Multiple sequence alignment - TraesCS3D01G356600

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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 TraesCS3D01G356600 chr3D 100.000 5873 0 0 1 5873 468980626 468974754 0.000000e+00 10846
1 TraesCS3D01G356600 chr3D 98.331 659 11 0 1 659 520592715 520593373 0.000000e+00 1157
2 TraesCS3D01G356600 chr3D 98.179 659 12 0 1 659 560889618 560890276 0.000000e+00 1151
3 TraesCS3D01G356600 chr3D 98.027 659 13 0 1 659 484116079 484115421 0.000000e+00 1146
4 TraesCS3D01G356600 chr3D 90.667 150 12 2 3564 3712 468976915 468977063 1.290000e-46 198
5 TraesCS3D01G356600 chr3A 95.800 2881 61 10 741 3567 611205159 611202285 0.000000e+00 4595
6 TraesCS3D01G356600 chr3A 96.114 1441 45 6 4438 5873 611200724 611199290 0.000000e+00 2340
7 TraesCS3D01G356600 chr3A 95.269 761 14 2 3709 4447 611202286 611201526 0.000000e+00 1186
8 TraesCS3D01G356600 chr3B 93.648 2015 56 13 722 2704 622778060 622776086 0.000000e+00 2946
9 TraesCS3D01G356600 chr3B 94.719 1477 60 11 4407 5873 622770829 622769361 0.000000e+00 2279
10 TraesCS3D01G356600 chr3B 96.746 799 23 1 2772 3567 622776092 622775294 0.000000e+00 1328
11 TraesCS3D01G356600 chr3B 94.467 723 20 2 3709 4411 622775295 622774573 0.000000e+00 1096
12 TraesCS3D01G356600 chr3B 97.674 86 2 0 3557 3642 581135782 581135867 1.320000e-31 148
13 TraesCS3D01G356600 chr7D 98.626 655 9 0 1 655 170954628 170955282 0.000000e+00 1160
14 TraesCS3D01G356600 chr7D 88.618 123 13 1 3589 3711 405876765 405876886 1.320000e-31 148
15 TraesCS3D01G356600 chr7D 85.366 123 17 1 3565 3687 405876886 405876765 6.180000e-25 126
16 TraesCS3D01G356600 chr5D 98.338 662 10 1 1 661 274780422 274779761 0.000000e+00 1160
17 TraesCS3D01G356600 chr5D 98.331 659 10 1 1 659 233733173 233733830 0.000000e+00 1155
18 TraesCS3D01G356600 chr5D 98.030 660 13 0 1 660 362188540 362187881 0.000000e+00 1147
19 TraesCS3D01G356600 chr5D 88.079 151 9 5 3571 3714 549792054 549792202 2.810000e-38 171
20 TraesCS3D01G356600 chr4D 98.480 658 10 0 2 659 461791929 461792586 0.000000e+00 1160
21 TraesCS3D01G356600 chr4D 98.478 657 10 0 1 657 469322979 469323635 0.000000e+00 1158
22 TraesCS3D01G356600 chr4B 92.105 152 8 4 3559 3710 286072588 286072441 1.660000e-50 211
23 TraesCS3D01G356600 chr4A 89.209 139 11 1 3572 3710 709886887 709886753 2.810000e-38 171
24 TraesCS3D01G356600 chr6A 86.301 146 16 4 3566 3710 525608001 525608143 7.880000e-34 156
25 TraesCS3D01G356600 chr1B 97.674 86 2 0 3557 3642 498863935 498863850 1.320000e-31 148
26 TraesCS3D01G356600 chr6B 84.298 121 15 3 3595 3713 604707066 604707184 1.340000e-21 115
27 TraesCS3D01G356600 chr6B 84.615 117 14 3 3594 3710 19033773 19033885 4.810000e-21 113


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 TraesCS3D01G356600 chr3D 468974754 468980626 5872 True 10846.00 10846 100.000000 1 5873 1 chr3D.!!$R1 5872
1 TraesCS3D01G356600 chr3D 520592715 520593373 658 False 1157.00 1157 98.331000 1 659 1 chr3D.!!$F2 658
2 TraesCS3D01G356600 chr3D 560889618 560890276 658 False 1151.00 1151 98.179000 1 659 1 chr3D.!!$F3 658
3 TraesCS3D01G356600 chr3D 484115421 484116079 658 True 1146.00 1146 98.027000 1 659 1 chr3D.!!$R2 658
4 TraesCS3D01G356600 chr3A 611199290 611205159 5869 True 2707.00 4595 95.727667 741 5873 3 chr3A.!!$R1 5132
5 TraesCS3D01G356600 chr3B 622769361 622778060 8699 True 1912.25 2946 94.895000 722 5873 4 chr3B.!!$R1 5151
6 TraesCS3D01G356600 chr7D 170954628 170955282 654 False 1160.00 1160 98.626000 1 655 1 chr7D.!!$F1 654
7 TraesCS3D01G356600 chr5D 274779761 274780422 661 True 1160.00 1160 98.338000 1 661 1 chr5D.!!$R1 660
8 TraesCS3D01G356600 chr5D 233733173 233733830 657 False 1155.00 1155 98.331000 1 659 1 chr5D.!!$F1 658
9 TraesCS3D01G356600 chr5D 362187881 362188540 659 True 1147.00 1147 98.030000 1 660 1 chr5D.!!$R2 659
10 TraesCS3D01G356600 chr4D 461791929 461792586 657 False 1160.00 1160 98.480000 2 659 1 chr4D.!!$F1 657
11 TraesCS3D01G356600 chr4D 469322979 469323635 656 False 1158.00 1158 98.478000 1 657 1 chr4D.!!$F2 656

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
718 720 0.248289 AAAGGGTATACACGCACGCT 59.752 50.000 5.01 0.0 39.99 5.07 F
720 722 0.459585 AGGGTATACACGCACGCTTG 60.460 55.000 5.01 0.0 39.99 4.01 F
1512 1523 0.830444 ACTACGGGCTCCAGTCACAA 60.830 55.000 0.00 0.0 0.00 3.33 F
