Multiple sequence alignment - TraesCS2A01G388400

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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 TraesCS2A01G388400 chr2A 100.000 6487 0 0 1 6487 635609766 635603280 0.000000e+00 11980.0
1 TraesCS2A01G388400 chr2A 100.000 41 0 0 1533 1573 635608111 635608071 6.970000e-10 76.8
2 TraesCS2A01G388400 chr2A 100.000 41 0 0 1656 1696 635608234 635608194 6.970000e-10 76.8
3 TraesCS2A01G388400 chr2B 95.982 2613 60 9 2293 4883 575874904 575872315 0.000000e+00 4202.0
4 TraesCS2A01G388400 chr2B 96.940 621 17 2 4881 5501 575872188 575871570 0.000000e+00 1040.0
5 TraesCS2A01G388400 chr2B 92.431 687 28 6 1690 2375 575876276 575875613 0.000000e+00 959.0
6 TraesCS2A01G388400 chr2B 94.711 605 25 4 1690 2294 575875583 575874986 0.000000e+00 933.0
7 TraesCS2A01G388400 chr2B 87.677 779 47 19 765 1526 575877941 575877195 0.000000e+00 861.0
8 TraesCS2A01G388400 chr2B 89.587 557 29 10 1603 2152 575877157 575876623 0.000000e+00 680.0
9 TraesCS2A01G388400 chr2B 96.847 222 7 0 2154 2375 575876527 575876306 7.940000e-99 372.0
10 TraesCS2A01G388400 chr2B 90.840 131 12 0 5499 5629 31587293 31587423 6.680000e-40 176.0
11 TraesCS2A01G388400 chr2B 90.769 130 12 0 5500 5629 24709178 24709307 2.400000e-39 174.0
12 TraesCS2A01G388400 chr2D 94.827 1759 64 9 1603 3340 491381769 491380017 0.000000e+00 2719.0
13 TraesCS2A01G388400 chr2D 95.634 1443 48 8 4064 5501 491378838 491377406 0.000000e+00 2302.0
14 TraesCS2A01G388400 chr2D 83.322 1505 151 42 60 1526 491383249 491381807 0.000000e+00 1297.0
15 TraesCS2A01G388400 chr2D 94.638 746 18 5 3339 4083 491379757 491379033 0.000000e+00 1136.0
16 TraesCS2A01G388400 chr2D 92.235 528 38 1 5946 6470 459840792 459841319 0.000000e+00 745.0
17 TraesCS2A01G388400 chr2D 91.856 528 40 1 5946 6470 579154304 579154831 0.000000e+00 734.0
18 TraesCS2A01G388400 chr2D 93.284 402 15 2 5543 5932 88705855 88705454 3.370000e-162 582.0
19 TraesCS2A01G388400 chr2D 92.289 402 18 3 5543 5932 88621001 88620601 5.680000e-155 558.0
20 TraesCS2A01G388400 chr6B 99.493 987 5 0 5501 6487 691822681 691823667 0.000000e+00 1796.0
21 TraesCS2A01G388400 chr3B 98.987 987 10 0 5501 6487 8689940 8690926 0.000000e+00 1768.0
22 TraesCS2A01G388400 chr3B 97.467 987 25 0 5501 6487 606343704 606342718 0.000000e+00 1685.0
23 TraesCS2A01G388400 chr3B 94.183 447 21 5 2428 2872 685953453 685953896 0.000000e+00 676.0
24 TraesCS2A01G388400 chr1D 92.523 535 34 2 5946 6477 465904409 465904940 0.000000e+00 761.0
25 TraesCS2A01G388400 chr5B 93.077 520 30 2 5954 6470 452228470 452227954 0.000000e+00 756.0
26 TraesCS2A01G388400 chr5B 93.960 447 25 2 2428 2872 447876001 447875555 0.000000e+00 675.0
27 TraesCS2A01G388400 chr5B 96.875 32 1 0 695 726 348967316 348967285 3.000000e-03 54.7
28 TraesCS2A01G388400 chr5A 91.667 528 41 1 5946 6470 671867721 671868248 0.000000e+00 728.0
29 TraesCS2A01G388400 chr5A 85.507 69 10 0 542 610 575318407 575318475 9.020000e-09 73.1
30 TraesCS2A01G388400 chr1B 91.045 536 41 3 5946 6477 642702741 642703273 0.000000e+00 717.0
31 TraesCS2A01G388400 chr1B 93.034 445 28 3 2430 2872 328514920 328515363 0.000000e+00 647.0
32 TraesCS2A01G388400 chr1B 89.552 134 13 1 5496 5629 461905397 461905265 1.120000e-37 169.0
33 TraesCS2A01G388400 chr1A 93.258 445 28 2 2430 2872 590531996 590532440 0.000000e+00 654.0
34 TraesCS2A01G388400 chr7B 96.203 316 11 1 5620 5934 415363272 415362957 3.470000e-142 516.0
35 TraesCS2A01G388400 chr7B 86.384 448 27 11 5500 5934 745621218 745620792 5.930000e-125 459.0
36 TraesCS2A01G388400 chr7B 88.923 325 23 7 5620 5931 210625118 210625442 7.890000e-104 388.0
37 TraesCS2A01G388400 chr7B 90.698 129 12 0 5501 5629 693337138 693337010 8.650000e-39 172.0
38 TraesCS2A01G388400 chr6D 87.696 447 20 4 5501 5934 97141403 97141827 7.560000e-134 488.0
39 TraesCS2A01G388400 chr3A 88.686 274 17 3 5674 5934 738461274 738461546 8.110000e-84 322.0
40 TraesCS2A01G388400 chrUn 88.400 250 15 3 5698 5934 439213069 439213317 8.230000e-74 289.0
41 TraesCS2A01G388400 chr4B 96.190 105 4 0 3104 3208 406208550 406208654 8.650000e-39 172.0


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 TraesCS2A01G388400 chr2A 635603280 635609766 6486 True 4044.533333 11980 100.000000 1 6487 3 chr2A.!!$R1 6486
1 TraesCS2A01G388400 chr2B 575871570 575877941 6371 True 1292.428571 4202 93.453571 765 5501 7 chr2B.!!$R1 4736
2 TraesCS2A01G388400 chr2D 491377406 491383249 5843 True 1863.500000 2719 92.105250 60 5501 4 chr2D.!!$R3 5441
3 TraesCS2A01G388400 chr2D 459840792 459841319 527 False 745.000000 745 92.235000 5946 6470 1 chr2D.!!$F1 524
4 TraesCS2A01G388400 chr2D 579154304 579154831 527 False 734.000000 734 91.856000 5946 6470 1 chr2D.!!$F2 524
5 TraesCS2A01G388400 chr6B 691822681 691823667 986 False 1796.000000 1796 99.493000 5501 6487 1 chr6B.!!$F1 986
6 TraesCS2A01G388400 chr3B 8689940 8690926 986 False 1768.000000 1768 98.987000 5501 6487 1 chr3B.!!$F1 986
7 TraesCS2A01G388400 chr3B 606342718 606343704 986 True 1685.000000 1685 97.467000 5501 6487 1 chr3B.!!$R1 986
8 TraesCS2A01G388400 chr1D 465904409 465904940 531 False 761.000000 761 92.523000 5946 6477 1 chr1D.!!$F1 531
