Multiple sequence alignment - TraesCS2A01G154600

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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 TraesCS2A01G154600 chr2A 100.000 4069 0 0 1 4069 101991518 101995586 0.000000e+00 7515.0
1 TraesCS2A01G154600 chr2A 83.586 396 47 7 1 390 101916005 101916388 5.000000e-94 355.0
2 TraesCS2A01G154600 chr2B 94.342 3376 113 33 733 4069 154269164 154272500 0.000000e+00 5105.0
3 TraesCS2A01G154600 chr2B 92.857 56 2 2 526 580 502922192 502922246 3.370000e-11 80.5
4 TraesCS2A01G154600 chr2B 86.957 69 6 3 513 580 590087138 590087204 1.570000e-09 75.0
5 TraesCS2A01G154600 chr2D 95.952 2495 65 16 1077 3548 102879383 102881864 0.000000e+00 4015.0
6 TraesCS2A01G154600 chr2D 94.466 524 28 1 3546 4069 102881946 102882468 0.000000e+00 806.0
7 TraesCS2A01G154600 chr2D 85.036 274 13 12 721 981 102878661 102878919 1.880000e-63 254.0
8 TraesCS2A01G154600 chr2D 84.681 235 29 6 1 235 102878083 102878310 1.140000e-55 228.0
9 TraesCS2A01G154600 chr2D 93.617 94 6 0 595 688 102878496 102878589 1.520000e-29 141.0
10 TraesCS2A01G154600 chr2D 96.000 50 2 0 531 580 612704883 612704834 9.370000e-12 82.4
11 TraesCS2A01G154600 chr4B 96.000 50 2 0 531 580 6957892 6957941 9.370000e-12 82.4
12 TraesCS2A01G154600 chr6B 92.857 56 1 3 526 580 649061179 649061232 1.210000e-10 78.7
13 TraesCS2A01G154600 chr6B 86.957 69 6 3 513 580 610451007 610450941 1.570000e-09 75.0
14 TraesCS2A01G154600 chr1B 91.379 58 4 1 523 580 400184634 400184578 1.210000e-10 78.7
15 TraesCS2A01G154600 chr1B 86.957 69 6 3 513 580 640815315 640815381 1.570000e-09 75.0
16 TraesCS2A01G154600 chr7D 91.228 57 4 1 524 580 30997898 30997953 4.360000e-10 76.8


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 TraesCS2A01G154600 chr2A 101991518 101995586 4068 False 7515.0 7515 100.0000 1 4069 1 chr2A.!!$F2 4068
1 TraesCS2A01G154600 chr2B 154269164 154272500 3336 False 5105.0 5105 94.3420 733 4069 1 chr2B.!!$F1 3336
2 TraesCS2A01G154600 chr2D 102878083 102882468 4385 False 1088.8 4015 90.7504 1 4069 5 chr2D.!!$F1 4068

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
728 771 0.029567 GGAAGATGATCGACGCGTCT 59.970 55.0 33.94 19.03 33.21 4.18 F
1363 1795 0.252927 CCCAACTCCTCCTTCCTCCT 60.253 60.0 0.00 0.00 0.00 3.69 F
2207 2669 0.767998 TGCCCACATACAAGGTGACA 59.232 50.0 0.00 0.00 38.54 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2669 0.323178 CCCTCTTCAGCTGCATTGGT 60.323 55.0 9.47 0.00 0.00 3.67 R
2679 3141 0.738063 ATGTACGCATCGAACGGCAA 60.738 50.0 14.62 1.40 34.00 4.52 R
3739 4290 0.388134 ACGACCGATTGTGAAGGACG 60.388 55.0 4.31 4.31 45.62 4.79 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
24 25 0.030908 GCTGATCTAAGGTCGGTCGG 59.969 60.000 0.00 0.00 0.00 4.79
38 39 0.594602 GGTCGGGGTAACACTTTTGC 59.405 55.000 0.00 0.00 38.54 3.68
53 54 6.468543 ACACTTTTGCCTTTGGACTTAAAAA 58.531 32.000 0.00 0.00 0.00 1.94
65 66 7.610580 TTGGACTTAAAAAGGGATGTTTGAT 57.389 32.000 0.00 0.00 0.00 2.57
76 77 2.033801 GGATGTTTGATCAAGGCGATGG 59.966 50.000 8.41 0.00 33.17 3.51
96 97 0.804989 CACCCGCCTCAAGAAATGTC 59.195 55.000 0.00 0.00 0.00 3.06
97 98 0.693049 ACCCGCCTCAAGAAATGTCT 59.307 50.000 0.00 0.00 34.72 3.41
103 104 3.557595 CGCCTCAAGAAATGTCTATGGTC 59.442 47.826 0.00 0.00 32.16 4.02
105 106 3.557595 CCTCAAGAAATGTCTATGGTCGC 59.442 47.826 0.00 0.00 32.16 5.19
106 107 4.437239 CTCAAGAAATGTCTATGGTCGCT 58.563 43.478 0.00 0.00 32.16 4.93
107 108 5.451937 CCTCAAGAAATGTCTATGGTCGCTA 60.452 44.000 0.00 0.00 32.16 4.26
108 109 5.348986 TCAAGAAATGTCTATGGTCGCTAC 58.651 41.667 0.00 0.00 32.16 3.58
109 110 3.966154 AGAAATGTCTATGGTCGCTACG 58.034 45.455 0.00 0.00 29.93 3.51
110 111 3.630769 AGAAATGTCTATGGTCGCTACGA 59.369 43.478 0.00 0.00 29.93 3.43
111 112 4.278669 AGAAATGTCTATGGTCGCTACGAT 59.721 41.667 0.00 0.00 32.83 3.73
112 113 4.585955 AATGTCTATGGTCGCTACGATT 57.414 40.909 0.00 0.00 38.42 3.34
113 114 5.700722 AATGTCTATGGTCGCTACGATTA 57.299 39.130 0.00 0.00 38.42 1.75
114 115 4.744136 TGTCTATGGTCGCTACGATTAG 57.256 45.455 0.00 0.00 38.42 1.73
115 116 4.132336 TGTCTATGGTCGCTACGATTAGT 58.868 43.478 0.00 0.00 38.42 2.24
154 155 3.810310 TGGGGTGAAAATGAAACACAC 57.190 42.857 0.00 0.00 37.24 3.82
155 156 3.370104 TGGGGTGAAAATGAAACACACT 58.630 40.909 0.00 0.00 37.95 3.55
