Multiple sequence alignment - TraesCS1A01G022900

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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 TraesCS1A01G022900 chr1A 100.000 3382 0 0 1 3382 11387647 11391028 0.000000e+00 6246.0
1 TraesCS1A01G022900 chr1A 90.999 911 57 12 399 1296 11205756 11204858 0.000000e+00 1205.0
2 TraesCS1A01G022900 chr1A 91.709 398 25 3 10 401 11206207 11205812 2.290000e-151 545.0
3 TraesCS1A01G022900 chr1A 94.574 129 7 0 1977 2105 11164699 11164571 2.060000e-47 200.0
4 TraesCS1A01G022900 chr1A 77.352 287 38 15 2712 2994 11163600 11163337 9.780000e-31 145.0
5 TraesCS1A01G022900 chr1B 96.589 3049 77 10 107 3135 14288104 14285063 0.000000e+00 5029.0
6 TraesCS1A01G022900 chr1B 100.000 37 0 0 8 44 14288137 14288101 6.060000e-08 69.4
7 TraesCS1A01G022900 chr3B 87.083 240 27 4 3144 3382 36469042 36468806 5.560000e-68 268.0
8 TraesCS1A01G022900 chr3B 86.235 247 30 3 3139 3382 155822830 155823075 7.200000e-67 265.0
9 TraesCS1A01G022900 chr7D 86.475 244 30 3 3141 3382 511927131 511926889 7.200000e-67 265.0
10 TraesCS1A01G022900 chr3D 86.475 244 29 3 3141 3382 442389618 442389377 7.200000e-67 265.0
11 TraesCS1A01G022900 chr3D 85.200 250 33 3 3136 3382 117880357 117880109 1.560000e-63 254.0
12 TraesCS1A01G022900 chr2A 86.475 244 30 2 3141 3382 733160012 733160254 7.200000e-67 265.0
13 TraesCS1A01G022900 chr7A 86.000 250 29 5 3137 3382 89977534 89977781 2.590000e-66 263.0
14 TraesCS1A01G022900 chr7B 86.235 247 25 6 3141 3382 710460332 710460090 3.350000e-65 259.0
15 TraesCS1A01G022900 chr4B 85.950 242 29 4 3144 3382 476260633 476260394 1.560000e-63 254.0


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 TraesCS1A01G022900 chr1A 11387647 11391028 3381 False 6246.0 6246 100.0000 1 3382 1 chr1A.!!$F1 3381
1 TraesCS1A01G022900 chr1A 11204858 11206207 1349 True 875.0 1205 91.3540 10 1296 2 chr1A.!!$R2 1286
2 TraesCS1A01G022900 chr1B 14285063 14288137 3074 True 2549.2 5029 98.2945 8 3135 2 chr1B.!!$R1 3127

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
69 140 0.118144 ACTGCCCCCTCTCTTCTTCT 59.882 55.0 0.00 0.00 0.00 2.85 F
155 226 0.249657 GAATCAGTGCGCTCCCTAGG 60.250 60.0 9.73 0.06 0.00 3.02 F
1959 2101 0.945813 GTAGCTACCGATCTGTCGCT 59.054 55.0 18.00 18.00 46.32 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2092 1.753649 AGATGCAGTACAGCGACAGAT 59.246 47.619 5.73 0.0 40.53 2.90 R
2023 2165 2.158986 TGCATGGACCCAACAACAAAAG 60.159 45.455 0.00 0.0 0.00 2.27 R
3189 3349 0.392461 GGCACGCCACTCAAATCCTA 60.392 55.000 2.36 0.0 35.81 2.94 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
44 115 3.569277 CGGCATCCAATCAAATCATGGTA 59.431 43.478 0.00 0.00 35.66 3.25
45 116 4.037803 CGGCATCCAATCAAATCATGGTAA 59.962 41.667 0.00 0.00 35.66 2.85
46 117 5.451659 CGGCATCCAATCAAATCATGGTAAA 60.452 40.000 0.00 0.00 35.66 2.01
47 118 6.527423 GGCATCCAATCAAATCATGGTAAAT 58.473 36.000 0.00 0.00 35.66 1.40
48 119 6.993902 GGCATCCAATCAAATCATGGTAAATT 59.006 34.615 0.00 0.00 35.66 1.82
49 120 7.172019 GGCATCCAATCAAATCATGGTAAATTC 59.828 37.037 0.00 0.00 35.66 2.17
50 121 7.711772 GCATCCAATCAAATCATGGTAAATTCA 59.288 33.333 0.00 0.00 35.66 2.57
51 122 9.037737 CATCCAATCAAATCATGGTAAATTCAC 57.962 33.333 0.00 0.00 35.66 3.18
52 123 8.365060 TCCAATCAAATCATGGTAAATTCACT 57.635 30.769 0.00 0.00 35.66 3.41
53 124 8.252417 TCCAATCAAATCATGGTAAATTCACTG 58.748 33.333 0.00 0.00 35.66 3.66
54 125 7.010738 CCAATCAAATCATGGTAAATTCACTGC 59.989 37.037 0.00 0.00 0.00 4.40
55 126 5.964758 TCAAATCATGGTAAATTCACTGCC 58.035 37.500 0.00 0.00 0.00 4.85
56 127 5.105392 TCAAATCATGGTAAATTCACTGCCC 60.105 40.000 0.00 0.00 0.00 5.36
57 128 2.733956 TCATGGTAAATTCACTGCCCC 58.266 47.619 0.00 0.00 0.00 5.80
58 129 1.756538 CATGGTAAATTCACTGCCCCC 59.243 52.381 0.00 0.00 0.00 5.40
59 130 1.080638 TGGTAAATTCACTGCCCCCT 58.919 50.000 0.00 0.00 0.00 4.79
60 131 1.005450 TGGTAAATTCACTGCCCCCTC 59.995 52.381 0.00 0.00 0.00 4.30
61 132 1.285078 GGTAAATTCACTGCCCCCTCT 59.715 52.381 0.00 0.00 0.00 3.69
62 133 2.644676 GTAAATTCACTGCCCCCTCTC 58.355 52.381 0.00 0.00 0.00 3.20
63 134 1.376649 AAATTCACTGCCCCCTCTCT 58.623 50.000 0.00 0.00 0.00 3.10
64 135 1.376649 AATTCACTGCCCCCTCTCTT 58.623 50.000 0.00 0.00 0.00 2.85
65 136 0.915364 ATTCACTGCCCCCTCTCTTC 59.085 55.000 0.00 0.00 0.00 2.87
66 137 0.178891 TTCACTGCCCCCTCTCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
67 138 0.178891 TCACTGCCCCCTCTCTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
68 139 0.251634 CACTGCCCCCTCTCTTCTTC 59.748 60.000 0.00 0.00 0.00 2.87
69 140 0.118144 ACTGCCCCCTCTCTTCTTCT 59.882 55.000 0.00 0.00 0.00 2.85
70 141 1.362932 ACTGCCCCCTCTCTTCTTCTA 59.637 52.381 0.00 0.00 0.00 2.10
71 142 2.038659 CTGCCCCCTCTCTTCTTCTAG 58.961 57.143 0.00 0.00 0.00 2.43
72 143 0.756294 GCCCCCTCTCTTCTTCTAGC 59.244 60.000 0.00 0.00 0.00 3.42
73 144 1.419381 CCCCCTCTCTTCTTCTAGCC 58.581 60.000 0.00 0.00 0.00 3.93
74 145 1.419381 CCCCTCTCTTCTTCTAGCCC 58.581 60.000 0.00 0.00 0.00 5.19
