Multiple sequence alignment - TraesCS6A01G292000

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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 TraesCS6A01G292000 chr6A 100.000 5220 0 0 1 5220 524066020 524071239 0.000000e+00 9640.0
1 TraesCS6A01G292000 chr6A 87.440 207 22 4 664 867 544165169 544164964 8.740000e-58 235.0
2 TraesCS6A01G292000 chr6A 83.333 84 13 1 4373 4456 524076574 524076656 5.610000e-10 76.8
3 TraesCS6A01G292000 chr6B 97.530 2065 49 2 1893 3956 571092988 571095051 0.000000e+00 3530.0
4 TraesCS6A01G292000 chr6B 91.803 1037 64 9 863 1886 571091605 571092633 0.000000e+00 1424.0
5 TraesCS6A01G292000 chr6B 84.756 656 23 20 1 635 571090981 571091580 2.090000e-163 586.0
6 TraesCS6A01G292000 chr6B 93.041 388 24 3 4068 4455 571095051 571095435 9.810000e-157 564.0
7 TraesCS6A01G292000 chr6B 88.095 210 23 2 660 867 38729873 38729664 1.120000e-61 248.0
8 TraesCS6A01G292000 chr6B 91.935 124 10 0 3955 4078 530129528 530129405 1.930000e-39 174.0
9 TraesCS6A01G292000 chr6B 83.333 84 13 1 4373 4456 571100428 571100510 5.610000e-10 76.8
10 TraesCS6A01G292000 chr6D 96.878 1217 33 3 3238 4453 382077690 382078902 0.000000e+00 2032.0
11 TraesCS6A01G292000 chr6D 91.728 1366 93 12 1885 3240 382076242 382077597 0.000000e+00 1879.0
12 TraesCS6A01G292000 chr6D 89.124 993 72 16 909 1886 382075081 382076052 0.000000e+00 1203.0
13 TraesCS6A01G292000 chr6D 85.462 509 13 19 35 543 382074410 382074857 1.700000e-129 473.0
14 TraesCS6A01G292000 chr6D 82.564 195 27 7 665 856 15601560 15601750 1.160000e-36 165.0
15 TraesCS6A01G292000 chr1A 96.181 707 16 6 4518 5220 559939819 559939120 0.000000e+00 1146.0
16 TraesCS6A01G292000 chr1A 86.101 554 63 8 4669 5219 581940140 581939598 7.530000e-163 584.0
17 TraesCS6A01G292000 chr2A 95.875 703 18 4 4521 5220 62396939 62396245 0.000000e+00 1127.0
18 TraesCS6A01G292000 chr2B 92.373 708 39 11 4518 5220 69557890 69558587 0.000000e+00 994.0
19 TraesCS6A01G292000 chr7B 91.571 700 37 6 4523 5220 446185767 446185088 0.000000e+00 946.0
20 TraesCS6A01G292000 chr7B 91.176 204 17 1 665 867 106733861 106734064 5.150000e-70 276.0
21 TraesCS6A01G292000 chr7B 94.958 119 6 0 3954 4072 434926024 434925906 2.480000e-43 187.0
22 TraesCS6A01G292000 chr2D 79.719 641 97 26 4599 5219 498095255 498095882 2.890000e-117 433.0
23 TraesCS6A01G292000 chr2D 94.017 117 7 0 3955 4071 155731005 155730889 1.490000e-40 178.0
24 TraesCS6A01G292000 chr3B 80.712 534 87 16 4618 5141 696677869 696678396 8.140000e-108 401.0
25 TraesCS6A01G292000 chr3B 91.339 127 10 1 3945 4071 740547592 740547467 6.950000e-39 172.0
26 TraesCS6A01G292000 chr5D 84.404 436 36 19 4520 4954 411163612 411163208 2.930000e-107 399.0
27 TraesCS6A01G292000 chr5D 92.233 206 15 1 663 867 25322689 25322484 1.840000e-74 291.0
28 TraesCS6A01G292000 chr5D 88.835 206 21 2 664 867 358024546 358024751 8.680000e-63 252.0
29 TraesCS6A01G292000 chr3D 78.720 625 103 23 4618 5220 511682847 511682231 1.760000e-104 390.0
30 TraesCS6A01G292000 chr3A 80.745 483 77 16 4601 5075 461839092 461838618 3.840000e-96 363.0
31 TraesCS6A01G292000 chr3A 90.821 207 15 4 664 867 17580391 17580596 1.850000e-69 274.0
32 TraesCS6A01G292000 chr3A 91.339 127 9 2 3947 4072 745931116 745931241 6.950000e-39 172.0
33 TraesCS6A01G292000 chr5A 91.787 207 15 2 663 867 502552094 502551888 2.380000e-73 287.0
34 TraesCS6A01G292000 chr1D 90.000 210 20 1 659 867 452249691 452249482 2.400000e-68 270.0
35 TraesCS6A01G292000 chr5B 88.210 229 22 4 640 867 438798559 438798783 8.620000e-68 268.0
36 TraesCS6A01G292000 chr5B 94.958 119 6 0 3954 4072 38365123 38365241 2.480000e-43 187.0
37 TraesCS6A01G292000 chr5B 94.068 118 7 0 3955 4072 517216988 517217105 4.150000e-41 180.0
38 TraesCS6A01G292000 chr4A 88.889 216 21 3 654 866 344025824 344026039 4.010000e-66 263.0
39 TraesCS6A01G292000 chr4A 89.756 205 19 2 664 866 82745713 82745509 1.440000e-65 261.0
40 TraesCS6A01G292000 chr4B 94.017 117 7 0 3955 4071 527282635 527282519 1.490000e-40 178.0
41 TraesCS6A01G292000 chr7A 80.220 91 14 3 5054 5143 635018851 635018938 1.210000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G292000 chr6A 524066020 524071239 5219 False 9640.00 9640 100.0000 1 5220 1 chr6A.!!$F1 5219
1 TraesCS6A01G292000 chr6B 571090981 571095435 4454 False 1526.00 3530 91.7825 1 4455 4 chr6B.!!$F2 4454
2 TraesCS6A01G292000 chr6D 382074410 382078902 4492 False 1396.75 2032 90.7980 35 4453 4 chr6D.!!$F2 4418
3 TraesCS6A01G292000 chr1A 559939120 559939819 699 True 1146.00 1146 96.1810 4518 5220 1 chr1A.!!$R1 702
4 TraesCS6A01G292000 chr1A 581939598 581940140 542 True 584.00 584 86.1010 4669 5219 1 chr1A.!!$R2 550
