Multiple sequence alignment - TraesCS2A01G194600

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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 TraesCS2A01G194600 chr2A 100.000 3380 0 0 1 3380 163668553 163671932 0.000000e+00 6242
1 TraesCS2A01G194600 chr2A 97.241 145 4 0 1 145 280100948 280101092 2.600000e-61 246
2 TraesCS2A01G194600 chr2D 96.052 2761 74 11 188 2927 138249400 138246654 0.000000e+00 4462
3 TraesCS2A01G194600 chr2D 87.209 258 29 1 2998 3251 138246423 138246166 1.190000e-74 291
4 TraesCS2A01G194600 chr2B 94.718 2840 80 25 195 2982 196194969 196192148 0.000000e+00 4349
5 TraesCS2A01G194600 chr2B 87.550 249 30 1 2997 3245 196192163 196191916 1.530000e-73 287
6 TraesCS2A01G194600 chr5A 98.582 141 2 0 1 141 575320264 575320404 2.010000e-62 250
7 TraesCS2A01G194600 chr5A 98.571 140 2 0 1 140 448842312 448842451 7.240000e-62 248
8 TraesCS2A01G194600 chr3A 98.582 141 2 0 1 141 726454220 726454080 2.010000e-62 250
9 TraesCS2A01G194600 chr3A 97.260 146 4 0 1 146 198424528 198424383 7.240000e-62 248
10 TraesCS2A01G194600 chr3A 98.571 140 2 0 2 141 593543663 593543524 7.240000e-62 248
11 TraesCS2A01G194600 chr1A 98.582 141 2 0 1 141 49277842 49277702 2.010000e-62 250
12 TraesCS2A01G194600 chr1A 88.112 143 16 1 3121 3262 506545382 506545524 5.800000e-38 169
13 TraesCS2A01G194600 chr6A 98.571 140 2 0 1 140 127610778 127610917 7.240000e-62 248
14 TraesCS2A01G194600 chr6A 97.887 142 3 0 1 142 448411453 448411312 2.600000e-61 246
15 TraesCS2A01G194600 chr6A 80.930 215 31 6 3045 3256 20520635 20520842 9.710000e-36 161
16 TraesCS2A01G194600 chr5D 81.985 272 43 4 2997 3263 5625728 5625998 3.390000e-55 226
17 TraesCS2A01G194600 chr5D 79.615 260 41 11 2999 3253 539019852 539019600 3.470000e-40 176
18 TraesCS2A01G194600 chr4B 83.036 224 35 3 3040 3261 17876730 17876508 2.060000e-47 200
19 TraesCS2A01G194600 chr1D 79.848 263 50 3 2997 3257 340526917 340526656 4.450000e-44 189
20 TraesCS2A01G194600 chr1B 89.510 143 14 1 3121 3262 553144781 553144923 2.680000e-41 180


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 TraesCS2A01G194600 chr2A 163668553 163671932 3379 False 6242.0 6242 100.0000 1 3380 1 chr2A.!!$F1 3379
1 TraesCS2A01G194600 chr2D 138246166 138249400 3234 True 2376.5 4462 91.6305 188 3251 2 chr2D.!!$R1 3063
2 TraesCS2A01G194600 chr2B 196191916 196194969 3053 True 2318.0 4349 91.1340 195 3245 2 chr2B.!!$R1 3050

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
344 345 0.392595 CCGGTAAACCTTCCTCCTGC 60.393 60.0 0.0 0.0 0.00 4.85 F
345 346 0.613777 CGGTAAACCTTCCTCCTGCT 59.386 55.0 0.0 0.0 0.00 4.24 F
2142 2170 0.108019 GGTGGAAGGTGGAGAACGTT 59.892 55.0 0.0 0.0 39.54 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1933 1.154188 GAGCGAGACCGACTGTGTC 60.154 63.158 0.00 0.0 38.22 3.67 R
2331 2359 1.826487 AACGTTGTGCCCCTTCCAC 60.826 57.895 0.00 0.0 0.00 4.02 R
3005 3257 0.035534 TGGTCGTGCCTTGCATGTAT 60.036 50.000 8.04 0.0 44.84 2.29 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 45 8.916628 TCATATTGTATAACTTTAGCATGGCA 57.083 30.769 0.00 0.00 0.00 4.92
45 46 9.348476 TCATATTGTATAACTTTAGCATGGCAA 57.652 29.630 0.00 0.00 0.00 4.52
46 47 9.964303 CATATTGTATAACTTTAGCATGGCAAA 57.036 29.630 0.00 0.00 0.00 3.68
48 49 8.876275 ATTGTATAACTTTAGCATGGCAAATG 57.124 30.769 0.00 0.00 0.00 2.32
49 50 7.403312 TGTATAACTTTAGCATGGCAAATGT 57.597 32.000 0.00 0.00 0.00 2.71
50 51 7.835822 TGTATAACTTTAGCATGGCAAATGTT 58.164 30.769 0.00 0.00 0.00 2.71
51 52 7.758980 TGTATAACTTTAGCATGGCAAATGTTG 59.241 33.333 9.77 0.00 0.00 3.33
52 53 4.870123 ACTTTAGCATGGCAAATGTTGA 57.130 36.364 0.00 0.00 0.00 3.18
53 54 5.410355 ACTTTAGCATGGCAAATGTTGAT 57.590 34.783 0.00 0.00 0.00 2.57
54 55 6.528537 ACTTTAGCATGGCAAATGTTGATA 57.471 33.333 0.00 0.00 0.00 2.15
55 56 7.116075 ACTTTAGCATGGCAAATGTTGATAT 57.884 32.000 0.00 0.00 0.00 1.63
56 57 7.558604 ACTTTAGCATGGCAAATGTTGATATT 58.441 30.769 0.00 0.00 0.00 1.28
57 58 8.042515 ACTTTAGCATGGCAAATGTTGATATTT 58.957 29.630 0.00 0.00 0.00 1.40
58 59 8.789825 TTTAGCATGGCAAATGTTGATATTTT 57.210 26.923 0.00 0.00 0.00 1.82
59 60 8.789825 TTAGCATGGCAAATGTTGATATTTTT 57.210 26.923 0.00 0.00 0.00 1.94
86 87 9.438228 TCATATAAATACGGTCAAACTTTGTGA 57.562 29.630 1.44 0.00 0.00 3.58
114 115 9.928236 GTTTGACTTCAGAGAATTCTAATATGC 57.072 33.333 8.25 0.00 30.73 3.14
115 116 9.671279 TTTGACTTCAGAGAATTCTAATATGCA 57.329 29.630 8.25 0.00 30.73 3.96
