Multiple sequence alignment - TraesCS2D01G294400

Loading Multiple Alignment...

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 TraesCS2D01G294400 chr2D 100.000 3647 0 0 1 3647 376690884 376694530 0.000000e+00 6735.0
1 TraesCS2D01G294400 chr2D 94.839 310 14 1 3338 3647 361254339 361254032 1.970000e-132 483.0
2 TraesCS2D01G294400 chr2D 94.249 313 14 3 3337 3647 409602218 409601908 3.300000e-130 475.0
3 TraesCS2D01G294400 chr2D 88.732 71 4 3 7 74 138296471 138296540 2.330000e-12 84.2
4 TraesCS2D01G294400 chr2B 94.778 3351 133 22 7 3337 448111925 448115253 0.000000e+00 5180.0
5 TraesCS2D01G294400 chr2B 79.394 165 25 6 755 914 764146569 764146729 1.380000e-19 108.0
6 TraesCS2D01G294400 chr2B 100.000 35 0 0 237 271 750129699 750129665 8.450000e-07 65.8
7 TraesCS2D01G294400 chr2A 92.802 3126 154 39 241 3317 510424786 510427889 0.000000e+00 4460.0
8 TraesCS2D01G294400 chr2A 77.778 144 29 3 525 666 668277190 668277048 6.490000e-13 86.1
9 TraesCS2D01G294400 chr4D 94.268 314 16 1 3334 3647 274462633 274462322 2.550000e-131 479.0
10 TraesCS2D01G294400 chr4D 86.207 58 6 2 214 271 486528309 486528254 1.090000e-05 62.1
11 TraesCS2D01G294400 chr4D 79.070 86 13 4 187 271 486534318 486534237 2.000000e-03 54.7
12 TraesCS2D01G294400 chr1A 94.534 311 16 1 3338 3647 292767512 292767202 2.550000e-131 479.0
13 TraesCS2D01G294400 chr6B 93.590 312 17 2 3338 3647 365706278 365705968 2.570000e-126 462.0
14 TraesCS2D01G294400 chr6B 92.523 321 15 4 3333 3647 439354018 439354335 5.550000e-123 451.0
15 TraesCS2D01G294400 chr3D 93.248 311 15 3 3337 3647 174054093 174054397 1.540000e-123 453.0
16 TraesCS2D01G294400 chr3D 81.522 92 11 6 525 612 67054869 67054958 1.820000e-08 71.3
17 TraesCS2D01G294400 chr5D 94.218 294 15 1 3354 3647 204292030 204291739 7.180000e-122 448.0
18 TraesCS2D01G294400 chr5D 77.241 145 19 13 242 380 418077018 418076882 5.050000e-09 73.1
19 TraesCS2D01G294400 chr7D 91.824 318 17 3 3338 3647 323963056 323962740 5.590000e-118 435.0
20 TraesCS2D01G294400 chr1D 78.495 186 27 11 524 704 347784324 347784501 3.850000e-20 110.0
21 TraesCS2D01G294400 chr1B 92.958 71 3 1 6 76 642732515 642732583 6.440000e-18 102.0
22 TraesCS2D01G294400 chr7A 75.362 207 34 13 171 373 696556235 696556428 2.330000e-12 84.2
23 TraesCS2D01G294400 chr6D 87.879 66 5 3 207 271 310412887 310412950 1.400000e-09 75.0
24 TraesCS2D01G294400 chrUn 90.909 55 2 2 218 271 21311768 21311820 1.820000e-08 71.3
25 TraesCS2D01G294400 chr5B 76.027 146 21 10 242 380 505562176 505562038 3.040000e-06 63.9
26 TraesCS2D01G294400 chr6A 95.000 40 1 1 525 563 426142906 426142945 1.090000e-05 62.1
27 TraesCS2D01G294400 chr6A 83.099 71 8 4 525 593 481744659 481744727 1.090000e-05 62.1
28 TraesCS2D01G294400 chr4B 92.308 39 3 0 244 282 620376456 620376494 5.090000e-04 56.5


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 TraesCS2D01G294400 chr2D 376690884 376694530 3646 False 6735 6735 100.000 1 3647 1 chr2D.!!$F2 3646
1 TraesCS2D01G294400 chr2B 448111925 448115253 3328 False 5180 5180 94.778 7 3337 1 chr2B.!!$F1 3330
2 TraesCS2D01G294400 chr2A 510424786 510427889 3103 False 4460 4460 92.802 241 3317 1 chr2A.!!$F1 3076

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
868 899 1.156736 GGAAGCGAACAAAGCAGCTA 58.843 50.0 0.00 0.0 39.25 3.32 F
1667 1725 1.415672 AAGTGCGGGGACTTGGAGAA 61.416 55.0 4.71 0.0 34.79 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1770 1.738908 CACCGATCAATGATGTGTGCA 59.261 47.619 0.0 0.0 0.0 4.57 R
3377 3448 0.029989 ATCCCTCCTTCCACCCCTAC 60.030 60.000 0.0 0.0 0.0 3.18 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
65 66 6.311200 TGATGTCTATTTTCTCACACACATCG 59.689 38.462 0.00 0.00 41.10 3.84
292 293 9.513906 TGTCATGACCATATTTCTTTTCAGTTA 57.486 29.630 22.85 0.00 0.00 2.24
407 410 9.684448 TTTAAATGTGACAAGCATATTTCGAAA 57.316 25.926 13.91 13.91 42.43 3.46
408 411 9.853555 TTAAATGTGACAAGCATATTTCGAAAT 57.146 25.926 25.48 25.48 42.43 2.17
409 412 7.745022 AATGTGACAAGCATATTTCGAAATG 57.255 32.000 29.20 18.29 35.09 2.32
410 413 7.201461 AAATGTGACAAGCATATTTCGAAATGC 60.201 33.333 29.20 25.85 42.43 3.56
452 455 7.424227 TTTTCTGAATGCCATCAACATTTTC 57.576 32.000 0.00 0.00 37.85 2.29
458 462 8.537049 TGAATGCCATCAACATTTTCTAAAAG 57.463 30.769 0.00 0.00 37.85 2.27
461 465 7.712264 TGCCATCAACATTTTCTAAAAGTTG 57.288 32.000 11.80 11.80 37.80 3.16
