Multiple sequence alignment - TraesCS1D01G427400

Loading Multiple Alignment...

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 TraesCS1D01G427400 chr1D 100.000 5340 0 0 1 5340 479893869 479888530 0.000000e+00 9862.0
1 TraesCS1D01G427400 chr1D 77.168 346 52 23 3959 4297 479878123 479877798 5.500000e-40 176.0
2 TraesCS1D01G427400 chr1A 90.776 4640 247 78 1 4556 576375705 576371163 0.000000e+00 6030.0
3 TraesCS1D01G427400 chr1A 89.524 210 16 3 5121 5327 576351646 576351440 1.480000e-65 261.0
4 TraesCS1D01G427400 chr1A 96.063 127 5 0 4554 4680 576371082 576370956 1.950000e-49 207.0
5 TraesCS1D01G427400 chr1B 91.387 3576 175 66 1568 5072 668131872 668128359 0.000000e+00 4774.0
6 TraesCS1D01G427400 chr1B 85.475 1253 89 41 376 1587 668133100 668131900 0.000000e+00 1219.0
7 TraesCS1D01G427400 chr1B 87.160 257 17 7 5086 5340 668128071 668127829 1.460000e-70 278.0
8 TraesCS1D01G427400 chr1B 89.091 55 4 2 4618 4672 668127242 668127190 3.450000e-07 67.6
9 TraesCS1D01G427400 chr5D 84.713 157 9 3 4863 5004 12157262 12157418 5.570000e-30 143.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G427400 chr1D 479888530 479893869 5339 True 9862.00 9862 100.00000 1 5340 1 chr1D.!!$R2 5339
1 TraesCS1D01G427400 chr1A 576370956 576375705 4749 True 3118.50 6030 93.41950 1 4680 2 chr1A.!!$R2 4679
2 TraesCS1D01G427400 chr1B 668127190 668133100 5910 True 1584.65 4774 88.27825 376 5340 4 chr1B.!!$R1 4964

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
111 112 0.030235 GTTGGGGCAAAACTGTCGAC 59.970 55.000 9.11 9.11 0.00 4.20 F
152 153 0.036388 GAGGACGGATCTTGTTGCCA 60.036 55.000 0.00 0.00 0.00 4.92 F
909 998 0.040058 ATGTGCCTTCCATGCTCCAA 59.960 50.000 0.00 0.00 0.00 3.53 F
910 999 0.040058 TGTGCCTTCCATGCTCCAAT 59.960 50.000 0.00 0.00 0.00 3.16 F
912 1001 0.627451 TGCCTTCCATGCTCCAATCT 59.373 50.000 0.00 0.00 0.00 2.40 F
2003 2156 1.004440 GCAGTTCAACTCGGCCTCT 60.004 57.895 0.00 0.00 0.00 3.69 F
2811 2970 1.009829 GGAAGCGATGGTTAGCACTG 58.990 55.000 0.00 0.00 35.48 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1440 0.031585 TCGGATCGGCGTAATTCCTG 59.968 55.000 6.85 6.61 0.00 3.86 R
1826 1979 1.521681 GACTGGACGGGCTACATGC 60.522 63.158 0.00 0.00 41.94 4.06 R
2305 2464 0.464554 GTATGAGGTGCAAGGAGGGC 60.465 60.000 0.00 0.00 0.00 5.19 R
2811 2970 2.891580 TCTGACACAGTGAGGTAAGACC 59.108 50.000 7.81 0.00 33.81 3.85 R
2886 3045 4.158949 CCACTTTCTGCAATGATCAATGGA 59.841 41.667 12.62 8.80 0.00 3.41 R
3485 3661 0.247460 GGGGGCTGCAATGAAGAAAC 59.753 55.000 0.50 0.00 0.00 2.78 R
4680 4962 0.232303 CACCACTCGAAAGCAACGTC 59.768 55.000 0.00 0.00 0.00 4.34 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
104 105 2.279851 GCGTGGTTGGGGCAAAAC 60.280 61.111 0.00 0.00 0.00 2.43
105 106 2.791868 GCGTGGTTGGGGCAAAACT 61.792 57.895 2.19 0.00 0.00 2.66
106 107 1.067250 CGTGGTTGGGGCAAAACTG 59.933 57.895 2.19 0.00 0.00 3.16
107 108 1.671901 CGTGGTTGGGGCAAAACTGT 61.672 55.000 2.19 0.00 0.00 3.55
108 109 0.104120 GTGGTTGGGGCAAAACTGTC 59.896 55.000 2.19 0.00 0.00 3.51
109 110 1.362355 GGTTGGGGCAAAACTGTCG 59.638 57.895 2.19 0.00 0.00 4.35
110 111 1.104577 GGTTGGGGCAAAACTGTCGA 61.105 55.000 2.19 0.00 0.00 4.20
111 112 0.030235 GTTGGGGCAAAACTGTCGAC 59.970 55.000 9.11 9.11 0.00 4.20
112 113 1.104577 TTGGGGCAAAACTGTCGACC 61.105 55.000 14.12 0.00 0.00 4.79
113 114 2.613506 GGGGCAAAACTGTCGACCG 61.614 63.158 14.12 9.58 0.00 4.79
116 117 2.943653 CAAAACTGTCGACCGGCC 59.056 61.111 14.12 0.00 0.00 6.13
152 153 0.036388 GAGGACGGATCTTGTTGCCA 60.036 55.000 0.00 0.00 0.00 4.92
175 176 1.948104 TAATTTCAGGATCACGGCCG 58.052 50.000 26.86 26.86 0.00 6.13
189 190 1.745489 GGCCGCTCGGTTTCTCATT 60.745 57.895 10.24 0.00 37.65 2.57
193 194 2.343101 CCGCTCGGTTTCTCATTAACA 58.657 47.619 0.00 0.00 0.00 2.41
194 195 2.093783 CCGCTCGGTTTCTCATTAACAC 59.906 50.000 0.00 0.00 0.00 3.32
195 196 2.993899 CGCTCGGTTTCTCATTAACACT 59.006 45.455 0.00 0.00 0.00 3.55
208 212 5.116180 TCATTAACACTAGCAGTACCATGC 58.884 41.667 0.00 0.00 46.88 4.06
224 236 5.859205 ACCATGCTGATTTATTTTCCTCC 57.141 39.130 0.00 0.00 0.00 4.30
238 250 9.807921 TTTATTTTCCTCCTGTCTGAATTAACT 57.192 29.630 0.00 0.00 0.00 2.24
239 251 7.693969 ATTTTCCTCCTGTCTGAATTAACTG 57.306 36.000 0.00 0.00 0.00 3.16
240 252 5.825593 TTCCTCCTGTCTGAATTAACTGT 57.174 39.130 0.00 0.00 0.00 3.55
