Multiple sequence alignment - TraesCS2D01G252200

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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 TraesCS2D01G252200 chr2D 100.000 4912 0 0 1 4912 302428622 302423711 0.000000e+00 9071.0
1 TraesCS2D01G252200 chr2B 94.943 2096 70 17 1008 3072 358050052 358047962 0.000000e+00 3251.0
2 TraesCS2D01G252200 chr2B 86.750 1766 97 49 3228 4912 358047970 358046261 0.000000e+00 1838.0
3 TraesCS2D01G252200 chr2B 97.619 168 3 1 3072 3238 244915613 244915780 2.240000e-73 287.0
4 TraesCS2D01G252200 chr2A 94.243 1928 80 18 1009 2918 379736607 379734693 0.000000e+00 2916.0
5 TraesCS2D01G252200 chr2A 89.518 1660 112 28 3268 4912 379734591 379732979 0.000000e+00 2045.0
6 TraesCS2D01G252200 chr2A 96.584 849 26 2 1 849 773301639 773302484 0.000000e+00 1404.0
7 TraesCS2D01G252200 chr2A 86.088 611 76 5 396 999 540767303 540766695 0.000000e+00 649.0
8 TraesCS2D01G252200 chr7A 96.016 1004 35 3 1 999 603297784 603296781 0.000000e+00 1628.0
9 TraesCS2D01G252200 chr7A 97.531 162 4 0 3065 3226 206943659 206943498 1.350000e-70 278.0
10 TraesCS2D01G252200 chr7A 92.593 54 4 0 3078 3131 474291093 474291040 1.470000e-10 78.7
11 TraesCS2D01G252200 chr7D 93.320 1003 60 5 1 998 184209440 184208440 0.000000e+00 1474.0
12 TraesCS2D01G252200 chr7D 96.622 148 4 1 3069 3215 264930966 264931113 1.370000e-60 244.0
13 TraesCS2D01G252200 chr7D 90.000 120 11 1 2914 3033 561921838 561921956 2.370000e-33 154.0
14 TraesCS2D01G252200 chr1A 84.756 984 143 7 1 981 169730136 169729157 0.000000e+00 979.0
15 TraesCS2D01G252200 chr1A 86.022 651 88 2 1 651 496006138 496006785 0.000000e+00 695.0
16 TraesCS2D01G252200 chr1A 89.254 335 36 0 645 979 496042279 496042613 2.110000e-113 420.0
17 TraesCS2D01G252200 chr1A 95.506 178 4 4 3072 3245 249045048 249045225 1.040000e-71 281.0
18 TraesCS2D01G252200 chr1A 89.256 121 11 2 2914 3032 463825451 463825331 3.060000e-32 150.0
19 TraesCS2D01G252200 chr1A 92.857 42 2 1 4020 4061 585692164 585692204 5.310000e-05 60.2
20 TraesCS2D01G252200 chrUn 83.682 1005 157 3 1 999 301348301 301349304 0.000000e+00 941.0
21 TraesCS2D01G252200 chrUn 82.615 650 113 0 1 650 402580845 402581494 4.260000e-160 575.0
22 TraesCS2D01G252200 chrUn 85.593 354 44 3 652 999 462853376 462853728 1.000000e-96 364.0
23 TraesCS2D01G252200 chr7B 98.765 162 2 0 3072 3233 134048609 134048448 6.220000e-74 289.0
24 TraesCS2D01G252200 chr7B 96.045 177 4 3 3072 3245 156950893 156951069 8.050000e-73 285.0
25 TraesCS2D01G252200 chr7B 98.693 153 2 0 3071 3223 711065878 711066030 6.270000e-69 272.0
26 TraesCS2D01G252200 chr4A 98.765 162 2 0 3072 3233 564649512 564649673 6.220000e-74 289.0
27 TraesCS2D01G252200 chr3B 98.765 162 2 0 3072 3233 689002703 689002864 6.220000e-74 289.0
28 TraesCS2D01G252200 chr6B 96.089 179 1 5 3072 3249 358303043 358303216 2.240000e-73 287.0
29 TraesCS2D01G252200 chr6B 98.734 158 2 0 3071 3228 308565617 308565774 1.040000e-71 281.0
30 TraesCS2D01G252200 chr6B 85.606 132 17 1 2914 3045 690558348 690558219 2.380000e-28 137.0
31 TraesCS2D01G252200 chr5B 97.059 170 3 1 3072 3241 609876003 609875836 8.050000e-73 285.0
32 TraesCS2D01G252200 chr5B 87.402 127 14 2 2907 3032 590183637 590183762 1.430000e-30 145.0
33 TraesCS2D01G252200 chr5A 97.059 170 2 2 3072 3241 439420920 439421086 2.890000e-72 283.0
34 TraesCS2D01G252200 chr5A 90.323 155 9 2 3074 3228 409327621 409327473 1.080000e-46 198.0
35 TraesCS2D01G252200 chr5D 97.436 156 3 1 3070 3225 61705207 61705053 1.050000e-66 265.0
36 TraesCS2D01G252200 chr5D 87.342 158 6 3 3071 3228 397028838 397028981 8.460000e-38 169.0
37 TraesCS2D01G252200 chr5D 88.333 120 14 0 2913 3032 421164945 421165064 1.430000e-30 145.0
38 TraesCS2D01G252200 chr3D 96.250 160 5 1 3069 3227 435586613 435586772 1.360000e-65 261.0
39 TraesCS2D01G252200 chr3D 86.822 129 15 2 2909 3037 28747759 28747633 5.130000e-30 143.0
40 TraesCS2D01G252200 chr4D 88.060 134 15 1 2903 3035 109274959 109275092 1.830000e-34 158.0
41 TraesCS2D01G252200 chr1D 87.402 127 14 2 2906 3032 406839698 406839822 1.430000e-30 145.0


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 TraesCS2D01G252200 chr2D 302423711 302428622 4911 True 9071.0 9071 100.0000 1 4912 1 chr2D.!!$R1 4911
1 TraesCS2D01G252200 chr2B 358046261 358050052 3791 True 2544.5 3251 90.8465 1008 4912 2 chr2B.!!$R1 3904
2 TraesCS2D01G252200 chr2A 379732979 379736607 3628 True 2480.5 2916 91.8805 1009 4912 2 chr2A.!!$R2 3903
3 TraesCS2D01G252200 chr2A 773301639 773302484 845 False 1404.0 1404 96.5840 1 849 1 chr2A.!!$F1 848
