Multiple sequence alignment - TraesCS5B01G257100

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 TraesCS5B01G257100 chr5B 100.000 5000 0 0 1 5000 439714910 439719909 0.000000e+00 9234.0
1 TraesCS5B01G257100 chr5B 93.720 207 13 0 1603 1809 688589695 688589489 1.350000e-80 311.0
2 TraesCS5B01G257100 chr5B 100.000 45 0 0 1509 1553 688590239 688590195 3.210000e-12 84.2
3 TraesCS5B01G257100 chr5A 90.452 5069 291 80 5 5000 473008796 473013744 0.000000e+00 6501.0
4 TraesCS5B01G257100 chr5A 94.872 39 2 0 4293 4331 450863605 450863643 1.500000e-05 62.1
5 TraesCS5B01G257100 chr5D 93.155 4047 193 34 266 4293 370462178 370466159 0.000000e+00 5862.0
6 TraesCS5B01G257100 chr5D 89.169 674 30 11 4336 5000 370466169 370466808 0.000000e+00 800.0
7 TraesCS5B01G257100 chr5D 92.373 118 4 1 131 248 370462004 370462116 4.010000e-36 163.0
8 TraesCS5B01G257100 chr5D 94.737 38 2 0 4294 4331 350371867 350371904 5.410000e-05 60.2
9 TraesCS5B01G257100 chr7D 75.924 2895 629 47 1149 4006 204109127 204111990 0.000000e+00 1423.0
10 TraesCS5B01G257100 chr7D 91.545 343 28 1 1467 1809 484694710 484694369 5.860000e-129 472.0
11 TraesCS5B01G257100 chr4B 97.872 47 1 0 3597 3643 526964735 526964689 1.150000e-11 82.4
12 TraesCS5B01G257100 chr2B 97.872 47 1 0 3597 3643 52455 52501 1.150000e-11 82.4
13 TraesCS5B01G257100 chr2D 93.182 44 1 2 4283 4324 648111234 648111277 4.180000e-06 63.9
14 TraesCS5B01G257100 chr3B 95.000 40 1 1 4294 4333 824388984 824389022 1.500000e-05 62.1
15 TraesCS5B01G257100 chr6D 92.857 42 2 1 4287 4327 29232332 29232291 5.410000e-05 60.2
16 TraesCS5B01G257100 chr2A 94.737 38 2 0 4294 4331 127156063 127156026 5.410000e-05 60.2
17 TraesCS5B01G257100 chr2A 91.111 45 3 1 4294 4338 699439239 699439196 5.410000e-05 60.2
18 TraesCS5B01G257100 chr1A 97.143 35 1 0 4294 4328 29287031 29287065 5.410000e-05 60.2
19 TraesCS5B01G257100 chr1A 94.737 38 2 0 4294 4331 338594738 338594775 5.410000e-05 60.2
20 TraesCS5B01G257100 chr7B 96.875 32 0 1 1458 1488 323817638 323817607 9.000000e-03 52.8


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 TraesCS5B01G257100 chr5B 439714910 439719909 4999 False 9234 9234 100.000000 1 5000 1 chr5B.!!$F1 4999
1 TraesCS5B01G257100 chr5A 473008796 473013744 4948 False 6501 6501 90.452000 5 5000 1 chr5A.!!$F2 4995
2 TraesCS5B01G257100 chr5D 370462004 370466808 4804 False 2275 5862 91.565667 131 5000 3 chr5D.!!$F2 4869
3 TraesCS5B01G257100 chr7D 204109127 204111990 2863 False 1423 1423 75.924000 1149 4006 1 chr7D.!!$F1 2857

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
190 217 0.034477 ATTAACAACCCCCTCCTGCG 60.034 55.0 0.00 0.00 0.00 5.18 F
711 813 0.255890 ACAATCCTAATGGCACCGCT 59.744 50.0 0.00 0.00 0.00 5.52 F
1804 1940 0.034670 GAGGAACCTGCTGCCAATCT 60.035 55.0 0.00 0.00 0.00 2.40 F