5 TraesCS6A01G292000 chr2A 62396245 62396939 694 True 1127.00 1127 95.8750 4521 5220 1 chr2A.!!$R1 699
6 TraesCS6A01G292000 chr2B 69557890 69558587 697 False 994.00 994 92.3730 4518 5220 1 chr2B.!!$F1 702
7 TraesCS6A01G292000 chr7B 446185088 446185767 679 True 946.00 946 91.5710 4523 5220 1 chr7B.!!$R2 697
8 TraesCS6A01G292000 chr2D 498095255 498095882 627 False 433.00 433 79.7190 4599 5219 1 chr2D.!!$F1 620
9 TraesCS6A01G292000 chr3B 696677869 696678396 527 False 401.00 401 80.7120 4618 5141 1 chr3B.!!$F1 523
10 TraesCS6A01G292000 chr3D 511682231 511682847 616 True 390.00 390 78.7200 4618 5220 1 chr3D.!!$R1 602

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
83 93 0.036952 ATCGCTTGCTGTGCTGTACT 60.037 50.000 0.00 0.00 0.00 2.73 F
759 813 0.179045 ACCTAATCAGACATGGCGGC 60.179 55.000 0.00 0.00 0.00 6.53 F
761 815 0.179048 CTAATCAGACATGGCGGCCA 60.179 55.000 26.11 26.11 38.19 5.36 F
965 1062 0.249657 GTCATCTCCTTGCTAGCCGG 60.250 60.000 13.29 12.92 0.00 6.13 F
1284 1389 0.674895 AGGCCGTCGACTACTACGTT 60.675 55.000 14.70 0.00 37.40 3.99 F
1580 1690 1.212935 TGGAAGCTCCAATTCTAGGGC 59.787 52.381 2.78 0.00 45.00 5.19 F
2680 3145 2.811410 TCCATTGCCAAGCAGAAATCT 58.189 42.857 0.00 0.00 40.61 2.40 F
2869 3338 3.139584 TCGGACATGATCCTTCTACCCTA 59.860 47.826 0.00 0.00 46.69 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1632 0.107993 TGCTCTGCACAGACATAGCC 60.108 55.000 0.00 0.00 38.59 3.93 R
1992 2457 0.617413 CCTTCTCTGGCACATCACCT 59.383 55.000 0.00 0.00 38.20 4.00 R
2483 2948 2.040813 ACTCCAGGAACATCTGTTGCAT 59.959 45.455 15.53 0.33 46.84 3.96 R
2954 3423 8.752005 TTAAGACATCAGGCTAATAAATTGCT 57.248 30.769 0.00 0.00 0.00 3.91 R
3282 3846 1.596477 GAGGGCATCGTCCATCTGC 60.596 63.158 0.00 0.00 34.33 4.26 R
3285 3849 1.596477 GCAGAGGGCATCGTCCATC 60.596 63.158 0.00 0.00 43.97 3.51 R
4041 4606 0.643820 GTCCGGAATTACTTGTCGCG 59.356 55.000 5.23 0.00 0.00 5.87 R
4361 4926 3.015327 GGAGAGCACCTCGTACTAAAGA 58.985 50.000 0.00 0.00 42.89 2.52 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
83 93 0.036952 ATCGCTTGCTGTGCTGTACT 60.037 50.000 0.00 0.00 0.00 2.73
99 109 0.318441 TACTCTGACAGGTGCTGCAC 59.682 55.000 24.02 24.02 34.37 4.57
100 110 1.370437 CTCTGACAGGTGCTGCACT 59.630 57.895 29.54 12.59 34.37 4.40
101 111 0.949588 CTCTGACAGGTGCTGCACTG 60.950 60.000 29.54 25.24 34.37 3.66
102 112 2.592574 TGACAGGTGCTGCACTGC 60.593 61.111 29.54 15.78 34.37 4.40
103 113 2.592574 GACAGGTGCTGCACTGCA 60.593 61.111 29.54 3.11 41.05 4.41
173 193 2.095252 GTGGAGAAAGCGACCGAGC 61.095 63.158 0.00 0.00 37.41 5.03
306 326 1.379977 GGGCCTTCCTACCTTTGGC 60.380 63.158 0.84 0.00 42.56 4.52
367 391 4.681978 GTGGTCCGCGCACCTTCT 62.682 66.667 21.92 0.00 37.34 2.85
368 392 4.373116 TGGTCCGCGCACCTTCTC 62.373 66.667 21.92 0.00 37.34 2.87
451 475 3.703127 GGACGGGGTGACTGGGAC 61.703 72.222 0.00 0.00 0.00 4.46
452 476 4.065281 GACGGGGTGACTGGGACG 62.065 72.222 0.00 0.00 0.00 4.79
453 477 4.928140 ACGGGGTGACTGGGACGT 62.928 66.667 0.00 0.00 0.00 4.34
454 478 4.373116 CGGGGTGACTGGGACGTG 62.373 72.222 0.00 0.00 0.00 4.49
562 586 4.760047 GGCTCGCTCCCGCTTCAA 62.760 66.667 0.00 0.00 0.00 2.69
564 588 2.815647 CTCGCTCCCGCTTCAACC 60.816 66.667 0.00 0.00 0.00 3.77
566 590 4.697756 CGCTCCCGCTTCAACCCA 62.698 66.667 0.00 0.00 0.00 4.51
567 591 2.282180 GCTCCCGCTTCAACCCAA 60.282 61.111 0.00 0.00 0.00 4.12
568 592 2.626780 GCTCCCGCTTCAACCCAAC 61.627 63.158 0.00 0.00 0.00 3.77
569 593 1.073199 CTCCCGCTTCAACCCAACT 59.927 57.895 0.00 0.00 0.00 3.16
570 594 1.228124 TCCCGCTTCAACCCAACTG 60.228 57.895 0.00 0.00 0.00 3.16
582 606 2.034066 CAACTGCCGGGTGGATGT 59.966 61.111 2.18 0.00 37.49 3.06
697 751 9.899226 AGACAAACTCATAAAGCTTTTATTCAC 57.101 29.630 18.47 0.69 0.00 3.18
698 752 9.129209 GACAAACTCATAAAGCTTTTATTCACC 57.871 33.333 18.47 0.00 0.00 4.02
699 753 8.088365 ACAAACTCATAAAGCTTTTATTCACCC 58.912 33.333 18.47 0.00 0.00 4.61
700 754 6.436843 ACTCATAAAGCTTTTATTCACCCG 57.563 37.500 18.47 0.00 0.00 5.28
701 755 5.944007 ACTCATAAAGCTTTTATTCACCCGT 59.056 36.000 18.47 0.51 0.00 5.28
702 756 6.093633 ACTCATAAAGCTTTTATTCACCCGTC 59.906 38.462 18.47 0.00 0.00 4.79
703 757 5.941058 TCATAAAGCTTTTATTCACCCGTCA 59.059 36.000 18.47 0.00 0.00 4.35
704 758 6.601613 TCATAAAGCTTTTATTCACCCGTCAT 59.398 34.615 18.47 0.00 0.00 3.06
705 759 7.771361 TCATAAAGCTTTTATTCACCCGTCATA 59.229 33.333 18.47 0.00 0.00 2.15
706 760 6.827586 AAAGCTTTTATTCACCCGTCATAA 57.172 33.333 5.69 0.00 0.00 1.90
707 761 7.404671 AAAGCTTTTATTCACCCGTCATAAT 57.595 32.000 5.69 0.00 0.00 1.28
708 762 8.514330 AAAGCTTTTATTCACCCGTCATAATA 57.486 30.769 5.69 0.00 0.00 0.98
709 763 8.691661 AAGCTTTTATTCACCCGTCATAATAT 57.308 30.769 0.00 0.00 0.00 1.28
710 764 8.691661 AGCTTTTATTCACCCGTCATAATATT 57.308 30.769 0.00 0.00 0.00 1.28