9 TraesCS2A01G388400 chr5B 452227954 452228470 516 True 756.000000 756 93.077000 5954 6470 1 chr5B.!!$R3 516
10 TraesCS2A01G388400 chr5A 671867721 671868248 527 False 728.000000 728 91.667000 5946 6470 1 chr5A.!!$F2 524
11 TraesCS2A01G388400 chr1B 642702741 642703273 532 False 717.000000 717 91.045000 5946 6477 1 chr1B.!!$F2 531

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
983 1005 0.098200 GCCGTTTATTGTTCTCGGGC 59.902 55.000 0.00 0.0 41.24 6.13 F
1529 1564 0.249120 TACTGTGCTTGATCGTGGGG 59.751 55.000 0.00 0.0 0.00 4.96 F
1790 2619 1.000394 CTGTCCGGATACACACACACA 60.000 52.381 7.81 0.0 0.00 3.72 F
2333 3938 0.936297 GTGCTTTGCCAAGTGAAGCG 60.936 55.000 0.00 0.0 46.59 4.68 F
2455 4060 2.092968 ACTGGCCACACATACTACATGG 60.093 50.000 0.00 0.0 0.00 3.66 F
3742 5631 1.002430 ACGCACAGTGGAGAACATCAT 59.998 47.619 1.84 0.0 0.00 2.45 F
5187 7432 1.315257 CGGAAGGTGAATGCAAGGGG 61.315 60.000 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2815 1.068541 CCGATCATCCTACGATTGCGA 60.069 52.381 0.00 0.0 41.64 5.10 R
2333 3938 1.337118 TGGGGTGCTGTTGAATTTCC 58.663 50.000 0.00 0.0 0.00 3.13 R
3034 4644 2.159014 TGAACGCGCCTTTCCATAGTAT 60.159 45.455 5.73 0.0 0.00 2.12 R
3478 5367 2.840296 GCATCAGCTTCTTGCCTTAC 57.160 50.000 1.66 0.0 44.23 2.34 R
4388 6492 2.825532 GGCACAGTTGATGGTTACCATT 59.174 45.455 18.78 0.0 45.26 3.16 R
5211 7456 0.840729 GCTCGCGTCTTTCGACATAG 59.159 55.000 5.77 0.0 42.86 2.23 R
6041 8290 4.702131 AGAGAGCCATTGTAACAATCAACC 59.298 41.667 0.00 0.0 0.00 3.77 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
31 32 9.627123 TTCTTTTATAGTCCAGATTTATGTGGG 57.373 33.333 6.11 0.00 41.28 4.61
32 33 8.217799 TCTTTTATAGTCCAGATTTATGTGGGG 58.782 37.037 6.11 0.00 41.28 4.96
33 34 7.460214 TTTATAGTCCAGATTTATGTGGGGT 57.540 36.000 6.11 0.00 41.28 4.95
34 35 5.994416 ATAGTCCAGATTTATGTGGGGTT 57.006 39.130 6.11 0.00 41.28 4.11
35 36 4.675063 AGTCCAGATTTATGTGGGGTTT 57.325 40.909 6.11 0.00 41.28 3.27
36 37 4.344104 AGTCCAGATTTATGTGGGGTTTG 58.656 43.478 6.11 0.00 41.28 2.93
37 38 4.086457 GTCCAGATTTATGTGGGGTTTGT 58.914 43.478 6.11 0.00 41.28 2.83
38 39 4.157840 GTCCAGATTTATGTGGGGTTTGTC 59.842 45.833 6.11 0.00 41.28 3.18
39 40 4.044065 TCCAGATTTATGTGGGGTTTGTCT 59.956 41.667 6.11 0.00 41.28 3.41
40 41 4.399303 CCAGATTTATGTGGGGTTTGTCTC 59.601 45.833 0.00 0.00 37.56 3.36
41 42 5.009631 CAGATTTATGTGGGGTTTGTCTCA 58.990 41.667 0.00 0.00 0.00 3.27
42 43 5.476599 CAGATTTATGTGGGGTTTGTCTCAA 59.523 40.000 0.00 0.00 0.00 3.02
43 44 6.015519 CAGATTTATGTGGGGTTTGTCTCAAA 60.016 38.462 0.00 0.00 0.00 2.69
44 45 6.553100 AGATTTATGTGGGGTTTGTCTCAAAA 59.447 34.615 0.00 0.00 0.00 2.44
45 46 6.546428 TTTATGTGGGGTTTGTCTCAAAAA 57.454 33.333 0.00 0.00 0.00 1.94
75 76 0.700564 ATGTGGGGTGTCAGAGCATT 59.299 50.000 0.00 0.00 0.00 3.56
109 110 5.824624 TGATGCAAAATAAGGCAACCAAAAA 59.175 32.000 0.00 0.00 44.20 1.94
145 146 4.362677 TGAGAGAGTAGGTTTTAGGGCAT 58.637 43.478 0.00 0.00 0.00 4.40
146 147 4.162320 TGAGAGAGTAGGTTTTAGGGCATG 59.838 45.833 0.00 0.00 0.00 4.06
148 149 4.162509 AGAGAGTAGGTTTTAGGGCATGAC 59.837 45.833 0.00 0.00 0.00 3.06
156 157 6.230472 AGGTTTTAGGGCATGACAAAAATTC 58.770 36.000 12.59 9.20 0.00 2.17
163 164 3.602483 GCATGACAAAAATTCCTGCCAT 58.398 40.909 0.00 0.00 30.74 4.40
164 165 3.372822 GCATGACAAAAATTCCTGCCATG 59.627 43.478 0.00 10.05 30.74 3.66
165 166 3.681593 TGACAAAAATTCCTGCCATGG 57.318 42.857 7.63 7.63 0.00 3.66
166 167 2.289569 TGACAAAAATTCCTGCCATGGC 60.290 45.455 30.54 30.54 42.35 4.40
186 187 2.806244 GCAGATAGTGTGAAACGGTTGT 59.194 45.455 0.00 0.00 42.39 3.32
190 191 2.413310 AGTGTGAAACGGTTGTCCTT 57.587 45.000 0.00 0.00 42.39 3.36
201 202 3.634910 ACGGTTGTCCTTAAACTTGCAAT 59.365 39.130 0.00 0.00 0.00 3.56
202 203 4.098807 ACGGTTGTCCTTAAACTTGCAATT 59.901 37.500 0.00 0.00 0.00 2.32
203 204 5.047188 CGGTTGTCCTTAAACTTGCAATTT 58.953 37.500 0.00 0.00 0.00 1.82
213 214 9.710900 CCTTAAACTTGCAATTTCTTTAGGAAT 57.289 29.630 0.00 0.00 33.53 3.01
224 225 4.280436 TCTTTAGGAATCACGAGGCAAA 57.720 40.909 0.00 0.00 0.00 3.68
226 227 3.410631 TTAGGAATCACGAGGCAAACA 57.589 42.857 0.00 0.00 0.00 2.83
248 249 5.364157 ACAGAGTTTGTTTGGTACTCTCTCT 59.636 40.000 0.00 0.00 45.01 3.10
249 250 5.694006 CAGAGTTTGTTTGGTACTCTCTCTG 59.306 44.000 0.00 0.00 45.01 3.35
250 251 4.381411 AGTTTGTTTGGTACTCTCTCTGC 58.619 43.478 0.00 0.00 0.00 4.26
309 310 9.562408 TGTAAACTACATGTGGACTAAAATGAA 57.438 29.630 16.98 0.00 32.89 2.57
313 314 8.498054 ACTACATGTGGACTAAAATGAATGAG 57.502 34.615 16.98 0.00 0.00 2.90
318 319 6.446318 TGTGGACTAAAATGAATGAGCAAAC 58.554 36.000 0.00 0.00 0.00 2.93
324 325 6.919662 ACTAAAATGAATGAGCAAACACACTG 59.080 34.615 0.00 0.00 0.00 3.66
328 329 4.671377 TGAATGAGCAAACACACTGAAAC 58.329 39.130 0.00 0.00 0.00 2.78
331 332 2.159585 TGAGCAAACACACTGAAACGTG 60.160 45.455 0.00 0.00 40.67 4.49
342 343 7.790000 ACACACTGAAACGTGTTTATATACAC 58.210 34.615 14.42 14.42 45.27 2.90
343 344 7.095523 ACACACTGAAACGTGTTTATATACACC 60.096 37.037 17.46 7.04 45.27 4.16
344 345 6.369615 ACACTGAAACGTGTTTATATACACCC 59.630 38.462 17.46 7.83 45.27 4.61
345 346 5.577945 ACTGAAACGTGTTTATATACACCCG 59.422 40.000 17.46 11.25 44.32 5.28
