Multiple sequence alignment - TraesCS2D01G433300

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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 TraesCS2D01G433300 chr2D 100.000 4415 0 0 1 4415 544889262 544884848 0.000000e+00 8154.0
1 TraesCS2D01G433300 chr2D 84.577 201 18 10 1 190 140937262 140937460 2.100000e-43 187.0
2 TraesCS2D01G433300 chr2D 79.661 177 26 7 190 362 82094201 82094371 7.760000e-23 119.0
3 TraesCS2D01G433300 chr2D 78.698 169 32 3 190 357 643292387 643292222 4.670000e-20 110.0
4 TraesCS2D01G433300 chr2D 87.356 87 10 1 4221 4307 82181924 82182009 1.010000e-16 99.0
5 TraesCS2D01G433300 chr2A 95.160 3347 139 9 923 4263 688616717 688620046 0.000000e+00 5262.0
6 TraesCS2D01G433300 chr2A 94.382 89 5 0 843 931 688616512 688616600 2.140000e-28 137.0
7 TraesCS2D01G433300 chr2A 79.775 178 27 8 189 362 15524731 15524903 2.160000e-23 121.0
8 TraesCS2D01G433300 chr2B 93.984 3424 150 18 843 4224 651365980 651362571 0.000000e+00 5131.0
9 TraesCS2D01G433300 chr2B 79.294 652 90 28 189 815 651368453 651367822 8.830000e-112 414.0
10 TraesCS2D01G433300 chr2B 94.118 153 9 0 4263 4415 651362575 651362423 2.660000e-57 233.0
11 TraesCS2D01G433300 chr2B 87.234 94 11 1 4221 4314 134045456 134045548 6.040000e-19 106.0
12 TraesCS2D01G433300 chr5B 87.179 195 17 6 1 187 354013357 354013163 9.620000e-52 215.0
13 TraesCS2D01G433300 chr5B 85.714 196 19 3 2 189 454652049 454652243 9.690000e-47 198.0
14 TraesCS2D01G433300 chr5B 79.882 169 24 7 190 355 619275574 619275735 1.000000e-21 115.0
15 TraesCS2D01G433300 chr4A 86.154 195 19 2 1 187 66160348 66160542 2.080000e-48 204.0
16 TraesCS2D01G433300 chr4A 79.641 167 29 3 190 355 520134467 520134305 1.000000e-21 115.0
17 TraesCS2D01G433300 chr7A 85.279 197 20 4 1 189 433960597 433960402 1.250000e-45 195.0
18 TraesCS2D01G433300 chr7A 83.673 196 24 8 1 189 254394048 254394242 1.260000e-40 178.0
19 TraesCS2D01G433300 chr7A 88.776 98 8 3 4220 4315 121396020 121396116 2.790000e-22 117.0
20 TraesCS2D01G433300 chr7A 80.255 157 27 2 198 353 393325327 393325174 1.000000e-21 115.0
21 TraesCS2D01G433300 chr3D 83.838 198 22 4 1 189 461023479 461023283 3.510000e-41 180.0
22 TraesCS2D01G433300 chr5D 83.582 201 22 5 1 191 272685238 272685039 1.260000e-40 178.0
23 TraesCS2D01G433300 chr5D 79.412 170 25 7 190 355 499065576 499065739 1.300000e-20 111.0
24 TraesCS2D01G433300 chr5A 83.333 198 21 8 1 190 411720009 411719816 5.870000e-39 172.0
25 TraesCS2D01G433300 chr7D 81.034 174 29 3 190 362 595869491 595869661 7.700000e-28 135.0
26 TraesCS2D01G433300 chr7D 80.240 167 29 2 190 355 251355245 251355408 6.000000e-24 122.0
27 TraesCS2D01G433300 chr7D 89.157 83 8 1 4225 4307 573982288 573982369 7.810000e-18 102.0
28 TraesCS2D01G433300 chr7D 88.608 79 8 1 4232 4310 117234500 117234577 1.310000e-15 95.3
29 TraesCS2D01G433300 chr1A 88.043 92 8 3 4227 4318 343398331 343398419 6.040000e-19 106.0
30 TraesCS2D01G433300 chr6B 89.024 82 8 1 4226 4307 124550507 124550587 2.810000e-17 100.0
31 TraesCS2D01G433300 chr6A 86.364 88 9 2 4220 4307 69358282 69358366 4.700000e-15 93.5
32 TraesCS2D01G433300 chr7B 81.818 77 7 2 509 578 704480006 704479930 1.720000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G433300 chr2D 544884848 544889262 4414 True 8154.0 8154 100.000 1 4415 1 chr2D.!!$R1 4414
1 TraesCS2D01G433300 chr2A 688616512 688620046 3534 False 2699.5 5262 94.771 843 4263 2 chr2A.!!$F2 3420
2 TraesCS2D01G433300 chr2B 651362423 651368453 6030 True 1926.0 5131 89.132 189 4415 3 chr2B.!!$R1 4226

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
377 380 0.108992 TCGGTGATACGTTGACAGGC 60.109 55.0 0.0 0.0 34.94 4.85 F
963 2928 0.686224 CAGGGGATGAGGAGATGAGC 59.314 60.0 0.0 0.0 0.00 4.26 F
1929 3903 0.109723 TGGGGTCAAAAGAGGTTCCG 59.890 55.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 3726 0.027194 CAGAGAACATGCCGATTGCG 59.973 55.0 0.00 0.00 45.60 4.85 R
2052 4026 0.037697 TCACGACAAGCGCATTACCT 60.038 50.0 11.47 0.00 46.04 3.08 R
3611 5590 0.109597 GCTCACTTTTCACCATGGCG 60.110 55.0 13.04 1.26 0.00 5.69 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
22 23 5.209818 ACAACACTTGAATCGGTCTTAGA 57.790 39.130 0.00 0.00 0.00 2.10
23 24 5.230942 ACAACACTTGAATCGGTCTTAGAG 58.769 41.667 0.00 0.00 0.00 2.43
24 25 4.457834 ACACTTGAATCGGTCTTAGAGG 57.542 45.455 0.00 0.00 0.00 3.69
25 26 3.190874 CACTTGAATCGGTCTTAGAGGC 58.809 50.000 0.00 0.00 0.00 4.70
26 27 2.832129 ACTTGAATCGGTCTTAGAGGCA 59.168 45.455 0.00 0.00 0.00 4.75
27 28 3.260884 ACTTGAATCGGTCTTAGAGGCAA 59.739 43.478 0.00 0.00 0.00 4.52
28 29 3.526931 TGAATCGGTCTTAGAGGCAAG 57.473 47.619 0.00 0.00 0.00 4.01
29 30 3.096852 TGAATCGGTCTTAGAGGCAAGA 58.903 45.455 0.00 0.00 32.11 3.02
33 34 3.742983 GTCTTAGAGGCAAGACCGG 57.257 57.895 0.00 0.00 45.75 5.28
34 35 1.183549 GTCTTAGAGGCAAGACCGGA 58.816 55.000 9.46 0.00 45.75 5.14
