Multiple sequence alignment - TraesCS4D01G352200

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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 TraesCS4D01G352200 chr4D 100.000 3954 0 0 1 3954 503616361 503620314 0.000000e+00 7302.0
1 TraesCS4D01G352200 chr4D 100.000 2045 0 0 4319 6363 503620679 503622723 0.000000e+00 3777.0
2 TraesCS4D01G352200 chr5A 92.547 2093 94 21 4319 6359 688141513 688143595 0.000000e+00 2944.0
3 TraesCS4D01G352200 chr5A 93.740 1214 49 15 2751 3954 688140228 688141424 0.000000e+00 1796.0
4 TraesCS4D01G352200 chr5A 91.294 1321 68 22 756 2069 688138312 688139592 0.000000e+00 1759.0
5 TraesCS4D01G352200 chr5A 96.341 574 20 1 2080 2652 688139542 688140115 0.000000e+00 942.0
6 TraesCS4D01G352200 chr5A 82.364 550 39 35 6 526 688137217 688137737 5.900000e-115 425.0
7 TraesCS4D01G352200 chr4B 90.659 2109 115 43 1 2069 649470112 649472178 0.000000e+00 2728.0
8 TraesCS4D01G352200 chr4B 92.308 1768 80 23 4324 6073 649474091 649475820 0.000000e+00 2460.0
9 TraesCS4D01G352200 chr4B 92.727 1210 60 16 2751 3942 649472817 649474016 0.000000e+00 1722.0
10 TraesCS4D01G352200 chr4B 94.783 575 28 2 2080 2652 649472127 649472701 0.000000e+00 894.0
11 TraesCS4D01G352200 chr3D 88.293 914 89 12 4451 5364 173709127 173708232 0.000000e+00 1079.0
12 TraesCS4D01G352200 chr3D 87.084 751 69 20 2751 3499 173710272 173709548 0.000000e+00 824.0
13 TraesCS4D01G352200 chr3D 89.149 470 49 2 2196 2664 173714120 173713652 9.190000e-163 584.0
14 TraesCS4D01G352200 chr3D 79.630 810 103 31 1220 2014 501271450 501270688 5.650000e-145 525.0
15 TraesCS4D01G352200 chr3D 88.480 408 38 6 3531 3936 173709555 173709155 9.590000e-133 484.0
16 TraesCS4D01G352200 chr3D 85.915 284 20 11 1736 2009 173714444 173714171 1.040000e-72 285.0
17 TraesCS4D01G352200 chr3D 84.694 98 12 2 664 758 482227854 482227757 1.890000e-15 95.3
18 TraesCS4D01G352200 chr3D 100.000 28 0 0 2114 2141 547429672 547429645 1.200000e-02 52.8
19 TraesCS4D01G352200 chr3B 88.004 917 89 16 4451 5364 252589534 252588636 0.000000e+00 1064.0
20 TraesCS4D01G352200 chr3B 86.818 751 71 20 2751 3499 252590679 252589955 0.000000e+00 813.0
21 TraesCS4D01G352200 chr3B 88.936 470 50 2 2196 2664 252594630 252594162 4.280000e-161 579.0
22 TraesCS4D01G352200 chr3B 88.480 408 38 6 3531 3936 252589962 252589562 9.590000e-133 484.0
23 TraesCS4D01G352200 chr3B 85.563 284 21 11 1736 2009 252594954 252594681 4.860000e-71 279.0
24 TraesCS4D01G352200 chr3A 87.527 938 96 15 4430 5364 212113608 212112689 0.000000e+00 1064.0
25 TraesCS4D01G352200 chr3A 86.818 751 71 20 2751 3499 212114733 212114009 0.000000e+00 813.0
26 TraesCS4D01G352200 chr3A 89.103 468 49 2 2196 2662 212130545 212130079 1.190000e-161 580.0
27 TraesCS4D01G352200 chr3A 88.509 409 37 7 3531 3936 212114016 212113615 2.670000e-133 486.0
28 TraesCS4D01G352200 chr3A 79.694 458 57 21 1215 1672 212131687 212131266 1.340000e-76 298.0
29 TraesCS4D01G352200 chr3A 85.563 284 21 11 1736 2009 212130869 212130596 4.860000e-71 279.0
30 TraesCS4D01G352200 chr3A 85.973 221 14 10 421 633 92676492 92676281 2.990000e-53 220.0
31 TraesCS4D01G352200 chr3A 87.421 159 15 4 1864 2018 265374136 265373979 1.820000e-40 178.0
32 TraesCS4D01G352200 chr3A 86.316 95 13 0 662 756 38429455 38429361 3.140000e-18 104.0
33 TraesCS4D01G352200 chr3A 100.000 28 0 0 2114 2141 744438516 744438489 1.200000e-02 52.8
34 TraesCS4D01G352200 chr6B 79.963 1093 131 45 954 2018 535442464 535443496 0.000000e+00 725.0
35 TraesCS4D01G352200 chr6B 88.800 500 36 8 5130 5625 704524588 704524105 4.250000e-166 595.0
36 TraesCS4D01G352200 chr6B 91.398 186 16 0 6083 6268 704517123 704516938 8.190000e-64 255.0
37 TraesCS4D01G352200 chr6B 82.182 275 27 10 1754 2014 661066838 661066572 3.860000e-52 217.0
38 TraesCS4D01G352200 chr6B 82.517 143 13 5 156 298 535441682 535441812 1.450000e-21 115.0
39 TraesCS4D01G352200 chr6B 97.619 42 1 0 5719 5760 704524095 704524054 8.850000e-09 73.1
40 TraesCS4D01G352200 chr6A 90.710 549 44 4 4924 5472 609055862 609056403 0.000000e+00 725.0
41 TraesCS4D01G352200 chr6A 90.217 460 41 2 5811 6268 609056737 609057194 1.180000e-166 597.0
42 TraesCS4D01G352200 chr6A 89.172 157 15 2 5469 5625 609056532 609056686 1.810000e-45 195.0
43 TraesCS4D01G352200 chr6D 79.050 1074 142 42 954 2001 410108789 410107773 0.000000e+00 660.0
44 TraesCS4D01G352200 chrUn 85.688 552 64 10 866 1416 236412599 236413136 9.260000e-158 568.0
45 TraesCS4D01G352200 chrUn 84.964 552 68 10 866 1416 35309340 35309877 4.340000e-151 545.0
46 TraesCS4D01G352200 chr2A 87.234 94 10 2 664 756 455350301 455350209 8.720000e-19 106.0
47 TraesCS4D01G352200 chr2A 86.170 94 11 2 664 756 455350209 455350301 4.060000e-17 100.0
48 TraesCS4D01G352200 chr2A 85.263 95 12 2 664 757 424544451 424544358 5.250000e-16 97.1
49 TraesCS4D01G352200 chr7B 75.258 291 34 25 16 293 537650238 537649973 3.140000e-18 104.0
50 TraesCS4D01G352200 chr7B 74.914 291 35 25 16 293 537653350 537653085 1.460000e-16 99.0
51 TraesCS4D01G352200 chr2B 85.106 94 12 2 663 756 732865163 732865254 1.890000e-15 95.3
52 TraesCS4D01G352200 chr2B 84.211 95 13 2 664 758 732865254 732865162 2.440000e-14 91.6
