Multiple sequence alignment - TraesCS6A01G030900

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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 TraesCS6A01G030900 chr6A 100.000 3524 0 0 1 3524 15746615 15750138 0.000000e+00 6508.0
1 TraesCS6A01G030900 chr6A 85.936 1998 238 32 615 2592 15727463 15729437 0.000000e+00 2093.0
2 TraesCS6A01G030900 chr6A 88.342 1707 169 17 849 2525 15734338 15736044 0.000000e+00 2023.0
3 TraesCS6A01G030900 chr6A 95.187 187 9 0 3054 3240 607063558 607063372 2.660000e-76 296.0
4 TraesCS6A01G030900 chr6A 80.412 194 27 5 615 806 15734076 15734260 1.710000e-28 137.0
5 TraesCS6A01G030900 chr6A 100.000 34 0 0 759 792 15756381 15756414 2.940000e-06 63.9
6 TraesCS6A01G030900 chr6D 91.780 3078 209 12 3 3054 14657592 14654533 0.000000e+00 4242.0
7 TraesCS6A01G030900 chr6D 86.424 2033 212 34 615 2604 14681181 14679170 0.000000e+00 2167.0
8 TraesCS6A01G030900 chr6D 90.103 1546 146 1 1001 2546 14664527 14662989 0.000000e+00 2001.0
9 TraesCS6A01G030900 chr6D 89.388 1536 163 0 1001 2536 14632985 14631450 0.000000e+00 1934.0
10 TraesCS6A01G030900 chr6D 94.359 195 8 3 3029 3223 333258859 333259050 2.660000e-76 296.0
11 TraesCS6A01G030900 chr6D 100.000 32 0 0 761 792 14633254 14633223 3.800000e-05 60.2
12 TraesCS6A01G030900 chr6B 91.261 3078 216 21 3 3055 26627918 26624869 0.000000e+00 4145.0
13 TraesCS6A01G030900 chr6B 89.181 1673 162 11 872 2525 26634940 26633268 0.000000e+00 2069.0
14 TraesCS6A01G030900 chr6B 85.032 2011 256 30 615 2604 26646017 26644031 0.000000e+00 2004.0
15 TraesCS6A01G030900 chr6B 90.033 1525 152 0 1001 2525 26597775 26596251 0.000000e+00 1975.0
16 TraesCS6A01G030900 chr6B 76.285 253 32 17 610 850 26635249 26635013 3.720000e-20 110.0
17 TraesCS6A01G030900 chr6B 97.368 38 1 0 755 792 26618682 26618645 8.170000e-07 65.8
18 TraesCS6A01G030900 chr6B 100.000 28 0 0 3436 3463 497232323 497232350 6.000000e-03 52.8
19 TraesCS6A01G030900 chr7B 84.974 386 52 6 3054 3436 585545117 585544735 1.530000e-103 387.0
20 TraesCS6A01G030900 chr5A 84.416 385 53 5 3054 3436 87574049 87573670 4.300000e-99 372.0
21 TraesCS6A01G030900 chr4A 94.521 219 12 0 3218 3436 75352632 75352850 4.360000e-89 339.0
22 TraesCS6A01G030900 chr4A 79.692 389 63 15 3054 3436 84532368 84531990 2.090000e-67 267.0
23 TraesCS6A01G030900 chr1A 92.760 221 16 0 3216 3436 570922808 570922588 1.580000e-83 320.0
24 TraesCS6A01G030900 chr3B 96.791 187 4 2 3038 3222 559731752 559731566 9.500000e-81 311.0
25 TraesCS6A01G030900 chr2B 91.928 223 17 1 3215 3436 401668948 401669170 9.500000e-81 311.0
26 TraesCS6A01G030900 chr4D 99.408 169 1 0 3054 3222 32130003 32130171 1.230000e-79 307.0
27 TraesCS6A01G030900 chr4D 99.408 169 1 0 3054 3222 111717972 111718140 1.230000e-79 307.0
28 TraesCS6A01G030900 chr5D 91.781 219 18 0 3218 3436 42063362 42063580 4.420000e-79 305.0
29 TraesCS6A01G030900 chr7D 91.743 218 18 0 3219 3436 592727407 592727624 1.590000e-78 303.0
30 TraesCS6A01G030900 chr2D 91.781 219 17 1 3219 3436 357894833 357895051 1.590000e-78 303.0
31 TraesCS6A01G030900 chr2D 96.216 185 6 1 3038 3222 267843852 267844035 5.720000e-78 302.0
32 TraesCS6A01G030900 chr5B 100.000 29 0 0 3434 3462 15035476 15035448 2.000000e-03 54.7
33 TraesCS6A01G030900 chr3A 100.000 29 0 0 3436 3464 593591764 593591736 2.000000e-03 54.7
34 TraesCS6A01G030900 chr3A 92.308 39 1 1 3425 3461 687499372 687499410 2.000000e-03 54.7
35 TraesCS6A01G030900 chr1D 100.000 29 0 0 3432 3460 447613125 447613153 2.000000e-03 54.7
36 TraesCS6A01G030900 chr1D 100.000 28 0 0 3432 3459 82712425 82712452 6.000000e-03 52.8
37 TraesCS6A01G030900 chr1B 100.000 29 0 0 3432 3460 248517006 248516978 2.000000e-03 54.7
38 TraesCS6A01G030900 chr2A 100.000 28 0 0 3434 3461 13405171 13405144 6.000000e-03 52.8
39 TraesCS6A01G030900 chr2A 100.000 28 0 0 3434 3461 36027930 36027903 6.000000e-03 52.8


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 TraesCS6A01G030900 chr6A 15746615 15750138 3523 False 6508.0 6508 100.000 1 3524 1 chr6A.!!$F2 3523
1 TraesCS6A01G030900 chr6A 15727463 15729437 1974 False 2093.0 2093 85.936 615 2592 1 chr6A.!!$F1 1977
2 TraesCS6A01G030900 chr6A 15734076 15736044 1968 False 1080.0 2023 84.377 615 2525 2 chr6A.!!$F4 1910
3 TraesCS6A01G030900 chr6D 14654533 14657592 3059 True 4242.0 4242 91.780 3 3054 1 chr6D.!!$R1 3051
4 TraesCS6A01G030900 chr6D 14679170 14681181 2011 True 2167.0 2167 86.424 615 2604 1 chr6D.!!$R3 1989
5 TraesCS6A01G030900 chr6D 14662989 14664527 1538 True 2001.0 2001 90.103 1001 2546 1 chr6D.!!$R2 1545
6 TraesCS6A01G030900 chr6D 14631450 14633254 1804 True 997.1 1934 94.694 761 2536 2 chr6D.!!$R4 1775
7 TraesCS6A01G030900 chr6B 26624869 26627918 3049 True 4145.0 4145 91.261 3 3055 1 chr6B.!!$R3 3052
8 TraesCS6A01G030900 chr6B 26644031 26646017 1986 True 2004.0 2004 85.032 615 2604 1 chr6B.!!$R4 1989
9 TraesCS6A01G030900 chr6B 26596251 26597775 1524 True 1975.0 1975 90.033 1001 2525 1 chr6B.!!$R1 1524
10 TraesCS6A01G030900 chr6B 26633268 26635249 1981 True 1089.5 2069 82.733 610 2525 2 chr6B.!!$R5 1915

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
451 453 0.167470 CGCTGTCCAAGTTGCATCAG 59.833 55.0 0.0 6.58 0.00 2.90 F
591 602 0.179111 TCGATTCTGGACACGCATCC 60.179 55.0 0.0 0.00 39.45 3.51 F
1012 1204 0.613777 GGTCGAAATGGAGGTGGAGT 59.386 55.0 0.0 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2109 0.589708 CCATAGGACGTGCGACGATA 59.410 55.0 14.18 5.88 46.05 2.92 R
