Multiple sequence alignment - TraesCS3D01G033800

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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 TraesCS3D01G033800 chr3D 100.000 2629 0 0 1 2629 12423374 12420746 0.000000e+00 4855.0
1 TraesCS3D01G033800 chr3D 81.510 768 93 26 887 1634 12462637 12463375 1.050000e-163 586.0
2 TraesCS3D01G033800 chr3D 94.306 281 13 3 35 313 12429235 12428956 6.720000e-116 427.0
3 TraesCS3D01G033800 chr3D 78.783 575 79 28 1093 1639 8851620 8851061 1.940000e-91 346.0
4 TraesCS3D01G033800 chr3D 95.122 123 6 0 2377 2499 533688327 533688449 7.420000e-46 195.0
5 TraesCS3D01G033800 chr3D 87.500 144 17 1 991 1134 12819512 12819654 5.820000e-37 165.0
6 TraesCS3D01G033800 chr3D 80.000 245 27 14 903 1132 12455074 12454837 7.530000e-36 161.0
7 TraesCS3D01G033800 chr3B 91.537 709 47 8 487 1190 18001612 18000912 0.000000e+00 965.0
8 TraesCS3D01G033800 chr3B 93.321 539 29 2 1216 1754 18000850 18000319 0.000000e+00 789.0
9 TraesCS3D01G033800 chr3B 80.380 841 101 40 825 1634 18155606 18156413 4.880000e-162 580.0
10 TraesCS3D01G033800 chr3B 80.881 795 98 34 895 1645 18568536 18567752 6.310000e-161 577.0
11 TraesCS3D01G033800 chr3B 90.956 387 32 2 1997 2382 17998537 17998153 3.880000e-143 518.0
12 TraesCS3D01G033800 chr3B 89.200 250 19 7 1752 1997 17998812 17998567 3.290000e-79 305.0
13 TraesCS3D01G033800 chr3B 93.333 195 12 1 35 229 18001866 18001673 1.190000e-73 287.0
14 TraesCS3D01G033800 chr3B 86.923 130 7 9 2500 2629 17998171 17998052 1.270000e-28 137.0
15 TraesCS3D01G033800 chr3B 83.654 104 13 4 1889 1989 583092398 583092296 7.750000e-16 95.3
16 TraesCS3D01G033800 chr3B 77.241 145 22 7 491 634 752665476 752665342 1.010000e-09 75.0
17 TraesCS3D01G033800 chr3A 90.174 631 34 13 592 1208 24758517 24759133 0.000000e+00 797.0
18 TraesCS3D01G033800 chr3A 94.988 419 18 1 1216 1634 24759170 24759585 0.000000e+00 654.0
19 TraesCS3D01G033800 chr3A 81.425 786 89 30 876 1639 24612666 24611916 8.100000e-165 590.0
20 TraesCS3D01G033800 chr3A 80.815 761 95 24 895 1634 24679133 24678403 1.380000e-152 549.0
21 TraesCS3D01G033800 chr3A 88.787 437 31 11 35 454 24757951 24758386 1.080000e-143 520.0
22 TraesCS3D01G033800 chr3A 81.503 173 26 1 1461 1633 24777087 24776921 1.270000e-28 137.0
23 TraesCS3D01G033800 chr3A 82.692 104 13 4 1889 1991 468728057 468727958 1.300000e-13 87.9
24 TraesCS3D01G033800 chr2B 97.581 124 3 0 2377 2500 63137611 63137734 2.050000e-51 213.0
25 TraesCS3D01G033800 chr2B 92.063 126 10 0 2377 2502 440569928 440569803 7.480000e-41 178.0
26 TraesCS3D01G033800 chr1B 96.774 124 4 0 2377 2500 41729024 41728901 9.540000e-50 207.0
27 TraesCS3D01G033800 chr7D 95.122 123 5 1 2377 2499 506637615 506637736 2.670000e-45 193.0
28 TraesCS3D01G033800 chr4A 94.262 122 7 0 2377 2498 634402401 634402522 1.240000e-43 187.0
29 TraesCS3D01G033800 chr4A 93.443 122 8 0 2377 2498 634434681 634434802 5.780000e-42 182.0
30 TraesCS3D01G033800 chr5B 91.935 124 10 0 2377 2500 331278479 331278602 9.670000e-40 174.0
31 TraesCS3D01G033800 chr5B 87.059 85 11 0 1891 1975 10408521 10408437 2.150000e-16 97.1
32 TraesCS3D01G033800 chrUn 91.057 123 11 0 2377 2499 88862892 88863014 1.620000e-37 167.0
33 TraesCS3D01G033800 chrUn 83.553 152 16 8 903 1050 430383112 430383258 1.640000e-27 134.0
34 TraesCS3D01G033800 chr1A 78.879 232 30 14 1997 2216 481657557 481657333 3.530000e-29 139.0
35 TraesCS3D01G033800 chr1A 81.818 154 16 6 487 640 56626421 56626562 4.600000e-23 119.0
36 TraesCS3D01G033800 chr1D 81.169 154 18 6 487 640 57505260 57505402 2.140000e-21 113.0
37 TraesCS3D01G033800 chr7A 86.598 97 11 2 1891 1987 492819667 492819761 3.580000e-19 106.0
38 TraesCS3D01G033800 chr2D 87.209 86 9 2 1891 1975 147472661 147472745 2.150000e-16 97.1
39 TraesCS3D01G033800 chr7B 84.536 97 13 2 1891 1987 458616015 458616109 7.750000e-16 95.3
40 TraesCS3D01G033800 chr6D 87.209 86 8 3 1892 1976 60550756 60550839 7.750000e-16 95.3
41 TraesCS3D01G033800 chr4D 84.694 98 12 3 1891 1987 12359630 12359725 7.750000e-16 95.3
42 TraesCS3D01G033800 chr4D 92.857 42 2 1 586 626 365865430 365865471 2.830000e-05 60.2
43 TraesCS3D01G033800 chr6A 79.085 153 16 9 488 639 181560831 181560694 1.000000e-14 91.6
44 TraesCS3D01G033800 chr5A 93.750 48 2 1 593 640 620406373 620406419 1.310000e-08 71.3
45 TraesCS3D01G033800 chr5D 96.875 32 1 0 590 621 496552794 496552825 1.000000e-03 54.7


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 TraesCS3D01G033800 chr3D 12420746 12423374 2628 True 4855.000000 4855 100.000000 1 2629 1 chr3D.!!$R2 2628
1 TraesCS3D01G033800 chr3D 12462637 12463375 738 False 586.000000 586 81.510000 887 1634 1 chr3D.!!$F1 747
