Multiple sequence alignment - TraesCS1A01G073000

Loading Multiple Alignment...

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 TraesCS1A01G073000 chr1A 100.000 4044 0 0 1 4044 57188874 57192917 0.000000e+00 7468.0
1 TraesCS1A01G073000 chr1A 87.735 2340 211 36 764 3055 57395000 57392689 0.000000e+00 2662.0
2 TraesCS1A01G073000 chr1A 91.276 619 33 8 157 756 57397168 57396552 0.000000e+00 824.0
3 TraesCS1A01G073000 chr1A 92.195 410 29 2 165 571 57310927 57310518 9.750000e-161 577.0
4 TraesCS1A01G073000 chr1A 86.131 411 33 15 513 914 57310533 57310138 4.830000e-114 422.0
5 TraesCS1A01G073000 chr1D 91.151 1763 121 20 853 2600 58448913 58450655 0.000000e+00 2359.0
6 TraesCS1A01G073000 chr1D 95.294 850 20 8 3195 4044 58451133 58451962 0.000000e+00 1330.0
7 TraesCS1A01G073000 chr1D 90.892 538 38 8 157 687 58620755 58620222 0.000000e+00 712.0
8 TraesCS1A01G073000 chr1D 92.347 392 19 5 2683 3070 58450698 58451082 7.640000e-152 547.0
9 TraesCS1A01G073000 chr1D 93.434 198 12 1 207 403 58448136 58448333 3.950000e-75 292.0
10 TraesCS1A01G073000 chr1D 87.243 243 11 9 451 679 58448462 58448698 4.010000e-65 259.0
11 TraesCS1A01G073000 chr1B 89.001 1191 105 17 878 2049 94208704 94207521 0.000000e+00 1450.0
12 TraesCS1A01G073000 chr1B 89.226 1021 91 7 2044 3055 94201894 94200884 0.000000e+00 1258.0
13 TraesCS1A01G073000 chr1B 90.406 886 43 19 3165 4044 94184856 94184007 0.000000e+00 1127.0
14 TraesCS1A01G073000 chr1B 87.790 647 60 8 857 1501 94186929 94186300 0.000000e+00 739.0
15 TraesCS1A01G073000 chr1B 89.608 587 49 9 3463 4044 94200146 94199567 0.000000e+00 736.0
16 TraesCS1A01G073000 chr1B 90.892 538 38 7 157 687 94209935 94209402 0.000000e+00 712.0
17 TraesCS1A01G073000 chr1B 86.348 586 54 10 2043 2617 94185863 94185293 2.070000e-172 616.0
18 TraesCS1A01G073000 chr1B 92.402 408 27 4 1572 1976 94186290 94185884 2.710000e-161 579.0
19 TraesCS1A01G073000 chr1B 85.476 420 30 17 2684 3101 94185253 94184863 3.760000e-110 409.0
20 TraesCS1A01G073000 chr1B 96.154 156 6 0 1 156 626492509 626492354 5.190000e-64 255.0
21 TraesCS1A01G073000 chr1B 95.541 157 7 0 1 157 524488026 524487870 6.710000e-63 252.0
22 TraesCS1A01G073000 chr1B 92.473 93 5 2 750 842 94208799 94208709 9.120000e-27 132.0
23 TraesCS1A01G073000 chr1B 88.889 54 4 2 760 812 94186991 94186939 9.380000e-07 65.8
24 TraesCS1A01G073000 chr7A 96.815 157 5 0 1 157 704890242 704890398 3.100000e-66 263.0
25 TraesCS1A01G073000 chrUn 96.178 157 6 0 1 157 38969422 38969578 1.440000e-64 257.0
26 TraesCS1A01G073000 chrUn 96.154 156 6 0 1 156 42262100 42261945 5.190000e-64 255.0
27 TraesCS1A01G073000 chr5B 95.541 157 7 0 1 157 14688241 14688397 6.710000e-63 252.0
28 TraesCS1A01G073000 chr5B 97.436 39 1 0 3126 3164 707411604 707411566 2.610000e-07 67.6
29 TraesCS1A01G073000 chr5B 97.297 37 1 0 3121 3157 136053307 136053343 3.370000e-06 63.9
30 TraesCS1A01G073000 chr4A 94.304 158 9 0 1 158 733780170 733780327 4.040000e-60 243.0
31 TraesCS1A01G073000 chr4A 97.436 39 1 0 3126 3164 585459854 585459892 2.610000e-07 67.6
32 TraesCS1A01G073000 chr2B 94.839 155 8 0 1 155 17575121 17575275 4.040000e-60 243.0
33 TraesCS1A01G073000 chr7B 93.293 164 9 1 1 164 725691679 725691518 1.450000e-59 241.0
34 TraesCS1A01G073000 chr5D 95.556 45 2 0 3120 3164 123089579 123089623 5.610000e-09 73.1
35 TraesCS1A01G073000 chr3D 97.436 39 1 0 3126 3164 143250804 143250766 2.610000e-07 67.6
36 TraesCS1A01G073000 chr2A 97.436 39 1 0 3124 3162 139434843 139434881 2.610000e-07 67.6
37 TraesCS1A01G073000 chr2A 97.436 39 1 0 3126 3164 756876990 756876952 2.610000e-07 67.6
38 TraesCS1A01G073000 chr6B 93.182 44 2 1 3114 3157 453407605 453407563 3.370000e-06 63.9
39 TraesCS1A01G073000 chr2D 97.368 38 0 1 3125 3162 472231210 472231174 3.370000e-06 63.9


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 TraesCS1A01G073000 chr1A 57188874 57192917 4043 False 7468.000000 7468 100.000000 1 4044 1 chr1A.!!$F1 4043
1 TraesCS1A01G073000 chr1A 57392689 57397168 4479 True 1743.000000 2662 89.505500 157 3055 2 chr1A.!!$R2 2898
2 TraesCS1A01G073000 chr1A 57310138 57310927 789 True 499.500000 577 89.163000 165 914 2 chr1A.!!$R1 749
3 TraesCS1A01G073000 chr1D 58448136 58451962 3826 False 957.400000 2359 91.893800 207 4044 5 chr1D.!!$F1 3837
4 TraesCS1A01G073000 chr1D 58620222 58620755 533 True 712.000000 712 90.892000 157 687 1 chr1D.!!$R1 530
5 TraesCS1A01G073000 chr1B 94199567 94201894 2327 True 997.000000 1258 89.417000 2044 4044 2 chr1B.!!$R4 2000
