Multiple sequence alignment - TraesCS3A01G226000

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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 TraesCS3A01G226000 chr3A 100.000 4092 0 0 1 4092 423618050 423622141 0.000000e+00 7557.0
1 TraesCS3A01G226000 chr3A 81.897 1044 117 51 772 1803 708322199 708323182 0.000000e+00 815.0
2 TraesCS3A01G226000 chr3A 77.467 608 62 37 2752 3325 708325376 708325942 1.110000e-75 294.0
3 TraesCS3A01G226000 chr3A 81.141 403 41 21 2945 3316 708323419 708323817 1.440000e-74 291.0
4 TraesCS3A01G226000 chr3A 95.270 148 6 1 2082 2229 714360773 714360627 2.460000e-57 233.0
5 TraesCS3A01G226000 chr3A 92.126 127 8 2 2210 2334 714956206 714956080 1.170000e-40 178.0
6 TraesCS3A01G226000 chr3A 93.478 92 6 0 1926 2017 708323179 708323270 1.980000e-28 137.0
7 TraesCS3A01G226000 chr3A 94.253 87 4 1 2752 2838 708323264 708323349 9.230000e-27 132.0
8 TraesCS3A01G226000 chr3D 92.693 2135 89 28 1 2084 305578634 305580752 0.000000e+00 3016.0
9 TraesCS3A01G226000 chr3D 90.044 1798 98 38 2328 4092 305580749 305582498 0.000000e+00 2254.0
10 TraesCS3A01G226000 chr3D 93.012 415 29 0 1389 1803 573690589 573691003 1.260000e-169 606.0
11 TraesCS3A01G226000 chr3D 79.888 537 60 26 770 1298 573690022 573690518 2.340000e-92 350.0
12 TraesCS3A01G226000 chr3D 81.250 432 49 16 2924 3325 573691217 573691646 1.840000e-83 320.0
13 TraesCS3A01G226000 chr3D 94.565 92 5 0 1926 2017 573691000 573691091 4.260000e-30 143.0
14 TraesCS3A01G226000 chr3D 94.545 55 3 0 2366 2420 582536283 582536337 7.290000e-13 86.1
15 TraesCS3A01G226000 chr3B 92.474 1900 77 24 1 1848 416153286 416151401 0.000000e+00 2656.0
16 TraesCS3A01G226000 chr3B 94.489 871 32 9 2398 3268 416150768 416149914 0.000000e+00 1328.0
17 TraesCS3A01G226000 chr3B 87.840 625 51 9 3490 4092 416139249 416138628 0.000000e+00 710.0
18 TraesCS3A01G226000 chr3B 92.289 415 32 0 1389 1803 763774074 763773660 1.270000e-164 590.0
19 TraesCS3A01G226000 chr3B 79.817 436 46 24 2924 3325 763773445 763773018 3.110000e-71 279.0
20 TraesCS3A01G226000 chr3B 77.007 548 70 37 772 1297 763774650 763774137 3.140000e-66 263.0
21 TraesCS3A01G226000 chr3B 93.000 100 6 1 1918 2017 763773670 763773572 1.190000e-30 145.0
22 TraesCS3A01G226000 chr3B 86.957 69 3 1 1882 1950 416151341 416151279 5.670000e-09 73.1
23 TraesCS3A01G226000 chr4A 95.946 148 5 1 2082 2229 552814952 552814806 5.290000e-59 239.0
24 TraesCS3A01G226000 chr4A 94.558 147 7 1 2083 2229 621673010 621673155 4.120000e-55 226.0
25 TraesCS3A01G226000 chr4A 91.803 122 8 2 2210 2330 533457284 533457404 7.030000e-38 169.0
26 TraesCS3A01G226000 chr5A 95.333 150 6 1 2080 2229 549412442 549412590 1.900000e-58 237.0
27 TraesCS3A01G226000 chr5A 97.321 112 3 0 2220 2331 549412552 549412663 1.500000e-44 191.0
28 TraesCS3A01G226000 chr2B 94.040 151 8 1 2079 2229 244883246 244883097 1.140000e-55 228.0
29 TraesCS3A01G226000 chr2B 93.805 113 7 0 2220 2332 41824763 41824875 1.960000e-38 171.0
30 TraesCS3A01G226000 chr2B 83.333 144 20 4 3921 4062 772648609 772648468 3.320000e-26 130.0
31 TraesCS3A01G226000 chr2B 80.952 147 24 3 3920 4064 233089530 233089674 3.340000e-21 113.0
32 TraesCS3A01G226000 chrUn 93.960 149 8 1 2081 2229 76956161 76956014 1.480000e-54 224.0
33 TraesCS3A01G226000 chrUn 92.258 155 11 1 2075 2229 15373514 15373667 6.890000e-53 219.0
34 TraesCS3A01G226000 chr5D 93.421 152 8 2 2079 2229 421982590 421982440 1.480000e-54 224.0
35 TraesCS3A01G226000 chr1D 91.772 158 11 2 2073 2229 50897808 50897964 6.890000e-53 219.0
36 TraesCS3A01G226000 chr6A 92.683 123 8 1 2210 2331 117403220 117403098 4.200000e-40 176.0
37 TraesCS3A01G226000 chr7A 90.840 131 11 1 2210 2339 57210566 57210436 1.510000e-39 174.0
38 TraesCS3A01G226000 chr7A 90.476 126 10 1 2220 2343 429734598 429734473 9.100000e-37 165.0
39 TraesCS3A01G226000 chr4B 91.870 123 9 1 2210 2331 189677667 189677789 1.960000e-38 171.0
40 TraesCS3A01G226000 chr4D 91.057 123 10 1 2210 2331 67339813 67339935 9.100000e-37 165.0
41 TraesCS3A01G226000 chr2D 79.592 147 26 3 3920 4064 176073173 176073317 7.240000e-18 102.0


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 TraesCS3A01G226000 chr3A 423618050 423622141 4091 False 7557.000000 7557 100.000000 1 4092 1 chr3A.!!$F1 4091
1 TraesCS3A01G226000 chr3A 708322199 708325942 3743 False 333.800000 815 85.647200 772 3325 5 chr3A.!!$F2 2553
2 TraesCS3A01G226000 chr3D 305578634 305582498 3864 False 2635.000000 3016 91.368500 1 4092 2 chr3D.!!$F2 4091
3 TraesCS3A01G226000 chr3D 573690022 573691646 1624 False 354.750000 606 87.178750 770 3325 4 chr3D.!!$F3 2555
