Multiple sequence alignment - TraesCS4D01G141000

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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 TraesCS4D01G141000 chr4D 100.000 4150 0 0 1 4150 125075226 125079375 0.000000e+00 7664.0
1 TraesCS4D01G141000 chr4D 93.186 587 27 1 3564 4150 21698367 21698940 0.000000e+00 850.0
2 TraesCS4D01G141000 chr4A 94.043 2283 89 20 1052 3305 445078023 445075759 0.000000e+00 3419.0
3 TraesCS4D01G141000 chr4A 92.875 407 20 6 616 1015 445078589 445078185 2.150000e-162 582.0
4 TraesCS4D01G141000 chr4B 91.185 1974 105 36 1384 3305 189014365 189016321 0.000000e+00 2617.0
5 TraesCS4D01G141000 chr4B 89.737 838 67 12 507 1329 189013239 189014072 0.000000e+00 1053.0
6 TraesCS4D01G141000 chr4B 81.857 474 65 13 11 482 189012793 189013247 3.030000e-101 379.0
7 TraesCS4D01G141000 chr4B 92.199 141 7 3 3427 3563 189016318 189016458 3.270000e-46 196.0
8 TraesCS4D01G141000 chr2D 96.036 555 21 1 3597 4150 641188275 641187721 0.000000e+00 902.0
9 TraesCS4D01G141000 chr1D 92.687 588 43 0 3563 4150 458149224 458149811 0.000000e+00 848.0
10 TraesCS4D01G141000 chr7A 92.530 589 43 1 3563 4150 521918837 521919425 0.000000e+00 843.0
11 TraesCS4D01G141000 chr7A 91.443 596 42 4 3564 4150 541332800 541333395 0.000000e+00 809.0
12 TraesCS4D01G141000 chr6A 90.803 598 47 6 3560 4149 60087696 60088293 0.000000e+00 793.0
13 TraesCS4D01G141000 chr1B 91.084 572 51 0 3579 4150 53862841 53863412 0.000000e+00 774.0
14 TraesCS4D01G141000 chr5B 93.361 241 16 0 3910 4150 116661708 116661948 1.420000e-94 357.0
15 TraesCS4D01G141000 chr6D 82.162 370 57 4 3564 3925 6765031 6765399 4.030000e-80 309.0
16 TraesCS4D01G141000 chr6D 95.402 174 8 0 3977 4150 464115789 464115962 1.140000e-70 278.0
17 TraesCS4D01G141000 chr6D 93.750 144 8 1 3301 3444 160470645 160470787 9.040000e-52 215.0
18 TraesCS4D01G141000 chr6D 96.183 131 5 0 3301 3431 237348850 237348720 9.040000e-52 215.0
19 TraesCS4D01G141000 chr3D 92.357 157 8 4 3287 3441 612269703 612269549 1.940000e-53 220.0
20 TraesCS4D01G141000 chr3D 96.183 131 5 0 3299 3429 261157000 261156870 9.040000e-52 215.0
21 TraesCS4D01G141000 chr7D 96.923 130 4 0 3302 3431 598598595 598598466 6.990000e-53 219.0
22 TraesCS4D01G141000 chr7D 96.212 132 5 0 3301 3432 266214253 266214384 2.510000e-52 217.0
23 TraesCS4D01G141000 chr5A 95.556 135 5 1 3299 3432 354537537 354537671 9.040000e-52 215.0
24 TraesCS4D01G141000 chr2B 95.522 134 6 0 3295 3428 598960843 598960976 9.040000e-52 215.0
25 TraesCS4D01G141000 chr2B 100.000 31 0 0 3533 3563 105379847 105379817 1.610000e-04 58.4
26 TraesCS4D01G141000 chr3B 94.891 137 6 1 3295 3431 236361941 236362076 3.250000e-51 213.0


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 TraesCS4D01G141000 chr4D 125075226 125079375 4149 False 7664.00 7664 100.0000 1 4150 1 chr4D.!!$F2 4149
1 TraesCS4D01G141000 chr4D 21698367 21698940 573 False 850.00 850 93.1860 3564 4150 1 chr4D.!!$F1 586
2 TraesCS4D01G141000 chr4A 445075759 445078589 2830 True 2000.50 3419 93.4590 616 3305 2 chr4A.!!$R1 2689
3 TraesCS4D01G141000 chr4B 189012793 189016458 3665 False 1061.25 2617 88.7445 11 3563 4 chr4B.!!$F1 3552
4 TraesCS4D01G141000 chr2D 641187721 641188275 554 True 902.00 902 96.0360 3597 4150 1 chr2D.!!$R1 553
5 TraesCS4D01G141000 chr1D 458149224 458149811 587 False 848.00 848 92.6870 3563 4150 1 chr1D.!!$F1 587
6 TraesCS4D01G141000 chr7A 521918837 521919425 588 False 843.00 843 92.5300 3563 4150 1 chr7A.!!$F1 587
7 TraesCS4D01G141000 chr7A 541332800 541333395 595 False 809.00 809 91.4430 3564 4150 1 chr7A.!!$F2 586
8 TraesCS4D01G141000 chr6A 60087696 60088293 597 False 793.00 793 90.8030 3560 4149 1 chr6A.!!$F1 589
9 TraesCS4D01G141000 chr1B 53862841 53863412 571 False 774.00 774 91.0840 3579 4150 1 chr1B.!!$F1 571

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
824 832 0.169009 GCCTTGCTGACGAATCAACC 59.831 55.0 0.00 0.0 33.30 3.77 F
1118 1254 0.037590 CGGAGGGACCAACCAATTCA 59.962 55.0 0.00 0.0 41.20 2.57 F
1352 1496 0.178831 ACCTGTGGGGGATCTCCTTT 60.179 55.0 12.53 0.0 40.03 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 2059 0.334676 CCATAAAACCCAGGGGAGCA 59.665 55.000 11.37 0.0 38.96 4.26 R
2999 3454 1.915141 CCTTGACAAGCTGGGTTCAT 58.085 50.000 9.85 0.0 0.00 2.57 R
3196 3658 1.864711 CGGAGTGGCATTTATGGTACG 59.135 52.381 0.00 0.0 0.00 3.67 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
53 55 6.428295 TGTTTTAAAAAGAAGAGAGGGACCA 58.572 36.000 1.31 0.00 0.00 4.02
54 56 7.066781 TGTTTTAAAAAGAAGAGAGGGACCAT 58.933 34.615 1.31 0.00 0.00 3.55
58 60 9.822727 TTTAAAAAGAAGAGAGGGACCATAATT 57.177 29.630 0.00 0.00 0.00 1.40
68 70 6.125029 AGAGGGACCATAATTGAAAGTGATG 58.875 40.000 0.00 0.00 0.00 3.07
83 85 0.895100 TGATGCCTGCAAACACCCTC 60.895 55.000 0.00 0.00 0.00 4.30
105 107 3.065371 CGACATCCAAGGCTTTGAATACC 59.935 47.826 10.61 0.00 36.36 2.73
