Multiple sequence alignment - TraesCS2A01G005100

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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 TraesCS2A01G005100 chr2A 100.000 3545 0 0 1 3545 2654812 2658356 0.000000e+00 6547.0
1 TraesCS2A01G005100 chr2A 91.667 48 3 1 293 340 680506561 680506607 8.210000e-07 65.8
2 TraesCS2A01G005100 chr2D 92.214 1066 56 14 832 1883 3035908 3034856 0.000000e+00 1483.0
3 TraesCS2A01G005100 chr2D 91.990 824 66 0 1878 2701 3034659 3033836 0.000000e+00 1157.0
4 TraesCS2A01G005100 chr2D 91.474 692 25 5 1 667 3761511 3760829 0.000000e+00 920.0
5 TraesCS2A01G005100 chr2D 89.267 382 35 4 3169 3545 3080222 3079842 1.150000e-129 473.0
6 TraesCS2A01G005100 chr2D 86.349 315 23 9 3168 3477 3629398 3629099 3.410000e-85 326.0
7 TraesCS2A01G005100 chr2D 90.833 240 22 0 3305 3544 3033104 3032865 4.410000e-84 322.0
8 TraesCS2A01G005100 chr2D 78.964 309 28 11 2758 3040 3033815 3033518 3.640000e-40 176.0
9 TraesCS2A01G005100 chr2D 88.435 147 16 1 2954 3099 3629709 3629563 3.640000e-40 176.0
10 TraesCS2A01G005100 chr2D 94.792 96 5 0 3038 3133 3033303 3033208 2.200000e-32 150.0
11 TraesCS2A01G005100 chr2D 88.281 128 10 2 793 920 3037432 3037310 7.930000e-32 148.0
12 TraesCS2A01G005100 chr2D 94.186 86 2 2 835 920 3036696 3036614 1.030000e-25 128.0
13 TraesCS2A01G005100 chr2D 89.610 77 4 3 793 868 3039301 3039228 1.050000e-15 95.3
14 TraesCS2A01G005100 chr2D 100.000 34 0 0 421 454 3761404 3761437 2.950000e-06 63.9
15 TraesCS2A01G005100 chr2D 97.297 37 1 0 388 424 48210355 48210391 2.950000e-06 63.9
16 TraesCS2A01G005100 chr2D 100.000 28 0 0 3 30 531967480 531967507 6.000000e-03 52.8
17 TraesCS2A01G005100 chr2B 89.498 657 40 9 1 632 7446896 7447548 0.000000e+00 804.0
18 TraesCS2A01G005100 chr2B 82.802 878 137 8 1016 1883 7565663 7566536 0.000000e+00 773.0
19 TraesCS2A01G005100 chr2B 79.556 900 169 14 1892 2784 7644443 7645334 2.320000e-176 628.0
20 TraesCS2A01G005100 chr2B 79.406 942 149 26 976 1883 6958847 6957917 1.080000e-174 623.0
21 TraesCS2A01G005100 chr2B 79.299 942 150 26 976 1883 6872263 6871333 5.030000e-173 617.0
22 TraesCS2A01G005100 chr2B 78.981 942 157 21 976 1883 7086383 7087317 3.910000e-169 604.0
23 TraesCS2A01G005100 chr2B 82.003 739 105 14 979 1693 7643063 7643797 1.410000e-168 603.0
24 TraesCS2A01G005100 chr2B 89.474 380 32 6 3169 3544 7645634 7646009 1.150000e-129 473.0
25 TraesCS2A01G005100 chr2B 90.756 119 7 4 3018 3133 7645518 7645635 4.740000e-34 156.0
26 TraesCS2A01G005100 chr2B 97.368 38 1 0 388 425 75711621 75711584 8.210000e-07 65.8
27 TraesCS2A01G005100 chr5B 81.490 913 143 17 993 1883 537964073 537963165 0.000000e+00 726.0
28 TraesCS2A01G005100 chr5B 76.627 830 183 6 1890 2719 537960975 537960157 6.980000e-122 448.0
29 TraesCS2A01G005100 chr5D 81.051 913 147 17 993 1883 441927052 441926144 0.000000e+00 704.0
30 TraesCS2A01G005100 chr5D 100.000 30 0 0 1 30 307091935 307091906 4.940000e-04 56.5
31 TraesCS2A01G005100 chr5A 80.280 857 140 20 1034 1868 558311919 558311070 1.400000e-173 619.0
32 TraesCS2A01G005100 chr3B 79.185 908 171 11 989 1881 796839509 796838605 6.500000e-172 614.0
33 TraesCS2A01G005100 chrUn 80.224 804 133 15 1105 1883 2390588 2391390 6.600000e-162 580.0
34 TraesCS2A01G005100 chrUn 93.000 100 7 0 976 1075 385833169 385833268 2.850000e-31 147.0
35 TraesCS2A01G005100 chr1B 80.124 805 132 23 1105 1883 13892870 13893672 3.070000e-160 575.0
36 TraesCS2A01G005100 chr7B 78.541 932 155 28 988 1883 244136348 244137270 3.970000e-159 571.0
37 TraesCS2A01G005100 chr7D 78.219 932 152 31 988 1883 263889978 263890894 1.860000e-152 549.0
38 TraesCS2A01G005100 chr7D 100.000 30 0 0 1 30 2145301 2145330 4.940000e-04 56.5
39 TraesCS2A01G005100 chr6B 77.707 157 19 7 127 283 703266667 703266807 8.160000e-12 82.4
40 TraesCS2A01G005100 chr4D 100.000 30 0 0 1 30 37539448 37539477 4.940000e-04 56.5
41 TraesCS2A01G005100 chr3D 100.000 30 0 0 1 30 562461650 562461679 4.940000e-04 56.5
42 TraesCS2A01G005100 chr7A 100.000 29 0 0 1 29 729061361 729061333 2.000000e-03 54.7
43 TraesCS2A01G005100 chr4A 100.000 29 0 0 1 29 552808601 552808573 2.000000e-03 54.7


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 TraesCS2A01G005100 chr2A 2654812 2658356 3544 False 6547.0000 6547 100.00000 1 3545 1 chr2A.!!$F1 3544
1 TraesCS2A01G005100 chr2D 3760829 3761511 682 True 920.0000 920 91.47400 1 667 1 chr2D.!!$R2 666
2 TraesCS2A01G005100 chr2D 3032865 3039301 6436 True 457.4125 1483 90.10875 793 3544 8 chr2D.!!$R3 2751
3 TraesCS2A01G005100 chr2D 3629099 3629709 610 True 251.0000 326 87.39200 2954 3477 2 chr2D.!!$R4 523
