Multiple sequence alignment - TraesCS6A01G118800

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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 TraesCS6A01G118800 chr6A 100.000 5141 0 0 1 5141 89891057 89896197 0.000000e+00 9494
1 TraesCS6A01G118800 chr6B 94.386 2547 97 22 605 3130 147677290 147679811 0.000000e+00 3869
2 TraesCS6A01G118800 chr6B 91.362 1887 97 28 3292 5141 147679812 147681669 0.000000e+00 2521
3 TraesCS6A01G118800 chr6D 95.022 2310 88 10 7 2296 73494639 73496941 0.000000e+00 3603
4 TraesCS6A01G118800 chr6D 93.085 1880 69 27 3292 5141 73497804 73499652 0.000000e+00 2695
5 TraesCS6A01G118800 chr6D 96.420 866 29 2 2266 3130 73496939 73497803 0.000000e+00 1426
6 TraesCS6A01G118800 chr3B 92.720 261 16 1 3518 3775 480376942 480377202 1.750000e-99 374
7 TraesCS6A01G118800 chr3A 92.720 261 16 3 3518 3775 76648141 76648401 1.750000e-99 374
8 TraesCS6A01G118800 chr3A 86.982 169 16 5 2562 2727 54660383 54660218 8.790000e-43 185
9 TraesCS6A01G118800 chr2B 92.395 263 17 1 3518 3777 42029561 42029823 6.290000e-99 372
10 TraesCS6A01G118800 chr2B 85.311 177 21 5 2547 2721 474614359 474614532 1.470000e-40 178
11 TraesCS6A01G118800 chr4B 91.791 268 18 2 3515 3778 438146336 438146069 2.260000e-98 370
12 TraesCS6A01G118800 chr1D 92.664 259 16 1 3518 3773 380609761 380610019 2.260000e-98 370
13 TraesCS6A01G118800 chr5D 91.241 274 19 3 3514 3784 517961359 517961088 8.130000e-98 368
14 TraesCS6A01G118800 chr5D 88.344 163 16 3 2562 2722 443898154 443898315 5.250000e-45 193
15 TraesCS6A01G118800 chr7D 88.776 294 25 6 3516 3805 164087472 164087183 2.280000e-93 353
16 TraesCS6A01G118800 chr5A 88.889 162 17 1 2562 2722 382336466 382336305 1.130000e-46 198
17 TraesCS6A01G118800 chr2A 87.879 165 14 5 2562 2722 218122410 218122248 6.800000e-44 189
18 TraesCS6A01G118800 chr2A 87.349 166 17 4 2562 2726 32548112 32548274 2.440000e-43 187
19 TraesCS6A01G118800 chr2D 87.654 162 18 2 2562 2722 22200812 22200972 2.440000e-43 187


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 TraesCS6A01G118800 chr6A 89891057 89896197 5140 False 9494.000000 9494 100.000000 1 5141 1 chr6A.!!$F1 5140
1 TraesCS6A01G118800 chr6B 147677290 147681669 4379 False 3195.000000 3869 92.874000 605 5141 2 chr6B.!!$F1 4536
2 TraesCS6A01G118800 chr6D 73494639 73499652 5013 False 2574.666667 3603 94.842333 7 5141 3 chr6D.!!$F1 5134

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
592 603 0.036010 CGGAAGCTCAGTGGTGGAAT 60.036 55.0 0.00 0.0 0.00 3.01 F
689 700 1.232119 GGTGTGTTTGTAAGGACCCG 58.768 55.0 0.00 0.0 0.00 5.28 F
1422 1450 1.880271 TCGTCTTCGAGTCTGTGTCT 58.120 50.0 0.00 0.0 41.35 3.41 F
2826 2887 0.840722 ACCGGATGGACCAAGGACTT 60.841 55.0 9.46 0.0 39.21 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1765 0.320374 TTTCGCGGAACCTCATCAGT 59.680 50.0 6.13 0.0 0.00 3.41 R
1979 2011 0.967380 CTTCCACTGCACCCCAATCC 60.967 60.0 0.00 0.0 0.00 3.01 R
2926 2987 0.321122 GAGCCTGCTGTAGTGCTGTT 60.321 55.0 11.94 0.0 34.43 3.16 R
4166 4232 0.534877 ACTCCATGACAAACGCAGCA 60.535 50.0 0.00 0.0 0.00 4.41 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
23 24 1.673168 GAGGAGCTGGTTGGCTATTG 58.327 55.000 0.00 0.00 43.20 1.90
24 25 1.210478 GAGGAGCTGGTTGGCTATTGA 59.790 52.381 0.00 0.00 43.20 2.57
25 26 1.635487 AGGAGCTGGTTGGCTATTGAA 59.365 47.619 0.00 0.00 43.20 2.69
34 35 1.448985 TGGCTATTGAAGGACAACGC 58.551 50.000 0.00 0.00 41.52 4.84
42 43 1.845809 GAAGGACAACGCCAGTGCTG 61.846 60.000 0.00 0.00 37.74 4.41
78 79 1.369091 GACAGGCGATGTTTGGCGAT 61.369 55.000 0.00 0.00 44.17 4.58
119 120 1.448013 GCGACTTGGCTAGGTCACC 60.448 63.158 12.73 0.00 33.19 4.02
121 122 1.874345 CGACTTGGCTAGGTCACCGT 61.874 60.000 12.73 0.00 33.19 4.83
158 159 1.409064 GCATGGTCCTAGATGACGACA 59.591 52.381 0.00 0.00 36.07 4.35
169 170 3.401577 TGACGACAAGCTCGACATC 57.598 52.632 0.37 0.00 46.14 3.06
174 175 1.263776 GACAAGCTCGACATCAGACG 58.736 55.000 0.00 0.00 0.00 4.18
180 181 0.179161 CTCGACATCAGACGTGGACC 60.179 60.000 0.00 0.00 34.59 4.46
191 192 2.594962 CGTGGACCTGTCGTGCAAC 61.595 63.158 0.00 0.00 45.31 4.17
212 213 5.766150 ACGACATGGATGTTTTTCTTCAA 57.234 34.783 0.00 0.00 41.95 2.69
247 248 3.031013 ACTCTTCAAGTTTGGTTTGGGG 58.969 45.455 0.00 0.00 33.03 4.96
252 253 2.035632 CAAGTTTGGTTTGGGGTAGCA 58.964 47.619 0.00 0.00 0.00 3.49
254 255 2.036387 AGTTTGGTTTGGGGTAGCAAC 58.964 47.619 0.00 0.00 33.21 4.17
270 271 0.365523 CAACGCAACGACACTATCCG 59.634 55.000 0.00 0.00 0.00 4.18
280 281 4.037690 ACGACACTATCCGCGTATAAAAC 58.962 43.478 4.92 0.00 34.93 2.43
319 330 2.066262 GTTGGTGTGTTCGTCATCGAT 58.934 47.619 0.00 0.00 45.65 3.59
322 333 1.403647 GGTGTGTTCGTCATCGATGGA 60.404 52.381 24.61 12.50 45.65 3.41