157 158 4.339814 TGGGGTGAAAATGAAACACACTAC 59.660 41.667 0.00 0.00 37.95 2.73
161 162 6.183360 GGGTGAAAATGAAACACACTACAAGA 60.183 38.462 0.00 0.00 35.41 3.02
167 168 4.127171 TGAAACACACTACAAGAAGAGCC 58.873 43.478 0.00 0.00 0.00 4.70
170 171 2.700897 ACACACTACAAGAAGAGCCTGT 59.299 45.455 0.00 0.00 0.00 4.00
190 191 4.724399 TGTGAGTAGCAAAATGGGAAAGA 58.276 39.130 0.00 0.00 0.00 2.52
193 194 6.095377 GTGAGTAGCAAAATGGGAAAGAATG 58.905 40.000 0.00 0.00 0.00 2.67
194 195 5.185635 TGAGTAGCAAAATGGGAAAGAATGG 59.814 40.000 0.00 0.00 0.00 3.16
197 198 2.743664 GCAAAATGGGAAAGAATGGTGC 59.256 45.455 0.00 0.00 0.00 5.01
231 232 7.036220 ACTACTCGGTGAAATTGAAGTAGATG 58.964 38.462 12.80 0.00 34.07 2.90
235 236 4.032900 CGGTGAAATTGAAGTAGATGACGG 59.967 45.833 0.00 0.00 0.00 4.79
237 238 5.175859 GTGAAATTGAAGTAGATGACGGGA 58.824 41.667 0.00 0.00 0.00 5.14
238 239 5.063564 GTGAAATTGAAGTAGATGACGGGAC 59.936 44.000 0.00 0.00 0.00 4.46
239 240 4.819105 AATTGAAGTAGATGACGGGACA 57.181 40.909 0.00 0.00 0.00 4.02
240 241 4.819105 ATTGAAGTAGATGACGGGACAA 57.181 40.909 0.00 0.00 0.00 3.18
241 242 3.587797 TGAAGTAGATGACGGGACAAC 57.412 47.619 0.00 0.00 0.00 3.32
242 243 2.894765 TGAAGTAGATGACGGGACAACA 59.105 45.455 0.00 0.00 0.00 3.33
243 244 3.056821 TGAAGTAGATGACGGGACAACAG 60.057 47.826 0.00 0.00 0.00 3.16
244 245 1.825474 AGTAGATGACGGGACAACAGG 59.175 52.381 0.00 0.00 0.00 4.00
245 246 1.822990 GTAGATGACGGGACAACAGGA 59.177 52.381 0.00 0.00 0.00 3.86
246 247 0.608640 AGATGACGGGACAACAGGAC 59.391 55.000 0.00 0.00 0.00 3.85
247 248 0.320374 GATGACGGGACAACAGGACA 59.680 55.000 0.00 0.00 0.00 4.02
248 249 0.984230 ATGACGGGACAACAGGACAT 59.016 50.000 0.00 0.00 0.00 3.06
249 250 0.034756 TGACGGGACAACAGGACATG 59.965 55.000 0.00 0.00 0.00 3.21
267 268 1.153127 GTGGGGGACACGACAAACA 60.153 57.895 0.00 0.00 40.85 2.83
269 270 0.536233 TGGGGGACACGACAAACATG 60.536 55.000 0.00 0.00 0.00 3.21
274 275 0.660488 GACACGACAAACATGCCACA 59.340 50.000 0.00 0.00 0.00 4.17
275 276 0.662619 ACACGACAAACATGCCACAG 59.337 50.000 0.00 0.00 0.00 3.66
281 282 2.616330 AAACATGCCACAGACGCCG 61.616 57.895 0.00 0.00 0.00 6.46
287 288 4.742201 CCACAGACGCCGGAGTGG 62.742 72.222 18.14 15.14 44.72 4.00
298 299 2.267961 GGAGTGGCCGTTCGGAAT 59.732 61.111 15.69 0.00 0.00 3.01
299 300 1.814169 GGAGTGGCCGTTCGGAATC 60.814 63.158 15.69 3.84 0.00 2.52
300 301 2.125673 AGTGGCCGTTCGGAATCG 60.126 61.111 15.69 0.00 37.82 3.34
301 302 2.125832 GTGGCCGTTCGGAATCGA 60.126 61.111 15.69 0.00 44.44 3.59
302 303 2.165301 GTGGCCGTTCGGAATCGAG 61.165 63.158 15.69 5.92 46.75 4.04
303 304 2.183555 GGCCGTTCGGAATCGAGT 59.816 61.111 15.69 0.00 46.75 4.18
304 305 2.165301 GGCCGTTCGGAATCGAGTG 61.165 63.158 15.69 1.00 46.75 3.51
305 306 1.153901 GCCGTTCGGAATCGAGTGA 60.154 57.895 15.69 0.00 46.75 3.41
342 343 5.106752 GCTTCAGCTTCGAGAAAGAAAGAAT 60.107 40.000 0.00 0.00 37.12 2.40
343 344 5.852738 TCAGCTTCGAGAAAGAAAGAATG 57.147 39.130 0.00 0.00 37.12 2.67
344 345 4.692625 TCAGCTTCGAGAAAGAAAGAATGG 59.307 41.667 0.00 0.00 37.12 3.16
346 347 5.180117 CAGCTTCGAGAAAGAAAGAATGGAA 59.820 40.000 0.00 0.00 37.12 3.53
402 406 9.941325 AATGTTTGATTAAATTTAGGTCATGCA 57.059 25.926 13.08 13.85 0.00 3.96
404 408 9.585099 TGTTTGATTAAATTTAGGTCATGCATC 57.415 29.630 13.08 6.00 0.00 3.91
407 411 8.750515 TGATTAAATTTAGGTCATGCATCTCA 57.249 30.769 0.00 0.00 0.00 3.27
408 412 9.187996 TGATTAAATTTAGGTCATGCATCTCAA 57.812 29.630 0.00 0.00 0.00 3.02
411 415 9.859427 TTAAATTTAGGTCATGCATCTCAAAAG 57.141 29.630 0.00 0.00 0.00 2.27
412 416 7.707624 AATTTAGGTCATGCATCTCAAAAGA 57.292 32.000 0.00 0.00 35.54 2.52
413 417 7.707624 ATTTAGGTCATGCATCTCAAAAGAA 57.292 32.000 0.00 0.00 34.49 2.52
414 418 6.748333 TTAGGTCATGCATCTCAAAAGAAG 57.252 37.500 0.00 0.00 34.49 2.85
415 419 3.442977 AGGTCATGCATCTCAAAAGAAGC 59.557 43.478 0.00 0.00 44.58 3.86
418 422 3.442625 TCATGCATCTCAAAAGAAGCCAG 59.557 43.478 0.00 0.00 43.89 4.85
420 424 3.489355 TGCATCTCAAAAGAAGCCAGAA 58.511 40.909 0.78 0.00 43.89 3.02
424 428 5.105837 GCATCTCAAAAGAAGCCAGAAGAAT 60.106 40.000 0.00 0.00 39.72 2.40
510 514 3.405823 AAAACGTCTTACATTCCGGGA 57.594 42.857 0.00 0.00 0.00 5.14
511 515 2.375173 AACGTCTTACATTCCGGGAC 57.625 50.000 0.00 0.00 0.00 4.46
527 531 3.908643 GGGACGAAGGGAGTAGATTTT 57.091 47.619 0.00 0.00 0.00 1.82