4 TraesCS2D01G252200 chr2A 540766695 540767303 608 True 649.0 649 86.0880 396 999 1 chr2A.!!$R1 603
5 TraesCS2D01G252200 chr7A 603296781 603297784 1003 True 1628.0 1628 96.0160 1 999 1 chr7A.!!$R3 998
6 TraesCS2D01G252200 chr7D 184208440 184209440 1000 True 1474.0 1474 93.3200 1 998 1 chr7D.!!$R1 997
7 TraesCS2D01G252200 chr1A 169729157 169730136 979 True 979.0 979 84.7560 1 981 1 chr1A.!!$R1 980
8 TraesCS2D01G252200 chr1A 496006138 496006785 647 False 695.0 695 86.0220 1 651 1 chr1A.!!$F2 650
9 TraesCS2D01G252200 chrUn 301348301 301349304 1003 False 941.0 941 83.6820 1 999 1 chrUn.!!$F1 998
10 TraesCS2D01G252200 chrUn 402580845 402581494 649 False 575.0 575 82.6150 1 650 1 chrUn.!!$F2 649

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
319 320 0.524862 CTTGATGTGAAGCAGGTGCC 59.475 55.000 0.00 0.0 43.38 5.01 F
1060 1072 1.890510 GTTCAGTTTCCCGCCGTGT 60.891 57.895 0.00 0.0 0.00 4.49 F
1966 1993 0.534203 GTCAGCTGAAACGGTTGGGA 60.534 55.000 20.19 0.0 0.00 4.37 F
3076 3131 0.038892 CTGGGCATAATGATTGGCGC 60.039 55.000 0.00 0.0 40.34 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1349 1.377987 GCATTACCTCGGCCACCAA 60.378 57.895 2.24 0.0 0.00 3.67 R
2922 2977 2.419667 ACGACAAGTAATTTGGGACGG 58.580 47.619 0.00 0.0 41.25 4.79 R
3125 3180 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.0 40.08 4.58 R
4197 4307 0.373716 GCTCATGAAACTTACGCGGG 59.626 55.000 12.47 0.0 0.00 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
107 108 4.530161 AGACATGTAGGCTCTAATGGATCC 59.470 45.833 4.20 4.20 0.00 3.36
319 320 0.524862 CTTGATGTGAAGCAGGTGCC 59.475 55.000 0.00 0.00 43.38 5.01
612 614 4.058124 TGCACAATGTCGCTATATTCCTC 58.942 43.478 8.69 0.00 0.00 3.71
1059 1071 2.613506 GGTTCAGTTTCCCGCCGTG 61.614 63.158 0.00 0.00 0.00 4.94
1060 1072 1.890510 GTTCAGTTTCCCGCCGTGT 60.891 57.895 0.00 0.00 0.00 4.49
1331 1349 0.689623 CCTGCAGGAGAAGGACAAGT 59.310 55.000 29.88 0.00 44.27 3.16
1345 1363 1.373435 CAAGTTGGTGGCCGAGGTA 59.627 57.895 0.00 0.00 0.00 3.08
1666 1684 5.974108 TGATGTAGTAAGGTAGAAAGTGGC 58.026 41.667 0.00 0.00 0.00 5.01
1774 1801 4.308899 ACAGCAAGTATGTCGAGGATAC 57.691 45.455 6.46 6.46 0.00 2.24
1857 1884 2.484594 GGCAAGATCTCTGAAGGTAGGC 60.485 54.545 0.00 0.00 0.00 3.93
1966 1993 0.534203 GTCAGCTGAAACGGTTGGGA 60.534 55.000 20.19 0.00 0.00 4.37
2265 2293 5.534278 TGTAAAAGCATCAACCACAATCTCA 59.466 36.000 0.00 0.00 0.00 3.27
2281 2309 6.690098 CACAATCTCAGAAAAATAAGGCATCG 59.310 38.462 0.00 0.00 0.00 3.84
2283 2311 7.284034 ACAATCTCAGAAAAATAAGGCATCGAT 59.716 33.333 0.00 0.00 0.00 3.59
2457 2509 3.944650 TCCATAACGTGCAGCATTAACAT 59.055 39.130 0.00 0.00 0.00 2.71
2546 2598 0.821517 ATCGGTTGATGGACGTAGCA 59.178 50.000 0.00 0.00 32.21 3.49
2554 2606 4.209307 TGATGGACGTAGCATTGGTAAA 57.791 40.909 0.00 0.00 0.00 2.01
2640 2694 1.549170 AGCTGGTTCCTAGTTGTACCG 59.451 52.381 0.00 0.00 33.29 4.02
2752 2807 4.803329 AAGAGCCAACCCATCTTATCAT 57.197 40.909 0.00 0.00 31.63 2.45
2758 2813 5.103940 AGCCAACCCATCTTATCATGTACTT 60.104 40.000 0.00 0.00 0.00 2.24
2846 2901 0.801251 GAGTTGCTTGCTACTGCTGG 59.199 55.000 13.71 0.00 40.48 4.85
2866 2921 5.221342 GCTGGTGCTACTAGTTCATGACTAT 60.221 44.000 0.00 0.00 36.92 2.12
2939 2994 2.290705 CCCTCCGTCCCAAATTACTTGT 60.291 50.000 0.00 0.00 32.65 3.16
2940 2995 3.007635 CCTCCGTCCCAAATTACTTGTC 58.992 50.000 0.00 0.00 32.65 3.18
2941 2996 2.671396 CTCCGTCCCAAATTACTTGTCG 59.329 50.000 0.00 0.00 32.65 4.35
2951 3006 6.373216 CCCAAATTACTTGTCGTAGAAATGGA 59.627 38.462 0.00 0.00 39.69 3.41
3008 3063 7.043961 TCTAGATACATTCATTTCTGCGACT 57.956 36.000 0.00 0.00 0.00 4.18
3022 3077 5.353394 TCTGCGACTAGTAATTTGGGATT 57.647 39.130 0.00 0.00 0.00 3.01
3025 3080 5.116180 TGCGACTAGTAATTTGGGATTGAG 58.884 41.667 0.00 0.00 0.00 3.02
3066 3121 2.818921 AGTGGCAATTTCTGGGCATAA 58.181 42.857 0.00 0.00 41.83 1.90
3067 3122 3.377573 AGTGGCAATTTCTGGGCATAAT 58.622 40.909 0.00 0.00 41.83 1.28
3068 3123 3.133362 AGTGGCAATTTCTGGGCATAATG 59.867 43.478 0.00 0.00 41.83 1.90
3069 3124 3.132646 GTGGCAATTTCTGGGCATAATGA 59.867 43.478 0.00 0.00 41.83 2.57
3070 3125 3.968649 TGGCAATTTCTGGGCATAATGAT 59.031 39.130 0.00 0.00 34.37 2.45
3071 3126 4.409574 TGGCAATTTCTGGGCATAATGATT 59.590 37.500 0.00 0.00 34.37 2.57
3072 3127 4.753107 GGCAATTTCTGGGCATAATGATTG 59.247 41.667 0.00 0.00 0.00 2.67
3073 3128 4.753107 GCAATTTCTGGGCATAATGATTGG 59.247 41.667 0.00 0.00 0.00 3.16
3074 3129 4.612264 ATTTCTGGGCATAATGATTGGC 57.388 40.909 0.00 0.00 38.82 4.52
3075 3130 1.608055 TCTGGGCATAATGATTGGCG 58.392 50.000 0.00 0.00 40.34 5.69
3076 3131 0.038892 CTGGGCATAATGATTGGCGC 60.039 55.000 0.00 0.00 40.34 6.53
