Multiple sequence alignment - TraesCS7A01G412700

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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 TraesCS7A01G412700 chr7A 100.000 3389 0 0 1 3389 603554258 603550870 0.000000e+00 6259
1 TraesCS7A01G412700 chr7A 87.675 1428 171 3 972 2398 603331692 603330269 0.000000e+00 1657
2 TraesCS7A01G412700 chr7A 86.662 1447 172 10 952 2394 566788201 566789630 0.000000e+00 1583
3 TraesCS7A01G412700 chr7A 88.121 564 54 4 1936 2489 603614703 603614143 0.000000e+00 658
4 TraesCS7A01G412700 chr7A 95.868 242 10 0 420 661 603558769 603558528 3.170000e-105 392
5 TraesCS7A01G412700 chr7A 88.119 101 9 1 785 885 603717254 603717157 2.140000e-22 117
6 TraesCS7A01G412700 chr7A 87.500 96 9 1 790 885 603703531 603703439 1.290000e-19 108
7 TraesCS7A01G412700 chr7B 94.412 1736 80 6 785 2510 557491815 557490087 0.000000e+00 2652
8 TraesCS7A01G412700 chr7B 86.445 1446 168 17 951 2389 528871600 528873024 0.000000e+00 1559
9 TraesCS7A01G412700 chr7B 86.121 1441 189 7 960 2398 557257472 557256041 0.000000e+00 1543
10 TraesCS7A01G412700 chr7D 92.111 1724 101 13 785 2499 523134012 523132315 0.000000e+00 2398
11 TraesCS7A01G412700 chr7D 88.286 1400 153 10 1003 2398 523057020 523055628 0.000000e+00 1666
12 TraesCS7A01G412700 chr7D 87.707 1391 153 11 961 2346 523128187 523126810 0.000000e+00 1605
13 TraesCS7A01G412700 chr7D 86.326 1448 175 11 952 2394 500773705 500775134 0.000000e+00 1555
14 TraesCS7A01G412700 chr7D 80.312 513 69 16 2785 3295 523130824 523130342 3.220000e-95 359
15 TraesCS7A01G412700 chr7D 83.033 389 36 12 3030 3389 523130158 523129771 3.260000e-85 326
16 TraesCS7A01G412700 chr2D 83.628 1356 203 12 1013 2351 569121055 569119702 0.000000e+00 1256
17 TraesCS7A01G412700 chr2D 83.555 1356 204 13 1013 2351 569153494 569152141 0.000000e+00 1251
18 TraesCS7A01G412700 chr2A 83.247 1355 208 12 1014 2351 708862315 708863667 0.000000e+00 1227
19 TraesCS7A01G412700 chr4D 96.084 664 22 2 1 661 507557617 507558279 0.000000e+00 1079
20 TraesCS7A01G412700 chr4D 90.855 667 47 7 1 661 3581993 3582651 0.000000e+00 881
21 TraesCS7A01G412700 chr4D 94.628 242 13 0 420 661 507553104 507553345 3.190000e-100 375
22 TraesCS7A01G412700 chr1B 90.855 667 53 6 1 661 58556491 58557155 0.000000e+00 887
23 TraesCS7A01G412700 chr1A 90.361 664 48 6 1 661 565136034 565136684 0.000000e+00 857
24 TraesCS7A01G412700 chr4A 89.759 664 51 7 1 661 626752689 626752040 0.000000e+00 833
25 TraesCS7A01G412700 chr3A 89.189 666 56 7 1 663 737513184 737513836 0.000000e+00 817
26 TraesCS7A01G412700 chr5A 89.039 666 54 10 1 661 35819421 35820072 0.000000e+00 808
27 TraesCS7A01G412700 chr3B 92.634 448 29 2 1 445 227423916 227424362 2.850000e-180 641
28 TraesCS7A01G412700 chr1D 88.082 537 50 11 2 529 6250243 6249712 2.870000e-175 625


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 TraesCS7A01G412700 chr7A 603550870 603554258 3388 True 6259 6259 100.00000 1 3389 1 chr7A.!!$R2 3388
1 TraesCS7A01G412700 chr7A 603330269 603331692 1423 True 1657 1657 87.67500 972 2398 1 chr7A.!!$R1 1426
2 TraesCS7A01G412700 chr7A 566788201 566789630 1429 False 1583 1583 86.66200 952 2394 1 chr7A.!!$F1 1442
3 TraesCS7A01G412700 chr7A 603614143 603614703 560 True 658 658 88.12100 1936 2489 1 chr7A.!!$R4 553
4 TraesCS7A01G412700 chr7B 557490087 557491815 1728 True 2652 2652 94.41200 785 2510 1 chr7B.!!$R2 1725
5 TraesCS7A01G412700 chr7B 528871600 528873024 1424 False 1559 1559 86.44500 951 2389 1 chr7B.!!$F1 1438
6 TraesCS7A01G412700 chr7B 557256041 557257472 1431 True 1543 1543 86.12100 960 2398 1 chr7B.!!$R1 1438
7 TraesCS7A01G412700 chr7D 523055628 523057020 1392 True 1666 1666 88.28600 1003 2398 1 chr7D.!!$R1 1395
8 TraesCS7A01G412700 chr7D 500773705 500775134 1429 False 1555 1555 86.32600 952 2394 1 chr7D.!!$F1 1442
9 TraesCS7A01G412700 chr7D 523126810 523134012 7202 True 1172 2398 85.79075 785 3389 4 chr7D.!!$R2 2604
10 TraesCS7A01G412700 chr2D 569119702 569121055 1353 True 1256 1256 83.62800 1013 2351 1 chr2D.!!$R1 1338
11 TraesCS7A01G412700 chr2D 569152141 569153494 1353 True 1251 1251 83.55500 1013 2351 1 chr2D.!!$R2 1338
12 TraesCS7A01G412700 chr2A 708862315 708863667 1352 False 1227 1227 83.24700 1014 2351 1 chr2A.!!$F1 1337
13 TraesCS7A01G412700 chr4D 507557617 507558279 662 False 1079 1079 96.08400 1 661 1 chr4D.!!$F3 660
14 TraesCS7A01G412700 chr4D 3581993 3582651 658 False 881 881 90.85500 1 661 1 chr4D.!!$F1 660
15 TraesCS7A01G412700 chr1B 58556491 58557155 664 False 887 887 90.85500 1 661 1 chr1B.!!$F1 660
16 TraesCS7A01G412700 chr1A 565136034 565136684 650 False 857 857 90.36100 1 661 1 chr1A.!!$F1 660
17 TraesCS7A01G412700 chr4A 626752040 626752689 649 True 833 833 89.75900 1 661 1 chr4A.!!$R1 660
18 TraesCS7A01G412700 chr3A 737513184 737513836 652 False 817 817 89.18900 1 663 1 chr3A.!!$F1 662
19 TraesCS7A01G412700 chr5A 35819421 35820072 651 False 808 808 89.03900 1 661 1 chr5A.!!$F1 660
20 TraesCS7A01G412700 chr1D 6249712 6250243 531 True 625 625 88.08200 2 529 1 chr1D.!!$R1 527

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
708 720 0.034616 ACCACTCTGCAGTCTTGAGC 59.965 55.0 14.67 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2741 0.178903 TCCAACACTGGGCTAGGAGT 60.179 55.0 2.02 0.0 43.71 3.85 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