711 765 9.131791 AGCTTTTATTCACCCGTCATAATATTT 57.868 29.630 0.00 0.00 0.00 1.40
715 769 9.761504 TTTATTCACCCGTCATAATATTTACGA 57.238 29.630 15.25 0.00 37.53 3.43
716 770 7.884816 ATTCACCCGTCATAATATTTACGAG 57.115 36.000 15.25 7.91 37.53 4.18
717 771 5.775686 TCACCCGTCATAATATTTACGAGG 58.224 41.667 15.25 15.37 37.53 4.63
718 772 5.535783 TCACCCGTCATAATATTTACGAGGA 59.464 40.000 19.67 12.17 37.53 3.71
719 773 5.632347 CACCCGTCATAATATTTACGAGGAC 59.368 44.000 19.67 9.71 37.53 3.85
720 774 4.855388 CCCGTCATAATATTTACGAGGACG 59.145 45.833 13.46 13.46 44.46 4.79
721 775 5.335113 CCCGTCATAATATTTACGAGGACGA 60.335 44.000 19.29 0.00 46.89 4.20
722 776 6.144854 CCGTCATAATATTTACGAGGACGAA 58.855 40.000 19.29 0.00 46.89 3.85
723 777 6.638063 CCGTCATAATATTTACGAGGACGAAA 59.362 38.462 19.29 0.00 46.89 3.46
724 778 7.327761 CCGTCATAATATTTACGAGGACGAAAT 59.672 37.037 19.29 0.00 46.89 2.17
725 779 8.697067 CGTCATAATATTTACGAGGACGAAATT 58.303 33.333 14.70 0.00 46.89 1.82
727 781 9.752961 TCATAATATTTACGAGGACGAAATTCA 57.247 29.630 0.00 0.00 42.66 2.57
732 786 9.931210 ATATTTACGAGGACGAAATTCAAATTC 57.069 29.630 0.00 0.00 42.66 2.17
733 787 6.788684 TTACGAGGACGAAATTCAAATTCA 57.211 33.333 0.00 0.00 42.66 2.57
734 788 5.880054 ACGAGGACGAAATTCAAATTCAT 57.120 34.783 0.00 0.00 42.66 2.57
735 789 5.631026 ACGAGGACGAAATTCAAATTCATG 58.369 37.500 0.00 0.00 42.66 3.07
736 790 5.030295 CGAGGACGAAATTCAAATTCATGG 58.970 41.667 0.00 0.00 42.66 3.66
737 791 5.329035 AGGACGAAATTCAAATTCATGGG 57.671 39.130 0.00 0.00 0.00 4.00
738 792 4.772100 AGGACGAAATTCAAATTCATGGGT 59.228 37.500 0.00 0.00 0.00 4.51
739 793 4.864247 GGACGAAATTCAAATTCATGGGTG 59.136 41.667 0.00 0.00 0.00 4.61
740 794 5.336372 GGACGAAATTCAAATTCATGGGTGA 60.336 40.000 0.00 0.00 0.00 4.02
741 795 5.469479 ACGAAATTCAAATTCATGGGTGAC 58.531 37.500 0.00 0.00 33.11 3.67
756 810 2.565841 GGTGACCTAATCAGACATGGC 58.434 52.381 0.00 0.00 38.28 4.40
757 811 2.205074 GTGACCTAATCAGACATGGCG 58.795 52.381 0.00 0.00 38.28 5.69
758 812 1.138859 TGACCTAATCAGACATGGCGG 59.861 52.381 0.00 0.00 31.91 6.13
759 813 0.179045 ACCTAATCAGACATGGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
760 814 0.886490 CCTAATCAGACATGGCGGCC 60.886 60.000 13.32 13.32 0.00 6.13
761 815 0.179048 CTAATCAGACATGGCGGCCA 60.179 55.000 26.11 26.11 38.19 5.36
762 816 0.254462 TAATCAGACATGGCGGCCAA 59.746 50.000 27.70 8.76 36.95 4.52
763 817 0.611618 AATCAGACATGGCGGCCAAA 60.612 50.000 27.70 3.00 36.95 3.28
764 818 0.611618 ATCAGACATGGCGGCCAAAA 60.612 50.000 27.70 2.09 36.95 2.44
765 819 1.080569 CAGACATGGCGGCCAAAAC 60.081 57.895 27.70 18.57 36.95 2.43
766 820 2.261361 GACATGGCGGCCAAAACC 59.739 61.111 27.70 11.73 36.95 3.27
767 821 3.295304 GACATGGCGGCCAAAACCC 62.295 63.158 27.70 9.92 36.95 4.11
768 822 3.309506 CATGGCGGCCAAAACCCA 61.310 61.111 27.70 0.00 36.95 4.51
769 823 2.996734 ATGGCGGCCAAAACCCAG 60.997 61.111 27.70 0.00 36.95 4.45
770 824 3.521765 ATGGCGGCCAAAACCCAGA 62.522 57.895 27.70 0.00 36.95 3.86
771 825 3.373565 GGCGGCCAAAACCCAGAG 61.374 66.667 15.62 0.00 0.00 3.35
772 826 2.282180 GCGGCCAAAACCCAGAGA 60.282 61.111 2.24 0.00 0.00 3.10
773 827 1.678970 GCGGCCAAAACCCAGAGAT 60.679 57.895 2.24 0.00 0.00 2.75
774 828 0.393808 GCGGCCAAAACCCAGAGATA 60.394 55.000 2.24 0.00 0.00 1.98
775 829 1.953311 GCGGCCAAAACCCAGAGATAA 60.953 52.381 2.24 0.00 0.00 1.75
776 830 2.654863 CGGCCAAAACCCAGAGATAAT 58.345 47.619 2.24 0.00 0.00 1.28
777 831 2.358898 CGGCCAAAACCCAGAGATAATG 59.641 50.000 2.24 0.00 0.00 1.90
778 832 2.101415 GGCCAAAACCCAGAGATAATGC 59.899 50.000 0.00 0.00 0.00 3.56
779 833 2.760092 GCCAAAACCCAGAGATAATGCA 59.240 45.455 0.00 0.00 0.00 3.96
780 834 3.385755 GCCAAAACCCAGAGATAATGCAT 59.614 43.478 0.00 0.00 0.00 3.96
781 835 4.738541 GCCAAAACCCAGAGATAATGCATG 60.739 45.833 0.00 0.00 0.00 4.06
782 836 4.365723 CAAAACCCAGAGATAATGCATGC 58.634 43.478 11.82 11.82 0.00 4.06
783 837 3.589951 AACCCAGAGATAATGCATGCT 57.410 42.857 20.33 1.26 0.00 3.79
784 838 3.589951 ACCCAGAGATAATGCATGCTT 57.410 42.857 20.33 10.16 0.00 3.91
785 839 3.907221 ACCCAGAGATAATGCATGCTTT 58.093 40.909 20.33 20.71 0.00 3.51
786 840 3.635373 ACCCAGAGATAATGCATGCTTTG 59.365 43.478 24.68 10.53 0.00 2.77
799 853 4.835199 CATGCTTTGCTAATTTGTGAGC 57.165 40.909 0.00 0.00 39.25 4.26
800 854 3.302365 TGCTTTGCTAATTTGTGAGCC 57.698 42.857 0.00 0.00 37.94 4.70
801 855 2.892852 TGCTTTGCTAATTTGTGAGCCT 59.107 40.909 0.00 0.00 37.94 4.58
802 856 3.057315 TGCTTTGCTAATTTGTGAGCCTC 60.057 43.478 0.00 0.00 37.94 4.70
803 857 3.057315 GCTTTGCTAATTTGTGAGCCTCA 60.057 43.478 0.00 0.00 37.94 3.86
804 858 4.559300 GCTTTGCTAATTTGTGAGCCTCAA 60.559 41.667 0.00 0.00 37.94 3.02
805 859 4.503741 TTGCTAATTTGTGAGCCTCAAC 57.496 40.909 0.00 0.00 37.94 3.18