2 TraesCS3D01G033800 chr3D 8851061 8851620 559 True 346.000000 346 78.783000 1093 1639 1 chr3D.!!$R1 546
3 TraesCS3D01G033800 chr3B 18155606 18156413 807 False 580.000000 580 80.380000 825 1634 1 chr3B.!!$F1 809
4 TraesCS3D01G033800 chr3B 18567752 18568536 784 True 577.000000 577 80.881000 895 1645 1 chr3B.!!$R1 750
5 TraesCS3D01G033800 chr3B 17998052 18001866 3814 True 500.166667 965 90.878333 35 2629 6 chr3B.!!$R4 2594
6 TraesCS3D01G033800 chr3A 24757951 24759585 1634 False 657.000000 797 91.316333 35 1634 3 chr3A.!!$F1 1599
7 TraesCS3D01G033800 chr3A 24611916 24612666 750 True 590.000000 590 81.425000 876 1639 1 chr3A.!!$R1 763
8 TraesCS3D01G033800 chr3A 24678403 24679133 730 True 549.000000 549 80.815000 895 1634 1 chr3A.!!$R2 739

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
447 465 0.178944 TCCCAACTTGACCCTCGAGA 60.179 55.0 15.71 0.0 32.2 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 4096 0.036388 GAGCCAATTCTCGGTCACCA 60.036 55.0 0.0 0.0 0.0 4.17 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
24 25 6.765915 ATAAAGCTCTCACAATTTTCCCTC 57.234 37.500 0.00 0.00 0.00 4.30
25 26 3.795688 AGCTCTCACAATTTTCCCTCA 57.204 42.857 0.00 0.00 0.00 3.86
26 27 4.104383 AGCTCTCACAATTTTCCCTCAA 57.896 40.909 0.00 0.00 0.00 3.02
27 28 4.473444 AGCTCTCACAATTTTCCCTCAAA 58.527 39.130 0.00 0.00 0.00 2.69
28 29 4.895297 AGCTCTCACAATTTTCCCTCAAAA 59.105 37.500 0.00 0.00 38.38 2.44
29 30 5.363580 AGCTCTCACAATTTTCCCTCAAAAA 59.636 36.000 0.00 0.00 37.52 1.94
98 99 3.430218 GTGTGAGAAAGTGAACCATCTCG 59.570 47.826 7.97 0.00 40.91 4.04
106 107 0.904649 TGAACCATCTCGCTGGACAT 59.095 50.000 5.63 0.00 39.73 3.06
124 125 4.866486 GGACATTCATCCAATGCTTTGTTC 59.134 41.667 11.03 0.00 45.37 3.18
167 168 5.118286 AGCTTTTCCAAAACCAGATTTGTG 58.882 37.500 0.59 0.00 38.37 3.33
189 190 4.224370 TGTTTTTAACTAGAGGCCCTCGAT 59.776 41.667 4.80 0.00 35.36 3.59
201 202 1.165270 CCCTCGATTGTCCAAACACC 58.835 55.000 0.00 0.00 34.35 4.16
212 213 2.542178 GTCCAAACACCGCAAAATTTCC 59.458 45.455 0.00 0.00 0.00 3.13
224 225 5.478407 CGCAAAATTTCCAATAGGTCCTTT 58.522 37.500 0.00 0.00 35.89 3.11
229 230 7.610580 AAATTTCCAATAGGTCCTTTCACAA 57.389 32.000 0.00 0.00 35.89 3.33
341 359 3.684788 GCCAATTACCGCTATATGTGAGG 59.315 47.826 0.00 0.00 0.00 3.86
355 373 9.743057 GCTATATGTGAGGTAATCTATGACATC 57.257 37.037 0.00 0.00 0.00 3.06
375 393 9.593565 TGACATCCAAGTGTATAGATAGATCTT 57.406 33.333 0.00 0.00 33.81 2.40
416 434 2.859992 CTGGAGTAAACAGGCCTGC 58.140 57.895 33.06 16.32 32.38 4.85
447 465 0.178944 TCCCAACTTGACCCTCGAGA 60.179 55.000 15.71 0.00 32.20 4.04
448 466 0.247736 CCCAACTTGACCCTCGAGAG 59.752 60.000 15.71 2.13 32.20 3.20
449 467 1.257743 CCAACTTGACCCTCGAGAGA 58.742 55.000 15.71 0.00 32.20 3.10
450 468 1.067495 CCAACTTGACCCTCGAGAGAC 60.067 57.143 15.71 0.75 32.20 3.36
451 469 0.882474 AACTTGACCCTCGAGAGACG 59.118 55.000 15.71 0.40 44.09 4.18
453 471 0.448593 CTTGACCCTCGAGAGACGAC 59.551 60.000 15.71 0.00 46.45 4.34
454 472 1.296755 TTGACCCTCGAGAGACGACG 61.297 60.000 15.71 0.00 46.45 5.12
455 473 1.447489 GACCCTCGAGAGACGACGA 60.447 63.158 15.71 0.00 46.45 4.20
460 478 3.511182 TCGAGAGACGACGAGAAGT 57.489 52.632 0.00 0.00 46.45 3.01
461 479 1.069255 TCGAGAGACGACGAGAAGTG 58.931 55.000 0.00 0.00 46.45 3.16
464 482 1.512310 GAGACGACGAGAAGTGCCG 60.512 63.158 0.00 0.00 0.00 5.69
471 489 1.207593 CGAGAAGTGCCGGCTTTTG 59.792 57.895 29.70 11.81 0.00 2.44
476 494 0.248866 AAGTGCCGGCTTTTGAAACG 60.249 50.000 29.70 0.00 0.00 3.60
540 589 7.555195 TGTCTCATCTAACTTCTATACCGTTGA 59.445 37.037 0.00 0.00 0.00 3.18
622 671 8.275758 TCAAGTAGTGTAGGAGTTAGATGAGAT 58.724 37.037 0.00 0.00 0.00 2.75
623 672 8.908903 CAAGTAGTGTAGGAGTTAGATGAGATT 58.091 37.037 0.00 0.00 0.00 2.40
657 706 3.390967 TCATCCAGCAAATCCGGATCTAA 59.609 43.478 19.43 3.09 37.44 2.10
664 713 5.760253 CAGCAAATCCGGATCTAACATTACT 59.240 40.000 19.43 4.26 0.00 2.24
756 808 2.412870 CTGTTCCATTGTCAGCGTACA 58.587 47.619 0.00 0.00 0.00 2.90
757 809 3.002791 CTGTTCCATTGTCAGCGTACAT 58.997 45.455 0.00 0.00 0.00 2.29
758 810 4.180817 CTGTTCCATTGTCAGCGTACATA 58.819 43.478 0.00 0.00 0.00 2.29
759 811 4.765273 TGTTCCATTGTCAGCGTACATAT 58.235 39.130 0.00 0.00 0.00 1.78
789 841 1.912001 ATCAATGGAAAACGCGCATG 58.088 45.000 5.73 0.00 0.00 4.06
826 878 8.119226 GTCAACACTTTGTCATCAATCTATAGC 58.881 37.037 0.00 0.00 34.02 2.97
840 893 5.746990 ATCTATAGCCCTTATCCACACAC 57.253 43.478 0.00 0.00 0.00 3.82
942 1001 1.533338 CGGTGTCACGAGGCTACATAC 60.533 57.143 0.00 0.00 35.47 2.39
1139 1236 0.536460 CAAGGCCAAGGTACGGTTGT 60.536 55.000 5.01 0.00 0.00 3.32
1163 1280 2.028165 GCGCGTGAACTCATTTCTCTAC 59.972 50.000 8.43 0.00 34.97 2.59
1199 1329 2.143122 TGCGTCCATGAAGAAACTGAC 58.857 47.619 0.00 0.00 0.00 3.51