125 126 4.471904 ACGTGAGGATTTGCTGATCTTA 57.528 40.909 0.00 0.00 0.00 2.10
139 140 5.001232 GCTGATCTTAAGTAACCCACACAA 58.999 41.667 1.63 0.00 0.00 3.33
288 292 1.056700 AGACCTGCACCTTCCACACT 61.057 55.000 0.00 0.00 0.00 3.55
510 519 8.982723 GCCAGGATAGATATAAGATTAGTTGGA 58.017 37.037 0.00 0.00 0.00 3.53
594 606 1.954146 CACAACACGCACGCCTACT 60.954 57.895 0.00 0.00 0.00 2.57
663 675 9.762062 CGTATATGTTTACAATGTTTAACAGCA 57.238 29.630 15.38 8.95 34.37 4.41
666 678 9.973450 ATATGTTTACAATGTTTAACAGCAACA 57.027 25.926 15.38 8.02 38.49 3.33
667 679 8.709386 ATGTTTACAATGTTTAACAGCAACAA 57.291 26.923 15.38 0.00 37.67 2.83
668 680 8.179148 TGTTTACAATGTTTAACAGCAACAAG 57.821 30.769 3.63 0.00 37.67 3.16
669 681 7.815068 TGTTTACAATGTTTAACAGCAACAAGT 59.185 29.630 3.63 0.00 37.67 3.16
670 682 9.291664 GTTTACAATGTTTAACAGCAACAAGTA 57.708 29.630 3.63 0.00 37.67 2.24
671 683 8.844441 TTACAATGTTTAACAGCAACAAGTAC 57.156 30.769 3.63 0.00 37.67 2.73
672 684 6.270064 ACAATGTTTAACAGCAACAAGTACC 58.730 36.000 3.63 0.00 37.67 3.34
673 685 4.904253 TGTTTAACAGCAACAAGTACCC 57.096 40.909 0.00 0.00 31.05 3.69
674 686 4.528920 TGTTTAACAGCAACAAGTACCCT 58.471 39.130 0.00 0.00 31.05 4.34
675 687 4.336993 TGTTTAACAGCAACAAGTACCCTG 59.663 41.667 0.00 0.00 31.05 4.45
676 688 4.425180 TTAACAGCAACAAGTACCCTGA 57.575 40.909 0.00 0.00 0.00 3.86
677 689 3.508845 AACAGCAACAAGTACCCTGAT 57.491 42.857 0.00 0.00 0.00 2.90
678 690 3.059352 ACAGCAACAAGTACCCTGATC 57.941 47.619 0.00 0.00 0.00 2.92
679 691 2.290323 ACAGCAACAAGTACCCTGATCC 60.290 50.000 0.00 0.00 0.00 3.36
680 692 1.985159 AGCAACAAGTACCCTGATCCA 59.015 47.619 0.00 0.00 0.00 3.41
681 693 2.578021 AGCAACAAGTACCCTGATCCAT 59.422 45.455 0.00 0.00 0.00 3.41
682 694 3.780294 AGCAACAAGTACCCTGATCCATA 59.220 43.478 0.00 0.00 0.00 2.74
683 695 3.877508 GCAACAAGTACCCTGATCCATAC 59.122 47.826 0.00 0.00 0.00 2.39
684 696 4.384208 GCAACAAGTACCCTGATCCATACT 60.384 45.833 0.00 0.00 0.00 2.12
685 697 5.163343 GCAACAAGTACCCTGATCCATACTA 60.163 44.000 0.00 0.00 0.00 1.82
686 698 6.631766 GCAACAAGTACCCTGATCCATACTAA 60.632 42.308 0.00 0.00 0.00 2.24
687 699 7.509546 CAACAAGTACCCTGATCCATACTAAT 58.490 38.462 0.00 0.00 0.00 1.73
688 700 7.304497 ACAAGTACCCTGATCCATACTAATC 57.696 40.000 0.00 0.00 0.00 1.75
689 701 6.844388 ACAAGTACCCTGATCCATACTAATCA 59.156 38.462 0.00 0.00 0.00 2.57
690 702 6.919775 AGTACCCTGATCCATACTAATCAC 57.080 41.667 0.00 0.00 0.00 3.06
691 703 5.780793 AGTACCCTGATCCATACTAATCACC 59.219 44.000 0.00 0.00 0.00 4.02
692 704 4.566837 ACCCTGATCCATACTAATCACCA 58.433 43.478 0.00 0.00 0.00 4.17
693 705 4.348168 ACCCTGATCCATACTAATCACCAC 59.652 45.833 0.00 0.00 0.00 4.16
694 706 4.594920 CCCTGATCCATACTAATCACCACT 59.405 45.833 0.00 0.00 0.00 4.00
695 707 5.279708 CCCTGATCCATACTAATCACCACTC 60.280 48.000 0.00 0.00 0.00 3.51
696 708 5.541868 CCTGATCCATACTAATCACCACTCT 59.458 44.000 0.00 0.00 0.00 3.24
697 709 6.410942 TGATCCATACTAATCACCACTCTG 57.589 41.667 0.00 0.00 0.00 3.35
698 710 4.672587 TCCATACTAATCACCACTCTGC 57.327 45.455 0.00 0.00 0.00 4.26
699 711 4.030216 TCCATACTAATCACCACTCTGCA 58.970 43.478 0.00 0.00 0.00 4.41
700 712 4.100035 TCCATACTAATCACCACTCTGCAG 59.900 45.833 7.63 7.63 0.00 4.41
701 713 4.141846 CCATACTAATCACCACTCTGCAGT 60.142 45.833 14.67 0.00 0.00 4.40
702 714 3.601443 ACTAATCACCACTCTGCAGTC 57.399 47.619 14.67 0.00 0.00 3.51
703 715 3.169099 ACTAATCACCACTCTGCAGTCT 58.831 45.455 14.67 0.00 0.00 3.24
704 716 3.580458 ACTAATCACCACTCTGCAGTCTT 59.420 43.478 14.67 0.00 0.00 3.01
705 717 2.469274 ATCACCACTCTGCAGTCTTG 57.531 50.000 14.67 9.11 0.00 3.02
706 718 1.413118 TCACCACTCTGCAGTCTTGA 58.587 50.000 14.67 7.76 0.00 3.02
707 719 1.342496 TCACCACTCTGCAGTCTTGAG 59.658 52.381 14.67 5.96 0.00 3.02
708 720 0.034616 ACCACTCTGCAGTCTTGAGC 59.965 55.000 14.67 0.00 0.00 4.26
709 721 0.321021 CCACTCTGCAGTCTTGAGCT 59.679 55.000 14.67 0.00 0.00 4.09
710 722 1.270732 CCACTCTGCAGTCTTGAGCTT 60.271 52.381 14.67 0.00 0.00 3.74
711 723 1.799403 CACTCTGCAGTCTTGAGCTTG 59.201 52.381 14.67 0.00 0.00 4.01
712 724 0.797542 CTCTGCAGTCTTGAGCTTGC 59.202 55.000 14.67 0.00 0.00 4.01
713 725 0.604780 TCTGCAGTCTTGAGCTTGCC 60.605 55.000 14.67 0.00 0.00 4.52
714 726 0.605860 CTGCAGTCTTGAGCTTGCCT 60.606 55.000 5.25 0.00 0.00 4.75
715 727 0.887836 TGCAGTCTTGAGCTTGCCTG 60.888 55.000 3.48 0.37 0.00 4.85
716 728 0.604780 GCAGTCTTGAGCTTGCCTGA 60.605 55.000 0.00 0.00 0.00 3.86
717 729 1.949547 GCAGTCTTGAGCTTGCCTGAT 60.950 52.381 0.00 0.00 0.00 2.90
718 730 2.008329 CAGTCTTGAGCTTGCCTGATC 58.992 52.381 0.00 0.00 0.00 2.92
719 731 1.065564 AGTCTTGAGCTTGCCTGATCC 60.066 52.381 0.00 0.00 0.00 3.36
720 732 0.986527 TCTTGAGCTTGCCTGATCCA 59.013 50.000 0.00 0.00 0.00 3.41
721 733 1.065636 TCTTGAGCTTGCCTGATCCAG 60.066 52.381 0.00 0.00 0.00 3.86
722 734 0.986527 TTGAGCTTGCCTGATCCAGA 59.013 50.000 0.00 0.00 32.44 3.86
723 735 0.251354 TGAGCTTGCCTGATCCAGAC 59.749 55.000 0.00 0.00 32.44 3.51
724 736 0.540923 GAGCTTGCCTGATCCAGACT 59.459 55.000 0.00 0.00 32.44 3.24
725 737 0.990374 AGCTTGCCTGATCCAGACTT 59.010 50.000 0.00 0.00 32.44 3.01
726 738 1.093159 GCTTGCCTGATCCAGACTTG 58.907 55.000 0.00 0.00 32.44 3.16
