Multiple sequence alignment - TraesCS3A01G250300

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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 TraesCS3A01G250300 chr3A 100.000 4026 0 0 1 4026 468734330 468730305 0.000000e+00 7435.0
1 TraesCS3A01G250300 chr3A 81.127 355 43 12 3287 3621 720411927 720412277 3.090000e-66 263.0
2 TraesCS3A01G250300 chr3A 89.375 160 15 2 3077 3234 581610820 581610979 2.450000e-47 200.0
3 TraesCS3A01G250300 chr3D 95.238 2394 77 12 703 3071 350877255 350874874 0.000000e+00 3755.0
4 TraesCS3A01G250300 chr3D 90.922 716 44 15 3312 4026 350873241 350872546 0.000000e+00 942.0
5 TraesCS3A01G250300 chr3B 95.153 2352 100 9 724 3071 449446812 449444471 0.000000e+00 3699.0
6 TraesCS3A01G250300 chr3B 89.863 730 53 18 3287 4011 449443338 449442625 0.000000e+00 918.0
7 TraesCS3A01G250300 chr3B 88.952 706 66 7 1 696 644321132 644321835 0.000000e+00 861.0
8 TraesCS3A01G250300 chr3B 88.968 698 64 8 7 696 29791079 29790387 0.000000e+00 850.0
9 TraesCS3A01G250300 chr1D 87.940 738 64 12 1 720 403202054 403201324 0.000000e+00 846.0
10 TraesCS3A01G250300 chr1D 84.274 248 32 6 3395 3641 488616828 488616587 6.730000e-58 235.0
11 TraesCS3A01G250300 chr7B 89.497 676 55 7 39 700 599799938 599800611 0.000000e+00 841.0
12 TraesCS3A01G250300 chr5D 88.062 712 68 4 1 695 404766814 404767525 0.000000e+00 828.0
13 TraesCS3A01G250300 chr5D 79.725 291 33 21 3287 3569 9549221 9549493 1.910000e-43 187.0
14 TraesCS3A01G250300 chr5D 90.411 73 7 0 3162 3234 547555581 547555509 3.310000e-16 97.1
15 TraesCS3A01G250300 chr1A 88.302 701 61 10 1 690 351471579 351472269 0.000000e+00 821.0
16 TraesCS3A01G250300 chr1A 76.647 501 61 35 3287 3735 587872535 587872039 4.050000e-55 226.0
17 TraesCS3A01G250300 chr1A 97.143 70 1 1 3083 3151 554011586 554011517 2.540000e-22 117.0
18 TraesCS3A01G250300 chr2B 87.822 698 77 4 7 696 216932991 216932294 0.000000e+00 811.0
19 TraesCS3A01G250300 chr2B 81.105 344 36 14 3300 3620 621957555 621957218 8.640000e-62 248.0
20 TraesCS3A01G250300 chr4D 89.177 656 55 7 48 695 442641672 442641025 0.000000e+00 804.0
21 TraesCS3A01G250300 chr5B 87.844 691 73 9 7 696 608314869 608314189 0.000000e+00 800.0
22 TraesCS3A01G250300 chr5B 92.025 163 9 2 3077 3235 429305116 429305278 4.050000e-55 226.0
23 TraesCS3A01G250300 chr5B 88.957 163 13 3 3078 3235 588915184 588915346 3.170000e-46 196.0
24 TraesCS3A01G250300 chr7A 79.794 485 42 25 3287 3729 83300192 83300662 6.540000e-78 302.0
25 TraesCS3A01G250300 chr7A 84.375 128 17 3 3884 4009 712084499 712084625 5.460000e-24 122.0
26 TraesCS3A01G250300 chr4A 83.090 343 31 11 3289 3612 441780948 441781282 1.830000e-73 287.0
27 TraesCS3A01G250300 chr6B 81.818 297 38 12 3287 3576 684145335 684145622 6.730000e-58 235.0
28 TraesCS3A01G250300 chr5A 89.571 163 12 2 3077 3234 599465579 599465417 6.820000e-48 202.0
29 TraesCS3A01G250300 chr2D 88.608 158 12 5 3077 3230 606633099 606633254 1.910000e-43 187.0
30 TraesCS3A01G250300 chr2D 87.681 138 12 2 3102 3234 615460772 615460909 5.390000e-34 156.0
31 TraesCS3A01G250300 chr2A 85.385 130 11 5 3110 3234 80889814 80889688 1.170000e-25 128.0
32 TraesCS3A01G250300 chr2A 87.619 105 9 4 3619 3722 661084908 661084807 7.070000e-23 119.0
33 TraesCS3A01G250300 chr2A 90.541 74 7 0 1 74 306110444 306110371 9.210000e-17 99.0
34 TraesCS3A01G250300 chr7D 81.250 144 22 4 3867 4009 618337047 618337186 1.180000e-20 111.0
35 TraesCS3A01G250300 chr6D 100.000 29 0 0 3202 3230 363014916 363014944 2.000000e-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 TraesCS3A01G250300 chr3A 468730305 468734330 4025 True 7435.0 7435 100.000 1 4026 1 chr3A.!!$R1 4025
1 TraesCS3A01G250300 chr3D 350872546 350877255 4709 True 2348.5 3755 93.080 703 4026 2 chr3D.!!$R1 3323
2 TraesCS3A01G250300 chr3B 449442625 449446812 4187 True 2308.5 3699 92.508 724 4011 2 chr3B.!!$R2 3287
3 TraesCS3A01G250300 chr3B 644321132 644321835 703 False 861.0 861 88.952 1 696 1 chr3B.!!$F1 695
4 TraesCS3A01G250300 chr3B 29790387 29791079 692 True 850.0 850 88.968 7 696 1 chr3B.!!$R1 689
5 TraesCS3A01G250300 chr1D 403201324 403202054 730 True 846.0 846 87.940 1 720 1 chr1D.!!$R1 719
6 TraesCS3A01G250300 chr7B 599799938 599800611 673 False 841.0 841 89.497 39 700 1 chr7B.!!$F1 661
7 TraesCS3A01G250300 chr5D 404766814 404767525 711 False 828.0 828 88.062 1 695 1 chr5D.!!$F2 694
