Multiple sequence alignment - TraesCS6D01G272800

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 TraesCS6D01G272800 chr6D 100.000 4224 0 0 1 4224 381545587 381549810 0.000000e+00 7801.0
1 TraesCS6D01G272800 chr6B 92.943 2593 115 20 754 3310 570147485 570150045 0.000000e+00 3712.0
2 TraesCS6D01G272800 chr6B 90.734 518 29 5 3594 4093 570150328 570150844 0.000000e+00 673.0
3 TraesCS6D01G272800 chr6A 95.749 1435 48 9 1866 3299 523065652 523067074 0.000000e+00 2300.0
4 TraesCS6D01G272800 chr6A 88.468 1925 147 42 1 1868 523062671 523064577 0.000000e+00 2255.0
5 TraesCS6D01G272800 chr6A 92.593 378 22 3 3847 4224 523067380 523067751 4.810000e-149 538.0
6 TraesCS6D01G272800 chr6A 86.348 293 20 6 3491 3771 523067081 523067365 6.860000e-78 302.0
7 TraesCS6D01G272800 chr4D 98.421 190 3 0 3306 3495 503922021 503922210 6.770000e-88 335.0
8 TraesCS6D01G272800 chr3D 98.421 190 3 0 3306 3495 142708776 142708587 6.770000e-88 335.0
9 TraesCS6D01G272800 chr3D 97.895 190 4 0 3307 3496 35671258 35671447 3.150000e-86 329.0
10 TraesCS6D01G272800 chr5D 98.413 189 3 0 3306 3494 121102664 121102476 2.430000e-87 333.0
11 TraesCS6D01G272800 chr5D 98.413 189 3 0 3307 3495 130661324 130661512 2.430000e-87 333.0
12 TraesCS6D01G272800 chr5B 98.404 188 3 0 3307 3494 447830849 447830662 8.750000e-87 331.0
13 TraesCS6D01G272800 chr7A 97.409 193 4 1 3307 3498 726986020 726986212 1.130000e-85 327.0
14 TraesCS6D01G272800 chr4B 96.923 195 5 1 3305 3499 52034700 52034893 4.070000e-85 326.0
15 TraesCS6D01G272800 chr7D 95.545 202 8 1 3306 3507 161844387 161844587 5.270000e-84 322.0
16 TraesCS6D01G272800 chr1D 76.923 273 52 5 2646 2913 97778243 97777977 1.220000e-30 145.0
17 TraesCS6D01G272800 chr2A 81.944 72 6 6 479 550 630086042 630085978 2.000000e-03 54.7


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 TraesCS6D01G272800 chr6D 381545587 381549810 4223 False 7801.00 7801 100.0000 1 4224 1 chr6D.!!$F1 4223
1 TraesCS6D01G272800 chr6B 570147485 570150844 3359 False 2192.50 3712 91.8385 754 4093 2 chr6B.!!$F1 3339
2 TraesCS6D01G272800 chr6A 523062671 523067751 5080 False 1348.75 2300 90.7895 1 4224 4 chr6A.!!$F1 4223

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
511 519 3.146066 CCGGGAACACTTCTCAAATTCA 58.854 45.455 0.0 0.0 0.0 2.57 F
1486 1551 1.006813 TGGATGGGTGGGTGCTTATT 58.993 50.000 0.0 0.0 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1553 1.529438 GGAAAACGACGCAACAGATCA 59.471 47.619 0.0 0.0 0.0 2.92 R
3473 4646 0.105709 AAGGGGGTGTTTGGTTCAGG 60.106 55.000 0.0 0.0 0.0 3.86 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
345 352 8.830201 TGAAATTCATGAACAATTTTCGGATT 57.170 26.923 19.71 3.25 34.30 3.01
354 361 4.344104 ACAATTTTCGGATTGGAGACCAT 58.656 39.130 10.37 0.00 40.50 3.55
361 368 5.023533 TCGGATTGGAGACCATCTTTAAG 57.976 43.478 0.00 0.00 31.53 1.85
370 377 5.423886 GAGACCATCTTTAAGTCTGGGAAG 58.576 45.833 16.28 0.00 40.87 3.46
374 381 7.403231 AGACCATCTTTAAGTCTGGGAAGAATA 59.597 37.037 16.28 0.00 39.36 1.75
389 396 5.532779 GGGAAGAATATTTGGAACTAGCAGG 59.467 44.000 0.00 0.00 0.00 4.85
407 414 6.308371 AGCAGGCATTTCTTTTGAATTTTG 57.692 33.333 0.00 0.00 38.37 2.44
411 418 7.863877 GCAGGCATTTCTTTTGAATTTTGAAAT 59.136 29.630 0.00 0.00 38.37 2.17
412 419 9.738832 CAGGCATTTCTTTTGAATTTTGAAATT 57.261 25.926 1.54 1.54 41.06 1.82
505 513 3.408634 GAAAATCCGGGAACACTTCTCA 58.591 45.455 0.00 0.00 0.00 3.27
510 518 3.408634 TCCGGGAACACTTCTCAAATTC 58.591 45.455 0.00 0.00 0.00 2.17
511 519 3.146066 CCGGGAACACTTCTCAAATTCA 58.854 45.455 0.00 0.00 0.00 2.57
704 716 6.438259 TCAAACTCGTGAACCATTTTTGTA 57.562 33.333 0.00 0.00 0.00 2.41
713 725 6.527722 CGTGAACCATTTTTGTATCCATGAAG 59.472 38.462 0.00 0.00 0.00 3.02
734 747 9.823647 ATGAAGATATATTGATATTCGGACCAC 57.176 33.333 0.00 0.00 31.08 4.16
749 762 3.753272 CGGACCACTTTCTGAATTCATGT 59.247 43.478 8.96 3.43 0.00 3.21
750 763 4.935205 CGGACCACTTTCTGAATTCATGTA 59.065 41.667 8.96 0.00 0.00 2.29
799 815 9.913451 TTTCAAATTCGTGAACATTTTGAAATC 57.087 25.926 20.48 0.00 44.71 2.17
997 1036 4.699522 GAGGGGTGCGCGTTTCCT 62.700 66.667 8.43 10.07 0.00 3.36
998 1037 4.699522 AGGGGTGCGCGTTTCCTC 62.700 66.667 8.43 8.08 0.00 3.71