107 109 2.871096 TCCAAGGCTTTGAATACCGT 57.129 45.000 10.61 0.00 36.36 4.83
108 110 2.432444 TCCAAGGCTTTGAATACCGTG 58.568 47.619 10.61 0.00 36.36 4.94
110 112 3.016736 CCAAGGCTTTGAATACCGTGAT 58.983 45.455 10.61 0.00 35.27 3.06
112 114 4.273480 CCAAGGCTTTGAATACCGTGATAG 59.727 45.833 10.61 0.00 35.27 2.08
114 116 2.548480 GGCTTTGAATACCGTGATAGCC 59.452 50.000 0.00 0.00 39.99 3.93
115 117 2.221055 GCTTTGAATACCGTGATAGCCG 59.779 50.000 0.00 0.00 0.00 5.52
120 122 1.170919 ATACCGTGATAGCCGCTCGT 61.171 55.000 0.00 0.00 0.00 4.18
152 154 4.456911 ACGAGATGTAGTAACCGTTGAAGA 59.543 41.667 0.00 0.00 0.00 2.87
155 157 6.183359 CGAGATGTAGTAACCGTTGAAGAAAC 60.183 42.308 0.00 0.00 35.25 2.78
156 158 6.518493 AGATGTAGTAACCGTTGAAGAAACA 58.482 36.000 0.00 0.00 38.84 2.83
157 159 6.645415 AGATGTAGTAACCGTTGAAGAAACAG 59.355 38.462 0.00 0.00 38.84 3.16
161 163 2.413310 ACCGTTGAAGAAACAGTGGT 57.587 45.000 0.00 0.00 38.84 4.16
162 164 2.718563 ACCGTTGAAGAAACAGTGGTT 58.281 42.857 0.00 0.00 38.84 3.67
166 168 3.020984 GTTGAAGAAACAGTGGTTGGGA 58.979 45.455 0.00 0.00 38.75 4.37
168 170 3.702792 TGAAGAAACAGTGGTTGGGAAA 58.297 40.909 0.00 0.00 37.30 3.13
171 173 3.909732 AGAAACAGTGGTTGGGAAATCA 58.090 40.909 0.00 0.00 37.30 2.57
186 188 2.496899 AATCACCCCAAGCAGTGTAG 57.503 50.000 0.00 0.00 35.45 2.74
187 189 0.620556 ATCACCCCAAGCAGTGTAGG 59.379 55.000 0.00 0.00 35.45 3.18
188 190 0.766674 TCACCCCAAGCAGTGTAGGT 60.767 55.000 0.00 0.00 35.45 3.08
197 199 2.862541 AGCAGTGTAGGTTTGCAATCA 58.137 42.857 0.00 0.00 40.22 2.57
198 200 3.424703 AGCAGTGTAGGTTTGCAATCAT 58.575 40.909 0.00 0.00 40.22 2.45
200 202 4.082571 AGCAGTGTAGGTTTGCAATCATTC 60.083 41.667 0.00 0.00 40.22 2.67
201 203 4.321156 GCAGTGTAGGTTTGCAATCATTCA 60.321 41.667 0.00 0.00 37.75 2.57
202 204 5.156355 CAGTGTAGGTTTGCAATCATTCAC 58.844 41.667 18.43 18.43 0.00 3.18
203 205 5.048504 CAGTGTAGGTTTGCAATCATTCACT 60.049 40.000 21.32 21.32 33.62 3.41
204 206 6.149308 CAGTGTAGGTTTGCAATCATTCACTA 59.851 38.462 24.40 9.20 32.42 2.74
205 207 6.149474 AGTGTAGGTTTGCAATCATTCACTAC 59.851 38.462 23.94 17.29 32.00 2.73
206 208 6.000840 TGTAGGTTTGCAATCATTCACTACA 58.999 36.000 14.44 14.44 36.79 2.74
207 209 6.488344 TGTAGGTTTGCAATCATTCACTACAA 59.512 34.615 15.38 5.67 36.37 2.41
208 210 6.403866 AGGTTTGCAATCATTCACTACAAA 57.596 33.333 0.00 0.00 0.00 2.83
209 211 6.996509 AGGTTTGCAATCATTCACTACAAAT 58.003 32.000 0.00 0.00 0.00 2.32
210 212 7.092716 AGGTTTGCAATCATTCACTACAAATC 58.907 34.615 0.00 0.00 0.00 2.17
211 213 6.311200 GGTTTGCAATCATTCACTACAAATCC 59.689 38.462 0.00 0.00 0.00 3.01
212 214 6.587206 TTGCAATCATTCACTACAAATCCA 57.413 33.333 0.00 0.00 0.00 3.41
213 215 6.778834 TGCAATCATTCACTACAAATCCAT 57.221 33.333 0.00 0.00 0.00 3.41
214 216 7.878547 TGCAATCATTCACTACAAATCCATA 57.121 32.000 0.00 0.00 0.00 2.74
233 235 6.202331 TCCATAAGGGATAGAGAAACTGACA 58.798 40.000 0.00 0.00 42.15 3.58
238 240 6.150396 AGGGATAGAGAAACTGACATTACG 57.850 41.667 0.00 0.00 0.00 3.18
239 241 5.069251 AGGGATAGAGAAACTGACATTACGG 59.931 44.000 0.00 0.00 0.00 4.02
242 244 2.301870 AGAGAAACTGACATTACGGCCA 59.698 45.455 2.24 0.00 0.00 5.36
254 256 6.587990 TGACATTACGGCCAAACAAATTAATG 59.412 34.615 2.24 4.94 33.56 1.90
275 277 3.560068 TGAAAAGAAGAGGTTGAAGTCGC 59.440 43.478 0.00 0.00 0.00 5.19
276 278 3.477210 AAAGAAGAGGTTGAAGTCGCT 57.523 42.857 0.00 0.00 0.00 4.93
291 293 2.687935 AGTCGCTGTGTCAAAAACCAAT 59.312 40.909 0.00 0.00 0.00 3.16
296 298 3.245990 GCTGTGTCAAAAACCAATCAAGC 59.754 43.478 0.00 0.00 0.00 4.01
297 299 4.431809 CTGTGTCAAAAACCAATCAAGCA 58.568 39.130 0.00 0.00 0.00 3.91
305 307 2.683211 ACCAATCAAGCAACTTCCCT 57.317 45.000 0.00 0.00 0.00 4.20
320 322 2.922740 TCCCTAGTTGACACACCAAC 57.077 50.000 0.00 0.00 44.92 3.77
332 334 6.850752 TGACACACCAACTATCAAGATCTA 57.149 37.500 0.00 0.00 0.00 1.98
335 337 8.154203 TGACACACCAACTATCAAGATCTAAAA 58.846 33.333 0.00 0.00 0.00 1.52
339 341 7.128331 CACCAACTATCAAGATCTAAAATGCG 58.872 38.462 0.00 0.00 0.00 4.73
346 348 9.299963 CTATCAAGATCTAAAATGCGGATCTAG 57.700 37.037 0.00 0.00 43.40 2.43
353 355 4.932789 TGCGGATCTAGCAACACC 57.067 55.556 12.66 0.00 42.18 4.16
356 358 1.136305 TGCGGATCTAGCAACACCTAC 59.864 52.381 12.66 0.00 42.18 3.18
360 362 2.365941 GGATCTAGCAACACCTACCCTC 59.634 54.545 0.00 0.00 0.00 4.30
362 364 3.116096 TCTAGCAACACCTACCCTCAT 57.884 47.619 0.00 0.00 0.00 2.90
364 366 4.215908 TCTAGCAACACCTACCCTCATAG 58.784 47.826 0.00 0.00 0.00 2.23
376 378 1.668419 CCTCATAGGTTCTTTGCCGG 58.332 55.000 0.00 0.00 0.00 6.13
378 380 0.742990 TCATAGGTTCTTTGCCGGCG 60.743 55.000 23.90 7.87 0.00 6.46
386 388 3.240606 CTTTGCCGGCGCCATATCG 62.241 63.158 28.98 11.99 0.00 2.92
390 392 3.027170 GCCGGCGCCATATCGAATG 62.027 63.158 28.98 6.19 0.00 2.67
406 408 2.790468 CGAATGTCGTCGAGGTAAGGAC 60.790 54.545 4.85 0.00 43.86 3.85
408 410 1.608055 TGTCGTCGAGGTAAGGACAA 58.392 50.000 4.85 0.00 38.26 3.18