1884 2020 0.332972 AGGGGATGGAAGCTTTGGAC 59.667 55.0 0.00 0.00 0.00 4.02 F
3415 3554 0.669318 GTTTCACCCGATCGTGCAGA 60.669 55.0 15.09 1.62 33.57 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1160 1.153628 GGATGTCGTCGTCCTTGGG 60.154 63.158 12.94 0.00 44.12 4.12 R
2484 2623 0.107017 CCTCGCCTCCAATCCACAAT 60.107 55.000 0.00 0.00 0.00 2.71 R
3782 3921 0.179100 ATGCCAGATGAACTCGTCGG 60.179 55.000 0.00 5.81 36.99 4.79 R
3990 4129 2.270923 TCCGCGTCATCTCAGATTTTG 58.729 47.619 4.92 0.00 0.00 2.44 R
4679 4832 0.040351 TGCAGAGGGCTGAGAGTACT 59.960 55.000 0.00 0.00 45.17 2.73 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
30 31 2.367202 GCAGCAGGGTGTAGGCCTA 61.367 63.158 8.91 8.91 0.00 3.93
44 45 3.785859 CCTAGCAGGGCGCCAAGA 61.786 66.667 30.85 7.20 44.04 3.02
62 63 3.762247 GCAGGCGTACCACCGGTA 61.762 66.667 6.87 0.00 39.06 4.02
66 67 0.320683 AGGCGTACCACCGGTAAAAC 60.321 55.000 6.87 4.37 40.12 2.43
67 68 0.602372 GGCGTACCACCGGTAAAACA 60.602 55.000 6.87 0.00 40.12 2.83
68 69 1.441738 GCGTACCACCGGTAAAACAT 58.558 50.000 6.87 0.00 40.12 2.71
69 70 1.129064 GCGTACCACCGGTAAAACATG 59.871 52.381 6.87 0.00 40.12 3.21
78 79 4.928615 CACCGGTAAAACATGCATGAATTT 59.071 37.500 32.75 28.76 0.00 1.82
82 83 4.094739 GGTAAAACATGCATGAATTTGCCC 59.905 41.667 33.06 27.33 42.06 5.36
85 86 1.208535 ACATGCATGAATTTGCCCTGG 59.791 47.619 32.75 1.77 42.06 4.45
87 88 0.905809 TGCATGAATTTGCCCTGGCT 60.906 50.000 9.97 0.00 42.06 4.75
88 89 0.179092 GCATGAATTTGCCCTGGCTC 60.179 55.000 9.97 0.00 42.51 4.70
100 111 2.045634 TGGCTCCAGCATGCAGAC 60.046 61.111 21.98 11.70 44.36 3.51
105 116 2.827190 CCAGCATGCAGACGCCAT 60.827 61.111 21.98 0.00 37.32 4.40
106 117 2.412323 CCAGCATGCAGACGCCATT 61.412 57.895 21.98 0.00 37.32 3.16
107 118 1.096967 CCAGCATGCAGACGCCATTA 61.097 55.000 21.98 0.00 37.32 1.90
108 119 0.734309 CAGCATGCAGACGCCATTAA 59.266 50.000 21.98 0.00 37.32 1.40
109 120 1.335810 CAGCATGCAGACGCCATTAAT 59.664 47.619 21.98 0.00 37.32 1.40
111 122 3.003585 CAGCATGCAGACGCCATTAATTA 59.996 43.478 21.98 0.00 37.32 1.40
112 123 3.631686 AGCATGCAGACGCCATTAATTAA 59.368 39.130 21.98 0.00 37.32 1.40
113 124 4.279169 AGCATGCAGACGCCATTAATTAAT 59.721 37.500 21.98 4.81 37.32 1.40
114 125 4.618489 GCATGCAGACGCCATTAATTAATC 59.382 41.667 14.21 0.00 37.32 1.75
116 127 5.422666 TGCAGACGCCATTAATTAATCTG 57.577 39.130 16.38 16.38 37.32 2.90
118 129 5.237127 TGCAGACGCCATTAATTAATCTGAG 59.763 40.000 21.70 14.29 37.32 3.35
119 130 5.683859 CAGACGCCATTAATTAATCTGAGC 58.316 41.667 15.93 11.90 0.00 4.26
120 131 5.237127 CAGACGCCATTAATTAATCTGAGCA 59.763 40.000 15.93 0.00 0.00 4.26
190 217 0.034477 ATTAACAACCCCCTCCTGCG 60.034 55.000 0.00 0.00 0.00 5.18
191 218 2.757980 TTAACAACCCCCTCCTGCGC 62.758 60.000 0.00 0.00 0.00 6.09
