Multiple sequence alignment - TraesCS3A01G167500

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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 TraesCS3A01G167500 chr3A 100.000 3870 0 0 1 3870 174277885 174281754 0.000000e+00 7147.0
1 TraesCS3A01G167500 chr3A 87.500 120 15 0 2492 2611 174280322 174280441 5.210000e-29 139.0
2 TraesCS3A01G167500 chr3A 87.500 120 15 0 2438 2557 174280376 174280495 5.210000e-29 139.0
3 TraesCS3A01G167500 chr3B 99.419 3445 19 1 427 3870 160141470 160144914 0.000000e+00 6250.0
4 TraesCS3A01G167500 chr3B 99.086 2408 21 1 1464 3870 52926252 52928659 0.000000e+00 4324.0
5 TraesCS3A01G167500 chr3B 98.752 1042 11 2 427 1467 52924722 52925762 0.000000e+00 1851.0
6 TraesCS3A01G167500 chr3B 92.017 238 13 4 188 422 226091210 226090976 2.880000e-86 329.0
7 TraesCS3A01G167500 chr3B 87.500 120 15 0 2492 2611 52927226 52927345 5.210000e-29 139.0
8 TraesCS3A01G167500 chr3B 87.500 120 15 0 2438 2557 52927280 52927399 5.210000e-29 139.0
9 TraesCS3A01G167500 chr3B 87.500 120 15 0 2492 2611 160143481 160143600 5.210000e-29 139.0
10 TraesCS3A01G167500 chr3B 87.500 120 15 0 2438 2557 160143535 160143654 5.210000e-29 139.0
11 TraesCS3A01G167500 chr2A 96.456 1326 31 6 2546 3870 762296480 762295170 0.000000e+00 2174.0
12 TraesCS3A01G167500 chr2A 96.839 1044 23 4 1460 2503 762297448 762296415 0.000000e+00 1736.0
13 TraesCS3A01G167500 chr2A 96.435 1038 31 5 432 1467 762298965 762297932 0.000000e+00 1707.0
14 TraesCS3A01G167500 chr2A 90.306 196 17 2 427 621 762293810 762294004 4.960000e-64 255.0
15 TraesCS3A01G167500 chr2A 96.970 66 2 0 2492 2557 762296480 762296415 1.140000e-20 111.0
16 TraesCS3A01G167500 chr7B 93.234 1212 67 9 2647 3856 571593636 571594834 0.000000e+00 1770.0
17 TraesCS3A01G167500 chr7B 94.118 901 53 0 1460 2360 571592668 571593568 0.000000e+00 1371.0
18 TraesCS3A01G167500 chr7B 81.989 1066 143 30 427 1467 571591141 571592182 0.000000e+00 859.0
19 TraesCS3A01G167500 chr7B 84.236 203 31 1 430 631 571596258 571596056 3.050000e-46 196.0
20 TraesCS3A01G167500 chr7B 77.193 171 32 6 2186 2352 713070675 713070508 4.120000e-15 93.5
21 TraesCS3A01G167500 chr6A 93.069 1212 69 9 2647 3856 584920801 584921999 0.000000e+00 1759.0
22 TraesCS3A01G167500 chr6A 94.007 901 54 0 1460 2360 584919833 584920733 0.000000e+00 1365.0
23 TraesCS3A01G167500 chr6A 81.759 1069 147 32 423 1467 584918303 584919347 0.000000e+00 850.0
24 TraesCS3A01G167500 chr6A 82.949 780 106 21 698 1467 273733334 273734096 0.000000e+00 678.0
25 TraesCS3A01G167500 chr6A 84.043 188 30 0 444 631 584923408 584923221 8.540000e-42 182.0
26 TraesCS3A01G167500 chr4A 93.004 1215 70 9 2647 3859 690104164 690102963 0.000000e+00 1759.0
27 TraesCS3A01G167500 chr4A 94.118 901 53 0 1460 2360 690105132 690104232 0.000000e+00 1371.0
28 TraesCS3A01G167500 chr4A 82.073 1071 141 32 423 1467 690106663 690105618 0.000000e+00 867.0
29 TraesCS3A01G167500 chr4A 83.981 206 32 1 427 631 690101538 690101743 3.050000e-46 196.0
30 TraesCS3A01G167500 chr2B 82.429 1161 186 14 2712 3859 23573820 23572665 0.000000e+00 998.0
31 TraesCS3A01G167500 chr6B 83.213 971 159 4 2727 3695 63421255 63420287 0.000000e+00 887.0
32 TraesCS3A01G167500 chr6B 76.159 1057 205 35 433 1461 666827760 666826723 2.670000e-141 512.0
33 TraesCS3A01G167500 chr1B 84.427 899 138 2 1460 2357 420604317 420603420 0.000000e+00 883.0
34 TraesCS3A01G167500 chr1B 78.068 766 142 21 712 1461 551219948 551219193 9.800000e-126 460.0
35 TraesCS3A01G167500 chr6D 83.007 971 162 3 2727 3695 469084785 469083816 0.000000e+00 876.0
36 TraesCS3A01G167500 chr7D 84.396 737 115 0 1460 2196 19557566 19558302 0.000000e+00 725.0
37 TraesCS3A01G167500 chr5D 83.853 737 118 1 1460 2196 532747573 532748308 0.000000e+00 701.0
38 TraesCS3A01G167500 chr3D 94.588 425 15 5 1 422 155555123 155555542 0.000000e+00 651.0
39 TraesCS3A01G167500 chr1D 73.311 296 61 15 2070 2354 325567857 325567569 4.120000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G167500 chr3A 174277885 174281754 3869 False 2475.000000 7147 91.666667 1 3870 3 chr3A.!!$F1 3869
1 TraesCS3A01G167500 chr3B 160141470 160144914 3444 False 2176.000000 6250 91.473000 427 3870 3 chr3B.!!$F2 3443
2 TraesCS3A01G167500 chr3B 52924722 52928659 3937 False 1613.250000 4324 93.209500 427 3870 4 chr3B.!!$F1 3443
3 TraesCS3A01G167500 chr2A 762295170 762298965 3795 True 1432.000000 2174 96.675000 432 3870 4 chr2A.!!$R1 3438
4 TraesCS3A01G167500 chr7B 571591141 571594834 3693 False 1333.333333 1770 89.780333 427 3856 3 chr7B.!!$F1 3429
5 TraesCS3A01G167500 chr6A 584918303 584921999 3696 False 1324.666667 1759 89.611667 423 3856 3 chr6A.!!$F2 3433
6 TraesCS3A01G167500 chr6A 273733334 273734096 762 False 678.000000 678 82.949000 698 1467 1 chr6A.!!$F1 769
7 TraesCS3A01G167500 chr4A 690102963 690106663 3700 True 1332.333333 1759 89.731667 423 3859 3 chr4A.!!$R1 3436
8 TraesCS3A01G167500 chr2B 23572665 23573820 1155 True 998.000000 998 82.429000 2712 3859 1 chr2B.!!$R1 1147
