Multiple sequence alignment - TraesCS1D01G412900

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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 TraesCS1D01G412900 chr1D 100.000 2763 0 0 1 2763 473878733 473881495 0.000000e+00 5103
1 TraesCS1D01G412900 chr1D 84.547 673 54 17 1070 1729 473961204 473961839 3.020000e-174 621
2 TraesCS1D01G412900 chr1D 89.623 424 31 5 1011 1425 473987273 473987692 6.780000e-146 527
3 TraesCS1D01G412900 chr1B 86.880 1189 106 17 1625 2763 659184130 659185318 0.000000e+00 1286
4 TraesCS1D01G412900 chr1B 86.678 1186 111 20 1624 2763 658972473 658973657 0.000000e+00 1271
5 TraesCS1D01G412900 chr1B 86.678 1186 111 15 1624 2763 659006060 659007244 0.000000e+00 1271
6 TraesCS1D01G412900 chr1B 86.650 1191 105 21 1624 2763 659288803 659289990 0.000000e+00 1269
7 TraesCS1D01G412900 chr1B 86.291 1189 113 24 1625 2763 659076323 659077511 0.000000e+00 1247
8 TraesCS1D01G412900 chr1B 86.088 1186 118 14 1624 2763 659271344 659272528 0.000000e+00 1232
9 TraesCS1D01G412900 chr1B 85.497 1186 125 14 1624 2763 659167392 659168576 0.000000e+00 1194
10 TraesCS1D01G412900 chr1B 93.035 603 33 6 1033 1627 659182454 659183055 0.000000e+00 872
11 TraesCS1D01G412900 chr1B 86.377 690 40 21 866 1513 659316610 659317287 0.000000e+00 704
12 TraesCS1D01G412900 chr1B 85.820 677 47 21 1017 1669 659002645 659003296 0.000000e+00 673
13 TraesCS1D01G412900 chr1B 81.603 886 86 39 872 1711 659033571 659034425 0.000000e+00 662
14 TraesCS1D01G412900 chr1B 85.100 698 48 23 1033 1711 659294663 659295323 0.000000e+00 662
15 TraesCS1D01G412900 chr1B 85.079 697 49 22 1033 1711 659285997 659286656 0.000000e+00 660
16 TraesCS1D01G412900 chr1B 91.086 359 26 5 1274 1627 659074889 659075246 5.350000e-132 481
17 TraesCS1D01G412900 chr1B 90.756 357 27 4 1274 1627 659004641 659004994 3.220000e-129 472
18 TraesCS1D01G412900 chr1B 92.517 147 10 1 1568 1713 659317674 659317820 2.790000e-50 209
19 TraesCS1D01G412900 chr1B 80.000 245 28 12 1 231 659032741 659032978 7.920000e-36 161
20 TraesCS1D01G412900 chr1B 80.342 234 19 14 1 214 659179452 659179678 4.770000e-33 152
21 TraesCS1D01G412900 chr1B 79.574 235 19 15 1 214 659282876 659283102 1.030000e-29 141
22 TraesCS1D01G412900 chr1B 78.390 236 25 14 14 231 659071926 659072153 2.230000e-26 130
23 TraesCS1D01G412900 chr1A 90.365 986 78 9 1792 2763 568140089 568141071 0.000000e+00 1279
24 TraesCS1D01G412900 chr1A 88.176 888 75 16 1624 2482 568268777 568269663 0.000000e+00 1031
25 TraesCS1D01G412900 chr1A 87.967 723 61 13 1011 1713 568388905 568389621 0.000000e+00 830
26 TraesCS1D01G412900 chr1A 87.068 665 46 15 1033 1682 568266002 568266641 0.000000e+00 715
27 TraesCS1D01G412900 chr1A 90.608 362 21 7 1274 1627 568268157 568268513 4.170000e-128 468
28 TraesCS1D01G412900 chr1A 82.056 535 45 18 1125 1641 568398646 568399147 2.560000e-110 409
29 TraesCS1D01G412900 chr1A 91.204 216 17 2 2550 2763 568269698 568269913 2.690000e-75 292
30 TraesCS1D01G412900 chr1A 89.441 161 14 2 1570 1727 568328597 568328757 1.680000e-47 200
31 TraesCS1D01G412900 chr1A 90.476 126 11 1 1607 1731 568122546 568122671 6.120000e-37 165
32 TraesCS1D01G412900 chr1A 77.204 329 36 23 1 302 568264510 568264826 3.680000e-34 156


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 TraesCS1D01G412900 chr1D 473878733 473881495 2762 False 5103.000000 5103 100.000000 1 2763 1 chr1D.!!$F1 2762
1 TraesCS1D01G412900 chr1D 473961204 473961839 635 False 621.000000 621 84.547000 1070 1729 1 chr1D.!!$F2 659
2 TraesCS1D01G412900 chr1B 658972473 658973657 1184 False 1271.000000 1271 86.678000 1624 2763 1 chr1B.!!$F1 1139
3 TraesCS1D01G412900 chr1B 659271344 659272528 1184 False 1232.000000 1232 86.088000 1624 2763 1 chr1B.!!$F3 1139
4 TraesCS1D01G412900 chr1B 659167392 659168576 1184 False 1194.000000 1194 85.497000 1624 2763 1 chr1B.!!$F2 1139
5 TraesCS1D01G412900 chr1B 659002645 659007244 4599 False 805.333333 1271 87.751333 1017 2763 3 chr1B.!!$F5 1746
6 TraesCS1D01G412900 chr1B 659179452 659185318 5866 False 770.000000 1286 86.752333 1 2763 3 chr1B.!!$F8 2762
7 TraesCS1D01G412900 chr1B 659282876 659289990 7114 False 690.000000 1269 83.767667 1 2763 3 chr1B.!!$F9 2762
8 TraesCS1D01G412900 chr1B 659294663 659295323 660 False 662.000000 662 85.100000 1033 1711 1 chr1B.!!$F4 678
9 TraesCS1D01G412900 chr1B 659071926 659077511 5585 False 619.333333 1247 85.255667 14 2763 3 chr1B.!!$F7 2749
10 TraesCS1D01G412900 chr1B 659316610 659317820 1210 False 456.500000 704 89.447000 866 1713 2 chr1B.!!$F10 847
11 TraesCS1D01G412900 chr1B 659032741 659034425 1684 False 411.500000 662 80.801500 1 1711 2 chr1B.!!$F6 1710