197 224 2.203126 CCCCTCCTGCGCTTCATC 60.203 66.667 9.73 0.00 0.00 2.92
217 244 7.242914 TCATCTCATCTCGTTTCATTCAATG 57.757 36.000 0.00 0.00 0.00 2.82
248 275 1.546773 TTGTGCACAGGGTACAATCCC 60.547 52.381 20.59 0.00 45.44 3.85
249 276 4.798252 TTGTGCACAGGGTACAATCCCC 62.798 54.545 20.59 0.00 45.44 4.81
257 294 0.468648 GGTACAATCCCCTCCCTTCG 59.531 60.000 0.00 0.00 0.00 3.79
278 315 2.573369 GAGCAGAGCATCATCATTGGT 58.427 47.619 0.00 0.00 37.82 3.67
287 366 0.522626 TCATCATTGGTGTTGCTGCG 59.477 50.000 0.00 0.00 0.00 5.18
288 367 0.457166 CATCATTGGTGTTGCTGCGG 60.457 55.000 0.00 0.00 0.00 5.69
289 368 2.216750 ATCATTGGTGTTGCTGCGGC 62.217 55.000 11.65 11.65 39.26 6.53
312 391 1.610886 CCGGTCTTGGTCTTCTTTCCC 60.611 57.143 0.00 0.00 0.00 3.97
313 392 1.610886 CGGTCTTGGTCTTCTTTCCCC 60.611 57.143 0.00 0.00 0.00 4.81
314 393 1.271982 GGTCTTGGTCTTCTTTCCCCC 60.272 57.143 0.00 0.00 0.00 5.40
336 418 0.619832 AGCTCTCATCTTCTGGGGCA 60.620 55.000 0.00 0.00 0.00 5.36
337 419 0.463474 GCTCTCATCTTCTGGGGCAC 60.463 60.000 0.00 0.00 0.00 5.01
357 439 0.961019 TGCCTGCCTTTTGATGTCAC 59.039 50.000 0.00 0.00 0.00 3.67
404 487 2.048603 GCTTTTGCCATCTCCGCCT 61.049 57.895 0.00 0.00 40.15 5.52
408 491 1.552799 TTTGCCATCTCCGCCTCTCA 61.553 55.000 0.00 0.00 0.00 3.27
412 498 2.841988 ATCTCCGCCTCTCAGCCC 60.842 66.667 0.00 0.00 0.00 5.19
494 587 8.488668 TCCCAAAGTTTCTTTACTTGTACTACT 58.511 33.333 0.00 0.00 38.33 2.57
495 588 8.557029 CCCAAAGTTTCTTTACTTGTACTACTG 58.443 37.037 0.00 0.00 38.33 2.74
496 589 8.068380 CCAAAGTTTCTTTACTTGTACTACTGC 58.932 37.037 0.00 0.00 38.33 4.40
498 591 8.959705 AAGTTTCTTTACTTGTACTACTGCTT 57.040 30.769 0.00 0.00 37.00 3.91
544 641 1.823648 GCTGGGACGAGATCATAGGGA 60.824 57.143 0.00 0.00 0.00 4.20
545 642 2.166829 CTGGGACGAGATCATAGGGAG 58.833 57.143 0.00 0.00 0.00 4.30
546 643 1.203063 TGGGACGAGATCATAGGGAGG 60.203 57.143 0.00 0.00 0.00 4.30
610 712 8.794335 AGAAGATTACTATCAAAAGTTGACCC 57.206 34.615 0.00 0.00 43.48 4.46
683 785 2.507992 CCGAGCTCTTCTGCCGTG 60.508 66.667 12.85 0.00 0.00 4.94
710 812 0.381801 CACAATCCTAATGGCACCGC 59.618 55.000 0.00 0.00 0.00 5.68
711 813 0.255890 ACAATCCTAATGGCACCGCT 59.744 50.000 0.00 0.00 0.00 5.52
729 831 1.747924 GCTGGATTCTTGAAGGCCTTC 59.252 52.381 34.48 34.48 39.91 3.46
753 856 4.261363 GCTGGTAATTAGCTTGCTCAATCC 60.261 45.833 15.27 0.00 38.14 3.01
756 859 4.024809 GGTAATTAGCTTGCTCAATCCGTC 60.025 45.833 7.42 0.00 0.00 4.79
843 949 1.985473 TGCCCTGAATCCATACATGC 58.015 50.000 0.00 0.00 0.00 4.06
849 955 3.496130 CCTGAATCCATACATGCTCGTTC 59.504 47.826 0.00 0.00 0.00 3.95
851 957 3.134623 TGAATCCATACATGCTCGTTCCT 59.865 43.478 0.00 0.00 0.00 3.36
852 958 2.602257 TCCATACATGCTCGTTCCTG 57.398 50.000 0.00 0.00 0.00 3.86
853 959 2.107366 TCCATACATGCTCGTTCCTGA 58.893 47.619 0.00 0.00 0.00 3.86