529 533 5.349061 GGGACGAAGGGAGTAGATTTTTA 57.651 43.478 0.00 0.00 0.00 1.52
549 553 8.726870 TTTTTATTTAGAATGTACTCCCTCCG 57.273 34.615 0.00 0.00 0.00 4.63
550 554 7.427989 TTTATTTAGAATGTACTCCCTCCGT 57.572 36.000 0.00 0.00 0.00 4.69
551 555 5.952347 ATTTAGAATGTACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
552 556 4.996788 TTAGAATGTACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
553 557 3.103080 AGAATGTACTCCCTCCGTTCT 57.897 47.619 0.00 0.00 31.33 3.01
554 558 4.246712 AGAATGTACTCCCTCCGTTCTA 57.753 45.455 0.00 0.00 33.77 2.10
555 559 4.607239 AGAATGTACTCCCTCCGTTCTAA 58.393 43.478 0.00 0.00 33.77 2.10
556 560 5.021458 AGAATGTACTCCCTCCGTTCTAAA 58.979 41.667 0.00 0.00 33.77 1.85
557 561 5.482878 AGAATGTACTCCCTCCGTTCTAAAA 59.517 40.000 0.00 0.00 33.77 1.52
558 562 5.952347 ATGTACTCCCTCCGTTCTAAAAT 57.048 39.130 0.00 0.00 0.00 1.82
559 563 7.343833 AGAATGTACTCCCTCCGTTCTAAAATA 59.656 37.037 0.00 0.00 33.77 1.40
560 564 6.461110 TGTACTCCCTCCGTTCTAAAATAG 57.539 41.667 0.00 0.00 0.00 1.73
561 565 6.189859 TGTACTCCCTCCGTTCTAAAATAGA 58.810 40.000 0.00 0.00 0.00 1.98
562 566 6.837568 TGTACTCCCTCCGTTCTAAAATAGAT 59.162 38.462 0.00 0.00 34.22 1.98
563 567 6.163135 ACTCCCTCCGTTCTAAAATAGATG 57.837 41.667 0.00 0.00 34.22 2.90
564 568 5.897824 ACTCCCTCCGTTCTAAAATAGATGA 59.102 40.000 0.00 0.00 34.22 2.92
565 569 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
566 570 5.070047 TCCCTCCGTTCTAAAATAGATGACC 59.930 44.000 0.00 0.00 34.22 4.02
567 571 5.298347 CCTCCGTTCTAAAATAGATGACCC 58.702 45.833 0.00 0.00 34.22 4.46
568 572 5.163343 CCTCCGTTCTAAAATAGATGACCCA 60.163 44.000 0.00 0.00 34.22 4.51
569 573 6.302535 TCCGTTCTAAAATAGATGACCCAA 57.697 37.500 0.00 0.00 34.22 4.12
570 574 6.110707 TCCGTTCTAAAATAGATGACCCAAC 58.889 40.000 0.00 0.00 34.22 3.77
571 575 6.070424 TCCGTTCTAAAATAGATGACCCAACT 60.070 38.462 0.00 0.00 34.22 3.16
572 576 6.598064 CCGTTCTAAAATAGATGACCCAACTT 59.402 38.462 0.00 0.00 34.22 2.66
573 577 7.120726 CCGTTCTAAAATAGATGACCCAACTTT 59.879 37.037 0.00 0.00 34.22 2.66
574 578 7.962918 CGTTCTAAAATAGATGACCCAACTTTG 59.037 37.037 0.00 0.00 34.22 2.77
575 579 8.793592 GTTCTAAAATAGATGACCCAACTTTGT 58.206 33.333 0.00 0.00 34.22 2.83
577 581 9.444600 TCTAAAATAGATGACCCAACTTTGTAC 57.555 33.333 0.00 0.00 0.00 2.90
578 582 9.449719 CTAAAATAGATGACCCAACTTTGTACT 57.550 33.333 0.00 0.00 0.00 2.73
580 584 9.449719 AAAATAGATGACCCAACTTTGTACTAG 57.550 33.333 0.00 0.00 0.00 2.57
581 585 5.422214 AGATGACCCAACTTTGTACTAGG 57.578 43.478 0.00 0.00 0.00 3.02
582 586 5.091552 AGATGACCCAACTTTGTACTAGGA 58.908 41.667 0.00 0.00 0.00 2.94
583 587 4.884668 TGACCCAACTTTGTACTAGGAG 57.115 45.455 0.00 0.00 0.00 3.69
584 588 4.228824 TGACCCAACTTTGTACTAGGAGT 58.771 43.478 0.00 0.00 0.00 3.85
585 589 5.396485 TGACCCAACTTTGTACTAGGAGTA 58.604 41.667 0.00 0.00 0.00 2.59
586 590 6.021030 TGACCCAACTTTGTACTAGGAGTAT 58.979 40.000 0.00 0.00 32.65 2.12
587 591 7.184161 TGACCCAACTTTGTACTAGGAGTATA 58.816 38.462 0.00 0.00 32.65 1.47
588 592 7.842743 TGACCCAACTTTGTACTAGGAGTATAT 59.157 37.037 0.00 0.00 32.65 0.86
589 593 8.019656 ACCCAACTTTGTACTAGGAGTATATG 57.980 38.462 0.00 0.00 32.65 1.78
590 594 7.622479 ACCCAACTTTGTACTAGGAGTATATGT 59.378 37.037 0.00 0.00 32.65 2.29
591 595 8.142551 CCCAACTTTGTACTAGGAGTATATGTC 58.857 40.741 0.00 0.00 32.65 3.06
592 596 8.915036 CCAACTTTGTACTAGGAGTATATGTCT 58.085 37.037 0.00 0.00 32.65 3.41
606 610 2.746279 ATGTCTTGTGTTCCCAACCA 57.254 45.000 0.00 0.00 0.00 3.67
608 612 2.582052 TGTCTTGTGTTCCCAACCATC 58.418 47.619 0.00 0.00 0.00 3.51
625 629 3.056035 ACCATCTTACTTCTTGTCCCGTC 60.056 47.826 0.00 0.00 0.00 4.79
627 631 4.322801 CCATCTTACTTCTTGTCCCGTCTT 60.323 45.833 0.00 0.00 0.00 3.01
630 634 0.759346 ACTTCTTGTCCCGTCTTGCT 59.241 50.000 0.00 0.00 0.00 3.91
671 675 1.111277 GCACTCCTCTCTCCTTCCTC 58.889 60.000 0.00 0.00 0.00 3.71
692 696 3.103911 GGTGAACTCGTCGCCGTG 61.104 66.667 0.00 0.00 46.80 4.94
693 697 3.764049 GTGAACTCGTCGCCGTGC 61.764 66.667 0.00 0.00 35.01 5.34
695 699 3.764049 GAACTCGTCGCCGTGCAC 61.764 66.667 6.82 6.82 35.01 4.57
714 718 1.911766 GGTGGTGAGGACGGGAAGA 60.912 63.158 0.00 0.00 0.00 2.87
718 761 1.123928 GGTGAGGACGGGAAGATGAT 58.876 55.000 0.00 0.00 0.00 2.45
719 762 1.069358 GGTGAGGACGGGAAGATGATC 59.931 57.143 0.00 0.00 0.00 2.92