53 TraesCS4D01G352200 chr1D 85.106 94 11 2 663 756 181632817 181632907 6.790000e-15 93.5
54 TraesCS4D01G352200 chr5D 100.000 28 0 0 2111 2138 318294670 318294643 1.200000e-02 52.8
55 TraesCS4D01G352200 chr2D 100.000 28 0 0 2114 2141 340258554 340258527 1.200000e-02 52.8


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 TraesCS4D01G352200 chr4D 503616361 503622723 6362 False 5539.500000 7302 100.000000 1 6363 2 chr4D.!!$F1 6362
1 TraesCS4D01G352200 chr5A 688137217 688143595 6378 False 1573.200000 2944 91.257200 6 6359 5 chr5A.!!$F1 6353
2 TraesCS4D01G352200 chr4B 649470112 649475820 5708 False 1951.000000 2728 92.619250 1 6073 4 chr4B.!!$F1 6072
3 TraesCS4D01G352200 chr3D 173708232 173714444 6212 True 651.200000 1079 87.784200 1736 5364 5 chr3D.!!$R4 3628
4 TraesCS4D01G352200 chr3D 501270688 501271450 762 True 525.000000 525 79.630000 1220 2014 1 chr3D.!!$R2 794
5 TraesCS4D01G352200 chr3B 252588636 252594954 6318 True 643.800000 1064 87.560200 1736 5364 5 chr3B.!!$R1 3628
6 TraesCS4D01G352200 chr3A 212112689 212114733 2044 True 787.666667 1064 87.618000 2751 5364 3 chr3A.!!$R5 2613
7 TraesCS4D01G352200 chr3A 212130079 212131687 1608 True 385.666667 580 84.786667 1215 2662 3 chr3A.!!$R6 1447
8 TraesCS4D01G352200 chr6B 535441682 535443496 1814 False 420.000000 725 81.240000 156 2018 2 chr6B.!!$F1 1862
9 TraesCS4D01G352200 chr6B 704524054 704524588 534 True 334.050000 595 93.209500 5130 5760 2 chr6B.!!$R3 630
10 TraesCS4D01G352200 chr6A 609055862 609057194 1332 False 505.666667 725 90.033000 4924 6268 3 chr6A.!!$F1 1344
11 TraesCS4D01G352200 chr6D 410107773 410108789 1016 True 660.000000 660 79.050000 954 2001 1 chr6D.!!$R1 1047
12 TraesCS4D01G352200 chrUn 236412599 236413136 537 False 568.000000 568 85.688000 866 1416 1 chrUn.!!$F2 550
13 TraesCS4D01G352200 chrUn 35309340 35309877 537 False 545.000000 545 84.964000 866 1416 1 chrUn.!!$F1 550

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
758 975 0.106167 TCGGGATGGAGGGAGTACTG 60.106 60.000 0.0 0.0 0.00 2.74 F
1650 2207 0.249573 TCGACAACCGTCTCCAAACC 60.250 55.000 0.0 0.0 40.23 3.27 F
2889 7237 1.675641 CTTTGGGGAGACAAGGCCG 60.676 63.158 0.0 0.0 0.00 6.13 F
3927 8302 0.320683 CAGCGACCACATCCTGTTCA 60.321 55.000 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 3297 0.392193 ATGCGCTTCCAGTTCTCCTG 60.392 55.0 9.73 0.0 41.15 3.86 R
3282 7635 0.742505 ATAACCGAACGATCCGCTCA 59.257 50.0 0.00 0.0 0.00 4.26 R
4675 9058 2.052782 ATTCCCGGTAATCTTGTGCC 57.947 50.0 0.00 0.0 0.00 5.01 R
5911 10494 0.178533 TCGACACCGGACACCTTTTT 59.821 50.0 9.46 0.0 36.24 1.94 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
34 35 0.875059 GCCGACAGCTTTTTACTGCT 59.125 50.000 0.00 0.00 38.79 4.24
48 49 4.689612 TTACTGCTGTTTCTGTCCTCTT 57.310 40.909 0.09 0.00 0.00 2.85
49 50 3.118905 ACTGCTGTTTCTGTCCTCTTC 57.881 47.619 0.00 0.00 0.00 2.87
50 51 2.224402 ACTGCTGTTTCTGTCCTCTTCC 60.224 50.000 0.00 0.00 0.00 3.46
51 52 1.768275 TGCTGTTTCTGTCCTCTTCCA 59.232 47.619 0.00 0.00 0.00 3.53
60 61 3.652869 TCTGTCCTCTTCCATCCAAGTTT 59.347 43.478 0.00 0.00 0.00 2.66
64 65 3.003480 CCTCTTCCATCCAAGTTTCGTC 58.997 50.000 0.00 0.00 0.00 4.20
66 67 4.319177 CTCTTCCATCCAAGTTTCGTCTT 58.681 43.478 0.00 0.00 0.00 3.01
92 93 8.666821 TGGAAAATATCTCTGGATCTGATTCAT 58.333 33.333 0.00 0.00 33.71 2.57
115 116 9.249053 TCATAGAGAGAGATTTAACACTCTGTT 57.751 33.333 13.22 0.00 42.51 3.16
119 120 9.267084 AGAGAGAGATTTAACACTCTGTTTTTC 57.733 33.333 13.22 5.72 42.51 2.29
121 122 9.620259 AGAGAGATTTAACACTCTGTTTTTCTT 57.380 29.630 13.22 0.00 42.51 2.52
122 123 9.871299 GAGAGATTTAACACTCTGTTTTTCTTC 57.129 33.333 13.22 0.00 42.51 2.87
129 130 6.685527 ACACTCTGTTTTTCTTCTTCTTCC 57.314 37.500 0.00 0.00 0.00 3.46
130 131 6.418946 ACACTCTGTTTTTCTTCTTCTTCCT 58.581 36.000 0.00 0.00 0.00 3.36
131 132 6.317391 ACACTCTGTTTTTCTTCTTCTTCCTG 59.683 38.462 0.00 0.00 0.00 3.86
132 133 6.317391 CACTCTGTTTTTCTTCTTCTTCCTGT 59.683 38.462 0.00 0.00 0.00 4.00
147 148 9.322769 TCTTCTTCCTGTTAAGTTTCCTATAGT 57.677 33.333 0.00 0.00 0.00 2.12
153 154 8.653191 TCCTGTTAAGTTTCCTATAGTTGACAA 58.347 33.333 0.00 0.00 28.14 3.18
225 226 1.741032 GAGCAGAGCAGACACCAGC 60.741 63.158 0.00 0.00 0.00 4.85
229 230 1.905843 AGAGCAGACACCAGCGAGT 60.906 57.895 0.00 0.00 35.48 4.18
255 256 0.734253 GTGAGTGAGCAGTACCAGCG 60.734 60.000 2.63 0.00 37.01 5.18
321 375 4.674101 GCTCTGTCTCTCTGATGTGTGTAC 60.674 50.000 0.00 0.00 0.00 2.90
327 381 7.896811 TGTCTCTCTGATGTGTGTACTTATTT 58.103 34.615 0.00 0.00 0.00 1.40
335 389 6.533723 TGATGTGTGTACTTATTTAGGCTTCG 59.466 38.462 0.00 0.00 0.00 3.79
350 411 1.535462 GCTTCGCCTTGCTGTTTTCTA 59.465 47.619 0.00 0.00 0.00 2.10
399 463 9.529325 GTTTAAGGTACAATCTTTGCTCTTTTT 57.471 29.630 0.00 0.00 0.00 1.94
403 467 4.607293 ACAATCTTTGCTCTTTTTCCCC 57.393 40.909 0.00 0.00 0.00 4.81
405 469 4.655649 ACAATCTTTGCTCTTTTTCCCCTT 59.344 37.500 0.00 0.00 0.00 3.95
406 470 5.221521 ACAATCTTTGCTCTTTTTCCCCTTC 60.222 40.000 0.00 0.00 0.00 3.46
407 471 3.230976 TCTTTGCTCTTTTTCCCCTTCC 58.769 45.455 0.00 0.00 0.00 3.46
421 485 1.073284 CCCTTCCCCTTCGAGTTTTCA 59.927 52.381 0.00 0.00 0.00 2.69
458 522 4.505313 AAAAGGAGAGCATTTCGTTTCC 57.495 40.909 0.00 0.00 33.10 3.13
