Multiple sequence alignment - TraesCS7B01G223100

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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 TraesCS7B01G223100 chr7B 100.000 4614 0 0 1 4614 419039096 419034483 0.000000e+00 8521.0
1 TraesCS7B01G223100 chr7A 93.827 3758 157 34 888 4614 466249893 466246180 0.000000e+00 5585.0
2 TraesCS7B01G223100 chr7A 90.687 451 15 9 1 428 466250687 466250241 4.000000e-160 575.0
3 TraesCS7B01G223100 chr7A 83.442 308 15 15 416 721 466250220 466249947 2.130000e-63 254.0
4 TraesCS7B01G223100 chr7D 92.086 2363 116 30 894 3217 407852368 407850038 0.000000e+00 3262.0
5 TraesCS7B01G223100 chr7D 95.187 1309 45 8 3317 4614 407849989 407848688 0.000000e+00 2052.0
6 TraesCS7B01G223100 chr7D 91.295 448 14 9 1 428 407853169 407852727 5.140000e-164 588.0
7 TraesCS7B01G223100 chr7D 89.744 195 10 5 529 721 407852620 407852434 1.660000e-59 241.0
8 TraesCS7B01G223100 chr6A 92.037 427 30 4 3976 4400 265993261 265993685 8.540000e-167 597.0
9 TraesCS7B01G223100 chr6A 92.233 103 8 0 4405 4507 265993777 265993879 3.720000e-31 147.0
10 TraesCS7B01G223100 chr6A 85.000 120 11 5 765 884 617147108 617146996 1.050000e-21 115.0
11 TraesCS7B01G223100 chr6B 88.000 125 10 4 764 885 539622085 539621963 4.810000e-30 143.0
12 TraesCS7B01G223100 chr2B 93.103 87 5 1 800 885 777562207 777562121 4.850000e-25 126.0
13 TraesCS7B01G223100 chr1D 84.211 133 11 8 764 886 462076150 462076018 2.250000e-23 121.0
14 TraesCS7B01G223100 chr1B 82.443 131 17 4 764 891 642611948 642612075 4.880000e-20 110.0
15 TraesCS7B01G223100 chrUn 83.200 125 13 7 764 884 43344522 43344642 1.760000e-19 108.0
16 TraesCS7B01G223100 chr5B 83.200 125 13 7 764 884 387095989 387095869 1.760000e-19 108.0
17 TraesCS7B01G223100 chr3A 83.065 124 15 4 764 884 657753944 657754064 1.760000e-19 108.0
18 TraesCS7B01G223100 chr3A 82.308 130 15 5 764 889 500740928 500740803 6.310000e-19 106.0
19 TraesCS7B01G223100 chr3B 93.478 46 3 0 616 661 122823337 122823292 8.280000e-08 69.4


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 TraesCS7B01G223100 chr7B 419034483 419039096 4613 True 8521.00 8521 100.000000 1 4614 1 chr7B.!!$R1 4613
1 TraesCS7B01G223100 chr7A 466246180 466250687 4507 True 2138.00 5585 89.318667 1 4614 3 chr7A.!!$R1 4613
2 TraesCS7B01G223100 chr7D 407848688 407853169 4481 True 1535.75 3262 92.078000 1 4614 4 chr7D.!!$R1 4613
3 TraesCS7B01G223100 chr6A 265993261 265993879 618 False 372.00 597 92.135000 3976 4507 2 chr6A.!!$F1 531

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
522 579 0.318441 CCGACATCAGCATCCGGTAT 59.682 55.0 0.00 0.0 35.83 2.73 F
1525 1621 0.329261 CAGCTCCCATGGGTGAAGAA 59.671 55.0 32.49 12.0 34.56 2.52 F
3036 3150 0.036010 GTGGGAGAGGTGTGGATGTG 60.036 60.0 0.00 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 2606 0.029834 CATGCCTCAAAGCGCCATAC 59.970 55.000 2.29 0.0 34.65 2.39 R
3090 3204 1.134670 ACAGCTTTACCTCCATCTCGC 60.135 52.381 0.00 0.0 0.00 5.03 R
3881 4006 2.354199 GCTAGCTGAGGATTCTTTGTGC 59.646 50.000 7.70 0.0 0.00 4.57 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
156 157 3.035363 TGCCGAGGGATTGTACAGATTA 58.965 45.455 0.00 0.00 0.00 1.75
162 163 6.439599 CGAGGGATTGTACAGATTACTACAG 58.560 44.000 0.00 0.00 0.00 2.74
175 176 7.121911 CAGATTACTACAGCATTCGTCAATTG 58.878 38.462 0.00 0.00 0.00 2.32
190 191 4.606961 GTCAATTGTTGGTTTCATCGTGT 58.393 39.130 5.13 0.00 0.00 4.49
197 202 6.415798 TGTTGGTTTCATCGTGTGTATATG 57.584 37.500 0.00 0.00 0.00 1.78
261 282 2.948315 GACAATCATTCTTGGAGGCCTC 59.052 50.000 25.59 25.59 0.00 4.70
288 309 5.222844 TGGATGGATATAGGAGGATTGGACT 60.223 44.000 0.00 0.00 0.00 3.85
313 337 0.389391 AGACAGACAGACACGGGTTG 59.611 55.000 0.00 0.00 0.00 3.77
378 402 4.091945 ACGATTGATTGTCTCGTGTCATTG 59.908 41.667 0.00 0.00 43.40 2.82
398 422 7.953173 GTCATTGTGTTGATTAATTTGCACATG 59.047 33.333 15.58 14.87 36.84 3.21
405 429 7.660617 TGTTGATTAATTTGCACATGTCCAATT 59.339 29.630 2.35 7.24 0.00 2.32
414 438 3.184986 GCACATGTCCAATTGTTTCAAGC 59.815 43.478 4.43 3.88 0.00 4.01
421 478 4.059511 TCCAATTGTTTCAAGCAATGCTG 58.940 39.130 9.14 3.28 39.62 4.41
445 502 2.870411 ACTTGTCGTTGAGTTACTTGGC 59.130 45.455 0.00 0.00 0.00 4.52
449 506 2.475487 GTCGTTGAGTTACTTGGCACTC 59.525 50.000 0.00 0.00 40.03 3.51
465 522 0.908198 ACTCCCTTTAGCAGCCTCTG 59.092 55.000 0.00 0.00 34.12 3.35
479 536 3.613737 CAGCCTCTGTGTTTGTTTGTTTG 59.386 43.478 0.00 0.00 0.00 2.93
480 537 3.258123 AGCCTCTGTGTTTGTTTGTTTGT 59.742 39.130 0.00 0.00 0.00 2.83
481 538 3.993736 GCCTCTGTGTTTGTTTGTTTGTT 59.006 39.130 0.00 0.00 0.00 2.83
482 539 4.450757 GCCTCTGTGTTTGTTTGTTTGTTT 59.549 37.500 0.00 0.00 0.00 2.83
