Multiple sequence alignment - TraesCS2A01G001100

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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 TraesCS2A01G001100 chr2A 100.000 3106 0 0 1 3106 526327 529432 0.000000e+00 5736
1 TraesCS2A01G001100 chr2B 87.555 1591 115 40 1396 2945 10785803 10784255 0.000000e+00 1764
2 TraesCS2A01G001100 chr2B 94.033 486 27 2 912 1396 10786217 10785733 0.000000e+00 736
3 TraesCS2A01G001100 chr2B 91.940 335 15 4 545 875 10786538 10786212 2.820000e-125 459
4 TraesCS2A01G001100 chr2B 95.172 145 5 1 2962 3106 10784273 10784131 8.670000e-56 228
5 TraesCS2A01G001100 chr2B 88.387 155 7 4 143 296 10786701 10786557 3.180000e-40 176
6 TraesCS2A01G001100 chr2D 86.675 1606 106 46 1396 2941 674483 676040 0.000000e+00 1681
7 TraesCS2A01G001100 chr2D 92.399 671 33 7 705 1375 673880 674532 0.000000e+00 941
8 TraesCS2A01G001100 chr2D 84.583 960 106 23 1404 2335 648747371 648748316 0.000000e+00 915
9 TraesCS2A01G001100 chr2D 89.497 457 39 9 928 1377 648746961 648747415 1.250000e-158 569
10 TraesCS2A01G001100 chr2D 85.124 363 24 13 1 356 673222 673561 8.250000e-91 344
11 TraesCS2A01G001100 chr2D 91.102 236 13 3 440 674 673652 673880 2.330000e-81 313
12 TraesCS2A01G001100 chr2D 97.917 144 3 0 2962 3105 676026 676169 1.850000e-62 250
13 TraesCS2A01G001100 chr5A 87.069 580 47 10 841 1396 219452005 219451430 5.650000e-177 630
14 TraesCS2A01G001100 chr5A 90.155 386 32 3 1407 1788 219451490 219451107 5.980000e-137 497
15 TraesCS2A01G001100 chr3D 87.269 542 41 11 841 1358 462477404 462476867 7.420000e-166 593
16 TraesCS2A01G001100 chr3D 90.828 338 28 3 1453 1790 462476866 462476532 1.700000e-122 449
17 TraesCS2A01G001100 chr6B 98.734 79 1 0 67 145 478479146 478479068 1.160000e-29 141
18 TraesCS2A01G001100 chr6B 93.617 94 5 1 67 159 526478327 526478234 4.180000e-29 139
19 TraesCS2A01G001100 chr4D 96.471 85 3 0 67 151 449455622 449455706 1.160000e-29 141
20 TraesCS2A01G001100 chr4D 88.333 120 4 4 149 268 182204565 182204674 5.400000e-28 135
21 TraesCS2A01G001100 chrUn 95.402 87 4 0 67 153 135090796 135090710 4.180000e-29 139
22 TraesCS2A01G001100 chrUn 95.402 87 4 0 67 153 152687652 152687566 4.180000e-29 139
23 TraesCS2A01G001100 chr3B 92.632 95 5 2 57 150 807080266 807080173 5.400000e-28 135
24 TraesCS2A01G001100 chr1B 88.991 109 9 3 39 145 345408297 345408190 6.990000e-27 132
25 TraesCS2A01G001100 chr7B 86.777 121 10 3 67 184 144686260 144686377 2.510000e-26 130


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 TraesCS2A01G001100 chr2A 526327 529432 3105 False 5736.0 5736 100.0000 1 3106 1 chr2A.!!$F1 3105
1 TraesCS2A01G001100 chr2B 10784131 10786701 2570 True 672.6 1764 91.4174 143 3106 5 chr2B.!!$R1 2963
2 TraesCS2A01G001100 chr2D 648746961 648748316 1355 False 742.0 915 87.0400 928 2335 2 chr2D.!!$F2 1407
3 TraesCS2A01G001100 chr2D 673222 676169 2947 False 705.8 1681 90.6434 1 3105 5 chr2D.!!$F1 3104
4 TraesCS2A01G001100 chr5A 219451107 219452005 898 True 563.5 630 88.6120 841 1788 2 chr5A.!!$R1 947
5 TraesCS2A01G001100 chr3D 462476532 462477404 872 True 521.0 593 89.0485 841 1790 2 chr3D.!!$R1 949

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
210 216 0.558712 AGCTAGGCTAGGCTAGGTGT 59.441 55.0 40.99 16.27 36.99 4.16 F
900 958 1.029408 GGCCACCGTGCATATGTCAA 61.029 55.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1486 0.108804 CGCAGCTAGGAAAGACGGAA 60.109 55.0 0.0 0.0 0.0 4.30 R
2811 3001 0.247894 GCGTTTGTTGTCGTGCTTGA 60.248 50.0 0.0 0.0 0.0 3.02 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
73 74 7.997773 ATGTATGTATGTATGTACTCCGTCT 57.002 36.000 0.00 0.00 0.00 4.18
74 75 7.430992 TGTATGTATGTATGTACTCCGTCTC 57.569 40.000 0.00 0.00 0.00 3.36
80 81 8.512138 TGTATGTATGTACTCCGTCTCATAATG 58.488 37.037 0.00 0.00 0.00 1.90
81 82 6.954487 TGTATGTACTCCGTCTCATAATGT 57.046 37.500 0.00 0.00 0.00 2.71
86 87 7.024340 TGTACTCCGTCTCATAATGTAAGAC 57.976 40.000 0.00 0.00 36.82 3.01
87 88 6.827251 TGTACTCCGTCTCATAATGTAAGACT 59.173 38.462 0.00 0.00 37.79 3.24
88 89 6.777213 ACTCCGTCTCATAATGTAAGACTT 57.223 37.500 0.00 0.00 37.79 3.01
142 143 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
144 145 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
145 146 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
146 147 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
160 166 5.151454 AGGGAGTAGTATTTAGCAGCAGAT 58.849 41.667 0.00 0.00 0.00 2.90
209 215 2.588464 TAGCTAGGCTAGGCTAGGTG 57.412 55.000 44.17 27.99 40.44 4.00
210 216 0.558712 AGCTAGGCTAGGCTAGGTGT 59.441 55.000 40.99 16.27 36.99 4.16
211 217 1.781529 AGCTAGGCTAGGCTAGGTGTA 59.218 52.381 40.99 18.20 36.99 2.90
212 218 1.887854 GCTAGGCTAGGCTAGGTGTAC 59.112 57.143 39.31 25.56 0.00 2.90
213 219 2.489437 GCTAGGCTAGGCTAGGTGTACT 60.489 54.545 39.31 13.46 0.00 2.73
219 225 4.205587 GCTAGGCTAGGTGTACTTACTCA 58.794 47.826 22.40 0.00 0.00 3.41