116 117 8.883954 TGACTTCAGAGAATTCTAATATGCAG 57.116 34.615 8.25 7.58 30.73 4.41
117 118 8.699130 TGACTTCAGAGAATTCTAATATGCAGA 58.301 33.333 8.25 0.00 30.73 4.26
118 119 9.195411 GACTTCAGAGAATTCTAATATGCAGAG 57.805 37.037 8.25 6.79 30.73 3.35
119 120 8.703743 ACTTCAGAGAATTCTAATATGCAGAGT 58.296 33.333 8.25 7.29 30.73 3.24
130 131 8.365399 TCTAATATGCAGAGTAAAAATGACCG 57.635 34.615 0.00 0.00 0.00 4.79
131 132 6.377327 AATATGCAGAGTAAAAATGACCGG 57.623 37.500 0.00 0.00 0.00 5.28
132 133 3.410631 TGCAGAGTAAAAATGACCGGA 57.589 42.857 9.46 0.00 0.00 5.14
133 134 3.334691 TGCAGAGTAAAAATGACCGGAG 58.665 45.455 9.46 0.00 0.00 4.63
151 152 5.883503 CGGAGGGAGTATGTCTTATACTC 57.116 47.826 15.33 15.33 45.91 2.59
152 153 4.392445 CGGAGGGAGTATGTCTTATACTCG 59.608 50.000 16.50 6.07 46.97 4.18
158 159 7.948278 GGAGTATGTCTTATACTCGCATTTT 57.052 36.000 16.50 0.00 46.97 1.82
159 160 8.366671 GGAGTATGTCTTATACTCGCATTTTT 57.633 34.615 16.50 0.00 46.97 1.94
160 161 8.276325 GGAGTATGTCTTATACTCGCATTTTTG 58.724 37.037 16.50 0.00 46.97 2.44
161 162 8.942338 AGTATGTCTTATACTCGCATTTTTGA 57.058 30.769 0.00 0.00 29.47 2.69
162 163 9.378551 AGTATGTCTTATACTCGCATTTTTGAA 57.621 29.630 0.00 0.00 29.47 2.69
163 164 9.422196 GTATGTCTTATACTCGCATTTTTGAAC 57.578 33.333 0.00 0.00 0.00 3.18
164 165 7.428282 TGTCTTATACTCGCATTTTTGAACA 57.572 32.000 0.00 0.00 0.00 3.18
165 166 7.866729 TGTCTTATACTCGCATTTTTGAACAA 58.133 30.769 0.00 0.00 0.00 2.83
166 167 8.346300 TGTCTTATACTCGCATTTTTGAACAAA 58.654 29.630 0.00 0.00 0.00 2.83
167 168 8.840867 GTCTTATACTCGCATTTTTGAACAAAG 58.159 33.333 0.46 0.00 0.00 2.77
168 169 8.020819 TCTTATACTCGCATTTTTGAACAAAGG 58.979 33.333 0.46 0.00 0.00 3.11
169 170 3.716601 ACTCGCATTTTTGAACAAAGGG 58.283 40.909 0.46 0.00 0.00 3.95
170 171 3.383185 ACTCGCATTTTTGAACAAAGGGA 59.617 39.130 0.46 3.34 0.00 4.20
171 172 3.976169 TCGCATTTTTGAACAAAGGGAG 58.024 40.909 0.46 0.00 0.00 4.30
172 173 3.383185 TCGCATTTTTGAACAAAGGGAGT 59.617 39.130 0.46 0.00 0.00 3.85
173 174 4.580995 TCGCATTTTTGAACAAAGGGAGTA 59.419 37.500 0.46 0.00 0.00 2.59
174 175 4.679654 CGCATTTTTGAACAAAGGGAGTAC 59.320 41.667 0.46 0.00 0.00 2.73
175 176 5.507315 CGCATTTTTGAACAAAGGGAGTACT 60.507 40.000 0.00 0.00 0.00 2.73
176 177 6.293735 CGCATTTTTGAACAAAGGGAGTACTA 60.294 38.462 0.00 0.00 0.00 1.82
177 178 6.861572 GCATTTTTGAACAAAGGGAGTACTAC 59.138 38.462 0.00 0.00 0.00 2.73
178 179 6.947644 TTTTTGAACAAAGGGAGTACTACC 57.052 37.500 17.30 17.30 0.00 3.18
180 181 6.999705 TTTGAACAAAGGGAGTACTACCTA 57.000 37.500 27.61 7.57 45.16 3.08
181 182 6.999705 TTGAACAAAGGGAGTACTACCTAA 57.000 37.500 27.61 13.62 45.16 2.69
182 183 6.600882 TGAACAAAGGGAGTACTACCTAAG 57.399 41.667 27.61 22.83 45.16 2.18
183 184 5.046807 TGAACAAAGGGAGTACTACCTAAGC 60.047 44.000 27.61 14.75 45.16 3.09
184 185 4.685807 ACAAAGGGAGTACTACCTAAGCT 58.314 43.478 27.61 8.80 45.16 3.74
185 186 5.835582 ACAAAGGGAGTACTACCTAAGCTA 58.164 41.667 27.61 0.00 45.16 3.32
186 187 6.442091 ACAAAGGGAGTACTACCTAAGCTAT 58.558 40.000 27.61 7.57 45.16 2.97
244 245 8.818141 TGATAATTGCAGTAGACTAATAGCAC 57.182 34.615 6.57 0.00 0.00 4.40
343 344 0.981943 ACCGGTAAACCTTCCTCCTG 59.018 55.000 4.49 0.00 0.00 3.86
344 345 0.392595 CCGGTAAACCTTCCTCCTGC 60.393 60.000 0.00 0.00 0.00 4.85
345 346 0.613777 CGGTAAACCTTCCTCCTGCT 59.386 55.000 0.00 0.00 0.00 4.24
346 347 1.003233 CGGTAAACCTTCCTCCTGCTT 59.997 52.381 0.00 0.00 0.00 3.91
347 348 2.552373 CGGTAAACCTTCCTCCTGCTTT 60.552 50.000 0.00 0.00 0.00 3.51
349 350 2.294449 AAACCTTCCTCCTGCTTTCC 57.706 50.000 0.00 0.00 0.00 3.13
406 424 4.417437 TCTCCTCCAGCTTACAAGTTACT 58.583 43.478 0.00 0.00 0.00 2.24
407 425 5.577100 TCTCCTCCAGCTTACAAGTTACTA 58.423 41.667 0.00 0.00 0.00 1.82
408 426 5.418209 TCTCCTCCAGCTTACAAGTTACTAC 59.582 44.000 0.00 0.00 0.00 2.73
465 484 3.941483 ACTCTTGGATTCAAATACCAGCG 59.059 43.478 0.00 0.00 35.08 5.18
509 528 5.220098 CGATATCAAGCATGCATGTACTACG 60.220 44.000 26.79 16.44 0.00 3.51
510 529 3.245518 TCAAGCATGCATGTACTACGT 57.754 42.857 26.79 6.23 0.00 3.57
511 530 4.379339 TCAAGCATGCATGTACTACGTA 57.621 40.909 26.79 0.00 0.00 3.57
512 531 4.109766 TCAAGCATGCATGTACTACGTAC 58.890 43.478 26.79 7.72 39.24 3.67
681 704 5.703130 CCAGCTAGCTAAATACAAATCCCTC 59.297 44.000 18.86 0.00 0.00 4.30
750 773 1.036707 CTCCATTCTCCGTCTCCCTC 58.963 60.000 0.00 0.00 0.00 4.30
766 789 1.562475 CCCTCGGTTTCCCCTTTGATA 59.438 52.381 0.00 0.00 0.00 2.15
