Multiple sequence alignment - TraesCS4D01G275100

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 TraesCS4D01G275100 chr4D 100.000 5197 0 0 1 5197 445503499 445498303 0 9598
1 TraesCS4D01G275100 chr4A 96.425 4532 110 25 1 4505 21624917 21629423 0 7424
2 TraesCS4D01G275100 chr4B 95.563 4553 135 28 1 4540 556076355 556071857 0 7227
3 TraesCS4D01G275100 chr4B 95.861 459 15 2 4742 5197 556071861 556071404 0 739


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 TraesCS4D01G275100 chr4D 445498303 445503499 5196 True 9598 9598 100.000 1 5197 1 chr4D.!!$R1 5196
1 TraesCS4D01G275100 chr4A 21624917 21629423 4506 False 7424 7424 96.425 1 4505 1 chr4A.!!$F1 4504
2 TraesCS4D01G275100 chr4B 556071404 556076355 4951 True 3983 7227 95.712 1 5197 2 chr4B.!!$R1 5196

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
45 46 0.108804 ATCCGCACAAATCTCGTCGT 60.109 50.000 0.0 0.0 0.00 4.34 F
384 393 0.316841 GCCAGGAGATCTAGCCTTCG 59.683 60.000 0.0 0.0 30.41 3.79 F
1125 1142 0.766131 ATGGTCCCGTGGTTGTTACA 59.234 50.000 0.0 0.0 0.00 2.41 F
2864 2886 1.528586 CAGCTTTGTGTGGAAGAGACG 59.471 52.381 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1142 1.056660 TCACGAAAGGGAAAGGAGCT 58.943 50.000 0.00 0.00 43.28 4.09 R
1296 1313 4.478843 CGCTTCATCGGAATCATTCAAT 57.521 40.909 0.00 0.00 31.34 2.57 R
3046 3068 0.031449 GTGACGGCAGCTCTAGGATC 59.969 60.000 0.00 0.00 0.00 3.36 R
4729 4766 0.032540 CATGAGACGGCGATGATCCA 59.967 55.000 16.62 2.67 0.00 3.41 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
45 46 0.108804 ATCCGCACAAATCTCGTCGT 60.109 50.000 0.00 0.00 0.00 4.34
167 168 3.667217 TACGGAAGGGGGAGGACGG 62.667 68.421 0.00 0.00 0.00 4.79
256 258 3.578688 GGCAGAATGTTGTGATTTGGTC 58.421 45.455 0.00 0.00 39.31 4.02
311 318 8.445275 TGCTATTTTCTTGTCTTGTTGTAGAA 57.555 30.769 0.00 0.00 0.00 2.10
312 319 8.559536 TGCTATTTTCTTGTCTTGTTGTAGAAG 58.440 33.333 0.00 0.00 0.00 2.85
313 320 8.774586 GCTATTTTCTTGTCTTGTTGTAGAAGA 58.225 33.333 0.00 0.00 0.00 2.87
328 335 6.531503 TGTAGAAGAAGAATCAGTAGTGGG 57.468 41.667 0.00 0.00 0.00 4.61
338 345 1.082954 AGTAGTGGGCTGATGGGGT 59.917 57.895 0.00 0.00 0.00 4.95
339 346 0.983378 AGTAGTGGGCTGATGGGGTC 60.983 60.000 0.00 0.00 0.00 4.46
340 347 0.983378 GTAGTGGGCTGATGGGGTCT 60.983 60.000 0.00 0.00 0.00 3.85
341 348 0.982852 TAGTGGGCTGATGGGGTCTG 60.983 60.000 0.00 0.00 0.00 3.51
342 349 2.204136 TGGGCTGATGGGGTCTGT 60.204 61.111 0.00 0.00 0.00 3.41
343 350 2.273449 GGGCTGATGGGGTCTGTG 59.727 66.667 0.00 0.00 0.00 3.66
384 393 0.316841 GCCAGGAGATCTAGCCTTCG 59.683 60.000 0.00 0.00 30.41 3.79
450 459 3.430374 GCACAAAGAGGGAGAATAGCGTA 60.430 47.826 0.00 0.00 0.00 4.42
551 561 5.491070 TGGATCACAGAAATTCGAACAGAT 58.509 37.500 0.00 0.00 0.00 2.90
555 565 5.056480 TCACAGAAATTCGAACAGATGTGT 58.944 37.500 23.51 13.37 36.65 3.72
671 686 2.985847 GTGGTGTTGGCCAGCTCC 60.986 66.667 28.14 28.14 42.19 4.70
932 948 5.020132 ACAACAACTATCTCTAGACTGGCT 58.980 41.667 0.00 0.00 0.00 4.75
1035 1052 5.689835 TCAGATGATGAGTACTCAGTAGCT 58.310 41.667 28.29 22.99 43.61 3.32
1125 1142 0.766131 ATGGTCCCGTGGTTGTTACA 59.234 50.000 0.00 0.00 0.00 2.41
1140 1157 3.751518 TGTTACAGCTCCTTTCCCTTTC 58.248 45.455 0.00 0.00 0.00 2.62
1296 1313 3.327464 TCTTGTCAATGATGAGACCACCA 59.673 43.478 0.00 0.00 35.88 4.17
2728 2750 7.742019 AATGCGCTACAAGATAGTTATATCG 57.258 36.000 9.73 0.00 42.34 2.92
2864 2886 1.528586 CAGCTTTGTGTGGAAGAGACG 59.471 52.381 0.00 0.00 0.00 4.18
3172 3194 2.065899 TCCCTGTTCTGTTTGTTGGG 57.934 50.000 0.00 0.00 34.76 4.12
3199 3221 1.959985 GGATGCGATGAGAGAGAAGGA 59.040 52.381 0.00 0.00 0.00 3.36
3328 3350 9.832445 ATTACTCCATATCGTCAACAAGTTAAT 57.168 29.630 0.00 0.00 0.00 1.40
3538 3560 0.179215 CTCGTGCCAAATCGTTGCTC 60.179 55.000 0.00 0.00 33.01 4.26
3556 3578 2.480845 CTCATTATCGTCGGAAACCCC 58.519 52.381 0.00 0.00 0.00 4.95
3585 3607 3.202906 TCACTAAGGTGTGTTGTTGCTC 58.797 45.455 0.00 0.00 43.41 4.26
3587 3609 3.002656 CACTAAGGTGTGTTGTTGCTCTG 59.997 47.826 0.00 0.00 38.54 3.35
3592 3614 1.006086 TGTGTTGTTGCTCTGTCACG 58.994 50.000 0.00 0.00 0.00 4.35
3599 3621 0.318441 TTGCTCTGTCACGCTAGCTT 59.682 50.000 13.93 0.00 35.95 3.74
3602 3624 1.801178 GCTCTGTCACGCTAGCTTTTT 59.199 47.619 13.93 0.00 32.18 1.94
3603 3625 2.993899 GCTCTGTCACGCTAGCTTTTTA 59.006 45.455 13.93 0.00 32.18 1.52
3604 3626 3.619038 GCTCTGTCACGCTAGCTTTTTAT 59.381 43.478 13.93 0.00 32.18 1.40
3605 3627 4.093556 GCTCTGTCACGCTAGCTTTTTATT 59.906 41.667 13.93 0.00 32.18 1.40
3638 3660 2.501261 GCTCTGCTTCCATATCATGCA 58.499 47.619 0.00 0.00 0.00 3.96
3642 3664 3.473625 CTGCTTCCATATCATGCAGTCA 58.526 45.455 0.00 0.00 44.04 3.41
3643 3665 4.072839 CTGCTTCCATATCATGCAGTCAT 58.927 43.478 0.00 0.00 44.04 3.06
3664 3686 2.224992 TGCCCTTATTCTGTTTCTGGCA 60.225 45.455 0.00 0.00 44.77 4.92
3891 3913 1.374758 CCGTCTGACAGTGGCTTCC 60.375 63.158 8.73 0.00 0.00 3.46
