Multiple sequence alignment - TraesCS4B01G079200

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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 TraesCS4B01G079200 chr4B 100.000 4278 0 0 1 4278 76812448 76816725 0.000000e+00 7901.0
1 TraesCS4B01G079200 chr4B 86.215 428 53 5 998 1422 76622196 76622620 3.900000e-125 459.0
2 TraesCS4B01G079200 chr4B 91.111 135 12 0 3480 3614 11930236 11930370 2.630000e-42 183.0
3 TraesCS4B01G079200 chr4D 95.121 2685 107 14 817 3493 52467340 52470008 0.000000e+00 4211.0
4 TraesCS4B01G079200 chr4D 88.623 334 21 9 3766 4089 52470116 52470442 1.440000e-104 390.0
5 TraesCS4B01G079200 chr4D 93.243 148 7 1 4131 4278 52470440 52470584 9.320000e-52 215.0
6 TraesCS4B01G079200 chr4D 92.366 131 10 0 3485 3615 614524 614654 2.030000e-43 187.0
7 TraesCS4B01G079200 chr4A 91.480 2629 160 37 892 3488 544204344 544201748 0.000000e+00 3555.0
8 TraesCS4B01G079200 chr4A 85.349 430 61 2 994 1422 544390833 544390405 1.090000e-120 444.0
9 TraesCS4B01G079200 chr4A 86.275 255 13 2 3858 4091 544201429 544201176 1.530000e-64 257.0
10 TraesCS4B01G079200 chr4A 95.270 148 4 1 4131 4278 544201180 544201036 9.250000e-57 231.0
11 TraesCS4B01G079200 chr4A 95.161 62 3 0 3762 3823 544201557 544201496 9.790000e-17 99.0
12 TraesCS4B01G079200 chr3A 96.970 693 18 3 1 690 378337675 378336983 0.000000e+00 1160.0
13 TraesCS4B01G079200 chr5B 96.691 695 20 1 1 692 63252290 63251596 0.000000e+00 1153.0
14 TraesCS4B01G079200 chr5B 95.397 717 24 8 1 713 686832066 686832777 0.000000e+00 1133.0
15 TraesCS4B01G079200 chr5B 80.241 911 155 20 2478 3376 595631941 595631044 0.000000e+00 662.0
16 TraesCS4B01G079200 chr5B 78.486 925 166 24 2478 3386 595645354 595644447 3.710000e-160 575.0
17 TraesCS4B01G079200 chr5B 77.957 930 160 32 2471 3376 541499740 541500648 1.350000e-149 540.0
18 TraesCS4B01G079200 chr5B 78.020 505 84 19 1008 1504 595633228 595632743 4.180000e-75 292.0
19 TraesCS4B01G079200 chr5B 93.284 134 7 2 3484 3617 695950978 695950847 3.370000e-46 196.0
20 TraesCS4B01G079200 chr5B 93.333 60 1 2 4190 4248 222724836 222724779 7.620000e-13 86.1
21 TraesCS4B01G079200 chr5A 96.557 697 20 1 1 693 664389561 664388865 0.000000e+00 1151.0
22 TraesCS4B01G079200 chr5A 96.681 693 19 2 1 690 653659864 653659173 0.000000e+00 1149.0
23 TraesCS4B01G079200 chr5A 78.947 893 150 27 2471 3343 561554306 561555180 1.330000e-159 573.0
24 TraesCS4B01G079200 chr5A 77.597 799 166 9 2475 3262 659822209 659821413 5.010000e-129 472.0
25 TraesCS4B01G079200 chr5A 80.412 485 74 14 1008 1488 606060581 606060114 2.450000e-92 350.0
26 TraesCS4B01G079200 chr5A 80.964 415 62 7 1008 1421 561553346 561553744 3.210000e-81 313.0
27 TraesCS4B01G079200 chr6B 96.413 697 22 2 1 695 67520450 67521145 0.000000e+00 1146.0
28 TraesCS4B01G079200 chr6B 93.130 131 9 0 3488 3618 209249735 209249865 4.370000e-45 193.0
29 TraesCS4B01G079200 chr6B 93.130 131 8 1 3487 3616 632877741 632877611 1.570000e-44 191.0
30 TraesCS4B01G079200 chr3B 96.275 698 23 2 1 696 94487467 94488163 0.000000e+00 1142.0
31 TraesCS4B01G079200 chr7B 96.017 703 23 3 1 699 664047480 664046779 0.000000e+00 1138.0
32 TraesCS4B01G079200 chr7B 80.020 976 179 11 2442 3416 86141072 86142032 0.000000e+00 708.0
33 TraesCS4B01G079200 chr7B 78.876 516 74 20 954 1445 86139274 86139778 2.480000e-82 316.0
34 TraesCS4B01G079200 chr1B 96.000 700 26 1 1 700 206978319 206979016 0.000000e+00 1136.0
35 TraesCS4B01G079200 chr7D 80.225 976 178 10 2442 3416 124300220 124301181 0.000000e+00 719.0
36 TraesCS4B01G079200 chr7D 80.198 505 80 15 954 1445 124298517 124299014 1.130000e-95 361.0
37 TraesCS4B01G079200 chr7A 79.482 1004 189 12 2415 3416 126866666 126867654 0.000000e+00 697.0
38 TraesCS4B01G079200 chr7A 79.010 505 86 14 954 1445 126865007 126865504 1.150000e-85 327.0
39 TraesCS4B01G079200 chr5D 79.585 916 152 26 2478 3376 484427553 484426656 1.310000e-174 623.0
40 TraesCS4B01G079200 chr5D 78.947 874 149 23 2493 3346 444712088 444712946 2.890000e-156 562.0
41 TraesCS4B01G079200 chr5D 80.808 495 72 17 1008 1496 484428841 484428364 2.430000e-97 366.0
42 TraesCS4B01G079200 chr5D 94.488 127 7 0 3488 3614 439810816 439810690 3.370000e-46 196.0
43 TraesCS4B01G079200 chr2B 95.312 128 6 0 3488 3615 65089831 65089958 2.020000e-48 204.0
44 TraesCS4B01G079200 chr2D 92.366 131 10 0 3487 3617 605712387 605712257 2.030000e-43 187.0
45 TraesCS4B01G079200 chr3D 89.116 147 12 4 3469 3614 35819164 35819021 3.400000e-41 180.0


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 TraesCS4B01G079200 chr4B 76812448 76816725 4277 False 7901.000000 7901 100.0000 1 4278 1 chr4B.!!$F3 4277
1 TraesCS4B01G079200 chr4D 52467340 52470584 3244 False 1605.333333 4211 92.3290 817 4278 3 chr4D.!!$F2 3461
2 TraesCS4B01G079200 chr4A 544201036 544204344 3308 True 1035.500000 3555 92.0465 892 4278 4 chr4A.!!$R2 3386
3 TraesCS4B01G079200 chr3A 378336983 378337675 692 True 1160.000000 1160 96.9700 1 690 1 chr3A.!!$R1 689
4 TraesCS4B01G079200 chr5B 63251596 63252290 694 True 1153.000000 1153 96.6910 1 692 1 chr5B.!!$R1 691
5 TraesCS4B01G079200 chr5B 686832066 686832777 711 False 1133.000000 1133 95.3970 1 713 1 chr5B.!!$F2 712
6 TraesCS4B01G079200 chr5B 595644447 595645354 907 True 575.000000 575 78.4860 2478 3386 1 chr5B.!!$R3 908