4 TraesCS3A01G226000 chr3B 416149914 416153286 3372 True 1352.366667 2656 91.306667 1 3268 3 chr3B.!!$R2 3267
5 TraesCS3A01G226000 chr3B 416138628 416139249 621 True 710.000000 710 87.840000 3490 4092 1 chr3B.!!$R1 602
6 TraesCS3A01G226000 chr3B 763773018 763774650 1632 True 319.250000 590 85.528250 772 3325 4 chr3B.!!$R3 2553

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
913 936 0.179045 AAGATCACCGCCCATACTGC 60.179 55.0 0.0 0.0 0.0 4.40 F
1915 2067 0.553333 TGTGTGGTGGGTTCATTCCA 59.447 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 3043 0.037139 ATACGCACACGCCCTGTAAA 60.037 50.0 0.0 0.0 45.53 2.01 R
3718 6831 0.036388 CAGGCGTTGTAGGACACCAT 60.036 55.0 0.0 0.0 0.00 3.55 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
81 85 1.713297 AAACTAGTCGTCCAGGGTGT 58.287 50.000 0.00 0.00 0.00 4.16
92 96 1.213296 CCAGGGTGTAGGGCAACTAT 58.787 55.000 0.00 0.00 34.56 2.12
112 117 1.301244 GCGATGGATCTGGCGTGAT 60.301 57.895 0.00 0.00 0.00 3.06
137 142 2.487265 CCTTAATAAGCTCGTGGGGCAT 60.487 50.000 0.00 0.00 0.00 4.40
146 151 1.889105 CGTGGGGCATCAGAATCCG 60.889 63.158 0.00 0.00 0.00 4.18
185 190 6.698380 TGTTTCTCTTCGTATTCTTAGCCTT 58.302 36.000 0.00 0.00 0.00 4.35
201 206 3.445008 AGCCTTCACATGGTAGAAGAGA 58.555 45.455 19.95 0.00 42.95 3.10
214 222 3.197927 AGAAGAGAAGGAGGTGGTGAT 57.802 47.619 0.00 0.00 0.00 3.06
222 230 3.191888 AGGAGGTGGTGATCTAGTGTT 57.808 47.619 0.00 0.00 0.00 3.32
302 310 3.176708 CCATTGCTTTGATTTGAGCTCG 58.823 45.455 9.64 0.00 39.60 5.03
348 356 0.321298 ACGACACCACCTATGTTGCC 60.321 55.000 0.00 0.00 35.20 4.52
357 365 2.684881 CACCTATGTTGCCTCAATGGTC 59.315 50.000 0.00 0.00 38.35 4.02
392 400 6.759272 TGATTGCTCTAAAGTTGAGTGTACT 58.241 36.000 0.00 0.00 34.30 2.73
415 423 0.320374 CGAAGGGTGGCTGTGTAGAA 59.680 55.000 0.00 0.00 0.00 2.10
441 449 2.014068 GCATCAGGCTAAACCGCTTCT 61.014 52.381 0.00 0.00 46.52 2.85
461 469 5.329191 TCTAGTTATTCCTCCCGACCATA 57.671 43.478 0.00 0.00 0.00 2.74
502 510 2.512515 GCTTCGGCTCGGCTTCAT 60.513 61.111 0.00 0.00 38.08 2.57
530 538 0.257039 ATCCCTGACATGAGTTGGCC 59.743 55.000 0.00 0.00 29.16 5.36
532 540 0.679002 CCCTGACATGAGTTGGCCTG 60.679 60.000 3.32 0.00 29.16 4.85
622 630 0.591659 GCCTCGAAAAAGGACCACAC 59.408 55.000 0.00 0.00 38.87 3.82
749 759 4.399303 ACTGCAAAGTTAGTGAAGTTGCTT 59.601 37.500 8.03 0.00 30.01 3.91
913 936 0.179045 AAGATCACCGCCCATACTGC 60.179 55.000 0.00 0.00 0.00 4.40
965 1013 2.032680 ACACCAACGCACAACTAACT 57.967 45.000 0.00 0.00 0.00 2.24
1020 1084 1.603739 GGTGAACTTGGTGGAGGCC 60.604 63.158 0.00 0.00 0.00 5.19
1050 1114 0.978907 TGCTGCACTTCCTGATCAGA 59.021 50.000 24.62 7.50 0.00 3.27
1195 1280 4.082523 CGCCGGCCTCCAAGAAGA 62.083 66.667 23.46 0.00 0.00 2.87
1301 1411 4.846779 TCCAGGTTTGCACTTTGTTATC 57.153 40.909 0.00 0.00 0.00 1.75
1308 1418 5.144359 GTTTGCACTTTGTTATCCTACGTG 58.856 41.667 0.00 0.00 0.00 4.49
1617 1743 4.813526 CTCGTCCGGTCGCTCGTG 62.814 72.222 16.54 5.12 0.00 4.35
1748 1874 4.521062 GGCGCTGCTCTCCATCGT 62.521 66.667 7.64 0.00 35.61 3.73
1812 1938 3.831651 CCTCCAGGTCCGTCTCTAT 57.168 57.895 0.00 0.00 0.00 1.98
1813 1939 1.611519 CCTCCAGGTCCGTCTCTATC 58.388 60.000 0.00 0.00 0.00 2.08
1814 1940 1.144093 CCTCCAGGTCCGTCTCTATCT 59.856 57.143 0.00 0.00 0.00 1.98
1815 1941 2.500229 CTCCAGGTCCGTCTCTATCTC 58.500 57.143 0.00 0.00 0.00 2.75
1816 1942 2.105821 CTCCAGGTCCGTCTCTATCTCT 59.894 54.545 0.00 0.00 0.00 3.10
1817 1943 3.315596 TCCAGGTCCGTCTCTATCTCTA 58.684 50.000 0.00 0.00 0.00 2.43
1877 2029 7.531857 TGATTTGTCCAGCTATTTTGGTTTA 57.468 32.000 0.00 0.00 37.02 2.01
1892 2044 7.415592 TTTTGGTTTATGGATGTGCATGATA 57.584 32.000 0.00 0.00 0.00 2.15
1911 2063 2.905415 ATGATGTGTGGTGGGTTCAT 57.095 45.000 0.00 0.00 0.00 2.57
1912 2064 2.673775 TGATGTGTGGTGGGTTCATT 57.326 45.000 0.00 0.00 0.00 2.57
1913 2065 2.513753 TGATGTGTGGTGGGTTCATTC 58.486 47.619 0.00 0.00 0.00 2.67
1914 2066 1.818674 GATGTGTGGTGGGTTCATTCC 59.181 52.381 0.00 0.00 0.00 3.01
1915 2067 0.553333 TGTGTGGTGGGTTCATTCCA 59.447 50.000 0.00 0.00 0.00 3.53
1916 2068 1.146774 TGTGTGGTGGGTTCATTCCAT 59.853 47.619 0.00 0.00 36.58 3.41
2089 3033 8.399284 TCTTAGTTAGTAACCTAGTACTCCCT 57.601 38.462 9.46 0.00 35.85 4.20
2090 3034 8.490311 TCTTAGTTAGTAACCTAGTACTCCCTC 58.510 40.741 9.46 0.00 35.85 4.30
2091 3035 6.906795 AGTTAGTAACCTAGTACTCCCTCT 57.093 41.667 9.46 0.00 35.85 3.69
2092 3036 6.899089 AGTTAGTAACCTAGTACTCCCTCTC 58.101 44.000 9.46 0.00 35.85 3.20
2093 3037 6.677965 AGTTAGTAACCTAGTACTCCCTCTCT 59.322 42.308 9.46 0.00 35.85 3.10
2094 3038 5.635278 AGTAACCTAGTACTCCCTCTCTC 57.365 47.826 0.00 0.00 27.56 3.20