224 230 5.185442 AGGCTAGGTGTACTTACTCAAACTC 59.815 44.000 0.00 0.00 0.00 3.01
291 297 2.185004 ACTGCTTGCTATTTCCACGT 57.815 45.000 0.00 0.00 0.00 4.49
292 298 2.076863 ACTGCTTGCTATTTCCACGTC 58.923 47.619 0.00 0.00 0.00 4.34
293 299 2.289694 ACTGCTTGCTATTTCCACGTCT 60.290 45.455 0.00 0.00 0.00 4.18
294 300 2.744202 CTGCTTGCTATTTCCACGTCTT 59.256 45.455 0.00 0.00 0.00 3.01
335 341 6.490566 ACATACAGTCAATAACCGGAAAAC 57.509 37.500 9.46 0.00 0.00 2.43
336 342 5.998981 ACATACAGTCAATAACCGGAAAACA 59.001 36.000 9.46 0.00 0.00 2.83
356 362 4.615513 ACAGTTAGCTAATCCTCCTCTGT 58.384 43.478 9.88 12.77 0.00 3.41
358 364 3.886505 AGTTAGCTAATCCTCCTCTGTCG 59.113 47.826 9.88 0.00 0.00 4.35
359 365 1.036707 AGCTAATCCTCCTCTGTCGC 58.963 55.000 0.00 0.00 0.00 5.19
362 368 2.623889 GCTAATCCTCCTCTGTCGCTAA 59.376 50.000 0.00 0.00 0.00 3.09
363 369 3.068307 GCTAATCCTCCTCTGTCGCTAAA 59.932 47.826 0.00 0.00 0.00 1.85
364 370 3.528597 AATCCTCCTCTGTCGCTAAAC 57.471 47.619 0.00 0.00 0.00 2.01
365 371 1.919240 TCCTCCTCTGTCGCTAAACA 58.081 50.000 0.00 0.00 0.00 2.83
366 372 2.244695 TCCTCCTCTGTCGCTAAACAA 58.755 47.619 0.00 0.00 0.00 2.83
367 373 2.631062 TCCTCCTCTGTCGCTAAACAAA 59.369 45.455 0.00 0.00 0.00 2.83
368 374 2.737252 CCTCCTCTGTCGCTAAACAAAC 59.263 50.000 0.00 0.00 0.00 2.93
369 375 3.390135 CTCCTCTGTCGCTAAACAAACA 58.610 45.455 0.00 0.00 0.00 2.83
370 376 3.390135 TCCTCTGTCGCTAAACAAACAG 58.610 45.455 0.00 0.00 40.34 3.16
371 377 3.131396 CCTCTGTCGCTAAACAAACAGT 58.869 45.455 0.00 0.00 40.01 3.55
372 378 3.560068 CCTCTGTCGCTAAACAAACAGTT 59.440 43.478 0.00 0.00 43.89 3.16
373 379 4.748102 CCTCTGTCGCTAAACAAACAGTTA 59.252 41.667 0.00 0.00 40.26 2.24
374 380 5.107453 CCTCTGTCGCTAAACAAACAGTTAG 60.107 44.000 0.00 0.00 40.26 2.34
377 383 5.291178 TGTCGCTAAACAAACAGTTAGCTA 58.709 37.500 12.19 0.00 40.26 3.32
378 384 5.754406 TGTCGCTAAACAAACAGTTAGCTAA 59.246 36.000 0.86 0.86 40.26 3.09
379 385 6.425721 TGTCGCTAAACAAACAGTTAGCTAAT 59.574 34.615 9.88 0.00 40.26 1.73
380 386 6.954297 GTCGCTAAACAAACAGTTAGCTAATC 59.046 38.462 9.88 3.85 40.26 1.75
381 387 6.091713 TCGCTAAACAAACAGTTAGCTAATCC 59.908 38.462 9.88 0.00 40.26 3.01
382 388 6.092259 CGCTAAACAAACAGTTAGCTAATCCT 59.908 38.462 9.88 0.00 40.26 3.24
383 389 7.465173 GCTAAACAAACAGTTAGCTAATCCTC 58.535 38.462 9.88 0.00 40.26 3.71
384 390 6.819397 AAACAAACAGTTAGCTAATCCTCC 57.181 37.500 9.88 0.00 40.26 4.30
385 391 5.763876 ACAAACAGTTAGCTAATCCTCCT 57.236 39.130 9.88 0.00 0.00 3.69
386 392 5.735766 ACAAACAGTTAGCTAATCCTCCTC 58.264 41.667 9.88 0.00 0.00 3.71
387 393 5.485708 ACAAACAGTTAGCTAATCCTCCTCT 59.514 40.000 9.88 0.00 0.00 3.69
390 396 4.647399 ACAGTTAGCTAATCCTCCTCTGTC 59.353 45.833 9.88 0.00 0.00 3.51
391 397 3.886505 AGTTAGCTAATCCTCCTCTGTCG 59.113 47.826 9.88 0.00 0.00 4.35
393 399 1.036707 GCTAATCCTCCTCTGTCGCT 58.963 55.000 0.00 0.00 0.00 4.93
394 400 2.158593 AGCTAATCCTCCTCTGTCGCTA 60.159 50.000 0.00 0.00 0.00 4.26
395 401 2.623889 GCTAATCCTCCTCTGTCGCTAA 59.376 50.000 0.00 0.00 0.00 3.09
396 402 3.068307 GCTAATCCTCCTCTGTCGCTAAA 59.932 47.826 0.00 0.00 0.00 1.85
397 403 3.528597 AATCCTCCTCTGTCGCTAAAC 57.471 47.619 0.00 0.00 0.00 2.01
398 404 1.919240 TCCTCCTCTGTCGCTAAACA 58.081 50.000 0.00 0.00 0.00 2.83
399 405 2.244695 TCCTCCTCTGTCGCTAAACAA 58.755 47.619 0.00 0.00 0.00 2.83
400 406 2.631062 TCCTCCTCTGTCGCTAAACAAA 59.369 45.455 0.00 0.00 0.00 2.83
401 407 2.737252 CCTCCTCTGTCGCTAAACAAAC 59.263 50.000 0.00 0.00 0.00 2.93
402 408 3.390135 CTCCTCTGTCGCTAAACAAACA 58.610 45.455 0.00 0.00 0.00 2.83
403 409 3.390135 TCCTCTGTCGCTAAACAAACAG 58.610 45.455 0.00 0.00 40.34 3.16
404 410 3.131396 CCTCTGTCGCTAAACAAACAGT 58.869 45.455 0.00 0.00 40.01 3.55
405 411 3.560068 CCTCTGTCGCTAAACAAACAGTT 59.440 43.478 0.00 0.00 43.89 3.16
406 412 4.748102 CCTCTGTCGCTAAACAAACAGTTA 59.252 41.667 0.00 0.00 40.26 2.24
419 442 5.675538 ACAAACAGTTAGCCATAGAGGATC 58.324 41.667 0.00 0.00 41.22 3.36
421 444 6.126652 ACAAACAGTTAGCCATAGAGGATCAT 60.127 38.462 0.00 0.00 41.22 2.45
423 446 7.618019 AACAGTTAGCCATAGAGGATCATAA 57.382 36.000 0.00 0.00 41.22 1.90
424 447 7.805083 ACAGTTAGCCATAGAGGATCATAAT 57.195 36.000 0.00 0.00 41.22 1.28
425 448 7.619050 ACAGTTAGCCATAGAGGATCATAATG 58.381 38.462 0.00 0.00 41.22 1.90
426 449 7.046652 CAGTTAGCCATAGAGGATCATAATGG 58.953 42.308 14.09 14.09 41.96 3.16
427 450 6.732862 AGTTAGCCATAGAGGATCATAATGGT 59.267 38.462 17.74 10.24 41.45 3.55
428 451 7.901322 AGTTAGCCATAGAGGATCATAATGGTA 59.099 37.037 17.74 9.55 41.45 3.25
429 452 8.709308 GTTAGCCATAGAGGATCATAATGGTAT 58.291 37.037 17.74 11.78 41.45 2.73
430 453 9.951866 TTAGCCATAGAGGATCATAATGGTATA 57.048 33.333 17.74 11.08 41.45 1.47
432 455 9.099071 AGCCATAGAGGATCATAATGGTATATC 57.901 37.037 17.74 5.76 41.45 1.63
433 456 9.099071 GCCATAGAGGATCATAATGGTATATCT 57.901 37.037 17.74 0.00 41.45 1.98
458 481 6.699895 TGTGTACTATCGCTAAACAAACAG 57.300 37.500 0.00 0.00 0.00 3.16