7 TraesCS4B01G079200 chr5B 541499740 541500648 908 False 540.000000 540 77.9570 2471 3376 1 chr5B.!!$F1 905
8 TraesCS4B01G079200 chr5B 595631044 595633228 2184 True 477.000000 662 79.1305 1008 3376 2 chr5B.!!$R5 2368
9 TraesCS4B01G079200 chr5A 664388865 664389561 696 True 1151.000000 1151 96.5570 1 693 1 chr5A.!!$R4 692
10 TraesCS4B01G079200 chr5A 653659173 653659864 691 True 1149.000000 1149 96.6810 1 690 1 chr5A.!!$R2 689
11 TraesCS4B01G079200 chr5A 659821413 659822209 796 True 472.000000 472 77.5970 2475 3262 1 chr5A.!!$R3 787
12 TraesCS4B01G079200 chr5A 561553346 561555180 1834 False 443.000000 573 79.9555 1008 3343 2 chr5A.!!$F1 2335
13 TraesCS4B01G079200 chr6B 67520450 67521145 695 False 1146.000000 1146 96.4130 1 695 1 chr6B.!!$F1 694
14 TraesCS4B01G079200 chr3B 94487467 94488163 696 False 1142.000000 1142 96.2750 1 696 1 chr3B.!!$F1 695
15 TraesCS4B01G079200 chr7B 664046779 664047480 701 True 1138.000000 1138 96.0170 1 699 1 chr7B.!!$R1 698
16 TraesCS4B01G079200 chr7B 86139274 86142032 2758 False 512.000000 708 79.4480 954 3416 2 chr7B.!!$F1 2462
17 TraesCS4B01G079200 chr1B 206978319 206979016 697 False 1136.000000 1136 96.0000 1 700 1 chr1B.!!$F1 699
18 TraesCS4B01G079200 chr7D 124298517 124301181 2664 False 540.000000 719 80.2115 954 3416 2 chr7D.!!$F1 2462
19 TraesCS4B01G079200 chr7A 126865007 126867654 2647 False 512.000000 697 79.2460 954 3416 2 chr7A.!!$F1 2462
20 TraesCS4B01G079200 chr5D 444712088 444712946 858 False 562.000000 562 78.9470 2493 3346 1 chr5D.!!$F1 853
21 TraesCS4B01G079200 chr5D 484426656 484428841 2185 True 494.500000 623 80.1965 1008 3376 2 chr5D.!!$R2 2368

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
813 821 0.036294 GTCCCTCCTTTTCTCCCACG 60.036 60.0 0.0 0.00 0.0 4.94 F
814 822 0.178915 TCCCTCCTTTTCTCCCACGA 60.179 55.0 0.0 0.00 0.0 4.35 F
949 957 0.180406 ATTGCACCTCCCGTACATCC 59.820 55.0 0.0 0.00 0.0 3.51 F
1467 1503 0.670546 ACACGACGGCAAGATCCTTG 60.671 55.0 0.0 2.54 0.0 3.61 F
2153 2728 0.740737 GCCTGGGGAATTTGTCGATG 59.259 55.0 0.0 0.00 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2795 3.133003 TGCAAGGCTCTAGACATTCCTAC 59.867 47.826 0.00 0.0 0.00 3.18 R
2357 2991 3.440173 ACATTGTGCAATACCACTACTGC 59.560 43.478 0.00 0.0 36.68 4.40 R
2948 3945 5.967674 CAGACGCTTCAAATCCAAATGATAC 59.032 40.000 0.00 0.0 31.83 2.24 R
3127 4130 0.599991 TAAGTGTGACCACAGCAGCG 60.600 55.000 2.68 0.0 44.39 5.18 R
4091 5154 0.033796 ATCTTGTGGGGGCATGAGTG 60.034 55.000 0.00 0.0 0.00 3.51 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
269 272 7.675062 TGCCATGAACCATAAACTAAAATTGT 58.325 30.769 0.00 0.00 0.00 2.71
700 708 8.525876 GGCGTTAACATTTCCGTATTTTATTTC 58.474 33.333 6.39 0.00 0.00 2.17
701 709 8.525876 GCGTTAACATTTCCGTATTTTATTTCC 58.474 33.333 6.39 0.00 0.00 3.13
702 710 9.557338 CGTTAACATTTCCGTATTTTATTTCCA 57.443 29.630 6.39 0.00 0.00 3.53
728 736 9.844790 AAAATAAAAATAGGGTTTGTAGTACGC 57.155 29.630 0.00 0.00 0.00 4.42
729 737 5.535043 AAAAATAGGGTTTGTAGTACGCG 57.465 39.130 3.53 3.53 34.06 6.01
730 738 2.877043 ATAGGGTTTGTAGTACGCGG 57.123 50.000 12.47 0.00 34.06 6.46
731 739 0.817013 TAGGGTTTGTAGTACGCGGG 59.183 55.000 12.47 0.00 34.06 6.13
732 740 0.899717 AGGGTTTGTAGTACGCGGGA 60.900 55.000 12.47 0.00 34.06 5.14
733 741 0.459063 GGGTTTGTAGTACGCGGGAG 60.459 60.000 12.47 0.00 0.00 4.30
734 742 0.527565 GGTTTGTAGTACGCGGGAGA 59.472 55.000 12.47 0.00 0.00 3.71
735 743 1.622232 GTTTGTAGTACGCGGGAGAC 58.378 55.000 12.47 3.59 0.00 3.36
746 754 3.041940 GGGAGACCGCACACGTTG 61.042 66.667 0.00 0.00 43.64 4.10
747 755 2.279918 GGAGACCGCACACGTTGT 60.280 61.111 0.00 0.00 37.70 3.32
748 756 2.308039 GGAGACCGCACACGTTGTC 61.308 63.158 0.00 0.00 37.70 3.18
749 757 1.590525 GAGACCGCACACGTTGTCA 60.591 57.895 0.00 0.00 34.22 3.58
750 758 1.818221 GAGACCGCACACGTTGTCAC 61.818 60.000 0.00 0.00 34.22 3.67
759 767 3.919386 CGTTGTCACGCACGCACA 61.919 61.111 0.00 0.00 40.18 4.57
760 768 2.401592 GTTGTCACGCACGCACAA 59.598 55.556 4.53 4.53 0.00 3.33
761 769 1.932564 GTTGTCACGCACGCACAAC 60.933 57.895 17.58 17.58 42.21 3.32
779 787 4.540735 GGCACACGATACCCCGGG 62.541 72.222 15.80 15.80 39.19 5.73
780 788 3.463585 GCACACGATACCCCGGGA 61.464 66.667 26.32 1.94 36.28 5.14
781 789 2.812499 CACACGATACCCCGGGAG 59.188 66.667 26.32 15.37 36.28 4.30
782 790 1.755395 CACACGATACCCCGGGAGA 60.755 63.158 26.32 9.91 36.28 3.71
783 791 1.755783 ACACGATACCCCGGGAGAC 60.756 63.158 26.32 9.50 36.28 3.36
794 802 3.041940 GGGAGACCGCACACGTTG 61.042 66.667 0.00 0.00 43.64 4.10
795 803 2.279918 GGAGACCGCACACGTTGT 60.280 61.111 0.00 0.00 37.70 3.32
796 804 2.308039 GGAGACCGCACACGTTGTC 61.308 63.158 0.00 0.00 37.70 3.18
797 805 2.279918 AGACCGCACACGTTGTCC 60.280 61.111 0.00 0.00 37.70 4.02
798 806 3.343421 GACCGCACACGTTGTCCC 61.343 66.667 0.00 0.00 37.70 4.46
799 807 3.802418 GACCGCACACGTTGTCCCT 62.802 63.158 0.00 0.00 37.70 4.20
800 808 3.041940 CCGCACACGTTGTCCCTC 61.042 66.667 0.00 0.00 37.70 4.30
801 809 3.041940 CGCACACGTTGTCCCTCC 61.042 66.667 0.00 0.00 33.53 4.30
802 810 2.426023 GCACACGTTGTCCCTCCT 59.574 61.111 0.00 0.00 0.00 3.69
803 811 1.227853 GCACACGTTGTCCCTCCTT 60.228 57.895 0.00 0.00 0.00 3.36
