Multiple sequence alignment - TraesCS2A01G414600

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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 TraesCS2A01G414600 chr2A 100.000 4537 0 0 1 4537 671708431 671703895 0.000000e+00 8379.0
1 TraesCS2A01G414600 chr2A 97.727 44 1 0 4407 4450 587741623 587741666 4.870000e-10 76.8
2 TraesCS2A01G414600 chr2B 93.123 4115 206 41 223 4290 622918221 622914137 0.000000e+00 5960.0
3 TraesCS2A01G414600 chr2B 91.852 135 11 0 4403 4537 622914059 622913925 5.990000e-44 189.0
4 TraesCS2A01G414600 chr2B 89.062 128 12 1 5 130 622918350 622918223 1.690000e-34 158.0
5 TraesCS2A01G414600 chr2B 92.453 106 4 2 123 224 694052142 694052247 1.020000e-31 148.0
6 TraesCS2A01G414600 chr2B 100.000 42 0 0 4408 4449 32892707 32892666 1.350000e-10 78.7
7 TraesCS2A01G414600 chr2B 95.745 47 2 0 4405 4451 622914061 622914107 4.870000e-10 76.8
8 TraesCS2A01G414600 chr2D 94.122 2807 123 21 773 3556 526519741 526516954 0.000000e+00 4231.0
9 TraesCS2A01G414600 chr2D 92.276 958 42 13 1824 2781 274923326 274924251 0.000000e+00 1330.0
10 TraesCS2A01G414600 chr2D 95.546 696 25 5 3596 4290 526516951 526516261 0.000000e+00 1109.0
11 TraesCS2A01G414600 chr2D 91.711 567 33 9 223 777 526520622 526520058 0.000000e+00 774.0
12 TraesCS2A01G414600 chr2D 94.611 167 9 0 4371 4537 526516262 526516096 4.500000e-65 259.0
13 TraesCS2A01G414600 chr2D 91.045 134 10 1 7 138 526520749 526520616 3.610000e-41 180.0
14 TraesCS2A01G414600 chr6B 92.902 958 44 10 1824 2781 27634227 27633294 0.000000e+00 1371.0
15 TraesCS2A01G414600 chr6B 96.842 95 1 2 132 224 448429821 448429727 1.690000e-34 158.0
16 TraesCS2A01G414600 chr6B 83.871 93 15 0 3989 4081 496988445 496988537 6.250000e-14 89.8
17 TraesCS2A01G414600 chr4D 92.797 958 37 13 1824 2781 455258961 455258036 0.000000e+00 1358.0
18 TraesCS2A01G414600 chr4D 95.000 80 4 0 4293 4372 434487677 434487598 4.760000e-25 126.0
19 TraesCS2A01G414600 chr4D 95.833 48 2 0 4408 4455 13062759 13062712 1.350000e-10 78.7
20 TraesCS2A01G414600 chr7B 92.133 966 44 11 1824 2781 145929508 145928567 0.000000e+00 1334.0
21 TraesCS2A01G414600 chr7B 91.148 610 37 11 2172 2781 4604450 4605042 0.000000e+00 811.0
22 TraesCS2A01G414600 chr5B 91.962 958 54 9 1824 2781 504043727 504044661 0.000000e+00 1321.0
23 TraesCS2A01G414600 chr6D 95.262 802 22 6 1824 2624 97558766 97559552 0.000000e+00 1256.0
24 TraesCS2A01G414600 chr6D 94.048 84 5 0 4293 4376 379576459 379576376 1.320000e-25 128.0
25 TraesCS2A01G414600 chr6D 82.075 106 17 2 3989 4093 325819719 325819615 6.250000e-14 89.8
26 TraesCS2A01G414600 chr3B 95.018 562 22 1 1824 2385 85095477 85094922 0.000000e+00 878.0
27 TraesCS2A01G414600 chr3B 85.666 293 25 9 2489 2781 85094710 85094435 4.440000e-75 292.0
28 TraesCS2A01G414600 chr3B 93.407 91 6 0 4121 4211 586051517 586051607 7.920000e-28 135.0
29 TraesCS2A01G414600 chr3B 93.976 83 5 0 4293 4375 517865725 517865807 4.760000e-25 126.0
30 TraesCS2A01G414600 chr3D 94.175 103 4 2 122 223 272281187 272281086 6.080000e-34 156.0
31 TraesCS2A01G414600 chr3D 93.333 105 2 4 128 227 530665414 530665310 2.830000e-32 150.0
32 TraesCS2A01G414600 chr3D 86.154 130 11 5 132 257 458561082 458561208 2.850000e-27 134.0
33 TraesCS2A01G414600 chr3D 89.831 59 4 2 4405 4462 131489213 131489156 1.750000e-09 75.0
34 TraesCS2A01G414600 chr1B 95.000 100 2 3 126 223 70703860 70703958 2.190000e-33 154.0
35 TraesCS2A01G414600 chr7D 90.991 111 6 4 125 231 157234999 157235109 3.660000e-31 147.0
36 TraesCS2A01G414600 chr7D 86.154 130 11 4 132 257 157235100 157234974 2.850000e-27 134.0
37 TraesCS2A01G414600 chr7D 95.000 80 4 0 4293 4372 367991537 367991458 4.760000e-25 126.0
38 TraesCS2A01G414600 chr1A 96.386 83 3 0 4293 4375 475654696 475654778 2.200000e-28 137.0
39 TraesCS2A01G414600 chr1D 86.614 127 11 5 132 257 269642755 269642634 7.920000e-28 135.0
40 TraesCS2A01G414600 chr7A 96.250 80 3 0 4293 4372 35618095 35618174 1.020000e-26 132.0
41 TraesCS2A01G414600 chr7A 93.976 83 5 0 4293 4375 93531638 93531720 4.760000e-25 126.0
42 TraesCS2A01G414600 chr5D 93.976 83 5 0 4293 4375 172264255 172264173 4.760000e-25 126.0
43 TraesCS2A01G414600 chr4B 95.000 80 4 0 4293 4372 147722653 147722732 4.760000e-25 126.0
44 TraesCS2A01G414600 chr4B 90.625 64 5 1 4408 4470 23667363 23667300 2.910000e-12 84.2
45 TraesCS2A01G414600 chr6A 82.075 106 17 2 3989 4093 464689285 464689181 6.250000e-14 89.8
46 TraesCS2A01G414600 chr5A 100.000 42 0 0 4408 4449 290393853 290393812 1.350000e-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 TraesCS2A01G414600 chr2A 671703895 671708431 4536 True 8379.000000 8379 100.000000 1 4537 1 chr2A.!!$R1 4536
1 TraesCS2A01G414600 chr2B 622913925 622918350 4425 True 2102.333333 5960 91.345667 5 4537 3 chr2B.!!$R2 4532
2 TraesCS2A01G414600 chr2D 274923326 274924251 925 False 1330.000000 1330 92.276000 1824 2781 1 chr2D.!!$F1 957
3 TraesCS2A01G414600 chr2D 526516096 526520749 4653 True 1310.600000 4231 93.407000 7 4537 5 chr2D.!!$R1 4530
4 TraesCS2A01G414600 chr6B 27633294 27634227 933 True 1371.000000 1371 92.902000 1824 2781 1 chr6B.!!$R1 957
