Multiple sequence alignment - TraesCS5B01G272700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G272700 chr5B 100.000 5876 0 0 1 5876 458151986 458146111 0.000000e+00 10852.0
1 TraesCS5B01G272700 chr5B 98.561 139 2 0 3536 3674 458148391 458148253 4.550000e-61 246.0
2 TraesCS5B01G272700 chr5B 98.561 139 2 0 3596 3734 458148451 458148313 4.550000e-61 246.0
3 TraesCS5B01G272700 chr5D 96.701 3637 73 14 1 3614 381917293 381913681 0.000000e+00 6008.0
4 TraesCS5B01G272700 chr5D 92.956 2229 93 30 3656 5871 381913759 381911582 0.000000e+00 3188.0
5 TraesCS5B01G272700 chr5D 95.918 49 2 0 3536 3584 381913729 381913681 4.880000e-11 80.5
6 TraesCS5B01G272700 chr5A 92.626 3282 146 36 344 3584 482125519 482122293 0.000000e+00 4632.0
7 TraesCS5B01G272700 chr5A 91.897 1086 45 12 4316 5397 482121527 482120481 0.000000e+00 1478.0
8 TraesCS5B01G272700 chr5A 92.073 656 29 8 3687 4319 482122340 482121685 0.000000e+00 902.0
9 TraesCS5B01G272700 chr5A 90.947 475 34 8 5399 5871 482120320 482119853 1.070000e-176 630.0
10 TraesCS5B01G272700 chr5A 95.143 350 10 4 1 343 482125958 482125609 4.000000e-151 545.0
11 TraesCS5B01G272700 chr5A 92.982 57 3 1 2794 2850 15849891 15849946 1.360000e-11 82.4
12 TraesCS5B01G272700 chr5A 92.727 55 4 0 2802 2856 624795511 624795565 4.880000e-11 80.5
13 TraesCS5B01G272700 chrUn 96.364 55 2 0 2802 2856 331535929 331535875 2.260000e-14 91.6
14 TraesCS5B01G272700 chrUn 96.364 55 2 0 2802 2856 331539266 331539320 2.260000e-14 91.6
15 TraesCS5B01G272700 chrUn 96.364 55 2 0 2802 2856 413738608 413738554 2.260000e-14 91.6
16 TraesCS5B01G272700 chr2A 94.545 55 3 0 2802 2856 29369269 29369215 1.050000e-12 86.1
17 TraesCS5B01G272700 chr2B 95.745 47 2 0 2801 2847 663781253 663781299 6.310000e-10 76.8


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 TraesCS5B01G272700 chr5B 458146111 458151986 5875 True 3781.333333 10852 99.040667 1 5876 3 chr5B.!!$R1 5875
1 TraesCS5B01G272700 chr5D 381911582 381917293 5711 True 3092.166667 6008 95.191667 1 5871 3 chr5D.!!$R1 5870
2 TraesCS5B01G272700 chr5A 482119853 482125958 6105 True 1637.400000 4632 92.537200 1 5871 5 chr5A.!!$R1 5870

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
459 563 0.238289 CTTGGGTTAGCAAGTGCACG 59.762 55.000 12.01 0.00 45.16 5.34 F
1207 1314 1.471119 ATCAGCTGCTTCCAATGTGG 58.529 50.000 9.47 0.00 39.43 4.17 F
2160 2288 0.532640 GTTTTGCCAGCCCCTTGTTG 60.533 55.000 0.00 0.00 0.00 3.33 F
2220 2348 0.839946 AGGTTTCAGTGCTGTCCTGT 59.160 50.000 10.42 0.00 0.00 4.00 F
3637 3788 1.562475 TGCTGTTAGTAATGGGACCCC 59.438 52.381 8.45 2.69 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2033 1.166531 AGTTCTGCACCGCCAAAGAC 61.167 55.000 0.00 0.0 0.00 3.01 R
2461 2602 0.181587 TTTTCCACCGCCTTCTGTCA 59.818 50.000 0.00 0.0 0.00 3.58 R
3930 4104 0.040058 TCCCTTCCGTAGCACTACCA 59.960 55.000 2.31 0.0 32.61 3.25 R
4042 4224 5.097529 TGAGTCGCACGTAGTAATTTTAGG 58.902 41.667 0.00 0.0 41.61 2.69 R
5510 6018 0.039256 TGTTTTGCTGCAGAATCGCC 60.039 50.000 20.43 0.0 0.00 5.54 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 6.500684 TGGAAGTGTGCAGAAAAATATCTC 57.499 37.500 0.00 0.00 0.00 2.75
217 222 4.201861 GCTGAGGCTTAAAGTTACTGCATC 60.202 45.833 1.08 1.08 35.41 3.91
366 463 5.531287 CGGAGGGAGTATTATTTTCCTTTGG 59.469 44.000 0.00 0.00 0.00 3.28
409 506 6.831353 TGGAACATAATGTACTATTTGGGTGG 59.169 38.462 0.00 0.00 0.00 4.61
453 557 6.817765 TTAGATCAAACTTGGGTTAGCAAG 57.182 37.500 0.00 0.00 34.90 4.01
459 563 0.238289 CTTGGGTTAGCAAGTGCACG 59.762 55.000 12.01 0.00 45.16 5.34
500 604 7.970384 TGATTAGTAAACGATCATGTTTCACC 58.030 34.615 2.47 0.00 40.99 4.02
722 826 7.141758 ACATGATCATTATGTACTTGGGAGT 57.858 36.000 5.16 0.00 37.02 3.85
1091 1198 4.154737 CCAATTTGAGAATGACGAGCTTCA 59.845 41.667 0.00 0.00 0.00 3.02
1207 1314 1.471119 ATCAGCTGCTTCCAATGTGG 58.529 50.000 9.47 0.00 39.43 4.17
1275 1382 3.064900 AGGTGCTTCAAATGGAGACTC 57.935 47.619 0.00 0.00 0.00 3.36
1573 1680 4.340381 GGCTATTTCTGCAAGGACATTGAT 59.660 41.667 3.57 0.00 41.83 2.57
1610 1719 7.634649 GCCTGCCACTTTATCTCTATATGCTAT 60.635 40.741 0.00 0.00 0.00 2.97
1760 1869 7.042335 AGTTCAAGTCGGGAATATAGAAACTG 58.958 38.462 0.00 0.00 0.00 3.16
1906 2033 6.771076 TGTGCTAGTTTAAATCACATTAGCG 58.229 36.000 9.79 0.00 35.90 4.26
1997 2124 4.102524 AGGAAATATGGTCGTAGGCATGAA 59.897 41.667 0.00 0.00 0.00 2.57
2160 2288 0.532640 GTTTTGCCAGCCCCTTGTTG 60.533 55.000 0.00 0.00 0.00 3.33
2220 2348 0.839946 AGGTTTCAGTGCTGTCCTGT 59.160 50.000 10.42 0.00 0.00 4.00
2252 2380 9.322773 TGATTCTATTCTGAAGCAAGTTCATAG 57.677 33.333 0.00 0.00 44.44 2.23
2293 2421 3.998913 TGATGGCCTATCAGTTTGACA 57.001 42.857 3.32 0.00 40.82 3.58
2294 2422 3.609853 TGATGGCCTATCAGTTTGACAC 58.390 45.455 3.32 0.00 40.82 3.67
2295 2423 3.264193 TGATGGCCTATCAGTTTGACACT 59.736 43.478 3.32 0.00 40.82 3.55
2296 2424 3.788227 TGGCCTATCAGTTTGACACTT 57.212 42.857 3.32 0.00 30.92 3.16