1938 2133 0.895530 CGCCAAGGTCAGAGAGGTAA 59.104 55.0 0.00 0.00 0.00 2.85 R
2903 3107 0.450983 GCAGCTCATGAGTCTTTGCC 59.549 55.0 23.38 5.42 0.00 4.52 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
82 83 4.015872 TCAATGGAAGAAAAGGCGTACT 57.984 40.909 0.00 0.00 0.00 2.73
83 84 4.394729 TCAATGGAAGAAAAGGCGTACTT 58.605 39.130 0.00 0.00 42.52 2.24
85 86 1.877443 TGGAAGAAAAGGCGTACTTGC 59.123 47.619 0.00 0.00 39.96 4.01
112 113 3.153919 GTCATTTACCTGTGCCCTTGAA 58.846 45.455 0.00 0.00 0.00 2.69
120 121 4.415596 ACCTGTGCCCTTGAATTTGAATA 58.584 39.130 0.00 0.00 0.00 1.75
121 122 4.220602 ACCTGTGCCCTTGAATTTGAATAC 59.779 41.667 0.00 0.00 0.00 1.89
180 182 3.505680 TGTTTGTGTTGCAAAGTCAGAGT 59.494 39.130 0.00 0.00 46.50 3.24
210 212 3.619233 GTGCAATGTACACGTCCTTTT 57.381 42.857 0.00 0.00 0.00 2.27
211 213 4.735662 GTGCAATGTACACGTCCTTTTA 57.264 40.909 0.00 0.00 0.00 1.52
236 238 4.137116 TGAGGAAGACCGGAATAATGTG 57.863 45.455 9.46 0.00 41.83 3.21
245 247 2.811431 CCGGAATAATGTGTGTGTGTGT 59.189 45.455 0.00 0.00 0.00 3.72
246 248 3.364864 CCGGAATAATGTGTGTGTGTGTG 60.365 47.826 0.00 0.00 0.00 3.82
247 249 3.249799 CGGAATAATGTGTGTGTGTGTGT 59.750 43.478 0.00 0.00 0.00 3.72
256 258 2.070028 GTGTGTGTGTGTGTGTGTACA 58.930 47.619 0.00 0.00 0.00 2.90
323 325 1.246649 CACCTGCTGCATGTAAACCA 58.753 50.000 10.22 0.00 0.00 3.67
327 329 3.016031 CCTGCTGCATGTAAACCATACA 58.984 45.455 1.31 0.00 30.71 2.29
344 346 5.104360 ACCATACACTTGCTTCATCCAGTAT 60.104 40.000 0.00 0.00 0.00 2.12
412 414 1.153349 GGCCGACATGGGTTCTCTC 60.153 63.158 0.00 0.00 38.63 3.20
451 453 0.167470 CGCTGTCCAAGTTGCATCAG 59.833 55.000 0.00 6.58 0.00 2.90
474 477 1.580893 CACGGATTGTTGCATCGCG 60.581 57.895 0.00 0.00 0.00 5.87
503 506 2.146342 ACCTGATGCTCAAACTGTTCG 58.854 47.619 0.00 0.00 0.00 3.95
508 519 2.031258 TGCTCAAACTGTTCGTGGAA 57.969 45.000 0.00 0.00 0.00 3.53
509 520 2.571212 TGCTCAAACTGTTCGTGGAAT 58.429 42.857 0.00 0.00 0.00 3.01
513 524 3.138304 TCAAACTGTTCGTGGAATCTGG 58.862 45.455 0.00 0.00 0.00 3.86
581 592 3.249091 CAGTTCAGACACTCGATTCTGG 58.751 50.000 15.21 0.00 39.86 3.86
591 602 0.179111 TCGATTCTGGACACGCATCC 60.179 55.000 0.00 0.00 39.45 3.51
599 610 3.612247 GACACGCATCCTGTGGGCT 62.612 63.158 0.00 0.00 44.09 5.19
626 637 1.602851 GCTGAGCTGTGCATATTCTGG 59.397 52.381 0.00 0.00 0.00 3.86
707 724 6.980978 GGTTATTCGTCATCATCTTTCTCTCA 59.019 38.462 0.00 0.00 0.00 3.27
746 768 6.304356 ACCGCTGTTTAAACCTTTACTAAC 57.696 37.500 15.59 0.00 0.00 2.34
748 770 5.376537 CGCTGTTTAAACCTTTACTAACCG 58.623 41.667 15.59 0.00 0.00 4.44
801 824 7.280876 TGCAATAATACATTCTTCTGTCTGTCC 59.719 37.037 0.00 0.00 0.00 4.02
869 943 0.798776 CCAATGTCAACTCCTGCGTC 59.201 55.000 0.00 0.00 0.00 5.19
870 944 1.511850 CAATGTCAACTCCTGCGTCA 58.488 50.000 0.00 0.00 0.00 4.35
888 986 6.558009 TGCGTCATATAAATACCCGATAGAC 58.442 40.000 0.00 0.00 39.76 2.59
908 1007 1.550072 CGGGGATTCAAAGCACCAAAT 59.450 47.619 0.00 0.00 37.89 2.32
1012 1204 0.613777 GGTCGAAATGGAGGTGGAGT 59.386 55.000 0.00 0.00 0.00 3.85
1056 1251 1.963338 GAGCAAGTTCACGCTGCCT 60.963 57.895 0.00 0.00 38.99 4.75
1158 1353 4.228210 TGGATATCCTTCTTCACCTGCTTT 59.772 41.667 22.35 0.00 36.82 3.51
1440 1635 1.966451 CCTCGCCACCTTTGTGTCC 60.966 63.158 0.00 0.00 41.09 4.02
1545 1740 1.795170 GCGGTGCCACACAACTCATT 61.795 55.000 0.00 0.00 35.86 2.57
1578 1773 0.896923 TCCATGCCATCCAAAAGTGC 59.103 50.000 0.00 0.00 0.00 4.40
1881 2076 2.181777 CTAGACCTTCGCGCTGCA 59.818 61.111 5.56 0.00 0.00 4.41
2079 2274 0.037303 CCTCAGTGACTGCCATGGTT 59.963 55.000 14.67 0.00 0.00 3.67
2127 2322 1.453015 TGGCGCTGTCTTTGGTGTT 60.453 52.632 7.64 0.00 0.00 3.32
2172 2367 2.173356 CCTTGGCATCATCTCTGGGTTA 59.827 50.000 0.00 0.00 0.00 2.85
2296 2491 3.574354 TCATGGCATGCACATTACCTA 57.426 42.857 22.56 0.00 0.00 3.08
2299 2494 3.574354 TGGCATGCACATTACCTATCA 57.426 42.857 21.36 0.00 0.00 2.15
2346 2541 1.002134 CATGTTCTTCCCGGCCAGT 60.002 57.895 2.24 0.00 0.00 4.00
2427 2622 0.320247 GTCTCCATATCGCAGGCCAG 60.320 60.000 5.01 0.00 0.00 4.85
2472 2667 3.573558 CGTGGTAGGCGCAATGTT 58.426 55.556 10.83 0.00 0.00 2.71
2478 2673 2.143925 GGTAGGCGCAATGTTATCCTC 58.856 52.381 10.83 0.00 0.00 3.71
2660 2859 5.930569 ACTAGTAAACTTAAGGAAACGCTGG 59.069 40.000 7.53 2.36 0.00 4.85
2680 2879 1.065551 GTTTTGCGTTCCTGCTCTGTT 59.934 47.619 0.00 0.00 35.36 3.16
2682 2881 0.179059 TTGCGTTCCTGCTCTGTTCA 60.179 50.000 0.00 0.00 35.36 3.18
2749 2950 4.027458 CAGTTTTGATGTTTGTGTGCTTCG 60.027 41.667 0.00 0.00 0.00 3.79
2767 2968 4.560108 GCTTCGTACACCTTCCTTCAAGTA 60.560 45.833 0.00 0.00 0.00 2.24
2808 3009 8.871862 GCACTTTCAATGTATTATCAAATTGCA 58.128 29.630 0.00 0.00 32.61 4.08
2903 3107 4.670896 ATTTGTTCTGACCCCAAAACTG 57.329 40.909 0.00 0.00 32.39 3.16
2936 3140 4.019919 TGAGCTGCAAAATCGAATAAGC 57.980 40.909 1.02 0.00 0.00 3.09
2940 3144 4.860907 AGCTGCAAAATCGAATAAGCAAAG 59.139 37.500 1.02 0.00 0.00 2.77
2947 3151 4.825546 ATCGAATAAGCAAAGCCATGAG 57.174 40.909 0.00 0.00 0.00 2.90
3000 3204 4.091509 CGATGCGTCCTAAATATTGTAGCC 59.908 45.833 0.00 0.00 0.00 3.93
3064 3268 9.503369 AGTACTAATAACCATTACTTCCTCCTT 57.497 33.333 0.00 0.00 0.00 3.36
3065 3269 9.761504 GTACTAATAACCATTACTTCCTCCTTC 57.238 37.037 0.00 0.00 0.00 3.46
3066 3270 7.803131 ACTAATAACCATTACTTCCTCCTTCC 58.197 38.462 0.00 0.00 0.00 3.46
3067 3271 6.652205 AATAACCATTACTTCCTCCTTCCA 57.348 37.500 0.00 0.00 0.00 3.53