1020 1074 1.891722 TTTTCCCCGCGTAGGTCTCC 61.892 60.000 4.92 0.00 38.74 3.71
1028 1082 1.041447 GCGTAGGTCTCCAGCCCTAA 61.041 60.000 0.00 0.00 35.16 2.69
1060 1114 4.452733 CCCCGTCGCAGTCTTCCC 62.453 72.222 0.00 0.00 0.00 3.97
1463 1528 7.003402 TGAATTGGAAAATTTTCTACTGGGG 57.997 36.000 25.86 0.00 37.35 4.96
1486 1551 1.006813 TGGATGGGTGGGTGCTTATT 58.993 50.000 0.00 0.00 0.00 1.40
1487 1552 2.209758 TGGATGGGTGGGTGCTTATTA 58.790 47.619 0.00 0.00 0.00 0.98
1488 1553 2.788807 TGGATGGGTGGGTGCTTATTAT 59.211 45.455 0.00 0.00 0.00 1.28
1514 1579 1.096416 TTGCGTCGTTTTCCAGGTTT 58.904 45.000 0.00 0.00 0.00 3.27
1655 1726 9.981114 ATTATGTAACTTGGGAAAACAGAAAAG 57.019 29.630 0.00 0.00 0.00 2.27
1715 1786 1.376424 CTGACGGGCAAGCATCAGT 60.376 57.895 10.35 0.00 35.00 3.41
1721 1792 1.468565 CGGGCAAGCATCAGTCATTTG 60.469 52.381 0.00 0.00 0.00 2.32
1745 1816 3.944055 AGTGTGTAGTAGTGCTTGAGG 57.056 47.619 0.00 0.00 0.00 3.86
1749 1820 3.838317 TGTGTAGTAGTGCTTGAGGGAAT 59.162 43.478 0.00 0.00 0.00 3.01
1752 1823 3.340814 AGTAGTGCTTGAGGGAATGTG 57.659 47.619 0.00 0.00 0.00 3.21
1828 1923 4.781934 ACTACTGCTTTCCTTTTGTCTGT 58.218 39.130 0.00 0.00 0.00 3.41
1906 3078 3.428532 AGCATTCCTCATTTGCTTGTCT 58.571 40.909 0.00 0.00 43.94 3.41
1937 3109 5.002516 CCATCTTTGGAGGCTTATCTGATC 58.997 45.833 0.00 0.00 46.92 2.92
1938 3110 4.696479 TCTTTGGAGGCTTATCTGATCC 57.304 45.455 0.00 0.00 0.00 3.36
1957 3129 5.366477 TGATCCTAGTATTGCAATCTGGTCA 59.634 40.000 16.86 14.73 0.00 4.02
1974 3146 7.062749 TCTGGTCAGACTGTGTTACTTTTAT 57.937 36.000 1.59 0.00 31.41 1.40
2058 3230 9.174166 GGCCATCTACTTATTCTTGAGTTTTTA 57.826 33.333 0.00 0.00 0.00 1.52
2188 3360 6.349243 TCCGAAGTATTTCCAAGTAAGTGA 57.651 37.500 0.00 0.00 0.00 3.41
2207 3379 6.536731 AGTGATCTAATTGCGAGCTTTATG 57.463 37.500 0.00 0.00 0.00 1.90
2210 3382 7.042187 AGTGATCTAATTGCGAGCTTTATGAAG 60.042 37.037 0.00 0.00 35.92 3.02
2256 3428 7.211573 TGAAAAATTGTGAATGCTCATCAGTT 58.788 30.769 0.00 0.00 33.05 3.16
2502 3675 5.720371 TGTGTATTAATTGCATATGGCCC 57.280 39.130 0.00 0.00 43.89 5.80
2941 4114 8.744652 TCAATGTAAAACAAGGAAGAACAGAAA 58.255 29.630 0.00 0.00 0.00 2.52
3026 4199 7.389330 TGGTGAATTCATGTAACTGAACGTATT 59.611 33.333 12.12 0.00 37.93 1.89
3195 4368 2.310538 CAAAAGAGCAGGGGAAGTGTT 58.689 47.619 0.00 0.00 0.00 3.32
3299 4472 9.177608 CAAAATTTGGTCCTCTTGTATCTATGA 57.822 33.333 0.00 0.00 0.00 2.15
3300 4473 9.927081 AAAATTTGGTCCTCTTGTATCTATGAT 57.073 29.630 0.00 0.00 0.00 2.45
3304 4477 4.158764 GGTCCTCTTGTATCTATGATCCGG 59.841 50.000 0.00 0.00 0.00 5.14
3305 4478 3.764434 TCCTCTTGTATCTATGATCCGGC 59.236 47.826 0.00 0.00 0.00 6.13
3306 4479 3.766591 CCTCTTGTATCTATGATCCGGCT 59.233 47.826 0.00 0.00 0.00 5.52
3307 4480 4.221703 CCTCTTGTATCTATGATCCGGCTT 59.778 45.833 0.00 0.00 0.00 4.35
3308 4481 5.419155 CCTCTTGTATCTATGATCCGGCTTA 59.581 44.000 0.00 0.00 0.00 3.09
3309 4482 6.405286 CCTCTTGTATCTATGATCCGGCTTAG 60.405 46.154 0.00 0.00 0.00 2.18
3310 4483 5.419155 TCTTGTATCTATGATCCGGCTTAGG 59.581 44.000 0.00 0.00 0.00 2.69
3311 4484 4.023980 TGTATCTATGATCCGGCTTAGGG 58.976 47.826 0.00 0.00 0.00 3.53
3312 4485 1.938585 TCTATGATCCGGCTTAGGGG 58.061 55.000 0.00 0.00 0.00 4.79
3313 4486 0.905357 CTATGATCCGGCTTAGGGGG 59.095 60.000 0.00 0.00 0.00 5.40
3314 4487 0.192566 TATGATCCGGCTTAGGGGGT 59.807 55.000 0.00 0.00 0.00 4.95
3315 4488 1.418908 ATGATCCGGCTTAGGGGGTG 61.419 60.000 0.00 0.00 0.00 4.61
3316 4489 2.042261 ATCCGGCTTAGGGGGTGT 59.958 61.111 0.00 0.00 0.00 4.16
3317 4490 1.618447 ATCCGGCTTAGGGGGTGTT 60.618 57.895 0.00 0.00 0.00 3.32
3318 4491 1.212250 ATCCGGCTTAGGGGGTGTTT 61.212 55.000 0.00 0.00 0.00 2.83
3319 4492 1.677633 CCGGCTTAGGGGGTGTTTG 60.678 63.158 0.00 0.00 0.00 2.93
3320 4493 1.677633 CGGCTTAGGGGGTGTTTGG 60.678 63.158 0.00 0.00 0.00 3.28
3321 4494 1.463375 GGCTTAGGGGGTGTTTGGT 59.537 57.895 0.00 0.00 0.00 3.67
3322 4495 0.178944 GGCTTAGGGGGTGTTTGGTT 60.179 55.000 0.00 0.00 0.00 3.67
3323 4496 1.254026 GCTTAGGGGGTGTTTGGTTC 58.746 55.000 0.00 0.00 0.00 3.62
3324 4497 1.479757 GCTTAGGGGGTGTTTGGTTCA 60.480 52.381 0.00 0.00 0.00 3.18
3325 4498 2.514803 CTTAGGGGGTGTTTGGTTCAG 58.485 52.381 0.00 0.00 0.00 3.02
