31
197 198 2.299013 CCAGATGGCCACGCTACTATAA 59.701 50.000 8.16 0.00 0.00 0.98
198 199 3.244078 CCAGATGGCCACGCTACTATAAA 60.244 47.826 8.16 0.00 0.00 1.40
199 200 3.990469 CAGATGGCCACGCTACTATAAAG 59.010 47.826 8.16 0.00 0.00 1.85
200 201 2.234300 TGGCCACGCTACTATAAAGC 57.766 50.000 0.00 0.00 36.60 3.51
201 202 1.483004 TGGCCACGCTACTATAAAGCA 59.517 47.619 0.00 0.00 40.08 3.91
202 203 2.135933 GGCCACGCTACTATAAAGCAG 58.864 52.381 0.00 3.53 40.08 4.24
203 204 1.527311 GCCACGCTACTATAAAGCAGC 59.473 52.381 7.35 0.00 40.08 5.25
204 205 2.821546 CCACGCTACTATAAAGCAGCA 58.178 47.619 0.00 0.00 41.53 4.41
205 206 2.797156 CCACGCTACTATAAAGCAGCAG 59.203 50.000 0.00 0.00 41.53 4.24
206 207 3.448686 CACGCTACTATAAAGCAGCAGT 58.551 45.455 0.00 0.00 41.53 4.40
207 208 4.499188 CCACGCTACTATAAAGCAGCAGTA 60.499 45.833 0.00 0.00 41.53 2.74
208 209 4.677378 CACGCTACTATAAAGCAGCAGTAG 59.323 45.833 11.02 11.02 41.53 2.57
222 223 4.752879 GTAGCGCGTGCAGGGGAA 62.753 66.667 25.42 10.69 46.23 3.97
223 224 4.752879 TAGCGCGTGCAGGGGAAC 62.753 66.667 25.42 9.89 46.23 3.62
235 236 2.499685 GGGAACCGCGCTACTGAT 59.500 61.111 5.56 0.00 40.86 2.90
236 237 1.737816 GGGAACCGCGCTACTGATA 59.262 57.895 5.56 0.00 40.86 2.15
237 238 0.103572 GGGAACCGCGCTACTGATAA 59.896 55.000 5.56 0.00 40.86 1.75
238 239 1.488527 GGAACCGCGCTACTGATAAG 58.511 55.000 5.56 0.00 0.00 1.73
239 240 0.853419 GAACCGCGCTACTGATAAGC 59.147 55.000 5.56 0.00 36.60 3.09
240 241 0.529992 AACCGCGCTACTGATAAGCC 60.530 55.000 5.56 0.00 36.60 4.35
241 242 1.364171 CCGCGCTACTGATAAGCCT 59.636 57.895 5.56 0.00 36.60 4.58
242 243 0.664767 CCGCGCTACTGATAAGCCTC 60.665 60.000 5.56 0.00 36.60 4.70
243 244 0.664767 CGCGCTACTGATAAGCCTCC 60.665 60.000 5.56 0.00 36.60 4.30
244 245 0.389391 GCGCTACTGATAAGCCTCCA 59.611 55.000 0.00 0.00 36.60 3.86
245 246 1.870167 GCGCTACTGATAAGCCTCCAC 60.870 57.143 0.00 0.00 36.60 4.02
246 247 1.269831 CGCTACTGATAAGCCTCCACC 60.270 57.143 0.00 0.00 36.60 4.61
247 248 2.043227 GCTACTGATAAGCCTCCACCT 58.957 52.381 0.00 0.00 33.73 4.00
248 249 3.231818 GCTACTGATAAGCCTCCACCTA 58.768 50.000 0.00 0.00 33.73 3.08
249 250 3.835395 GCTACTGATAAGCCTCCACCTAT 59.165 47.826 0.00 0.00 33.73 2.57
250 251 5.017490 GCTACTGATAAGCCTCCACCTATA 58.983 45.833 0.00 0.00 33.73 1.31
251 252 5.480772 GCTACTGATAAGCCTCCACCTATAA 59.519 44.000 0.00 0.00 33.73 0.98
252 253 6.350612 GCTACTGATAAGCCTCCACCTATAAG 60.351 46.154 0.00 0.00 33.73 1.73
253 254 4.841246 ACTGATAAGCCTCCACCTATAAGG 59.159 45.833 0.00 0.00 42.49 2.69
318 319 9.905713 AAGGAATACAAAAGTGCTCATCTATTA 57.094 29.630 0.00 0.00 0.00 0.98
335 336 9.612066 TCATCTATTAACAATAATCAGCACACA 57.388 29.630 0.00 0.00 33.75 3.72
443 444 8.622948 AGGATTAGCTAACTAAATTACCATGC 57.377 34.615 8.70 0.00 41.62 4.06
473 474 6.263842 CACATCACAAATTGCAGGGATACTAT 59.736 38.462 0.00 0.00 0.00 2.12
477 478 8.394971 TCACAAATTGCAGGGATACTATATTG 57.605 34.615 0.00 0.00 0.00 1.90
487 488 7.220030 CAGGGATACTATATTGAGCACAACTT 58.780 38.462 0.00 0.00 38.90 2.66
540 541 4.733077 TTCAGGTAAACAAAGATGGGGA 57.267 40.909 0.00 0.00 0.00 4.81
585 586 5.321927 TGCAAGCATGAATAGGATGATGAT 58.678 37.500 0.00 0.00 0.00 2.45
602 603 3.433984 ATGGTGGTGTGTGCAGGCA 62.434 57.895 0.00 0.00 0.00 4.75
603 604 2.598394 GGTGGTGTGTGCAGGCAT 60.598 61.111 0.00 0.00 0.00 4.40
639 640 2.999355 GCCTAGTGAGCTCTTGAAACTG 59.001 50.000 16.19 4.80 0.00 3.16
641 642 1.506493 AGTGAGCTCTTGAAACTGCG 58.494 50.000 16.19 0.00 0.00 5.18
643 644 0.392706 TGAGCTCTTGAAACTGCGGA 59.607 50.000 16.19 0.00 0.00 5.54
649 650 1.153329 TTGAAACTGCGGACACGGT 60.153 52.632 0.00 0.00 41.36 4.83
679 1377 2.513753 TGAATTTCATGGGCACGAACT 58.486 42.857 0.00 0.00 0.00 3.01
684 1382 0.535335 TCATGGGCACGAACTAGTCC 59.465 55.000 0.00 0.00 0.00 3.85
