Multiple sequence alignment - TraesCS7A01G305600

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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 TraesCS7A01G305600 chr7A 100.000 3361 0 0 1 3361 430489995 430493355 0.000000e+00 6207
1 TraesCS7A01G305600 chr7A 88.632 475 37 16 71 540 22640858 22641320 2.260000e-156 562
2 TraesCS7A01G305600 chr7D 96.628 2165 59 6 542 2695 382378592 382380753 0.000000e+00 3581
3 TraesCS7A01G305600 chr7D 89.601 577 36 9 2781 3355 382380755 382381309 0.000000e+00 712
4 TraesCS7A01G305600 chr7B 96.667 2160 47 9 542 2697 376800989 376803127 0.000000e+00 3567
5 TraesCS7A01G305600 chr7B 95.667 577 18 3 2779 3355 376803125 376803694 0.000000e+00 920
6 TraesCS7A01G305600 chr7B 89.384 471 36 13 75 542 459801829 459802288 6.250000e-162 580
7 TraesCS7A01G305600 chr7B 93.333 105 6 1 2680 2784 544131547 544131650 1.610000e-33 154
8 TraesCS7A01G305600 chr7B 94.000 100 5 1 2695 2794 715301935 715302033 2.090000e-32 150
9 TraesCS7A01G305600 chr2D 91.239 468 31 10 75 540 577604858 577605317 2.200000e-176 628
10 TraesCS7A01G305600 chr2D 90.316 475 33 11 70 540 291994727 291994262 7.970000e-171 610
11 TraesCS7A01G305600 chr1D 90.638 470 33 11 75 541 359480536 359480075 6.160000e-172 614
12 TraesCS7A01G305600 chr6D 89.619 472 37 9 70 540 14160232 14159772 1.040000e-164 590
13 TraesCS7A01G305600 chr6D 93.878 98 6 0 2695 2792 26359302 26359205 7.510000e-32 148
14 TraesCS7A01G305600 chr3B 90.086 464 33 12 75 534 162473355 162472901 1.040000e-164 590
15 TraesCS7A01G305600 chr6A 89.677 465 40 7 70 533 71112925 71113382 1.340000e-163 586
16 TraesCS7A01G305600 chr6A 96.739 92 3 0 2695 2786 51946554 51946463 1.610000e-33 154
17 TraesCS7A01G305600 chr6B 88.387 465 40 13 78 540 635267742 635267290 6.340000e-152 547
18 TraesCS7A01G305600 chr4B 94.792 96 5 0 2694 2789 6067739 6067644 2.090000e-32 150
19 TraesCS7A01G305600 chr1A 95.699 93 4 0 2696 2788 504269086 504269178 2.090000e-32 150
20 TraesCS7A01G305600 chr2A 93.069 101 5 2 2695 2793 193876552 193876452 2.700000e-31 147
21 TraesCS7A01G305600 chr2B 90.179 112 8 3 2695 2804 593680831 593680721 3.500000e-30 143
22 TraesCS7A01G305600 chr4A 86.047 129 13 5 2677 2803 731306800 731306675 2.100000e-27 134


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 TraesCS7A01G305600 chr7A 430489995 430493355 3360 False 6207.0 6207 100.0000 1 3361 1 chr7A.!!$F2 3360
1 TraesCS7A01G305600 chr7D 382378592 382381309 2717 False 2146.5 3581 93.1145 542 3355 2 chr7D.!!$F1 2813
2 TraesCS7A01G305600 chr7B 376800989 376803694 2705 False 2243.5 3567 96.1670 542 3355 2 chr7B.!!$F4 2813

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
490 491 0.036010 GCCCATGCTAGTGACACAGT 60.036 55.0 8.59 0.0 33.53 3.55 F
1155 1163 1.217882 GGCGAAATGTCTGGGTATCG 58.782 55.0 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1321 1.209127 CACGGCCGGATTTGACAAC 59.791 57.895 31.76 0.0 0.0 3.32 R
2765 2777 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.0 0.0 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 6.867519 TTTTTCTCTTTTTCTTCCTGGGTT 57.132 33.333 0.00 0.00 0.00 4.11
64 65 6.867519 TTTTCTCTTTTTCTTCCTGGGTTT 57.132 33.333 0.00 0.00 0.00 3.27
65 66 5.852282 TTCTCTTTTTCTTCCTGGGTTTG 57.148 39.130 0.00 0.00 0.00 2.93
66 67 5.124036 TCTCTTTTTCTTCCTGGGTTTGA 57.876 39.130 0.00 0.00 0.00 2.69
67 68 5.705400 TCTCTTTTTCTTCCTGGGTTTGAT 58.295 37.500 0.00 0.00 0.00 2.57
68 69 5.536161 TCTCTTTTTCTTCCTGGGTTTGATG 59.464 40.000 0.00 0.00 0.00 3.07
69 70 4.039124 TCTTTTTCTTCCTGGGTTTGATGC 59.961 41.667 0.00 0.00 0.00 3.91
70 71 2.673775 TTCTTCCTGGGTTTGATGCA 57.326 45.000 0.00 0.00 0.00 3.96
71 72 2.673775 TCTTCCTGGGTTTGATGCAA 57.326 45.000 0.00 0.00 0.00 4.08
72 73 2.956132 TCTTCCTGGGTTTGATGCAAA 58.044 42.857 0.00 0.00 0.00 3.68
73 74 3.303938 TCTTCCTGGGTTTGATGCAAAA 58.696 40.909 0.00 0.00 35.03 2.44
74 75 3.903090 TCTTCCTGGGTTTGATGCAAAAT 59.097 39.130 0.00 0.00 35.03 1.82
75 76 3.959535 TCCTGGGTTTGATGCAAAATC 57.040 42.857 0.00 0.00 35.03 2.17
76 77 2.230992 TCCTGGGTTTGATGCAAAATCG 59.769 45.455 0.00 0.00 35.03 3.34
77 78 2.230992 CCTGGGTTTGATGCAAAATCGA 59.769 45.455 0.00 0.00 35.03 3.59
78 79 3.119029 CCTGGGTTTGATGCAAAATCGAT 60.119 43.478 0.00 0.00 35.03 3.59
79 80 3.847542 TGGGTTTGATGCAAAATCGATG 58.152 40.909 0.00 0.00 35.03 3.84
80 81 3.509184 TGGGTTTGATGCAAAATCGATGA 59.491 39.130 0.00 0.00 35.03 2.92
81 82 4.021632 TGGGTTTGATGCAAAATCGATGAA 60.022 37.500 0.00 0.00 35.03 2.57
82 83 4.327087 GGGTTTGATGCAAAATCGATGAAC 59.673 41.667 0.00 0.00 35.03 3.18
83 84 5.163513 GGTTTGATGCAAAATCGATGAACT 58.836 37.500 0.00 0.00 35.03 3.01
84 85 5.634859 GGTTTGATGCAAAATCGATGAACTT 59.365 36.000 0.00 0.00 35.03 2.66
85 86 6.146021 GGTTTGATGCAAAATCGATGAACTTT 59.854 34.615 0.00 0.00 35.03 2.66
86 87 7.307337 GGTTTGATGCAAAATCGATGAACTTTT 60.307 33.333 0.00 0.00 35.03 2.27
87 88 7.712264 TTGATGCAAAATCGATGAACTTTTT 57.288 28.000 0.00 0.00 0.00 1.94
