Multiple sequence alignment - TraesCS2D01G318800

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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 TraesCS2D01G318800 chr2D 100.000 7001 0 0 1 7001 409254473 409261473 0.000000e+00 12929.0
1 TraesCS2D01G318800 chr2D 80.994 342 47 14 4664 4996 106350597 106350265 9.010000e-64 255.0
2 TraesCS2D01G318800 chr2B 98.177 2853 44 6 1178 4025 483996487 483999336 0.000000e+00 4974.0
3 TraesCS2D01G318800 chr2B 97.793 1042 18 3 4996 6035 483999332 484000370 0.000000e+00 1792.0
4 TraesCS2D01G318800 chr2B 98.057 978 14 3 6028 7001 484004748 484005724 0.000000e+00 1696.0
5 TraesCS2D01G318800 chr2B 90.541 814 46 15 325 1112 483995380 483996188 0.000000e+00 1048.0
6 TraesCS2D01G318800 chr2B 94.419 215 11 1 15 229 520903479 520903266 5.240000e-86 329.0
7 TraesCS2D01G318800 chr2B 90.698 215 18 2 15 229 122259076 122259288 1.150000e-72 285.0
8 TraesCS2D01G318800 chr2B 86.740 181 23 1 4026 4205 526388507 526388327 4.280000e-47 200.0
9 TraesCS2D01G318800 chr2B 94.643 112 6 0 233 344 483995248 483995359 2.600000e-39 174.0
10 TraesCS2D01G318800 chr5B 88.386 2738 181 65 895 3609 13280656 13278033 0.000000e+00 3168.0
11 TraesCS2D01G318800 chr5B 89.150 1742 106 42 5219 6925 13277356 13275663 0.000000e+00 2093.0
12 TraesCS2D01G318800 chr5B 91.489 423 31 3 3606 4025 13277982 13277562 1.690000e-160 577.0
13 TraesCS2D01G318800 chr5B 95.175 228 8 3 1 227 557322328 557322103 2.400000e-94 357.0
14 TraesCS2D01G318800 chr5B 94.470 217 10 1 14 230 557348755 557348969 4.050000e-87 333.0
15 TraesCS2D01G318800 chr5B 96.364 55 2 0 5125 5179 13277420 13277366 2.690000e-14 91.6
16 TraesCS2D01G318800 chr5D 90.143 2242 137 34 1392 3609 13900741 13898560 0.000000e+00 2839.0
17 TraesCS2D01G318800 chr5D 90.066 1832 114 33 5125 6925 13897144 13895350 0.000000e+00 2313.0
18 TraesCS2D01G318800 chr5D 88.031 518 44 10 894 1406 13901269 13900765 1.300000e-166 597.0
19 TraesCS2D01G318800 chr5D 90.968 310 23 4 3606 3912 13898509 13898202 5.050000e-111 412.0
20 TraesCS2D01G318800 chr5D 81.871 342 49 11 4664 4998 374382598 374382933 6.920000e-70 276.0
21 TraesCS2D01G318800 chr5D 91.150 113 10 0 3913 4025 13897398 13897286 3.380000e-33 154.0
22 TraesCS2D01G318800 chr5A 90.152 1838 114 33 5125 6925 10932497 10930690 0.000000e+00 2329.0
23 TraesCS2D01G318800 chr5A 89.276 1893 103 33 894 2763 10935265 10933450 0.000000e+00 2279.0
24 TraesCS2D01G318800 chr5A 91.962 423 28 5 3606 4025 10933060 10932641 7.820000e-164 588.0
25 TraesCS2D01G318800 chr5A 91.691 337 25 1 3276 3609 10933447 10933111 1.380000e-126 464.0
26 TraesCS2D01G318800 chr5A 89.855 207 20 1 23 229 485461707 485461502 1.500000e-66 265.0
27 TraesCS2D01G318800 chr5A 78.571 182 32 3 642 817 10935581 10935401 5.740000e-21 113.0
28 TraesCS2D01G318800 chr7A 96.133 931 27 3 4074 4996 592059385 592058456 0.000000e+00 1511.0
29 TraesCS2D01G318800 chr7A 94.760 229 9 2 1 229 630360579 630360354 3.110000e-93 353.0
30 TraesCS2D01G318800 chr7A 95.455 220 8 2 14 232 630387078 630387296 4.020000e-92 350.0
31 TraesCS2D01G318800 chr3B 93.724 972 32 8 4025 4996 715008582 715009524 0.000000e+00 1430.0
32 TraesCS2D01G318800 chr3B 78.850 487 72 22 4530 4996 369405265 369404790 4.100000e-77 300.0
33 TraesCS2D01G318800 chr3B 91.667 216 17 1 14 229 791765661 791765447 1.480000e-76 298.0
34 TraesCS2D01G318800 chr3B 82.891 339 43 12 4664 4990 387433567 387433902 2.470000e-74 291.0
35 TraesCS2D01G318800 chr3B 86.522 230 23 6 4765 4990 512523821 512524046 5.420000e-61 246.0
36 TraesCS2D01G318800 chrUn 79.386 1009 164 27 4026 4995 23394357 23395360 0.000000e+00 671.0
37 TraesCS2D01G318800 chrUn 79.386 1009 164 27 4026 4995 267108364 267109367 0.000000e+00 671.0
38 TraesCS2D01G318800 chrUn 79.386 1009 164 27 4026 4995 267125957 267126960 0.000000e+00 671.0
39 TraesCS2D01G318800 chr7B 78.615 491 76 20 4530 5001 339605362 339605842 1.480000e-76 298.0
40 TraesCS2D01G318800 chr7B 88.940 217 19 3 14 230 679106035 679105824 5.390000e-66 263.0
41 TraesCS2D01G318800 chr1B 81.792 346 48 11 4664 4997 614177844 614178186 6.920000e-70 276.0
42 TraesCS2D01G318800 chr7D 75.749 367 56 22 2763 3105 130138621 130138978 3.380000e-33 154.0
43 TraesCS2D01G318800 chr6D 88.406 69 8 0 4026 4094 469404960 469404892 4.500000e-12 84.2
44 TraesCS2D01G318800 chr6A 91.525 59 5 0 4026 4084 614529779 614529721 1.620000e-11 82.4
45 TraesCS2D01G318800 chr1A 96.875 32 1 0 3286 3317 290552269 290552238 4.000000e-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 TraesCS2D01G318800 chr2D 409254473 409261473 7000 False 12929.0 12929 100.00000 1 7001 1 chr2D.!!$F1 7000
1 TraesCS2D01G318800 chr2B 483995248 484000370 5122 False 1997.0 4974 95.28850 233 6035 4 chr2B.!!$F3 5802
2 TraesCS2D01G318800 chr2B 484004748 484005724 976 False 1696.0 1696 98.05700 6028 7001 1 chr2B.!!$F2 973
3 TraesCS2D01G318800 chr5B 13275663 13280656 4993 True 1482.4 3168 91.34725 895 6925 4 chr5B.!!$R2 6030
4 TraesCS2D01G318800 chr5D 13895350 13901269 5919 True 1263.0 2839 90.07160 894 6925 5 chr5D.!!$R1 6031
5 TraesCS2D01G318800 chr5A 10930690 10935581 4891 True 1154.6 2329 88.33040 642 6925 5 chr5A.!!$R2 6283
6 TraesCS2D01G318800 chr7A 592058456 592059385 929 True 1511.0 1511 96.13300 4074 4996 1 chr7A.!!$R1 922