35 36 1.549170 GTCTTAGAGGCAAGACCGGAA 59.451 52.381 9.46 0.00 45.75 4.30
36 37 2.028385 GTCTTAGAGGCAAGACCGGAAA 60.028 50.000 9.46 0.00 45.75 3.13
37 38 2.028385 TCTTAGAGGCAAGACCGGAAAC 60.028 50.000 9.46 0.00 46.52 2.78
38 39 0.611714 TAGAGGCAAGACCGGAAACC 59.388 55.000 9.46 1.49 46.52 3.27
39 40 1.128188 AGAGGCAAGACCGGAAACCT 61.128 55.000 9.46 7.27 46.52 3.50
40 41 0.611714 GAGGCAAGACCGGAAACCTA 59.388 55.000 9.46 0.00 46.52 3.08
41 42 1.209747 GAGGCAAGACCGGAAACCTAT 59.790 52.381 9.46 0.00 46.52 2.57
42 43 2.433239 GAGGCAAGACCGGAAACCTATA 59.567 50.000 9.46 0.00 46.52 1.31
43 44 3.046374 AGGCAAGACCGGAAACCTATAT 58.954 45.455 9.46 0.00 46.52 0.86
44 45 3.458487 AGGCAAGACCGGAAACCTATATT 59.542 43.478 9.46 0.00 46.52 1.28
45 46 4.657039 AGGCAAGACCGGAAACCTATATTA 59.343 41.667 9.46 0.00 46.52 0.98
46 47 5.309806 AGGCAAGACCGGAAACCTATATTAT 59.690 40.000 9.46 0.00 46.52 1.28
47 48 6.499350 AGGCAAGACCGGAAACCTATATTATA 59.501 38.462 9.46 0.00 46.52 0.98
48 49 7.182206 AGGCAAGACCGGAAACCTATATTATAT 59.818 37.037 9.46 0.00 46.52 0.86
49 50 7.494952 GGCAAGACCGGAAACCTATATTATATC 59.505 40.741 9.46 0.00 0.00 1.63
50 51 7.222224 GCAAGACCGGAAACCTATATTATATCG 59.778 40.741 9.46 0.00 0.00 2.92
51 52 7.951347 AGACCGGAAACCTATATTATATCGT 57.049 36.000 9.46 0.00 0.00 3.73
52 53 8.358582 AGACCGGAAACCTATATTATATCGTT 57.641 34.615 9.46 0.00 0.00 3.85
53 54 8.810041 AGACCGGAAACCTATATTATATCGTTT 58.190 33.333 9.46 8.94 0.00 3.60
71 72 7.734924 ATCGTTTATCATGTGCATATGAGTT 57.265 32.000 27.00 16.22 40.16 3.01
72 73 7.552458 TCGTTTATCATGTGCATATGAGTTT 57.448 32.000 27.00 15.59 40.16 2.66
73 74 7.984391 TCGTTTATCATGTGCATATGAGTTTT 58.016 30.769 27.00 15.28 40.16 2.43
74 75 8.122330 TCGTTTATCATGTGCATATGAGTTTTC 58.878 33.333 27.00 16.13 40.16 2.29
75 76 7.909641 CGTTTATCATGTGCATATGAGTTTTCA 59.090 33.333 27.00 6.73 40.16 2.69
76 77 9.013490 GTTTATCATGTGCATATGAGTTTTCAC 57.987 33.333 27.00 15.22 40.16 3.18
77 78 8.510243 TTATCATGTGCATATGAGTTTTCACT 57.490 30.769 27.00 13.08 40.16 3.41
78 79 6.185852 TCATGTGCATATGAGTTTTCACTG 57.814 37.500 20.85 4.90 35.83 3.66
79 80 5.939296 TCATGTGCATATGAGTTTTCACTGA 59.061 36.000 20.85 6.85 35.83 3.41
80 81 6.430616 TCATGTGCATATGAGTTTTCACTGAA 59.569 34.615 20.85 0.00 35.83 3.02
81 82 6.822667 TGTGCATATGAGTTTTCACTGAAT 57.177 33.333 6.97 0.00 35.83 2.57
82 83 6.845302 TGTGCATATGAGTTTTCACTGAATC 58.155 36.000 6.97 0.00 35.83 2.52
83 84 6.430616 TGTGCATATGAGTTTTCACTGAATCA 59.569 34.615 6.97 0.00 35.83 2.57
84 85 6.744537 GTGCATATGAGTTTTCACTGAATCAC 59.255 38.462 6.97 0.00 35.83 3.06
85 86 6.430616 TGCATATGAGTTTTCACTGAATCACA 59.569 34.615 6.97 0.00 35.83 3.58
86 87 7.121611 TGCATATGAGTTTTCACTGAATCACAT 59.878 33.333 6.97 3.36 35.83 3.21
87 88 8.615211 GCATATGAGTTTTCACTGAATCACATA 58.385 33.333 6.97 12.32 35.83 2.29
91 92 8.044060 TGAGTTTTCACTGAATCACATATTCC 57.956 34.615 0.00 0.00 31.22 3.01
92 93 7.665145 TGAGTTTTCACTGAATCACATATTCCA 59.335 33.333 0.00 0.00 31.22 3.53
93 94 8.048534 AGTTTTCACTGAATCACATATTCCAG 57.951 34.615 0.00 0.00 0.00 3.86
94 95 7.667219 AGTTTTCACTGAATCACATATTCCAGT 59.333 33.333 0.00 0.00 0.00 4.00
95 96 8.946085 GTTTTCACTGAATCACATATTCCAGTA 58.054 33.333 0.00 0.00 0.00 2.74
96 97 9.685276 TTTTCACTGAATCACATATTCCAGTAT 57.315 29.630 0.00 0.00 0.00 2.12
97 98 8.893219 TTCACTGAATCACATATTCCAGTATC 57.107 34.615 0.00 0.00 0.00 2.24
98 99 8.021898 TCACTGAATCACATATTCCAGTATCA 57.978 34.615 0.00 0.00 0.00 2.15
99 100 7.928167 TCACTGAATCACATATTCCAGTATCAC 59.072 37.037 0.00 0.00 0.00 3.06
100 101 7.712205 CACTGAATCACATATTCCAGTATCACA 59.288 37.037 0.00 0.00 0.00 3.58
101 102 8.267183 ACTGAATCACATATTCCAGTATCACAA 58.733 33.333 0.00 0.00 0.00 3.33
102 103 8.437360 TGAATCACATATTCCAGTATCACAAC 57.563 34.615 0.00 0.00 0.00 3.32
103 104 8.046107 TGAATCACATATTCCAGTATCACAACA 58.954 33.333 0.00 0.00 0.00 3.33
104 105 8.442632 AATCACATATTCCAGTATCACAACAG 57.557 34.615 0.00 0.00 0.00 3.16
105 106 6.946340 TCACATATTCCAGTATCACAACAGT 58.054 36.000 0.00 0.00 0.00 3.55
106 107 7.394016 TCACATATTCCAGTATCACAACAGTT 58.606 34.615 0.00 0.00 0.00 3.16
107 108 8.536175 TCACATATTCCAGTATCACAACAGTTA 58.464 33.333 0.00 0.00 0.00 2.24
108 109 9.330063 CACATATTCCAGTATCACAACAGTTAT 57.670 33.333 0.00 0.00 0.00 1.89
115 116 9.416284 TCCAGTATCACAACAGTTATAGTATGA 57.584 33.333 0.00 0.00 0.00 2.15
177 178 8.978874 AACACAATATTATTGTCTCTATGGCA 57.021 30.769 17.21 0.00 0.00 4.92
178 179 9.578576 AACACAATATTATTGTCTCTATGGCAT 57.421 29.630 17.21 4.88 0.00 4.40
186 187 9.812347 ATTATTGTCTCTATGGCATATTTCCAA 57.188 29.630 7.81 9.40 37.13 3.53
187 188 6.942532 TTGTCTCTATGGCATATTTCCAAC 57.057 37.500 7.81 2.37 37.13 3.77
209 210 6.394345 ACAGGAGAACCTTATTCCATCTTT 57.606 37.500 0.00 0.00 45.36 2.52
211 212 7.569240 ACAGGAGAACCTTATTCCATCTTTAG 58.431 38.462 0.00 0.00 45.36 1.85
213 214 7.497249 CAGGAGAACCTTATTCCATCTTTAGTG 59.503 40.741 0.00 0.00 45.36 2.74
215 216 7.713073 GGAGAACCTTATTCCATCTTTAGTGAG 59.287 40.741 0.00 0.00 0.00 3.51