142 143 9.878599 ATTTTAGTGTACTTTGTCTCAAATTCG 57.121 29.630 0.00 0.00 0.00 3.34
143 144 8.651391 TTTAGTGTACTTTGTCTCAAATTCGA 57.349 30.769 0.00 0.00 0.00 3.71
144 145 8.827177 TTAGTGTACTTTGTCTCAAATTCGAT 57.173 30.769 0.00 0.00 0.00 3.59
145 146 7.121974 AGTGTACTTTGTCTCAAATTCGATG 57.878 36.000 0.00 0.00 0.00 3.84
146 147 6.929049 AGTGTACTTTGTCTCAAATTCGATGA 59.071 34.615 0.00 0.00 0.00 2.92
147 148 7.441157 AGTGTACTTTGTCTCAAATTCGATGAA 59.559 33.333 0.00 0.00 0.00 2.57
148 149 7.530861 GTGTACTTTGTCTCAAATTCGATGAAC 59.469 37.037 0.00 0.00 0.00 3.18
149 150 6.867662 ACTTTGTCTCAAATTCGATGAACT 57.132 33.333 0.00 0.00 0.00 3.01
150 151 7.264373 ACTTTGTCTCAAATTCGATGAACTT 57.736 32.000 0.00 0.00 0.00 2.66
151 152 7.707104 ACTTTGTCTCAAATTCGATGAACTTT 58.293 30.769 0.00 0.00 0.00 2.66
152 153 8.190784 ACTTTGTCTCAAATTCGATGAACTTTT 58.809 29.630 0.00 0.00 0.00 2.27
153 154 8.925161 TTTGTCTCAAATTCGATGAACTTTTT 57.075 26.923 0.00 0.00 0.00 1.94
235 236 6.377327 TTTTCAAGCTCGATGAACTTTTCT 57.623 33.333 0.00 0.00 36.57 2.52
236 237 4.997905 TCAAGCTCGATGAACTTTTCTG 57.002 40.909 0.00 0.00 0.00 3.02
237 238 4.631131 TCAAGCTCGATGAACTTTTCTGA 58.369 39.130 0.00 0.00 0.00 3.27
238 239 5.056480 TCAAGCTCGATGAACTTTTCTGAA 58.944 37.500 0.00 0.00 0.00 3.02
239 240 5.527214 TCAAGCTCGATGAACTTTTCTGAAA 59.473 36.000 0.00 0.00 0.00 2.69
240 241 5.349824 AGCTCGATGAACTTTTCTGAAAC 57.650 39.130 1.58 0.00 0.00 2.78
241 242 4.816385 AGCTCGATGAACTTTTCTGAAACA 59.184 37.500 1.58 0.00 0.00 2.83
242 243 4.906437 GCTCGATGAACTTTTCTGAAACAC 59.094 41.667 1.58 0.00 0.00 3.32
243 244 5.078153 TCGATGAACTTTTCTGAAACACG 57.922 39.130 1.58 5.16 0.00 4.49
244 245 4.806775 TCGATGAACTTTTCTGAAACACGA 59.193 37.500 1.58 7.05 0.00 4.35
245 246 5.465390 TCGATGAACTTTTCTGAAACACGAT 59.535 36.000 1.58 0.00 0.00 3.73
246 247 5.561499 CGATGAACTTTTCTGAAACACGATG 59.439 40.000 1.58 0.00 0.00 3.84
247 248 6.563939 CGATGAACTTTTCTGAAACACGATGA 60.564 38.462 1.58 0.00 0.00 2.92
248 249 6.048073 TGAACTTTTCTGAAACACGATGAG 57.952 37.500 1.58 0.00 0.00 2.90
249 250 4.474226 ACTTTTCTGAAACACGATGAGC 57.526 40.909 1.58 0.00 0.00 4.26
250 251 4.130118 ACTTTTCTGAAACACGATGAGCT 58.870 39.130 1.58 0.00 0.00 4.09
251 252 4.576463 ACTTTTCTGAAACACGATGAGCTT 59.424 37.500 1.58 0.00 0.00 3.74
252 253 5.066505 ACTTTTCTGAAACACGATGAGCTTT 59.933 36.000 1.58 0.00 0.00 3.51
253 254 5.499139 TTTCTGAAACACGATGAGCTTTT 57.501 34.783 0.00 0.00 0.00 2.27
254 255 5.499139 TTCTGAAACACGATGAGCTTTTT 57.501 34.783 0.00 0.00 0.00 1.94
323 324 8.211116 TCTAAGACAAGAGTACATACAGTAGC 57.789 38.462 0.00 0.00 32.19 3.58
324 325 6.835819 AAGACAAGAGTACATACAGTAGCA 57.164 37.500 0.00 0.00 32.19 3.49
325 326 6.835819 AGACAAGAGTACATACAGTAGCAA 57.164 37.500 0.00 0.00 32.19 3.91
326 327 7.228314 AGACAAGAGTACATACAGTAGCAAA 57.772 36.000 0.00 0.00 32.19 3.68
327 328 7.091443 AGACAAGAGTACATACAGTAGCAAAC 58.909 38.462 0.00 0.00 32.19 2.93
328 329 6.164176 ACAAGAGTACATACAGTAGCAAACC 58.836 40.000 0.00 0.00 32.19 3.27
329 330 4.995124 AGAGTACATACAGTAGCAAACCG 58.005 43.478 0.00 0.00 32.19 4.44
330 331 4.110482 GAGTACATACAGTAGCAAACCGG 58.890 47.826 0.00 0.00 32.19 5.28
331 332 3.512724 AGTACATACAGTAGCAAACCGGT 59.487 43.478 0.00 0.00 32.19 5.28
332 333 3.412237 ACATACAGTAGCAAACCGGTT 57.588 42.857 15.86 15.86 0.00 4.44
333 334 3.746940 ACATACAGTAGCAAACCGGTTT 58.253 40.909 26.87 26.87 0.00 3.27
334 335 4.139038 ACATACAGTAGCAAACCGGTTTT 58.861 39.130 29.74 18.83 0.00 2.43
335 336 4.581409 ACATACAGTAGCAAACCGGTTTTT 59.419 37.500 29.74 21.78 0.00 1.94
363 364 9.856488 CTAAGAAAAATAGTCTGTACTGTAGCA 57.144 33.333 0.00 0.00 36.36 3.49
364 365 8.764524 AAGAAAAATAGTCTGTACTGTAGCAG 57.235 34.615 9.64 9.64 36.36 4.24
366 367 8.368668 AGAAAAATAGTCTGTACTGTAGCAGTT 58.631 33.333 7.11 8.50 42.59 3.16
367 368 8.904099 AAAAATAGTCTGTACTGTAGCAGTTT 57.096 30.769 7.11 7.21 42.59 2.66
368 369 8.904099 AAAATAGTCTGTACTGTAGCAGTTTT 57.096 30.769 7.11 10.79 42.59 2.43
369 370 8.904099 AAATAGTCTGTACTGTAGCAGTTTTT 57.096 30.769 7.11 8.76 42.59 1.94
370 371 9.991906 AAATAGTCTGTACTGTAGCAGTTTTTA 57.008 29.630 7.11 0.00 42.59 1.52
371 372 9.640963 AATAGTCTGTACTGTAGCAGTTTTTAG 57.359 33.333 7.11 2.35 42.59 1.85
372 373 7.286215 AGTCTGTACTGTAGCAGTTTTTAGA 57.714 36.000 7.11 4.36 42.59 2.10
373 374 7.723324 AGTCTGTACTGTAGCAGTTTTTAGAA 58.277 34.615 7.11 0.00 42.59 2.10
374 375 8.368668 AGTCTGTACTGTAGCAGTTTTTAGAAT 58.631 33.333 7.11 3.83 42.59 2.40
375 376 8.436200 GTCTGTACTGTAGCAGTTTTTAGAATG 58.564 37.037 7.11 0.00 42.59 2.67
376 377 8.364894 TCTGTACTGTAGCAGTTTTTAGAATGA 58.635 33.333 7.11 0.00 42.59 2.57
377 378 8.896320 TGTACTGTAGCAGTTTTTAGAATGAA 57.104 30.769 7.11 0.00 42.59 2.57
378 379 8.988934 TGTACTGTAGCAGTTTTTAGAATGAAG 58.011 33.333 7.11 0.00 42.59 3.02
379 380 9.204570 GTACTGTAGCAGTTTTTAGAATGAAGA 57.795 33.333 7.11 0.00 42.59 2.87
380 381 8.677148 ACTGTAGCAGTTTTTAGAATGAAGAA 57.323 30.769 0.00 0.00 42.59 2.52
381 382 9.120538 ACTGTAGCAGTTTTTAGAATGAAGAAA 57.879 29.630 0.00 0.00 42.59 2.52