1517 1683 2.811317 GCTCCGACCTGCAAGACG 60.811 66.667 0.00 0.00 34.07 4.18
1639 1808 3.176578 TAACTAGCACGCACGCGC 61.177 61.111 12.02 0.00 44.19 6.86
1640 1809 3.900393 TAACTAGCACGCACGCGCA 62.900 57.895 12.02 0.00 44.19 6.09
1666 1835 3.441244 GTGTGCACCATGATCGAGA 57.559 52.632 15.69 0.00 0.00 4.04
1685 1854 0.747283 ACGCTACGTCCCTACTCCTG 60.747 60.000 0.00 0.00 33.69 3.86
1688 1857 0.395311 CTACGTCCCTACTCCTGCCA 60.395 60.000 0.00 0.00 0.00 4.92
1717 1886 1.008079 GCAGCCTGCAGTTTGTGAC 60.008 57.895 12.82 0.00 44.26 3.67
1765 3443 7.279536 ACAAGCAATCATGTATAAGACAGAGTG 59.720 37.037 0.00 0.00 42.79 3.51
1806 3484 2.507407 ATAACTGAATGGTGCGGGTT 57.493 45.000 0.00 0.00 0.00 4.11
1893 3571 8.956426 TGACCAAAGTCCTATTTCAAATATCAC 58.044 33.333 0.00 0.00 42.81 3.06
1930 3612 6.622833 AAGTTGCCTGAATTTTGAATTTGG 57.377 33.333 0.00 0.00 0.00 3.28
1934 3616 3.679502 GCCTGAATTTTGAATTTGGGTCG 59.320 43.478 7.80 0.00 0.00 4.79
1937 3619 5.405269 CCTGAATTTTGAATTTGGGTCGTTC 59.595 40.000 0.00 0.00 0.00 3.95
1948 3630 2.235016 TGGGTCGTTCAATTTCTTGGG 58.765 47.619 0.00 0.00 32.95 4.12
1949 3631 1.067846 GGGTCGTTCAATTTCTTGGGC 60.068 52.381 0.00 0.00 32.95 5.36
1964 3646 1.686355 TGGGCGTTGATTGTTGTTCT 58.314 45.000 0.00 0.00 0.00 3.01
1979 3661 5.053811 TGTTGTTCTAAGATTCGTGCTTCA 58.946 37.500 0.00 0.00 0.00 3.02
1981 3663 6.204688 TGTTGTTCTAAGATTCGTGCTTCATT 59.795 34.615 0.00 0.00 0.00 2.57
1982 3664 7.386573 TGTTGTTCTAAGATTCGTGCTTCATTA 59.613 33.333 0.00 0.00 0.00 1.90
2016 3728 5.013079 TGACTCAACTGACCTCATATTTGGT 59.987 40.000 0.00 0.00 39.60 3.67
2035 3747 2.673368 GGTTCAGTCGATTTGCTACTGG 59.327 50.000 0.00 0.00 39.90 4.00
2036 3748 2.672961 TCAGTCGATTTGCTACTGGG 57.327 50.000 0.00 0.00 39.90 4.45
2038 3750 0.107654 AGTCGATTTGCTACTGGGCC 60.108 55.000 0.00 0.00 0.00 5.80
2071 3783 3.157252 TGCGATCCAGCCCTCCTC 61.157 66.667 0.00 0.00 36.02 3.71
2113 3825 7.658179 TTTCTGTTTTTATGTGTGTTTTGCA 57.342 28.000 0.00 0.00 0.00 4.08
2124 3836 5.455392 TGTGTGTTTTGCATTTGTTTTTGG 58.545 33.333 0.00 0.00 0.00 3.28
2132 3844 8.423973 GTTTTGCATTTGTTTTTGGTTTTTCTC 58.576 29.630 0.00 0.00 0.00 2.87
2134 3846 7.071014 TGCATTTGTTTTTGGTTTTTCTCTC 57.929 32.000 0.00 0.00 0.00 3.20
2141 3853 9.634163 TTGTTTTTGGTTTTTCTCTCTTACTTC 57.366 29.630 0.00 0.00 0.00 3.01
2206 3919 8.862325 TGAGTGGAAATGTACTCACATAAATT 57.138 30.769 3.18 0.00 45.97 1.82
2212 3925 9.884465 GGAAATGTACTCACATAAATTCTATGC 57.116 33.333 0.00 0.00 44.83 3.14
2220 3933 8.834465 ACTCACATAAATTCTATGCAATGTCTC 58.166 33.333 0.00 0.00 0.00 3.36
2265 3978 5.871465 TTATCGCATGCTACAAAAAGTGA 57.129 34.783 17.13 1.34 0.00 3.41
2296 4009 2.666022 GCGAAGTTGTGTGCAAGTTTTT 59.334 40.909 0.00 0.00 45.32 1.94
2373 4086 8.794335 AGAAGGTAAGTGTCCAAATCTTATTC 57.206 34.615 0.00 0.00 0.00 1.75
2374 4087 8.383175 AGAAGGTAAGTGTCCAAATCTTATTCA 58.617 33.333 0.00 0.00 0.00 2.57
2375 4088 8.934023 AAGGTAAGTGTCCAAATCTTATTCAA 57.066 30.769 0.00 0.00 0.00 2.69
2376 4089 9.533831 AAGGTAAGTGTCCAAATCTTATTCAAT 57.466 29.630 0.00 0.00 0.00 2.57
2377 4090 9.178758 AGGTAAGTGTCCAAATCTTATTCAATC 57.821 33.333 0.00 0.00 0.00 2.67
2378 4091 8.122952 GGTAAGTGTCCAAATCTTATTCAATCG 58.877 37.037 0.00 0.00 0.00 3.34
2379 4092 6.124088 AGTGTCCAAATCTTATTCAATCGC 57.876 37.500 0.00 0.00 0.00 4.58
2380 4093 5.882557 AGTGTCCAAATCTTATTCAATCGCT 59.117 36.000 0.00 0.00 0.00 4.93
2381 4094 5.967674 GTGTCCAAATCTTATTCAATCGCTG 59.032 40.000 0.00 0.00 0.00 5.18
2382 4095 5.647658 TGTCCAAATCTTATTCAATCGCTGT 59.352 36.000 0.00 0.00 0.00 4.40
2383 4096 6.150976 TGTCCAAATCTTATTCAATCGCTGTT 59.849 34.615 0.00 0.00 0.00 3.16
2384 4097 6.470235 GTCCAAATCTTATTCAATCGCTGTTG 59.530 38.462 0.00 0.00 0.00 3.33
2385 4098 5.745294 CCAAATCTTATTCAATCGCTGTTGG 59.255 40.000 0.00 0.00 0.00 3.77
2386 4099 6.324819 CAAATCTTATTCAATCGCTGTTGGT 58.675 36.000 0.00 0.00 0.00 3.67
2387 4100 4.944962 TCTTATTCAATCGCTGTTGGTG 57.055 40.909 0.00 0.00 0.00 4.17
2388 4101 4.574892 TCTTATTCAATCGCTGTTGGTGA 58.425 39.130 0.00 0.00 38.92 4.02
2389 4102 4.391830 TCTTATTCAATCGCTGTTGGTGAC 59.608 41.667 0.00 0.00 37.27 3.67
2390 4103 1.234821 TTCAATCGCTGTTGGTGACC 58.765 50.000 0.00 0.00 37.27 4.02
2391 4104 0.948623 TCAATCGCTGTTGGTGACCG 60.949 55.000 0.00 0.00 37.27 4.79
2392 4105 0.948623 CAATCGCTGTTGGTGACCGA 60.949 55.000 0.00 0.00 37.27 4.69
2393 4106 0.670546 AATCGCTGTTGGTGACCGAG 60.671 55.000 0.00 0.00 37.27 4.63
2394 4107 1.532604 ATCGCTGTTGGTGACCGAGA 61.533 55.000 0.00 0.00 37.27 4.04
2395 4108 1.300620 CGCTGTTGGTGACCGAGAA 60.301 57.895 0.00 0.00 0.00 2.87
2396 4109 0.670546 CGCTGTTGGTGACCGAGAAT 60.671 55.000 0.00 0.00 0.00 2.40
2397 4110 1.523758 GCTGTTGGTGACCGAGAATT 58.476 50.000 0.00 0.00 0.00 2.17
2398 4111 1.197721 GCTGTTGGTGACCGAGAATTG 59.802 52.381 0.00 0.00 0.00 2.32