793 820 5.220854 CGTTCCCAAAGTTCTATTGGCATAG 60.221 44.000 0.00 0.00 44.87 2.23
807 834 1.406341 GGCATAGGGAAAGCACGTGTA 60.406 52.381 18.38 0.00 0.00 2.90
808 835 2.561569 GCATAGGGAAAGCACGTGTAT 58.438 47.619 18.38 3.23 0.00 2.29
809 836 2.287915 GCATAGGGAAAGCACGTGTATG 59.712 50.000 18.38 15.13 0.00 2.39
810 837 3.531538 CATAGGGAAAGCACGTGTATGT 58.468 45.455 18.38 0.81 0.00 2.29
1908 1936 3.311110 GGGTCGGTGAGCCTGACA 61.311 66.667 7.75 0.00 45.63 3.58
2142 2170 0.108019 GGTGGAAGGTGGAGAACGTT 59.892 55.000 0.00 0.00 39.54 3.99
2331 2359 1.869574 CGACGACCTCATGCTCACG 60.870 63.158 0.00 0.00 0.00 4.35
2361 2389 1.088306 ACAACGTTGTTTTCGCCTCA 58.912 45.000 27.70 0.00 38.47 3.86
2753 2797 3.126343 GGTAAGTACAAATGCCGACCAAG 59.874 47.826 0.00 0.00 0.00 3.61
2779 2823 4.657814 AGGACCAAATGAAGCTTTCCTA 57.342 40.909 11.14 0.00 0.00 2.94
2956 3208 2.105649 TGTGCCCATGTGTCTTACTTGA 59.894 45.455 0.00 0.00 36.76 3.02
2960 3212 3.559171 GCCCATGTGTCTTACTTGAAGGA 60.559 47.826 0.00 0.00 36.76 3.36
2961 3213 4.256920 CCCATGTGTCTTACTTGAAGGAG 58.743 47.826 0.00 0.00 36.76 3.69
2962 3214 4.263068 CCCATGTGTCTTACTTGAAGGAGT 60.263 45.833 0.00 0.00 36.76 3.85
2963 3215 4.692625 CCATGTGTCTTACTTGAAGGAGTG 59.307 45.833 0.00 0.00 36.76 3.51
2964 3216 5.300752 CATGTGTCTTACTTGAAGGAGTGT 58.699 41.667 0.00 0.00 36.76 3.55
2965 3217 5.353394 TGTGTCTTACTTGAAGGAGTGTT 57.647 39.130 0.00 0.00 35.67 3.32
2966 3218 6.474140 TGTGTCTTACTTGAAGGAGTGTTA 57.526 37.500 0.00 0.00 35.67 2.41
2967 3219 6.513180 TGTGTCTTACTTGAAGGAGTGTTAG 58.487 40.000 0.00 0.00 35.67 2.34
2968 3220 6.097839 TGTGTCTTACTTGAAGGAGTGTTAGT 59.902 38.462 0.00 0.00 35.67 2.24
2969 3221 7.286087 TGTGTCTTACTTGAAGGAGTGTTAGTA 59.714 37.037 0.00 0.00 35.67 1.82
2970 3222 8.139989 GTGTCTTACTTGAAGGAGTGTTAGTAA 58.860 37.037 0.00 0.00 35.67 2.24
2971 3223 8.867097 TGTCTTACTTGAAGGAGTGTTAGTAAT 58.133 33.333 0.00 0.00 35.67 1.89
2972 3224 9.356433 GTCTTACTTGAAGGAGTGTTAGTAATC 57.644 37.037 0.00 0.00 35.67 1.75
2973 3225 8.242053 TCTTACTTGAAGGAGTGTTAGTAATCG 58.758 37.037 0.00 0.00 35.67 3.34
2974 3226 6.342338 ACTTGAAGGAGTGTTAGTAATCGT 57.658 37.500 0.00 0.00 0.00 3.73
2975 3227 6.157211 ACTTGAAGGAGTGTTAGTAATCGTG 58.843 40.000 0.00 0.00 0.00 4.35
2976 3228 4.491676 TGAAGGAGTGTTAGTAATCGTGC 58.508 43.478 0.00 0.00 0.00 5.34
2977 3229 4.219944 TGAAGGAGTGTTAGTAATCGTGCT 59.780 41.667 0.00 0.00 0.00 4.40
2978 3230 4.373348 AGGAGTGTTAGTAATCGTGCTC 57.627 45.455 0.00 0.00 0.00 4.26
2979 3231 3.762288 AGGAGTGTTAGTAATCGTGCTCA 59.238 43.478 0.00 0.00 0.00 4.26
2980 3232 4.402793 AGGAGTGTTAGTAATCGTGCTCAT 59.597 41.667 0.00 0.00 0.00 2.90
2981 3233 4.504461 GGAGTGTTAGTAATCGTGCTCATG 59.496 45.833 0.00 0.00 0.00 3.07
2982 3234 5.324784 AGTGTTAGTAATCGTGCTCATGA 57.675 39.130 0.00 0.00 0.00 3.07
2983 3235 5.344066 AGTGTTAGTAATCGTGCTCATGAG 58.656 41.667 18.84 18.84 0.00 2.90
3090 3346 8.761575 TGTTGATTCCAAGATTAATTGCTTTC 57.238 30.769 0.00 0.00 32.06 2.62
3091 3347 8.366401 TGTTGATTCCAAGATTAATTGCTTTCA 58.634 29.630 0.00 0.00 32.06 2.69
3092 3348 8.866956 GTTGATTCCAAGATTAATTGCTTTCAG 58.133 33.333 0.00 0.00 32.06 3.02
3209 3465 4.202326 ACGTTGGGTATAGATGGTTGGATC 60.202 45.833 0.00 0.00 0.00 3.36
3214 3470 3.258372 GGTATAGATGGTTGGATCGCTCA 59.742 47.826 0.00 0.00 0.00 4.26
3251 3507 2.159627 CCAAACTCGCGCTTTCATAAGT 59.840 45.455 5.56 0.00 33.74 2.24
3252 3508 3.369756 CCAAACTCGCGCTTTCATAAGTA 59.630 43.478 5.56 0.00 33.74 2.24
3253 3509 4.492570 CCAAACTCGCGCTTTCATAAGTAG 60.493 45.833 5.56 0.00 33.74 2.57
3254 3510 3.505464 ACTCGCGCTTTCATAAGTAGT 57.495 42.857 5.56 0.00 33.74 2.73
3255 3511 4.627611 ACTCGCGCTTTCATAAGTAGTA 57.372 40.909 5.56 0.00 33.74 1.82
3256 3512 4.599047 ACTCGCGCTTTCATAAGTAGTAG 58.401 43.478 5.56 0.00 33.74 2.57
3257 3513 4.096081 ACTCGCGCTTTCATAAGTAGTAGT 59.904 41.667 5.56 0.00 33.74 2.73
3258 3514 5.295292 ACTCGCGCTTTCATAAGTAGTAGTA 59.705 40.000 5.56 0.00 33.74 1.82
3259 3515 5.745514 TCGCGCTTTCATAAGTAGTAGTAG 58.254 41.667 5.56 0.00 33.74 2.57
3260 3516 5.525012 TCGCGCTTTCATAAGTAGTAGTAGA 59.475 40.000 5.56 0.00 33.74 2.59
3261 3517 6.204301 TCGCGCTTTCATAAGTAGTAGTAGAT 59.796 38.462 5.56 0.00 33.74 1.98
3262 3518 7.386025 TCGCGCTTTCATAAGTAGTAGTAGATA 59.614 37.037 5.56 0.00 33.74 1.98
3263 3519 7.688989 CGCGCTTTCATAAGTAGTAGTAGATAG 59.311 40.741 5.56 0.00 33.74 2.08
3264 3520 8.505625 GCGCTTTCATAAGTAGTAGTAGATAGT 58.494 37.037 0.00 0.00 33.74 2.12
3302 3558 8.992835 AGAAAACATCCAAAATAAATCTGAGC 57.007 30.769 0.00 0.00 0.00 4.26