382 383 9.604626 CTGTAGCAGTTTTTAGAATGAAGAAAG 57.395 33.333 0.00 0.00 0.00 2.62
383 384 8.567948 TGTAGCAGTTTTTAGAATGAAGAAAGG 58.432 33.333 0.00 0.00 0.00 3.11
384 385 7.823745 AGCAGTTTTTAGAATGAAGAAAGGA 57.176 32.000 0.00 0.00 0.00 3.36
385 386 8.237811 AGCAGTTTTTAGAATGAAGAAAGGAA 57.762 30.769 0.00 0.00 0.00 3.36
386 387 8.355913 AGCAGTTTTTAGAATGAAGAAAGGAAG 58.644 33.333 0.00 0.00 0.00 3.46
387 388 8.352942 GCAGTTTTTAGAATGAAGAAAGGAAGA 58.647 33.333 0.00 0.00 0.00 2.87
393 394 6.756299 AGAATGAAGAAAGGAAGATCAAGC 57.244 37.500 0.00 0.00 0.00 4.01
394 395 5.353678 AGAATGAAGAAAGGAAGATCAAGCG 59.646 40.000 0.00 0.00 0.00 4.68
395 396 3.338249 TGAAGAAAGGAAGATCAAGCGG 58.662 45.455 0.00 0.00 0.00 5.52
396 397 2.409948 AGAAAGGAAGATCAAGCGGG 57.590 50.000 0.00 0.00 0.00 6.13
397 398 1.909302 AGAAAGGAAGATCAAGCGGGA 59.091 47.619 0.00 0.00 0.00 5.14
398 399 2.093235 AGAAAGGAAGATCAAGCGGGAG 60.093 50.000 0.00 0.00 0.00 4.30
410 411 4.637489 CGGGAGCCAGCGATCGAG 62.637 72.222 21.57 10.27 0.00 4.04
411 412 4.959596 GGGAGCCAGCGATCGAGC 62.960 72.222 21.57 17.61 37.41 5.03
436 437 2.148687 CGATAGCCAGCGATCAAGC 58.851 57.895 12.31 0.00 34.91 4.01
437 438 1.612469 CGATAGCCAGCGATCAAGCG 61.612 60.000 12.31 0.00 43.00 4.68
438 439 0.319040 GATAGCCAGCGATCAAGCGA 60.319 55.000 7.73 0.00 43.00 4.93
439 440 0.319383 ATAGCCAGCGATCAAGCGAG 60.319 55.000 0.00 0.00 43.00 5.03
440 441 2.960957 TAGCCAGCGATCAAGCGAGC 62.961 60.000 0.00 0.00 43.00 5.03
482 483 3.813724 GGCCAGGCCCATGCTAGT 61.814 66.667 21.62 0.00 44.06 2.57
483 484 2.517875 GCCAGGCCCATGCTAGTG 60.518 66.667 0.00 0.00 37.74 2.74
484 485 3.047807 GCCAGGCCCATGCTAGTGA 62.048 63.158 0.00 0.00 37.74 3.41
485 486 1.153086 CCAGGCCCATGCTAGTGAC 60.153 63.158 0.00 0.00 37.74 3.67
486 487 1.603842 CAGGCCCATGCTAGTGACA 59.396 57.895 0.00 0.00 37.74 3.58
487 488 0.745845 CAGGCCCATGCTAGTGACAC 60.746 60.000 0.00 0.00 37.74 3.67
488 489 1.200760 AGGCCCATGCTAGTGACACA 61.201 55.000 8.59 0.00 37.74 3.72
489 490 0.745845 GGCCCATGCTAGTGACACAG 60.746 60.000 8.59 4.66 37.74 3.66
490 491 0.036010 GCCCATGCTAGTGACACAGT 60.036 55.000 8.59 0.00 33.53 3.55
491 492 1.730501 CCCATGCTAGTGACACAGTG 58.269 55.000 8.59 0.00 0.00 3.66
492 493 1.676916 CCCATGCTAGTGACACAGTGG 60.677 57.143 8.59 7.84 0.00 4.00
493 494 1.676916 CCATGCTAGTGACACAGTGGG 60.677 57.143 8.59 0.00 0.00 4.61
494 495 0.036010 ATGCTAGTGACACAGTGGGC 60.036 55.000 8.59 5.05 0.00 5.36
495 496 1.738099 GCTAGTGACACAGTGGGCG 60.738 63.158 8.59 0.00 0.00 6.13
496 497 1.738099 CTAGTGACACAGTGGGCGC 60.738 63.158 8.59 0.00 0.00 6.53
497 498 2.159819 CTAGTGACACAGTGGGCGCT 62.160 60.000 7.64 10.72 0.00 5.92
498 499 2.434658 TAGTGACACAGTGGGCGCTG 62.435 60.000 17.34 0.00 41.92 5.18
499 500 4.624364 TGACACAGTGGGCGCTGG 62.624 66.667 7.64 0.00 40.59 4.85
500 501 4.314440 GACACAGTGGGCGCTGGA 62.314 66.667 7.64 0.00 40.59 3.86
501 502 3.825160 GACACAGTGGGCGCTGGAA 62.825 63.158 7.64 0.00 40.59 3.53
502 503 2.360350 CACAGTGGGCGCTGGAAT 60.360 61.111 7.64 0.00 40.59 3.01
503 504 2.045926 ACAGTGGGCGCTGGAATC 60.046 61.111 7.64 0.00 40.59 2.52
504 505 3.197790 CAGTGGGCGCTGGAATCG 61.198 66.667 7.64 0.00 33.11 3.34
531 532 3.130160 GCTGAAGGCGCCAAGGAG 61.130 66.667 31.54 18.92 0.00 3.69
532 533 2.437359 CTGAAGGCGCCAAGGAGG 60.437 66.667 31.54 9.49 41.84 4.30
533 534 2.927856 TGAAGGCGCCAAGGAGGA 60.928 61.111 31.54 1.21 41.22 3.71
534 535 2.124942 GAAGGCGCCAAGGAGGAG 60.125 66.667 31.54 0.00 41.22 3.69
539 540 2.498726 CGCCAAGGAGGAGCTCTC 59.501 66.667 14.64 9.01 41.22 3.20
540 541 2.498726 GCCAAGGAGGAGCTCTCG 59.501 66.667 14.64 0.00 43.34 4.04
682 683 4.222847 CCCCGCTTCCCGCTACTC 62.223 72.222 0.00 0.00 36.13 2.59
765 773 4.511454 GGGCACAATTTTCTTGTTCTTTCC 59.489 41.667 0.00 0.00 0.00 3.13
863 871 2.623878 TTTGCCCTAAGTTCGTGACA 57.376 45.000 0.00 0.00 0.00 3.58
912 920 3.585862 TCTTGTCTAGCCAACACGAATC 58.414 45.455 0.00 0.00 0.00 2.52
959 967 1.273327 GCTGTATTTTTGGCTGCAGGT 59.727 47.619 17.12 0.00 0.00 4.00
1043 1051 3.952508 TGGCAGCACCGGTGACAT 61.953 61.111 38.30 19.63 44.55 3.06
1077 1085 1.892819 CTGACGACCTGCTCCACCAT 61.893 60.000 0.00 0.00 0.00 3.55
1155 1163 1.217882 GGCGAAATGTCTGGGTATCG 58.782 55.000 0.00 0.00 0.00 2.92
1326 1334 4.970662 AGATGATTGTTGTCAAATCCGG 57.029 40.909 0.00 0.00 37.11 5.14
1871 1879 7.073883 CGCTGGATTTTACATTGACTGATATG 58.926 38.462 0.00 0.00 0.00 1.78
1932 1940 4.339247 CAGGTGGCAATAAAGGTATTGGAG 59.661 45.833 8.19 0.00 44.65 3.86
1973 1981 3.253188 GCTACATTCAACAGCCTGACAAA 59.747 43.478 0.00 0.00 0.00 2.83
2074 2082 6.595716 ACAGAAACTTATCCTGCATCTTACAC 59.404 38.462 0.00 0.00 0.00 2.90
2084 2092 4.456911 CCTGCATCTTACACATGTGAGTTT 59.543 41.667 31.94 12.27 33.85 2.66
2095 2103 3.951680 ACATGTGAGTTTTCCGTTTTCCT 59.048 39.130 0.00 0.00 0.00 3.36
2100 2108 5.008217 TGTGAGTTTTCCGTTTTCCTATGTG 59.992 40.000 0.00 0.00 0.00 3.21
2111 2120 6.350110 CCGTTTTCCTATGTGGATCATTGTTT 60.350 38.462 0.00 0.00 45.68 2.83