332 343 0.462581 CATCGATGGAGGGTGTGTGG 60.463 60.000 17.96 0.00 0.00 4.17
385 396 4.634443 CCGATTGGTTTAGGTTTCTAGTGG 59.366 45.833 0.00 0.00 0.00 4.00
388 399 6.258068 CGATTGGTTTAGGTTTCTAGTGGATC 59.742 42.308 0.00 0.00 0.00 3.36
420 431 6.753897 TTCGACATACATTCATGATCTTCG 57.246 37.500 0.00 0.00 0.00 3.79
463 474 0.602905 CCTTTTCGTCTCCAAGGCGT 60.603 55.000 0.51 0.00 44.83 5.68
513 524 3.027412 ACTTCTCCTAGTGTGCATCGAT 58.973 45.455 0.00 0.00 0.00 3.59
537 548 3.985925 ACTTTTCAGCCGTTACTTCTACG 59.014 43.478 0.00 0.00 38.67 3.51
541 552 2.417933 TCAGCCGTTACTTCTACGAGTC 59.582 50.000 0.00 0.00 41.33 3.36
561 572 5.924356 AGTCCTTGGGGTTTAAAATGTTTG 58.076 37.500 0.00 0.00 0.00 2.93
566 577 3.970640 TGGGGTTTAAAATGTTTGCTCCT 59.029 39.130 0.00 0.00 0.00 3.69
572 583 7.090808 GGTTTAAAATGTTTGCTCCTCTAAGG 58.909 38.462 0.00 0.00 36.46 2.69
592 603 0.036010 CGGAAGCTCAGTGGTGGAAT 60.036 55.000 0.00 0.00 0.00 3.01
619 630 3.719268 TTGCTATGCAGGAGGAAGAAA 57.281 42.857 1.74 0.00 40.61 2.52
635 646 2.807676 AGAAAATTTCGGCACCCTCAT 58.192 42.857 0.00 0.00 34.02 2.90
689 700 1.232119 GGTGTGTTTGTAAGGACCCG 58.768 55.000 0.00 0.00 0.00 5.28
698 709 3.880047 TGTAAGGACCCGTGATACTTG 57.120 47.619 0.00 0.00 0.00 3.16
702 713 4.667519 AAGGACCCGTGATACTTGATAC 57.332 45.455 0.00 0.00 0.00 2.24
706 717 6.017192 AGGACCCGTGATACTTGATACATAT 58.983 40.000 0.00 0.00 0.00 1.78
708 719 7.839705 AGGACCCGTGATACTTGATACATATAT 59.160 37.037 0.00 0.00 0.00 0.86
709 720 7.921214 GGACCCGTGATACTTGATACATATATG 59.079 40.741 11.29 11.29 0.00 1.78
710 721 8.589701 ACCCGTGATACTTGATACATATATGA 57.410 34.615 19.63 3.73 0.00 2.15
711 722 8.467598 ACCCGTGATACTTGATACATATATGAC 58.532 37.037 19.63 10.23 0.00 3.06
713 724 8.687242 CCGTGATACTTGATACATATATGACCT 58.313 37.037 19.63 3.21 0.00 3.85
721 732 8.621532 TTGATACATATATGACCTTGCCTTTC 57.378 34.615 19.63 0.42 0.00 2.62
1290 1318 4.162690 ATGGACGAGGAAGGCGCC 62.163 66.667 21.89 21.89 0.00 6.53
1422 1450 1.880271 TCGTCTTCGAGTCTGTGTCT 58.120 50.000 0.00 0.00 41.35 3.41
1464 1492 2.692041 CTGATCCCTTCCCTGCAAATTC 59.308 50.000 0.00 0.00 0.00 2.17
1522 1550 8.093927 TGGAAATGAATCCTTTGATTTGGTAAC 58.906 33.333 0.00 0.00 41.30 2.50
1649 1677 5.181009 TCTCTTGGTGAGCTGTATCATTTG 58.819 41.667 0.00 0.00 42.38 2.32
1695 1723 3.073678 GTGGTGCTCATGTCATTGTGTA 58.926 45.455 0.00 0.00 0.00 2.90
1696 1724 3.073678 TGGTGCTCATGTCATTGTGTAC 58.926 45.455 0.00 0.00 0.00 2.90
1697 1725 3.244526 TGGTGCTCATGTCATTGTGTACT 60.245 43.478 0.00 0.00 0.00 2.73
1735 1765 2.643995 ATTCACATCGGATGGCATCA 57.356 45.000 27.39 9.84 33.60 3.07
2200 2232 1.080161 GCGCAGGATAGCTAGGAGC 60.080 63.158 0.30 0.00 42.84 4.70
2221 2253 3.989167 GCTTTGCTGTTATGAACAATGCA 59.011 39.130 0.00 0.00 41.61 3.96
2402 2462 5.049129 GCATCTATCATTGTTACCAAGGCTC 60.049 44.000 0.00 0.00 32.52 4.70
2477 2537 6.097839 GGTATTAGTTGGAGTACCTGTGATCA 59.902 42.308 0.00 0.00 34.98 2.92
2498 2558 5.198207 TCATTGGATGACATGAGATGCTTT 58.802 37.500 0.00 0.00 33.59 3.51
2525 2585 8.846943 TGAACACTTCTATTTGTACATGTCAT 57.153 30.769 0.00 0.00 0.00 3.06
2565 2625 5.939883 ACAGCTTGCTTCAGAATACAATGTA 59.060 36.000 0.00 0.00 0.00 2.29
2646 2707 5.705441 AGAAAGAAAATACCTGCACGAATCA 59.295 36.000 0.00 0.00 0.00 2.57
2783 2844 6.263168 GCCAGCATTGTGGTATTAGTTCTAAT 59.737 38.462 9.54 9.54 40.09 1.73
2826 2887 0.840722 ACCGGATGGACCAAGGACTT 60.841 55.000 9.46 0.00 39.21 3.01
2858 2919 2.746277 GGACTCGCGTGGGCAAAT 60.746 61.111 13.32 0.00 39.92 2.32
2988 3049 2.537143 TGTAAAGAGGTCCTGTCTCCC 58.463 52.381 0.00 0.00 31.96 4.30
3031 3092 7.015292 ACAATCTCTTAGTTGTCTACAGTCCAA 59.985 37.037 0.00 0.00 33.53 3.53
3093 3154 5.221601 GGATGCTGGTTCTCTGATATTCTGA 60.222 44.000 0.00 0.00 0.00 3.27
3094 3155 5.883685 TGCTGGTTCTCTGATATTCTGAT 57.116 39.130 0.00 0.00 0.00 2.90
3144 3205 8.356533 ACAATGTGCTTGTTTATTTTCTTCTG 57.643 30.769 0.00 0.00 45.98 3.02
3145 3206 7.439056 ACAATGTGCTTGTTTATTTTCTTCTGG 59.561 33.333 0.00 0.00 45.98 3.86
3146 3207 6.707440 TGTGCTTGTTTATTTTCTTCTGGA 57.293 33.333 0.00 0.00 0.00 3.86
3147 3208 7.288810 TGTGCTTGTTTATTTTCTTCTGGAT 57.711 32.000 0.00 0.00 0.00 3.41
3148 3209 8.402798 TGTGCTTGTTTATTTTCTTCTGGATA 57.597 30.769 0.00 0.00 0.00 2.59
3149 3210 8.296713 TGTGCTTGTTTATTTTCTTCTGGATAC 58.703 33.333 0.00 0.00 0.00 2.24
3150 3211 8.515414 GTGCTTGTTTATTTTCTTCTGGATACT 58.485 33.333 0.00 0.00 37.61 2.12
3151 3212 9.733556 TGCTTGTTTATTTTCTTCTGGATACTA 57.266 29.630 0.00 0.00 37.61 1.82
3155 3216 9.667107 TGTTTATTTTCTTCTGGATACTAGGTG 57.333 33.333 0.00 0.00 37.61 4.00
3156 3217 9.886132 GTTTATTTTCTTCTGGATACTAGGTGA 57.114 33.333 0.00 0.00 37.61 4.02
3161 3222 9.886132 TTTTCTTCTGGATACTAGGTGATAAAC 57.114 33.333 0.00 0.00 37.61 2.01