2297 2425 3.674997 TGGCCTATCAGTTTGACACTTC 58.325 45.455 3.32 0.00 30.92 3.01
2298 2426 3.010420 GGCCTATCAGTTTGACACTTCC 58.990 50.000 0.00 0.00 30.92 3.46
2299 2427 3.559171 GGCCTATCAGTTTGACACTTCCA 60.559 47.826 0.00 0.00 30.92 3.53
2300 2428 4.265073 GCCTATCAGTTTGACACTTCCAT 58.735 43.478 0.00 0.00 30.92 3.41
2301 2429 4.095483 GCCTATCAGTTTGACACTTCCATG 59.905 45.833 0.00 0.00 30.92 3.66
2302 2430 5.491070 CCTATCAGTTTGACACTTCCATGA 58.509 41.667 0.00 0.00 30.92 3.07
2303 2431 6.118170 CCTATCAGTTTGACACTTCCATGAT 58.882 40.000 0.00 0.00 30.92 2.45
2304 2432 5.892160 ATCAGTTTGACACTTCCATGATG 57.108 39.130 0.00 0.00 30.92 3.07
2305 2433 4.971939 TCAGTTTGACACTTCCATGATGA 58.028 39.130 0.00 0.00 30.92 2.92
2377 2518 6.148480 ACATTGCTATCGATTATTGGAGAAGC 59.852 38.462 1.71 3.45 0.00 3.86
2434 2575 6.770785 ACTAAAAACAACTGCTGATTGGAGTA 59.229 34.615 0.00 0.00 46.85 2.59
2461 2602 4.431416 TGACGCATATGGGAATTAAGGT 57.569 40.909 25.04 0.92 0.00 3.50
2549 2690 8.646004 AGTAATATAAGCTGCAAAGATGAGAGA 58.354 33.333 1.02 0.00 0.00 3.10
2559 2701 7.279758 GCTGCAAAGATGAGAGACTTAGTTAAT 59.720 37.037 0.00 0.00 0.00 1.40
2564 2706 7.354751 AGATGAGAGACTTAGTTAATGGACC 57.645 40.000 0.00 0.00 0.00 4.46
2576 2718 8.561738 TTAGTTAATGGACCTTTCATCTTGTC 57.438 34.615 0.00 0.00 0.00 3.18
2827 2969 7.690256 ACTCCCTCTGTAAACAAATGTAAGAT 58.310 34.615 0.00 0.00 0.00 2.40
3094 3237 5.611796 TGTCCTTTCAACATCAATCTTCG 57.388 39.130 0.00 0.00 0.00 3.79
3244 3387 8.430801 AGTATGTAGTTACTACTAACGGAGTG 57.569 38.462 21.20 0.00 38.21 3.51
3245 3388 6.690194 ATGTAGTTACTACTAACGGAGTGG 57.310 41.667 21.20 2.44 42.26 4.00
3365 3516 7.791029 TCCATAGTGTAGAAATAGATTGTGCA 58.209 34.615 0.00 0.00 0.00 4.57
3366 3517 7.710907 TCCATAGTGTAGAAATAGATTGTGCAC 59.289 37.037 10.75 10.75 44.68 4.57
3474 3625 7.399245 TTTAGGCAAATAATTAAGACCGCTT 57.601 32.000 0.00 0.00 38.15 4.68
3525 3676 3.048501 GCCTCTCTTTTATACGGCGTAC 58.951 50.000 23.50 0.74 0.00 3.67
3600 3751 7.173907 CCCCTCTTATTTGTGCTGATAGTAATG 59.826 40.741 0.00 0.00 0.00 1.90
3601 3752 7.173907 CCCTCTTATTTGTGCTGATAGTAATGG 59.826 40.741 0.00 0.00 0.00 3.16
3602 3753 7.173907 CCTCTTATTTGTGCTGATAGTAATGGG 59.826 40.741 0.00 0.00 0.00 4.00
3603 3754 7.801104 TCTTATTTGTGCTGATAGTAATGGGA 58.199 34.615 0.00 0.00 0.00 4.37
3604 3755 8.439971 TCTTATTTGTGCTGATAGTAATGGGAT 58.560 33.333 0.00 0.00 0.00 3.85
3605 3756 8.621532 TTATTTGTGCTGATAGTAATGGGATC 57.378 34.615 0.00 0.00 0.00 3.36
3606 3757 4.623932 TGTGCTGATAGTAATGGGATCC 57.376 45.455 1.92 1.92 0.00 3.36
3607 3758 3.327757 TGTGCTGATAGTAATGGGATCCC 59.672 47.826 25.22 25.22 0.00 3.85
3608 3759 3.584848 GTGCTGATAGTAATGGGATCCCT 59.415 47.826 31.05 15.06 36.94 4.20
3609 3760 3.840666 TGCTGATAGTAATGGGATCCCTC 59.159 47.826 31.05 18.37 36.94 4.30
3610 3761 4.100373 GCTGATAGTAATGGGATCCCTCT 58.900 47.826 31.05 22.92 36.94 3.69
3611 3762 4.534103 GCTGATAGTAATGGGATCCCTCTT 59.466 45.833 31.05 24.27 36.94 2.85
3612 3763 5.721960 GCTGATAGTAATGGGATCCCTCTTA 59.278 44.000 31.05 23.30 36.94 2.10
3613 3764 6.385467 GCTGATAGTAATGGGATCCCTCTTAT 59.615 42.308 31.05 19.42 36.94 1.73
3614 3765 7.092668 GCTGATAGTAATGGGATCCCTCTTATT 60.093 40.741 31.05 22.76 36.94 1.40
3615 3766 8.757307 TGATAGTAATGGGATCCCTCTTATTT 57.243 34.615 31.05 19.70 36.94 1.40
3616 3767 8.605947 TGATAGTAATGGGATCCCTCTTATTTG 58.394 37.037 31.05 0.00 36.94 2.32
3617 3768 6.848562 AGTAATGGGATCCCTCTTATTTGT 57.151 37.500 31.05 10.21 36.94 2.83
3618 3769 6.605119 AGTAATGGGATCCCTCTTATTTGTG 58.395 40.000 31.05 0.00 36.94 3.33
3619 3770 3.297134 TGGGATCCCTCTTATTTGTGC 57.703 47.619 31.05 0.39 36.94 4.57
3620 3771 2.852449 TGGGATCCCTCTTATTTGTGCT 59.148 45.455 31.05 0.00 36.94 4.40
3621 3772 3.217626 GGGATCCCTCTTATTTGTGCTG 58.782 50.000 24.69 0.00 0.00 4.41
3622 3773 3.372025 GGGATCCCTCTTATTTGTGCTGT 60.372 47.826 24.69 0.00 0.00 4.40
3623 3774 4.273318 GGATCCCTCTTATTTGTGCTGTT 58.727 43.478 0.00 0.00 0.00 3.16
3624 3775 5.437060 GGATCCCTCTTATTTGTGCTGTTA 58.563 41.667 0.00 0.00 0.00 2.41
3625 3776 5.529060 GGATCCCTCTTATTTGTGCTGTTAG 59.471 44.000 0.00 0.00 0.00 2.34
3626 3777 5.499004 TCCCTCTTATTTGTGCTGTTAGT 57.501 39.130 0.00 0.00 0.00 2.24
3627 3778 6.614694 TCCCTCTTATTTGTGCTGTTAGTA 57.385 37.500 0.00 0.00 0.00 1.82
3628 3779 7.011499 TCCCTCTTATTTGTGCTGTTAGTAA 57.989 36.000 0.00 0.00 0.00 2.24
3629 3780 7.630082 TCCCTCTTATTTGTGCTGTTAGTAAT 58.370 34.615 0.00 0.00 0.00 1.89
3630 3781 7.552687 TCCCTCTTATTTGTGCTGTTAGTAATG 59.447 37.037 0.00 0.00 0.00 1.90
3631 3782 7.201732 CCCTCTTATTTGTGCTGTTAGTAATGG 60.202 40.741 0.00 0.00 0.00 3.16
3632 3783 7.201732 CCTCTTATTTGTGCTGTTAGTAATGGG 60.202 40.741 0.00 0.00 0.00 4.00
3633 3784 7.398829 TCTTATTTGTGCTGTTAGTAATGGGA 58.601 34.615 0.00 0.00 0.00 4.37
3634 3785 5.897377 ATTTGTGCTGTTAGTAATGGGAC 57.103 39.130 0.00 0.00 0.00 4.46
