Multiple sequence alignment - TraesCS7D01G114400

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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 TraesCS7D01G114400 chr7D 100.000 3615 0 0 1 3615 69953221 69956835 0.000000e+00 6676.0
1 TraesCS7D01G114400 chr7D 91.727 2067 115 20 706 2747 70154269 70152234 0.000000e+00 2819.0
2 TraesCS7D01G114400 chr7D 91.606 2061 118 20 711 2747 70048043 70050072 0.000000e+00 2796.0
3 TraesCS7D01G114400 chr7D 91.732 1270 62 13 963 2222 70736792 70735556 0.000000e+00 1724.0
4 TraesCS7D01G114400 chr7D 97.000 400 11 1 757 1155 70361689 70362088 0.000000e+00 671.0
5 TraesCS7D01G114400 chr7D 88.753 489 36 8 2251 2735 70735561 70735088 6.730000e-162 580.0
6 TraesCS7D01G114400 chr7D 98.857 175 2 0 1916 2090 70362288 70362114 2.710000e-81 313.0
7 TraesCS7D01G114400 chr7D 77.895 190 16 14 706 884 70737001 70736827 1.070000e-15 95.3
8 TraesCS7D01G114400 chr7B 93.236 2809 127 25 706 3502 12719646 12716889 0.000000e+00 4076.0
9 TraesCS7D01G114400 chr7B 93.569 2379 115 14 770 3147 12951740 12954081 0.000000e+00 3511.0
10 TraesCS7D01G114400 chr7B 86.767 597 27 23 748 1321 12716216 12716783 5.130000e-173 617.0
11 TraesCS7D01G114400 chr7B 91.339 254 16 4 3195 3444 12954087 12954338 3.460000e-90 342.0
12 TraesCS7D01G114400 chr6D 90.424 731 36 19 1 708 445062730 445063449 0.000000e+00 931.0
13 TraesCS7D01G114400 chr6D 90.741 270 16 6 1 269 447511993 447512254 5.740000e-93 351.0
14 TraesCS7D01G114400 chr6D 91.503 153 12 1 259 410 447520567 447520719 3.660000e-50 209.0
15 TraesCS7D01G114400 chr6D 82.110 218 29 8 17 229 436869093 436869305 1.030000e-40 178.0
16 TraesCS7D01G114400 chr6D 80.392 153 24 5 554 703 436869656 436869805 1.060000e-20 111.0
17 TraesCS7D01G114400 chr6B 89.779 724 44 19 1 703 638498735 638499449 0.000000e+00 900.0
18 TraesCS7D01G114400 chr7A 90.684 526 42 6 2225 2747 76550199 76550720 0.000000e+00 693.0
19 TraesCS7D01G114400 chr7A 86.375 411 36 13 314 706 639785577 639785169 7.170000e-117 431.0
20 TraesCS7D01G114400 chr7A 89.591 269 23 4 32 299 639785925 639785661 1.610000e-88 337.0
21 TraesCS7D01G114400 chr7A 86.408 103 3 4 749 851 76819166 76819257 6.390000e-18 102.0
22 TraesCS7D01G114400 chr2B 84.892 417 42 15 26 427 678008899 678008489 5.620000e-108 401.0
23 TraesCS7D01G114400 chr2B 82.380 437 51 18 26 449 63163519 63163942 1.230000e-94 357.0
24 TraesCS7D01G114400 chr2B 86.667 105 13 1 583 686 63163026 63162922 8.200000e-22 115.0
25 TraesCS7D01G114400 chr2B 81.955 133 23 1 572 703 1757055 1757187 1.060000e-20 111.0
26 TraesCS7D01G114400 chr2B 81.955 133 23 1 572 703 1772317 1772449 1.060000e-20 111.0
27 TraesCS7D01G114400 chr2B 82.812 128 19 3 578 703 637869109 637869235 1.060000e-20 111.0
28 TraesCS7D01G114400 chr5A 84.382 429 35 20 1 408 55176813 55176396 3.380000e-105 392.0
29 TraesCS7D01G114400 chr5A 89.474 114 11 1 407 519 55176163 55176050 3.760000e-30 143.0
30 TraesCS7D01G114400 chr5D 87.048 332 29 11 1 330 65950127 65949808 2.650000e-96 363.0
31 TraesCS7D01G114400 chr5D 89.474 114 11 1 407 519 65949480 65949367 3.760000e-30 143.0
32 TraesCS7D01G114400 chr3B 82.781 302 29 17 161 449 758347637 758347928 7.750000e-62 248.0
33 TraesCS7D01G114400 chr5B 82.313 147 24 2 559 703 404181410 404181264 3.790000e-25 126.0


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 TraesCS7D01G114400 chr7D 69953221 69956835 3614 False 6676.000000 6676 100.000000 1 3615 1 chr7D.!!$F1 3614
1 TraesCS7D01G114400 chr7D 70152234 70154269 2035 True 2819.000000 2819 91.727000 706 2747 1 chr7D.!!$R1 2041
2 TraesCS7D01G114400 chr7D 70048043 70050072 2029 False 2796.000000 2796 91.606000 711 2747 1 chr7D.!!$F2 2036
3 TraesCS7D01G114400 chr7D 70735088 70737001 1913 True 799.766667 1724 86.126667 706 2735 3 chr7D.!!$R3 2029
4 TraesCS7D01G114400 chr7B 12716889 12719646 2757 True 4076.000000 4076 93.236000 706 3502 1 chr7B.!!$R1 2796
5 TraesCS7D01G114400 chr7B 12951740 12954338 2598 False 1926.500000 3511 92.454000 770 3444 2 chr7B.!!$F2 2674
6 TraesCS7D01G114400 chr7B 12716216 12716783 567 False 617.000000 617 86.767000 748 1321 1 chr7B.!!$F1 573
7 TraesCS7D01G114400 chr6D 445062730 445063449 719 False 931.000000 931 90.424000 1 708 1 chr6D.!!$F1 707
8 TraesCS7D01G114400 chr6B 638498735 638499449 714 False 900.000000 900 89.779000 1 703 1 chr6B.!!$F1 702
9 TraesCS7D01G114400 chr7A 76550199 76550720 521 False 693.000000 693 90.684000 2225 2747 1 chr7A.!!$F1 522
10 TraesCS7D01G114400 chr7A 639785169 639785925 756 True 384.000000 431 87.983000 32 706 2 chr7A.!!$R1 674
11 TraesCS7D01G114400 chr5A 55176050 55176813 763 True 267.500000 392 86.928000 1 519 2 chr5A.!!$R1 518
12 TraesCS7D01G114400 chr5D 65949367 65950127 760 True 253.000000 363 88.261000 1 519 2 chr5D.!!$R1 518

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
371 472 0.032515 TCGAATCCTCCTGGGCACTA 60.033 55.0 0.0 0.0 34.39 2.74 F
577 915 0.037447 TGCCACGTGATCAAATCCCA 59.963 50.0 19.3 0.0 0.00 4.37 F
