Multiple sequence alignment - TraesCS6A01G125000

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 TraesCS6A01G125000 chr6A 100.000 5177 0 0 1 5177 98324849 98319673 0.000000e+00 9561.0
1 TraesCS6A01G125000 chr6A 88.860 3815 375 34 483 4287 98814098 98810324 0.000000e+00 4645.0
2 TraesCS6A01G125000 chr6A 83.469 3321 515 25 839 4146 98256589 98253290 0.000000e+00 3061.0
3 TraesCS6A01G125000 chr6A 84.630 2674 368 34 1825 4471 98916398 98913741 0.000000e+00 2621.0
4 TraesCS6A01G125000 chr6D 96.802 4534 122 13 1 4518 81936388 81931862 0.000000e+00 7548.0
5 TraesCS6A01G125000 chr6D 87.395 3800 426 33 483 4273 82139624 82135869 0.000000e+00 4314.0
6 TraesCS6A01G125000 chr6D 83.413 3328 504 35 839 4146 81764090 81760791 0.000000e+00 3044.0
7 TraesCS6A01G125000 chr6D 93.333 405 27 0 4773 5177 81931842 81931438 2.670000e-167 599.0
8 TraesCS6A01G125000 chr6D 95.833 240 10 0 4531 4770 80054076 80054315 6.290000e-104 388.0
9 TraesCS6A01G125000 chr6D 95.436 241 11 0 4533 4773 227007762 227008002 8.130000e-103 385.0
10 TraesCS6A01G125000 chr6D 85.000 80 7 4 203 282 82139704 82139630 5.560000e-10 76.8
11 TraesCS6A01G125000 chr6B 95.980 4552 145 19 1 4534 156741993 156737462 0.000000e+00 7358.0
12 TraesCS6A01G125000 chr6B 86.976 3793 446 28 483 4266 157027897 157024144 0.000000e+00 4224.0
13 TraesCS6A01G125000 chr6B 83.544 3324 507 31 839 4146 156533346 156530047 0.000000e+00 3072.0
14 TraesCS6A01G125000 chr6B 81.148 3904 629 63 481 4353 157489764 157485937 0.000000e+00 3033.0
15 TraesCS6A01G125000 chr6B 89.258 782 68 5 3755 4534 156686243 156685476 0.000000e+00 965.0
16 TraesCS6A01G125000 chr6B 90.732 410 30 3 4770 5177 156685479 156685076 1.640000e-149 540.0
17 TraesCS6A01G125000 chr6B 89.630 405 33 4 4773 5177 156737465 156737070 1.660000e-139 507.0
18 TraesCS6A01G125000 chr4D 96.281 242 9 0 4532 4773 30506425 30506666 1.040000e-106 398.0
19 TraesCS6A01G125000 chr4D 94.821 251 12 1 4523 4773 76611934 76612183 1.750000e-104 390.0
20 TraesCS6A01G125000 chr4D 95.021 241 12 0 4533 4773 11504115 11504355 3.780000e-101 379.0
21 TraesCS6A01G125000 chr4D 88.636 176 14 4 297 467 509822279 509822453 5.250000e-50 209.0
22 TraesCS6A01G125000 chr4D 88.889 108 11 1 360 467 220360561 220360455 1.170000e-26 132.0
23 TraesCS6A01G125000 chr2D 94.758 248 12 1 4530 4776 459810945 459810698 8.130000e-103 385.0
24 TraesCS6A01G125000 chr2D 94.694 245 11 2 4533 4777 642827074 642827316 3.780000e-101 379.0
25 TraesCS6A01G125000 chr2D 85.795 176 13 4 297 467 30487791 30487623 5.330000e-40 176.0
26 TraesCS6A01G125000 chr2D 88.356 146 11 3 327 467 617437150 617437294 2.480000e-38 171.0
27 TraesCS6A01G125000 chr7A 93.077 260 16 2 4515 4773 362740125 362740383 3.780000e-101 379.0
28 TraesCS6A01G125000 chr7A 89.041 146 10 3 327 467 501154056 501154200 5.330000e-40 176.0
29 TraesCS6A01G125000 chr2A 94.000 250 15 0 4532 4781 612829527 612829776 3.780000e-101 379.0
30 TraesCS6A01G125000 chr2A 88.356 146 11 3 327 467 240475384 240475240 2.480000e-38 171.0
31 TraesCS6A01G125000 chr5B 87.500 152 14 2 327 473 448597897 448597746 2.480000e-38 171.0
32 TraesCS6A01G125000 chr2B 87.838 148 12 3 327 468 654443266 654443119 8.920000e-38 169.0
33 TraesCS6A01G125000 chr3B 100.000 28 0 0 297 324 755710503 755710530 9.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G125000 chr6A 98319673 98324849 5176 True 9561.0 9561 100.0000 1 5177 1 chr6A.!!$R2 5176
1 TraesCS6A01G125000 chr6A 98810324 98814098 3774 True 4645.0 4645 88.8600 483 4287 1 chr6A.!!$R3 3804
2 TraesCS6A01G125000 chr6A 98253290 98256589 3299 True 3061.0 3061 83.4690 839 4146 1 chr6A.!!$R1 3307
3 TraesCS6A01G125000 chr6A 98913741 98916398 2657 True 2621.0 2621 84.6300 1825 4471 1 chr6A.!!$R4 2646
4 TraesCS6A01G125000 chr6D 81931438 81936388 4950 True 4073.5 7548 95.0675 1 5177 2 chr6D.!!$R2 5176
5 TraesCS6A01G125000 chr6D 81760791 81764090 3299 True 3044.0 3044 83.4130 839 4146 1 chr6D.!!$R1 3307
6 TraesCS6A01G125000 chr6D 82135869 82139704 3835 True 2195.4 4314 86.1975 203 4273 2 chr6D.!!$R3 4070
7 TraesCS6A01G125000 chr6B 157024144 157027897 3753 True 4224.0 4224 86.9760 483 4266 1 chr6B.!!$R2 3783
8 TraesCS6A01G125000 chr6B 156737070 156741993 4923 True 3932.5 7358 92.8050 1 5177 2 chr6B.!!$R5 5176
9 TraesCS6A01G125000 chr6B 156530047 156533346 3299 True 3072.0 3072 83.5440 839 4146 1 chr6B.!!$R1 3307