854 960 2.499693 TCCATACATGCTCGTTCCTGAA 59.500 45.455 0.00 0.00 0.00 3.02
855 961 3.134623 TCCATACATGCTCGTTCCTGAAT 59.865 43.478 0.00 0.00 0.00 2.57
856 962 3.496130 CCATACATGCTCGTTCCTGAATC 59.504 47.826 0.00 0.00 0.00 2.52
857 963 2.029838 ACATGCTCGTTCCTGAATCC 57.970 50.000 0.00 0.00 0.00 3.01
858 964 1.556911 ACATGCTCGTTCCTGAATCCT 59.443 47.619 0.00 0.00 0.00 3.24
859 965 1.938577 CATGCTCGTTCCTGAATCCTG 59.061 52.381 0.00 0.00 0.00 3.86
860 966 1.266178 TGCTCGTTCCTGAATCCTGA 58.734 50.000 0.00 0.00 0.00 3.86
861 967 1.833630 TGCTCGTTCCTGAATCCTGAT 59.166 47.619 0.00 0.00 0.00 2.90
862 968 2.208431 GCTCGTTCCTGAATCCTGATG 58.792 52.381 0.00 0.00 0.00 3.07
864 970 3.715495 CTCGTTCCTGAATCCTGATGAG 58.285 50.000 0.00 0.00 0.00 2.90
868 974 2.837947 TCCTGAATCCTGATGAGTGGT 58.162 47.619 0.00 0.00 0.00 4.16
869 975 2.502947 TCCTGAATCCTGATGAGTGGTG 59.497 50.000 0.00 0.00 0.00 4.17
870 976 2.502947 CCTGAATCCTGATGAGTGGTGA 59.497 50.000 0.00 0.00 0.00 4.02
871 977 3.136077 CCTGAATCCTGATGAGTGGTGAT 59.864 47.826 0.00 0.00 0.00 3.06
872 978 4.346127 CCTGAATCCTGATGAGTGGTGATA 59.654 45.833 0.00 0.00 0.00 2.15
873 979 5.282055 TGAATCCTGATGAGTGGTGATAC 57.718 43.478 0.00 0.00 0.00 2.24
874 980 4.964897 TGAATCCTGATGAGTGGTGATACT 59.035 41.667 0.00 0.00 0.00 2.12
875 981 6.136155 TGAATCCTGATGAGTGGTGATACTA 58.864 40.000 0.00 0.00 0.00 1.82
877 983 5.130705 TCCTGATGAGTGGTGATACTAGT 57.869 43.478 0.00 0.00 0.00 2.57
878 984 5.133941 TCCTGATGAGTGGTGATACTAGTC 58.866 45.833 0.00 0.00 30.67 2.59
879 985 4.279671 CCTGATGAGTGGTGATACTAGTCC 59.720 50.000 0.00 0.00 29.08 3.85
881 987 4.889995 TGATGAGTGGTGATACTAGTCCAG 59.110 45.833 0.00 0.00 29.08 3.86
882 988 4.586306 TGAGTGGTGATACTAGTCCAGA 57.414 45.455 0.00 0.00 29.08 3.86
883 989 4.930696 TGAGTGGTGATACTAGTCCAGAA 58.069 43.478 0.00 0.00 29.08 3.02
884 990 5.519808 TGAGTGGTGATACTAGTCCAGAAT 58.480 41.667 0.00 0.00 29.08 2.40
885 991 5.958380 TGAGTGGTGATACTAGTCCAGAATT 59.042 40.000 0.00 0.00 29.08 2.17
887 993 7.618117 TGAGTGGTGATACTAGTCCAGAATTTA 59.382 37.037 0.00 0.00 29.08 1.40
888 994 8.375493 AGTGGTGATACTAGTCCAGAATTTAA 57.625 34.615 0.00 0.00 0.00 1.52
890 996 8.038944 GTGGTGATACTAGTCCAGAATTTAACA 58.961 37.037 0.00 0.00 0.00 2.41
891 997 8.258007 TGGTGATACTAGTCCAGAATTTAACAG 58.742 37.037 0.00 0.00 0.00 3.16
892 998 8.475639 GGTGATACTAGTCCAGAATTTAACAGA 58.524 37.037 0.00 0.00 0.00 3.41
902 1008 9.788960 GTCCAGAATTTAACAGATTGTTATTCC 57.211 33.333 11.17 1.28 41.83 3.01
903 1009 9.753674 TCCAGAATTTAACAGATTGTTATTCCT 57.246 29.630 11.17 2.89 41.83 3.36
914 1020 9.965902 ACAGATTGTTATTCCTTTCTTATCTGT 57.034 29.630 0.00 0.00 42.68 3.41
916 1022 9.401058 AGATTGTTATTCCTTTCTTATCTGTGG 57.599 33.333 0.00 0.00 0.00 4.17
917 1023 9.396022 GATTGTTATTCCTTTCTTATCTGTGGA 57.604 33.333 0.00 0.00 0.00 4.02