409 411 1.267806 TGTCGTCGAGGTAAGGACAAC 59.732 52.381 4.85 0.00 38.26 3.32
412 414 0.971386 GTCGAGGTAAGGACAACCCA 59.029 55.000 0.00 0.00 37.77 4.51
413 415 1.067071 GTCGAGGTAAGGACAACCCAG 60.067 57.143 0.00 0.00 37.77 4.45
417 419 0.391263 GGTAAGGACAACCCAGAGCG 60.391 60.000 0.00 0.00 37.41 5.03
419 421 1.207329 GTAAGGACAACCCAGAGCGAT 59.793 52.381 0.00 0.00 37.41 4.58
420 422 1.568504 AAGGACAACCCAGAGCGATA 58.431 50.000 0.00 0.00 37.41 2.92
422 424 2.119495 AGGACAACCCAGAGCGATATT 58.881 47.619 0.00 0.00 37.41 1.28
423 425 3.305720 AGGACAACCCAGAGCGATATTA 58.694 45.455 0.00 0.00 37.41 0.98
424 426 3.069729 AGGACAACCCAGAGCGATATTAC 59.930 47.826 0.00 0.00 37.41 1.89
425 427 3.391049 GACAACCCAGAGCGATATTACC 58.609 50.000 0.00 0.00 0.00 2.85
454 456 3.938963 CGTTATTGTTGCCACTACCTCAT 59.061 43.478 0.00 0.00 0.00 2.90
458 460 3.500448 TGTTGCCACTACCTCATCAAA 57.500 42.857 0.00 0.00 0.00 2.69
482 484 5.884792 AGCCATGAGAGAACCAAAATCTAAG 59.115 40.000 0.00 0.00 0.00 2.18
483 485 5.067023 GCCATGAGAGAACCAAAATCTAAGG 59.933 44.000 0.00 0.00 0.00 2.69
484 486 5.591877 CCATGAGAGAACCAAAATCTAAGGG 59.408 44.000 0.00 0.00 0.00 3.95
485 487 6.418101 CATGAGAGAACCAAAATCTAAGGGA 58.582 40.000 0.00 0.00 0.00 4.20
486 488 6.448369 TGAGAGAACCAAAATCTAAGGGAA 57.552 37.500 0.00 0.00 0.00 3.97
487 489 6.476378 TGAGAGAACCAAAATCTAAGGGAAG 58.524 40.000 0.00 0.00 0.00 3.46
488 490 5.257262 AGAGAACCAAAATCTAAGGGAAGC 58.743 41.667 0.00 0.00 0.00 3.86
489 491 4.998051 AGAACCAAAATCTAAGGGAAGCA 58.002 39.130 0.00 0.00 0.00 3.91
490 492 5.393866 AGAACCAAAATCTAAGGGAAGCAA 58.606 37.500 0.00 0.00 0.00 3.91
491 493 5.243954 AGAACCAAAATCTAAGGGAAGCAAC 59.756 40.000 0.00 0.00 0.00 4.17
492 494 3.506067 ACCAAAATCTAAGGGAAGCAACG 59.494 43.478 0.00 0.00 0.00 4.10
493 495 3.756434 CCAAAATCTAAGGGAAGCAACGA 59.244 43.478 0.00 0.00 0.00 3.85
494 496 4.379499 CCAAAATCTAAGGGAAGCAACGAC 60.379 45.833 0.00 0.00 0.00 4.34
495 497 3.695830 AATCTAAGGGAAGCAACGACA 57.304 42.857 0.00 0.00 0.00 4.35
496 498 3.914426 ATCTAAGGGAAGCAACGACAT 57.086 42.857 0.00 0.00 0.00 3.06
497 499 5.353394 AATCTAAGGGAAGCAACGACATA 57.647 39.130 0.00 0.00 0.00 2.29
498 500 4.119442 TCTAAGGGAAGCAACGACATAC 57.881 45.455 0.00 0.00 0.00 2.39
499 501 3.767673 TCTAAGGGAAGCAACGACATACT 59.232 43.478 0.00 0.00 0.00 2.12
500 502 3.418684 AAGGGAAGCAACGACATACTT 57.581 42.857 0.00 0.00 0.00 2.24
501 503 2.699954 AGGGAAGCAACGACATACTTG 58.300 47.619 0.00 0.00 0.00 3.16
502 504 2.301870 AGGGAAGCAACGACATACTTGA 59.698 45.455 0.00 0.00 0.00 3.02
503 505 3.071479 GGGAAGCAACGACATACTTGAA 58.929 45.455 0.00 0.00 0.00 2.69
504 506 3.125316 GGGAAGCAACGACATACTTGAAG 59.875 47.826 0.00 0.00 0.00 3.02
505 507 3.746492 GGAAGCAACGACATACTTGAAGT 59.254 43.478 2.37 2.37 0.00 3.01
506 508 4.927425 GGAAGCAACGACATACTTGAAGTA 59.073 41.667 7.60 7.60 34.82 2.24
507 509 5.407387 GGAAGCAACGACATACTTGAAGTAA 59.593 40.000 9.35 0.00 33.89 2.24
508 510 6.073440 GGAAGCAACGACATACTTGAAGTAAA 60.073 38.462 9.35 0.00 33.89 2.01
509 511 6.854496 AGCAACGACATACTTGAAGTAAAA 57.146 33.333 9.35 0.00 33.89 1.52
510 512 7.435068 AGCAACGACATACTTGAAGTAAAAT 57.565 32.000 9.35 0.00 33.89 1.82
511 513 7.871853 AGCAACGACATACTTGAAGTAAAATT 58.128 30.769 9.35 0.00 33.89 1.82
512 514 8.995220 AGCAACGACATACTTGAAGTAAAATTA 58.005 29.630 9.35 0.00 33.89 1.40
513 515 9.601971 GCAACGACATACTTGAAGTAAAATTAA 57.398 29.630 9.35 0.00 33.89 1.40
524 526 9.810545 CTTGAAGTAAAATTAACAAAAGGGACA 57.189 29.630 0.00 0.00 0.00 4.02
527 529 9.758651 GAAGTAAAATTAACAAAAGGGACATGT 57.241 29.630 0.00 0.00 0.00 3.21
559 561 1.113517 GGCCGCCTATGAGGTCAGTA 61.114 60.000 0.71 0.00 37.80 2.74
560 562 0.315568 GCCGCCTATGAGGTCAGTAG 59.684 60.000 0.00 0.00 37.80 2.57
561 563 0.962489 CCGCCTATGAGGTCAGTAGG 59.038 60.000 9.44 9.44 37.80 3.18
572 574 2.650322 AGGTCAGTAGGTGGAAGAGAGA 59.350 50.000 0.00 0.00 0.00 3.10
576 578 3.511934 TCAGTAGGTGGAAGAGAGAAAGC 59.488 47.826 0.00 0.00 0.00 3.51
577 579 2.494073 AGTAGGTGGAAGAGAGAAAGCG 59.506 50.000 0.00 0.00 0.00 4.68
580 582 1.673329 GGTGGAAGAGAGAAAGCGGAC 60.673 57.143 0.00 0.00 0.00 4.79
583 585 0.458716 GAAGAGAGAAAGCGGACCGG 60.459 60.000 17.22 0.00 0.00 5.28
611 613 1.002773 GGCGAAGGAAACCTTAGGTGA 59.997 52.381 3.99 0.00 44.82 4.02
628 630 3.141272 AGGTGACAATTAGGGTTTGGGAA 59.859 43.478 0.00 0.00 0.00 3.97
631 633 3.096852 GACAATTAGGGTTTGGGAAGGG 58.903 50.000 0.00 0.00 0.00 3.95
634 639 0.407918 TTAGGGTTTGGGAAGGGCAG 59.592 55.000 0.00 0.00 0.00 4.85
642 647 1.301293 GGGAAGGGCAGTGAAGGAG 59.699 63.158 0.00 0.00 0.00 3.69
644 649 1.743252 GAAGGGCAGTGAAGGAGCG 60.743 63.158 0.00 0.00 0.00 5.03
646 651 2.738213 AAGGGCAGTGAAGGAGCGTG 62.738 60.000 0.00 0.00 0.00 5.34
650 655 1.374758 CAGTGAAGGAGCGTGGACC 60.375 63.158 0.00 0.00 0.00 4.46
692 698 9.341899 GCAGTGGAGTAAAATATTTTTACAGTG 57.658 33.333 19.74 19.74 37.35 3.66
720 726 1.134560 CGGTAACCTGTCTAGCTGACC 59.865 57.143 11.99 0.00 44.75 4.02