2400 4113 0.521735 GTTGGTGACCGAGAATTGGC 59.478 55.000 0.00 0.00 46.70 4.52
2401 4114 0.400213 TTGGTGACCGAGAATTGGCT 59.600 50.000 0.00 0.00 46.70 4.75
2402 4115 0.036388 TGGTGACCGAGAATTGGCTC 60.036 55.000 0.00 0.00 46.70 4.70
2410 4123 2.949451 GAGAATTGGCTCGACTCTGA 57.051 50.000 0.00 0.00 0.00 3.27
2411 4124 3.238108 GAGAATTGGCTCGACTCTGAA 57.762 47.619 0.00 0.00 0.00 3.02
2412 4125 2.926838 GAGAATTGGCTCGACTCTGAAC 59.073 50.000 0.00 0.00 0.00 3.18
2413 4126 2.003301 GAATTGGCTCGACTCTGAACC 58.997 52.381 0.00 0.00 0.00 3.62
2414 4127 0.250513 ATTGGCTCGACTCTGAACCC 59.749 55.000 0.00 0.00 0.00 4.11
2415 4128 0.832135 TTGGCTCGACTCTGAACCCT 60.832 55.000 0.00 0.00 0.00 4.34
2416 4129 1.251527 TGGCTCGACTCTGAACCCTC 61.252 60.000 0.00 0.00 0.00 4.30
2417 4130 1.137825 GCTCGACTCTGAACCCTCG 59.862 63.158 0.00 0.00 0.00 4.63
2418 4131 1.587933 GCTCGACTCTGAACCCTCGT 61.588 60.000 0.00 0.00 0.00 4.18
2419 4132 0.882474 CTCGACTCTGAACCCTCGTT 59.118 55.000 0.00 0.00 33.88 3.85
2421 4134 0.109226 CGACTCTGAACCCTCGTTCC 60.109 60.000 0.83 0.00 46.67 3.62
2422 4135 1.258676 GACTCTGAACCCTCGTTCCT 58.741 55.000 0.83 0.00 46.67 3.36
2423 4136 0.969894 ACTCTGAACCCTCGTTCCTG 59.030 55.000 0.83 0.00 46.67 3.86
2424 4137 1.257743 CTCTGAACCCTCGTTCCTGA 58.742 55.000 0.83 0.00 46.67 3.86
2425 4138 1.827969 CTCTGAACCCTCGTTCCTGAT 59.172 52.381 0.83 0.00 46.67 2.90
2426 4139 1.825474 TCTGAACCCTCGTTCCTGATC 59.175 52.381 0.83 0.00 46.67 2.92
2427 4140 1.550524 CTGAACCCTCGTTCCTGATCA 59.449 52.381 0.00 0.00 46.67 2.92
2428 4141 1.550524 TGAACCCTCGTTCCTGATCAG 59.449 52.381 16.24 16.24 46.67 2.90
2429 4142 1.550976 GAACCCTCGTTCCTGATCAGT 59.449 52.381 21.11 0.00 42.26 3.41
2430 4143 2.526888 ACCCTCGTTCCTGATCAGTA 57.473 50.000 21.11 2.36 0.00 2.74
2431 4144 2.379972 ACCCTCGTTCCTGATCAGTAG 58.620 52.381 21.11 7.28 0.00 2.57
2432 4145 1.067821 CCCTCGTTCCTGATCAGTAGC 59.932 57.143 21.11 7.03 0.00 3.58
2433 4146 1.067821 CCTCGTTCCTGATCAGTAGCC 59.932 57.143 21.11 5.55 0.00 3.93
2434 4147 2.028130 CTCGTTCCTGATCAGTAGCCT 58.972 52.381 21.11 0.00 0.00 4.58
2435 4148 1.751351 TCGTTCCTGATCAGTAGCCTG 59.249 52.381 21.11 5.09 40.25 4.85
2446 4159 3.635591 TCAGTAGCCTGATGACTGATGA 58.364 45.455 0.00 0.00 43.52 2.92
2447 4160 4.221530 TCAGTAGCCTGATGACTGATGAT 58.778 43.478 0.00 0.00 43.52 2.45
2448 4161 4.280425 TCAGTAGCCTGATGACTGATGATC 59.720 45.833 0.00 0.00 43.52 2.92
2449 4162 3.577848 AGTAGCCTGATGACTGATGATCC 59.422 47.826 0.00 0.00 0.00 3.36
2450 4163 1.698532 AGCCTGATGACTGATGATCCC 59.301 52.381 0.00 0.00 0.00 3.85
2451 4164 1.419012 GCCTGATGACTGATGATCCCA 59.581 52.381 0.00 0.00 0.00 4.37
2452 4165 2.550423 GCCTGATGACTGATGATCCCAG 60.550 54.545 9.80 9.80 37.64 4.45
2453 4166 2.038689 CCTGATGACTGATGATCCCAGG 59.961 54.545 14.33 0.00 36.03 4.45
2454 4167 2.970640 CTGATGACTGATGATCCCAGGA 59.029 50.000 14.33 0.00 36.03 3.86
2455 4168 2.970640 TGATGACTGATGATCCCAGGAG 59.029 50.000 14.33 0.00 36.03 3.69
2456 4169 1.126488 TGACTGATGATCCCAGGAGC 58.874 55.000 14.33 0.00 36.03 4.70
2457 4170 1.343782 TGACTGATGATCCCAGGAGCT 60.344 52.381 14.33 0.00 36.03 4.09
2458 4171 1.344114 GACTGATGATCCCAGGAGCTC 59.656 57.143 4.71 4.71 36.03 4.09
2459 4172 1.062275 ACTGATGATCCCAGGAGCTCT 60.062 52.381 14.64 0.00 36.03 4.09
2460 4173 2.048601 CTGATGATCCCAGGAGCTCTT 58.951 52.381 14.64 2.08 0.00 2.85
2461 4174 2.438763 CTGATGATCCCAGGAGCTCTTT 59.561 50.000 14.64 0.00 0.00 2.52
2462 4175 2.848694 TGATGATCCCAGGAGCTCTTTT 59.151 45.455 14.64 0.00 0.00 2.27
2463 4176 2.795231 TGATCCCAGGAGCTCTTTTG 57.205 50.000 14.64 9.75 0.00 2.44
2464 4177 1.988107 TGATCCCAGGAGCTCTTTTGT 59.012 47.619 14.64 0.00 0.00 2.83
2465 4178 2.376518 TGATCCCAGGAGCTCTTTTGTT 59.623 45.455 14.64 0.00 0.00 2.83
2466 4179 3.181429 TGATCCCAGGAGCTCTTTTGTTT 60.181 43.478 14.64 0.00 0.00 2.83
2467 4180 2.586425 TCCCAGGAGCTCTTTTGTTTG 58.414 47.619 14.64 1.56 0.00 2.93
2468 4181 2.174639 TCCCAGGAGCTCTTTTGTTTGA 59.825 45.455 14.64 4.15 0.00 2.69
2469 4182 2.958355 CCCAGGAGCTCTTTTGTTTGAA 59.042 45.455 14.64 0.00 0.00 2.69
2470 4183 3.575687 CCCAGGAGCTCTTTTGTTTGAAT 59.424 43.478 14.64 0.00 0.00 2.57
2471 4184 4.766891 CCCAGGAGCTCTTTTGTTTGAATA 59.233 41.667 14.64 0.00 0.00 1.75
2472 4185 5.243730 CCCAGGAGCTCTTTTGTTTGAATAA 59.756 40.000 14.64 0.00 0.00 1.40
2473 4186 6.239289 CCCAGGAGCTCTTTTGTTTGAATAAA 60.239 38.462 14.64 0.00 0.00 1.40
2474 4187 6.865205 CCAGGAGCTCTTTTGTTTGAATAAAG 59.135 38.462 14.64 0.00 0.00 1.85
2475 4188 6.364435 CAGGAGCTCTTTTGTTTGAATAAAGC 59.636 38.462 14.64 0.00 0.00 3.51
2476 4189 6.266330 AGGAGCTCTTTTGTTTGAATAAAGCT 59.734 34.615 14.64 0.00 0.00 3.74
2477 4190 6.584184 GGAGCTCTTTTGTTTGAATAAAGCTC 59.416 38.462 14.64 11.11 35.78 4.09