7 TraesCS2D01G318800 chr3B 715008582 715009524 942 False 1430.0 1430 93.72400 4025 4996 1 chr3B.!!$F3 971
8 TraesCS2D01G318800 chrUn 23394357 23395360 1003 False 671.0 671 79.38600 4026 4995 1 chrUn.!!$F1 969
9 TraesCS2D01G318800 chrUn 267108364 267109367 1003 False 671.0 671 79.38600 4026 4995 1 chrUn.!!$F2 969
10 TraesCS2D01G318800 chrUn 267125957 267126960 1003 False 671.0 671 79.38600 4026 4995 1 chrUn.!!$F3 969

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
47 48 0.106419 ACCGGGCAGAAAAGACCAAA 60.106 50.000 6.32 0.00 35.99 3.28 F
51 52 0.318441 GGCAGAAAAGACCAAAGGGC 59.682 55.000 0.00 0.00 37.90 5.19 F
889 1000 0.749091 AGCACTGCACTGACAAAGCA 60.749 50.000 3.30 2.00 36.72 3.91 F
2205 2642 5.152934 ACAGAACCTTCCACTACTAAGGAA 58.847 41.667 8.06 0.00 44.27 3.36 F
2897 3354 1.539827 ACATTAGTTTTCTGGCACGGC 59.460 47.619 0.00 0.00 32.53 5.68 F
3460 3922 3.582647 TGAGCCTCTAAGGTCAATGACAA 59.417 43.478 15.86 0.00 37.80 3.18 F
4382 5725 2.507944 CTCTAGCCAGCCGCCATT 59.492 61.111 0.00 0.00 38.78 3.16 F
4416 5760 0.035458 AAGTAGCCTGACAGGTGTGC 59.965 55.000 22.58 13.52 37.80 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 1600 0.250124 TCCCTTGTCAACAACGCGAT 60.250 50.000 15.93 0.0 0.00 4.58 R
1316 1698 3.058914 AGTTGCACGCAAGAAAGACATAC 60.059 43.478 4.35 0.0 43.62 2.39 R
2472 2911 2.916702 ATCATCATCTACGCAAGGCA 57.083 45.000 0.00 0.0 46.39 4.75 R
3024 3481 0.393077 AGACACGTCCCTTGGTGAAG 59.607 55.000 0.00 0.0 37.58 3.02 R
4228 5553 0.320247 CGGAGCTGCTTGTCTGACTT 60.320 55.000 2.53 0.0 0.00 3.01 R
4416 5760 0.939577 CCATATTCGTGACGGAGCGG 60.940 60.000 4.70 0.0 0.00 5.52 R
5879 7303 2.028658 TCACAACTGTCATCTGGCTCTC 60.029 50.000 0.00 0.0 0.00 3.20 R
6328 7758 2.753296 CTAAGAGCAGGAGCATACAGC 58.247 52.381 0.00 0.0 45.49 4.40 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
19 20 2.171341 ATCATCTCGTCTCCGATCGA 57.829 50.000 18.66 1.60 43.27 3.59
20 21 1.949465 TCATCTCGTCTCCGATCGAA 58.051 50.000 18.66 0.00 43.27 3.71
21 22 2.285977 TCATCTCGTCTCCGATCGAAA 58.714 47.619 18.66 3.09 43.27 3.46
22 23 2.031807 TCATCTCGTCTCCGATCGAAAC 59.968 50.000 18.66 10.31 43.27 2.78
23 24 1.735386 TCTCGTCTCCGATCGAAACT 58.265 50.000 18.66 0.00 43.27 2.66
24 25 1.397343 TCTCGTCTCCGATCGAAACTG 59.603 52.381 18.66 3.42 43.27 3.16
25 26 1.130749 CTCGTCTCCGATCGAAACTGT 59.869 52.381 18.66 0.00 43.27 3.55
26 27 1.538512 TCGTCTCCGATCGAAACTGTT 59.461 47.619 18.66 0.00 38.40 3.16
27 28 1.649171 CGTCTCCGATCGAAACTGTTG 59.351 52.381 18.66 0.00 35.63 3.33
28 29 2.667448 CGTCTCCGATCGAAACTGTTGA 60.667 50.000 18.66 1.18 35.63 3.18
29 30 2.662156 GTCTCCGATCGAAACTGTTGAC 59.338 50.000 18.66 8.63 0.00 3.18
30 31 1.993370 CTCCGATCGAAACTGTTGACC 59.007 52.381 18.66 0.00 0.00 4.02
31 32 0.713883 CCGATCGAAACTGTTGACCG 59.286 55.000 18.66 0.00 0.00 4.79
32 33 0.713883 CGATCGAAACTGTTGACCGG 59.286 55.000 10.26 0.00 0.00 5.28
33 34 1.076332 GATCGAAACTGTTGACCGGG 58.924 55.000 6.32 0.00 0.00 5.73
34 35 0.953960 ATCGAAACTGTTGACCGGGC 60.954 55.000 6.32 1.57 0.00 6.13
35 36 1.890041 CGAAACTGTTGACCGGGCA 60.890 57.895 5.41 5.41 0.00 5.36
36 37 1.841663 CGAAACTGTTGACCGGGCAG 61.842 60.000 11.51 12.82 36.41 4.85
37 38 0.534203 GAAACTGTTGACCGGGCAGA 60.534 55.000 11.51 0.00 34.60 4.26
38 39 0.106918 AAACTGTTGACCGGGCAGAA 60.107 50.000 11.51 0.95 34.60 3.02
39 40 0.106918 AACTGTTGACCGGGCAGAAA 60.107 50.000 11.51 0.00 34.60 2.52
40 41 0.106918 ACTGTTGACCGGGCAGAAAA 60.107 50.000 11.51 0.00 34.60 2.29
41 42 0.593128 CTGTTGACCGGGCAGAAAAG 59.407 55.000 11.51 0.00 32.39 2.27
42 43 0.181587 TGTTGACCGGGCAGAAAAGA 59.818 50.000 11.51 0.00 0.00 2.52
43 44 0.591659 GTTGACCGGGCAGAAAAGAC 59.408 55.000 11.51 0.00 0.00 3.01
44 45 0.536460 TTGACCGGGCAGAAAAGACC 60.536 55.000 11.51 0.00 0.00 3.85
45 46 1.072505 GACCGGGCAGAAAAGACCA 59.927 57.895 0.00 0.00 35.99 4.02
46 47 0.536460 GACCGGGCAGAAAAGACCAA 60.536 55.000 0.00 0.00 35.99 3.67
47 48 0.106419 ACCGGGCAGAAAAGACCAAA 60.106 50.000 6.32 0.00 35.99 3.28
48 49 0.598065 CCGGGCAGAAAAGACCAAAG 59.402 55.000 0.00 0.00 35.99 2.77
49 50 0.598065 CGGGCAGAAAAGACCAAAGG 59.402 55.000 0.00 0.00 35.99 3.11
50 51 0.969149 GGGCAGAAAAGACCAAAGGG 59.031 55.000 0.00 0.00 36.38 3.95
51 52 0.318441 GGCAGAAAAGACCAAAGGGC 59.682 55.000 0.00 0.00 37.90 5.19
52 53 1.039856 GCAGAAAAGACCAAAGGGCA 58.960 50.000 0.00 0.00 37.90 5.36
53 54 1.412343 GCAGAAAAGACCAAAGGGCAA 59.588 47.619 0.00 0.00 37.90 4.52
54 55 2.158971 GCAGAAAAGACCAAAGGGCAAA 60.159 45.455 0.00 0.00 37.90 3.68
55 56 3.681313 GCAGAAAAGACCAAAGGGCAAAA 60.681 43.478 0.00 0.00 37.90 2.44
56 57 4.707105 CAGAAAAGACCAAAGGGCAAAAT 58.293 39.130 0.00 0.00 37.90 1.82
57 58 4.751600 CAGAAAAGACCAAAGGGCAAAATC 59.248 41.667 0.00 0.00 37.90 2.17
58 59 3.385193 AAAGACCAAAGGGCAAAATCG 57.615 42.857 0.00 0.00 37.90 3.34
59 60 1.995376 AGACCAAAGGGCAAAATCGT 58.005 45.000 0.00 0.00 37.90 3.73
60 61 1.886542 AGACCAAAGGGCAAAATCGTC 59.113 47.619 0.00 0.00 37.90 4.20
61 62 0.966179 ACCAAAGGGCAAAATCGTCC 59.034 50.000 0.00 0.00 37.90 4.79
62 63 0.965439 CCAAAGGGCAAAATCGTCCA 59.035 50.000 0.00 0.00 30.91 4.02
63 64 1.342819 CCAAAGGGCAAAATCGTCCAA 59.657 47.619 0.00 0.00 30.91 3.53
64 65 2.224161 CCAAAGGGCAAAATCGTCCAAA 60.224 45.455 0.00 0.00 30.91 3.28
