Multiple sequence alignment - TraesCS3D01G489700

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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 TraesCS3D01G489700 chr3D 100.000 3111 0 0 1 3111 584047747 584050857 0.000000e+00 5746.0
1 TraesCS3D01G489700 chr3D 86.184 1339 127 32 830 2127 584129660 584130981 0.000000e+00 1395.0
2 TraesCS3D01G489700 chr3D 89.586 941 74 10 924 1841 584456977 584456038 0.000000e+00 1173.0
3 TraesCS3D01G489700 chr3D 78.148 270 36 17 1869 2130 584453907 584453653 1.930000e-32 150.0
4 TraesCS3D01G489700 chr3D 92.308 78 2 3 3031 3104 584050699 584050776 1.180000e-19 108.0
5 TraesCS3D01G489700 chr3D 92.308 78 2 3 2953 3030 584050777 584050850 1.180000e-19 108.0
6 TraesCS3D01G489700 chr3D 90.164 61 5 1 3039 3098 584451271 584451211 9.250000e-11 78.7
7 TraesCS3D01G489700 chr3B 89.481 2139 164 20 926 3030 781344499 781346610 0.000000e+00 2647.0
8 TraesCS3D01G489700 chr3B 87.789 1425 96 27 699 2110 781210244 781211603 0.000000e+00 1596.0
9 TraesCS3D01G489700 chr3B 88.738 1101 67 17 799 1855 781355990 781357077 0.000000e+00 1293.0
10 TraesCS3D01G489700 chr3B 88.314 1044 89 19 924 1958 781494902 781493883 0.000000e+00 1221.0
11 TraesCS3D01G489700 chr3B 86.106 583 42 12 1 573 781209653 781210206 2.670000e-165 592.0
12 TraesCS3D01G489700 chr3B 83.733 584 68 10 1 579 781341970 781342531 7.640000e-146 527.0
13 TraesCS3D01G489700 chr3B 82.986 288 33 10 2746 3030 781488822 781488548 2.400000e-61 246.0
14 TraesCS3D01G489700 chr3B 77.129 411 90 3 2117 2524 26575199 26575608 5.190000e-58 235.0
15 TraesCS3D01G489700 chr3B 85.165 182 15 6 2823 2996 781217074 781217251 3.190000e-40 176.0
16 TraesCS3D01G489700 chr3B 95.181 83 2 1 3031 3111 781346535 781346617 2.520000e-26 130.0
17 TraesCS3D01G489700 chr3B 89.552 67 7 0 3039 3105 781488613 781488547 5.530000e-13 86.1
18 TraesCS3D01G489700 chr3A 87.829 1101 96 18 924 1992 21360391 21359297 0.000000e+00 1256.0
19 TraesCS3D01G489700 chr3A 93.333 105 4 2 574 676 647618288 647618185 5.370000e-33 152.0
20 TraesCS3D01G489700 chr3A 91.753 97 4 1 825 917 21360543 21360447 7.000000e-27 132.0
21 TraesCS3D01G489700 chr7D 86.295 1131 102 26 924 2026 588419740 588420845 0.000000e+00 1181.0
22 TraesCS3D01G489700 chr7D 78.904 602 111 14 2137 2730 118868972 118868379 8.090000e-106 394.0
23 TraesCS3D01G489700 chr7D 78.559 555 113 4 2180 2730 236001364 236000812 8.200000e-96 361.0
24 TraesCS3D01G489700 chr7D 95.876 97 4 0 580 676 474338721 474338817 1.150000e-34 158.0
25 TraesCS3D01G489700 chr7D 87.805 123 7 2 799 917 588419566 588419684 1.500000e-28 137.0
26 TraesCS3D01G489700 chrUn 84.164 1244 121 38 924 2126 45483347 45482139 0.000000e+00 1136.0
27 TraesCS3D01G489700 chrUn 92.537 67 5 0 3039 3105 45500697 45500763 2.550000e-16 97.1
28 TraesCS3D01G489700 chr4D 77.488 613 125 9 2124 2730 16303695 16303090 3.820000e-94 355.0
29 TraesCS3D01G489700 chr4D 76.961 612 130 7 2124 2730 16328934 16328329 3.840000e-89 339.0
30 TraesCS3D01G489700 chr5B 77.915 566 117 6 2170 2730 54508263 54507701 2.300000e-91 346.0
31 TraesCS3D01G489700 chr4A 75.941 611 130 14 2128 2730 666154193 666153592 6.520000e-77 298.0
32 TraesCS3D01G489700 chr4A 76.660 527 117 6 2126 2649 584075370 584075893 1.410000e-73 287.0
33 TraesCS3D01G489700 chr1B 74.291 564 115 19 2136 2682 679721551 679722101 8.740000e-51 211.0
34 TraesCS3D01G489700 chr5D 93.636 110 6 1 567 676 205794633 205794741 2.480000e-36 163.0
35 TraesCS3D01G489700 chr5D 95.000 100 5 0 577 676 521371681 521371582 1.150000e-34 158.0
36 TraesCS3D01G489700 chr2B 95.050 101 5 0 576 676 601206842 601206942 3.210000e-35 159.0
37 TraesCS3D01G489700 chr1D 95.050 101 5 0 576 676 483907577 483907677 3.210000e-35 159.0
38 TraesCS3D01G489700 chr7B 95.000 100 5 0 577 676 562993166 562993067 1.150000e-34 158.0
39 TraesCS3D01G489700 chr7A 94.118 102 6 0 575 676 60728522 60728623 4.150000e-34 156.0
40 TraesCS3D01G489700 chr7A 87.302 126 9 4 552 676 510625287 510625406 1.500000e-28 137.0


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 TraesCS3D01G489700 chr3D 584047747 584050857 3110 False 1987.333333 5746 94.8720 1 3111 3 chr3D.!!$F2 3110
1 TraesCS3D01G489700 chr3D 584129660 584130981 1321 False 1395.000000 1395 86.1840 830 2127 1 chr3D.!!$F1 1297
2 TraesCS3D01G489700 chr3D 584451211 584456977 5766 True 467.233333 1173 85.9660 924 3098 3 chr3D.!!$R1 2174
3 TraesCS3D01G489700 chr3B 781355990 781357077 1087 False 1293.000000 1293 88.7380 799 1855 1 chr3B.!!$F3 1056
