Multiple sequence alignment - TraesCS2A01G448000

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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 TraesCS2A01G448000 chr2A 100.000 4695 0 0 1 4695 696926529 696921835 0.000000e+00 8671.0
1 TraesCS2A01G448000 chr2A 86.620 142 12 5 2449 2590 754108734 754108600 2.930000e-32 150.0
2 TraesCS2A01G448000 chr2A 89.423 104 8 3 455 556 717955004 717955106 1.370000e-25 128.0
3 TraesCS2A01G448000 chr2D 94.441 3508 146 21 550 4032 556952238 556948755 0.000000e+00 5352.0
4 TraesCS2A01G448000 chr2D 94.549 587 23 6 4078 4664 556948737 556948160 0.000000e+00 898.0
5 TraesCS2A01G448000 chr2D 91.667 192 14 2 261 452 556952436 556952247 1.000000e-66 265.0
6 TraesCS2A01G448000 chr2D 91.818 110 8 1 2448 2557 622392476 622392368 8.140000e-33 152.0
7 TraesCS2A01G448000 chr2D 91.667 72 5 1 190 260 91365544 91365615 1.080000e-16 99.0
8 TraesCS2A01G448000 chr2B 93.300 3642 175 34 545 4170 664222691 664219103 0.000000e+00 5310.0
9 TraesCS2A01G448000 chr2B 90.150 467 25 7 4204 4666 664219107 664218658 5.230000e-164 588.0
10 TraesCS2A01G448000 chr2B 80.808 198 22 12 1 184 664223028 664222833 1.760000e-29 141.0
11 TraesCS2A01G448000 chr2B 92.391 92 7 0 457 548 315661560 315661651 1.060000e-26 132.0
12 TraesCS2A01G448000 chr4D 95.349 86 4 0 464 549 100820422 100820507 2.280000e-28 137.0
13 TraesCS2A01G448000 chr5B 92.391 92 7 0 464 555 8355944 8355853 1.060000e-26 132.0
14 TraesCS2A01G448000 chr5B 93.333 75 3 2 187 260 304128350 304128423 4.970000e-20 110.0
15 TraesCS2A01G448000 chr6B 92.308 91 7 0 460 550 713009719 713009629 3.810000e-26 130.0
16 TraesCS2A01G448000 chr1D 91.579 95 7 1 456 549 22957731 22957637 3.810000e-26 130.0
17 TraesCS2A01G448000 chr6A 89.423 104 8 3 451 552 182320846 182320744 1.370000e-25 128.0
18 TraesCS2A01G448000 chr6A 87.069 116 10 5 437 548 614018547 614018661 4.930000e-25 126.0
19 TraesCS2A01G448000 chr1A 88.350 103 12 0 448 550 288508786 288508684 1.770000e-24 124.0
20 TraesCS2A01G448000 chr1A 91.781 73 5 1 189 260 580149201 580149129 2.990000e-17 100.0
21 TraesCS2A01G448000 chrUn 89.286 84 7 2 178 260 8090042 8089960 2.310000e-18 104.0
22 TraesCS2A01G448000 chr5A 90.909 77 6 1 185 260 596040917 596040993 8.310000e-18 102.0
23 TraesCS2A01G448000 chr4B 91.781 73 5 1 189 260 437405211 437405139 2.990000e-17 100.0
24 TraesCS2A01G448000 chr5D 89.873 79 5 2 185 260 288133271 288133349 1.080000e-16 99.0
25 TraesCS2A01G448000 chr3B 90.667 75 6 1 187 260 240267885 240267811 1.080000e-16 99.0
26 TraesCS2A01G448000 chr7B 89.610 77 6 2 186 260 589915764 589915840 3.870000e-16 97.1


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 TraesCS2A01G448000 chr2A 696921835 696926529 4694 True 8671.000000 8671 100.000000 1 4695 1 chr2A.!!$R1 4694
1 TraesCS2A01G448000 chr2D 556948160 556952436 4276 True 2171.666667 5352 93.552333 261 4664 3 chr2D.!!$R2 4403
2 TraesCS2A01G448000 chr2B 664218658 664223028 4370 True 2013.000000 5310 88.086000 1 4666 3 chr2B.!!$R1 4665

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
306 324 0.096976 CGCCACGCTTTATGAGGTTG 59.903 55.0 0.00 0.0 0.00 3.77 F
399 423 0.177373 GGGTAGGGTGGTAAAGCGAG 59.823 60.0 0.00 0.0 0.00 5.03 F
2212 2332 0.036732 AAGCTGCTGACCAAATCGGA 59.963 50.0 1.35 0.0 38.63 4.55 F
2857 2977 0.179051 CAGCTGAATCCAGAGAGGCC 60.179 60.0 8.42 0.0 43.02 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2329 0.036952 TCTCTGCCTCAAGCTTTCCG 60.037 55.0 0.00 0.0 44.23 4.30 R
2374 2494 1.889545 ACAGCTGCACCTTCTTCTTC 58.110 50.0 15.27 0.0 0.00 2.87 R
3622 3742 0.102844 TTTGCTGCTGCTGTTTGGTC 59.897 50.0 17.00 0.0 40.48 4.02 R
4668 4798 0.318441 TGCTGCAGGTACACTCTGTC 59.682 55.0 17.12 0.0 34.89 3.51 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
29 30 0.732538 CGCCTTTCATGCGTTTTCCC 60.733 55.000 0.00 0.00 46.59 3.97
69 70 4.463879 CCGAGCAGCAGGGACCAG 62.464 72.222 0.00 0.00 0.00 4.00
71 72 2.947532 CGAGCAGCAGGGACCAGAA 61.948 63.158 0.00 0.00 0.00 3.02
72 73 1.376553 GAGCAGCAGGGACCAGAAC 60.377 63.158 0.00 0.00 0.00 3.01
73 74 2.116983 GAGCAGCAGGGACCAGAACA 62.117 60.000 0.00 0.00 0.00 3.18
74 75 1.001641 GCAGCAGGGACCAGAACAT 60.002 57.895 0.00 0.00 0.00 2.71
76 77 1.340017 GCAGCAGGGACCAGAACATAA 60.340 52.381 0.00 0.00 0.00 1.90
77 78 2.879756 GCAGCAGGGACCAGAACATAAA 60.880 50.000 0.00 0.00 0.00 1.40
80 81 5.380043 CAGCAGGGACCAGAACATAAATAT 58.620 41.667 0.00 0.00 0.00 1.28
81 82 6.533730 CAGCAGGGACCAGAACATAAATATA 58.466 40.000 0.00 0.00 0.00 0.86
82 83 7.170965 CAGCAGGGACCAGAACATAAATATAT 58.829 38.462 0.00 0.00 0.00 0.86
83 84 7.120285 CAGCAGGGACCAGAACATAAATATATG 59.880 40.741 0.00 0.00 43.79 1.78
86 102 9.170734 CAGGGACCAGAACATAAATATATGATG 57.829 37.037 3.03 6.40 41.25 3.07
88 104 9.911788 GGGACCAGAACATAAATATATGATGAT 57.088 33.333 12.62 3.54 41.25 2.45
105 121 7.634671 ATGATGATGATAAAAAGAGCACACA 57.365 32.000 0.00 0.00 0.00 3.72
106 122 6.845302 TGATGATGATAAAAAGAGCACACAC 58.155 36.000 0.00 0.00 0.00 3.82