462 466 7.271511 TGCCATCAACATTTTCTAAAAGTTGT 58.728 30.769 15.51 8.47 37.75 3.32
466 470 8.901748 CATCAACATTTTCTAAAAGTTGTACGG 58.098 33.333 15.51 5.30 37.75 4.02
519 523 7.728580 TTTACGAAAATGATAAATGCCGAAC 57.271 32.000 0.00 0.00 0.00 3.95
520 524 5.303747 ACGAAAATGATAAATGCCGAACA 57.696 34.783 0.00 0.00 0.00 3.18
582 587 3.713858 TTTAATGATGCAAGGATGGCG 57.286 42.857 0.00 0.00 38.51 5.69
602 607 3.799035 CGAGTTTAGTTGACACACATGC 58.201 45.455 0.00 0.00 0.00 4.06
647 652 2.792500 CACGGATTTGCCATGCCTA 58.208 52.632 0.00 0.00 35.94 3.93
668 673 2.110011 ACCAACTAAACTTGCCATCCCT 59.890 45.455 0.00 0.00 0.00 4.20
671 676 1.355720 ACTAAACTTGCCATCCCTGCT 59.644 47.619 0.00 0.00 0.00 4.24
672 677 2.225117 ACTAAACTTGCCATCCCTGCTT 60.225 45.455 0.00 0.00 0.00 3.91
712 717 7.434492 TCGAAAACTTTTAATTTGCCATGGTA 58.566 30.769 14.67 5.86 0.00 3.25
868 899 1.156736 GGAAGCGAACAAAGCAGCTA 58.843 50.000 0.00 0.00 39.25 3.32
869 900 1.740025 GGAAGCGAACAAAGCAGCTAT 59.260 47.619 0.00 0.00 39.25 2.97
876 907 4.554973 GCGAACAAAGCAGCTATACTTTTG 59.445 41.667 0.00 0.00 33.92 2.44
884 915 3.356290 CAGCTATACTTTTGTTGGGCCT 58.644 45.455 4.53 0.00 0.00 5.19
1392 1450 2.034687 ACTGGCTCCGCTTTGCAT 59.965 55.556 0.00 0.00 0.00 3.96
1594 1652 2.978018 GCCCGGGAGCTTTTTGACG 61.978 63.158 29.31 0.00 0.00 4.35
1637 1695 2.234143 TCATTGGAACGCAATGGTTGA 58.766 42.857 12.42 0.00 39.69 3.18
1644 1702 2.435372 ACGCAATGGTTGATGGGTAT 57.565 45.000 0.00 0.00 40.43 2.73
1667 1725 1.415672 AAGTGCGGGGACTTGGAGAA 61.416 55.000 4.71 0.00 34.79 2.87
1743 1801 1.745232 TGATCGGTGGGTATGCAAAC 58.255 50.000 0.00 0.00 0.00 2.93
1752 1810 1.135402 GGGTATGCAAACGCAGGAAAG 60.135 52.381 0.00 0.00 44.13 2.62
1815 1873 2.616256 GGATGTGTTCTCATGGTCAGCA 60.616 50.000 0.00 0.00 0.00 4.41
1833 1891 3.063588 CAGCAATGATATCAGGCTATGCG 59.936 47.826 25.60 14.69 38.04 4.73
1864 1922 2.642171 TCCTGGAGAGGCTTTAAGGA 57.358 50.000 5.18 5.18 39.57 3.36
1931 1989 5.308014 TGTTATTGTTGCTCTGATGACAGT 58.692 37.500 0.00 0.00 43.81 3.55
1938 1996 1.067000 GCTCTGATGACAGTGTGCTCT 60.067 52.381 0.00 0.00 43.81 4.09
1984 2042 5.516339 GCAAAATGGATTGAAGGTTACATCG 59.484 40.000 0.00 0.00 31.84 3.84
2071 2129 1.225704 GGGAACATGGAGAGGGCTG 59.774 63.158 0.00 0.00 0.00 4.85
2133 2191 1.089920 ACTGTTCGATGATGCAAGGC 58.910 50.000 0.00 0.00 0.00 4.35
2217 2275 2.441001 CCTCTCCCCAGATAATGCTGTT 59.559 50.000 0.00 0.00 34.06 3.16
2220 2278 4.526970 TCTCCCCAGATAATGCTGTTTTC 58.473 43.478 0.00 0.00 34.06 2.29
2301 2359 8.430801 ACTTTGCTATGATGAAGAATGAGTAC 57.569 34.615 0.00 0.00 0.00 2.73
2419 2477 0.912486 AGGAAAACCTCATCCGGGAG 59.088 55.000 0.00 0.20 40.78 4.30
2453 2511 2.029666 GCGCGGATGCATACTCCT 59.970 61.111 8.83 0.00 42.97 3.69
2568 2626 2.025981 TGCTAACATTGACAGATGGGCT 60.026 45.455 0.00 0.00 0.00 5.19
2625 2683 4.801330 AGGGTTAACAAAAATAGCAGGC 57.199 40.909 8.10 0.00 0.00 4.85
2894 2960 8.188139 AGAAAACATGTTAGTTTACAACCTGTG 58.812 33.333 12.39 0.00 40.60 3.66
2920 2986 4.511826 GGGTTAATAAGAGTCATCAAGCCG 59.488 45.833 0.00 0.00 0.00 5.52
2960 3027 5.047021 TCACTTCTGCATAGTGCTTCTAGTT 60.047 40.000 19.17 0.00 45.31 2.24
3007 3074 9.178758 GTTAAGAACCAGAGGATAATGTGATTT 57.821 33.333 0.00 0.00 0.00 2.17
3116 3183 7.817418 TTCTTTACTGCCTATTCAGTTTGTT 57.183 32.000 1.55 0.00 44.26 2.83
3211 3278 5.458041 ACTGAAATCATCCAACCTTGTTG 57.542 39.130 0.00 0.00 0.00 3.33
3257 3328 7.067008 AGGTATAATGAACTCGTGAAAAATGGG 59.933 37.037 0.00 0.00 0.00 4.00
3287 3358 3.550561 TCACTTTTGTTTCTTATGCGCG 58.449 40.909 0.00 0.00 0.00 6.86
3296 3367 2.798834 TCTTATGCGCGTACTTTTGC 57.201 45.000 9.30 0.00 0.00 3.68
3327 3398 3.619483 CCTGCATACGTTTTTCCGTGATA 59.381 43.478 0.00 0.00 41.92 2.15
3337 3408 8.091385 ACGTTTTTCCGTGATATTTAGAAACT 57.909 30.769 0.00 0.00 40.08 2.66
3338 3409 8.013378 ACGTTTTTCCGTGATATTTAGAAACTG 58.987 33.333 0.00 0.00 40.08 3.16
3339 3410 7.480542 CGTTTTTCCGTGATATTTAGAAACTGG 59.519 37.037 0.00 0.00 0.00 4.00
3340 3411 7.989416 TTTTCCGTGATATTTAGAAACTGGT 57.011 32.000 0.00 0.00 0.00 4.00
3341 3412 9.504708 TTTTTCCGTGATATTTAGAAACTGGTA 57.495 29.630 0.00 0.00 0.00 3.25
3342 3413 8.712285 TTTCCGTGATATTTAGAAACTGGTAG 57.288 34.615 0.00 0.00 0.00 3.18
3343 3414 6.812998 TCCGTGATATTTAGAAACTGGTAGG 58.187 40.000 0.00 0.00 0.00 3.18
3344 3415 6.608405 TCCGTGATATTTAGAAACTGGTAGGA 59.392 38.462 0.00 0.00 0.00 2.94