431 434 1.064060 GCAATGGCTTATCGTGGTCAC 59.936 52.381 0.00 0.00 36.96 3.67
432 435 2.355197 CAATGGCTTATCGTGGTCACA 58.645 47.619 1.90 0.00 0.00 3.58
446 449 6.745116 TCGTGGTCACAGGAGTATTATTATG 58.255 40.000 1.90 0.00 36.65 1.90
474 477 6.276832 ACATTGCATGTTCTCAGCTTTATT 57.723 33.333 0.00 0.00 41.63 1.40
501 504 9.650539 ATTATTTCCTCATCATGTCTATCTTCG 57.349 33.333 0.00 0.00 0.00 3.79
504 507 4.764308 TCCTCATCATGTCTATCTTCGGAG 59.236 45.833 0.00 0.00 0.00 4.63
512 515 6.980978 TCATGTCTATCTTCGGAGATGTTTTC 59.019 38.462 16.93 3.36 42.55 2.29
550 553 6.716173 GGTGTTCCTATAAAAGGTTGTTGGTA 59.284 38.462 0.00 0.00 46.62 3.25
551 554 7.308770 GGTGTTCCTATAAAAGGTTGTTGGTAC 60.309 40.741 0.00 0.00 46.62 3.34
557 560 1.153353 AAGGTTGTTGGTACGATGCG 58.847 50.000 0.00 0.00 0.00 4.73
563 566 1.004320 TTGGTACGATGCGCTGGTT 60.004 52.632 9.73 0.00 0.00 3.67
585 588 0.326595 TTTGGGCCTTAGCATGACGA 59.673 50.000 4.53 0.00 42.56 4.20
586 589 0.546122 TTGGGCCTTAGCATGACGAT 59.454 50.000 4.53 0.00 42.56 3.73
595 598 4.872691 CCTTAGCATGACGATTTTCTGACT 59.127 41.667 0.00 0.00 0.00 3.41
599 602 4.153117 AGCATGACGATTTTCTGACTGTTC 59.847 41.667 0.00 0.00 0.00 3.18
611 614 4.119862 TCTGACTGTTCACTACAACAAGC 58.880 43.478 0.00 0.00 35.83 4.01
612 615 3.867857 TGACTGTTCACTACAACAAGCA 58.132 40.909 0.00 0.00 35.83 3.91
629 632 0.738412 GCATTGTTCAGCCCATGTGC 60.738 55.000 0.00 0.00 0.00 4.57
631 634 0.604578 ATTGTTCAGCCCATGTGCAC 59.395 50.000 10.75 10.75 0.00 4.57
632 635 1.462731 TTGTTCAGCCCATGTGCACC 61.463 55.000 15.69 0.00 0.00 5.01
633 636 1.604593 GTTCAGCCCATGTGCACCT 60.605 57.895 15.69 0.23 0.00 4.00
634 637 1.153524 TTCAGCCCATGTGCACCTT 59.846 52.632 15.69 0.00 0.00 3.50
635 638 0.895100 TTCAGCCCATGTGCACCTTC 60.895 55.000 15.69 0.00 0.00 3.46
636 639 2.360350 AGCCCATGTGCACCTTCG 60.360 61.111 15.69 0.23 0.00 3.79
637 640 4.120331 GCCCATGTGCACCTTCGC 62.120 66.667 15.69 7.35 0.00 4.70
638 641 2.360350 CCCATGTGCACCTTCGCT 60.360 61.111 15.69 0.00 0.00 4.93
639 642 2.401766 CCCATGTGCACCTTCGCTC 61.402 63.158 15.69 0.00 0.00 5.03
640 643 2.743752 CCATGTGCACCTTCGCTCG 61.744 63.158 15.69 0.00 0.00 5.03
641 644 3.121030 ATGTGCACCTTCGCTCGC 61.121 61.111 15.69 0.00 0.00 5.03
653 674 2.447887 CGCTCGCCTAGTGCTTGTG 61.448 63.158 2.39 0.00 37.22 3.33
660 681 0.732880 CCTAGTGCTTGTGGTCGTCG 60.733 60.000 0.00 0.00 0.00 5.12
663 684 1.372499 GTGCTTGTGGTCGTCGCTA 60.372 57.895 0.00 0.00 0.00 4.26
664 685 1.372499 TGCTTGTGGTCGTCGCTAC 60.372 57.895 0.00 0.00 0.00 3.58
668 689 2.798499 GCTTGTGGTCGTCGCTACATAT 60.798 50.000 6.67 0.00 0.00 1.78
669 690 3.444916 CTTGTGGTCGTCGCTACATATT 58.555 45.455 6.67 0.00 0.00 1.28
670 691 3.513680 TGTGGTCGTCGCTACATATTT 57.486 42.857 2.67 0.00 0.00 1.40
681 702 3.247411 CGCTACATATTTTGCGGACATGA 59.753 43.478 9.40 0.00 43.97 3.07
687 708 6.728200 ACATATTTTGCGGACATGAATGTAG 58.272 36.000 0.00 0.00 41.95 2.74
692 713 3.407698 TGCGGACATGAATGTAGTTTGT 58.592 40.909 0.00 0.00 41.95 2.83
697 718 6.403200 GCGGACATGAATGTAGTTTGTGTTAT 60.403 38.462 0.00 0.00 41.95 1.89
700 721 9.691362 GGACATGAATGTAGTTTGTGTTATTTT 57.309 29.630 0.00 0.00 41.95 1.82
726 747 5.756195 TGTTCTTTATACTGCCATGATGC 57.244 39.130 0.00 0.00 0.00 3.91
729 750 6.183360 TGTTCTTTATACTGCCATGATGCTTG 60.183 38.462 0.00 0.00 0.00 4.01
735 756 2.426024 ACTGCCATGATGCTTGATGAAC 59.574 45.455 0.46 0.00 0.00 3.18
737 758 3.028130 TGCCATGATGCTTGATGAACAT 58.972 40.909 0.46 0.00 0.00 2.71
749 770 8.920509 TGCTTGATGAACATATCTCAAATTTG 57.079 30.769 12.15 12.15 30.25 2.32
751 772 9.017669 GCTTGATGAACATATCTCAAATTTGTC 57.982 33.333 17.47 6.20 30.25 3.18
782 803 6.846325 AAGTTCTTTCAAAGTCTACTTCCG 57.154 37.500 0.00 0.00 34.61 4.30
865 886 1.077787 CAGGCGGTTGGCAGGATAA 60.078 57.895 0.00 0.00 46.16 1.75
868 889 0.963355 GGCGGTTGGCAGGATAAACA 60.963 55.000 0.00 0.00 46.16 2.83
869 890 0.170339 GCGGTTGGCAGGATAAACAC 59.830 55.000 0.00 0.00 42.87 3.32
870 891 1.529226 CGGTTGGCAGGATAAACACA 58.471 50.000 0.00 0.00 0.00 3.72
871 892 1.468520 CGGTTGGCAGGATAAACACAG 59.531 52.381 0.00 0.00 0.00 3.66
872 893 1.202348 GGTTGGCAGGATAAACACAGC 59.798 52.381 0.00 0.00 0.00 4.40
873 894 1.202348 GTTGGCAGGATAAACACAGCC 59.798 52.381 0.00 0.00 42.32 4.85
903 925 4.831307 CGTCTCCTCGGCCGAACG 62.831 72.222 29.07 29.07 0.00 3.95
904 926 3.437795 GTCTCCTCGGCCGAACGA 61.438 66.667 30.53 24.53 41.13 3.85
905 927 2.674033 TCTCCTCGGCCGAACGAA 60.674 61.111 30.53 12.56 42.98 3.85
906 928 2.506438 CTCCTCGGCCGAACGAAC 60.506 66.667 30.53 0.00 42.98 3.95
907 929 3.984200 CTCCTCGGCCGAACGAACC 62.984 68.421 30.53 0.00 42.98 3.62
908 930 4.367023 CCTCGGCCGAACGAACCA 62.367 66.667 30.53 3.64 42.98 3.67
909 931 2.125673 CTCGGCCGAACGAACCAT 60.126 61.111 30.53 0.00 42.98 3.55
910 932 2.125832 TCGGCCGAACGAACCATC 60.126 61.111 28.99 0.00 40.34 3.51
911 933 2.433491 CGGCCGAACGAACCATCA 60.433 61.111 24.07 0.00 35.47 3.07
912 934 2.736682 CGGCCGAACGAACCATCAC 61.737 63.158 24.07 0.00 35.47 3.06
913 935 2.736682 GGCCGAACGAACCATCACG 61.737 63.158 0.00 0.00 0.00 4.35
914 936 2.776072 CCGAACGAACCATCACGC 59.224 61.111 0.00 0.00 0.00 5.34
915 937 2.736682 CCGAACGAACCATCACGCC 61.737 63.158 0.00 0.00 0.00 5.68
916 938 2.736682 CGAACGAACCATCACGCCC 61.737 63.158 0.00 0.00 0.00 6.13