65 66 3.462021 CAAAGGGCAAAATCGTCCAAAA 58.538 40.909 0.00 0.00 30.91 2.44
66 67 4.064388 CAAAGGGCAAAATCGTCCAAAAT 58.936 39.130 0.00 0.00 30.91 1.82
67 68 5.233988 CAAAGGGCAAAATCGTCCAAAATA 58.766 37.500 0.00 0.00 30.91 1.40
68 69 5.675684 AAGGGCAAAATCGTCCAAAATAT 57.324 34.783 0.00 0.00 30.91 1.28
69 70 5.675684 AGGGCAAAATCGTCCAAAATATT 57.324 34.783 0.00 0.00 30.91 1.28
70 71 6.783708 AGGGCAAAATCGTCCAAAATATTA 57.216 33.333 0.00 0.00 30.91 0.98
71 72 7.360113 AGGGCAAAATCGTCCAAAATATTAT 57.640 32.000 0.00 0.00 30.91 1.28
72 73 7.209475 AGGGCAAAATCGTCCAAAATATTATG 58.791 34.615 0.00 0.00 30.91 1.90
73 74 7.069331 AGGGCAAAATCGTCCAAAATATTATGA 59.931 33.333 0.00 0.00 30.91 2.15
74 75 7.872483 GGGCAAAATCGTCCAAAATATTATGAT 59.128 33.333 0.00 0.00 0.00 2.45
75 76 8.702438 GGCAAAATCGTCCAAAATATTATGATG 58.298 33.333 0.00 0.00 0.00 3.07
76 77 9.248291 GCAAAATCGTCCAAAATATTATGATGT 57.752 29.630 0.00 0.00 0.00 3.06
82 83 9.378551 TCGTCCAAAATATTATGATGTATAGGC 57.621 33.333 0.00 0.00 0.00 3.93
83 84 8.612619 CGTCCAAAATATTATGATGTATAGGCC 58.387 37.037 0.00 0.00 0.00 5.19
84 85 8.903820 GTCCAAAATATTATGATGTATAGGCCC 58.096 37.037 0.00 0.00 0.00 5.80
85 86 8.619281 TCCAAAATATTATGATGTATAGGCCCA 58.381 33.333 0.00 0.00 0.00 5.36
86 87 9.425248 CCAAAATATTATGATGTATAGGCCCAT 57.575 33.333 0.00 0.00 0.00 4.00
90 91 8.812894 ATATTATGATGTATAGGCCCATACCA 57.187 34.615 17.36 10.12 31.52 3.25
91 92 6.560003 TTATGATGTATAGGCCCATACCAG 57.440 41.667 17.36 0.00 31.52 4.00
92 93 4.140575 TGATGTATAGGCCCATACCAGA 57.859 45.455 17.36 0.97 31.52 3.86
93 94 4.498493 TGATGTATAGGCCCATACCAGAA 58.502 43.478 17.36 0.63 31.52 3.02
94 95 4.910913 TGATGTATAGGCCCATACCAGAAA 59.089 41.667 17.36 0.27 31.52 2.52
95 96 5.371176 TGATGTATAGGCCCATACCAGAAAA 59.629 40.000 17.36 0.00 31.52 2.29
96 97 5.922960 TGTATAGGCCCATACCAGAAAAT 57.077 39.130 17.36 0.00 31.52 1.82
97 98 6.274322 TGTATAGGCCCATACCAGAAAATT 57.726 37.500 17.36 0.00 31.52 1.82
98 99 6.068010 TGTATAGGCCCATACCAGAAAATTG 58.932 40.000 17.36 0.00 31.52 2.32
99 100 3.756082 AGGCCCATACCAGAAAATTGA 57.244 42.857 0.00 0.00 0.00 2.57
100 101 3.635591 AGGCCCATACCAGAAAATTGAG 58.364 45.455 0.00 0.00 0.00 3.02
101 102 3.269381 AGGCCCATACCAGAAAATTGAGA 59.731 43.478 0.00 0.00 0.00 3.27
102 103 4.023291 GGCCCATACCAGAAAATTGAGAA 58.977 43.478 0.00 0.00 0.00 2.87
103 104 4.466015 GGCCCATACCAGAAAATTGAGAAA 59.534 41.667 0.00 0.00 0.00 2.52
104 105 5.046663 GGCCCATACCAGAAAATTGAGAAAA 60.047 40.000 0.00 0.00 0.00 2.29
105 106 6.463360 GCCCATACCAGAAAATTGAGAAAAA 58.537 36.000 0.00 0.00 0.00 1.94
131 132 7.759489 AAATCAGTTTGTGCTACTTTATCCA 57.241 32.000 0.00 0.00 0.00 3.41
132 133 6.992063 ATCAGTTTGTGCTACTTTATCCAG 57.008 37.500 0.00 0.00 0.00 3.86
133 134 4.695455 TCAGTTTGTGCTACTTTATCCAGC 59.305 41.667 0.00 0.00 35.82 4.85
134 135 4.010349 AGTTTGTGCTACTTTATCCAGCC 58.990 43.478 0.00 0.00 34.31 4.85
135 136 3.712016 TTGTGCTACTTTATCCAGCCA 57.288 42.857 0.00 0.00 34.31 4.75
136 137 3.931907 TGTGCTACTTTATCCAGCCAT 57.068 42.857 0.00 0.00 34.31 4.40
137 138 3.544684 TGTGCTACTTTATCCAGCCATG 58.455 45.455 0.00 0.00 34.31 3.66
148 149 1.805254 CAGCCATGGAGGAAAAGCG 59.195 57.895 18.40 0.00 41.22 4.68
149 150 0.962356 CAGCCATGGAGGAAAAGCGT 60.962 55.000 18.40 0.00 41.22 5.07
150 151 0.962356 AGCCATGGAGGAAAAGCGTG 60.962 55.000 18.40 0.00 41.22 5.34
151 152 1.244019 GCCATGGAGGAAAAGCGTGT 61.244 55.000 18.40 0.00 41.22 4.49
152 153 0.804989 CCATGGAGGAAAAGCGTGTC 59.195 55.000 5.56 0.00 41.22 3.67
153 154 1.522668 CATGGAGGAAAAGCGTGTCA 58.477 50.000 0.00 0.00 0.00 3.58
154 155 2.086869 CATGGAGGAAAAGCGTGTCAT 58.913 47.619 0.00 0.00 0.00 3.06
155 156 2.270352 TGGAGGAAAAGCGTGTCATT 57.730 45.000 0.00 0.00 0.00 2.57
156 157 2.582052 TGGAGGAAAAGCGTGTCATTT 58.418 42.857 0.00 0.00 0.00 2.32
157 158 3.745799 TGGAGGAAAAGCGTGTCATTTA 58.254 40.909 0.00 0.00 0.00 1.40
158 159 4.138290 TGGAGGAAAAGCGTGTCATTTAA 58.862 39.130 0.00 0.00 0.00 1.52
159 160 4.764823 TGGAGGAAAAGCGTGTCATTTAAT 59.235 37.500 0.00 0.00 0.00 1.40
160 161 5.106317 TGGAGGAAAAGCGTGTCATTTAATC 60.106 40.000 0.00 0.00 0.00 1.75
161 162 5.106317 GGAGGAAAAGCGTGTCATTTAATCA 60.106 40.000 0.00 0.00 0.00 2.57
162 163 6.325919 AGGAAAAGCGTGTCATTTAATCAA 57.674 33.333 0.00 0.00 0.00 2.57
163 164 6.744112 AGGAAAAGCGTGTCATTTAATCAAA 58.256 32.000 0.00 0.00 0.00 2.69
164 165 6.640907 AGGAAAAGCGTGTCATTTAATCAAAC 59.359 34.615 0.00 0.00 0.00 2.93
165 166 6.419413 GGAAAAGCGTGTCATTTAATCAAACA 59.581 34.615 0.00 0.00 0.00 2.83
166 167 7.043059 GGAAAAGCGTGTCATTTAATCAAACAA 60.043 33.333 0.00 0.00 0.00 2.83
167 168 7.763172 AAAGCGTGTCATTTAATCAAACAAA 57.237 28.000 0.00 0.00 0.00 2.83
168 169 7.763172 AAGCGTGTCATTTAATCAAACAAAA 57.237 28.000 0.00 0.00 0.00 2.44
169 170 7.763172 AGCGTGTCATTTAATCAAACAAAAA 57.237 28.000 0.00 0.00 0.00 1.94
170 171 7.840489 AGCGTGTCATTTAATCAAACAAAAAG 58.160 30.769 0.00 0.00 0.00 2.27
171 172 7.704472 AGCGTGTCATTTAATCAAACAAAAAGA 59.296 29.630 0.00 0.00 0.00 2.52
172 173 8.324567 GCGTGTCATTTAATCAAACAAAAAGAA 58.675 29.630 0.00 0.00 0.00 2.52
180 181 9.818796 TTTAATCAAACAAAAAGAAAAGTGTGC 57.181 25.926 0.00 0.00 0.00 4.57
181 182 7.671495 AATCAAACAAAAAGAAAAGTGTGCT 57.329 28.000 0.00 0.00 0.00 4.40
182 183 8.770438 AATCAAACAAAAAGAAAAGTGTGCTA 57.230 26.923 0.00 0.00 0.00 3.49
