Multiple sequence alignment - TraesCS4A01G498700

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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 TraesCS4A01G498700 chr4A 100.000 2841 0 0 1506 4346 743977626 743980466 0.000000e+00 5247.0
1 TraesCS4A01G498700 chr4A 100.000 598 0 0 560 1157 743976680 743977277 0.000000e+00 1105.0
2 TraesCS4A01G498700 chr4A 100.000 328 0 0 1 328 743976121 743976448 1.340000e-169 606.0
3 TraesCS4A01G498700 chr7D 91.701 2639 146 29 1506 4110 1320452 1323051 0.000000e+00 3592.0
4 TraesCS4A01G498700 chr7D 91.867 332 21 5 1 328 126989019 126988690 3.960000e-125 459.0
5 TraesCS4A01G498700 chr7D 90.274 329 12 10 835 1157 1320063 1320377 3.130000e-111 412.0
6 TraesCS4A01G498700 chr7D 92.118 203 16 0 560 762 56936991 56936789 1.980000e-73 287.0
7 TraesCS4A01G498700 chr7D 92.118 203 16 0 560 762 408471505 408471303 1.980000e-73 287.0
8 TraesCS4A01G498700 chr7D 87.660 235 10 5 4114 4346 1323145 1323362 5.580000e-64 255.0
9 TraesCS4A01G498700 chr7A 92.547 2442 108 28 1524 3922 1322118 1319708 0.000000e+00 3434.0
10 TraesCS4A01G498700 chr7A 84.519 239 23 6 4113 4346 1319008 1318779 1.570000e-54 224.0
11 TraesCS4A01G498700 chr6D 89.559 680 35 7 1506 2157 57044181 57044852 0.000000e+00 830.0
12 TraesCS4A01G498700 chr6D 92.401 329 20 4 1 328 943999 944323 8.510000e-127 464.0
13 TraesCS4A01G498700 chr3D 88.726 683 40 7 1506 2160 237607983 237607310 0.000000e+00 800.0
14 TraesCS4A01G498700 chr3D 91.343 335 19 9 1 327 580656938 580656606 2.380000e-122 449.0
15 TraesCS4A01G498700 chr3D 90.208 337 21 11 1 328 442774443 442774776 3.110000e-116 429.0
16 TraesCS4A01G498700 chr1D 92.012 338 16 9 1 328 278101887 278102223 8.510000e-127 464.0
17 TraesCS4A01G498700 chr1D 90.332 331 23 7 1 328 139134695 139135019 4.020000e-115 425.0
18 TraesCS4A01G498700 chr4D 91.098 337 20 9 1 328 486565202 486565537 8.570000e-122 448.0
19 TraesCS4A01G498700 chr4D 92.611 203 15 0 560 762 486565579 486565781 4.250000e-75 292.0
20 TraesCS4A01G498700 chr5D 91.159 328 20 5 3 328 495795649 495795969 1.860000e-118 436.0
21 TraesCS4A01G498700 chr5D 85.714 91 9 2 1651 1737 21423238 21423328 4.630000e-15 93.5
22 TraesCS4A01G498700 chr4B 89.851 335 26 7 1 328 671183665 671183332 1.440000e-114 424.0
23 TraesCS4A01G498700 chr1B 91.880 234 16 2 4114 4346 25315571 25315802 1.510000e-84 324.0
24 TraesCS4A01G498700 chr1B 80.612 392 51 11 3722 4110 25315117 25315486 3.310000e-71 279.0
25 TraesCS4A01G498700 chr5B 91.453 234 17 2 4114 4346 585081480 585081711 7.010000e-83 318.0
26 TraesCS4A01G498700 chr5B 78.718 390 59 6 3722 4109 585081027 585081394 5.620000e-59 239.0
27 TraesCS4A01G498700 chr6B 91.026 234 17 3 4114 4346 110897412 110897642 3.260000e-81 313.0
28 TraesCS4A01G498700 chr2B 91.827 208 17 0 560 767 396181758 396181965 1.530000e-74 291.0
29 TraesCS4A01G498700 chr2B 80.513 390 53 5 3722 4110 148013981 148014348 1.190000e-70 278.0
30 TraesCS4A01G498700 chr2B 80.513 390 52 6 3722 4110 434394343 434394709 1.190000e-70 278.0
31 TraesCS4A01G498700 chr2B 92.045 176 11 2 4117 4291 434394797 434394970 1.210000e-60 244.0
32 TraesCS4A01G498700 chr2B 90.503 179 14 2 4114 4291 148014433 148014609 2.610000e-57 233.0
33 TraesCS4A01G498700 chrUn 91.787 207 17 0 560 766 105335761 105335967 5.500000e-74 289.0
34 TraesCS4A01G498700 chr2D 92.118 203 16 0 560 762 50138862 50139064 1.980000e-73 287.0
35 TraesCS4A01G498700 chr2D 91.748 206 17 0 563 768 236135039 236134834 1.980000e-73 287.0
36 TraesCS4A01G498700 chr2D 92.118 203 16 0 560 762 498273523 498273321 1.980000e-73 287.0
37 TraesCS4A01G498700 chr2D 92.118 203 16 0 560 762 500667009 500667211 1.980000e-73 287.0
38 TraesCS4A01G498700 chr3B 80.818 391 51 6 3722 4110 290763555 290763923 7.110000e-73 285.0
39 TraesCS4A01G498700 chr3B 92.614 176 10 2 4117 4291 290764011 290764184 2.590000e-62 250.0
40 TraesCS4A01G498700 chr3B 90.533 169 14 2 4120 4288 789959322 789959156 5.660000e-54 222.0
41 TraesCS4A01G498700 chr7B 84.211 171 12 1 3722 3892 531002795 531002950 7.530000e-33 152.0


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 TraesCS4A01G498700 chr4A 743976121 743980466 4345 False 2319.333333 5247 100.000000 1 4346 3 chr4A.!!$F1 4345
1 TraesCS4A01G498700 chr7D 1320063 1323362 3299 False 1419.666667 3592 89.878333 835 4346 3 chr7D.!!$F1 3511
2 TraesCS4A01G498700 chr7A 1318779 1322118 3339 True 1829.000000 3434 88.533000 1524 4346 2 chr7A.!!$R1 2822
3 TraesCS4A01G498700 chr6D 57044181 57044852 671 False 830.000000 830 89.559000 1506 2157 1 chr6D.!!$F2 651
4 TraesCS4A01G498700 chr3D 237607310 237607983 673 True 800.000000 800 88.726000 1506 2160 1 chr3D.!!$R1 654