255 270 1.967319 ACTGTTGCCAACGACTGAAT 58.033 45.000 2.68 0.00 34.20 2.57
260 275 4.260985 TGTTGCCAACGACTGAATATCAT 58.739 39.130 2.68 0.00 0.00 2.45
268 283 6.237942 CCAACGACTGAATATCATCACTTCAC 60.238 42.308 0.00 0.00 0.00 3.18
292 310 5.617609 TCATTTCATTCGTCGCTGTAAAAG 58.382 37.500 0.00 0.00 0.00 2.27
322 340 4.096003 CCGGTGATTGGGGCGAGT 62.096 66.667 0.00 0.00 0.00 4.18
324 342 2.124695 GGTGATTGGGGCGAGTCC 60.125 66.667 0.00 0.00 0.00 3.85
349 373 4.647399 CCTTTCCTTTCCTCGATCTCTACT 59.353 45.833 0.00 0.00 0.00 2.57
365 389 1.003580 CTACTTGTGCCCAGTGGTGAT 59.996 52.381 8.74 0.00 0.00 3.06
404 428 3.294079 GTTCCCGACGACAGGAAAA 57.706 52.632 4.12 0.00 43.62 2.29
629 698 2.234143 GGATATTCTGCCTTGCTTCCC 58.766 52.381 0.00 0.00 0.00 3.97
654 728 2.734079 GAGTTCAGAAGAGGAAACAGCG 59.266 50.000 0.00 0.00 0.00 5.18
735 809 3.869065 TGAAAAGTCACAAAGTCCTCGT 58.131 40.909 0.00 0.00 0.00 4.18
762 836 1.196012 CCCACTCTTCCACTAGTCCC 58.804 60.000 0.00 0.00 0.00 4.46
836 921 1.443802 CGTGAGAGAGGGGAAAAAGC 58.556 55.000 0.00 0.00 0.00 3.51
876 965 5.977635 TCGACCTGTAAATTCATCAGTGAT 58.022 37.500 0.00 0.00 33.56 3.06
896 985 1.470996 TTTGGGCCAAGTCATGTGCC 61.471 55.000 19.90 0.00 41.81 5.01
897 986 2.036256 GGGCCAAGTCATGTGCCT 59.964 61.111 4.39 0.00 42.05 4.75
899 988 1.598701 GGGCCAAGTCATGTGCCTTC 61.599 60.000 4.39 0.00 42.05 3.46
900 989 1.598701 GGCCAAGTCATGTGCCTTCC 61.599 60.000 0.00 0.00 40.33 3.46
902 991 1.843368 CCAAGTCATGTGCCTTCCAT 58.157 50.000 0.00 0.00 0.00 3.41
904 993 1.135199 CAAGTCATGTGCCTTCCATGC 60.135 52.381 0.00 0.00 39.60 4.06
905 994 0.330604 AGTCATGTGCCTTCCATGCT 59.669 50.000 0.00 0.00 39.60 3.79
906 995 0.737219 GTCATGTGCCTTCCATGCTC 59.263 55.000 0.00 0.00 39.60 4.26
907 996 0.394762 TCATGTGCCTTCCATGCTCC 60.395 55.000 0.00 0.00 39.60 4.70
908 997 0.681887 CATGTGCCTTCCATGCTCCA 60.682 55.000 0.00 0.00 33.90 3.86
909 998 0.040058 ATGTGCCTTCCATGCTCCAA 59.960 50.000 0.00 0.00 0.00 3.53
910 999 0.040058 TGTGCCTTCCATGCTCCAAT 59.960 50.000 0.00 0.00 0.00 3.16
911 1000 0.743097 GTGCCTTCCATGCTCCAATC 59.257 55.000 0.00 0.00 0.00 2.67
912 1001 0.627451 TGCCTTCCATGCTCCAATCT 59.373 50.000 0.00 0.00 0.00 2.40
913 1002 1.845791 TGCCTTCCATGCTCCAATCTA 59.154 47.619 0.00 0.00 0.00 1.98
914 1003 2.158711 TGCCTTCCATGCTCCAATCTAG 60.159 50.000 0.00 0.00 0.00 2.43
915 1004 2.158696 GCCTTCCATGCTCCAATCTAGT 60.159 50.000 0.00 0.00 0.00 2.57
916 1005 3.737850 CCTTCCATGCTCCAATCTAGTC 58.262 50.000 0.00 0.00 0.00 2.59
917 1006 3.390639 CCTTCCATGCTCCAATCTAGTCT 59.609 47.826 0.00 0.00 0.00 3.24
918 1007 4.590647 CCTTCCATGCTCCAATCTAGTCTA 59.409 45.833 0.00 0.00 0.00 2.59
919 1008 5.510520 CCTTCCATGCTCCAATCTAGTCTAC 60.511 48.000 0.00 0.00 0.00 2.59
920 1009 3.898123 TCCATGCTCCAATCTAGTCTACC 59.102 47.826 0.00 0.00 0.00 3.18
921 1010 3.643320 CCATGCTCCAATCTAGTCTACCA 59.357 47.826 0.00 0.00 0.00 3.25
922 1011 4.262377 CCATGCTCCAATCTAGTCTACCAG 60.262 50.000 0.00 0.00 0.00 4.00
923 1012 3.982516 TGCTCCAATCTAGTCTACCAGT 58.017 45.455 0.00 0.00 0.00 4.00
924 1013 4.353777 TGCTCCAATCTAGTCTACCAGTT 58.646 43.478 0.00 0.00 0.00 3.16
925 1014 5.516044 TGCTCCAATCTAGTCTACCAGTTA 58.484 41.667 0.00 0.00 0.00 2.24
926 1015 5.955959 TGCTCCAATCTAGTCTACCAGTTAA 59.044 40.000 0.00 0.00 0.00 2.01
927 1016 6.611642 TGCTCCAATCTAGTCTACCAGTTAAT 59.388 38.462 0.00 0.00 0.00 1.40
928 1017 6.926272 GCTCCAATCTAGTCTACCAGTTAATG 59.074 42.308 0.00 0.00 0.00 1.90
1237 1326 3.828451 CACCCTTGTGAGTTTCATTCCAT 59.172 43.478 0.00 0.00 45.76 3.41
1238 1327 4.082125 ACCCTTGTGAGTTTCATTCCATC 58.918 43.478 0.00 0.00 0.00 3.51
1239 1328 3.445096 CCCTTGTGAGTTTCATTCCATCC 59.555 47.826 0.00 0.00 0.00 3.51
1240 1329 3.127548 CCTTGTGAGTTTCATTCCATCCG 59.872 47.826 0.00 0.00 0.00 4.18
1241 1330 3.694043 TGTGAGTTTCATTCCATCCGA 57.306 42.857 0.00 0.00 0.00 4.55
1242 1331 4.014569 TGTGAGTTTCATTCCATCCGAA 57.985 40.909 0.00 0.00 34.14 4.30
1243 1332 3.751175 TGTGAGTTTCATTCCATCCGAAC 59.249 43.478 0.00 0.00 31.79 3.95
1258 1347 2.693074 TCCGAACCAGATGATGATCGAA 59.307 45.455 0.00 0.00 39.16 3.71
1265 1354 4.825634 ACCAGATGATGATCGAATTGCAAT 59.174 37.500 5.99 5.99 33.34 3.56
1372 1467 2.278661 GCCGATCCGAACGAGGTC 60.279 66.667 0.00 0.00 0.00 3.85
1459 1554 4.005650 CACCTGCTGTAAGATGACACATT 58.994 43.478 0.00 0.00 34.07 2.71
1540 1636 7.371936 AGTTTGACACTAGTACATCTCAGTTC 58.628 38.462 0.00 0.00 31.97 3.01