183 184 8.947055 ATCAAACAAAAAGAAAAGTGTGCTAT 57.053 26.923 0.00 0.00 0.00 2.97
184 185 8.770438 TCAAACAAAAAGAAAAGTGTGCTATT 57.230 26.923 0.00 0.00 0.00 1.73
185 186 9.213799 TCAAACAAAAAGAAAAGTGTGCTATTT 57.786 25.926 0.00 0.00 0.00 1.40
186 187 9.824534 CAAACAAAAAGAAAAGTGTGCTATTTT 57.175 25.926 0.00 0.00 0.00 1.82
193 194 9.696917 AAAGAAAAGTGTGCTATTTTATGAAGG 57.303 29.630 0.00 0.00 0.00 3.46
194 195 8.409358 AGAAAAGTGTGCTATTTTATGAAGGT 57.591 30.769 0.00 0.00 0.00 3.50
195 196 8.299570 AGAAAAGTGTGCTATTTTATGAAGGTG 58.700 33.333 0.00 0.00 0.00 4.00
196 197 5.567138 AGTGTGCTATTTTATGAAGGTGC 57.433 39.130 0.00 0.00 0.00 5.01
197 198 5.009631 AGTGTGCTATTTTATGAAGGTGCA 58.990 37.500 0.00 0.00 0.00 4.57
198 199 5.476599 AGTGTGCTATTTTATGAAGGTGCAA 59.523 36.000 0.00 0.00 0.00 4.08
199 200 5.801947 GTGTGCTATTTTATGAAGGTGCAAG 59.198 40.000 0.00 0.00 0.00 4.01
200 201 5.105797 TGTGCTATTTTATGAAGGTGCAAGG 60.106 40.000 0.00 0.00 0.00 3.61
201 202 5.125417 GTGCTATTTTATGAAGGTGCAAGGA 59.875 40.000 0.00 0.00 0.00 3.36
202 203 5.714333 TGCTATTTTATGAAGGTGCAAGGAA 59.286 36.000 0.00 0.00 0.00 3.36
203 204 6.210385 TGCTATTTTATGAAGGTGCAAGGAAA 59.790 34.615 0.00 0.00 0.00 3.13
204 205 6.753744 GCTATTTTATGAAGGTGCAAGGAAAG 59.246 38.462 0.00 0.00 0.00 2.62
205 206 6.916360 ATTTTATGAAGGTGCAAGGAAAGA 57.084 33.333 0.00 0.00 0.00 2.52
206 207 5.705609 TTTATGAAGGTGCAAGGAAAGAC 57.294 39.130 0.00 0.00 0.00 3.01
207 208 1.593196 TGAAGGTGCAAGGAAAGACG 58.407 50.000 0.00 0.00 0.00 4.18
208 209 1.134220 TGAAGGTGCAAGGAAAGACGT 60.134 47.619 0.00 0.00 0.00 4.34
209 210 1.264288 GAAGGTGCAAGGAAAGACGTG 59.736 52.381 0.00 0.00 0.00 4.49
210 211 1.166531 AGGTGCAAGGAAAGACGTGC 61.167 55.000 0.00 0.00 0.00 5.34
211 212 1.166531 GGTGCAAGGAAAGACGTGCT 61.167 55.000 0.00 0.00 0.00 4.40
212 213 1.508632 GTGCAAGGAAAGACGTGCTA 58.491 50.000 0.00 0.00 0.00 3.49
213 214 2.076863 GTGCAAGGAAAGACGTGCTAT 58.923 47.619 0.00 0.00 0.00 2.97
214 215 2.484264 GTGCAAGGAAAGACGTGCTATT 59.516 45.455 0.00 0.00 0.00 1.73
215 216 3.058224 GTGCAAGGAAAGACGTGCTATTT 60.058 43.478 0.00 0.00 0.00 1.40
216 217 3.568007 TGCAAGGAAAGACGTGCTATTTT 59.432 39.130 0.00 0.00 0.00 1.82
217 218 4.757657 TGCAAGGAAAGACGTGCTATTTTA 59.242 37.500 0.00 0.00 0.00 1.52
218 219 5.414454 TGCAAGGAAAGACGTGCTATTTTAT 59.586 36.000 0.00 0.00 0.00 1.40
219 220 5.965918 GCAAGGAAAGACGTGCTATTTTATC 59.034 40.000 0.00 0.00 0.00 1.75
220 221 6.403200 GCAAGGAAAGACGTGCTATTTTATCA 60.403 38.462 0.00 0.00 0.00 2.15
221 222 7.526608 CAAGGAAAGACGTGCTATTTTATCAA 58.473 34.615 0.00 0.00 0.00 2.57
222 223 7.681939 AGGAAAGACGTGCTATTTTATCAAA 57.318 32.000 0.00 0.00 0.00 2.69
223 224 8.281212 AGGAAAGACGTGCTATTTTATCAAAT 57.719 30.769 0.00 0.00 36.52 2.32
224 225 8.739972 AGGAAAGACGTGCTATTTTATCAAATT 58.260 29.630 0.00 0.00 34.29 1.82
225 226 8.798153 GGAAAGACGTGCTATTTTATCAAATTG 58.202 33.333 0.00 0.00 34.29 2.32
226 227 7.740519 AAGACGTGCTATTTTATCAAATTGC 57.259 32.000 10.61 10.61 45.80 3.56
227 228 7.088589 AGACGTGCTATTTTATCAAATTGCT 57.911 32.000 16.18 1.19 45.80 3.91
228 229 7.189512 AGACGTGCTATTTTATCAAATTGCTC 58.810 34.615 16.18 12.70 45.80 4.26
229 230 6.265577 ACGTGCTATTTTATCAAATTGCTCC 58.734 36.000 16.18 8.61 45.80 4.70
230 231 5.396362 CGTGCTATTTTATCAAATTGCTCCG 59.604 40.000 16.18 14.22 45.80 4.63
231 232 6.265577 GTGCTATTTTATCAAATTGCTCCGT 58.734 36.000 16.18 0.00 45.80 4.69
293 294 2.741985 CTGATCGGGCACGTGCAA 60.742 61.111 38.60 24.69 44.36 4.08
333 334 2.357517 ACGTGTGCACTGCCTAGC 60.358 61.111 19.41 0.00 0.00 3.42
420 462 2.587473 TGTGCGTGCATGTCGTGT 60.587 55.556 7.93 0.00 0.00 4.49
444 502 0.852777 GGCGAGTATACGTGCATGTG 59.147 55.000 21.92 4.64 35.59 3.21
470 528 1.018910 TCCATCAGATTGCATGCACG 58.981 50.000 22.58 9.57 0.00 5.34
491 549 2.597713 CGAGCGTGCTGTTGCTTGA 61.598 57.895 0.00 0.00 43.89 3.02
556 614 4.567958 CCGGGTAATCAGCTAGGAGAGATA 60.568 50.000 0.00 0.00 0.00 1.98
639 703 5.234466 AGAGATTCCAGCAGTTTGTTAGT 57.766 39.130 0.00 0.00 0.00 2.24
649 719 3.374058 GCAGTTTGTTAGTATGTGGCGAT 59.626 43.478 0.00 0.00 0.00 4.58
655 725 5.950758 TGTTAGTATGTGGCGATTTTGTT 57.049 34.783 0.00 0.00 0.00 2.83
664 734 9.562583 GTATGTGGCGATTTTGTTAATCTTAAA 57.437 29.630 0.00 0.00 0.00 1.52
676 746 7.384439 TGTTAATCTTAAATTGATGTGCCGA 57.616 32.000 0.00 0.00 0.00 5.54
685 755 3.610040 TTGATGTGCCGACTCAGTATT 57.390 42.857 0.00 0.00 0.00 1.89
687 757 3.937814 TGATGTGCCGACTCAGTATTTT 58.062 40.909 0.00 0.00 0.00 1.82
695 765 4.381718 GCCGACTCAGTATTTTAGAGGTGT 60.382 45.833 0.00 0.00 33.76 4.16
756 828 8.712285 AATTAAGTATGTGCGTGTATGTAAGT 57.288 30.769 0.00 0.00 0.00 2.24
844 955 2.409948 AGATGTAGTGGGCTTGCTTC 57.590 50.000 0.00 0.00 0.00 3.86
889 1000 0.749091 AGCACTGCACTGACAAAGCA 60.749 50.000 3.30 2.00 36.72 3.91
1221 1600 5.771469 TCACTATCCTGTTTCGAAAACGTA 58.229 37.500 13.10 0.00 0.00 3.57
1548 1979 6.691754 TCATGAGTGTTTGTTTGCTTCTTA 57.308 33.333 0.00 0.00 0.00 2.10
1556 1987 8.682710 AGTGTTTGTTTGCTTCTTATGTTTCTA 58.317 29.630 0.00 0.00 0.00 2.10
1565 1996 9.725019 TTGCTTCTTATGTTTCTATTCTTCTGA 57.275 29.630 0.00 0.00 0.00 3.27
2205 2642 5.152934 ACAGAACCTTCCACTACTAAGGAA 58.847 41.667 8.06 0.00 44.27 3.36
2370 2809 5.488341 ACTTATGGAACTGCGTCTTGTATT 58.512 37.500 0.00 0.00 0.00 1.89
