Multiple sequence alignment - TraesCS7A01G514600

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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 TraesCS7A01G514600 chr7A 100.000 7242 0 0 1 7242 700671086 700678327 0.000000e+00 13374
1 TraesCS7A01G514600 chr7A 95.732 328 12 2 3875 4202 631667067 631666742 1.790000e-145 527
2 TraesCS7A01G514600 chr7A 95.062 324 16 0 3875 4198 683559840 683560163 1.800000e-140 510
3 TraesCS7A01G514600 chr7A 94.444 324 18 0 3875 4198 721272993 721273316 3.900000e-137 499
4 TraesCS7A01G514600 chr7A 93.750 304 12 2 2576 2878 700673366 700673663 3.980000e-122 449
5 TraesCS7A01G514600 chr7A 93.750 304 12 2 2281 2578 700673661 700673963 3.980000e-122 449
6 TraesCS7A01G514600 chr7A 87.636 275 13 3 3522 3778 683559572 683559843 4.250000e-77 300
7 TraesCS7A01G514600 chr7A 87.500 272 13 4 3525 3778 631667332 631667064 1.980000e-75 294
8 TraesCS7A01G514600 chr7A 85.455 275 19 5 3522 3778 721272725 721272996 4.310000e-67 267
9 TraesCS7A01G514600 chr7D 94.889 5439 135 40 1734 7088 610775316 610780695 0.000000e+00 8371
10 TraesCS7A01G514600 chr7D 97.471 1107 28 0 589 1695 610774219 610775325 0.000000e+00 1890
11 TraesCS7A01G514600 chr7D 92.279 531 33 6 1 524 610773540 610774069 0.000000e+00 747
12 TraesCS7A01G514600 chr7D 95.973 298 12 0 2281 2578 610776158 610776455 1.090000e-132 484
13 TraesCS7A01G514600 chr7D 94.737 304 9 2 2576 2878 610775863 610776160 3.960000e-127 466
14 TraesCS7A01G514600 chr7D 93.277 119 7 1 7121 7239 610781241 610781358 2.690000e-39 174
15 TraesCS7A01G514600 chr7D 100.000 64 0 0 2901 2964 307160169 307160106 1.280000e-22 119
16 TraesCS7A01G514600 chr7D 100.000 64 0 0 2901 2964 382087044 382086981 1.280000e-22 119
17 TraesCS7A01G514600 chr7D 100.000 64 0 0 2901 2964 606883738 606883675 1.280000e-22 119
18 TraesCS7A01G514600 chr7B 95.776 2675 97 8 3632 6298 699377276 699374610 0.000000e+00 4300
19 TraesCS7A01G514600 chr7B 95.601 1887 63 11 1735 3619 699380190 699378322 0.000000e+00 3007
20 TraesCS7A01G514600 chr7B 94.858 1128 55 3 582 1706 699381304 699380177 0.000000e+00 1759
21 TraesCS7A01G514600 chr7B 91.657 839 35 14 6269 7085 699374610 699373785 0.000000e+00 1129
22 TraesCS7A01G514600 chr7B 93.310 583 37 2 2965 3546 703575925 703576506 0.000000e+00 859
23 TraesCS7A01G514600 chr7B 93.466 551 25 4 3005 3546 619069303 619068755 0.000000e+00 808
24 TraesCS7A01G514600 chr7B 90.244 533 41 5 1 524 699382110 699381580 0.000000e+00 686
25 TraesCS7A01G514600 chr7B 95.638 298 10 1 2281 2578 699379349 699379055 6.570000e-130 475
26 TraesCS7A01G514600 chr7B 94.079 304 11 2 2576 2878 699379644 699379347 8.560000e-124 455
27 TraesCS7A01G514600 chr6B 94.349 584 30 3 2965 3546 72321506 72320924 0.000000e+00 893
28 TraesCS7A01G514600 chr6B 94.168 583 32 2 2965 3546 72318712 72318131 0.000000e+00 887
29 TraesCS7A01G514600 chr6B 94.007 584 32 3 2965 3546 72315919 72315337 0.000000e+00 881
30 TraesCS7A01G514600 chr6B 94.007 584 32 3 2965 3546 72327102 72326520 0.000000e+00 881
31 TraesCS7A01G514600 chr6B 93.836 584 33 3 2965 3546 72324306 72323724 0.000000e+00 876
32 TraesCS7A01G514600 chr6B 95.652 230 10 0 3969 4198 687274859 687274630 3.190000e-98 370
33 TraesCS7A01G514600 chr6B 86.408 206 8 2 3525 3712 687275070 687274867 2.650000e-49 207
34 TraesCS7A01G514600 chr3A 95.988 324 13 0 3875 4198 497908878 497909201 1.790000e-145 527
35 TraesCS7A01G514600 chr3A 87.273 275 14 3 3522 3778 497908610 497908881 1.980000e-75 294
36 TraesCS7A01G514600 chr5A 94.753 324 17 0 3875 4198 195559037 195559360 8.380000e-139 505
37 TraesCS7A01G514600 chr5A 87.636 275 13 3 3522 3778 195558769 195559040 4.250000e-77 300
38 TraesCS7A01G514600 chr1A 94.512 328 17 1 3875 4202 174399850 174399524 8.380000e-139 505
39 TraesCS7A01G514600 chr1A 87.132 272 14 3 3525 3778 174400115 174399847 9.190000e-74 289
40 TraesCS7A01G514600 chr6D 93.617 329 19 2 2965 3292 292687963 292687636 2.350000e-134 490
41 TraesCS7A01G514600 chr3B 85.308 211 11 2 3520 3712 752874051 752874259 4.430000e-47 200
42 TraesCS7A01G514600 chrUn 100.000 64 0 0 2901 2964 171005526 171005463 1.280000e-22 119
43 TraesCS7A01G514600 chr4D 100.000 64 0 0 2901 2964 123398764 123398701 1.280000e-22 119
44 TraesCS7A01G514600 chr4B 100.000 64 0 0 2901 2964 623344603 623344540 1.280000e-22 119
45 TraesCS7A01G514600 chr1D 100.000 64 0 0 2901 2964 212448328 212448391 1.280000e-22 119


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 TraesCS7A01G514600 chr7A 700671086 700678327 7241 False 13374.000000 13374 100.000000 1 7242 1 chr7A.!!$F1 7241
1 TraesCS7A01G514600 chr7A 700673366 700673963 597 False 449.000000 449 93.750000 2281 2878 2 chr7A.!!$F3 597
2 TraesCS7A01G514600 chr7A 631666742 631667332 590 True 410.500000 527 91.616000 3525 4202 2 chr7A.!!$R1 677
3 TraesCS7A01G514600 chr7A 683559572 683560163 591 False 405.000000 510 91.349000 3522 4198 2 chr7A.!!$F2 676