3345 3416 7.124599 TCCGTGATATTTAGAAACTGGTAGGAA 59.875 37.037 0.00 0.00 0.00 3.36
3346 3417 7.224167 CCGTGATATTTAGAAACTGGTAGGAAC 59.776 40.741 0.00 0.00 0.00 3.62
3347 3418 7.224167 CGTGATATTTAGAAACTGGTAGGAACC 59.776 40.741 0.00 0.00 46.98 3.62
3362 3433 0.468648 GAACCGGATTCCTACCAGGG 59.531 60.000 9.46 0.00 35.59 4.45
3363 3434 1.632965 AACCGGATTCCTACCAGGGC 61.633 60.000 9.46 0.00 35.59 5.19
3364 3435 2.421739 CGGATTCCTACCAGGGCG 59.578 66.667 0.30 0.00 35.59 6.13
3365 3436 2.432300 CGGATTCCTACCAGGGCGT 61.432 63.158 0.30 0.00 35.59 5.68
3366 3437 1.146263 GGATTCCTACCAGGGCGTG 59.854 63.158 0.00 0.00 35.59 5.34
3374 3445 4.087892 CCAGGGCGTGGTCTCAGG 62.088 72.222 17.92 0.00 42.17 3.86
3375 3446 3.314331 CAGGGCGTGGTCTCAGGT 61.314 66.667 0.00 0.00 0.00 4.00
3376 3447 2.526873 AGGGCGTGGTCTCAGGTT 60.527 61.111 0.00 0.00 0.00 3.50
3377 3448 2.358737 GGGCGTGGTCTCAGGTTG 60.359 66.667 0.00 0.00 0.00 3.77
3378 3449 2.426023 GGCGTGGTCTCAGGTTGT 59.574 61.111 0.00 0.00 0.00 3.32
3379 3450 1.669440 GGCGTGGTCTCAGGTTGTA 59.331 57.895 0.00 0.00 0.00 2.41
3380 3451 0.389948 GGCGTGGTCTCAGGTTGTAG 60.390 60.000 0.00 0.00 0.00 2.74
3381 3452 0.389948 GCGTGGTCTCAGGTTGTAGG 60.390 60.000 0.00 0.00 0.00 3.18
3382 3453 0.246635 CGTGGTCTCAGGTTGTAGGG 59.753 60.000 0.00 0.00 0.00 3.53
3383 3454 0.613777 GTGGTCTCAGGTTGTAGGGG 59.386 60.000 0.00 0.00 0.00 4.79
3384 3455 0.192566 TGGTCTCAGGTTGTAGGGGT 59.807 55.000 0.00 0.00 0.00 4.95
3385 3456 0.613777 GGTCTCAGGTTGTAGGGGTG 59.386 60.000 0.00 0.00 0.00 4.61
3386 3457 0.613777 GTCTCAGGTTGTAGGGGTGG 59.386 60.000 0.00 0.00 0.00 4.61
3387 3458 0.490017 TCTCAGGTTGTAGGGGTGGA 59.510 55.000 0.00 0.00 0.00 4.02
3388 3459 1.132657 TCTCAGGTTGTAGGGGTGGAA 60.133 52.381 0.00 0.00 0.00 3.53
3389 3460 1.279271 CTCAGGTTGTAGGGGTGGAAG 59.721 57.143 0.00 0.00 0.00 3.46
3390 3461 0.328258 CAGGTTGTAGGGGTGGAAGG 59.672 60.000 0.00 0.00 0.00 3.46
3391 3462 0.195096 AGGTTGTAGGGGTGGAAGGA 59.805 55.000 0.00 0.00 0.00 3.36
3392 3463 0.618981 GGTTGTAGGGGTGGAAGGAG 59.381 60.000 0.00 0.00 0.00 3.69
3393 3464 0.618981 GTTGTAGGGGTGGAAGGAGG 59.381 60.000 0.00 0.00 0.00 4.30
3394 3465 0.549169 TTGTAGGGGTGGAAGGAGGG 60.549 60.000 0.00 0.00 0.00 4.30
3395 3466 1.394963 GTAGGGGTGGAAGGAGGGA 59.605 63.158 0.00 0.00 0.00 4.20
3396 3467 0.029989 GTAGGGGTGGAAGGAGGGAT 60.030 60.000 0.00 0.00 0.00 3.85
3397 3468 0.030092 TAGGGGTGGAAGGAGGGATG 60.030 60.000 0.00 0.00 0.00 3.51
3398 3469 2.386935 GGGGTGGAAGGAGGGATGG 61.387 68.421 0.00 0.00 0.00 3.51
3399 3470 2.597903 GGTGGAAGGAGGGATGGC 59.402 66.667 0.00 0.00 0.00 4.40
3400 3471 2.190578 GTGGAAGGAGGGATGGCG 59.809 66.667 0.00 0.00 0.00 5.69
3401 3472 2.285368 TGGAAGGAGGGATGGCGT 60.285 61.111 0.00 0.00 0.00 5.68
3402 3473 2.190578 GGAAGGAGGGATGGCGTG 59.809 66.667 0.00 0.00 0.00 5.34
3403 3474 2.190578 GAAGGAGGGATGGCGTGG 59.809 66.667 0.00 0.00 0.00 4.94
3404 3475 2.610859 AAGGAGGGATGGCGTGGT 60.611 61.111 0.00 0.00 0.00 4.16
3405 3476 2.595009 GAAGGAGGGATGGCGTGGTC 62.595 65.000 0.00 0.00 0.00 4.02
3406 3477 4.530857 GGAGGGATGGCGTGGTCG 62.531 72.222 0.00 0.00 40.37 4.79
3454 3525 3.568743 GCGCGCGAGAGAGAGAGA 61.569 66.667 37.18 0.00 31.43 3.10
3455 3526 2.625906 CGCGCGAGAGAGAGAGAG 59.374 66.667 28.94 0.00 31.43 3.20
3456 3527 1.880796 CGCGCGAGAGAGAGAGAGA 60.881 63.158 28.94 0.00 31.43 3.10
3457 3528 1.821241 CGCGCGAGAGAGAGAGAGAG 61.821 65.000 28.94 0.00 31.43 3.20
3458 3529 1.934463 CGCGAGAGAGAGAGAGAGC 59.066 63.158 0.00 0.00 0.00 4.09
3459 3530 0.809636 CGCGAGAGAGAGAGAGAGCA 60.810 60.000 0.00 0.00 0.00 4.26
3460 3531 0.940126 GCGAGAGAGAGAGAGAGCAG 59.060 60.000 0.00 0.00 0.00 4.24
3461 3532 1.586422 CGAGAGAGAGAGAGAGCAGG 58.414 60.000 0.00 0.00 0.00 4.85
3462 3533 1.811558 CGAGAGAGAGAGAGAGCAGGG 60.812 61.905 0.00 0.00 0.00 4.45
3463 3534 0.552848 AGAGAGAGAGAGAGCAGGGG 59.447 60.000 0.00 0.00 0.00 4.79
3464 3535 1.076044 AGAGAGAGAGAGCAGGGGC 60.076 63.158 0.00 0.00 41.61 5.80
3478 3549 3.085296 GGGCGGTGGCTAGGGTTA 61.085 66.667 0.00 0.00 39.81 2.85
3479 3550 2.504519 GGCGGTGGCTAGGGTTAG 59.495 66.667 0.00 0.00 39.81 2.34
3480 3551 2.504519 GCGGTGGCTAGGGTTAGG 59.495 66.667 0.00 0.00 35.83 2.69
3481 3552 2.364780 GCGGTGGCTAGGGTTAGGT 61.365 63.158 0.00 0.00 35.83 3.08
3482 3553 1.821258 CGGTGGCTAGGGTTAGGTC 59.179 63.158 0.00 0.00 0.00 3.85