3162 3223 8.840200 TTCTTCTGGATACTAGGTGATAAACT 57.160 34.615 0.00 0.00 37.61 2.66
3163 3224 9.931698 TTCTTCTGGATACTAGGTGATAAACTA 57.068 33.333 0.00 0.00 37.61 2.24
3164 3225 9.352191 TCTTCTGGATACTAGGTGATAAACTAC 57.648 37.037 0.00 0.00 37.61 2.73
3165 3226 9.132923 CTTCTGGATACTAGGTGATAAACTACA 57.867 37.037 0.00 0.00 37.61 2.74
3166 3227 9.656323 TTCTGGATACTAGGTGATAAACTACAT 57.344 33.333 0.00 0.00 37.61 2.29
3167 3228 9.078990 TCTGGATACTAGGTGATAAACTACATG 57.921 37.037 0.00 0.00 37.61 3.21
3168 3229 8.777578 TGGATACTAGGTGATAAACTACATGT 57.222 34.615 2.69 2.69 37.61 3.21
3169 3230 9.209048 TGGATACTAGGTGATAAACTACATGTT 57.791 33.333 2.30 0.00 37.87 2.71
3170 3231 9.477484 GGATACTAGGTGATAAACTACATGTTG 57.523 37.037 2.30 4.29 39.13 3.33
3173 3234 7.903145 ACTAGGTGATAAACTACATGTTGTCA 58.097 34.615 13.34 4.61 39.13 3.58
3174 3235 8.035394 ACTAGGTGATAAACTACATGTTGTCAG 58.965 37.037 13.34 2.55 39.13 3.51
3175 3236 6.769512 AGGTGATAAACTACATGTTGTCAGT 58.230 36.000 13.34 3.23 39.13 3.41
3176 3237 7.903145 AGGTGATAAACTACATGTTGTCAGTA 58.097 34.615 13.34 7.06 39.13 2.74
3177 3238 8.372459 AGGTGATAAACTACATGTTGTCAGTAA 58.628 33.333 13.34 0.00 39.13 2.24
3178 3239 9.162764 GGTGATAAACTACATGTTGTCAGTAAT 57.837 33.333 13.34 4.13 39.13 1.89
3186 3247 9.730420 ACTACATGTTGTCAGTAATTTGTTTTC 57.270 29.630 2.30 0.00 0.00 2.29
3187 3248 9.729023 CTACATGTTGTCAGTAATTTGTTTTCA 57.271 29.630 2.30 0.00 0.00 2.69
3188 3249 8.633075 ACATGTTGTCAGTAATTTGTTTTCAG 57.367 30.769 0.00 0.00 0.00 3.02
3189 3250 7.222611 ACATGTTGTCAGTAATTTGTTTTCAGC 59.777 33.333 0.00 0.00 0.00 4.26
3190 3251 6.862209 TGTTGTCAGTAATTTGTTTTCAGCT 58.138 32.000 0.00 0.00 0.00 4.24
3191 3252 7.990917 TGTTGTCAGTAATTTGTTTTCAGCTA 58.009 30.769 0.00 0.00 0.00 3.32
3192 3253 8.128582 TGTTGTCAGTAATTTGTTTTCAGCTAG 58.871 33.333 0.00 0.00 0.00 3.42
3193 3254 6.668323 TGTCAGTAATTTGTTTTCAGCTAGC 58.332 36.000 6.62 6.62 0.00 3.42
3194 3255 6.086871 GTCAGTAATTTGTTTTCAGCTAGCC 58.913 40.000 12.13 0.00 0.00 3.93
3195 3256 6.003950 TCAGTAATTTGTTTTCAGCTAGCCT 58.996 36.000 12.13 0.00 0.00 4.58
3196 3257 6.072508 TCAGTAATTTGTTTTCAGCTAGCCTG 60.073 38.462 12.13 9.38 43.17 4.85
3206 3267 4.551702 TCAGCTAGCCTGATTTGTAACA 57.448 40.909 12.13 0.00 45.44 2.41
3207 3268 5.102953 TCAGCTAGCCTGATTTGTAACAT 57.897 39.130 12.13 0.00 45.44 2.71
3208 3269 4.877823 TCAGCTAGCCTGATTTGTAACATG 59.122 41.667 12.13 0.00 45.44 3.21
3209 3270 4.877823 CAGCTAGCCTGATTTGTAACATGA 59.122 41.667 12.13 0.00 44.64 3.07
3210 3271 5.007430 CAGCTAGCCTGATTTGTAACATGAG 59.993 44.000 12.13 0.00 44.64 2.90
3211 3272 4.260948 GCTAGCCTGATTTGTAACATGAGC 60.261 45.833 2.29 0.00 0.00 4.26
3212 3273 3.960571 AGCCTGATTTGTAACATGAGCT 58.039 40.909 0.00 0.00 0.00 4.09
3213 3274 4.338879 AGCCTGATTTGTAACATGAGCTT 58.661 39.130 0.00 0.00 0.00 3.74
3214 3275 4.397417 AGCCTGATTTGTAACATGAGCTTC 59.603 41.667 0.00 0.00 0.00 3.86
3215 3276 4.728882 GCCTGATTTGTAACATGAGCTTCG 60.729 45.833 0.00 0.00 0.00 3.79
3216 3277 4.393062 CCTGATTTGTAACATGAGCTTCGT 59.607 41.667 0.00 0.00 0.00 3.85
3217 3278 5.281693 TGATTTGTAACATGAGCTTCGTG 57.718 39.130 0.00 0.00 39.24 4.35
3218 3279 4.994217 TGATTTGTAACATGAGCTTCGTGA 59.006 37.500 0.00 0.00 36.89 4.35
3219 3280 5.468409 TGATTTGTAACATGAGCTTCGTGAA 59.532 36.000 0.00 0.00 36.89 3.18
3220 3281 5.743026 TTTGTAACATGAGCTTCGTGAAA 57.257 34.783 0.00 1.32 36.89 2.69
3221 3282 5.743026 TTGTAACATGAGCTTCGTGAAAA 57.257 34.783 0.00 0.00 36.89 2.29
3222 3283 5.940192 TGTAACATGAGCTTCGTGAAAAT 57.060 34.783 0.00 0.60 36.89 1.82
3223 3284 7.428282 TTGTAACATGAGCTTCGTGAAAATA 57.572 32.000 0.00 0.00 36.89 1.40
3224 3285 7.428282 TGTAACATGAGCTTCGTGAAAATAA 57.572 32.000 0.00 0.00 36.89 1.40
3225 3286 7.518161 TGTAACATGAGCTTCGTGAAAATAAG 58.482 34.615 0.00 0.00 36.89 1.73
3226 3287 6.801539 AACATGAGCTTCGTGAAAATAAGA 57.198 33.333 0.00 0.00 36.89 2.10
3227 3288 6.801539 ACATGAGCTTCGTGAAAATAAGAA 57.198 33.333 0.00 0.00 36.89 2.52
3228 3289 7.202016 ACATGAGCTTCGTGAAAATAAGAAA 57.798 32.000 0.00 0.00 36.89 2.52
3229 3290 7.648142 ACATGAGCTTCGTGAAAATAAGAAAA 58.352 30.769 0.00 0.00 36.89 2.29
3230 3291 7.591426 ACATGAGCTTCGTGAAAATAAGAAAAC 59.409 33.333 0.00 0.00 36.89 2.43
3231 3292 7.259290 TGAGCTTCGTGAAAATAAGAAAACT 57.741 32.000 0.00 0.00 0.00 2.66
3232 3293 7.132213 TGAGCTTCGTGAAAATAAGAAAACTG 58.868 34.615 0.00 0.00 0.00 3.16
3233 3294 7.011950 TGAGCTTCGTGAAAATAAGAAAACTGA 59.988 33.333 0.00 0.00 0.00 3.41
3234 3295 7.703328 AGCTTCGTGAAAATAAGAAAACTGAA 58.297 30.769 0.00 0.00 0.00 3.02
3235 3296 7.644157 AGCTTCGTGAAAATAAGAAAACTGAAC 59.356 33.333 0.00 0.00 0.00 3.18
3236 3297 7.431084 GCTTCGTGAAAATAAGAAAACTGAACA 59.569 33.333 0.00 0.00 0.00 3.18