921 1027 4.778213 TCCTTTCTTATCTGTGGATGGG 57.222 45.455 0.00 0.00 33.71 4.00
934 1040 1.630369 TGGATGGGTTTCTGACAGGAG 59.370 52.381 1.81 0.00 0.00 3.69
981 1087 2.902486 TCTTGCACTGAGATCTCCAACT 59.098 45.455 20.03 0.00 0.00 3.16
987 1093 5.129980 TGCACTGAGATCTCCAACTGATTAT 59.870 40.000 20.03 0.00 0.00 1.28
1051 1160 4.481112 CTGATGCGCCGCCCAAAC 62.481 66.667 6.63 0.00 0.00 2.93
1058 1167 4.986708 GCCGCCCAAACCCAAGGA 62.987 66.667 0.00 0.00 0.00 3.36
1059 1168 2.989253 CCGCCCAAACCCAAGGAC 60.989 66.667 0.00 0.00 0.00 3.85
1102 1211 0.108138 GTCCCTCACCATCAAGACCG 60.108 60.000 0.00 0.00 0.00 4.79
1250 1368 0.568192 CCTCCTCCTCCTAATCCCCA 59.432 60.000 0.00 0.00 0.00 4.96
1253 1371 1.130678 CCTCCTCCTAATCCCCAGCC 61.131 65.000 0.00 0.00 0.00 4.85
1274 1392 1.079127 CGCATCGAGGAACCAAGGT 60.079 57.895 0.00 0.00 0.00 3.50
1591 1727 4.785453 CCCTCGCCAGGTTCTGCC 62.785 72.222 0.00 0.00 38.30 4.85
1800 1936 1.130054 AGAAGAGGAACCTGCTGCCA 61.130 55.000 0.00 0.00 0.00 4.92
1804 1940 0.034670 GAGGAACCTGCTGCCAATCT 60.035 55.000 0.00 0.00 0.00 2.40
1809 1945 1.708341 ACCTGCTGCCAATCTTGTTT 58.292 45.000 0.00 0.00 0.00 2.83
1820 1956 2.958355 CAATCTTGTTTGACACCAGGGT 59.042 45.455 0.00 0.00 0.00 4.34
1878 2014 2.089696 AGATAAGGAGGGGATGGAAGCT 60.090 50.000 0.00 0.00 0.00 3.74
1881 2017 0.627986 AGGAGGGGATGGAAGCTTTG 59.372 55.000 0.00 0.00 0.00 2.77
1884 2020 0.332972 AGGGGATGGAAGCTTTGGAC 59.667 55.000 0.00 0.00 0.00 4.02
1887 2023 1.657751 GGATGGAAGCTTTGGACGGC 61.658 60.000 0.00 0.00 0.00 5.68
1890 2026 1.298667 GGAAGCTTTGGACGGCCTA 59.701 57.895 9.82 0.00 34.31 3.93
1992 2128 3.253838 AAGCTTGGCCGGGGTACA 61.254 61.111 2.18 0.00 0.00 2.90
2275 2414 0.947244 CAATCGGCCTATGTTGGAGC 59.053 55.000 0.00 0.00 0.00 4.70
2285 2424 1.315257 ATGTTGGAGCCATCGGTTGC 61.315 55.000 0.00 0.00 0.00 4.17
2448 2587 1.377202 GACGGAGCTGGCATTGGAA 60.377 57.895 0.00 0.00 0.00 3.53
2484 2623 2.165641 CTCACAGCGGTACAAGATGGTA 59.834 50.000 9.94 0.00 0.00 3.25
2505 2644 3.008517 TGGATTGGAGGCGAGGCA 61.009 61.111 0.00 0.00 0.00 4.75
2538 2677 6.366061 TGAGACAGAACATACTGAATTTGTCG 59.634 38.462 0.00 0.00 40.63 4.35
2550 2689 3.245300 TGAATTTGTCGGGGTATTTGGGA 60.245 43.478 0.00 0.00 0.00 4.37
2733 2872 3.766051 GGAAGGACCTGCAAGATTTCATT 59.234 43.478 0.65 0.00 34.07 2.57
2925 3064 4.828925 GAGCAGCTGGGGCGAGTC 62.829 72.222 17.12 0.00 44.37 3.36
2973 3112 4.219725 TCACTGTTGTCCGAGTTGATGATA 59.780 41.667 0.00 0.00 0.00 2.15
2979 3118 2.036089 GTCCGAGTTGATGATAGACCCC 59.964 54.545 0.00 0.00 0.00 4.95
3087 3226 8.352201 CAGAACAATTTGTTTCTGATCAAGGTA 58.648 33.333 23.14 0.00 41.28 3.08
3112 3251 4.077108 AGTCTTCTGCTTTGCATTGATGA 58.923 39.130 0.00 0.00 38.13 2.92
3129 3268 1.518367 TGAACCAGGTGAAAGGAGGT 58.482 50.000 0.00 0.00 0.00 3.85
