Multiple sequence alignment - TraesCS2D01G029900

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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 TraesCS2D01G029900 chr2D 100.000 3583 0 0 1 3583 12306051 12302469 0.000000e+00 6617
1 TraesCS2D01G029900 chr2D 83.840 1875 244 39 995 2826 12525142 12523284 0.000000e+00 1729
2 TraesCS2D01G029900 chr2D 82.064 1589 236 28 1085 2632 12290296 12291876 0.000000e+00 1310
3 TraesCS2D01G029900 chr2D 94.533 750 36 5 2837 3583 538595237 538595984 0.000000e+00 1153
4 TraesCS2D01G029900 chr2D 76.471 714 150 15 1165 1869 12324579 12323875 4.370000e-99 372
5 TraesCS2D01G029900 chr2D 75.211 831 145 35 76 888 12378346 12377559 1.590000e-88 337
6 TraesCS2D01G029900 chrUn 97.862 1029 17 1 913 1941 12461767 12462790 0.000000e+00 1773
7 TraesCS2D01G029900 chrUn 95.213 940 27 6 1909 2837 12462797 12463729 0.000000e+00 1471
8 TraesCS2D01G029900 chrUn 81.340 1597 249 28 1085 2640 12473520 12471932 0.000000e+00 1253
9 TraesCS2D01G029900 chrUn 93.114 668 37 4 1 661 12461101 12461766 0.000000e+00 970
10 TraesCS2D01G029900 chr5D 84.285 1559 216 22 1084 2632 560883668 560885207 0.000000e+00 1495
11 TraesCS2D01G029900 chr5D 92.961 753 42 7 2837 3583 227450389 227449642 0.000000e+00 1086
12 TraesCS2D01G029900 chr2A 82.979 1551 223 21 1084 2632 34157500 34155989 0.000000e+00 1363
13 TraesCS2D01G029900 chr2A 81.984 1482 225 27 1160 2606 12805355 12803881 0.000000e+00 1219
14 TraesCS2D01G029900 chr2A 87.859 453 51 1 1439 1891 12940294 12939846 2.450000e-146 529
15 TraesCS2D01G029900 chr2A 78.060 670 96 27 477 1104 12954498 12953838 3.380000e-100 375
16 TraesCS2D01G029900 chr2A 83.516 182 27 3 2647 2828 12921865 12921687 2.210000e-37 167
17 TraesCS2D01G029900 chr7D 93.227 753 44 6 2836 3583 254982947 254982197 0.000000e+00 1101
18 TraesCS2D01G029900 chr1D 92.885 759 42 8 2836 3583 58116643 58117400 0.000000e+00 1092
19 TraesCS2D01G029900 chr1D 93.067 750 46 6 2836 3583 247865319 247866064 0.000000e+00 1092
20 TraesCS2D01G029900 chr1D 92.529 763 45 11 2829 3583 96912684 96911926 0.000000e+00 1083
21 TraesCS2D01G029900 chr5A 92.838 754 45 8 2836 3583 156855322 156854572 0.000000e+00 1085
22 TraesCS2D01G029900 chr5A 92.696 753 45 9 2837 3583 482924507 482925255 0.000000e+00 1077
23 TraesCS2D01G029900 chr5A 78.947 114 21 3 307 419 224386410 224386521 1.380000e-09 75
24 TraesCS2D01G029900 chr7A 92.602 757 48 6 2832 3583 35179216 35179969 0.000000e+00 1081
25 TraesCS2D01G029900 chr2B 86.466 665 83 6 1901 2563 52717965 52718624 0.000000e+00 723
26 TraesCS2D01G029900 chr2B 81.398 887 153 4 995 1869 52716964 52717850 0.000000e+00 713
27 TraesCS2D01G029900 chr2B 77.157 788 151 20 990 1753 636823217 636822435 7.110000e-117 431


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 TraesCS2D01G029900 chr2D 12302469 12306051 3582 True 6617.000000 6617 100.000000 1 3583 1 chr2D.!!$R1 3582
1 TraesCS2D01G029900 chr2D 12523284 12525142 1858 True 1729.000000 1729 83.840000 995 2826 1 chr2D.!!$R4 1831
2 TraesCS2D01G029900 chr2D 12290296 12291876 1580 False 1310.000000 1310 82.064000 1085 2632 1 chr2D.!!$F1 1547
3 TraesCS2D01G029900 chr2D 538595237 538595984 747 False 1153.000000 1153 94.533000 2837 3583 1 chr2D.!!$F2 746
4 TraesCS2D01G029900 chr2D 12323875 12324579 704 True 372.000000 372 76.471000 1165 1869 1 chr2D.!!$R2 704
5 TraesCS2D01G029900 chr2D 12377559 12378346 787 True 337.000000 337 75.211000 76 888 1 chr2D.!!$R3 812
6 TraesCS2D01G029900 chrUn 12461101 12463729 2628 False 1404.666667 1773 95.396333 1 2837 3 chrUn.!!$F1 2836
7 TraesCS2D01G029900 chrUn 12471932 12473520 1588 True 1253.000000 1253 81.340000 1085 2640 1 chrUn.!!$R1 1555
8 TraesCS2D01G029900 chr5D 560883668 560885207 1539 False 1495.000000 1495 84.285000 1084 2632 1 chr5D.!!$F1 1548
9 TraesCS2D01G029900 chr5D 227449642 227450389 747 True 1086.000000 1086 92.961000 2837 3583 1 chr5D.!!$R1 746
10 TraesCS2D01G029900 chr2A 34155989 34157500 1511 True 1363.000000 1363 82.979000 1084 2632 1 chr2A.!!$R5 1548
11 TraesCS2D01G029900 chr2A 12803881 12805355 1474 True 1219.000000 1219 81.984000 1160 2606 1 chr2A.!!$R1 1446
12 TraesCS2D01G029900 chr2A 12953838 12954498 660 True 375.000000 375 78.060000 477 1104 1 chr2A.!!$R4 627
13 TraesCS2D01G029900 chr7D 254982197 254982947 750 True 1101.000000 1101 93.227000 2836 3583 1 chr7D.!!$R1 747
14 TraesCS2D01G029900 chr1D 58116643 58117400 757 False 1092.000000 1092 92.885000 2836 3583 1 chr1D.!!$F1 747
15 TraesCS2D01G029900 chr1D 247865319 247866064 745 False 1092.000000 1092 93.067000 2836 3583 1 chr1D.!!$F2 747
16 TraesCS2D01G029900 chr1D 96911926 96912684 758 True 1083.000000 1083 92.529000 2829 3583 1 chr1D.!!$R1 754
17 TraesCS2D01G029900 chr5A 156854572 156855322 750 True 1085.000000 1085 92.838000 2836 3583 1 chr5A.!!$R1 747
18 TraesCS2D01G029900 chr5A 482924507 482925255 748 False 1077.000000 1077 92.696000 2837 3583 1 chr5A.!!$F2 746
