Multiple sequence alignment - TraesCS1B01G418900

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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 TraesCS1B01G418900 chr1B 100.000 4051 0 0 1 4051 642525977 642530027 0.000000e+00 7481
1 TraesCS1B01G418900 chr1B 85.724 1541 148 19 2539 4051 642620032 642621528 0.000000e+00 1561
2 TraesCS1B01G418900 chr1B 86.282 503 46 13 1829 2316 642617345 642617839 3.590000e-145 525
3 TraesCS1B01G418900 chr1B 84.559 544 56 17 844 1374 642636979 642637507 7.760000e-142 514
4 TraesCS1B01G418900 chr1B 79.467 750 105 27 13 759 413971503 413970800 1.690000e-133 486
5 TraesCS1B01G418900 chr1B 83.990 381 36 12 3686 4049 642545531 642545903 3.880000e-90 342
6 TraesCS1B01G418900 chr1B 81.768 362 32 17 1518 1845 642610123 642610484 5.160000e-69 272
7 TraesCS1B01G418900 chr1B 95.425 153 6 1 2312 2463 642619881 642620033 4.050000e-60 243
8 TraesCS1B01G418900 chr1A 91.888 1849 109 20 1735 3571 558131134 558132953 0.000000e+00 2545
9 TraesCS1B01G418900 chr1A 92.415 646 33 8 883 1523 558130314 558130948 0.000000e+00 907
10 TraesCS1B01G418900 chr1A 75.361 1039 188 41 2037 3053 558149121 558150113 4.810000e-119 438
11 TraesCS1B01G418900 chr1A 84.578 415 41 13 980 1384 558148121 558148522 1.370000e-104 390
12 TraesCS1B01G418900 chr1A 93.711 159 9 1 1504 1662 558130959 558131116 1.880000e-58 237
13 TraesCS1B01G418900 chr1D 84.709 981 121 19 2083 3053 465813098 465814059 0.000000e+00 953
14 TraesCS1B01G418900 chr1D 91.598 488 31 8 883 1368 465812028 465812507 0.000000e+00 665
15 TraesCS1B01G418900 chr1D 85.514 428 44 13 961 1377 465820813 465821233 8.040000e-117 431
16 TraesCS1B01G418900 chr1D 75.187 669 136 23 2039 2693 465821628 465822280 5.120000e-74 289
17 TraesCS1B01G418900 chr3B 81.673 753 119 12 7 746 429415127 429414381 3.460000e-170 608
18 TraesCS1B01G418900 chr3B 79.401 801 116 25 9 764 206427272 206428068 1.670000e-143 520
19 TraesCS1B01G418900 chr3B 83.333 300 42 7 8 305 463226491 463226784 1.860000e-68 270
20 TraesCS1B01G418900 chr3B 95.833 72 3 0 1011 1082 673098166 673098095 2.560000e-22 117
21 TraesCS1B01G418900 chr4D 81.596 777 97 22 12 764 13046201 13045447 5.790000e-168 601
22 TraesCS1B01G418900 chr4D 85.591 465 65 2 301 764 50458451 50458914 1.690000e-133 486
23 TraesCS1B01G418900 chr4D 92.771 83 4 2 1002 1082 477089471 477089389 7.110000e-23 119
24 TraesCS1B01G418900 chr2A 80.420 761 127 10 8 764 706881768 706881026 9.830000e-156 560
25 TraesCS1B01G418900 chr3A 83.667 600 89 7 1 593 23466323 23465726 1.270000e-154 556
26 TraesCS1B01G418900 chr3A 95.833 72 3 0 1011 1082 647499720 647499649 2.560000e-22 117
27 TraesCS1B01G418900 chr6D 80.000 770 118 23 7 770 460484179 460483440 1.660000e-148 536
28 TraesCS1B01G418900 chr5D 80.450 578 104 6 8 580 349998461 349999034 2.240000e-117 433
29 TraesCS1B01G418900 chr5A 78.466 678 125 17 1 661 25121070 25121743 1.350000e-114 424
30 TraesCS1B01G418900 chr3D 95.833 72 3 0 1011 1082 511444270 511444199 2.560000e-22 117


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 TraesCS1B01G418900 chr1B 642525977 642530027 4050 False 7481.000000 7481 100.000000 1 4051 1 chr1B.!!$F1 4050
1 TraesCS1B01G418900 chr1B 642617345 642621528 4183 False 776.333333 1561 89.143667 1829 4051 3 chr1B.!!$F5 2222
2 TraesCS1B01G418900 chr1B 642636979 642637507 528 False 514.000000 514 84.559000 844 1374 1 chr1B.!!$F4 530
3 TraesCS1B01G418900 chr1B 413970800 413971503 703 True 486.000000 486 79.467000 13 759 1 chr1B.!!$R1 746
4 TraesCS1B01G418900 chr1A 558130314 558132953 2639 False 1229.666667 2545 92.671333 883 3571 3 chr1A.!!$F1 2688
5 TraesCS1B01G418900 chr1A 558148121 558150113 1992 False 414.000000 438 79.969500 980 3053 2 chr1A.!!$F2 2073
6 TraesCS1B01G418900 chr1D 465812028 465814059 2031 False 809.000000 953 88.153500 883 3053 2 chr1D.!!$F1 2170
7 TraesCS1B01G418900 chr1D 465820813 465822280 1467 False 360.000000 431 80.350500 961 2693 2 chr1D.!!$F2 1732
8 TraesCS1B01G418900 chr3B 429414381 429415127 746 True 608.000000 608 81.673000 7 746 1 chr3B.!!$R1 739
9 TraesCS1B01G418900 chr3B 206427272 206428068 796 False 520.000000 520 79.401000 9 764 1 chr3B.!!$F1 755
10 TraesCS1B01G418900 chr4D 13045447 13046201 754 True 601.000000 601 81.596000 12 764 1 chr4D.!!$R1 752
11 TraesCS1B01G418900 chr2A 706881026 706881768 742 True 560.000000 560 80.420000 8 764 1 chr2A.!!$R1 756
12 TraesCS1B01G418900 chr3A 23465726 23466323 597 True 556.000000 556 83.667000 1 593 1 chr3A.!!$R1 592
13 TraesCS1B01G418900 chr6D 460483440 460484179 739 True 536.000000 536 80.000000 7 770 1 chr6D.!!$R1 763
14 TraesCS1B01G418900 chr5D 349998461 349999034 573 False 433.000000 433 80.450000 8 580 1 chr5D.!!$F1 572
15 TraesCS1B01G418900 chr5A 25121070 25121743 673 False 424.000000 424 78.466000 1 661 1 chr5A.!!$F1 660

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
959 1056 0.034756 ACACAAGTACAGCGGCATCA 59.965 50.0 1.45 0.0 0.0 3.07 F
1406 1537 0.524862 TCGACGGCTCAAAGGTAGTC 59.475 55.0 0.00 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2482 0.816018 TGGCCGTCACATCGTGTTTT 60.816 50.0 0.00 0.0 34.79 2.43 R
3111 5808 0.036875 GCCTCCACTTAAGCACCACT 59.963 55.0 1.29 0.0 0.00 4.00 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
74 75 2.895372 GACCGGCGGCATCGAAAT 60.895 61.111 28.71 2.71 39.00 2.17