12 TraesCS1D01G412900 chr1A 568140089 568141071 982 False 1279.000000 1279 90.365000 1792 2763 1 chr1A.!!$F2 971
13 TraesCS1D01G412900 chr1A 568388905 568389621 716 False 830.000000 830 87.967000 1011 1713 1 chr1A.!!$F4 702
14 TraesCS1D01G412900 chr1A 568264510 568269913 5403 False 532.400000 1031 86.852000 1 2763 5 chr1A.!!$F6 2762
15 TraesCS1D01G412900 chr1A 568398646 568399147 501 False 409.000000 409 82.056000 1125 1641 1 chr1A.!!$F5 516

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
846 3278 0.02577 CGTTTCGTCACACACACCAC 59.974 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 12833 0.106268 ATGTTGTGGCCACTTGGTGA 60.106 50.0 34.75 12.54 35.23 4.02 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
22 23 3.117491 TGGAAATGAGCATCGAGATCC 57.883 47.619 0.00 0.00 38.61 3.36
46 53 0.600557 TTTTTGGGTATGCGCACCTG 59.399 50.000 14.90 0.00 38.73 4.00
47 54 1.872197 TTTTGGGTATGCGCACCTGC 61.872 55.000 14.90 0.00 38.73 4.85
66 73 0.096628 CGCAGCTCTGTTGATCAAGC 59.903 55.000 8.80 8.78 33.60 4.01
67 74 1.162698 GCAGCTCTGTTGATCAAGCA 58.837 50.000 17.19 13.08 34.82 3.91
68 75 1.135746 GCAGCTCTGTTGATCAAGCAC 60.136 52.381 17.19 4.67 34.82 4.40
70 77 0.807496 GCTCTGTTGATCAAGCACCC 59.193 55.000 8.80 0.00 33.61 4.61
71 78 1.883638 GCTCTGTTGATCAAGCACCCA 60.884 52.381 8.80 1.84 33.61 4.51
72 79 2.082231 CTCTGTTGATCAAGCACCCAG 58.918 52.381 8.80 12.05 0.00 4.45
73 80 1.171308 CTGTTGATCAAGCACCCAGG 58.829 55.000 8.80 0.00 0.00 4.45
74 81 0.478072 TGTTGATCAAGCACCCAGGT 59.522 50.000 8.80 0.00 0.00 4.00
75 82 1.702401 TGTTGATCAAGCACCCAGGTA 59.298 47.619 8.80 0.00 0.00 3.08
76 83 2.084546 GTTGATCAAGCACCCAGGTAC 58.915 52.381 8.80 0.00 0.00 3.34
77 84 0.249120 TGATCAAGCACCCAGGTACG 59.751 55.000 0.00 0.00 0.00 3.67
78 85 0.249398 GATCAAGCACCCAGGTACGT 59.751 55.000 0.00 0.00 0.00 3.57
79 86 0.249398 ATCAAGCACCCAGGTACGTC 59.751 55.000 0.00 0.00 0.00 4.34
82 89 1.542187 AAGCACCCAGGTACGTCCTC 61.542 60.000 0.00 0.00 46.24 3.71
94 107 2.607750 GTCCTCCTCCTGTGGGCA 60.608 66.667 0.00 0.00 32.37 5.36
95 108 1.997874 GTCCTCCTCCTGTGGGCAT 60.998 63.158 0.00 0.00 32.37 4.40
140 157 1.339291 CATACGATGAGCTCTCTGCCA 59.661 52.381 16.19 0.00 44.23 4.92
162 186 0.462581 CCATGTCAGGATCACACGGG 60.463 60.000 0.00 0.00 0.00 5.28
163 187 1.091771 CATGTCAGGATCACACGGGC 61.092 60.000 0.00 0.00 0.00 6.13
164 188 2.125106 GTCAGGATCACACGGGCC 60.125 66.667 0.00 0.00 0.00 5.80
165 189 2.284625 TCAGGATCACACGGGCCT 60.285 61.111 0.84 0.00 0.00 5.19
166 190 2.187946 CAGGATCACACGGGCCTC 59.812 66.667 0.84 0.00 0.00 4.70
214 238 1.271325 TGCTTCCGTTGGTGATGTGAT 60.271 47.619 0.00 0.00 0.00 3.06
215 239 1.398390 GCTTCCGTTGGTGATGTGATC 59.602 52.381 0.00 0.00 0.00 2.92
216 240 2.698803 CTTCCGTTGGTGATGTGATCA 58.301 47.619 0.00 0.00 36.84 2.92
217 241 2.849294 TCCGTTGGTGATGTGATCAA 57.151 45.000 0.00 0.00 41.69 2.57
226 250 2.703416 TGATGTGATCAACAGAGCACC 58.297 47.619 10.84 0.00 45.52 5.01
241 265 1.829456 CACCCAGCATCGGTCCATA 59.171 57.895 0.00 0.00 0.00 2.74
243 267 1.071471 CCCAGCATCGGTCCATACC 59.929 63.158 0.00 0.00 42.95 2.73
245 269 0.250038 CCAGCATCGGTCCATACCTG 60.250 60.000 0.00 0.00 44.35 4.00
247 271 1.050988 AGCATCGGTCCATACCTGCT 61.051 55.000 5.69 5.69 46.89 4.24
248 272 0.882042 GCATCGGTCCATACCTGCTG 60.882 60.000 0.00 0.00 44.35 4.41
249 273 0.882042 CATCGGTCCATACCTGCTGC 60.882 60.000 0.00 0.00 44.35 5.25
250 274 2.369257 ATCGGTCCATACCTGCTGCG 62.369 60.000 0.00 0.00 44.35 5.18
252 276 1.820581 GGTCCATACCTGCTGCGTA 59.179 57.895 0.00 0.00 43.08 4.42
253 277 0.177141 GGTCCATACCTGCTGCGTAA 59.823 55.000 0.00 0.00 43.08 3.18
260 284 2.332063 ACCTGCTGCGTAATTGCTAT 57.668 45.000 0.00 0.00 35.36 2.97
261 285 1.942657 ACCTGCTGCGTAATTGCTATG 59.057 47.619 0.00 0.00 35.36 2.23
262 286 2.212652 CCTGCTGCGTAATTGCTATGA 58.787 47.619 0.00 0.00 35.36 2.15
263 287 2.810274 CCTGCTGCGTAATTGCTATGAT 59.190 45.455 0.00 0.00 35.36 2.45
265 289 3.465871 TGCTGCGTAATTGCTATGATGA 58.534 40.909 0.00 0.00 35.36 2.92
269 293 4.692228 TGCGTAATTGCTATGATGACAGA 58.308 39.130 0.00 0.00 35.36 3.41
291 316 3.425577 AGCACTGTGTGTCAAAATGTG 57.574 42.857 9.86 0.00 35.75 3.21
302 330 4.328712 GTGTCAAAATGTGTTTGGAACCAC 59.671 41.667 0.00 0.00 29.25 4.16
303 331 4.221703 TGTCAAAATGTGTTTGGAACCACT 59.778 37.500 0.00 0.00 29.25 4.00
307 335 1.388547 TGTGTTTGGAACCACTGAGC 58.611 50.000 0.00 0.00 0.00 4.26
309 337 1.748493 GTGTTTGGAACCACTGAGCAA 59.252 47.619 0.00 0.00 0.00 3.91
310 338 2.023673 TGTTTGGAACCACTGAGCAAG 58.976 47.619 0.00 0.00 0.00 4.01
311 339 2.024414 GTTTGGAACCACTGAGCAAGT 58.976 47.619 0.00 0.00 40.93 3.16
320 348 2.001812 ACTGAGCAAGTGAGCATACG 57.998 50.000 0.00 0.00 37.88 3.06
326 354 1.795768 CAAGTGAGCATACGTGTGGT 58.204 50.000 17.19 17.19 0.00 4.16