10 TraesCS6A01G125000 chr6B 157485937 157489764 3827 True 3033.0 3033 81.1480 481 4353 1 chr6B.!!$R3 3872
11 TraesCS6A01G125000 chr6B 156685076 156686243 1167 True 752.5 965 89.9950 3755 5177 2 chr6B.!!$R4 1422

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
360 375 0.316689 CACGGGTTGTTCGAAACAGC 60.317 55.000 0.0 2.81 43.27 4.40 F
1060 1095 0.831307 ACTCGGCATACCTTCCCTTC 59.169 55.000 0.0 0.00 0.00 3.46 F
1068 1103 2.193087 TACCTTCCCTTCGCCTTGCC 62.193 60.000 0.0 0.00 0.00 4.52 F
2384 2422 0.964860 TTGGACATGGATGGTTGCCG 60.965 55.000 0.0 0.00 0.00 5.69 F
3518 3556 1.447314 GTTACTGCGTCCGGGGAAG 60.447 63.158 0.0 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1343 1.814169 GTACTGCAGCCCGGTTAGC 60.814 63.158 15.27 0.84 34.16 3.09 R
2285 2323 6.567687 TGAAATTGAACGAAATAAGCAGGA 57.432 33.333 0.00 0.00 0.00 3.86 R
2404 2442 9.112725 CAGTTGTGTCAATCTTGATATCCATAA 57.887 33.333 0.00 0.00 39.73 1.90 R
3596 3637 0.694771 AGGCCAGTCAAGCAATGAGA 59.305 50.000 5.01 0.00 39.19 3.27 R
4731 4826 0.032017 AGTGCTTCCTCTATCCCCGT 60.032 55.000 0.00 0.00 0.00 5.28 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
125 132 3.009473 ACATATCACCCAGCAAGTCAACT 59.991 43.478 0.00 0.00 0.00 3.16
140 147 3.008049 AGTCAACTATCCACCTTGTCCAC 59.992 47.826 0.00 0.00 0.00 4.02
301 315 1.450312 ATCTTCTGAAAGGGGCGCG 60.450 57.895 0.00 0.00 33.03 6.86
360 375 0.316689 CACGGGTTGTTCGAAACAGC 60.317 55.000 0.00 2.81 43.27 4.40
454 471 2.363925 AGGGAGCTACGTCCACCC 60.364 66.667 11.97 11.97 38.52 4.61
455 472 2.682494 GGGAGCTACGTCCACCCA 60.682 66.667 14.15 0.00 38.52 4.51
456 473 2.722201 GGGAGCTACGTCCACCCAG 61.722 68.421 14.15 0.00 38.52 4.45
457 474 2.722201 GGAGCTACGTCCACCCAGG 61.722 68.421 0.00 0.00 36.51 4.45
472 489 0.890683 CCAGGCTGCCCTTTAAACAG 59.109 55.000 16.57 1.00 40.33 3.16
532 549 8.718734 GGATACGTGAAGAAGTAATTTTTCTGT 58.281 33.333 0.00 8.21 35.20 3.41
533 550 9.742552 GATACGTGAAGAAGTAATTTTTCTGTC 57.257 33.333 0.00 6.63 35.20 3.51
1044 1079 4.533225 CAAGACATGCAGCAAGATACTC 57.467 45.455 4.23 0.00 0.00 2.59
1060 1095 0.831307 ACTCGGCATACCTTCCCTTC 59.169 55.000 0.00 0.00 0.00 3.46
1068 1103 2.193087 TACCTTCCCTTCGCCTTGCC 62.193 60.000 0.00 0.00 0.00 4.52
1305 1343 4.157289 CACATCTCACAATCCCTTGGAAAG 59.843 45.833 0.00 0.00 45.69 2.62
2285 2323 2.307098 AGAGCAGCAAGAACCTTACCAT 59.693 45.455 0.00 0.00 0.00 3.55
2384 2422 0.964860 TTGGACATGGATGGTTGCCG 60.965 55.000 0.00 0.00 0.00 5.69
2389 2427 2.948979 GACATGGATGGTTGCCGATTAA 59.051 45.455 0.00 0.00 0.00 1.40
2404 2442 5.712917 TGCCGATTAACTGGAAAAATACCTT 59.287 36.000 0.00 0.00 0.00 3.50
2962 3000 5.652452 GGAGGCCAGTTTAATACATTTCAGT 59.348 40.000 5.01 0.00 0.00 3.41
3129 3167 2.627221 TGCTATTCTTTTGTTGCTGGCA 59.373 40.909 0.00 0.00 0.00 4.92
3212 3250 6.373005 TGGAGATGTTGAAGAACCTTCATA 57.627 37.500 9.83 4.07 0.00 2.15
3280 3318 3.394606 AGGCAAGGGAGTAGAAAACAAGA 59.605 43.478 0.00 0.00 0.00 3.02
3282 3320 5.250774 AGGCAAGGGAGTAGAAAACAAGATA 59.749 40.000 0.00 0.00 0.00 1.98
3310 3348 3.058293 TGCTGACATTTTGAAAGCTACGG 60.058 43.478 0.00 0.00 33.04 4.02
3512 3550 2.433664 GTGGGGTTACTGCGTCCG 60.434 66.667 0.00 0.00 0.00 4.79
3518 3556 1.447314 GTTACTGCGTCCGGGGAAG 60.447 63.158 0.00 0.00 0.00 3.46
3596 3637 4.263639 CCATAACAGGGATGATGGTGCTAT 60.264 45.833 0.00 0.00 35.17 2.97
3933 3975 0.868406 GAAGGCGACCTGTTTCAGTG 59.132 55.000 0.00 0.00 32.13 3.66
3967 4009 3.328535 AAGAACTTGTCCCATGGGTTT 57.671 42.857 30.28 15.83 36.47 3.27
4029 4071 1.202651 CCAACACTTCGAGGAACAGGT 60.203 52.381 0.00 0.00 0.00 4.00
4045 4087 5.183904 GGAACAGGTTATGAAGAGCAAATGT 59.816 40.000 0.00 0.00 0.00 2.71
4098 4140 4.149511 TGACCATAATCAATTCAGGCGA 57.850 40.909 0.00 0.00 0.00 5.54
4137 4179 1.137872 GTCTCCTGCCTGTCCAGTATG 59.862 57.143 0.00 0.00 0.00 2.39
4146 4188 2.534298 CTGTCCAGTATGAACGCTGAG 58.466 52.381 0.00 0.00 39.69 3.35
4261 4320 3.764434 TCCACTAGAACTACTGCTTCTGG 59.236 47.826 0.00 0.00 33.58 3.86
4267 4347 6.663953 ACTAGAACTACTGCTTCTGGTAATCA 59.336 38.462 0.00 0.00 37.60 2.57
4300 4380 4.882842 TTGTACATAGCCTGACAAGACA 57.117 40.909 0.00 0.00 0.00 3.41
4482 4567 5.163322 TGGTTTCCATTCAGATGTTTGCTTT 60.163 36.000 0.00 0.00 0.00 3.51
4537 4632 3.500558 GGTGAGTTACCGAACTACTCC 57.499 52.381 0.00 0.00 46.23 3.85
4538 4633 2.165234 GGTGAGTTACCGAACTACTCCC 59.835 54.545 0.00 0.00 46.23 4.30
4539 4634 3.087781 GTGAGTTACCGAACTACTCCCT 58.912 50.000 0.00 0.00 46.23 4.20