6 TraesCS1A01G073000 chr1B 94207521 94209935 2414 True 764.666667 1450 90.788667 157 2049 3 chr1B.!!$R5 1892
7 TraesCS1A01G073000 chr1B 94184007 94186991 2984 True 589.300000 1127 88.551833 760 4044 6 chr1B.!!$R3 3284

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
945 2866 1.653151 GCTGGTTGATTCCTACGGTC 58.347 55.0 0.0 0.0 0.00 4.79 F
2066 4026 0.817654 TAGCGTGATCAGTGGTCCTG 59.182 55.0 0.0 0.0 42.97 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 4446 0.798776 CAAGCAGGTTTCTGTAGGCG 59.201 55.0 0.0 0.0 42.78 5.52 R
3149 5152 0.380378 TGCTGGCTTGACAAACGTTC 59.620 50.0 0.0 0.0 0.00 3.95 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
46 47 8.899427 TTGAAAAATATTTGATTTCCTGTGCA 57.101 26.923 0.39 0.00 33.23 4.57
47 48 8.309163 TGAAAAATATTTGATTTCCTGTGCAC 57.691 30.769 10.75 10.75 33.23 4.57
48 49 8.149647 TGAAAAATATTTGATTTCCTGTGCACT 58.850 29.630 19.41 0.00 33.23 4.40
49 50 9.638239 GAAAAATATTTGATTTCCTGTGCACTA 57.362 29.630 19.41 3.54 0.00 2.74
50 51 8.986477 AAAATATTTGATTTCCTGTGCACTAC 57.014 30.769 19.41 2.43 0.00 2.73
51 52 7.944729 AATATTTGATTTCCTGTGCACTACT 57.055 32.000 19.41 0.00 0.00 2.57
52 53 5.633830 ATTTGATTTCCTGTGCACTACTG 57.366 39.130 19.41 5.64 0.00 2.74
53 54 4.350368 TTGATTTCCTGTGCACTACTGA 57.650 40.909 19.41 6.26 0.00 3.41
54 55 4.350368 TGATTTCCTGTGCACTACTGAA 57.650 40.909 19.41 11.87 0.00 3.02
55 56 4.910195 TGATTTCCTGTGCACTACTGAAT 58.090 39.130 19.41 11.36 0.00 2.57
56 57 5.316167 TGATTTCCTGTGCACTACTGAATT 58.684 37.500 19.41 10.84 0.00 2.17
57 58 5.769662 TGATTTCCTGTGCACTACTGAATTT 59.230 36.000 19.41 6.24 0.00 1.82
58 59 5.437289 TTTCCTGTGCACTACTGAATTTG 57.563 39.130 19.41 0.00 0.00 2.32
59 60 4.085357 TCCTGTGCACTACTGAATTTGT 57.915 40.909 19.41 0.00 0.00 2.83
60 61 4.460263 TCCTGTGCACTACTGAATTTGTT 58.540 39.130 19.41 0.00 0.00 2.83
61 62 4.275689 TCCTGTGCACTACTGAATTTGTTG 59.724 41.667 19.41 0.00 0.00 3.33
62 63 4.275689 CCTGTGCACTACTGAATTTGTTGA 59.724 41.667 19.41 0.00 0.00 3.18
63 64 5.221028 CCTGTGCACTACTGAATTTGTTGAA 60.221 40.000 19.41 0.00 0.00 2.69
64 65 6.201226 TGTGCACTACTGAATTTGTTGAAA 57.799 33.333 19.41 0.00 0.00 2.69
65 66 6.804677 TGTGCACTACTGAATTTGTTGAAAT 58.195 32.000 19.41 0.00 32.87 2.17
66 67 7.935520 TGTGCACTACTGAATTTGTTGAAATA 58.064 30.769 19.41 0.00 31.18 1.40
67 68 8.575589 TGTGCACTACTGAATTTGTTGAAATAT 58.424 29.630 19.41 0.00 31.18 1.28
68 69 9.410556 GTGCACTACTGAATTTGTTGAAATATT 57.589 29.630 10.32 0.00 31.18 1.28
69 70 9.979578 TGCACTACTGAATTTGTTGAAATATTT 57.020 25.926 0.00 0.00 31.18 1.40
74 75 8.017587 ACTGAATTTGTTGAAATATTTTCGCC 57.982 30.769 1.43 0.00 31.18 5.54
75 76 7.043454 TGAATTTGTTGAAATATTTTCGCCG 57.957 32.000 1.43 0.00 31.18 6.46
76 77 6.863645 TGAATTTGTTGAAATATTTTCGCCGA 59.136 30.769 1.43 0.00 31.18 5.54
77 78 7.382488 TGAATTTGTTGAAATATTTTCGCCGAA 59.618 29.630 1.43 0.00 31.18 4.30
78 79 7.644986 ATTTGTTGAAATATTTTCGCCGAAA 57.355 28.000 8.43 8.43 29.49 3.46
79 80 6.441099 TTGTTGAAATATTTTCGCCGAAAC 57.559 33.333 12.49 0.09 30.83 2.78
80 81 4.613448 TGTTGAAATATTTTCGCCGAAACG 59.387 37.500 12.49 0.00 30.83 3.60
81 82 4.407496 TGAAATATTTTCGCCGAAACGT 57.593 36.364 12.49 6.82 30.83 3.99
82 83 5.527511 TGAAATATTTTCGCCGAAACGTA 57.472 34.783 12.49 8.84 30.83 3.57
83 84 5.924786 TGAAATATTTTCGCCGAAACGTAA 58.075 33.333 12.49 0.00 30.83 3.18
84 85 6.544622 TGAAATATTTTCGCCGAAACGTAAT 58.455 32.000 12.49 5.77 30.83 1.89
85 86 7.682824 TGAAATATTTTCGCCGAAACGTAATA 58.317 30.769 12.49 7.87 30.83 0.98
86 87 8.336806 TGAAATATTTTCGCCGAAACGTAATAT 58.663 29.630 12.49 9.81 35.24 1.28
87 88 9.161684 GAAATATTTTCGCCGAAACGTAATATT 57.838 29.630 12.49 14.74 39.71 1.28
88 89 9.505995 AAATATTTTCGCCGAAACGTAATATTT 57.494 25.926 22.16 22.16 40.76 1.40
89 90 8.703823 ATATTTTCGCCGAAACGTAATATTTC 57.296 30.769 12.49 0.00 32.69 2.17
90 91 5.527511 TTTCGCCGAAACGTAATATTTCA 57.472 34.783 8.43 0.00 36.09 2.69
91 92 4.765281 TCGCCGAAACGTAATATTTCAG 57.235 40.909 0.00 0.00 36.09 3.02
92 93 4.175516 TCGCCGAAACGTAATATTTCAGT 58.824 39.130 0.00 0.00 36.09 3.41
93 94 4.031991 TCGCCGAAACGTAATATTTCAGTG 59.968 41.667 0.00 0.00 36.09 3.66
94 95 4.201647 CGCCGAAACGTAATATTTCAGTGT 60.202 41.667 0.00 0.00 36.09 3.55
95 96 5.253335 GCCGAAACGTAATATTTCAGTGTC 58.747 41.667 0.00 0.00 36.09 3.67
96 97 5.063060 GCCGAAACGTAATATTTCAGTGTCT 59.937 40.000 0.00 0.00 36.09 3.41
97 98 6.254157 GCCGAAACGTAATATTTCAGTGTCTA 59.746 38.462 0.00 0.00 36.09 2.59