3068 3272 6.848562 ATAACCATTACTTCCTCCTTCCAT 57.151 37.500 0.00 0.00 0.00 3.41
3069 3273 4.779993 ACCATTACTTCCTCCTTCCATC 57.220 45.455 0.00 0.00 0.00 3.51
3070 3274 4.375313 ACCATTACTTCCTCCTTCCATCT 58.625 43.478 0.00 0.00 0.00 2.90
3071 3275 5.538877 ACCATTACTTCCTCCTTCCATCTA 58.461 41.667 0.00 0.00 0.00 1.98
3072 3276 6.153924 ACCATTACTTCCTCCTTCCATCTAT 58.846 40.000 0.00 0.00 0.00 1.98
3073 3277 7.313731 ACCATTACTTCCTCCTTCCATCTATA 58.686 38.462 0.00 0.00 0.00 1.31
3074 3278 7.964293 ACCATTACTTCCTCCTTCCATCTATAT 59.036 37.037 0.00 0.00 0.00 0.86
3075 3279 9.494055 CCATTACTTCCTCCTTCCATCTATATA 57.506 37.037 0.00 0.00 0.00 0.86
3077 3281 9.722317 ATTACTTCCTCCTTCCATCTATATAGG 57.278 37.037 9.89 0.00 0.00 2.57
3078 3282 6.507568 ACTTCCTCCTTCCATCTATATAGGG 58.492 44.000 9.89 4.49 0.00 3.53
3079 3283 4.884961 TCCTCCTTCCATCTATATAGGGC 58.115 47.826 9.89 0.00 0.00 5.19
3080 3284 3.970640 CCTCCTTCCATCTATATAGGGCC 59.029 52.174 9.89 0.00 0.00 5.80
3081 3285 4.327332 CCTCCTTCCATCTATATAGGGCCT 60.327 50.000 12.58 12.58 0.00 5.19
3082 3286 5.103043 CCTCCTTCCATCTATATAGGGCCTA 60.103 48.000 17.16 17.16 0.00 3.93
3083 3287 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
3084 3288 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
3085 3289 6.846505 TCCTTCCATCTATATAGGGCCTAATG 59.153 42.308 18.91 15.42 0.00 1.90
3086 3290 6.465035 CCTTCCATCTATATAGGGCCTAATGC 60.465 46.154 18.91 0.00 40.16 3.56
3087 3291 4.588951 TCCATCTATATAGGGCCTAATGCG 59.411 45.833 18.91 10.04 42.61 4.73
3088 3292 4.345257 CCATCTATATAGGGCCTAATGCGT 59.655 45.833 18.91 2.76 42.61 5.24
3089 3293 5.163301 CCATCTATATAGGGCCTAATGCGTT 60.163 44.000 18.91 1.94 42.61 4.84
3090 3294 6.349300 CATCTATATAGGGCCTAATGCGTTT 58.651 40.000 18.91 1.12 42.61 3.60
3091 3295 6.368779 TCTATATAGGGCCTAATGCGTTTT 57.631 37.500 18.91 0.30 42.61 2.43
3092 3296 6.775708 TCTATATAGGGCCTAATGCGTTTTT 58.224 36.000 18.91 0.00 42.61 1.94
3093 3297 5.959618 ATATAGGGCCTAATGCGTTTTTC 57.040 39.130 18.91 0.00 42.61 2.29
3094 3298 0.808755 AGGGCCTAATGCGTTTTTCG 59.191 50.000 2.82 0.00 42.61 3.46
3095 3299 0.806241 GGGCCTAATGCGTTTTTCGA 59.194 50.000 0.84 0.00 42.61 3.71
3096 3300 1.202143 GGGCCTAATGCGTTTTTCGAG 60.202 52.381 0.84 0.00 42.61 4.04
3097 3301 1.202143 GGCCTAATGCGTTTTTCGAGG 60.202 52.381 0.00 0.00 42.61 4.63
3098 3302 1.794076 GCCTAATGCGTTTTTCGAGGC 60.794 52.381 12.47 12.47 44.30 4.70
3099 3303 1.737793 CCTAATGCGTTTTTCGAGGCT 59.262 47.619 0.00 0.00 42.86 4.58
3100 3304 2.933906 CCTAATGCGTTTTTCGAGGCTA 59.066 45.455 0.00 0.00 42.86 3.93
3101 3305 3.372822 CCTAATGCGTTTTTCGAGGCTAA 59.627 43.478 0.00 0.00 42.86 3.09
3102 3306 2.894307 ATGCGTTTTTCGAGGCTAAC 57.106 45.000 0.00 0.00 42.86 2.34
3103 3307 1.873698 TGCGTTTTTCGAGGCTAACT 58.126 45.000 0.00 0.00 42.86 2.24
3104 3308 2.215196 TGCGTTTTTCGAGGCTAACTT 58.785 42.857 0.00 0.00 42.86 2.66
3105 3309 2.614983 TGCGTTTTTCGAGGCTAACTTT 59.385 40.909 0.00 0.00 42.86 2.66
3106 3310 2.971261 GCGTTTTTCGAGGCTAACTTTG 59.029 45.455 0.00 0.00 42.86 2.77
3107 3311 3.303526 GCGTTTTTCGAGGCTAACTTTGA 60.304 43.478 0.00 0.00 42.86 2.69
3108 3312 4.209112 CGTTTTTCGAGGCTAACTTTGAC 58.791 43.478 0.00 0.00 42.86 3.18
3109 3313 4.534168 GTTTTTCGAGGCTAACTTTGACC 58.466 43.478 0.00 0.00 0.00 4.02
3110 3314 3.478857 TTTCGAGGCTAACTTTGACCA 57.521 42.857 0.00 0.00 0.00 4.02
3111 3315 3.478857 TTCGAGGCTAACTTTGACCAA 57.521 42.857 0.00 0.00 0.00 3.67
3112 3316 3.478857 TCGAGGCTAACTTTGACCAAA 57.521 42.857 0.00 0.00 0.00 3.28
3113 3317 4.015872 TCGAGGCTAACTTTGACCAAAT 57.984 40.909 0.00 0.00 0.00 2.32
3114 3318 5.155278 TCGAGGCTAACTTTGACCAAATA 57.845 39.130 0.00 0.00 0.00 1.40
3115 3319 5.741011 TCGAGGCTAACTTTGACCAAATAT 58.259 37.500 0.00 0.00 0.00 1.28
3116 3320 6.177610 TCGAGGCTAACTTTGACCAAATATT 58.822 36.000 0.00 0.00 0.00 1.28
3117 3321 7.332557 TCGAGGCTAACTTTGACCAAATATTA 58.667 34.615 0.00 0.00 0.00 0.98
3118 3322 7.494625 TCGAGGCTAACTTTGACCAAATATTAG 59.505 37.037 15.32 15.32 34.88 1.73
3119 3323 7.494625 CGAGGCTAACTTTGACCAAATATTAGA 59.505 37.037 19.82 0.15 34.31 2.10
3120 3324 8.738645 AGGCTAACTTTGACCAAATATTAGAG 57.261 34.615 19.82 7.39 34.31 2.43
3121 3325 7.283354 AGGCTAACTTTGACCAAATATTAGAGC 59.717 37.037 19.82 13.12 34.31 4.09
3122 3326 7.067008 GGCTAACTTTGACCAAATATTAGAGCA 59.933 37.037 19.82 0.00 34.31 4.26
3123 3327 8.458843 GCTAACTTTGACCAAATATTAGAGCAA 58.541 33.333 19.82 0.00 34.31 3.91
3142 3346 8.859236 AGAGCAATAATATATGACATGCAACT 57.141 30.769 10.78 7.52 34.89 3.16
3143 3347 9.293404 AGAGCAATAATATATGACATGCAACTT 57.707 29.630 10.78 0.00 34.89 2.66
3152 3356 3.963665 TGACATGCAACTTACACAAAGC 58.036 40.909 0.00 0.00 38.93 3.51
3153 3357 3.379688 TGACATGCAACTTACACAAAGCA 59.620 39.130 0.00 0.00 38.93 3.91
3154 3358 3.705604 ACATGCAACTTACACAAAGCAC 58.294 40.909 0.00 0.00 38.93 4.40
3155 3359 3.130164 ACATGCAACTTACACAAAGCACA 59.870 39.130 0.00 0.00 38.93 4.57
3156 3360 3.143807 TGCAACTTACACAAAGCACAC 57.856 42.857 0.00 0.00 38.93 3.82
3157 3361 2.159310 TGCAACTTACACAAAGCACACC 60.159 45.455 0.00 0.00 38.93 4.16
3158 3362 2.715268 CAACTTACACAAAGCACACCG 58.285 47.619 0.00 0.00 38.93 4.94
3159 3363 2.032680 ACTTACACAAAGCACACCGT 57.967 45.000 0.00 0.00 38.93 4.83
3160 3364 2.361789 ACTTACACAAAGCACACCGTT 58.638 42.857 0.00 0.00 38.93 4.44
3161 3365 3.533547 ACTTACACAAAGCACACCGTTA 58.466 40.909 0.00 0.00 38.93 3.18
3162 3366 3.940221 ACTTACACAAAGCACACCGTTAA 59.060 39.130 0.00 0.00 38.93 2.01