75 146 1.036707 CCCTCTCTTCTTCTAGCCCG 58.963 60.000 0.00 0.00 0.00 6.13
76 147 1.686741 CCCTCTCTTCTTCTAGCCCGT 60.687 57.143 0.00 0.00 0.00 5.28
77 148 2.104170 CCTCTCTTCTTCTAGCCCGTT 58.896 52.381 0.00 0.00 0.00 4.44
78 149 2.498078 CCTCTCTTCTTCTAGCCCGTTT 59.502 50.000 0.00 0.00 0.00 3.60
79 150 3.055747 CCTCTCTTCTTCTAGCCCGTTTT 60.056 47.826 0.00 0.00 0.00 2.43
80 151 3.926616 TCTCTTCTTCTAGCCCGTTTTG 58.073 45.455 0.00 0.00 0.00 2.44
81 152 3.323979 TCTCTTCTTCTAGCCCGTTTTGT 59.676 43.478 0.00 0.00 0.00 2.83
82 153 3.660865 TCTTCTTCTAGCCCGTTTTGTC 58.339 45.455 0.00 0.00 0.00 3.18
83 154 3.323979 TCTTCTTCTAGCCCGTTTTGTCT 59.676 43.478 0.00 0.00 0.00 3.41
84 155 3.764237 TCTTCTAGCCCGTTTTGTCTT 57.236 42.857 0.00 0.00 0.00 3.01
85 156 3.399330 TCTTCTAGCCCGTTTTGTCTTG 58.601 45.455 0.00 0.00 0.00 3.02
86 157 1.519408 TCTAGCCCGTTTTGTCTTGC 58.481 50.000 0.00 0.00 0.00 4.01
87 158 1.071699 TCTAGCCCGTTTTGTCTTGCT 59.928 47.619 0.00 0.00 0.00 3.91
88 159 2.300723 TCTAGCCCGTTTTGTCTTGCTA 59.699 45.455 0.00 0.00 0.00 3.49
89 160 1.235724 AGCCCGTTTTGTCTTGCTAC 58.764 50.000 0.00 0.00 0.00 3.58
90 161 1.202770 AGCCCGTTTTGTCTTGCTACT 60.203 47.619 0.00 0.00 0.00 2.57
91 162 2.038033 AGCCCGTTTTGTCTTGCTACTA 59.962 45.455 0.00 0.00 0.00 1.82
92 163 2.809696 GCCCGTTTTGTCTTGCTACTAA 59.190 45.455 0.00 0.00 0.00 2.24
93 164 3.439129 GCCCGTTTTGTCTTGCTACTAAT 59.561 43.478 0.00 0.00 0.00 1.73
94 165 4.632688 GCCCGTTTTGTCTTGCTACTAATA 59.367 41.667 0.00 0.00 0.00 0.98
95 166 5.296035 GCCCGTTTTGTCTTGCTACTAATAT 59.704 40.000 0.00 0.00 0.00 1.28
96 167 6.183360 GCCCGTTTTGTCTTGCTACTAATATT 60.183 38.462 0.00 0.00 0.00 1.28
97 168 7.407337 CCCGTTTTGTCTTGCTACTAATATTC 58.593 38.462 0.00 0.00 0.00 1.75
98 169 7.280205 CCCGTTTTGTCTTGCTACTAATATTCT 59.720 37.037 0.00 0.00 0.00 2.40
99 170 8.328864 CCGTTTTGTCTTGCTACTAATATTCTC 58.671 37.037 0.00 0.00 0.00 2.87
100 171 9.088512 CGTTTTGTCTTGCTACTAATATTCTCT 57.911 33.333 0.00 0.00 0.00 3.10
102 173 9.601217 TTTTGTCTTGCTACTAATATTCTCTCC 57.399 33.333 0.00 0.00 0.00 3.71
103 174 8.540507 TTGTCTTGCTACTAATATTCTCTCCT 57.459 34.615 0.00 0.00 0.00 3.69
104 175 8.540507 TGTCTTGCTACTAATATTCTCTCCTT 57.459 34.615 0.00 0.00 0.00 3.36
105 176 8.982723 TGTCTTGCTACTAATATTCTCTCCTTT 58.017 33.333 0.00 0.00 0.00 3.11
106 177 9.825109 GTCTTGCTACTAATATTCTCTCCTTTT 57.175 33.333 0.00 0.00 0.00 2.27
107 178 9.823647 TCTTGCTACTAATATTCTCTCCTTTTG 57.176 33.333 0.00 0.00 0.00 2.44
108 179 8.964476 TTGCTACTAATATTCTCTCCTTTTGG 57.036 34.615 0.00 0.00 42.21 3.28
109 180 8.090788 TGCTACTAATATTCTCTCCTTTTGGT 57.909 34.615 0.00 0.00 41.38 3.67
129 200 1.588824 TTTGCAGAGCCAAGATGCCG 61.589 55.000 0.00 0.00 39.22 5.69
131 202 2.178890 GCAGAGCCAAGATGCCGAG 61.179 63.158 0.00 0.00 33.81 4.63
155 226 0.249657 GAATCAGTGCGCTCCCTAGG 60.250 60.000 9.73 0.06 0.00 3.02
189 260 2.633488 GAATCCTTGAACTCCTTCCGG 58.367 52.381 0.00 0.00 0.00 5.14
329 400 1.594293 GATCATGGGGGCGTACACG 60.594 63.158 0.00 0.00 43.27 4.49
332 403 3.467226 ATGGGGGCGTACACGGAG 61.467 66.667 3.67 0.00 40.23 4.63
418 547 8.818622 AGACTTACCTTTTACCTTTCAAAACT 57.181 30.769 0.00 0.00 0.00 2.66
429 558 4.935205 ACCTTTCAAAACTTTTCTTGTGCC 59.065 37.500 0.00 0.00 0.00 5.01
730 859 1.075970 TCCTCAGCATAGACGCCCT 60.076 57.895 0.00 0.00 0.00 5.19
854 987 1.996292 CTGTGACCACACCTATGTCG 58.004 55.000 0.00 0.00 45.40 4.35
855 988 1.544246 CTGTGACCACACCTATGTCGA 59.456 52.381 0.00 0.00 45.40 4.20
856 989 2.166459 CTGTGACCACACCTATGTCGAT 59.834 50.000 0.00 0.00 45.40 3.59
857 990 2.165641 TGTGACCACACCTATGTCGATC 59.834 50.000 0.00 0.00 45.40 3.69
1314 1454 2.101783 TCTATGCCATTTGCCCACTTG 58.898 47.619 0.00 0.00 40.16 3.16
1319 1459 3.106054 TGCCATTTGCCCACTTGATATT 58.894 40.909 0.00 0.00 40.16 1.28
1378 1519 6.433847 AACTATATACCAGCATGCCACTAA 57.566 37.500 15.66 0.00 31.97 2.24
1415 1556 6.206243 CACCAATAATAAAGATGAGAGCAGGG 59.794 42.308 0.00 0.00 0.00 4.45
1649 1790 5.990120 AAACATGGATTTTCTTGGGAGAG 57.010 39.130 0.00 0.00 32.44 3.20
1681 1822 8.636213 CCATGCAAGATAATGTTAGAATTCCTT 58.364 33.333 0.65 0.00 0.00 3.36
1758 1899 3.593096 TGTTTCAGAGAGCTGTATGCAG 58.407 45.455 6.42 6.42 45.94 4.41
1857 1999 4.692625 CCTCCGATATTGATGCAGGTTTAG 59.307 45.833 0.00 0.00 0.00 1.85
1950 2092 6.282930 ACTTGTAAGTTTTTGTAGCTACCGA 58.717 36.000 21.01 7.17 35.21 4.69
1959 2101 0.945813 GTAGCTACCGATCTGTCGCT 59.054 55.000 18.00 18.00 46.32 4.93
2081 2223 4.157656 TCTTGTGAACCCAACAAGTTTGAG 59.842 41.667 14.12 0.00 40.98 3.02
2093 2235 5.649782 ACAAGTTTGAGGATATTGCCAAG 57.350 39.130 0.00 0.00 0.00 3.61
2169 2311 3.857010 GCTGTTCATGAAAGGGTTTTCGG 60.857 47.826 10.35 1.37 44.55 4.30
2304 2446 3.250040 CGAGTGTTTAAGGTTTCCTGTGG 59.750 47.826 0.00 0.00 32.13 4.17
2411 2553 1.823470 AAGCAGTGCGCAGAACCAA 60.823 52.632 12.22 0.00 46.13 3.67
2414 2556 2.024918 CAGTGCGCAGAACCAAGTT 58.975 52.632 12.22 0.00 0.00 2.66
2437 2579 1.091537 TGCTTAGCACGCCCATTAAC 58.908 50.000 1.39 0.00 31.71 2.01
2499 2655 6.769512 TGTAGGCTTACTTTTTCAGAGACAT 58.230 36.000 7.57 0.00 0.00 3.06