686 1384 1.754803 CATGGGCACGAACTAGTCCTA 59.245 52.381 0.00 0.00 0.00 2.94
698 1396 3.280295 ACTAGTCCTAGTGATGACGTGG 58.720 50.000 6.19 0.00 44.11 4.94
702 1400 1.831106 TCCTAGTGATGACGTGGCAAT 59.169 47.619 0.00 0.00 0.00 3.56
712 1410 2.029288 CGTGGCAATGTGAGCTCGT 61.029 57.895 9.64 0.00 0.00 4.18
733 1431 3.126858 GTCAAGATTCGTGCAATGGCTTA 59.873 43.478 0.00 0.00 41.91 3.09
749 1447 2.893637 GCTTAGAAGGCATTCAGACGA 58.106 47.619 14.34 0.00 37.94 4.20
756 1454 1.059994 GCATTCAGACGAAGCAGCG 59.940 57.895 0.00 0.00 33.74 5.18
758 1456 1.070821 CATTCAGACGAAGCAGCGAA 58.929 50.000 5.21 0.00 33.74 4.70
761 1459 2.647529 TCAGACGAAGCAGCGAAATA 57.352 45.000 5.21 0.00 34.83 1.40
763 1461 2.860136 TCAGACGAAGCAGCGAAATATG 59.140 45.455 5.21 0.00 34.83 1.78
822 1521 9.862371 ATAGTCTATTCGAAGCATTATTGGTAG 57.138 33.333 3.35 0.00 32.06 3.18
824 1523 8.204836 AGTCTATTCGAAGCATTATTGGTAGTT 58.795 33.333 3.35 0.00 32.06 2.24
861 1564 4.871513 TGATAGCATCACGACAATCTACC 58.128 43.478 0.00 0.00 33.59 3.18
1297 2848 3.061403 CGTAAAGCATCGCTAACCTTACG 60.061 47.826 13.18 13.18 41.59 3.18
1319 2870 3.491619 GCTAGCAGTGGATCTTGATTCGA 60.492 47.826 10.63 0.00 0.00 3.71
1324 2875 4.248859 CAGTGGATCTTGATTCGAACTGT 58.751 43.478 0.00 0.00 0.00 3.55
1400 2951 4.155644 GCCTGAGAAGAAGAAAAGATGGTG 59.844 45.833 0.00 0.00 0.00 4.17
1525 3079 2.481795 CCTGGAATGCTTATTTTGGCCG 60.482 50.000 0.00 0.00 0.00 6.13
1526 3080 1.134848 TGGAATGCTTATTTTGGCCGC 60.135 47.619 0.00 0.00 0.00 6.53
1541 3095 1.090052 GCCGCCGCTTAGACTTTCAT 61.090 55.000 0.00 0.00 0.00 2.57
1574 3128 0.675522 AGAAACGGCATGGTTACGGG 60.676 55.000 0.00 0.00 0.00 5.28
1643 3197 1.047002 TGCCATGGTGGTTTTGAAGG 58.953 50.000 14.67 0.00 40.46 3.46
1644 3198 1.337118 GCCATGGTGGTTTTGAAGGA 58.663 50.000 14.67 0.00 40.46 3.36
1722 3283 5.284660 CAGAATTTGCTGCTCAATTAACGAC 59.715 40.000 0.00 0.00 34.12 4.34
1735 3296 7.465916 GCTCAATTAACGACAATGCTATCTTGA 60.466 37.037 0.00 0.00 0.00 3.02
1749 3310 7.111247 TGCTATCTTGATTTTGGTAATTGGG 57.889 36.000 0.00 0.00 0.00 4.12
1779 3340 1.676006 ACCTTCTTTTGTCAGGCAACG 59.324 47.619 0.00 0.00 46.39 4.10
1821 3383 5.107109 TGTCAAATTCCTGTTGTGATTCG 57.893 39.130 0.00 0.00 0.00 3.34
1829 3391 1.800586 CTGTTGTGATTCGGTGGTCAG 59.199 52.381 0.00 0.00 0.00 3.51
1835 3397 3.268103 ATTCGGTGGTCAGGGGCAC 62.268 63.158 0.00 0.00 0.00 5.01
1844 3406 0.681243 GTCAGGGGCACATTTCTCCC 60.681 60.000 0.00 0.00 39.67 4.30
1858 3420 6.093219 CACATTTCTCCCTGTTGAATAGTCTG 59.907 42.308 0.00 0.00 0.00 3.51
1871 3433 4.532126 TGAATAGTCTGGTTCACTCATGGT 59.468 41.667 0.00 0.00 29.93 3.55
1892 3454 4.142687 GGTGATTTCCTGTCATGTTTACGG 60.143 45.833 0.00 0.00 0.00 4.02
1897 3459 4.280436 TCCTGTCATGTTTACGGAATGT 57.720 40.909 0.00 0.00 0.00 2.71
1957 3519 4.613925 ACTTCTTGATGCACAGAGAAGA 57.386 40.909 27.87 13.32 41.06 2.87
1978 3540 8.390921 AGAAGAAACAATACTTCTTGGGGAATA 58.609 33.333 0.00 0.00 46.86 1.75
2152 3732 1.995542 AGGAACAACAGATCATGGGGT 59.004 47.619 0.00 0.00 0.00 4.95
2973 4608 5.068198 CAGCCAAGCATACATGGATTTAGTT 59.932 40.000 0.00 0.00 36.75 2.24
3468 5153 6.398918 ACTCTGCATTAGTACTTGGTACTTG 58.601 40.000 14.27 9.51 45.68 3.16
3469 5154 5.730550 TCTGCATTAGTACTTGGTACTTGG 58.269 41.667 14.27 7.04 45.68 3.61
3470 5155 5.482526 TCTGCATTAGTACTTGGTACTTGGA 59.517 40.000 14.27 8.86 45.68 3.53
3471 5156 5.730550 TGCATTAGTACTTGGTACTTGGAG 58.269 41.667 14.27 5.65 45.68 3.86
3472 5157 4.571176 GCATTAGTACTTGGTACTTGGAGC 59.429 45.833 14.27 10.44 45.68 4.70
3473 5158 5.627040 GCATTAGTACTTGGTACTTGGAGCT 60.627 44.000 14.27 0.00 45.68 4.09
3474 5159 6.407202 CATTAGTACTTGGTACTTGGAGCTT 58.593 40.000 14.27 0.00 45.68 3.74
3475 5160 4.538746 AGTACTTGGTACTTGGAGCTTC 57.461 45.455 4.72 0.00 45.68 3.86
3476 5161 3.901844 AGTACTTGGTACTTGGAGCTTCA 59.098 43.478 0.00 0.00 45.68 3.02