728 771 0.029567 GGAAGATGATCGACGCGTCT 59.970 55.000 33.94 19.03 33.21 4.18
730 773 2.300042 GAAGATGATCGACGCGTCTAC 58.700 52.381 33.94 24.03 31.66 2.59
745 788 3.064987 CTACACCCACCTCTCGGCG 62.065 68.421 0.00 0.00 0.00 6.46
807 853 0.827368 GTGCGATCTCCTTTCTCCCT 59.173 55.000 0.00 0.00 0.00 4.20
809 855 0.391228 GCGATCTCCTTTCTCCCTCC 59.609 60.000 0.00 0.00 0.00 4.30
811 857 1.044611 GATCTCCTTTCTCCCTCCCG 58.955 60.000 0.00 0.00 0.00 5.14
839 885 1.087501 AAAGCGCGATCTTTCTTCCC 58.912 50.000 12.10 0.00 31.07 3.97
847 893 3.628032 GCGATCTTTCTTCCCCCTAAAAG 59.372 47.826 0.00 0.00 0.00 2.27
888 940 1.370414 CCACGCAACGCAAAGGAAG 60.370 57.895 0.00 0.00 0.00 3.46
889 941 1.370414 CACGCAACGCAAAGGAAGG 60.370 57.895 0.00 0.00 0.00 3.46
890 942 1.525077 ACGCAACGCAAAGGAAGGA 60.525 52.632 0.00 0.00 0.00 3.36
891 943 1.098712 ACGCAACGCAAAGGAAGGAA 61.099 50.000 0.00 0.00 0.00 3.36
996 1069 3.706373 CACCACTCCCACTCCCCG 61.706 72.222 0.00 0.00 0.00 5.73
1021 1094 0.678048 GCTCCAACCAAATCTCGCCT 60.678 55.000 0.00 0.00 0.00 5.52
1023 1096 0.391130 TCCAACCAAATCTCGCCTCG 60.391 55.000 0.00 0.00 0.00 4.63
1071 1144 3.083349 CCGCCATGTCCTCCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
1097 1526 2.648102 GATCACGACGAGGACGCG 60.648 66.667 3.53 3.53 43.96 6.01
1363 1795 0.252927 CCCAACTCCTCCTTCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
1364 1796 1.199615 CCAACTCCTCCTTCCTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
1413 1845 4.040198 ACTTCCCCTCCCCCTCCC 62.040 72.222 0.00 0.00 0.00 4.30
1799 2261 2.037847 CCCAAGGGCCCCAAGAAG 59.962 66.667 21.43 0.90 0.00 2.85
1868 2330 4.796231 CTCGTTGGGTCGGAGGCG 62.796 72.222 0.00 0.00 0.00 5.52
1952 2414 2.903798 CAGTTCATCTGGAGCTTCCTC 58.096 52.381 0.00 0.00 40.23 3.71
2001 2463 0.870307 CCGGACGTTCGTGATGGATC 60.870 60.000 16.40 0.00 0.00 3.36
2123 2585 1.229529 TCTGGTGGAGGAAGGGGAC 60.230 63.158 0.00 0.00 0.00 4.46
2207 2669 0.767998 TGCCCACATACAAGGTGACA 59.232 50.000 0.00 0.00 38.54 3.58
2256 2718 4.321899 GCAACATCATTTGGAGGCAGTTTA 60.322 41.667 0.00 0.00 0.00 2.01
2369 2831 3.119602 CCAAGAGGCTGATGAACATTGTG 60.120 47.826 0.00 0.00 0.00 3.33
2679 3141 3.392616 AGCGATCAATAATGGGAAGGACT 59.607 43.478 0.00 0.00 0.00 3.85
2851 3313 9.475620 TGATAATTATCGGTGTCCATATACTCT 57.524 33.333 18.35 0.00 35.48 3.24
2875 3337 2.486966 GCTGGCGCAATGGAACTC 59.513 61.111 10.83 0.00 35.78 3.01
3092 3558 2.229062 TCTTAGTGTCTGGACTTCTGCG 59.771 50.000 2.38 0.00 0.00 5.18
3157 3624 9.964303 TCATTTATTGTATGTTTCCATATGTGC 57.036 29.630 1.24 0.00 36.02 4.57
3327 3794 2.224354 TGCTCTGTGAGAATTGCAGACA 60.224 45.455 0.00 0.00 35.65 3.41
3518 3985 3.879892 GGCCAGTCTAGTCCAAATGAATC 59.120 47.826 0.00 0.00 0.00 2.52
3571 4122 7.209475 ACATTGGTGCATATTTTAGGTTATGC 58.791 34.615 7.73 7.73 46.96 3.14
3713 4264 4.521130 AGTCATTAGTTCAGACTTCGCA 57.479 40.909 0.00 0.00 39.45 5.10
3739 4290 2.706190 AGGAAGATGGTAGGTGGCATAC 59.294 50.000 0.00 0.00 0.00 2.39
3759 4310 1.792006 GTCCTTCACAATCGGTCGTT 58.208 50.000 0.00 0.00 0.00 3.85
3771 4322 5.182001 ACAATCGGTCGTTACACTAGTAGTT 59.818 40.000 0.00 0.00 0.00 2.24
3828 4379 2.512515 ATCTCTTTGAGCGGCCGC 60.513 61.111 42.34 42.34 42.33 6.53
3860 4411 4.734398 ATGTTTCAACTGGCTGTTTTCA 57.266 36.364 7.06 5.26 36.63 2.69
3875 4426 5.261209 TGTTTTCAACTTGAGGATGTTGG 57.739 39.130 0.00 0.00 42.48 3.77
3879 4430 6.817765 TTTCAACTTGAGGATGTTGGATAC 57.182 37.500 0.00 0.00 42.48 2.24
3900 4451 1.274596 GAAGCCATTCTGCGCATTTG 58.725 50.000 12.24 9.04 36.02 2.32
3966 4517 5.459107 GCTTGATGAATTCACAATGATGCTC 59.541 40.000 11.07 1.60 32.84 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.533753 TGTTACCCCGACCGACCTT 60.534 57.895 0.00 0.00 0.00 3.50
16 17 0.033920 AAAGTGTTACCCCGACCGAC 59.966 55.000 0.00 0.00 0.00 4.79
17 18 0.758123 AAAAGTGTTACCCCGACCGA 59.242 50.000 0.00 0.00 0.00 4.69
24 25 2.696187 TCCAAAGGCAAAAGTGTTACCC 59.304 45.455 0.00 0.00 0.00 3.69
38 39 6.419484 AACATCCCTTTTTAAGTCCAAAGG 57.581 37.500 8.78 8.78 46.10 3.11
53 54 1.281867 TCGCCTTGATCAAACATCCCT 59.718 47.619 9.88 0.00 0.00 4.20
65 66 4.776322 CGGGTGCCATCGCCTTGA 62.776 66.667 0.00 0.00 42.48 3.02
76 77 1.244019 ACATTTCTTGAGGCGGGTGC 61.244 55.000 0.00 0.00 41.71 5.01
96 97 5.444350 CGTCTACTAATCGTAGCGACCATAG 60.444 48.000 8.95 0.77 44.29 2.23