640 978 0.109532 TTGGTGTGCTGATTTCCGGA 59.890 50.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2540 0.247736 CTGAAACAGAGAGGGACCGG 59.752 60.0 0.00 0.0 32.44 5.28 R
2508 2951 0.317770 ATCAACAAACTGCAACGCGG 60.318 50.0 12.47 0.0 41.29 6.46 R
2645 3103 2.025887 ACCAAGGAATTGACCTAGCCAG 60.026 50.0 0.00 0.0 39.62 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
121 125 5.010213 ACGTGTATTTGGCAAAATGTTACCT 59.990 36.000 17.70 0.00 36.65 3.08
122 126 5.344665 CGTGTATTTGGCAAAATGTTACCTG 59.655 40.000 17.70 6.27 36.65 4.00
257 263 8.574196 AAAATTCAGGAATGTTAAACACTTCG 57.426 30.769 0.00 0.00 0.00 3.79
312 387 2.032894 CGCGCTATACAAAATCACCAGG 60.033 50.000 5.56 0.00 0.00 4.45
371 472 0.032515 TCGAATCCTCCTGGGCACTA 60.033 55.000 0.00 0.00 34.39 2.74
519 857 2.273370 TAAACAAGTAGAGCGAGCGG 57.727 50.000 0.00 0.00 0.00 5.52
520 858 1.014564 AAACAAGTAGAGCGAGCGGC 61.015 55.000 0.00 0.00 44.05 6.53
521 859 2.583593 CAAGTAGAGCGAGCGGCC 60.584 66.667 0.00 0.00 45.17 6.13
522 860 3.839432 AAGTAGAGCGAGCGGCCC 61.839 66.667 0.00 0.00 45.17 5.80
524 862 3.917760 GTAGAGCGAGCGGCCCAT 61.918 66.667 0.00 0.00 45.17 4.00
525 863 3.154473 TAGAGCGAGCGGCCCATT 61.154 61.111 0.00 0.00 45.17 3.16
526 864 1.830847 TAGAGCGAGCGGCCCATTA 60.831 57.895 0.00 0.00 45.17 1.90
527 865 1.806461 TAGAGCGAGCGGCCCATTAG 61.806 60.000 0.00 0.00 45.17 1.73
528 866 4.918201 AGCGAGCGGCCCATTAGC 62.918 66.667 0.00 0.00 45.17 3.09
530 868 2.281070 CGAGCGGCCCATTAGCAT 60.281 61.111 0.00 0.00 0.00 3.79
531 869 2.320587 CGAGCGGCCCATTAGCATC 61.321 63.158 0.00 0.00 0.00 3.91
532 870 1.968540 GAGCGGCCCATTAGCATCC 60.969 63.158 0.00 0.00 0.00 3.51
533 871 2.113986 GCGGCCCATTAGCATCCT 59.886 61.111 0.00 0.00 0.00 3.24
534 872 1.127567 AGCGGCCCATTAGCATCCTA 61.128 55.000 0.00 0.00 0.00 2.94
535 873 0.674895 GCGGCCCATTAGCATCCTAG 60.675 60.000 0.00 0.00 0.00 3.02
536 874 0.687354 CGGCCCATTAGCATCCTAGT 59.313 55.000 0.00 0.00 0.00 2.57
537 875 1.609061 CGGCCCATTAGCATCCTAGTG 60.609 57.143 0.00 0.00 32.70 2.74
538 876 1.421646 GGCCCATTAGCATCCTAGTGT 59.578 52.381 0.00 0.00 31.41 3.55
539 877 2.551071 GGCCCATTAGCATCCTAGTGTC 60.551 54.545 0.00 0.00 31.41 3.67
540 878 2.551071 GCCCATTAGCATCCTAGTGTCC 60.551 54.545 0.00 0.00 31.41 4.02
541 879 2.705658 CCCATTAGCATCCTAGTGTCCA 59.294 50.000 0.00 0.00 31.41 4.02
542 880 3.244353 CCCATTAGCATCCTAGTGTCCAG 60.244 52.174 0.00 0.00 31.41 3.86
543 881 3.397482 CATTAGCATCCTAGTGTCCAGC 58.603 50.000 0.00 0.00 0.00 4.85
544 882 1.032794 TAGCATCCTAGTGTCCAGCG 58.967 55.000 0.00 0.00 0.00 5.18
545 883 0.684479 AGCATCCTAGTGTCCAGCGA 60.684 55.000 0.00 0.00 0.00 4.93
546 884 0.249238 GCATCCTAGTGTCCAGCGAG 60.249 60.000 0.00 0.00 0.00 5.03
547 885 1.107114 CATCCTAGTGTCCAGCGAGT 58.893 55.000 0.00 0.00 0.00 4.18
548 886 1.066303 CATCCTAGTGTCCAGCGAGTC 59.934 57.143 0.00 0.00 0.00 3.36
549 887 0.037734 TCCTAGTGTCCAGCGAGTCA 59.962 55.000 0.00 0.00 0.00 3.41
550 888 0.888619 CCTAGTGTCCAGCGAGTCAA 59.111 55.000 0.00 0.00 0.00 3.18
551 889 1.402984 CCTAGTGTCCAGCGAGTCAAC 60.403 57.143 0.00 0.00 0.00 3.18
552 890 0.240145 TAGTGTCCAGCGAGTCAACG 59.760 55.000 0.00 0.00 0.00 4.10
553 891 1.007734 GTGTCCAGCGAGTCAACGA 60.008 57.895 0.00 0.00 35.09 3.85
554 892 0.388649 GTGTCCAGCGAGTCAACGAT 60.389 55.000 0.00 0.00 35.09 3.73
555 893 0.388520 TGTCCAGCGAGTCAACGATG 60.389 55.000 0.00 0.00 46.78 3.84
556 894 1.446099 TCCAGCGAGTCAACGATGC 60.446 57.895 0.00 0.00 46.06 3.91
557 895 1.446792 CCAGCGAGTCAACGATGCT 60.447 57.895 0.00 0.00 46.06 3.79
558 896 1.016130 CCAGCGAGTCAACGATGCTT 61.016 55.000 0.00 0.00 46.06 3.91
559 897 0.094216 CAGCGAGTCAACGATGCTTG 59.906 55.000 0.00 0.00 42.22 4.01
560 898 1.225854 GCGAGTCAACGATGCTTGC 60.226 57.895 11.47 11.47 34.90 4.01
561 899 1.421485 CGAGTCAACGATGCTTGCC 59.579 57.895 0.00 0.00 35.09 4.52
562 900 1.291184 CGAGTCAACGATGCTTGCCA 61.291 55.000 0.00 0.00 35.09 4.92
563 901 0.166814 GAGTCAACGATGCTTGCCAC 59.833 55.000 0.00 0.00 0.00 5.01
564 902 1.154413 GTCAACGATGCTTGCCACG 60.154 57.895 0.00 6.89 0.00 4.94
565 903 1.596752 TCAACGATGCTTGCCACGT 60.597 52.632 7.93 7.93 40.64 4.49
566 904 1.440850 CAACGATGCTTGCCACGTG 60.441 57.895 9.08 9.08 38.92 4.49
567 905 1.596752 AACGATGCTTGCCACGTGA 60.597 52.632 19.30 0.00 38.92 4.35
568 906 0.955428 AACGATGCTTGCCACGTGAT 60.955 50.000 19.30 0.00 38.92 3.06
569 907 1.349627 CGATGCTTGCCACGTGATC 59.650 57.895 19.30 9.81 0.00 2.92
570 908 1.360931 CGATGCTTGCCACGTGATCA 61.361 55.000 19.30 11.77 0.00 2.92
571 909 0.804364 GATGCTTGCCACGTGATCAA 59.196 50.000 19.30 18.35 0.00 2.57
572 910 1.199789 GATGCTTGCCACGTGATCAAA 59.800 47.619 19.30 7.18 0.00 2.69
573 911 1.246649 TGCTTGCCACGTGATCAAAT 58.753 45.000 19.30 0.00 0.00 2.32
574 912 1.199789 TGCTTGCCACGTGATCAAATC 59.800 47.619 19.30 14.04 0.00 2.17
575 913 1.468054 GCTTGCCACGTGATCAAATCC 60.468 52.381 19.30 8.07 0.00 3.01
576 914 1.133025 CTTGCCACGTGATCAAATCCC 59.867 52.381 19.30 0.00 0.00 3.85
577 915 0.037447 TGCCACGTGATCAAATCCCA 59.963 50.000 19.30 0.00 0.00 4.37
578 916 0.734889 GCCACGTGATCAAATCCCAG 59.265 55.000 19.30 0.00 0.00 4.45