917 939 1.375523 GAACGAACCATCACGCCCT 60.376 57.895 0.00 0.00 0.00 5.19
918 940 1.359459 GAACGAACCATCACGCCCTC 61.359 60.000 0.00 0.00 0.00 4.30
919 941 2.511600 CGAACCATCACGCCCTCC 60.512 66.667 0.00 0.00 0.00 4.30
920 942 2.124695 GAACCATCACGCCCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
921 943 3.699134 GAACCATCACGCCCTCCCC 62.699 68.421 0.00 0.00 0.00 4.81
924 946 3.151710 CATCACGCCCTCCCCGTA 61.152 66.667 0.00 0.00 37.12 4.02
925 947 2.838225 ATCACGCCCTCCCCGTAG 60.838 66.667 0.00 0.00 37.12 3.51
978 1000 2.344025 GACCGAGCCGTTTATTGTTCT 58.656 47.619 0.00 0.00 0.00 3.01
983 1005 0.098200 GCCGTTTATTGTTCTCGGGC 59.902 55.000 0.00 0.00 41.24 6.13
1112 1134 7.147966 GGTCAGAAAACCAAAAGTAAAAGGAGA 60.148 37.037 0.00 0.00 39.27 3.71
1122 1144 5.906772 AAGTAAAAGGAGAGGAGACCAAA 57.093 39.130 0.00 0.00 0.00 3.28
1123 1145 5.230323 AGTAAAAGGAGAGGAGACCAAAC 57.770 43.478 0.00 0.00 0.00 2.93
1131 1153 2.741211 GAGACCAAACCGCCGTCC 60.741 66.667 0.00 0.00 0.00 4.79
1369 1404 2.258591 CGCGCACACAGTAGAGGT 59.741 61.111 8.75 0.00 0.00 3.85
1370 1405 1.801913 CGCGCACACAGTAGAGGTC 60.802 63.158 8.75 0.00 0.00 3.85
1411 1446 2.029838 AATTGGCTCGGTGTCTGATC 57.970 50.000 0.00 0.00 0.00 2.92
1419 1454 2.031870 TCGGTGTCTGATCTATGTGGG 58.968 52.381 0.00 0.00 0.00 4.61
1489 1524 4.322349 GGAGACCGGAGAAATGGATAGATG 60.322 50.000 9.46 0.00 0.00 2.90
1515 1550 3.525800 AGAGGGTTGGCAATTTACTGT 57.474 42.857 1.92 0.00 0.00 3.55
1526 1561 3.848019 GCAATTTACTGTGCTTGATCGTG 59.152 43.478 0.00 0.00 37.78 4.35
1528 1563 2.093306 TTACTGTGCTTGATCGTGGG 57.907 50.000 0.00 0.00 0.00 4.61
1529 1564 0.249120 TACTGTGCTTGATCGTGGGG 59.751 55.000 0.00 0.00 0.00 4.96
1530 1565 1.746615 CTGTGCTTGATCGTGGGGG 60.747 63.158 0.00 0.00 0.00 5.40
1547 1582 1.644337 GGGGGAAGGGAATACAGGTTT 59.356 52.381 0.00 0.00 0.00 3.27
1548 1583 2.623239 GGGGGAAGGGAATACAGGTTTG 60.623 54.545 0.00 0.00 0.00 2.93
1549 1584 2.310647 GGGGAAGGGAATACAGGTTTGA 59.689 50.000 0.00 0.00 0.00 2.69
1550 1585 3.052869 GGGGAAGGGAATACAGGTTTGAT 60.053 47.826 0.00 0.00 0.00 2.57
1552 1587 5.023452 GGGAAGGGAATACAGGTTTGATTT 58.977 41.667 0.00 0.00 0.00 2.17
1553 1588 5.105351 GGGAAGGGAATACAGGTTTGATTTG 60.105 44.000 0.00 0.00 0.00 2.32
1554 1589 5.714806 GGAAGGGAATACAGGTTTGATTTGA 59.285 40.000 0.00 0.00 0.00 2.69
1555 1590 6.210584 GGAAGGGAATACAGGTTTGATTTGAA 59.789 38.462 0.00 0.00 0.00 2.69
1556 1591 6.840780 AGGGAATACAGGTTTGATTTGAAG 57.159 37.500 0.00 0.00 0.00 3.02
1557 1592 6.314917 AGGGAATACAGGTTTGATTTGAAGT 58.685 36.000 0.00 0.00 0.00 3.01
1558 1593 7.466804 AGGGAATACAGGTTTGATTTGAAGTA 58.533 34.615 0.00 0.00 0.00 2.24
1593 1628 9.614792 AGGTTTGATTTGAAGTATACATAGACC 57.385 33.333 5.50 0.00 0.00 3.85
1594 1629 8.548721 GGTTTGATTTGAAGTATACATAGACCG 58.451 37.037 5.50 0.00 0.00 4.79
1595 1630 8.548721 GTTTGATTTGAAGTATACATAGACCGG 58.451 37.037 0.00 0.00 0.00 5.28
1596 1631 7.591421 TGATTTGAAGTATACATAGACCGGA 57.409 36.000 9.46 0.00 0.00 5.14
1597 1632 7.658261 TGATTTGAAGTATACATAGACCGGAG 58.342 38.462 9.46 0.00 0.00 4.63
1598 1633 7.504574 TGATTTGAAGTATACATAGACCGGAGA 59.495 37.037 9.46 0.00 0.00 3.71
1599 1634 7.649533 TTTGAAGTATACATAGACCGGAGAA 57.350 36.000 9.46 0.00 0.00 2.87
1600 1635 7.649533 TTGAAGTATACATAGACCGGAGAAA 57.350 36.000 9.46 0.00 0.00 2.52
1601 1636 7.834881 TGAAGTATACATAGACCGGAGAAAT 57.165 36.000 9.46 0.00 0.00 2.17
1653 1689 9.872757 TTCTAAAATAACTGAGTTTTTACAGCG 57.127 29.630 1.97 0.00 37.61 5.18
1664 1700 6.072893 TGAGTTTTTACAGCGAAAGGGAATAC 60.073 38.462 0.00 0.00 0.00 1.89
1680 1716 6.314917 AGGGAATACAGGTTTGATTTGAAGT 58.685 36.000 0.00 0.00 0.00 3.01
1731 2560 5.580911 TGCTCATGAATCATCGTTAATCG 57.419 39.130 0.00 0.00 41.41 3.34
1760 2589 6.891306 ATATAGAACTGCCATAAGCCCATA 57.109 37.500 0.00 0.00 42.71 2.74
1787 2616 2.930040 CAATCTGTCCGGATACACACAC 59.070 50.000 7.81 0.00 0.00 3.82
1788 2617 1.623163 TCTGTCCGGATACACACACA 58.377 50.000 7.81 0.00 0.00 3.72
1789 2618 1.271379 TCTGTCCGGATACACACACAC 59.729 52.381 7.81 0.00 0.00 3.82
1790 2619 1.000394 CTGTCCGGATACACACACACA 60.000 52.381 7.81 0.00 0.00 3.72
1791 2620 1.413077 TGTCCGGATACACACACACAA 59.587 47.619 7.81 0.00 0.00 3.33
1797 2626 4.201970 CCGGATACACACACACAAAAACTT 60.202 41.667 0.00 0.00 0.00 2.66
1887 2716 2.442084 GGCACGTACGGAGAACAAG 58.558 57.895 21.06 0.03 0.00 3.16
1890 2719 1.324718 CACGTACGGAGAACAAGACG 58.675 55.000 21.06 0.00 36.42 4.18
1955 2785 6.756299 ACACTGTTTAGACTAGTACCTAGC 57.244 41.667 0.00 0.00 37.57 3.42
1957 2787 6.374894 ACACTGTTTAGACTAGTACCTAGCTG 59.625 42.308 0.00 0.00 37.57 4.24
1962 2792 3.917300 AGACTAGTACCTAGCTGCCAAT 58.083 45.455 0.00 0.00 37.57 3.16
1985 2815 4.464951 TCTGATTGCTTTGCATCCATCTTT 59.535 37.500 0.00 0.00 38.76 2.52
2057 3579 2.755650 CACTCGGGCTGATGGTATTAC 58.244 52.381 0.00 0.00 0.00 1.89
2139 3661 2.229784 CTGGAAATGCAGAAGGTGGTTC 59.770 50.000 0.00 0.00 35.08 3.62
2148 3670 3.003378 GCAGAAGGTGGTTCACTGTTAAC 59.997 47.826 0.00 0.00 37.67 2.01
2258 3780 3.555139 GCGATCTCAAGATTCTGAAGTGG 59.445 47.826 0.00 0.00 34.37 4.00
2333 3938 0.936297 GTGCTTTGCCAAGTGAAGCG 60.936 55.000 0.00 0.00 46.59 4.68
2455 4060 2.092968 ACTGGCCACACATACTACATGG 60.093 50.000 0.00 0.00 0.00 3.66