3562 5251 1.002659 TCAATCCCACAGTGGTTACCG 59.997 52.381 18.82 2.59 35.17 4.02
3563 5252 0.322187 AATCCCACAGTGGTTACCGC 60.322 55.000 18.82 6.88 35.17 5.68
3573 5262 1.274447 GTGGTTACCGCTACTCCTGTT 59.726 52.381 7.82 0.00 0.00 3.16
3577 5266 2.735134 GTTACCGCTACTCCTGTTGTTG 59.265 50.000 0.00 0.00 0.00 3.33
3674 5367 7.921786 TTTGTTGCATTTCTAGCTAGTGTAT 57.078 32.000 20.10 9.39 0.00 2.29
3781 5474 3.438434 GGTTCAAGAAGGAAGCTGCTAAG 59.562 47.826 0.90 0.00 40.99 2.18
3848 5625 3.954904 GGAGTACTGCAGGTTGATCTCTA 59.045 47.826 19.93 0.00 0.00 2.43
4043 5820 5.488341 TGCATAGAAGAAGGTAACAAGACC 58.512 41.667 0.00 0.00 40.08 3.85
4139 5916 3.129502 GCTGATCGCTGCTTGGCA 61.130 61.111 0.00 0.00 36.21 4.92
4193 5976 0.178990 AGGCTTTTCTTCGGGTGCTT 60.179 50.000 0.00 0.00 0.00 3.91
4194 5977 1.073284 AGGCTTTTCTTCGGGTGCTTA 59.927 47.619 0.00 0.00 0.00 3.09
4202 5985 0.398696 TTCGGGTGCTTAAGCTGGAA 59.601 50.000 26.90 19.68 42.66 3.53
4231 6014 3.784178 TCTGGGACATGAGTTCTTCTCT 58.216 45.455 0.00 0.00 43.13 3.10
4280 6070 0.035439 ACCCTGCATTACTTGGACGG 60.035 55.000 0.00 0.00 0.00 4.79
4287 6077 4.439057 TGCATTACTTGGACGGAATAGAC 58.561 43.478 0.00 0.00 0.00 2.59
4323 6114 5.324409 TCAGCATTTTACTGTCATTTCCCT 58.676 37.500 0.00 0.00 36.50 4.20
4342 6133 4.019321 TCCCTTGTATCTTGGTTTCTCTGG 60.019 45.833 0.00 0.00 0.00 3.86
4442 6233 5.717119 TCACGTATCTAGGTTTCTTTGGTC 58.283 41.667 0.00 0.00 0.00 4.02
4444 6235 5.577164 CACGTATCTAGGTTTCTTTGGTCAG 59.423 44.000 0.00 0.00 0.00 3.51
4448 6239 1.308998 AGGTTTCTTTGGTCAGCACG 58.691 50.000 0.00 0.00 0.00 5.34
4525 6316 1.856265 CTGAAAACCTCGGCTGCACC 61.856 60.000 0.50 0.00 0.00 5.01
4546 6337 5.121142 CACCGTCGGTATAGATGTTTTTGTT 59.879 40.000 18.38 0.00 32.11 2.83
4650 6547 5.543507 TGTTGCCATGTGAAAACCTAAAT 57.456 34.783 0.00 0.00 0.00 1.40
4681 6578 4.320714 CCAGTTGCTAAGTACAGTACGTCA 60.321 45.833 2.04 0.00 0.00 4.35
4696 6593 6.150318 CAGTACGTCAATATGACCCTACATC 58.850 44.000 0.00 0.00 44.20 3.06
4748 6648 4.689071 AGTAAAAGCAAAGGGGAAAAACG 58.311 39.130 0.00 0.00 0.00 3.60
4753 6653 2.703536 AGCAAAGGGGAAAAACGGATTT 59.296 40.909 0.00 0.00 0.00 2.17
4758 6658 6.038382 GCAAAGGGGAAAAACGGATTTAAAAA 59.962 34.615 0.00 0.00 0.00 1.94
4886 6786 1.270571 TGCGCCACTCTGATTTGTGTA 60.271 47.619 4.18 0.00 32.76 2.90
4887 6787 2.009774 GCGCCACTCTGATTTGTGTAT 58.990 47.619 0.00 0.00 32.76 2.29
4888 6788 2.223112 GCGCCACTCTGATTTGTGTATG 60.223 50.000 0.00 0.00 32.76 2.39
4919 6819 9.453572 AATTGAAGTCTTACTTGATTAGCATGA 57.546 29.630 0.00 0.00 38.80 3.07
5080 6984 1.140161 CCAAGATGCCAATGTGCCG 59.860 57.895 0.00 0.00 0.00 5.69
5117 7021 0.249073 GCTACCGCTCATGATGACGT 60.249 55.000 13.41 0.00 0.00 4.34
5134 7038 2.751436 TCCGGCAATGGCAGAAGC 60.751 61.111 7.75 0.00 43.71 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.986135 GCTTTCTGATACGTCTCCAATGTAT 59.014 40.000 0.00 0.00 41.77 2.29
49 50 5.105513 TGCTTTCTGATACGTCTCCAATGTA 60.106 40.000 0.00 0.00 33.91 2.29
50 51 4.184629 GCTTTCTGATACGTCTCCAATGT 58.815 43.478 0.00 0.00 0.00 2.71
51 52 4.033358 GTGCTTTCTGATACGTCTCCAATG 59.967 45.833 0.00 0.00 0.00 2.82
52 53 4.184629 GTGCTTTCTGATACGTCTCCAAT 58.815 43.478 0.00 0.00 0.00 3.16
53 54 3.006430 TGTGCTTTCTGATACGTCTCCAA 59.994 43.478 0.00 0.00 0.00 3.53
54 55 2.560981 TGTGCTTTCTGATACGTCTCCA 59.439 45.455 0.00 0.00 0.00 3.86
55 56 3.232213 TGTGCTTTCTGATACGTCTCC 57.768 47.619 0.00 0.00 0.00 3.71
56 57 4.493220 GCAATGTGCTTTCTGATACGTCTC 60.493 45.833 0.00 0.00 40.96 3.36
57 58 3.372206 GCAATGTGCTTTCTGATACGTCT 59.628 43.478 0.00 0.00 40.96 4.18
58 59 3.674423 GCAATGTGCTTTCTGATACGTC 58.326 45.455 0.00 0.00 40.96 4.34
59 60 3.747099 GCAATGTGCTTTCTGATACGT 57.253 42.857 0.00 0.00 40.96 3.57