3237 3298 8.609478 TTCGTGAAAATAAGAAAACTGAACAC 57.391 30.769 0.00 0.00 0.00 3.32
3238 3299 7.190871 TCGTGAAAATAAGAAAACTGAACACC 58.809 34.615 0.00 0.00 0.00 4.16
3239 3300 6.416750 CGTGAAAATAAGAAAACTGAACACCC 59.583 38.462 0.00 0.00 0.00 4.61
3240 3301 6.700081 GTGAAAATAAGAAAACTGAACACCCC 59.300 38.462 0.00 0.00 0.00 4.95
3241 3302 5.801531 AAATAAGAAAACTGAACACCCCC 57.198 39.130 0.00 0.00 0.00 5.40
3258 3319 2.448926 CCCCCGTTTGAAATTTCCAC 57.551 50.000 15.48 10.89 0.00 4.02
3259 3320 1.001520 CCCCCGTTTGAAATTTCCACC 59.998 52.381 15.48 0.00 0.00 4.61
3260 3321 1.967779 CCCCGTTTGAAATTTCCACCT 59.032 47.619 15.48 0.00 0.00 4.00
3261 3322 3.158676 CCCCGTTTGAAATTTCCACCTA 58.841 45.455 15.48 0.00 0.00 3.08
3262 3323 3.574826 CCCCGTTTGAAATTTCCACCTAA 59.425 43.478 15.48 0.00 0.00 2.69
3263 3324 4.039366 CCCCGTTTGAAATTTCCACCTAAA 59.961 41.667 15.48 6.18 0.00 1.85
3264 3325 5.279758 CCCCGTTTGAAATTTCCACCTAAAT 60.280 40.000 15.48 0.00 0.00 1.40
3265 3326 6.227522 CCCGTTTGAAATTTCCACCTAAATT 58.772 36.000 15.48 0.00 40.02 1.82
3266 3327 6.147000 CCCGTTTGAAATTTCCACCTAAATTG 59.853 38.462 15.48 6.11 38.68 2.32
3267 3328 6.704050 CCGTTTGAAATTTCCACCTAAATTGT 59.296 34.615 15.48 0.00 38.68 2.71
3268 3329 7.225734 CCGTTTGAAATTTCCACCTAAATTGTT 59.774 33.333 15.48 0.00 38.68 2.83
3269 3330 8.061268 CGTTTGAAATTTCCACCTAAATTGTTG 58.939 33.333 15.48 0.00 38.68 3.33
3270 3331 8.341903 GTTTGAAATTTCCACCTAAATTGTTGG 58.658 33.333 15.48 0.00 38.68 3.77
3271 3332 6.529220 TGAAATTTCCACCTAAATTGTTGGG 58.471 36.000 15.48 0.00 38.68 4.12
3273 3334 6.508030 AATTTCCACCTAAATTGTTGGGTT 57.492 33.333 0.00 0.00 45.82 4.11
3274 3335 7.619512 AATTTCCACCTAAATTGTTGGGTTA 57.380 32.000 0.00 0.00 45.82 2.85
3275 3336 6.658188 TTTCCACCTAAATTGTTGGGTTAG 57.342 37.500 0.00 0.00 45.82 2.34
3276 3337 5.327737 TCCACCTAAATTGTTGGGTTAGT 57.672 39.130 0.00 0.00 45.82 2.24
3277 3338 6.451292 TCCACCTAAATTGTTGGGTTAGTA 57.549 37.500 0.00 0.00 45.82 1.82
3278 3339 6.240145 TCCACCTAAATTGTTGGGTTAGTAC 58.760 40.000 0.00 0.00 45.82 2.73
3279 3340 6.044637 TCCACCTAAATTGTTGGGTTAGTACT 59.955 38.462 0.00 0.00 45.82 2.73
3280 3341 6.717997 CCACCTAAATTGTTGGGTTAGTACTT 59.282 38.462 0.00 0.00 45.82 2.24
3281 3342 7.094506 CCACCTAAATTGTTGGGTTAGTACTTC 60.095 40.741 0.00 0.00 45.82 3.01
3282 3343 7.446013 CACCTAAATTGTTGGGTTAGTACTTCA 59.554 37.037 0.00 0.00 45.82 3.02
3283 3344 8.000127 ACCTAAATTGTTGGGTTAGTACTTCAA 59.000 33.333 0.00 0.00 45.82 2.69
3284 3345 9.020731 CCTAAATTGTTGGGTTAGTACTTCAAT 57.979 33.333 0.00 0.00 30.81 2.57
3285 3346 9.840427 CTAAATTGTTGGGTTAGTACTTCAATG 57.160 33.333 0.00 0.00 0.00 2.82
3286 3347 8.472007 AAATTGTTGGGTTAGTACTTCAATGA 57.528 30.769 0.00 0.00 0.00 2.57
3287 3348 8.472007 AATTGTTGGGTTAGTACTTCAATGAA 57.528 30.769 0.00 0.00 0.00 2.57
3288 3349 7.883391 TTGTTGGGTTAGTACTTCAATGAAA 57.117 32.000 0.00 0.00 0.00 2.69
3289 3350 8.472007 TTGTTGGGTTAGTACTTCAATGAAAT 57.528 30.769 0.00 0.00 0.00 2.17
3290 3351 7.881142 TGTTGGGTTAGTACTTCAATGAAATG 58.119 34.615 0.00 0.00 0.00 2.32
3307 3368 9.811995 CAATGAAATGACATCAATACAGGAAAT 57.188 29.630 0.00 0.00 0.00 2.17
3382 3445 9.988350 ATATGTTAATGATTCTTCAACGTGTTC 57.012 29.630 0.00 0.00 34.96 3.18
3420 3483 3.259374 TGATGAGAGAGGTCAAAGGTCAC 59.741 47.826 0.00 0.00 0.00 3.67
3527 3590 4.361783 TCAGATTTGATGTACTCCCTCCA 58.638 43.478 0.00 0.00 0.00 3.86
3589 3652 5.600696 ACCATTTGAATGTTTGACCAAGAC 58.399 37.500 3.30 0.00 34.60 3.01
3726 3790 6.403866 AAAACTTGGTCAAATATGCACTCA 57.596 33.333 0.00 0.00 0.00 3.41
3765 3829 8.637281 AAAACAAAACCTTATGTAAAGGAACG 57.363 30.769 10.67 0.00 39.81 3.95
3828 3892 3.122948 CCTGAAGTCGAAATTGTGTACCG 59.877 47.826 0.00 0.00 0.00 4.02
3858 3922 7.332926 TCTGAACTGCTAGAAGCTTCTATTTTG 59.667 37.037 31.24 21.83 42.97 2.44
4146 4210 1.741706 GGCCATGATTCATAGCCATCG 59.258 52.381 25.38 1.81 45.46 3.84
4148 4212 2.877300 GCCATGATTCATAGCCATCGGT 60.877 50.000 5.84 0.00 0.00 4.69
4149 4213 2.745821 CCATGATTCATAGCCATCGGTG 59.254 50.000 0.00 0.00 0.00 4.94
4166 4232 1.211457 GGTGGTGATGCTTCAGAGGAT 59.789 52.381 1.91 0.00 36.56 3.24
4303 4373 7.323895 CCGCATGTGTATATAGATAATAGACGC 59.676 40.741 5.38 0.00 41.22 5.19
4720 4807 1.098050 GACCATGGATCTTTGCGCTT 58.902 50.000 21.47 0.00 0.00 4.68
4721 4808 0.813184 ACCATGGATCTTTGCGCTTG 59.187 50.000 21.47 0.00 0.00 4.01
4741 4828 5.359194 TTGATGGGAGAGATTTGGTCTAC 57.641 43.478 0.00 0.00 37.29 2.59
4742 4829 4.624913 TGATGGGAGAGATTTGGTCTACT 58.375 43.478 0.00 0.00 37.29 2.57
4743 4830 5.777449 TGATGGGAGAGATTTGGTCTACTA 58.223 41.667 0.00 0.00 37.29 1.82
4744 4831 5.835819 TGATGGGAGAGATTTGGTCTACTAG 59.164 44.000 0.00 0.00 37.29 2.57
4745 4832 4.547671 TGGGAGAGATTTGGTCTACTAGG 58.452 47.826 0.00 0.00 37.29 3.02