3954 3976 1.278127 GGTCCGAAGAATGGTCCAAGA 59.722 52.381 0.00 0.00 0.00 3.02
3986 4008 2.371841 CGGGGACTTCCATTCATATCCA 59.628 50.000 0.00 0.00 37.91 3.41
4056 4078 2.130193 TCGAGGAAGGGGCTACTACTA 58.870 52.381 0.00 0.00 0.00 1.82
4057 4079 2.158696 TCGAGGAAGGGGCTACTACTAC 60.159 54.545 0.00 0.00 0.00 2.73
4058 4080 2.596346 GAGGAAGGGGCTACTACTACC 58.404 57.143 0.00 0.00 0.00 3.18
4102 4127 2.661866 GTGCTCAGCCAACGACGT 60.662 61.111 0.00 0.00 0.00 4.34
4111 4136 2.352686 CAACGACGTCGACGGTGT 60.353 61.111 41.52 31.14 42.42 4.16
4207 4236 0.970937 TGGGAGTGACCGACCAGATC 60.971 60.000 0.00 0.00 40.11 2.75
4424 4461 2.004733 GGTGGACGTGCTAAATACCAC 58.995 52.381 8.99 9.36 44.50 4.16
4450 4487 8.917088 CCCCTGTTTGTTGAATAGAAATATGAT 58.083 33.333 0.00 0.00 0.00 2.45
4534 4571 0.255033 GTGTTAGGGCCTTAGGGGTG 59.745 60.000 13.45 0.00 37.43 4.61
4535 4572 0.178855 TGTTAGGGCCTTAGGGGTGT 60.179 55.000 13.45 0.00 37.43 4.16
4536 4573 0.997363 GTTAGGGCCTTAGGGGTGTT 59.003 55.000 13.45 0.00 37.43 3.32
4537 4574 1.064906 GTTAGGGCCTTAGGGGTGTTC 60.065 57.143 13.45 0.00 37.43 3.18
4538 4575 0.420272 TAGGGCCTTAGGGGTGTTCT 59.580 55.000 13.45 0.00 37.43 3.01
4539 4576 0.914902 AGGGCCTTAGGGGTGTTCTC 60.915 60.000 0.00 0.00 37.43 2.87
4540 4577 0.914902 GGGCCTTAGGGGTGTTCTCT 60.915 60.000 0.84 0.00 37.43 3.10
4541 4578 0.542333 GGCCTTAGGGGTGTTCTCTC 59.458 60.000 0.00 0.00 37.43 3.20
4542 4579 0.542333 GCCTTAGGGGTGTTCTCTCC 59.458 60.000 0.00 0.00 37.43 3.71
4543 4580 1.902141 GCCTTAGGGGTGTTCTCTCCT 60.902 57.143 0.00 0.00 37.43 3.69
4544 4581 1.834263 CCTTAGGGGTGTTCTCTCCTG 59.166 57.143 3.85 0.00 0.00 3.86
4545 4582 1.834263 CTTAGGGGTGTTCTCTCCTGG 59.166 57.143 3.85 0.00 0.00 4.45
4546 4583 0.790993 TAGGGGTGTTCTCTCCTGGT 59.209 55.000 3.85 0.00 0.00 4.00
4547 4584 0.790993 AGGGGTGTTCTCTCCTGGTA 59.209 55.000 0.00 0.00 0.00 3.25
4548 4585 1.366435 AGGGGTGTTCTCTCCTGGTAT 59.634 52.381 0.00 0.00 0.00 2.73
4549 4586 2.197465 GGGGTGTTCTCTCCTGGTATT 58.803 52.381 0.00 0.00 0.00 1.89
4550 4587 2.576648 GGGGTGTTCTCTCCTGGTATTT 59.423 50.000 0.00 0.00 0.00 1.40
4551 4588 3.610911 GGGTGTTCTCTCCTGGTATTTG 58.389 50.000 0.00 0.00 0.00 2.32
4552 4589 3.009143 GGGTGTTCTCTCCTGGTATTTGT 59.991 47.826 0.00 0.00 0.00 2.83
4553 4590 4.224370 GGGTGTTCTCTCCTGGTATTTGTA 59.776 45.833 0.00 0.00 0.00 2.41
4554 4591 5.420409 GGTGTTCTCTCCTGGTATTTGTAG 58.580 45.833 0.00 0.00 0.00 2.74
4555 4592 5.420409 GTGTTCTCTCCTGGTATTTGTAGG 58.580 45.833 0.00 0.00 0.00 3.18
4556 4593 4.469945 TGTTCTCTCCTGGTATTTGTAGGG 59.530 45.833 0.00 0.00 0.00 3.53
4557 4594 4.348020 TCTCTCCTGGTATTTGTAGGGT 57.652 45.455 0.00 0.00 0.00 4.34
4558 4595 4.030913 TCTCTCCTGGTATTTGTAGGGTG 58.969 47.826 0.00 0.00 0.00 4.61
4559 4596 3.112263 TCTCCTGGTATTTGTAGGGTGG 58.888 50.000 0.00 0.00 0.00 4.61
4560 4597 2.844348 CTCCTGGTATTTGTAGGGTGGT 59.156 50.000 0.00 0.00 0.00 4.16
4561 4598 3.261962 TCCTGGTATTTGTAGGGTGGTT 58.738 45.455 0.00 0.00 0.00 3.67
4562 4599 3.264964 TCCTGGTATTTGTAGGGTGGTTC 59.735 47.826 0.00 0.00 0.00 3.62
4563 4600 3.265995 CCTGGTATTTGTAGGGTGGTTCT 59.734 47.826 0.00 0.00 0.00 3.01
4564 4601 4.261801 CTGGTATTTGTAGGGTGGTTCTG 58.738 47.826 0.00 0.00 0.00 3.02
4565 4602 3.653836 TGGTATTTGTAGGGTGGTTCTGT 59.346 43.478 0.00 0.00 0.00 3.41
4566 4603 4.259356 GGTATTTGTAGGGTGGTTCTGTC 58.741 47.826 0.00 0.00 0.00 3.51
4567 4604 2.943036 TTTGTAGGGTGGTTCTGTCC 57.057 50.000 0.00 0.00 0.00 4.02
4568 4605 2.112279 TTGTAGGGTGGTTCTGTCCT 57.888 50.000 0.00 0.00 0.00 3.85
4569 4606 1.348064 TGTAGGGTGGTTCTGTCCTG 58.652 55.000 0.00 0.00 0.00 3.86
4570 4607 1.132977 TGTAGGGTGGTTCTGTCCTGA 60.133 52.381 0.00 0.00 0.00 3.86
4571 4608 1.275573 GTAGGGTGGTTCTGTCCTGAC 59.724 57.143 0.00 0.00 0.00 3.51
4572 4609 0.399949 AGGGTGGTTCTGTCCTGACA 60.400 55.000 0.00 0.00 39.32 3.58
4573 4610 0.250338 GGGTGGTTCTGTCCTGACAC 60.250 60.000 0.00 0.00 36.21 3.67
4574 4611 0.759346 GGTGGTTCTGTCCTGACACT 59.241 55.000 0.00 0.00 36.21 3.55
4575 4612 1.541233 GGTGGTTCTGTCCTGACACTG 60.541 57.143 0.00 0.00 36.21 3.66
4576 4613 1.412710 GTGGTTCTGTCCTGACACTGA 59.587 52.381 0.00 0.00 36.21 3.41
4577 4614 1.412710 TGGTTCTGTCCTGACACTGAC 59.587 52.381 0.00 0.00 36.21 3.51
4578 4615 1.412710 GGTTCTGTCCTGACACTGACA 59.587 52.381 0.00 3.69 39.08 3.58
4584 4621 3.891817 CTGACACTGACAGGGGGT 58.108 61.111 10.07 2.98 0.00 4.95
4585 4622 2.145865 CTGACACTGACAGGGGGTT 58.854 57.895 10.07 0.00 0.00 4.11
4586 4623 0.474184 CTGACACTGACAGGGGGTTT 59.526 55.000 10.07 0.00 0.00 3.27
4587 4624 0.472471 TGACACTGACAGGGGGTTTC 59.528 55.000 10.07 0.00 0.00 2.78
4588 4625 0.472471 GACACTGACAGGGGGTTTCA 59.528 55.000 10.07 0.00 0.00 2.69
4589 4626 1.073923 GACACTGACAGGGGGTTTCAT 59.926 52.381 10.07 0.00 0.00 2.57
4590 4627 1.499007 ACACTGACAGGGGGTTTCATT 59.501 47.619 10.07 0.00 0.00 2.57
4591 4628 2.162681 CACTGACAGGGGGTTTCATTC 58.837 52.381 7.51 0.00 0.00 2.67