3163 3367 4.395542 ACTTACACAAAGCACACCGTTAAA 59.604 37.500 0.00 0.00 38.93 1.52
3164 3368 5.066764 ACTTACACAAAGCACACCGTTAAAT 59.933 36.000 0.00 0.00 38.93 1.40
3165 3369 4.379339 ACACAAAGCACACCGTTAAATT 57.621 36.364 0.00 0.00 0.00 1.82
3166 3370 4.356289 ACACAAAGCACACCGTTAAATTC 58.644 39.130 0.00 0.00 0.00 2.17
3167 3371 3.420576 CACAAAGCACACCGTTAAATTCG 59.579 43.478 0.00 0.00 0.00 3.34
3168 3372 3.065648 ACAAAGCACACCGTTAAATTCGT 59.934 39.130 0.00 0.00 0.00 3.85
3169 3373 2.961522 AGCACACCGTTAAATTCGTG 57.038 45.000 0.00 0.00 0.00 4.35
3170 3374 2.215196 AGCACACCGTTAAATTCGTGT 58.785 42.857 0.00 0.00 0.00 4.49
3171 3375 2.032377 AGCACACCGTTAAATTCGTGTG 60.032 45.455 13.39 13.39 40.02 3.82
3172 3376 2.286536 GCACACCGTTAAATTCGTGTGT 60.287 45.455 17.54 12.66 40.37 3.72
3173 3377 3.284914 CACACCGTTAAATTCGTGTGTG 58.715 45.455 17.05 17.05 44.50 3.82
3174 3378 3.196463 ACACCGTTAAATTCGTGTGTGA 58.804 40.909 9.71 0.00 39.31 3.58
3175 3379 3.622163 ACACCGTTAAATTCGTGTGTGAA 59.378 39.130 9.71 0.00 39.31 3.18
3176 3380 4.094590 ACACCGTTAAATTCGTGTGTGAAA 59.905 37.500 9.71 0.00 39.31 2.69
3177 3381 4.668837 CACCGTTAAATTCGTGTGTGAAAG 59.331 41.667 0.00 0.00 0.00 2.62
3178 3382 4.215965 CCGTTAAATTCGTGTGTGAAAGG 58.784 43.478 0.00 0.00 0.00 3.11
3179 3383 4.024725 CCGTTAAATTCGTGTGTGAAAGGA 60.025 41.667 0.00 0.00 0.00 3.36
3180 3384 5.137403 CGTTAAATTCGTGTGTGAAAGGAG 58.863 41.667 0.00 0.00 0.00 3.69
3181 3385 3.626028 AAATTCGTGTGTGAAAGGAGC 57.374 42.857 0.00 0.00 0.00 4.70
3182 3386 2.550830 ATTCGTGTGTGAAAGGAGCT 57.449 45.000 0.00 0.00 0.00 4.09
3183 3387 2.325583 TTCGTGTGTGAAAGGAGCTT 57.674 45.000 0.00 0.00 0.00 3.74
3184 3388 2.325583 TCGTGTGTGAAAGGAGCTTT 57.674 45.000 0.00 0.00 36.29 3.51
3185 3389 2.210116 TCGTGTGTGAAAGGAGCTTTC 58.790 47.619 0.00 0.00 46.88 2.62
3214 3418 9.518906 TGATATAATTTTCACATTGTGCATGTC 57.481 29.630 12.04 6.55 43.17 3.06
3215 3419 9.518906 GATATAATTTTCACATTGTGCATGTCA 57.481 29.630 12.04 0.00 43.17 3.58
3217 3421 6.474819 AATTTTCACATTGTGCATGTCATG 57.525 33.333 12.04 8.56 43.17 3.07
3218 3422 4.587584 TTTCACATTGTGCATGTCATGT 57.412 36.364 14.26 0.00 43.17 3.21
3219 3423 5.702349 TTTCACATTGTGCATGTCATGTA 57.298 34.783 14.26 7.11 43.17 2.29
3220 3424 4.683501 TCACATTGTGCATGTCATGTAC 57.316 40.909 22.84 22.84 43.17 2.90
3221 3425 4.325972 TCACATTGTGCATGTCATGTACT 58.674 39.130 27.47 11.55 43.17 2.73
3222 3426 4.392754 TCACATTGTGCATGTCATGTACTC 59.607 41.667 27.47 9.41 43.17 2.59
3223 3427 3.691118 ACATTGTGCATGTCATGTACTCC 59.309 43.478 27.47 8.79 43.17 3.85
3224 3428 2.401583 TGTGCATGTCATGTACTCCC 57.598 50.000 27.47 8.49 44.74 4.30
3225 3429 1.908619 TGTGCATGTCATGTACTCCCT 59.091 47.619 27.47 0.00 44.74 4.20
3226 3430 2.093500 TGTGCATGTCATGTACTCCCTC 60.093 50.000 27.47 7.56 44.74 4.30
3227 3431 1.486310 TGCATGTCATGTACTCCCTCC 59.514 52.381 14.26 0.00 0.00 4.30
3228 3432 1.486310 GCATGTCATGTACTCCCTCCA 59.514 52.381 14.26 0.00 0.00 3.86
3229 3433 2.105477 GCATGTCATGTACTCCCTCCAT 59.895 50.000 14.26 0.00 0.00 3.41
3230 3434 3.434167 GCATGTCATGTACTCCCTCCATT 60.434 47.826 14.26 0.00 0.00 3.16
3231 3435 4.785301 CATGTCATGTACTCCCTCCATTT 58.215 43.478 4.53 0.00 0.00 2.32
3232 3436 4.927267 TGTCATGTACTCCCTCCATTTT 57.073 40.909 0.00 0.00 0.00 1.82
3233 3437 5.255397 TGTCATGTACTCCCTCCATTTTT 57.745 39.130 0.00 0.00 0.00 1.94
3234 3438 6.381498 TGTCATGTACTCCCTCCATTTTTA 57.619 37.500 0.00 0.00 0.00 1.52
3235 3439 6.969043 TGTCATGTACTCCCTCCATTTTTAT 58.031 36.000 0.00 0.00 0.00 1.40
3236 3440 7.410174 TGTCATGTACTCCCTCCATTTTTATT 58.590 34.615 0.00 0.00 0.00 1.40
3237 3441 7.893302 TGTCATGTACTCCCTCCATTTTTATTT 59.107 33.333 0.00 0.00 0.00 1.40
3238 3442 9.403583 GTCATGTACTCCCTCCATTTTTATTTA 57.596 33.333 0.00 0.00 0.00 1.40
3239 3443 9.403583 TCATGTACTCCCTCCATTTTTATTTAC 57.596 33.333 0.00 0.00 0.00 2.01
3240 3444 9.408648 CATGTACTCCCTCCATTTTTATTTACT 57.591 33.333 0.00 0.00 0.00 2.24
3241 3445 9.628500 ATGTACTCCCTCCATTTTTATTTACTC 57.372 33.333 0.00 0.00 0.00 2.59
3242 3446 8.832735 TGTACTCCCTCCATTTTTATTTACTCT 58.167 33.333 0.00 0.00 0.00 3.24
3243 3447 9.110502 GTACTCCCTCCATTTTTATTTACTCTG 57.889 37.037 0.00 0.00 0.00 3.35
3244 3448 6.603599 ACTCCCTCCATTTTTATTTACTCTGC 59.396 38.462 0.00 0.00 0.00 4.26
3245 3449 6.489603 TCCCTCCATTTTTATTTACTCTGCA 58.510 36.000 0.00 0.00 0.00 4.41
3246 3450 7.125391 TCCCTCCATTTTTATTTACTCTGCAT 58.875 34.615 0.00 0.00 0.00 3.96
3247 3451 8.278639 TCCCTCCATTTTTATTTACTCTGCATA 58.721 33.333 0.00 0.00 0.00 3.14
3248 3452 9.082313 CCCTCCATTTTTATTTACTCTGCATAT 57.918 33.333 0.00 0.00 0.00 1.78
3263 3467 7.697352 CTCTGCATATTAGAGTTGACAGAAG 57.303 40.000 5.84 0.00 37.48 2.85
3264 3468 7.175347 TCTGCATATTAGAGTTGACAGAAGT 57.825 36.000 0.00 0.00 30.46 3.01
3265 3469 7.261325 TCTGCATATTAGAGTTGACAGAAGTC 58.739 38.462 0.00 0.00 45.19 3.01
3291 3495 6.115450 ACTTCGTAAAGTTTGACCAAGTTC 57.885 37.500 0.00 0.00 43.28 3.01
3292 3496 5.644636 ACTTCGTAAAGTTTGACCAAGTTCA 59.355 36.000 0.00 0.00 43.28 3.18
3293 3497 6.317893 ACTTCGTAAAGTTTGACCAAGTTCAT 59.682 34.615 0.00 0.00 43.28 2.57
3294 3498 7.496591 ACTTCGTAAAGTTTGACCAAGTTCATA 59.503 33.333 0.00 0.00 43.28 2.15
3295 3499 7.416154 TCGTAAAGTTTGACCAAGTTCATAG 57.584 36.000 0.00 0.00 0.00 2.23
3296 3500 7.211573 TCGTAAAGTTTGACCAAGTTCATAGA 58.788 34.615 0.00 0.00 0.00 1.98
3297 3501 7.711772 TCGTAAAGTTTGACCAAGTTCATAGAA 59.288 33.333 0.00 0.00 0.00 2.10
3298 3502 8.339714 CGTAAAGTTTGACCAAGTTCATAGAAA 58.660 33.333 0.00 0.00 0.00 2.52