327 355 2.143122 CAAGTGAGCATACGTGTGGTT 58.857 47.619 18.18 0.00 0.00 3.67
329 357 3.671008 AGTGAGCATACGTGTGGTTAA 57.329 42.857 18.18 7.50 0.00 2.01
330 358 4.202245 AGTGAGCATACGTGTGGTTAAT 57.798 40.909 18.18 10.77 0.00 1.40
333 361 5.810587 AGTGAGCATACGTGTGGTTAATTAG 59.189 40.000 18.18 0.00 0.00 1.73
339 367 8.423349 AGCATACGTGTGGTTAATTAGGTATTA 58.577 33.333 11.47 0.00 0.00 0.98
340 368 8.490355 GCATACGTGTGGTTAATTAGGTATTAC 58.510 37.037 14.49 0.00 0.00 1.89
377 406 5.629849 CGAAAAGGAAATATAGCGATCGACT 59.370 40.000 21.57 17.42 0.00 4.18
378 407 6.183359 CGAAAAGGAAATATAGCGATCGACTC 60.183 42.308 21.57 0.32 0.00 3.36
391 420 4.571372 GATCGACTCGAGGGATTTAGTT 57.429 45.455 18.41 0.00 39.91 2.24
393 422 4.889832 TCGACTCGAGGGATTTAGTTAC 57.110 45.455 18.41 0.00 0.00 2.50
394 423 3.310774 TCGACTCGAGGGATTTAGTTACG 59.689 47.826 18.41 5.04 0.00 3.18
396 425 4.349501 GACTCGAGGGATTTAGTTACGTG 58.650 47.826 18.41 0.00 0.00 4.49
397 426 3.129988 ACTCGAGGGATTTAGTTACGTGG 59.870 47.826 18.41 0.00 0.00 4.94
398 427 3.355378 TCGAGGGATTTAGTTACGTGGA 58.645 45.455 0.00 0.00 0.00 4.02
400 429 4.110482 CGAGGGATTTAGTTACGTGGAAG 58.890 47.826 0.00 0.00 0.00 3.46
401 430 4.142315 CGAGGGATTTAGTTACGTGGAAGA 60.142 45.833 0.00 0.00 0.00 2.87
402 431 5.622914 CGAGGGATTTAGTTACGTGGAAGAA 60.623 44.000 0.00 0.00 0.00 2.52
406 435 7.336176 AGGGATTTAGTTACGTGGAAGAAAATC 59.664 37.037 0.00 6.38 33.45 2.17
413 465 0.094730 GTGGAAGAAAATCCGACGCG 59.905 55.000 3.53 3.53 42.76 6.01
439 491 1.180907 TGTTCACAACAAAGCTGCCA 58.819 45.000 0.00 0.00 38.72 4.92
440 492 1.134753 TGTTCACAACAAAGCTGCCAG 59.865 47.619 0.00 0.00 38.72 4.85
469 536 3.438360 CACAAGTGAAAAGCTGAACACC 58.562 45.455 11.85 0.00 34.33 4.16
470 537 3.129287 CACAAGTGAAAAGCTGAACACCT 59.871 43.478 11.85 0.00 34.33 4.00
474 541 4.016444 AGTGAAAAGCTGAACACCTGAAA 58.984 39.130 11.85 0.00 34.33 2.69
475 542 4.646492 AGTGAAAAGCTGAACACCTGAAAT 59.354 37.500 11.85 0.00 34.33 2.17
476 543 5.827797 AGTGAAAAGCTGAACACCTGAAATA 59.172 36.000 11.85 0.00 34.33 1.40
477 544 6.491403 AGTGAAAAGCTGAACACCTGAAATAT 59.509 34.615 11.85 0.00 34.33 1.28
478 545 6.803807 GTGAAAAGCTGAACACCTGAAATATC 59.196 38.462 0.00 0.00 0.00 1.63
479 546 5.904362 AAAGCTGAACACCTGAAATATCC 57.096 39.130 0.00 0.00 0.00 2.59
504 580 2.364647 TGAGAGCTAGGCATGTGATCAG 59.635 50.000 0.00 0.00 0.00 2.90
510 586 2.865119 AGGCATGTGATCAGTGTGAA 57.135 45.000 0.00 0.00 0.00 3.18
513 589 3.261643 AGGCATGTGATCAGTGTGAACTA 59.738 43.478 0.00 0.00 0.00 2.24
514 590 3.620374 GGCATGTGATCAGTGTGAACTAG 59.380 47.826 0.00 0.00 0.00 2.57
515 591 4.498241 GCATGTGATCAGTGTGAACTAGA 58.502 43.478 0.00 0.00 0.00 2.43
516 592 5.114780 GCATGTGATCAGTGTGAACTAGAT 58.885 41.667 0.00 0.00 0.00 1.98
517 593 5.583854 GCATGTGATCAGTGTGAACTAGATT 59.416 40.000 0.00 0.00 0.00 2.40
518 594 6.758416 GCATGTGATCAGTGTGAACTAGATTA 59.242 38.462 0.00 0.00 0.00 1.75
521 597 8.707938 TGTGATCAGTGTGAACTAGATTATTG 57.292 34.615 0.00 0.00 0.00 1.90
522 598 8.531146 TGTGATCAGTGTGAACTAGATTATTGA 58.469 33.333 0.00 0.00 0.00 2.57
523 599 8.812329 GTGATCAGTGTGAACTAGATTATTGAC 58.188 37.037 0.00 0.00 0.00 3.18
527 2776 9.462606 TCAGTGTGAACTAGATTATTGACTAGA 57.537 33.333 0.00 0.00 39.25 2.43
541 2795 8.634475 TTATTGACTAGAATGTTGATGAGACG 57.366 34.615 0.00 0.00 0.00 4.18
542 2796 4.998788 TGACTAGAATGTTGATGAGACGG 58.001 43.478 0.00 0.00 0.00 4.79
556 2810 4.730949 TGAGACGGTGGTTTTCTATAGG 57.269 45.455 0.00 0.00 0.00 2.57
561 2815 2.878406 CGGTGGTTTTCTATAGGCATGG 59.122 50.000 0.00 0.00 0.00 3.66
565 2819 4.816925 GTGGTTTTCTATAGGCATGGAGAC 59.183 45.833 0.00 0.00 0.00 3.36
585 2845 5.942872 AGACTTTCAAGTTCAAACACAGTG 58.057 37.500 0.00 0.00 39.88 3.66
597 2857 5.283294 TCAAACACAGTGCAGATTCATTTG 58.717 37.500 0.00 1.79 0.00 2.32
604 2864 3.306917 TGCAGATTCATTTGCAAGGTG 57.693 42.857 0.00 3.33 46.42 4.00
606 2866 2.613691 CAGATTCATTTGCAAGGTGGC 58.386 47.619 12.28 4.90 0.00 5.01
614 2930 2.530460 TTGCAAGGTGGCCAGAATAT 57.470 45.000 5.11 0.00 0.00 1.28
618 2934 2.313317 CAAGGTGGCCAGAATATGCAT 58.687 47.619 5.11 3.79 0.00 3.96
660 2998 2.573462 TCCCTTTGAGATGCAGCTTAGT 59.427 45.455 5.67 0.00 0.00 2.24
668 3006 3.604582 AGATGCAGCTTAGTCAGGAAAC 58.395 45.455 0.00 0.00 0.00 2.78
669 3007 2.928801 TGCAGCTTAGTCAGGAAACA 57.071 45.000 0.00 0.00 0.00 2.83
670 3008 3.423539 TGCAGCTTAGTCAGGAAACAT 57.576 42.857 0.00 0.00 0.00 2.71
682 3083 5.411669 AGTCAGGAAACATATCAAACCGAAC 59.588 40.000 0.00 0.00 0.00 3.95
697 3098 6.148811 TCAAACCGAACCACTAATTCAGATTC 59.851 38.462 0.00 0.00 0.00 2.52
707 3109 6.642950 CCACTAATTCAGATTCAGATACGACC 59.357 42.308 0.00 0.00 0.00 4.79
708 3110 7.203218 CACTAATTCAGATTCAGATACGACCA 58.797 38.462 0.00 0.00 0.00 4.02
730 3143 9.780413 GACCAATTCAAGAGTTAATTCAGATTC 57.220 33.333 0.44 0.00 0.00 2.52