804 812 0.818040 GCACACGTTGTCCCTCCTTT 60.818 55.000 0.00 0.00 0.00 3.11
805 813 1.675552 CACACGTTGTCCCTCCTTTT 58.324 50.000 0.00 0.00 0.00 2.27
806 814 1.602377 CACACGTTGTCCCTCCTTTTC 59.398 52.381 0.00 0.00 0.00 2.29
807 815 1.489230 ACACGTTGTCCCTCCTTTTCT 59.511 47.619 0.00 0.00 0.00 2.52
808 816 2.143925 CACGTTGTCCCTCCTTTTCTC 58.856 52.381 0.00 0.00 0.00 2.87
809 817 1.071857 ACGTTGTCCCTCCTTTTCTCC 59.928 52.381 0.00 0.00 0.00 3.71
810 818 1.610886 CGTTGTCCCTCCTTTTCTCCC 60.611 57.143 0.00 0.00 0.00 4.30
811 819 1.423921 GTTGTCCCTCCTTTTCTCCCA 59.576 52.381 0.00 0.00 0.00 4.37
812 820 1.064825 TGTCCCTCCTTTTCTCCCAC 58.935 55.000 0.00 0.00 0.00 4.61
813 821 0.036294 GTCCCTCCTTTTCTCCCACG 60.036 60.000 0.00 0.00 0.00 4.94
814 822 0.178915 TCCCTCCTTTTCTCCCACGA 60.179 55.000 0.00 0.00 0.00 4.35
815 823 0.690762 CCCTCCTTTTCTCCCACGAA 59.309 55.000 0.00 0.00 0.00 3.85
819 827 1.202722 TCCTTTTCTCCCACGAACACC 60.203 52.381 0.00 0.00 0.00 4.16
846 854 4.708726 ATTAATGCCAACTCTGTTCAGC 57.291 40.909 0.00 0.00 0.00 4.26
912 920 2.481449 CCCGCTACATAACCAGTGAGAC 60.481 54.545 0.00 0.00 0.00 3.36
949 957 0.180406 ATTGCACCTCCCGTACATCC 59.820 55.000 0.00 0.00 0.00 3.51
1449 1485 5.646577 TCCTTGTCTAGCTAGTTCTTGAC 57.353 43.478 20.10 10.64 38.63 3.18
1467 1503 0.670546 ACACGACGGCAAGATCCTTG 60.671 55.000 0.00 2.54 0.00 3.61
1507 1547 9.390795 CATAGTACAGATTTGCTCATTATTTGC 57.609 33.333 0.00 0.00 0.00 3.68
1617 1701 8.971073 TGATGTGATGTAGATATGAATATCGGT 58.029 33.333 4.97 0.00 43.01 4.69
1675 1777 9.787435 TTTGAAATTTAGTACTCCATACAGTGT 57.213 29.630 0.00 0.00 36.09 3.55
1677 1779 9.214957 TGAAATTTAGTACTCCATACAGTGTTG 57.785 33.333 0.00 0.00 36.09 3.33
1678 1780 9.216117 GAAATTTAGTACTCCATACAGTGTTGT 57.784 33.333 0.00 0.00 41.39 3.32
1691 1793 9.307121 CCATACAGTGTTGTAATTTTGTTGAAA 57.693 29.630 0.00 0.00 42.72 2.69
1792 1901 3.908382 GTCTGCTGTTTTCGTAAATGCAG 59.092 43.478 24.85 24.85 45.03 4.41
2083 2217 9.817365 CTAGTCTGTTACTTTTGTGATCAAATG 57.183 33.333 0.00 0.00 42.14 2.32
2153 2728 0.740737 GCCTGGGGAATTTGTCGATG 59.259 55.000 0.00 0.00 0.00 3.84
2240 2831 1.543802 CCTTGCAAATTCGTTGGCCTA 59.456 47.619 3.32 0.00 37.73 3.93
2285 2918 7.312899 CCCTTTCGTGCTTTTCATTTATTACT 58.687 34.615 0.00 0.00 0.00 2.24
2397 3036 1.204704 TGTCGCTTCTAGATGGTGTGG 59.795 52.381 7.66 0.00 0.00 4.17
2770 3767 4.100963 TCTGACAGCTTGAAGGTACTGAAA 59.899 41.667 0.00 0.00 40.86 2.69
2948 3945 2.494059 TCAAGCTTCCGAAGTTCAAGG 58.506 47.619 9.87 0.00 0.00 3.61
3335 4342 2.804527 CAACTGTCACATGTGAGTGGAG 59.195 50.000 28.54 21.44 40.75 3.86
3395 4405 3.447586 TCCGGTGGATGTTTTTGTTTTCA 59.552 39.130 0.00 0.00 0.00 2.69
3432 4442 3.523157 TGATGTATGGAGGTTGTGGTGAT 59.477 43.478 0.00 0.00 0.00 3.06
3436 4446 5.882040 TGTATGGAGGTTGTGGTGATTTAA 58.118 37.500 0.00 0.00 0.00 1.52
3461 4471 5.300034 TGACAATAATCCAGGATTGATGTGC 59.700 40.000 27.18 20.65 34.65 4.57
3464 4474 3.377253 AATCCAGGATTGATGTGCAGT 57.623 42.857 14.45 0.00 30.42 4.40
3472 4482 3.742369 GGATTGATGTGCAGTTTTTGTGG 59.258 43.478 0.00 0.00 0.00 4.17
3493 4503 3.440522 GGTTTCAGTTGCTTGATACTCCC 59.559 47.826 0.00 0.00 32.03 4.30
3494 4504 4.327680 GTTTCAGTTGCTTGATACTCCCT 58.672 43.478 0.00 0.00 0.00 4.20
3496 4506 2.501723 TCAGTTGCTTGATACTCCCTCC 59.498 50.000 0.00 0.00 0.00 4.30
3498 4508 1.207329 GTTGCTTGATACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
3499 4509 1.112113 TGCTTGATACTCCCTCCGTC 58.888 55.000 0.00 0.00 0.00 4.79
3500 4510 0.389757 GCTTGATACTCCCTCCGTCC 59.610 60.000 0.00 0.00 0.00 4.79
3501 4511 1.041437 CTTGATACTCCCTCCGTCCC 58.959 60.000 0.00 0.00 0.00 4.46
3502 4512 0.337082 TTGATACTCCCTCCGTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
3503 4513 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
3504 4514 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
3505 4515 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
3506 4516 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3507 4517 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3508 4518 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3509 4519 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3510 4520 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3513 4523 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3514 4524 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3515 4525 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3516 4526 3.818773 TCCGTCCCAAAATTCTTGTCTTC 59.181 43.478 0.00 0.00 0.00 2.87
3517 4527 3.568007 CCGTCCCAAAATTCTTGTCTTCA 59.432 43.478 0.00 0.00 0.00 3.02
3519 4529 5.278957 CCGTCCCAAAATTCTTGTCTTCAAT 60.279 40.000 0.00 0.00 32.82 2.57
3520 4530 6.215845 CGTCCCAAAATTCTTGTCTTCAATT 58.784 36.000 0.00 0.00 32.82 2.32
3521 4531 6.701400 CGTCCCAAAATTCTTGTCTTCAATTT 59.299 34.615 0.00 0.00 32.30 1.82
3522 4532 7.865385 CGTCCCAAAATTCTTGTCTTCAATTTA 59.135 33.333 0.00 0.00 31.06 1.40
3523 4533 9.710900 GTCCCAAAATTCTTGTCTTCAATTTAT 57.289 29.630 0.00 0.00 31.06 1.40
3524 4534 9.927668 TCCCAAAATTCTTGTCTTCAATTTATC 57.072 29.630 0.00 0.00 31.06 1.75
3555 4565 8.858003 ACGAATGTATCTAACAGTAAGATGTG 57.142 34.615 0.00 0.00 42.70 3.21
3556 4566 8.683615 ACGAATGTATCTAACAGTAAGATGTGA 58.316 33.333 0.00 0.00 42.70 3.58
3557 4567 8.959058 CGAATGTATCTAACAGTAAGATGTGAC 58.041 37.037 0.00 0.00 42.70 3.67