4 TraesCS3D01G489700 chr3B 781493883 781494902 1019 True 1221.000000 1221 88.3140 924 1958 1 chr3B.!!$R1 1034
5 TraesCS3D01G489700 chr3B 781341970 781346617 4647 False 1101.333333 2647 89.4650 1 3111 3 chr3B.!!$F5 3110
6 TraesCS3D01G489700 chr3B 781209653 781211603 1950 False 1094.000000 1596 86.9475 1 2110 2 chr3B.!!$F4 2109
7 TraesCS3D01G489700 chr3A 21359297 21360543 1246 True 694.000000 1256 89.7910 825 1992 2 chr3A.!!$R2 1167
8 TraesCS3D01G489700 chr7D 588419566 588420845 1279 False 659.000000 1181 87.0500 799 2026 2 chr7D.!!$F2 1227
9 TraesCS3D01G489700 chr7D 118868379 118868972 593 True 394.000000 394 78.9040 2137 2730 1 chr7D.!!$R1 593
10 TraesCS3D01G489700 chr7D 236000812 236001364 552 True 361.000000 361 78.5590 2180 2730 1 chr7D.!!$R2 550
11 TraesCS3D01G489700 chrUn 45482139 45483347 1208 True 1136.000000 1136 84.1640 924 2126 1 chrUn.!!$R1 1202
12 TraesCS3D01G489700 chr4D 16303090 16303695 605 True 355.000000 355 77.4880 2124 2730 1 chr4D.!!$R1 606
13 TraesCS3D01G489700 chr4D 16328329 16328934 605 True 339.000000 339 76.9610 2124 2730 1 chr4D.!!$R2 606
14 TraesCS3D01G489700 chr5B 54507701 54508263 562 True 346.000000 346 77.9150 2170 2730 1 chr5B.!!$R1 560
15 TraesCS3D01G489700 chr4A 666153592 666154193 601 True 298.000000 298 75.9410 2128 2730 1 chr4A.!!$R1 602
16 TraesCS3D01G489700 chr4A 584075370 584075893 523 False 287.000000 287 76.6600 2126 2649 1 chr4A.!!$F1 523
17 TraesCS3D01G489700 chr1B 679721551 679722101 550 False 211.000000 211 74.2910 2136 2682 1 chr1B.!!$F1 546

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
676 689 1.073098 ATTTTGGGACGGAGGGAGTT 58.927 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 8302 0.248289 TGGACGAAGAATTCCCGACC 59.752 55.0 22.51 22.51 43.81 4.79 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
55 56 5.804639 TGCTGGAGTATAATGTTGTCACTT 58.195 37.500 0.00 0.00 0.00 3.16
77 78 3.915536 ACTTTCTCTTAGTTCGGACTGC 58.084 45.455 6.62 0.00 36.60 4.40
102 103 2.586425 ACTAGTTGGTGCATGCAGTTT 58.414 42.857 23.41 7.94 0.00 2.66
169 171 3.639094 AGCACGCCTCTCTCTATTTGTAT 59.361 43.478 0.00 0.00 0.00 2.29
190 192 7.367285 TGTATACATCAGAAAGTGTTTTTGGC 58.633 34.615 0.08 0.00 0.00 4.52
192 194 4.432712 ACATCAGAAAGTGTTTTTGGCAC 58.567 39.130 0.00 0.00 37.13 5.01
195 197 6.040842 ACATCAGAAAGTGTTTTTGGCACTAT 59.959 34.615 0.00 0.00 45.36 2.12
196 198 5.830912 TCAGAAAGTGTTTTTGGCACTATG 58.169 37.500 0.00 0.08 45.36 2.23
198 200 4.649218 AGAAAGTGTTTTTGGCACTATGGT 59.351 37.500 0.00 0.00 45.36 3.55
199 201 5.128663 AGAAAGTGTTTTTGGCACTATGGTT 59.871 36.000 0.00 0.00 45.36 3.67
200 202 4.320608 AGTGTTTTTGGCACTATGGTTG 57.679 40.909 0.00 0.00 44.41 3.77
209 211 5.854010 TGGCACTATGGTTGTTGTTAAAA 57.146 34.783 0.00 0.00 0.00 1.52
555 568 8.921205 GGGATACAACCTAGACTTACTGATTAA 58.079 37.037 0.00 0.00 39.74 1.40
563 576 7.447853 ACCTAGACTTACTGATTAATACTCCCG 59.552 40.741 0.00 0.00 0.00 5.14
573 586 1.755393 AATACTCCCGCCGTCCCATC 61.755 60.000 0.00 0.00 0.00 3.51
580 593 1.209504 CCCGCCGTCCCATCATATAAT 59.790 52.381 0.00 0.00 0.00 1.28
581 594 2.432874 CCCGCCGTCCCATCATATAATA 59.567 50.000 0.00 0.00 0.00 0.98
582 595 3.071023 CCCGCCGTCCCATCATATAATAT 59.929 47.826 0.00 0.00 0.00 1.28
583 596 4.444306 CCCGCCGTCCCATCATATAATATT 60.444 45.833 0.00 0.00 0.00 1.28
584 597 4.750098 CCGCCGTCCCATCATATAATATTC 59.250 45.833 0.00 0.00 0.00 1.75
585 598 4.750098 CGCCGTCCCATCATATAATATTCC 59.250 45.833 0.00 0.00 0.00 3.01
586 599 5.063880 GCCGTCCCATCATATAATATTCCC 58.936 45.833 0.00 0.00 0.00 3.97
587 600 5.163195 GCCGTCCCATCATATAATATTCCCT 60.163 44.000 0.00 0.00 0.00 4.20
588 601 6.525629 CCGTCCCATCATATAATATTCCCTC 58.474 44.000 0.00 0.00 0.00 4.30
589 602 6.464465 CCGTCCCATCATATAATATTCCCTCC 60.464 46.154 0.00 0.00 0.00 4.30
590 603 6.525629 GTCCCATCATATAATATTCCCTCCG 58.474 44.000 0.00 0.00 0.00 4.63
591 604 6.099845 GTCCCATCATATAATATTCCCTCCGT 59.900 42.308 0.00 0.00 0.00 4.69
592 605 6.326583 TCCCATCATATAATATTCCCTCCGTC 59.673 42.308 0.00 0.00 0.00 4.79
593 606 6.464465 CCCATCATATAATATTCCCTCCGTCC 60.464 46.154 0.00 0.00 0.00 4.79
594 607 6.464465 CCATCATATAATATTCCCTCCGTCCC 60.464 46.154 0.00 0.00 0.00 4.46
595 608 5.595770 TCATATAATATTCCCTCCGTCCCA 58.404 41.667 0.00 0.00 0.00 4.37
596 609 6.026834 TCATATAATATTCCCTCCGTCCCAA 58.973 40.000 0.00 0.00 0.00 4.12
597 610 6.502510 TCATATAATATTCCCTCCGTCCCAAA 59.497 38.462 0.00 0.00 0.00 3.28
598 611 5.656549 ATAATATTCCCTCCGTCCCAAAA 57.343 39.130 0.00 0.00 0.00 2.44