770 778 0.250124 ATCTCAAACCGCGTGGACAA 60.250 50.000 24.59 2.94 39.21 3.18
771 779 1.155424 TCTCAAACCGCGTGGACAAC 61.155 55.000 24.59 0.00 39.21 3.32
824 832 0.169009 GCCTTGCTGACGAATCAACC 59.831 55.000 0.00 0.00 33.30 3.77
832 840 1.142060 TGACGAATCAACCAACCCACT 59.858 47.619 0.00 0.00 0.00 4.00
908 916 4.147322 CACCATCCGACGCGCAAC 62.147 66.667 5.73 0.00 0.00 4.17
912 923 4.063967 ATCCGACGCGCAACAGGA 62.064 61.111 5.73 10.88 35.24 3.86
962 973 0.679002 CACAGTCCAGCCCAATCCAG 60.679 60.000 0.00 0.00 0.00 3.86
1042 1053 1.827399 GAAGACCCCAGCTGGTTCGA 61.827 60.000 30.63 0.00 39.24 3.71
1043 1054 1.201429 AAGACCCCAGCTGGTTCGAT 61.201 55.000 30.63 16.93 39.24 3.59
1044 1055 1.153349 GACCCCAGCTGGTTCGATC 60.153 63.158 30.63 15.99 39.24 3.69
1045 1056 1.613630 ACCCCAGCTGGTTCGATCT 60.614 57.895 30.63 2.29 33.91 2.75
1046 1057 1.144936 CCCCAGCTGGTTCGATCTC 59.855 63.158 30.63 0.00 0.00 2.75
1047 1058 1.333636 CCCCAGCTGGTTCGATCTCT 61.334 60.000 30.63 0.00 0.00 3.10
1048 1059 0.103937 CCCAGCTGGTTCGATCTCTC 59.896 60.000 30.63 0.00 0.00 3.20
1049 1060 0.103937 CCAGCTGGTTCGATCTCTCC 59.896 60.000 25.53 0.00 0.00 3.71
1050 1061 0.103937 CAGCTGGTTCGATCTCTCCC 59.896 60.000 5.57 0.00 0.00 4.30
1067 1203 0.624500 CCCCCTCCTCCTGGATTTCA 60.625 60.000 0.00 0.00 42.29 2.69
1073 1209 3.556633 CCTCCTCCTGGATTTCATGATCG 60.557 52.174 0.00 0.00 42.29 3.69
1083 1219 7.279981 CCTGGATTTCATGATCGTACTTGTTTA 59.720 37.037 0.00 0.00 0.00 2.01
1095 1231 2.762745 ACTTGTTTACCTGTGCTACCG 58.237 47.619 0.00 0.00 0.00 4.02
1118 1254 0.037590 CGGAGGGACCAACCAATTCA 59.962 55.000 0.00 0.00 41.20 2.57
1124 1260 0.958822 GACCAACCAATTCAACGCCT 59.041 50.000 0.00 0.00 0.00 5.52
1136 1272 3.974871 TCAACGCCTTTTTACCTTGTC 57.025 42.857 0.00 0.00 0.00 3.18
1143 1279 3.473625 CCTTTTTACCTTGTCGTGGACT 58.526 45.455 0.00 0.00 33.15 3.85
1170 1308 4.356442 CCCGCCCGTGCCTTTTTG 62.356 66.667 0.00 0.00 0.00 2.44
1186 1324 2.488204 TTTGGTCGGCTTGATCATCA 57.512 45.000 0.00 0.00 37.61 3.07
1191 1329 3.191162 TGGTCGGCTTGATCATCAAAAAG 59.809 43.478 0.75 0.00 35.73 2.27
1229 1369 3.344515 GTTAATCTCGCCCAGGTTCTTT 58.655 45.455 0.00 0.00 0.00 2.52
1302 1445 7.617041 AGTATCTTTATTGACTTGGTTGAGC 57.383 36.000 0.00 0.00 0.00 4.26
1348 1492 1.132500 CCTAACCTGTGGGGGATCTC 58.868 60.000 0.00 0.00 40.03 2.75
1352 1496 0.178831 ACCTGTGGGGGATCTCCTTT 60.179 55.000 12.53 0.00 40.03 3.11
1452 1843 2.288961 CAAGCAATGCAAGGGACATC 57.711 50.000 8.35 0.00 0.00 3.06
1531 1922 7.769272 TTTGCTGAAGAAACCAAATAACTTG 57.231 32.000 0.00 0.00 34.52 3.16
1595 1992 6.994421 ATTTACTTTGGTGTTGATTTCCCT 57.006 33.333 0.00 0.00 0.00 4.20
1638 2059 2.422127 CACAAGACAACGTTGGAGGTTT 59.578 45.455 30.34 14.39 0.00 3.27
1835 2257 2.338577 AGCAAGGACAGATGGTATGC 57.661 50.000 0.00 0.00 35.21 3.14
1837 2259 1.743772 GCAAGGACAGATGGTATGCGT 60.744 52.381 0.00 0.00 0.00 5.24
2046 2471 6.458751 GCATTGAAGATCATACGAACACCAAT 60.459 38.462 0.00 0.00 0.00 3.16
2101 2553 9.303116 TGGTAAGTTAATTGAAATATGGTGTGT 57.697 29.630 0.00 0.00 0.00 3.72
2114 2566 1.134521 TGGTGTGTCATTATCCTCGGC 60.135 52.381 0.00 0.00 0.00 5.54
2480 2933 3.265791 CCAGTTGCAAGGTGTATCTCTC 58.734 50.000 0.00 0.00 0.00 3.20
2486 2939 3.318275 TGCAAGGTGTATCTCTCCGTATC 59.682 47.826 0.00 0.00 35.13 2.24
2570 3023 3.144657 ACAATGTGATGAGGTCAAGCA 57.855 42.857 0.00 0.00 38.90 3.91
2768 3223 2.922335 GCGGGACTTTGAGATGCAAAAC 60.922 50.000 0.00 0.00 45.26 2.43
2942 3397 8.331022 CCTGTATTTTCGTGTTGATTCTATCAG 58.669 37.037 0.00 0.00 40.94 2.90
3150 3605 6.373005 TTGATAACCTGAGGAAGATGTGAA 57.627 37.500 4.99 0.00 0.00 3.18
3196 3658 4.434857 GCGCAATTCTCTGTCTGTAGTTTC 60.435 45.833 0.30 0.00 0.00 2.78
3259 3723 1.687660 TGCAGTGTGTTTGGCATTGAT 59.312 42.857 0.00 0.00 0.00 2.57
3310 3775 8.697507 ATTTCAATAAATCACATACTCCCTCC 57.302 34.615 0.00 0.00 28.88 4.30
3311 3776 5.853936 TCAATAAATCACATACTCCCTCCG 58.146 41.667 0.00 0.00 0.00 4.63
3312 3777 5.365605 TCAATAAATCACATACTCCCTCCGT 59.634 40.000 0.00 0.00 0.00 4.69
3313 3778 3.821421 AAATCACATACTCCCTCCGTC 57.179 47.619 0.00 0.00 0.00 4.79
3314 3779 1.705873 ATCACATACTCCCTCCGTCC 58.294 55.000 0.00 0.00 0.00 4.79
3315 3780 0.629596 TCACATACTCCCTCCGTCCT 59.370 55.000 0.00 0.00 0.00 3.85
3316 3781 1.848388 TCACATACTCCCTCCGTCCTA 59.152 52.381 0.00 0.00 0.00 2.94
3317 3782 2.242965 TCACATACTCCCTCCGTCCTAA 59.757 50.000 0.00 0.00 0.00 2.69
3318 3783 3.028850 CACATACTCCCTCCGTCCTAAA 58.971 50.000 0.00 0.00 0.00 1.85
3319 3784 3.449737 CACATACTCCCTCCGTCCTAAAA 59.550 47.826 0.00 0.00 0.00 1.52
3320 3785 4.101119 CACATACTCCCTCCGTCCTAAAAT 59.899 45.833 0.00 0.00 0.00 1.82
3321 3786 4.720273 ACATACTCCCTCCGTCCTAAAATT 59.280 41.667 0.00 0.00 0.00 1.82
3322 3787 3.908643 ACTCCCTCCGTCCTAAAATTC 57.091 47.619 0.00 0.00 0.00 2.17
3323 3788 3.451890 ACTCCCTCCGTCCTAAAATTCT 58.548 45.455 0.00 0.00 0.00 2.40
3324 3789 3.844804 ACTCCCTCCGTCCTAAAATTCTT 59.155 43.478 0.00 0.00 0.00 2.52