5 TraesCS2A01G414600 chr4D 455258036 455258961 925 True 1358.000000 1358 92.797000 1824 2781 1 chr4D.!!$R3 957
6 TraesCS2A01G414600 chr7B 145928567 145929508 941 True 1334.000000 1334 92.133000 1824 2781 1 chr7B.!!$R1 957
7 TraesCS2A01G414600 chr7B 4604450 4605042 592 False 811.000000 811 91.148000 2172 2781 1 chr7B.!!$F1 609
8 TraesCS2A01G414600 chr5B 504043727 504044661 934 False 1321.000000 1321 91.962000 1824 2781 1 chr5B.!!$F1 957
9 TraesCS2A01G414600 chr6D 97558766 97559552 786 False 1256.000000 1256 95.262000 1824 2624 1 chr6D.!!$F1 800
10 TraesCS2A01G414600 chr3B 85094435 85095477 1042 True 585.000000 878 90.342000 1824 2781 2 chr3B.!!$R1 957

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
144 147 0.105039 CTATGCACTCCCTCCGTTCC 59.895 60.0 0.00 0.0 0.00 3.62 F
485 489 0.109342 CCGGATCTTAAGCAGCCCAT 59.891 55.0 0.00 0.0 0.00 4.00 F
1410 1766 0.110056 CGCACCACTTAGCAAGCAAG 60.110 55.0 0.00 0.0 0.00 4.01 F
1412 1768 0.242017 CACCACTTAGCAAGCAAGCC 59.758 55.0 0.00 0.0 34.23 4.35 F
2743 3254 0.035458 ACAAGAAGCTGGACCCTTCG 59.965 55.0 5.22 0.0 42.63 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1745 1.207593 GCTTGCTAAGTGGTGCGTG 59.792 57.895 0.00 0.00 0.00 5.34 R
1473 1829 1.270094 TGCTCTGTAAACTCACACCGG 60.270 52.381 0.00 0.00 0.00 5.28 R
2649 3155 0.179100 CTGGGATCATCGTCGCACTT 60.179 55.000 0.00 0.00 36.32 3.16 R
3363 3874 0.684153 AGATTGGGGGCGTCAAATGG 60.684 55.000 0.00 0.00 0.00 3.16 R
3705 4217 1.061131 GAACGGTTCATCAGTGATGCG 59.939 52.381 25.53 23.67 39.63 4.73 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
21 22 4.985044 CCTGTTGTAGTCTTTGTTACCG 57.015 45.455 0.00 0.00 0.00 4.02
38 39 3.998672 GTCCGACCCGTGGAGCAA 61.999 66.667 0.00 0.00 35.82 3.91
88 89 1.132453 CATTGCATGTGGTCTGCTCAG 59.868 52.381 0.00 0.00 40.34 3.35
90 91 0.321034 TGCATGTGGTCTGCTCAGTC 60.321 55.000 0.00 0.00 40.34 3.51
96 97 1.188219 TGGTCTGCTCAGTCTGGTCC 61.188 60.000 0.00 0.00 0.00 4.46
102 103 1.502640 CTCAGTCTGGTCCGTCGAC 59.497 63.158 5.18 5.18 38.38 4.20
104 105 2.281345 AGTCTGGTCCGTCGACGT 60.281 61.111 33.49 12.26 40.17 4.34
139 142 3.142174 GCATTTACTATGCACTCCCTCC 58.858 50.000 4.95 0.00 44.00 4.30
140 143 3.393800 CATTTACTATGCACTCCCTCCG 58.606 50.000 0.00 0.00 0.00 4.63
141 144 2.154567 TTACTATGCACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
142 145 2.154567 TACTATGCACTCCCTCCGTT 57.845 50.000 0.00 0.00 0.00 4.44
143 146 0.824759 ACTATGCACTCCCTCCGTTC 59.175 55.000 0.00 0.00 0.00 3.95
144 147 0.105039 CTATGCACTCCCTCCGTTCC 59.895 60.000 0.00 0.00 0.00 3.62
145 148 0.616395 TATGCACTCCCTCCGTTCCA 60.616 55.000 0.00 0.00 0.00 3.53
146 149 1.488705 ATGCACTCCCTCCGTTCCAA 61.489 55.000 0.00 0.00 0.00 3.53
147 150 1.072505 GCACTCCCTCCGTTCCAAA 59.927 57.895 0.00 0.00 0.00 3.28
148 151 0.536460 GCACTCCCTCCGTTCCAAAA 60.536 55.000 0.00 0.00 0.00 2.44
149 152 1.886655 GCACTCCCTCCGTTCCAAAAT 60.887 52.381 0.00 0.00 0.00 1.82
150 153 2.617021 GCACTCCCTCCGTTCCAAAATA 60.617 50.000 0.00 0.00 0.00 1.40
151 154 3.270877 CACTCCCTCCGTTCCAAAATAG 58.729 50.000 0.00 0.00 0.00 1.73
152 155 3.055385 CACTCCCTCCGTTCCAAAATAGA 60.055 47.826 0.00 0.00 0.00 1.98
153 156 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
154 157 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
155 158 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
156 159 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
157 160 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
158 161 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
159 162 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
160 163 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
161 164 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
162 165 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
163 166 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
164 167 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
165 168 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
166 169 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
167 170 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
168 171 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
169 172 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
170 173 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
171 174 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
172 175 9.975218 AAATAGATGACCCAACTTTGTACTAAT 57.025 29.630 0.00 0.00 0.00 1.73
173 176 9.975218 AATAGATGACCCAACTTTGTACTAATT 57.025 29.630 0.00 0.00 0.00 1.40
174 177 9.975218 ATAGATGACCCAACTTTGTACTAATTT 57.025 29.630 0.00 0.00 0.00 1.82
176 179 9.449719 AGATGACCCAACTTTGTACTAATTTAG 57.550 33.333 1.79 1.79 0.00 1.85
177 180 9.227777 GATGACCCAACTTTGTACTAATTTAGT 57.772 33.333 13.36 13.36 42.68 2.24
198 201 9.546428 TTTAGTAAGTTAGTACAAAGTTGGGTC 57.454 33.333 0.00 0.00 0.00 4.46
199 202 7.128234 AGTAAGTTAGTACAAAGTTGGGTCA 57.872 36.000 0.00 0.00 0.00 4.02
200 203 7.742767 AGTAAGTTAGTACAAAGTTGGGTCAT 58.257 34.615 0.00 0.00 0.00 3.06
201 204 7.876582 AGTAAGTTAGTACAAAGTTGGGTCATC 59.123 37.037 0.00 0.00 0.00 2.92