462 485 7.115947 GTGTACTATCGCTAAACAAACAGTTCT 59.884 37.037 0.00 0.00 40.26 3.01
463 486 7.654520 TGTACTATCGCTAAACAAACAGTTCTT 59.345 33.333 0.00 0.00 40.26 2.52
464 487 7.118422 ACTATCGCTAAACAAACAGTTCTTC 57.882 36.000 0.00 0.00 40.26 2.87
465 488 6.704493 ACTATCGCTAAACAAACAGTTCTTCA 59.296 34.615 0.00 0.00 40.26 3.02
466 489 5.804692 TCGCTAAACAAACAGTTCTTCAA 57.195 34.783 0.00 0.00 40.26 2.69
518 542 8.582437 CATTTATCATGGGCAGACTTCATAATT 58.418 33.333 0.00 0.00 0.00 1.40
577 601 3.436704 ACCACATGCTCTGTACAATTTCG 59.563 43.478 0.00 0.00 35.91 3.46
654 678 6.426025 TGAGATGCTATATTGATCTGTTGTGC 59.574 38.462 0.00 0.00 0.00 4.57
673 697 4.202000 TGTGCGATGTGTTCTGTTGAAAAT 60.202 37.500 0.00 0.00 33.52 1.82
674 698 4.739716 GTGCGATGTGTTCTGTTGAAAATT 59.260 37.500 0.00 0.00 33.52 1.82
675 699 5.231991 GTGCGATGTGTTCTGTTGAAAATTT 59.768 36.000 0.00 0.00 33.52 1.82
676 700 5.458452 TGCGATGTGTTCTGTTGAAAATTTC 59.542 36.000 0.00 0.00 33.52 2.17
677 701 5.687285 GCGATGTGTTCTGTTGAAAATTTCT 59.313 36.000 7.29 0.00 33.52 2.52
678 702 6.855914 GCGATGTGTTCTGTTGAAAATTTCTA 59.144 34.615 7.29 0.00 33.52 2.10
679 703 7.059945 GCGATGTGTTCTGTTGAAAATTTCTAG 59.940 37.037 7.29 3.63 33.52 2.43
680 704 7.535258 CGATGTGTTCTGTTGAAAATTTCTAGG 59.465 37.037 7.29 0.00 33.52 3.02
681 705 7.873719 TGTGTTCTGTTGAAAATTTCTAGGA 57.126 32.000 7.29 0.00 33.52 2.94
682 706 8.287439 TGTGTTCTGTTGAAAATTTCTAGGAA 57.713 30.769 7.29 4.80 33.52 3.36
683 707 8.912988 TGTGTTCTGTTGAAAATTTCTAGGAAT 58.087 29.630 7.29 0.00 33.52 3.01
684 708 9.750125 GTGTTCTGTTGAAAATTTCTAGGAATT 57.250 29.630 2.89 2.89 33.52 2.17
698 722 9.991906 ATTTCTAGGAATTATTTGAATGGCATG 57.008 29.630 0.00 0.00 0.00 4.06
699 723 8.765488 TTCTAGGAATTATTTGAATGGCATGA 57.235 30.769 0.00 0.00 0.00 3.07
700 724 8.169977 TCTAGGAATTATTTGAATGGCATGAC 57.830 34.615 0.00 0.00 0.00 3.06
701 725 8.000709 TCTAGGAATTATTTGAATGGCATGACT 58.999 33.333 0.00 0.00 0.00 3.41
702 726 9.288576 CTAGGAATTATTTGAATGGCATGACTA 57.711 33.333 0.00 0.00 0.00 2.59
703 727 8.174733 AGGAATTATTTGAATGGCATGACTAG 57.825 34.615 0.00 0.00 0.00 2.57
716 774 6.414732 TGGCATGACTAGTGCTTAAGTAATT 58.585 36.000 0.00 0.00 42.16 1.40
743 801 2.399580 ACTACCCTGCCTGGAAGTATC 58.600 52.381 0.00 0.00 38.35 2.24
744 802 1.694696 CTACCCTGCCTGGAAGTATCC 59.305 57.143 0.00 0.00 46.76 2.59
777 835 1.821088 ACTCTGTTCCCCCTTGTCTT 58.179 50.000 0.00 0.00 0.00 3.01
825 883 6.037830 ACGGTTGCACCTTATGTTATGTTATC 59.962 38.462 0.00 0.00 35.66 1.75
900 958 1.029408 GGCCACCGTGCATATGTCAA 61.029 55.000 0.00 0.00 0.00 3.18
924 982 8.865978 CAATATCCATTTATCAATTCGCATTGG 58.134 33.333 7.93 0.00 40.41 3.16
944 1003 9.617975 GCATTGGATTTATTATAACTCTGCTTC 57.382 33.333 7.36 0.00 0.00 3.86
981 1040 7.119846 GCCATGTATGATAACTACAGAAATCCC 59.880 40.741 0.00 0.00 32.91 3.85
1044 1103 4.508943 CCTGGCCCATATGACAATCCATTA 60.509 45.833 3.65 0.00 0.00 1.90
1155 1214 2.708861 TGTAAGGAGCCTCCAAAGAACA 59.291 45.455 14.46 6.55 39.61 3.18
1162 1221 4.268359 GAGCCTCCAAAGAACATTGATCT 58.732 43.478 0.00 0.00 31.84 2.75
1183 1266 1.613437 CCCTGGTGTTTCAAATCGCTT 59.387 47.619 0.00 0.00 0.00 4.68
1362 1449 7.248976 TCCCATCTACACTGGATATGTATCTT 58.751 38.462 0.51 0.00 35.70 2.40
1401 1488 9.871238 ATATATCGGGTGTACTGAAATATGTTC 57.129 33.333 0.00 0.00 38.16 3.18
1403 1490 3.554324 CGGGTGTACTGAAATATGTTCCG 59.446 47.826 0.00 0.00 0.00 4.30
1404 1491 4.510571 GGGTGTACTGAAATATGTTCCGT 58.489 43.478 0.00 0.00 0.00 4.69
1405 1492 4.569564 GGGTGTACTGAAATATGTTCCGTC 59.430 45.833 0.00 0.00 0.00 4.79
1406 1493 5.416947 GGTGTACTGAAATATGTTCCGTCT 58.583 41.667 0.00 0.00 0.00 4.18
1407 1494 5.873164 GGTGTACTGAAATATGTTCCGTCTT 59.127 40.000 0.00 0.00 0.00 3.01
1408 1495 6.370718 GGTGTACTGAAATATGTTCCGTCTTT 59.629 38.462 0.00 0.00 0.00 2.52
1409 1496 7.412672 GGTGTACTGAAATATGTTCCGTCTTTC 60.413 40.741 0.00 0.00 0.00 2.62
1410 1497 6.592607 TGTACTGAAATATGTTCCGTCTTTCC 59.407 38.462 0.00 0.00 0.00 3.13
1411 1498 5.805728 ACTGAAATATGTTCCGTCTTTCCT 58.194 37.500 0.00 0.00 0.00 3.36
1412 1499 6.942976 ACTGAAATATGTTCCGTCTTTCCTA 58.057 36.000 0.00 0.00 0.00 2.94
1413 1500 7.042335 ACTGAAATATGTTCCGTCTTTCCTAG 58.958 38.462 0.00 0.00 0.00 3.02
1414 1501 5.815740 TGAAATATGTTCCGTCTTTCCTAGC 59.184 40.000 0.00 0.00 0.00 3.42
1415 1502 5.615925 AATATGTTCCGTCTTTCCTAGCT 57.384 39.130 0.00 0.00 0.00 3.32
1416 1503 2.743636 TGTTCCGTCTTTCCTAGCTG 57.256 50.000 0.00 0.00 0.00 4.24
1417 1504 1.337823 TGTTCCGTCTTTCCTAGCTGC 60.338 52.381 0.00 0.00 0.00 5.25
1418 1505 0.108804 TTCCGTCTTTCCTAGCTGCG 60.109 55.000 0.00 0.00 0.00 5.18
1419 1506 2.167861 CCGTCTTTCCTAGCTGCGC 61.168 63.158 0.00 0.00 0.00 6.09
1420 1507 1.153745 CGTCTTTCCTAGCTGCGCT 60.154 57.895 9.73 8.09 43.41 5.92
1421 1508 1.416813 CGTCTTTCCTAGCTGCGCTG 61.417 60.000 9.73 10.04 40.10 5.18
1422 1509 1.086634 GTCTTTCCTAGCTGCGCTGG 61.087 60.000 16.47 9.55 40.10 4.85
1423 1510 1.219124 CTTTCCTAGCTGCGCTGGA 59.781 57.895 16.47 13.48 39.54 3.86