599 612 4.536295 AATATTCCCTCCGTCCCAAAAT 57.464 40.909 0.00 0.00 0.00 1.82
600 613 5.656549 AATATTCCCTCCGTCCCAAAATA 57.343 39.130 0.00 0.00 0.00 1.40
601 614 5.656549 ATATTCCCTCCGTCCCAAAATAA 57.343 39.130 0.00 0.00 0.00 1.40
602 615 3.359695 TTCCCTCCGTCCCAAAATAAG 57.640 47.619 0.00 0.00 0.00 1.73
603 616 2.271777 TCCCTCCGTCCCAAAATAAGT 58.728 47.619 0.00 0.00 0.00 2.24
604 617 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
605 618 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
606 619 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
607 620 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
608 621 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
609 622 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
610 623 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
611 624 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
612 625 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
613 626 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
614 627 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
615 628 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
616 629 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
617 630 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
618 631 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
619 632 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
625 638 8.788325 AAGTGTCTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
626 639 9.880157 AAGTGTCTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
627 640 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
628 641 9.310716 GTGTCTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
652 665 6.803154 ACAAAATTGTACTAAGCCTGAGAC 57.197 37.500 0.00 0.00 40.16 3.36
653 666 6.296026 ACAAAATTGTACTAAGCCTGAGACA 58.704 36.000 0.00 0.00 40.16 3.41
654 667 6.428159 ACAAAATTGTACTAAGCCTGAGACAG 59.572 38.462 0.00 0.00 40.16 3.51
655 668 5.746990 AATTGTACTAAGCCTGAGACAGT 57.253 39.130 0.00 0.00 0.00 3.55
656 669 5.746990 ATTGTACTAAGCCTGAGACAGTT 57.253 39.130 0.00 0.00 0.00 3.16
657 670 6.852420 ATTGTACTAAGCCTGAGACAGTTA 57.148 37.500 0.00 0.00 0.00 2.24
658 671 6.852420 TTGTACTAAGCCTGAGACAGTTAT 57.148 37.500 0.00 0.00 0.00 1.89
659 672 6.852420 TGTACTAAGCCTGAGACAGTTATT 57.148 37.500 0.00 0.00 0.00 1.40
660 673 7.241042 TGTACTAAGCCTGAGACAGTTATTT 57.759 36.000 0.00 0.00 0.00 1.40
661 674 7.676947 TGTACTAAGCCTGAGACAGTTATTTT 58.323 34.615 0.00 0.00 0.00 1.82
662 675 7.602644 TGTACTAAGCCTGAGACAGTTATTTTG 59.397 37.037 0.00 0.00 0.00 2.44
663 676 5.940470 ACTAAGCCTGAGACAGTTATTTTGG 59.060 40.000 0.00 0.00 0.00 3.28
664 677 3.690460 AGCCTGAGACAGTTATTTTGGG 58.310 45.455 0.00 0.00 0.00 4.12
665 678 3.330701 AGCCTGAGACAGTTATTTTGGGA 59.669 43.478 0.00 0.00 0.00 4.37
666 679 3.440522 GCCTGAGACAGTTATTTTGGGAC 59.559 47.826 0.00 0.00 0.00 4.46
667 680 3.684788 CCTGAGACAGTTATTTTGGGACG 59.315 47.826 0.00 0.00 0.00 4.79
668 681 3.670625 TGAGACAGTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
669 682 3.325425 TGAGACAGTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
670 683 3.933332 GAGACAGTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
671 684 3.007635 GACAGTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
672 685 2.290705 ACAGTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
676 689 1.073098 ATTTTGGGACGGAGGGAGTT 58.927 50.000 0.00 0.00 0.00 3.01
692 705 3.555518 GGAGTTCGTTTTTGCAAGCTAG 58.444 45.455 0.00 0.00 0.00 3.42
693 706 3.003378 GGAGTTCGTTTTTGCAAGCTAGT 59.997 43.478 0.00 0.00 0.00 2.57
695 708 5.091910 AGTTCGTTTTTGCAAGCTAGTAC 57.908 39.130 0.00 0.00 0.00 2.73
696 709 3.781341 TCGTTTTTGCAAGCTAGTACG 57.219 42.857 0.00 5.16 0.00 3.67
697 710 3.125316 TCGTTTTTGCAAGCTAGTACGT 58.875 40.909 0.00 0.00 0.00 3.57
743 763 4.546829 ATGAAGCATGTGCAAATTTCCT 57.453 36.364 7.83 0.00 45.16 3.36
744 764 3.916761 TGAAGCATGTGCAAATTTCCTC 58.083 40.909 7.83 0.00 45.16 3.71
758 1042 2.093306 TTCCTCGTTGAACGCATCAT 57.907 45.000 13.62 0.00 42.21 2.45
769 1053 7.490079 TCGTTGAACGCATCATAGTTTAGTAAT 59.510 33.333 13.62 0.00 42.21 1.89
770 1054 7.787935 CGTTGAACGCATCATAGTTTAGTAATC 59.212 37.037 4.26 0.00 38.03 1.75
775 1059 7.265673 ACGCATCATAGTTTAGTAATCACAGT 58.734 34.615 0.00 0.00 0.00 3.55
793 1077 1.899814 AGTACCAGCTTTGGTCGATCA 59.100 47.619 0.00 0.00 42.99 2.92
820 1123 3.877874 ACGCGAGTACATGACACAA 57.122 47.368 15.93 0.00 46.88 3.33
821 1124 2.143008 ACGCGAGTACATGACACAAA 57.857 45.000 15.93 0.00 46.88 2.83
822 1125 2.683968 ACGCGAGTACATGACACAAAT 58.316 42.857 15.93 0.00 46.88 2.32