3326 4499 1.822425 TAGGGGGTGTTTGGTTCAGA 58.178 50.000 0.00 0.00 0.00 3.27
3327 4500 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
3328 4501 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
3329 4502 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
3330 4503 1.954382 GGGGTGTTTGGTTCAGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
3331 4504 1.954382 GGGTGTTTGGTTCAGAAGTCC 59.046 52.381 0.00 0.00 0.00 3.85
3332 4505 2.422945 GGGTGTTTGGTTCAGAAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
3333 4506 3.181448 GGGTGTTTGGTTCAGAAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
3334 4507 4.065789 GGTGTTTGGTTCAGAAGTCCTAG 58.934 47.826 0.00 0.00 0.00 3.02
3335 4508 4.065789 GTGTTTGGTTCAGAAGTCCTAGG 58.934 47.826 0.82 0.82 0.00 3.02
3336 4509 3.971305 TGTTTGGTTCAGAAGTCCTAGGA 59.029 43.478 7.62 7.62 0.00 2.94
3337 4510 4.202326 TGTTTGGTTCAGAAGTCCTAGGAC 60.202 45.833 31.29 31.29 44.86 3.85
3396 4569 9.106070 CTCTCTAGTAGAGTCTTTTTCTAGTCC 57.894 40.741 23.51 0.00 45.85 3.85
3397 4570 8.048514 TCTCTAGTAGAGTCTTTTTCTAGTCCC 58.951 40.741 23.51 0.00 42.83 4.46
3398 4571 7.931046 TCTAGTAGAGTCTTTTTCTAGTCCCT 58.069 38.462 0.00 0.00 33.84 4.20
3399 4572 6.844097 AGTAGAGTCTTTTTCTAGTCCCTG 57.156 41.667 0.00 0.00 0.00 4.45
3400 4573 6.316513 AGTAGAGTCTTTTTCTAGTCCCTGT 58.683 40.000 0.00 0.00 0.00 4.00
3401 4574 7.468496 AGTAGAGTCTTTTTCTAGTCCCTGTA 58.532 38.462 0.00 0.00 0.00 2.74
3402 4575 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
3403 4576 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
3404 4577 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
3405 4578 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
3411 4584 7.613551 TTTCTAGTCCCTGTAGAAAAAGTCT 57.386 36.000 3.39 0.00 41.43 3.24
3412 4585 6.837471 TCTAGTCCCTGTAGAAAAAGTCTC 57.163 41.667 0.00 0.00 37.84 3.36
3413 4586 6.553857 TCTAGTCCCTGTAGAAAAAGTCTCT 58.446 40.000 0.00 0.00 37.84 3.10
3414 4587 5.731957 AGTCCCTGTAGAAAAAGTCTCTC 57.268 43.478 0.00 0.00 37.84 3.20
3415 4588 4.528987 AGTCCCTGTAGAAAAAGTCTCTCC 59.471 45.833 0.00 0.00 37.84 3.71
3416 4589 4.528987 GTCCCTGTAGAAAAAGTCTCTCCT 59.471 45.833 0.00 0.00 37.84 3.69
3417 4590 4.528596 TCCCTGTAGAAAAAGTCTCTCCTG 59.471 45.833 0.00 0.00 37.84 3.86
3418 4591 4.284746 CCCTGTAGAAAAAGTCTCTCCTGT 59.715 45.833 0.00 0.00 37.84 4.00
3419 4592 5.221742 CCCTGTAGAAAAAGTCTCTCCTGTT 60.222 44.000 0.00 0.00 37.84 3.16
3420 4593 6.292150 CCTGTAGAAAAAGTCTCTCCTGTTT 58.708 40.000 0.00 0.00 37.84 2.83
3421 4594 6.203723 CCTGTAGAAAAAGTCTCTCCTGTTTG 59.796 42.308 0.00 0.00 37.84 2.93
3422 4595 6.055588 TGTAGAAAAAGTCTCTCCTGTTTGG 58.944 40.000 0.00 0.00 37.84 3.28
3423 4596 5.117406 AGAAAAAGTCTCTCCTGTTTGGT 57.883 39.130 0.00 0.00 37.07 3.67
3424 4597 5.510430 AGAAAAAGTCTCTCCTGTTTGGTT 58.490 37.500 0.00 0.00 37.07 3.67
3425 4598 5.590663 AGAAAAAGTCTCTCCTGTTTGGTTC 59.409 40.000 0.00 0.00 37.07 3.62
3426 4599 3.493767 AAGTCTCTCCTGTTTGGTTCC 57.506 47.619 0.00 0.00 37.07 3.62
3427 4600 2.695585 AGTCTCTCCTGTTTGGTTCCT 58.304 47.619 0.00 0.00 37.07 3.36
3428 4601 3.858135 AGTCTCTCCTGTTTGGTTCCTA 58.142 45.455 0.00 0.00 37.07 2.94
3429 4602 3.835395 AGTCTCTCCTGTTTGGTTCCTAG 59.165 47.826 0.00 0.00 37.07 3.02
3430 4603 3.055747 GTCTCTCCTGTTTGGTTCCTAGG 60.056 52.174 0.82 0.82 37.07 3.02
3431 4604 2.237392 CTCTCCTGTTTGGTTCCTAGGG 59.763 54.545 9.46 0.00 37.07 3.53
3432 4605 2.158066 TCTCCTGTTTGGTTCCTAGGGA 60.158 50.000 9.46 0.00 37.07 4.20
3433 4606 1.982958 TCCTGTTTGGTTCCTAGGGAC 59.017 52.381 12.35 12.35 37.07 4.46
3434 4607 1.985895 CCTGTTTGGTTCCTAGGGACT 59.014 52.381 20.08 0.00 46.37 3.85
3435 4608 2.375509 CCTGTTTGGTTCCTAGGGACTT 59.624 50.000 20.08 0.00 41.75 3.01
3436 4609 3.181433 CCTGTTTGGTTCCTAGGGACTTT 60.181 47.826 20.08 0.00 41.75 2.66
3437 4610 4.470602 CTGTTTGGTTCCTAGGGACTTTT 58.529 43.478 20.08 0.00 41.75 2.27
3438 4611 4.874199 TGTTTGGTTCCTAGGGACTTTTT 58.126 39.130 20.08 0.00 41.75 1.94
3439 4612 6.015991 TGTTTGGTTCCTAGGGACTTTTTA 57.984 37.500 20.08 1.82 41.75 1.52
3440 4613 6.066032 TGTTTGGTTCCTAGGGACTTTTTAG 58.934 40.000 20.08 0.00 41.75 1.85
3441 4614 4.921644 TGGTTCCTAGGGACTTTTTAGG 57.078 45.455 20.08 0.00 41.75 2.69
