Multiple sequence alignment - TraesCS6B01G176200

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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 TraesCS6B01G176200 chr6B 100.000 6597 0 0 1 6597 192355653 192349057 0.000000e+00 12183.0
1 TraesCS6B01G176200 chr6B 95.070 142 1 4 3731 3867 224208465 224208325 1.110000e-52 219.0
2 TraesCS6B01G176200 chr6B 98.913 92 1 0 6021 6112 192349541 192349450 1.470000e-36 165.0
3 TraesCS6B01G176200 chr6B 98.913 92 1 0 6113 6204 192349633 192349542 1.470000e-36 165.0
4 TraesCS6B01G176200 chr6D 95.258 3416 91 25 6 3399 105825131 105821765 0.000000e+00 5345.0
5 TraesCS6B01G176200 chr6D 96.751 1816 44 8 4306 6112 105821764 105819955 0.000000e+00 3013.0
6 TraesCS6B01G176200 chr6D 96.502 486 14 3 6113 6597 105820045 105819562 0.000000e+00 800.0
7 TraesCS6B01G176200 chr6D 79.422 277 36 16 1608 1868 472714714 472714985 6.800000e-40 176.0
8 TraesCS6B01G176200 chr6D 74.558 283 53 14 1636 1906 78467878 78468153 9.050000e-19 106.0
9 TraesCS6B01G176200 chr6A 94.725 2256 72 14 3868 6112 128445079 128442860 0.000000e+00 3463.0
10 TraesCS6B01G176200 chr6A 94.637 1417 39 7 469 1873 128448654 128447263 0.000000e+00 2161.0
11 TraesCS6B01G176200 chr6A 95.798 1285 45 6 2468 3745 128446360 128445078 0.000000e+00 2065.0
12 TraesCS6B01G176200 chr6A 93.705 699 38 4 1873 2566 128447051 128446354 0.000000e+00 1042.0
13 TraesCS6B01G176200 chr6A 96.313 434 15 1 6 439 128449615 128449183 0.000000e+00 712.0
14 TraesCS6B01G176200 chr6A 96.296 216 7 1 6113 6327 128442951 128442736 2.930000e-93 353.0
15 TraesCS6B01G176200 chr6A 100.000 133 0 0 6465 6597 128440869 128440737 5.110000e-61 246.0
16 TraesCS6B01G176200 chr6A 76.503 366 53 25 1567 1909 594287424 594287069 1.140000e-37 169.0
17 TraesCS6B01G176200 chr6A 91.964 112 7 1 6327 6438 128440971 128440862 8.860000e-34 156.0
18 TraesCS6B01G176200 chr6A 89.796 98 5 3 5296 5392 551840517 551840424 3.230000e-23 121.0
19 TraesCS6B01G176200 chr5A 85.559 367 24 7 1555 1909 559739227 559738878 2.260000e-94 357.0
20 TraesCS6B01G176200 chr5A 79.239 289 41 4 1588 1871 476025028 476025302 4.060000e-42 183.0
21 TraesCS6B01G176200 chr5A 89.796 98 5 3 5296 5392 5695991 5695898 3.230000e-23 121.0
22 TraesCS6B01G176200 chr5A 91.011 89 4 2 5296 5384 493820308 493820224 4.180000e-22 117.0
23 TraesCS6B01G176200 chr1A 84.073 383 39 13 1537 1908 518769161 518769532 3.790000e-92 350.0
24 TraesCS6B01G176200 chr1A 80.973 226 29 10 1614 1826 24335218 24335442 4.090000e-37 167.0
25 TraesCS6B01G176200 chr1A 78.313 249 35 9 1567 1800 63861653 63861897 6.900000e-30 143.0
26 TraesCS6B01G176200 chr1A 89.796 98 5 3 5296 5392 478362861 478362954 3.230000e-23 121.0
27 TraesCS6B01G176200 chr1A 89.000 100 6 3 5296 5394 146184625 146184720 1.160000e-22 119.0
28 TraesCS6B01G176200 chr7A 87.338 308 31 7 1569 1873 216353679 216353377 4.900000e-91 346.0
29 TraesCS6B01G176200 chr7A 84.083 289 32 11 1569 1852 25338065 25337786 3.920000e-67 267.0
30 TraesCS6B01G176200 chr7A 73.117 677 146 32 4349 5012 692879381 692880034 6.700000e-50 209.0
31 TraesCS6B01G176200 chr7A 73.975 561 102 32 2751 3285 692877825 692878367 3.140000e-43 187.0
32 TraesCS6B01G176200 chr7A 90.400 125 12 0 5410 5534 692880354 692880478 1.470000e-36 165.0
33 TraesCS6B01G176200 chr7A 86.538 104 9 5 5294 5396 506684318 506684219 6.990000e-20 110.0
34 TraesCS6B01G176200 chr5D 84.282 369 27 8 1555 1909 443498480 443498129 1.370000e-86 331.0
35 TraesCS6B01G176200 chr5D 79.623 265 33 6 1612 1871 374201201 374201449 3.160000e-38 171.0
36 TraesCS6B01G176200 chr5D 78.369 282 40 14 1567 1835 391310730 391310457 5.290000e-36 163.0
37 TraesCS6B01G176200 chr7D 87.912 273 26 5 1605 1873 204256287 204256018 1.380000e-81 315.0
38 TraesCS6B01G176200 chr7D 74.332 561 97 34 2751 3285 600884135 600884674 1.880000e-45 195.0
39 TraesCS6B01G176200 chr7D 72.566 678 149 32 4349 5012 600885696 600886350 3.140000e-43 187.0
40 TraesCS6B01G176200 chr7D 90.400 125 12 0 5410 5534 600886672 600886796 1.470000e-36 165.0
41 TraesCS6B01G176200 chr2D 80.263 380 47 17 1541 1907 539412731 539413095 1.820000e-65 261.0
42 TraesCS6B01G176200 chr2D 96.324 136 4 1 3736 3870 536091159 536091024 8.610000e-54 222.0
43 TraesCS6B01G176200 chr3A 87.391 230 24 3 1625 1851 57231402 57231629 6.560000e-65 259.0
44 TraesCS6B01G176200 chr4D 82.578 287 39 8 1538 1820 496870623 496870902 6.610000e-60 243.0
45 TraesCS6B01G176200 chr4D 96.269 134 4 1 3737 3869 106682247 106682380 1.110000e-52 219.0
46 TraesCS6B01G176200 chr4D 79.264 299 43 15 1567 1851 46141737 46142030 2.430000e-44 191.0
47 TraesCS6B01G176200 chr4D 78.616 159 29 4 1567 1724 483234256 483234410 4.210000e-17 100.0
48 TraesCS6B01G176200 chr4A 83.270 263 38 5 1614 1872 485510878 485511138 3.070000e-58 237.0
49 TraesCS6B01G176200 chr4A 92.810 153 6 5 3742 3890 736061080 736061231 4.010000e-52 217.0
50 TraesCS6B01G176200 chr4A 77.232 224 25 14 1630 1851 60882465 60882664 2.520000e-19 108.0
51 TraesCS6B01G176200 chr7B 96.992 133 3 1 3742 3873 678632358 678632490 8.610000e-54 222.0
52 TraesCS6B01G176200 chr7B 73.225 676 147 30 4349 5012 680115871 680116524 1.440000e-51 215.0
53 TraesCS6B01G176200 chr7B 90.400 125 12 0 5410 5534 680116845 680116969 1.470000e-36 165.0