217 218 6.567602 ACCTTATTCCATCTTTAGTGAGCT 57.432 37.500 0.00 0.00 0.00 4.09
223 224 2.877168 CCATCTTTAGTGAGCTGCCATC 59.123 50.000 0.00 0.00 0.00 3.51
224 225 3.433314 CCATCTTTAGTGAGCTGCCATCT 60.433 47.826 0.00 0.00 0.00 2.90
229 230 0.175302 AGTGAGCTGCCATCTTCTCG 59.825 55.000 0.00 0.00 0.00 4.04
234 236 0.807496 GCTGCCATCTTCTCGCTTTT 59.193 50.000 0.00 0.00 0.00 2.27
255 257 4.440826 TTTAGCAGGACACAAACCCTAA 57.559 40.909 0.00 0.00 0.00 2.69
263 265 4.643334 AGGACACAAACCCTAACAAAACTC 59.357 41.667 0.00 0.00 0.00 3.01
306 308 2.270850 CCCTCCGGCCGAAAATGA 59.729 61.111 30.73 14.30 0.00 2.57
307 309 1.152963 CCCTCCGGCCGAAAATGAT 60.153 57.895 30.73 0.00 0.00 2.45
308 310 0.751643 CCCTCCGGCCGAAAATGATT 60.752 55.000 30.73 0.00 0.00 2.57
309 311 0.381801 CCTCCGGCCGAAAATGATTG 59.618 55.000 30.73 6.27 0.00 2.67
311 313 1.034838 TCCGGCCGAAAATGATTGGG 61.035 55.000 30.73 4.77 0.00 4.12
312 314 1.437160 CGGCCGAAAATGATTGGGG 59.563 57.895 24.07 0.00 0.00 4.96
313 315 1.319614 CGGCCGAAAATGATTGGGGT 61.320 55.000 24.07 0.00 0.00 4.95
315 317 0.459899 GCCGAAAATGATTGGGGTCC 59.540 55.000 0.00 0.00 0.00 4.46
316 318 1.846007 CCGAAAATGATTGGGGTCCA 58.154 50.000 0.00 0.00 0.00 4.02
317 319 2.387757 CCGAAAATGATTGGGGTCCAT 58.612 47.619 0.00 0.00 31.53 3.41
318 320 2.362077 CCGAAAATGATTGGGGTCCATC 59.638 50.000 0.00 0.00 31.53 3.51
319 321 3.023119 CGAAAATGATTGGGGTCCATCA 58.977 45.455 0.00 0.00 31.53 3.07
320 322 3.181487 CGAAAATGATTGGGGTCCATCAC 60.181 47.826 0.00 0.00 31.53 3.06
321 323 2.057137 AATGATTGGGGTCCATCACG 57.943 50.000 0.00 0.00 31.53 4.35
323 325 1.224592 GATTGGGGTCCATCACGCT 59.775 57.895 0.00 0.00 38.07 5.07
331 333 2.903855 CCATCACGCTCCCATGGC 60.904 66.667 6.09 0.00 30.94 4.40
337 339 2.305607 ACGCTCCCATGGCCCTAAA 61.306 57.895 6.09 0.00 0.00 1.85
362 364 1.118356 GGGAGATGAGGCAGATCGGT 61.118 60.000 0.00 0.00 0.00 4.69
370 373 1.067212 GAGGCAGATCGGTGATACGTT 59.933 52.381 0.00 0.00 34.94 3.99
374 377 2.734175 GCAGATCGGTGATACGTTGACA 60.734 50.000 0.00 0.00 34.94 3.58
377 380 0.108992 TCGGTGATACGTTGACAGGC 60.109 55.000 0.00 0.00 34.94 4.85
392 395 3.068562 AGGCGACTGGAACCTTAGT 57.931 52.632 0.00 0.00 41.13 2.24
394 397 1.002087 AGGCGACTGGAACCTTAGTTG 59.998 52.381 0.00 0.00 41.13 3.16
395 398 1.270678 GGCGACTGGAACCTTAGTTGT 60.271 52.381 0.00 0.00 35.94 3.32
414 417 1.705745 GTCTTTTCCCTTGGGAGGAGT 59.294 52.381 8.55 0.00 46.74 3.85
428 431 2.933260 GGAGGAGTGAAGAAATCGAAGC 59.067 50.000 0.00 0.00 0.00 3.86
430 433 3.997021 GAGGAGTGAAGAAATCGAAGCAA 59.003 43.478 0.00 0.00 0.00 3.91
446 449 4.319694 CGAAGCAACACAGACATGAAATCA 60.320 41.667 0.00 0.00 0.00 2.57
448 451 5.717078 AGCAACACAGACATGAAATCAAT 57.283 34.783 0.00 0.00 0.00 2.57
449 452 5.466819 AGCAACACAGACATGAAATCAATG 58.533 37.500 0.00 0.00 0.00 2.82
456 459 6.972901 CACAGACATGAAATCAATGGAATCTG 59.027 38.462 0.00 0.00 36.70 2.90
458 461 7.395206 ACAGACATGAAATCAATGGAATCTGAA 59.605 33.333 0.00 0.00 35.09 3.02
463 466 6.980593 TGAAATCAATGGAATCTGAACGTTT 58.019 32.000 0.46 0.00 0.00 3.60
469 472 3.399330 TGGAATCTGAACGTTTCACCTC 58.601 45.455 0.46 0.00 35.46 3.85
485 489 9.357652 CGTTTCACCTCAAAAATCAATATCATT 57.642 29.630 0.00 0.00 0.00 2.57
512 516 2.035632 AGCAAGAAGATACTCCCTCCG 58.964 52.381 0.00 0.00 0.00 4.63
514 518 2.168728 GCAAGAAGATACTCCCTCCGTT 59.831 50.000 0.00 0.00 0.00 4.44
515 519 3.738590 GCAAGAAGATACTCCCTCCGTTC 60.739 52.174 0.00 0.00 0.00 3.95
516 520 3.383698 AGAAGATACTCCCTCCGTTCA 57.616 47.619 0.00 0.00 0.00 3.18
517 521 3.709587 AGAAGATACTCCCTCCGTTCAA 58.290 45.455 0.00 0.00 0.00 2.69
518 522 4.094476 AGAAGATACTCCCTCCGTTCAAA 58.906 43.478 0.00 0.00 0.00 2.69
522 527 6.163135 AGATACTCCCTCCGTTCAAAATAG 57.837 41.667 0.00 0.00 0.00 1.73
539 544 7.816640 TCAAAATAGGTGTCTCAACTTTATGC 58.183 34.615 0.00 0.00 31.86 3.14
540 545 7.665559 TCAAAATAGGTGTCTCAACTTTATGCT 59.334 33.333 0.00 0.00 31.86 3.79
641 660 7.837202 AAACTTTCGATAATGTTATCCGACA 57.163 32.000 7.08 0.00 36.95 4.35
644 663 7.681903 ACTTTCGATAATGTTATCCGACAAAC 58.318 34.615 7.08 0.00 36.95 2.93
659 680 3.530910 AAACGTCGTCAGCTGGGGG 62.531 63.158 15.13 3.48 0.00 5.40
721 742 7.968405 AGTTGTTTTGTAAGATCAAACAGTGAC 59.032 33.333 0.00 5.20 39.72 3.67
729 750 9.168451 TGTAAGATCAAACAGTGACAGTTTTAA 57.832 29.630 3.22 0.00 39.72 1.52
730 751 9.997482 GTAAGATCAAACAGTGACAGTTTTAAA 57.003 29.630 3.22 0.00 39.72 1.52
731 752 8.911247 AAGATCAAACAGTGACAGTTTTAAAC 57.089 30.769 3.22 0.00 39.72 2.01
732 753 8.050778 AGATCAAACAGTGACAGTTTTAAACA 57.949 30.769 10.60 0.00 39.72 2.83
778 800 9.288576 TGAAACTATCATGTTGTTCTGAAGAAT 57.711 29.630 3.16 0.00 32.71 2.40
781 803 9.903682 AACTATCATGTTGTTCTGAAGAATTTG 57.096 29.630 3.16 5.03 36.33 2.32
815 837 4.342092 ACAACTAAAGCTGCCAGTGAAATT 59.658 37.500 0.00 0.00 0.00 1.82
816 838 5.534654 ACAACTAAAGCTGCCAGTGAAATTA 59.465 36.000 0.00 0.00 0.00 1.40
817 839 6.040391 ACAACTAAAGCTGCCAGTGAAATTAA 59.960 34.615 0.00 0.00 0.00 1.40