9 TraesCS3A01G167500 chr6B 63420287 63421255 968 True 887.000000 887 83.213000 2727 3695 1 chr6B.!!$R1 968
10 TraesCS3A01G167500 chr6B 666826723 666827760 1037 True 512.000000 512 76.159000 433 1461 1 chr6B.!!$R2 1028
11 TraesCS3A01G167500 chr1B 420603420 420604317 897 True 883.000000 883 84.427000 1460 2357 1 chr1B.!!$R1 897
12 TraesCS3A01G167500 chr1B 551219193 551219948 755 True 460.000000 460 78.068000 712 1461 1 chr1B.!!$R2 749
13 TraesCS3A01G167500 chr6D 469083816 469084785 969 True 876.000000 876 83.007000 2727 3695 1 chr6D.!!$R1 968
14 TraesCS3A01G167500 chr7D 19557566 19558302 736 False 725.000000 725 84.396000 1460 2196 1 chr7D.!!$F1 736
15 TraesCS3A01G167500 chr5D 532747573 532748308 735 False 701.000000 701 83.853000 1460 2196 1 chr5D.!!$F1 736

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
393 394 0.026285 CAACGCCCAAATCGATCGAC 59.974 55.0 22.06 5.46 0.00 4.20 F
401 402 0.107848 AAATCGATCGACCCACCCAC 60.108 55.0 22.06 0.00 0.00 4.61 F
413 414 0.250727 CCACCCACCGAAACACAGAT 60.251 55.0 0.00 0.00 0.00 2.90 F
1690 2710 0.323725 GTGTGGATGGCCTGGATGTT 60.324 55.0 3.32 0.00 34.31 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 2598 1.980765 AGTGCCTTCCTCATCTGTTCA 59.019 47.619 0.00 0.0 0.0 3.18 R
1721 2741 6.166279 GTGATCACCTGAAATCTAGAACACA 58.834 40.000 15.31 0.0 0.0 3.72 R
2114 3134 6.404074 CCCAATAACTCTTCTGCAAGCTTTAG 60.404 42.308 0.00 0.0 0.0 1.85 R
3180 4201 0.486879 ACCCTTCCTTGCCATTCCAA 59.513 50.000 0.00 0.0 0.0 3.53 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
61 62 7.686438 AGATGACTAAAAACACATACATGCA 57.314 32.000 0.00 0.00 0.00 3.96
62 63 8.109705 AGATGACTAAAAACACATACATGCAA 57.890 30.769 0.00 0.00 0.00 4.08
63 64 8.575589 AGATGACTAAAAACACATACATGCAAA 58.424 29.630 0.00 0.00 0.00 3.68
64 65 8.746922 ATGACTAAAAACACATACATGCAAAG 57.253 30.769 0.00 0.00 0.00 2.77
65 66 6.640499 TGACTAAAAACACATACATGCAAAGC 59.360 34.615 0.00 0.00 0.00 3.51
66 67 6.511416 ACTAAAAACACATACATGCAAAGCA 58.489 32.000 0.00 0.00 44.86 3.91
81 82 5.900425 TGCAAAGCATGTTTTAGAAGTTCA 58.100 33.333 7.25 0.00 31.71 3.18
82 83 6.514947 TGCAAAGCATGTTTTAGAAGTTCAT 58.485 32.000 7.25 0.00 31.71 2.57
83 84 6.642131 TGCAAAGCATGTTTTAGAAGTTCATC 59.358 34.615 7.25 0.00 31.71 2.92
84 85 6.865205 GCAAAGCATGTTTTAGAAGTTCATCT 59.135 34.615 7.25 0.00 0.00 2.90
85 86 7.383300 GCAAAGCATGTTTTAGAAGTTCATCTT 59.617 33.333 7.25 0.00 39.32 2.40
86 87 9.252962 CAAAGCATGTTTTAGAAGTTCATCTTT 57.747 29.630 7.25 0.00 36.40 2.52
87 88 9.822185 AAAGCATGTTTTAGAAGTTCATCTTTT 57.178 25.926 5.65 0.00 36.40 2.27
88 89 9.822185 AAGCATGTTTTAGAAGTTCATCTTTTT 57.178 25.926 5.50 0.00 36.40 1.94
115 116 2.209838 ACGGCTCGTGAATACTCATG 57.790 50.000 0.00 0.00 39.18 3.07
116 117 1.476891 ACGGCTCGTGAATACTCATGT 59.523 47.619 0.00 0.00 39.18 3.21
117 118 2.094182 ACGGCTCGTGAATACTCATGTT 60.094 45.455 0.00 0.00 39.18 2.71
118 119 2.930040 CGGCTCGTGAATACTCATGTTT 59.070 45.455 0.00 0.00 39.30 2.83
119 120 3.370978 CGGCTCGTGAATACTCATGTTTT 59.629 43.478 0.00 0.00 39.30 2.43
120 121 4.142902 CGGCTCGTGAATACTCATGTTTTT 60.143 41.667 0.00 0.00 39.30 1.94
121 122 5.062934 CGGCTCGTGAATACTCATGTTTTTA 59.937 40.000 0.00 0.00 39.30 1.52
122 123 6.248631 GGCTCGTGAATACTCATGTTTTTAC 58.751 40.000 0.00 0.00 39.30 2.01
123 124 6.128391 GGCTCGTGAATACTCATGTTTTTACA 60.128 38.462 0.00 0.00 39.30 2.41
124 125 7.295201 GCTCGTGAATACTCATGTTTTTACAA 58.705 34.615 0.00 0.00 39.30 2.41
125 126 7.268447 GCTCGTGAATACTCATGTTTTTACAAC 59.732 37.037 0.00 0.00 39.30 3.32
126 127 8.144155 TCGTGAATACTCATGTTTTTACAACA 57.856 30.769 0.00 0.00 39.30 3.33
127 128 8.779303 TCGTGAATACTCATGTTTTTACAACAT 58.221 29.630 0.00 0.00 41.18 2.71
128 129 9.393249 CGTGAATACTCATGTTTTTACAACATT 57.607 29.630 0.00 0.00 38.69 2.71
135 136 9.651913 ACTCATGTTTTTACAACATTTTTGTCT 57.348 25.926 0.00 0.00 38.69 3.41
136 137 9.904647 CTCATGTTTTTACAACATTTTTGTCTG 57.095 29.630 0.00 0.00 38.69 3.51
137 138 9.645059 TCATGTTTTTACAACATTTTTGTCTGA 57.355 25.926 0.00 0.00 38.69 3.27
140 141 9.482627 TGTTTTTACAACATTTTTGTCTGAACT 57.517 25.926 0.00 0.00 34.11 3.01
146 147 8.687824 ACAACATTTTTGTCTGAACTTACTTG 57.312 30.769 0.00 0.00 0.00 3.16
147 148 7.275560 ACAACATTTTTGTCTGAACTTACTTGC 59.724 33.333 0.00 0.00 0.00 4.01
148 149 6.862209 ACATTTTTGTCTGAACTTACTTGCA 58.138 32.000 0.00 0.00 0.00 4.08
149 150 6.751888 ACATTTTTGTCTGAACTTACTTGCAC 59.248 34.615 0.00 0.00 0.00 4.57
150 151 5.888691 TTTTGTCTGAACTTACTTGCACA 57.111 34.783 0.00 0.00 0.00 4.57
151 152 6.449635 TTTTGTCTGAACTTACTTGCACAT 57.550 33.333 0.00 0.00 0.00 3.21
152 153 5.422666 TTGTCTGAACTTACTTGCACATG 57.577 39.130 0.00 0.00 0.00 3.21
153 154 3.250762 TGTCTGAACTTACTTGCACATGC 59.749 43.478 0.00 0.00 42.50 4.06
183 184 6.046885 ACAACAAAATTTACTTGCACATGC 57.953 33.333 0.00 0.00 42.50 4.06
196 197 3.770263 GCACATGCATGTACACATTCT 57.230 42.857 30.92 3.26 39.39 2.40
197 198 3.688272 GCACATGCATGTACACATTCTC 58.312 45.455 30.92 8.74 39.39 2.87
198 199 3.376234 GCACATGCATGTACACATTCTCT 59.624 43.478 30.92 1.90 39.39 3.10