3483 3554 0.686769 CGGTGGCTAGGGTTAGGTCT 60.687 60.000 0.00 0.00 0.00 3.85
3484 3555 1.121378 GGTGGCTAGGGTTAGGTCTC 58.879 60.000 0.00 0.00 0.00 3.36
3485 3556 1.121378 GTGGCTAGGGTTAGGTCTCC 58.879 60.000 0.00 0.00 0.00 3.71
3486 3557 0.031414 TGGCTAGGGTTAGGTCTCCC 60.031 60.000 0.00 0.00 43.71 4.30
3490 3561 2.365237 GGGTTAGGTCTCCCGGCT 60.365 66.667 0.00 0.00 33.97 5.52
3491 3562 2.433146 GGGTTAGGTCTCCCGGCTC 61.433 68.421 0.00 0.00 33.97 4.70
3492 3563 2.433146 GGTTAGGTCTCCCGGCTCC 61.433 68.421 0.00 0.00 35.12 4.70
3493 3564 2.042230 TTAGGTCTCCCGGCTCCC 60.042 66.667 0.00 0.00 35.12 4.30
3494 3565 2.633557 TTAGGTCTCCCGGCTCCCT 61.634 63.158 0.00 0.06 35.12 4.20
3495 3566 1.291459 TTAGGTCTCCCGGCTCCCTA 61.291 60.000 0.00 0.00 35.12 3.53
3496 3567 1.291459 TAGGTCTCCCGGCTCCCTAA 61.291 60.000 0.00 0.00 35.12 2.69
3497 3568 2.134933 GGTCTCCCGGCTCCCTAAG 61.135 68.421 0.00 0.00 0.00 2.18
3498 3569 2.134933 GTCTCCCGGCTCCCTAAGG 61.135 68.421 0.00 0.00 0.00 2.69
3499 3570 2.282446 CTCCCGGCTCCCTAAGGA 59.718 66.667 0.00 0.00 41.08 3.36
3500 3571 1.382695 CTCCCGGCTCCCTAAGGAA 60.383 63.158 0.00 0.00 43.40 3.36
3501 3572 1.382695 TCCCGGCTCCCTAAGGAAG 60.383 63.158 0.00 0.00 43.40 3.46
3502 3573 2.506472 CCGGCTCCCTAAGGAAGC 59.494 66.667 0.00 0.00 43.40 3.86
3503 3574 2.506472 CGGCTCCCTAAGGAAGCC 59.494 66.667 12.57 12.57 45.65 4.35
3504 3575 2.506472 GGCTCCCTAAGGAAGCCG 59.494 66.667 8.09 0.00 43.40 5.52
3505 3576 2.064581 GGCTCCCTAAGGAAGCCGA 61.065 63.158 8.09 0.00 43.40 5.54
3506 3577 1.443828 GCTCCCTAAGGAAGCCGAG 59.556 63.158 0.00 0.00 43.40 4.63
3507 3578 1.443828 CTCCCTAAGGAAGCCGAGC 59.556 63.158 0.00 0.00 43.40 5.03
3508 3579 1.305802 TCCCTAAGGAAGCCGAGCA 60.306 57.895 0.00 0.00 40.08 4.26
3509 3580 0.907704 TCCCTAAGGAAGCCGAGCAA 60.908 55.000 0.00 0.00 40.08 3.91
3510 3581 0.035439 CCCTAAGGAAGCCGAGCAAA 60.035 55.000 0.00 0.00 33.47 3.68
3511 3582 1.408822 CCCTAAGGAAGCCGAGCAAAT 60.409 52.381 0.00 0.00 33.47 2.32
3512 3583 2.158813 CCCTAAGGAAGCCGAGCAAATA 60.159 50.000 0.00 0.00 33.47 1.40
3513 3584 3.541632 CCTAAGGAAGCCGAGCAAATAA 58.458 45.455 0.00 0.00 0.00 1.40
3514 3585 3.561725 CCTAAGGAAGCCGAGCAAATAAG 59.438 47.826 0.00 0.00 0.00 1.73
3515 3586 3.350219 AAGGAAGCCGAGCAAATAAGA 57.650 42.857 0.00 0.00 0.00 2.10
3516 3587 3.567478 AGGAAGCCGAGCAAATAAGAT 57.433 42.857 0.00 0.00 0.00 2.40
3517 3588 3.891049 AGGAAGCCGAGCAAATAAGATT 58.109 40.909 0.00 0.00 0.00 2.40
3518 3589 3.629398 AGGAAGCCGAGCAAATAAGATTG 59.371 43.478 0.00 0.00 0.00 2.67
3533 3604 9.028185 CAAATAAGATTGCTTCTTGCTTAATCC 57.972 33.333 11.34 0.00 44.54 3.01
3534 3605 5.588958 AAGATTGCTTCTTGCTTAATCCC 57.411 39.130 2.24 0.00 43.21 3.85
3535 3606 4.603131 AGATTGCTTCTTGCTTAATCCCA 58.397 39.130 0.00 0.00 43.37 4.37
3536 3607 5.018809 AGATTGCTTCTTGCTTAATCCCAA 58.981 37.500 0.00 0.00 43.37 4.12
3537 3608 5.481473 AGATTGCTTCTTGCTTAATCCCAAA 59.519 36.000 0.00 0.00 43.37 3.28
3538 3609 5.543507 TTGCTTCTTGCTTAATCCCAAAA 57.456 34.783 0.00 0.00 43.37 2.44
3539 3610 4.881920 TGCTTCTTGCTTAATCCCAAAAC 58.118 39.130 0.00 0.00 43.37 2.43
3540 3611 3.920412 GCTTCTTGCTTAATCCCAAAACG 59.080 43.478 0.00 0.00 38.95 3.60
3541 3612 4.485163 CTTCTTGCTTAATCCCAAAACGG 58.515 43.478 0.00 0.00 0.00 4.44
3566 3637 9.159364 GGGTCCTTACACGAAATTATATAATCC 57.841 37.037 8.42 3.67 0.00 3.01
3567 3638 9.939802 GGTCCTTACACGAAATTATATAATCCT 57.060 33.333 8.42 0.00 0.00 3.24
3586 3657 6.628644 ATCCTCCTAATAAGATAACTGGGC 57.371 41.667 0.00 0.00 0.00 5.36
3587 3658 5.727630 TCCTCCTAATAAGATAACTGGGCT 58.272 41.667 0.00 0.00 0.00 5.19
3588 3659 6.871035 TCCTCCTAATAAGATAACTGGGCTA 58.129 40.000 0.00 0.00 0.00 3.93
3589 3660 7.310634 TCCTCCTAATAAGATAACTGGGCTAA 58.689 38.462 0.00 0.00 0.00 3.09
3590 3661 7.455008 TCCTCCTAATAAGATAACTGGGCTAAG 59.545 40.741 0.00 0.00 0.00 2.18
3591 3662 7.005709 TCCTAATAAGATAACTGGGCTAAGC 57.994 40.000 0.00 0.00 0.00 3.09
3604 3675 3.697619 GGCTAAGCCCCTAATAACGAT 57.302 47.619 0.00 0.00 44.06 3.73
3605 3676 4.813750 GGCTAAGCCCCTAATAACGATA 57.186 45.455 0.00 0.00 44.06 2.92
3606 3677 5.156608 GGCTAAGCCCCTAATAACGATAA 57.843 43.478 0.00 0.00 44.06 1.75
3607 3678 5.176592 GGCTAAGCCCCTAATAACGATAAG 58.823 45.833 0.00 0.00 44.06 1.73
3608 3679 5.046807 GGCTAAGCCCCTAATAACGATAAGA 60.047 44.000 0.00 0.00 44.06 2.10
3609 3680 6.351966 GGCTAAGCCCCTAATAACGATAAGAT 60.352 42.308 0.00 0.00 44.06 2.40