3442 4615 3.590182 TGGTTCCTAGGGACTTTTTAGGG 59.410 47.826 20.08 0.00 41.75 3.53
3443 4616 3.848377 GGTTCCTAGGGACTTTTTAGGGA 59.152 47.826 20.08 0.00 41.75 4.20
3444 4617 4.324099 GGTTCCTAGGGACTTTTTAGGGAC 60.324 50.000 20.08 0.45 40.79 4.46
3445 4618 4.431158 TCCTAGGGACTTTTTAGGGACT 57.569 45.455 9.46 0.00 41.75 3.85
3446 4619 4.771338 TCCTAGGGACTTTTTAGGGACTT 58.229 43.478 9.46 0.00 39.49 3.01
3447 4620 5.167921 TCCTAGGGACTTTTTAGGGACTTT 58.832 41.667 9.46 0.00 39.49 2.66
3448 4621 5.613973 TCCTAGGGACTTTTTAGGGACTTTT 59.386 40.000 9.46 0.00 39.49 2.27
3449 4622 6.103649 TCCTAGGGACTTTTTAGGGACTTTTT 59.896 38.462 9.46 0.00 39.49 1.94
3450 4623 6.433404 CCTAGGGACTTTTTAGGGACTTTTTC 59.567 42.308 0.00 0.00 39.49 2.29
3451 4624 6.027025 AGGGACTTTTTAGGGACTTTTTCT 57.973 37.500 0.00 0.00 34.75 2.52
3452 4625 7.157947 AGGGACTTTTTAGGGACTTTTTCTA 57.842 36.000 0.00 0.00 34.75 2.10
3453 4626 7.232188 AGGGACTTTTTAGGGACTTTTTCTAG 58.768 38.462 0.00 0.00 34.75 2.43
3454 4627 7.002879 GGGACTTTTTAGGGACTTTTTCTAGT 58.997 38.462 0.00 0.00 41.75 2.57
3455 4628 7.174599 GGGACTTTTTAGGGACTTTTTCTAGTC 59.825 40.741 0.00 0.00 43.05 2.59
3456 4629 7.937942 GGACTTTTTAGGGACTTTTTCTAGTCT 59.062 37.037 0.00 0.00 43.26 3.24
3457 4630 8.905660 ACTTTTTAGGGACTTTTTCTAGTCTC 57.094 34.615 0.00 0.00 44.42 3.36
3461 4634 4.209307 GGGACTTTTTCTAGTCTCTGGG 57.791 50.000 0.00 0.00 41.50 4.45
3462 4635 3.838903 GGGACTTTTTCTAGTCTCTGGGA 59.161 47.826 0.00 0.00 41.50 4.37
3463 4636 4.322877 GGGACTTTTTCTAGTCTCTGGGAC 60.323 50.000 0.00 0.00 41.50 4.46
3484 4657 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
3485 4658 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
3486 4659 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
3487 4660 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
3488 4661 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
3489 4662 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
3511 4684 4.384647 CCCTTAGCTTGGCTGAGTAGAAAT 60.385 45.833 9.75 0.00 40.06 2.17
3534 4708 0.322322 CTTTGGGCCATGTTGTGCAT 59.678 50.000 7.26 0.00 38.60 3.96
3541 4715 3.397482 GGCCATGTTGTGCATTTTGTTA 58.603 40.909 0.00 0.00 35.19 2.41
3547 4721 6.456181 CCATGTTGTGCATTTTGTTACGTTTT 60.456 34.615 0.00 0.00 35.19 2.43
3552 4726 4.026393 GTGCATTTTGTTACGTTTTGTCCC 60.026 41.667 0.00 0.00 0.00 4.46
3553 4727 4.142138 TGCATTTTGTTACGTTTTGTCCCT 60.142 37.500 0.00 0.00 0.00 4.20
3554 4728 4.806775 GCATTTTGTTACGTTTTGTCCCTT 59.193 37.500 0.00 0.00 0.00 3.95
3555 4729 5.051307 GCATTTTGTTACGTTTTGTCCCTTC 60.051 40.000 0.00 0.00 0.00 3.46
3556 4730 4.635833 TTTGTTACGTTTTGTCCCTTCC 57.364 40.909 0.00 0.00 0.00 3.46
3577 4751 1.200716 CTTGCATTGCACCGTTGATCT 59.799 47.619 11.66 0.00 38.71 2.75
3622 4985 1.199097 GACGGCATGTGTGGTTTAAGG 59.801 52.381 0.00 0.00 0.00 2.69
3623 4986 1.202830 ACGGCATGTGTGGTTTAAGGA 60.203 47.619 0.00 0.00 0.00 3.36
3642 5005 2.730928 GGATGAACAAATGCAAACCACG 59.269 45.455 0.00 0.00 0.00 4.94
3643 5006 2.949451 TGAACAAATGCAAACCACGT 57.051 40.000 0.00 0.00 0.00 4.49
3682 5045 1.150536 TGTTGTTCTGCTCACCCCC 59.849 57.895 0.00 0.00 0.00 5.40
3702 5065 5.221904 CCCCCTTTCAAAAATGGTGATCTTT 60.222 40.000 0.00 0.00 0.00 2.52
3778 5158 4.023980 TCACACAGATACCTAGAAGGGTG 58.976 47.826 0.00 0.00 40.58 4.61
3789 5169 4.349930 ACCTAGAAGGGTGCAGTTTTAAGA 59.650 41.667 0.00 0.00 40.58 2.10
3804 5184 8.801913 GCAGTTTTAAGACAGCAAAATATCATC 58.198 33.333 8.41 0.00 32.91 2.92
3825 5205 8.746922 TCATCAGTTTTCAGCAAAATATTCAC 57.253 30.769 0.00 0.00 33.98 3.18
3845 5225 2.831526 ACAGTTTCCAGCAAAAGGTGTT 59.168 40.909 0.00 0.00 0.00 3.32
3955 5335 3.368571 GCTGAACCTGCACCCAGC 61.369 66.667 8.48 8.48 44.00 4.85
4021 5401 3.384789 CCGAATGTAGAATCACCTCCTCA 59.615 47.826 0.00 0.00 0.00 3.86
4026 5406 1.479709 AGAATCACCTCCTCAGGACG 58.520 55.000 0.00 0.00 43.65 4.79
4093 5473 4.792189 CGTTCTTGATCTACACGTAGAACC 59.208 45.833 10.78 6.94 44.44 3.62
4140 5520 1.986575 GCTCAAGCTTTAGCCTGCGG 61.987 60.000 19.87 0.00 43.38 5.69
4162 5542 1.546923 CAAGCATGGGCAAAGACATCA 59.453 47.619 0.00 0.00 44.61 3.07
4166 5546 0.038166 ATGGGCAAAGACATCACCGT 59.962 50.000 0.00 0.00 0.00 4.83
4168 5548 0.605319 GGGCAAAGACATCACCGTCA 60.605 55.000 0.00 0.00 38.43 4.35