3077 3132 0.754587 TGGGCATAATGATTGGCGCA 60.755 50.000 10.83 15.58 45.21 6.09
3078 3133 0.038892 GGGCATAATGATTGGCGCAG 60.039 55.000 10.83 0.00 40.34 5.18
3079 3134 0.670162 GGCATAATGATTGGCGCAGT 59.330 50.000 10.83 0.00 0.00 4.40
3080 3135 1.601162 GGCATAATGATTGGCGCAGTG 60.601 52.381 10.83 0.00 0.00 3.66
3081 3136 1.601162 GCATAATGATTGGCGCAGTGG 60.601 52.381 10.83 0.00 0.00 4.00
3082 3137 1.677576 CATAATGATTGGCGCAGTGGT 59.322 47.619 10.83 0.00 0.00 4.16
3083 3138 1.093972 TAATGATTGGCGCAGTGGTG 58.906 50.000 10.83 0.00 0.00 4.17
3084 3139 0.608856 AATGATTGGCGCAGTGGTGA 60.609 50.000 10.83 0.00 0.00 4.02
3085 3140 0.608856 ATGATTGGCGCAGTGGTGAA 60.609 50.000 10.83 0.00 0.00 3.18
3086 3141 1.236616 TGATTGGCGCAGTGGTGAAG 61.237 55.000 10.83 0.00 0.00 3.02
3087 3142 1.228245 ATTGGCGCAGTGGTGAAGT 60.228 52.632 10.83 0.00 0.00 3.01
3088 3143 0.823356 ATTGGCGCAGTGGTGAAGTT 60.823 50.000 10.83 0.00 0.00 2.66
3089 3144 1.444119 TTGGCGCAGTGGTGAAGTTC 61.444 55.000 10.83 0.00 0.00 3.01
3090 3145 1.598130 GGCGCAGTGGTGAAGTTCT 60.598 57.895 10.83 0.00 0.00 3.01
3091 3146 1.569479 GGCGCAGTGGTGAAGTTCTC 61.569 60.000 10.83 0.00 0.00 2.87
3092 3147 1.569479 GCGCAGTGGTGAAGTTCTCC 61.569 60.000 15.67 15.67 0.00 3.71
3093 3148 0.951040 CGCAGTGGTGAAGTTCTCCC 60.951 60.000 18.90 12.09 0.00 4.30
3094 3149 0.606673 GCAGTGGTGAAGTTCTCCCC 60.607 60.000 18.90 9.54 0.00 4.81
3095 3150 0.764890 CAGTGGTGAAGTTCTCCCCA 59.235 55.000 18.90 12.08 0.00 4.96
3096 3151 0.765510 AGTGGTGAAGTTCTCCCCAC 59.234 55.000 22.08 22.08 44.69 4.61
3097 3152 0.765510 GTGGTGAAGTTCTCCCCACT 59.234 55.000 22.20 0.00 41.83 4.00
3098 3153 1.143073 GTGGTGAAGTTCTCCCCACTT 59.857 52.381 22.20 0.00 41.83 3.16
3099 3154 1.142870 TGGTGAAGTTCTCCCCACTTG 59.857 52.381 18.90 0.00 34.49 3.16
3100 3155 1.143073 GGTGAAGTTCTCCCCACTTGT 59.857 52.381 12.17 0.00 34.49 3.16
3101 3156 2.222027 GTGAAGTTCTCCCCACTTGTG 58.778 52.381 4.17 0.00 34.49 3.33
3102 3157 1.239347 GAAGTTCTCCCCACTTGTGC 58.761 55.000 0.00 0.00 34.49 4.57
3103 3158 0.178990 AAGTTCTCCCCACTTGTGCC 60.179 55.000 0.00 0.00 33.04 5.01
3104 3159 1.150536 GTTCTCCCCACTTGTGCCA 59.849 57.895 0.00 0.00 0.00 4.92
3105 3160 0.467290 GTTCTCCCCACTTGTGCCAA 60.467 55.000 0.00 0.00 0.00 4.52
3106 3161 0.178992 TTCTCCCCACTTGTGCCAAG 60.179 55.000 11.87 11.87 0.00 3.61
3107 3162 1.059584 TCTCCCCACTTGTGCCAAGA 61.060 55.000 18.22 0.00 0.00 3.02
3108 3163 0.607489 CTCCCCACTTGTGCCAAGAG 60.607 60.000 18.22 11.85 0.00 2.85
3109 3164 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
3110 3165 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
3111 3166 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
3112 3167 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
3113 3168 0.109342 CACTTGTGCCAAGAGGTCCT 59.891 55.000 18.22 0.00 37.19 3.85
3114 3169 0.109342 ACTTGTGCCAAGAGGTCCTG 59.891 55.000 18.22 0.00 37.19 3.86
3115 3170 0.607489 CTTGTGCCAAGAGGTCCTGG 60.607 60.000 0.00 0.00 37.19 4.45
3116 3171 2.067932 TTGTGCCAAGAGGTCCTGGG 62.068 60.000 0.00 0.00 39.14 4.45
3117 3172 2.121963 TGCCAAGAGGTCCTGGGT 60.122 61.111 0.00 0.00 38.32 4.51
3118 3173 1.774217 TGCCAAGAGGTCCTGGGTT 60.774 57.895 0.00 0.00 38.32 4.11
3119 3174 1.002011 GCCAAGAGGTCCTGGGTTC 60.002 63.158 0.00 0.00 38.32 3.62
3120 3175 1.296715 CCAAGAGGTCCTGGGTTCG 59.703 63.158 0.00 0.00 30.82 3.95
3121 3176 1.192146 CCAAGAGGTCCTGGGTTCGA 61.192 60.000 0.00 0.00 30.82 3.71
3122 3177 0.685097 CAAGAGGTCCTGGGTTCGAA 59.315 55.000 0.00 0.00 0.00 3.71
3123 3178 0.685660 AAGAGGTCCTGGGTTCGAAC 59.314 55.000 20.14 20.14 0.00 3.95
3134 3189 3.129792 GTTCGAACCAGCCTCTCTG 57.870 57.895 17.68 0.00 42.49 3.35
3135 3190 1.016653 GTTCGAACCAGCCTCTCTGC 61.017 60.000 17.68 0.00 41.50 4.26
3136 3191 1.471829 TTCGAACCAGCCTCTCTGCA 61.472 55.000 0.00 0.00 41.50 4.41
3137 3192 1.220206 CGAACCAGCCTCTCTGCAT 59.780 57.895 0.00 0.00 41.50 3.96
3138 3193 0.392193 CGAACCAGCCTCTCTGCATT 60.392 55.000 0.00 0.00 41.50 3.56
3139 3194 1.093159 GAACCAGCCTCTCTGCATTG 58.907 55.000 0.00 0.00 41.50 2.82
3140 3195 0.964358 AACCAGCCTCTCTGCATTGC 60.964 55.000 0.46 0.46 41.50 3.56
3141 3196 1.378119 CCAGCCTCTCTGCATTGCA 60.378 57.895 11.50 11.50 41.50 4.08
3142 3197 1.654954 CCAGCCTCTCTGCATTGCAC 61.655 60.000 7.38 0.00 41.50 4.57
3143 3198 0.677098 CAGCCTCTCTGCATTGCACT 60.677 55.000 7.38 0.00 35.78 4.40
3144 3199 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.000 7.38 0.00 33.79 3.16
3145 3200 0.886563 GCCTCTCTGCATTGCACTTT 59.113 50.000 7.38 0.00 33.79 2.66
3146 3201 1.402456 GCCTCTCTGCATTGCACTTTG 60.402 52.381 7.38 0.00 33.79 2.77