579 917 0.734889 CCACGTGATCAAATCCCAGC 59.265 55.000 19.30 0.00 0.00 4.85
580 918 1.679944 CCACGTGATCAAATCCCAGCT 60.680 52.381 19.30 0.00 0.00 4.24
581 919 2.419990 CCACGTGATCAAATCCCAGCTA 60.420 50.000 19.30 0.00 0.00 3.32
582 920 3.270027 CACGTGATCAAATCCCAGCTAA 58.730 45.455 10.90 0.00 0.00 3.09
583 921 3.689161 CACGTGATCAAATCCCAGCTAAA 59.311 43.478 10.90 0.00 0.00 1.85
584 922 3.689649 ACGTGATCAAATCCCAGCTAAAC 59.310 43.478 0.00 0.00 0.00 2.01
585 923 3.065371 CGTGATCAAATCCCAGCTAAACC 59.935 47.826 0.00 0.00 0.00 3.27
586 924 3.381590 GTGATCAAATCCCAGCTAAACCC 59.618 47.826 0.00 0.00 0.00 4.11
587 925 2.525105 TCAAATCCCAGCTAAACCCC 57.475 50.000 0.00 0.00 0.00 4.95
588 926 1.006639 TCAAATCCCAGCTAAACCCCC 59.993 52.381 0.00 0.00 0.00 5.40
589 927 1.007118 CAAATCCCAGCTAAACCCCCT 59.993 52.381 0.00 0.00 0.00 4.79
590 928 0.927029 AATCCCAGCTAAACCCCCTC 59.073 55.000 0.00 0.00 0.00 4.30
591 929 1.345715 ATCCCAGCTAAACCCCCTCG 61.346 60.000 0.00 0.00 0.00 4.63
592 930 1.993391 CCCAGCTAAACCCCCTCGA 60.993 63.158 0.00 0.00 0.00 4.04
593 931 1.522569 CCAGCTAAACCCCCTCGAG 59.477 63.158 5.13 5.13 0.00 4.04
594 932 1.522569 CAGCTAAACCCCCTCGAGG 59.477 63.158 25.36 25.36 0.00 4.63
595 933 1.080538 AGCTAAACCCCCTCGAGGT 59.919 57.895 29.25 13.53 40.14 3.85
599 937 4.324521 AACCCCCTCGAGGTTTGA 57.675 55.556 29.25 0.00 45.46 2.69
600 938 2.547171 AACCCCCTCGAGGTTTGAA 58.453 52.632 29.25 0.00 45.46 2.69
601 939 0.848053 AACCCCCTCGAGGTTTGAAA 59.152 50.000 29.25 0.00 45.46 2.69
602 940 1.073098 ACCCCCTCGAGGTTTGAAAT 58.927 50.000 29.25 5.33 32.05 2.17
603 941 2.271777 ACCCCCTCGAGGTTTGAAATA 58.728 47.619 29.25 0.00 32.05 1.40
604 942 2.026542 ACCCCCTCGAGGTTTGAAATAC 60.027 50.000 29.25 0.00 32.05 1.89
605 943 2.026636 CCCCCTCGAGGTTTGAAATACA 60.027 50.000 29.25 0.00 0.00 2.29
606 944 3.007635 CCCCTCGAGGTTTGAAATACAC 58.992 50.000 29.25 0.00 0.00 2.90
607 945 3.007635 CCCTCGAGGTTTGAAATACACC 58.992 50.000 29.25 0.00 0.00 4.16
608 946 2.671396 CCTCGAGGTTTGAAATACACCG 59.329 50.000 24.04 0.00 0.00 4.94
609 947 2.671396 CTCGAGGTTTGAAATACACCGG 59.329 50.000 3.91 0.00 0.00 5.28
610 948 1.735571 CGAGGTTTGAAATACACCGGG 59.264 52.381 6.32 0.00 0.00 5.73
611 949 2.613474 CGAGGTTTGAAATACACCGGGA 60.613 50.000 6.32 0.00 0.00 5.14
612 950 3.617284 GAGGTTTGAAATACACCGGGAT 58.383 45.455 6.32 0.00 0.00 3.85
613 951 3.617284 AGGTTTGAAATACACCGGGATC 58.383 45.455 6.32 0.00 0.00 3.36
614 952 3.009695 AGGTTTGAAATACACCGGGATCA 59.990 43.478 6.32 0.00 0.00 2.92
615 953 3.759618 GGTTTGAAATACACCGGGATCAA 59.240 43.478 6.32 4.12 0.00 2.57
616 954 4.218852 GGTTTGAAATACACCGGGATCAAA 59.781 41.667 6.32 10.04 35.20 2.69
617 955 5.399013 GTTTGAAATACACCGGGATCAAAG 58.601 41.667 6.32 0.00 37.43 2.77
618 956 4.561500 TGAAATACACCGGGATCAAAGA 57.438 40.909 6.32 0.00 0.00 2.52
619 957 4.513442 TGAAATACACCGGGATCAAAGAG 58.487 43.478 6.32 0.00 0.00 2.85
620 958 4.019681 TGAAATACACCGGGATCAAAGAGT 60.020 41.667 6.32 0.00 0.00 3.24
621 959 4.569719 AATACACCGGGATCAAAGAGTT 57.430 40.909 6.32 0.00 0.00 3.01
622 960 2.951229 ACACCGGGATCAAAGAGTTT 57.049 45.000 6.32 0.00 0.00 2.66
623 961 2.504367 ACACCGGGATCAAAGAGTTTG 58.496 47.619 6.32 0.00 41.96 2.93
624 962 1.812571 CACCGGGATCAAAGAGTTTGG 59.187 52.381 6.32 0.00 40.98 3.28
625 963 1.423921 ACCGGGATCAAAGAGTTTGGT 59.576 47.619 6.32 0.00 40.98 3.67
626 964 1.812571 CCGGGATCAAAGAGTTTGGTG 59.187 52.381 0.00 0.00 40.98 4.17
627 965 2.504367 CGGGATCAAAGAGTTTGGTGT 58.496 47.619 0.00 0.00 40.98 4.16
628 966 2.226437 CGGGATCAAAGAGTTTGGTGTG 59.774 50.000 0.00 0.00 40.98 3.82
629 967 2.029918 GGGATCAAAGAGTTTGGTGTGC 60.030 50.000 0.00 0.00 40.98 4.57
630 968 2.887152 GGATCAAAGAGTTTGGTGTGCT 59.113 45.455 0.00 0.00 40.98 4.40
631 969 3.304928 GGATCAAAGAGTTTGGTGTGCTG 60.305 47.826 0.00 0.00 40.98 4.41
632 970 2.997980 TCAAAGAGTTTGGTGTGCTGA 58.002 42.857 0.00 0.00 40.98 4.26
633 971 3.554934 TCAAAGAGTTTGGTGTGCTGAT 58.445 40.909 0.00 0.00 40.98 2.90
634 972 3.953612 TCAAAGAGTTTGGTGTGCTGATT 59.046 39.130 0.00 0.00 40.98 2.57
635 973 4.402155 TCAAAGAGTTTGGTGTGCTGATTT 59.598 37.500 0.00 0.00 40.98 2.17
636 974 4.574599 AAGAGTTTGGTGTGCTGATTTC 57.425 40.909 0.00 0.00 0.00 2.17
637 975 2.887152 AGAGTTTGGTGTGCTGATTTCC 59.113 45.455 0.00 0.00 0.00 3.13
638 976 1.608590 AGTTTGGTGTGCTGATTTCCG 59.391 47.619 0.00 0.00 0.00 4.30
639 977 0.958091 TTTGGTGTGCTGATTTCCGG 59.042 50.000 0.00 0.00 0.00 5.14
640 978 0.109532 TTGGTGTGCTGATTTCCGGA 59.890 50.000 0.00 0.00 0.00 5.14
641 979 0.327924 TGGTGTGCTGATTTCCGGAT 59.672 50.000 4.15 0.00 0.00 4.18
642 980 1.271871 TGGTGTGCTGATTTCCGGATT 60.272 47.619 4.15 0.00 0.00 3.01
643 981 2.026729 TGGTGTGCTGATTTCCGGATTA 60.027 45.455 4.15 0.00 0.00 1.75
644 982 3.214328 GGTGTGCTGATTTCCGGATTAT 58.786 45.455 4.15 1.31 0.00 1.28
645 983 4.141597 TGGTGTGCTGATTTCCGGATTATA 60.142 41.667 4.15 0.00 0.00 0.98
646 984 4.819630 GGTGTGCTGATTTCCGGATTATAA 59.180 41.667 4.15 0.00 0.00 0.98
647 985 5.298276 GGTGTGCTGATTTCCGGATTATAAA 59.702 40.000 4.15 0.00 0.00 1.40
648 986 6.016276 GGTGTGCTGATTTCCGGATTATAAAT 60.016 38.462 4.15 0.34 0.00 1.40