733 3146 9.784680 CAATTCAAGAGTTAATTCAGATTCAGG 57.215 33.333 0.44 0.00 0.00 3.86
742 3174 7.824779 AGTTAATTCAGATTCAGGTACAACTCC 59.175 37.037 0.00 0.00 0.00 3.85
750 3182 1.887198 CAGGTACAACTCCAGACGACT 59.113 52.381 0.00 0.00 0.00 4.18
751 3183 1.887198 AGGTACAACTCCAGACGACTG 59.113 52.381 7.98 7.98 43.12 3.51
752 3184 1.612463 GGTACAACTCCAGACGACTGT 59.388 52.381 13.67 0.00 42.05 3.55
753 3185 2.035576 GGTACAACTCCAGACGACTGTT 59.964 50.000 13.67 0.00 42.05 3.16
755 3187 1.480954 ACAACTCCAGACGACTGTTGT 59.519 47.619 13.67 13.67 42.05 3.32
756 3188 2.128035 CAACTCCAGACGACTGTTGTC 58.872 52.381 18.49 18.49 42.05 3.18
757 3189 1.399714 ACTCCAGACGACTGTTGTCA 58.600 50.000 25.73 8.38 43.06 3.58
758 3190 1.964223 ACTCCAGACGACTGTTGTCAT 59.036 47.619 25.73 11.32 43.06 3.06
759 3191 2.288457 ACTCCAGACGACTGTTGTCATG 60.288 50.000 25.73 19.76 43.06 3.07
760 3192 0.792640 CCAGACGACTGTTGTCATGC 59.207 55.000 25.73 4.04 43.06 4.06
761 3193 0.436150 CAGACGACTGTTGTCATGCG 59.564 55.000 25.73 10.55 43.06 4.73
763 3195 0.435008 GACGACTGTTGTCATGCGTC 59.565 55.000 20.66 10.94 43.06 5.19
765 3197 1.781555 GACTGTTGTCATGCGTCGG 59.218 57.895 0.00 0.00 42.48 4.79
766 3198 1.626654 GACTGTTGTCATGCGTCGGG 61.627 60.000 0.00 0.00 42.48 5.14
767 3199 1.374125 CTGTTGTCATGCGTCGGGA 60.374 57.895 0.00 0.00 0.00 5.14
796 3228 1.676006 CATATGGACGGACCCAAAAGC 59.324 52.381 0.00 0.00 40.04 3.51
804 3236 4.011698 GACGGACCCAAAAGCCTTAATTA 58.988 43.478 0.00 0.00 0.00 1.40
821 3253 6.375455 CCTTAATTACTCAAACAGGCTGTCAT 59.625 38.462 22.31 10.44 0.00 3.06
824 3256 3.996150 ACTCAAACAGGCTGTCATTTG 57.004 42.857 22.31 20.71 34.11 2.32
827 3259 4.202050 ACTCAAACAGGCTGTCATTTGAAC 60.202 41.667 25.20 0.00 39.78 3.18
828 3260 3.044986 CAAACAGGCTGTCATTTGAACG 58.955 45.455 22.31 0.00 34.62 3.95
829 3261 1.967319 ACAGGCTGTCATTTGAACGT 58.033 45.000 15.88 0.00 0.00 3.99
833 3265 2.032030 AGGCTGTCATTTGAACGTTTCG 60.032 45.455 0.46 0.00 0.00 3.46
835 3267 2.964768 GCTGTCATTTGAACGTTTCGTC 59.035 45.455 0.46 0.00 39.99 4.20
836 3268 3.545228 GCTGTCATTTGAACGTTTCGTCA 60.545 43.478 0.46 0.00 39.99 4.35
838 3270 3.371285 TGTCATTTGAACGTTTCGTCACA 59.629 39.130 0.46 0.00 39.99 3.58
839 3271 3.717404 GTCATTTGAACGTTTCGTCACAC 59.283 43.478 0.46 0.00 39.99 3.82
841 3273 2.791417 TTGAACGTTTCGTCACACAC 57.209 45.000 0.46 0.00 39.99 3.82
844 3276 0.722848 AACGTTTCGTCACACACACC 59.277 50.000 0.00 0.00 39.99 4.16
845 3277 0.390078 ACGTTTCGTCACACACACCA 60.390 50.000 0.00 0.00 33.69 4.17
846 3278 0.025770 CGTTTCGTCACACACACCAC 59.974 55.000 0.00 0.00 0.00 4.16
847 3279 1.080298 GTTTCGTCACACACACCACA 58.920 50.000 0.00 0.00 0.00 4.17
848 3280 1.080298 TTTCGTCACACACACCACAC 58.920 50.000 0.00 0.00 0.00 3.82
849 3281 1.079317 TTCGTCACACACACCACACG 61.079 55.000 0.00 0.00 0.00 4.49
850 3282 2.707039 GTCACACACACCACACGC 59.293 61.111 0.00 0.00 0.00 5.34
851 3283 1.813753 GTCACACACACCACACGCT 60.814 57.895 0.00 0.00 0.00 5.07
852 3284 1.078778 TCACACACACCACACGCTT 60.079 52.632 0.00 0.00 0.00 4.68
853 3285 1.087202 TCACACACACCACACGCTTC 61.087 55.000 0.00 0.00 0.00 3.86
854 3286 1.817941 ACACACACCACACGCTTCC 60.818 57.895 0.00 0.00 0.00 3.46
855 3287 2.203153 ACACACCACACGCTTCCC 60.203 61.111 0.00 0.00 0.00 3.97
856 3288 2.203139 CACACCACACGCTTCCCA 60.203 61.111 0.00 0.00 0.00 4.37
857 3289 1.600636 CACACCACACGCTTCCCAT 60.601 57.895 0.00 0.00 0.00 4.00
858 3290 1.600636 ACACCACACGCTTCCCATG 60.601 57.895 0.00 0.00 0.00 3.66
859 3291 1.600636 CACCACACGCTTCCCATGT 60.601 57.895 0.00 0.00 0.00 3.21
860 3292 1.600636 ACCACACGCTTCCCATGTG 60.601 57.895 0.00 0.00 42.75 3.21
861 3293 2.562912 CACACGCTTCCCATGTGC 59.437 61.111 0.00 0.00 37.52 4.57
862 3294 2.112928 ACACGCTTCCCATGTGCA 59.887 55.556 0.00 0.00 37.11 4.57
863 3295 1.528076 ACACGCTTCCCATGTGCAA 60.528 52.632 0.00 0.00 37.11 4.08
864 3296 1.106351 ACACGCTTCCCATGTGCAAA 61.106 50.000 0.00 0.00 37.11 3.68
879 3311 1.628340 TGCAAACCCTAGCTAGCTCAA 59.372 47.619 23.26 3.28 0.00 3.02
902 3338 0.593128 ACCTGCGAGAACATTGTTGC 59.407 50.000 6.80 5.13 0.00 4.17
922 3358 0.607489 CCTGTCCTCAGCCACCTTTG 60.607 60.000 0.00 0.00 40.09 2.77
948 3384 5.474825 GTTTTAACCCAGAGAGAGAGACAG 58.525 45.833 0.00 0.00 0.00 3.51
955 3402 1.091537 GAGAGAGAGACAGGACACGG 58.908 60.000 0.00 0.00 0.00 4.94
976 3423 1.285078 CCCCAGGGCCTATAAATAGCC 59.715 57.143 5.28 0.00 0.00 3.93
979 3426 1.279271 CAGGGCCTATAAATAGCCGCT 59.721 52.381 5.28 0.00 32.36 5.52
1009 3462 3.644966 AGAGAGACACCAAACCAAACA 57.355 42.857 0.00 0.00 0.00 2.83
1293 3779 0.526211 CCAGATCCTTGTCGACGACA 59.474 55.000 26.04 26.04 41.09 4.35
1381 3882 9.257651 CTAGTAAAAGGTATAATTCTCAACGGG 57.742 37.037 0.00 0.00 0.00 5.28