111 127 4.278170 TGATAAAAAGAGCACACACCCAAG 59.722 41.667 0.00 0.00 0.00 3.61
112 128 1.402787 AAAAGAGCACACACCCAAGG 58.597 50.000 0.00 0.00 0.00 3.61
133 149 2.159240 GGGCGAATGAAAACAAGGGATC 60.159 50.000 0.00 0.00 0.00 3.36
134 150 2.491693 GGCGAATGAAAACAAGGGATCA 59.508 45.455 0.00 0.00 0.00 2.92
141 157 7.273381 CGAATGAAAACAAGGGATCACATTTAC 59.727 37.037 0.00 0.00 0.00 2.01
147 163 1.647084 GGATCACATTTACGCGGCC 59.353 57.895 12.47 0.00 0.00 6.13
168 184 3.181450 CCTTATTTTCCTCATCTCCGCCT 60.181 47.826 0.00 0.00 0.00 5.52
192 210 3.090598 CGCACACGCATCAAACAAT 57.909 47.368 0.00 0.00 38.40 2.71
193 211 2.239751 CGCACACGCATCAAACAATA 57.760 45.000 0.00 0.00 38.40 1.90
195 213 3.170505 CGCACACGCATCAAACAATAAT 58.829 40.909 0.00 0.00 38.40 1.28
198 216 5.455201 CGCACACGCATCAAACAATAATAAT 59.545 36.000 0.00 0.00 38.40 1.28
200 218 7.164990 CGCACACGCATCAAACAATAATAATAA 59.835 33.333 0.00 0.00 38.40 1.40
203 221 9.005180 ACACGCATCAAACAATAATAATAAACG 57.995 29.630 0.00 0.00 0.00 3.60
204 222 9.005180 CACGCATCAAACAATAATAATAAACGT 57.995 29.630 0.00 0.00 0.00 3.99
220 238 4.442350 AAACGTACAAAGAGTTACACGC 57.558 40.909 0.00 0.00 32.90 5.34
221 239 3.082698 ACGTACAAAGAGTTACACGCA 57.917 42.857 0.00 0.00 32.90 5.24
222 240 3.446799 ACGTACAAAGAGTTACACGCAA 58.553 40.909 0.00 0.00 32.90 4.85
223 241 4.053295 ACGTACAAAGAGTTACACGCAAT 58.947 39.130 0.00 0.00 32.90 3.56
224 242 4.508861 ACGTACAAAGAGTTACACGCAATT 59.491 37.500 0.00 0.00 32.90 2.32
225 243 5.691305 ACGTACAAAGAGTTACACGCAATTA 59.309 36.000 0.00 0.00 32.90 1.40
226 244 6.005289 CGTACAAAGAGTTACACGCAATTAC 58.995 40.000 0.00 0.00 0.00 1.89
227 245 5.994887 ACAAAGAGTTACACGCAATTACA 57.005 34.783 0.00 0.00 0.00 2.41
228 246 5.744490 ACAAAGAGTTACACGCAATTACAC 58.256 37.500 0.00 0.00 0.00 2.90
229 247 4.640805 AAGAGTTACACGCAATTACACG 57.359 40.909 0.00 0.00 0.00 4.49
230 248 2.410730 AGAGTTACACGCAATTACACGC 59.589 45.455 0.00 0.00 0.00 5.34
231 249 2.409975 AGTTACACGCAATTACACGCT 58.590 42.857 0.00 0.00 0.00 5.07
232 250 2.156891 AGTTACACGCAATTACACGCTG 59.843 45.455 0.00 0.00 0.00 5.18
233 251 2.067414 TACACGCAATTACACGCTGA 57.933 45.000 0.00 0.00 0.00 4.26
234 252 1.438651 ACACGCAATTACACGCTGAT 58.561 45.000 0.00 0.00 0.00 2.90
235 253 1.804151 ACACGCAATTACACGCTGATT 59.196 42.857 0.00 0.00 0.00 2.57
236 254 2.997303 ACACGCAATTACACGCTGATTA 59.003 40.909 0.00 0.00 0.00 1.75
237 255 3.062099 ACACGCAATTACACGCTGATTAG 59.938 43.478 0.00 0.00 0.00 1.73
238 256 2.607635 ACGCAATTACACGCTGATTAGG 59.392 45.455 0.00 0.00 0.00 2.69
239 257 2.863740 CGCAATTACACGCTGATTAGGA 59.136 45.455 0.00 0.00 0.00 2.94
240 258 3.494626 CGCAATTACACGCTGATTAGGAT 59.505 43.478 0.00 0.00 0.00 3.24
241 259 4.024893 CGCAATTACACGCTGATTAGGATT 60.025 41.667 0.00 0.00 0.00 3.01
242 260 5.504010 CGCAATTACACGCTGATTAGGATTT 60.504 40.000 0.00 0.00 0.00 2.17
243 261 6.265577 GCAATTACACGCTGATTAGGATTTT 58.734 36.000 0.00 0.00 0.00 1.82
244 262 6.751888 GCAATTACACGCTGATTAGGATTTTT 59.248 34.615 0.00 0.00 0.00 1.94
306 324 0.096976 CGCCACGCTTTATGAGGTTG 59.903 55.000 0.00 0.00 0.00 3.77
328 352 4.570772 TGCACAGAATAGAATTAGAACGGC 59.429 41.667 0.00 0.00 0.00 5.68
393 417 2.040935 CCCGGGGTAGGGTGGTAA 59.959 66.667 14.71 0.00 46.38 2.85
394 418 1.616025 CCCGGGGTAGGGTGGTAAA 60.616 63.158 14.71 0.00 46.38 2.01
395 419 1.629181 CCCGGGGTAGGGTGGTAAAG 61.629 65.000 14.71 0.00 46.38 1.85
396 420 1.222661 CGGGGTAGGGTGGTAAAGC 59.777 63.158 0.00 0.00 0.00 3.51
397 421 1.222661 GGGGTAGGGTGGTAAAGCG 59.777 63.158 0.00 0.00 0.00 4.68
398 422 1.266867 GGGGTAGGGTGGTAAAGCGA 61.267 60.000 0.00 0.00 0.00 4.93
399 423 0.177373 GGGTAGGGTGGTAAAGCGAG 59.823 60.000 0.00 0.00 0.00 5.03
400 424 0.461516 GGTAGGGTGGTAAAGCGAGC 60.462 60.000 0.00 0.00 0.00 5.03
401 425 0.804933 GTAGGGTGGTAAAGCGAGCG 60.805 60.000 0.00 0.00 0.00 5.03
402 426 0.966875 TAGGGTGGTAAAGCGAGCGA 60.967 55.000 0.00 0.00 0.00 4.93
403 427 1.810030 GGGTGGTAAAGCGAGCGAG 60.810 63.158 0.00 0.00 0.00 5.03
404 428 2.453638 GGTGGTAAAGCGAGCGAGC 61.454 63.158 0.00 0.00 37.41 5.03
424 448 3.945434 GCTGGCGCGGTGATCATG 61.945 66.667 8.83 0.00 0.00 3.07
425 449 2.202919 CTGGCGCGGTGATCATGA 60.203 61.111 8.83 0.00 0.00 3.07
426 450 2.511373 TGGCGCGGTGATCATGAC 60.511 61.111 8.83 0.00 0.00 3.06
427 451 3.630148 GGCGCGGTGATCATGACG 61.630 66.667 8.83 5.86 0.00 4.35
428 452 3.630148 GCGCGGTGATCATGACGG 61.630 66.667 8.83 9.23 0.00 4.79
429 453 2.961721 CGCGGTGATCATGACGGG 60.962 66.667 15.84 15.84 0.00 5.28
430 454 2.499205 GCGGTGATCATGACGGGA 59.501 61.111 15.82 0.00 0.00 5.14
431 455 1.153449 GCGGTGATCATGACGGGAA 60.153 57.895 15.82 0.00 0.00 3.97
432 456 0.532862 GCGGTGATCATGACGGGAAT 60.533 55.000 15.82 0.00 0.00 3.01
433 457 1.220529 CGGTGATCATGACGGGAATG 58.779 55.000 0.00 0.00 0.00 2.67
434 458 1.202521 CGGTGATCATGACGGGAATGA 60.203 52.381 0.00 0.29 38.37 2.57
435 459 2.213499 GGTGATCATGACGGGAATGAC 58.787 52.381 0.00 0.00 36.89 3.06