199 200 4.729746 GCACATGCATGTACACATTCTCTG 60.730 45.833 30.92 15.33 39.39 3.35
200 201 3.376234 ACATGCATGTACACATTCTCTGC 59.624 43.478 30.50 2.70 39.68 4.26
201 202 3.056588 TGCATGTACACATTCTCTGCA 57.943 42.857 12.71 12.71 33.61 4.41
202 203 2.743664 TGCATGTACACATTCTCTGCAC 59.256 45.455 12.71 0.00 33.61 4.57
203 204 2.222886 GCATGTACACATTCTCTGCACG 60.223 50.000 9.82 0.00 33.61 5.34
204 205 1.428448 TGTACACATTCTCTGCACGC 58.572 50.000 0.00 0.00 0.00 5.34
205 206 0.366871 GTACACATTCTCTGCACGCG 59.633 55.000 3.53 3.53 0.00 6.01
206 207 0.242555 TACACATTCTCTGCACGCGA 59.757 50.000 15.93 0.00 0.00 5.87
207 208 0.390340 ACACATTCTCTGCACGCGAT 60.390 50.000 15.93 0.00 0.00 4.58
208 209 1.135112 ACACATTCTCTGCACGCGATA 60.135 47.619 15.93 0.00 0.00 2.92
209 210 1.520174 CACATTCTCTGCACGCGATAG 59.480 52.381 15.93 7.97 0.00 2.08
210 211 1.405463 ACATTCTCTGCACGCGATAGA 59.595 47.619 15.93 12.19 39.76 1.98
211 212 2.049959 CATTCTCTGCACGCGATAGAG 58.950 52.381 15.93 20.95 43.65 2.43
212 213 1.379527 TTCTCTGCACGCGATAGAGA 58.620 50.000 25.78 25.78 43.68 3.10
213 214 0.940833 TCTCTGCACGCGATAGAGAG 59.059 55.000 25.78 21.65 41.33 3.20
214 215 0.940833 CTCTGCACGCGATAGAGAGA 59.059 55.000 24.14 11.83 40.21 3.10
215 216 0.940833 TCTGCACGCGATAGAGAGAG 59.059 55.000 15.93 0.00 40.06 3.20
216 217 0.940833 CTGCACGCGATAGAGAGAGA 59.059 55.000 15.93 0.00 40.06 3.10
217 218 1.332065 CTGCACGCGATAGAGAGAGAA 59.668 52.381 15.93 0.00 40.06 2.87
218 219 1.064208 TGCACGCGATAGAGAGAGAAC 59.936 52.381 15.93 0.00 40.06 3.01
219 220 1.598430 GCACGCGATAGAGAGAGAACC 60.598 57.143 15.93 0.00 40.06 3.62
220 221 1.002251 CACGCGATAGAGAGAGAACCC 60.002 57.143 15.93 0.00 40.06 4.11
221 222 1.134037 ACGCGATAGAGAGAGAACCCT 60.134 52.381 15.93 0.00 40.06 4.34
222 223 1.950909 CGCGATAGAGAGAGAACCCTT 59.049 52.381 0.00 0.00 38.63 3.95
223 224 2.287308 CGCGATAGAGAGAGAACCCTTG 60.287 54.545 0.00 0.00 38.63 3.61
224 225 2.544903 GCGATAGAGAGAGAACCCTTGC 60.545 54.545 0.00 0.00 39.76 4.01
225 226 2.035321 CGATAGAGAGAGAACCCTTGCC 59.965 54.545 0.00 0.00 39.76 4.52
226 227 1.867363 TAGAGAGAGAACCCTTGCCC 58.133 55.000 0.00 0.00 0.00 5.36
227 228 0.178891 AGAGAGAGAACCCTTGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
228 229 0.915364 GAGAGAGAACCCTTGCCCAT 59.085 55.000 0.00 0.00 0.00 4.00
229 230 1.283321 GAGAGAGAACCCTTGCCCATT 59.717 52.381 0.00 0.00 0.00 3.16
230 231 1.713078 AGAGAGAACCCTTGCCCATTT 59.287 47.619 0.00 0.00 0.00 2.32
231 232 2.110721 AGAGAGAACCCTTGCCCATTTT 59.889 45.455 0.00 0.00 0.00 1.82
232 233 2.493675 GAGAGAACCCTTGCCCATTTTC 59.506 50.000 0.00 0.00 0.00 2.29
233 234 2.110721 AGAGAACCCTTGCCCATTTTCT 59.889 45.455 0.00 0.00 0.00 2.52
234 235 2.232208 GAGAACCCTTGCCCATTTTCTG 59.768 50.000 0.00 0.00 0.00 3.02
235 236 0.686789 AACCCTTGCCCATTTTCTGC 59.313 50.000 0.00 0.00 0.00 4.26
236 237 0.471591 ACCCTTGCCCATTTTCTGCA 60.472 50.000 0.00 0.00 0.00 4.41
237 238 0.037046 CCCTTGCCCATTTTCTGCAC 60.037 55.000 0.00 0.00 34.16 4.57
238 239 0.388907 CCTTGCCCATTTTCTGCACG 60.389 55.000 0.00 0.00 34.16 5.34
239 240 0.314935 CTTGCCCATTTTCTGCACGT 59.685 50.000 0.00 0.00 34.16 4.49
240 241 0.031857 TTGCCCATTTTCTGCACGTG 59.968 50.000 12.28 12.28 34.16 4.49
241 242 1.734117 GCCCATTTTCTGCACGTGC 60.734 57.895 33.11 33.11 42.50 5.34
242 243 1.442520 CCCATTTTCTGCACGTGCG 60.443 57.895 33.22 26.60 45.83 5.34
244 245 2.082366 CATTTTCTGCACGTGCGGC 61.082 57.895 38.49 16.74 46.62 6.53
245 246 3.593551 ATTTTCTGCACGTGCGGCG 62.594 57.895 38.49 26.55 46.62 6.46
251 252 4.007940 GCACGTGCGGCGAGAAAA 62.008 61.111 26.77 0.00 44.77 2.29
252 253 2.127758 CACGTGCGGCGAGAAAAC 60.128 61.111 12.98 0.00 44.77 2.43
253 254 2.279918 ACGTGCGGCGAGAAAACT 60.280 55.556 12.98 0.00 44.77 2.66
254 255 1.007038 ACGTGCGGCGAGAAAACTA 60.007 52.632 12.98 0.00 44.77 2.24
255 256 1.280206 ACGTGCGGCGAGAAAACTAC 61.280 55.000 12.98 0.00 44.77 2.73
256 257 1.785951 GTGCGGCGAGAAAACTACC 59.214 57.895 12.98 0.00 0.00 3.18
257 258 0.669625 GTGCGGCGAGAAAACTACCT 60.670 55.000 12.98 0.00 0.00 3.08
258 259 0.389426 TGCGGCGAGAAAACTACCTC 60.389 55.000 12.98 0.00 0.00 3.85
267 268 5.888105 CGAGAAAACTACCTCGGATTTAGA 58.112 41.667 0.00 0.00 45.93 2.10
268 269 5.972382 CGAGAAAACTACCTCGGATTTAGAG 59.028 44.000 0.00 0.00 45.93 2.43
269 270 6.183360 CGAGAAAACTACCTCGGATTTAGAGA 60.183 42.308 0.00 0.00 45.93 3.10
270 271 7.102847 AGAAAACTACCTCGGATTTAGAGAG 57.897 40.000 0.00 0.00 37.93 3.20
271 272 6.890814 AGAAAACTACCTCGGATTTAGAGAGA 59.109 38.462 0.00 0.00 37.93 3.10
272 273 7.562088 AGAAAACTACCTCGGATTTAGAGAGAT 59.438 37.037 0.00 0.00 37.93 2.75
273 274 6.887626 AACTACCTCGGATTTAGAGAGATC 57.112 41.667 0.00 0.00 37.93 2.75
274 275 5.942961 ACTACCTCGGATTTAGAGAGATCA 58.057 41.667 0.00 0.00 37.93 2.92
275 276 5.766174 ACTACCTCGGATTTAGAGAGATCAC 59.234 44.000 0.00 0.00 37.93 3.06
276 277 3.892588 ACCTCGGATTTAGAGAGATCACC 59.107 47.826 0.00 0.00 37.93 4.02
277 278 3.891977 CCTCGGATTTAGAGAGATCACCA 59.108 47.826 0.00 0.00 37.93 4.17
278 279 4.261825 CCTCGGATTTAGAGAGATCACCAC 60.262 50.000 0.00 0.00 37.93 4.16