3303 3559 8.810041 AGAAAACATCCAAAATAAATCTGAGCT 58.190 29.630 0.00 0.00 0.00 4.09
3304 3560 8.767478 AAAACATCCAAAATAAATCTGAGCTG 57.233 30.769 0.00 0.00 0.00 4.24
3305 3561 7.707624 AACATCCAAAATAAATCTGAGCTGA 57.292 32.000 0.00 0.00 0.00 4.26
3306 3562 7.330900 ACATCCAAAATAAATCTGAGCTGAG 57.669 36.000 0.00 0.00 0.00 3.35
3307 3563 6.888632 ACATCCAAAATAAATCTGAGCTGAGT 59.111 34.615 0.00 0.00 0.00 3.41
3308 3564 6.748333 TCCAAAATAAATCTGAGCTGAGTG 57.252 37.500 0.00 0.00 0.00 3.51
3309 3565 5.649395 TCCAAAATAAATCTGAGCTGAGTGG 59.351 40.000 0.00 0.00 0.00 4.00
3310 3566 5.416952 CCAAAATAAATCTGAGCTGAGTGGT 59.583 40.000 0.00 0.00 0.00 4.16
3311 3567 6.320171 CAAAATAAATCTGAGCTGAGTGGTG 58.680 40.000 0.00 0.00 0.00 4.17
3312 3568 4.833478 ATAAATCTGAGCTGAGTGGTGT 57.167 40.909 0.00 0.00 0.00 4.16
3313 3569 3.498774 AAATCTGAGCTGAGTGGTGTT 57.501 42.857 0.00 0.00 0.00 3.32
3314 3570 3.498774 AATCTGAGCTGAGTGGTGTTT 57.501 42.857 0.00 0.00 0.00 2.83
3315 3571 4.623932 AATCTGAGCTGAGTGGTGTTTA 57.376 40.909 0.00 0.00 0.00 2.01
3316 3572 4.833478 ATCTGAGCTGAGTGGTGTTTAT 57.167 40.909 0.00 0.00 0.00 1.40
3317 3573 4.623932 TCTGAGCTGAGTGGTGTTTATT 57.376 40.909 0.00 0.00 0.00 1.40
3318 3574 4.973168 TCTGAGCTGAGTGGTGTTTATTT 58.027 39.130 0.00 0.00 0.00 1.40
3319 3575 4.997395 TCTGAGCTGAGTGGTGTTTATTTC 59.003 41.667 0.00 0.00 0.00 2.17
3320 3576 4.973168 TGAGCTGAGTGGTGTTTATTTCT 58.027 39.130 0.00 0.00 0.00 2.52
3321 3577 4.997395 TGAGCTGAGTGGTGTTTATTTCTC 59.003 41.667 0.00 0.00 0.00 2.87
3322 3578 4.973168 AGCTGAGTGGTGTTTATTTCTCA 58.027 39.130 0.00 0.00 0.00 3.27
3323 3579 5.564550 AGCTGAGTGGTGTTTATTTCTCAT 58.435 37.500 0.00 0.00 32.73 2.90
3324 3580 6.006449 AGCTGAGTGGTGTTTATTTCTCATT 58.994 36.000 0.00 0.00 32.73 2.57
3325 3581 6.491403 AGCTGAGTGGTGTTTATTTCTCATTT 59.509 34.615 0.00 0.00 32.73 2.32
3326 3582 6.803807 GCTGAGTGGTGTTTATTTCTCATTTC 59.196 38.462 0.00 0.00 32.73 2.17
3327 3583 7.214467 TGAGTGGTGTTTATTTCTCATTTCC 57.786 36.000 0.00 0.00 0.00 3.13
3328 3584 7.004086 TGAGTGGTGTTTATTTCTCATTTCCT 58.996 34.615 0.00 0.00 0.00 3.36
3329 3585 7.505585 TGAGTGGTGTTTATTTCTCATTTCCTT 59.494 33.333 0.00 0.00 0.00 3.36
3330 3586 7.661040 AGTGGTGTTTATTTCTCATTTCCTTG 58.339 34.615 0.00 0.00 0.00 3.61
3331 3587 6.366061 GTGGTGTTTATTTCTCATTTCCTTGC 59.634 38.462 0.00 0.00 0.00 4.01
3332 3588 5.869344 GGTGTTTATTTCTCATTTCCTTGCC 59.131 40.000 0.00 0.00 0.00 4.52
3333 3589 6.295292 GGTGTTTATTTCTCATTTCCTTGCCT 60.295 38.462 0.00 0.00 0.00 4.75
3334 3590 7.093945 GGTGTTTATTTCTCATTTCCTTGCCTA 60.094 37.037 0.00 0.00 0.00 3.93
3335 3591 8.470002 GTGTTTATTTCTCATTTCCTTGCCTAT 58.530 33.333 0.00 0.00 0.00 2.57
3336 3592 9.034800 TGTTTATTTCTCATTTCCTTGCCTATT 57.965 29.630 0.00 0.00 0.00 1.73
3337 3593 9.875691 GTTTATTTCTCATTTCCTTGCCTATTT 57.124 29.630 0.00 0.00 0.00 1.40
3339 3595 7.722949 ATTTCTCATTTCCTTGCCTATTTCA 57.277 32.000 0.00 0.00 0.00 2.69
3340 3596 6.515272 TTCTCATTTCCTTGCCTATTTCAC 57.485 37.500 0.00 0.00 0.00 3.18
3341 3597 4.949856 TCTCATTTCCTTGCCTATTTCACC 59.050 41.667 0.00 0.00 0.00 4.02
3342 3598 4.023291 TCATTTCCTTGCCTATTTCACCC 58.977 43.478 0.00 0.00 0.00 4.61
3343 3599 3.534357 TTTCCTTGCCTATTTCACCCA 57.466 42.857 0.00 0.00 0.00 4.51
3344 3600 3.534357 TTCCTTGCCTATTTCACCCAA 57.466 42.857 0.00 0.00 0.00 4.12
3345 3601 3.534357 TCCTTGCCTATTTCACCCAAA 57.466 42.857 0.00 0.00 0.00 3.28
3346 3602 4.059773 TCCTTGCCTATTTCACCCAAAT 57.940 40.909 0.00 0.00 38.35 2.32
3347 3603 5.199982 TCCTTGCCTATTTCACCCAAATA 57.800 39.130 0.00 0.00 36.09 1.40
3348 3604 5.776358 TCCTTGCCTATTTCACCCAAATAT 58.224 37.500 0.00 0.00 36.53 1.28
3349 3605 6.201591 TCCTTGCCTATTTCACCCAAATATT 58.798 36.000 0.00 0.00 36.53 1.28
3350 3606 7.358263 TCCTTGCCTATTTCACCCAAATATTA 58.642 34.615 0.00 0.00 36.53 0.98
3351 3607 7.505585 TCCTTGCCTATTTCACCCAAATATTAG 59.494 37.037 0.00 0.00 36.53 1.73
3352 3608 7.255942 CCTTGCCTATTTCACCCAAATATTAGG 60.256 40.741 3.43 3.43 36.53 2.69
3353 3609 6.678547 TGCCTATTTCACCCAAATATTAGGT 58.321 36.000 4.59 4.59 36.53 3.08
3359 3615 4.589216 CACCCAAATATTAGGTGGCATG 57.411 45.455 21.88 9.77 46.01 4.06
3360 3616 3.960102 CACCCAAATATTAGGTGGCATGT 59.040 43.478 21.88 5.03 46.01 3.21
3361 3617 3.960102 ACCCAAATATTAGGTGGCATGTG 59.040 43.478 8.86 0.00 30.97 3.21
3362 3618 3.960102 CCCAAATATTAGGTGGCATGTGT 59.040 43.478 0.00 0.00 0.00 3.72
3363 3619 4.202141 CCCAAATATTAGGTGGCATGTGTG 60.202 45.833 0.00 0.00 0.00 3.82