3610 3681 7.147776 GGCTAAGCCCCTAATAACGATAAGATA 60.148 40.741 0.00 0.00 44.06 1.98
3611 3682 8.255905 GCTAAGCCCCTAATAACGATAAGATAA 58.744 37.037 0.00 0.00 0.00 1.75
3613 3684 8.843885 AAGCCCCTAATAACGATAAGATAAAC 57.156 34.615 0.00 0.00 0.00 2.01
3614 3685 8.203681 AGCCCCTAATAACGATAAGATAAACT 57.796 34.615 0.00 0.00 0.00 2.66
3615 3686 8.095169 AGCCCCTAATAACGATAAGATAAACTG 58.905 37.037 0.00 0.00 0.00 3.16
3616 3687 7.333672 GCCCCTAATAACGATAAGATAAACTGG 59.666 40.741 0.00 0.00 0.00 4.00
3617 3688 7.822822 CCCCTAATAACGATAAGATAAACTGGG 59.177 40.741 0.00 0.00 0.00 4.45
3618 3689 7.333672 CCCTAATAACGATAAGATAAACTGGGC 59.666 40.741 0.00 0.00 0.00 5.36
3619 3690 7.333672 CCTAATAACGATAAGATAAACTGGGCC 59.666 40.741 0.00 0.00 0.00 5.80
3620 3691 4.497291 AACGATAAGATAAACTGGGCCA 57.503 40.909 5.85 5.85 0.00 5.36
3621 3692 3.805207 ACGATAAGATAAACTGGGCCAC 58.195 45.455 0.00 0.00 0.00 5.01
3622 3693 3.199071 ACGATAAGATAAACTGGGCCACA 59.801 43.478 0.00 0.00 0.00 4.17
3623 3694 4.196193 CGATAAGATAAACTGGGCCACAA 58.804 43.478 0.00 0.00 0.00 3.33
3624 3695 4.035208 CGATAAGATAAACTGGGCCACAAC 59.965 45.833 0.00 0.00 0.00 3.32
3625 3696 3.525800 AAGATAAACTGGGCCACAACT 57.474 42.857 0.00 0.00 0.00 3.16
3626 3697 4.650972 AAGATAAACTGGGCCACAACTA 57.349 40.909 0.00 0.00 0.00 2.24
3627 3698 4.650972 AGATAAACTGGGCCACAACTAA 57.349 40.909 0.00 0.00 0.00 2.24
3628 3699 4.332828 AGATAAACTGGGCCACAACTAAC 58.667 43.478 0.00 0.00 0.00 2.34
3629 3700 2.748209 AAACTGGGCCACAACTAACT 57.252 45.000 0.00 0.00 0.00 2.24
3630 3701 1.981256 AACTGGGCCACAACTAACTG 58.019 50.000 0.00 0.00 0.00 3.16
3631 3702 0.110486 ACTGGGCCACAACTAACTGG 59.890 55.000 0.00 0.00 0.00 4.00
3632 3703 0.609131 CTGGGCCACAACTAACTGGG 60.609 60.000 0.00 0.00 0.00 4.45
3633 3704 3.681473 GGCCACAACTAACTGGGC 58.319 61.111 0.00 0.00 45.01 5.36
3634 3705 4.821935 GCCACAACTAACTGGGCT 57.178 55.556 0.00 0.00 41.39 5.19
3635 3706 3.948735 GCCACAACTAACTGGGCTA 57.051 52.632 0.00 0.00 41.39 3.93
3636 3707 2.194201 GCCACAACTAACTGGGCTAA 57.806 50.000 0.00 0.00 41.39 3.09
3637 3708 2.084546 GCCACAACTAACTGGGCTAAG 58.915 52.381 0.00 0.00 41.39 2.18
3638 3709 2.084546 CCACAACTAACTGGGCTAAGC 58.915 52.381 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 9.622004 TGTTTCAACGTGTATTTGAACTTTTTA 57.378 25.926 0.00 0.00 41.55 1.52
165 166 8.696410 ATGTTTCAACGTGTATTTGAACTTTT 57.304 26.923 0.00 0.00 41.55 2.27
384 385 7.201461 GCATTTCGAAATATGCTTGTCACATTT 60.201 33.333 22.33 0.00 42.91 2.32
395 398 2.017357 TCGCGCATTTCGAAATATGC 57.983 45.000 25.27 25.27 42.82 3.14
403 406 4.736872 ACATTAAAAATCGCGCATTTCG 57.263 36.364 8.75 0.00 33.16 3.46
404 407 9.471742 AAAAATACATTAAAAATCGCGCATTTC 57.528 25.926 8.75 0.00 33.16 2.17
458 462 7.638683 GCAGTGTTAAAATGATATCCGTACAAC 59.361 37.037 0.00 0.64 0.00 3.32
461 465 7.241663 TGCAGTGTTAAAATGATATCCGTAC 57.758 36.000 0.00 0.00 0.00 3.67
462 466 9.549078 TTATGCAGTGTTAAAATGATATCCGTA 57.451 29.630 0.00 0.00 0.00 4.02
553 558 9.752961 CATCCTTGCATCATTAAAATTGTCATA 57.247 29.630 0.00 0.00 0.00 2.15
582 587 3.563808 TGGCATGTGTGTCAACTAAACTC 59.436 43.478 0.00 0.00 36.93 3.01
647 652 2.110011 AGGGATGGCAAGTTTAGTTGGT 59.890 45.455 0.00 0.00 0.00 3.67
668 673 8.751335 GTTTTCGATGAAAAATTTAGTGAAGCA 58.249 29.630 6.31 0.00 42.09 3.91
824 854 8.076178 CCTTTAGATCACTCGTTTGTTTCAATT 58.924 33.333 0.00 0.00 0.00 2.32
825 855 7.444183 TCCTTTAGATCACTCGTTTGTTTCAAT 59.556 33.333 0.00 0.00 0.00 2.57
868 899 2.158385 TGGACAGGCCCAACAAAAGTAT 60.158 45.455 0.00 0.00 34.97 2.12
869 900 1.215673 TGGACAGGCCCAACAAAAGTA 59.784 47.619 0.00 0.00 34.97 2.24
876 907 1.182667 GGTAAATGGACAGGCCCAAC 58.817 55.000 0.00 0.00 40.04 3.77
884 915 1.876799 CAGCGTTGTGGTAAATGGACA 59.123 47.619 0.00 0.00 0.00 4.02
1554 1612 0.750249 ACACGATGTCACCACAGTCA 59.250 50.000 0.00 0.00 35.41 3.41
1594 1652 0.889186 ACGTTCCTGTGTGGCATTCC 60.889 55.000 0.00 0.00 35.26 3.01
1629 1687 4.706476 CACTTCACATACCCATCAACCATT 59.294 41.667 0.00 0.00 0.00 3.16
1637 1695 0.107214 CCCGCACTTCACATACCCAT 60.107 55.000 0.00 0.00 0.00 4.00
1644 1702 1.227823 CAAGTCCCCGCACTTCACA 60.228 57.895 0.00 0.00 34.17 3.58
1667 1725 0.036732 TTCGAACAGCCTCCTTGCAT 59.963 50.000 0.00 0.00 0.00 3.96
1712 1770 1.738908 CACCGATCAATGATGTGTGCA 59.261 47.619 0.00 0.00 0.00 4.57
1743 1801 1.973138 CAACTTGCATCTTTCCTGCG 58.027 50.000 0.00 0.00 42.62 5.18