54 TraesCS6B01G176200 chr7B 77.027 296 43 17 2747 3023 680114318 680114607 5.330000e-31 147.0
55 TraesCS6B01G176200 chr7B 87.629 97 8 2 5293 5389 8925179 8925271 6.990000e-20 110.0
56 TraesCS6B01G176200 chrUn 95.620 137 4 2 3737 3872 11031655 11031790 1.110000e-52 219.0
57 TraesCS6B01G176200 chr4B 95.620 137 5 1 3742 3877 671676822 671676686 1.110000e-52 219.0
58 TraesCS6B01G176200 chr4B 79.655 290 48 8 1567 1851 500080858 500081141 1.450000e-46 198.0
59 TraesCS6B01G176200 chr3D 95.620 137 4 2 3737 3871 267286404 267286540 1.110000e-52 219.0
60 TraesCS6B01G176200 chr3D 78.882 322 46 15 1567 1872 346092169 346091854 1.450000e-46 198.0
61 TraesCS6B01G176200 chr3D 76.000 300 52 17 1564 1851 10670713 10670422 3.210000e-28 137.0
62 TraesCS6B01G176200 chr3D 73.432 271 50 16 1567 1821 557269011 557268747 1.520000e-11 82.4
63 TraesCS6B01G176200 chr2B 95.588 136 5 1 3739 3873 423662678 423662813 4.010000e-52 217.0
64 TraesCS6B01G176200 chr2A 89.796 98 5 3 5296 5392 80987383 80987290 3.230000e-23 121.0


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 TraesCS6B01G176200 chr6B 192349057 192355653 6596 True 12183.000000 12183 100.000000 1 6597 1 chr6B.!!$R1 6596
1 TraesCS6B01G176200 chr6D 105819562 105825131 5569 True 3052.666667 5345 96.170333 6 6597 3 chr6D.!!$R1 6591
2 TraesCS6B01G176200 chr6A 128440737 128449615 8878 True 1274.750000 3463 95.429750 6 6597 8 chr6A.!!$R3 6591

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
207 208 0.039618 GAATTGGGAGCTGTTGGGGA 59.960 55.000 0.00 0.00 0.00 4.81 F
458 701 0.321671 AGATGTGTTCCCAGGACGTG 59.678 55.000 0.00 0.00 0.00 4.49 F
804 1325 1.134995 TCTCCACTGCTATTGTCTGCG 60.135 52.381 0.00 0.00 0.00 5.18 F
2324 3061 0.393808 ACTTGGCGTGGACTTTGTGT 60.394 50.000 0.00 0.00 0.00 3.72 F
3542 4385 0.041312 GGTGTTTACGCTGCACAGTG 60.041 55.000 9.59 9.59 44.11 3.66 F
4487 5331 0.030092 TCTAGGGCTGGCCAGGTATT 60.030 55.000 33.46 2.65 37.98 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1730 3.150458 TCGGTCTTTGGAGTACTGAGA 57.850 47.619 0.00 0.0 0.00 3.27 R
2324 3061 3.181492 ACACGTCAAATGTTTCATGTGCA 60.181 39.130 2.23 0.0 0.00 4.57 R
2519 3350 8.525316 TCACTGCAACATTGATTCATTAGAATT 58.475 29.630 0.00 0.0 44.30 2.17 R
3742 4585 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.0 0.00 3.85 R
5265 6110 1.278238 GTGCAACGTAATCTCCTCCG 58.722 55.000 0.00 0.0 0.00 4.63 R
5616 6461 0.107703 CCAGTGGAGCCTTCGCATAA 60.108 55.000 1.68 0.0 37.52 1.90 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
134 135 1.946475 GAGGTCGGGTTTCTCGAGGG 61.946 65.000 13.56 0.00 37.31 4.30
167 168 2.297315 TGCTGGTATCATGGTCGATCTC 59.703 50.000 0.00 0.00 0.00 2.75
175 176 0.178961 ATGGTCGATCTCGGGATGGA 60.179 55.000 0.20 3.47 40.29 3.41
207 208 0.039618 GAATTGGGAGCTGTTGGGGA 59.960 55.000 0.00 0.00 0.00 4.81
229 230 5.047377 GGAGTGGAGTGGAGATGATAGATTC 60.047 48.000 0.00 0.00 0.00 2.52
234 235 5.106317 GGAGTGGAGATGATAGATTCGAGAC 60.106 48.000 0.00 0.00 0.00 3.36
255 256 2.553466 CCCGGGAATGGTTTCTGTGTAA 60.553 50.000 18.48 0.00 32.16 2.41
348 349 1.355381 ACTTGGAATGTGCTCCATGGA 59.645 47.619 15.27 15.27 45.03 3.41
458 701 0.321671 AGATGTGTTCCCAGGACGTG 59.678 55.000 0.00 0.00 0.00 4.49
498 1000 9.520204 CATCTTGTGTCTTACATTTTGAAAAGT 57.480 29.630 0.00 0.00 39.48 2.66
499 1001 8.909708 TCTTGTGTCTTACATTTTGAAAAGTG 57.090 30.769 0.00 0.00 39.48 3.16
762 1283 3.422546 CGACTGTCTTTCGTTCTTGTCTC 59.577 47.826 6.21 0.00 0.00 3.36
763 1284 4.612943 GACTGTCTTTCGTTCTTGTCTCT 58.387 43.478 0.00 0.00 0.00 3.10
764 1285 4.363999 ACTGTCTTTCGTTCTTGTCTCTG 58.636 43.478 0.00 0.00 0.00 3.35
804 1325 1.134995 TCTCCACTGCTATTGTCTGCG 60.135 52.381 0.00 0.00 0.00 5.18
939 1460 6.153851 TCTGTTTGATGATGATTCTTGCCATT 59.846 34.615 0.00 0.00 0.00 3.16
1015 1536 5.945191 TGAGATTTGATGCACTGGAATGTTA 59.055 36.000 0.00 0.00 0.00 2.41
1209 1730 3.269381 TCCTTGCCAAGATGGGAGTTTAT 59.731 43.478 5.89 0.00 39.66 1.40
1487 2008 1.269448 CAATGGTGGGAACGACCAAAG 59.731 52.381 7.21 0.12 43.34 2.77
1896 2631 2.884639 GTGCAATGAACTTGGGTGTAGT 59.115 45.455 0.00 0.00 35.25 2.73
1911 2646 6.762333 TGGGTGTAGTTACTACTTTTCCTTC 58.238 40.000 21.20 8.89 37.78 3.46
2324 3061 0.393808 ACTTGGCGTGGACTTTGTGT 60.394 50.000 0.00 0.00 0.00 3.72
2519 3350 7.765695 AGCTCTTGTTTATCAATCTTTCCAA 57.234 32.000 0.00 0.00 35.35 3.53
2741 3579 6.330278 TCTCTCATGTACTGTTTAATGTCCG 58.670 40.000 0.00 0.00 0.00 4.79
2949 3787 6.647212 TTCTGTGCAAAATATCTACACTCG 57.353 37.500 0.00 0.00 32.49 4.18
2985 3823 5.181748 AGTGAAGCATATTCTTCTGGTGAC 58.818 41.667 14.87 5.76 42.15 3.67
3056 3894 9.859152 TTGGATCACCACATGAAACAATATATA 57.141 29.630 0.00 0.00 46.80 0.86
3288 4131 5.109479 ACTGGGCTCTAGAGGAGGTATATA 58.891 45.833 21.23 0.00 42.08 0.86
3383 4226 7.069331 TGTGGACCTTATTTGTGTTTGATTCTT 59.931 33.333 0.00 0.00 0.00 2.52
3542 4385 0.041312 GGTGTTTACGCTGCACAGTG 60.041 55.000 9.59 9.59 44.11 3.66
3574 4417 4.681942 GTGACAGTACAGTTCTGTGCTTAG 59.318 45.833 16.91 11.94 44.68 2.18
3657 4500 8.745590 TGCCTCTATTGTTTTAAAAAGATACCC 58.254 33.333 1.31 0.00 0.00 3.69
3670 4513 1.559682 AGATACCCATGTCCACCACAC 59.440 52.381 0.00 0.00 38.04 3.82
3729 4572 2.512692 TACCATGCATTGCCTCAAGT 57.487 45.000 6.12 0.00 0.00 3.16