4592 4629 1.780309 ACTGACAGGGGGTTTCATTCA 59.220 47.619 7.51 0.00 0.00 2.57
4593 4630 2.379907 ACTGACAGGGGGTTTCATTCAT 59.620 45.455 7.51 0.00 0.00 2.57
4594 4631 3.019564 CTGACAGGGGGTTTCATTCATC 58.980 50.000 0.00 0.00 0.00 2.92
4595 4632 2.649312 TGACAGGGGGTTTCATTCATCT 59.351 45.455 0.00 0.00 0.00 2.90
4596 4633 3.849574 TGACAGGGGGTTTCATTCATCTA 59.150 43.478 0.00 0.00 0.00 1.98
4597 4634 4.478317 TGACAGGGGGTTTCATTCATCTAT 59.522 41.667 0.00 0.00 0.00 1.98
4598 4635 5.053978 ACAGGGGGTTTCATTCATCTATC 57.946 43.478 0.00 0.00 0.00 2.08
4599 4636 4.067896 CAGGGGGTTTCATTCATCTATCG 58.932 47.826 0.00 0.00 0.00 2.92
4600 4637 3.073062 AGGGGGTTTCATTCATCTATCGG 59.927 47.826 0.00 0.00 0.00 4.18
4601 4638 3.181443 GGGGGTTTCATTCATCTATCGGT 60.181 47.826 0.00 0.00 0.00 4.69
4602 4639 3.815401 GGGGTTTCATTCATCTATCGGTG 59.185 47.826 0.00 0.00 0.00 4.94
4603 4640 4.444306 GGGGTTTCATTCATCTATCGGTGA 60.444 45.833 0.00 0.00 0.00 4.02
4604 4641 4.511826 GGGTTTCATTCATCTATCGGTGAC 59.488 45.833 0.00 0.00 0.00 3.67
4605 4642 5.360591 GGTTTCATTCATCTATCGGTGACT 58.639 41.667 0.00 0.00 0.00 3.41
4606 4643 5.235186 GGTTTCATTCATCTATCGGTGACTG 59.765 44.000 0.00 0.00 0.00 3.51
4607 4644 4.590850 TCATTCATCTATCGGTGACTGG 57.409 45.455 0.00 0.00 0.00 4.00
4608 4645 3.321968 TCATTCATCTATCGGTGACTGGG 59.678 47.826 0.00 0.00 0.00 4.45
4609 4646 2.748209 TCATCTATCGGTGACTGGGA 57.252 50.000 0.00 0.00 0.00 4.37
4610 4647 3.244887 TCATCTATCGGTGACTGGGAT 57.755 47.619 0.00 0.00 0.00 3.85
4611 4648 3.576861 TCATCTATCGGTGACTGGGATT 58.423 45.455 0.00 0.00 0.00 3.01
4612 4649 3.574396 TCATCTATCGGTGACTGGGATTC 59.426 47.826 0.00 0.00 0.00 2.52
4613 4650 3.026707 TCTATCGGTGACTGGGATTCA 57.973 47.619 0.00 0.00 0.00 2.57
4614 4651 3.576861 TCTATCGGTGACTGGGATTCAT 58.423 45.455 0.00 0.00 0.00 2.57
4615 4652 2.627515 ATCGGTGACTGGGATTCATG 57.372 50.000 0.00 0.00 0.00 3.07
4616 4653 0.107703 TCGGTGACTGGGATTCATGC 60.108 55.000 0.00 0.00 0.00 4.06
4617 4654 1.431488 CGGTGACTGGGATTCATGCG 61.431 60.000 0.00 0.00 0.00 4.73
4618 4655 1.718757 GGTGACTGGGATTCATGCGC 61.719 60.000 0.00 0.00 0.00 6.09
4619 4656 1.451927 TGACTGGGATTCATGCGCC 60.452 57.895 4.18 0.00 0.00 6.53
4620 4657 1.451927 GACTGGGATTCATGCGCCA 60.452 57.895 4.18 0.00 0.00 5.69
4621 4658 1.001020 ACTGGGATTCATGCGCCAA 60.001 52.632 4.18 0.00 0.00 4.52
4622 4659 1.315257 ACTGGGATTCATGCGCCAAC 61.315 55.000 4.18 0.00 0.00 3.77
4623 4660 1.303970 TGGGATTCATGCGCCAACA 60.304 52.632 4.18 0.00 0.00 3.33
4624 4661 0.683828 TGGGATTCATGCGCCAACAT 60.684 50.000 4.18 0.00 0.00 2.71
4625 4662 1.317613 GGGATTCATGCGCCAACATA 58.682 50.000 4.18 0.00 0.00 2.29
4626 4663 1.267806 GGGATTCATGCGCCAACATAG 59.732 52.381 4.18 0.00 0.00 2.23
4627 4664 2.221169 GGATTCATGCGCCAACATAGA 58.779 47.619 4.18 0.00 0.00 1.98
4628 4665 2.816087 GGATTCATGCGCCAACATAGAT 59.184 45.455 4.18 0.00 0.00 1.98
4629 4666 3.365666 GGATTCATGCGCCAACATAGATG 60.366 47.826 4.18 0.00 0.00 2.90
4630 4667 2.330440 TCATGCGCCAACATAGATGT 57.670 45.000 4.18 0.00 44.20 3.06
4631 4668 1.941975 TCATGCGCCAACATAGATGTG 59.058 47.619 4.18 0.00 41.61 3.21
4632 4669 1.672363 CATGCGCCAACATAGATGTGT 59.328 47.619 4.18 0.00 41.61 3.72
4633 4670 1.085893 TGCGCCAACATAGATGTGTG 58.914 50.000 4.18 0.00 41.61 3.82
4634 4671 0.378257 GCGCCAACATAGATGTGTGG 59.622 55.000 0.00 14.49 41.61 4.17
4635 4672 1.016627 CGCCAACATAGATGTGTGGG 58.983 55.000 17.82 9.13 44.61 4.61
4636 4673 1.406751 CGCCAACATAGATGTGTGGGA 60.407 52.381 7.29 0.00 44.59 4.37
4637 4674 2.292267 GCCAACATAGATGTGTGGGAG 58.708 52.381 7.29 0.61 44.59 4.30
4638 4675 2.092968 GCCAACATAGATGTGTGGGAGA 60.093 50.000 7.29 0.00 44.59 3.71
4639 4676 3.622206 GCCAACATAGATGTGTGGGAGAA 60.622 47.826 7.29 0.00 44.59 2.87
4640 4677 4.588899 CCAACATAGATGTGTGGGAGAAA 58.411 43.478 0.00 0.00 44.59 2.52
4641 4678 4.637534 CCAACATAGATGTGTGGGAGAAAG 59.362 45.833 0.00 0.00 44.59 2.62
4642 4679 5.491070 CAACATAGATGTGTGGGAGAAAGA 58.509 41.667 0.00 0.00 41.61 2.52
4643 4680 5.965033 ACATAGATGTGTGGGAGAAAGAT 57.035 39.130 0.00 0.00 40.03 2.40
4644 4681 6.319048 ACATAGATGTGTGGGAGAAAGATT 57.681 37.500 0.00 0.00 40.03 2.40
4645 4682 6.118170 ACATAGATGTGTGGGAGAAAGATTG 58.882 40.000 0.00 0.00 40.03 2.67
4646 4683 4.647564 AGATGTGTGGGAGAAAGATTGT 57.352 40.909 0.00 0.00 0.00 2.71
4647 4684 4.990526 AGATGTGTGGGAGAAAGATTGTT 58.009 39.130 0.00 0.00 0.00 2.83
4648 4685 5.388654 AGATGTGTGGGAGAAAGATTGTTT 58.611 37.500 0.00 0.00 0.00 2.83
4649 4686 5.835280 AGATGTGTGGGAGAAAGATTGTTTT 59.165 36.000 0.00 0.00 0.00 2.43
4650 4687 7.004086 AGATGTGTGGGAGAAAGATTGTTTTA 58.996 34.615 0.00 0.00 0.00 1.52
4651 4688 7.505585 AGATGTGTGGGAGAAAGATTGTTTTAA 59.494 33.333 0.00 0.00 0.00 1.52
4652 4689 7.411486 TGTGTGGGAGAAAGATTGTTTTAAA 57.589 32.000 0.00 0.00 0.00 1.52
4653 4690 7.841956 TGTGTGGGAGAAAGATTGTTTTAAAA 58.158 30.769 0.00 0.00 0.00 1.52
4654 4691 7.762159 TGTGTGGGAGAAAGATTGTTTTAAAAC 59.238 33.333 21.66 21.66 39.33 2.43