2180 2189 2.608623 TCTCAGTGTGATCACCCTGAA 58.391 47.619 31.88 22.61 43.35 3.02
2192 2201 1.682854 CACCCTGAACAACATGCTGTT 59.317 47.619 14.15 14.15 42.08 3.16
2235 2244 4.282068 CAGTGAAACACAAAGACCATTCG 58.718 43.478 4.75 0.00 41.43 3.34
2236 2245 3.315191 AGTGAAACACAAAGACCATTCGG 59.685 43.478 4.75 0.00 41.43 4.30
2285 2294 3.585289 TCAACTGCCCACTAGGTGATAAA 59.415 43.478 0.00 0.00 36.98 1.40
2587 2599 5.392767 TGTGGCTTGTTTTGTTTAACTGA 57.607 34.783 0.00 0.00 0.00 3.41
2590 2602 5.635700 GTGGCTTGTTTTGTTTAACTGACAA 59.364 36.000 0.00 4.42 35.36 3.18
2591 2603 6.312672 GTGGCTTGTTTTGTTTAACTGACAAT 59.687 34.615 10.14 0.00 36.92 2.71
2631 2643 9.405587 GTGCTTGCTGTTATTCTTTAATTAACA 57.594 29.630 0.00 0.00 0.00 2.41
2696 2708 9.179909 CATAACTGTTATGGTAATTGGTTGGTA 57.820 33.333 25.74 0.00 39.42 3.25
2697 2709 7.457024 AACTGTTATGGTAATTGGTTGGTAC 57.543 36.000 0.00 0.00 0.00 3.34
2698 2710 6.786122 ACTGTTATGGTAATTGGTTGGTACT 58.214 36.000 0.00 0.00 0.00 2.73
2699 2711 6.882678 ACTGTTATGGTAATTGGTTGGTACTC 59.117 38.462 0.00 0.00 0.00 2.59
2700 2712 6.181908 TGTTATGGTAATTGGTTGGTACTCC 58.818 40.000 0.00 0.00 0.00 3.85
2701 2713 3.724732 TGGTAATTGGTTGGTACTCCC 57.275 47.619 0.00 0.00 0.00 4.30
2702 2714 3.261962 TGGTAATTGGTTGGTACTCCCT 58.738 45.455 0.00 0.00 0.00 4.20
2703 2715 3.264964 TGGTAATTGGTTGGTACTCCCTC 59.735 47.826 0.00 0.00 0.00 4.30
2704 2716 3.371273 GGTAATTGGTTGGTACTCCCTCC 60.371 52.174 0.00 0.00 0.00 4.30
2705 2717 0.909623 ATTGGTTGGTACTCCCTCCG 59.090 55.000 0.00 0.00 32.88 4.63
2706 2718 0.472352 TTGGTTGGTACTCCCTCCGT 60.472 55.000 0.00 0.00 32.88 4.69
2707 2719 0.472352 TGGTTGGTACTCCCTCCGTT 60.472 55.000 0.00 0.00 32.88 4.44
2708 2720 0.248565 GGTTGGTACTCCCTCCGTTC 59.751 60.000 0.00 0.00 0.00 3.95
2709 2721 0.248565 GTTGGTACTCCCTCCGTTCC 59.751 60.000 0.00 0.00 0.00 3.62
2710 2722 0.178926 TTGGTACTCCCTCCGTTCCA 60.179 55.000 0.00 0.00 31.17 3.53
2711 2723 0.178926 TGGTACTCCCTCCGTTCCAA 60.179 55.000 0.00 0.00 30.28 3.53
2712 2724 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2713 2725 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
2714 2726 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
2715 2727 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
2716 2728 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2717 2729 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2718 2730 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2719 2731 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2720 2732 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2721 2733 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2722 2734 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2723 2735 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2724 2736 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2725 2737 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2726 2738 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2727 2739 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2728 2740 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2729 2741 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2730 2742 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2731 2743 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2732 2744 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2733 2745 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2734 2746 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2772 2784 9.855021 AAAATTAAGTCATCTATTTTGGAACGG 57.145 29.630 0.00 0.00 31.14 4.44
2773 2785 8.801882 AATTAAGTCATCTATTTTGGAACGGA 57.198 30.769 0.00 0.00 0.00 4.69
2774 2786 7.843490 TTAAGTCATCTATTTTGGAACGGAG 57.157 36.000 0.00 0.00 0.00 4.63
2775 2787 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2776 2788 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2777 2789 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2778 2790 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2779 2791 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2900 2913 2.035632 AGTAGGTAGCATGTGAGAGGC 58.964 52.381 0.00 0.00 0.00 4.70
2958 2971 4.963276 ATTAGTTGCTTAAGCGCATTGA 57.037 36.364 21.97 6.01 45.83 2.57
2960 2973 2.154462 AGTTGCTTAAGCGCATTGACT 58.846 42.857 21.97 14.50 45.83 3.41
3080 3094 8.870879 GTCTGTTGTGAATAACTTACTGATACC 58.129 37.037 0.00 0.00 30.75 2.73
3088 3102 8.656806 TGAATAACTTACTGATACCCCTATTGG 58.343 37.037 0.00 0.00 0.00 3.16
3093 3107 6.619852 ACTTACTGATACCCCTATTGGACAAT 59.380 38.462 2.80 2.80 35.39 2.71
3153 3167 6.528537 TTTGTAGTGCATGCTTCCATAATT 57.471 33.333 20.33 0.00 0.00 1.40
3165 3179 9.017509 CATGCTTCCATAATTTACTATCATGGT 57.982 33.333 0.00 0.00 37.87 3.55
3237 3251 8.396272 AGCCATTATGTAGATCCAACATTAAC 57.604 34.615 14.54 3.50 38.49 2.01
3302 3316 8.694581 AAATTGGAATCATTTCAACCATGTTT 57.305 26.923 0.00 0.00 33.23 2.83
3355 3369 4.166725 TGCTCCCATTCTCCTACATTTGAT 59.833 41.667 0.00 0.00 0.00 2.57
3356 3370 4.759183 GCTCCCATTCTCCTACATTTGATC 59.241 45.833 0.00 0.00 0.00 2.92