3749 4592 4.652421 GTAGTGGCTTTACTACTCCCTC 57.348 50.000 14.80 0.00 46.00 4.30
3750 4593 2.468915 AGTGGCTTTACTACTCCCTCC 58.531 52.381 0.00 0.00 34.47 4.30
3751 4594 1.136500 GTGGCTTTACTACTCCCTCCG 59.864 57.143 0.00 0.00 0.00 4.63
3752 4595 1.272872 TGGCTTTACTACTCCCTCCGT 60.273 52.381 0.00 0.00 0.00 4.69
3753 4596 1.408340 GGCTTTACTACTCCCTCCGTC 59.592 57.143 0.00 0.00 0.00 4.79
3754 4597 1.408340 GCTTTACTACTCCCTCCGTCC 59.592 57.143 0.00 0.00 0.00 4.79
3755 4598 2.030371 CTTTACTACTCCCTCCGTCCC 58.970 57.143 0.00 0.00 0.00 4.46
3756 4599 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3757 4600 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3758 4601 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3759 4602 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
3760 4603 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
3761 4604 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3762 4605 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3763 4606 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3764 4607 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3765 4608 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3766 4609 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3767 4610 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3768 4611 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3769 4612 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3770 4613 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3771 4614 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3772 4615 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3773 4616 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3774 4617 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3775 4618 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3776 4619 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3777 4620 7.329471 GTCCCAAAATTCTTGTCTTAGATTTGC 59.671 37.037 0.00 0.00 29.17 3.68
3778 4621 6.591448 CCCAAAATTCTTGTCTTAGATTTGCC 59.409 38.462 0.00 0.00 29.17 4.52
3779 4622 7.381323 CCAAAATTCTTGTCTTAGATTTGCCT 58.619 34.615 0.00 0.00 29.17 4.75
3780 4623 8.522830 CCAAAATTCTTGTCTTAGATTTGCCTA 58.477 33.333 0.00 0.00 29.17 3.93
3781 4624 9.565213 CAAAATTCTTGTCTTAGATTTGCCTAG 57.435 33.333 0.00 0.00 0.00 3.02
3782 4625 9.520515 AAAATTCTTGTCTTAGATTTGCCTAGA 57.479 29.630 0.00 0.00 0.00 2.43
3783 4626 9.692325 AAATTCTTGTCTTAGATTTGCCTAGAT 57.308 29.630 0.00 0.00 0.00 1.98
3785 4628 9.771534 ATTCTTGTCTTAGATTTGCCTAGATAC 57.228 33.333 0.00 0.00 0.00 2.24
3786 4629 7.426410 TCTTGTCTTAGATTTGCCTAGATACG 58.574 38.462 0.00 0.00 0.00 3.06
3787 4630 6.085555 TGTCTTAGATTTGCCTAGATACGG 57.914 41.667 0.00 0.00 0.00 4.02
3788 4631 5.831525 TGTCTTAGATTTGCCTAGATACGGA 59.168 40.000 0.00 0.00 0.00 4.69
3789 4632 6.493802 TGTCTTAGATTTGCCTAGATACGGAT 59.506 38.462 0.00 0.00 0.00 4.18
3790 4633 6.809196 GTCTTAGATTTGCCTAGATACGGATG 59.191 42.308 0.00 0.00 0.00 3.51
3791 4634 6.493802 TCTTAGATTTGCCTAGATACGGATGT 59.506 38.462 0.00 0.00 0.00 3.06
3792 4635 7.668469 TCTTAGATTTGCCTAGATACGGATGTA 59.332 37.037 0.00 0.00 34.45 2.29
3793 4636 6.859112 AGATTTGCCTAGATACGGATGTAT 57.141 37.500 0.00 0.00 43.97 2.29
3823 4666 7.539712 ACTAAAACATGACTTGATACATCCG 57.460 36.000 0.00 0.00 0.00 4.18
3824 4667 7.103641 ACTAAAACATGACTTGATACATCCGT 58.896 34.615 0.00 0.00 0.00 4.69
3825 4668 8.255206 ACTAAAACATGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 0.00 4.02
3826 4669 9.261180 CTAAAACATGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
3827 4670 8.506168 AAAACATGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
3828 4671 8.506168 AAACATGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
3829 4672 9.607988 AAACATGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
3830 4673 8.818141 ACATGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
3831 4674 8.638873 ACATGACTTGATACATCCGTATTTAGA 58.361 33.333 0.00 0.00 38.48 2.10
3832 4675 8.916654 CATGACTTGATACATCCGTATTTAGAC 58.083 37.037 0.00 0.00 38.48 2.59
3833 4676 8.002984 TGACTTGATACATCCGTATTTAGACA 57.997 34.615 0.00 0.00 38.48 3.41
3834 4677 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
3835 4678 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
3836 4679 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
3843 4686 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
3844 4687 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
3846 4689 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3847 4690 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
3858 4701 7.602517 AATCTAAGACAAGATTTTGAGACGG 57.397 36.000 2.48 0.00 42.28 4.79
3859 4702 6.340962 TCTAAGACAAGATTTTGAGACGGA 57.659 37.500 2.48 0.00 37.73 4.69
3860 4703 6.390721 TCTAAGACAAGATTTTGAGACGGAG 58.609 40.000 2.48 0.00 37.73 4.63
3861 4704 3.931578 AGACAAGATTTTGAGACGGAGG 58.068 45.455 2.48 0.00 37.73 4.30
3862 4705 3.003480 GACAAGATTTTGAGACGGAGGG 58.997 50.000 2.48 0.00 37.73 4.30
3863 4706 2.637872 ACAAGATTTTGAGACGGAGGGA 59.362 45.455 2.48 0.00 37.73 4.20
3864 4707 3.265791 CAAGATTTTGAGACGGAGGGAG 58.734 50.000 0.00 0.00 36.36 4.30
3865 4708 2.541466 AGATTTTGAGACGGAGGGAGT 58.459 47.619 0.00 0.00 0.00 3.85
3866 4709 3.709587 AGATTTTGAGACGGAGGGAGTA 58.290 45.455 0.00 0.00 0.00 2.59