1424 1511 0.179062 CTTTCCTAGCTGCGCTGGAT 60.179 55.000 16.47 6.68 39.54 3.41
1425 1512 1.069204 CTTTCCTAGCTGCGCTGGATA 59.931 52.381 16.47 7.51 39.54 2.59
1426 1513 1.342074 TTCCTAGCTGCGCTGGATAT 58.658 50.000 16.47 0.00 39.54 1.63
1427 1514 0.605083 TCCTAGCTGCGCTGGATATG 59.395 55.000 16.47 5.90 39.54 1.78
1428 1515 0.319728 CCTAGCTGCGCTGGATATGT 59.680 55.000 16.47 0.00 39.54 2.29
1429 1516 1.270518 CCTAGCTGCGCTGGATATGTT 60.271 52.381 16.47 0.00 39.54 2.71
1430 1517 2.487934 CTAGCTGCGCTGGATATGTTT 58.512 47.619 16.47 0.00 39.54 2.83
1431 1518 1.303309 AGCTGCGCTGGATATGTTTC 58.697 50.000 16.47 0.00 37.57 2.78
1432 1519 1.134280 AGCTGCGCTGGATATGTTTCT 60.134 47.619 16.47 0.00 37.57 2.52
1433 1520 1.003116 GCTGCGCTGGATATGTTTCTG 60.003 52.381 16.47 0.00 0.00 3.02
1434 1521 1.600957 CTGCGCTGGATATGTTTCTGG 59.399 52.381 9.73 0.00 0.00 3.86
1435 1522 1.065491 TGCGCTGGATATGTTTCTGGT 60.065 47.619 9.73 0.00 0.00 4.00
1436 1523 2.017049 GCGCTGGATATGTTTCTGGTT 58.983 47.619 0.00 0.00 0.00 3.67
1437 1524 2.032178 GCGCTGGATATGTTTCTGGTTC 59.968 50.000 0.00 0.00 0.00 3.62
1438 1525 3.535561 CGCTGGATATGTTTCTGGTTCT 58.464 45.455 0.00 0.00 0.00 3.01
1439 1526 3.941483 CGCTGGATATGTTTCTGGTTCTT 59.059 43.478 0.00 0.00 0.00 2.52
1440 1527 4.396166 CGCTGGATATGTTTCTGGTTCTTT 59.604 41.667 0.00 0.00 0.00 2.52
1441 1528 5.106157 CGCTGGATATGTTTCTGGTTCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
1442 1529 6.093495 CGCTGGATATGTTTCTGGTTCTTTTA 59.907 38.462 0.00 0.00 0.00 1.52
1443 1530 7.201732 CGCTGGATATGTTTCTGGTTCTTTTAT 60.202 37.037 0.00 0.00 0.00 1.40
1444 1531 8.131731 GCTGGATATGTTTCTGGTTCTTTTATC 58.868 37.037 0.00 0.00 0.00 1.75
1445 1532 9.401058 CTGGATATGTTTCTGGTTCTTTTATCT 57.599 33.333 0.00 0.00 0.00 1.98
1451 1538 8.792830 TGTTTCTGGTTCTTTTATCTATCTGG 57.207 34.615 0.00 0.00 0.00 3.86
1452 1539 8.383175 TGTTTCTGGTTCTTTTATCTATCTGGT 58.617 33.333 0.00 0.00 0.00 4.00
1453 1540 8.669243 GTTTCTGGTTCTTTTATCTATCTGGTG 58.331 37.037 0.00 0.00 0.00 4.17
1454 1541 7.496346 TCTGGTTCTTTTATCTATCTGGTGT 57.504 36.000 0.00 0.00 0.00 4.16
1455 1542 8.603898 TCTGGTTCTTTTATCTATCTGGTGTA 57.396 34.615 0.00 0.00 0.00 2.90
1456 1543 8.475639 TCTGGTTCTTTTATCTATCTGGTGTAC 58.524 37.037 0.00 0.00 0.00 2.90
1457 1544 8.375493 TGGTTCTTTTATCTATCTGGTGTACT 57.625 34.615 0.00 0.00 0.00 2.73
1458 1545 8.258007 TGGTTCTTTTATCTATCTGGTGTACTG 58.742 37.037 0.00 0.00 0.00 2.74
1459 1546 8.475639 GGTTCTTTTATCTATCTGGTGTACTGA 58.524 37.037 0.00 0.00 0.00 3.41
1460 1547 9.871238 GTTCTTTTATCTATCTGGTGTACTGAA 57.129 33.333 0.00 0.00 0.00 3.02
1642 1729 0.899717 TGGGCTTCATGGGAAAGTGC 60.900 55.000 0.00 0.00 31.35 4.40
1644 1731 1.244019 GGCTTCATGGGAAAGTGCGT 61.244 55.000 0.00 0.00 31.35 5.24
1716 1817 2.107950 TCCTAATGCACTTGAACCCG 57.892 50.000 0.00 0.00 0.00 5.28
1961 2063 1.076485 GAGCCTGTGCATGGGGATT 60.076 57.895 10.15 0.00 41.13 3.01
1964 2066 0.614812 GCCTGTGCATGGGGATTTTT 59.385 50.000 10.15 0.00 37.47 1.94
2123 2243 6.499172 CGCATGAGATAGTCTTCTCTGTAAA 58.501 40.000 0.00 0.00 42.22 2.01
2141 2261 7.145323 TCTGTAAATTTGGCACTAGAAAAAGC 58.855 34.615 0.00 0.00 0.00 3.51
2221 2361 7.285172 TCATCATATATGTTTTGTTGACAGGGG 59.715 37.037 12.42 0.00 0.00 4.79
2263 2403 8.795786 TGTATAAAGTTGTGAATTTTGCAGTC 57.204 30.769 0.00 0.00 0.00 3.51
2295 2435 8.924691 CCATTTTGTAGTATGTTTGTTGGAATG 58.075 33.333 0.00 0.00 0.00 2.67
2405 2559 4.370917 ACTGGCATTGTTTGAATGTTCAC 58.629 39.130 0.00 0.00 36.83 3.18
2428 2603 5.102953 TCAGTGAAAGTATATGCCAGCTT 57.897 39.130 0.00 0.00 0.00 3.74
2447 2622 3.686726 GCTTCAGTCTGTCATTTGGTAGG 59.313 47.826 0.00 0.00 0.00 3.18
2554 2733 4.398319 TGATTTCCTCAGAGTTTTGGTCC 58.602 43.478 0.00 0.00 0.00 4.46
2560 2739 2.291741 CTCAGAGTTTTGGTCCAACAGC 59.708 50.000 2.98 0.00 0.00 4.40
2585 2764 8.067189 GCTTTTCTCAAAACAAGACAAACAAAA 58.933 29.630 0.00 0.00 0.00 2.44
2629 2808 7.712205 ACTGATTTTCTTTGGATTTTTGGTGAG 59.288 33.333 0.00 0.00 0.00 3.51
2698 2877 4.336153 AGATGCGTGCAATGTATGAAATGA 59.664 37.500 0.00 0.00 0.00 2.57
2720 2899 7.561021 TGAATTAGCAACAAGTGAACAAGTA 57.439 32.000 0.00 0.00 0.00 2.24
2722 2901 7.282224 TGAATTAGCAACAAGTGAACAAGTACT 59.718 33.333 0.00 0.00 0.00 2.73
2726 2905 6.782150 AGCAACAAGTGAACAAGTACTTAAC 58.218 36.000 8.04 4.97 35.50 2.01
2727 2906 6.373216 AGCAACAAGTGAACAAGTACTTAACA 59.627 34.615 8.04 6.17 35.50 2.41
2729 2908 7.007995 GCAACAAGTGAACAAGTACTTAACAAC 59.992 37.037 8.04 5.31 35.50 3.32
2730 2909 6.768078 ACAAGTGAACAAGTACTTAACAACG 58.232 36.000 8.04 0.00 35.50 4.10
2731 2910 6.369615 ACAAGTGAACAAGTACTTAACAACGT 59.630 34.615 8.04 0.00 35.50 3.99
2734 2921 8.477984 AGTGAACAAGTACTTAACAACGTTTA 57.522 30.769 8.04 1.51 0.00 2.01
2763 2950 7.326063 GGATAAATTCTGAACGACCAAAAACAG 59.674 37.037 0.00 0.00 0.00 3.16
2820 3010 3.686241 CCAGAATTCATTCTCAAGCACGA 59.314 43.478 8.44 0.00 44.84 4.35
2829 3019 1.326245 TCTCAAGCACGACAACAAACG 59.674 47.619 0.00 0.00 0.00 3.60