8 TraesCS3A01G250300 chr1A 351471579 351472269 690 False 821.0 821 88.302 1 690 1 chr1A.!!$F1 689
9 TraesCS3A01G250300 chr2B 216932294 216932991 697 True 811.0 811 87.822 7 696 1 chr2B.!!$R1 689
10 TraesCS3A01G250300 chr4D 442641025 442641672 647 True 804.0 804 89.177 48 695 1 chr4D.!!$R1 647
11 TraesCS3A01G250300 chr5B 608314189 608314869 680 True 800.0 800 87.844 7 696 1 chr5B.!!$R1 689

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
280 306 1.148157 CGCGCGACAATGAAGAGGAT 61.148 55.0 28.94 0.0 0.00 3.24 F
581 627 1.227999 TGCTGCAGTTTAGCACGTCC 61.228 55.0 16.64 0.0 45.52 4.79 F
1617 1667 0.462759 AGTCGATGCCAAAGCTAGCC 60.463 55.0 12.13 0.0 40.80 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1352 0.394488 ACGAGAGCGAAGGGAGATCA 60.394 55.0 0.00 0.00 41.64 2.92 R
1812 1883 1.172180 CCACCGCCGCCATTATCATT 61.172 55.0 0.00 0.00 0.00 2.57 R
3274 3345 0.039346 GAATACTAGACGAGGCCCGC 60.039 60.0 12.78 6.71 43.32 6.13 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
170 196 2.584608 CTCCGGGTGACATGGGTC 59.415 66.667 0.00 0.00 44.57 4.46
257 283 2.597455 TCCGAGCTCCACATGATGATA 58.403 47.619 8.47 0.00 0.00 2.15
280 306 1.148157 CGCGCGACAATGAAGAGGAT 61.148 55.000 28.94 0.00 0.00 3.24
365 409 3.080319 TGATTGTTGATGTGCCATTCGA 58.920 40.909 0.00 0.00 0.00 3.71
393 437 8.465999 TGTGTGAACTTTTATGTCATGAACTTT 58.534 29.630 0.00 0.00 0.00 2.66
412 456 4.803613 ACTTTGTTCGGATTTTGAACTTGC 59.196 37.500 7.30 0.00 44.67 4.01
451 496 7.173047 GTGGGCATGAATTTGAACTTTTATGTT 59.827 33.333 0.00 0.00 0.00 2.71
470 516 5.508200 TGTTATGAACTTGTTTGGGTGAC 57.492 39.130 0.00 0.00 0.00 3.67
549 595 5.880054 AATGCAATATATGGTAAGCGTCC 57.120 39.130 0.00 0.00 0.00 4.79
581 627 1.227999 TGCTGCAGTTTAGCACGTCC 61.228 55.000 16.64 0.00 45.52 4.79
582 628 1.912371 GCTGCAGTTTAGCACGTCCC 61.912 60.000 16.64 0.00 40.11 4.46
586 632 1.876416 GCAGTTTAGCACGTCCCTTGA 60.876 52.381 0.00 0.00 0.00 3.02
591 637 1.529152 TAGCACGTCCCTTGAAGCGA 61.529 55.000 0.00 0.00 0.00 4.93
656 702 2.896801 CGGCGTGCAAAAGCTGACT 61.897 57.895 12.03 0.00 42.01 3.41
662 708 2.483877 CGTGCAAAAGCTGACTATTCCA 59.516 45.455 0.00 0.00 0.00 3.53
705 752 3.541831 CGCGCGTTCGTGTATGCT 61.542 61.111 24.19 0.00 40.97 3.79
708 755 2.316687 GCGTTCGTGTATGCTCGC 59.683 61.111 0.08 0.00 37.17 5.03
730 777 4.390297 GCAGATTTTAAACAGAGAGCGTCT 59.610 41.667 0.00 0.00 35.00 4.18
757 804 1.676967 GCCAGCAGTTTCCCCTCTG 60.677 63.158 0.00 0.00 35.12 3.35
816 863 2.126071 CTCACGTTCCCGCGTCAT 60.126 61.111 4.92 0.00 43.83 3.06
850 897 1.690985 CCTTCCCTCCTGGACCTCC 60.691 68.421 0.00 0.00 45.11 4.30
854 901 2.443016 CCTCCTGGACCTCCCTCG 60.443 72.222 0.00 0.00 35.38 4.63
855 902 3.151022 CTCCTGGACCTCCCTCGC 61.151 72.222 0.00 0.00 35.38 5.03
856 903 3.670629 CTCCTGGACCTCCCTCGCT 62.671 68.421 0.00 0.00 35.38 4.93
857 904 3.151022 CCTGGACCTCCCTCGCTC 61.151 72.222 0.00 0.00 35.38 5.03
858 905 3.151022 CTGGACCTCCCTCGCTCC 61.151 72.222 0.00 0.00 35.38 4.70
859 906 4.779733 TGGACCTCCCTCGCTCCC 62.780 72.222 0.00 0.00 35.38 4.30
860 907 4.467107 GGACCTCCCTCGCTCCCT 62.467 72.222 0.00 0.00 0.00 4.20
867 914 4.465446 CCTCGCTCCCTCCTCCCA 62.465 72.222 0.00 0.00 0.00 4.37
932 982 2.124236 CTCCTCCGCGTCCCTACT 60.124 66.667 4.92 0.00 0.00 2.57
998 1048 4.080129 AGCCCTGCAATCTCTGATCTTTTA 60.080 41.667 0.00 0.00 0.00 1.52
1326 1376 1.139947 CCCTTCGCTCTCGTTCCTC 59.860 63.158 0.00 0.00 36.96 3.71
1344 1394 2.486191 CCTCAGCCTCAAGAACAACACT 60.486 50.000 0.00 0.00 0.00 3.55
1578 1628 3.454574 CGCAATTCGTTCGTCGGA 58.545 55.556 0.00 0.00 40.32 4.55
1617 1667 0.462759 AGTCGATGCCAAAGCTAGCC 60.463 55.000 12.13 0.00 40.80 3.93
1812 1883 2.352821 CGACCGGTGGATGGTGGTA 61.353 63.158 14.63 0.00 40.63 3.25
1818 1889 2.370519 CCGGTGGATGGTGGTAATGATA 59.629 50.000 0.00 0.00 0.00 2.15
1939 2010 2.887568 GCACCAGCTCGATGTCGG 60.888 66.667 2.25 0.00 40.29 4.79
2145 2216 0.707024 TGAAGAGGCTGAGGAGGAGA 59.293 55.000 0.00 0.00 0.00 3.71
2500 2571 3.142838 GCCTACCTCCACGGCGTA 61.143 66.667 14.22 0.00 35.61 4.42
2986 3057 3.329688 CTCGTCTCCTTGCGCGTCT 62.330 63.158 8.43 0.00 0.00 4.18
3046 3117 2.591429 TGCGCACAAGTCACCAGG 60.591 61.111 5.66 0.00 0.00 4.45
3047 3118 2.280797 GCGCACAAGTCACCAGGA 60.281 61.111 0.30 0.00 0.00 3.86
3048 3119 2.320587 GCGCACAAGTCACCAGGAG 61.321 63.158 0.30 0.00 0.00 3.69