3876 4719 4.166531 AGACGGAGGGAGTACTTTAGAGAT 59.833 45.833 0.00 0.00 0.00 2.75
3888 4731 9.660180 GAGTACTTTAGAGATGATCCTTTGTTT 57.340 33.333 0.00 0.00 0.00 2.83
3930 4773 7.020827 TGAAAGGGAAGAGTATTCAGACATT 57.979 36.000 0.00 0.00 0.00 2.71
3935 4778 5.363939 GGAAGAGTATTCAGACATTCCTGG 58.636 45.833 0.00 0.00 35.83 4.45
3940 4783 6.013379 AGAGTATTCAGACATTCCTGGTTTGA 60.013 38.462 5.80 0.00 34.99 2.69
3947 4790 7.685481 TCAGACATTCCTGGTTTGATTACTTA 58.315 34.615 5.80 0.00 34.99 2.24
4032 4875 5.415701 GTGATATCCACACTTTGGTGATGTT 59.584 40.000 0.00 0.00 46.97 2.71
4033 4876 5.647658 TGATATCCACACTTTGGTGATGTTC 59.352 40.000 0.00 0.00 46.97 3.18
4034 4877 2.217750 TCCACACTTTGGTGATGTTCG 58.782 47.619 3.06 0.00 46.97 3.95
4035 4878 1.946768 CCACACTTTGGTGATGTTCGT 59.053 47.619 3.06 0.00 45.61 3.85
4036 4879 2.032030 CCACACTTTGGTGATGTTCGTC 60.032 50.000 3.06 0.00 45.61 4.20
4037 4880 2.611751 CACACTTTGGTGATGTTCGTCA 59.388 45.455 3.06 0.00 45.61 4.35
4038 4881 3.064682 CACACTTTGGTGATGTTCGTCAA 59.935 43.478 3.06 0.00 45.61 3.18
4076 4919 4.744867 GCTGCAAGATAATAGCCAGAGGAA 60.745 45.833 0.00 0.00 34.07 3.36
4104 4947 6.699204 TGACAAATTGCATGTAAATTCAACGT 59.301 30.769 0.00 0.00 0.00 3.99
4111 4954 5.105957 TGCATGTAAATTCAACGTATTGGCT 60.106 36.000 0.00 0.00 36.39 4.75
4147 4990 9.942850 CATATAGATGTGGTGGTTCATACATAA 57.057 33.333 0.00 0.00 34.18 1.90
4190 5033 7.038154 TCTGTAATGTTTGCTTAGCTTTTGT 57.962 32.000 5.60 0.00 0.00 2.83
4227 5070 3.160679 ACCAACCTGCAAGCTAAGAAT 57.839 42.857 0.00 0.00 0.00 2.40
4233 5076 5.382618 ACCTGCAAGCTAAGAATGAAAAG 57.617 39.130 0.00 0.00 0.00 2.27
4282 5125 8.671921 CATTGTCTTGAAGATGCAGTTACTATT 58.328 33.333 0.00 0.00 0.00 1.73
4285 5128 7.877612 TGTCTTGAAGATGCAGTTACTATTTCA 59.122 33.333 0.00 0.00 0.00 2.69
4286 5129 8.171840 GTCTTGAAGATGCAGTTACTATTTCAC 58.828 37.037 0.00 0.00 0.00 3.18
4287 5130 7.877612 TCTTGAAGATGCAGTTACTATTTCACA 59.122 33.333 0.00 0.00 0.00 3.58
4288 5131 7.601073 TGAAGATGCAGTTACTATTTCACAG 57.399 36.000 0.00 0.00 0.00 3.66
4311 5154 7.927629 ACAGCCATTTTTATGTATGCCTAATTG 59.072 33.333 0.00 0.00 0.00 2.32
4455 5299 1.154225 GGCAAACGCTGGTGATTCG 60.154 57.895 0.00 0.00 0.00 3.34
4487 5331 0.030092 TCTAGGGCTGGCCAGGTATT 60.030 55.000 33.46 2.65 37.98 1.89
4494 5338 3.566351 GGCTGGCCAGGTATTTATTCTT 58.434 45.455 33.46 0.00 35.81 2.52
4741 5586 8.774183 TCCCTTTTATTAGTATGTTCTGCCTTA 58.226 33.333 0.00 0.00 0.00 2.69
4863 5708 4.009675 GACATCAATGTTGTAAGCCCTCA 58.990 43.478 0.00 0.00 41.95 3.86
4884 5729 1.549203 AATGCTGGCACCACCTTAAG 58.451 50.000 0.00 0.00 40.22 1.85
5151 5996 4.999950 CACTCAAGTCCTAACAGAAGCAAT 59.000 41.667 0.00 0.00 0.00 3.56
5615 6460 4.696899 TGAGGTTCAGTGAGTATACGTG 57.303 45.455 0.00 0.00 0.00 4.49
5616 6461 4.077108 TGAGGTTCAGTGAGTATACGTGT 58.923 43.478 0.00 0.00 0.00 4.49
5673 6520 1.264749 TTGACACGGGCTAGGATGCT 61.265 55.000 0.00 0.00 0.00 3.79
5786 6633 4.498009 CGAACCCAGGATAAATCACATTGC 60.498 45.833 0.00 0.00 0.00 3.56
5822 6669 2.777832 ATCCTGGCACTCAACTTCTC 57.222 50.000 0.00 0.00 0.00 2.87
5824 6671 2.050144 TCCTGGCACTCAACTTCTCTT 58.950 47.619 0.00 0.00 0.00 2.85
5948 6802 0.673985 GCTGGGGTGTTCCTTTGTTC 59.326 55.000 0.00 0.00 35.33 3.18
5972 6826 3.052329 TGGTGGTATATTCCATGCCTCA 58.948 45.455 4.18 0.00 39.81 3.86
5974 6828 3.073062 GGTGGTATATTCCATGCCTCAGT 59.927 47.826 4.18 0.00 39.81 3.41
5988 6842 1.512996 CTCAGTGGCTGTGGCTGTTG 61.513 60.000 0.00 0.00 38.73 3.33
6119 6974 9.725019 TTACTTCATATTTCAAGATCAGTGTGT 57.275 29.630 0.00 0.00 0.00 3.72
6120 6975 8.627208 ACTTCATATTTCAAGATCAGTGTGTT 57.373 30.769 0.00 0.00 0.00 3.32
6121 6976 9.071276 ACTTCATATTTCAAGATCAGTGTGTTT 57.929 29.630 0.00 0.00 0.00 2.83
6122 6977 9.552114 CTTCATATTTCAAGATCAGTGTGTTTC 57.448 33.333 0.00 0.00 0.00 2.78
6123 6978 8.853077 TCATATTTCAAGATCAGTGTGTTTCT 57.147 30.769 0.00 0.00 0.00 2.52
6124 6979 8.724229 TCATATTTCAAGATCAGTGTGTTTCTG 58.276 33.333 0.00 0.00 0.00 3.02
6125 6980 6.949352 ATTTCAAGATCAGTGTGTTTCTGT 57.051 33.333 0.00 0.00 34.86 3.41
6126 6981 6.757897 TTTCAAGATCAGTGTGTTTCTGTT 57.242 33.333 0.00 0.00 34.86 3.16
6127 6982 5.991328 TCAAGATCAGTGTGTTTCTGTTC 57.009 39.130 0.00 0.00 34.86 3.18
6128 6983 5.674525 TCAAGATCAGTGTGTTTCTGTTCT 58.325 37.500 0.00 0.00 41.07 3.01
6129 6984 6.115446 TCAAGATCAGTGTGTTTCTGTTCTT 58.885 36.000 11.17 11.17 45.10 2.52
6130 6985 6.599244 TCAAGATCAGTGTGTTTCTGTTCTTT 59.401 34.615 13.19 2.17 43.41 2.52
6131 6986 6.369059 AGATCAGTGTGTTTCTGTTCTTTG 57.631 37.500 0.00 0.00 38.20 2.77
6132 6987 4.355543 TCAGTGTGTTTCTGTTCTTTGC 57.644 40.909 0.00 0.00 34.86 3.68
6133 6988 3.128589 TCAGTGTGTTTCTGTTCTTTGCC 59.871 43.478 0.00 0.00 34.86 4.52
6134 6989 3.088532 AGTGTGTTTCTGTTCTTTGCCA 58.911 40.909 0.00 0.00 0.00 4.92
6135 6990 3.119495 AGTGTGTTTCTGTTCTTTGCCAC 60.119 43.478 0.00 0.00 0.00 5.01
6136 6991 2.159448 TGTGTTTCTGTTCTTTGCCACG 60.159 45.455 0.00 0.00 0.00 4.94
6137 6992 2.096819 GTGTTTCTGTTCTTTGCCACGA 59.903 45.455 0.00 0.00 0.00 4.35
6138 6993 2.750166 TGTTTCTGTTCTTTGCCACGAA 59.250 40.909 0.00 0.00 0.00 3.85
6139 6994 3.380004 TGTTTCTGTTCTTTGCCACGAAT 59.620 39.130 0.00 0.00 0.00 3.34
6140 6995 4.576873 TGTTTCTGTTCTTTGCCACGAATA 59.423 37.500 0.00 0.00 0.00 1.75
