Multiple sequence alignment - TraesCS4A01G059200

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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 TraesCS4A01G059200 chr4A 100.000 4237 0 0 1 4237 55380737 55376501 0.000000e+00 7825
1 TraesCS4A01G059200 chr4D 89.475 4323 186 80 14 4230 397669525 397665366 0.000000e+00 5214
2 TraesCS4A01G059200 chr4B 89.021 4044 165 82 278 4230 489650942 489647087 0.000000e+00 4750
3 TraesCS4A01G059200 chr4B 83.026 271 19 10 1 267 489651358 489651111 1.980000e-53 220
4 TraesCS4A01G059200 chr1D 87.255 102 9 2 944 1044 444882821 444882723 3.460000e-21 113


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 TraesCS4A01G059200 chr4A 55376501 55380737 4236 True 7825 7825 100.0000 1 4237 1 chr4A.!!$R1 4236
1 TraesCS4A01G059200 chr4D 397665366 397669525 4159 True 5214 5214 89.4750 14 4230 1 chr4D.!!$R1 4216
2 TraesCS4A01G059200 chr4B 489647087 489651358 4271 True 2485 4750 86.0235 1 4230 2 chr4B.!!$R1 4229

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
815 992 0.032615 GGGGGAGAGAGAGAGAAGCA 60.033 60.0 0.0 0.0 0.0 3.91 F
932 1109 0.179215 CAACAGTGGAAAGATCGCGC 60.179 55.0 0.0 0.0 0.0 6.86 F
2830 3064 0.036010 CCCACTACCAGCTCCAACAG 60.036 60.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1856 0.742505 CGGAGTAGCCCGTGATGTTA 59.257 55.000 0.0 0.0 44.23 2.41 R
2920 3154 1.136336 CGTAGCCGTTCTTGTTCTTGC 60.136 52.381 0.0 0.0 0.00 4.01 R
4044 4336 0.325602 ACCCCCACGCTTTATTCGAA 59.674 50.000 0.0 0.0 0.00 3.71 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
27 32 3.509266 GACGCGATCCAAAATTCGG 57.491 52.632 15.93 0.00 35.93 4.30
53 58 0.179037 GCATGGCTGATGGCTCTGTA 60.179 55.000 0.00 0.00 41.46 2.74
54 59 1.544982 GCATGGCTGATGGCTCTGTAT 60.545 52.381 0.00 0.00 41.46 2.29
55 60 2.289882 GCATGGCTGATGGCTCTGTATA 60.290 50.000 0.00 0.00 41.46 1.47
56 61 3.621709 GCATGGCTGATGGCTCTGTATAT 60.622 47.826 0.00 0.00 41.46 0.86
69 74 5.121298 GGCTCTGTATATACATACGACGTCA 59.879 44.000 15.81 0.00 40.04 4.35
82 87 0.317938 GACGTCATGGGTAGCTAGCG 60.318 60.000 16.33 3.58 0.00 4.26
88 93 2.159099 TCATGGGTAGCTAGCGAAAGTG 60.159 50.000 16.33 8.49 0.00 3.16
99 104 5.065988 AGCTAGCGAAAGTGAAAAAGTTGAA 59.934 36.000 9.55 0.00 0.00 2.69
103 108 4.265320 GCGAAAGTGAAAAAGTTGAAGTGG 59.735 41.667 0.00 0.00 0.00 4.00
105 110 5.621329 CGAAAGTGAAAAAGTTGAAGTGGGT 60.621 40.000 0.00 0.00 0.00 4.51
108 113 4.334481 AGTGAAAAAGTTGAAGTGGGTACG 59.666 41.667 0.00 0.00 0.00 3.67
173 178 0.456312 CGTGTAGGTCAAGCGGAGAC 60.456 60.000 0.00 0.00 35.29 3.36
185 190 2.833582 GGAGACGCCTGGGATCGA 60.834 66.667 0.00 0.00 0.00 3.59
186 191 2.413765 GAGACGCCTGGGATCGAC 59.586 66.667 0.00 0.00 0.00 4.20
187 192 3.140225 GAGACGCCTGGGATCGACC 62.140 68.421 0.00 0.00 38.08 4.79
211 216 4.255510 TCCCAAACCCTACTCTACGTAT 57.744 45.455 0.00 0.00 0.00 3.06
212 217 5.387113 TCCCAAACCCTACTCTACGTATA 57.613 43.478 0.00 0.00 0.00 1.47
213 218 5.133221 TCCCAAACCCTACTCTACGTATAC 58.867 45.833 0.00 0.00 0.00 1.47
214 219 5.103940 TCCCAAACCCTACTCTACGTATACT 60.104 44.000 0.00 0.00 0.00 2.12
215 220 6.101150 TCCCAAACCCTACTCTACGTATACTA 59.899 42.308 0.00 0.00 0.00 1.82
227 232 2.223433 ACGTATACTACAGTTCGGCAGC 60.223 50.000 0.56 0.00 0.00 5.25
315 478 0.038618 GGCAAAAGCAACGGGGTAAG 60.039 55.000 0.00 0.00 0.00 2.34
449 618 1.271434 GCGAAGGGATAGGGGAATTCC 60.271 57.143 16.74 16.74 0.00 3.01
485 654 2.035442 GCCGAGCCAACTTCACTCC 61.035 63.158 0.00 0.00 0.00 3.85
490 659 2.087646 GAGCCAACTTCACTCCATTCC 58.912 52.381 0.00 0.00 0.00 3.01
494 663 2.350522 CAACTTCACTCCATTCCTCCG 58.649 52.381 0.00 0.00 0.00 4.63
542 713 4.598406 TCCATTCGTGTTCATTCATTCG 57.402 40.909 0.00 0.00 0.00 3.34
546 717 3.698420 TCGTGTTCATTCATTCGTTCG 57.302 42.857 0.00 0.00 0.00 3.95
557 728 2.935849 TCATTCGTTCGTTCCATGATGG 59.064 45.455 4.74 4.74 39.43 3.51