4764 4863 7.730364 ACTAGGTTATGTTCTCTTGTTTGTG 57.270 36.000 0.00 0.00 0.00 3.33
4765 4864 5.438761 AGGTTATGTTCTCTTGTTTGTGC 57.561 39.130 0.00 0.00 0.00 4.57
4795 4894 2.046314 CGTCGGCCCAGTGGAATT 60.046 61.111 11.95 0.00 0.00 2.17
4871 4970 3.391296 GGGCATGTAGGGTTTCTGAGATA 59.609 47.826 0.00 0.00 0.00 1.98
4916 5015 6.015772 TGTGGGTATCTTTTTGCCTTAGTTTC 60.016 38.462 0.00 0.00 0.00 2.78
4944 5043 8.815141 TTGACACCAATCTTTTCAATAACATG 57.185 30.769 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.621571 AGCCAACCAGCTCCTCCATA 60.622 55.000 0.00 0.00 39.48 2.74
1 2 0.621571 TAGCCAACCAGCTCCTCCAT 60.622 55.000 0.00 0.00 43.67 3.41
2 3 0.621571 ATAGCCAACCAGCTCCTCCA 60.622 55.000 0.00 0.00 43.67 3.86
3 4 0.548510 AATAGCCAACCAGCTCCTCC 59.451 55.000 0.00 0.00 43.67 4.30
4 5 1.210478 TCAATAGCCAACCAGCTCCTC 59.790 52.381 0.00 0.00 43.67 3.71
5 6 1.289160 TCAATAGCCAACCAGCTCCT 58.711 50.000 0.00 0.00 43.67 3.69
13 14 2.414161 GCGTTGTCCTTCAATAGCCAAC 60.414 50.000 0.00 0.00 38.38 3.77
17 18 1.398390 CTGGCGTTGTCCTTCAATAGC 59.602 52.381 0.00 0.00 39.74 2.97
23 24 2.946762 GCACTGGCGTTGTCCTTC 59.053 61.111 0.00 0.00 0.00 3.46
34 35 0.675837 CCACATCCTGACAGCACTGG 60.676 60.000 2.21 0.00 34.19 4.00
42 43 1.270094 TGTCGACAACCACATCCTGAC 60.270 52.381 17.62 0.00 0.00 3.51
72 73 2.545742 CGGATCACTAACATCATCGCCA 60.546 50.000 0.00 0.00 0.00 5.69
78 79 0.529773 GCGCCGGATCACTAACATCA 60.530 55.000 5.05 0.00 0.00 3.07
102 103 1.153823 CGGTGACCTAGCCAAGTCG 60.154 63.158 0.00 0.00 35.71 4.18
119 120 3.797039 TGCATCAAATCCCTCTTCTACG 58.203 45.455 0.00 0.00 0.00 3.51
121 122 4.166725 ACCATGCATCAAATCCCTCTTCTA 59.833 41.667 0.00 0.00 0.00 2.10
158 159 0.109086 CCACGTCTGATGTCGAGCTT 60.109 55.000 0.00 0.00 0.00 3.74
167 168 0.894184 ACGACAGGTCCACGTCTGAT 60.894 55.000 8.80 0.00 35.33 2.90
169 170 1.371758 CACGACAGGTCCACGTCTG 60.372 63.158 9.16 0.74 38.18 3.51
174 175 2.594962 CGTTGCACGACAGGTCCAC 61.595 63.158 3.04 0.00 46.05 4.02
191 192 5.762045 ACTTGAAGAAAAACATCCATGTCG 58.238 37.500 0.00 0.00 40.80 4.35
212 213 5.841783 ACTTGAAGAGTCCCTAAAGAGAACT 59.158 40.000 0.00 0.00 31.20 3.01
247 248 1.411394 TAGTGTCGTTGCGTTGCTAC 58.589 50.000 0.00 0.00 0.00 3.58
252 253 1.349259 GCGGATAGTGTCGTTGCGTT 61.349 55.000 0.00 0.00 0.00 4.84
254 255 2.845739 CGCGGATAGTGTCGTTGCG 61.846 63.158 0.00 5.65 37.32 4.85
270 271 6.870439 ACCGGGAGAATATTAGTTTTATACGC 59.130 38.462 6.32 0.00 0.00 4.42
280 281 4.510340 CCAACGAAACCGGGAGAATATTAG 59.490 45.833 6.32 0.00 0.00 1.73
319 330 3.249189 GGCTCCACACACCCTCCA 61.249 66.667 0.00 0.00 0.00 3.86
322 333 3.941188 CACGGCTCCACACACCCT 61.941 66.667 0.00 0.00 0.00 4.34
344 355 2.107141 GTCCCGGAAGATCAGCCG 59.893 66.667 16.62 16.62 46.80 5.52
365 376 6.424032 GGATCCACTAGAAACCTAAACCAAT 58.576 40.000 6.95 0.00 0.00 3.16
388 399 5.227152 TGAATGTATGTCGAATCCATACGG 58.773 41.667 15.75 0.00 44.87 4.02
403 414 8.954950 AGAAACTTCGAAGATCATGAATGTAT 57.045 30.769 31.08 0.99 35.04 2.29
420 431 6.258947 GGCTGATAAGGTCATGTAGAAACTTC 59.741 42.308 0.00 0.00 35.97 3.01
463 474 2.223502 CGCAATCTACAGAGCTAACCGA 60.224 50.000 0.00 0.00 0.00 4.69
513 524 4.067972 AGAAGTAACGGCTGAAAAGTCA 57.932 40.909 0.00 0.00 0.00 3.41
537 548 5.801531 AACATTTTAAACCCCAAGGACTC 57.198 39.130 0.00 0.00 36.73 3.36
541 552 4.713553 AGCAAACATTTTAAACCCCAAGG 58.286 39.130 0.00 0.00 40.04 3.61
561 572 1.227409 GCTTCCGCCTTAGAGGAGC 60.227 63.158 0.00 0.00 43.48 4.70
566 577 0.532573 CACTGAGCTTCCGCCTTAGA 59.467 55.000 0.00 0.00 36.60 2.10
572 583 2.731691 TTCCACCACTGAGCTTCCGC 62.732 60.000 0.00 0.00 0.00 5.54
584 595 2.270352 AGCAAAACTCGATTCCACCA 57.730 45.000 0.00 0.00 0.00 4.17
592 603 2.621338 CTCCTGCATAGCAAAACTCGA 58.379 47.619 0.00 0.00 38.41 4.04
619 630 2.214376 TTCATGAGGGTGCCGAAATT 57.786 45.000 0.00 0.00 0.00 1.82
698 709 7.097192 TCGAAAGGCAAGGTCATATATGTATC 58.903 38.462 12.42 5.03 0.00 2.24
702 713 6.618287 TTTCGAAAGGCAAGGTCATATATG 57.382 37.500 6.47 6.36 0.00 1.78
805 824 4.702612 TGCCGATGCTTTTGGAATAGTTTA 59.297 37.500 0.00 0.00 38.71 2.01
808 827 2.684881 CTGCCGATGCTTTTGGAATAGT 59.315 45.455 0.00 0.00 38.71 2.12
1356 1384 2.280592 GTGTTCGACGGGGCTTGT 60.281 61.111 0.00 0.00 0.00 3.16
1464 1492 3.160047 ATCAGGGCAGGAGAGCGG 61.160 66.667 0.00 0.00 34.64 5.52
1522 1550 1.447317 AACCGCTTGCACCTGACAAG 61.447 55.000 0.00 0.00 45.88 3.16
1649 1677 1.779569 TCGAAAGCTTCTCAACGGAC 58.220 50.000 0.00 0.00 0.00 4.79
1695 1723 8.200792 GTGAATTCAACCTCTATATCACAGAGT 58.799 37.037 10.35 0.00 38.29 3.24
1696 1724 8.200120 TGTGAATTCAACCTCTATATCACAGAG 58.800 37.037 10.35 0.00 40.48 3.35
1697 1725 8.078060 TGTGAATTCAACCTCTATATCACAGA 57.922 34.615 10.35 0.00 40.48 3.41