2472 2911 8.688747 TTTAACCATGCTGGATTTTCAATTTT 57.311 26.923 8.91 0.00 40.96 1.82
2546 2994 9.463443 GTTTAACACATCTAATGTTTGCTTCTT 57.537 29.630 0.00 0.00 42.70 2.52
2897 3354 1.539827 ACATTAGTTTTCTGGCACGGC 59.460 47.619 0.00 0.00 32.53 5.68
3024 3481 5.816919 TGTTTTTCCGTGAAGAAAGATCAC 58.183 37.500 0.00 0.00 42.94 3.06
3170 3628 9.855021 CAAGGGATGTGTTATTTAACTAAAAGG 57.145 33.333 2.45 0.00 37.12 3.11
3460 3922 3.582647 TGAGCCTCTAAGGTCAATGACAA 59.417 43.478 15.86 0.00 37.80 3.18
3465 3927 5.938125 GCCTCTAAGGTCAATGACAAAACTA 59.062 40.000 15.86 0.00 37.80 2.24
3821 4342 4.456911 TGCCTTGAAGCTCACAAATAGAAG 59.543 41.667 7.51 0.00 0.00 2.85
3822 4343 4.697352 GCCTTGAAGCTCACAAATAGAAGA 59.303 41.667 7.51 0.00 0.00 2.87
3889 4410 5.931441 AGAGCATAAGAACAAAGACACAC 57.069 39.130 0.00 0.00 0.00 3.82
3893 4414 4.377431 GCATAAGAACAAAGACACACGAGG 60.377 45.833 0.00 0.00 0.00 4.63
4023 5347 9.020731 ACCCAAAACCTAGTACAATTCATTTAG 57.979 33.333 0.00 0.00 0.00 1.85
4086 5410 6.795144 ATTGGCTTCAATATCAAATCACCA 57.205 33.333 0.00 0.00 39.15 4.17
4382 5725 2.507944 CTCTAGCCAGCCGCCATT 59.492 61.111 0.00 0.00 38.78 3.16
4416 5760 0.035458 AAGTAGCCTGACAGGTGTGC 59.965 55.000 22.58 13.52 37.80 4.57
4440 5784 2.858344 CTCCGTCACGAATATGGTTGTC 59.142 50.000 0.00 0.00 0.00 3.18
4549 5911 1.377202 ATCTTGCAACGGCGACCAT 60.377 52.632 16.62 0.00 45.35 3.55
4561 5924 2.436109 GACCATGCCCACCACTGT 59.564 61.111 0.00 0.00 0.00 3.55
4795 6173 1.675219 GCCAAGTCGAAGGGGTACA 59.325 57.895 0.00 0.00 0.00 2.90
4996 6374 4.553330 ATCTACATCCAAACGGAGTGTT 57.447 40.909 0.00 0.00 45.00 3.32
4997 6375 5.670792 ATCTACATCCAAACGGAGTGTTA 57.329 39.130 0.00 0.00 45.00 2.41
5009 6387 3.244630 ACGGAGTGTTAGGGCATGTTTAA 60.245 43.478 0.00 0.00 42.51 1.52
5246 6657 1.621672 TATGTGGCCCTGTCATCGCA 61.622 55.000 0.00 0.00 0.00 5.10
5255 6666 0.671472 CTGTCATCGCACTTGGCTCA 60.671 55.000 0.00 0.00 41.67 4.26
5583 7000 4.006319 GCTTGCTCTGACAGGTTAGATTT 58.994 43.478 1.81 0.00 0.00 2.17
5605 7022 8.593492 ATTTTTATTCTGTGCTGTTCTTTTCC 57.407 30.769 0.00 0.00 0.00 3.13
5615 7032 2.430332 CTGTTCTTTTCCCTGTGCCAAA 59.570 45.455 0.00 0.00 0.00 3.28
5790 7214 2.435059 GTGGTTGGAGAGGAGCGC 60.435 66.667 0.00 0.00 0.00 5.92
5879 7303 7.444629 TTCACAGAAGAGAAGAATTTGATGG 57.555 36.000 0.00 0.00 0.00 3.51
6090 7515 4.993584 CCATCAGCTGACATTAGGATGTAC 59.006 45.833 20.97 0.00 46.27 2.90
6269 7694 4.687018 TGAGCTTGCATTATTTGTTGCTTG 59.313 37.500 0.00 0.00 31.19 4.01
6271 7696 4.687483 AGCTTGCATTATTTGTTGCTTGTC 59.313 37.500 0.00 0.00 0.00 3.18
6272 7697 4.448395 GCTTGCATTATTTGTTGCTTGTCA 59.552 37.500 0.00 0.00 0.00 3.58
6274 7699 6.469139 TTGCATTATTTGTTGCTTGTCATG 57.531 33.333 0.00 0.00 0.00 3.07
6275 7700 4.930405 TGCATTATTTGTTGCTTGTCATGG 59.070 37.500 0.00 0.00 0.00 3.66
6277 7702 5.409214 GCATTATTTGTTGCTTGTCATGGTT 59.591 36.000 0.00 0.00 0.00 3.67
6278 7703 6.073112 GCATTATTTGTTGCTTGTCATGGTTT 60.073 34.615 0.00 0.00 0.00 3.27
6279 7704 7.512297 CATTATTTGTTGCTTGTCATGGTTTC 58.488 34.615 0.00 0.00 0.00 2.78
6280 7705 2.772568 TGTTGCTTGTCATGGTTTCG 57.227 45.000 0.00 0.00 0.00 3.46
6328 7758 6.294731 CCCTCTTTGTTAATTTCTCTGTTGGG 60.295 42.308 0.00 0.00 0.00 4.12
6411 7847 9.606849 TGATTGATATCGCTAACCTGCTAGGTG 62.607 44.444 8.37 0.00 39.69 4.00
6455 7891 9.626045 TGTATTCATGATATATCGAAGTCACAC 57.374 33.333 8.19 1.02 0.00 3.82
6605 8042 0.250901 TCAGCTTGGAGGTTTGCTCC 60.251 55.000 0.00 0.00 41.21 4.70
6975 8427 2.289133 GCTAGAAGATCCGGAATCCACC 60.289 54.545 9.01 0.00 34.67 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.662156 GTCAACAGTTTCGATCGGAGAC 59.338 50.000 16.41 11.32 42.51 3.36
9 10 2.352421 GGTCAACAGTTTCGATCGGAGA 60.352 50.000 16.41 0.00 45.75 3.71
10 11 1.993370 GGTCAACAGTTTCGATCGGAG 59.007 52.381 16.41 0.00 0.00 4.63
11 12 1.667756 CGGTCAACAGTTTCGATCGGA 60.668 52.381 16.41 2.60 29.70 4.55
12 13 0.713883 CGGTCAACAGTTTCGATCGG 59.286 55.000 16.41 0.47 29.70 4.18
13 14 0.713883 CCGGTCAACAGTTTCGATCG 59.286 55.000 9.36 9.36 33.11 3.69
14 15 1.076332 CCCGGTCAACAGTTTCGATC 58.924 55.000 0.00 0.00 0.00 3.69
15 16 0.953960 GCCCGGTCAACAGTTTCGAT 60.954 55.000 0.00 0.00 0.00 3.59
16 17 1.595929 GCCCGGTCAACAGTTTCGA 60.596 57.895 0.00 0.00 0.00 3.71
17 18 1.841663 CTGCCCGGTCAACAGTTTCG 61.842 60.000 0.00 0.00 0.00 3.46
18 19 0.534203 TCTGCCCGGTCAACAGTTTC 60.534 55.000 0.00 0.00 33.12 2.78
19 20 0.106918 TTCTGCCCGGTCAACAGTTT 60.107 50.000 0.00 0.00 33.12 2.66
20 21 0.106918 TTTCTGCCCGGTCAACAGTT 60.107 50.000 0.00 0.00 33.12 3.16
21 22 0.106918 TTTTCTGCCCGGTCAACAGT 60.107 50.000 0.00 0.00 33.12 3.55
22 23 0.593128 CTTTTCTGCCCGGTCAACAG 59.407 55.000 0.00 2.48 0.00 3.16
23 24 0.181587 TCTTTTCTGCCCGGTCAACA 59.818 50.000 0.00 0.00 0.00 3.33
24 25 0.591659 GTCTTTTCTGCCCGGTCAAC 59.408 55.000 0.00 0.00 0.00 3.18
25 26 0.536460 GGTCTTTTCTGCCCGGTCAA 60.536 55.000 0.00 0.00 0.00 3.18
26 27 1.072505 GGTCTTTTCTGCCCGGTCA 59.927 57.895 0.00 0.00 0.00 4.02
27 28 0.536460 TTGGTCTTTTCTGCCCGGTC 60.536 55.000 0.00 0.00 0.00 4.79
28 29 0.106419 TTTGGTCTTTTCTGCCCGGT 60.106 50.000 0.00 0.00 0.00 5.28
29 30 0.598065 CTTTGGTCTTTTCTGCCCGG 59.402 55.000 0.00 0.00 0.00 5.73
30 31 0.598065 CCTTTGGTCTTTTCTGCCCG 59.402 55.000 0.00 0.00 0.00 6.13
31 32 0.969149 CCCTTTGGTCTTTTCTGCCC 59.031 55.000 0.00 0.00 0.00 5.36