3364 3620 4.644234 CCAAATATTAGGTGGCATGTGTGA 59.356 41.667 0.00 0.00 0.00 3.58
3365 3621 5.126869 CCAAATATTAGGTGGCATGTGTGAA 59.873 40.000 0.00 0.00 0.00 3.18
3366 3622 6.350864 CCAAATATTAGGTGGCATGTGTGAAA 60.351 38.462 0.00 0.00 0.00 2.69
3367 3623 6.455360 AATATTAGGTGGCATGTGTGAAAG 57.545 37.500 0.00 0.00 0.00 2.62
3368 3624 2.198827 TAGGTGGCATGTGTGAAAGG 57.801 50.000 0.00 0.00 0.00 3.11
3369 3625 0.185901 AGGTGGCATGTGTGAAAGGT 59.814 50.000 0.00 0.00 0.00 3.50
3370 3626 1.423541 AGGTGGCATGTGTGAAAGGTA 59.576 47.619 0.00 0.00 0.00 3.08
3371 3627 2.041620 AGGTGGCATGTGTGAAAGGTAT 59.958 45.455 0.00 0.00 0.00 2.73
3372 3628 2.164219 GGTGGCATGTGTGAAAGGTATG 59.836 50.000 0.00 0.00 0.00 2.39
3373 3629 2.164219 GTGGCATGTGTGAAAGGTATGG 59.836 50.000 0.00 0.00 0.00 2.74
3374 3630 2.224992 TGGCATGTGTGAAAGGTATGGT 60.225 45.455 0.00 0.00 0.00 3.55
3375 3631 2.825532 GGCATGTGTGAAAGGTATGGTT 59.174 45.455 0.00 0.00 0.00 3.67
3376 3632 4.013728 GGCATGTGTGAAAGGTATGGTTA 58.986 43.478 0.00 0.00 0.00 2.85
3377 3633 4.644685 GGCATGTGTGAAAGGTATGGTTAT 59.355 41.667 0.00 0.00 0.00 1.89
3378 3634 5.825679 GGCATGTGTGAAAGGTATGGTTATA 59.174 40.000 0.00 0.00 0.00 0.98
3379 3635 6.490040 GGCATGTGTGAAAGGTATGGTTATAT 59.510 38.462 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.348476 TGCCATGCTAAAGTTATACAATATGAA 57.652 29.630 0.00 0.00 0.00 2.57
19 20 8.916628 TGCCATGCTAAAGTTATACAATATGA 57.083 30.769 0.00 0.00 0.00 2.15
20 21 9.964303 TTTGCCATGCTAAAGTTATACAATATG 57.036 29.630 0.00 0.00 0.00 1.78
22 23 9.964303 CATTTGCCATGCTAAAGTTATACAATA 57.036 29.630 0.00 0.00 0.00 1.90
23 24 8.477256 ACATTTGCCATGCTAAAGTTATACAAT 58.523 29.630 0.00 0.00 0.00 2.71
24 25 7.835822 ACATTTGCCATGCTAAAGTTATACAA 58.164 30.769 0.00 0.00 0.00 2.41
25 26 7.403312 ACATTTGCCATGCTAAAGTTATACA 57.597 32.000 0.00 0.00 0.00 2.29
26 27 7.973388 TCAACATTTGCCATGCTAAAGTTATAC 59.027 33.333 4.21 0.00 34.41 1.47
27 28 8.060931 TCAACATTTGCCATGCTAAAGTTATA 57.939 30.769 4.21 0.00 34.41 0.98
28 29 6.934056 TCAACATTTGCCATGCTAAAGTTAT 58.066 32.000 4.21 0.00 34.41 1.89
29 30 6.338214 TCAACATTTGCCATGCTAAAGTTA 57.662 33.333 4.21 0.00 34.41 2.24
30 31 5.212532 TCAACATTTGCCATGCTAAAGTT 57.787 34.783 0.00 0.00 36.19 2.66
31 32 4.870123 TCAACATTTGCCATGCTAAAGT 57.130 36.364 0.00 0.00 28.32 2.66
32 33 8.428186 AAATATCAACATTTGCCATGCTAAAG 57.572 30.769 0.00 0.00 0.00 1.85
33 34 8.789825 AAAATATCAACATTTGCCATGCTAAA 57.210 26.923 0.00 0.00 0.00 1.85
34 35 8.789825 AAAAATATCAACATTTGCCATGCTAA 57.210 26.923 0.00 0.00 0.00 3.09
60 61 9.438228 TCACAAAGTTTGACCGTATTTATATGA 57.562 29.630 22.23 7.49 0.00 2.15
63 64 9.275398 ACTTCACAAAGTTTGACCGTATTTATA 57.725 29.630 22.23 0.00 43.28 0.98
64 65 8.161699 ACTTCACAAAGTTTGACCGTATTTAT 57.838 30.769 22.23 0.00 43.28 1.40
65 66 7.556733 ACTTCACAAAGTTTGACCGTATTTA 57.443 32.000 22.23 0.00 43.28 1.40
66 67 6.445357 ACTTCACAAAGTTTGACCGTATTT 57.555 33.333 22.23 0.00 43.28 1.40
88 89 9.928236 GCATATTAGAATTCTCTGAAGTCAAAC 57.072 33.333 12.24 0.00 32.70 2.93
89 90 9.671279 TGCATATTAGAATTCTCTGAAGTCAAA 57.329 29.630 12.24 0.00 32.70 2.69
90 91 9.322773 CTGCATATTAGAATTCTCTGAAGTCAA 57.677 33.333 12.24 0.00 32.70 3.18
91 92 8.699130 TCTGCATATTAGAATTCTCTGAAGTCA 58.301 33.333 12.24 3.02 32.70 3.41
92 93 9.195411 CTCTGCATATTAGAATTCTCTGAAGTC 57.805 37.037 12.24 0.25 32.70 3.01
93 94 8.703743 ACTCTGCATATTAGAATTCTCTGAAGT 58.296 33.333 12.24 7.56 32.70 3.01
104 105 8.826710 CGGTCATTTTTACTCTGCATATTAGAA 58.173 33.333 0.00 0.00 0.00 2.10
105 106 7.441157 CCGGTCATTTTTACTCTGCATATTAGA 59.559 37.037 0.00 0.00 0.00 2.10
106 107 7.441157 TCCGGTCATTTTTACTCTGCATATTAG 59.559 37.037 0.00 0.00 0.00 1.73
107 108 7.276658 TCCGGTCATTTTTACTCTGCATATTA 58.723 34.615 0.00 0.00 0.00 0.98
108 109 6.119536 TCCGGTCATTTTTACTCTGCATATT 58.880 36.000 0.00 0.00 0.00 1.28
109 110 5.680619 TCCGGTCATTTTTACTCTGCATAT 58.319 37.500 0.00 0.00 0.00 1.78
110 111 5.092554 TCCGGTCATTTTTACTCTGCATA 57.907 39.130 0.00 0.00 0.00 3.14
111 112 3.941483 CTCCGGTCATTTTTACTCTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
112 113 3.334691 CTCCGGTCATTTTTACTCTGCA 58.665 45.455 0.00 0.00 0.00 4.41
113 114 2.678336 CCTCCGGTCATTTTTACTCTGC 59.322 50.000 0.00 0.00 0.00 4.26
114 115 3.055385 TCCCTCCGGTCATTTTTACTCTG 60.055 47.826 0.00 0.00 0.00 3.35
115 116 3.178865 TCCCTCCGGTCATTTTTACTCT 58.821 45.455 0.00 0.00 0.00 3.24