436 460 2.419990 GGTGATCATGACGGGAATGACA 60.420 50.000 0.00 0.00 36.89 3.58
437 461 2.609459 GTGATCATGACGGGAATGACAC 59.391 50.000 0.00 6.63 36.89 3.67
438 462 2.501316 TGATCATGACGGGAATGACACT 59.499 45.455 0.00 0.00 36.89 3.55
439 463 2.385013 TCATGACGGGAATGACACTG 57.615 50.000 0.00 0.00 0.00 3.66
440 464 0.729116 CATGACGGGAATGACACTGC 59.271 55.000 0.00 0.00 0.00 4.40
441 465 0.615331 ATGACGGGAATGACACTGCT 59.385 50.000 0.00 0.00 0.00 4.24
442 466 0.320683 TGACGGGAATGACACTGCTG 60.321 55.000 0.00 0.00 0.00 4.41
443 467 1.639298 GACGGGAATGACACTGCTGC 61.639 60.000 0.00 0.00 0.00 5.25
444 468 2.401766 CGGGAATGACACTGCTGCC 61.402 63.158 0.00 0.00 0.00 4.85
445 469 1.303561 GGGAATGACACTGCTGCCA 60.304 57.895 0.00 0.00 0.00 4.92
446 470 1.310933 GGGAATGACACTGCTGCCAG 61.311 60.000 0.00 0.00 44.80 4.85
458 482 4.555348 CTGCTGCCAGTAGTAGTAGTAC 57.445 50.000 7.01 7.01 36.41 2.73
459 483 4.200874 CTGCTGCCAGTAGTAGTAGTACT 58.799 47.826 14.57 14.57 42.49 2.73
460 484 4.597004 TGCTGCCAGTAGTAGTAGTACTT 58.403 43.478 15.34 0.00 40.23 2.24
461 485 5.748402 TGCTGCCAGTAGTAGTAGTACTTA 58.252 41.667 15.34 4.70 40.23 2.24
462 486 5.587844 TGCTGCCAGTAGTAGTAGTACTTAC 59.412 44.000 15.34 6.11 40.23 2.34
463 487 5.821995 GCTGCCAGTAGTAGTAGTACTTACT 59.178 44.000 15.34 8.36 44.71 2.24
464 488 6.989169 GCTGCCAGTAGTAGTAGTACTTACTA 59.011 42.308 15.34 5.52 42.57 1.82
476 500 5.700402 AGTACTTACTACTCCCTCCGTAA 57.300 43.478 0.00 0.00 34.13 3.18
477 501 6.067217 AGTACTTACTACTCCCTCCGTAAA 57.933 41.667 0.00 0.00 34.13 2.01
478 502 5.883115 AGTACTTACTACTCCCTCCGTAAAC 59.117 44.000 0.00 0.00 34.13 2.01
479 503 4.928263 ACTTACTACTCCCTCCGTAAACT 58.072 43.478 0.00 0.00 0.00 2.66
480 504 6.067217 ACTTACTACTCCCTCCGTAAACTA 57.933 41.667 0.00 0.00 0.00 2.24
481 505 6.485171 ACTTACTACTCCCTCCGTAAACTAA 58.515 40.000 0.00 0.00 0.00 2.24
482 506 7.122048 ACTTACTACTCCCTCCGTAAACTAAT 58.878 38.462 0.00 0.00 0.00 1.73
483 507 8.275040 ACTTACTACTCCCTCCGTAAACTAATA 58.725 37.037 0.00 0.00 0.00 0.98
484 508 9.294614 CTTACTACTCCCTCCGTAAACTAATAT 57.705 37.037 0.00 0.00 0.00 1.28
487 511 9.646522 ACTACTCCCTCCGTAAACTAATATAAA 57.353 33.333 0.00 0.00 0.00 1.40
490 514 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
491 515 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
492 516 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
493 517 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
494 518 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
605 703 2.633509 GCTGCCTTGCCCTTCACTG 61.634 63.158 0.00 0.00 0.00 3.66
618 716 1.768684 TTCACTGCACCTCCCTCCAC 61.769 60.000 0.00 0.00 0.00 4.02
619 717 2.205462 ACTGCACCTCCCTCCACT 59.795 61.111 0.00 0.00 0.00 4.00
620 718 1.915769 ACTGCACCTCCCTCCACTC 60.916 63.158 0.00 0.00 0.00 3.51
621 719 1.611851 CTGCACCTCCCTCCACTCT 60.612 63.158 0.00 0.00 0.00 3.24
622 720 1.610673 TGCACCTCCCTCCACTCTC 60.611 63.158 0.00 0.00 0.00 3.20
646 744 2.896745 AAAAACAGAGGCAGCAAAGG 57.103 45.000 0.00 0.00 0.00 3.11
700 798 4.023707 CACAAGAGACACTGATCAAAACCC 60.024 45.833 0.00 0.00 0.00 4.11
770 874 4.759205 AATTCCGCAGCCCCACCC 62.759 66.667 0.00 0.00 0.00 4.61
885 995 0.251209 GAAAACACCACCTCCCCCTC 60.251 60.000 0.00 0.00 0.00 4.30
905 1015 2.596851 CCCTCACCCACCACTCCTG 61.597 68.421 0.00 0.00 0.00 3.86
911 1021 3.721706 CCACCACTCCTGCCTCCC 61.722 72.222 0.00 0.00 0.00 4.30
932 1042 3.955234 GACTTCGCGCTCGCTGAGT 62.955 63.158 5.56 15.51 39.32 3.41
1050 1161 1.880340 CCGACGCTCTCTGCATTCC 60.880 63.158 0.00 0.00 43.06 3.01
1051 1162 1.880340 CGACGCTCTCTGCATTCCC 60.880 63.158 0.00 0.00 43.06 3.97
1053 1164 1.965754 GACGCTCTCTGCATTCCCCT 61.966 60.000 0.00 0.00 43.06 4.79
1074 1185 6.598064 CCCCTACGATTCTTTTATCACTGTTT 59.402 38.462 0.00 0.00 0.00 2.83
1075 1187 7.201617 CCCCTACGATTCTTTTATCACTGTTTC 60.202 40.741 0.00 0.00 0.00 2.78
1094 1206 5.710099 TGTTTCTATTTTGGAGTGATGGGTC 59.290 40.000 0.00 0.00 0.00 4.46
1099 1211 2.125106 GGAGTGATGGGTCGGCAC 60.125 66.667 0.00 0.00 0.00 5.01
1160 1277 2.235650 TGGAGCATAGCATAGATCTGGC 59.764 50.000 5.18 9.29 0.00 4.85
1192 1309 4.113815 TTGGGGATGGAGCTGCCG 62.114 66.667 1.53 0.00 40.66 5.69
1211 1328 2.422479 CCGAGTTCTTGATCTGACGGTA 59.578 50.000 0.00 0.00 35.40 4.02
1212 1329 3.487711 CCGAGTTCTTGATCTGACGGTAG 60.488 52.174 0.00 0.00 35.40 3.18
1535 1652 3.011517 CCACCACCCCTCCTCCTG 61.012 72.222 0.00 0.00 0.00 3.86
1588 1705 3.117589 GCACAAAGCATGCTTCCTG 57.882 52.632 32.01 27.58 44.79 3.86
1589 1706 1.012486 GCACAAAGCATGCTTCCTGC 61.012 55.000 31.07 31.07 44.79 4.85
1595 1712 3.637297 GCATGCTTCCTGCTTTAGC 57.363 52.632 11.37 0.00 43.37 3.09
1613 1730 7.549488 TGCTTTAGCTTTAGTGGAATCTTAGTC 59.451 37.037 0.00 0.00 42.66 2.59
1619 1739 6.367969 GCTTTAGTGGAATCTTAGTCGTTTGA 59.632 38.462 0.00 0.00 0.00 2.69
1648 1768 3.651980 GAAGCAGGGGAAGGCTGGG 62.652 68.421 0.00 0.00 40.93 4.45
1660 1780 2.194326 GCTGGGAAGCCATCTCCC 59.806 66.667 0.64 0.64 43.82 4.30