3420 3624 9.945904 TTTTTGTTTATAAACCTGGTCAAAGTT 57.054 25.926 22.47 0.00 38.11 2.66
3421 3625 9.945904 TTTTGTTTATAAACCTGGTCAAAGTTT 57.054 25.926 22.47 0.00 38.11 2.66
3431 3635 9.594478 AAACCTGGTCAAAGTTTATAAAACTTG 57.406 29.630 16.20 6.80 40.10 3.16
3432 3636 8.528044 ACCTGGTCAAAGTTTATAAAACTTGA 57.472 30.769 16.20 14.72 40.10 3.02
3433 3637 8.410912 ACCTGGTCAAAGTTTATAAAACTTGAC 58.589 33.333 27.00 27.00 40.10 3.18
3434 3638 8.630037 CCTGGTCAAAGTTTATAAAACTTGACT 58.370 33.333 29.93 13.29 40.10 3.41
3452 3656 8.429237 ACTTGACTTATATAGATGGAAGGAGG 57.571 38.462 0.00 0.00 0.00 4.30
3453 3657 7.456269 ACTTGACTTATATAGATGGAAGGAGGG 59.544 40.741 0.00 0.00 0.00 4.30
3454 3658 7.116089 TGACTTATATAGATGGAAGGAGGGA 57.884 40.000 0.00 0.00 0.00 4.20
3455 3659 7.185565 TGACTTATATAGATGGAAGGAGGGAG 58.814 42.308 0.00 0.00 0.00 4.30
3456 3660 7.122311 ACTTATATAGATGGAAGGAGGGAGT 57.878 40.000 0.00 0.00 0.00 3.85
3457 3661 8.245929 ACTTATATAGATGGAAGGAGGGAGTA 57.754 38.462 0.00 0.00 0.00 2.59
3458 3662 8.340757 ACTTATATAGATGGAAGGAGGGAGTAG 58.659 40.741 0.00 0.00 0.00 2.57
3459 3663 2.095604 AGATGGAAGGAGGGAGTAGC 57.904 55.000 0.00 0.00 0.00 3.58
3460 3664 1.292242 AGATGGAAGGAGGGAGTAGCA 59.708 52.381 0.00 0.00 0.00 3.49
3461 3665 2.090267 AGATGGAAGGAGGGAGTAGCAT 60.090 50.000 0.00 0.00 0.00 3.79
3462 3666 3.142977 AGATGGAAGGAGGGAGTAGCATA 59.857 47.826 0.00 0.00 0.00 3.14
3463 3667 3.414759 TGGAAGGAGGGAGTAGCATAA 57.585 47.619 0.00 0.00 0.00 1.90
3464 3668 3.309296 TGGAAGGAGGGAGTAGCATAAG 58.691 50.000 0.00 0.00 0.00 1.73
3465 3669 2.037902 GGAAGGAGGGAGTAGCATAAGC 59.962 54.545 0.00 0.00 42.56 3.09
3475 3679 4.876701 GCATAAGCGGGATCCACA 57.123 55.556 15.23 0.00 0.00 4.17
3476 3680 3.329300 GCATAAGCGGGATCCACAT 57.671 52.632 15.23 0.15 0.00 3.21
3477 3681 0.877071 GCATAAGCGGGATCCACATG 59.123 55.000 15.23 9.58 0.00 3.21
3478 3682 1.527034 CATAAGCGGGATCCACATGG 58.473 55.000 15.23 0.00 0.00 3.66
3479 3683 0.250901 ATAAGCGGGATCCACATGGC 60.251 55.000 15.23 8.37 34.44 4.40
3480 3684 1.631071 TAAGCGGGATCCACATGGCA 61.631 55.000 15.23 0.00 34.44 4.92
3481 3685 2.898920 AAGCGGGATCCACATGGCAG 62.899 60.000 15.23 0.00 34.44 4.85
3482 3686 2.910360 CGGGATCCACATGGCAGA 59.090 61.111 15.23 0.00 34.44 4.26
3483 3687 1.227764 CGGGATCCACATGGCAGAG 60.228 63.158 15.23 0.00 34.44 3.35
3484 3688 1.527844 GGGATCCACATGGCAGAGC 60.528 63.158 15.23 0.00 34.44 4.09
3496 3700 2.947127 GGCAGAGCCTGGAAGATAAT 57.053 50.000 0.00 0.00 46.69 1.28
3497 3701 2.777094 GGCAGAGCCTGGAAGATAATC 58.223 52.381 0.00 0.00 46.69 1.75
3498 3702 2.371510 GGCAGAGCCTGGAAGATAATCT 59.628 50.000 0.00 0.00 46.69 2.40
3499 3703 3.181446 GGCAGAGCCTGGAAGATAATCTT 60.181 47.826 0.00 0.00 46.69 2.40
3500 3704 4.040952 GGCAGAGCCTGGAAGATAATCTTA 59.959 45.833 0.00 0.00 46.69 2.10
3501 3705 5.237048 GCAGAGCCTGGAAGATAATCTTAG 58.763 45.833 0.00 0.00 32.41 2.18
3502 3706 5.221621 GCAGAGCCTGGAAGATAATCTTAGT 60.222 44.000 0.00 0.00 32.41 2.24
3503 3707 6.687647 GCAGAGCCTGGAAGATAATCTTAGTT 60.688 42.308 0.00 0.00 32.41 2.24
3504 3708 6.705381 CAGAGCCTGGAAGATAATCTTAGTTG 59.295 42.308 0.00 0.00 36.73 3.16
3505 3709 6.385467 AGAGCCTGGAAGATAATCTTAGTTGT 59.615 38.462 0.00 0.00 36.73 3.32
3506 3710 6.963322 AGCCTGGAAGATAATCTTAGTTGTT 58.037 36.000 0.00 0.00 36.73 2.83
3507 3711 7.406104 AGCCTGGAAGATAATCTTAGTTGTTT 58.594 34.615 0.00 0.00 36.73 2.83
3508 3712 7.890655 AGCCTGGAAGATAATCTTAGTTGTTTT 59.109 33.333 0.00 0.00 36.73 2.43
3509 3713 8.523658 GCCTGGAAGATAATCTTAGTTGTTTTT 58.476 33.333 0.00 0.00 36.73 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.990426 CGCCTTTTCTTCCATTGAATGTTT 59.010 37.500 4.27 0.00 0.00 2.83
60 61 4.394729 AGTACGCCTTTTCTTCCATTGAA 58.605 39.130 0.00 0.00 0.00 2.69
100 101 5.389859 TGTATTCAAATTCAAGGGCACAG 57.610 39.130 0.00 0.00 0.00 3.66
104 105 4.807304 CAGCATGTATTCAAATTCAAGGGC 59.193 41.667 0.00 0.00 0.00 5.19
121 122 0.035881 ACCCTGACACTGACAGCATG 59.964 55.000 1.25 0.00 46.00 4.06
180 182 2.190161 GTACATTGCACGCAGTCGATA 58.810 47.619 0.00 0.00 41.61 2.92
210 212 7.282224 CACATTATTCCGGTCTTCCTCAAAATA 59.718 37.037 0.00 0.00 0.00 1.40
211 213 6.095440 CACATTATTCCGGTCTTCCTCAAAAT 59.905 38.462 0.00 0.00 0.00 1.82
236 238 2.070028 TGTACACACACACACACACAC 58.930 47.619 0.00 0.00 0.00 3.82
245 247 3.194062 CGATGGCATATGTACACACACA 58.806 45.455 0.00 0.00 37.54 3.72
246 248 2.032894 GCGATGGCATATGTACACACAC 60.033 50.000 0.00 0.00 36.91 3.82
247 249 2.209273 GCGATGGCATATGTACACACA 58.791 47.619 0.00 0.00 39.62 3.72
283 285 0.887933 AACTTTTGCCGCGATCCAAT 59.112 45.000 8.23 0.00 0.00 3.16
320 322 3.009473 ACTGGATGAAGCAAGTGTATGGT 59.991 43.478 0.00 0.00 0.00 3.55
323 325 5.994250 ACATACTGGATGAAGCAAGTGTAT 58.006 37.500 6.92 0.00 39.06 2.29
327 329 4.081642 ACGTACATACTGGATGAAGCAAGT 60.082 41.667 6.92 0.00 39.06 3.16
364 366 1.029681 AAAGTGAGAAAACGGGGCAC 58.970 50.000 0.00 0.00 0.00 5.01
412 414 0.391793 GAAGCTTCAGGTTCCCTCCG 60.392 60.000 21.67 0.00 44.29 4.63
451 453 2.584791 GATGCAACAATCCGTGTGAAC 58.415 47.619 0.00 0.00 40.60 3.18
489 492 2.031258 TTCCACGAACAGTTTGAGCA 57.969 45.000 7.60 0.00 0.00 4.26
503 506 2.359850 TGCGGTGCCAGATTCCAC 60.360 61.111 0.00 0.00 0.00 4.02
508 519 1.078426 GTTACCTGCGGTGCCAGAT 60.078 57.895 10.01 0.00 36.19 2.90
509 520 1.764571 AAGTTACCTGCGGTGCCAGA 61.765 55.000 10.01 0.00 36.19 3.86
513 524 1.791103 TTGCAAGTTACCTGCGGTGC 61.791 55.000 10.01 3.78 36.19 5.01