19 TraesCS2D01G029900 chr7A 35179216 35179969 753 False 1081.000000 1081 92.602000 2832 3583 1 chr7A.!!$F1 751
20 TraesCS2D01G029900 chr2B 52716964 52718624 1660 False 718.000000 723 83.932000 995 2563 2 chr2B.!!$F1 1568
21 TraesCS2D01G029900 chr2B 636822435 636823217 782 True 431.000000 431 77.157000 990 1753 1 chr2B.!!$R1 763

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
681 689 0.036388 ATGGGTGGACACATGTCGTC 60.036 55.0 15.77 15.77 45.65 4.20 F
685 693 0.039437 GTGGACACATGTCGTCTCGT 60.039 55.0 20.43 6.25 45.65 4.18 F
737 745 0.388659 AGCGTTTTTGCCAGCATTCA 59.611 45.0 0.00 0.00 34.65 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 2080 2.119611 TCAAGCTCCCCCTCGTCA 59.880 61.111 0.00 0.00 0.00 4.35 R
2219 2736 2.509964 GGTACCCTCCATGACCTCAAAT 59.490 50.000 0.00 0.00 0.00 2.32 R
2693 3224 2.223572 GCCATCCCATGACGATGAAAAC 60.224 50.000 18.94 6.73 39.64 2.43 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
37 38 0.919710 AAGCCCCACTAGACCCAATC 59.080 55.000 0.00 0.00 0.00 2.67
74 75 0.385098 AATCAATGCATGCGCGATCG 60.385 50.000 12.10 11.69 42.97 3.69
113 114 1.723870 GGCAGACAATCATGCGGAC 59.276 57.895 0.00 0.00 43.49 4.79
158 159 2.863809 AGGGACAATGTTCCAGTCAAC 58.136 47.619 14.07 0.00 37.40 3.18
184 185 4.688770 ACCTCTCGGGGTCAGATC 57.311 61.111 0.00 0.00 40.03 2.75
190 191 1.305297 TCGGGGTCAGATCTGCTGT 60.305 57.895 18.36 0.00 45.14 4.40
191 192 1.153489 CGGGGTCAGATCTGCTGTG 60.153 63.158 18.36 2.88 45.14 3.66
241 243 1.383248 GGAGAAGAGCTAGGGGGCA 60.383 63.158 0.00 0.00 34.17 5.36
257 259 1.413227 GGGCAGAGGGGACTATAGTGT 60.413 57.143 10.90 0.00 44.43 3.55
264 266 4.105057 AGAGGGGACTATAGTGTAGTGGAG 59.895 50.000 10.90 0.00 44.43 3.86
282 284 3.074687 TGGAGTGGCTATGGTTTGGTAAA 59.925 43.478 0.00 0.00 0.00 2.01
285 287 4.332828 AGTGGCTATGGTTTGGTAAAGAC 58.667 43.478 0.00 0.00 0.00 3.01
307 309 7.249715 AGACTATGGATAGGGCTGTATTTAGT 58.750 38.462 0.00 0.00 34.69 2.24
314 316 1.583054 GGCTGTATTTAGTGAGGCCG 58.417 55.000 0.00 0.00 0.00 6.13
343 345 0.398522 ATAGTGGGCTGGATCCGACA 60.399 55.000 7.39 0.09 37.31 4.35
377 379 2.606587 GGCATCCCCATATCCGCCT 61.607 63.158 0.00 0.00 36.58 5.52
385 387 2.158900 CCCCATATCCGCCTCACATATC 60.159 54.545 0.00 0.00 0.00 1.63
386 388 2.481969 CCCATATCCGCCTCACATATCG 60.482 54.545 0.00 0.00 0.00 2.92
406 408 2.550978 GACTGGATATGGGTGTTGACG 58.449 52.381 0.00 0.00 0.00 4.35
414 416 2.668550 GGTGTTGACGGTCTGCCC 60.669 66.667 9.88 0.80 0.00 5.36
416 418 1.525077 GTGTTGACGGTCTGCCCAA 60.525 57.895 9.88 0.00 0.00 4.12
450 452 4.680237 CGAGCGTCTGGTTGGGCA 62.680 66.667 0.00 0.00 0.00 5.36
501 503 1.743995 CCGTCCGGACATTTGGGAC 60.744 63.158 32.80 4.66 45.34 4.46
505 507 4.954933 CGGACATTTGGGACGGAT 57.045 55.556 0.00 0.00 0.00 4.18
511 513 2.105821 GACATTTGGGACGGATATGGGA 59.894 50.000 0.00 0.00 0.00 4.37
530 532 0.606604 ACGTCCGGTTGTAGATGCTT 59.393 50.000 0.00 0.00 0.00 3.91
562 566 5.747248 GCTCAAGAGATACCCAATTATGCCT 60.747 44.000 0.32 0.00 0.00 4.75
613 617 2.596904 GCACTCGGCATAGACCTTAA 57.403 50.000 0.00 0.00 43.97 1.85
614 618 2.202566 GCACTCGGCATAGACCTTAAC 58.797 52.381 0.00 0.00 43.97 2.01
615 619 2.822764 CACTCGGCATAGACCTTAACC 58.177 52.381 0.00 0.00 0.00 2.85
616 620 1.407979 ACTCGGCATAGACCTTAACCG 59.592 52.381 0.00 0.00 41.92 4.44
629 637 3.248266 CCTTAACCGAGTGTCCGTTAAG 58.752 50.000 15.35 15.35 35.49 1.85
634 642 2.096496 ACCGAGTGTCCGTTAAGATACG 59.904 50.000 0.00 0.00 41.06 3.06
657 665 4.215399 GCTTGGCAATGTTTACTACACTCA 59.785 41.667 0.00 0.00 40.19 3.41
661 669 4.396166 GGCAATGTTTACTACACTCAGCAT 59.604 41.667 0.00 0.00 40.19 3.79
662 670 5.584649 GGCAATGTTTACTACACTCAGCATA 59.415 40.000 0.00 0.00 40.19 3.14
663 671 6.260936 GGCAATGTTTACTACACTCAGCATAT 59.739 38.462 0.00 0.00 40.19 1.78
664 672 7.128331 GCAATGTTTACTACACTCAGCATATG 58.872 38.462 0.00 0.00 40.19 1.78
665 673 7.633621 CAATGTTTACTACACTCAGCATATGG 58.366 38.462 4.56 0.00 40.19 2.74
666 674 5.670485 TGTTTACTACACTCAGCATATGGG 58.330 41.667 4.56 0.00 34.51 4.00
667 675 5.188948 TGTTTACTACACTCAGCATATGGGT 59.811 40.000 4.56 0.00 46.48 4.51
672 680 1.583556 ACTCAGCATATGGGTGGACA 58.416 50.000 4.56 0.00 42.71 4.02
673 681 1.210478 ACTCAGCATATGGGTGGACAC 59.790 52.381 4.56 0.00 42.71 3.67
674 682 1.210234 CTCAGCATATGGGTGGACACA 59.790 52.381 4.56 0.00 45.09 3.72
675 683 1.845791 TCAGCATATGGGTGGACACAT 59.154 47.619 4.56 0.00 45.09 3.21
676 684 1.951602 CAGCATATGGGTGGACACATG 59.048 52.381 4.71 0.00 40.78 3.21
677 685 1.565759 AGCATATGGGTGGACACATGT 59.434 47.619 4.71 0.00 40.78 3.21
678 686 1.949525 GCATATGGGTGGACACATGTC 59.050 52.381 4.71 3.27 40.78 3.06
679 687 2.212652 CATATGGGTGGACACATGTCG 58.787 52.381 4.71 0.00 45.65 4.35
680 688 1.271856 TATGGGTGGACACATGTCGT 58.728 50.000 4.71 0.00 45.65 4.34
681 689 0.036388 ATGGGTGGACACATGTCGTC 60.036 55.000 15.77 15.77 45.65 4.20
682 690 1.118965 TGGGTGGACACATGTCGTCT 61.119 55.000 20.43 0.00 45.65 4.18