823 1126 3.064207 ACGCGAGTACATGACACAAATT 58.936 40.909 15.93 0.00 46.88 1.82
1012 2782 3.395054 TCTCATCCAGTCATCCTCAGT 57.605 47.619 0.00 0.00 0.00 3.41
1226 3013 1.080298 CCTCGACGGCCGTAAGTTT 60.080 57.895 34.36 7.22 39.75 2.66
1235 3022 1.810755 GGCCGTAAGTTTTGCTAGCTT 59.189 47.619 17.23 3.72 0.00 3.74
1247 3034 6.608808 AGTTTTGCTAGCTTTTCCATCCATAT 59.391 34.615 17.23 0.00 0.00 1.78
1248 3035 7.779798 AGTTTTGCTAGCTTTTCCATCCATATA 59.220 33.333 17.23 0.00 0.00 0.86
1249 3036 7.750229 TTTGCTAGCTTTTCCATCCATATAG 57.250 36.000 17.23 0.00 0.00 1.31
1878 3737 0.251341 GCATGAGGTTGGTTGGGTCT 60.251 55.000 0.00 0.00 0.00 3.85
2013 3885 1.053424 TTTAGTGAAGGGTGTCGCCT 58.947 50.000 1.66 0.00 37.43 5.52
2048 3922 6.660887 AATTGTTGCTTTTTGTTCACGAAT 57.339 29.167 0.00 0.00 0.00 3.34
2051 3925 4.797868 TGTTGCTTTTTGTTCACGAATGAG 59.202 37.500 0.00 0.00 35.83 2.90
2104 3978 4.339872 TTGCTGAAAATGAATGTGCCTT 57.660 36.364 0.00 0.00 0.00 4.35
2115 3989 7.832503 AATGAATGTGCCTTATTGCTTTAAC 57.167 32.000 0.00 0.00 0.00 2.01
2124 3998 6.208402 TGCCTTATTGCTTTAACTGTCATGAA 59.792 34.615 0.00 0.00 0.00 2.57
2260 8251 3.671411 AGAACGAGCCGCTGACGT 61.671 61.111 0.00 0.00 41.97 4.34
2278 8270 0.942410 GTGCCGTTGTCGTTGCTCTA 60.942 55.000 0.00 0.00 35.01 2.43
2279 8271 0.666274 TGCCGTTGTCGTTGCTCTAG 60.666 55.000 0.00 0.00 35.01 2.43
2310 8302 1.514228 CCTGACCGTGTCGATGACG 60.514 63.158 11.77 11.77 34.95 4.35
2337 8329 0.903454 ATTCTTCGTCCACGTCCCCT 60.903 55.000 0.00 0.00 40.80 4.79
2350 8349 3.098445 TCCCCTTAAGGACCTGTGG 57.902 57.895 23.74 13.93 38.24 4.17
2391 8390 4.026062 CGCCGTTGAATTCTTGAATCGATA 60.026 41.667 7.05 0.00 0.00 2.92
2392 8391 5.198274 GCCGTTGAATTCTTGAATCGATAC 58.802 41.667 7.05 0.00 0.00 2.24
2455 8457 1.488261 GAAACCCTAATCTCGCCGCG 61.488 60.000 6.39 6.39 0.00 6.46
2460 8462 1.878522 CTAATCTCGCCGCGCAAGT 60.879 57.895 8.75 0.00 41.68 3.16
2499 8501 1.567504 TAGAGCTCCGTTTAATGCGC 58.432 50.000 10.93 0.00 0.00 6.09
2531 8533 2.040442 TTGGGGAGGATCGGAGCA 59.960 61.111 0.00 0.00 34.37 4.26
2532 8534 1.384502 TTGGGGAGGATCGGAGCAT 60.385 57.895 0.00 0.00 34.37 3.79
2554 8556 6.597280 GCATGGAAGACTAACTCAAAGAAGAT 59.403 38.462 0.00 0.00 0.00 2.40
2638 8643 1.467920 GAGGCACCAGAAAATCCCTG 58.532 55.000 0.00 0.00 0.00 4.45
2673 8678 4.792804 GAGTGGCAGGCAGAGGGC 62.793 72.222 0.00 0.00 43.74 5.19
2692 8697 0.329261 CAGGTGAATCCTTGGGCTCA 59.671 55.000 0.00 0.00 45.67 4.26
2696 8701 1.198094 TGAATCCTTGGGCTCACCGA 61.198 55.000 0.00 0.00 44.64 4.69
2714 8720 0.974383 GACAAAGTTCGAGGGGAGGA 59.026 55.000 0.00 0.00 0.00 3.71
2755 8761 9.671279 TGATGTACAAGTCACATGATAAAGAAT 57.329 29.630 0.00 0.00 36.76 2.40
2879 8890 3.791973 TGATTTGCACCGACAGTTTTT 57.208 38.095 0.00 0.00 0.00 1.94
2980 8993 4.147135 GGCTCTACCAACCTCCCA 57.853 61.111 0.00 0.00 38.86 4.37
2981 8994 1.602771 GGCTCTACCAACCTCCCAC 59.397 63.158 0.00 0.00 38.86 4.61
2982 8995 1.218316 GCTCTACCAACCTCCCACG 59.782 63.158 0.00 0.00 0.00 4.94
2983 8996 1.542187 GCTCTACCAACCTCCCACGT 61.542 60.000 0.00 0.00 0.00 4.49
2984 8997 0.531200 CTCTACCAACCTCCCACGTC 59.469 60.000 0.00 0.00 0.00 4.34
2985 8998 0.901580 TCTACCAACCTCCCACGTCC 60.902 60.000 0.00 0.00 0.00 4.79
2986 8999 1.152290 TACCAACCTCCCACGTCCA 60.152 57.895 0.00 0.00 0.00 4.02
2987 9000 1.474332 TACCAACCTCCCACGTCCAC 61.474 60.000 0.00 0.00 0.00 4.02
2988 9001 2.813726 CCAACCTCCCACGTCCACA 61.814 63.158 0.00 0.00 0.00 4.17
2989 9002 1.597027 CAACCTCCCACGTCCACAC 60.597 63.158 0.00 0.00 0.00 3.82
2999 9012 4.750460 GTCCACACGAAGCTGTGA 57.250 55.556 10.91 0.00 42.55 3.58
3000 9013 2.986311 GTCCACACGAAGCTGTGAA 58.014 52.632 10.91 0.00 42.55 3.18
3001 9014 0.582005 GTCCACACGAAGCTGTGAAC 59.418 55.000 10.91 0.00 42.55 3.18
3002 9015 0.531974 TCCACACGAAGCTGTGAACC 60.532 55.000 10.91 0.00 42.55 3.62
3003 9016 0.532862 CCACACGAAGCTGTGAACCT 60.533 55.000 10.91 0.00 42.55 3.50
3004 9017 1.299541 CACACGAAGCTGTGAACCTT 58.700 50.000 10.91 0.00 42.55 3.50
3005 9018 1.261619 CACACGAAGCTGTGAACCTTC 59.738 52.381 10.91 0.00 42.55 3.46
3006 9019 0.868406 CACGAAGCTGTGAACCTTCC 59.132 55.000 0.00 0.00 42.55 3.46
3007 9020 0.759346 ACGAAGCTGTGAACCTTCCT 59.241 50.000 0.00 0.00 35.23 3.36
3008 9021 1.270358 ACGAAGCTGTGAACCTTCCTC 60.270 52.381 0.00 0.00 35.23 3.71
3009 9022 1.001406 CGAAGCTGTGAACCTTCCTCT 59.999 52.381 0.00 0.00 35.23 3.69
3010 9023 2.548920 CGAAGCTGTGAACCTTCCTCTT 60.549 50.000 0.00 0.00 35.23 2.85
3011 9024 2.849294 AGCTGTGAACCTTCCTCTTC 57.151 50.000 0.00 0.00 0.00 2.87