570 741 0.535102 ATGATGGAAATCGGTCCGGC 60.535 55.000 12.29 0.00 40.96 6.13
693 870 2.034879 ACATTGCGACCCGAAGCAG 61.035 57.895 0.00 0.00 44.72 4.24
707 884 2.876219 GCAGGCAGCAAAGAGAGC 59.124 61.111 0.00 0.00 44.79 4.09
708 885 3.036783 GCAGGCAGCAAAGAGAGCG 62.037 63.158 0.00 0.00 44.79 5.03
709 886 2.745492 AGGCAGCAAAGAGAGCGC 60.745 61.111 0.00 0.00 37.01 5.92
753 930 3.715097 AGCCAGCCTCACCTCTGC 61.715 66.667 0.00 0.00 0.00 4.26
773 950 1.675641 CAGGAGACCAAAAGGCCGG 60.676 63.158 0.00 0.00 0.00 6.13
778 955 1.971695 GACCAAAAGGCCGGACCAG 60.972 63.158 1.76 0.00 43.14 4.00
797 974 2.035626 AAGCACCAATCCCACGGG 59.964 61.111 0.00 0.00 0.00 5.28
814 991 2.820845 GGGGGAGAGAGAGAGAAGC 58.179 63.158 0.00 0.00 0.00 3.86
815 992 0.032615 GGGGGAGAGAGAGAGAAGCA 60.033 60.000 0.00 0.00 0.00 3.91
817 994 1.064017 GGGGAGAGAGAGAGAAGCAGA 60.064 57.143 0.00 0.00 0.00 4.26
818 995 2.301346 GGGAGAGAGAGAGAAGCAGAG 58.699 57.143 0.00 0.00 0.00 3.35
819 996 2.092429 GGGAGAGAGAGAGAAGCAGAGA 60.092 54.545 0.00 0.00 0.00 3.10
820 997 3.620488 GGAGAGAGAGAGAAGCAGAGAA 58.380 50.000 0.00 0.00 0.00 2.87
821 998 4.016444 GGAGAGAGAGAGAAGCAGAGAAA 58.984 47.826 0.00 0.00 0.00 2.52
822 999 4.096984 GGAGAGAGAGAGAAGCAGAGAAAG 59.903 50.000 0.00 0.00 0.00 2.62
823 1000 3.445096 AGAGAGAGAGAAGCAGAGAAAGC 59.555 47.826 0.00 0.00 0.00 3.51
824 1001 3.434309 AGAGAGAGAAGCAGAGAAAGCT 58.566 45.455 0.00 0.00 45.97 3.74
825 1002 3.194116 AGAGAGAGAAGCAGAGAAAGCTG 59.806 47.826 0.00 0.00 42.53 4.24
826 1003 2.234414 AGAGAGAAGCAGAGAAAGCTGG 59.766 50.000 0.00 0.00 42.53 4.85
827 1004 1.278699 AGAGAAGCAGAGAAAGCTGGG 59.721 52.381 0.00 0.00 42.53 4.45
828 1005 1.003003 GAGAAGCAGAGAAAGCTGGGT 59.997 52.381 0.00 0.00 42.53 4.51
829 1006 1.163554 GAAGCAGAGAAAGCTGGGTG 58.836 55.000 0.00 0.00 42.53 4.61
879 1056 0.322098 TTGTACCGCCCACCAATCAG 60.322 55.000 0.00 0.00 0.00 2.90
931 1108 3.955429 CAACAGTGGAAAGATCGCG 57.045 52.632 0.00 0.00 0.00 5.87
932 1109 0.179215 CAACAGTGGAAAGATCGCGC 60.179 55.000 0.00 0.00 0.00 6.86
936 1113 2.819595 TGGAAAGATCGCGCCAGC 60.820 61.111 0.00 0.00 40.74 4.85
937 1114 3.577313 GGAAAGATCGCGCCAGCC 61.577 66.667 0.00 0.00 41.18 4.85
941 1118 4.521062 AGATCGCGCCAGCCAGAC 62.521 66.667 0.00 0.00 41.18 3.51
1107 1311 2.567049 CACCACGAGGAGGACGAC 59.433 66.667 5.68 0.00 38.69 4.34
1108 1312 3.054503 ACCACGAGGAGGACGACG 61.055 66.667 5.68 0.00 38.69 5.12
1109 1313 2.745100 CCACGAGGAGGACGACGA 60.745 66.667 0.00 0.00 36.89 4.20
1110 1314 2.479650 CACGAGGAGGACGACGAC 59.520 66.667 0.00 0.00 34.70 4.34
1111 1315 3.117171 ACGAGGAGGACGACGACG 61.117 66.667 5.58 5.58 45.75 5.12
1112 1316 2.812609 CGAGGAGGACGACGACGA 60.813 66.667 15.32 0.00 42.66 4.20
1155 1359 0.750850 TGGCGCTCTCCAAGGTATAC 59.249 55.000 7.64 0.00 32.18 1.47
1156 1360 0.318784 GGCGCTCTCCAAGGTATACG 60.319 60.000 7.64 0.00 0.00 3.06
1157 1361 0.940047 GCGCTCTCCAAGGTATACGC 60.940 60.000 0.00 0.00 38.17 4.42
1158 1362 0.660595 CGCTCTCCAAGGTATACGCG 60.661 60.000 3.53 3.53 0.00 6.01
1159 1363 0.940047 GCTCTCCAAGGTATACGCGC 60.940 60.000 5.73 0.00 0.00 6.86
1160 1364 0.660595 CTCTCCAAGGTATACGCGCG 60.661 60.000 30.96 30.96 0.00 6.86
1161 1365 2.278989 TCCAAGGTATACGCGCGC 60.279 61.111 32.58 23.91 0.00 6.86
1200 1404 2.159296 ACGTGTAGATGCGCACATTCTA 60.159 45.455 14.90 14.20 36.35 2.10
1203 1407 4.679654 CGTGTAGATGCGCACATTCTATAA 59.320 41.667 14.90 6.51 36.35 0.98
1208 1412 5.174395 AGATGCGCACATTCTATAATCTCC 58.826 41.667 14.90 0.00 36.35 3.71
1213 1417 4.993584 CGCACATTCTATAATCTCCAGCTT 59.006 41.667 0.00 0.00 0.00 3.74
1218 1422 6.013812 ACATTCTATAATCTCCAGCTTCCTCC 60.014 42.308 0.00 0.00 0.00 4.30
1264 1478 4.858935 CCGGTAAATTTCATACTGGCATG 58.141 43.478 4.81 0.00 41.55 4.06
1305 1519 2.478831 GGTAGACATTCAGCTGCTAGC 58.521 52.381 9.47 8.10 42.84 3.42