2511 2667 0.837691 AGAGACATGGTGAGTGCCCA 60.838 55.000 0.00 0.00 36.16 5.36
2530 2686 0.467844 ATGTGTTGCAACAGGAGCCA 60.468 50.000 31.81 24.40 40.05 4.75
2572 2732 6.491062 ACAAGGTATTGGGTTAAACTAACACC 59.509 38.462 8.92 8.92 41.35 4.16
2672 2832 6.263344 CAGACAATGGATATCAAAGCAACAG 58.737 40.000 4.83 0.00 0.00 3.16
2761 2921 5.306678 TCCTTCCAAACAAAATGTAATGGCT 59.693 36.000 9.28 0.00 37.38 4.75
2781 2941 3.983344 GCTGGTTATTGAAAGTGCACAAG 59.017 43.478 21.04 0.00 0.00 3.16
2807 2967 2.034432 TGCAAGCGAGAATGAAAAAGCA 59.966 40.909 0.00 0.00 0.00 3.91
2813 2973 4.455533 AGCGAGAATGAAAAAGCATGTGTA 59.544 37.500 0.00 0.00 0.00 2.90
2943 3103 7.346751 ACAGAAGTGACACCAAACATATTTT 57.653 32.000 0.84 0.00 0.00 1.82
3031 3191 7.342026 ACAGTATTGTGGTAGACAGTCATATCA 59.658 37.037 2.66 0.00 35.83 2.15
3041 3201 8.355169 GGTAGACAGTCATATCAACGGTTATTA 58.645 37.037 2.66 0.00 0.00 0.98
3099 3259 4.093743 TGCTCCTGTTACCTAATCTCACA 58.906 43.478 0.00 0.00 0.00 3.58
3132 3292 9.760077 ACGTAATAGGTAGAACATATTTTGGAG 57.240 33.333 2.72 0.00 36.59 3.86
3142 3302 8.525290 AGAACATATTTTGGAGATAACTTGGG 57.475 34.615 0.00 0.00 0.00 4.12
3143 3303 6.715347 ACATATTTTGGAGATAACTTGGGC 57.285 37.500 0.00 0.00 0.00 5.36
3144 3304 5.598417 ACATATTTTGGAGATAACTTGGGCC 59.402 40.000 0.00 0.00 0.00 5.80
3145 3305 3.825908 TTTTGGAGATAACTTGGGCCT 57.174 42.857 4.53 0.00 0.00 5.19
3146 3306 3.366052 TTTGGAGATAACTTGGGCCTC 57.634 47.619 4.53 0.00 0.00 4.70
3147 3307 2.270434 TGGAGATAACTTGGGCCTCT 57.730 50.000 4.53 0.00 0.00 3.69
3148 3308 2.562296 TGGAGATAACTTGGGCCTCTT 58.438 47.619 4.53 0.00 0.00 2.85
3149 3309 2.919602 TGGAGATAACTTGGGCCTCTTT 59.080 45.455 4.53 0.00 0.00 2.52
3150 3310 3.282885 GGAGATAACTTGGGCCTCTTTG 58.717 50.000 4.53 0.00 0.00 2.77
3151 3311 3.054361 GGAGATAACTTGGGCCTCTTTGA 60.054 47.826 4.53 0.00 0.00 2.69
3152 3312 4.385754 GGAGATAACTTGGGCCTCTTTGAT 60.386 45.833 4.53 0.00 0.00 2.57
3153 3313 5.196695 GAGATAACTTGGGCCTCTTTGATT 58.803 41.667 4.53 0.00 0.00 2.57
3154 3314 5.196695 AGATAACTTGGGCCTCTTTGATTC 58.803 41.667 4.53 0.00 0.00 2.52
3155 3315 2.978156 ACTTGGGCCTCTTTGATTCA 57.022 45.000 4.53 0.00 0.00 2.57
3156 3316 2.519013 ACTTGGGCCTCTTTGATTCAC 58.481 47.619 4.53 0.00 0.00 3.18
3157 3317 2.158475 ACTTGGGCCTCTTTGATTCACA 60.158 45.455 4.53 0.00 0.00 3.58
3158 3318 2.205022 TGGGCCTCTTTGATTCACAG 57.795 50.000 4.53 0.00 0.00 3.66
3159 3319 1.272092 TGGGCCTCTTTGATTCACAGG 60.272 52.381 4.53 1.39 0.00 4.00
3160 3320 1.467920 GGCCTCTTTGATTCACAGGG 58.532 55.000 0.00 0.00 0.00 4.45
3161 3321 1.272147 GGCCTCTTTGATTCACAGGGT 60.272 52.381 0.00 0.00 0.00 4.34
3162 3322 2.519013 GCCTCTTTGATTCACAGGGTT 58.481 47.619 0.00 0.00 0.00 4.11
3163 3323 2.893489 GCCTCTTTGATTCACAGGGTTT 59.107 45.455 0.00 0.00 0.00 3.27
3164 3324 3.321968 GCCTCTTTGATTCACAGGGTTTT 59.678 43.478 0.00 0.00 0.00 2.43
3165 3325 4.559502 GCCTCTTTGATTCACAGGGTTTTC 60.560 45.833 0.00 0.00 0.00 2.29
3166 3326 4.584325 CCTCTTTGATTCACAGGGTTTTCA 59.416 41.667 0.00 0.00 0.00 2.69
3167 3327 5.068987 CCTCTTTGATTCACAGGGTTTTCAA 59.931 40.000 0.00 0.00 0.00 2.69
3168 3328 6.406849 CCTCTTTGATTCACAGGGTTTTCAAA 60.407 38.462 0.00 0.00 33.47 2.69
3169 3329 6.940739 TCTTTGATTCACAGGGTTTTCAAAA 58.059 32.000 0.19 0.00 33.97 2.44
3170 3330 6.816140 TCTTTGATTCACAGGGTTTTCAAAAC 59.184 34.615 4.25 4.25 33.97 2.43
3171 3331 4.677584 TGATTCACAGGGTTTTCAAAACG 58.322 39.130 6.92 0.00 0.00 3.60
3172 3332 4.158764 TGATTCACAGGGTTTTCAAAACGT 59.841 37.500 6.92 0.00 0.00 3.99
3173 3333 5.357314 TGATTCACAGGGTTTTCAAAACGTA 59.643 36.000 6.92 0.00 0.00 3.57
3174 3334 4.886247 TCACAGGGTTTTCAAAACGTAG 57.114 40.909 6.92 1.90 0.00 3.51
3176 3336 5.426504 TCACAGGGTTTTCAAAACGTAGTA 58.573 37.500 6.92 0.00 45.00 1.82
3177 3337 5.524646 TCACAGGGTTTTCAAAACGTAGTAG 59.475 40.000 6.92 0.00 45.00 2.57
3178 3338 4.274214 ACAGGGTTTTCAAAACGTAGTAGC 59.726 41.667 6.92 0.00 45.00 3.58
3179 3339 4.273969 CAGGGTTTTCAAAACGTAGTAGCA 59.726 41.667 6.92 0.00 45.00 3.49
3180 3340 4.883006 AGGGTTTTCAAAACGTAGTAGCAA 59.117 37.500 6.92 0.00 45.00 3.91
3181 3341 4.971830 GGGTTTTCAAAACGTAGTAGCAAC 59.028 41.667 6.92 0.00 45.00 4.17
3182 3342 5.448904 GGGTTTTCAAAACGTAGTAGCAACA 60.449 40.000 6.92 0.00 45.00 3.33
3183 3343 5.679792 GGTTTTCAAAACGTAGTAGCAACAG 59.320 40.000 6.92 0.00 45.00 3.16
3184 3344 6.457257 GGTTTTCAAAACGTAGTAGCAACAGA 60.457 38.462 6.92 0.00 45.00 3.41
3185 3345 6.665474 TTTCAAAACGTAGTAGCAACAGAA 57.335 33.333 0.00 0.00 45.00 3.02
3186 3346 5.900339 TCAAAACGTAGTAGCAACAGAAG 57.100 39.130 0.00 0.00 45.00 2.85
3187 3347 5.353938 TCAAAACGTAGTAGCAACAGAAGT 58.646 37.500 0.00 0.00 45.00 3.01
3188 3348 6.506147 TCAAAACGTAGTAGCAACAGAAGTA 58.494 36.000 0.00 0.00 45.00 2.24
3189 3349 7.149973 TCAAAACGTAGTAGCAACAGAAGTAT 58.850 34.615 0.00 0.00 45.00 2.12
3190 3350 8.298854 TCAAAACGTAGTAGCAACAGAAGTATA 58.701 33.333 0.00 0.00 45.00 1.47
3191 3351 8.584600 CAAAACGTAGTAGCAACAGAAGTATAG 58.415 37.037 0.00 0.00 45.00 1.31
3192 3352 6.374565 ACGTAGTAGCAACAGAAGTATAGG 57.625 41.667 0.00 0.00 41.94 2.57