3357 3371 5.455899 GCTCCCATTCTCCTACATTTGATCT 60.456 44.000 0.00 0.00 0.00 2.75
3358 3372 6.581388 TCCCATTCTCCTACATTTGATCTT 57.419 37.500 0.00 0.00 0.00 2.40
3359 3373 6.973642 TCCCATTCTCCTACATTTGATCTTT 58.026 36.000 0.00 0.00 0.00 2.52
3360 3374 7.413446 TCCCATTCTCCTACATTTGATCTTTT 58.587 34.615 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.867519 AACCCAGGAAGAAAAAGAGAAAAA 57.132 33.333 0.00 0.00 0.00 1.94
41 42 6.439058 TCAAACCCAGGAAGAAAAAGAGAAAA 59.561 34.615 0.00 0.00 0.00 2.29
42 43 5.955355 TCAAACCCAGGAAGAAAAAGAGAAA 59.045 36.000 0.00 0.00 0.00 2.52
43 44 5.515106 TCAAACCCAGGAAGAAAAAGAGAA 58.485 37.500 0.00 0.00 0.00 2.87
44 45 5.124036 TCAAACCCAGGAAGAAAAAGAGA 57.876 39.130 0.00 0.00 0.00 3.10
45 46 5.776744 CATCAAACCCAGGAAGAAAAAGAG 58.223 41.667 0.00 0.00 0.00 2.85
46 47 4.039124 GCATCAAACCCAGGAAGAAAAAGA 59.961 41.667 0.00 0.00 0.00 2.52
47 48 4.202243 TGCATCAAACCCAGGAAGAAAAAG 60.202 41.667 0.00 0.00 0.00 2.27
48 49 3.708631 TGCATCAAACCCAGGAAGAAAAA 59.291 39.130 0.00 0.00 0.00 1.94
49 50 3.303938 TGCATCAAACCCAGGAAGAAAA 58.696 40.909 0.00 0.00 0.00 2.29
50 51 2.956132 TGCATCAAACCCAGGAAGAAA 58.044 42.857 0.00 0.00 0.00 2.52
51 52 2.673775 TGCATCAAACCCAGGAAGAA 57.326 45.000 0.00 0.00 0.00 2.52
52 53 2.673775 TTGCATCAAACCCAGGAAGA 57.326 45.000 0.00 0.00 0.00 2.87
53 54 3.749665 TTTTGCATCAAACCCAGGAAG 57.250 42.857 0.00 0.00 32.79 3.46
54 55 3.305950 CGATTTTGCATCAAACCCAGGAA 60.306 43.478 0.00 0.00 32.79 3.36
55 56 2.230992 CGATTTTGCATCAAACCCAGGA 59.769 45.455 0.00 0.00 32.79 3.86
56 57 2.230992 TCGATTTTGCATCAAACCCAGG 59.769 45.455 0.00 0.00 32.79 4.45
57 58 3.574284 TCGATTTTGCATCAAACCCAG 57.426 42.857 0.00 0.00 32.79 4.45
58 59 3.509184 TCATCGATTTTGCATCAAACCCA 59.491 39.130 0.00 0.00 32.79 4.51
59 60 4.108699 TCATCGATTTTGCATCAAACCC 57.891 40.909 0.00 0.00 32.79 4.11
60 61 5.163513 AGTTCATCGATTTTGCATCAAACC 58.836 37.500 0.00 0.00 32.79 3.27
61 62 6.695292 AAGTTCATCGATTTTGCATCAAAC 57.305 33.333 0.00 0.00 32.79 2.93
62 63 7.712264 AAAAGTTCATCGATTTTGCATCAAA 57.288 28.000 0.00 0.00 0.00 2.69
63 64 7.712264 AAAAAGTTCATCGATTTTGCATCAA 57.288 28.000 0.00 0.00 0.00 2.57
116 117 9.878599 CGAATTTGAGACAAAGTACACTAAAAT 57.121 29.630 0.00 0.00 0.00 1.82
117 118 9.100554 TCGAATTTGAGACAAAGTACACTAAAA 57.899 29.630 0.00 0.00 0.00 1.52
118 119 8.651391 TCGAATTTGAGACAAAGTACACTAAA 57.349 30.769 0.00 0.00 0.00 1.85
119 120 8.708742 CATCGAATTTGAGACAAAGTACACTAA 58.291 33.333 1.10 0.00 0.00 2.24
120 121 8.085909 TCATCGAATTTGAGACAAAGTACACTA 58.914 33.333 1.10 0.00 0.00 2.74
121 122 6.929049 TCATCGAATTTGAGACAAAGTACACT 59.071 34.615 1.10 0.00 0.00 3.55
122 123 7.117241 TCATCGAATTTGAGACAAAGTACAC 57.883 36.000 1.10 0.00 0.00 2.90
123 124 7.441157 AGTTCATCGAATTTGAGACAAAGTACA 59.559 33.333 1.10 0.00 0.00 2.90
124 125 7.797819 AGTTCATCGAATTTGAGACAAAGTAC 58.202 34.615 1.10 0.00 0.00 2.73
125 126 7.962964 AGTTCATCGAATTTGAGACAAAGTA 57.037 32.000 1.10 0.00 0.00 2.24
126 127 6.867662 AGTTCATCGAATTTGAGACAAAGT 57.132 33.333 1.10 0.00 0.00 2.66
127 128 8.566008 AAAAGTTCATCGAATTTGAGACAAAG 57.434 30.769 1.10 0.00 0.00 2.77
128 129 8.925161 AAAAAGTTCATCGAATTTGAGACAAA 57.075 26.923 1.10 0.00 0.00 2.83
211 212 6.692681 CAGAAAAGTTCATCGAGCTTGAAAAA 59.307 34.615 7.99 2.52 33.62 1.94
212 213 6.038161 TCAGAAAAGTTCATCGAGCTTGAAAA 59.962 34.615 7.99 2.90 33.62 2.29
213 214 5.527214 TCAGAAAAGTTCATCGAGCTTGAAA 59.473 36.000 7.99 0.00 33.62 2.69
214 215 5.056480 TCAGAAAAGTTCATCGAGCTTGAA 58.944 37.500 7.99 0.90 33.62 2.69
215 216 4.631131 TCAGAAAAGTTCATCGAGCTTGA 58.369 39.130 6.01 6.01 33.62 3.02
216 217 4.997905 TCAGAAAAGTTCATCGAGCTTG 57.002 40.909 0.00 0.00 33.62 4.01
217 218 5.296780 TGTTTCAGAAAAGTTCATCGAGCTT 59.703 36.000 0.00 0.00 34.73 3.74
218 219 4.816385 TGTTTCAGAAAAGTTCATCGAGCT 59.184 37.500 0.00 0.00 0.00 4.09
219 220 4.906437 GTGTTTCAGAAAAGTTCATCGAGC 59.094 41.667 0.00 0.00 0.00 5.03
220 221 5.051039 TCGTGTTTCAGAAAAGTTCATCGAG 60.051 40.000 0.00 0.00 0.00 4.04
221 222 4.806775 TCGTGTTTCAGAAAAGTTCATCGA 59.193 37.500 0.00 0.00 0.00 3.59
222 223 5.078153 TCGTGTTTCAGAAAAGTTCATCG 57.922 39.130 0.00 0.00 0.00 3.84
223 224 6.658831 TCATCGTGTTTCAGAAAAGTTCATC 58.341 36.000 0.00 0.00 0.00 2.92
224 225 6.618287 TCATCGTGTTTCAGAAAAGTTCAT 57.382 33.333 0.00 0.00 0.00 2.57
225 226 5.504010 GCTCATCGTGTTTCAGAAAAGTTCA 60.504 40.000 0.00 0.00 0.00 3.18
226 227 4.906437 GCTCATCGTGTTTCAGAAAAGTTC 59.094 41.667 0.00 0.00 0.00 3.01
227 228 4.576463 AGCTCATCGTGTTTCAGAAAAGTT 59.424 37.500 0.00 0.00 0.00 2.66
228 229 4.130118 AGCTCATCGTGTTTCAGAAAAGT 58.870 39.130 0.00 0.00 0.00 2.66
229 230 4.739046 AGCTCATCGTGTTTCAGAAAAG 57.261 40.909 0.00 0.00 0.00 2.27
230 231 5.499139 AAAGCTCATCGTGTTTCAGAAAA 57.501 34.783 0.00 0.00 0.00 2.29
231 232 5.499139 AAAAGCTCATCGTGTTTCAGAAA 57.501 34.783 0.00 0.00 0.00 2.52
232 233 5.499139 AAAAAGCTCATCGTGTTTCAGAA 57.501 34.783 0.00 0.00 0.00 3.02
