Multiple sequence alignment - TraesCS6D01G187600

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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 TraesCS6D01G187600 chr6D 100.000 4517 0 0 1 4517 254135919 254140435 0.000000e+00 8342.0
1 TraesCS6D01G187600 chr6D 86.184 152 13 1 1755 1906 293805682 293805825 1.680000e-34 158.0
2 TraesCS6D01G187600 chr6B 95.023 3657 83 26 446 4060 345627433 345623834 0.000000e+00 5653.0
3 TraesCS6D01G187600 chr6B 91.184 397 29 4 4050 4444 345603898 345603506 6.650000e-148 534.0
4 TraesCS6D01G187600 chr6B 88.327 257 24 5 63 317 277619667 277619919 2.040000e-78 303.0
5 TraesCS6D01G187600 chr6B 100.000 40 0 0 373 412 345631873 345631834 1.740000e-09 75.0
6 TraesCS6D01G187600 chr6A 95.717 3479 96 24 426 3881 340189935 340186487 0.000000e+00 5550.0
7 TraesCS6D01G187600 chr6A 93.858 521 27 3 3926 4444 340099399 340098882 0.000000e+00 780.0
8 TraesCS6D01G187600 chr6A 98.214 56 1 0 1235 1290 340189041 340188986 1.030000e-16 99.0
9 TraesCS6D01G187600 chr6A 97.500 40 0 1 368 407 340194165 340194127 2.920000e-07 67.6
10 TraesCS6D01G187600 chr7D 95.402 261 1 1 68 317 474532174 474532434 5.440000e-109 405.0
11 TraesCS6D01G187600 chr7D 88.710 186 20 1 1699 1883 197919326 197919141 4.550000e-55 226.0
12 TraesCS6D01G187600 chr7D 88.108 185 21 1 1699 1883 595597164 595596981 7.610000e-53 219.0
13 TraesCS6D01G187600 chr3D 95.076 264 2 1 65 317 553424112 553423849 5.440000e-109 405.0
14 TraesCS6D01G187600 chr3D 100.000 28 0 0 384 411 3025071 3025044 8.000000e-03 52.8
15 TraesCS6D01G187600 chr2B 91.603 262 11 5 68 318 742453293 742453554 7.190000e-93 351.0
16 TraesCS6D01G187600 chr2B 88.168 262 19 4 68 317 796674339 796674600 7.340000e-78 302.0
17 TraesCS6D01G187600 chr2D 91.700 253 19 2 67 317 30440801 30440549 2.590000e-92 350.0
18 TraesCS6D01G187600 chr2D 89.883 257 24 1 68 322 638884198 638884454 3.370000e-86 329.0
19 TraesCS6D01G187600 chr2D 88.000 250 24 2 68 317 121353344 121353587 1.590000e-74 291.0
20 TraesCS6D01G187600 chr2D 87.324 71 7 2 4326 4394 470060930 470060860 3.750000e-11 80.5
21 TraesCS6D01G187600 chr5D 91.732 254 15 2 64 317 241959997 241960244 9.300000e-92 348.0
22 TraesCS6D01G187600 chr5D 88.000 175 21 0 1709 1883 526035853 526036027 1.650000e-49 207.0
23 TraesCS6D01G187600 chr5D 100.000 28 0 0 382 409 379391314 379391341 8.000000e-03 52.8
24 TraesCS6D01G187600 chr7A 88.976 254 23 5 68 319 715441966 715441716 4.390000e-80 309.0
25 TraesCS6D01G187600 chr5B 88.327 257 23 3 67 317 309661649 309661904 7.340000e-78 302.0
26 TraesCS6D01G187600 chr5B 87.568 185 23 0 1699 1883 403648853 403648669 9.840000e-52 215.0
27 TraesCS6D01G187600 chr5B 87.209 172 21 1 1699 1869 95256328 95256499 1.280000e-45 195.0
28 TraesCS6D01G187600 chr5B 87.135 171 22 0 1699 1869 135754497 135754327 1.280000e-45 195.0
29 TraesCS6D01G187600 chr5B 95.238 42 2 0 4273 4314 520368919 520368960 2.920000e-07 67.6
30 TraesCS6D01G187600 chr5B 95.122 41 1 1 4270 4309 50646739 50646779 3.770000e-06 63.9
31 TraesCS6D01G187600 chr5B 100.000 29 0 0 4242 4270 684918533 684918505 2.000000e-03 54.7
32 TraesCS6D01G187600 chr7B 87.719 171 21 0 1699 1869 29232068 29231898 2.760000e-47 200.0
33 TraesCS6D01G187600 chr7B 100.000 29 0 0 4243 4271 723837607 723837579 2.000000e-03 54.7
34 TraesCS6D01G187600 chr4D 95.122 41 1 1 4273 4313 339233852 339233891 3.770000e-06 63.9
35 TraesCS6D01G187600 chr2A 95.000 40 2 0 4270 4309 25042473 25042512 3.770000e-06 63.9
36 TraesCS6D01G187600 chr1D 97.297 37 1 0 4273 4309 366680770 366680806 3.770000e-06 63.9
37 TraesCS6D01G187600 chr1D 95.000 40 1 1 4274 4313 483018321 483018359 1.360000e-05 62.1
38 TraesCS6D01G187600 chr3A 95.000 40 1 1 4273 4312 213258792 213258754 1.360000e-05 62.1
39 TraesCS6D01G187600 chr5A 100.000 31 0 0 381 411 694011532 694011502 1.760000e-04 58.4
40 TraesCS6D01G187600 chr3B 100.000 29 0 0 4242 4270 667714481 667714453 2.000000e-03 54.7
41 TraesCS6D01G187600 chr1B 100.000 29 0 0 4242 4270 360348821 360348849 2.000000e-03 54.7


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 TraesCS6D01G187600 chr6D 254135919 254140435 4516 False 8342.0 8342 100.0000 1 4517 1 chr6D.!!$F1 4516
1 TraesCS6D01G187600 chr6B 345623834 345627433 3599 True 5653.0 5653 95.0230 446 4060 1 chr6B.!!$R2 3614
2 TraesCS6D01G187600 chr6A 340186487 340189935 3448 True 2824.5 5550 96.9655 426 3881 2 chr6A.!!$R3 3455
3 TraesCS6D01G187600 chr6A 340098882 340099399 517 True 780.0 780 93.8580 3926 4444 1 chr6A.!!$R1 518

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
395 396 0.171903 GTGCAGCCCAATTAGTGCAG 59.828 55.000 0.00 0.0 46.18 4.41 F
1317 1334 0.326264 AGAGCGAATTGGCAGTCCTT 59.674 50.000 15.20 0.0 34.64 3.36 F
2440 2480 0.175760 TGGACATCTCTACGCTTGGC 59.824 55.000 0.00 0.0 0.00 4.52 F