2095 3039 5.291161 AGTAACCTAGTACTCCCTCTCTCT 58.709 45.833 0.00 0.00 27.56 3.10
2096 3040 4.783560 AACCTAGTACTCCCTCTCTCTC 57.216 50.000 0.00 0.00 0.00 3.20
2097 3041 3.738434 ACCTAGTACTCCCTCTCTCTCA 58.262 50.000 0.00 0.00 0.00 3.27
2098 3042 3.714798 ACCTAGTACTCCCTCTCTCTCAG 59.285 52.174 0.00 0.00 0.00 3.35
2099 3043 3.714798 CCTAGTACTCCCTCTCTCTCAGT 59.285 52.174 0.00 0.00 0.00 3.41
2100 3044 4.165372 CCTAGTACTCCCTCTCTCTCAGTT 59.835 50.000 0.00 0.00 0.00 3.16
2101 3045 4.668138 AGTACTCCCTCTCTCTCAGTTT 57.332 45.455 0.00 0.00 0.00 2.66
2102 3046 5.782677 AGTACTCCCTCTCTCTCAGTTTA 57.217 43.478 0.00 0.00 0.00 2.01
2103 3047 5.503002 AGTACTCCCTCTCTCTCAGTTTAC 58.497 45.833 0.00 0.00 0.00 2.01
2104 3048 4.390129 ACTCCCTCTCTCTCAGTTTACA 57.610 45.455 0.00 0.00 0.00 2.41
2105 3049 4.340617 ACTCCCTCTCTCTCAGTTTACAG 58.659 47.826 0.00 0.00 0.00 2.74
2106 3050 3.699038 CTCCCTCTCTCTCAGTTTACAGG 59.301 52.174 0.00 0.00 0.00 4.00
2107 3051 2.763448 CCCTCTCTCTCAGTTTACAGGG 59.237 54.545 0.00 0.00 33.59 4.45
2108 3052 2.167487 CCTCTCTCTCAGTTTACAGGGC 59.833 54.545 0.00 0.00 0.00 5.19
2109 3053 1.819288 TCTCTCTCAGTTTACAGGGCG 59.181 52.381 0.00 0.00 0.00 6.13
2110 3054 1.546476 CTCTCTCAGTTTACAGGGCGT 59.454 52.381 0.00 0.00 0.00 5.68
2111 3055 1.272490 TCTCTCAGTTTACAGGGCGTG 59.728 52.381 5.50 5.50 0.00 5.34
2112 3056 1.000955 CTCTCAGTTTACAGGGCGTGT 59.999 52.381 17.69 17.69 43.86 4.49
2113 3057 1.148310 CTCAGTTTACAGGGCGTGTG 58.852 55.000 22.09 5.80 40.69 3.82
2114 3058 0.882927 TCAGTTTACAGGGCGTGTGC 60.883 55.000 22.09 12.04 40.69 4.57
2115 3059 1.959226 AGTTTACAGGGCGTGTGCG 60.959 57.895 22.09 0.00 44.10 5.34
2116 3060 2.109387 TTTACAGGGCGTGTGCGT 59.891 55.556 22.09 0.00 44.10 5.24
2117 3061 0.945265 GTTTACAGGGCGTGTGCGTA 60.945 55.000 22.09 0.00 44.10 4.42
2118 3062 0.037139 TTTACAGGGCGTGTGCGTAT 60.037 50.000 22.09 0.00 44.10 3.06
2119 3063 0.458889 TTACAGGGCGTGTGCGTATC 60.459 55.000 22.09 0.00 44.10 2.24
2120 3064 2.287457 TACAGGGCGTGTGCGTATCC 62.287 60.000 22.09 0.00 44.10 2.59
2121 3065 4.157120 AGGGCGTGTGCGTATCCC 62.157 66.667 0.00 0.00 44.10 3.85
2122 3066 4.157120 GGGCGTGTGCGTATCCCT 62.157 66.667 0.00 0.00 44.10 4.20
2123 3067 2.788640 GGGCGTGTGCGTATCCCTA 61.789 63.158 0.00 0.00 44.10 3.53
2124 3068 1.299926 GGCGTGTGCGTATCCCTAG 60.300 63.158 0.00 0.00 44.10 3.02
2125 3069 1.731433 GGCGTGTGCGTATCCCTAGA 61.731 60.000 0.00 0.00 44.10 2.43
2126 3070 0.314302 GCGTGTGCGTATCCCTAGAT 59.686 55.000 0.00 0.00 40.81 1.98
2127 3071 1.666311 GCGTGTGCGTATCCCTAGATC 60.666 57.143 0.00 0.00 40.81 2.75
2128 3072 1.399855 CGTGTGCGTATCCCTAGATCG 60.400 57.143 0.00 0.00 33.67 3.69
2129 3073 1.607628 GTGTGCGTATCCCTAGATCGT 59.392 52.381 0.00 0.00 33.67 3.73
2130 3074 1.878088 TGTGCGTATCCCTAGATCGTC 59.122 52.381 0.00 0.00 33.67 4.20
2131 3075 1.878088 GTGCGTATCCCTAGATCGTCA 59.122 52.381 0.00 0.00 33.67 4.35
2132 3076 2.292569 GTGCGTATCCCTAGATCGTCAA 59.707 50.000 0.00 0.00 33.67 3.18
2133 3077 3.057456 GTGCGTATCCCTAGATCGTCAAT 60.057 47.826 0.00 0.00 33.67 2.57
2134 3078 3.572682 TGCGTATCCCTAGATCGTCAATT 59.427 43.478 0.00 0.00 33.67 2.32
2135 3079 4.038763 TGCGTATCCCTAGATCGTCAATTT 59.961 41.667 0.00 0.00 33.67 1.82
2136 3080 4.386049 GCGTATCCCTAGATCGTCAATTTG 59.614 45.833 0.00 0.00 33.67 2.32
2137 3081 5.769367 CGTATCCCTAGATCGTCAATTTGA 58.231 41.667 0.00 0.00 33.67 2.69
2138 3082 6.390721 CGTATCCCTAGATCGTCAATTTGAT 58.609 40.000 1.78 0.00 33.67 2.57
2139 3083 6.528423 CGTATCCCTAGATCGTCAATTTGATC 59.472 42.308 1.78 0.00 41.02 2.92
2140 3084 5.869649 TCCCTAGATCGTCAATTTGATCA 57.130 39.130 1.78 0.00 42.72 2.92
2141 3085 6.233905 TCCCTAGATCGTCAATTTGATCAA 57.766 37.500 3.38 3.38 42.72 2.57
2142 3086 6.830912 TCCCTAGATCGTCAATTTGATCAAT 58.169 36.000 9.40 0.00 42.72 2.57
2143 3087 6.931281 TCCCTAGATCGTCAATTTGATCAATC 59.069 38.462 9.40 1.07 42.72 2.67
2144 3088 6.933521 CCCTAGATCGTCAATTTGATCAATCT 59.066 38.462 9.40 17.67 42.72 2.40
2145 3089 8.090831 CCCTAGATCGTCAATTTGATCAATCTA 58.909 37.037 9.40 17.88 42.72 1.98
2146 3090 9.481340 CCTAGATCGTCAATTTGATCAATCTAA 57.519 33.333 9.40 0.00 42.72 2.10
2208 3152 8.558973 ACTTCAGATGTTCTATTTTCAGAAGG 57.441 34.615 0.00 0.00 36.56 3.46
2209 3153 8.160106 ACTTCAGATGTTCTATTTTCAGAAGGT 58.840 33.333 0.00 0.00 36.56 3.50
2210 3154 9.658799 CTTCAGATGTTCTATTTTCAGAAGGTA 57.341 33.333 0.00 0.00 35.25 3.08
2301 3245 7.766219 AAATTGACAACTTAGATATACGCGT 57.234 32.000 19.17 19.17 0.00 6.01
2302 3246 8.861033 AAATTGACAACTTAGATATACGCGTA 57.139 30.769 22.94 22.94 0.00 4.42
2303 3247 8.503486 AATTGACAACTTAGATATACGCGTAG 57.497 34.615 24.78 13.09 0.00 3.51