3325 3790 4.192317 CTCCCTCCGTCCTAAAATTCTTG 58.808 47.826 0.00 0.00 0.00 3.02
3326 3791 3.585732 TCCCTCCGTCCTAAAATTCTTGT 59.414 43.478 0.00 0.00 0.00 3.16
3327 3792 3.939592 CCCTCCGTCCTAAAATTCTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
3328 3793 4.323562 CCCTCCGTCCTAAAATTCTTGTCT 60.324 45.833 0.00 0.00 0.00 3.41
3329 3794 5.246307 CCTCCGTCCTAAAATTCTTGTCTT 58.754 41.667 0.00 0.00 0.00 3.01
3330 3795 6.403878 CCTCCGTCCTAAAATTCTTGTCTTA 58.596 40.000 0.00 0.00 0.00 2.10
3331 3796 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
3332 3797 7.235935 TCCGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
3333 3798 7.848128 TCCGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
3334 3799 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
3335 3800 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
3336 3801 9.760660 CGTCCTAAAATTCTTGTCTTAGATTTG 57.239 33.333 0.00 0.00 0.00 2.32
3347 3812 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3348 3813 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3349 3814 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3350 3815 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3351 3816 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3352 3817 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3406 3871 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3407 3872 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
3418 3883 9.760660 CAAATCTAAGACAAGAATTTTAGGACG 57.239 33.333 0.00 0.00 0.00 4.79
3419 3884 8.494016 AATCTAAGACAAGAATTTTAGGACGG 57.506 34.615 0.00 0.00 0.00 4.79
3420 3885 7.235935 TCTAAGACAAGAATTTTAGGACGGA 57.764 36.000 0.00 0.00 0.00 4.69
3421 3886 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
3422 3887 4.833390 AGACAAGAATTTTAGGACGGAGG 58.167 43.478 0.00 0.00 0.00 4.30
3423 3888 3.939592 GACAAGAATTTTAGGACGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
3424 3889 3.585732 ACAAGAATTTTAGGACGGAGGGA 59.414 43.478 0.00 0.00 0.00 4.20
3425 3890 4.192317 CAAGAATTTTAGGACGGAGGGAG 58.808 47.826 0.00 0.00 0.00 4.30
3426 3891 3.451890 AGAATTTTAGGACGGAGGGAGT 58.548 45.455 0.00 0.00 0.00 3.85
3427 3892 4.617593 AGAATTTTAGGACGGAGGGAGTA 58.382 43.478 0.00 0.00 0.00 2.59
3428 3893 4.405036 AGAATTTTAGGACGGAGGGAGTAC 59.595 45.833 0.00 0.00 0.00 2.73
3429 3894 3.463048 TTTTAGGACGGAGGGAGTACT 57.537 47.619 0.00 0.00 36.60 2.73
3470 3935 0.391661 ATTTGCCGCACTCTCGTCAT 60.392 50.000 0.00 0.00 0.00 3.06
3477 3942 2.534298 CGCACTCTCGTCATGATTCTT 58.466 47.619 0.00 0.00 0.00 2.52
3479 3944 4.294232 CGCACTCTCGTCATGATTCTTAT 58.706 43.478 0.00 0.00 0.00 1.73
3480 3945 4.742167 CGCACTCTCGTCATGATTCTTATT 59.258 41.667 0.00 0.00 0.00 1.40
3481 3946 5.233050 CGCACTCTCGTCATGATTCTTATTT 59.767 40.000 0.00 0.00 0.00 1.40
3515 3983 5.010415 AGCAGTAAAGTAGTGACCTAAACGT 59.990 40.000 0.00 0.00 0.00 3.99
3520 3988 5.479124 AAGTAGTGACCTAAACGTTGGAT 57.521 39.130 11.37 0.00 0.00 3.41
3565 4034 4.325030 CCACACACCCCTATATGAAAAGGT 60.325 45.833 0.00 0.00 0.00 3.50
3568 4037 6.542370 CACACACCCCTATATGAAAAGGTAAG 59.458 42.308 0.00 0.00 0.00 2.34
3673 4142 2.629137 ACATTCTTTGCAACAGCCATGA 59.371 40.909 0.00 0.00 0.00 3.07
3705 4174 2.969628 TCCTCATCTCCTCAATCTCCC 58.030 52.381 0.00 0.00 0.00 4.30
3737 4206 1.375908 GTGCCAAGCGAGATGGTCA 60.376 57.895 0.00 0.00 40.23 4.02
3796 4272 2.934932 TGGCAGCCATCCTCACCA 60.935 61.111 11.22 0.00 0.00 4.17
3827 4303 1.153329 TTTGCCGTCGTCACCAGTT 60.153 52.632 0.00 0.00 0.00 3.16
3959 4438 3.878519 GTCGTCGCTCCTCCCTCG 61.879 72.222 0.00 0.00 0.00 4.63
4034 4513 2.948979 TCAGGAATTGTTTCTGCAACGT 59.051 40.909 0.00 0.00 38.36 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.643379 TTCTTTTATTGTCCATCCAGTGC 57.357 39.130 0.00 0.00 0.00 4.40
44 46 5.779241 TCACTTTCAATTATGGTCCCTCT 57.221 39.130 0.00 0.00 0.00 3.69
50 52 4.142093 GCAGGCATCACTTTCAATTATGGT 60.142 41.667 0.00 0.00 0.00 3.55
53 55 5.664294 TTGCAGGCATCACTTTCAATTAT 57.336 34.783 0.00 0.00 0.00 1.28
54 56 5.221402 TGTTTGCAGGCATCACTTTCAATTA 60.221 36.000 0.00 0.00 0.00 1.40
58 60 2.030371 TGTTTGCAGGCATCACTTTCA 58.970 42.857 0.00 0.00 0.00 2.69
68 70 2.281484 TCGAGGGTGTTTGCAGGC 60.281 61.111 0.00 0.00 0.00 4.85
83 85 3.065371 GGTATTCAAAGCCTTGGATGTCG 59.935 47.826 0.00 0.00 32.63 4.35
105 107 2.722548 CGACGAGCGGCTATCACG 60.723 66.667 0.60 4.69 36.03 4.35
120 122 2.014857 ACTACATCTCGTTGCTAGCGA 58.985 47.619 10.77 5.12 36.85 4.93
152 154 2.698274 GGTGATTTCCCAACCACTGTTT 59.302 45.455 0.00 0.00 30.42 2.83
155 157 1.256812 GGGTGATTTCCCAACCACTG 58.743 55.000 0.00 0.00 46.30 3.66
156 158 3.765968 GGGTGATTTCCCAACCACT 57.234 52.632 0.00 0.00 46.30 4.00
166 168 2.555227 CCTACACTGCTTGGGGTGATTT 60.555 50.000 0.00 0.00 37.22 2.17
168 170 0.620556 CCTACACTGCTTGGGGTGAT 59.379 55.000 0.00 0.00 37.22 3.06
171 173 0.850784 AAACCTACACTGCTTGGGGT 59.149 50.000 0.00 0.00 37.12 4.95