4 TraesCS7A01G514600 chr7A 721272725 721273316 591 False 383.000000 499 89.949500 3522 4198 2 chr7A.!!$F4 676
5 TraesCS7A01G514600 chr7D 610773540 610780695 7155 False 3669.333333 8371 94.879667 1 7088 3 chr7D.!!$F2 7087
6 TraesCS7A01G514600 chr7D 610775863 610776455 592 False 475.000000 484 95.355000 2281 2878 2 chr7D.!!$F3 597
7 TraesCS7A01G514600 chr7B 699373785 699382110 8325 True 1687.285714 4300 93.979000 1 7085 7 chr7B.!!$R2 7084
8 TraesCS7A01G514600 chr7B 703575925 703576506 581 False 859.000000 859 93.310000 2965 3546 1 chr7B.!!$F1 581
9 TraesCS7A01G514600 chr7B 619068755 619069303 548 True 808.000000 808 93.466000 3005 3546 1 chr7B.!!$R1 541
10 TraesCS7A01G514600 chr6B 72315337 72327102 11765 True 883.600000 893 94.073400 2965 3546 5 chr6B.!!$R1 581
11 TraesCS7A01G514600 chr3A 497908610 497909201 591 False 410.500000 527 91.630500 3522 4198 2 chr3A.!!$F1 676
12 TraesCS7A01G514600 chr5A 195558769 195559360 591 False 402.500000 505 91.194500 3522 4198 2 chr5A.!!$F1 676
13 TraesCS7A01G514600 chr1A 174399524 174400115 591 True 397.000000 505 90.822000 3525 4202 2 chr1A.!!$R1 677

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
535 550 0.100503 CCACCAATTTCCCGCGATTC 59.899 55.000 8.23 0.00 0.00 2.52 F
1553 1786 0.533308 ACGCGAAGTGGGCTTGTTAA 60.533 50.000 15.93 0.00 45.78 2.01 F
1982 2224 1.115467 ACTCAAGGATAGCCCAGACG 58.885 55.000 0.00 0.00 37.41 4.18 F
3043 8883 2.026356 TGCCTCCTAGCATGCTTTTACA 60.026 45.455 28.02 13.98 38.00 2.41 F
4365 16053 1.901948 AACCGGTCTCTCGACAGCA 60.902 57.895 8.04 0.00 42.05 4.41 F
4795 16486 0.108186 CAGATGCTGCCGTTCCAGTA 60.108 55.000 0.00 0.00 35.28 2.74 F
5867 17564 0.097674 GCAAATAGACGCAGCACCTG 59.902 55.000 0.00 0.00 34.12 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2224 1.285078 ACTTCCATCTGGCCCCTTAAC 59.715 52.381 0.00 0.00 34.44 2.01 R
3043 8883 5.123936 TGACTATCACGTAGTAGATGCAGT 58.876 41.667 11.94 2.12 43.66 4.40 R
3571 9421 7.330900 ACGATACCTACATACATATAGCACC 57.669 40.000 0.00 0.00 0.00 5.01 R
4795 16486 0.036952 CAGTGCCCTCGTTGATCTGT 60.037 55.000 0.00 0.00 0.00 3.41 R
5866 17563 0.181587 TTGCCGAGGAGGTTTCAACA 59.818 50.000 0.00 0.00 43.70 3.33 R
6019 17716 0.249868 CTGTGAGGGTCTTGAACGCA 60.250 55.000 0.00 0.00 43.06 5.24 R
6913 18713 0.035725 TCGGAACTAGGAGTCGAGCA 60.036 55.000 0.00 0.00 0.00 4.26 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
68 69 1.634753 GATAAACGAAGTCCCGCGC 59.365 57.895 0.00 0.00 45.00 6.86
147 149 1.905215 AGGAAGGTCTCTGGTGATGTG 59.095 52.381 0.00 0.00 0.00 3.21
189 191 2.483188 CGTTGGGACTAGATAGGTTGCC 60.483 54.545 0.00 0.00 0.00 4.52
192 194 2.771943 TGGGACTAGATAGGTTGCCTTG 59.228 50.000 0.00 0.00 34.61 3.61
217 219 2.540101 CCTATTCGCGCTAAAAGACAGG 59.460 50.000 5.56 0.43 0.00 4.00
219 221 0.601576 TTCGCGCTAAAAGACAGGCA 60.602 50.000 5.56 0.00 0.00 4.75
248 250 3.852536 GGCGCGTAGATATAGCAACTTAG 59.147 47.826 8.43 0.00 0.00 2.18
298 304 0.392998 GGACATTCTCCATGTGCCGT 60.393 55.000 0.00 0.00 46.96 5.68
302 308 2.482796 ATTCTCCATGTGCCGTGCCA 62.483 55.000 0.00 0.00 0.00 4.92
342 352 2.542824 CCTTTTGGTGCCGTTTAGTGTG 60.543 50.000 0.00 0.00 34.07 3.82
371 381 5.821995 TGGATGCGTGAAGATGATTTTATCA 59.178 36.000 0.00 0.00 44.55 2.15
409 423 2.526432 GATCGTAGATAGAAGCCCCCA 58.474 52.381 0.00 0.00 45.12 4.96
430 444 4.571984 CCATGTTGTCGTGTGTCATATCAT 59.428 41.667 0.00 0.00 0.00 2.45
453 467 1.283029 TGCCTCCAATCCAAAGAGAGG 59.717 52.381 0.00 0.00 45.74 3.69
527 542 8.896320 AAAGTTTTAATGTACCACCAATTTCC 57.104 30.769 0.00 0.00 0.00 3.13
528 543 6.999950 AGTTTTAATGTACCACCAATTTCCC 58.000 36.000 0.00 0.00 0.00 3.97
530 545 1.470051 ATGTACCACCAATTTCCCGC 58.530 50.000 0.00 0.00 0.00 6.13
531 546 0.956410 TGTACCACCAATTTCCCGCG 60.956 55.000 0.00 0.00 0.00 6.46
534 549 0.610785 ACCACCAATTTCCCGCGATT 60.611 50.000 8.23 0.00 0.00 3.34
535 550 0.100503 CCACCAATTTCCCGCGATTC 59.899 55.000 8.23 0.00 0.00 2.52
537 552 1.201181 CACCAATTTCCCGCGATTCAA 59.799 47.619 8.23 0.00 0.00 2.69
540 555 2.859538 CCAATTTCCCGCGATTCAAATG 59.140 45.455 8.23 0.00 0.00 2.32
542 557 4.362279 CAATTTCCCGCGATTCAAATGAT 58.638 39.130 8.23 0.00 0.00 2.45
543 558 4.654091 ATTTCCCGCGATTCAAATGATT 57.346 36.364 8.23 0.00 0.00 2.57
544 559 4.448537 TTTCCCGCGATTCAAATGATTT 57.551 36.364 8.23 0.00 0.00 2.17
545 560 3.691049 TCCCGCGATTCAAATGATTTC 57.309 42.857 8.23 0.00 0.00 2.17
547 562 3.694072 TCCCGCGATTCAAATGATTTCTT 59.306 39.130 8.23 0.00 0.00 2.52
548 563 4.157656 TCCCGCGATTCAAATGATTTCTTT 59.842 37.500 8.23 0.00 0.00 2.52
551 566 5.801947 CCGCGATTCAAATGATTTCTTTTCT 59.198 36.000 8.23 0.00 0.00 2.52
552 567 6.308766 CCGCGATTCAAATGATTTCTTTTCTT 59.691 34.615 8.23 0.00 0.00 2.52
553 568 7.148755 CCGCGATTCAAATGATTTCTTTTCTTT 60.149 33.333 8.23 0.00 0.00 2.52
554 569 8.216453 CGCGATTCAAATGATTTCTTTTCTTTT 58.784 29.630 0.00 0.00 0.00 2.27
645 878 6.969043 TCCAGACAAATACACCCTATCAAAT 58.031 36.000 0.00 0.00 0.00 2.32
646 879 6.828273 TCCAGACAAATACACCCTATCAAATG 59.172 38.462 0.00 0.00 0.00 2.32