2304 3248 6.609237 TGACAACTTAGATATACGCGTAGT 57.391 37.500 24.78 15.42 0.00 2.73
2305 3249 7.713764 TGACAACTTAGATATACGCGTAGTA 57.286 36.000 24.78 16.10 40.03 1.82
2306 3250 7.567571 TGACAACTTAGATATACGCGTAGTAC 58.432 38.462 24.78 16.38 38.29 2.73
2307 3251 7.439356 TGACAACTTAGATATACGCGTAGTACT 59.561 37.037 24.78 21.73 38.29 2.73
2308 3252 8.147642 ACAACTTAGATATACGCGTAGTACTT 57.852 34.615 24.78 9.82 38.29 2.24
2309 3253 8.066595 ACAACTTAGATATACGCGTAGTACTTG 58.933 37.037 24.78 17.06 38.29 3.16
2310 3254 7.721286 ACTTAGATATACGCGTAGTACTTGT 57.279 36.000 24.78 18.16 38.29 3.16
2311 3255 8.818141 ACTTAGATATACGCGTAGTACTTGTA 57.182 34.615 24.78 10.35 38.29 2.41
2312 3256 9.261180 ACTTAGATATACGCGTAGTACTTGTAA 57.739 33.333 24.78 13.37 38.29 2.41
2314 3258 9.864034 TTAGATATACGCGTAGTACTTGTAAAC 57.136 33.333 24.78 8.64 38.29 2.01
2315 3259 8.147642 AGATATACGCGTAGTACTTGTAAACT 57.852 34.615 24.78 10.47 38.29 2.66
2316 3260 8.066595 AGATATACGCGTAGTACTTGTAAACTG 58.933 37.037 24.78 0.00 38.29 3.16
2317 3261 4.228912 ACGCGTAGTACTTGTAAACTGT 57.771 40.909 11.67 0.00 0.00 3.55
2318 3262 3.976942 ACGCGTAGTACTTGTAAACTGTG 59.023 43.478 11.67 0.00 0.00 3.66
2319 3263 4.221342 CGCGTAGTACTTGTAAACTGTGA 58.779 43.478 0.00 0.00 0.00 3.58
2320 3264 4.087648 CGCGTAGTACTTGTAAACTGTGAC 59.912 45.833 0.00 0.00 0.00 3.67
2321 3265 4.087648 GCGTAGTACTTGTAAACTGTGACG 59.912 45.833 0.00 1.04 0.00 4.35
2322 3266 4.614284 CGTAGTACTTGTAAACTGTGACGG 59.386 45.833 0.00 0.00 0.00 4.79
2323 3267 4.924305 AGTACTTGTAAACTGTGACGGA 57.076 40.909 0.00 0.00 0.00 4.69
2324 3268 4.868067 AGTACTTGTAAACTGTGACGGAG 58.132 43.478 0.00 0.00 0.00 4.63
2325 3269 3.107642 ACTTGTAAACTGTGACGGAGG 57.892 47.619 0.00 0.00 0.00 4.30
2326 3270 2.224209 ACTTGTAAACTGTGACGGAGGG 60.224 50.000 0.00 0.00 0.00 4.30
2377 3321 1.305201 AACAGTACACCAGTTTGCCG 58.695 50.000 0.00 0.00 0.00 5.69
2390 3334 3.057596 CAGTTTGCCGATTGGTTGTACAT 60.058 43.478 0.00 0.00 37.67 2.29
2424 3368 4.980434 TGTTTGACTCTTTGTACTCGTAGC 59.020 41.667 0.00 0.00 0.00 3.58
2425 3369 4.841443 TTGACTCTTTGTACTCGTAGCA 57.159 40.909 0.00 0.00 0.00 3.49
2426 3370 4.421033 TGACTCTTTGTACTCGTAGCAG 57.579 45.455 0.00 0.00 0.00 4.24
2438 3382 4.525024 ACTCGTAGCAGTAGTAGTCCAAT 58.475 43.478 0.00 0.00 0.00 3.16
2443 3387 5.915758 CGTAGCAGTAGTAGTCCAATTGATC 59.084 44.000 7.12 0.00 0.00 2.92
2472 3416 2.943690 CAGGAGGACAGAAGCATTGATG 59.056 50.000 0.00 0.00 0.00 3.07
2491 3435 2.283834 TGGGTATTCATGGTTGGGAGT 58.716 47.619 0.00 0.00 0.00 3.85
2542 3487 3.672781 GCTGAAGGCTTTCAATGCTCTTC 60.673 47.826 12.74 14.45 42.48 2.87
2563 3508 2.436646 AAGCGGATGGCCTGTTCG 60.437 61.111 3.32 4.45 45.17 3.95
2573 3518 0.951040 GGCCTGTTCGACTTGACAGG 60.951 60.000 23.86 23.86 43.26 4.00
2595 3540 4.262851 GGAACACAAACCAGCCCATAATTT 60.263 41.667 0.00 0.00 0.00 1.82
2613 3558 7.253950 CCATAATTTACAAAACATGCTTACCGC 60.254 37.037 0.00 0.00 39.77 5.68
2649 3594 0.106521 GTGCACCAAAGCCACCAAAT 59.893 50.000 5.22 0.00 0.00 2.32
2716 3661 4.766375 CAATTCCCGTGATTACCAGTAGT 58.234 43.478 0.00 0.00 0.00 2.73
2722 3667 4.441079 CCCGTGATTACCAGTAGTACCAAG 60.441 50.000 0.00 0.00 0.00 3.61
2725 3670 5.337009 CGTGATTACCAGTAGTACCAAGGTT 60.337 44.000 13.07 0.00 33.91 3.50
2813 3758 2.299993 TTCAACATAGAGCTCGCCAG 57.700 50.000 8.37 2.52 0.00 4.85
2866 3811 5.048013 TGCTCTTGAGATTTCAGACGACTTA 60.048 40.000 1.30 0.00 34.15 2.24
2914 3859 1.613925 TCTGAAGCTAAGCGTGTGAGT 59.386 47.619 0.00 0.00 0.00 3.41
2920 3865 0.179161 CTAAGCGTGTGAGTCGAGGG 60.179 60.000 0.00 0.00 0.00 4.30
2965 3916 4.436998 GTACGCAGGCAGCTCGGT 62.437 66.667 0.00 0.00 42.61 4.69
3085 6152 1.949525 GTCACTGCTGAAGCTTCCAAA 59.050 47.619 23.42 7.83 42.66 3.28
3215 6306 6.908870 TTGTGAGTGTGATGCATAATACTC 57.091 37.500 26.50 26.50 36.11 2.59
3216 6307 5.359756 TGTGAGTGTGATGCATAATACTCC 58.640 41.667 28.75 22.01 35.02 3.85
3217 6308 5.129320 TGTGAGTGTGATGCATAATACTCCT 59.871 40.000 28.75 15.28 35.02 3.69
3218 6309 6.323739 TGTGAGTGTGATGCATAATACTCCTA 59.676 38.462 28.75 18.81 35.02 2.94
3219 6310 7.015584 TGTGAGTGTGATGCATAATACTCCTAT 59.984 37.037 28.75 4.28 35.02 2.57
3233 6325 1.411977 CTCCTATGGAGTCAGCACTGG 59.588 57.143 5.50 0.00 44.25 4.00
3275 6374 5.568685 TTTGCAGCTAAACAGTTGTGTAA 57.431 34.783 0.00 0.00 35.08 2.41
3329 6428 5.163437 ACGGATTGAGGTAATAAGAGTGGAC 60.163 44.000 0.00 0.00 0.00 4.02
3360 6459 6.787085 AATCTTTAACTCTCAAACGGTCAG 57.213 37.500 0.00 0.00 0.00 3.51
3384 6484 9.801873 CAGAAGACAAAATTTGAAGGAGTTAAA 57.198 29.630 13.19 0.00 0.00 1.52
3404 6504 2.715763 TTTGAGACCCACCCTACTCT 57.284 50.000 0.00 0.00 0.00 3.24