98 99 7.607005 CCGAAACGTAATATTTCAGTGTCTAC 58.393 38.462 0.00 0.00 36.09 2.59
99 100 7.487189 CCGAAACGTAATATTTCAGTGTCTACT 59.513 37.037 0.00 0.00 36.09 2.57
161 162 3.244146 TGAAAGTGAAAACCATGGGCATG 60.244 43.478 18.09 0.00 38.51 4.06
163 164 2.173519 AGTGAAAACCATGGGCATGAG 58.826 47.619 18.09 0.00 41.20 2.90
249 258 9.809096 TTACAGTTCACTGATGATCTTAATCTC 57.191 33.333 14.00 0.00 46.59 2.75
294 303 5.242838 TGTTTCAGGCTTTATTTGGTACCAG 59.757 40.000 15.65 3.28 0.00 4.00
395 405 8.375493 TCCTTGTTATACTCTACCAAGAATGT 57.625 34.615 0.00 0.00 35.64 2.71
399 409 9.787435 TTGTTATACTCTACCAAGAATGTTGTT 57.213 29.630 0.00 0.00 0.00 2.83
406 416 6.223852 TCTACCAAGAATGTTGTTGAGTCTC 58.776 40.000 4.40 0.00 33.69 3.36
491 584 4.154195 CCCTGGAAATTAAGACAAGACACG 59.846 45.833 0.00 0.00 0.00 4.49
563 716 4.023107 GCCCCTCTTTTGTGTAAACTCTTC 60.023 45.833 0.00 0.00 0.00 2.87
741 1032 6.039493 AGTCTCTGTCGTCTCTTGAGTTTTTA 59.961 38.462 0.00 0.00 0.00 1.52
819 2707 4.106925 GGGGCCTGGCAGAGAGTG 62.107 72.222 22.05 0.00 0.00 3.51
897 2811 2.643272 GAGGTCGCTGACGTGTGA 59.357 61.111 0.00 0.00 41.18 3.58
922 2842 4.910585 CCGGCTATCCACCACGCC 62.911 72.222 0.00 0.00 39.14 5.68
945 2866 1.653151 GCTGGTTGATTCCTACGGTC 58.347 55.000 0.00 0.00 0.00 4.79
1060 2981 4.100084 CCGCACTCCCATCCTGCA 62.100 66.667 0.00 0.00 0.00 4.41
1093 3014 1.160870 TCCTTCTCAGCCCCCTCAA 59.839 57.895 0.00 0.00 0.00 3.02
1137 3058 3.417275 CTCCCGGCTGTACTGCTCG 62.417 68.421 22.05 21.20 0.00 5.03
1335 3258 2.029666 GTGAGCCCCATCGATCCG 59.970 66.667 0.00 0.00 0.00 4.18
1362 3290 3.077695 TCCCCTTCTTCTCTCTACTTGGT 59.922 47.826 0.00 0.00 0.00 3.67
1378 3306 4.208746 ACTTGGTTACCTATCTCCTCTCG 58.791 47.826 2.07 0.00 0.00 4.04
1461 3389 7.023197 TGACTGCAGAAATTATGACATGATG 57.977 36.000 23.35 0.00 0.00 3.07
1537 3475 4.072131 TCTTTGCTGGTTGGATAGAACAC 58.928 43.478 0.00 0.00 0.00 3.32
1575 3513 3.755378 CAGAGACTGAATTCCACCCTTTG 59.245 47.826 2.27 0.00 32.44 2.77
1579 3517 1.962807 CTGAATTCCACCCTTTGCACA 59.037 47.619 2.27 0.00 0.00 4.57
1617 3565 9.495754 GTTACATCTGTTAATTTCTCTCATTGC 57.504 33.333 0.00 0.00 0.00 3.56
1713 3663 1.408683 CGCCTCATGATCAAGGGGAAA 60.409 52.381 21.09 0.00 45.81 3.13
1722 3672 2.746279 TCAAGGGGAAAAGTGCTTCA 57.254 45.000 0.00 0.00 0.00 3.02
1862 3819 4.969484 ACAAATTTCAGGTCCGAGTACTT 58.031 39.130 0.00 0.00 0.00 2.24
1937 3894 1.631405 TTGCTAATGGCCAACTTGCT 58.369 45.000 10.96 0.00 40.92 3.91
1972 3929 3.565482 GGTGAGTTCATTGCAAGTCAGAA 59.435 43.478 4.94 3.90 36.57 3.02
1973 3930 4.217118 GGTGAGTTCATTGCAAGTCAGAAT 59.783 41.667 4.94 0.00 36.57 2.40
1976 3933 6.361748 GTGAGTTCATTGCAAGTCAGAATTTC 59.638 38.462 4.94 8.94 36.57 2.17
1977 3934 6.039605 TGAGTTCATTGCAAGTCAGAATTTCA 59.960 34.615 4.94 10.96 31.89 2.69
1978 3935 6.444633 AGTTCATTGCAAGTCAGAATTTCAG 58.555 36.000 4.94 0.00 0.00 3.02
1981 3938 2.585330 TGCAAGTCAGAATTTCAGGCA 58.415 42.857 0.00 0.00 0.00 4.75
1982 3939 2.294233 TGCAAGTCAGAATTTCAGGCAC 59.706 45.455 0.00 0.00 0.00 5.01
1984 3941 3.753272 GCAAGTCAGAATTTCAGGCACTA 59.247 43.478 0.00 0.00 36.02 2.74
1985 3942 4.397417 GCAAGTCAGAATTTCAGGCACTAT 59.603 41.667 0.00 0.00 36.02 2.12
1989 3946 7.129457 AGTCAGAATTTCAGGCACTATGATA 57.871 36.000 0.00 0.00 36.02 2.15
1990 3947 6.989169 AGTCAGAATTTCAGGCACTATGATAC 59.011 38.462 0.00 0.00 36.02 2.24
1991 3948 5.985530 TCAGAATTTCAGGCACTATGATACG 59.014 40.000 0.00 0.00 36.02 3.06
2005 3965 3.510388 TGATACGCTTTCAGGACTCAG 57.490 47.619 0.00 0.00 0.00 3.35
2009 3969 1.270358 ACGCTTTCAGGACTCAGTTCC 60.270 52.381 0.00 0.00 35.66 3.62
2023 3983 5.276440 ACTCAGTTCCCTGTAGAGATCAAT 58.724 41.667 0.00 0.00 39.82 2.57
2030 3990 4.100653 TCCCTGTAGAGATCAATTGCAGAG 59.899 45.833 0.00 0.00 0.00 3.35
2035 3995 7.010923 CCTGTAGAGATCAATTGCAGAGTTAAC 59.989 40.741 0.00 0.00 0.00 2.01
2037 3997 7.761704 TGTAGAGATCAATTGCAGAGTTAACTC 59.238 37.037 25.24 25.24 43.17 3.01
2064 4024 1.204941 ACTTAGCGTGATCAGTGGTCC 59.795 52.381 0.00 0.00 0.00 4.46
2066 4026 0.817654 TAGCGTGATCAGTGGTCCTG 59.182 55.000 0.00 0.00 42.97 3.86
2086 4046 6.262273 GTCCTGTTTTTCTTACTTGTGATCCA 59.738 38.462 0.00 0.00 0.00 3.41
2090 4050 9.185192 CTGTTTTTCTTACTTGTGATCCATTTC 57.815 33.333 0.00 0.00 0.00 2.17
2209 4169 2.945668 GTGGGGTATTGATCTGTTCAGC 59.054 50.000 0.00 0.00 35.27 4.26
2229 4193 6.378582 TCAGCCTTCAATTTACATTTCGTTC 58.621 36.000 0.00 0.00 0.00 3.95
2231 4195 6.808212 CAGCCTTCAATTTACATTTCGTTCAT 59.192 34.615 0.00 0.00 0.00 2.57
2242 4206 6.618287 ACATTTCGTTCATGAAGACTTTCA 57.382 33.333 8.80 0.00 46.67 2.69