4 TraesCS2A01G005100 chr2B 7446896 7447548 652 False 804.0000 804 89.49800 1 632 1 chr2B.!!$F2 631
5 TraesCS2A01G005100 chr2B 7565663 7566536 873 False 773.0000 773 82.80200 1016 1883 1 chr2B.!!$F3 867
6 TraesCS2A01G005100 chr2B 6957917 6958847 930 True 623.0000 623 79.40600 976 1883 1 chr2B.!!$R2 907
7 TraesCS2A01G005100 chr2B 6871333 6872263 930 True 617.0000 617 79.29900 976 1883 1 chr2B.!!$R1 907
8 TraesCS2A01G005100 chr2B 7086383 7087317 934 False 604.0000 604 78.98100 976 1883 1 chr2B.!!$F1 907
9 TraesCS2A01G005100 chr2B 7643063 7646009 2946 False 465.0000 628 85.44725 979 3544 4 chr2B.!!$F4 2565
10 TraesCS2A01G005100 chr5B 537960157 537964073 3916 True 587.0000 726 79.05850 993 2719 2 chr5B.!!$R1 1726
11 TraesCS2A01G005100 chr5D 441926144 441927052 908 True 704.0000 704 81.05100 993 1883 1 chr5D.!!$R2 890
12 TraesCS2A01G005100 chr5A 558311070 558311919 849 True 619.0000 619 80.28000 1034 1868 1 chr5A.!!$R1 834
13 TraesCS2A01G005100 chr3B 796838605 796839509 904 True 614.0000 614 79.18500 989 1881 1 chr3B.!!$R1 892
14 TraesCS2A01G005100 chrUn 2390588 2391390 802 False 580.0000 580 80.22400 1105 1883 1 chrUn.!!$F1 778
15 TraesCS2A01G005100 chr1B 13892870 13893672 802 False 575.0000 575 80.12400 1105 1883 1 chr1B.!!$F1 778
16 TraesCS2A01G005100 chr7B 244136348 244137270 922 False 571.0000 571 78.54100 988 1883 1 chr7B.!!$F1 895
17 TraesCS2A01G005100 chr7D 263889978 263890894 916 False 549.0000 549 78.21900 988 1883 1 chr7D.!!$F2 895

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
688 714 0.249073 CTGATTCCCTAGCCACGTCG 60.249 60.0 0.0 0.0 0.0 5.12 F
1103 3679 0.035630 GAGCCACAGAAGCACCATCT 60.036 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 7162 0.167689 GTCGAGTTTAGCGAGGTCGT 59.832 55.000 0.69 0.0 42.22 4.34 R
2997 8214 1.070914 GTCCTAAGATAGGTGCCCTGC 59.929 57.143 4.16 0.0 46.32 4.85 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
49 50 0.974383 AGTACAAAGTGACGGAGGGG 59.026 55.000 0.00 0.00 0.00 4.79
85 86 5.073417 ACTGGACCGAGGAAGACTAGTATAT 59.927 44.000 0.00 0.00 0.00 0.86
90 91 7.023171 ACCGAGGAAGACTAGTATATGATCT 57.977 40.000 0.00 0.00 0.00 2.75
91 92 6.882140 ACCGAGGAAGACTAGTATATGATCTG 59.118 42.308 0.00 0.00 0.00 2.90
95 96 7.531317 AGGAAGACTAGTATATGATCTGTGGT 58.469 38.462 0.00 0.00 0.00 4.16
109 110 7.718334 TGATCTGTGGTCTTTAAGTGAGATA 57.282 36.000 0.00 0.00 0.00 1.98
110 111 8.311395 TGATCTGTGGTCTTTAAGTGAGATAT 57.689 34.615 0.00 0.00 0.00 1.63
217 221 6.593770 ACTCCAAAACAAATCAACTCAAAACC 59.406 34.615 0.00 0.00 0.00 3.27
283 287 6.712095 TGAATAGTGTCAGCTTTGAGTGAATT 59.288 34.615 0.00 0.00 0.00 2.17
308 312 5.999205 ATTTGCCACTATTCACATCCAAA 57.001 34.783 0.00 0.00 0.00 3.28
594 620 8.481314 TCATTTCTAGACTTCTAGTGCATGAAT 58.519 33.333 12.11 3.84 44.74 2.57
677 703 4.780815 TGGTACATGACATTCTGATTCCC 58.219 43.478 0.00 0.00 0.00 3.97
678 704 4.474651 TGGTACATGACATTCTGATTCCCT 59.525 41.667 0.00 0.00 0.00 4.20
680 706 6.183361 TGGTACATGACATTCTGATTCCCTAG 60.183 42.308 0.00 0.00 0.00 3.02
682 708 3.845781 TGACATTCTGATTCCCTAGCC 57.154 47.619 0.00 0.00 0.00 3.93
683 709 3.114606 TGACATTCTGATTCCCTAGCCA 58.885 45.455 0.00 0.00 0.00 4.75
684 710 3.118261 TGACATTCTGATTCCCTAGCCAC 60.118 47.826 0.00 0.00 0.00 5.01
686 712 1.568504 TTCTGATTCCCTAGCCACGT 58.431 50.000 0.00 0.00 0.00 4.49
688 714 0.249073 CTGATTCCCTAGCCACGTCG 60.249 60.000 0.00 0.00 0.00 5.12
689 715 0.681887 TGATTCCCTAGCCACGTCGA 60.682 55.000 0.00 0.00 0.00 4.20
690 716 0.458669 GATTCCCTAGCCACGTCGAA 59.541 55.000 0.00 0.00 0.00 3.71
691 717 0.899720 ATTCCCTAGCCACGTCGAAA 59.100 50.000 0.00 0.00 0.00 3.46
692 718 0.680618 TTCCCTAGCCACGTCGAAAA 59.319 50.000 0.00 0.00 0.00 2.29
693 719 0.899720 TCCCTAGCCACGTCGAAAAT 59.100 50.000 0.00 0.00 0.00 1.82
694 720 1.276989 TCCCTAGCCACGTCGAAAATT 59.723 47.619 0.00 0.00 0.00 1.82
695 721 1.664151 CCCTAGCCACGTCGAAAATTC 59.336 52.381 0.00 0.00 0.00 2.17
696 722 2.618053 CCTAGCCACGTCGAAAATTCT 58.382 47.619 0.00 0.00 0.00 2.40
697 723 2.348666 CCTAGCCACGTCGAAAATTCTG 59.651 50.000 0.00 0.00 0.00 3.02
699 725 2.489971 AGCCACGTCGAAAATTCTGAA 58.510 42.857 0.00 0.00 0.00 3.02
701 727 3.502211 AGCCACGTCGAAAATTCTGAAAT 59.498 39.130 0.00 0.00 0.00 2.17
703 729 5.180492 AGCCACGTCGAAAATTCTGAAATAA 59.820 36.000 0.00 0.00 0.00 1.40
706 732 7.061789 GCCACGTCGAAAATTCTGAAATAAATT 59.938 33.333 0.00 0.00 0.00 1.82
707 733 8.575454 CCACGTCGAAAATTCTGAAATAAATTC 58.425 33.333 0.00 0.00 38.60 2.17
708 734 9.329913 CACGTCGAAAATTCTGAAATAAATTCT 57.670 29.630 0.00 0.00 38.92 2.40