3049 3120 1.069765 CGCACAAGTCACCAGGAGT 59.930 57.895 0.00 0.00 0.00 3.85
3050 3121 0.532862 CGCACAAGTCACCAGGAGTT 60.533 55.000 0.00 0.00 39.80 3.01
3063 3134 0.964358 AGGAGTTGCTTGCATGCTCC 60.964 55.000 25.31 25.31 44.37 4.70
3071 3142 2.275547 CTTGCATGCTCCTTTCCGGC 62.276 60.000 20.33 0.00 0.00 6.13
3072 3143 2.751436 GCATGCTCCTTTCCGGCA 60.751 61.111 11.37 0.00 40.32 5.69
3073 3144 2.768492 GCATGCTCCTTTCCGGCAG 61.768 63.158 11.37 0.00 39.38 4.85
3074 3145 2.117156 CATGCTCCTTTCCGGCAGG 61.117 63.158 12.34 12.34 39.38 4.85
3080 3151 4.489771 CTTTCCGGCAGGCGGGAT 62.490 66.667 33.26 0.00 43.41 3.85
3081 3152 3.995506 CTTTCCGGCAGGCGGGATT 62.996 63.158 33.26 0.00 43.41 3.01
3082 3153 3.577334 TTTCCGGCAGGCGGGATTT 62.577 57.895 33.26 0.00 43.41 2.17
3086 3157 2.180204 CGGCAGGCGGGATTTACAG 61.180 63.158 8.89 0.00 0.00 2.74
3087 3158 1.823899 GGCAGGCGGGATTTACAGG 60.824 63.158 0.00 0.00 0.00 4.00
3089 3160 0.815615 GCAGGCGGGATTTACAGGAG 60.816 60.000 0.00 0.00 0.00 3.69
3091 3162 1.065418 CAGGCGGGATTTACAGGAGTT 60.065 52.381 0.00 0.00 0.00 3.01
3094 3165 3.264964 AGGCGGGATTTACAGGAGTTTTA 59.735 43.478 0.00 0.00 0.00 1.52
3095 3166 3.376234 GGCGGGATTTACAGGAGTTTTAC 59.624 47.826 0.00 0.00 0.00 2.01
3096 3167 3.063045 GCGGGATTTACAGGAGTTTTACG 59.937 47.826 0.00 0.00 0.00 3.18
3097 3168 3.619929 CGGGATTTACAGGAGTTTTACGG 59.380 47.826 0.00 0.00 0.00 4.02
3098 3169 3.943381 GGGATTTACAGGAGTTTTACGGG 59.057 47.826 0.00 0.00 0.00 5.28
3099 3170 3.376234 GGATTTACAGGAGTTTTACGGGC 59.624 47.826 0.00 0.00 0.00 6.13
3100 3171 3.775261 TTTACAGGAGTTTTACGGGCT 57.225 42.857 0.00 0.00 0.00 5.19
3101 3172 4.888326 TTTACAGGAGTTTTACGGGCTA 57.112 40.909 0.00 0.00 0.00 3.93
3102 3173 4.460948 TTACAGGAGTTTTACGGGCTAG 57.539 45.455 0.00 0.00 0.00 3.42
3103 3174 1.553704 ACAGGAGTTTTACGGGCTAGG 59.446 52.381 0.00 0.00 0.00 3.02
3104 3175 0.540454 AGGAGTTTTACGGGCTAGGC 59.460 55.000 8.00 8.00 0.00 3.93
3105 3176 0.540454 GGAGTTTTACGGGCTAGGCT 59.460 55.000 16.80 0.00 0.00 4.58
3106 3177 1.653151 GAGTTTTACGGGCTAGGCTG 58.347 55.000 22.85 22.85 0.00 4.85
3107 3178 1.206371 GAGTTTTACGGGCTAGGCTGA 59.794 52.381 30.28 12.04 0.00 4.26
3108 3179 1.207329 AGTTTTACGGGCTAGGCTGAG 59.793 52.381 30.28 16.92 0.00 3.35
3109 3180 0.539986 TTTTACGGGCTAGGCTGAGG 59.460 55.000 30.28 12.86 0.00 3.86
3113 3184 3.483869 GGGCTAGGCTGAGGTGGG 61.484 72.222 16.80 0.00 0.00 4.61
3114 3185 3.483869 GGCTAGGCTGAGGTGGGG 61.484 72.222 9.46 0.00 0.00 4.96
3115 3186 2.689034 GCTAGGCTGAGGTGGGGT 60.689 66.667 0.00 0.00 0.00 4.95
3116 3187 3.036429 GCTAGGCTGAGGTGGGGTG 62.036 68.421 0.00 0.00 0.00 4.61
3117 3188 1.613630 CTAGGCTGAGGTGGGGTGT 60.614 63.158 0.00 0.00 0.00 4.16
3119 3190 2.689573 TAGGCTGAGGTGGGGTGTGT 62.690 60.000 0.00 0.00 0.00 3.72
3120 3191 2.515901 GCTGAGGTGGGGTGTGTT 59.484 61.111 0.00 0.00 0.00 3.32
3121 3192 1.898574 GCTGAGGTGGGGTGTGTTG 60.899 63.158 0.00 0.00 0.00 3.33
3122 3193 1.836391 CTGAGGTGGGGTGTGTTGA 59.164 57.895 0.00 0.00 0.00 3.18
3123 3194 0.401738 CTGAGGTGGGGTGTGTTGAT 59.598 55.000 0.00 0.00 0.00 2.57
3124 3195 0.850100 TGAGGTGGGGTGTGTTGATT 59.150 50.000 0.00 0.00 0.00 2.57
3126 3197 0.178964 AGGTGGGGTGTGTTGATTGG 60.179 55.000 0.00 0.00 0.00 3.16
3129 3200 2.588620 GTGGGGTGTGTTGATTGGTTA 58.411 47.619 0.00 0.00 0.00 2.85
3132 3203 4.767928 GTGGGGTGTGTTGATTGGTTATTA 59.232 41.667 0.00 0.00 0.00 0.98
3134 3205 5.478679 TGGGGTGTGTTGATTGGTTATTAAG 59.521 40.000 0.00 0.00 0.00 1.85
3135 3206 5.712917 GGGGTGTGTTGATTGGTTATTAAGA 59.287 40.000 0.00 0.00 0.00 2.10
3139 3210 8.519526 GGTGTGTTGATTGGTTATTAAGATGAA 58.480 33.333 0.00 0.00 0.00 2.57
3141 3212 8.243426 TGTGTTGATTGGTTATTAAGATGAAGC 58.757 33.333 0.00 0.00 0.00 3.86
3142 3213 7.429340 GTGTTGATTGGTTATTAAGATGAAGCG 59.571 37.037 0.00 0.00 0.00 4.68
3143 3214 6.618287 TGATTGGTTATTAAGATGAAGCGG 57.382 37.500 0.00 0.00 0.00 5.52
3146 3217 2.552743 GGTTATTAAGATGAAGCGGCCC 59.447 50.000 0.00 0.00 0.00 5.80
3147 3218 2.552743 GTTATTAAGATGAAGCGGCCCC 59.447 50.000 0.00 0.00 0.00 5.80
3148 3219 0.550914 ATTAAGATGAAGCGGCCCCA 59.449 50.000 0.00 0.00 0.00 4.96
3149 3220 0.393808 TTAAGATGAAGCGGCCCCAC 60.394 55.000 0.00 0.00 0.00 4.61
3158 3229 3.966543 CGGCCCCACCCTGAAAGT 61.967 66.667 0.00 0.00 33.26 2.66
3159 3230 2.035783 GGCCCCACCCTGAAAGTC 59.964 66.667 0.00 0.00 0.00 3.01