1328 1550 2.095364 AGCTACAGTACGTGAAAGGTCG 60.095 50.000 0.00 0.00 35.89 4.79
1369 1591 2.088423 TGTTTATTTACTGCCTGGCCG 58.912 47.619 17.53 12.95 0.00 6.13
1445 1679 1.810755 TGAGCTGATCGACTTACGTGT 59.189 47.619 0.00 0.00 43.13 4.49
2009 2243 3.449227 CTCCTCGTGGTGCGCCTA 61.449 66.667 18.96 0.57 41.07 3.93
2075 2309 4.400961 AACCTGCTCCTGGCGCTC 62.401 66.667 7.64 0.00 45.43 5.03
2078 2312 4.834453 CTGCTCCTGGCGCTCCTG 62.834 72.222 7.64 0.00 45.43 3.86
2107 2341 4.181010 CATCTCGGGGGCCCACAG 62.181 72.222 27.55 20.41 35.37 3.66
2243 2477 2.031516 CGTGCTGTCTGGGCTTCTG 61.032 63.158 0.00 0.00 0.00 3.02
2435 2669 3.554692 CTCGTCATTGGCGCCGTC 61.555 66.667 23.90 8.92 0.00 4.79
2555 2789 3.782244 CTGTGCGAGCTCGGCAAC 61.782 66.667 35.10 23.98 40.23 4.17
2645 2879 0.683504 TGGCCTCCTTCTACCTCGTC 60.684 60.000 3.32 0.00 0.00 4.20
2830 3064 0.036010 CCCACTACCAGCTCCAACAG 60.036 60.000 0.00 0.00 0.00 3.16
2844 3078 0.453282 CAACAGCTCCGAATGCAACG 60.453 55.000 9.21 9.21 0.00 4.10
2860 3094 2.176546 CGCCAACACATCAAGCGG 59.823 61.111 0.00 0.00 42.93 5.52
2890 3124 1.210155 CTAGCACCAAAACAGCGGC 59.790 57.895 0.00 0.00 0.00 6.53
2895 3129 0.871163 CACCAAAACAGCGGCAACTG 60.871 55.000 1.45 3.82 43.59 3.16
2900 3134 1.515521 AAACAGCGGCAACTGCTACC 61.516 55.000 1.45 0.00 42.95 3.18
2920 3154 2.879907 CAGCAATGCCGGTGGAAG 59.120 61.111 1.90 0.00 0.00 3.46
2930 3164 0.593128 CCGGTGGAAGCAAGAACAAG 59.407 55.000 0.00 0.00 0.00 3.16
3000 3234 1.153005 CTGGAGGAAGGGCTCATGC 60.153 63.158 0.00 0.00 38.76 4.06
3059 3302 0.179084 ACACGAATGCGGTGGATAGG 60.179 55.000 0.00 0.00 43.17 2.57
3065 3308 1.410850 ATGCGGTGGATAGGGACAGG 61.411 60.000 0.00 0.00 0.00 4.00
3138 3387 4.427661 AGCAGTGCGTCTCGGAGC 62.428 66.667 10.00 0.00 0.00 4.70
3178 3427 2.760385 GGACGTGGAGGAGGAGGG 60.760 72.222 0.00 0.00 0.00 4.30
3179 3428 2.760385 GACGTGGAGGAGGAGGGG 60.760 72.222 0.00 0.00 0.00 4.79
3180 3429 4.400251 ACGTGGAGGAGGAGGGGG 62.400 72.222 0.00 0.00 0.00 5.40
3181 3430 4.075793 CGTGGAGGAGGAGGGGGA 62.076 72.222 0.00 0.00 0.00 4.81
3182 3431 2.041405 GTGGAGGAGGAGGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
3183 3432 3.368501 TGGAGGAGGAGGGGGAGG 61.369 72.222 0.00 0.00 0.00 4.30
3184 3433 3.036959 GGAGGAGGAGGGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
3185 3434 2.612251 GAGGAGGAGGGGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
3186 3435 3.039526 AGGAGGAGGGGGAGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
3246 3495 2.363925 AGGTCTAGGGTGGTCGCC 60.364 66.667 0.00 0.00 0.00 5.54
3308 3561 3.993081 GCTATTGACTTGATCCATCTCCG 59.007 47.826 0.00 0.00 0.00 4.63
3316 3569 3.245668 ATCCATCTCCGCGCCATCC 62.246 63.158 0.00 0.00 0.00 3.51
3358 3615 1.335182 TGATAAAGAGCGAGCGAGAGG 59.665 52.381 0.00 0.00 0.00 3.69
3370 3627 0.468226 GCGAGAGGGAGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
3371 3628 1.541233 GCGAGAGGGAGAGAGAGAGAG 60.541 61.905 0.00 0.00 0.00 3.20
3372 3629 2.039418 CGAGAGGGAGAGAGAGAGAGA 58.961 57.143 0.00 0.00 0.00 3.10
3373 3630 2.036475 CGAGAGGGAGAGAGAGAGAGAG 59.964 59.091 0.00 0.00 0.00 3.20
3374 3631 3.309296 GAGAGGGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
3375 3632 3.312890 AGAGGGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
3376 3633 3.051803 AGAGGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
3377 3634 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
3378 3635 3.051803 AGGGAGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
3379 3636 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
3380 3637 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
3381 3638 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
3447 3704 8.592105 TTTTCACCTTTTCTTGCTTATCATTG 57.408 30.769 0.00 0.00 0.00 2.82