202 205 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
203 206 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
204 207 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
205 208 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
206 209 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
207 210 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
208 211 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
209 212 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
210 213 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
211 214 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
212 215 6.840780 AAGTTGGGTCATCTATTTTGGAAG 57.159 37.500 0.00 0.00 0.00 3.46
213 216 5.264395 AGTTGGGTCATCTATTTTGGAAGG 58.736 41.667 0.00 0.00 0.00 3.46
214 217 4.249638 TGGGTCATCTATTTTGGAAGGG 57.750 45.455 0.00 0.00 0.00 3.95
215 218 3.855599 TGGGTCATCTATTTTGGAAGGGA 59.144 43.478 0.00 0.00 0.00 4.20
216 219 4.079787 TGGGTCATCTATTTTGGAAGGGAG 60.080 45.833 0.00 0.00 0.00 4.30
217 220 4.464947 GGTCATCTATTTTGGAAGGGAGG 58.535 47.826 0.00 0.00 0.00 4.30
218 221 4.464947 GTCATCTATTTTGGAAGGGAGGG 58.535 47.826 0.00 0.00 0.00 4.30
219 222 4.166144 GTCATCTATTTTGGAAGGGAGGGA 59.834 45.833 0.00 0.00 0.00 4.20
220 223 4.413520 TCATCTATTTTGGAAGGGAGGGAG 59.586 45.833 0.00 0.00 0.00 4.30
221 224 3.815507 TCTATTTTGGAAGGGAGGGAGT 58.184 45.455 0.00 0.00 0.00 3.85
259 262 1.985614 CCTGTCTGTCCATGGCTGA 59.014 57.895 6.96 9.11 0.00 4.26
275 278 1.138047 CTGATACGTCGTTCGGTGCC 61.138 60.000 1.78 0.00 44.69 5.01
296 299 2.201732 GCAATGCCATCAGATTTGCAG 58.798 47.619 11.24 1.29 41.67 4.41
343 347 8.626526 TCTTCACAAATTAAACTTGGGTCTAAC 58.373 33.333 3.58 0.00 0.00 2.34
381 385 2.125106 GGCGCAGGGAATCGTCTT 60.125 61.111 10.83 0.00 0.00 3.01
419 423 4.202000 TGCTAATGGTGTGTGTTCAGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
438 442 0.179179 GCTCAAGCGAAGATGCCAAC 60.179 55.000 0.00 0.00 34.65 3.77
467 471 2.606826 AGAACGGTGGGGAGGACC 60.607 66.667 0.00 0.00 39.11 4.46
485 489 0.109342 CCGGATCTTAAGCAGCCCAT 59.891 55.000 0.00 0.00 0.00 4.00
512 516 1.687494 GATCAACGACAGCGAGTGGC 61.687 60.000 0.00 0.00 41.64 5.01
531 535 5.350640 AGTGGCGCTTTGTTTATAAGTAGAC 59.649 40.000 7.64 0.00 0.00 2.59
535 539 5.701469 CGCTTTGTTTATAAGTAGACGTCG 58.299 41.667 10.46 0.00 0.00 5.12
536 540 5.509272 CGCTTTGTTTATAAGTAGACGTCGA 59.491 40.000 10.46 0.94 0.00 4.20
557 561 5.123820 TCGAAAAATTCTGTGCTTATCAGGG 59.876 40.000 0.00 0.00 34.15 4.45
558 562 5.123820 CGAAAAATTCTGTGCTTATCAGGGA 59.876 40.000 0.00 0.00 34.15 4.20
559 563 6.521151 AAAAATTCTGTGCTTATCAGGGAG 57.479 37.500 0.00 0.00 34.15 4.30
567 571 2.224281 TGCTTATCAGGGAGTATTGCGG 60.224 50.000 0.00 0.00 0.00 5.69
640 655 1.068434 ACCACTGGCAAATTTGTTCGG 59.932 47.619 19.03 17.20 0.00 4.30
673 689 4.539152 GCATTTGGTGACTGTGCG 57.461 55.556 0.00 0.00 0.00 5.34
682 698 0.859232 GTGACTGTGCGAACGAACAT 59.141 50.000 8.49 0.02 32.47 2.71
700 716 0.839946 ATCCCTTGGATTCCACTCCG 59.160 55.000 4.45 0.00 39.79 4.63
727 743 0.243636 CAACGATTCCCTGCCCAAAC 59.756 55.000 0.00 0.00 0.00 2.93
777 1114 1.153628 CTCGCTCCAAACCCCTACG 60.154 63.158 0.00 0.00 0.00 3.51
779 1116 1.740296 CGCTCCAAACCCCTACGTG 60.740 63.158 0.00 0.00 0.00 4.49
798 1135 7.594015 CCTACGTGTACCATCTGATGTTTATAC 59.406 40.741 15.95 12.82 0.00 1.47
799 1136 6.869695 ACGTGTACCATCTGATGTTTATACA 58.130 36.000 15.95 14.22 38.95 2.29
800 1137 6.978659 ACGTGTACCATCTGATGTTTATACAG 59.021 38.462 15.95 12.16 37.77 2.74
913 1251 0.658536 GCGCAACTTGTCACTCTTGC 60.659 55.000 0.30 0.00 36.47 4.01
917 1255 1.070309 CAACTTGTCACTCTTGCGAGC 60.070 52.381 0.00 0.00 41.09 5.03
952 1290 2.523015 CGGGCGTTATTATAGGCTACG 58.477 52.381 0.00 0.00 35.48 3.51
957 1295 3.605486 GCGTTATTATAGGCTACGAACCG 59.395 47.826 9.25 3.71 34.36 4.44
959 1297 4.549458 GTTATTATAGGCTACGAACCGCA 58.451 43.478 0.00 0.00 0.00 5.69
961 1299 2.787601 TATAGGCTACGAACCGCAAG 57.212 50.000 0.00 0.00 0.00 4.01
995 1339 2.380410 CCGAAAGAGACCAACGCCG 61.380 63.158 0.00 0.00 0.00 6.46
1065 1409 4.087892 CACCACCCTCGCCTCCAG 62.088 72.222 0.00 0.00 0.00 3.86
1396 1752 3.419759 CAAGGTACGCCACGCACC 61.420 66.667 1.06 1.06 42.96 5.01
1400 1756 2.663852 GTACGCCACGCACCACTT 60.664 61.111 0.00 0.00 0.00 3.16
1405 1761 2.258013 GCCACGCACCACTTAGCAA 61.258 57.895 0.00 0.00 0.00 3.91
1408 1764 1.227823 ACGCACCACTTAGCAAGCA 60.228 52.632 0.00 0.00 0.00 3.91
1410 1766 0.110056 CGCACCACTTAGCAAGCAAG 60.110 55.000 0.00 0.00 0.00 4.01
1411 1767 0.387750 GCACCACTTAGCAAGCAAGC 60.388 55.000 0.00 0.00 0.00 4.01
1412 1768 0.242017 CACCACTTAGCAAGCAAGCC 59.758 55.000 0.00 0.00 34.23 4.35
1413 1769 1.237285 ACCACTTAGCAAGCAAGCCG 61.237 55.000 0.00 0.00 34.23 5.52
1437 1793 1.595093 CCGTGCCACCTTGGGAATTC 61.595 60.000 0.00 0.00 40.43 2.17
1449 1805 2.699212 GAATTCGGCGGCGTGTAC 59.301 61.111 31.06 16.82 0.00 2.90
1453 1809 1.936436 ATTCGGCGGCGTGTACTGTA 61.936 55.000 31.06 6.10 0.00 2.74
1454 1810 2.126385 CGGCGGCGTGTACTGTAA 60.126 61.111 24.74 0.00 0.00 2.41
1457 1813 0.738412 GGCGGCGTGTACTGTAATGT 60.738 55.000 9.37 0.00 0.00 2.71
1458 1814 0.643820 GCGGCGTGTACTGTAATGTC 59.356 55.000 9.37 0.00 0.00 3.06