710 736 8.306923 CGTCGAAAATTCTGAAATAAATTCTGC 58.693 33.333 0.00 0.00 38.92 4.26
711 737 9.128107 GTCGAAAATTCTGAAATAAATTCTGCA 57.872 29.630 0.00 0.00 38.92 4.41
712 738 9.859427 TCGAAAATTCTGAAATAAATTCTGCAT 57.141 25.926 0.00 0.00 38.92 3.96
725 751 6.544038 AAATTCTGCATAAAAACAAGCACC 57.456 33.333 0.00 0.00 32.87 5.01
726 752 4.662468 TTCTGCATAAAAACAAGCACCA 57.338 36.364 0.00 0.00 32.87 4.17
727 753 4.870123 TCTGCATAAAAACAAGCACCAT 57.130 36.364 0.00 0.00 32.87 3.55
728 754 4.558178 TCTGCATAAAAACAAGCACCATG 58.442 39.130 0.00 0.00 32.87 3.66
729 755 4.280425 TCTGCATAAAAACAAGCACCATGA 59.720 37.500 0.00 0.00 32.87 3.07
730 756 5.047164 TCTGCATAAAAACAAGCACCATGAT 60.047 36.000 0.00 0.00 32.87 2.45
731 757 5.549347 TGCATAAAAACAAGCACCATGATT 58.451 33.333 0.00 0.00 31.05 2.57
732 758 5.996513 TGCATAAAAACAAGCACCATGATTT 59.003 32.000 0.00 0.00 31.05 2.17
734 760 7.658982 TGCATAAAAACAAGCACCATGATTTAA 59.341 29.630 0.00 0.00 31.05 1.52
735 761 8.502387 GCATAAAAACAAGCACCATGATTTAAA 58.498 29.630 0.00 0.00 0.00 1.52
736 762 9.810231 CATAAAAACAAGCACCATGATTTAAAC 57.190 29.630 0.00 0.00 0.00 2.01
737 763 6.859420 AAAACAAGCACCATGATTTAAACC 57.141 33.333 0.00 0.00 0.00 3.27
739 765 3.260632 ACAAGCACCATGATTTAAACCCC 59.739 43.478 0.00 0.00 0.00 4.95
740 766 2.099405 AGCACCATGATTTAAACCCCG 58.901 47.619 0.00 0.00 0.00 5.73
741 767 2.096248 GCACCATGATTTAAACCCCGA 58.904 47.619 0.00 0.00 0.00 5.14
742 768 2.693074 GCACCATGATTTAAACCCCGAT 59.307 45.455 0.00 0.00 0.00 4.18
745 771 4.400884 CACCATGATTTAAACCCCGATGAA 59.599 41.667 0.00 0.00 0.00 2.57
746 772 4.401202 ACCATGATTTAAACCCCGATGAAC 59.599 41.667 0.00 0.00 0.00 3.18
747 773 4.644685 CCATGATTTAAACCCCGATGAACT 59.355 41.667 0.00 0.00 0.00 3.01
749 775 4.912586 TGATTTAAACCCCGATGAACTGA 58.087 39.130 0.00 0.00 0.00 3.41
750 776 5.317808 TGATTTAAACCCCGATGAACTGAA 58.682 37.500 0.00 0.00 0.00 3.02
751 777 5.770663 TGATTTAAACCCCGATGAACTGAAA 59.229 36.000 0.00 0.00 0.00 2.69
752 778 6.265649 TGATTTAAACCCCGATGAACTGAAAA 59.734 34.615 0.00 0.00 0.00 2.29
753 779 6.658188 TTTAAACCCCGATGAACTGAAAAT 57.342 33.333 0.00 0.00 0.00 1.82
754 780 6.658188 TTAAACCCCGATGAACTGAAAATT 57.342 33.333 0.00 0.00 0.00 1.82
755 781 4.783764 AACCCCGATGAACTGAAAATTC 57.216 40.909 0.00 0.00 0.00 2.17
757 783 3.088532 CCCCGATGAACTGAAAATTCCA 58.911 45.455 0.00 0.00 0.00 3.53
760 786 4.941263 CCCGATGAACTGAAAATTCCACTA 59.059 41.667 0.00 0.00 0.00 2.74
761 787 5.590259 CCCGATGAACTGAAAATTCCACTAT 59.410 40.000 0.00 0.00 0.00 2.12
763 789 6.540189 CCGATGAACTGAAAATTCCACTATCT 59.460 38.462 0.00 0.00 0.00 1.98
764 790 7.066284 CCGATGAACTGAAAATTCCACTATCTT 59.934 37.037 0.00 0.00 0.00 2.40
765 791 8.454106 CGATGAACTGAAAATTCCACTATCTTT 58.546 33.333 0.00 0.00 0.00 2.52
766 792 9.780413 GATGAACTGAAAATTCCACTATCTTTC 57.220 33.333 0.00 0.00 0.00 2.62
767 793 8.924511 TGAACTGAAAATTCCACTATCTTTCT 57.075 30.769 0.00 0.00 0.00 2.52
779 805 9.784531 TTCCACTATCTTTCTAATCATCCAATC 57.215 33.333 0.00 0.00 0.00 2.67
781 807 9.736414 CCACTATCTTTCTAATCATCCAATCAT 57.264 33.333 0.00 0.00 0.00 2.45
791 817 9.730705 TCTAATCATCCAATCATAGATTGGTTC 57.269 33.333 28.38 0.00 46.47 3.62
794 820 7.754851 TCATCCAATCATAGATTGGTTCATG 57.245 36.000 28.38 24.51 46.47 3.07
797 823 6.131264 TCCAATCATAGATTGGTTCATGCTT 58.869 36.000 28.38 0.00 46.47 3.91
798 824 6.608405 TCCAATCATAGATTGGTTCATGCTTT 59.392 34.615 28.38 0.00 46.47 3.51
799 825 6.921857 CCAATCATAGATTGGTTCATGCTTTC 59.078 38.462 24.00 0.00 42.63 2.62
800 826 7.201884 CCAATCATAGATTGGTTCATGCTTTCT 60.202 37.037 24.00 0.00 42.63 2.52
801 827 8.843262 CAATCATAGATTGGTTCATGCTTTCTA 58.157 33.333 11.00 0.00 0.00 2.10
803 829 7.568349 TCATAGATTGGTTCATGCTTTCTAGT 58.432 34.615 0.00 0.00 0.00 2.57
804 830 8.704668 TCATAGATTGGTTCATGCTTTCTAGTA 58.295 33.333 0.00 0.00 0.00 1.82
811 1887 5.515626 GGTTCATGCTTTCTAGTACACGTAG 59.484 44.000 0.00 0.00 0.00 3.51
815 1891 5.130292 TGCTTTCTAGTACACGTAGCTTT 57.870 39.130 0.00 0.00 0.00 3.51
816 1892 5.159209 TGCTTTCTAGTACACGTAGCTTTC 58.841 41.667 0.00 0.00 0.00 2.62
884 2656 0.608582 AGCCAGGCAAGAGAAAGCTG 60.609 55.000 15.80 0.00 0.00 4.24
891 2663 1.376553 AAGAGAAAGCTGCTCGCCC 60.377 57.895 1.00 0.00 40.39 6.13
892 2664 3.191539 GAGAAAGCTGCTCGCCCG 61.192 66.667 1.00 0.00 40.39 6.13
893 2665 3.941657 GAGAAAGCTGCTCGCCCGT 62.942 63.158 1.00 0.00 40.39 5.28
894 2666 3.491652 GAAAGCTGCTCGCCCGTC 61.492 66.667 1.00 0.00 40.39 4.79
925 3368 0.533755 CCTGGCCTATGAAAGCTCCG 60.534 60.000 3.32 0.00 0.00 4.63
929 3372 0.810031 GCCTATGAAAGCTCCGCGAA 60.810 55.000 8.23 0.00 0.00 4.70