3579 3855 4.142513 GGATGATGAGAGTTGAAAAGTGCC 60.143 45.833 0.00 0.00 0.00 5.01
3612 3888 3.434319 CACGCAGCCATCCACCAC 61.434 66.667 0.00 0.00 0.00 4.16
3627 3903 3.379445 CACGGGCGTGGAGGTACT 61.379 66.667 0.00 0.00 42.00 2.73
3628 3904 3.379445 ACGGGCGTGGAGGTACTG 61.379 66.667 0.00 0.00 41.55 2.74
3629 3905 4.143333 CGGGCGTGGAGGTACTGG 62.143 72.222 0.00 0.00 41.55 4.00
3638 3914 2.026641 TGGAGGTACTGGTACGTATGC 58.973 52.381 0.00 1.54 41.55 3.14
3674 3950 5.114780 CCTGATGATTTGAGACGAGTTGAT 58.885 41.667 0.00 0.00 0.00 2.57
3805 4091 3.372060 CTCCTTTTTGTGCGTTTCCTTC 58.628 45.455 0.00 0.00 0.00 3.46
3806 4092 2.100087 TCCTTTTTGTGCGTTTCCTTCC 59.900 45.455 0.00 0.00 0.00 3.46
3807 4093 2.100749 CCTTTTTGTGCGTTTCCTTCCT 59.899 45.455 0.00 0.00 0.00 3.36
3808 4094 3.430236 CCTTTTTGTGCGTTTCCTTCCTT 60.430 43.478 0.00 0.00 0.00 3.36
3810 4096 3.878160 TTTGTGCGTTTCCTTCCTTTT 57.122 38.095 0.00 0.00 0.00 2.27
3811 4097 2.861462 TGTGCGTTTCCTTCCTTTTG 57.139 45.000 0.00 0.00 0.00 2.44
3813 4099 2.955660 TGTGCGTTTCCTTCCTTTTGAT 59.044 40.909 0.00 0.00 0.00 2.57
3814 4100 4.138290 TGTGCGTTTCCTTCCTTTTGATA 58.862 39.130 0.00 0.00 0.00 2.15
3815 4101 4.580995 TGTGCGTTTCCTTCCTTTTGATAA 59.419 37.500 0.00 0.00 0.00 1.75
3816 4102 5.067936 TGTGCGTTTCCTTCCTTTTGATAAA 59.932 36.000 0.00 0.00 0.00 1.40
3817 4103 5.629435 GTGCGTTTCCTTCCTTTTGATAAAG 59.371 40.000 0.00 0.00 40.38 1.85
3818 4104 5.533154 TGCGTTTCCTTCCTTTTGATAAAGA 59.467 36.000 0.00 0.00 42.78 2.52
3819 4105 6.208599 TGCGTTTCCTTCCTTTTGATAAAGAT 59.791 34.615 0.00 0.00 42.78 2.40
3820 4106 6.747739 GCGTTTCCTTCCTTTTGATAAAGATC 59.252 38.462 0.00 0.00 42.78 2.75
3822 4108 7.360946 CGTTTCCTTCCTTTTGATAAAGATCGT 60.361 37.037 0.00 0.00 42.78 3.73
3823 4109 8.943002 GTTTCCTTCCTTTTGATAAAGATCGTA 58.057 33.333 0.00 0.00 42.78 3.43
3855 4146 2.726760 CCGATATCTACAAAGCACTCGC 59.273 50.000 0.34 0.00 38.99 5.03
3856 4147 2.726760 CGATATCTACAAAGCACTCGCC 59.273 50.000 0.34 0.00 39.83 5.54
3859 4150 0.109272 TCTACAAAGCACTCGCCGAG 60.109 55.000 13.52 13.52 39.83 4.63
3904 4195 6.129221 TGCGATTTTGCGAAGAATAAACTTTG 60.129 34.615 0.00 0.00 37.81 2.77
3925 4216 2.126734 CGCAGCGCAAAGGAAAGG 60.127 61.111 11.47 0.00 0.00 3.11
3926 4217 2.616330 CGCAGCGCAAAGGAAAGGA 61.616 57.895 11.47 0.00 0.00 3.36
3927 4218 1.659794 GCAGCGCAAAGGAAAGGAA 59.340 52.632 11.47 0.00 0.00 3.36
3928 4219 0.664466 GCAGCGCAAAGGAAAGGAAC 60.664 55.000 11.47 0.00 0.00 3.62
3929 4220 0.385974 CAGCGCAAAGGAAAGGAACG 60.386 55.000 11.47 0.00 0.00 3.95
3930 4221 0.534203 AGCGCAAAGGAAAGGAACGA 60.534 50.000 11.47 0.00 0.00 3.85
3931 4222 0.521735 GCGCAAAGGAAAGGAACGAT 59.478 50.000 0.30 0.00 0.00 3.73
3932 4223 1.729149 GCGCAAAGGAAAGGAACGATG 60.729 52.381 0.30 0.00 0.00 3.84
3933 4224 1.729149 CGCAAAGGAAAGGAACGATGC 60.729 52.381 0.00 0.00 0.00 3.91
3934 4225 1.402852 GCAAAGGAAAGGAACGATGCC 60.403 52.381 0.00 0.00 0.00 4.40
3935 4226 2.162681 CAAAGGAAAGGAACGATGCCT 58.837 47.619 0.00 0.00 37.35 4.75
3936 4227 1.826385 AAGGAAAGGAACGATGCCTG 58.174 50.000 0.00 0.00 35.50 4.85
3937 4228 0.678048 AGGAAAGGAACGATGCCTGC 60.678 55.000 0.00 0.00 35.50 4.85
3938 4229 0.678048 GGAAAGGAACGATGCCTGCT 60.678 55.000 0.00 0.00 35.50 4.24
3939 4230 0.449388 GAAAGGAACGATGCCTGCTG 59.551 55.000 0.00 0.00 35.50 4.41
3940 4231 1.589716 AAAGGAACGATGCCTGCTGC 61.590 55.000 0.00 0.00 35.50 5.25
3941 4232 2.437359 GGAACGATGCCTGCTGCT 60.437 61.111 0.00 0.00 42.00 4.24
3942 4233 2.758089 GGAACGATGCCTGCTGCTG 61.758 63.158 0.00 0.00 42.00 4.41
3943 4234 3.392595 GAACGATGCCTGCTGCTGC 62.393 63.158 8.89 8.89 42.00 5.25
3944 4235 3.914579 AACGATGCCTGCTGCTGCT 62.915 57.895 17.00 0.00 42.00 4.24
3945 4236 3.877357 CGATGCCTGCTGCTGCTG 61.877 66.667 17.00 15.58 42.00 4.41
3946 4237 4.194720 GATGCCTGCTGCTGCTGC 62.195 66.667 22.51 22.51 42.00 5.25