71 72 4.246458 GGCTAGGTATAGTAGCAATGTGC 58.754 47.826 13.57 0.00 44.08 4.57
72 73 4.618460 CGGGCTAGGTATAGTAGCAATGTG 60.618 50.000 13.57 0.00 44.08 3.21
73 74 3.510360 CGGGCTAGGTATAGTAGCAATGT 59.490 47.826 13.57 0.00 44.08 2.71
74 75 3.119101 CCGGGCTAGGTATAGTAGCAATG 60.119 52.174 13.57 5.12 44.08 2.82
75 76 3.097614 CCGGGCTAGGTATAGTAGCAAT 58.902 50.000 13.57 0.00 44.08 3.56
76 77 2.158415 ACCGGGCTAGGTATAGTAGCAA 60.158 50.000 6.32 0.00 44.08 3.91
77 78 1.426598 ACCGGGCTAGGTATAGTAGCA 59.573 52.381 6.32 0.00 44.08 3.49
78 79 1.817447 CACCGGGCTAGGTATAGTAGC 59.183 57.143 6.32 5.73 43.89 3.58
79 80 2.224967 ACCACCGGGCTAGGTATAGTAG 60.225 54.545 6.32 0.00 43.89 2.57
80 81 1.782752 ACCACCGGGCTAGGTATAGTA 59.217 52.381 6.32 0.00 43.89 1.82
81 82 0.559699 ACCACCGGGCTAGGTATAGT 59.440 55.000 6.32 1.82 43.89 2.12
82 83 1.713297 AACCACCGGGCTAGGTATAG 58.287 55.000 6.32 1.29 43.89 1.31
83 84 2.597455 GTAACCACCGGGCTAGGTATA 58.403 52.381 6.32 1.68 43.89 1.47
84 85 1.417288 GTAACCACCGGGCTAGGTAT 58.583 55.000 6.32 2.57 43.89 2.73
85 86 1.037030 CGTAACCACCGGGCTAGGTA 61.037 60.000 6.32 0.00 43.89 3.08
87 88 2.497770 CGTAACCACCGGGCTAGG 59.502 66.667 6.32 4.50 37.90 3.02
88 89 2.497770 CCGTAACCACCGGGCTAG 59.502 66.667 6.32 0.00 41.78 3.42
94 95 4.317444 TGGCCACCGTAACCACCG 62.317 66.667 0.00 0.00 0.00 4.94
95 96 2.670592 GTGGCCACCGTAACCACC 60.671 66.667 26.31 0.00 46.65 4.61
106 107 2.034066 GCTGCTAAGTGGTGGCCA 59.966 61.111 0.00 0.00 0.00 5.36
107 108 1.603455 TTGCTGCTAAGTGGTGGCC 60.603 57.895 0.00 0.00 0.00 5.36
108 109 1.581447 GTTGCTGCTAAGTGGTGGC 59.419 57.895 0.00 0.00 0.00 5.01
109 110 0.884704 ACGTTGCTGCTAAGTGGTGG 60.885 55.000 0.00 0.00 0.00 4.61
110 111 0.512952 GACGTTGCTGCTAAGTGGTG 59.487 55.000 7.40 0.00 0.00 4.17
111 112 0.944311 CGACGTTGCTGCTAAGTGGT 60.944 55.000 7.40 0.00 0.00 4.16
112 113 0.944311 ACGACGTTGCTGCTAAGTGG 60.944 55.000 7.40 8.74 0.00 4.00
113 114 0.859232 AACGACGTTGCTGCTAAGTG 59.141 50.000 13.38 3.45 0.00 3.16
114 115 1.260561 CAAACGACGTTGCTGCTAAGT 59.739 47.619 15.01 2.22 0.00 2.24
115 116 1.398451 CCAAACGACGTTGCTGCTAAG 60.398 52.381 15.01 0.00 0.00 2.18
116 117 0.584396 CCAAACGACGTTGCTGCTAA 59.416 50.000 15.01 0.00 0.00 3.09
117 118 1.837538 GCCAAACGACGTTGCTGCTA 61.838 55.000 15.01 0.00 0.00 3.49
118 119 3.022287 CCAAACGACGTTGCTGCT 58.978 55.556 15.01 0.00 0.00 4.24
119 120 2.725815 GCCAAACGACGTTGCTGC 60.726 61.111 15.01 13.10 0.00 5.25
120 121 1.654137 GTGCCAAACGACGTTGCTG 60.654 57.895 15.01 9.65 0.00 4.41
121 122 1.649390 TTGTGCCAAACGACGTTGCT 61.649 50.000 15.01 0.00 0.00 3.91
122 123 0.798771 TTTGTGCCAAACGACGTTGC 60.799 50.000 15.01 14.56 0.00 4.17
123 124 0.911184 GTTTGTGCCAAACGACGTTG 59.089 50.000 15.01 8.43 0.00 4.10
124 125 0.522180 TGTTTGTGCCAAACGACGTT 59.478 45.000 19.30 7.57 33.05 3.99
125 126 0.736053 ATGTTTGTGCCAAACGACGT 59.264 45.000 19.30 0.00 33.05 4.34
126 127 1.119635 CATGTTTGTGCCAAACGACG 58.880 50.000 19.30 0.00 33.05 5.12
127 128 1.202359 ACCATGTTTGTGCCAAACGAC 60.202 47.619 19.30 4.60 33.05 4.34
128 129 1.107114 ACCATGTTTGTGCCAAACGA 58.893 45.000 19.30 12.36 33.05 3.85
129 130 2.034053 AGTACCATGTTTGTGCCAAACG 59.966 45.455 19.30 11.62 33.05 3.60
130 131 3.380142 CAGTACCATGTTTGTGCCAAAC 58.620 45.455 18.38 18.38 0.00 2.93
131 132 2.223923 GCAGTACCATGTTTGTGCCAAA 60.224 45.455 0.00 0.00 0.00 3.28
132 133 1.339610 GCAGTACCATGTTTGTGCCAA 59.660 47.619 0.00 0.00 0.00 4.52
133 134 0.958091 GCAGTACCATGTTTGTGCCA 59.042 50.000 0.00 0.00 0.00 4.92
134 135 1.247567 AGCAGTACCATGTTTGTGCC 58.752 50.000 0.00 0.00 0.00 5.01
135 136 4.497473 TTTAGCAGTACCATGTTTGTGC 57.503 40.909 0.00 0.00 0.00 4.57
136 137 6.012658 ACATTTAGCAGTACCATGTTTGTG 57.987 37.500 0.00 0.00 0.00 3.33
137 138 7.938140 ATACATTTAGCAGTACCATGTTTGT 57.062 32.000 0.00 0.00 30.70 2.83