672 905 5.772169 GCCCTAAGCCTATTTTGATGATCTT 59.228 40.000 0.00 0.00 34.35 2.40
686 919 1.909302 TGATCTTGACAGGACTTCCCC 59.091 52.381 0.00 0.00 36.42 4.81
819 1052 3.924686 TCCTCAGTTATTTCGACGAAAGC 59.075 43.478 25.45 17.91 34.92 3.51
997 1230 6.797033 GGTCTTTGTGAATTGAAGTAACATCG 59.203 38.462 0.00 0.00 0.00 3.84
1073 1306 4.145052 GGAAACAATATCAGGGATCCCAC 58.855 47.826 32.69 6.74 38.92 4.61
1138 1371 1.203038 ACAGCAACATGGATCCCAACA 60.203 47.619 9.90 0.00 36.95 3.33
1143 1376 1.843368 ACATGGATCCCAACAAGCTG 58.157 50.000 9.90 0.00 36.95 4.24
1197 1430 9.185680 GTTAGGGTAAACAATATTGTGGATTCT 57.814 33.333 21.46 17.01 41.31 2.40
1511 1744 7.123547 TGTTAGGGGAAACATTGTTATGGATTC 59.876 37.037 1.76 0.00 34.50 2.52
1513 1746 4.962362 GGGGAAACATTGTTATGGATTCCT 59.038 41.667 12.92 0.00 43.86 3.36
1553 1786 0.533308 ACGCGAAGTGGGCTTGTTAA 60.533 50.000 15.93 0.00 45.78 2.01
1630 1866 1.518792 GTTAGAAGACGCCCCGCTC 60.519 63.158 0.00 0.00 0.00 5.03
1695 1931 2.418692 TGGGTGCAACGTATTAGTGTG 58.581 47.619 0.00 0.00 38.12 3.82
1696 1932 2.224329 TGGGTGCAACGTATTAGTGTGT 60.224 45.455 0.00 0.00 38.12 3.72
1697 1933 2.158841 GGGTGCAACGTATTAGTGTGTG 59.841 50.000 0.00 0.00 38.12 3.82
1698 1934 2.803956 GGTGCAACGTATTAGTGTGTGT 59.196 45.455 0.00 0.00 38.12 3.72
1699 1935 3.120786 GGTGCAACGTATTAGTGTGTGTC 60.121 47.826 0.00 0.00 38.12 3.67
1700 1936 3.739300 GTGCAACGTATTAGTGTGTGTCT 59.261 43.478 0.00 0.00 0.00 3.41
1701 1937 4.919168 GTGCAACGTATTAGTGTGTGTCTA 59.081 41.667 0.00 0.00 0.00 2.59
1702 1938 5.575606 GTGCAACGTATTAGTGTGTGTCTAT 59.424 40.000 0.00 0.00 0.00 1.98
1703 1939 6.748658 GTGCAACGTATTAGTGTGTGTCTATA 59.251 38.462 0.00 0.00 0.00 1.31
1704 1940 7.434307 GTGCAACGTATTAGTGTGTGTCTATAT 59.566 37.037 0.00 0.00 0.00 0.86
1705 1941 8.623030 TGCAACGTATTAGTGTGTGTCTATATA 58.377 33.333 0.00 0.00 0.00 0.86
1706 1942 9.622004 GCAACGTATTAGTGTGTGTCTATATAT 57.378 33.333 0.00 0.00 0.00 0.86
1982 2224 1.115467 ACTCAAGGATAGCCCAGACG 58.885 55.000 0.00 0.00 37.41 4.18
2021 2263 5.183904 GGAAGTTGCAAAGAAGACATACCAT 59.816 40.000 0.00 0.00 0.00 3.55
2062 2304 5.965033 ACAAGAGTGATCAGGTATTCCAT 57.035 39.130 0.00 0.00 35.89 3.41
2067 2309 4.649692 AGTGATCAGGTATTCCATGATGC 58.350 43.478 0.00 0.00 34.34 3.91
2074 2316 6.808829 TCAGGTATTCCATGATGCATTTTTC 58.191 36.000 0.00 0.00 35.89 2.29
3043 8883 2.026356 TGCCTCCTAGCATGCTTTTACA 60.026 45.455 28.02 13.98 38.00 2.41
3224 9064 4.348198 CTTACTGAGCTGCCTTTTTAGC 57.652 45.455 0.00 0.00 40.18 3.09
3279 9129 9.301897 GTTATAGAATGCCTCCCAAAAATCTAT 57.698 33.333 0.00 0.00 34.33 1.98
4365 16053 1.901948 AACCGGTCTCTCGACAGCA 60.902 57.895 8.04 0.00 42.05 4.41
4446 16134 5.180492 CCAAGAAGCGTAAAACCATGTCTAA 59.820 40.000 0.00 0.00 0.00 2.10
4447 16135 6.293735 CCAAGAAGCGTAAAACCATGTCTAAA 60.294 38.462 0.00 0.00 0.00 1.85
4448 16136 6.481954 AGAAGCGTAAAACCATGTCTAAAG 57.518 37.500 0.00 0.00 0.00 1.85
4713 16404 2.124403 GGATGTGAGCCAGGCAGG 60.124 66.667 15.80 0.00 41.84 4.85
4795 16486 0.108186 CAGATGCTGCCGTTCCAGTA 60.108 55.000 0.00 0.00 35.28 2.74
4804 16498 2.000447 GCCGTTCCAGTACAGATCAAC 59.000 52.381 0.00 0.00 0.00 3.18
5179 16876 5.938125 ACAGAAATACGTTGCCAATTACTCT 59.062 36.000 0.00 0.00 0.00 3.24
5218 16915 2.815503 TGGAAGCACTGTGAATCACATG 59.184 45.455 17.10 16.51 43.71 3.21
5370 17067 1.089920 CACATGCAGAGTAACCAGGC 58.910 55.000 0.00 0.00 0.00 4.85
5379 17076 2.030958 GTAACCAGGCGAACACCGG 61.031 63.158 0.00 0.00 39.04 5.28
5393 17090 2.428491 ACACCGGCATTCGATTACAAA 58.572 42.857 0.00 0.00 42.43 2.83
5444 17141 0.328258 AACCGTGCAGGGAAATAGCT 59.672 50.000 31.22 4.45 46.96 3.32
5671 17368 1.171308 CACAGCTGATCCAGGGTTTG 58.829 55.000 23.35 0.00 31.21 2.93
5765 17462 4.713792 ATCCAACAGTCTGGTTTCTCTT 57.286 40.909 4.53 0.00 37.74 2.85
5800 17497 2.034532 CATGGAGCACCTGCCACA 59.965 61.111 0.71 0.00 43.38 4.17
5812 17509 3.673599 GCCACAGGCTTCTGGAAC 58.326 61.111 11.49 0.00 46.69 3.62
5820 17517 4.460382 CACAGGCTTCTGGAACAATAATGT 59.540 41.667 0.00 0.00 42.60 2.71
5837 17534 4.410492 AATGTTGAACATCAGAAGTCGC 57.590 40.909 11.70 0.00 37.97 5.19
5839 17536 2.143122 GTTGAACATCAGAAGTCGCCA 58.857 47.619 0.00 0.00 0.00 5.69
5841 17538 0.723981 GAACATCAGAAGTCGCCAGC 59.276 55.000 0.00 0.00 0.00 4.85
5866 17563 0.321564 TGCAAATAGACGCAGCACCT 60.322 50.000 0.00 0.00 33.34 4.00
5867 17564 0.097674 GCAAATAGACGCAGCACCTG 59.902 55.000 0.00 0.00 34.12 4.00
5871 17568 0.608130 ATAGACGCAGCACCTGTTGA 59.392 50.000 0.00 0.00 33.43 3.18
5896 17593 0.243636 CCTCGGCAAATGTTGAACCC 59.756 55.000 0.00 0.00 0.00 4.11
5917 17614 3.865383 TATGCGCCTGCCCCAGAG 61.865 66.667 4.18 0.00 41.78 3.35
5935 17632 1.069049 GAGCCTGTTTTGCCAACACAT 59.931 47.619 0.00 0.00 0.00 3.21
6019 17716 3.118738 GGTCAGACCCATGTATCGAGTTT 60.119 47.826 8.65 0.00 30.04 2.66
6156 17853 5.913514 CCGTTGACGATACTAGAAACCATAG 59.086 44.000 4.91 0.00 43.02 2.23
6181 17878 0.896940 ATGTCAACCAAGGCAGCCAG 60.897 55.000 15.80 5.46 0.00 4.85