727 739 1.339438 GCTTGCCTGATCCAGACTTGA 60.339 52.381 0.00 0.00 32.44 3.02
728 740 2.877300 GCTTGCCTGATCCAGACTTGAA 60.877 50.000 0.00 0.00 32.44 2.69
729 741 2.479566 TGCCTGATCCAGACTTGAAC 57.520 50.000 0.00 0.00 32.44 3.18
730 742 1.980765 TGCCTGATCCAGACTTGAACT 59.019 47.619 0.00 0.00 32.44 3.01
731 743 2.289882 TGCCTGATCCAGACTTGAACTG 60.290 50.000 0.00 0.00 32.44 3.16
732 744 2.027745 GCCTGATCCAGACTTGAACTGA 60.028 50.000 0.00 0.00 37.54 3.41
733 745 3.557898 GCCTGATCCAGACTTGAACTGAA 60.558 47.826 0.00 0.00 37.54 3.02
734 746 4.841422 CCTGATCCAGACTTGAACTGAAT 58.159 43.478 0.00 0.00 37.54 2.57
735 747 5.251764 CCTGATCCAGACTTGAACTGAATT 58.748 41.667 0.00 0.00 37.54 2.17
736 748 5.353678 CCTGATCCAGACTTGAACTGAATTC 59.646 44.000 0.00 0.00 37.54 2.17
737 749 6.119240 TGATCCAGACTTGAACTGAATTCT 57.881 37.500 7.05 0.00 38.25 2.40
738 750 5.936372 TGATCCAGACTTGAACTGAATTCTG 59.064 40.000 10.51 10.51 38.25 3.02
739 751 5.296151 TCCAGACTTGAACTGAATTCTGT 57.704 39.130 11.82 11.82 38.25 3.41
740 752 5.684704 TCCAGACTTGAACTGAATTCTGTT 58.315 37.500 25.33 25.33 40.07 3.16
741 753 6.122277 TCCAGACTTGAACTGAATTCTGTTT 58.878 36.000 25.66 13.86 37.99 2.83
742 754 6.603201 TCCAGACTTGAACTGAATTCTGTTTT 59.397 34.615 25.66 14.06 37.99 2.43
743 755 7.122650 TCCAGACTTGAACTGAATTCTGTTTTT 59.877 33.333 25.66 13.78 37.99 1.94
744 756 7.221452 CCAGACTTGAACTGAATTCTGTTTTTG 59.779 37.037 25.66 20.14 37.99 2.44
745 757 7.756722 CAGACTTGAACTGAATTCTGTTTTTGT 59.243 33.333 25.66 22.30 37.99 2.83
746 758 7.756722 AGACTTGAACTGAATTCTGTTTTTGTG 59.243 33.333 25.66 17.62 37.99 3.33
747 759 6.311200 ACTTGAACTGAATTCTGTTTTTGTGC 59.689 34.615 25.66 15.24 37.99 4.57
748 760 5.718146 TGAACTGAATTCTGTTTTTGTGCA 58.282 33.333 25.66 17.13 37.99 4.57
749 761 5.806502 TGAACTGAATTCTGTTTTTGTGCAG 59.193 36.000 25.66 6.51 37.99 4.41
750 762 4.685924 ACTGAATTCTGTTTTTGTGCAGG 58.314 39.130 11.82 0.00 33.81 4.85
751 763 4.053295 CTGAATTCTGTTTTTGTGCAGGG 58.947 43.478 7.05 0.00 33.81 4.45
752 764 2.531522 ATTCTGTTTTTGTGCAGGGC 57.468 45.000 0.00 0.00 33.81 5.19
753 765 1.189752 TTCTGTTTTTGTGCAGGGCA 58.810 45.000 0.00 0.00 35.60 5.36
754 766 1.412079 TCTGTTTTTGTGCAGGGCAT 58.588 45.000 0.00 0.00 41.91 4.40
755 767 1.068895 TCTGTTTTTGTGCAGGGCATG 59.931 47.619 0.00 0.00 41.91 4.06
764 776 2.124612 CAGGGCATGCCGATGACA 60.125 61.111 29.90 0.00 39.74 3.58
765 777 2.184830 CAGGGCATGCCGATGACAG 61.185 63.158 29.90 9.22 39.74 3.51
766 778 3.589881 GGGCATGCCGATGACAGC 61.590 66.667 29.90 10.13 39.74 4.40
767 779 2.515523 GGCATGCCGATGACAGCT 60.516 61.111 23.48 0.00 37.57 4.24
768 780 2.541120 GGCATGCCGATGACAGCTC 61.541 63.158 23.48 0.00 37.57 4.09
769 781 1.523258 GCATGCCGATGACAGCTCT 60.523 57.895 6.36 0.00 0.00 4.09
770 782 1.497223 GCATGCCGATGACAGCTCTC 61.497 60.000 6.36 0.00 0.00 3.20
771 783 0.104487 CATGCCGATGACAGCTCTCT 59.896 55.000 0.00 0.00 0.00 3.10
772 784 0.388659 ATGCCGATGACAGCTCTCTC 59.611 55.000 0.00 0.00 0.00 3.20
773 785 1.067250 GCCGATGACAGCTCTCTCC 59.933 63.158 0.00 0.00 0.00 3.71
774 786 1.358402 CCGATGACAGCTCTCTCCG 59.642 63.158 0.00 0.00 0.00 4.63
775 787 1.299014 CGATGACAGCTCTCTCCGC 60.299 63.158 0.00 0.00 0.00 5.54
776 788 1.299014 GATGACAGCTCTCTCCGCG 60.299 63.158 0.00 0.00 0.00 6.46
777 789 1.999071 GATGACAGCTCTCTCCGCGT 61.999 60.000 4.92 0.00 0.00 6.01
778 790 0.748367 ATGACAGCTCTCTCCGCGTA 60.748 55.000 4.92 0.00 0.00 4.42
779 791 1.062845 GACAGCTCTCTCCGCGTAC 59.937 63.158 4.92 0.00 0.00 3.67
780 792 2.325666 GACAGCTCTCTCCGCGTACC 62.326 65.000 4.92 0.00 0.00 3.34
781 793 2.115911 CAGCTCTCTCCGCGTACCT 61.116 63.158 4.92 0.00 0.00 3.08
782 794 2.115911 AGCTCTCTCCGCGTACCTG 61.116 63.158 4.92 0.00 0.00 4.00
783 795 2.409651 CTCTCTCCGCGTACCTGC 59.590 66.667 4.92 0.00 0.00 4.85
893 905 1.081892 CTGGAGTGTTCTGATTGCCG 58.918 55.000 0.00 0.00 0.00 5.69
914 926 2.951229 TGGTTTGTTCCTTCTCCCTC 57.049 50.000 0.00 0.00 0.00 4.30
947 959 2.485795 GGACGCCAAGCAACACCAA 61.486 57.895 0.00 0.00 0.00 3.67
948 960 1.299089 GACGCCAAGCAACACCAAC 60.299 57.895 0.00 0.00 0.00 3.77
949 961 2.027460 CGCCAAGCAACACCAACC 59.973 61.111 0.00 0.00 0.00 3.77
1008 1020 1.133025 CCGTTTGCCAGAATGATGGAC 59.867 52.381 0.60 0.00 43.57 4.02
1721 1751 4.626081 ACTGCACGCCAGGTCCAC 62.626 66.667 8.34 0.00 46.14 4.02
1730 1760 3.822192 CAGGTCCACGATCGCCGA 61.822 66.667 16.60 7.90 41.76 5.54
1818 1848 2.632544 CGTGTACGTGAGCCTGGGA 61.633 63.158 0.00 0.00 34.11 4.37
1866 1896 2.630580 GTTCACTGAGTTCCTCTCTGGT 59.369 50.000 6.67 0.00 43.42 4.00
1934 1964 0.615331 GTCCAGATGACCAGCTCCAA 59.385 55.000 0.00 0.00 38.09 3.53
2216 2246 1.609501 TGGAGAAGACGGTGAGGGG 60.610 63.158 0.00 0.00 0.00 4.79
2277 2307 2.558313 GCGCAACAGTTGAGGCTC 59.442 61.111 17.99 7.79 0.00 4.70
2278 2308 2.253758 GCGCAACAGTTGAGGCTCA 61.254 57.895 17.99 14.43 0.00 4.26
2308 2338 2.202703 CGGGGTCGTCGTCATTCC 60.203 66.667 0.00 0.00 0.00 3.01
2335 2365 2.956964 GGCTCGTCCGCTTCATCG 60.957 66.667 0.00 0.00 0.00 3.84
2361 2395 2.692557 GCTCAACATCAGCTCCTCTCTA 59.307 50.000 0.00 0.00 33.75 2.43
2379 2413 5.431765 TCTCTAATGAAGCCCAGAATGAAC 58.568 41.667 0.00 0.00 39.69 3.18
2401 2436 3.312973 CGAAGACTAGTACAGGCTGGTAG 59.687 52.174 20.34 17.32 44.33 3.18
2475 2522 7.854337 TCAATTATGGAGATATATGCAGAGCA 58.146 34.615 0.00 0.00 44.86 4.26