138 139 8.070171 GCTATACATTTAGCAGTACCATGTTTG 58.930 37.037 0.00 0.00 43.33 2.93
139 140 8.154649 GCTATACATTTAGCAGTACCATGTTT 57.845 34.615 0.00 0.00 43.33 2.83
140 141 7.730364 GCTATACATTTAGCAGTACCATGTT 57.270 36.000 0.00 0.00 43.33 2.71
151 152 5.462405 ACTCGCTACTGCTATACATTTAGC 58.538 41.667 0.00 0.00 43.98 3.09
152 153 6.583050 GGAACTCGCTACTGCTATACATTTAG 59.417 42.308 0.00 0.00 36.97 1.85
153 154 6.040054 TGGAACTCGCTACTGCTATACATTTA 59.960 38.462 0.00 0.00 36.97 1.40
154 155 5.163447 TGGAACTCGCTACTGCTATACATTT 60.163 40.000 0.00 0.00 36.97 2.32
155 156 4.341235 TGGAACTCGCTACTGCTATACATT 59.659 41.667 0.00 0.00 36.97 2.71
156 157 3.889538 TGGAACTCGCTACTGCTATACAT 59.110 43.478 0.00 0.00 36.97 2.29
157 158 3.284617 TGGAACTCGCTACTGCTATACA 58.715 45.455 0.00 0.00 36.97 2.29
158 159 3.564644 TCTGGAACTCGCTACTGCTATAC 59.435 47.826 0.00 0.00 36.97 1.47
159 160 3.816994 TCTGGAACTCGCTACTGCTATA 58.183 45.455 0.00 0.00 36.97 1.31
160 161 2.656002 TCTGGAACTCGCTACTGCTAT 58.344 47.619 0.00 0.00 36.97 2.97
161 162 2.124277 TCTGGAACTCGCTACTGCTA 57.876 50.000 0.00 0.00 36.97 3.49
162 163 1.135915 CATCTGGAACTCGCTACTGCT 59.864 52.381 0.00 0.00 36.97 4.24
163 164 1.565305 CATCTGGAACTCGCTACTGC 58.435 55.000 0.00 0.00 0.00 4.40
164 165 1.804372 GCCATCTGGAACTCGCTACTG 60.804 57.143 0.00 0.00 37.39 2.74
165 166 0.461961 GCCATCTGGAACTCGCTACT 59.538 55.000 0.00 0.00 37.39 2.57
166 167 0.530870 GGCCATCTGGAACTCGCTAC 60.531 60.000 0.00 0.00 37.39 3.58
167 168 0.975556 TGGCCATCTGGAACTCGCTA 60.976 55.000 0.00 0.00 37.39 4.26
168 169 2.293318 TGGCCATCTGGAACTCGCT 61.293 57.895 0.00 0.00 37.39 4.93
169 170 2.109126 GTGGCCATCTGGAACTCGC 61.109 63.158 9.72 0.00 37.39 5.03
170 171 1.811266 CGTGGCCATCTGGAACTCG 60.811 63.158 9.72 0.00 37.39 4.18
171 172 2.109126 GCGTGGCCATCTGGAACTC 61.109 63.158 9.72 0.00 37.39 3.01
172 173 1.264749 TAGCGTGGCCATCTGGAACT 61.265 55.000 9.72 1.38 37.39 3.01
173 174 1.090052 GTAGCGTGGCCATCTGGAAC 61.090 60.000 9.72 1.11 37.39 3.62
174 175 1.220749 GTAGCGTGGCCATCTGGAA 59.779 57.895 9.72 0.00 37.39 3.53
175 176 0.396556 TAGTAGCGTGGCCATCTGGA 60.397 55.000 9.72 0.00 37.39 3.86
176 177 0.681733 ATAGTAGCGTGGCCATCTGG 59.318 55.000 9.72 0.00 38.53 3.86
177 178 3.660501 TTATAGTAGCGTGGCCATCTG 57.339 47.619 9.72 2.98 0.00 2.90
178 179 3.555168 GCTTTATAGTAGCGTGGCCATCT 60.555 47.826 9.72 12.44 0.00 2.90
179 180 2.737252 GCTTTATAGTAGCGTGGCCATC 59.263 50.000 9.72 3.89 0.00 3.51
180 181 2.104111 TGCTTTATAGTAGCGTGGCCAT 59.896 45.455 9.72 0.00 41.54 4.40
181 182 1.483004 TGCTTTATAGTAGCGTGGCCA 59.517 47.619 0.00 0.00 41.54 5.36
182 183 2.135933 CTGCTTTATAGTAGCGTGGCC 58.864 52.381 0.00 0.00 41.54 5.36
189 190 3.670991 GCGCTACTGCTGCTTTATAGTAG 59.329 47.826 15.78 15.78 43.32 2.57
190 191 3.639538 GCGCTACTGCTGCTTTATAGTA 58.360 45.455 0.00 0.00 36.40 1.82
191 192 2.474816 GCGCTACTGCTGCTTTATAGT 58.525 47.619 0.00 0.00 36.40 2.12
192 193 1.453524 CGCGCTACTGCTGCTTTATAG 59.546 52.381 5.56 0.00 36.87 1.31
193 194 1.202371 ACGCGCTACTGCTGCTTTATA 60.202 47.619 5.73 0.00 36.87 0.98
194 195 0.460284 ACGCGCTACTGCTGCTTTAT 60.460 50.000 5.73 0.00 36.87 1.40
195 196 1.080093 ACGCGCTACTGCTGCTTTA 60.080 52.632 5.73 0.00 36.87 1.85
196 197 2.357517 ACGCGCTACTGCTGCTTT 60.358 55.556 5.73 0.00 36.87 3.51
197 198 3.114616 CACGCGCTACTGCTGCTT 61.115 61.111 5.73 0.00 36.87 3.91
200 201 3.846590 CTGCACGCGCTACTGCTG 61.847 66.667 18.50 14.65 39.64 4.41
205 206 4.752879 TTCCCCTGCACGCGCTAC 62.753 66.667 5.73 0.00 39.64 3.58
206 207 4.752879 GTTCCCCTGCACGCGCTA 62.753 66.667 5.73 0.00 39.64 4.26
215 216 3.771160 AGTAGCGCGGTTCCCCTG 61.771 66.667 19.09 0.00 0.00 4.45
216 217 3.771160 CAGTAGCGCGGTTCCCCT 61.771 66.667 19.09 4.81 0.00 4.79