459 523 3.425162 AAGGAGAGCATTTCGTTTCCT 57.575 42.857 0.00 0.00 36.65 3.36
460 524 2.979240 AGGAGAGCATTTCGTTTCCTC 58.021 47.619 0.00 0.00 29.27 3.71
461 525 2.569404 AGGAGAGCATTTCGTTTCCTCT 59.431 45.455 0.00 0.00 35.72 3.69
462 526 2.675348 GGAGAGCATTTCGTTTCCTCTG 59.325 50.000 0.00 0.00 33.35 3.35
463 527 3.330267 GAGAGCATTTCGTTTCCTCTGT 58.670 45.455 0.00 0.00 33.35 3.41
464 528 4.495422 GAGAGCATTTCGTTTCCTCTGTA 58.505 43.478 0.00 0.00 33.35 2.74
466 530 5.112686 AGAGCATTTCGTTTCCTCTGTATC 58.887 41.667 0.00 0.00 32.07 2.24
467 531 5.091261 AGCATTTCGTTTCCTCTGTATCT 57.909 39.130 0.00 0.00 0.00 1.98
468 532 5.112686 AGCATTTCGTTTCCTCTGTATCTC 58.887 41.667 0.00 0.00 0.00 2.75
469 533 4.271291 GCATTTCGTTTCCTCTGTATCTCC 59.729 45.833 0.00 0.00 0.00 3.71
527 601 7.595819 TTGGGTTCAGTCAAATTTCTGTTAT 57.404 32.000 6.74 0.00 33.89 1.89
539 613 9.283768 TCAAATTTCTGTTATGCTCTTACTTCA 57.716 29.630 0.00 0.00 0.00 3.02
552 626 5.452496 GCTCTTACTTCAGTGGATGATGCTA 60.452 44.000 0.00 0.00 37.89 3.49
580 654 1.055040 CCCCCTTGGAGAGATGCTAG 58.945 60.000 0.00 0.00 35.39 3.42
581 655 0.396060 CCCCTTGGAGAGATGCTAGC 59.604 60.000 8.10 8.10 0.00 3.42
582 656 1.422531 CCCTTGGAGAGATGCTAGCT 58.577 55.000 17.23 0.83 0.00 3.32
583 657 2.603021 CCCTTGGAGAGATGCTAGCTA 58.397 52.381 17.23 2.58 0.00 3.32
584 658 2.562298 CCCTTGGAGAGATGCTAGCTAG 59.438 54.545 16.84 16.84 0.00 3.42
605 679 1.401409 GCTAGCTAGATCTGAGCAGCG 60.401 57.143 25.15 11.66 42.69 5.18
611 685 0.107945 AGATCTGAGCAGCGGGAAAC 60.108 55.000 0.00 0.00 0.00 2.78
624 698 2.102588 GCGGGAAACTAGCTAGGAATCA 59.897 50.000 24.35 0.00 0.00 2.57
636 853 6.916360 AGCTAGGAATCAGATAGAAAGAGG 57.084 41.667 0.00 0.00 0.00 3.69
649 866 4.993029 AGAAAGAGGGATCTAACACTCG 57.007 45.455 0.00 0.00 44.12 4.18
667 884 3.570550 ACTCGCTCTGTTCTCTTGTACTT 59.429 43.478 0.00 0.00 0.00 2.24
691 908 1.659098 CTGTCCGGAATTACTTGTCGC 59.341 52.381 5.23 0.00 0.00 5.19
699 916 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
714 931 6.090493 CGCAGAAATGGATGTATCTAGATGTG 59.910 42.308 15.79 0.00 0.00 3.21
728 945 6.305272 TCTAGATGTGCTTTCCATTTCTCT 57.695 37.500 0.00 0.00 0.00 3.10
741 958 6.968131 TCCATTTCTCTGACAAGTAATTCG 57.032 37.500 0.00 0.00 0.00 3.34
745 962 5.677319 TTCTCTGACAAGTAATTCGGGAT 57.323 39.130 0.00 0.00 0.00 3.85
758 975 0.106167 TCGGGATGGAGGGAGTACTG 60.106 60.000 0.00 0.00 0.00 2.74
799 1303 7.232941 TCCTTAAGTTGTACAGTAAGCTCTTCT 59.767 37.037 13.58 0.00 0.00 2.85
846 1353 6.985653 TCTATTTGTGGATAGAAGAGGAGG 57.014 41.667 0.00 0.00 36.08 4.30
848 1355 3.776731 TTGTGGATAGAAGAGGAGGGA 57.223 47.619 0.00 0.00 0.00 4.20
849 1356 3.320610 TGTGGATAGAAGAGGAGGGAG 57.679 52.381 0.00 0.00 0.00 4.30
851 1358 3.469006 TGTGGATAGAAGAGGAGGGAGAT 59.531 47.826 0.00 0.00 0.00 2.75
900 1409 2.038557 TGAAAAGGGGCAGTCAGTAGTC 59.961 50.000 0.00 0.00 0.00 2.59
999 1510 5.013808 TGGGGTTAGGTAAAAGAAGAAGGAG 59.986 44.000 0.00 0.00 0.00 3.69
1047 1558 0.387878 GAGCCACTGAGTCTGACACG 60.388 60.000 10.88 3.44 0.00 4.49
1083 1600 2.861147 ACAGTGGGAACTTAGAAGGC 57.139 50.000 0.00 0.00 0.00 4.35
1088 1605 3.394606 AGTGGGAACTTAGAAGGCTCAAA 59.605 43.478 0.00 0.00 0.00 2.69
1395 1922 4.035208 GGGAAATGCATCGGTAACTACTTG 59.965 45.833 0.00 0.00 0.00 3.16
1486 2036 7.199766 TCAAGTAGTAATTGCTTTTGGTTGTG 58.800 34.615 15.39 1.44 28.30 3.33
1487 2037 6.709018 AGTAGTAATTGCTTTTGGTTGTGT 57.291 33.333 0.00 0.00 0.00 3.72
1488 2038 6.503524 AGTAGTAATTGCTTTTGGTTGTGTG 58.496 36.000 0.00 0.00 0.00 3.82
1489 2039 5.337578 AGTAATTGCTTTTGGTTGTGTGT 57.662 34.783 0.00 0.00 0.00 3.72
1650 2207 0.249573 TCGACAACCGTCTCCAAACC 60.250 55.000 0.00 0.00 40.23 3.27
1705 2262 7.226523 GCTAAATGTTTTGTCATGGTTTCCTTT 59.773 33.333 0.00 0.00 0.00 3.11
1813 2704 2.609747 AGGAGGTTAGTCACAGCTGAA 58.390 47.619 23.35 4.92 0.00 3.02
2014 2936 6.852420 TGGGCTACATAGAGGTATTATGTC 57.148 41.667 1.52 0.00 40.95 3.06
2037 2959 4.878397 CCAATCAAGTACATCCTCTGTTCC 59.122 45.833 0.00 0.00 39.39 3.62
2045 2967 4.437682 ACATCCTCTGTTCCTTGTTCAA 57.562 40.909 0.00 0.00 32.90 2.69
2047 2969 5.200483 ACATCCTCTGTTCCTTGTTCAAAA 58.800 37.500 0.00 0.00 32.90 2.44
2070 2992 6.884280 AAAAAGTACATCCTCTGTTCCTTG 57.116 37.500 0.00 0.00 39.39 3.61
2071 2993 5.568620 AAAGTACATCCTCTGTTCCTTGT 57.431 39.130 0.00 0.00 39.39 3.16
2072 2994 5.568620 AAGTACATCCTCTGTTCCTTGTT 57.431 39.130 0.00 0.00 39.39 2.83
2073 2995 5.568620 AGTACATCCTCTGTTCCTTGTTT 57.431 39.130 0.00 0.00 39.39 2.83
2074 2996 6.681729 AGTACATCCTCTGTTCCTTGTTTA 57.318 37.500 0.00 0.00 39.39 2.01
2075 2997 7.074653 AGTACATCCTCTGTTCCTTGTTTAA 57.925 36.000 0.00 0.00 39.39 1.52
2076 2998 7.514721 AGTACATCCTCTGTTCCTTGTTTAAA 58.485 34.615 0.00 0.00 39.39 1.52
2077 2999 7.996644 AGTACATCCTCTGTTCCTTGTTTAAAA 59.003 33.333 0.00 0.00 39.39 1.52
2078 3000 7.654022 ACATCCTCTGTTCCTTGTTTAAAAA 57.346 32.000 0.00 0.00 32.90 1.94
2099 3021 6.884280 AAAAAGTACATCCTCTGTTCCTTG 57.116 37.500 0.00 0.00 39.39 3.61
2100 3022 5.568620 AAAGTACATCCTCTGTTCCTTGT 57.431 39.130 0.00 0.00 39.39 3.16
2101 3023 5.568620 AAGTACATCCTCTGTTCCTTGTT 57.431 39.130 0.00 0.00 39.39 2.83
2102 3024 6.681729 AAGTACATCCTCTGTTCCTTGTTA 57.318 37.500 0.00 0.00 39.39 2.41
2103 3025 6.681729 AGTACATCCTCTGTTCCTTGTTAA 57.318 37.500 0.00 0.00 39.39 2.01