3978 4269 0.394899 CATGCCTCTGTTTCCCCTCC 60.395 60.000 0.00 0.00 0.00 4.30
3984 4275 1.488393 CTCTGTTTCCCCTCCCAGATC 59.512 57.143 0.00 0.00 33.77 2.75
3989 4280 1.837533 TTCCCCTCCCAGATCACCCT 61.838 60.000 0.00 0.00 0.00 4.34
3990 4281 1.308216 CCCCTCCCAGATCACCCTT 60.308 63.158 0.00 0.00 0.00 3.95
3991 4282 0.921256 CCCCTCCCAGATCACCCTTT 60.921 60.000 0.00 0.00 0.00 3.11
4044 4336 0.250166 GCCCTGTCACCGTACAAACT 60.250 55.000 0.00 0.00 0.00 2.66
4056 4348 4.143263 ACCGTACAAACTTCGAATAAAGCG 60.143 41.667 0.00 0.00 0.00 4.68
4062 4355 1.014352 CTTCGAATAAAGCGTGGGGG 58.986 55.000 0.00 0.00 0.00 5.40
4107 4403 4.338379 ACTACTCGGATATGGAAAAGGC 57.662 45.455 0.00 0.00 0.00 4.35
4152 4448 2.698797 TCACGACCACTTCCTCTTTCTT 59.301 45.455 0.00 0.00 0.00 2.52
4153 4449 2.802816 CACGACCACTTCCTCTTTCTTG 59.197 50.000 0.00 0.00 0.00 3.02
4157 4454 4.024809 CGACCACTTCCTCTTTCTTGTTTC 60.025 45.833 0.00 0.00 0.00 2.78
4166 4463 2.755655 TCTTTCTTGTTTCGGGTTTGCA 59.244 40.909 0.00 0.00 0.00 4.08
4199 4496 5.411977 TCGTGTGGTTTTTGTGAACTCTTTA 59.588 36.000 0.00 0.00 0.00 1.85
4206 4503 8.124199 TGGTTTTTGTGAACTCTTTATACGTTC 58.876 33.333 0.00 0.00 37.97 3.95
4207 4504 8.124199 GGTTTTTGTGAACTCTTTATACGTTCA 58.876 33.333 0.00 0.00 43.18 3.18
4214 4511 7.792508 GTGAACTCTTTATACGTTCAGTTTGTG 59.207 37.037 0.00 0.00 45.18 3.33
4216 4513 7.639162 ACTCTTTATACGTTCAGTTTGTGAG 57.361 36.000 0.00 0.00 36.21 3.51
4223 4520 5.751243 ACGTTCAGTTTGTGAGCTTTAAT 57.249 34.783 0.00 0.00 36.21 1.40
4226 4523 7.699566 ACGTTCAGTTTGTGAGCTTTAATTAA 58.300 30.769 0.00 0.00 36.21 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.867329 GCTGCCGAATTTTGGATCGC 60.867 55.000 6.88 1.79 37.73 4.58
22 27 3.125607 CCATGCATGCTGCCGAAT 58.874 55.556 21.69 0.00 44.23 3.34
53 58 5.163683 GCTACCCATGACGTCGTATGTATAT 60.164 44.000 10.54 0.00 0.00 0.86
54 59 4.154737 GCTACCCATGACGTCGTATGTATA 59.845 45.833 10.54 3.62 0.00 1.47
55 60 3.057736 GCTACCCATGACGTCGTATGTAT 60.058 47.826 10.54 2.65 0.00 2.29
56 61 2.291465 GCTACCCATGACGTCGTATGTA 59.709 50.000 10.54 13.01 0.00 2.29
69 74 2.108168 TCACTTTCGCTAGCTACCCAT 58.892 47.619 13.93 0.00 0.00 4.00
82 87 5.720202 ACCCACTTCAACTTTTTCACTTTC 58.280 37.500 0.00 0.00 0.00 2.62
88 93 3.878699 TCCGTACCCACTTCAACTTTTTC 59.121 43.478 0.00 0.00 0.00 2.29
99 104 4.503817 GGTTACTTCTTTTCCGTACCCACT 60.504 45.833 0.00 0.00 0.00 4.00
103 108 2.995939 CGGGTTACTTCTTTTCCGTACC 59.004 50.000 0.00 0.00 33.63 3.34
108 113 2.991866 CTCGACGGGTTACTTCTTTTCC 59.008 50.000 0.00 0.00 0.00 3.13
154 159 0.456312 GTCTCCGCTTGACCTACACG 60.456 60.000 0.00 0.00 0.00 4.49
155 160 0.456312 CGTCTCCGCTTGACCTACAC 60.456 60.000 0.00 0.00 0.00 2.90
179 184 0.465642 GGTTTGGGATGGGTCGATCC 60.466 60.000 8.12 8.12 41.28 3.36
180 185 0.465642 GGGTTTGGGATGGGTCGATC 60.466 60.000 0.00 0.00 0.00 3.69
181 186 0.919289 AGGGTTTGGGATGGGTCGAT 60.919 55.000 0.00 0.00 0.00 3.59
182 187 0.252789 TAGGGTTTGGGATGGGTCGA 60.253 55.000 0.00 0.00 0.00 4.20
183 188 0.107361 GTAGGGTTTGGGATGGGTCG 60.107 60.000 0.00 0.00 0.00 4.79
184 189 1.212195 GAGTAGGGTTTGGGATGGGTC 59.788 57.143 0.00 0.00 0.00 4.46
185 190 1.203570 AGAGTAGGGTTTGGGATGGGT 60.204 52.381 0.00 0.00 0.00 4.51
186 191 1.596496 AGAGTAGGGTTTGGGATGGG 58.404 55.000 0.00 0.00 0.00 4.00
187 192 2.102588 CGTAGAGTAGGGTTTGGGATGG 59.897 54.545 0.00 0.00 0.00 3.51
188 193 2.764572 ACGTAGAGTAGGGTTTGGGATG 59.235 50.000 0.00 0.00 0.00 3.51
211 216 0.450583 CTCGCTGCCGAACTGTAGTA 59.549 55.000 0.00 0.00 43.87 1.82
212 217 1.213013 CTCGCTGCCGAACTGTAGT 59.787 57.895 0.00 0.00 43.87 2.73
213 218 2.161486 GCTCGCTGCCGAACTGTAG 61.161 63.158 0.00 0.00 43.87 2.74
214 219 2.126071 GCTCGCTGCCGAACTGTA 60.126 61.111 0.00 0.00 43.87 2.74
227 232 1.217882 GGTGAATAATCGGTGGCTCG 58.782 55.000 0.00 0.00 0.00 5.03
259 264 1.986378 CTACTACTGTGTCACGCAAGC 59.014 52.381 0.00 0.00 45.62 4.01