945 3388 2.969628 CGAAGCCAGAGGACTGTTAT 57.030 50.000 0.00 0.00 42.05 1.89
947 3390 4.386867 CGAAGCCAGAGGACTGTTATAA 57.613 45.455 0.00 0.00 42.05 0.98
948 3391 4.950050 CGAAGCCAGAGGACTGTTATAAT 58.050 43.478 0.00 0.00 42.05 1.28
949 3392 6.085555 CGAAGCCAGAGGACTGTTATAATA 57.914 41.667 0.00 0.00 42.05 0.98
950 3393 6.692486 CGAAGCCAGAGGACTGTTATAATAT 58.308 40.000 0.00 0.00 42.05 1.28
953 3396 9.998106 GAAGCCAGAGGACTGTTATAATATTTA 57.002 33.333 0.00 0.00 42.05 1.40
1008 3566 2.679092 CTGCCTGCCATGGAGGAA 59.321 61.111 25.77 18.21 41.22 3.36
1023 3584 1.200948 GAGGAATGGTTCAGCTTGTGC 59.799 52.381 0.00 0.00 40.05 4.57
1084 3657 3.031964 CTCGCCGGCAGCAAGAAAG 62.032 63.158 28.98 6.54 44.04 2.62
1101 3677 0.403271 AAGAGCCACAGAAGCACCAT 59.597 50.000 0.00 0.00 0.00 3.55
1103 3679 0.035630 GAGCCACAGAAGCACCATCT 60.036 55.000 0.00 0.00 0.00 2.90
1255 3831 2.102357 CCACCGTGATCGTCTCCG 59.898 66.667 0.00 0.00 35.01 4.63
1875 4514 1.730902 CGAGATCATAGGCGCCGTG 60.731 63.158 23.20 23.48 0.00 4.94
1903 7008 2.644992 GTGCTTTCCACGGCCTTG 59.355 61.111 1.29 1.29 34.22 3.61
2052 7157 0.252197 AAGACCGGGCTGTCATTACC 59.748 55.000 12.91 0.00 37.73 2.85
2057 7162 2.240160 ACCGGGCTGTCATTACCAATAA 59.760 45.455 6.32 0.00 0.00 1.40
2106 7211 2.879103 TGGTCATCAAGGAAACCCTC 57.121 50.000 0.00 0.00 32.44 4.30
2200 7305 2.357637 CCCAAAGGCACCAATGTATACG 59.642 50.000 0.00 0.00 0.00 3.06
2250 7355 1.678101 GCATACTGGAACAATCCTGGC 59.322 52.381 6.69 0.00 46.13 4.85
2258 7363 3.279434 GGAACAATCCTGGCGAGTTTAT 58.721 45.455 0.00 0.00 42.93 1.40
2279 7384 2.224378 TGCCAGAGAGGTTTGAGAACAG 60.224 50.000 0.00 0.00 40.61 3.16
2299 7404 4.202243 ACAGCAACACAAATTACAATGGCT 60.202 37.500 0.00 0.00 0.00 4.75
2301 7406 3.679502 GCAACACAAATTACAATGGCTCC 59.320 43.478 0.00 0.00 0.00 4.70
2325 7430 1.821216 TTGAATTCACTCCCTTCGGC 58.179 50.000 7.89 0.00 0.00 5.54
2328 7433 2.463589 AATTCACTCCCTTCGGCGCA 62.464 55.000 10.83 0.00 0.00 6.09
2397 7502 8.948631 TGGAGATGACACTAACAAATATTCTC 57.051 34.615 0.00 0.00 0.00 2.87
2517 7622 2.288273 ACTTGAAGCTACTCCACACGTC 60.288 50.000 0.00 0.00 0.00 4.34
2571 7676 4.098349 GGAAAGCTTGCATATTCATGTGGA 59.902 41.667 6.80 0.00 34.40 4.02
2579 7684 5.110598 TGCATATTCATGTGGAAATGCAAC 58.889 37.500 15.97 0.00 45.72 4.17
2594 7699 7.448777 TGGAAATGCAACTTAACATACCTACAA 59.551 33.333 0.00 0.00 0.00 2.41
2601 7706 8.726988 GCAACTTAACATACCTACAATTTCAGA 58.273 33.333 0.00 0.00 0.00 3.27
2712 7817 8.018520 TCGTATCAACAAAAACATTGTGGTATC 58.981 33.333 0.00 0.00 32.22 2.24
2721 7826 4.202245 ACATTGTGGTATCGTACTGCTT 57.798 40.909 0.00 0.00 0.00 3.91
2723 7828 5.726397 ACATTGTGGTATCGTACTGCTTTA 58.274 37.500 0.00 0.00 0.00 1.85
2725 7830 6.479001 ACATTGTGGTATCGTACTGCTTTATC 59.521 38.462 0.00 0.00 0.00 1.75
2756 7861 9.676861 ATGAACTTCTGAATAATCATGACAGAA 57.323 29.630 19.09 19.09 42.59 3.02
2838 7947 9.738832 ACACATTTACCATTATTTAATTACCGC 57.261 29.630 0.00 0.00 0.00 5.68
2839 7948 9.737427 CACATTTACCATTATTTAATTACCGCA 57.263 29.630 0.00 0.00 0.00 5.69
2840 7949 9.738832 ACATTTACCATTATTTAATTACCGCAC 57.261 29.630 0.00 0.00 0.00 5.34
2841 7950 8.897809 CATTTACCATTATTTAATTACCGCACG 58.102 33.333 0.00 0.00 0.00 5.34
2842 7951 7.783090 TTACCATTATTTAATTACCGCACGA 57.217 32.000 0.00 0.00 0.00 4.35
2843 7952 6.051646 ACCATTATTTAATTACCGCACGAC 57.948 37.500 0.00 0.00 0.00 4.34
2844 7953 5.134640 CCATTATTTAATTACCGCACGACG 58.865 41.667 0.00 0.00 43.15 5.12
2845 7954 5.276963 CCATTATTTAATTACCGCACGACGT 60.277 40.000 0.00 0.00 41.42 4.34
2846 7955 3.644805 ATTTAATTACCGCACGACGTG 57.355 42.857 23.43 23.43 41.42 4.49
2864 7973 5.179368 CGACGTGCTTATGGAATGGATTTAT 59.821 40.000 0.00 0.00 0.00 1.40
2926 8035 6.141560 TGTGTGTGTTCTATGCAATTTTCA 57.858 33.333 0.00 0.00 0.00 2.69
2935 8044 9.176460 TGTTCTATGCAATTTTCATATCAGTGA 57.824 29.630 0.00 0.00 0.00 3.41
2952 8061 6.356186 TCAGTGAATATGCTCAGCTCATAT 57.644 37.500 0.00 1.50 38.40 1.78
2953 8062 7.472334 TCAGTGAATATGCTCAGCTCATATA 57.528 36.000 0.00 0.00 36.43 0.86
2954 8063 8.075761 TCAGTGAATATGCTCAGCTCATATAT 57.924 34.615 0.00 0.00 36.43 0.86
2991 8204 5.755861 GGTCCAGTACAGCTCTTGATATTTC 59.244 44.000 0.00 0.00 0.00 2.17
2997 8214 4.467769 ACAGCTCTTGATATTTCCCCATG 58.532 43.478 0.00 0.00 0.00 3.66
3042 8477 6.519679 ACCGACACACTTGACTGTAATATA 57.480 37.500 0.00 0.00 0.00 0.86
3138 8709 2.824689 TCAGCCATCTGAGAGAGACT 57.175 50.000 0.00 0.00 43.95 3.24
3139 8710 2.377073 TCAGCCATCTGAGAGAGACTG 58.623 52.381 0.00 0.00 43.95 3.51
3140 8711 2.025510 TCAGCCATCTGAGAGAGACTGA 60.026 50.000 0.79 0.79 43.95 3.41
3141 8712 2.359848 CAGCCATCTGAGAGAGACTGAG 59.640 54.545 0.00 0.00 42.95 3.35