100 105 0.331278 ATCCACATTTTCCTCCGCCA 59.669 50.000 0.00 0.00 0.00 5.69
124 129 4.093952 CGCCGCAGCCACTTTCTG 62.094 66.667 0.00 0.00 34.57 3.02
153 164 2.807107 CGCCTAGTAGCCATGCCCA 61.807 63.158 0.00 0.00 0.00 5.36
159 170 4.027173 TAGCCATGCCCACACGCA 62.027 61.111 0.00 0.00 44.35 5.24
180 194 2.904131 GGGTGAGGAGCTAGCCAC 59.096 66.667 12.13 12.04 34.66 5.01
209 223 3.518998 GAGTGCCGGCTCGAGCTA 61.519 66.667 34.46 17.08 41.70 3.32
281 298 3.476740 GGATGCAGTGGATCCGAAA 57.523 52.632 25.73 0.00 30.30 3.46
296 313 2.951457 CGAAAGGAGAAGAGGAGGAC 57.049 55.000 0.00 0.00 0.00 3.85
299 316 1.842052 AAGGAGAAGAGGAGGACGAC 58.158 55.000 0.00 0.00 0.00 4.34
328 369 0.831711 GAGGAGGAGGAGGAGGATGC 60.832 65.000 0.00 0.00 0.00 3.91
383 424 2.569059 CAACATGCCATCCTCGATTCT 58.431 47.619 0.00 0.00 0.00 2.40
390 431 0.038709 CATCCTCGATTCTCTCCGCC 60.039 60.000 0.00 0.00 0.00 6.13
499 567 1.002662 AGCAGGAGGAGGATGAGCA 59.997 57.895 0.00 0.00 0.00 4.26
523 591 3.528370 CTCCTACCTGCCCGTCCG 61.528 72.222 0.00 0.00 0.00 4.79
580 650 4.202441 ACGACGAAGATTAGCTAGGGTAA 58.798 43.478 0.00 0.00 0.00 2.85
617 705 7.944729 AGTATGTAGGATTTCTTTTGCATGT 57.055 32.000 0.00 0.00 0.00 3.21
619 707 8.462016 AGTATGTAGGATTTCTTTTGCATGTTC 58.538 33.333 0.00 0.00 0.00 3.18
621 709 7.288810 TGTAGGATTTCTTTTGCATGTTCTT 57.711 32.000 0.00 0.00 0.00 2.52
632 720 8.677300 TCTTTTGCATGTTCTTTATGGATCTAC 58.323 33.333 0.00 0.00 0.00 2.59
637 726 5.272283 TGTTCTTTATGGATCTACGGGTC 57.728 43.478 0.00 0.00 0.00 4.46
639 728 2.889045 TCTTTATGGATCTACGGGTCGG 59.111 50.000 0.00 0.00 0.00 4.79
640 729 2.369983 TTATGGATCTACGGGTCGGT 57.630 50.000 0.00 0.00 0.00 4.69
649 738 4.564782 TCTACGGGTCGGTATATGAGAT 57.435 45.455 0.00 0.00 0.00 2.75
732 821 4.302509 TCCGCGGGCGTTTGAAGA 62.303 61.111 27.83 0.00 37.81 2.87
750 839 1.808945 AGAGCCAGATTTGCAAAGTCG 59.191 47.619 18.19 7.68 37.67 4.18
764 853 0.905357 AAGTCGGGCTGTAGATGCTT 59.095 50.000 0.00 0.00 0.00 3.91
766 855 1.009829 GTCGGGCTGTAGATGCTTTG 58.990 55.000 0.00 0.00 0.00 2.77
770 859 1.740025 GGGCTGTAGATGCTTTGACAC 59.260 52.381 0.00 0.00 0.00 3.67
771 860 1.740025 GGCTGTAGATGCTTTGACACC 59.260 52.381 0.00 0.00 0.00 4.16
772 861 2.426522 GCTGTAGATGCTTTGACACCA 58.573 47.619 0.00 0.00 0.00 4.17
773 862 2.813754 GCTGTAGATGCTTTGACACCAA 59.186 45.455 0.00 0.00 0.00 3.67
774 863 3.365364 GCTGTAGATGCTTTGACACCAAC 60.365 47.826 0.00 0.00 30.88 3.77
775 864 3.814625 TGTAGATGCTTTGACACCAACA 58.185 40.909 0.00 0.00 30.88 3.33
776 865 4.203226 TGTAGATGCTTTGACACCAACAA 58.797 39.130 0.00 0.00 30.88 2.83
777 866 4.642437 TGTAGATGCTTTGACACCAACAAA 59.358 37.500 0.00 0.00 36.15 2.83
778 867 4.045636 AGATGCTTTGACACCAACAAAC 57.954 40.909 0.00 0.00 34.30 2.93
779 868 3.701040 AGATGCTTTGACACCAACAAACT 59.299 39.130 0.00 0.00 34.30 2.66
780 869 4.887071 AGATGCTTTGACACCAACAAACTA 59.113 37.500 0.00 0.00 34.30 2.24
781 870 4.364415 TGCTTTGACACCAACAAACTAC 57.636 40.909 0.00 0.00 34.30 2.73
782 871 3.759086 TGCTTTGACACCAACAAACTACA 59.241 39.130 0.00 0.00 34.30 2.74
783 872 4.218635 TGCTTTGACACCAACAAACTACAA 59.781 37.500 0.00 0.00 34.30 2.41
784 873 4.798387 GCTTTGACACCAACAAACTACAAG 59.202 41.667 0.00 0.00 34.30 3.16
785 874 5.392595 GCTTTGACACCAACAAACTACAAGA 60.393 40.000 0.00 0.00 34.30 3.02
786 875 5.811399 TTGACACCAACAAACTACAAGAG 57.189 39.130 0.00 0.00 0.00 2.85
787 876 3.625764 TGACACCAACAAACTACAAGAGC 59.374 43.478 0.00 0.00 0.00 4.09
788 877 3.616219 ACACCAACAAACTACAAGAGCA 58.384 40.909 0.00 0.00 0.00 4.26
789 878 4.013728 ACACCAACAAACTACAAGAGCAA 58.986 39.130 0.00 0.00 0.00 3.91
790 879 4.142469 ACACCAACAAACTACAAGAGCAAC 60.142 41.667 0.00 0.00 0.00 4.17
791 880 4.013728 ACCAACAAACTACAAGAGCAACA 58.986 39.130 0.00 0.00 0.00 3.33
792 881 4.461081 ACCAACAAACTACAAGAGCAACAA 59.539 37.500 0.00 0.00 0.00 2.83
793 882 5.127031 ACCAACAAACTACAAGAGCAACAAT 59.873 36.000 0.00 0.00 0.00 2.71
794 883 5.687285 CCAACAAACTACAAGAGCAACAATC 59.313 40.000 0.00 0.00 0.00 2.67
795 884 5.438761 ACAAACTACAAGAGCAACAATCC 57.561 39.130 0.00 0.00 0.00 3.01
796 885 4.887071 ACAAACTACAAGAGCAACAATCCA 59.113 37.500 0.00 0.00 0.00 3.41
797 886 5.359576 ACAAACTACAAGAGCAACAATCCAA 59.640 36.000 0.00 0.00 0.00 3.53
798 887 5.438761 AACTACAAGAGCAACAATCCAAC 57.561 39.130 0.00 0.00 0.00 3.77
799 888 4.718961 ACTACAAGAGCAACAATCCAACT 58.281 39.130 0.00 0.00 0.00 3.16
800 889 5.865085 ACTACAAGAGCAACAATCCAACTA 58.135 37.500 0.00 0.00 0.00 2.24
801 890 6.476378 ACTACAAGAGCAACAATCCAACTAT 58.524 36.000 0.00 0.00 0.00 2.12
802 891 5.886960 ACAAGAGCAACAATCCAACTATC 57.113 39.130 0.00 0.00 0.00 2.08
803 892 4.702131 ACAAGAGCAACAATCCAACTATCC 59.298 41.667 0.00 0.00 0.00 2.59
804 893 3.535561 AGAGCAACAATCCAACTATCCG 58.464 45.455 0.00 0.00 0.00 4.18
805 894 2.614057 GAGCAACAATCCAACTATCCGG 59.386 50.000 0.00 0.00 0.00 5.14
806 895 1.065551 GCAACAATCCAACTATCCGGC 59.934 52.381 0.00 0.00 0.00 6.13
807 896 1.676006 CAACAATCCAACTATCCGGCC 59.324 52.381 0.00 0.00 0.00 6.13
808 897 1.213296 ACAATCCAACTATCCGGCCT 58.787 50.000 0.00 0.00 0.00 5.19
809 898 1.134098 ACAATCCAACTATCCGGCCTG 60.134 52.381 0.00 0.00 0.00 4.85
810 899 0.179018 AATCCAACTATCCGGCCTGC 60.179 55.000 0.00 0.00 0.00 4.85
811 900 1.056700 ATCCAACTATCCGGCCTGCT 61.057 55.000 0.00 0.00 0.00 4.24
812 901 1.227674 CCAACTATCCGGCCTGCTC 60.228 63.158 0.00 0.00 0.00 4.26