2831 3021 0.248054 CAAGCACGACAACAAACGCT 60.248 50.000 0.00 0.00 0.00 5.07
2873 3063 2.222007 GCAGTTGCACATTCCAACAA 57.778 45.000 6.98 0.00 43.74 2.83
2884 3074 3.634448 ACATTCCAACAACCATTCGTCAA 59.366 39.130 0.00 0.00 0.00 3.18
2885 3075 4.098654 ACATTCCAACAACCATTCGTCAAA 59.901 37.500 0.00 0.00 0.00 2.69
2888 3078 5.269505 TCCAACAACCATTCGTCAAAAAT 57.730 34.783 0.00 0.00 0.00 1.82
2889 3079 5.046529 TCCAACAACCATTCGTCAAAAATG 58.953 37.500 0.00 0.00 34.55 2.32
2930 3123 0.366196 CGCGCCGTTCGTATTAAACA 59.634 50.000 0.00 0.00 41.07 2.83
2931 3124 1.588082 CGCGCCGTTCGTATTAAACAG 60.588 52.381 0.00 0.00 41.07 3.16
2932 3125 1.391144 GCGCCGTTCGTATTAAACAGT 59.609 47.619 0.00 0.00 41.07 3.55
2933 3126 2.781973 GCGCCGTTCGTATTAAACAGTG 60.782 50.000 0.00 0.00 41.07 3.66
2934 3127 2.765918 GCCGTTCGTATTAAACAGTGC 58.234 47.619 0.00 0.00 0.00 4.40
2935 3128 2.158058 GCCGTTCGTATTAAACAGTGCA 59.842 45.455 0.00 0.00 0.00 4.57
2936 3129 3.364167 GCCGTTCGTATTAAACAGTGCAA 60.364 43.478 0.00 0.00 0.00 4.08
2937 3130 4.774586 CCGTTCGTATTAAACAGTGCAAA 58.225 39.130 0.00 0.00 0.00 3.68
2938 3131 4.843984 CCGTTCGTATTAAACAGTGCAAAG 59.156 41.667 0.00 0.00 0.00 2.77
2939 3132 4.843984 CGTTCGTATTAAACAGTGCAAAGG 59.156 41.667 0.00 0.00 0.00 3.11
2940 3133 5.559417 CGTTCGTATTAAACAGTGCAAAGGT 60.559 40.000 0.00 0.00 0.00 3.50
2941 3134 5.600908 TCGTATTAAACAGTGCAAAGGTC 57.399 39.130 0.00 0.00 0.00 3.85
2942 3135 4.453136 TCGTATTAAACAGTGCAAAGGTCC 59.547 41.667 0.00 0.00 0.00 4.46
2943 3136 3.915437 ATTAAACAGTGCAAAGGTCCG 57.085 42.857 0.00 0.00 0.00 4.79
2944 3137 2.623878 TAAACAGTGCAAAGGTCCGA 57.376 45.000 0.00 0.00 0.00 4.55
2945 3138 1.981256 AAACAGTGCAAAGGTCCGAT 58.019 45.000 0.00 0.00 0.00 4.18
2946 3139 1.238439 AACAGTGCAAAGGTCCGATG 58.762 50.000 0.00 0.00 0.00 3.84
2947 3140 1.237285 ACAGTGCAAAGGTCCGATGC 61.237 55.000 13.29 13.29 40.45 3.91
2948 3141 1.073025 AGTGCAAAGGTCCGATGCA 59.927 52.632 17.51 17.51 46.97 3.96
2949 3142 4.490696 TGCAAAGGTCCGATGCAA 57.509 50.000 18.70 6.20 46.23 4.08
2950 3143 2.725811 TGCAAAGGTCCGATGCAAA 58.274 47.368 18.70 1.09 46.23 3.68
2951 3144 1.035923 TGCAAAGGTCCGATGCAAAA 58.964 45.000 18.70 0.47 46.23 2.44
2952 3145 1.410517 TGCAAAGGTCCGATGCAAAAA 59.589 42.857 18.70 0.16 46.23 1.94
3021 3214 5.458891 CAAGAAGAAACTTTGGCATCTCAG 58.541 41.667 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
118 119 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
124 125 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
160 166 7.903995 ATGTTGTTTTCTTTCTTTCTTTGCA 57.096 28.000 0.00 0.00 0.00 4.08
164 170 9.822185 AGCATTATGTTGTTTTCTTTCTTTCTT 57.178 25.926 0.00 0.00 0.00 2.52
203 209 6.978338 TGTGAGTTTGAGTAAGTACACCTAG 58.022 40.000 0.00 0.00 0.00 3.02
204 210 6.964807 TGTGAGTTTGAGTAAGTACACCTA 57.035 37.500 0.00 0.00 0.00 3.08
205 211 5.864418 TGTGAGTTTGAGTAAGTACACCT 57.136 39.130 0.00 0.00 0.00 4.00
206 212 6.456501 AGATGTGAGTTTGAGTAAGTACACC 58.543 40.000 0.00 0.00 0.00 4.16
207 213 7.755822 CCTAGATGTGAGTTTGAGTAAGTACAC 59.244 40.741 0.00 0.00 0.00 2.90
208 214 7.668469 TCCTAGATGTGAGTTTGAGTAAGTACA 59.332 37.037 0.00 0.00 0.00 2.90
209 215 8.053026 TCCTAGATGTGAGTTTGAGTAAGTAC 57.947 38.462 0.00 0.00 0.00 2.73
210 216 8.645814 TTCCTAGATGTGAGTTTGAGTAAGTA 57.354 34.615 0.00 0.00 0.00 2.24
211 217 7.540474 TTCCTAGATGTGAGTTTGAGTAAGT 57.460 36.000 0.00 0.00 0.00 2.24
212 218 8.253810 TCATTCCTAGATGTGAGTTTGAGTAAG 58.746 37.037 0.00 0.00 0.00 2.34
213 219 8.134202 TCATTCCTAGATGTGAGTTTGAGTAA 57.866 34.615 0.00 0.00 0.00 2.24
219 225 6.319048 ACCATCATTCCTAGATGTGAGTTT 57.681 37.500 0.00 0.00 40.93 2.66
224 230 5.922053 TCAGAACCATCATTCCTAGATGTG 58.078 41.667 0.00 0.00 40.93 3.21
319 325 5.180680 AGCTAACTGTTTTCCGGTTATTGAC 59.819 40.000 0.00 0.00 42.58 3.18
327 333 4.514401 AGGATTAGCTAACTGTTTTCCGG 58.486 43.478 8.70 0.00 0.00 5.14
335 341 4.261405 CGACAGAGGAGGATTAGCTAACTG 60.261 50.000 8.70 11.77 0.00 3.16
336 342 3.886505 CGACAGAGGAGGATTAGCTAACT 59.113 47.826 8.70 1.93 0.00 2.24
356 362 6.091713 GGATTAGCTAACTGTTTGTTTAGCGA 59.908 38.462 8.70 0.00 38.77 4.93
358 364 7.379098 AGGATTAGCTAACTGTTTGTTTAGC 57.621 36.000 8.70 0.93 39.89 3.09
359 365 7.824779 AGGAGGATTAGCTAACTGTTTGTTTAG 59.175 37.037 8.70 0.00 39.89 1.85
362 368 6.013293 AGAGGAGGATTAGCTAACTGTTTGTT 60.013 38.462 8.70 0.00 42.31 2.83
363 369 5.485708 AGAGGAGGATTAGCTAACTGTTTGT 59.514 40.000 8.70 0.00 0.00 2.83
364 370 5.814705 CAGAGGAGGATTAGCTAACTGTTTG 59.185 44.000 8.70 0.00 0.00 2.93
365 371 5.485708 ACAGAGGAGGATTAGCTAACTGTTT 59.514 40.000 8.70 0.00 33.29 2.83
366 372 5.026790 ACAGAGGAGGATTAGCTAACTGTT 58.973 41.667 8.70 0.00 33.29 3.16
367 373 4.615513 ACAGAGGAGGATTAGCTAACTGT 58.384 43.478 8.70 12.40 0.00 3.55
368 374 4.261405 CGACAGAGGAGGATTAGCTAACTG 60.261 50.000 8.70 11.77 0.00 3.16
369 375 3.886505 CGACAGAGGAGGATTAGCTAACT 59.113 47.826 8.70 1.93 0.00 2.24