1703 1856 6.090088 CAGTTGAAGTACAGCTCATTCAGTAC 59.910 42.308 0.00 2.39 37.96 2.73
1826 1979 3.464907 CTCAAGGCTATCAGTGACCATG 58.535 50.000 0.00 0.00 0.00 3.66
1931 2084 2.968574 AGGATGTTACAGGCTCATCGAT 59.031 45.455 7.56 0.00 38.86 3.59
2003 2156 1.004440 GCAGTTCAACTCGGCCTCT 60.004 57.895 0.00 0.00 0.00 3.69
2330 2489 4.323485 CCTCCTTGCACCTCATACTTGTAA 60.323 45.833 0.00 0.00 0.00 2.41
2638 2797 4.760530 TCTTGTACATCCCAGATCCTTG 57.239 45.455 0.00 0.00 0.00 3.61
2811 2970 1.009829 GGAAGCGATGGTTAGCACTG 58.990 55.000 0.00 0.00 35.48 3.66
2818 2977 3.187700 CGATGGTTAGCACTGGTCTTAC 58.812 50.000 0.00 0.00 0.00 2.34
2935 3095 4.168760 CCAGTTTTCTCAATTTCGCCATC 58.831 43.478 0.00 0.00 0.00 3.51
3031 3191 6.103330 CCTTCTAAAGTAAGAACCTGCTCTC 58.897 44.000 0.00 0.00 32.18 3.20
3072 3232 6.778069 TCCTGTCGGTCTGAATTCTAATATCT 59.222 38.462 7.05 0.00 0.00 1.98
3244 3406 8.391106 CAGTCTGTAAAACTATTTCCTATGTGC 58.609 37.037 0.00 0.00 0.00 4.57
3270 3432 1.880027 GAAGTGGCCGTTCATTTGACT 59.120 47.619 11.84 0.00 0.00 3.41
3613 3789 2.890311 TGTTAGAACCAACCTGCCATTG 59.110 45.455 0.00 0.00 0.00 2.82
3770 3946 0.390735 GCCTAAACTCCGGAAGCGAA 60.391 55.000 5.23 0.00 0.00 4.70
3804 3980 3.840890 TTTTCGCACCGAATTAATGCT 57.159 38.095 0.59 0.00 45.28 3.79
3829 4006 4.681025 GTGGTGCATGTCAACTGTAAAATG 59.319 41.667 6.71 0.00 32.28 2.32
3834 4011 5.476254 TGCATGTCAACTGTAAAATGATCCA 59.524 36.000 0.00 0.00 0.00 3.41
3835 4012 6.153170 TGCATGTCAACTGTAAAATGATCCAT 59.847 34.615 0.00 0.00 0.00 3.41
3895 4072 0.465705 AGAACGCGATGATGATGGGT 59.534 50.000 15.93 0.00 0.00 4.51
3901 4078 0.321034 CGATGATGATGGGTGCGGAT 60.321 55.000 0.00 0.00 0.00 4.18
3919 4096 1.872313 GATTCGTACGAGACCGAGGAT 59.128 52.381 18.64 6.29 39.50 3.24
3940 4117 1.269448 GAGATCTCGAGGCTGATGTCC 59.731 57.143 13.56 0.00 29.93 4.02
4040 4217 0.800683 TATCGTTCGGCGCAAGTGAG 60.801 55.000 10.83 0.00 41.07 3.51
4044 4221 1.664649 TTCGGCGCAAGTGAGACAG 60.665 57.895 10.83 0.00 41.68 3.51
4064 4242 7.217200 AGACAGTATCTCTAACACTTTTTGCA 58.783 34.615 0.00 0.00 28.16 4.08
4066 4244 8.034058 ACAGTATCTCTAACACTTTTTGCATC 57.966 34.615 0.00 0.00 0.00 3.91
4147 4325 6.314896 GTCATCTCAAACAAGGAGGTAAGATG 59.685 42.308 0.00 0.00 39.97 2.90
4163 4341 1.836802 AGATGCCCTCCTTCAGAGTTC 59.163 52.381 0.00 0.00 41.47 3.01
4172 4351 1.882623 CCTTCAGAGTTCAAACCTGGC 59.117 52.381 0.00 0.00 31.98 4.85
4199 4378 7.010460 CCCAAAATTCTGAAGAAAACAACACTC 59.990 37.037 0.00 0.00 37.61 3.51
4217 4396 0.684535 TCGTCTCTGAAACCATGCCA 59.315 50.000 0.00 0.00 0.00 4.92
4343 4522 2.257371 GCACCGTCGTGTAGAGCA 59.743 61.111 0.00 0.00 42.39 4.26
4368 4548 4.353437 GTCGGCGTGACGGGTTCT 62.353 66.667 7.25 0.00 37.96 3.01
4415 4598 4.176851 GTCGTCGTCTCGAGGCCC 62.177 72.222 12.25 0.98 40.78 5.80
4465 4659 0.951558 GGAGGCGTTTGAAGCTTGAA 59.048 50.000 2.10 0.00 34.52 2.69
4469 4663 2.030805 AGGCGTTTGAAGCTTGAATGAC 60.031 45.455 2.10 6.40 34.52 3.06
4470 4664 2.030805 GGCGTTTGAAGCTTGAATGACT 60.031 45.455 2.10 0.00 34.52 3.41
4547 4745 7.852454 GGAACAAAGTAATAGTCGTTCGTTTTT 59.148 33.333 0.00 0.00 34.87 1.94
4671 4953 4.719273 TGTGAAATTTTCAGGGGGTTTTCT 59.281 37.500 12.02 0.00 41.01 2.52
4672 4954 5.190726 TGTGAAATTTTCAGGGGGTTTTCTT 59.809 36.000 12.02 0.00 41.01 2.52
4677 4959 1.133363 TCAGGGGGTTTTCTTGTCGA 58.867 50.000 0.00 0.00 0.00 4.20
4680 4962 1.202770 AGGGGGTTTTCTTGTCGACTG 60.203 52.381 17.92 9.81 0.00 3.51
4681 4963 1.202722 GGGGGTTTTCTTGTCGACTGA 60.203 52.381 17.92 12.06 0.00 3.41
4682 4964 1.871676 GGGGTTTTCTTGTCGACTGAC 59.128 52.381 17.92 6.12 45.71 3.51
4693 4990 0.029700 TCGACTGACGTTGCTTTCGA 59.970 50.000 0.00 0.00 43.13 3.71
4744 5041 2.338500 GAAAGACCATTTCGAGACGCT 58.662 47.619 0.00 0.00 0.00 5.07
4754 5051 2.671177 CGAGACGCTGCCACTTTGG 61.671 63.158 0.00 0.00 41.55 3.28
4769 5068 1.332144 TTTGGTAGCTATCGGGCGGT 61.332 55.000 0.00 0.00 37.29 5.68
4793 5093 0.464735 AGAGTATCGGCGTCAGCTCT 60.465 55.000 6.85 12.70 42.67 4.09
4797 5097 0.593618 TATCGGCGTCAGCTCTGATC 59.406 55.000 6.85 0.00 42.18 2.92
4801 5101 2.804167 CGTCAGCTCTGATCGCCT 59.196 61.111 2.62 0.00 42.18 5.52
4802 5102 1.299014 CGTCAGCTCTGATCGCCTC 60.299 63.158 2.62 0.00 42.18 4.70
4804 5104 1.380380 TCAGCTCTGATCGCCTCCA 60.380 57.895 0.00 0.00 34.14 3.86
4806 5106 2.107953 GCTCTGATCGCCTCCACC 59.892 66.667 0.00 0.00 0.00 4.61