683 691 0.389948 GGGTGGACACATGTCGTCTC 60.390 60.000 20.43 15.49 45.65 3.36
684 692 0.732880 GGTGGACACATGTCGTCTCG 60.733 60.000 20.43 3.40 45.65 4.04
685 693 0.039437 GTGGACACATGTCGTCTCGT 60.039 55.000 20.43 6.25 45.65 4.18
686 694 0.671796 TGGACACATGTCGTCTCGTT 59.328 50.000 20.43 0.00 45.65 3.85
687 695 1.067974 TGGACACATGTCGTCTCGTTT 59.932 47.619 20.43 0.00 45.65 3.60
688 696 1.719780 GGACACATGTCGTCTCGTTTC 59.280 52.381 20.43 6.45 45.65 2.78
689 697 1.719780 GACACATGTCGTCTCGTTTCC 59.280 52.381 16.43 0.00 35.12 3.13
690 698 1.340248 ACACATGTCGTCTCGTTTCCT 59.660 47.619 0.00 0.00 0.00 3.36
691 699 2.223971 ACACATGTCGTCTCGTTTCCTT 60.224 45.455 0.00 0.00 0.00 3.36
692 700 3.005050 ACACATGTCGTCTCGTTTCCTTA 59.995 43.478 0.00 0.00 0.00 2.69
693 701 3.608506 CACATGTCGTCTCGTTTCCTTAG 59.391 47.826 0.00 0.00 0.00 2.18
694 702 3.255149 ACATGTCGTCTCGTTTCCTTAGT 59.745 43.478 0.00 0.00 0.00 2.24
695 703 3.996150 TGTCGTCTCGTTTCCTTAGTT 57.004 42.857 0.00 0.00 0.00 2.24
696 704 3.635331 TGTCGTCTCGTTTCCTTAGTTG 58.365 45.455 0.00 0.00 0.00 3.16
697 705 3.316029 TGTCGTCTCGTTTCCTTAGTTGA 59.684 43.478 0.00 0.00 0.00 3.18
698 706 3.667726 GTCGTCTCGTTTCCTTAGTTGAC 59.332 47.826 0.00 0.00 0.00 3.18
699 707 2.655474 CGTCTCGTTTCCTTAGTTGACG 59.345 50.000 0.00 0.00 39.61 4.35
700 708 2.985139 GTCTCGTTTCCTTAGTTGACGG 59.015 50.000 0.00 0.00 34.72 4.79
701 709 1.725164 CTCGTTTCCTTAGTTGACGGC 59.275 52.381 0.00 0.00 34.72 5.68
702 710 1.068895 TCGTTTCCTTAGTTGACGGCA 59.931 47.619 0.00 0.00 34.72 5.69
703 711 2.073816 CGTTTCCTTAGTTGACGGCAT 58.926 47.619 0.00 0.00 0.00 4.40
704 712 2.159707 CGTTTCCTTAGTTGACGGCATG 60.160 50.000 0.00 0.00 0.00 4.06
705 713 2.107950 TTCCTTAGTTGACGGCATGG 57.892 50.000 0.00 0.00 0.00 3.66
706 714 0.981183 TCCTTAGTTGACGGCATGGT 59.019 50.000 0.00 0.00 0.00 3.55
707 715 2.181125 TCCTTAGTTGACGGCATGGTA 58.819 47.619 0.00 0.00 0.00 3.25
708 716 2.568062 TCCTTAGTTGACGGCATGGTAA 59.432 45.455 0.00 0.00 0.00 2.85
709 717 2.676342 CCTTAGTTGACGGCATGGTAAC 59.324 50.000 0.00 0.00 0.00 2.50
710 718 2.389962 TAGTTGACGGCATGGTAACC 57.610 50.000 0.00 0.00 0.00 2.85
711 719 0.690762 AGTTGACGGCATGGTAACCT 59.309 50.000 0.00 0.00 0.00 3.50
712 720 1.903860 AGTTGACGGCATGGTAACCTA 59.096 47.619 0.00 0.00 0.00 3.08
713 721 2.504175 AGTTGACGGCATGGTAACCTAT 59.496 45.455 0.00 0.00 0.00 2.57
714 722 2.612212 GTTGACGGCATGGTAACCTATG 59.388 50.000 0.00 0.00 0.00 2.23
715 723 1.226746 GACGGCATGGTAACCTATGC 58.773 55.000 12.67 12.67 46.76 3.14
720 728 2.427506 GCATGGTAACCTATGCCTAGC 58.572 52.381 10.76 0.00 42.88 3.42
721 729 2.688507 CATGGTAACCTATGCCTAGCG 58.311 52.381 0.00 0.00 34.34 4.26
722 730 1.784358 TGGTAACCTATGCCTAGCGT 58.216 50.000 0.00 0.00 34.34 5.07
723 731 2.112998 TGGTAACCTATGCCTAGCGTT 58.887 47.619 7.59 7.59 34.34 4.84
724 732 2.502538 TGGTAACCTATGCCTAGCGTTT 59.497 45.455 7.71 0.00 34.34 3.60
725 733 3.054948 TGGTAACCTATGCCTAGCGTTTT 60.055 43.478 7.71 0.00 34.34 2.43
726 734 3.943381 GGTAACCTATGCCTAGCGTTTTT 59.057 43.478 7.71 0.00 0.00 1.94
727 735 4.201881 GGTAACCTATGCCTAGCGTTTTTG 60.202 45.833 7.71 0.00 0.00 2.44
728 736 1.743394 ACCTATGCCTAGCGTTTTTGC 59.257 47.619 0.00 0.00 0.00 3.68
729 737 1.065551 CCTATGCCTAGCGTTTTTGCC 59.934 52.381 0.00 0.00 34.65 4.52
730 738 1.742831 CTATGCCTAGCGTTTTTGCCA 59.257 47.619 0.00 0.00 34.65 4.92
731 739 0.527565 ATGCCTAGCGTTTTTGCCAG 59.472 50.000 0.00 0.00 34.65 4.85
732 740 1.444383 GCCTAGCGTTTTTGCCAGC 60.444 57.895 0.00 0.00 34.65 4.85
733 741 1.956043 CCTAGCGTTTTTGCCAGCA 59.044 52.632 0.00 0.00 34.65 4.41
734 742 0.527565 CCTAGCGTTTTTGCCAGCAT 59.472 50.000 0.00 0.00 34.65 3.79
735 743 1.067635 CCTAGCGTTTTTGCCAGCATT 60.068 47.619 0.00 0.00 34.65 3.56
736 744 2.253603 CTAGCGTTTTTGCCAGCATTC 58.746 47.619 0.00 0.00 34.65 2.67
737 745 0.388659 AGCGTTTTTGCCAGCATTCA 59.611 45.000 0.00 0.00 34.65 2.57
738 746 0.785979 GCGTTTTTGCCAGCATTCAG 59.214 50.000 0.00 0.00 0.00 3.02
739 747 0.785979 CGTTTTTGCCAGCATTCAGC 59.214 50.000 0.00 0.00 46.19 4.26
756 764 8.609478 GCATTCAGCAAATTTTTAATCCATTG 57.391 30.769 0.00 0.00 44.79 2.82
757 765 7.698970 GCATTCAGCAAATTTTTAATCCATTGG 59.301 33.333 0.00 0.00 44.79 3.16
758 766 8.732531 CATTCAGCAAATTTTTAATCCATTGGT 58.267 29.630 1.86 0.00 0.00 3.67
759 767 9.956640 ATTCAGCAAATTTTTAATCCATTGGTA 57.043 25.926 1.86 0.00 0.00 3.25
760 768 9.956640 TTCAGCAAATTTTTAATCCATTGGTAT 57.043 25.926 1.86 0.00 0.00 2.73
761 769 9.956640 TCAGCAAATTTTTAATCCATTGGTATT 57.043 25.926 1.86 4.40 0.00 1.89
788 796 7.972832 TCATCTTTATGTTTTCCGTTGTACT 57.027 32.000 0.00 0.00 34.50 2.73
789 797 8.025243 TCATCTTTATGTTTTCCGTTGTACTC 57.975 34.615 0.00 0.00 34.50 2.59
790 798 6.456447 TCTTTATGTTTTCCGTTGTACTCG 57.544 37.500 0.00 0.00 0.00 4.18
792 800 1.219646 TGTTTTCCGTTGTACTCGGC 58.780 50.000 19.75 10.18 46.49 5.54
793 801 1.219646 GTTTTCCGTTGTACTCGGCA 58.780 50.000 19.75 10.55 46.49 5.69