3012 9025 2.334023 AGCTGTGAACCTTCCTCTTCT 58.666 47.619 0.00 0.00 0.00 2.85
3013 9026 2.301583 AGCTGTGAACCTTCCTCTTCTC 59.698 50.000 0.00 0.00 0.00 2.87
3014 9027 2.301583 GCTGTGAACCTTCCTCTTCTCT 59.698 50.000 0.00 0.00 0.00 3.10
3015 9028 3.616317 GCTGTGAACCTTCCTCTTCTCTC 60.616 52.174 0.00 0.00 0.00 3.20
3016 9029 3.576118 CTGTGAACCTTCCTCTTCTCTCA 59.424 47.826 0.00 0.00 0.00 3.27
3017 9030 3.322254 TGTGAACCTTCCTCTTCTCTCAC 59.678 47.826 0.00 0.00 34.03 3.51
3018 9031 2.558795 TGAACCTTCCTCTTCTCTCACG 59.441 50.000 0.00 0.00 0.00 4.35
3019 9032 0.892063 ACCTTCCTCTTCTCTCACGC 59.108 55.000 0.00 0.00 0.00 5.34
3020 9033 0.174617 CCTTCCTCTTCTCTCACGCC 59.825 60.000 0.00 0.00 0.00 5.68
3021 9034 1.181786 CTTCCTCTTCTCTCACGCCT 58.818 55.000 0.00 0.00 0.00 5.52
3022 9035 2.370349 CTTCCTCTTCTCTCACGCCTA 58.630 52.381 0.00 0.00 0.00 3.93
3023 9036 2.509166 TCCTCTTCTCTCACGCCTAA 57.491 50.000 0.00 0.00 0.00 2.69
3024 9037 3.019799 TCCTCTTCTCTCACGCCTAAT 57.980 47.619 0.00 0.00 0.00 1.73
3025 9038 3.366396 TCCTCTTCTCTCACGCCTAATT 58.634 45.455 0.00 0.00 0.00 1.40
3026 9039 3.131223 TCCTCTTCTCTCACGCCTAATTG 59.869 47.826 0.00 0.00 0.00 2.32
3027 9040 3.452474 CTCTTCTCTCACGCCTAATTGG 58.548 50.000 0.00 0.00 39.35 3.16
3028 9041 2.832129 TCTTCTCTCACGCCTAATTGGT 59.168 45.455 0.00 0.00 38.35 3.67
3029 9042 3.260884 TCTTCTCTCACGCCTAATTGGTT 59.739 43.478 0.00 0.00 38.35 3.67
3030 9043 3.695830 TCTCTCACGCCTAATTGGTTT 57.304 42.857 0.00 0.00 38.35 3.27
3031 9044 3.334691 TCTCTCACGCCTAATTGGTTTG 58.665 45.455 0.00 0.00 38.35 2.93
3032 9045 3.007506 TCTCTCACGCCTAATTGGTTTGA 59.992 43.478 0.00 0.00 38.35 2.69
3033 9046 3.334691 TCTCACGCCTAATTGGTTTGAG 58.665 45.455 14.11 14.11 42.90 3.02
3034 9047 3.074412 CTCACGCCTAATTGGTTTGAGT 58.926 45.455 13.06 0.00 39.73 3.41
3035 9048 4.020928 TCTCACGCCTAATTGGTTTGAGTA 60.021 41.667 16.84 8.75 42.51 2.59
3036 9049 4.839121 TCACGCCTAATTGGTTTGAGTAT 58.161 39.130 0.00 0.00 38.35 2.12
3037 9050 4.634004 TCACGCCTAATTGGTTTGAGTATG 59.366 41.667 0.00 0.00 38.35 2.39
3038 9051 3.945285 ACGCCTAATTGGTTTGAGTATGG 59.055 43.478 0.00 0.00 38.35 2.74
3039 9052 3.243068 CGCCTAATTGGTTTGAGTATGGC 60.243 47.826 0.00 0.00 38.35 4.40
3040 9053 3.954258 GCCTAATTGGTTTGAGTATGGCT 59.046 43.478 0.00 0.00 38.35 4.75
3041 9054 4.202050 GCCTAATTGGTTTGAGTATGGCTG 60.202 45.833 0.00 0.00 38.35 4.85
3042 9055 4.339247 CCTAATTGGTTTGAGTATGGCTGG 59.661 45.833 0.00 0.00 0.00 4.85
3043 9056 1.544724 TTGGTTTGAGTATGGCTGGC 58.455 50.000 0.00 0.00 0.00 4.85
3044 9057 0.698238 TGGTTTGAGTATGGCTGGCT 59.302 50.000 2.00 0.00 0.00 4.75
3045 9058 1.340017 TGGTTTGAGTATGGCTGGCTC 60.340 52.381 2.00 0.00 0.00 4.70
3046 9059 1.065126 GGTTTGAGTATGGCTGGCTCT 60.065 52.381 2.00 0.00 0.00 4.09
3047 9060 2.170607 GGTTTGAGTATGGCTGGCTCTA 59.829 50.000 2.00 0.00 0.00 2.43
3048 9061 3.198872 GTTTGAGTATGGCTGGCTCTAC 58.801 50.000 2.00 4.76 0.00 2.59
3049 9062 1.414158 TGAGTATGGCTGGCTCTACC 58.586 55.000 2.00 0.85 39.84 3.18
3098 9114 4.090819 ACCTTCCTCTTCTCTCACCTAAC 58.909 47.826 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.379186 CGCAGTCCGAACTAAGAGAAAGTA 60.379 45.833 0.00 0.00 40.02 2.24
77 78 2.482336 TGCATGCACCAACTAGTTTACG 59.518 45.455 18.46 0.00 0.00 3.18
134 136 4.270325 AGAGGCGTGCTTTATTCGTAATTC 59.730 41.667 0.00 0.00 0.00 2.17
169 171 5.359576 AGTGCCAAAAACACTTTCTGATGTA 59.640 36.000 0.00 0.00 46.01 2.29
233 235 5.515270 GCCCGCTTTCAATTCAATTAAGTAC 59.485 40.000 0.00 0.00 0.00 2.73
344 347 6.222389 TGGCCACACTTGAATTTAATTTGAG 58.778 36.000 0.00 0.00 0.00 3.02
462 473 6.825721 AGGCTCAGTCAATAAGATTTAACTGG 59.174 38.462 0.00 0.00 35.86 4.00
476 487 5.893824 TCATTGTATCTCTAGGCTCAGTCAA 59.106 40.000 0.00 0.00 0.00 3.18
481 492 9.716531 CAATTTATCATTGTATCTCTAGGCTCA 57.283 33.333 0.00 0.00 0.00 4.26
522 535 2.104967 CTAGGTTGTATCCCACGGACA 58.895 52.381 0.00 0.00 32.98 4.02
555 568 2.122989 ATGGGACGGCGGGAGTAT 60.123 61.111 13.24 0.00 0.00 2.12
563 576 5.063880 GGGAATATTATATGATGGGACGGC 58.936 45.833 0.00 0.00 0.00 5.68
573 586 5.950544 TGGGACGGAGGGAATATTATATG 57.049 43.478 0.00 0.00 0.00 1.78
580 593 4.475747 ACTTATTTTGGGACGGAGGGAATA 59.524 41.667 0.00 0.00 0.00 1.75
581 594 3.268595 ACTTATTTTGGGACGGAGGGAAT 59.731 43.478 0.00 0.00 0.00 3.01
582 595 2.645797 ACTTATTTTGGGACGGAGGGAA 59.354 45.455 0.00 0.00 0.00 3.97
583 596 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
584 597 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
585 598 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