269 274 5.047519 CCCCCGGTAATTATCTACTACTGTG 60.048 48.000 0.00 0.00 0.00 3.66
315 478 1.838943 GAAGTCGTCGACGCAGATTAC 59.161 52.381 32.19 22.83 37.67 1.89
359 522 3.787001 CAACCTCGCCTCCCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
360 523 2.593956 AACAACCTCGCCTCCCTCC 61.594 63.158 0.00 0.00 0.00 4.30
361 524 1.376037 CAACAACCTCGCCTCCCTC 60.376 63.158 0.00 0.00 0.00 4.30
362 525 2.750350 CAACAACCTCGCCTCCCT 59.250 61.111 0.00 0.00 0.00 4.20
363 526 2.359975 CCAACAACCTCGCCTCCC 60.360 66.667 0.00 0.00 0.00 4.30
364 527 2.359975 CCCAACAACCTCGCCTCC 60.360 66.667 0.00 0.00 0.00 4.30
365 528 1.671379 GACCCAACAACCTCGCCTC 60.671 63.158 0.00 0.00 0.00 4.70
372 539 1.271379 GGAAAATCGGACCCAACAACC 59.729 52.381 0.00 0.00 0.00 3.77
449 618 0.994995 GCATATATGCGCCTGTCTCG 59.005 55.000 21.33 0.00 44.67 4.04
469 638 1.734465 GAATGGAGTGAAGTTGGCTCG 59.266 52.381 0.00 0.00 0.00 5.03
494 663 6.887626 TGTATTATTATTTTCTTCCGGGCC 57.112 37.500 0.00 0.00 0.00 5.80
523 694 4.488449 CGAACGAATGAATGAACACGAATG 59.512 41.667 0.00 0.00 0.00 2.67
524 695 4.151689 ACGAACGAATGAATGAACACGAAT 59.848 37.500 0.14 0.00 0.00 3.34
525 696 3.491639 ACGAACGAATGAATGAACACGAA 59.508 39.130 0.14 0.00 0.00 3.85
526 697 3.054166 ACGAACGAATGAATGAACACGA 58.946 40.909 0.14 0.00 0.00 4.35
527 698 3.433709 ACGAACGAATGAATGAACACG 57.566 42.857 0.14 0.00 0.00 4.49
528 699 4.148891 GGAACGAACGAATGAATGAACAC 58.851 43.478 0.14 0.00 0.00 3.32
529 700 3.810386 TGGAACGAACGAATGAATGAACA 59.190 39.130 0.14 0.00 0.00 3.18
530 701 4.398549 TGGAACGAACGAATGAATGAAC 57.601 40.909 0.14 0.00 0.00 3.18
531 702 4.693095 TCATGGAACGAACGAATGAATGAA 59.307 37.500 0.14 0.00 0.00 2.57
532 703 4.249661 TCATGGAACGAACGAATGAATGA 58.750 39.130 0.14 1.69 0.00 2.57
533 704 4.598406 TCATGGAACGAACGAATGAATG 57.402 40.909 0.14 0.00 0.00 2.67
534 705 4.035558 CCATCATGGAACGAACGAATGAAT 59.964 41.667 0.00 0.00 40.96 2.57
535 706 3.373748 CCATCATGGAACGAACGAATGAA 59.626 43.478 0.00 0.00 40.96 2.57
536 707 2.935849 CCATCATGGAACGAACGAATGA 59.064 45.455 0.00 5.42 40.96 2.57
636 813 1.194495 GCCCGTATATATACACGCGC 58.806 55.000 20.24 7.70 36.85 6.86
637 814 1.132834 TGGCCCGTATATATACACGCG 59.867 52.381 20.24 3.53 36.85 6.01
638 815 2.805845 CTGGCCCGTATATATACACGC 58.194 52.381 20.24 18.57 36.85 5.34
639 816 2.480759 GGCTGGCCCGTATATATACACG 60.481 54.545 20.24 6.58 37.89 4.49
693 870 3.808656 GGCGCTCTCTTTGCTGCC 61.809 66.667 7.64 0.00 40.53 4.85
705 882 2.042537 TGATGAGGAGGAGGCGCT 60.043 61.111 7.64 0.00 0.00 5.92
706 883 2.107953 GTGATGAGGAGGAGGCGC 59.892 66.667 0.00 0.00 0.00 6.53
707 884 1.739049 GAGTGATGAGGAGGAGGCG 59.261 63.158 0.00 0.00 0.00 5.52
708 885 1.739049 CGAGTGATGAGGAGGAGGC 59.261 63.158 0.00 0.00 0.00 4.70
709 886 1.739049 GCGAGTGATGAGGAGGAGG 59.261 63.158 0.00 0.00 0.00 4.30
753 930 1.304464 GGCCTTTTGGTCTCCTGGG 60.304 63.158 0.00 0.00 42.03 4.45
773 950 1.598701 GGGATTGGTGCTTGCTGGTC 61.599 60.000 0.00 0.00 0.00 4.02
778 955 2.568090 CGTGGGATTGGTGCTTGC 59.432 61.111 0.00 0.00 0.00 4.01
797 974 1.064017 TCTGCTTCTCTCTCTCTCCCC 60.064 57.143 0.00 0.00 0.00 4.81
799 976 3.281727 TCTCTGCTTCTCTCTCTCTCC 57.718 52.381 0.00 0.00 0.00 3.71
812 989 1.377994 CCACCCAGCTTTCTCTGCT 59.622 57.895 0.00 0.00 42.06 4.24
814 991 2.704572 CTTACCACCCAGCTTTCTCTG 58.295 52.381 0.00 0.00 0.00 3.35
815 992 1.003696 GCTTACCACCCAGCTTTCTCT 59.996 52.381 0.00 0.00 32.87 3.10
817 994 1.068121 AGCTTACCACCCAGCTTTCT 58.932 50.000 0.00 0.00 44.28 2.52
818 995 2.747989 GTTAGCTTACCACCCAGCTTTC 59.252 50.000 0.00 0.00 44.28 2.62
819 996 2.791655 GTTAGCTTACCACCCAGCTTT 58.208 47.619 0.00 0.00 44.28 3.51
820 997 1.338769 CGTTAGCTTACCACCCAGCTT 60.339 52.381 0.00 0.00 44.28 3.74
822 999 0.248289 TCGTTAGCTTACCACCCAGC 59.752 55.000 0.00 0.00 36.16 4.85