794 802 1.598601 GTTTTCCGTTGTACTCGGCAA 59.401 47.619 19.75 14.82 46.49 4.52
795 803 1.950828 TTTCCGTTGTACTCGGCAAA 58.049 45.000 19.75 17.23 46.49 3.68
796 804 1.219646 TTCCGTTGTACTCGGCAAAC 58.780 50.000 19.75 3.88 46.49 2.93
797 805 0.390124 TCCGTTGTACTCGGCAAACT 59.610 50.000 19.75 0.00 46.49 2.66
798 806 1.202557 TCCGTTGTACTCGGCAAACTT 60.203 47.619 19.75 0.00 46.49 2.66
799 807 1.070175 CCGTTGTACTCGGCAAACTTG 60.070 52.381 14.70 0.00 41.48 3.16
800 808 1.595794 CGTTGTACTCGGCAAACTTGT 59.404 47.619 0.00 0.00 0.00 3.16
801 809 2.031191 CGTTGTACTCGGCAAACTTGTT 59.969 45.455 0.00 0.00 0.00 2.83
802 810 3.486209 CGTTGTACTCGGCAAACTTGTTT 60.486 43.478 0.00 0.00 0.00 2.83
803 811 4.417506 GTTGTACTCGGCAAACTTGTTTT 58.582 39.130 0.00 0.00 0.00 2.43
804 812 5.571277 GTTGTACTCGGCAAACTTGTTTTA 58.429 37.500 0.00 0.00 0.00 1.52
805 813 6.203647 GTTGTACTCGGCAAACTTGTTTTAT 58.796 36.000 0.00 0.00 0.00 1.40
806 814 5.992729 TGTACTCGGCAAACTTGTTTTATC 58.007 37.500 0.00 0.00 0.00 1.75
807 815 5.761234 TGTACTCGGCAAACTTGTTTTATCT 59.239 36.000 0.00 0.00 0.00 1.98
808 816 5.767816 ACTCGGCAAACTTGTTTTATCTT 57.232 34.783 0.00 0.00 0.00 2.40
809 817 5.519722 ACTCGGCAAACTTGTTTTATCTTG 58.480 37.500 0.00 0.00 0.00 3.02
810 818 5.298276 ACTCGGCAAACTTGTTTTATCTTGA 59.702 36.000 0.00 0.00 0.00 3.02
811 819 6.016276 ACTCGGCAAACTTGTTTTATCTTGAT 60.016 34.615 0.00 0.00 0.00 2.57
812 820 7.174253 ACTCGGCAAACTTGTTTTATCTTGATA 59.826 33.333 0.00 0.00 0.00 2.15
813 821 8.050778 TCGGCAAACTTGTTTTATCTTGATAT 57.949 30.769 0.00 0.00 0.00 1.63
814 822 8.519526 TCGGCAAACTTGTTTTATCTTGATATT 58.480 29.630 0.00 0.00 0.00 1.28
815 823 9.139174 CGGCAAACTTGTTTTATCTTGATATTT 57.861 29.630 0.00 0.00 0.00 1.40
838 846 7.579589 TTTTTCATGCGGTAAATTTGATGAG 57.420 32.000 0.00 0.00 0.00 2.90
839 847 6.507958 TTTCATGCGGTAAATTTGATGAGA 57.492 33.333 0.00 0.00 0.00 3.27
840 848 5.739752 TCATGCGGTAAATTTGATGAGAG 57.260 39.130 0.00 0.00 0.00 3.20
841 849 5.185454 TCATGCGGTAAATTTGATGAGAGT 58.815 37.500 0.00 0.00 0.00 3.24
842 850 6.345298 TCATGCGGTAAATTTGATGAGAGTA 58.655 36.000 0.00 0.00 0.00 2.59
843 851 6.992123 TCATGCGGTAAATTTGATGAGAGTAT 59.008 34.615 0.00 0.00 0.00 2.12
844 852 7.498900 TCATGCGGTAAATTTGATGAGAGTATT 59.501 33.333 0.00 0.00 0.00 1.89
845 853 7.624360 TGCGGTAAATTTGATGAGAGTATTT 57.376 32.000 0.00 0.00 0.00 1.40
846 854 8.050778 TGCGGTAAATTTGATGAGAGTATTTT 57.949 30.769 0.00 0.00 0.00 1.82
847 855 8.181573 TGCGGTAAATTTGATGAGAGTATTTTC 58.818 33.333 0.00 0.00 0.00 2.29
848 856 7.373441 GCGGTAAATTTGATGAGAGTATTTTCG 59.627 37.037 0.00 0.00 0.00 3.46
849 857 7.850982 CGGTAAATTTGATGAGAGTATTTTCGG 59.149 37.037 0.00 0.00 0.00 4.30
850 858 8.674607 GGTAAATTTGATGAGAGTATTTTCGGT 58.325 33.333 0.00 0.00 0.00 4.69
852 860 8.970691 AAATTTGATGAGAGTATTTTCGGTTG 57.029 30.769 0.00 0.00 0.00 3.77
853 861 7.921786 ATTTGATGAGAGTATTTTCGGTTGA 57.078 32.000 0.00 0.00 0.00 3.18
854 862 6.968131 TTGATGAGAGTATTTTCGGTTGAG 57.032 37.500 0.00 0.00 0.00 3.02
855 863 6.280855 TGATGAGAGTATTTTCGGTTGAGA 57.719 37.500 0.00 0.00 0.00 3.27
856 864 6.878317 TGATGAGAGTATTTTCGGTTGAGAT 58.122 36.000 0.00 0.00 0.00 2.75
857 865 6.758416 TGATGAGAGTATTTTCGGTTGAGATG 59.242 38.462 0.00 0.00 0.00 2.90
858 866 5.419542 TGAGAGTATTTTCGGTTGAGATGG 58.580 41.667 0.00 0.00 0.00 3.51
859 867 5.186992 TGAGAGTATTTTCGGTTGAGATGGA 59.813 40.000 0.00 0.00 0.00 3.41
860 868 5.665459 AGAGTATTTTCGGTTGAGATGGAG 58.335 41.667 0.00 0.00 0.00 3.86
861 869 5.187967 AGAGTATTTTCGGTTGAGATGGAGT 59.812 40.000 0.00 0.00 0.00 3.85
862 870 6.380274 AGAGTATTTTCGGTTGAGATGGAGTA 59.620 38.462 0.00 0.00 0.00 2.59
863 871 6.942976 AGTATTTTCGGTTGAGATGGAGTAA 58.057 36.000 0.00 0.00 0.00 2.24
864 872 7.391620 AGTATTTTCGGTTGAGATGGAGTAAA 58.608 34.615 0.00 0.00 0.00 2.01
865 873 8.047310 AGTATTTTCGGTTGAGATGGAGTAAAT 58.953 33.333 0.00 0.00 0.00 1.40
866 874 7.703058 ATTTTCGGTTGAGATGGAGTAAATT 57.297 32.000 0.00 0.00 0.00 1.82
867 875 7.519032 TTTTCGGTTGAGATGGAGTAAATTT 57.481 32.000 0.00 0.00 0.00 1.82
868 876 6.494893 TTCGGTTGAGATGGAGTAAATTTG 57.505 37.500 0.00 0.00 0.00 2.32
869 877 5.800296 TCGGTTGAGATGGAGTAAATTTGA 58.200 37.500 0.00 0.00 0.00 2.69
870 878 6.414732 TCGGTTGAGATGGAGTAAATTTGAT 58.585 36.000 0.00 0.00 0.00 2.57
871 879 6.884295 TCGGTTGAGATGGAGTAAATTTGATT 59.116 34.615 0.00 0.00 0.00 2.57
872 880 8.044309 TCGGTTGAGATGGAGTAAATTTGATTA 58.956 33.333 0.00 0.00 0.00 1.75
873 881 8.840321 CGGTTGAGATGGAGTAAATTTGATTAT 58.160 33.333 0.00 0.00 0.00 1.28
899 907 7.843490 TTTTTCGGACATGATCTTTACCTAG 57.157 36.000 0.00 0.00 0.00 3.02
900 908 5.531122 TTCGGACATGATCTTTACCTAGG 57.469 43.478 7.41 7.41 0.00 3.02
901 909 4.800023 TCGGACATGATCTTTACCTAGGA 58.200 43.478 17.98 0.00 0.00 2.94
902 910 4.583489 TCGGACATGATCTTTACCTAGGAC 59.417 45.833 17.98 0.00 0.00 3.85
903 911 4.585162 CGGACATGATCTTTACCTAGGACT 59.415 45.833 17.98 0.00 0.00 3.85
904 912 5.508153 CGGACATGATCTTTACCTAGGACTG 60.508 48.000 17.98 2.64 0.00 3.51