3130 3269 1.142870 TGAACCAGGTGAAAGGAGGTG 59.857 52.381 0.00 0.00 31.86 4.00
3132 3271 0.697854 ACCAGGTGAAAGGAGGTGGT 60.698 55.000 0.00 0.00 33.35 4.16
3213 3352 0.982852 TACTAGCTGCCATGGCCAGT 60.983 55.000 33.44 28.16 41.09 4.00
3229 3368 2.482839 GCCAGTAAGCTGCCAACAAAAA 60.483 45.455 0.00 0.00 41.26 1.94
3267 3406 3.745975 TGTTGAGTGAATCACTTAAGGCG 59.254 43.478 18.94 0.00 45.44 5.52
3297 3436 1.280746 CGGCACACACTGCTTTCTG 59.719 57.895 0.00 0.00 46.25 3.02
3363 3502 2.136196 TAAAACTTGGCTTGGCGCGG 62.136 55.000 8.83 0.00 40.44 6.46
3415 3554 0.669318 GTTTCACCCGATCGTGCAGA 60.669 55.000 15.09 1.62 33.57 4.26
3439 3578 2.467826 GGCAAGATCAGCGGCAGTC 61.468 63.158 1.45 0.00 0.00 3.51
3480 3619 4.740934 GCAGTATCTGGTGTCATAAGGACC 60.741 50.000 0.00 0.00 37.57 4.46
3525 3664 1.820519 CACATGTGGGCTAGTGCATTT 59.179 47.619 18.51 0.00 41.91 2.32
3628 3767 3.830192 CCCTGGCAATCCAAGCGC 61.830 66.667 0.00 0.00 42.91 5.92
3990 4129 4.192317 CAAAGGTGGTTAGATACAGGAGC 58.808 47.826 0.00 0.00 0.00 4.70
4038 4177 2.733517 GAGCTGTTCGACATAGGTAGC 58.266 52.381 0.00 0.00 0.00 3.58
4220 4364 6.209788 GTCCAGTCTCCTAAATCTACCTATGG 59.790 46.154 0.00 0.00 0.00 2.74
4263 4409 6.095021 TCTGAGCAAATTGGATGAATTCTCTG 59.905 38.462 7.05 0.00 32.76 3.35
4293 4439 5.425217 ACATGTGACCTGGAGATGTTATGTA 59.575 40.000 0.00 0.00 0.00 2.29
4294 4440 6.070251 ACATGTGACCTGGAGATGTTATGTAA 60.070 38.462 0.00 0.00 0.00 2.41
4295 4441 5.730550 TGTGACCTGGAGATGTTATGTAAC 58.269 41.667 0.00 0.00 36.74 2.50
4296 4442 4.804139 GTGACCTGGAGATGTTATGTAACG 59.196 45.833 0.00 0.00 39.00 3.18
4297 4443 4.464951 TGACCTGGAGATGTTATGTAACGT 59.535 41.667 0.00 0.00 39.00 3.99
4300 4446 5.187186 ACCTGGAGATGTTATGTAACGTTCT 59.813 40.000 2.82 0.00 39.00 3.01
4301 4447 6.106673 CCTGGAGATGTTATGTAACGTTCTT 58.893 40.000 2.82 0.00 39.00 2.52
4302 4448 7.093640 ACCTGGAGATGTTATGTAACGTTCTTA 60.094 37.037 2.82 0.00 39.00 2.10
4304 4450 9.961265 CTGGAGATGTTATGTAACGTTCTTATA 57.039 33.333 2.82 0.00 39.00 0.98
4319 4465 8.943909 ACGTTCTTATATTTCTTTACAGAGGG 57.056 34.615 0.00 0.00 0.00 4.30
4346 4492 8.610035 AGTAGTAACTAGTGTTTGTTTTTGCTC 58.390 33.333 0.00 0.00 37.59 4.26
4351 4497 5.861787 ACTAGTGTTTGTTTTTGCTCAACAC 59.138 36.000 0.00 5.52 33.81 3.32
4401 4547 5.300286 CCAGTGAAGAATATTTAGCAAGGGG 59.700 44.000 0.00 0.00 0.00 4.79
4461 4614 2.318908 TGCAGTCTTCCCTTGCAATTT 58.681 42.857 0.00 0.00 44.13 1.82
4481 4634 7.201496 GCAATTTTGATGCTGAATTTAGTCTGG 60.201 37.037 0.00 0.00 40.64 3.86
4510 4663 1.677576 CAGCAAAGTTCTCCTGCACAA 59.322 47.619 0.44 0.00 38.58 3.33
4526 4679 4.831107 TGCACAAAGTAGCAGACATGATA 58.169 39.130 0.00 0.00 35.51 2.15
4527 4680 5.244755 TGCACAAAGTAGCAGACATGATAA 58.755 37.500 0.00 0.00 35.51 1.75
4528 4681 5.882000 TGCACAAAGTAGCAGACATGATAAT 59.118 36.000 0.00 0.00 35.51 1.28