483 540 5.635700 GCCTCTGTGTTTGTTTGTTTGTTTA 59.364 36.000 0.00 0.00 0.00 2.01
484 541 6.183360 GCCTCTGTGTTTGTTTGTTTGTTTAG 60.183 38.462 0.00 0.00 0.00 1.85
485 542 6.866248 CCTCTGTGTTTGTTTGTTTGTTTAGT 59.134 34.615 0.00 0.00 0.00 2.24
486 543 7.148820 CCTCTGTGTTTGTTTGTTTGTTTAGTG 60.149 37.037 0.00 0.00 0.00 2.74
487 544 7.426410 TCTGTGTTTGTTTGTTTGTTTAGTGA 58.574 30.769 0.00 0.00 0.00 3.41
488 545 8.085296 TCTGTGTTTGTTTGTTTGTTTAGTGAT 58.915 29.630 0.00 0.00 0.00 3.06
489 546 8.012151 TGTGTTTGTTTGTTTGTTTAGTGATG 57.988 30.769 0.00 0.00 0.00 3.07
490 547 7.867909 TGTGTTTGTTTGTTTGTTTAGTGATGA 59.132 29.630 0.00 0.00 0.00 2.92
491 548 8.868916 GTGTTTGTTTGTTTGTTTAGTGATGAT 58.131 29.630 0.00 0.00 0.00 2.45
511 568 3.033368 TGATGAAAACGACCGACATCA 57.967 42.857 0.00 0.00 42.85 3.07
512 569 2.993220 TGATGAAAACGACCGACATCAG 59.007 45.455 0.00 0.00 41.12 2.90
520 577 2.501128 CCGACATCAGCATCCGGT 59.499 61.111 0.00 0.00 35.83 5.28
521 578 1.739667 CCGACATCAGCATCCGGTA 59.260 57.895 0.00 0.00 35.83 4.02
522 579 0.318441 CCGACATCAGCATCCGGTAT 59.682 55.000 0.00 0.00 35.83 2.73
523 580 1.670087 CCGACATCAGCATCCGGTATC 60.670 57.143 0.00 0.00 35.83 2.24
524 581 1.000274 CGACATCAGCATCCGGTATCA 60.000 52.381 0.00 0.00 0.00 2.15
525 582 2.545742 CGACATCAGCATCCGGTATCAA 60.546 50.000 0.00 0.00 0.00 2.57
526 583 3.668447 GACATCAGCATCCGGTATCAAT 58.332 45.455 0.00 0.00 0.00 2.57
527 584 4.067896 GACATCAGCATCCGGTATCAATT 58.932 43.478 0.00 0.00 0.00 2.32
528 585 3.817084 ACATCAGCATCCGGTATCAATTG 59.183 43.478 0.00 0.00 0.00 2.32
529 586 3.558931 TCAGCATCCGGTATCAATTGT 57.441 42.857 5.13 0.00 0.00 2.71
530 587 3.466836 TCAGCATCCGGTATCAATTGTC 58.533 45.455 5.13 0.00 0.00 3.18
531 588 3.118445 TCAGCATCCGGTATCAATTGTCA 60.118 43.478 5.13 0.00 0.00 3.58
532 589 3.817084 CAGCATCCGGTATCAATTGTCAT 59.183 43.478 5.13 0.00 0.00 3.06
533 590 4.067896 AGCATCCGGTATCAATTGTCATC 58.932 43.478 5.13 0.00 0.00 2.92
534 591 3.189287 GCATCCGGTATCAATTGTCATCC 59.811 47.826 5.13 3.89 0.00 3.51
535 592 4.388485 CATCCGGTATCAATTGTCATCCA 58.612 43.478 5.13 0.00 0.00 3.41
590 647 5.109662 TCTCCGAGAATAAACTATGAGCG 57.890 43.478 0.00 0.00 0.00 5.03
614 671 1.200948 GTTGCCTTCCTGTTGAGCATC 59.799 52.381 0.00 0.00 32.67 3.91
623 681 1.391485 CTGTTGAGCATCGGTCTTTCG 59.609 52.381 0.00 0.00 38.61 3.46
631 689 2.159517 GCATCGGTCTTTCGATTTGCTT 60.160 45.455 0.00 0.00 46.23 3.91
683 741 4.989279 AGCAGTTGAAGAAACATGTGTT 57.011 36.364 0.00 0.00 41.61 3.32
684 742 6.765989 AGTAGCAGTTGAAGAAACATGTGTTA 59.234 34.615 0.00 0.00 41.61 2.41
685 743 6.064846 AGCAGTTGAAGAAACATGTGTTAG 57.935 37.500 0.00 0.00 41.61 2.34
687 745 6.318648 AGCAGTTGAAGAAACATGTGTTAGAA 59.681 34.615 0.00 0.00 41.61 2.10
688 746 6.972328 GCAGTTGAAGAAACATGTGTTAGAAA 59.028 34.615 0.00 0.00 41.61 2.52
689 747 7.044052 GCAGTTGAAGAAACATGTGTTAGAAAC 60.044 37.037 0.00 1.42 41.61 2.78
690 748 7.967854 CAGTTGAAGAAACATGTGTTAGAAACA 59.032 33.333 0.00 0.00 41.61 2.83
691 749 8.519526 AGTTGAAGAAACATGTGTTAGAAACAA 58.480 29.630 0.00 0.00 41.36 2.83
692 750 9.134734 GTTGAAGAAACATGTGTTAGAAACAAA 57.865 29.630 0.00 0.00 39.84 2.83
693 751 8.909708 TGAAGAAACATGTGTTAGAAACAAAG 57.090 30.769 0.00 0.00 44.16 2.77
708 766 6.037098 AGAAACAAAGAGTCCTAATCGATCG 58.963 40.000 9.36 9.36 0.00 3.69
723 790 0.594110 GATCGGATCGGTCCTCTGAC 59.406 60.000 14.05 0.00 42.73 3.51
770 837 6.986904 ATTTAACTGAAAAGATCTCCGTCC 57.013 37.500 0.00 0.00 0.00 4.79
771 838 5.477607 TTAACTGAAAAGATCTCCGTCCA 57.522 39.130 0.00 0.00 0.00 4.02
773 840 4.351874 ACTGAAAAGATCTCCGTCCAAA 57.648 40.909 0.00 0.00 0.00 3.28
774 841 4.714632 ACTGAAAAGATCTCCGTCCAAAA 58.285 39.130 0.00 0.00 0.00 2.44
777 844 6.940298 ACTGAAAAGATCTCCGTCCAAAAATA 59.060 34.615 0.00 0.00 0.00 1.40
778 845 7.094762 ACTGAAAAGATCTCCGTCCAAAAATAC 60.095 37.037 0.00 0.00 0.00 1.89
779 846 6.940298 TGAAAAGATCTCCGTCCAAAAATACT 59.060 34.615 0.00 0.00 0.00 2.12
780 847 7.447238 TGAAAAGATCTCCGTCCAAAAATACTT 59.553 33.333 0.00 0.00 0.00 2.24
781 848 6.743575 AAGATCTCCGTCCAAAAATACTTG 57.256 37.500 0.00 0.00 0.00 3.16
782 849 5.805728 AGATCTCCGTCCAAAAATACTTGT 58.194 37.500 0.00 0.00 0.00 3.16
783 850 5.875359 AGATCTCCGTCCAAAAATACTTGTC 59.125 40.000 0.00 0.00 0.00 3.18
784 851 4.963373 TCTCCGTCCAAAAATACTTGTCA 58.037 39.130 0.00 0.00 0.00 3.58
785 852 5.556915 TCTCCGTCCAAAAATACTTGTCAT 58.443 37.500 0.00 0.00 0.00 3.06
786 853 5.642063 TCTCCGTCCAAAAATACTTGTCATC 59.358 40.000 0.00 0.00 0.00 2.92
787 854 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
788 855 5.765677 TCCGTCCAAAAATACTTGTCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
789 856 6.263392 TCCGTCCAAAAATACTTGTCATCAAA 59.737 34.615 0.00 0.00 32.87 2.69