823 1000 1.549170 ACTCGTTAGCTTACCACCCAG 59.451 52.381 0.00 0.00 0.00 4.45
824 1001 1.547372 GACTCGTTAGCTTACCACCCA 59.453 52.381 0.00 0.00 0.00 4.51
825 1002 1.547372 TGACTCGTTAGCTTACCACCC 59.453 52.381 0.00 0.00 0.00 4.61
826 1003 3.308438 TTGACTCGTTAGCTTACCACC 57.692 47.619 0.00 0.00 0.00 4.61
827 1004 4.689345 ACATTTGACTCGTTAGCTTACCAC 59.311 41.667 0.00 0.00 0.00 4.16
828 1005 4.890088 ACATTTGACTCGTTAGCTTACCA 58.110 39.130 0.00 0.00 0.00 3.25
829 1006 6.098017 AGTACATTTGACTCGTTAGCTTACC 58.902 40.000 0.00 0.00 0.00 2.85
969 1161 1.302832 CCGGCTGGAAAGTGCTTCT 60.303 57.895 5.28 0.00 37.49 2.85
970 1162 2.982744 GCCGGCTGGAAAGTGCTTC 61.983 63.158 22.15 0.00 37.49 3.86
971 1163 2.985847 GCCGGCTGGAAAGTGCTT 60.986 61.111 22.15 0.00 37.49 3.91
1047 1251 3.157087 GTGGGAGGAATTCTTGAAGCAA 58.843 45.455 5.23 0.00 0.00 3.91
1098 1302 2.479650 CTGTCGTCGTCGTCCTCC 59.520 66.667 1.33 0.00 38.33 4.30
1101 1305 4.034258 TGGCTGTCGTCGTCGTCC 62.034 66.667 1.33 1.01 38.33 4.79
1181 1385 6.587990 AGATTATAGAATGTGCGCATCTACAC 59.412 38.462 18.74 11.46 33.50 2.90
1200 1404 2.708325 GGTGGAGGAAGCTGGAGATTAT 59.292 50.000 0.00 0.00 0.00 1.28
1203 1407 0.043940 AGGTGGAGGAAGCTGGAGAT 59.956 55.000 0.00 0.00 0.00 2.75
1208 1412 0.747283 GATGCAGGTGGAGGAAGCTG 60.747 60.000 0.00 0.00 46.20 4.24
1213 1417 2.993008 GCAGATGCAGGTGGAGGA 59.007 61.111 0.00 0.00 41.59 3.71
1261 1475 0.520847 TTGTACGTGTGCATGCCATG 59.479 50.000 16.68 18.96 0.00 3.66
1262 1476 0.804364 CTTGTACGTGTGCATGCCAT 59.196 50.000 16.68 1.61 0.00 4.40
1263 1477 1.851021 GCTTGTACGTGTGCATGCCA 61.851 55.000 16.68 10.08 39.29 4.92
1264 1478 1.154225 GCTTGTACGTGTGCATGCC 60.154 57.895 16.68 7.25 39.29 4.40
1305 1519 4.660105 GACCTTTCACGTACTGTAGCTAG 58.340 47.826 0.00 0.00 0.00 3.42
1306 1520 3.125829 CGACCTTTCACGTACTGTAGCTA 59.874 47.826 0.00 0.00 0.00 3.32
1307 1521 2.095364 CGACCTTTCACGTACTGTAGCT 60.095 50.000 0.00 0.00 0.00 3.32
1308 1522 2.248487 CGACCTTTCACGTACTGTAGC 58.752 52.381 0.00 0.00 0.00 3.58
1369 1591 3.428282 CGGCCGGTTGCTGTTACC 61.428 66.667 20.10 0.00 41.73 2.85
1622 1856 0.742505 CGGAGTAGCCCGTGATGTTA 59.257 55.000 0.00 0.00 44.23 2.41
1703 1937 4.648626 AGCGCCAGAAGCTTGCCA 62.649 61.111 2.10 0.00 43.24 4.92
2042 2276 4.717629 TTGAGGTCGGTGAGCGCG 62.718 66.667 0.00 0.00 35.00 6.86
2075 2309 1.817099 GATGGCGAGGAAGCACAGG 60.817 63.158 0.00 0.00 39.27 4.00
2078 2312 1.880340 CGAGATGGCGAGGAAGCAC 60.880 63.158 0.00 0.00 39.27 4.40
2107 2341 3.703127 GACCCACCCACGAGTCCC 61.703 72.222 0.00 0.00 0.00 4.46
2402 2636 3.723235 GAGGCCGATGAAGAGCGCA 62.723 63.158 11.47 0.00 0.00 6.09
2435 2669 3.070018 GGATATCATGAAGGTGGAAGCG 58.930 50.000 0.00 0.00 40.95 4.68
2830 3064 2.976840 TTGGCGTTGCATTCGGAGC 61.977 57.895 12.40 1.52 0.00 4.70
2844 3078 2.126346 GCCGCTTGATGTGTTGGC 60.126 61.111 0.00 0.00 35.04 4.52
2920 3154 1.136336 CGTAGCCGTTCTTGTTCTTGC 60.136 52.381 0.00 0.00 0.00 4.01
3059 3302 2.583520 CTGCTGCTCTCCCTGTCC 59.416 66.667 0.00 0.00 0.00 4.02
3308 3561 1.305930 ACCGAAAAAGAGGATGGCGC 61.306 55.000 0.00 0.00 0.00 6.53
3316 3569 0.602905 ACCTCGCCACCGAAAAAGAG 60.603 55.000 0.00 0.00 43.87 2.85
3358 3615 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
3370 3627 5.072329 CCTCCTCAATACTCTCTCTCTCTCT 59.928 48.000 0.00 0.00 0.00 3.10
3371 3628 5.071788 TCCTCCTCAATACTCTCTCTCTCTC 59.928 48.000 0.00 0.00 0.00 3.20
3372 3629 4.975147 TCCTCCTCAATACTCTCTCTCTCT 59.025 45.833 0.00 0.00 0.00 3.10
3373 3630 5.304686 TCCTCCTCAATACTCTCTCTCTC 57.695 47.826 0.00 0.00 0.00 3.20
3374 3631 5.725551 TTCCTCCTCAATACTCTCTCTCT 57.274 43.478 0.00 0.00 0.00 3.10
3375 3632 6.549364 TCATTTCCTCCTCAATACTCTCTCTC 59.451 42.308 0.00 0.00 0.00 3.20
3376 3633 6.439487 TCATTTCCTCCTCAATACTCTCTCT 58.561 40.000 0.00 0.00 0.00 3.10
3377 3634 6.723298 TCATTTCCTCCTCAATACTCTCTC 57.277 41.667 0.00 0.00 0.00 3.20