116 117 3.055312 ACTCCCTCCGGTCATTTTTACTC 60.055 47.826 0.00 0.00 0.00 2.59
117 118 2.910977 ACTCCCTCCGGTCATTTTTACT 59.089 45.455 0.00 0.00 0.00 2.24
118 119 3.345508 ACTCCCTCCGGTCATTTTTAC 57.654 47.619 0.00 0.00 0.00 2.01
119 120 4.472108 ACATACTCCCTCCGGTCATTTTTA 59.528 41.667 0.00 0.00 0.00 1.52
120 121 3.265995 ACATACTCCCTCCGGTCATTTTT 59.734 43.478 0.00 0.00 0.00 1.94
121 122 2.844348 ACATACTCCCTCCGGTCATTTT 59.156 45.455 0.00 0.00 0.00 1.82
122 123 2.434702 GACATACTCCCTCCGGTCATTT 59.565 50.000 0.00 0.00 0.00 2.32
123 124 2.040178 GACATACTCCCTCCGGTCATT 58.960 52.381 0.00 0.00 0.00 2.57
124 125 1.218196 AGACATACTCCCTCCGGTCAT 59.782 52.381 0.00 0.00 0.00 3.06
125 126 0.629596 AGACATACTCCCTCCGGTCA 59.370 55.000 0.00 0.00 0.00 4.02
126 127 1.777941 AAGACATACTCCCTCCGGTC 58.222 55.000 0.00 0.00 0.00 4.79
127 128 3.614568 ATAAGACATACTCCCTCCGGT 57.385 47.619 0.00 0.00 0.00 5.28
128 129 4.664392 AGTATAAGACATACTCCCTCCGG 58.336 47.826 0.00 0.00 29.47 5.14
129 130 4.392445 CGAGTATAAGACATACTCCCTCCG 59.608 50.000 15.36 4.28 44.58 4.63
130 131 4.156373 GCGAGTATAAGACATACTCCCTCC 59.844 50.000 15.36 2.79 44.58 4.30
131 132 4.760715 TGCGAGTATAAGACATACTCCCTC 59.239 45.833 15.36 8.15 44.58 4.30
132 133 4.726583 TGCGAGTATAAGACATACTCCCT 58.273 43.478 15.36 0.00 44.58 4.20
133 134 5.646577 ATGCGAGTATAAGACATACTCCC 57.353 43.478 15.36 9.44 44.58 4.30
134 135 7.948278 AAAATGCGAGTATAAGACATACTCC 57.052 36.000 15.36 10.42 44.58 3.85
135 136 9.031360 TCAAAAATGCGAGTATAAGACATACTC 57.969 33.333 12.41 12.41 44.19 2.59
136 137 8.942338 TCAAAAATGCGAGTATAAGACATACT 57.058 30.769 0.00 0.00 37.53 2.12
137 138 9.422196 GTTCAAAAATGCGAGTATAAGACATAC 57.578 33.333 0.00 0.00 0.00 2.39
138 139 9.157104 TGTTCAAAAATGCGAGTATAAGACATA 57.843 29.630 0.00 0.00 0.00 2.29
139 140 8.039603 TGTTCAAAAATGCGAGTATAAGACAT 57.960 30.769 0.00 0.00 0.00 3.06
140 141 7.428282 TGTTCAAAAATGCGAGTATAAGACA 57.572 32.000 0.00 0.00 0.00 3.41
141 142 8.722342 TTTGTTCAAAAATGCGAGTATAAGAC 57.278 30.769 0.00 0.00 0.00 3.01
142 143 8.020819 CCTTTGTTCAAAAATGCGAGTATAAGA 58.979 33.333 0.00 0.00 0.00 2.10
143 144 7.273381 CCCTTTGTTCAAAAATGCGAGTATAAG 59.727 37.037 0.00 0.00 0.00 1.73
144 145 7.040340 TCCCTTTGTTCAAAAATGCGAGTATAA 60.040 33.333 0.00 0.00 0.00 0.98
145 146 6.431543 TCCCTTTGTTCAAAAATGCGAGTATA 59.568 34.615 0.00 0.00 0.00 1.47
146 147 5.242838 TCCCTTTGTTCAAAAATGCGAGTAT 59.757 36.000 0.00 0.00 0.00 2.12
147 148 4.580995 TCCCTTTGTTCAAAAATGCGAGTA 59.419 37.500 0.00 0.00 0.00 2.59
148 149 3.383185 TCCCTTTGTTCAAAAATGCGAGT 59.617 39.130 0.00 0.00 0.00 4.18
149 150 3.976169 TCCCTTTGTTCAAAAATGCGAG 58.024 40.909 0.00 0.00 0.00 5.03
150 151 3.383185 ACTCCCTTTGTTCAAAAATGCGA 59.617 39.130 0.00 0.00 0.00 5.10
151 152 3.716601 ACTCCCTTTGTTCAAAAATGCG 58.283 40.909 0.00 0.00 0.00 4.73
152 153 5.842907 AGTACTCCCTTTGTTCAAAAATGC 58.157 37.500 0.00 0.00 0.00 3.56
153 154 7.230712 AGGTAGTACTCCCTTTGTTCAAAAATG 59.769 37.037 0.11 0.00 0.00 2.32
154 155 7.295340 AGGTAGTACTCCCTTTGTTCAAAAAT 58.705 34.615 0.11 0.00 0.00 1.82
155 156 6.665695 AGGTAGTACTCCCTTTGTTCAAAAA 58.334 36.000 0.11 0.00 0.00 1.94
156 157 6.256643 AGGTAGTACTCCCTTTGTTCAAAA 57.743 37.500 0.11 0.00 0.00 2.44
157 158 5.899631 AGGTAGTACTCCCTTTGTTCAAA 57.100 39.130 0.11 0.00 0.00 2.69
158 159 6.519551 GCTTAGGTAGTACTCCCTTTGTTCAA 60.520 42.308 12.85 0.00 32.08 2.69
159 160 5.046807 GCTTAGGTAGTACTCCCTTTGTTCA 60.047 44.000 12.85 0.00 32.08 3.18
160 161 5.187381 AGCTTAGGTAGTACTCCCTTTGTTC 59.813 44.000 12.85 0.00 32.08 3.18
161 162 5.092259 AGCTTAGGTAGTACTCCCTTTGTT 58.908 41.667 12.85 1.58 32.08 2.83
162 163 4.685807 AGCTTAGGTAGTACTCCCTTTGT 58.314 43.478 12.85 0.00 32.08 2.83
163 164 6.980416 ATAGCTTAGGTAGTACTCCCTTTG 57.020 41.667 12.85 7.13 32.08 2.77
164 165 8.288081 AGTAATAGCTTAGGTAGTACTCCCTTT 58.712 37.037 20.96 2.41 41.37 3.11
165 166 7.824671 AGTAATAGCTTAGGTAGTACTCCCTT 58.175 38.462 20.96 0.00 41.37 3.95
166 167 7.405228 AGTAATAGCTTAGGTAGTACTCCCT 57.595 40.000 20.96 12.22 41.37 4.20
167 168 9.752228 AATAGTAATAGCTTAGGTAGTACTCCC 57.248 37.037 27.11 0.00 41.37 4.30
343 344 0.033991 GAAGAAGGGGAGGGGAAAGC 60.034 60.000 0.00 0.00 0.00 3.51
344 345 1.562008 GAGAAGAAGGGGAGGGGAAAG 59.438 57.143 0.00 0.00 0.00 2.62
345 346 1.670059 GAGAAGAAGGGGAGGGGAAA 58.330 55.000 0.00 0.00 0.00 3.13
346 347 0.617820 CGAGAAGAAGGGGAGGGGAA 60.618 60.000 0.00 0.00 0.00 3.97
347 348 1.001760 CGAGAAGAAGGGGAGGGGA 59.998 63.158 0.00 0.00 0.00 4.81