813 902 1.690219 CCAACTATCCGGCCTGCTCT 61.690 60.000 0.00 0.00 0.00 4.09
814 903 1.040646 CAACTATCCGGCCTGCTCTA 58.959 55.000 0.00 0.00 0.00 2.43
815 904 1.620819 CAACTATCCGGCCTGCTCTAT 59.379 52.381 0.00 0.00 0.00 1.98
816 905 2.826128 CAACTATCCGGCCTGCTCTATA 59.174 50.000 0.00 0.00 0.00 1.31
817 906 2.448453 ACTATCCGGCCTGCTCTATAC 58.552 52.381 0.00 0.00 0.00 1.47
818 907 1.402259 CTATCCGGCCTGCTCTATACG 59.598 57.143 0.00 0.00 0.00 3.06
819 908 0.251209 ATCCGGCCTGCTCTATACGA 60.251 55.000 0.00 0.00 0.00 3.43
820 909 1.170919 TCCGGCCTGCTCTATACGAC 61.171 60.000 0.00 0.00 0.00 4.34
821 910 1.452953 CCGGCCTGCTCTATACGACA 61.453 60.000 0.00 0.00 0.00 4.35
822 911 0.384309 CGGCCTGCTCTATACGACAA 59.616 55.000 0.00 0.00 0.00 3.18
823 912 1.600663 CGGCCTGCTCTATACGACAAG 60.601 57.143 0.00 0.00 0.00 3.16
824 913 1.409427 GGCCTGCTCTATACGACAAGT 59.591 52.381 0.00 0.00 0.00 3.16
825 914 2.464865 GCCTGCTCTATACGACAAGTG 58.535 52.381 0.00 0.00 0.00 3.16
826 915 2.799917 GCCTGCTCTATACGACAAGTGG 60.800 54.545 0.00 0.00 0.00 4.00
827 916 2.464865 CTGCTCTATACGACAAGTGGC 58.535 52.381 0.00 0.00 0.00 5.01
828 917 2.099921 CTGCTCTATACGACAAGTGGCT 59.900 50.000 0.00 0.00 0.00 4.75
829 918 2.159240 TGCTCTATACGACAAGTGGCTG 60.159 50.000 0.00 0.00 0.00 4.85
830 919 2.799917 GCTCTATACGACAAGTGGCTGG 60.800 54.545 0.00 0.00 0.00 4.85
831 920 2.688446 CTCTATACGACAAGTGGCTGGA 59.312 50.000 0.00 0.00 0.00 3.86
832 921 3.296854 TCTATACGACAAGTGGCTGGAT 58.703 45.455 0.00 0.00 0.00 3.41
833 922 3.704566 TCTATACGACAAGTGGCTGGATT 59.295 43.478 0.00 0.00 0.00 3.01
834 923 4.891168 TCTATACGACAAGTGGCTGGATTA 59.109 41.667 0.00 0.00 0.00 1.75
835 924 4.689612 ATACGACAAGTGGCTGGATTAT 57.310 40.909 0.00 0.00 0.00 1.28
836 925 3.350219 ACGACAAGTGGCTGGATTATT 57.650 42.857 0.00 0.00 0.00 1.40
837 926 4.481368 ACGACAAGTGGCTGGATTATTA 57.519 40.909 0.00 0.00 0.00 0.98
838 927 4.442706 ACGACAAGTGGCTGGATTATTAG 58.557 43.478 0.00 0.00 0.00 1.73
839 928 4.081087 ACGACAAGTGGCTGGATTATTAGT 60.081 41.667 0.00 0.00 0.00 2.24
840 929 4.876107 CGACAAGTGGCTGGATTATTAGTT 59.124 41.667 0.00 0.00 0.00 2.24
841 930 5.354234 CGACAAGTGGCTGGATTATTAGTTT 59.646 40.000 0.00 0.00 0.00 2.66
842 931 6.537301 CGACAAGTGGCTGGATTATTAGTTTA 59.463 38.462 0.00 0.00 0.00 2.01
843 932 7.226720 CGACAAGTGGCTGGATTATTAGTTTAT 59.773 37.037 0.00 0.00 0.00 1.40
844 933 9.555727 GACAAGTGGCTGGATTATTAGTTTATA 57.444 33.333 0.00 0.00 0.00 0.98
870 959 3.044059 CTTGGCTTAGCACGGCAGC 62.044 63.158 6.53 0.19 38.23 5.25
875 964 1.790387 CTTAGCACGGCAGCAACTC 59.210 57.895 0.00 0.00 36.85 3.01
959 1056 0.034756 ACACAAGTACAGCGGCATCA 59.965 50.000 1.45 0.00 0.00 3.07
971 1068 0.867746 CGGCATCAATCATACACCCG 59.132 55.000 0.00 0.00 0.00 5.28
1082 1183 2.419574 GCAGCAAAGGAATAGGGTACGA 60.420 50.000 0.00 0.00 0.00 3.43
1098 1220 4.984785 GGGTACGAAATATACGTTTCCCTC 59.015 45.833 23.36 11.13 44.44 4.30
1100 1222 4.637483 ACGAAATATACGTTTCCCTCGA 57.363 40.909 13.61 0.00 41.18 4.04
1101 1223 4.604976 ACGAAATATACGTTTCCCTCGAG 58.395 43.478 5.13 5.13 41.18 4.04
1102 1224 3.424529 CGAAATATACGTTTCCCTCGAGC 59.575 47.826 6.99 0.00 35.23 5.03
1103 1225 4.618965 GAAATATACGTTTCCCTCGAGCT 58.381 43.478 6.99 0.00 33.10 4.09
1111 1233 3.001414 GTTTCCCTCGAGCTAGTTTTCC 58.999 50.000 6.99 0.00 0.00 3.13
1117 1239 1.343142 TCGAGCTAGTTTTCCAGTGCA 59.657 47.619 0.00 0.00 0.00 4.57
1325 1456 1.950484 GCGAGGGAAAAGCTCATGGAA 60.950 52.381 0.00 0.00 0.00 3.53
1333 1464 2.270352 AAGCTCATGGAAACGGTCAA 57.730 45.000 0.00 0.00 0.00 3.18
1404 1535 1.336517 TGTTCGACGGCTCAAAGGTAG 60.337 52.381 0.00 0.00 0.00 3.18
1406 1537 0.524862 TCGACGGCTCAAAGGTAGTC 59.475 55.000 0.00 0.00 0.00 2.59
1452 1685 3.430929 GGTCCGATCAATGAGTAAGTGCT 60.431 47.826 0.00 0.00 0.00 4.40
1453 1686 4.202121 GGTCCGATCAATGAGTAAGTGCTA 60.202 45.833 0.00 0.00 0.00 3.49
1475 1708 1.140052 AGGACCACGTCAAATCACACA 59.860 47.619 0.00 0.00 33.68 3.72
1553 1978 2.428890 CGACCTCTCCAAATGCTCTACT 59.571 50.000 0.00 0.00 0.00 2.57
1579 2009 8.325421 TCATTGTGCCGTTTCTTAAACTTATA 57.675 30.769 1.49 0.00 39.23 0.98
1623 2054 2.096013 GCACCGAATTAGTGGAGAAAGC 59.904 50.000 9.48 0.00 35.71 3.51
1668 2127 7.376072 GCTAAATACGGTCTTCACATAAAATGC 59.624 37.037 0.00 0.00 0.00 3.56
1671 2130 2.791158 CGGTCTTCACATAAAATGCGGC 60.791 50.000 0.00 0.00 0.00 6.53
1673 2132 3.171277 GTCTTCACATAAAATGCGGCAC 58.829 45.455 4.03 0.00 0.00 5.01
1674 2133 2.816672 TCTTCACATAAAATGCGGCACA 59.183 40.909 4.03 0.00 0.00 4.57
1675 2134 3.254411 TCTTCACATAAAATGCGGCACAA 59.746 39.130 4.03 0.00 0.00 3.33
1676 2135 3.865011 TCACATAAAATGCGGCACAAT 57.135 38.095 4.03 0.00 0.00 2.71
1677 2136 4.972514 TCACATAAAATGCGGCACAATA 57.027 36.364 4.03 0.00 0.00 1.90
1680 2139 4.503734 CACATAAAATGCGGCACAATAAGG 59.496 41.667 4.03 0.00 0.00 2.69
1681 2140 4.159506 ACATAAAATGCGGCACAATAAGGT 59.840 37.500 4.03 0.00 0.00 3.50
1682 2141 2.939460 AAATGCGGCACAATAAGGTC 57.061 45.000 4.03 0.00 0.00 3.85
1683 2142 2.128771 AATGCGGCACAATAAGGTCT 57.871 45.000 4.03 0.00 0.00 3.85
1684 2143 1.668419 ATGCGGCACAATAAGGTCTC 58.332 50.000 4.03 0.00 0.00 3.36
1687 2146 1.941325 CGGCACAATAAGGTCTCTCC 58.059 55.000 0.00 0.00 0.00 3.71
1688 2147 1.473434 CGGCACAATAAGGTCTCTCCC 60.473 57.143 0.00 0.00 36.75 4.30
1689 2148 1.134068 GGCACAATAAGGTCTCTCCCC 60.134 57.143 0.00 0.00 36.75 4.81
1690 2149 1.473434 GCACAATAAGGTCTCTCCCCG 60.473 57.143 0.00 0.00 36.75 5.73