2352 4316 1.312371 ACACGTGCAAACTGCCAACT 61.312 50.000 17.22 0.00 44.23 3.16
2463 4437 9.241317 GTGATATCAATTTAGCAAACTGGAATG 57.759 33.333 7.07 0.00 0.00 2.67
2472 4446 7.817418 TTAGCAAACTGGAATGGTATAATCC 57.183 36.000 0.00 0.00 30.45 3.01
2475 4449 3.418684 ACTGGAATGGTATAATCCGCC 57.581 47.619 0.00 0.00 35.96 6.13
2479 4455 3.904965 TGGAATGGTATAATCCGCCTACA 59.095 43.478 0.00 0.00 35.96 2.74
2567 4548 3.633986 CCAAAATTCTACCAGATCCAGCC 59.366 47.826 0.00 0.00 0.00 4.85
2568 4549 2.918712 AATTCTACCAGATCCAGCCG 57.081 50.000 0.00 0.00 0.00 5.52
2584 4565 0.171231 GCCGGAAATGCTCCTTGAAC 59.829 55.000 5.05 0.00 42.85 3.18
2590 4571 3.694566 GGAAATGCTCCTTGAACGGTTAT 59.305 43.478 0.00 0.00 41.61 1.89
2600 4581 5.765677 TCCTTGAACGGTTATGTTTCAATCA 59.234 36.000 0.00 0.00 30.75 2.57
2613 4594 1.372582 TCAATCACGCATTGGAGCTC 58.627 50.000 4.71 4.71 42.18 4.09
2619 4600 4.883354 GCATTGGAGCTCCGGGGG 62.883 72.222 27.43 17.18 39.43 5.40
2625 4608 1.378646 GGAGCTCCGGGGGAAAAAG 60.379 63.158 19.06 0.00 0.00 2.27
2633 4618 1.074244 CCGGGGGAAAAAGTACTTCCA 59.926 52.381 8.95 0.00 43.64 3.53
2635 4620 3.427573 CGGGGGAAAAAGTACTTCCATT 58.572 45.455 8.95 4.85 43.64 3.16
2647 4632 6.128138 AGTACTTCCATTGCCTAAAAGAGT 57.872 37.500 0.00 0.00 0.00 3.24
2650 4635 4.944317 ACTTCCATTGCCTAAAAGAGTAGC 59.056 41.667 0.00 0.00 0.00 3.58
2656 4641 7.283127 TCCATTGCCTAAAAGAGTAGCTTATTG 59.717 37.037 0.00 0.00 35.24 1.90
2659 4644 6.947464 TGCCTAAAAGAGTAGCTTATTGAGT 58.053 36.000 0.00 0.00 35.24 3.41
2661 4646 6.819146 GCCTAAAAGAGTAGCTTATTGAGTGT 59.181 38.462 0.00 0.00 35.24 3.55
2667 4652 7.897575 AGAGTAGCTTATTGAGTGTCTTTTG 57.102 36.000 0.00 0.00 0.00 2.44
2678 4663 6.509418 TGAGTGTCTTTTGCTAAAAACTGT 57.491 33.333 7.62 0.00 31.94 3.55
2777 4774 3.430453 TGCCAGGTAAAGGAAATTCAGG 58.570 45.455 0.00 0.00 0.00 3.86
2778 4775 3.075283 TGCCAGGTAAAGGAAATTCAGGA 59.925 43.478 0.00 0.00 0.00 3.86
2779 4776 4.086457 GCCAGGTAAAGGAAATTCAGGAA 58.914 43.478 0.00 0.00 0.00 3.36
2780 4777 4.711846 GCCAGGTAAAGGAAATTCAGGAAT 59.288 41.667 0.00 0.00 0.00 3.01
2781 4778 5.163509 GCCAGGTAAAGGAAATTCAGGAATC 60.164 44.000 0.00 0.00 0.00 2.52
2782 4779 5.951747 CCAGGTAAAGGAAATTCAGGAATCA 59.048 40.000 0.00 0.00 0.00 2.57
2783 4780 6.096001 CCAGGTAAAGGAAATTCAGGAATCAG 59.904 42.308 0.00 0.00 0.00 2.90
2849 4851 8.200120 AGCTATGCTCATTTTTATCCCTTTTTC 58.800 33.333 0.00 0.00 30.62 2.29
2864 4866 3.433456 CCTTTTTCCAACCAAATGCCACT 60.433 43.478 0.00 0.00 0.00 4.00
2874 4876 2.352421 CCAAATGCCACTGAAGAAGCAG 60.352 50.000 0.00 0.00 38.89 4.24
2983 4986 1.819928 TGGACATATGCACAAACGCT 58.180 45.000 1.58 0.00 0.00 5.07
3075 5078 4.574892 TCTGAAAGGACGCACATGATAAA 58.425 39.130 0.00 0.00 0.00 1.40
3076 5079 5.185454 TCTGAAAGGACGCACATGATAAAT 58.815 37.500 0.00 0.00 0.00 1.40
3077 5080 6.345298 TCTGAAAGGACGCACATGATAAATA 58.655 36.000 0.00 0.00 0.00 1.40
3078 5081 6.257849 TCTGAAAGGACGCACATGATAAATAC 59.742 38.462 0.00 0.00 0.00 1.89
3079 5082 6.112734 TGAAAGGACGCACATGATAAATACT 58.887 36.000 0.00 0.00 0.00 2.12
3134 5137 5.945191 GGCTAAGTACGAATATACTCCCTCT 59.055 44.000 0.00 0.00 34.18 3.69
3135 5138 6.127952 GGCTAAGTACGAATATACTCCCTCTG 60.128 46.154 0.00 0.00 34.18 3.35
3136 5139 6.430616 GCTAAGTACGAATATACTCCCTCTGT 59.569 42.308 0.00 0.00 34.18 3.41
3137 5140 6.880942 AAGTACGAATATACTCCCTCTGTC 57.119 41.667 0.00 0.00 34.18 3.51
3145 5148 2.642171 ACTCCCTCTGTCCCACAATA 57.358 50.000 0.00 0.00 0.00 1.90
3148 5151 4.631234 ACTCCCTCTGTCCCACAATATAA 58.369 43.478 0.00 0.00 0.00 0.98
3149 5152 4.656112 ACTCCCTCTGTCCCACAATATAAG 59.344 45.833 0.00 0.00 0.00 1.73
3150 5153 4.890988 TCCCTCTGTCCCACAATATAAGA 58.109 43.478 0.00 0.00 0.00 2.10
3151 5154 5.285401 TCCCTCTGTCCCACAATATAAGAA 58.715 41.667 0.00 0.00 0.00 2.52
3152 5155 5.130477 TCCCTCTGTCCCACAATATAAGAAC 59.870 44.000 0.00 0.00 0.00 3.01
3153 5156 5.050490 CCTCTGTCCCACAATATAAGAACG 58.950 45.833 0.00 0.00 0.00 3.95
3154 5157 5.395324 CCTCTGTCCCACAATATAAGAACGT 60.395 44.000 0.00 0.00 0.00 3.99
3155 5158 6.045072 TCTGTCCCACAATATAAGAACGTT 57.955 37.500 0.00 0.00 0.00 3.99
3156 5159 6.469410 TCTGTCCCACAATATAAGAACGTTT 58.531 36.000 0.46 0.00 0.00 3.60
3157 5160 6.370442 TCTGTCCCACAATATAAGAACGTTTG 59.630 38.462 0.46 0.00 0.00 2.93
3158 5161 5.998981 TGTCCCACAATATAAGAACGTTTGT 59.001 36.000 0.46 0.00 0.00 2.83
3159 5162 6.148150 TGTCCCACAATATAAGAACGTTTGTC 59.852 38.462 0.46 0.00 0.00 3.18
3160 5163 6.148150 GTCCCACAATATAAGAACGTTTGTCA 59.852 38.462 0.46 0.00 0.00 3.58