4170 5550 0.517316 GCAAAGACATCACCGTCACC 59.483 55.000 0.00 0.00 38.43 4.02
4174 5554 1.118965 AGACATCACCGTCACCACCA 61.119 55.000 0.00 0.00 38.43 4.17
4175 5555 0.949105 GACATCACCGTCACCACCAC 60.949 60.000 0.00 0.00 35.88 4.16
4176 5556 1.371183 CATCACCGTCACCACCACT 59.629 57.895 0.00 0.00 0.00 4.00
4177 5557 0.950555 CATCACCGTCACCACCACTG 60.951 60.000 0.00 0.00 0.00 3.66
4178 5558 2.731691 ATCACCGTCACCACCACTGC 62.732 60.000 0.00 0.00 0.00 4.40
4179 5559 3.475494 ACCGTCACCACCACTGCA 61.475 61.111 0.00 0.00 0.00 4.41
4180 5560 2.666190 CCGTCACCACCACTGCAG 60.666 66.667 13.48 13.48 0.00 4.41
4181 5561 3.349006 CGTCACCACCACTGCAGC 61.349 66.667 15.27 0.00 0.00 5.25
4182 5562 2.980233 GTCACCACCACTGCAGCC 60.980 66.667 15.27 0.00 0.00 4.85
4183 5563 3.170672 TCACCACCACTGCAGCCT 61.171 61.111 15.27 0.00 0.00 4.58
4184 5564 2.670934 CACCACCACTGCAGCCTC 60.671 66.667 15.27 0.00 0.00 4.70
4211 5591 1.065764 CCGACATCTCGATCCGCAA 59.934 57.895 0.00 0.00 43.06 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.773976 ACCATCAAAGTCAAAGAGAAAACA 57.226 33.333 0.00 0.00 0.00 2.83
143 148 6.870971 TTATGTGCGACTTTCTAAAAAGGT 57.129 33.333 3.24 0.00 45.15 3.50
286 293 8.436046 TCCAAAATTTCAAAAATGTTCTCTGG 57.564 30.769 0.00 0.00 0.00 3.86
288 295 7.769970 TGCTCCAAAATTTCAAAAATGTTCTCT 59.230 29.630 0.00 0.00 0.00 3.10
329 336 4.217550 GGTCTCCAATCCGAAAATTGTTCA 59.782 41.667 0.00 0.00 35.31 3.18
340 347 4.770795 ACTTAAAGATGGTCTCCAATCCG 58.229 43.478 0.00 0.00 36.95 4.18
345 352 3.519510 CCCAGACTTAAAGATGGTCTCCA 59.480 47.826 0.00 0.00 38.12 3.86
354 361 8.611257 TCCAAATATTCTTCCCAGACTTAAAGA 58.389 33.333 0.00 0.00 0.00 2.52
361 368 6.261158 GCTAGTTCCAAATATTCTTCCCAGAC 59.739 42.308 0.00 0.00 0.00 3.51
370 377 6.396829 AATGCCTGCTAGTTCCAAATATTC 57.603 37.500 0.00 0.00 0.00 1.75
374 381 4.347607 AGAAATGCCTGCTAGTTCCAAAT 58.652 39.130 0.00 0.00 0.00 2.32
483 491 2.415512 GAGAAGTGTTCCCGGATTTTCG 59.584 50.000 0.73 0.00 0.00 3.46
484 492 3.408634 TGAGAAGTGTTCCCGGATTTTC 58.591 45.455 0.73 0.00 0.00 2.29
491 499 5.376854 AATGAATTTGAGAAGTGTTCCCG 57.623 39.130 0.00 0.00 0.00 5.14
659 671 9.709495 TTTGAAAAATATGTTCCAGGATTTCAG 57.291 29.630 10.60 0.00 37.01 3.02
660 672 9.487790 GTTTGAAAAATATGTTCCAGGATTTCA 57.512 29.630 7.71 7.71 34.72 2.69
666 678 6.582295 CACGAGTTTGAAAAATATGTTCCAGG 59.418 38.462 0.00 0.00 0.00 4.45
668 680 7.265647 TCACGAGTTTGAAAAATATGTTCCA 57.734 32.000 0.00 0.00 0.00 3.53
713 725 9.877178 AGAAAGTGGTCCGAATATCAATATATC 57.123 33.333 0.00 0.00 0.00 1.63
718 730 5.989477 TCAGAAAGTGGTCCGAATATCAAT 58.011 37.500 0.00 0.00 0.00 2.57
925 946 2.351447 GCGGCCCTTGTTTTACTTCTTC 60.351 50.000 0.00 0.00 0.00 2.87
928 949 0.109919 CGCGGCCCTTGTTTTACTTC 60.110 55.000 0.00 0.00 0.00 3.01
932 971 0.952010 GAGACGCGGCCCTTGTTTTA 60.952 55.000 9.25 0.00 0.00 1.52
980 1019 4.699522 AGGAAACGCGCACCCCTC 62.700 66.667 5.73 0.00 0.00 4.30
990 1029 1.873863 GGGGAAAAGCGAGGAAACG 59.126 57.895 0.00 0.00 0.00 3.60
991 1030 1.873863 CGGGGAAAAGCGAGGAAAC 59.126 57.895 0.00 0.00 0.00 2.78
992 1031 1.969589 GCGGGGAAAAGCGAGGAAA 60.970 57.895 0.00 0.00 0.00 3.13
993 1032 2.359478 GCGGGGAAAAGCGAGGAA 60.359 61.111 0.00 0.00 0.00 3.36
999 1038 2.046604 ACCTACGCGGGGAAAAGC 60.047 61.111 23.53 0.00 36.97 3.51
1000 1039 0.459759 GAGACCTACGCGGGGAAAAG 60.460 60.000 23.53 5.78 36.97 2.27
1001 1040 1.593265 GAGACCTACGCGGGGAAAA 59.407 57.895 23.53 0.00 36.97 2.29
1002 1041 2.353610 GGAGACCTACGCGGGGAAA 61.354 63.158 23.53 0.00 36.97 3.13
1020 1074 2.156774 GGGGAGGGGATTAGGGCTG 61.157 68.421 0.00 0.00 0.00 4.85
1028 1082 3.462501 GGGGAGAGGGGAGGGGAT 61.463 72.222 0.00 0.00 0.00 3.85
1112 1177 3.627714 CGTTGTTGGGTTACGCGA 58.372 55.556 15.93 0.00 0.00 5.87
1256 1321 2.046507 CGAGCCCTTCTTGCTGCT 60.047 61.111 0.00 0.00 39.69 4.24
1463 1528 1.678970 GCACCCACCCATCCAAGAC 60.679 63.158 0.00 0.00 0.00 3.01
1486 1551 3.369756 GGAAAACGACGCAACAGATCATA 59.630 43.478 0.00 0.00 0.00 2.15
1487 1552 2.159627 GGAAAACGACGCAACAGATCAT 59.840 45.455 0.00 0.00 0.00 2.45
1488 1553 1.529438 GGAAAACGACGCAACAGATCA 59.471 47.619 0.00 0.00 0.00 2.92
1655 1726 5.458779 CCTAAATGCTAAATTAAACAGGCGC 59.541 40.000 0.00 0.00 0.00 6.53