3147 3202 1.402456 CCTCTCTGCATTGCACTTTGC 60.402 52.381 7.38 8.20 45.29 3.68
3157 3212 3.339547 GCACTTTGCAGGGGTAAGA 57.660 52.632 2.16 0.00 44.26 2.10
3158 3213 0.881796 GCACTTTGCAGGGGTAAGAC 59.118 55.000 2.16 0.00 44.26 3.01
3159 3214 1.545651 GCACTTTGCAGGGGTAAGACT 60.546 52.381 2.16 0.00 44.26 3.24
3160 3215 2.290071 GCACTTTGCAGGGGTAAGACTA 60.290 50.000 2.16 0.00 44.26 2.59
3161 3216 3.600388 CACTTTGCAGGGGTAAGACTAG 58.400 50.000 2.16 0.00 0.00 2.57
3162 3217 2.572104 ACTTTGCAGGGGTAAGACTAGG 59.428 50.000 2.16 0.00 0.00 3.02
3163 3218 2.337359 TTGCAGGGGTAAGACTAGGT 57.663 50.000 0.00 0.00 0.00 3.08
3164 3219 2.337359 TGCAGGGGTAAGACTAGGTT 57.663 50.000 0.00 0.00 0.00 3.50
3165 3220 2.185387 TGCAGGGGTAAGACTAGGTTC 58.815 52.381 0.00 0.00 0.00 3.62
3166 3221 1.485480 GCAGGGGTAAGACTAGGTTCC 59.515 57.143 0.00 0.00 0.00 3.62
3167 3222 2.893153 GCAGGGGTAAGACTAGGTTCCT 60.893 54.545 0.00 0.00 0.00 3.36
3168 3223 3.629282 GCAGGGGTAAGACTAGGTTCCTA 60.629 52.174 0.00 0.00 0.00 2.94
3169 3224 4.817286 CAGGGGTAAGACTAGGTTCCTAT 58.183 47.826 0.00 0.00 0.00 2.57
3170 3225 5.694949 GCAGGGGTAAGACTAGGTTCCTATA 60.695 48.000 0.00 0.00 0.00 1.31
3171 3226 6.379579 CAGGGGTAAGACTAGGTTCCTATAA 58.620 44.000 0.00 0.00 0.00 0.98
3172 3227 7.017531 CAGGGGTAAGACTAGGTTCCTATAAT 58.982 42.308 0.00 0.00 0.00 1.28
3173 3228 7.178805 CAGGGGTAAGACTAGGTTCCTATAATC 59.821 44.444 0.00 0.00 0.00 1.75
3174 3229 6.440010 GGGGTAAGACTAGGTTCCTATAATCC 59.560 46.154 0.00 0.00 0.00 3.01
3175 3230 6.440010 GGGTAAGACTAGGTTCCTATAATCCC 59.560 46.154 0.00 4.36 0.00 3.85
3176 3231 7.247500 GGTAAGACTAGGTTCCTATAATCCCT 58.753 42.308 0.00 0.00 0.00 4.20
3177 3232 7.396907 GGTAAGACTAGGTTCCTATAATCCCTC 59.603 44.444 0.00 0.00 0.00 4.30
3178 3233 5.906254 AGACTAGGTTCCTATAATCCCTCC 58.094 45.833 0.00 0.00 0.00 4.30
3179 3234 5.024785 GACTAGGTTCCTATAATCCCTCCC 58.975 50.000 0.00 0.00 0.00 4.30
3180 3235 3.293215 AGGTTCCTATAATCCCTCCCC 57.707 52.381 0.00 0.00 0.00 4.81
3181 3236 2.531463 AGGTTCCTATAATCCCTCCCCA 59.469 50.000 0.00 0.00 0.00 4.96
3182 3237 2.913617 GGTTCCTATAATCCCTCCCCAG 59.086 54.545 0.00 0.00 0.00 4.45
3183 3238 3.441054 GGTTCCTATAATCCCTCCCCAGA 60.441 52.174 0.00 0.00 0.00 3.86
3184 3239 3.562108 TCCTATAATCCCTCCCCAGAC 57.438 52.381 0.00 0.00 0.00 3.51
3185 3240 2.113777 TCCTATAATCCCTCCCCAGACC 59.886 54.545 0.00 0.00 0.00 3.85
3186 3241 2.552367 CTATAATCCCTCCCCAGACCC 58.448 57.143 0.00 0.00 0.00 4.46
3187 3242 0.103876 ATAATCCCTCCCCAGACCCC 60.104 60.000 0.00 0.00 0.00 4.95
3188 3243 1.542093 TAATCCCTCCCCAGACCCCA 61.542 60.000 0.00 0.00 0.00 4.96
3189 3244 3.660092 ATCCCTCCCCAGACCCCAC 62.660 68.421 0.00 0.00 0.00 4.61
3191 3246 4.354943 CCTCCCCAGACCCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
3192 3247 2.204151 CTCCCCAGACCCCACCTT 60.204 66.667 0.00 0.00 0.00 3.50
3193 3248 2.531685 TCCCCAGACCCCACCTTG 60.532 66.667 0.00 0.00 0.00 3.61
3194 3249 2.858974 CCCCAGACCCCACCTTGT 60.859 66.667 0.00 0.00 0.00 3.16
3195 3250 2.436109 CCCAGACCCCACCTTGTG 59.564 66.667 0.00 0.00 0.00 3.33
3196 3251 2.460853 CCCAGACCCCACCTTGTGT 61.461 63.158 0.00 0.00 0.00 3.72
3197 3252 1.228245 CCAGACCCCACCTTGTGTG 60.228 63.158 0.00 0.00 45.01 3.82
3204 3259 4.907457 CACCTTGTGTGGGAGCTT 57.093 55.556 0.00 0.00 41.52 3.74
3205 3260 2.633860 CACCTTGTGTGGGAGCTTC 58.366 57.895 0.00 0.00 41.52 3.86
3206 3261 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.000 0.00 0.00 41.52 2.85
3207 3262 1.347707 CACCTTGTGTGGGAGCTTCTA 59.652 52.381 0.00 0.00 41.52 2.10
3208 3263 2.026822 CACCTTGTGTGGGAGCTTCTAT 60.027 50.000 0.00 0.00 41.52 1.98
3209 3264 2.026822 ACCTTGTGTGGGAGCTTCTATG 60.027 50.000 0.00 0.00 0.00 2.23
3210 3265 2.012673 CTTGTGTGGGAGCTTCTATGC 58.987 52.381 0.00 0.00 0.00 3.14
3211 3266 0.983467 TGTGTGGGAGCTTCTATGCA 59.017 50.000 0.00 0.00 34.99 3.96
3212 3267 1.339055 TGTGTGGGAGCTTCTATGCAC 60.339 52.381 0.00 0.00 34.99 4.57
3213 3268 1.065854 GTGTGGGAGCTTCTATGCACT 60.066 52.381 0.00 0.00 34.99 4.40
3214 3269 1.065926 TGTGGGAGCTTCTATGCACTG 60.066 52.381 0.00 0.00 34.99 3.66
3215 3270 0.543277 TGGGAGCTTCTATGCACTGG 59.457 55.000 0.00 0.00 34.99 4.00
3216 3271 0.179034 GGGAGCTTCTATGCACTGGG 60.179 60.000 0.00 0.00 34.99 4.45
3217 3272 0.543749 GGAGCTTCTATGCACTGGGT 59.456 55.000 0.00 0.00 34.99 4.51
3218 3273 1.474143 GGAGCTTCTATGCACTGGGTC 60.474 57.143 0.00 0.00 34.99 4.46
3219 3274 1.484240 GAGCTTCTATGCACTGGGTCT 59.516 52.381 0.00 0.00 34.99 3.85
3220 3275 1.209019 AGCTTCTATGCACTGGGTCTG 59.791 52.381 0.00 0.00 34.99 3.51
3221 3276 1.065854 GCTTCTATGCACTGGGTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