649 987 7.425606 GTGTGCTGATTTCCGGATTATAAATT 58.574 34.615 4.15 0.00 0.00 1.82
650 988 7.920682 GTGTGCTGATTTCCGGATTATAAATTT 59.079 33.333 4.15 0.00 0.00 1.82
651 989 9.126151 TGTGCTGATTTCCGGATTATAAATTTA 57.874 29.630 4.15 0.00 0.00 1.40
652 990 9.612620 GTGCTGATTTCCGGATTATAAATTTAG 57.387 33.333 4.15 5.91 0.00 1.85
653 991 8.792633 TGCTGATTTCCGGATTATAAATTTAGG 58.207 33.333 4.15 0.00 0.00 2.69
654 992 8.244113 GCTGATTTCCGGATTATAAATTTAGGG 58.756 37.037 4.15 0.00 0.00 3.53
655 993 9.297037 CTGATTTCCGGATTATAAATTTAGGGT 57.703 33.333 4.15 0.00 0.00 4.34
656 994 9.649316 TGATTTCCGGATTATAAATTTAGGGTT 57.351 29.630 4.15 0.00 0.00 4.11
658 996 7.733402 TTCCGGATTATAAATTTAGGGTTCG 57.267 36.000 4.15 5.35 0.00 3.95
659 997 7.065120 TCCGGATTATAAATTTAGGGTTCGA 57.935 36.000 0.00 0.00 0.00 3.71
660 998 7.682628 TCCGGATTATAAATTTAGGGTTCGAT 58.317 34.615 0.00 0.00 0.00 3.59
661 999 8.158789 TCCGGATTATAAATTTAGGGTTCGATT 58.841 33.333 0.00 0.00 0.00 3.34
662 1000 8.789762 CCGGATTATAAATTTAGGGTTCGATTT 58.210 33.333 0.00 0.00 0.00 2.17
670 1008 7.696992 AATTTAGGGTTCGATTTAGCTTTCA 57.303 32.000 0.00 0.00 0.00 2.69
671 1009 6.490566 TTTAGGGTTCGATTTAGCTTTCAC 57.509 37.500 0.00 0.00 0.00 3.18
672 1010 4.287766 AGGGTTCGATTTAGCTTTCACT 57.712 40.909 0.00 0.00 0.00 3.41
673 1011 4.652822 AGGGTTCGATTTAGCTTTCACTT 58.347 39.130 0.00 0.00 0.00 3.16
674 1012 5.801380 AGGGTTCGATTTAGCTTTCACTTA 58.199 37.500 0.00 0.00 0.00 2.24
675 1013 6.415573 AGGGTTCGATTTAGCTTTCACTTAT 58.584 36.000 0.00 0.00 0.00 1.73
676 1014 7.562135 AGGGTTCGATTTAGCTTTCACTTATA 58.438 34.615 0.00 0.00 0.00 0.98
677 1015 8.044908 AGGGTTCGATTTAGCTTTCACTTATAA 58.955 33.333 0.00 0.00 0.00 0.98
678 1016 8.336080 GGGTTCGATTTAGCTTTCACTTATAAG 58.664 37.037 11.05 11.05 0.00 1.73
679 1017 8.880750 GGTTCGATTTAGCTTTCACTTATAAGT 58.119 33.333 12.50 12.50 40.60 2.24
690 1028 9.961265 GCTTTCACTTATAAGTTTAAGGTTTGT 57.039 29.630 24.33 1.02 37.08 2.83
701 1039 8.911918 AAGTTTAAGGTTTGTTTTGGACTTTT 57.088 26.923 0.00 0.00 0.00 2.27
702 1040 8.911918 AGTTTAAGGTTTGTTTTGGACTTTTT 57.088 26.923 0.00 0.00 0.00 1.94
703 1041 9.999660 AGTTTAAGGTTTGTTTTGGACTTTTTA 57.000 25.926 0.00 0.00 0.00 1.52
715 1053 0.187361 ACTTTTTACTGCCTGGCCCA 59.813 50.000 17.53 0.00 0.00 5.36
773 1118 4.218852 TCCGGCGTTTGGATTAAAGAAAAT 59.781 37.500 6.01 0.00 0.00 1.82
793 1144 5.494632 AATAAAAGGCGTTTCTTATCCCG 57.505 39.130 4.63 0.00 0.00 5.14
795 1146 2.019948 AAGGCGTTTCTTATCCCGTC 57.980 50.000 0.00 0.00 0.00 4.79
888 1244 4.359434 AAGTTTCTTCCTCACCTCTTCC 57.641 45.455 0.00 0.00 0.00 3.46
889 1245 2.640332 AGTTTCTTCCTCACCTCTTCCC 59.360 50.000 0.00 0.00 0.00 3.97
890 1246 2.640332 GTTTCTTCCTCACCTCTTCCCT 59.360 50.000 0.00 0.00 0.00 4.20
891 1247 3.838903 GTTTCTTCCTCACCTCTTCCCTA 59.161 47.826 0.00 0.00 0.00 3.53
892 1248 3.390175 TCTTCCTCACCTCTTCCCTAG 57.610 52.381 0.00 0.00 0.00 3.02
893 1249 2.655407 TCTTCCTCACCTCTTCCCTAGT 59.345 50.000 0.00 0.00 0.00 2.57
894 1250 3.077695 TCTTCCTCACCTCTTCCCTAGTT 59.922 47.826 0.00 0.00 0.00 2.24
895 1251 4.294168 TCTTCCTCACCTCTTCCCTAGTTA 59.706 45.833 0.00 0.00 0.00 2.24
896 1252 4.687262 TCCTCACCTCTTCCCTAGTTAA 57.313 45.455 0.00 0.00 0.00 2.01
897 1253 5.222278 TCCTCACCTCTTCCCTAGTTAAT 57.778 43.478 0.00 0.00 0.00 1.40
898 1254 5.600749 TCCTCACCTCTTCCCTAGTTAATT 58.399 41.667 0.00 0.00 0.00 1.40
899 1255 6.030082 TCCTCACCTCTTCCCTAGTTAATTT 58.970 40.000 0.00 0.00 0.00 1.82
900 1256 6.156429 TCCTCACCTCTTCCCTAGTTAATTTC 59.844 42.308 0.00 0.00 0.00 2.17
901 1257 6.157123 CCTCACCTCTTCCCTAGTTAATTTCT 59.843 42.308 0.00 0.00 0.00 2.52
902 1258 7.311360 CCTCACCTCTTCCCTAGTTAATTTCTT 60.311 40.741 0.00 0.00 0.00 2.52
903 1259 7.621796 TCACCTCTTCCCTAGTTAATTTCTTC 58.378 38.462 0.00 0.00 0.00 2.87
904 1260 6.824196 CACCTCTTCCCTAGTTAATTTCTTCC 59.176 42.308 0.00 0.00 0.00 3.46
905 1261 6.069556 ACCTCTTCCCTAGTTAATTTCTTCCC 60.070 42.308 0.00 0.00 0.00 3.97
906 1262 5.985911 TCTTCCCTAGTTAATTTCTTCCCG 58.014 41.667 0.00 0.00 0.00 5.14
907 1263 5.722923 TCTTCCCTAGTTAATTTCTTCCCGA 59.277 40.000 0.00 0.00 0.00 5.14
908 1264 6.386050 TCTTCCCTAGTTAATTTCTTCCCGAT 59.614 38.462 0.00 0.00 0.00 4.18
909 1265 6.570654 TCCCTAGTTAATTTCTTCCCGATT 57.429 37.500 0.00 0.00 0.00 3.34
910 1266 6.965607 TCCCTAGTTAATTTCTTCCCGATTT 58.034 36.000 0.00 0.00 0.00 2.17
911 1267 7.407729 TCCCTAGTTAATTTCTTCCCGATTTT 58.592 34.615 0.00 0.00 0.00 1.82
912 1268 7.555195 TCCCTAGTTAATTTCTTCCCGATTTTC 59.445 37.037 0.00 0.00 0.00 2.29
1164 1598 3.015753 GGTCCCTCCTTGGTCCCC 61.016 72.222 0.00 0.00 0.00 4.81
1364 1798 2.681778 CAGACCGGACCTCTGGCT 60.682 66.667 9.46 0.00 46.43 4.75
1446 1880 1.300620 CTTCTTCCACACGCGGACA 60.301 57.895 12.47 0.00 33.75 4.02
1503 1937 1.472552 CGCCACAGGATCATCGGTTTA 60.473 52.381 0.00 0.00 0.00 2.01
1717 2157 1.599518 TTCCCGTGGACACATGTGC 60.600 57.895 25.68 17.27 36.87 4.57
1778 2218 0.902531 CACCGAGGGCTCTTCCTTAA 59.097 55.000 0.00 0.00 37.25 1.85
1779 2219 1.278127 CACCGAGGGCTCTTCCTTAAA 59.722 52.381 0.00 0.00 37.25 1.52