6141 6996 5.240623 TGTTTCTGTTCTTTGCCACGAATAT 59.759 36.000 0.00 0.00 0.00 1.28
6142 6997 6.428465 TGTTTCTGTTCTTTGCCACGAATATA 59.572 34.615 0.00 0.00 0.00 0.86
6143 6998 7.120579 TGTTTCTGTTCTTTGCCACGAATATAT 59.879 33.333 0.00 0.00 0.00 0.86
6144 6999 7.624360 TTCTGTTCTTTGCCACGAATATATT 57.376 32.000 0.00 0.00 0.00 1.28
6145 7000 7.246674 TCTGTTCTTTGCCACGAATATATTC 57.753 36.000 14.45 14.45 0.00 1.75
6146 7001 7.047891 TCTGTTCTTTGCCACGAATATATTCT 58.952 34.615 20.47 7.52 34.69 2.40
6147 7002 7.552687 TCTGTTCTTTGCCACGAATATATTCTT 59.447 33.333 20.47 10.73 34.69 2.52
6148 7003 8.050778 TGTTCTTTGCCACGAATATATTCTTT 57.949 30.769 20.47 7.15 34.69 2.52
6149 7004 9.168451 TGTTCTTTGCCACGAATATATTCTTTA 57.832 29.630 20.47 3.20 34.69 1.85
6150 7005 9.651718 GTTCTTTGCCACGAATATATTCTTTAG 57.348 33.333 20.47 9.49 34.69 1.85
6151 7006 8.958119 TCTTTGCCACGAATATATTCTTTAGT 57.042 30.769 20.47 10.05 34.69 2.24
6152 7007 9.391006 TCTTTGCCACGAATATATTCTTTAGTT 57.609 29.630 20.47 0.00 34.69 2.24
6153 7008 9.438291 CTTTGCCACGAATATATTCTTTAGTTG 57.562 33.333 20.47 9.79 34.69 3.16
6154 7009 8.500753 TTGCCACGAATATATTCTTTAGTTGT 57.499 30.769 20.47 8.51 34.69 3.32
6155 7010 8.500753 TGCCACGAATATATTCTTTAGTTGTT 57.499 30.769 20.47 0.00 34.69 2.83
6156 7011 8.952278 TGCCACGAATATATTCTTTAGTTGTTT 58.048 29.630 20.47 0.00 34.69 2.83
6157 7012 9.221775 GCCACGAATATATTCTTTAGTTGTTTG 57.778 33.333 20.47 5.71 34.69 2.93
6158 7013 9.221775 CCACGAATATATTCTTTAGTTGTTTGC 57.778 33.333 20.47 0.00 34.69 3.68
6159 7014 9.221775 CACGAATATATTCTTTAGTTGTTTGCC 57.778 33.333 20.47 0.00 34.69 4.52
6160 7015 8.952278 ACGAATATATTCTTTAGTTGTTTGCCA 58.048 29.630 20.47 0.00 34.69 4.92
6161 7016 9.781834 CGAATATATTCTTTAGTTGTTTGCCAA 57.218 29.630 20.47 0.00 34.69 4.52
6167 7022 8.962884 ATTCTTTAGTTGTTTGCCAAGAAAAT 57.037 26.923 0.00 0.00 34.73 1.82
6170 7025 9.691362 TCTTTAGTTGTTTGCCAAGAAAATATC 57.309 29.630 0.00 0.00 32.51 1.63
6171 7026 9.696917 CTTTAGTTGTTTGCCAAGAAAATATCT 57.303 29.630 0.00 0.00 41.32 1.98
6174 7029 7.315890 AGTTGTTTGCCAAGAAAATATCTAGC 58.684 34.615 0.00 0.00 37.42 3.42
6175 7030 6.207691 TGTTTGCCAAGAAAATATCTAGCC 57.792 37.500 0.00 0.00 37.42 3.93
6176 7031 5.951747 TGTTTGCCAAGAAAATATCTAGCCT 59.048 36.000 0.00 0.00 37.42 4.58
6177 7032 7.116075 TGTTTGCCAAGAAAATATCTAGCCTA 58.884 34.615 0.00 0.00 37.42 3.93
6178 7033 7.779798 TGTTTGCCAAGAAAATATCTAGCCTAT 59.220 33.333 0.00 0.00 37.42 2.57
6179 7034 7.750229 TTGCCAAGAAAATATCTAGCCTATG 57.250 36.000 0.00 0.00 37.42 2.23
6180 7035 6.841601 TGCCAAGAAAATATCTAGCCTATGT 58.158 36.000 0.00 0.00 37.42 2.29
6181 7036 7.290061 TGCCAAGAAAATATCTAGCCTATGTT 58.710 34.615 0.00 0.00 37.42 2.71
6182 7037 7.779798 TGCCAAGAAAATATCTAGCCTATGTTT 59.220 33.333 0.00 0.00 37.42 2.83
6183 7038 8.633561 GCCAAGAAAATATCTAGCCTATGTTTT 58.366 33.333 0.00 0.00 37.42 2.43
6270 7125 8.755018 GTTTAATGGTTTATGCATGCAATAGTC 58.245 33.333 26.68 14.71 0.00 2.59
6376 8997 5.646793 CCCTCTGATGCACATATAATTCTGG 59.353 44.000 0.00 0.00 0.00 3.86
6422 9043 7.067372 CCCTACATGAATGTTTTAAGATCTGCA 59.933 37.037 0.00 0.00 41.97 4.41
6426 9047 8.188799 ACATGAATGTTTTAAGATCTGCATGAG 58.811 33.333 0.00 0.00 37.90 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.987715 CTTGCATGACGACTGACGAG 59.012 55.000 6.52 0.00 45.77 4.18
1 2 0.388520 CCTTGCATGACGACTGACGA 60.389 55.000 6.52 0.00 45.77 4.20
3 4 1.993370 GTACCTTGCATGACGACTGAC 59.007 52.381 0.00 0.00 0.00 3.51
4 5 1.616374 TGTACCTTGCATGACGACTGA 59.384 47.619 0.00 0.00 0.00 3.41
8 9 6.183360 GGATTTTATTGTACCTTGCATGACGA 60.183 38.462 0.00 0.00 0.00 4.20
143 144 1.831106 TCGACCATGATACCAGCAGTT 59.169 47.619 0.00 0.00 0.00 3.16
167 168 0.804989 GCAACAAGAACTCCATCCCG 59.195 55.000 0.00 0.00 0.00 5.14
175 176 1.613437 CCCAATTCGGCAACAAGAACT 59.387 47.619 0.00 0.00 0.00 3.01
207 208 4.522405 CGAATCTATCATCTCCACTCCACT 59.478 45.833 0.00 0.00 0.00 4.00
229 230 0.743345 GAAACCATTCCCGGGTCTCG 60.743 60.000 22.86 9.62 37.77 4.04
234 235 0.251165 ACACAGAAACCATTCCCGGG 60.251 55.000 16.85 16.85 36.12 5.73
255 256 9.462606 TGACAGAGTATATAATGATACGACCAT 57.537 33.333 0.00 0.00 37.37 3.55
273 274 1.219773 ATGCCCCATGATGACAGAGT 58.780 50.000 0.00 0.00 0.00 3.24
275 276 2.242965 AGAAATGCCCCATGATGACAGA 59.757 45.455 0.00 0.00 0.00 3.41
348 349 4.262207 CCTGTACTGCTTCGTATGATCCAT 60.262 45.833 0.00 0.00 0.00 3.41
440 443 0.034896 ACACGTCCTGGGAACACATC 59.965 55.000 0.00 0.00 35.60 3.06
448 691 2.809696 ACGAATTAAAACACGTCCTGGG 59.190 45.455 0.00 0.00 33.80 4.45
530 1035 3.300388 TGGCACTTTATTCAACCACCAA 58.700 40.909 0.00 0.00 0.00 3.67
679 1200 5.701224 AGTTTCCCAACTCCAACTTATCAA 58.299 37.500 0.00 0.00 39.15 2.57
762 1283 7.914346 GGAGATGAAACAGAATGAAAATAGCAG 59.086 37.037 0.00 0.00 39.69 4.24
763 1284 7.394077 TGGAGATGAAACAGAATGAAAATAGCA 59.606 33.333 0.00 0.00 39.69 3.49
764 1285 7.699812 GTGGAGATGAAACAGAATGAAAATAGC 59.300 37.037 0.00 0.00 39.69 2.97
804 1325 6.882678 ACTACCCAAATTACCACATAACAGAC 59.117 38.462 0.00 0.00 0.00 3.51
939 1460 7.973944 GCTAAAAAGTTCCTGAAGAAAGTCAAA 59.026 33.333 0.00 0.00 35.85 2.69
1015 1536 6.769512 TCAAGTAGCTCTGAACCTTGTTAAT 58.230 36.000 0.00 0.00 35.26 1.40
1209 1730 3.150458 TCGGTCTTTGGAGTACTGAGA 57.850 47.619 0.00 0.00 0.00 3.27