2459 4064 4.902448 TGGCCACACATACTACATGGTATA 59.098 41.667 0.00 0.00 31.96 1.47
2574 4179 2.107950 TGTATGTACTGTTGCAGGGC 57.892 50.000 0.00 0.00 35.51 5.19
2706 4311 3.000041 TGCTGCCAAAGTATGAGTAACG 59.000 45.455 0.00 0.00 0.00 3.18
2794 4399 2.664698 GCATTTTCAAAGGGACGTCGTC 60.665 50.000 17.16 17.16 0.00 4.20
3001 4611 6.314400 AGAAATATGGCATTGAAAACACATGC 59.686 34.615 4.78 0.00 37.51 4.06
3034 4644 6.485830 AATACTTTATCCAGAGCTGCTACA 57.514 37.500 0.15 0.00 0.00 2.74
3153 4763 6.126739 ACCCTTTACCTTATGACAAGATCCTC 60.127 42.308 0.00 0.00 0.00 3.71
3167 4777 6.670617 ACAAGATCCTCCTGATGAATTTCAT 58.329 36.000 11.64 11.64 40.34 2.57
3314 4943 8.657074 TTATCATTTGGAGTATAACCGAACAG 57.343 34.615 0.00 0.00 34.18 3.16
3367 5256 9.649167 GTGTGTAACCAGGGTATAATATGTATC 57.351 37.037 0.00 0.00 34.36 2.24
3478 5367 4.661222 TCTAGCCCAGAGATATGACAGAG 58.339 47.826 0.00 0.00 0.00 3.35
3527 5416 6.914757 GTGAAAATCCTTGCTCACATATAAGC 59.085 38.462 0.00 0.00 38.43 3.09
3600 5489 6.557568 TGGAATTCCCTTGTAGTTATTTGGT 58.442 36.000 21.90 0.00 35.38 3.67
3742 5631 1.002430 ACGCACAGTGGAGAACATCAT 59.998 47.619 1.84 0.00 0.00 2.45
3743 5632 2.233676 ACGCACAGTGGAGAACATCATA 59.766 45.455 1.84 0.00 0.00 2.15
3744 5633 3.118629 ACGCACAGTGGAGAACATCATAT 60.119 43.478 1.84 0.00 0.00 1.78
3745 5634 3.246936 CGCACAGTGGAGAACATCATATG 59.753 47.826 1.84 0.00 0.00 1.78
3747 5636 4.034858 GCACAGTGGAGAACATCATATGTG 59.965 45.833 1.84 3.41 44.07 3.21
3748 5637 5.181009 CACAGTGGAGAACATCATATGTGT 58.819 41.667 1.90 4.04 44.07 3.72
3749 5638 6.340522 CACAGTGGAGAACATCATATGTGTA 58.659 40.000 1.90 0.00 44.07 2.90
3750 5639 6.478016 CACAGTGGAGAACATCATATGTGTAG 59.522 42.308 1.90 0.00 44.07 2.74
3751 5640 6.381133 ACAGTGGAGAACATCATATGTGTAGA 59.619 38.462 1.90 0.00 44.07 2.59
3752 5641 6.922407 CAGTGGAGAACATCATATGTGTAGAG 59.078 42.308 1.90 0.00 44.07 2.43
3753 5642 6.609212 AGTGGAGAACATCATATGTGTAGAGT 59.391 38.462 1.90 0.00 44.07 3.24
3754 5643 7.780271 AGTGGAGAACATCATATGTGTAGAGTA 59.220 37.037 1.90 0.00 44.07 2.59
3755 5644 8.414003 GTGGAGAACATCATATGTGTAGAGTAA 58.586 37.037 1.90 0.00 44.07 2.24
3756 5645 8.977412 TGGAGAACATCATATGTGTAGAGTAAA 58.023 33.333 1.90 0.00 44.07 2.01
3757 5646 9.988815 GGAGAACATCATATGTGTAGAGTAAAT 57.011 33.333 1.90 0.00 44.07 1.40
3912 5802 3.251484 TCTCATCTGAAGGGTGTTTCCT 58.749 45.455 0.00 0.00 39.17 3.36
3968 5858 5.433526 AGCAGCAATATCAATGCCAATTTT 58.566 33.333 0.00 0.00 44.91 1.82
4033 5923 7.555965 TCAGCAGTTCTGATAAGCTTATGTTA 58.444 34.615 23.51 8.75 46.34 2.41
4150 6254 2.558359 CTCGGGGCACTTCATTTCTTTT 59.442 45.455 0.00 0.00 0.00 2.27
4244 6348 5.902431 AGTAAGAGAATCAGCTGGGAATAGT 59.098 40.000 15.13 0.00 37.82 2.12
4388 6492 2.158559 ACATTACAACGCCTCATTGCA 58.841 42.857 0.00 0.00 0.00 4.08
4414 6518 2.014010 ACCATCAACTGTGCCCATTT 57.986 45.000 0.00 0.00 0.00 2.32
4655 6765 4.811908 TGGAAACACTGATGCATGAATTG 58.188 39.130 2.46 0.00 33.40 2.32
4745 6855 3.245284 CAGAAAGTTATATGTCACCGCCG 59.755 47.826 0.00 0.00 0.00 6.46
4879 7119 3.389002 AGATAGCATGCCAGATGTACACA 59.611 43.478 15.66 0.00 0.00 3.72
5021 7262 7.628286 TCGTTATCGTCCGGAAGGTAAATAGT 61.628 42.308 22.36 1.00 43.67 2.12
5070 7315 6.603599 AGCTTCTCCCAAGTTAATAATGTTCC 59.396 38.462 0.00 0.00 0.00 3.62
5187 7432 1.315257 CGGAAGGTGAATGCAAGGGG 61.315 60.000 0.00 0.00 0.00 4.79
5211 7456 1.039233 CAGGATGGTTCCCACATGCC 61.039 60.000 0.00 0.00 43.76 4.40
5432 7677 2.228822 CAGAACACCAAACTGGCCATAC 59.771 50.000 5.51 0.00 42.67 2.39
5467 7712 8.750416 TGTATTGTTGTTTGAAACGATTGAATG 58.250 29.630 0.70 0.00 35.99 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.217799 CCCCACATAAATCTGGACTATAAAAGA 58.782 37.037 0.00 0.00 0.00 2.52
7 8 7.998964 ACCCCACATAAATCTGGACTATAAAAG 59.001 37.037 0.00 0.00 0.00 2.27
8 9 7.878495 ACCCCACATAAATCTGGACTATAAAA 58.122 34.615 0.00 0.00 0.00 1.52
9 10 7.460214 ACCCCACATAAATCTGGACTATAAA 57.540 36.000 0.00 0.00 0.00 1.40
10 11 7.460214 AACCCCACATAAATCTGGACTATAA 57.540 36.000 0.00 0.00 0.00 0.98
11 12 7.092174 ACAAACCCCACATAAATCTGGACTATA 60.092 37.037 0.00 0.00 0.00 1.31
12 13 5.994416 AACCCCACATAAATCTGGACTAT 57.006 39.130 0.00 0.00 0.00 2.12
13 14 5.014755 ACAAACCCCACATAAATCTGGACTA 59.985 40.000 0.00 0.00 0.00 2.59
14 15 4.202673 ACAAACCCCACATAAATCTGGACT 60.203 41.667 0.00 0.00 0.00 3.85
15 16 4.086457 ACAAACCCCACATAAATCTGGAC 58.914 43.478 0.00 0.00 0.00 4.02
16 17 4.044065 AGACAAACCCCACATAAATCTGGA 59.956 41.667 0.00 0.00 0.00 3.86
17 18 4.344104 AGACAAACCCCACATAAATCTGG 58.656 43.478 0.00 0.00 0.00 3.86
18 19 5.009631 TGAGACAAACCCCACATAAATCTG 58.990 41.667 0.00 0.00 0.00 2.90
19 20 5.255397 TGAGACAAACCCCACATAAATCT 57.745 39.130 0.00 0.00 0.00 2.40
20 21 5.975693 TTGAGACAAACCCCACATAAATC 57.024 39.130 0.00 0.00 0.00 2.17
21 22 6.739331 TTTTGAGACAAACCCCACATAAAT 57.261 33.333 0.00 0.00 0.00 1.40
22 23 6.546428 TTTTTGAGACAAACCCCACATAAA 57.454 33.333 0.00 0.00 0.00 1.40
46 47 6.074648 TCTGACACCCCACATAAATCTTTTT 58.925 36.000 0.00 0.00 0.00 1.94
47 48 5.640147 TCTGACACCCCACATAAATCTTTT 58.360 37.500 0.00 0.00 0.00 2.27
48 49 5.255397 TCTGACACCCCACATAAATCTTT 57.745 39.130 0.00 0.00 0.00 2.52
49 50 4.848357 CTCTGACACCCCACATAAATCTT 58.152 43.478 0.00 0.00 0.00 2.40