818 840 6.648879 ACTAAAGCTGCCAGTGAAATTAAA 57.351 33.333 0.00 0.00 0.00 1.52
819 841 7.049799 ACTAAAGCTGCCAGTGAAATTAAAA 57.950 32.000 0.00 0.00 0.00 1.52
898 2734 2.161486 GTCGATGCGTCTGTGGCTC 61.161 63.158 4.05 0.00 0.00 4.70
960 2925 1.415659 GTCACAGGGGATGAGGAGATG 59.584 57.143 0.00 0.00 0.00 2.90
961 2926 1.291939 TCACAGGGGATGAGGAGATGA 59.708 52.381 0.00 0.00 0.00 2.92
962 2927 1.693062 CACAGGGGATGAGGAGATGAG 59.307 57.143 0.00 0.00 0.00 2.90
963 2928 0.686224 CAGGGGATGAGGAGATGAGC 59.314 60.000 0.00 0.00 0.00 4.26
964 2929 0.831288 AGGGGATGAGGAGATGAGCG 60.831 60.000 0.00 0.00 0.00 5.03
965 2930 0.829602 GGGGATGAGGAGATGAGCGA 60.830 60.000 0.00 0.00 0.00 4.93
998 2966 4.436998 GGAGGAGCGACACCACCG 62.437 72.222 0.00 0.00 0.00 4.94
1026 2994 1.923227 CTACTCAGTGCGCCGTCTCA 61.923 60.000 4.18 0.00 0.00 3.27
1027 2995 2.196382 TACTCAGTGCGCCGTCTCAC 62.196 60.000 4.18 0.00 0.00 3.51
1512 3486 2.680913 GCTGTTCGACGCAATGCCT 61.681 57.895 0.00 0.00 0.00 4.75
1702 3676 3.181483 GCCATTCTTGCTCTATGGTTTGG 60.181 47.826 0.00 0.00 40.73 3.28
1752 3726 2.094494 TGATCTCTTCGTTGTCAGCTCC 60.094 50.000 0.00 0.00 0.00 4.70
1755 3729 1.664649 CTTCGTTGTCAGCTCCGCA 60.665 57.895 0.00 0.00 0.00 5.69
1779 3753 2.295885 GGCATGTTCTCTGAGATTGGG 58.704 52.381 8.42 0.84 0.00 4.12
1783 3757 4.202398 GCATGTTCTCTGAGATTGGGGATA 60.202 45.833 8.42 0.00 0.00 2.59
1789 3763 1.349026 CTGAGATTGGGGATATGCGGT 59.651 52.381 0.00 0.00 0.00 5.68
1791 3765 0.321671 AGATTGGGGATATGCGGTCG 59.678 55.000 0.00 0.00 0.00 4.79
1800 3774 0.963856 ATATGCGGTCGGCTCGGATA 60.964 55.000 12.66 12.66 43.00 2.59
1929 3903 0.109723 TGGGGTCAAAAGAGGTTCCG 59.890 55.000 0.00 0.00 0.00 4.30
1932 3906 1.071857 GGGTCAAAAGAGGTTCCGTCT 59.928 52.381 0.00 0.00 0.00 4.18
1995 3969 1.001641 ACAAGATGTCAGGCTGGGC 60.002 57.895 15.73 8.78 0.00 5.36
2265 4239 2.416747 GTGACATTGACTGCAGTGCTA 58.583 47.619 27.27 12.96 35.36 3.49
2377 4351 6.183360 GGAGAGCTATCTGATAGACATGTACG 60.183 46.154 25.04 0.43 35.30 3.67
2408 4382 1.495878 CGCATAGACATGGCTCAGAC 58.504 55.000 2.95 0.00 32.36 3.51
2517 4491 0.107703 CAGTCTTAGCATTCCGGGCA 60.108 55.000 0.00 0.00 0.00 5.36
2574 4548 1.174712 TTGCTTCAGTGCTTCCTGCC 61.175 55.000 0.00 0.00 42.00 4.85
2676 4650 4.924462 GTCTTTGTAGGTACAGCTCTTGTC 59.076 45.833 0.00 0.00 41.29 3.18
2827 4801 5.309638 CACTATCCCTCTTCTACTCGATGA 58.690 45.833 0.00 0.00 0.00 2.92
2967 4941 1.307343 AGCTACCCCTCAGCACCAT 60.307 57.895 0.00 0.00 41.66 3.55
2982 4956 2.564771 CACCATTGCTGTATCGTGGAT 58.435 47.619 0.00 0.00 34.13 3.41
3048 5022 0.846427 AAAGCCTGGGTGAGGATGGA 60.846 55.000 0.00 0.00 40.73 3.41
3057 5031 3.075882 TGGGTGAGGATGGAAACTTCATT 59.924 43.478 0.00 0.00 36.27 2.57
3072 5046 1.224436 TCATTGCCATCTGGGGATCA 58.776 50.000 0.00 0.00 36.59 2.92
3078 5052 1.213926 GCCATCTGGGGATCACTTCTT 59.786 52.381 0.00 0.00 37.04 2.52
3144 5118 2.999355 GACTGAGAAGGTGCTCAACATC 59.001 50.000 0.00 0.00 43.75 3.06
3226 5200 2.464865 GTAACTGGAGTAGCGCTGATG 58.535 52.381 22.90 6.65 0.00 3.07
3256 5230 1.296523 AGGAGATGAGATTGAGGGGGT 59.703 52.381 0.00 0.00 0.00 4.95
3269 5243 1.000771 GGGGGTTGAGGAAAGAGGC 60.001 63.158 0.00 0.00 0.00 4.70
3270 5244 1.501654 GGGGGTTGAGGAAAGAGGCT 61.502 60.000 0.00 0.00 0.00 4.58
3278 5252 2.567615 TGAGGAAAGAGGCTGGTTCTAC 59.432 50.000 0.00 0.00 0.00 2.59
3327 5301 2.732763 CAGGACAGATCTGTGGAGAGA 58.267 52.381 32.50 0.00 45.05 3.10
3344 5318 5.816777 TGGAGAGAAACCAAAAGCAAAATTG 59.183 36.000 0.00 0.00 34.25 2.32
3361 5335 1.916506 TTGCCCCGAAAATGATCACA 58.083 45.000 0.00 0.00 0.00 3.58
3380 5354 1.263484 CATGTTCTCGATGCTGGATGC 59.737 52.381 0.00 0.00 43.25 3.91
3444 5418 5.392767 AGTACTTATGGCACGGATAGATG 57.607 43.478 0.00 0.00 0.00 2.90
3446 5420 3.239449 ACTTATGGCACGGATAGATGGA 58.761 45.455 0.00 0.00 0.00 3.41
3498 5472 5.453903 GGTGGTGATTAGCTCATACTGTCAT 60.454 44.000 0.00 0.00 35.97 3.06
3556 5531 2.551270 TGCCTTCTCCCAGAATACAGT 58.449 47.619 0.00 0.00 33.13 3.55
3561 5536 4.141824 CCTTCTCCCAGAATACAGTTCCTC 60.142 50.000 0.00 0.00 33.13 3.71
3574 5549 3.924144 CAGTTCCTCTGGAGTCTTTGAG 58.076 50.000 0.00 0.00 40.23 3.02
3682 5662 5.476599 TCCATCGGAAATGAAACAAGTTGAT 59.523 36.000 10.54 0.00 0.00 2.57
3727 5707 7.333672 CAGAGATGAAACAAGATGTTGAGATCA 59.666 37.037 9.96 10.20 40.14 2.92
3805 5787 0.460284 CCTGACATGTGAGTACGCCC 60.460 60.000 11.54 0.00 0.00 6.13
4017 6023 3.246619 GCACTCTGCACTCTGTACTAAC 58.753 50.000 0.00 0.00 44.26 2.34
4072 6079 5.458041 TTACTACAAGCCTCAAACGTACT 57.542 39.130 0.00 0.00 0.00 2.73
4151 6160 3.192633 ACCAGCAAAAGAACTGAAACGTT 59.807 39.130 0.00 0.00 35.90 3.99
4152 6161 3.547468 CCAGCAAAAGAACTGAAACGTTG 59.453 43.478 0.00 0.00 35.90 4.10
4222 6231 5.121380 ACCCAGCAGTGAAAGAATCATAT 57.879 39.130 0.00 0.00 40.97 1.78
4229 6238 5.240403 GCAGTGAAAGAATCATATTCCCTCC 59.760 44.000 0.00 0.00 40.97 4.30
4245 6254 5.732331 TCCCTCCATTCCATAATTCTTGT 57.268 39.130 0.00 0.00 0.00 3.16