4540 4635 3.128415 GTGAGTTACCGAACTACTCCCTC 59.872 52.174 0.00 0.00 46.23 4.30
4541 4636 2.687425 GAGTTACCGAACTACTCCCTCC 59.313 54.545 0.00 0.00 46.23 4.30
4542 4637 2.042162 AGTTACCGAACTACTCCCTCCA 59.958 50.000 0.00 0.00 44.36 3.86
4543 4638 3.029570 GTTACCGAACTACTCCCTCCAT 58.970 50.000 0.00 0.00 32.40 3.41
4544 4639 2.249309 ACCGAACTACTCCCTCCATT 57.751 50.000 0.00 0.00 0.00 3.16
4545 4640 2.108970 ACCGAACTACTCCCTCCATTC 58.891 52.381 0.00 0.00 0.00 2.67
4546 4641 1.413077 CCGAACTACTCCCTCCATTCC 59.587 57.143 0.00 0.00 0.00 3.01
4547 4642 2.108168 CGAACTACTCCCTCCATTCCA 58.892 52.381 0.00 0.00 0.00 3.53
4548 4643 2.500098 CGAACTACTCCCTCCATTCCAA 59.500 50.000 0.00 0.00 0.00 3.53
4549 4644 3.055385 CGAACTACTCCCTCCATTCCAAA 60.055 47.826 0.00 0.00 0.00 3.28
4550 4645 4.564821 CGAACTACTCCCTCCATTCCAAAA 60.565 45.833 0.00 0.00 0.00 2.44
4551 4646 5.510430 GAACTACTCCCTCCATTCCAAAAT 58.490 41.667 0.00 0.00 0.00 1.82
4552 4647 6.631766 CGAACTACTCCCTCCATTCCAAAATA 60.632 42.308 0.00 0.00 0.00 1.40
4553 4648 6.848562 ACTACTCCCTCCATTCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
4554 4649 7.947782 ACTACTCCCTCCATTCCAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
4555 4650 7.978925 ACTACTCCCTCCATTCCAAAATATAG 58.021 38.462 0.00 0.00 0.00 1.31
4556 4651 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
4557 4652 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
4558 4653 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
4559 4654 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
4560 4655 4.320494 CCTCCATTCCAAAATATAGTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
4561 4656 4.460263 TCCATTCCAAAATATAGTGCGCT 58.540 39.130 9.73 4.58 0.00 5.92
4562 4657 4.515191 TCCATTCCAAAATATAGTGCGCTC 59.485 41.667 9.73 4.74 0.00 5.03
4563 4658 4.457810 CATTCCAAAATATAGTGCGCTCG 58.542 43.478 9.73 0.00 0.00 5.03
4564 4659 1.864711 TCCAAAATATAGTGCGCTCGC 59.135 47.619 9.73 7.38 42.35 5.03
4565 4660 1.397190 CCAAAATATAGTGCGCTCGCG 60.397 52.381 9.73 6.98 45.51 5.87
4577 4672 4.856607 CTCGCGCTTCCCGAGGTC 62.857 72.222 5.56 0.00 46.15 3.85
4579 4674 4.735132 CGCGCTTCCCGAGGTCAA 62.735 66.667 5.56 0.00 40.02 3.18
4580 4675 2.358247 GCGCTTCCCGAGGTCAAA 60.358 61.111 0.00 0.00 40.02 2.69
4581 4676 2.677979 GCGCTTCCCGAGGTCAAAC 61.678 63.158 0.00 0.00 40.02 2.93
4582 4677 1.004918 CGCTTCCCGAGGTCAAACT 60.005 57.895 0.00 0.00 40.02 2.66
4583 4678 0.602905 CGCTTCCCGAGGTCAAACTT 60.603 55.000 0.00 0.00 40.02 2.66
4584 4679 1.605753 GCTTCCCGAGGTCAAACTTT 58.394 50.000 0.00 0.00 0.00 2.66
4585 4680 1.266989 GCTTCCCGAGGTCAAACTTTG 59.733 52.381 0.00 0.00 0.00 2.77
4586 4681 2.846193 CTTCCCGAGGTCAAACTTTGA 58.154 47.619 0.00 0.00 37.33 2.69
4609 4704 9.715121 TTGACTATAAATTTAACGAACCAGACT 57.285 29.630 1.21 0.00 0.00 3.24
4610 4705 9.146984 TGACTATAAATTTAACGAACCAGACTG 57.853 33.333 1.21 0.00 0.00 3.51
4611 4706 9.362539 GACTATAAATTTAACGAACCAGACTGA 57.637 33.333 3.32 0.00 0.00 3.41
4612 4707 9.148104 ACTATAAATTTAACGAACCAGACTGAC 57.852 33.333 3.32 0.00 0.00 3.51
4613 4708 9.367444 CTATAAATTTAACGAACCAGACTGACT 57.633 33.333 3.32 0.00 0.00 3.41
4614 4709 5.924475 AATTTAACGAACCAGACTGACTG 57.076 39.130 3.32 0.00 45.36 3.51
4615 4710 2.433868 TAACGAACCAGACTGACTGC 57.566 50.000 3.32 0.00 44.52 4.40
4616 4711 0.597637 AACGAACCAGACTGACTGCG 60.598 55.000 3.32 1.44 44.52 5.18
4617 4712 1.734477 CGAACCAGACTGACTGCGG 60.734 63.158 3.32 0.00 44.52 5.69
4618 4713 2.029844 GAACCAGACTGACTGCGGC 61.030 63.158 3.32 0.00 44.52 6.53
4619 4714 3.865929 AACCAGACTGACTGCGGCG 62.866 63.158 0.51 0.51 44.52 6.46
4623 4718 4.803426 GACTGACTGCGGCGGGAG 62.803 72.222 14.26 11.31 37.67 4.30
4625 4720 4.069232 CTGACTGCGGCGGGAGAA 62.069 66.667 19.55 6.32 35.29 2.87
4626 4721 3.589654 CTGACTGCGGCGGGAGAAA 62.590 63.158 19.55 5.98 35.29 2.52
4627 4722 2.358247 GACTGCGGCGGGAGAAAA 60.358 61.111 19.55 0.00 35.29 2.29
4628 4723 1.964373 GACTGCGGCGGGAGAAAAA 60.964 57.895 19.55 0.00 35.29 1.94
4629 4724 1.912371 GACTGCGGCGGGAGAAAAAG 61.912 60.000 19.55 0.00 35.29 2.27
4630 4725 1.966451 CTGCGGCGGGAGAAAAAGT 60.966 57.895 9.78 0.00 32.53 2.66
4631 4726 1.515521 CTGCGGCGGGAGAAAAAGTT 61.516 55.000 9.78 0.00 32.53 2.66
4632 4727 0.250381 TGCGGCGGGAGAAAAAGTTA 60.250 50.000 9.78 0.00 0.00 2.24
4633 4728 0.167470 GCGGCGGGAGAAAAAGTTAC 59.833 55.000 9.78 0.00 0.00 2.50