1549 1560 1.080329 AGTTGGGGTTTGGGGCATAAT 59.920 47.619 0.00 0.0 0.00 1.28 F
3279 3380 0.039256 CCCAACAACAGCATTCACCG 60.039 55.000 0.00 0.0 0.00 4.94 F
3535 3636 2.222953 GCACAGGTAATTAACGGCTTCG 60.223 50.000 0.09 0.0 40.22 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2416 3.437049 GCTGCAGTAACAGGAAAGGTTAG 59.563 47.826 16.64 0.0 38.16 2.34 R
2751 2849 3.637911 TTCATATTGCCCCGTAACACT 57.362 42.857 0.00 0.0 0.00 3.55 R
2930 3028 0.668535 AGCCTTTGCAAAACCGAGAC 59.331 50.000 13.84 0.0 41.13 3.36 R
3535 3636 0.968405 TGCATGTTCCCAGAAAAGGC 59.032 50.000 0.00 0.0 0.00 4.35 R
4628 9310 0.179089 AGAGGCGCAGATGCAAGTAG 60.179 55.000 10.83 0.0 42.21 2.57 R
4906 9589 0.179234 TGCCGAAACAGTGGACTTGA 59.821 50.000 0.00 0.0 0.00 3.02 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
200 201 2.542595 CGTGTTGCGTCCTCTACTTTTT 59.457 45.455 0.00 0.00 35.54 1.94
362 363 7.126268 TGAGAGGAGGAAGATGATGATTTTGTA 59.874 37.037 0.00 0.00 0.00 2.41
603 605 5.417580 TGTTAAAAAGTGGCACTTCTCAACT 59.582 36.000 31.24 13.43 37.47 3.16
637 639 6.549364 TGCTTTAAAGATTTGAGGGTTTGAGA 59.451 34.615 19.48 0.00 0.00 3.27
671 673 0.801251 GCTCTAAGCAGCAAGTGTGG 59.199 55.000 0.00 0.00 41.89 4.17
672 674 1.879796 GCTCTAAGCAGCAAGTGTGGT 60.880 52.381 0.00 0.00 41.89 4.16
673 675 2.612972 GCTCTAAGCAGCAAGTGTGGTA 60.613 50.000 0.00 0.00 41.89 3.25
674 676 3.664107 CTCTAAGCAGCAAGTGTGGTAA 58.336 45.455 0.00 0.00 33.05 2.85
675 677 3.664107 TCTAAGCAGCAAGTGTGGTAAG 58.336 45.455 0.00 0.00 33.05 2.34
676 678 0.954452 AAGCAGCAAGTGTGGTAAGC 59.046 50.000 0.00 0.00 33.05 3.09
677 679 0.890996 AGCAGCAAGTGTGGTAAGCC 60.891 55.000 0.00 0.00 33.05 4.35
678 680 1.172180 GCAGCAAGTGTGGTAAGCCA 61.172 55.000 0.00 0.00 43.73 4.75
688 690 2.570415 TGGTAAGCCATTTCACCGAA 57.430 45.000 0.00 0.00 40.46 4.30
689 691 2.865079 TGGTAAGCCATTTCACCGAAA 58.135 42.857 0.00 0.00 40.46 3.46
690 692 2.554893 TGGTAAGCCATTTCACCGAAAC 59.445 45.455 0.00 0.00 40.46 2.78
691 693 2.554893 GGTAAGCCATTTCACCGAAACA 59.445 45.455 0.00 0.00 34.23 2.83
692 694 3.192633 GGTAAGCCATTTCACCGAAACAT 59.807 43.478 0.00 0.00 34.23 2.71
693 695 4.396790 GGTAAGCCATTTCACCGAAACATA 59.603 41.667 0.00 0.00 34.23 2.29
694 696 5.106078 GGTAAGCCATTTCACCGAAACATAA 60.106 40.000 0.00 0.00 34.23 1.90
695 697 5.461032 AAGCCATTTCACCGAAACATAAA 57.539 34.783 0.00 0.00 34.23 1.40
696 698 4.805219 AGCCATTTCACCGAAACATAAAC 58.195 39.130 0.00 0.00 34.23 2.01
697 699 4.279671 AGCCATTTCACCGAAACATAAACA 59.720 37.500 0.00 0.00 34.23 2.83
698 700 4.621034 GCCATTTCACCGAAACATAAACAG 59.379 41.667 0.00 0.00 34.23 3.16
699 701 5.563867 GCCATTTCACCGAAACATAAACAGA 60.564 40.000 0.00 0.00 34.23 3.41
700 702 6.442952 CCATTTCACCGAAACATAAACAGAA 58.557 36.000 0.00 0.00 34.23 3.02
701 703 6.920758 CCATTTCACCGAAACATAAACAGAAA 59.079 34.615 0.00 0.00 34.23 2.52
702 704 7.114811 CCATTTCACCGAAACATAAACAGAAAG 59.885 37.037 0.00 0.00 34.23 2.62
703 705 5.682943 TCACCGAAACATAAACAGAAAGG 57.317 39.130 0.00 0.00 0.00 3.11
704 706 4.517453 TCACCGAAACATAAACAGAAAGGG 59.483 41.667 0.00 0.00 0.00 3.95
705 707 4.277423 CACCGAAACATAAACAGAAAGGGT 59.723 41.667 0.00 0.00 0.00 4.34
706 708 5.470777 CACCGAAACATAAACAGAAAGGGTA 59.529 40.000 0.00 0.00 0.00 3.69
707 709 6.150474 CACCGAAACATAAACAGAAAGGGTAT 59.850 38.462 0.00 0.00 0.00 2.73
708 710 7.334921 CACCGAAACATAAACAGAAAGGGTATA 59.665 37.037 0.00 0.00 0.00 1.47
709 711 7.335171 ACCGAAACATAAACAGAAAGGGTATAC 59.665 37.037 0.00 0.00 0.00 1.47
710 712 7.334921 CCGAAACATAAACAGAAAGGGTATACA 59.665 37.037 5.01 0.00 0.00 2.29
711 713 8.173130 CGAAACATAAACAGAAAGGGTATACAC 58.827 37.037 5.01 0.00 0.00 2.90
712 714 7.605410 AACATAAACAGAAAGGGTATACACG 57.395 36.000 5.01 0.00 0.00 4.49
713 715 5.583457 ACATAAACAGAAAGGGTATACACGC 59.417 40.000 5.01 0.00 37.87 5.34
714 716 3.688694 AACAGAAAGGGTATACACGCA 57.311 42.857 5.01 0.00 39.99 5.24
715 717 2.968675 ACAGAAAGGGTATACACGCAC 58.031 47.619 5.01 0.00 39.99 5.34
716 718 1.924524 CAGAAAGGGTATACACGCACG 59.075 52.381 5.01 0.00 39.99 5.34
717 719 0.648958 GAAAGGGTATACACGCACGC 59.351 55.000 5.01 0.00 39.99 5.34
718 720 0.248289 AAAGGGTATACACGCACGCT 59.752 50.000 5.01 0.00 39.99 5.07
719 721 0.248289 AAGGGTATACACGCACGCTT 59.752 50.000 5.01 0.00 41.49 4.68
720 722 0.459585 AGGGTATACACGCACGCTTG 60.460 55.000 5.01 0.00 39.99 4.01