1815 2255 1.012486 AAGGAAGGCTTTACGCGACG 61.012 55.000 15.93 0.00 40.44 5.12
1883 2323 1.642037 CCACATCCTGTGCTTGCTCG 61.642 60.000 1.71 0.00 46.51 5.03
1911 2351 4.761975 CAAATGATTTTGGTGATCAGGGG 58.238 43.478 0.00 0.00 38.85 4.79
1917 2357 1.595311 TTGGTGATCAGGGGCTATGT 58.405 50.000 0.00 0.00 0.00 2.29
1947 2387 4.394712 GTGGAGTCCGGTGGGCAG 62.395 72.222 4.30 0.00 0.00 4.85
2008 2448 3.267974 CGGAGCCCTTTCAGCAAC 58.732 61.111 0.00 0.00 0.00 4.17
2370 2811 3.884693 TCTTCTTTGCATGTGTCATGTGT 59.115 39.130 10.68 0.00 0.00 3.72
2508 2951 7.678927 GCAAAAGATTCTAAACTACGGATTCCC 60.679 40.741 0.00 0.00 0.00 3.97
2572 3015 2.875672 GCACCTCACACTAGCCATTGAA 60.876 50.000 0.00 0.00 0.00 2.69
2573 3016 3.614092 CACCTCACACTAGCCATTGAAT 58.386 45.455 0.00 0.00 0.00 2.57
2575 3018 4.813161 CACCTCACACTAGCCATTGAATAG 59.187 45.833 0.00 0.00 0.00 1.73
2645 3103 1.734465 CGCTCAGTTGGGATCTTTGTC 59.266 52.381 0.00 0.00 0.00 3.18
2701 3161 6.401688 CGCATTGTGCATGATCTTTTGATTTT 60.402 34.615 0.00 0.00 45.36 1.82
2702 3162 7.302524 GCATTGTGCATGATCTTTTGATTTTT 58.697 30.769 0.00 0.00 44.26 1.94
2910 3372 1.460255 CCGGCATGGGTATTGGGAT 59.540 57.895 0.00 0.00 0.00 3.85
2913 3375 1.478471 CGGCATGGGTATTGGGATCAA 60.478 52.381 0.00 0.00 37.28 2.57
3029 3491 1.632965 GCGGTGGGGGACTAGGAATT 61.633 60.000 0.00 0.00 0.00 2.17
3039 3501 5.437946 GGGGACTAGGAATTGAAACCTAAG 58.562 45.833 0.00 0.00 38.14 2.18
3131 3594 5.594926 CAGGGATTGCAAATATTTGGAGAC 58.405 41.667 25.61 19.50 39.65 3.36
3132 3595 4.339247 AGGGATTGCAAATATTTGGAGACG 59.661 41.667 25.61 3.80 39.65 4.18
3176 3639 4.036734 CAGTCAGGTTTGCATTACAGTTGT 59.963 41.667 0.00 0.00 0.00 3.32
3301 3765 0.960364 TTGCTGGAGTTCATTCGGCC 60.960 55.000 0.00 0.00 0.00 6.13
3306 3770 0.678048 GGAGTTCATTCGGCCAGCTT 60.678 55.000 2.24 0.00 0.00 3.74
3397 3864 2.175878 AGATAATTGCCTGGCTAGCG 57.824 50.000 21.03 0.00 0.00 4.26
3409 3876 4.381612 GCCTGGCTAGCGTATACAATATCA 60.382 45.833 12.43 0.00 0.00 2.15
3500 4005 7.040478 GCCATGTTATCAGCATTTATGGTCTTA 60.040 37.037 0.00 0.00 36.17 2.10
3508 4013 9.976511 ATCAGCATTTATGGTCTTATTTTGATG 57.023 29.630 0.00 0.00 36.17 3.07
3553 4058 8.675705 TGGTTATATGATTCAACCACTACATG 57.324 34.615 4.20 0.00 45.15 3.21
3562 4067 3.933879 CCACTACATGGTGAGTGCA 57.066 52.632 15.53 0.00 44.46 4.57
3563 4068 2.183478 CCACTACATGGTGAGTGCAA 57.817 50.000 15.53 0.00 44.46 4.08
3564 4069 2.503331 CCACTACATGGTGAGTGCAAA 58.497 47.619 15.53 0.00 44.46 3.68
3565 4070 3.084039 CCACTACATGGTGAGTGCAAAT 58.916 45.455 15.53 0.00 44.46 2.32
3566 4071 4.260985 CCACTACATGGTGAGTGCAAATA 58.739 43.478 15.53 0.00 44.46 1.40
3567 4072 4.699735 CCACTACATGGTGAGTGCAAATAA 59.300 41.667 15.53 0.00 44.46 1.40
3568 4073 5.163723 CCACTACATGGTGAGTGCAAATAAG 60.164 44.000 15.53 1.76 44.46 1.73
3569 4074 5.412594 CACTACATGGTGAGTGCAAATAAGT 59.587 40.000 10.56 0.00 39.34 2.24
3570 4075 6.593770 CACTACATGGTGAGTGCAAATAAGTA 59.406 38.462 10.56 0.00 39.34 2.24
3571 4076 5.880054 ACATGGTGAGTGCAAATAAGTAC 57.120 39.130 0.00 0.00 0.00 2.73
3572 4077 5.560724 ACATGGTGAGTGCAAATAAGTACT 58.439 37.500 0.00 0.00 37.15 2.73
3582 4087 9.804758 GAGTGCAAATAAGTACTCTATGTAACT 57.195 33.333 0.00 2.72 44.59 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 240 6.264518 ACCGAAGTGTTTAACATTCCTGAATT 59.735 34.615 0.00 0.00 0.00 2.17
235 241 5.768164 ACCGAAGTGTTTAACATTCCTGAAT 59.232 36.000 0.00 0.00 0.00 2.57
371 472 0.037975 CCAGCAGCCGCAAAAGAATT 60.038 50.000 0.00 0.00 42.27 2.17
498 836 3.794475 GCCGCTCGCTCTACTTGTTTATA 60.794 47.826 0.00 0.00 0.00 0.98
500 838 1.734707 GCCGCTCGCTCTACTTGTTTA 60.735 52.381 0.00 0.00 0.00 2.01
519 857 2.551071 GGACACTAGGATGCTAATGGGC 60.551 54.545 7.63 0.00 0.00 5.36
520 858 2.705658 TGGACACTAGGATGCTAATGGG 59.294 50.000 7.63 0.00 0.00 4.00
521 859 3.805108 GCTGGACACTAGGATGCTAATGG 60.805 52.174 7.63 0.00 0.00 3.16
522 860 3.397482 GCTGGACACTAGGATGCTAATG 58.603 50.000 0.75 0.75 0.00 1.90
523 861 2.036475 CGCTGGACACTAGGATGCTAAT 59.964 50.000 0.00 0.00 0.00 1.73
524 862 1.409064 CGCTGGACACTAGGATGCTAA 59.591 52.381 0.00 0.00 0.00 3.09
525 863 1.032794 CGCTGGACACTAGGATGCTA 58.967 55.000 0.00 0.00 0.00 3.49
526 864 0.684479 TCGCTGGACACTAGGATGCT 60.684 55.000 0.00 0.00 0.00 3.79
527 865 0.249238 CTCGCTGGACACTAGGATGC 60.249 60.000 0.00 0.00 0.00 3.91
528 866 1.066303 GACTCGCTGGACACTAGGATG 59.934 57.143 0.00 0.00 0.00 3.51
529 867 1.341089 TGACTCGCTGGACACTAGGAT 60.341 52.381 0.00 0.00 0.00 3.24
530 868 0.037734 TGACTCGCTGGACACTAGGA 59.962 55.000 0.00 0.00 0.00 2.94
531 869 0.888619 TTGACTCGCTGGACACTAGG 59.111 55.000 0.00 0.00 0.00 3.02
532 870 1.729472 CGTTGACTCGCTGGACACTAG 60.729 57.143 0.00 0.00 0.00 2.57
533 871 0.240145 CGTTGACTCGCTGGACACTA 59.760 55.000 0.00 0.00 0.00 2.74
534 872 1.007271 CGTTGACTCGCTGGACACT 60.007 57.895 0.00 0.00 0.00 3.55
535 873 0.388649 ATCGTTGACTCGCTGGACAC 60.389 55.000 0.00 0.00 0.00 3.67
536 874 0.388520 CATCGTTGACTCGCTGGACA 60.389 55.000 0.00 0.00 0.00 4.02
537 875 1.687494 GCATCGTTGACTCGCTGGAC 61.687 60.000 0.00 0.00 0.00 4.02
538 876 1.446099 GCATCGTTGACTCGCTGGA 60.446 57.895 0.00 0.00 0.00 3.86