2655 2705 1.138247 GCTGCTGCTAACATGCACC 59.862 57.895 8.53 0.0 38.12 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2185 1.765904 TGCTAGTGGTTCACAACTGGA 59.234 47.619 2.10 0.0 36.74 3.86 R
3041 3092 3.756434 GGTGTAAAATTGCAGCAGGAGTA 59.244 43.478 8.27 0.0 40.31 2.59 R
3388 3439 1.153489 CACTGATCCTGCCGTCCAG 60.153 63.158 0.00 0.0 41.41 3.86 R
4482 4538 0.462047 GGATGTCTGCGGTCGGAAAT 60.462 55.000 0.00 0.0 0.00 2.17 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
19 20 2.405892 GCACGCACTTGTCATTTCTT 57.594 45.000 0.00 0.00 0.00 2.52
20 21 2.731217 GCACGCACTTGTCATTTCTTT 58.269 42.857 0.00 0.00 0.00 2.52
21 22 3.884169 GCACGCACTTGTCATTTCTTTA 58.116 40.909 0.00 0.00 0.00 1.85
22 23 3.664025 GCACGCACTTGTCATTTCTTTAC 59.336 43.478 0.00 0.00 0.00 2.01
23 24 4.554723 GCACGCACTTGTCATTTCTTTACT 60.555 41.667 0.00 0.00 0.00 2.24
24 25 4.905866 CACGCACTTGTCATTTCTTTACTG 59.094 41.667 0.00 0.00 0.00 2.74
25 26 4.814234 ACGCACTTGTCATTTCTTTACTGA 59.186 37.500 0.00 0.00 0.00 3.41
26 27 5.470098 ACGCACTTGTCATTTCTTTACTGAT 59.530 36.000 0.00 0.00 0.00 2.90
27 28 6.017109 ACGCACTTGTCATTTCTTTACTGATT 60.017 34.615 0.00 0.00 0.00 2.57
28 29 6.857964 CGCACTTGTCATTTCTTTACTGATTT 59.142 34.615 0.00 0.00 0.00 2.17
29 30 8.015087 CGCACTTGTCATTTCTTTACTGATTTA 58.985 33.333 0.00 0.00 0.00 1.40
30 31 9.846248 GCACTTGTCATTTCTTTACTGATTTAT 57.154 29.630 0.00 0.00 0.00 1.40
44 45 9.609346 TTTACTGATTTATACAAAGTAGGGAGC 57.391 33.333 0.00 0.00 0.00 4.70
45 46 7.195374 ACTGATTTATACAAAGTAGGGAGCA 57.805 36.000 0.00 0.00 0.00 4.26
46 47 7.806180 ACTGATTTATACAAAGTAGGGAGCAT 58.194 34.615 0.00 0.00 0.00 3.79
47 48 8.275040 ACTGATTTATACAAAGTAGGGAGCATT 58.725 33.333 0.00 0.00 0.00 3.56
48 49 8.677148 TGATTTATACAAAGTAGGGAGCATTC 57.323 34.615 0.00 0.00 0.00 2.67
49 50 7.441157 TGATTTATACAAAGTAGGGAGCATTCG 59.559 37.037 0.00 0.00 0.00 3.34
50 51 6.474140 TTATACAAAGTAGGGAGCATTCGA 57.526 37.500 0.00 0.00 0.00 3.71
51 52 3.914426 ACAAAGTAGGGAGCATTCGAT 57.086 42.857 0.00 0.00 0.00 3.59
52 53 3.535561 ACAAAGTAGGGAGCATTCGATG 58.464 45.455 0.00 0.00 0.00 3.84
53 54 2.874701 CAAAGTAGGGAGCATTCGATGG 59.125 50.000 0.00 0.00 0.00 3.51
54 55 1.051812 AGTAGGGAGCATTCGATGGG 58.948 55.000 0.00 0.00 0.00 4.00
55 56 1.048601 GTAGGGAGCATTCGATGGGA 58.951 55.000 0.00 0.00 0.00 4.37
56 57 1.625818 GTAGGGAGCATTCGATGGGAT 59.374 52.381 0.00 0.00 0.00 3.85
57 58 0.399454 AGGGAGCATTCGATGGGATG 59.601 55.000 0.00 0.00 0.00 3.51
58 59 0.397941 GGGAGCATTCGATGGGATGA 59.602 55.000 0.00 0.00 0.00 2.92
59 60 1.610102 GGGAGCATTCGATGGGATGAG 60.610 57.143 0.00 0.00 0.00 2.90
60 61 1.345741 GGAGCATTCGATGGGATGAGA 59.654 52.381 0.00 0.00 0.00 3.27
61 62 2.224378 GGAGCATTCGATGGGATGAGAA 60.224 50.000 0.00 0.00 0.00 2.87
62 63 3.470709 GAGCATTCGATGGGATGAGAAA 58.529 45.455 0.00 0.00 0.00 2.52
63 64 3.209410 AGCATTCGATGGGATGAGAAAC 58.791 45.455 0.00 0.00 0.00 2.78
64 65 2.945008 GCATTCGATGGGATGAGAAACA 59.055 45.455 0.00 0.00 0.00 2.83
65 66 3.003068 GCATTCGATGGGATGAGAAACAG 59.997 47.826 0.00 0.00 0.00 3.16
66 67 4.445453 CATTCGATGGGATGAGAAACAGA 58.555 43.478 0.00 0.00 0.00 3.41
67 68 4.760530 TTCGATGGGATGAGAAACAGAT 57.239 40.909 0.00 0.00 0.00 2.90
68 69 5.869649 TTCGATGGGATGAGAAACAGATA 57.130 39.130 0.00 0.00 0.00 1.98
69 70 5.201713 TCGATGGGATGAGAAACAGATAC 57.798 43.478 0.00 0.00 0.00 2.24
70 71 4.895889 TCGATGGGATGAGAAACAGATACT 59.104 41.667 0.00 0.00 0.00 2.12
71 72 5.010112 TCGATGGGATGAGAAACAGATACTC 59.990 44.000 0.00 0.00 0.00 2.59
72 73 5.546526 GATGGGATGAGAAACAGATACTCC 58.453 45.833 0.00 0.00 0.00 3.85
73 74 3.711704 TGGGATGAGAAACAGATACTCCC 59.288 47.826 0.00 0.00 41.01 4.30
74 75 3.970640 GGGATGAGAAACAGATACTCCCT 59.029 47.826 0.00 0.00 38.86 4.20
75 76 4.039852 GGGATGAGAAACAGATACTCCCTC 59.960 50.000 0.00 0.00 38.86 4.30
76 77 4.039852 GGATGAGAAACAGATACTCCCTCC 59.960 50.000 0.00 0.00 0.00 4.30
77 78 3.024547 TGAGAAACAGATACTCCCTCCG 58.975 50.000 0.00 0.00 0.00 4.63
78 79 3.025262 GAGAAACAGATACTCCCTCCGT 58.975 50.000 0.00 0.00 0.00 4.69
79 80 3.442076 AGAAACAGATACTCCCTCCGTT 58.558 45.455 0.00 0.00 0.00 4.44
80 81 3.838903 AGAAACAGATACTCCCTCCGTTT 59.161 43.478 0.00 0.00 0.00 3.60
81 82 4.286291 AGAAACAGATACTCCCTCCGTTTT 59.714 41.667 0.00 0.00 0.00 2.43
82 83 4.635699 AACAGATACTCCCTCCGTTTTT 57.364 40.909 0.00 0.00 0.00 1.94
83 84 5.750352 AACAGATACTCCCTCCGTTTTTA 57.250 39.130 0.00 0.00 0.00 1.52
84 85 5.952347 ACAGATACTCCCTCCGTTTTTAT 57.048 39.130 0.00 0.00 0.00 1.40
85 86 6.309389 ACAGATACTCCCTCCGTTTTTATT 57.691 37.500 0.00 0.00 0.00 1.40
86 87 6.718294 ACAGATACTCCCTCCGTTTTTATTT 58.282 36.000 0.00 0.00 0.00 1.40
87 88 7.854337 ACAGATACTCCCTCCGTTTTTATTTA 58.146 34.615 0.00 0.00 0.00 1.40
88 89 7.767659 ACAGATACTCCCTCCGTTTTTATTTAC 59.232 37.037 0.00 0.00 0.00 2.01