279 280 3.315470 TCGGATTTAGAGAGATCACCACG 59.685 47.826 0.00 0.00 0.00 4.94
280 281 3.315470 CGGATTTAGAGAGATCACCACGA 59.685 47.826 0.00 0.00 0.00 4.35
281 282 4.022762 CGGATTTAGAGAGATCACCACGAT 60.023 45.833 0.00 0.00 36.91 3.73
282 283 5.226396 GGATTTAGAGAGATCACCACGATG 58.774 45.833 0.00 0.00 33.17 3.84
283 284 3.717400 TTAGAGAGATCACCACGATGC 57.283 47.619 0.00 0.00 33.17 3.91
284 285 1.478631 AGAGAGATCACCACGATGCA 58.521 50.000 0.00 0.00 33.17 3.96
285 286 1.827344 AGAGAGATCACCACGATGCAA 59.173 47.619 0.00 0.00 33.17 4.08
286 287 2.234661 AGAGAGATCACCACGATGCAAA 59.765 45.455 0.00 0.00 33.17 3.68
287 288 3.002791 GAGAGATCACCACGATGCAAAA 58.997 45.455 0.00 0.00 33.17 2.44
288 289 3.411446 AGAGATCACCACGATGCAAAAA 58.589 40.909 0.00 0.00 33.17 1.94
289 290 3.438087 AGAGATCACCACGATGCAAAAAG 59.562 43.478 0.00 0.00 33.17 2.27
290 291 2.095059 AGATCACCACGATGCAAAAAGC 60.095 45.455 0.00 0.00 45.96 3.51
291 292 0.313672 TCACCACGATGCAAAAAGCC 59.686 50.000 0.00 0.00 44.83 4.35
292 293 0.667184 CACCACGATGCAAAAAGCCC 60.667 55.000 0.00 0.00 44.83 5.19
293 294 1.112315 ACCACGATGCAAAAAGCCCA 61.112 50.000 0.00 0.00 44.83 5.36
294 295 0.388907 CCACGATGCAAAAAGCCCAG 60.389 55.000 0.00 0.00 44.83 4.45
295 296 0.597568 CACGATGCAAAAAGCCCAGA 59.402 50.000 0.00 0.00 44.83 3.86
296 297 1.000385 CACGATGCAAAAAGCCCAGAA 60.000 47.619 0.00 0.00 44.83 3.02
297 298 1.270550 ACGATGCAAAAAGCCCAGAAG 59.729 47.619 0.00 0.00 44.83 2.85
298 299 1.718396 GATGCAAAAAGCCCAGAAGC 58.282 50.000 0.00 0.00 44.83 3.86
299 300 1.001181 GATGCAAAAAGCCCAGAAGCA 59.999 47.619 0.00 0.00 44.83 3.91
300 301 0.390124 TGCAAAAAGCCCAGAAGCAG 59.610 50.000 0.00 0.00 44.83 4.24
301 302 0.320160 GCAAAAAGCCCAGAAGCAGG 60.320 55.000 0.00 0.00 37.23 4.85
307 308 4.748144 CCCAGAAGCAGGCCCACC 62.748 72.222 0.00 0.00 0.00 4.61
321 322 4.680237 CACCTGTCGGCTCCGCAA 62.680 66.667 2.96 0.00 39.59 4.85
322 323 4.379243 ACCTGTCGGCTCCGCAAG 62.379 66.667 2.96 3.55 39.59 4.01
323 324 4.069232 CCTGTCGGCTCCGCAAGA 62.069 66.667 2.96 0.00 43.02 3.02
324 325 2.048222 CTGTCGGCTCCGCAAGAA 60.048 61.111 2.96 0.00 43.02 2.52
325 326 1.667830 CTGTCGGCTCCGCAAGAAA 60.668 57.895 2.96 0.00 43.02 2.52
326 327 1.227704 TGTCGGCTCCGCAAGAAAA 60.228 52.632 2.96 0.00 43.02 2.29
327 328 1.227999 TGTCGGCTCCGCAAGAAAAG 61.228 55.000 2.96 0.00 43.02 2.27
328 329 2.176792 CGGCTCCGCAAGAAAAGC 59.823 61.111 0.00 0.00 43.02 3.51
329 330 2.568612 GGCTCCGCAAGAAAAGCC 59.431 61.111 0.00 0.00 43.02 4.35
330 331 2.568612 GCTCCGCAAGAAAAGCCC 59.431 61.111 0.00 0.00 43.02 5.19
331 332 2.994671 GCTCCGCAAGAAAAGCCCC 61.995 63.158 0.00 0.00 43.02 5.80
332 333 1.303643 CTCCGCAAGAAAAGCCCCT 60.304 57.895 0.00 0.00 43.02 4.79
333 334 1.589716 CTCCGCAAGAAAAGCCCCTG 61.590 60.000 0.00 0.00 43.02 4.45
334 335 2.259511 CGCAAGAAAAGCCCCTGC 59.740 61.111 0.00 0.00 43.02 4.85
335 336 2.659016 GCAAGAAAAGCCCCTGCC 59.341 61.111 0.00 0.00 38.69 4.85
336 337 2.947532 GCAAGAAAAGCCCCTGCCC 61.948 63.158 0.00 0.00 38.69 5.36
337 338 2.120496 AAGAAAAGCCCCTGCCCC 59.880 61.111 0.00 0.00 38.69 5.80
338 339 3.886550 AAGAAAAGCCCCTGCCCCG 62.887 63.158 0.00 0.00 38.69 5.73
339 340 4.678743 GAAAAGCCCCTGCCCCGT 62.679 66.667 0.00 0.00 38.69 5.28
340 341 4.678743 AAAAGCCCCTGCCCCGTC 62.679 66.667 0.00 0.00 38.69 4.79
352 353 4.248842 CCCGTCACACCACCAGCA 62.249 66.667 0.00 0.00 0.00 4.41
353 354 2.972505 CCGTCACACCACCAGCAC 60.973 66.667 0.00 0.00 0.00 4.40
354 355 2.203001 CGTCACACCACCAGCACA 60.203 61.111 0.00 0.00 0.00 4.57
355 356 2.246739 CGTCACACCACCAGCACAG 61.247 63.158 0.00 0.00 0.00 3.66
356 357 2.203195 TCACACCACCAGCACAGC 60.203 61.111 0.00 0.00 0.00 4.40
357 358 3.289834 CACACCACCAGCACAGCC 61.290 66.667 0.00 0.00 0.00 4.85
358 359 4.935495 ACACCACCAGCACAGCCG 62.935 66.667 0.00 0.00 0.00 5.52
366 367 4.269523 AGCACAGCCGCCCTCAAA 62.270 61.111 0.00 0.00 0.00 2.69
367 368 3.294493 GCACAGCCGCCCTCAAAA 61.294 61.111 0.00 0.00 0.00 2.44
368 369 2.639327 GCACAGCCGCCCTCAAAAT 61.639 57.895 0.00 0.00 0.00 1.82
369 370 1.508088 CACAGCCGCCCTCAAAATC 59.492 57.895 0.00 0.00 0.00 2.17
370 371 1.074775 ACAGCCGCCCTCAAAATCA 59.925 52.632 0.00 0.00 0.00 2.57
371 372 0.962356 ACAGCCGCCCTCAAAATCAG 60.962 55.000 0.00 0.00 0.00 2.90
372 373 2.048603 AGCCGCCCTCAAAATCAGC 61.049 57.895 0.00 0.00 0.00 4.26
373 374 2.793946 CCGCCCTCAAAATCAGCG 59.206 61.111 0.00 0.00 46.04 5.18
374 375 2.100991 CGCCCTCAAAATCAGCGC 59.899 61.111 0.00 0.00 40.35 5.92
375 376 2.689785 CGCCCTCAAAATCAGCGCA 61.690 57.895 11.47 0.00 40.35 6.09
376 377 1.586028 GCCCTCAAAATCAGCGCAA 59.414 52.632 11.47 0.00 0.00 4.85
377 378 0.733909 GCCCTCAAAATCAGCGCAAC 60.734 55.000 11.47 0.00 0.00 4.17
378 379 0.454957 CCCTCAAAATCAGCGCAACG 60.455 55.000 11.47 0.00 0.00 4.10
389 390 2.791256 CGCAACGCCCAAATCGAT 59.209 55.556 0.00 0.00 0.00 3.59
390 391 1.297598 CGCAACGCCCAAATCGATC 60.298 57.895 0.00 0.00 0.00 3.69
391 392 1.297598 GCAACGCCCAAATCGATCG 60.298 57.895 9.36 9.36 0.00 3.69
392 393 1.701545 GCAACGCCCAAATCGATCGA 61.702 55.000 21.86 21.86 0.00 3.59