4818 5118 3.851845 CTCCACCGTTGCGACCGAA 62.852 63.158 0.00 0.00 0.00 4.30
4854 5154 5.935789 CCGGATACAGTTAGGAACTTTGAAA 59.064 40.000 0.00 0.00 40.46 2.69
4908 5208 2.100631 GTGGTGAAGTCCCGATGCG 61.101 63.158 0.00 0.00 0.00 4.73
4941 5256 1.075970 CCCTCGGTCCTCCTCATCA 60.076 63.158 0.00 0.00 0.00 3.07
4943 5258 0.684479 CCTCGGTCCTCCTCATCACA 60.684 60.000 0.00 0.00 0.00 3.58
4962 5277 1.761784 CACCATCTGAAGGAGAGGAGG 59.238 57.143 5.85 0.00 34.14 4.30
4963 5278 1.648568 ACCATCTGAAGGAGAGGAGGA 59.351 52.381 5.85 0.00 34.14 3.71
4964 5279 2.318908 CCATCTGAAGGAGAGGAGGAG 58.681 57.143 0.00 0.00 34.14 3.69
4965 5280 1.688197 CATCTGAAGGAGAGGAGGAGC 59.312 57.143 0.00 0.00 34.14 4.70
4966 5281 0.395036 TCTGAAGGAGAGGAGGAGCG 60.395 60.000 0.00 0.00 0.00 5.03
4967 5282 1.380515 TGAAGGAGAGGAGGAGCGG 60.381 63.158 0.00 0.00 0.00 5.52
4968 5283 2.762043 AAGGAGAGGAGGAGCGGC 60.762 66.667 0.00 0.00 0.00 6.53
4985 5300 2.824041 CGGTGCCGCCTATTTGCT 60.824 61.111 0.00 0.00 34.25 3.91
4986 5301 2.823829 CGGTGCCGCCTATTTGCTC 61.824 63.158 0.00 0.00 34.25 4.26
5038 5359 1.818642 AGGATGCAGCACAAGTCTTC 58.181 50.000 3.51 0.00 0.00 2.87
5051 5372 0.247736 AGTCTTCATGGCCGTCTGTC 59.752 55.000 0.00 0.00 0.00 3.51
5074 5395 2.952714 CACCCTTGGAAGCTTCTGG 58.047 57.895 25.05 21.77 0.00 3.86
5075 5396 0.111253 CACCCTTGGAAGCTTCTGGT 59.889 55.000 25.05 21.15 0.00 4.00
5076 5397 0.853530 ACCCTTGGAAGCTTCTGGTT 59.146 50.000 25.05 11.33 36.51 3.67
5077 5398 1.217942 ACCCTTGGAAGCTTCTGGTTT 59.782 47.619 25.05 11.30 33.64 3.27
5078 5399 2.319844 CCCTTGGAAGCTTCTGGTTTT 58.680 47.619 25.05 0.00 33.64 2.43
5079 5400 2.297315 CCCTTGGAAGCTTCTGGTTTTC 59.703 50.000 25.05 7.94 33.64 2.29
5080 5401 2.958355 CCTTGGAAGCTTCTGGTTTTCA 59.042 45.455 25.05 10.48 33.64 2.69
5081 5402 3.005155 CCTTGGAAGCTTCTGGTTTTCAG 59.995 47.826 25.05 9.70 44.68 3.02
5115 5710 0.906756 TCAGGCAGCTGCTACCTTCT 60.907 55.000 35.82 21.38 41.70 2.85
5116 5711 0.461693 CAGGCAGCTGCTACCTTCTC 60.462 60.000 35.82 17.96 41.70 2.87
5117 5712 1.153269 GGCAGCTGCTACCTTCTCC 60.153 63.158 35.82 14.01 41.70 3.71
5118 5713 1.599047 GCAGCTGCTACCTTCTCCA 59.401 57.895 31.33 0.00 38.21 3.86
5119 5714 0.179936 GCAGCTGCTACCTTCTCCAT 59.820 55.000 31.33 0.00 38.21 3.41
5120 5715 1.407989 GCAGCTGCTACCTTCTCCATT 60.408 52.381 31.33 0.00 38.21 3.16
5121 5716 2.158900 GCAGCTGCTACCTTCTCCATTA 60.159 50.000 31.33 0.00 38.21 1.90
5122 5717 3.726607 CAGCTGCTACCTTCTCCATTAG 58.273 50.000 0.00 0.00 0.00 1.73
5123 5718 3.386078 CAGCTGCTACCTTCTCCATTAGA 59.614 47.826 0.00 0.00 0.00 2.10
5124 5719 4.040217 CAGCTGCTACCTTCTCCATTAGAT 59.960 45.833 0.00 0.00 33.05 1.98
5125 5720 4.283212 AGCTGCTACCTTCTCCATTAGATC 59.717 45.833 0.00 0.00 33.05 2.75
5126 5721 4.039730 GCTGCTACCTTCTCCATTAGATCA 59.960 45.833 0.00 0.00 33.05 2.92
5130 5725 5.468409 GCTACCTTCTCCATTAGATCAAAGC 59.532 44.000 0.00 0.00 33.05 3.51
5133 5728 6.118852 ACCTTCTCCATTAGATCAAAGCTTC 58.881 40.000 0.00 0.00 33.05 3.86
5144 5739 5.244755 AGATCAAAGCTTCTTGTTCCTCTC 58.755 41.667 0.00 0.00 0.00 3.20
5196 5791 1.876156 CTTCAACCTCCTCTGTTGCAC 59.124 52.381 0.00 0.00 42.17 4.57
5205 5800 1.880027 CCTCTGTTGCACAAGGGTAAC 59.120 52.381 0.00 0.00 34.47 2.50
5290 5885 3.566130 AGGCACATCCTCTTGAAGC 57.434 52.632 0.00 0.00 43.20 3.86
5291 5886 0.694771 AGGCACATCCTCTTGAAGCA 59.305 50.000 0.00 0.00 43.20 3.91
5292 5887 1.074405 AGGCACATCCTCTTGAAGCAA 59.926 47.619 0.00 0.00 43.20 3.91
5298 5894 5.340803 CACATCCTCTTGAAGCAAATGATG 58.659 41.667 7.27 0.00 33.23 3.07
5300 5896 5.105877 ACATCCTCTTGAAGCAAATGATGTG 60.106 40.000 13.39 0.00 36.03 3.21
5305 5901 4.038282 TCTTGAAGCAAATGATGTGCAGTT 59.962 37.500 10.66 0.00 44.74 3.16
5309 5905 1.990563 GCAAATGATGTGCAGTTCAGC 59.009 47.619 1.98 0.00 41.80 4.26
5310 5906 2.602878 CAAATGATGTGCAGTTCAGCC 58.397 47.619 4.94 0.00 31.43 4.85
5327 5923 3.266772 TCAGCCTTGTCAACCATAGGAAT 59.733 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.179174 TCACTCACTCACCTCACGGG 61.179 60.000 0.00 0.00 41.89 5.28
42 43 0.242286 CTCACTCACTCACCTCACGG 59.758 60.000 0.00 0.00 0.00 4.94
49 50 1.600663 CGGTGTCACTCACTCACTCAC 60.601 57.143 2.35 0.00 45.50 3.51
50 51 0.668535 CGGTGTCACTCACTCACTCA 59.331 55.000 2.35 0.00 45.50 3.41
51 52 0.664767 GCGGTGTCACTCACTCACTC 60.665 60.000 2.35 0.00 45.50 3.51