349 350 1.044611 GATCGAGAAGAAGGGGAGGG 58.955 60.000 0.00 0.00 0.00 4.30
406 424 2.321719 TGTGCTTGTGGGTCTGTAGTA 58.678 47.619 0.00 0.00 0.00 1.82
407 425 1.128200 TGTGCTTGTGGGTCTGTAGT 58.872 50.000 0.00 0.00 0.00 2.73
408 426 2.254546 TTGTGCTTGTGGGTCTGTAG 57.745 50.000 0.00 0.00 0.00 2.74
681 704 4.679662 ACGTACAGGGAATATTTCAGTCG 58.320 43.478 0.00 3.42 0.00 4.18
726 749 1.336755 GAGACGGAGAATGGAGAGAGC 59.663 57.143 0.00 0.00 0.00 4.09
766 789 2.467566 ATAGAACTTTGGGAACGCGT 57.532 45.000 5.58 5.58 0.00 6.01
793 820 1.664151 GCTACATACACGTGCTTTCCC 59.336 52.381 17.22 0.00 0.00 3.97
807 834 4.278669 CGGAGATACAACCTACAGCTACAT 59.721 45.833 0.00 0.00 0.00 2.29
808 835 3.630769 CGGAGATACAACCTACAGCTACA 59.369 47.826 0.00 0.00 0.00 2.74
809 836 3.881688 TCGGAGATACAACCTACAGCTAC 59.118 47.826 0.00 0.00 0.00 3.58
810 837 4.160642 TCGGAGATACAACCTACAGCTA 57.839 45.455 0.00 0.00 0.00 3.32
953 980 1.147473 GGAAGGCAACAAATTTGCGG 58.853 50.000 18.12 11.21 45.78 5.69
1578 1606 1.592669 CATGTCGATGAGGGTCGGC 60.593 63.158 0.00 0.00 45.83 5.54
1644 1672 4.758251 CCGCTGCACCCGACATCA 62.758 66.667 0.00 0.00 0.00 3.07
1905 1933 1.154188 GAGCGAGACCGACTGTGTC 60.154 63.158 0.00 0.00 38.22 3.67
1974 2002 2.892425 GCATCCTCTTCGGCCACG 60.892 66.667 2.24 0.00 42.74 4.94
2331 2359 1.826487 AACGTTGTGCCCCTTCCAC 60.826 57.895 0.00 0.00 0.00 4.02
2405 2433 5.056480 CACACTCACTTACCTTGTCAATCA 58.944 41.667 0.00 0.00 0.00 2.57
2407 2435 5.036117 ACACACTCACTTACCTTGTCAAT 57.964 39.130 0.00 0.00 0.00 2.57
2418 2446 3.306780 GGCATACACCTACACACTCACTT 60.307 47.826 0.00 0.00 0.00 3.16
2581 2609 6.327934 TCTTCTACGGTGTATTTGTAAGAGC 58.672 40.000 0.00 0.00 0.00 4.09
2586 2614 8.089597 TGTTCATTCTTCTACGGTGTATTTGTA 58.910 33.333 0.00 0.00 0.00 2.41
2753 2797 5.163509 GGAAAGCTTCATTTGGTCCTTATCC 60.164 44.000 0.00 0.00 0.00 2.59
2797 2841 9.261180 TCGATCAGTCACCAAAATATATTCTTC 57.739 33.333 0.00 0.00 0.00 2.87
2816 2860 2.288702 CCCTAACCTCAGCATCGATCAG 60.289 54.545 0.00 0.00 0.00 2.90
2850 2894 5.776716 AGATTTGTCAAGGTCCACATTCAAT 59.223 36.000 0.00 0.00 0.00 2.57
2916 2976 8.370940 TGGGCACATTTCTACAATAAAATTTCA 58.629 29.630 0.00 0.00 0.00 2.69
2956 3208 4.219944 TGAGCACGATTACTAACACTCCTT 59.780 41.667 0.00 0.00 0.00 3.36
2960 3212 5.324784 TCATGAGCACGATTACTAACACT 57.675 39.130 0.00 0.00 0.00 3.55
2961 3213 5.627802 CTCATGAGCACGATTACTAACAC 57.372 43.478 10.38 0.00 0.00 3.32
2992 3244 7.148154 TGCCTTGCATGTATACGATTACTTTTT 60.148 33.333 0.00 0.00 31.71 1.94
2993 3245 6.317642 TGCCTTGCATGTATACGATTACTTTT 59.682 34.615 0.00 0.00 31.71 2.27
2994 3246 5.820423 TGCCTTGCATGTATACGATTACTTT 59.180 36.000 0.00 0.00 31.71 2.66
2995 3247 5.236478 GTGCCTTGCATGTATACGATTACTT 59.764 40.000 0.00 0.00 41.91 2.24
3005 3257 0.035534 TGGTCGTGCCTTGCATGTAT 60.036 50.000 8.04 0.00 44.84 2.29
3015 3267 2.604174 CCGTCAAACTGGTCGTGCC 61.604 63.158 0.00 0.00 37.90 5.01
3061 3317 8.195436 AGCAATTAATCTTGGAATCAACATCAG 58.805 33.333 0.00 0.00 0.00 2.90
3063 3319 8.937634 AAGCAATTAATCTTGGAATCAACATC 57.062 30.769 0.00 0.00 0.00 3.06
3193 3449 4.218635 TCTGAGCGATCCAACCATCTATAC 59.781 45.833 0.00 0.00 0.00 1.47
3209 3465 3.003068 GGTGAATCCAAATGATCTGAGCG 59.997 47.826 0.00 0.00 35.97 5.03
3276 3532 9.428097 GCTCAGATTTATTTTGGATGTTTTCTT 57.572 29.630 0.00 0.00 0.00 2.52
3277 3533 8.810041 AGCTCAGATTTATTTTGGATGTTTTCT 58.190 29.630 0.00 0.00 0.00 2.52
3278 3534 8.866956 CAGCTCAGATTTATTTTGGATGTTTTC 58.133 33.333 0.00 0.00 0.00 2.29
3279 3535 8.587608 TCAGCTCAGATTTATTTTGGATGTTTT 58.412 29.630 0.00 0.00 0.00 2.43
3280 3536 8.125978 TCAGCTCAGATTTATTTTGGATGTTT 57.874 30.769 0.00 0.00 0.00 2.83
3281 3537 7.395489 ACTCAGCTCAGATTTATTTTGGATGTT 59.605 33.333 0.00 0.00 0.00 2.71
3282 3538 6.888632 ACTCAGCTCAGATTTATTTTGGATGT 59.111 34.615 0.00 0.00 0.00 3.06
3283 3539 7.194278 CACTCAGCTCAGATTTATTTTGGATG 58.806 38.462 0.00 0.00 0.00 3.51
3284 3540 6.320672 CCACTCAGCTCAGATTTATTTTGGAT 59.679 38.462 0.00 0.00 0.00 3.41
3285 3541 5.649395 CCACTCAGCTCAGATTTATTTTGGA 59.351 40.000 0.00 0.00 0.00 3.53
3286 3542 5.416952 ACCACTCAGCTCAGATTTATTTTGG 59.583 40.000 0.00 0.00 0.00 3.28
3287 3543 6.072286 ACACCACTCAGCTCAGATTTATTTTG 60.072 38.462 0.00 0.00 0.00 2.44
3288 3544 6.006449 ACACCACTCAGCTCAGATTTATTTT 58.994 36.000 0.00 0.00 0.00 1.82
3289 3545 5.564550 ACACCACTCAGCTCAGATTTATTT 58.435 37.500 0.00 0.00 0.00 1.40
3290 3546 5.171339 ACACCACTCAGCTCAGATTTATT 57.829 39.130 0.00 0.00 0.00 1.40