32 33 0.318441 GCCCTTTGGTCTTTTCTGCC 59.682 55.000 0.00 0.00 0.00 4.85
33 34 1.039856 TGCCCTTTGGTCTTTTCTGC 58.960 50.000 0.00 0.00 0.00 4.26
34 35 3.817709 TTTGCCCTTTGGTCTTTTCTG 57.182 42.857 0.00 0.00 0.00 3.02
35 36 4.501400 CGATTTTGCCCTTTGGTCTTTTCT 60.501 41.667 0.00 0.00 0.00 2.52
36 37 3.740832 CGATTTTGCCCTTTGGTCTTTTC 59.259 43.478 0.00 0.00 0.00 2.29
37 38 3.133901 ACGATTTTGCCCTTTGGTCTTTT 59.866 39.130 0.00 0.00 0.00 2.27
38 39 2.698274 ACGATTTTGCCCTTTGGTCTTT 59.302 40.909 0.00 0.00 0.00 2.52
39 40 2.296190 GACGATTTTGCCCTTTGGTCTT 59.704 45.455 0.00 0.00 0.00 3.01
40 41 1.886542 GACGATTTTGCCCTTTGGTCT 59.113 47.619 0.00 0.00 0.00 3.85
41 42 1.067846 GGACGATTTTGCCCTTTGGTC 60.068 52.381 0.00 0.00 0.00 4.02
42 43 0.966179 GGACGATTTTGCCCTTTGGT 59.034 50.000 0.00 0.00 0.00 3.67
43 44 0.965439 TGGACGATTTTGCCCTTTGG 59.035 50.000 0.00 0.00 0.00 3.28
44 45 2.810439 TTGGACGATTTTGCCCTTTG 57.190 45.000 0.00 0.00 0.00 2.77
45 46 3.828875 TTTTGGACGATTTTGCCCTTT 57.171 38.095 0.00 0.00 0.00 3.11
46 47 5.675684 ATATTTTGGACGATTTTGCCCTT 57.324 34.783 0.00 0.00 0.00 3.95
47 48 5.675684 AATATTTTGGACGATTTTGCCCT 57.324 34.783 0.00 0.00 0.00 5.19
48 49 7.206687 TCATAATATTTTGGACGATTTTGCCC 58.793 34.615 6.12 0.00 0.00 5.36
49 50 8.702438 CATCATAATATTTTGGACGATTTTGCC 58.298 33.333 6.12 0.00 0.00 4.52
50 51 9.248291 ACATCATAATATTTTGGACGATTTTGC 57.752 29.630 6.12 0.00 0.00 3.68
56 57 9.378551 GCCTATACATCATAATATTTTGGACGA 57.621 33.333 6.12 0.00 0.00 4.20
57 58 8.612619 GGCCTATACATCATAATATTTTGGACG 58.387 37.037 0.00 0.00 0.00 4.79
58 59 8.903820 GGGCCTATACATCATAATATTTTGGAC 58.096 37.037 0.84 0.00 0.00 4.02
59 60 8.619281 TGGGCCTATACATCATAATATTTTGGA 58.381 33.333 4.53 0.00 0.00 3.53
60 61 8.821686 TGGGCCTATACATCATAATATTTTGG 57.178 34.615 4.53 0.00 0.00 3.28
64 65 9.236498 TGGTATGGGCCTATACATCATAATATT 57.764 33.333 32.75 0.00 35.67 1.28
65 66 8.812894 TGGTATGGGCCTATACATCATAATAT 57.187 34.615 32.75 0.00 35.67 1.28
66 67 8.071229 TCTGGTATGGGCCTATACATCATAATA 58.929 37.037 32.75 11.99 35.67 0.98
67 68 6.908593 TCTGGTATGGGCCTATACATCATAAT 59.091 38.462 32.75 0.00 35.67 1.28
68 69 6.268414 TCTGGTATGGGCCTATACATCATAA 58.732 40.000 32.75 15.29 35.67 1.90
69 70 5.849140 TCTGGTATGGGCCTATACATCATA 58.151 41.667 32.75 16.85 35.67 2.15
70 71 4.698895 TCTGGTATGGGCCTATACATCAT 58.301 43.478 32.75 15.82 35.67 2.45
71 72 4.140575 TCTGGTATGGGCCTATACATCA 57.859 45.455 32.75 23.31 35.67 3.07
72 73 5.499004 TTTCTGGTATGGGCCTATACATC 57.501 43.478 32.75 20.57 35.67 3.06
73 74 5.922960 TTTTCTGGTATGGGCCTATACAT 57.077 39.130 32.75 17.48 35.67 2.29
74 75 5.922960 ATTTTCTGGTATGGGCCTATACA 57.077 39.130 32.75 20.74 35.67 2.29
75 76 6.303839 TCAATTTTCTGGTATGGGCCTATAC 58.696 40.000 26.73 26.73 33.71 1.47
76 77 6.331572 TCTCAATTTTCTGGTATGGGCCTATA 59.668 38.462 4.39 4.39 0.00 1.31
77 78 5.134339 TCTCAATTTTCTGGTATGGGCCTAT 59.866 40.000 6.88 6.88 0.00 2.57
78 79 4.476846 TCTCAATTTTCTGGTATGGGCCTA 59.523 41.667 4.53 0.00 0.00 3.93
79 80 3.269381 TCTCAATTTTCTGGTATGGGCCT 59.731 43.478 4.53 0.00 0.00 5.19
80 81 3.631250 TCTCAATTTTCTGGTATGGGCC 58.369 45.455 0.00 0.00 0.00 5.80
81 82 5.659440 TTTCTCAATTTTCTGGTATGGGC 57.341 39.130 0.00 0.00 0.00 5.36
105 106 8.637986 TGGATAAAGTAGCACAAACTGATTTTT 58.362 29.630 0.00 0.00 0.00 1.94
106 107 8.177119 TGGATAAAGTAGCACAAACTGATTTT 57.823 30.769 0.00 0.00 0.00 1.82
107 108 7.575720 GCTGGATAAAGTAGCACAAACTGATTT 60.576 37.037 0.00 0.00 37.40 2.17
108 109 6.127897 GCTGGATAAAGTAGCACAAACTGATT 60.128 38.462 0.00 0.00 37.40 2.57
109 110 5.355350 GCTGGATAAAGTAGCACAAACTGAT 59.645 40.000 0.00 0.00 37.40 2.90
110 111 4.695455 GCTGGATAAAGTAGCACAAACTGA 59.305 41.667 0.00 0.00 37.40 3.41
111 112 4.142600 GGCTGGATAAAGTAGCACAAACTG 60.143 45.833 0.00 0.00 39.15 3.16
112 113 4.010349 GGCTGGATAAAGTAGCACAAACT 58.990 43.478 0.00 0.00 39.15 2.66
113 114 3.756434 TGGCTGGATAAAGTAGCACAAAC 59.244 43.478 0.00 0.00 39.15 2.93
114 115 4.027674 TGGCTGGATAAAGTAGCACAAA 57.972 40.909 0.00 0.00 39.15 2.83
115 116 3.712016 TGGCTGGATAAAGTAGCACAA 57.288 42.857 0.00 0.00 39.15 3.33
116 117 3.544684 CATGGCTGGATAAAGTAGCACA 58.455 45.455 0.00 0.00 39.15 4.57
117 118 2.880890 CCATGGCTGGATAAAGTAGCAC 59.119 50.000 0.00 0.00 46.37 4.40
118 119 2.777114 TCCATGGCTGGATAAAGTAGCA 59.223 45.455 6.96 0.00 46.95 3.49
119 120 3.492102 TCCATGGCTGGATAAAGTAGC 57.508 47.619 6.96 0.00 46.95 3.58
129 130 1.660560 CGCTTTTCCTCCATGGCTGG 61.661 60.000 6.96 12.03 44.64 4.85
130 131 0.962356 ACGCTTTTCCTCCATGGCTG 60.962 55.000 6.96 1.90 35.26 4.85
131 132 0.962356 CACGCTTTTCCTCCATGGCT 60.962 55.000 6.96 0.00 35.26 4.75
132 133 1.244019 ACACGCTTTTCCTCCATGGC 61.244 55.000 6.96 0.00 35.26 4.40
133 134 0.804989 GACACGCTTTTCCTCCATGG 59.195 55.000 4.97 4.97 37.10 3.66
134 135 1.522668 TGACACGCTTTTCCTCCATG 58.477 50.000 0.00 0.00 0.00 3.66
135 136 2.496899 ATGACACGCTTTTCCTCCAT 57.503 45.000 0.00 0.00 0.00 3.41
136 137 2.270352 AATGACACGCTTTTCCTCCA 57.730 45.000 0.00 0.00 0.00 3.86
137 138 4.759516 TTAAATGACACGCTTTTCCTCC 57.240 40.909 0.00 0.00 0.00 4.30
138 139 5.938322 TGATTAAATGACACGCTTTTCCTC 58.062 37.500 0.00 0.00 0.00 3.71
139 140 5.957842 TGATTAAATGACACGCTTTTCCT 57.042 34.783 0.00 0.00 0.00 3.36
140 141 6.419413 TGTTTGATTAAATGACACGCTTTTCC 59.581 34.615 0.00 0.00 0.00 3.13