370 376 3.551250 GCGACAGAGGAGGATTAGCTAAC 60.551 52.174 8.70 3.03 0.00 2.34
371 377 2.623889 GCGACAGAGGAGGATTAGCTAA 59.376 50.000 8.99 8.99 0.00 3.09
372 378 2.158593 AGCGACAGAGGAGGATTAGCTA 60.159 50.000 0.00 0.00 0.00 3.32
373 379 1.036707 GCGACAGAGGAGGATTAGCT 58.963 55.000 0.00 0.00 0.00 3.32
374 380 1.036707 AGCGACAGAGGAGGATTAGC 58.963 55.000 0.00 0.00 0.00 3.09
377 383 2.832129 TGTTTAGCGACAGAGGAGGATT 59.168 45.455 0.00 0.00 0.00 3.01
378 384 2.457598 TGTTTAGCGACAGAGGAGGAT 58.542 47.619 0.00 0.00 0.00 3.24
379 385 1.919240 TGTTTAGCGACAGAGGAGGA 58.081 50.000 0.00 0.00 0.00 3.71
380 386 2.737252 GTTTGTTTAGCGACAGAGGAGG 59.263 50.000 0.00 0.00 0.00 4.30
381 387 3.390135 TGTTTGTTTAGCGACAGAGGAG 58.610 45.455 0.00 0.00 0.00 3.69
382 388 3.181469 ACTGTTTGTTTAGCGACAGAGGA 60.181 43.478 9.10 0.00 41.46 3.71
383 389 3.131396 ACTGTTTGTTTAGCGACAGAGG 58.869 45.455 9.10 0.00 41.46 3.69
384 390 4.795970 AACTGTTTGTTTAGCGACAGAG 57.204 40.909 9.10 0.00 41.46 3.35
385 391 4.210537 GCTAACTGTTTGTTTAGCGACAGA 59.789 41.667 9.10 0.00 41.46 3.41
386 392 4.455124 GCTAACTGTTTGTTTAGCGACAG 58.545 43.478 0.00 0.00 43.81 3.51
387 393 3.249080 GGCTAACTGTTTGTTTAGCGACA 59.751 43.478 0.00 0.00 39.89 4.35
390 396 3.889196 TGGCTAACTGTTTGTTTAGCG 57.111 42.857 0.00 0.00 39.89 4.26
391 397 6.183360 CCTCTATGGCTAACTGTTTGTTTAGC 60.183 42.308 0.00 0.72 39.89 3.09
393 399 7.011499 TCCTCTATGGCTAACTGTTTGTTTA 57.989 36.000 0.00 0.00 36.57 2.01
394 400 5.876357 TCCTCTATGGCTAACTGTTTGTTT 58.124 37.500 0.00 0.00 36.57 2.83
395 401 5.499004 TCCTCTATGGCTAACTGTTTGTT 57.501 39.130 0.00 0.00 37.96 2.83
396 402 5.189736 TGATCCTCTATGGCTAACTGTTTGT 59.810 40.000 0.00 0.00 35.26 2.83
397 403 5.674525 TGATCCTCTATGGCTAACTGTTTG 58.325 41.667 0.00 0.00 35.26 2.93
398 404 5.957771 TGATCCTCTATGGCTAACTGTTT 57.042 39.130 0.00 0.00 35.26 2.83
399 405 7.618019 TTATGATCCTCTATGGCTAACTGTT 57.382 36.000 0.00 0.00 35.26 3.16
400 406 7.310921 CCATTATGATCCTCTATGGCTAACTGT 60.311 40.741 0.00 0.00 35.26 3.55
401 407 7.046652 CCATTATGATCCTCTATGGCTAACTG 58.953 42.308 0.00 0.00 35.26 3.16
402 408 6.732862 ACCATTATGATCCTCTATGGCTAACT 59.267 38.462 11.15 0.00 39.46 2.24
403 409 6.951971 ACCATTATGATCCTCTATGGCTAAC 58.048 40.000 11.15 0.00 39.46 2.34
404 410 8.860517 ATACCATTATGATCCTCTATGGCTAA 57.139 34.615 11.15 1.87 39.46 3.09
406 412 9.099071 GATATACCATTATGATCCTCTATGGCT 57.901 37.037 11.15 4.67 39.46 4.75
421 444 9.850628 GCGATAGTACACAAAGATATACCATTA 57.149 33.333 0.00 0.00 39.35 1.90
423 446 8.123639 AGCGATAGTACACAAAGATATACCAT 57.876 34.615 0.00 0.00 39.35 3.55
424 447 7.520451 AGCGATAGTACACAAAGATATACCA 57.480 36.000 0.00 0.00 39.35 3.25
425 448 9.903682 TTTAGCGATAGTACACAAAGATATACC 57.096 33.333 0.00 0.00 39.35 2.73
428 451 9.811995 TTGTTTAGCGATAGTACACAAAGATAT 57.188 29.630 0.00 0.00 39.35 1.63
429 452 9.642327 TTTGTTTAGCGATAGTACACAAAGATA 57.358 29.630 0.00 0.00 32.63 1.98
430 453 8.440833 GTTTGTTTAGCGATAGTACACAAAGAT 58.559 33.333 8.77 0.00 35.30 2.40
431 454 7.438757 TGTTTGTTTAGCGATAGTACACAAAGA 59.561 33.333 8.77 6.34 35.30 2.52
432 455 7.569297 TGTTTGTTTAGCGATAGTACACAAAG 58.431 34.615 8.77 0.00 35.30 2.77
433 456 7.225145 ACTGTTTGTTTAGCGATAGTACACAAA 59.775 33.333 0.00 0.00 33.83 2.83
434 457 6.702723 ACTGTTTGTTTAGCGATAGTACACAA 59.297 34.615 0.00 0.00 39.35 3.33
435 458 6.218019 ACTGTTTGTTTAGCGATAGTACACA 58.782 36.000 0.00 0.00 39.35 3.72
436 459 6.701432 ACTGTTTGTTTAGCGATAGTACAC 57.299 37.500 0.00 0.00 39.35 2.90
438 461 7.578169 AGAACTGTTTGTTTAGCGATAGTAC 57.422 36.000 0.00 0.00 39.30 2.73
442 465 7.307751 CCTTGAAGAACTGTTTGTTTAGCGATA 60.308 37.037 0.00 0.00 39.30 2.92
446 469 5.743872 CACCTTGAAGAACTGTTTGTTTAGC 59.256 40.000 0.00 0.00 39.30 3.09
458 481 4.354587 CAGAAACTTGCACCTTGAAGAAC 58.645 43.478 0.00 0.00 0.00 3.01
462 485 2.869233 GCAGAAACTTGCACCTTGAA 57.131 45.000 0.00 0.00 43.53 2.69
540 564 4.396166 GCATGTGGTATAATATCTGCCACC 59.604 45.833 17.32 4.71 46.44 4.61
541 565 5.248640 AGCATGTGGTATAATATCTGCCAC 58.751 41.667 14.73 14.73 46.97 5.01
542 566 5.249163 AGAGCATGTGGTATAATATCTGCCA 59.751 40.000 0.00 0.00 0.00 4.92
543 567 5.583854 CAGAGCATGTGGTATAATATCTGCC 59.416 44.000 0.00 0.00 0.00 4.85
559 583 3.125829 ACAGCGAAATTGTACAGAGCATG 59.874 43.478 0.00 0.00 0.00 4.06
563 587 4.867047 AGATGACAGCGAAATTGTACAGAG 59.133 41.667 0.00 0.00 0.00 3.35
577 601 8.909671 CAAGTGAAAATTTCTAAAGATGACAGC 58.090 33.333 7.29 0.00 0.00 4.40
630 654 6.400834 CGCACAACAGATCAATATAGCATCTC 60.401 42.308 0.00 0.00 0.00 2.75
648 672 2.031560 TCAACAGAACACATCGCACAAC 59.968 45.455 0.00 0.00 0.00 3.32
654 678 7.535258 CCTAGAAATTTTCAACAGAACACATCG 59.465 37.037 11.53 0.00 0.00 3.84
673 697 9.199645 TCATGCCATTCAAATAATTCCTAGAAA 57.800 29.630 0.00 0.00 0.00 2.52
674 698 8.632679 GTCATGCCATTCAAATAATTCCTAGAA 58.367 33.333 0.00 0.00 0.00 2.10
675 699 8.000709 AGTCATGCCATTCAAATAATTCCTAGA 58.999 33.333 0.00 0.00 0.00 2.43