790 857 6.920758 CCGTCCAAAAATACTTGTCATCAAAA 59.079 34.615 0.00 0.00 32.87 2.44
791 858 7.598493 CCGTCCAAAAATACTTGTCATCAAAAT 59.402 33.333 0.00 0.00 32.87 1.82
792 859 8.427012 CGTCCAAAAATACTTGTCATCAAAATG 58.573 33.333 0.00 0.00 32.87 2.32
793 860 8.711457 GTCCAAAAATACTTGTCATCAAAATGG 58.289 33.333 0.00 0.00 33.42 3.16
794 861 8.646004 TCCAAAAATACTTGTCATCAAAATGGA 58.354 29.630 0.00 0.00 33.42 3.41
795 862 8.711457 CCAAAAATACTTGTCATCAAAATGGAC 58.289 33.333 0.00 0.00 33.42 4.02
796 863 9.258826 CAAAAATACTTGTCATCAAAATGGACA 57.741 29.630 0.00 0.00 33.42 4.02
797 864 9.829507 AAAAATACTTGTCATCAAAATGGACAA 57.170 25.926 0.00 0.00 34.59 3.18
798 865 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
799 866 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
800 867 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
824 891 9.829507 AAAAATACTTGTCATCAAAATGGACAA 57.170 25.926 0.00 0.00 34.59 3.18
825 892 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
826 893 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
827 894 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
828 895 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
829 896 7.555087 ACTTGTCATCAAAATGGACAAAAAGA 58.445 30.769 7.70 0.00 34.98 2.52
830 897 7.707893 ACTTGTCATCAAAATGGACAAAAAGAG 59.292 33.333 7.70 0.00 34.98 2.85
831 898 7.345422 TGTCATCAAAATGGACAAAAAGAGA 57.655 32.000 0.00 0.00 33.42 3.10
832 899 7.954835 TGTCATCAAAATGGACAAAAAGAGAT 58.045 30.769 0.00 0.00 33.42 2.75
833 900 9.076781 TGTCATCAAAATGGACAAAAAGAGATA 57.923 29.630 0.00 0.00 33.42 1.98
834 901 9.346725 GTCATCAAAATGGACAAAAAGAGATAC 57.653 33.333 0.00 0.00 33.42 2.24
835 902 9.076781 TCATCAAAATGGACAAAAAGAGATACA 57.923 29.630 0.00 0.00 33.42 2.29
836 903 9.865321 CATCAAAATGGACAAAAAGAGATACAT 57.135 29.630 0.00 0.00 0.00 2.29
838 905 8.522830 TCAAAATGGACAAAAAGAGATACATCC 58.477 33.333 0.00 0.00 0.00 3.51
839 906 8.526147 CAAAATGGACAAAAAGAGATACATCCT 58.474 33.333 0.00 0.00 0.00 3.24
840 907 7.872113 AATGGACAAAAAGAGATACATCCTC 57.128 36.000 0.00 0.00 0.00 3.71
841 908 6.627087 TGGACAAAAAGAGATACATCCTCT 57.373 37.500 0.00 0.00 42.37 3.69
863 930 9.918630 CCTCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
871 938 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
872 939 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
873 940 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
874 941 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
875 942 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
876 943 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
877 944 4.196626 TGACAAGTATTTTCGGACGGAT 57.803 40.909 0.00 0.00 0.00 4.18
878 945 3.930229 TGACAAGTATTTTCGGACGGATG 59.070 43.478 0.00 0.00 0.00 3.51
879 946 3.267483 ACAAGTATTTTCGGACGGATGG 58.733 45.455 0.00 0.00 0.00 3.51
880 947 3.055675 ACAAGTATTTTCGGACGGATGGA 60.056 43.478 0.00 0.00 0.00 3.41
881 948 3.454371 AGTATTTTCGGACGGATGGAG 57.546 47.619 0.00 0.00 0.00 3.86
882 949 2.764572 AGTATTTTCGGACGGATGGAGT 59.235 45.455 0.00 0.00 0.00 3.85
883 950 3.956199 AGTATTTTCGGACGGATGGAGTA 59.044 43.478 0.00 0.00 0.00 2.59
884 951 4.587684 AGTATTTTCGGACGGATGGAGTAT 59.412 41.667 0.00 0.00 0.00 2.12
885 952 3.899052 TTTTCGGACGGATGGAGTATT 57.101 42.857 0.00 0.00 0.00 1.89
886 953 2.882927 TTCGGACGGATGGAGTATTG 57.117 50.000 0.00 0.00 0.00 1.90
887 954 1.037493 TCGGACGGATGGAGTATTGG 58.963 55.000 0.00 0.00 0.00 3.16
888 955 0.750850 CGGACGGATGGAGTATTGGT 59.249 55.000 0.00 0.00 0.00 3.67
889 956 1.958579 CGGACGGATGGAGTATTGGTA 59.041 52.381 0.00 0.00 0.00 3.25
890 957 2.561419 CGGACGGATGGAGTATTGGTAT 59.439 50.000 0.00 0.00 0.00 2.73
891 958 3.760151 CGGACGGATGGAGTATTGGTATA 59.240 47.826 0.00 0.00 0.00 1.47
892 959 4.219070 CGGACGGATGGAGTATTGGTATAA 59.781 45.833 0.00 0.00 0.00 0.98
951 1021 2.928801 TAGACCAGCAAGACAGCAAA 57.071 45.000 0.00 0.00 36.85 3.68
970 1040 4.262506 GCAAAGGAGTAGAGTAGTTGGTGT 60.263 45.833 0.00 0.00 0.00 4.16
971 1041 5.742255 GCAAAGGAGTAGAGTAGTTGGTGTT 60.742 44.000 0.00 0.00 0.00 3.32
1006 1076 3.064324 GCAGGCACACCATGTCCC 61.064 66.667 0.00 0.00 39.06 4.46
1017 1087 3.083997 ATGTCCCTCTCCACCGCC 61.084 66.667 0.00 0.00 0.00 6.13
1288 1367 4.059773 AGATGAACTCCCTCTGTTCTCT 57.940 45.455 7.89 5.80 42.86 3.10
1337 1419 8.413899 AGAGAAATTTCTAGTAAACGATGCTC 57.586 34.615 20.51 3.75 37.73 4.26
1338 1420 8.254508 AGAGAAATTTCTAGTAAACGATGCTCT 58.745 33.333 20.51 5.93 37.73 4.09
1339 1421 8.190888 AGAAATTTCTAGTAAACGATGCTCTG 57.809 34.615 19.17 0.00 35.34 3.35
1343 1429 6.997239 TTCTAGTAAACGATGCTCTGACTA 57.003 37.500 0.00 0.00 0.00 2.59
1347 1433 2.285827 AACGATGCTCTGACTACTGC 57.714 50.000 0.00 0.00 0.00 4.40