3161 5164 6.711194 TCCCACAATATAAGAACGTTTGTCAA 59.289 34.615 0.46 0.00 0.00 3.18
3162 5165 7.021196 CCCACAATATAAGAACGTTTGTCAAG 58.979 38.462 0.46 0.00 0.00 3.02
3193 5412 4.666253 TGCCCCTGCTTCACCTGC 62.666 66.667 0.00 0.00 38.71 4.85
3213 5446 4.769688 TGCGACTGAAGATGGATTTGTAT 58.230 39.130 0.00 0.00 0.00 2.29
3215 5466 4.572389 GCGACTGAAGATGGATTTGTATGT 59.428 41.667 0.00 0.00 0.00 2.29
3249 5500 2.506472 GCCGGCTTCTTCCCTAGG 59.494 66.667 22.15 0.06 0.00 3.02
3397 5771 3.587797 AGCAAAGAATTGGCACTGATG 57.412 42.857 0.00 0.00 37.02 3.07
3453 5827 7.601886 AGCTACGTATATACTACCTGTGTGTAG 59.398 40.741 11.05 11.26 43.13 2.74
3478 5917 3.853355 ACATCATTGAGGGATCCTGTC 57.147 47.619 12.58 9.59 31.76 3.51
3525 5966 3.368220 CCATCTCATCATCATCGTCTCCC 60.368 52.174 0.00 0.00 0.00 4.30
3526 5967 3.235750 TCTCATCATCATCGTCTCCCT 57.764 47.619 0.00 0.00 0.00 4.20
3527 5968 3.153130 TCTCATCATCATCGTCTCCCTC 58.847 50.000 0.00 0.00 0.00 4.30
3528 5969 2.889678 CTCATCATCATCGTCTCCCTCA 59.110 50.000 0.00 0.00 0.00 3.86
3529 5970 2.889678 TCATCATCATCGTCTCCCTCAG 59.110 50.000 0.00 0.00 0.00 3.35
3541 5985 0.619832 TCCCTCAGAGCTGGCATTCT 60.620 55.000 0.00 0.00 0.00 2.40
3631 6075 0.944311 ACGTGCACTGTTCCATCGTC 60.944 55.000 16.19 0.00 0.00 4.20
3634 6078 0.602638 TGCACTGTTCCATCGTCCAC 60.603 55.000 0.00 0.00 0.00 4.02
3656 6100 1.227409 GCCTAGAGAGCGGCCTTTC 60.227 63.158 0.00 0.00 40.43 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.334947 TGCACAGGAAATCAAATATTTTTCAAA 57.665 25.926 11.38 0.00 32.30 2.69
21 22 8.772705 GTGCACAGGAAATCAAATATTTTTCAA 58.227 29.630 13.17 0.00 32.30 2.69
22 23 8.149647 AGTGCACAGGAAATCAAATATTTTTCA 58.850 29.630 21.04 0.00 32.30 2.69
23 24 8.538409 AGTGCACAGGAAATCAAATATTTTTC 57.462 30.769 21.04 0.49 0.00 2.29
24 25 9.423061 GTAGTGCACAGGAAATCAAATATTTTT 57.577 29.630 21.04 0.00 0.00 1.94
25 26 8.806146 AGTAGTGCACAGGAAATCAAATATTTT 58.194 29.630 21.04 0.00 0.00 1.82
26 27 8.246180 CAGTAGTGCACAGGAAATCAAATATTT 58.754 33.333 21.04 0.00 0.00 1.40
27 28 7.611467 TCAGTAGTGCACAGGAAATCAAATATT 59.389 33.333 21.04 0.00 0.00 1.28
28 29 7.112122 TCAGTAGTGCACAGGAAATCAAATAT 58.888 34.615 21.04 0.00 0.00 1.28
29 30 6.472016 TCAGTAGTGCACAGGAAATCAAATA 58.528 36.000 21.04 0.00 0.00 1.40
30 31 5.316167 TCAGTAGTGCACAGGAAATCAAAT 58.684 37.500 21.04 0.00 0.00 2.32
31 32 4.713553 TCAGTAGTGCACAGGAAATCAAA 58.286 39.130 21.04 0.00 0.00 2.69
32 33 4.350368 TCAGTAGTGCACAGGAAATCAA 57.650 40.909 21.04 0.00 0.00 2.57
33 34 4.350368 TTCAGTAGTGCACAGGAAATCA 57.650 40.909 21.04 0.00 0.00 2.57
34 35 5.886960 AATTCAGTAGTGCACAGGAAATC 57.113 39.130 21.04 1.02 0.00 2.17
35 36 5.536161 ACAAATTCAGTAGTGCACAGGAAAT 59.464 36.000 21.04 8.92 0.00 2.17
36 37 4.887071 ACAAATTCAGTAGTGCACAGGAAA 59.113 37.500 21.04 6.87 0.00 3.13
37 38 4.460263 ACAAATTCAGTAGTGCACAGGAA 58.540 39.130 21.04 15.95 0.00 3.36
38 39 4.085357 ACAAATTCAGTAGTGCACAGGA 57.915 40.909 21.04 7.63 0.00 3.86
39 40 4.275689 TCAACAAATTCAGTAGTGCACAGG 59.724 41.667 21.04 5.16 0.00 4.00
40 41 5.422666 TCAACAAATTCAGTAGTGCACAG 57.577 39.130 21.04 5.94 0.00 3.66
41 42 5.826601 TTCAACAAATTCAGTAGTGCACA 57.173 34.783 21.04 1.84 0.00 4.57
42 43 8.970691 ATATTTCAACAAATTCAGTAGTGCAC 57.029 30.769 9.40 9.40 33.95 4.57
43 44 9.979578 AAATATTTCAACAAATTCAGTAGTGCA 57.020 25.926 0.00 0.00 33.95 4.57
48 49 9.134734 GGCGAAAATATTTCAACAAATTCAGTA 57.865 29.630 0.10 0.00 33.95 2.74
49 50 7.148820 CGGCGAAAATATTTCAACAAATTCAGT 60.149 33.333 0.00 0.00 33.95 3.41
50 51 7.061673 TCGGCGAAAATATTTCAACAAATTCAG 59.938 33.333 7.35 0.00 33.95 3.02
51 52 6.863645 TCGGCGAAAATATTTCAACAAATTCA 59.136 30.769 7.35 0.00 33.95 2.57
52 53 7.271936 TCGGCGAAAATATTTCAACAAATTC 57.728 32.000 7.35 0.00 33.95 2.17
53 54 7.644986 TTCGGCGAAAATATTTCAACAAATT 57.355 28.000 21.53 0.00 33.95 1.82
54 55 7.506474 GTTTCGGCGAAAATATTTCAACAAAT 58.494 30.769 33.66 0.00 33.14 2.32
55 56 6.345093 CGTTTCGGCGAAAATATTTCAACAAA 60.345 34.615 33.66 6.71 33.14 2.83
56 57 5.115773 CGTTTCGGCGAAAATATTTCAACAA 59.884 36.000 33.66 7.18 33.14 2.83
57 58 4.613448 CGTTTCGGCGAAAATATTTCAACA 59.387 37.500 33.66 7.39 33.14 3.33
58 59 4.613866 ACGTTTCGGCGAAAATATTTCAAC 59.386 37.500 33.66 18.83 33.14 3.18
59 60 4.785417 ACGTTTCGGCGAAAATATTTCAA 58.215 34.783 33.66 8.72 33.14 2.69
60 61 4.407496 ACGTTTCGGCGAAAATATTTCA 57.593 36.364 33.66 9.49 33.14 2.69
61 62 8.703823 ATATTACGTTTCGGCGAAAATATTTC 57.296 30.769 33.66 19.92 34.15 2.17
62 63 9.505995 AAATATTACGTTTCGGCGAAAATATTT 57.494 25.926 32.03 32.03 41.59 1.40