3222 3277 2.898705 CTTCTATGCACTGGGTCTGTC 58.101 52.381 0.00 0.00 0.00 3.51
3223 3278 1.195115 TCTATGCACTGGGTCTGTCC 58.805 55.000 0.00 0.00 0.00 4.02
3224 3279 1.198713 CTATGCACTGGGTCTGTCCT 58.801 55.000 0.00 0.00 36.25 3.85
3225 3280 1.556911 CTATGCACTGGGTCTGTCCTT 59.443 52.381 0.00 0.00 36.25 3.36
3226 3281 0.773644 ATGCACTGGGTCTGTCCTTT 59.226 50.000 0.00 0.00 36.25 3.11
3227 3282 0.550914 TGCACTGGGTCTGTCCTTTT 59.449 50.000 0.00 0.00 36.25 2.27
3228 3283 1.771854 TGCACTGGGTCTGTCCTTTTA 59.228 47.619 0.00 0.00 36.25 1.52
3277 3363 4.697514 GCTTGTAGAGATTATCAGTGGCA 58.302 43.478 0.00 0.00 0.00 4.92
3299 3385 2.222027 GCAAATACCCTCCTGAATCCG 58.778 52.381 0.00 0.00 0.00 4.18
3360 3446 8.737168 AACTAAATTGAAGATTGATCCGATCA 57.263 30.769 7.00 7.00 37.55 2.92
3529 3615 4.013728 TCAATTTCCATTCAGGGGTAACG 58.986 43.478 0.00 0.00 38.24 3.18
3556 3643 2.416431 CCTATGTTTCAGGCTTTGCTGC 60.416 50.000 0.00 0.00 0.00 5.25
3593 3680 2.153247 CAGTACAACGACGAACTTGAGC 59.847 50.000 0.00 0.00 0.00 4.26
3598 3685 0.109226 ACGACGAACTTGAGCTAGGC 60.109 55.000 0.00 0.00 0.00 3.93
3715 3807 0.803740 GAGACGCCTAAGACGTGACT 59.196 55.000 0.00 0.00 45.24 3.41
3716 3808 1.199558 GAGACGCCTAAGACGTGACTT 59.800 52.381 0.00 0.00 45.24 3.01
3827 3920 0.107654 AACCGGAGCTGCATAAGTCC 60.108 55.000 9.46 0.00 0.00 3.85
3828 3921 1.264749 ACCGGAGCTGCATAAGTCCA 61.265 55.000 9.46 0.00 0.00 4.02
3829 3922 0.811616 CCGGAGCTGCATAAGTCCAC 60.812 60.000 5.91 0.00 0.00 4.02
3830 3923 1.148157 CGGAGCTGCATAAGTCCACG 61.148 60.000 5.91 0.00 0.00 4.94
3919 4012 0.867746 TTGTCTGTCACGATTGCAGC 59.132 50.000 0.00 0.00 30.99 5.25
3923 4016 0.376152 CTGTCACGATTGCAGCCATC 59.624 55.000 0.00 0.00 0.00 3.51
3930 4023 1.329906 CGATTGCAGCCATCTCAACTC 59.670 52.381 5.01 0.00 0.00 3.01
3999 4097 7.671302 ACTTATAGAAGAAGAAAGCAGTGTCA 58.329 34.615 3.65 0.00 36.45 3.58
4009 4107 5.865085 AGAAAGCAGTGTCACCTTATAACA 58.135 37.500 0.00 0.00 0.00 2.41
4166 4276 1.003812 CGAACCTTCCCCAATACCACA 59.996 52.381 0.00 0.00 0.00 4.17
4196 4306 3.733709 CTGGAAGCAACAACCCTCT 57.266 52.632 0.00 0.00 0.00 3.69
4197 4307 1.528129 CTGGAAGCAACAACCCTCTC 58.472 55.000 0.00 0.00 0.00 3.20
4200 4310 0.955919 GAAGCAACAACCCTCTCCCG 60.956 60.000 0.00 0.00 0.00 5.14
4201 4311 3.056328 GCAACAACCCTCTCCCGC 61.056 66.667 0.00 0.00 0.00 6.13
4202 4312 2.742372 CAACAACCCTCTCCCGCG 60.742 66.667 0.00 0.00 0.00 6.46
4235 4347 0.752658 CACATCCATCTCCCGCTACA 59.247 55.000 0.00 0.00 0.00 2.74
4303 4417 2.816958 CGCTCTTGTGCTGCCGAT 60.817 61.111 0.00 0.00 0.00 4.18
4338 4452 0.673644 CCACCCTCGACCAACATCAC 60.674 60.000 0.00 0.00 0.00 3.06
4364 4478 1.090052 GGCCTAAGCGCACAGTAAGG 61.090 60.000 11.47 7.74 41.24 2.69
4377 4491 2.289694 ACAGTAAGGCATGTGACCTGTC 60.290 50.000 0.00 0.00 37.67 3.51
4378 4492 1.279271 AGTAAGGCATGTGACCTGTCC 59.721 52.381 0.00 0.00 37.67 4.02
4383 4497 1.514678 GCATGTGACCTGTCCGCAAA 61.515 55.000 0.00 0.00 0.00 3.68
4387 4501 2.281484 GACCTGTCCGCAAAGGCA 60.281 61.111 0.00 0.00 41.24 4.75
4416 4530 2.033194 GGAAGGAGGCAACGTTCCG 61.033 63.158 15.98 0.00 42.22 4.30
4425 4539 1.209127 CAACGTTCCGCATTGGGTC 59.791 57.895 0.00 0.00 38.76 4.46
4430 4544 3.229156 TTCCGCATTGGGTCGTCGT 62.229 57.895 0.00 0.00 38.76 4.34
4449 4563 4.016706 CCGACCAAGAAGCCCCGT 62.017 66.667 0.00 0.00 0.00 5.28
4478 4615 2.657237 CTTCGGCCTCCTTCACGT 59.343 61.111 0.00 0.00 0.00 4.49
4492 4629 0.391528 TCACGTAGATGTCCCGACGA 60.392 55.000 0.00 0.00 38.29 4.20
4503 4640 2.995574 CCGACGACCCCACCTTCT 60.996 66.667 0.00 0.00 0.00 2.85
4504 4641 2.580601 CCGACGACCCCACCTTCTT 61.581 63.158 0.00 0.00 0.00 2.52
4505 4642 1.080025 CGACGACCCCACCTTCTTC 60.080 63.158 0.00 0.00 0.00 2.87
4511 4648 2.294078 CCCCACCTTCTTCGAGGCT 61.294 63.158 0.00 0.00 40.65 4.58
4514 4651 1.294780 CACCTTCTTCGAGGCTGCT 59.705 57.895 0.00 0.00 40.65 4.24
4538 4675 3.863424 CCGATTTCTACATGTACAACGCT 59.137 43.478 0.08 0.00 0.00 5.07
4566 4703 4.083110 AGTTGTTCGATGAAATGCAGGAAG 60.083 41.667 0.00 0.00 0.00 3.46
4568 4705 2.749621 GTTCGATGAAATGCAGGAAGGT 59.250 45.455 0.00 0.00 0.00 3.50
4569 4706 3.904800 TCGATGAAATGCAGGAAGGTA 57.095 42.857 0.00 0.00 0.00 3.08
4717 4885 1.272769 GTAGACTCTTTGTCCACGCCT 59.727 52.381 0.00 0.00 46.46 5.52
4760 4928 1.374758 GAGTGAGGGGTGTTGCTCG 60.375 63.158 0.00 0.00 0.00 5.03
4871 5041 6.744112 TCATTTCAAGGATTTGCTACGTTTT 58.256 32.000 0.00 0.00 34.21 2.43
4877 5047 7.136119 TCAAGGATTTGCTACGTTTTACTTTG 58.864 34.615 0.00 0.00 34.21 2.77
4888 5058 9.494479 GCTACGTTTTACTTTGAACTTTTACTT 57.506 29.630 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 2.090400 CCTGATGGCATATCGGACAG 57.910 55.000 0.00 2.06 0.00 3.51