3419 6528 5.068855 ACCCTACTCTCTTATTTTACTCGGC 59.931 44.000 0.00 0.00 0.00 5.54
3424 6533 4.703897 TCTCTTATTTTACTCGGCCATGG 58.296 43.478 7.63 7.63 0.00 3.66
3442 6552 1.173913 GGCACCGCTCCTTAAACAAT 58.826 50.000 0.00 0.00 0.00 2.71
3445 6555 3.554129 GGCACCGCTCCTTAAACAATTTT 60.554 43.478 0.00 0.00 0.00 1.82
3451 6561 5.278758 CCGCTCCTTAAACAATTTTCCTTGA 60.279 40.000 0.00 0.00 0.00 3.02
3457 6567 7.777910 TCCTTAAACAATTTTCCTTGACTCTCA 59.222 33.333 0.00 0.00 0.00 3.27
3469 6579 3.842923 CTCTCATCCACCGCCGCT 61.843 66.667 0.00 0.00 0.00 5.52
3501 6611 1.003118 CCCTGGTGACCGAGAAAATGA 59.997 52.381 0.00 0.00 0.00 2.57
3525 6636 2.420568 CCTACGCCCCGCAACTCTA 61.421 63.158 0.00 0.00 0.00 2.43
3578 6689 3.171277 GGCCAGAAATTTCGTGAAATCG 58.829 45.455 12.42 1.09 39.88 3.34
3584 6695 5.399301 CAGAAATTTCGTGAAATCGTGCTTT 59.601 36.000 12.42 0.00 39.88 3.51
3589 6700 1.334059 CGTGAAATCGTGCTTTGTGCT 60.334 47.619 0.00 0.00 43.37 4.40
3603 6714 1.013596 TGTGCTGTTATGCATACGCC 58.986 50.000 5.74 5.02 45.23 5.68
3655 6766 2.501222 CGTCGTCGTGGTCCTTCG 60.501 66.667 0.00 0.00 0.00 3.79
3665 6776 2.433436 GTGGTCCTTCGTAGCCAATTT 58.567 47.619 0.00 0.00 32.26 1.82
3671 6784 4.915667 GTCCTTCGTAGCCAATTTTTGAAC 59.084 41.667 0.00 0.00 0.00 3.18
3675 6788 2.605823 CGTAGCCAATTTTTGAACGCCA 60.606 45.455 0.00 0.00 0.00 5.69
3693 6806 1.227380 AAGGCCTTCTAGCGCATCG 60.227 57.895 13.78 0.00 0.00 3.84
3697 6810 1.355563 CCTTCTAGCGCATCGTCGA 59.644 57.895 11.47 0.00 0.00 4.20
3700 6813 1.988834 TTCTAGCGCATCGTCGAGCA 61.989 55.000 11.47 0.00 33.67 4.26
3702 6815 2.654421 CTAGCGCATCGTCGAGCAGT 62.654 60.000 11.47 5.67 33.67 4.40
3717 6830 0.179124 GCAGTGTTCCTAGAGCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
3718 6831 1.464734 CAGTGTTCCTAGAGCCTCGA 58.535 55.000 0.00 0.00 0.00 4.04
3765 6878 2.586792 CGCCAAGGCCTTCTAGCT 59.413 61.111 17.29 0.00 37.98 3.32
3799 6912 0.103572 ACCAAGCACGACAAGTACGT 59.896 50.000 0.00 0.00 44.83 3.57
3845 6962 1.176619 TCTGAAACTCCTCGCCGACA 61.177 55.000 0.00 0.00 0.00 4.35
3881 7014 0.250467 GTGACATGCCAGAGGTGTGT 60.250 55.000 0.00 0.00 0.00 3.72
3982 7115 6.648879 TTGAGGACTTAAATTTGAGGGTTG 57.351 37.500 13.89 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 85 0.317160 CCATCGCGATAGTTGCCCTA 59.683 55.000 23.22 0.00 39.35 3.53
92 96 3.527427 ACGCCAGATCCATCGCGA 61.527 61.111 13.09 13.09 0.00 5.87
109 114 5.453339 CCCACGAGCTTATTAAGGAAGATCA 60.453 44.000 14.85 0.00 38.88 2.92
112 117 3.134081 CCCCACGAGCTTATTAAGGAAGA 59.866 47.826 5.61 0.00 0.00 2.87
137 142 3.557054 CCTCCAACTTCAACGGATTCTGA 60.557 47.826 0.00 0.00 0.00 3.27
146 151 4.640647 AGAGAAACAACCTCCAACTTCAAC 59.359 41.667 0.00 0.00 0.00 3.18
185 190 4.026744 CCTCCTTCTCTTCTACCATGTGA 58.973 47.826 0.00 0.00 0.00 3.58
201 206 3.191888 ACACTAGATCACCACCTCCTT 57.808 47.619 0.00 0.00 0.00 3.36
214 222 6.657966 TCGATCTAAGGAAGTTGAACACTAGA 59.342 38.462 0.00 0.00 32.94 2.43
222 230 6.098266 TCCAATGATCGATCTAAGGAAGTTGA 59.902 38.462 25.02 3.04 0.00 3.18
302 310 0.110644 CTTCAAAACGCCGCTGAGAC 60.111 55.000 0.00 0.00 0.00 3.36
348 356 1.519455 GACCGGCTCGACCATTGAG 60.519 63.158 0.00 0.00 39.03 3.02
357 365 1.424493 GAGCAATCAAGACCGGCTCG 61.424 60.000 0.00 0.00 41.18 5.03
415 423 0.107654 GTTTAGCCTGATGCCGGAGT 60.108 55.000 5.05 0.00 42.71 3.85
441 449 5.842328 ACATTATGGTCGGGAGGAATAACTA 59.158 40.000 0.00 0.00 0.00 2.24
461 469 4.038402 CACTTTGCCTCTCCTTTTGACATT 59.962 41.667 0.00 0.00 0.00 2.71
502 510 4.971282 ACTCATGTCAGGGATGGAAGATAA 59.029 41.667 0.00 0.00 0.00 1.75
530 538 0.600255 AACCTTGTCGTCGCTTCCAG 60.600 55.000 0.00 0.00 0.00 3.86
532 540 1.860078 CAACCTTGTCGTCGCTTCC 59.140 57.895 0.00 0.00 0.00 3.46
567 575 0.032678 GATCGCCATCATCGTGGACT 59.967 55.000 0.00 0.00 42.02 3.85
575 583 3.405831 CACATACCAAGATCGCCATCAT 58.594 45.455 0.00 0.00 0.00 2.45
947 995 4.742438 AATAGTTAGTTGTGCGTTGGTG 57.258 40.909 0.00 0.00 0.00 4.17
1186 1265 2.628178 TCGTCTTGCTCTTCTTCTTGGA 59.372 45.455 0.00 0.00 0.00 3.53
1195 1280 1.876156 CTTGGCTTTCGTCTTGCTCTT 59.124 47.619 0.00 0.00 0.00 2.85
1301 1411 2.159184 ACATCTCACTCATGCACGTAGG 60.159 50.000 0.00 0.00 0.00 3.18
1308 1418 0.107312 AGGCCACATCTCACTCATGC 60.107 55.000 5.01 0.00 0.00 4.06
1382 1504 3.423154 GCACACCAGCCTACGCAC 61.423 66.667 0.00 0.00 37.52 5.34
1383 1505 3.625897 AGCACACCAGCCTACGCA 61.626 61.111 0.00 0.00 37.52 5.24
1384 1506 3.121030 CAGCACACCAGCCTACGC 61.121 66.667 0.00 0.00 34.23 4.42
1385 1507 2.434884 CCAGCACACCAGCCTACG 60.435 66.667 0.00 0.00 34.23 3.51
1748 1874 1.371183 CAGAGTTTCCTGTGGGCGA 59.629 57.895 0.00 0.00 0.00 5.54