179 181 5.048504 AGTGAATGATTGCAAACCTACACTG 60.049 40.000 21.76 0.00 34.39 3.66
186 188 6.311200 GGATTTGTAGTGAATGATTGCAAACC 59.689 38.462 1.71 0.00 0.00 3.27
187 189 6.867816 TGGATTTGTAGTGAATGATTGCAAAC 59.132 34.615 1.71 0.04 0.00 2.93
188 190 6.990798 TGGATTTGTAGTGAATGATTGCAAA 58.009 32.000 1.71 0.00 0.00 3.68
210 212 6.485830 TGTCAGTTTCTCTATCCCTTATGG 57.514 41.667 0.00 0.00 0.00 2.74
211 213 9.482627 GTAATGTCAGTTTCTCTATCCCTTATG 57.517 37.037 0.00 0.00 0.00 1.90
212 214 8.361139 CGTAATGTCAGTTTCTCTATCCCTTAT 58.639 37.037 0.00 0.00 0.00 1.73
213 215 7.201884 CCGTAATGTCAGTTTCTCTATCCCTTA 60.202 40.741 0.00 0.00 0.00 2.69
214 216 6.407074 CCGTAATGTCAGTTTCTCTATCCCTT 60.407 42.308 0.00 0.00 0.00 3.95
219 221 4.161565 TGGCCGTAATGTCAGTTTCTCTAT 59.838 41.667 0.00 0.00 0.00 1.98
233 235 8.608844 TTTTCATTAATTTGTTTGGCCGTAAT 57.391 26.923 0.00 0.00 0.00 1.89
238 240 8.376889 TCTTCTTTTCATTAATTTGTTTGGCC 57.623 30.769 0.00 0.00 0.00 5.36
239 241 8.498358 CCTCTTCTTTTCATTAATTTGTTTGGC 58.502 33.333 0.00 0.00 0.00 4.52
254 256 3.810386 AGCGACTTCAACCTCTTCTTTTC 59.190 43.478 0.00 0.00 0.00 2.29
275 277 4.431809 TGCTTGATTGGTTTTTGACACAG 58.568 39.130 0.00 0.00 0.00 3.66
276 278 4.462508 TGCTTGATTGGTTTTTGACACA 57.537 36.364 0.00 0.00 0.00 3.72
320 322 9.299963 CTAGATCCGCATTTTAGATCTTGATAG 57.700 37.037 0.00 0.00 43.23 2.08
322 324 6.593382 GCTAGATCCGCATTTTAGATCTTGAT 59.407 38.462 0.00 0.00 43.23 2.57
324 326 5.698089 TGCTAGATCCGCATTTTAGATCTTG 59.302 40.000 0.00 6.68 43.23 3.02
332 334 2.423538 GGTGTTGCTAGATCCGCATTTT 59.576 45.455 7.97 0.00 37.22 1.82
335 337 0.833287 AGGTGTTGCTAGATCCGCAT 59.167 50.000 7.97 0.00 37.22 4.73
339 341 2.365941 GAGGGTAGGTGTTGCTAGATCC 59.634 54.545 0.00 0.00 0.00 3.36
346 348 2.622064 CCTATGAGGGTAGGTGTTGC 57.378 55.000 0.00 0.00 37.13 4.17
353 355 3.741388 CGGCAAAGAACCTATGAGGGTAG 60.741 52.174 0.00 0.00 33.59 3.18
356 358 1.668419 CGGCAAAGAACCTATGAGGG 58.332 55.000 0.00 0.00 40.58 4.30
360 362 1.721487 CGCCGGCAAAGAACCTATG 59.279 57.895 28.98 0.37 0.00 2.23
362 364 2.744709 GCGCCGGCAAAGAACCTA 60.745 61.111 28.98 0.00 39.62 3.08
372 374 2.742372 ATTCGATATGGCGCCGGC 60.742 61.111 23.90 19.07 38.90 6.13
378 380 1.979469 CTCGACGACATTCGATATGGC 59.021 52.381 1.94 7.61 46.53 4.40
386 388 2.163010 TGTCCTTACCTCGACGACATTC 59.837 50.000 0.00 0.00 0.00 2.67
390 392 1.402062 GGTTGTCCTTACCTCGACGAC 60.402 57.143 0.00 0.00 41.03 4.34
401 403 1.568504 TATCGCTCTGGGTTGTCCTT 58.431 50.000 0.00 0.00 36.20 3.36
406 408 3.131396 GTGGTAATATCGCTCTGGGTTG 58.869 50.000 0.00 0.00 0.00 3.77
408 410 2.394632 TGTGGTAATATCGCTCTGGGT 58.605 47.619 0.00 0.00 0.00 4.51
409 411 3.131396 GTTGTGGTAATATCGCTCTGGG 58.869 50.000 0.00 0.00 0.00 4.45
412 414 3.119245 ACGTGTTGTGGTAATATCGCTCT 60.119 43.478 0.00 0.00 0.00 4.09
413 415 3.184541 ACGTGTTGTGGTAATATCGCTC 58.815 45.455 0.00 0.00 0.00 5.03
443 445 2.787473 TGGCTTTGATGAGGTAGTGG 57.213 50.000 0.00 0.00 0.00 4.00
454 456 3.507162 TTGGTTCTCTCATGGCTTTGA 57.493 42.857 0.00 0.00 0.00 2.69
458 460 4.313020 AGATTTTGGTTCTCTCATGGCT 57.687 40.909 0.00 0.00 0.00 4.75
482 484 2.695359 TCAAGTATGTCGTTGCTTCCC 58.305 47.619 0.00 0.00 0.00 3.97
483 485 3.746492 ACTTCAAGTATGTCGTTGCTTCC 59.254 43.478 0.00 0.00 0.00 3.46
484 486 4.992381 ACTTCAAGTATGTCGTTGCTTC 57.008 40.909 0.00 0.00 0.00 3.86
485 487 6.854496 TTTACTTCAAGTATGTCGTTGCTT 57.146 33.333 0.00 0.00 29.64 3.91
486 488 6.854496 TTTTACTTCAAGTATGTCGTTGCT 57.146 33.333 0.00 0.00 29.64 3.91
487 489 9.601971 TTAATTTTACTTCAAGTATGTCGTTGC 57.398 29.630 0.00 0.00 29.64 4.17
497 499 9.811995 GTCCCTTTTGTTAATTTTACTTCAAGT 57.188 29.630 0.00 0.00 0.00 3.16
498 500 9.810545 TGTCCCTTTTGTTAATTTTACTTCAAG 57.189 29.630 0.00 0.00 0.00 3.02
500 502 9.757227 CATGTCCCTTTTGTTAATTTTACTTCA 57.243 29.630 0.00 0.00 0.00 3.02
501 503 9.758651 ACATGTCCCTTTTGTTAATTTTACTTC 57.241 29.630 0.00 0.00 0.00 3.01
502 504 9.758651 GACATGTCCCTTTTGTTAATTTTACTT 57.241 29.630 15.31 0.00 0.00 2.24
503 505 8.364894 GGACATGTCCCTTTTGTTAATTTTACT 58.635 33.333 31.37 0.00 43.94 2.24
504 506 8.528917 GGACATGTCCCTTTTGTTAATTTTAC 57.471 34.615 31.37 2.15 43.94 2.01
521 523 2.360165 GCCAATGGAATGAGGACATGTC 59.640 50.000 17.91 17.91 36.79 3.06
524 526 1.751733 CGGCCAATGGAATGAGGACAT 60.752 52.381 2.05 0.00 38.50 3.06
527 529 1.453745 GCGGCCAATGGAATGAGGA 60.454 57.895 2.05 0.00 0.00 3.71
533 535 0.179020 CTCATAGGCGGCCAATGGAA 60.179 55.000 23.09 0.15 0.00 3.53
536 538 0.886490 GACCTCATAGGCGGCCAATG 60.886 60.000 23.09 10.55 39.63 2.82
559 561 0.610687 CCGCTTTCTCTCTTCCACCT 59.389 55.000 0.00 0.00 0.00 4.00
560 562 0.608640 TCCGCTTTCTCTCTTCCACC 59.391 55.000 0.00 0.00 0.00 4.61
561 563 1.673329 GGTCCGCTTTCTCTCTTCCAC 60.673 57.143 0.00 0.00 0.00 4.02
588 590 0.743345 CTAAGGTTTCCTTCGCCCCG 60.743 60.000 4.21 0.00 43.57 5.73
591 593 1.002773 TCACCTAAGGTTTCCTTCGCC 59.997 52.381 4.21 0.00 43.57 5.54