393 394 0.026285 CAACGCCCAAATCGATCGAC 59.974 55.000 22.06 5.46 0.00 4.20
394 395 1.087771 AACGCCCAAATCGATCGACC 61.088 55.000 22.06 4.00 0.00 4.79
395 396 2.244651 CGCCCAAATCGATCGACCC 61.245 63.158 22.06 4.36 0.00 4.46
396 397 1.153249 GCCCAAATCGATCGACCCA 60.153 57.895 22.06 0.00 0.00 4.51
397 398 1.436983 GCCCAAATCGATCGACCCAC 61.437 60.000 22.06 4.45 0.00 4.61
398 399 0.814010 CCCAAATCGATCGACCCACC 60.814 60.000 22.06 0.00 0.00 4.61
399 400 0.814010 CCAAATCGATCGACCCACCC 60.814 60.000 22.06 0.00 0.00 4.61
400 401 0.107897 CAAATCGATCGACCCACCCA 60.108 55.000 22.06 0.00 0.00 4.51
401 402 0.107848 AAATCGATCGACCCACCCAC 60.108 55.000 22.06 0.00 0.00 4.61
402 403 1.968050 AATCGATCGACCCACCCACC 61.968 60.000 22.06 0.00 0.00 4.61
403 404 4.508128 CGATCGACCCACCCACCG 62.508 72.222 10.26 0.00 0.00 4.94
404 405 3.072468 GATCGACCCACCCACCGA 61.072 66.667 0.00 0.00 35.43 4.69
405 406 2.605295 ATCGACCCACCCACCGAA 60.605 61.111 0.00 0.00 34.59 4.30
406 407 2.175035 GATCGACCCACCCACCGAAA 62.175 60.000 0.00 0.00 34.59 3.46
407 408 2.459202 ATCGACCCACCCACCGAAAC 62.459 60.000 0.00 0.00 34.59 2.78
408 409 2.511900 GACCCACCCACCGAAACA 59.488 61.111 0.00 0.00 0.00 2.83
409 410 1.895231 GACCCACCCACCGAAACAC 60.895 63.158 0.00 0.00 0.00 3.32
410 411 2.193517 CCCACCCACCGAAACACA 59.806 61.111 0.00 0.00 0.00 3.72
411 412 1.896660 CCCACCCACCGAAACACAG 60.897 63.158 0.00 0.00 0.00 3.66
412 413 1.147376 CCACCCACCGAAACACAGA 59.853 57.895 0.00 0.00 0.00 3.41
413 414 0.250727 CCACCCACCGAAACACAGAT 60.251 55.000 0.00 0.00 0.00 2.90
414 415 1.002659 CCACCCACCGAAACACAGATA 59.997 52.381 0.00 0.00 0.00 1.98
415 416 2.346803 CACCCACCGAAACACAGATAG 58.653 52.381 0.00 0.00 0.00 2.08
416 417 2.028476 CACCCACCGAAACACAGATAGA 60.028 50.000 0.00 0.00 0.00 1.98
417 418 2.838202 ACCCACCGAAACACAGATAGAT 59.162 45.455 0.00 0.00 0.00 1.98
418 419 4.028131 ACCCACCGAAACACAGATAGATA 58.972 43.478 0.00 0.00 0.00 1.98
419 420 4.099573 ACCCACCGAAACACAGATAGATAG 59.900 45.833 0.00 0.00 0.00 2.08
420 421 4.341235 CCCACCGAAACACAGATAGATAGA 59.659 45.833 0.00 0.00 0.00 1.98
421 422 5.011125 CCCACCGAAACACAGATAGATAGAT 59.989 44.000 0.00 0.00 0.00 1.98
494 496 5.252863 TCAAACCCTGAATTGAGAATCCCTA 59.747 40.000 0.00 0.00 32.14 3.53
687 711 1.589414 CCCTGTTTCTCTCCCTGGAT 58.411 55.000 0.00 0.00 0.00 3.41
825 849 4.008330 TCTATTCGTCTTCTCGTCCTTGT 58.992 43.478 0.00 0.00 0.00 3.16
1343 1381 3.473923 TGATCAGAGTGCAAGTGACAA 57.526 42.857 0.00 0.00 0.00 3.18
1578 2598 3.903090 TGGGAATGTTTTTCAGGAGCAAT 59.097 39.130 0.00 0.00 0.00 3.56
1690 2710 0.323725 GTGTGGATGGCCTGGATGTT 60.324 55.000 3.32 0.00 34.31 2.71
2114 3134 5.578336 GCTTCAATGCTATGAAAAAGGGTTC 59.422 40.000 6.28 0.00 38.75 3.62
3180 4201 3.181462 TGACTCAGTTCTGTGATGTGCTT 60.181 43.478 8.54 0.00 0.00 3.91
3685 4706 4.096081 CAGGCAGGAAAATGAAGTCATCTC 59.904 45.833 0.00 0.00 35.10 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.394767 TGCATGTATGTGTTTTTAGTCATCTAT 57.605 29.630 0.00 0.00 0.00 1.98
36 37 8.785329 TGCATGTATGTGTTTTTAGTCATCTA 57.215 30.769 0.00 0.00 0.00 1.98
37 38 7.686438 TGCATGTATGTGTTTTTAGTCATCT 57.314 32.000 0.00 0.00 0.00 2.90
38 39 8.741101 TTTGCATGTATGTGTTTTTAGTCATC 57.259 30.769 0.00 0.00 0.00 2.92
39 40 7.329226 GCTTTGCATGTATGTGTTTTTAGTCAT 59.671 33.333 0.00 0.00 0.00 3.06
40 41 6.640499 GCTTTGCATGTATGTGTTTTTAGTCA 59.360 34.615 0.00 0.00 0.00 3.41
41 42 6.640499 TGCTTTGCATGTATGTGTTTTTAGTC 59.360 34.615 0.00 0.00 31.71 2.59
42 43 6.511416 TGCTTTGCATGTATGTGTTTTTAGT 58.489 32.000 0.00 0.00 31.71 2.24
58 59 5.900425 TGAACTTCTAAAACATGCTTTGCA 58.100 33.333 4.33 0.00 44.86 4.08
59 60 6.865205 AGATGAACTTCTAAAACATGCTTTGC 59.135 34.615 4.33 0.00 0.00 3.68
60 61 8.807667 AAGATGAACTTCTAAAACATGCTTTG 57.192 30.769 4.33 0.00 32.91 2.77
61 62 9.822185 AAAAGATGAACTTCTAAAACATGCTTT 57.178 25.926 0.00 0.00 37.93 3.51
62 63 9.822185 AAAAAGATGAACTTCTAAAACATGCTT 57.178 25.926 0.00 0.00 37.93 3.91
96 97 1.476891 ACATGAGTATTCACGAGCCGT 59.523 47.619 0.00 0.00 42.36 5.68
97 98 2.209838 ACATGAGTATTCACGAGCCG 57.790 50.000 0.00 0.00 35.83 5.52
98 99 4.946784 AAAACATGAGTATTCACGAGCC 57.053 40.909 0.00 0.00 35.83 4.70
99 100 6.827641 TGTAAAAACATGAGTATTCACGAGC 58.172 36.000 0.00 0.00 35.83 5.03
100 101 8.279800 TGTTGTAAAAACATGAGTATTCACGAG 58.720 33.333 0.00 0.00 35.83 4.18
101 102 8.144155 TGTTGTAAAAACATGAGTATTCACGA 57.856 30.769 0.00 0.00 35.83 4.35
102 103 8.948853 ATGTTGTAAAAACATGAGTATTCACG 57.051 30.769 0.00 0.00 39.22 4.35
109 110 9.651913 AGACAAAAATGTTGTAAAAACATGAGT 57.348 25.926 0.00 2.31 40.43 3.41
110 111 9.904647 CAGACAAAAATGTTGTAAAAACATGAG 57.095 29.630 0.00 0.00 40.43 2.90
111 112 9.645059 TCAGACAAAAATGTTGTAAAAACATGA 57.355 25.926 0.00 0.00 40.43 3.07
114 115 9.482627 AGTTCAGACAAAAATGTTGTAAAAACA 57.517 25.926 8.74 0.00 31.96 2.83
120 121 9.781834 CAAGTAAGTTCAGACAAAAATGTTGTA 57.218 29.630 0.00 0.00 31.96 2.41
121 122 7.275560 GCAAGTAAGTTCAGACAAAAATGTTGT 59.724 33.333 0.00 0.00 34.97 3.32
122 123 7.275341 TGCAAGTAAGTTCAGACAAAAATGTTG 59.725 33.333 0.00 0.00 0.00 3.33