4634 4729 1.515081 CGGCGGGAGAAAAAGTTACA 58.485 50.000 0.00 0.00 0.00 2.41
4635 4730 2.081462 CGGCGGGAGAAAAAGTTACAT 58.919 47.619 0.00 0.00 0.00 2.29
4636 4731 3.264104 CGGCGGGAGAAAAAGTTACATA 58.736 45.455 0.00 0.00 0.00 2.29
4637 4732 3.685756 CGGCGGGAGAAAAAGTTACATAA 59.314 43.478 0.00 0.00 0.00 1.90
4638 4733 4.334481 CGGCGGGAGAAAAAGTTACATAAT 59.666 41.667 0.00 0.00 0.00 1.28
4639 4734 5.163693 CGGCGGGAGAAAAAGTTACATAATT 60.164 40.000 0.00 0.00 0.00 1.40
4640 4735 6.037391 CGGCGGGAGAAAAAGTTACATAATTA 59.963 38.462 0.00 0.00 0.00 1.40
4641 4736 7.414319 CGGCGGGAGAAAAAGTTACATAATTAA 60.414 37.037 0.00 0.00 0.00 1.40
4642 4737 8.245491 GGCGGGAGAAAAAGTTACATAATTAAA 58.755 33.333 0.00 0.00 0.00 1.52
4643 4738 9.628746 GCGGGAGAAAAAGTTACATAATTAAAA 57.371 29.630 0.00 0.00 0.00 1.52
4667 4762 8.797266 AAACTTCTTTCAAATACGAAATCACC 57.203 30.769 0.00 0.00 34.50 4.02
4668 4763 6.599437 ACTTCTTTCAAATACGAAATCACCG 58.401 36.000 0.00 0.00 34.50 4.94
4669 4764 6.425721 ACTTCTTTCAAATACGAAATCACCGA 59.574 34.615 0.00 0.00 34.50 4.69
4670 4765 6.978343 TCTTTCAAATACGAAATCACCGAT 57.022 33.333 0.00 0.00 34.50 4.18
4671 4766 8.481974 TTCTTTCAAATACGAAATCACCGATA 57.518 30.769 0.00 0.00 34.50 2.92
4672 4767 8.657074 TCTTTCAAATACGAAATCACCGATAT 57.343 30.769 0.00 0.00 34.50 1.63
4673 4768 9.752961 TCTTTCAAATACGAAATCACCGATATA 57.247 29.630 0.00 0.00 34.50 0.86
4676 4771 9.537192 TTCAAATACGAAATCACCGATATAACT 57.463 29.630 0.00 0.00 0.00 2.24
4677 4772 9.537192 TCAAATACGAAATCACCGATATAACTT 57.463 29.630 0.00 0.00 0.00 2.66
4681 4776 6.483687 ACGAAATCACCGATATAACTTTTGC 58.516 36.000 0.00 0.00 0.00 3.68
4682 4777 6.315393 ACGAAATCACCGATATAACTTTTGCT 59.685 34.615 0.00 0.00 0.00 3.91
4683 4778 6.846283 CGAAATCACCGATATAACTTTTGCTC 59.154 38.462 0.00 0.00 0.00 4.26
4684 4779 6.619801 AATCACCGATATAACTTTTGCTCC 57.380 37.500 0.00 0.00 0.00 4.70
4685 4780 4.448210 TCACCGATATAACTTTTGCTCCC 58.552 43.478 0.00 0.00 0.00 4.30
4686 4781 3.247648 CACCGATATAACTTTTGCTCCCG 59.752 47.826 0.00 0.00 0.00 5.14
4687 4782 2.223377 CCGATATAACTTTTGCTCCCGC 59.777 50.000 0.00 0.00 0.00 6.13
4688 4783 2.223377 CGATATAACTTTTGCTCCCGCC 59.777 50.000 0.00 0.00 34.43 6.13
4689 4784 1.658994 TATAACTTTTGCTCCCGCCG 58.341 50.000 0.00 0.00 34.43 6.46
4690 4785 1.654023 ATAACTTTTGCTCCCGCCGC 61.654 55.000 0.00 0.00 34.43 6.53
4691 4786 4.887932 TATAACTTTTGCTCCCGCCGCA 62.888 50.000 0.00 0.00 35.22 5.69
4692 4787 3.669344 CTTTTGCTCCCGCCGCAA 61.669 61.111 0.00 0.00 44.83 4.85
4693 4788 2.988684 TTTTGCTCCCGCCGCAAT 60.989 55.556 5.33 0.00 45.67 3.56
4694 4789 2.872337 CTTTTGCTCCCGCCGCAATC 62.872 60.000 5.33 0.00 45.67 2.67
4710 4805 5.712217 CGCAATCGGTCTTGATAGTTAAA 57.288 39.130 0.00 0.00 0.00 1.52
4711 4806 6.287107 CGCAATCGGTCTTGATAGTTAAAT 57.713 37.500 0.00 0.00 0.00 1.40
4712 4807 6.715464 CGCAATCGGTCTTGATAGTTAAATT 58.285 36.000 0.00 0.00 0.00 1.82
4713 4808 7.186804 CGCAATCGGTCTTGATAGTTAAATTT 58.813 34.615 0.00 0.00 0.00 1.82
4714 4809 8.332464 CGCAATCGGTCTTGATAGTTAAATTTA 58.668 33.333 0.00 0.00 0.00 1.40
4718 4813 9.847224 ATCGGTCTTGATAGTTAAATTTATGGT 57.153 29.630 0.00 0.00 0.00 3.55
4719 4814 9.321562 TCGGTCTTGATAGTTAAATTTATGGTC 57.678 33.333 0.00 0.00 0.00 4.02
4720 4815 9.104965 CGGTCTTGATAGTTAAATTTATGGTCA 57.895 33.333 0.00 0.00 0.00 4.02
4730 4825 9.476202 AGTTAAATTTATGGTCAAAGTTGAAGC 57.524 29.630 0.00 0.00 39.21 3.86
4731 4826 9.255304 GTTAAATTTATGGTCAAAGTTGAAGCA 57.745 29.630 0.00 0.00 39.21 3.91
4732 4827 7.713764 AAATTTATGGTCAAAGTTGAAGCAC 57.286 32.000 0.00 0.00 39.21 4.40
4733 4828 4.481930 TTATGGTCAAAGTTGAAGCACG 57.518 40.909 0.00 0.00 39.21 5.34
4734 4829 1.021202 TGGTCAAAGTTGAAGCACGG 58.979 50.000 0.00 0.00 39.21 4.94
4735 4830 0.310854 GGTCAAAGTTGAAGCACGGG 59.689 55.000 0.00 0.00 39.21 5.28
4736 4831 0.310854 GTCAAAGTTGAAGCACGGGG 59.689 55.000 0.00 0.00 39.21 5.73
4737 4832 0.181587 TCAAAGTTGAAGCACGGGGA 59.818 50.000 0.00 0.00 33.55 4.81
4738 4833 1.202879 TCAAAGTTGAAGCACGGGGAT 60.203 47.619 0.00 0.00 33.55 3.85
4739 4834 2.039216 TCAAAGTTGAAGCACGGGGATA 59.961 45.455 0.00 0.00 33.55 2.59
4740 4835 2.403252 AAGTTGAAGCACGGGGATAG 57.597 50.000 0.00 0.00 0.00 2.08
4741 4836 1.568504 AGTTGAAGCACGGGGATAGA 58.431 50.000 0.00 0.00 0.00 1.98
4742 4837 1.482593 AGTTGAAGCACGGGGATAGAG 59.517 52.381 0.00 0.00 0.00 2.43
4743 4838 0.830648 TTGAAGCACGGGGATAGAGG 59.169 55.000 0.00 0.00 0.00 3.69