2478 4191 7.282332 AGCTCTTTTGTTTGAATAAAGCTCT 57.718 32.000 0.00 0.00 0.00 4.09
2479 4192 7.366513 AGCTCTTTTGTTTGAATAAAGCTCTC 58.633 34.615 0.00 0.00 0.00 3.20
2480 4193 7.013655 AGCTCTTTTGTTTGAATAAAGCTCTCA 59.986 33.333 0.00 0.00 0.00 3.27
2481 4194 7.811713 GCTCTTTTGTTTGAATAAAGCTCTCAT 59.188 33.333 0.00 0.00 0.00 2.90
2482 4195 9.125906 CTCTTTTGTTTGAATAAAGCTCTCATG 57.874 33.333 0.00 0.00 0.00 3.07
2483 4196 8.849168 TCTTTTGTTTGAATAAAGCTCTCATGA 58.151 29.630 0.00 0.00 0.00 3.07
2484 4197 9.635520 CTTTTGTTTGAATAAAGCTCTCATGAT 57.364 29.630 0.00 0.00 0.00 2.45
2485 4198 9.985730 TTTTGTTTGAATAAAGCTCTCATGATT 57.014 25.926 0.00 0.00 0.00 2.57
2486 4199 9.985730 TTTGTTTGAATAAAGCTCTCATGATTT 57.014 25.926 0.00 0.00 0.00 2.17
2487 4200 9.630098 TTGTTTGAATAAAGCTCTCATGATTTC 57.370 29.630 0.00 0.00 0.00 2.17
2488 4201 8.246180 TGTTTGAATAAAGCTCTCATGATTTCC 58.754 33.333 0.00 0.00 0.00 3.13
2489 4202 6.949352 TGAATAAAGCTCTCATGATTTCCC 57.051 37.500 0.00 0.00 0.00 3.97
2490 4203 5.528690 TGAATAAAGCTCTCATGATTTCCCG 59.471 40.000 0.00 0.00 0.00 5.14
2491 4204 1.673168 AAGCTCTCATGATTTCCCGC 58.327 50.000 0.00 0.00 0.00 6.13
2492 4205 0.543277 AGCTCTCATGATTTCCCGCA 59.457 50.000 0.00 0.00 0.00 5.69
2493 4206 1.065199 AGCTCTCATGATTTCCCGCAA 60.065 47.619 0.00 0.00 0.00 4.85
2494 4207 1.745087 GCTCTCATGATTTCCCGCAAA 59.255 47.619 0.00 0.00 0.00 3.68
2495 4208 2.164219 GCTCTCATGATTTCCCGCAAAA 59.836 45.455 0.00 0.00 0.00 2.44
2496 4209 3.367292 GCTCTCATGATTTCCCGCAAAAA 60.367 43.478 0.00 0.00 0.00 1.94
2572 4285 2.677199 AGTGCTACAACATCAGACACG 58.323 47.619 0.00 0.00 0.00 4.49
2573 4286 2.035961 AGTGCTACAACATCAGACACGT 59.964 45.455 0.00 0.00 0.00 4.49
2581 4294 1.474478 ACATCAGACACGTCAGCTAGG 59.526 52.381 0.00 0.00 0.00 3.02
2582 4295 0.457851 ATCAGACACGTCAGCTAGGC 59.542 55.000 0.00 0.00 0.00 3.93
2583 4296 0.893727 TCAGACACGTCAGCTAGGCA 60.894 55.000 0.00 0.00 0.00 4.75
2584 4297 0.457509 CAGACACGTCAGCTAGGCAG 60.458 60.000 0.00 0.00 0.00 4.85
2598 4311 2.181021 GCAGCTAGCACCGTACGT 59.819 61.111 18.83 0.00 44.79 3.57
2599 4312 1.872679 GCAGCTAGCACCGTACGTC 60.873 63.158 18.83 2.93 44.79 4.34
2600 4313 1.226603 CAGCTAGCACCGTACGTCC 60.227 63.158 18.83 1.70 0.00 4.79
2601 4314 1.676635 AGCTAGCACCGTACGTCCA 60.677 57.895 18.83 0.00 0.00 4.02
2605 4318 1.002684 CTAGCACCGTACGTCCATCTC 60.003 57.143 15.21 0.00 0.00 2.75
2617 4330 2.542178 CGTCCATCTCGAACAACAAACA 59.458 45.455 0.00 0.00 0.00 2.83
2623 4336 6.313658 TCCATCTCGAACAACAAACAGATATG 59.686 38.462 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.721208 TGAGGGAAAATTGTGAGAGCTTTATT 59.279 34.615 0.00 0.00 0.00 1.40
1 2 6.248433 TGAGGGAAAATTGTGAGAGCTTTAT 58.752 36.000 0.00 0.00 0.00 1.40
2 3 5.630121 TGAGGGAAAATTGTGAGAGCTTTA 58.370 37.500 0.00 0.00 0.00 1.85
3 4 4.473444 TGAGGGAAAATTGTGAGAGCTTT 58.527 39.130 0.00 0.00 0.00 3.51
4 5 4.104383 TGAGGGAAAATTGTGAGAGCTT 57.896 40.909 0.00 0.00 0.00 3.74
5 6 3.795688 TGAGGGAAAATTGTGAGAGCT 57.204 42.857 0.00 0.00 0.00 4.09
6 7 4.853924 TTTGAGGGAAAATTGTGAGAGC 57.146 40.909 0.00 0.00 0.00 4.09
27 28 1.762370 CAGGTGTCCCTTTGCCTTTTT 59.238 47.619 0.00 0.00 39.89 1.94
28 29 1.063266 TCAGGTGTCCCTTTGCCTTTT 60.063 47.619 0.00 0.00 39.89 2.27
29 30 0.555769 TCAGGTGTCCCTTTGCCTTT 59.444 50.000 0.00 0.00 39.89 3.11
30 31 0.779997 ATCAGGTGTCCCTTTGCCTT 59.220 50.000 0.00 0.00 39.89 4.35
31 32 0.038744 CATCAGGTGTCCCTTTGCCT 59.961 55.000 0.00 0.00 39.89 4.75
32 33 0.967380 CCATCAGGTGTCCCTTTGCC 60.967 60.000 0.00 0.00 39.89 4.52
33 34 0.038166 TCCATCAGGTGTCCCTTTGC 59.962 55.000 0.00 0.00 39.89 3.68
106 107 4.583907 TGAGTGAACAAAGCATTGGATGAA 59.416 37.500 6.62 0.00 41.01 2.57
124 125 6.749923 AGCTTTAAAAGGCTAGATTGAGTG 57.250 37.500 1.32 0.00 37.00 3.51
167 168 4.198028 TCGAGGGCCTCTAGTTAAAAAC 57.802 45.455 29.81 1.00 0.00 2.43
189 190 2.969628 ATTTTGCGGTGTTTGGACAA 57.030 40.000 0.00 0.00 37.57 3.18
201 202 4.718940 AGGACCTATTGGAAATTTTGCG 57.281 40.909 0.00 0.00 37.04 4.85
212 213 4.154918 GCTCAGTTGTGAAAGGACCTATTG 59.845 45.833 0.00 0.00 30.14 1.90
224 225 5.005094 TGAATCAATGATGCTCAGTTGTGA 58.995 37.500 2.49 0.00 0.00 3.58
291 295 8.403236 TCTCTGCATCTGATGAACAATAAAATG 58.597 33.333 21.30 0.00 0.00 2.32
292 296 8.404000 GTCTCTGCATCTGATGAACAATAAAAT 58.596 33.333 21.30 0.00 0.00 1.82
293 297 7.413328 CGTCTCTGCATCTGATGAACAATAAAA 60.413 37.037 21.30 0.00 0.00 1.52
298 302 3.256558 CGTCTCTGCATCTGATGAACAA 58.743 45.455 21.30 0.00 0.00 2.83
303 307 0.179092 TGGCGTCTCTGCATCTGATG 60.179 55.000 13.26 13.26 36.28 3.07
312 316 0.460284 AGCGGTAATTGGCGTCTCTG 60.460 55.000 0.00 0.00 0.00 3.35
375 393 0.994247 ATGGACCACAGCCATCTCAA 59.006 50.000 0.00 0.00 42.31 3.02
447 465 2.561885 CGGCACTTCTCGTCGTCT 59.438 61.111 0.00 0.00 0.00 4.18