1459 1815 0.911856 CGGCGTGTACTGTAATGTCG 59.088 55.000 0.00 0.00 0.00 4.35
1460 1816 1.730121 CGGCGTGTACTGTAATGTCGT 60.730 52.381 0.00 0.00 0.00 4.34
1461 1817 1.916000 GGCGTGTACTGTAATGTCGTC 59.084 52.381 0.00 0.00 0.00 4.20
1462 1818 1.916000 GCGTGTACTGTAATGTCGTCC 59.084 52.381 0.00 0.00 0.00 4.79
1463 1819 2.171567 CGTGTACTGTAATGTCGTCCG 58.828 52.381 0.00 0.00 0.00 4.79
1464 1820 2.413239 CGTGTACTGTAATGTCGTCCGT 60.413 50.000 0.00 0.00 0.00 4.69
1487 1843 1.067354 ACGATCCCGGTGTGAGTTTAC 60.067 52.381 0.00 0.00 40.78 2.01
1501 1857 3.127376 TGAGTTTACAGAGCACGCGTATA 59.873 43.478 13.44 0.00 0.00 1.47
1502 1858 3.432782 AGTTTACAGAGCACGCGTATAC 58.567 45.455 13.44 4.42 0.00 1.47
1597 1953 3.241530 TTCTCGGTGCTGCAGGGT 61.242 61.111 17.12 0.00 0.00 4.34
2404 2801 3.390521 CCGGTCTACCTGCTGCCA 61.391 66.667 0.00 0.00 0.00 4.92
2634 3140 2.677199 TCAGTTGATCTTCGTCTGCAC 58.323 47.619 0.00 0.00 0.00 4.57
2643 3149 5.862323 TGATCTTCGTCTGCACTTTTACTAC 59.138 40.000 0.00 0.00 0.00 2.73
2647 3153 3.005472 TCGTCTGCACTTTTACTACTGCT 59.995 43.478 0.00 0.00 0.00 4.24
2648 3154 3.365220 CGTCTGCACTTTTACTACTGCTC 59.635 47.826 0.00 0.00 0.00 4.26
2649 3155 4.307432 GTCTGCACTTTTACTACTGCTCA 58.693 43.478 0.00 0.00 0.00 4.26
2650 3156 4.750098 GTCTGCACTTTTACTACTGCTCAA 59.250 41.667 0.00 0.00 0.00 3.02
2651 3157 4.991056 TCTGCACTTTTACTACTGCTCAAG 59.009 41.667 0.00 0.00 0.00 3.02
2652 3158 4.703897 TGCACTTTTACTACTGCTCAAGT 58.296 39.130 0.00 0.00 43.40 3.16
2657 3163 2.631418 TACTACTGCTCAAGTGCGAC 57.369 50.000 0.00 0.00 40.26 5.19
2698 3208 4.156622 CTGTGCTGCGATGGTGCG 62.157 66.667 0.00 0.00 37.81 5.34
2743 3254 0.035458 ACAAGAAGCTGGACCCTTCG 59.965 55.000 5.22 0.00 42.63 3.79
2785 3296 2.048603 GGAAATGCTGCCTCGCCTT 61.049 57.895 0.00 0.00 0.00 4.35
2814 3325 5.761234 AGGTGAACGAATGCTTGTTTTAGTA 59.239 36.000 0.00 0.00 0.00 1.82
2898 3409 0.546122 TGCTTGTTCGGGCCTATGAT 59.454 50.000 0.84 0.00 0.00 2.45
2904 3415 5.472137 GCTTGTTCGGGCCTATGATAATTTA 59.528 40.000 0.84 0.00 0.00 1.40
3001 3512 3.181475 GGAGATGCACCGTGAAGAGATTA 60.181 47.826 1.65 0.00 0.00 1.75
3034 3545 2.120718 AGACCGGCAGACTTCCCT 59.879 61.111 0.00 0.00 0.00 4.20
3052 3563 2.417719 CCTGCGATAAATCCAGGCTAC 58.582 52.381 11.92 0.00 37.95 3.58
3069 3580 3.467803 GCTACGCCAACAAGAGGAATAT 58.532 45.455 0.00 0.00 0.00 1.28
3107 3618 1.745489 GCCTCCGGTTCTCGCAAAT 60.745 57.895 0.00 0.00 37.59 2.32
3136 3647 4.472286 CATATTTTCCGTTTGACAGCGTT 58.528 39.130 1.83 0.00 0.00 4.84
3172 3683 4.473520 AATGGGTCAGCGAGGCGG 62.474 66.667 0.00 0.00 0.00 6.13
3291 3802 5.474578 ACTACATATGCCCTGTCAGTATG 57.525 43.478 1.58 3.25 37.54 2.39
3296 3807 5.307976 ACATATGCCCTGTCAGTATGTACAT 59.692 40.000 13.93 13.93 35.03 2.29
3378 3889 2.282816 CACCATTTGACGCCCCCA 60.283 61.111 0.00 0.00 0.00 4.96
3556 4067 0.108520 ATGGCAAAAATCGCAGGCAG 60.109 50.000 0.00 0.00 39.97 4.85
3566 4077 2.271497 GCAGGCAGCCACTCTGAT 59.729 61.111 15.80 0.00 45.72 2.90
3577 4088 4.157289 CAGCCACTCTGATAAGCAATTGTT 59.843 41.667 7.40 0.00 45.72 2.83
3584 4095 4.811024 TCTGATAAGCAATTGTTAGGCTCG 59.189 41.667 7.40 0.00 36.76 5.03
3675 4187 7.261325 CCATATCCTGATCCGTTCTTATACAG 58.739 42.308 0.00 0.00 0.00 2.74
3685 4197 4.634004 CCGTTCTTATACAGCAACCATTCA 59.366 41.667 0.00 0.00 0.00 2.57
3689 4201 7.307396 CGTTCTTATACAGCAACCATTCATAGG 60.307 40.741 0.00 0.00 0.00 2.57
3705 4217 5.028549 TCATAGGGAGCTTGTCAAATCTC 57.971 43.478 0.00 6.13 0.00 2.75
3738 4250 3.676172 TGAACCGTTCGTACTGCATTTAG 59.324 43.478 6.78 0.00 0.00 1.85
3739 4251 3.308438 ACCGTTCGTACTGCATTTAGT 57.692 42.857 0.00 0.00 34.71 2.24
3740 4252 4.439305 ACCGTTCGTACTGCATTTAGTA 57.561 40.909 0.00 0.00 32.19 1.82
3796 4309 8.596293 TGCAGTTGATATGAACTATGGATGATA 58.404 33.333 7.28 0.00 34.29 2.15
3818 4331 9.930693 TGATAAAAACAATTATTACCACAACCC 57.069 29.630 0.00 0.00 0.00 4.11
3859 4372 7.874940 TGAATTTCCACTGAGAATTGTAACAG 58.125 34.615 0.00 0.00 36.58 3.16
4288 4801 3.668141 TGCAGATCCACCCAACATAAT 57.332 42.857 0.00 0.00 0.00 1.28
4289 4802 4.787135 TGCAGATCCACCCAACATAATA 57.213 40.909 0.00 0.00 0.00 0.98
4290 4803 4.460263 TGCAGATCCACCCAACATAATAC 58.540 43.478 0.00 0.00 0.00 1.89
4291 4804 4.165950 TGCAGATCCACCCAACATAATACT 59.834 41.667 0.00 0.00 0.00 2.12
4292 4805 4.516698 GCAGATCCACCCAACATAATACTG 59.483 45.833 0.00 0.00 0.00 2.74
4293 4806 5.065914 CAGATCCACCCAACATAATACTGG 58.934 45.833 0.00 0.00 0.00 4.00
4294 4807 4.975147 AGATCCACCCAACATAATACTGGA 59.025 41.667 0.00 0.00 31.38 3.86
4295 4808 5.431731 AGATCCACCCAACATAATACTGGAA 59.568 40.000 0.00 0.00 31.38 3.53
4296 4809 5.725551 TCCACCCAACATAATACTGGAAT 57.274 39.130 0.00 0.00 31.38 3.01
4297 4810 6.086011 TCCACCCAACATAATACTGGAATT 57.914 37.500 0.00 0.00 31.38 2.17
4298 4811 5.890985 TCCACCCAACATAATACTGGAATTG 59.109 40.000 0.00 0.00 31.38 2.32
4299 4812 5.068987 CCACCCAACATAATACTGGAATTGG 59.931 44.000 0.00 0.00 35.84 3.16
4300 4813 5.890985 CACCCAACATAATACTGGAATTGGA 59.109 40.000 1.70 0.00 37.85 3.53
4301 4814 6.379703 CACCCAACATAATACTGGAATTGGAA 59.620 38.462 1.70 0.00 37.85 3.53
4302 4815 6.607198 ACCCAACATAATACTGGAATTGGAAG 59.393 38.462 1.70 0.00 37.85 3.46