4561 4714 4.047142 GAGCAAAAACAGCTTCTTCCTTG 58.953 43.478 0.00 0.00 43.58 3.61
4564 4717 4.677779 GCAAAAACAGCTTCTTCCTTGTCA 60.678 41.667 0.00 0.00 0.00 3.58
4602 4755 0.378257 CGCCGATTTTGTGAGATGGG 59.622 55.000 0.00 0.00 0.00 4.00
4675 4828 4.874396 TGATCATGCATCAAGTCTGAACTC 59.126 41.667 0.00 0.00 38.68 3.01
4676 4829 4.548451 TCATGCATCAAGTCTGAACTCT 57.452 40.909 0.00 0.00 33.48 3.24
4677 4830 4.251268 TCATGCATCAAGTCTGAACTCTG 58.749 43.478 0.00 0.00 33.48 3.35
4678 4831 4.020839 TCATGCATCAAGTCTGAACTCTGA 60.021 41.667 0.00 0.00 33.48 3.27
4679 4832 4.341366 TGCATCAAGTCTGAACTCTGAA 57.659 40.909 0.00 0.00 33.48 3.02
4680 4833 4.313282 TGCATCAAGTCTGAACTCTGAAG 58.687 43.478 0.00 0.00 33.48 3.02
4681 4834 4.202295 TGCATCAAGTCTGAACTCTGAAGT 60.202 41.667 0.00 0.00 33.48 3.01
4684 4837 6.686630 CATCAAGTCTGAACTCTGAAGTACT 58.313 40.000 0.00 0.00 33.48 2.73
4691 4844 3.508012 TGAACTCTGAAGTACTCTCAGCC 59.492 47.826 20.97 13.89 33.48 4.85
4700 4853 0.332972 TACTCTCAGCCCTCTGCAGA 59.667 55.000 17.19 17.19 44.83 4.26
4701 4854 0.543883 ACTCTCAGCCCTCTGCAGAA 60.544 55.000 18.85 0.00 44.83 3.02
4702 4855 0.176219 CTCTCAGCCCTCTGCAGAAG 59.824 60.000 18.85 11.99 44.83 2.85
4703 4856 1.221293 CTCAGCCCTCTGCAGAAGG 59.779 63.158 24.76 24.76 44.83 3.46
4706 4859 3.313874 GCCCTCTGCAGAAGGCTA 58.686 61.111 38.21 9.57 45.79 3.93
4707 4860 1.604378 GCCCTCTGCAGAAGGCTAA 59.396 57.895 38.21 8.85 45.79 3.09
4708 4861 0.182299 GCCCTCTGCAGAAGGCTAAT 59.818 55.000 38.21 0.00 45.79 1.73
4709 4862 1.964552 CCCTCTGCAGAAGGCTAATG 58.035 55.000 18.36 3.43 45.15 1.90
4710 4863 1.476471 CCCTCTGCAGAAGGCTAATGG 60.476 57.143 18.36 12.34 45.15 3.16
4711 4864 1.487976 CCTCTGCAGAAGGCTAATGGA 59.512 52.381 18.85 0.00 45.15 3.41
4712 4865 2.106166 CCTCTGCAGAAGGCTAATGGAT 59.894 50.000 18.85 0.00 45.15 3.41
4713 4866 3.139850 CTCTGCAGAAGGCTAATGGATG 58.860 50.000 18.85 0.00 45.15 3.51
4714 4867 2.158711 TCTGCAGAAGGCTAATGGATGG 60.159 50.000 15.67 0.00 45.15 3.51
4715 4868 1.845791 TGCAGAAGGCTAATGGATGGA 59.154 47.619 0.00 0.00 45.15 3.41
4716 4869 2.444388 TGCAGAAGGCTAATGGATGGAT 59.556 45.455 0.00 0.00 45.15 3.41
4717 4870 2.818432 GCAGAAGGCTAATGGATGGATG 59.182 50.000 0.00 0.00 40.25 3.51
4784 4938 3.134401 ACGCAGTGCATTCTCTCAG 57.866 52.632 16.83 0.00 42.51 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.741770 CTGCTGCGTAACTGTCCCC 60.742 63.158 0.00 0.00 0.00 4.81
1 2 1.741770 CCTGCTGCGTAACTGTCCC 60.742 63.158 0.00 0.00 0.00 4.46
2 3 1.741770 CCCTGCTGCGTAACTGTCC 60.742 63.158 0.00 0.00 0.00 4.02
3 4 1.004918 ACCCTGCTGCGTAACTGTC 60.005 57.895 0.00 0.00 0.00 3.51
12 13 2.317149 CTAGGCCTACACCCTGCTGC 62.317 65.000 8.91 0.00 33.88 5.25
69 70 0.179092 GAGCCAGGGCAAATTCATGC 60.179 55.000 13.63 0.00 45.67 4.06