4247 6256 5.193527 TCCCTCCATTCCATAATTCTTGTCA 59.806 40.000 0.00 0.00 0.00 3.58
4259 6268 9.573133 CCATAATTCTTGTCATGGTTTTAGTTC 57.427 33.333 0.00 0.00 34.46 3.01
4297 6306 3.443681 ACCAAGGCAAGAATTATGGAACG 59.556 43.478 0.00 0.00 0.00 3.95
4298 6307 3.694072 CCAAGGCAAGAATTATGGAACGA 59.306 43.478 0.00 0.00 0.00 3.85
4308 6317 5.897824 AGAATTATGGAACGAAGGGAGTAGA 59.102 40.000 0.00 0.00 0.00 2.59
4327 6336 9.032420 GGAGTAGAATTTAGTTCCAGAATAACG 57.968 37.037 0.00 0.00 37.56 3.18
4356 6365 8.296211 ACATGATATCATTGAATTCCACAACA 57.704 30.769 15.74 0.00 33.61 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.209818 TCTAAGACCGATTCAAGTGTTGT 57.790 39.130 0.00 0.00 0.00 3.32
1 2 4.627467 CCTCTAAGACCGATTCAAGTGTTG 59.373 45.833 0.00 0.00 0.00 3.33
2 3 4.822026 CCTCTAAGACCGATTCAAGTGTT 58.178 43.478 0.00 0.00 0.00 3.32
3 4 3.368531 GCCTCTAAGACCGATTCAAGTGT 60.369 47.826 0.00 0.00 0.00 3.55
4 5 3.190874 GCCTCTAAGACCGATTCAAGTG 58.809 50.000 0.00 0.00 0.00 3.16
5 6 2.832129 TGCCTCTAAGACCGATTCAAGT 59.168 45.455 0.00 0.00 0.00 3.16
6 7 3.526931 TGCCTCTAAGACCGATTCAAG 57.473 47.619 0.00 0.00 0.00 3.02
7 8 3.513912 TCTTGCCTCTAAGACCGATTCAA 59.486 43.478 0.00 0.00 32.02 2.69
8 9 3.096852 TCTTGCCTCTAAGACCGATTCA 58.903 45.455 0.00 0.00 32.02 2.57
9 10 3.449632 GTCTTGCCTCTAAGACCGATTC 58.550 50.000 7.27 0.00 46.84 2.52
10 11 3.528597 GTCTTGCCTCTAAGACCGATT 57.471 47.619 7.27 0.00 46.84 3.34
16 17 1.933021 TTCCGGTCTTGCCTCTAAGA 58.067 50.000 0.00 0.00 34.46 2.10
17 18 2.347731 GTTTCCGGTCTTGCCTCTAAG 58.652 52.381 0.00 0.00 34.25 2.18
18 19 1.002773 GGTTTCCGGTCTTGCCTCTAA 59.997 52.381 0.00 0.00 34.25 2.10
19 20 0.611714 GGTTTCCGGTCTTGCCTCTA 59.388 55.000 0.00 0.00 34.25 2.43
20 21 1.128188 AGGTTTCCGGTCTTGCCTCT 61.128 55.000 0.00 0.00 34.25 3.69
21 22 0.611714 TAGGTTTCCGGTCTTGCCTC 59.388 55.000 0.00 0.00 34.25 4.70
22 23 1.286248 ATAGGTTTCCGGTCTTGCCT 58.714 50.000 0.00 6.21 34.25 4.75
23 24 2.994186 TATAGGTTTCCGGTCTTGCC 57.006 50.000 0.00 0.00 0.00 4.52
24 25 7.222224 CGATATAATATAGGTTTCCGGTCTTGC 59.778 40.741 0.00 0.00 0.00 4.01
25 26 8.248945 ACGATATAATATAGGTTTCCGGTCTTG 58.751 37.037 0.00 0.00 0.00 3.02
26 27 8.358582 ACGATATAATATAGGTTTCCGGTCTT 57.641 34.615 0.00 0.00 0.00 3.01
27 28 7.951347 ACGATATAATATAGGTTTCCGGTCT 57.049 36.000 0.00 0.00 0.00 3.85
28 29 8.992835 AAACGATATAATATAGGTTTCCGGTC 57.007 34.615 0.00 0.00 0.00 4.79
45 46 9.440773 AACTCATATGCACATGATAAACGATAT 57.559 29.630 8.37 0.00 34.50 1.63
46 47 8.831715 AACTCATATGCACATGATAAACGATA 57.168 30.769 8.37 0.00 34.50 2.92
47 48 7.734924 AACTCATATGCACATGATAAACGAT 57.265 32.000 8.37 0.00 34.50 3.73
48 49 7.552458 AAACTCATATGCACATGATAAACGA 57.448 32.000 8.37 0.00 34.50 3.85
49 50 7.909641 TGAAAACTCATATGCACATGATAAACG 59.090 33.333 8.37 0.00 34.50 3.60
50 51 9.013490 GTGAAAACTCATATGCACATGATAAAC 57.987 33.333 8.37 0.91 34.50 2.01
51 52 8.959548 AGTGAAAACTCATATGCACATGATAAA 58.040 29.630 8.37 0.00 34.50 1.40
52 53 8.400186 CAGTGAAAACTCATATGCACATGATAA 58.600 33.333 8.37 0.00 34.50 1.75
53 54 7.769970 TCAGTGAAAACTCATATGCACATGATA 59.230 33.333 8.37 0.00 34.50 2.15
54 55 6.600427 TCAGTGAAAACTCATATGCACATGAT 59.400 34.615 8.37 0.00 34.50 2.45
55 56 5.939296 TCAGTGAAAACTCATATGCACATGA 59.061 36.000 7.57 7.57 33.88 3.07
56 57 6.185852 TCAGTGAAAACTCATATGCACATG 57.814 37.500 0.00 0.00 0.00 3.21
57 58 6.822667 TTCAGTGAAAACTCATATGCACAT 57.177 33.333 2.20 0.00 0.00 3.21
58 59 6.430616 TGATTCAGTGAAAACTCATATGCACA 59.569 34.615 10.14 0.00 0.00 4.57
59 60 6.744537 GTGATTCAGTGAAAACTCATATGCAC 59.255 38.462 10.14 0.00 0.00 4.57
60 61 6.430616 TGTGATTCAGTGAAAACTCATATGCA 59.569 34.615 10.14 1.41 0.00 3.96
61 62 6.845302 TGTGATTCAGTGAAAACTCATATGC 58.155 36.000 10.14 0.00 0.00 3.14
65 66 8.680903 GGAATATGTGATTCAGTGAAAACTCAT 58.319 33.333 22.17 22.17 0.00 2.90
66 67 7.665145 TGGAATATGTGATTCAGTGAAAACTCA 59.335 33.333 10.14 13.50 0.00 3.41
67 68 8.044060 TGGAATATGTGATTCAGTGAAAACTC 57.956 34.615 10.14 3.82 0.00 3.01
68 69 7.667219 ACTGGAATATGTGATTCAGTGAAAACT 59.333 33.333 10.14 0.00 0.00 2.66
69 70 7.820648 ACTGGAATATGTGATTCAGTGAAAAC 58.179 34.615 10.14 11.77 0.00 2.43
70 71 9.685276 ATACTGGAATATGTGATTCAGTGAAAA 57.315 29.630 10.14 0.00 0.00 2.29
71 72 9.330063 GATACTGGAATATGTGATTCAGTGAAA 57.670 33.333 10.14 0.00 0.00 2.69
72 73 8.485392 TGATACTGGAATATGTGATTCAGTGAA 58.515 33.333 8.27 8.27 0.00 3.18
73 74 7.928167 GTGATACTGGAATATGTGATTCAGTGA 59.072 37.037 0.00 0.00 0.00 3.41
74 75 7.712205 TGTGATACTGGAATATGTGATTCAGTG 59.288 37.037 0.00 0.00 0.00 3.66
75 76 7.795047 TGTGATACTGGAATATGTGATTCAGT 58.205 34.615 0.00 0.00 0.00 3.41
76 77 8.554528 GTTGTGATACTGGAATATGTGATTCAG 58.445 37.037 0.17 0.00 0.00 3.02
77 78 8.046107 TGTTGTGATACTGGAATATGTGATTCA 58.954 33.333 0.17 0.00 0.00 2.57
78 79 8.437360 TGTTGTGATACTGGAATATGTGATTC 57.563 34.615 0.00 0.00 0.00 2.52
79 80 8.049117 ACTGTTGTGATACTGGAATATGTGATT 58.951 33.333 0.00 0.00 0.00 2.57