1467 1561 1.602377 GAGGTTCGTTTGACTTGGGTG 59.398 52.381 0.00 0.00 0.00 4.61
1486 1580 1.693606 TGTGCATCCTGTGACTCTGAA 59.306 47.619 0.00 0.00 0.00 3.02
1492 1586 2.520069 TCCTGTGACTCTGAAGACTCC 58.480 52.381 0.00 0.00 0.00 3.85
1494 1588 1.548269 CTGTGACTCTGAAGACTCCCC 59.452 57.143 0.00 0.00 0.00 4.81
1495 1589 1.133167 TGTGACTCTGAAGACTCCCCA 60.133 52.381 0.00 0.00 0.00 4.96
1521 1617 0.915872 ATGTCAGCTCCCATGGGTGA 60.916 55.000 32.49 24.57 38.60 4.02
1522 1618 1.133181 TGTCAGCTCCCATGGGTGAA 61.133 55.000 32.49 13.51 41.75 3.18
1523 1619 0.393537 GTCAGCTCCCATGGGTGAAG 60.394 60.000 32.49 22.72 41.75 3.02
1524 1620 0.547471 TCAGCTCCCATGGGTGAAGA 60.547 55.000 32.49 24.67 38.09 2.87
1525 1621 0.329261 CAGCTCCCATGGGTGAAGAA 59.671 55.000 32.49 12.00 34.56 2.52
1526 1622 1.064166 CAGCTCCCATGGGTGAAGAAT 60.064 52.381 32.49 12.51 34.56 2.40
1527 1623 1.642762 AGCTCCCATGGGTGAAGAATT 59.357 47.619 32.49 9.92 36.47 2.17
1536 1632 6.838612 CCCATGGGTGAAGAATTAATCCTAAA 59.161 38.462 23.93 0.00 0.00 1.85
1554 1650 6.778821 TCCTAAAGTTTTCATCTGACATGGA 58.221 36.000 0.00 0.00 0.00 3.41
1558 1654 5.495926 AGTTTTCATCTGACATGGACTCT 57.504 39.130 0.00 0.00 0.00 3.24
1637 1733 1.454847 TTTCGCCAGCCCTTGTGTT 60.455 52.632 0.00 0.00 0.00 3.32
1732 1828 1.680735 ACCGATGCAGCTGAAAACAAA 59.319 42.857 20.43 0.00 0.00 2.83
1751 1849 7.826260 AACAAAAGACAACACCTGTTTATTG 57.174 32.000 0.00 0.00 38.84 1.90
1770 1868 9.320352 GTTTATTGTTAGGCTTTTCTTTGGAAA 57.680 29.630 0.00 0.00 39.38 3.13
1776 1874 8.210265 TGTTAGGCTTTTCTTTGGAAAATCAAT 58.790 29.630 0.00 0.00 46.27 2.57
1787 1886 5.191727 TGGAAAATCAATCCTGCTTAGGA 57.808 39.130 0.00 0.00 42.91 2.94
1800 1899 5.076182 CCTGCTTAGGATGATGACTAGAGA 58.924 45.833 0.00 0.00 0.00 3.10
1808 1907 5.601729 AGGATGATGACTAGAGATGCTTCAA 59.398 40.000 0.00 0.00 0.00 2.69
1842 1941 1.000396 GGCCCCTTGAGAGTTGCAT 60.000 57.895 0.00 0.00 0.00 3.96
1892 1991 8.066612 TGGATTTCCATCTGATTACCTTTTTC 57.933 34.615 0.00 0.00 42.01 2.29
1976 2076 6.312918 TCAACGCTATTCACTTATCCAACTTC 59.687 38.462 0.00 0.00 0.00 3.01
1994 2094 3.117512 ACTTCCTGATGGTGGTTTTCTGT 60.118 43.478 0.00 0.00 34.23 3.41
2017 2117 4.754411 ACTAATCGGTTATCCCTCCCTA 57.246 45.455 0.00 0.00 0.00 3.53
2137 2238 4.224147 TGGATCAGACCATCCTTTACGAAA 59.776 41.667 0.00 0.00 42.79 3.46
2364 2465 6.513806 AGTGTTGCTGATGTTATTGCAATA 57.486 33.333 15.21 15.21 45.25 1.90
2505 2606 2.498761 GATGTGCTGTGTTCACCGCG 62.499 60.000 12.88 0.00 33.71 6.46
2738 2852 2.004583 CTTCCGAAGTCATTGCGGTA 57.995 50.000 0.00 0.00 45.02 4.02
2747 2861 4.207891 AGTCATTGCGGTAGATGTTCTT 57.792 40.909 0.00 0.00 0.00 2.52
2759 2873 6.591834 CGGTAGATGTTCTTGATGAGAAACTT 59.408 38.462 0.00 0.00 45.59 2.66
2850 2964 6.627395 TCAAGGTATACAACAAGTTTGTGG 57.373 37.500 5.01 0.00 41.31 4.17
2853 2967 6.628919 AGGTATACAACAAGTTTGTGGTTC 57.371 37.500 10.10 2.99 42.53 3.62
2874 2988 7.123997 TGGTTCACCCATATAACGTCTAAAGTA 59.876 37.037 0.00 0.00 38.72 2.24
2936 3050 4.405036 CGATATCTCATCCTGATCATGGGT 59.595 45.833 0.00 0.00 0.00 4.51
2989 3103 2.421424 GTGCTCCCATTCAGATGTGAAC 59.579 50.000 7.55 0.00 45.58 3.18
3036 3150 0.036010 GTGGGAGAGGTGTGGATGTG 60.036 60.000 0.00 0.00 0.00 3.21
3117 3231 6.904626 AGATGGAGGTAAAGCTGTTATGATT 58.095 36.000 0.00 0.00 0.00 2.57
3198 3312 3.260380 AGGTATGCATCTAGCTCCATCAC 59.740 47.826 0.19 0.00 45.94 3.06
3200 3314 2.904697 TGCATCTAGCTCCATCACAG 57.095 50.000 0.00 0.00 45.94 3.66
3229 3343 4.515361 TCGTTTGTTGTCCAGACCTTAAA 58.485 39.130 0.00 0.00 0.00 1.52
3234 3348 5.881923 TGTTGTCCAGACCTTAAACTAGT 57.118 39.130 0.00 0.00 0.00 2.57
3251 3365 6.552445 AACTAGTTCCTGCAGATATGTTCT 57.448 37.500 17.39 6.08 33.90 3.01
3259 3373 6.817184 TCCTGCAGATATGTTCTAACTTACC 58.183 40.000 17.39 0.00 31.77 2.85
3261 3375 7.125811 TCCTGCAGATATGTTCTAACTTACCTT 59.874 37.037 17.39 0.00 31.77 3.50
3266 3380 9.522804 CAGATATGTTCTAACTTACCTTGTCTC 57.477 37.037 0.00 0.00 31.77 3.36
3267 3381 9.256228 AGATATGTTCTAACTTACCTTGTCTCA 57.744 33.333 0.00 0.00 30.96 3.27
3274 3388 2.224305 ACTTACCTTGTCTCAGGCACAC 60.224 50.000 0.00 0.00 37.47 3.82
3280 3394 1.937191 TGTCTCAGGCACACATAGGA 58.063 50.000 0.00 0.00 0.00 2.94
3304 3418 7.437565 GGACCTTTCCTCAAATTACTCGTATAC 59.562 40.741 0.00 0.00 39.13 1.47
3306 3420 8.537858 ACCTTTCCTCAAATTACTCGTATACTT 58.462 33.333 0.56 0.00 0.00 2.24
3321 3435 8.036575 ACTCGTATACTTTTAGTGCAATACCAA 58.963 33.333 0.00 0.00 0.00 3.67
3344 3458 5.664294 TTGCATCCATTTTGAATGCTACT 57.336 34.783 7.92 0.00 38.88 2.57
3346 3460 6.135290 TGCATCCATTTTGAATGCTACTAC 57.865 37.500 7.92 0.00 38.88 2.73
3347 3461 5.067674 TGCATCCATTTTGAATGCTACTACC 59.932 40.000 7.92 0.00 38.88 3.18
3352 3466 8.189119 TCCATTTTGAATGCTACTACCTTTTT 57.811 30.769 0.00 0.00 0.00 1.94