806 860 3.485394 TGCTAATTTGTGAGCCTCAACA 58.515 40.909 0.00 0.00 37.94 3.33
807 861 4.081406 TGCTAATTTGTGAGCCTCAACAT 58.919 39.130 0.00 0.00 37.94 2.71
808 862 4.523943 TGCTAATTTGTGAGCCTCAACATT 59.476 37.500 0.00 0.00 37.94 2.71
809 863 5.098211 GCTAATTTGTGAGCCTCAACATTC 58.902 41.667 0.00 0.00 32.25 2.67
810 864 3.837213 ATTTGTGAGCCTCAACATTCG 57.163 42.857 0.00 0.00 0.00 3.34
811 865 2.542020 TTGTGAGCCTCAACATTCGA 57.458 45.000 0.00 0.00 0.00 3.71
812 866 2.084610 TGTGAGCCTCAACATTCGAG 57.915 50.000 0.00 0.00 0.00 4.04
822 876 6.743575 CCTCAACATTCGAGGTTCTAAATT 57.256 37.500 1.98 0.00 44.35 1.82
823 877 6.776094 CCTCAACATTCGAGGTTCTAAATTC 58.224 40.000 1.98 0.00 44.35 2.17
824 878 6.371548 CCTCAACATTCGAGGTTCTAAATTCA 59.628 38.462 1.98 0.00 44.35 2.57
825 879 7.066284 CCTCAACATTCGAGGTTCTAAATTCAT 59.934 37.037 1.98 0.00 44.35 2.57
826 880 7.751732 TCAACATTCGAGGTTCTAAATTCATG 58.248 34.615 1.98 0.00 0.00 3.07
827 881 7.606073 TCAACATTCGAGGTTCTAAATTCATGA 59.394 33.333 0.00 0.00 0.00 3.07
828 882 8.400947 CAACATTCGAGGTTCTAAATTCATGAT 58.599 33.333 0.00 0.00 0.00 2.45
829 883 8.511604 ACATTCGAGGTTCTAAATTCATGATT 57.488 30.769 0.00 0.00 0.00 2.57
830 884 9.613428 ACATTCGAGGTTCTAAATTCATGATTA 57.387 29.630 0.00 0.00 0.00 1.75
883 937 3.200593 GGGCTCACTGCTCGCATG 61.201 66.667 0.00 0.00 42.39 4.06
902 956 2.985847 GGCCCACAGCTTCCACAC 60.986 66.667 0.00 0.00 43.05 3.82
904 958 2.839098 CCCACAGCTTCCACACCT 59.161 61.111 0.00 0.00 0.00 4.00
920 1017 4.363999 CACACCTCCACGAGATATTTCTC 58.636 47.826 3.27 3.27 44.24 2.87
936 1033 1.153745 CTCTCTTTCTCGGCCCACG 60.154 63.158 0.00 0.00 46.11 4.94
937 1034 2.125512 CTCTTTCTCGGCCCACGG 60.126 66.667 0.00 0.00 44.45 4.94
965 1062 0.249657 GTCATCTCCTTGCTAGCCGG 60.250 60.000 13.29 12.92 0.00 6.13
966 1063 0.687757 TCATCTCCTTGCTAGCCGGT 60.688 55.000 13.29 0.00 0.00 5.28
998 1103 2.363018 CGAGCTCCCACCTCTGGA 60.363 66.667 8.47 0.00 40.55 3.86
999 1104 2.716017 CGAGCTCCCACCTCTGGAC 61.716 68.421 8.47 0.00 40.55 4.02
1100 1205 0.921896 ATCCCACACATCTCCCCTTG 59.078 55.000 0.00 0.00 0.00 3.61
1107 1212 2.982488 ACACATCTCCCCTTGTTCTCTT 59.018 45.455 0.00 0.00 0.00 2.85
1284 1389 0.674895 AGGCCGTCGACTACTACGTT 60.675 55.000 14.70 0.00 37.40 3.99
1323 1428 3.830755 TGTTGGGAAGGTGACTCTACTAC 59.169 47.826 0.00 0.00 42.68 2.73
1342 1447 6.051179 ACTACTTTTCCCTTCTGTATCCAC 57.949 41.667 0.00 0.00 0.00 4.02
1390 1498 6.939730 TGTTTTTACTGCAATCTCTGATACCA 59.060 34.615 0.00 0.00 0.00 3.25
1392 1500 3.550437 ACTGCAATCTCTGATACCACC 57.450 47.619 0.00 0.00 0.00 4.61
1393 1501 2.171448 ACTGCAATCTCTGATACCACCC 59.829 50.000 0.00 0.00 0.00 4.61
1522 1632 5.224888 AGCTTGCAAGTATGTTGTTGAATG 58.775 37.500 26.55 0.00 0.00 2.67
1580 1690 1.212935 TGGAAGCTCCAATTCTAGGGC 59.787 52.381 2.78 0.00 45.00 5.19
1634 1744 3.624410 CGATTCTGCTGGATTGTGATGAA 59.376 43.478 0.00 0.00 0.00 2.57
1779 1889 8.424918 TGGTAGTATGGTAGTAGACTAGTACAC 58.575 40.741 23.03 15.18 36.52 2.90
1788 1898 7.175641 GGTAGTAGACTAGTACACTTTGACCAA 59.824 40.741 23.03 0.00 36.52 3.67
1789 1899 7.778185 AGTAGACTAGTACACTTTGACCAAT 57.222 36.000 0.00 0.00 0.00 3.16
1790 1900 8.191534 AGTAGACTAGTACACTTTGACCAATT 57.808 34.615 0.00 0.00 0.00 2.32
1791 1901 8.648693 AGTAGACTAGTACACTTTGACCAATTT 58.351 33.333 0.00 0.00 0.00 1.82
1815 1928 9.478768 TTTTATAGTGTCAGATTTTGTCGTACA 57.521 29.630 0.00 0.00 0.00 2.90
1831 1944 5.126384 TGTCGTACATATGACTGATTCACCA 59.874 40.000 10.38 0.00 41.60 4.17
1838 1951 3.423539 TGACTGATTCACCAGGAAAGG 57.576 47.619 0.00 0.00 39.39 3.11
1876 1990 4.022068 ACGAACGGGTAGTACTCATGAAAA 60.022 41.667 0.00 0.00 0.00 2.29
1992 2457 7.284820 GGGTATTAGCTGTTAGGATGGTTAAA 58.715 38.462 0.00 0.00 0.00 1.52
2019 2484 4.679373 TGTGCCAGAGAAGGATAATCTC 57.321 45.455 0.00 0.00 42.95 2.75
2178 2643 5.014966 GGTAGACCACTATACCCAGATCCTA 59.985 48.000 0.00 0.00 36.26 2.94
2223 2688 3.658725 AGAGTATCATTGGCCACCTACT 58.341 45.455 3.88 10.18 37.82 2.57
2226 2691 5.665812 AGAGTATCATTGGCCACCTACTTAA 59.334 40.000 3.88 0.00 37.82 1.85
2305 2770 4.154918 CCTAGTGAAAAGGATGCACAAGTC 59.845 45.833 0.00 0.00 36.08 3.01
2680 3145 2.811410 TCCATTGCCAAGCAGAAATCT 58.189 42.857 0.00 0.00 40.61 2.40
2869 3338 3.139584 TCGGACATGATCCTTCTACCCTA 59.860 47.826 0.00 0.00 46.69 3.53
2873 3342 4.484912 ACATGATCCTTCTACCCTACTCC 58.515 47.826 0.00 0.00 0.00 3.85
2883 3352 3.596956 TCTACCCTACTCCTTCTTGTCCT 59.403 47.826 0.00 0.00 0.00 3.85
2957 3426 5.302568 AGGACATCATTTCTTGTTTCAAGCA 59.697 36.000 4.82 0.00 0.00 3.91
3161 3630 4.263462 TGTGGTTTCAGGTGATGATAGCTT 60.263 41.667 0.00 0.00 37.97 3.74
3282 3846 8.472683 TTGTTTGTTTGATCACTTAAACCTTG 57.527 30.769 18.01 0.00 36.27 3.61
3285 3849 5.830912 TGTTTGATCACTTAAACCTTGCAG 58.169 37.500 0.00 0.00 36.27 4.41