1692 2151 1.831736 ACAATAAGGTCTCTCCCCGTG 59.168 52.381 0.00 0.00 36.75 4.94
1693 2152 0.831307 AATAAGGTCTCTCCCCGTGC 59.169 55.000 0.00 0.00 36.75 5.34
1696 2155 1.831652 AAGGTCTCTCCCCGTGCAAG 61.832 60.000 0.00 0.00 36.75 4.01
1697 2156 2.584391 GGTCTCTCCCCGTGCAAGT 61.584 63.158 0.00 0.00 0.00 3.16
1698 2157 1.255667 GGTCTCTCCCCGTGCAAGTA 61.256 60.000 0.00 0.00 0.00 2.24
1699 2158 0.824759 GTCTCTCCCCGTGCAAGTAT 59.175 55.000 0.00 0.00 0.00 2.12
1702 2161 0.535335 TCTCCCCGTGCAAGTATCAC 59.465 55.000 0.00 0.00 0.00 3.06
1712 2171 4.982999 GTGCAAGTATCACGAGAACTAGA 58.017 43.478 0.00 0.00 0.00 2.43
1713 2172 5.583495 GTGCAAGTATCACGAGAACTAGAT 58.417 41.667 0.00 0.00 0.00 1.98
1714 2173 5.683743 GTGCAAGTATCACGAGAACTAGATC 59.316 44.000 0.00 0.00 0.00 2.75
1715 2174 4.907010 GCAAGTATCACGAGAACTAGATCG 59.093 45.833 12.81 12.81 44.36 3.69
1725 2184 3.452474 AGAACTAGATCGTTGATGCTGC 58.548 45.455 0.00 0.00 0.00 5.25
1726 2185 1.845266 ACTAGATCGTTGATGCTGCG 58.155 50.000 0.00 0.00 0.00 5.18
1728 2187 0.875908 TAGATCGTTGATGCTGCGCC 60.876 55.000 4.18 0.00 0.00 6.53
1965 2492 5.432885 AAAACTGGACCTAAAACACGATG 57.567 39.130 0.00 0.00 0.00 3.84
1992 2526 3.253230 GCCAGAAAAACATGAAATCCGG 58.747 45.455 0.00 0.00 0.00 5.14
2351 5009 2.232298 CTCCTCCTCAACGCCTCCAC 62.232 65.000 0.00 0.00 0.00 4.02
2549 5213 4.396357 TTTCCCCTCAATATGTGTTGGT 57.604 40.909 0.00 0.00 0.00 3.67
2653 5317 3.676093 CTCCATCCATGATCATGACTGG 58.324 50.000 32.71 31.78 41.20 4.00
2879 5576 2.750166 TCAACGGCTTTTGTTGTTCTCA 59.250 40.909 5.83 0.00 45.33 3.27
2893 5590 5.939883 TGTTGTTCTCAATCCAACAGATAGG 59.060 40.000 0.00 0.00 42.41 2.57
2963 5660 3.241530 AAGCCAGTGGAGGTCGCA 61.242 61.111 15.20 0.00 0.00 5.10
2978 5675 1.671054 CGCATCGGTGGTGTCCTTT 60.671 57.895 0.00 0.00 0.00 3.11
3057 5754 5.635700 GGTCGATCTATTTGTTAGAGGATGC 59.364 44.000 0.00 0.00 40.27 3.91
3058 5755 6.216569 GTCGATCTATTTGTTAGAGGATGCA 58.783 40.000 0.00 0.00 40.27 3.96
3059 5756 6.870965 GTCGATCTATTTGTTAGAGGATGCAT 59.129 38.462 0.00 0.00 40.27 3.96
3060 5757 6.870439 TCGATCTATTTGTTAGAGGATGCATG 59.130 38.462 2.46 0.00 40.27 4.06
3206 5906 8.931775 GTTGAACAGTTTGGACTTTGTTTTATT 58.068 29.630 0.00 0.00 32.54 1.40
3233 5933 4.152402 GGTATGTAGCACTGTTGTGTCAAG 59.848 45.833 0.00 0.00 45.44 3.02
3254 5954 7.845622 GTCAAGCAATTATGTTGTTTGTTTGTC 59.154 33.333 16.16 3.37 40.35 3.18
3344 6044 3.914435 AGGGGCGGGTATGTATTAGAAAT 59.086 43.478 0.00 0.00 0.00 2.17
3364 6065 8.570068 AGAAATAAAACTAAAGGCGGTGATTA 57.430 30.769 0.00 0.00 0.00 1.75
3369 6070 5.410355 AACTAAAGGCGGTGATTAGTACA 57.590 39.130 0.00 0.00 38.55 2.90
3410 6113 6.743575 AAAGACATTGGAAGAGGTTATTCG 57.256 37.500 0.00 0.00 0.00 3.34
3437 6140 1.307355 CCGCATGCACTGTCCATGAA 61.307 55.000 19.57 0.00 41.97 2.57
3441 6144 2.029649 GCATGCACTGTCCATGAAACTT 60.030 45.455 15.65 0.00 41.97 2.66
3444 6147 4.829064 TGCACTGTCCATGAAACTTAAC 57.171 40.909 0.00 0.00 0.00 2.01
3459 6162 4.820894 ACTTAACGTGATTTCCCTAGCT 57.179 40.909 0.00 0.00 0.00 3.32
3464 6167 1.291132 GTGATTTCCCTAGCTGTCGC 58.709 55.000 0.00 0.00 0.00 5.19
3465 6168 0.179111 TGATTTCCCTAGCTGTCGCG 60.179 55.000 0.00 0.00 42.32 5.87
3489 6192 2.063266 GTTCCAAGTATTGTCGACGCA 58.937 47.619 11.62 0.00 46.99 5.24
3490 6193 2.665649 TCCAAGTATTGTCGACGCAT 57.334 45.000 11.62 8.14 46.99 4.73
3499 6202 1.225854 GTCGACGCATGCTTTGAGC 60.226 57.895 17.13 7.12 42.82 4.26
3505 6208 0.454600 CGCATGCTTTGAGCTGGAAT 59.545 50.000 17.13 0.00 42.97 3.01
3506 6209 1.672363 CGCATGCTTTGAGCTGGAATA 59.328 47.619 17.13 0.00 42.97 1.75
3519 6222 1.227853 GGAATATGGAACCGCCGCT 60.228 57.895 0.00 0.00 40.66 5.52
3522 6225 1.978455 AATATGGAACCGCCGCTGGA 61.978 55.000 8.04 0.00 40.66 3.86
3546 6249 3.485947 TGCATGAAAATCGCCTACAAC 57.514 42.857 0.00 0.00 0.00 3.32
3576 6279 4.445452 TTATACGACTGGAAGACACCAC 57.555 45.455 0.00 0.00 37.43 4.16
3580 6283 1.270839 CGACTGGAAGACACCACCAAT 60.271 52.381 0.00 0.00 37.43 3.16
3581 6284 2.154462 GACTGGAAGACACCACCAATG 58.846 52.381 0.00 0.00 37.43 2.82
3595 6298 1.474077 ACCAATGCAAAAGCTCGGATC 59.526 47.619 0.00 0.00 0.00 3.36
3599 6302 0.036732 TGCAAAAGCTCGGATCTGGT 59.963 50.000 0.62 0.00 0.00 4.00
3613 6316 4.097437 CGGATCTGGTGTTAACTAGCACTA 59.903 45.833 7.22 0.00 37.53 2.74
3617 6320 4.282449 TCTGGTGTTAACTAGCACTAGCAA 59.718 41.667 7.22 0.00 42.66 3.91
3618 6321 4.963373 TGGTGTTAACTAGCACTAGCAAA 58.037 39.130 7.22 0.00 45.49 3.68
3626 6329 4.601084 ACTAGCACTAGCAAAGGAGACTA 58.399 43.478 4.58 0.00 45.49 2.59
3629 6332 4.826556 AGCACTAGCAAAGGAGACTAAAG 58.173 43.478 0.00 0.00 45.49 1.85
3634 6337 2.816672 AGCAAAGGAGACTAAAGCAAGC 59.183 45.455 0.00 0.00 42.68 4.01
3638 6341 1.825474 AGGAGACTAAAGCAAGCGCTA 59.175 47.619 12.05 0.00 45.15 4.26
3654 6357 1.439679 GCTAACACCCTTTCTCCACG 58.560 55.000 0.00 0.00 0.00 4.94
3657 6360 0.108019 AACACCCTTTCTCCACGGTC 59.892 55.000 0.00 0.00 0.00 4.79
3658 6361 1.052124 ACACCCTTTCTCCACGGTCA 61.052 55.000 0.00 0.00 0.00 4.02
3681 6384 3.758554 CCATGACAGTAGAAAACAAGGGG 59.241 47.826 0.00 0.00 0.00 4.79
3683 6386 4.351874 TGACAGTAGAAAACAAGGGGAG 57.648 45.455 0.00 0.00 0.00 4.30
3692 6395 2.359975 CAAGGGGAGAACCACCGC 60.360 66.667 0.00 0.00 41.27 5.68
3708 6411 3.458163 GCGACACCCTCCGATCCA 61.458 66.667 0.00 0.00 0.00 3.41
3716 6419 1.995626 CCTCCGATCCACCCAACCT 60.996 63.158 0.00 0.00 0.00 3.50