3635 3786 3.343941 TGTGCTGTTAGTAATGGGACC 57.656 47.619 7.05 0.00 0.00 4.46
3636 3787 2.026636 TGTGCTGTTAGTAATGGGACCC 60.027 50.000 2.45 2.45 0.00 4.46
3637 3788 1.562475 TGCTGTTAGTAATGGGACCCC 59.438 52.381 8.45 2.69 0.00 4.95
3638 3789 1.844497 GCTGTTAGTAATGGGACCCCT 59.156 52.381 8.45 0.00 36.94 4.79
3639 3790 2.158798 GCTGTTAGTAATGGGACCCCTC 60.159 54.545 8.45 0.00 36.94 4.30
3640 3791 3.385115 CTGTTAGTAATGGGACCCCTCT 58.615 50.000 8.45 3.71 36.94 3.69
3641 3792 3.780850 CTGTTAGTAATGGGACCCCTCTT 59.219 47.826 8.45 1.57 36.94 2.85
3642 3793 4.962839 TGTTAGTAATGGGACCCCTCTTA 58.037 43.478 8.45 0.53 36.94 2.10
3643 3794 5.544682 TGTTAGTAATGGGACCCCTCTTAT 58.455 41.667 8.45 0.00 36.94 1.73
3644 3795 5.974370 TGTTAGTAATGGGACCCCTCTTATT 59.026 40.000 8.45 3.03 36.94 1.40
3645 3796 6.449041 TGTTAGTAATGGGACCCCTCTTATTT 59.551 38.462 8.45 0.19 36.94 1.40
3646 3797 5.648330 AGTAATGGGACCCCTCTTATTTC 57.352 43.478 8.45 0.00 36.94 2.17
3647 3798 5.297799 AGTAATGGGACCCCTCTTATTTCT 58.702 41.667 8.45 1.03 36.94 2.52
3648 3799 4.526438 AATGGGACCCCTCTTATTTCTG 57.474 45.455 8.45 0.00 36.94 3.02
3649 3800 1.564348 TGGGACCCCTCTTATTTCTGC 59.436 52.381 8.45 0.00 36.94 4.26
3650 3801 1.847088 GGGACCCCTCTTATTTCTGCT 59.153 52.381 0.00 0.00 0.00 4.24
3651 3802 2.422093 GGGACCCCTCTTATTTCTGCTG 60.422 54.545 0.00 0.00 0.00 4.41
3652 3803 2.505819 GGACCCCTCTTATTTCTGCTGA 59.494 50.000 0.00 0.00 0.00 4.26
3653 3804 3.137360 GGACCCCTCTTATTTCTGCTGAT 59.863 47.826 0.00 0.00 0.00 2.90
3654 3805 4.348168 GGACCCCTCTTATTTCTGCTGATA 59.652 45.833 0.00 0.00 0.00 2.15
3655 3806 5.512232 GGACCCCTCTTATTTCTGCTGATAG 60.512 48.000 0.00 0.00 0.00 2.08
3656 3807 4.971924 ACCCCTCTTATTTCTGCTGATAGT 59.028 41.667 0.00 0.00 0.00 2.12
3657 3808 6.143915 ACCCCTCTTATTTCTGCTGATAGTA 58.856 40.000 0.00 0.00 0.00 1.82
3658 3809 6.615726 ACCCCTCTTATTTCTGCTGATAGTAA 59.384 38.462 0.00 0.00 0.00 2.24
3659 3810 7.293535 ACCCCTCTTATTTCTGCTGATAGTAAT 59.706 37.037 0.00 0.00 0.00 1.89
3660 3811 7.605691 CCCCTCTTATTTCTGCTGATAGTAATG 59.394 40.741 0.00 0.00 0.00 1.90
3661 3812 7.605691 CCCTCTTATTTCTGCTGATAGTAATGG 59.394 40.741 0.00 1.55 0.00 3.16
3662 3813 7.605691 CCTCTTATTTCTGCTGATAGTAATGGG 59.394 40.741 0.00 0.00 0.00 4.00
3663 3814 8.262601 TCTTATTTCTGCTGATAGTAATGGGA 57.737 34.615 0.00 0.00 0.00 4.37
3664 3815 8.884323 TCTTATTTCTGCTGATAGTAATGGGAT 58.116 33.333 0.00 0.00 0.00 3.85
3665 3816 9.160496 CTTATTTCTGCTGATAGTAATGGGATC 57.840 37.037 0.00 0.00 0.00 3.36
3666 3817 5.489792 TTCTGCTGATAGTAATGGGATCC 57.510 43.478 1.92 1.92 0.00 3.36
3667 3818 3.840666 TCTGCTGATAGTAATGGGATCCC 59.159 47.826 25.22 25.22 0.00 3.85
3668 3819 3.843027 CTGCTGATAGTAATGGGATCCCT 59.157 47.826 31.05 15.06 36.94 4.20
3669 3820 3.840666 TGCTGATAGTAATGGGATCCCTC 59.159 47.826 31.05 18.37 36.94 4.30
3670 3821 4.100373 GCTGATAGTAATGGGATCCCTCT 58.900 47.826 31.05 22.92 36.94 3.69
3671 3822 4.534103 GCTGATAGTAATGGGATCCCTCTT 59.466 45.833 31.05 24.27 36.94 2.85
3672 3823 5.721960 GCTGATAGTAATGGGATCCCTCTTA 59.278 44.000 31.05 23.30 36.94 2.10
3673 3824 6.385467 GCTGATAGTAATGGGATCCCTCTTAT 59.615 42.308 31.05 19.42 36.94 1.73
3674 3825 7.092668 GCTGATAGTAATGGGATCCCTCTTATT 60.093 40.741 31.05 22.76 36.94 1.40
3675 3826 8.757307 TGATAGTAATGGGATCCCTCTTATTT 57.243 34.615 31.05 19.70 36.94 1.40
3676 3827 8.605947 TGATAGTAATGGGATCCCTCTTATTTG 58.394 37.037 31.05 0.00 36.94 2.32
3677 3828 6.848562 AGTAATGGGATCCCTCTTATTTGT 57.151 37.500 31.05 10.21 36.94 2.83
3678 3829 6.605119 AGTAATGGGATCCCTCTTATTTGTG 58.395 40.000 31.05 0.00 36.94 3.33
3679 3830 3.297134 TGGGATCCCTCTTATTTGTGC 57.703 47.619 31.05 0.39 36.94 4.57
3680 3831 2.852449 TGGGATCCCTCTTATTTGTGCT 59.148 45.455 31.05 0.00 36.94 4.40
3681 3832 3.217626 GGGATCCCTCTTATTTGTGCTG 58.782 50.000 24.69 0.00 0.00 4.41
3682 3833 3.372025 GGGATCCCTCTTATTTGTGCTGT 60.372 47.826 24.69 0.00 0.00 4.40
3683 3834 4.273318 GGATCCCTCTTATTTGTGCTGTT 58.727 43.478 0.00 0.00 0.00 3.16
3684 3835 5.437060 GGATCCCTCTTATTTGTGCTGTTA 58.563 41.667 0.00 0.00 0.00 2.41
3685 3836 5.529060 GGATCCCTCTTATTTGTGCTGTTAG 59.471 44.000 0.00 0.00 0.00 2.34
3686 3837 5.499004 TCCCTCTTATTTGTGCTGTTAGT 57.501 39.130 0.00 0.00 0.00 2.24
3687 3838 6.614694 TCCCTCTTATTTGTGCTGTTAGTA 57.385 37.500 0.00 0.00 0.00 1.82
3688 3839 7.011499 TCCCTCTTATTTGTGCTGTTAGTAA 57.989 36.000 0.00 0.00 0.00 2.24
3689 3840 7.630082 TCCCTCTTATTTGTGCTGTTAGTAAT 58.370 34.615 0.00 0.00 0.00 1.89
3690 3841 7.552687 TCCCTCTTATTTGTGCTGTTAGTAATG 59.447 37.037 0.00 0.00 0.00 1.90
3691 3842 7.201732 CCCTCTTATTTGTGCTGTTAGTAATGG 60.202 40.741 0.00 0.00 0.00 3.16
3692 3843 7.201732 CCTCTTATTTGTGCTGTTAGTAATGGG 60.202 40.741 0.00 0.00 0.00 4.00
3693 3844 7.398829 TCTTATTTGTGCTGTTAGTAATGGGA 58.601 34.615 0.00 0.00 0.00 4.37
3694 3845 5.897377 ATTTGTGCTGTTAGTAATGGGAC 57.103 39.130 0.00 0.00 0.00 4.46
3695 3846 3.343941 TGTGCTGTTAGTAATGGGACC 57.656 47.619 7.05 0.00 0.00 4.46