905 913 5.364157 GGACATGATCTTTACCTAGGACTGT 59.636 44.000 17.98 4.88 0.00 3.55
906 914 6.227298 ACATGATCTTTACCTAGGACTGTG 57.773 41.667 17.98 1.52 0.00 3.66
907 915 5.958380 ACATGATCTTTACCTAGGACTGTGA 59.042 40.000 17.98 7.21 0.00 3.58
908 916 6.613271 ACATGATCTTTACCTAGGACTGTGAT 59.387 38.462 17.98 11.65 0.00 3.06
909 917 7.126421 ACATGATCTTTACCTAGGACTGTGATT 59.874 37.037 17.98 0.00 0.00 2.57
910 918 7.113658 TGATCTTTACCTAGGACTGTGATTC 57.886 40.000 17.98 3.36 0.00 2.52
911 919 5.934402 TCTTTACCTAGGACTGTGATTCC 57.066 43.478 17.98 0.00 0.00 3.01
968 976 3.325870 GCTTACAAAAGGCCATCAAACC 58.674 45.455 5.01 0.00 32.98 3.27
1098 1118 4.069232 CCAAGTCGGCGAGCTCCA 62.069 66.667 11.20 0.00 0.00 3.86
1389 1458 3.490759 CGGACGCTGCGCAAGATT 61.491 61.111 23.51 0.04 43.02 2.40
1900 2327 5.758296 AGTGAAACGCTCTCAATTTTCTACA 59.242 36.000 0.00 0.00 45.86 2.74
1901 2328 6.073548 AGTGAAACGCTCTCAATTTTCTACAG 60.074 38.462 0.00 0.00 45.86 2.74
1902 2329 5.758296 TGAAACGCTCTCAATTTTCTACAGT 59.242 36.000 0.00 0.00 0.00 3.55
1903 2330 6.926826 TGAAACGCTCTCAATTTTCTACAGTA 59.073 34.615 0.00 0.00 0.00 2.74
1904 2331 6.707599 AACGCTCTCAATTTTCTACAGTAC 57.292 37.500 0.00 0.00 0.00 2.73
1941 2378 6.734137 TCCATTGTGTTTGTTCTTCATGTAC 58.266 36.000 0.00 0.00 0.00 2.90
1944 2381 5.150342 TGTGTTTGTTCTTCATGTACGTG 57.850 39.130 8.90 8.90 0.00 4.49
1945 2382 4.870991 TGTGTTTGTTCTTCATGTACGTGA 59.129 37.500 13.87 13.87 0.00 4.35
1946 2383 5.525745 TGTGTTTGTTCTTCATGTACGTGAT 59.474 36.000 18.26 0.00 0.00 3.06
2295 2812 1.330655 CCCCGAGTACTGGCATGAGT 61.331 60.000 0.00 0.00 0.00 3.41
2345 2862 2.094659 CGGCACTGCGACCTACAAG 61.095 63.158 0.00 0.00 0.00 3.16
2411 2928 4.323477 CCCGGCGACACCTTTGGA 62.323 66.667 9.30 0.00 35.61 3.53
2471 2988 1.078848 CTTTGACTGGAGCCTCCCG 60.079 63.158 8.62 4.13 35.03 5.14
2612 3131 8.767478 AACTTAACTTATGCACGTTGTAGTAT 57.233 30.769 7.82 0.00 0.00 2.12
2729 3260 3.607741 GGATGGCATGACTATCAGATGG 58.392 50.000 3.81 0.00 37.98 3.51
2859 3391 0.384353 GCAAAAGAGTCCGTGCGTTC 60.384 55.000 0.00 0.00 0.00 3.95
2976 3508 0.613260 TGTGTTGCCGCTTATCCTCT 59.387 50.000 0.00 0.00 0.00 3.69
3050 3584 8.361139 AAAACGTGTTTGAATATGGTTAATCCA 58.639 29.630 0.00 0.18 40.69 3.41
3077 3622 3.243569 CGTCTCTCTCTCTCTCTCTCTCC 60.244 56.522 0.00 0.00 0.00 3.71
3079 3624 2.036475 CTCTCTCTCTCTCTCTCTCCCG 59.964 59.091 0.00 0.00 0.00 5.14
3105 3656 0.307453 CTCTCACTCTCGCGATGAGG 59.693 60.000 28.52 19.11 45.32 3.86
3128 3679 1.202879 TCTGTTGTTTTCCCCTGCGAT 60.203 47.619 0.00 0.00 0.00 4.58
3236 3788 2.223525 CCGCCGGTACAAAAGAAAAACA 60.224 45.455 1.90 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.525629 TTGTGGAGGGAGGCACGA 60.526 61.111 0.00 0.00 0.00 4.35
98 99 0.460284 GGACGTCCGCATGATTGTCT 60.460 55.000 20.85 0.00 33.85 3.41
113 114 1.690219 CCCCTTGGAGGAGATGGACG 61.690 65.000 0.00 0.00 37.67 4.79
190 191 0.108019 CATCTCAGGCATGGCTAGCA 59.892 55.000 22.88 8.54 0.00 3.49
191 192 0.605860 CCATCTCAGGCATGGCTAGC 60.606 60.000 22.88 6.04 34.59 3.42
241 243 4.052922 TCCACTACACTATAGTCCCCTCT 58.947 47.826 1.26 0.00 0.00 3.69
257 259 2.238646 CCAAACCATAGCCACTCCACTA 59.761 50.000 0.00 0.00 0.00 2.74
264 266 4.332828 AGTCTTTACCAAACCATAGCCAC 58.667 43.478 0.00 0.00 0.00 5.01
282 284 7.179338 CACTAAATACAGCCCTATCCATAGTCT 59.821 40.741 0.00 0.00 0.00 3.24
285 287 7.364232 CCTCACTAAATACAGCCCTATCCATAG 60.364 44.444 0.00 0.00 0.00 2.23
314 316 2.189521 CCCACTATGGCCCGTCAC 59.810 66.667 0.00 0.00 35.79 3.67
352 354 2.129555 ATATGGGGATGCCTGGACGC 62.130 60.000 2.19 0.00 0.00 5.19
385 387 2.550978 GTCAACACCCATATCCAGTCG 58.449 52.381 0.00 0.00 0.00 4.18
386 388 2.550978 CGTCAACACCCATATCCAGTC 58.449 52.381 0.00 0.00 0.00 3.51
420 422 2.637025 GCTCGAAACGCAGCCAAA 59.363 55.556 0.00 0.00 0.00 3.28
428 430 1.487231 CAACCAGACGCTCGAAACG 59.513 57.895 6.00 6.00 0.00 3.60
450 452 1.372872 GCTCGGGCGCAAAATTGTT 60.373 52.632 10.83 0.00 0.00 2.83
486 488 1.914263 TCCGTCCCAAATGTCCGGA 60.914 57.895 0.00 0.00 44.74 5.14
505 507 1.105457 CTACAACCGGACGTCCCATA 58.895 55.000 28.52 12.37 34.14 2.74
511 513 0.606604 AAGCATCTACAACCGGACGT 59.393 50.000 9.46 7.17 0.00 4.34
530 532 5.473273 TGGGTATCTCTTGAGCCCTATAAA 58.527 41.667 11.33 0.00 40.09 1.40
562 566 6.829229 TGAATGTTTTCTCTAGTACTCGGA 57.171 37.500 0.00 0.00 32.78 4.55
607 611 1.043022 AACGGACACTCGGTTAAGGT 58.957 50.000 0.00 0.00 38.01 3.50
611 615 4.201812 CGTATCTTAACGGACACTCGGTTA 60.202 45.833 0.00 0.00 39.93 2.85
612 616 3.426695 CGTATCTTAACGGACACTCGGTT 60.427 47.826 0.00 1.47 41.71 4.44
613 617 2.096496 CGTATCTTAACGGACACTCGGT 59.904 50.000 0.00 0.00 39.19 4.69
614 618 2.713011 CGTATCTTAACGGACACTCGG 58.287 52.381 0.00 0.00 39.19 4.63
615 619 2.107178 GCGTATCTTAACGGACACTCG 58.893 52.381 0.00 0.00 43.06 4.18
616 620 3.417690 AGCGTATCTTAACGGACACTC 57.582 47.619 0.00 0.00 43.06 3.51
629 637 4.616181 AGTAAACATTGCCAAGCGTATC 57.384 40.909 0.00 0.00 0.00 2.24