732 734 1.596954 GCACGCTTGCTTTCTCGAAAA 60.597 47.619 8.12 0.00 46.17 2.29
1512 1523 0.830444 ACTACGGGCTCCAGTCACAA 60.830 55.000 0.00 0.00 0.00 3.33
1549 1560 1.080329 AGTTGGGGTTTGGGGCATAAT 59.920 47.619 0.00 0.00 0.00 1.28
1551 1562 1.577736 TGGGGTTTGGGGCATAATTG 58.422 50.000 0.00 0.00 0.00 2.32
1627 1639 7.344134 AGAGGGAAAACTACGCCTTTAATTAT 58.656 34.615 0.00 0.00 0.00 1.28
1669 1682 6.604735 AGATCACGATTAATTGTGGTTAGC 57.395 37.500 28.01 16.18 41.50 3.09
1695 1708 3.191162 TGCTTGTTTTCTTATCGCTGCAT 59.809 39.130 0.00 0.00 0.00 3.96
1696 1709 4.168760 GCTTGTTTTCTTATCGCTGCATT 58.831 39.130 0.00 0.00 0.00 3.56
1697 1710 4.622740 GCTTGTTTTCTTATCGCTGCATTT 59.377 37.500 0.00 0.00 0.00 2.32
1698 1711 5.443693 GCTTGTTTTCTTATCGCTGCATTTG 60.444 40.000 0.00 0.00 0.00 2.32
1699 1712 5.119931 TGTTTTCTTATCGCTGCATTTGT 57.880 34.783 0.00 0.00 0.00 2.83
1700 1713 4.916831 TGTTTTCTTATCGCTGCATTTGTG 59.083 37.500 0.00 0.00 0.00 3.33
1886 1900 2.479560 GCCTCCAAAAATACCACGATGC 60.480 50.000 0.00 0.00 0.00 3.91
1893 1907 2.192664 AATACCACGATGCACAACCA 57.807 45.000 0.00 0.00 0.00 3.67
2169 2235 7.010183 ACTCATTCGAATAGTAAATGTTGGTCG 59.990 37.037 10.97 0.00 33.22 4.79
2175 2241 7.760794 TCGAATAGTAAATGTTGGTCGTTATGT 59.239 33.333 0.00 0.00 0.00 2.29
2323 2416 4.698304 TGGTTATAAGCCTTGCAGTGTAAC 59.302 41.667 11.96 0.00 0.00 2.50
2591 2684 7.602644 TGACTTTTGATCTGTATAAGCGAAAGT 59.397 33.333 6.48 6.48 37.47 2.66
2751 2849 6.294120 CCAATATCTCTGCCGCATTTTATTCA 60.294 38.462 0.00 0.00 0.00 2.57
2861 2959 3.194755 TGTGCTCCATGTTACACGAGTAT 59.805 43.478 11.38 0.00 35.79 2.12
2930 3028 2.553602 TGCTGCCATAGTCACTTGTTTG 59.446 45.455 0.00 0.00 0.00 2.93
2958 3056 4.096231 GGTTTTGCAAAGGCTTTCATGTTT 59.904 37.500 10.08 0.00 41.91 2.83
3093 3191 0.107456 AACTGCCTGGAGTGTCACAG 59.893 55.000 5.62 0.00 34.54 3.66
3274 3375 1.122227 ACAAGCCCAACAACAGCATT 58.878 45.000 0.00 0.00 0.00 3.56
3279 3380 0.039256 CCCAACAACAGCATTCACCG 60.039 55.000 0.00 0.00 0.00 4.94
3535 3636 2.222953 GCACAGGTAATTAACGGCTTCG 60.223 50.000 0.09 0.00 40.22 3.79
3567 3668 8.682710 TCTGGGAACATGCATTTTAACTTATAC 58.317 33.333 0.00 0.00 41.51 1.47
3568 3669 8.588290 TGGGAACATGCATTTTAACTTATACT 57.412 30.769 0.00 0.00 33.40 2.12
3569 3670 8.682710 TGGGAACATGCATTTTAACTTATACTC 58.317 33.333 0.00 0.00 33.40 2.59
3570 3671 8.135529 GGGAACATGCATTTTAACTTATACTCC 58.864 37.037 0.00 0.00 0.00 3.85
3571 3672 8.135529 GGAACATGCATTTTAACTTATACTCCC 58.864 37.037 0.00 0.00 0.00 4.30
3572 3673 8.823220 AACATGCATTTTAACTTATACTCCCT 57.177 30.769 0.00 0.00 0.00 4.20
3573 3674 8.451908 ACATGCATTTTAACTTATACTCCCTC 57.548 34.615 0.00 0.00 0.00 4.30
3574 3675 7.502561 ACATGCATTTTAACTTATACTCCCTCC 59.497 37.037 0.00 0.00 0.00 4.30
3575 3676 6.053005 TGCATTTTAACTTATACTCCCTCCG 58.947 40.000 0.00 0.00 0.00 4.63
3576 3677 6.053650 GCATTTTAACTTATACTCCCTCCGT 58.946 40.000 0.00 0.00 0.00 4.69
3577 3678 6.541278 GCATTTTAACTTATACTCCCTCCGTT 59.459 38.462 0.00 0.00 0.00 4.44
3578 3679 7.254692 GCATTTTAACTTATACTCCCTCCGTTC 60.255 40.741 0.00 0.00 0.00 3.95
3579 3680 5.859205 TTAACTTATACTCCCTCCGTTCC 57.141 43.478 0.00 0.00 0.00 3.62
3580 3681 3.393426 ACTTATACTCCCTCCGTTCCA 57.607 47.619 0.00 0.00 0.00 3.53
3581 3682 3.716431 ACTTATACTCCCTCCGTTCCAA 58.284 45.455 0.00 0.00 0.00 3.53
3582 3683 4.098894 ACTTATACTCCCTCCGTTCCAAA 58.901 43.478 0.00 0.00 0.00 3.28
3583 3684 4.533311 ACTTATACTCCCTCCGTTCCAAAA 59.467 41.667 0.00 0.00 0.00 2.44
3584 3685 5.191124 ACTTATACTCCCTCCGTTCCAAAAT 59.809 40.000 0.00 0.00 0.00 1.82
3585 3686 6.384886 ACTTATACTCCCTCCGTTCCAAAATA 59.615 38.462 0.00 0.00 0.00 1.40
3586 3687 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3587 3688 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3588 3689 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3589 3690 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3590 3691 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3591 3692 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3592 3693 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
3593 3694 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
3594 3695 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
3595 3696 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
3596 3697 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