5 TraesCS4A01G498700 chr4D 486565202 486565781 579 False 370.000000 448 91.854500 1 762 2 chr4D.!!$F1 761
6 TraesCS4A01G498700 chr1B 25315117 25315802 685 False 301.500000 324 86.246000 3722 4346 2 chr1B.!!$F1 624
7 TraesCS4A01G498700 chr5B 585081027 585081711 684 False 278.500000 318 85.085500 3722 4346 2 chr5B.!!$F1 624
8 TraesCS4A01G498700 chr2B 434394343 434394970 627 False 261.000000 278 86.279000 3722 4291 2 chr2B.!!$F3 569
9 TraesCS4A01G498700 chr2B 148013981 148014609 628 False 255.500000 278 85.508000 3722 4291 2 chr2B.!!$F2 569
10 TraesCS4A01G498700 chr3B 290763555 290764184 629 False 267.500000 285 86.716000 3722 4291 2 chr3B.!!$F1 569

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
720 729 0.035056 AACATGCCTCTTCCTTCCCG 60.035 55.0 0.0 0.0 0.0 5.14 F
2345 2401 0.038744 CACAAGACCTGCCCCAAGAT 59.961 55.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2631 2687 0.458669 GCAGATTGACCAGCAATGGG 59.541 55.0 0.0 0.0 46.90 4.00 R
4057 4634 0.108329 CTGAATACGCCTCCCAACGT 60.108 55.0 0.0 0.0 45.85 3.99 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
25 26 2.019951 CGACGGTTCGTTCAGTGGG 61.020 63.158 0.00 0.00 41.37 4.61
35 36 2.496070 TCGTTCAGTGGGAAATCGATCT 59.504 45.455 0.00 0.00 37.23 2.75
36 37 3.697542 TCGTTCAGTGGGAAATCGATCTA 59.302 43.478 0.00 0.00 37.23 1.98
37 38 3.797256 CGTTCAGTGGGAAATCGATCTAC 59.203 47.826 0.00 0.00 37.23 2.59
38 39 4.676986 CGTTCAGTGGGAAATCGATCTACA 60.677 45.833 0.00 0.00 37.23 2.74
39 40 4.386867 TCAGTGGGAAATCGATCTACAC 57.613 45.455 0.00 6.39 0.00 2.90
42 43 2.169769 GTGGGAAATCGATCTACACCCA 59.830 50.000 17.70 17.70 42.70 4.51
72 74 3.003480 GCCTAACCACTGAGCTAACAAG 58.997 50.000 0.00 0.00 0.00 3.16
94 96 2.361230 GGGGGTGGTGCTGCTTAC 60.361 66.667 0.00 0.00 0.00 2.34
114 116 2.105128 GCACCGGAGATGAGGACG 59.895 66.667 9.46 0.00 0.00 4.79
117 119 2.835431 CCGGAGATGAGGACGGCT 60.835 66.667 0.00 0.00 39.85 5.52
149 151 1.668151 GGCACAGACAAGGTCGACC 60.668 63.158 27.67 27.67 37.67 4.79
193 195 2.436646 ACCAGATCCGCCGCAAAG 60.437 61.111 0.00 0.00 0.00 2.77
319 328 0.335019 GGGGGTGAGGCTAATTTGGT 59.665 55.000 0.00 0.00 0.00 3.67
622 631 2.270923 CTCACGAGAAATTGCCGATCA 58.729 47.619 0.00 0.00 0.00 2.92
640 649 2.738521 GAGCGTTTCCAGCGAGCA 60.739 61.111 0.00 0.00 40.04 4.26
658 667 3.826282 AGGCTCTGGGCTGCTTTA 58.174 55.556 0.00 0.00 46.90 1.85
682 691 4.120331 GTGCGATGCAGGCCCAAC 62.120 66.667 0.00 0.00 40.08 3.77
683 692 4.657408 TGCGATGCAGGCCCAACA 62.657 61.111 0.00 0.00 33.32 3.33
684 693 3.818787 GCGATGCAGGCCCAACAG 61.819 66.667 0.00 0.00 0.00 3.16
685 694 2.046023 CGATGCAGGCCCAACAGA 60.046 61.111 0.00 0.00 0.00 3.41
686 695 1.675310 CGATGCAGGCCCAACAGAA 60.675 57.895 0.00 0.00 0.00 3.02
687 696 1.243342 CGATGCAGGCCCAACAGAAA 61.243 55.000 0.00 0.00 0.00 2.52
688 697 0.968405 GATGCAGGCCCAACAGAAAA 59.032 50.000 0.00 0.00 0.00 2.29
689 698 1.344114 GATGCAGGCCCAACAGAAAAA 59.656 47.619 0.00 0.00 0.00 1.94
690 699 0.463620 TGCAGGCCCAACAGAAAAAC 59.536 50.000 0.00 0.00 0.00 2.43
691 700 0.249868 GCAGGCCCAACAGAAAAACC 60.250 55.000 0.00 0.00 0.00 3.27
692 701 1.118838 CAGGCCCAACAGAAAAACCA 58.881 50.000 0.00 0.00 0.00 3.67
693 702 1.069049 CAGGCCCAACAGAAAAACCAG 59.931 52.381 0.00 0.00 0.00 4.00
694 703 0.392706 GGCCCAACAGAAAAACCAGG 59.607 55.000 0.00 0.00 0.00 4.45
695 704 0.249868 GCCCAACAGAAAAACCAGGC 60.250 55.000 0.00 0.00 0.00 4.85
696 705 1.118838 CCCAACAGAAAAACCAGGCA 58.881 50.000 0.00 0.00 0.00 4.75
697 706 1.484240 CCCAACAGAAAAACCAGGCAA 59.516 47.619 0.00 0.00 0.00 4.52
698 707 2.549926 CCAACAGAAAAACCAGGCAAC 58.450 47.619 0.00 0.00 0.00 4.17
699 708 2.093764 CCAACAGAAAAACCAGGCAACA 60.094 45.455 0.00 0.00 41.41 3.33
700 709 3.594134 CAACAGAAAAACCAGGCAACAA 58.406 40.909 0.00 0.00 41.41 2.83
701 710 3.971245 ACAGAAAAACCAGGCAACAAA 57.029 38.095 0.00 0.00 41.41 2.83
702 711 4.278975 ACAGAAAAACCAGGCAACAAAA 57.721 36.364 0.00 0.00 41.41 2.44
703 712 4.000325 ACAGAAAAACCAGGCAACAAAAC 59.000 39.130 0.00 0.00 41.41 2.43
704 713 3.999663 CAGAAAAACCAGGCAACAAAACA 59.000 39.130 0.00 0.00 41.41 2.83
705 714 4.635324 CAGAAAAACCAGGCAACAAAACAT 59.365 37.500 0.00 0.00 41.41 2.71
706 715 4.635324 AGAAAAACCAGGCAACAAAACATG 59.365 37.500 0.00 0.00 41.41 3.21
707 716 1.952193 AACCAGGCAACAAAACATGC 58.048 45.000 0.00 0.00 41.82 4.06
714 723 2.407090 GCAACAAAACATGCCTCTTCC 58.593 47.619 0.00 0.00 36.56 3.46
715 724 2.036346 GCAACAAAACATGCCTCTTCCT 59.964 45.455 0.00 0.00 36.56 3.36
716 725 3.493176 GCAACAAAACATGCCTCTTCCTT 60.493 43.478 0.00 0.00 36.56 3.36
717 726 4.301628 CAACAAAACATGCCTCTTCCTTC 58.698 43.478 0.00 0.00 0.00 3.46
718 727 2.893489 ACAAAACATGCCTCTTCCTTCC 59.107 45.455 0.00 0.00 0.00 3.46