3193 3353 6.118170 ACGTAGTAGCAACAGAAGTATAGGA 58.882 40.000 0.00 0.00 41.94 2.94
3194 3354 6.771749 ACGTAGTAGCAACAGAAGTATAGGAT 59.228 38.462 0.00 0.00 41.94 3.24
3195 3355 7.284944 ACGTAGTAGCAACAGAAGTATAGGATT 59.715 37.037 0.00 0.00 41.94 3.01
3196 3356 8.136165 CGTAGTAGCAACAGAAGTATAGGATTT 58.864 37.037 0.00 0.00 0.00 2.17
3197 3357 9.250624 GTAGTAGCAACAGAAGTATAGGATTTG 57.749 37.037 0.00 0.00 0.00 2.32
3198 3358 8.079211 AGTAGCAACAGAAGTATAGGATTTGA 57.921 34.615 0.00 0.00 0.00 2.69
3199 3359 8.200792 AGTAGCAACAGAAGTATAGGATTTGAG 58.799 37.037 0.00 0.00 0.00 3.02
3200 3360 6.951971 AGCAACAGAAGTATAGGATTTGAGT 58.048 36.000 0.00 0.00 0.00 3.41
3201 3361 6.820656 AGCAACAGAAGTATAGGATTTGAGTG 59.179 38.462 0.00 0.00 0.00 3.51
3202 3362 6.037610 GCAACAGAAGTATAGGATTTGAGTGG 59.962 42.308 0.00 0.00 0.00 4.00
3203 3363 5.675538 ACAGAAGTATAGGATTTGAGTGGC 58.324 41.667 0.00 0.00 0.00 5.01
3204 3364 4.747108 CAGAAGTATAGGATTTGAGTGGCG 59.253 45.833 0.00 0.00 0.00 5.69
3205 3365 4.406003 AGAAGTATAGGATTTGAGTGGCGT 59.594 41.667 0.00 0.00 0.00 5.68
3206 3366 4.060038 AGTATAGGATTTGAGTGGCGTG 57.940 45.455 0.00 0.00 0.00 5.34
3207 3367 1.668419 ATAGGATTTGAGTGGCGTGC 58.332 50.000 0.00 0.00 0.00 5.34
3208 3368 0.392461 TAGGATTTGAGTGGCGTGCC 60.392 55.000 3.30 3.30 0.00 5.01
3209 3369 2.700773 GGATTTGAGTGGCGTGCCC 61.701 63.158 8.69 0.00 34.56 5.36
3210 3370 1.971167 GATTTGAGTGGCGTGCCCA 60.971 57.895 8.69 0.00 42.79 5.36
3217 3377 2.115052 TGGCGTGCCCACTTGAAT 59.885 55.556 8.69 0.00 39.18 2.57
3218 3378 1.376848 TGGCGTGCCCACTTGAATA 59.623 52.632 8.69 0.00 39.18 1.75
3219 3379 0.958382 TGGCGTGCCCACTTGAATAC 60.958 55.000 8.69 0.00 39.18 1.89
3220 3380 0.676782 GGCGTGCCCACTTGAATACT 60.677 55.000 0.00 0.00 0.00 2.12
3221 3381 1.406341 GGCGTGCCCACTTGAATACTA 60.406 52.381 0.00 0.00 0.00 1.82
3222 3382 2.352388 GCGTGCCCACTTGAATACTAA 58.648 47.619 0.00 0.00 0.00 2.24
3223 3383 2.745281 GCGTGCCCACTTGAATACTAAA 59.255 45.455 0.00 0.00 0.00 1.85
3224 3384 3.181510 GCGTGCCCACTTGAATACTAAAG 60.182 47.826 0.00 0.00 0.00 1.85
3225 3385 3.374058 CGTGCCCACTTGAATACTAAAGG 59.626 47.826 0.00 0.00 0.00 3.11
3226 3386 4.585879 GTGCCCACTTGAATACTAAAGGA 58.414 43.478 0.00 0.00 0.00 3.36
3227 3387 5.193679 GTGCCCACTTGAATACTAAAGGAT 58.806 41.667 0.00 0.00 0.00 3.24
3228 3388 5.652452 GTGCCCACTTGAATACTAAAGGATT 59.348 40.000 0.00 0.00 0.00 3.01
3229 3389 6.826741 GTGCCCACTTGAATACTAAAGGATTA 59.173 38.462 0.00 0.00 0.00 1.75
3230 3390 7.012421 GTGCCCACTTGAATACTAAAGGATTAG 59.988 40.741 0.00 0.00 43.48 1.73
3231 3391 6.017026 GCCCACTTGAATACTAAAGGATTAGC 60.017 42.308 0.00 0.00 41.92 3.09
3232 3392 7.054124 CCCACTTGAATACTAAAGGATTAGCA 58.946 38.462 0.00 0.00 41.92 3.49
3233 3393 7.556275 CCCACTTGAATACTAAAGGATTAGCAA 59.444 37.037 0.00 0.00 41.92 3.91
3234 3394 8.956426 CCACTTGAATACTAAAGGATTAGCAAA 58.044 33.333 0.00 0.00 41.92 3.68
3235 3395 9.994432 CACTTGAATACTAAAGGATTAGCAAAG 57.006 33.333 0.00 0.00 41.92 2.77
3236 3396 9.178758 ACTTGAATACTAAAGGATTAGCAAAGG 57.821 33.333 0.00 0.00 41.92 3.11
3237 3397 9.396022 CTTGAATACTAAAGGATTAGCAAAGGA 57.604 33.333 0.00 0.00 41.92 3.36
3238 3398 8.964476 TGAATACTAAAGGATTAGCAAAGGAG 57.036 34.615 0.00 0.00 41.92 3.69
3239 3399 8.548877 TGAATACTAAAGGATTAGCAAAGGAGT 58.451 33.333 0.00 0.00 41.92 3.85
3240 3400 8.738645 AATACTAAAGGATTAGCAAAGGAGTG 57.261 34.615 0.00 0.00 41.92 3.51
3241 3401 4.944317 ACTAAAGGATTAGCAAAGGAGTGC 59.056 41.667 0.00 0.00 41.92 4.40
3248 3408 3.413522 GCAAAGGAGTGCTTGATGC 57.586 52.632 5.45 5.45 41.51 3.91
3249 3409 0.108945 GCAAAGGAGTGCTTGATGCC 60.109 55.000 9.29 0.00 41.51 4.40
3250 3410 1.250328 CAAAGGAGTGCTTGATGCCA 58.750 50.000 0.00 0.00 42.00 4.92
3251 3411 1.068055 CAAAGGAGTGCTTGATGCCAC 60.068 52.381 0.00 0.00 42.00 5.01
3252 3412 0.111061 AAGGAGTGCTTGATGCCACA 59.889 50.000 0.00 0.00 42.00 4.17
3253 3413 0.111061 AGGAGTGCTTGATGCCACAA 59.889 50.000 0.00 0.00 42.00 3.33
3254 3414 0.524862 GGAGTGCTTGATGCCACAAG 59.475 55.000 13.33 13.33 46.69 3.16
3255 3415 1.527034 GAGTGCTTGATGCCACAAGA 58.473 50.000 19.39 6.25 46.85 3.02
3256 3416 1.467734 GAGTGCTTGATGCCACAAGAG 59.532 52.381 19.39 0.78 46.85 2.85
3257 3417 1.072806 AGTGCTTGATGCCACAAGAGA 59.927 47.619 19.39 6.24 46.85 3.10
3258 3418 1.881973 GTGCTTGATGCCACAAGAGAA 59.118 47.619 19.39 5.64 46.85 2.87
3259 3419 2.294233 GTGCTTGATGCCACAAGAGAAA 59.706 45.455 19.39 3.75 46.85 2.52
3260 3420 2.294233 TGCTTGATGCCACAAGAGAAAC 59.706 45.455 19.39 6.09 46.85 2.78
3261 3421 2.294233 GCTTGATGCCACAAGAGAAACA 59.706 45.455 19.39 0.00 46.85 2.83
3262 3422 3.243501 GCTTGATGCCACAAGAGAAACAA 60.244 43.478 19.39 0.00 46.85 2.83
3263 3423 4.737352 GCTTGATGCCACAAGAGAAACAAA 60.737 41.667 19.39 0.00 46.85 2.83
3264 3424 4.572985 TGATGCCACAAGAGAAACAAAG 57.427 40.909 0.00 0.00 0.00 2.77
3265 3425 4.206375 TGATGCCACAAGAGAAACAAAGA 58.794 39.130 0.00 0.00 0.00 2.52
3266 3426 4.644234 TGATGCCACAAGAGAAACAAAGAA 59.356 37.500 0.00 0.00 0.00 2.52
3267 3427 5.126869 TGATGCCACAAGAGAAACAAAGAAA 59.873 36.000 0.00 0.00 0.00 2.52