89 90 7.985752 CAGATACTCCCTCCGTTTTTATTTACT 59.014 37.037 0.00 0.00 0.00 2.24
90 91 8.546322 AGATACTCCCTCCGTTTTTATTTACTT 58.454 33.333 0.00 0.00 0.00 2.24
91 92 8.728337 ATACTCCCTCCGTTTTTATTTACTTC 57.272 34.615 0.00 0.00 0.00 3.01
92 93 5.640783 ACTCCCTCCGTTTTTATTTACTTCG 59.359 40.000 0.00 0.00 0.00 3.79
93 94 4.392754 TCCCTCCGTTTTTATTTACTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
94 95 4.154556 CCCTCCGTTTTTATTTACTTCGCA 59.845 41.667 0.00 0.00 0.00 5.10
95 96 5.163693 CCCTCCGTTTTTATTTACTTCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
96 97 6.037391 CCCTCCGTTTTTATTTACTTCGCATA 59.963 38.462 0.00 0.00 0.00 3.14
97 98 7.255001 CCCTCCGTTTTTATTTACTTCGCATAT 60.255 37.037 0.00 0.00 0.00 1.78
98 99 8.126700 CCTCCGTTTTTATTTACTTCGCATATT 58.873 33.333 0.00 0.00 0.00 1.28
109 110 7.908827 TTACTTCGCATATTAACTTTGGTCA 57.091 32.000 0.00 0.00 0.00 4.02
110 111 6.811253 ACTTCGCATATTAACTTTGGTCAA 57.189 33.333 0.00 0.00 0.00 3.18
111 112 7.209471 ACTTCGCATATTAACTTTGGTCAAA 57.791 32.000 0.00 0.00 0.00 2.69
131 132 5.535043 AAAGTCAAGCTTTGCAAACTTTG 57.465 34.783 18.97 18.62 45.00 2.77
132 133 4.454728 AGTCAAGCTTTGCAAACTTTGA 57.545 36.364 21.12 21.12 0.00 2.69
133 134 4.176271 AGTCAAGCTTTGCAAACTTTGAC 58.824 39.130 32.35 32.35 0.00 3.18
134 135 3.925913 GTCAAGCTTTGCAAACTTTGACA 59.074 39.130 33.27 16.71 0.00 3.58
135 136 4.388469 GTCAAGCTTTGCAAACTTTGACAA 59.612 37.500 33.27 16.24 0.00 3.18
136 137 4.993584 TCAAGCTTTGCAAACTTTGACAAA 59.006 33.333 21.12 16.44 36.24 2.83
137 138 5.120519 TCAAGCTTTGCAAACTTTGACAAAG 59.879 36.000 26.71 26.71 46.01 2.77
211 212 6.951062 TTCATTGTTGAATGTACTTCCACA 57.049 33.333 0.00 1.71 40.09 4.17
212 213 7.523293 TTCATTGTTGAATGTACTTCCACAT 57.477 32.000 10.54 0.00 38.77 3.21
214 215 8.628630 TCATTGTTGAATGTACTTCCACATTA 57.371 30.769 10.54 2.04 46.53 1.90
215 216 9.241919 TCATTGTTGAATGTACTTCCACATTAT 57.758 29.630 10.54 3.59 46.53 1.28
283 284 9.567848 TTTACAAAGTTTGACTTCATTCAACTC 57.432 29.630 22.23 0.00 37.47 3.01
284 285 7.396540 ACAAAGTTTGACTTCATTCAACTCT 57.603 32.000 22.23 0.00 37.47 3.24
285 286 8.506168 ACAAAGTTTGACTTCATTCAACTCTA 57.494 30.769 22.23 0.00 37.47 2.43
286 287 8.956426 ACAAAGTTTGACTTCATTCAACTCTAA 58.044 29.630 22.23 0.00 37.47 2.10
287 288 9.956720 CAAAGTTTGACTTCATTCAACTCTAAT 57.043 29.630 10.19 0.00 37.47 1.73
291 292 9.495754 GTTTGACTTCATTCAACTCTAATATGC 57.504 33.333 0.00 0.00 35.18 3.14
292 293 7.468922 TGACTTCATTCAACTCTAATATGCG 57.531 36.000 0.00 0.00 0.00 4.73
293 294 6.479990 TGACTTCATTCAACTCTAATATGCGG 59.520 38.462 0.00 0.00 0.00 5.69
294 295 6.582636 ACTTCATTCAACTCTAATATGCGGA 58.417 36.000 0.00 0.00 0.00 5.54
295 296 6.703607 ACTTCATTCAACTCTAATATGCGGAG 59.296 38.462 0.00 0.00 0.00 4.63
296 297 6.161855 TCATTCAACTCTAATATGCGGAGT 57.838 37.500 0.00 0.00 41.37 3.85
297 298 7.284919 TCATTCAACTCTAATATGCGGAGTA 57.715 36.000 6.10 0.00 39.09 2.59
298 299 7.722363 TCATTCAACTCTAATATGCGGAGTAA 58.278 34.615 6.10 0.80 39.09 2.24
299 300 8.201464 TCATTCAACTCTAATATGCGGAGTAAA 58.799 33.333 6.10 5.29 39.09 2.01
300 301 8.993121 CATTCAACTCTAATATGCGGAGTAAAT 58.007 33.333 6.10 6.73 39.09 1.40
307 308 9.793245 CTCTAATATGCGGAGTAAATAAAAACG 57.207 33.333 0.00 0.00 0.00 3.60
308 309 8.767085 TCTAATATGCGGAGTAAATAAAAACGG 58.233 33.333 0.00 0.00 0.00 4.44
309 310 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
310 311 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
311 312 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
312 313 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
313 314 4.506758 CGGAGTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
314 315 4.569564 CGGAGTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
315 316 5.494724 GGAGTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
316 317 6.627953 CGGAGTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
317 318 6.536582 GGAGTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
318 319 7.250032 AGTAAATAAAAACGGAGGGAGTACT 57.750 36.000 0.00 0.00 0.00 2.73
319 320 7.683578 AGTAAATAAAAACGGAGGGAGTACTT 58.316 34.615 0.00 0.00 0.00 2.24
320 321 8.159447 AGTAAATAAAAACGGAGGGAGTACTTT 58.841 33.333 0.00 0.00 0.00 2.66
321 322 7.828508 AAATAAAAACGGAGGGAGTACTTTT 57.171 32.000 0.00 0.00 0.00 2.27
322 323 7.828508 AATAAAAACGGAGGGAGTACTTTTT 57.171 32.000 0.00 0.00 0.00 1.94
378 379 9.994432 ATTATTCTTTTTCTAATGAAGCTCGTG 57.006 29.630 0.00 0.00 32.82 4.35
379 380 5.283060 TCTTTTTCTAATGAAGCTCGTGC 57.717 39.130 0.07 0.07 40.05 5.34
380 381 4.754618 TCTTTTTCTAATGAAGCTCGTGCA 59.245 37.500 12.58 0.00 42.74 4.57
381 382 4.668576 TTTTCTAATGAAGCTCGTGCAG 57.331 40.909 12.58 0.00 42.74 4.41
389 390 3.903783 GCTCGTGCAGCCCAATTA 58.096 55.556 4.26 0.00 43.17 1.40
390 391 1.723870 GCTCGTGCAGCCCAATTAG 59.276 57.895 4.26 0.00 43.17 1.73
391 392 1.026718 GCTCGTGCAGCCCAATTAGT 61.027 55.000 4.26 0.00 43.17 2.24