52 53 1.364171 GCGGTGTCACTCACTCACT 59.636 57.895 2.35 0.00 45.50 3.41
97 98 2.943653 CCGGTCGACAGTTTTGCC 59.056 61.111 18.91 0.00 0.00 4.52
99 100 2.943653 GGCCGGTCGACAGTTTTG 59.056 61.111 18.91 1.48 0.00 2.44
100 101 2.663852 CGGCCGGTCGACAGTTTT 60.664 61.111 27.65 0.00 0.00 2.43
116 117 4.521062 CTTCCCTCCTCGCCAGCG 62.521 72.222 5.50 5.50 41.35 5.18
119 120 2.364317 CCTCTTCCCTCCTCGCCA 60.364 66.667 0.00 0.00 0.00 5.69
130 131 2.003301 GCAACAAGATCCGTCCTCTTC 58.997 52.381 0.00 0.00 30.60 2.87
132 133 0.250513 GGCAACAAGATCCGTCCTCT 59.749 55.000 0.00 0.00 0.00 3.69
152 153 3.694566 GGCCGTGATCCTGAAATTAAGTT 59.305 43.478 0.00 0.00 0.00 2.66
175 176 4.033014 GCTAGTGTTAATGAGAAACCGAGC 59.967 45.833 0.00 0.00 0.00 5.03
208 212 7.928307 TTCAGACAGGAGGAAAATAAATCAG 57.072 36.000 0.00 0.00 0.00 2.90
220 232 4.154918 GCAACAGTTAATTCAGACAGGAGG 59.845 45.833 0.00 0.00 0.00 4.30
239 251 4.332543 TGATGATATTCAGTCGTTGGCAAC 59.667 41.667 20.27 20.27 0.00 4.17
240 252 4.332543 GTGATGATATTCAGTCGTTGGCAA 59.667 41.667 0.00 0.00 0.00 4.52
255 270 7.765819 ACGAATGAAATGAGTGAAGTGATGATA 59.234 33.333 0.00 0.00 0.00 2.15
260 275 4.385748 CGACGAATGAAATGAGTGAAGTGA 59.614 41.667 0.00 0.00 0.00 3.41
268 283 4.840401 TTACAGCGACGAATGAAATGAG 57.160 40.909 0.00 0.00 0.00 2.90
318 336 1.903183 AGGAAAGGAAAGGAGGACTCG 59.097 52.381 0.00 0.00 0.00 4.18
319 337 2.093921 CGAGGAAAGGAAAGGAGGACTC 60.094 54.545 0.00 0.00 0.00 3.36
320 338 1.903183 CGAGGAAAGGAAAGGAGGACT 59.097 52.381 0.00 0.00 0.00 3.85
321 339 1.900486 TCGAGGAAAGGAAAGGAGGAC 59.100 52.381 0.00 0.00 0.00 3.85
322 340 2.320681 TCGAGGAAAGGAAAGGAGGA 57.679 50.000 0.00 0.00 0.00 3.71
324 342 3.704061 AGAGATCGAGGAAAGGAAAGGAG 59.296 47.826 0.00 0.00 0.00 3.69
349 373 1.462731 GCAATCACCACTGGGCACAA 61.463 55.000 0.00 0.00 37.90 3.33
399 423 2.236395 TCCAAGGAGGACTCGATTTTCC 59.764 50.000 0.00 0.00 43.07 3.13
400 424 3.611766 TCCAAGGAGGACTCGATTTTC 57.388 47.619 0.00 0.00 43.07 2.29
437 470 7.603784 AGAAGCCGCAATATTTGAAGAAAATTT 59.396 29.630 0.00 0.00 39.29 1.82
514 548 3.079578 AGGAAAGATGCACATGTGAGTG 58.920 45.455 29.80 3.04 42.37 3.51
607 676 2.234143 GAAGCAAGGCAGAATATCCCC 58.766 52.381 0.00 0.00 0.00 4.81
629 698 5.277731 GCTGTTTCCTCTTCTGAACTCAAAG 60.278 44.000 0.00 0.00 0.00 2.77
654 728 1.302511 TGGCTGGCGTTCTTCCTTC 60.303 57.895 0.00 0.00 0.00 3.46
735 809 1.420138 GTGGAAGAGTGGGAAAGGTGA 59.580 52.381 0.00 0.00 0.00 4.02
762 836 6.519679 TCAGAACAATGATCATGGGAAAAG 57.480 37.500 14.72 1.00 0.00 2.27
850 935 4.183865 CTGATGAATTTACAGGTCGAGCA 58.816 43.478 18.15 0.00 0.00 4.26
851 936 4.033358 CACTGATGAATTTACAGGTCGAGC 59.967 45.833 6.48 6.48 36.17 5.03
853 938 5.400066 TCACTGATGAATTTACAGGTCGA 57.600 39.130 0.00 0.00 36.17 4.20
855 940 7.756722 CCAAAATCACTGATGAATTTACAGGTC 59.243 37.037 0.00 0.00 36.07 3.85
856 941 7.309990 CCCAAAATCACTGATGAATTTACAGGT 60.310 37.037 0.00 0.00 36.07 4.00
857 942 7.037438 CCCAAAATCACTGATGAATTTACAGG 58.963 38.462 0.00 0.00 36.07 4.00
858 943 6.532657 GCCCAAAATCACTGATGAATTTACAG 59.467 38.462 0.00 0.00 36.07 2.74
859 944 6.397272 GCCCAAAATCACTGATGAATTTACA 58.603 36.000 0.00 0.00 36.07 2.41
860 945 5.812127 GGCCCAAAATCACTGATGAATTTAC 59.188 40.000 0.00 0.00 36.07 2.01
876 965 0.392336 GCACATGACTTGGCCCAAAA 59.608 50.000 0.00 0.00 0.00 2.44
896 985 4.686191 AGACTAGATTGGAGCATGGAAG 57.314 45.455 0.00 0.00 0.00 3.46
897 986 4.345257 GGTAGACTAGATTGGAGCATGGAA 59.655 45.833 0.00 0.00 0.00 3.53
899 988 3.643320 TGGTAGACTAGATTGGAGCATGG 59.357 47.826 0.00 0.00 0.00 3.66
900 989 4.343526 ACTGGTAGACTAGATTGGAGCATG 59.656 45.833 0.00 0.00 0.00 4.06
902 991 3.982516 ACTGGTAGACTAGATTGGAGCA 58.017 45.455 0.00 0.00 0.00 4.26
904 993 7.287927 TCCATTAACTGGTAGACTAGATTGGAG 59.712 40.741 0.00 0.00 46.08 3.86
905 994 7.130099 TCCATTAACTGGTAGACTAGATTGGA 58.870 38.462 0.00 4.15 46.08 3.53
906 995 7.361457 TCCATTAACTGGTAGACTAGATTGG 57.639 40.000 0.00 2.13 46.08 3.16
907 996 9.482627 GAATCCATTAACTGGTAGACTAGATTG 57.517 37.037 0.00 0.00 46.08 2.67
908 997 9.440761 AGAATCCATTAACTGGTAGACTAGATT 57.559 33.333 0.00 0.00 46.08 2.40
909 998 8.865090 CAGAATCCATTAACTGGTAGACTAGAT 58.135 37.037 0.00 0.00 46.08 1.98
910 999 8.059461 TCAGAATCCATTAACTGGTAGACTAGA 58.941 37.037 0.00 0.00 46.08 2.43
911 1000 8.239038 TCAGAATCCATTAACTGGTAGACTAG 57.761 38.462 0.00 0.00 46.08 2.57