3696 3847 2.026636 TGTGCTGTTAGTAATGGGACCC 60.027 50.000 2.45 2.45 0.00 4.46
3697 3848 1.562475 TGCTGTTAGTAATGGGACCCC 59.438 52.381 8.45 2.69 0.00 4.95
3698 3849 1.844497 GCTGTTAGTAATGGGACCCCT 59.156 52.381 8.45 0.00 36.94 4.79
3699 3850 2.158798 GCTGTTAGTAATGGGACCCCTC 60.159 54.545 8.45 0.00 36.94 4.30
3700 3851 3.385115 CTGTTAGTAATGGGACCCCTCT 58.615 50.000 8.45 3.71 36.94 3.69
3701 3852 3.780850 CTGTTAGTAATGGGACCCCTCTT 59.219 47.826 8.45 1.57 36.94 2.85
3702 3853 4.962839 TGTTAGTAATGGGACCCCTCTTA 58.037 43.478 8.45 0.53 36.94 2.10
3703 3854 5.544682 TGTTAGTAATGGGACCCCTCTTAT 58.455 41.667 8.45 0.00 36.94 1.73
3704 3855 5.974370 TGTTAGTAATGGGACCCCTCTTATT 59.026 40.000 8.45 3.03 36.94 1.40
3705 3856 6.449041 TGTTAGTAATGGGACCCCTCTTATTT 59.551 38.462 8.45 0.19 36.94 1.40
3706 3857 5.648330 AGTAATGGGACCCCTCTTATTTC 57.352 43.478 8.45 0.00 36.94 2.17
3707 3858 5.297799 AGTAATGGGACCCCTCTTATTTCT 58.702 41.667 8.45 1.03 36.94 2.52
3708 3859 4.526438 AATGGGACCCCTCTTATTTCTG 57.474 45.455 8.45 0.00 36.94 3.02
3709 3860 1.564348 TGGGACCCCTCTTATTTCTGC 59.436 52.381 8.45 0.00 36.94 4.26
3710 3861 1.847088 GGGACCCCTCTTATTTCTGCT 59.153 52.381 0.00 0.00 0.00 4.24
3711 3862 2.422093 GGGACCCCTCTTATTTCTGCTG 60.422 54.545 0.00 0.00 0.00 4.41
3712 3863 2.505819 GGACCCCTCTTATTTCTGCTGA 59.494 50.000 0.00 0.00 0.00 4.26
3713 3864 3.137360 GGACCCCTCTTATTTCTGCTGAT 59.863 47.826 0.00 0.00 0.00 2.90
3714 3865 4.348168 GGACCCCTCTTATTTCTGCTGATA 59.652 45.833 0.00 0.00 0.00 2.15
3715 3866 5.512232 GGACCCCTCTTATTTCTGCTGATAG 60.512 48.000 0.00 0.00 0.00 2.08
3716 3867 4.971924 ACCCCTCTTATTTCTGCTGATAGT 59.028 41.667 0.00 0.00 0.00 2.12
3717 3868 6.143915 ACCCCTCTTATTTCTGCTGATAGTA 58.856 40.000 0.00 0.00 0.00 1.82
3718 3869 6.615726 ACCCCTCTTATTTCTGCTGATAGTAA 59.384 38.462 0.00 0.00 0.00 2.24
3719 3870 7.293535 ACCCCTCTTATTTCTGCTGATAGTAAT 59.706 37.037 0.00 0.00 0.00 1.89
3760 3911 8.982723 AGCGTATAATATTGGACTAATGGATCT 58.017 33.333 0.00 0.00 0.00 2.75
3790 3941 5.486526 ACTCAAAGGTTCAAATTTGTGCAA 58.513 33.333 17.47 2.54 37.60 4.08
3791 3942 5.581874 ACTCAAAGGTTCAAATTTGTGCAAG 59.418 36.000 17.47 8.30 37.60 4.01
3852 4012 8.076178 GTCAAATTAGTTTTGTGTCATGCTACT 58.924 33.333 0.00 0.00 44.25 2.57
3881 4041 7.224557 GTGCAAAAGGTTACAAATTCAACTCAT 59.775 33.333 0.00 0.00 0.00 2.90
4364 4707 8.006590 GCTTTGCTAGATTATATCTTTGTCGTG 58.993 37.037 0.00 0.00 40.76 4.35
4365 4708 8.942338 TTTGCTAGATTATATCTTTGTCGTGT 57.058 30.769 0.00 0.00 40.76 4.49
4366 4709 8.575565 TTGCTAGATTATATCTTTGTCGTGTC 57.424 34.615 0.00 0.00 40.76 3.67
4367 4710 6.856426 TGCTAGATTATATCTTTGTCGTGTCG 59.144 38.462 0.00 0.00 40.76 4.35
4368 4711 6.856938 GCTAGATTATATCTTTGTCGTGTCGT 59.143 38.462 0.00 0.00 40.76 4.34
4405 4748 9.563898 CATGAATTACGATTATCCATCCAAATG 57.436 33.333 0.00 0.00 0.00 2.32
4521 4864 6.266786 TCAAGACACTAGTTGAACCATACTGA 59.733 38.462 0.00 0.00 29.66 3.41
4576 4919 0.601057 ATTGGTAACGGTTGCTTGGC 59.399 50.000 8.82 0.00 42.51 4.52
4700 5044 0.326264 AGTGAGGCTAAGGCAAGTGG 59.674 55.000 0.00 0.00 40.87 4.00
4774 5118 1.276421 TCCGGAAGAGGAAAGCAGAAG 59.724 52.381 0.00 0.00 37.36 2.85
4775 5119 1.677217 CCGGAAGAGGAAAGCAGAAGG 60.677 57.143 0.00 0.00 0.00 3.46
4776 5120 1.458398 GGAAGAGGAAAGCAGAAGGC 58.542 55.000 0.00 0.00 45.30 4.35
4820 5164 3.426695 GCTAACAACCATGTGTCTGATGC 60.427 47.826 0.00 0.00 40.46 3.91
4892 5236 1.534595 CTGAAAAGCTGCAGTCTGACC 59.465 52.381 16.64 0.00 0.00 4.02
4904 5248 2.264794 CTGACCGTACCCAGTGCC 59.735 66.667 0.00 0.00 0.00 5.01
5080 5424 6.688578 AGTTGACTGAATGTTGTAGTATCGT 58.311 36.000 0.00 0.00 0.00 3.73
5167 5511 4.570772 GTCGTGCAAGATTAGATGCCTTTA 59.429 41.667 5.42 0.00 41.87 1.85
5205 5549 4.287552 AGATACAGAAATGTCGGTAGGGT 58.712 43.478 2.29 0.00 37.76 4.34
5262 5606 9.173021 ACTCTTCTATTATCTATCGAGACATGG 57.827 37.037 0.00 0.00 33.41 3.66
5268 5612 4.679373 ATCTATCGAGACATGGCAGTTT 57.321 40.909 0.00 0.00 33.41 2.66
5342 5690 4.290459 TCCTATATTTGCCAGCATGATCCT 59.710 41.667 0.00 0.00 39.69 3.24
5350 5698 2.658285 CCAGCATGATCCTTGCCTTTA 58.342 47.619 12.65 0.00 41.06 1.85
5355 5703 3.382546 GCATGATCCTTGCCTTTACACAT 59.617 43.478 0.00 0.00 33.95 3.21
5356 5704 4.580167 GCATGATCCTTGCCTTTACACATA 59.420 41.667 0.00 0.00 33.95 2.29
5362 5710 5.192927 TCCTTGCCTTTACACATATGGAAG 58.807 41.667 7.80 5.70 27.47 3.46
5397 5745 5.998454 ATCTATGCATGAACAACACTAGC 57.002 39.130 10.16 0.00 0.00 3.42
5422 5929 3.521947 TTCTAAACCCTAGAGCTTCGC 57.478 47.619 0.00 0.00 0.00 4.70
5429 5936 2.208431 CCCTAGAGCTTCGCATTTCTG 58.792 52.381 0.00 0.00 0.00 3.02
5438 5945 4.455533 AGCTTCGCATTTCTGTACATGAAA 59.544 37.500 17.19 17.19 37.74 2.69
5440 5947 5.801947 GCTTCGCATTTCTGTACATGAAAAT 59.198 36.000 18.18 12.20 37.05 1.82
5443 5950 7.087409 TCGCATTTCTGTACATGAAAATCAT 57.913 32.000 18.18 5.67 37.65 2.45
5451 5958 8.492673 TCTGTACATGAAAATCATTAGTGTCC 57.507 34.615 0.00 0.00 34.28 4.02