4744 4839 0.032515 TGAAGCACGGGGATAGAGGA 60.033 55.000 0.00 0.00 0.00 3.71
4745 4840 1.120530 GAAGCACGGGGATAGAGGAA 58.879 55.000 0.00 0.00 0.00 3.36
4746 4841 1.069358 GAAGCACGGGGATAGAGGAAG 59.931 57.143 0.00 0.00 0.00 3.46
4747 4842 1.069935 GCACGGGGATAGAGGAAGC 59.930 63.158 0.00 0.00 0.00 3.86
4748 4843 1.686325 GCACGGGGATAGAGGAAGCA 61.686 60.000 0.00 0.00 0.00 3.91
4749 4844 0.105039 CACGGGGATAGAGGAAGCAC 59.895 60.000 0.00 0.00 0.00 4.40
4750 4845 0.032017 ACGGGGATAGAGGAAGCACT 60.032 55.000 0.00 0.00 0.00 4.40
4751 4846 1.217183 ACGGGGATAGAGGAAGCACTA 59.783 52.381 0.00 0.00 0.00 2.74
4752 4847 1.614413 CGGGGATAGAGGAAGCACTAC 59.386 57.143 0.00 0.00 0.00 2.73
4753 4848 2.679082 GGGGATAGAGGAAGCACTACA 58.321 52.381 0.00 0.00 0.00 2.74
4754 4849 3.243724 GGGGATAGAGGAAGCACTACAT 58.756 50.000 0.00 0.00 0.00 2.29
4755 4850 3.648545 GGGGATAGAGGAAGCACTACATT 59.351 47.826 0.00 0.00 0.00 2.71
4756 4851 4.503991 GGGGATAGAGGAAGCACTACATTG 60.504 50.000 0.00 0.00 0.00 2.82
4757 4852 4.101741 GGGATAGAGGAAGCACTACATTGT 59.898 45.833 0.00 0.00 0.00 2.71
4758 4853 5.053145 GGATAGAGGAAGCACTACATTGTG 58.947 45.833 0.00 0.00 40.62 3.33
4759 4854 3.340814 AGAGGAAGCACTACATTGTGG 57.659 47.619 0.00 0.00 38.31 4.17
4760 4855 2.906389 AGAGGAAGCACTACATTGTGGA 59.094 45.455 7.20 0.00 38.31 4.02
4761 4856 3.327757 AGAGGAAGCACTACATTGTGGAA 59.672 43.478 7.20 0.00 38.31 3.53
4762 4857 4.018960 AGAGGAAGCACTACATTGTGGAAT 60.019 41.667 7.20 0.00 38.31 3.01
4763 4858 4.012374 AGGAAGCACTACATTGTGGAATG 58.988 43.478 7.20 0.00 44.11 2.67
4764 4859 3.129287 GGAAGCACTACATTGTGGAATGG 59.871 47.826 7.20 0.00 43.00 3.16
4765 4860 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
4769 4864 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
4770 4865 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
4771 4866 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
4823 4918 3.496884 TCAAGTGCCGAATGAAGTGTAAC 59.503 43.478 0.00 0.00 0.00 2.50
4938 5033 4.177026 CGAAATGGTTGTGTTGTTTTCCA 58.823 39.130 0.00 0.00 0.00 3.53
4974 5069 4.686191 AATGTTTCCCATTCAAGTGCAA 57.314 36.364 0.00 0.00 39.66 4.08
5008 5103 2.225491 GCCACTGTTTGCTTCGTATCAA 59.775 45.455 0.00 0.00 0.00 2.57
5075 5172 1.549203 GTGGTCCATTGTCCAAGCAT 58.451 50.000 0.00 0.00 35.38 3.79
5155 5252 2.383298 ACTTTGAAATGCACGTCACG 57.617 45.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.437085 TCGATTCTCCTGCTCCACTA 57.563 50.000 0.00 0.00 0.00 2.74
140 147 2.806608 AGTGCAATCTTGTTGCTTGG 57.193 45.000 13.17 0.00 45.13 3.61
301 315 1.524008 AAGGCAACAGCTTTACCGCC 61.524 55.000 0.00 0.00 39.90 6.13
437 454 2.363925 GGGTGGACGTAGCTCCCT 60.364 66.667 0.00 0.00 35.63 4.20
454 471 1.909700 TCTGTTTAAAGGGCAGCCTG 58.090 50.000 12.43 0.00 0.00 4.85
455 472 2.310052 AGATCTGTTTAAAGGGCAGCCT 59.690 45.455 12.43 0.00 0.00 4.58
456 473 2.728007 AGATCTGTTTAAAGGGCAGCC 58.272 47.619 1.26 1.26 0.00 4.85
457 474 4.013050 AGAAGATCTGTTTAAAGGGCAGC 58.987 43.478 0.00 0.00 0.00 5.25
472 489 5.413309 TTGAACAGGAGAAGGAGAAGATC 57.587 43.478 0.00 0.00 0.00 2.75
514 531 7.379797 GCACTTGGACAGAAAAATTACTTCTTC 59.620 37.037 0.95 3.46 30.58 2.87
532 549 2.024176 TCTTCCCACTAGCACTTGGA 57.976 50.000 0.00 0.00 34.46 3.53
533 550 2.039084 ACTTCTTCCCACTAGCACTTGG 59.961 50.000 0.00 0.00 0.00 3.61
754 784 0.535102 ACTGGCGTTTCCCTGTTCTG 60.535 55.000 0.00 0.00 33.84 3.02
755 785 0.535102 CACTGGCGTTTCCCTGTTCT 60.535 55.000 0.00 0.00 35.19 3.01
1044 1079 1.887707 GCGAAGGGAAGGTATGCCG 60.888 63.158 0.00 0.00 45.98 5.69
1060 1095 4.047059 CAGCACAAGGGCAAGGCG 62.047 66.667 0.00 0.00 35.83 5.52
1068 1103 1.170919 AGCAGAACAGCAGCACAAGG 61.171 55.000 0.00 0.00 36.85 3.61
1305 1343 1.814169 GTACTGCAGCCCGGTTAGC 60.814 63.158 15.27 0.84 34.16 3.09
1519 1557 2.041485 TCTCCATTGCTTTCCATGTGGA 59.959 45.455 0.00 0.00 43.73 4.02
2285 2323 6.567687 TGAAATTGAACGAAATAAGCAGGA 57.432 33.333 0.00 0.00 0.00 3.86
2404 2442 9.112725 CAGTTGTGTCAATCTTGATATCCATAA 57.887 33.333 0.00 0.00 39.73 1.90
2962 3000 9.189156 CTTTGGATTCCCATTGAAACTAGAATA 57.811 33.333 0.00 0.00 43.12 1.75
3129 3167 3.368531 GCCTAATTGAGACAAGGAGACGT 60.369 47.826 0.00 0.00 0.00 4.34
3212 3250 3.388024 TGTTTGCTCTGAACTGGAGTAGT 59.612 43.478 0.00 0.00 42.89 2.73
3280 3318 9.059260 AGCTTTCAAAATGTCAGCAAATTTTAT 57.941 25.926 0.00 0.00 34.92 1.40
3282 3320 7.324354 AGCTTTCAAAATGTCAGCAAATTTT 57.676 28.000 0.00 0.00 36.63 1.82