603 605 4.705023 CCCAAACCCTAATTGTCACCTAAG 59.295 45.833 0.00 0.00 0.00 2.18
611 613 2.825457 GCCCTTCCCAAACCCTAATTGT 60.825 50.000 0.00 0.00 0.00 2.71
628 630 2.925170 ACGCTCCTTCACTGCCCT 60.925 61.111 0.00 0.00 0.00 5.19
631 633 2.029844 GTCCACGCTCCTTCACTGC 61.030 63.158 0.00 0.00 0.00 4.40
634 639 2.432628 CGGTCCACGCTCCTTCAC 60.433 66.667 0.00 0.00 34.82 3.18
642 647 4.090588 TGATTCCCCGGTCCACGC 62.091 66.667 0.00 0.00 42.52 5.34
644 649 2.271173 GGTGATTCCCCGGTCCAC 59.729 66.667 0.00 0.49 0.00 4.02
678 683 8.732746 ACCGCTAAGATCACTGTAAAAATATT 57.267 30.769 0.00 0.00 0.00 1.28
679 684 9.826574 TTACCGCTAAGATCACTGTAAAAATAT 57.173 29.630 0.00 0.00 0.00 1.28
680 685 9.090692 GTTACCGCTAAGATCACTGTAAAAATA 57.909 33.333 0.00 0.00 0.00 1.40
681 686 7.065443 GGTTACCGCTAAGATCACTGTAAAAAT 59.935 37.037 0.00 0.00 0.00 1.82
692 698 4.557097 GCTAGACAGGTTACCGCTAAGATC 60.557 50.000 0.00 0.00 0.00 2.75
697 703 2.022195 CAGCTAGACAGGTTACCGCTA 58.978 52.381 0.00 0.00 0.00 4.26
720 726 4.848357 TCCCTGCTTTATTCTTTCCTCTG 58.152 43.478 0.00 0.00 0.00 3.35
770 778 0.319083 TGGGTTCGTTGCTGATACGT 59.681 50.000 0.00 0.00 39.84 3.57
771 779 1.127951 GTTGGGTTCGTTGCTGATACG 59.872 52.381 0.00 0.00 40.23 3.06
824 832 2.352323 GCGGATTGGTTTTAGTGGGTTG 60.352 50.000 0.00 0.00 0.00 3.77
832 840 2.219458 TGTTGACGCGGATTGGTTTTA 58.781 42.857 12.47 0.00 0.00 1.52
908 916 1.001641 CTGGCTGTTCCCCTTCCTG 60.002 63.158 0.00 0.00 0.00 3.86
912 923 0.909610 TCGATCTGGCTGTTCCCCTT 60.910 55.000 0.00 0.00 0.00 3.95
1042 1053 1.673928 CCAGGAGGAGGGGGAGAGAT 61.674 65.000 0.00 0.00 36.89 2.75
1043 1054 2.328589 CCAGGAGGAGGGGGAGAGA 61.329 68.421 0.00 0.00 36.89 3.10
1044 1055 2.285180 CCAGGAGGAGGGGGAGAG 59.715 72.222 0.00 0.00 36.89 3.20
1045 1056 2.204624 TCCAGGAGGAGGGGGAGA 60.205 66.667 0.00 0.00 39.61 3.71
1067 1203 4.630069 GCACAGGTAAACAAGTACGATCAT 59.370 41.667 0.00 0.00 0.00 2.45
1073 1209 3.676646 CGGTAGCACAGGTAAACAAGTAC 59.323 47.826 0.00 0.00 0.00 2.73
1083 1219 2.423898 CCGGATCGGTAGCACAGGT 61.424 63.158 0.00 0.00 42.73 4.00
1095 1231 1.559065 TTGGTTGGTCCCTCCGGATC 61.559 60.000 3.57 0.00 41.40 3.36
1112 1248 5.047188 ACAAGGTAAAAAGGCGTTGAATTG 58.953 37.500 0.00 0.00 0.00 2.32
1118 1254 2.032426 CACGACAAGGTAAAAAGGCGTT 59.968 45.455 0.00 0.00 0.00 4.84
1124 1260 4.060205 GCTAGTCCACGACAAGGTAAAAA 58.940 43.478 0.00 0.00 34.60 1.94
1136 1272 1.883084 GGCGGATTGCTAGTCCACG 60.883 63.158 0.00 0.00 45.43 4.94
1170 1308 3.191371 ACTTTTTGATGATCAAGCCGACC 59.809 43.478 8.01 0.00 37.70 4.79
1191 1329 7.839837 CGAGATTAACGCAATAGTAAACTTCAC 59.160 37.037 0.00 0.00 0.00 3.18
1219 1359 3.500343 AGGGTTTGATGAAAGAACCTGG 58.500 45.455 4.69 0.00 41.93 4.45
1221 1361 4.043435 AGCTAGGGTTTGATGAAAGAACCT 59.957 41.667 4.69 0.00 41.93 3.50
1256 1396 6.565234 ACTAGTACTACAATCTGCACATGAC 58.435 40.000 0.00 0.00 0.00 3.06
1302 1445 2.176273 GCATCCTGGTAGCGCAGTG 61.176 63.158 11.47 0.00 0.00 3.66
1348 1492 9.620259 AGATTATAACAGCTAAAGAGGAAAAGG 57.380 33.333 0.00 0.00 0.00 3.11
1352 1496 9.601217 GACAAGATTATAACAGCTAAAGAGGAA 57.399 33.333 0.00 0.00 0.00 3.36
1420 1811 0.741326 TTGCTTGCTTGTTAACGGCA 59.259 45.000 18.01 18.01 0.00 5.69
1452 1843 9.573133 GAATCAAGTAACTCCAAACCAATATTG 57.427 33.333 8.58 8.58 0.00 1.90
1531 1922 1.286248 TTAGAGGGCCCCAGTTTCTC 58.714 55.000 21.43 7.63 0.00 2.87
1595 1992 3.644738 GTCCCCCATATTCCGAAGTCTTA 59.355 47.826 0.00 0.00 0.00 2.10
1638 2059 0.334676 CCATAAAACCCAGGGGAGCA 59.665 55.000 11.37 0.00 38.96 4.26
1835 2257 3.997021 AGAGATTTGGCAGTTTCAGTACG 59.003 43.478 0.00 0.00 0.00 3.67
1837 2259 4.245660 CGAGAGATTTGGCAGTTTCAGTA 58.754 43.478 0.00 0.00 0.00 2.74
2046 2471 8.868522 AAGAATGAATTACAGTGGAAGAATGA 57.131 30.769 0.00 0.00 0.00 2.57
2101 2553 3.136443 ACAATCAAGGCCGAGGATAATGA 59.864 43.478 0.00 0.00 0.00 2.57
2206 2659 5.980116 CCTATTCAGGAGACATCAACGTAAG 59.020 44.000 0.00 0.00 45.91 2.34
2347 2800 3.942739 TCAAATCAAAACACGTTCCGTC 58.057 40.909 0.00 0.00 38.32 4.79
2480 2933 2.910688 ACAATGCTACCTGGATACGG 57.089 50.000 0.00 0.00 45.15 4.02
2486 2939 3.316308 GCTTGGATTACAATGCTACCTGG 59.684 47.826 0.00 0.00 38.65 4.45
2570 3023 7.573710 TCCACAATATAATGAAGCCTACTGTT 58.426 34.615 0.00 0.00 0.00 3.16
2657 3112 2.361567 GGCTTCCCCCATTGCTTGG 61.362 63.158 0.00 0.00 46.00 3.61
2768 3223 2.611292 GCTGACCATTTCCATCTTCTCG 59.389 50.000 0.00 0.00 0.00 4.04
2942 3397 4.836825 TCATCCTGGTGTTTCAATCTCTC 58.163 43.478 0.00 0.00 0.00 3.20
2999 3454 1.915141 CCTTGACAAGCTGGGTTCAT 58.085 50.000 9.85 0.00 0.00 2.57
3196 3658 1.864711 CGGAGTGGCATTTATGGTACG 59.135 52.381 0.00 0.00 0.00 3.67
3225 3689 4.083855 ACACACTGCAAATGATACGTCAAG 60.084 41.667 4.68 0.00 38.01 3.02
3305 3770 3.939592 GACAAGAATTTTAGGACGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
3306 3771 4.833390 AGACAAGAATTTTAGGACGGAGG 58.167 43.478 0.00 0.00 0.00 4.30