1833 1891 3.495806 CCTCTCCAGGATAACCATTCTGC 60.496 52.174 0.00 0.00 43.65 4.26
1864 1922 8.290325 GTCTTTCTCACGGAACTCATTAAAAAT 58.710 33.333 0.00 0.00 33.13 1.82
1931 1989 1.765904 TGTTACCCAGTTGAGAGCACA 59.234 47.619 0.00 0.00 0.00 4.57
1938 1996 4.078537 CCAACATGATGTTACCCAGTTGA 58.921 43.478 10.89 0.00 38.77 3.18
1984 2042 8.534333 TTGTTCATATCTATGGAATAAGTCGC 57.466 34.615 0.00 0.00 34.50 5.19
2071 2129 4.176271 GGCATGGACTCAAATAAAACAGC 58.824 43.478 0.00 0.00 0.00 4.40
2217 2275 4.782019 AGCTGTCAAAACAACTGTGAAA 57.218 36.364 0.00 0.00 34.24 2.69
2220 2278 2.599973 GCAAGCTGTCAAAACAACTGTG 59.400 45.455 0.00 0.00 32.22 3.66
2439 2497 2.239400 TCACCTAGGAGTATGCATCCG 58.761 52.381 17.98 0.00 42.02 4.18
2453 2511 6.721318 ACTTTTCCAAGCTCAATATCACCTA 58.279 36.000 0.00 0.00 32.57 3.08
2568 2626 6.101650 TCAGCTCTAACTTCAGAAACATCA 57.898 37.500 0.00 0.00 0.00 3.07
2691 2749 3.347216 TCCAATAAGGTCAGCAAAGCTC 58.653 45.455 0.00 0.00 36.04 4.09
2811 2869 3.499157 CCAAACTTGGGTGCAAATCATTG 59.501 43.478 0.09 0.00 44.70 2.82
2894 2960 6.183360 GGCTTGATGACTCTTATTAACCCAAC 60.183 42.308 0.00 0.00 0.00 3.77
2960 3027 5.784578 ACACGAGGTAATGTCAGCATATA 57.215 39.130 0.00 0.00 34.39 0.86
3101 3168 3.831715 AAGCGAACAAACTGAATAGGC 57.168 42.857 0.00 0.00 0.00 3.93
3116 3183 4.868171 CACTACCTTGTATGCTAAAAGCGA 59.132 41.667 0.00 0.00 46.26 4.93
3211 3278 4.869861 ACCTGAAATGTTCTGTTTTTGTGC 59.130 37.500 0.00 0.00 0.00 4.57
3287 3358 4.226761 GCAGGTACATTGTGCAAAAGTAC 58.773 43.478 15.49 15.49 37.16 2.73
3296 3367 4.678509 AAACGTATGCAGGTACATTGTG 57.321 40.909 0.00 0.00 0.00 3.33
3327 3398 4.533311 TCCGGTTCCTACCAGTTTCTAAAT 59.467 41.667 0.00 0.00 45.31 1.40
3343 3414 0.468648 CCCTGGTAGGAATCCGGTTC 59.531 60.000 0.00 4.72 37.67 3.62
3344 3415 1.632965 GCCCTGGTAGGAATCCGGTT 61.633 60.000 0.00 0.00 37.67 4.44
3345 3416 2.070650 GCCCTGGTAGGAATCCGGT 61.071 63.158 0.00 0.00 37.67 5.28
3346 3417 2.829592 GCCCTGGTAGGAATCCGG 59.170 66.667 0.00 0.00 37.67 5.14
3347 3418 2.421739 CGCCCTGGTAGGAATCCG 59.578 66.667 0.00 0.00 37.67 4.18
3348 3419 1.146263 CACGCCCTGGTAGGAATCC 59.854 63.158 0.00 0.00 37.67 3.01
3349 3420 1.146263 CCACGCCCTGGTAGGAATC 59.854 63.158 0.00 0.00 37.67 2.52
3350 3421 3.320359 CCACGCCCTGGTAGGAAT 58.680 61.111 0.00 0.00 37.67 3.01
3358 3429 2.883828 AACCTGAGACCACGCCCTG 61.884 63.158 0.00 0.00 0.00 4.45
3359 3430 2.526873 AACCTGAGACCACGCCCT 60.527 61.111 0.00 0.00 0.00 5.19
3360 3431 1.823169 TACAACCTGAGACCACGCCC 61.823 60.000 0.00 0.00 0.00 6.13
3361 3432 0.389948 CTACAACCTGAGACCACGCC 60.390 60.000 0.00 0.00 0.00 5.68
3362 3433 0.389948 CCTACAACCTGAGACCACGC 60.390 60.000 0.00 0.00 0.00 5.34
3363 3434 0.246635 CCCTACAACCTGAGACCACG 59.753 60.000 0.00 0.00 0.00 4.94
3364 3435 0.613777 CCCCTACAACCTGAGACCAC 59.386 60.000 0.00 0.00 0.00 4.16
3365 3436 0.192566 ACCCCTACAACCTGAGACCA 59.807 55.000 0.00 0.00 0.00 4.02
3366 3437 0.613777 CACCCCTACAACCTGAGACC 59.386 60.000 0.00 0.00 0.00 3.85
3367 3438 0.613777 CCACCCCTACAACCTGAGAC 59.386 60.000 0.00 0.00 0.00 3.36
3368 3439 0.490017 TCCACCCCTACAACCTGAGA 59.510 55.000 0.00 0.00 0.00 3.27
3369 3440 1.279271 CTTCCACCCCTACAACCTGAG 59.721 57.143 0.00 0.00 0.00 3.35
3370 3441 1.358152 CTTCCACCCCTACAACCTGA 58.642 55.000 0.00 0.00 0.00 3.86
3371 3442 0.328258 CCTTCCACCCCTACAACCTG 59.672 60.000 0.00 0.00 0.00 4.00
3372 3443 0.195096 TCCTTCCACCCCTACAACCT 59.805 55.000 0.00 0.00 0.00 3.50
3373 3444 0.618981 CTCCTTCCACCCCTACAACC 59.381 60.000 0.00 0.00 0.00 3.77
3374 3445 0.618981 CCTCCTTCCACCCCTACAAC 59.381 60.000 0.00 0.00 0.00 3.32
3375 3446 0.549169 CCCTCCTTCCACCCCTACAA 60.549 60.000 0.00 0.00 0.00 2.41
3376 3447 1.082206 CCCTCCTTCCACCCCTACA 59.918 63.158 0.00 0.00 0.00 2.74
3377 3448 0.029989 ATCCCTCCTTCCACCCCTAC 60.030 60.000 0.00 0.00 0.00 3.18
3378 3449 0.030092 CATCCCTCCTTCCACCCCTA 60.030 60.000 0.00 0.00 0.00 3.53
3379 3450 1.308216 CATCCCTCCTTCCACCCCT 60.308 63.158 0.00 0.00 0.00 4.79
3380 3451 2.386935 CCATCCCTCCTTCCACCCC 61.387 68.421 0.00 0.00 0.00 4.95
3381 3452 3.061905 GCCATCCCTCCTTCCACCC 62.062 68.421 0.00 0.00 0.00 4.61
3382 3453 2.597903 GCCATCCCTCCTTCCACC 59.402 66.667 0.00 0.00 0.00 4.61
3383 3454 2.190578 CGCCATCCCTCCTTCCAC 59.809 66.667 0.00 0.00 0.00 4.02
3384 3455 2.285368 ACGCCATCCCTCCTTCCA 60.285 61.111 0.00 0.00 0.00 3.53