539 877 1.016130 AAGCATCGTTGACTCGCTGG 61.016 55.000 0.00 0.00 32.14 4.85
540 878 0.094216 CAAGCATCGTTGACTCGCTG 59.906 55.000 0.00 0.00 32.14 5.18
541 879 1.630244 GCAAGCATCGTTGACTCGCT 61.630 55.000 0.00 0.00 33.45 4.93
542 880 1.225854 GCAAGCATCGTTGACTCGC 60.226 57.895 0.00 0.00 0.00 5.03
543 881 1.291184 TGGCAAGCATCGTTGACTCG 61.291 55.000 0.00 0.00 36.30 4.18
544 882 0.166814 GTGGCAAGCATCGTTGACTC 59.833 55.000 0.00 0.00 36.30 3.36
545 883 1.568612 CGTGGCAAGCATCGTTGACT 61.569 55.000 0.00 0.00 36.30 3.41
546 884 1.154413 CGTGGCAAGCATCGTTGAC 60.154 57.895 0.00 0.00 35.83 3.18
547 885 1.596752 ACGTGGCAAGCATCGTTGA 60.597 52.632 0.00 0.00 32.62 3.18
548 886 1.440850 CACGTGGCAAGCATCGTTG 60.441 57.895 7.95 0.00 34.30 4.10
549 887 0.955428 ATCACGTGGCAAGCATCGTT 60.955 50.000 17.00 0.00 34.30 3.85
550 888 1.361668 GATCACGTGGCAAGCATCGT 61.362 55.000 17.00 0.00 36.99 3.73
551 889 1.349627 GATCACGTGGCAAGCATCG 59.650 57.895 17.00 0.00 0.00 3.84
552 890 0.804364 TTGATCACGTGGCAAGCATC 59.196 50.000 17.00 10.52 0.00 3.91
553 891 1.246649 TTTGATCACGTGGCAAGCAT 58.753 45.000 17.00 0.00 0.00 3.79
554 892 1.199789 GATTTGATCACGTGGCAAGCA 59.800 47.619 17.00 2.13 0.00 3.91
555 893 1.468054 GGATTTGATCACGTGGCAAGC 60.468 52.381 17.00 14.52 0.00 4.01
556 894 1.133025 GGGATTTGATCACGTGGCAAG 59.867 52.381 17.00 0.00 0.00 4.01
557 895 1.173043 GGGATTTGATCACGTGGCAA 58.827 50.000 17.00 17.00 0.00 4.52
558 896 0.037447 TGGGATTTGATCACGTGGCA 59.963 50.000 17.00 11.73 34.70 4.92
559 897 0.734889 CTGGGATTTGATCACGTGGC 59.265 55.000 17.00 9.03 34.70 5.01
560 898 0.734889 GCTGGGATTTGATCACGTGG 59.265 55.000 17.00 0.00 34.70 4.94
561 899 1.742761 AGCTGGGATTTGATCACGTG 58.257 50.000 9.94 9.94 34.70 4.49
562 900 3.627395 TTAGCTGGGATTTGATCACGT 57.373 42.857 0.00 0.00 34.70 4.49
563 901 3.065371 GGTTTAGCTGGGATTTGATCACG 59.935 47.826 0.00 0.00 34.70 4.35
564 902 3.381590 GGGTTTAGCTGGGATTTGATCAC 59.618 47.826 0.00 0.00 0.00 3.06
565 903 3.627237 GGGGTTTAGCTGGGATTTGATCA 60.627 47.826 0.00 0.00 0.00 2.92
566 904 2.959030 GGGGTTTAGCTGGGATTTGATC 59.041 50.000 0.00 0.00 0.00 2.92
567 905 2.359249 GGGGGTTTAGCTGGGATTTGAT 60.359 50.000 0.00 0.00 0.00 2.57
568 906 1.006639 GGGGGTTTAGCTGGGATTTGA 59.993 52.381 0.00 0.00 0.00 2.69
569 907 1.007118 AGGGGGTTTAGCTGGGATTTG 59.993 52.381 0.00 0.00 0.00 2.32
570 908 1.288037 GAGGGGGTTTAGCTGGGATTT 59.712 52.381 0.00 0.00 0.00 2.17
571 909 0.927029 GAGGGGGTTTAGCTGGGATT 59.073 55.000 0.00 0.00 0.00 3.01
572 910 1.345715 CGAGGGGGTTTAGCTGGGAT 61.346 60.000 0.00 0.00 0.00 3.85
573 911 1.993391 CGAGGGGGTTTAGCTGGGA 60.993 63.158 0.00 0.00 0.00 4.37
574 912 1.972660 CTCGAGGGGGTTTAGCTGGG 61.973 65.000 3.91 0.00 0.00 4.45
575 913 1.522569 CTCGAGGGGGTTTAGCTGG 59.477 63.158 3.91 0.00 0.00 4.85
576 914 1.265454 ACCTCGAGGGGGTTTAGCTG 61.265 60.000 34.04 5.90 40.27 4.24
577 915 0.546988 AACCTCGAGGGGGTTTAGCT 60.547 55.000 34.04 8.06 43.66 3.32
578 916 1.988817 AACCTCGAGGGGGTTTAGC 59.011 57.895 34.04 0.00 43.66 3.09
583 921 1.073098 ATTTCAAACCTCGAGGGGGT 58.927 50.000 34.04 16.92 40.27 4.95
584 922 2.026636 TGTATTTCAAACCTCGAGGGGG 60.027 50.000 34.04 22.14 40.27 5.40
585 923 3.007635 GTGTATTTCAAACCTCGAGGGG 58.992 50.000 34.04 22.49 40.27 4.79
586 924 3.007635 GGTGTATTTCAAACCTCGAGGG 58.992 50.000 34.04 17.51 40.27 4.30
587 925 2.671396 CGGTGTATTTCAAACCTCGAGG 59.329 50.000 30.11 30.11 42.17 4.63
588 926 2.671396 CCGGTGTATTTCAAACCTCGAG 59.329 50.000 5.13 5.13 0.00 4.04
589 927 2.613474 CCCGGTGTATTTCAAACCTCGA 60.613 50.000 0.00 0.00 0.00 4.04
590 928 1.735571 CCCGGTGTATTTCAAACCTCG 59.264 52.381 0.00 0.00 0.00 4.63
591 929 3.062122 TCCCGGTGTATTTCAAACCTC 57.938 47.619 0.00 0.00 0.00 3.85
592 930 3.009695 TGATCCCGGTGTATTTCAAACCT 59.990 43.478 0.00 0.00 0.00 3.50
593 931 3.349022 TGATCCCGGTGTATTTCAAACC 58.651 45.455 0.00 0.00 0.00 3.27
594 932 5.182380 TCTTTGATCCCGGTGTATTTCAAAC 59.818 40.000 0.00 0.00 31.78 2.93
595 933 5.317808 TCTTTGATCCCGGTGTATTTCAAA 58.682 37.500 0.00 5.74 33.47 2.69
596 934 4.912586 TCTTTGATCCCGGTGTATTTCAA 58.087 39.130 0.00 0.00 0.00 2.69
597 935 4.019681 ACTCTTTGATCCCGGTGTATTTCA 60.020 41.667 0.00 0.00 0.00 2.69
598 936 4.514401 ACTCTTTGATCCCGGTGTATTTC 58.486 43.478 0.00 0.00 0.00 2.17
599 937 4.569719 ACTCTTTGATCCCGGTGTATTT 57.430 40.909 0.00 0.00 0.00 1.40
600 938 4.569719 AACTCTTTGATCCCGGTGTATT 57.430 40.909 0.00 0.00 0.00 1.89
601 939 4.261801 CAAACTCTTTGATCCCGGTGTAT 58.738 43.478 0.00 0.00 43.26 2.29
602 940 3.558321 CCAAACTCTTTGATCCCGGTGTA 60.558 47.826 0.00 0.00 43.26 2.90
603 941 2.504367 CAAACTCTTTGATCCCGGTGT 58.496 47.619 0.00 0.00 43.26 4.16
604 942 1.812571 CCAAACTCTTTGATCCCGGTG 59.187 52.381 0.00 0.00 43.26 4.94
605 943 1.423921 ACCAAACTCTTTGATCCCGGT 59.576 47.619 0.00 0.00 43.26 5.28
606 944 1.812571 CACCAAACTCTTTGATCCCGG 59.187 52.381 0.00 0.00 43.26 5.73
607 945 2.226437 CACACCAAACTCTTTGATCCCG 59.774 50.000 0.00 0.00 43.26 5.14
608 946 2.029918 GCACACCAAACTCTTTGATCCC 60.030 50.000 0.00 0.00 43.26 3.85