141 142 7.388290 TGTTTGATTAAATGACACGCTTTTC 57.612 32.000 0.00 0.00 0.00 2.29
142 143 7.763172 TTGTTTGATTAAATGACACGCTTTT 57.237 28.000 0.00 0.00 0.00 2.27
143 144 7.763172 TTTGTTTGATTAAATGACACGCTTT 57.237 28.000 0.00 0.00 0.00 3.51
144 145 7.763172 TTTTGTTTGATTAAATGACACGCTT 57.237 28.000 0.00 0.00 0.00 4.68
145 146 7.704472 TCTTTTTGTTTGATTAAATGACACGCT 59.296 29.630 0.00 0.00 0.00 5.07
146 147 7.836512 TCTTTTTGTTTGATTAAATGACACGC 58.163 30.769 0.00 0.00 0.00 5.34
154 155 9.818796 GCACACTTTTCTTTTTGTTTGATTAAA 57.181 25.926 0.00 0.00 0.00 1.52
155 156 9.213799 AGCACACTTTTCTTTTTGTTTGATTAA 57.786 25.926 0.00 0.00 0.00 1.40
156 157 8.770438 AGCACACTTTTCTTTTTGTTTGATTA 57.230 26.923 0.00 0.00 0.00 1.75
157 158 7.671495 AGCACACTTTTCTTTTTGTTTGATT 57.329 28.000 0.00 0.00 0.00 2.57
158 159 8.947055 ATAGCACACTTTTCTTTTTGTTTGAT 57.053 26.923 0.00 0.00 0.00 2.57
159 160 8.770438 AATAGCACACTTTTCTTTTTGTTTGA 57.230 26.923 0.00 0.00 0.00 2.69
160 161 9.824534 AAAATAGCACACTTTTCTTTTTGTTTG 57.175 25.926 0.00 0.00 0.00 2.93
167 168 9.696917 CCTTCATAAAATAGCACACTTTTCTTT 57.303 29.630 0.00 0.00 0.00 2.52
168 169 8.860088 ACCTTCATAAAATAGCACACTTTTCTT 58.140 29.630 0.00 0.00 0.00 2.52
169 170 8.299570 CACCTTCATAAAATAGCACACTTTTCT 58.700 33.333 0.00 0.00 0.00 2.52
170 171 7.062255 GCACCTTCATAAAATAGCACACTTTTC 59.938 37.037 0.00 0.00 0.00 2.29
171 172 6.868339 GCACCTTCATAAAATAGCACACTTTT 59.132 34.615 0.00 0.00 0.00 2.27
172 173 6.015519 TGCACCTTCATAAAATAGCACACTTT 60.016 34.615 0.00 0.00 0.00 2.66
173 174 5.476599 TGCACCTTCATAAAATAGCACACTT 59.523 36.000 0.00 0.00 0.00 3.16
174 175 5.009631 TGCACCTTCATAAAATAGCACACT 58.990 37.500 0.00 0.00 0.00 3.55
175 176 5.309323 TGCACCTTCATAAAATAGCACAC 57.691 39.130 0.00 0.00 0.00 3.82
176 177 5.105797 CCTTGCACCTTCATAAAATAGCACA 60.106 40.000 0.00 0.00 0.00 4.57
177 178 5.125417 TCCTTGCACCTTCATAAAATAGCAC 59.875 40.000 0.00 0.00 0.00 4.40
178 179 5.260424 TCCTTGCACCTTCATAAAATAGCA 58.740 37.500 0.00 0.00 0.00 3.49
179 180 5.835113 TCCTTGCACCTTCATAAAATAGC 57.165 39.130 0.00 0.00 0.00 2.97
180 181 7.970614 GTCTTTCCTTGCACCTTCATAAAATAG 59.029 37.037 0.00 0.00 0.00 1.73
181 182 7.361713 CGTCTTTCCTTGCACCTTCATAAAATA 60.362 37.037 0.00 0.00 0.00 1.40
182 183 6.570378 CGTCTTTCCTTGCACCTTCATAAAAT 60.570 38.462 0.00 0.00 0.00 1.82
183 184 5.278266 CGTCTTTCCTTGCACCTTCATAAAA 60.278 40.000 0.00 0.00 0.00 1.52
184 185 4.215399 CGTCTTTCCTTGCACCTTCATAAA 59.785 41.667 0.00 0.00 0.00 1.40
185 186 3.751175 CGTCTTTCCTTGCACCTTCATAA 59.249 43.478 0.00 0.00 0.00 1.90
186 187 3.244422 ACGTCTTTCCTTGCACCTTCATA 60.244 43.478 0.00 0.00 0.00 2.15
187 188 2.154462 CGTCTTTCCTTGCACCTTCAT 58.846 47.619 0.00 0.00 0.00 2.57
188 189 1.134220 ACGTCTTTCCTTGCACCTTCA 60.134 47.619 0.00 0.00 0.00 3.02
189 190 1.264288 CACGTCTTTCCTTGCACCTTC 59.736 52.381 0.00 0.00 0.00 3.46
190 191 1.308998 CACGTCTTTCCTTGCACCTT 58.691 50.000 0.00 0.00 0.00 3.50
191 192 1.166531 GCACGTCTTTCCTTGCACCT 61.167 55.000 0.00 0.00 34.97 4.00
192 193 1.166531 AGCACGTCTTTCCTTGCACC 61.167 55.000 0.00 0.00 37.44 5.01
193 194 1.508632 TAGCACGTCTTTCCTTGCAC 58.491 50.000 0.00 0.00 37.44 4.57
194 195 2.472695 ATAGCACGTCTTTCCTTGCA 57.527 45.000 0.00 0.00 37.44 4.08
195 196 3.831715 AAATAGCACGTCTTTCCTTGC 57.168 42.857 0.00 0.00 35.08 4.01
196 197 7.072177 TGATAAAATAGCACGTCTTTCCTTG 57.928 36.000 0.00 0.00 0.00 3.61
197 198 7.681939 TTGATAAAATAGCACGTCTTTCCTT 57.318 32.000 0.00 0.00 0.00 3.36
198 199 7.681939 TTTGATAAAATAGCACGTCTTTCCT 57.318 32.000 0.00 0.00 0.00 3.36
199 200 8.798153 CAATTTGATAAAATAGCACGTCTTTCC 58.202 33.333 0.00 0.00 0.00 3.13
200 201 8.313931 GCAATTTGATAAAATAGCACGTCTTTC 58.686 33.333 0.00 0.00 0.00 2.62
201 202 8.028938 AGCAATTTGATAAAATAGCACGTCTTT 58.971 29.630 0.00 0.00 0.00 2.52
202 203 7.538575 AGCAATTTGATAAAATAGCACGTCTT 58.461 30.769 0.00 0.00 0.00 3.01
203 204 7.088589 AGCAATTTGATAAAATAGCACGTCT 57.911 32.000 0.00 0.00 0.00 4.18
204 205 6.414987 GGAGCAATTTGATAAAATAGCACGTC 59.585 38.462 0.00 0.00 0.00 4.34
205 206 6.265577 GGAGCAATTTGATAAAATAGCACGT 58.734 36.000 0.00 0.00 0.00 4.49
206 207 5.396362 CGGAGCAATTTGATAAAATAGCACG 59.604 40.000 0.00 0.00 0.00 5.34
207 208 6.265577 ACGGAGCAATTTGATAAAATAGCAC 58.734 36.000 0.00 0.00 0.00 4.40
208 209 6.449635 ACGGAGCAATTTGATAAAATAGCA 57.550 33.333 0.00 0.00 0.00 3.49
209 210 5.621228 CGACGGAGCAATTTGATAAAATAGC 59.379 40.000 0.00 0.00 0.00 2.97
210 211 6.715464 ACGACGGAGCAATTTGATAAAATAG 58.285 36.000 0.00 0.00 0.00 1.73
211 212 6.671614 ACGACGGAGCAATTTGATAAAATA 57.328 33.333 0.00 0.00 0.00 1.40
212 213 5.560966 ACGACGGAGCAATTTGATAAAAT 57.439 34.783 0.00 0.00 0.00 1.82
213 214 5.446741 GCTACGACGGAGCAATTTGATAAAA 60.447 40.000 27.04 0.00 39.84 1.52
214 215 4.033587 GCTACGACGGAGCAATTTGATAAA 59.966 41.667 27.04 0.00 39.84 1.40
215 216 3.554324 GCTACGACGGAGCAATTTGATAA 59.446 43.478 27.04 0.00 39.84 1.75
216 217 3.120792 GCTACGACGGAGCAATTTGATA 58.879 45.455 27.04 0.00 39.84 2.15
217 218 1.933853 GCTACGACGGAGCAATTTGAT 59.066 47.619 27.04 0.00 39.84 2.57
218 219 1.355971 GCTACGACGGAGCAATTTGA 58.644 50.000 27.04 0.00 39.84 2.69
219 220 0.373716 GGCTACGACGGAGCAATTTG 59.626 55.000 31.87 0.00 41.98 2.32
220 221 1.082117 CGGCTACGACGGAGCAATTT 61.082 55.000 31.87 0.00 44.60 1.82