3597 3698 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
3598 3699 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
3599 3700 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
3600 3701 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
3601 3702 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
3602 3703 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
3603 3704 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
3604 3705 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
3605 3706 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
3606 3707 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
3607 3708 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
3608 3709 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
3609 3710 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
3611 3712 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
3612 3713 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
3613 3714 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
3614 3715 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
3637 3738 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3638 3739 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3639 3740 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3640 3741 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3641 3742 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
3642 3743 6.464222 AGTTGAGTCATCTATTTTGGAACGA 58.536 36.000 1.70 0.00 0.00 3.85
3643 3744 7.106239 AGTTGAGTCATCTATTTTGGAACGAT 58.894 34.615 1.70 0.00 0.00 3.73
3644 3745 8.258007 AGTTGAGTCATCTATTTTGGAACGATA 58.742 33.333 1.70 0.00 0.00 2.92
3645 3746 8.543774 GTTGAGTCATCTATTTTGGAACGATAG 58.456 37.037 0.00 0.00 46.19 2.08
3646 3747 8.007405 TGAGTCATCTATTTTGGAACGATAGA 57.993 34.615 0.00 0.00 36.96 1.98
3647 3748 8.642432 TGAGTCATCTATTTTGGAACGATAGAT 58.358 33.333 0.00 0.00 41.44 1.98
3652 3753 6.522054 TCTATTTTGGAACGATAGATGACCC 58.478 40.000 0.00 0.00 41.38 4.46
3653 3754 4.561500 TTTTGGAACGATAGATGACCCA 57.438 40.909 0.00 0.00 41.38 4.51
3654 3755 4.561500 TTTGGAACGATAGATGACCCAA 57.438 40.909 0.00 0.00 41.38 4.12
3655 3756 3.536956 TGGAACGATAGATGACCCAAC 57.463 47.619 0.00 0.00 41.38 3.77
3656 3757 3.104512 TGGAACGATAGATGACCCAACT 58.895 45.455 0.00 0.00 41.38 3.16
3657 3758 3.517901 TGGAACGATAGATGACCCAACTT 59.482 43.478 0.00 0.00 41.38 2.66
3658 3759 4.019681 TGGAACGATAGATGACCCAACTTT 60.020 41.667 0.00 0.00 41.38 2.66
3659 3760 4.332819 GGAACGATAGATGACCCAACTTTG 59.667 45.833 0.00 0.00 41.38 2.77
3660 3761 4.553330 ACGATAGATGACCCAACTTTGT 57.447 40.909 0.00 0.00 41.38 2.83
3661 3762 5.670792 ACGATAGATGACCCAACTTTGTA 57.329 39.130 0.00 0.00 41.38 2.41
3662 3763 5.416947 ACGATAGATGACCCAACTTTGTAC 58.583 41.667 0.00 0.00 41.38 2.90
3663 3764 5.187186 ACGATAGATGACCCAACTTTGTACT 59.813 40.000 0.00 0.00 41.38 2.73
3664 3765 6.379133 ACGATAGATGACCCAACTTTGTACTA 59.621 38.462 0.00 0.00 41.38 1.82
3665 3766 7.093640 ACGATAGATGACCCAACTTTGTACTAA 60.094 37.037 0.00 0.00 41.38 2.24
3666 3767 7.762615 CGATAGATGACCCAACTTTGTACTAAA 59.237 37.037 0.00 0.00 39.76 1.85
3667 3768 9.099454 GATAGATGACCCAACTTTGTACTAAAG 57.901 37.037 13.08 13.08 0.00 1.85
3668 3769 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
3670 3771 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
3671 3772 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
3672 3773 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
3673 3774 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
3696 3797 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3697 3798 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3698 3799 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3699 3800 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3700 3801 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
3701 3802 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
3702 3803 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3703 3804 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
3704 3805 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
3705 3806 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3706 3807 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3707 3808 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3708 3809 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