1812 1938 6.842437 AGCTAGTGTTTGATTGAGTAGAGA 57.158 37.500 0.00 0.00 0.00 3.10
1813 1939 7.093354 TGAAGCTAGTGTTTGATTGAGTAGAG 58.907 38.462 0.00 0.00 0.00 2.43
1814 1940 6.993079 TGAAGCTAGTGTTTGATTGAGTAGA 58.007 36.000 0.00 0.00 0.00 2.59
1815 1941 7.840342 ATGAAGCTAGTGTTTGATTGAGTAG 57.160 36.000 0.00 0.00 0.00 2.57
1816 1942 7.877612 TGAATGAAGCTAGTGTTTGATTGAGTA 59.122 33.333 0.00 0.00 0.00 2.59
1817 1943 6.712095 TGAATGAAGCTAGTGTTTGATTGAGT 59.288 34.615 0.00 0.00 0.00 3.41
1877 2029 5.183140 CACACATCATATCATGCACATCCAT 59.817 40.000 0.00 0.00 0.00 3.41
1892 2044 2.905415 ATGAACCCACCACACATCAT 57.095 45.000 0.00 0.00 0.00 2.45
1911 2063 2.601240 TCACCTGCATGGAAATGGAA 57.399 45.000 8.91 0.00 39.71 3.53
1912 2064 2.291735 ACATCACCTGCATGGAAATGGA 60.292 45.455 8.91 0.00 39.71 3.41
1913 2065 2.104967 ACATCACCTGCATGGAAATGG 58.895 47.619 8.91 0.00 39.71 3.16
1914 2066 3.193903 TGAACATCACCTGCATGGAAATG 59.806 43.478 8.91 12.03 39.71 2.32
1915 2067 3.194116 GTGAACATCACCTGCATGGAAAT 59.806 43.478 8.91 0.42 41.37 2.17
1916 2068 2.557924 GTGAACATCACCTGCATGGAAA 59.442 45.455 8.91 0.00 41.37 3.13
2073 3017 5.130809 TGAGAGAGAGGGAGTACTAGGTTAC 59.869 48.000 0.00 0.00 0.00 2.50
2074 3018 5.287042 TGAGAGAGAGGGAGTACTAGGTTA 58.713 45.833 0.00 0.00 0.00 2.85
2075 3019 4.113085 TGAGAGAGAGGGAGTACTAGGTT 58.887 47.826 0.00 0.00 0.00 3.50
2076 3020 3.714798 CTGAGAGAGAGGGAGTACTAGGT 59.285 52.174 0.00 0.00 0.00 3.08
2077 3021 3.714798 ACTGAGAGAGAGGGAGTACTAGG 59.285 52.174 0.00 0.00 0.00 3.02
2078 3022 5.367945 AACTGAGAGAGAGGGAGTACTAG 57.632 47.826 0.00 0.00 0.00 2.57
2079 3023 5.782677 AAACTGAGAGAGAGGGAGTACTA 57.217 43.478 0.00 0.00 0.00 1.82
2080 3024 4.668138 AAACTGAGAGAGAGGGAGTACT 57.332 45.455 0.00 0.00 0.00 2.73
2081 3025 5.254901 TGTAAACTGAGAGAGAGGGAGTAC 58.745 45.833 0.00 0.00 0.00 2.73
2082 3026 5.502079 CTGTAAACTGAGAGAGAGGGAGTA 58.498 45.833 0.00 0.00 0.00 2.59
2083 3027 4.340617 CTGTAAACTGAGAGAGAGGGAGT 58.659 47.826 0.00 0.00 0.00 3.85
2084 3028 3.699038 CCTGTAAACTGAGAGAGAGGGAG 59.301 52.174 0.00 0.00 0.00 4.30
2085 3029 3.564571 CCCTGTAAACTGAGAGAGAGGGA 60.565 52.174 8.74 0.00 41.40 4.20
2086 3030 2.763448 CCCTGTAAACTGAGAGAGAGGG 59.237 54.545 0.00 0.00 33.23 4.30
2087 3031 2.167487 GCCCTGTAAACTGAGAGAGAGG 59.833 54.545 0.00 0.00 0.00 3.69
2088 3032 2.159310 CGCCCTGTAAACTGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
2089 3033 1.819288 CGCCCTGTAAACTGAGAGAGA 59.181 52.381 0.00 0.00 0.00 3.10
2090 3034 1.546476 ACGCCCTGTAAACTGAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
2091 3035 1.272490 CACGCCCTGTAAACTGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
2092 3036 1.000955 ACACGCCCTGTAAACTGAGAG 59.999 52.381 0.00 0.00 0.00 3.20
2093 3037 1.045407 ACACGCCCTGTAAACTGAGA 58.955 50.000 0.00 0.00 0.00 3.27
2094 3038 1.148310 CACACGCCCTGTAAACTGAG 58.852 55.000 0.00 0.00 0.00 3.35
2095 3039 0.882927 GCACACGCCCTGTAAACTGA 60.883 55.000 0.00 0.00 0.00 3.41
2096 3040 1.574428 GCACACGCCCTGTAAACTG 59.426 57.895 0.00 0.00 0.00 3.16
2097 3041 1.959226 CGCACACGCCCTGTAAACT 60.959 57.895 0.00 0.00 33.11 2.66
2098 3042 0.945265 TACGCACACGCCCTGTAAAC 60.945 55.000 0.00 0.00 45.53 2.01
2099 3043 0.037139 ATACGCACACGCCCTGTAAA 60.037 50.000 0.00 0.00 45.53 2.01
2100 3044 0.458889 GATACGCACACGCCCTGTAA 60.459 55.000 0.00 0.00 45.53 2.41
2101 3045 1.140161 GATACGCACACGCCCTGTA 59.860 57.895 0.00 0.00 45.53 2.74
2102 3046 2.125673 GATACGCACACGCCCTGT 60.126 61.111 0.00 0.00 45.53 4.00
2103 3047 2.890474 GGATACGCACACGCCCTG 60.890 66.667 0.00 0.00 45.53 4.45
2104 3048 4.157120 GGGATACGCACACGCCCT 62.157 66.667 0.00 0.00 45.53 5.19
2105 3049 2.694829 CTAGGGATACGCACACGCCC 62.695 65.000 0.00 0.00 45.53 6.13
2106 3050 1.299926 CTAGGGATACGCACACGCC 60.300 63.158 0.00 0.00 45.53 5.68
2107 3051 0.314302 ATCTAGGGATACGCACACGC 59.686 55.000 0.00 0.00 45.53 5.34
2108 3052 1.399855 CGATCTAGGGATACGCACACG 60.400 57.143 0.00 0.00 37.56 4.49
2109 3053 1.607628 ACGATCTAGGGATACGCACAC 59.392 52.381 0.00 0.00 37.60 3.82
2110 3054 1.878088 GACGATCTAGGGATACGCACA 59.122 52.381 0.00 0.00 37.60 4.57
2111 3055 1.878088 TGACGATCTAGGGATACGCAC 59.122 52.381 0.00 0.00 37.60 5.34
2112 3056 2.265589 TGACGATCTAGGGATACGCA 57.734 50.000 0.00 0.00 37.60 5.24
2113 3057 3.851976 ATTGACGATCTAGGGATACGC 57.148 47.619 0.00 0.00 37.60 4.42
2114 3058 5.769367 TCAAATTGACGATCTAGGGATACG 58.231 41.667 0.00 0.00 37.60 3.06
2115 3059 7.378966 TGATCAAATTGACGATCTAGGGATAC 58.621 38.462 0.00 0.00 39.06 2.24
2116 3060 7.539034 TGATCAAATTGACGATCTAGGGATA 57.461 36.000 0.00 0.00 39.06 2.59