719 728 2.222227 AAACATGCCTCTTCCTTCCC 57.778 50.000 0.00 0.00 0.00 3.97
720 729 0.035056 AACATGCCTCTTCCTTCCCG 60.035 55.000 0.00 0.00 0.00 5.14
721 730 1.821332 CATGCCTCTTCCTTCCCGC 60.821 63.158 0.00 0.00 0.00 6.13
722 731 3.391665 ATGCCTCTTCCTTCCCGCG 62.392 63.158 0.00 0.00 0.00 6.46
744 753 2.825836 CCTGGTTGGGCTCGATGC 60.826 66.667 0.00 0.00 41.94 3.91
745 754 2.046023 CTGGTTGGGCTCGATGCA 60.046 61.111 8.71 0.00 45.15 3.96
746 755 2.046023 TGGTTGGGCTCGATGCAG 60.046 61.111 8.71 0.00 45.15 4.41
747 756 2.825836 GGTTGGGCTCGATGCAGG 60.826 66.667 8.71 0.00 45.15 4.85
748 757 3.512516 GTTGGGCTCGATGCAGGC 61.513 66.667 8.71 0.00 45.15 4.85
749 758 4.032452 TTGGGCTCGATGCAGGCA 62.032 61.111 0.00 0.00 45.15 4.75
750 759 3.565961 TTGGGCTCGATGCAGGCAA 62.566 57.895 0.00 0.00 45.15 4.52
751 760 3.512516 GGGCTCGATGCAGGCAAC 61.513 66.667 0.00 0.00 45.15 4.17
752 761 3.512516 GGCTCGATGCAGGCAACC 61.513 66.667 0.00 0.00 45.15 3.77
753 762 2.747460 GCTCGATGCAGGCAACCA 60.747 61.111 0.00 0.00 42.31 3.67
754 763 2.334946 GCTCGATGCAGGCAACCAA 61.335 57.895 0.00 0.00 42.31 3.67
755 764 1.865788 GCTCGATGCAGGCAACCAAA 61.866 55.000 0.00 0.00 42.31 3.28
756 765 0.109597 CTCGATGCAGGCAACCAAAC 60.110 55.000 0.00 0.00 37.17 2.93
757 766 0.821301 TCGATGCAGGCAACCAAACA 60.821 50.000 0.00 0.00 37.17 2.83
758 767 0.244450 CGATGCAGGCAACCAAACAT 59.756 50.000 0.00 0.00 37.17 2.71
759 768 1.717194 GATGCAGGCAACCAAACATG 58.283 50.000 0.00 0.00 37.17 3.21
760 769 0.320946 ATGCAGGCAACCAAACATGC 60.321 50.000 0.00 0.00 41.82 4.06
785 794 5.675684 AAAAAGCACTTTCAAGGAAGGAA 57.324 34.783 0.00 0.00 31.45 3.36
786 795 4.926140 AAAGCACTTTCAAGGAAGGAAG 57.074 40.909 0.00 0.00 0.00 3.46
787 796 3.864789 AGCACTTTCAAGGAAGGAAGA 57.135 42.857 0.00 0.00 0.00 2.87
788 797 3.749226 AGCACTTTCAAGGAAGGAAGAG 58.251 45.455 0.00 0.00 0.00 2.85
789 798 2.816672 GCACTTTCAAGGAAGGAAGAGG 59.183 50.000 0.00 0.00 0.00 3.69
790 799 3.416156 CACTTTCAAGGAAGGAAGAGGG 58.584 50.000 0.00 0.00 0.00 4.30
791 800 2.376855 ACTTTCAAGGAAGGAAGAGGGG 59.623 50.000 0.00 0.00 0.00 4.79
792 801 1.372501 TTCAAGGAAGGAAGAGGGGG 58.627 55.000 0.00 0.00 0.00 5.40
793 802 0.496382 TCAAGGAAGGAAGAGGGGGA 59.504 55.000 0.00 0.00 0.00 4.81
794 803 0.915364 CAAGGAAGGAAGAGGGGGAG 59.085 60.000 0.00 0.00 0.00 4.30
795 804 0.800239 AAGGAAGGAAGAGGGGGAGA 59.200 55.000 0.00 0.00 0.00 3.71
796 805 0.341609 AGGAAGGAAGAGGGGGAGAG 59.658 60.000 0.00 0.00 0.00 3.20
797 806 1.341913 GGAAGGAAGAGGGGGAGAGC 61.342 65.000 0.00 0.00 0.00 4.09
798 807 0.618968 GAAGGAAGAGGGGGAGAGCA 60.619 60.000 0.00 0.00 0.00 4.26
799 808 0.045469 AAGGAAGAGGGGGAGAGCAT 59.955 55.000 0.00 0.00 0.00 3.79
800 809 0.693767 AGGAAGAGGGGGAGAGCATG 60.694 60.000 0.00 0.00 0.00 4.06
801 810 1.704007 GGAAGAGGGGGAGAGCATGG 61.704 65.000 0.00 0.00 0.00 3.66
802 811 2.336484 GAAGAGGGGGAGAGCATGGC 62.336 65.000 0.00 0.00 0.00 4.40
803 812 4.247380 GAGGGGGAGAGCATGGCG 62.247 72.222 0.00 0.00 0.00 5.69
804 813 4.804420 AGGGGGAGAGCATGGCGA 62.804 66.667 0.00 0.00 0.00 5.54
805 814 4.247380 GGGGGAGAGCATGGCGAG 62.247 72.222 0.00 0.00 0.00 5.03
806 815 4.247380 GGGGAGAGCATGGCGAGG 62.247 72.222 0.00 0.00 0.00 4.63
807 816 4.247380 GGGAGAGCATGGCGAGGG 62.247 72.222 0.00 0.00 0.00 4.30
808 817 3.157252 GGAGAGCATGGCGAGGGA 61.157 66.667 0.00 0.00 0.00 4.20
809 818 2.420890 GAGAGCATGGCGAGGGAG 59.579 66.667 0.00 0.00 0.00 4.30
810 819 2.364842 AGAGCATGGCGAGGGAGT 60.365 61.111 0.00 0.00 0.00 3.85
811 820 2.202987 GAGCATGGCGAGGGAGTG 60.203 66.667 0.00 0.00 0.00 3.51
812 821 3.746949 GAGCATGGCGAGGGAGTGG 62.747 68.421 0.00 0.00 0.00 4.00
813 822 4.864334 GCATGGCGAGGGAGTGGG 62.864 72.222 0.00 0.00 0.00 4.61
814 823 3.083349 CATGGCGAGGGAGTGGGA 61.083 66.667 0.00 0.00 0.00 4.37
815 824 2.765807 ATGGCGAGGGAGTGGGAG 60.766 66.667 0.00 0.00 0.00 4.30
817 826 4.779733 GGCGAGGGAGTGGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
818 827 2.683933 GCGAGGGAGTGGGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
819 828 2.726351 GCGAGGGAGTGGGAGGAAG 61.726 68.421 0.00 0.00 0.00 3.46
820 829 1.000486 CGAGGGAGTGGGAGGAAGA 60.000 63.158 0.00 0.00 0.00 2.87
821 830 0.397816 CGAGGGAGTGGGAGGAAGAT 60.398 60.000 0.00 0.00 0.00 2.40
822 831 1.886422 GAGGGAGTGGGAGGAAGATT 58.114 55.000 0.00 0.00 0.00 2.40
823 832 1.765904 GAGGGAGTGGGAGGAAGATTC 59.234 57.143 0.00 0.00 0.00 2.52
848 857 2.231964 CCATTCCATTGGTGGTGTGAAG 59.768 50.000 1.86 0.00 46.16 3.02
849 858 2.746279 TTCCATTGGTGGTGTGAAGT 57.254 45.000 1.86 0.00 46.16 3.01
850 859 2.746279 TCCATTGGTGGTGTGAAGTT 57.254 45.000 1.86 0.00 46.16 2.66
851 860 2.582052 TCCATTGGTGGTGTGAAGTTC 58.418 47.619 1.86 0.00 46.16 3.01