1425 5056 7.755582 AACAAAGTTTTCAGTTGAGCATAAC 57.244 32.000 0.00 0.00 0.00 1.89
1491 6857 2.058798 CTACGCATGACTGTGTCGTTT 58.941 47.619 0.00 0.00 44.75 3.60
1714 12669 4.935352 TCAGAACAAAAACTTGGATGGG 57.065 40.909 0.00 0.00 0.00 4.00
1718 12673 4.584743 AGAACAAAAACTTGGATGGGTCTC 59.415 41.667 0.00 0.00 0.00 3.36
1744 12699 7.545965 CGAAGTCTTTCTCTAAATAGGCTTTCA 59.454 37.037 0.00 0.00 0.00 2.69
1746 12701 6.814146 AGTCTTTCTCTAAATAGGCTTTCACG 59.186 38.462 0.00 0.00 0.00 4.35
1747 12702 6.812160 GTCTTTCTCTAAATAGGCTTTCACGA 59.188 38.462 0.00 0.00 0.00 4.35
1748 12703 6.812160 TCTTTCTCTAAATAGGCTTTCACGAC 59.188 38.462 0.00 0.00 0.00 4.34
1788 12753 2.514458 AACCAATCCTAGCAAGGTGG 57.486 50.000 0.00 0.71 44.09 4.61
1803 12769 4.509970 GCAAGGTGGCGAAAAATAAAAGTT 59.490 37.500 0.00 0.00 0.00 2.66
1806 12772 5.666462 AGGTGGCGAAAAATAAAAGTTTGT 58.334 33.333 0.00 0.00 0.00 2.83
1904 12876 3.771160 GGTCACCGGTGGAGCGAT 61.771 66.667 33.40 0.00 0.00 4.58
1926 12898 0.673644 GCCAAGCCGTGTCATGTAGT 60.674 55.000 0.00 0.00 0.00 2.73
1949 12921 2.036098 CAACATCTGCCCCAGCCA 59.964 61.111 0.00 0.00 38.69 4.75
1953 12925 3.415087 ATCTGCCCCAGCCAGTCC 61.415 66.667 0.00 0.00 38.69 3.85
1969 12941 1.229496 TCCCAGTCCTGCTGCCTAA 60.229 57.895 0.00 0.00 43.71 2.69
1982 12954 2.332654 GCCTAACCAACAGGTGCCG 61.333 63.158 0.00 0.00 35.32 5.69
2140 13118 1.209504 TGCCTAACCTCATGCCTACAC 59.790 52.381 0.00 0.00 0.00 2.90
2277 13262 4.534500 TGTATAAACTCCAGTGGTGGACAT 59.466 41.667 15.44 7.38 46.77 3.06
2428 13419 5.235516 CCTATGTTGTTGTAGGTTCTCGTT 58.764 41.667 0.00 0.00 34.14 3.85
2439 13430 6.460781 TGTAGGTTCTCGTTTACATTCATGT 58.539 36.000 0.00 0.00 44.48 3.21
2454 13447 6.521162 ACATTCATGTACTGTGTGTTGTCTA 58.479 36.000 0.00 0.00 39.68 2.59
2584 13603 0.617820 AGTAAGGCAGGGTGATCCGT 60.618 55.000 0.00 0.00 41.52 4.69
2608 13629 7.252543 CGTTCTCAATTACTATTTGTTTTCGCG 60.253 37.037 0.00 0.00 0.00 5.87
2613 13634 1.259316 CTATTTGTTTTCGCGGCTGC 58.741 50.000 7.70 7.70 37.91 5.25
2679 13701 1.423161 GCAGCCCCCTATCAGATTCTT 59.577 52.381 0.00 0.00 0.00 2.52
2693 13715 5.224888 TCAGATTCTTTTCATGCACAAAGC 58.775 37.500 9.15 0.00 45.96 3.51
2723 13745 9.833917 CTATTCTCCAATATGCAGATGATACAT 57.166 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.338769 ACCCAAAAACCTCGGATCTCG 60.339 52.381 0.00 0.00 40.90 4.04
21 22 0.450184 CGCATACCCAAAAACCTCGG 59.550 55.000 0.00 0.00 0.00 4.63
22 23 0.179174 GCGCATACCCAAAAACCTCG 60.179 55.000 0.30 0.00 0.00 4.63
25 26 0.389296 GGTGCGCATACCCAAAAACC 60.389 55.000 15.91 1.08 34.56 3.27
46 53 0.096628 CTTGATCAACAGAGCTGCGC 59.903 55.000 3.38 0.00 0.00 6.09
47 54 0.096628 GCTTGATCAACAGAGCTGCG 59.903 55.000 3.38 0.00 33.36 5.18
59 66 0.249398 ACGTACCTGGGTGCTTGATC 59.751 55.000 2.07 0.00 0.00 2.92
61 68 1.669440 GACGTACCTGGGTGCTTGA 59.331 57.895 2.07 0.00 0.00 3.02
62 69 1.375523 GGACGTACCTGGGTGCTTG 60.376 63.158 2.07 0.00 35.41 4.01
72 79 1.321074 CCACAGGAGGAGGACGTACC 61.321 65.000 0.00 0.00 39.35 3.34
73 80 1.321074 CCCACAGGAGGAGGACGTAC 61.321 65.000 0.00 0.00 33.47 3.67
74 81 1.000019 CCCACAGGAGGAGGACGTA 60.000 63.158 0.00 0.00 33.47 3.57
75 82 2.283966 CCCACAGGAGGAGGACGT 60.284 66.667 0.00 0.00 33.47 4.34
76 83 3.775654 GCCCACAGGAGGAGGACG 61.776 72.222 0.00 0.00 33.47 4.79
77 84 1.977293 GATGCCCACAGGAGGAGGAC 61.977 65.000 0.00 0.00 33.47 3.85
78 85 1.690633 GATGCCCACAGGAGGAGGA 60.691 63.158 0.00 0.00 33.47 3.71
79 86 1.277580 AAGATGCCCACAGGAGGAGG 61.278 60.000 0.00 0.00 33.47 4.30
81 88 1.993653 CAAGATGCCCACAGGAGGA 59.006 57.895 0.00 0.00 33.47 3.71
82 89 1.751927 GCAAGATGCCCACAGGAGG 60.752 63.158 0.00 0.00 37.42 4.30
94 107 1.384989 GCATCAGCCTGCTGCAAGAT 61.385 55.000 15.24 2.44 44.83 2.40
95 108 2.044555 GCATCAGCCTGCTGCAAGA 61.045 57.895 15.24 0.00 44.83 3.02
113 130 2.932083 GCTCATCGTATGGCGTGCG 61.932 63.158 11.12 11.12 42.13 5.34
120 137 1.339291 TGGCAGAGAGCTCATCGTATG 59.661 52.381 17.77 3.60 44.79 2.39
121 138 1.697284 TGGCAGAGAGCTCATCGTAT 58.303 50.000 17.77 0.00 44.79 3.06
127 144 1.134189 CATGGATTGGCAGAGAGCTCA 60.134 52.381 17.77 0.00 44.79 4.26
128 145 1.134159 ACATGGATTGGCAGAGAGCTC 60.134 52.381 5.27 5.27 44.79 4.09
129 146 0.917533 ACATGGATTGGCAGAGAGCT 59.082 50.000 0.00 0.00 44.79 4.09
130 147 1.307097 GACATGGATTGGCAGAGAGC 58.693 55.000 0.00 0.00 44.65 4.09
140 157 2.910199 CGTGTGATCCTGACATGGATT 58.090 47.619 0.00 0.00 46.00 3.01
162 186 0.393402 TGCATGGTGATGTCTGAGGC 60.393 55.000 0.00 0.00 31.50 4.70
163 187 1.947456 CATGCATGGTGATGTCTGAGG 59.053 52.381 19.40 0.00 31.50 3.86
164 188 1.333931 GCATGCATGGTGATGTCTGAG 59.666 52.381 27.34 0.00 31.50 3.35
165 189 1.340211 TGCATGCATGGTGATGTCTGA 60.340 47.619 27.34 0.00 31.50 3.27
166 190 1.065551 CTGCATGCATGGTGATGTCTG 59.934 52.381 27.34 9.34 31.50 3.51