3142 8713 1.682854 GCCATCTGAGAGAGACTGAGG 59.317 57.143 0.00 0.00 31.75 3.86
3143 8714 2.686416 GCCATCTGAGAGAGACTGAGGA 60.686 54.545 0.00 0.00 31.75 3.71
3144 8715 3.216800 CCATCTGAGAGAGACTGAGGAG 58.783 54.545 0.00 0.00 31.75 3.69
3145 8716 2.418368 TCTGAGAGAGACTGAGGAGC 57.582 55.000 0.00 0.00 30.91 4.70
3146 8717 1.632920 TCTGAGAGAGACTGAGGAGCA 59.367 52.381 0.00 0.00 30.91 4.26
3147 8718 2.040947 TCTGAGAGAGACTGAGGAGCAA 59.959 50.000 0.00 0.00 30.91 3.91
3148 8719 3.025978 CTGAGAGAGACTGAGGAGCAAT 58.974 50.000 0.00 0.00 0.00 3.56
3149 8720 2.759535 TGAGAGAGACTGAGGAGCAATG 59.240 50.000 0.00 0.00 0.00 2.82
3150 8721 2.760092 GAGAGAGACTGAGGAGCAATGT 59.240 50.000 0.00 0.00 0.00 2.71
3151 8722 3.172339 AGAGAGACTGAGGAGCAATGTT 58.828 45.455 0.00 0.00 0.00 2.71
3152 8723 3.582208 AGAGAGACTGAGGAGCAATGTTT 59.418 43.478 0.00 0.00 0.00 2.83
3153 8724 4.041444 AGAGAGACTGAGGAGCAATGTTTT 59.959 41.667 0.00 0.00 0.00 2.43
3154 8725 4.723309 AGAGACTGAGGAGCAATGTTTTT 58.277 39.130 0.00 0.00 0.00 1.94
3178 8749 2.107953 GCGGGATGACTGAGGAGC 59.892 66.667 0.00 0.00 0.00 4.70
3223 8799 9.829507 AGATCATTTTTATCTACCTCTCAGTTG 57.170 33.333 0.00 0.00 31.88 3.16
3224 8800 9.606631 GATCATTTTTATCTACCTCTCAGTTGT 57.393 33.333 0.00 0.00 0.00 3.32
3230 8806 3.483421 TCTACCTCTCAGTTGTGTCGAA 58.517 45.455 0.00 0.00 0.00 3.71
3232 8808 1.269831 ACCTCTCAGTTGTGTCGAAGC 60.270 52.381 0.00 0.00 0.00 3.86
3269 8845 6.053650 TGAGCATGAGAATACATTTCCAGAG 58.946 40.000 0.00 0.00 0.00 3.35
3271 8847 4.820716 GCATGAGAATACATTTCCAGAGCT 59.179 41.667 0.00 0.00 0.00 4.09
3275 8881 4.775236 AGAATACATTTCCAGAGCTCACC 58.225 43.478 17.77 0.00 0.00 4.02
3276 8882 3.567478 ATACATTTCCAGAGCTCACCC 57.433 47.619 17.77 0.00 0.00 4.61
3277 8883 1.067295 ACATTTCCAGAGCTCACCCA 58.933 50.000 17.77 0.00 0.00 4.51
3278 8884 1.425066 ACATTTCCAGAGCTCACCCAA 59.575 47.619 17.77 3.66 0.00 4.12
3279 8885 2.089980 CATTTCCAGAGCTCACCCAAG 58.910 52.381 17.77 0.00 0.00 3.61
3280 8886 0.401738 TTTCCAGAGCTCACCCAAGG 59.598 55.000 17.77 7.66 0.00 3.61
3281 8887 0.768221 TTCCAGAGCTCACCCAAGGT 60.768 55.000 17.77 0.00 35.62 3.50
3282 8888 0.768221 TCCAGAGCTCACCCAAGGTT 60.768 55.000 17.77 0.00 31.02 3.50
3283 8889 0.984230 CCAGAGCTCACCCAAGGTTA 59.016 55.000 17.77 0.00 31.02 2.85
3284 8890 1.339151 CCAGAGCTCACCCAAGGTTAC 60.339 57.143 17.77 0.00 31.02 2.50
3285 8891 1.625818 CAGAGCTCACCCAAGGTTACT 59.374 52.381 17.77 0.00 31.02 2.24
3286 8892 2.832129 CAGAGCTCACCCAAGGTTACTA 59.168 50.000 17.77 0.00 31.02 1.82
3287 8893 3.452627 CAGAGCTCACCCAAGGTTACTAT 59.547 47.826 17.77 0.00 31.02 2.12
3288 8894 3.707102 AGAGCTCACCCAAGGTTACTATC 59.293 47.826 17.77 0.00 31.02 2.08
3289 8895 3.450904 AGCTCACCCAAGGTTACTATCA 58.549 45.455 0.00 0.00 31.02 2.15
3290 8896 3.452627 AGCTCACCCAAGGTTACTATCAG 59.547 47.826 0.00 0.00 31.02 2.90
3291 8897 3.432326 GCTCACCCAAGGTTACTATCAGG 60.432 52.174 0.00 0.00 31.02 3.86
3292 8898 2.504175 TCACCCAAGGTTACTATCAGGC 59.496 50.000 0.00 0.00 31.02 4.85
3293 8899 2.505819 CACCCAAGGTTACTATCAGGCT 59.494 50.000 0.00 0.00 31.02 4.58
3294 8900 3.709653 CACCCAAGGTTACTATCAGGCTA 59.290 47.826 0.00 0.00 31.02 3.93
3295 8901 3.967987 ACCCAAGGTTACTATCAGGCTAG 59.032 47.826 0.00 0.00 27.29 3.42
3296 8902 4.223953 CCCAAGGTTACTATCAGGCTAGA 58.776 47.826 0.00 0.00 0.00 2.43
3297 8903 4.282195 CCCAAGGTTACTATCAGGCTAGAG 59.718 50.000 0.00 0.00 0.00 2.43
3298 8904 4.262249 CCAAGGTTACTATCAGGCTAGAGC 60.262 50.000 0.00 0.00 41.14 4.09
3299 8905 4.186077 AGGTTACTATCAGGCTAGAGCA 57.814 45.455 3.54 0.00 44.36 4.26
3300 8906 4.547671 AGGTTACTATCAGGCTAGAGCAA 58.452 43.478 3.54 0.00 44.36 3.91
3301 8907 4.962995 AGGTTACTATCAGGCTAGAGCAAA 59.037 41.667 3.54 0.00 44.36 3.68
3302 8908 5.051153 GGTTACTATCAGGCTAGAGCAAAC 58.949 45.833 3.54 0.00 44.36 2.93
3303 8909 5.163395 GGTTACTATCAGGCTAGAGCAAACT 60.163 44.000 3.54 0.00 44.36 2.66
3304 8910 4.664150 ACTATCAGGCTAGAGCAAACTC 57.336 45.455 3.54 0.00 44.36 3.01
3325 8931 3.250040 TCTTCGCTTTGCAAGTTCCTAAC 59.750 43.478 0.00 0.00 0.00 2.34
3341 8947 2.116736 TAACGAACGTCACGCCGAGT 62.117 55.000 17.75 8.59 32.52 4.18
3376 8982 0.675633 ATTTTGAGTTTGCGGCTGCT 59.324 45.000 20.27 0.00 43.34 4.24
3388 8994 2.202349 GCTGCTAAAAGTGCCGCG 60.202 61.111 0.00 0.00 31.74 6.46
3442 9048 1.074405 ACAATGTGCTCCATGTCCTGT 59.926 47.619 0.00 0.00 32.82 4.00
3544 9150 1.421646 ACCACTGTTCTTCTCCCCAAG 59.578 52.381 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.369182 CTCGGTCCAGTTTGATATGTACC 58.631 47.826 0.00 0.00 0.00 3.34
85 86 6.611613 ATCTCACTTAAAGACCACAGATCA 57.388 37.500 0.00 0.00 0.00 2.92