2104 3026 7.074653 AGTACATCCTCTGTTCCTTGTTAAA 57.925 36.000 0.00 0.00 39.39 1.52
2105 3027 7.514721 AGTACATCCTCTGTTCCTTGTTAAAA 58.485 34.615 0.00 0.00 39.39 1.52
2106 3028 6.884280 ACATCCTCTGTTCCTTGTTAAAAG 57.116 37.500 0.00 0.00 32.90 2.27
2107 3029 6.601332 ACATCCTCTGTTCCTTGTTAAAAGA 58.399 36.000 0.00 0.00 32.90 2.52
2166 3088 4.959596 AGTAACAACTAGAGATTCGCGA 57.040 40.909 3.71 3.71 0.00 5.87
2375 3297 4.320275 GGCTGCAGTTTACCTTCTTTGTAC 60.320 45.833 16.64 0.00 0.00 2.90
2406 3328 3.349006 GCGCATATGGGTCGCTGG 61.349 66.667 19.73 0.00 44.79 4.85
2476 3398 2.573941 ACCGTAACCGAGCTGTATTC 57.426 50.000 0.00 0.00 35.63 1.75
2654 3576 8.966868 ACATAAACTTCCATAAGGTAATGTTGG 58.033 33.333 0.00 0.00 37.01 3.77
2657 3579 7.933215 AACTTCCATAAGGTAATGTTGGTAC 57.067 36.000 0.00 0.00 37.01 3.34
2668 3590 9.720769 AAGGTAATGTTGGTACTATGTATATGC 57.279 33.333 0.00 0.00 0.00 3.14
2669 3591 8.033038 AGGTAATGTTGGTACTATGTATATGCG 58.967 37.037 0.00 0.00 0.00 4.73
2670 3592 7.277098 GGTAATGTTGGTACTATGTATATGCGG 59.723 40.741 0.00 0.00 0.00 5.69
2672 3594 6.897706 TGTTGGTACTATGTATATGCGGTA 57.102 37.500 0.00 0.00 0.00 4.02
2674 3596 7.147312 TGTTGGTACTATGTATATGCGGTAAC 58.853 38.462 0.00 0.00 0.00 2.50
2716 3696 9.732130 AAAGAACAAATTACATAGAGAGAGCTT 57.268 29.630 0.00 0.00 0.00 3.74
2719 3699 9.810545 GAACAAATTACATAGAGAGAGCTTAGT 57.189 33.333 0.00 0.00 0.00 2.24
2720 3700 9.593134 AACAAATTACATAGAGAGAGCTTAGTG 57.407 33.333 0.00 0.00 0.00 2.74
2721 3701 8.200792 ACAAATTACATAGAGAGAGCTTAGTGG 58.799 37.037 0.00 0.00 0.00 4.00
2722 3702 8.417106 CAAATTACATAGAGAGAGCTTAGTGGA 58.583 37.037 0.00 0.00 0.00 4.02
2723 3703 8.719645 AATTACATAGAGAGAGCTTAGTGGAT 57.280 34.615 0.00 0.00 0.00 3.41
2725 3705 5.454062 ACATAGAGAGAGCTTAGTGGATGT 58.546 41.667 0.00 0.00 0.00 3.06
2726 3706 5.896678 ACATAGAGAGAGCTTAGTGGATGTT 59.103 40.000 0.00 0.00 0.00 2.71
2727 3707 7.063593 ACATAGAGAGAGCTTAGTGGATGTTA 58.936 38.462 0.00 0.00 0.00 2.41
2728 3708 5.845391 AGAGAGAGCTTAGTGGATGTTAC 57.155 43.478 0.00 0.00 0.00 2.50
2731 3711 7.063593 AGAGAGAGCTTAGTGGATGTTACATA 58.936 38.462 0.00 0.00 0.00 2.29
2732 3712 7.561722 AGAGAGAGCTTAGTGGATGTTACATAA 59.438 37.037 0.00 0.00 0.00 1.90
2734 3714 8.364142 AGAGAGCTTAGTGGATGTTACATAATC 58.636 37.037 0.00 0.00 0.00 1.75
2736 3716 8.147058 AGAGCTTAGTGGATGTTACATAATCTG 58.853 37.037 0.00 0.00 0.00 2.90
2737 3717 8.023021 AGCTTAGTGGATGTTACATAATCTGA 57.977 34.615 0.00 0.00 0.00 3.27
2738 3718 8.486210 AGCTTAGTGGATGTTACATAATCTGAA 58.514 33.333 0.00 0.00 0.00 3.02
2739 3719 8.552034 GCTTAGTGGATGTTACATAATCTGAAC 58.448 37.037 0.00 0.00 0.00 3.18
2740 3720 8.642908 TTAGTGGATGTTACATAATCTGAACG 57.357 34.615 0.00 0.00 0.00 3.95
2741 3721 6.640518 AGTGGATGTTACATAATCTGAACGT 58.359 36.000 0.00 0.00 0.00 3.99
2742 3722 6.757010 AGTGGATGTTACATAATCTGAACGTC 59.243 38.462 0.00 0.00 37.18 4.34
2743 3723 6.533723 GTGGATGTTACATAATCTGAACGTCA 59.466 38.462 0.00 0.00 38.84 4.35
2745 3725 7.768582 TGGATGTTACATAATCTGAACGTCATT 59.231 33.333 0.00 0.00 38.84 2.57
2746 3726 8.064222 GGATGTTACATAATCTGAACGTCATTG 58.936 37.037 0.00 0.00 38.84 2.82
2747 3727 7.899178 TGTTACATAATCTGAACGTCATTGT 57.101 32.000 0.00 0.00 0.00 2.71
2748 3728 7.959733 TGTTACATAATCTGAACGTCATTGTC 58.040 34.615 0.00 0.00 0.00 3.18
2749 3729 7.600752 TGTTACATAATCTGAACGTCATTGTCA 59.399 33.333 0.00 0.00 0.00 3.58
2889 7237 1.675641 CTTTGGGGAGACAAGGCCG 60.676 63.158 0.00 0.00 0.00 6.13
3012 7360 1.798813 CGTAACAAGCTCAAGGACACC 59.201 52.381 0.00 0.00 0.00 4.16
3015 7363 1.680338 ACAAGCTCAAGGACACCAAC 58.320 50.000 0.00 0.00 0.00 3.77
3162 7510 6.951062 ACGGTAAAAGTCTATCTACTACCC 57.049 41.667 0.00 0.00 33.46 3.69
3163 7511 6.667661 ACGGTAAAAGTCTATCTACTACCCT 58.332 40.000 0.00 0.00 33.46 4.34
3282 7635 9.717942 GCTTATCCTGTCTTCTTATATTCATGT 57.282 33.333 0.00 0.00 0.00 3.21
3288 7641 5.985530 TGTCTTCTTATATTCATGTGAGCGG 59.014 40.000 0.00 0.00 0.00 5.52
3315 7668 5.231568 CGTTCGGTTATTTAGGAGACATGAC 59.768 44.000 0.00 0.00 0.00 3.06
3353 7706 3.904717 AGGTACCACCATGACAAAAACA 58.095 40.909 15.94 0.00 41.95 2.83
3394 7747 8.925161 TTCATTGTTTGTCTTTTTGACCTTAG 57.075 30.769 0.00 0.00 44.75 2.18
3469 7830 1.134431 GCCAAGCCATTTAACATGGGG 60.134 52.381 14.57 10.22 39.53 4.96
3575 7947 1.416401 CAGGTTGCGGTATATCCTGGT 59.584 52.381 0.00 0.00 41.10 4.00
3626 7998 1.743394 CCTGGTTTCAAATACCGGAGC 59.257 52.381 9.46 0.00 43.44 4.70
3691 8064 1.328430 TGGTACCCACGTCACACACA 61.328 55.000 10.07 0.00 0.00 3.72
3706 8079 6.021468 CGTCACACACATTGAGAAAAAGAAAC 60.021 38.462 0.00 0.00 0.00 2.78
3855 8229 0.613777 GGGGTGATTGGACTTCTCGT 59.386 55.000 0.00 0.00 0.00 4.18
3926 8301 1.021390 CCAGCGACCACATCCTGTTC 61.021 60.000 0.00 0.00 0.00 3.18
3927 8302 0.320683 CAGCGACCACATCCTGTTCA 60.321 55.000 0.00 0.00 0.00 3.18
4370 8745 8.579682 AAAACTTAAATGTCTGAAGCATTGTC 57.420 30.769 0.00 0.00 36.75 3.18
4407 8782 7.925043 TTTGATTTTTCATAGCAATGCCATT 57.075 28.000 0.00 0.00 32.76 3.16
4408 8783 7.542534 TTGATTTTTCATAGCAATGCCATTC 57.457 32.000 0.00 0.00 32.76 2.67
4409 8784 6.050432 TGATTTTTCATAGCAATGCCATTCC 58.950 36.000 0.00 0.00 32.76 3.01
4410 8785 4.405116 TTTTCATAGCAATGCCATTCCC 57.595 40.909 0.00 0.00 32.76 3.97
4411 8786 3.317455 TTCATAGCAATGCCATTCCCT 57.683 42.857 0.00 0.00 32.76 4.20