319 320 2.158900 AGATACCAGAATCCAACAGCCG 60.159 50.000 0.00 0.00 0.00 5.52
486 488 7.714703 ACGTTAACTTTTACAAATTTGGGCTA 58.285 30.769 21.74 3.19 0.00 3.93
612 614 1.672030 TCACCACATCCGCTGCAAG 60.672 57.895 0.00 0.00 0.00 4.01
892 896 2.490903 GGCTCGTCTGTCCAACTACTAA 59.509 50.000 0.00 0.00 0.00 2.24
1073 1085 2.349155 CGGTTTGTTTTCGTGGTAGAGC 60.349 50.000 0.00 0.00 0.00 4.09
1105 1117 0.833949 GGAGCAGAAGAACCCTAGGG 59.166 60.000 27.36 27.36 42.03 3.53
1331 1349 1.377987 GCATTACCTCGGCCACCAA 60.378 57.895 2.24 0.00 0.00 3.67
1666 1684 4.358851 CTCGAGGTCATTCTTAAGCTCAG 58.641 47.826 3.91 0.00 39.42 3.35
1857 1884 3.181467 TGTGGGAAAAAGAACCAGCAATG 60.181 43.478 0.00 0.00 34.39 2.82
1925 1952 2.549349 GCCAAAGGTCCTCTGAAACGTA 60.549 50.000 0.00 0.00 0.00 3.57
1966 1993 6.825721 GGTGGTTCTCATCAGTCTCATTTAAT 59.174 38.462 0.00 0.00 0.00 1.40
2265 2293 7.716998 ACATACAGATCGATGCCTTATTTTTCT 59.283 33.333 0.54 0.00 0.00 2.52
2392 2420 8.985315 AAACATCATTTTGAGAGGATAGCATA 57.015 30.769 0.00 0.00 0.00 3.14
2538 2590 5.519206 CCTAGTTCTTTACCAATGCTACGTC 59.481 44.000 0.00 0.00 0.00 4.34
2542 2594 5.045869 AGCACCTAGTTCTTTACCAATGCTA 60.046 40.000 0.00 0.00 37.89 3.49
2546 2598 5.186409 TCGTAGCACCTAGTTCTTTACCAAT 59.814 40.000 0.00 0.00 0.00 3.16
2554 2606 6.531923 TCAGTATATCGTAGCACCTAGTTCT 58.468 40.000 0.00 0.00 0.00 3.01
2640 2694 7.750769 AGAGTTCATAGTCTAGACGTGTTTAC 58.249 38.462 22.41 18.91 32.18 2.01
2922 2977 2.419667 ACGACAAGTAATTTGGGACGG 58.580 47.619 0.00 0.00 41.25 4.79
2983 3038 7.665690 AGTCGCAGAAATGAATGTATCTAGAT 58.334 34.615 10.73 10.73 39.69 1.98
3008 3063 6.906901 AGTACTCCCTCAATCCCAAATTACTA 59.093 38.462 0.00 0.00 0.00 1.82
3022 3077 3.371702 CCTGTGCTACTAGTACTCCCTCA 60.372 52.174 0.00 0.00 31.77 3.86
3025 3080 3.015675 ACCTGTGCTACTAGTACTCCC 57.984 52.381 0.00 0.00 31.77 4.30
3066 3121 0.608856 TTCACCACTGCGCCAATCAT 60.609 50.000 4.18 0.00 0.00 2.45
3067 3122 1.228094 TTCACCACTGCGCCAATCA 60.228 52.632 4.18 0.00 0.00 2.57
3068 3123 1.237285 ACTTCACCACTGCGCCAATC 61.237 55.000 4.18 0.00 0.00 2.67
3069 3124 0.823356 AACTTCACCACTGCGCCAAT 60.823 50.000 4.18 0.00 0.00 3.16
3070 3125 1.444119 GAACTTCACCACTGCGCCAA 61.444 55.000 4.18 0.00 0.00 4.52
3071 3126 1.891919 GAACTTCACCACTGCGCCA 60.892 57.895 4.18 0.00 0.00 5.69
3072 3127 1.569479 GAGAACTTCACCACTGCGCC 61.569 60.000 4.18 0.00 0.00 6.53
3073 3128 1.569479 GGAGAACTTCACCACTGCGC 61.569 60.000 0.00 0.00 0.00 6.09
3074 3129 0.951040 GGGAGAACTTCACCACTGCG 60.951 60.000 7.47 0.00 0.00 5.18
3075 3130 2.934083 GGGAGAACTTCACCACTGC 58.066 57.895 7.47 0.00 0.00 4.40
3081 3136 2.222027 CACAAGTGGGGAGAACTTCAC 58.778 52.381 0.00 0.00 35.70 3.18
3082 3137 1.476833 GCACAAGTGGGGAGAACTTCA 60.477 52.381 2.00 0.00 35.70 3.02
3083 3138 1.239347 GCACAAGTGGGGAGAACTTC 58.761 55.000 2.00 0.00 35.70 3.01
3084 3139 0.178990 GGCACAAGTGGGGAGAACTT 60.179 55.000 2.00 0.00 38.40 2.66
3085 3140 1.352622 TGGCACAAGTGGGGAGAACT 61.353 55.000 2.00 0.00 31.92 3.01
3086 3141 1.150536 TGGCACAAGTGGGGAGAAC 59.849 57.895 2.00 0.00 31.92 3.01
3087 3142 3.667476 TGGCACAAGTGGGGAGAA 58.333 55.556 2.00 0.00 31.92 2.87
3098 3153 2.528818 CCCAGGACCTCTTGGCACA 61.529 63.158 0.00 0.00 41.31 4.57
3099 3154 2.069165 AACCCAGGACCTCTTGGCAC 62.069 60.000 0.00 0.00 41.31 5.01
3100 3155 1.774217 AACCCAGGACCTCTTGGCA 60.774 57.895 0.00 0.00 41.31 4.92
3101 3156 1.002011 GAACCCAGGACCTCTTGGC 60.002 63.158 0.00 0.00 41.31 4.52
3102 3157 1.192146 TCGAACCCAGGACCTCTTGG 61.192 60.000 0.00 0.00 42.20 3.61
3103 3158 0.685097 TTCGAACCCAGGACCTCTTG 59.315 55.000 0.00 0.00 0.00 3.02
3104 3159 0.685660 GTTCGAACCCAGGACCTCTT 59.314 55.000 17.68 0.00 0.00 2.85
3105 3160 1.192803 GGTTCGAACCCAGGACCTCT 61.193 60.000 33.02 0.00 43.43 3.69
3106 3161 1.295746 GGTTCGAACCCAGGACCTC 59.704 63.158 33.02 7.79 43.43 3.85
3107 3162 3.479979 GGTTCGAACCCAGGACCT 58.520 61.111 33.02 0.00 43.43 3.85
3116 3171 1.016653 GCAGAGAGGCTGGTTCGAAC 61.017 60.000 20.14 20.14 45.03 3.95
3117 3172 1.293498 GCAGAGAGGCTGGTTCGAA 59.707 57.895 0.00 0.00 45.03 3.71
3118 3173 1.260538 ATGCAGAGAGGCTGGTTCGA 61.261 55.000 0.00 0.00 45.03 3.71
3119 3174 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.000 0.00 0.00 45.03 3.95
3120 3175 1.093159 CAATGCAGAGAGGCTGGTTC 58.907 55.000 0.00 0.00 45.03 3.62
3121 3176 0.964358 GCAATGCAGAGAGGCTGGTT 60.964 55.000 0.00 0.00 45.03 3.67
3122 3177 1.378250 GCAATGCAGAGAGGCTGGT 60.378 57.895 0.00 0.00 45.03 4.00
3123 3178 1.378119 TGCAATGCAGAGAGGCTGG 60.378 57.895 2.72 0.00 45.03 4.85
3125 3180 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.00 40.08 4.58