3709 3810 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
3786 3887 2.708051 CTGACTGTACTCTGGTCCGTA 58.292 52.381 0.00 0.00 0.00 4.02
3920 4021 5.587388 TCTTTGTAGATCGTCCCGTATTT 57.413 39.130 0.00 0.00 0.00 1.40
4107 4208 4.788201 GCACTTACGTATGCTCTCTCTCTG 60.788 50.000 12.79 1.03 38.84 3.35
4115 4236 3.719268 TGCTCTCTCTCTGTCTCTCTT 57.281 47.619 0.00 0.00 0.00 2.85
4218 4341 3.066203 TGGTTTTTCGAAGGAAGACAAGC 59.934 43.478 0.00 0.00 32.80 4.01
4356 4479 5.568825 GCACAAATCCCACTGAACTCTACTA 60.569 44.000 0.00 0.00 0.00 1.82
4415 8286 2.397044 ATGTTTGGGGCTTTTCCAGA 57.603 45.000 0.00 0.00 35.48 3.86
4522 9204 3.489355 TCTGCTCATTTTGTGGTCATGT 58.511 40.909 0.00 0.00 0.00 3.21
4628 9310 2.029365 GTGCCTTCTTCGTAATCGCTTC 59.971 50.000 0.00 0.00 36.96 3.86
4659 9341 1.468520 TGCGCCTCTGCTTTTAACATC 59.531 47.619 4.18 0.00 35.36 3.06
4828 9510 0.250234 TCCGGTTGCAGATCCTTCAG 59.750 55.000 0.00 0.00 0.00 3.02
4906 9589 1.283905 CCCCTCGGTGGAAGGTAATTT 59.716 52.381 0.00 0.00 38.35 1.82
4999 9682 4.290985 TCTTTAATGGTTGGGAGATGTGGA 59.709 41.667 0.00 0.00 0.00 4.02
5006 9689 4.229353 TGGTTGGGAGATGTGGATCATAAA 59.771 41.667 0.00 0.00 36.83 1.40
5148 9831 4.081862 TCTGAACAAATACCCCTGACTACG 60.082 45.833 0.00 0.00 0.00 3.51
5156 9839 2.444421 ACCCCTGACTACGTAGAGTTG 58.556 52.381 28.74 14.29 0.00 3.16
5191 9874 2.809696 TGATATTGGCATGATCGTGCAG 59.190 45.455 34.49 4.38 46.81 4.41
5207 9890 4.461431 TCGTGCAGTGAAGACCTTCTATTA 59.539 41.667 10.67 0.00 40.14 0.98
5211 9894 6.818644 GTGCAGTGAAGACCTTCTATTATCAA 59.181 38.462 10.67 0.00 40.14 2.57
5283 9966 8.049117 TCCACTCTTGCATATATTCTTTCTTGT 58.951 33.333 0.00 0.00 0.00 3.16
5454 10137 1.922570 CCGATCGTTTACCTGTCCAG 58.077 55.000 15.09 0.00 0.00 3.86
5460 10143 0.672711 GTTTACCTGTCCAGACCGGC 60.673 60.000 0.00 0.00 39.01 6.13
5516 10199 1.630369 TGCTAGCTGACTGGGTCATTT 59.370 47.619 17.23 0.00 41.94 2.32
5578 10261 3.371917 CCATGAATCTTTGTAGCTCCCCA 60.372 47.826 0.00 0.00 0.00 4.96
5715 10403 2.448477 CGCAAGGAAATTGGCAAGC 58.552 52.632 5.96 0.34 39.47 4.01
5723 10411 2.419667 GAAATTGGCAAGCTTGTGCAT 58.580 42.857 26.55 13.31 46.81 3.96
5765 10453 3.265791 GCTATCAGGGCATTAATCCTCG 58.734 50.000 0.00 0.00 0.00 4.63
5773 10461 1.401552 GCATTAATCCTCGTTGCTGCA 59.598 47.619 0.00 0.00 0.00 4.41
5821 10509 8.400947 GTGAGACAGATATGTTTGTGCAAATAT 58.599 33.333 10.76 10.76 36.37 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.068691 TCTCCTCCAACTCGGCCG 61.069 66.667 22.12 22.12 33.14 6.13
200 201 1.177401 CTCATCGGAGTGTCACCTCA 58.823 55.000 0.00 0.00 36.36 3.86
533 535 6.185511 GGGCAAATACTAGAACCCTTAAACT 58.814 40.000 0.00 0.00 34.34 2.66
603 605 9.965824 CCTCAAATCTTTAAAGCAGTTTTAAGA 57.034 29.630 10.51 3.34 42.50 2.10
620 622 5.574970 AGAACTCTCAAACCCTCAAATCT 57.425 39.130 0.00 0.00 0.00 2.40
670 672 2.554893 TGTTTCGGTGAAATGGCTTACC 59.445 45.455 0.00 0.00 33.97 2.85
671 673 3.907894 TGTTTCGGTGAAATGGCTTAC 57.092 42.857 0.00 0.00 33.97 2.34
672 674 6.016192 TGTTTATGTTTCGGTGAAATGGCTTA 60.016 34.615 0.00 0.00 33.97 3.09
673 675 5.221342 TGTTTATGTTTCGGTGAAATGGCTT 60.221 36.000 0.00 0.00 33.97 4.35
674 676 4.279671 TGTTTATGTTTCGGTGAAATGGCT 59.720 37.500 0.00 0.00 33.97 4.75
675 677 4.551388 TGTTTATGTTTCGGTGAAATGGC 58.449 39.130 0.00 0.00 33.97 4.40
676 678 6.007936 TCTGTTTATGTTTCGGTGAAATGG 57.992 37.500 0.00 0.00 33.97 3.16
677 679 7.114811 CCTTTCTGTTTATGTTTCGGTGAAATG 59.885 37.037 0.00 0.00 33.97 2.32
678 680 7.145323 CCTTTCTGTTTATGTTTCGGTGAAAT 58.855 34.615 0.00 0.00 33.97 2.17
679 681 6.460399 CCCTTTCTGTTTATGTTTCGGTGAAA 60.460 38.462 0.00 0.00 0.00 2.69
680 682 5.009210 CCCTTTCTGTTTATGTTTCGGTGAA 59.991 40.000 0.00 0.00 0.00 3.18
681 683 4.517453 CCCTTTCTGTTTATGTTTCGGTGA 59.483 41.667 0.00 0.00 0.00 4.02
682 684 4.277423 ACCCTTTCTGTTTATGTTTCGGTG 59.723 41.667 0.00 0.00 0.00 4.94
683 685 4.466827 ACCCTTTCTGTTTATGTTTCGGT 58.533 39.130 0.00 0.00 0.00 4.69
684 686 6.753107 ATACCCTTTCTGTTTATGTTTCGG 57.247 37.500 0.00 0.00 0.00 4.30
685 687 8.173130 GTGTATACCCTTTCTGTTTATGTTTCG 58.827 37.037 0.00 0.00 0.00 3.46
686 688 8.173130 CGTGTATACCCTTTCTGTTTATGTTTC 58.827 37.037 0.00 0.00 0.00 2.78
687 689 7.361457 GCGTGTATACCCTTTCTGTTTATGTTT 60.361 37.037 0.00 0.00 0.00 2.83