90 91 8.078060 TGATCATATCTCACTTAAAGACCACA 57.922 34.615 0.00 0.00 0.00 4.17
91 92 8.821894 GTTGATCATATCTCACTTAAAGACCAC 58.178 37.037 0.00 0.00 0.00 4.16
95 96 8.981659 TGGAGTTGATCATATCTCACTTAAAGA 58.018 33.333 18.19 0.00 0.00 2.52
161 165 3.627395 CCCTGCAGGTATGTTGTCTAA 57.373 47.619 30.63 0.00 0.00 2.10
283 287 5.504853 TGGATGTGAATAGTGGCAAATACA 58.495 37.500 0.00 0.00 0.00 2.29
494 520 0.819582 GATGCCCCCAGTTTGACATG 59.180 55.000 0.00 0.00 0.00 3.21
543 569 7.229228 TCATGTCATGTTACGTATAACTTGC 57.771 36.000 12.54 7.76 42.26 4.01
594 620 3.055819 GTCCTTCATACTCAGTCTTGCCA 60.056 47.826 0.00 0.00 0.00 4.92
667 693 1.480954 GACGTGGCTAGGGAATCAGAA 59.519 52.381 0.00 0.00 0.00 3.02
668 694 1.112113 GACGTGGCTAGGGAATCAGA 58.888 55.000 0.00 0.00 0.00 3.27
670 696 0.681887 TCGACGTGGCTAGGGAATCA 60.682 55.000 0.00 0.00 0.00 2.57
671 697 0.458669 TTCGACGTGGCTAGGGAATC 59.541 55.000 0.00 0.00 0.00 2.52
672 698 0.899720 TTTCGACGTGGCTAGGGAAT 59.100 50.000 0.00 0.00 0.00 3.01
673 699 0.680618 TTTTCGACGTGGCTAGGGAA 59.319 50.000 0.00 0.00 0.00 3.97
674 700 0.899720 ATTTTCGACGTGGCTAGGGA 59.100 50.000 0.00 0.00 0.00 4.20
675 701 1.664151 GAATTTTCGACGTGGCTAGGG 59.336 52.381 0.00 0.00 0.00 3.53
677 703 3.250744 TCAGAATTTTCGACGTGGCTAG 58.749 45.455 0.00 0.00 0.00 3.42
678 704 3.306917 TCAGAATTTTCGACGTGGCTA 57.693 42.857 0.00 0.00 0.00 3.93
680 706 2.961522 TTCAGAATTTTCGACGTGGC 57.038 45.000 0.00 0.00 0.00 5.01
682 708 9.329913 AGAATTTATTTCAGAATTTTCGACGTG 57.670 29.630 0.00 0.00 36.75 4.49
683 709 9.329913 CAGAATTTATTTCAGAATTTTCGACGT 57.670 29.630 0.00 0.00 36.75 4.34
684 710 8.306923 GCAGAATTTATTTCAGAATTTTCGACG 58.693 33.333 0.00 0.00 36.75 5.12
686 712 9.859427 ATGCAGAATTTATTTCAGAATTTTCGA 57.141 25.926 0.00 0.00 36.75 3.71
699 725 8.720562 GGTGCTTGTTTTTATGCAGAATTTATT 58.279 29.630 0.00 0.00 36.03 1.40
701 727 7.212976 TGGTGCTTGTTTTTATGCAGAATTTA 58.787 30.769 0.00 0.00 36.03 1.40
703 729 5.609423 TGGTGCTTGTTTTTATGCAGAATT 58.391 33.333 0.00 0.00 36.03 2.17
706 732 4.280425 TCATGGTGCTTGTTTTTATGCAGA 59.720 37.500 0.00 0.00 36.03 4.26
707 733 4.558178 TCATGGTGCTTGTTTTTATGCAG 58.442 39.130 0.00 0.00 36.03 4.41
708 734 4.597404 TCATGGTGCTTGTTTTTATGCA 57.403 36.364 0.00 0.00 0.00 3.96
710 736 9.810231 GTTTAAATCATGGTGCTTGTTTTTATG 57.190 29.630 0.00 0.00 0.00 1.90
711 737 8.998377 GGTTTAAATCATGGTGCTTGTTTTTAT 58.002 29.630 0.00 0.00 0.00 1.40
712 738 7.442666 GGGTTTAAATCATGGTGCTTGTTTTTA 59.557 33.333 0.00 0.00 0.00 1.52
713 739 6.262049 GGGTTTAAATCATGGTGCTTGTTTTT 59.738 34.615 0.00 0.00 0.00 1.94
715 741 5.304778 GGGTTTAAATCATGGTGCTTGTTT 58.695 37.500 0.00 0.00 0.00 2.83
716 742 4.262851 GGGGTTTAAATCATGGTGCTTGTT 60.263 41.667 0.00 0.00 0.00 2.83
717 743 3.260632 GGGGTTTAAATCATGGTGCTTGT 59.739 43.478 0.00 0.00 0.00 3.16
719 745 2.495669 CGGGGTTTAAATCATGGTGCTT 59.504 45.455 0.00 0.00 0.00 3.91
720 746 2.099405 CGGGGTTTAAATCATGGTGCT 58.901 47.619 0.00 0.00 0.00 4.40
721 747 2.096248 TCGGGGTTTAAATCATGGTGC 58.904 47.619 0.00 0.00 0.00 5.01
723 749 4.243793 TCATCGGGGTTTAAATCATGGT 57.756 40.909 0.00 0.00 0.00 3.55
724 750 4.644685 AGTTCATCGGGGTTTAAATCATGG 59.355 41.667 0.00 0.00 0.00 3.66
725 751 5.356751 TCAGTTCATCGGGGTTTAAATCATG 59.643 40.000 0.00 0.00 0.00 3.07
726 752 5.505780 TCAGTTCATCGGGGTTTAAATCAT 58.494 37.500 0.00 0.00 0.00 2.45
727 753 4.912586 TCAGTTCATCGGGGTTTAAATCA 58.087 39.130 0.00 0.00 0.00 2.57
728 754 5.890424 TTCAGTTCATCGGGGTTTAAATC 57.110 39.130 0.00 0.00 0.00 2.17
729 755 6.658188 TTTTCAGTTCATCGGGGTTTAAAT 57.342 33.333 0.00 0.00 0.00 1.40
730 756 6.658188 ATTTTCAGTTCATCGGGGTTTAAA 57.342 33.333 0.00 0.00 0.00 1.52
731 757 6.294843 GGAATTTTCAGTTCATCGGGGTTTAA 60.295 38.462 0.00 0.00 0.00 1.52
732 758 5.184287 GGAATTTTCAGTTCATCGGGGTTTA 59.816 40.000 0.00 0.00 0.00 2.01
734 760 3.509967 GGAATTTTCAGTTCATCGGGGTT 59.490 43.478 0.00 0.00 0.00 4.11
735 761 3.089284 GGAATTTTCAGTTCATCGGGGT 58.911 45.455 0.00 0.00 0.00 4.95
736 762 3.088532 TGGAATTTTCAGTTCATCGGGG 58.911 45.455 0.00 0.00 0.00 5.73
737 763 3.758554 AGTGGAATTTTCAGTTCATCGGG 59.241 43.478 0.00 0.00 0.00 5.14
739 765 7.545362 AGATAGTGGAATTTTCAGTTCATCG 57.455 36.000 0.00 0.00 0.00 3.84
740 766 9.780413 GAAAGATAGTGGAATTTTCAGTTCATC 57.220 33.333 0.00 0.00 0.00 2.92
741 767 9.525826 AGAAAGATAGTGGAATTTTCAGTTCAT 57.474 29.630 0.00 0.00 31.83 2.57
742 768 8.924511 AGAAAGATAGTGGAATTTTCAGTTCA 57.075 30.769 0.00 0.00 31.83 3.18
753 779 9.784531 GATTGGATGATTAGAAAGATAGTGGAA 57.215 33.333 0.00 0.00 0.00 3.53
754 780 8.937835 TGATTGGATGATTAGAAAGATAGTGGA 58.062 33.333 0.00 0.00 0.00 4.02