3720 6423 2.438434 GATCCACCCAACCTGCCG 60.438 66.667 0.00 0.00 0.00 5.69
3732 6435 0.180406 ACCTGCCGTCAACTTCAACT 59.820 50.000 0.00 0.00 0.00 3.16
3743 6446 3.055094 TCAACTTCAACTCCTATCAGCCC 60.055 47.826 0.00 0.00 0.00 5.19
3749 6452 1.051812 ACTCCTATCAGCCCCAATCG 58.948 55.000 0.00 0.00 0.00 3.34
3752 6455 0.179020 CCTATCAGCCCCAATCGCAA 60.179 55.000 0.00 0.00 0.00 4.85
3753 6456 1.233019 CTATCAGCCCCAATCGCAAG 58.767 55.000 0.00 0.00 0.00 4.01
3754 6457 0.546122 TATCAGCCCCAATCGCAAGT 59.454 50.000 0.00 0.00 39.48 3.16
3768 6471 7.148239 CCCAATCGCAAGTAGTAGAAGAAAAAT 60.148 37.037 0.00 0.00 39.48 1.82
3773 6476 9.784680 TCGCAAGTAGTAGAAGAAAAATAGTAG 57.215 33.333 0.00 0.00 39.48 2.57
3812 6526 4.048470 GGACCAAGCCCACTCCCC 62.048 72.222 0.00 0.00 0.00 4.81
3813 6527 4.048470 GACCAAGCCCACTCCCCC 62.048 72.222 0.00 0.00 0.00 5.40
3831 6545 2.309504 CCCTCCCTCCACCCCTTTC 61.310 68.421 0.00 0.00 0.00 2.62
3845 6559 0.392998 CCTTTCTGGGGACATCACCG 60.393 60.000 0.00 0.00 44.25 4.94
3854 6568 1.541233 GGGACATCACCGCCATAAGAG 60.541 57.143 0.00 0.00 0.00 2.85
3867 6581 1.221781 CATAAGAGGGAGGGAGGGAGT 59.778 57.143 0.00 0.00 0.00 3.85
3868 6582 0.935194 TAAGAGGGAGGGAGGGAGTC 59.065 60.000 0.00 0.00 0.00 3.36
3895 6609 1.072930 AAAGGGGTGTGGAGGAGGT 60.073 57.895 0.00 0.00 0.00 3.85
3907 6621 2.869689 TGGAGGAGGTATTAGAAGGGGA 59.130 50.000 0.00 0.00 0.00 4.81
3911 6625 4.821940 AGGAGGTATTAGAAGGGGAAGAG 58.178 47.826 0.00 0.00 0.00 2.85
3929 6660 3.003763 ACGGGAGGAAGGCAGTCC 61.004 66.667 0.00 0.00 38.03 3.85
3930 6661 3.003173 CGGGAGGAAGGCAGTCCA 61.003 66.667 9.61 0.00 40.48 4.02
3935 6666 2.529632 GGAGGAAGGCAGTCCAAAAAT 58.470 47.619 9.61 0.00 40.48 1.82
3942 6673 4.112634 AGGCAGTCCAAAAATTCTGGTA 57.887 40.909 6.46 0.00 35.30 3.25
3947 6678 4.154195 CAGTCCAAAAATTCTGGTAGTCCG 59.846 45.833 6.46 0.00 35.30 4.79
3948 6679 3.078837 TCCAAAAATTCTGGTAGTCCGC 58.921 45.455 6.46 0.00 35.30 5.54
4000 6731 3.370104 ACTCTACTTGGGTCTCATCTGG 58.630 50.000 0.00 0.00 0.00 3.86
4005 6736 0.614697 TTGGGTCTCATCTGGCGAGA 60.615 55.000 0.00 0.00 37.18 4.04
4006 6737 0.397675 TGGGTCTCATCTGGCGAGAT 60.398 55.000 5.25 5.25 41.39 2.75
4008 6739 1.270041 GGGTCTCATCTGGCGAGATTC 60.270 57.143 8.71 0.72 41.39 2.52
4009 6740 1.686052 GGTCTCATCTGGCGAGATTCT 59.314 52.381 8.71 0.00 41.39 2.40
4010 6741 2.545532 GGTCTCATCTGGCGAGATTCTG 60.546 54.545 8.71 0.00 41.39 3.02
4016 6747 1.833630 TCTGGCGAGATTCTGACCAAT 59.166 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 4.771114 AATGTGGATGGTAGGATTTCGA 57.229 40.909 0.00 0.00 0.00 3.71
74 75 3.202151 GGAGGAAAATGTGGATGGTAGGA 59.798 47.826 0.00 0.00 0.00 2.94
113 118 2.759795 GGGGAGCAGAAAGTGGCT 59.240 61.111 0.00 0.00 44.48 4.75
159 170 2.443016 CTAGCTCCTCACCCGGCT 60.443 66.667 0.00 0.00 38.62 5.52
180 194 1.810030 GGCACTCCGGCGTTAGAAG 60.810 63.158 6.01 3.13 33.57 2.85
209 223 1.841302 TTGCCCGGATCTGCTCAAGT 61.841 55.000 0.73 0.00 0.00 3.16
281 298 0.393267 CGTCGTCCTCCTCTTCTCCT 60.393 60.000 0.00 0.00 0.00 3.69
283 300 1.011333 CTCGTCGTCCTCCTCTTCTC 58.989 60.000 0.00 0.00 0.00 2.87
287 304 1.222387 CTCCTCGTCGTCCTCCTCT 59.778 63.158 0.00 0.00 0.00 3.69
296 313 1.525077 CTCCTCCTCCTCCTCGTCG 60.525 68.421 0.00 0.00 0.00 5.12
299 316 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
328 369 4.842091 CGTCGCTAACGTCCCCCG 62.842 72.222 0.00 0.00 46.42 5.73
347 388 2.958281 TTGCTCCGCCTGCAGATCA 61.958 57.895 17.39 0.39 41.71 2.92
390 431 2.105128 CTCCGCAGCTAACTCCGG 59.895 66.667 0.00 0.00 41.97 5.14
397 438 2.407428 CGTCTGGTCTCCGCAGCTA 61.407 63.158 0.00 0.00 0.00 3.32
417 459 4.147449 CATCTCCTGCCGGCGACA 62.147 66.667 23.90 0.20 0.00 4.35
542 611 0.242825 TCGTCGGAGATGTTCACACC 59.757 55.000 0.00 0.00 45.22 4.16
597 683 6.899393 AGAACATGCAAAAGAAATCCTACA 57.101 33.333 0.00 0.00 0.00 2.74
598 684 9.860898 ATAAAGAACATGCAAAAGAAATCCTAC 57.139 29.630 0.00 0.00 0.00 3.18
617 705 3.319972 CCGACCCGTAGATCCATAAAGAA 59.680 47.826 0.00 0.00 0.00 2.52
619 707 2.626743 ACCGACCCGTAGATCCATAAAG 59.373 50.000 0.00 0.00 0.00 1.85
621 709 2.369983 ACCGACCCGTAGATCCATAA 57.630 50.000 0.00 0.00 0.00 1.90
632 720 5.589050 TCTGAATATCTCATATACCGACCCG 59.411 44.000 0.00 0.00 32.14 5.28
637 726 7.710896 TCTGCATCTGAATATCTCATATACCG 58.289 38.462 0.00 0.00 32.14 4.02
639 728 9.518906 CACTCTGCATCTGAATATCTCATATAC 57.481 37.037 0.00 0.00 32.14 1.47
640 729 9.471702 TCACTCTGCATCTGAATATCTCATATA 57.528 33.333 0.00 0.00 32.14 0.86
649 738 8.260114 TCAAATTAGTCACTCTGCATCTGAATA 58.740 33.333 0.00 0.00 0.00 1.75
732 821 0.883833 CCGACTTTGCAAATCTGGCT 59.116 50.000 13.23 0.00 0.00 4.75
750 839 1.740025 GTGTCAAAGCATCTACAGCCC 59.260 52.381 0.00 0.00 0.00 5.19
764 853 4.095782 GCTCTTGTAGTTTGTTGGTGTCAA 59.904 41.667 0.00 0.00 0.00 3.18
766 855 3.625764 TGCTCTTGTAGTTTGTTGGTGTC 59.374 43.478 0.00 0.00 0.00 3.67
770 859 4.630894 TGTTGCTCTTGTAGTTTGTTGG 57.369 40.909 0.00 0.00 0.00 3.77
771 860 5.687285 GGATTGTTGCTCTTGTAGTTTGTTG 59.313 40.000 0.00 0.00 0.00 3.33
772 861 5.359576 TGGATTGTTGCTCTTGTAGTTTGTT 59.640 36.000 0.00 0.00 0.00 2.83
773 862 4.887071 TGGATTGTTGCTCTTGTAGTTTGT 59.113 37.500 0.00 0.00 0.00 2.83
774 863 5.437289 TGGATTGTTGCTCTTGTAGTTTG 57.563 39.130 0.00 0.00 0.00 2.93
775 864 5.594317 AGTTGGATTGTTGCTCTTGTAGTTT 59.406 36.000 0.00 0.00 0.00 2.66
776 865 5.133221 AGTTGGATTGTTGCTCTTGTAGTT 58.867 37.500 0.00 0.00 0.00 2.24