688 690 6.093082 GCGTGTATACCCTTTCTGTTTATGTT 59.907 38.462 0.00 0.00 0.00 2.71
689 691 5.583457 GCGTGTATACCCTTTCTGTTTATGT 59.417 40.000 0.00 0.00 0.00 2.29
690 692 5.583061 TGCGTGTATACCCTTTCTGTTTATG 59.417 40.000 0.00 0.00 0.00 1.90
691 693 5.583457 GTGCGTGTATACCCTTTCTGTTTAT 59.417 40.000 0.00 0.00 0.00 1.40
692 694 4.931002 GTGCGTGTATACCCTTTCTGTTTA 59.069 41.667 0.00 0.00 0.00 2.01
693 695 3.749609 GTGCGTGTATACCCTTTCTGTTT 59.250 43.478 0.00 0.00 0.00 2.83
694 696 3.332034 GTGCGTGTATACCCTTTCTGTT 58.668 45.455 0.00 0.00 0.00 3.16
695 697 2.673043 CGTGCGTGTATACCCTTTCTGT 60.673 50.000 0.00 0.00 0.00 3.41
696 698 1.924524 CGTGCGTGTATACCCTTTCTG 59.075 52.381 0.00 0.00 0.00 3.02
697 699 1.738030 GCGTGCGTGTATACCCTTTCT 60.738 52.381 0.00 0.00 0.00 2.52
698 700 0.648958 GCGTGCGTGTATACCCTTTC 59.351 55.000 0.00 0.00 0.00 2.62
699 701 0.248289 AGCGTGCGTGTATACCCTTT 59.752 50.000 0.00 0.00 0.00 3.11
700 702 0.248289 AAGCGTGCGTGTATACCCTT 59.752 50.000 0.00 0.00 0.00 3.95
701 703 0.459585 CAAGCGTGCGTGTATACCCT 60.460 55.000 0.00 0.00 0.00 4.34
702 704 2.003672 CAAGCGTGCGTGTATACCC 58.996 57.895 0.00 0.00 0.00 3.69
703 705 1.347221 GCAAGCGTGCGTGTATACC 59.653 57.895 9.33 0.00 41.93 2.73
704 706 4.946766 GCAAGCGTGCGTGTATAC 57.053 55.556 9.33 0.00 41.93 1.47
713 715 2.383298 TTTTCGAGAAAGCAAGCGTG 57.617 45.000 0.00 0.00 0.00 5.34
714 716 3.626028 ATTTTTCGAGAAAGCAAGCGT 57.374 38.095 7.25 0.00 0.00 5.07
715 717 5.147162 AGTTATTTTTCGAGAAAGCAAGCG 58.853 37.500 7.25 0.00 0.00 4.68
716 718 8.502161 TTTAGTTATTTTTCGAGAAAGCAAGC 57.498 30.769 7.25 0.00 0.00 4.01
717 719 9.118236 CCTTTAGTTATTTTTCGAGAAAGCAAG 57.882 33.333 7.25 3.28 0.00 4.01
718 720 8.626526 ACCTTTAGTTATTTTTCGAGAAAGCAA 58.373 29.630 7.25 1.46 0.00 3.91
719 721 8.161699 ACCTTTAGTTATTTTTCGAGAAAGCA 57.838 30.769 7.25 0.00 0.00 3.91
720 722 9.539139 GTACCTTTAGTTATTTTTCGAGAAAGC 57.461 33.333 7.25 0.80 0.00 3.51
772 774 1.330213 CGCATGACACGCAAATCCATA 59.670 47.619 0.00 0.00 0.00 2.74
1316 1318 1.630369 AGTATTGTGGAAGCTGGCTGA 59.370 47.619 0.00 0.00 0.00 4.26
1512 1523 2.559668 CAACTTCACCTGTGCCATCATT 59.440 45.455 0.00 0.00 0.00 2.57
1549 1560 7.512130 AGGCTAATGTGTGATATTCAGATCAA 58.488 34.615 0.00 0.00 37.58 2.57
1551 1562 7.976135 AAGGCTAATGTGTGATATTCAGATC 57.024 36.000 0.00 0.00 0.00 2.75
1596 1607 4.067192 GGCGTAGTTTTCCCTCTTGTTAA 58.933 43.478 0.00 0.00 0.00 2.01
1669 1682 4.560035 CAGCGATAAGAAAACAAGCAATGG 59.440 41.667 0.00 0.00 0.00 3.16
1689 1702 3.862267 TGTTACACAAACACAAATGCAGC 59.138 39.130 0.00 0.00 43.22 5.25
1700 1713 7.250569 CCTCCATGTATGAATGTTACACAAAC 58.749 38.462 0.00 0.00 38.67 2.93
2175 2241 9.155975 GAGCATCTAGTCTTGAATTCTTACAAA 57.844 33.333 7.05 0.00 0.00 2.83
2259 2345 9.813080 GCAAAGACAAGAGTTACAAAATACTAG 57.187 33.333 0.00 0.00 0.00 2.57
2260 2346 9.555727 AGCAAAGACAAGAGTTACAAAATACTA 57.444 29.630 0.00 0.00 0.00 1.82
2261 2347 8.345565 CAGCAAAGACAAGAGTTACAAAATACT 58.654 33.333 0.00 0.00 0.00 2.12
2262 2348 8.129211 ACAGCAAAGACAAGAGTTACAAAATAC 58.871 33.333 0.00 0.00 0.00 1.89
2263 2349 8.220755 ACAGCAAAGACAAGAGTTACAAAATA 57.779 30.769 0.00 0.00 0.00 1.40
2264 2350 7.067494 AGACAGCAAAGACAAGAGTTACAAAAT 59.933 33.333 0.00 0.00 0.00 1.82
2265 2351 6.374333 AGACAGCAAAGACAAGAGTTACAAAA 59.626 34.615 0.00 0.00 0.00 2.44
2266 2352 5.880332 AGACAGCAAAGACAAGAGTTACAAA 59.120 36.000 0.00 0.00 0.00 2.83
2267 2353 5.428253 AGACAGCAAAGACAAGAGTTACAA 58.572 37.500 0.00 0.00 0.00 2.41
2268 2354 5.023533 AGACAGCAAAGACAAGAGTTACA 57.976 39.130 0.00 0.00 0.00 2.41
2269 2355 5.405873 GGTAGACAGCAAAGACAAGAGTTAC 59.594 44.000 0.00 0.00 0.00 2.50
2270 2356 5.304614 AGGTAGACAGCAAAGACAAGAGTTA 59.695 40.000 0.00 0.00 0.00 2.24
2271 2357 4.101741 AGGTAGACAGCAAAGACAAGAGTT 59.898 41.667 0.00 0.00 0.00 3.01
2272 2358 3.643792 AGGTAGACAGCAAAGACAAGAGT 59.356 43.478 0.00 0.00 0.00 3.24
2273 2359 3.993081 CAGGTAGACAGCAAAGACAAGAG 59.007 47.826 0.00 0.00 0.00 2.85
2274 2360 3.803715 GCAGGTAGACAGCAAAGACAAGA 60.804 47.826 0.00 0.00 0.00 3.02
2323 2416 3.437049 GCTGCAGTAACAGGAAAGGTTAG 59.563 47.826 16.64 0.00 38.16 2.34
2751 2849 3.637911 TTCATATTGCCCCGTAACACT 57.362 42.857 0.00 0.00 0.00 3.55
2839 2937 1.343142 ACTCGTGTAACATGGAGCACA 59.657 47.619 13.47 2.77 35.74 4.57
2840 2938 2.080286 ACTCGTGTAACATGGAGCAC 57.920 50.000 0.00 1.75 35.74 4.40