3357 3471 8.458573 TTTGAATGCTACTACCTTTTTCTTGA 57.541 30.769 0.00 0.00 0.00 3.02
3361 3475 9.346725 GAATGCTACTACCTTTTTCTTGAATTG 57.653 33.333 0.00 0.00 0.00 2.32
3399 3513 1.308069 ACATTGGCTGGCTGCTAACG 61.308 55.000 16.75 11.80 44.72 3.18
3541 3655 3.367292 GGAAATGCAAATTCGAAGAGGCA 60.367 43.478 18.59 18.59 38.43 4.75
3586 3700 3.508840 GGCAAGATCGTTGGCCGG 61.509 66.667 15.78 0.00 38.83 6.13
3605 3719 2.223340 CGGGCTGTAGTTGAAATCATGC 60.223 50.000 0.00 0.00 0.00 4.06
3881 4006 7.292292 TGGTTTCTAATGTTACAAAATCGTCG 58.708 34.615 0.00 0.00 0.00 5.12
3952 4077 8.299570 AGAGTAAAACAAAATACAGGCAATGAG 58.700 33.333 0.00 0.00 0.00 2.90
4174 4299 0.764271 TCAGCCACATGTCTGGTTCA 59.236 50.000 13.06 0.00 33.30 3.18
4180 4305 0.603707 ACATGTCTGGTTCACGCAGG 60.604 55.000 0.00 0.00 0.00 4.85
4251 4376 1.001746 CTGGAAGTGAGCAGCTTCTCA 59.998 52.381 12.33 12.33 41.36 3.27
4325 4451 8.193438 CACAGATGACAGTGAAAGAGATACATA 58.807 37.037 0.00 0.00 35.94 2.29
4380 4506 5.173774 TGAAATGTTTGCTCAGTGAGTTC 57.826 39.130 21.06 14.45 31.39 3.01
4427 4641 3.875134 ACAACCTCGACAACAAAAGTAGG 59.125 43.478 0.00 0.00 0.00 3.18
4547 4761 2.869801 TGTGGTAAGCAACTTCTGAACG 59.130 45.455 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.037579 ACGACGGGATGATGCTCAGA 61.038 55.000 0.00 0.00 0.00 3.27
131 132 0.811616 GTACAATCCCTCGGCAGCAG 60.812 60.000 0.00 0.00 0.00 4.24
135 136 1.496060 ATCTGTACAATCCCTCGGCA 58.504 50.000 0.00 0.00 0.00 5.69
156 157 4.083324 CCAACAATTGACGAATGCTGTAGT 60.083 41.667 13.59 0.00 0.00 2.73
162 163 4.047822 TGAAACCAACAATTGACGAATGC 58.952 39.130 13.59 0.00 0.00 3.56
175 176 6.238103 CCTCATATACACACGATGAAACCAAC 60.238 42.308 0.00 0.00 0.00 3.77
190 191 9.674068 TTTGTACATTTAAGCACCTCATATACA 57.326 29.630 0.00 0.00 0.00 2.29
197 202 7.084486 CCTTCTTTTGTACATTTAAGCACCTC 58.916 38.462 0.00 0.00 0.00 3.85
240 246 2.948315 GAGGCCTCCAAGAATGATTGTC 59.052 50.000 23.19 0.00 0.00 3.18
241 247 2.579860 AGAGGCCTCCAAGAATGATTGT 59.420 45.455 29.54 2.46 0.00 2.71
242 248 2.950309 CAGAGGCCTCCAAGAATGATTG 59.050 50.000 29.54 12.78 0.00 2.67
243 249 2.579860 ACAGAGGCCTCCAAGAATGATT 59.420 45.455 29.54 3.28 0.00 2.57
261 282 5.104610 CCAATCCTCCTATATCCATCCACAG 60.105 48.000 0.00 0.00 0.00 3.66
288 309 2.552743 CCGTGTCTGTCTGTCTGTCTTA 59.447 50.000 0.00 0.00 0.00 2.10
313 337 1.035385 CATCCTTGGTTTACCGGCCC 61.035 60.000 0.00 0.00 39.43 5.80
362 386 4.126437 TCAACACAATGACACGAGACAAT 58.874 39.130 0.00 0.00 0.00 2.71
363 387 3.526534 TCAACACAATGACACGAGACAA 58.473 40.909 0.00 0.00 0.00 3.18
364 388 3.172229 TCAACACAATGACACGAGACA 57.828 42.857 0.00 0.00 0.00 3.41
365 389 4.732285 AATCAACACAATGACACGAGAC 57.268 40.909 0.00 0.00 30.82 3.36
370 394 7.042858 TGTGCAAATTAATCAACACAATGACAC 60.043 33.333 12.42 0.00 35.28 3.67
378 402 5.925397 TGGACATGTGCAAATTAATCAACAC 59.075 36.000 18.56 7.42 0.00 3.32
398 422 4.060205 AGCATTGCTTGAAACAATTGGAC 58.940 39.130 10.83 1.34 33.89 4.02
414 438 2.124011 AACGACAAGTTGCAGCATTG 57.876 45.000 2.55 7.12 42.39 2.82
440 497 1.457346 CTGCTAAAGGGAGTGCCAAG 58.543 55.000 2.50 0.00 35.15 3.61
445 502 0.908198 AGAGGCTGCTAAAGGGAGTG 59.092 55.000 0.00 0.00 35.71 3.51
449 506 0.326264 ACACAGAGGCTGCTAAAGGG 59.674 55.000 0.00 0.00 34.37 3.95
465 522 8.233692 TCATCACTAAACAAACAAACAAACAC 57.766 30.769 0.00 0.00 0.00 3.32
479 536 6.961554 GGTCGTTTTCATCATCATCACTAAAC 59.038 38.462 0.00 0.00 0.00 2.01
480 537 6.183360 CGGTCGTTTTCATCATCATCACTAAA 60.183 38.462 0.00 0.00 0.00 1.85
481 538 5.290885 CGGTCGTTTTCATCATCATCACTAA 59.709 40.000 0.00 0.00 0.00 2.24
482 539 4.803613 CGGTCGTTTTCATCATCATCACTA 59.196 41.667 0.00 0.00 0.00 2.74
483 540 3.618594 CGGTCGTTTTCATCATCATCACT 59.381 43.478 0.00 0.00 0.00 3.41
484 541 3.616821 TCGGTCGTTTTCATCATCATCAC 59.383 43.478 0.00 0.00 0.00 3.06
485 542 3.616821 GTCGGTCGTTTTCATCATCATCA 59.383 43.478 0.00 0.00 0.00 3.07
486 543 3.616821 TGTCGGTCGTTTTCATCATCATC 59.383 43.478 0.00 0.00 0.00 2.92
487 544 3.595173 TGTCGGTCGTTTTCATCATCAT 58.405 40.909 0.00 0.00 0.00 2.45
488 545 3.033368 TGTCGGTCGTTTTCATCATCA 57.967 42.857 0.00 0.00 0.00 3.07
489 546 3.616821 TGATGTCGGTCGTTTTCATCATC 59.383 43.478 0.00 0.00 39.53 2.92
490 547 3.595173 TGATGTCGGTCGTTTTCATCAT 58.405 40.909 0.00 0.00 39.53 2.45
491 548 2.993220 CTGATGTCGGTCGTTTTCATCA 59.007 45.455 0.00 0.00 41.27 3.07
499 556 1.141881 GGATGCTGATGTCGGTCGT 59.858 57.895 0.00 0.00 0.00 4.34
511 568 3.558931 TGACAATTGATACCGGATGCT 57.441 42.857 13.59 0.00 0.00 3.79
512 569 3.189287 GGATGACAATTGATACCGGATGC 59.811 47.826 13.59 0.00 0.00 3.91
526 583 3.118075 TGCGGATAAGGATTGGATGACAA 60.118 43.478 0.00 0.00 44.54 3.18
527 584 2.437651 TGCGGATAAGGATTGGATGACA 59.562 45.455 0.00 0.00 0.00 3.58