3160 3231 2.840753 GGCCCCACCCTGAAAGTCA 61.841 63.158 0.00 0.00 0.00 3.41
3161 3232 1.303643 GCCCCACCCTGAAAGTCAG 60.304 63.158 0.00 0.00 43.91 3.51
3172 3243 4.414337 CTGAAAGTCAGGGGGAGATTAG 57.586 50.000 0.00 0.00 40.71 1.73
3174 3245 2.198334 AAGTCAGGGGGAGATTAGGG 57.802 55.000 0.00 0.00 0.00 3.53
3176 3247 1.221781 AGTCAGGGGGAGATTAGGGAG 59.778 57.143 0.00 0.00 0.00 4.30
3177 3248 0.568192 TCAGGGGGAGATTAGGGAGG 59.432 60.000 0.00 0.00 0.00 4.30
3178 3249 0.474660 CAGGGGGAGATTAGGGAGGG 60.475 65.000 0.00 0.00 0.00 4.30
3179 3250 1.151788 GGGGGAGATTAGGGAGGGG 60.152 68.421 0.00 0.00 0.00 4.79
3180 3251 1.686060 GGGGGAGATTAGGGAGGGGA 61.686 65.000 0.00 0.00 0.00 4.81
3181 3252 0.178888 GGGGAGATTAGGGAGGGGAG 60.179 65.000 0.00 0.00 0.00 4.30
3182 3253 0.868186 GGGAGATTAGGGAGGGGAGA 59.132 60.000 0.00 0.00 0.00 3.71
3183 3254 1.223337 GGGAGATTAGGGAGGGGAGAA 59.777 57.143 0.00 0.00 0.00 2.87
3184 3255 2.615391 GGAGATTAGGGAGGGGAGAAG 58.385 57.143 0.00 0.00 0.00 2.85
3185 3256 2.615391 GAGATTAGGGAGGGGAGAAGG 58.385 57.143 0.00 0.00 0.00 3.46
3186 3257 1.948243 AGATTAGGGAGGGGAGAAGGT 59.052 52.381 0.00 0.00 0.00 3.50
3187 3258 2.322543 AGATTAGGGAGGGGAGAAGGTT 59.677 50.000 0.00 0.00 0.00 3.50
3188 3259 3.540687 AGATTAGGGAGGGGAGAAGGTTA 59.459 47.826 0.00 0.00 0.00 2.85
3189 3260 3.416414 TTAGGGAGGGGAGAAGGTTAG 57.584 52.381 0.00 0.00 0.00 2.34
3190 3261 1.102938 AGGGAGGGGAGAAGGTTAGT 58.897 55.000 0.00 0.00 0.00 2.24
3191 3262 1.008571 AGGGAGGGGAGAAGGTTAGTC 59.991 57.143 0.00 0.00 0.00 2.59
3192 3263 1.498264 GGAGGGGAGAAGGTTAGTCC 58.502 60.000 0.00 0.00 0.00 3.85
3193 3264 1.112950 GAGGGGAGAAGGTTAGTCCG 58.887 60.000 0.00 0.00 41.99 4.79
3194 3265 0.412640 AGGGGAGAAGGTTAGTCCGT 59.587 55.000 0.00 0.00 41.99 4.69
3196 3267 2.043526 AGGGGAGAAGGTTAGTCCGTTA 59.956 50.000 0.00 0.00 41.99 3.18
3197 3268 2.833943 GGGGAGAAGGTTAGTCCGTTAA 59.166 50.000 0.00 0.00 41.99 2.01
3198 3269 3.453717 GGGGAGAAGGTTAGTCCGTTAAT 59.546 47.826 0.00 0.00 41.99 1.40
3202 3273 6.432162 GGGAGAAGGTTAGTCCGTTAATTTTT 59.568 38.462 0.00 0.00 41.99 1.94
3203 3274 7.303261 GGAGAAGGTTAGTCCGTTAATTTTTG 58.697 38.462 0.00 0.00 41.99 2.44
3204 3275 7.040892 GGAGAAGGTTAGTCCGTTAATTTTTGT 60.041 37.037 0.00 0.00 41.99 2.83
3205 3276 8.907222 AGAAGGTTAGTCCGTTAATTTTTGTA 57.093 30.769 0.00 0.00 41.99 2.41
3209 3280 9.955208 AGGTTAGTCCGTTAATTTTTGTAAAAG 57.045 29.630 0.00 0.00 41.99 2.27
3210 3281 9.734620 GGTTAGTCCGTTAATTTTTGTAAAAGT 57.265 29.630 0.00 0.00 0.00 2.66
3214 3285 9.304731 AGTCCGTTAATTTTTGTAAAAGTTTCC 57.695 29.630 3.69 0.00 31.54 3.13
3216 3287 7.434602 TCCGTTAATTTTTGTAAAAGTTTCCCG 59.565 33.333 3.69 4.55 31.54 5.14
3222 3293 5.402464 TTTGTAAAAGTTTCCCGTACGTC 57.598 39.130 15.21 0.00 0.00 4.34
3223 3294 4.320608 TGTAAAAGTTTCCCGTACGTCT 57.679 40.909 15.21 1.79 0.00 4.18
3224 3295 5.446143 TGTAAAAGTTTCCCGTACGTCTA 57.554 39.130 15.21 0.00 0.00 2.59
3225 3296 5.460646 TGTAAAAGTTTCCCGTACGTCTAG 58.539 41.667 15.21 0.00 0.00 2.43
3226 3297 2.643933 AAGTTTCCCGTACGTCTAGC 57.356 50.000 15.21 1.52 0.00 3.42
3227 3298 1.538047 AGTTTCCCGTACGTCTAGCA 58.462 50.000 15.21 0.00 0.00 3.49
3229 3300 2.494870 AGTTTCCCGTACGTCTAGCATT 59.505 45.455 15.21 0.00 0.00 3.56
3231 3302 2.048444 TCCCGTACGTCTAGCATTCT 57.952 50.000 15.21 0.00 0.00 2.40
3232 3303 2.372264 TCCCGTACGTCTAGCATTCTT 58.628 47.619 15.21 0.00 0.00 2.52
3234 3305 2.098607 CCCGTACGTCTAGCATTCTTGA 59.901 50.000 15.21 0.00 0.00 3.02
3235 3306 3.428452 CCCGTACGTCTAGCATTCTTGAA 60.428 47.826 15.21 0.00 0.00 2.69
3236 3307 3.546670 CCGTACGTCTAGCATTCTTGAAC 59.453 47.826 15.21 0.00 0.00 3.18
3237 3308 4.163552 CGTACGTCTAGCATTCTTGAACA 58.836 43.478 7.22 0.00 0.00 3.18
3240 3311 6.183360 CGTACGTCTAGCATTCTTGAACATTT 60.183 38.462 7.22 0.00 0.00 2.32
3241 3312 6.560253 ACGTCTAGCATTCTTGAACATTTT 57.440 33.333 0.00 0.00 0.00 1.82
3265 3336 3.570550 TGTAAAAGTTTCCGTTGGGGATG 59.429 43.478 0.00 0.00 46.62 3.51
3268 3339 2.484742 AGTTTCCGTTGGGGATGTAC 57.515 50.000 0.00 0.00 46.62 2.90
3270 3341 0.686224 TTTCCGTTGGGGATGTACGT 59.314 50.000 0.00 0.00 46.62 3.57
3271 3342 0.247185 TTCCGTTGGGGATGTACGTC 59.753 55.000 6.53 6.53 46.62 4.34
3272 3343 0.612732 TCCGTTGGGGATGTACGTCT 60.613 55.000 14.61 0.00 40.94 4.18
3274 3345 1.066605 CCGTTGGGGATGTACGTCTAG 59.933 57.143 14.61 1.25 38.47 2.43
3277 3348 1.105167 TGGGGATGTACGTCTAGCGG 61.105 60.000 14.61 0.00 46.52 5.52