634 642 4.215399 TGAGTGTAGTAAACATTGCCAAGC 59.785 41.667 0.00 0.00 41.10 4.01
657 665 1.565759 ACATGTGTCCACCCATATGCT 59.434 47.619 0.00 0.00 37.43 3.79
661 669 1.206132 GACGACATGTGTCCACCCATA 59.794 52.381 1.15 0.00 41.86 2.74
662 670 0.036388 GACGACATGTGTCCACCCAT 60.036 55.000 1.15 0.00 41.86 4.00
663 671 1.118965 AGACGACATGTGTCCACCCA 61.119 55.000 18.71 0.00 41.86 4.51
664 672 0.389948 GAGACGACATGTGTCCACCC 60.390 60.000 18.71 7.73 41.86 4.61
665 673 0.732880 CGAGACGACATGTGTCCACC 60.733 60.000 18.71 11.10 41.86 4.61
666 674 0.039437 ACGAGACGACATGTGTCCAC 60.039 55.000 18.71 14.10 41.86 4.02
667 675 0.671796 AACGAGACGACATGTGTCCA 59.328 50.000 18.71 0.00 41.86 4.02
668 676 1.719780 GAAACGAGACGACATGTGTCC 59.280 52.381 18.71 12.29 41.86 4.02
669 677 1.719780 GGAAACGAGACGACATGTGTC 59.280 52.381 1.15 11.49 41.47 3.67
670 678 1.340248 AGGAAACGAGACGACATGTGT 59.660 47.619 1.15 1.22 0.00 3.72
671 679 2.065993 AGGAAACGAGACGACATGTG 57.934 50.000 1.15 0.00 0.00 3.21
672 680 2.814280 AAGGAAACGAGACGACATGT 57.186 45.000 0.00 0.00 0.00 3.21
673 681 3.834610 ACTAAGGAAACGAGACGACATG 58.165 45.455 0.00 0.00 0.00 3.21
674 682 4.022589 TCAACTAAGGAAACGAGACGACAT 60.023 41.667 0.00 0.00 0.00 3.06
675 683 3.316029 TCAACTAAGGAAACGAGACGACA 59.684 43.478 0.00 0.00 0.00 4.35
676 684 3.667726 GTCAACTAAGGAAACGAGACGAC 59.332 47.826 0.00 0.00 0.00 4.34
677 685 3.893720 GTCAACTAAGGAAACGAGACGA 58.106 45.455 0.00 0.00 0.00 4.20
678 686 2.655474 CGTCAACTAAGGAAACGAGACG 59.345 50.000 0.00 0.00 41.00 4.18
679 687 2.985139 CCGTCAACTAAGGAAACGAGAC 59.015 50.000 0.00 0.00 35.45 3.36
680 688 2.608752 GCCGTCAACTAAGGAAACGAGA 60.609 50.000 0.00 0.00 35.45 4.04
681 689 1.725164 GCCGTCAACTAAGGAAACGAG 59.275 52.381 0.00 0.00 35.45 4.18
682 690 1.068895 TGCCGTCAACTAAGGAAACGA 59.931 47.619 0.00 0.00 35.45 3.85
683 691 1.504359 TGCCGTCAACTAAGGAAACG 58.496 50.000 0.00 0.00 0.00 3.60
684 692 2.161609 CCATGCCGTCAACTAAGGAAAC 59.838 50.000 0.00 0.00 0.00 2.78
685 693 2.224670 ACCATGCCGTCAACTAAGGAAA 60.225 45.455 0.00 0.00 0.00 3.13
686 694 1.349688 ACCATGCCGTCAACTAAGGAA 59.650 47.619 0.00 0.00 0.00 3.36
687 695 0.981183 ACCATGCCGTCAACTAAGGA 59.019 50.000 0.00 0.00 0.00 3.36
688 696 2.676342 GTTACCATGCCGTCAACTAAGG 59.324 50.000 0.00 0.00 0.00 2.69
689 697 2.676342 GGTTACCATGCCGTCAACTAAG 59.324 50.000 0.00 0.00 0.00 2.18
690 698 2.303600 AGGTTACCATGCCGTCAACTAA 59.696 45.455 3.51 0.00 0.00 2.24
691 699 1.903860 AGGTTACCATGCCGTCAACTA 59.096 47.619 3.51 0.00 0.00 2.24
692 700 0.690762 AGGTTACCATGCCGTCAACT 59.309 50.000 3.51 0.00 0.00 3.16
693 701 2.389962 TAGGTTACCATGCCGTCAAC 57.610 50.000 3.51 0.00 0.00 3.18
694 702 2.912771 CATAGGTTACCATGCCGTCAA 58.087 47.619 3.51 0.00 0.00 3.18
695 703 1.474320 GCATAGGTTACCATGCCGTCA 60.474 52.381 20.37 0.00 41.36 4.35
696 704 1.226746 GCATAGGTTACCATGCCGTC 58.773 55.000 20.37 2.32 41.36 4.79
697 705 3.396951 GCATAGGTTACCATGCCGT 57.603 52.632 20.37 0.00 41.36 5.68
700 708 2.427506 GCTAGGCATAGGTTACCATGC 58.572 52.381 21.85 21.85 45.47 4.06
701 709 2.037251 ACGCTAGGCATAGGTTACCATG 59.963 50.000 7.62 6.80 0.00 3.66
702 710 2.326428 ACGCTAGGCATAGGTTACCAT 58.674 47.619 7.62 0.00 0.00 3.55
703 711 1.784358 ACGCTAGGCATAGGTTACCA 58.216 50.000 7.62 0.00 0.00 3.25
704 712 2.904697 AACGCTAGGCATAGGTTACC 57.095 50.000 7.62 0.00 0.00 2.85
705 713 4.729746 GCAAAAACGCTAGGCATAGGTTAC 60.730 45.833 7.62 0.00 0.00 2.50
706 714 3.375922 GCAAAAACGCTAGGCATAGGTTA 59.624 43.478 7.62 0.00 0.00 2.85
707 715 2.163613 GCAAAAACGCTAGGCATAGGTT 59.836 45.455 7.62 6.95 0.00 3.50
708 716 1.743394 GCAAAAACGCTAGGCATAGGT 59.257 47.619 7.62 0.70 0.00 3.08
709 717 1.065551 GGCAAAAACGCTAGGCATAGG 59.934 52.381 7.62 0.06 0.00 2.57
710 718 1.742831 TGGCAAAAACGCTAGGCATAG 59.257 47.619 0.00 0.00 0.00 2.23
711 719 1.742831 CTGGCAAAAACGCTAGGCATA 59.257 47.619 0.00 0.00 36.88 3.14
712 720 0.527565 CTGGCAAAAACGCTAGGCAT 59.472 50.000 0.00 0.00 36.88 4.40
713 721 1.956043 CTGGCAAAAACGCTAGGCA 59.044 52.632 0.00 0.00 36.88 4.75
714 722 1.444383 GCTGGCAAAAACGCTAGGC 60.444 57.895 0.00 0.00 40.58 3.93
715 723 0.527565 ATGCTGGCAAAAACGCTAGG 59.472 50.000 0.00 0.00 40.58 3.02
716 724 2.253603 GAATGCTGGCAAAAACGCTAG 58.746 47.619 0.00 0.00 42.92 3.42
717 725 1.611006 TGAATGCTGGCAAAAACGCTA 59.389 42.857 0.00 0.00 0.00 4.26
718 726 0.388659 TGAATGCTGGCAAAAACGCT 59.611 45.000 0.00 0.00 0.00 5.07
719 727 0.785979 CTGAATGCTGGCAAAAACGC 59.214 50.000 0.00 0.00 0.00 4.84
720 728 0.785979 GCTGAATGCTGGCAAAAACG 59.214 50.000 0.00 0.00 38.95 3.60
721 729 1.868469 TGCTGAATGCTGGCAAAAAC 58.132 45.000 0.00 0.00 43.37 2.43
722 730 2.616634 TTGCTGAATGCTGGCAAAAA 57.383 40.000 0.00 0.00 41.96 1.94
725 733 2.843401 AATTTGCTGAATGCTGGCAA 57.157 40.000 0.00 0.00 42.97 4.52
726 734 2.843401 AAATTTGCTGAATGCTGGCA 57.157 40.000 0.00 0.00 43.37 4.92
727 735 5.610235 TTAAAAATTTGCTGAATGCTGGC 57.390 34.783 0.00 0.00 43.37 4.85