528 585 3.070018 CTGCGGATAAGGATTGGATGAC 58.930 50.000 0.00 0.00 0.00 3.06
529 586 2.705658 ACTGCGGATAAGGATTGGATGA 59.294 45.455 0.00 0.00 0.00 2.92
530 587 2.810274 CACTGCGGATAAGGATTGGATG 59.190 50.000 0.00 0.00 0.00 3.51
531 588 2.811873 GCACTGCGGATAAGGATTGGAT 60.812 50.000 0.00 0.00 0.00 3.41
532 589 1.475034 GCACTGCGGATAAGGATTGGA 60.475 52.381 0.00 0.00 0.00 3.53
533 590 0.947244 GCACTGCGGATAAGGATTGG 59.053 55.000 0.00 0.00 0.00 3.16
534 591 0.947244 GGCACTGCGGATAAGGATTG 59.053 55.000 0.00 0.00 0.00 2.67
535 592 0.532862 CGGCACTGCGGATAAGGATT 60.533 55.000 0.00 0.00 0.00 3.01
599 656 1.066573 AGACCGATGCTCAACAGGAAG 60.067 52.381 0.00 0.00 0.00 3.46
603 660 1.391485 CGAAAGACCGATGCTCAACAG 59.609 52.381 0.00 0.00 0.00 3.16
614 671 1.978782 GCAAAGCAAATCGAAAGACCG 59.021 47.619 0.00 0.00 46.97 4.79
623 681 6.275335 TGCATTAGGATTAGCAAAGCAAATC 58.725 36.000 0.00 0.00 33.48 2.17
631 689 7.384660 CACTTGTTTTTGCATTAGGATTAGCAA 59.615 33.333 0.00 0.00 44.36 3.91
672 730 7.644157 GGACTCTTTGTTTCTAACACATGTTTC 59.356 37.037 1.98 0.00 41.97 2.78
683 741 7.194278 CGATCGATTAGGACTCTTTGTTTCTA 58.806 38.462 10.26 0.00 0.00 2.10
684 742 6.037098 CGATCGATTAGGACTCTTTGTTTCT 58.963 40.000 10.26 0.00 0.00 2.52
685 743 5.232414 CCGATCGATTAGGACTCTTTGTTTC 59.768 44.000 18.66 0.00 0.00 2.78
687 745 4.401519 TCCGATCGATTAGGACTCTTTGTT 59.598 41.667 18.66 0.00 0.00 2.83
688 746 3.952323 TCCGATCGATTAGGACTCTTTGT 59.048 43.478 18.66 0.00 0.00 2.83
689 747 4.569761 TCCGATCGATTAGGACTCTTTG 57.430 45.455 18.66 0.00 0.00 2.77
690 748 5.379732 GATCCGATCGATTAGGACTCTTT 57.620 43.478 18.66 8.95 36.81 2.52
708 766 0.312416 CATCGTCAGAGGACCGATCC 59.688 60.000 0.00 0.00 46.69 3.36
744 811 8.297426 GGACGGAGATCTTTTCAGTTAAATTTT 58.703 33.333 0.00 0.00 0.00 1.82
745 812 7.447238 TGGACGGAGATCTTTTCAGTTAAATTT 59.553 33.333 0.00 0.00 0.00 1.82
746 813 6.940298 TGGACGGAGATCTTTTCAGTTAAATT 59.060 34.615 0.00 0.00 0.00 1.82
748 815 5.860611 TGGACGGAGATCTTTTCAGTTAAA 58.139 37.500 0.00 0.00 0.00 1.52
749 816 5.477607 TGGACGGAGATCTTTTCAGTTAA 57.522 39.130 0.00 0.00 0.00 2.01
751 818 4.351874 TTGGACGGAGATCTTTTCAGTT 57.648 40.909 0.00 0.00 0.00 3.16
753 820 5.689383 TTTTTGGACGGAGATCTTTTCAG 57.311 39.130 0.00 0.00 0.00 3.02
761 828 5.556915 TGACAAGTATTTTTGGACGGAGAT 58.443 37.500 0.00 0.00 32.32 2.75
763 830 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
764 831 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
765 832 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
766 833 7.922505 TTTTGATGACAAGTATTTTTGGACG 57.077 32.000 0.00 0.00 37.32 4.79
767 834 8.711457 CCATTTTGATGACAAGTATTTTTGGAC 58.289 33.333 0.00 0.00 37.32 4.02
768 835 8.646004 TCCATTTTGATGACAAGTATTTTTGGA 58.354 29.630 0.00 0.00 37.32 3.53
770 837 9.258826 TGTCCATTTTGATGACAAGTATTTTTG 57.741 29.630 0.00 0.00 37.32 2.44
771 838 9.829507 TTGTCCATTTTGATGACAAGTATTTTT 57.170 25.926 0.00 0.00 37.32 1.94
773 840 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
774 841 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
798 865 9.829507 TTGTCCATTTTGATGACAAGTATTTTT 57.170 25.926 0.00 0.00 37.32 1.94
799 866 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
800 867 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
801 868 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
802 869 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
803 870 8.690884 TCTTTTTGTCCATTTTGATGACAAGTA 58.309 29.630 0.00 0.00 37.13 2.24
804 871 7.555087 TCTTTTTGTCCATTTTGATGACAAGT 58.445 30.769 0.00 0.00 37.13 3.16
805 872 7.922278 TCTCTTTTTGTCCATTTTGATGACAAG 59.078 33.333 0.00 0.00 37.13 3.16
806 873 7.780064 TCTCTTTTTGTCCATTTTGATGACAA 58.220 30.769 0.00 0.00 34.47 3.18
807 874 7.345422 TCTCTTTTTGTCCATTTTGATGACA 57.655 32.000 0.00 0.00 0.00 3.58
808 875 9.346725 GTATCTCTTTTTGTCCATTTTGATGAC 57.653 33.333 0.00 0.00 0.00 3.06
809 876 9.076781 TGTATCTCTTTTTGTCCATTTTGATGA 57.923 29.630 0.00 0.00 0.00 2.92
810 877 9.865321 ATGTATCTCTTTTTGTCCATTTTGATG 57.135 29.630 0.00 0.00 0.00 3.07
812 879 8.522830 GGATGTATCTCTTTTTGTCCATTTTGA 58.477 33.333 0.00 0.00 0.00 2.69
813 880 8.526147 AGGATGTATCTCTTTTTGTCCATTTTG 58.474 33.333 0.00 0.00 0.00 2.44
814 881 8.655935 AGGATGTATCTCTTTTTGTCCATTTT 57.344 30.769 0.00 0.00 0.00 1.82
815 882 8.112183 AGAGGATGTATCTCTTTTTGTCCATTT 58.888 33.333 0.00 0.00 38.32 2.32
816 883 7.637511 AGAGGATGTATCTCTTTTTGTCCATT 58.362 34.615 0.00 0.00 38.32 3.16
817 884 7.205515 AGAGGATGTATCTCTTTTTGTCCAT 57.794 36.000 0.00 0.00 38.32 3.41
818 885 6.627087 AGAGGATGTATCTCTTTTTGTCCA 57.373 37.500 0.00 0.00 38.32 4.02
837 904 9.918630 ACTTGTCATCAAAATGAATAAAAGAGG 57.081 29.630 0.00 0.00 43.42 3.69