3378 3635 7.688918 AATCATTTCCTCCTCAATACTCTCT 57.311 36.000 0.00 0.00 0.00 3.10
3379 3636 9.434420 CATAATCATTTCCTCCTCAATACTCTC 57.566 37.037 0.00 0.00 0.00 3.20
3380 3637 8.943085 ACATAATCATTTCCTCCTCAATACTCT 58.057 33.333 0.00 0.00 0.00 3.24
3426 3683 4.866486 GGCAATGATAAGCAAGAAAAGGTG 59.134 41.667 0.00 0.00 0.00 4.00
3427 3684 4.081476 GGGCAATGATAAGCAAGAAAAGGT 60.081 41.667 0.00 0.00 0.00 3.50
3428 3685 4.436332 GGGCAATGATAAGCAAGAAAAGG 58.564 43.478 0.00 0.00 0.00 3.11
3447 3704 0.181350 CAGGAGTACCAATCTGGGGC 59.819 60.000 0.00 0.00 43.37 5.80
3537 3811 5.761726 TCATCCATTGATAATGTGCACTCTC 59.238 40.000 19.41 9.62 37.18 3.20
3556 3832 4.142513 GGCACTTTTCAACTCTCATCATCC 60.143 45.833 0.00 0.00 0.00 3.51
3612 3888 4.143333 CCAGTACCTCCACGCCCG 62.143 72.222 0.00 0.00 0.00 6.13
3616 3892 1.737838 TACGTACCAGTACCTCCACG 58.262 55.000 2.46 6.23 32.61 4.94
3617 3893 2.223665 GCATACGTACCAGTACCTCCAC 60.224 54.545 0.00 0.00 32.61 4.02
3618 3894 2.026641 GCATACGTACCAGTACCTCCA 58.973 52.381 0.00 0.00 32.61 3.86
3619 3895 1.339291 GGCATACGTACCAGTACCTCC 59.661 57.143 0.00 0.00 32.61 4.30
3620 3896 2.026641 TGGCATACGTACCAGTACCTC 58.973 52.381 0.00 0.00 32.61 3.85
3621 3897 1.753073 GTGGCATACGTACCAGTACCT 59.247 52.381 5.21 0.00 36.38 3.08
3622 3898 1.753073 AGTGGCATACGTACCAGTACC 59.247 52.381 10.11 1.64 37.85 3.34
3623 3899 2.165030 ACAGTGGCATACGTACCAGTAC 59.835 50.000 11.18 0.00 37.51 2.73
3624 3900 2.449464 ACAGTGGCATACGTACCAGTA 58.551 47.619 11.18 0.00 37.51 2.74
3625 3901 1.263356 ACAGTGGCATACGTACCAGT 58.737 50.000 5.21 6.02 40.32 4.00
3626 3902 1.999735 CAACAGTGGCATACGTACCAG 59.000 52.381 5.21 0.00 36.38 4.00
3627 3903 1.338294 CCAACAGTGGCATACGTACCA 60.338 52.381 0.00 0.00 38.35 3.25
3628 3904 1.365699 CCAACAGTGGCATACGTACC 58.634 55.000 0.00 0.00 38.35 3.34
3674 3950 2.047274 GGGAACAGCGCTACAGCA 60.047 61.111 10.99 0.00 42.21 4.41
3732 4018 2.180017 GCGTGGAAATGGCAGCAG 59.820 61.111 0.00 0.00 0.00 4.24
3758 4044 1.903877 ATGAGTTGGAGGTGGGAGCG 61.904 60.000 0.00 0.00 0.00 5.03
3759 4045 0.329596 AATGAGTTGGAGGTGGGAGC 59.670 55.000 0.00 0.00 0.00 4.70
3766 4052 0.962356 AGCGGCAAATGAGTTGGAGG 60.962 55.000 1.45 0.00 37.73 4.30
3770 4056 0.883833 AAGGAGCGGCAAATGAGTTG 59.116 50.000 1.45 0.00 40.50 3.16
3820 4106 2.099141 TATCGGGGGATCGTACTACG 57.901 55.000 1.93 1.93 44.19 3.51
3822 4108 4.471025 TGTAGATATCGGGGGATCGTACTA 59.529 45.833 0.00 0.00 0.00 1.82
3823 4109 3.265221 TGTAGATATCGGGGGATCGTACT 59.735 47.826 0.00 0.00 0.00 2.73
3833 4124 3.309388 CGAGTGCTTTGTAGATATCGGG 58.691 50.000 0.00 0.00 0.00 5.14
3855 4146 2.437359 CAGGGGCAGCTTTCTCGG 60.437 66.667 0.00 0.00 0.00 4.63
3856 4147 2.437359 CCAGGGGCAGCTTTCTCG 60.437 66.667 0.00 0.00 0.00 4.04
3859 4150 1.973812 GACACCAGGGGCAGCTTTC 60.974 63.158 0.00 0.00 0.00 2.62
3923 4214 2.437359 GCAGCAGGCATCGTTCCT 60.437 61.111 0.00 0.00 43.97 3.36
4027 4318 1.790623 CGAAGTTTGTACGGTGACAGG 59.209 52.381 0.00 0.00 0.00 4.00
4044 4336 0.325602 ACCCCCACGCTTTATTCGAA 59.674 50.000 0.00 0.00 0.00 3.71
4056 4348 1.304879 TGCTGCCATAAACCCCCAC 60.305 57.895 0.00 0.00 0.00 4.61
4062 4355 1.677633 ACCGGGTGCTGCCATAAAC 60.678 57.895 6.32 0.00 39.65 2.01
4065 4358 3.326578 ACACCGGGTGCTGCCATA 61.327 61.111 26.62 0.00 36.98 2.74
4107 4403 1.213537 CCACTGATGCGCAAAAGGG 59.786 57.895 17.11 16.40 0.00 3.95
4152 4448 3.252974 ACAAAATGCAAACCCGAAACA 57.747 38.095 0.00 0.00 0.00 2.83
4153 4449 5.387958 CGATTACAAAATGCAAACCCGAAAC 60.388 40.000 0.00 0.00 0.00 2.78
4157 4454 3.363426 CACGATTACAAAATGCAAACCCG 59.637 43.478 0.00 0.00 0.00 5.28
4166 4463 7.036220 TCACAAAAACCACACGATTACAAAAT 58.964 30.769 0.00 0.00 0.00 1.82
4199 4496 6.854496 TTAAAGCTCACAAACTGAACGTAT 57.146 33.333 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.