5452 5959 8.321353 TCTGTACATGAAAATCATTAGTGTCCT 58.679 33.333 0.00 0.00 34.28 3.85
5453 5960 8.267620 TGTACATGAAAATCATTAGTGTCCTG 57.732 34.615 0.00 0.00 34.28 3.86
5454 5961 7.882791 TGTACATGAAAATCATTAGTGTCCTGT 59.117 33.333 0.00 0.00 34.28 4.00
5455 5962 7.383102 ACATGAAAATCATTAGTGTCCTGTC 57.617 36.000 0.00 0.00 34.28 3.51
5466 5974 4.199432 AGTGTCCTGTCATTCTAGCAAG 57.801 45.455 0.00 0.00 0.00 4.01
5469 5977 4.808364 GTGTCCTGTCATTCTAGCAAGATC 59.192 45.833 0.00 0.00 0.00 2.75
5470 5978 4.141846 TGTCCTGTCATTCTAGCAAGATCC 60.142 45.833 0.00 0.00 0.00 3.36
5512 6020 3.562567 TTTAGGCATGTAAAACACGGC 57.437 42.857 0.00 0.00 37.11 5.68
5600 6108 1.200020 CTTCCTTGGATCACGTTTGCC 59.800 52.381 0.00 0.00 0.00 4.52
5631 6140 2.426024 CCCTCACAAATGGCTCAATCAG 59.574 50.000 0.00 0.00 0.00 2.90
5765 6274 5.112686 GCCTATGTTCAGTTCGAATTCTCT 58.887 41.667 0.00 0.00 35.63 3.10
5842 6351 3.167291 TGGTACACACCCAGGCTAA 57.833 52.632 0.00 0.00 45.11 3.09
5848 6357 3.026707 ACACACCCAGGCTAAAGTTTT 57.973 42.857 0.00 0.00 0.00 2.43
5864 6373 7.328493 GCTAAAGTTTTCCCAATTCACATACAC 59.672 37.037 0.00 0.00 0.00 2.90
5868 6377 3.719268 TCCCAATTCACATACACAGCT 57.281 42.857 0.00 0.00 0.00 4.24
5871 6380 3.624861 CCCAATTCACATACACAGCTCTC 59.375 47.826 0.00 0.00 0.00 3.20
5872 6381 3.308053 CCAATTCACATACACAGCTCTCG 59.692 47.826 0.00 0.00 0.00 4.04
5873 6382 2.654749 TTCACATACACAGCTCTCGG 57.345 50.000 0.00 0.00 0.00 4.63
5874 6383 1.834188 TCACATACACAGCTCTCGGA 58.166 50.000 0.00 0.00 0.00 4.55
5875 6384 2.379005 TCACATACACAGCTCTCGGAT 58.621 47.619 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 0.606401 ATGAACAGGCCGTCAGTTGG 60.606 55.000 11.68 0.00 0.00 3.77
217 222 4.261801 CTGGGGGTAGTAGTTCAACAATG 58.738 47.826 0.00 0.00 0.00 2.82
453 557 5.923684 TCAATAAAAATTTCTTCCCGTGCAC 59.076 36.000 6.82 6.82 0.00 4.57
500 604 7.021196 CACACAAATTTAGAACGGATAACCAG 58.979 38.462 0.00 0.00 35.59 4.00
722 826 2.453521 ACCAGTATTAGCCACGAGACA 58.546 47.619 0.00 0.00 0.00 3.41
758 862 7.306515 CCAACAATAATTTTGAACGTTGTCCAG 60.307 37.037 5.00 0.00 32.39 3.86
1116 1223 4.526650 ACTGTTTCAAACTTCAAACCAGGT 59.473 37.500 1.10 0.00 32.43 4.00
1203 1310 1.142965 CGATCCACGGTATGCCACA 59.857 57.895 0.00 0.00 38.46 4.17
1207 1314 1.301716 ATGGCGATCCACGGTATGC 60.302 57.895 0.00 0.00 46.92 3.14
1275 1382 6.968131 TCATACTTCTCTTTCGTTGGAATG 57.032 37.500 0.00 0.00 30.88 2.67
1532 1639 2.019984 GCCTGACAAGCAAATAGAGGG 58.980 52.381 0.00 0.00 0.00 4.30
1610 1719 9.941325 ATTTCCATGTGCATTAAAAACTGATTA 57.059 25.926 0.00 0.00 0.00 1.75
1906 2033 1.166531 AGTTCTGCACCGCCAAAGAC 61.167 55.000 0.00 0.00 0.00 3.01
1990 2117 7.768120 TGTCAATAATAAATGGGTTTTCATGCC 59.232 33.333 0.00 0.00 0.00 4.40
2190 2318 3.654414 CACTGAAACCTAGACTGACCAC 58.346 50.000 0.00 0.00 0.00 4.16
2220 2348 7.124901 ACTTGCTTCAGAATAGAATCAGGAGTA 59.875 37.037 0.00 0.00 29.06 2.59
2276 2404 3.559171 GGAAGTGTCAAACTGATAGGCCA 60.559 47.826 5.01 0.00 39.81 5.36
2292 2420 4.862574 CAGCAAAATGTCATCATGGAAGTG 59.137 41.667 0.00 0.00 34.19 3.16
2293 2421 4.525487 ACAGCAAAATGTCATCATGGAAGT 59.475 37.500 0.00 0.00 34.19 3.01
2294 2422 4.862574 CACAGCAAAATGTCATCATGGAAG 59.137 41.667 0.00 0.00 34.19 3.46
2295 2423 4.281435 ACACAGCAAAATGTCATCATGGAA 59.719 37.500 0.00 0.00 34.19 3.53
2296 2424 3.827876 ACACAGCAAAATGTCATCATGGA 59.172 39.130 0.00 0.00 34.19 3.41
2297 2425 4.182693 ACACAGCAAAATGTCATCATGG 57.817 40.909 0.00 0.00 34.19 3.66
2298 2426 6.641723 TGTTTACACAGCAAAATGTCATCATG 59.358 34.615 0.00 0.00 34.19 3.07
2299 2427 6.747125 TGTTTACACAGCAAAATGTCATCAT 58.253 32.000 0.00 0.00 35.59 2.45
2300 2428 6.141560 TGTTTACACAGCAAAATGTCATCA 57.858 33.333 0.00 0.00 0.00 3.07
2301 2429 7.086376 AGATGTTTACACAGCAAAATGTCATC 58.914 34.615 0.00 0.00 42.17 2.92
2302 2430 6.985117 AGATGTTTACACAGCAAAATGTCAT 58.015 32.000 0.00 0.00 42.17 3.06
2303 2431 6.389830 AGATGTTTACACAGCAAAATGTCA 57.610 33.333 0.00 0.00 42.17 3.58
2304 2432 7.698836 AAAGATGTTTACACAGCAAAATGTC 57.301 32.000 0.00 0.00 42.17 3.06
2305 2433 8.491331 AAAAAGATGTTTACACAGCAAAATGT 57.509 26.923 0.00 0.00 42.17 2.71
2346 2487 7.445096 TCCAATAATCGATAGCAATGTCAACAT 59.555 33.333 0.00 0.00 38.41 2.71
2377 2518 5.006358 CCGGATCAACTAAAGTTATTGGTCG 59.994 44.000 0.00 0.00 34.82 4.79
2434 2575 7.121168 CCTTAATTCCCATATGCGTCATACATT 59.879 37.037 0.00 1.23 0.00 2.71
2461 2602 0.181587 TTTTCCACCGCCTTCTGTCA 59.818 50.000 0.00 0.00 0.00 3.58
2549 2690 8.164070 ACAAGATGAAAGGTCCATTAACTAAGT 58.836 33.333 0.00 0.00 0.00 2.24
2564 2706 3.190118 GCTGTTCTGGGACAAGATGAAAG 59.810 47.826 0.00 0.00 38.70 2.62
2576 2718 3.258872 TGAAAATGGAATGCTGTTCTGGG 59.741 43.478 3.12 0.00 0.00 4.45
2931 3073 6.801718 ACTGTAGCAAGGGTACATGTTATA 57.198 37.500 2.30 0.00 43.86 0.98
2932 3074 5.693769 ACTGTAGCAAGGGTACATGTTAT 57.306 39.130 2.30 0.00 43.86 1.89