4655 4692 7.979537 GTGTGGGAGAAAGATTGTTTTAAAACT 59.020 33.333 26.76 11.76 39.59 2.66
4656 4693 8.536175 TGTGGGAGAAAGATTGTTTTAAAACTT 58.464 29.630 26.76 16.72 39.59 2.66
4657 4694 8.817100 GTGGGAGAAAGATTGTTTTAAAACTTG 58.183 33.333 26.76 0.00 39.59 3.16
4658 4695 7.494298 TGGGAGAAAGATTGTTTTAAAACTTGC 59.506 33.333 26.76 14.32 39.59 4.01
4659 4696 7.710907 GGGAGAAAGATTGTTTTAAAACTTGCT 59.289 33.333 26.76 18.05 39.59 3.91
4660 4697 9.744468 GGAGAAAGATTGTTTTAAAACTTGCTA 57.256 29.630 26.76 8.06 39.59 3.49
4666 4703 9.233232 AGATTGTTTTAAAACTTGCTAAACTCG 57.767 29.630 26.76 0.00 39.59 4.18
4667 4704 8.920509 ATTGTTTTAAAACTTGCTAAACTCGT 57.079 26.923 26.76 0.48 39.59 4.18
4668 4705 7.728580 TGTTTTAAAACTTGCTAAACTCGTG 57.271 32.000 26.76 0.00 39.59 4.35
4669 4706 6.251801 TGTTTTAAAACTTGCTAAACTCGTGC 59.748 34.615 26.76 0.50 39.59 5.34
4670 4707 5.744666 TTAAAACTTGCTAAACTCGTGCT 57.255 34.783 0.00 0.00 0.00 4.40
4671 4708 4.632538 AAAACTTGCTAAACTCGTGCTT 57.367 36.364 0.00 0.00 0.00 3.91
4672 4709 4.632538 AAACTTGCTAAACTCGTGCTTT 57.367 36.364 0.00 0.00 0.00 3.51
4673 4710 4.632538 AACTTGCTAAACTCGTGCTTTT 57.367 36.364 0.00 0.00 0.00 2.27
4674 4711 4.632538 ACTTGCTAAACTCGTGCTTTTT 57.367 36.364 0.00 0.00 0.00 1.94
4675 4712 4.598062 ACTTGCTAAACTCGTGCTTTTTC 58.402 39.130 0.00 0.00 0.00 2.29
4676 4713 3.619233 TGCTAAACTCGTGCTTTTTCC 57.381 42.857 0.00 0.00 0.00 3.13
4677 4714 2.292292 TGCTAAACTCGTGCTTTTTCCC 59.708 45.455 0.00 0.00 0.00 3.97
4678 4715 2.351447 GCTAAACTCGTGCTTTTTCCCC 60.351 50.000 0.00 0.00 0.00 4.81
4679 4716 1.037493 AAACTCGTGCTTTTTCCCCC 58.963 50.000 0.00 0.00 0.00 5.40
4680 4717 0.106419 AACTCGTGCTTTTTCCCCCA 60.106 50.000 0.00 0.00 0.00 4.96
4681 4718 0.822121 ACTCGTGCTTTTTCCCCCAC 60.822 55.000 0.00 0.00 0.00 4.61
4682 4719 1.524008 CTCGTGCTTTTTCCCCCACC 61.524 60.000 0.00 0.00 0.00 4.61
4683 4720 1.530655 CGTGCTTTTTCCCCCACCT 60.531 57.895 0.00 0.00 0.00 4.00
4684 4721 1.805428 CGTGCTTTTTCCCCCACCTG 61.805 60.000 0.00 0.00 0.00 4.00
4685 4722 0.469144 GTGCTTTTTCCCCCACCTGA 60.469 55.000 0.00 0.00 0.00 3.86
4686 4723 0.263172 TGCTTTTTCCCCCACCTGAA 59.737 50.000 0.00 0.00 0.00 3.02
4687 4724 0.679505 GCTTTTTCCCCCACCTGAAC 59.320 55.000 0.00 0.00 0.00 3.18
4688 4725 2.032151 GCTTTTTCCCCCACCTGAACA 61.032 52.381 0.00 0.00 0.00 3.18
4689 4726 2.393646 CTTTTTCCCCCACCTGAACAA 58.606 47.619 0.00 0.00 0.00 2.83
4690 4727 1.783071 TTTTCCCCCACCTGAACAAC 58.217 50.000 0.00 0.00 0.00 3.32
4691 4728 0.631753 TTTCCCCCACCTGAACAACA 59.368 50.000 0.00 0.00 0.00 3.33
4692 4729 0.631753 TTCCCCCACCTGAACAACAA 59.368 50.000 0.00 0.00 0.00 2.83
4693 4730 0.856982 TCCCCCACCTGAACAACAAT 59.143 50.000 0.00 0.00 0.00 2.71
4694 4731 1.219213 TCCCCCACCTGAACAACAATT 59.781 47.619 0.00 0.00 0.00 2.32
4695 4732 2.046292 CCCCCACCTGAACAACAATTT 58.954 47.619 0.00 0.00 0.00 1.82
4696 4733 2.437651 CCCCCACCTGAACAACAATTTT 59.562 45.455 0.00 0.00 0.00 1.82
4697 4734 3.643792 CCCCCACCTGAACAACAATTTTA 59.356 43.478 0.00 0.00 0.00 1.52
4698 4735 4.262420 CCCCCACCTGAACAACAATTTTAG 60.262 45.833 0.00 0.00 0.00 1.85
4699 4736 4.343814 CCCCACCTGAACAACAATTTTAGT 59.656 41.667 0.00 0.00 0.00 2.24
4700 4737 5.163353 CCCCACCTGAACAACAATTTTAGTT 60.163 40.000 0.00 0.00 0.00 2.24
4713 4750 9.820229 CAACAATTTTAGTTGTATCTTCGCTAA 57.180 29.630 0.00 0.00 41.22 3.09
4726 4763 9.151471 TGTATCTTCGCTAAAGAATATATTGCC 57.849 33.333 1.78 0.00 46.85 4.52
4727 4764 9.372369 GTATCTTCGCTAAAGAATATATTGCCT 57.628 33.333 1.78 0.00 46.85 4.75
4728 4765 8.854614 ATCTTCGCTAAAGAATATATTGCCTT 57.145 30.769 1.78 0.00 46.85 4.35
4729 4766 8.677148 TCTTCGCTAAAGAATATATTGCCTTT 57.323 30.769 1.78 9.53 41.10 3.11
4730 4767 8.559536 TCTTCGCTAAAGAATATATTGCCTTTG 58.440 33.333 16.71 10.68 41.10 2.77
4731 4768 7.202016 TCGCTAAAGAATATATTGCCTTTGG 57.798 36.000 16.71 15.32 32.55 3.28
4732 4769 6.995686 TCGCTAAAGAATATATTGCCTTTGGA 59.004 34.615 18.99 12.23 31.49 3.53
4733 4770 7.665559 TCGCTAAAGAATATATTGCCTTTGGAT 59.334 33.333 18.99 2.59 31.49 3.41
4734 4771 7.965107 CGCTAAAGAATATATTGCCTTTGGATC 59.035 37.037 18.99 7.95 31.49 3.36
4735 4772 8.796475 GCTAAAGAATATATTGCCTTTGGATCA 58.204 33.333 18.99 4.31 31.49 2.92
4738 4775 7.621428 AGAATATATTGCCTTTGGATCATCG 57.379 36.000 1.78 0.00 0.00 3.84
4739 4776 5.824904 ATATATTGCCTTTGGATCATCGC 57.175 39.130 0.00 0.00 0.00 4.58
4740 4777 1.035139 ATTGCCTTTGGATCATCGCC 58.965 50.000 0.00 0.00 0.00 5.54
4748 4785 0.032540 TGGATCATCGCCGTCTCATG 59.967 55.000 0.00 0.00 0.00 3.07
4824 4861 2.101750 TGTGTTTCTACCGAGCAAGTGA 59.898 45.455 0.00 0.00 0.00 3.41
4834 4871 3.004734 ACCGAGCAAGTGAATTTCCTTTG 59.995 43.478 0.00 0.55 0.00 2.77
4860 4897 2.289882 CCATGTGAGCTTTCCAGTCTCA 60.290 50.000 0.00 0.00 33.42 3.27
4871 4908 1.134491 TCCAGTCTCAGCTCATGCATG 60.134 52.381 21.07 21.07 42.74 4.06
4878 4915 0.678684 CAGCTCATGCATGGTGTGGA 60.679 55.000 25.97 5.09 42.74 4.02