1715 1786 7.611770 AGCACTACTACACACTTATCAAATGA 58.388 34.615 0.00 0.00 0.00 2.57
1721 1792 6.037098 CCTCAAGCACTACTACACACTTATC 58.963 44.000 0.00 0.00 0.00 1.75
1767 1838 7.902087 AGAAGCCTAGCTATCCTAAATAACAG 58.098 38.462 0.00 0.00 38.25 3.16
1937 3109 5.053145 GTCTGACCAGATTGCAATACTAGG 58.947 45.833 12.97 13.66 39.97 3.02
1938 3110 5.752472 CAGTCTGACCAGATTGCAATACTAG 59.248 44.000 12.97 7.26 38.13 2.57
1957 3129 8.958119 TTCAGTTCATAAAAGTAACACAGTCT 57.042 30.769 0.00 0.00 0.00 3.24
2058 3230 4.526262 TGTGCTTAAGCCACCAAAACATAT 59.474 37.500 24.30 0.00 41.18 1.78
2188 3360 8.839310 ATACTTCATAAAGCTCGCAATTAGAT 57.161 30.769 0.00 0.00 35.81 1.98
2207 3379 9.349713 TCAATGGTATGGTATCCAAAATACTTC 57.650 33.333 0.00 0.00 36.95 3.01
2237 3409 5.717078 AACAACTGATGAGCATTCACAAT 57.283 34.783 0.00 0.00 35.83 2.71
2256 3428 7.811653 TCATCAAAATATTCAGCACGTTAACA 58.188 30.769 6.39 0.00 0.00 2.41
2502 3675 4.118410 CCGATGAACTCTTTGATCTGGAG 58.882 47.826 0.00 1.71 0.00 3.86
2511 3684 7.972832 TTGTATAACAACCGATGAACTCTTT 57.027 32.000 0.00 0.00 32.34 2.52
2941 4114 2.558359 CCATTTCTCTTTGGCTCCGTTT 59.442 45.455 0.00 0.00 0.00 3.60
2996 4169 6.741992 TCAGTTACATGAATTCACCACATC 57.258 37.500 11.07 0.65 0.00 3.06
3026 4199 0.472471 AGTGCGGGGAGAAAAGTTCA 59.528 50.000 0.00 0.00 0.00 3.18
3195 4368 6.867816 GGATTCAGAATGTGTGCAAATGTTAA 59.132 34.615 0.00 0.00 37.40 2.01
3299 4472 1.212250 AAACACCCCCTAAGCCGGAT 61.212 55.000 5.05 0.00 0.00 4.18
3300 4473 1.848895 AAACACCCCCTAAGCCGGA 60.849 57.895 5.05 0.00 0.00 5.14
3304 4477 1.254026 GAACCAAACACCCCCTAAGC 58.746 55.000 0.00 0.00 0.00 3.09
3305 4478 2.107552 TCTGAACCAAACACCCCCTAAG 59.892 50.000 0.00 0.00 0.00 2.18
3306 4479 2.136863 TCTGAACCAAACACCCCCTAA 58.863 47.619 0.00 0.00 0.00 2.69
3307 4480 1.822425 TCTGAACCAAACACCCCCTA 58.178 50.000 0.00 0.00 0.00 3.53
3308 4481 0.930726 TTCTGAACCAAACACCCCCT 59.069 50.000 0.00 0.00 0.00 4.79
3309 4482 1.328279 CTTCTGAACCAAACACCCCC 58.672 55.000 0.00 0.00 0.00 5.40
3310 4483 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95
3311 4484 1.954382 GGACTTCTGAACCAAACACCC 59.046 52.381 0.00 0.00 0.00 4.61
3312 4485 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16
3313 4486 4.065789 CCTAGGACTTCTGAACCAAACAC 58.934 47.826 1.05 0.00 0.00 3.32
3314 4487 3.971305 TCCTAGGACTTCTGAACCAAACA 59.029 43.478 7.62 0.00 0.00 2.83
3315 4488 4.316645 GTCCTAGGACTTCTGAACCAAAC 58.683 47.826 31.12 3.26 41.57 2.93
3316 4489 4.618920 GTCCTAGGACTTCTGAACCAAA 57.381 45.455 31.12 0.00 41.57 3.28
3371 4544 8.048514 GGGACTAGAAAAAGACTCTACTAGAGA 58.951 40.741 18.41 0.00 45.07 3.10
3372 4545 8.050930 AGGGACTAGAAAAAGACTCTACTAGAG 58.949 40.741 11.06 11.06 42.94 2.43
3373 4546 7.830201 CAGGGACTAGAAAAAGACTCTACTAGA 59.170 40.741 0.00 0.00 36.02 2.43
3374 4547 7.612633 ACAGGGACTAGAAAAAGACTCTACTAG 59.387 40.741 0.00 0.00 36.02 2.57
3375 4548 7.468496 ACAGGGACTAGAAAAAGACTCTACTA 58.532 38.462 0.00 0.00 36.02 1.82
3376 4549 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
3377 4550 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
3378 4551 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
3379 4552 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
3380 4553 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
3381 4554 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
3382 4555 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
3386 4559 8.030913 AGACTTTTTCTACAGGGACTAGAAAA 57.969 34.615 0.00 8.58 43.60 2.29
3387 4560 7.509659 AGAGACTTTTTCTACAGGGACTAGAAA 59.490 37.037 0.00 0.00 38.08 2.52
3388 4561 7.011382 AGAGACTTTTTCTACAGGGACTAGAA 58.989 38.462 0.00 0.00 31.59 2.10
3389 4562 6.553857 AGAGACTTTTTCTACAGGGACTAGA 58.446 40.000 0.00 0.00 31.59 2.43
3390 4563 6.127563 GGAGAGACTTTTTCTACAGGGACTAG 60.128 46.154 0.00 0.00 31.59 2.57
3391 4564 5.715753 GGAGAGACTTTTTCTACAGGGACTA 59.284 44.000 0.00 0.00 31.59 2.59
3392 4565 4.528987 GGAGAGACTTTTTCTACAGGGACT 59.471 45.833 0.00 0.00 33.64 3.85
3393 4566 4.528987 AGGAGAGACTTTTTCTACAGGGAC 59.471 45.833 0.00 0.00 33.22 4.46
3394 4567 4.528596 CAGGAGAGACTTTTTCTACAGGGA 59.471 45.833 0.00 0.00 33.22 4.20
3395 4568 4.284746 ACAGGAGAGACTTTTTCTACAGGG 59.715 45.833 0.00 0.00 33.22 4.45