2476 2523 8.323567 TCAATTATGGAGATATATGCAGAGCAA 58.676 33.333 0.00 0.00 43.62 3.91
2518 2646 7.478520 AACTAGATAATTGTCCGTGTATTGC 57.521 36.000 0.00 0.00 0.00 3.56
2530 2658 6.259167 TGTCCGTGTATTGCAAAGGAATATAC 59.741 38.462 1.71 0.00 37.72 1.47
2579 2717 7.645058 TTCTCAAAGAAAAAGTTGATCCAGT 57.355 32.000 0.00 0.00 33.45 4.00
2580 2718 7.031226 TCTCAAAGAAAAAGTTGATCCAGTG 57.969 36.000 0.00 0.00 33.45 3.66
2581 2719 6.828273 TCTCAAAGAAAAAGTTGATCCAGTGA 59.172 34.615 0.00 0.00 33.45 3.41
2582 2720 7.503566 TCTCAAAGAAAAAGTTGATCCAGTGAT 59.496 33.333 0.00 0.00 33.45 3.06
2583 2721 8.010733 TCAAAGAAAAAGTTGATCCAGTGATT 57.989 30.769 0.00 0.00 0.00 2.57
2584 2722 9.130661 TCAAAGAAAAAGTTGATCCAGTGATTA 57.869 29.630 0.00 0.00 0.00 1.75
2585 2723 9.403110 CAAAGAAAAAGTTGATCCAGTGATTAG 57.597 33.333 0.00 0.00 0.00 1.73
2586 2724 8.697507 AAGAAAAAGTTGATCCAGTGATTAGT 57.302 30.769 0.00 0.00 0.00 2.24
2587 2725 9.793259 AAGAAAAAGTTGATCCAGTGATTAGTA 57.207 29.630 0.00 0.00 0.00 1.82
2588 2726 9.965902 AGAAAAAGTTGATCCAGTGATTAGTAT 57.034 29.630 0.00 0.00 0.00 2.12
2591 2729 9.911788 AAAAGTTGATCCAGTGATTAGTATGAT 57.088 29.630 0.00 0.00 0.00 2.45
2603 2741 6.998074 GTGATTAGTATGATTTGGTGGATGGA 59.002 38.462 0.00 0.00 0.00 3.41
2615 2753 0.399091 TGGATGGACTCCTAGCCCAG 60.399 60.000 0.00 0.00 45.21 4.45
2616 2754 0.399233 GGATGGACTCCTAGCCCAGT 60.399 60.000 0.00 0.00 41.29 4.00
2617 2755 0.755686 GATGGACTCCTAGCCCAGTG 59.244 60.000 0.00 0.00 32.90 3.66
2618 2756 0.043334 ATGGACTCCTAGCCCAGTGT 59.957 55.000 0.00 0.00 32.90 3.55
2619 2757 0.178903 TGGACTCCTAGCCCAGTGTT 60.179 55.000 0.00 0.00 0.00 3.32
2620 2758 0.250513 GGACTCCTAGCCCAGTGTTG 59.749 60.000 0.00 0.00 0.00 3.33
2621 2759 0.250513 GACTCCTAGCCCAGTGTTGG 59.749 60.000 0.00 0.00 44.60 3.77
2633 2771 1.009675 GTGTTGGAGTGCAGTTGCG 60.010 57.895 0.00 0.00 45.83 4.85
2634 2772 1.451207 TGTTGGAGTGCAGTTGCGT 60.451 52.632 0.00 0.00 45.83 5.24
2635 2773 1.009675 GTTGGAGTGCAGTTGCGTG 60.010 57.895 0.00 0.00 45.83 5.34
2637 2775 2.974698 GGAGTGCAGTTGCGTGCT 60.975 61.111 0.00 0.00 44.32 4.40
2638 2776 2.553268 GAGTGCAGTTGCGTGCTC 59.447 61.111 0.00 3.96 44.32 4.26
2639 2777 2.959357 GAGTGCAGTTGCGTGCTCC 61.959 63.158 0.00 0.00 44.32 4.70
2640 2778 4.030452 GTGCAGTTGCGTGCTCCC 62.030 66.667 7.01 0.00 44.32 4.30
2641 2779 4.560743 TGCAGTTGCGTGCTCCCA 62.561 61.111 7.01 0.00 44.32 4.37
2642 2780 4.030452 GCAGTTGCGTGCTCCCAC 62.030 66.667 0.00 0.00 40.54 4.61
2644 2782 4.988598 AGTTGCGTGCTCCCACCG 62.989 66.667 0.00 0.00 38.79 4.94
2645 2783 4.980805 GTTGCGTGCTCCCACCGA 62.981 66.667 0.00 0.00 38.79 4.69
2660 2798 3.170585 CGACGCGGGTTCTCGAAC 61.171 66.667 12.47 1.22 40.45 3.95
2681 2819 3.016736 CCCTGTGGGTGTTTATCATCAC 58.983 50.000 0.00 0.00 38.25 3.06
2683 2821 3.941483 CCTGTGGGTGTTTATCATCACTC 59.059 47.826 0.00 0.00 35.62 3.51
2684 2822 3.941483 CTGTGGGTGTTTATCATCACTCC 59.059 47.826 0.00 0.00 34.52 3.85
2686 2824 4.780554 TGTGGGTGTTTATCATCACTCCTA 59.219 41.667 0.00 0.00 34.52 2.94
2688 2826 6.069673 TGTGGGTGTTTATCATCACTCCTAAT 60.070 38.462 0.00 0.00 34.52 1.73
2689 2827 6.828785 GTGGGTGTTTATCATCACTCCTAATT 59.171 38.462 0.00 0.00 34.52 1.40
2690 2828 7.990886 GTGGGTGTTTATCATCACTCCTAATTA 59.009 37.037 0.00 0.00 34.52 1.40
2692 2830 9.403583 GGGTGTTTATCATCACTCCTAATTAAA 57.596 33.333 0.00 0.00 35.26 1.52
2709 2847 3.946242 AAAAAGCCACACCTTCCCT 57.054 47.368 0.00 0.00 0.00 4.20
2710 2848 1.413118 AAAAAGCCACACCTTCCCTG 58.587 50.000 0.00 0.00 0.00 4.45
2713 2851 0.468029 AAGCCACACCTTCCCTGTTG 60.468 55.000 0.00 0.00 0.00 3.33
2714 2852 1.903404 GCCACACCTTCCCTGTTGG 60.903 63.158 0.00 0.00 0.00 3.77
2715 2853 1.843421 CCACACCTTCCCTGTTGGA 59.157 57.895 0.00 0.00 43.18 3.53
2716 2854 0.405585 CCACACCTTCCCTGTTGGAT 59.594 55.000 0.00 0.00 44.66 3.41
2718 2856 2.162681 CACACCTTCCCTGTTGGATTC 58.837 52.381 0.00 0.00 44.66 2.52
2719 2857 1.780309 ACACCTTCCCTGTTGGATTCA 59.220 47.619 0.00 0.00 44.66 2.57
2720 2858 2.176798 ACACCTTCCCTGTTGGATTCAA 59.823 45.455 0.00 0.00 44.66 2.69
2721 2859 3.230134 CACCTTCCCTGTTGGATTCAAA 58.770 45.455 0.00 0.00 44.66 2.69
2723 2861 5.016173 CACCTTCCCTGTTGGATTCAAATA 58.984 41.667 0.00 0.00 44.66 1.40
2725 2863 6.155049 CACCTTCCCTGTTGGATTCAAATAAT 59.845 38.462 0.00 0.00 44.66 1.28
2726 2864 6.730507 ACCTTCCCTGTTGGATTCAAATAATT 59.269 34.615 0.00 0.00 44.66 1.40
2727 2865 7.043565 CCTTCCCTGTTGGATTCAAATAATTG 58.956 38.462 0.00 0.00 44.66 2.32
2728 2866 5.976458 TCCCTGTTGGATTCAAATAATTGC 58.024 37.500 0.00 0.00 38.61 3.56
2729 2867 5.721000 TCCCTGTTGGATTCAAATAATTGCT 59.279 36.000 0.00 0.00 38.61 3.91
2730 2868 5.813672 CCCTGTTGGATTCAAATAATTGCTG 59.186 40.000 0.00 0.00 34.40 4.41
2731 2869 5.292589 CCTGTTGGATTCAAATAATTGCTGC 59.707 40.000 0.00 0.00 34.14 5.25
2732 2870 5.177326 TGTTGGATTCAAATAATTGCTGCC 58.823 37.500 0.00 0.00 36.45 4.85
2733 2871 5.177326 GTTGGATTCAAATAATTGCTGCCA 58.823 37.500 0.00 0.00 36.45 4.92
2734 2872 4.757594 TGGATTCAAATAATTGCTGCCAC 58.242 39.130 0.00 0.00 36.45 5.01
2737 2875 5.394443 GGATTCAAATAATTGCTGCCACAGA 60.394 40.000 0.00 0.00 36.45 3.41
2738 2876 4.439305 TCAAATAATTGCTGCCACAGAC 57.561 40.909 0.00 0.00 36.45 3.51
2740 2878 2.113860 ATAATTGCTGCCACAGACGT 57.886 45.000 0.00 0.00 32.44 4.34
2741 2879 2.753055 TAATTGCTGCCACAGACGTA 57.247 45.000 0.00 0.00 32.44 3.57