3561 4571 9.901172 TGTATCTAACAGTAAGATGTGACTAGA 57.099 33.333 0.00 0.00 35.36 2.43
3565 4575 9.901172 TCTAACAGTAAGATGTGACTAGATACA 57.099 33.333 0.00 1.16 32.52 2.29
3589 4599 9.988815 ACATCCATATGTAGACAAATCTAAGAC 57.011 33.333 1.24 0.00 44.66 3.01
3590 4600 9.987272 CATCCATATGTAGACAAATCTAAGACA 57.013 33.333 1.24 0.00 39.20 3.41
3601 4611 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3602 4612 7.670364 ACAAATCTAAGACAAGAATTTTGGGG 58.330 34.615 0.00 0.00 33.04 4.96
3603 4613 5.921962 ATCTAAGACAAGAATTTTGGGGC 57.078 39.130 5.68 0.00 0.00 5.80
3604 4614 3.756434 TCTAAGACAAGAATTTTGGGGCG 59.244 43.478 5.68 0.00 0.00 6.13
3605 4615 2.286365 AGACAAGAATTTTGGGGCGA 57.714 45.000 0.00 0.00 0.00 5.54
3606 4616 2.593026 AGACAAGAATTTTGGGGCGAA 58.407 42.857 0.00 0.00 0.00 4.70
3607 4617 2.558359 AGACAAGAATTTTGGGGCGAAG 59.442 45.455 0.00 0.00 0.00 3.79
3608 4618 1.618343 ACAAGAATTTTGGGGCGAAGG 59.382 47.619 0.00 0.00 0.00 3.46
3609 4619 1.066929 CAAGAATTTTGGGGCGAAGGG 60.067 52.381 0.00 0.00 0.00 3.95
3610 4620 0.407918 AGAATTTTGGGGCGAAGGGA 59.592 50.000 0.00 0.00 0.00 4.20
3611 4621 0.817654 GAATTTTGGGGCGAAGGGAG 59.182 55.000 0.00 0.00 0.00 4.30
3612 4622 0.114364 AATTTTGGGGCGAAGGGAGT 59.886 50.000 0.00 0.00 0.00 3.85
3613 4623 0.996583 ATTTTGGGGCGAAGGGAGTA 59.003 50.000 0.00 0.00 0.00 2.59
3617 4627 1.335132 TGGGGCGAAGGGAGTACATC 61.335 60.000 0.00 0.00 0.00 3.06
3623 4633 2.362397 GCGAAGGGAGTACATCAGATGA 59.638 50.000 17.81 0.00 0.00 2.92
3667 4677 4.111375 AGCGAAGTACTGTATCAACCAG 57.889 45.455 0.00 0.00 36.01 4.00
3730 4740 9.757227 TTTGTTAATCTGGATTGTTTTACTTGG 57.243 29.630 6.13 0.00 32.50 3.61
3731 4741 7.891561 TGTTAATCTGGATTGTTTTACTTGGG 58.108 34.615 6.13 0.00 32.50 4.12
3733 4743 6.994421 AATCTGGATTGTTTTACTTGGGTT 57.006 33.333 0.00 0.00 0.00 4.11
3734 4744 6.994421 ATCTGGATTGTTTTACTTGGGTTT 57.006 33.333 0.00 0.00 0.00 3.27
3735 4745 6.155475 TCTGGATTGTTTTACTTGGGTTTG 57.845 37.500 0.00 0.00 0.00 2.93
3736 4746 5.069781 TCTGGATTGTTTTACTTGGGTTTGG 59.930 40.000 0.00 0.00 0.00 3.28
3737 4747 4.717280 TGGATTGTTTTACTTGGGTTTGGT 59.283 37.500 0.00 0.00 0.00 3.67
3738 4748 5.189934 TGGATTGTTTTACTTGGGTTTGGTT 59.810 36.000 0.00 0.00 0.00 3.67
3739 4749 5.525745 GGATTGTTTTACTTGGGTTTGGTTG 59.474 40.000 0.00 0.00 0.00 3.77
3740 4750 5.740290 TTGTTTTACTTGGGTTTGGTTGA 57.260 34.783 0.00 0.00 0.00 3.18
3741 4751 5.074584 TGTTTTACTTGGGTTTGGTTGAC 57.925 39.130 0.00 0.00 0.00 3.18
3742 4752 4.773149 TGTTTTACTTGGGTTTGGTTGACT 59.227 37.500 0.00 0.00 0.00 3.41
3743 4753 5.246429 TGTTTTACTTGGGTTTGGTTGACTT 59.754 36.000 0.00 0.00 0.00 3.01
3744 4754 6.167685 GTTTTACTTGGGTTTGGTTGACTTT 58.832 36.000 0.00 0.00 0.00 2.66
3745 4755 3.885724 ACTTGGGTTTGGTTGACTTTG 57.114 42.857 0.00 0.00 0.00 2.77
3746 4756 3.169908 ACTTGGGTTTGGTTGACTTTGT 58.830 40.909 0.00 0.00 0.00 2.83
3747 4757 3.056179 ACTTGGGTTTGGTTGACTTTGTG 60.056 43.478 0.00 0.00 0.00 3.33
3748 4758 2.530701 TGGGTTTGGTTGACTTTGTGT 58.469 42.857 0.00 0.00 0.00 3.72
3749 4759 2.900546 TGGGTTTGGTTGACTTTGTGTT 59.099 40.909 0.00 0.00 0.00 3.32
3750 4760 3.325135 TGGGTTTGGTTGACTTTGTGTTT 59.675 39.130 0.00 0.00 0.00 2.83
3751 4761 4.202367 TGGGTTTGGTTGACTTTGTGTTTT 60.202 37.500 0.00 0.00 0.00 2.43
3752 4762 4.757657 GGGTTTGGTTGACTTTGTGTTTTT 59.242 37.500 0.00 0.00 0.00 1.94
3842 4853 2.282462 GTGTGCCTTGACTGGGGG 60.282 66.667 0.00 0.00 0.00 5.40
3884 4926 5.709164 AGAGAAAGATTCCACAATGGTTCAG 59.291 40.000 0.00 0.00 39.03 3.02
3899 4941 7.451255 ACAATGGTTCAGAATTTATTCACTCCA 59.549 33.333 5.36 7.76 39.23 3.86
3911 4953 7.730364 TTTATTCACTCCAGAACTTCTCAAC 57.270 36.000 0.00 0.00 0.00 3.18
3940 4982 1.417517 TGAGCCCACGATATGCTGAAT 59.582 47.619 0.00 0.00 34.99 2.57
3952 4994 9.964253 CACGATATGCTGAATTCTGATATTAAC 57.036 33.333 15.79 0.00 0.00 2.01
3973 5015 3.805422 ACATGCACAACTCAAAATTGCTG 59.195 39.130 0.00 0.00 34.18 4.41
4003 5066 2.573462 AGTGCATATCTCAACACCTGGT 59.427 45.455 0.00 0.00 33.46 4.00
4047 5110 3.935203 ACTGAATCATAGCAAGAACCACG 59.065 43.478 0.00 0.00 0.00 4.94
4061 5124 1.229428 ACCACGATGCAGAAACACAG 58.771 50.000 0.00 0.00 0.00 3.66
4091 5154 2.296012 GAACTGAAAGGTCGAAACGC 57.704 50.000 0.00 0.00 43.22 4.84
4092 5155 1.595794 GAACTGAAAGGTCGAAACGCA 59.404 47.619 0.00 0.00 43.22 5.24
4093 5156 0.935196 ACTGAAAGGTCGAAACGCAC 59.065 50.000 0.00 0.00 39.30 5.34
4094 5157 1.217882 CTGAAAGGTCGAAACGCACT 58.782 50.000 0.00 0.00 0.00 4.40
4095 5158 1.192534 CTGAAAGGTCGAAACGCACTC 59.807 52.381 0.00 0.00 0.00 3.51
4096 5159 1.214367 GAAAGGTCGAAACGCACTCA 58.786 50.000 0.00 0.00 0.00 3.41
4097 5160 1.798813 GAAAGGTCGAAACGCACTCAT 59.201 47.619 0.00 0.00 0.00 2.90
4098 5161 1.148310 AAGGTCGAAACGCACTCATG 58.852 50.000 0.00 0.00 0.00 3.07
4107 5170 2.283101 GCACTCATGCCCCCACAA 60.283 61.111 0.00 0.00 46.97 3.33
4108 5171 2.345760 GCACTCATGCCCCCACAAG 61.346 63.158 0.00 0.00 46.97 3.16
4109 5172 1.379916 CACTCATGCCCCCACAAGA 59.620 57.895 0.00 0.00 0.00 3.02
4110 5173 0.033796 CACTCATGCCCCCACAAGAT 60.034 55.000 0.00 0.00 0.00 2.40
4111 5174 0.033796 ACTCATGCCCCCACAAGATG 60.034 55.000 0.00 0.00 0.00 2.90
4112 5175 1.380246 TCATGCCCCCACAAGATGC 60.380 57.895 0.00 0.00 0.00 3.91
4113 5176 1.380785 CATGCCCCCACAAGATGCT 60.381 57.895 0.00 0.00 0.00 3.79