3396 4569 5.476091 ACAGGAGAGACTTTTTCTACAGG 57.524 43.478 0.00 0.00 33.22 4.00
3397 4570 6.203723 CCAAACAGGAGAGACTTTTTCTACAG 59.796 42.308 0.00 0.00 41.22 2.74
3398 4571 6.055588 CCAAACAGGAGAGACTTTTTCTACA 58.944 40.000 0.00 0.00 41.22 2.74
3399 4572 6.056236 ACCAAACAGGAGAGACTTTTTCTAC 58.944 40.000 0.00 0.00 41.22 2.59
3400 4573 6.248569 ACCAAACAGGAGAGACTTTTTCTA 57.751 37.500 0.00 0.00 41.22 2.10
3401 4574 5.117406 ACCAAACAGGAGAGACTTTTTCT 57.883 39.130 0.00 0.00 41.22 2.52
3402 4575 5.221067 GGAACCAAACAGGAGAGACTTTTTC 60.221 44.000 0.00 0.00 41.22 2.29
3403 4576 4.645136 GGAACCAAACAGGAGAGACTTTTT 59.355 41.667 0.00 0.00 41.22 1.94
3404 4577 4.079730 AGGAACCAAACAGGAGAGACTTTT 60.080 41.667 0.00 0.00 41.22 2.27
3405 4578 3.459969 AGGAACCAAACAGGAGAGACTTT 59.540 43.478 0.00 0.00 41.22 2.66
3406 4579 3.049344 AGGAACCAAACAGGAGAGACTT 58.951 45.455 0.00 0.00 41.22 3.01
3407 4580 2.695585 AGGAACCAAACAGGAGAGACT 58.304 47.619 0.00 0.00 41.22 3.24
3408 4581 3.055747 CCTAGGAACCAAACAGGAGAGAC 60.056 52.174 1.05 0.00 41.22 3.36
3409 4582 3.173965 CCTAGGAACCAAACAGGAGAGA 58.826 50.000 1.05 0.00 41.22 3.10
3410 4583 2.237392 CCCTAGGAACCAAACAGGAGAG 59.763 54.545 11.48 0.00 41.22 3.20
3411 4584 2.158066 TCCCTAGGAACCAAACAGGAGA 60.158 50.000 11.48 0.00 41.22 3.71
3412 4585 2.027100 GTCCCTAGGAACCAAACAGGAG 60.027 54.545 11.48 0.00 42.07 3.69
3413 4586 1.982958 GTCCCTAGGAACCAAACAGGA 59.017 52.381 11.48 0.00 42.07 3.86
3414 4587 1.985895 AGTCCCTAGGAACCAAACAGG 59.014 52.381 11.48 0.00 45.67 4.00
3415 4588 3.790089 AAGTCCCTAGGAACCAAACAG 57.210 47.619 11.48 0.00 31.38 3.16
3416 4589 4.529716 AAAAGTCCCTAGGAACCAAACA 57.470 40.909 11.48 0.00 31.38 2.83
3417 4590 5.475909 CCTAAAAAGTCCCTAGGAACCAAAC 59.524 44.000 11.48 0.00 35.17 2.93
3418 4591 5.458508 CCCTAAAAAGTCCCTAGGAACCAAA 60.459 44.000 11.48 0.00 35.17 3.28
3419 4592 4.043686 CCCTAAAAAGTCCCTAGGAACCAA 59.956 45.833 11.48 0.00 35.17 3.67
3420 4593 3.590182 CCCTAAAAAGTCCCTAGGAACCA 59.410 47.826 11.48 0.00 35.17 3.67
3421 4594 3.848377 TCCCTAAAAAGTCCCTAGGAACC 59.152 47.826 11.48 0.00 35.17 3.62
3422 4595 4.535294 AGTCCCTAAAAAGTCCCTAGGAAC 59.465 45.833 11.48 0.00 35.17 3.62
3423 4596 4.771338 AGTCCCTAAAAAGTCCCTAGGAA 58.229 43.478 11.48 0.00 35.17 3.36
3424 4597 4.431158 AGTCCCTAAAAAGTCCCTAGGA 57.569 45.455 11.48 0.00 35.17 2.94
3425 4598 5.516059 AAAGTCCCTAAAAAGTCCCTAGG 57.484 43.478 0.06 0.06 33.30 3.02
3426 4599 7.232188 AGAAAAAGTCCCTAAAAAGTCCCTAG 58.768 38.462 0.00 0.00 0.00 3.02
3427 4600 7.157947 AGAAAAAGTCCCTAAAAAGTCCCTA 57.842 36.000 0.00 0.00 0.00 3.53
3428 4601 6.027025 AGAAAAAGTCCCTAAAAAGTCCCT 57.973 37.500 0.00 0.00 0.00 4.20
3429 4602 7.002879 ACTAGAAAAAGTCCCTAAAAAGTCCC 58.997 38.462 0.00 0.00 0.00 4.46
3430 4603 7.937942 AGACTAGAAAAAGTCCCTAAAAAGTCC 59.062 37.037 0.00 0.00 45.86 3.85
3431 4604 8.905660 AGACTAGAAAAAGTCCCTAAAAAGTC 57.094 34.615 0.00 0.00 45.86 3.01
3432 4605 8.715842 AGAGACTAGAAAAAGTCCCTAAAAAGT 58.284 33.333 0.00 0.00 45.86 2.66
3433 4606 8.994170 CAGAGACTAGAAAAAGTCCCTAAAAAG 58.006 37.037 0.00 0.00 45.86 2.27
3434 4607 7.937394 CCAGAGACTAGAAAAAGTCCCTAAAAA 59.063 37.037 0.00 0.00 45.86 1.94
3435 4608 7.450903 CCAGAGACTAGAAAAAGTCCCTAAAA 58.549 38.462 0.00 0.00 45.86 1.52
3436 4609 6.013639 CCCAGAGACTAGAAAAAGTCCCTAAA 60.014 42.308 0.00 0.00 45.86 1.85
3437 4610 5.484290 CCCAGAGACTAGAAAAAGTCCCTAA 59.516 44.000 0.00 0.00 45.86 2.69
3438 4611 5.024118 CCCAGAGACTAGAAAAAGTCCCTA 58.976 45.833 0.00 0.00 45.86 3.53
3439 4612 3.841255 CCCAGAGACTAGAAAAAGTCCCT 59.159 47.826 0.00 0.00 45.86 4.20
3440 4613 3.838903 TCCCAGAGACTAGAAAAAGTCCC 59.161 47.826 0.00 0.00 45.86 4.46
3441 4614 4.823157 GTCCCAGAGACTAGAAAAAGTCC 58.177 47.826 0.00 0.00 45.86 3.85
3461 4634 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
3462 4635 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
3463 4636 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
3464 4637 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
3465 4638 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
3466 4639 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
3467 4640 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