755 781 9.736414 ATGATTGGATGATTAGAAAGATAGTGG 57.264 33.333 0.00 0.00 0.00 4.00
776 802 7.893124 AGAAAGCATGAACCAATCTATGATT 57.107 32.000 0.00 0.00 31.26 2.57
777 803 8.216423 ACTAGAAAGCATGAACCAATCTATGAT 58.784 33.333 0.00 0.00 0.00 2.45
778 804 7.568349 ACTAGAAAGCATGAACCAATCTATGA 58.432 34.615 0.00 0.00 0.00 2.15
779 805 7.798596 ACTAGAAAGCATGAACCAATCTATG 57.201 36.000 0.00 0.00 0.00 2.23
781 807 7.764443 GTGTACTAGAAAGCATGAACCAATCTA 59.236 37.037 0.00 0.00 0.00 1.98
782 808 6.595716 GTGTACTAGAAAGCATGAACCAATCT 59.404 38.462 0.00 0.00 0.00 2.40
783 809 6.455646 CGTGTACTAGAAAGCATGAACCAATC 60.456 42.308 0.00 0.00 0.00 2.67
784 810 5.351465 CGTGTACTAGAAAGCATGAACCAAT 59.649 40.000 0.00 0.00 0.00 3.16
785 811 4.688879 CGTGTACTAGAAAGCATGAACCAA 59.311 41.667 0.00 0.00 0.00 3.67
786 812 4.242475 CGTGTACTAGAAAGCATGAACCA 58.758 43.478 0.00 0.00 0.00 3.67
788 814 5.004535 GCTACGTGTACTAGAAAGCATGAAC 59.995 44.000 0.00 0.00 0.00 3.18
789 815 5.100259 GCTACGTGTACTAGAAAGCATGAA 58.900 41.667 0.00 0.00 0.00 2.57
790 816 4.398358 AGCTACGTGTACTAGAAAGCATGA 59.602 41.667 0.00 0.00 0.00 3.07
791 817 4.673441 AGCTACGTGTACTAGAAAGCATG 58.327 43.478 0.00 0.00 0.00 4.06
794 820 4.262510 CGAAAGCTACGTGTACTAGAAAGC 59.737 45.833 0.00 0.00 0.00 3.51
797 823 6.668541 ATACGAAAGCTACGTGTACTAGAA 57.331 37.500 22.87 6.45 43.73 2.10
798 824 6.668541 AATACGAAAGCTACGTGTACTAGA 57.331 37.500 22.87 7.04 43.73 2.43
799 825 6.572989 GCTAATACGAAAGCTACGTGTACTAG 59.427 42.308 22.87 17.12 43.73 2.57
800 826 6.422223 GCTAATACGAAAGCTACGTGTACTA 58.578 40.000 22.87 10.12 43.73 1.82
801 827 5.269313 GCTAATACGAAAGCTACGTGTACT 58.731 41.667 22.87 9.63 43.73 2.73
803 829 4.498009 GGGCTAATACGAAAGCTACGTGTA 60.498 45.833 22.87 15.45 43.73 2.90
804 830 3.442100 GGCTAATACGAAAGCTACGTGT 58.558 45.455 22.87 16.27 43.73 4.49
811 1887 2.152016 GGGATGGGCTAATACGAAAGC 58.848 52.381 0.00 0.00 38.03 3.51
815 1891 2.358039 CCGGGATGGGCTAATACGA 58.642 57.895 0.00 0.00 0.00 3.43
891 2663 1.227089 CAGGGGAGAAGCATCGACG 60.227 63.158 0.00 0.00 0.00 5.12
892 2664 1.144936 CCAGGGGAGAAGCATCGAC 59.855 63.158 0.00 0.00 0.00 4.20
893 2665 2.735772 GCCAGGGGAGAAGCATCGA 61.736 63.158 0.00 0.00 0.00 3.59
894 2666 2.203126 GCCAGGGGAGAAGCATCG 60.203 66.667 0.00 0.00 0.00 3.84
925 3368 0.246635 TAACAGTCCTCTGGCTTCGC 59.753 55.000 0.47 0.00 45.14 4.70
945 3388 7.041916 CCGACGGCACCAAAGTATTAAATATTA 60.042 37.037 0.00 0.00 0.00 0.98
946 3389 6.238538 CCGACGGCACCAAAGTATTAAATATT 60.239 38.462 0.00 0.00 0.00 1.28
947 3390 5.237779 CCGACGGCACCAAAGTATTAAATAT 59.762 40.000 0.00 0.00 0.00 1.28
948 3391 4.571580 CCGACGGCACCAAAGTATTAAATA 59.428 41.667 0.00 0.00 0.00 1.40
949 3392 3.375922 CCGACGGCACCAAAGTATTAAAT 59.624 43.478 0.00 0.00 0.00 1.40
950 3393 2.743126 CCGACGGCACCAAAGTATTAAA 59.257 45.455 0.00 0.00 0.00 1.52
953 3396 2.849081 CCGACGGCACCAAAGTATT 58.151 52.632 0.00 0.00 0.00 1.89
954 3397 4.609995 CCGACGGCACCAAAGTAT 57.390 55.556 0.00 0.00 0.00 2.12
1023 3584 1.528586 GGCGTGCATAGTGCTATGAAG 59.471 52.381 19.89 11.82 45.31 3.02
1084 3657 0.035630 AGATGGTGCTTCTGTGGCTC 60.036 55.000 0.00 0.00 0.00 4.70
1875 4514 3.242712 CGTGGAAAGCACAATCAAACAAC 59.757 43.478 0.00 0.00 0.00 3.32
1898 7003 5.650543 CAAATATGTCCTGTAAACCAAGGC 58.349 41.667 0.00 0.00 0.00 4.35
1903 7008 4.705023 ACCTGCAAATATGTCCTGTAAACC 59.295 41.667 0.00 0.00 0.00 3.27
1963 7068 3.782244 GCGCACAAGCTCCGACAG 61.782 66.667 0.30 0.00 39.10 3.51
2000 7105 0.534203 TCGGACTTCTTGTTGTGCCC 60.534 55.000 0.00 0.00 0.00 5.36
2052 7157 3.239941 CGAGTTTAGCGAGGTCGTTATTG 59.760 47.826 0.69 0.00 42.22 1.90
2057 7162 0.167689 GTCGAGTTTAGCGAGGTCGT 59.832 55.000 0.69 0.00 42.22 4.34
2200 7305 4.264614 TCGAGAAATCGCGAAGACATTAAC 59.735 41.667 15.24 0.78 44.59 2.01
2250 7355 2.969628 ACCTCTCTGGCATAAACTCG 57.030 50.000 0.00 0.00 40.22 4.18
2258 7363 1.768275 TGTTCTCAAACCTCTCTGGCA 59.232 47.619 0.00 0.00 40.22 4.92
2279 7384 3.679502 GGAGCCATTGTAATTTGTGTTGC 59.320 43.478 0.00 0.00 0.00 4.17
2299 7404 5.568825 CGAAGGGAGTGAATTCAAAGTAGGA 60.569 44.000 10.35 0.00 0.00 2.94
2301 7406 5.786401 CGAAGGGAGTGAATTCAAAGTAG 57.214 43.478 10.35 0.00 0.00 2.57
2517 7622 1.331756 GACCGCATAGCATTGAACCAG 59.668 52.381 0.00 0.00 0.00 4.00
2594 7699 7.457024 TGACATCATTGACATGTTCTGAAAT 57.543 32.000 0.00 0.00 34.49 2.17
2601 7706 7.548967 TGCAATAATGACATCATTGACATGTT 58.451 30.769 14.48 0.00 45.34 2.71
2661 7766 3.501828 ACACGATGTTTGCAATGAGCTTA 59.498 39.130 0.00 0.00 45.94 3.09
2813 7922 9.737427 TGCGGTAATTAAATAATGGTAAATGTG 57.263 29.630 0.00 0.00 0.00 3.21