1693 1813 3.710722 AAGCCGTCCCAGGAGCTG 61.711 66.667 0.00 0.00 35.30 4.24
1759 1879 0.687354 GTCAGCTGGTGGAGAAGGAA 59.313 55.000 15.13 0.00 0.00 3.36
1786 1906 0.772124 AGGGCAAGGTTCTGGAGGAA 60.772 55.000 0.00 0.00 0.00 3.36
1909 2029 3.978272 CCTGAGCAGGTGAGCAAC 58.022 61.111 8.38 0.00 43.61 4.17
1910 2030 1.071987 CCTGAGCAGGTGAGCAACA 59.928 57.895 8.38 0.00 43.61 3.33
1921 2041 2.416431 GGTGAGCAACAATGATTCTGCC 60.416 50.000 5.42 0.04 35.33 4.85
2204 2324 2.125350 CGAGGGAAGCTGCTGACC 60.125 66.667 1.35 8.94 0.00 4.02
2209 2329 0.813821 GGGAAGCTGCTGACCAAATC 59.186 55.000 21.61 7.41 0.00 2.17
2212 2332 0.036732 AAGCTGCTGACCAAATCGGA 59.963 50.000 1.35 0.00 38.63 4.55
2249 2369 6.489361 AGAGAATTCTGTGTTGAAGCTTGAAT 59.511 34.615 14.00 1.55 30.72 2.57
2252 2372 3.968649 TCTGTGTTGAAGCTTGAATTGC 58.031 40.909 2.10 0.00 0.00 3.56
2362 2482 5.391736 GGAATGCTCAAAGTCAGATGAGTTG 60.392 44.000 3.74 2.45 43.91 3.16
2366 2486 4.825422 CTCAAAGTCAGATGAGTTGGCTA 58.175 43.478 3.74 0.00 38.57 3.93
2369 2489 5.645067 TCAAAGTCAGATGAGTTGGCTAATG 59.355 40.000 3.74 0.00 37.72 1.90
2372 2492 5.999044 AGTCAGATGAGTTGGCTAATGAAT 58.001 37.500 0.00 0.00 0.00 2.57
2374 2494 6.318144 AGTCAGATGAGTTGGCTAATGAATTG 59.682 38.462 0.00 0.00 0.00 2.32
2419 2539 0.918983 TCCAATTGGAGGAAGCCGAT 59.081 50.000 23.63 0.00 39.78 4.18
2425 2545 0.324738 TGGAGGAAGCCGATCAGTCT 60.325 55.000 0.00 0.00 0.00 3.24
2590 2710 5.409643 AAGAAATTGACGTGACAAGTGAG 57.590 39.130 0.00 0.00 33.22 3.51
2684 2804 5.702670 CAGGCAGTAGAAGATGAGAAAACAA 59.297 40.000 0.00 0.00 0.00 2.83
2758 2878 2.548480 ACAAAAGAACGAGCTAGCCAAC 59.452 45.455 12.13 2.48 0.00 3.77
2857 2977 0.179051 CAGCTGAATCCAGAGAGGCC 60.179 60.000 8.42 0.00 43.02 5.19
2980 3100 5.232414 GGTGATGCTCGATGAAGTAAACTAC 59.768 44.000 0.00 0.00 0.00 2.73
3079 3199 6.038714 CCAAAGAGCTAAGTTTTGTCAACTCT 59.961 38.462 0.00 0.00 34.85 3.24
3091 3211 8.429641 AGTTTTGTCAACTCTATTAGGAAGTCA 58.570 33.333 0.00 0.00 0.00 3.41
3110 3230 3.611986 GTCAGAAGAAGAGATCGTTGCTG 59.388 47.826 0.00 0.00 0.00 4.41
3280 3400 9.831737 CAATTGAAGGACAAACTATTAGACAAG 57.168 33.333 0.00 0.00 42.03 3.16
3337 3457 0.883833 ACTTGCAGGCAAAGGAATCG 59.116 50.000 8.20 0.00 35.33 3.34
3424 3544 6.433766 CAACAAGGAAGAAGACAATGAGAAC 58.566 40.000 0.00 0.00 0.00 3.01
3445 3565 2.509336 GGCGGTGTGGATGACGAG 60.509 66.667 0.00 0.00 0.00 4.18
3451 3571 2.264794 GTGGATGACGAGCCGGTT 59.735 61.111 1.90 0.00 0.00 4.44
3487 3607 0.550914 TGTGGGAGAACAGCAAGGTT 59.449 50.000 0.00 0.00 0.00 3.50
3567 3687 1.192146 TCCAACAAGGGAGACTCCGG 61.192 60.000 15.46 9.69 37.43 5.14
3571 3691 2.122954 AAGGGAGACTCCGGCCTT 59.877 61.111 15.46 10.15 37.43 4.35
4000 4120 6.530534 CAGAGATTTCCAAATCAATGCAGTTC 59.469 38.462 13.30 1.58 45.59 3.01
4017 4140 5.107143 TGCAGTTCTTTGTTTTTGTTGAAGC 60.107 36.000 0.00 0.00 0.00 3.86
4029 4152 8.562892 TGTTTTTGTTGAAGCAAATTCTTTGAA 58.437 25.926 3.87 0.00 43.26 2.69
4032 4155 6.890663 TGTTGAAGCAAATTCTTTGAACAG 57.109 33.333 3.87 0.00 43.26 3.16
4034 4157 7.267128 TGTTGAAGCAAATTCTTTGAACAGAT 58.733 30.769 3.87 0.00 43.26 2.90
4076 4199 4.217550 GGAGTACTATCATGGTGCTCTCTC 59.782 50.000 16.90 0.00 42.91 3.20
4126 4249 1.075076 ATGATGGTGGCAATGGGGG 60.075 57.895 0.00 0.00 0.00 5.40
4132 4259 1.203364 TGGTGGCAATGGGGGTAAAAT 60.203 47.619 0.00 0.00 0.00 1.82
4185 4312 0.618680 ATGTGAGCCAGCCAGGAGTA 60.619 55.000 0.00 0.00 41.22 2.59
4226 4353 4.567959 GCTGTTGCCCATCAATCAAATAAC 59.432 41.667 0.00 0.00 36.99 1.89
4317 4444 4.785453 CGGCACAAGAGGGGAGGC 62.785 72.222 0.00 0.00 0.00 4.70
4375 4502 3.561310 TGACTCACAACTCACAAAGATGC 59.439 43.478 0.00 0.00 31.17 3.91
4389 4516 4.826733 ACAAAGATGCAGTACATGTTGGAA 59.173 37.500 2.30 0.00 41.16 3.53
4390 4517 5.048504 ACAAAGATGCAGTACATGTTGGAAG 60.049 40.000 2.30 0.00 41.16 3.46
4392 4519 4.655963 AGATGCAGTACATGTTGGAAGTT 58.344 39.130 2.30 0.00 39.84 2.66
4393 4520 4.697352 AGATGCAGTACATGTTGGAAGTTC 59.303 41.667 2.30 0.00 39.84 3.01
4394 4521 4.085357 TGCAGTACATGTTGGAAGTTCT 57.915 40.909 2.30 0.00 0.00 3.01
4429 4559 1.610624 GGTGGAGCGATGAACTTTCCA 60.611 52.381 0.00 0.00 35.67 3.53
4444 4574 4.379652 ACTTTCCAATGACAAAATGCACC 58.620 39.130 0.00 0.00 0.00 5.01
4489 4619 2.498885 GTGGTAGTAGTGGTACCTTGGG 59.501 54.545 14.36 0.00 40.70 4.12
4490 4620 2.113807 GGTAGTAGTGGTACCTTGGGG 58.886 57.143 14.36 0.00 37.54 4.96
4491 4621 1.483827 GTAGTAGTGGTACCTTGGGGC 59.516 57.143 14.36 0.00 35.63 5.80
4492 4622 1.219935 GTAGTGGTACCTTGGGGCG 59.780 63.158 14.36 0.00 35.63 6.13
4516 4646 0.463620 GCTAGCCTGTCTCTGAAGGG 59.536 60.000 2.29 0.00 33.87 3.95
4526 4656 2.046892 CTGAAGGGTGGCCACTCG 60.047 66.667 33.91 14.91 36.76 4.18
4545 4675 0.393944 GGTACAAAGGCCCCTACTGC 60.394 60.000 0.00 0.00 0.00 4.40
4573 4703 2.669569 CAGGTCAACACAGGCCCG 60.670 66.667 0.00 0.00 0.00 6.13
4577 4707 4.641645 TCAACACAGGCCCGCCAG 62.642 66.667 8.74 1.99 38.92 4.85
4619 4749 7.770801 TGTGTATGTACAGCAGAATTGATAC 57.229 36.000 0.33 0.00 36.78 2.24