586 599 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
587 600 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
588 601 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
589 602 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
590 603 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
591 604 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
592 605 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
593 606 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
599 612 9.880157 AAAGTTAGTACAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
600 613 8.788325 AAAGTTAGTACAAAGTTGAGACACTT 57.212 30.769 0.00 0.98 38.74 3.16
601 614 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
602 615 9.310716 ACTAAAGTTAGTACAAAGTTGAGACAC 57.689 33.333 1.81 0.00 41.92 3.67
628 641 7.446769 TGTCTCAGGCTTAGTACAATTTTGTA 58.553 34.615 0.00 0.00 42.35 2.41
629 642 6.296026 TGTCTCAGGCTTAGTACAATTTTGT 58.704 36.000 1.08 1.08 44.86 2.83
630 643 6.428159 ACTGTCTCAGGCTTAGTACAATTTTG 59.572 38.462 0.00 0.00 35.51 2.44
631 644 6.534634 ACTGTCTCAGGCTTAGTACAATTTT 58.465 36.000 0.00 0.00 35.51 1.82
632 645 6.115448 ACTGTCTCAGGCTTAGTACAATTT 57.885 37.500 0.00 0.00 35.51 1.82
633 646 5.746990 ACTGTCTCAGGCTTAGTACAATT 57.253 39.130 0.00 0.00 35.51 2.32
634 647 5.746990 AACTGTCTCAGGCTTAGTACAAT 57.253 39.130 0.00 0.00 35.51 2.71
635 648 6.852420 ATAACTGTCTCAGGCTTAGTACAA 57.148 37.500 0.00 0.00 35.51 2.41
636 649 6.852420 AATAACTGTCTCAGGCTTAGTACA 57.148 37.500 0.00 0.00 35.51 2.90
637 650 7.064728 CCAAAATAACTGTCTCAGGCTTAGTAC 59.935 40.741 0.00 0.00 35.51 2.73
638 651 7.103641 CCAAAATAACTGTCTCAGGCTTAGTA 58.896 38.462 0.00 0.00 35.51 1.82
639 652 5.940470 CCAAAATAACTGTCTCAGGCTTAGT 59.060 40.000 0.00 0.00 35.51 2.24
640 653 5.355350 CCCAAAATAACTGTCTCAGGCTTAG 59.645 44.000 1.90 0.00 35.51 2.18
641 654 5.013704 TCCCAAAATAACTGTCTCAGGCTTA 59.986 40.000 1.90 0.00 35.51 3.09
642 655 4.082125 CCCAAAATAACTGTCTCAGGCTT 58.918 43.478 1.90 0.00 35.51 4.35
643 656 3.330701 TCCCAAAATAACTGTCTCAGGCT 59.669 43.478 1.90 0.00 35.51 4.58
644 657 3.440522 GTCCCAAAATAACTGTCTCAGGC 59.559 47.826 1.90 0.00 35.51 4.85
645 658 3.684788 CGTCCCAAAATAACTGTCTCAGG 59.315 47.826 1.90 0.00 35.51 3.86
646 659 3.684788 CCGTCCCAAAATAACTGTCTCAG 59.315 47.826 0.00 0.00 37.52 3.35
647 660 3.325425 TCCGTCCCAAAATAACTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
648 661 3.933332 CTCCGTCCCAAAATAACTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
649 662 3.307480 CCTCCGTCCCAAAATAACTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
650 663 3.007635 CCTCCGTCCCAAAATAACTGTC 58.992 50.000 0.00 0.00 0.00 3.51
651 664 2.290705 CCCTCCGTCCCAAAATAACTGT 60.291 50.000 0.00 0.00 0.00 3.55
652 665 2.026636 TCCCTCCGTCCCAAAATAACTG 60.027 50.000 0.00 0.00 0.00 3.16
653 666 2.238898 CTCCCTCCGTCCCAAAATAACT 59.761 50.000 0.00 0.00 0.00 2.24
654 667 2.026542 ACTCCCTCCGTCCCAAAATAAC 60.027 50.000 0.00 0.00 0.00 1.89
655 668 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
656 669 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
657 670 1.004394 GAACTCCCTCCGTCCCAAAAT 59.996 52.381 0.00 0.00 0.00 1.82
658 671 0.399075 GAACTCCCTCCGTCCCAAAA 59.601 55.000 0.00 0.00 0.00 2.44
659 672 1.823169 CGAACTCCCTCCGTCCCAAA 61.823 60.000 0.00 0.00 0.00 3.28
660 673 2.280552 CGAACTCCCTCCGTCCCAA 61.281 63.158 0.00 0.00 0.00 4.12
661 674 2.678934 CGAACTCCCTCCGTCCCA 60.679 66.667 0.00 0.00 0.00 4.37
662 675 1.824224 AAACGAACTCCCTCCGTCCC 61.824 60.000 0.00 0.00 35.28 4.46
663 676 0.034476 AAAACGAACTCCCTCCGTCC 59.966 55.000 0.00 0.00 35.28 4.79
664 677 1.529865 CAAAAACGAACTCCCTCCGTC 59.470 52.381 0.00 0.00 35.28 4.79
665 678 1.589803 CAAAAACGAACTCCCTCCGT 58.410 50.000 0.00 0.00 38.24 4.69
666 679 0.237498 GCAAAAACGAACTCCCTCCG 59.763 55.000 0.00 0.00 0.00 4.63
667 680 1.314730 TGCAAAAACGAACTCCCTCC 58.685 50.000 0.00 0.00 0.00 4.30
668 681 2.858646 GCTTGCAAAAACGAACTCCCTC 60.859 50.000 0.00 0.00 0.00 4.30
669 682 1.067060 GCTTGCAAAAACGAACTCCCT 59.933 47.619 0.00 0.00 0.00 4.20
670 683 1.067060 AGCTTGCAAAAACGAACTCCC 59.933 47.619 0.00 0.00 0.00 4.30
671 684 2.492019 AGCTTGCAAAAACGAACTCC 57.508 45.000 0.00 0.00 0.00 3.85
672 685 4.210832 ACTAGCTTGCAAAAACGAACTC 57.789 40.909 0.00 0.00 0.00 3.01
676 689 3.125316 ACGTACTAGCTTGCAAAAACGA 58.875 40.909 16.52 0.86 33.59 3.85
727 747 2.352503 ACGAGGAAATTTGCACATGC 57.647 45.000 12.54 0.00 42.50 4.06
743 763 5.165676 ACTAAACTATGATGCGTTCAACGA 58.834 37.500 15.79 0.00 46.05 3.85