4891 4928 0.102300 GTGTGGAGTGGGTTTGCAAC 59.898 55.000 0.00 0.00 0.00 4.17
4956 4993 0.457166 CGCATGTGGCTTTCATGTGG 60.457 55.000 16.97 8.75 44.76 4.17
4962 4999 1.541588 GTGGCTTTCATGTGGGAGAAC 59.458 52.381 0.00 0.00 0.00 3.01
4987 5024 4.941609 CCAGCGGCAATGAGTACT 57.058 55.556 1.45 0.00 0.00 2.73
5087 5124 9.182214 AGTAGCAGTTGATTTGATCATTTGTAT 57.818 29.630 0.00 0.00 39.39 2.29
5124 5161 6.806739 GGACAAACTCTTAATGGCATGTTTAC 59.193 38.462 0.00 4.85 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.375908 GCCACGCTCACCAAGATCA 60.376 57.895 0.00 0.00 0.00 2.92
117 118 9.563748 AAGGTGCGGCTTTTACTAATTATTATA 57.436 29.630 0.00 0.00 0.00 0.98
167 168 4.862823 CCGTCCCCTCCCCTCTCC 62.863 77.778 0.00 0.00 0.00 3.71
236 238 4.232221 CTGACCAAATCACAACATTCTGC 58.768 43.478 0.00 0.00 32.37 4.26
256 258 5.105716 CCGTTACAGACATATATCCCTCCTG 60.106 48.000 0.00 0.00 0.00 3.86
311 318 3.445008 TCAGCCCACTACTGATTCTTCT 58.555 45.455 0.00 0.00 39.21 2.85
312 319 3.895232 TCAGCCCACTACTGATTCTTC 57.105 47.619 0.00 0.00 39.21 2.87
328 335 0.251341 AAACCACAGACCCCATCAGC 60.251 55.000 0.00 0.00 0.00 4.26
338 345 3.720002 ACTAGAAGGGGAAAAACCACAGA 59.280 43.478 0.00 0.00 46.31 3.41
339 346 4.100279 ACTAGAAGGGGAAAAACCACAG 57.900 45.455 0.00 0.00 46.31 3.66
340 347 4.529716 AACTAGAAGGGGAAAAACCACA 57.470 40.909 0.00 0.00 46.31 4.17
341 348 5.417894 CCATAACTAGAAGGGGAAAAACCAC 59.582 44.000 0.00 0.00 43.70 4.16
342 349 5.576128 CCATAACTAGAAGGGGAAAAACCA 58.424 41.667 0.00 0.00 41.20 3.67
343 350 4.401519 GCCATAACTAGAAGGGGAAAAACC 59.598 45.833 0.00 0.00 38.08 3.27
384 393 0.960861 GCAACCCCACTCCTTACAGC 60.961 60.000 0.00 0.00 0.00 4.40
450 459 3.041211 TGGACAGAGGCATTATGCTACT 58.959 45.455 17.13 12.87 44.28 2.57
548 558 3.582647 TCATAGGACCACAACACACATCT 59.417 43.478 0.00 0.00 0.00 2.90
551 561 4.071423 CAATCATAGGACCACAACACACA 58.929 43.478 0.00 0.00 0.00 3.72
555 565 3.609853 GAGCAATCATAGGACCACAACA 58.390 45.455 0.00 0.00 0.00 3.33
671 686 2.328099 GGGTTCAAGCGCTGTGGAG 61.328 63.158 12.58 0.00 0.00 3.86
932 948 5.360714 AGTTCCATTGAGCAGAAACAAGAAA 59.639 36.000 0.00 0.00 0.00 2.52
1035 1052 2.693591 CTCTACTTCCGGCTTATCACCA 59.306 50.000 0.00 0.00 0.00 4.17
1125 1142 1.056660 TCACGAAAGGGAAAGGAGCT 58.943 50.000 0.00 0.00 43.28 4.09
1140 1157 3.000727 AGATTTAGGCTTTCCGTTCACG 58.999 45.455 0.00 0.00 37.47 4.35
1296 1313 4.478843 CGCTTCATCGGAATCATTCAAT 57.521 40.909 0.00 0.00 31.34 2.57
2728 2750 4.080863 AGGGTTGATGAACTCATGTAGGTC 60.081 45.833 0.00 0.00 42.83 3.85
2864 2886 0.593128 CCTGCTAACACAACCACTGC 59.407 55.000 0.00 0.00 0.00 4.40
3046 3068 0.031449 GTGACGGCAGCTCTAGGATC 59.969 60.000 0.00 0.00 0.00 3.36
3058 3080 0.438830 CGTAGAAAAGCTGTGACGGC 59.561 55.000 8.67 8.67 35.73 5.68
3172 3194 0.972134 TCTCATCGCATCCCTGGATC 59.028 55.000 0.00 0.00 31.62 3.36
3199 3221 5.539574 TCTGTTGAACCATGATGGATTGTTT 59.460 36.000 20.11 0.50 40.96 2.83
3328 3350 5.535406 CGTCTCTAGGGCCTTCTTTATCTTA 59.465 44.000 13.45 0.00 0.00 2.10
3538 3560 1.134340 TGGGGGTTTCCGACGATAATG 60.134 52.381 0.00 0.00 36.01 1.90
3611 3633 4.467795 TGATATGGAAGCAGAGCCTATACC 59.532 45.833 0.00 0.00 0.00 2.73
3615 3637 3.307269 GCATGATATGGAAGCAGAGCCTA 60.307 47.826 0.00 0.00 0.00 3.93
3638 3660 4.946157 CAGAAACAGAATAAGGGCATGACT 59.054 41.667 0.00 0.00 0.00 3.41
3639 3661 4.096984 CCAGAAACAGAATAAGGGCATGAC 59.903 45.833 0.00 0.00 0.00 3.06
3640 3662 4.272489 CCAGAAACAGAATAAGGGCATGA 58.728 43.478 0.00 0.00 0.00 3.07
3641 3663 3.181483 GCCAGAAACAGAATAAGGGCATG 60.181 47.826 0.00 0.00 39.88 4.06
3642 3664 3.026694 GCCAGAAACAGAATAAGGGCAT 58.973 45.455 0.00 0.00 39.88 4.40
3643 3665 2.224992 TGCCAGAAACAGAATAAGGGCA 60.225 45.455 0.00 0.00 46.95 5.36
3644 3666 2.446435 TGCCAGAAACAGAATAAGGGC 58.554 47.619 0.00 0.00 40.51 5.19
3645 3667 5.011023 AGTTTTGCCAGAAACAGAATAAGGG 59.989 40.000 9.26 0.00 40.98 3.95
3646 3668 6.089249 AGTTTTGCCAGAAACAGAATAAGG 57.911 37.500 9.26 0.00 40.98 2.69
3647 3669 8.134895 TGTTAGTTTTGCCAGAAACAGAATAAG 58.865 33.333 9.26 0.00 40.98 1.73
3648 3670 8.001881 TGTTAGTTTTGCCAGAAACAGAATAA 57.998 30.769 9.26 0.00 40.98 1.40
3664 3686 5.524646 TGCAGTAGTAACGCTTGTTAGTTTT 59.475 36.000 1.29 0.00 41.05 2.43
3891 3913 3.487202 CCGGCCATTGTCGTGTCG 61.487 66.667 2.24 0.00 38.09 4.35
3923 3945 4.617253 TTCTTCGGACCATTCTTCTTCA 57.383 40.909 0.00 0.00 0.00 3.02
3954 3976 1.128188 AAGTCCCCGTCTGGCTTCTT 61.128 55.000 0.00 0.00 0.00 2.52
3986 4008 1.882989 GAGGTTCTGCTCCTGCGTCT 61.883 60.000 0.00 0.00 43.34 4.18
4081 4103 3.052082 CGTTGGCTGAGCACTGGG 61.052 66.667 6.82 0.00 0.00 4.45
4102 4127 1.829096 TCTTGGACCACACCGTCGA 60.829 57.895 0.00 0.00 33.30 4.20
4111 4136 2.011548 GCACATATGCGTCTTGGACCA 61.012 52.381 1.58 0.00 43.33 4.02
4207 4236 5.205565 CCGACGGAAAAGAAAAGAAAAGAG 58.794 41.667 8.64 0.00 0.00 2.85
4424 4461 8.292444 TCATATTTCTATTCAACAAACAGGGG 57.708 34.615 0.00 0.00 0.00 4.79