3288 3326 3.058293 CCGTAGCTTTCAAAATGTCAGCA 60.058 43.478 0.00 0.00 32.58 4.41
3310 3348 4.742438 TGTTCGCCTTATCAAAGTTGTC 57.258 40.909 0.00 0.00 0.00 3.18
3512 3550 1.889170 CAAGAAACCTTGAGCTTCCCC 59.111 52.381 0.00 0.00 42.71 4.81
3518 3556 7.988028 AGTAGGAATATACAAGAAACCTTGAGC 59.012 37.037 11.60 0.00 42.71 4.26
3552 3590 1.450531 GCCAATCATCCAGGCTTCCG 61.451 60.000 0.00 0.00 44.92 4.30
3596 3637 0.694771 AGGCCAGTCAAGCAATGAGA 59.305 50.000 5.01 0.00 39.19 3.27
4029 4071 6.680810 CACCTTCAACATTTGCTCTTCATAA 58.319 36.000 0.00 0.00 0.00 1.90
4045 4087 1.795170 GCGGCTTCAAGCACCTTCAA 61.795 55.000 12.53 0.00 44.75 2.69
4098 4140 5.364157 GGAGACTACTTCCATGATAGTTGGT 59.636 44.000 0.00 0.44 35.64 3.67
4137 4179 1.427592 GCATCTCTGGCTCAGCGTTC 61.428 60.000 0.00 0.00 0.00 3.95
4146 4188 1.334243 GCTGATCTTTGCATCTCTGGC 59.666 52.381 0.00 0.00 0.00 4.85
4267 4347 7.663905 TCAGGCTATGTACAAAACAAACTGTAT 59.336 33.333 0.00 0.00 42.70 2.29
4300 4380 6.059787 AGACTTACAAAGATCAGAATGGCT 57.940 37.500 0.00 0.00 36.16 4.75
4482 4567 5.163343 ACGGCTCCTAAAATCTGCTTATACA 60.163 40.000 0.00 0.00 0.00 2.29
4531 4626 7.880195 CACTATATTTTGGAATGGAGGGAGTAG 59.120 40.741 0.00 0.00 0.00 2.57
4532 4627 7.691791 GCACTATATTTTGGAATGGAGGGAGTA 60.692 40.741 0.00 0.00 0.00 2.59
4533 4628 6.605119 CACTATATTTTGGAATGGAGGGAGT 58.395 40.000 0.00 0.00 0.00 3.85
4534 4629 5.474876 GCACTATATTTTGGAATGGAGGGAG 59.525 44.000 0.00 0.00 0.00 4.30
4535 4630 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
4536 4631 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
4537 4632 4.320494 GCGCACTATATTTTGGAATGGAGG 60.320 45.833 0.30 0.00 0.00 4.30
4538 4633 4.516698 AGCGCACTATATTTTGGAATGGAG 59.483 41.667 11.47 0.00 0.00 3.86
4539 4634 4.460263 AGCGCACTATATTTTGGAATGGA 58.540 39.130 11.47 0.00 0.00 3.41
4540 4635 4.611355 CGAGCGCACTATATTTTGGAATGG 60.611 45.833 11.47 0.00 0.00 3.16
4541 4636 4.457810 CGAGCGCACTATATTTTGGAATG 58.542 43.478 11.47 0.00 0.00 2.67
4542 4637 3.058914 GCGAGCGCACTATATTTTGGAAT 60.059 43.478 11.47 0.00 41.49 3.01
4543 4638 2.286833 GCGAGCGCACTATATTTTGGAA 59.713 45.455 11.47 0.00 41.49 3.53
4544 4639 1.864711 GCGAGCGCACTATATTTTGGA 59.135 47.619 11.47 0.00 41.49 3.53
4545 4640 1.397190 CGCGAGCGCACTATATTTTGG 60.397 52.381 11.47 0.00 42.06 3.28
4546 4641 1.924408 CGCGAGCGCACTATATTTTG 58.076 50.000 11.47 0.00 42.06 2.44
4562 4657 4.735132 TTGACCTCGGGAAGCGCG 62.735 66.667 0.00 0.00 41.10 6.86
4563 4658 2.358247 TTTGACCTCGGGAAGCGC 60.358 61.111 0.00 0.00 0.00 5.92
4564 4659 0.602905 AAGTTTGACCTCGGGAAGCG 60.603 55.000 0.00 0.00 0.00 4.68
4565 4660 1.266989 CAAAGTTTGACCTCGGGAAGC 59.733 52.381 10.19 0.00 0.00 3.86
4566 4661 2.846193 TCAAAGTTTGACCTCGGGAAG 58.154 47.619 14.35 0.00 34.08 3.46
4583 4678 9.715121 AGTCTGGTTCGTTAAATTTATAGTCAA 57.285 29.630 0.00 0.00 0.00 3.18
4584 4679 9.146984 CAGTCTGGTTCGTTAAATTTATAGTCA 57.853 33.333 0.00 0.00 0.00 3.41
4585 4680 9.362539 TCAGTCTGGTTCGTTAAATTTATAGTC 57.637 33.333 0.00 0.00 0.00 2.59
4586 4681 9.148104 GTCAGTCTGGTTCGTTAAATTTATAGT 57.852 33.333 0.00 0.00 0.00 2.12
4587 4682 9.367444 AGTCAGTCTGGTTCGTTAAATTTATAG 57.633 33.333 0.00 0.00 0.00 1.31
4588 4683 9.146984 CAGTCAGTCTGGTTCGTTAAATTTATA 57.853 33.333 0.00 0.00 40.23 0.98
4589 4684 7.360946 GCAGTCAGTCTGGTTCGTTAAATTTAT 60.361 37.037 0.00 0.00 43.78 1.40
4590 4685 6.073440 GCAGTCAGTCTGGTTCGTTAAATTTA 60.073 38.462 0.00 0.00 43.78 1.40
4591 4686 5.277828 GCAGTCAGTCTGGTTCGTTAAATTT 60.278 40.000 0.00 0.00 43.78 1.82
4592 4687 4.213482 GCAGTCAGTCTGGTTCGTTAAATT 59.787 41.667 0.00 0.00 43.78 1.82
4593 4688 3.746492 GCAGTCAGTCTGGTTCGTTAAAT 59.254 43.478 0.00 0.00 43.78 1.40
4594 4689 3.128349 GCAGTCAGTCTGGTTCGTTAAA 58.872 45.455 0.00 0.00 43.78 1.52
4595 4690 2.750948 GCAGTCAGTCTGGTTCGTTAA 58.249 47.619 0.00 0.00 43.78 2.01
4596 4691 1.335597 CGCAGTCAGTCTGGTTCGTTA 60.336 52.381 0.00 0.00 43.78 3.18
4597 4692 0.597637 CGCAGTCAGTCTGGTTCGTT 60.598 55.000 0.00 0.00 43.78 3.85
4598 4693 1.007271 CGCAGTCAGTCTGGTTCGT 60.007 57.895 0.00 0.00 43.78 3.85
4599 4694 1.734477 CCGCAGTCAGTCTGGTTCG 60.734 63.158 0.00 0.00 43.78 3.95
4600 4695 2.029844 GCCGCAGTCAGTCTGGTTC 61.030 63.158 0.00 0.00 43.78 3.62
4601 4696 2.031163 GCCGCAGTCAGTCTGGTT 59.969 61.111 0.00 0.00 43.78 3.67
4602 4697 4.363990 CGCCGCAGTCAGTCTGGT 62.364 66.667 0.00 0.00 43.78 4.00
4606 4701 4.803426 CTCCCGCCGCAGTCAGTC 62.803 72.222 0.00 0.00 0.00 3.51