3468 4641 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
3469 4642 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
3470 4643 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
3471 4644 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
3472 4645 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
3473 4646 0.105709 AAGGGGGTGTTTGGTTCAGG 60.106 55.000 0.00 0.00 0.00 3.86
3474 4647 2.514803 CTAAGGGGGTGTTTGGTTCAG 58.485 52.381 0.00 0.00 0.00 3.02
3475 4648 1.479757 GCTAAGGGGGTGTTTGGTTCA 60.480 52.381 0.00 0.00 0.00 3.18
3476 4649 1.203013 AGCTAAGGGGGTGTTTGGTTC 60.203 52.381 0.00 0.00 0.00 3.62
3477 4650 0.857675 AGCTAAGGGGGTGTTTGGTT 59.142 50.000 0.00 0.00 0.00 3.67
3478 4651 0.857675 AAGCTAAGGGGGTGTTTGGT 59.142 50.000 0.00 0.00 0.00 3.67
3479 4652 1.256812 CAAGCTAAGGGGGTGTTTGG 58.743 55.000 0.00 0.00 0.00 3.28
3480 4653 1.256812 CCAAGCTAAGGGGGTGTTTG 58.743 55.000 0.00 0.00 0.00 2.93
3481 4654 0.541998 GCCAAGCTAAGGGGGTGTTT 60.542 55.000 7.20 0.00 0.00 2.83
3482 4655 1.076727 GCCAAGCTAAGGGGGTGTT 59.923 57.895 7.20 0.00 0.00 3.32
3483 4656 1.852626 AGCCAAGCTAAGGGGGTGT 60.853 57.895 7.20 0.00 36.99 4.16
3484 4657 1.379044 CAGCCAAGCTAAGGGGGTG 60.379 63.158 10.23 10.23 42.93 4.61
3485 4658 1.541368 TCAGCCAAGCTAAGGGGGT 60.541 57.895 7.20 0.44 36.40 4.95
3486 4659 1.225704 CTCAGCCAAGCTAAGGGGG 59.774 63.158 7.20 0.00 36.40 5.40
3487 4660 1.139853 CTACTCAGCCAAGCTAAGGGG 59.860 57.143 7.20 0.00 36.40 4.79
3488 4661 2.111384 TCTACTCAGCCAAGCTAAGGG 58.889 52.381 7.20 1.25 36.40 3.95
3489 4662 3.895232 TTCTACTCAGCCAAGCTAAGG 57.105 47.619 0.79 0.79 36.40 2.69
3511 4684 1.967066 CACAACATGGCCCAAAGGTTA 59.033 47.619 0.00 0.00 34.57 2.85
3534 4708 4.142204 GGGAAGGGACAAAACGTAACAAAA 60.142 41.667 0.00 0.00 0.00 2.44
3541 4715 1.687563 CAAGGGAAGGGACAAAACGT 58.312 50.000 0.00 0.00 0.00 3.99
3547 4721 0.899717 GCAATGCAAGGGAAGGGACA 60.900 55.000 0.00 0.00 0.00 4.02
3552 4726 1.213537 CGGTGCAATGCAAGGGAAG 59.786 57.895 10.44 0.00 41.47 3.46
3553 4727 1.112315 AACGGTGCAATGCAAGGGAA 61.112 50.000 10.44 0.00 41.47 3.97
3554 4728 1.530419 AACGGTGCAATGCAAGGGA 60.530 52.632 10.44 0.00 41.47 4.20
3555 4729 1.373246 CAACGGTGCAATGCAAGGG 60.373 57.895 10.44 4.60 41.47 3.95
3556 4730 0.244450 ATCAACGGTGCAATGCAAGG 59.756 50.000 10.44 7.40 41.47 3.61
3577 4751 6.587990 CCAAACAACACAACAGACACAAAATA 59.412 34.615 0.00 0.00 0.00 1.40
3622 4985 3.380142 ACGTGGTTTGCATTTGTTCATC 58.620 40.909 0.00 0.00 0.00 2.92
3623 4986 3.068024 AGACGTGGTTTGCATTTGTTCAT 59.932 39.130 0.00 0.00 0.00 2.57
3642 5005 2.645730 TTGCACACAACCAAACAGAC 57.354 45.000 0.00 0.00 0.00 3.51
3643 5006 2.495270 ACATTGCACACAACCAAACAGA 59.505 40.909 0.00 0.00 38.99 3.41
3778 5158 8.693542 ATGATATTTTGCTGTCTTAAAACTGC 57.306 30.769 4.00 4.00 42.49 4.40
3789 5169 6.810182 GCTGAAAACTGATGATATTTTGCTGT 59.190 34.615 0.00 0.00 0.00 4.40
3804 5184 7.935338 ACTGTGAATATTTTGCTGAAAACTG 57.065 32.000 0.00 0.00 33.86 3.16
3825 5205 3.119173 TCAACACCTTTTGCTGGAAACTG 60.119 43.478 0.00 0.00 0.00 3.16
3845 5225 4.412207 CGACATACTCGTTGTCAAGATCA 58.588 43.478 0.00 0.00 42.90 2.92
3955 5335 0.593128 GCTGGCAAGTGGTGTAACTG 59.407 55.000 0.00 0.00 36.74 3.16
4093 5473 0.036388 ATAGAACCAGTGCCACACCG 60.036 55.000 0.00 0.00 34.49 4.94
4150 5530 0.517316 GTGACGGTGATGTCTTTGCC 59.483 55.000 0.00 0.00 39.64 4.52
4154 5534 0.034896 GGTGGTGACGGTGATGTCTT 59.965 55.000 0.00 0.00 39.64 3.01
4162 5542 3.460672 CTGCAGTGGTGGTGACGGT 62.461 63.158 5.25 0.00 0.00 4.83
4166 5546 3.170672 AGGCTGCAGTGGTGGTGA 61.171 61.111 16.64 0.00 0.00 4.02
4168 5548 3.958860 GGAGGCTGCAGTGGTGGT 61.959 66.667 16.64 0.00 0.00 4.16
4170 5550 3.618780 GAGGGAGGCTGCAGTGGTG 62.619 68.421 16.64 0.00 0.00 4.17
4174 5554 2.686835 GAGGAGGGAGGCTGCAGT 60.687 66.667 16.64 0.00 0.00 4.40
4175 5555 3.478274 GGAGGAGGGAGGCTGCAG 61.478 72.222 10.11 10.11 0.00 4.41
4181 5561 3.396822 ATGTCGGGGAGGAGGGAGG 62.397 68.421 0.00 0.00 0.00 4.30
4182 5562 1.834822 GATGTCGGGGAGGAGGGAG 60.835 68.421 0.00 0.00 0.00 4.30
4183 5563 2.282446 GATGTCGGGGAGGAGGGA 59.718 66.667 0.00 0.00 0.00 4.20
4184 5564 1.834822 GAGATGTCGGGGAGGAGGG 60.835 68.421 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.