4450 4487 7.643579 CAGATGAGAAGACGACTACATTCATA 58.356 38.462 0.00 0.00 0.00 2.15
4453 4490 4.737765 GCAGATGAGAAGACGACTACATTC 59.262 45.833 0.00 0.00 0.00 2.67
4456 4493 3.127721 CAGCAGATGAGAAGACGACTACA 59.872 47.826 0.00 0.00 0.00 2.74
4457 4494 3.488384 CCAGCAGATGAGAAGACGACTAC 60.488 52.174 0.00 0.00 0.00 2.73
4458 4495 2.685388 CCAGCAGATGAGAAGACGACTA 59.315 50.000 0.00 0.00 0.00 2.59
4459 4496 1.476085 CCAGCAGATGAGAAGACGACT 59.524 52.381 0.00 0.00 0.00 4.18
4534 4571 4.470304 ACCCTACAAATACCAGGAGAGAAC 59.530 45.833 0.00 0.00 0.00 3.01
4535 4572 4.469945 CACCCTACAAATACCAGGAGAGAA 59.530 45.833 0.00 0.00 0.00 2.87
4536 4573 4.030913 CACCCTACAAATACCAGGAGAGA 58.969 47.826 0.00 0.00 0.00 3.10
4537 4574 3.134804 CCACCCTACAAATACCAGGAGAG 59.865 52.174 0.00 0.00 0.00 3.20
4538 4575 3.112263 CCACCCTACAAATACCAGGAGA 58.888 50.000 0.00 0.00 0.00 3.71
4539 4576 2.844348 ACCACCCTACAAATACCAGGAG 59.156 50.000 0.00 0.00 0.00 3.69
4540 4577 2.923908 ACCACCCTACAAATACCAGGA 58.076 47.619 0.00 0.00 0.00 3.86
4541 4578 3.265995 AGAACCACCCTACAAATACCAGG 59.734 47.826 0.00 0.00 0.00 4.45
4542 4579 4.261801 CAGAACCACCCTACAAATACCAG 58.738 47.826 0.00 0.00 0.00 4.00
4543 4580 3.653836 ACAGAACCACCCTACAAATACCA 59.346 43.478 0.00 0.00 0.00 3.25
4544 4581 4.259356 GACAGAACCACCCTACAAATACC 58.741 47.826 0.00 0.00 0.00 2.73
4545 4582 4.019591 AGGACAGAACCACCCTACAAATAC 60.020 45.833 0.00 0.00 0.00 1.89
4546 4583 4.019681 CAGGACAGAACCACCCTACAAATA 60.020 45.833 0.00 0.00 0.00 1.40
4547 4584 2.986728 AGGACAGAACCACCCTACAAAT 59.013 45.455 0.00 0.00 0.00 2.32
4548 4585 2.105821 CAGGACAGAACCACCCTACAAA 59.894 50.000 0.00 0.00 0.00 2.83
4549 4586 1.697432 CAGGACAGAACCACCCTACAA 59.303 52.381 0.00 0.00 0.00 2.41
4550 4587 1.132977 TCAGGACAGAACCACCCTACA 60.133 52.381 0.00 0.00 0.00 2.74
4551 4588 1.275573 GTCAGGACAGAACCACCCTAC 59.724 57.143 0.00 0.00 0.00 3.18
4552 4589 1.132977 TGTCAGGACAGAACCACCCTA 60.133 52.381 0.00 0.00 36.21 3.53
4553 4590 0.399949 TGTCAGGACAGAACCACCCT 60.400 55.000 0.00 0.00 36.21 4.34
4554 4591 0.250338 GTGTCAGGACAGAACCACCC 60.250 60.000 1.66 0.00 42.74 4.61
4555 4592 0.759346 AGTGTCAGGACAGAACCACC 59.241 55.000 1.66 0.00 42.74 4.61
4556 4593 1.412710 TCAGTGTCAGGACAGAACCAC 59.587 52.381 1.66 0.00 42.74 4.16
4557 4594 1.412710 GTCAGTGTCAGGACAGAACCA 59.587 52.381 1.66 0.00 42.74 3.67
4558 4595 1.412710 TGTCAGTGTCAGGACAGAACC 59.587 52.381 1.66 0.00 42.74 3.62
4559 4596 2.890808 TGTCAGTGTCAGGACAGAAC 57.109 50.000 1.66 2.62 42.74 3.01
4567 4604 0.474184 AAACCCCCTGTCAGTGTCAG 59.526 55.000 10.07 10.07 0.00 3.51
4568 4605 0.472471 GAAACCCCCTGTCAGTGTCA 59.528 55.000 0.00 0.00 0.00 3.58
4569 4606 0.472471 TGAAACCCCCTGTCAGTGTC 59.528 55.000 0.00 0.00 0.00 3.67
4570 4607 1.149101 ATGAAACCCCCTGTCAGTGT 58.851 50.000 0.00 0.00 0.00 3.55
4571 4608 2.162681 GAATGAAACCCCCTGTCAGTG 58.837 52.381 0.00 0.00 0.00 3.66
4572 4609 1.780309 TGAATGAAACCCCCTGTCAGT 59.220 47.619 0.00 0.00 0.00 3.41
4573 4610 2.584835 TGAATGAAACCCCCTGTCAG 57.415 50.000 0.00 0.00 0.00 3.51
4574 4611 2.649312 AGATGAATGAAACCCCCTGTCA 59.351 45.455 0.00 0.00 0.00 3.58
4575 4612 3.372440 AGATGAATGAAACCCCCTGTC 57.628 47.619 0.00 0.00 0.00 3.51
4576 4613 4.444876 CGATAGATGAATGAAACCCCCTGT 60.445 45.833 0.00 0.00 39.76 4.00
4577 4614 4.067896 CGATAGATGAATGAAACCCCCTG 58.932 47.826 0.00 0.00 39.76 4.45
4578 4615 3.073062 CCGATAGATGAATGAAACCCCCT 59.927 47.826 0.00 0.00 39.76 4.79
4579 4616 3.181443 ACCGATAGATGAATGAAACCCCC 60.181 47.826 0.00 0.00 39.76 5.40
4580 4617 3.815401 CACCGATAGATGAATGAAACCCC 59.185 47.826 0.00 0.00 39.76 4.95
4581 4618 4.511826 GTCACCGATAGATGAATGAAACCC 59.488 45.833 0.00 0.00 43.06 4.11
4582 4619 5.360591 AGTCACCGATAGATGAATGAAACC 58.639 41.667 0.00 0.00 43.06 3.27
4588 4625 3.576861 TCCCAGTCACCGATAGATGAAT 58.423 45.455 0.00 0.00 43.06 2.57
4589 4626 3.026707 TCCCAGTCACCGATAGATGAA 57.973 47.619 0.00 0.00 43.06 2.57
4590 4627 2.748209 TCCCAGTCACCGATAGATGA 57.252 50.000 0.00 0.00 35.07 2.92
4591 4628 3.321968 TGAATCCCAGTCACCGATAGATG 59.678 47.826 0.00 0.00 39.76 2.90
4592 4629 3.576861 TGAATCCCAGTCACCGATAGAT 58.423 45.455 0.00 0.00 39.76 1.98
4593 4630 3.026707 TGAATCCCAGTCACCGATAGA 57.973 47.619 0.00 0.00 39.76 1.98
4594 4631 3.657634 CATGAATCCCAGTCACCGATAG 58.342 50.000 0.00 0.00 0.00 2.08
4595 4632 2.224281 GCATGAATCCCAGTCACCGATA 60.224 50.000 0.00 0.00 0.00 2.92
4596 4633 1.475751 GCATGAATCCCAGTCACCGAT 60.476 52.381 0.00 0.00 0.00 4.18
4597 4634 0.107703 GCATGAATCCCAGTCACCGA 60.108 55.000 0.00 0.00 0.00 4.69
4598 4635 1.431488 CGCATGAATCCCAGTCACCG 61.431 60.000 0.00 0.00 0.00 4.94
4599 4636 1.718757 GCGCATGAATCCCAGTCACC 61.719 60.000 0.30 0.00 0.00 4.02
4600 4637 1.718757 GGCGCATGAATCCCAGTCAC 61.719 60.000 10.83 0.00 0.00 3.67
4601 4638 1.451927 GGCGCATGAATCCCAGTCA 60.452 57.895 10.83 0.00 0.00 3.41
4602 4639 1.031571 TTGGCGCATGAATCCCAGTC 61.032 55.000 10.83 0.00 0.00 3.51