744 764 5.450376 ACTAAACTATGATGCGTTCAACG 57.550 39.130 5.28 5.28 45.88 4.10
758 1042 7.713734 AGCTGGTACTGTGATTACTAAACTA 57.286 36.000 0.00 0.00 0.00 2.24
820 1123 6.849085 TTGTCAAGCACCATACCATTAATT 57.151 33.333 0.00 0.00 0.00 1.40
821 1124 7.422465 AATTGTCAAGCACCATACCATTAAT 57.578 32.000 0.00 0.00 0.00 1.40
822 1125 6.849085 AATTGTCAAGCACCATACCATTAA 57.151 33.333 0.00 0.00 0.00 1.40
823 1126 6.435591 TCAAATTGTCAAGCACCATACCATTA 59.564 34.615 0.00 0.00 0.00 1.90
901 2608 2.093658 AGACACGCGGTTTTATGAGGAT 60.094 45.455 12.47 0.00 0.00 3.24
1226 3013 6.841601 ACTATATGGATGGAAAAGCTAGCAA 58.158 36.000 18.83 0.00 0.00 3.91
1235 3022 5.504853 TGTGCACAACTATATGGATGGAAA 58.495 37.500 19.28 0.00 0.00 3.13
1247 3034 6.424812 GCATGATCTATACATGTGCACAACTA 59.575 38.462 25.72 15.85 44.52 2.24
1248 3035 5.237996 GCATGATCTATACATGTGCACAACT 59.762 40.000 25.72 14.06 44.52 3.16
1249 3036 5.446709 GCATGATCTATACATGTGCACAAC 58.553 41.667 25.72 7.38 44.52 3.32
1730 3584 3.799755 GGCACCGAACATCGCCAC 61.800 66.667 0.00 0.00 44.25 5.01
1811 3665 1.271379 CGGGAACTTGGACTTGATGGT 60.271 52.381 0.00 0.00 0.00 3.55
2048 3922 4.839121 ACAAATTAATCACCGGTAGCTCA 58.161 39.130 6.87 0.00 0.00 4.26
2051 3925 6.037830 ACACATACAAATTAATCACCGGTAGC 59.962 38.462 6.87 0.00 0.00 3.58
2156 8111 7.043391 GGTGCTTTGTACTTTCAATGAAACTTC 60.043 37.037 4.03 0.00 0.00 3.01
2168 8127 3.692593 ACGTTTGAGGTGCTTTGTACTTT 59.307 39.130 0.00 0.00 0.00 2.66
2199 8190 7.758609 TCCATGGTTCATAATCCTTGATGTAT 58.241 34.615 12.58 0.00 32.78 2.29
2222 8213 2.746277 AGCGGCAATGGTCGTTCC 60.746 61.111 1.45 0.00 45.79 3.62
2260 8251 0.666274 CTAGAGCAACGACAACGGCA 60.666 55.000 0.00 0.00 44.46 5.69
2278 8270 1.303888 TCAGGACGGCTTCGGTACT 60.304 57.895 0.00 0.00 38.38 2.73
2279 8271 1.153881 GTCAGGACGGCTTCGGTAC 60.154 63.158 0.00 0.00 38.38 3.34
2310 8302 0.248289 TGGACGAAGAATTCCCGACC 59.752 55.000 22.51 22.51 43.81 4.79
2392 8391 9.573102 CGATGATATTTGATGTAAGTTTCTTCG 57.427 33.333 0.00 0.00 32.48 3.79
2455 8457 1.020437 GATTCCTGCCAGCTACTTGC 58.980 55.000 0.00 0.00 43.29 4.01
2460 8462 1.776662 ACGTAGATTCCTGCCAGCTA 58.223 50.000 0.00 0.00 0.00 3.32
2499 8501 0.739813 CCCAAGTTCGCTCGTTAGGG 60.740 60.000 0.00 0.00 37.02 3.53
2531 8533 6.597280 GCATCTTCTTTGAGTTAGTCTTCCAT 59.403 38.462 0.00 0.00 0.00 3.41
2532 8534 5.934625 GCATCTTCTTTGAGTTAGTCTTCCA 59.065 40.000 0.00 0.00 0.00 3.53
2554 8556 1.002359 GACGCTCAGATAGATGACGCA 60.002 52.381 0.00 0.00 31.39 5.24
2563 8568 3.277142 TGTAGGAGTGACGCTCAGATA 57.723 47.619 17.46 4.82 45.88 1.98
2654 8659 3.324930 CCTCTGCCTGCCACTCCA 61.325 66.667 0.00 0.00 0.00 3.86
2684 8689 0.106918 AACTTTGTCGGTGAGCCCAA 60.107 50.000 0.00 0.00 0.00 4.12
2692 8697 1.117142 TCCCCTCGAACTTTGTCGGT 61.117 55.000 0.00 0.00 41.43 4.69
2696 8701 1.430992 TTCCTCCCCTCGAACTTTGT 58.569 50.000 0.00 0.00 0.00 2.83
2714 8720 4.288626 TGTACATCACTAGGGAAAGCCTTT 59.711 41.667 0.00 0.00 0.00 3.11
2755 8761 3.264998 TGTACAGCTGCATGCAATCTA 57.735 42.857 22.88 5.93 45.94 1.98
2759 8765 3.663995 AAATTGTACAGCTGCATGCAA 57.336 38.095 22.88 11.90 45.94 4.08
2814 8825 9.853555 AAACTATCACGCATTCAATAATTTCAA 57.146 25.926 0.00 0.00 0.00 2.69
2815 8826 9.288124 CAAACTATCACGCATTCAATAATTTCA 57.712 29.630 0.00 0.00 0.00 2.69
2816 8827 8.261908 GCAAACTATCACGCATTCAATAATTTC 58.738 33.333 0.00 0.00 0.00 2.17
2817 8828 7.758980 TGCAAACTATCACGCATTCAATAATTT 59.241 29.630 0.00 0.00 0.00 1.82
2818 8829 7.257003 TGCAAACTATCACGCATTCAATAATT 58.743 30.769 0.00 0.00 0.00 1.40
2819 8830 6.794374 TGCAAACTATCACGCATTCAATAAT 58.206 32.000 0.00 0.00 0.00 1.28
2820 8831 6.188400 TGCAAACTATCACGCATTCAATAA 57.812 33.333 0.00 0.00 0.00 1.40
2821 8832 5.809719 TGCAAACTATCACGCATTCAATA 57.190 34.783 0.00 0.00 0.00 1.90
2879 8890 3.243367 GCCAAACAGTGTTGCTTGATACA 60.243 43.478 9.79 0.00 33.25 2.29
2975 8988 1.372997 CTTCGTGTGGACGTGGGAG 60.373 63.158 0.00 0.00 46.20 4.30
2976 8989 2.732016 CTTCGTGTGGACGTGGGA 59.268 61.111 0.00 0.00 46.20 4.37
2977 8990 3.041940 GCTTCGTGTGGACGTGGG 61.042 66.667 0.00 0.00 46.20 4.61
2978 8991 2.029073 AGCTTCGTGTGGACGTGG 59.971 61.111 0.00 0.00 46.20 4.94
2979 8992 1.591594 ACAGCTTCGTGTGGACGTG 60.592 57.895 0.00 0.00 46.20 4.49
2980 8993 1.591594 CACAGCTTCGTGTGGACGT 60.592 57.895 0.00 0.00 46.20 4.34
2981 8994 0.874175 TTCACAGCTTCGTGTGGACG 60.874 55.000 4.29 0.00 46.65 4.79
2982 8995 2.986311 TTCACAGCTTCGTGTGGAC 58.014 52.632 4.29 0.00 46.65 4.02
2983 8996 0.531974 GGTTCACAGCTTCGTGTGGA 60.532 55.000 4.29 0.00 46.65 4.02