214 238 0.321919 GATGCTGGGTGCTCTGTTGA 60.322 55.000 0.00 0.00 43.37 3.18
215 239 1.642037 CGATGCTGGGTGCTCTGTTG 61.642 60.000 0.00 0.00 43.37 3.33
216 240 1.376424 CGATGCTGGGTGCTCTGTT 60.376 57.895 0.00 0.00 43.37 3.16
217 241 2.267006 CGATGCTGGGTGCTCTGT 59.733 61.111 0.00 0.00 43.37 3.41
226 250 4.779475 GGTATGGACCGATGCTGG 57.221 61.111 0.00 0.00 35.52 4.85
241 265 1.942657 CATAGCAATTACGCAGCAGGT 59.057 47.619 0.00 0.00 0.00 4.00
243 267 3.495753 TCATCATAGCAATTACGCAGCAG 59.504 43.478 0.00 0.00 0.00 4.24
245 269 3.248363 TGTCATCATAGCAATTACGCAGC 59.752 43.478 0.00 0.00 0.00 5.25
247 271 4.692228 TCTGTCATCATAGCAATTACGCA 58.308 39.130 0.00 0.00 0.00 5.24
248 272 5.852738 ATCTGTCATCATAGCAATTACGC 57.147 39.130 0.00 0.00 0.00 4.42
249 273 6.587608 TGCTATCTGTCATCATAGCAATTACG 59.412 38.462 18.12 0.00 45.96 3.18
250 274 7.895975 TGCTATCTGTCATCATAGCAATTAC 57.104 36.000 18.12 0.00 45.96 1.89
260 284 3.259123 ACACACAGTGCTATCTGTCATCA 59.741 43.478 0.00 0.00 45.37 3.07
261 285 3.854666 ACACACAGTGCTATCTGTCATC 58.145 45.455 0.00 0.00 45.37 2.92
262 286 3.259123 TGACACACAGTGCTATCTGTCAT 59.741 43.478 16.24 0.00 45.37 3.06
263 287 2.627699 TGACACACAGTGCTATCTGTCA 59.372 45.455 16.24 16.24 45.37 3.58
269 293 4.580167 ACACATTTTGACACACAGTGCTAT 59.420 37.500 0.00 0.00 36.98 2.97
275 299 4.742417 TCCAAACACATTTTGACACACAG 58.258 39.130 0.00 0.00 0.00 3.66
282 306 4.464244 TCAGTGGTTCCAAACACATTTTGA 59.536 37.500 10.08 2.19 39.99 2.69
291 316 2.024414 ACTTGCTCAGTGGTTCCAAAC 58.976 47.619 0.00 0.00 32.83 2.93
302 330 1.657594 CACGTATGCTCACTTGCTCAG 59.342 52.381 0.00 0.00 0.00 3.35
303 331 1.000843 ACACGTATGCTCACTTGCTCA 59.999 47.619 0.00 0.00 0.00 4.26
307 335 1.795768 ACCACACGTATGCTCACTTG 58.204 50.000 0.00 0.00 0.00 3.16
309 337 3.671008 TTAACCACACGTATGCTCACT 57.329 42.857 0.00 0.00 0.00 3.41
310 338 4.939509 AATTAACCACACGTATGCTCAC 57.060 40.909 0.00 0.00 0.00 3.51
311 339 5.113383 CCTAATTAACCACACGTATGCTCA 58.887 41.667 0.00 0.00 0.00 4.26
312 340 5.114081 ACCTAATTAACCACACGTATGCTC 58.886 41.667 0.00 0.00 0.00 4.26
313 341 5.093849 ACCTAATTAACCACACGTATGCT 57.906 39.130 0.00 0.00 0.00 3.79
314 342 7.486802 AATACCTAATTAACCACACGTATGC 57.513 36.000 0.00 0.00 0.00 3.14
315 343 9.531942 TGTAATACCTAATTAACCACACGTATG 57.468 33.333 0.00 0.00 31.82 2.39
317 345 9.935241 TTTGTAATACCTAATTAACCACACGTA 57.065 29.630 0.00 0.00 31.82 3.57
318 346 8.845413 TTTGTAATACCTAATTAACCACACGT 57.155 30.769 0.00 0.00 31.82 4.49
319 347 9.545611 GTTTTGTAATACCTAATTAACCACACG 57.454 33.333 0.00 0.00 31.82 4.49
352 380 5.628193 GTCGATCGCTATATTTCCTTTTCGA 59.372 40.000 11.09 0.00 0.00 3.71
354 382 6.183359 CGAGTCGATCGCTATATTTCCTTTTC 60.183 42.308 11.09 0.00 45.98 2.29
356 384 5.154932 CGAGTCGATCGCTATATTTCCTTT 58.845 41.667 11.09 0.00 45.98 3.11
377 406 3.355378 TCCACGTAACTAAATCCCTCGA 58.645 45.455 0.00 0.00 0.00 4.04
378 407 3.788333 TCCACGTAACTAAATCCCTCG 57.212 47.619 0.00 0.00 0.00 4.63
379 408 5.334724 TCTTCCACGTAACTAAATCCCTC 57.665 43.478 0.00 0.00 0.00 4.30
380 409 5.750352 TTCTTCCACGTAACTAAATCCCT 57.250 39.130 0.00 0.00 0.00 4.20
381 410 6.806388 TTTTCTTCCACGTAACTAAATCCC 57.194 37.500 0.00 0.00 0.00 3.85
383 412 7.063780 TCGGATTTTCTTCCACGTAACTAAATC 59.936 37.037 0.00 0.00 35.34 2.17
385 414 6.146021 GTCGGATTTTCTTCCACGTAACTAAA 59.854 38.462 0.00 0.00 35.34 1.85
386 415 5.634859 GTCGGATTTTCTTCCACGTAACTAA 59.365 40.000 0.00 0.00 35.34 2.24
387 416 5.163513 GTCGGATTTTCTTCCACGTAACTA 58.836 41.667 0.00 0.00 35.34 2.24
388 417 3.992427 GTCGGATTTTCTTCCACGTAACT 59.008 43.478 0.00 0.00 35.34 2.24
389 418 3.181537 CGTCGGATTTTCTTCCACGTAAC 60.182 47.826 0.00 0.00 36.46 2.50
390 419 2.988493 CGTCGGATTTTCTTCCACGTAA 59.012 45.455 0.00 0.00 36.46 3.18
391 420 2.598589 CGTCGGATTTTCTTCCACGTA 58.401 47.619 0.00 0.00 36.46 3.57
393 422 0.094730 GCGTCGGATTTTCTTCCACG 59.905 55.000 0.00 9.54 40.30 4.94
394 423 0.094730 CGCGTCGGATTTTCTTCCAC 59.905 55.000 0.00 0.00 35.34 4.02
439 491 1.401761 TTTCACTTGTGCACCATGCT 58.598 45.000 15.69 0.00 45.31 3.79
440 492 2.129607 CTTTTCACTTGTGCACCATGC 58.870 47.619 15.69 0.00 45.29 4.06
448 515 3.129287 AGGTGTTCAGCTTTTCACTTGTG 59.871 43.478 10.38 0.00 0.00 3.33
450 517 3.378112 TCAGGTGTTCAGCTTTTCACTTG 59.622 43.478 13.85 13.85 38.58 3.16
455 522 6.151817 AGGATATTTCAGGTGTTCAGCTTTTC 59.848 38.462 1.59 0.00 0.00 2.29
456 523 6.012745 AGGATATTTCAGGTGTTCAGCTTTT 58.987 36.000 1.59 0.00 0.00 2.27
469 536 4.686191 AGCTCTCACCAGGATATTTCAG 57.314 45.455 0.00 0.00 0.00 3.02
470 537 4.590647 CCTAGCTCTCACCAGGATATTTCA 59.409 45.833 0.00 0.00 0.00 2.69
474 541 2.158249 TGCCTAGCTCTCACCAGGATAT 60.158 50.000 1.97 0.00 0.00 1.63
475 542 1.217942 TGCCTAGCTCTCACCAGGATA 59.782 52.381 1.97 0.00 0.00 2.59