609 947 2.887152 AGCACACCAAACTCTTTGATCC 59.113 45.455 0.00 0.00 43.26 3.36
610 948 3.565482 TCAGCACACCAAACTCTTTGATC 59.435 43.478 0.00 0.00 43.26 2.92
611 949 3.554934 TCAGCACACCAAACTCTTTGAT 58.445 40.909 0.00 0.00 43.26 2.57
612 950 2.997980 TCAGCACACCAAACTCTTTGA 58.002 42.857 0.00 0.00 43.26 2.69
613 951 3.996150 ATCAGCACACCAAACTCTTTG 57.004 42.857 0.00 0.00 40.32 2.77
614 952 4.202151 GGAAATCAGCACACCAAACTCTTT 60.202 41.667 0.00 0.00 0.00 2.52
615 953 3.319122 GGAAATCAGCACACCAAACTCTT 59.681 43.478 0.00 0.00 0.00 2.85
616 954 2.887152 GGAAATCAGCACACCAAACTCT 59.113 45.455 0.00 0.00 0.00 3.24
617 955 2.350772 CGGAAATCAGCACACCAAACTC 60.351 50.000 0.00 0.00 0.00 3.01
618 956 1.608590 CGGAAATCAGCACACCAAACT 59.391 47.619 0.00 0.00 0.00 2.66
619 957 1.335872 CCGGAAATCAGCACACCAAAC 60.336 52.381 0.00 0.00 0.00 2.93
620 958 0.958091 CCGGAAATCAGCACACCAAA 59.042 50.000 0.00 0.00 0.00 3.28
621 959 0.109532 TCCGGAAATCAGCACACCAA 59.890 50.000 0.00 0.00 0.00 3.67
622 960 0.327924 ATCCGGAAATCAGCACACCA 59.672 50.000 9.01 0.00 0.00 4.17
623 961 1.463674 AATCCGGAAATCAGCACACC 58.536 50.000 9.01 0.00 0.00 4.16
624 962 6.371809 TTTATAATCCGGAAATCAGCACAC 57.628 37.500 9.01 0.00 0.00 3.82
625 963 7.581213 AATTTATAATCCGGAAATCAGCACA 57.419 32.000 9.01 0.00 0.00 4.57
626 964 9.612620 CTAAATTTATAATCCGGAAATCAGCAC 57.387 33.333 9.01 0.00 0.00 4.40
627 965 8.792633 CCTAAATTTATAATCCGGAAATCAGCA 58.207 33.333 9.01 0.00 0.00 4.41
628 966 8.244113 CCCTAAATTTATAATCCGGAAATCAGC 58.756 37.037 9.01 0.00 0.00 4.26
629 967 9.297037 ACCCTAAATTTATAATCCGGAAATCAG 57.703 33.333 9.01 4.52 0.00 2.90
630 968 9.649316 AACCCTAAATTTATAATCCGGAAATCA 57.351 29.630 9.01 0.00 0.00 2.57
632 970 8.789762 CGAACCCTAAATTTATAATCCGGAAAT 58.210 33.333 9.01 8.19 0.00 2.17
633 971 7.992033 TCGAACCCTAAATTTATAATCCGGAAA 59.008 33.333 9.01 0.00 0.00 3.13
634 972 7.507829 TCGAACCCTAAATTTATAATCCGGAA 58.492 34.615 9.01 0.00 0.00 4.30
635 973 7.065120 TCGAACCCTAAATTTATAATCCGGA 57.935 36.000 6.61 6.61 0.00 5.14
636 974 7.916914 ATCGAACCCTAAATTTATAATCCGG 57.083 36.000 0.00 0.00 0.00 5.14
644 982 9.233649 TGAAAGCTAAATCGAACCCTAAATTTA 57.766 29.630 0.00 0.00 0.00 1.40
645 983 8.027189 GTGAAAGCTAAATCGAACCCTAAATTT 58.973 33.333 0.00 0.00 0.00 1.82
646 984 7.393515 AGTGAAAGCTAAATCGAACCCTAAATT 59.606 33.333 0.00 0.00 0.00 1.82
647 985 6.884836 AGTGAAAGCTAAATCGAACCCTAAAT 59.115 34.615 0.00 0.00 0.00 1.40
648 986 6.235664 AGTGAAAGCTAAATCGAACCCTAAA 58.764 36.000 0.00 0.00 0.00 1.85
649 987 5.801380 AGTGAAAGCTAAATCGAACCCTAA 58.199 37.500 0.00 0.00 0.00 2.69
650 988 5.416271 AGTGAAAGCTAAATCGAACCCTA 57.584 39.130 0.00 0.00 0.00 3.53
651 989 4.287766 AGTGAAAGCTAAATCGAACCCT 57.712 40.909 0.00 0.00 0.00 4.34
652 990 6.679327 ATAAGTGAAAGCTAAATCGAACCC 57.321 37.500 0.00 0.00 0.00 4.11
653 991 8.880750 ACTTATAAGTGAAAGCTAAATCGAACC 58.119 33.333 17.35 0.00 37.98 3.62
664 1002 9.961265 ACAAACCTTAAACTTATAAGTGAAAGC 57.039 29.630 18.70 0.00 39.66 3.51
675 1013 9.999660 AAAAGTCCAAAACAAACCTTAAACTTA 57.000 25.926 0.00 0.00 0.00 2.24
676 1014 8.911918 AAAAGTCCAAAACAAACCTTAAACTT 57.088 26.923 0.00 0.00 0.00 2.66
677 1015 8.911918 AAAAAGTCCAAAACAAACCTTAAACT 57.088 26.923 0.00 0.00 0.00 2.66
679 1017 9.999660 AGTAAAAAGTCCAAAACAAACCTTAAA 57.000 25.926 0.00 0.00 0.00 1.52
680 1018 9.425577 CAGTAAAAAGTCCAAAACAAACCTTAA 57.574 29.630 0.00 0.00 0.00 1.85
681 1019 7.546316 GCAGTAAAAAGTCCAAAACAAACCTTA 59.454 33.333 0.00 0.00 0.00 2.69
682 1020 6.370442 GCAGTAAAAAGTCCAAAACAAACCTT 59.630 34.615 0.00 0.00 0.00 3.50
683 1021 5.872617 GCAGTAAAAAGTCCAAAACAAACCT 59.127 36.000 0.00 0.00 0.00 3.50
684 1022 5.064198 GGCAGTAAAAAGTCCAAAACAAACC 59.936 40.000 0.00 0.00 0.00 3.27
685 1023 5.872617 AGGCAGTAAAAAGTCCAAAACAAAC 59.127 36.000 0.00 0.00 0.00 2.93
686 1024 5.872070 CAGGCAGTAAAAAGTCCAAAACAAA 59.128 36.000 0.00 0.00 0.00 2.83
687 1025 5.415221 CAGGCAGTAAAAAGTCCAAAACAA 58.585 37.500 0.00 0.00 0.00 2.83
688 1026 4.142049 CCAGGCAGTAAAAAGTCCAAAACA 60.142 41.667 0.00 0.00 0.00 2.83
689 1027 4.368315 CCAGGCAGTAAAAAGTCCAAAAC 58.632 43.478 0.00 0.00 0.00 2.43
690 1028 3.181470 GCCAGGCAGTAAAAAGTCCAAAA 60.181 43.478 6.55 0.00 0.00 2.44
691 1029 2.364002 GCCAGGCAGTAAAAAGTCCAAA 59.636 45.455 6.55 0.00 0.00 3.28
692 1030 1.960689 GCCAGGCAGTAAAAAGTCCAA 59.039 47.619 6.55 0.00 0.00 3.53
693 1031 1.616159 GCCAGGCAGTAAAAAGTCCA 58.384 50.000 6.55 0.00 0.00 4.02
694 1032 0.888619 GGCCAGGCAGTAAAAAGTCC 59.111 55.000 15.19 0.00 0.00 3.85
695 1033 0.888619 GGGCCAGGCAGTAAAAAGTC 59.111 55.000 15.19 0.00 0.00 3.01
696 1034 0.187361 TGGGCCAGGCAGTAAAAAGT 59.813 50.000 15.19 0.00 0.00 2.66
697 1035 0.890683 CTGGGCCAGGCAGTAAAAAG 59.109 55.000 26.34 0.00 0.00 2.27
698 1036 0.541764 CCTGGGCCAGGCAGTAAAAA 60.542 55.000 38.22 0.00 45.13 1.94
699 1037 1.076549 CCTGGGCCAGGCAGTAAAA 59.923 57.895 38.22 0.00 45.13 1.52
700 1038 2.763215 CCTGGGCCAGGCAGTAAA 59.237 61.111 38.22 0.00 45.13 2.01
737 1075 4.020617 CCGGAGCAGAACTGGGCA 62.021 66.667 0.00 0.00 0.00 5.36
744 1089 2.463589 ATCCAAACGCCGGAGCAGAA 62.464 55.000 5.05 0.00 39.83 3.02