217 218 1.741327 TATCAGTAGCGCGGTTCCCC 61.741 60.000 19.09 2.20 0.00 4.81
218 219 0.103572 TTATCAGTAGCGCGGTTCCC 59.896 55.000 19.09 5.05 0.00 3.97
219 220 1.488527 CTTATCAGTAGCGCGGTTCC 58.511 55.000 19.09 7.96 0.00 3.62
220 221 0.853419 GCTTATCAGTAGCGCGGTTC 59.147 55.000 19.09 12.41 0.00 3.62
221 222 0.529992 GGCTTATCAGTAGCGCGGTT 60.530 55.000 19.09 0.00 39.54 4.44
222 223 1.067582 GGCTTATCAGTAGCGCGGT 59.932 57.895 17.70 17.70 39.54 5.68
223 224 0.664767 GAGGCTTATCAGTAGCGCGG 60.665 60.000 8.83 0.00 39.54 6.46
224 225 0.664767 GGAGGCTTATCAGTAGCGCG 60.665 60.000 0.00 0.00 39.54 6.86
225 226 0.389391 TGGAGGCTTATCAGTAGCGC 59.611 55.000 0.00 0.00 39.54 5.92
226 227 1.269831 GGTGGAGGCTTATCAGTAGCG 60.270 57.143 0.00 0.00 39.54 4.26
227 228 2.043227 AGGTGGAGGCTTATCAGTAGC 58.957 52.381 0.00 0.00 37.91 3.58
228 229 6.153680 CCTTATAGGTGGAGGCTTATCAGTAG 59.846 46.154 0.00 0.00 0.00 2.57
229 230 6.017192 CCTTATAGGTGGAGGCTTATCAGTA 58.983 44.000 0.00 0.00 0.00 2.74
230 231 4.841246 CCTTATAGGTGGAGGCTTATCAGT 59.159 45.833 0.00 0.00 0.00 3.41
231 232 5.413309 CCTTATAGGTGGAGGCTTATCAG 57.587 47.826 0.00 0.00 0.00 2.90
245 246 5.522824 GCACTACTCGGAAAAACCTTATAGG 59.477 44.000 0.00 0.00 42.49 2.57
246 247 6.103997 TGCACTACTCGGAAAAACCTTATAG 58.896 40.000 0.00 0.00 36.31 1.31
247 248 6.040209 TGCACTACTCGGAAAAACCTTATA 57.960 37.500 0.00 0.00 36.31 0.98
248 249 4.901868 TGCACTACTCGGAAAAACCTTAT 58.098 39.130 0.00 0.00 36.31 1.73
249 250 4.339872 TGCACTACTCGGAAAAACCTTA 57.660 40.909 0.00 0.00 36.31 2.69
250 251 3.202829 TGCACTACTCGGAAAAACCTT 57.797 42.857 0.00 0.00 36.31 3.50
251 252 2.922740 TGCACTACTCGGAAAAACCT 57.077 45.000 0.00 0.00 36.31 3.50
252 253 3.071479 TGATGCACTACTCGGAAAAACC 58.929 45.455 0.00 0.00 0.00 3.27
253 254 3.746492 AGTGATGCACTACTCGGAAAAAC 59.254 43.478 0.00 0.00 43.46 2.43
254 255 4.002906 AGTGATGCACTACTCGGAAAAA 57.997 40.909 0.00 0.00 43.46 1.94
255 256 3.678056 AGTGATGCACTACTCGGAAAA 57.322 42.857 0.00 0.00 43.46 2.29
264 265 5.813513 ATGATGATGGTAGTGATGCACTA 57.186 39.130 3.32 3.32 43.46 2.74
266 267 5.762825 AAATGATGATGGTAGTGATGCAC 57.237 39.130 0.00 0.00 34.10 4.57
267 268 7.878547 TTTAAATGATGATGGTAGTGATGCA 57.121 32.000 0.00 0.00 0.00 3.96
268 269 9.241317 CTTTTTAAATGATGATGGTAGTGATGC 57.759 33.333 0.00 0.00 0.00 3.91
443 444 1.068402 TGCAATTTGTGATGTGAGCCG 60.068 47.619 0.00 0.00 0.00 5.52
473 474 4.199310 GCCCATAGAAGTTGTGCTCAATA 58.801 43.478 4.26 0.00 35.92 1.90
477 478 1.009829 CGCCCATAGAAGTTGTGCTC 58.990 55.000 0.00 0.00 0.00 4.26
487 488 2.821546 CGAGATTTGAACGCCCATAGA 58.178 47.619 0.00 0.00 0.00 1.98
530 531 2.584608 CGCGACCTCCCCATCTTT 59.415 61.111 0.00 0.00 0.00 2.52
565 566 5.710567 CACCATCATCATCCTATTCATGCTT 59.289 40.000 0.00 0.00 0.00 3.91
585 586 3.433984 ATGCCTGCACACACCACCA 62.434 57.895 0.00 0.00 0.00 4.17
611 612 3.827898 GCTCACTAGGCCGACGCT 61.828 66.667 0.00 0.00 34.44 5.07
643 644 4.697756 CATGACCGGCCACCGTGT 62.698 66.667 0.00 2.71 46.80 4.49
649 650 2.142356 ATGAAATTCATGACCGGCCA 57.858 45.000 7.79 0.00 35.43 5.36
661 662 3.686016 ACTAGTTCGTGCCCATGAAATT 58.314 40.909 8.25 2.30 37.99 1.82
679 1377 2.022195 GCCACGTCATCACTAGGACTA 58.978 52.381 0.00 0.00 34.24 2.59
684 1382 2.349580 CACATTGCCACGTCATCACTAG 59.650 50.000 0.00 0.00 0.00 2.57
686 1384 1.159285 CACATTGCCACGTCATCACT 58.841 50.000 0.00 0.00 0.00 3.41
698 1396 1.432514 TCTTGACGAGCTCACATTGC 58.567 50.000 15.40 0.00 0.00 3.56
702 1400 1.269723 ACGAATCTTGACGAGCTCACA 59.730 47.619 15.40 10.43 0.00 3.58
712 1410 1.825090 AGCCATTGCACGAATCTTGA 58.175 45.000 0.00 0.00 41.13 3.02
733 1431 1.002430 TGCTTCGTCTGAATGCCTTCT 59.998 47.619 3.32 0.00 32.61 2.85
744 1442 2.604914 CACATATTTCGCTGCTTCGTCT 59.395 45.455 0.00 0.00 0.00 4.18
749 1447 2.346803 ACGTCACATATTTCGCTGCTT 58.653 42.857 0.00 0.00 0.00 3.91