1388 1909 4.159693 ACGCATCAAGGTATGTGTTCTAGA 59.840 41.667 0.00 0.00 45.82 2.43
1506 2027 6.706295 TCAATGTTGTTTTGGTTTCCTCTTT 58.294 32.000 0.00 0.00 0.00 2.52
1896 2631 8.157476 AGAAATGAGCTGAAGGAAAAGTAGTAA 58.843 33.333 0.00 0.00 0.00 2.24
2324 3061 3.181492 ACACGTCAAATGTTTCATGTGCA 60.181 39.130 2.23 0.00 0.00 4.57
2428 3165 9.541884 ACCTATGACCCAAAACTAAAACAATAT 57.458 29.630 0.00 0.00 0.00 1.28
2519 3350 8.525316 TCACTGCAACATTGATTCATTAGAATT 58.475 29.630 0.00 0.00 44.30 2.17
2741 3579 8.545420 CAATGCTGAATGCTGAAAAATTATACC 58.455 33.333 0.00 0.00 43.37 2.73
2949 3787 4.032703 TGCTTCACTTTTGAGAACTTGC 57.967 40.909 0.00 0.00 31.71 4.01
3056 3894 7.933033 AGTAATGTCAAAACAAATGCCAAATCT 59.067 29.630 0.00 0.00 39.30 2.40
3066 3904 8.791675 TGATGCTATCAGTAATGTCAAAACAAA 58.208 29.630 0.00 0.00 34.90 2.83
3067 3905 8.334263 TGATGCTATCAGTAATGTCAAAACAA 57.666 30.769 0.00 0.00 34.90 2.83
3068 3906 7.920160 TGATGCTATCAGTAATGTCAAAACA 57.080 32.000 0.00 0.00 35.42 2.83
3069 3907 8.236586 TGTTGATGCTATCAGTAATGTCAAAAC 58.763 33.333 0.00 0.00 40.94 2.43
3070 3908 8.334263 TGTTGATGCTATCAGTAATGTCAAAA 57.666 30.769 0.00 0.00 40.94 2.44
3288 4131 1.640670 AGGGTTGTACTCCCATTGCAT 59.359 47.619 22.24 4.49 46.82 3.96
3406 4249 6.173427 AGGTTTTGAAATTGTTGCACCTAT 57.827 33.333 0.00 0.00 31.39 2.57
3407 4250 5.606348 AGGTTTTGAAATTGTTGCACCTA 57.394 34.783 0.00 0.00 31.39 3.08
3505 4348 5.726980 ACACCATTTTGACAACATAGCAT 57.273 34.783 0.00 0.00 0.00 3.79
3542 4385 9.587772 ACAGAACTGTACTGTCACATTTATATC 57.412 33.333 5.81 0.00 43.84 1.63
3608 4451 6.481134 CAACAATTGATGGTACTTCGAGATG 58.519 40.000 13.59 0.00 0.00 2.90
3657 4500 1.153353 GGTTACGTGTGGTGGACATG 58.847 55.000 0.00 0.00 45.83 3.21
3670 4513 6.183360 CCAAGAATTCTAGCTGAAAGGTTACG 60.183 42.308 8.75 0.00 46.63 3.18
3707 4550 3.577848 ACTTGAGGCAATGCATGGTAAAA 59.422 39.130 7.79 0.00 0.00 1.52
3729 4572 3.639952 GGAGGGAGTAGTAAAGCCACTA 58.360 50.000 0.00 0.00 0.00 2.74
3742 4585 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3743 4586 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3744 4587 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3745 4588 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3746 4589 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3747 4590 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3748 4591 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3749 4592 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3750 4593 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3751 4594 7.329471 GCAAATCTAAGACAAGAATTTTGGGAC 59.671 37.037 0.00 0.00 30.97 4.46
3752 4595 7.378181 GCAAATCTAAGACAAGAATTTTGGGA 58.622 34.615 0.00 0.00 30.97 4.37
3753 4596 6.591448 GGCAAATCTAAGACAAGAATTTTGGG 59.409 38.462 0.00 0.00 30.97 4.12
3754 4597 7.381323 AGGCAAATCTAAGACAAGAATTTTGG 58.619 34.615 0.00 0.00 30.97 3.28
3755 4598 9.565213 CTAGGCAAATCTAAGACAAGAATTTTG 57.435 33.333 0.00 0.00 32.40 2.44
3756 4599 9.520515 TCTAGGCAAATCTAAGACAAGAATTTT 57.479 29.630 0.00 0.00 0.00 1.82
3757 4600 9.692325 ATCTAGGCAAATCTAAGACAAGAATTT 57.308 29.630 0.00 0.00 0.00 1.82
3759 4602 9.771534 GTATCTAGGCAAATCTAAGACAAGAAT 57.228 33.333 0.00 0.00 0.00 2.40
3760 4603 7.921214 CGTATCTAGGCAAATCTAAGACAAGAA 59.079 37.037 0.00 0.00 0.00 2.52
3761 4604 7.426410 CGTATCTAGGCAAATCTAAGACAAGA 58.574 38.462 0.00 0.00 0.00 3.02
3762 4605 6.642950 CCGTATCTAGGCAAATCTAAGACAAG 59.357 42.308 0.00 0.00 0.00 3.16
3763 4606 6.322969 TCCGTATCTAGGCAAATCTAAGACAA 59.677 38.462 0.00 0.00 0.00 3.18
3764 4607 5.831525 TCCGTATCTAGGCAAATCTAAGACA 59.168 40.000 0.00 0.00 0.00 3.41
3765 4608 6.328641 TCCGTATCTAGGCAAATCTAAGAC 57.671 41.667 0.00 0.00 0.00 3.01
3766 4609 6.493802 ACATCCGTATCTAGGCAAATCTAAGA 59.506 38.462 0.00 0.00 0.00 2.10
3767 4610 6.692486 ACATCCGTATCTAGGCAAATCTAAG 58.308 40.000 0.00 0.00 0.00 2.18
3768 4611 6.665992 ACATCCGTATCTAGGCAAATCTAA 57.334 37.500 0.00 0.00 0.00 2.10
3769 4612 7.956328 ATACATCCGTATCTAGGCAAATCTA 57.044 36.000 0.00 0.00 32.66 1.98
3770 4613 6.859112 ATACATCCGTATCTAGGCAAATCT 57.141 37.500 0.00 0.00 32.66 2.40
3797 4640 9.261180 CGGATGTATCAAGTCATGTTTTAGTAT 57.739 33.333 0.00 0.00 0.00 2.12
3798 4641 8.255206 ACGGATGTATCAAGTCATGTTTTAGTA 58.745 33.333 0.00 0.00 0.00 1.82
3799 4642 7.103641 ACGGATGTATCAAGTCATGTTTTAGT 58.896 34.615 0.00 0.00 0.00 2.24
3800 4643 7.539712 ACGGATGTATCAAGTCATGTTTTAG 57.460 36.000 0.00 0.00 0.00 1.85
3801 4644 9.607988 AATACGGATGTATCAAGTCATGTTTTA 57.392 29.630 0.00 0.00 40.42 1.52
3802 4645 8.506168 AATACGGATGTATCAAGTCATGTTTT 57.494 30.769 0.00 0.00 40.42 2.43
3803 4646 8.506168 AAATACGGATGTATCAAGTCATGTTT 57.494 30.769 0.00 0.00 40.42 2.83
3804 4647 9.261180 CTAAATACGGATGTATCAAGTCATGTT 57.739 33.333 0.00 0.00 40.42 2.71
3805 4648 8.638873 TCTAAATACGGATGTATCAAGTCATGT 58.361 33.333 0.00 0.00 40.42 3.21
3806 4649 8.916654 GTCTAAATACGGATGTATCAAGTCATG 58.083 37.037 0.00 0.00 40.42 3.07
3807 4650 8.638873 TGTCTAAATACGGATGTATCAAGTCAT 58.361 33.333 0.00 0.00 40.42 3.06
3808 4651 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
3809 4652 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
3810 4653 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
3817 4660 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