2861 2959 2.254152 ACCCTGGCTATGAGAACTCA 57.746 50.000 6.98 6.98 44.59 3.41
2930 3028 0.668535 AGCCTTTGCAAAACCGAGAC 59.331 50.000 13.84 0.00 41.13 3.36
2958 3056 2.427453 TGGCAAAAAGAAACTACCGCAA 59.573 40.909 0.00 0.00 0.00 4.85
3535 3636 0.968405 TGCATGTTCCCAGAAAAGGC 59.032 50.000 0.00 0.00 0.00 4.35
3567 3668 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3568 3669 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3569 3670 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3570 3671 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
3571 3672 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
3572 3673 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
3573 3674 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
3574 3675 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
3575 3676 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
3576 3677 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
3577 3678 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
3578 3679 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
3579 3680 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
3580 3681 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
3581 3682 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
3582 3683 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
3583 3684 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
3584 3685 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
3585 3686 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
3586 3687 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
3587 3688 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
3588 3689 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
3611 3712 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3612 3713 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3613 3714 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3614 3715 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3615 3716 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
3616 3717 7.444183 TCGTTCCAAAATAGATGACTCAACTTT 59.556 33.333 0.00 0.00 0.00 2.66
3617 3718 6.934645 TCGTTCCAAAATAGATGACTCAACTT 59.065 34.615 0.00 0.00 0.00 2.66
3618 3719 6.464222 TCGTTCCAAAATAGATGACTCAACT 58.536 36.000 0.00 0.00 0.00 3.16
3619 3720 6.721571 TCGTTCCAAAATAGATGACTCAAC 57.278 37.500 0.00 0.00 0.00 3.18
3620 3721 8.474831 TCTATCGTTCCAAAATAGATGACTCAA 58.525 33.333 0.00 0.00 29.31 3.02
3621 3722 8.007405 TCTATCGTTCCAAAATAGATGACTCA 57.993 34.615 0.00 0.00 29.31 3.41
3627 3728 7.162082 GGGTCATCTATCGTTCCAAAATAGAT 58.838 38.462 0.00 0.00 41.28 1.98
3628 3729 6.099125 TGGGTCATCTATCGTTCCAAAATAGA 59.901 38.462 0.00 0.00 36.67 1.98
3629 3730 6.288294 TGGGTCATCTATCGTTCCAAAATAG 58.712 40.000 0.00 0.00 0.00 1.73
3630 3731 6.241882 TGGGTCATCTATCGTTCCAAAATA 57.758 37.500 0.00 0.00 0.00 1.40
3631 3732 5.110814 TGGGTCATCTATCGTTCCAAAAT 57.889 39.130 0.00 0.00 0.00 1.82
3632 3733 4.561500 TGGGTCATCTATCGTTCCAAAA 57.438 40.909 0.00 0.00 0.00 2.44
3633 3734 4.019681 AGTTGGGTCATCTATCGTTCCAAA 60.020 41.667 0.00 0.00 35.03 3.28
3634 3735 3.517901 AGTTGGGTCATCTATCGTTCCAA 59.482 43.478 0.00 0.00 0.00 3.53
3635 3736 3.104512 AGTTGGGTCATCTATCGTTCCA 58.895 45.455 0.00 0.00 0.00 3.53
3636 3737 3.821421 AGTTGGGTCATCTATCGTTCC 57.179 47.619 0.00 0.00 0.00 3.62
3637 3738 4.935808 ACAAAGTTGGGTCATCTATCGTTC 59.064 41.667 0.00 0.00 0.00 3.95
3638 3739 4.906618 ACAAAGTTGGGTCATCTATCGTT 58.093 39.130 0.00 0.00 0.00 3.85
3639 3740 4.553330 ACAAAGTTGGGTCATCTATCGT 57.447 40.909 0.00 0.00 0.00 3.73
3640 3741 5.661458 AGTACAAAGTTGGGTCATCTATCG 58.339 41.667 0.00 0.00 0.00 2.92
3641 3742 9.099454 CTTTAGTACAAAGTTGGGTCATCTATC 57.901 37.037 0.00 0.00 0.00 2.08
3642 3743 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
3643 3744 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
3644 3745 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
3645 3746 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
3646 3747 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
3647 3748 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
3670 3771 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3671 3772 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3672 3773 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3673 3774 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3674 3775 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