80 81 7.568349 ACTGTTGTGATACTGGAATATGTGAT 58.432 34.615 0.00 0.00 0.00 3.06
81 82 6.946340 ACTGTTGTGATACTGGAATATGTGA 58.054 36.000 0.00 0.00 0.00 3.58
82 83 7.615582 AACTGTTGTGATACTGGAATATGTG 57.384 36.000 0.00 0.00 0.00 3.21
89 90 9.416284 TCATACTATAACTGTTGTGATACTGGA 57.584 33.333 2.69 0.00 0.00 3.86
152 153 8.978874 TGCCATAGAGACAATAATATTGTGTT 57.021 30.769 21.80 10.65 31.96 3.32
160 161 9.812347 TTGGAAATATGCCATAGAGACAATAAT 57.188 29.630 0.00 0.00 34.90 1.28
161 162 9.066892 GTTGGAAATATGCCATAGAGACAATAA 57.933 33.333 0.00 0.00 34.90 1.40
162 163 8.217111 TGTTGGAAATATGCCATAGAGACAATA 58.783 33.333 0.00 0.00 34.90 1.90
163 164 7.062322 TGTTGGAAATATGCCATAGAGACAAT 58.938 34.615 0.00 0.00 34.90 2.71
164 165 6.422333 TGTTGGAAATATGCCATAGAGACAA 58.578 36.000 0.00 0.00 34.90 3.18
165 166 6.000246 TGTTGGAAATATGCCATAGAGACA 58.000 37.500 0.00 0.00 34.90 3.41
166 167 5.471456 CCTGTTGGAAATATGCCATAGAGAC 59.529 44.000 0.00 0.00 34.90 3.36
167 168 5.369404 TCCTGTTGGAAATATGCCATAGAGA 59.631 40.000 0.00 0.53 39.87 3.10
168 169 5.624159 TCCTGTTGGAAATATGCCATAGAG 58.376 41.667 0.00 0.28 39.87 2.43
169 170 5.369404 TCTCCTGTTGGAAATATGCCATAGA 59.631 40.000 0.00 0.00 42.66 1.98
170 171 5.624159 TCTCCTGTTGGAAATATGCCATAG 58.376 41.667 0.00 2.05 42.66 2.23
171 172 5.645056 TCTCCTGTTGGAAATATGCCATA 57.355 39.130 0.00 0.00 42.66 2.74
172 173 4.524802 TCTCCTGTTGGAAATATGCCAT 57.475 40.909 0.00 0.00 42.66 4.40
173 174 4.016444 GTTCTCCTGTTGGAAATATGCCA 58.984 43.478 0.00 0.00 42.66 4.92
174 175 3.381590 GGTTCTCCTGTTGGAAATATGCC 59.618 47.826 0.00 0.00 42.66 4.40
175 176 4.273318 AGGTTCTCCTGTTGGAAATATGC 58.727 43.478 0.00 0.00 43.33 3.14
176 177 8.525290 AATAAGGTTCTCCTGTTGGAAATATG 57.475 34.615 0.00 0.00 44.35 1.78
177 178 7.780271 GGAATAAGGTTCTCCTGTTGGAAATAT 59.220 37.037 0.00 0.00 44.35 1.28
178 179 7.116736 GGAATAAGGTTCTCCTGTTGGAAATA 58.883 38.462 0.00 0.00 44.35 1.40
179 180 5.952347 GGAATAAGGTTCTCCTGTTGGAAAT 59.048 40.000 0.00 0.00 44.35 2.17
180 181 5.163034 TGGAATAAGGTTCTCCTGTTGGAAA 60.163 40.000 0.00 0.00 44.35 3.13
181 182 4.352595 TGGAATAAGGTTCTCCTGTTGGAA 59.647 41.667 0.00 0.00 44.35 3.53
182 183 3.913799 TGGAATAAGGTTCTCCTGTTGGA 59.086 43.478 0.00 0.00 44.35 3.53
183 184 4.301072 TGGAATAAGGTTCTCCTGTTGG 57.699 45.455 0.00 0.00 44.35 3.77
184 185 5.749462 AGATGGAATAAGGTTCTCCTGTTG 58.251 41.667 0.00 0.00 44.35 3.33
185 186 6.394345 AAGATGGAATAAGGTTCTCCTGTT 57.606 37.500 0.00 0.00 44.35 3.16
186 187 6.394345 AAAGATGGAATAAGGTTCTCCTGT 57.606 37.500 0.00 0.00 44.35 4.00
187 188 7.497249 CACTAAAGATGGAATAAGGTTCTCCTG 59.503 40.741 0.00 0.00 44.35 3.86
209 210 1.406898 CGAGAAGATGGCAGCTCACTA 59.593 52.381 5.40 0.00 0.00 2.74
211 212 1.427592 GCGAGAAGATGGCAGCTCAC 61.428 60.000 5.40 3.60 31.94 3.51
213 214 0.461693 AAGCGAGAAGATGGCAGCTC 60.462 55.000 5.40 2.56 34.56 4.09
215 216 0.807496 AAAAGCGAGAAGATGGCAGC 59.193 50.000 0.00 0.00 34.56 5.25
234 236 4.139038 GTTAGGGTTTGTGTCCTGCTAAA 58.861 43.478 0.00 0.00 34.75 1.85
236 238 2.706723 TGTTAGGGTTTGTGTCCTGCTA 59.293 45.455 0.00 0.00 34.75 3.49
238 240 1.975660 TGTTAGGGTTTGTGTCCTGC 58.024 50.000 0.00 0.00 34.75 4.85
269 271 5.580022 AGGGCTCCATTTTTATGTGTTAGT 58.420 37.500 0.00 0.00 0.00 2.24
270 272 6.136541 GAGGGCTCCATTTTTATGTGTTAG 57.863 41.667 0.00 0.00 0.00 2.34
295 297 0.459899 GACCCCAATCATTTTCGGCC 59.540 55.000 0.00 0.00 0.00 6.13
296 298 0.459899 GGACCCCAATCATTTTCGGC 59.540 55.000 0.00 0.00 0.00 5.54
298 300 3.023119 TGATGGACCCCAATCATTTTCG 58.977 45.455 0.00 0.00 36.95 3.46
303 305 0.466189 GCGTGATGGACCCCAATCAT 60.466 55.000 0.00 0.00 36.95 2.45
304 306 1.077787 GCGTGATGGACCCCAATCA 60.078 57.895 0.00 0.00 36.95 2.57
305 307 0.815615 GAGCGTGATGGACCCCAATC 60.816 60.000 0.00 0.00 36.95 2.67
306 308 1.224592 GAGCGTGATGGACCCCAAT 59.775 57.895 0.00 0.00 36.95 3.16
307 309 2.668632 GAGCGTGATGGACCCCAA 59.331 61.111 0.00 0.00 36.95 4.12
308 310 3.399181 GGAGCGTGATGGACCCCA 61.399 66.667 0.00 0.00 38.19 4.96
309 311 4.176752 GGGAGCGTGATGGACCCC 62.177 72.222 0.00 0.00 35.00 4.95
311 313 1.524621 CATGGGAGCGTGATGGACC 60.525 63.158 0.00 0.00 0.00 4.46
312 314 1.524621 CCATGGGAGCGTGATGGAC 60.525 63.158 2.85 0.00 39.29 4.02
313 315 2.910360 CCATGGGAGCGTGATGGA 59.090 61.111 2.85 0.00 39.29 3.41
315 317 2.903855 GGCCATGGGAGCGTGATG 60.904 66.667 15.13 0.00 0.00 3.07
316 318 4.195334 GGGCCATGGGAGCGTGAT 62.195 66.667 15.13 0.00 0.00 3.06
317 319 3.993865 TAGGGCCATGGGAGCGTGA 62.994 63.158 15.13 0.00 0.00 4.35
318 320 2.550699 TTTAGGGCCATGGGAGCGTG 62.551 60.000 15.13 0.00 0.00 5.34
319 321 2.270874 CTTTAGGGCCATGGGAGCGT 62.271 60.000 15.13 0.00 0.00 5.07
320 322 1.526917 CTTTAGGGCCATGGGAGCG 60.527 63.158 15.13 0.00 0.00 5.03
321 323 1.829970 GCTTTAGGGCCATGGGAGC 60.830 63.158 15.13 5.33 0.00 4.70
331 333 0.179045 CATCTCCCGTGGCTTTAGGG 60.179 60.000 0.00 0.00 46.40 3.53
334 336 0.830648 CCTCATCTCCCGTGGCTTTA 59.169 55.000 0.00 0.00 0.00 1.85