392 393 0.729116 CTCGTGCAGCCCAATTAGTG 59.271 55.000 0.00 0.00 0.00 2.74
393 394 1.137404 CGTGCAGCCCAATTAGTGC 59.863 57.895 0.00 0.00 36.42 4.40
394 395 1.585267 CGTGCAGCCCAATTAGTGCA 61.585 55.000 0.00 0.00 43.50 4.57
395 396 0.171903 GTGCAGCCCAATTAGTGCAG 59.828 55.000 0.00 0.00 46.18 4.41
396 397 1.140375 GCAGCCCAATTAGTGCAGC 59.860 57.895 0.00 0.00 35.91 5.25
397 398 1.318158 GCAGCCCAATTAGTGCAGCT 61.318 55.000 0.00 0.00 36.15 4.24
398 399 0.454600 CAGCCCAATTAGTGCAGCTG 59.545 55.000 10.11 10.11 42.88 4.24
399 400 1.140375 GCCCAATTAGTGCAGCTGC 59.860 57.895 31.89 31.89 42.50 5.25
414 415 5.088141 GCAGCTGCACTATTAAGTACATG 57.912 43.478 33.36 0.00 41.59 3.21
415 416 4.811024 GCAGCTGCACTATTAAGTACATGA 59.189 41.667 33.36 0.00 41.59 3.07
416 417 5.294306 GCAGCTGCACTATTAAGTACATGAA 59.706 40.000 33.36 0.00 41.59 2.57
417 418 6.183360 GCAGCTGCACTATTAAGTACATGAAA 60.183 38.462 33.36 0.00 41.59 2.69
418 419 7.626240 GCAGCTGCACTATTAAGTACATGAAAA 60.626 37.037 33.36 0.00 41.59 2.29
419 420 8.400947 CAGCTGCACTATTAAGTACATGAAAAT 58.599 33.333 0.00 0.00 33.48 1.82
420 421 9.613428 AGCTGCACTATTAAGTACATGAAAATA 57.387 29.630 0.00 0.00 33.48 1.40
421 422 9.869844 GCTGCACTATTAAGTACATGAAAATAG 57.130 33.333 0.00 7.54 36.60 1.73
435 436 5.957771 TGAAAATAGATAGCCTGGTGACT 57.042 39.130 0.00 0.00 0.00 3.41
543 544 4.347865 GAGTCGCTTCTCCTCCCT 57.652 61.111 0.00 0.00 0.00 4.20
773 789 0.971959 ACCTCTCTGCTCCTGCTCTG 60.972 60.000 0.00 0.00 40.48 3.35
833 849 2.627945 TCTCGCGAGCAATTTGGTATT 58.372 42.857 30.97 0.00 0.00 1.89
940 956 4.035102 GTGGCTGGGAGTGGGACC 62.035 72.222 0.00 0.00 0.00 4.46
1317 1334 0.326264 AGAGCGAATTGGCAGTCCTT 59.674 50.000 15.20 0.00 34.64 3.36
1515 1542 0.950555 TGCGTGAGATGTTGCCAGTC 60.951 55.000 0.00 0.00 0.00 3.51
1976 2016 7.891183 AAAAAGCTGTATGTACTGACAGTAG 57.109 36.000 15.69 6.03 44.10 2.57
2031 2071 9.566432 AAGTTGAACTTTCTATTGAATCTGTCT 57.434 29.630 4.45 0.00 34.11 3.41
2068 2108 4.640789 AGAATTAGCTCTGTAGTGGACG 57.359 45.455 0.00 0.00 0.00 4.79
2086 2126 4.699735 TGGACGCATGTGTTCTTAATCAAT 59.300 37.500 18.36 0.00 0.00 2.57
2364 2404 2.563179 ACAAGTAGTGGGAGTGCTACTG 59.437 50.000 11.01 0.00 44.84 2.74
2391 2431 7.986085 ATGTAATATGCCCTATGAAGTGTTC 57.014 36.000 0.00 0.00 0.00 3.18
2440 2480 0.175760 TGGACATCTCTACGCTTGGC 59.824 55.000 0.00 0.00 0.00 4.52
2655 2705 1.138247 GCTGCTGCTAACATGCACC 59.862 57.895 8.53 0.00 38.12 5.01
3407 3458 2.512515 GGACGGCAGGATCAGTGC 60.513 66.667 10.16 10.16 40.42 4.40
3617 3668 6.897966 TCAATGGTAAACTGACTCTAGAGGAT 59.102 38.462 23.50 3.46 0.00 3.24
3662 3714 7.893124 ACTGGAAATAGAGGAATAGTCGTAA 57.107 36.000 0.00 0.00 0.00 3.18
3663 3715 8.480133 ACTGGAAATAGAGGAATAGTCGTAAT 57.520 34.615 0.00 0.00 0.00 1.89
3664 3716 8.361139 ACTGGAAATAGAGGAATAGTCGTAATG 58.639 37.037 0.00 0.00 0.00 1.90
3883 3938 2.033801 CGACCTTGAATTGGATCATGGC 59.966 50.000 8.61 2.85 44.45 4.40
3912 3967 5.348724 AGCACAAATATAGTGACACGTCTTG 59.651 40.000 11.29 4.09 39.30 3.02
3918 3973 6.946229 ATATAGTGACACGTCTTGAACAAC 57.054 37.500 0.00 0.00 0.00 3.32
4060 4115 5.563475 CGAATGATTAGAATGGGCAACATCC 60.563 44.000 0.00 0.00 39.40 3.51
4062 4117 5.645056 TGATTAGAATGGGCAACATCCTA 57.355 39.130 0.00 0.00 39.40 2.94
4100 4155 2.415491 GGCTTCATGTCTTTTAACGGCC 60.415 50.000 0.00 0.00 0.00 6.13
4101 4156 2.727916 GCTTCATGTCTTTTAACGGCCG 60.728 50.000 26.86 26.86 0.00 6.13
4140 4195 2.609459 GGACTGCCAATATGTCTTGTCG 59.391 50.000 0.00 0.00 0.00 4.35
4148 4203 5.163764 GCCAATATGTCTTGTCGAAACATGA 60.164 40.000 0.00 2.55 37.26 3.07
4155 4210 1.698165 TGTCGAAACATGACGAGAGC 58.302 50.000 0.00 0.00 39.22 4.09
4174 4229 3.568538 AGCGAATCAATGAACTTTGCAC 58.431 40.909 10.42 0.00 32.73 4.57
4196 4251 6.090898 GCACCCTATATTAAGCGTACATCTTG 59.909 42.308 7.43 0.00 0.00 3.02
4253 4308 0.708802 TCTTTACCTCCCTCCGTCCT 59.291 55.000 0.00 0.00 0.00 3.85
4262 4317 3.494573 CCTCCCTCCGTCCTAAAATAAGC 60.495 52.174 0.00 0.00 0.00 3.09
4263 4318 2.101917 TCCCTCCGTCCTAAAATAAGCG 59.898 50.000 0.00 0.00 0.00 4.68
4295 4350 9.832445 ACTCTAAGTTTGAGACACTTATTTTGA 57.168 29.630 19.28 0.00 36.39 2.69
4332 4387 0.618981 AACACGGATCCCTTCTTCCC 59.381 55.000 6.06 0.00 0.00 3.97
4338 4394 1.490910 GGATCCCTTCTTCCCGTCAAT 59.509 52.381 0.00 0.00 0.00 2.57
4349 4405 6.494893 TCTTCCCGTCAATGTCATTAAAAG 57.505 37.500 0.00 0.00 0.00 2.27
4353 4409 5.180492 TCCCGTCAATGTCATTAAAAGTGTC 59.820 40.000 0.00 0.00 0.00 3.67
4354 4410 5.390613 CCGTCAATGTCATTAAAAGTGTCC 58.609 41.667 0.00 0.00 0.00 4.02
4398 4454 4.067896 ACACTGCCATCTGTAAGTCAAAG 58.932 43.478 0.00 0.00 33.76 2.77
4401 4457 5.239306 CACTGCCATCTGTAAGTCAAAGAAA 59.761 40.000 0.00 0.00 33.76 2.52
4402 4458 5.827797 ACTGCCATCTGTAAGTCAAAGAAAA 59.172 36.000 0.00 0.00 33.76 2.29
4403 4459 6.321181 ACTGCCATCTGTAAGTCAAAGAAAAA 59.679 34.615 0.00 0.00 33.76 1.94