845 912 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
846 913 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
847 914 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
848 915 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
849 916 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
850 917 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
851 918 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
852 919 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
853 920 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
854 921 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
855 922 4.196626 TCCGTCCGAAAATACTTGTCAT 57.803 40.909 0.00 0.00 0.00 3.06
856 923 3.663995 TCCGTCCGAAAATACTTGTCA 57.336 42.857 0.00 0.00 0.00 3.58
857 924 3.308866 CCATCCGTCCGAAAATACTTGTC 59.691 47.826 0.00 0.00 0.00 3.18
858 925 3.055675 TCCATCCGTCCGAAAATACTTGT 60.056 43.478 0.00 0.00 0.00 3.16
859 926 3.527533 TCCATCCGTCCGAAAATACTTG 58.472 45.455 0.00 0.00 0.00 3.16
860 927 3.197116 ACTCCATCCGTCCGAAAATACTT 59.803 43.478 0.00 0.00 0.00 2.24
861 928 2.764572 ACTCCATCCGTCCGAAAATACT 59.235 45.455 0.00 0.00 0.00 2.12
862 929 3.175109 ACTCCATCCGTCCGAAAATAC 57.825 47.619 0.00 0.00 0.00 1.89
863 930 5.294356 CAATACTCCATCCGTCCGAAAATA 58.706 41.667 0.00 0.00 0.00 1.40
864 931 4.127171 CAATACTCCATCCGTCCGAAAAT 58.873 43.478 0.00 0.00 0.00 1.82
865 932 3.527533 CAATACTCCATCCGTCCGAAAA 58.472 45.455 0.00 0.00 0.00 2.29
866 933 2.159014 CCAATACTCCATCCGTCCGAAA 60.159 50.000 0.00 0.00 0.00 3.46
867 934 1.411246 CCAATACTCCATCCGTCCGAA 59.589 52.381 0.00 0.00 0.00 4.30
868 935 1.037493 CCAATACTCCATCCGTCCGA 58.963 55.000 0.00 0.00 0.00 4.55
869 936 0.750850 ACCAATACTCCATCCGTCCG 59.249 55.000 0.00 0.00 0.00 4.79
870 937 5.733620 TTATACCAATACTCCATCCGTCC 57.266 43.478 0.00 0.00 0.00 4.79
871 938 8.504005 CATTTTTATACCAATACTCCATCCGTC 58.496 37.037 0.00 0.00 0.00 4.79
872 939 7.040686 GCATTTTTATACCAATACTCCATCCGT 60.041 37.037 0.00 0.00 0.00 4.69
873 940 7.174946 AGCATTTTTATACCAATACTCCATCCG 59.825 37.037 0.00 0.00 0.00 4.18
874 941 8.409358 AGCATTTTTATACCAATACTCCATCC 57.591 34.615 0.00 0.00 0.00 3.51
875 942 9.683069 CAAGCATTTTTATACCAATACTCCATC 57.317 33.333 0.00 0.00 0.00 3.51
876 943 8.641541 CCAAGCATTTTTATACCAATACTCCAT 58.358 33.333 0.00 0.00 0.00 3.41
877 944 7.836685 TCCAAGCATTTTTATACCAATACTCCA 59.163 33.333 0.00 0.00 0.00 3.86
878 945 8.232913 TCCAAGCATTTTTATACCAATACTCC 57.767 34.615 0.00 0.00 0.00 3.85
879 946 8.903820 ACTCCAAGCATTTTTATACCAATACTC 58.096 33.333 0.00 0.00 0.00 2.59
880 947 8.823220 ACTCCAAGCATTTTTATACCAATACT 57.177 30.769 0.00 0.00 0.00 2.12
881 948 9.301153 CAACTCCAAGCATTTTTATACCAATAC 57.699 33.333 0.00 0.00 0.00 1.89
882 949 9.030452 ACAACTCCAAGCATTTTTATACCAATA 57.970 29.630 0.00 0.00 0.00 1.90
883 950 7.906327 ACAACTCCAAGCATTTTTATACCAAT 58.094 30.769 0.00 0.00 0.00 3.16
884 951 7.296628 ACAACTCCAAGCATTTTTATACCAA 57.703 32.000 0.00 0.00 0.00 3.67
885 952 6.909550 ACAACTCCAAGCATTTTTATACCA 57.090 33.333 0.00 0.00 0.00 3.25
886 953 7.151976 ACAACAACTCCAAGCATTTTTATACC 58.848 34.615 0.00 0.00 0.00 2.73
887 954 9.855021 ATACAACAACTCCAAGCATTTTTATAC 57.145 29.630 0.00 0.00 0.00 1.47
891 958 9.777297 ATTAATACAACAACTCCAAGCATTTTT 57.223 25.926 0.00 0.00 0.00 1.94
932 1002 2.550855 CCTTTGCTGTCTTGCTGGTCTA 60.551 50.000 0.00 0.00 0.00 2.59
951 1021 4.481072 ACAACACCAACTACTCTACTCCT 58.519 43.478 0.00 0.00 0.00 3.69
970 1040 1.021202 CCAACGGAACTCTGCAACAA 58.979 50.000 0.00 0.00 0.00 2.83
971 1041 1.444119 GCCAACGGAACTCTGCAACA 61.444 55.000 0.00 0.00 0.00 3.33
1230 1306 1.842381 AAGGAAGAGTGGCGGGGAAG 61.842 60.000 0.00 0.00 0.00 3.46
1231 1307 1.838073 GAAGGAAGAGTGGCGGGGAA 61.838 60.000 0.00 0.00 0.00 3.97
1232 1308 2.203938 AAGGAAGAGTGGCGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
1337 1419 4.098654 ACAGCATACCTAAGCAGTAGTCAG 59.901 45.833 0.00 0.00 0.00 3.51
1338 1420 4.023980 ACAGCATACCTAAGCAGTAGTCA 58.976 43.478 0.00 0.00 0.00 3.41
1339 1421 4.363999 CACAGCATACCTAAGCAGTAGTC 58.636 47.826 0.00 0.00 0.00 2.59
1343 1429 1.278985 TGCACAGCATACCTAAGCAGT 59.721 47.619 0.00 0.00 31.71 4.40
1388 1474 4.722526 ATAATCATCCATTCCCCGTCAA 57.277 40.909 0.00 0.00 0.00 3.18
1390 1476 4.576463 GCATATAATCATCCATTCCCCGTC 59.424 45.833 0.00 0.00 0.00 4.79
1391 1477 4.526970 GCATATAATCATCCATTCCCCGT 58.473 43.478 0.00 0.00 0.00 5.28
1392 1478 3.885297 GGCATATAATCATCCATTCCCCG 59.115 47.826 0.00 0.00 0.00 5.73
1467 1561 2.028658 TCTTCAGAGTCACAGGATGCAC 60.029 50.000 0.00 0.00 42.53 4.57
1502 1596 0.915872 TCACCCATGGGAGCTGACAT 60.916 55.000 38.07 9.39 38.96 3.06