2117 3061 6.425210 TGATCAAATTGACGATCTAGGGAT 57.575 37.500 0.00 0.00 39.06 3.85
2118 3062 5.869649 TGATCAAATTGACGATCTAGGGA 57.130 39.130 0.00 0.00 39.06 4.20
2119 3063 6.933521 AGATTGATCAAATTGACGATCTAGGG 59.066 38.462 13.09 0.00 39.06 3.53
2120 3064 7.959689 AGATTGATCAAATTGACGATCTAGG 57.040 36.000 13.09 0.00 39.06 3.02
2182 3126 9.007901 CCTTCTGAAAATAGAACATCTGAAGTT 57.992 33.333 15.39 0.00 41.97 2.66
2183 3127 8.160106 ACCTTCTGAAAATAGAACATCTGAAGT 58.840 33.333 15.39 5.92 41.97 3.01
2184 3128 8.558973 ACCTTCTGAAAATAGAACATCTGAAG 57.441 34.615 11.82 11.82 42.59 3.02
2275 3219 9.304731 ACGCGTATATCTAAGTTGTCAATTTTA 57.695 29.630 11.67 0.00 0.00 1.52
2276 3220 8.193250 ACGCGTATATCTAAGTTGTCAATTTT 57.807 30.769 11.67 0.00 0.00 1.82
2277 3221 7.766219 ACGCGTATATCTAAGTTGTCAATTT 57.234 32.000 11.67 0.00 0.00 1.82
2278 3222 8.133627 ACTACGCGTATATCTAAGTTGTCAATT 58.866 33.333 20.91 0.00 0.00 2.32
2279 3223 7.646314 ACTACGCGTATATCTAAGTTGTCAAT 58.354 34.615 20.91 0.00 0.00 2.57
2280 3224 7.019774 ACTACGCGTATATCTAAGTTGTCAA 57.980 36.000 20.91 0.00 0.00 3.18
2281 3225 6.609237 ACTACGCGTATATCTAAGTTGTCA 57.391 37.500 20.91 0.00 0.00 3.58
2282 3226 7.791949 AGTACTACGCGTATATCTAAGTTGTC 58.208 38.462 20.91 8.13 0.00 3.18
2283 3227 7.721286 AGTACTACGCGTATATCTAAGTTGT 57.279 36.000 20.91 12.10 0.00 3.32
2284 3228 8.066595 ACAAGTACTACGCGTATATCTAAGTTG 58.933 37.037 20.91 19.17 0.00 3.16
2285 3229 8.147642 ACAAGTACTACGCGTATATCTAAGTT 57.852 34.615 20.91 7.92 0.00 2.66
2286 3230 7.721286 ACAAGTACTACGCGTATATCTAAGT 57.279 36.000 20.91 16.18 0.00 2.24
2288 3232 9.864034 GTTTACAAGTACTACGCGTATATCTAA 57.136 33.333 20.91 6.60 0.00 2.10
2289 3233 9.261180 AGTTTACAAGTACTACGCGTATATCTA 57.739 33.333 20.91 4.36 0.00 1.98
2290 3234 8.066595 CAGTTTACAAGTACTACGCGTATATCT 58.933 37.037 20.91 14.33 0.00 1.98
2291 3235 7.852945 ACAGTTTACAAGTACTACGCGTATATC 59.147 37.037 20.91 12.33 0.00 1.63
2292 3236 7.641411 CACAGTTTACAAGTACTACGCGTATAT 59.359 37.037 20.91 13.59 0.00 0.86
2293 3237 6.960992 CACAGTTTACAAGTACTACGCGTATA 59.039 38.462 20.91 11.37 0.00 1.47
2294 3238 5.796935 CACAGTTTACAAGTACTACGCGTAT 59.203 40.000 20.91 12.37 0.00 3.06
2295 3239 5.049749 TCACAGTTTACAAGTACTACGCGTA 60.050 40.000 19.40 19.40 0.00 4.42
2296 3240 3.976942 CACAGTTTACAAGTACTACGCGT 59.023 43.478 19.17 19.17 0.00 6.01
2297 3241 4.087648 GTCACAGTTTACAAGTACTACGCG 59.912 45.833 3.53 3.53 0.00 6.01
2298 3242 4.087648 CGTCACAGTTTACAAGTACTACGC 59.912 45.833 0.00 0.00 0.00 4.42
2299 3243 4.614284 CCGTCACAGTTTACAAGTACTACG 59.386 45.833 0.00 0.00 0.00 3.51
2300 3244 5.762045 TCCGTCACAGTTTACAAGTACTAC 58.238 41.667 0.00 0.00 0.00 2.73
2301 3245 5.048504 CCTCCGTCACAGTTTACAAGTACTA 60.049 44.000 0.00 0.00 0.00 1.82
2302 3246 4.261909 CCTCCGTCACAGTTTACAAGTACT 60.262 45.833 0.00 0.00 0.00 2.73
2303 3247 3.985925 CCTCCGTCACAGTTTACAAGTAC 59.014 47.826 0.00 0.00 0.00 2.73
2304 3248 3.006110 CCCTCCGTCACAGTTTACAAGTA 59.994 47.826 0.00 0.00 0.00 2.24
2305 3249 2.224209 CCCTCCGTCACAGTTTACAAGT 60.224 50.000 0.00 0.00 0.00 3.16
2306 3250 2.036733 TCCCTCCGTCACAGTTTACAAG 59.963 50.000 0.00 0.00 0.00 3.16
2307 3251 2.036733 CTCCCTCCGTCACAGTTTACAA 59.963 50.000 0.00 0.00 0.00 2.41
2308 3252 1.616865 CTCCCTCCGTCACAGTTTACA 59.383 52.381 0.00 0.00 0.00 2.41
2309 3253 1.617357 ACTCCCTCCGTCACAGTTTAC 59.383 52.381 0.00 0.00 0.00 2.01
2310 3254 2.005370 ACTCCCTCCGTCACAGTTTA 57.995 50.000 0.00 0.00 0.00 2.01
2311 3255 2.005370 TACTCCCTCCGTCACAGTTT 57.995 50.000 0.00 0.00 0.00 2.66
2312 3256 2.005370 TTACTCCCTCCGTCACAGTT 57.995 50.000 0.00 0.00 0.00 3.16
2313 3257 2.005370 TTTACTCCCTCCGTCACAGT 57.995 50.000 0.00 0.00 0.00 3.55
2314 3258 2.496070 TGATTTACTCCCTCCGTCACAG 59.504 50.000 0.00 0.00 0.00 3.66
2315 3259 2.531771 TGATTTACTCCCTCCGTCACA 58.468 47.619 0.00 0.00 0.00 3.58
2316 3260 3.821421 ATGATTTACTCCCTCCGTCAC 57.179 47.619 0.00 0.00 0.00 3.67
2317 3261 4.837093 AAATGATTTACTCCCTCCGTCA 57.163 40.909 0.00 0.00 0.00 4.35
2318 3262 5.183228 TGAAAATGATTTACTCCCTCCGTC 58.817 41.667 0.00 0.00 0.00 4.79
2319 3263 5.174037 TGAAAATGATTTACTCCCTCCGT 57.826 39.130 0.00 0.00 0.00 4.69
2320 3264 7.661437 TGATATGAAAATGATTTACTCCCTCCG 59.339 37.037 0.00 0.00 0.00 4.63
2321 3265 8.924511 TGATATGAAAATGATTTACTCCCTCC 57.075 34.615 0.00 0.00 0.00 4.30
2370 3314 3.057876 TGATGTACAACCAATCGGCAAAC 60.058 43.478 0.00 0.00 34.57 2.93
2377 3321 5.762825 ATCATGCTGATGTACAACCAATC 57.237 39.130 0.00 0.00 35.43 2.67
2390 3334 6.656270 ACAAAGAGTCAAACATATCATGCTGA 59.344 34.615 0.00 0.00 0.00 4.26
2424 3368 5.651530 ACGTGATCAATTGGACTACTACTG 58.348 41.667 5.42 0.00 0.00 2.74