4603 4640 1.001020 TTGGCGCATGAATCCCAGT 60.001 52.632 10.83 0.00 0.00 4.00
4604 4641 1.314534 TGTTGGCGCATGAATCCCAG 61.315 55.000 10.83 0.00 0.00 4.45
4605 4642 0.683828 ATGTTGGCGCATGAATCCCA 60.684 50.000 10.83 0.00 0.00 4.37
4606 4643 1.267806 CTATGTTGGCGCATGAATCCC 59.732 52.381 10.83 0.00 0.00 3.85
4607 4644 2.221169 TCTATGTTGGCGCATGAATCC 58.779 47.619 10.83 0.00 0.00 3.01
4608 4645 3.251729 ACATCTATGTTGGCGCATGAATC 59.748 43.478 10.83 0.00 37.90 2.52
4609 4646 3.004002 CACATCTATGTTGGCGCATGAAT 59.996 43.478 10.83 0.00 39.39 2.57
4610 4647 2.355444 CACATCTATGTTGGCGCATGAA 59.645 45.455 10.83 0.00 39.39 2.57
4611 4648 1.941975 CACATCTATGTTGGCGCATGA 59.058 47.619 10.83 0.00 39.39 3.07
4612 4649 1.672363 ACACATCTATGTTGGCGCATG 59.328 47.619 10.83 3.90 39.39 4.06
4613 4650 1.672363 CACACATCTATGTTGGCGCAT 59.328 47.619 10.83 0.00 39.39 4.73
4614 4651 1.085893 CACACATCTATGTTGGCGCA 58.914 50.000 10.83 0.00 39.39 6.09
4615 4652 0.378257 CCACACATCTATGTTGGCGC 59.622 55.000 0.00 0.00 39.39 6.53
4616 4653 1.016627 CCCACACATCTATGTTGGCG 58.983 55.000 14.05 7.76 39.39 5.69
4617 4654 2.092968 TCTCCCACACATCTATGTTGGC 60.093 50.000 14.05 0.00 39.39 4.52
4618 4655 3.912496 TCTCCCACACATCTATGTTGG 57.088 47.619 13.16 13.16 39.39 3.77
4619 4656 5.491070 TCTTTCTCCCACACATCTATGTTG 58.509 41.667 0.00 0.00 39.39 3.33
4620 4657 5.762179 TCTTTCTCCCACACATCTATGTT 57.238 39.130 0.00 0.00 39.39 2.71
4621 4658 5.965033 ATCTTTCTCCCACACATCTATGT 57.035 39.130 0.00 0.00 42.84 2.29
4622 4659 6.118170 ACAATCTTTCTCCCACACATCTATG 58.882 40.000 0.00 0.00 0.00 2.23
4623 4660 6.319048 ACAATCTTTCTCCCACACATCTAT 57.681 37.500 0.00 0.00 0.00 1.98
4624 4661 5.762179 ACAATCTTTCTCCCACACATCTA 57.238 39.130 0.00 0.00 0.00 1.98
4625 4662 4.647564 ACAATCTTTCTCCCACACATCT 57.352 40.909 0.00 0.00 0.00 2.90
4626 4663 5.712152 AAACAATCTTTCTCCCACACATC 57.288 39.130 0.00 0.00 0.00 3.06
4627 4664 7.595819 TTAAAACAATCTTTCTCCCACACAT 57.404 32.000 0.00 0.00 0.00 3.21
4628 4665 7.411486 TTTAAAACAATCTTTCTCCCACACA 57.589 32.000 0.00 0.00 0.00 3.72
4629 4666 7.979537 AGTTTTAAAACAATCTTTCTCCCACAC 59.020 33.333 28.03 0.57 41.30 3.82
4630 4667 8.073467 AGTTTTAAAACAATCTTTCTCCCACA 57.927 30.769 28.03 0.00 41.30 4.17
4631 4668 8.817100 CAAGTTTTAAAACAATCTTTCTCCCAC 58.183 33.333 28.03 1.25 41.30 4.61
4632 4669 7.494298 GCAAGTTTTAAAACAATCTTTCTCCCA 59.506 33.333 28.03 0.00 41.30 4.37
4633 4670 7.710907 AGCAAGTTTTAAAACAATCTTTCTCCC 59.289 33.333 28.03 1.72 41.30 4.30
4634 4671 8.648557 AGCAAGTTTTAAAACAATCTTTCTCC 57.351 30.769 28.03 8.14 41.30 3.71
4640 4677 9.233232 CGAGTTTAGCAAGTTTTAAAACAATCT 57.767 29.630 28.03 21.84 41.30 2.40
4641 4678 9.016623 ACGAGTTTAGCAAGTTTTAAAACAATC 57.983 29.630 28.03 17.21 41.30 2.67
4642 4679 8.803799 CACGAGTTTAGCAAGTTTTAAAACAAT 58.196 29.630 28.03 16.22 41.30 2.71
4643 4680 7.201367 GCACGAGTTTAGCAAGTTTTAAAACAA 60.201 33.333 28.03 13.56 41.30 2.83
4644 4681 6.251801 GCACGAGTTTAGCAAGTTTTAAAACA 59.748 34.615 28.03 8.60 41.30 2.83
4645 4682 6.471198 AGCACGAGTTTAGCAAGTTTTAAAAC 59.529 34.615 21.06 21.06 39.17 2.43
4646 4683 6.557110 AGCACGAGTTTAGCAAGTTTTAAAA 58.443 32.000 0.00 0.00 0.00 1.52
4647 4684 6.126568 AGCACGAGTTTAGCAAGTTTTAAA 57.873 33.333 0.00 0.00 0.00 1.52
4648 4685 5.744666 AGCACGAGTTTAGCAAGTTTTAA 57.255 34.783 0.00 0.00 0.00 1.52
4649 4686 5.744666 AAGCACGAGTTTAGCAAGTTTTA 57.255 34.783 0.00 0.00 0.00 1.52
4650 4687 4.632538 AAGCACGAGTTTAGCAAGTTTT 57.367 36.364 0.00 0.00 0.00 2.43
4651 4688 4.632538 AAAGCACGAGTTTAGCAAGTTT 57.367 36.364 0.00 0.00 0.00 2.66
4652 4689 4.632538 AAAAGCACGAGTTTAGCAAGTT 57.367 36.364 0.00 0.00 0.00 2.66
4653 4690 4.497507 GGAAAAAGCACGAGTTTAGCAAGT 60.498 41.667 0.00 0.00 0.00 3.16
4654 4691 3.975035 GGAAAAAGCACGAGTTTAGCAAG 59.025 43.478 0.00 0.00 0.00 4.01
4655 4692 3.243267 GGGAAAAAGCACGAGTTTAGCAA 60.243 43.478 0.00 0.00 0.00 3.91
4656 4693 2.292292 GGGAAAAAGCACGAGTTTAGCA 59.708 45.455 0.00 0.00 0.00 3.49
4657 4694 2.351447 GGGGAAAAAGCACGAGTTTAGC 60.351 50.000 0.00 0.00 0.00 3.09
4658 4695 2.228103 GGGGGAAAAAGCACGAGTTTAG 59.772 50.000 0.00 0.00 0.00 1.85
4659 4696 2.232399 GGGGGAAAAAGCACGAGTTTA 58.768 47.619 0.00 0.00 0.00 2.01
4660 4697 1.037493 GGGGGAAAAAGCACGAGTTT 58.963 50.000 0.00 0.00 0.00 2.66
4661 4698 0.106419 TGGGGGAAAAAGCACGAGTT 60.106 50.000 0.00 0.00 0.00 3.01
4662 4699 0.822121 GTGGGGGAAAAAGCACGAGT 60.822 55.000 0.00 0.00 0.00 4.18
4663 4700 1.524008 GGTGGGGGAAAAAGCACGAG 61.524 60.000 0.00 0.00 0.00 4.18
4664 4701 1.529713 GGTGGGGGAAAAAGCACGA 60.530 57.895 0.00 0.00 0.00 4.35
4665 4702 1.530655 AGGTGGGGGAAAAAGCACG 60.531 57.895 0.00 0.00 0.00 5.34
4666 4703 0.469144 TCAGGTGGGGGAAAAAGCAC 60.469 55.000 0.00 0.00 0.00 4.40
4667 4704 0.263172 TTCAGGTGGGGGAAAAAGCA 59.737 50.000 0.00 0.00 0.00 3.91
4668 4705 0.679505 GTTCAGGTGGGGGAAAAAGC 59.320 55.000 0.00 0.00 0.00 3.51