1527 1623 9.177608 CCATGTCAGATGAAAACTTTAGGATTA 57.822 33.333 0.00 0.00 0.00 1.75
1536 1632 5.495926 AGAGTCCATGTCAGATGAAAACT 57.504 39.130 0.00 0.00 0.00 2.66
1554 1650 2.874701 CACAAGCTGCACAAGTTAGAGT 59.125 45.455 1.02 0.00 0.00 3.24
1558 1654 2.221169 CTCCACAAGCTGCACAAGTTA 58.779 47.619 1.02 0.00 0.00 2.24
1637 1733 0.392863 CGGTGATCTCATGGCCAACA 60.393 55.000 10.96 0.00 0.00 3.33
1732 1828 6.238925 GCCTAACAATAAACAGGTGTTGTCTT 60.239 38.462 0.00 0.00 39.73 3.01
1787 1886 7.991460 TCAAATTGAAGCATCTCTAGTCATCAT 59.009 33.333 0.00 0.00 0.00 2.45
1792 1891 8.206325 TCAATCAAATTGAAGCATCTCTAGTC 57.794 34.615 0.00 0.00 45.57 2.59
1808 1907 2.092807 GGGGCCAAGCATTCAATCAAAT 60.093 45.455 4.39 0.00 0.00 2.32
1842 1941 7.019774 GCATCTATCTGTGCTGTAAATTTCA 57.980 36.000 0.00 0.00 38.30 2.69
1931 2030 1.527034 TGACAGTGCTTCCATGCTTC 58.473 50.000 0.00 0.00 0.00 3.86
1976 2076 4.398319 AGTTACAGAAAACCACCATCAGG 58.602 43.478 0.00 0.00 42.21 3.86
1994 2094 5.083953 AGGGAGGGATAACCGATTAGTTA 57.916 43.478 0.00 0.00 46.96 2.24
2137 2238 3.429410 GGTCAAGAAAACAAAGCAGCACT 60.429 43.478 0.00 0.00 0.00 4.40
2364 2465 0.258774 ACACTGGTTTTCCTGCAGGT 59.741 50.000 31.58 7.59 41.75 4.00
2505 2606 0.029834 CATGCCTCAAAGCGCCATAC 59.970 55.000 2.29 0.00 34.65 2.39
2738 2852 7.448420 TCTGAAGTTTCTCATCAAGAACATCT 58.552 34.615 0.00 0.00 43.75 2.90
2747 2861 6.638096 TTTGCATTCTGAAGTTTCTCATCA 57.362 33.333 0.00 0.00 0.00 3.07
2759 2873 4.737352 GCTCCAAGTGTTTTTGCATTCTGA 60.737 41.667 0.00 0.00 0.00 3.27
2850 2964 9.538508 AATACTTTAGACGTTATATGGGTGAAC 57.461 33.333 0.00 0.00 0.00 3.18
2881 2995 5.031066 ACCTAAACAAACTGCACTGAGTA 57.969 39.130 0.00 0.00 0.00 2.59
2887 3001 4.766404 ATGCTACCTAAACAAACTGCAC 57.234 40.909 0.00 0.00 31.92 4.57
2936 3050 5.316167 ACTGAAGAAGCAACATATGGACAA 58.684 37.500 7.80 0.00 0.00 3.18
2943 3057 6.042638 AGCTAAGACTGAAGAAGCAACATA 57.957 37.500 0.00 0.00 35.63 2.29
2974 3088 4.436332 TGAGATCGTTCACATCTGAATGG 58.564 43.478 3.46 0.00 41.90 3.16
2989 3103 9.265901 AGTAATTTCCTGTGAATAATGAGATCG 57.734 33.333 0.00 0.00 0.00 3.69
3036 3150 2.674380 CCAAGTGCCTCCACAGCC 60.674 66.667 0.00 0.00 44.53 4.85
3090 3204 1.134670 ACAGCTTTACCTCCATCTCGC 60.135 52.381 0.00 0.00 0.00 5.03
3117 3231 1.143620 GTTTGTTGCAGCAAGCCCA 59.856 52.632 17.36 0.00 44.83 5.36
3198 3312 3.619483 TGGACAACAAACGAACAGTACTG 59.381 43.478 21.44 21.44 0.00 2.74
3200 3314 3.866910 TCTGGACAACAAACGAACAGTAC 59.133 43.478 0.00 0.00 0.00 2.73
3229 3343 7.343316 AGTTAGAACATATCTGCAGGAACTAGT 59.657 37.037 15.13 2.82 39.30 2.57
3234 3348 7.125811 AGGTAAGTTAGAACATATCTGCAGGAA 59.874 37.037 15.13 2.22 39.30 3.36
3251 3365 3.644265 TGTGCCTGAGACAAGGTAAGTTA 59.356 43.478 0.00 0.00 39.75 2.24
3259 3373 2.234661 TCCTATGTGTGCCTGAGACAAG 59.765 50.000 0.00 0.00 30.25 3.16
3261 3375 1.550524 GTCCTATGTGTGCCTGAGACA 59.449 52.381 0.00 0.00 31.20 3.41
3266 3380 2.359900 GAAAGGTCCTATGTGTGCCTG 58.640 52.381 0.00 0.00 0.00 4.85
3267 3381 1.282157 GGAAAGGTCCTATGTGTGCCT 59.718 52.381 0.00 0.00 41.24 4.75
3280 3394 8.075761 AGTATACGAGTAATTTGAGGAAAGGT 57.924 34.615 0.00 0.00 0.00 3.50
3321 3435 6.229936 AGTAGCATTCAAAATGGATGCAAT 57.770 33.333 22.05 8.13 40.41 3.56
3344 3458 5.070313 AGCAAGGCAATTCAAGAAAAAGGTA 59.930 36.000 0.00 0.00 0.00 3.08
3346 3460 4.383173 AGCAAGGCAATTCAAGAAAAAGG 58.617 39.130 0.00 0.00 0.00 3.11
3347 3461 5.744490 CAAGCAAGGCAATTCAAGAAAAAG 58.256 37.500 0.00 0.00 0.00 2.27
3352 3466 1.965643 AGCAAGCAAGGCAATTCAAGA 59.034 42.857 0.00 0.00 0.00 3.02
3357 3471 2.215196 CACAAAGCAAGCAAGGCAATT 58.785 42.857 0.00 0.00 0.00 2.32
3361 3475 2.127251 GTTACACAAAGCAAGCAAGGC 58.873 47.619 0.00 0.00 0.00 4.35
3399 3513 3.695830 TGACCTGGTTCCAGTAATCAC 57.304 47.619 16.33 3.68 32.56 3.06
3541 3655 1.765314 AGATCCTCATAGGCGCTGTTT 59.235 47.619 7.64 0.00 34.61 2.83
3586 3700 3.441572 ACTGCATGATTTCAACTACAGCC 59.558 43.478 0.00 0.00 0.00 4.85
3605 3719 2.573941 TGATCATCTCGTCAGCACTG 57.426 50.000 0.00 0.00 0.00 3.66
3825 3950 4.096984 GGCTGCAGAACTGTATAAGCAAAT 59.903 41.667 20.43 0.00 31.45 2.32
3881 4006 2.354199 GCTAGCTGAGGATTCTTTGTGC 59.646 50.000 7.70 0.00 0.00 4.57
4180 4305 6.200097 GCTAGCTAACTCATAAGCAGAGAAAC 59.800 42.308 7.70 0.00 41.32 2.78
4251 4376 5.360591 GTGGAAGATGTATTCGGTGAGATT 58.639 41.667 0.00 0.00 0.00 2.40
4349 4475 9.146984 CACTGAGCAAACATTTCATAATCATTT 57.853 29.630 0.00 0.00 0.00 2.32
4350 4476 8.525316 TCACTGAGCAAACATTTCATAATCATT 58.475 29.630 0.00 0.00 0.00 2.57
4380 4506 7.751732 TGCACTATATAGAGCAACAACAAAAG 58.248 34.615 26.38 0.00 44.73 2.27
4427 4641 4.889409 TGTTCCTCCATGGCATTCTTTATC 59.111 41.667 6.96 0.00 35.26 1.75


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

AutoCloner maintained by Alex Coulton.