777 866 4.718961 AGTTGGATTGTTGCTCTTGTAGT 58.281 39.130 0.00 0.00 0.00 2.73
778 867 6.037610 GGATAGTTGGATTGTTGCTCTTGTAG 59.962 42.308 0.00 0.00 0.00 2.74
779 868 5.880332 GGATAGTTGGATTGTTGCTCTTGTA 59.120 40.000 0.00 0.00 0.00 2.41
780 869 4.702131 GGATAGTTGGATTGTTGCTCTTGT 59.298 41.667 0.00 0.00 0.00 3.16
781 870 4.201851 CGGATAGTTGGATTGTTGCTCTTG 60.202 45.833 0.00 0.00 0.00 3.02
782 871 3.941483 CGGATAGTTGGATTGTTGCTCTT 59.059 43.478 0.00 0.00 0.00 2.85
783 872 3.535561 CGGATAGTTGGATTGTTGCTCT 58.464 45.455 0.00 0.00 0.00 4.09
784 873 2.614057 CCGGATAGTTGGATTGTTGCTC 59.386 50.000 0.00 0.00 0.00 4.26
785 874 2.643551 CCGGATAGTTGGATTGTTGCT 58.356 47.619 0.00 0.00 0.00 3.91
786 875 1.065551 GCCGGATAGTTGGATTGTTGC 59.934 52.381 5.05 0.00 0.00 4.17
787 876 1.676006 GGCCGGATAGTTGGATTGTTG 59.324 52.381 5.05 0.00 0.00 3.33
788 877 1.564348 AGGCCGGATAGTTGGATTGTT 59.436 47.619 5.05 0.00 0.00 2.83
789 878 1.134098 CAGGCCGGATAGTTGGATTGT 60.134 52.381 5.05 0.00 0.00 2.71
790 879 1.597742 CAGGCCGGATAGTTGGATTG 58.402 55.000 5.05 0.00 0.00 2.67
791 880 0.179018 GCAGGCCGGATAGTTGGATT 60.179 55.000 5.05 0.00 0.00 3.01
792 881 1.056700 AGCAGGCCGGATAGTTGGAT 61.057 55.000 5.05 0.00 0.00 3.41
793 882 1.686325 GAGCAGGCCGGATAGTTGGA 61.686 60.000 5.05 0.00 0.00 3.53
794 883 1.227674 GAGCAGGCCGGATAGTTGG 60.228 63.158 5.05 0.00 0.00 3.77
795 884 1.040646 TAGAGCAGGCCGGATAGTTG 58.959 55.000 5.05 0.00 0.00 3.16
796 885 2.016905 ATAGAGCAGGCCGGATAGTT 57.983 50.000 5.05 0.00 0.00 2.24
797 886 2.448453 GTATAGAGCAGGCCGGATAGT 58.552 52.381 5.05 0.00 0.00 2.12
798 887 1.402259 CGTATAGAGCAGGCCGGATAG 59.598 57.143 5.05 0.00 0.00 2.08
799 888 1.003928 TCGTATAGAGCAGGCCGGATA 59.996 52.381 5.05 0.00 0.00 2.59
800 889 0.251209 TCGTATAGAGCAGGCCGGAT 60.251 55.000 5.05 0.00 0.00 4.18
801 890 1.149854 TCGTATAGAGCAGGCCGGA 59.850 57.895 5.05 0.00 0.00 5.14
802 891 1.286260 GTCGTATAGAGCAGGCCGG 59.714 63.158 0.00 0.00 0.00 6.13
803 892 0.384309 TTGTCGTATAGAGCAGGCCG 59.616 55.000 0.00 0.00 0.00 6.13
804 893 1.409427 ACTTGTCGTATAGAGCAGGCC 59.591 52.381 0.00 0.00 0.00 5.19
805 894 2.464865 CACTTGTCGTATAGAGCAGGC 58.535 52.381 0.00 0.00 0.00 4.85
806 895 2.799917 GCCACTTGTCGTATAGAGCAGG 60.800 54.545 0.00 0.00 0.00 4.85
807 896 2.099921 AGCCACTTGTCGTATAGAGCAG 59.900 50.000 0.00 0.00 0.00 4.24
808 897 2.100197 AGCCACTTGTCGTATAGAGCA 58.900 47.619 0.00 0.00 0.00 4.26
809 898 2.464865 CAGCCACTTGTCGTATAGAGC 58.535 52.381 0.00 0.00 0.00 4.09
810 899 2.688446 TCCAGCCACTTGTCGTATAGAG 59.312 50.000 0.00 0.00 0.00 2.43
811 900 2.730382 TCCAGCCACTTGTCGTATAGA 58.270 47.619 0.00 0.00 0.00 1.98
812 901 3.735237 ATCCAGCCACTTGTCGTATAG 57.265 47.619 0.00 0.00 0.00 1.31
813 902 5.801531 ATAATCCAGCCACTTGTCGTATA 57.198 39.130 0.00 0.00 0.00 1.47
814 903 4.689612 ATAATCCAGCCACTTGTCGTAT 57.310 40.909 0.00 0.00 0.00 3.06
815 904 4.481368 AATAATCCAGCCACTTGTCGTA 57.519 40.909 0.00 0.00 0.00 3.43
816 905 3.350219 AATAATCCAGCCACTTGTCGT 57.650 42.857 0.00 0.00 0.00 4.34
817 906 4.442706 ACTAATAATCCAGCCACTTGTCG 58.557 43.478 0.00 0.00 0.00 4.35
818 907 6.759497 AAACTAATAATCCAGCCACTTGTC 57.241 37.500 0.00 0.00 0.00 3.18
837 926 9.627123 TGCTAAGCCAAGAAACATATATAAACT 57.373 29.630 0.00 0.00 0.00 2.66
838 927 9.665264 GTGCTAAGCCAAGAAACATATATAAAC 57.335 33.333 0.00 0.00 0.00 2.01
839 928 8.556194 CGTGCTAAGCCAAGAAACATATATAAA 58.444 33.333 0.00 0.00 0.00 1.40
840 929 7.172532 CCGTGCTAAGCCAAGAAACATATATAA 59.827 37.037 0.00 0.00 0.00 0.98
841 930 6.649141 CCGTGCTAAGCCAAGAAACATATATA 59.351 38.462 0.00 0.00 0.00 0.86
842 931 5.470098 CCGTGCTAAGCCAAGAAACATATAT 59.530 40.000 0.00 0.00 0.00 0.86
843 932 4.814234 CCGTGCTAAGCCAAGAAACATATA 59.186 41.667 0.00 0.00 0.00 0.86
844 933 3.627577 CCGTGCTAAGCCAAGAAACATAT 59.372 43.478 0.00 0.00 0.00 1.78
845 934 3.006940 CCGTGCTAAGCCAAGAAACATA 58.993 45.455 0.00 0.00 0.00 2.29
846 935 1.812571 CCGTGCTAAGCCAAGAAACAT 59.187 47.619 0.00 0.00 0.00 2.71
847 936 1.234821 CCGTGCTAAGCCAAGAAACA 58.765 50.000 0.00 0.00 0.00 2.83
848 937 0.109735 GCCGTGCTAAGCCAAGAAAC 60.110 55.000 0.00 0.00 0.00 2.78
849 938 0.536233 TGCCGTGCTAAGCCAAGAAA 60.536 50.000 0.00 0.00 0.00 2.52
858 947 2.027073 CGAGTTGCTGCCGTGCTAA 61.027 57.895 0.00 0.00 0.00 3.09
870 959 3.589988 AGAGGTAATGCAAGACGAGTTG 58.410 45.455 0.00 0.00 0.00 3.16
875 964 6.842163 ACAAATTAAGAGGTAATGCAAGACG 58.158 36.000 0.00 0.00 32.47 4.18
905 994 6.994421 TCCTCACATCTACATTGCCTATTA 57.006 37.500 0.00 0.00 0.00 0.98
906 995 5.894298 TCCTCACATCTACATTGCCTATT 57.106 39.130 0.00 0.00 0.00 1.73
907 996 6.183361 ACAATCCTCACATCTACATTGCCTAT 60.183 38.462 0.00 0.00 0.00 2.57
908 997 5.130975 ACAATCCTCACATCTACATTGCCTA 59.869 40.000 0.00 0.00 0.00 3.93
959 1056 2.612212 GCAACGAATCGGGTGTATGATT 59.388 45.455 7.80 0.00 37.52 2.57
989 1086 2.545952 CCCGTCGTCATATCTCCCTTTG 60.546 54.545 0.00 0.00 0.00 2.77
991 1088 1.329256 CCCGTCGTCATATCTCCCTT 58.671 55.000 0.00 0.00 0.00 3.95
993 1090 1.289380 GCCCGTCGTCATATCTCCC 59.711 63.158 0.00 0.00 0.00 4.30
1082 1183 4.667519 AGCTCGAGGGAAACGTATATTT 57.332 40.909 15.58 0.00 0.00 1.40
1098 1220 1.795768 TGCACTGGAAAACTAGCTCG 58.204 50.000 0.00 0.00 0.00 5.03
1100 1222 4.911390 AGTAATGCACTGGAAAACTAGCT 58.089 39.130 0.00 0.00 35.62 3.32
1101 1223 5.629079 AAGTAATGCACTGGAAAACTAGC 57.371 39.130 0.00 0.00 37.63 3.42