2742 2880 1.442769 AATTGCTGCCACAGACGTAG 58.557 50.000 0.00 0.00 32.44 3.51
2748 2886 2.457080 GCCACAGACGTAGGCTTTC 58.543 57.895 12.05 0.00 44.92 2.62
2749 2887 1.352156 GCCACAGACGTAGGCTTTCG 61.352 60.000 12.05 0.54 44.92 3.46
2750 2888 0.038526 CCACAGACGTAGGCTTTCGT 60.039 55.000 15.09 15.09 43.00 3.85
2754 2892 3.808583 GACGTAGGCTTTCGTCCTT 57.191 52.632 24.15 3.85 46.83 3.36
2756 2894 0.963962 ACGTAGGCTTTCGTCCTTCA 59.036 50.000 10.68 0.00 35.30 3.02
2757 2895 1.336609 ACGTAGGCTTTCGTCCTTCAC 60.337 52.381 10.68 0.00 35.30 3.18
2766 2904 3.050275 GTCCTTCACGCTGGGTGC 61.050 66.667 18.86 2.18 46.56 5.01
2767 2905 3.555324 TCCTTCACGCTGGGTGCA 61.555 61.111 18.86 8.43 46.56 4.57
2768 2906 3.357079 CCTTCACGCTGGGTGCAC 61.357 66.667 18.86 8.80 46.56 4.57
2770 2908 2.591429 TTCACGCTGGGTGCACAG 60.591 61.111 20.43 9.70 46.56 3.66
2869 4138 6.439375 TGGAGCTTCTAGTGTCAATACCTTTA 59.561 38.462 0.00 0.00 0.00 1.85
2873 4142 8.035984 AGCTTCTAGTGTCAATACCTTTAGAAC 58.964 37.037 0.00 0.00 0.00 3.01
2928 4197 9.859427 TGTCTTAATTTTGATGATTCAATCCAC 57.141 29.630 0.00 0.00 41.38 4.02
2950 4219 7.017645 CCACTTATTTCACTCAATCTGTTTCG 58.982 38.462 0.00 0.00 0.00 3.46
2954 4223 5.862924 TTTCACTCAATCTGTTTCGATCC 57.137 39.130 0.00 0.00 0.00 3.36
2960 4229 6.536582 CACTCAATCTGTTTCGATCCACTTAT 59.463 38.462 0.00 0.00 0.00 1.73
2961 4230 7.065085 CACTCAATCTGTTTCGATCCACTTATT 59.935 37.037 0.00 0.00 0.00 1.40
2966 4235 7.737972 TCTGTTTCGATCCACTTATTCAAAA 57.262 32.000 0.00 0.00 0.00 2.44
2971 4240 8.638565 GTTTCGATCCACTTATTCAAAAATGTG 58.361 33.333 0.00 0.00 0.00 3.21
2999 4268 7.524294 AATTTTGAACAACAACATGAGTGAC 57.476 32.000 0.00 0.00 38.29 3.67
3011 4280 8.902540 ACAACATGAGTGACATAAGTTTTCTA 57.097 30.769 0.00 0.00 37.46 2.10
3012 4281 9.337396 ACAACATGAGTGACATAAGTTTTCTAA 57.663 29.630 0.00 0.00 37.46 2.10
3097 4583 8.419076 AAACAAACCTATTTCACACATTTCAC 57.581 30.769 0.00 0.00 0.00 3.18
3103 4589 8.402798 ACCTATTTCACACATTTCACATGTTA 57.597 30.769 0.00 0.00 0.00 2.41
3155 4854 1.188863 ATGTGTGGGGACTACGTACC 58.811 55.000 0.00 0.00 35.36 3.34
3165 4865 3.882288 GGGACTACGTACCCAAAACAAAA 59.118 43.478 14.81 0.00 44.96 2.44
3193 4893 9.520204 AATGAGTAAAATGTGTTTTTGAGTGAG 57.480 29.630 0.00 0.00 38.03 3.51
3314 5043 9.643693 ATTTCACATTCCATATGTTGAAACTTC 57.356 29.630 1.24 0.00 34.85 3.01
3349 5078 3.307691 GGATGAGTGAAATCTGTGTGGGA 60.308 47.826 0.00 0.00 0.00 4.37
3351 5080 4.371624 TGAGTGAAATCTGTGTGGGAAT 57.628 40.909 0.00 0.00 0.00 3.01
3361 6188 7.454260 AATCTGTGTGGGAATTTCTTAGAAC 57.546 36.000 0.00 0.00 0.00 3.01
3367 6194 5.888724 TGTGGGAATTTCTTAGAACAACACA 59.111 36.000 10.74 10.74 0.00 3.72
3372 6199 8.141268 GGGAATTTCTTAGAACAACACAAATGA 58.859 33.333 0.00 0.00 0.00 2.57
3376 6203 6.618287 TCTTAGAACAACACAAATGAGTGG 57.382 37.500 0.00 0.00 43.72 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 2.884639 GAGCATGTTGTGTGGGTTACTT 59.115 45.455 0.00 0.00 0.00 2.24
139 140 2.045926 GCCGAACCCTGAGCATGT 60.046 61.111 0.00 0.00 0.00 3.21
288 292 2.041350 ACTGACCCGAGAGAACTTCCTA 59.959 50.000 0.00 0.00 0.00 2.94
360 364 2.284258 AGCTCCTCCTCAGCCGTT 60.284 61.111 0.00 0.00 37.63 4.44
458 464 0.309922 CCCTATATCGACACGCACGT 59.690 55.000 0.00 0.00 0.00 4.49
468 475 4.913126 GCTTCGGCCCCTATATCG 57.087 61.111 0.00 0.00 34.32 2.92
497 505 6.785337 TCAATCCGAGTCCAACTAATCTTA 57.215 37.500 0.00 0.00 0.00 2.10
560 571 4.578928 GTGTTGTGTATTCAGTTGGGTCTT 59.421 41.667 0.00 0.00 0.00 3.01
594 606 9.373603 GTATATGTGTTGTATTTGTACAGGTGA 57.626 33.333 0.00 0.00 0.00 4.02
663 675 7.347222 TGATTAGTATGGATCAGGGTACTTGTT 59.653 37.037 0.00 0.00 0.00 2.83
664 676 6.844388 TGATTAGTATGGATCAGGGTACTTGT 59.156 38.462 0.00 0.00 0.00 3.16
665 677 7.155328 GTGATTAGTATGGATCAGGGTACTTG 58.845 42.308 0.00 0.00 33.27 3.16
666 678 6.270231 GGTGATTAGTATGGATCAGGGTACTT 59.730 42.308 0.00 0.00 33.27 2.24
667 679 5.780793 GGTGATTAGTATGGATCAGGGTACT 59.219 44.000 0.00 0.00 33.27 2.73
668 680 5.542635 TGGTGATTAGTATGGATCAGGGTAC 59.457 44.000 0.00 0.00 33.27 3.34
669 681 5.542635 GTGGTGATTAGTATGGATCAGGGTA 59.457 44.000 0.00 0.00 33.27 3.69
670 682 4.348168 GTGGTGATTAGTATGGATCAGGGT 59.652 45.833 0.00 0.00 33.27 4.34
671 683 4.594920 AGTGGTGATTAGTATGGATCAGGG 59.405 45.833 0.00 0.00 33.27 4.45
672 684 5.541868 AGAGTGGTGATTAGTATGGATCAGG 59.458 44.000 0.00 0.00 33.27 3.86
673 685 6.453943 CAGAGTGGTGATTAGTATGGATCAG 58.546 44.000 0.00 0.00 33.27 2.90
674 686 5.221521 GCAGAGTGGTGATTAGTATGGATCA 60.222 44.000 0.00 0.00 0.00 2.92
675 687 5.221521 TGCAGAGTGGTGATTAGTATGGATC 60.222 44.000 0.00 0.00 0.00 3.36
676 688 4.655649 TGCAGAGTGGTGATTAGTATGGAT 59.344 41.667 0.00 0.00 0.00 3.41
677 689 4.030216 TGCAGAGTGGTGATTAGTATGGA 58.970 43.478 0.00 0.00 0.00 3.41
678 690 4.141846 ACTGCAGAGTGGTGATTAGTATGG 60.142 45.833 23.35 0.00 0.00 2.74
679 691 5.016051 ACTGCAGAGTGGTGATTAGTATG 57.984 43.478 23.35 0.00 0.00 2.39
680 692 4.959210 AGACTGCAGAGTGGTGATTAGTAT 59.041 41.667 23.35 0.00 30.16 2.12
681 693 4.344978 AGACTGCAGAGTGGTGATTAGTA 58.655 43.478 23.35 0.00 30.16 1.82
682 694 3.169099 AGACTGCAGAGTGGTGATTAGT 58.831 45.455 23.35 0.00 30.16 2.24
683 695 3.883830 AGACTGCAGAGTGGTGATTAG 57.116 47.619 23.35 0.00 30.16 1.73
684 696 3.578282 TCAAGACTGCAGAGTGGTGATTA 59.422 43.478 23.35 0.00 30.16 1.75