728 736 6.372103 TGGATTAAAAATTTGCTGAATGCTGG 59.628 34.615 0.00 0.00 43.37 4.85
729 737 7.367159 TGGATTAAAAATTTGCTGAATGCTG 57.633 32.000 0.00 0.00 43.37 4.41
730 738 8.455682 CAATGGATTAAAAATTTGCTGAATGCT 58.544 29.630 0.00 0.00 43.37 3.79
731 739 7.698970 CCAATGGATTAAAAATTTGCTGAATGC 59.301 33.333 0.00 0.00 43.25 3.56
732 740 8.732531 ACCAATGGATTAAAAATTTGCTGAATG 58.267 29.630 6.16 0.00 0.00 2.67
733 741 8.866970 ACCAATGGATTAAAAATTTGCTGAAT 57.133 26.923 6.16 0.00 0.00 2.57
734 742 9.956640 ATACCAATGGATTAAAAATTTGCTGAA 57.043 25.926 6.16 0.00 0.00 3.02
735 743 9.956640 AATACCAATGGATTAAAAATTTGCTGA 57.043 25.926 6.16 0.00 0.00 4.26
762 770 9.010029 AGTACAACGGAAAACATAAAGATGAAT 57.990 29.630 0.00 0.00 36.48 2.57
763 771 8.385898 AGTACAACGGAAAACATAAAGATGAA 57.614 30.769 0.00 0.00 36.48 2.57
764 772 7.148705 CGAGTACAACGGAAAACATAAAGATGA 60.149 37.037 0.00 0.00 36.48 2.92
765 773 6.953743 CGAGTACAACGGAAAACATAAAGATG 59.046 38.462 0.00 0.00 39.16 2.90
766 774 7.057149 CGAGTACAACGGAAAACATAAAGAT 57.943 36.000 0.00 0.00 0.00 2.40
767 775 6.456447 CGAGTACAACGGAAAACATAAAGA 57.544 37.500 0.00 0.00 0.00 2.52
780 788 1.595794 ACAAGTTTGCCGAGTACAACG 59.404 47.619 0.00 0.19 0.00 4.10
781 789 3.685836 AACAAGTTTGCCGAGTACAAC 57.314 42.857 0.00 0.00 0.00 3.32
782 790 4.705337 AAAACAAGTTTGCCGAGTACAA 57.295 36.364 0.00 0.00 32.36 2.41
783 791 5.761234 AGATAAAACAAGTTTGCCGAGTACA 59.239 36.000 0.00 0.00 32.36 2.90
784 792 6.237313 AGATAAAACAAGTTTGCCGAGTAC 57.763 37.500 0.00 0.00 32.36 2.73
785 793 6.483974 TCAAGATAAAACAAGTTTGCCGAGTA 59.516 34.615 0.00 0.00 32.36 2.59
786 794 5.298276 TCAAGATAAAACAAGTTTGCCGAGT 59.702 36.000 0.00 0.00 32.36 4.18
787 795 5.757886 TCAAGATAAAACAAGTTTGCCGAG 58.242 37.500 0.00 0.00 32.36 4.63
788 796 5.759506 TCAAGATAAAACAAGTTTGCCGA 57.240 34.783 0.00 0.00 32.36 5.54
789 797 8.687824 AATATCAAGATAAAACAAGTTTGCCG 57.312 30.769 0.00 0.00 32.36 5.69
814 822 7.374272 TCTCATCAAATTTACCGCATGAAAAA 58.626 30.769 0.00 0.00 0.00 1.94
815 823 6.918626 TCTCATCAAATTTACCGCATGAAAA 58.081 32.000 0.00 0.00 0.00 2.29
816 824 6.150976 ACTCTCATCAAATTTACCGCATGAAA 59.849 34.615 0.00 0.00 0.00 2.69
817 825 5.647658 ACTCTCATCAAATTTACCGCATGAA 59.352 36.000 0.00 0.00 0.00 2.57
818 826 5.185454 ACTCTCATCAAATTTACCGCATGA 58.815 37.500 0.00 0.00 0.00 3.07
819 827 5.490139 ACTCTCATCAAATTTACCGCATG 57.510 39.130 0.00 0.00 0.00 4.06
820 828 7.807977 AATACTCTCATCAAATTTACCGCAT 57.192 32.000 0.00 0.00 0.00 4.73
821 829 7.624360 AAATACTCTCATCAAATTTACCGCA 57.376 32.000 0.00 0.00 0.00 5.69
822 830 7.373441 CGAAAATACTCTCATCAAATTTACCGC 59.627 37.037 0.00 0.00 0.00 5.68
823 831 7.850982 CCGAAAATACTCTCATCAAATTTACCG 59.149 37.037 0.00 0.00 0.00 4.02
824 832 8.674607 ACCGAAAATACTCTCATCAAATTTACC 58.325 33.333 0.00 0.00 0.00 2.85
827 835 8.792633 TCAACCGAAAATACTCTCATCAAATTT 58.207 29.630 0.00 0.00 0.00 1.82
828 836 8.335532 TCAACCGAAAATACTCTCATCAAATT 57.664 30.769 0.00 0.00 0.00 1.82
829 837 7.824289 TCTCAACCGAAAATACTCTCATCAAAT 59.176 33.333 0.00 0.00 0.00 2.32
830 838 7.158697 TCTCAACCGAAAATACTCTCATCAAA 58.841 34.615 0.00 0.00 0.00 2.69
831 839 6.697395 TCTCAACCGAAAATACTCTCATCAA 58.303 36.000 0.00 0.00 0.00 2.57
832 840 6.280855 TCTCAACCGAAAATACTCTCATCA 57.719 37.500 0.00 0.00 0.00 3.07
833 841 6.201806 CCATCTCAACCGAAAATACTCTCATC 59.798 42.308 0.00 0.00 0.00 2.92
834 842 6.051717 CCATCTCAACCGAAAATACTCTCAT 58.948 40.000 0.00 0.00 0.00 2.90
835 843 5.186992 TCCATCTCAACCGAAAATACTCTCA 59.813 40.000 0.00 0.00 0.00 3.27
836 844 5.661458 TCCATCTCAACCGAAAATACTCTC 58.339 41.667 0.00 0.00 0.00 3.20
837 845 5.187967 ACTCCATCTCAACCGAAAATACTCT 59.812 40.000 0.00 0.00 0.00 3.24
838 846 5.420409 ACTCCATCTCAACCGAAAATACTC 58.580 41.667 0.00 0.00 0.00 2.59
839 847 5.422214 ACTCCATCTCAACCGAAAATACT 57.578 39.130 0.00 0.00 0.00 2.12
840 848 7.605410 TTTACTCCATCTCAACCGAAAATAC 57.395 36.000 0.00 0.00 0.00 1.89
841 849 8.801882 AATTTACTCCATCTCAACCGAAAATA 57.198 30.769 0.00 0.00 0.00 1.40
842 850 7.703058 AATTTACTCCATCTCAACCGAAAAT 57.297 32.000 0.00 0.00 0.00 1.82
843 851 7.229707 TCAAATTTACTCCATCTCAACCGAAAA 59.770 33.333 0.00 0.00 0.00 2.29
844 852 6.712998 TCAAATTTACTCCATCTCAACCGAAA 59.287 34.615 0.00 0.00 0.00 3.46
845 853 6.234920 TCAAATTTACTCCATCTCAACCGAA 58.765 36.000 0.00 0.00 0.00 4.30
846 854 5.800296 TCAAATTTACTCCATCTCAACCGA 58.200 37.500 0.00 0.00 0.00 4.69
847 855 6.683974 ATCAAATTTACTCCATCTCAACCG 57.316 37.500 0.00 0.00 0.00 4.44
875 883 6.821665 CCTAGGTAAAGATCATGTCCGAAAAA 59.178 38.462 0.00 0.00 0.00 1.94
876 884 6.155565 TCCTAGGTAAAGATCATGTCCGAAAA 59.844 38.462 9.08 0.00 0.00 2.29
877 885 5.659525 TCCTAGGTAAAGATCATGTCCGAAA 59.340 40.000 9.08 0.00 0.00 3.46
878 886 5.068723 GTCCTAGGTAAAGATCATGTCCGAA 59.931 44.000 9.08 0.00 0.00 4.30
879 887 4.583489 GTCCTAGGTAAAGATCATGTCCGA 59.417 45.833 9.08 0.00 0.00 4.55
880 888 4.585162 AGTCCTAGGTAAAGATCATGTCCG 59.415 45.833 9.08 0.00 0.00 4.79