3278 3349 1.658673 GGGATGTACGTCTAGCGGG 59.341 63.158 14.61 0.00 46.52 6.13
3279 3350 1.007618 GGATGTACGTCTAGCGGGC 60.008 63.158 14.61 4.40 46.52 6.13
3280 3351 1.007618 GATGTACGTCTAGCGGGCC 60.008 63.158 7.88 0.00 46.52 5.80
3282 3353 1.453762 ATGTACGTCTAGCGGGCCTC 61.454 60.000 0.84 0.00 46.52 4.70
3284 3355 3.687321 TACGTCTAGCGGGCCTCGT 62.687 63.158 13.97 5.57 46.52 4.18
3285 3356 4.253257 CGTCTAGCGGGCCTCGTC 62.253 72.222 13.97 7.46 41.72 4.20
3287 3358 1.525535 GTCTAGCGGGCCTCGTCTA 60.526 63.158 13.97 13.40 41.72 2.59
3288 3359 1.227883 TCTAGCGGGCCTCGTCTAG 60.228 63.158 23.14 23.14 41.93 2.43
3290 3361 0.250209 CTAGCGGGCCTCGTCTAGTA 60.250 60.000 22.05 8.14 38.99 1.82
3293 3364 0.039346 GCGGGCCTCGTCTAGTATTC 60.039 60.000 13.97 0.00 41.72 1.75
3294 3365 1.315690 CGGGCCTCGTCTAGTATTCA 58.684 55.000 0.84 0.00 0.00 2.57
3295 3366 1.887198 CGGGCCTCGTCTAGTATTCAT 59.113 52.381 0.84 0.00 0.00 2.57
3296 3367 3.079578 CGGGCCTCGTCTAGTATTCATA 58.920 50.000 0.84 0.00 0.00 2.15
3297 3368 3.127203 CGGGCCTCGTCTAGTATTCATAG 59.873 52.174 0.84 0.00 0.00 2.23
3397 5557 9.624697 TGAAACTATTGCACTCATTGTATTTTC 57.375 29.630 0.00 0.00 0.00 2.29
3469 5629 7.864686 TCCAGATTTCAGTATTAATTCATGCG 58.135 34.615 0.00 0.00 0.00 4.73
3624 5784 5.912396 TCATCGCAATTTTACATATTTCCGC 59.088 36.000 0.00 0.00 0.00 5.54
3722 5882 7.636259 GCTGTTTGCATGTTTTTACTATTGA 57.364 32.000 0.00 0.00 42.31 2.57
3781 5941 6.430925 TGACATTGGTGTTATCCTTCAAGAAG 59.569 38.462 2.83 2.83 39.09 2.85
3782 5942 6.542821 ACATTGGTGTTATCCTTCAAGAAGA 58.457 36.000 11.25 0.00 36.46 2.87
3783 5943 7.004086 ACATTGGTGTTATCCTTCAAGAAGAA 58.996 34.615 11.25 0.00 36.46 2.52
3795 5955 8.292444 TCCTTCAAGAAGAAAAAGTGAAATCA 57.708 30.769 11.25 0.00 40.79 2.57
3799 5959 9.573133 TTCAAGAAGAAAAAGTGAAATCAGAAC 57.427 29.630 0.00 0.00 32.05 3.01
3854 6014 4.736793 GCAAGAATGAATTAGCGACATTGG 59.263 41.667 0.00 0.00 34.94 3.16
3855 6015 4.558538 AGAATGAATTAGCGACATTGGC 57.441 40.909 0.00 0.00 34.94 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.060614 ATGCCGCCCATGGTAGCTT 62.061 57.895 11.73 5.78 31.48 3.74
170 196 0.652592 GGCACATCGGAAGACATTCG 59.347 55.000 0.00 0.00 46.97 3.34
257 283 2.716828 CTTCATTGTCGCGCGTCGT 61.717 57.895 30.98 14.17 39.67 4.34
365 409 8.632679 AGTTCATGACATAAAAGTTCACACAAT 58.367 29.630 0.00 0.00 0.00 2.71
393 437 4.358851 CAAGCAAGTTCAAAATCCGAACA 58.641 39.130 5.89 0.00 44.22 3.18
412 456 2.061509 TGCCCACATCATCATCCAAG 57.938 50.000 0.00 0.00 0.00 3.61
451 496 7.883391 TTAAAGTCACCCAAACAAGTTCATA 57.117 32.000 0.00 0.00 0.00 2.15
581 627 2.815647 GCCCGAGTCGCTTCAAGG 60.816 66.667 7.12 2.73 0.00 3.61
582 628 3.181967 CGCCCGAGTCGCTTCAAG 61.182 66.667 7.12 0.00 0.00 3.02
591 637 2.210116 CAAAATATAGTGCGCCCGAGT 58.790 47.619 4.18 0.00 0.00 4.18
656 702 6.380095 AAAACAGTTTACAGCGTTGGAATA 57.620 33.333 3.74 0.00 0.00 1.75
696 743 4.514545 TTAAAATCTGCGAGCATACACG 57.485 40.909 0.00 0.00 0.00 4.49
697 744 5.627172 TGTTTAAAATCTGCGAGCATACAC 58.373 37.500 0.00 0.00 0.00 2.90
698 745 5.641636 TCTGTTTAAAATCTGCGAGCATACA 59.358 36.000 0.00 0.00 0.00 2.29
699 746 6.036083 TCTCTGTTTAAAATCTGCGAGCATAC 59.964 38.462 0.00 0.00 0.00 2.39
700 747 6.106003 TCTCTGTTTAAAATCTGCGAGCATA 58.894 36.000 0.00 0.00 0.00 3.14
701 748 4.937620 TCTCTGTTTAAAATCTGCGAGCAT 59.062 37.500 0.00 0.00 0.00 3.79
705 752 3.367932 CGCTCTCTGTTTAAAATCTGCGA 59.632 43.478 12.78 0.00 41.79 5.10
708 755 5.852005 CAGACGCTCTCTGTTTAAAATCTG 58.148 41.667 0.00 0.00 41.60 2.90
730 777 4.873810 ACTGCTGGCGGTGCAACA 62.874 61.111 0.98 0.00 40.13 3.33
757 804 1.000866 AGGGGATTGGAGCCAAAGC 59.999 57.895 5.98 1.84 39.55 3.51
835 882 2.540910 AGGGAGGTCCAGGAGGGA 60.541 66.667 0.00 0.00 45.89 4.20
850 897 4.465446 TGGGAGGAGGGAGCGAGG 62.465 72.222 0.00 0.00 0.00 4.63
854 901 1.225704 CAATGTGGGAGGAGGGAGC 59.774 63.158 0.00 0.00 0.00 4.70
855 902 1.918253 CCAATGTGGGAGGAGGGAG 59.082 63.158 0.00 0.00 32.67 4.30
856 903 2.308722 GCCAATGTGGGAGGAGGGA 61.309 63.158 0.00 0.00 38.19 4.20
857 904 2.276740 GCCAATGTGGGAGGAGGG 59.723 66.667 0.00 0.00 38.19 4.30
858 905 1.941403 ATGGCCAATGTGGGAGGAGG 61.941 60.000 10.96 0.00 38.19 4.30
859 906 0.032813 AATGGCCAATGTGGGAGGAG 60.033 55.000 10.96 0.00 38.19 3.69
860 907 1.303898 TAATGGCCAATGTGGGAGGA 58.696 50.000 10.96 0.00 38.19 3.71