912 1001 8.603898 TTCAGAATCCATTAACTGGTAGACTA 57.396 34.615 0.00 0.00 46.08 2.59
913 1002 7.400339 TCTTCAGAATCCATTAACTGGTAGACT 59.600 37.037 0.00 0.00 46.08 3.24
914 1003 7.556844 TCTTCAGAATCCATTAACTGGTAGAC 58.443 38.462 0.00 0.00 46.08 2.59
915 1004 7.733773 TCTTCAGAATCCATTAACTGGTAGA 57.266 36.000 0.00 0.00 46.08 2.59
916 1005 8.970859 AATCTTCAGAATCCATTAACTGGTAG 57.029 34.615 0.00 0.00 46.08 3.18
917 1006 7.993183 GGAATCTTCAGAATCCATTAACTGGTA 59.007 37.037 6.10 0.00 46.08 3.25
918 1007 6.830838 GGAATCTTCAGAATCCATTAACTGGT 59.169 38.462 6.10 0.00 46.08 4.00
919 1008 6.830324 TGGAATCTTCAGAATCCATTAACTGG 59.170 38.462 9.25 0.00 46.19 4.00
920 1009 7.870509 TGGAATCTTCAGAATCCATTAACTG 57.129 36.000 9.25 0.00 46.19 3.16
928 1017 4.202090 GCAACCATGGAATCTTCAGAATCC 60.202 45.833 21.47 4.16 42.96 3.01
929 1018 4.643784 AGCAACCATGGAATCTTCAGAATC 59.356 41.667 21.47 0.00 0.00 2.52
930 1019 4.401519 CAGCAACCATGGAATCTTCAGAAT 59.598 41.667 21.47 0.00 0.00 2.40
939 1028 2.425143 ACGATCAGCAACCATGGAAT 57.575 45.000 21.47 3.48 0.00 3.01
1209 1298 0.839946 AACTCACAAGGGTGTCTGCT 59.160 50.000 0.00 0.00 45.45 4.24
1224 1313 3.343617 TGGTTCGGATGGAATGAAACTC 58.656 45.455 0.00 0.00 36.92 3.01
1237 1326 2.306847 TCGATCATCATCTGGTTCGGA 58.693 47.619 0.00 0.00 34.04 4.55
1238 1327 2.800881 TCGATCATCATCTGGTTCGG 57.199 50.000 0.00 0.00 34.04 4.30
1239 1328 4.610007 GCAATTCGATCATCATCTGGTTCG 60.610 45.833 0.00 0.00 34.34 3.95
1240 1329 4.274214 TGCAATTCGATCATCATCTGGTTC 59.726 41.667 0.00 0.00 0.00 3.62
1241 1330 4.201657 TGCAATTCGATCATCATCTGGTT 58.798 39.130 0.00 0.00 0.00 3.67
1242 1331 3.812262 TGCAATTCGATCATCATCTGGT 58.188 40.909 0.00 0.00 0.00 4.00
1243 1332 4.823790 TTGCAATTCGATCATCATCTGG 57.176 40.909 0.00 0.00 0.00 3.86
1258 1347 3.430042 ACAGAGTGTCTCCATTGCAAT 57.570 42.857 5.99 5.99 0.00 3.56
1265 1354 4.526650 TGCTAACATAACAGAGTGTCTCCA 59.473 41.667 0.00 0.00 0.00 3.86
1345 1440 0.031585 TCGGATCGGCGTAATTCCTG 59.968 55.000 6.85 6.61 0.00 3.86
1589 1685 7.404980 TCCTATCTACCTAAAACTGGGAAATGT 59.595 37.037 0.00 0.00 0.00 2.71
1703 1856 4.033129 CACAACACAATGCAGAAAACTTGG 59.967 41.667 0.00 0.00 0.00 3.61
1743 1896 1.878102 CGGCTACAGAAACCACTGCTT 60.878 52.381 0.00 0.00 41.06 3.91
1826 1979 1.521681 GACTGGACGGGCTACATGC 60.522 63.158 0.00 0.00 41.94 4.06
1955 2108 5.670485 ACGAATATCTTGTTGATGCCACTA 58.330 37.500 0.00 0.00 36.65 2.74
2003 2156 2.927477 GCGGTGAATGTGACGATTAAGA 59.073 45.455 0.00 0.00 0.00 2.10
2130 2286 4.265073 CTGTAGTCAGCTAAAAGCCCAAT 58.735 43.478 0.00 0.00 43.77 3.16
2248 2404 3.694072 CCCAGATAAATTTTCTGACGGCA 59.306 43.478 21.76 0.00 42.63 5.69
2305 2464 0.464554 GTATGAGGTGCAAGGAGGGC 60.465 60.000 0.00 0.00 0.00 5.19
2330 2489 8.814038 AAGCATTACTTTAACAGATCCAGATT 57.186 30.769 0.00 0.00 33.71 2.40
2530 2689 7.936496 TGTTTCTGTAAAGGATGCATGAATA 57.064 32.000 2.46 0.00 0.00 1.75
2531 2690 6.839124 TGTTTCTGTAAAGGATGCATGAAT 57.161 33.333 2.46 0.00 0.00 2.57
2532 2691 6.209192 ACATGTTTCTGTAAAGGATGCATGAA 59.791 34.615 2.46 0.00 36.19 2.57
2533 2692 5.711506 ACATGTTTCTGTAAAGGATGCATGA 59.288 36.000 2.46 0.00 36.19 3.07
2537 2696 4.458989 TCCACATGTTTCTGTAAAGGATGC 59.541 41.667 0.00 0.00 0.00 3.91
2811 2970 2.891580 TCTGACACAGTGAGGTAAGACC 59.108 50.000 7.81 0.00 33.81 3.85
2818 2977 4.282957 AGGCATATATCTGACACAGTGAGG 59.717 45.833 7.81 0.00 32.61 3.86
2850 3009 9.726438 AGATACTGCAACTTATTTAAGACAGTT 57.274 29.630 19.87 13.02 41.20 3.16
2886 3045 4.158949 CCACTTTCTGCAATGATCAATGGA 59.841 41.667 12.62 8.80 0.00 3.41
2935 3095 2.035449 TGGATATTTAGCAGGGTCGTCG 59.965 50.000 0.00 0.00 0.00 5.12
3072 3232 3.785486 CGTATCTTGACCTGAGAATGCA 58.215 45.455 0.00 0.00 0.00 3.96
3244 3406 2.954753 GAACGGCCACTTCGTGCAG 61.955 63.158 2.24 0.00 40.96 4.41
3270 3432 5.376625 AGACATAAGCCTGACAAAAACAGA 58.623 37.500 0.00 0.00 37.54 3.41
3485 3661 0.247460 GGGGGCTGCAATGAAGAAAC 59.753 55.000 0.50 0.00 0.00 2.78
3489 3665 0.248289 CTTTGGGGGCTGCAATGAAG 59.752 55.000 0.50 0.00 0.00 3.02
3600 3776 2.787473 TAGTCTCAATGGCAGGTTGG 57.213 50.000 0.00 0.00 0.00 3.77
3613 3789 4.926238 CCGATGCTTGTATGGAATAGTCTC 59.074 45.833 0.00 0.00 0.00 3.36
3770 3946 3.146066 TGCGAAAAAGCATACCTTGAGT 58.854 40.909 0.00 0.00 42.92 3.41
3804 3980 1.761449 ACAGTTGACATGCACCACAA 58.239 45.000 0.00 0.00 0.00 3.33
3829 4006 2.349886 GACAGCGTTCAGACAATGGATC 59.650 50.000 0.00 0.00 0.00 3.36