6242 17939 0.916358 CTGGTTCCCTCCCCAGTGAT 60.916 60.000 0.00 0.00 42.72 3.06
6247 17944 3.813724 CCTCCCCAGTGATGCCCC 61.814 72.222 0.00 0.00 0.00 5.80
6289 17986 0.305617 GCTTGTGCTTGCAAAAAGGC 59.694 50.000 16.10 0.32 36.03 4.35
6342 18090 1.391826 GCTCGAAGCAGTAGTCTTTGC 59.608 52.381 2.53 1.79 41.89 3.68
6346 18094 3.128068 TCGAAGCAGTAGTCTTTGCGATA 59.872 43.478 0.00 0.00 44.80 2.92
6630 18406 2.147958 TGCGGATAATAAATGGCGGTC 58.852 47.619 0.00 0.00 0.00 4.79
6631 18407 1.467342 GCGGATAATAAATGGCGGTCC 59.533 52.381 0.00 0.00 0.00 4.46
6632 18408 1.730064 CGGATAATAAATGGCGGTCCG 59.270 52.381 6.99 6.99 40.74 4.79
6633 18409 3.048337 GGATAATAAATGGCGGTCCGA 57.952 47.619 17.49 0.00 34.14 4.55
6634 18410 3.404899 GGATAATAAATGGCGGTCCGAA 58.595 45.455 17.49 1.85 34.14 4.30
6635 18411 4.007659 GGATAATAAATGGCGGTCCGAAT 58.992 43.478 17.49 4.60 34.14 3.34
6636 18412 4.094442 GGATAATAAATGGCGGTCCGAATC 59.906 45.833 17.49 4.03 34.14 2.52
6637 18413 1.508632 ATAAATGGCGGTCCGAATCG 58.491 50.000 17.49 0.00 34.14 3.34
6638 18414 0.460722 TAAATGGCGGTCCGAATCGA 59.539 50.000 17.49 0.00 34.14 3.59
6639 18415 1.087771 AAATGGCGGTCCGAATCGAC 61.088 55.000 17.49 0.20 34.14 4.20
6640 18416 3.375239 TGGCGGTCCGAATCGACA 61.375 61.111 17.49 0.00 42.60 4.35
6641 18417 2.582498 GGCGGTCCGAATCGACAG 60.582 66.667 17.49 2.78 34.24 3.51
6642 18418 3.255379 GCGGTCCGAATCGACAGC 61.255 66.667 17.49 9.18 44.59 4.40
6643 18419 2.949678 CGGTCCGAATCGACAGCG 60.950 66.667 4.91 7.98 34.24 5.18
6644 18420 2.181021 GGTCCGAATCGACAGCGT 59.819 61.111 3.36 0.00 38.98 5.07
6645 18421 1.872679 GGTCCGAATCGACAGCGTC 60.873 63.158 3.36 0.00 38.98 5.19
6650 18426 0.640768 CGAATCGACAGCGTCTTTCC 59.359 55.000 0.00 0.00 38.98 3.13
6733 18512 8.890472 ACCATTGCCAGTATCTAATATTCCTTA 58.110 33.333 0.00 0.00 0.00 2.69
6761 18544 9.622004 CTAAAGTGCATTTTCATATGATGGATC 57.378 33.333 10.79 0.00 32.01 3.36
6808 18591 5.010012 CCCTTGCTCATTGTTTTAGTGTCTT 59.990 40.000 0.00 0.00 0.00 3.01
6877 18661 4.970003 CGTGAATTGGTGTCTTTGAAGTTC 59.030 41.667 0.00 0.00 0.00 3.01
6892 18692 4.894798 GAAGTTCTGCTTCGTGTTCTAG 57.105 45.455 0.00 0.00 43.41 2.43
6893 18693 4.299978 GAAGTTCTGCTTCGTGTTCTAGT 58.700 43.478 0.00 0.00 43.41 2.57
6894 18694 5.449107 AAGTTCTGCTTCGTGTTCTAGTA 57.551 39.130 0.00 0.00 30.06 1.82
6895 18695 4.796369 AGTTCTGCTTCGTGTTCTAGTAC 58.204 43.478 0.00 0.00 0.00 2.73
6896 18696 3.466712 TCTGCTTCGTGTTCTAGTACG 57.533 47.619 9.53 9.53 41.38 3.67
6897 18697 3.069289 TCTGCTTCGTGTTCTAGTACGA 58.931 45.455 12.95 12.95 46.31 3.43
6906 18706 7.369803 TCGTGTTCTAGTACGAATTAGTTCT 57.630 36.000 14.05 0.00 45.18 3.01
6907 18707 7.810658 TCGTGTTCTAGTACGAATTAGTTCTT 58.189 34.615 14.05 0.00 45.18 2.52
6908 18708 7.747799 TCGTGTTCTAGTACGAATTAGTTCTTG 59.252 37.037 14.05 2.51 45.18 3.02
6909 18709 7.747799 CGTGTTCTAGTACGAATTAGTTCTTGA 59.252 37.037 3.36 4.65 42.54 3.02
6910 18710 9.570488 GTGTTCTAGTACGAATTAGTTCTTGAT 57.430 33.333 9.28 0.00 32.00 2.57
6914 18714 9.952188 TCTAGTACGAATTAGTTCTTGATGATG 57.048 33.333 3.36 0.00 32.00 3.07
6916 18716 7.268586 AGTACGAATTAGTTCTTGATGATGCT 58.731 34.615 0.00 0.00 32.00 3.79
6917 18717 6.595772 ACGAATTAGTTCTTGATGATGCTC 57.404 37.500 0.00 0.00 32.00 4.26
6920 18720 6.561166 CGAATTAGTTCTTGATGATGCTCGAC 60.561 42.308 0.00 0.00 32.00 4.20
6922 18722 3.779759 AGTTCTTGATGATGCTCGACTC 58.220 45.455 0.00 0.00 0.00 3.36
6923 18723 2.863137 GTTCTTGATGATGCTCGACTCC 59.137 50.000 0.00 0.00 0.00 3.85
6924 18724 2.382882 TCTTGATGATGCTCGACTCCT 58.617 47.619 0.00 0.00 0.00 3.69
6925 18725 3.555966 TCTTGATGATGCTCGACTCCTA 58.444 45.455 0.00 0.00 0.00 2.94
6965 18765 2.149578 CTCCTGTTCAAAGCTCACCAG 58.850 52.381 0.00 0.00 0.00 4.00
6980 18780 4.142730 GCTCACCAGTTAAATTCTCAGCAG 60.143 45.833 0.00 0.00 0.00 4.24
7059 18863 8.630054 ACAAACTACAGAAAAATAGCACCATA 57.370 30.769 0.00 0.00 0.00 2.74
7076 18880 7.820648 AGCACCATAAGTCAGTTAAAATCTTG 58.179 34.615 0.00 0.00 0.00 3.02
7088 18892 5.700832 AGTTAAAATCTTGAGTGCGATGACA 59.299 36.000 0.00 0.00 0.00 3.58
7089 18893 6.204688 AGTTAAAATCTTGAGTGCGATGACAA 59.795 34.615 0.00 0.00 0.00 3.18
7090 18894 4.675190 AAATCTTGAGTGCGATGACAAG 57.325 40.909 0.00 0.00 40.37 3.16
7091 18895 1.432514 TCTTGAGTGCGATGACAAGC 58.567 50.000 0.00 0.00 39.33 4.01
7092 18896 1.150827 CTTGAGTGCGATGACAAGCA 58.849 50.000 5.04 5.04 41.55 3.91
7096 18900 4.453093 TGCGATGACAAGCACACA 57.547 50.000 5.04 0.00 38.59 3.72
7097 18901 2.931246 TGCGATGACAAGCACACAT 58.069 47.368 5.04 0.00 38.59 3.21
7098 18902 2.091852 TGCGATGACAAGCACACATA 57.908 45.000 5.04 0.00 38.59 2.29
7099 18903 2.631267 TGCGATGACAAGCACACATAT 58.369 42.857 5.04 0.00 38.59 1.78
7100 18904 3.009026 TGCGATGACAAGCACACATATT 58.991 40.909 5.04 0.00 38.59 1.28
7101 18905 3.181508 TGCGATGACAAGCACACATATTG 60.182 43.478 5.04 0.00 38.59 1.90
7102 18906 3.181507 GCGATGACAAGCACACATATTGT 60.182 43.478 0.00 0.00 39.76 2.71
7113 18917 2.168384 CACATATTGTGTCGCAAAGCG 58.832 47.619 4.83 4.83 45.70 4.68