2425 3369 5.916661 ACGTGATCAATTGGACTACTACT 57.083 39.130 5.42 0.00 0.00 2.57
2426 3370 6.793349 AGTACGTGATCAATTGGACTACTAC 58.207 40.000 5.42 0.18 0.00 2.73
2438 3382 2.753452 GTCCTCCTGAGTACGTGATCAA 59.247 50.000 0.00 0.00 0.00 2.57
2443 3387 1.822506 TCTGTCCTCCTGAGTACGTG 58.177 55.000 0.00 0.00 0.00 4.49
2472 3416 3.382083 AACTCCCAACCATGAATACCC 57.618 47.619 0.00 0.00 0.00 3.69
2491 3435 2.805295 CGCCGCTCATGACCCTTATTAA 60.805 50.000 0.00 0.00 0.00 1.40
2563 3508 3.013921 TGGTTTGTGTTCCTGTCAAGTC 58.986 45.455 0.00 0.00 0.00 3.01
2573 3518 4.535526 AATTATGGGCTGGTTTGTGTTC 57.464 40.909 0.00 0.00 0.00 3.18
2613 3558 4.320202 GGTGCACCAACTTTGTACTGTATG 60.320 45.833 31.23 0.00 35.64 2.39
2649 3594 5.541845 CTGCTTATATTCTTCACGGATGGA 58.458 41.667 0.00 0.00 0.00 3.41
2716 3661 1.944024 CGTTTGTCAGCAACCTTGGTA 59.056 47.619 0.00 0.00 37.09 3.25
2722 3667 2.844122 AGAAACGTTTGTCAGCAACC 57.156 45.000 20.10 0.00 33.82 3.77
2813 3758 9.418045 GATAGATAGCTTACTCTTTCATTGTCC 57.582 37.037 0.00 0.00 0.00 4.02
2866 3811 3.988976 TTGGATTGTGAAGCTAGCTCT 57.011 42.857 19.65 8.45 0.00 4.09
2914 3859 6.381994 ACCATTTGTTAGTATCTAACCCTCGA 59.618 38.462 14.41 0.00 0.00 4.04
2920 3865 8.179615 CCCGAAAACCATTTGTTAGTATCTAAC 58.820 37.037 11.32 11.32 35.67 2.34
2965 3916 0.967380 TCTGCAGCATCGTCTCCTCA 60.967 55.000 9.47 0.00 0.00 3.86
3085 6152 6.405953 CGATGGACCTACTAATTTGTCACTCT 60.406 42.308 0.00 0.00 0.00 3.24
3215 6306 0.179062 GCCAGTGCTGACTCCATAGG 60.179 60.000 0.02 0.00 33.53 2.57
3216 6307 0.179062 GGCCAGTGCTGACTCCATAG 60.179 60.000 0.00 0.00 37.74 2.23
3217 6308 0.909133 TGGCCAGTGCTGACTCCATA 60.909 55.000 0.00 0.00 37.74 2.74
3218 6309 1.782201 TTGGCCAGTGCTGACTCCAT 61.782 55.000 5.11 0.00 37.74 3.41
3219 6310 1.782201 ATTGGCCAGTGCTGACTCCA 61.782 55.000 5.11 2.80 37.74 3.86
3231 6323 6.916360 AAAGAGAAATAGACAAATTGGCCA 57.084 33.333 0.00 0.00 0.00 5.36
3233 6325 6.646240 TGCAAAAGAGAAATAGACAAATTGGC 59.354 34.615 0.00 0.00 0.00 4.52
3275 6374 6.741992 TGTATGAAGCATTTCGAGTTGATT 57.258 33.333 0.50 0.50 36.04 2.57
3283 6382 6.073369 CGTTATCCATGTATGAAGCATTTCG 58.927 40.000 0.00 0.00 36.04 3.46
3329 6428 7.371159 GTTTGAGAGTTAAAGATTTTGAGGGG 58.629 38.462 0.00 0.00 0.00 4.79
3384 6484 3.108376 GAGAGTAGGGTGGGTCTCAAAT 58.892 50.000 0.00 0.00 36.29 2.32
3388 6488 2.535836 AAGAGAGTAGGGTGGGTCTC 57.464 55.000 0.00 0.00 36.48 3.36
3390 6490 5.695424 AAAATAAGAGAGTAGGGTGGGTC 57.305 43.478 0.00 0.00 0.00 4.46
3404 6504 3.211045 GCCATGGCCGAGTAAAATAAGA 58.789 45.455 27.24 0.00 34.56 2.10
3419 6528 0.679640 TTTAAGGAGCGGTGCCATGG 60.680 55.000 7.63 7.63 0.00 3.66
3424 6533 3.297830 AAATTGTTTAAGGAGCGGTGC 57.702 42.857 0.00 0.00 0.00 5.01
3442 6552 3.557054 CGGTGGATGAGAGTCAAGGAAAA 60.557 47.826 0.00 0.00 0.00 2.29
3445 6555 1.186200 CGGTGGATGAGAGTCAAGGA 58.814 55.000 0.00 0.00 0.00 3.36
3451 6561 4.148825 GCGGCGGTGGATGAGAGT 62.149 66.667 9.78 0.00 0.00 3.24
3469 6579 2.935481 CCAGGGAGGTGGAGGCAA 60.935 66.667 0.00 0.00 40.44 4.52
3501 6611 4.185286 GCGGGGCGTAGGGGATTT 62.185 66.667 0.00 0.00 0.00 2.17
3589 6700 2.241190 CGCCGGCGTATGCATAACA 61.241 57.895 39.71 0.00 45.35 2.41
3614 6725 0.763652 AGGCCATAGAGGTGAGCATG 59.236 55.000 5.01 0.00 40.61 4.06
3615 6726 1.055040 GAGGCCATAGAGGTGAGCAT 58.945 55.000 5.01 0.00 40.61 3.79
3655 6766 3.019933 TGGCGTTCAAAAATTGGCTAC 57.980 42.857 0.00 0.00 0.00 3.58
3665 6776 0.467290 AGAAGGCCTTGGCGTTCAAA 60.467 50.000 33.86 0.00 37.14 2.69
3671 6784 2.892425 CGCTAGAAGGCCTTGGCG 60.892 66.667 29.37 29.37 38.64 5.69
3675 6788 1.227380 CGATGCGCTAGAAGGCCTT 60.227 57.895 20.65 20.65 0.00 4.35
3693 6806 1.468395 GCTCTAGGAACACTGCTCGAC 60.468 57.143 0.00 0.00 0.00 4.20
3697 6810 1.190643 GAGGCTCTAGGAACACTGCT 58.809 55.000 7.40 0.00 0.00 4.24
3700 6813 2.028130 CATCGAGGCTCTAGGAACACT 58.972 52.381 13.50 0.00 0.00 3.55
3702 6815 1.342076 ACCATCGAGGCTCTAGGAACA 60.342 52.381 19.33 0.00 43.14 3.18
3717 6830 0.249398 AGGCGTTGTAGGACACCATC 59.751 55.000 0.00 0.00 0.00 3.51
3718 6831 0.036388 CAGGCGTTGTAGGACACCAT 60.036 55.000 0.00 0.00 0.00 3.55
3748 6861 1.522580 GAGCTAGAAGGCCTTGGCG 60.523 63.158 26.25 11.40 0.00 5.69
3812 6927 1.011968 TTCAGAAATAGTGCGCGCGT 61.012 50.000 32.35 18.96 0.00 6.01
3863 6996 0.250424 CACACACCTCTGGCATGTCA 60.250 55.000 0.00 0.00 0.00 3.58
3881 7014 3.596066 GAGAAGCACCTCAGCCGCA 62.596 63.158 0.00 0.00 33.50 5.69
3982 7115 1.129058 ATGATGACCGGACCTAACCC 58.871 55.000 9.46 0.00 0.00 4.11
4064 7197 2.447408 TAGGGCATCTCTAACCGACA 57.553 50.000 0.00 0.00 0.00 4.35
4065 7198 2.694109 ACTTAGGGCATCTCTAACCGAC 59.306 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.