4444 4500 5.711036 ACCTACTGTTATGTCTCTTCGTCTT 59.289 40.000 0.00 0.00 0.00 3.01
4445 4501 6.883217 ACCTACTGTTATGTCTCTTCGTCTTA 59.117 38.462 0.00 0.00 0.00 2.10
4446 4502 7.392673 ACCTACTGTTATGTCTCTTCGTCTTAA 59.607 37.037 0.00 0.00 0.00 1.85
4447 4503 8.407064 CCTACTGTTATGTCTCTTCGTCTTAAT 58.593 37.037 0.00 0.00 0.00 1.40
4448 4504 9.440784 CTACTGTTATGTCTCTTCGTCTTAATC 57.559 37.037 0.00 0.00 0.00 1.75
4449 4505 8.057536 ACTGTTATGTCTCTTCGTCTTAATCT 57.942 34.615 0.00 0.00 0.00 2.40
4450 4506 9.175312 ACTGTTATGTCTCTTCGTCTTAATCTA 57.825 33.333 0.00 0.00 0.00 1.98
4452 4508 9.784680 TGTTATGTCTCTTCGTCTTAATCTAAC 57.215 33.333 0.00 0.00 0.00 2.34
4453 4509 8.945930 GTTATGTCTCTTCGTCTTAATCTAACG 58.054 37.037 0.00 0.00 37.74 3.18
4454 4510 5.330295 TGTCTCTTCGTCTTAATCTAACGC 58.670 41.667 0.00 0.00 36.40 4.84
4455 4511 4.433945 GTCTCTTCGTCTTAATCTAACGCG 59.566 45.833 3.53 3.53 36.40 6.01
4456 4512 3.103738 TCTTCGTCTTAATCTAACGCGC 58.896 45.455 5.73 0.00 36.40 6.86
4457 4513 1.459756 TCGTCTTAATCTAACGCGCG 58.540 50.000 30.96 30.96 36.40 6.86
4458 4514 0.112266 CGTCTTAATCTAACGCGCGC 60.112 55.000 32.58 23.91 0.00 6.86
4479 4535 4.271816 CGTCCTAGATGGCGCGCT 62.272 66.667 32.29 12.85 35.26 5.92
4480 4536 2.355244 GTCCTAGATGGCGCGCTC 60.355 66.667 32.29 21.73 35.26 5.03
4481 4537 3.966104 TCCTAGATGGCGCGCTCG 61.966 66.667 32.29 9.52 39.07 5.03
4482 4538 3.966104 CCTAGATGGCGCGCTCGA 61.966 66.667 32.29 16.68 38.10 4.04
4483 4539 2.256764 CTAGATGGCGCGCTCGAT 59.743 61.111 32.29 19.98 38.10 3.59
4484 4540 1.372251 CTAGATGGCGCGCTCGATT 60.372 57.895 32.29 15.22 38.10 3.34
4485 4541 0.941463 CTAGATGGCGCGCTCGATTT 60.941 55.000 32.29 17.14 38.10 2.17
4486 4542 0.939577 TAGATGGCGCGCTCGATTTC 60.940 55.000 32.29 17.35 38.10 2.17
4487 4543 3.228688 GATGGCGCGCTCGATTTCC 62.229 63.158 32.29 12.15 38.10 3.13
4490 4546 4.267013 GCGCGCTCGATTTCCGAC 62.267 66.667 26.67 0.00 43.23 4.79
4491 4547 3.617538 CGCGCTCGATTTCCGACC 61.618 66.667 5.56 0.00 43.23 4.79
4492 4548 3.617538 GCGCTCGATTTCCGACCG 61.618 66.667 0.00 0.00 45.95 4.79
4493 4549 3.617538 CGCTCGATTTCCGACCGC 61.618 66.667 0.00 0.00 43.23 5.68
4494 4550 2.508439 GCTCGATTTCCGACCGCA 60.508 61.111 0.00 0.00 43.23 5.69
4495 4551 2.517450 GCTCGATTTCCGACCGCAG 61.517 63.158 0.00 0.00 43.23 5.18
4496 4552 1.138883 CTCGATTTCCGACCGCAGA 59.861 57.895 0.00 0.00 43.23 4.26
4497 4553 1.140407 CTCGATTTCCGACCGCAGAC 61.140 60.000 0.00 0.00 43.23 3.51
4498 4554 1.445410 CGATTTCCGACCGCAGACA 60.445 57.895 0.00 0.00 41.76 3.41
4499 4555 0.806102 CGATTTCCGACCGCAGACAT 60.806 55.000 0.00 0.00 41.76 3.06
4500 4556 0.931005 GATTTCCGACCGCAGACATC 59.069 55.000 0.00 0.00 0.00 3.06
4501 4557 0.462047 ATTTCCGACCGCAGACATCC 60.462 55.000 0.00 0.00 0.00 3.51
4502 4558 2.515996 TTTCCGACCGCAGACATCCC 62.516 60.000 0.00 0.00 0.00 3.85
4503 4559 4.873129 CCGACCGCAGACATCCCG 62.873 72.222 0.00 0.00 0.00 5.14
4504 4560 4.129737 CGACCGCAGACATCCCGT 62.130 66.667 0.00 0.00 0.00 5.28
4505 4561 2.509336 GACCGCAGACATCCCGTG 60.509 66.667 0.00 0.00 0.00 4.94
4506 4562 3.296709 GACCGCAGACATCCCGTGT 62.297 63.158 0.00 0.00 45.83 4.49
4515 4571 1.129058 ACATCCCGTGTCCTATTCCC 58.871 55.000 0.00 0.00 35.77 3.97
4516 4572 1.344087 ACATCCCGTGTCCTATTCCCT 60.344 52.381 0.00 0.00 35.77 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.905866 CAGTAAAGAAATGACAAGTGCGTG 59.094 41.667 0.00 0.00 0.00 5.34
4 5 9.846248 ATAAATCAGTAAAGAAATGACAAGTGC 57.154 29.630 0.00 0.00 0.00 4.40
18 19 9.609346 GCTCCCTACTTTGTATAAATCAGTAAA 57.391 33.333 0.00 0.00 0.00 2.01
19 20 8.764558 TGCTCCCTACTTTGTATAAATCAGTAA 58.235 33.333 0.00 0.00 0.00 2.24
20 21 8.313944 TGCTCCCTACTTTGTATAAATCAGTA 57.686 34.615 0.00 0.00 0.00 2.74
21 22 7.195374 TGCTCCCTACTTTGTATAAATCAGT 57.805 36.000 0.00 0.00 0.00 3.41
22 23 8.682936 AATGCTCCCTACTTTGTATAAATCAG 57.317 34.615 0.00 0.00 0.00 2.90
23 24 7.441157 CGAATGCTCCCTACTTTGTATAAATCA 59.559 37.037 0.00 0.00 0.00 2.57
24 25 7.656137 TCGAATGCTCCCTACTTTGTATAAATC 59.344 37.037 0.00 0.00 0.00 2.17
25 26 7.506114 TCGAATGCTCCCTACTTTGTATAAAT 58.494 34.615 0.00 0.00 0.00 1.40
26 27 6.880484 TCGAATGCTCCCTACTTTGTATAAA 58.120 36.000 0.00 0.00 0.00 1.40
27 28 6.474140 TCGAATGCTCCCTACTTTGTATAA 57.526 37.500 0.00 0.00 0.00 0.98
28 29 6.455647 CATCGAATGCTCCCTACTTTGTATA 58.544 40.000 0.00 0.00 0.00 1.47
29 30 5.300752 CATCGAATGCTCCCTACTTTGTAT 58.699 41.667 0.00 0.00 0.00 2.29
30 31 4.442893 CCATCGAATGCTCCCTACTTTGTA 60.443 45.833 0.00 0.00 0.00 2.41
31 32 3.535561 CATCGAATGCTCCCTACTTTGT 58.464 45.455 0.00 0.00 0.00 2.83
32 33 2.874701 CCATCGAATGCTCCCTACTTTG 59.125 50.000 0.00 0.00 0.00 2.77
33 34 2.158755 CCCATCGAATGCTCCCTACTTT 60.159 50.000 0.00 0.00 0.00 2.66
34 35 1.417890 CCCATCGAATGCTCCCTACTT 59.582 52.381 0.00 0.00 0.00 2.24