4608 4703 3.589654 TTTCTCCCGCCGCAGTCAG 62.590 63.158 0.00 0.00 0.00 3.51
4609 4704 2.668185 TTTTTCTCCCGCCGCAGTCA 62.668 55.000 0.00 0.00 0.00 3.41
4610 4705 1.912371 CTTTTTCTCCCGCCGCAGTC 61.912 60.000 0.00 0.00 0.00 3.51
4611 4706 1.966451 CTTTTTCTCCCGCCGCAGT 60.966 57.895 0.00 0.00 0.00 4.40
4612 4707 1.515521 AACTTTTTCTCCCGCCGCAG 61.516 55.000 0.00 0.00 0.00 5.18
4613 4708 0.250381 TAACTTTTTCTCCCGCCGCA 60.250 50.000 0.00 0.00 0.00 5.69
4614 4709 0.167470 GTAACTTTTTCTCCCGCCGC 59.833 55.000 0.00 0.00 0.00 6.53
4615 4710 1.515081 TGTAACTTTTTCTCCCGCCG 58.485 50.000 0.00 0.00 0.00 6.46
4616 4711 5.830000 ATTATGTAACTTTTTCTCCCGCC 57.170 39.130 0.00 0.00 0.00 6.13
4617 4712 9.628746 TTTTAATTATGTAACTTTTTCTCCCGC 57.371 29.630 0.00 0.00 0.00 6.13
4641 4736 9.244799 GGTGATTTCGTATTTGAAAGAAGTTTT 57.755 29.630 0.00 0.00 40.86 2.43
4642 4737 7.589954 CGGTGATTTCGTATTTGAAAGAAGTTT 59.410 33.333 0.00 0.00 40.86 2.66
4643 4738 7.041644 TCGGTGATTTCGTATTTGAAAGAAGTT 60.042 33.333 0.00 0.00 40.86 2.66
4644 4739 6.425721 TCGGTGATTTCGTATTTGAAAGAAGT 59.574 34.615 0.00 0.00 40.86 3.01
4645 4740 6.827641 TCGGTGATTTCGTATTTGAAAGAAG 58.172 36.000 0.00 0.00 40.86 2.85
4646 4741 6.788684 TCGGTGATTTCGTATTTGAAAGAA 57.211 33.333 0.00 0.00 40.86 2.52
4647 4742 6.978343 ATCGGTGATTTCGTATTTGAAAGA 57.022 33.333 0.00 0.00 40.86 2.52
4650 4745 9.537192 AGTTATATCGGTGATTTCGTATTTGAA 57.463 29.630 0.00 0.00 0.00 2.69
4651 4746 9.537192 AAGTTATATCGGTGATTTCGTATTTGA 57.463 29.630 0.00 0.00 0.00 2.69
4655 4750 8.280497 GCAAAAGTTATATCGGTGATTTCGTAT 58.720 33.333 0.00 0.00 0.00 3.06
4656 4751 7.493320 AGCAAAAGTTATATCGGTGATTTCGTA 59.507 33.333 0.00 0.00 0.00 3.43
4657 4752 6.315393 AGCAAAAGTTATATCGGTGATTTCGT 59.685 34.615 0.00 0.00 0.00 3.85
4658 4753 6.715464 AGCAAAAGTTATATCGGTGATTTCG 58.285 36.000 0.00 0.00 0.00 3.46
4659 4754 7.132863 GGAGCAAAAGTTATATCGGTGATTTC 58.867 38.462 0.00 0.00 0.00 2.17
4660 4755 6.039382 GGGAGCAAAAGTTATATCGGTGATTT 59.961 38.462 0.00 0.00 0.00 2.17
4661 4756 5.531287 GGGAGCAAAAGTTATATCGGTGATT 59.469 40.000 0.00 0.00 0.00 2.57
4662 4757 5.063880 GGGAGCAAAAGTTATATCGGTGAT 58.936 41.667 0.00 0.00 0.00 3.06
4663 4758 4.448210 GGGAGCAAAAGTTATATCGGTGA 58.552 43.478 0.00 0.00 0.00 4.02
4664 4759 3.247648 CGGGAGCAAAAGTTATATCGGTG 59.752 47.826 0.00 0.00 0.00 4.94
4665 4760 3.463944 CGGGAGCAAAAGTTATATCGGT 58.536 45.455 0.00 0.00 0.00 4.69
4688 4783 5.712217 TTTAACTATCAAGACCGATTGCG 57.288 39.130 0.00 0.00 37.24 4.85
4692 4787 9.847224 ACCATAAATTTAACTATCAAGACCGAT 57.153 29.630 1.21 0.00 0.00 4.18
4693 4788 9.321562 GACCATAAATTTAACTATCAAGACCGA 57.678 33.333 1.21 0.00 0.00 4.69
4694 4789 9.104965 TGACCATAAATTTAACTATCAAGACCG 57.895 33.333 1.21 0.00 0.00 4.79
4704 4799 9.476202 GCTTCAACTTTGACCATAAATTTAACT 57.524 29.630 1.21 0.00 36.83 2.24
4705 4800 9.255304 TGCTTCAACTTTGACCATAAATTTAAC 57.745 29.630 1.21 0.00 36.83 2.01
4706 4801 9.255304 GTGCTTCAACTTTGACCATAAATTTAA 57.745 29.630 1.21 0.00 36.83 1.52
4707 4802 7.593273 CGTGCTTCAACTTTGACCATAAATTTA 59.407 33.333 0.00 0.00 36.83 1.40
4708 4803 6.420604 CGTGCTTCAACTTTGACCATAAATTT 59.579 34.615 0.00 0.00 36.83 1.82
4709 4804 5.920273 CGTGCTTCAACTTTGACCATAAATT 59.080 36.000 0.00 0.00 36.83 1.82
4710 4805 5.460646 CGTGCTTCAACTTTGACCATAAAT 58.539 37.500 0.00 0.00 36.83 1.40
4711 4806 4.261405 CCGTGCTTCAACTTTGACCATAAA 60.261 41.667 0.00 0.00 36.83 1.40
4712 4807 3.252215 CCGTGCTTCAACTTTGACCATAA 59.748 43.478 0.00 0.00 36.83 1.90
4713 4808 2.811431 CCGTGCTTCAACTTTGACCATA 59.189 45.455 0.00 0.00 36.83 2.74
4714 4809 1.608590 CCGTGCTTCAACTTTGACCAT 59.391 47.619 0.00 0.00 36.83 3.55
4715 4810 1.021202 CCGTGCTTCAACTTTGACCA 58.979 50.000 0.00 0.00 36.83 4.02
4716 4811 0.310854 CCCGTGCTTCAACTTTGACC 59.689 55.000 0.00 0.00 36.83 4.02
4717 4812 0.310854 CCCCGTGCTTCAACTTTGAC 59.689 55.000 0.00 0.00 36.83 3.18
4718 4813 0.181587 TCCCCGTGCTTCAACTTTGA 59.818 50.000 0.00 0.00 34.92 2.69
4719 4814 1.247567 ATCCCCGTGCTTCAACTTTG 58.752 50.000 0.00 0.00 0.00 2.77
4720 4815 2.304761 TCTATCCCCGTGCTTCAACTTT 59.695 45.455 0.00 0.00 0.00 2.66
4721 4816 1.906574 TCTATCCCCGTGCTTCAACTT 59.093 47.619 0.00 0.00 0.00 2.66
4722 4817 1.482593 CTCTATCCCCGTGCTTCAACT 59.517 52.381 0.00 0.00 0.00 3.16
4723 4818 1.473434 CCTCTATCCCCGTGCTTCAAC 60.473 57.143 0.00 0.00 0.00 3.18
4724 4819 0.830648 CCTCTATCCCCGTGCTTCAA 59.169 55.000 0.00 0.00 0.00 2.69