4114 5177 1.380785 ATGCCCCCACAAGATGCTG 60.381 57.895 0.00 0.00 0.00 4.41
4115 5178 2.757099 GCCCCCACAAGATGCTGG 60.757 66.667 0.00 0.00 0.00 4.85
4116 5179 3.089838 CCCCCACAAGATGCTGGA 58.910 61.111 0.00 0.00 0.00 3.86
4117 5180 1.383799 CCCCCACAAGATGCTGGAA 59.616 57.895 0.00 0.00 0.00 3.53
4118 5181 0.251742 CCCCCACAAGATGCTGGAAA 60.252 55.000 0.00 0.00 0.00 3.13
4119 5182 1.620524 CCCCCACAAGATGCTGGAAAT 60.621 52.381 0.00 0.00 0.00 2.17
4120 5183 1.479323 CCCCACAAGATGCTGGAAATG 59.521 52.381 0.00 0.00 0.00 2.32
4121 5184 1.479323 CCCACAAGATGCTGGAAATGG 59.521 52.381 0.00 0.00 0.00 3.16
4122 5185 1.134907 CCACAAGATGCTGGAAATGGC 60.135 52.381 0.00 0.00 0.00 4.40
4123 5186 1.546923 CACAAGATGCTGGAAATGGCA 59.453 47.619 0.00 0.00 42.80 4.92
4124 5187 1.822990 ACAAGATGCTGGAAATGGCAG 59.177 47.619 0.00 0.00 41.88 4.85
4125 5188 1.136305 CAAGATGCTGGAAATGGCAGG 59.864 52.381 0.00 0.00 41.88 4.85
4126 5189 1.041447 AGATGCTGGAAATGGCAGGC 61.041 55.000 0.00 0.00 41.88 4.85
4127 5190 1.305465 ATGCTGGAAATGGCAGGCA 60.305 52.632 0.00 0.00 41.88 4.75
4128 5191 1.327690 ATGCTGGAAATGGCAGGCAG 61.328 55.000 1.89 0.00 41.88 4.85
4129 5192 2.890371 CTGGAAATGGCAGGCAGC 59.110 61.111 1.89 0.00 44.65 5.25
4154 5217 6.526566 AACGAAACTGATCAAACTGTAGTC 57.473 37.500 0.00 0.00 0.00 2.59
4245 5308 3.849911 TCTACCAGTTCTCAAATCAGCG 58.150 45.455 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 272 5.970612 GCAATTTTACGTGCATGTATCATGA 59.029 36.000 19.17 0.00 40.58 3.07
319 322 5.221843 TGGCAACTCTAGTACTTTGACCATT 60.222 40.000 0.00 0.00 37.61 3.16
426 429 4.072131 AGAAGTTGCCACGATGTTTACAT 58.928 39.130 0.00 0.00 39.70 2.29
464 472 9.936329 AACTAGACCCCATGTTGATATATTTTT 57.064 29.630 0.00 0.00 0.00 1.94
671 679 1.828979 ACGGAAATGTTAACGCCCAT 58.171 45.000 0.26 0.00 0.00 4.00
702 710 9.844790 GCGTACTACAAACCCTATTTTTATTTT 57.155 29.630 0.00 0.00 0.00 1.82
703 711 8.177013 CGCGTACTACAAACCCTATTTTTATTT 58.823 33.333 0.00 0.00 0.00 1.40
704 712 7.201635 CCGCGTACTACAAACCCTATTTTTATT 60.202 37.037 4.92 0.00 0.00 1.40
705 713 6.258507 CCGCGTACTACAAACCCTATTTTTAT 59.741 38.462 4.92 0.00 0.00 1.40
706 714 5.580297 CCGCGTACTACAAACCCTATTTTTA 59.420 40.000 4.92 0.00 0.00 1.52
707 715 4.392754 CCGCGTACTACAAACCCTATTTTT 59.607 41.667 4.92 0.00 0.00 1.94
708 716 3.934579 CCGCGTACTACAAACCCTATTTT 59.065 43.478 4.92 0.00 0.00 1.82
709 717 3.524541 CCGCGTACTACAAACCCTATTT 58.475 45.455 4.92 0.00 0.00 1.40
710 718 2.159057 CCCGCGTACTACAAACCCTATT 60.159 50.000 4.92 0.00 0.00 1.73
711 719 1.410153 CCCGCGTACTACAAACCCTAT 59.590 52.381 4.92 0.00 0.00 2.57
712 720 0.817013 CCCGCGTACTACAAACCCTA 59.183 55.000 4.92 0.00 0.00 3.53
713 721 0.899717 TCCCGCGTACTACAAACCCT 60.900 55.000 4.92 0.00 0.00 4.34
714 722 0.459063 CTCCCGCGTACTACAAACCC 60.459 60.000 4.92 0.00 0.00 4.11
715 723 0.527565 TCTCCCGCGTACTACAAACC 59.472 55.000 4.92 0.00 0.00 3.27
716 724 1.622232 GTCTCCCGCGTACTACAAAC 58.378 55.000 4.92 0.00 0.00 2.93
717 725 0.527565 GGTCTCCCGCGTACTACAAA 59.472 55.000 4.92 0.00 0.00 2.83
718 726 2.183409 GGTCTCCCGCGTACTACAA 58.817 57.895 4.92 0.00 0.00 2.41
719 727 3.909662 GGTCTCCCGCGTACTACA 58.090 61.111 4.92 0.00 0.00 2.74
729 737 3.041940 CAACGTGTGCGGTCTCCC 61.042 66.667 0.00 0.00 43.45 4.30
730 738 2.279918 ACAACGTGTGCGGTCTCC 60.280 61.111 0.00 0.00 43.45 3.71
731 739 1.590525 TGACAACGTGTGCGGTCTC 60.591 57.895 0.00 0.00 43.45 3.36
732 740 1.881252 GTGACAACGTGTGCGGTCT 60.881 57.895 0.00 0.00 43.45 3.85
733 741 2.624264 GTGACAACGTGTGCGGTC 59.376 61.111 0.00 0.00 43.45 4.79
734 742 3.259020 CGTGACAACGTGTGCGGT 61.259 61.111 0.00 0.00 44.93 5.68
743 751 1.932564 GTTGTGCGTGCGTGACAAC 60.933 57.895 18.40 18.40 41.83 3.32
744 752 2.401592 GTTGTGCGTGCGTGACAA 59.598 55.556 7.05 7.05 0.00 3.18
745 753 3.919386 CGTTGTGCGTGCGTGACA 61.919 61.111 0.00 0.00 35.54 3.58
746 754 4.643385 CCGTTGTGCGTGCGTGAC 62.643 66.667 0.00 0.00 39.32 3.67
752 760 4.936248 CGTGTGCCGTTGTGCGTG 62.936 66.667 0.00 0.00 39.32 5.34
754 762 2.376538 TATCGTGTGCCGTTGTGCG 61.377 57.895 0.00 0.00 37.94 5.34
755 763 1.131826 GTATCGTGTGCCGTTGTGC 59.868 57.895 0.00 0.00 37.94 4.57
756 764 1.632046 GGGTATCGTGTGCCGTTGTG 61.632 60.000 0.00 0.00 37.94 3.33
757 765 1.375013 GGGTATCGTGTGCCGTTGT 60.375 57.895 0.00 0.00 37.94 3.32
758 766 2.104253 GGGGTATCGTGTGCCGTTG 61.104 63.158 0.00 0.00 37.94 4.10
759 767 2.266689 GGGGTATCGTGTGCCGTT 59.733 61.111 0.00 0.00 37.94 4.44
760 768 4.137872 CGGGGTATCGTGTGCCGT 62.138 66.667 0.00 0.00 37.94 5.68
761 769 4.884257 CCGGGGTATCGTGTGCCG 62.884 72.222 0.00 0.00 32.54 5.69
762 770 4.540735 CCCGGGGTATCGTGTGCC 62.541 72.222 14.71 0.00 0.00 5.01
763 771 3.441011 CTCCCGGGGTATCGTGTGC 62.441 68.421 23.50 0.00 0.00 4.57
764 772 1.755395 TCTCCCGGGGTATCGTGTG 60.755 63.158 23.50 0.01 0.00 3.82
765 773 1.755783 GTCTCCCGGGGTATCGTGT 60.756 63.158 23.50 0.00 0.00 4.49
766 774 2.496291 GGTCTCCCGGGGTATCGTG 61.496 68.421 23.50 2.58 0.00 4.35
767 775 2.123554 GGTCTCCCGGGGTATCGT 60.124 66.667 23.50 0.00 0.00 3.73
777 785 3.041940 CAACGTGTGCGGTCTCCC 61.042 66.667 0.00 0.00 43.45 4.30
778 786 2.279918 ACAACGTGTGCGGTCTCC 60.280 61.111 0.00 0.00 43.45 3.71
779 787 2.308039 GGACAACGTGTGCGGTCTC 61.308 63.158 0.00 0.00 43.45 3.36