761 1459 9.559958 GAAAAATGATAATTCTGAACGTCACAT 57.440 29.630 0.00 0.00 0.00 3.21
763 1461 9.612620 AAGAAAAATGATAATTCTGAACGTCAC 57.387 29.630 0.00 0.00 33.86 3.67
819 1518 8.989980 GCTATCATATTTGTGGAGGTTAACTAC 58.010 37.037 5.42 0.07 0.00 2.73
821 1520 7.573710 TGCTATCATATTTGTGGAGGTTAACT 58.426 34.615 5.42 0.00 0.00 2.24
822 1521 7.801716 TGCTATCATATTTGTGGAGGTTAAC 57.198 36.000 0.00 0.00 0.00 2.01
824 1523 7.661437 GTGATGCTATCATATTTGTGGAGGTTA 59.339 37.037 2.80 0.00 42.04 2.85
834 1537 9.144747 GTAGATTGTCGTGATGCTATCATATTT 57.855 33.333 2.80 0.00 42.04 1.40
861 1564 6.596888 ACATTGATGAGTGTCTTATCTTGTGG 59.403 38.462 0.00 0.00 29.89 4.17
928 2478 5.560722 TGGAGTTTCTGGTGAACATTAGA 57.439 39.130 0.00 0.00 31.02 2.10
929 2479 5.707298 ACATGGAGTTTCTGGTGAACATTAG 59.293 40.000 0.00 0.00 31.02 1.73
930 2480 5.630121 ACATGGAGTTTCTGGTGAACATTA 58.370 37.500 0.00 0.00 31.02 1.90
932 2482 4.074970 GACATGGAGTTTCTGGTGAACAT 58.925 43.478 0.00 0.00 31.02 2.71
933 2483 3.476552 GACATGGAGTTTCTGGTGAACA 58.523 45.455 0.00 0.00 31.02 3.18
934 2484 2.814336 GGACATGGAGTTTCTGGTGAAC 59.186 50.000 0.00 0.00 31.02 3.18
936 2486 2.054021 TGGACATGGAGTTTCTGGTGA 58.946 47.619 0.00 0.00 0.00 4.02
937 2487 2.566833 TGGACATGGAGTTTCTGGTG 57.433 50.000 0.00 0.00 0.00 4.17
938 2488 3.077484 CATGGACATGGAGTTTCTGGT 57.923 47.619 4.39 0.00 35.24 4.00
1187 2738 3.186943 AAATTGGGGGTGGGGTGGG 62.187 63.158 0.00 0.00 0.00 4.61
1254 2805 2.906458 CAGGAGCCGCTCAATCCT 59.094 61.111 21.76 7.87 44.41 3.24
1297 2848 2.799412 CGAATCAAGATCCACTGCTAGC 59.201 50.000 8.10 8.10 0.00 3.42
1319 2870 3.505680 TCAGTGCAAAAAGTCACACAGTT 59.494 39.130 0.00 0.00 35.47 3.16
1324 2875 5.182487 TCTAAGTCAGTGCAAAAAGTCACA 58.818 37.500 0.00 0.00 35.76 3.58
1378 2929 5.180868 CACACCATCTTTTCTTCTTCTCAGG 59.819 44.000 0.00 0.00 0.00 3.86
1400 2951 1.682087 GCCTTATGAAGTCCCACCCAC 60.682 57.143 0.00 0.00 0.00 4.61
1525 3079 2.024176 TGGATGAAAGTCTAAGCGGC 57.976 50.000 0.00 0.00 0.00 6.53
1526 3080 3.600388 AGTTGGATGAAAGTCTAAGCGG 58.400 45.455 0.00 0.00 0.00 5.52
1541 3095 4.000988 GCCGTTTCTCAGATTAAGTTGGA 58.999 43.478 0.00 0.00 0.00 3.53
1574 3128 3.202829 TCACACTCCAGGTTTGGTAAC 57.797 47.619 0.00 0.00 45.26 2.50
1599 3153 3.118038 AGTCCCAGCACACTTTCAGTTTA 60.118 43.478 0.00 0.00 0.00 2.01
1663 3224 8.910351 AATTTCAATCCTAGCTAACATCCTAC 57.090 34.615 0.00 0.00 0.00 3.18
1722 3283 9.037737 CCAATTACCAAAATCAAGATAGCATTG 57.962 33.333 0.00 0.00 0.00 2.82
1735 3296 5.549619 TCCAACATTCCCCAATTACCAAAAT 59.450 36.000 0.00 0.00 0.00 1.82
1749 3310 4.340950 TGACAAAAGAAGGTCCAACATTCC 59.659 41.667 1.26 0.00 39.49 3.01
1795 3356 1.608590 ACAACAGGAATTTGACAGCCG 59.391 47.619 0.00 0.00 0.00 5.52
1821 3383 1.228862 AAATGTGCCCCTGACCACC 60.229 57.895 0.00 0.00 0.00 4.61
1829 3391 0.251787 AACAGGGAGAAATGTGCCCC 60.252 55.000 0.00 0.00 43.08 5.80
1835 3397 5.587844 CCAGACTATTCAACAGGGAGAAATG 59.412 44.000 0.00 0.00 0.00 2.32
1844 3406 5.541845 TGAGTGAACCAGACTATTCAACAG 58.458 41.667 3.51 0.00 36.62 3.16
1871 3433 4.900684 TCCGTAAACATGACAGGAAATCA 58.099 39.130 0.00 0.00 0.00 2.57
1892 3454 6.200665 TGCAAGTAACAAAAAGCATCACATTC 59.799 34.615 0.00 0.00 0.00 2.67
1897 3459 7.205992 TGTAATGCAAGTAACAAAAAGCATCA 58.794 30.769 0.00 0.00 41.37 3.07
2152 3732 5.415221 GTTTTGGGTGACATCAAGTTTTCA 58.585 37.500 0.00 0.00 0.00 2.69
2621 4255 6.098982 TGGGATGGACAAAATTTACACTGTTT 59.901 34.615 0.00 0.00 0.00 2.83
2973 4608 4.348461 TGGGATAGTTCGGGCAATTATACA 59.652 41.667 0.00 0.00 0.00 2.29
3468 5153 5.605534 TCTAACTAGCATCAATGAAGCTCC 58.394 41.667 16.60 0.00 37.73 4.70
3469 5154 7.440556 TGAATCTAACTAGCATCAATGAAGCTC 59.559 37.037 16.60 0.34 37.73 4.09
3470 5155 7.278135 TGAATCTAACTAGCATCAATGAAGCT 58.722 34.615 17.24 17.24 39.88 3.74