581 592 3.127533 GCCCACAGGATGCGTGTC 61.128 66.667 7.99 0.00 42.53 3.67
599 610 2.029518 CACAGCTCAGCACGTGGA 59.970 61.111 18.88 5.99 32.92 4.02
626 637 0.179006 GGATGGGCCAAGGATCAGAC 60.179 60.000 11.89 0.00 36.34 3.51
748 770 1.636988 GAATCATGGCTGCAACTTGC 58.363 50.000 6.82 6.82 45.29 4.01
801 824 2.414293 CGAAGGGTAAGACAGACAGACG 60.414 54.545 0.00 0.00 0.00 4.18
888 986 0.965439 TTTGGTGCTTTGAATCCCCG 59.035 50.000 0.00 0.00 0.00 5.73
908 1007 0.253044 GGAGGTGCTAATGGCTGTGA 59.747 55.000 0.00 0.00 42.39 3.58
1056 1251 1.367471 CTTGTGCTCGGAGTCCACA 59.633 57.895 10.49 12.55 37.66 4.17
1158 1353 4.373116 GCGGCGAAGGTGGAGACA 62.373 66.667 12.98 0.00 38.70 3.41
1440 1635 1.945394 GTGCTCATCCAGTATTGGCAG 59.055 52.381 0.00 0.00 44.63 4.85
1545 1740 2.233431 GGCATGGAAAACAAGTGGCATA 59.767 45.455 0.00 0.00 35.41 3.14
1824 2019 1.443702 CTCGGCGATGACGTTGTCA 60.444 57.895 11.27 1.65 46.90 3.58
1914 2109 0.589708 CCATAGGACGTGCGACGATA 59.410 55.000 14.18 5.88 46.05 2.92
1938 2133 0.895530 CGCCAAGGTCAGAGAGGTAA 59.104 55.000 0.00 0.00 0.00 2.85
2079 2274 1.680522 GGGCGCAGATGGAGAAGAGA 61.681 60.000 10.83 0.00 0.00 3.10
2127 2322 1.523154 GCCTGGAAACGAATGGTGCA 61.523 55.000 0.00 0.00 0.00 4.57
2299 2494 1.344953 TGTGGGAAGTGCACCAGAGT 61.345 55.000 14.63 0.00 37.45 3.24
2346 2541 1.395045 CCTCCTCCGTAGCATCAGCA 61.395 60.000 0.00 0.00 45.49 4.41
2427 2622 1.801178 CGGGAGTTCTCTGCAAACTTC 59.199 52.381 3.86 1.93 37.10 3.01
2472 2667 2.734591 GCGGATGTGGCGAGGATA 59.265 61.111 0.00 0.00 0.00 2.59
2660 2859 0.663153 ACAGAGCAGGAACGCAAAAC 59.337 50.000 0.00 0.00 0.00 2.43
2701 2900 6.037172 GTGCATGTAGTAATTTCGGACTCAAT 59.963 38.462 0.00 0.00 0.00 2.57
2749 2950 7.172019 TCGAAATTTACTTGAAGGAAGGTGTAC 59.828 37.037 0.00 0.00 35.78 2.90
2767 2968 5.049167 TGAAAGTGCAAGCATTCGAAATTT 58.951 33.333 0.00 0.00 0.00 1.82
2808 3009 3.181487 GCACATTGGCTGTAATTTCGGAT 60.181 43.478 0.00 0.00 35.91 4.18
2848 3052 3.730662 CGGCAAAATGGACTTTGTATCCG 60.731 47.826 0.00 0.00 39.30 4.18
2903 3107 0.450983 GCAGCTCATGAGTCTTTGCC 59.549 55.000 23.38 5.42 0.00 4.52
2936 3140 9.859427 TTTAAATTGAATAGTCTCATGGCTTTG 57.141 29.630 0.00 0.00 0.00 2.77
2940 3144 6.912591 CCGTTTAAATTGAATAGTCTCATGGC 59.087 38.462 0.00 0.00 0.00 4.40
2947 3151 8.911247 ATTCAAGCCGTTTAAATTGAATAGTC 57.089 30.769 19.01 0.00 45.67 2.59
3000 3204 1.341209 TCTATATCTGGCGTGGCAGTG 59.659 52.381 20.97 9.17 0.00 3.66
3043 3247 7.758820 TGGAAGGAGGAAGTAATGGTTATTA 57.241 36.000 0.00 0.00 0.00 0.98
3055 3259 5.365314 GCCCTATATAGATGGAAGGAGGAAG 59.635 48.000 11.53 0.00 0.00 3.46
3056 3260 5.281314 GCCCTATATAGATGGAAGGAGGAA 58.719 45.833 11.53 0.00 0.00 3.36
3057 3261 4.327010 GGCCCTATATAGATGGAAGGAGGA 60.327 50.000 11.53 0.00 0.00 3.71
3058 3262 3.970640 GGCCCTATATAGATGGAAGGAGG 59.029 52.174 11.53 1.87 0.00 4.30
3059 3263 4.889780 AGGCCCTATATAGATGGAAGGAG 58.110 47.826 11.53 0.00 0.00 3.69
3060 3264 4.994411 AGGCCCTATATAGATGGAAGGA 57.006 45.455 11.53 0.00 0.00 3.36
3061 3265 6.465035 GCATTAGGCCCTATATAGATGGAAGG 60.465 46.154 11.53 3.94 36.11 3.46
3062 3266 6.529220 GCATTAGGCCCTATATAGATGGAAG 58.471 44.000 11.53 0.00 36.11 3.46
3063 3267 5.070446 CGCATTAGGCCCTATATAGATGGAA 59.930 44.000 11.53 0.00 40.31 3.53
3064 3268 4.588951 CGCATTAGGCCCTATATAGATGGA 59.411 45.833 11.53 0.00 40.31 3.41
3065 3269 4.345257 ACGCATTAGGCCCTATATAGATGG 59.655 45.833 11.53 6.04 40.31 3.51
3066 3270 5.537300 ACGCATTAGGCCCTATATAGATG 57.463 43.478 11.53 6.87 40.31 2.90
3067 3271 6.561519 AAACGCATTAGGCCCTATATAGAT 57.438 37.500 11.53 0.00 40.31 1.98
3068 3272 6.368779 AAAACGCATTAGGCCCTATATAGA 57.631 37.500 11.53 0.00 40.31 1.98
3069 3273 6.183360 CGAAAAACGCATTAGGCCCTATATAG 60.183 42.308 0.00 2.46 40.31 1.31
3070 3274 5.640357 CGAAAAACGCATTAGGCCCTATATA 59.360 40.000 0.00 0.00 40.31 0.86
3071 3275 4.454504 CGAAAAACGCATTAGGCCCTATAT 59.545 41.667 0.00 0.00 40.31 0.86
3072 3276 3.810941 CGAAAAACGCATTAGGCCCTATA 59.189 43.478 0.00 0.00 40.31 1.31
3073 3277 2.616842 CGAAAAACGCATTAGGCCCTAT 59.383 45.455 0.00 0.00 40.31 2.57
3074 3278 2.011222 CGAAAAACGCATTAGGCCCTA 58.989 47.619 0.00 0.00 40.31 3.53
3075 3279 0.808755 CGAAAAACGCATTAGGCCCT 59.191 50.000 0.00 0.00 40.31 5.19
3076 3280 0.806241 TCGAAAAACGCATTAGGCCC 59.194 50.000 0.00 0.00 42.26 5.80
3077 3281 1.202143 CCTCGAAAAACGCATTAGGCC 60.202 52.381 0.00 0.00 42.26 5.19
3078 3282 1.794076 GCCTCGAAAAACGCATTAGGC 60.794 52.381 0.00 0.00 45.73 3.93
3079 3283 1.737793 AGCCTCGAAAAACGCATTAGG 59.262 47.619 0.00 0.00 42.26 2.69
3080 3284 4.092968 AGTTAGCCTCGAAAAACGCATTAG 59.907 41.667 0.00 0.00 42.26 1.73
3081 3285 3.998341 AGTTAGCCTCGAAAAACGCATTA 59.002 39.130 0.00 0.00 42.26 1.90
3082 3286 2.812011 AGTTAGCCTCGAAAAACGCATT 59.188 40.909 0.00 0.00 42.26 3.56
3083 3287 2.423577 AGTTAGCCTCGAAAAACGCAT 58.576 42.857 0.00 0.00 42.26 4.73
3084 3288 1.873698 AGTTAGCCTCGAAAAACGCA 58.126 45.000 0.00 0.00 42.26 5.24
3085 3289 2.963498 AAGTTAGCCTCGAAAAACGC 57.037 45.000 0.00 0.00 42.26 4.84
3086 3290 4.209112 GTCAAAGTTAGCCTCGAAAAACG 58.791 43.478 0.00 0.00 44.09 3.60
3087 3291 4.035909 TGGTCAAAGTTAGCCTCGAAAAAC 59.964 41.667 0.00 0.00 0.00 2.43
3088 3292 4.200874 TGGTCAAAGTTAGCCTCGAAAAA 58.799 39.130 0.00 0.00 0.00 1.94
3089 3293 3.811083 TGGTCAAAGTTAGCCTCGAAAA 58.189 40.909 0.00 0.00 0.00 2.29
3090 3294 3.478857 TGGTCAAAGTTAGCCTCGAAA 57.521 42.857 0.00 0.00 0.00 3.46
3091 3295 3.478857 TTGGTCAAAGTTAGCCTCGAA 57.521 42.857 0.00 0.00 0.00 3.71