773 1118 3.934579 GACGGGATAAGAAACGCCTTTTA 59.065 43.478 0.00 0.00 0.00 1.52
888 1244 7.466860 CGGAAAATCGGGAAGAAATTAACTAGG 60.467 40.741 0.00 0.00 0.00 3.02
889 1245 7.407337 CGGAAAATCGGGAAGAAATTAACTAG 58.593 38.462 0.00 0.00 0.00 2.57
890 1246 6.316890 CCGGAAAATCGGGAAGAAATTAACTA 59.683 38.462 0.00 0.00 45.78 2.24
891 1247 5.124936 CCGGAAAATCGGGAAGAAATTAACT 59.875 40.000 0.00 0.00 45.78 2.24
892 1248 5.337554 CCGGAAAATCGGGAAGAAATTAAC 58.662 41.667 0.00 0.00 45.78 2.01
893 1249 5.570234 CCGGAAAATCGGGAAGAAATTAA 57.430 39.130 0.00 0.00 45.78 1.40
894 1250 5.442391 ATCCGGAAAATCGGGAAGAAATTA 58.558 37.500 9.01 0.00 46.76 1.40
895 1251 4.278310 ATCCGGAAAATCGGGAAGAAATT 58.722 39.130 9.01 0.00 46.76 1.82
896 1252 3.883489 GATCCGGAAAATCGGGAAGAAAT 59.117 43.478 9.01 0.00 46.76 2.17
897 1253 3.275999 GATCCGGAAAATCGGGAAGAAA 58.724 45.455 9.01 0.00 46.76 2.52
898 1254 2.420967 GGATCCGGAAAATCGGGAAGAA 60.421 50.000 9.01 0.00 46.76 2.52
899 1255 1.140252 GGATCCGGAAAATCGGGAAGA 59.860 52.381 9.01 0.00 46.76 2.87
900 1256 1.594331 GGATCCGGAAAATCGGGAAG 58.406 55.000 9.01 0.00 46.76 3.46
901 1257 0.179067 CGGATCCGGAAAATCGGGAA 60.179 55.000 26.95 0.00 46.76 3.97
905 1261 1.590525 TCGCGGATCCGGAAAATCG 60.591 57.895 33.98 26.03 40.19 3.34
906 1262 1.818221 CGTCGCGGATCCGGAAAATC 61.818 60.000 33.98 15.97 40.19 2.17
907 1263 1.881252 CGTCGCGGATCCGGAAAAT 60.881 57.895 33.98 0.00 40.19 1.82
908 1264 2.507547 CGTCGCGGATCCGGAAAA 60.508 61.111 33.98 7.27 40.19 2.29
909 1265 3.688475 GACGTCGCGGATCCGGAAA 62.688 63.158 33.98 7.96 40.19 3.13
910 1266 4.183686 GACGTCGCGGATCCGGAA 62.184 66.667 33.98 12.14 40.19 4.30
1035 1447 5.137551 GCCCTCTCCTCCATCTATATCTAC 58.862 50.000 0.00 0.00 0.00 2.59
1503 1937 2.566746 AGAATGATCAGTCCCTGGGTT 58.433 47.619 18.99 0.00 31.51 4.11
1617 2051 0.679505 CAGAGTTCCGGTTCCTGACA 59.320 55.000 0.00 0.00 0.00 3.58
1778 2218 1.897802 CTTGGAAGGGCAAGATGCTTT 59.102 47.619 2.00 0.00 44.28 3.51
1779 2219 1.553706 CTTGGAAGGGCAAGATGCTT 58.446 50.000 2.00 0.00 44.28 3.91
1907 2347 1.132500 GAAGTAGCCACATAGCCCCT 58.868 55.000 0.00 0.00 0.00 4.79
1911 2351 1.409427 ACGAGGAAGTAGCCACATAGC 59.591 52.381 0.00 0.00 0.00 2.97
1917 2357 0.251653 ACTCCACGAGGAAGTAGCCA 60.252 55.000 2.41 0.00 45.19 4.75
1991 2431 0.962356 ATGTTGCTGAAAGGGCTCCG 60.962 55.000 0.00 0.00 0.00 4.63
2001 2441 3.565764 AGCTTATAGGCATGTTGCTGA 57.434 42.857 9.75 0.00 44.28 4.26
2008 2448 5.149273 CAACGCAAATAGCTTATAGGCATG 58.851 41.667 9.75 3.99 42.61 4.06
2100 2540 0.247736 CTGAAACAGAGAGGGACCGG 59.752 60.000 0.00 0.00 32.44 5.28
2508 2951 0.317770 ATCAACAAACTGCAACGCGG 60.318 50.000 12.47 0.00 41.29 6.46
2645 3103 2.025887 ACCAAGGAATTGACCTAGCCAG 60.026 50.000 0.00 0.00 39.62 4.85
2701 3161 4.082787 GCATAGACAAACTGCTGGCTAAAA 60.083 41.667 0.00 0.00 40.35 1.52
2702 3162 3.440173 GCATAGACAAACTGCTGGCTAAA 59.560 43.478 0.00 0.00 40.35 1.85
2895 3357 2.564062 CCATTGATCCCAATACCCATGC 59.436 50.000 0.00 0.00 40.81 4.06
2910 3372 3.102972 CTCTCTCCCACTTCTCCATTGA 58.897 50.000 0.00 0.00 0.00 2.57
2913 3375 1.494960 GCTCTCTCCCACTTCTCCAT 58.505 55.000 0.00 0.00 0.00 3.41
2969 3431 0.950836 TCCACGTCACAAGGCATTTG 59.049 50.000 0.00 0.00 42.68 2.32
2982 3444 0.179094 TGAACGACTTTGCTCCACGT 60.179 50.000 0.00 0.00 38.81 4.49
3029 3491 0.991920 CCCTGGAGCCTTAGGTTTCA 59.008 55.000 0.00 0.00 31.99 2.69
3131 3594 1.359848 ATACGAGCCTTGCAGAAACG 58.640 50.000 0.00 0.00 0.00 3.60
3132 3595 3.188460 TGAAATACGAGCCTTGCAGAAAC 59.812 43.478 0.00 0.00 0.00 2.78
3176 3639 4.365111 GATGTGCCTGCCACCCCA 62.365 66.667 0.00 0.00 44.01 4.96
3301 3765 1.333619 AGCAAACGGTACACAAAGCTG 59.666 47.619 0.00 0.00 0.00 4.24
3306 3770 5.786311 AGATAGTAAGCAAACGGTACACAA 58.214 37.500 0.00 0.00 0.00 3.33
3409 3876 1.075601 TCCCATTCAGGTCCAAAGCT 58.924 50.000 0.00 0.00 34.66 3.74
3435 3902 3.753294 AGGTATGGTTCGGCTAATCAG 57.247 47.619 0.00 0.00 29.80 2.90
3529 4034 8.099364 CCATGTAGTGGTTGAATCATATAACC 57.901 38.462 0.00 0.00 43.44 2.85
3545 4050 5.412594 ACTTATTTGCACTCACCATGTAGTG 59.587 40.000 13.12 13.12 44.79 2.74
3546 4051 5.560724 ACTTATTTGCACTCACCATGTAGT 58.439 37.500 0.00 0.00 0.00 2.73
3547 4052 6.818644 AGTACTTATTTGCACTCACCATGTAG 59.181 38.462 0.00 0.00 0.00 2.74
3548 4053 6.707290 AGTACTTATTTGCACTCACCATGTA 58.293 36.000 0.00 0.00 0.00 2.29
3549 4054 5.560724 AGTACTTATTTGCACTCACCATGT 58.439 37.500 0.00 0.00 0.00 3.21
3550 4055 5.877012 AGAGTACTTATTTGCACTCACCATG 59.123 40.000 0.00 0.00 39.90 3.66
3551 4056 6.054860 AGAGTACTTATTTGCACTCACCAT 57.945 37.500 0.00 0.00 39.90 3.55
3552 4057 5.483685 AGAGTACTTATTTGCACTCACCA 57.516 39.130 0.00 0.00 39.90 4.17
3553 4058 7.042335 ACATAGAGTACTTATTTGCACTCACC 58.958 38.462 0.00 0.00 39.90 4.02
3554 4059 9.582431 TTACATAGAGTACTTATTTGCACTCAC 57.418 33.333 0.00 0.00 39.90 3.51
3555 4060 9.582431 GTTACATAGAGTACTTATTTGCACTCA 57.418 33.333 0.00 0.00 39.90 3.41
3556 4061 9.804758 AGTTACATAGAGTACTTATTTGCACTC 57.195 33.333 0.00 0.00 38.13 3.51


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

AutoCloner maintained by Alex Coulton.