4303 4816 6.833416 CCCAACATAATACTGGAATTGGAAGA 59.167 38.462 1.70 0.00 37.85 2.87
4304 4817 7.341769 CCCAACATAATACTGGAATTGGAAGAA 59.658 37.037 1.70 0.00 37.85 2.52
4305 4818 8.748412 CCAACATAATACTGGAATTGGAAGAAA 58.252 33.333 0.00 0.00 37.85 2.52
4311 4824 7.881775 ATACTGGAATTGGAAGAAATACACC 57.118 36.000 0.00 0.00 0.00 4.16
4312 4825 5.892348 ACTGGAATTGGAAGAAATACACCT 58.108 37.500 0.00 0.00 0.00 4.00
4313 4826 6.314917 ACTGGAATTGGAAGAAATACACCTT 58.685 36.000 0.00 0.00 0.00 3.50
4314 4827 6.209391 ACTGGAATTGGAAGAAATACACCTTG 59.791 38.462 0.00 0.00 0.00 3.61
4315 4828 5.047377 TGGAATTGGAAGAAATACACCTTGC 60.047 40.000 0.00 0.00 0.00 4.01
4316 4829 5.047377 GGAATTGGAAGAAATACACCTTGCA 60.047 40.000 0.00 0.00 38.62 4.08
4317 4830 6.351286 GGAATTGGAAGAAATACACCTTGCAT 60.351 38.462 0.00 0.00 39.75 3.96
4318 4831 6.610075 ATTGGAAGAAATACACCTTGCATT 57.390 33.333 0.00 0.00 39.75 3.56
4319 4832 6.418057 TTGGAAGAAATACACCTTGCATTT 57.582 33.333 0.00 0.00 39.75 2.32
4320 4833 6.418057 TGGAAGAAATACACCTTGCATTTT 57.582 33.333 0.00 0.00 36.14 1.82
4321 4834 6.222389 TGGAAGAAATACACCTTGCATTTTG 58.778 36.000 0.00 0.00 36.14 2.44
4322 4835 5.639082 GGAAGAAATACACCTTGCATTTTGG 59.361 40.000 0.00 0.00 32.10 3.28
4323 4836 6.418057 AAGAAATACACCTTGCATTTTGGA 57.582 33.333 0.00 0.00 0.00 3.53
4324 4837 6.418057 AGAAATACACCTTGCATTTTGGAA 57.582 33.333 0.00 0.00 0.00 3.53
4325 4838 7.008021 AGAAATACACCTTGCATTTTGGAAT 57.992 32.000 0.00 0.00 0.00 3.01
4326 4839 7.452562 AGAAATACACCTTGCATTTTGGAATT 58.547 30.769 0.00 0.00 0.00 2.17
4327 4840 7.938490 AGAAATACACCTTGCATTTTGGAATTT 59.062 29.630 0.00 0.00 0.00 1.82
4328 4841 8.462589 AAATACACCTTGCATTTTGGAATTTT 57.537 26.923 0.00 0.00 0.00 1.82
4329 4842 9.566432 AAATACACCTTGCATTTTGGAATTTTA 57.434 25.926 0.00 0.00 0.00 1.52
4330 4843 9.737844 AATACACCTTGCATTTTGGAATTTTAT 57.262 25.926 0.00 0.00 0.00 1.40
4331 4844 7.671495 ACACCTTGCATTTTGGAATTTTATC 57.329 32.000 0.00 0.00 0.00 1.75
4332 4845 7.222872 ACACCTTGCATTTTGGAATTTTATCA 58.777 30.769 0.00 0.00 0.00 2.15
4333 4846 7.718753 ACACCTTGCATTTTGGAATTTTATCAA 59.281 29.630 0.00 0.00 0.00 2.57
4334 4847 8.566260 CACCTTGCATTTTGGAATTTTATCAAA 58.434 29.630 0.00 0.00 0.00 2.69
4335 4848 9.129532 ACCTTGCATTTTGGAATTTTATCAAAA 57.870 25.926 0.00 0.00 42.22 2.44
4336 4849 9.962783 CCTTGCATTTTGGAATTTTATCAAAAA 57.037 25.926 0.00 0.00 41.63 1.94
4367 4880 7.138054 ACACCTTATATAAAGGAACAGAGGG 57.862 40.000 10.67 4.11 39.81 4.30
4368 4881 6.906901 ACACCTTATATAAAGGAACAGAGGGA 59.093 38.462 10.67 0.00 39.81 4.20
4369 4882 7.071321 ACACCTTATATAAAGGAACAGAGGGAG 59.929 40.741 10.67 3.30 39.81 4.30
4450 5010 2.599408 TATGGATCGGAGGGAGTACC 57.401 55.000 0.00 0.00 40.67 3.34
4451 5011 0.561184 ATGGATCGGAGGGAGTACCA 59.439 55.000 0.00 0.00 43.89 3.25
4457 5017 2.332117 TCGGAGGGAGTACCAAAGTTT 58.668 47.619 0.00 0.00 43.89 2.66
4514 5074 6.313658 TCTTTCATCCACGTCAAGTCAATATG 59.686 38.462 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.374399 ACGGTAACAAAGACTACAACAGG 58.626 43.478 0.00 0.00 0.00 4.00
1 2 4.446719 GGACGGTAACAAAGACTACAACAG 59.553 45.833 0.00 0.00 0.00 3.16
2 3 4.370917 GGACGGTAACAAAGACTACAACA 58.629 43.478 0.00 0.00 0.00 3.33
3 4 3.426525 CGGACGGTAACAAAGACTACAAC 59.573 47.826 0.00 0.00 0.00 3.32
21 22 2.798148 AATTGCTCCACGGGTCGGAC 62.798 60.000 0.00 0.00 0.00 4.79
37 38 6.829849 TGAAAAATCAAGGGAAGCTCAAATT 58.170 32.000 0.00 0.00 0.00 1.82
38 39 6.423776 TGAAAAATCAAGGGAAGCTCAAAT 57.576 33.333 0.00 0.00 0.00 2.32
88 89 0.179205 CTTACGTCGACGGACCAGAC 60.179 60.000 37.89 0.00 44.95 3.51
90 91 0.453950 CACTTACGTCGACGGACCAG 60.454 60.000 37.89 27.89 44.95 4.00
96 97 2.921126 ACTTTACCACTTACGTCGACG 58.079 47.619 34.58 34.58 46.33 5.12
102 103 6.894828 AGTAAATGCAACTTTACCACTTACG 58.105 36.000 15.92 0.00 40.77 3.18
104 105 8.455682 GCATAGTAAATGCAACTTTACCACTTA 58.544 33.333 15.92 5.97 44.00 2.24
131 134 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
132 135 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
133 136 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
134 137 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
135 138 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
136 139 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
137 140 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
138 141 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
139 142 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
140 143 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
141 144 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
142 145 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
143 146 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
144 147 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
145 148 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
146 149 9.975218 ATTAGTACAAAGTTGGGTCATCTATTT 57.025 29.630 0.00 0.00 0.00 1.40
147 150 9.975218 AATTAGTACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
148 151 9.975218 AAATTAGTACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