3092 3296 3.478857 TTTGGTCAAAGTTAGCCTCGA 57.521 42.857 0.00 0.00 0.00 4.04
3093 3297 6.436843 AATATTTGGTCAAAGTTAGCCTCG 57.563 37.500 2.55 0.00 33.32 4.63
3094 3298 8.732746 TCTAATATTTGGTCAAAGTTAGCCTC 57.267 34.615 17.32 0.00 35.14 4.70
3095 3299 7.283354 GCTCTAATATTTGGTCAAAGTTAGCCT 59.717 37.037 17.32 0.41 35.14 4.58
3096 3300 7.067008 TGCTCTAATATTTGGTCAAAGTTAGCC 59.933 37.037 17.32 13.62 35.14 3.93
3097 3301 7.985476 TGCTCTAATATTTGGTCAAAGTTAGC 58.015 34.615 17.32 13.47 35.14 3.09
3116 3320 9.948964 AGTTGCATGTCATATATTATTGCTCTA 57.051 29.630 0.00 0.00 0.00 2.43
3117 3321 8.859236 AGTTGCATGTCATATATTATTGCTCT 57.141 30.769 0.00 0.00 0.00 4.09
3126 3330 8.131100 GCTTTGTGTAAGTTGCATGTCATATAT 58.869 33.333 0.00 0.00 36.19 0.86
3127 3331 7.120432 TGCTTTGTGTAAGTTGCATGTCATATA 59.880 33.333 0.00 0.00 36.19 0.86
3128 3332 6.072008 TGCTTTGTGTAAGTTGCATGTCATAT 60.072 34.615 0.00 0.00 36.19 1.78
3129 3333 5.240403 TGCTTTGTGTAAGTTGCATGTCATA 59.760 36.000 0.00 0.00 36.19 2.15
3130 3334 4.037803 TGCTTTGTGTAAGTTGCATGTCAT 59.962 37.500 0.00 0.00 36.19 3.06
3131 3335 3.379688 TGCTTTGTGTAAGTTGCATGTCA 59.620 39.130 0.00 0.00 36.19 3.58
3132 3336 3.730715 GTGCTTTGTGTAAGTTGCATGTC 59.269 43.478 0.00 0.00 36.19 3.06
3133 3337 3.130164 TGTGCTTTGTGTAAGTTGCATGT 59.870 39.130 0.00 0.00 36.19 3.21
3134 3338 3.486841 GTGTGCTTTGTGTAAGTTGCATG 59.513 43.478 0.00 0.00 36.19 4.06
3135 3339 3.490761 GGTGTGCTTTGTGTAAGTTGCAT 60.491 43.478 0.00 0.00 36.19 3.96
3136 3340 2.159310 GGTGTGCTTTGTGTAAGTTGCA 60.159 45.455 0.00 0.00 36.19 4.08
3137 3341 2.459934 GGTGTGCTTTGTGTAAGTTGC 58.540 47.619 0.00 0.00 36.19 4.17
3138 3342 2.096819 ACGGTGTGCTTTGTGTAAGTTG 59.903 45.455 0.00 0.00 36.19 3.16
3139 3343 2.361789 ACGGTGTGCTTTGTGTAAGTT 58.638 42.857 0.00 0.00 36.19 2.66
3140 3344 2.032680 ACGGTGTGCTTTGTGTAAGT 57.967 45.000 0.00 0.00 36.19 2.24
3141 3345 4.539509 TTAACGGTGTGCTTTGTGTAAG 57.460 40.909 0.00 0.00 36.90 2.34
3142 3346 4.959596 TTTAACGGTGTGCTTTGTGTAA 57.040 36.364 0.00 0.00 0.00 2.41
3143 3347 5.502153 AATTTAACGGTGTGCTTTGTGTA 57.498 34.783 0.00 0.00 0.00 2.90
3144 3348 4.356289 GAATTTAACGGTGTGCTTTGTGT 58.644 39.130 0.00 0.00 0.00 3.72
3145 3349 3.420576 CGAATTTAACGGTGTGCTTTGTG 59.579 43.478 0.00 0.00 0.00 3.33
3146 3350 3.065648 ACGAATTTAACGGTGTGCTTTGT 59.934 39.130 0.00 0.00 34.93 2.83
3147 3351 3.420576 CACGAATTTAACGGTGTGCTTTG 59.579 43.478 0.00 0.00 34.93 2.77
3148 3352 3.065648 ACACGAATTTAACGGTGTGCTTT 59.934 39.130 0.00 0.00 34.93 3.51
3149 3353 2.614983 ACACGAATTTAACGGTGTGCTT 59.385 40.909 0.00 0.00 34.93 3.91
3150 3354 2.032377 CACACGAATTTAACGGTGTGCT 60.032 45.455 9.81 0.00 36.70 4.40
3151 3355 2.286536 ACACACGAATTTAACGGTGTGC 60.287 45.455 19.53 0.00 41.40 4.57
3152 3356 3.284914 CACACACGAATTTAACGGTGTG 58.715 45.455 18.39 18.39 45.49 3.82
3153 3357 3.196463 TCACACACGAATTTAACGGTGT 58.804 40.909 0.00 0.00 41.61 4.16
3154 3358 3.863396 TCACACACGAATTTAACGGTG 57.137 42.857 0.00 0.00 37.66 4.94
3155 3359 4.260866 CCTTTCACACACGAATTTAACGGT 60.261 41.667 0.00 0.00 34.93 4.83
3156 3360 4.024725 TCCTTTCACACACGAATTTAACGG 60.025 41.667 0.00 0.00 34.93 4.44
3157 3361 5.085636 TCCTTTCACACACGAATTTAACG 57.914 39.130 0.00 0.00 0.00 3.18
3158 3362 4.909880 GCTCCTTTCACACACGAATTTAAC 59.090 41.667 0.00 0.00 0.00 2.01
3159 3363 4.819630 AGCTCCTTTCACACACGAATTTAA 59.180 37.500 0.00 0.00 0.00 1.52
3160 3364 4.385825 AGCTCCTTTCACACACGAATTTA 58.614 39.130 0.00 0.00 0.00 1.40
3161 3365 3.214328 AGCTCCTTTCACACACGAATTT 58.786 40.909 0.00 0.00 0.00 1.82
3162 3366 2.851195 AGCTCCTTTCACACACGAATT 58.149 42.857 0.00 0.00 0.00 2.17
3163 3367 2.550830 AGCTCCTTTCACACACGAAT 57.449 45.000 0.00 0.00 0.00 3.34
3164 3368 2.325583 AAGCTCCTTTCACACACGAA 57.674 45.000 0.00 0.00 0.00 3.85
3165 3369 2.210116 GAAAGCTCCTTTCACACACGA 58.790 47.619 11.65 0.00 46.23 4.35
3166 3370 2.670401 GAAAGCTCCTTTCACACACG 57.330 50.000 11.65 0.00 46.23 4.49
3202 3406 3.065786 GGGAGTACATGACATGCACAATG 59.934 47.826 18.79 0.00 42.48 2.82
3203 3407 3.054139 AGGGAGTACATGACATGCACAAT 60.054 43.478 18.79 3.69 0.00 2.71
3204 3408 2.305635 AGGGAGTACATGACATGCACAA 59.694 45.455 18.79 0.00 0.00 3.33
3205 3409 1.908619 AGGGAGTACATGACATGCACA 59.091 47.619 18.79 1.79 0.00 4.57
3206 3410 2.555199 GAGGGAGTACATGACATGCAC 58.445 52.381 15.49 12.79 0.00 4.57
3207 3411 1.486310 GGAGGGAGTACATGACATGCA 59.514 52.381 15.49 0.00 0.00 3.96
3208 3412 1.486310 TGGAGGGAGTACATGACATGC 59.514 52.381 15.49 0.11 0.00 4.06
3209 3413 4.428294 AATGGAGGGAGTACATGACATG 57.572 45.455 14.02 14.02 0.00 3.21
3210 3414 5.456921 AAAATGGAGGGAGTACATGACAT 57.543 39.130 0.00 0.00 0.00 3.06
3211 3415 4.927267 AAAATGGAGGGAGTACATGACA 57.073 40.909 0.00 0.00 0.00 3.58
3212 3416 7.881775 AATAAAAATGGAGGGAGTACATGAC 57.118 36.000 0.00 0.00 0.00 3.06
3213 3417 9.403583 GTAAATAAAAATGGAGGGAGTACATGA 57.596 33.333 0.00 0.00 0.00 3.07
3214 3418 9.408648 AGTAAATAAAAATGGAGGGAGTACATG 57.591 33.333 0.00 0.00 0.00 3.21
3215 3419 9.628500 GAGTAAATAAAAATGGAGGGAGTACAT 57.372 33.333 0.00 0.00 0.00 2.29
3216 3420 8.832735 AGAGTAAATAAAAATGGAGGGAGTACA 58.167 33.333 0.00 0.00 0.00 2.90
3217 3421 9.110502 CAGAGTAAATAAAAATGGAGGGAGTAC 57.889 37.037 0.00 0.00 0.00 2.73
3218 3422 7.773690 GCAGAGTAAATAAAAATGGAGGGAGTA 59.226 37.037 0.00 0.00 0.00 2.59
3219 3423 6.603599 GCAGAGTAAATAAAAATGGAGGGAGT 59.396 38.462 0.00 0.00 0.00 3.85
3220 3424 6.603201 TGCAGAGTAAATAAAAATGGAGGGAG 59.397 38.462 0.00 0.00 0.00 4.30