3094 3237 8.045176 AGGAAATAAATTACAGCTCAACAGAC 57.955 34.615 0.00 0.00 0.00 3.51
3224 3367 6.765512 AGATCCACTCCGTTAGTAGTAACTAC 59.234 42.308 16.51 0.00 37.94 2.73
3282 3428 2.165167 CCCAGTTCTCGTGTACCACTA 58.835 52.381 0.00 0.00 31.34 2.74
3365 3516 3.803715 GCATAGCTTCCCACATATGTCGT 60.804 47.826 5.07 0.00 0.00 4.34
3366 3517 2.738846 GCATAGCTTCCCACATATGTCG 59.261 50.000 5.07 0.00 0.00 4.35
3367 3518 3.499918 GTGCATAGCTTCCCACATATGTC 59.500 47.826 5.07 0.00 0.00 3.06
3474 3625 3.716353 AGTGCATCATAAGGGGTATGTGA 59.284 43.478 0.00 0.00 40.58 3.58
3525 3676 0.313043 ATCCCATTACCGTACGCTCG 59.687 55.000 10.49 0.00 0.00 5.03
3600 3751 3.217626 CAGCACAAATAAGAGGGATCCC 58.782 50.000 24.59 24.59 0.00 3.85
3601 3752 3.891049 ACAGCACAAATAAGAGGGATCC 58.109 45.455 1.92 1.92 0.00 3.36
3602 3753 6.116126 ACTAACAGCACAAATAAGAGGGATC 58.884 40.000 0.00 0.00 0.00 3.36
3603 3754 6.067217 ACTAACAGCACAAATAAGAGGGAT 57.933 37.500 0.00 0.00 0.00 3.85
3604 3755 5.499004 ACTAACAGCACAAATAAGAGGGA 57.501 39.130 0.00 0.00 0.00 4.20
3605 3756 7.201732 CCATTACTAACAGCACAAATAAGAGGG 60.202 40.741 0.00 0.00 0.00 4.30
3606 3757 7.201732 CCCATTACTAACAGCACAAATAAGAGG 60.202 40.741 0.00 0.00 0.00 3.69
3607 3758 7.552687 TCCCATTACTAACAGCACAAATAAGAG 59.447 37.037 0.00 0.00 0.00 2.85
3608 3759 7.335924 GTCCCATTACTAACAGCACAAATAAGA 59.664 37.037 0.00 0.00 0.00 2.10
3609 3760 7.415206 GGTCCCATTACTAACAGCACAAATAAG 60.415 40.741 0.00 0.00 0.00 1.73
3610 3761 6.376018 GGTCCCATTACTAACAGCACAAATAA 59.624 38.462 0.00 0.00 0.00 1.40
3611 3762 5.883673 GGTCCCATTACTAACAGCACAAATA 59.116 40.000 0.00 0.00 0.00 1.40
3612 3763 4.705023 GGTCCCATTACTAACAGCACAAAT 59.295 41.667 0.00 0.00 0.00 2.32
3613 3764 4.076394 GGTCCCATTACTAACAGCACAAA 58.924 43.478 0.00 0.00 0.00 2.83
3614 3765 3.560453 GGGTCCCATTACTAACAGCACAA 60.560 47.826 1.78 0.00 0.00 3.33
3615 3766 2.026636 GGGTCCCATTACTAACAGCACA 60.027 50.000 1.78 0.00 0.00 4.57
3616 3767 2.640184 GGGTCCCATTACTAACAGCAC 58.360 52.381 1.78 0.00 0.00 4.40
3617 3768 1.562475 GGGGTCCCATTACTAACAGCA 59.438 52.381 10.98 0.00 35.81 4.41
3618 3769 1.844497 AGGGGTCCCATTACTAACAGC 59.156 52.381 10.98 0.00 38.92 4.40
3619 3770 3.385115 AGAGGGGTCCCATTACTAACAG 58.615 50.000 10.98 0.00 38.92 3.16
3620 3771 3.502051 AGAGGGGTCCCATTACTAACA 57.498 47.619 10.98 0.00 38.92 2.41
3621 3772 6.511017 AATAAGAGGGGTCCCATTACTAAC 57.489 41.667 10.98 0.00 38.92 2.34
3622 3773 6.912561 AGAAATAAGAGGGGTCCCATTACTAA 59.087 38.462 10.98 0.00 38.92 2.24
3623 3774 6.329197 CAGAAATAAGAGGGGTCCCATTACTA 59.671 42.308 10.98 0.00 38.92 1.82
3624 3775 5.132816 CAGAAATAAGAGGGGTCCCATTACT 59.867 44.000 10.98 0.00 38.92 2.24
3625 3776 5.377478 CAGAAATAAGAGGGGTCCCATTAC 58.623 45.833 10.98 0.00 38.92 1.89
3626 3777 4.141251 GCAGAAATAAGAGGGGTCCCATTA 60.141 45.833 10.98 6.10 38.92 1.90
3627 3778 3.373110 GCAGAAATAAGAGGGGTCCCATT 60.373 47.826 10.98 3.85 38.92 3.16
3628 3779 2.175715 GCAGAAATAAGAGGGGTCCCAT 59.824 50.000 10.98 0.89 38.92 4.00
3629 3780 1.564348 GCAGAAATAAGAGGGGTCCCA 59.436 52.381 10.98 0.00 38.92 4.37
3630 3781 1.847088 AGCAGAAATAAGAGGGGTCCC 59.153 52.381 0.00 0.00 0.00 4.46
3631 3782 2.505819 TCAGCAGAAATAAGAGGGGTCC 59.494 50.000 0.00 0.00 0.00 4.46
3632 3783 3.914426 TCAGCAGAAATAAGAGGGGTC 57.086 47.619 0.00 0.00 0.00 4.46
3633 3784 4.971924 ACTATCAGCAGAAATAAGAGGGGT 59.028 41.667 0.00 0.00 0.00 4.95
3634 3785 5.559148 ACTATCAGCAGAAATAAGAGGGG 57.441 43.478 0.00 0.00 0.00 4.79
3635 3786 7.605691 CCATTACTATCAGCAGAAATAAGAGGG 59.394 40.741 0.00 0.00 0.00 4.30
3636 3787 7.605691 CCCATTACTATCAGCAGAAATAAGAGG 59.394 40.741 0.00 0.00 0.00 3.69
3637 3788 8.370940 TCCCATTACTATCAGCAGAAATAAGAG 58.629 37.037 0.00 0.00 0.00 2.85
3638 3789 8.262601 TCCCATTACTATCAGCAGAAATAAGA 57.737 34.615 0.00 0.00 0.00 2.10
3639 3790 9.160496 GATCCCATTACTATCAGCAGAAATAAG 57.840 37.037 0.00 0.00 0.00 1.73
3640 3791 8.103305 GGATCCCATTACTATCAGCAGAAATAA 58.897 37.037 0.00 0.00 0.00 1.40
3641 3792 7.311297 GGGATCCCATTACTATCAGCAGAAATA 60.311 40.741 26.95 0.00 35.81 1.40
3642 3793 6.479884 GGATCCCATTACTATCAGCAGAAAT 58.520 40.000 0.00 0.00 0.00 2.17
3643 3794 5.221925 GGGATCCCATTACTATCAGCAGAAA 60.222 44.000 26.95 0.00 35.81 2.52
3644 3795 4.287067 GGGATCCCATTACTATCAGCAGAA 59.713 45.833 26.95 0.00 35.81 3.02
3645 3796 3.840666 GGGATCCCATTACTATCAGCAGA 59.159 47.826 26.95 0.00 35.81 4.26
3646 3797 3.843027 AGGGATCCCATTACTATCAGCAG 59.157 47.826 32.69 0.00 38.92 4.24
3647 3798 3.840666 GAGGGATCCCATTACTATCAGCA 59.159 47.826 32.69 0.00 38.92 4.41
3648 3799 4.100373 AGAGGGATCCCATTACTATCAGC 58.900 47.826 32.69 0.25 38.92 4.26
3649 3800 7.986553 ATAAGAGGGATCCCATTACTATCAG 57.013 40.000 32.69 0.00 38.92 2.90
3650 3801 8.605947 CAAATAAGAGGGATCCCATTACTATCA 58.394 37.037 32.69 10.78 38.92 2.15
3651 3802 8.606830 ACAAATAAGAGGGATCCCATTACTATC 58.393 37.037 32.69 18.68 38.92 2.08
3652 3803 8.386264 CACAAATAAGAGGGATCCCATTACTAT 58.614 37.037 32.69 17.08 38.92 2.12