4623 4753 3.865164 TGTACAGCAGAATTGATACGCAG 59.135 43.478 0.00 0.00 0.00 5.18
4629 4759 0.652592 GAATTGATACGCAGCGTGCT 59.347 50.000 30.67 17.31 42.25 4.40
4659 4789 4.406456 TCAGTTAATGTGTGCCAAAGGAT 58.594 39.130 0.00 0.00 0.00 3.24
4666 4796 1.270550 GTGTGCCAAAGGATTGACAGG 59.729 52.381 0.00 0.00 38.94 4.00
4667 4797 0.244721 GTGCCAAAGGATTGACAGGC 59.755 55.000 0.00 0.00 38.94 4.85
4668 4798 1.243342 TGCCAAAGGATTGACAGGCG 61.243 55.000 0.00 0.00 44.83 5.52
4669 4799 0.960364 GCCAAAGGATTGACAGGCGA 60.960 55.000 0.00 0.00 38.94 5.54
4670 4800 0.804989 CCAAAGGATTGACAGGCGAC 59.195 55.000 0.00 0.00 38.94 5.19
4671 4801 1.522668 CAAAGGATTGACAGGCGACA 58.477 50.000 0.00 0.00 38.94 4.35
4672 4802 1.466167 CAAAGGATTGACAGGCGACAG 59.534 52.381 0.00 0.00 38.94 3.51
4673 4803 0.976641 AAGGATTGACAGGCGACAGA 59.023 50.000 0.00 0.00 0.00 3.41
4674 4804 0.534412 AGGATTGACAGGCGACAGAG 59.466 55.000 0.00 0.00 0.00 3.35
4675 4805 0.247736 GGATTGACAGGCGACAGAGT 59.752 55.000 0.00 0.00 0.00 3.24
4676 4806 1.354040 GATTGACAGGCGACAGAGTG 58.646 55.000 0.00 0.00 0.00 3.51
4677 4807 0.681733 ATTGACAGGCGACAGAGTGT 59.318 50.000 0.00 0.00 0.00 3.55
4678 4808 1.324383 TTGACAGGCGACAGAGTGTA 58.676 50.000 0.00 0.00 0.00 2.90
4679 4809 0.596577 TGACAGGCGACAGAGTGTAC 59.403 55.000 0.00 0.00 0.00 2.90
4680 4810 0.109226 GACAGGCGACAGAGTGTACC 60.109 60.000 0.00 0.00 0.00 3.34
4681 4811 0.539901 ACAGGCGACAGAGTGTACCT 60.540 55.000 0.00 0.00 37.46 3.08
4682 4812 0.109086 CAGGCGACAGAGTGTACCTG 60.109 60.000 12.01 12.01 43.73 4.00
4683 4813 1.446272 GGCGACAGAGTGTACCTGC 60.446 63.158 0.00 0.00 35.14 4.85
4684 4814 1.289066 GCGACAGAGTGTACCTGCA 59.711 57.895 0.00 0.00 35.14 4.41
4685 4815 0.734253 GCGACAGAGTGTACCTGCAG 60.734 60.000 6.78 6.78 35.14 4.41
4686 4816 0.734253 CGACAGAGTGTACCTGCAGC 60.734 60.000 8.66 0.00 35.14 5.25
4687 4817 0.318441 GACAGAGTGTACCTGCAGCA 59.682 55.000 8.66 0.00 35.14 4.41
4688 4818 0.319728 ACAGAGTGTACCTGCAGCAG 59.680 55.000 16.23 16.23 35.14 4.24
4689 4819 1.018226 CAGAGTGTACCTGCAGCAGC 61.018 60.000 17.81 4.14 42.57 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.732538 CGGGAAAACGCATGAAAGGC 60.733 55.000 0.00 0.00 42.44 4.35
80 81 8.615211 GTGTGTGCTCTTTTTATCATCATCATA 58.385 33.333 0.00 0.00 0.00 2.15
81 82 7.415989 GGTGTGTGCTCTTTTTATCATCATCAT 60.416 37.037 0.00 0.00 0.00 2.45
82 83 6.127925 GGTGTGTGCTCTTTTTATCATCATCA 60.128 38.462 0.00 0.00 0.00 3.07
83 84 6.261118 GGTGTGTGCTCTTTTTATCATCATC 58.739 40.000 0.00 0.00 0.00 2.92
86 102 4.458989 TGGGTGTGTGCTCTTTTTATCATC 59.541 41.667 0.00 0.00 0.00 2.92
88 104 3.826524 TGGGTGTGTGCTCTTTTTATCA 58.173 40.909 0.00 0.00 0.00 2.15
105 121 0.178947 TTTTCATTCGCCCCTTGGGT 60.179 50.000 4.84 0.00 46.51 4.51
111 127 0.246360 CCCTTGTTTTCATTCGCCCC 59.754 55.000 0.00 0.00 0.00 5.80
112 128 1.253100 TCCCTTGTTTTCATTCGCCC 58.747 50.000 0.00 0.00 0.00 6.13
120 136 4.857037 GCGTAAATGTGATCCCTTGTTTTC 59.143 41.667 0.00 0.00 0.00 2.29
133 149 3.414549 AAATAAGGCCGCGTAAATGTG 57.585 42.857 4.92 0.00 0.00 3.21
134 150 3.181494 GGAAAATAAGGCCGCGTAAATGT 60.181 43.478 4.92 0.00 0.00 2.71
141 157 1.264288 GATGAGGAAAATAAGGCCGCG 59.736 52.381 0.00 0.00 0.00 6.46
147 163 4.078639 AGGCGGAGATGAGGAAAATAAG 57.921 45.455 0.00 0.00 0.00 1.73
195 213 7.380870 TGCGTGTAACTCTTTGTACGTTTATTA 59.619 33.333 0.00 0.00 34.37 0.98
198 216 5.039984 TGCGTGTAACTCTTTGTACGTTTA 58.960 37.500 0.00 0.00 34.37 2.01
200 218 3.446799 TGCGTGTAACTCTTTGTACGTT 58.553 40.909 0.00 0.00 34.37 3.99
202 220 4.640805 ATTGCGTGTAACTCTTTGTACG 57.359 40.909 0.00 0.00 34.93 3.67
203 221 6.788930 GTGTAATTGCGTGTAACTCTTTGTAC 59.211 38.462 0.00 0.00 31.75 2.90
204 222 6.345961 CGTGTAATTGCGTGTAACTCTTTGTA 60.346 38.462 0.00 0.00 31.75 2.41
205 223 5.557514 CGTGTAATTGCGTGTAACTCTTTGT 60.558 40.000 0.00 0.00 31.75 2.83
206 224 4.838642 CGTGTAATTGCGTGTAACTCTTTG 59.161 41.667 0.00 0.00 31.75 2.77
207 225 4.609783 GCGTGTAATTGCGTGTAACTCTTT 60.610 41.667 0.00 0.00 31.75 2.52
208 226 3.120786 GCGTGTAATTGCGTGTAACTCTT 60.121 43.478 0.00 0.00 31.75 2.85
209 227 2.410730 GCGTGTAATTGCGTGTAACTCT 59.589 45.455 0.00 0.00 31.75 3.24
210 228 2.410730 AGCGTGTAATTGCGTGTAACTC 59.589 45.455 0.00 0.00 35.87 3.01
211 229 2.156891 CAGCGTGTAATTGCGTGTAACT 59.843 45.455 0.00 0.00 35.87 2.24
212 230 2.156117 TCAGCGTGTAATTGCGTGTAAC 59.844 45.455 0.00 0.00 35.87 2.50
213 231 2.405172 TCAGCGTGTAATTGCGTGTAA 58.595 42.857 0.00 0.00 35.87 2.41
214 232 2.067414 TCAGCGTGTAATTGCGTGTA 57.933 45.000 0.00 0.00 35.87 2.90
215 233 1.438651 ATCAGCGTGTAATTGCGTGT 58.561 45.000 0.00 0.00 35.87 4.49
216 234 2.525750 AATCAGCGTGTAATTGCGTG 57.474 45.000 0.00 0.00 35.87 5.34
217 235 2.607635 CCTAATCAGCGTGTAATTGCGT 59.392 45.455 0.00 0.00 35.87 5.24
218 236 2.863740 TCCTAATCAGCGTGTAATTGCG 59.136 45.455 0.00 0.00 35.87 4.85
219 237 5.424121 AATCCTAATCAGCGTGTAATTGC 57.576 39.130 0.00 0.00 0.00 3.56
259 277 6.100279 AGCCAATTCTTTCCCTCTTTCTTTTT 59.900 34.615 0.00 0.00 0.00 1.94