853 862 2.217750 CATTGGTGGTGTGAAGTTCGA 58.782 47.619 0.00 0.00 0.00 3.71
854 863 2.404923 TTGGTGGTGTGAAGTTCGAA 57.595 45.000 0.00 0.00 0.00 3.71
856 865 1.226746 GGTGGTGTGAAGTTCGAAGG 58.773 55.000 0.00 0.00 0.00 3.46
858 867 2.135933 GTGGTGTGAAGTTCGAAGGAG 58.864 52.381 0.00 0.00 0.00 3.69
859 868 1.149148 GGTGTGAAGTTCGAAGGAGC 58.851 55.000 0.00 0.00 0.00 4.70
860 869 0.784778 GTGTGAAGTTCGAAGGAGCG 59.215 55.000 0.00 0.00 0.00 5.03
914 934 2.240667 CAAACCCACTCTCCATCTCCAT 59.759 50.000 0.00 0.00 0.00 3.41
915 935 1.799933 ACCCACTCTCCATCTCCATC 58.200 55.000 0.00 0.00 0.00 3.51
916 936 1.293458 ACCCACTCTCCATCTCCATCT 59.707 52.381 0.00 0.00 0.00 2.90
917 937 1.969923 CCCACTCTCCATCTCCATCTC 59.030 57.143 0.00 0.00 0.00 2.75
918 938 1.969923 CCACTCTCCATCTCCATCTCC 59.030 57.143 0.00 0.00 0.00 3.71
919 939 2.675583 CACTCTCCATCTCCATCTCCA 58.324 52.381 0.00 0.00 0.00 3.86
920 940 2.629137 CACTCTCCATCTCCATCTCCAG 59.371 54.545 0.00 0.00 0.00 3.86
921 941 2.250031 CTCTCCATCTCCATCTCCAGG 58.750 57.143 0.00 0.00 0.00 4.45
922 942 1.132913 TCTCCATCTCCATCTCCAGGG 60.133 57.143 0.00 0.00 0.00 4.45
923 943 0.944238 TCCATCTCCATCTCCAGGGA 59.056 55.000 0.00 0.00 0.00 4.20
926 946 4.309879 CTCCATCTCCAGGGAGGG 57.690 66.667 15.08 9.51 45.62 4.30
927 947 1.628727 CTCCATCTCCAGGGAGGGA 59.371 63.158 15.08 13.00 45.62 4.20
933 953 2.454941 TCCAGGGAGGGAGGAACC 59.545 66.667 0.00 0.00 38.24 3.62
934 954 3.083997 CCAGGGAGGGAGGAACCG 61.084 72.222 0.00 0.00 40.11 4.44
935 955 3.787001 CAGGGAGGGAGGAACCGC 61.787 72.222 0.00 0.00 40.11 5.68
1750 1787 5.188434 TCCATCAGATTTCACACCTCAATC 58.812 41.667 0.00 0.00 0.00 2.67
1781 1828 1.745489 GACTGCCGTTGATCCCCAC 60.745 63.158 0.00 0.00 0.00 4.61
1888 1941 2.049156 CTCAGCGACGACAAGCCA 60.049 61.111 0.00 0.00 0.00 4.75
2122 2175 0.252467 CTCCCTCTGTGAAGTCCCCT 60.252 60.000 0.00 0.00 0.00 4.79
2131 2184 1.700186 GTGAAGTCCCCTATCATCCCC 59.300 57.143 0.00 0.00 0.00 4.81
2176 2229 2.729479 CGAGCTGATGCAGGACCCT 61.729 63.158 0.00 0.00 42.74 4.34
2194 2247 1.938657 CTGTCATCGTCTCCAGCGGT 61.939 60.000 0.00 0.00 0.00 5.68
2200 2253 2.044555 CGTCTCCAGCGGTCAGGTA 61.045 63.158 0.00 0.00 0.00 3.08
2201 2254 1.810532 GTCTCCAGCGGTCAGGTAG 59.189 63.158 0.00 0.00 0.00 3.18
2202 2255 0.966370 GTCTCCAGCGGTCAGGTAGT 60.966 60.000 0.00 0.00 0.00 2.73
2203 2256 0.622136 TCTCCAGCGGTCAGGTAGTA 59.378 55.000 0.00 0.00 0.00 1.82
2204 2257 1.025812 CTCCAGCGGTCAGGTAGTAG 58.974 60.000 0.00 0.00 0.00 2.57
2205 2258 0.395311 TCCAGCGGTCAGGTAGTAGG 60.395 60.000 0.00 0.00 0.00 3.18
2209 2262 0.175073 GCGGTCAGGTAGTAGGGTTG 59.825 60.000 0.00 0.00 0.00 3.77
2210 2263 1.553706 CGGTCAGGTAGTAGGGTTGT 58.446 55.000 0.00 0.00 0.00 3.32
2211 2264 1.897802 CGGTCAGGTAGTAGGGTTGTT 59.102 52.381 0.00 0.00 0.00 2.83
2212 2265 2.353406 CGGTCAGGTAGTAGGGTTGTTG 60.353 54.545 0.00 0.00 0.00 3.33
2213 2266 2.901839 GGTCAGGTAGTAGGGTTGTTGA 59.098 50.000 0.00 0.00 0.00 3.18
2214 2267 3.325716 GGTCAGGTAGTAGGGTTGTTGAA 59.674 47.826 0.00 0.00 0.00 2.69
2217 2270 5.642491 GTCAGGTAGTAGGGTTGTTGAATTC 59.358 44.000 0.00 0.00 0.00 2.17
2220 2273 6.817140 CAGGTAGTAGGGTTGTTGAATTCTAC 59.183 42.308 12.40 12.40 0.00 2.59
2223 2276 2.073816 AGGGTTGTTGAATTCTACGCG 58.926 47.619 3.53 3.53 0.00 6.01
2224 2277 2.070783 GGGTTGTTGAATTCTACGCGA 58.929 47.619 15.93 0.00 0.00 5.87
2225 2278 2.676342 GGGTTGTTGAATTCTACGCGAT 59.324 45.455 15.93 0.00 0.00 4.58
2226 2279 3.485216 GGGTTGTTGAATTCTACGCGATG 60.485 47.826 15.93 4.70 0.00 3.84
2227 2280 3.369756 GGTTGTTGAATTCTACGCGATGA 59.630 43.478 15.93 7.51 0.00 2.92
2268 2322 6.345298 TCAAGCACATTTATCCTAACGATCA 58.655 36.000 0.00 0.00 31.92 2.92
2345 2401 0.038744 CACAAGACCTGCCCCAAGAT 59.961 55.000 0.00 0.00 0.00 2.40
2358 2414 1.225426 CAAGATGCAGCTGGCCCTA 59.775 57.895 17.12 0.00 43.89 3.53
2481 2537 3.013921 TGACAAGAAAGCGGTGAAAAGT 58.986 40.909 0.00 0.00 0.00 2.66
2592 2648 1.270550 CGGTTGCTTGCCAAGAGAAAT 59.729 47.619 9.04 0.00 33.21 2.17
2595 2651 3.311966 GTTGCTTGCCAAGAGAAATGTC 58.688 45.455 9.04 0.00 33.21 3.06
2631 2687 2.832201 GCTGAAGCAGGGGCCATC 60.832 66.667 4.39 0.00 42.56 3.51
2715 2771 2.158885 GCTCCTTAACCTCTCCATCCAC 60.159 54.545 0.00 0.00 0.00 4.02
2754 2810 1.671054 CGTGGACTCCAACGCCATT 60.671 57.895 0.00 0.00 34.18 3.16
2781 2837 4.973168 AGATAGTGGAAGTGCTGAAAACA 58.027 39.130 0.00 0.00 0.00 2.83
2818 2874 4.609018 AGAACGCAGCAGCCACGT 62.609 61.111 4.52 4.52 42.81 4.49
2862 2918 8.573035 GTGGATGAAAACAAAGTAACTATTGGA 58.427 33.333 0.00 0.00 0.00 3.53
2970 3026 2.816087 CCTGTGCATATATCAGGGCAAC 59.184 50.000 11.57 1.71 43.30 4.17
2998 3054 1.425428 GCGGTGAAAGCTGGAATCG 59.575 57.895 0.00 0.00 0.00 3.34