150 153 9.449719 CTAAATTAGTACAAAGTTGGGTCATCT 57.550 33.333 0.00 0.00 0.00 2.90
151 154 9.227777 ACTAAATTAGTACAAAGTTGGGTCATC 57.772 33.333 3.48 0.00 37.23 2.92
172 175 9.546428 GACCCAACTTTGTACTAACTTACTAAA 57.454 33.333 0.00 0.00 0.00 1.85
173 176 8.703743 TGACCCAACTTTGTACTAACTTACTAA 58.296 33.333 0.00 0.00 0.00 2.24
174 177 8.248904 TGACCCAACTTTGTACTAACTTACTA 57.751 34.615 0.00 0.00 0.00 1.82
175 178 7.128234 TGACCCAACTTTGTACTAACTTACT 57.872 36.000 0.00 0.00 0.00 2.24
176 179 7.876582 AGATGACCCAACTTTGTACTAACTTAC 59.123 37.037 0.00 0.00 0.00 2.34
177 180 7.970102 AGATGACCCAACTTTGTACTAACTTA 58.030 34.615 0.00 0.00 0.00 2.24
178 181 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
179 182 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
180 183 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
181 184 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
182 185 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
183 186 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
184 187 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
185 188 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
186 189 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
187 190 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
188 191 6.211384 CCTTCCAAAATAGATGACCCAACTTT 59.789 38.462 0.00 0.00 0.00 2.66
189 192 5.716703 CCTTCCAAAATAGATGACCCAACTT 59.283 40.000 0.00 0.00 0.00 2.66
190 193 5.264395 CCTTCCAAAATAGATGACCCAACT 58.736 41.667 0.00 0.00 0.00 3.16
191 194 4.402474 CCCTTCCAAAATAGATGACCCAAC 59.598 45.833 0.00 0.00 0.00 3.77
192 195 4.293634 TCCCTTCCAAAATAGATGACCCAA 59.706 41.667 0.00 0.00 0.00 4.12
193 196 3.855599 TCCCTTCCAAAATAGATGACCCA 59.144 43.478 0.00 0.00 0.00 4.51
194 197 4.464947 CTCCCTTCCAAAATAGATGACCC 58.535 47.826 0.00 0.00 0.00 4.46
195 198 4.464947 CCTCCCTTCCAAAATAGATGACC 58.535 47.826 0.00 0.00 0.00 4.02
196 199 4.166144 TCCCTCCCTTCCAAAATAGATGAC 59.834 45.833 0.00 0.00 0.00 3.06
197 200 4.379875 TCCCTCCCTTCCAAAATAGATGA 58.620 43.478 0.00 0.00 0.00 2.92
198 201 4.166919 ACTCCCTCCCTTCCAAAATAGATG 59.833 45.833 0.00 0.00 0.00 2.90
199 202 4.384465 ACTCCCTCCCTTCCAAAATAGAT 58.616 43.478 0.00 0.00 0.00 1.98
200 203 3.815507 ACTCCCTCCCTTCCAAAATAGA 58.184 45.455 0.00 0.00 0.00 1.98
201 204 5.710409 TTACTCCCTCCCTTCCAAAATAG 57.290 43.478 0.00 0.00 0.00 1.73
202 205 5.734140 TGATTACTCCCTCCCTTCCAAAATA 59.266 40.000 0.00 0.00 0.00 1.40
203 206 4.544152 TGATTACTCCCTCCCTTCCAAAAT 59.456 41.667 0.00 0.00 0.00 1.82
204 207 3.920197 TGATTACTCCCTCCCTTCCAAAA 59.080 43.478 0.00 0.00 0.00 2.44
205 208 3.265995 GTGATTACTCCCTCCCTTCCAAA 59.734 47.826 0.00 0.00 0.00 3.28
206 209 2.844348 GTGATTACTCCCTCCCTTCCAA 59.156 50.000 0.00 0.00 0.00 3.53
207 210 2.045885 AGTGATTACTCCCTCCCTTCCA 59.954 50.000 0.00 0.00 28.79 3.53
208 211 2.765502 AGTGATTACTCCCTCCCTTCC 58.234 52.381 0.00 0.00 28.79 3.46
209 212 3.118223 CCAAGTGATTACTCCCTCCCTTC 60.118 52.174 0.00 0.00 35.69 3.46
210 213 2.846827 CCAAGTGATTACTCCCTCCCTT 59.153 50.000 0.00 0.00 35.69 3.95
211 214 2.482494 CCAAGTGATTACTCCCTCCCT 58.518 52.381 0.00 0.00 35.69 4.20
212 215 1.490910 CCCAAGTGATTACTCCCTCCC 59.509 57.143 0.00 0.00 35.69 4.30
213 216 1.490910 CCCCAAGTGATTACTCCCTCC 59.509 57.143 0.00 0.00 35.69 4.30
214 217 1.134068 GCCCCAAGTGATTACTCCCTC 60.134 57.143 0.00 0.00 35.69 4.30
215 218 0.919710 GCCCCAAGTGATTACTCCCT 59.080 55.000 0.00 0.00 35.69 4.20
216 219 0.919710 AGCCCCAAGTGATTACTCCC 59.080 55.000 0.00 0.00 35.69 4.30
217 220 3.136626 ACATAGCCCCAAGTGATTACTCC 59.863 47.826 0.00 0.00 35.69 3.85
218 221 4.130118 CACATAGCCCCAAGTGATTACTC 58.870 47.826 0.00 0.00 35.69 2.59
219 222 3.685550 GCACATAGCCCCAAGTGATTACT 60.686 47.826 0.00 0.00 36.43 2.24
220 223 2.618709 GCACATAGCCCCAAGTGATTAC 59.381 50.000 0.00 0.00 37.23 1.89
221 224 2.930950 GCACATAGCCCCAAGTGATTA 58.069 47.619 0.00 0.00 37.23 1.75
259 262 2.202518 CGGCACCGAACGACGTAT 60.203 61.111 2.01 0.00 42.83 3.06
275 278 1.205657 GCAAATCTGATGGCATTGCG 58.794 50.000 0.00 0.00 37.27 4.85
296 299 1.867233 ACGTGATGCACACTTGAGAAC 59.133 47.619 14.60 0.00 46.24 3.01
343 347 1.414181 ACGTGGCCTCTGAATAGATGG 59.586 52.381 3.32 0.00 31.21 3.51
381 385 4.294523 GCACCAGGCAATACGACA 57.705 55.556 0.00 0.00 43.97 4.35
419 423 0.179179 GTTGGCATCTTCGCTTGAGC 60.179 55.000 0.00 0.00 37.78 4.26
438 442 1.797933 CCGTTCTGTCTCGAGCGTG 60.798 63.158 7.81 0.00 36.14 5.34
467 471 1.605710 CAATGGGCTGCTTAAGATCCG 59.394 52.381 6.67 0.00 0.00 4.18
485 489 2.143122 GCTGTCGTTGATCAGTTCCAA 58.857 47.619 0.00 0.00 34.57 3.53
512 516 5.509272 TCGACGTCTACTTATAAACAAAGCG 59.491 40.000 14.70 0.00 0.00 4.68
524 528 5.333111 GCACAGAATTTTTCGACGTCTACTT 60.333 40.000 14.70 0.00 34.02 2.24
531 535 5.617609 TGATAAGCACAGAATTTTTCGACG 58.382 37.500 0.00 0.00 34.02 5.12
535 539 6.151817 ACTCCCTGATAAGCACAGAATTTTTC 59.848 38.462 0.00 0.00 37.54 2.29
536 540 6.012745 ACTCCCTGATAAGCACAGAATTTTT 58.987 36.000 0.00 0.00 37.54 1.94
557 561 5.054477 TGACTAATTAAGGCCGCAATACTC 58.946 41.667 0.00 0.00 28.59 2.59
558 562 5.031066 TGACTAATTAAGGCCGCAATACT 57.969 39.130 0.00 0.00 28.59 2.12