260 278 5.604231 AGCCAATTCTTTCCCTCTTTCTTTT 59.396 36.000 0.00 0.00 0.00 2.27
261 279 5.011431 CAGCCAATTCTTTCCCTCTTTCTTT 59.989 40.000 0.00 0.00 0.00 2.52
262 280 4.525874 CAGCCAATTCTTTCCCTCTTTCTT 59.474 41.667 0.00 0.00 0.00 2.52
263 281 4.085009 CAGCCAATTCTTTCCCTCTTTCT 58.915 43.478 0.00 0.00 0.00 2.52
264 282 3.367806 GCAGCCAATTCTTTCCCTCTTTC 60.368 47.826 0.00 0.00 0.00 2.62
290 308 1.535028 TGTGCAACCTCATAAAGCGTG 59.465 47.619 0.00 0.00 34.36 5.34
306 324 4.318121 CGCCGTTCTAATTCTATTCTGTGC 60.318 45.833 0.00 0.00 0.00 4.57
328 352 1.683790 CGCTTTCGCTAACCACCTCG 61.684 60.000 0.00 0.00 0.00 4.63
377 401 1.909975 CTTTACCACCCTACCCCGG 59.090 63.158 0.00 0.00 0.00 5.73
381 405 0.461516 GCTCGCTTTACCACCCTACC 60.462 60.000 0.00 0.00 0.00 3.18
382 406 0.804933 CGCTCGCTTTACCACCCTAC 60.805 60.000 0.00 0.00 0.00 3.18
383 407 0.966875 TCGCTCGCTTTACCACCCTA 60.967 55.000 0.00 0.00 0.00 3.53
384 408 2.227089 CTCGCTCGCTTTACCACCCT 62.227 60.000 0.00 0.00 0.00 4.34
385 409 1.810030 CTCGCTCGCTTTACCACCC 60.810 63.158 0.00 0.00 0.00 4.61
386 410 2.453638 GCTCGCTCGCTTTACCACC 61.454 63.158 0.00 0.00 0.00 4.61
387 411 1.446272 AGCTCGCTCGCTTTACCAC 60.446 57.895 0.00 0.00 36.74 4.16
388 412 1.446099 CAGCTCGCTCGCTTTACCA 60.446 57.895 0.00 0.00 38.41 3.25
389 413 2.167861 CCAGCTCGCTCGCTTTACC 61.168 63.158 0.00 0.00 38.41 2.85
390 414 2.803713 GCCAGCTCGCTCGCTTTAC 61.804 63.158 0.00 0.00 38.41 2.01
391 415 2.509336 GCCAGCTCGCTCGCTTTA 60.509 61.111 0.00 0.00 38.41 1.85
392 416 4.385405 AGCCAGCTCGCTCGCTTT 62.385 61.111 0.00 0.00 37.20 3.51
407 431 3.945434 CATGATCACCGCGCCAGC 61.945 66.667 0.00 0.00 40.74 4.85
408 432 2.202919 TCATGATCACCGCGCCAG 60.203 61.111 0.00 0.00 0.00 4.85
409 433 2.511373 GTCATGATCACCGCGCCA 60.511 61.111 0.00 0.00 0.00 5.69
410 434 3.630148 CGTCATGATCACCGCGCC 61.630 66.667 0.00 0.00 0.00 6.53
411 435 3.630148 CCGTCATGATCACCGCGC 61.630 66.667 0.00 0.00 0.00 6.86
412 436 2.899345 TTCCCGTCATGATCACCGCG 62.899 60.000 0.00 0.00 0.00 6.46
413 437 0.532862 ATTCCCGTCATGATCACCGC 60.533 55.000 0.00 0.00 0.00 5.68
414 438 1.202521 TCATTCCCGTCATGATCACCG 60.203 52.381 0.00 0.46 0.00 4.94
415 439 2.213499 GTCATTCCCGTCATGATCACC 58.787 52.381 0.00 0.00 33.22 4.02
416 440 2.609459 GTGTCATTCCCGTCATGATCAC 59.391 50.000 0.00 0.00 33.22 3.06
417 441 2.501316 AGTGTCATTCCCGTCATGATCA 59.499 45.455 0.00 0.00 33.22 2.92
418 442 2.868583 CAGTGTCATTCCCGTCATGATC 59.131 50.000 0.00 0.00 33.22 2.92
419 443 2.910199 CAGTGTCATTCCCGTCATGAT 58.090 47.619 0.00 0.00 33.22 2.45
420 444 1.675714 GCAGTGTCATTCCCGTCATGA 60.676 52.381 0.00 0.00 0.00 3.07
421 445 0.729116 GCAGTGTCATTCCCGTCATG 59.271 55.000 0.00 0.00 0.00 3.07
422 446 0.615331 AGCAGTGTCATTCCCGTCAT 59.385 50.000 0.00 0.00 0.00 3.06
423 447 0.320683 CAGCAGTGTCATTCCCGTCA 60.321 55.000 0.00 0.00 0.00 4.35
424 448 1.639298 GCAGCAGTGTCATTCCCGTC 61.639 60.000 0.00 0.00 0.00 4.79
425 449 1.672356 GCAGCAGTGTCATTCCCGT 60.672 57.895 0.00 0.00 0.00 5.28
426 450 2.401766 GGCAGCAGTGTCATTCCCG 61.402 63.158 0.00 0.00 0.00 5.14
427 451 1.303561 TGGCAGCAGTGTCATTCCC 60.304 57.895 0.00 0.00 31.64 3.97
428 452 0.607489 ACTGGCAGCAGTGTCATTCC 60.607 55.000 15.89 0.00 37.75 3.01
429 453 2.005451 CTACTGGCAGCAGTGTCATTC 58.995 52.381 15.89 0.00 37.75 2.67
430 454 1.349026 ACTACTGGCAGCAGTGTCATT 59.651 47.619 19.37 0.00 37.75 2.57
431 455 0.979665 ACTACTGGCAGCAGTGTCAT 59.020 50.000 19.37 0.00 37.75 3.06
432 456 1.546029 CTACTACTGGCAGCAGTGTCA 59.454 52.381 26.87 9.30 35.32 3.58
433 457 1.546476 ACTACTACTGGCAGCAGTGTC 59.454 52.381 26.87 0.00 36.68 3.67
434 458 1.633774 ACTACTACTGGCAGCAGTGT 58.366 50.000 26.87 19.53 36.68 3.55
435 459 2.755655 ACTACTACTACTGGCAGCAGTG 59.244 50.000 26.87 18.98 36.68 3.66
436 460 3.088789 ACTACTACTACTGGCAGCAGT 57.911 47.619 23.05 23.05 39.08 4.40
437 461 4.200874 AGTACTACTACTACTGGCAGCAG 58.799 47.826 15.89 14.45 30.81 4.24
438 462 4.232188 AGTACTACTACTACTGGCAGCA 57.768 45.455 15.89 0.00 30.81 4.41
439 463 5.821995 AGTAAGTACTACTACTACTGGCAGC 59.178 44.000 15.89 0.00 39.20 5.25
453 477 6.808321 TTACGGAGGGAGTAGTAAGTACTA 57.192 41.667 0.00 0.00 42.48 1.82
454 478 5.700402 TTACGGAGGGAGTAGTAAGTACT 57.300 43.478 0.00 0.00 45.34 2.73
455 479 5.883115 AGTTTACGGAGGGAGTAGTAAGTAC 59.117 44.000 0.00 0.00 31.77 2.73
456 480 6.067217 AGTTTACGGAGGGAGTAGTAAGTA 57.933 41.667 0.00 0.00 31.77 2.24
457 481 4.928263 AGTTTACGGAGGGAGTAGTAAGT 58.072 43.478 0.00 0.00 31.77 2.24
458 482 7.579761 ATTAGTTTACGGAGGGAGTAGTAAG 57.420 40.000 0.00 0.00 31.77 2.34
461 485 9.646522 TTTATATTAGTTTACGGAGGGAGTAGT 57.353 33.333 0.00 0.00 0.00 2.73
464 488 7.930325 GCTTTTATATTAGTTTACGGAGGGAGT 59.070 37.037 0.00 0.00 0.00 3.85
465 489 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
466 490 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
467 491 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
468 492 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