3126 3181 0.886563 AAAGTGCAATGCAGAGAGGC 59.113 50.000 8.73 0.00 40.08 4.70
3127 3182 1.402456 GCAAAGTGCAATGCAGAGAGG 60.402 52.381 8.73 0.00 44.26 3.69
3128 3183 1.978542 GCAAAGTGCAATGCAGAGAG 58.021 50.000 8.73 0.33 44.26 3.20
3139 3194 0.881796 GTCTTACCCCTGCAAAGTGC 59.118 55.000 0.00 0.00 45.29 4.40
3140 3195 2.568623 AGTCTTACCCCTGCAAAGTG 57.431 50.000 0.00 0.00 0.00 3.16
3141 3196 2.572104 CCTAGTCTTACCCCTGCAAAGT 59.428 50.000 0.00 0.00 0.00 2.66
3142 3197 2.572104 ACCTAGTCTTACCCCTGCAAAG 59.428 50.000 0.00 0.00 0.00 2.77
3143 3198 2.627933 ACCTAGTCTTACCCCTGCAAA 58.372 47.619 0.00 0.00 0.00 3.68
3144 3199 2.337359 ACCTAGTCTTACCCCTGCAA 57.663 50.000 0.00 0.00 0.00 4.08
3145 3200 2.185387 GAACCTAGTCTTACCCCTGCA 58.815 52.381 0.00 0.00 0.00 4.41
3146 3201 1.485480 GGAACCTAGTCTTACCCCTGC 59.515 57.143 0.00 0.00 0.00 4.85
3147 3202 3.117552 AGGAACCTAGTCTTACCCCTG 57.882 52.381 0.00 0.00 0.00 4.45
3148 3203 6.618836 TTATAGGAACCTAGTCTTACCCCT 57.381 41.667 6.72 0.00 31.45 4.79
3149 3204 6.440010 GGATTATAGGAACCTAGTCTTACCCC 59.560 46.154 6.72 0.00 31.45 4.95
3150 3205 6.440010 GGGATTATAGGAACCTAGTCTTACCC 59.560 46.154 6.72 9.62 31.45 3.69
3151 3206 7.247500 AGGGATTATAGGAACCTAGTCTTACC 58.753 42.308 6.72 4.95 31.45 2.85
3152 3207 7.396907 GGAGGGATTATAGGAACCTAGTCTTAC 59.603 44.444 6.72 0.00 31.45 2.34
3153 3208 7.477008 GGAGGGATTATAGGAACCTAGTCTTA 58.523 42.308 6.72 0.00 31.45 2.10
3154 3209 6.324544 GGAGGGATTATAGGAACCTAGTCTT 58.675 44.000 6.72 0.00 31.45 3.01
3155 3210 5.222589 GGGAGGGATTATAGGAACCTAGTCT 60.223 48.000 6.72 0.00 31.45 3.24
3156 3211 5.024785 GGGAGGGATTATAGGAACCTAGTC 58.975 50.000 6.72 4.93 31.45 2.59
3157 3212 4.202912 GGGGAGGGATTATAGGAACCTAGT 60.203 50.000 6.72 0.00 31.45 2.57
3158 3213 4.202901 TGGGGAGGGATTATAGGAACCTAG 60.203 50.000 6.72 0.00 31.45 3.02
3159 3214 3.741438 TGGGGAGGGATTATAGGAACCTA 59.259 47.826 2.93 2.93 0.00 3.08
3160 3215 2.531463 TGGGGAGGGATTATAGGAACCT 59.469 50.000 0.00 0.00 0.00 3.50
3161 3216 2.913617 CTGGGGAGGGATTATAGGAACC 59.086 54.545 0.00 0.00 0.00 3.62
3162 3217 3.583526 GTCTGGGGAGGGATTATAGGAAC 59.416 52.174 0.00 0.00 0.00 3.62
3163 3218 3.441054 GGTCTGGGGAGGGATTATAGGAA 60.441 52.174 0.00 0.00 0.00 3.36
3164 3219 2.113777 GGTCTGGGGAGGGATTATAGGA 59.886 54.545 0.00 0.00 0.00 2.94
3165 3220 2.552367 GGTCTGGGGAGGGATTATAGG 58.448 57.143 0.00 0.00 0.00 2.57
3166 3221 2.552367 GGGTCTGGGGAGGGATTATAG 58.448 57.143 0.00 0.00 0.00 1.31
3167 3222 1.153565 GGGGTCTGGGGAGGGATTATA 59.846 57.143 0.00 0.00 0.00 0.98
3168 3223 0.103876 GGGGTCTGGGGAGGGATTAT 60.104 60.000 0.00 0.00 0.00 1.28
3169 3224 1.320512 GGGGTCTGGGGAGGGATTA 59.679 63.158 0.00 0.00 0.00 1.75
3170 3225 2.044620 GGGGTCTGGGGAGGGATT 59.955 66.667 0.00 0.00 0.00 3.01
3171 3226 3.300962 TGGGGTCTGGGGAGGGAT 61.301 66.667 0.00 0.00 0.00 3.85
3172 3227 4.348495 GTGGGGTCTGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
3174 3229 3.891432 AAGGTGGGGTCTGGGGAGG 62.891 68.421 0.00 0.00 0.00 4.30
3175 3230 2.204151 AAGGTGGGGTCTGGGGAG 60.204 66.667 0.00 0.00 0.00 4.30
3176 3231 2.531685 CAAGGTGGGGTCTGGGGA 60.532 66.667 0.00 0.00 0.00 4.81
3177 3232 2.858974 ACAAGGTGGGGTCTGGGG 60.859 66.667 0.00 0.00 0.00 4.96
3178 3233 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.00 0.00 0.00 4.45
3179 3234 1.228245 CACACAAGGTGGGGTCTGG 60.228 63.158 1.07 0.00 44.04 3.86
3180 3235 4.481195 CACACAAGGTGGGGTCTG 57.519 61.111 1.07 0.00 44.04 3.51
3188 3243 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
3189 3244 2.636830 CATAGAAGCTCCCACACAAGG 58.363 52.381 0.00 0.00 0.00 3.61
3190 3245 2.012673 GCATAGAAGCTCCCACACAAG 58.987 52.381 0.00 0.00 0.00 3.16
3191 3246 1.350684 TGCATAGAAGCTCCCACACAA 59.649 47.619 0.00 0.00 34.99 3.33
3192 3247 0.983467 TGCATAGAAGCTCCCACACA 59.017 50.000 0.00 0.00 34.99 3.72
3193 3248 1.065854 AGTGCATAGAAGCTCCCACAC 60.066 52.381 0.00 0.00 34.99 3.82
3194 3249 1.065926 CAGTGCATAGAAGCTCCCACA 60.066 52.381 0.00 0.00 34.99 4.17
3195 3250 1.661341 CAGTGCATAGAAGCTCCCAC 58.339 55.000 0.00 0.00 34.99 4.61
3196 3251 0.543277 CCAGTGCATAGAAGCTCCCA 59.457 55.000 0.00 0.00 34.99 4.37
3197 3252 0.179034 CCCAGTGCATAGAAGCTCCC 60.179 60.000 0.00 0.00 34.99 4.30
3198 3253 0.543749 ACCCAGTGCATAGAAGCTCC 59.456 55.000 0.00 0.00 34.99 4.70
3199 3254 1.484240 AGACCCAGTGCATAGAAGCTC 59.516 52.381 0.00 0.00 34.99 4.09
3200 3255 1.209019 CAGACCCAGTGCATAGAAGCT 59.791 52.381 0.00 0.00 34.99 3.74
3201 3256 1.065854 ACAGACCCAGTGCATAGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
3202 3257 2.419297 GGACAGACCCAGTGCATAGAAG 60.419 54.545 0.00 0.00 0.00 2.85