3438 4003 7.554118 TCAGACAATTCAACCCTATTTGAGATC 59.446 37.037 0.00 0.00 36.84 2.75
3693 4258 4.227197 TCTGAGAAAACTCTGAGGGAAGT 58.773 43.478 9.85 0.00 0.00 3.01
3955 4520 7.276658 TGTTTTCGGATAGCCTTTACATGATA 58.723 34.615 0.00 0.00 0.00 2.15
3967 4532 4.931661 TTACATGATACTCCTTCCGTCC 57.068 45.455 0.00 0.00 0.00 4.79
3994 4559 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
4074 4639 1.453762 CCGGACGGAGGGAGTATGAC 61.454 65.000 4.40 0.00 37.50 3.06
4295 4860 3.915437 AGGTTTAATGCCACAGTTTCG 57.085 42.857 0.33 0.00 0.00 3.46
4361 4926 5.136068 TGAGGGAGATGATAGTGACTTCT 57.864 43.478 0.00 0.00 0.00 2.85
4435 5000 9.005777 TGTAAAAGTACCTGATATTCACCAAAC 57.994 33.333 0.00 0.00 0.00 2.93
4443 5008 7.125391 ACCTGATATTCACCAAACCAATATGT 58.875 34.615 0.00 0.00 0.00 2.29
4455 5020 8.522830 ACCAAACCAATATGTTAACTTCAGATG 58.477 33.333 7.22 0.00 0.00 2.90
4456 5021 8.522830 CCAAACCAATATGTTAACTTCAGATGT 58.477 33.333 7.22 0.00 0.00 3.06
4495 5060 9.606631 AATAAGTAAATGCAACTTCCAAAAACA 57.393 25.926 5.55 0.00 0.00 2.83
4496 5061 9.777297 ATAAGTAAATGCAACTTCCAAAAACAT 57.223 25.926 5.55 0.00 0.00 2.71
4498 5063 9.777297 AAGTAAATGCAACTTCCAAAAACATAT 57.223 25.926 0.00 0.00 0.00 1.78
4499 5064 9.777297 AGTAAATGCAACTTCCAAAAACATATT 57.223 25.926 0.00 0.00 0.00 1.28
4500 5065 9.810231 GTAAATGCAACTTCCAAAAACATATTG 57.190 29.630 0.00 0.00 0.00 1.90
4501 5066 8.449251 AAATGCAACTTCCAAAAACATATTGT 57.551 26.923 0.00 0.00 0.00 2.71
4502 5067 9.553064 AAATGCAACTTCCAAAAACATATTGTA 57.447 25.926 0.00 0.00 0.00 2.41
4503 5068 9.723601 AATGCAACTTCCAAAAACATATTGTAT 57.276 25.926 0.00 0.00 0.00 2.29
4504 5069 8.531622 TGCAACTTCCAAAAACATATTGTATG 57.468 30.769 0.00 0.00 0.00 2.39
4505 5070 8.363390 TGCAACTTCCAAAAACATATTGTATGA 58.637 29.630 4.12 0.00 0.00 2.15
4506 5071 9.369904 GCAACTTCCAAAAACATATTGTATGAT 57.630 29.630 4.12 0.00 0.00 2.45
4986 5563 6.248433 TCTGGCCATAAAAATGACTTCTTCT 58.752 36.000 5.51 0.00 0.00 2.85
5038 5616 3.758554 AGTGCGGAAAAGCTAATGTCATT 59.241 39.130 3.06 3.06 38.13 2.57
5106 5684 3.694566 ACCGCTTGTTAGATCCAAAATCC 59.305 43.478 0.00 0.00 0.00 3.01
5119 5698 8.950208 AGATCCAAAATCCGTTTTTACAAAAA 57.050 26.923 0.00 0.00 35.75 1.94
5196 5806 6.371595 TTGGGTCAAAAATTATCATGCCTT 57.628 33.333 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.182030 GACGAACCCAGCTCCGAG 59.818 66.667 0.00 0.00 0.00 4.63
83 93 1.070275 CAGTGCAGCACCTGTCAGA 59.930 57.895 22.41 0.00 34.49 3.27
99 109 0.322277 ATCAGTGAGGTTGCCTGCAG 60.322 55.000 6.78 6.78 31.76 4.41
100 110 0.111061 AATCAGTGAGGTTGCCTGCA 59.889 50.000 0.00 0.00 31.76 4.41
101 111 0.524862 CAATCAGTGAGGTTGCCTGC 59.475 55.000 0.00 0.00 31.76 4.85
102 112 0.524862 GCAATCAGTGAGGTTGCCTG 59.475 55.000 17.16 0.24 41.67 4.85
103 113 2.952714 GCAATCAGTGAGGTTGCCT 58.047 52.632 17.16 0.00 41.67 4.75
157 167 2.881352 CGCTCGGTCGCTTTCTCC 60.881 66.667 0.00 0.00 0.00 3.71
290 310 1.478105 CATTGCCAAAGGTAGGAAGGC 59.522 52.381 0.00 0.00 45.41 4.35
306 326 2.819595 CCTGACCCGACGGCATTG 60.820 66.667 8.86 0.00 0.00 2.82
441 465 4.664677 AGCGCACGTCCCAGTCAC 62.665 66.667 11.47 0.00 0.00 3.67
442 466 3.454587 AAAGCGCACGTCCCAGTCA 62.455 57.895 11.47 0.00 0.00 3.41
443 467 2.665185 AAAGCGCACGTCCCAGTC 60.665 61.111 11.47 0.00 0.00 3.51
444 468 2.665185 GAAAGCGCACGTCCCAGT 60.665 61.111 11.47 0.00 0.00 4.00
445 469 3.423154 GGAAAGCGCACGTCCCAG 61.423 66.667 11.47 0.00 0.00 4.45
555 579 2.644992 GGCAGTTGGGTTGAAGCG 59.355 61.111 0.00 0.00 0.00 4.68
556 580 2.644992 CGGCAGTTGGGTTGAAGC 59.355 61.111 0.00 0.00 0.00 3.86
557 581 2.268076 CCCGGCAGTTGGGTTGAAG 61.268 63.158 0.00 0.00 42.07 3.02
558 582 2.203422 CCCGGCAGTTGGGTTGAA 60.203 61.111 0.00 0.00 42.07 2.69
564 588 2.751436 CATCCACCCGGCAGTTGG 60.751 66.667 0.00 0.00 0.00 3.77
566 590 2.351276 GACATCCACCCGGCAGTT 59.649 61.111 0.00 0.00 0.00 3.16
567 591 2.927856 TGACATCCACCCGGCAGT 60.928 61.111 0.00 0.00 0.00 4.40
568 592 2.124983 CTGACATCCACCCGGCAG 60.125 66.667 0.00 0.00 0.00 4.85
569 593 2.606213 TCTGACATCCACCCGGCA 60.606 61.111 0.00 0.00 0.00 5.69
570 594 2.185310 AACTCTGACATCCACCCGGC 62.185 60.000 0.00 0.00 0.00 6.13
582 606 2.493035 TCAGCATTTTCGCAACTCTGA 58.507 42.857 0.00 0.00 0.00 3.27
671 725 9.899226 GTGAATAAAAGCTTTATGAGTTTGTCT 57.101 29.630 13.10 0.00 0.00 3.41
672 726 9.129209 GGTGAATAAAAGCTTTATGAGTTTGTC 57.871 33.333 13.10 1.40 0.00 3.18
673 727 8.088365 GGGTGAATAAAAGCTTTATGAGTTTGT 58.912 33.333 13.10 0.00 0.00 2.83
674 728 7.273381 CGGGTGAATAAAAGCTTTATGAGTTTG 59.727 37.037 13.10 0.00 0.00 2.93
675 729 7.039993 ACGGGTGAATAAAAGCTTTATGAGTTT 60.040 33.333 13.10 0.00 0.00 2.66
676 730 6.433093 ACGGGTGAATAAAAGCTTTATGAGTT 59.567 34.615 13.10 3.37 0.00 3.01
677 731 5.944007 ACGGGTGAATAAAAGCTTTATGAGT 59.056 36.000 13.10 0.00 0.00 3.41