685 697 2.369860 TCAAGACTGCAGAGTGGTGATT 59.630 45.455 23.35 0.00 30.16 2.57
686 698 1.973515 TCAAGACTGCAGAGTGGTGAT 59.026 47.619 23.35 0.00 30.16 3.06
687 699 1.342496 CTCAAGACTGCAGAGTGGTGA 59.658 52.381 23.35 14.18 30.16 4.02
688 700 1.793258 CTCAAGACTGCAGAGTGGTG 58.207 55.000 23.35 10.65 30.16 4.17
689 701 0.034616 GCTCAAGACTGCAGAGTGGT 59.965 55.000 23.35 0.00 30.16 4.16
690 702 0.321021 AGCTCAAGACTGCAGAGTGG 59.679 55.000 23.35 4.27 30.16 4.00
691 703 1.799403 CAAGCTCAAGACTGCAGAGTG 59.201 52.381 23.35 14.62 30.16 3.51
692 704 1.877258 GCAAGCTCAAGACTGCAGAGT 60.877 52.381 23.35 3.35 33.98 3.24
693 705 0.797542 GCAAGCTCAAGACTGCAGAG 59.202 55.000 23.35 8.25 0.00 3.35
694 706 0.604780 GGCAAGCTCAAGACTGCAGA 60.605 55.000 23.35 0.00 0.00 4.26
695 707 0.605860 AGGCAAGCTCAAGACTGCAG 60.606 55.000 13.48 13.48 0.00 4.41
696 708 0.887836 CAGGCAAGCTCAAGACTGCA 60.888 55.000 8.01 0.00 0.00 4.41
697 709 0.604780 TCAGGCAAGCTCAAGACTGC 60.605 55.000 10.83 4.68 0.00 4.40
698 710 2.008329 GATCAGGCAAGCTCAAGACTG 58.992 52.381 9.68 9.68 0.00 3.51
699 711 1.065564 GGATCAGGCAAGCTCAAGACT 60.066 52.381 0.00 0.00 0.00 3.24
700 712 1.339438 TGGATCAGGCAAGCTCAAGAC 60.339 52.381 0.00 0.00 0.00 3.01
701 713 0.986527 TGGATCAGGCAAGCTCAAGA 59.013 50.000 0.00 0.00 0.00 3.02
702 714 1.065636 TCTGGATCAGGCAAGCTCAAG 60.066 52.381 0.00 0.00 31.51 3.02
703 715 0.986527 TCTGGATCAGGCAAGCTCAA 59.013 50.000 0.00 0.00 31.51 3.02
704 716 0.251354 GTCTGGATCAGGCAAGCTCA 59.749 55.000 0.00 0.00 35.96 4.26
705 717 0.540923 AGTCTGGATCAGGCAAGCTC 59.459 55.000 2.30 0.00 38.73 4.09
706 718 0.990374 AAGTCTGGATCAGGCAAGCT 59.010 50.000 2.30 0.00 38.73 3.74
707 719 1.093159 CAAGTCTGGATCAGGCAAGC 58.907 55.000 2.30 0.00 38.73 4.01
708 720 2.746362 GTTCAAGTCTGGATCAGGCAAG 59.254 50.000 2.30 0.00 38.73 4.01
709 721 2.373169 AGTTCAAGTCTGGATCAGGCAA 59.627 45.455 2.30 0.00 38.73 4.52
710 722 1.980765 AGTTCAAGTCTGGATCAGGCA 59.019 47.619 2.30 0.00 38.73 4.75
711 723 2.027745 TCAGTTCAAGTCTGGATCAGGC 60.028 50.000 0.00 0.00 36.18 4.85
712 724 3.969287 TCAGTTCAAGTCTGGATCAGG 57.031 47.619 0.00 0.00 34.15 3.86
713 725 6.092396 CAGAATTCAGTTCAAGTCTGGATCAG 59.908 42.308 8.44 0.00 42.29 2.90
714 726 5.936372 CAGAATTCAGTTCAAGTCTGGATCA 59.064 40.000 8.44 0.00 42.29 2.92
715 727 6.419980 CAGAATTCAGTTCAAGTCTGGATC 57.580 41.667 8.44 0.00 42.29 3.36
720 732 7.756722 CACAAAAACAGAATTCAGTTCAAGTCT 59.243 33.333 15.60 0.00 39.39 3.24
721 733 7.463251 GCACAAAAACAGAATTCAGTTCAAGTC 60.463 37.037 15.60 2.54 39.39 3.01
722 734 6.311200 GCACAAAAACAGAATTCAGTTCAAGT 59.689 34.615 15.60 11.34 39.39 3.16
723 735 6.310956 TGCACAAAAACAGAATTCAGTTCAAG 59.689 34.615 15.60 10.81 39.39 3.02
724 736 6.162079 TGCACAAAAACAGAATTCAGTTCAA 58.838 32.000 15.60 0.00 39.39 2.69
725 737 5.718146 TGCACAAAAACAGAATTCAGTTCA 58.282 33.333 15.60 6.57 39.39 3.18
726 738 5.232838 CCTGCACAAAAACAGAATTCAGTTC 59.767 40.000 15.60 4.26 35.90 3.01
727 739 5.111293 CCTGCACAAAAACAGAATTCAGTT 58.889 37.500 10.19 10.19 35.90 3.16
728 740 4.441913 CCCTGCACAAAAACAGAATTCAGT 60.442 41.667 8.44 2.42 35.90 3.41
729 741 4.053295 CCCTGCACAAAAACAGAATTCAG 58.947 43.478 8.44 1.65 35.90 3.02
730 742 3.740764 GCCCTGCACAAAAACAGAATTCA 60.741 43.478 8.44 0.00 35.90 2.57
731 743 2.802247 GCCCTGCACAAAAACAGAATTC 59.198 45.455 0.00 0.00 35.90 2.17
732 744 2.170187 TGCCCTGCACAAAAACAGAATT 59.830 40.909 0.00 0.00 35.90 2.17
733 745 1.761784 TGCCCTGCACAAAAACAGAAT 59.238 42.857 0.00 0.00 35.90 2.40
734 746 1.189752 TGCCCTGCACAAAAACAGAA 58.810 45.000 0.00 0.00 35.90 3.02
735 747 1.068895 CATGCCCTGCACAAAAACAGA 59.931 47.619 0.00 0.00 43.04 3.41
736 748 1.504359 CATGCCCTGCACAAAAACAG 58.496 50.000 0.00 0.00 43.04 3.16
737 749 3.682766 CATGCCCTGCACAAAAACA 57.317 47.368 0.00 0.00 43.04 2.83
747 759 2.124612 TGTCATCGGCATGCCCTG 60.125 61.111 30.79 25.95 0.00 4.45
748 760 2.191375 CTGTCATCGGCATGCCCT 59.809 61.111 30.79 15.87 0.00 5.19
749 761 3.589881 GCTGTCATCGGCATGCCC 61.590 66.667 30.79 16.67 44.61 5.36
755 767 1.067250 GGAGAGAGCTGTCATCGGC 59.933 63.158 14.08 0.00 45.49 5.54
756 768 1.358402 CGGAGAGAGCTGTCATCGG 59.642 63.158 14.08 8.23 0.00 4.18
757 769 1.299014 GCGGAGAGAGCTGTCATCG 60.299 63.158 14.08 15.97 0.00 3.84
758 770 1.299014 CGCGGAGAGAGCTGTCATC 60.299 63.158 14.08 7.59 0.00 2.92
759 771 0.748367 TACGCGGAGAGAGCTGTCAT 60.748 55.000 14.08 0.00 0.00 3.06
760 772 1.376812 TACGCGGAGAGAGCTGTCA 60.377 57.895 14.08 0.00 0.00 3.58
761 773 1.062845 GTACGCGGAGAGAGCTGTC 59.937 63.158 12.47 1.81 0.00 3.51
762 774 2.408241 GGTACGCGGAGAGAGCTGT 61.408 63.158 12.47 0.00 0.00 4.40
763 775 2.115911 AGGTACGCGGAGAGAGCTG 61.116 63.158 12.47 0.00 0.00 4.24
764 776 2.115911 CAGGTACGCGGAGAGAGCT 61.116 63.158 12.47 1.90 0.00 4.09
765 777 2.409651 CAGGTACGCGGAGAGAGC 59.590 66.667 12.47 0.00 0.00 4.09
766 778 2.409651 GCAGGTACGCGGAGAGAG 59.590 66.667 12.47 0.00 0.00 3.20
767 779 3.138798 GGCAGGTACGCGGAGAGA 61.139 66.667 12.47 0.00 0.00 3.10
768 780 4.554363 CGGCAGGTACGCGGAGAG 62.554 72.222 12.47 0.00 34.36 3.20
775 787 4.690719 TTGGTGGCGGCAGGTACG 62.691 66.667 13.91 0.00 0.00 3.67
776 788 3.053896 GTTGGTGGCGGCAGGTAC 61.054 66.667 13.91 6.72 0.00 3.34
777 789 3.545124 CTGTTGGTGGCGGCAGGTA 62.545 63.158 13.91 0.00 0.00 3.08