63 64 9.161684 GAAATATTACGTTTCGGCGAAAATATT 57.838 29.630 33.66 29.96 40.68 1.28
64 65 8.336806 TGAAATATTACGTTTCGGCGAAAATAT 58.663 29.630 33.66 26.92 38.18 1.28
65 66 7.682824 TGAAATATTACGTTTCGGCGAAAATA 58.317 30.769 33.66 26.07 38.18 1.40
66 67 6.544622 TGAAATATTACGTTTCGGCGAAAAT 58.455 32.000 33.66 26.05 38.18 1.82
67 68 5.924786 TGAAATATTACGTTTCGGCGAAAA 58.075 33.333 33.66 20.26 38.18 2.29
68 69 5.120519 ACTGAAATATTACGTTTCGGCGAAA 59.879 36.000 29.31 29.31 42.81 3.46
69 70 4.626604 ACTGAAATATTACGTTTCGGCGAA 59.373 37.500 19.83 19.83 42.81 4.70
70 71 4.031991 CACTGAAATATTACGTTTCGGCGA 59.968 41.667 4.99 4.99 42.81 5.54
71 72 4.201647 ACACTGAAATATTACGTTTCGGCG 60.202 41.667 0.00 0.00 42.81 6.46
72 73 5.063060 AGACACTGAAATATTACGTTTCGGC 59.937 40.000 0.00 0.00 42.81 5.54
73 74 6.642683 AGACACTGAAATATTACGTTTCGG 57.357 37.500 0.00 0.00 43.98 4.30
74 75 8.390854 AGTAGACACTGAAATATTACGTTTCG 57.609 34.615 0.00 0.00 38.18 3.46
137 138 2.365293 GCCCATGGTTTTCACTTTCAGT 59.635 45.455 11.73 0.00 0.00 3.41
138 139 2.364970 TGCCCATGGTTTTCACTTTCAG 59.635 45.455 11.73 0.00 0.00 3.02
139 140 2.392662 TGCCCATGGTTTTCACTTTCA 58.607 42.857 11.73 0.00 0.00 2.69
140 141 3.006752 TCATGCCCATGGTTTTCACTTTC 59.993 43.478 11.73 0.00 39.24 2.62
141 142 2.971330 TCATGCCCATGGTTTTCACTTT 59.029 40.909 11.73 0.00 39.24 2.66
142 143 2.564062 CTCATGCCCATGGTTTTCACTT 59.436 45.455 11.73 0.00 39.24 3.16
143 144 2.173519 CTCATGCCCATGGTTTTCACT 58.826 47.619 11.73 0.00 39.24 3.41
144 145 1.895131 ACTCATGCCCATGGTTTTCAC 59.105 47.619 11.73 0.00 39.24 3.18
145 146 1.894466 CACTCATGCCCATGGTTTTCA 59.106 47.619 11.73 3.38 39.24 2.69
146 147 1.205417 CCACTCATGCCCATGGTTTTC 59.795 52.381 11.73 0.00 39.24 2.29
147 148 1.269012 CCACTCATGCCCATGGTTTT 58.731 50.000 11.73 0.00 39.24 2.43
148 149 0.615544 CCCACTCATGCCCATGGTTT 60.616 55.000 11.73 0.00 39.24 3.27
149 150 1.000739 CCCACTCATGCCCATGGTT 59.999 57.895 11.73 0.00 39.24 3.67
150 151 2.685366 CCCACTCATGCCCATGGT 59.315 61.111 11.73 3.17 39.24 3.55
151 152 2.123597 CCCCACTCATGCCCATGG 60.124 66.667 4.14 4.14 39.24 3.66
152 153 1.000739 AACCCCACTCATGCCCATG 59.999 57.895 1.86 1.86 40.09 3.66
153 154 1.000739 CAACCCCACTCATGCCCAT 59.999 57.895 0.00 0.00 0.00 4.00
154 155 2.440147 CAACCCCACTCATGCCCA 59.560 61.111 0.00 0.00 0.00 5.36
155 156 2.362889 CCAACCCCACTCATGCCC 60.363 66.667 0.00 0.00 0.00 5.36
161 162 1.152756 AGTGTTGCCAACCCCACTC 60.153 57.895 4.90 0.00 32.97 3.51
163 164 1.152756 AGAGTGTTGCCAACCCCAC 60.153 57.895 4.90 0.00 0.00 4.61
198 199 6.073331 ACAAACACAAACTTGTCCAAAACATG 60.073 34.615 0.00 0.00 39.91 3.21
249 258 4.700213 ACAATTCTCAGAATACCCCAAACG 59.300 41.667 0.00 0.00 0.00 3.60
384 394 5.991606 CAGAGACTCAACAACATTCTTGGTA 59.008 40.000 5.02 0.00 0.00 3.25
395 405 0.318441 CCCGAGCAGAGACTCAACAA 59.682 55.000 5.02 0.00 36.42 2.83
399 409 1.188219 AAAGCCCGAGCAGAGACTCA 61.188 55.000 5.02 0.00 43.56 3.41
406 416 1.399791 GATTGAGAAAAGCCCGAGCAG 59.600 52.381 0.00 0.00 43.56 4.24
491 584 6.014156 AGTTTCAGCTACCATATGTAGGGATC 60.014 42.308 1.24 0.00 45.97 3.36
563 716 7.874528 TCTGCAATCCATGTATACAAGACATAG 59.125 37.037 10.14 7.27 35.75 2.23
687 850 6.148645 ACCAAATTGTCCAAAAGTTTCACAAC 59.851 34.615 8.95 0.00 30.04 3.32
689 852 5.641209 CACCAAATTGTCCAAAAGTTTCACA 59.359 36.000 0.00 0.00 0.00 3.58
690 853 5.064579 CCACCAAATTGTCCAAAAGTTTCAC 59.935 40.000 0.00 0.00 0.00 3.18
691 854 5.181748 CCACCAAATTGTCCAAAAGTTTCA 58.818 37.500 0.00 0.00 0.00 2.69
819 2707 3.043999 AATGCGGCCCAGACTACCC 62.044 63.158 0.00 0.00 0.00 3.69
875 2787 3.680786 CGTCAGCGACCTCCACCA 61.681 66.667 0.00 0.00 41.33 4.17
922 2842 1.743772 CGTAGGAATCAACCAGCCAGG 60.744 57.143 0.00 0.00 45.67 4.45
945 2866 3.963222 GCTGTGAGCCTGTGACAG 58.037 61.111 5.42 5.42 40.14 3.51
986 2907 4.802051 CCATGGGCGTGGACTGGG 62.802 72.222 2.85 0.00 42.02 4.45
1047 2968 3.017581 GGGGTGCAGGATGGGAGT 61.018 66.667 0.00 0.00 35.86 3.85
1079 3000 0.984961 CTGGATTGAGGGGGCTGAGA 60.985 60.000 0.00 0.00 0.00 3.27
1137 3058 2.387125 TAATACGTACCGGCGGCGAC 62.387 60.000 34.49 22.92 35.98 5.19
1263 3186 4.728110 TCGTCGGCGAAGGAGGGA 62.728 66.667 21.95 5.58 44.92 4.20
1335 3258 1.962321 GAGAGAAGAAGGGGACGGGC 61.962 65.000 0.00 0.00 0.00 6.13
1378 3306 2.769893 ACAAAAATCACTTGCATGGCC 58.230 42.857 0.00 0.00 0.00 5.36
1494 3429 8.927721 CAAAGATTGAAATATGTTGCATGTGAA 58.072 29.630 0.00 0.00 0.00 3.18
1537 3475 6.758416 TCAGTCTCTGGTTTATCAATTCATCG 59.242 38.462 0.00 0.00 31.51 3.84