3105 3161 6.549952 CAATCAAGAAGGCAAGTCTGTAATC 58.450 40.000 0.00 0.00 0.00 1.75
3189 3245 1.813753 GAACGCGGCAGCCATTCTA 60.814 57.895 13.30 0.00 41.18 2.10
3237 3293 2.438951 AAACCATGGCTGCAAAGGCG 62.439 55.000 13.04 0.00 45.35 5.52
3255 3311 2.203126 GCTGGAGGGGAAGATGCG 60.203 66.667 0.00 0.00 0.00 4.73
3367 3434 4.102035 AGATTTTCTTGAAATGCGAGGC 57.898 40.909 0.00 0.00 38.06 4.70
3405 3472 1.193650 CCAATTGTACACACGACACGG 59.806 52.381 4.43 0.00 0.00 4.94
3579 3646 5.359576 TCTGTGTGGTTTACTTTGCTGATTT 59.640 36.000 0.00 0.00 0.00 2.17
3600 3667 7.337689 TGATTTTTATCAGTTCTGGTCTCATGG 59.662 37.037 0.00 0.00 0.00 3.66
3668 3736 2.474410 AAAGGAAGCGACGAGGAATT 57.526 45.000 0.00 0.00 0.00 2.17
3670 3738 0.895530 AGGAAGCGACGAGGAATTCA 59.104 50.000 7.93 0.00 0.00 2.57
3677 3745 2.737252 GCGACGAGGAATTCAGAAGTTT 59.263 45.455 7.93 0.00 0.00 2.66
3812 3895 9.739276 TTTGTGTCTAAATCTCAAGTATGGATT 57.261 29.630 0.00 0.00 31.74 3.01
4026 4142 7.715249 TCCATTTTGAGGTGAGCTATGTATAAC 59.285 37.037 0.00 0.00 0.00 1.89
4050 4627 2.189594 TTCTGAGTCCACATGCAAGG 57.810 50.000 0.00 0.00 0.00 3.61
4057 4634 2.375174 AGTCCACATGCAAGGAACCTTA 59.625 45.455 5.75 0.00 35.29 2.69
4058 4635 2.488153 GTCCACATGCAAGGAACCTTAC 59.512 50.000 5.75 1.38 35.29 2.34
4065 4642 1.543871 GCAAGGAACCTTACGTTGGGA 60.544 52.381 12.44 0.00 33.74 4.37
4087 4664 2.290641 GGCGTATTCAGTGCATTAAGGG 59.709 50.000 0.00 0.00 0.00 3.95
4110 4687 5.338365 GTCATGGGTACAGTACTCGTTTAG 58.662 45.833 10.62 0.00 29.54 1.85
4111 4688 4.400251 TCATGGGTACAGTACTCGTTTAGG 59.600 45.833 10.62 0.00 29.54 2.69
4115 4782 4.142513 GGGTACAGTACTCGTTTAGGTGAG 60.143 50.000 10.62 0.00 38.21 3.51
4118 4785 5.312120 ACAGTACTCGTTTAGGTGAGATG 57.688 43.478 0.00 0.00 36.11 2.90
4229 4899 5.313280 TCACTGGGCTCCTTTTACTTTTA 57.687 39.130 0.00 0.00 0.00 1.52
4305 4978 3.616379 GCAGTTGCTGACTCACTATTCTC 59.384 47.826 0.00 0.00 36.10 2.87
4306 4979 4.180057 CAGTTGCTGACTCACTATTCTCC 58.820 47.826 0.00 0.00 36.10 3.71
4307 4980 3.834813 AGTTGCTGACTCACTATTCTCCA 59.165 43.478 0.00 0.00 31.20 3.86
4308 4981 4.284490 AGTTGCTGACTCACTATTCTCCAA 59.716 41.667 0.00 0.00 31.20 3.53
4309 4982 5.046014 AGTTGCTGACTCACTATTCTCCAAT 60.046 40.000 0.00 0.00 31.20 3.16
4310 4983 4.763073 TGCTGACTCACTATTCTCCAATG 58.237 43.478 0.00 0.00 0.00 2.82
4311 4984 4.125703 GCTGACTCACTATTCTCCAATGG 58.874 47.826 0.00 0.00 0.00 3.16
4312 4985 4.141846 GCTGACTCACTATTCTCCAATGGA 60.142 45.833 0.48 0.48 0.00 3.41
4313 4986 5.627735 GCTGACTCACTATTCTCCAATGGAA 60.628 44.000 2.61 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.237755 CGTTAAGTTGGGTGTAGATCGATTTC 60.238 42.308 0.00 0.00 0.00 2.17
35 36 1.058284 AGGCCGTTAAGTTGGGTGTA 58.942 50.000 0.00 0.00 0.00 2.90
36 37 1.058284 TAGGCCGTTAAGTTGGGTGT 58.942 50.000 0.00 0.00 0.00 4.16
37 38 1.808343 GTTAGGCCGTTAAGTTGGGTG 59.192 52.381 0.00 0.00 0.00 4.61
38 39 1.271543 GGTTAGGCCGTTAAGTTGGGT 60.272 52.381 0.00 0.00 0.00 4.51
39 40 1.271488 TGGTTAGGCCGTTAAGTTGGG 60.271 52.381 0.00 0.00 41.21 4.12
42 43 2.369532 TCAGTGGTTAGGCCGTTAAGTT 59.630 45.455 0.00 0.00 41.21 2.66
79 81 2.746277 CGGTAAGCAGCACCACCC 60.746 66.667 2.96 0.00 35.67 4.61
80 82 2.746277 CCGGTAAGCAGCACCACC 60.746 66.667 0.00 1.90 35.67 4.61
82 84 3.947459 TGCCGGTAAGCAGCACCA 61.947 61.111 1.90 0.00 38.00 4.17
100 102 1.107538 TAAGCCGTCCTCATCTCCGG 61.108 60.000 0.00 0.00 43.22 5.14
107 109 2.365105 CCCCCTAAGCCGTCCTCA 60.365 66.667 0.00 0.00 0.00 3.86
117 119 2.286808 TGCCATGGCTCCCCCTAA 60.287 61.111 35.53 11.81 42.51 2.69
149 151 1.380403 TTGTTGTTGGCCACCGTCTG 61.380 55.000 3.88 0.00 0.00 3.51
153 155 2.727544 CCTTGTTGTTGGCCACCG 59.272 61.111 3.88 0.00 0.00 4.94
208 216 5.175673 CGATTTCAAATCTGCGCTATAGACA 59.824 40.000 9.73 0.00 0.00 3.41
210 218 4.150627 GCGATTTCAAATCTGCGCTATAGA 59.849 41.667 9.73 3.10 41.09 1.98
224 232 3.798650 CGGCGGCTGCGATTTCAA 61.799 61.111 12.29 0.00 44.10 2.69
598 607 1.324736 CGGCAATTTCTCGTGAGCTAC 59.675 52.381 0.00 0.00 0.00 3.58
600 609 0.037326 TCGGCAATTTCTCGTGAGCT 60.037 50.000 0.00 0.00 0.00 4.09
605 614 2.544685 CTCTGATCGGCAATTTCTCGT 58.455 47.619 0.00 0.00 0.00 4.18
613 622 1.019278 GGAAACGCTCTGATCGGCAA 61.019 55.000 5.85 0.00 0.00 4.52
622 631 2.433318 GCTCGCTGGAAACGCTCT 60.433 61.111 0.00 0.00 0.00 4.09
640 649 0.405585 TTAAAGCAGCCCAGAGCCTT 59.594 50.000 0.00 0.00 45.47 4.35
654 663 1.128507 TGCATCGCACGCTTCTTAAAG 59.871 47.619 0.00 0.00 31.71 1.85
658 667 2.393768 CCTGCATCGCACGCTTCTT 61.394 57.895 0.00 0.00 33.79 2.52
678 687 2.093764 TGTTGCCTGGTTTTTCTGTTGG 60.094 45.455 0.00 0.00 0.00 3.77
679 688 3.244033 TGTTGCCTGGTTTTTCTGTTG 57.756 42.857 0.00 0.00 0.00 3.33