123 124 7.275560 GTGCAAGTAAGTTCAGACAAAAATGTT 59.724 33.333 0.00 0.00 0.00 2.71
124 125 6.751888 GTGCAAGTAAGTTCAGACAAAAATGT 59.248 34.615 0.00 0.00 0.00 2.71
125 126 6.751425 TGTGCAAGTAAGTTCAGACAAAAATG 59.249 34.615 0.00 0.00 0.00 2.32
126 127 6.862209 TGTGCAAGTAAGTTCAGACAAAAAT 58.138 32.000 0.00 0.00 0.00 1.82
127 128 6.260870 TGTGCAAGTAAGTTCAGACAAAAA 57.739 33.333 0.00 0.00 0.00 1.94
128 129 5.888691 TGTGCAAGTAAGTTCAGACAAAA 57.111 34.783 0.00 0.00 0.00 2.44
129 130 5.733091 GCATGTGCAAGTAAGTTCAGACAAA 60.733 40.000 0.00 0.00 41.59 2.83
130 131 4.261155 GCATGTGCAAGTAAGTTCAGACAA 60.261 41.667 0.00 0.00 41.59 3.18
131 132 3.250762 GCATGTGCAAGTAAGTTCAGACA 59.749 43.478 0.00 0.00 41.59 3.41
132 133 3.814945 GCATGTGCAAGTAAGTTCAGAC 58.185 45.455 0.00 0.00 41.59 3.51
157 158 8.920665 GCATGTGCAAGTAAATTTTGTTGTATA 58.079 29.630 0.00 0.00 41.59 1.47
158 159 7.795859 GCATGTGCAAGTAAATTTTGTTGTAT 58.204 30.769 0.00 0.00 41.59 2.29
159 160 7.171447 GCATGTGCAAGTAAATTTTGTTGTA 57.829 32.000 0.00 0.00 41.59 2.41
160 161 6.046885 GCATGTGCAAGTAAATTTTGTTGT 57.953 33.333 0.00 0.00 41.59 3.32
176 177 3.376234 AGAGAATGTGTACATGCATGTGC 59.624 43.478 36.72 34.86 41.89 4.57
177 178 4.729746 GCAGAGAATGTGTACATGCATGTG 60.730 45.833 36.72 19.13 41.89 3.21
178 179 3.376234 GCAGAGAATGTGTACATGCATGT 59.624 43.478 33.20 33.20 44.48 3.21
179 180 3.375922 TGCAGAGAATGTGTACATGCATG 59.624 43.478 25.09 25.09 36.56 4.06
180 181 3.376234 GTGCAGAGAATGTGTACATGCAT 59.624 43.478 18.08 7.15 44.21 3.96
181 182 2.743664 GTGCAGAGAATGTGTACATGCA 59.256 45.455 12.71 12.71 44.21 3.96
182 183 2.222886 CGTGCAGAGAATGTGTACATGC 60.223 50.000 0.00 3.41 45.03 4.06
183 184 2.222886 GCGTGCAGAGAATGTGTACATG 60.223 50.000 0.00 0.00 45.03 3.21
184 185 2.002586 GCGTGCAGAGAATGTGTACAT 58.997 47.619 0.00 0.00 45.03 2.29
185 186 1.428448 GCGTGCAGAGAATGTGTACA 58.572 50.000 0.00 0.00 45.03 2.90
186 187 0.366871 CGCGTGCAGAGAATGTGTAC 59.633 55.000 0.00 0.00 41.46 2.90
187 188 0.242555 TCGCGTGCAGAGAATGTGTA 59.757 50.000 5.77 0.00 0.00 2.90
188 189 0.390340 ATCGCGTGCAGAGAATGTGT 60.390 50.000 5.77 0.00 31.00 3.72
189 190 1.520174 CTATCGCGTGCAGAGAATGTG 59.480 52.381 5.77 0.00 31.00 3.21
190 191 1.405463 TCTATCGCGTGCAGAGAATGT 59.595 47.619 5.77 0.00 31.00 2.71
191 192 2.049959 CTCTATCGCGTGCAGAGAATG 58.950 52.381 21.56 3.80 38.46 2.67
192 193 1.950216 TCTCTATCGCGTGCAGAGAAT 59.050 47.619 24.36 6.32 41.33 2.40
193 194 1.332065 CTCTCTATCGCGTGCAGAGAA 59.668 52.381 25.52 15.72 43.10 2.87
194 195 0.940833 CTCTCTATCGCGTGCAGAGA 59.059 55.000 24.66 24.66 41.87 3.10
195 196 0.940833 TCTCTCTATCGCGTGCAGAG 59.059 55.000 20.66 20.66 37.70 3.35
196 197 0.940833 CTCTCTCTATCGCGTGCAGA 59.059 55.000 5.77 6.45 0.00 4.26
197 198 0.940833 TCTCTCTCTATCGCGTGCAG 59.059 55.000 5.77 1.70 0.00 4.41
198 199 1.064208 GTTCTCTCTCTATCGCGTGCA 59.936 52.381 5.77 0.00 0.00 4.57
199 200 1.598430 GGTTCTCTCTCTATCGCGTGC 60.598 57.143 5.77 0.00 0.00 5.34
200 201 1.002251 GGGTTCTCTCTCTATCGCGTG 60.002 57.143 5.77 0.00 0.00 5.34
201 202 1.134037 AGGGTTCTCTCTCTATCGCGT 60.134 52.381 5.77 0.00 0.00 6.01
202 203 1.600023 AGGGTTCTCTCTCTATCGCG 58.400 55.000 0.00 0.00 0.00 5.87
203 204 2.544903 GCAAGGGTTCTCTCTCTATCGC 60.545 54.545 0.00 0.00 0.00 4.58
204 205 2.035321 GGCAAGGGTTCTCTCTCTATCG 59.965 54.545 0.00 0.00 0.00 2.92
205 206 2.367241 GGGCAAGGGTTCTCTCTCTATC 59.633 54.545 0.00 0.00 0.00 2.08
206 207 2.293184 TGGGCAAGGGTTCTCTCTCTAT 60.293 50.000 0.00 0.00 0.00 1.98
207 208 1.078823 TGGGCAAGGGTTCTCTCTCTA 59.921 52.381 0.00 0.00 0.00 2.43
208 209 0.178891 TGGGCAAGGGTTCTCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
209 210 0.915364 ATGGGCAAGGGTTCTCTCTC 59.085 55.000 0.00 0.00 0.00 3.20
210 211 1.376649 AATGGGCAAGGGTTCTCTCT 58.623 50.000 0.00 0.00 0.00 3.10
211 212 2.222227 AAATGGGCAAGGGTTCTCTC 57.778 50.000 0.00 0.00 0.00 3.20
212 213 2.110721 AGAAAATGGGCAAGGGTTCTCT 59.889 45.455 0.00 0.00 0.00 3.10
213 214 2.232208 CAGAAAATGGGCAAGGGTTCTC 59.768 50.000 0.00 0.00 0.00 2.87
214 215 2.250924 CAGAAAATGGGCAAGGGTTCT 58.749 47.619 0.00 0.00 0.00 3.01
215 216 1.338105 GCAGAAAATGGGCAAGGGTTC 60.338 52.381 0.00 0.00 0.00 3.62
216 217 0.686789 GCAGAAAATGGGCAAGGGTT 59.313 50.000 0.00 0.00 0.00 4.11
217 218 0.471591 TGCAGAAAATGGGCAAGGGT 60.472 50.000 0.00 0.00 34.05 4.34
218 219 0.037046 GTGCAGAAAATGGGCAAGGG 60.037 55.000 0.00 0.00 39.57 3.95
219 220 0.388907 CGTGCAGAAAATGGGCAAGG 60.389 55.000 0.00 0.00 39.57 3.61
220 221 0.314935 ACGTGCAGAAAATGGGCAAG 59.685 50.000 0.00 0.00 41.69 4.01
221 222 0.031857 CACGTGCAGAAAATGGGCAA 59.968 50.000 0.82 0.00 39.57 4.52
222 223 1.659233 CACGTGCAGAAAATGGGCA 59.341 52.632 0.82 0.00 34.70 5.36
223 224 1.734117 GCACGTGCAGAAAATGGGC 60.734 57.895 34.52 2.63 41.59 5.36
224 225 1.442520 CGCACGTGCAGAAAATGGG 60.443 57.895 37.03 15.87 42.21 4.00
225 226 1.442520 CCGCACGTGCAGAAAATGG 60.443 57.895 37.03 24.73 42.21 3.16
226 227 2.082366 GCCGCACGTGCAGAAAATG 61.082 57.895 37.03 20.12 42.21 2.32
227 228 2.255252 GCCGCACGTGCAGAAAAT 59.745 55.556 37.03 0.00 42.21 1.82