676 700 8.174733 AGTCATGCCATTCAAATAATTCCTAG 57.825 34.615 0.00 0.00 0.00 3.02
677 701 9.288576 CTAGTCATGCCATTCAAATAATTCCTA 57.711 33.333 0.00 0.00 0.00 2.94
678 702 7.781693 ACTAGTCATGCCATTCAAATAATTCCT 59.218 33.333 0.00 0.00 0.00 3.36
679 703 7.864379 CACTAGTCATGCCATTCAAATAATTCC 59.136 37.037 0.00 0.00 0.00 3.01
680 704 7.380602 GCACTAGTCATGCCATTCAAATAATTC 59.619 37.037 0.00 0.00 37.08 2.17
681 705 7.069085 AGCACTAGTCATGCCATTCAAATAATT 59.931 33.333 0.00 0.00 44.53 1.40
682 706 6.548622 AGCACTAGTCATGCCATTCAAATAAT 59.451 34.615 0.00 0.00 44.53 1.28
683 707 5.887598 AGCACTAGTCATGCCATTCAAATAA 59.112 36.000 0.00 0.00 44.53 1.40
684 708 5.439721 AGCACTAGTCATGCCATTCAAATA 58.560 37.500 0.00 0.00 44.53 1.40
685 709 4.275810 AGCACTAGTCATGCCATTCAAAT 58.724 39.130 0.00 0.00 44.53 2.32
686 710 3.689347 AGCACTAGTCATGCCATTCAAA 58.311 40.909 0.00 0.00 44.53 2.69
687 711 3.354948 AGCACTAGTCATGCCATTCAA 57.645 42.857 0.00 0.00 44.53 2.69
688 712 3.354948 AAGCACTAGTCATGCCATTCA 57.645 42.857 0.00 0.00 44.53 2.57
689 713 4.878397 ACTTAAGCACTAGTCATGCCATTC 59.122 41.667 1.29 0.00 44.53 2.67
690 714 4.848357 ACTTAAGCACTAGTCATGCCATT 58.152 39.130 1.29 0.00 44.53 3.16
691 715 4.494091 ACTTAAGCACTAGTCATGCCAT 57.506 40.909 1.29 0.00 44.53 4.40
692 716 3.981071 ACTTAAGCACTAGTCATGCCA 57.019 42.857 1.29 0.00 44.53 4.92
693 717 6.538742 TCAATTACTTAAGCACTAGTCATGCC 59.461 38.462 1.29 0.00 44.53 4.40
694 718 7.539712 TCAATTACTTAAGCACTAGTCATGC 57.460 36.000 1.29 0.00 43.74 4.06
716 774 3.186283 TCCAGGCAGGGTAGTAATTTCA 58.814 45.455 0.00 0.00 38.24 2.69
743 801 5.412904 GGAACAGAGTTTATCTTGGTCTTGG 59.587 44.000 0.00 0.00 35.47 3.61
744 802 5.412904 GGGAACAGAGTTTATCTTGGTCTTG 59.587 44.000 0.00 0.00 35.47 3.02
745 803 5.515008 GGGGAACAGAGTTTATCTTGGTCTT 60.515 44.000 0.00 0.00 35.47 3.01
746 804 4.019231 GGGGAACAGAGTTTATCTTGGTCT 60.019 45.833 0.00 0.00 35.47 3.85
747 805 4.262617 GGGGAACAGAGTTTATCTTGGTC 58.737 47.826 0.00 0.00 35.47 4.02
748 806 3.010250 GGGGGAACAGAGTTTATCTTGGT 59.990 47.826 0.00 0.00 35.47 3.67
777 835 5.048364 GTGCAAAACCAACAGGTACATGATA 60.048 40.000 15.54 0.00 33.53 2.15
848 906 9.445786 AATTAACTGAAGTAAAATGTCAACACG 57.554 29.630 0.00 0.00 0.00 4.49
900 958 8.352137 TCCAATGCGAATTGATAAATGGATAT 57.648 30.769 18.19 0.00 33.55 1.63
917 975 7.810658 AGCAGAGTTATAATAAATCCAATGCG 58.189 34.615 0.00 0.00 32.92 4.73
932 990 5.620738 TGCATAGAAGGAAGCAGAGTTAT 57.379 39.130 0.00 0.00 32.48 1.89
944 1003 4.011966 TCATACATGGCTGCATAGAAGG 57.988 45.455 0.50 0.00 0.00 3.46
950 1009 5.868454 TGTAGTTATCATACATGGCTGCAT 58.132 37.500 0.50 0.00 0.00 3.96
1044 1103 1.895707 GCCTGAGCTTGCGCCATAT 60.896 57.895 4.18 0.00 36.60 1.78
1155 1214 4.387026 TTGAAACACCAGGGAGATCAAT 57.613 40.909 0.00 0.00 0.00 2.57
1162 1221 1.202879 AGCGATTTGAAACACCAGGGA 60.203 47.619 0.00 0.00 0.00 4.20
1362 1449 6.776116 ACACCCGATATATAGACAGAAGAACA 59.224 38.462 0.00 0.00 0.00 3.18
1382 1469 4.510571 ACGGAACATATTTCAGTACACCC 58.489 43.478 0.00 0.00 0.00 4.61
1397 1484 1.337823 GCAGCTAGGAAAGACGGAACA 60.338 52.381 0.00 0.00 0.00 3.18
1398 1485 1.360820 GCAGCTAGGAAAGACGGAAC 58.639 55.000 0.00 0.00 0.00 3.62
1399 1486 0.108804 CGCAGCTAGGAAAGACGGAA 60.109 55.000 0.00 0.00 0.00 4.30
1400 1487 1.511305 CGCAGCTAGGAAAGACGGA 59.489 57.895 0.00 0.00 0.00 4.69
1401 1488 4.094684 CGCAGCTAGGAAAGACGG 57.905 61.111 0.00 0.00 0.00 4.79
1414 1501 1.600957 CCAGAAACATATCCAGCGCAG 59.399 52.381 11.47 0.00 0.00 5.18
1415 1502 1.065491 ACCAGAAACATATCCAGCGCA 60.065 47.619 11.47 0.00 0.00 6.09
1416 1503 1.668419 ACCAGAAACATATCCAGCGC 58.332 50.000 0.00 0.00 0.00 5.92
1417 1504 3.535561 AGAACCAGAAACATATCCAGCG 58.464 45.455 0.00 0.00 0.00 5.18
1418 1505 5.904362 AAAGAACCAGAAACATATCCAGC 57.096 39.130 0.00 0.00 0.00 4.85
1419 1506 9.401058 AGATAAAAGAACCAGAAACATATCCAG 57.599 33.333 0.00 0.00 0.00 3.86
1425 1512 9.401058 CCAGATAGATAAAAGAACCAGAAACAT 57.599 33.333 0.00 0.00 0.00 2.71
1426 1513 8.383175 ACCAGATAGATAAAAGAACCAGAAACA 58.617 33.333 0.00 0.00 0.00 2.83
1427 1514 8.669243 CACCAGATAGATAAAAGAACCAGAAAC 58.331 37.037 0.00 0.00 0.00 2.78
1428 1515 8.383175 ACACCAGATAGATAAAAGAACCAGAAA 58.617 33.333 0.00 0.00 0.00 2.52
1429 1516 7.918076 ACACCAGATAGATAAAAGAACCAGAA 58.082 34.615 0.00 0.00 0.00 3.02
1430 1517 7.496346 ACACCAGATAGATAAAAGAACCAGA 57.504 36.000 0.00 0.00 0.00 3.86
1431 1518 8.478877 AGTACACCAGATAGATAAAAGAACCAG 58.521 37.037 0.00 0.00 0.00 4.00
1432 1519 8.258007 CAGTACACCAGATAGATAAAAGAACCA 58.742 37.037 0.00 0.00 0.00 3.67
1433 1520 8.475639 TCAGTACACCAGATAGATAAAAGAACC 58.524 37.037 0.00 0.00 0.00 3.62
1434 1521 9.871238 TTCAGTACACCAGATAGATAAAAGAAC 57.129 33.333 0.00 0.00 0.00 3.01
1467 1554 4.277921 GCCCCTGAAAAATCATTGCAAAAA 59.722 37.500 1.71 0.00 0.00 1.94
1468 1555 3.819902 GCCCCTGAAAAATCATTGCAAAA 59.180 39.130 1.71 0.00 0.00 2.44
1478 1565 1.632589 GTCCAGTGCCCCTGAAAAAT 58.367 50.000 2.23 0.00 44.49 1.82