97 98 4.386954 CGTCTACTAATCGTAGCGACCATA 59.613 45.833 8.95 0.00 44.29 2.74
103 104 3.055591 TCCTCGTCTACTAATCGTAGCG 58.944 50.000 0.00 0.00 44.29 4.26
105 106 4.083908 GGCTTCCTCGTCTACTAATCGTAG 60.084 50.000 0.00 0.00 45.68 3.51
106 107 3.812053 GGCTTCCTCGTCTACTAATCGTA 59.188 47.826 0.00 0.00 0.00 3.43
107 108 2.617774 GGCTTCCTCGTCTACTAATCGT 59.382 50.000 0.00 0.00 0.00 3.73
108 109 2.879646 AGGCTTCCTCGTCTACTAATCG 59.120 50.000 0.00 0.00 0.00 3.34
109 110 4.820716 TGTAGGCTTCCTCGTCTACTAATC 59.179 45.833 0.00 0.00 34.61 1.75
110 111 4.789807 TGTAGGCTTCCTCGTCTACTAAT 58.210 43.478 0.00 0.00 34.61 1.73
111 112 4.226427 TGTAGGCTTCCTCGTCTACTAA 57.774 45.455 0.00 0.00 34.61 2.24
112 113 3.920231 TGTAGGCTTCCTCGTCTACTA 57.080 47.619 0.00 0.00 34.61 1.82
113 114 2.803030 TGTAGGCTTCCTCGTCTACT 57.197 50.000 0.00 0.00 34.61 2.57
114 115 3.491104 CCATTGTAGGCTTCCTCGTCTAC 60.491 52.174 0.00 0.00 34.61 2.59
115 116 2.693591 CCATTGTAGGCTTCCTCGTCTA 59.306 50.000 0.00 0.00 34.61 2.59
120 121 0.919710 ACCCCATTGTAGGCTTCCTC 59.080 55.000 0.00 0.00 34.61 3.71
123 124 2.507407 TTCACCCCATTGTAGGCTTC 57.493 50.000 0.00 0.00 0.00 3.86
154 155 3.951775 ACTCACAGGCTCTTCTTGTAG 57.048 47.619 0.00 0.00 0.00 2.74
155 156 3.193691 GCTACTCACAGGCTCTTCTTGTA 59.806 47.826 0.00 0.00 0.00 2.41
157 158 2.028658 TGCTACTCACAGGCTCTTCTTG 60.029 50.000 0.00 0.00 0.00 3.02
161 162 3.492102 TTTTGCTACTCACAGGCTCTT 57.508 42.857 0.00 0.00 0.00 2.85
167 168 4.761739 TCTTTCCCATTTTGCTACTCACAG 59.238 41.667 0.00 0.00 0.00 3.66
170 171 5.185635 CCATTCTTTCCCATTTTGCTACTCA 59.814 40.000 0.00 0.00 0.00 3.41
197 198 2.348888 ACCGAGTAGTTGCCTCCGG 61.349 63.158 0.00 0.00 0.00 5.14
210 211 5.004821 CGTCATCTACTTCAATTTCACCGAG 59.995 44.000 0.00 0.00 0.00 4.63
213 214 4.332819 CCCGTCATCTACTTCAATTTCACC 59.667 45.833 0.00 0.00 0.00 4.02
215 216 5.175859 GTCCCGTCATCTACTTCAATTTCA 58.824 41.667 0.00 0.00 0.00 2.69
217 218 5.160607 TGTCCCGTCATCTACTTCAATTT 57.839 39.130 0.00 0.00 0.00 1.82
218 219 4.819105 TGTCCCGTCATCTACTTCAATT 57.181 40.909 0.00 0.00 0.00 2.32
231 232 0.034896 ACATGTCCTGTTGTCCCGTC 59.965 55.000 0.00 0.00 32.90 4.79
235 236 0.609131 CCCCACATGTCCTGTTGTCC 60.609 60.000 0.00 0.00 35.29 4.02
237 238 1.065410 TCCCCCACATGTCCTGTTGT 61.065 55.000 0.00 0.00 35.29 3.32
238 239 0.609131 GTCCCCCACATGTCCTGTTG 60.609 60.000 0.00 0.00 35.29 3.33
239 240 1.065410 TGTCCCCCACATGTCCTGTT 61.065 55.000 0.00 0.00 35.29 3.16
240 241 1.463214 TGTCCCCCACATGTCCTGT 60.463 57.895 0.00 0.00 39.20 4.00
241 242 1.002134 GTGTCCCCCACATGTCCTG 60.002 63.158 0.00 0.00 43.92 3.86
242 243 2.592993 CGTGTCCCCCACATGTCCT 61.593 63.158 0.00 0.00 44.78 3.85
243 244 2.046314 CGTGTCCCCCACATGTCC 60.046 66.667 0.00 0.00 44.78 4.02
244 245 1.375523 GTCGTGTCCCCCACATGTC 60.376 63.158 0.00 0.00 44.78 3.06
245 246 1.701031 TTGTCGTGTCCCCCACATGT 61.701 55.000 0.00 0.00 44.78 3.21
246 247 0.536233 TTTGTCGTGTCCCCCACATG 60.536 55.000 0.00 0.00 44.78 3.21
247 248 0.536460 GTTTGTCGTGTCCCCCACAT 60.536 55.000 0.00 0.00 44.78 3.21
248 249 1.153127 GTTTGTCGTGTCCCCCACA 60.153 57.895 0.00 0.00 44.78 4.17
249 250 0.536460 ATGTTTGTCGTGTCCCCCAC 60.536 55.000 0.00 0.00 40.89 4.61
259 260 0.110688 CGTCTGTGGCATGTTTGTCG 60.111 55.000 0.00 0.00 0.00 4.35
263 264 2.616330 CGGCGTCTGTGGCATGTTT 61.616 57.895 0.00 0.00 0.00 2.83
267 268 4.457496 CTCCGGCGTCTGTGGCAT 62.457 66.667 6.01 0.00 0.00 4.40
281 282 1.814169 GATTCCGAACGGCCACTCC 60.814 63.158 2.24 0.00 34.68 3.85
285 286 2.183300 CTCGATTCCGAACGGCCA 59.817 61.111 2.24 0.00 45.04 5.36
286 287 2.165301 CACTCGATTCCGAACGGCC 61.165 63.158 8.48 0.00 45.04 6.13
287 288 0.734942 TTCACTCGATTCCGAACGGC 60.735 55.000 8.48 0.00 45.04 5.68
288 289 1.269166 CTTCACTCGATTCCGAACGG 58.731 55.000 6.94 6.94 45.04 4.44
289 290 1.269166 CCTTCACTCGATTCCGAACG 58.731 55.000 0.00 0.00 45.04 3.95
290 291 2.365408 ACCTTCACTCGATTCCGAAC 57.635 50.000 0.00 0.00 45.04 3.95
291 292 3.697542 TGATACCTTCACTCGATTCCGAA 59.302 43.478 0.00 0.00 45.04 4.30
292 293 3.284617 TGATACCTTCACTCGATTCCGA 58.715 45.455 0.00 0.00 43.35 4.55
293 294 3.710326 TGATACCTTCACTCGATTCCG 57.290 47.619 0.00 0.00 37.07 4.30
303 304 2.237143 CTGAAGCTGGGTGATACCTTCA 59.763 50.000 0.00 0.00 39.44 3.02
304 305 2.911484 CTGAAGCTGGGTGATACCTTC 58.089 52.381 0.00 0.00 38.64 3.46