780 788 2.279918 GGACAACGTGTGCGGTCT 60.280 61.111 0.00 0.00 43.45 3.85
781 789 3.343421 GGGACAACGTGTGCGGTC 61.343 66.667 0.00 0.00 39.79 4.79
782 790 3.802418 GAGGGACAACGTGTGCGGT 62.802 63.158 0.00 0.00 39.79 5.68
783 791 3.041940 GAGGGACAACGTGTGCGG 61.042 66.667 0.00 0.00 39.79 5.69
784 792 2.989055 AAGGAGGGACAACGTGTGCG 62.989 60.000 0.00 0.00 39.79 5.34
785 793 0.818040 AAAGGAGGGACAACGTGTGC 60.818 55.000 0.00 0.00 38.03 4.57
786 794 1.602377 GAAAAGGAGGGACAACGTGTG 59.398 52.381 0.00 0.00 0.00 3.82
787 795 1.489230 AGAAAAGGAGGGACAACGTGT 59.511 47.619 0.00 0.00 0.00 4.49
788 796 2.143925 GAGAAAAGGAGGGACAACGTG 58.856 52.381 0.00 0.00 0.00 4.49
789 797 1.071857 GGAGAAAAGGAGGGACAACGT 59.928 52.381 0.00 0.00 0.00 3.99
790 798 1.610886 GGGAGAAAAGGAGGGACAACG 60.611 57.143 0.00 0.00 0.00 4.10
791 799 1.423921 TGGGAGAAAAGGAGGGACAAC 59.576 52.381 0.00 0.00 0.00 3.32
792 800 1.423921 GTGGGAGAAAAGGAGGGACAA 59.576 52.381 0.00 0.00 0.00 3.18
793 801 1.064825 GTGGGAGAAAAGGAGGGACA 58.935 55.000 0.00 0.00 0.00 4.02
794 802 0.036294 CGTGGGAGAAAAGGAGGGAC 60.036 60.000 0.00 0.00 0.00 4.46
795 803 0.178915 TCGTGGGAGAAAAGGAGGGA 60.179 55.000 0.00 0.00 0.00 4.20
796 804 0.690762 TTCGTGGGAGAAAAGGAGGG 59.309 55.000 0.00 0.00 0.00 4.30
797 805 1.071699 TGTTCGTGGGAGAAAAGGAGG 59.928 52.381 0.00 0.00 0.00 4.30
798 806 2.143925 GTGTTCGTGGGAGAAAAGGAG 58.856 52.381 0.00 0.00 0.00 3.69
799 807 1.202722 GGTGTTCGTGGGAGAAAAGGA 60.203 52.381 0.00 0.00 0.00 3.36
800 808 1.235724 GGTGTTCGTGGGAGAAAAGG 58.764 55.000 0.00 0.00 0.00 3.11
801 809 0.865769 CGGTGTTCGTGGGAGAAAAG 59.134 55.000 0.00 0.00 0.00 2.27
802 810 1.161563 GCGGTGTTCGTGGGAGAAAA 61.162 55.000 0.00 0.00 41.72 2.29
803 811 1.595929 GCGGTGTTCGTGGGAGAAA 60.596 57.895 0.00 0.00 41.72 2.52
804 812 2.029964 GCGGTGTTCGTGGGAGAA 59.970 61.111 0.00 0.00 41.72 2.87
805 813 4.351938 CGCGGTGTTCGTGGGAGA 62.352 66.667 0.00 0.00 44.78 3.71
811 819 2.726681 GCATTAATTTCGCGGTGTTCGT 60.727 45.455 6.13 0.00 41.72 3.85
812 820 1.837747 GCATTAATTTCGCGGTGTTCG 59.162 47.619 6.13 0.00 42.76 3.95
813 821 2.182014 GGCATTAATTTCGCGGTGTTC 58.818 47.619 6.13 0.00 0.00 3.18
814 822 1.542030 TGGCATTAATTTCGCGGTGTT 59.458 42.857 6.13 0.77 0.00 3.32
815 823 1.169577 TGGCATTAATTTCGCGGTGT 58.830 45.000 6.13 0.00 0.00 4.16
819 827 3.100817 CAGAGTTGGCATTAATTTCGCG 58.899 45.455 0.00 0.00 0.00 5.87
912 920 3.806858 GCAATTTTCAAGGGTTTCAGGGG 60.807 47.826 0.00 0.00 0.00 4.79
1449 1485 0.389817 TCAAGGATCTTGCCGTCGTG 60.390 55.000 3.01 0.00 0.00 4.35
1507 1547 2.025155 ACTACCAGCTAGTGATGTCCG 58.975 52.381 0.00 0.00 34.08 4.79
1579 1660 5.204409 ACATCACATCAGCACAAAACAAT 57.796 34.783 0.00 0.00 0.00 2.71
1617 1701 4.098807 GGTTGAAAGACCTAGCAAAACCAA 59.901 41.667 0.00 0.00 36.63 3.67
1662 1764 7.817418 ACAAAATTACAACACTGTATGGAGT 57.183 32.000 0.00 0.00 37.86 3.85
1663 1765 8.349245 TCAACAAAATTACAACACTGTATGGAG 58.651 33.333 0.00 0.00 37.86 3.86
1665 1767 8.864069 TTCAACAAAATTACAACACTGTATGG 57.136 30.769 0.00 0.00 37.86 2.74
1669 1771 7.657761 TGGTTTTCAACAAAATTACAACACTGT 59.342 29.630 0.00 0.00 35.39 3.55
1671 1773 7.333174 CCTGGTTTTCAACAAAATTACAACACT 59.667 33.333 0.00 0.00 33.98 3.55
1675 1777 6.536941 GCTCCTGGTTTTCAACAAAATTACAA 59.463 34.615 0.00 0.00 33.98 2.41
1677 1779 6.280643 AGCTCCTGGTTTTCAACAAAATTAC 58.719 36.000 0.00 0.00 33.98 1.89
1678 1780 6.478512 AGCTCCTGGTTTTCAACAAAATTA 57.521 33.333 0.00 0.00 33.98 1.40
1679 1781 5.357742 AGCTCCTGGTTTTCAACAAAATT 57.642 34.783 0.00 0.00 33.98 1.82
1691 1793 4.102681 ACAACAGTACTAAAGCTCCTGGTT 59.897 41.667 0.00 0.00 35.14 3.67
1816 1925 9.077885 TGAGAAGGAAATAAATTGCAAGTTAGT 57.922 29.630 22.13 17.93 0.00 2.24
1833 1959 7.581213 TCACATTTTTAAGCTTGAGAAGGAA 57.419 32.000 9.86 0.00 0.00 3.36
1971 2105 4.252073 AGAGAGCAAGTTAGCAACATGAG 58.748 43.478 0.00 0.00 36.85 2.90
2204 2795 3.133003 TGCAAGGCTCTAGACATTCCTAC 59.867 47.826 0.00 0.00 0.00 3.18
2260 2851 7.312899 AGTAATAAATGAAAAGCACGAAAGGG 58.687 34.615 0.00 0.00 37.78 3.95
2285 2918 9.116067 TCTTCTTAGAAAGAAAATTCCGTGAAA 57.884 29.630 3.88 0.00 46.13 2.69
2357 2991 3.440173 ACATTGTGCAATACCACTACTGC 59.560 43.478 0.00 0.00 36.68 4.40
2948 3945 5.967674 CAGACGCTTCAAATCCAAATGATAC 59.032 40.000 0.00 0.00 31.83 2.24
3127 4130 0.599991 TAAGTGTGACCACAGCAGCG 60.600 55.000 2.68 0.00 44.39 5.18
3335 4342 4.706962 AGCATGATCTAAAGTTGAAACCCC 59.293 41.667 0.00 0.00 0.00 4.95
3395 4405 6.324512 TCCATACATCAAGCAAGCCATTATTT 59.675 34.615 0.00 0.00 0.00 1.40
3436 4446 6.015688 GCACATCAATCCTGGATTATTGTCAT 60.016 38.462 20.95 4.57 35.16 3.06
3456 4466 4.183101 CTGAAACCACAAAAACTGCACAT 58.817 39.130 0.00 0.00 0.00 3.21
3461 4471 4.244862 AGCAACTGAAACCACAAAAACTG 58.755 39.130 0.00 0.00 0.00 3.16
3464 4474 4.887748 TCAAGCAACTGAAACCACAAAAA 58.112 34.783 0.00 0.00 0.00 1.94
3472 4482 4.327680 AGGGAGTATCAAGCAACTGAAAC 58.672 43.478 0.00 0.00 36.25 2.78
3493 4503 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3494 4504 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3496 4506 4.829064 TGAAGACAAGAATTTTGGGACG 57.171 40.909 5.68 0.00 0.00 4.79
3498 4508 9.927668 GATAAATTGAAGACAAGAATTTTGGGA 57.072 29.630 0.00 0.00 39.46 4.37
3499 4509 9.933723 AGATAAATTGAAGACAAGAATTTTGGG 57.066 29.630 0.00 0.00 39.46 4.12