1479 1566 0.469144 GGTCCAGTGCCCCTGAAAAA 60.469 55.000 2.23 0.00 44.49 1.94
1498 1585 1.656652 CAACAGGCTCACTTATCCGG 58.343 55.000 0.00 0.00 0.00 5.14
1669 1769 7.151308 TGTGATTTTGAAGTGTCACTGTTTTT 58.849 30.769 6.18 0.00 41.08 1.94
1716 1817 3.265791 CTTCTGGAGTGAACCTGCATAC 58.734 50.000 0.00 0.00 41.10 2.39
1964 2066 1.808411 GCTTCATCGTCCTCACCAAA 58.192 50.000 0.00 0.00 0.00 3.28
2123 2243 4.100808 TGGTTGCTTTTTCTAGTGCCAAAT 59.899 37.500 0.00 0.00 0.00 2.32
2141 2261 2.154462 CCTAAGCTTCACAGGTGGTTG 58.846 52.381 0.00 0.00 0.00 3.77
2263 2403 5.873179 AACATACTACAAAATGGTGACCG 57.127 39.130 0.00 0.00 0.00 4.79
2348 2502 4.712337 AGTGAACTAGGGTAGATCCAACAG 59.288 45.833 0.00 0.00 38.11 3.16
2405 2559 4.701765 AGCTGGCATATACTTTCACTGAG 58.298 43.478 0.00 0.00 0.00 3.35
2422 2576 2.486982 CCAAATGACAGACTGAAGCTGG 59.513 50.000 10.08 5.35 37.69 4.85
2428 2603 3.557054 GCACCTACCAAATGACAGACTGA 60.557 47.826 10.08 0.00 0.00 3.41
2463 2638 9.952030 TTATGTGGTGAATTTTCTGACAGTATA 57.048 29.630 1.59 0.00 0.00 1.47
2464 2639 8.862325 TTATGTGGTGAATTTTCTGACAGTAT 57.138 30.769 1.59 0.00 0.00 2.12
2535 2713 3.943671 TGGACCAAAACTCTGAGGAAA 57.056 42.857 9.85 0.00 0.00 3.13
2537 2715 2.507886 TGTTGGACCAAAACTCTGAGGA 59.492 45.455 8.94 0.00 0.00 3.71
2538 2716 2.880890 CTGTTGGACCAAAACTCTGAGG 59.119 50.000 8.94 0.00 0.00 3.86
2539 2718 2.291741 GCTGTTGGACCAAAACTCTGAG 59.708 50.000 8.94 2.45 0.00 3.35
2540 2719 2.092429 AGCTGTTGGACCAAAACTCTGA 60.092 45.455 8.94 0.00 0.00 3.27
2541 2720 2.301346 AGCTGTTGGACCAAAACTCTG 58.699 47.619 8.94 1.93 0.00 3.35
2546 2725 3.766591 TGAGAAAAGCTGTTGGACCAAAA 59.233 39.130 8.94 1.88 0.00 2.44
2554 2733 5.863397 TGTCTTGTTTTGAGAAAAGCTGTTG 59.137 36.000 0.00 0.00 0.00 3.33
2603 2782 7.563906 TCACCAAAAATCCAAAGAAAATCAGT 58.436 30.769 0.00 0.00 0.00 3.41
2629 2808 3.088194 TCACGCGTAAATCTGGATACC 57.912 47.619 13.44 0.00 0.00 2.73
2672 2851 3.469739 TCATACATTGCACGCATCTCAT 58.530 40.909 0.00 0.00 0.00 2.90
2673 2852 2.903798 TCATACATTGCACGCATCTCA 58.096 42.857 0.00 0.00 0.00 3.27
2676 2855 4.600032 TCATTTCATACATTGCACGCATC 58.400 39.130 0.00 0.00 0.00 3.91
2678 2857 4.431661 TTCATTTCATACATTGCACGCA 57.568 36.364 0.00 0.00 0.00 5.24
2679 2858 5.954434 AATTCATTTCATACATTGCACGC 57.046 34.783 0.00 0.00 0.00 5.34
2680 2859 6.692249 TGCTAATTCATTTCATACATTGCACG 59.308 34.615 0.00 0.00 0.00 5.34
2682 2861 8.033626 TGTTGCTAATTCATTTCATACATTGCA 58.966 29.630 0.00 0.00 0.00 4.08
2698 2877 7.568199 AGTACTTGTTCACTTGTTGCTAATT 57.432 32.000 0.00 0.00 0.00 1.40
2726 2905 8.785101 CGTTCAGAATTTATCCATTAAACGTTG 58.215 33.333 0.00 0.00 32.71 4.10
2727 2906 8.723311 TCGTTCAGAATTTATCCATTAAACGTT 58.277 29.630 0.00 0.00 37.57 3.99
2729 2908 7.638683 GGTCGTTCAGAATTTATCCATTAAACG 59.361 37.037 0.00 0.00 37.64 3.60
2730 2909 8.455682 TGGTCGTTCAGAATTTATCCATTAAAC 58.544 33.333 0.00 0.00 32.71 2.01
2731 2910 8.568676 TGGTCGTTCAGAATTTATCCATTAAA 57.431 30.769 0.00 0.00 34.37 1.52
2734 2921 7.461182 TTTGGTCGTTCAGAATTTATCCATT 57.539 32.000 0.00 0.00 0.00 3.16
2748 2935 3.692791 AAGCTCTGTTTTTGGTCGTTC 57.307 42.857 0.00 0.00 0.00 3.95
2763 2950 1.981256 TTGTGTTCCCTCCAAAGCTC 58.019 50.000 0.00 0.00 0.00 4.09
2811 3001 0.247894 GCGTTTGTTGTCGTGCTTGA 60.248 50.000 0.00 0.00 0.00 3.02
2829 3019 3.829948 CTGTGAAATCCATGACAACAGC 58.170 45.455 0.00 0.00 0.00 4.40
2831 3021 3.220940 TGCTGTGAAATCCATGACAACA 58.779 40.909 0.00 0.00 0.00 3.33
2835 3025 2.164827 TGCATGCTGTGAAATCCATGAC 59.835 45.455 20.33 0.00 37.78 3.06
2873 3063 7.383687 TCTACTACTCATTTTTGACGAATGGT 58.616 34.615 0.00 0.00 35.66 3.55
2884 3074 9.067986 CCCTTTCAAGTTTCTACTACTCATTTT 57.932 33.333 0.00 0.00 33.17 1.82
2885 3075 7.175119 GCCCTTTCAAGTTTCTACTACTCATTT 59.825 37.037 0.00 0.00 33.17 2.32
2888 3078 5.548406 GCCCTTTCAAGTTTCTACTACTCA 58.452 41.667 0.00 0.00 33.17 3.41
2889 3079 4.626172 CGCCCTTTCAAGTTTCTACTACTC 59.374 45.833 0.00 0.00 33.17 2.59
2930 3123 0.537143 TTGCATCGGACCTTTGCACT 60.537 50.000 15.48 0.00 45.35 4.40
2931 3124 0.313672 TTTGCATCGGACCTTTGCAC 59.686 50.000 15.48 0.00 45.35 4.57
2932 3125 1.035923 TTTTGCATCGGACCTTTGCA 58.964 45.000 12.68 12.68 44.12 4.08
2933 3126 2.147436 TTTTTGCATCGGACCTTTGC 57.853 45.000 8.22 8.22 36.91 3.68
2959 3152 3.486209 CGTCGTACCTTTGCACTGTTTTT 60.486 43.478 0.00 0.00 0.00 1.94
2960 3153 2.031191 CGTCGTACCTTTGCACTGTTTT 59.969 45.455 0.00 0.00 0.00 2.43
2961 3154 1.595794 CGTCGTACCTTTGCACTGTTT 59.404 47.619 0.00 0.00 0.00 2.83
2962 3155 1.202440 TCGTCGTACCTTTGCACTGTT 60.202 47.619 0.00 0.00 0.00 3.16
2963 3156 0.386476 TCGTCGTACCTTTGCACTGT 59.614 50.000 0.00 0.00 0.00 3.55
2964 3157 0.782384 GTCGTCGTACCTTTGCACTG 59.218 55.000 0.00 0.00 0.00 3.66
3021 3214 0.104671 TTTGCTTGTTGCCAGGCTTC 59.895 50.000 14.15 6.24 43.63 3.86
3078 3271 1.341852 TCGTGACAATGACGAAAGGGA 59.658 47.619 0.00 0.00 42.63 4.20


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

AutoCloner maintained by Alex Coulton.