297 298 8.675504 GCTACTGTATGTACTCTTGTCTTAGAA 58.324 37.037 0.00 0.00 0.00 2.10
298 299 7.827729 TGCTACTGTATGTACTCTTGTCTTAGA 59.172 37.037 0.00 0.00 0.00 2.10
299 300 7.986562 TGCTACTGTATGTACTCTTGTCTTAG 58.013 38.462 0.00 0.00 0.00 2.18
300 301 7.933215 TGCTACTGTATGTACTCTTGTCTTA 57.067 36.000 0.00 0.00 0.00 2.10
301 302 6.835819 TGCTACTGTATGTACTCTTGTCTT 57.164 37.500 0.00 0.00 0.00 3.01
302 303 6.835819 TTGCTACTGTATGTACTCTTGTCT 57.164 37.500 0.00 0.00 0.00 3.41
303 304 6.310711 GGTTTGCTACTGTATGTACTCTTGTC 59.689 42.308 0.00 0.00 0.00 3.18
304 305 6.164176 GGTTTGCTACTGTATGTACTCTTGT 58.836 40.000 0.00 0.00 0.00 3.16
305 306 5.288712 CGGTTTGCTACTGTATGTACTCTTG 59.711 44.000 0.00 0.00 0.00 3.02
306 307 5.408356 CGGTTTGCTACTGTATGTACTCTT 58.592 41.667 0.00 0.00 0.00 2.85
307 308 4.142227 CCGGTTTGCTACTGTATGTACTCT 60.142 45.833 0.00 0.00 0.00 3.24
308 309 4.110482 CCGGTTTGCTACTGTATGTACTC 58.890 47.826 0.00 0.00 0.00 2.59
309 310 3.512724 ACCGGTTTGCTACTGTATGTACT 59.487 43.478 0.00 0.00 0.00 2.73
310 311 3.853475 ACCGGTTTGCTACTGTATGTAC 58.147 45.455 0.00 0.00 0.00 2.90
311 312 4.540359 AACCGGTTTGCTACTGTATGTA 57.460 40.909 15.86 0.00 0.00 2.29
312 313 3.412237 AACCGGTTTGCTACTGTATGT 57.588 42.857 15.86 0.00 0.00 2.29
313 314 4.759516 AAAACCGGTTTGCTACTGTATG 57.240 40.909 32.23 0.00 32.36 2.39
337 338 9.856488 TGCTACAGTACAGACTATTTTTCTTAG 57.144 33.333 0.00 0.00 33.32 2.18
338 339 9.856488 CTGCTACAGTACAGACTATTTTTCTTA 57.144 33.333 0.00 0.00 35.90 2.10
339 340 8.368668 ACTGCTACAGTACAGACTATTTTTCTT 58.631 33.333 13.84 0.00 43.46 2.52
340 341 7.897864 ACTGCTACAGTACAGACTATTTTTCT 58.102 34.615 13.84 0.00 43.46 2.52
341 342 8.535690 AACTGCTACAGTACAGACTATTTTTC 57.464 34.615 13.84 0.00 44.62 2.29
342 343 8.904099 AAACTGCTACAGTACAGACTATTTTT 57.096 30.769 13.84 4.14 44.62 1.94
343 344 8.904099 AAAACTGCTACAGTACAGACTATTTT 57.096 30.769 13.84 8.84 44.62 1.82
344 345 8.904099 AAAAACTGCTACAGTACAGACTATTT 57.096 30.769 13.84 0.00 44.62 1.40
345 346 9.640963 CTAAAAACTGCTACAGTACAGACTATT 57.359 33.333 13.84 7.90 44.62 1.73
346 347 9.021807 TCTAAAAACTGCTACAGTACAGACTAT 57.978 33.333 13.84 4.29 44.62 2.12
347 348 8.400184 TCTAAAAACTGCTACAGTACAGACTA 57.600 34.615 13.84 3.34 44.62 2.59
348 349 7.286215 TCTAAAAACTGCTACAGTACAGACT 57.714 36.000 13.84 2.51 44.62 3.24
349 350 7.941795 TTCTAAAAACTGCTACAGTACAGAC 57.058 36.000 13.84 0.00 44.62 3.51
350 351 8.364894 TCATTCTAAAAACTGCTACAGTACAGA 58.635 33.333 13.84 0.00 44.62 3.41
351 352 8.534333 TCATTCTAAAAACTGCTACAGTACAG 57.466 34.615 0.00 8.02 44.62 2.74
352 353 8.896320 TTCATTCTAAAAACTGCTACAGTACA 57.104 30.769 0.00 0.00 44.62 2.90
353 354 9.204570 TCTTCATTCTAAAAACTGCTACAGTAC 57.795 33.333 0.00 0.00 44.62 2.73
354 355 9.772973 TTCTTCATTCTAAAAACTGCTACAGTA 57.227 29.630 0.00 0.00 44.62 2.74
356 357 9.604626 CTTTCTTCATTCTAAAAACTGCTACAG 57.395 33.333 0.00 0.00 37.52 2.74
357 358 8.567948 CCTTTCTTCATTCTAAAAACTGCTACA 58.432 33.333 0.00 0.00 0.00 2.74
358 359 8.784043 TCCTTTCTTCATTCTAAAAACTGCTAC 58.216 33.333 0.00 0.00 0.00 3.58
359 360 8.918202 TCCTTTCTTCATTCTAAAAACTGCTA 57.082 30.769 0.00 0.00 0.00 3.49
360 361 7.823745 TCCTTTCTTCATTCTAAAAACTGCT 57.176 32.000 0.00 0.00 0.00 4.24
361 362 8.352942 TCTTCCTTTCTTCATTCTAAAAACTGC 58.647 33.333 0.00 0.00 0.00 4.40
367 368 8.734386 GCTTGATCTTCCTTTCTTCATTCTAAA 58.266 33.333 0.00 0.00 0.00 1.85
368 369 7.065085 CGCTTGATCTTCCTTTCTTCATTCTAA 59.935 37.037 0.00 0.00 0.00 2.10
369 370 6.536582 CGCTTGATCTTCCTTTCTTCATTCTA 59.463 38.462 0.00 0.00 0.00 2.10
370 371 5.353678 CGCTTGATCTTCCTTTCTTCATTCT 59.646 40.000 0.00 0.00 0.00 2.40
371 372 5.448360 CCGCTTGATCTTCCTTTCTTCATTC 60.448 44.000 0.00 0.00 0.00 2.67
372 373 4.397417 CCGCTTGATCTTCCTTTCTTCATT 59.603 41.667 0.00 0.00 0.00 2.57
373 374 3.944015 CCGCTTGATCTTCCTTTCTTCAT 59.056 43.478 0.00 0.00 0.00 2.57
374 375 3.338249 CCGCTTGATCTTCCTTTCTTCA 58.662 45.455 0.00 0.00 0.00 3.02
375 376 2.680339 CCCGCTTGATCTTCCTTTCTTC 59.320 50.000 0.00 0.00 0.00 2.87
376 377 2.305927 TCCCGCTTGATCTTCCTTTCTT 59.694 45.455 0.00 0.00 0.00 2.52
377 378 1.909302 TCCCGCTTGATCTTCCTTTCT 59.091 47.619 0.00 0.00 0.00 2.52
378 379 2.284190 CTCCCGCTTGATCTTCCTTTC 58.716 52.381 0.00 0.00 0.00 2.62
379 380 1.680249 GCTCCCGCTTGATCTTCCTTT 60.680 52.381 0.00 0.00 0.00 3.11
380 381 0.107459 GCTCCCGCTTGATCTTCCTT 60.107 55.000 0.00 0.00 0.00 3.36
381 382 1.524482 GCTCCCGCTTGATCTTCCT 59.476 57.895 0.00 0.00 0.00 3.36
382 383 1.524849 GGCTCCCGCTTGATCTTCC 60.525 63.158 0.00 0.00 36.09 3.46
383 384 0.813210 CTGGCTCCCGCTTGATCTTC 60.813 60.000 0.00 0.00 36.09 2.87
384 385 1.222936 CTGGCTCCCGCTTGATCTT 59.777 57.895 0.00 0.00 36.09 2.40
385 386 2.906458 CTGGCTCCCGCTTGATCT 59.094 61.111 0.00 0.00 36.09 2.75
386 387 2.899339 GCTGGCTCCCGCTTGATC 60.899 66.667 0.00 0.00 36.09 2.92
387 388 4.845580 CGCTGGCTCCCGCTTGAT 62.846 66.667 1.05 0.00 36.09 2.57
389 390 4.845580 ATCGCTGGCTCCCGCTTG 62.846 66.667 1.05 0.00 36.09 4.01