4669 4706 2.080654 TGTTCAGGTGGGGGAAAAAG 57.919 50.000 0.00 0.00 0.00 2.27
4670 4707 2.112190 GTTGTTCAGGTGGGGGAAAAA 58.888 47.619 0.00 0.00 0.00 1.94
4671 4708 1.007238 TGTTGTTCAGGTGGGGGAAAA 59.993 47.619 0.00 0.00 0.00 2.29
4672 4709 0.631753 TGTTGTTCAGGTGGGGGAAA 59.368 50.000 0.00 0.00 0.00 3.13
4673 4710 0.631753 TTGTTGTTCAGGTGGGGGAA 59.368 50.000 0.00 0.00 0.00 3.97
4674 4711 0.856982 ATTGTTGTTCAGGTGGGGGA 59.143 50.000 0.00 0.00 0.00 4.81
4675 4712 1.715785 AATTGTTGTTCAGGTGGGGG 58.284 50.000 0.00 0.00 0.00 5.40
4676 4713 3.836365 AAAATTGTTGTTCAGGTGGGG 57.164 42.857 0.00 0.00 0.00 4.96
4677 4714 5.529581 ACTAAAATTGTTGTTCAGGTGGG 57.470 39.130 0.00 0.00 0.00 4.61
4678 4715 6.826893 CAACTAAAATTGTTGTTCAGGTGG 57.173 37.500 0.00 0.00 39.69 4.61
4700 4737 9.151471 GGCAATATATTCTTTAGCGAAGATACA 57.849 33.333 6.44 0.00 43.65 2.29
4701 4738 9.372369 AGGCAATATATTCTTTAGCGAAGATAC 57.628 33.333 6.44 0.00 43.65 2.24
4702 4739 9.944376 AAGGCAATATATTCTTTAGCGAAGATA 57.056 29.630 6.44 0.00 43.65 1.98
4703 4740 8.854614 AAGGCAATATATTCTTTAGCGAAGAT 57.145 30.769 6.44 0.00 43.65 2.40
4704 4741 8.559536 CAAAGGCAATATATTCTTTAGCGAAGA 58.440 33.333 10.30 1.99 42.56 2.87
4705 4742 7.805071 CCAAAGGCAATATATTCTTTAGCGAAG 59.195 37.037 10.30 0.00 36.67 3.79
4706 4743 7.500892 TCCAAAGGCAATATATTCTTTAGCGAA 59.499 33.333 10.30 0.00 0.00 4.70
4707 4744 6.995686 TCCAAAGGCAATATATTCTTTAGCGA 59.004 34.615 10.30 5.90 0.00 4.93
4708 4745 7.202016 TCCAAAGGCAATATATTCTTTAGCG 57.798 36.000 10.30 4.32 0.00 4.26
4709 4746 8.796475 TGATCCAAAGGCAATATATTCTTTAGC 58.204 33.333 10.30 4.59 0.00 3.09
4712 4749 8.517878 CGATGATCCAAAGGCAATATATTCTTT 58.482 33.333 6.40 6.40 0.00 2.52
4713 4750 7.362401 GCGATGATCCAAAGGCAATATATTCTT 60.362 37.037 0.00 0.00 0.00 2.52
4714 4751 6.094603 GCGATGATCCAAAGGCAATATATTCT 59.905 38.462 0.00 0.00 0.00 2.40
4715 4752 6.261118 GCGATGATCCAAAGGCAATATATTC 58.739 40.000 0.00 0.00 0.00 1.75
4716 4753 5.126061 GGCGATGATCCAAAGGCAATATATT 59.874 40.000 0.00 0.00 0.00 1.28
4717 4754 4.641989 GGCGATGATCCAAAGGCAATATAT 59.358 41.667 0.00 0.00 0.00 0.86
4718 4755 4.009675 GGCGATGATCCAAAGGCAATATA 58.990 43.478 0.00 0.00 0.00 0.86
4719 4756 2.821969 GGCGATGATCCAAAGGCAATAT 59.178 45.455 0.00 0.00 0.00 1.28
4720 4757 2.229792 GGCGATGATCCAAAGGCAATA 58.770 47.619 0.00 0.00 0.00 1.90
4721 4758 1.035139 GGCGATGATCCAAAGGCAAT 58.965 50.000 0.00 0.00 0.00 3.56
4722 4759 1.375853 CGGCGATGATCCAAAGGCAA 61.376 55.000 0.00 0.00 0.00 4.52
4723 4760 1.819208 CGGCGATGATCCAAAGGCA 60.819 57.895 0.00 0.00 0.00 4.75
4724 4761 1.776034 GACGGCGATGATCCAAAGGC 61.776 60.000 16.62 0.00 0.00 4.35
4725 4762 0.179073 AGACGGCGATGATCCAAAGG 60.179 55.000 16.62 0.00 0.00 3.11
4726 4763 1.212616 GAGACGGCGATGATCCAAAG 58.787 55.000 16.62 0.00 0.00 2.77
4727 4764 0.534873 TGAGACGGCGATGATCCAAA 59.465 50.000 16.62 0.00 0.00 3.28
4728 4765 0.752658 ATGAGACGGCGATGATCCAA 59.247 50.000 16.62 0.00 0.00 3.53
4729 4766 0.032540 CATGAGACGGCGATGATCCA 59.967 55.000 16.62 2.67 0.00 3.41
4730 4767 1.287730 GCATGAGACGGCGATGATCC 61.288 60.000 16.62 0.00 0.00 3.36
4731 4768 0.319383 AGCATGAGACGGCGATGATC 60.319 55.000 16.62 0.00 34.54 2.92
4732 4769 0.105593 AAGCATGAGACGGCGATGAT 59.894 50.000 16.62 1.75 34.54 2.45
4733 4770 0.807275 CAAGCATGAGACGGCGATGA 60.807 55.000 16.62 0.00 34.54 2.92
4734 4771 0.807275 TCAAGCATGAGACGGCGATG 60.807 55.000 16.62 8.06 34.54 3.84
4735 4772 0.108186 TTCAAGCATGAGACGGCGAT 60.108 50.000 16.62 0.11 36.78 4.58
4736 4773 0.320334 TTTCAAGCATGAGACGGCGA 60.320 50.000 16.62 0.00 36.78 5.54
4737 4774 0.729116 ATTTCAAGCATGAGACGGCG 59.271 50.000 4.80 4.80 36.78 6.46
4738 4775 2.012673 AGATTTCAAGCATGAGACGGC 58.987 47.619 0.00 0.00 36.78 5.68
4739 4776 4.269603 CAGTAGATTTCAAGCATGAGACGG 59.730 45.833 0.00 0.00 36.78 4.79
4740 4777 4.260132 GCAGTAGATTTCAAGCATGAGACG 60.260 45.833 0.00 0.00 36.78 4.18
4748 4785 3.726190 GCTTCGTGCAGTAGATTTCAAGC 60.726 47.826 0.00 0.00 42.31 4.01
4824 4861 0.249955 CATGGCCGGCAAAGGAAATT 59.750 50.000 30.85 0.00 0.00 1.82
4834 4871 3.056313 GAAAGCTCACATGGCCGGC 62.056 63.158 21.18 21.18 0.00 6.13
4860 4897 0.393944 CTCCACACCATGCATGAGCT 60.394 55.000 28.31 6.96 42.74 4.09
4871 4908 1.040339 TTGCAAACCCACTCCACACC 61.040 55.000 0.00 0.00 0.00 4.16
4912 4949 0.978146 CCTGTCCTCCTCCGGTTCAT 60.978 60.000 0.00 0.00 0.00 2.57
4956 4993 0.737715 CGCTGGCTGTACTGTTCTCC 60.738 60.000 1.46 0.00 0.00 3.71
4987 5024 2.032528 CAGCCCAAGTTCTGCCGA 59.967 61.111 0.00 0.00 0.00 5.54
5087 5124 3.882888 AGAGTTTGTCCGAAGAATGCAAA 59.117 39.130 0.00 0.00 0.00 3.68
5124 5161 5.051816 AGAGGCAAATGTTGTTTCAACATG 58.948 37.500 22.81 16.22 40.43 3.21
5127 5164 6.421377 AAAAGAGGCAAATGTTGTTTCAAC 57.579 33.333 5.78 5.78 0.00 3.18
5163 5203 7.284489 AGTTTGAACAAGGCAAATACTGTTCTA 59.716 33.333 13.23 4.99 37.54 2.10


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

AutoCloner maintained by Alex Coulton.