3203 3258 1.555075 GGACAGACCCAGTGCATAGAA 59.445 52.381 0.00 0.00 0.00 2.10
3204 3259 1.195115 GGACAGACCCAGTGCATAGA 58.805 55.000 0.00 0.00 0.00 1.98
3205 3260 1.198713 AGGACAGACCCAGTGCATAG 58.801 55.000 0.00 0.00 40.05 2.23
3206 3261 1.656587 AAGGACAGACCCAGTGCATA 58.343 50.000 0.00 0.00 40.05 3.14
3207 3262 0.773644 AAAGGACAGACCCAGTGCAT 59.226 50.000 0.00 0.00 40.05 3.96
3208 3263 0.550914 AAAAGGACAGACCCAGTGCA 59.449 50.000 0.00 0.00 40.05 4.57
3209 3264 2.561478 TAAAAGGACAGACCCAGTGC 57.439 50.000 0.00 0.00 40.05 4.40
3210 3265 5.070001 TCAATTAAAAGGACAGACCCAGTG 58.930 41.667 0.00 0.00 40.05 3.66
3211 3266 5.319043 TCAATTAAAAGGACAGACCCAGT 57.681 39.130 0.00 0.00 40.05 4.00
3212 3267 6.840780 AATCAATTAAAAGGACAGACCCAG 57.159 37.500 0.00 0.00 40.05 4.45
3213 3268 6.210584 GGAAATCAATTAAAAGGACAGACCCA 59.789 38.462 0.00 0.00 40.05 4.51
3214 3269 6.210584 TGGAAATCAATTAAAAGGACAGACCC 59.789 38.462 0.00 0.00 40.05 4.46
3215 3270 7.227049 TGGAAATCAATTAAAAGGACAGACC 57.773 36.000 0.00 0.00 39.35 3.85
3216 3271 8.522830 TGATGGAAATCAATTAAAAGGACAGAC 58.477 33.333 0.00 0.00 0.00 3.51
3217 3272 8.648698 TGATGGAAATCAATTAAAAGGACAGA 57.351 30.769 0.00 0.00 0.00 3.41
3218 3273 9.309516 CATGATGGAAATCAATTAAAAGGACAG 57.690 33.333 0.00 0.00 33.83 3.51
3219 3274 9.033711 TCATGATGGAAATCAATTAAAAGGACA 57.966 29.630 0.00 0.00 33.83 4.02
3227 3282 9.645128 ACAGGTTATCATGATGGAAATCAATTA 57.355 29.630 18.72 0.00 33.83 1.40
3228 3283 8.543293 ACAGGTTATCATGATGGAAATCAATT 57.457 30.769 18.72 0.00 33.83 2.32
3277 3363 2.175715 GGATTCAGGAGGGTATTTGCCT 59.824 50.000 0.00 0.00 0.00 4.75
3299 3385 2.094700 TCTGACTCTACAATGCGACACC 60.095 50.000 0.00 0.00 0.00 4.16
3360 3446 4.202253 GGCAAAAAGAGGATTGGTCAAACT 60.202 41.667 0.00 0.00 0.00 2.66
3556 3643 5.661056 TGTACTGATGAGTTTAGACTGGG 57.339 43.478 0.00 0.00 35.88 4.45
3772 3865 3.865929 CTGAACTGCCACCGCGACT 62.866 63.158 8.23 0.00 38.08 4.18
3829 3922 0.796312 AAAGCCACGTAGAATGCACG 59.204 50.000 0.00 0.00 44.80 5.34
3830 3923 1.535462 ACAAAGCCACGTAGAATGCAC 59.465 47.619 0.00 0.00 0.00 4.57
3919 4012 5.947228 TGCTAAACTTTGAGTTGAGATGG 57.053 39.130 8.97 0.00 38.70 3.51
3923 4016 8.345565 ACAGTTTATGCTAAACTTTGAGTTGAG 58.654 33.333 14.69 1.51 39.28 3.02
4019 4117 5.662657 CCCAACTCCCCAATATCAGATTTTT 59.337 40.000 0.00 0.00 0.00 1.94
4144 4242 2.092592 GTGGTATTGGGGAAGGTTCGAT 60.093 50.000 0.00 0.00 0.00 3.59
4146 4244 1.003812 TGTGGTATTGGGGAAGGTTCG 59.996 52.381 0.00 0.00 0.00 3.95
4147 4245 2.443416 GTGTGGTATTGGGGAAGGTTC 58.557 52.381 0.00 0.00 0.00 3.62
4149 4247 0.702316 GGTGTGGTATTGGGGAAGGT 59.298 55.000 0.00 0.00 0.00 3.50
4150 4248 0.701731 TGGTGTGGTATTGGGGAAGG 59.298 55.000 0.00 0.00 0.00 3.46
4151 4249 2.595750 TTGGTGTGGTATTGGGGAAG 57.404 50.000 0.00 0.00 0.00 3.46
4194 4304 1.546923 TCATGAAACTTACGCGGGAGA 59.453 47.619 12.47 0.00 0.00 3.71
4195 4305 1.927174 CTCATGAAACTTACGCGGGAG 59.073 52.381 12.47 10.46 0.00 4.30
4196 4306 2.004583 CTCATGAAACTTACGCGGGA 57.995 50.000 12.47 0.00 0.00 5.14
4197 4307 0.373716 GCTCATGAAACTTACGCGGG 59.626 55.000 12.47 0.00 0.00 6.13
4200 4310 3.485877 GGATGTGCTCATGAAACTTACGC 60.486 47.826 5.89 0.00 34.06 4.42
4201 4311 3.684305 TGGATGTGCTCATGAAACTTACG 59.316 43.478 5.89 0.00 34.06 3.18
4202 4312 5.587844 AGATGGATGTGCTCATGAAACTTAC 59.412 40.000 5.89 0.00 34.06 2.34
4235 4347 0.692419 AGGATCGGTGGCCTTCATCT 60.692 55.000 3.32 0.00 0.00 2.90
4303 4417 1.098712 GTGGAGGTGGTTTGCAACGA 61.099 55.000 0.00 0.00 0.00 3.85
4357 4471 2.350522 GACAGGTCACATGCCTTACTG 58.649 52.381 0.00 0.00 33.31 2.74
4364 4478 1.514678 TTTGCGGACAGGTCACATGC 61.515 55.000 1.41 0.76 0.00 4.06
4387 4501 4.475444 TCCTTCCTCCCCCGCGAT 62.475 66.667 8.23 0.00 0.00 4.58
4416 4530 3.799755 GGCACGACGACCCAATGC 61.800 66.667 0.00 0.00 35.51 3.56
4430 4544 4.344865 GGGGCTTCTTGGTCGGCA 62.345 66.667 0.00 0.00 0.00 5.69
4449 4563 1.671054 GCCGAAGCAGTTGTGGCTA 60.671 57.895 0.00 0.00 41.66 3.93
4492 4629 2.593956 GCCTCGAAGAAGGTGGGGT 61.594 63.158 0.00 0.00 34.09 4.95
4511 4648 2.401583 ACATGTAGAAATCGGCAGCA 57.598 45.000 0.00 0.00 0.00 4.41
4514 4651 3.615056 CGTTGTACATGTAGAAATCGGCA 59.385 43.478 16.30 1.05 0.00 5.69
4520 4657 8.991243 ACTTATTAGCGTTGTACATGTAGAAA 57.009 30.769 16.30 6.89 0.00 2.52
4538 4675 7.335673 TCCTGCATTTCATCGAACAACTTATTA 59.664 33.333 0.00 0.00 0.00 0.98
4614 4768 5.051816 CGAGCATTGGAAATTGCCATTTAT 58.948 37.500 5.81 0.00 39.72 1.40
4717 4885 0.762418 ACCGTTCACATTCCCACTCA 59.238 50.000 0.00 0.00 0.00 3.41
4760 4928 4.753107 TCACCTAAACACGAAGATCAAACC 59.247 41.667 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.