3529 4539 9.946165 CACATCTTACTGTTAGATACATTCGTA 57.054 33.333 8.80 0.00 35.85 3.43
3530 4540 8.683615 TCACATCTTACTGTTAGATACATTCGT 58.316 33.333 8.80 0.33 35.85 3.85
3531 4541 8.959058 GTCACATCTTACTGTTAGATACATTCG 58.041 37.037 8.80 0.00 35.85 3.34
3535 4545 9.901172 TCTAGTCACATCTTACTGTTAGATACA 57.099 33.333 8.80 0.00 31.32 2.29
3539 4549 9.901172 TGTATCTAGTCACATCTTACTGTTAGA 57.099 33.333 0.00 0.00 0.00 2.10
3542 4552 8.634444 GGATGTATCTAGTCACATCTTACTGTT 58.366 37.037 25.12 2.95 46.67 3.16
3543 4553 7.780271 TGGATGTATCTAGTCACATCTTACTGT 59.220 37.037 25.12 0.00 46.67 3.55
3544 4554 8.171164 TGGATGTATCTAGTCACATCTTACTG 57.829 38.462 25.12 0.00 46.67 2.74
3545 4555 8.948401 ATGGATGTATCTAGTCACATCTTACT 57.052 34.615 25.12 13.24 46.67 2.24
3548 4558 9.319060 ACATATGGATGTATCTAGTCACATCTT 57.681 33.333 25.12 19.11 46.67 2.40
3549 4559 8.891985 ACATATGGATGTATCTAGTCACATCT 57.108 34.615 25.12 16.04 46.67 2.90
3551 4561 9.981460 TCTACATATGGATGTATCTAGTCACAT 57.019 33.333 7.80 10.46 45.42 3.21
3553 4563 9.232473 TGTCTACATATGGATGTATCTAGTCAC 57.768 37.037 7.80 0.00 45.42 3.67
3554 4564 9.807921 TTGTCTACATATGGATGTATCTAGTCA 57.192 33.333 7.80 0.00 45.42 3.41
3564 4574 9.987272 TGTCTTAGATTTGTCTACATATGGATG 57.013 33.333 7.80 0.00 39.16 3.51
3575 4585 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3576 4586 7.814587 CCCCAAAATTCTTGTCTTAGATTTGTC 59.185 37.037 0.00 0.00 28.79 3.18
3577 4587 7.670364 CCCCAAAATTCTTGTCTTAGATTTGT 58.330 34.615 0.00 0.00 28.79 2.83
3578 4588 6.591448 GCCCCAAAATTCTTGTCTTAGATTTG 59.409 38.462 0.00 0.00 29.84 2.32
3579 4589 6.572314 CGCCCCAAAATTCTTGTCTTAGATTT 60.572 38.462 0.00 0.00 0.00 2.17
3580 4590 5.105756 CGCCCCAAAATTCTTGTCTTAGATT 60.106 40.000 0.00 0.00 0.00 2.40
3581 4591 4.399303 CGCCCCAAAATTCTTGTCTTAGAT 59.601 41.667 0.00 0.00 0.00 1.98
3582 4592 3.756434 CGCCCCAAAATTCTTGTCTTAGA 59.244 43.478 0.00 0.00 0.00 2.10
3583 4593 3.756434 TCGCCCCAAAATTCTTGTCTTAG 59.244 43.478 0.00 0.00 0.00 2.18
3584 4594 3.757270 TCGCCCCAAAATTCTTGTCTTA 58.243 40.909 0.00 0.00 0.00 2.10
3585 4595 2.593026 TCGCCCCAAAATTCTTGTCTT 58.407 42.857 0.00 0.00 0.00 3.01
3586 4596 2.286365 TCGCCCCAAAATTCTTGTCT 57.714 45.000 0.00 0.00 0.00 3.41
3587 4597 2.352715 CCTTCGCCCCAAAATTCTTGTC 60.353 50.000 0.00 0.00 0.00 3.18
3588 4598 1.618343 CCTTCGCCCCAAAATTCTTGT 59.382 47.619 0.00 0.00 0.00 3.16
3589 4599 1.066929 CCCTTCGCCCCAAAATTCTTG 60.067 52.381 0.00 0.00 0.00 3.02
3590 4600 1.203125 TCCCTTCGCCCCAAAATTCTT 60.203 47.619 0.00 0.00 0.00 2.52
3591 4601 0.407918 TCCCTTCGCCCCAAAATTCT 59.592 50.000 0.00 0.00 0.00 2.40
3592 4602 0.817654 CTCCCTTCGCCCCAAAATTC 59.182 55.000 0.00 0.00 0.00 2.17
3593 4603 0.114364 ACTCCCTTCGCCCCAAAATT 59.886 50.000 0.00 0.00 0.00 1.82
3594 4604 0.996583 TACTCCCTTCGCCCCAAAAT 59.003 50.000 0.00 0.00 0.00 1.82
3595 4605 0.037160 GTACTCCCTTCGCCCCAAAA 59.963 55.000 0.00 0.00 0.00 2.44
3596 4606 1.128809 TGTACTCCCTTCGCCCCAAA 61.129 55.000 0.00 0.00 0.00 3.28
3597 4607 0.912487 ATGTACTCCCTTCGCCCCAA 60.912 55.000 0.00 0.00 0.00 4.12
3598 4608 1.306654 ATGTACTCCCTTCGCCCCA 60.307 57.895 0.00 0.00 0.00 4.96
3599 4609 1.335132 TGATGTACTCCCTTCGCCCC 61.335 60.000 0.00 0.00 0.00 5.80
3600 4610 0.105039 CTGATGTACTCCCTTCGCCC 59.895 60.000 0.00 0.00 0.00 6.13
3601 4611 1.112113 TCTGATGTACTCCCTTCGCC 58.888 55.000 0.00 0.00 0.00 5.54
3602 4612 2.362397 TCATCTGATGTACTCCCTTCGC 59.638 50.000 16.66 0.00 0.00 4.70
3603 4613 3.243569 GGTCATCTGATGTACTCCCTTCG 60.244 52.174 16.66 0.00 0.00 3.79
3604 4614 3.706594 TGGTCATCTGATGTACTCCCTTC 59.293 47.826 16.66 2.62 0.00 3.46
3605 4615 3.724478 TGGTCATCTGATGTACTCCCTT 58.276 45.455 16.66 0.00 0.00 3.95
3606 4616 3.404869 TGGTCATCTGATGTACTCCCT 57.595 47.619 16.66 0.00 0.00 4.20
3607 4617 3.805108 GCATGGTCATCTGATGTACTCCC 60.805 52.174 16.66 10.52 0.00 4.30
3608 4618 3.070734 AGCATGGTCATCTGATGTACTCC 59.929 47.826 16.66 14.32 0.00 3.85
3609 4619 4.056740 CAGCATGGTCATCTGATGTACTC 58.943 47.826 16.66 6.87 0.00 2.59
3610 4620 4.069300 CAGCATGGTCATCTGATGTACT 57.931 45.455 16.66 4.75 0.00 2.73
3655 4665 2.749621 GCAAAGACCCTGGTTGATACAG 59.250 50.000 0.00 0.00 35.74 2.74
3656 4666 2.107378 TGCAAAGACCCTGGTTGATACA 59.893 45.455 0.00 0.00 0.00 2.29
3657 4667 2.790433 TGCAAAGACCCTGGTTGATAC 58.210 47.619 0.00 0.00 0.00 2.24
3659 4669 2.610438 ATGCAAAGACCCTGGTTGAT 57.390 45.000 0.00 0.00 0.00 2.57
3660 4670 3.517296 TTATGCAAAGACCCTGGTTGA 57.483 42.857 0.00 0.00 0.00 3.18
3661 4671 4.806640 AATTATGCAAAGACCCTGGTTG 57.193 40.909 0.00 0.00 0.00 3.77
3662 4672 5.151297 CAAATTATGCAAAGACCCTGGTT 57.849 39.130 0.00 0.00 0.00 3.67
3663 4673 4.806640 CAAATTATGCAAAGACCCTGGT 57.193 40.909 0.00 0.00 0.00 4.00
3730 4740 5.933187 AAAAACACAAAGTCAACCAAACC 57.067 34.783 0.00 0.00 0.00 3.27
3749 4759 3.445987 ACCAAACCCAAGTCCTCAAAAA 58.554 40.909 0.00 0.00 0.00 1.94
3750 4760 3.108847 ACCAAACCCAAGTCCTCAAAA 57.891 42.857 0.00 0.00 0.00 2.44
3751 4761 2.763448 CAACCAAACCCAAGTCCTCAAA 59.237 45.455 0.00 0.00 0.00 2.69
3752 4762 2.024846 TCAACCAAACCCAAGTCCTCAA 60.025 45.455 0.00 0.00 0.00 3.02
3753 4763 1.566703 TCAACCAAACCCAAGTCCTCA 59.433 47.619 0.00 0.00 0.00 3.86
3754 4764 1.954382 GTCAACCAAACCCAAGTCCTC 59.046 52.381 0.00 0.00 0.00 3.71
3755 4765 1.749286 CGTCAACCAAACCCAAGTCCT 60.749 52.381 0.00 0.00 0.00 3.85