4412 8787 4.451891 TTCATAGCAATGCCATTCCCTA 57.548 40.909 0.00 0.00 32.76 3.53
4413 8788 4.662966 TCATAGCAATGCCATTCCCTAT 57.337 40.909 0.00 0.00 32.76 2.57
4439 8814 5.406780 GCTCTACTTGATGGAACCGATAATG 59.593 44.000 0.00 0.00 0.00 1.90
4442 8817 5.097742 ACTTGATGGAACCGATAATGACA 57.902 39.130 0.00 0.00 0.00 3.58
4508 8883 2.225394 TGGACTCCTTAGAGCTGACCTT 60.225 50.000 0.00 0.00 44.65 3.50
4569 8946 6.560493 GAACTTCTTCAGTTGCTTGAAAAC 57.440 37.500 0.00 0.00 46.53 2.43
4618 9001 9.273016 CAAACTCTTGTTCTGATCCTAAACTTA 57.727 33.333 0.00 0.00 34.96 2.24
4732 9115 1.377725 CGGACTTGGCATTGGAGCT 60.378 57.895 0.00 0.00 34.17 4.09
5169 9562 1.016130 ACGTCTTCTCGCTGCCATTG 61.016 55.000 0.00 0.00 0.00 2.82
5173 9566 1.065926 TCTTCTCGCTGCCATTGTCAT 60.066 47.619 0.00 0.00 0.00 3.06
5189 9582 7.254137 CCATTGTCATATCGATCTGGTACTAG 58.746 42.308 0.00 0.00 0.00 2.57
5481 10026 5.810587 TGGTTTAGACGCTTTATCATGAGAC 59.189 40.000 0.09 0.00 0.00 3.36
5487 10032 5.028549 ACGCTTTATCATGAGACCTTGAT 57.971 39.130 0.09 0.00 39.55 2.57
5586 10132 5.336744 TGAAAATCAACTCCGACAACAAAC 58.663 37.500 0.00 0.00 0.00 2.93
5685 10231 5.126061 GCTCCATTTGGATTAGTGACAATGT 59.874 40.000 0.00 0.00 44.46 2.71
5687 10233 7.624360 TCCATTTGGATTAGTGACAATGTAC 57.376 36.000 0.00 0.00 39.78 2.90
5688 10234 6.601613 TCCATTTGGATTAGTGACAATGTACC 59.398 38.462 0.00 0.00 39.78 3.34
5689 10235 6.183360 CCATTTGGATTAGTGACAATGTACCC 60.183 42.308 0.00 0.00 37.39 3.69
5717 10276 8.567948 AGTACACAATAAGTTCATTTCACAAGG 58.432 33.333 0.00 0.00 0.00 3.61
5819 10382 5.066893 CACCCACAATAAGTCATTCTCCATG 59.933 44.000 0.00 0.00 0.00 3.66
5830 10393 5.363562 TCATTCTCCATGACAGCTGTATT 57.636 39.130 21.73 7.33 36.94 1.89
5831 10394 5.748402 TCATTCTCCATGACAGCTGTATTT 58.252 37.500 21.73 4.44 36.94 1.40
5832 10395 5.819379 TCATTCTCCATGACAGCTGTATTTC 59.181 40.000 21.73 7.93 36.94 2.17
5833 10396 5.426689 TTCTCCATGACAGCTGTATTTCT 57.573 39.130 21.73 0.00 0.00 2.52
5839 10422 5.183713 CCATGACAGCTGTATTTCTTCCAAA 59.816 40.000 21.73 0.00 0.00 3.28
5958 10543 7.158099 TCTAAGATGAACGAGACATTTCTGA 57.842 36.000 0.00 0.00 29.47 3.27
6089 10674 6.614657 TCTGGAAGTCTGGAGATGATATGTA 58.385 40.000 0.00 0.00 33.76 2.29
6130 10715 1.396301 GAGAAGAAGCGCATCCTTGTG 59.604 52.381 11.47 0.00 36.41 3.33
6255 10840 0.731994 GTCGGAACCGTCTCTACTCC 59.268 60.000 12.93 0.00 40.74 3.85
6275 10860 1.135960 CCAATTCCTCCTCCTCCTCC 58.864 60.000 0.00 0.00 0.00 4.30
6296 10890 2.627221 CTCATCATCACCATCCTCGTCT 59.373 50.000 0.00 0.00 0.00 4.18
6305 10899 1.000827 CCATCCTCGTCTTCATCCTCG 60.001 57.143 0.00 0.00 0.00 4.63
6311 10905 0.586748 CGTCTTCATCCTCGTCGTCG 60.587 60.000 0.00 0.00 38.55 5.12
6317 10911 3.182472 ATCCTCGTCGTCGCCATCG 62.182 63.158 0.00 0.00 36.96 3.84
6323 10917 4.509883 TCGTCGCCATCGTCGTCG 62.510 66.667 0.00 0.00 44.86 5.12
6359 10953 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
6360 10954 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
6361 10955 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
6362 10956 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.978978 TGGATGGAAGAGGACAGAAACA 59.021 45.455 0.00 0.00 0.00 2.83
60 61 5.932619 TCCAGAGATATTTTCCAAGACGA 57.067 39.130 0.00 0.00 0.00 4.20
64 65 8.921353 AATCAGATCCAGAGATATTTTCCAAG 57.079 34.615 0.00 0.00 30.90 3.61
66 67 8.037723 TGAATCAGATCCAGAGATATTTTCCA 57.962 34.615 0.00 0.00 30.90 3.53
93 94 9.267084 GAAAAACAGAGTGTTAAATCTCTCTCT 57.733 33.333 7.45 0.00 40.14 3.10
96 97 9.871299 GAAGAAAAACAGAGTGTTAAATCTCTC 57.129 33.333 7.45 0.00 40.14 3.20
115 116 8.683615 GGAAACTTAACAGGAAGAAGAAGAAAA 58.316 33.333 0.00 0.00 0.00 2.29
121 122 9.322769 ACTATAGGAAACTTAACAGGAAGAAGA 57.677 33.333 4.43 0.00 43.67 2.87
122 123 9.945904 AACTATAGGAAACTTAACAGGAAGAAG 57.054 33.333 4.43 0.00 43.67 2.85
124 125 9.096823 TCAACTATAGGAAACTTAACAGGAAGA 57.903 33.333 4.43 0.00 43.67 2.87
125 126 9.152595 GTCAACTATAGGAAACTTAACAGGAAG 57.847 37.037 4.43 0.00 43.67 3.46
127 128 8.197592 TGTCAACTATAGGAAACTTAACAGGA 57.802 34.615 4.43 0.00 43.67 3.86
128 129 8.718734 GTTGTCAACTATAGGAAACTTAACAGG 58.281 37.037 8.53 0.00 43.67 4.00
129 130 9.268268 TGTTGTCAACTATAGGAAACTTAACAG 57.732 33.333 16.45 0.00 43.67 3.16
130 131 9.616156 TTGTTGTCAACTATAGGAAACTTAACA 57.384 29.630 16.45 4.36 43.67 2.41
147 148 3.133721 CAGGGGAAATTGGTTGTTGTCAA 59.866 43.478 0.00 0.00 0.00 3.18
153 154 2.316108 GACACAGGGGAAATTGGTTGT 58.684 47.619 0.00 0.00 0.00 3.32
205 206 2.125753 GGTGTCTGCTCTGCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
209 210 3.117171 CGCTGGTGTCTGCTCTGC 61.117 66.667 0.00 0.00 35.96 4.26
210 211 1.445754 CTCGCTGGTGTCTGCTCTG 60.446 63.158 0.00 0.00 35.96 3.35
225 226 1.400888 GCTCACTCACTCACTCACTCG 60.401 57.143 0.00 0.00 0.00 4.18
229 230 1.697284 ACTGCTCACTCACTCACTCA 58.303 50.000 0.00 0.00 0.00 3.41
255 256 1.006922 GCAAGCACCAACCAAGCTC 60.007 57.895 0.00 0.00 37.70 4.09
335 389 3.610349 GCAGAAGTAGAAAACAGCAAGGC 60.610 47.826 0.00 0.00 0.00 4.35
337 391 4.512944 TCAGCAGAAGTAGAAAACAGCAAG 59.487 41.667 0.00 0.00 0.00 4.01
343 397 5.063312 GCATCTCTCAGCAGAAGTAGAAAAC 59.937 44.000 0.00 0.00 0.00 2.43
350 411 1.481772 GGAGCATCTCTCAGCAGAAGT 59.518 52.381 0.00 0.00 43.70 3.01