7114 18918 3.038047 CACATATTGTGTCGCAAAGCGG 61.038 50.000 11.72 0.00 45.01 5.52
7129 18933 2.103143 CGGGCAGCAGTACTCTCG 59.897 66.667 0.00 0.00 0.00 4.04
7130 18934 2.202810 GGGCAGCAGTACTCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
7131 18935 2.580867 GGCAGCAGTACTCTCGCG 60.581 66.667 0.00 0.00 0.00 5.87
7132 18936 2.179517 GCAGCAGTACTCTCGCGT 59.820 61.111 5.77 0.00 0.00 6.01
7133 18937 1.444553 GCAGCAGTACTCTCGCGTT 60.445 57.895 5.77 0.00 0.00 4.84
7134 18938 1.406970 GCAGCAGTACTCTCGCGTTC 61.407 60.000 5.77 0.00 0.00 3.95
7135 18939 0.109735 CAGCAGTACTCTCGCGTTCA 60.110 55.000 5.77 0.00 0.00 3.18
7136 18940 0.169230 AGCAGTACTCTCGCGTTCAG 59.831 55.000 5.77 2.87 0.00 3.02
7137 18941 0.109689 GCAGTACTCTCGCGTTCAGT 60.110 55.000 5.77 9.24 0.00 3.41
7138 18942 1.129998 GCAGTACTCTCGCGTTCAGTA 59.870 52.381 5.77 8.19 0.00 2.74
7139 18943 2.771689 CAGTACTCTCGCGTTCAGTAC 58.228 52.381 24.66 24.66 41.91 2.73
7151 18955 1.060698 GTTCAGTACGAAGAATGCGGC 59.939 52.381 0.00 0.00 46.02 6.53
7152 18956 0.800683 TCAGTACGAAGAATGCGGCG 60.801 55.000 0.51 0.51 46.02 6.46
7153 18957 0.800683 CAGTACGAAGAATGCGGCGA 60.801 55.000 12.98 0.00 46.02 5.54
7154 18958 0.108992 AGTACGAAGAATGCGGCGAA 60.109 50.000 12.98 0.00 46.02 4.70
7155 18959 0.297820 GTACGAAGAATGCGGCGAAG 59.702 55.000 12.98 0.00 46.02 3.79
7156 18960 0.108992 TACGAAGAATGCGGCGAAGT 60.109 50.000 12.98 0.00 46.02 3.01
7157 18961 0.949105 ACGAAGAATGCGGCGAAGTT 60.949 50.000 12.98 0.37 46.02 2.66
7158 18962 0.996462 CGAAGAATGCGGCGAAGTTA 59.004 50.000 12.98 0.00 29.15 2.24
7159 18963 1.392168 CGAAGAATGCGGCGAAGTTAA 59.608 47.619 12.98 0.00 29.15 2.01
7160 18964 2.770532 GAAGAATGCGGCGAAGTTAAC 58.229 47.619 12.98 0.00 0.00 2.01
7161 18965 2.094762 AGAATGCGGCGAAGTTAACT 57.905 45.000 12.98 1.12 0.00 2.24
7162 18966 2.423577 AGAATGCGGCGAAGTTAACTT 58.576 42.857 20.67 20.67 39.23 2.66
7163 18967 2.415512 AGAATGCGGCGAAGTTAACTTC 59.584 45.455 30.40 30.40 46.63 3.01
7172 18976 3.808116 GAAGTTAACTTCCGGCAGAAC 57.192 47.619 30.17 9.13 44.93 3.01
7173 18977 2.180432 AGTTAACTTCCGGCAGAACC 57.820 50.000 8.52 0.00 0.00 3.62
7174 18978 1.162698 GTTAACTTCCGGCAGAACCC 58.837 55.000 8.52 0.00 33.26 4.11
7175 18979 0.037160 TTAACTTCCGGCAGAACCCC 59.963 55.000 8.52 0.00 33.26 4.95
7176 18980 1.844544 TAACTTCCGGCAGAACCCCC 61.845 60.000 8.52 0.00 33.26 5.40
7201 19005 7.455641 CGATAGGATTCCAGTACTATTGTCT 57.544 40.000 5.29 0.00 0.00 3.41
7202 19006 7.887381 CGATAGGATTCCAGTACTATTGTCTT 58.113 38.462 5.29 0.00 0.00 3.01
7203 19007 8.024285 CGATAGGATTCCAGTACTATTGTCTTC 58.976 40.741 5.29 0.00 0.00 2.87
7204 19008 8.783660 ATAGGATTCCAGTACTATTGTCTTCA 57.216 34.615 5.29 0.00 0.00 3.02
7205 19009 7.118496 AGGATTCCAGTACTATTGTCTTCAG 57.882 40.000 5.29 0.00 0.00 3.02
7206 19010 6.897966 AGGATTCCAGTACTATTGTCTTCAGA 59.102 38.462 5.29 0.00 0.00 3.27
7207 19011 7.566879 AGGATTCCAGTACTATTGTCTTCAGAT 59.433 37.037 5.29 0.00 0.00 2.90
7208 19012 7.655328 GGATTCCAGTACTATTGTCTTCAGATG 59.345 40.741 0.00 0.00 0.00 2.90
7209 19013 7.718334 TTCCAGTACTATTGTCTTCAGATGA 57.282 36.000 0.00 0.00 0.00 2.92
7210 19014 7.340122 TCCAGTACTATTGTCTTCAGATGAG 57.660 40.000 0.00 0.00 0.00 2.90
7211 19015 6.892456 TCCAGTACTATTGTCTTCAGATGAGT 59.108 38.462 0.00 0.00 0.00 3.41
7212 19016 8.053355 TCCAGTACTATTGTCTTCAGATGAGTA 58.947 37.037 0.00 0.00 0.00 2.59
7213 19017 8.855110 CCAGTACTATTGTCTTCAGATGAGTAT 58.145 37.037 0.00 0.00 0.00 2.12
7214 19018 9.891828 CAGTACTATTGTCTTCAGATGAGTATC 57.108 37.037 0.00 0.00 0.00 2.24
7233 19037 9.276590 TGAGTATCAAGGCAATGTGATATAAAG 57.723 33.333 0.00 0.00 45.97 1.85
7234 19038 8.627208 AGTATCAAGGCAATGTGATATAAAGG 57.373 34.615 0.00 0.00 38.60 3.11
7235 19039 8.220559 AGTATCAAGGCAATGTGATATAAAGGT 58.779 33.333 0.00 0.00 38.60 3.50
7236 19040 7.902920 ATCAAGGCAATGTGATATAAAGGTT 57.097 32.000 0.00 0.00 32.68 3.50
7237 19041 7.333528 TCAAGGCAATGTGATATAAAGGTTC 57.666 36.000 0.00 0.00 0.00 3.62
7238 19042 6.321181 TCAAGGCAATGTGATATAAAGGTTCC 59.679 38.462 0.00 0.00 0.00 3.62
7239 19043 5.140454 AGGCAATGTGATATAAAGGTTCCC 58.860 41.667 0.00 0.00 0.00 3.97
7240 19044 4.892934 GGCAATGTGATATAAAGGTTCCCA 59.107 41.667 0.00 0.00 0.00 4.37
7241 19045 5.539955 GGCAATGTGATATAAAGGTTCCCAT 59.460 40.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.119708 GCAAGCTCTGTACCAATTTGAGG 60.120 47.826 0.00 0.00 0.00 3.86
50 51 1.634753 GCGCGGGACTTCGTTTATC 59.365 57.895 8.83 0.00 0.00 1.75
120 122 4.467795 TCACCAGAGACCTTCCTTTCTATG 59.532 45.833 0.00 0.00 32.00 2.23
189 191 5.290158 TCTTTTAGCGCGAATAGGTAACAAG 59.710 40.000 12.10 9.86 41.41 3.16
192 194 4.563976 TGTCTTTTAGCGCGAATAGGTAAC 59.436 41.667 12.10 10.88 32.23 2.50
219 221 1.731433 ATATCTACGCGCCACCACGT 61.731 55.000 5.73 0.00 45.85 4.49
331 337 3.426159 GCATCCATCAACACACTAAACGG 60.426 47.826 0.00 0.00 0.00 4.44
342 352 2.938451 TCATCTTCACGCATCCATCAAC 59.062 45.455 0.00 0.00 0.00 3.18
371 381 0.042131 TCGACACCTTACCCCTCCAT 59.958 55.000 0.00 0.00 0.00 3.41