228 229 4.306471 CGCCGCACGTGCAGAAAA 62.306 61.111 37.03 0.00 42.21 2.29
234 235 4.007940 TTTTCTCGCCGCACGTGC 62.008 61.111 30.42 30.42 44.19 5.34
235 236 1.279527 TAGTTTTCTCGCCGCACGTG 61.280 55.000 12.28 12.28 44.19 4.49
236 237 1.007038 TAGTTTTCTCGCCGCACGT 60.007 52.632 0.00 0.00 44.19 4.49
237 238 1.414897 GTAGTTTTCTCGCCGCACG 59.585 57.895 0.00 0.00 45.62 5.34
238 239 0.669625 AGGTAGTTTTCTCGCCGCAC 60.670 55.000 0.00 0.00 32.74 5.34
239 240 0.389426 GAGGTAGTTTTCTCGCCGCA 60.389 55.000 0.00 0.00 32.74 5.69
240 241 1.411493 CGAGGTAGTTTTCTCGCCGC 61.411 60.000 0.00 0.00 44.68 6.53
241 242 2.650163 CGAGGTAGTTTTCTCGCCG 58.350 57.895 0.00 0.00 44.68 6.46
245 246 7.067251 TCTCTCTAAATCCGAGGTAGTTTTCTC 59.933 40.741 0.00 0.00 0.00 2.87
246 247 6.890814 TCTCTCTAAATCCGAGGTAGTTTTCT 59.109 38.462 0.00 0.00 0.00 2.52
247 248 7.098074 TCTCTCTAAATCCGAGGTAGTTTTC 57.902 40.000 0.00 0.00 0.00 2.29
248 249 7.342284 TGATCTCTCTAAATCCGAGGTAGTTTT 59.658 37.037 0.00 0.00 0.00 2.43
249 250 6.834451 TGATCTCTCTAAATCCGAGGTAGTTT 59.166 38.462 0.00 0.00 0.00 2.66
250 251 6.263617 GTGATCTCTCTAAATCCGAGGTAGTT 59.736 42.308 0.00 0.00 0.00 2.24
251 252 5.766174 GTGATCTCTCTAAATCCGAGGTAGT 59.234 44.000 0.00 0.00 0.00 2.73
252 253 5.182380 GGTGATCTCTCTAAATCCGAGGTAG 59.818 48.000 0.00 0.00 0.00 3.18
253 254 5.071370 GGTGATCTCTCTAAATCCGAGGTA 58.929 45.833 0.00 0.00 0.00 3.08
254 255 3.892588 GGTGATCTCTCTAAATCCGAGGT 59.107 47.826 0.00 0.00 0.00 3.85
255 256 3.891977 TGGTGATCTCTCTAAATCCGAGG 59.108 47.826 0.00 0.00 0.00 4.63
256 257 4.555708 CGTGGTGATCTCTCTAAATCCGAG 60.556 50.000 0.00 0.00 0.00 4.63
257 258 3.315470 CGTGGTGATCTCTCTAAATCCGA 59.685 47.826 0.00 0.00 0.00 4.55
258 259 3.315470 TCGTGGTGATCTCTCTAAATCCG 59.685 47.826 0.00 0.00 0.00 4.18
259 260 4.920640 TCGTGGTGATCTCTCTAAATCC 57.079 45.455 0.00 0.00 0.00 3.01
260 261 4.683781 GCATCGTGGTGATCTCTCTAAATC 59.316 45.833 0.00 0.00 34.13 2.17
261 262 4.100035 TGCATCGTGGTGATCTCTCTAAAT 59.900 41.667 0.00 0.00 34.13 1.40
262 263 3.447229 TGCATCGTGGTGATCTCTCTAAA 59.553 43.478 0.00 0.00 34.13 1.85
263 264 3.023832 TGCATCGTGGTGATCTCTCTAA 58.976 45.455 0.00 0.00 34.13 2.10
264 265 2.654863 TGCATCGTGGTGATCTCTCTA 58.345 47.619 0.00 0.00 34.13 2.43
265 266 1.478631 TGCATCGTGGTGATCTCTCT 58.521 50.000 0.00 0.00 34.13 3.10
266 267 2.299993 TTGCATCGTGGTGATCTCTC 57.700 50.000 0.00 0.00 34.13 3.20
267 268 2.768253 TTTGCATCGTGGTGATCTCT 57.232 45.000 0.00 0.00 34.13 3.10
268 269 3.751621 CTTTTTGCATCGTGGTGATCTC 58.248 45.455 0.00 0.00 34.13 2.75
269 270 2.095059 GCTTTTTGCATCGTGGTGATCT 60.095 45.455 0.00 0.00 42.31 2.75
270 271 2.253603 GCTTTTTGCATCGTGGTGATC 58.746 47.619 0.00 0.00 42.31 2.92
271 272 1.067635 GGCTTTTTGCATCGTGGTGAT 60.068 47.619 0.00 0.00 45.15 3.06
272 273 0.313672 GGCTTTTTGCATCGTGGTGA 59.686 50.000 0.00 0.00 45.15 4.02
273 274 0.667184 GGGCTTTTTGCATCGTGGTG 60.667 55.000 0.00 0.00 45.15 4.17
274 275 1.112315 TGGGCTTTTTGCATCGTGGT 61.112 50.000 0.00 0.00 45.15 4.16
275 276 0.388907 CTGGGCTTTTTGCATCGTGG 60.389 55.000 0.00 0.00 45.15 4.94
276 277 0.597568 TCTGGGCTTTTTGCATCGTG 59.402 50.000 0.00 0.00 45.15 4.35
277 278 1.270550 CTTCTGGGCTTTTTGCATCGT 59.729 47.619 0.00 0.00 45.15 3.73
278 279 1.986698 CTTCTGGGCTTTTTGCATCG 58.013 50.000 0.00 0.00 45.15 3.84
279 280 1.001181 TGCTTCTGGGCTTTTTGCATC 59.999 47.619 0.00 0.00 45.15 3.91
280 281 1.001633 CTGCTTCTGGGCTTTTTGCAT 59.998 47.619 0.00 0.00 45.15 3.96
281 282 0.390124 CTGCTTCTGGGCTTTTTGCA 59.610 50.000 0.00 0.00 45.15 4.08
282 283 0.320160 CCTGCTTCTGGGCTTTTTGC 60.320 55.000 0.00 0.00 41.94 3.68
283 284 0.320160 GCCTGCTTCTGGGCTTTTTG 60.320 55.000 0.00 0.00 44.48 2.44
284 285 1.475169 GGCCTGCTTCTGGGCTTTTT 61.475 55.000 0.00 0.00 46.80 1.94
285 286 1.910276 GGCCTGCTTCTGGGCTTTT 60.910 57.895 0.00 0.00 46.80 2.27
286 287 2.283460 GGCCTGCTTCTGGGCTTT 60.283 61.111 0.00 0.00 46.80 3.51
287 288 4.372999 GGGCCTGCTTCTGGGCTT 62.373 66.667 0.84 0.00 46.80 4.35
290 291 4.748144 GGTGGGCCTGCTTCTGGG 62.748 72.222 4.53 0.00 0.00 4.45
291 292 3.655211 AGGTGGGCCTGCTTCTGG 61.655 66.667 4.53 0.00 45.05 3.86
314 315 1.303643 AGGGGCTTTTCTTGCGGAG 60.304 57.895 0.00 0.00 0.00 4.63
315 316 1.603455 CAGGGGCTTTTCTTGCGGA 60.603 57.895 0.00 0.00 0.00 5.54
316 317 2.964978 CAGGGGCTTTTCTTGCGG 59.035 61.111 0.00 0.00 0.00 5.69
317 318 2.259511 GCAGGGGCTTTTCTTGCG 59.740 61.111 0.00 0.00 36.96 4.85
318 319 2.659016 GGCAGGGGCTTTTCTTGC 59.341 61.111 0.00 0.00 40.87 4.01
319 320 2.285773 GGGGCAGGGGCTTTTCTTG 61.286 63.158 0.00 0.00 40.87 3.02
320 321 2.120496 GGGGCAGGGGCTTTTCTT 59.880 61.111 0.00 0.00 40.87 2.52
321 322 4.366684 CGGGGCAGGGGCTTTTCT 62.367 66.667 0.00 0.00 40.87 2.52
322 323 4.678743 ACGGGGCAGGGGCTTTTC 62.679 66.667 0.00 0.00 40.87 2.29
323 324 4.678743 GACGGGGCAGGGGCTTTT 62.679 66.667 0.00 0.00 40.87 2.27
335 336 4.248842 TGCTGGTGGTGTGACGGG 62.249 66.667 0.00 0.00 0.00 5.28
336 337 2.972505 GTGCTGGTGGTGTGACGG 60.973 66.667 0.00 0.00 0.00 4.79
337 338 2.203001 TGTGCTGGTGGTGTGACG 60.203 61.111 0.00 0.00 0.00 4.35