536 560 8.027771 CGAGTGTTTAATTAGTACTTCCTCTGT 58.972 37.037 0.00 0.00 0.00 3.41
537 561 7.488471 CCGAGTGTTTAATTAGTACTTCCTCTG 59.512 40.741 0.00 0.00 0.00 3.35
538 562 7.395489 TCCGAGTGTTTAATTAGTACTTCCTCT 59.605 37.037 0.00 0.00 0.00 3.69
539 563 7.542025 TCCGAGTGTTTAATTAGTACTTCCTC 58.458 38.462 0.00 0.00 0.00 3.71
540 564 7.472334 TCCGAGTGTTTAATTAGTACTTCCT 57.528 36.000 0.00 0.00 0.00 3.36
541 565 8.713737 AATCCGAGTGTTTAATTAGTACTTCC 57.286 34.615 0.00 0.00 0.00 3.46
596 694 2.190488 GAGGGAGGTGCAGTGAAGGG 62.190 65.000 0.00 0.00 0.00 3.95
605 703 2.716017 CGAGAGTGGAGGGAGGTGC 61.716 68.421 0.00 0.00 0.00 5.01
618 716 3.861840 TGCCTCTGTTTTTATCCGAGAG 58.138 45.455 0.00 0.00 0.00 3.20
619 717 3.861840 CTGCCTCTGTTTTTATCCGAGA 58.138 45.455 0.00 0.00 0.00 4.04
620 718 2.352960 GCTGCCTCTGTTTTTATCCGAG 59.647 50.000 0.00 0.00 0.00 4.63
621 719 2.290008 TGCTGCCTCTGTTTTTATCCGA 60.290 45.455 0.00 0.00 0.00 4.55
622 720 2.083774 TGCTGCCTCTGTTTTTATCCG 58.916 47.619 0.00 0.00 0.00 4.18
646 744 1.202031 CGCTCGCATTAACCTTTCCAC 60.202 52.381 0.00 0.00 0.00 4.02
700 798 1.443802 GAGAGGAAAAAGCAGGGACG 58.556 55.000 0.00 0.00 0.00 4.79
741 845 0.315382 GCGGAATTTCACTCGATGCG 60.315 55.000 0.00 0.00 0.00 4.73
831 940 1.202698 GGTTATGGCAGGCAGAGTAGG 60.203 57.143 1.89 0.00 0.00 3.18
885 995 3.330720 GAGTGGTGGGTGAGGGGG 61.331 72.222 0.00 0.00 0.00 5.40
888 998 3.072476 CAGGAGTGGTGGGTGAGG 58.928 66.667 0.00 0.00 0.00 3.86
986 1097 1.001641 AGCATTGTGGACTCCCTGC 60.002 57.895 0.00 0.00 32.00 4.85
987 1098 0.679002 CCAGCATTGTGGACTCCCTG 60.679 60.000 0.00 0.00 40.44 4.45
1050 1161 7.549488 AGAAACAGTGATAAAAGAATCGTAGGG 59.451 37.037 0.00 0.00 0.00 3.53
1051 1162 8.480643 AGAAACAGTGATAAAAGAATCGTAGG 57.519 34.615 0.00 0.00 0.00 3.18
1074 1185 3.118408 CCGACCCATCACTCCAAAATAGA 60.118 47.826 0.00 0.00 0.00 1.98
1075 1187 3.206150 CCGACCCATCACTCCAAAATAG 58.794 50.000 0.00 0.00 0.00 1.73
1099 1211 1.750399 CCAAGAACCATCCAGCCCG 60.750 63.158 0.00 0.00 0.00 6.13
1104 1216 2.945440 GCATGCTACCAAGAACCATCCA 60.945 50.000 11.37 0.00 0.00 3.41
1105 1217 1.678101 GCATGCTACCAAGAACCATCC 59.322 52.381 11.37 0.00 0.00 3.51
1107 1219 2.756760 CAAGCATGCTACCAAGAACCAT 59.243 45.455 23.00 0.00 0.00 3.55
1160 1277 0.392998 CCCAACCACCAAGATCCGAG 60.393 60.000 0.00 0.00 0.00 4.63
1192 1309 4.705337 ACTACCGTCAGATCAAGAACTC 57.295 45.455 0.00 0.00 0.00 3.01
1399 1516 3.508840 GCATTCGCCTTGGGGACG 61.509 66.667 5.89 2.48 34.90 4.79
1535 1652 1.146358 GGAATCGTGCGTACCTCTGC 61.146 60.000 0.00 0.00 0.00 4.26
1581 1698 3.127721 CCACTAAAGCTAAAGCAGGAAGC 59.872 47.826 4.54 0.00 45.16 3.86
1582 1699 4.579869 TCCACTAAAGCTAAAGCAGGAAG 58.420 43.478 4.54 0.00 45.16 3.46
1584 1701 4.634012 TTCCACTAAAGCTAAAGCAGGA 57.366 40.909 4.54 0.00 45.16 3.86
1586 1703 6.749923 AAGATTCCACTAAAGCTAAAGCAG 57.250 37.500 4.54 0.00 45.16 4.24
1587 1704 7.394816 ACTAAGATTCCACTAAAGCTAAAGCA 58.605 34.615 4.54 0.00 45.16 3.91
1588 1705 7.254151 CGACTAAGATTCCACTAAAGCTAAAGC 60.254 40.741 0.00 0.00 42.49 3.51
1589 1706 7.760340 ACGACTAAGATTCCACTAAAGCTAAAG 59.240 37.037 0.00 0.00 0.00 1.85
1590 1707 7.609056 ACGACTAAGATTCCACTAAAGCTAAA 58.391 34.615 0.00 0.00 0.00 1.85
1591 1708 7.166691 ACGACTAAGATTCCACTAAAGCTAA 57.833 36.000 0.00 0.00 0.00 3.09
1592 1709 6.770746 ACGACTAAGATTCCACTAAAGCTA 57.229 37.500 0.00 0.00 0.00 3.32
1593 1710 5.662674 ACGACTAAGATTCCACTAAAGCT 57.337 39.130 0.00 0.00 0.00 3.74
1594 1711 6.367969 TCAAACGACTAAGATTCCACTAAAGC 59.632 38.462 0.00 0.00 0.00 3.51
1595 1712 7.884816 TCAAACGACTAAGATTCCACTAAAG 57.115 36.000 0.00 0.00 0.00 1.85
1613 1730 2.322161 CTTCTGCAAGCCAATCAAACG 58.678 47.619 0.00 0.00 0.00 3.60
1648 1768 2.110006 GGCTCGGGAGATGGCTTC 59.890 66.667 0.00 0.00 38.80 3.86
1675 1795 3.710722 AGCTCCTGGGACGGCTTG 61.711 66.667 0.00 0.00 0.00 4.01
1759 1879 2.039613 CAGAACCTTGCCCTTCTCTTCT 59.960 50.000 0.00 0.00 0.00 2.85
1786 1906 1.302033 CTTCTTGGCGCACTCCAGT 60.302 57.895 10.83 0.00 37.44 4.00
1894 2014 1.202794 TCATTGTTGCTCACCTGCTCA 60.203 47.619 0.00 0.00 0.00 4.26
1921 2041 1.227089 CTCATCTTCCTCGCCGTGG 60.227 63.158 0.00 0.00 0.00 4.94
1929 2049 1.684386 CCTCCGCAGCTCATCTTCCT 61.684 60.000 0.00 0.00 0.00 3.36
1993 2113 1.079819 CTCCACCGTCGAATGCAGT 60.080 57.895 0.00 0.00 0.00 4.40
2204 2324 1.541147 TGCCTCAAGCTTTCCGATTTG 59.459 47.619 0.00 0.00 44.23 2.32
2209 2329 0.036952 TCTCTGCCTCAAGCTTTCCG 60.037 55.000 0.00 0.00 44.23 4.30
2212 2332 3.757493 CAGAATTCTCTGCCTCAAGCTTT 59.243 43.478 4.57 0.00 42.66 3.51
2252 2372 3.332919 TCTCAGCTAGCTTTGCTTTCTG 58.667 45.455 16.46 0.98 40.44 3.02
2362 2482 6.558909 CACCTTCTTCTTCAATTCATTAGCC 58.441 40.000 0.00 0.00 0.00 3.93
2366 2486 5.566230 GCTGCACCTTCTTCTTCAATTCATT 60.566 40.000 0.00 0.00 0.00 2.57
2369 2489 3.505293 AGCTGCACCTTCTTCTTCAATTC 59.495 43.478 1.02 0.00 0.00 2.17
2372 2492 2.224606 CAGCTGCACCTTCTTCTTCAA 58.775 47.619 0.00 0.00 0.00 2.69
2374 2494 1.889545 ACAGCTGCACCTTCTTCTTC 58.110 50.000 15.27 0.00 0.00 2.87