1575 3513 8.948936 CAGATGTAACAATCACACAGCTGTGC 62.949 46.154 39.95 23.39 46.41 4.57
1579 3517 4.645535 ACAGATGTAACAATCACACAGCT 58.354 39.130 0.00 0.00 39.36 4.24
1616 3564 0.239347 CTACAGCTTTGTGCACAGGC 59.761 55.000 27.97 27.97 45.94 4.85
1617 3565 0.877071 CCTACAGCTTTGTGCACAGG 59.123 55.000 20.59 17.21 45.94 4.00
1713 3663 1.690893 TGCTCAGTCTCTGAAGCACTT 59.309 47.619 14.65 0.00 40.18 3.16
1819 3776 4.462834 TGTAAGAGAAGAGATGCCGAGAAA 59.537 41.667 0.00 0.00 0.00 2.52
1825 3782 7.383102 TGAAATTTGTAAGAGAAGAGATGCC 57.617 36.000 0.00 0.00 0.00 4.40
1862 3819 1.768684 GAGGTGGGAACAGTGCCTGA 61.769 60.000 8.91 0.00 44.46 3.86
1877 3834 3.391296 TGAAAAGGACTAGCAACAGAGGT 59.609 43.478 0.00 0.00 0.00 3.85
1937 3894 3.843619 TGAACTCACCTACCATCATGGAA 59.156 43.478 11.90 0.00 40.96 3.53
1972 3929 4.342862 AGCGTATCATAGTGCCTGAAAT 57.657 40.909 0.00 0.00 0.00 2.17
1973 3930 3.819564 AGCGTATCATAGTGCCTGAAA 57.180 42.857 0.00 0.00 0.00 2.69
1976 3933 3.457234 TGAAAGCGTATCATAGTGCCTG 58.543 45.455 0.00 0.00 0.00 4.85
1977 3934 3.493350 CCTGAAAGCGTATCATAGTGCCT 60.493 47.826 0.00 0.00 0.00 4.75
1978 3935 2.802816 CCTGAAAGCGTATCATAGTGCC 59.197 50.000 0.00 0.00 0.00 5.01
1981 3938 4.645136 TGAGTCCTGAAAGCGTATCATAGT 59.355 41.667 0.00 0.00 0.00 2.12
1982 3939 5.188327 TGAGTCCTGAAAGCGTATCATAG 57.812 43.478 0.00 0.00 0.00 2.23
1984 3941 3.449018 ACTGAGTCCTGAAAGCGTATCAT 59.551 43.478 0.00 0.00 0.00 2.45
1985 3942 2.826128 ACTGAGTCCTGAAAGCGTATCA 59.174 45.455 0.00 0.00 0.00 2.15
1989 3946 1.270358 GGAACTGAGTCCTGAAAGCGT 60.270 52.381 0.00 0.00 34.56 5.07
1990 3947 1.433534 GGAACTGAGTCCTGAAAGCG 58.566 55.000 0.00 0.00 34.56 4.68
1991 3948 1.349357 AGGGAACTGAGTCCTGAAAGC 59.651 52.381 0.00 0.00 41.13 3.51
2005 3965 4.517285 TGCAATTGATCTCTACAGGGAAC 58.483 43.478 10.34 0.00 0.00 3.62
2009 3969 5.021033 ACTCTGCAATTGATCTCTACAGG 57.979 43.478 10.34 2.55 0.00 4.00
2023 3983 2.902705 ACGGTGAGTTAACTCTGCAA 57.097 45.000 30.47 12.38 43.25 4.08
2030 3990 4.089065 CACGCTAAGTTACGGTGAGTTAAC 59.911 45.833 0.00 0.00 0.00 2.01
2035 3995 2.624316 TCACGCTAAGTTACGGTGAG 57.376 50.000 7.02 0.00 0.00 3.51
2037 3997 2.852413 CTGATCACGCTAAGTTACGGTG 59.148 50.000 0.00 6.19 0.00 4.94
2064 4024 9.185192 GAAATGGATCACAAGTAAGAAAAACAG 57.815 33.333 0.00 0.00 0.00 3.16
2090 4050 1.989165 GTTGCTCTAGCTTCACGAGTG 59.011 52.381 3.26 0.00 42.66 3.51
2132 4092 2.291209 TCACTGAACATGTGCCCATT 57.709 45.000 0.00 0.00 35.58 3.16
2183 4143 5.905331 TGAACAGATCAATACCCCACTAGAT 59.095 40.000 0.00 0.00 34.30 1.98
2186 4146 4.141711 GCTGAACAGATCAATACCCCACTA 60.142 45.833 5.97 0.00 37.67 2.74
2209 4169 8.741101 TTCATGAACGAAATGTAAATTGAAGG 57.259 30.769 3.38 0.00 0.00 3.46
2352 4316 5.784578 ATATAACGCATAGACACACCTGA 57.215 39.130 0.00 0.00 0.00 3.86
2409 4373 6.663523 CCCTTTGGAAGACATAAAGGTATTGT 59.336 38.462 12.42 0.00 45.66 2.71
2463 4437 4.040095 AGGTTTCTGTAGGCGGATTATACC 59.960 45.833 0.00 0.00 0.00 2.73
2472 4446 0.798776 CAAGCAGGTTTCTGTAGGCG 59.201 55.000 0.00 0.00 42.78 5.52
2526 4506 4.751767 TGGGTGAGCAAAAAGTTTTCAT 57.248 36.364 0.32 0.00 0.00 2.57
2539 4519 3.686016 TCTGGTAGAATTTTGGGTGAGC 58.314 45.455 0.00 0.00 0.00 4.26
2584 4565 3.463533 TGCGTGATTGAAACATAACCG 57.536 42.857 0.00 0.00 0.00 4.44
2590 4571 2.351641 GCTCCAATGCGTGATTGAAACA 60.352 45.455 9.98 0.00 43.87 2.83
2600 4581 4.473520 CCCGGAGCTCCAATGCGT 62.474 66.667 31.67 0.00 38.13 5.24
2613 4594 1.074244 TGGAAGTACTTTTTCCCCCGG 59.926 52.381 10.02 0.00 42.79 5.73
2618 4599 6.584185 TTAGGCAATGGAAGTACTTTTTCC 57.416 37.500 10.02 7.36 43.56 3.13
2619 4600 8.357402 TCTTTTAGGCAATGGAAGTACTTTTTC 58.643 33.333 10.02 3.82 0.00 2.29
2625 4608 6.037281 GCTACTCTTTTAGGCAATGGAAGTAC 59.963 42.308 0.00 0.00 0.00 2.73
2633 4618 8.049721 ACTCAATAAGCTACTCTTTTAGGCAAT 58.950 33.333 0.00 0.00 36.25 3.56
2635 4620 6.818644 CACTCAATAAGCTACTCTTTTAGGCA 59.181 38.462 0.00 0.00 36.25 4.75
2647 4632 8.615878 TTTAGCAAAAGACACTCAATAAGCTA 57.384 30.769 0.00 0.00 0.00 3.32
2650 4635 9.736023 AGTTTTTAGCAAAAGACACTCAATAAG 57.264 29.630 0.00 0.00 33.28 1.73
2656 4641 6.806739 ACAACAGTTTTTAGCAAAAGACACTC 59.193 34.615 0.00 0.00 33.28 3.51
2659 4644 6.919721 AGACAACAGTTTTTAGCAAAAGACA 58.080 32.000 0.00 0.00 33.28 3.41
2661 4646 9.120538 AGATAGACAACAGTTTTTAGCAAAAGA 57.879 29.630 0.00 0.00 32.32 2.52
2667 4652 8.774586 TCTGAAAGATAGACAACAGTTTTTAGC 58.225 33.333 0.00 0.00 38.67 3.09
2777 4774 6.485984 AGCAAGATGTACATGATTCCTGATTC 59.514 38.462 14.43 0.00 0.00 2.52