3268 3428 5.596836 TGCCACAAGAGAAACAAAGAAAT 57.403 34.783 0.00 0.00 0.00 2.17
3269 3429 5.976458 TGCCACAAGAGAAACAAAGAAATT 58.024 33.333 0.00 0.00 0.00 1.82
3270 3430 5.811613 TGCCACAAGAGAAACAAAGAAATTG 59.188 36.000 0.00 0.00 44.95 2.32
3288 3448 9.847224 AAGAAATTGTAAAGAGGTTGAAGTAGA 57.153 29.630 0.00 0.00 0.00 2.59
3291 3451 9.574516 AAATTGTAAAGAGGTTGAAGTAGATGT 57.425 29.630 0.00 0.00 0.00 3.06
3292 3452 9.574516 AATTGTAAAGAGGTTGAAGTAGATGTT 57.425 29.630 0.00 0.00 0.00 2.71
3294 3454 9.706691 TTGTAAAGAGGTTGAAGTAGATGTTAG 57.293 33.333 0.00 0.00 0.00 2.34
3295 3455 9.085645 TGTAAAGAGGTTGAAGTAGATGTTAGA 57.914 33.333 0.00 0.00 0.00 2.10
3300 3460 9.660180 AGAGGTTGAAGTAGATGTTAGATTTTC 57.340 33.333 0.00 0.00 0.00 2.29
3301 3461 9.660180 GAGGTTGAAGTAGATGTTAGATTTTCT 57.340 33.333 0.00 0.00 0.00 2.52
3370 3530 8.797438 GGATCCAATCCTATAAATCAAAGAACC 58.203 37.037 6.95 0.00 46.19 3.62
3371 3531 9.354673 GATCCAATCCTATAAATCAAAGAACCA 57.645 33.333 0.00 0.00 0.00 3.67
3372 3532 9.713684 ATCCAATCCTATAAATCAAAGAACCAA 57.286 29.630 0.00 0.00 0.00 3.67
3373 3533 8.966868 TCCAATCCTATAAATCAAAGAACCAAC 58.033 33.333 0.00 0.00 0.00 3.77
3374 3534 7.915397 CCAATCCTATAAATCAAAGAACCAACG 59.085 37.037 0.00 0.00 0.00 4.10
3375 3535 8.458843 CAATCCTATAAATCAAAGAACCAACGT 58.541 33.333 0.00 0.00 0.00 3.99
3376 3536 9.675464 AATCCTATAAATCAAAGAACCAACGTA 57.325 29.630 0.00 0.00 0.00 3.57
3377 3537 8.712285 TCCTATAAATCAAAGAACCAACGTAG 57.288 34.615 0.00 0.00 0.00 3.51
3378 3538 7.767198 TCCTATAAATCAAAGAACCAACGTAGG 59.233 37.037 0.00 0.00 0.00 3.18
3379 3539 7.767198 CCTATAAATCAAAGAACCAACGTAGGA 59.233 37.037 0.00 0.00 0.00 2.94
3380 3540 7.989416 ATAAATCAAAGAACCAACGTAGGAA 57.011 32.000 0.00 0.00 0.00 3.36
3381 3541 6.702716 AAATCAAAGAACCAACGTAGGAAA 57.297 33.333 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179037 GCAGATGGATGCACAGCCTA 60.179 55.000 6.48 0.00 45.77 3.93
1 2 1.453379 GCAGATGGATGCACAGCCT 60.453 57.895 6.48 0.00 45.77 4.58
2 3 3.117372 GCAGATGGATGCACAGCC 58.883 61.111 0.00 0.00 45.77 4.85
44 115 1.376649 AGAGAGGGGGCAGTGAATTT 58.623 50.000 0.00 0.00 0.00 1.82
45 116 1.283321 GAAGAGAGGGGGCAGTGAATT 59.717 52.381 0.00 0.00 0.00 2.17
46 117 0.915364 GAAGAGAGGGGGCAGTGAAT 59.085 55.000 0.00 0.00 0.00 2.57
47 118 0.178891 AGAAGAGAGGGGGCAGTGAA 60.179 55.000 0.00 0.00 0.00 3.18
48 119 0.178891 AAGAAGAGAGGGGGCAGTGA 60.179 55.000 0.00 0.00 0.00 3.41
49 120 0.251634 GAAGAAGAGAGGGGGCAGTG 59.748 60.000 0.00 0.00 0.00 3.66
50 121 0.118144 AGAAGAAGAGAGGGGGCAGT 59.882 55.000 0.00 0.00 0.00 4.40
51 122 2.038659 CTAGAAGAAGAGAGGGGGCAG 58.961 57.143 0.00 0.00 0.00 4.85
52 123 1.967274 GCTAGAAGAAGAGAGGGGGCA 60.967 57.143 0.00 0.00 0.00 5.36
53 124 0.756294 GCTAGAAGAAGAGAGGGGGC 59.244 60.000 0.00 0.00 0.00 5.80
54 125 1.419381 GGCTAGAAGAAGAGAGGGGG 58.581 60.000 0.00 0.00 0.00 5.40
55 126 1.419381 GGGCTAGAAGAAGAGAGGGG 58.581 60.000 0.00 0.00 0.00 4.79
56 127 1.036707 CGGGCTAGAAGAAGAGAGGG 58.963 60.000 0.00 0.00 0.00 4.30
57 128 1.770294 ACGGGCTAGAAGAAGAGAGG 58.230 55.000 0.00 0.00 0.00 3.69
58 129 3.878160 AAACGGGCTAGAAGAAGAGAG 57.122 47.619 0.00 0.00 0.00 3.20
59 130 3.323979 ACAAAACGGGCTAGAAGAAGAGA 59.676 43.478 0.00 0.00 0.00 3.10
60 131 3.665190 ACAAAACGGGCTAGAAGAAGAG 58.335 45.455 0.00 0.00 0.00 2.85
61 132 3.323979 AGACAAAACGGGCTAGAAGAAGA 59.676 43.478 0.00 0.00 0.00 2.87
62 133 3.665190 AGACAAAACGGGCTAGAAGAAG 58.335 45.455 0.00 0.00 0.00 2.85
63 134 3.764237 AGACAAAACGGGCTAGAAGAA 57.236 42.857 0.00 0.00 0.00 2.52
64 135 3.399330 CAAGACAAAACGGGCTAGAAGA 58.601 45.455 0.00 0.00 0.00 2.87
65 136 2.095718 GCAAGACAAAACGGGCTAGAAG 60.096 50.000 0.00 0.00 0.00 2.85
66 137 1.877443 GCAAGACAAAACGGGCTAGAA 59.123 47.619 0.00 0.00 0.00 2.10
67 138 1.071699 AGCAAGACAAAACGGGCTAGA 59.928 47.619 0.00 0.00 0.00 2.43
68 139 1.523758 AGCAAGACAAAACGGGCTAG 58.476 50.000 0.00 0.00 0.00 3.42
69 140 2.038033 AGTAGCAAGACAAAACGGGCTA 59.962 45.455 0.00 0.00 33.10 3.93
70 141 1.202770 AGTAGCAAGACAAAACGGGCT 60.203 47.619 0.00 0.00 35.50 5.19
71 142 1.235724 AGTAGCAAGACAAAACGGGC 58.764 50.000 0.00 0.00 0.00 6.13
72 143 6.920569 ATATTAGTAGCAAGACAAAACGGG 57.079 37.500 0.00 0.00 0.00 5.28
73 144 8.197988 AGAATATTAGTAGCAAGACAAAACGG 57.802 34.615 0.00 0.00 0.00 4.44
74 145 9.088512 AGAGAATATTAGTAGCAAGACAAAACG 57.911 33.333 0.00 0.00 0.00 3.60
76 147 9.601217 GGAGAGAATATTAGTAGCAAGACAAAA 57.399 33.333 0.00 0.00 0.00 2.44
77 148 8.982723 AGGAGAGAATATTAGTAGCAAGACAAA 58.017 33.333 0.00 0.00 0.00 2.83
78 149 8.540507 AGGAGAGAATATTAGTAGCAAGACAA 57.459 34.615 0.00 0.00 0.00 3.18
79 150 8.540507 AAGGAGAGAATATTAGTAGCAAGACA 57.459 34.615 0.00 0.00 0.00 3.41
80 151 9.825109 AAAAGGAGAGAATATTAGTAGCAAGAC 57.175 33.333 0.00 0.00 0.00 3.01
81 152 9.823647 CAAAAGGAGAGAATATTAGTAGCAAGA 57.176 33.333 0.00 0.00 0.00 3.02
82 153 9.050601 CCAAAAGGAGAGAATATTAGTAGCAAG 57.949 37.037 0.00 0.00 0.00 4.01
83 154 8.548877 ACCAAAAGGAGAGAATATTAGTAGCAA 58.451 33.333 0.00 0.00 0.00 3.91
84 155 8.090788 ACCAAAAGGAGAGAATATTAGTAGCA 57.909 34.615 0.00 0.00 0.00 3.49