3385 3456 2.190578 CACGCCATCCCTCCTTCC 59.809 66.667 0.00 0.00 0.00 3.46
3386 3457 2.190578 CCACGCCATCCCTCCTTC 59.809 66.667 0.00 0.00 0.00 3.46
3387 3458 2.610859 ACCACGCCATCCCTCCTT 60.611 61.111 0.00 0.00 0.00 3.36
3388 3459 3.083997 GACCACGCCATCCCTCCT 61.084 66.667 0.00 0.00 0.00 3.69
3389 3460 4.530857 CGACCACGCCATCCCTCC 62.531 72.222 0.00 0.00 0.00 4.30
3436 3507 4.936248 CTCTCTCTCTCGCGCGCG 62.936 72.222 44.84 44.84 41.35 6.86
3437 3508 3.506312 CTCTCTCTCTCTCGCGCGC 62.506 68.421 27.95 23.91 0.00 6.86
3438 3509 1.821241 CTCTCTCTCTCTCTCGCGCG 61.821 65.000 26.76 26.76 0.00 6.86
3439 3510 1.934463 CTCTCTCTCTCTCTCGCGC 59.066 63.158 0.00 0.00 0.00 6.86
3440 3511 0.809636 TGCTCTCTCTCTCTCTCGCG 60.810 60.000 0.00 0.00 0.00 5.87
3441 3512 0.940126 CTGCTCTCTCTCTCTCTCGC 59.060 60.000 0.00 0.00 0.00 5.03
3442 3513 1.586422 CCTGCTCTCTCTCTCTCTCG 58.414 60.000 0.00 0.00 0.00 4.04
3443 3514 1.477558 CCCCTGCTCTCTCTCTCTCTC 60.478 61.905 0.00 0.00 0.00 3.20
3444 3515 0.552848 CCCCTGCTCTCTCTCTCTCT 59.447 60.000 0.00 0.00 0.00 3.10
3445 3516 1.109323 GCCCCTGCTCTCTCTCTCTC 61.109 65.000 0.00 0.00 33.53 3.20
3446 3517 1.076044 GCCCCTGCTCTCTCTCTCT 60.076 63.158 0.00 0.00 33.53 3.10
3447 3518 2.489275 CGCCCCTGCTCTCTCTCTC 61.489 68.421 0.00 0.00 34.43 3.20
3448 3519 2.441901 CGCCCCTGCTCTCTCTCT 60.442 66.667 0.00 0.00 34.43 3.10
3449 3520 3.535962 CCGCCCCTGCTCTCTCTC 61.536 72.222 0.00 0.00 34.43 3.20
3450 3521 4.390556 ACCGCCCCTGCTCTCTCT 62.391 66.667 0.00 0.00 34.43 3.10
3451 3522 4.154347 CACCGCCCCTGCTCTCTC 62.154 72.222 0.00 0.00 34.43 3.20
3461 3532 3.085296 TAACCCTAGCCACCGCCC 61.085 66.667 0.00 0.00 34.57 6.13
3462 3533 2.504519 CTAACCCTAGCCACCGCC 59.495 66.667 0.00 0.00 34.57 6.13
3463 3534 2.307611 GACCTAACCCTAGCCACCGC 62.308 65.000 0.00 0.00 0.00 5.68
3464 3535 0.686769 AGACCTAACCCTAGCCACCG 60.687 60.000 0.00 0.00 0.00 4.94
3465 3536 1.121378 GAGACCTAACCCTAGCCACC 58.879 60.000 0.00 0.00 0.00 4.61
3466 3537 1.121378 GGAGACCTAACCCTAGCCAC 58.879 60.000 0.00 0.00 0.00 5.01
3467 3538 3.629220 GGAGACCTAACCCTAGCCA 57.371 57.895 0.00 0.00 0.00 4.75
3480 3551 2.134933 CCTTAGGGAGCCGGGAGAC 61.135 68.421 2.18 0.00 33.58 3.36
3481 3552 1.882189 TTCCTTAGGGAGCCGGGAGA 61.882 60.000 2.18 0.00 43.29 3.71
3482 3553 1.382695 TTCCTTAGGGAGCCGGGAG 60.383 63.158 2.18 0.00 43.29 4.30
3483 3554 1.382695 CTTCCTTAGGGAGCCGGGA 60.383 63.158 2.18 0.00 43.29 5.14
3484 3555 3.108288 GCTTCCTTAGGGAGCCGGG 62.108 68.421 20.68 0.00 43.29 5.73
3485 3556 2.506472 GCTTCCTTAGGGAGCCGG 59.494 66.667 20.68 0.00 43.29 6.13
3486 3557 2.506472 GGCTTCCTTAGGGAGCCG 59.494 66.667 32.66 0.00 43.29 5.52
3487 3558 2.034048 CTCGGCTTCCTTAGGGAGCC 62.034 65.000 35.24 35.24 44.75 4.70
3488 3559 1.443828 CTCGGCTTCCTTAGGGAGC 59.556 63.158 22.98 22.98 43.29 4.70
3489 3560 1.330655 TGCTCGGCTTCCTTAGGGAG 61.331 60.000 1.20 1.20 43.29 4.30
3490 3561 0.907704 TTGCTCGGCTTCCTTAGGGA 60.908 55.000 0.00 0.00 40.36 4.20
3491 3562 0.035439 TTTGCTCGGCTTCCTTAGGG 60.035 55.000 0.00 0.00 0.00 3.53
3492 3563 2.044123 ATTTGCTCGGCTTCCTTAGG 57.956 50.000 0.00 0.00 0.00 2.69
3493 3564 4.442706 TCTTATTTGCTCGGCTTCCTTAG 58.557 43.478 0.00 0.00 0.00 2.18
3494 3565 4.481368 TCTTATTTGCTCGGCTTCCTTA 57.519 40.909 0.00 0.00 0.00 2.69
3495 3566 3.350219 TCTTATTTGCTCGGCTTCCTT 57.650 42.857 0.00 0.00 0.00 3.36
3496 3567 3.567478 ATCTTATTTGCTCGGCTTCCT 57.433 42.857 0.00 0.00 0.00 3.36
3497 3568 3.793465 GCAATCTTATTTGCTCGGCTTCC 60.793 47.826 2.08 0.00 46.66 3.46
3498 3569 3.366719 GCAATCTTATTTGCTCGGCTTC 58.633 45.455 2.08 0.00 46.66 3.86
3499 3570 3.427161 GCAATCTTATTTGCTCGGCTT 57.573 42.857 2.08 0.00 46.66 4.35
3506 3577 7.816945 TTAAGCAAGAAGCAATCTTATTTGC 57.183 32.000 13.94 13.94 46.80 3.68
3507 3578 9.028185 GGATTAAGCAAGAAGCAATCTTATTTG 57.972 33.333 4.66 0.00 46.80 2.32
3508 3579 8.200120 GGGATTAAGCAAGAAGCAATCTTATTT 58.800 33.333 4.66 5.48 46.80 1.40
3509 3580 7.342799 TGGGATTAAGCAAGAAGCAATCTTATT 59.657 33.333 4.66 6.01 46.80 1.40
3510 3581 6.835488 TGGGATTAAGCAAGAAGCAATCTTAT 59.165 34.615 4.66 0.00 46.80 1.73
3511 3582 6.186957 TGGGATTAAGCAAGAAGCAATCTTA 58.813 36.000 4.66 0.00 46.80 2.10
3518 3589 3.920412 CGTTTTGGGATTAAGCAAGAAGC 59.080 43.478 0.00 0.00 46.19 3.86
3519 3590 4.485163 CCGTTTTGGGATTAAGCAAGAAG 58.515 43.478 0.00 0.00 0.00 2.85
3520 3591 4.513198 CCGTTTTGGGATTAAGCAAGAA 57.487 40.909 0.00 0.00 0.00 2.52