3653 3804 7.691791 GCACAAATAAGAGGGATCCCATTACTA 60.692 40.741 32.69 15.65 38.92 1.82
3654 3805 6.605119 CACAAATAAGAGGGATCCCATTACT 58.395 40.000 32.69 20.98 38.92 2.24
3655 3806 5.241728 GCACAAATAAGAGGGATCCCATTAC 59.758 44.000 32.69 19.19 38.92 1.89
3656 3807 5.134339 AGCACAAATAAGAGGGATCCCATTA 59.866 40.000 32.69 27.37 38.92 1.90
3657 3808 4.078980 AGCACAAATAAGAGGGATCCCATT 60.079 41.667 32.69 26.21 38.92 3.16
3658 3809 3.464833 AGCACAAATAAGAGGGATCCCAT 59.535 43.478 32.69 19.76 38.92 4.00
3659 3810 2.852449 AGCACAAATAAGAGGGATCCCA 59.148 45.455 32.69 12.63 38.92 4.37
3660 3811 3.217626 CAGCACAAATAAGAGGGATCCC 58.782 50.000 24.59 24.59 0.00 3.85
3661 3812 3.891049 ACAGCACAAATAAGAGGGATCC 58.109 45.455 1.92 1.92 0.00 3.36
3662 3813 6.116126 ACTAACAGCACAAATAAGAGGGATC 58.884 40.000 0.00 0.00 0.00 3.36
3663 3814 6.067217 ACTAACAGCACAAATAAGAGGGAT 57.933 37.500 0.00 0.00 0.00 3.85
3664 3815 5.499004 ACTAACAGCACAAATAAGAGGGA 57.501 39.130 0.00 0.00 0.00 4.20
3665 3816 7.201732 CCATTACTAACAGCACAAATAAGAGGG 60.202 40.741 0.00 0.00 0.00 4.30
3666 3817 7.201732 CCCATTACTAACAGCACAAATAAGAGG 60.202 40.741 0.00 0.00 0.00 3.69
3667 3818 7.552687 TCCCATTACTAACAGCACAAATAAGAG 59.447 37.037 0.00 0.00 0.00 2.85
3668 3819 7.335924 GTCCCATTACTAACAGCACAAATAAGA 59.664 37.037 0.00 0.00 0.00 2.10
3669 3820 7.415206 GGTCCCATTACTAACAGCACAAATAAG 60.415 40.741 0.00 0.00 0.00 1.73
3670 3821 6.376018 GGTCCCATTACTAACAGCACAAATAA 59.624 38.462 0.00 0.00 0.00 1.40
3671 3822 5.883673 GGTCCCATTACTAACAGCACAAATA 59.116 40.000 0.00 0.00 0.00 1.40
3672 3823 4.705023 GGTCCCATTACTAACAGCACAAAT 59.295 41.667 0.00 0.00 0.00 2.32
3673 3824 4.076394 GGTCCCATTACTAACAGCACAAA 58.924 43.478 0.00 0.00 0.00 2.83
3674 3825 3.560453 GGGTCCCATTACTAACAGCACAA 60.560 47.826 1.78 0.00 0.00 3.33
3675 3826 2.026636 GGGTCCCATTACTAACAGCACA 60.027 50.000 1.78 0.00 0.00 4.57
3676 3827 2.640184 GGGTCCCATTACTAACAGCAC 58.360 52.381 1.78 0.00 0.00 4.40
3677 3828 1.562475 GGGGTCCCATTACTAACAGCA 59.438 52.381 10.98 0.00 35.81 4.41
3678 3829 1.844497 AGGGGTCCCATTACTAACAGC 59.156 52.381 10.98 0.00 38.92 4.40
3679 3830 3.385115 AGAGGGGTCCCATTACTAACAG 58.615 50.000 10.98 0.00 38.92 3.16
3680 3831 3.502051 AGAGGGGTCCCATTACTAACA 57.498 47.619 10.98 0.00 38.92 2.41
3681 3832 6.511017 AATAAGAGGGGTCCCATTACTAAC 57.489 41.667 10.98 0.00 38.92 2.34
3682 3833 6.912561 AGAAATAAGAGGGGTCCCATTACTAA 59.087 38.462 10.98 0.00 38.92 2.24
3683 3834 6.329197 CAGAAATAAGAGGGGTCCCATTACTA 59.671 42.308 10.98 0.00 38.92 1.82
3684 3835 5.132816 CAGAAATAAGAGGGGTCCCATTACT 59.867 44.000 10.98 0.00 38.92 2.24
3685 3836 5.377478 CAGAAATAAGAGGGGTCCCATTAC 58.623 45.833 10.98 0.00 38.92 1.89
3686 3837 4.141251 GCAGAAATAAGAGGGGTCCCATTA 60.141 45.833 10.98 6.10 38.92 1.90
3687 3838 3.373110 GCAGAAATAAGAGGGGTCCCATT 60.373 47.826 10.98 3.85 38.92 3.16
3688 3839 2.175715 GCAGAAATAAGAGGGGTCCCAT 59.824 50.000 10.98 0.89 38.92 4.00
3689 3840 1.564348 GCAGAAATAAGAGGGGTCCCA 59.436 52.381 10.98 0.00 38.92 4.37
3690 3841 1.847088 AGCAGAAATAAGAGGGGTCCC 59.153 52.381 0.00 0.00 0.00 4.46
3691 3842 2.505819 TCAGCAGAAATAAGAGGGGTCC 59.494 50.000 0.00 0.00 0.00 4.46
3692 3843 3.914426 TCAGCAGAAATAAGAGGGGTC 57.086 47.619 0.00 0.00 0.00 4.46
3693 3844 4.971924 ACTATCAGCAGAAATAAGAGGGGT 59.028 41.667 0.00 0.00 0.00 4.95
3694 3845 5.559148 ACTATCAGCAGAAATAAGAGGGG 57.441 43.478 0.00 0.00 0.00 4.79
3695 3846 7.605691 CCATTACTATCAGCAGAAATAAGAGGG 59.394 40.741 0.00 0.00 0.00 4.30
3696 3847 7.605691 CCCATTACTATCAGCAGAAATAAGAGG 59.394 40.741 0.00 0.00 0.00 3.69
3697 3848 8.370940 TCCCATTACTATCAGCAGAAATAAGAG 58.629 37.037 0.00 0.00 0.00 2.85
3698 3849 8.262601 TCCCATTACTATCAGCAGAAATAAGA 57.737 34.615 0.00 0.00 0.00 2.10
3699 3850 9.160496 GATCCCATTACTATCAGCAGAAATAAG 57.840 37.037 0.00 0.00 0.00 1.73
3700 3851 8.103305 GGATCCCATTACTATCAGCAGAAATAA 58.897 37.037 0.00 0.00 0.00 1.40
3701 3852 7.311297 GGGATCCCATTACTATCAGCAGAAATA 60.311 40.741 26.95 0.00 35.81 1.40
3702 3853 6.479884 GGATCCCATTACTATCAGCAGAAAT 58.520 40.000 0.00 0.00 0.00 2.17
3703 3854 5.221925 GGGATCCCATTACTATCAGCAGAAA 60.222 44.000 26.95 0.00 35.81 2.52
3704 3855 4.287067 GGGATCCCATTACTATCAGCAGAA 59.713 45.833 26.95 0.00 35.81 3.02
3705 3856 3.840666 GGGATCCCATTACTATCAGCAGA 59.159 47.826 26.95 0.00 35.81 4.26
3706 3857 3.843027 AGGGATCCCATTACTATCAGCAG 59.157 47.826 32.69 0.00 38.92 4.24
3707 3858 3.840666 GAGGGATCCCATTACTATCAGCA 59.159 47.826 32.69 0.00 38.92 4.41
3708 3859 4.100373 AGAGGGATCCCATTACTATCAGC 58.900 47.826 32.69 0.25 38.92 4.26
3709 3860 7.986553 ATAAGAGGGATCCCATTACTATCAG 57.013 40.000 32.69 0.00 38.92 2.90
3710 3861 7.565398 GCTATAAGAGGGATCCCATTACTATCA 59.435 40.741 32.69 10.78 38.92 2.15
3711 3862 7.255660 CGCTATAAGAGGGATCCCATTACTATC 60.256 44.444 32.69 18.68 40.59 2.08
3712 3863 6.551601 CGCTATAAGAGGGATCCCATTACTAT 59.448 42.308 32.69 20.66 40.59 2.12