85 156 8.966069 AACCAAAAGGAGAGAATATTAGTAGC 57.034 34.615 0.00 0.00 0.00 3.58
88 159 8.523658 GCAAAACCAAAAGGAGAGAATATTAGT 58.476 33.333 0.00 0.00 0.00 2.24
89 160 8.522830 TGCAAAACCAAAAGGAGAGAATATTAG 58.477 33.333 0.00 0.00 0.00 1.73
90 161 8.415950 TGCAAAACCAAAAGGAGAGAATATTA 57.584 30.769 0.00 0.00 0.00 0.98
91 162 7.233348 TCTGCAAAACCAAAAGGAGAGAATATT 59.767 33.333 0.00 0.00 0.00 1.28
92 163 6.721208 TCTGCAAAACCAAAAGGAGAGAATAT 59.279 34.615 0.00 0.00 0.00 1.28
93 164 6.068010 TCTGCAAAACCAAAAGGAGAGAATA 58.932 36.000 0.00 0.00 0.00 1.75
94 165 4.895297 TCTGCAAAACCAAAAGGAGAGAAT 59.105 37.500 0.00 0.00 0.00 2.40
95 166 4.277476 TCTGCAAAACCAAAAGGAGAGAA 58.723 39.130 0.00 0.00 0.00 2.87
96 167 3.885297 CTCTGCAAAACCAAAAGGAGAGA 59.115 43.478 4.10 0.00 45.77 3.10
97 168 3.551659 GCTCTGCAAAACCAAAAGGAGAG 60.552 47.826 0.00 0.00 45.69 3.20
98 169 2.362077 GCTCTGCAAAACCAAAAGGAGA 59.638 45.455 0.00 0.00 0.00 3.71
99 170 2.546584 GGCTCTGCAAAACCAAAAGGAG 60.547 50.000 0.00 0.00 0.00 3.69
100 171 1.412343 GGCTCTGCAAAACCAAAAGGA 59.588 47.619 0.00 0.00 0.00 3.36
101 172 1.138661 TGGCTCTGCAAAACCAAAAGG 59.861 47.619 0.00 0.00 0.00 3.11
102 173 2.600470 TGGCTCTGCAAAACCAAAAG 57.400 45.000 0.00 0.00 0.00 2.27
103 174 2.499289 TCTTGGCTCTGCAAAACCAAAA 59.501 40.909 13.25 0.36 41.44 2.44
104 175 2.106566 TCTTGGCTCTGCAAAACCAAA 58.893 42.857 13.25 4.59 41.44 3.28
105 176 1.774110 TCTTGGCTCTGCAAAACCAA 58.226 45.000 12.06 12.06 39.81 3.67
106 177 1.614903 CATCTTGGCTCTGCAAAACCA 59.385 47.619 0.00 0.00 0.00 3.67
107 178 1.670967 GCATCTTGGCTCTGCAAAACC 60.671 52.381 0.00 0.00 35.96 3.27
108 179 1.670967 GGCATCTTGGCTCTGCAAAAC 60.671 52.381 0.00 0.00 40.14 2.43
109 180 0.604578 GGCATCTTGGCTCTGCAAAA 59.395 50.000 0.00 0.00 40.14 2.44
129 200 0.108424 AGCGCACTGATTCTGTCCTC 60.108 55.000 11.47 0.00 0.00 3.71
131 202 1.086634 GGAGCGCACTGATTCTGTCC 61.087 60.000 11.47 0.00 0.00 4.02
155 226 4.040461 TCAAGGATTCGGATAAGGATGTCC 59.960 45.833 0.00 0.00 33.68 4.02
329 400 0.248702 GCAATCTCCTCGTCGTCTCC 60.249 60.000 0.00 0.00 0.00 3.71
332 403 2.663334 CGATAGCAATCTCCTCGTCGTC 60.663 54.545 0.00 0.00 0.00 4.20
372 443 2.115291 GGCTCTTGATGGAACGGCC 61.115 63.158 0.00 0.00 37.10 6.13
557 686 1.072965 ACAGGGCAAGAGTGGAAGAAG 59.927 52.381 0.00 0.00 0.00 2.85
730 859 2.902486 AGTTTCTGGAGCTCTGATGACA 59.098 45.455 14.64 0.47 0.00 3.58
854 987 1.546029 GGGGAACAAAGCCACAAGATC 59.454 52.381 0.00 0.00 0.00 2.75
855 988 1.133199 TGGGGAACAAAGCCACAAGAT 60.133 47.619 0.00 0.00 35.47 2.40
856 989 0.260230 TGGGGAACAAAGCCACAAGA 59.740 50.000 0.00 0.00 35.47 3.02
857 990 1.118838 TTGGGGAACAAAGCCACAAG 58.881 50.000 0.00 0.00 43.57 3.16
1378 1519 3.678056 TTATTGGTGACAGAAGAGCGT 57.322 42.857 0.00 0.00 44.54 5.07
1443 1584 3.374678 CCACAAGTGCTTTTGTTTGCAAT 59.625 39.130 0.00 0.00 39.17 3.56
1599 1740 7.662669 AGAATTTCTACCTTTTTGCATTGCATT 59.337 29.630 12.95 0.00 38.76 3.56
1724 1865 2.146342 CTGAAACAGGAATGACGCTGT 58.854 47.619 0.00 0.00 33.67 4.40
1727 1868 2.670414 CTCTCTGAAACAGGAATGACGC 59.330 50.000 0.00 0.00 31.51 5.19
1758 1899 5.325239 CCCTCATATGGTTTTAGGGGAATC 58.675 45.833 15.71 0.00 42.79 2.52
1896 2038 9.442062 TGTACTACTCCCTCCAATCAATATTAA 57.558 33.333 0.00 0.00 0.00 1.40
1907 2049 6.021030 ACAAGTAAATGTACTACTCCCTCCA 58.979 40.000 0.00 0.00 39.79 3.86
1950 2092 1.753649 AGATGCAGTACAGCGACAGAT 59.246 47.619 5.73 0.00 40.53 2.90
1959 2101 8.935844 CAATACTAGTTTTCAAGATGCAGTACA 58.064 33.333 0.00 0.00 0.00 2.90
2017 2159 3.183754 GACCCAACAACAAAAGAAACGG 58.816 45.455 0.00 0.00 0.00 4.44
2023 2165 2.158986 TGCATGGACCCAACAACAAAAG 60.159 45.455 0.00 0.00 0.00 2.27
2081 2223 2.872858 GTCGGTCTTCTTGGCAATATCC 59.127 50.000 0.00 0.00 0.00 2.59
2169 2311 4.751767 AGTTCATCACCTTCTCATCCTC 57.248 45.455 0.00 0.00 0.00 3.71
2304 2446 1.789464 CCGACGCTTGCTAGATTCATC 59.211 52.381 0.00 0.00 0.00 2.92
2389 2531 0.239347 GTTCTGCGCACTGCTTGATT 59.761 50.000 5.66 0.00 46.63 2.57
2411 2553 1.439679 GGCGTGCTAAGCAACTAACT 58.560 50.000 0.00 0.00 41.47 2.24
2414 2556 0.251916 ATGGGCGTGCTAAGCAACTA 59.748 50.000 0.00 0.00 41.47 2.24
2460 2608 2.927014 GCCTACATATGCTCGCACCTAC 60.927 54.545 1.58 0.00 0.00 3.18
2499 2655 0.822944 CAACACATGGGCACTCACCA 60.823 55.000 0.00 0.00 43.22 4.17
2511 2667 0.467844 TGGCTCCTGTTGCAACACAT 60.468 50.000 27.96 0.00 34.70 3.21
2672 2832 1.073177 GCTCACATGGTTGCATTTGC 58.927 50.000 0.00 0.00 42.50 3.68
2752 2912 5.336372 GCACTTTCAATAACCAGCCATTACA 60.336 40.000 0.00 0.00 0.00 2.41
2761 2921 5.359576 ACTTCTTGTGCACTTTCAATAACCA 59.640 36.000 19.41 0.00 0.00 3.67
2781 2941 3.542712 TTCATTCTCGCTTGCAACTTC 57.457 42.857 0.00 0.00 0.00 3.01
2807 2967 3.192541 TGCTGGAACGCATATACACAT 57.807 42.857 0.00 0.00 33.58 3.21
2813 2973 2.415893 GCTTTGTTGCTGGAACGCATAT 60.416 45.455 7.54 0.00 37.64 1.78
2915 3075 5.054390 TGTTTGGTGTCACTTCTGTTTTC 57.946 39.130 2.35 0.00 0.00 2.29
2977 3137 3.118738 CGGCTACATTATGGATAGGTCCC 60.119 52.174 0.00 0.00 44.41 4.46
2978 3138 3.118738 CCGGCTACATTATGGATAGGTCC 60.119 52.174 0.00 0.00 45.31 4.46