399 463 0.475048 AAACTCGAAGGGGAAGGGGA 60.475 55.000 0.00 0.00 0.00 4.81
403 467 3.402628 TCTGAAAACTCGAAGGGGAAG 57.597 47.619 0.00 0.00 0.00 3.46
405 469 3.849563 TTTCTGAAAACTCGAAGGGGA 57.150 42.857 0.00 0.00 0.00 4.81
406 470 4.134563 TCTTTTCTGAAAACTCGAAGGGG 58.865 43.478 11.33 0.00 0.00 4.79
407 471 5.278022 CCTTCTTTTCTGAAAACTCGAAGGG 60.278 44.000 31.03 21.52 38.44 3.95
441 505 2.675348 CAGAGGAAACGAAATGCTCTCC 59.325 50.000 7.62 0.00 42.81 3.71
445 509 5.091261 AGATACAGAGGAAACGAAATGCT 57.909 39.130 0.00 0.00 0.00 3.79
446 510 4.271291 GGAGATACAGAGGAAACGAAATGC 59.729 45.833 0.00 0.00 0.00 3.56
447 511 4.504461 CGGAGATACAGAGGAAACGAAATG 59.496 45.833 0.00 0.00 0.00 2.32
453 517 3.889520 AACCGGAGATACAGAGGAAAC 57.110 47.619 9.46 0.00 0.00 2.78
456 520 3.053842 ACACTAACCGGAGATACAGAGGA 60.054 47.826 9.46 0.00 0.00 3.71
458 522 5.531659 ACATACACTAACCGGAGATACAGAG 59.468 44.000 9.46 0.00 0.00 3.35
459 523 5.443283 ACATACACTAACCGGAGATACAGA 58.557 41.667 9.46 0.00 0.00 3.41
460 524 5.769484 ACATACACTAACCGGAGATACAG 57.231 43.478 9.46 0.00 0.00 2.74
461 525 6.071221 ACAAACATACACTAACCGGAGATACA 60.071 38.462 9.46 0.00 0.00 2.29
462 526 6.335777 ACAAACATACACTAACCGGAGATAC 58.664 40.000 9.46 0.00 0.00 2.24
463 527 6.534475 ACAAACATACACTAACCGGAGATA 57.466 37.500 9.46 0.00 0.00 1.98
464 528 5.416271 ACAAACATACACTAACCGGAGAT 57.584 39.130 9.46 0.00 0.00 2.75
466 530 5.699458 AGAAACAAACATACACTAACCGGAG 59.301 40.000 9.46 0.00 0.00 4.63
467 531 5.613329 AGAAACAAACATACACTAACCGGA 58.387 37.500 9.46 0.00 0.00 5.14
468 532 5.699458 AGAGAAACAAACATACACTAACCGG 59.301 40.000 0.00 0.00 0.00 5.28
469 533 6.780706 AGAGAAACAAACATACACTAACCG 57.219 37.500 0.00 0.00 0.00 4.44
501 575 6.293004 ACAGAAATTTGACTGAACCCAAAA 57.707 33.333 12.48 0.00 36.10 2.44
504 578 6.516527 GCATAACAGAAATTTGACTGAACCCA 60.517 38.462 12.48 0.00 37.54 4.51
527 601 4.763073 CATCATCCACTGAAGTAAGAGCA 58.237 43.478 0.00 0.00 37.44 4.26
539 613 3.133721 GGAGTGAAGTAGCATCATCCACT 59.866 47.826 0.00 0.00 36.27 4.00
581 655 3.684908 TGCTCAGATCTAGCTAGCCTAG 58.315 50.000 16.35 12.32 44.09 3.02
582 656 3.684908 CTGCTCAGATCTAGCTAGCCTA 58.315 50.000 16.35 0.00 40.73 3.93
583 657 2.517959 CTGCTCAGATCTAGCTAGCCT 58.482 52.381 16.35 12.10 40.73 4.58
584 658 1.067635 GCTGCTCAGATCTAGCTAGCC 60.068 57.143 16.35 10.02 40.73 3.93
605 679 5.816955 ATCTGATTCCTAGCTAGTTTCCC 57.183 43.478 19.31 5.43 0.00 3.97
611 685 7.122650 CCCTCTTTCTATCTGATTCCTAGCTAG 59.877 44.444 14.20 14.20 0.00 3.42
624 698 6.488683 CGAGTGTTAGATCCCTCTTTCTATCT 59.511 42.308 0.00 0.00 32.66 1.98
636 853 3.129638 AGAACAGAGCGAGTGTTAGATCC 59.870 47.826 1.94 0.00 38.26 3.36
649 866 4.219725 AGAGGAAGTACAAGAGAACAGAGC 59.780 45.833 0.00 0.00 0.00 4.09
667 884 3.170717 ACAAGTAATTCCGGACAGAGGA 58.829 45.455 1.83 0.00 35.69 3.71
691 908 7.160049 AGCACATCTAGATACATCCATTTCTG 58.840 38.462 4.54 0.00 0.00 3.02
699 916 7.976135 AATGGAAAGCACATCTAGATACATC 57.024 36.000 4.54 1.87 0.00 3.06
714 931 6.560253 TTACTTGTCAGAGAAATGGAAAGC 57.440 37.500 0.00 0.00 0.00 3.51
728 945 3.118408 CCTCCATCCCGAATTACTTGTCA 60.118 47.826 0.00 0.00 0.00 3.58
741 958 0.031010 ACCAGTACTCCCTCCATCCC 60.031 60.000 0.00 0.00 0.00 3.85
745 962 2.715763 AGAAACCAGTACTCCCTCCA 57.284 50.000 0.00 0.00 0.00 3.86
758 975 7.447545 ACAACTTAAGGAACAGGAATAGAAACC 59.552 37.037 7.53 0.00 0.00 3.27
808 1312 8.417884 TCCACAAATAGAAAGGTAAACCAAAAG 58.582 33.333 1.26 0.00 38.89 2.27
848 1355 7.605691 CAGAACAAACTTGGAGAAGATGTATCT 59.394 37.037 0.00 0.00 39.22 1.98
849 1356 7.625185 GCAGAACAAACTTGGAGAAGATGTATC 60.625 40.741 0.00 0.00 34.13 2.24
851 1358 5.470098 GCAGAACAAACTTGGAGAAGATGTA 59.530 40.000 0.00 0.00 34.13 2.29
862 1369 5.517770 CCTTTTCAGAAGCAGAACAAACTTG 59.482 40.000 0.00 0.00 0.00 3.16
900 1409 1.202806 TCCAAGAGGGCAAGTCAAGTG 60.203 52.381 0.00 0.00 36.21 3.16
1047 1558 2.299867 ACTGTTTGGGATCAATGTTGCC 59.700 45.455 0.00 0.00 32.28 4.52
1083 1600 1.338020 GTCTTTGTGGCCCTGTTTGAG 59.662 52.381 0.00 0.00 0.00 3.02
1088 1605 1.151450 CAGGTCTTTGTGGCCCTGT 59.849 57.895 0.00 0.00 42.71 4.00
1225 1748 1.849219 GCTCTTGCTTCTGTCGTATCG 59.151 52.381 0.00 0.00 36.03 2.92
1395 1922 6.586082 ACATTCACTGAAACAAACTGTTCAAC 59.414 34.615 0.00 0.00 40.14 3.18
1486 2036 0.819259 ATCCCTGCACACACACACAC 60.819 55.000 0.00 0.00 0.00 3.82
1487 2037 0.818852 CATCCCTGCACACACACACA 60.819 55.000 0.00 0.00 0.00 3.72
1488 2038 1.518056 CCATCCCTGCACACACACAC 61.518 60.000 0.00 0.00 0.00 3.82
1489 2039 1.228215 CCATCCCTGCACACACACA 60.228 57.895 0.00 0.00 0.00 3.72
1518 2071 0.534877 ACATCTGCACCGCAAACTCA 60.535 50.000 0.00 0.00 38.41 3.41
1650 2207 7.476667 AGAGAAGTACTAACATGTCGATGAAG 58.523 38.462 0.00 0.00 33.36 3.02
1705 2262 3.368843 GCTGTGCACCTATCTTCAGAAGA 60.369 47.826 15.44 15.44 42.69 2.87
1813 2704 6.373759 ACTAGATCTTTTCAGTTTGGGGTTT 58.626 36.000 0.00 0.00 0.00 3.27
2014 2936 4.878397 GGAACAGAGGATGTACTTGATTGG 59.122 45.833 0.00 0.00 43.00 3.16
2047 2969 6.365520 ACAAGGAACAGAGGATGTACTTTTT 58.634 36.000 0.00 0.00 43.00 1.94
2051 2973 5.568620 AAACAAGGAACAGAGGATGTACT 57.431 39.130 0.00 0.00 43.00 2.73
2052 2974 7.739498 TTTAAACAAGGAACAGAGGATGTAC 57.261 36.000 0.00 0.00 43.00 2.90