3713 3864 5.892119 CGCTATAAGAGGGATCCCATTACTA 59.108 44.000 32.69 19.35 40.59 1.82
3714 3865 4.712337 CGCTATAAGAGGGATCCCATTACT 59.288 45.833 32.69 20.98 40.59 2.24
3715 3866 4.466726 ACGCTATAAGAGGGATCCCATTAC 59.533 45.833 32.69 19.19 40.59 1.89
3716 3867 4.684724 ACGCTATAAGAGGGATCCCATTA 58.315 43.478 32.69 27.37 40.59 1.90
3717 3868 3.521727 ACGCTATAAGAGGGATCCCATT 58.478 45.455 32.69 26.21 40.59 3.16
3718 3869 3.191888 ACGCTATAAGAGGGATCCCAT 57.808 47.619 32.69 19.03 40.59 4.00
3719 3870 2.696526 ACGCTATAAGAGGGATCCCA 57.303 50.000 32.69 12.63 40.59 4.37
3760 3911 8.966868 ACAAATTTGAACCTTTGAGTTTCTAGA 58.033 29.630 24.64 0.00 36.19 2.43
3790 3941 1.831652 CGACTTTCAGTCTGCCCCCT 61.832 60.000 0.00 0.00 42.92 4.79
3791 3942 1.376037 CGACTTTCAGTCTGCCCCC 60.376 63.158 0.00 0.00 42.92 5.40
3852 4012 7.389053 AGTTGAATTTGTAACCTTTTGCACAAA 59.611 29.630 1.68 1.68 42.98 2.83
3881 4041 4.818863 CCCATCGGCCCATGCACA 62.819 66.667 4.56 0.00 40.13 4.57
3924 4098 4.098960 CCTTCCGTAGCACTACCATAAAGA 59.901 45.833 2.31 0.00 32.61 2.52
3930 4104 0.040058 TCCCTTCCGTAGCACTACCA 59.960 55.000 2.31 0.00 32.61 3.25
4042 4224 5.097529 TGAGTCGCACGTAGTAATTTTAGG 58.902 41.667 0.00 0.00 41.61 2.69
4325 4668 6.313744 TCTAGCAAAGCAGTAAGAAAAACC 57.686 37.500 0.00 0.00 0.00 3.27
4364 4707 7.433131 TCGTAATTCATGACTACCATTTACGAC 59.567 37.037 14.13 3.25 44.68 4.34
4365 4708 7.482474 TCGTAATTCATGACTACCATTTACGA 58.518 34.615 14.13 14.13 45.87 3.43
4366 4709 7.688478 TCGTAATTCATGACTACCATTTACG 57.312 36.000 0.00 7.35 43.64 3.18
4405 4748 7.633361 TGAGTTCTCACGTTATAGTTGAAAC 57.367 36.000 0.00 0.00 0.00 2.78
4440 4783 8.630917 CCGATACTTCTCAAGTAGATTAAAGGA 58.369 37.037 2.76 0.00 46.32 3.36
4521 4864 3.022557 AGGAGCATACATGTGCCAAAT 57.977 42.857 9.11 0.00 46.19 2.32
4576 4919 5.422666 TGAAAAGCACCTGATAATATGCG 57.577 39.130 0.00 0.00 42.98 4.73
4700 5044 1.086634 GTCGGCATGAGAAGCTGGTC 61.087 60.000 0.00 0.00 38.87 4.02
4775 5119 3.219224 CCTCTCCTGGCTCAGAGC 58.781 66.667 14.69 14.69 41.46 4.09
4820 5164 1.079405 TCTAGCTTGGTTTCCGGCG 60.079 57.895 0.00 0.00 32.06 6.46
4904 5248 1.215655 GAGGAAATCATCGACGCGGG 61.216 60.000 12.47 1.12 0.00 6.13
5080 5424 2.747686 GGTTCGACAGGGCTTCCA 59.252 61.111 0.00 0.00 0.00 3.53
5205 5549 4.447290 ACATACAGCACAACACAACAGTA 58.553 39.130 0.00 0.00 0.00 2.74
5262 5606 1.210155 CCGCCACTGCTAAAACTGC 59.790 57.895 0.00 0.00 34.43 4.40
5268 5612 2.437518 TAACGCACCGCCACTGCTAA 62.438 55.000 0.00 0.00 34.43 3.09
5319 5664 4.290459 AGGATCATGCTGGCAAATATAGGA 59.710 41.667 0.00 0.00 0.00 2.94
5321 5666 5.621555 GCAAGGATCATGCTGGCAAATATAG 60.622 44.000 13.72 0.00 34.57 1.31
5342 5690 4.339748 TGCTTCCATATGTGTAAAGGCAA 58.660 39.130 1.24 0.00 0.00 4.52
5350 5698 6.357579 TGGAAATTTTGCTTCCATATGTGT 57.642 33.333 1.24 0.00 45.88 3.72
5362 5710 8.706035 GTTCATGCATAGATATGGAAATTTTGC 58.294 33.333 0.00 0.00 37.57 3.68
5397 5745 5.694006 CGAAGCTCTAGGGTTTAGAATCATG 59.306 44.000 0.00 0.00 35.61 3.07
5429 5936 8.268850 ACAGGACACTAATGATTTTCATGTAC 57.731 34.615 0.00 0.00 37.15 2.90
5438 5945 6.989169 GCTAGAATGACAGGACACTAATGATT 59.011 38.462 0.00 0.00 0.00 2.57
5440 5947 5.422012 TGCTAGAATGACAGGACACTAATGA 59.578 40.000 0.00 0.00 0.00 2.57
5443 5950 5.480422 TCTTGCTAGAATGACAGGACACTAA 59.520 40.000 0.00 0.00 0.00 2.24
5448 5955 4.376146 GGATCTTGCTAGAATGACAGGAC 58.624 47.826 0.99 0.00 33.20 3.85
5451 5958 3.181471 ACGGGATCTTGCTAGAATGACAG 60.181 47.826 0.99 0.00 33.20 3.51
5452 5959 2.766263 ACGGGATCTTGCTAGAATGACA 59.234 45.455 0.99 0.00 33.20 3.58
5453 5960 3.460857 ACGGGATCTTGCTAGAATGAC 57.539 47.619 0.99 0.00 33.20 3.06
5454 5961 5.601662 CTTAACGGGATCTTGCTAGAATGA 58.398 41.667 0.99 0.00 33.20 2.57
5455 5962 4.212214 GCTTAACGGGATCTTGCTAGAATG 59.788 45.833 0.99 0.00 33.20 2.67
5510 6018 0.039256 TGTTTTGCTGCAGAATCGCC 60.039 50.000 20.43 0.00 0.00 5.54
5511 6019 1.055338 GTGTTTTGCTGCAGAATCGC 58.945 50.000 20.43 2.17 0.00 4.58
5512 6020 2.313234 CTGTGTTTTGCTGCAGAATCG 58.687 47.619 20.43 0.00 0.00 3.34
5600 6108 1.631405 TTTGTGAGGGGCCATCTTTG 58.369 50.000 20.14 0.00 0.00 2.77
5765 6274 8.669946 TTTGTGTCACACATATGTCTAAAGAA 57.330 30.769 12.49 0.00 44.16 2.52
5794 6303 8.786898 TGTCCATTTTCATTTGTTTTTGTTTCA 58.213 25.926 0.00 0.00 0.00 2.69
5795 6304 9.060547 GTGTCCATTTTCATTTGTTTTTGTTTC 57.939 29.630 0.00 0.00 0.00 2.78
5796 6305 8.026026 GGTGTCCATTTTCATTTGTTTTTGTTT 58.974 29.630 0.00 0.00 0.00 2.83
5799 6308 6.183360 ACGGTGTCCATTTTCATTTGTTTTTG 60.183 34.615 0.00 0.00 0.00 2.44
5800 6309 5.877564 ACGGTGTCCATTTTCATTTGTTTTT 59.122 32.000 0.00 0.00 0.00 1.94
5808 6317 2.286365 ACCACGGTGTCCATTTTCAT 57.714 45.000 7.45 0.00 0.00 2.57
5842 6351 6.723298 TGTGTATGTGAATTGGGAAAACTT 57.277 33.333 0.00 0.00 0.00 2.66
5848 6357 3.264193 AGAGCTGTGTATGTGAATTGGGA 59.736 43.478 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.