305 306 1.065126 GCTGAAGCTGGGTGATACCTT 60.065 52.381 0.00 0.00 36.89 3.50
357 361 4.827284 ACATTTCAAATCCTTCCGAAGTGT 59.173 37.500 7.37 0.00 34.63 3.55
359 363 6.040391 TCAAACATTTCAAATCCTTCCGAAGT 59.960 34.615 7.37 0.00 0.00 3.01
362 366 6.588719 ATCAAACATTTCAAATCCTTCCGA 57.411 33.333 0.00 0.00 0.00 4.55
392 396 4.637534 GCTTCTTTTGAGATGCATGACCTA 59.362 41.667 2.46 0.00 38.40 3.08
394 398 3.428589 GGCTTCTTTTGAGATGCATGACC 60.429 47.826 2.46 0.00 39.72 4.02
396 400 3.423749 TGGCTTCTTTTGAGATGCATGA 58.576 40.909 2.46 0.00 39.72 3.07
397 401 3.442625 TCTGGCTTCTTTTGAGATGCATG 59.557 43.478 2.46 0.00 39.72 4.06
398 402 3.693807 TCTGGCTTCTTTTGAGATGCAT 58.306 40.909 0.00 0.00 39.72 3.96
400 404 3.755378 TCTTCTGGCTTCTTTTGAGATGC 59.245 43.478 5.91 5.91 37.98 3.91
401 405 5.954296 TTCTTCTGGCTTCTTTTGAGATG 57.046 39.130 0.00 0.00 0.00 2.90
402 406 6.150809 GTGATTCTTCTGGCTTCTTTTGAGAT 59.849 38.462 0.00 0.00 0.00 2.75
403 407 5.471456 GTGATTCTTCTGGCTTCTTTTGAGA 59.529 40.000 0.00 0.00 0.00 3.27
404 408 5.240183 TGTGATTCTTCTGGCTTCTTTTGAG 59.760 40.000 0.00 0.00 0.00 3.02
406 410 5.009410 ACTGTGATTCTTCTGGCTTCTTTTG 59.991 40.000 0.00 0.00 0.00 2.44
407 411 5.009410 CACTGTGATTCTTCTGGCTTCTTTT 59.991 40.000 0.32 0.00 0.00 2.27
408 412 4.518211 CACTGTGATTCTTCTGGCTTCTTT 59.482 41.667 0.32 0.00 0.00 2.52
409 413 4.070716 CACTGTGATTCTTCTGGCTTCTT 58.929 43.478 0.32 0.00 0.00 2.52
410 414 3.072184 ACACTGTGATTCTTCTGGCTTCT 59.928 43.478 15.86 0.00 0.00 2.85
411 415 3.406764 ACACTGTGATTCTTCTGGCTTC 58.593 45.455 15.86 0.00 0.00 3.86
412 416 3.498774 ACACTGTGATTCTTCTGGCTT 57.501 42.857 15.86 0.00 0.00 4.35
413 417 3.498774 AACACTGTGATTCTTCTGGCT 57.501 42.857 15.86 0.00 0.00 4.75
414 418 4.574599 AAAACACTGTGATTCTTCTGGC 57.425 40.909 15.86 0.00 0.00 4.85
489 493 3.499537 GTCCCGGAATGTAAGACGTTTTT 59.500 43.478 0.73 0.00 0.00 1.94
490 494 3.069289 GTCCCGGAATGTAAGACGTTTT 58.931 45.455 0.73 0.00 0.00 2.43
491 495 2.691927 GTCCCGGAATGTAAGACGTTT 58.308 47.619 0.73 0.00 0.00 3.60
492 496 1.403249 CGTCCCGGAATGTAAGACGTT 60.403 52.381 16.05 0.00 43.89 3.99
493 497 0.171903 CGTCCCGGAATGTAAGACGT 59.828 55.000 16.05 0.00 43.89 4.34
494 498 2.953669 CGTCCCGGAATGTAAGACG 58.046 57.895 0.73 8.03 43.52 4.18
495 499 2.537401 CTTCGTCCCGGAATGTAAGAC 58.463 52.381 0.73 0.00 0.00 3.01
496 500 1.479323 CCTTCGTCCCGGAATGTAAGA 59.521 52.381 0.73 0.00 0.00 2.10
497 501 1.472728 CCCTTCGTCCCGGAATGTAAG 60.473 57.143 0.73 0.00 0.00 2.34
498 502 0.538118 CCCTTCGTCCCGGAATGTAA 59.462 55.000 0.73 0.00 0.00 2.41
499 503 0.324552 TCCCTTCGTCCCGGAATGTA 60.325 55.000 0.73 0.00 0.00 2.29
500 504 1.611261 TCCCTTCGTCCCGGAATGT 60.611 57.895 0.73 0.00 0.00 2.71
501 505 1.144057 CTCCCTTCGTCCCGGAATG 59.856 63.158 0.73 0.00 0.00 2.67
502 506 0.032813 TACTCCCTTCGTCCCGGAAT 60.033 55.000 0.73 0.00 0.00 3.01
503 507 0.682209 CTACTCCCTTCGTCCCGGAA 60.682 60.000 0.73 0.00 0.00 4.30
504 508 1.077212 CTACTCCCTTCGTCCCGGA 60.077 63.158 0.73 0.00 0.00 5.14
505 509 0.467659 ATCTACTCCCTTCGTCCCGG 60.468 60.000 0.00 0.00 0.00 5.73
506 510 1.400737 AATCTACTCCCTTCGTCCCG 58.599 55.000 0.00 0.00 0.00 5.14
507 511 3.908643 AAAATCTACTCCCTTCGTCCC 57.091 47.619 0.00 0.00 0.00 4.46
508 512 7.860918 AAATAAAAATCTACTCCCTTCGTCC 57.139 36.000 0.00 0.00 0.00 4.79
509 513 9.813446 TCTAAATAAAAATCTACTCCCTTCGTC 57.187 33.333 0.00 0.00 0.00 4.20
525 529 7.854337 ACGGAGGGAGTACATTCTAAATAAAA 58.146 34.615 0.00 0.00 0.00 1.52
527 531 7.343833 AGAACGGAGGGAGTACATTCTAAATAA 59.656 37.037 0.00 0.00 0.00 1.40
529 533 5.661759 AGAACGGAGGGAGTACATTCTAAAT 59.338 40.000 0.00 0.00 0.00 1.40
539 543 7.014038 GTCATCTATTTTAGAACGGAGGGAGTA 59.986 40.741 0.00 0.00 38.50 2.59
541 545 6.217294 GTCATCTATTTTAGAACGGAGGGAG 58.783 44.000 0.00 0.00 38.50 4.30
542 546 5.070047 GGTCATCTATTTTAGAACGGAGGGA 59.930 44.000 0.00 0.00 38.50 4.20
543 547 5.298347 GGTCATCTATTTTAGAACGGAGGG 58.702 45.833 0.00 0.00 38.50 4.30
544 548 5.163343 TGGGTCATCTATTTTAGAACGGAGG 60.163 44.000 0.00 0.00 38.50 4.30
545 549 5.914033 TGGGTCATCTATTTTAGAACGGAG 58.086 41.667 0.00 0.00 38.50 4.63
546 550 5.943349 TGGGTCATCTATTTTAGAACGGA 57.057 39.130 0.00 0.00 38.50 4.69
547 551 6.113411 AGTTGGGTCATCTATTTTAGAACGG 58.887 40.000 0.00 0.00 38.50 4.44
548 552 7.611213 AAGTTGGGTCATCTATTTTAGAACG 57.389 36.000 0.00 0.00 38.50 3.95