3675 3776 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
3676 3777 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
3677 3778 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
3678 3779 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
3679 3780 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3680 3781 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3681 3782 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
3682 3783 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
3683 3784 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3684 3785 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3685 3786 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3686 3787 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3687 3788 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3688 3789 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3689 3790 6.294899 CGATATACTCCCTCCGTTCCAAAATA 60.295 42.308 0.00 0.00 0.00 1.40
3690 3791 5.510861 CGATATACTCCCTCCGTTCCAAAAT 60.511 44.000 0.00 0.00 0.00 1.82
3691 3792 4.202182 CGATATACTCCCTCCGTTCCAAAA 60.202 45.833 0.00 0.00 0.00 2.44
3692 3793 3.319972 CGATATACTCCCTCCGTTCCAAA 59.680 47.826 0.00 0.00 0.00 3.28
3693 3794 2.889045 CGATATACTCCCTCCGTTCCAA 59.111 50.000 0.00 0.00 0.00 3.53
3694 3795 2.158564 ACGATATACTCCCTCCGTTCCA 60.159 50.000 0.00 0.00 0.00 3.53
3695 3796 2.512705 ACGATATACTCCCTCCGTTCC 58.487 52.381 0.00 0.00 0.00 3.62
3696 3797 3.305199 CCAACGATATACTCCCTCCGTTC 60.305 52.174 0.00 0.00 38.02 3.95
3697 3798 2.626743 CCAACGATATACTCCCTCCGTT 59.373 50.000 0.00 0.00 40.25 4.44
3698 3799 2.236766 CCAACGATATACTCCCTCCGT 58.763 52.381 0.00 0.00 0.00 4.69
3699 3800 1.067776 GCCAACGATATACTCCCTCCG 60.068 57.143 0.00 0.00 0.00 4.63
3700 3801 1.067776 CGCCAACGATATACTCCCTCC 60.068 57.143 0.00 0.00 43.93 4.30
3701 3802 1.884579 TCGCCAACGATATACTCCCTC 59.115 52.381 0.00 0.00 45.12 4.30
3702 3803 1.991121 TCGCCAACGATATACTCCCT 58.009 50.000 0.00 0.00 45.12 4.20
4107 4208 2.771089 TGCACCACATGAAAGAGAGAC 58.229 47.619 0.00 0.00 0.00 3.36
4115 4236 3.472283 AAATTGCTTGCACCACATGAA 57.528 38.095 0.00 0.00 0.00 2.57
4166 4289 2.031807 CAGATGCCAATTTCTCTCTGCG 59.968 50.000 0.00 0.00 0.00 5.18
4218 4341 9.551734 TCATCTTACATAATTTCTCTGTGGATG 57.448 33.333 0.00 0.00 36.68 3.51
4356 4479 2.226315 TCAGGACAGTGCCATGGCT 61.226 57.895 35.53 17.44 42.51 4.75
4415 8286 1.535462 CCGGCTTGTCAACTTCGAAAT 59.465 47.619 0.00 0.00 0.00 2.17
4522 9204 7.716998 AGAGCAAAGACTATTTCAGTTTTCAGA 59.283 33.333 0.00 0.00 37.72 3.27
4567 9249 6.079424 ACACCGCACACATTAAAGTTAATT 57.921 33.333 0.00 0.00 31.28 1.40
4628 9310 0.179089 AGAGGCGCAGATGCAAGTAG 60.179 55.000 10.83 0.00 42.21 2.57
4659 9341 3.194542 TCCAGTCAACCTTTTGTTTGTGG 59.805 43.478 0.00 0.00 34.00 4.17
4828 9510 1.279271 AGGACCCACTGTAGATGTTGC 59.721 52.381 0.00 0.00 0.00 4.17
4906 9589 0.179234 TGCCGAAACAGTGGACTTGA 59.821 50.000 0.00 0.00 0.00 3.02
5006 9689 5.707066 ACCAGAAGGCTCTCAATAGATTT 57.293 39.130 0.00 0.00 39.06 2.17
5148 9831 4.627467 CACTACCACTGAATGCAACTCTAC 59.373 45.833 0.00 0.00 0.00 2.59
5156 9839 4.023707 GCCAATATCACTACCACTGAATGC 60.024 45.833 0.00 0.00 0.00 3.56
5191 9874 8.723942 ACATGTTGATAATAGAAGGTCTTCAC 57.276 34.615 12.54 1.28 41.84 3.18
5260 9943 7.555554 AGCACAAGAAAGAATATATGCAAGAGT 59.444 33.333 0.00 0.00 34.27 3.24
5283 9966 3.398406 ACATCGTGTGATACAACAAGCA 58.602 40.909 0.00 0.00 32.18 3.91
5454 10137 0.884704 TTTGAGACAAGCAGCCGGTC 60.885 55.000 1.90 6.02 0.00 4.79
5460 10143 2.478134 CCTTCGACTTTGAGACAAGCAG 59.522 50.000 0.00 0.00 0.00 4.24
5707 10395 3.355378 AGTATATGCACAAGCTTGCCAA 58.645 40.909 26.27 11.91 42.25 4.52
5709 10397 3.876914 TGTAGTATATGCACAAGCTTGCC 59.123 43.478 26.27 17.32 42.25 4.52
5715 10403 6.258160 GGCAAGTTTGTAGTATATGCACAAG 58.742 40.000 0.00 1.66 33.96 3.16
5723 10411 3.680937 GCACACGGCAAGTTTGTAGTATA 59.319 43.478 0.00 0.00 43.97 1.47
5765 10453 0.675633 ACCACTGGAAATGCAGCAAC 59.324 50.000 0.00 0.00 0.00 4.17
5773 10461 1.451449 TACCACCCACCACTGGAAAT 58.549 50.000 0.71 0.00 40.55 2.17
5830 10518 7.322664 CAGCCACATAAATTCAGTAAACCATT 58.677 34.615 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.