3834 4011 3.668447 AGAATGACAGCGTTCAGACAAT 58.332 40.909 0.00 0.00 41.50 2.71
3835 4012 3.111853 AGAATGACAGCGTTCAGACAA 57.888 42.857 0.00 0.00 41.50 3.18
3895 4072 1.430632 GGTCTCGTACGAATCCGCA 59.569 57.895 20.00 0.00 39.95 5.69
3901 4078 1.012086 CATCCTCGGTCTCGTACGAA 58.988 55.000 20.00 7.68 38.79 3.85
3919 4096 1.952990 GACATCAGCCTCGAGATCTCA 59.047 52.381 22.31 8.81 0.00 3.27
4040 4217 7.421530 TGCAAAAAGTGTTAGAGATACTGTC 57.578 36.000 0.00 0.00 29.24 3.51
4044 4221 7.290857 TCGATGCAAAAAGTGTTAGAGATAC 57.709 36.000 0.00 0.00 0.00 2.24
4064 4242 3.957671 CAGTTGCTGCAATGTATCGAT 57.042 42.857 19.11 2.16 0.00 3.59
4147 4325 2.155279 GTTTGAACTCTGAAGGAGGGC 58.845 52.381 0.00 0.00 45.83 5.19
4163 4341 1.699083 AGAATTTTGGGGCCAGGTTTG 59.301 47.619 4.39 0.00 0.00 2.93
4172 4351 6.037062 GTGTTGTTTTCTTCAGAATTTTGGGG 59.963 38.462 0.00 0.00 33.54 4.96
4199 4378 0.798776 GTGGCATGGTTTCAGAGACG 59.201 55.000 0.00 0.00 0.00 4.18
4358 4537 1.593209 GTTGTCGCAGAACCCGTCA 60.593 57.895 0.00 0.00 39.69 4.35
4415 4598 0.247736 CACTTCTTCAGTCCCTCCCG 59.752 60.000 0.00 0.00 30.92 5.14
4416 4599 1.276705 GTCACTTCTTCAGTCCCTCCC 59.723 57.143 0.00 0.00 30.92 4.30
4417 4600 1.276705 GGTCACTTCTTCAGTCCCTCC 59.723 57.143 0.00 0.00 30.92 4.30
4418 4601 1.276705 GGGTCACTTCTTCAGTCCCTC 59.723 57.143 0.00 0.00 36.82 4.30
4419 4602 1.353091 GGGTCACTTCTTCAGTCCCT 58.647 55.000 0.00 0.00 36.82 4.20
4450 4633 2.975851 CAGTCATTCAAGCTTCAAACGC 59.024 45.455 0.00 0.00 0.00 4.84
4465 4659 2.510238 GCGCGCCTTCTCAGTCAT 60.510 61.111 23.24 0.00 0.00 3.06
4485 4679 5.532664 ACTACTTACTACTAATGCTGCCC 57.467 43.478 0.00 0.00 0.00 5.36
4514 4712 5.062308 CGACTATTACTTTGTTCCACTGCTC 59.938 44.000 0.00 0.00 0.00 4.26
4547 4745 5.670361 ACAGCCTCTTATTTATTACAGGGGA 59.330 40.000 0.00 0.00 0.00 4.81
4647 4929 4.687901 AAACCCCCTGAAAATTTCACAG 57.312 40.909 4.03 14.48 35.46 3.66
4671 4953 1.591158 GAAAGCAACGTCAGTCGACAA 59.409 47.619 19.50 1.95 42.74 3.18
4672 4954 1.205657 GAAAGCAACGTCAGTCGACA 58.794 50.000 19.50 0.00 42.74 4.35
4677 4959 1.209128 CACTCGAAAGCAACGTCAGT 58.791 50.000 0.00 0.00 0.00 3.41
4680 4962 0.232303 CACCACTCGAAAGCAACGTC 59.768 55.000 0.00 0.00 0.00 4.34
4681 4963 1.157870 CCACCACTCGAAAGCAACGT 61.158 55.000 0.00 0.00 0.00 3.99
4682 4964 1.157870 ACCACCACTCGAAAGCAACG 61.158 55.000 0.00 0.00 0.00 4.10
4683 4965 1.021968 AACCACCACTCGAAAGCAAC 58.978 50.000 0.00 0.00 0.00 4.17
4684 4966 1.021202 CAACCACCACTCGAAAGCAA 58.979 50.000 0.00 0.00 0.00 3.91
4685 4967 1.444119 GCAACCACCACTCGAAAGCA 61.444 55.000 0.00 0.00 0.00 3.91
4693 4990 5.435686 TCATAGATAAAGCAACCACCACT 57.564 39.130 0.00 0.00 0.00 4.00
4729 5026 1.741770 GGCAGCGTCTCGAAATGGT 60.742 57.895 0.00 0.00 0.00 3.55
4731 5028 1.016130 AGTGGCAGCGTCTCGAAATG 61.016 55.000 0.00 0.00 0.00 2.32
4738 5035 0.320771 CTACCAAAGTGGCAGCGTCT 60.321 55.000 0.00 0.00 42.67 4.18
4754 5051 1.006454 GGAACCGCCCGATAGCTAC 60.006 63.158 0.00 0.00 0.00 3.58
4769 5068 0.681887 TGACGCCGATACTCTGGGAA 60.682 55.000 0.00 0.00 0.00 3.97
4774 5073 0.464735 AGAGCTGACGCCGATACTCT 60.465 55.000 0.00 0.00 36.60 3.24
4793 5093 2.264480 CAACGGTGGAGGCGATCA 59.736 61.111 0.00 0.00 0.00 2.92
4801 5101 3.851845 CTTCGGTCGCAACGGTGGA 62.852 63.158 0.90 0.00 0.00 4.02
4802 5102 3.411351 CTTCGGTCGCAACGGTGG 61.411 66.667 0.90 0.00 0.00 4.61
4804 5104 3.920196 ACCTTCGGTCGCAACGGT 61.920 61.111 0.00 0.00 0.00 4.83
4806 5106 3.411351 CCACCTTCGGTCGCAACG 61.411 66.667 0.00 0.00 31.02 4.10
4818 5118 2.170607 CTGTATCCGGTCATTTCCACCT 59.829 50.000 0.00 0.00 0.00 4.00
4854 5154 3.008049 ACCGAGGCTTCACAGTTCTAAAT 59.992 43.478 0.00 0.00 0.00 1.40
4865 5165 0.532573 CTCTTGCTACCGAGGCTTCA 59.467 55.000 0.00 0.00 0.00 3.02
4930 5230 2.113807 CAGATGGTGTGATGAGGAGGA 58.886 52.381 0.00 0.00 0.00 3.71
4941 5256 2.465813 CTCCTCTCCTTCAGATGGTGT 58.534 52.381 2.31 0.00 0.00 4.16
4943 5258 1.648568 TCCTCCTCTCCTTCAGATGGT 59.351 52.381 2.31 0.00 0.00 3.55
4968 5283 2.823829 GAGCAAATAGGCGGCACCG 61.824 63.158 13.08 4.30 46.52 4.94
4969 5284 2.823829 CGAGCAAATAGGCGGCACC 61.824 63.158 13.08 0.00 39.27 5.01
4970 5285 1.766143 CTCGAGCAAATAGGCGGCAC 61.766 60.000 13.08 0.00 39.27 5.01
4971 5286 1.521457 CTCGAGCAAATAGGCGGCA 60.521 57.895 13.08 0.00 39.27 5.69
4972 5287 2.886782 GCTCGAGCAAATAGGCGGC 61.887 63.158 31.91 0.00 41.59 6.53