448 466 2.504244 CCGGCACTTCTCGTCGTC 60.504 66.667 0.00 0.00 0.00 4.20
449 467 4.719369 GCCGGCACTTCTCGTCGT 62.719 66.667 24.80 0.00 0.00 4.34
450 468 3.916392 AAGCCGGCACTTCTCGTCG 62.916 63.158 31.54 0.00 0.00 5.12
451 469 1.228657 AAAAGCCGGCACTTCTCGTC 61.229 55.000 31.54 0.00 0.00 4.20
452 470 1.227853 AAAAGCCGGCACTTCTCGT 60.228 52.632 31.54 0.76 0.00 4.18
453 471 1.207593 CAAAAGCCGGCACTTCTCG 59.792 57.895 31.54 9.70 0.00 4.04
454 472 0.951558 TTCAAAAGCCGGCACTTCTC 59.048 50.000 31.54 0.00 0.00 2.87
455 473 1.067060 GTTTCAAAAGCCGGCACTTCT 59.933 47.619 31.54 3.61 0.00 2.85
456 474 1.487482 GTTTCAAAAGCCGGCACTTC 58.513 50.000 31.54 5.23 0.00 3.01
457 475 0.248866 CGTTTCAAAAGCCGGCACTT 60.249 50.000 31.54 18.90 0.00 3.16
460 478 0.671251 AATCGTTTCAAAAGCCGGCA 59.329 45.000 31.54 3.61 0.00 5.69
461 479 1.778334 AAATCGTTTCAAAAGCCGGC 58.222 45.000 21.89 21.89 0.00 6.13
464 482 7.755373 AGCTAATTCTAAATCGTTTCAAAAGCC 59.245 33.333 0.00 0.00 0.00 4.35
532 578 2.406130 CCAGCGTAAAACTCAACGGTA 58.594 47.619 0.00 0.00 46.92 4.02
534 580 0.515564 CCCAGCGTAAAACTCAACGG 59.484 55.000 0.00 0.00 39.46 4.44
540 589 2.467566 ACGAATCCCAGCGTAAAACT 57.532 45.000 0.00 0.00 39.21 2.66
580 629 8.524487 ACACTACTTGATTAACAAACAACCAAA 58.476 29.630 0.00 0.00 38.08 3.28
582 631 7.633193 ACACTACTTGATTAACAAACAACCA 57.367 32.000 0.00 0.00 38.08 3.67
583 632 8.287503 CCTACACTACTTGATTAACAAACAACC 58.712 37.037 0.00 0.00 38.08 3.77
587 636 8.828688 ACTCCTACACTACTTGATTAACAAAC 57.171 34.615 0.00 0.00 38.08 2.93
590 639 9.524496 TCTAACTCCTACACTACTTGATTAACA 57.476 33.333 0.00 0.00 0.00 2.41
617 666 8.246180 GCTGGATGAGAATTAACAAAAATCTCA 58.754 33.333 7.70 7.70 37.20 3.27
622 671 9.206870 GATTTGCTGGATGAGAATTAACAAAAA 57.793 29.630 0.00 0.00 0.00 1.94
623 672 7.818930 GGATTTGCTGGATGAGAATTAACAAAA 59.181 33.333 0.00 0.00 0.00 2.44
657 706 4.238514 GCTTCTTCACTCGTGAGTAATGT 58.761 43.478 1.54 0.00 40.20 2.71
756 808 8.362639 GTTTTCCATTGATTGTAGCATGGATAT 58.637 33.333 0.64 0.00 37.93 1.63
757 809 7.468494 CGTTTTCCATTGATTGTAGCATGGATA 60.468 37.037 0.64 0.00 37.93 2.59
758 810 6.576185 GTTTTCCATTGATTGTAGCATGGAT 58.424 36.000 0.64 0.00 37.93 3.41
759 811 5.392919 CGTTTTCCATTGATTGTAGCATGGA 60.393 40.000 0.00 0.00 36.52 3.41
789 841 6.110543 ACAAAGTGTTGACTAAAACCGTAC 57.889 37.500 0.00 0.00 38.20 3.67
840 893 2.904697 TGGCAGCTCTCTATCACATG 57.095 50.000 0.00 0.00 0.00 3.21
1139 1236 2.493088 GAAATGAGTTCACGCGCGCA 62.493 55.000 32.58 19.24 36.15 6.09
1154 1264 6.656902 TGATGAAGCCATGAAGTAGAGAAAT 58.343 36.000 0.00 0.00 32.09 2.17
1163 1280 1.674441 ACGCATGATGAAGCCATGAAG 59.326 47.619 0.00 3.25 42.89 3.02
1211 1341 1.236616 CCGCCATGACTGCTTGTTCA 61.237 55.000 0.00 0.00 0.00 3.18
1212 1342 1.503542 CCGCCATGACTGCTTGTTC 59.496 57.895 0.00 0.00 0.00 3.18
1213 1343 2.629656 GCCGCCATGACTGCTTGTT 61.630 57.895 0.00 0.00 0.00 2.83
1214 1344 3.058160 GCCGCCATGACTGCTTGT 61.058 61.111 0.00 0.00 0.00 3.16
1666 1835 0.747283 CAGGAGTAGGGACGTAGCGT 60.747 60.000 0.00 0.00 45.10 5.07
1740 1909 7.628235 CACTCTGTCTTATACATGATTGCTTG 58.372 38.462 0.00 0.00 37.50 4.01
1781 3459 5.244178 ACCCGCACCATTCAGTTATTAAAAA 59.756 36.000 0.00 0.00 0.00 1.94
1782 3460 4.767928 ACCCGCACCATTCAGTTATTAAAA 59.232 37.500 0.00 0.00 0.00 1.52
1888 3566 7.548075 GGCAACTTACAAGTAGCTAAAGTGATA 59.452 37.037 8.22 0.00 38.57 2.15
1919 3601 7.044798 AGAAATTGAACGACCCAAATTCAAAA 58.955 30.769 14.32 0.00 43.50 2.44
1930 3612 1.401018 CGCCCAAGAAATTGAACGACC 60.401 52.381 0.00 0.00 0.00 4.79
1934 3616 3.363341 TCAACGCCCAAGAAATTGAAC 57.637 42.857 0.00 0.00 0.00 3.18
1937 3619 3.652274 ACAATCAACGCCCAAGAAATTG 58.348 40.909 0.00 0.00 0.00 2.32
1948 3630 5.504755 CGAATCTTAGAACAACAATCAACGC 59.495 40.000 0.00 0.00 0.00 4.84
1949 3631 6.516355 CACGAATCTTAGAACAACAATCAACG 59.484 38.462 0.00 0.00 0.00 4.10
1992 3674 5.013079 ACCAAATATGAGGTCAGTTGAGTCA 59.987 40.000 0.00 0.00 30.79 3.41
2000 3712 4.568359 CGACTGAACCAAATATGAGGTCAG 59.432 45.833 11.49 11.49 42.48 3.51
2006 3718 5.647658 AGCAAATCGACTGAACCAAATATGA 59.352 36.000 0.56 0.00 0.00 2.15
2036 3748 0.451783 CACATTTACTGGGCTTCGGC 59.548 55.000 0.00 0.00 40.88 5.54
2044 3756 1.331756 GCTGGATCGCACATTTACTGG 59.668 52.381 0.00 0.00 0.00 4.00
2045 3757 1.331756 GGCTGGATCGCACATTTACTG 59.668 52.381 0.00 0.00 0.00 2.74
2102 3814 5.456265 ACCAAAAACAAATGCAAAACACAC 58.544 33.333 0.00 0.00 0.00 3.82
2103 3815 5.695851 ACCAAAAACAAATGCAAAACACA 57.304 30.435 0.00 0.00 0.00 3.72
2104 3816 6.999956 AAACCAAAAACAAATGCAAAACAC 57.000 29.167 0.00 0.00 0.00 3.32
2147 3859 8.485578 TCCAAAAATACCCACAAAATAGAAGT 57.514 30.769 0.00 0.00 0.00 3.01
2148 3860 9.942850 ATTCCAAAAATACCCACAAAATAGAAG 57.057 29.630 0.00 0.00 0.00 2.85