337 339 3.474570 GCCTCATCTCCCGTGGCT 61.475 66.667 0.00 0.00 40.36 4.75
362 364 0.885879 AGTCGCCTGTCAACGTATCA 59.114 50.000 0.00 0.00 0.00 2.15
370 373 1.407656 AAGGTTCCAGTCGCCTGTCA 61.408 55.000 0.00 0.00 36.95 3.58
374 377 1.002087 CAACTAAGGTTCCAGTCGCCT 59.998 52.381 0.00 0.00 32.73 5.52
377 380 3.662247 AGACAACTAAGGTTCCAGTCG 57.338 47.619 0.00 0.00 33.73 4.18
383 386 5.009710 CCAAGGGAAAAGACAACTAAGGTTC 59.990 44.000 0.00 0.00 32.73 3.62
388 391 4.447180 CCTCCCAAGGGAAAAGACAACTAA 60.447 45.833 9.52 0.00 44.66 2.24
392 395 2.108250 CTCCTCCCAAGGGAAAAGACAA 59.892 50.000 9.52 0.00 44.66 3.18
394 397 1.705745 ACTCCTCCCAAGGGAAAAGAC 59.294 52.381 18.46 0.00 44.66 3.01
395 398 1.705186 CACTCCTCCCAAGGGAAAAGA 59.295 52.381 18.46 11.09 44.66 2.52
414 417 4.024893 GTCTGTGTTGCTTCGATTTCTTCA 60.025 41.667 0.00 0.00 0.00 3.02
428 431 6.016213 TCCATTGATTTCATGTCTGTGTTG 57.984 37.500 0.00 0.00 0.00 3.33
430 433 6.662234 AGATTCCATTGATTTCATGTCTGTGT 59.338 34.615 0.00 0.00 0.00 3.72
446 449 4.398319 AGGTGAAACGTTCAGATTCCATT 58.602 39.130 0.00 0.00 41.01 3.16
448 451 3.181459 TGAGGTGAAACGTTCAGATTCCA 60.181 43.478 0.00 0.00 41.01 3.53
449 452 3.399330 TGAGGTGAAACGTTCAGATTCC 58.601 45.455 0.00 0.00 41.01 3.01
456 459 8.742554 ATATTGATTTTTGAGGTGAAACGTTC 57.257 30.769 0.00 0.00 38.12 3.95
458 461 7.881142 TGATATTGATTTTTGAGGTGAAACGT 58.119 30.769 0.00 0.00 38.12 3.99
485 489 9.036980 GGAGGGAGTATCTTCTTGCTAATATAA 57.963 37.037 0.00 0.00 33.73 0.98
486 490 7.339721 CGGAGGGAGTATCTTCTTGCTAATATA 59.660 40.741 0.00 0.00 33.73 0.86
490 494 3.637229 CGGAGGGAGTATCTTCTTGCTAA 59.363 47.826 0.00 0.00 33.73 3.09
506 510 3.007635 GACACCTATTTTGAACGGAGGG 58.992 50.000 0.00 0.00 0.00 4.30
512 516 9.612620 CATAAAGTTGAGACACCTATTTTGAAC 57.387 33.333 0.00 0.00 0.00 3.18
514 518 7.665559 AGCATAAAGTTGAGACACCTATTTTGA 59.334 33.333 0.00 0.00 0.00 2.69
515 519 7.820648 AGCATAAAGTTGAGACACCTATTTTG 58.179 34.615 0.00 0.00 0.00 2.44
516 520 9.515226 TTAGCATAAAGTTGAGACACCTATTTT 57.485 29.630 0.00 0.00 0.00 1.82
517 521 8.947115 GTTAGCATAAAGTTGAGACACCTATTT 58.053 33.333 0.00 0.00 0.00 1.40
518 522 8.322091 AGTTAGCATAAAGTTGAGACACCTATT 58.678 33.333 0.00 0.00 0.00 1.73
522 527 6.803154 AAGTTAGCATAAAGTTGAGACACC 57.197 37.500 0.00 0.00 0.00 4.16
599 609 9.284594 CGAAAGTTTTATTCTTTTGACACTGAA 57.715 29.630 0.00 0.00 38.08 3.02
618 637 7.837202 TTGTCGGATAACATTATCGAAAGTT 57.163 32.000 5.72 0.00 40.30 2.66
624 643 5.630896 ACGTTTGTCGGATAACATTATCG 57.369 39.130 5.72 2.63 44.69 2.92
641 660 2.030562 CCCCAGCTGACGACGTTT 59.969 61.111 17.39 0.00 0.00 3.60
644 663 4.742201 CACCCCCAGCTGACGACG 62.742 72.222 17.39 0.00 0.00 5.12
648 667 4.284550 TTGCCACCCCCAGCTGAC 62.285 66.667 17.39 0.00 0.00 3.51
649 668 3.970410 CTTGCCACCCCCAGCTGA 61.970 66.667 17.39 0.00 0.00 4.26
653 672 4.659172 TTCGCTTGCCACCCCCAG 62.659 66.667 0.00 0.00 0.00 4.45
654 673 4.966787 GTTCGCTTGCCACCCCCA 62.967 66.667 0.00 0.00 0.00 4.96
700 721 7.624360 ACTGTCACTGTTTGATCTTACAAAA 57.376 32.000 0.00 0.00 40.62 2.44
705 726 9.997482 GTTTAAAACTGTCACTGTTTGATCTTA 57.003 29.630 13.03 0.00 36.08 2.10
752 773 8.675705 TTCTTCAGAACAACATGATAGTTTCA 57.324 30.769 0.00 0.00 39.12 2.69
757 779 9.552114 GACAAATTCTTCAGAACAACATGATAG 57.448 33.333 0.00 0.00 36.80 2.08
759 781 7.944061 TGACAAATTCTTCAGAACAACATGAT 58.056 30.769 0.00 0.00 36.80 2.45
761 783 7.327761 GGATGACAAATTCTTCAGAACAACATG 59.672 37.037 0.00 0.00 36.80 3.21
778 800 4.715534 TTAGTTGTGAGGGGATGACAAA 57.284 40.909 0.00 0.00 31.62 2.83
781 803 3.010420 GCTTTAGTTGTGAGGGGATGAC 58.990 50.000 0.00 0.00 0.00 3.06
960 2925 2.024588 CAGCTCTCGCTCTCGCTC 59.975 66.667 0.00 0.00 45.15 5.03
961 2926 4.191950 GCAGCTCTCGCTCTCGCT 62.192 66.667 0.00 0.00 45.15 4.93
962 2927 2.715864 CTAGCAGCTCTCGCTCTCGC 62.716 65.000 0.00 0.00 45.15 5.03
963 2928 1.279539 CTAGCAGCTCTCGCTCTCG 59.720 63.158 0.00 0.00 45.15 4.04
964 2929 0.817634 TCCTAGCAGCTCTCGCTCTC 60.818 60.000 0.00 0.00 45.15 3.20
965 2930 0.819259 CTCCTAGCAGCTCTCGCTCT 60.819 60.000 0.00 0.00 45.15 4.09
998 2966 0.813210 GCACTGAGTAGGAGCCATGC 60.813 60.000 0.00 0.00 0.00 4.06
1009 2977 3.295273 TGAGACGGCGCACTGAGT 61.295 61.111 10.83 0.00 0.00 3.41
1482 3456 3.858868 GAACAGCCTGCGGACGACA 62.859 63.158 0.00 0.00 0.00 4.35
1512 3486 3.044986 CCACGAAACGACGTTCTTCTTA 58.955 45.455 14.58 0.00 44.76 2.10
1702 3676 2.301346 CTCCACCCCATGCTTTATCAC 58.699 52.381 0.00 0.00 0.00 3.06
1752 3726 0.027194 CAGAGAACATGCCGATTGCG 59.973 55.000 0.00 0.00 45.60 4.85
1755 3729 3.834489 ATCTCAGAGAACATGCCGATT 57.166 42.857 3.63 0.00 0.00 3.34
1779 3753 2.430921 CGAGCCGACCGCATATCC 60.431 66.667 0.00 0.00 41.38 2.59
1783 3757 2.910479 TATCCGAGCCGACCGCAT 60.910 61.111 0.00 0.00 41.38 4.73
1789 3763 1.135199 GTCAAACACTATCCGAGCCGA 60.135 52.381 0.00 0.00 0.00 5.54
1791 3765 1.653151 GGTCAAACACTATCCGAGCC 58.347 55.000 0.00 0.00 0.00 4.70