678 732 6.093495 TGACGGGTGAATAAAAGCTTTATGAG 59.907 38.462 13.10 0.57 0.00 2.90
679 733 5.941058 TGACGGGTGAATAAAAGCTTTATGA 59.059 36.000 13.10 1.27 0.00 2.15
680 734 6.189677 TGACGGGTGAATAAAAGCTTTATG 57.810 37.500 13.10 0.00 0.00 1.90
681 735 8.514330 TTATGACGGGTGAATAAAAGCTTTAT 57.486 30.769 13.10 5.68 0.00 1.40
682 736 7.925043 TTATGACGGGTGAATAAAAGCTTTA 57.075 32.000 13.10 1.49 0.00 1.85
683 737 6.827586 TTATGACGGGTGAATAAAAGCTTT 57.172 33.333 5.69 5.69 0.00 3.51
684 738 8.691661 ATATTATGACGGGTGAATAAAAGCTT 57.308 30.769 0.00 0.00 0.00 3.74
685 739 8.691661 AATATTATGACGGGTGAATAAAAGCT 57.308 30.769 0.00 0.00 0.00 3.74
689 743 9.761504 TCGTAAATATTATGACGGGTGAATAAA 57.238 29.630 14.08 0.00 36.02 1.40
690 744 9.414295 CTCGTAAATATTATGACGGGTGAATAA 57.586 33.333 14.08 0.00 36.02 1.40
691 745 8.030692 CCTCGTAAATATTATGACGGGTGAATA 58.969 37.037 13.31 0.00 33.93 1.75
692 746 6.872020 CCTCGTAAATATTATGACGGGTGAAT 59.128 38.462 13.31 0.00 33.93 2.57
693 747 6.040729 TCCTCGTAAATATTATGACGGGTGAA 59.959 38.462 13.31 1.05 33.93 3.18
694 748 5.535783 TCCTCGTAAATATTATGACGGGTGA 59.464 40.000 13.31 9.06 33.93 4.02
695 749 5.632347 GTCCTCGTAAATATTATGACGGGTG 59.368 44.000 13.31 7.52 33.93 4.61
696 750 5.563475 CGTCCTCGTAAATATTATGACGGGT 60.563 44.000 13.31 0.00 40.27 5.28
697 751 4.855388 CGTCCTCGTAAATATTATGACGGG 59.145 45.833 14.08 11.78 40.27 5.28
698 752 5.692814 TCGTCCTCGTAAATATTATGACGG 58.307 41.667 14.08 7.68 43.14 4.79
699 753 7.613247 TTTCGTCCTCGTAAATATTATGACG 57.387 36.000 9.89 9.89 43.98 4.35
701 755 9.752961 TGAATTTCGTCCTCGTAAATATTATGA 57.247 29.630 0.00 0.00 38.33 2.15
706 760 9.931210 GAATTTGAATTTCGTCCTCGTAAATAT 57.069 29.630 0.00 0.00 38.33 1.28
707 761 8.937884 TGAATTTGAATTTCGTCCTCGTAAATA 58.062 29.630 0.00 0.00 38.33 1.40
708 762 7.812648 TGAATTTGAATTTCGTCCTCGTAAAT 58.187 30.769 0.00 0.00 38.33 1.40
709 763 7.192148 TGAATTTGAATTTCGTCCTCGTAAA 57.808 32.000 0.00 0.00 38.33 2.01
710 764 6.788684 TGAATTTGAATTTCGTCCTCGTAA 57.211 33.333 0.00 0.00 38.33 3.18
711 765 6.183360 CCATGAATTTGAATTTCGTCCTCGTA 60.183 38.462 0.00 0.00 38.33 3.43
712 766 5.391950 CCATGAATTTGAATTTCGTCCTCGT 60.392 40.000 0.00 0.00 38.33 4.18
713 767 5.030295 CCATGAATTTGAATTTCGTCCTCG 58.970 41.667 0.00 0.00 38.55 4.63
714 768 5.105756 ACCCATGAATTTGAATTTCGTCCTC 60.106 40.000 0.00 0.00 0.00 3.71
715 769 4.772100 ACCCATGAATTTGAATTTCGTCCT 59.228 37.500 0.00 0.00 0.00 3.85
716 770 4.864247 CACCCATGAATTTGAATTTCGTCC 59.136 41.667 0.00 0.00 0.00 4.79
717 771 5.572896 GTCACCCATGAATTTGAATTTCGTC 59.427 40.000 0.00 0.00 36.31 4.20
718 772 5.469479 GTCACCCATGAATTTGAATTTCGT 58.531 37.500 0.00 0.00 36.31 3.85
719 773 4.864247 GGTCACCCATGAATTTGAATTTCG 59.136 41.667 0.00 0.00 36.31 3.46
720 774 6.041423 AGGTCACCCATGAATTTGAATTTC 57.959 37.500 0.00 0.00 36.31 2.17
721 775 7.552050 TTAGGTCACCCATGAATTTGAATTT 57.448 32.000 0.00 0.00 36.31 1.82
722 776 7.399765 TGATTAGGTCACCCATGAATTTGAATT 59.600 33.333 0.00 0.00 36.31 2.17
723 777 6.896860 TGATTAGGTCACCCATGAATTTGAAT 59.103 34.615 0.00 0.00 36.31 2.57
724 778 6.252233 TGATTAGGTCACCCATGAATTTGAA 58.748 36.000 0.00 0.00 36.31 2.69
725 779 5.825532 TGATTAGGTCACCCATGAATTTGA 58.174 37.500 0.00 0.00 36.31 2.69
726 780 5.887598 TCTGATTAGGTCACCCATGAATTTG 59.112 40.000 0.00 0.00 36.31 2.32
727 781 5.888161 GTCTGATTAGGTCACCCATGAATTT 59.112 40.000 0.00 0.00 36.31 1.82
728 782 5.044919 TGTCTGATTAGGTCACCCATGAATT 60.045 40.000 0.00 0.00 36.31 2.17
729 783 4.474651 TGTCTGATTAGGTCACCCATGAAT 59.525 41.667 0.00 0.00 36.31 2.57
730 784 3.843619 TGTCTGATTAGGTCACCCATGAA 59.156 43.478 0.00 0.00 36.31 2.57
731 785 3.449918 TGTCTGATTAGGTCACCCATGA 58.550 45.455 0.00 0.00 32.22 3.07
732 786 3.912496 TGTCTGATTAGGTCACCCATG 57.088 47.619 0.00 0.00 32.22 3.66
733 787 3.137176 CCATGTCTGATTAGGTCACCCAT 59.863 47.826 0.00 0.00 32.22 4.00
734 788 2.505407 CCATGTCTGATTAGGTCACCCA 59.495 50.000 0.00 0.00 32.22 4.51
735 789 2.746472 GCCATGTCTGATTAGGTCACCC 60.746 54.545 0.00 0.00 32.22 4.61
736 790 2.565841 GCCATGTCTGATTAGGTCACC 58.434 52.381 0.00 0.00 32.22 4.02
737 791 2.205074 CGCCATGTCTGATTAGGTCAC 58.795 52.381 0.00 0.00 32.22 3.67
738 792 1.138859 CCGCCATGTCTGATTAGGTCA 59.861 52.381 0.00 0.00 35.05 4.02
739 793 1.871080 CCGCCATGTCTGATTAGGTC 58.129 55.000 0.00 0.00 0.00 3.85
740 794 0.179045 GCCGCCATGTCTGATTAGGT 60.179 55.000 0.00 0.00 0.00 3.08
741 795 0.886490 GGCCGCCATGTCTGATTAGG 60.886 60.000 3.91 0.00 0.00 2.69
742 796 0.179048 TGGCCGCCATGTCTGATTAG 60.179 55.000 8.43 0.00 0.00 1.73
743 797 0.254462 TTGGCCGCCATGTCTGATTA 59.746 50.000 14.30 0.00 31.53 1.75
744 798 0.611618 TTTGGCCGCCATGTCTGATT 60.612 50.000 14.30 0.00 31.53 2.57