476 543 0.031716 TGCCTAGCTCTCACCAGGAT 60.032 55.000 1.97 0.00 0.00 3.24
477 544 0.031716 ATGCCTAGCTCTCACCAGGA 60.032 55.000 1.97 0.00 0.00 3.86
478 545 0.106335 CATGCCTAGCTCTCACCAGG 59.894 60.000 0.00 0.00 0.00 4.45
479 546 0.829333 ACATGCCTAGCTCTCACCAG 59.171 55.000 0.00 0.00 0.00 4.00
515 591 9.254133 CGTCTCATCAACATTCTAGTCAATAAT 57.746 33.333 0.00 0.00 0.00 1.28
516 592 7.706607 CCGTCTCATCAACATTCTAGTCAATAA 59.293 37.037 0.00 0.00 0.00 1.40
517 593 7.147897 ACCGTCTCATCAACATTCTAGTCAATA 60.148 37.037 0.00 0.00 0.00 1.90
518 594 6.045318 CCGTCTCATCAACATTCTAGTCAAT 58.955 40.000 0.00 0.00 0.00 2.57
521 597 4.800993 CACCGTCTCATCAACATTCTAGTC 59.199 45.833 0.00 0.00 0.00 2.59
522 598 4.382040 CCACCGTCTCATCAACATTCTAGT 60.382 45.833 0.00 0.00 0.00 2.57
523 599 4.115516 CCACCGTCTCATCAACATTCTAG 58.884 47.826 0.00 0.00 0.00 2.43
527 2776 2.859165 ACCACCGTCTCATCAACATT 57.141 45.000 0.00 0.00 0.00 2.71
535 2789 3.118884 GCCTATAGAAAACCACCGTCTCA 60.119 47.826 0.00 0.00 0.00 3.27
540 2794 2.878406 CCATGCCTATAGAAAACCACCG 59.122 50.000 0.00 0.00 0.00 4.94
541 2795 4.137543 CTCCATGCCTATAGAAAACCACC 58.862 47.826 0.00 0.00 0.00 4.61
542 2796 4.816925 GTCTCCATGCCTATAGAAAACCAC 59.183 45.833 0.00 0.00 0.00 4.16
556 2810 4.836125 TTGAACTTGAAAGTCTCCATGC 57.164 40.909 0.00 0.00 38.57 4.06
561 2815 6.024049 CACTGTGTTTGAACTTGAAAGTCTC 58.976 40.000 0.00 0.00 38.57 3.36
565 2819 4.484236 TGCACTGTGTTTGAACTTGAAAG 58.516 39.130 9.86 0.00 0.00 2.62
585 2845 2.613691 CCACCTTGCAAATGAATCTGC 58.386 47.619 11.12 0.00 39.09 4.26
597 2857 0.386838 GCATATTCTGGCCACCTTGC 59.613 55.000 0.00 3.28 0.00 4.01
604 2864 5.772825 TTTTCTGTATGCATATTCTGGCC 57.227 39.130 10.16 0.00 0.00 5.36
660 2998 4.698304 GGTTCGGTTTGATATGTTTCCTGA 59.302 41.667 0.00 0.00 0.00 3.86
668 3006 7.279981 TCTGAATTAGTGGTTCGGTTTGATATG 59.720 37.037 0.00 0.00 34.37 1.78
669 3007 7.335627 TCTGAATTAGTGGTTCGGTTTGATAT 58.664 34.615 0.00 0.00 34.37 1.63
670 3008 6.703319 TCTGAATTAGTGGTTCGGTTTGATA 58.297 36.000 0.00 0.00 34.37 2.15
682 3083 6.642950 GGTCGTATCTGAATCTGAATTAGTGG 59.357 42.308 0.00 0.00 0.00 4.00
697 3098 7.827819 TTAACTCTTGAATTGGTCGTATCTG 57.172 36.000 0.00 0.00 0.00 2.90
707 3109 9.784680 CCTGAATCTGAATTAACTCTTGAATTG 57.215 33.333 0.00 0.00 0.00 2.32
708 3110 9.525826 ACCTGAATCTGAATTAACTCTTGAATT 57.474 29.630 0.00 0.00 0.00 2.17
730 3143 1.887198 AGTCGTCTGGAGTTGTACCTG 59.113 52.381 0.00 0.00 0.00 4.00
733 3146 3.050619 CAACAGTCGTCTGGAGTTGTAC 58.949 50.000 14.13 0.00 45.14 2.90
742 3174 0.436150 CGCATGACAACAGTCGTCTG 59.564 55.000 8.17 8.17 46.18 3.51
750 3182 1.018752 CATCCCGACGCATGACAACA 61.019 55.000 0.00 0.00 0.00 3.33
751 3183 1.715585 CATCCCGACGCATGACAAC 59.284 57.895 0.00 0.00 0.00 3.32
752 3184 2.106074 GCATCCCGACGCATGACAA 61.106 57.895 0.00 0.00 0.00 3.18
753 3185 2.511373 GCATCCCGACGCATGACA 60.511 61.111 0.00 0.00 0.00 3.58
774 3206 0.462937 TTTGGGTCCGTCCATATGCG 60.463 55.000 0.00 0.00 36.58 4.73
775 3207 1.676006 CTTTTGGGTCCGTCCATATGC 59.324 52.381 0.00 0.00 36.58 3.14
776 3208 1.676006 GCTTTTGGGTCCGTCCATATG 59.324 52.381 0.00 0.00 36.58 1.78
777 3209 1.409661 GGCTTTTGGGTCCGTCCATAT 60.410 52.381 0.00 0.00 36.58 1.78
778 3210 0.034863 GGCTTTTGGGTCCGTCCATA 60.035 55.000 0.00 0.00 36.58 2.74
779 3211 1.304134 GGCTTTTGGGTCCGTCCAT 60.304 57.895 0.00 0.00 36.58 3.41
780 3212 2.002018 AAGGCTTTTGGGTCCGTCCA 62.002 55.000 0.00 0.00 38.11 4.02
781 3213 0.037160 TAAGGCTTTTGGGTCCGTCC 59.963 55.000 4.45 0.00 0.00 4.79
782 3214 1.900245 TTAAGGCTTTTGGGTCCGTC 58.100 50.000 4.45 0.00 0.00 4.79
783 3215 2.597578 ATTAAGGCTTTTGGGTCCGT 57.402 45.000 4.45 0.00 0.00 4.69
784 3216 4.014406 AGTAATTAAGGCTTTTGGGTCCG 58.986 43.478 4.45 0.00 0.00 4.79
796 3228 5.705441 TGACAGCCTGTTTGAGTAATTAAGG 59.295 40.000 0.00 0.00 0.00 2.69
804 3236 3.554934 TCAAATGACAGCCTGTTTGAGT 58.445 40.909 6.39 0.00 36.11 3.41
821 3253 2.479275 TGTGTGTGACGAAACGTTCAAA 59.521 40.909 0.00 0.00 41.37 2.69
824 3256 1.267186 GGTGTGTGTGACGAAACGTTC 60.267 52.381 0.00 0.00 41.37 3.95
827 3259 0.025770 GTGGTGTGTGTGACGAAACG 59.974 55.000 0.00 0.00 0.00 3.60
828 3260 1.080298 TGTGGTGTGTGTGACGAAAC 58.920 50.000 0.00 0.00 0.00 2.78
829 3261 1.080298 GTGTGGTGTGTGTGACGAAA 58.920 50.000 0.00 0.00 0.00 3.46
833 3265 1.366111 AAGCGTGTGGTGTGTGTGAC 61.366 55.000 0.00 0.00 0.00 3.67
835 3267 1.351707 GAAGCGTGTGGTGTGTGTG 59.648 57.895 0.00 0.00 0.00 3.82
836 3268 1.817941 GGAAGCGTGTGGTGTGTGT 60.818 57.895 0.00 0.00 0.00 3.72
838 3270 2.203153 GGGAAGCGTGTGGTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
839 3271 1.600636 ATGGGAAGCGTGTGGTGTG 60.601 57.895 0.00 0.00 0.00 3.82
841 3273 1.600636 ACATGGGAAGCGTGTGGTG 60.601 57.895 0.00 0.00 0.00 4.17