35 36 1.051812 CCCATCGAATGCTCCCTACT 58.948 55.000 0.00 0.00 0.00 2.57
36 37 1.048601 TCCCATCGAATGCTCCCTAC 58.951 55.000 0.00 0.00 0.00 3.18
37 38 1.625315 CATCCCATCGAATGCTCCCTA 59.375 52.381 0.00 0.00 0.00 3.53
38 39 0.399454 CATCCCATCGAATGCTCCCT 59.601 55.000 0.00 0.00 0.00 4.20
39 40 0.397941 TCATCCCATCGAATGCTCCC 59.602 55.000 0.00 0.00 0.00 4.30
40 41 1.345741 TCTCATCCCATCGAATGCTCC 59.654 52.381 0.00 0.00 0.00 4.70
41 42 2.827800 TCTCATCCCATCGAATGCTC 57.172 50.000 0.00 0.00 0.00 4.26
42 43 3.209410 GTTTCTCATCCCATCGAATGCT 58.791 45.455 0.00 0.00 0.00 3.79
43 44 2.945008 TGTTTCTCATCCCATCGAATGC 59.055 45.455 0.00 0.00 0.00 3.56
44 45 4.445453 TCTGTTTCTCATCCCATCGAATG 58.555 43.478 0.00 0.00 0.00 2.67
45 46 4.760530 TCTGTTTCTCATCCCATCGAAT 57.239 40.909 0.00 0.00 0.00 3.34
46 47 4.760530 ATCTGTTTCTCATCCCATCGAA 57.239 40.909 0.00 0.00 0.00 3.71
47 48 4.895889 AGTATCTGTTTCTCATCCCATCGA 59.104 41.667 0.00 0.00 0.00 3.59
48 49 5.207110 AGTATCTGTTTCTCATCCCATCG 57.793 43.478 0.00 0.00 0.00 3.84
49 50 5.512232 GGGAGTATCTGTTTCTCATCCCATC 60.512 48.000 2.06 0.00 43.86 3.51
50 51 4.349342 GGGAGTATCTGTTTCTCATCCCAT 59.651 45.833 2.06 0.00 43.86 4.00
51 52 3.711704 GGGAGTATCTGTTTCTCATCCCA 59.288 47.826 2.06 0.00 43.86 4.37
52 53 3.970640 AGGGAGTATCTGTTTCTCATCCC 59.029 47.826 0.00 0.00 44.60 3.85
53 54 4.039852 GGAGGGAGTATCTGTTTCTCATCC 59.960 50.000 0.00 0.00 33.73 3.51
54 55 4.261825 CGGAGGGAGTATCTGTTTCTCATC 60.262 50.000 0.00 0.00 33.73 2.92
55 56 3.639094 CGGAGGGAGTATCTGTTTCTCAT 59.361 47.826 0.00 0.00 33.73 2.90
56 57 3.024547 CGGAGGGAGTATCTGTTTCTCA 58.975 50.000 0.00 0.00 33.73 3.27
57 58 3.025262 ACGGAGGGAGTATCTGTTTCTC 58.975 50.000 0.00 0.00 32.24 2.87
58 59 3.103080 ACGGAGGGAGTATCTGTTTCT 57.897 47.619 0.00 0.00 32.24 2.52
59 60 3.889520 AACGGAGGGAGTATCTGTTTC 57.110 47.619 0.00 0.00 42.28 2.78
61 62 4.635699 AAAAACGGAGGGAGTATCTGTT 57.364 40.909 0.00 0.00 45.88 3.16
62 63 5.952347 ATAAAAACGGAGGGAGTATCTGT 57.048 39.130 0.00 0.00 37.90 3.41
63 64 7.985752 AGTAAATAAAAACGGAGGGAGTATCTG 59.014 37.037 0.00 0.00 33.73 2.90
64 65 8.087303 AGTAAATAAAAACGGAGGGAGTATCT 57.913 34.615 0.00 0.00 33.73 1.98
65 66 8.728337 AAGTAAATAAAAACGGAGGGAGTATC 57.272 34.615 0.00 0.00 0.00 2.24
66 67 7.493645 CGAAGTAAATAAAAACGGAGGGAGTAT 59.506 37.037 0.00 0.00 0.00 2.12
67 68 6.813152 CGAAGTAAATAAAAACGGAGGGAGTA 59.187 38.462 0.00 0.00 0.00 2.59
68 69 5.640783 CGAAGTAAATAAAAACGGAGGGAGT 59.359 40.000 0.00 0.00 0.00 3.85
69 70 5.446875 GCGAAGTAAATAAAAACGGAGGGAG 60.447 44.000 0.00 0.00 0.00 4.30
70 71 4.392754 GCGAAGTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
71 72 4.154556 TGCGAAGTAAATAAAAACGGAGGG 59.845 41.667 0.00 0.00 0.00 4.30
72 73 5.285798 TGCGAAGTAAATAAAAACGGAGG 57.714 39.130 0.00 0.00 0.00 4.30
83 84 8.952278 TGACCAAAGTTAATATGCGAAGTAAAT 58.048 29.630 0.00 0.00 0.00 1.40
84 85 8.325421 TGACCAAAGTTAATATGCGAAGTAAA 57.675 30.769 0.00 0.00 0.00 2.01
85 86 7.908827 TGACCAAAGTTAATATGCGAAGTAA 57.091 32.000 0.00 0.00 0.00 2.24
86 87 7.908827 TTGACCAAAGTTAATATGCGAAGTA 57.091 32.000 0.00 0.00 0.00 2.24
87 88 6.811253 TTGACCAAAGTTAATATGCGAAGT 57.189 33.333 0.00 0.00 0.00 3.01
88 89 7.725610 CTTTGACCAAAGTTAATATGCGAAG 57.274 36.000 12.91 0.00 42.02 3.79
188 189 6.951062 TGTGGAAGTACATTCAACAATGAA 57.049 33.333 10.88 0.00 46.75 2.57
257 258 9.567848 GAGTTGAATGAAGTCAAACTTTGTAAA 57.432 29.630 1.44 0.00 38.80 2.01
258 259 8.956426 AGAGTTGAATGAAGTCAAACTTTGTAA 58.044 29.630 1.44 0.00 38.80 2.41
259 260 8.506168 AGAGTTGAATGAAGTCAAACTTTGTA 57.494 30.769 1.44 0.00 38.80 2.41
260 261 7.396540 AGAGTTGAATGAAGTCAAACTTTGT 57.603 32.000 1.44 0.00 38.80 2.83
261 262 9.956720 ATTAGAGTTGAATGAAGTCAAACTTTG 57.043 29.630 0.00 0.00 38.80 2.77
265 266 9.495754 GCATATTAGAGTTGAATGAAGTCAAAC 57.504 33.333 0.00 0.00 39.18 2.93
266 267 8.390354 CGCATATTAGAGTTGAATGAAGTCAAA 58.610 33.333 0.00 0.00 39.18 2.69
267 268 7.011389 CCGCATATTAGAGTTGAATGAAGTCAA 59.989 37.037 0.00 0.00 36.57 3.18
268 269 6.479990 CCGCATATTAGAGTTGAATGAAGTCA 59.520 38.462 0.00 0.00 36.57 3.41
269 270 6.701841 TCCGCATATTAGAGTTGAATGAAGTC 59.298 38.462 0.00 0.00 34.56 3.01
270 271 6.582636 TCCGCATATTAGAGTTGAATGAAGT 58.417 36.000 0.00 0.00 0.00 3.01
271 272 6.703607 ACTCCGCATATTAGAGTTGAATGAAG 59.296 38.462 0.00 0.00 37.60 3.02
272 273 6.582636 ACTCCGCATATTAGAGTTGAATGAA 58.417 36.000 0.00 0.00 37.60 2.57
273 274 6.161855 ACTCCGCATATTAGAGTTGAATGA 57.838 37.500 0.00 0.00 37.60 2.57
274 275 7.946655 TTACTCCGCATATTAGAGTTGAATG 57.053 36.000 4.78 0.00 41.09 2.67
281 282 9.793245 CGTTTTTATTTACTCCGCATATTAGAG 57.207 33.333 0.00 0.00 0.00 2.43
282 283 8.767085 CCGTTTTTATTTACTCCGCATATTAGA 58.233 33.333 0.00 0.00 0.00 2.10
283 284 8.767085 TCCGTTTTTATTTACTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
284 285 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