50 51 3.370953 GCTCTGACACCCCACATAAATCT 60.371 47.826 0.00 0.00 0.00 2.40
51 52 2.945668 GCTCTGACACCCCACATAAATC 59.054 50.000 0.00 0.00 0.00 2.17
52 53 2.308570 TGCTCTGACACCCCACATAAAT 59.691 45.455 0.00 0.00 0.00 1.40
53 54 1.702401 TGCTCTGACACCCCACATAAA 59.298 47.619 0.00 0.00 0.00 1.40
54 55 1.357137 TGCTCTGACACCCCACATAA 58.643 50.000 0.00 0.00 0.00 1.90
55 56 1.583556 ATGCTCTGACACCCCACATA 58.416 50.000 0.00 0.00 0.00 2.29
56 57 0.700564 AATGCTCTGACACCCCACAT 59.299 50.000 0.00 0.00 0.00 3.21
57 58 0.478072 AAATGCTCTGACACCCCACA 59.522 50.000 0.00 0.00 0.00 4.17
58 59 1.168714 GAAATGCTCTGACACCCCAC 58.831 55.000 0.00 0.00 0.00 4.61
59 60 0.038166 GGAAATGCTCTGACACCCCA 59.962 55.000 0.00 0.00 0.00 4.96
60 61 0.329596 AGGAAATGCTCTGACACCCC 59.670 55.000 0.00 0.00 0.00 4.95
61 62 2.501723 TCTAGGAAATGCTCTGACACCC 59.498 50.000 0.00 0.00 0.00 4.61
62 63 3.449018 TCTCTAGGAAATGCTCTGACACC 59.551 47.826 0.00 0.00 0.00 4.16
63 64 4.727507 TCTCTAGGAAATGCTCTGACAC 57.272 45.455 0.00 0.00 0.00 3.67
64 65 4.958581 TCATCTCTAGGAAATGCTCTGACA 59.041 41.667 0.00 0.00 0.00 3.58
65 66 5.528043 TCATCTCTAGGAAATGCTCTGAC 57.472 43.478 0.00 0.00 0.00 3.51
66 67 5.511031 GCATCATCTCTAGGAAATGCTCTGA 60.511 44.000 16.26 4.22 40.72 3.27
67 68 4.691685 GCATCATCTCTAGGAAATGCTCTG 59.308 45.833 16.26 7.73 40.72 3.35
75 76 6.488006 GCCTTATTTTGCATCATCTCTAGGAA 59.512 38.462 0.00 0.00 0.00 3.36
112 113 9.847224 AAAACCTACTCTCTCATTCTTAAAACA 57.153 29.630 0.00 0.00 0.00 2.83
117 118 7.147707 GCCCTAAAACCTACTCTCTCATTCTTA 60.148 40.741 0.00 0.00 0.00 2.10
119 120 5.129650 GCCCTAAAACCTACTCTCTCATTCT 59.870 44.000 0.00 0.00 0.00 2.40
120 121 5.104900 TGCCCTAAAACCTACTCTCTCATTC 60.105 44.000 0.00 0.00 0.00 2.67
121 122 4.783227 TGCCCTAAAACCTACTCTCTCATT 59.217 41.667 0.00 0.00 0.00 2.57
126 127 4.081087 TGTCATGCCCTAAAACCTACTCTC 60.081 45.833 0.00 0.00 0.00 3.20
137 138 4.322650 GCAGGAATTTTTGTCATGCCCTAA 60.323 41.667 0.00 0.00 44.80 2.69
145 146 2.289569 GCCATGGCAGGAATTTTTGTCA 60.290 45.455 32.08 0.74 41.49 3.58
146 147 2.349590 GCCATGGCAGGAATTTTTGTC 58.650 47.619 32.08 0.00 41.49 3.18
163 164 1.346395 ACCGTTTCACACTATCTGCCA 59.654 47.619 0.00 0.00 0.00 4.92
164 165 2.094762 ACCGTTTCACACTATCTGCC 57.905 50.000 0.00 0.00 0.00 4.85
165 166 2.806244 ACAACCGTTTCACACTATCTGC 59.194 45.455 0.00 0.00 0.00 4.26
166 167 3.432252 GGACAACCGTTTCACACTATCTG 59.568 47.826 0.00 0.00 0.00 2.90
167 168 3.323979 AGGACAACCGTTTCACACTATCT 59.676 43.478 0.00 0.00 41.83 1.98
168 169 3.660865 AGGACAACCGTTTCACACTATC 58.339 45.455 0.00 0.00 41.83 2.08
169 170 3.764237 AGGACAACCGTTTCACACTAT 57.236 42.857 0.00 0.00 41.83 2.12
170 171 3.547054 AAGGACAACCGTTTCACACTA 57.453 42.857 0.00 0.00 41.83 2.74
171 172 2.413310 AAGGACAACCGTTTCACACT 57.587 45.000 0.00 0.00 41.83 3.55
172 173 4.095334 AGTTTAAGGACAACCGTTTCACAC 59.905 41.667 0.00 0.00 41.83 3.82
173 174 4.263435 AGTTTAAGGACAACCGTTTCACA 58.737 39.130 0.00 0.00 41.83 3.58
174 175 4.888038 AGTTTAAGGACAACCGTTTCAC 57.112 40.909 0.00 0.00 41.83 3.18
186 187 8.472007 TCCTAAAGAAATTGCAAGTTTAAGGA 57.528 30.769 14.04 17.84 0.00 3.36
190 191 9.691362 GTGATTCCTAAAGAAATTGCAAGTTTA 57.309 29.630 14.04 9.17 38.21 2.01
201 202 4.280436 TGCCTCGTGATTCCTAAAGAAA 57.720 40.909 0.00 0.00 38.21 2.52
202 203 3.973206 TGCCTCGTGATTCCTAAAGAA 57.027 42.857 0.00 0.00 39.32 2.52
203 204 3.973206 TTGCCTCGTGATTCCTAAAGA 57.027 42.857 0.00 0.00 0.00 2.52
213 214 1.939934 CAAACTCTGTTTGCCTCGTGA 59.060 47.619 9.73 0.00 0.00 4.35
282 283 8.995220 TCATTTTAGTCCACATGTAGTTTACAC 58.005 33.333 0.00 0.00 42.23 2.90
294 295 6.040278 TGTTTGCTCATTCATTTTAGTCCACA 59.960 34.615 0.00 0.00 0.00 4.17
295 296 6.363357 GTGTTTGCTCATTCATTTTAGTCCAC 59.637 38.462 0.00 0.00 0.00 4.02
296 297 6.040278 TGTGTTTGCTCATTCATTTTAGTCCA 59.960 34.615 0.00 0.00 0.00 4.02
297 298 6.363357 GTGTGTTTGCTCATTCATTTTAGTCC 59.637 38.462 0.00 0.00 0.00 3.85
298 299 7.113965 CAGTGTGTTTGCTCATTCATTTTAGTC 59.886 37.037 0.00 0.00 0.00 2.59
299 300 6.919662 CAGTGTGTTTGCTCATTCATTTTAGT 59.080 34.615 0.00 0.00 0.00 2.24
300 301 7.140705 TCAGTGTGTTTGCTCATTCATTTTAG 58.859 34.615 0.00 0.00 0.00 1.85
309 310 2.682856 ACGTTTCAGTGTGTTTGCTCAT 59.317 40.909 0.00 0.00 0.00 2.90
368 371 9.699410 AAGTATTCCCTTCATTCACAAATATGA 57.301 29.630 0.00 0.00 0.00 2.15
401 404 5.820423 ACGATAAGCCATTGCACATAGTAAA 59.180 36.000 0.00 0.00 41.13 2.01
423 426 6.420903 CACATAATAATACTCCTGTGACCACG 59.579 42.308 0.00 0.00 36.89 4.94
535 538 3.186817 CGCATCGTACCAACAACCTTTTA 59.813 43.478 0.00 0.00 0.00 1.52
568 571 0.546122 AATCGTCATGCTAAGGCCCA 59.454 50.000 0.00 0.00 37.74 5.36
571 574 3.623060 TCAGAAAATCGTCATGCTAAGGC 59.377 43.478 0.00 0.00 39.26 4.35
577 580 4.083855 TGAACAGTCAGAAAATCGTCATGC 60.084 41.667 0.00 0.00 0.00 4.06
582 585 5.597806 TGTAGTGAACAGTCAGAAAATCGT 58.402 37.500 0.00 0.00 33.27 3.73
585 588 7.624360 TTGTTGTAGTGAACAGTCAGAAAAT 57.376 32.000 0.00 0.00 39.87 1.82
586 589 6.403200 GCTTGTTGTAGTGAACAGTCAGAAAA 60.403 38.462 0.00 0.00 39.87 2.29
611 614 0.604073 TGCACATGGGCTGAACAATG 59.396 50.000 22.81 0.00 34.04 2.82
612 615 0.604578 GTGCACATGGGCTGAACAAT 59.395 50.000 22.81 0.00 34.04 2.71