3307 3772 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
3308 3773 7.235935 TCTAAGACAAGAATTTTAGGACGGA 57.764 36.000 0.00 0.00 0.00 4.69
3309 3774 8.494016 AATCTAAGACAAGAATTTTAGGACGG 57.506 34.615 0.00 0.00 0.00 4.79
3310 3775 9.760660 CAAATCTAAGACAAGAATTTTAGGACG 57.239 33.333 0.00 0.00 0.00 4.79
3321 3786 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3322 3787 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3323 3788 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3324 3789 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3325 3790 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3326 3791 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3380 3845 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3381 3846 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3392 3857 9.760660 CGTCCTAAAATTCTTGTCTTAGATTTG 57.239 33.333 0.00 0.00 0.00 2.32
3393 3858 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
3394 3859 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
3395 3860 7.848128 TCCGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
3396 3861 7.235935 TCCGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
3397 3862 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
3398 3863 6.403878 CCTCCGTCCTAAAATTCTTGTCTTA 58.596 40.000 0.00 0.00 0.00 2.10
3399 3864 5.246307 CCTCCGTCCTAAAATTCTTGTCTT 58.754 41.667 0.00 0.00 0.00 3.01
3400 3865 4.323562 CCCTCCGTCCTAAAATTCTTGTCT 60.324 45.833 0.00 0.00 0.00 3.41
3401 3866 3.939592 CCCTCCGTCCTAAAATTCTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
3402 3867 3.585732 TCCCTCCGTCCTAAAATTCTTGT 59.414 43.478 0.00 0.00 0.00 3.16
3403 3868 4.192317 CTCCCTCCGTCCTAAAATTCTTG 58.808 47.826 0.00 0.00 0.00 3.02
3404 3869 3.844804 ACTCCCTCCGTCCTAAAATTCTT 59.155 43.478 0.00 0.00 0.00 2.52
3405 3870 3.451890 ACTCCCTCCGTCCTAAAATTCT 58.548 45.455 0.00 0.00 0.00 2.40
3406 3871 3.908643 ACTCCCTCCGTCCTAAAATTC 57.091 47.619 0.00 0.00 0.00 2.17
3407 3872 4.359996 AGTACTCCCTCCGTCCTAAAATT 58.640 43.478 0.00 0.00 0.00 1.82
3408 3873 3.991683 AGTACTCCCTCCGTCCTAAAAT 58.008 45.455 0.00 0.00 0.00 1.82
3409 3874 3.463048 AGTACTCCCTCCGTCCTAAAA 57.537 47.619 0.00 0.00 0.00 1.52
3410 3875 3.117738 CCTAGTACTCCCTCCGTCCTAAA 60.118 52.174 0.00 0.00 0.00 1.85
3411 3876 2.441001 CCTAGTACTCCCTCCGTCCTAA 59.559 54.545 0.00 0.00 0.00 2.69
3412 3877 2.053244 CCTAGTACTCCCTCCGTCCTA 58.947 57.143 0.00 0.00 0.00 2.94
3413 3878 0.845337 CCTAGTACTCCCTCCGTCCT 59.155 60.000 0.00 0.00 0.00 3.85
3414 3879 0.822944 GCCTAGTACTCCCTCCGTCC 60.823 65.000 0.00 0.00 0.00 4.79
3415 3880 0.183252 AGCCTAGTACTCCCTCCGTC 59.817 60.000 0.00 0.00 0.00 4.79
3416 3881 0.630134 AAGCCTAGTACTCCCTCCGT 59.370 55.000 0.00 0.00 0.00 4.69
3417 3882 1.033574 CAAGCCTAGTACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
3418 3883 1.343176 ACCAAGCCTAGTACTCCCTCC 60.343 57.143 0.00 0.00 0.00 4.30
3419 3884 2.033372 GACCAAGCCTAGTACTCCCTC 58.967 57.143 0.00 0.00 0.00 4.30
3420 3885 1.646977 AGACCAAGCCTAGTACTCCCT 59.353 52.381 0.00 0.00 0.00 4.20
3421 3886 2.162264 AGACCAAGCCTAGTACTCCC 57.838 55.000 0.00 0.00 0.00 4.30
3422 3887 3.770388 AGAAAGACCAAGCCTAGTACTCC 59.230 47.826 0.00 0.00 0.00 3.85
3423 3888 5.653330 ACTAGAAAGACCAAGCCTAGTACTC 59.347 44.000 0.00 0.00 38.47 2.59
3424 3889 5.581975 ACTAGAAAGACCAAGCCTAGTACT 58.418 41.667 0.00 0.00 38.47 2.73
3425 3890 5.918426 ACTAGAAAGACCAAGCCTAGTAC 57.082 43.478 0.00 0.00 38.47 2.73
3426 3891 5.421374 GGAACTAGAAAGACCAAGCCTAGTA 59.579 44.000 0.00 0.00 39.08 1.82
3427 3892 4.223255 GGAACTAGAAAGACCAAGCCTAGT 59.777 45.833 0.00 0.00 41.01 2.57
3428 3893 4.223032 TGGAACTAGAAAGACCAAGCCTAG 59.777 45.833 0.00 0.00 32.84 3.02
3429 3894 4.164981 TGGAACTAGAAAGACCAAGCCTA 58.835 43.478 0.00 0.00 32.84 3.93
3515 3983 3.293337 AGAGCTGCAATGCATTATCCAA 58.707 40.909 12.53 0.00 38.13 3.53
3520 3988 1.302366 CCGAGAGCTGCAATGCATTA 58.698 50.000 12.53 0.00 38.13 1.90
3546 4015 5.686650 CGCTTACCTTTTCATATAGGGGTGT 60.687 44.000 0.00 0.00 35.79 4.16
3565 4034 1.545136 TCGGGTGATGTGTAACGCTTA 59.455 47.619 0.00 0.00 42.39 3.09
3568 4037 1.680105 CGTCGGGTGATGTGTAACGC 61.680 60.000 0.00 0.00 42.39 4.84
3639 4108 1.672356 GAATGTGCTGGTGCGGTCT 60.672 57.895 0.00 0.00 43.34 3.85
3673 4142 4.105057 AGGAGATGAGGATAAGGTACGAGT 59.895 45.833 0.00 0.00 0.00 4.18
3705 4174 1.817099 GGCACCGCTGATTCAGGAG 60.817 63.158 15.28 0.89 31.21 3.69
3844 4320 2.203126 GCGAGGCCTAGCTGCAAT 60.203 61.111 28.57 0.00 0.00 3.56
3869 4346 4.524318 AGCGGGTGATAACGGCGG 62.524 66.667 13.24 0.00 38.93 6.13
3877 4354 1.077501 CATGGTGGAAGCGGGTGAT 60.078 57.895 0.00 0.00 36.92 3.06
3931 4410 1.664965 GCGACGACAAGCTCACCTT 60.665 57.895 0.00 0.00 0.00 3.50
3959 4438 2.750888 GCTTCCGTCGAATGGTGGC 61.751 63.158 4.98 6.91 0.00 5.01
4034 4513 1.339610 CAATTCCTGAAACAACGGCCA 59.660 47.619 2.24 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.