559 563 4.814771 ACTGACTAATTAAGGCCGCAATAC 59.185 41.667 0.00 0.00 28.59 1.89
597 601 3.817647 GCCTCTGCTTATTCTACATTGGG 59.182 47.826 0.00 0.00 33.53 4.12
673 689 2.683362 GGAATCCAAGGGATGTTCGTTC 59.317 50.000 0.00 0.00 42.27 3.95
682 698 1.271840 CCGGAGTGGAATCCAAGGGA 61.272 60.000 2.31 0.00 42.00 4.20
700 716 3.181490 GGCAGGGAATCGTTGTTATTTCC 60.181 47.826 0.00 0.00 37.49 3.13
727 743 1.971695 GTGAGGCGTTTTGGAGGGG 60.972 63.158 0.00 0.00 0.00 4.79
777 1114 6.986817 AGCTGTATAAACATCAGATGGTACAC 59.013 38.462 15.13 7.54 36.40 2.90
779 1116 9.712305 AATAGCTGTATAAACATCAGATGGTAC 57.288 33.333 15.13 11.45 34.37 3.34
798 1135 4.026475 GGAAGAATCGACGTTCAATAGCTG 60.026 45.833 0.00 0.00 0.00 4.24
799 1136 4.113354 GGAAGAATCGACGTTCAATAGCT 58.887 43.478 11.08 0.00 0.00 3.32
800 1137 3.245519 GGGAAGAATCGACGTTCAATAGC 59.754 47.826 11.08 0.00 0.00 2.97
857 1195 6.148811 TGGAATACTTCATTTTTGTCTCGTCC 59.851 38.462 0.00 0.00 0.00 4.79
913 1251 1.517257 CTGGTACTTCCGCAGCTCG 60.517 63.158 0.00 0.00 39.52 5.03
917 1255 2.509336 CCGCTGGTACTTCCGCAG 60.509 66.667 0.00 0.00 39.52 5.18
952 1290 1.162698 GGTTAGGTTCCTTGCGGTTC 58.837 55.000 0.00 0.00 0.00 3.62
957 1295 1.534163 GTCGTTGGTTAGGTTCCTTGC 59.466 52.381 0.00 0.00 0.00 4.01
959 1297 1.270465 CGGTCGTTGGTTAGGTTCCTT 60.270 52.381 0.00 0.00 0.00 3.36
961 1299 0.318120 TCGGTCGTTGGTTAGGTTCC 59.682 55.000 0.00 0.00 0.00 3.62
962 1300 2.153366 TTCGGTCGTTGGTTAGGTTC 57.847 50.000 0.00 0.00 0.00 3.62
964 1302 1.688197 TCTTTCGGTCGTTGGTTAGGT 59.312 47.619 0.00 0.00 0.00 3.08
965 1303 2.029649 TCTCTTTCGGTCGTTGGTTAGG 60.030 50.000 0.00 0.00 0.00 2.69
966 1304 2.985139 GTCTCTTTCGGTCGTTGGTTAG 59.015 50.000 0.00 0.00 0.00 2.34
1012 1356 2.885644 GTGCATGGTCGCGATCGT 60.886 61.111 14.06 11.20 36.96 3.73
1370 1726 1.877165 GCGTACCTTGCGGAGTAGC 60.877 63.158 0.00 0.00 37.71 3.58
1375 1731 4.728102 CGTGGCGTACCTTGCGGA 62.728 66.667 0.00 0.00 36.63 5.54
1389 1745 1.207593 GCTTGCTAAGTGGTGCGTG 59.792 57.895 0.00 0.00 0.00 5.34
1396 1752 1.503542 CCGGCTTGCTTGCTAAGTG 59.496 57.895 0.00 0.00 0.00 3.16
1417 1773 4.966787 TTCCCAAGGTGGCACGGC 62.967 66.667 12.17 0.00 35.79 5.68
1428 1784 4.708386 ACGCCGCCGAATTCCCAA 62.708 61.111 0.00 0.00 38.29 4.12
1437 1793 1.517694 ATTACAGTACACGCCGCCG 60.518 57.895 0.00 0.00 41.14 6.46
1449 1805 3.982213 TCGACGGACGACATTACAG 57.018 52.632 0.00 0.00 46.45 2.74
1462 1818 3.807538 ACACCGGGATCGTCGACG 61.808 66.667 31.30 31.30 41.45 5.12
1463 1819 2.202570 CACACCGGGATCGTCGAC 60.203 66.667 6.32 5.18 33.95 4.20
1464 1820 2.360225 TCACACCGGGATCGTCGA 60.360 61.111 6.32 0.00 33.95 4.20
1473 1829 1.270094 TGCTCTGTAAACTCACACCGG 60.270 52.381 0.00 0.00 0.00 5.28
1501 1857 2.960170 GTCTCCACGTACCTGCGT 59.040 61.111 0.00 0.00 46.88 5.24
1502 1858 2.202440 CGTCTCCACGTACCTGCG 60.202 66.667 0.00 0.00 41.42 5.18
2208 2597 3.119096 GCACGAACTCCCGCTTCC 61.119 66.667 0.00 0.00 0.00 3.46
2634 3140 3.987868 TCGCACTTGAGCAGTAGTAAAAG 59.012 43.478 0.00 0.00 32.76 2.27
2643 3149 0.733909 TCATCGTCGCACTTGAGCAG 60.734 55.000 0.00 0.00 0.00 4.24
2647 3153 0.179111 GGGATCATCGTCGCACTTGA 60.179 55.000 0.00 0.00 0.00 3.02
2648 3154 0.460109 TGGGATCATCGTCGCACTTG 60.460 55.000 0.00 0.00 36.32 3.16
2649 3155 0.179100 CTGGGATCATCGTCGCACTT 60.179 55.000 0.00 0.00 36.32 3.16
2650 3156 1.323271 ACTGGGATCATCGTCGCACT 61.323 55.000 0.00 0.00 36.32 4.40
2651 3157 1.141881 ACTGGGATCATCGTCGCAC 59.858 57.895 0.00 0.00 36.32 5.34
2652 3158 1.141665 CACTGGGATCATCGTCGCA 59.858 57.895 0.00 0.00 38.54 5.10
2657 3163 1.478105 TGTCAGTCACTGGGATCATCG 59.522 52.381 4.57 0.00 31.51 3.84
2698 3208 4.894784 TCCAGTTGTAACCTGTGAGAATC 58.105 43.478 0.00 0.00 0.00 2.52
2743 3254 1.136336 GTCTTGACCGCGTTCATGAAC 60.136 52.381 25.68 25.68 32.97 3.18
2758 3269 1.067354 GGCAGCATTTCCTTGGTCTTG 60.067 52.381 0.00 0.00 0.00 3.02
2785 3296 2.254546 AGCATTCGTTCACCTTCACA 57.745 45.000 0.00 0.00 0.00 3.58
2846 3357 7.996644 ACAGGACTCAAATTTAACTGAAACCTA 59.003 33.333 11.33 0.00 30.83 3.08
3001 3512 1.482593 GGTCTGTTCCACTGATCGGAT 59.517 52.381 9.00 0.00 30.35 4.18
3034 3545 2.148916 CGTAGCCTGGATTTATCGCA 57.851 50.000 0.00 0.00 0.00 5.10
3052 3563 3.689161 TGAACATATTCCTCTTGTTGGCG 59.311 43.478 0.00 0.00 33.92 5.69
3069 3580 3.029564 GCGCCCGCGTAAATGAACA 62.030 57.895 11.18 0.00 42.09 3.18
3107 3618 6.239396 TGTCAAACGGAAAATATGGGAGTAA 58.761 36.000 0.00 0.00 0.00 2.24
3172 3683 4.452733 CGCCCCTCGGAAGACCAC 62.453 72.222 0.00 0.00 35.39 4.16
3296 3807 9.832445 AATTCCAATAATAGCTTCGAAGAGTTA 57.168 29.630 28.95 20.60 38.43 2.24
3363 3874 0.684153 AGATTGGGGGCGTCAAATGG 60.684 55.000 0.00 0.00 0.00 3.16
3556 4067 4.708726 AACAATTGCTTATCAGAGTGGC 57.291 40.909 5.05 0.00 0.00 5.01
3566 4077 2.705730 TGCGAGCCTAACAATTGCTTA 58.294 42.857 5.05 3.17 34.99 3.09
3577 4088 1.674322 GCCCAGTTTTGCGAGCCTA 60.674 57.895 0.00 0.00 0.00 3.93
3584 4095 3.110447 TCAGATTTTGCCCAGTTTTGC 57.890 42.857 0.00 0.00 0.00 3.68
3675 4187 2.355010 AGCTCCCTATGAATGGTTGC 57.645 50.000 0.00 0.00 0.00 4.17
3685 4197 3.742640 GCGAGATTTGACAAGCTCCCTAT 60.743 47.826 12.04 0.00 41.66 2.57
3689 4201 1.442769 TGCGAGATTTGACAAGCTCC 58.557 50.000 12.04 7.56 41.66 4.70