3533 3604 0.869730 CGTGTAAGGACCCGTTTTGG 59.130 55.000 0.00 0.00 37.55 3.28
3534 3605 1.868469 TCGTGTAAGGACCCGTTTTG 58.132 50.000 0.00 0.00 0.00 2.44
3535 3606 2.618442 TTCGTGTAAGGACCCGTTTT 57.382 45.000 0.00 0.00 0.00 2.43
3536 3607 2.618442 TTTCGTGTAAGGACCCGTTT 57.382 45.000 0.00 0.00 0.00 3.60
3537 3608 2.845363 ATTTCGTGTAAGGACCCGTT 57.155 45.000 0.00 0.00 0.00 4.44
3538 3609 2.845363 AATTTCGTGTAAGGACCCGT 57.155 45.000 0.00 0.00 0.00 5.28
3539 3610 8.767478 ATTATATAATTTCGTGTAAGGACCCG 57.233 34.615 1.91 0.00 0.00 5.28
3540 3611 9.159364 GGATTATATAATTTCGTGTAAGGACCC 57.841 37.037 9.33 0.00 0.00 4.46
3541 3612 9.939802 AGGATTATATAATTTCGTGTAAGGACC 57.060 33.333 9.33 2.00 0.00 4.46
3560 3631 8.773216 GCCCAGTTATCTTATTAGGAGGATTAT 58.227 37.037 0.00 0.00 0.00 1.28
3561 3632 7.962003 AGCCCAGTTATCTTATTAGGAGGATTA 59.038 37.037 0.00 0.00 0.00 1.75
3562 3633 6.795000 AGCCCAGTTATCTTATTAGGAGGATT 59.205 38.462 0.00 0.00 0.00 3.01
3563 3634 6.335115 AGCCCAGTTATCTTATTAGGAGGAT 58.665 40.000 0.00 0.00 0.00 3.24
3564 3635 5.727630 AGCCCAGTTATCTTATTAGGAGGA 58.272 41.667 0.00 0.00 0.00 3.71
3565 3636 7.554959 TTAGCCCAGTTATCTTATTAGGAGG 57.445 40.000 0.00 0.00 0.00 4.30
3566 3637 7.100409 GCTTAGCCCAGTTATCTTATTAGGAG 58.900 42.308 0.00 0.00 0.00 3.69
3567 3638 6.013639 GGCTTAGCCCAGTTATCTTATTAGGA 60.014 42.308 13.12 0.00 44.06 2.94
3568 3639 6.174049 GGCTTAGCCCAGTTATCTTATTAGG 58.826 44.000 13.12 0.00 44.06 2.69
3585 3656 6.034161 TCTTATCGTTATTAGGGGCTTAGC 57.966 41.667 0.00 0.00 0.00 3.09
3587 3658 9.933723 GTTTATCTTATCGTTATTAGGGGCTTA 57.066 33.333 0.00 0.00 0.00 3.09
3588 3659 8.657712 AGTTTATCTTATCGTTATTAGGGGCTT 58.342 33.333 0.00 0.00 0.00 4.35
3589 3660 8.095169 CAGTTTATCTTATCGTTATTAGGGGCT 58.905 37.037 0.00 0.00 0.00 5.19
3590 3661 7.333672 CCAGTTTATCTTATCGTTATTAGGGGC 59.666 40.741 0.00 0.00 0.00 5.80
3591 3662 7.822822 CCCAGTTTATCTTATCGTTATTAGGGG 59.177 40.741 0.00 0.00 0.00 4.79
3592 3663 7.333672 GCCCAGTTTATCTTATCGTTATTAGGG 59.666 40.741 0.00 0.00 0.00 3.53
3593 3664 7.333672 GGCCCAGTTTATCTTATCGTTATTAGG 59.666 40.741 0.00 0.00 0.00 2.69
3594 3665 7.876068 TGGCCCAGTTTATCTTATCGTTATTAG 59.124 37.037 0.00 0.00 0.00 1.73
3595 3666 7.658575 GTGGCCCAGTTTATCTTATCGTTATTA 59.341 37.037 0.00 0.00 0.00 0.98
3596 3667 6.485648 GTGGCCCAGTTTATCTTATCGTTATT 59.514 38.462 0.00 0.00 0.00 1.40
3597 3668 5.995897 GTGGCCCAGTTTATCTTATCGTTAT 59.004 40.000 0.00 0.00 0.00 1.89
3598 3669 5.104859 TGTGGCCCAGTTTATCTTATCGTTA 60.105 40.000 0.00 0.00 0.00 3.18
3599 3670 4.196971 GTGGCCCAGTTTATCTTATCGTT 58.803 43.478 0.00 0.00 0.00 3.85
3600 3671 3.199071 TGTGGCCCAGTTTATCTTATCGT 59.801 43.478 0.00 0.00 0.00 3.73
3601 3672 3.804036 TGTGGCCCAGTTTATCTTATCG 58.196 45.455 0.00 0.00 0.00 2.92
3602 3673 5.193679 AGTTGTGGCCCAGTTTATCTTATC 58.806 41.667 0.00 0.00 0.00 1.75
3603 3674 5.193099 AGTTGTGGCCCAGTTTATCTTAT 57.807 39.130 0.00 0.00 0.00 1.73
3604 3675 4.650972 AGTTGTGGCCCAGTTTATCTTA 57.349 40.909 0.00 0.00 0.00 2.10
3605 3676 3.525800 AGTTGTGGCCCAGTTTATCTT 57.474 42.857 0.00 0.00 0.00 2.40
3606 3677 4.042934 AGTTAGTTGTGGCCCAGTTTATCT 59.957 41.667 0.00 0.00 0.00 1.98
3607 3678 4.156008 CAGTTAGTTGTGGCCCAGTTTATC 59.844 45.833 0.00 0.00 0.00 1.75
3608 3679 4.079253 CAGTTAGTTGTGGCCCAGTTTAT 58.921 43.478 0.00 0.00 0.00 1.40
3609 3680 3.482436 CAGTTAGTTGTGGCCCAGTTTA 58.518 45.455 0.00 0.00 0.00 2.01
3610 3681 2.306847 CAGTTAGTTGTGGCCCAGTTT 58.693 47.619 0.00 0.00 0.00 2.66
3611 3682 1.478654 CCAGTTAGTTGTGGCCCAGTT 60.479 52.381 0.00 0.00 0.00 3.16
3612 3683 0.110486 CCAGTTAGTTGTGGCCCAGT 59.890 55.000 0.00 0.00 0.00 4.00
3613 3684 0.609131 CCCAGTTAGTTGTGGCCCAG 60.609 60.000 0.00 0.00 31.85 4.45
3614 3685 1.458486 CCCAGTTAGTTGTGGCCCA 59.542 57.895 0.00 0.00 31.85 5.36
3615 3686 1.977009 GCCCAGTTAGTTGTGGCCC 60.977 63.158 0.00 0.00 36.07 5.80
3616 3687 0.326927 TAGCCCAGTTAGTTGTGGCC 59.673 55.000 0.00 0.00 43.18 5.36
3617 3688 2.084546 CTTAGCCCAGTTAGTTGTGGC 58.915 52.381 0.00 0.00 42.48 5.01
3618 3689 2.084546 GCTTAGCCCAGTTAGTTGTGG 58.915 52.381 0.00 0.00 0.00 4.17
3619 3690 2.084546 GGCTTAGCCCAGTTAGTTGTG 58.915 52.381 13.12 0.00 44.06 3.33
3620 3691 2.491675 GGCTTAGCCCAGTTAGTTGT 57.508 50.000 13.12 0.00 44.06 3.32


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

AutoCloner maintained by Alex Coulton.