3818 4661 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
3820 4663 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3821 4664 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3834 4677 7.386851 TCCGTCTCAAAATCTTGTCTTAGATT 58.613 34.615 0.00 0.00 44.62 2.40
3835 4678 6.936279 TCCGTCTCAAAATCTTGTCTTAGAT 58.064 36.000 0.00 0.00 36.44 1.98
3836 4679 6.340962 TCCGTCTCAAAATCTTGTCTTAGA 57.659 37.500 0.00 0.00 33.94 2.10
3837 4680 5.578727 CCTCCGTCTCAAAATCTTGTCTTAG 59.421 44.000 0.00 0.00 33.94 2.18
3838 4681 5.479306 CCTCCGTCTCAAAATCTTGTCTTA 58.521 41.667 0.00 0.00 33.94 2.10
3839 4682 4.319177 CCTCCGTCTCAAAATCTTGTCTT 58.681 43.478 0.00 0.00 33.94 3.01
3840 4683 3.307059 CCCTCCGTCTCAAAATCTTGTCT 60.307 47.826 0.00 0.00 33.94 3.41
3841 4684 3.003480 CCCTCCGTCTCAAAATCTTGTC 58.997 50.000 0.00 0.00 33.94 3.18
3842 4685 2.637872 TCCCTCCGTCTCAAAATCTTGT 59.362 45.455 0.00 0.00 33.94 3.16
3843 4686 3.265791 CTCCCTCCGTCTCAAAATCTTG 58.734 50.000 0.00 0.00 0.00 3.02
3844 4687 2.907042 ACTCCCTCCGTCTCAAAATCTT 59.093 45.455 0.00 0.00 0.00 2.40
3845 4688 2.541466 ACTCCCTCCGTCTCAAAATCT 58.459 47.619 0.00 0.00 0.00 2.40
3846 4689 3.447944 AGTACTCCCTCCGTCTCAAAATC 59.552 47.826 0.00 0.00 0.00 2.17
3847 4690 3.442076 AGTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
3848 4691 2.885616 AGTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
3849 4692 2.599408 AGTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
3850 4693 2.599408 AAGTACTCCCTCCGTCTCAA 57.401 50.000 0.00 0.00 0.00 3.02
3851 4694 2.599408 AAAGTACTCCCTCCGTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
3852 4695 3.878699 CTCTAAAGTACTCCCTCCGTCTC 59.121 52.174 0.00 0.00 0.00 3.36
3853 4696 3.522750 TCTCTAAAGTACTCCCTCCGTCT 59.477 47.826 0.00 0.00 0.00 4.18
3854 4697 3.883669 TCTCTAAAGTACTCCCTCCGTC 58.116 50.000 0.00 0.00 0.00 4.79
3855 4698 4.079901 TCATCTCTAAAGTACTCCCTCCGT 60.080 45.833 0.00 0.00 0.00 4.69
3856 4699 4.462133 TCATCTCTAAAGTACTCCCTCCG 58.538 47.826 0.00 0.00 0.00 4.63
3857 4700 5.479027 GGATCATCTCTAAAGTACTCCCTCC 59.521 48.000 0.00 0.00 0.00 4.30
3858 4701 6.311735 AGGATCATCTCTAAAGTACTCCCTC 58.688 44.000 0.00 0.00 0.00 4.30
3859 4702 6.288096 AGGATCATCTCTAAAGTACTCCCT 57.712 41.667 0.00 0.00 0.00 4.20
3860 4703 6.987403 AAGGATCATCTCTAAAGTACTCCC 57.013 41.667 0.00 0.00 0.00 4.30
3861 4704 7.787028 ACAAAGGATCATCTCTAAAGTACTCC 58.213 38.462 0.00 0.00 0.00 3.85
3862 4705 9.660180 AAACAAAGGATCATCTCTAAAGTACTC 57.340 33.333 0.00 0.00 0.00 2.59
3863 4706 9.442047 CAAACAAAGGATCATCTCTAAAGTACT 57.558 33.333 0.00 0.00 0.00 2.73
3864 4707 9.220767 ACAAACAAAGGATCATCTCTAAAGTAC 57.779 33.333 0.00 0.00 0.00 2.73
3865 4708 9.793259 AACAAACAAAGGATCATCTCTAAAGTA 57.207 29.630 0.00 0.00 0.00 2.24
3866 4709 8.697507 AACAAACAAAGGATCATCTCTAAAGT 57.302 30.769 0.00 0.00 0.00 2.66
3876 4719 7.719633 GGGATAGCTATAACAAACAAAGGATCA 59.280 37.037 6.13 0.00 0.00 2.92
3888 4731 6.409234 CCCTTTCAGTTGGGATAGCTATAACA 60.409 42.308 16.49 11.61 46.15 2.41
3930 4773 7.202186 CCCCAGATATAAGTAATCAAACCAGGA 60.202 40.741 0.00 0.00 0.00 3.86
3935 4778 9.628500 AGAAACCCCAGATATAAGTAATCAAAC 57.372 33.333 0.00 0.00 0.00 2.93
3940 4783 9.004231 ACAGAAGAAACCCCAGATATAAGTAAT 57.996 33.333 0.00 0.00 0.00 1.89
3947 4790 5.395324 CGTACACAGAAGAAACCCCAGATAT 60.395 44.000 0.00 0.00 0.00 1.63
4032 4875 4.661125 GCAAATATGTTGCTGATTGACGA 58.339 39.130 12.51 0.00 41.87 4.20
4056 4899 6.488006 TCAATTTCCTCTGGCTATTATCTTGC 59.512 38.462 0.00 0.00 0.00 4.01
4076 4919 9.881529 GTTGAATTTACATGCAATTTGTCAATT 57.118 25.926 9.67 9.67 34.98 2.32
4104 4947 4.999469 ATATGTGATCACCCAGCCAATA 57.001 40.909 22.85 12.00 0.00 1.90
4167 5010 6.346040 GCACAAAAGCTAAGCAAACATTACAG 60.346 38.462 0.00 0.00 0.00 2.74
4203 5046 2.472695 TAGCTTGCAGGTTGGTACTG 57.527 50.000 0.00 0.00 38.95 2.74
4205 5048 3.053831 TCTTAGCTTGCAGGTTGGTAC 57.946 47.619 0.00 0.00 0.00 3.34
4263 5106 7.361201 GCTGTGAAATAGTAACTGCATCTTCAA 60.361 37.037 0.00 0.00 38.29 2.69
4264 5107 6.092670 GCTGTGAAATAGTAACTGCATCTTCA 59.907 38.462 0.00 0.00 38.29 3.02
4282 5125 5.659463 GGCATACATAAAAATGGCTGTGAA 58.341 37.500 2.02 0.00 43.33 3.18
4288 5131 7.710475 ACACAATTAGGCATACATAAAAATGGC 59.290 33.333 1.01 1.01 46.09 4.40
4414 5258 5.646360 CCACGACAAGTTGGTTATTCCTTAT 59.354 40.000 7.96 0.00 37.07 1.73
4455 5299 1.669265 GCCCTAGAAATAACACACCGC 59.331 52.381 0.00 0.00 0.00 5.68
4487 5331 6.542370 GTGCCTAATAGCAGGAACAAGAATAA 59.458 38.462 0.00 0.00 43.13 1.40
4713 5557 7.556635 AGGCAGAACATACTAATAAAAGGGAAC 59.443 37.037 0.00 0.00 0.00 3.62
4863 5708 2.008242 TAAGGTGGTGCCAGCATTTT 57.992 45.000 20.63 10.08 45.79 1.82
4884 5729 5.505286 CAGATCATGATTAAGTGCGGAAAC 58.495 41.667 10.14 0.00 0.00 2.78
5151 5996 9.474313 ACAGTCCCTGCTCATTAAATAAATTTA 57.526 29.630 0.00 0.00 34.37 1.40
5265 6110 1.278238 GTGCAACGTAATCTCCTCCG 58.722 55.000 0.00 0.00 0.00 4.63
5575 6420 4.140536 CTCAAGACTCTTCCTTGCCTTTT 58.859 43.478 0.00 0.00 40.45 2.27
5615 6460 1.009829 CAGTGGAGCCTTCGCATAAC 58.990 55.000 0.00 0.00 37.52 1.89
5616 6461 0.107703 CCAGTGGAGCCTTCGCATAA 60.108 55.000 1.68 0.00 37.52 1.90
5673 6520 6.475076 GCACACAATTTCACATTGACAACTTA 59.525 34.615 1.59 0.00 33.51 2.24
5786 6633 1.538276 GATTTCGATGTTGCGCCAAG 58.462 50.000 4.18 0.00 0.00 3.61