2984 8997 0.532862 AGGTTCACAGCTTCGTGTGG 60.533 55.000 4.29 0.00 46.65 4.17
2985 8998 1.261619 GAAGGTTCACAGCTTCGTGTG 59.738 52.381 4.29 1.04 45.25 3.82
2986 8999 1.583054 GAAGGTTCACAGCTTCGTGT 58.417 50.000 4.29 0.00 45.25 4.49
2991 9004 2.708325 AGAAGAGGAAGGTTCACAGCTT 59.292 45.455 0.00 0.00 43.69 3.74
2992 9005 2.301583 GAGAAGAGGAAGGTTCACAGCT 59.698 50.000 0.00 0.00 0.00 4.24
2993 9006 2.301583 AGAGAAGAGGAAGGTTCACAGC 59.698 50.000 0.00 0.00 0.00 4.40
2994 9007 3.576118 TGAGAGAAGAGGAAGGTTCACAG 59.424 47.826 0.00 0.00 0.00 3.66
2995 9008 3.322254 GTGAGAGAAGAGGAAGGTTCACA 59.678 47.826 0.00 0.00 35.13 3.58
2996 9009 3.612955 CGTGAGAGAAGAGGAAGGTTCAC 60.613 52.174 0.00 0.00 0.00 3.18
2997 9010 2.558795 CGTGAGAGAAGAGGAAGGTTCA 59.441 50.000 0.00 0.00 0.00 3.18
2998 9011 2.672760 GCGTGAGAGAAGAGGAAGGTTC 60.673 54.545 0.00 0.00 0.00 3.62
2999 9012 1.273886 GCGTGAGAGAAGAGGAAGGTT 59.726 52.381 0.00 0.00 0.00 3.50
3000 9013 0.892063 GCGTGAGAGAAGAGGAAGGT 59.108 55.000 0.00 0.00 0.00 3.50
3001 9014 0.174617 GGCGTGAGAGAAGAGGAAGG 59.825 60.000 0.00 0.00 0.00 3.46
3002 9015 1.181786 AGGCGTGAGAGAAGAGGAAG 58.818 55.000 0.00 0.00 0.00 3.46
3003 9016 2.509166 TAGGCGTGAGAGAAGAGGAA 57.491 50.000 0.00 0.00 0.00 3.36
3004 9017 2.509166 TTAGGCGTGAGAGAAGAGGA 57.491 50.000 0.00 0.00 0.00 3.71
3005 9018 3.452474 CAATTAGGCGTGAGAGAAGAGG 58.548 50.000 0.00 0.00 0.00 3.69
3006 9019 3.118956 ACCAATTAGGCGTGAGAGAAGAG 60.119 47.826 0.00 0.00 43.14 2.85
3007 9020 2.832129 ACCAATTAGGCGTGAGAGAAGA 59.168 45.455 0.00 0.00 43.14 2.87
3008 9021 3.252974 ACCAATTAGGCGTGAGAGAAG 57.747 47.619 0.00 0.00 43.14 2.85
3009 9022 3.695830 AACCAATTAGGCGTGAGAGAA 57.304 42.857 0.00 0.00 43.14 2.87
3010 9023 3.007506 TCAAACCAATTAGGCGTGAGAGA 59.992 43.478 0.00 0.00 43.14 3.10
3011 9024 3.334691 TCAAACCAATTAGGCGTGAGAG 58.665 45.455 0.00 0.00 43.14 3.20
3012 9025 3.244422 ACTCAAACCAATTAGGCGTGAGA 60.244 43.478 21.29 5.49 46.92 3.27
3013 9026 3.747099 CTCAAACCAATTAGGCGTGAG 57.253 47.619 10.36 10.36 42.12 3.51
3014 9027 3.134574 ACTCAAACCAATTAGGCGTGA 57.865 42.857 0.00 0.00 43.14 4.35
3015 9028 4.201910 CCATACTCAAACCAATTAGGCGTG 60.202 45.833 0.00 0.00 43.14 5.34
3016 9029 3.945285 CCATACTCAAACCAATTAGGCGT 59.055 43.478 0.00 0.00 43.14 5.68
3017 9030 3.243068 GCCATACTCAAACCAATTAGGCG 60.243 47.826 0.00 0.00 43.14 5.52
3018 9031 3.954258 AGCCATACTCAAACCAATTAGGC 59.046 43.478 0.00 0.00 43.14 3.93
3019 9032 4.339247 CCAGCCATACTCAAACCAATTAGG 59.661 45.833 0.00 0.00 45.67 2.69
3020 9033 4.202050 GCCAGCCATACTCAAACCAATTAG 60.202 45.833 0.00 0.00 0.00 1.73
3021 9034 3.699038 GCCAGCCATACTCAAACCAATTA 59.301 43.478 0.00 0.00 0.00 1.40
3022 9035 2.497273 GCCAGCCATACTCAAACCAATT 59.503 45.455 0.00 0.00 0.00 2.32
3023 9036 2.102578 GCCAGCCATACTCAAACCAAT 58.897 47.619 0.00 0.00 0.00 3.16
3024 9037 1.075374 AGCCAGCCATACTCAAACCAA 59.925 47.619 0.00 0.00 0.00 3.67
3025 9038 0.698238 AGCCAGCCATACTCAAACCA 59.302 50.000 0.00 0.00 0.00 3.67
3026 9039 1.065126 AGAGCCAGCCATACTCAAACC 60.065 52.381 0.00 0.00 32.71 3.27
3027 9040 2.409948 AGAGCCAGCCATACTCAAAC 57.590 50.000 0.00 0.00 32.71 2.93
3028 9041 2.170607 GGTAGAGCCAGCCATACTCAAA 59.829 50.000 0.00 0.00 37.17 2.69
3029 9042 1.762957 GGTAGAGCCAGCCATACTCAA 59.237 52.381 0.00 0.00 37.17 3.02
3030 9043 1.342975 TGGTAGAGCCAGCCATACTCA 60.343 52.381 0.00 0.00 43.61 3.41
3031 9044 1.414158 TGGTAGAGCCAGCCATACTC 58.586 55.000 2.91 0.00 43.61 2.59
3032 9045 3.635099 TGGTAGAGCCAGCCATACT 57.365 52.632 2.91 0.00 43.61 2.12
3041 9054 0.173708 CGTGAGAGGTTGGTAGAGCC 59.826 60.000 0.00 0.00 37.90 4.70
3042 9055 0.889306 ACGTGAGAGGTTGGTAGAGC 59.111 55.000 0.00 0.00 0.00 4.09
3043 9056 3.079578 TGTACGTGAGAGGTTGGTAGAG 58.920 50.000 0.00 0.00 0.00 2.43
3044 9057 2.816087 GTGTACGTGAGAGGTTGGTAGA 59.184 50.000 0.00 0.00 0.00 2.59
3045 9058 2.413765 CGTGTACGTGAGAGGTTGGTAG 60.414 54.545 0.00 0.00 34.11 3.18
3046 9059 1.536766 CGTGTACGTGAGAGGTTGGTA 59.463 52.381 0.00 0.00 34.11 3.25
3047 9060 0.313043 CGTGTACGTGAGAGGTTGGT 59.687 55.000 0.00 0.00 34.11 3.67
3048 9061 0.594602 TCGTGTACGTGAGAGGTTGG 59.405 55.000 0.00 0.00 40.80 3.77
3049 9062 2.316792 CTTCGTGTACGTGAGAGGTTG 58.683 52.381 0.00 0.00 40.80 3.77
3050 9063 1.335689 GCTTCGTGTACGTGAGAGGTT 60.336 52.381 0.00 0.00 40.80 3.50
3051 9064 0.240411 GCTTCGTGTACGTGAGAGGT 59.760 55.000 0.00 0.00 40.80 3.85
3052 9065 0.522180 AGCTTCGTGTACGTGAGAGG 59.478 55.000 0.00 0.00 40.80 3.69


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

AutoCloner maintained by Alex Coulton.