745 799 0.611618 TTTTGGCCGCCATGTCTGAT 60.612 50.000 14.30 0.00 31.53 2.90
746 800 1.228398 TTTTGGCCGCCATGTCTGA 60.228 52.632 14.30 0.00 31.53 3.27
747 801 1.080569 GTTTTGGCCGCCATGTCTG 60.081 57.895 14.30 0.00 31.53 3.51
748 802 2.275380 GGTTTTGGCCGCCATGTCT 61.275 57.895 14.30 0.00 31.53 3.41
749 803 2.261361 GGTTTTGGCCGCCATGTC 59.739 61.111 14.30 6.32 31.53 3.06
750 804 3.310307 GGGTTTTGGCCGCCATGT 61.310 61.111 14.30 0.00 31.53 3.21
751 805 3.299524 CTGGGTTTTGGCCGCCATG 62.300 63.158 14.30 0.00 31.53 3.66
752 806 2.996734 CTGGGTTTTGGCCGCCAT 60.997 61.111 14.30 0.00 31.53 4.40
753 807 4.211330 TCTGGGTTTTGGCCGCCA 62.211 61.111 8.43 8.43 0.00 5.69
754 808 3.373565 CTCTGGGTTTTGGCCGCC 61.374 66.667 1.04 1.04 0.00 6.13
755 809 0.393808 TATCTCTGGGTTTTGGCCGC 60.394 55.000 0.00 0.00 0.00 6.53
756 810 2.122783 TTATCTCTGGGTTTTGGCCG 57.877 50.000 0.00 0.00 0.00 6.13
757 811 2.101415 GCATTATCTCTGGGTTTTGGCC 59.899 50.000 0.00 0.00 0.00 5.36
758 812 2.760092 TGCATTATCTCTGGGTTTTGGC 59.240 45.455 0.00 0.00 0.00 4.52
759 813 4.738541 GCATGCATTATCTCTGGGTTTTGG 60.739 45.833 14.21 0.00 0.00 3.28
760 814 4.098960 AGCATGCATTATCTCTGGGTTTTG 59.901 41.667 21.98 0.00 0.00 2.44
761 815 4.284178 AGCATGCATTATCTCTGGGTTTT 58.716 39.130 21.98 0.00 0.00 2.43
762 816 3.907221 AGCATGCATTATCTCTGGGTTT 58.093 40.909 21.98 0.00 0.00 3.27
763 817 3.589951 AGCATGCATTATCTCTGGGTT 57.410 42.857 21.98 0.00 0.00 4.11
764 818 3.589951 AAGCATGCATTATCTCTGGGT 57.410 42.857 21.98 0.00 0.00 4.51
765 819 4.238761 CAAAGCATGCATTATCTCTGGG 57.761 45.455 21.98 0.00 0.00 4.45
778 832 3.615496 GGCTCACAAATTAGCAAAGCATG 59.385 43.478 0.66 0.00 40.61 4.06
779 833 3.512724 AGGCTCACAAATTAGCAAAGCAT 59.487 39.130 0.66 0.00 40.61 3.79
780 834 2.892852 AGGCTCACAAATTAGCAAAGCA 59.107 40.909 0.66 0.00 40.61 3.91
781 835 3.057315 TGAGGCTCACAAATTAGCAAAGC 60.057 43.478 14.43 0.00 40.61 3.51
782 836 4.771590 TGAGGCTCACAAATTAGCAAAG 57.228 40.909 14.43 0.00 40.61 2.77
783 837 4.340666 TGTTGAGGCTCACAAATTAGCAAA 59.659 37.500 18.55 0.00 40.61 3.68
784 838 3.888323 TGTTGAGGCTCACAAATTAGCAA 59.112 39.130 18.55 0.00 40.61 3.91
785 839 3.485394 TGTTGAGGCTCACAAATTAGCA 58.515 40.909 18.55 0.00 40.61 3.49
786 840 4.708726 ATGTTGAGGCTCACAAATTAGC 57.291 40.909 18.55 0.00 38.03 3.09
787 841 5.122239 TCGAATGTTGAGGCTCACAAATTAG 59.878 40.000 18.55 15.92 0.00 1.73
788 842 5.000591 TCGAATGTTGAGGCTCACAAATTA 58.999 37.500 18.55 0.00 0.00 1.40
789 843 3.820467 TCGAATGTTGAGGCTCACAAATT 59.180 39.130 18.55 16.25 0.00 1.82
790 844 3.411446 TCGAATGTTGAGGCTCACAAAT 58.589 40.909 18.55 8.28 0.00 2.32
791 845 2.807967 CTCGAATGTTGAGGCTCACAAA 59.192 45.455 18.55 6.04 0.00 2.83
792 846 2.416747 CTCGAATGTTGAGGCTCACAA 58.583 47.619 18.55 8.84 0.00 3.33
793 847 1.338105 CCTCGAATGTTGAGGCTCACA 60.338 52.381 18.55 18.08 45.99 3.58
794 848 1.363744 CCTCGAATGTTGAGGCTCAC 58.636 55.000 18.55 12.93 45.99 3.51
795 849 3.840831 CCTCGAATGTTGAGGCTCA 57.159 52.632 14.43 14.43 45.99 4.26
800 854 7.364522 TGAATTTAGAACCTCGAATGTTGAG 57.635 36.000 4.84 0.00 0.00 3.02
801 855 7.606073 TCATGAATTTAGAACCTCGAATGTTGA 59.394 33.333 4.84 0.00 0.00 3.18
802 856 7.751732 TCATGAATTTAGAACCTCGAATGTTG 58.248 34.615 4.84 0.00 0.00 3.33
803 857 7.921786 TCATGAATTTAGAACCTCGAATGTT 57.078 32.000 0.00 0.00 0.00 2.71
804 858 8.511604 AATCATGAATTTAGAACCTCGAATGT 57.488 30.769 0.00 0.00 0.00 2.71
845 899 4.141914 CCCATAGACCGCTCTAGAGTTTTT 60.142 45.833 20.75 3.52 32.24 1.94
846 900 3.385111 CCCATAGACCGCTCTAGAGTTTT 59.615 47.826 20.75 5.31 32.24 2.43
847 901 2.959707 CCCATAGACCGCTCTAGAGTTT 59.040 50.000 20.75 5.67 32.24 2.66
848 902 2.588620 CCCATAGACCGCTCTAGAGTT 58.411 52.381 20.75 6.03 32.24 3.01
849 903 1.820090 GCCCATAGACCGCTCTAGAGT 60.820 57.143 20.75 1.97 32.24 3.24
850 904 0.885196 GCCCATAGACCGCTCTAGAG 59.115 60.000 15.85 15.85 32.24 2.43
851 905 0.478942 AGCCCATAGACCGCTCTAGA 59.521 55.000 0.00 0.00 32.24 2.43
852 906 0.885196 GAGCCCATAGACCGCTCTAG 59.115 60.000 1.14 0.00 44.52 2.43
853 907 3.037941 GAGCCCATAGACCGCTCTA 57.962 57.895 1.14 0.00 44.52 2.43
854 908 3.863606 GAGCCCATAGACCGCTCT 58.136 61.111 1.14 0.00 44.52 4.09
856 910 1.381872 AGTGAGCCCATAGACCGCT 60.382 57.895 0.00 0.00 34.97 5.52
857 911 1.227380 CAGTGAGCCCATAGACCGC 60.227 63.158 0.00 0.00 0.00 5.68
858 912 1.227380 GCAGTGAGCCCATAGACCG 60.227 63.158 0.00 0.00 37.23 4.79
859 913 4.865865 GCAGTGAGCCCATAGACC 57.134 61.111 0.00 0.00 37.23 3.85
920 1017 2.125512 CCGTGGGCCGAGAAAGAG 60.126 66.667 0.00 0.00 39.56 2.85
936 1033 1.590259 GGAGATGACGAGCTTCGCC 60.590 63.158 5.63 0.00 45.12 5.54
937 1034 0.179124 AAGGAGATGACGAGCTTCGC 60.179 55.000 5.63 0.00 45.12 4.70
965 1062 2.895372 CGCGGGAATGGCTGGTAC 60.895 66.667 0.00 0.00 0.00 3.34