378 388 4.993584 TCTATCTACGATCGACACCTTACC 59.006 45.833 24.34 0.00 0.00 2.85
409 423 4.571984 CCATGATATGACACACGACAACAT 59.428 41.667 0.00 0.00 0.00 2.71
453 467 0.108851 AAATCGCGGGAAATTGGTGC 60.109 50.000 6.13 0.00 0.00 5.01
524 539 3.694072 AGAAATCATTTGAATCGCGGGAA 59.306 39.130 6.13 0.00 0.00 3.97
525 540 3.278574 AGAAATCATTTGAATCGCGGGA 58.721 40.909 6.13 4.03 0.00 5.14
526 541 3.698029 AGAAATCATTTGAATCGCGGG 57.302 42.857 6.13 0.00 0.00 6.13
527 542 5.801947 AGAAAAGAAATCATTTGAATCGCGG 59.198 36.000 6.13 0.00 0.00 6.46
528 543 6.859715 AGAAAAGAAATCATTTGAATCGCG 57.140 33.333 0.00 0.00 0.00 5.87
567 582 5.721480 CCATCTAGGATGTATGTGGTCCATA 59.279 44.000 0.00 0.00 41.22 2.74
569 584 3.903714 CCATCTAGGATGTATGTGGTCCA 59.096 47.826 6.75 0.00 41.22 4.02
573 588 2.909006 AGCCCATCTAGGATGTATGTGG 59.091 50.000 6.75 2.27 41.22 4.17
574 589 3.935315 CAGCCCATCTAGGATGTATGTG 58.065 50.000 6.75 0.00 38.54 3.21
645 878 3.730215 TCAAAATAGGCTTAGGGCACA 57.270 42.857 0.10 0.00 44.01 4.57
646 879 4.207165 TCATCAAAATAGGCTTAGGGCAC 58.793 43.478 0.10 0.00 44.01 5.01
813 1046 8.594881 AGACTATATTTCCAAGTATGCTTTCG 57.405 34.615 0.00 0.00 31.49 3.46
948 1181 1.609580 CCAATTGGCAATTGCACAGCT 60.610 47.619 36.11 14.15 45.36 4.24
997 1230 2.362717 AGCTCCCGCTAGAAGACATAAC 59.637 50.000 0.00 0.00 46.79 1.89
1073 1306 4.183865 TGTTCTAGCAGATGAATTGTCGG 58.816 43.478 0.00 0.00 0.00 4.79
1197 1430 5.483937 TGCTTTAGAAGATGAACCCTCACTA 59.516 40.000 0.00 0.00 33.30 2.74
1553 1786 4.103311 GGGTATCCATAGCAGAGTTTCCTT 59.897 45.833 0.00 0.00 32.63 3.36
1630 1866 8.358148 AGAATTTAGAGATTTGCATGCCTTATG 58.642 33.333 16.68 0.00 39.88 1.90
1754 1995 7.170965 AGCAAGGAAAAGAGAAGTGATGATTA 58.829 34.615 0.00 0.00 0.00 1.75
1982 2224 1.285078 ACTTCCATCTGGCCCCTTAAC 59.715 52.381 0.00 0.00 34.44 2.01
2021 2263 9.667107 ACTCTTGTAATTCAATCGATCCTTTAA 57.333 29.630 0.00 0.00 35.35 1.52
2062 2304 1.826720 GGCAGGAGGAAAAATGCATCA 59.173 47.619 0.00 0.00 40.46 3.07
2067 2309 1.475682 GAGCAGGCAGGAGGAAAAATG 59.524 52.381 0.00 0.00 0.00 2.32
2074 2316 5.690464 ATTTATATAGAGCAGGCAGGAGG 57.310 43.478 0.00 0.00 0.00 4.30
3043 8883 5.123936 TGACTATCACGTAGTAGATGCAGT 58.876 41.667 11.94 2.12 43.66 4.40
3215 9055 8.649973 AGTATATCTTCAGAACGCTAAAAAGG 57.350 34.615 0.00 0.00 0.00 3.11
3224 9064 7.911205 AGAAAACTCGAGTATATCTTCAGAACG 59.089 37.037 20.39 0.00 0.00 3.95
3279 9129 8.091449 AGTACACAAAACAATGTCAAGGAAAAA 58.909 29.630 0.00 0.00 0.00 1.94
3568 9418 9.286170 CGATACCTACATACATATAGCACCTAT 57.714 37.037 0.00 0.00 0.00 2.57
3571 9421 7.330900 ACGATACCTACATACATATAGCACC 57.669 40.000 0.00 0.00 0.00 5.01
3577 9427 9.964354 TGGTAACTACGATACCTACATACATAT 57.036 33.333 4.53 0.00 42.73 1.78
4365 16053 3.526841 AGATCTCTTTCCCCTTGAAGCAT 59.473 43.478 0.00 0.00 33.63 3.79
4446 16134 0.182775 AGGTGTGGCGACCTTTTCTT 59.817 50.000 2.24 0.00 44.53 2.52
4447 16135 1.837090 AGGTGTGGCGACCTTTTCT 59.163 52.632 2.24 0.00 44.53 2.52
4448 16136 4.475527 AGGTGTGGCGACCTTTTC 57.524 55.556 2.24 0.00 44.53 2.29
4656 16347 3.931578 AGCTGTACCTGATTGACAAGAC 58.068 45.455 0.00 0.00 0.00 3.01
4713 16404 3.184986 GGTTTGCATTTGAATGACAGTGC 59.815 43.478 7.86 0.00 38.70 4.40
4795 16486 0.036952 CAGTGCCCTCGTTGATCTGT 60.037 55.000 0.00 0.00 0.00 3.41
4804 16498 1.811266 CCGATTGACAGTGCCCTCG 60.811 63.158 0.00 0.00 0.00 4.63
5114 16811 2.612212 GTGACTTTTCTTGGCTCGAACA 59.388 45.455 0.00 0.00 0.00 3.18
5179 16876 2.107378 TCCATGGCTTTGTGGTAACTGA 59.893 45.455 6.96 0.00 36.84 3.41
5218 16915 3.976942 CAGTGTGTTGCTGATTAGTTTGC 59.023 43.478 0.00 0.00 36.12 3.68
5370 17067 1.005347 GTAATCGAATGCCGGTGTTCG 60.005 52.381 26.81 26.81 46.20 3.95
5379 17076 5.909610 GCTTGACCTATTTGTAATCGAATGC 59.090 40.000 0.00 0.00 0.00 3.56
5444 17141 0.900182 ACCAGCTGTGACCGATCAGA 60.900 55.000 13.81 0.00 34.75 3.27
5481 17178 9.003658 AGTATTCCTGAATAGTTTGTGTTTGAG 57.996 33.333 0.00 0.00 34.24 3.02
5671 17368 3.412386 AGCCTGTATTTGGTTGACAGTC 58.588 45.455 0.00 0.00 39.16 3.51
5765 17462 3.992641 TCCCCACTCAGGAGCCGA 61.993 66.667 0.00 0.00 41.22 5.54
5800 17497 5.324409 TCAACATTATTGTTCCAGAAGCCT 58.676 37.500 0.02 0.00 44.24 4.58
5812 17509 6.467047 GCGACTTCTGATGTTCAACATTATTG 59.533 38.462 4.04 0.00 39.27 1.90
5820 17517 2.416747 CTGGCGACTTCTGATGTTCAA 58.583 47.619 0.00 0.00 0.00 2.69
5837 17534 1.869767 GTCTATTTGCATCGGAGCTGG 59.130 52.381 0.00 0.00 34.99 4.85
5839 17536 1.858091 CGTCTATTTGCATCGGAGCT 58.142 50.000 0.00 0.00 34.99 4.09
5841 17538 1.524355 CTGCGTCTATTTGCATCGGAG 59.476 52.381 0.00 0.00 40.89 4.63
5866 17563 0.181587 TTGCCGAGGAGGTTTCAACA 59.818 50.000 0.00 0.00 43.70 3.33
5867 17564 1.314730 TTTGCCGAGGAGGTTTCAAC 58.685 50.000 0.00 0.00 43.70 3.18
5871 17568 1.613437 CAACATTTGCCGAGGAGGTTT 59.387 47.619 0.00 0.00 43.70 3.27
5917 17614 2.035832 AGTATGTGTTGGCAAAACAGGC 59.964 45.455 25.93 20.06 0.00 4.85
5935 17632 3.390521 CCTCCAGGCACCGCAGTA 61.391 66.667 0.00 0.00 0.00 2.74
6019 17716 0.249868 CTGTGAGGGTCTTGAACGCA 60.250 55.000 0.00 0.00 43.06 5.24