778 790 4.954970 CTGTTGGTGGCGGCAGGT 62.955 66.667 13.91 0.00 0.00 4.00
779 791 4.954970 ACTGTTGGTGGCGGCAGG 62.955 66.667 13.91 1.14 33.62 4.85
780 792 3.663176 CACTGTTGGTGGCGGCAG 61.663 66.667 13.91 1.13 41.90 4.85
781 793 4.182433 TCACTGTTGGTGGCGGCA 62.182 61.111 7.97 7.97 45.38 5.69
782 794 3.357079 CTCACTGTTGGTGGCGGC 61.357 66.667 0.00 0.00 45.38 6.53
783 795 2.669569 CCTCACTGTTGGTGGCGG 60.670 66.667 0.00 0.00 45.38 6.13
893 905 3.348119 GAGGGAGAAGGAACAAACCATC 58.652 50.000 0.00 0.00 0.00 3.51
914 926 3.111098 GGCGTCCTATATATAAACGGCG 58.889 50.000 24.97 4.80 46.32 6.46
947 959 1.847798 TTAATGGCGGCTCTGGTGGT 61.848 55.000 11.43 0.00 0.00 4.16
948 960 0.679640 TTTAATGGCGGCTCTGGTGG 60.680 55.000 11.43 0.00 0.00 4.61
949 961 1.334869 GATTTAATGGCGGCTCTGGTG 59.665 52.381 11.43 0.00 0.00 4.17
1098 1110 1.270907 GGAGGAAGCTGACTTGGAGA 58.729 55.000 0.00 0.00 35.82 3.71
1160 1172 4.284550 AAAGCAAGCGGAGGCCCA 62.285 61.111 0.00 0.00 41.24 5.36
1200 1215 1.073897 GAAGCTGCAGGGTTGGTCT 59.926 57.895 17.12 0.00 35.61 3.85
1818 1848 2.125512 GTGATCACGGCGAGGCTT 60.126 61.111 16.62 0.00 0.00 4.35
1946 1976 2.738521 CCACTGCCTCGACGGTTG 60.739 66.667 0.00 0.00 34.25 3.77
2216 2246 1.136305 TCTCGTCCGAAATCATGACCC 59.864 52.381 0.00 0.00 0.00 4.46
2229 2259 1.066587 CGCCTCCTTGATCTCGTCC 59.933 63.158 0.00 0.00 0.00 4.79
2335 2365 1.606531 AGCTGATGTTGAGCTCCCC 59.393 57.895 12.15 1.67 43.54 4.81
2361 2395 3.071874 TCGTTCATTCTGGGCTTCATT 57.928 42.857 0.00 0.00 0.00 2.57
2379 2413 2.093106 ACCAGCCTGTACTAGTCTTCG 58.907 52.381 0.00 0.00 0.00 3.79
2401 2436 1.610522 ACTCAGTGTCTGGCAAATTGC 59.389 47.619 9.87 9.87 44.08 3.56
2506 2632 5.751243 ATATTCCTTTGCAATACACGGAC 57.249 39.130 0.00 0.00 30.00 4.79
2507 2633 6.588204 AGTATATTCCTTTGCAATACACGGA 58.412 36.000 0.00 0.00 0.00 4.69
2555 2693 7.339212 TCACTGGATCAACTTTTTCTTTGAGAA 59.661 33.333 0.00 0.00 35.25 2.87
2557 2695 7.031226 TCACTGGATCAACTTTTTCTTTGAG 57.969 36.000 0.00 0.00 35.25 3.02
2558 2696 7.587037 ATCACTGGATCAACTTTTTCTTTGA 57.413 32.000 0.00 0.00 36.21 2.69
2559 2697 9.403110 CTAATCACTGGATCAACTTTTTCTTTG 57.597 33.333 0.00 0.00 31.88 2.77
2560 2698 9.136323 ACTAATCACTGGATCAACTTTTTCTTT 57.864 29.630 0.00 0.00 31.88 2.52
2561 2699 8.697507 ACTAATCACTGGATCAACTTTTTCTT 57.302 30.769 0.00 0.00 31.88 2.52
2562 2700 9.965902 ATACTAATCACTGGATCAACTTTTTCT 57.034 29.630 0.00 0.00 31.88 2.52
2564 2702 9.739276 TCATACTAATCACTGGATCAACTTTTT 57.261 29.630 0.00 0.00 31.88 1.94
2565 2703 9.911788 ATCATACTAATCACTGGATCAACTTTT 57.088 29.630 0.00 0.00 31.88 2.27
2567 2705 9.911788 AAATCATACTAATCACTGGATCAACTT 57.088 29.630 0.00 0.00 31.88 2.66
2568 2706 9.334947 CAAATCATACTAATCACTGGATCAACT 57.665 33.333 0.00 0.00 31.88 3.16
2569 2707 8.562892 CCAAATCATACTAATCACTGGATCAAC 58.437 37.037 0.00 0.00 31.88 3.18
2570 2708 8.274322 ACCAAATCATACTAATCACTGGATCAA 58.726 33.333 0.00 0.00 31.88 2.57
2571 2709 7.716560 CACCAAATCATACTAATCACTGGATCA 59.283 37.037 0.00 0.00 31.88 2.92
2572 2710 7.173907 CCACCAAATCATACTAATCACTGGATC 59.826 40.741 0.00 0.00 31.88 3.36
2573 2711 7.000472 CCACCAAATCATACTAATCACTGGAT 59.000 38.462 0.00 0.00 34.43 3.41
2574 2712 6.157820 TCCACCAAATCATACTAATCACTGGA 59.842 38.462 0.00 0.00 0.00 3.86
2575 2713 6.356556 TCCACCAAATCATACTAATCACTGG 58.643 40.000 0.00 0.00 0.00 4.00
2576 2714 7.040892 CCATCCACCAAATCATACTAATCACTG 60.041 40.741 0.00 0.00 0.00 3.66
2577 2715 7.000472 CCATCCACCAAATCATACTAATCACT 59.000 38.462 0.00 0.00 0.00 3.41
2578 2716 6.998074 TCCATCCACCAAATCATACTAATCAC 59.002 38.462 0.00 0.00 0.00 3.06
2579 2717 6.998074 GTCCATCCACCAAATCATACTAATCA 59.002 38.462 0.00 0.00 0.00 2.57
2580 2718 7.227156 AGTCCATCCACCAAATCATACTAATC 58.773 38.462 0.00 0.00 0.00 1.75
2581 2719 7.154191 AGTCCATCCACCAAATCATACTAAT 57.846 36.000 0.00 0.00 0.00 1.73
2582 2720 6.575244 AGTCCATCCACCAAATCATACTAA 57.425 37.500 0.00 0.00 0.00 2.24
2583 2721 6.174720 GAGTCCATCCACCAAATCATACTA 57.825 41.667 0.00 0.00 0.00 1.82
2584 2722 5.041191 GAGTCCATCCACCAAATCATACT 57.959 43.478 0.00 0.00 0.00 2.12
2603 2741 0.178903 TCCAACACTGGGCTAGGAGT 60.179 55.000 2.02 0.00 43.71 3.85
2615 2753 1.009675 CGCAACTGCACTCCAACAC 60.010 57.895 2.12 0.00 42.21 3.32
2616 2754 1.451207 ACGCAACTGCACTCCAACA 60.451 52.632 2.12 0.00 42.21 3.33
2617 2755 1.009675 CACGCAACTGCACTCCAAC 60.010 57.895 2.12 0.00 42.21 3.77
2618 2756 2.833533 GCACGCAACTGCACTCCAA 61.834 57.895 2.12 0.00 42.21 3.53
2619 2757 3.279116 GCACGCAACTGCACTCCA 61.279 61.111 2.12 0.00 42.21 3.86
2620 2758 2.959357 GAGCACGCAACTGCACTCC 61.959 63.158 2.12 0.00 42.21 3.85
2621 2759 2.553268 GAGCACGCAACTGCACTC 59.447 61.111 2.12 2.01 42.21 3.51
2623 2761 4.030452 GGGAGCACGCAACTGCAC 62.030 66.667 2.12 0.00 42.21 4.57
2624 2762 4.560743 TGGGAGCACGCAACTGCA 62.561 61.111 0.00 0.00 42.21 4.41
2625 2763 4.030452 GTGGGAGCACGCAACTGC 62.030 66.667 1.76 0.00 40.47 4.40
2626 2764 3.357079 GGTGGGAGCACGCAACTG 61.357 66.667 8.99 0.00 42.25 3.16
2627 2765 4.988598 CGGTGGGAGCACGCAACT 62.989 66.667 13.94 0.00 43.14 3.16
2628 2766 4.980805 TCGGTGGGAGCACGCAAC 62.981 66.667 6.16 6.16 42.13 4.17
2629 2767 4.980805 GTCGGTGGGAGCACGCAA 62.981 66.667 1.76 0.00 40.47 4.85
2661 2799 3.941483 GAGTGATGATAAACACCCACAGG 59.059 47.826 0.00 0.00 37.65 4.00