617 620 1.303561 GAAGGTGCACATGGGCTGA 60.304 57.895 22.81 0.00 34.04 4.26
618 621 2.693762 CGAAGGTGCACATGGGCTG 61.694 63.158 22.81 0.00 34.04 4.85
619 622 2.360350 CGAAGGTGCACATGGGCT 60.360 61.111 22.81 0.00 34.04 5.19
621 624 2.360350 AGCGAAGGTGCACATGGG 60.360 61.111 20.43 8.45 36.17 4.00
622 625 2.743752 CGAGCGAAGGTGCACATGG 61.744 63.158 20.43 8.84 39.88 3.66
624 627 3.121030 GCGAGCGAAGGTGCACAT 61.121 61.111 20.43 9.24 39.88 3.21
629 632 1.517257 CACTAGGCGAGCGAAGGTG 60.517 63.158 0.00 0.00 39.88 4.00
631 634 2.583593 GCACTAGGCGAGCGAAGG 60.584 66.667 0.00 0.00 0.00 3.46
640 643 1.004918 ACGACCACAAGCACTAGGC 60.005 57.895 0.00 0.00 45.30 3.93
641 644 0.732880 CGACGACCACAAGCACTAGG 60.733 60.000 0.00 0.00 0.00 3.02
653 674 3.234596 GCAAAATATGTAGCGACGACC 57.765 47.619 0.00 0.00 0.00 4.79
660 681 4.811555 TCATGTCCGCAAAATATGTAGC 57.188 40.909 0.00 0.00 0.00 3.58
663 684 5.581126 ACATTCATGTCCGCAAAATATGT 57.419 34.783 0.00 0.00 35.87 2.29
664 685 6.728200 ACTACATTCATGTCCGCAAAATATG 58.272 36.000 0.00 0.00 41.97 1.78
668 689 5.218885 CAAACTACATTCATGTCCGCAAAA 58.781 37.500 0.00 0.00 41.97 2.44
669 690 4.277174 ACAAACTACATTCATGTCCGCAAA 59.723 37.500 0.00 0.00 41.97 3.68
670 691 3.818210 ACAAACTACATTCATGTCCGCAA 59.182 39.130 0.00 0.00 41.97 4.85
697 718 8.417106 TCATGGCAGTATAAAGAACAACAAAAA 58.583 29.630 0.00 0.00 0.00 1.94
700 721 7.537715 CATCATGGCAGTATAAAGAACAACAA 58.462 34.615 0.00 0.00 0.00 2.83
711 732 5.231702 TCATCAAGCATCATGGCAGTATA 57.768 39.130 0.00 0.00 35.83 1.47
717 738 3.728076 ATGTTCATCAAGCATCATGGC 57.272 42.857 0.00 0.00 0.00 4.40
760 781 5.915175 ACGGAAGTAGACTTTGAAAGAACT 58.085 37.500 12.53 12.18 46.88 3.01
814 835 9.662545 CAAGCATTCCAATTTATTTTTCGTTTT 57.337 25.926 0.00 0.00 0.00 2.43
815 836 7.802720 GCAAGCATTCCAATTTATTTTTCGTTT 59.197 29.630 0.00 0.00 0.00 3.60
816 837 7.297391 GCAAGCATTCCAATTTATTTTTCGTT 58.703 30.769 0.00 0.00 0.00 3.85
817 838 6.400940 CGCAAGCATTCCAATTTATTTTTCGT 60.401 34.615 0.00 0.00 0.00 3.85
818 839 5.953205 CGCAAGCATTCCAATTTATTTTTCG 59.047 36.000 0.00 0.00 0.00 3.46
851 872 1.468520 CTGTGTTTATCCTGCCAACCG 59.531 52.381 0.00 0.00 0.00 4.44
860 881 1.922545 GTACGTCGGCTGTGTTTATCC 59.077 52.381 0.00 0.00 0.00 2.59
903 925 2.124695 GGGAGGGCGTGATGGTTC 60.125 66.667 0.00 0.00 0.00 3.62
904 926 3.728373 GGGGAGGGCGTGATGGTT 61.728 66.667 0.00 0.00 0.00 3.67
907 929 3.151710 TACGGGGAGGGCGTGATG 61.152 66.667 0.00 0.00 0.00 3.07
908 930 2.838225 CTACGGGGAGGGCGTGAT 60.838 66.667 0.00 0.00 0.00 3.06
914 936 3.841353 TAGGGCCTACGGGGAGGG 61.841 72.222 9.81 0.00 37.06 4.30
915 937 2.523657 GTAGGGCCTACGGGGAGG 60.524 72.222 26.87 0.00 39.88 4.30
1031 1053 2.519780 TTTCGGTGGTGGTTGGCC 60.520 61.111 0.00 0.00 0.00 5.36
1045 1067 1.831736 TCCTTCCTCGGAGGATGTTTC 59.168 52.381 26.54 0.00 45.34 2.78
1112 1134 3.236003 GACGGCGGTTTGGTCTCCT 62.236 63.158 13.24 0.00 0.00 3.69
1308 1343 0.823769 CTCCACCCAGATCGATCGGA 60.824 60.000 27.16 21.60 0.00 4.55
1309 1344 1.109920 ACTCCACCCAGATCGATCGG 61.110 60.000 19.33 20.83 0.00 4.18
1355 1390 0.969894 ACCAGACCTCTACTGTGTGC 59.030 55.000 0.00 0.00 34.04 4.57
1357 1392 2.677542 TCACCAGACCTCTACTGTGT 57.322 50.000 0.00 0.00 34.04 3.72
1358 1393 3.092301 TCATCACCAGACCTCTACTGTG 58.908 50.000 0.00 0.00 34.04 3.66
1366 1401 2.421107 GCACATCATCATCACCAGACCT 60.421 50.000 0.00 0.00 0.00 3.85
1369 1404 1.841919 AGGCACATCATCATCACCAGA 59.158 47.619 0.00 0.00 0.00 3.86
1370 1405 1.947456 CAGGCACATCATCATCACCAG 59.053 52.381 0.00 0.00 0.00 4.00
1411 1446 4.152647 TCTCTAGCACATACCCCACATAG 58.847 47.826 0.00 0.00 0.00 2.23
1419 1454 2.035632 ACTGCCTCTCTAGCACATACC 58.964 52.381 0.00 0.00 36.01 2.73
1489 1524 3.584733 AATTGCCAACCCTCTATCTCC 57.415 47.619 0.00 0.00 0.00 3.71
1528 1563 2.310647 TCAAACCTGTATTCCCTTCCCC 59.689 50.000 0.00 0.00 0.00 4.81
1529 1564 3.732048 TCAAACCTGTATTCCCTTCCC 57.268 47.619 0.00 0.00 0.00 3.97
1530 1565 5.714806 TCAAATCAAACCTGTATTCCCTTCC 59.285 40.000 0.00 0.00 0.00 3.46
1532 1567 6.782494 ACTTCAAATCAAACCTGTATTCCCTT 59.218 34.615 0.00 0.00 0.00 3.95
1534 1569 6.590234 ACTTCAAATCAAACCTGTATTCCC 57.410 37.500 0.00 0.00 0.00 3.97
1567 1602 9.614792 GGTCTATGTATACTTCAAATCAAACCT 57.385 33.333 4.17 0.00 0.00 3.50
1568 1603 8.548721 CGGTCTATGTATACTTCAAATCAAACC 58.451 37.037 4.17 0.00 0.00 3.27
1569 1604 8.548721 CCGGTCTATGTATACTTCAAATCAAAC 58.451 37.037 4.17 0.00 0.00 2.93
1570 1605 8.479689 TCCGGTCTATGTATACTTCAAATCAAA 58.520 33.333 0.00 0.00 0.00 2.69
1571 1606 8.014070 TCCGGTCTATGTATACTTCAAATCAA 57.986 34.615 0.00 0.00 0.00 2.57
1572 1607 7.504574 TCTCCGGTCTATGTATACTTCAAATCA 59.495 37.037 0.00 0.00 0.00 2.57
1573 1608 7.883217 TCTCCGGTCTATGTATACTTCAAATC 58.117 38.462 0.00 0.00 0.00 2.17
1574 1609 7.834881 TCTCCGGTCTATGTATACTTCAAAT 57.165 36.000 0.00 0.00 0.00 2.32
1575 1610 7.649533 TTCTCCGGTCTATGTATACTTCAAA 57.350 36.000 0.00 0.00 0.00 2.69
1576 1611 7.649533 TTTCTCCGGTCTATGTATACTTCAA 57.350 36.000 0.00 0.00 0.00 2.69
1577 1612 7.658261 CATTTCTCCGGTCTATGTATACTTCA 58.342 38.462 0.00 0.00 0.00 3.02
1578 1613 6.586844 GCATTTCTCCGGTCTATGTATACTTC 59.413 42.308 0.00 0.00 0.00 3.01
1579 1614 6.267928 AGCATTTCTCCGGTCTATGTATACTT 59.732 38.462 0.00 0.08 0.00 2.24