6247 17944 2.686915 GTTCATCCATTCAGCCTTCCAG 59.313 50.000 0.00 0.00 0.00 3.86
6289 17986 3.204526 GGCATTCCTCTCTGAACATCAG 58.795 50.000 0.88 0.88 45.59 2.90
6346 18094 8.960591 CCCTTTCACAAAATATATCACAGAAGT 58.039 33.333 0.00 0.00 0.00 3.01
6503 18263 0.322322 TTACCGGGCAACTACACAGG 59.678 55.000 6.32 0.00 0.00 4.00
6630 18406 0.640768 GAAAGACGCTGTCGATTCGG 59.359 55.000 6.18 0.00 37.67 4.30
6631 18407 0.640768 GGAAAGACGCTGTCGATTCG 59.359 55.000 0.00 0.00 37.67 3.34
6632 18408 0.640768 CGGAAAGACGCTGTCGATTC 59.359 55.000 15.02 15.02 37.67 2.52
6633 18409 2.738147 CGGAAAGACGCTGTCGATT 58.262 52.632 0.00 3.71 37.67 3.34
6634 18410 4.478195 CGGAAAGACGCTGTCGAT 57.522 55.556 0.00 0.00 37.67 3.59
6642 18418 0.512952 CAGGAACTTGCGGAAAGACG 59.487 55.000 1.86 0.00 39.38 4.18
6643 18419 0.875059 CCAGGAACTTGCGGAAAGAC 59.125 55.000 1.86 0.00 39.38 3.01
6644 18420 0.762418 TCCAGGAACTTGCGGAAAGA 59.238 50.000 1.86 0.00 39.38 2.52
6645 18421 0.875059 GTCCAGGAACTTGCGGAAAG 59.125 55.000 0.00 0.00 42.07 2.62
6650 18426 0.804989 GAATGGTCCAGGAACTTGCG 59.195 55.000 5.94 0.00 34.60 4.85
6733 18512 8.970020 TCCATCATATGAAAATGCACTTTAGTT 58.030 29.630 9.99 0.00 0.00 2.24
6808 18591 6.540914 ACTTTAGAACCGAAATGAAGTGTTCA 59.459 34.615 0.00 0.00 45.01 3.18
6877 18661 3.466712 TCGTACTAGAACACGAAGCAG 57.533 47.619 13.74 0.00 43.63 4.24
6891 18691 7.268586 AGCATCATCAAGAACTAATTCGTACT 58.731 34.615 0.00 0.00 40.04 2.73
6892 18692 7.470289 AGCATCATCAAGAACTAATTCGTAC 57.530 36.000 0.00 0.00 40.04 3.67
6893 18693 6.417930 CGAGCATCATCAAGAACTAATTCGTA 59.582 38.462 0.00 0.00 35.82 3.43
6894 18694 5.233050 CGAGCATCATCAAGAACTAATTCGT 59.767 40.000 0.00 0.00 35.82 3.85
6895 18695 5.460091 TCGAGCATCATCAAGAACTAATTCG 59.540 40.000 0.00 0.00 35.82 3.34
6896 18696 6.478344 AGTCGAGCATCATCAAGAACTAATTC 59.522 38.462 0.00 0.00 33.17 2.17
6897 18697 6.344500 AGTCGAGCATCATCAAGAACTAATT 58.656 36.000 0.00 0.00 33.17 1.40
6898 18698 5.911752 AGTCGAGCATCATCAAGAACTAAT 58.088 37.500 0.00 0.00 33.17 1.73
6901 18701 3.430098 GGAGTCGAGCATCATCAAGAACT 60.430 47.826 0.00 0.00 33.17 3.01
6902 18702 2.863137 GGAGTCGAGCATCATCAAGAAC 59.137 50.000 0.00 0.00 33.17 3.01
6903 18703 2.762887 AGGAGTCGAGCATCATCAAGAA 59.237 45.455 0.00 0.00 33.17 2.52
6905 18705 2.886862 AGGAGTCGAGCATCATCAAG 57.113 50.000 0.00 0.00 33.17 3.02
6906 18706 3.291584 ACTAGGAGTCGAGCATCATCAA 58.708 45.455 0.00 0.00 33.17 2.57
6907 18707 2.937519 ACTAGGAGTCGAGCATCATCA 58.062 47.619 0.00 0.00 33.17 3.07
6908 18708 3.305064 GGAACTAGGAGTCGAGCATCATC 60.305 52.174 0.00 0.00 33.17 2.92
6909 18709 2.625790 GGAACTAGGAGTCGAGCATCAT 59.374 50.000 0.00 0.00 33.17 2.45
6910 18710 2.025155 GGAACTAGGAGTCGAGCATCA 58.975 52.381 0.00 0.00 33.17 3.07
6913 18713 0.035725 TCGGAACTAGGAGTCGAGCA 60.036 55.000 0.00 0.00 0.00 4.26
6914 18714 1.310904 ATCGGAACTAGGAGTCGAGC 58.689 55.000 0.00 0.00 29.92 5.03
6916 18716 2.681848 GTGAATCGGAACTAGGAGTCGA 59.318 50.000 0.00 0.00 30.76 4.20
6917 18717 2.422479 TGTGAATCGGAACTAGGAGTCG 59.578 50.000 0.00 0.00 30.36 4.18
6920 18720 2.166459 TGCTGTGAATCGGAACTAGGAG 59.834 50.000 0.00 0.00 0.00 3.69
6922 18722 2.271800 GTGCTGTGAATCGGAACTAGG 58.728 52.381 0.00 0.00 0.00 3.02
6923 18723 2.668457 GTGTGCTGTGAATCGGAACTAG 59.332 50.000 0.00 0.00 32.27 2.57
6924 18724 2.611971 GGTGTGCTGTGAATCGGAACTA 60.612 50.000 0.00 0.00 32.27 2.24
6925 18725 1.512926 GTGTGCTGTGAATCGGAACT 58.487 50.000 0.00 0.00 32.27 3.01
6965 18765 7.748847 TCGGTTATTTCTGCTGAGAATTTAAC 58.251 34.615 0.00 0.00 38.05 2.01
7059 18863 5.758296 TCGCACTCAAGATTTTAACTGACTT 59.242 36.000 0.00 0.00 0.00 3.01
7106 18910 3.055719 TACTGCTGCCCGCTTTGC 61.056 61.111 0.00 0.00 40.11 3.68
7107 18911 1.639298 GAGTACTGCTGCCCGCTTTG 61.639 60.000 0.00 0.00 40.11 2.77
7108 18912 1.376037 GAGTACTGCTGCCCGCTTT 60.376 57.895 0.00 0.00 40.11 3.51
7109 18913 2.232298 GAGAGTACTGCTGCCCGCTT 62.232 60.000 0.00 0.00 40.11 4.68
7110 18914 2.681778 AGAGTACTGCTGCCCGCT 60.682 61.111 0.00 0.00 40.11 5.52
7111 18915 2.202810 GAGAGTACTGCTGCCCGC 60.203 66.667 0.00 0.00 39.77 6.13
7112 18916 2.103143 CGAGAGTACTGCTGCCCG 59.897 66.667 0.00 0.00 0.00 6.13
7113 18917 2.202810 GCGAGAGTACTGCTGCCC 60.203 66.667 0.00 0.00 0.00 5.36
7114 18918 2.580867 CGCGAGAGTACTGCTGCC 60.581 66.667 0.00 0.00 0.00 4.85
7115 18919 1.406970 GAACGCGAGAGTACTGCTGC 61.407 60.000 15.93 0.00 0.00 5.25
7116 18920 0.109735 TGAACGCGAGAGTACTGCTG 60.110 55.000 15.93 0.00 0.00 4.41
7117 18921 0.169230 CTGAACGCGAGAGTACTGCT 59.831 55.000 15.93 0.00 0.00 4.24
7118 18922 0.109689 ACTGAACGCGAGAGTACTGC 60.110 55.000 15.93 0.00 0.00 4.40
7119 18923 2.771689 GTACTGAACGCGAGAGTACTG 58.228 52.381 25.66 13.08 39.24 2.74
7120 18924 1.392853 CGTACTGAACGCGAGAGTACT 59.607 52.381 27.70 0.00 46.10 2.73
7121 18925 1.795536 CGTACTGAACGCGAGAGTAC 58.204 55.000 24.31 24.31 46.10 2.73
7131 18935 1.060698 GCCGCATTCTTCGTACTGAAC 59.939 52.381 0.00 0.00 31.87 3.18