2419 2539 4.717877 TGCCTTTCAAAATGAGAGACTGA 58.282 39.130 0.00 0.00 30.88 3.41
2425 2545 6.275335 CAAAGACTTGCCTTTCAAAATGAGA 58.725 36.000 0.00 0.00 34.41 3.27
2590 2710 0.738762 TCTCTGCAGCATCAAGACGC 60.739 55.000 9.47 0.00 0.00 5.19
2618 2738 3.954258 TCGATCTCTGCAATTAGGTCAGA 59.046 43.478 4.94 0.00 35.74 3.27
2651 2771 4.026744 TCTTCTACTGCCTGTAGCTTCAT 58.973 43.478 4.03 0.00 46.15 2.57
2684 2804 0.537143 TGGTCATTGTTCAGCGCCTT 60.537 50.000 2.29 0.00 0.00 4.35
2857 2977 5.500234 TGTTTGATGAGGTATTTCTCCTGG 58.500 41.667 0.00 0.00 35.20 4.45
2980 3100 3.561725 ACTTCTTGAGGCAAACTTTCTCG 59.438 43.478 0.00 0.00 0.00 4.04
3079 3199 7.776030 ACGATCTCTTCTTCTGACTTCCTAATA 59.224 37.037 0.00 0.00 0.00 0.98
3091 3211 3.256879 TGACAGCAACGATCTCTTCTTCT 59.743 43.478 0.00 0.00 0.00 2.85
3110 3230 4.574599 ACTTGTCCATTTGAGCTTTGAC 57.425 40.909 0.00 0.00 0.00 3.18
3199 3319 0.979665 TGGCTTCAACTAGCTGAGCT 59.020 50.000 13.25 13.25 43.41 4.09
3280 3400 7.544566 TCTTGTATGTTCTGTAATTCGTTCTCC 59.455 37.037 0.00 0.00 0.00 3.71
3337 3457 2.604046 TTATCTTCTCCGAAGCAGCC 57.396 50.000 0.00 0.00 0.00 4.85
3369 3489 1.002624 GTTCCATTCGGCACCAGGA 60.003 57.895 0.00 0.00 0.00 3.86
3370 3490 0.893270 TTGTTCCATTCGGCACCAGG 60.893 55.000 0.00 0.00 0.00 4.45
3373 3493 0.671251 TTGTTGTTCCATTCGGCACC 59.329 50.000 0.00 0.00 0.00 5.01
3415 3535 1.079127 ACCGCCTCCGTTCTCATTG 60.079 57.895 0.00 0.00 0.00 2.82
3418 3538 2.915659 ACACCGCCTCCGTTCTCA 60.916 61.111 0.00 0.00 0.00 3.27
3424 3544 3.770040 TCATCCACACCGCCTCCG 61.770 66.667 0.00 0.00 0.00 4.63
3445 3565 4.279043 GCAACCACCACAACCGGC 62.279 66.667 0.00 0.00 0.00 6.13
3451 3571 0.106268 ACATCTTGGCAACCACCACA 60.106 50.000 0.00 0.00 40.19 4.17
3487 3607 0.246360 TGGACGAGTCGTAGTCGGTA 59.754 55.000 19.93 0.00 44.80 4.02
3567 3687 4.043200 GCCCGTTGCTGTCAAGGC 62.043 66.667 0.00 0.00 36.69 4.35
3622 3742 0.102844 TTTGCTGCTGCTGTTTGGTC 59.897 50.000 17.00 0.00 40.48 4.02
4000 4120 8.953507 AAGAATTTGCTTCAACAAAAACAAAG 57.046 26.923 0.00 0.00 42.45 2.77
4041 4164 9.177608 CCATGATAGTACTCCTTCAAAATTTCA 57.822 33.333 0.00 0.00 0.00 2.69
4042 4165 9.178758 ACCATGATAGTACTCCTTCAAAATTTC 57.821 33.333 0.00 0.00 0.00 2.17
4043 4166 8.960591 CACCATGATAGTACTCCTTCAAAATTT 58.039 33.333 0.00 0.00 0.00 1.82
4044 4167 7.067494 GCACCATGATAGTACTCCTTCAAAATT 59.933 37.037 0.00 0.00 0.00 1.82
4045 4168 6.543831 GCACCATGATAGTACTCCTTCAAAAT 59.456 38.462 0.00 0.00 0.00 1.82
4046 4169 5.880332 GCACCATGATAGTACTCCTTCAAAA 59.120 40.000 0.00 0.00 0.00 2.44
4058 4181 3.037851 TGGAGAGAGCACCATGATAGT 57.962 47.619 0.00 0.00 29.24 2.12
4076 4199 2.566833 TCAGGTCAACAGGAACATGG 57.433 50.000 0.00 0.00 34.85 3.66
4185 4312 1.055040 GCCTCATCAGGAGCCATACT 58.945 55.000 0.00 0.00 43.65 2.12
4194 4321 3.915575 GGCAACAGCCTCATCAGG 58.084 61.111 0.00 0.00 45.21 3.86
4211 4338 5.108517 CAAACCCCGTTATTTGATTGATGG 58.891 41.667 0.00 0.00 37.91 3.51
4226 4353 2.359975 GGAGTGGAGCAAACCCCG 60.360 66.667 0.00 0.00 0.00 5.73
4263 4390 1.177401 GGTTGGGAGAAATGTGGAGC 58.823 55.000 0.00 0.00 0.00 4.70
4375 4502 6.223852 ACAGTAGAACTTCCAACATGTACTG 58.776 40.000 13.75 13.75 42.27 2.74
4389 4516 5.202004 CACCATAGGACCTACAGTAGAACT 58.798 45.833 9.38 6.53 0.00 3.01
4390 4517 4.341520 CCACCATAGGACCTACAGTAGAAC 59.658 50.000 9.38 2.70 0.00 3.01
4392 4519 3.789840 TCCACCATAGGACCTACAGTAGA 59.210 47.826 9.38 0.23 31.23 2.59
4393 4520 4.145807 CTCCACCATAGGACCTACAGTAG 58.854 52.174 2.46 0.00 33.19 2.57
4394 4521 3.690438 GCTCCACCATAGGACCTACAGTA 60.690 52.174 2.46 0.00 33.19 2.74
4429 4559 3.512978 GCGGGTGCATTTTGTCATT 57.487 47.368 0.00 0.00 42.15 2.57
4444 4574 2.023673 TCTGGAGCCAATAATTTGCGG 58.976 47.619 0.00 0.00 0.00 5.69
4516 4646 0.953960 CCTTTGTACCGAGTGGCCAC 60.954 60.000 29.22 29.22 39.70 5.01
4526 4656 0.393944 GCAGTAGGGGCCTTTGTACC 60.394 60.000 0.84 0.00 0.00 3.34
4573 4703 3.545703 ACACATTGCCTACTAATCTGGC 58.454 45.455 0.00 0.00 46.26 4.85
4577 4707 5.880054 ACACAACACATTGCCTACTAATC 57.120 39.130 0.00 0.00 39.66 1.75
4623 4753 1.921243 AACTGAACCAAAAAGCACGC 58.079 45.000 0.00 0.00 0.00 5.34
4629 4759 5.112686 GGCACACATTAACTGAACCAAAAA 58.887 37.500 0.00 0.00 0.00 1.94
4659 4789 1.000607 GTACACTCTGTCGCCTGTCAA 60.001 52.381 0.00 0.00 0.00 3.18
4666 4796 0.734253 CTGCAGGTACACTCTGTCGC 60.734 60.000 5.57 0.00 34.89 5.19
4667 4797 0.734253 GCTGCAGGTACACTCTGTCG 60.734 60.000 17.12 0.00 34.89 4.35
4668 4798 0.318441 TGCTGCAGGTACACTCTGTC 59.682 55.000 17.12 0.00 34.89 3.51
4669 4799 0.319728 CTGCTGCAGGTACACTCTGT 59.680 55.000 21.71 0.00 34.89 3.41
4670 4800 1.018226 GCTGCTGCAGGTACACTCTG 61.018 60.000 29.05 2.86 39.41 3.35
4671 4801 1.294780 GCTGCTGCAGGTACACTCT 59.705 57.895 29.05 0.00 39.41 3.24
4672 4802 1.004560 TGCTGCTGCAGGTACACTC 60.005 57.895 29.05 12.29 45.31 3.51
4673 4803 3.150949 TGCTGCTGCAGGTACACT 58.849 55.556 29.05 0.00 45.31 3.55


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

AutoCloner maintained by Alex Coulton.