1735 1765 0.320374 TTTCGCGGAACCTCATCAGT 59.680 50.000 6.13 0.00 0.00 3.41
1979 2011 0.967380 CTTCCACTGCACCCCAATCC 60.967 60.000 0.00 0.00 0.00 3.01
2012 2044 2.033194 GTGGACTTACACAGGCGCC 61.033 63.158 21.89 21.89 40.99 6.53
2131 2163 6.869913 CCTAACTTCGGTACTGATTTACAACA 59.130 38.462 4.94 0.00 0.00 3.33
2194 2226 4.905429 TGTTCATAACAGCAAAGCTCCTA 58.095 39.130 0.00 0.00 36.40 2.94
2200 2232 5.062934 CCATGCATTGTTCATAACAGCAAAG 59.937 40.000 0.00 6.75 43.06 2.77
2221 2253 4.569943 CACTGCACTAGACACTAAACCAT 58.430 43.478 0.00 0.00 0.00 3.55
2356 2416 4.797349 GCATGTCTTCAAGCTAGCATTTTC 59.203 41.667 18.83 1.71 35.70 2.29
2449 2509 6.270463 TCACAGGTACTCCAACTAATACCAAA 59.730 38.462 2.37 0.00 39.72 3.28
2463 2523 5.053145 GTCATCCAATGATCACAGGTACTC 58.947 45.833 13.38 2.87 42.04 2.59
2477 2537 6.153851 TCAAAAAGCATCTCATGTCATCCAAT 59.846 34.615 0.00 0.00 0.00 3.16
2498 2558 9.114952 TGACATGTACAAATAGAAGTGTTCAAA 57.885 29.630 0.00 0.00 30.30 2.69
2565 2625 6.156256 TCACTTAGATGTGCAATAACTAGGGT 59.844 38.462 0.00 0.00 37.81 4.34
2640 2701 5.451908 CCAATGATTTTACCCGATGATTCG 58.548 41.667 0.00 0.00 45.08 3.34
2646 2707 3.360867 TGTGCCAATGATTTTACCCGAT 58.639 40.909 0.00 0.00 0.00 4.18
2783 2844 4.082949 CCTCGACGCATCATAGGTGTATTA 60.083 45.833 0.00 0.00 0.00 0.98
2826 2887 1.270274 GAGTCCACATGCATTGCACAA 59.730 47.619 14.66 0.00 43.04 3.33
2883 2944 8.999431 ACAAGGTAAATGAACATACTAACACAG 58.001 33.333 0.00 0.00 0.00 3.66
2926 2987 0.321122 GAGCCTGCTGTAGTGCTGTT 60.321 55.000 11.94 0.00 34.43 3.16
2971 3032 2.424684 AAGGGAGACAGGACCTCTTT 57.575 50.000 0.00 0.00 32.29 2.52
3031 3092 8.358148 CGGTACAGAAGGATATATTGTTACAGT 58.642 37.037 0.00 0.00 0.00 3.55
3093 3154 8.579850 TGCTGATGAAGTTAAAACCATCTTAT 57.420 30.769 11.09 0.00 37.06 1.73
3094 3155 7.994425 TGCTGATGAAGTTAAAACCATCTTA 57.006 32.000 11.09 0.30 37.06 2.10
3130 3191 9.886132 TCACCTAGTATCCAGAAGAAAATAAAC 57.114 33.333 0.00 0.00 0.00 2.01
3135 3196 9.886132 GTTTATCACCTAGTATCCAGAAGAAAA 57.114 33.333 0.00 0.00 0.00 2.29
3136 3197 9.268282 AGTTTATCACCTAGTATCCAGAAGAAA 57.732 33.333 0.00 0.00 0.00 2.52
3137 3198 8.840200 AGTTTATCACCTAGTATCCAGAAGAA 57.160 34.615 0.00 0.00 0.00 2.52
3138 3199 9.352191 GTAGTTTATCACCTAGTATCCAGAAGA 57.648 37.037 0.00 0.00 0.00 2.87
3139 3200 9.132923 TGTAGTTTATCACCTAGTATCCAGAAG 57.867 37.037 0.00 0.00 0.00 2.85
3140 3201 9.656323 ATGTAGTTTATCACCTAGTATCCAGAA 57.344 33.333 0.00 0.00 0.00 3.02
3141 3202 9.078990 CATGTAGTTTATCACCTAGTATCCAGA 57.921 37.037 0.00 0.00 0.00 3.86
3142 3203 8.861086 ACATGTAGTTTATCACCTAGTATCCAG 58.139 37.037 0.00 0.00 0.00 3.86
3143 3204 8.777578 ACATGTAGTTTATCACCTAGTATCCA 57.222 34.615 0.00 0.00 0.00 3.41
3144 3205 9.477484 CAACATGTAGTTTATCACCTAGTATCC 57.523 37.037 0.00 0.00 38.74 2.59
3147 3208 9.027202 TGACAACATGTAGTTTATCACCTAGTA 57.973 33.333 0.00 0.00 38.74 1.82
3148 3209 7.903145 TGACAACATGTAGTTTATCACCTAGT 58.097 34.615 0.00 0.00 38.74 2.57
3149 3210 8.035394 ACTGACAACATGTAGTTTATCACCTAG 58.965 37.037 0.00 0.00 38.74 3.02
3150 3211 7.903145 ACTGACAACATGTAGTTTATCACCTA 58.097 34.615 0.00 0.00 38.74 3.08
3151 3212 6.769512 ACTGACAACATGTAGTTTATCACCT 58.230 36.000 0.00 0.00 38.74 4.00
3152 3213 8.542497 TTACTGACAACATGTAGTTTATCACC 57.458 34.615 0.00 0.00 38.74 4.02
3160 3221 9.730420 GAAAACAAATTACTGACAACATGTAGT 57.270 29.630 0.00 0.88 0.00 2.73
3161 3222 9.729023 TGAAAACAAATTACTGACAACATGTAG 57.271 29.630 0.00 0.00 0.00 2.74
3162 3223 9.729023 CTGAAAACAAATTACTGACAACATGTA 57.271 29.630 0.00 0.00 0.00 2.29
3163 3224 7.222611 GCTGAAAACAAATTACTGACAACATGT 59.777 33.333 0.00 0.00 0.00 3.21
3164 3225 7.436080 AGCTGAAAACAAATTACTGACAACATG 59.564 33.333 0.00 0.00 0.00 3.21
3165 3226 7.491682 AGCTGAAAACAAATTACTGACAACAT 58.508 30.769 0.00 0.00 0.00 2.71
3166 3227 6.862209 AGCTGAAAACAAATTACTGACAACA 58.138 32.000 0.00 0.00 0.00 3.33
3167 3228 7.113544 GCTAGCTGAAAACAAATTACTGACAAC 59.886 37.037 7.70 0.00 0.00 3.32
3168 3229 7.138736 GCTAGCTGAAAACAAATTACTGACAA 58.861 34.615 7.70 0.00 0.00 3.18
3169 3230 6.293955 GGCTAGCTGAAAACAAATTACTGACA 60.294 38.462 15.72 0.00 0.00 3.58
3170 3231 6.072452 AGGCTAGCTGAAAACAAATTACTGAC 60.072 38.462 15.72 0.00 0.00 3.51
3171 3232 6.003950 AGGCTAGCTGAAAACAAATTACTGA 58.996 36.000 15.72 0.00 0.00 3.41
3172 3233 6.072508 TCAGGCTAGCTGAAAACAAATTACTG 60.073 38.462 15.72 7.99 0.00 2.74
3173 3234 6.003950 TCAGGCTAGCTGAAAACAAATTACT 58.996 36.000 15.72 0.00 0.00 2.24
3174 3235 6.254281 TCAGGCTAGCTGAAAACAAATTAC 57.746 37.500 15.72 0.00 0.00 1.89
3175 3236 7.466746 AATCAGGCTAGCTGAAAACAAATTA 57.533 32.000 15.72 0.00 34.26 1.40
3176 3237 5.990120 ATCAGGCTAGCTGAAAACAAATT 57.010 34.783 15.72 0.00 34.26 1.82