2151 3863 9.500785 AACATTCCAAAAATACCCACAAAATAG 57.499 29.630 0.00 0.00 0.00 1.73
2206 3919 8.668353 GTGTAATTTTCAGAGACATTGCATAGA 58.332 33.333 0.00 0.00 0.00 1.98
2239 3952 8.620416 TCACTTTTTGTAGCATGCGATAATAAT 58.380 29.630 13.01 0.00 0.00 1.28
2244 3957 5.871465 TTCACTTTTTGTAGCATGCGATA 57.129 34.783 13.01 1.81 0.00 2.92
2247 3960 4.290155 ACTTTCACTTTTTGTAGCATGCG 58.710 39.130 13.01 0.00 0.00 4.73
2262 3975 5.798434 ACACAACTTCGCTTTAAACTTTCAC 59.202 36.000 0.00 0.00 0.00 3.18
2265 3978 4.561213 GCACACAACTTCGCTTTAAACTTT 59.439 37.500 0.00 0.00 0.00 2.66
2275 3988 1.908065 AAACTTGCACACAACTTCGC 58.092 45.000 0.00 0.00 0.00 4.70
2372 4085 0.948623 CGGTCACCAACAGCGATTGA 60.949 55.000 0.00 0.00 36.89 2.57
2373 4086 0.948623 TCGGTCACCAACAGCGATTG 60.949 55.000 0.00 0.00 38.77 2.67
2374 4087 0.670546 CTCGGTCACCAACAGCGATT 60.671 55.000 0.00 0.00 42.45 3.34
2375 4088 1.079819 CTCGGTCACCAACAGCGAT 60.080 57.895 0.00 0.00 42.45 4.58
2376 4089 1.740332 TTCTCGGTCACCAACAGCGA 61.740 55.000 0.00 0.00 41.24 4.93
2377 4090 0.670546 ATTCTCGGTCACCAACAGCG 60.671 55.000 0.00 0.00 36.08 5.18
2378 4091 1.197721 CAATTCTCGGTCACCAACAGC 59.802 52.381 0.00 0.00 0.00 4.40
2379 4092 1.806542 CCAATTCTCGGTCACCAACAG 59.193 52.381 0.00 0.00 0.00 3.16
2380 4093 1.890876 CCAATTCTCGGTCACCAACA 58.109 50.000 0.00 0.00 0.00 3.33
2381 4094 0.521735 GCCAATTCTCGGTCACCAAC 59.478 55.000 0.00 0.00 0.00 3.77
2382 4095 0.400213 AGCCAATTCTCGGTCACCAA 59.600 50.000 0.00 0.00 0.00 3.67
2383 4096 0.036388 GAGCCAATTCTCGGTCACCA 60.036 55.000 0.00 0.00 0.00 4.17
2384 4097 2.768834 GAGCCAATTCTCGGTCACC 58.231 57.895 0.00 0.00 0.00 4.02
2391 4104 2.926838 GTTCAGAGTCGAGCCAATTCTC 59.073 50.000 0.00 0.00 0.00 2.87
2392 4105 2.354203 GGTTCAGAGTCGAGCCAATTCT 60.354 50.000 11.14 0.00 36.37 2.40
2393 4106 2.003301 GGTTCAGAGTCGAGCCAATTC 58.997 52.381 11.14 0.00 36.37 2.17
2394 4107 1.339151 GGGTTCAGAGTCGAGCCAATT 60.339 52.381 15.66 0.00 37.98 2.32
2395 4108 0.250513 GGGTTCAGAGTCGAGCCAAT 59.749 55.000 15.66 0.00 37.98 3.16
2396 4109 0.832135 AGGGTTCAGAGTCGAGCCAA 60.832 55.000 15.66 0.00 37.98 4.52
2397 4110 1.228894 AGGGTTCAGAGTCGAGCCA 60.229 57.895 15.66 0.00 37.98 4.75
2398 4111 1.513622 GAGGGTTCAGAGTCGAGCC 59.486 63.158 8.60 8.60 35.65 4.70
2399 4112 1.137825 CGAGGGTTCAGAGTCGAGC 59.862 63.158 0.00 0.00 34.28 5.03
2400 4113 0.882474 AACGAGGGTTCAGAGTCGAG 59.118 55.000 0.00 0.00 36.30 4.04
2401 4114 3.031916 AACGAGGGTTCAGAGTCGA 57.968 52.632 0.00 0.00 36.30 4.20
2410 4123 1.645710 ACTGATCAGGAACGAGGGTT 58.354 50.000 26.08 0.00 39.63 4.11
2411 4124 2.379972 CTACTGATCAGGAACGAGGGT 58.620 52.381 26.08 5.73 0.00 4.34
2412 4125 1.067821 GCTACTGATCAGGAACGAGGG 59.932 57.143 26.08 6.47 0.00 4.30
2413 4126 1.067821 GGCTACTGATCAGGAACGAGG 59.932 57.143 26.08 7.20 0.00 4.63
2414 4127 2.028130 AGGCTACTGATCAGGAACGAG 58.972 52.381 26.08 14.92 0.00 4.18
2415 4128 2.145397 AGGCTACTGATCAGGAACGA 57.855 50.000 26.08 5.65 0.00 3.85
2426 4139 4.558178 GATCATCAGTCATCAGGCTACTG 58.442 47.826 8.54 8.54 46.30 2.74
2427 4140 3.577848 GGATCATCAGTCATCAGGCTACT 59.422 47.826 0.00 0.00 0.00 2.57
2428 4141 3.306641 GGGATCATCAGTCATCAGGCTAC 60.307 52.174 0.00 0.00 0.00 3.58
2429 4142 2.902486 GGGATCATCAGTCATCAGGCTA 59.098 50.000 0.00 0.00 0.00 3.93
2430 4143 1.698532 GGGATCATCAGTCATCAGGCT 59.301 52.381 0.00 0.00 0.00 4.58
2431 4144 1.419012 TGGGATCATCAGTCATCAGGC 59.581 52.381 0.00 0.00 0.00 4.85
2432 4145 2.038689 CCTGGGATCATCAGTCATCAGG 59.961 54.545 12.38 0.00 34.58 3.86
2433 4146 2.970640 TCCTGGGATCATCAGTCATCAG 59.029 50.000 12.38 0.00 0.00 2.90
2434 4147 2.970640 CTCCTGGGATCATCAGTCATCA 59.029 50.000 12.38 0.00 0.00 3.07
2435 4148 2.289569 GCTCCTGGGATCATCAGTCATC 60.290 54.545 12.38 0.00 0.00 2.92
2436 4149 1.698532 GCTCCTGGGATCATCAGTCAT 59.301 52.381 12.38 0.00 0.00 3.06
2437 4150 1.126488 GCTCCTGGGATCATCAGTCA 58.874 55.000 12.38 1.32 0.00 3.41
2438 4151 1.344114 GAGCTCCTGGGATCATCAGTC 59.656 57.143 0.87 2.71 0.00 3.51
2439 4152 1.062275 AGAGCTCCTGGGATCATCAGT 60.062 52.381 10.93 0.00 0.00 3.41
2440 4153 1.719529 AGAGCTCCTGGGATCATCAG 58.280 55.000 10.93 7.97 0.00 2.90
2441 4154 2.187239 AAGAGCTCCTGGGATCATCA 57.813 50.000 10.93 0.00 0.00 3.07
2442 4155 3.212685 CAAAAGAGCTCCTGGGATCATC 58.787 50.000 10.93 0.00 0.00 2.92
2443 4156 2.579860 ACAAAAGAGCTCCTGGGATCAT 59.420 45.455 10.93 0.00 0.00 2.45
2444 4157 1.988107 ACAAAAGAGCTCCTGGGATCA 59.012 47.619 10.93 0.00 0.00 2.92
2445 4158 2.797177 ACAAAAGAGCTCCTGGGATC 57.203 50.000 10.93 0.00 0.00 3.36
2446 4159 3.160269 CAAACAAAAGAGCTCCTGGGAT 58.840 45.455 10.93 0.00 0.00 3.85
2447 4160 2.174639 TCAAACAAAAGAGCTCCTGGGA 59.825 45.455 10.93 3.20 0.00 4.37
2448 4161 2.586425 TCAAACAAAAGAGCTCCTGGG 58.414 47.619 10.93 0.45 0.00 4.45