4973 5288 2.247437 GGCTCGAGCAAATAGGCGG 61.247 63.158 36.27 0.00 44.36 6.13
4974 5289 1.218230 GAGGCTCGAGCAAATAGGCG 61.218 60.000 36.27 0.00 44.36 5.52
4975 5290 1.218230 CGAGGCTCGAGCAAATAGGC 61.218 60.000 36.27 18.46 43.74 3.93
4976 5291 1.218230 GCGAGGCTCGAGCAAATAGG 61.218 60.000 38.56 19.81 43.74 2.57
4977 5292 1.218230 GGCGAGGCTCGAGCAAATAG 61.218 60.000 38.56 22.22 43.74 1.73
4978 5293 1.227263 GGCGAGGCTCGAGCAAATA 60.227 57.895 38.56 0.00 43.74 1.40
4979 5294 2.512515 GGCGAGGCTCGAGCAAAT 60.513 61.111 38.56 22.57 43.74 2.32
4983 5298 4.908877 GTACGGCGAGGCTCGAGC 62.909 72.222 38.56 29.38 43.74 5.03
4984 5299 3.203412 AGTACGGCGAGGCTCGAG 61.203 66.667 38.56 30.48 43.74 4.04
4985 5300 3.506096 CAGTACGGCGAGGCTCGA 61.506 66.667 38.56 16.60 43.74 4.04
4986 5301 4.554363 CCAGTACGGCGAGGCTCG 62.554 72.222 31.40 31.40 43.89 5.03
4998 5313 0.774908 CCCCTCAACCCAAACCAGTA 59.225 55.000 0.00 0.00 0.00 2.74
5059 5380 2.958355 TGAAAACCAGAAGCTTCCAAGG 59.042 45.455 22.81 22.31 0.00 3.61
5072 5393 2.746279 TTGCCTTCCTCTGAAAACCA 57.254 45.000 0.00 0.00 0.00 3.67
5073 5394 2.893489 ACATTGCCTTCCTCTGAAAACC 59.107 45.455 0.00 0.00 0.00 3.27
5074 5395 5.415701 TGATACATTGCCTTCCTCTGAAAAC 59.584 40.000 0.00 0.00 0.00 2.43
5075 5396 5.569355 TGATACATTGCCTTCCTCTGAAAA 58.431 37.500 0.00 0.00 0.00 2.29
5076 5397 5.178096 TGATACATTGCCTTCCTCTGAAA 57.822 39.130 0.00 0.00 0.00 2.69
5077 5398 4.384537 CCTGATACATTGCCTTCCTCTGAA 60.385 45.833 0.00 0.00 0.00 3.02
5078 5399 3.135348 CCTGATACATTGCCTTCCTCTGA 59.865 47.826 0.00 0.00 0.00 3.27
5079 5400 3.474600 CCTGATACATTGCCTTCCTCTG 58.525 50.000 0.00 0.00 0.00 3.35
5080 5401 2.158696 GCCTGATACATTGCCTTCCTCT 60.159 50.000 0.00 0.00 0.00 3.69
5081 5402 2.225467 GCCTGATACATTGCCTTCCTC 58.775 52.381 0.00 0.00 0.00 3.71
5082 5403 1.565759 TGCCTGATACATTGCCTTCCT 59.434 47.619 0.00 0.00 0.00 3.36
5084 5405 1.336125 GCTGCCTGATACATTGCCTTC 59.664 52.381 0.00 0.00 0.00 3.46
5115 5710 6.375455 GGAACAAGAAGCTTTGATCTAATGGA 59.625 38.462 0.00 0.00 32.39 3.41
5116 5711 6.376581 AGGAACAAGAAGCTTTGATCTAATGG 59.623 38.462 0.00 0.00 32.39 3.16
5117 5712 7.336427 AGAGGAACAAGAAGCTTTGATCTAATG 59.664 37.037 0.00 0.00 32.39 1.90
5118 5713 7.401246 AGAGGAACAAGAAGCTTTGATCTAAT 58.599 34.615 0.00 0.00 32.39 1.73
5119 5714 6.773638 AGAGGAACAAGAAGCTTTGATCTAA 58.226 36.000 0.00 0.00 32.39 2.10
5120 5715 6.365970 AGAGGAACAAGAAGCTTTGATCTA 57.634 37.500 0.00 0.00 32.39 1.98
5121 5716 5.240013 AGAGGAACAAGAAGCTTTGATCT 57.760 39.130 0.00 0.00 32.39 2.75
5122 5717 4.092675 CGAGAGGAACAAGAAGCTTTGATC 59.907 45.833 0.00 0.00 0.00 2.92
5123 5718 3.999663 CGAGAGGAACAAGAAGCTTTGAT 59.000 43.478 0.00 0.00 0.00 2.57
5124 5719 3.069586 TCGAGAGGAACAAGAAGCTTTGA 59.930 43.478 0.00 0.00 0.00 2.69
5125 5720 3.393800 TCGAGAGGAACAAGAAGCTTTG 58.606 45.455 0.00 0.00 0.00 2.77
5126 5721 3.753294 TCGAGAGGAACAAGAAGCTTT 57.247 42.857 0.00 0.00 0.00 3.51
5130 5725 3.876274 TCCATCGAGAGGAACAAGAAG 57.124 47.619 6.91 0.00 30.71 2.85
5144 5739 4.571984 TGCACAATTCATCTAGTTCCATCG 59.428 41.667 0.00 0.00 0.00 3.84
5152 5747 4.769688 TGGTACCTGCACAATTCATCTAG 58.230 43.478 14.36 0.00 0.00 2.43
5158 5753 1.826385 AGCTGGTACCTGCACAATTC 58.174 50.000 36.18 12.94 42.23 2.17
5196 5791 4.510167 ATCTCATTCTGGGTTACCCTTG 57.490 45.455 22.29 14.09 45.70 3.61
5205 5800 6.435277 TCTTCCAAGAAAAATCTCATTCTGGG 59.565 38.462 3.04 3.04 44.81 4.45
5206 5801 7.458409 TCTTCCAAGAAAAATCTCATTCTGG 57.542 36.000 0.00 0.00 36.09 3.86
5282 5877 3.570975 ACTGCACATCATTTGCTTCAAGA 59.429 39.130 0.00 0.00 40.86 3.02
5287 5882 3.859627 GCTGAACTGCACATCATTTGCTT 60.860 43.478 0.00 0.00 40.86 3.91
5288 5883 2.352421 GCTGAACTGCACATCATTTGCT 60.352 45.455 0.00 0.00 40.86 3.91
5289 5884 1.990563 GCTGAACTGCACATCATTTGC 59.009 47.619 0.00 0.00 40.63 3.68
5290 5885 2.230508 AGGCTGAACTGCACATCATTTG 59.769 45.455 6.09 0.00 34.04 2.32
5291 5886 2.522185 AGGCTGAACTGCACATCATTT 58.478 42.857 6.09 0.00 34.04 2.32
5292 5887 2.211250 AGGCTGAACTGCACATCATT 57.789 45.000 6.09 0.00 34.04 2.57
5298 5894 1.024271 TTGACAAGGCTGAACTGCAC 58.976 50.000 6.09 0.00 34.04 4.57
5300 5896 0.312102 GGTTGACAAGGCTGAACTGC 59.688 55.000 0.00 0.00 0.00 4.40
5305 5901 2.265367 TCCTATGGTTGACAAGGCTGA 58.735 47.619 0.00 0.00 31.47 4.26


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

AutoCloner maintained by Alex Coulton.