3177 3238 5.990120 AATCAGGCTAGCTGAAAACAAAT 57.010 34.783 15.72 0.00 34.26 2.32
3178 3239 5.068987 ACAAATCAGGCTAGCTGAAAACAAA 59.931 36.000 15.72 0.00 34.26 2.83
3179 3240 4.584325 ACAAATCAGGCTAGCTGAAAACAA 59.416 37.500 15.72 0.00 34.26 2.83
3180 3241 4.144297 ACAAATCAGGCTAGCTGAAAACA 58.856 39.130 15.72 0.00 34.26 2.83
3181 3242 4.773323 ACAAATCAGGCTAGCTGAAAAC 57.227 40.909 15.72 0.00 34.26 2.43
3182 3243 5.767665 TGTTACAAATCAGGCTAGCTGAAAA 59.232 36.000 15.72 1.90 34.26 2.29
3183 3244 5.312895 TGTTACAAATCAGGCTAGCTGAAA 58.687 37.500 15.72 4.74 34.26 2.69
3184 3245 4.905429 TGTTACAAATCAGGCTAGCTGAA 58.095 39.130 15.72 0.00 34.26 3.02
3185 3246 4.551702 TGTTACAAATCAGGCTAGCTGA 57.448 40.909 15.72 15.88 35.13 4.26
3186 3247 4.877823 TCATGTTACAAATCAGGCTAGCTG 59.122 41.667 15.72 10.96 0.00 4.24
3187 3248 5.102953 TCATGTTACAAATCAGGCTAGCT 57.897 39.130 15.72 0.00 0.00 3.32
3188 3249 4.260948 GCTCATGTTACAAATCAGGCTAGC 60.261 45.833 6.04 6.04 0.00 3.42
3189 3250 5.121811 AGCTCATGTTACAAATCAGGCTAG 58.878 41.667 0.00 0.00 0.00 3.42
3190 3251 5.102953 AGCTCATGTTACAAATCAGGCTA 57.897 39.130 0.00 0.00 0.00 3.93
3191 3252 3.960571 AGCTCATGTTACAAATCAGGCT 58.039 40.909 0.00 0.00 0.00 4.58
3192 3253 4.666237 GAAGCTCATGTTACAAATCAGGC 58.334 43.478 0.00 0.00 0.00 4.85
3193 3254 4.393062 ACGAAGCTCATGTTACAAATCAGG 59.607 41.667 0.00 0.00 0.00 3.86
3194 3255 5.120674 TCACGAAGCTCATGTTACAAATCAG 59.879 40.000 0.00 0.00 0.00 2.90
3195 3256 4.994217 TCACGAAGCTCATGTTACAAATCA 59.006 37.500 0.00 0.00 0.00 2.57
3196 3257 5.530519 TCACGAAGCTCATGTTACAAATC 57.469 39.130 0.00 0.00 0.00 2.17
3197 3258 5.940192 TTCACGAAGCTCATGTTACAAAT 57.060 34.783 0.00 0.00 0.00 2.32
3198 3259 5.743026 TTTCACGAAGCTCATGTTACAAA 57.257 34.783 0.00 0.00 0.00 2.83
3199 3260 5.743026 TTTTCACGAAGCTCATGTTACAA 57.257 34.783 0.00 0.00 0.00 2.41
3200 3261 5.940192 ATTTTCACGAAGCTCATGTTACA 57.060 34.783 0.00 0.00 0.00 2.41
3201 3262 7.739295 TCTTATTTTCACGAAGCTCATGTTAC 58.261 34.615 0.00 0.00 0.00 2.50
3202 3263 7.899178 TCTTATTTTCACGAAGCTCATGTTA 57.101 32.000 0.00 0.00 0.00 2.41
3203 3264 6.801539 TCTTATTTTCACGAAGCTCATGTT 57.198 33.333 0.00 0.00 0.00 2.71
3204 3265 6.801539 TTCTTATTTTCACGAAGCTCATGT 57.198 33.333 0.00 0.00 0.00 3.21
3205 3266 7.805071 AGTTTTCTTATTTTCACGAAGCTCATG 59.195 33.333 0.00 0.00 0.00 3.07
3206 3267 7.805071 CAGTTTTCTTATTTTCACGAAGCTCAT 59.195 33.333 0.00 0.00 0.00 2.90
3207 3268 7.011950 TCAGTTTTCTTATTTTCACGAAGCTCA 59.988 33.333 0.00 0.00 0.00 4.26
3208 3269 7.352739 TCAGTTTTCTTATTTTCACGAAGCTC 58.647 34.615 0.00 0.00 0.00 4.09
3209 3270 7.259290 TCAGTTTTCTTATTTTCACGAAGCT 57.741 32.000 0.00 0.00 0.00 3.74
3210 3271 7.431084 TGTTCAGTTTTCTTATTTTCACGAAGC 59.569 33.333 0.00 0.00 0.00 3.86
3211 3272 8.734030 GTGTTCAGTTTTCTTATTTTCACGAAG 58.266 33.333 0.00 0.00 0.00 3.79
3212 3273 7.698970 GGTGTTCAGTTTTCTTATTTTCACGAA 59.301 33.333 0.00 0.00 0.00 3.85
3213 3274 7.190871 GGTGTTCAGTTTTCTTATTTTCACGA 58.809 34.615 0.00 0.00 0.00 4.35
3214 3275 6.416750 GGGTGTTCAGTTTTCTTATTTTCACG 59.583 38.462 0.00 0.00 0.00 4.35
3215 3276 6.700081 GGGGTGTTCAGTTTTCTTATTTTCAC 59.300 38.462 0.00 0.00 0.00 3.18
3216 3277 6.183360 GGGGGTGTTCAGTTTTCTTATTTTCA 60.183 38.462 0.00 0.00 0.00 2.69
3217 3278 6.220930 GGGGGTGTTCAGTTTTCTTATTTTC 58.779 40.000 0.00 0.00 0.00 2.29
3218 3279 6.169557 GGGGGTGTTCAGTTTTCTTATTTT 57.830 37.500 0.00 0.00 0.00 1.82
3219 3280 5.801531 GGGGGTGTTCAGTTTTCTTATTT 57.198 39.130 0.00 0.00 0.00 1.40
3239 3300 1.001520 GGTGGAAATTTCAAACGGGGG 59.998 52.381 19.49 0.00 0.00 5.40
3240 3301 1.967779 AGGTGGAAATTTCAAACGGGG 59.032 47.619 19.49 0.00 0.00 5.73
3241 3302 4.857509 TTAGGTGGAAATTTCAAACGGG 57.142 40.909 19.49 0.00 0.00 5.28
3242 3303 6.704050 ACAATTTAGGTGGAAATTTCAAACGG 59.296 34.615 19.49 8.98 36.99 4.44
3243 3304 7.707774 ACAATTTAGGTGGAAATTTCAAACG 57.292 32.000 19.49 8.45 36.99 3.60
3244 3305 8.341903 CCAACAATTTAGGTGGAAATTTCAAAC 58.658 33.333 19.49 11.58 36.99 2.93
3245 3306 7.500559 CCCAACAATTTAGGTGGAAATTTCAAA 59.499 33.333 19.49 11.02 36.99 2.69
3246 3307 6.995091 CCCAACAATTTAGGTGGAAATTTCAA 59.005 34.615 19.49 5.77 36.99 2.69
3247 3308 6.100424 ACCCAACAATTTAGGTGGAAATTTCA 59.900 34.615 19.49 3.64 36.99 2.69
3248 3309 6.530120 ACCCAACAATTTAGGTGGAAATTTC 58.470 36.000 9.83 9.83 36.99 2.17
3249 3310 6.508030 ACCCAACAATTTAGGTGGAAATTT 57.492 33.333 1.41 0.00 36.99 1.82
3250 3311 6.508030 AACCCAACAATTTAGGTGGAAATT 57.492 33.333 1.41 0.00 39.13 1.82
3251 3312 6.785466 ACTAACCCAACAATTTAGGTGGAAAT 59.215 34.615 1.41 0.00 31.45 2.17
3252 3313 6.137559 ACTAACCCAACAATTTAGGTGGAAA 58.862 36.000 1.41 0.00 31.45 3.13
3253 3314 5.707495 ACTAACCCAACAATTTAGGTGGAA 58.293 37.500 1.41 0.00 31.45 3.53