3291 3547 4.833478 ACACCACTCAGCTCAGATTTAT 57.167 40.909 0.00 0.00 0.00 1.40
3292 3548 4.623932 AACACCACTCAGCTCAGATTTA 57.376 40.909 0.00 0.00 0.00 1.40
3293 3549 3.498774 AACACCACTCAGCTCAGATTT 57.501 42.857 0.00 0.00 0.00 2.17
3294 3550 3.498774 AAACACCACTCAGCTCAGATT 57.501 42.857 0.00 0.00 0.00 2.40
3295 3551 4.833478 ATAAACACCACTCAGCTCAGAT 57.167 40.909 0.00 0.00 0.00 2.90
3296 3552 4.623932 AATAAACACCACTCAGCTCAGA 57.376 40.909 0.00 0.00 0.00 3.27
3297 3553 4.999950 AGAAATAAACACCACTCAGCTCAG 59.000 41.667 0.00 0.00 0.00 3.35
3298 3554 4.973168 AGAAATAAACACCACTCAGCTCA 58.027 39.130 0.00 0.00 0.00 4.26
3299 3555 4.997395 TGAGAAATAAACACCACTCAGCTC 59.003 41.667 0.00 0.00 32.04 4.09
3300 3556 4.973168 TGAGAAATAAACACCACTCAGCT 58.027 39.130 0.00 0.00 32.04 4.24
3301 3557 5.886960 ATGAGAAATAAACACCACTCAGC 57.113 39.130 0.00 0.00 37.70 4.26
3302 3558 7.175641 AGGAAATGAGAAATAAACACCACTCAG 59.824 37.037 0.00 0.00 37.70 3.35
3303 3559 7.004086 AGGAAATGAGAAATAAACACCACTCA 58.996 34.615 0.00 0.00 38.44 3.41
3304 3560 7.454260 AGGAAATGAGAAATAAACACCACTC 57.546 36.000 0.00 0.00 0.00 3.51
3305 3561 7.661040 CAAGGAAATGAGAAATAAACACCACT 58.339 34.615 0.00 0.00 0.00 4.00
3306 3562 6.366061 GCAAGGAAATGAGAAATAAACACCAC 59.634 38.462 0.00 0.00 0.00 4.16
3307 3563 6.454795 GCAAGGAAATGAGAAATAAACACCA 58.545 36.000 0.00 0.00 0.00 4.17
3308 3564 5.869344 GGCAAGGAAATGAGAAATAAACACC 59.131 40.000 0.00 0.00 0.00 4.16
3309 3565 6.691508 AGGCAAGGAAATGAGAAATAAACAC 58.308 36.000 0.00 0.00 0.00 3.32
3310 3566 6.916360 AGGCAAGGAAATGAGAAATAAACA 57.084 33.333 0.00 0.00 0.00 2.83
3311 3567 9.875691 AAATAGGCAAGGAAATGAGAAATAAAC 57.124 29.630 0.00 0.00 0.00 2.01
3313 3569 9.253832 TGAAATAGGCAAGGAAATGAGAAATAA 57.746 29.630 0.00 0.00 0.00 1.40
3314 3570 8.686334 GTGAAATAGGCAAGGAAATGAGAAATA 58.314 33.333 0.00 0.00 0.00 1.40
3315 3571 7.364144 GGTGAAATAGGCAAGGAAATGAGAAAT 60.364 37.037 0.00 0.00 0.00 2.17
3316 3572 6.071391 GGTGAAATAGGCAAGGAAATGAGAAA 60.071 38.462 0.00 0.00 0.00 2.52
3317 3573 5.418840 GGTGAAATAGGCAAGGAAATGAGAA 59.581 40.000 0.00 0.00 0.00 2.87
3318 3574 4.949856 GGTGAAATAGGCAAGGAAATGAGA 59.050 41.667 0.00 0.00 0.00 3.27
3319 3575 4.098501 GGGTGAAATAGGCAAGGAAATGAG 59.901 45.833 0.00 0.00 0.00 2.90
3320 3576 4.023291 GGGTGAAATAGGCAAGGAAATGA 58.977 43.478 0.00 0.00 0.00 2.57
3321 3577 3.768757 TGGGTGAAATAGGCAAGGAAATG 59.231 43.478 0.00 0.00 0.00 2.32
3322 3578 4.059773 TGGGTGAAATAGGCAAGGAAAT 57.940 40.909 0.00 0.00 0.00 2.17
3323 3579 3.534357 TGGGTGAAATAGGCAAGGAAA 57.466 42.857 0.00 0.00 0.00 3.13
3324 3580 3.534357 TTGGGTGAAATAGGCAAGGAA 57.466 42.857 0.00 0.00 0.00 3.36
3325 3581 3.534357 TTTGGGTGAAATAGGCAAGGA 57.466 42.857 0.00 0.00 0.00 3.36
3326 3582 6.484364 AATATTTGGGTGAAATAGGCAAGG 57.516 37.500 0.00 0.00 39.40 3.61
3327 3583 7.287696 ACCTAATATTTGGGTGAAATAGGCAAG 59.712 37.037 18.42 0.00 43.54 4.01
3328 3584 7.129425 ACCTAATATTTGGGTGAAATAGGCAA 58.871 34.615 18.42 0.00 43.54 4.52
3329 3585 6.678547 ACCTAATATTTGGGTGAAATAGGCA 58.321 36.000 18.42 0.00 43.54 4.75
3339 3595 3.960102 CACATGCCACCTAATATTTGGGT 59.040 43.478 18.42 12.47 46.45 4.51
3340 3596 3.960102 ACACATGCCACCTAATATTTGGG 59.040 43.478 18.42 11.91 37.31 4.12
3341 3597 4.644234 TCACACATGCCACCTAATATTTGG 59.356 41.667 13.59 13.59 0.00 3.28
3342 3598 5.833406 TCACACATGCCACCTAATATTTG 57.167 39.130 0.00 0.00 0.00 2.32
3343 3599 6.127366 CCTTTCACACATGCCACCTAATATTT 60.127 38.462 0.00 0.00 0.00 1.40
3344 3600 5.360714 CCTTTCACACATGCCACCTAATATT 59.639 40.000 0.00 0.00 0.00 1.28
3345 3601 4.889409 CCTTTCACACATGCCACCTAATAT 59.111 41.667 0.00 0.00 0.00 1.28
3346 3602 4.263727 ACCTTTCACACATGCCACCTAATA 60.264 41.667 0.00 0.00 0.00 0.98
3347 3603 3.091545 CCTTTCACACATGCCACCTAAT 58.908 45.455 0.00 0.00 0.00 1.73
3348 3604 2.158534 ACCTTTCACACATGCCACCTAA 60.159 45.455 0.00 0.00 0.00 2.69
3349 3605 1.423541 ACCTTTCACACATGCCACCTA 59.576 47.619 0.00 0.00 0.00 3.08
3350 3606 0.185901 ACCTTTCACACATGCCACCT 59.814 50.000 0.00 0.00 0.00 4.00
3351 3607 1.904287 TACCTTTCACACATGCCACC 58.096 50.000 0.00 0.00 0.00 4.61
3352 3608 2.164219 CCATACCTTTCACACATGCCAC 59.836 50.000 0.00 0.00 0.00 5.01
3353 3609 2.224992 ACCATACCTTTCACACATGCCA 60.225 45.455 0.00 0.00 0.00 4.92
3354 3610 2.446435 ACCATACCTTTCACACATGCC 58.554 47.619 0.00 0.00 0.00 4.40
3355 3611 5.835113 ATAACCATACCTTTCACACATGC 57.165 39.130 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.