867 914 3.318839 CGTGATGGATTAATGGCCAATGT 59.681 43.478 10.96 0.00 37.78 2.71
906 953 1.811266 CGCGGAGGAGGTGTTGATG 60.811 63.158 0.00 0.00 0.00 3.07
1302 1352 0.394488 ACGAGAGCGAAGGGAGATCA 60.394 55.000 0.00 0.00 41.64 2.92
1326 1376 3.378112 TGAAAGTGTTGTTCTTGAGGCTG 59.622 43.478 0.00 0.00 0.00 4.85
1344 1394 2.183300 CGGAGCGATCCCGTGAAA 59.817 61.111 15.35 0.00 41.91 2.69
1398 1448 2.617840 TTCCGGAGAGGTAAAGGAGT 57.382 50.000 3.34 0.00 41.99 3.85
1677 1727 1.293267 GAAACGATGACGCCGGGAAA 61.293 55.000 2.18 0.00 43.96 3.13
1744 1794 1.292860 GCACTCTCTGCTGCTGTCT 59.707 57.895 0.00 0.00 43.33 3.41
1782 1853 2.572284 CGGTCGTGGGAACTCCTC 59.428 66.667 0.00 0.00 36.20 3.71
1812 1883 1.172180 CCACCGCCGCCATTATCATT 61.172 55.000 0.00 0.00 0.00 2.57
2096 2167 3.068691 CGCCCTTGGTCTCCTCGA 61.069 66.667 0.00 0.00 0.00 4.04
2623 2694 2.034687 TGCTTCTGCAGGGCCTTC 59.965 61.111 22.82 0.00 45.31 3.46
2986 3057 0.472925 TAGACTTGGTGGTGCCCTCA 60.473 55.000 0.00 0.00 36.04 3.86
3046 3117 0.886563 AAGGAGCATGCAAGCAACTC 59.113 50.000 21.98 15.92 36.85 3.01
3047 3118 1.271656 GAAAGGAGCATGCAAGCAACT 59.728 47.619 21.98 10.47 36.85 3.16
3048 3119 1.670967 GGAAAGGAGCATGCAAGCAAC 60.671 52.381 21.98 8.19 36.85 4.17
3049 3120 0.604578 GGAAAGGAGCATGCAAGCAA 59.395 50.000 21.98 0.00 36.85 3.91
3050 3121 1.588824 CGGAAAGGAGCATGCAAGCA 61.589 55.000 21.98 0.00 36.85 3.91
3051 3122 1.138247 CGGAAAGGAGCATGCAAGC 59.862 57.895 21.98 5.62 0.00 4.01
3052 3123 1.805254 CCGGAAAGGAGCATGCAAG 59.195 57.895 21.98 1.36 45.00 4.01
3071 3142 0.541863 ACTCCTGTAAATCCCGCCTG 59.458 55.000 0.00 0.00 0.00 4.85
3072 3143 1.286248 AACTCCTGTAAATCCCGCCT 58.714 50.000 0.00 0.00 0.00 5.52
3073 3144 2.124277 AAACTCCTGTAAATCCCGCC 57.876 50.000 0.00 0.00 0.00 6.13
3074 3145 3.063045 CGTAAAACTCCTGTAAATCCCGC 59.937 47.826 0.00 0.00 0.00 6.13
3076 3147 3.943381 CCCGTAAAACTCCTGTAAATCCC 59.057 47.826 0.00 0.00 0.00 3.85
3077 3148 3.376234 GCCCGTAAAACTCCTGTAAATCC 59.624 47.826 0.00 0.00 0.00 3.01
3078 3149 4.259356 AGCCCGTAAAACTCCTGTAAATC 58.741 43.478 0.00 0.00 0.00 2.17
3080 3151 3.775261 AGCCCGTAAAACTCCTGTAAA 57.225 42.857 0.00 0.00 0.00 2.01
3081 3152 3.196254 CCTAGCCCGTAAAACTCCTGTAA 59.804 47.826 0.00 0.00 0.00 2.41
3082 3153 2.762327 CCTAGCCCGTAAAACTCCTGTA 59.238 50.000 0.00 0.00 0.00 2.74
3086 3157 0.540454 AGCCTAGCCCGTAAAACTCC 59.460 55.000 0.00 0.00 0.00 3.85
3087 3158 1.206371 TCAGCCTAGCCCGTAAAACTC 59.794 52.381 0.00 0.00 0.00 3.01
3089 3160 1.653151 CTCAGCCTAGCCCGTAAAAC 58.347 55.000 0.00 0.00 0.00 2.43
3091 3162 0.616679 ACCTCAGCCTAGCCCGTAAA 60.617 55.000 0.00 0.00 0.00 2.01
3094 3165 3.077556 CACCTCAGCCTAGCCCGT 61.078 66.667 0.00 0.00 0.00 5.28
3095 3166 3.854669 CCACCTCAGCCTAGCCCG 61.855 72.222 0.00 0.00 0.00 6.13
3096 3167 3.483869 CCCACCTCAGCCTAGCCC 61.484 72.222 0.00 0.00 0.00 5.19
3097 3168 3.483869 CCCCACCTCAGCCTAGCC 61.484 72.222 0.00 0.00 0.00 3.93
3098 3169 2.689034 ACCCCACCTCAGCCTAGC 60.689 66.667 0.00 0.00 0.00 3.42
3099 3170 1.613630 ACACCCCACCTCAGCCTAG 60.614 63.158 0.00 0.00 0.00 3.02
3100 3171 1.918293 CACACCCCACCTCAGCCTA 60.918 63.158 0.00 0.00 0.00 3.93
3101 3172 3.252284 CACACCCCACCTCAGCCT 61.252 66.667 0.00 0.00 0.00 4.58
3102 3173 3.133365 AACACACCCCACCTCAGCC 62.133 63.158 0.00 0.00 0.00 4.85
3103 3174 1.898574 CAACACACCCCACCTCAGC 60.899 63.158 0.00 0.00 0.00 4.26
3104 3175 0.401738 ATCAACACACCCCACCTCAG 59.598 55.000 0.00 0.00 0.00 3.35
3105 3176 0.850100 AATCAACACACCCCACCTCA 59.150 50.000 0.00 0.00 0.00 3.86
3106 3177 1.247567 CAATCAACACACCCCACCTC 58.752 55.000 0.00 0.00 0.00 3.85
3107 3178 0.178964 CCAATCAACACACCCCACCT 60.179 55.000 0.00 0.00 0.00 4.00
3108 3179 0.469144 ACCAATCAACACACCCCACC 60.469 55.000 0.00 0.00 0.00 4.61
3109 3180 1.408969 AACCAATCAACACACCCCAC 58.591 50.000 0.00 0.00 0.00 4.61
3113 3184 8.050778 TCATCTTAATAACCAATCAACACACC 57.949 34.615 0.00 0.00 0.00 4.16
3114 3185 9.559958 CTTCATCTTAATAACCAATCAACACAC 57.440 33.333 0.00 0.00 0.00 3.82
3115 3186 8.243426 GCTTCATCTTAATAACCAATCAACACA 58.757 33.333 0.00 0.00 0.00 3.72
3116 3187 7.429340 CGCTTCATCTTAATAACCAATCAACAC 59.571 37.037 0.00 0.00 0.00 3.32
3117 3188 7.415095 CCGCTTCATCTTAATAACCAATCAACA 60.415 37.037 0.00 0.00 0.00 3.33
3119 3190 6.459573 GCCGCTTCATCTTAATAACCAATCAA 60.460 38.462 0.00 0.00 0.00 2.57
3120 3191 5.008613 GCCGCTTCATCTTAATAACCAATCA 59.991 40.000 0.00 0.00 0.00 2.57