285 286 7.255001 CCTCCGTTTTTATTTACTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
286 287 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
287 288 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
288 289 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
289 290 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
290 291 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
291 292 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
292 293 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
293 294 7.326454 AGTACTCCCTCCGTTTTTATTTACTC 58.674 38.462 0.00 0.00 0.00 2.59
294 295 7.250032 AGTACTCCCTCCGTTTTTATTTACT 57.750 36.000 0.00 0.00 0.00 2.24
295 296 7.912056 AAGTACTCCCTCCGTTTTTATTTAC 57.088 36.000 0.00 0.00 0.00 2.01
296 297 8.922931 AAAAGTACTCCCTCCGTTTTTATTTA 57.077 30.769 0.00 0.00 0.00 1.40
297 298 7.828508 AAAAGTACTCCCTCCGTTTTTATTT 57.171 32.000 0.00 0.00 0.00 1.40
298 299 7.828508 AAAAAGTACTCCCTCCGTTTTTATT 57.171 32.000 0.00 0.00 0.00 1.40
352 353 9.994432 CACGAGCTTCATTAGAAAAAGAATAAT 57.006 29.630 0.00 0.00 32.35 1.28
353 354 7.962918 GCACGAGCTTCATTAGAAAAAGAATAA 59.037 33.333 0.00 0.00 37.91 1.40
354 355 7.119116 TGCACGAGCTTCATTAGAAAAAGAATA 59.881 33.333 6.36 0.00 42.74 1.75
355 356 6.072508 TGCACGAGCTTCATTAGAAAAAGAAT 60.073 34.615 6.36 0.00 42.74 2.40
356 357 5.238432 TGCACGAGCTTCATTAGAAAAAGAA 59.762 36.000 6.36 0.00 42.74 2.52
357 358 4.754618 TGCACGAGCTTCATTAGAAAAAGA 59.245 37.500 6.36 0.00 42.74 2.52
358 359 5.034554 TGCACGAGCTTCATTAGAAAAAG 57.965 39.130 6.36 0.00 42.74 2.27
359 360 4.613622 GCTGCACGAGCTTCATTAGAAAAA 60.614 41.667 6.36 0.00 45.21 1.94
360 361 3.120199 GCTGCACGAGCTTCATTAGAAAA 60.120 43.478 6.36 0.00 45.21 2.29
361 362 2.416547 GCTGCACGAGCTTCATTAGAAA 59.583 45.455 6.36 0.00 45.21 2.52
362 363 2.002586 GCTGCACGAGCTTCATTAGAA 58.997 47.619 6.36 0.00 45.21 2.10
363 364 1.645034 GCTGCACGAGCTTCATTAGA 58.355 50.000 6.36 0.00 45.21 2.10
373 374 0.729116 CACTAATTGGGCTGCACGAG 59.271 55.000 0.50 0.00 0.00 4.18
374 375 1.305219 GCACTAATTGGGCTGCACGA 61.305 55.000 0.50 0.00 43.01 4.35
375 376 1.137404 GCACTAATTGGGCTGCACG 59.863 57.895 0.50 0.00 43.01 5.34
404 405 9.778741 CCAGGCTATCTATTTTCATGTACTTAA 57.221 33.333 0.00 0.00 0.00 1.85
405 406 8.934697 ACCAGGCTATCTATTTTCATGTACTTA 58.065 33.333 0.00 0.00 0.00 2.24
406 407 7.716998 CACCAGGCTATCTATTTTCATGTACTT 59.283 37.037 0.00 0.00 0.00 2.24
407 408 7.071196 TCACCAGGCTATCTATTTTCATGTACT 59.929 37.037 0.00 0.00 0.00 2.73
408 409 7.171678 GTCACCAGGCTATCTATTTTCATGTAC 59.828 40.741 0.00 0.00 0.00 2.90
409 410 7.071196 AGTCACCAGGCTATCTATTTTCATGTA 59.929 37.037 0.00 0.00 0.00 2.29
410 411 6.058183 GTCACCAGGCTATCTATTTTCATGT 58.942 40.000 0.00 0.00 0.00 3.21
411 412 6.204301 CAGTCACCAGGCTATCTATTTTCATG 59.796 42.308 0.00 0.00 0.00 3.07
412 413 6.294473 CAGTCACCAGGCTATCTATTTTCAT 58.706 40.000 0.00 0.00 0.00 2.57
413 414 5.396772 CCAGTCACCAGGCTATCTATTTTCA 60.397 44.000 0.00 0.00 0.00 2.69
414 415 5.059833 CCAGTCACCAGGCTATCTATTTTC 58.940 45.833 0.00 0.00 0.00 2.29
415 416 4.475016 ACCAGTCACCAGGCTATCTATTTT 59.525 41.667 0.00 0.00 0.00 1.82
416 417 4.040755 ACCAGTCACCAGGCTATCTATTT 58.959 43.478 0.00 0.00 0.00 1.40
417 418 3.389329 CACCAGTCACCAGGCTATCTATT 59.611 47.826 0.00 0.00 0.00 1.73
418 419 2.968574 CACCAGTCACCAGGCTATCTAT 59.031 50.000 0.00 0.00 0.00 1.98
419 420 2.024369 TCACCAGTCACCAGGCTATCTA 60.024 50.000 0.00 0.00 0.00 1.98
420 421 1.198713 CACCAGTCACCAGGCTATCT 58.801 55.000 0.00 0.00 0.00 1.98
421 422 1.134670 GTCACCAGTCACCAGGCTATC 60.135 57.143 0.00 0.00 0.00 2.08
422 423 0.905357 GTCACCAGTCACCAGGCTAT 59.095 55.000 0.00 0.00 0.00 2.97
423 424 0.178932 AGTCACCAGTCACCAGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
424 425 1.460305 AGTCACCAGTCACCAGGCT 60.460 57.895 0.00 0.00 0.00 4.58
435 436 6.206634 CAGCCTATTTTTCTTTACAGTCACCA 59.793 38.462 0.00 0.00 0.00 4.17
773 789 0.743345 CAGCCTAACCTAACACCGCC 60.743 60.000 0.00 0.00 0.00 6.13
833 849 0.824109 CTCTGCTGATCCAACCGGTA 59.176 55.000 8.00 0.00 0.00 4.02
862 878 3.499157 TGGATTCCCGACTAACAAAAACG 59.501 43.478 0.00 0.00 34.29 3.60
940 956 1.196200 CCAACGAAAAACAAGCACCG 58.804 50.000 0.00 0.00 0.00 4.94
1024 1040 1.216990 GGTCTCCCATCCCATGAACT 58.783 55.000 0.00 0.00 0.00 3.01
1154 1171 2.572104 GTGGATCTGGGGAAGTACAAGT 59.428 50.000 0.00 0.00 0.00 3.16
1200 1217 4.127907 GGCCTGGTATAGTTTAAGCTCAC 58.872 47.826 0.00 0.00 0.00 3.51
1317 1334 4.710865 TCAAATTATCAGCCCTCATTTGCA 59.289 37.500 0.00 0.00 35.62 4.08
1515 1542 2.957491 AGCTCTCCTTGAAGATCACG 57.043 50.000 0.00 0.00 0.00 4.35
1956 1996 7.054751 TGATACTACTGTCAGTACATACAGCT 58.945 38.462 21.17 13.69 45.65 4.24
2068 2108 4.266976 GCAGCATTGATTAAGAACACATGC 59.733 41.667 0.00 0.00 0.00 4.06