338 339 2.546494 GCTGTGCTGGTGGTGTGAC 61.546 63.158 0.00 0.00 0.00 3.67
339 340 2.203195 GCTGTGCTGGTGGTGTGA 60.203 61.111 0.00 0.00 0.00 3.58
340 341 3.289834 GGCTGTGCTGGTGGTGTG 61.290 66.667 0.00 0.00 0.00 3.82
341 342 4.935495 CGGCTGTGCTGGTGGTGT 62.935 66.667 0.00 0.00 0.00 4.16
349 350 3.790416 TTTTGAGGGCGGCTGTGCT 62.790 57.895 9.56 0.00 34.52 4.40
350 351 2.548127 GATTTTGAGGGCGGCTGTGC 62.548 60.000 9.56 0.00 0.00 4.57
351 352 1.243342 TGATTTTGAGGGCGGCTGTG 61.243 55.000 9.56 0.00 0.00 3.66
352 353 0.962356 CTGATTTTGAGGGCGGCTGT 60.962 55.000 9.56 0.00 0.00 4.40
353 354 1.805254 CTGATTTTGAGGGCGGCTG 59.195 57.895 9.56 0.00 0.00 4.85
354 355 2.048603 GCTGATTTTGAGGGCGGCT 61.049 57.895 9.56 0.00 0.00 5.52
355 356 2.491621 GCTGATTTTGAGGGCGGC 59.508 61.111 0.00 0.00 0.00 6.53
356 357 2.793946 CGCTGATTTTGAGGGCGG 59.206 61.111 0.00 0.00 41.77 6.13
358 359 0.733909 GTTGCGCTGATTTTGAGGGC 60.734 55.000 9.73 0.00 46.68 5.19
359 360 0.454957 CGTTGCGCTGATTTTGAGGG 60.455 55.000 9.73 0.00 0.00 4.30
360 361 3.005823 CGTTGCGCTGATTTTGAGG 57.994 52.632 9.73 0.00 0.00 3.86
372 373 1.297598 GATCGATTTGGGCGTTGCG 60.298 57.895 0.00 0.00 0.00 4.85
373 374 1.297598 CGATCGATTTGGGCGTTGC 60.298 57.895 10.26 0.00 0.00 4.17
374 375 0.026285 GTCGATCGATTTGGGCGTTG 59.974 55.000 22.50 0.00 0.00 4.10
375 376 1.087771 GGTCGATCGATTTGGGCGTT 61.088 55.000 22.50 0.00 0.00 4.84
376 377 1.520787 GGTCGATCGATTTGGGCGT 60.521 57.895 22.50 0.00 0.00 5.68
377 378 2.244651 GGGTCGATCGATTTGGGCG 61.245 63.158 22.50 0.00 0.00 6.13
378 379 1.153249 TGGGTCGATCGATTTGGGC 60.153 57.895 22.50 6.85 0.00 5.36
379 380 0.814010 GGTGGGTCGATCGATTTGGG 60.814 60.000 22.50 0.00 0.00 4.12
380 381 0.814010 GGGTGGGTCGATCGATTTGG 60.814 60.000 22.50 0.00 0.00 3.28
381 382 0.107897 TGGGTGGGTCGATCGATTTG 60.108 55.000 22.50 0.00 0.00 2.32
382 383 0.107848 GTGGGTGGGTCGATCGATTT 60.108 55.000 22.50 0.00 0.00 2.17
383 384 1.520666 GTGGGTGGGTCGATCGATT 59.479 57.895 22.50 0.00 0.00 3.34
384 385 2.432300 GGTGGGTGGGTCGATCGAT 61.432 63.158 22.50 0.00 0.00 3.59
385 386 3.072468 GGTGGGTGGGTCGATCGA 61.072 66.667 15.15 15.15 0.00 3.59
386 387 4.508128 CGGTGGGTGGGTCGATCG 62.508 72.222 9.36 9.36 0.00 3.69
387 388 2.175035 TTTCGGTGGGTGGGTCGATC 62.175 60.000 0.00 0.00 0.00 3.69
388 389 2.218454 TTTCGGTGGGTGGGTCGAT 61.218 57.895 0.00 0.00 0.00 3.59
389 390 2.843411 TTTCGGTGGGTGGGTCGA 60.843 61.111 0.00 0.00 0.00 4.20
390 391 2.667199 GTTTCGGTGGGTGGGTCG 60.667 66.667 0.00 0.00 0.00 4.79
391 392 1.895231 GTGTTTCGGTGGGTGGGTC 60.895 63.158 0.00 0.00 0.00 4.46
392 393 2.193786 GTGTTTCGGTGGGTGGGT 59.806 61.111 0.00 0.00 0.00 4.51
393 394 1.896660 CTGTGTTTCGGTGGGTGGG 60.897 63.158 0.00 0.00 0.00 4.61
394 395 0.250727 ATCTGTGTTTCGGTGGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
395 396 2.028476 TCTATCTGTGTTTCGGTGGGTG 60.028 50.000 0.00 0.00 0.00 4.61
396 397 2.253610 TCTATCTGTGTTTCGGTGGGT 58.746 47.619 0.00 0.00 0.00 4.51
397 398 3.543680 ATCTATCTGTGTTTCGGTGGG 57.456 47.619 0.00 0.00 0.00 4.61
398 399 5.515797 TCTATCTATCTGTGTTTCGGTGG 57.484 43.478 0.00 0.00 0.00 4.61
399 400 8.100508 TCTATCTATCTATCTGTGTTTCGGTG 57.899 38.462 0.00 0.00 0.00 4.94
400 401 8.735315 CATCTATCTATCTATCTGTGTTTCGGT 58.265 37.037 0.00 0.00 0.00 4.69
401 402 8.187480 CCATCTATCTATCTATCTGTGTTTCGG 58.813 40.741 0.00 0.00 0.00 4.30
402 403 7.700234 GCCATCTATCTATCTATCTGTGTTTCG 59.300 40.741 0.00 0.00 0.00 3.46
403 404 8.526978 TGCCATCTATCTATCTATCTGTGTTTC 58.473 37.037 0.00 0.00 0.00 2.78
404 405 8.427902 TGCCATCTATCTATCTATCTGTGTTT 57.572 34.615 0.00 0.00 0.00 2.83
405 406 8.427902 TTGCCATCTATCTATCTATCTGTGTT 57.572 34.615 0.00 0.00 0.00 3.32
406 407 8.427902 TTTGCCATCTATCTATCTATCTGTGT 57.572 34.615 0.00 0.00 0.00 3.72
407 408 9.368674 CTTTTGCCATCTATCTATCTATCTGTG 57.631 37.037 0.00 0.00 0.00 3.66
408 409 9.099071 ACTTTTGCCATCTATCTATCTATCTGT 57.901 33.333 0.00 0.00 0.00 3.41
409 410 9.585099 GACTTTTGCCATCTATCTATCTATCTG 57.415 37.037 0.00 0.00 0.00 2.90
410 411 9.545928 AGACTTTTGCCATCTATCTATCTATCT 57.454 33.333 0.00 0.00 0.00 1.98
494 496 7.639113 TTAACAAAGACAAGGTGACAATTCT 57.361 32.000 0.00 0.00 0.00 2.40
687 711 2.522367 GGGGAAGGAACGGGTGACA 61.522 63.158 0.00 0.00 0.00 3.58
1343 1381 8.472413 CCATCTCATTTTCAAAATCACTACCAT 58.528 33.333 0.00 0.00 0.00 3.55
1578 2598 1.980765 AGTGCCTTCCTCATCTGTTCA 59.019 47.619 0.00 0.00 0.00 3.18
1690 2710 7.832685 ACTATAAGCACCATATATAGTCCACGA 59.167 37.037 0.00 0.00 38.02 4.35
1721 2741 6.166279 GTGATCACCTGAAATCTAGAACACA 58.834 40.000 15.31 0.00 0.00 3.72
2114 3134 6.404074 CCCAATAACTCTTCTGCAAGCTTTAG 60.404 42.308 0.00 0.00 0.00 1.85
3180 4201 0.486879 ACCCTTCCTTGCCATTCCAA 59.513 50.000 0.00 0.00 0.00 3.53
3685 4706 8.023050 CAAGAGAGTGAACTTGTATTTACCTG 57.977 38.462 0.00 0.00 38.72 4.00
3774 4803 7.307337 GCATTAGTGTTTGCTTGCTGTTAAAAT 60.307 33.333 0.00 0.00 35.95 1.82
3796 4825 4.021229 TGGCTTGATCTGATTTGAGCATT 58.979 39.130 16.94 0.00 32.18 3.56


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

AutoCloner maintained by Alex Coulton.