7132 18936 1.355971 GCCGCATTCTTCGTACTGAA 58.644 50.000 0.00 0.00 34.74 3.02
7133 18937 0.800683 CGCCGCATTCTTCGTACTGA 60.801 55.000 0.00 0.00 0.00 3.41
7134 18938 0.800683 TCGCCGCATTCTTCGTACTG 60.801 55.000 0.00 0.00 0.00 2.74
7135 18939 0.108992 TTCGCCGCATTCTTCGTACT 60.109 50.000 0.00 0.00 0.00 2.73
7136 18940 0.297820 CTTCGCCGCATTCTTCGTAC 59.702 55.000 0.00 0.00 0.00 3.67
7137 18941 0.108992 ACTTCGCCGCATTCTTCGTA 60.109 50.000 0.00 0.00 0.00 3.43
7138 18942 0.949105 AACTTCGCCGCATTCTTCGT 60.949 50.000 0.00 0.00 0.00 3.85
7139 18943 0.996462 TAACTTCGCCGCATTCTTCG 59.004 50.000 0.00 0.00 0.00 3.79
7140 18944 2.415512 AGTTAACTTCGCCGCATTCTTC 59.584 45.455 1.12 0.00 0.00 2.87
7141 18945 2.423577 AGTTAACTTCGCCGCATTCTT 58.576 42.857 1.12 0.00 0.00 2.52
7142 18946 2.094762 AGTTAACTTCGCCGCATTCT 57.905 45.000 1.12 0.00 0.00 2.40
7143 18947 2.770532 GAAGTTAACTTCGCCGCATTC 58.229 47.619 27.73 7.39 42.33 2.67
7144 18948 2.894307 GAAGTTAACTTCGCCGCATT 57.106 45.000 27.73 1.56 42.33 3.56
7153 18957 2.501261 GGTTCTGCCGGAAGTTAACTT 58.499 47.619 20.67 20.67 39.23 2.66
7154 18958 1.271217 GGGTTCTGCCGGAAGTTAACT 60.271 52.381 9.98 1.12 38.44 2.24
7155 18959 1.162698 GGGTTCTGCCGGAAGTTAAC 58.837 55.000 9.98 7.44 38.44 2.01
7156 18960 0.037160 GGGGTTCTGCCGGAAGTTAA 59.963 55.000 9.98 0.00 38.44 2.01
7157 18961 1.681076 GGGGTTCTGCCGGAAGTTA 59.319 57.895 9.98 0.00 38.44 2.24
7158 18962 2.434774 GGGGTTCTGCCGGAAGTT 59.565 61.111 9.98 0.00 38.44 2.66
7159 18963 3.647771 GGGGGTTCTGCCGGAAGT 61.648 66.667 9.98 0.00 38.44 3.01
7173 18977 1.900486 GTACTGGAATCCTATCGGGGG 59.100 57.143 0.00 0.00 35.33 5.40
7174 18978 2.890814 AGTACTGGAATCCTATCGGGG 58.109 52.381 0.00 0.00 35.33 5.73
7175 18979 5.480772 ACAATAGTACTGGAATCCTATCGGG 59.519 44.000 5.39 0.00 0.00 5.14
7176 18980 6.434652 AGACAATAGTACTGGAATCCTATCGG 59.565 42.308 5.39 0.00 0.00 4.18
7177 18981 7.455641 AGACAATAGTACTGGAATCCTATCG 57.544 40.000 5.39 0.00 0.00 2.92
7178 18982 8.861086 TGAAGACAATAGTACTGGAATCCTATC 58.139 37.037 5.39 0.00 0.00 2.08
7179 18983 8.783660 TGAAGACAATAGTACTGGAATCCTAT 57.216 34.615 5.39 0.00 0.00 2.57
7180 18984 8.059461 TCTGAAGACAATAGTACTGGAATCCTA 58.941 37.037 5.39 0.00 0.00 2.94
7181 18985 6.897966 TCTGAAGACAATAGTACTGGAATCCT 59.102 38.462 5.39 0.00 0.00 3.24
7182 18986 7.113658 TCTGAAGACAATAGTACTGGAATCC 57.886 40.000 5.39 0.00 0.00 3.01
7183 18987 8.417106 TCATCTGAAGACAATAGTACTGGAATC 58.583 37.037 5.39 0.00 0.00 2.52
7184 18988 8.311395 TCATCTGAAGACAATAGTACTGGAAT 57.689 34.615 5.39 0.00 0.00 3.01
7185 18989 7.397476 ACTCATCTGAAGACAATAGTACTGGAA 59.603 37.037 5.39 0.00 0.00 3.53
7186 18990 6.892456 ACTCATCTGAAGACAATAGTACTGGA 59.108 38.462 5.39 0.00 0.00 3.86
7187 18991 7.106439 ACTCATCTGAAGACAATAGTACTGG 57.894 40.000 5.39 0.00 0.00 4.00
7188 18992 9.891828 GATACTCATCTGAAGACAATAGTACTG 57.108 37.037 5.39 0.00 0.00 2.74
7189 18993 9.634021 TGATACTCATCTGAAGACAATAGTACT 57.366 33.333 0.00 0.00 31.93 2.73
7192 18996 8.420222 CCTTGATACTCATCTGAAGACAATAGT 58.580 37.037 0.00 0.00 31.93 2.12
7193 18997 7.384660 GCCTTGATACTCATCTGAAGACAATAG 59.615 40.741 0.00 0.00 31.93 1.73
7194 18998 7.147672 TGCCTTGATACTCATCTGAAGACAATA 60.148 37.037 0.00 0.00 31.93 1.90
7195 18999 6.054295 GCCTTGATACTCATCTGAAGACAAT 58.946 40.000 0.00 0.00 31.93 2.71
7196 19000 5.046376 TGCCTTGATACTCATCTGAAGACAA 60.046 40.000 0.00 0.00 31.93 3.18
7197 19001 4.467438 TGCCTTGATACTCATCTGAAGACA 59.533 41.667 0.00 0.00 31.93 3.41
7198 19002 5.016051 TGCCTTGATACTCATCTGAAGAC 57.984 43.478 0.00 0.00 31.93 3.01
7199 19003 5.682234 TTGCCTTGATACTCATCTGAAGA 57.318 39.130 0.00 0.00 31.93 2.87
7200 19004 5.821470 ACATTGCCTTGATACTCATCTGAAG 59.179 40.000 0.00 0.00 31.93 3.02
7201 19005 5.587443 CACATTGCCTTGATACTCATCTGAA 59.413 40.000 0.00 0.00 31.93 3.02
7202 19006 5.104817 TCACATTGCCTTGATACTCATCTGA 60.105 40.000 0.00 0.00 31.93 3.27
7203 19007 5.121105 TCACATTGCCTTGATACTCATCTG 58.879 41.667 0.00 0.00 31.93 2.90
7204 19008 5.363562 TCACATTGCCTTGATACTCATCT 57.636 39.130 0.00 0.00 31.93 2.90
7205 19009 7.918536 ATATCACATTGCCTTGATACTCATC 57.081 36.000 0.00 0.00 37.50 2.92
7206 19010 9.797642 TTTATATCACATTGCCTTGATACTCAT 57.202 29.630 0.00 0.00 37.50 2.90
7207 19011 9.276590 CTTTATATCACATTGCCTTGATACTCA 57.723 33.333 0.00 0.00 37.50 3.41
7208 19012 8.725148 CCTTTATATCACATTGCCTTGATACTC 58.275 37.037 0.00 0.00 37.50 2.59
7209 19013 8.220559 ACCTTTATATCACATTGCCTTGATACT 58.779 33.333 0.00 0.00 37.50 2.12
7210 19014 8.396272 ACCTTTATATCACATTGCCTTGATAC 57.604 34.615 0.00 0.00 37.50 2.24
7211 19015 8.995027 AACCTTTATATCACATTGCCTTGATA 57.005 30.769 0.00 0.00 38.70 2.15
7212 19016 7.014615 GGAACCTTTATATCACATTGCCTTGAT 59.985 37.037 0.00 0.00 36.43 2.57
7213 19017 6.321181 GGAACCTTTATATCACATTGCCTTGA 59.679 38.462 0.00 0.00 0.00 3.02
7214 19018 6.507023 GGAACCTTTATATCACATTGCCTTG 58.493 40.000 0.00 0.00 0.00 3.61
7215 19019 6.715347 GGAACCTTTATATCACATTGCCTT 57.285 37.500 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.