2814 7923 9.738832 GTGCGGTAATTAAATAATGGTAAATGT 57.261 29.630 0.00 0.00 0.00 2.71
2818 7927 7.516470 CGTCGTGCGGTAATTAAATAATGGTAA 60.516 37.037 0.00 0.00 36.85 2.85
2822 7931 5.613983 CACGTCGTGCGGTAATTAAATAATG 59.386 40.000 13.22 0.00 46.52 1.90
2838 7947 1.327460 CCATTCCATAAGCACGTCGTG 59.673 52.381 21.02 21.02 36.51 4.35
2839 7948 1.206132 TCCATTCCATAAGCACGTCGT 59.794 47.619 0.00 0.00 0.00 4.34
2840 7949 1.934589 TCCATTCCATAAGCACGTCG 58.065 50.000 0.00 0.00 0.00 5.12
2841 7950 4.900635 AAATCCATTCCATAAGCACGTC 57.099 40.909 0.00 0.00 0.00 4.34
2842 7951 6.959639 AATAAATCCATTCCATAAGCACGT 57.040 33.333 0.00 0.00 0.00 4.49
2843 7952 8.783093 TCTAAATAAATCCATTCCATAAGCACG 58.217 33.333 0.00 0.00 0.00 5.34
2900 8009 8.522003 TGAAAATTGCATAGAACACACACATAT 58.478 29.630 0.00 0.00 0.00 1.78
2901 8010 7.880105 TGAAAATTGCATAGAACACACACATA 58.120 30.769 0.00 0.00 0.00 2.29
2902 8011 6.747125 TGAAAATTGCATAGAACACACACAT 58.253 32.000 0.00 0.00 0.00 3.21
2903 8012 6.141560 TGAAAATTGCATAGAACACACACA 57.858 33.333 0.00 0.00 0.00 3.72
2904 8013 8.915871 ATATGAAAATTGCATAGAACACACAC 57.084 30.769 0.00 0.00 32.28 3.82
2905 8014 8.738106 TGATATGAAAATTGCATAGAACACACA 58.262 29.630 0.00 0.00 32.28 3.72
2906 8015 9.229784 CTGATATGAAAATTGCATAGAACACAC 57.770 33.333 0.00 0.00 32.28 3.82
2920 8029 8.512956 GCTGAGCATATTCACTGATATGAAAAT 58.487 33.333 0.00 0.00 41.78 1.82
2926 8035 6.356186 TGAGCTGAGCATATTCACTGATAT 57.644 37.500 7.39 0.00 0.00 1.63
2935 8044 7.092979 ACCACTGATATATGAGCTGAGCATATT 60.093 37.037 7.39 0.00 39.14 1.28
2997 8214 1.070914 GTCCTAAGATAGGTGCCCTGC 59.929 57.143 4.16 0.00 46.32 4.85
3007 8224 4.084287 AGTGTGTCGGTTGTCCTAAGATA 58.916 43.478 0.00 0.00 0.00 1.98
3012 8229 2.033372 TCAAGTGTGTCGGTTGTCCTA 58.967 47.619 0.00 0.00 0.00 2.94
3020 8237 9.181805 CTATTATATTACAGTCAAGTGTGTCGG 57.818 37.037 0.68 0.00 31.46 4.79
3156 8727 1.073125 TCCTCAGTCATCCCGCAAAAA 59.927 47.619 0.00 0.00 0.00 1.94
3157 8728 0.690192 TCCTCAGTCATCCCGCAAAA 59.310 50.000 0.00 0.00 0.00 2.44
3158 8729 0.250234 CTCCTCAGTCATCCCGCAAA 59.750 55.000 0.00 0.00 0.00 3.68
3159 8730 1.900351 CTCCTCAGTCATCCCGCAA 59.100 57.895 0.00 0.00 0.00 4.85
3160 8731 2.725312 GCTCCTCAGTCATCCCGCA 61.725 63.158 0.00 0.00 0.00 5.69
3161 8732 2.107953 GCTCCTCAGTCATCCCGC 59.892 66.667 0.00 0.00 0.00 6.13
3162 8733 0.467384 ATTGCTCCTCAGTCATCCCG 59.533 55.000 0.00 0.00 0.00 5.14
3163 8734 1.211457 ACATTGCTCCTCAGTCATCCC 59.789 52.381 0.00 0.00 0.00 3.85
3164 8735 2.681848 CAACATTGCTCCTCAGTCATCC 59.318 50.000 0.00 0.00 0.00 3.51
3165 8736 3.603532 TCAACATTGCTCCTCAGTCATC 58.396 45.455 0.00 0.00 0.00 2.92
3166 8737 3.708403 TCAACATTGCTCCTCAGTCAT 57.292 42.857 0.00 0.00 0.00 3.06
3167 8738 3.490439 TTCAACATTGCTCCTCAGTCA 57.510 42.857 0.00 0.00 0.00 3.41
3168 8739 3.817647 ACTTTCAACATTGCTCCTCAGTC 59.182 43.478 0.00 0.00 0.00 3.51
3169 8740 3.817647 GACTTTCAACATTGCTCCTCAGT 59.182 43.478 0.00 0.00 0.00 3.41
3178 8749 8.981724 ATGATCTTCATTGACTTTCAACATTG 57.018 30.769 0.00 0.00 39.45 2.82
3204 8780 6.208007 TCGACACAACTGAGAGGTAGATAAAA 59.792 38.462 0.00 0.00 0.00 1.52
3223 8799 5.753438 TCAGGAACATATATTGCTTCGACAC 59.247 40.000 0.00 0.00 0.00 3.67
3224 8800 5.912892 TCAGGAACATATATTGCTTCGACA 58.087 37.500 0.00 0.00 0.00 4.35
3230 8806 5.872963 TCATGCTCAGGAACATATATTGCT 58.127 37.500 0.00 0.00 0.00 3.91
3232 8808 7.974482 TTCTCATGCTCAGGAACATATATTG 57.026 36.000 0.00 0.00 0.00 1.90
3269 8845 3.432326 CCTGATAGTAACCTTGGGTGAGC 60.432 52.174 0.00 0.00 35.34 4.26
3271 8847 2.504175 GCCTGATAGTAACCTTGGGTGA 59.496 50.000 0.00 0.00 35.34 4.02
3275 8881 4.262249 GCTCTAGCCTGATAGTAACCTTGG 60.262 50.000 0.00 0.00 34.31 3.61
3276 8882 4.342378 TGCTCTAGCCTGATAGTAACCTTG 59.658 45.833 0.00 0.00 41.18 3.61
3277 8883 4.547671 TGCTCTAGCCTGATAGTAACCTT 58.452 43.478 0.00 0.00 41.18 3.50
3278 8884 4.186077 TGCTCTAGCCTGATAGTAACCT 57.814 45.455 0.00 0.00 41.18 3.50
3279 8885 4.939052 TTGCTCTAGCCTGATAGTAACC 57.061 45.455 0.00 0.00 41.18 2.85
3280 8886 5.908341 AGTTTGCTCTAGCCTGATAGTAAC 58.092 41.667 0.00 0.00 41.18 2.50
3281 8887 6.150396 GAGTTTGCTCTAGCCTGATAGTAA 57.850 41.667 0.00 0.00 41.18 2.24
3282 8888 5.776173 GAGTTTGCTCTAGCCTGATAGTA 57.224 43.478 0.00 0.00 41.18 1.82
3283 8889 4.664150 GAGTTTGCTCTAGCCTGATAGT 57.336 45.455 0.00 0.00 41.18 2.12
3325 8931 3.458579 CACTCGGCGTGACGTTCG 61.459 66.667 16.57 11.47 46.81 3.95
3341 8947 1.758936 AAATATGCAGCAGCTCAGCA 58.241 45.000 9.71 9.71 41.53 4.41
3376 8982 2.435234 ATCGGCGCGGCACTTTTA 60.435 55.556 32.60 10.18 0.00 1.52


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

AutoCloner maintained by Alex Coulton.