1580 1615 5.775701 AGCATTTCTCCGGTCTATGTATACT 59.224 40.000 0.00 0.00 0.00 2.12
1581 1616 6.026947 AGCATTTCTCCGGTCTATGTATAC 57.973 41.667 0.00 0.00 0.00 1.47
1582 1617 6.266786 TCAAGCATTTCTCCGGTCTATGTATA 59.733 38.462 0.00 0.00 0.00 1.47
1583 1618 5.070446 TCAAGCATTTCTCCGGTCTATGTAT 59.930 40.000 0.00 0.00 0.00 2.29
1584 1619 4.404394 TCAAGCATTTCTCCGGTCTATGTA 59.596 41.667 0.00 0.00 0.00 2.29
1585 1620 3.197766 TCAAGCATTTCTCCGGTCTATGT 59.802 43.478 0.00 0.00 0.00 2.29
1586 1621 3.797039 TCAAGCATTTCTCCGGTCTATG 58.203 45.455 0.00 2.85 0.00 2.23
1587 1622 3.181461 CCTCAAGCATTTCTCCGGTCTAT 60.181 47.826 0.00 0.00 0.00 1.98
1588 1623 2.168521 CCTCAAGCATTTCTCCGGTCTA 59.831 50.000 0.00 0.00 0.00 2.59
1589 1624 1.065854 CCTCAAGCATTTCTCCGGTCT 60.066 52.381 0.00 0.00 0.00 3.85
1590 1625 1.339151 ACCTCAAGCATTTCTCCGGTC 60.339 52.381 0.00 0.00 0.00 4.79
1591 1626 0.693049 ACCTCAAGCATTTCTCCGGT 59.307 50.000 0.00 0.00 0.00 5.28
1592 1627 1.089920 CACCTCAAGCATTTCTCCGG 58.910 55.000 0.00 0.00 0.00 5.14
1593 1628 2.099141 TCACCTCAAGCATTTCTCCG 57.901 50.000 0.00 0.00 0.00 4.63
1594 1629 3.614092 TGATCACCTCAAGCATTTCTCC 58.386 45.455 0.00 0.00 0.00 3.71
1595 1630 5.633830 TTTGATCACCTCAAGCATTTCTC 57.366 39.130 0.00 0.00 44.48 2.87
1596 1631 6.395629 CAATTTGATCACCTCAAGCATTTCT 58.604 36.000 0.00 0.00 44.48 2.52
1597 1632 5.579511 CCAATTTGATCACCTCAAGCATTTC 59.420 40.000 0.00 0.00 44.48 2.17
1598 1633 5.484715 CCAATTTGATCACCTCAAGCATTT 58.515 37.500 0.00 0.00 44.48 2.32
1599 1634 4.622220 GCCAATTTGATCACCTCAAGCATT 60.622 41.667 0.00 0.00 44.48 3.56
1600 1635 3.118884 GCCAATTTGATCACCTCAAGCAT 60.119 43.478 0.00 0.00 44.48 3.79
1601 1636 2.231964 GCCAATTTGATCACCTCAAGCA 59.768 45.455 0.00 0.00 44.48 3.91
1653 1689 7.227049 TCAAATCAAACCTGTATTCCCTTTC 57.773 36.000 0.00 0.00 0.00 2.62
1702 1739 4.514441 ACGATGATTCATGAGCAATCCTTC 59.486 41.667 3.32 0.00 30.30 3.46
1731 2560 6.072452 GGCTTATGGCAGTTCTATATTTGGAC 60.072 42.308 0.00 0.00 44.01 4.02
1760 2589 4.454504 GTGTATCCGGACAGATTGTGTTTT 59.545 41.667 6.12 0.00 40.56 2.43
1787 2616 2.158971 CCCCAAGGGTCAAGTTTTTGTG 60.159 50.000 4.11 0.00 38.25 3.33
1788 2617 2.115427 CCCCAAGGGTCAAGTTTTTGT 58.885 47.619 4.11 0.00 38.25 2.83
1789 2618 2.908688 CCCCAAGGGTCAAGTTTTTG 57.091 50.000 4.11 0.00 38.25 2.44
1832 2661 1.489481 CTGTCATGGCTGGAGACCTA 58.511 55.000 0.00 0.00 0.00 3.08
1833 2662 1.908340 GCTGTCATGGCTGGAGACCT 61.908 60.000 6.32 0.00 0.00 3.85
1890 2719 3.741830 GAGTAAGGCCCCTCGCTGC 62.742 68.421 0.00 0.00 37.74 5.25
1955 2785 2.268298 GCAAAGCAATCAGATTGGCAG 58.732 47.619 22.25 10.85 40.57 4.85
1957 2787 2.373540 TGCAAAGCAATCAGATTGGC 57.626 45.000 22.25 17.09 40.57 4.52
1962 2792 3.628008 AGATGGATGCAAAGCAATCAGA 58.372 40.909 0.00 0.00 43.62 3.27
1985 2815 1.068541 CCGATCATCCTACGATTGCGA 60.069 52.381 0.00 0.00 41.64 5.10
2333 3938 1.337118 TGGGGTGCTGTTGAATTTCC 58.663 50.000 0.00 0.00 0.00 3.13
2574 4179 1.601914 GCCCCAAACTGCTTAAACACG 60.602 52.381 0.00 0.00 0.00 4.49
2706 4311 7.080724 AGAAAGAAAAGAGACGATGAAATTGC 58.919 34.615 0.00 0.00 0.00 3.56
3001 4611 7.011482 GCTCTGGATAAAGTATTACCACTTGTG 59.989 40.741 0.00 0.00 38.74 3.33
3034 4644 2.159014 TGAACGCGCCTTTCCATAGTAT 60.159 45.455 5.73 0.00 0.00 2.12
3153 4763 6.802608 ACTATGTGCAATGAAATTCATCAGG 58.197 36.000 9.11 3.75 35.76 3.86
3478 5367 2.840296 GCATCAGCTTCTTGCCTTAC 57.160 50.000 1.66 0.00 44.23 2.34
3576 5465 6.557568 ACCAAATAACTACAAGGGAATTCCA 58.442 36.000 25.67 4.02 38.24 3.53
3755 5644 9.261180 CCGTCATTTTACTCTACACATATGATT 57.739 33.333 10.38 0.00 0.00 2.57
3756 5645 8.638873 TCCGTCATTTTACTCTACACATATGAT 58.361 33.333 10.38 0.00 0.00 2.45
3757 5646 8.002984 TCCGTCATTTTACTCTACACATATGA 57.997 34.615 10.38 0.00 0.00 2.15
3758 5647 8.818141 ATCCGTCATTTTACTCTACACATATG 57.182 34.615 0.00 0.00 0.00 1.78
3968 5858 4.400251 GGACATTGAAGAGCATGAATTGGA 59.600 41.667 0.00 0.00 0.00 3.53
4033 5923 9.715121 AAAATGATGCATGAAGTTCTTAAATGT 57.285 25.926 2.46 0.00 0.00 2.71
4139 6243 6.125327 TGCTGTTCGTACAAAAGAAATGAA 57.875 33.333 0.00 0.00 32.92 2.57
4150 6254 8.464404 AGTAAGATAAATACTGCTGTTCGTACA 58.536 33.333 15.37 0.00 32.50 2.90
4244 6348 4.503910 CCTCCAACTTTGATATCACGTCA 58.496 43.478 4.48 0.00 0.00 4.35
4388 6492 2.825532 GGCACAGTTGATGGTTACCATT 59.174 45.455 18.78 0.00 45.26 3.16
4435 6539 9.825109 TGACCACATAATTTTCTCACGATAATA 57.175 29.630 0.00 0.00 0.00 0.98
4495 6599 6.983890 GGACTTTCTGATGATAAGTTCTCTCC 59.016 42.308 0.00 0.00 32.58 3.71
4655 6765 8.844244 ACCATCTAGCAATCAAAATAGTCATTC 58.156 33.333 0.00 0.00 0.00 2.67
4745 6855 2.838736 ACTTCGTCATATGATGGTGGC 58.161 47.619 21.97 2.29 0.00 5.01
4879 7119 4.414846 AGCCTCCCAGATATGATCAACTTT 59.585 41.667 0.00 0.00 0.00 2.66
5021 7262 8.932945 CTTACAGAGCACAGATATGAAAAGTA 57.067 34.615 0.00 0.00 0.00 2.24
5070 7315 1.269831 GCTTCTAGGACCACGCATAGG 60.270 57.143 0.00 0.00 0.00 2.57
5211 7456 0.840729 GCTCGCGTCTTTCGACATAG 59.159 55.000 5.77 0.00 42.86 2.23
5432 7677 4.502282 TCAAACAACAATACAAAGCTTGCG 59.498 37.500 0.00 0.00 0.00 4.85
5467 7712 2.234908 ACTATGAACTCCACCAGTGAGC 59.765 50.000 0.00 0.00 34.56 4.26
6041 8290 4.702131 AGAGAGCCATTGTAACAATCAACC 59.298 41.667 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.