549 553 8.793592 ACAAAGTTGGGTCATCTATTTTAGAAC 58.206 33.333 0.00 0.00 38.50 3.01
550 554 8.934023 ACAAAGTTGGGTCATCTATTTTAGAA 57.066 30.769 0.00 0.00 38.50 2.10
551 555 9.444600 GTACAAAGTTGGGTCATCTATTTTAGA 57.555 33.333 0.00 0.00 39.50 2.10
552 556 9.449719 AGTACAAAGTTGGGTCATCTATTTTAG 57.550 33.333 0.00 0.00 0.00 1.85
554 558 9.449719 CTAGTACAAAGTTGGGTCATCTATTTT 57.550 33.333 0.00 0.00 0.00 1.82
555 559 8.047310 CCTAGTACAAAGTTGGGTCATCTATTT 58.953 37.037 0.00 0.00 0.00 1.40
556 560 7.402071 TCCTAGTACAAAGTTGGGTCATCTATT 59.598 37.037 0.00 0.00 0.00 1.73
557 561 6.901300 TCCTAGTACAAAGTTGGGTCATCTAT 59.099 38.462 0.00 0.00 0.00 1.98
558 562 6.258354 TCCTAGTACAAAGTTGGGTCATCTA 58.742 40.000 0.00 0.00 0.00 1.98
559 563 5.091552 TCCTAGTACAAAGTTGGGTCATCT 58.908 41.667 0.00 0.00 0.00 2.90
560 564 5.046520 ACTCCTAGTACAAAGTTGGGTCATC 60.047 44.000 0.00 0.00 0.00 2.92
561 565 4.844655 ACTCCTAGTACAAAGTTGGGTCAT 59.155 41.667 0.00 0.00 0.00 3.06
562 566 4.228824 ACTCCTAGTACAAAGTTGGGTCA 58.771 43.478 0.00 0.00 0.00 4.02
563 567 4.886496 ACTCCTAGTACAAAGTTGGGTC 57.114 45.455 0.00 0.00 0.00 4.46
564 568 7.622479 ACATATACTCCTAGTACAAAGTTGGGT 59.378 37.037 0.00 0.00 32.84 4.51
565 569 8.019656 ACATATACTCCTAGTACAAAGTTGGG 57.980 38.462 0.00 0.00 32.84 4.12
566 570 8.915036 AGACATATACTCCTAGTACAAAGTTGG 58.085 37.037 0.00 0.00 32.84 3.77
569 573 9.476928 ACAAGACATATACTCCTAGTACAAAGT 57.523 33.333 0.00 0.00 32.84 2.66
570 574 9.737427 CACAAGACATATACTCCTAGTACAAAG 57.263 37.037 0.00 0.00 32.84 2.77
571 575 9.251440 ACACAAGACATATACTCCTAGTACAAA 57.749 33.333 0.00 0.00 32.84 2.83
572 576 8.818622 ACACAAGACATATACTCCTAGTACAA 57.181 34.615 0.00 0.00 32.84 2.41
573 577 8.818622 AACACAAGACATATACTCCTAGTACA 57.181 34.615 0.00 0.00 32.84 2.90
574 578 8.351461 GGAACACAAGACATATACTCCTAGTAC 58.649 40.741 0.00 0.00 32.84 2.73
575 579 7.504911 GGGAACACAAGACATATACTCCTAGTA 59.495 40.741 0.00 0.00 34.82 1.82
576 580 6.324254 GGGAACACAAGACATATACTCCTAGT 59.676 42.308 0.00 0.00 0.00 2.57
577 581 6.323996 TGGGAACACAAGACATATACTCCTAG 59.676 42.308 0.00 0.00 33.40 3.02
578 582 6.199376 TGGGAACACAAGACATATACTCCTA 58.801 40.000 0.00 0.00 33.40 2.94
579 583 5.030147 TGGGAACACAAGACATATACTCCT 58.970 41.667 0.00 0.00 33.40 3.69
580 584 5.353394 TGGGAACACAAGACATATACTCC 57.647 43.478 0.00 0.00 33.40 3.85
581 585 5.585047 GGTTGGGAACACAAGACATATACTC 59.415 44.000 0.00 0.00 42.67 2.59
582 586 5.013704 TGGTTGGGAACACAAGACATATACT 59.986 40.000 0.00 0.00 42.67 2.12
583 587 5.250200 TGGTTGGGAACACAAGACATATAC 58.750 41.667 0.00 0.00 42.67 1.47
584 588 5.506730 TGGTTGGGAACACAAGACATATA 57.493 39.130 0.00 0.00 42.67 0.86
585 589 4.380843 TGGTTGGGAACACAAGACATAT 57.619 40.909 0.00 0.00 42.67 1.78
586 590 3.866703 TGGTTGGGAACACAAGACATA 57.133 42.857 0.00 0.00 42.67 2.29
587 591 2.746279 TGGTTGGGAACACAAGACAT 57.254 45.000 0.00 0.00 42.67 3.06
588 592 2.174639 AGATGGTTGGGAACACAAGACA 59.825 45.455 0.00 0.00 42.67 3.41
589 593 2.863809 AGATGGTTGGGAACACAAGAC 58.136 47.619 0.00 0.00 42.67 3.01
590 594 3.593442 AAGATGGTTGGGAACACAAGA 57.407 42.857 0.00 0.00 42.67 3.02
591 595 4.398319 AGTAAGATGGTTGGGAACACAAG 58.602 43.478 0.00 0.00 42.67 3.16
592 596 4.447138 AGTAAGATGGTTGGGAACACAA 57.553 40.909 0.00 0.00 42.67 3.33
593 597 4.104102 AGAAGTAAGATGGTTGGGAACACA 59.896 41.667 0.00 0.00 42.67 3.72
606 610 4.822026 CAAGACGGGACAAGAAGTAAGAT 58.178 43.478 0.00 0.00 0.00 2.40
608 612 2.737252 GCAAGACGGGACAAGAAGTAAG 59.263 50.000 0.00 0.00 0.00 2.34
625 629 3.243336 GACGGTGTACAGAGTAAGCAAG 58.757 50.000 0.00 0.00 0.00 4.01
627 631 1.198408 CGACGGTGTACAGAGTAAGCA 59.802 52.381 0.00 0.00 0.00 3.91
630 634 1.460743 CGTCGACGGTGTACAGAGTAA 59.539 52.381 29.70 0.00 35.37 2.24
691 695 4.293648 CGTCCTCACCACCGTGCA 62.294 66.667 0.00 0.00 40.04 4.57
693 697 4.373116 CCCGTCCTCACCACCGTG 62.373 72.222 0.00 0.00 41.72 4.94
695 699 3.296709 CTTCCCGTCCTCACCACCG 62.297 68.421 0.00 0.00 0.00 4.94
697 701 0.108138 CATCTTCCCGTCCTCACCAC 60.108 60.000 0.00 0.00 0.00 4.16
698 702 0.252057 TCATCTTCCCGTCCTCACCA 60.252 55.000 0.00 0.00 0.00 4.17
700 704 1.269309 CGATCATCTTCCCGTCCTCAC 60.269 57.143 0.00 0.00 0.00 3.51
701 705 1.032794 CGATCATCTTCCCGTCCTCA 58.967 55.000 0.00 0.00 0.00 3.86