5822 6669 0.109272 TGACGAACAGAGCGGCTAAG 60.109 55.000 0.60 0.33 37.73 2.18
5824 6671 0.530744 AATGACGAACAGAGCGGCTA 59.469 50.000 0.60 0.00 37.73 3.93
5897 6751 7.737972 ACAGCATACACACAAACTATAACAA 57.262 32.000 0.00 0.00 0.00 2.83
5900 6754 8.436970 CGTTTACAGCATACACACAAACTATAA 58.563 33.333 0.00 0.00 0.00 0.98
5948 6802 4.473444 AGGCATGGAATATACCACCAAAG 58.527 43.478 0.00 0.00 43.03 2.77
5972 6826 1.076777 AACAACAGCCACAGCCACT 60.077 52.632 0.00 0.00 41.25 4.00
5974 6828 1.102809 CAGAACAACAGCCACAGCCA 61.103 55.000 0.00 0.00 41.25 4.75
6095 6950 8.627208 AACACACTGATCTTGAAATATGAAGT 57.373 30.769 0.00 0.00 0.00 3.01
6096 6951 9.552114 GAAACACACTGATCTTGAAATATGAAG 57.448 33.333 0.00 0.00 0.00 3.02
6097 6952 9.288576 AGAAACACACTGATCTTGAAATATGAA 57.711 29.630 0.00 0.00 0.00 2.57
6098 6953 8.724229 CAGAAACACACTGATCTTGAAATATGA 58.276 33.333 0.00 0.00 37.54 2.15
6099 6954 8.509690 ACAGAAACACACTGATCTTGAAATATG 58.490 33.333 0.00 0.00 38.55 1.78
6100 6955 8.627208 ACAGAAACACACTGATCTTGAAATAT 57.373 30.769 0.00 0.00 38.55 1.28
6101 6956 8.450578 AACAGAAACACACTGATCTTGAAATA 57.549 30.769 0.00 0.00 38.55 1.40
6102 6957 6.949352 ACAGAAACACACTGATCTTGAAAT 57.051 33.333 0.00 0.00 38.55 2.17
6103 6958 6.599244 AGAACAGAAACACACTGATCTTGAAA 59.401 34.615 0.00 0.00 42.05 2.69
6104 6959 6.115446 AGAACAGAAACACACTGATCTTGAA 58.885 36.000 0.00 0.00 42.05 2.69
6105 6960 5.674525 AGAACAGAAACACACTGATCTTGA 58.325 37.500 0.00 0.00 42.05 3.02
6106 6961 5.998454 AGAACAGAAACACACTGATCTTG 57.002 39.130 0.00 0.00 42.05 3.02
6108 6963 5.220931 GCAAAGAACAGAAACACACTGATCT 60.221 40.000 0.00 0.00 44.92 2.75
6109 6964 4.972440 GCAAAGAACAGAAACACACTGATC 59.028 41.667 0.00 0.00 38.55 2.92
6110 6965 4.202050 GGCAAAGAACAGAAACACACTGAT 60.202 41.667 0.00 0.00 38.55 2.90
6111 6966 3.128589 GGCAAAGAACAGAAACACACTGA 59.871 43.478 0.00 0.00 38.55 3.41
6112 6967 3.119531 TGGCAAAGAACAGAAACACACTG 60.120 43.478 0.00 0.00 40.68 3.66
6113 6968 3.088532 TGGCAAAGAACAGAAACACACT 58.911 40.909 0.00 0.00 0.00 3.55
6114 6969 3.179048 GTGGCAAAGAACAGAAACACAC 58.821 45.455 0.00 0.00 0.00 3.82
6115 6970 2.159448 CGTGGCAAAGAACAGAAACACA 60.159 45.455 0.00 0.00 0.00 3.72
6116 6971 2.096819 TCGTGGCAAAGAACAGAAACAC 59.903 45.455 0.00 0.00 0.00 3.32
6117 6972 2.360844 TCGTGGCAAAGAACAGAAACA 58.639 42.857 0.00 0.00 0.00 2.83
6118 6973 3.414549 TTCGTGGCAAAGAACAGAAAC 57.585 42.857 2.97 0.00 0.00 2.78
6119 6974 5.957842 ATATTCGTGGCAAAGAACAGAAA 57.042 34.783 8.53 0.00 0.00 2.52
6120 6975 7.552687 AGAATATATTCGTGGCAAAGAACAGAA 59.447 33.333 17.69 0.00 41.56 3.02
6121 6976 7.047891 AGAATATATTCGTGGCAAAGAACAGA 58.952 34.615 17.69 0.00 41.56 3.41
6122 6977 7.251704 AGAATATATTCGTGGCAAAGAACAG 57.748 36.000 17.69 0.00 41.56 3.16
6123 6978 7.624360 AAGAATATATTCGTGGCAAAGAACA 57.376 32.000 17.69 0.00 41.56 3.18
6124 6979 9.651718 CTAAAGAATATATTCGTGGCAAAGAAC 57.348 33.333 17.69 0.00 41.56 3.01
6125 6980 9.391006 ACTAAAGAATATATTCGTGGCAAAGAA 57.609 29.630 17.69 8.75 41.56 2.52
6126 6981 8.958119 ACTAAAGAATATATTCGTGGCAAAGA 57.042 30.769 17.69 0.00 41.56 2.52
6127 6982 9.438291 CAACTAAAGAATATATTCGTGGCAAAG 57.562 33.333 17.69 12.15 41.56 2.77
6128 6983 8.952278 ACAACTAAAGAATATATTCGTGGCAAA 58.048 29.630 17.69 2.83 41.56 3.68
6129 6984 8.500753 ACAACTAAAGAATATATTCGTGGCAA 57.499 30.769 17.69 3.74 41.56 4.52
6130 6985 8.500753 AACAACTAAAGAATATATTCGTGGCA 57.499 30.769 17.69 5.47 41.56 4.92
6131 6986 9.221775 CAAACAACTAAAGAATATATTCGTGGC 57.778 33.333 17.69 0.00 41.56 5.01
6132 6987 9.221775 GCAAACAACTAAAGAATATATTCGTGG 57.778 33.333 17.69 14.20 41.56 4.94
6133 6988 9.221775 GGCAAACAACTAAAGAATATATTCGTG 57.778 33.333 17.69 12.61 41.56 4.35
6134 6989 8.952278 TGGCAAACAACTAAAGAATATATTCGT 58.048 29.630 17.69 13.02 41.56 3.85
6135 6990 9.781834 TTGGCAAACAACTAAAGAATATATTCG 57.218 29.630 17.69 7.89 36.67 3.34
6142 6997 8.962884 ATTTTCTTGGCAAACAACTAAAGAAT 57.037 26.923 0.00 0.00 34.59 2.40
6144 6999 9.691362 GATATTTTCTTGGCAAACAACTAAAGA 57.309 29.630 0.00 0.00 34.76 2.52
6145 7000 9.696917 AGATATTTTCTTGGCAAACAACTAAAG 57.303 29.630 0.00 0.00 34.76 1.85
6148 7003 8.458843 GCTAGATATTTTCTTGGCAAACAACTA 58.541 33.333 0.00 0.00 35.79 2.24
6149 7004 7.315890 GCTAGATATTTTCTTGGCAAACAACT 58.684 34.615 0.00 0.00 35.79 3.16
6150 7005 6.531594 GGCTAGATATTTTCTTGGCAAACAAC 59.468 38.462 0.00 0.00 46.94 3.32
6151 7006 6.630071 GGCTAGATATTTTCTTGGCAAACAA 58.370 36.000 0.00 0.00 46.94 2.83
6152 7007 6.207691 GGCTAGATATTTTCTTGGCAAACA 57.792 37.500 0.00 0.00 46.94 2.83
6183 7038 9.973661 TGACCTATCTTGAAATATGAAGGAAAA 57.026 29.630 0.00 0.00 0.00 2.29
6184 7039 9.618890 CTGACCTATCTTGAAATATGAAGGAAA 57.381 33.333 0.00 0.00 0.00 3.13
6185 7040 8.992349 TCTGACCTATCTTGAAATATGAAGGAA 58.008 33.333 0.00 0.00 0.00 3.36
6186 7041 8.553085 TCTGACCTATCTTGAAATATGAAGGA 57.447 34.615 0.00 0.00 0.00 3.36
6187 7042 9.790344 ATTCTGACCTATCTTGAAATATGAAGG 57.210 33.333 0.00 0.00 0.00 3.46
6325 8946 5.592587 TTCCCTGTCTAATTCTTCCCAAA 57.407 39.130 0.00 0.00 0.00 3.28
6376 8997 1.278413 GGGAACACCCTGACTCCTTAC 59.722 57.143 0.00 0.00 40.49 2.34
6444 9065 4.615513 AGTCCTAGACAGGCCATATATCC 58.384 47.826 5.01 0.00 42.30 2.59


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

AutoCloner maintained by Alex Coulton.