3121 3192 5.452777 GCCGCTTCATCTTAATAACCAATC 58.547 41.667 0.00 0.00 0.00 2.67
3122 3193 4.278419 GGCCGCTTCATCTTAATAACCAAT 59.722 41.667 0.00 0.00 0.00 3.16
3123 3194 3.630312 GGCCGCTTCATCTTAATAACCAA 59.370 43.478 0.00 0.00 0.00 3.67
3124 3195 3.211045 GGCCGCTTCATCTTAATAACCA 58.789 45.455 0.00 0.00 0.00 3.67
3126 3197 2.552743 GGGGCCGCTTCATCTTAATAAC 59.447 50.000 13.57 0.00 0.00 1.89
3129 3200 0.550914 TGGGGCCGCTTCATCTTAAT 59.449 50.000 21.80 0.00 0.00 1.40
3132 3203 2.044946 GTGGGGCCGCTTCATCTT 60.045 61.111 21.80 0.00 0.00 2.40
3141 3212 3.920093 GACTTTCAGGGTGGGGCCG 62.920 68.421 0.00 0.00 38.44 6.13
3142 3213 2.035783 GACTTTCAGGGTGGGGCC 59.964 66.667 0.00 0.00 0.00 5.80
3143 3214 1.303643 CTGACTTTCAGGGTGGGGC 60.304 63.158 0.00 0.00 40.71 5.80
3151 3222 3.135530 CCTAATCTCCCCCTGACTTTCAG 59.864 52.174 0.00 0.00 43.91 3.02
3152 3223 3.115390 CCTAATCTCCCCCTGACTTTCA 58.885 50.000 0.00 0.00 0.00 2.69
3153 3224 2.439880 CCCTAATCTCCCCCTGACTTTC 59.560 54.545 0.00 0.00 0.00 2.62
3155 3226 1.657162 TCCCTAATCTCCCCCTGACTT 59.343 52.381 0.00 0.00 0.00 3.01
3156 3227 1.221781 CTCCCTAATCTCCCCCTGACT 59.778 57.143 0.00 0.00 0.00 3.41
3158 3229 0.568192 CCTCCCTAATCTCCCCCTGA 59.432 60.000 0.00 0.00 0.00 3.86
3159 3230 0.474660 CCCTCCCTAATCTCCCCCTG 60.475 65.000 0.00 0.00 0.00 4.45
3160 3231 1.690148 CCCCTCCCTAATCTCCCCCT 61.690 65.000 0.00 0.00 0.00 4.79
3161 3232 1.151788 CCCCTCCCTAATCTCCCCC 60.152 68.421 0.00 0.00 0.00 5.40
3163 3234 0.868186 TCTCCCCTCCCTAATCTCCC 59.132 60.000 0.00 0.00 0.00 4.30
3164 3235 2.615391 CTTCTCCCCTCCCTAATCTCC 58.385 57.143 0.00 0.00 0.00 3.71
3165 3236 2.090437 ACCTTCTCCCCTCCCTAATCTC 60.090 54.545 0.00 0.00 0.00 2.75
3166 3237 1.948243 ACCTTCTCCCCTCCCTAATCT 59.052 52.381 0.00 0.00 0.00 2.40
3167 3238 2.498473 ACCTTCTCCCCTCCCTAATC 57.502 55.000 0.00 0.00 0.00 1.75
3168 3239 2.993604 AACCTTCTCCCCTCCCTAAT 57.006 50.000 0.00 0.00 0.00 1.73
3169 3240 2.663675 ACTAACCTTCTCCCCTCCCTAA 59.336 50.000 0.00 0.00 0.00 2.69
3170 3241 2.246849 GACTAACCTTCTCCCCTCCCTA 59.753 54.545 0.00 0.00 0.00 3.53
3171 3242 1.008571 GACTAACCTTCTCCCCTCCCT 59.991 57.143 0.00 0.00 0.00 4.20
3172 3243 1.498264 GACTAACCTTCTCCCCTCCC 58.502 60.000 0.00 0.00 0.00 4.30
3174 3245 1.112950 CGGACTAACCTTCTCCCCTC 58.887 60.000 0.00 0.00 36.31 4.30
3176 3247 1.273759 AACGGACTAACCTTCTCCCC 58.726 55.000 0.00 0.00 36.31 4.81
3177 3248 4.750021 ATTAACGGACTAACCTTCTCCC 57.250 45.455 0.00 0.00 36.31 4.30
3178 3249 7.040892 ACAAAAATTAACGGACTAACCTTCTCC 60.041 37.037 0.00 0.00 36.31 3.71
3179 3250 7.868775 ACAAAAATTAACGGACTAACCTTCTC 58.131 34.615 0.00 0.00 36.31 2.87
3180 3251 7.812690 ACAAAAATTAACGGACTAACCTTCT 57.187 32.000 0.00 0.00 36.31 2.85
3181 3252 9.949174 TTTACAAAAATTAACGGACTAACCTTC 57.051 29.630 0.00 0.00 36.31 3.46
3183 3254 9.955208 CTTTTACAAAAATTAACGGACTAACCT 57.045 29.630 0.00 0.00 36.31 3.50
3184 3255 9.734620 ACTTTTACAAAAATTAACGGACTAACC 57.265 29.630 0.00 0.00 0.00 2.85
3188 3259 9.304731 GGAAACTTTTACAAAAATTAACGGACT 57.695 29.630 0.00 0.00 0.00 3.85
3189 3260 8.542132 GGGAAACTTTTACAAAAATTAACGGAC 58.458 33.333 0.00 0.00 0.00 4.79
3190 3261 7.434602 CGGGAAACTTTTACAAAAATTAACGGA 59.565 33.333 0.00 0.00 0.00 4.69
3191 3262 7.222417 ACGGGAAACTTTTACAAAAATTAACGG 59.778 33.333 0.00 0.00 0.00 4.44
3192 3263 8.117758 ACGGGAAACTTTTACAAAAATTAACG 57.882 30.769 0.00 0.00 0.00 3.18
3194 3265 9.230932 CGTACGGGAAACTTTTACAAAAATTAA 57.769 29.630 7.57 0.00 0.00 1.40
3196 3267 7.257003 ACGTACGGGAAACTTTTACAAAAATT 58.743 30.769 21.06 0.00 0.00 1.82
3197 3268 6.794374 ACGTACGGGAAACTTTTACAAAAAT 58.206 32.000 21.06 0.00 0.00 1.82
3198 3269 6.093357 AGACGTACGGGAAACTTTTACAAAAA 59.907 34.615 21.06 0.00 0.00 1.94
3202 3273 4.320608 AGACGTACGGGAAACTTTTACA 57.679 40.909 21.06 0.00 0.00 2.41
3203 3274 4.324669 GCTAGACGTACGGGAAACTTTTAC 59.675 45.833 21.06 0.00 0.00 2.01
3204 3275 4.022416 TGCTAGACGTACGGGAAACTTTTA 60.022 41.667 21.06 0.00 0.00 1.52
3205 3276 3.243839 TGCTAGACGTACGGGAAACTTTT 60.244 43.478 21.06 0.00 0.00 2.27
3209 3280 2.573941 ATGCTAGACGTACGGGAAAC 57.426 50.000 21.06 6.57 0.00 2.78
3210 3281 2.756760 AGAATGCTAGACGTACGGGAAA 59.243 45.455 21.06 0.91 0.00 3.13
3211 3282 2.372264 AGAATGCTAGACGTACGGGAA 58.628 47.619 21.06 2.82 0.00 3.97
3212 3283 2.048444 AGAATGCTAGACGTACGGGA 57.952 50.000 21.06 2.78 0.00 5.14