1102 1224 7.201444 CGAGTAAGTAATGCACTGGAAAACTAG 60.201 40.741 0.00 0.00 37.63 2.57
1103 1225 6.588756 CGAGTAAGTAATGCACTGGAAAACTA 59.411 38.462 0.00 0.00 37.63 2.24
1111 1233 3.487574 GCTAGCGAGTAAGTAATGCACTG 59.512 47.826 0.00 0.00 37.63 3.66
1117 1239 3.568853 ACGATGGCTAGCGAGTAAGTAAT 59.431 43.478 16.52 0.00 38.09 1.89
1149 1272 2.817834 GATGGCGCGCCTACACAA 60.818 61.111 45.79 28.70 36.94 3.33
1313 1444 2.270352 TGACCGTTTCCATGAGCTTT 57.730 45.000 0.00 0.00 0.00 3.51
1325 1456 3.064931 GTCGAAAGATTCCTTGACCGTT 58.935 45.455 0.00 0.00 45.19 4.44
1333 1464 1.726853 CTTGCCGTCGAAAGATTCCT 58.273 50.000 0.00 0.00 45.19 3.36
1404 1535 3.027974 ACTTTTCTAGTGGCGACTGAC 57.972 47.619 12.14 0.00 35.19 3.51
1406 1537 6.307155 CAAATAACTTTTCTAGTGGCGACTG 58.693 40.000 12.14 1.98 37.12 3.51
1452 1685 2.365941 TGTGATTTGACGTGGTCCTGTA 59.634 45.455 0.00 0.00 0.00 2.74
1453 1686 1.140052 TGTGATTTGACGTGGTCCTGT 59.860 47.619 0.00 0.00 0.00 4.00
1475 1708 5.581126 ATGTTGATAATTTGGATGCGTGT 57.419 34.783 0.00 0.00 0.00 4.49
1553 1978 5.508200 AGTTTAAGAAACGGCACAATGAA 57.492 34.783 0.00 0.00 45.88 2.57
1579 2009 5.358160 GCCACCTTAGCTAAAATCTGACAAT 59.642 40.000 7.74 0.00 0.00 2.71
1668 2127 1.473434 GGGAGAGACCTTATTGTGCCG 60.473 57.143 0.00 0.00 38.98 5.69
1671 2130 1.831736 ACGGGGAGAGACCTTATTGTG 59.168 52.381 0.00 0.00 38.98 3.33
1673 2132 1.473434 GCACGGGGAGAGACCTTATTG 60.473 57.143 0.00 0.00 38.98 1.90
1674 2133 0.831307 GCACGGGGAGAGACCTTATT 59.169 55.000 0.00 0.00 38.98 1.40
1675 2134 0.325296 TGCACGGGGAGAGACCTTAT 60.325 55.000 0.00 0.00 38.98 1.73
1676 2135 0.543410 TTGCACGGGGAGAGACCTTA 60.543 55.000 0.00 0.00 38.98 2.69
1677 2136 1.831652 CTTGCACGGGGAGAGACCTT 61.832 60.000 0.00 0.00 38.98 3.50
1680 2139 0.824759 ATACTTGCACGGGGAGAGAC 59.175 55.000 0.00 0.00 0.00 3.36
1681 2140 1.112113 GATACTTGCACGGGGAGAGA 58.888 55.000 0.00 0.00 0.00 3.10
1682 2141 0.824109 TGATACTTGCACGGGGAGAG 59.176 55.000 0.00 0.00 0.00 3.20
1683 2142 0.535335 GTGATACTTGCACGGGGAGA 59.465 55.000 0.00 0.00 0.00 3.71
1684 2143 3.065575 GTGATACTTGCACGGGGAG 57.934 57.895 0.00 0.00 0.00 4.30
1690 2149 4.982999 TCTAGTTCTCGTGATACTTGCAC 58.017 43.478 0.00 0.00 0.00 4.57
1692 2151 4.907010 CGATCTAGTTCTCGTGATACTTGC 59.093 45.833 7.34 0.00 0.00 4.01
1693 2152 6.050454 ACGATCTAGTTCTCGTGATACTTG 57.950 41.667 13.98 6.39 45.63 3.16
1696 2155 6.045698 TCAACGATCTAGTTCTCGTGATAC 57.954 41.667 14.99 0.00 46.59 2.24
1697 2156 6.659776 CATCAACGATCTAGTTCTCGTGATA 58.340 40.000 14.99 7.33 46.59 2.15
1698 2157 5.515184 CATCAACGATCTAGTTCTCGTGAT 58.485 41.667 14.99 15.15 46.59 3.06
1699 2158 4.730903 GCATCAACGATCTAGTTCTCGTGA 60.731 45.833 14.99 14.09 46.59 4.35
1702 2161 3.728221 CAGCATCAACGATCTAGTTCTCG 59.272 47.826 9.48 9.48 40.62 4.04
1703 2162 3.489047 GCAGCATCAACGATCTAGTTCTC 59.511 47.826 0.00 0.00 30.96 2.87
1705 2164 2.217393 CGCAGCATCAACGATCTAGTTC 59.783 50.000 0.00 0.00 30.96 3.01
1819 2334 6.403866 ACTTTTCAACTATTTGCACCATCA 57.596 33.333 0.00 0.00 32.17 3.07
1955 2482 0.816018 TGGCCGTCACATCGTGTTTT 60.816 50.000 0.00 0.00 34.79 2.43
1965 2492 1.606668 TCATGTTTTTCTGGCCGTCAC 59.393 47.619 0.00 0.00 0.00 3.67
1992 2526 1.019278 TCTCTCATGTTTTCGGCCGC 61.019 55.000 23.51 6.96 0.00 6.53
2001 2535 3.118956 CCTAAACCGAGCTCTCTCATGTT 60.119 47.826 12.85 2.87 39.30 2.71
2093 2699 9.628746 TGTTAAGAGGAAACTTTAAACAACAAC 57.371 29.630 0.00 0.00 44.43 3.32
2122 2728 3.697542 GCCCCTTGGTTGACGTATTTTAT 59.302 43.478 0.00 0.00 0.00 1.40
2123 2729 3.083293 GCCCCTTGGTTGACGTATTTTA 58.917 45.455 0.00 0.00 0.00 1.52
2351 5009 2.158900 ACAATACTTCCTCCTCCGCATG 60.159 50.000 0.00 0.00 0.00 4.06
2549 5213 3.084039 GTTCATTCCTCCTGCATGTGAA 58.916 45.455 0.00 0.00 0.00 3.18
2653 5317 4.548916 CGACACGTACATCTTTGATCATGC 60.549 45.833 0.00 0.00 0.00 4.06
2823 5515 8.694540 TGCTATTTTTGTATAAGTAGTACCCGA 58.305 33.333 0.00 0.00 0.00 5.14
2824 5516 8.876275 TGCTATTTTTGTATAAGTAGTACCCG 57.124 34.615 0.00 0.00 0.00 5.28
2879 5576 2.700897 CTCCGACCCTATCTGTTGGATT 59.299 50.000 0.03 0.00 43.68 3.01
2893 5590 4.779733 TCTCCAGGGCCTCCGACC 62.780 72.222 0.95 0.00 38.33 4.79
2941 5638 2.360852 CCTCCACTGGCTTGCCAG 60.361 66.667 32.66 32.66 42.90 4.85
2953 5650 3.770040 CCACCGATGCGACCTCCA 61.770 66.667 0.00 0.00 0.00 3.86
2963 5660 1.276421 CAGAGAAAGGACACCACCGAT 59.724 52.381 0.00 0.00 34.73 4.18
3058 5755 3.748083 ACATTAGAATCATGCTCGCCAT 58.252 40.909 0.00 0.00 33.39 4.40
3059 5756 3.198409 ACATTAGAATCATGCTCGCCA 57.802 42.857 0.00 0.00 0.00 5.69
3060 5757 3.304257 CCAACATTAGAATCATGCTCGCC 60.304 47.826 0.00 0.00 0.00 5.54
3111 5808 0.036875 GCCTCCACTTAAGCACCACT 59.963 55.000 1.29 0.00 0.00 4.00
3187 5887 7.390823 ACCACAAATAAAACAAAGTCCAAACT 58.609 30.769 0.00 0.00 37.32 2.66
3206 5906 3.812609 CACAACAGTGCTACATACCACAA 59.187 43.478 0.00 0.00 34.48 3.33
3233 5933 9.743937 CATATGACAAACAAACAACATAATTGC 57.256 29.630 0.00 0.00 0.00 3.56
3275 5975 8.909671 GCAACTGAATTAGAACTGAAATTCAAG 58.090 33.333 10.62 8.06 46.14 3.02
3318 6018 0.472471 ATACATACCCGCCCCTGTTG 59.528 55.000 0.00 0.00 0.00 3.33
3320 6020 1.975680 CTAATACATACCCGCCCCTGT 59.024 52.381 0.00 0.00 0.00 4.00
3344 6044 7.385267 TGTACTAATCACCGCCTTTAGTTTTA 58.615 34.615 0.00 0.00 37.37 1.52
3364 6065 2.561478 ACCGCAGATGGTTTTGTACT 57.439 45.000 0.00 0.00 39.99 2.73
3390 6093 4.201822 GCACGAATAACCTCTTCCAATGTC 60.202 45.833 0.00 0.00 0.00 3.06