3041 3201 0.392998 GATATTGGGGCGATCGGCAT 60.393 55.000 37.72 26.26 46.16 4.40
3099 3259 7.642082 ATGTTCTACCTATTACGTGTCTTCT 57.358 36.000 0.00 0.00 0.00 2.85
3132 3292 4.949856 TGAATCAAAGAGGCCCAAGTTATC 59.050 41.667 0.00 0.00 0.00 1.75
3135 3295 2.893489 GTGAATCAAAGAGGCCCAAGTT 59.107 45.455 0.00 0.00 0.00 2.66
3136 3296 2.158475 TGTGAATCAAAGAGGCCCAAGT 60.158 45.455 0.00 0.00 0.00 3.16
3137 3297 2.490903 CTGTGAATCAAAGAGGCCCAAG 59.509 50.000 0.00 0.00 0.00 3.61
3138 3298 2.517959 CTGTGAATCAAAGAGGCCCAA 58.482 47.619 0.00 0.00 0.00 4.12
3139 3299 1.272092 CCTGTGAATCAAAGAGGCCCA 60.272 52.381 1.15 0.00 0.00 5.36
3140 3300 1.467920 CCTGTGAATCAAAGAGGCCC 58.532 55.000 1.15 0.00 0.00 5.80
3141 3301 1.272147 ACCCTGTGAATCAAAGAGGCC 60.272 52.381 1.15 0.00 0.00 5.19
3142 3302 2.206576 ACCCTGTGAATCAAAGAGGC 57.793 50.000 1.15 0.00 0.00 4.70
3143 3303 4.584325 TGAAAACCCTGTGAATCAAAGAGG 59.416 41.667 1.15 4.37 0.00 3.69
3144 3304 5.772825 TGAAAACCCTGTGAATCAAAGAG 57.227 39.130 1.15 0.00 0.00 2.85
3145 3305 6.537453 TTTGAAAACCCTGTGAATCAAAGA 57.463 33.333 1.15 0.00 33.32 2.52
3146 3306 6.237808 CGTTTTGAAAACCCTGTGAATCAAAG 60.238 38.462 14.50 0.00 37.86 2.77
3147 3307 5.578727 CGTTTTGAAAACCCTGTGAATCAAA 59.421 36.000 14.50 0.00 35.63 2.69
3148 3308 5.105752 CGTTTTGAAAACCCTGTGAATCAA 58.894 37.500 14.50 0.00 0.00 2.57
3149 3309 4.158764 ACGTTTTGAAAACCCTGTGAATCA 59.841 37.500 14.50 0.00 0.00 2.57
3150 3310 4.678622 ACGTTTTGAAAACCCTGTGAATC 58.321 39.130 14.50 0.00 0.00 2.52
3151 3311 4.729227 ACGTTTTGAAAACCCTGTGAAT 57.271 36.364 14.50 0.00 0.00 2.57
3152 3312 4.701171 ACTACGTTTTGAAAACCCTGTGAA 59.299 37.500 14.50 0.00 0.00 3.18
3153 3313 4.263435 ACTACGTTTTGAAAACCCTGTGA 58.737 39.130 14.50 0.00 0.00 3.58
3154 3314 4.625972 ACTACGTTTTGAAAACCCTGTG 57.374 40.909 14.50 3.54 0.00 3.66
3155 3315 4.274214 GCTACTACGTTTTGAAAACCCTGT 59.726 41.667 14.50 12.09 0.00 4.00
3156 3316 4.273969 TGCTACTACGTTTTGAAAACCCTG 59.726 41.667 14.50 7.43 0.00 4.45
3157 3317 4.453751 TGCTACTACGTTTTGAAAACCCT 58.546 39.130 14.50 3.47 0.00 4.34
3158 3318 4.816786 TGCTACTACGTTTTGAAAACCC 57.183 40.909 14.50 0.00 0.00 4.11
3159 3319 5.571277 TGTTGCTACTACGTTTTGAAAACC 58.429 37.500 14.50 0.36 0.00 3.27
3160 3320 6.480285 TCTGTTGCTACTACGTTTTGAAAAC 58.520 36.000 10.62 10.62 0.00 2.43
3161 3321 6.665474 TCTGTTGCTACTACGTTTTGAAAA 57.335 33.333 0.00 0.00 0.00 2.29
3162 3322 6.314400 ACTTCTGTTGCTACTACGTTTTGAAA 59.686 34.615 0.00 0.00 0.00 2.69
3163 3323 5.813672 ACTTCTGTTGCTACTACGTTTTGAA 59.186 36.000 0.00 0.00 0.00 2.69
3164 3324 5.353938 ACTTCTGTTGCTACTACGTTTTGA 58.646 37.500 0.00 0.00 0.00 2.69
3165 3325 5.652744 ACTTCTGTTGCTACTACGTTTTG 57.347 39.130 0.00 0.00 0.00 2.44
3166 3326 7.758528 CCTATACTTCTGTTGCTACTACGTTTT 59.241 37.037 0.00 0.00 0.00 2.43
3167 3327 7.121759 TCCTATACTTCTGTTGCTACTACGTTT 59.878 37.037 0.00 0.00 0.00 3.60
3168 3328 6.600822 TCCTATACTTCTGTTGCTACTACGTT 59.399 38.462 0.00 0.00 0.00 3.99
3169 3329 6.118170 TCCTATACTTCTGTTGCTACTACGT 58.882 40.000 0.00 0.00 0.00 3.57
3170 3330 6.615264 TCCTATACTTCTGTTGCTACTACG 57.385 41.667 0.00 0.00 0.00 3.51
3171 3331 9.250624 CAAATCCTATACTTCTGTTGCTACTAC 57.749 37.037 0.00 0.00 0.00 2.73
3172 3332 9.197306 TCAAATCCTATACTTCTGTTGCTACTA 57.803 33.333 0.00 0.00 0.00 1.82
3173 3333 8.079211 TCAAATCCTATACTTCTGTTGCTACT 57.921 34.615 0.00 0.00 0.00 2.57
3174 3334 7.982354 ACTCAAATCCTATACTTCTGTTGCTAC 59.018 37.037 0.00 0.00 0.00 3.58
3175 3335 7.981789 CACTCAAATCCTATACTTCTGTTGCTA 59.018 37.037 0.00 0.00 0.00 3.49
3176 3336 6.820656 CACTCAAATCCTATACTTCTGTTGCT 59.179 38.462 0.00 0.00 0.00 3.91
3177 3337 6.037610 CCACTCAAATCCTATACTTCTGTTGC 59.962 42.308 0.00 0.00 0.00 4.17
3178 3338 6.037610 GCCACTCAAATCCTATACTTCTGTTG 59.962 42.308 0.00 0.00 0.00 3.33
3179 3339 6.116126 GCCACTCAAATCCTATACTTCTGTT 58.884 40.000 0.00 0.00 0.00 3.16
3180 3340 5.675538 GCCACTCAAATCCTATACTTCTGT 58.324 41.667 0.00 0.00 0.00 3.41
3181 3341 4.747108 CGCCACTCAAATCCTATACTTCTG 59.253 45.833 0.00 0.00 0.00 3.02
3182 3342 4.406003 ACGCCACTCAAATCCTATACTTCT 59.594 41.667 0.00 0.00 0.00 2.85
3183 3343 4.508124 CACGCCACTCAAATCCTATACTTC 59.492 45.833 0.00 0.00 0.00 3.01
3184 3344 4.442706 CACGCCACTCAAATCCTATACTT 58.557 43.478 0.00 0.00 0.00 2.24
3185 3345 3.741388 GCACGCCACTCAAATCCTATACT 60.741 47.826 0.00 0.00 0.00 2.12
3186 3346 2.544267 GCACGCCACTCAAATCCTATAC 59.456 50.000 0.00 0.00 0.00 1.47
3187 3347 2.484770 GGCACGCCACTCAAATCCTATA 60.485 50.000 2.36 0.00 35.81 1.31
3188 3348 1.668419 GCACGCCACTCAAATCCTAT 58.332 50.000 0.00 0.00 0.00 2.57
3189 3349 0.392461 GGCACGCCACTCAAATCCTA 60.392 55.000 2.36 0.00 35.81 2.94
3190 3350 1.675641 GGCACGCCACTCAAATCCT 60.676 57.895 2.36 0.00 35.81 3.24
3191 3351 2.700773 GGGCACGCCACTCAAATCC 61.701 63.158 10.83 0.00 37.98 3.01
3192 3352 1.971167 TGGGCACGCCACTCAAATC 60.971 57.895 10.83 0.00 37.98 2.17
3193 3353 2.115052 TGGGCACGCCACTCAAAT 59.885 55.556 10.83 0.00 37.98 2.32
3194 3354 2.902423 AAGTGGGCACGCCACTCAAA 62.902 55.000 12.82 0.00 46.24 2.69