3705 4217 1.061131 GAACGGTTCATCAGTGATGCG 59.939 52.381 25.53 23.67 39.63 4.73
3738 4250 5.123820 TGCTTGTTATCCTGCTGTGAAATAC 59.876 40.000 0.00 0.00 0.00 1.89
3739 4251 5.252547 TGCTTGTTATCCTGCTGTGAAATA 58.747 37.500 0.00 0.00 0.00 1.40
3740 4252 4.081406 TGCTTGTTATCCTGCTGTGAAAT 58.919 39.130 0.00 0.00 0.00 2.17
3796 4309 7.565680 TGTGGGTTGTGGTAATAATTGTTTTT 58.434 30.769 0.00 0.00 0.00 1.94
3799 4312 6.071984 TCTGTGGGTTGTGGTAATAATTGTT 58.928 36.000 0.00 0.00 0.00 2.83
3818 4331 9.559958 GTGGAAATTCAATATGTTTACTCTGTG 57.440 33.333 0.00 0.00 0.00 3.66
3859 4372 3.638484 AGAACATTAAAAGTTGCCGTGC 58.362 40.909 1.85 0.00 0.00 5.34
4224 4737 8.870075 ACTTTTCAGCTAAGGAAACTGATAAT 57.130 30.769 0.05 0.00 42.68 1.28
4288 4801 7.027874 AGGTGTATTTCTTCCAATTCCAGTA 57.972 36.000 0.00 0.00 0.00 2.74
4289 4802 5.892348 AGGTGTATTTCTTCCAATTCCAGT 58.108 37.500 0.00 0.00 0.00 4.00
4290 4803 6.624423 CAAGGTGTATTTCTTCCAATTCCAG 58.376 40.000 0.00 0.00 0.00 3.86
4291 4804 5.047377 GCAAGGTGTATTTCTTCCAATTCCA 60.047 40.000 0.00 0.00 0.00 3.53
4292 4805 5.047377 TGCAAGGTGTATTTCTTCCAATTCC 60.047 40.000 0.00 0.00 0.00 3.01
4293 4806 6.024552 TGCAAGGTGTATTTCTTCCAATTC 57.975 37.500 0.00 0.00 0.00 2.17
4294 4807 6.610075 ATGCAAGGTGTATTTCTTCCAATT 57.390 33.333 0.00 0.00 0.00 2.32
4295 4808 6.610075 AATGCAAGGTGTATTTCTTCCAAT 57.390 33.333 0.00 0.00 28.11 3.16
4296 4809 6.418057 AAATGCAAGGTGTATTTCTTCCAA 57.582 33.333 0.00 0.00 38.03 3.53
4297 4810 6.222389 CAAAATGCAAGGTGTATTTCTTCCA 58.778 36.000 5.03 0.00 40.82 3.53
4298 4811 5.639082 CCAAAATGCAAGGTGTATTTCTTCC 59.361 40.000 5.03 0.00 40.82 3.46
4299 4812 6.454795 TCCAAAATGCAAGGTGTATTTCTTC 58.545 36.000 5.03 0.00 40.82 2.87
4300 4813 6.418057 TCCAAAATGCAAGGTGTATTTCTT 57.582 33.333 5.03 0.00 40.82 2.52
4301 4814 6.418057 TTCCAAAATGCAAGGTGTATTTCT 57.582 33.333 5.03 0.00 40.82 2.52
4302 4815 7.671495 AATTCCAAAATGCAAGGTGTATTTC 57.329 32.000 5.03 0.00 40.82 2.17
4303 4816 8.462589 AAAATTCCAAAATGCAAGGTGTATTT 57.537 26.923 0.00 0.00 42.93 1.40
4304 4817 9.737844 ATAAAATTCCAAAATGCAAGGTGTATT 57.262 25.926 0.00 0.00 34.13 1.89
4305 4818 9.382275 GATAAAATTCCAAAATGCAAGGTGTAT 57.618 29.630 0.00 0.00 0.00 2.29
4306 4819 8.370940 TGATAAAATTCCAAAATGCAAGGTGTA 58.629 29.630 0.00 0.00 0.00 2.90
4307 4820 7.222872 TGATAAAATTCCAAAATGCAAGGTGT 58.777 30.769 0.00 0.00 0.00 4.16
4308 4821 7.670009 TGATAAAATTCCAAAATGCAAGGTG 57.330 32.000 0.00 0.00 0.00 4.00
4309 4822 8.688747 TTTGATAAAATTCCAAAATGCAAGGT 57.311 26.923 0.00 0.00 0.00 3.50
4310 4823 9.962783 TTTTTGATAAAATTCCAAAATGCAAGG 57.037 25.926 0.00 0.00 38.87 3.61
4341 4854 8.881262 CCCTCTGTTCCTTTATATAAGGTGTAT 58.119 37.037 4.13 0.00 38.55 2.29
4342 4855 8.069356 TCCCTCTGTTCCTTTATATAAGGTGTA 58.931 37.037 4.13 0.00 38.55 2.90
4343 4856 6.906901 TCCCTCTGTTCCTTTATATAAGGTGT 59.093 38.462 4.13 0.00 38.55 4.16
4344 4857 7.071321 ACTCCCTCTGTTCCTTTATATAAGGTG 59.929 40.741 4.13 0.00 38.55 4.00
4345 4858 7.140304 ACTCCCTCTGTTCCTTTATATAAGGT 58.860 38.462 4.13 0.00 38.55 3.50
4346 4859 7.619512 ACTCCCTCTGTTCCTTTATATAAGG 57.380 40.000 0.00 0.00 38.78 2.69
4347 4860 9.589461 TCTACTCCCTCTGTTCCTTTATATAAG 57.411 37.037 0.00 0.00 0.00 1.73
4349 4862 9.535170 CATCTACTCCCTCTGTTCCTTTATATA 57.465 37.037 0.00 0.00 0.00 0.86
4350 4863 7.038658 GCATCTACTCCCTCTGTTCCTTTATAT 60.039 40.741 0.00 0.00 0.00 0.86
4351 4864 6.267928 GCATCTACTCCCTCTGTTCCTTTATA 59.732 42.308 0.00 0.00 0.00 0.98
4352 4865 5.071115 GCATCTACTCCCTCTGTTCCTTTAT 59.929 44.000 0.00 0.00 0.00 1.40
4353 4866 4.406003 GCATCTACTCCCTCTGTTCCTTTA 59.594 45.833 0.00 0.00 0.00 1.85
4354 4867 3.198853 GCATCTACTCCCTCTGTTCCTTT 59.801 47.826 0.00 0.00 0.00 3.11
4355 4868 2.769095 GCATCTACTCCCTCTGTTCCTT 59.231 50.000 0.00 0.00 0.00 3.36
4356 4869 2.393646 GCATCTACTCCCTCTGTTCCT 58.606 52.381 0.00 0.00 0.00 3.36
4357 4870 1.067821 CGCATCTACTCCCTCTGTTCC 59.932 57.143 0.00 0.00 0.00 3.62
4358 4871 2.025155 TCGCATCTACTCCCTCTGTTC 58.975 52.381 0.00 0.00 0.00 3.18
4359 4872 1.751924 GTCGCATCTACTCCCTCTGTT 59.248 52.381 0.00 0.00 0.00 3.16
4360 4873 1.064314 AGTCGCATCTACTCCCTCTGT 60.064 52.381 0.00 0.00 0.00 3.41
4361 4874 1.686355 AGTCGCATCTACTCCCTCTG 58.314 55.000 0.00 0.00 0.00 3.35
4362 4875 2.428890 CAAAGTCGCATCTACTCCCTCT 59.571 50.000 0.00 0.00 0.00 3.69
4363 4876 2.427453 TCAAAGTCGCATCTACTCCCTC 59.573 50.000 0.00 0.00 0.00 4.30
4364 4877 2.457598 TCAAAGTCGCATCTACTCCCT 58.542 47.619 0.00 0.00 0.00 4.20
4365 4878 2.961526 TCAAAGTCGCATCTACTCCC 57.038 50.000 0.00 0.00 0.00 4.30
4366 4879 3.126831 CCATCAAAGTCGCATCTACTCC 58.873 50.000 0.00 0.00 0.00 3.85
4367 4880 4.046938 TCCATCAAAGTCGCATCTACTC 57.953 45.455 0.00 0.00 0.00 2.59
4368 4881 4.184629 GTTCCATCAAAGTCGCATCTACT 58.815 43.478 0.00 0.00 0.00 2.57
4369 4882 3.932710 TGTTCCATCAAAGTCGCATCTAC 59.067 43.478 0.00 0.00 0.00 2.59
4421 4981 5.785423 TCCCTCCGATCCATATTAATTGTCT 59.215 40.000 0.00 0.00 0.00 3.41
4476 5036 7.176690 ACGTGGATGAAAGATAACCTTTTGATT 59.823 33.333 0.00 0.00 44.63 2.57


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

AutoCloner maintained by Alex Coulton.