221 222 1.518572 CGGCTACGACGGAGCAATT 60.519 57.895 31.87 0.00 44.60 2.32
222 223 2.104331 CGGCTACGACGGAGCAAT 59.896 61.111 31.87 0.00 44.60 3.56
223 224 3.057548 TCGGCTACGACGGAGCAA 61.058 61.111 31.87 17.52 45.59 3.91
273 274 2.740714 GCACGTGCCCGATCAGTTC 61.741 63.158 30.12 0.00 37.88 3.01
316 317 1.532604 TAGCTAGGCAGTGCACACGT 61.533 55.000 21.04 14.36 36.20 4.49
318 319 1.086634 GCTAGCTAGGCAGTGCACAC 61.087 60.000 22.10 10.63 0.00 3.82
420 462 1.723273 CACGTATACTCGCCACGGA 59.277 57.895 0.56 0.00 39.91 4.69
470 528 1.557443 AAGCAACAGCACGCTCGTAC 61.557 55.000 0.00 0.00 37.54 3.67
512 570 4.158025 CGGTCTACACCTGAGTCAAACTAT 59.842 45.833 0.00 0.00 41.17 2.12
514 572 2.296471 CGGTCTACACCTGAGTCAAACT 59.704 50.000 0.00 0.00 41.17 2.66
536 594 6.337356 GCATTATCTCTCCTAGCTGATTACC 58.663 44.000 0.00 0.00 0.00 2.85
556 614 1.382522 CACACTATTCGGCTGGCATT 58.617 50.000 1.08 0.00 0.00 3.56
595 653 2.268298 CACGCCAGCTACGAAACTAAT 58.732 47.619 14.58 0.00 0.00 1.73
596 654 1.670674 CCACGCCAGCTACGAAACTAA 60.671 52.381 14.58 0.00 0.00 2.24
597 655 0.108992 CCACGCCAGCTACGAAACTA 60.109 55.000 14.58 0.00 0.00 2.24
598 656 1.374252 CCACGCCAGCTACGAAACT 60.374 57.895 14.58 0.00 0.00 2.66
602 660 2.360726 TCTCCACGCCAGCTACGA 60.361 61.111 14.58 0.00 0.00 3.43
649 719 8.920665 CGGCACATCAATTTAAGATTAACAAAA 58.079 29.630 0.00 0.00 0.00 2.44
655 725 6.821160 TGAGTCGGCACATCAATTTAAGATTA 59.179 34.615 0.00 0.00 0.00 1.75
664 734 3.827008 ATACTGAGTCGGCACATCAAT 57.173 42.857 0.00 0.00 0.00 2.57
665 735 3.610040 AATACTGAGTCGGCACATCAA 57.390 42.857 0.00 0.00 0.00 2.57
704 774 6.120905 ACGAAGGCACGTATCTATATCCTAT 58.879 40.000 7.87 0.00 44.72 2.57
735 805 7.648112 CAGATACTTACATACACGCACATACTT 59.352 37.037 0.00 0.00 0.00 2.24
753 825 8.615878 TTAACACAGTACAAATGCAGATACTT 57.384 30.769 0.00 0.00 0.00 2.24
889 1000 1.059913 ACAAGTTAGGACTGCTGGCT 58.940 50.000 0.00 0.00 35.91 4.75
890 1001 2.762535 TACAAGTTAGGACTGCTGGC 57.237 50.000 0.00 0.00 35.91 4.85
891 1002 3.437049 GCTTTACAAGTTAGGACTGCTGG 59.563 47.826 0.00 0.00 35.91 4.85
1221 1600 0.250124 TCCCTTGTCAACAACGCGAT 60.250 50.000 15.93 0.00 0.00 4.58
1316 1698 3.058914 AGTTGCACGCAAGAAAGACATAC 60.059 43.478 4.35 0.00 43.62 2.39
1556 1987 8.510505 GTTGCAAGAAAGTAATCTCAGAAGAAT 58.489 33.333 0.00 0.00 34.49 2.40
1558 1989 7.172190 CAGTTGCAAGAAAGTAATCTCAGAAGA 59.828 37.037 0.00 0.00 35.54 2.87
1559 1990 7.172190 TCAGTTGCAAGAAAGTAATCTCAGAAG 59.828 37.037 0.00 0.00 0.00 2.85
1561 1992 6.524734 TCAGTTGCAAGAAAGTAATCTCAGA 58.475 36.000 0.00 0.00 0.00 3.27
1564 1995 7.369803 TCATCAGTTGCAAGAAAGTAATCTC 57.630 36.000 0.00 0.00 0.00 2.75
1565 1996 7.750229 TTCATCAGTTGCAAGAAAGTAATCT 57.250 32.000 0.00 0.00 0.00 2.40
2472 2911 2.916702 ATCATCATCTACGCAAGGCA 57.083 45.000 0.00 0.00 46.39 4.75
2546 2994 6.154363 ACAAGCCCAAGCAGCTATTAATTAAA 59.846 34.615 1.21 0.00 40.49 1.52
2547 2995 5.656416 ACAAGCCCAAGCAGCTATTAATTAA 59.344 36.000 0.00 0.00 40.49 1.40
2656 3104 9.136952 GCAATTCTATGAATGGAATTAATGAGC 57.863 33.333 12.55 8.97 43.30 4.26
2897 3354 2.094545 GCCACCATTGAAACTGCCTTAG 60.095 50.000 0.00 0.00 0.00 2.18
3024 3481 0.393077 AGACACGTCCCTTGGTGAAG 59.607 55.000 0.00 0.00 37.58 3.02
3501 3963 6.374333 TGTTTTTCCTGGTATCTACTGCAATC 59.626 38.462 0.00 0.00 0.00 2.67
3503 3965 5.626142 TGTTTTTCCTGGTATCTACTGCAA 58.374 37.500 0.00 0.00 0.00 4.08
3821 4342 4.962693 GCATATGTGCCGTGAATAAGATC 58.037 43.478 2.47 0.00 45.76 2.75
3889 4410 3.475566 TTCCTGGCATCTATTTCCTCG 57.524 47.619 0.00 0.00 0.00 4.63
4023 5347 2.622064 ATCTACATCCAAACGGAGCC 57.378 50.000 0.00 0.00 35.52 4.70
4086 5410 6.777580 GGGTTGAATATCAATACCAATGTCCT 59.222 38.462 10.18 0.00 38.79 3.85
4148 5472 5.050490 ACATCGATCTTTCCTTGAATACCG 58.950 41.667 0.00 0.00 0.00 4.02
4151 5475 8.737168 AATCAACATCGATCTTTCCTTGAATA 57.263 30.769 0.00 0.00 0.00 1.75
4228 5553 0.320247 CGGAGCTGCTTGTCTGACTT 60.320 55.000 2.53 0.00 0.00 3.01
4416 5760 0.939577 CCATATTCGTGACGGAGCGG 60.940 60.000 4.70 0.00 0.00 5.52
4424 5768 2.494471 AGACGGACAACCATATTCGTGA 59.506 45.455 0.00 0.00 35.59 4.35
4427 5771 2.470821 GGAGACGGACAACCATATTCG 58.529 52.381 0.00 0.00 35.59 3.34
4549 5911 2.510411 CTGTCACAGTGGTGGGCA 59.490 61.111 0.00 0.00 45.32 5.36
4734 6112 3.598715 ACCGGTCGACGCAACTCA 61.599 61.111 9.92 0.00 42.52 3.41
4795 6173 1.367840 GATATTGCCTCGCTCCCGT 59.632 57.895 0.00 0.00 35.54 5.28
4996 6374 5.417580 GTGGAAGTCAATTAAACATGCCCTA 59.582 40.000 0.00 0.00 0.00 3.53
4997 6375 4.220602 GTGGAAGTCAATTAAACATGCCCT 59.779 41.667 0.00 0.00 0.00 5.19
5009 6387 3.704566 TGAGGTATAGCGTGGAAGTCAAT 59.295 43.478 0.00 0.00 0.00 2.57
5354 6769 3.485394 TGCACTCACTTGAATAAAGGCA 58.515 40.909 0.00 0.00 40.51 4.75
5583 7000 5.833131 AGGGAAAAGAACAGCACAGAATAAA 59.167 36.000 0.00 0.00 0.00 1.40
5605 7022 6.128472 GCTTTTCAGATAATTTTTGGCACAGG 60.128 38.462 0.00 0.00 42.39 4.00
5879 7303 2.028658 TCACAACTGTCATCTGGCTCTC 60.029 50.000 0.00 0.00 0.00 3.20
6090 7515 8.474025 GTGATCCTCAAACCCTCATATATCTAG 58.526 40.741 0.00 0.00 0.00 2.43
6328 7758 2.753296 CTAAGAGCAGGAGCATACAGC 58.247 52.381 0.00 0.00 45.49 4.40
6455 7891 3.622163 CCAGCTAGCAGTGAATTGAAGAG 59.378 47.826 18.83 0.00 0.00 2.85
6605 8042 2.032894 CCAACTTTGCTACACACACTCG 60.033 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.