4725 4820 0.032515 TCCTCTATCCCCGTGCTTCA 60.033 55.000 0.00 0.00 0.00 3.02
4726 4821 1.069358 CTTCCTCTATCCCCGTGCTTC 59.931 57.143 0.00 0.00 0.00 3.86
4727 4822 1.123928 CTTCCTCTATCCCCGTGCTT 58.876 55.000 0.00 0.00 0.00 3.91
4728 4823 1.403687 GCTTCCTCTATCCCCGTGCT 61.404 60.000 0.00 0.00 0.00 4.40
4729 4824 1.069935 GCTTCCTCTATCCCCGTGC 59.930 63.158 0.00 0.00 0.00 5.34
4730 4825 0.105039 GTGCTTCCTCTATCCCCGTG 59.895 60.000 0.00 0.00 0.00 4.94
4731 4826 0.032017 AGTGCTTCCTCTATCCCCGT 60.032 55.000 0.00 0.00 0.00 5.28
4732 4827 1.614413 GTAGTGCTTCCTCTATCCCCG 59.386 57.143 0.00 0.00 0.00 5.73
4733 4828 2.679082 TGTAGTGCTTCCTCTATCCCC 58.321 52.381 0.00 0.00 0.00 4.81
4734 4829 4.101741 ACAATGTAGTGCTTCCTCTATCCC 59.898 45.833 0.00 0.00 0.00 3.85
4735 4830 5.053145 CACAATGTAGTGCTTCCTCTATCC 58.947 45.833 0.00 0.00 32.04 2.59
4736 4831 5.053145 CCACAATGTAGTGCTTCCTCTATC 58.947 45.833 0.00 0.00 38.18 2.08
4737 4832 4.716784 TCCACAATGTAGTGCTTCCTCTAT 59.283 41.667 0.00 0.00 38.18 1.98
4738 4833 4.093743 TCCACAATGTAGTGCTTCCTCTA 58.906 43.478 0.00 0.00 38.18 2.43
4739 4834 2.906389 TCCACAATGTAGTGCTTCCTCT 59.094 45.455 0.00 0.00 38.18 3.69
4740 4835 3.334583 TCCACAATGTAGTGCTTCCTC 57.665 47.619 0.00 0.00 38.18 3.71
4741 4836 3.788227 TTCCACAATGTAGTGCTTCCT 57.212 42.857 0.00 0.00 38.18 3.36
4742 4837 3.129287 CCATTCCACAATGTAGTGCTTCC 59.871 47.826 0.00 0.00 38.22 3.46
4743 4838 4.009675 TCCATTCCACAATGTAGTGCTTC 58.990 43.478 0.00 0.00 38.22 3.86
4744 4839 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
4745 4840 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
4746 4841 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
4747 4842 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
4748 4843 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
4749 4844 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
4750 4845 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
4751 4846 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
4752 4847 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
4753 4848 3.464828 ACTACTCCCTCCATTCCACAAT 58.535 45.455 0.00 0.00 0.00 2.71
4754 4849 2.915869 ACTACTCCCTCCATTCCACAA 58.084 47.619 0.00 0.00 0.00 3.33
4755 4850 2.642171 ACTACTCCCTCCATTCCACA 57.358 50.000 0.00 0.00 0.00 4.17
4756 4851 5.395611 AGTATACTACTCCCTCCATTCCAC 58.604 45.833 2.75 0.00 32.47 4.02
4757 4852 5.681494 AGTATACTACTCCCTCCATTCCA 57.319 43.478 2.75 0.00 32.47 3.53
4758 4853 6.997942 AAAGTATACTACTCCCTCCATTCC 57.002 41.667 5.65 0.00 38.26 3.01
4759 4854 8.474710 TGTAAAGTATACTACTCCCTCCATTC 57.525 38.462 5.65 0.00 38.26 2.67
4760 4855 8.702819 GTTGTAAAGTATACTACTCCCTCCATT 58.297 37.037 5.65 0.00 38.26 3.16
4761 4856 7.842743 TGTTGTAAAGTATACTACTCCCTCCAT 59.157 37.037 5.65 0.00 38.26 3.41
4762 4857 7.184161 TGTTGTAAAGTATACTACTCCCTCCA 58.816 38.462 5.65 0.00 38.26 3.86
4763 4858 7.651027 TGTTGTAAAGTATACTACTCCCTCC 57.349 40.000 5.65 0.00 38.26 4.30
4764 4859 8.747471 ACTTGTTGTAAAGTATACTACTCCCTC 58.253 37.037 5.65 0.00 38.62 4.30
4765 4860 8.529476 CACTTGTTGTAAAGTATACTACTCCCT 58.471 37.037 5.65 0.00 38.34 4.20
4766 4861 8.309656 ACACTTGTTGTAAAGTATACTACTCCC 58.690 37.037 5.65 0.00 38.34 4.30
4767 4862 9.702494 AACACTTGTTGTAAAGTATACTACTCC 57.298 33.333 5.65 0.00 38.34 3.85
4798 4893 1.531149 ACTTCATTCGGCACTTGAACG 59.469 47.619 0.00 0.00 0.00 3.95
4823 4918 4.677378 CGGTAGTTGCATTAGATTCTCTCG 59.323 45.833 0.00 0.00 0.00 4.04
4871 4966 5.635280 TGCTCATCGAACTTAAGCATATAGC 59.365 40.000 1.29 4.39 46.19 2.97
4887 4982 1.033746 ACTTTGCCCCATGCTCATCG 61.034 55.000 0.00 0.00 42.00 3.84
4890 4985 2.240921 TGTATACTTTGCCCCATGCTCA 59.759 45.455 4.17 0.00 42.00 4.26
4910 5005 3.555139 ACAACACAACCATTTCGCATTTG 59.445 39.130 0.00 0.00 0.00 2.32
4938 5033 5.478332 GGGAAACATTCTCAATCCTTCACTT 59.522 40.000 0.00 0.00 0.00 3.16
4974 5069 0.816825 CAGTGGCAGCACACAGTCTT 60.817 55.000 14.26 0.00 43.72 3.01
5008 5103 0.540365 TTCGGTAACTCACCTCCGGT 60.540 55.000 0.00 0.00 46.19 5.28
5035 5132 2.217620 CGACCAACCAAAAATTTGACGC 59.782 45.455 7.44 0.00 40.55 5.19
5075 5172 6.605194 TCATTCCATTCCATATTTCCGTTCAA 59.395 34.615 0.00 0.00 0.00 2.69
5080 5177 6.882610 TTCTCATTCCATTCCATATTTCCG 57.117 37.500 0.00 0.00 0.00 4.30
5155 5252 0.734889 ATGCCTGTTATGCGTTCTGC 59.265 50.000 0.00 0.00 46.70 4.26


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

AutoCloner maintained by Alex Coulton.