2449 4162 4.861102 ATTCAAACAAAAGAGCTCCTGG 57.139 40.909 10.93 0.00 0.00 4.45
2450 4163 6.364435 GCTTTATTCAAACAAAAGAGCTCCTG 59.636 38.462 10.93 8.30 33.05 3.86
2451 4164 6.266330 AGCTTTATTCAAACAAAAGAGCTCCT 59.734 34.615 10.93 0.00 33.00 3.69
2452 4165 6.450545 AGCTTTATTCAAACAAAAGAGCTCC 58.549 36.000 10.93 0.00 33.00 4.70
2453 4166 7.559835 GAGCTTTATTCAAACAAAAGAGCTC 57.440 36.000 5.27 5.27 44.35 4.09
2454 4167 7.013655 TGAGAGCTTTATTCAAACAAAAGAGCT 59.986 33.333 0.00 0.00 40.33 4.09
2455 4168 7.141363 TGAGAGCTTTATTCAAACAAAAGAGC 58.859 34.615 0.00 0.00 33.05 4.09
2456 4169 9.125906 CATGAGAGCTTTATTCAAACAAAAGAG 57.874 33.333 0.00 0.00 33.05 2.85
2457 4170 8.849168 TCATGAGAGCTTTATTCAAACAAAAGA 58.151 29.630 0.00 0.00 33.05 2.52
2458 4171 9.635520 ATCATGAGAGCTTTATTCAAACAAAAG 57.364 29.630 0.09 0.00 34.14 2.27
2459 4172 9.985730 AATCATGAGAGCTTTATTCAAACAAAA 57.014 25.926 0.09 0.00 0.00 2.44
2460 4173 9.985730 AAATCATGAGAGCTTTATTCAAACAAA 57.014 25.926 0.09 0.00 0.00 2.83
2461 4174 9.630098 GAAATCATGAGAGCTTTATTCAAACAA 57.370 29.630 0.09 0.00 0.00 2.83
2462 4175 8.246180 GGAAATCATGAGAGCTTTATTCAAACA 58.754 33.333 0.09 0.00 0.00 2.83
2463 4176 7.704047 GGGAAATCATGAGAGCTTTATTCAAAC 59.296 37.037 0.09 0.00 0.00 2.93
2464 4177 7.415541 CGGGAAATCATGAGAGCTTTATTCAAA 60.416 37.037 0.09 0.00 0.00 2.69
2465 4178 6.038603 CGGGAAATCATGAGAGCTTTATTCAA 59.961 38.462 0.09 0.00 0.00 2.69
2466 4179 5.528690 CGGGAAATCATGAGAGCTTTATTCA 59.471 40.000 0.09 0.00 0.00 2.57
2467 4180 5.561725 GCGGGAAATCATGAGAGCTTTATTC 60.562 44.000 0.09 0.00 0.00 1.75
2468 4181 4.276926 GCGGGAAATCATGAGAGCTTTATT 59.723 41.667 0.09 0.00 0.00 1.40
2469 4182 3.817647 GCGGGAAATCATGAGAGCTTTAT 59.182 43.478 0.09 0.00 0.00 1.40
2470 4183 3.206150 GCGGGAAATCATGAGAGCTTTA 58.794 45.455 0.09 0.00 0.00 1.85
2471 4184 2.019984 GCGGGAAATCATGAGAGCTTT 58.980 47.619 0.09 0.00 0.00 3.51
2472 4185 1.065199 TGCGGGAAATCATGAGAGCTT 60.065 47.619 0.09 0.00 0.00 3.74
2473 4186 0.543277 TGCGGGAAATCATGAGAGCT 59.457 50.000 0.09 0.00 0.00 4.09
2474 4187 1.382522 TTGCGGGAAATCATGAGAGC 58.617 50.000 0.09 1.04 0.00 4.09
2475 4188 4.439305 TTTTTGCGGGAAATCATGAGAG 57.561 40.909 0.09 0.00 0.00 3.20
2497 4210 5.036737 CGGCAGCGATTGAATAAGATTTTT 58.963 37.500 0.00 0.00 0.00 1.94
2498 4211 4.096382 ACGGCAGCGATTGAATAAGATTTT 59.904 37.500 0.00 0.00 0.00 1.82
2499 4212 3.627577 ACGGCAGCGATTGAATAAGATTT 59.372 39.130 0.00 0.00 0.00 2.17
2500 4213 3.206150 ACGGCAGCGATTGAATAAGATT 58.794 40.909 0.00 0.00 0.00 2.40
2501 4214 2.838736 ACGGCAGCGATTGAATAAGAT 58.161 42.857 0.00 0.00 0.00 2.40
2502 4215 2.309528 ACGGCAGCGATTGAATAAGA 57.690 45.000 0.00 0.00 0.00 2.10
2503 4216 2.863740 TGTACGGCAGCGATTGAATAAG 59.136 45.455 0.00 0.00 0.00 1.73
2504 4217 2.863740 CTGTACGGCAGCGATTGAATAA 59.136 45.455 0.00 0.00 38.52 1.40
2505 4218 2.469826 CTGTACGGCAGCGATTGAATA 58.530 47.619 0.00 0.00 38.52 1.75
2506 4219 1.290203 CTGTACGGCAGCGATTGAAT 58.710 50.000 0.00 0.00 38.52 2.57
2507 4220 2.749541 CTGTACGGCAGCGATTGAA 58.250 52.632 0.00 0.00 38.52 2.69
2567 4280 1.807573 GCTGCCTAGCTGACGTGTC 60.808 63.158 0.00 0.00 46.57 3.67
2581 4294 1.872679 GACGTACGGTGCTAGCTGC 60.873 63.158 21.06 8.75 43.25 5.25
2582 4295 1.226603 GGACGTACGGTGCTAGCTG 60.227 63.158 21.06 8.41 33.58 4.24
2583 4296 1.035932 ATGGACGTACGGTGCTAGCT 61.036 55.000 21.06 0.00 37.93 3.32
2584 4297 0.594284 GATGGACGTACGGTGCTAGC 60.594 60.000 21.06 8.10 37.93 3.42
2585 4298 1.002684 GAGATGGACGTACGGTGCTAG 60.003 57.143 21.06 0.00 37.93 3.42
2586 4299 1.019673 GAGATGGACGTACGGTGCTA 58.980 55.000 21.06 6.88 37.93 3.49
2587 4300 1.807886 GAGATGGACGTACGGTGCT 59.192 57.895 21.06 9.00 37.93 4.40
2588 4301 1.585521 CGAGATGGACGTACGGTGC 60.586 63.158 21.06 10.94 37.52 5.01
2589 4302 0.448990 TTCGAGATGGACGTACGGTG 59.551 55.000 21.06 0.00 0.00 4.94
2590 4303 0.449388 GTTCGAGATGGACGTACGGT 59.551 55.000 21.06 5.07 0.00 4.83
2592 4305 1.909532 GTTGTTCGAGATGGACGTACG 59.090 52.381 15.01 15.01 34.72 3.67
2593 4306 2.937591 TGTTGTTCGAGATGGACGTAC 58.062 47.619 0.00 0.00 0.00 3.67
2594 4307 3.646611 TTGTTGTTCGAGATGGACGTA 57.353 42.857 0.00 0.00 0.00 3.57
2595 4308 2.519377 TTGTTGTTCGAGATGGACGT 57.481 45.000 0.00 0.00 0.00 4.34
2596 4309 2.542178 TGTTTGTTGTTCGAGATGGACG 59.458 45.455 0.00 0.00 0.00 4.79
2597 4310 3.807622 TCTGTTTGTTGTTCGAGATGGAC 59.192 43.478 0.00 0.00 0.00 4.02
2598 4311 4.066646 TCTGTTTGTTGTTCGAGATGGA 57.933 40.909 0.00 0.00 0.00 3.41
2599 4312 6.313658 TCATATCTGTTTGTTGTTCGAGATGG 59.686 38.462 0.00 0.00 0.00 3.51
2600 4313 7.276438 TCTCATATCTGTTTGTTGTTCGAGATG 59.724 37.037 0.00 0.00 0.00 2.90
2601 4314 7.323420 TCTCATATCTGTTTGTTGTTCGAGAT 58.677 34.615 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.