3437 6140 4.935808 CAGCTAGGGAAATCACGTTAAGTT 59.064 41.667 0.00 0.00 0.00 2.66
3441 6144 3.428452 CGACAGCTAGGGAAATCACGTTA 60.428 47.826 0.00 0.00 0.00 3.18
3444 6147 1.560923 CGACAGCTAGGGAAATCACG 58.439 55.000 0.00 0.00 0.00 4.35
3459 6162 2.089887 TACTTGGAACAGCCGCGACA 62.090 55.000 8.23 0.00 42.39 4.35
3464 6167 1.393539 CGACAATACTTGGAACAGCCG 59.606 52.381 0.00 0.00 42.39 5.52
3465 6168 2.415512 GTCGACAATACTTGGAACAGCC 59.584 50.000 11.55 0.00 42.39 4.85
3481 6184 1.225854 GCTCAAAGCATGCGTCGAC 60.226 57.895 13.01 5.18 41.89 4.20
3489 6192 4.174704 TCCATATTCCAGCTCAAAGCAT 57.825 40.909 1.29 0.00 45.56 3.79
3490 6193 3.650281 TCCATATTCCAGCTCAAAGCA 57.350 42.857 1.29 0.00 45.56 3.91
3499 6202 1.507141 GCGGCGGTTCCATATTCCAG 61.507 60.000 9.78 0.00 34.01 3.86
3505 6208 3.078196 TCCAGCGGCGGTTCCATA 61.078 61.111 9.73 0.00 34.01 2.74
3506 6209 4.778143 GTCCAGCGGCGGTTCCAT 62.778 66.667 9.73 0.00 34.01 3.41
3519 6222 1.134753 GCGATTTTCATGCATGGTCCA 59.865 47.619 25.97 4.13 0.00 4.02
3522 6225 1.477553 AGGCGATTTTCATGCATGGT 58.522 45.000 25.97 10.29 0.00 3.55
3546 6249 3.624900 TCCAGTCGTATAAAATCGAGCG 58.375 45.455 0.00 0.00 36.76 5.03
3595 6298 4.188247 TGCTAGTGCTAGTTAACACCAG 57.812 45.455 8.61 3.13 40.48 4.00
3599 6302 5.245301 TCTCCTTTGCTAGTGCTAGTTAACA 59.755 40.000 8.61 0.00 40.48 2.41
3613 6316 2.816672 GCTTGCTTTAGTCTCCTTTGCT 59.183 45.455 0.00 0.00 0.00 3.91
3617 6320 1.443802 GCGCTTGCTTTAGTCTCCTT 58.556 50.000 0.00 0.00 35.07 3.36
3618 6321 3.145228 GCGCTTGCTTTAGTCTCCT 57.855 52.632 0.00 0.00 35.07 3.69
3629 6332 0.109735 GAAAGGGTGTTAGCGCTTGC 60.110 55.000 18.68 9.86 40.71 4.01
3634 6337 1.439679 GTGGAGAAAGGGTGTTAGCG 58.560 55.000 0.00 0.00 0.00 4.26
3638 6341 0.108019 GACCGTGGAGAAAGGGTGTT 59.892 55.000 0.00 0.00 38.41 3.32
3654 6357 4.385825 TGTTTTCTACTGTCATGGTGACC 58.614 43.478 7.55 0.00 46.40 4.02
3657 6360 4.216257 CCCTTGTTTTCTACTGTCATGGTG 59.784 45.833 0.00 0.00 0.00 4.17
3658 6361 4.398319 CCCTTGTTTTCTACTGTCATGGT 58.602 43.478 0.00 0.00 0.00 3.55
3668 6371 3.181437 GGTGGTTCTCCCCTTGTTTTCTA 60.181 47.826 0.00 0.00 0.00 2.10
3674 6377 3.157680 CGGTGGTTCTCCCCTTGT 58.842 61.111 0.00 0.00 0.00 3.16
3681 6384 2.737376 GGTGTCGCGGTGGTTCTC 60.737 66.667 6.13 0.00 0.00 2.87
3683 6386 4.309950 AGGGTGTCGCGGTGGTTC 62.310 66.667 6.13 0.00 0.00 3.62
3692 6395 2.494918 GTGGATCGGAGGGTGTCG 59.505 66.667 0.00 0.00 0.00 4.35
3694 6397 2.687566 GGGTGGATCGGAGGGTGT 60.688 66.667 0.00 0.00 0.00 4.16
3702 6405 2.438434 GGCAGGTTGGGTGGATCG 60.438 66.667 0.00 0.00 0.00 3.69
3708 6411 2.203294 GTTGACGGCAGGTTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
3716 6419 0.468226 AGGAGTTGAAGTTGACGGCA 59.532 50.000 0.00 0.00 0.00 5.69
3720 6423 3.935828 GGCTGATAGGAGTTGAAGTTGAC 59.064 47.826 0.00 0.00 0.00 3.18
3732 6435 1.053835 TGCGATTGGGGCTGATAGGA 61.054 55.000 0.00 0.00 0.00 2.94
3743 6446 6.721571 TTTTCTTCTACTACTTGCGATTGG 57.278 37.500 0.00 0.00 0.00 3.16
3768 6471 7.177184 TGTAGTGTCCACAATAGGTTCTACTA 58.823 38.462 0.00 0.00 33.33 1.82
3773 6476 4.504858 CCTGTAGTGTCCACAATAGGTTC 58.495 47.826 0.00 0.00 0.00 3.62
3780 6483 1.053424 GGTCCCTGTAGTGTCCACAA 58.947 55.000 0.00 0.00 0.00 3.33
3782 6485 1.002087 CTTGGTCCCTGTAGTGTCCAC 59.998 57.143 0.00 0.00 0.00 4.02
3812 6526 3.910646 AAAGGGGTGGAGGGAGGGG 62.911 68.421 0.00 0.00 0.00 4.79
3813 6527 2.204306 AAAGGGGTGGAGGGAGGG 60.204 66.667 0.00 0.00 0.00 4.30
3827 6541 1.026718 GCGGTGATGTCCCCAGAAAG 61.027 60.000 0.00 0.00 0.00 2.62
3828 6542 1.002624 GCGGTGATGTCCCCAGAAA 60.003 57.895 0.00 0.00 0.00 2.52
3831 6545 1.695114 TATGGCGGTGATGTCCCCAG 61.695 60.000 0.00 0.00 33.62 4.45
3836 6550 1.541233 CCCTCTTATGGCGGTGATGTC 60.541 57.143 0.00 0.00 0.00 3.06
3838 6552 0.758734 TCCCTCTTATGGCGGTGATG 59.241 55.000 0.00 0.00 0.00 3.07
3839 6553 1.051812 CTCCCTCTTATGGCGGTGAT 58.948 55.000 0.00 0.00 0.00 3.06
3840 6554 1.048724 CCTCCCTCTTATGGCGGTGA 61.049 60.000 0.00 0.00 0.00 4.02
3841 6555 1.447643 CCTCCCTCTTATGGCGGTG 59.552 63.158 0.00 0.00 0.00 4.94
3842 6556 1.766461 CCCTCCCTCTTATGGCGGT 60.766 63.158 0.00 0.00 0.00 5.68
3845 6559 1.130678 CCCTCCCTCCCTCTTATGGC 61.131 65.000 0.00 0.00 0.00 4.40
3854 6568 4.862823 CCGGACTCCCTCCCTCCC 62.863 77.778 0.00 0.00 35.21 4.30
3870 6584 2.983592 CACACCCCTTTCACCGCC 60.984 66.667 0.00 0.00 0.00 6.13
3871 6585 2.983592 CCACACCCCTTTCACCGC 60.984 66.667 0.00 0.00 0.00 5.68
3876 6590 1.134438 ACCTCCTCCACACCCCTTTC 61.134 60.000 0.00 0.00 0.00 2.62
3895 6609 3.205959 TCCCGTCTCTTCCCCTTCTAATA 59.794 47.826 0.00 0.00 0.00 0.98
3907 6621 1.229209 TGCCTTCCTCCCGTCTCTT 60.229 57.895 0.00 0.00 0.00 2.85
3911 6625 2.579738 GACTGCCTTCCTCCCGTC 59.420 66.667 0.00 0.00 0.00 4.79
3929 6660 4.497473 TTGCGGACTACCAGAATTTTTG 57.503 40.909 0.00 0.00 35.59 2.44
3930 6661 4.825085 TCTTTGCGGACTACCAGAATTTTT 59.175 37.500 0.00 0.00 35.59 1.94
3935 6666 3.135994 GTTTCTTTGCGGACTACCAGAA 58.864 45.455 0.00 0.00 35.59 3.02
3942 6673 5.411669 CACTAATAAGGTTTCTTTGCGGACT 59.588 40.000 0.00 0.00 34.59 3.85
3947 6678 7.041372 TGTGTCTCACTAATAAGGTTTCTTTGC 60.041 37.037 1.72 0.00 35.11 3.68
3948 6679 8.378172 TGTGTCTCACTAATAAGGTTTCTTTG 57.622 34.615 1.72 0.00 35.11 2.77
4000 6731 2.421424 AGCAAATTGGTCAGAATCTCGC 59.579 45.455 0.00 0.00 0.00 5.03
4006 6737 9.241919 TCAGAAATAATAGCAAATTGGTCAGAA 57.758 29.630 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.