3214 3285 3.416119 TCAAGAATGCTAGACGTACGG 57.584 47.619 21.06 2.24 0.00 4.02
3216 3287 6.648725 AATGTTCAAGAATGCTAGACGTAC 57.351 37.500 0.00 0.00 0.00 3.67
3240 3311 4.465305 TCCCCAACGGAAACTTTTACAAAA 59.535 37.500 0.00 0.00 37.88 2.44
3241 3312 4.021916 TCCCCAACGGAAACTTTTACAAA 58.978 39.130 0.00 0.00 37.88 2.83
3245 3316 3.834938 ACATCCCCAACGGAAACTTTTA 58.165 40.909 0.00 0.00 46.47 1.52
3246 3317 2.673258 ACATCCCCAACGGAAACTTTT 58.327 42.857 0.00 0.00 46.47 2.27
3247 3318 2.375014 ACATCCCCAACGGAAACTTT 57.625 45.000 0.00 0.00 46.47 2.66
3248 3319 2.786777 GTACATCCCCAACGGAAACTT 58.213 47.619 0.00 0.00 46.47 2.66
3249 3320 1.338389 CGTACATCCCCAACGGAAACT 60.338 52.381 0.00 0.00 46.47 2.66
3252 3323 0.247185 GACGTACATCCCCAACGGAA 59.753 55.000 0.00 0.00 46.47 4.30
3255 3326 1.535437 GCTAGACGTACATCCCCAACG 60.535 57.143 0.00 0.00 42.17 4.10
3261 3332 1.007618 GCCCGCTAGACGTACATCC 60.008 63.158 0.00 0.00 41.42 3.51
3265 3336 2.720605 GAGGCCCGCTAGACGTAC 59.279 66.667 0.00 0.00 41.42 3.67
3268 3339 4.253257 GACGAGGCCCGCTAGACG 62.253 72.222 12.78 0.00 43.32 4.18
3270 3341 1.227883 CTAGACGAGGCCCGCTAGA 60.228 63.158 23.92 7.87 42.29 2.43
3271 3342 0.250209 TACTAGACGAGGCCCGCTAG 60.250 60.000 25.11 25.11 43.72 3.42
3272 3343 0.399454 ATACTAGACGAGGCCCGCTA 59.601 55.000 12.78 12.91 43.32 4.26
3274 3345 0.039346 GAATACTAGACGAGGCCCGC 60.039 60.000 12.78 6.71 43.32 6.13
3276 3347 4.080687 ACTATGAATACTAGACGAGGCCC 58.919 47.826 0.00 0.00 0.00 5.80
3277 3348 7.393841 AATACTATGAATACTAGACGAGGCC 57.606 40.000 0.00 0.00 0.00 5.19
3371 5531 9.624697 GAAAATACAATGAGTGCAATAGTTTCA 57.375 29.630 0.00 0.00 31.95 2.69
3372 5532 9.624697 TGAAAATACAATGAGTGCAATAGTTTC 57.375 29.630 0.00 0.00 32.10 2.78
3373 5533 9.410556 GTGAAAATACAATGAGTGCAATAGTTT 57.589 29.630 0.00 0.00 0.00 2.66
3375 5535 8.109705 TGTGAAAATACAATGAGTGCAATAGT 57.890 30.769 0.00 0.00 0.00 2.12
3376 5536 9.016623 CATGTGAAAATACAATGAGTGCAATAG 57.983 33.333 0.00 0.00 33.69 1.73
3378 5538 7.380536 ACATGTGAAAATACAATGAGTGCAAT 58.619 30.769 0.00 0.00 33.69 3.56
3381 5541 7.381948 TGAAACATGTGAAAATACAATGAGTGC 59.618 33.333 0.00 0.00 33.69 4.40
3382 5542 8.800231 TGAAACATGTGAAAATACAATGAGTG 57.200 30.769 0.00 0.00 33.69 3.51
3383 5543 9.985730 AATGAAACATGTGAAAATACAATGAGT 57.014 25.926 0.00 0.00 33.69 3.41
3461 5621 6.469782 AATAGAAATGAAACCCGCATGAAT 57.530 33.333 0.00 0.00 0.00 2.57
3533 5693 2.283821 GCCCAGCCCAACCATGAA 60.284 61.111 0.00 0.00 0.00 2.57
3553 5713 9.559958 AAATAATATGCGAAGAGAACACTTTTG 57.440 29.630 0.00 0.00 0.00 2.44
3617 5777 7.151999 TGTGTAATGAAACAATAGCGGAAAT 57.848 32.000 0.00 0.00 0.00 2.17
3637 5797 3.454719 TGGGACATGGATGAATTGTGT 57.545 42.857 0.00 0.00 0.00 3.72
3698 5858 7.382218 AGTCAATAGTAAAAACATGCAAACAGC 59.618 33.333 0.00 0.00 45.96 4.40
3700 5860 8.409371 TGAGTCAATAGTAAAAACATGCAAACA 58.591 29.630 0.00 0.00 0.00 2.83
3716 5876 3.697045 AGAGAACCGGAGTGAGTCAATAG 59.303 47.826 9.46 0.00 0.00 1.73
3722 5882 3.436577 TCTTAGAGAACCGGAGTGAGT 57.563 47.619 9.46 0.00 0.00 3.41
3755 5915 6.484288 TCTTGAAGGATAACACCAATGTCAT 58.516 36.000 0.00 0.00 38.45 3.06
3770 5930 8.292444 TGATTTCACTTTTTCTTCTTGAAGGA 57.708 30.769 10.08 0.00 35.89 3.36
3817 5977 8.822652 ATTCATTCTTGCTTGGAAAACTTTAG 57.177 30.769 0.00 0.00 0.00 1.85
3825 5985 4.699735 TCGCTAATTCATTCTTGCTTGGAA 59.300 37.500 0.00 0.00 0.00 3.53
3832 5992 4.736793 GCCAATGTCGCTAATTCATTCTTG 59.263 41.667 0.00 0.00 30.74 3.02
3872 6032 9.212687 GAAATTTGTGTCATTTGTGTCATTTTG 57.787 29.630 0.00 0.00 0.00 2.44
3873 6033 8.397148 GGAAATTTGTGTCATTTGTGTCATTTT 58.603 29.630 0.00 0.00 0.00 1.82
3875 6035 7.011295 GTGGAAATTTGTGTCATTTGTGTCATT 59.989 33.333 0.00 0.00 0.00 2.57
3876 6036 6.479660 GTGGAAATTTGTGTCATTTGTGTCAT 59.520 34.615 0.00 0.00 0.00 3.06
3877 6037 5.809562 GTGGAAATTTGTGTCATTTGTGTCA 59.190 36.000 0.00 0.00 0.00 3.58
3878 6038 6.019640 CAGTGGAAATTTGTGTCATTTGTGTC 60.020 38.462 0.00 0.00 0.00 3.67
3879 6039 5.811613 CAGTGGAAATTTGTGTCATTTGTGT 59.188 36.000 0.00 0.00 0.00 3.72
3880 6040 6.041511 TCAGTGGAAATTTGTGTCATTTGTG 58.958 36.000 0.00 0.00 0.00 3.33
3881 6041 6.219417 TCAGTGGAAATTTGTGTCATTTGT 57.781 33.333 0.00 0.00 0.00 2.83
3882 6042 7.536895 TTTCAGTGGAAATTTGTGTCATTTG 57.463 32.000 0.00 0.00 38.07 2.32


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

AutoCloner maintained by Alex Coulton.