2778 4775 6.363065 AGCAAGATGTACATGATTCCTGATT 58.637 36.000 14.43 0.00 0.00 2.57
2779 4776 5.938279 AGCAAGATGTACATGATTCCTGAT 58.062 37.500 14.43 0.00 0.00 2.90
2780 4777 5.363562 AGCAAGATGTACATGATTCCTGA 57.636 39.130 14.43 0.00 0.00 3.86
2781 4778 6.348295 GCATAGCAAGATGTACATGATTCCTG 60.348 42.308 14.43 0.61 0.00 3.86
2782 4779 5.704515 GCATAGCAAGATGTACATGATTCCT 59.295 40.000 14.43 6.11 0.00 3.36
2783 4780 5.704515 AGCATAGCAAGATGTACATGATTCC 59.295 40.000 14.43 0.00 0.00 3.01
2849 4851 1.962807 TCTTCAGTGGCATTTGGTTGG 59.037 47.619 0.00 0.00 0.00 3.77
2864 4866 5.227569 TGTTATTGGAGACTGCTTCTTCA 57.772 39.130 0.00 0.00 38.18 3.02
2874 4876 4.154195 ACGAGCAACATTGTTATTGGAGAC 59.846 41.667 0.86 0.00 0.00 3.36
2931 4934 2.358737 GGGCCTTGTCCGTGTCAG 60.359 66.667 0.84 0.00 0.00 3.51
2932 4935 2.847234 AGGGCCTTGTCCGTGTCA 60.847 61.111 0.00 0.00 29.39 3.58
3104 5107 8.579863 GGAGTATATTCGTACTTAGCCCTAAAA 58.420 37.037 0.00 0.00 35.14 1.52
3105 5108 7.177392 GGGAGTATATTCGTACTTAGCCCTAAA 59.823 40.741 0.00 0.00 35.16 1.85
3106 5109 6.660949 GGGAGTATATTCGTACTTAGCCCTAA 59.339 42.308 0.00 0.00 35.16 2.69
3107 5110 6.012157 AGGGAGTATATTCGTACTTAGCCCTA 60.012 42.308 9.05 0.00 41.36 3.53
3108 5111 5.015515 GGGAGTATATTCGTACTTAGCCCT 58.984 45.833 0.00 0.00 35.16 5.19
3109 5112 5.015515 AGGGAGTATATTCGTACTTAGCCC 58.984 45.833 0.00 0.00 36.89 5.19
3110 5113 5.945191 AGAGGGAGTATATTCGTACTTAGCC 59.055 44.000 0.00 0.00 35.14 3.93
3111 5114 6.430616 ACAGAGGGAGTATATTCGTACTTAGC 59.569 42.308 0.00 0.00 35.14 3.09
3112 5115 7.119553 GGACAGAGGGAGTATATTCGTACTTAG 59.880 44.444 0.00 0.00 35.14 2.18
3113 5116 6.939163 GGACAGAGGGAGTATATTCGTACTTA 59.061 42.308 0.00 0.00 35.14 2.24
3114 5117 5.769162 GGACAGAGGGAGTATATTCGTACTT 59.231 44.000 0.00 0.00 35.14 2.24
3115 5118 5.315348 GGACAGAGGGAGTATATTCGTACT 58.685 45.833 0.00 0.00 37.61 2.73
3116 5119 4.458642 GGGACAGAGGGAGTATATTCGTAC 59.541 50.000 0.00 0.00 0.00 3.67
3117 5120 4.105217 TGGGACAGAGGGAGTATATTCGTA 59.895 45.833 0.00 0.00 0.00 3.43
3118 5121 3.117246 TGGGACAGAGGGAGTATATTCGT 60.117 47.826 0.00 0.00 0.00 3.85
3119 5122 3.256136 GTGGGACAGAGGGAGTATATTCG 59.744 52.174 0.00 0.00 41.80 3.34
3120 5123 4.223953 TGTGGGACAGAGGGAGTATATTC 58.776 47.826 0.00 0.00 41.80 1.75
3121 5124 4.280789 TGTGGGACAGAGGGAGTATATT 57.719 45.455 0.00 0.00 41.80 1.28
3122 5125 3.993658 TGTGGGACAGAGGGAGTATAT 57.006 47.619 0.00 0.00 41.80 0.86
3123 5126 3.769189 TTGTGGGACAGAGGGAGTATA 57.231 47.619 0.00 0.00 41.80 1.47
3124 5127 2.642171 TTGTGGGACAGAGGGAGTAT 57.358 50.000 0.00 0.00 41.80 2.12
3134 5137 5.998981 ACAAACGTTCTTATATTGTGGGACA 59.001 36.000 0.00 0.00 33.29 4.02
3135 5138 6.148150 TGACAAACGTTCTTATATTGTGGGAC 59.852 38.462 0.00 0.00 34.59 4.46
3136 5139 6.231951 TGACAAACGTTCTTATATTGTGGGA 58.768 36.000 0.00 0.00 34.59 4.37
3137 5140 6.489127 TGACAAACGTTCTTATATTGTGGG 57.511 37.500 0.00 0.00 34.59 4.61
3145 5148 3.058224 GCTGGCTTGACAAACGTTCTTAT 60.058 43.478 0.00 0.00 0.00 1.73
3148 5151 0.663153 GCTGGCTTGACAAACGTTCT 59.337 50.000 0.00 0.00 0.00 3.01
3149 5152 0.380378 TGCTGGCTTGACAAACGTTC 59.620 50.000 0.00 0.00 0.00 3.95
3150 5153 0.814457 TTGCTGGCTTGACAAACGTT 59.186 45.000 0.00 0.00 0.00 3.99
3151 5154 1.032014 ATTGCTGGCTTGACAAACGT 58.968 45.000 0.00 0.00 0.00 3.99
3152 5155 1.411394 CATTGCTGGCTTGACAAACG 58.589 50.000 0.00 0.00 0.00 3.60
3153 5156 1.787012 CCATTGCTGGCTTGACAAAC 58.213 50.000 0.00 0.00 35.23 2.93
3193 5412 5.007039 CCACATACAAATCCATCTTCAGTCG 59.993 44.000 0.00 0.00 0.00 4.18
3236 5487 1.405661 CCGTTCACCTAGGGAAGAAGC 60.406 57.143 14.81 8.11 0.00 3.86
3249 5500 4.715520 CACATCATGCTATACCGTTCAC 57.284 45.455 0.00 0.00 0.00 3.18
3293 5552 2.430332 ACATCCCAATTAAACCCATGCG 59.570 45.455 0.00 0.00 0.00 4.73
3397 5771 3.001736 GCGATAAAGAGGACAGAACATGC 59.998 47.826 0.00 0.00 0.00 4.06
3398 5772 4.269603 CAGCGATAAAGAGGACAGAACATG 59.730 45.833 0.00 0.00 0.00 3.21
3399 5773 4.160439 TCAGCGATAAAGAGGACAGAACAT 59.840 41.667 0.00 0.00 0.00 2.71
3400 5774 3.509967 TCAGCGATAAAGAGGACAGAACA 59.490 43.478 0.00 0.00 0.00 3.18
3453 5827 2.417719 GATCCCTCAATGATGTACGCC 58.582 52.381 0.00 0.00 0.00 5.68
3478 5917 3.059597 ACGCAAGAACAAATCTGAGAACG 60.060 43.478 0.00 0.00 38.79 3.95
3528 5969 1.913722 CCCAGAGAATGCCAGCTCT 59.086 57.895 0.00 0.00 41.95 4.09
3529 5970 1.823041 GCCCAGAGAATGCCAGCTC 60.823 63.158 0.00 0.00 0.00 4.09
3631 6075 1.007964 CGCTCTCTAGGCATCGTGG 60.008 63.158 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.