2145 2185 1.765904 TGCTAGTGGTTCACAACTGGA 59.234 47.619 2.10 0.00 36.74 3.86
2232 2272 5.065731 GTGCCAACTGAAGGATCTCTATTTG 59.934 44.000 0.00 0.00 0.00 2.32
2364 2404 9.672673 AACACTTCATAGGGCATATTACATATC 57.327 33.333 0.00 0.00 0.00 1.63
2391 2431 7.672983 TTGTTTCTAAAGAAGCTAGTCCATG 57.327 36.000 7.87 0.00 36.42 3.66
2440 2480 6.684979 TCATGCATTTTTATTACGCTACGTTG 59.315 34.615 0.00 0.00 41.54 4.10
2655 2705 5.401550 TGTTGGTTAGAAATAGACCGTACG 58.598 41.667 8.69 8.69 36.22 3.67
3041 3092 3.756434 GGTGTAAAATTGCAGCAGGAGTA 59.244 43.478 8.27 0.00 40.31 2.59
3276 3327 3.986006 TCGGTTGGAGCGACGCTT 61.986 61.111 25.30 7.72 43.66 4.68
3388 3439 1.153489 CACTGATCCTGCCGTCCAG 60.153 63.158 0.00 0.00 41.41 3.86
3407 3458 4.100084 TCTGCTGTGATGGGCCGG 62.100 66.667 0.00 0.00 0.00 6.13
3617 3668 6.940298 CCAGTACAAGATTAGACCTTTTTCCA 59.060 38.462 0.00 0.00 0.00 3.53
3744 3796 9.845214 ACAATTAATATGGATAGGAGGAGTACT 57.155 33.333 0.00 0.00 0.00 2.73
3746 3798 9.837681 TGACAATTAATATGGATAGGAGGAGTA 57.162 33.333 0.00 0.00 0.00 2.59
3747 3799 8.598041 GTGACAATTAATATGGATAGGAGGAGT 58.402 37.037 0.00 0.00 0.00 3.85
3748 3800 8.820831 AGTGACAATTAATATGGATAGGAGGAG 58.179 37.037 0.00 0.00 0.00 3.69
3749 3801 8.597167 CAGTGACAATTAATATGGATAGGAGGA 58.403 37.037 0.00 0.00 0.00 3.71
3750 3802 8.597167 TCAGTGACAATTAATATGGATAGGAGG 58.403 37.037 0.00 0.00 0.00 4.30
3883 3938 6.257849 ACGTGTCACTATATTTGTGCTTATGG 59.742 38.462 0.65 0.00 35.58 2.74
3912 3967 7.753132 TCCATATATTTTTCGCACTTGTTGTTC 59.247 33.333 0.00 0.00 0.00 3.18
3918 3973 4.905866 CGCTCCATATATTTTTCGCACTTG 59.094 41.667 0.00 0.00 0.00 3.16
4048 4103 3.201930 TGTGTGTATAGGATGTTGCCCAT 59.798 43.478 0.00 0.00 36.13 4.00
4060 4115 3.066900 AGCCGCTTCTAGTGTGTGTATAG 59.933 47.826 0.00 0.00 0.00 1.31
4062 4117 1.825474 AGCCGCTTCTAGTGTGTGTAT 59.175 47.619 0.00 0.00 0.00 2.29
4100 4155 3.735746 GTCCAAAGGAAAAACAAGCATCG 59.264 43.478 0.00 0.00 31.38 3.84
4101 4156 4.746611 CAGTCCAAAGGAAAAACAAGCATC 59.253 41.667 0.00 0.00 31.38 3.91
4140 4195 2.923655 TGATTCGCTCTCGTCATGTTTC 59.076 45.455 0.00 0.00 36.96 2.78
4148 4203 3.238108 AGTTCATTGATTCGCTCTCGT 57.762 42.857 0.00 0.00 36.96 4.18
4155 4210 3.057315 AGGGTGCAAAGTTCATTGATTCG 60.057 43.478 0.00 0.00 31.84 3.34
4174 4229 7.603651 AGACAAGATGTACGCTTAATATAGGG 58.396 38.462 1.07 0.00 0.00 3.53
4247 4302 3.777478 TGAGACGCTTATTTTAGGACGG 58.223 45.455 0.00 0.00 0.00 4.79
4253 4308 9.485206 AAACTTAGAGTTGAGACGCTTATTTTA 57.515 29.630 0.00 0.00 38.66 1.52
4295 4350 4.320788 CGTGTTTTACTACTCCTTCCGTCT 60.321 45.833 0.00 0.00 0.00 4.18
4332 4387 6.241207 AGGACACTTTTAATGACATTGACG 57.759 37.500 11.05 0.00 0.00 4.35
4338 4394 9.179909 TCAACTTTTAGGACACTTTTAATGACA 57.820 29.630 0.00 0.00 0.00 3.58
4371 4427 3.326588 ACTTACAGATGGCAGTGTGGTAA 59.673 43.478 13.95 7.43 0.00 2.85
4376 4432 3.769739 TTGACTTACAGATGGCAGTGT 57.230 42.857 9.90 9.90 0.00 3.55
4402 4458 9.490083 ACAGTAGGTATAGATTAGGACAGTTTT 57.510 33.333 0.00 0.00 0.00 2.43
4403 4459 9.490083 AACAGTAGGTATAGATTAGGACAGTTT 57.510 33.333 0.00 0.00 0.00 2.66
4431 4487 5.330295 GCGTTAGATTAAGACGAAGAGACA 58.670 41.667 0.00 0.00 38.99 3.41
4462 4518 4.271816 AGCGCGCCATCTAGGACG 62.272 66.667 30.33 0.00 41.22 4.79
4463 4519 2.355244 GAGCGCGCCATCTAGGAC 60.355 66.667 30.33 4.35 41.22 3.85
4464 4520 3.966104 CGAGCGCGCCATCTAGGA 61.966 66.667 30.33 0.00 41.22 2.94
4465 4521 2.755542 AATCGAGCGCGCCATCTAGG 62.756 60.000 30.33 9.34 41.84 3.02
4466 4522 0.941463 AAATCGAGCGCGCCATCTAG 60.941 55.000 30.33 9.91 37.46 2.43
4467 4523 0.939577 GAAATCGAGCGCGCCATCTA 60.940 55.000 30.33 12.58 37.46 1.98
4468 4524 2.202932 AAATCGAGCGCGCCATCT 60.203 55.556 30.33 9.44 37.46 2.90
4469 4525 2.246687 GAAATCGAGCGCGCCATC 59.753 61.111 30.33 19.30 37.46 3.51
4470 4526 3.272334 GGAAATCGAGCGCGCCAT 61.272 61.111 30.33 15.09 37.46 4.40
4479 4535 1.153901 GTCTGCGGTCGGAAATCGA 60.154 57.895 0.00 0.00 46.77 3.59
4480 4536 0.806102 ATGTCTGCGGTCGGAAATCG 60.806 55.000 0.00 0.00 40.90 3.34
4481 4537 0.931005 GATGTCTGCGGTCGGAAATC 59.069 55.000 0.00 0.00 35.72 2.17
4482 4538 0.462047 GGATGTCTGCGGTCGGAAAT 60.462 55.000 0.00 0.00 0.00 2.17
4483 4539 1.079405 GGATGTCTGCGGTCGGAAA 60.079 57.895 0.00 0.00 0.00 3.13
4484 4540 2.577059 GGATGTCTGCGGTCGGAA 59.423 61.111 0.00 0.00 0.00 4.30
4485 4541 3.458163 GGGATGTCTGCGGTCGGA 61.458 66.667 0.00 0.00 0.00 4.55
4486 4542 4.873129 CGGGATGTCTGCGGTCGG 62.873 72.222 0.00 0.00 0.00 4.79
4487 4543 4.129737 ACGGGATGTCTGCGGTCG 62.130 66.667 0.00 0.00 0.00 4.79
4488 4544 2.509336 CACGGGATGTCTGCGGTC 60.509 66.667 0.00 0.00 0.00 4.79
4489 4545 3.311110 ACACGGGATGTCTGCGGT 61.311 61.111 0.00 0.00 36.54 5.68
4497 4553 1.424638 AGGGAATAGGACACGGGATG 58.575 55.000 0.00 0.00 0.00 3.51
4498 4554 3.970426 AGGGAATAGGACACGGGAT 57.030 52.632 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.