3756 4766 0.666374 CGTCAACCAAACCCAAGTCC 59.334 55.000 0.00 0.00 0.00 3.85
3757 4767 1.602377 CTCGTCAACCAAACCCAAGTC 59.398 52.381 0.00 0.00 0.00 3.01
3758 4768 1.675552 CTCGTCAACCAAACCCAAGT 58.324 50.000 0.00 0.00 0.00 3.16
3759 4769 0.951558 CCTCGTCAACCAAACCCAAG 59.048 55.000 0.00 0.00 0.00 3.61
3760 4770 1.104577 GCCTCGTCAACCAAACCCAA 61.105 55.000 0.00 0.00 0.00 4.12
3842 4853 3.953612 TCTCTCTGCATCTCTTTCTCTCC 59.046 47.826 0.00 0.00 0.00 3.71
3844 4855 5.716228 TCTTTCTCTCTGCATCTCTTTCTCT 59.284 40.000 0.00 0.00 0.00 3.10
3849 4860 5.189342 TGGAATCTTTCTCTCTGCATCTCTT 59.811 40.000 0.00 0.00 0.00 2.85
3853 4864 4.511527 TGTGGAATCTTTCTCTCTGCATC 58.488 43.478 0.00 0.00 0.00 3.91
3854 4865 4.564782 TGTGGAATCTTTCTCTCTGCAT 57.435 40.909 0.00 0.00 0.00 3.96
3855 4866 4.356405 TTGTGGAATCTTTCTCTCTGCA 57.644 40.909 0.00 0.00 0.00 4.41
3856 4867 4.096081 CCATTGTGGAATCTTTCTCTCTGC 59.904 45.833 0.00 0.00 40.96 4.26
3884 4926 8.553459 TGAGAAGTTCTGGAGTGAATAAATTC 57.447 34.615 10.90 0.00 37.31 2.17
3899 4941 6.672266 TCATCTTACCTGTTGAGAAGTTCT 57.328 37.500 4.68 4.68 0.00 3.01
3911 4953 0.824109 TCGTGGGCTCATCTTACCTG 59.176 55.000 0.00 0.00 0.00 4.00
3940 4982 7.920160 TGAGTTGTGCATGTTAATATCAGAA 57.080 32.000 0.00 0.00 0.00 3.02
3952 4994 4.052608 TCAGCAATTTTGAGTTGTGCATG 58.947 39.130 0.00 0.00 37.68 4.06
3973 5015 8.930760 GGTGTTGAGATATGCACTCTATTATTC 58.069 37.037 4.63 0.00 35.66 1.75
4003 5066 3.451540 TGTATCCATTTACGTGCAGGGTA 59.548 43.478 11.67 2.28 0.00 3.69
4047 5110 4.818534 TGAGTTTCTGTGTTTCTGCATC 57.181 40.909 0.00 0.00 0.00 3.91
4061 5124 5.107298 CGACCTTTCAGTTCAGATGAGTTTC 60.107 44.000 0.00 0.00 0.00 2.78
4091 5154 0.033796 ATCTTGTGGGGGCATGAGTG 60.034 55.000 0.00 0.00 0.00 3.51
4092 5155 0.033796 CATCTTGTGGGGGCATGAGT 60.034 55.000 0.00 0.00 0.00 3.41
4093 5156 1.389609 GCATCTTGTGGGGGCATGAG 61.390 60.000 0.00 0.00 0.00 2.90
4094 5157 1.380246 GCATCTTGTGGGGGCATGA 60.380 57.895 0.00 0.00 0.00 3.07
4095 5158 1.380785 AGCATCTTGTGGGGGCATG 60.381 57.895 0.00 0.00 0.00 4.06
4096 5159 1.380785 CAGCATCTTGTGGGGGCAT 60.381 57.895 0.00 0.00 0.00 4.40
4097 5160 2.036098 CAGCATCTTGTGGGGGCA 59.964 61.111 0.00 0.00 0.00 5.36
4098 5161 2.757099 CCAGCATCTTGTGGGGGC 60.757 66.667 0.00 0.00 0.00 5.80
4099 5162 0.251742 TTTCCAGCATCTTGTGGGGG 60.252 55.000 0.00 0.00 34.27 5.40
4100 5163 1.479323 CATTTCCAGCATCTTGTGGGG 59.521 52.381 0.00 0.00 34.27 4.96
4101 5164 1.479323 CCATTTCCAGCATCTTGTGGG 59.521 52.381 0.00 0.00 34.27 4.61
4102 5165 1.134907 GCCATTTCCAGCATCTTGTGG 60.135 52.381 0.00 0.00 34.87 4.17
4103 5166 1.546923 TGCCATTTCCAGCATCTTGTG 59.453 47.619 0.00 0.00 33.08 3.33
4104 5167 1.822990 CTGCCATTTCCAGCATCTTGT 59.177 47.619 0.00 0.00 38.56 3.16
4105 5168 1.136305 CCTGCCATTTCCAGCATCTTG 59.864 52.381 0.00 0.00 38.56 3.02
4106 5169 1.481871 CCTGCCATTTCCAGCATCTT 58.518 50.000 0.00 0.00 38.56 2.40
4107 5170 1.041447 GCCTGCCATTTCCAGCATCT 61.041 55.000 0.00 0.00 38.56 2.90
4108 5171 1.324740 TGCCTGCCATTTCCAGCATC 61.325 55.000 0.00 0.00 38.56 3.91
4109 5172 1.305465 TGCCTGCCATTTCCAGCAT 60.305 52.632 0.00 0.00 38.56 3.79
4110 5173 1.980232 CTGCCTGCCATTTCCAGCA 60.980 57.895 0.00 0.00 37.46 4.41
4111 5174 2.890371 CTGCCTGCCATTTCCAGC 59.110 61.111 0.00 0.00 0.00 4.85
4112 5175 1.537814 TTGCTGCCTGCCATTTCCAG 61.538 55.000 0.00 0.00 42.00 3.86
4113 5176 1.120184 TTTGCTGCCTGCCATTTCCA 61.120 50.000 0.00 0.00 42.00 3.53
4114 5177 0.671472 GTTTGCTGCCTGCCATTTCC 60.671 55.000 0.00 0.00 42.00 3.13
4115 5178 1.010419 CGTTTGCTGCCTGCCATTTC 61.010 55.000 0.00 0.00 42.00 2.17
4116 5179 1.005867 CGTTTGCTGCCTGCCATTT 60.006 52.632 0.00 0.00 42.00 2.32
4117 5180 1.462731 TTCGTTTGCTGCCTGCCATT 61.463 50.000 0.00 0.00 42.00 3.16
4118 5181 1.462731 TTTCGTTTGCTGCCTGCCAT 61.463 50.000 0.00 0.00 42.00 4.40
4119 5182 2.124060 TTTCGTTTGCTGCCTGCCA 61.124 52.632 0.00 0.00 42.00 4.92
4120 5183 1.661509 GTTTCGTTTGCTGCCTGCC 60.662 57.895 0.00 0.00 42.00 4.85
4121 5184 0.936297 CAGTTTCGTTTGCTGCCTGC 60.936 55.000 0.00 0.00 43.25 4.85
4122 5185 0.662619 TCAGTTTCGTTTGCTGCCTG 59.337 50.000 0.00 0.00 0.00 4.85
4123 5186 1.537202 GATCAGTTTCGTTTGCTGCCT 59.463 47.619 0.00 0.00 0.00 4.75
4124 5187 1.266718 TGATCAGTTTCGTTTGCTGCC 59.733 47.619 0.00 0.00 0.00 4.85
4125 5188 2.686558 TGATCAGTTTCGTTTGCTGC 57.313 45.000 0.00 0.00 0.00 5.25
4126 5189 4.438797 CAGTTTGATCAGTTTCGTTTGCTG 59.561 41.667 0.00 0.00 0.00 4.41
4127 5190 4.096382 ACAGTTTGATCAGTTTCGTTTGCT 59.904 37.500 0.00 0.00 0.00 3.91
4128 5191 4.351192 ACAGTTTGATCAGTTTCGTTTGC 58.649 39.130 0.00 0.00 0.00 3.68
4129 5192 6.715464 ACTACAGTTTGATCAGTTTCGTTTG 58.285 36.000 0.00 0.00 0.00 2.93
4130 5193 6.761714 AGACTACAGTTTGATCAGTTTCGTTT 59.238 34.615 0.00 0.00 0.00 3.60
4131 5194 6.281405 AGACTACAGTTTGATCAGTTTCGTT 58.719 36.000 0.00 0.00 0.00 3.85
4154 5217 6.992063 ATGTGTTGTAGGCAAATAAGAGAG 57.008 37.500 0.00 0.00 36.22 3.20
4208 5271 2.963782 GGTAGATCATCTGTAACCCCGT 59.036 50.000 0.00 0.00 0.00 5.28
4209 5272 2.963101 TGGTAGATCATCTGTAACCCCG 59.037 50.000 0.00 0.00 0.00 5.73
4210 5273 3.967987 ACTGGTAGATCATCTGTAACCCC 59.032 47.826 0.00 0.00 0.00 4.95
4245 5308 3.624861 CCAATGCTGTGTTGACTATCTCC 59.375 47.826 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.