680 689 3.971245 TTGTTGCCTGGTTTTTCTGTT 57.029 38.095 0.00 0.00 0.00 3.16
681 690 3.971245 TTTGTTGCCTGGTTTTTCTGT 57.029 38.095 0.00 0.00 0.00 3.41
682 691 3.999663 TGTTTTGTTGCCTGGTTTTTCTG 59.000 39.130 0.00 0.00 0.00 3.02
683 692 4.278975 TGTTTTGTTGCCTGGTTTTTCT 57.721 36.364 0.00 0.00 0.00 2.52
684 693 4.730324 GCATGTTTTGTTGCCTGGTTTTTC 60.730 41.667 0.00 0.00 32.66 2.29
685 694 3.128415 GCATGTTTTGTTGCCTGGTTTTT 59.872 39.130 0.00 0.00 32.66 1.94
686 695 2.682352 GCATGTTTTGTTGCCTGGTTTT 59.318 40.909 0.00 0.00 32.66 2.43
687 696 2.287769 GCATGTTTTGTTGCCTGGTTT 58.712 42.857 0.00 0.00 32.66 3.27
688 697 1.952193 GCATGTTTTGTTGCCTGGTT 58.048 45.000 0.00 0.00 32.66 3.67
689 698 3.684693 GCATGTTTTGTTGCCTGGT 57.315 47.368 0.00 0.00 32.66 4.00
694 703 2.036346 AGGAAGAGGCATGTTTTGTTGC 59.964 45.455 0.00 0.00 38.14 4.17
695 704 4.301628 GAAGGAAGAGGCATGTTTTGTTG 58.698 43.478 0.00 0.00 0.00 3.33
696 705 3.321968 GGAAGGAAGAGGCATGTTTTGTT 59.678 43.478 0.00 0.00 0.00 2.83
697 706 2.893489 GGAAGGAAGAGGCATGTTTTGT 59.107 45.455 0.00 0.00 0.00 2.83
698 707 2.232208 GGGAAGGAAGAGGCATGTTTTG 59.768 50.000 0.00 0.00 0.00 2.44
699 708 2.529632 GGGAAGGAAGAGGCATGTTTT 58.470 47.619 0.00 0.00 0.00 2.43
700 709 1.614317 CGGGAAGGAAGAGGCATGTTT 60.614 52.381 0.00 0.00 0.00 2.83
701 710 0.035056 CGGGAAGGAAGAGGCATGTT 60.035 55.000 0.00 0.00 0.00 2.71
702 711 1.604378 CGGGAAGGAAGAGGCATGT 59.396 57.895 0.00 0.00 0.00 3.21
703 712 1.821332 GCGGGAAGGAAGAGGCATG 60.821 63.158 0.00 0.00 0.00 4.06
704 713 2.592308 GCGGGAAGGAAGAGGCAT 59.408 61.111 0.00 0.00 0.00 4.40
705 714 4.082523 CGCGGGAAGGAAGAGGCA 62.083 66.667 0.00 0.00 0.00 4.75
727 736 2.825836 GCATCGAGCCCAACCAGG 60.826 66.667 0.00 0.00 37.23 4.45
728 737 2.046023 TGCATCGAGCCCAACCAG 60.046 61.111 0.00 0.00 44.83 4.00
729 738 2.046023 CTGCATCGAGCCCAACCA 60.046 61.111 0.00 0.00 44.83 3.67
730 739 2.825836 CCTGCATCGAGCCCAACC 60.826 66.667 0.00 0.00 44.83 3.77
731 740 3.512516 GCCTGCATCGAGCCCAAC 61.513 66.667 0.00 0.00 44.83 3.77
732 741 3.565961 TTGCCTGCATCGAGCCCAA 62.566 57.895 0.00 0.00 44.83 4.12
733 742 4.032452 TTGCCTGCATCGAGCCCA 62.032 61.111 0.00 0.00 44.83 5.36
734 743 3.512516 GTTGCCTGCATCGAGCCC 61.513 66.667 0.00 0.00 44.83 5.19
735 744 3.512516 GGTTGCCTGCATCGAGCC 61.513 66.667 0.00 0.00 44.83 4.70
736 745 1.865788 TTTGGTTGCCTGCATCGAGC 61.866 55.000 0.00 0.00 45.96 5.03
737 746 0.109597 GTTTGGTTGCCTGCATCGAG 60.110 55.000 0.00 0.00 0.00 4.04
738 747 0.821301 TGTTTGGTTGCCTGCATCGA 60.821 50.000 0.00 0.00 0.00 3.59
739 748 0.244450 ATGTTTGGTTGCCTGCATCG 59.756 50.000 0.00 0.00 0.00 3.84
740 749 1.717194 CATGTTTGGTTGCCTGCATC 58.283 50.000 0.00 0.00 0.00 3.91
741 750 0.320946 GCATGTTTGGTTGCCTGCAT 60.321 50.000 0.00 0.00 32.66 3.96
742 751 1.069427 GCATGTTTGGTTGCCTGCA 59.931 52.632 0.00 0.00 32.66 4.41
743 752 3.955775 GCATGTTTGGTTGCCTGC 58.044 55.556 0.00 0.00 32.66 4.85
763 772 5.422012 TCTTCCTTCCTTGAAAGTGCTTTTT 59.578 36.000 0.00 0.00 32.11 1.94
764 773 4.956075 TCTTCCTTCCTTGAAAGTGCTTTT 59.044 37.500 0.00 0.00 32.11 2.27
765 774 4.536765 TCTTCCTTCCTTGAAAGTGCTTT 58.463 39.130 0.00 0.00 35.14 3.51
766 775 4.140536 CTCTTCCTTCCTTGAAAGTGCTT 58.859 43.478 0.00 0.00 0.00 3.91
767 776 3.497584 CCTCTTCCTTCCTTGAAAGTGCT 60.498 47.826 0.00 0.00 0.00 4.40
768 777 2.816672 CCTCTTCCTTCCTTGAAAGTGC 59.183 50.000 0.00 0.00 0.00 4.40
769 778 3.416156 CCCTCTTCCTTCCTTGAAAGTG 58.584 50.000 0.00 0.00 0.00 3.16
770 779 2.376855 CCCCTCTTCCTTCCTTGAAAGT 59.623 50.000 0.00 0.00 0.00 2.66
771 780 2.291217 CCCCCTCTTCCTTCCTTGAAAG 60.291 54.545 0.00 0.00 0.00 2.62
772 781 1.710809 CCCCCTCTTCCTTCCTTGAAA 59.289 52.381 0.00 0.00 0.00 2.69
773 782 1.132201 TCCCCCTCTTCCTTCCTTGAA 60.132 52.381 0.00 0.00 0.00 2.69
774 783 0.496382 TCCCCCTCTTCCTTCCTTGA 59.504 55.000 0.00 0.00 0.00 3.02
775 784 0.915364 CTCCCCCTCTTCCTTCCTTG 59.085 60.000 0.00 0.00 0.00 3.61
776 785 0.800239 TCTCCCCCTCTTCCTTCCTT 59.200 55.000 0.00 0.00 0.00 3.36
777 786 0.341609 CTCTCCCCCTCTTCCTTCCT 59.658 60.000 0.00 0.00 0.00 3.36
778 787 1.341913 GCTCTCCCCCTCTTCCTTCC 61.342 65.000 0.00 0.00 0.00 3.46
779 788 0.618968 TGCTCTCCCCCTCTTCCTTC 60.619 60.000 0.00 0.00 0.00 3.46
780 789 0.045469 ATGCTCTCCCCCTCTTCCTT 59.955 55.000 0.00 0.00 0.00 3.36
781 790 0.693767 CATGCTCTCCCCCTCTTCCT 60.694 60.000 0.00 0.00 0.00 3.36
782 791 1.704007 CCATGCTCTCCCCCTCTTCC 61.704 65.000 0.00 0.00 0.00 3.46
783 792 1.835693 CCATGCTCTCCCCCTCTTC 59.164 63.158 0.00 0.00 0.00 2.87
784 793 2.381941 GCCATGCTCTCCCCCTCTT 61.382 63.158 0.00 0.00 0.00 2.85
785 794 2.771762 GCCATGCTCTCCCCCTCT 60.772 66.667 0.00 0.00 0.00 3.69
786 795 4.247380 CGCCATGCTCTCCCCCTC 62.247 72.222 0.00 0.00 0.00 4.30