2053 2975 8.754991 TTTTTAAACAAGGAACAGAGGATGTA 57.245 30.769 0.00 0.00 43.00 2.29
2054 2976 7.654022 TTTTTAAACAAGGAACAGAGGATGT 57.346 32.000 0.00 0.00 46.97 3.06
2076 2998 6.365520 ACAAGGAACAGAGGATGTACTTTTT 58.634 36.000 0.00 0.00 43.00 1.94
2077 2999 5.941788 ACAAGGAACAGAGGATGTACTTTT 58.058 37.500 0.00 0.00 43.00 2.27
2078 3000 5.568620 ACAAGGAACAGAGGATGTACTTT 57.431 39.130 0.00 0.00 43.00 2.66
2079 3001 5.568620 AACAAGGAACAGAGGATGTACTT 57.431 39.130 0.00 0.00 43.00 2.24
2080 3002 6.681729 TTAACAAGGAACAGAGGATGTACT 57.318 37.500 0.00 0.00 43.00 2.73
2081 3003 7.660208 TCTTTTAACAAGGAACAGAGGATGTAC 59.340 37.037 0.00 0.00 43.00 2.90
2082 3004 7.741785 TCTTTTAACAAGGAACAGAGGATGTA 58.258 34.615 0.00 0.00 43.00 2.29
2083 3005 6.601332 TCTTTTAACAAGGAACAGAGGATGT 58.399 36.000 0.00 0.00 46.97 3.06
2084 3006 7.510549 TTCTTTTAACAAGGAACAGAGGATG 57.489 36.000 0.00 0.00 0.00 3.51
2085 3007 8.533569 TTTTCTTTTAACAAGGAACAGAGGAT 57.466 30.769 0.00 0.00 28.13 3.24
2086 3008 7.948034 TTTTCTTTTAACAAGGAACAGAGGA 57.052 32.000 0.00 0.00 28.13 3.71
2087 3009 8.251026 ACTTTTTCTTTTAACAAGGAACAGAGG 58.749 33.333 9.61 0.00 28.13 3.69
2090 3012 9.849166 TGTACTTTTTCTTTTAACAAGGAACAG 57.151 29.630 0.00 4.41 28.13 3.16
2094 3016 9.416284 AGGATGTACTTTTTCTTTTAACAAGGA 57.584 29.630 0.00 0.00 0.00 3.36
2095 3017 9.678941 GAGGATGTACTTTTTCTTTTAACAAGG 57.321 33.333 0.00 0.00 0.00 3.61
2098 3020 9.403583 ACAGAGGATGTACTTTTTCTTTTAACA 57.596 29.630 0.00 0.00 41.60 2.41
2101 3023 9.063615 GGAACAGAGGATGTACTTTTTCTTTTA 57.936 33.333 0.00 0.00 43.00 1.52
2102 3024 7.780271 AGGAACAGAGGATGTACTTTTTCTTTT 59.220 33.333 0.00 0.00 43.00 2.27
2103 3025 7.290813 AGGAACAGAGGATGTACTTTTTCTTT 58.709 34.615 0.00 0.00 43.00 2.52
2104 3026 6.842676 AGGAACAGAGGATGTACTTTTTCTT 58.157 36.000 0.00 0.00 43.00 2.52
2105 3027 6.441088 AGGAACAGAGGATGTACTTTTTCT 57.559 37.500 0.00 0.00 43.00 2.52
2106 3028 8.617290 TTTAGGAACAGAGGATGTACTTTTTC 57.383 34.615 0.00 0.00 43.00 2.29
2153 3075 2.783828 ACCATGTCGCGAATCTCTAG 57.216 50.000 12.06 0.00 0.00 2.43
2375 3297 0.392193 ATGCGCTTCCAGTTCTCCTG 60.392 55.000 9.73 0.00 41.15 3.86
2476 3398 2.421073 CACACAGTAGCCCATGATGTTG 59.579 50.000 0.00 0.00 0.00 3.33
2653 3575 5.335127 CCGTTACCGCATATACATAGTACC 58.665 45.833 0.00 0.00 0.00 3.34
2654 3576 4.795278 GCCGTTACCGCATATACATAGTAC 59.205 45.833 0.00 0.00 0.00 2.73
2657 3579 3.840468 TGCCGTTACCGCATATACATAG 58.160 45.455 0.00 0.00 0.00 2.23
2664 3586 2.823924 ATACATGCCGTTACCGCATA 57.176 45.000 10.48 0.00 32.31 3.14
2665 3587 2.036733 AGTATACATGCCGTTACCGCAT 59.963 45.455 5.50 5.41 33.26 4.73
2668 3590 5.050644 TGATAGTATACATGCCGTTACCG 57.949 43.478 5.50 0.00 0.00 4.02
2669 3591 7.149973 TCTTTGATAGTATACATGCCGTTACC 58.850 38.462 5.50 0.00 0.00 2.85
2670 3592 8.485591 GTTCTTTGATAGTATACATGCCGTTAC 58.514 37.037 5.50 0.00 0.00 2.50
2672 3594 7.045416 TGTTCTTTGATAGTATACATGCCGTT 58.955 34.615 5.50 0.00 0.00 4.44
2674 3596 7.477144 TTGTTCTTTGATAGTATACATGCCG 57.523 36.000 5.50 0.00 0.00 5.69
2703 3679 6.403866 AACATCCACTAAGCTCTCTCTATG 57.596 41.667 0.00 0.00 0.00 2.23
2705 3681 6.424032 TGTAACATCCACTAAGCTCTCTCTA 58.576 40.000 0.00 0.00 0.00 2.43
2716 3696 7.778083 ACGTTCAGATTATGTAACATCCACTA 58.222 34.615 0.00 0.00 0.00 2.74
2717 3697 6.640518 ACGTTCAGATTATGTAACATCCACT 58.359 36.000 0.00 0.00 0.00 4.00
2718 3698 6.533723 TGACGTTCAGATTATGTAACATCCAC 59.466 38.462 0.00 0.00 0.00 4.02
2719 3699 6.635755 TGACGTTCAGATTATGTAACATCCA 58.364 36.000 0.00 0.00 0.00 3.41
2720 3700 7.715265 ATGACGTTCAGATTATGTAACATCC 57.285 36.000 0.00 0.00 0.00 3.51
2721 3701 8.604035 ACAATGACGTTCAGATTATGTAACATC 58.396 33.333 0.00 0.00 0.00 3.06
2722 3702 8.492673 ACAATGACGTTCAGATTATGTAACAT 57.507 30.769 0.00 0.00 0.00 2.71
2723 3703 7.600752 TGACAATGACGTTCAGATTATGTAACA 59.399 33.333 0.00 0.00 0.00 2.41
2725 3705 8.603181 CATGACAATGACGTTCAGATTATGTAA 58.397 33.333 0.00 0.00 35.67 2.41
2726 3706 7.254421 GCATGACAATGACGTTCAGATTATGTA 60.254 37.037 0.00 0.00 35.67 2.29
2727 3707 6.457392 GCATGACAATGACGTTCAGATTATGT 60.457 38.462 0.00 0.00 35.67 2.29
2728 3708 5.905733 GCATGACAATGACGTTCAGATTATG 59.094 40.000 0.00 0.00 35.67 1.90
2731 3711 3.752747 TGCATGACAATGACGTTCAGATT 59.247 39.130 0.00 0.00 35.67 2.40
2732 3712 3.337358 TGCATGACAATGACGTTCAGAT 58.663 40.909 0.00 0.00 35.67 2.90
2734 3714 2.159612 CCTGCATGACAATGACGTTCAG 60.160 50.000 0.00 0.00 35.67 3.02
2736 3716 1.806542 ACCTGCATGACAATGACGTTC 59.193 47.619 0.00 0.00 35.67 3.95
2737 3717 1.896220 ACCTGCATGACAATGACGTT 58.104 45.000 0.00 0.00 35.67 3.99
2738 3718 2.760634 TACCTGCATGACAATGACGT 57.239 45.000 0.00 0.00 35.67 4.34
2739 3719 4.319046 GCTATTACCTGCATGACAATGACG 60.319 45.833 0.00 0.00 35.67 4.35
2740 3720 4.576053 TGCTATTACCTGCATGACAATGAC 59.424 41.667 0.00 0.00 35.67 3.06
2741 3721 4.779696 TGCTATTACCTGCATGACAATGA 58.220 39.130 0.00 0.00 35.67 2.57
2742 3722 4.556104 GCTGCTATTACCTGCATGACAATG 60.556 45.833 0.00 0.00 38.59 2.82
2743 3723 3.567164 GCTGCTATTACCTGCATGACAAT 59.433 43.478 0.00 0.00 38.59 2.71
2745 3725 2.093021 TGCTGCTATTACCTGCATGACA 60.093 45.455 0.00 0.00 38.59 3.58
2746 3726 2.547211 CTGCTGCTATTACCTGCATGAC 59.453 50.000 0.00 0.00 38.59 3.06
2747 3727 2.486013 CCTGCTGCTATTACCTGCATGA 60.486 50.000 0.00 0.00 38.59 3.07