3221 3425 6.489603 TGCAGAGTAAATAAAAATGGAGGGA 58.510 36.000 0.00 0.00 0.00 4.20
3222 3426 6.773976 TGCAGAGTAAATAAAAATGGAGGG 57.226 37.500 0.00 0.00 0.00 4.30
3239 3443 7.264221 ACTTCTGTCAACTCTAATATGCAGAG 58.736 38.462 11.37 11.37 44.28 3.35
3240 3444 7.175347 ACTTCTGTCAACTCTAATATGCAGA 57.825 36.000 0.00 0.00 0.00 4.26
3241 3445 7.462109 GACTTCTGTCAACTCTAATATGCAG 57.538 40.000 0.00 0.00 42.48 4.41
3269 3473 6.114221 TGAACTTGGTCAAACTTTACGAAG 57.886 37.500 0.00 0.00 37.43 3.79
3270 3474 6.687081 ATGAACTTGGTCAAACTTTACGAA 57.313 33.333 0.00 0.00 0.00 3.85
3271 3475 7.211573 TCTATGAACTTGGTCAAACTTTACGA 58.788 34.615 0.00 0.00 0.00 3.43
3272 3476 7.416154 TCTATGAACTTGGTCAAACTTTACG 57.584 36.000 0.00 0.00 0.00 3.18
3394 3598 9.945904 AACTTTGACCAGGTTTATAAACAAAAA 57.054 25.926 25.59 15.36 40.63 1.94
3395 3599 9.945904 AAACTTTGACCAGGTTTATAAACAAAA 57.054 25.926 25.59 15.10 40.63 2.44
3405 3609 9.594478 CAAGTTTTATAAACTTTGACCAGGTTT 57.406 29.630 13.29 0.00 38.32 3.27
3406 3610 8.973182 TCAAGTTTTATAAACTTTGACCAGGTT 58.027 29.630 13.29 0.00 38.32 3.50
3407 3611 8.410912 GTCAAGTTTTATAAACTTTGACCAGGT 58.589 33.333 25.87 0.00 38.32 4.00
3408 3612 8.630037 AGTCAAGTTTTATAAACTTTGACCAGG 58.370 33.333 28.94 12.85 38.32 4.45
3426 3630 8.875168 CCTCCTTCCATCTATATAAGTCAAGTT 58.125 37.037 0.00 0.00 0.00 2.66
3427 3631 7.456269 CCCTCCTTCCATCTATATAAGTCAAGT 59.544 40.741 0.00 0.00 0.00 3.16
3428 3632 7.676043 TCCCTCCTTCCATCTATATAAGTCAAG 59.324 40.741 0.00 0.00 0.00 3.02
3429 3633 7.544650 TCCCTCCTTCCATCTATATAAGTCAA 58.455 38.462 0.00 0.00 0.00 3.18
3430 3634 7.116089 TCCCTCCTTCCATCTATATAAGTCA 57.884 40.000 0.00 0.00 0.00 3.41
3431 3635 7.186268 ACTCCCTCCTTCCATCTATATAAGTC 58.814 42.308 0.00 0.00 0.00 3.01
3432 3636 7.122311 ACTCCCTCCTTCCATCTATATAAGT 57.878 40.000 0.00 0.00 0.00 2.24
3433 3637 7.286775 GCTACTCCCTCCTTCCATCTATATAAG 59.713 44.444 0.00 0.00 0.00 1.73
3434 3638 7.126733 GCTACTCCCTCCTTCCATCTATATAA 58.873 42.308 0.00 0.00 0.00 0.98
3435 3639 6.219772 TGCTACTCCCTCCTTCCATCTATATA 59.780 42.308 0.00 0.00 0.00 0.86
3436 3640 5.016782 TGCTACTCCCTCCTTCCATCTATAT 59.983 44.000 0.00 0.00 0.00 0.86
3437 3641 4.357097 TGCTACTCCCTCCTTCCATCTATA 59.643 45.833 0.00 0.00 0.00 1.31
3438 3642 3.142977 TGCTACTCCCTCCTTCCATCTAT 59.857 47.826 0.00 0.00 0.00 1.98
3439 3643 2.518407 TGCTACTCCCTCCTTCCATCTA 59.482 50.000 0.00 0.00 0.00 1.98
3440 3644 1.292242 TGCTACTCCCTCCTTCCATCT 59.708 52.381 0.00 0.00 0.00 2.90
3441 3645 1.794714 TGCTACTCCCTCCTTCCATC 58.205 55.000 0.00 0.00 0.00 3.51
3442 3646 2.503869 ATGCTACTCCCTCCTTCCAT 57.496 50.000 0.00 0.00 0.00 3.41
3443 3647 3.309296 CTTATGCTACTCCCTCCTTCCA 58.691 50.000 0.00 0.00 0.00 3.53
3444 3648 2.037902 GCTTATGCTACTCCCTCCTTCC 59.962 54.545 0.00 0.00 36.03 3.46
3445 3649 2.288518 CGCTTATGCTACTCCCTCCTTC 60.289 54.545 0.00 0.00 36.97 3.46
3446 3650 1.689273 CGCTTATGCTACTCCCTCCTT 59.311 52.381 0.00 0.00 36.97 3.36
3447 3651 1.333177 CGCTTATGCTACTCCCTCCT 58.667 55.000 0.00 0.00 36.97 3.69
3448 3652 0.318762 CCGCTTATGCTACTCCCTCC 59.681 60.000 0.00 0.00 36.97 4.30
3449 3653 0.318762 CCCGCTTATGCTACTCCCTC 59.681 60.000 0.00 0.00 36.97 4.30
3450 3654 0.105658 TCCCGCTTATGCTACTCCCT 60.106 55.000 0.00 0.00 36.97 4.20
3451 3655 0.977395 ATCCCGCTTATGCTACTCCC 59.023 55.000 0.00 0.00 36.97 4.30
3452 3656 1.066787 GGATCCCGCTTATGCTACTCC 60.067 57.143 0.00 0.00 36.97 3.85
3453 3657 1.618837 TGGATCCCGCTTATGCTACTC 59.381 52.381 9.90 0.00 36.97 2.59
3454 3658 1.344763 GTGGATCCCGCTTATGCTACT 59.655 52.381 9.90 0.00 36.97 2.57
3455 3659 1.070134 TGTGGATCCCGCTTATGCTAC 59.930 52.381 9.90 0.00 34.70 3.58
3456 3660 1.419381 TGTGGATCCCGCTTATGCTA 58.581 50.000 9.90 0.00 34.70 3.49
3457 3661 0.767375 ATGTGGATCCCGCTTATGCT 59.233 50.000 9.90 0.00 34.70 3.79
3458 3662 0.877071 CATGTGGATCCCGCTTATGC 59.123 55.000 9.90 0.00 34.70 3.14
3459 3663 1.527034 CCATGTGGATCCCGCTTATG 58.473 55.000 9.90 6.56 37.39 1.90
3460 3664 0.250901 GCCATGTGGATCCCGCTTAT 60.251 55.000 9.90 0.00 37.39 1.73
3461 3665 1.148273 GCCATGTGGATCCCGCTTA 59.852 57.895 9.90 0.00 37.39 3.09
3462 3666 2.124151 GCCATGTGGATCCCGCTT 60.124 61.111 9.90 0.00 37.39 4.68
3463 3667 3.410628 TGCCATGTGGATCCCGCT 61.411 61.111 9.90 0.00 37.39 5.52
3464 3668 2.903855 CTGCCATGTGGATCCCGC 60.904 66.667 9.90 2.62 37.39 6.13
3465 3669 1.227764 CTCTGCCATGTGGATCCCG 60.228 63.158 9.90 0.00 37.39 5.14
3466 3670 1.527844 GCTCTGCCATGTGGATCCC 60.528 63.158 9.90 0.85 37.39 3.85
3467 3671 4.154296 GCTCTGCCATGTGGATCC 57.846 61.111 4.20 4.20 37.39 3.36
3474 3678 8.878324 AAGATTATCTTCCAGGCTCTGCCATG 62.878 46.154 11.38 6.27 41.43 3.66
3475 3679 6.937875 AAGATTATCTTCCAGGCTCTGCCAT 61.938 44.000 11.38 0.00 41.43 4.40
3476 3680 5.677621 AAGATTATCTTCCAGGCTCTGCCA 61.678 45.833 11.38 0.00 41.43 4.92
3477 3681 3.181446 AAGATTATCTTCCAGGCTCTGCC 60.181 47.826 0.99 0.00 39.97 4.85
3478 3682 3.767902 AGATTATCTTCCAGGCTCTGC 57.232 47.619 0.00 0.00 0.00 4.26
3479 3683 6.418057 ACTAAGATTATCTTCCAGGCTCTG 57.582 41.667 11.06 0.00 37.89 3.35
3480 3684 6.385467 ACAACTAAGATTATCTTCCAGGCTCT 59.615 38.462 11.06 0.00 37.89 4.09
3481 3685 6.587273 ACAACTAAGATTATCTTCCAGGCTC 58.413 40.000 11.06 0.00 37.89 4.70
3482 3686 6.567602 ACAACTAAGATTATCTTCCAGGCT 57.432 37.500 11.06 0.00 37.89 4.58
3483 3687 7.631717 AAACAACTAAGATTATCTTCCAGGC 57.368 36.000 11.06 0.00 37.89 4.85


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

AutoCloner maintained by Alex Coulton.