787 796 4.804420 TCGCCATGCTCTCCCCCT 62.804 66.667 0.00 0.00 0.00 4.79
788 797 4.247380 CTCGCCATGCTCTCCCCC 62.247 72.222 0.00 0.00 0.00 5.40
789 798 4.247380 CCTCGCCATGCTCTCCCC 62.247 72.222 0.00 0.00 0.00 4.81
790 799 4.247380 CCCTCGCCATGCTCTCCC 62.247 72.222 0.00 0.00 0.00 4.30
791 800 3.157252 TCCCTCGCCATGCTCTCC 61.157 66.667 0.00 0.00 0.00 3.71
792 801 2.420890 CTCCCTCGCCATGCTCTC 59.579 66.667 0.00 0.00 0.00 3.20
793 802 2.364842 ACTCCCTCGCCATGCTCT 60.365 61.111 0.00 0.00 0.00 4.09
794 803 2.202987 CACTCCCTCGCCATGCTC 60.203 66.667 0.00 0.00 0.00 4.26
795 804 3.790437 CCACTCCCTCGCCATGCT 61.790 66.667 0.00 0.00 0.00 3.79
796 805 4.864334 CCCACTCCCTCGCCATGC 62.864 72.222 0.00 0.00 0.00 4.06
797 806 3.083349 TCCCACTCCCTCGCCATG 61.083 66.667 0.00 0.00 0.00 3.66
798 807 2.765807 CTCCCACTCCCTCGCCAT 60.766 66.667 0.00 0.00 0.00 4.40
800 809 4.779733 TCCTCCCACTCCCTCGCC 62.780 72.222 0.00 0.00 0.00 5.54
801 810 2.683933 TTCCTCCCACTCCCTCGC 60.684 66.667 0.00 0.00 0.00 5.03
802 811 0.397816 ATCTTCCTCCCACTCCCTCG 60.398 60.000 0.00 0.00 0.00 4.63
803 812 1.765904 GAATCTTCCTCCCACTCCCTC 59.234 57.143 0.00 0.00 0.00 4.30
804 813 1.626631 GGAATCTTCCTCCCACTCCCT 60.627 57.143 1.57 0.00 44.11 4.20
805 814 0.840617 GGAATCTTCCTCCCACTCCC 59.159 60.000 1.57 0.00 44.11 4.30
816 825 4.958581 ACCAATGGAATGGAAGGAATCTTC 59.041 41.667 6.16 0.00 46.47 2.87
817 826 4.713321 CACCAATGGAATGGAAGGAATCTT 59.287 41.667 6.16 0.00 43.54 2.40
818 827 4.284178 CACCAATGGAATGGAAGGAATCT 58.716 43.478 6.16 0.00 43.54 2.40
819 828 4.660789 CACCAATGGAATGGAAGGAATC 57.339 45.455 6.16 0.00 43.54 2.52
833 842 2.217750 TCGAACTTCACACCACCAATG 58.782 47.619 0.00 0.00 0.00 2.82
848 857 3.119096 GCCCACGCTCCTTCGAAC 61.119 66.667 0.00 0.00 0.00 3.95
849 858 4.388499 GGCCCACGCTCCTTCGAA 62.388 66.667 0.00 0.00 34.44 3.71
853 862 4.351054 CAAGGGCCCACGCTCCTT 62.351 66.667 27.56 4.03 42.80 3.36
856 865 4.115199 ATCCAAGGGCCCACGCTC 62.115 66.667 27.56 0.00 38.30 5.03
859 868 4.856801 CGGATCCAAGGGCCCACG 62.857 72.222 27.56 14.66 0.00 4.94
860 869 4.506255 CCGGATCCAAGGGCCCAC 62.506 72.222 27.56 7.54 0.00 4.61
916 936 2.454941 GGTTCCTCCCTCCCTGGA 59.545 66.667 0.00 0.00 38.35 3.86
917 937 3.083997 CGGTTCCTCCCTCCCTGG 61.084 72.222 0.00 0.00 0.00 4.45
918 938 3.787001 GCGGTTCCTCCCTCCCTG 61.787 72.222 0.00 0.00 0.00 4.45
921 941 4.144703 GACGCGGTTCCTCCCTCC 62.145 72.222 12.47 0.00 0.00 4.30
922 942 4.493747 CGACGCGGTTCCTCCCTC 62.494 72.222 12.47 0.00 0.00 4.30
1506 1531 0.691413 GGTGGTAGAGGAAGAGGGGG 60.691 65.000 0.00 0.00 0.00 5.40
1507 1532 1.043673 CGGTGGTAGAGGAAGAGGGG 61.044 65.000 0.00 0.00 0.00 4.79
1508 1533 1.677637 GCGGTGGTAGAGGAAGAGGG 61.678 65.000 0.00 0.00 0.00 4.30
1509 1534 1.677637 GGCGGTGGTAGAGGAAGAGG 61.678 65.000 0.00 0.00 0.00 3.69
1510 1535 0.970937 TGGCGGTGGTAGAGGAAGAG 60.971 60.000 0.00 0.00 0.00 2.85
1511 1536 1.077805 TGGCGGTGGTAGAGGAAGA 59.922 57.895 0.00 0.00 0.00 2.87
1514 1539 2.682494 GGTGGCGGTGGTAGAGGA 60.682 66.667 0.00 0.00 0.00 3.71
1750 1787 1.466167 CGGCAGTCAGAACAGAATTGG 59.534 52.381 0.00 0.00 0.00 3.16
2008 2061 4.194720 ATCTCGTCGACGCAGCCC 62.195 66.667 32.19 0.00 39.60 5.19
2122 2175 1.954382 CTGAACTCGTCGGGGATGATA 59.046 52.381 0.00 0.00 0.00 2.15
2131 2184 1.519455 GGGGCATCTGAACTCGTCG 60.519 63.158 0.00 0.00 0.00 5.12
2176 2229 1.934220 GACCGCTGGAGACGATGACA 61.934 60.000 1.50 0.00 0.00 3.58
2194 2247 5.546499 AGAATTCAACAACCCTACTACCTGA 59.454 40.000 8.44 0.00 0.00 3.86
2200 2253 4.251268 GCGTAGAATTCAACAACCCTACT 58.749 43.478 8.44 0.00 0.00 2.57
2201 2254 3.061697 CGCGTAGAATTCAACAACCCTAC 59.938 47.826 8.44 0.00 0.00 3.18
2202 2255 3.056678 TCGCGTAGAATTCAACAACCCTA 60.057 43.478 5.77 0.00 0.00 3.53
2203 2256 2.073816 CGCGTAGAATTCAACAACCCT 58.926 47.619 8.44 0.00 0.00 4.34
2204 2257 2.070783 TCGCGTAGAATTCAACAACCC 58.929 47.619 5.77 0.00 0.00 4.11
2205 2258 3.369756 TCATCGCGTAGAATTCAACAACC 59.630 43.478 5.77 0.00 0.00 3.77
2209 2262 3.246226 AGCATCATCGCGTAGAATTCAAC 59.754 43.478 5.77 0.00 36.85 3.18
2210 2263 3.457234 AGCATCATCGCGTAGAATTCAA 58.543 40.909 5.77 0.00 36.85 2.69
2211 2264 3.097877 AGCATCATCGCGTAGAATTCA 57.902 42.857 5.77 0.00 36.85 2.57
2212 2265 4.230657 ACTAGCATCATCGCGTAGAATTC 58.769 43.478 5.77 0.00 36.85 2.17
2213 2266 4.230657 GACTAGCATCATCGCGTAGAATT 58.769 43.478 5.77 0.00 36.85 2.17
2214 2267 3.253432 TGACTAGCATCATCGCGTAGAAT 59.747 43.478 5.77 0.00 36.85 2.40
2217 2270 2.688364 TGACTAGCATCATCGCGTAG 57.312 50.000 5.77 0.46 36.85 3.51
2220 2273 1.723542 GGAATGACTAGCATCATCGCG 59.276 52.381 0.00 0.00 38.40 5.87
2223 2276 5.851720 TGAAGAGGAATGACTAGCATCATC 58.148 41.667 0.00 0.00 38.40 2.92