3471 5156 7.440556 TCTGAATCTAACTAGCATCAATGAAGC 59.559 37.037 1.78 1.78 0.00 3.86
3472 5157 8.763356 GTCTGAATCTAACTAGCATCAATGAAG 58.237 37.037 0.00 0.00 0.00 3.02
3473 5158 7.436376 CGTCTGAATCTAACTAGCATCAATGAA 59.564 37.037 0.00 0.00 0.00 2.57
3474 5159 6.920210 CGTCTGAATCTAACTAGCATCAATGA 59.080 38.462 0.00 0.00 0.00 2.57
3475 5160 6.699204 ACGTCTGAATCTAACTAGCATCAATG 59.301 38.462 0.00 0.00 0.00 2.82
3476 5161 6.810911 ACGTCTGAATCTAACTAGCATCAAT 58.189 36.000 0.00 0.00 0.00 2.57
3562 5251 2.675348 GAGCATCAACAACAGGAGTAGC 59.325 50.000 0.00 0.00 33.17 3.58
3563 5252 2.926200 CGAGCATCAACAACAGGAGTAG 59.074 50.000 0.00 0.00 33.17 2.57
3573 5262 6.493449 TTTATTTCATCACGAGCATCAACA 57.507 33.333 0.00 0.00 33.17 3.33
3577 5266 9.539139 CAGATATTTTATTTCATCACGAGCATC 57.461 33.333 0.00 0.00 0.00 3.91
3674 5367 2.754552 ACTCTTTGCAACACTTGAGCAA 59.245 40.909 0.00 8.91 45.53 3.91
3781 5474 1.021390 CGGCCAGATCAACACTCCAC 61.021 60.000 2.24 0.00 0.00 4.02
3914 5691 1.547372 CTTTGGAGAAACCTGGCCATG 59.453 52.381 5.51 6.06 39.86 3.66
4064 5841 1.451028 GCTGCCCCATCTCTGACAC 60.451 63.158 0.00 0.00 0.00 3.67
4139 5916 0.244450 CAACATCAGGTGGCGCATTT 59.756 50.000 10.83 0.00 0.00 2.32
4187 5970 2.825532 TCCAATTTCCAGCTTAAGCACC 59.174 45.455 28.39 0.05 45.16 5.01
4193 5976 4.017591 TCCCAGAATCCAATTTCCAGCTTA 60.018 41.667 0.00 0.00 0.00 3.09
4194 5977 3.102204 CCCAGAATCCAATTTCCAGCTT 58.898 45.455 0.00 0.00 0.00 3.74
4202 5985 4.598036 ACTCATGTCCCAGAATCCAATT 57.402 40.909 0.00 0.00 0.00 2.32
4231 6014 0.961857 TGTAGTCGCCGCTTAGGACA 60.962 55.000 0.00 0.00 45.00 4.02
4280 6070 1.883084 CCCACTGCGGCGTCTATTC 60.883 63.158 9.37 0.00 0.00 1.75
4323 6114 5.560722 TCACCAGAGAAACCAAGATACAA 57.439 39.130 0.00 0.00 0.00 2.41
4342 6133 1.877443 AGGTTATTGCACGGTGTTCAC 59.123 47.619 10.24 0.45 0.00 3.18
4429 6220 1.308998 CGTGCTGACCAAAGAAACCT 58.691 50.000 0.00 0.00 0.00 3.50
4442 6233 1.468520 CCAAGTAATTCCACCGTGCTG 59.531 52.381 0.00 0.00 0.00 4.41
4444 6235 1.467342 GTCCAAGTAATTCCACCGTGC 59.533 52.381 0.00 0.00 0.00 5.34
4448 6239 2.484742 ACCGTCCAAGTAATTCCACC 57.515 50.000 0.00 0.00 0.00 4.61
4525 6316 5.121142 ACCAACAAAAACATCTATACCGACG 59.879 40.000 0.00 0.00 0.00 5.12
4546 6337 6.833416 AGAAGCCAGCATAAAAATACATACCA 59.167 34.615 0.00 0.00 0.00 3.25
4650 6547 3.275617 ACTTAGCAACTGGTTGTGACA 57.724 42.857 13.85 0.00 42.31 3.58
4681 6578 6.479972 TCAGAAACGATGTAGGGTCATATT 57.520 37.500 0.00 0.00 0.00 1.28
4696 6593 2.847901 CAGCATGCTCTTTCAGAAACG 58.152 47.619 19.68 0.00 0.00 3.60
4720 6620 5.578157 TCCCCTTTGCTTTTACTAGTTCT 57.422 39.130 0.00 0.00 0.00 3.01
4723 6623 6.460537 CGTTTTTCCCCTTTGCTTTTACTAGT 60.461 38.462 0.00 0.00 0.00 2.57
4724 6624 5.918576 CGTTTTTCCCCTTTGCTTTTACTAG 59.081 40.000 0.00 0.00 0.00 2.57
4725 6625 5.221283 CCGTTTTTCCCCTTTGCTTTTACTA 60.221 40.000 0.00 0.00 0.00 1.82
4786 6686 9.947433 TGATATTTTTCCTTCATTTTTGCAGAT 57.053 25.926 0.00 0.00 0.00 2.90
4787 6687 9.426837 CTGATATTTTTCCTTCATTTTTGCAGA 57.573 29.630 0.00 0.00 0.00 4.26
4902 6802 6.090088 GCGAGGTATCATGCTAATCAAGTAAG 59.910 42.308 0.00 0.00 0.00 2.34
4903 6803 5.926542 GCGAGGTATCATGCTAATCAAGTAA 59.073 40.000 0.00 0.00 0.00 2.24
4904 6804 5.010617 TGCGAGGTATCATGCTAATCAAGTA 59.989 40.000 0.00 0.00 0.00 2.24
4909 6809 2.670414 GCTGCGAGGTATCATGCTAATC 59.330 50.000 0.00 0.00 0.00 1.75
4919 6819 0.745845 CAAGGCAAGCTGCGAGGTAT 60.746 55.000 0.00 0.00 46.21 2.73
5027 6930 5.918608 TGGTTTGTTGCTTTATTTGGCTTA 58.081 33.333 0.00 0.00 0.00 3.09
5080 6984 1.427020 CTTCTGGCTTAGCTTGCGC 59.573 57.895 0.00 0.00 0.00 6.09
5117 7021 2.751436 GCTTCTGCCATTGCCGGA 60.751 61.111 5.05 0.00 36.33 5.14


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

AutoCloner maintained by Alex Coulton.