390 391 4.537433 GATCGCTGGCTCCCGCTT 62.537 66.667 1.05 0.00 36.09 4.68
393 394 4.637489 CTCGATCGCTGGCTCCCG 62.637 72.222 11.09 0.00 0.00 5.14
394 395 4.959596 GCTCGATCGCTGGCTCCC 62.960 72.222 11.09 0.00 0.00 4.30
395 396 3.910490 AGCTCGATCGCTGGCTCC 61.910 66.667 18.97 1.35 39.16 4.70
401 402 4.887987 GCTGCCAGCTCGATCGCT 62.888 66.667 10.04 0.00 41.90 4.93
403 404 2.463675 TATCGCTGCCAGCTCGATCG 62.464 60.000 15.80 9.36 42.18 3.69
404 405 0.732196 CTATCGCTGCCAGCTCGATC 60.732 60.000 15.80 0.00 42.18 3.69
405 406 1.288439 CTATCGCTGCCAGCTCGAT 59.712 57.895 15.80 13.10 44.05 3.59
406 407 2.724377 CTATCGCTGCCAGCTCGA 59.276 61.111 15.80 5.91 39.60 4.04
407 408 3.034923 GCTATCGCTGCCAGCTCG 61.035 66.667 15.80 0.00 39.60 5.03
414 415 2.356793 ATCGCTGGCTATCGCTGC 60.357 61.111 0.00 0.00 36.09 5.25
415 416 0.598419 TTGATCGCTGGCTATCGCTG 60.598 55.000 3.35 0.00 36.09 5.18
416 417 0.319383 CTTGATCGCTGGCTATCGCT 60.319 55.000 3.35 0.00 36.09 4.93
417 418 1.895280 GCTTGATCGCTGGCTATCGC 61.895 60.000 3.35 0.00 0.00 4.58
418 419 1.612469 CGCTTGATCGCTGGCTATCG 61.612 60.000 3.35 0.00 0.00 2.92
419 420 0.319040 TCGCTTGATCGCTGGCTATC 60.319 55.000 0.94 0.94 0.00 2.08
420 421 0.319383 CTCGCTTGATCGCTGGCTAT 60.319 55.000 0.00 0.00 0.00 2.97
421 422 1.066422 CTCGCTTGATCGCTGGCTA 59.934 57.895 0.00 0.00 0.00 3.93
422 423 2.202851 CTCGCTTGATCGCTGGCT 60.203 61.111 0.00 0.00 0.00 4.75
423 424 3.934684 GCTCGCTTGATCGCTGGC 61.935 66.667 0.00 0.00 0.00 4.85
424 425 3.624300 CGCTCGCTTGATCGCTGG 61.624 66.667 0.00 0.00 0.00 4.85
425 426 3.624300 CCGCTCGCTTGATCGCTG 61.624 66.667 0.00 0.00 30.18 5.18
428 429 3.624300 CTGCCGCTCGCTTGATCG 61.624 66.667 0.00 0.00 38.78 3.69
429 430 3.934684 GCTGCCGCTCGCTTGATC 61.935 66.667 0.00 0.00 38.78 2.92
430 431 4.765449 TGCTGCCGCTCGCTTGAT 62.765 61.111 0.70 0.00 38.78 2.57
466 467 2.517875 CACTAGCATGGGCCTGGC 60.518 66.667 11.05 11.05 42.56 4.85
467 468 1.153086 GTCACTAGCATGGGCCTGG 60.153 63.158 4.53 0.00 42.56 4.45
468 469 0.745845 GTGTCACTAGCATGGGCCTG 60.746 60.000 4.53 1.41 42.56 4.85
469 470 1.200760 TGTGTCACTAGCATGGGCCT 61.201 55.000 4.53 0.00 42.56 5.19
470 471 0.745845 CTGTGTCACTAGCATGGGCC 60.746 60.000 4.27 0.00 42.56 5.80
471 472 0.036010 ACTGTGTCACTAGCATGGGC 60.036 55.000 4.27 0.00 41.61 5.36
472 473 1.676916 CCACTGTGTCACTAGCATGGG 60.677 57.143 7.08 0.00 0.00 4.00
473 474 1.676916 CCCACTGTGTCACTAGCATGG 60.677 57.143 7.08 4.85 0.00 3.66
474 475 1.730501 CCCACTGTGTCACTAGCATG 58.269 55.000 7.08 0.00 0.00 4.06
475 476 0.036010 GCCCACTGTGTCACTAGCAT 60.036 55.000 7.08 0.00 0.00 3.79
476 477 1.371183 GCCCACTGTGTCACTAGCA 59.629 57.895 7.08 0.00 0.00 3.49
477 478 1.738099 CGCCCACTGTGTCACTAGC 60.738 63.158 7.08 0.00 0.00 3.42
478 479 1.738099 GCGCCCACTGTGTCACTAG 60.738 63.158 7.08 3.01 0.00 2.57
479 480 2.207229 AGCGCCCACTGTGTCACTA 61.207 57.895 2.29 0.00 0.00 2.74
480 481 3.550431 AGCGCCCACTGTGTCACT 61.550 61.111 2.29 0.00 0.00 3.41
481 482 3.349006 CAGCGCCCACTGTGTCAC 61.349 66.667 2.29 0.00 32.78 3.67
482 483 4.624364 CCAGCGCCCACTGTGTCA 62.624 66.667 2.29 0.00 35.83 3.58
483 484 3.825160 TTCCAGCGCCCACTGTGTC 62.825 63.158 2.29 0.00 35.83 3.67
484 485 3.196207 ATTCCAGCGCCCACTGTGT 62.196 57.895 2.29 0.00 35.83 3.72
485 486 2.360350 ATTCCAGCGCCCACTGTG 60.360 61.111 2.29 0.00 35.83 3.66
486 487 2.045926 GATTCCAGCGCCCACTGT 60.046 61.111 2.29 0.00 35.83 3.55
487 488 3.197790 CGATTCCAGCGCCCACTG 61.198 66.667 2.29 0.00 37.42 3.66
514 515 3.130160 CTCCTTGGCGCCTTCAGC 61.130 66.667 29.70 0.00 38.52 4.26
515 516 2.437359 CCTCCTTGGCGCCTTCAG 60.437 66.667 29.70 19.80 0.00 3.02
516 517 2.927856 TCCTCCTTGGCGCCTTCA 60.928 61.111 29.70 10.82 35.26 3.02
517 518 2.124942 CTCCTCCTTGGCGCCTTC 60.125 66.667 29.70 0.50 35.26 3.46
518 519 4.416738 GCTCCTCCTTGGCGCCTT 62.417 66.667 29.70 0.00 40.51 4.35
521 522 3.731653 GAGAGCTCCTCCTTGGCGC 62.732 68.421 10.93 0.00 46.39 6.53
522 523 2.498726 GAGAGCTCCTCCTTGGCG 59.501 66.667 10.93 0.00 35.87 5.69
523 524 2.498726 CGAGAGCTCCTCCTTGGC 59.501 66.667 10.93 0.00 38.71 4.52
524 525 2.430610 CCCGAGAGCTCCTCCTTGG 61.431 68.421 10.93 5.00 38.71 3.61
525 526 3.087666 GCCCGAGAGCTCCTCCTTG 62.088 68.421 10.93 0.00 38.71 3.61
526 527 2.762043 GCCCGAGAGCTCCTCCTT 60.762 66.667 10.93 0.00 38.71 3.36
564 565 3.729906 GATTTGCCGCTCGCTGCTG 62.730 63.158 6.84 0.00 40.11 4.41
565 566 3.503363 GATTTGCCGCTCGCTGCT 61.503 61.111 6.84 0.00 40.11 4.24
682 683 1.337917 CCAGAGCAGGATGATGGATCG 60.338 57.143 0.00 0.00 39.69 3.69
765 773 4.473477 AAACCTTATCAGAAGACGAGGG 57.527 45.455 0.00 0.00 34.87 4.30
912 920 8.430801 ACCTACATACAGTAAAGTACTACTCG 57.569 38.462 0.00 0.00 37.23 4.18
959 967 1.758440 GAGCAGGTGGTGTGTGAGGA 61.758 60.000 0.00 0.00 0.00 3.71
1313 1321 1.209127 CACGGCCGGATTTGACAAC 59.791 57.895 31.76 0.00 0.00 3.32
1396 1404 1.405933 GGTGAAGGCATTTCCAATGGC 60.406 52.381 13.66 13.66 43.88 4.40
1876 1884 9.612066 CACCCAAAATGTAAAATATGCCTAAAT 57.388 29.630 0.00 0.00 0.00 1.40
1932 1940 2.014068 GCACACCTTAGCACATCCCTC 61.014 57.143 0.00 0.00 0.00 4.30