2224 2277 5.883685 TGAAGAGGAATGACTAGCATCAT 57.116 39.130 0.00 0.00 41.20 2.45
2225 2278 5.668471 CTTGAAGAGGAATGACTAGCATCA 58.332 41.667 0.00 0.00 35.78 3.07
2226 2279 4.511082 GCTTGAAGAGGAATGACTAGCATC 59.489 45.833 0.00 0.00 35.78 3.91
2227 2280 4.080695 TGCTTGAAGAGGAATGACTAGCAT 60.081 41.667 0.00 0.00 39.43 3.79
2268 2322 7.113124 CGCTCGTACGTCTGAAAATAAGATAAT 59.887 37.037 16.05 0.00 0.00 1.28
2276 2330 1.068055 ACCGCTCGTACGTCTGAAAAT 60.068 47.619 16.05 0.00 0.00 1.82
2358 2414 1.338769 GGTGTGAGGGAAGTATGCGTT 60.339 52.381 0.00 0.00 0.00 4.84
2430 2486 1.819305 GCCTTGTTCTTGGGAAGCTCA 60.819 52.381 0.00 0.00 31.46 4.26
2481 2537 2.236146 ACCAGCATTGTCATAGTCGGAA 59.764 45.455 0.00 0.00 0.00 4.30
2592 2648 2.481289 TGCATATCCGGTTGTTGACA 57.519 45.000 0.00 0.00 0.00 3.58
2595 2651 1.334059 GCGATGCATATCCGGTTGTTG 60.334 52.381 0.00 0.00 0.00 3.33
2631 2687 0.458669 GCAGATTGACCAGCAATGGG 59.541 55.000 0.00 0.00 46.90 4.00
2694 2750 2.119495 TGGATGGAGAGGTTAAGGAGC 58.881 52.381 0.00 0.00 0.00 4.70
2715 2771 0.662619 TGCTTGCCTTGTTGTTCTCG 59.337 50.000 0.00 0.00 0.00 4.04
2754 2810 4.610333 TCAGCACTTCCACTATCTTAGGA 58.390 43.478 0.00 0.00 0.00 2.94
2781 2837 1.292242 TCTCTGGCTTCCATACTCCCT 59.708 52.381 0.00 0.00 30.82 4.20
2818 2874 2.948979 CCACAACTGACAGGCTAAACAA 59.051 45.455 7.51 0.00 0.00 2.83
2883 2939 3.257393 GTCGCACAGAAGATTGATGAGT 58.743 45.455 0.00 0.00 0.00 3.41
2970 3026 3.835790 TTTCACCGCCCGGACCTTG 62.836 63.158 14.44 1.11 38.96 3.61
2998 3054 4.213564 AGAAGTTCATCAGATGGGTGAC 57.786 45.455 10.67 5.09 0.00 3.67
3105 3161 1.135199 GGCATTGGCTCTGATTGTGTG 60.135 52.381 2.42 0.00 40.87 3.82
3189 3245 2.533916 TCAGCAGAACAGAGAGACCAT 58.466 47.619 0.00 0.00 0.00 3.55
3237 3293 2.194326 GCATCTTCCCCTCCAGCC 59.806 66.667 0.00 0.00 0.00 4.85
3579 3646 5.762179 ACCATGAGACCAGAACTGATAAA 57.238 39.130 3.19 0.00 0.00 1.40
3590 3657 6.239176 GGAATGTGTTTAAAACCATGAGACCA 60.239 38.462 0.00 0.00 0.00 4.02
3600 3667 7.561021 ACCAAAATGGGAATGTGTTTAAAAC 57.439 32.000 0.87 0.00 43.37 2.43
3812 3895 6.383147 AGAAGCTAAGCCACATTAACCTAGTA 59.617 38.462 0.00 0.00 0.00 1.82
3928 4044 8.950007 AGAGAAAATATTGTACCCCTCAAAAA 57.050 30.769 0.00 0.00 0.00 1.94
3929 4045 8.802267 CAAGAGAAAATATTGTACCCCTCAAAA 58.198 33.333 0.00 0.00 0.00 2.44
3930 4046 8.167392 TCAAGAGAAAATATTGTACCCCTCAAA 58.833 33.333 0.00 0.00 31.82 2.69
3931 4047 7.695055 TCAAGAGAAAATATTGTACCCCTCAA 58.305 34.615 0.00 0.00 31.82 3.02
3932 4048 7.265599 TCAAGAGAAAATATTGTACCCCTCA 57.734 36.000 0.00 0.00 31.82 3.86
3933 4049 9.847224 TTATCAAGAGAAAATATTGTACCCCTC 57.153 33.333 0.00 0.00 31.82 4.30
3934 4050 9.853177 CTTATCAAGAGAAAATATTGTACCCCT 57.147 33.333 0.00 0.00 31.82 4.79
3935 4051 9.628500 ACTTATCAAGAGAAAATATTGTACCCC 57.372 33.333 0.00 0.00 31.82 4.95
3948 4064 9.177608 CCCATCATGTTTTACTTATCAAGAGAA 57.822 33.333 0.00 0.00 0.00 2.87
3949 4065 8.548025 TCCCATCATGTTTTACTTATCAAGAGA 58.452 33.333 0.00 0.00 0.00 3.10
3991 4107 6.293845 GCTCACCTCAAAATGGATCATGTATC 60.294 42.308 0.00 0.00 0.00 2.24
3998 4114 5.128919 ACATAGCTCACCTCAAAATGGATC 58.871 41.667 0.00 0.00 0.00 3.36
4026 4142 2.821378 TGCATGTGGACTCAGAAAATGG 59.179 45.455 0.00 0.00 0.00 3.16
4050 4627 1.017701 CGCCTCCCAACGTAAGGTTC 61.018 60.000 6.26 0.00 46.39 3.62
4057 4634 0.108329 CTGAATACGCCTCCCAACGT 60.108 55.000 0.00 0.00 45.85 3.99
4058 4635 0.108329 ACTGAATACGCCTCCCAACG 60.108 55.000 0.00 0.00 0.00 4.10
4065 4642 3.206150 CCTTAATGCACTGAATACGCCT 58.794 45.455 0.00 0.00 0.00 5.52
4087 4664 3.863142 AACGAGTACTGTACCCATGAC 57.137 47.619 14.05 0.00 0.00 3.06
4110 4687 9.832445 TTATTCTTAATCCTAACACATCTCACC 57.168 33.333 0.00 0.00 0.00 4.02
4157 4826 5.921153 AAAAGGGGAAATGATGGGAAAAA 57.079 34.783 0.00 0.00 0.00 1.94
4158 4827 5.921153 AAAAAGGGGAAATGATGGGAAAA 57.079 34.783 0.00 0.00 0.00 2.29
4229 4899 2.234908 CAAGCACACTAACTAGGGCTCT 59.765 50.000 0.00 0.00 31.86 4.09
4305 4978 2.621055 TCGTTTTGTCTGGTTCCATTGG 59.379 45.455 0.00 0.00 0.00 3.16
4306 4979 3.980646 TCGTTTTGTCTGGTTCCATTG 57.019 42.857 0.00 0.00 0.00 2.82
4307 4980 4.261994 CCATTCGTTTTGTCTGGTTCCATT 60.262 41.667 0.00 0.00 0.00 3.16
4308 4981 3.255642 CCATTCGTTTTGTCTGGTTCCAT 59.744 43.478 0.00 0.00 0.00 3.41
4309 4982 2.621055 CCATTCGTTTTGTCTGGTTCCA 59.379 45.455 0.00 0.00 0.00 3.53
4310 4983 2.621526 ACCATTCGTTTTGTCTGGTTCC 59.378 45.455 0.00 0.00 36.86 3.62
4311 4984 3.066203 ACACCATTCGTTTTGTCTGGTTC 59.934 43.478 0.00 0.00 38.13 3.62
4312 4985 3.020984 ACACCATTCGTTTTGTCTGGTT 58.979 40.909 0.00 0.00 38.13 3.67
4313 4986 2.616842 GACACCATTCGTTTTGTCTGGT 59.383 45.455 0.00 0.00 40.79 4.00


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

AutoCloner maintained by Alex Coulton.