844 3276 1.794151 TTGCACATGGGAAGCGTGTG 61.794 55.000 0.00 0.00 44.51 3.82
845 3277 1.106351 TTTGCACATGGGAAGCGTGT 61.106 50.000 0.00 0.00 33.13 4.49
846 3278 0.664166 GTTTGCACATGGGAAGCGTG 60.664 55.000 0.00 0.00 0.00 5.34
847 3279 1.659794 GTTTGCACATGGGAAGCGT 59.340 52.632 0.00 0.00 0.00 5.07
848 3280 1.080569 GGTTTGCACATGGGAAGCG 60.081 57.895 0.00 0.00 0.00 4.68
849 3281 1.187567 AGGGTTTGCACATGGGAAGC 61.188 55.000 0.00 0.00 0.00 3.86
850 3282 2.094675 CTAGGGTTTGCACATGGGAAG 58.905 52.381 0.00 0.00 0.00 3.46
851 3283 1.890573 GCTAGGGTTTGCACATGGGAA 60.891 52.381 0.00 0.00 0.00 3.97
852 3284 0.323360 GCTAGGGTTTGCACATGGGA 60.323 55.000 0.00 0.00 0.00 4.37
853 3285 0.323725 AGCTAGGGTTTGCACATGGG 60.324 55.000 0.00 0.00 0.00 4.00
854 3286 2.292267 CTAGCTAGGGTTTGCACATGG 58.708 52.381 13.32 0.00 0.00 3.66
855 3287 1.672881 GCTAGCTAGGGTTTGCACATG 59.327 52.381 22.10 0.00 0.00 3.21
856 3288 1.561542 AGCTAGCTAGGGTTTGCACAT 59.438 47.619 17.69 0.00 0.00 3.21
857 3289 0.984230 AGCTAGCTAGGGTTTGCACA 59.016 50.000 17.69 0.00 0.00 4.57
858 3290 1.066143 TGAGCTAGCTAGGGTTTGCAC 60.066 52.381 19.38 6.86 0.00 4.57
859 3291 1.275666 TGAGCTAGCTAGGGTTTGCA 58.724 50.000 19.38 5.75 0.00 4.08
860 3292 2.403252 TTGAGCTAGCTAGGGTTTGC 57.597 50.000 19.38 7.57 0.00 3.68
879 3311 4.111916 CAACAATGTTCTCGCAGGTTTTT 58.888 39.130 0.00 0.00 0.00 1.94
895 3327 0.610232 GCTGAGGACAGGGCAACAAT 60.610 55.000 0.00 0.00 43.62 2.71
902 3338 1.783250 AAAGGTGGCTGAGGACAGGG 61.783 60.000 0.00 0.00 43.62 4.45
925 3361 5.470047 TGTCTCTCTCTCTGGGTTAAAAC 57.530 43.478 0.00 0.00 0.00 2.43
926 3362 4.528596 CCTGTCTCTCTCTCTGGGTTAAAA 59.471 45.833 0.00 0.00 0.00 1.52
927 3363 4.090090 CCTGTCTCTCTCTCTGGGTTAAA 58.910 47.826 0.00 0.00 0.00 1.52
928 3364 3.333980 TCCTGTCTCTCTCTCTGGGTTAA 59.666 47.826 0.00 0.00 0.00 2.01
929 3365 2.920271 TCCTGTCTCTCTCTCTGGGTTA 59.080 50.000 0.00 0.00 0.00 2.85
931 3367 1.005450 GTCCTGTCTCTCTCTCTGGGT 59.995 57.143 0.00 0.00 0.00 4.51
934 3370 1.737236 CGTGTCCTGTCTCTCTCTCTG 59.263 57.143 0.00 0.00 0.00 3.35
935 3371 1.339631 CCGTGTCCTGTCTCTCTCTCT 60.340 57.143 0.00 0.00 0.00 3.10
936 3372 1.091537 CCGTGTCCTGTCTCTCTCTC 58.908 60.000 0.00 0.00 0.00 3.20
979 3426 0.242286 GTGTCTCTCTTGCTGCGAGA 59.758 55.000 18.20 18.20 34.50 4.04
1009 3462 0.402121 GGCTCCTGGAAGTCCTTTGT 59.598 55.000 0.00 0.00 36.82 2.83
1241 3727 1.203187 ACCTCCTCAGCAGACTTGGTA 60.203 52.381 0.00 0.00 32.80 3.25
1293 3779 1.078709 CCGTGCTCGATGTTGTTGAT 58.921 50.000 10.21 0.00 39.71 2.57
1381 3882 8.662781 TTTGTTAACATCAGAGTATCCTATGC 57.337 34.615 9.56 0.00 32.63 3.14
1425 5056 3.795623 ATACAGCAGTAACTGGTACGG 57.204 47.619 0.00 0.00 40.40 4.02
1557 7107 4.556592 TGGTGGTAAGTAACGCCTAAAT 57.443 40.909 7.45 0.00 0.00 1.40
1714 12669 6.693978 GCCTATTTAGAGAAAGACTTCGAGAC 59.306 42.308 0.00 0.00 36.61 3.36
1718 12673 7.545965 TGAAAGCCTATTTAGAGAAAGACTTCG 59.454 37.037 0.00 0.00 36.61 3.79
1768 12723 2.356741 GCCACCTTGCTAGGATTGGTTA 60.357 50.000 21.63 0.00 45.05 2.85
1777 12732 4.695217 TTATTTTTCGCCACCTTGCTAG 57.305 40.909 0.00 0.00 0.00 3.42
1788 12753 5.743467 CCCCAACAAACTTTTATTTTTCGC 58.257 37.500 0.00 0.00 0.00 4.70
1806 12772 1.260538 TGCTTGTGTTGTTGCCCCAA 61.261 50.000 0.00 0.00 0.00 4.12
1860 12831 1.454847 TTGTGGCCACTTGGTGACC 60.455 57.895 34.75 7.37 36.61 4.02
1862 12833 0.106268 ATGTTGTGGCCACTTGGTGA 60.106 50.000 34.75 12.54 35.23 4.02
1910 12882 1.014044 CGCACTACATGACACGGCTT 61.014 55.000 0.00 0.00 0.00 4.35
1926 12898 2.359850 GGGCAGATGTTGGACGCA 60.360 61.111 0.00 0.00 0.00 5.24
1982 12954 1.024271 TCTTGTGTTCTTGCAGCACC 58.976 50.000 0.00 0.00 32.62 5.01
1996 12968 6.266103 TCTGATGCCTTCTTCAAATTTCTTGT 59.734 34.615 0.00 0.00 0.00 3.16
2026 12998 3.165875 AGGGAGAAAGACTCATTCGACA 58.834 45.455 0.00 0.00 46.54 4.35
2100 13078 7.013823 AGGCAAATGTGTATCTAGATAGCAT 57.986 36.000 12.87 15.76 0.00 3.79
2120 13098 1.209504 GTGTAGGCATGAGGTTAGGCA 59.790 52.381 0.00 0.00 0.00 4.75
2140 13118 9.797473 GTTCTTTCTTTCTTTTGTTTTGTTCTG 57.203 29.630 0.00 0.00 0.00 3.02
2277 13262 8.519526 AGATGAAGTTTGTACAACTTTGTTCAA 58.480 29.630 8.07 9.36 43.53 2.69
2428 13419 6.989759 AGACAACACACAGTACATGAATGTAA 59.010 34.615 0.00 0.00 44.11 2.41
2518 13537 8.842358 TTCCTAGGAACACTGTTTAACATAAG 57.158 34.615 20.72 0.00 0.00 1.73
2520 13539 7.970102 ACTTCCTAGGAACACTGTTTAACATA 58.030 34.615 20.72 0.00 0.00 2.29
2584 13603 7.018826 CCGCGAAAACAAATAGTAATTGAGAA 58.981 34.615 8.23 0.00 0.00 2.87
2636 13658 2.082140 ATGCTCATGTCCATGGCATT 57.918 45.000 20.74 11.51 45.02 3.56
2679 13701 7.362056 GGAGAATAGTAAGCTTTGTGCATGAAA 60.362 37.037 3.20 0.00 45.94 2.69
2723 13745 8.809066 TGTTGGACTAGCTTGTAAGACTATTAA 58.191 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.