966 1063 3.078196 TCGCGGGAATGGCTGGTA 61.078 61.111 6.13 0.00 0.00 3.25
1100 1205 0.402121 AGTGGCCCAAGGAAGAGAAC 59.598 55.000 0.00 0.00 0.00 3.01
1176 1281 4.570663 CGCGGGCGGGTAGAAGAG 62.571 72.222 4.92 0.00 35.56 2.85
1179 1284 4.745751 CAACGCGGGCGGGTAGAA 62.746 66.667 18.03 0.00 44.69 2.10
1342 1447 8.927675 ACAAGAGATAATCTACCTACTACCAG 57.072 38.462 0.00 0.00 37.23 4.00
1370 1478 4.141711 GGGTGGTATCAGAGATTGCAGTAA 60.142 45.833 0.00 0.00 0.00 2.24
1425 1535 2.026860 CGACGCGTCATATATGCACATC 59.973 50.000 35.71 7.38 40.39 3.06
1457 1567 1.472878 TCTCGCAGCAGAATTCGTAGT 59.527 47.619 0.00 0.00 0.00 2.73
1522 1632 0.107993 TGCTCTGCACAGACATAGCC 60.108 55.000 0.00 0.00 38.59 3.93
1569 1679 3.733337 AGCAACTATCGCCCTAGAATTG 58.267 45.455 0.00 0.00 0.00 2.32
1580 1690 6.019801 ACGCTATTAACTGAAAGCAACTATCG 60.020 38.462 0.00 0.00 37.60 2.92
1610 1720 2.621338 TCACAATCCAGCAGAATCGAC 58.379 47.619 0.00 0.00 0.00 4.20
1634 1744 7.041372 ACAATTGTCACTTGCGTTACTCTATTT 60.041 33.333 4.92 0.00 0.00 1.40
1719 1829 9.719355 TTTGATGTCTACTACAACATACACAAT 57.281 29.630 0.00 0.00 42.70 2.71
1789 1899 9.478768 TGTACGACAAAATCTGACACTATAAAA 57.521 29.630 0.00 0.00 0.00 1.52
1790 1900 9.647797 ATGTACGACAAAATCTGACACTATAAA 57.352 29.630 0.00 0.00 0.00 1.40
1793 1903 9.249457 CATATGTACGACAAAATCTGACACTAT 57.751 33.333 0.00 0.00 0.00 2.12
1794 1904 8.463607 TCATATGTACGACAAAATCTGACACTA 58.536 33.333 1.90 0.00 0.00 2.74
1815 1928 5.429762 TCCTTTCCTGGTGAATCAGTCATAT 59.570 40.000 0.00 0.00 38.90 1.78
1831 1944 5.048713 CGTTATTCAAAGTTGCTCCTTTCCT 60.049 40.000 0.00 0.00 32.42 3.36
1838 1951 4.148891 CCGTTCGTTATTCAAAGTTGCTC 58.851 43.478 0.00 0.00 0.00 4.26
1992 2457 0.617413 CCTTCTCTGGCACATCACCT 59.383 55.000 0.00 0.00 38.20 4.00
2019 2484 2.282147 CTGGTGAGAGGCTCGAGCTG 62.282 65.000 34.46 9.61 41.70 4.24
2178 2643 6.388619 ACATACTTCCCCAATACTTTCACT 57.611 37.500 0.00 0.00 0.00 3.41
2305 2770 4.996758 TCCCATGAAACGTGATATATGCTG 59.003 41.667 0.00 0.00 0.00 4.41
2483 2948 2.040813 ACTCCAGGAACATCTGTTGCAT 59.959 45.455 15.53 0.33 46.84 3.96
2954 3423 8.752005 TTAAGACATCAGGCTAATAAATTGCT 57.248 30.769 0.00 0.00 0.00 3.91
3021 3490 5.599999 ACTAGGTATGCTCTTGGTTAGTG 57.400 43.478 0.00 0.00 0.00 2.74
3161 3630 4.161189 CCTGAGTAGCTTCTGAGGATTTCA 59.839 45.833 19.07 0.00 40.42 2.69
3282 3846 1.596477 GAGGGCATCGTCCATCTGC 60.596 63.158 0.00 0.00 34.33 4.26
3285 3849 1.596477 GCAGAGGGCATCGTCCATC 60.596 63.158 0.00 0.00 43.97 3.51
3423 3987 7.496346 TCAACACTAGATCTCAAATAGGGTT 57.504 36.000 0.00 0.68 42.44 4.11
3438 4003 9.901724 CTTAGCACGTTTAAATATCAACACTAG 57.098 33.333 0.00 0.00 0.00 2.57
3624 4189 5.818678 ACTAGACCAAATTAGTGACACCA 57.181 39.130 0.84 0.00 0.00 4.17
3967 4532 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
4040 4605 1.079875 TCCGGAATTACTTGTCGCGC 61.080 55.000 0.00 0.00 0.00 6.86
4041 4606 0.643820 GTCCGGAATTACTTGTCGCG 59.356 55.000 5.23 0.00 0.00 5.87
4274 4839 3.634910 ACGAAACTGTGGCATTAAACCTT 59.365 39.130 0.00 0.00 0.00 3.50
4295 4860 5.812642 ACATGAAAATACAGTCTCGGATCAC 59.187 40.000 0.00 0.00 0.00 3.06
4361 4926 3.015327 GGAGAGCACCTCGTACTAAAGA 58.985 50.000 0.00 0.00 42.89 2.52
4428 4993 7.881142 TCTGAAGTTAACATATTGGTTTGGTG 58.119 34.615 8.61 0.00 32.29 4.17
4469 5034 9.606631 TGTTTTTGGAAGTTGCATTTACTTATT 57.393 25.926 2.29 0.00 36.04 1.40
4470 5035 9.777297 ATGTTTTTGGAAGTTGCATTTACTTAT 57.223 25.926 2.29 0.00 36.04 1.73
4472 5037 9.777297 ATATGTTTTTGGAAGTTGCATTTACTT 57.223 25.926 1.89 1.89 38.49 2.24
4473 5038 9.777297 AATATGTTTTTGGAAGTTGCATTTACT 57.223 25.926 0.00 0.00 0.00 2.24
4474 5039 9.810231 CAATATGTTTTTGGAAGTTGCATTTAC 57.190 29.630 0.00 0.00 0.00 2.01
4475 5040 9.553064 ACAATATGTTTTTGGAAGTTGCATTTA 57.447 25.926 0.00 0.00 0.00 1.40
4476 5041 8.449251 ACAATATGTTTTTGGAAGTTGCATTT 57.551 26.923 0.00 0.00 0.00 2.32
4477 5042 9.723601 ATACAATATGTTTTTGGAAGTTGCATT 57.276 25.926 0.00 0.00 0.00 3.56
4478 5043 9.153721 CATACAATATGTTTTTGGAAGTTGCAT 57.846 29.630 0.00 0.00 0.00 3.96
4479 5044 8.363390 TCATACAATATGTTTTTGGAAGTTGCA 58.637 29.630 0.00 0.00 0.00 4.08
4480 5045 8.755696 TCATACAATATGTTTTTGGAAGTTGC 57.244 30.769 0.00 0.00 0.00 4.17
4510 5075 9.520204 GTGCGTTAGTACAGTCCTTATATTTAA 57.480 33.333 0.00 0.00 32.98 1.52
4511 5076 8.685427 TGTGCGTTAGTACAGTCCTTATATTTA 58.315 33.333 0.00 0.00 38.05 1.40
4512 5077 7.549839 TGTGCGTTAGTACAGTCCTTATATTT 58.450 34.615 0.00 0.00 38.05 1.40
4513 5078 7.104043 TGTGCGTTAGTACAGTCCTTATATT 57.896 36.000 0.00 0.00 38.05 1.28
4514 5079 6.704289 TGTGCGTTAGTACAGTCCTTATAT 57.296 37.500 0.00 0.00 38.05 0.86
4535 5100 5.064962 TGTTGTTTAAAATCCGAACGACTGT 59.935 36.000 0.00 0.00 38.12 3.55
4986 5563 1.762957 CGGAATCAGGGGAGAAAGCTA 59.237 52.381 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.