2748 3728 1.878088 CCTGCTGCTATTACCTGCATG 59.122 52.381 0.00 0.00 38.59 4.06
2749 3729 1.202855 CCCTGCTGCTATTACCTGCAT 60.203 52.381 0.00 0.00 38.59 3.96
2889 7237 3.744238 ACAAACCACCAGTAATTTGGC 57.256 42.857 9.48 0.00 42.18 4.52
3012 7360 3.750130 CAGTCATCTTCTTGAGTGGGTTG 59.250 47.826 2.09 0.00 41.40 3.77
3282 7635 0.742505 ATAACCGAACGATCCGCTCA 59.257 50.000 0.00 0.00 0.00 4.26
3288 7641 5.585390 TGTCTCCTAAATAACCGAACGATC 58.415 41.667 0.00 0.00 0.00 3.69
3315 7668 6.814146 GTGGTACCTTCTGAATCTTAACTGAG 59.186 42.308 14.36 0.00 0.00 3.35
3353 7706 9.054922 CAAACAATGAAAAACCATATGAAAGGT 57.945 29.630 3.65 0.00 40.61 3.50
3469 7830 4.460382 TCTTTGCTGTTCAGAAATCCATCC 59.540 41.667 3.84 0.00 0.00 3.51
3532 7900 7.706100 TGTTTAGGACACAAAAGTTAAAGGT 57.294 32.000 0.00 0.00 32.00 3.50
3575 7947 7.342581 TGGACATATAAAGAGCCAACACATTA 58.657 34.615 0.00 0.00 0.00 1.90
3626 7998 5.751680 CAATTTATGAAGATGTACTGCCCG 58.248 41.667 0.00 0.00 0.00 6.13
3691 8064 5.976458 TGCAACTGGTTTCTTTTTCTCAAT 58.024 33.333 0.00 0.00 0.00 2.57
3855 8229 4.043561 ACCTCAGAGAAGACAGTCCTAAGA 59.956 45.833 0.00 0.00 0.00 2.10
3926 8301 6.616947 TGTTTCTCCTGTTACACAAACTTTG 58.383 36.000 0.00 0.00 38.99 2.77
3927 8302 6.827586 TGTTTCTCCTGTTACACAAACTTT 57.172 33.333 0.00 0.00 38.99 2.66
4397 8772 2.159327 GCAATAGGGAATGGCATTGC 57.841 50.000 21.87 21.87 44.39 3.56
4407 8782 4.556697 TCCATCAAGTAGAGCAATAGGGA 58.443 43.478 0.00 0.00 0.00 4.20
4408 8783 4.963318 TCCATCAAGTAGAGCAATAGGG 57.037 45.455 0.00 0.00 0.00 3.53
4409 8784 5.059833 GGTTCCATCAAGTAGAGCAATAGG 58.940 45.833 0.00 0.00 0.00 2.57
4410 8785 4.747108 CGGTTCCATCAAGTAGAGCAATAG 59.253 45.833 0.00 0.00 0.00 1.73
4411 8786 4.404394 TCGGTTCCATCAAGTAGAGCAATA 59.596 41.667 0.00 0.00 0.00 1.90
4412 8787 3.197766 TCGGTTCCATCAAGTAGAGCAAT 59.802 43.478 0.00 0.00 0.00 3.56
4413 8788 2.565391 TCGGTTCCATCAAGTAGAGCAA 59.435 45.455 0.00 0.00 0.00 3.91
4439 8814 5.092781 CACGCCTGGTTTACATTTAATGTC 58.907 41.667 14.29 0.86 43.67 3.06
4442 8817 4.142773 CGACACGCCTGGTTTACATTTAAT 60.143 41.667 0.00 0.00 0.00 1.40
4618 9001 7.200434 AGGGAATCTAGTACATGTCAAACAT 57.800 36.000 0.00 0.00 39.91 2.71
4675 9058 2.052782 ATTCCCGGTAATCTTGTGCC 57.947 50.000 0.00 0.00 0.00 5.01
4732 9115 3.010027 TCACAATGCTGATCAAAGGGGTA 59.990 43.478 0.00 0.00 0.00 3.69
4810 9193 2.443577 TTTGCCTTGCCACTGCCA 60.444 55.556 0.00 0.00 36.33 4.92
5169 9562 8.516234 ACATTTCTAGTACCAGATCGATATGAC 58.484 37.037 21.24 12.09 0.00 3.06
5173 9566 6.148976 CCGACATTTCTAGTACCAGATCGATA 59.851 42.308 11.87 0.00 29.12 2.92
5189 9582 6.142480 CGATGATAACTAGTCACCGACATTTC 59.858 42.308 0.00 0.00 34.53 2.17
5371 9764 7.095910 ACATGCTCTTACATCAGCTACATATC 58.904 38.462 0.00 0.00 36.53 1.63
5481 10026 6.480524 TCACGATTTGTTCAGTAATCAAGG 57.519 37.500 0.00 0.00 31.70 3.61
5487 10032 5.587043 ACCAGTTTCACGATTTGTTCAGTAA 59.413 36.000 0.00 0.00 0.00 2.24
5586 10132 7.487189 GCTCAAGGTGATTTTTAGATGTGATTG 59.513 37.037 0.00 0.00 0.00 2.67
5685 10231 9.880157 GAAATGAACTTATTGTGTACTAGGGTA 57.120 33.333 0.00 0.00 0.00 3.69
5687 10233 8.665685 GTGAAATGAACTTATTGTGTACTAGGG 58.334 37.037 0.00 0.00 0.00 3.53
5688 10234 9.214957 TGTGAAATGAACTTATTGTGTACTAGG 57.785 33.333 0.00 0.00 0.00 3.02
5717 10276 9.923143 ACTTTAGTTATTTTGATTAGCAAACCC 57.077 29.630 0.00 0.00 45.64 4.11
5809 10372 5.821470 AGAAATACAGCTGTCATGGAGAATG 59.179 40.000 25.56 0.00 37.66 2.67
5810 10373 5.999044 AGAAATACAGCTGTCATGGAGAAT 58.001 37.500 25.56 5.55 0.00 2.40
5819 10382 5.003804 TCCTTTGGAAGAAATACAGCTGTC 58.996 41.667 25.56 9.12 0.00 3.51
5823 10386 7.826690 TGTAATTCCTTTGGAAGAAATACAGC 58.173 34.615 5.27 0.00 45.48 4.40
5828 10391 9.320295 TGGTTATGTAATTCCTTTGGAAGAAAT 57.680 29.630 5.27 0.04 45.48 2.17
5829 10392 8.581578 GTGGTTATGTAATTCCTTTGGAAGAAA 58.418 33.333 5.27 0.00 45.48 2.52
5830 10393 7.726291 TGTGGTTATGTAATTCCTTTGGAAGAA 59.274 33.333 5.27 0.00 45.48 2.52
5831 10394 7.235079 TGTGGTTATGTAATTCCTTTGGAAGA 58.765 34.615 5.27 0.00 45.48 2.87
5832 10395 7.461182 TGTGGTTATGTAATTCCTTTGGAAG 57.539 36.000 5.27 0.00 45.48 3.46
5833 10396 7.726291 TCTTGTGGTTATGTAATTCCTTTGGAA 59.274 33.333 1.24 1.24 46.39 3.53
5839 10422 7.065803 CGACATTCTTGTGGTTATGTAATTCCT 59.934 37.037 0.00 0.00 35.79 3.36
5872 10455 4.147653 CACCGTACGTTCTTTAGTGAGTTG 59.852 45.833 15.21 0.00 0.00 3.16
5910 10493 1.411977 TCGACACCGGACACCTTTTTA 59.588 47.619 9.46 0.00 36.24 1.52
5911 10494 0.178533 TCGACACCGGACACCTTTTT 59.821 50.000 9.46 0.00 36.24 1.94
5958 10543 1.884075 TACGTTGATGCACTCCCGCT 61.884 55.000 0.00 0.00 0.00 5.52
6089 10674 2.882137 CAAATTTAGTGACACGGTGGGT 59.118 45.455 13.48 0.00 0.00 4.51
6217 10802 2.753452 GACTACTCATGGAACTCGGACA 59.247 50.000 0.00 0.00 0.00 4.02
6255 10840 1.135960 GAGGAGGAGGAGGAATTGGG 58.864 60.000 0.00 0.00 0.00 4.12
6275 10860 2.627221 AGACGAGGATGGTGATGATGAG 59.373 50.000 0.00 0.00 0.00 2.90
6296 10890 1.663379 ATGGCGACGACGAGGATGAA 61.663 55.000 12.29 0.00 42.66 2.57
6311 10905 2.914797 ATGACGACGACGACGATGGC 62.915 60.000 25.15 8.31 42.66 4.40
6317 10911 2.037649 GATGATGATGACGACGACGAC 58.962 52.381 15.32 8.68 42.66 4.34
6323 10917 5.867716 TGATGATGATGATGATGATGACGAC 59.132 40.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.