1800 3774 2.186826 GGCAGCACGGTCAAACACT 61.187 57.895 0.00 0.00 0.00 3.55
1909 3883 1.617322 GGAACCTCTTTTGACCCCAC 58.383 55.000 0.00 0.00 0.00 4.61
1929 3903 5.294306 TGACAAGAAAGTCACAACATCAGAC 59.706 40.000 0.00 0.00 43.18 3.51
1932 3906 4.035558 GCTGACAAGAAAGTCACAACATCA 59.964 41.667 0.00 0.00 43.18 3.07
1967 3941 1.068434 TGACATCTTGTGACTGCGACA 59.932 47.619 0.00 0.00 0.00 4.35
1995 3969 0.679002 AGTAGCCATGCAGTTGCTGG 60.679 55.000 15.38 8.13 42.66 4.85
2052 4026 0.037697 TCACGACAAGCGCATTACCT 60.038 50.000 11.47 0.00 46.04 3.08
2265 4239 4.135306 CTCCTGTATTTGATGCTGCAGAT 58.865 43.478 20.43 8.20 0.00 2.90
2408 4382 3.003394 TCCCATAGCCATCAAACACTG 57.997 47.619 0.00 0.00 0.00 3.66
2517 4491 0.107508 CCACACCTGCCTCGATCATT 60.108 55.000 0.00 0.00 0.00 2.57
2574 4548 2.347490 CCTCCAACGGGGTCACAG 59.653 66.667 0.00 0.00 38.11 3.66
2827 4801 2.040412 CAGGCTTTAACCCCTTGTCTCT 59.960 50.000 0.00 0.00 0.00 3.10
2868 4842 5.300286 AGAGTAATTACATGCTGAAATGGCC 59.700 40.000 17.65 0.00 31.46 5.36
2948 4922 1.630126 ATGGTGCTGAGGGGTAGCTG 61.630 60.000 0.00 0.00 41.66 4.24
2967 4941 3.190327 CCAACAAATCCACGATACAGCAA 59.810 43.478 0.00 0.00 0.00 3.91
3012 4986 3.063588 GGCTTTCTACAAAGTCGTATGCC 59.936 47.826 0.00 0.00 41.18 4.40
3048 5022 2.181975 CCCCAGATGGCAATGAAGTTT 58.818 47.619 4.76 0.00 0.00 2.66
3057 5031 0.548031 GAAGTGATCCCCAGATGGCA 59.452 55.000 0.00 0.00 30.90 4.92
3091 5065 2.129555 AACTCCATCTTGCCCTGCGT 62.130 55.000 0.00 0.00 0.00 5.24
3096 5070 1.304381 TGCCAACTCCATCTTGCCC 60.304 57.895 0.00 0.00 0.00 5.36
3144 5118 1.550065 CGTGACCATACTGCTTCTCG 58.450 55.000 0.00 0.00 0.00 4.04
3162 5136 1.068333 AGCAAAACATTGTAGCCTGCG 60.068 47.619 0.00 0.00 33.61 5.18
3226 5200 5.128499 TCAATCTCATCTCCTTTCTCAGACC 59.872 44.000 0.00 0.00 0.00 3.85
3256 5230 2.057922 AGAACCAGCCTCTTTCCTCAA 58.942 47.619 0.00 0.00 0.00 3.02
3269 5243 4.938226 GGACTTTGATCCAAGTAGAACCAG 59.062 45.833 11.89 0.00 38.77 4.00
3270 5244 4.349636 TGGACTTTGATCCAAGTAGAACCA 59.650 41.667 11.89 11.74 46.08 3.67
3344 5318 1.750778 ACATGTGATCATTTTCGGGGC 59.249 47.619 0.00 0.00 31.15 5.80
3357 5331 1.550072 TCCAGCATCGAGAACATGTGA 59.450 47.619 0.00 0.00 0.00 3.58
3361 5335 1.590932 GCATCCAGCATCGAGAACAT 58.409 50.000 0.00 0.00 44.79 2.71
3380 5354 5.966503 GCGTCTGTACTGTAAGAAGTATCTG 59.033 44.000 0.00 0.00 35.20 2.90
3381 5355 5.646793 TGCGTCTGTACTGTAAGAAGTATCT 59.353 40.000 0.00 0.00 35.20 1.98
3389 5363 6.408858 AAATGATTGCGTCTGTACTGTAAG 57.591 37.500 0.00 0.00 42.29 2.34
3390 5364 7.385478 TGTTAAATGATTGCGTCTGTACTGTAA 59.615 33.333 0.00 0.00 0.00 2.41
3391 5365 6.869388 TGTTAAATGATTGCGTCTGTACTGTA 59.131 34.615 0.00 0.00 0.00 2.74
3392 5366 5.699001 TGTTAAATGATTGCGTCTGTACTGT 59.301 36.000 0.00 0.00 0.00 3.55
3444 5418 5.745227 TCTCCAGGTATCAACAAATCTTCC 58.255 41.667 0.00 0.00 0.00 3.46
3446 5420 7.500559 GCTAATCTCCAGGTATCAACAAATCTT 59.499 37.037 0.00 0.00 0.00 2.40
3498 5472 1.112113 GGTAGCAGGAGTTCGATCCA 58.888 55.000 7.77 0.00 42.26 3.41
3556 5531 2.634940 CCACTCAAAGACTCCAGAGGAA 59.365 50.000 0.00 0.00 32.52 3.36
3561 5536 3.969287 TCATCCACTCAAAGACTCCAG 57.031 47.619 0.00 0.00 0.00 3.86
3574 5549 2.896685 TGGGGTTTCATGTTTCATCCAC 59.103 45.455 0.00 0.00 0.00 4.02
3608 5587 2.179018 CTTTTCACCATGGCGGCG 59.821 61.111 13.04 0.51 39.03 6.46
3611 5590 0.109597 GCTCACTTTTCACCATGGCG 60.110 55.000 13.04 1.26 0.00 5.69
3624 5604 4.299547 TCGGCGCACTTGCTCACT 62.300 61.111 10.83 0.00 39.32 3.41
3682 5662 7.645058 TCTCTGATGGATGCGTATATTGATA 57.355 36.000 0.00 0.00 0.00 2.15
3727 5707 2.291153 CCATCCAGTGGTTCATGGTCTT 60.291 50.000 16.86 0.00 43.44 3.01
3748 5730 1.079819 TACGCTGCAGCTGGTTCTC 60.080 57.895 34.22 5.37 39.32 2.87
3805 5787 6.558771 TTTGATGTACACTTCATTCACAGG 57.441 37.500 0.00 0.00 31.40 4.00
3970 5969 6.294473 AGCTGGGTAATCATGTGATCTTAAG 58.706 40.000 0.00 0.00 32.75 1.85
4017 6023 7.501559 ACCTTGATCTGAGTGATTCCAAATATG 59.498 37.037 0.00 0.00 35.14 1.78
4151 6160 4.901197 TTAGTGCTTTGGTGTATCTCCA 57.099 40.909 0.00 0.00 0.00 3.86
4152 6161 5.246307 ACTTTAGTGCTTTGGTGTATCTCC 58.754 41.667 0.00 0.00 0.00 3.71
4222 6231 6.091076 ACAAGAATTATGGAATGGAGGGAA 57.909 37.500 0.00 0.00 0.00 3.97
4259 6268 9.235537 CTTGCCTTGGTTTTATTTCAAAATTTG 57.764 29.630 0.00 0.00 0.00 2.32
4270 6279 7.732222 TCCATAATTCTTGCCTTGGTTTTAT 57.268 32.000 0.00 0.00 0.00 1.40
4279 6288 3.947834 CCTTCGTTCCATAATTCTTGCCT 59.052 43.478 0.00 0.00 0.00 4.75
4281 6290 3.945285 TCCCTTCGTTCCATAATTCTTGC 59.055 43.478 0.00 0.00 0.00 4.01
4297 6306 7.184067 TCTGGAACTAAATTCTACTCCCTTC 57.816 40.000 0.00 0.00 37.48 3.46
4298 6307 7.569599 TTCTGGAACTAAATTCTACTCCCTT 57.430 36.000 0.00 0.00 37.48 3.95
4308 6317 8.385898 TGTCAACGTTATTCTGGAACTAAATT 57.614 30.769 0.00 0.00 0.00 1.82
4327 6336 8.407832 TGTGGAATTCAATGATATCATGTCAAC 58.592 33.333 18.85 13.88 36.56 3.18


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

AutoCloner maintained by Alex Coulton.