1973 1981 3.470709 CACCATTCACCAAGCGATAGAT 58.529 45.455 0.00 0.00 39.76 1.98
2074 2082 4.568152 AGGAAAACGGAAAACTCACATG 57.432 40.909 0.00 0.00 0.00 3.21
2111 2120 4.925054 GTGCATTAGCTTCATCTGCAAAAA 59.075 37.500 0.00 0.00 43.73 1.94
2192 2201 3.031736 GCAGGTTGGATCTCCTACTACA 58.968 50.000 10.03 0.00 40.75 2.74
2235 2244 8.029642 TCGATTTTCTTAAGATTCTCACAACC 57.970 34.615 5.89 0.00 0.00 3.77
2236 2245 9.878599 TTTCGATTTTCTTAAGATTCTCACAAC 57.121 29.630 5.89 0.00 0.00 3.32
2285 2294 3.007940 TCCTCACAATGACGTGGATTCTT 59.992 43.478 0.00 0.00 37.50 2.52
2587 2599 2.836262 CACAAACATGTGGGCAATTGT 58.164 42.857 7.40 1.90 36.24 2.71
2631 2643 7.654022 TGTCAAAGATAAAGTTTTGGGAGTT 57.346 32.000 0.00 0.00 35.52 3.01
2642 2654 9.490663 GATGTTCCGTAAATGTCAAAGATAAAG 57.509 33.333 0.00 0.00 0.00 1.85
2696 2708 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2697 2709 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2698 2710 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2699 2711 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2700 2712 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2701 2713 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2702 2714 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2703 2715 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2704 2716 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2705 2717 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2706 2718 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2707 2719 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2708 2720 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2746 2758 9.855021 CCGTTCCAAAATAGATGACTTAATTTT 57.145 29.630 0.00 0.00 33.07 1.82
2747 2759 9.238368 TCCGTTCCAAAATAGATGACTTAATTT 57.762 29.630 0.00 0.00 0.00 1.82
2748 2760 8.801882 TCCGTTCCAAAATAGATGACTTAATT 57.198 30.769 0.00 0.00 0.00 1.40
2749 2761 7.499232 CCTCCGTTCCAAAATAGATGACTTAAT 59.501 37.037 0.00 0.00 0.00 1.40
2750 2762 6.821665 CCTCCGTTCCAAAATAGATGACTTAA 59.178 38.462 0.00 0.00 0.00 1.85
2751 2763 6.346096 CCTCCGTTCCAAAATAGATGACTTA 58.654 40.000 0.00 0.00 0.00 2.24
2752 2764 5.186198 CCTCCGTTCCAAAATAGATGACTT 58.814 41.667 0.00 0.00 0.00 3.01
2753 2765 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2754 2766 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2755 2767 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2756 2768 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2757 2769 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2758 2770 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2759 2771 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2760 2772 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
2761 2773 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
2762 2774 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
2763 2775 2.027561 CACATACTCCCTCCGTTCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
2764 2776 1.553248 CACATACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
2765 2777 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2766 2778 1.192428 ACACATACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62
2767 2779 3.329929 AAACACATACTCCCTCCGTTC 57.670 47.619 0.00 0.00 0.00 3.95
2768 2780 5.183228 CAATAAACACATACTCCCTCCGTT 58.817 41.667 0.00 0.00 0.00 4.44
2769 2781 4.224370 ACAATAAACACATACTCCCTCCGT 59.776 41.667 0.00 0.00 0.00 4.69
2770 2782 4.766375 ACAATAAACACATACTCCCTCCG 58.234 43.478 0.00 0.00 0.00 4.63
2771 2783 7.336396 AGTTACAATAAACACATACTCCCTCC 58.664 38.462 0.00 0.00 0.00 4.30
2772 2784 7.222224 CGAGTTACAATAAACACATACTCCCTC 59.778 40.741 0.00 0.00 0.00 4.30
2773 2785 7.039882 CGAGTTACAATAAACACATACTCCCT 58.960 38.462 0.00 0.00 0.00 4.20
2774 2786 6.257193 CCGAGTTACAATAAACACATACTCCC 59.743 42.308 0.00 0.00 0.00 4.30
2775 2787 6.815142 ACCGAGTTACAATAAACACATACTCC 59.185 38.462 0.00 0.00 0.00 3.85
2776 2788 7.823149 ACCGAGTTACAATAAACACATACTC 57.177 36.000 0.00 0.00 0.00 2.59
2777 2789 9.880157 ATAACCGAGTTACAATAAACACATACT 57.120 29.630 0.00 0.00 30.49 2.12
2779 2791 9.872721 TGATAACCGAGTTACAATAAACACATA 57.127 29.630 0.00 0.00 30.49 2.29
2820 2832 5.533528 TCAAATACCTCGTCAGGAATCGATA 59.466 40.000 0.00 0.00 43.65 2.92
2900 2913 3.951680 ACAAGTTGGTCCTAAAACACAGG 59.048 43.478 7.96 0.00 34.20 4.00
3070 3084 8.014263 TCTATTGTCCAATAGGGGTATCAGTAA 58.986 37.037 21.09 1.57 46.32 2.24
3080 3094 7.922811 GCTTTTTCAATCTATTGTCCAATAGGG 59.077 37.037 21.09 13.71 46.32 3.53
3088 3102 9.561270 GGTTAGAAGCTTTTTCAATCTATTGTC 57.439 33.333 0.00 0.00 38.84 3.18
3093 3107 5.123344 GGCGGTTAGAAGCTTTTTCAATCTA 59.877 40.000 0.00 0.00 0.00 1.98
3190 3204 8.551440 TGGCTACATTATAGCTCATATTCCAAT 58.449 33.333 5.94 0.00 40.25 3.16
3237 3251 1.688197 ACCACCCTTCATGCAACTTTG 59.312 47.619 0.00 0.00 0.00 2.77
3302 3316 2.093921 TCTCACAAGTCACAACGAACCA 60.094 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.