881 889 5.364157 ACAGTCCTAGGTAAAGATCATGTCC 59.636 44.000 9.08 0.00 0.00 4.02
882 890 6.096987 TCACAGTCCTAGGTAAAGATCATGTC 59.903 42.308 9.08 0.00 0.00 3.06
883 891 5.958380 TCACAGTCCTAGGTAAAGATCATGT 59.042 40.000 9.08 0.00 0.00 3.21
884 892 6.471233 TCACAGTCCTAGGTAAAGATCATG 57.529 41.667 9.08 0.00 0.00 3.07
885 893 7.202047 GGAATCACAGTCCTAGGTAAAGATCAT 60.202 40.741 9.08 0.00 31.94 2.45
886 894 6.098409 GGAATCACAGTCCTAGGTAAAGATCA 59.902 42.308 9.08 0.00 31.94 2.92
887 895 6.517605 GGAATCACAGTCCTAGGTAAAGATC 58.482 44.000 9.08 0.00 31.94 2.75
888 896 5.069251 CGGAATCACAGTCCTAGGTAAAGAT 59.931 44.000 9.08 4.84 32.53 2.40
889 897 4.401519 CGGAATCACAGTCCTAGGTAAAGA 59.598 45.833 9.08 2.57 32.53 2.52
890 898 4.159879 ACGGAATCACAGTCCTAGGTAAAG 59.840 45.833 9.08 0.24 32.53 1.85
891 899 4.081862 CACGGAATCACAGTCCTAGGTAAA 60.082 45.833 9.08 0.00 32.53 2.01
892 900 3.446161 CACGGAATCACAGTCCTAGGTAA 59.554 47.826 9.08 0.00 32.53 2.85
893 901 3.021695 CACGGAATCACAGTCCTAGGTA 58.978 50.000 9.08 0.00 32.53 3.08
894 902 1.825474 CACGGAATCACAGTCCTAGGT 59.175 52.381 9.08 0.00 32.53 3.08
895 903 2.100197 TCACGGAATCACAGTCCTAGG 58.900 52.381 0.82 0.82 32.53 3.02
896 904 2.492088 TGTCACGGAATCACAGTCCTAG 59.508 50.000 0.00 0.00 32.53 3.02
897 905 2.521126 TGTCACGGAATCACAGTCCTA 58.479 47.619 0.00 0.00 32.53 2.94
898 906 1.338107 TGTCACGGAATCACAGTCCT 58.662 50.000 0.00 0.00 32.53 3.85
899 907 2.002586 CATGTCACGGAATCACAGTCC 58.997 52.381 0.00 0.00 0.00 3.85
900 908 1.394917 GCATGTCACGGAATCACAGTC 59.605 52.381 0.00 0.00 0.00 3.51
901 909 1.442769 GCATGTCACGGAATCACAGT 58.557 50.000 0.00 0.00 0.00 3.55
902 910 0.371301 CGCATGTCACGGAATCACAG 59.629 55.000 0.00 0.00 0.00 3.66
903 911 1.634757 GCGCATGTCACGGAATCACA 61.635 55.000 0.30 0.00 0.00 3.58
904 912 1.060937 GCGCATGTCACGGAATCAC 59.939 57.895 0.30 0.00 0.00 3.06
905 913 0.744057 ATGCGCATGTCACGGAATCA 60.744 50.000 24.69 0.00 33.57 2.57
906 914 0.316442 CATGCGCATGTCACGGAATC 60.316 55.000 36.45 0.00 33.57 2.52
907 915 0.744057 TCATGCGCATGTCACGGAAT 60.744 50.000 40.57 8.70 39.72 3.01
908 916 1.375268 TCATGCGCATGTCACGGAA 60.375 52.632 40.57 23.00 39.72 4.30
909 917 2.100031 GTCATGCGCATGTCACGGA 61.100 57.895 40.57 23.68 39.72 4.69
910 918 2.300597 CTGTCATGCGCATGTCACGG 62.301 60.000 40.57 33.29 39.72 4.94
911 919 1.059838 CTGTCATGCGCATGTCACG 59.940 57.895 40.57 29.80 39.72 4.35
959 967 4.082245 ACTTAATTTGGCGAGGTTTGATGG 60.082 41.667 0.00 0.00 0.00 3.51
968 976 3.334691 TCAGTGGACTTAATTTGGCGAG 58.665 45.455 0.00 0.00 0.00 5.03
1066 1077 1.003262 CTTGGTGTTGATTTGCGGCG 61.003 55.000 0.51 0.51 0.00 6.46
1098 1118 3.626924 GGCAGACACCGTGGTCCT 61.627 66.667 3.03 0.00 38.59 3.85
1248 1268 3.909086 GAGCACCTCCTTTGCCGCT 62.909 63.158 0.00 0.00 41.18 5.52
1389 1458 3.240134 GAGGAGCTCCACCGTGCAA 62.240 63.158 33.90 0.00 38.89 4.08
1502 1697 2.281484 GCCTGCCGAGGTTGAACA 60.281 61.111 0.00 0.00 42.15 3.18
1809 2080 2.119611 TCAAGCTCCCCCTCGTCA 59.880 61.111 0.00 0.00 0.00 4.35
1900 2327 6.312918 CACAATGGAAAAGTATACTGCGTACT 59.687 38.462 6.06 0.00 33.98 2.73
1901 2328 6.091713 ACACAATGGAAAAGTATACTGCGTAC 59.908 38.462 6.06 0.00 0.00 3.67
1902 2329 6.167685 ACACAATGGAAAAGTATACTGCGTA 58.832 36.000 6.06 0.00 0.00 4.42
1903 2330 5.001232 ACACAATGGAAAAGTATACTGCGT 58.999 37.500 6.06 0.00 0.00 5.24
1904 2331 5.545658 ACACAATGGAAAAGTATACTGCG 57.454 39.130 6.06 0.00 0.00 5.18
2219 2736 2.509964 GGTACCCTCCATGACCTCAAAT 59.490 50.000 0.00 0.00 0.00 2.32
2345 2862 3.443045 TACTCGAACCGCGACCCC 61.443 66.667 8.23 0.00 45.59 4.95
2563 3080 7.358830 TTTTAATTAAAAACTGCATGCCTTGC 58.641 30.769 18.74 1.95 40.76 4.01
2612 3131 3.454447 ACCACTCGACCATTATCATTCCA 59.546 43.478 0.00 0.00 0.00 3.53
2693 3224 2.223572 GCCATCCCATGACGATGAAAAC 60.224 50.000 18.94 6.73 39.64 2.43
2798 3330 2.224018 TGCATGCAAAGTTCCAAACCTC 60.224 45.455 20.30 0.00 0.00 3.85
2799 3331 1.761784 TGCATGCAAAGTTCCAAACCT 59.238 42.857 20.30 0.00 0.00 3.50
2859 3391 4.069304 TGTTATGTTTTCTCTCCCGTTGG 58.931 43.478 0.00 0.00 0.00 3.77
2929 3461 4.219507 TGATGCCTCGCAAAAATAAAGGAA 59.780 37.500 0.00 0.00 43.62 3.36
2976 3508 4.388499 GCCGGCGAGGGTGAGAAA 62.388 66.667 12.58 0.00 41.48 2.52
2996 3528 0.546122 TTGTGTGAACACTGAGGCCT 59.454 50.000 3.86 3.86 46.55 5.19
3050 3584 2.026262 AGAGAGAGAGAGAGACGCCTTT 60.026 50.000 0.00 0.00 0.00 3.11
3077 3622 0.800300 GAGAGTGAGAGAAAGCGCGG 60.800 60.000 8.83 0.00 0.00 6.46
3079 3624 1.409982 GCGAGAGTGAGAGAAAGCGC 61.410 60.000 0.00 0.00 36.35 5.92
3105 3656 2.351738 CGCAGGGGAAAACAACAGATTC 60.352 50.000 0.00 0.00 0.00 2.52
3128 3679 8.046708 ACTACACATGCATACCTCTGAAAAATA 58.953 33.333 0.00 0.00 0.00 1.40
3224 3775 4.741676 AGCGCAAGATCTGTTTTTCTTTTG 59.258 37.500 11.47 0.00 43.02 2.44
3225 3776 4.936891 AGCGCAAGATCTGTTTTTCTTTT 58.063 34.783 11.47 0.00 43.02 2.27
3362 3916 9.486857 GTATCTTTTAAACCGTAGCTTTGATTC 57.513 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.