3254 3315 5.327737 ACTAACCCAACAATTTAGGTGGA 57.672 39.130 1.41 0.00 31.45 4.02
3255 3316 6.243148 AGTACTAACCCAACAATTTAGGTGG 58.757 40.000 0.00 0.00 31.45 4.61
3256 3317 7.446013 TGAAGTACTAACCCAACAATTTAGGTG 59.554 37.037 0.00 0.00 31.45 4.00
3257 3318 7.519927 TGAAGTACTAACCCAACAATTTAGGT 58.480 34.615 0.00 0.00 0.00 3.08
3258 3319 7.989416 TGAAGTACTAACCCAACAATTTAGG 57.011 36.000 0.00 0.00 0.00 2.69
3259 3320 9.840427 CATTGAAGTACTAACCCAACAATTTAG 57.160 33.333 0.00 0.00 0.00 1.85
3260 3321 9.575868 TCATTGAAGTACTAACCCAACAATTTA 57.424 29.630 0.00 0.00 0.00 1.40
3261 3322 8.472007 TCATTGAAGTACTAACCCAACAATTT 57.528 30.769 0.00 0.00 0.00 1.82
3262 3323 8.472007 TTCATTGAAGTACTAACCCAACAATT 57.528 30.769 0.00 0.00 0.00 2.32
3263 3324 8.472007 TTTCATTGAAGTACTAACCCAACAAT 57.528 30.769 0.00 0.00 0.00 2.71
3264 3325 7.883391 TTTCATTGAAGTACTAACCCAACAA 57.117 32.000 0.00 0.00 0.00 2.83
3265 3326 7.721842 TCATTTCATTGAAGTACTAACCCAACA 59.278 33.333 0.00 0.00 0.00 3.33
3266 3327 8.021396 GTCATTTCATTGAAGTACTAACCCAAC 58.979 37.037 0.00 0.00 0.00 3.77
3267 3328 7.721842 TGTCATTTCATTGAAGTACTAACCCAA 59.278 33.333 0.00 0.00 0.00 4.12
3268 3329 7.227873 TGTCATTTCATTGAAGTACTAACCCA 58.772 34.615 0.00 0.00 0.00 4.51
3269 3330 7.681939 TGTCATTTCATTGAAGTACTAACCC 57.318 36.000 0.00 0.00 0.00 4.11
3270 3331 8.946085 TGATGTCATTTCATTGAAGTACTAACC 58.054 33.333 0.00 0.00 0.00 2.85
3277 3338 8.464404 CCTGTATTGATGTCATTTCATTGAAGT 58.536 33.333 0.00 0.00 0.00 3.01
3278 3339 8.680001 TCCTGTATTGATGTCATTTCATTGAAG 58.320 33.333 0.00 0.00 0.00 3.02
3279 3340 8.578448 TCCTGTATTGATGTCATTTCATTGAA 57.422 30.769 0.00 0.00 0.00 2.69
3280 3341 8.578448 TTCCTGTATTGATGTCATTTCATTGA 57.422 30.769 0.00 0.00 0.00 2.57
3281 3342 9.811995 ATTTCCTGTATTGATGTCATTTCATTG 57.188 29.630 0.00 0.00 0.00 2.82
3288 3349 9.685276 TGACTTTATTTCCTGTATTGATGTCAT 57.315 29.630 0.00 0.00 0.00 3.06
3289 3350 8.946085 GTGACTTTATTTCCTGTATTGATGTCA 58.054 33.333 0.00 0.00 0.00 3.58
3290 3351 8.946085 TGTGACTTTATTTCCTGTATTGATGTC 58.054 33.333 0.00 0.00 0.00 3.06
3307 3368 7.333423 GCATGAGGTACTAACATTGTGACTTTA 59.667 37.037 0.00 0.00 41.55 1.85
3309 3370 5.643777 GCATGAGGTACTAACATTGTGACTT 59.356 40.000 0.00 0.00 41.55 3.01
3747 3811 4.324022 CCCTCCGTTCCTTTACATAAGGTT 60.324 45.833 3.68 0.00 38.55 3.50
3755 3819 7.530426 TTATATACTCCCTCCGTTCCTTTAC 57.470 40.000 0.00 0.00 0.00 2.01
3828 3892 5.468409 AGAAGCTTCTAGCAGTTCAGAAAAC 59.532 40.000 27.47 0.00 45.56 2.43
4146 4210 0.615331 TCCTCTGAAGCATCACCACC 59.385 55.000 0.00 0.00 0.00 4.61
4148 4212 1.407851 GCATCCTCTGAAGCATCACCA 60.408 52.381 0.00 0.00 35.33 4.17
4149 4213 1.134159 AGCATCCTCTGAAGCATCACC 60.134 52.381 0.00 0.00 37.67 4.02
4151 4215 1.746171 GCAGCATCCTCTGAAGCATCA 60.746 52.381 0.00 0.00 37.67 3.07
4166 4232 0.534877 ACTCCATGACAAACGCAGCA 60.535 50.000 0.00 0.00 0.00 4.41
4309 4379 5.200483 TGAACACTCAGAAAAACCCATCTT 58.800 37.500 0.00 0.00 0.00 2.40
4311 4381 5.712152 ATGAACACTCAGAAAAACCCATC 57.288 39.130 0.00 0.00 34.23 3.51
4396 4467 6.535150 TCTCATACGATTCTAAAGCAACCAAG 59.465 38.462 0.00 0.00 0.00 3.61
4399 4470 8.589335 TTATCTCATACGATTCTAAAGCAACC 57.411 34.615 0.00 0.00 0.00 3.77
4428 4499 4.572389 GTCATCCTGACGCATTTGTCTAAT 59.428 41.667 0.00 0.00 37.67 1.73
4507 4587 3.470709 ACATCTTCATGTAGCCAATCGG 58.529 45.455 0.00 0.00 41.81 4.18
4508 4588 5.490139 AAACATCTTCATGTAGCCAATCG 57.510 39.130 0.00 0.00 42.89 3.34
4510 4590 7.944729 AGTTAAACATCTTCATGTAGCCAAT 57.055 32.000 0.00 0.00 42.89 3.16
4720 4807 4.624913 AGTAGACCAAATCTCTCCCATCA 58.375 43.478 0.00 0.00 39.04 3.07
4721 4808 5.245075 CCTAGTAGACCAAATCTCTCCCATC 59.755 48.000 0.00 0.00 39.04 3.51
4741 4828 6.204688 TGCACAAACAAGAGAACATAACCTAG 59.795 38.462 0.00 0.00 0.00 3.02
4742 4829 6.058833 TGCACAAACAAGAGAACATAACCTA 58.941 36.000 0.00 0.00 0.00 3.08
4743 4830 4.887071 TGCACAAACAAGAGAACATAACCT 59.113 37.500 0.00 0.00 0.00 3.50
4744 4831 5.008613 TCTGCACAAACAAGAGAACATAACC 59.991 40.000 0.00 0.00 0.00 2.85
4745 4832 6.060028 TCTGCACAAACAAGAGAACATAAC 57.940 37.500 0.00 0.00 0.00 1.89
4764 4863 2.512515 GACGCCTCCACCATCTGC 60.513 66.667 0.00 0.00 0.00 4.26
4765 4864 2.202797 CGACGCCTCCACCATCTG 60.203 66.667 0.00 0.00 0.00 2.90
4795 4894 1.001048 CACAACGAGGACGGAACACTA 60.001 52.381 0.00 0.00 44.46 2.74
4809 4908 2.094957 AGAAACCAACAACACCACAACG 60.095 45.455 0.00 0.00 0.00 4.10
4857 4956 4.526262 CGAGGATCATATCTCAGAAACCCT 59.474 45.833 0.00 0.00 33.17 4.34
4871 4970 0.833287 CTCACAACCCCGAGGATCAT 59.167 55.000 0.00 0.00 36.73 2.45
4916 5015 7.871973 TGTTATTGAAAAGATTGGTGTCAATGG 59.128 33.333 7.31 0.00 43.08 3.16
4944 5043 5.105756 ACAATCCAAAGCAATAAGGTGTAGC 60.106 40.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.