3195 3355 3.414136 AAGTGGGCACGCCACTCAA 62.414 57.895 12.82 0.00 46.24 3.02
3196 3356 3.872603 AAGTGGGCACGCCACTCA 61.873 61.111 12.82 0.00 46.24 3.41
3197 3357 3.357079 CAAGTGGGCACGCCACTC 61.357 66.667 12.82 0.86 46.24 3.51
3199 3359 0.958382 TATTCAAGTGGGCACGCCAC 60.958 55.000 10.83 0.00 37.98 5.01
3200 3360 0.958382 GTATTCAAGTGGGCACGCCA 60.958 55.000 10.83 0.00 37.98 5.69
3201 3361 0.676782 AGTATTCAAGTGGGCACGCC 60.677 55.000 0.00 0.00 36.20 5.68
3202 3362 2.018542 TAGTATTCAAGTGGGCACGC 57.981 50.000 0.00 0.00 36.20 5.34
3203 3363 3.374058 CCTTTAGTATTCAAGTGGGCACG 59.626 47.826 0.00 0.00 36.20 5.34
3204 3364 4.585879 TCCTTTAGTATTCAAGTGGGCAC 58.414 43.478 0.00 0.00 0.00 5.01
3205 3365 4.919774 TCCTTTAGTATTCAAGTGGGCA 57.080 40.909 0.00 0.00 0.00 5.36
3206 3366 6.017026 GCTAATCCTTTAGTATTCAAGTGGGC 60.017 42.308 0.00 0.00 37.68 5.36
3207 3367 7.054124 TGCTAATCCTTTAGTATTCAAGTGGG 58.946 38.462 0.00 0.00 37.68 4.61
3208 3368 8.506168 TTGCTAATCCTTTAGTATTCAAGTGG 57.494 34.615 0.00 0.00 37.68 4.00
3209 3369 9.994432 CTTTGCTAATCCTTTAGTATTCAAGTG 57.006 33.333 0.00 0.00 37.68 3.16
3210 3370 9.178758 CCTTTGCTAATCCTTTAGTATTCAAGT 57.821 33.333 0.00 0.00 37.68 3.16
3211 3371 9.396022 TCCTTTGCTAATCCTTTAGTATTCAAG 57.604 33.333 0.00 0.00 37.68 3.02
3212 3372 9.396022 CTCCTTTGCTAATCCTTTAGTATTCAA 57.604 33.333 0.00 0.00 37.68 2.69
3213 3373 8.548877 ACTCCTTTGCTAATCCTTTAGTATTCA 58.451 33.333 0.00 0.00 37.68 2.57
3214 3374 8.831550 CACTCCTTTGCTAATCCTTTAGTATTC 58.168 37.037 0.00 0.00 37.68 1.75
3215 3375 7.283354 GCACTCCTTTGCTAATCCTTTAGTATT 59.717 37.037 0.00 0.00 39.59 1.89
3216 3376 6.768381 GCACTCCTTTGCTAATCCTTTAGTAT 59.232 38.462 0.00 0.00 39.59 2.12
3217 3377 6.113411 GCACTCCTTTGCTAATCCTTTAGTA 58.887 40.000 0.00 0.00 39.59 1.82
3218 3378 4.944317 GCACTCCTTTGCTAATCCTTTAGT 59.056 41.667 0.00 0.00 39.59 2.24
3219 3379 5.491635 GCACTCCTTTGCTAATCCTTTAG 57.508 43.478 0.00 0.00 39.59 1.85
3230 3390 3.413522 GCATCAAGCACTCCTTTGC 57.586 52.632 0.00 0.00 44.79 3.68
3240 3400 2.294233 TGTTTCTCTTGTGGCATCAAGC 59.706 45.455 18.78 9.55 42.90 4.01
3241 3401 4.572985 TTGTTTCTCTTGTGGCATCAAG 57.427 40.909 17.98 17.98 44.08 3.02
3242 3402 4.644234 TCTTTGTTTCTCTTGTGGCATCAA 59.356 37.500 0.00 0.00 0.00 2.57
3243 3403 4.206375 TCTTTGTTTCTCTTGTGGCATCA 58.794 39.130 0.00 0.00 0.00 3.07
3244 3404 4.836125 TCTTTGTTTCTCTTGTGGCATC 57.164 40.909 0.00 0.00 0.00 3.91
3245 3405 5.596836 TTTCTTTGTTTCTCTTGTGGCAT 57.403 34.783 0.00 0.00 0.00 4.40
3246 3406 5.596836 ATTTCTTTGTTTCTCTTGTGGCA 57.403 34.783 0.00 0.00 0.00 4.92
3247 3407 5.812127 ACAATTTCTTTGTTTCTCTTGTGGC 59.188 36.000 0.00 0.00 46.51 5.01
3248 3408 8.925161 TTACAATTTCTTTGTTTCTCTTGTGG 57.075 30.769 0.00 0.00 46.51 4.17
3253 3413 9.190317 ACCTCTTTACAATTTCTTTGTTTCTCT 57.810 29.630 0.00 0.00 46.51 3.10
3254 3414 9.803315 AACCTCTTTACAATTTCTTTGTTTCTC 57.197 29.630 0.00 0.00 46.51 2.87
3255 3415 9.586435 CAACCTCTTTACAATTTCTTTGTTTCT 57.414 29.630 0.00 0.00 46.51 2.52
3256 3416 9.581099 TCAACCTCTTTACAATTTCTTTGTTTC 57.419 29.630 0.00 0.00 46.51 2.78
3257 3417 9.936759 TTCAACCTCTTTACAATTTCTTTGTTT 57.063 25.926 0.00 0.00 46.51 2.83
3258 3418 9.586435 CTTCAACCTCTTTACAATTTCTTTGTT 57.414 29.630 0.00 0.00 46.51 2.83
3262 3422 9.847224 TCTACTTCAACCTCTTTACAATTTCTT 57.153 29.630 0.00 0.00 0.00 2.52
3265 3425 9.574516 ACATCTACTTCAACCTCTTTACAATTT 57.425 29.630 0.00 0.00 0.00 1.82
3266 3426 9.574516 AACATCTACTTCAACCTCTTTACAATT 57.425 29.630 0.00 0.00 0.00 2.32
3268 3428 9.706691 CTAACATCTACTTCAACCTCTTTACAA 57.293 33.333 0.00 0.00 0.00 2.41
3269 3429 9.085645 TCTAACATCTACTTCAACCTCTTTACA 57.914 33.333 0.00 0.00 0.00 2.41
3274 3434 9.660180 GAAAATCTAACATCTACTTCAACCTCT 57.340 33.333 0.00 0.00 0.00 3.69
3275 3435 9.660180 AGAAAATCTAACATCTACTTCAACCTC 57.340 33.333 0.00 0.00 0.00 3.85
3345 3505 9.354673 TGGTTCTTTGATTTATAGGATTGGATC 57.645 33.333 0.00 0.00 0.00 3.36
3346 3506 9.713684 TTGGTTCTTTGATTTATAGGATTGGAT 57.286 29.630 0.00 0.00 0.00 3.41
3347 3507 8.966868 GTTGGTTCTTTGATTTATAGGATTGGA 58.033 33.333 0.00 0.00 0.00 3.53
3348 3508 7.915397 CGTTGGTTCTTTGATTTATAGGATTGG 59.085 37.037 0.00 0.00 0.00 3.16
3349 3509 8.458843 ACGTTGGTTCTTTGATTTATAGGATTG 58.541 33.333 0.00 0.00 0.00 2.67
3350 3510 8.575649 ACGTTGGTTCTTTGATTTATAGGATT 57.424 30.769 0.00 0.00 0.00 3.01
3351 3511 9.326413 CTACGTTGGTTCTTTGATTTATAGGAT 57.674 33.333 0.00 0.00 0.00 3.24
3352 3512 7.767198 CCTACGTTGGTTCTTTGATTTATAGGA 59.233 37.037 7.97 0.00 0.00 2.94
3353 3513 7.767198 TCCTACGTTGGTTCTTTGATTTATAGG 59.233 37.037 15.74 0.00 0.00 2.57
3354 3514 8.712285 TCCTACGTTGGTTCTTTGATTTATAG 57.288 34.615 15.74 0.00 0.00 1.31
3355 3515 9.504708 TTTCCTACGTTGGTTCTTTGATTTATA 57.495 29.630 15.74 0.00 0.00 0.98
3356 3516 7.989416 TTCCTACGTTGGTTCTTTGATTTAT 57.011 32.000 15.74 0.00 0.00 1.40
3357 3517 7.804843 TTTCCTACGTTGGTTCTTTGATTTA 57.195 32.000 15.74 0.00 0.00 1.40
3358 3518 6.702716 TTTCCTACGTTGGTTCTTTGATTT 57.297 33.333 15.74 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.