2662 2800 3.941483 GGAGTGATGATAAACACCCACAG 59.059 47.826 0.00 0.00 37.65 3.66
2663 2801 3.587061 AGGAGTGATGATAAACACCCACA 59.413 43.478 0.00 0.00 37.65 4.17
2664 2802 4.222124 AGGAGTGATGATAAACACCCAC 57.778 45.455 0.00 0.00 37.69 4.61
2665 2803 6.575244 ATTAGGAGTGATGATAAACACCCA 57.425 37.500 0.00 0.00 37.69 4.51
2666 2804 8.974060 TTAATTAGGAGTGATGATAAACACCC 57.026 34.615 0.00 0.00 37.69 4.61
2692 2830 0.261696 ACAGGGAAGGTGTGGCTTTT 59.738 50.000 0.00 0.00 0.00 2.27
2693 2831 0.261696 AACAGGGAAGGTGTGGCTTT 59.738 50.000 0.00 0.00 0.00 3.51
2695 2833 1.151450 CAACAGGGAAGGTGTGGCT 59.849 57.895 0.00 0.00 0.00 4.75
2696 2834 1.903404 CCAACAGGGAAGGTGTGGC 60.903 63.158 0.00 0.00 40.01 5.01
2701 2839 7.310609 CAATTATTTGAATCCAACAGGGAAGGT 60.311 37.037 0.00 0.00 41.54 3.50
2703 2841 6.536224 GCAATTATTTGAATCCAACAGGGAAG 59.464 38.462 1.55 0.00 41.54 3.46
2704 2842 6.213195 AGCAATTATTTGAATCCAACAGGGAA 59.787 34.615 1.55 0.00 41.54 3.97
2705 2843 5.721000 AGCAATTATTTGAATCCAACAGGGA 59.279 36.000 1.55 0.00 42.08 4.20
2706 2844 5.813672 CAGCAATTATTTGAATCCAACAGGG 59.186 40.000 1.55 0.00 34.60 4.45
2707 2845 5.292589 GCAGCAATTATTTGAATCCAACAGG 59.707 40.000 1.55 0.00 34.60 4.00
2708 2846 5.292589 GGCAGCAATTATTTGAATCCAACAG 59.707 40.000 0.00 0.00 34.60 3.16
2709 2847 5.177326 GGCAGCAATTATTTGAATCCAACA 58.823 37.500 0.00 0.00 34.60 3.33
2710 2848 5.063817 GTGGCAGCAATTATTTGAATCCAAC 59.936 40.000 0.00 0.00 34.60 3.77
2713 2851 4.757594 TGTGGCAGCAATTATTTGAATCC 58.242 39.130 0.00 0.00 34.60 3.01
2714 2852 5.517770 GTCTGTGGCAGCAATTATTTGAATC 59.482 40.000 0.00 0.00 34.60 2.52
2715 2853 5.413499 GTCTGTGGCAGCAATTATTTGAAT 58.587 37.500 0.00 0.00 34.60 2.57
2716 2854 4.615682 CGTCTGTGGCAGCAATTATTTGAA 60.616 41.667 0.00 0.00 34.60 2.69
2718 2856 3.173599 CGTCTGTGGCAGCAATTATTTG 58.826 45.455 0.00 0.00 35.85 2.32
2719 2857 2.819608 ACGTCTGTGGCAGCAATTATTT 59.180 40.909 0.00 0.00 0.00 1.40
2720 2858 2.436417 ACGTCTGTGGCAGCAATTATT 58.564 42.857 0.00 0.00 0.00 1.40
2721 2859 2.113860 ACGTCTGTGGCAGCAATTAT 57.886 45.000 0.00 0.00 0.00 1.28
2723 2861 1.442769 CTACGTCTGTGGCAGCAATT 58.557 50.000 0.00 0.00 0.00 2.32
2725 2863 1.005037 CCTACGTCTGTGGCAGCAA 60.005 57.895 0.00 0.00 0.00 3.91
2726 2864 2.656646 CCTACGTCTGTGGCAGCA 59.343 61.111 0.00 0.00 0.00 4.41
2727 2865 2.788191 AAGCCTACGTCTGTGGCAGC 62.788 60.000 19.10 0.00 41.71 5.25
2728 2866 0.320771 AAAGCCTACGTCTGTGGCAG 60.321 55.000 19.10 0.00 41.71 4.85
2729 2867 0.320421 GAAAGCCTACGTCTGTGGCA 60.320 55.000 19.10 0.00 41.71 4.92
2730 2868 1.352156 CGAAAGCCTACGTCTGTGGC 61.352 60.000 12.06 12.06 40.45 5.01
2731 2869 0.038526 ACGAAAGCCTACGTCTGTGG 60.039 55.000 0.00 0.00 38.34 4.17
2732 2870 3.491581 ACGAAAGCCTACGTCTGTG 57.508 52.632 0.00 0.00 38.34 3.66
2737 2875 0.963962 TGAAGGACGAAAGCCTACGT 59.036 50.000 0.00 0.00 45.32 3.57
2738 2876 1.347320 GTGAAGGACGAAAGCCTACG 58.653 55.000 0.00 0.00 36.77 3.51
2749 2887 3.050275 GCACCCAGCGTGAAGGAC 61.050 66.667 0.00 0.00 46.20 3.85
2776 2914 2.663826 TGATTAAAATTGCGGTGGCC 57.336 45.000 0.00 0.00 38.85 5.36
2778 2916 4.420168 ACGAATGATTAAAATTGCGGTGG 58.580 39.130 0.00 0.00 0.00 4.61
2779 2917 7.132213 AGATACGAATGATTAAAATTGCGGTG 58.868 34.615 0.00 0.00 0.00 4.94
2780 2918 7.259290 AGATACGAATGATTAAAATTGCGGT 57.741 32.000 0.00 0.00 0.00 5.68
2781 2919 8.560576 AAAGATACGAATGATTAAAATTGCGG 57.439 30.769 0.00 0.00 0.00 5.69
2782 2920 9.819750 CAAAAGATACGAATGATTAAAATTGCG 57.180 29.630 0.00 0.00 0.00 4.85
2845 4114 5.346181 AAGGTATTGACACTAGAAGCTCC 57.654 43.478 0.00 0.00 0.00 4.70
2869 4138 9.981460 AAATTTATCCTAGATTGACCTTGTTCT 57.019 29.630 0.00 0.00 0.00 3.01
2913 4182 8.812513 AGTGAAATAAGTGGATTGAATCATCA 57.187 30.769 7.56 0.00 0.00 3.07
2914 4183 8.896744 TGAGTGAAATAAGTGGATTGAATCATC 58.103 33.333 7.56 0.00 0.00 2.92
2916 4185 8.634335 TTGAGTGAAATAAGTGGATTGAATCA 57.366 30.769 7.56 0.00 0.00 2.57
2918 4187 9.471702 AGATTGAGTGAAATAAGTGGATTGAAT 57.528 29.630 0.00 0.00 0.00 2.57
2928 4197 8.119226 GGATCGAAACAGATTGAGTGAAATAAG 58.881 37.037 0.00 0.00 0.00 1.73
2971 4240 9.687717 CACTCATGTTGTTGTTCAAAATTAAAC 57.312 29.630 0.00 0.00 37.81 2.01
3107 4593 8.062065 TCGCTCCTCCAAATATTTTACAATTT 57.938 30.769 0.00 0.00 0.00 1.82
3108 4594 7.639113 TCGCTCCTCCAAATATTTTACAATT 57.361 32.000 0.00 0.00 0.00 2.32
3109 4595 7.639113 TTCGCTCCTCCAAATATTTTACAAT 57.361 32.000 0.00 0.00 0.00 2.71
3124 4823 2.213499 CCCACACATATTTCGCTCCTC 58.787 52.381 0.00 0.00 0.00 3.71
3126 4825 1.134220 TCCCCACACATATTTCGCTCC 60.134 52.381 0.00 0.00 0.00 4.70
3130 4829 3.120792 CGTAGTCCCCACACATATTTCG 58.879 50.000 0.00 0.00 0.00 3.46
3155 4854 9.919348 CACATTTTACTCATTCTTTTGTTTTGG 57.081 29.630 0.00 0.00 0.00 3.28
3165 4865 9.520204 CACTCAAAAACACATTTTACTCATTCT 57.480 29.630 0.00 0.00 39.20 2.40
3285 5014 9.023967 GTTTCAACATATGGAATGTGAAATAGC 57.976 33.333 7.80 1.25 37.69 2.97
3314 5043 6.990341 TTCACTCATCCACATATTTCACAG 57.010 37.500 0.00 0.00 0.00 3.66
3349 5078 9.520204 CACTCATTTGTGTTGTTCTAAGAAATT 57.480 29.630 0.00 0.00 33.61 1.82
3351 5080 7.338196 TCCACTCATTTGTGTTGTTCTAAGAAA 59.662 33.333 0.00 0.00 36.30 2.52
3361 6188 5.443185 ACTCATTCCACTCATTTGTGTTG 57.557 39.130 0.00 0.00 36.30 3.33


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

AutoCloner maintained by Alex Coulton.