703 707 1.033574 GTCGATCATCTTCCCGTCCT 58.966 55.000 0.00 0.00 0.00 3.85
704 708 0.317938 CGTCGATCATCTTCCCGTCC 60.318 60.000 0.00 0.00 0.00 4.79
705 709 0.935366 GCGTCGATCATCTTCCCGTC 60.935 60.000 0.00 0.00 0.00 4.79
706 710 1.065928 GCGTCGATCATCTTCCCGT 59.934 57.895 0.00 0.00 0.00 5.28
707 711 2.011349 CGCGTCGATCATCTTCCCG 61.011 63.158 0.00 0.00 0.00 5.14
709 713 0.029567 AGACGCGTCGATCATCTTCC 59.970 55.000 31.56 5.81 34.09 3.46
714 718 0.029035 GGTGTAGACGCGTCGATCAT 59.971 55.000 31.56 17.63 34.09 2.45
718 761 2.669229 TGGGTGTAGACGCGTCGA 60.669 61.111 31.56 25.37 37.86 4.20
719 762 2.503375 GTGGGTGTAGACGCGTCG 60.503 66.667 31.56 0.00 37.86 5.12
745 788 1.000955 TCAGTCGTTTTCCCTGCTCTC 59.999 52.381 0.00 0.00 0.00 3.20
785 831 1.272781 GAGAAAGGAGATCGCACACG 58.727 55.000 0.00 0.00 42.01 4.49
786 832 1.646189 GGAGAAAGGAGATCGCACAC 58.354 55.000 0.00 0.00 0.00 3.82
787 833 0.537188 GGGAGAAAGGAGATCGCACA 59.463 55.000 0.00 0.00 0.00 4.57
788 834 0.827368 AGGGAGAAAGGAGATCGCAC 59.173 55.000 0.00 0.00 0.00 5.34
839 885 2.480845 CGCCGGAGTAATCTTTTAGGG 58.519 52.381 5.05 0.00 0.00 3.53
847 893 2.657620 GTCGGCGCCGGAGTAATC 60.658 66.667 44.95 22.96 40.25 1.75
888 940 1.448717 GCTCGGCTGTCTTCCTTCC 60.449 63.158 0.00 0.00 0.00 3.46
889 941 1.016653 GTGCTCGGCTGTCTTCCTTC 61.017 60.000 0.00 0.00 0.00 3.46
890 942 1.004440 GTGCTCGGCTGTCTTCCTT 60.004 57.895 0.00 0.00 0.00 3.36
891 943 2.659610 GTGCTCGGCTGTCTTCCT 59.340 61.111 0.00 0.00 0.00 3.36
996 1069 1.304134 ATTTGGTTGGAGCGGGGAC 60.304 57.895 0.00 0.00 0.00 4.46
1008 1081 2.125106 GCCGAGGCGAGATTTGGT 60.125 61.111 0.00 0.00 0.00 3.67
1071 1144 0.611062 TCGTCGTGATCCTCCTGGTT 60.611 55.000 0.00 0.00 34.23 3.67
1150 1579 4.150454 AGGAGGAGGAGGCGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1151 1580 2.520741 GAGGAGGAGGAGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
1152 1581 4.144727 GGAGGAGGAGGAGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
1158 1590 4.816984 GACGGCGGAGGAGGAGGA 62.817 72.222 13.24 0.00 0.00 3.71
1448 1904 2.106683 GTTGATGCCCGAGGGAACG 61.107 63.158 13.28 0.00 37.50 3.95
1450 1906 2.267642 CGTTGATGCCCGAGGGAA 59.732 61.111 13.28 0.35 37.50 3.97
1451 1907 4.467084 GCGTTGATGCCCGAGGGA 62.467 66.667 13.28 0.00 37.50 4.20
1673 2135 3.117372 CGGCGGTAGTCCCTGTAG 58.883 66.667 0.00 0.00 0.00 2.74
1826 2288 2.497092 CGTGTCGTTGATCTCCGCG 61.497 63.158 0.00 0.00 0.00 6.46
1868 2330 0.980423 ACTTGCCTCTCCTGAACTCC 59.020 55.000 0.00 0.00 0.00 3.85
1940 2402 2.186384 CCGCAGAGGAAGCTCCAG 59.814 66.667 5.21 0.00 45.00 3.86
2001 2463 0.518636 CCGGACAAGCACATGTTCAG 59.481 55.000 0.00 0.00 32.57 3.02
2123 2585 1.301677 GCCGCCAGTCCTTCAAGAAG 61.302 60.000 2.83 2.83 38.14 2.85
2207 2669 0.323178 CCCTCTTCAGCTGCATTGGT 60.323 55.000 9.47 0.00 0.00 3.67
2369 2831 1.227205 CCTGCCTGCGATCTCAGTC 60.227 63.158 11.60 0.00 32.32 3.51
2679 3141 0.738063 ATGTACGCATCGAACGGCAA 60.738 50.000 14.62 1.40 34.00 4.52
2851 3313 1.450134 CATTGCGCCAGCCAGTAGA 60.450 57.895 4.18 0.00 44.33 2.59
2924 3386 1.134729 TGAGCATGCTATGACAAGCGA 60.135 47.619 22.74 0.00 45.85 4.93
3092 3558 5.632034 AACTAATGGGGACTCAAGATACC 57.368 43.478 0.00 0.00 0.00 2.73
3157 3624 6.436261 TCCGACTAGAGAATATTTAGCAACG 58.564 40.000 0.00 0.00 0.00 4.10
3204 3671 9.607988 TCTGTTCTGACTTTTGACAGTAAAATA 57.392 29.630 5.20 0.00 41.65 1.40
3327 3794 7.807977 ATACACAAGAGAAACACAACTGATT 57.192 32.000 0.00 0.00 0.00 2.57
3667 4218 8.593945 TTAAATTGATAGGCTTCCTTTGTGAT 57.406 30.769 0.00 0.00 34.61 3.06
3713 4264 2.840651 CCACCTACCATCTTCCTTGAGT 59.159 50.000 0.00 0.00 0.00 3.41
3739 4290 0.388134 ACGACCGATTGTGAAGGACG 60.388 55.000 4.31 4.31 45.62 4.79
3759 4310 9.635520 GCTGATCAAACTTAAACTACTAGTGTA 57.364 33.333 5.39 0.00 0.00 2.90
3771 4322 7.542890 TGAAAACAACAGCTGATCAAACTTAA 58.457 30.769 23.35 0.00 0.00 1.85
3828 4379 5.284079 CCAGTTGAAACATTCCTTGAAGTG 58.716 41.667 0.00 0.00 0.00 3.16
3860 4411 5.762179 TCAGTATCCAACATCCTCAAGTT 57.238 39.130 0.00 0.00 0.00 2.66
3875 4426 1.262683 GCGCAGAATGGCTTCAGTATC 59.737 52.381 0.30 0.00 35.86 2.24
3879 4430 0.454600 AATGCGCAGAATGGCTTCAG 59.545 50.000 18.32 0.00 35.86 3.02
3966 4517 6.884096 TGCGCAGAAATAAATTTAACCATG 57.116 33.333 5.66 1.42 0.00 3.66


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

AutoCloner maintained by Alex Coulton.