78 79 4.435970 CATGCTGGAGCCAGGGCA 62.436 66.667 17.64 11.69 43.77 5.36
82 83 2.113433 GTCTGCATGCTGGAGCCAG 61.113 63.158 22.54 12.17 46.15 4.85
85 86 3.873883 GCGTCTGCATGCTGGAGC 61.874 66.667 22.54 21.94 42.15 4.70
87 88 2.825075 AATGGCGTCTGCATGCTGGA 62.825 55.000 22.54 15.69 45.35 3.86
88 89 1.096967 TAATGGCGTCTGCATGCTGG 61.097 55.000 22.54 13.72 45.35 4.85
100 111 5.679734 ACTGCTCAGATTAATTAATGGCG 57.320 39.130 15.39 11.39 0.00 5.69
105 116 7.801104 TGGACCATACTGCTCAGATTAATTAA 58.199 34.615 3.60 0.00 0.00 1.40
106 117 7.373617 TGGACCATACTGCTCAGATTAATTA 57.626 36.000 3.60 0.00 0.00 1.40
107 118 6.252599 TGGACCATACTGCTCAGATTAATT 57.747 37.500 3.60 0.00 0.00 1.40
108 119 5.894298 TGGACCATACTGCTCAGATTAAT 57.106 39.130 3.60 0.00 0.00 1.40
109 120 5.692115 TTGGACCATACTGCTCAGATTAA 57.308 39.130 3.60 0.00 0.00 1.40
111 122 4.574674 TTTGGACCATACTGCTCAGATT 57.425 40.909 3.60 0.00 0.00 2.40
112 123 4.018960 AGTTTTGGACCATACTGCTCAGAT 60.019 41.667 8.55 0.00 0.00 2.90
113 124 3.327757 AGTTTTGGACCATACTGCTCAGA 59.672 43.478 8.55 0.00 0.00 3.27
114 125 3.679389 AGTTTTGGACCATACTGCTCAG 58.321 45.455 8.55 0.00 0.00 3.35
116 127 3.944087 AGAGTTTTGGACCATACTGCTC 58.056 45.455 13.02 8.57 0.00 4.26
118 129 5.880332 TCATAAGAGTTTTGGACCATACTGC 59.120 40.000 13.02 6.57 0.00 4.40
119 130 7.278868 GTCTCATAAGAGTTTTGGACCATACTG 59.721 40.741 13.02 2.18 42.66 2.74
120 131 7.331791 GTCTCATAAGAGTTTTGGACCATACT 58.668 38.462 9.00 9.00 42.66 2.12
138 159 4.519350 CCTAGTACTTGGATGCGTCTCATA 59.481 45.833 17.42 0.00 35.05 2.15
190 217 5.292834 TGAATGAAACGAGATGAGATGAAGC 59.707 40.000 0.00 0.00 0.00 3.86
191 218 6.898912 TGAATGAAACGAGATGAGATGAAG 57.101 37.500 0.00 0.00 0.00 3.02
197 224 9.430838 GAAATACATTGAATGAAACGAGATGAG 57.569 33.333 12.80 0.00 0.00 2.90
257 294 1.880675 CCAATGATGATGCTCTGCTCC 59.119 52.381 0.00 0.00 0.00 4.70
263 300 2.426024 AGCAACACCAATGATGATGCTC 59.574 45.455 6.54 0.00 30.30 4.26
287 366 3.553095 AAGACCAAGACCGGCTGCC 62.553 63.158 9.11 9.11 0.00 4.85
288 367 2.032681 AAGACCAAGACCGGCTGC 59.967 61.111 0.00 0.00 0.00 5.25
289 368 0.035458 AAGAAGACCAAGACCGGCTG 59.965 55.000 0.00 0.00 0.00 4.85
290 369 0.765510 AAAGAAGACCAAGACCGGCT 59.234 50.000 0.00 0.00 0.00 5.52
291 370 1.157585 GAAAGAAGACCAAGACCGGC 58.842 55.000 0.00 0.00 0.00 6.13
312 391 0.530211 CAGAAGATGAGAGCTGCGGG 60.530 60.000 0.00 0.00 0.00 6.13
313 392 0.530211 CCAGAAGATGAGAGCTGCGG 60.530 60.000 0.00 0.00 0.00 5.69
314 393 0.530211 CCCAGAAGATGAGAGCTGCG 60.530 60.000 0.00 0.00 0.00 5.18
336 418 1.251251 GACATCAAAAGGCAGGCAGT 58.749 50.000 0.00 0.00 0.00 4.40
337 419 1.068055 GTGACATCAAAAGGCAGGCAG 60.068 52.381 0.00 0.00 0.00 4.85
357 439 1.562672 AAACAGATCGGGTGGGGAGG 61.563 60.000 0.00 0.00 0.00 4.30
404 487 0.332632 CTTGGAAATGGGGGCTGAGA 59.667 55.000 0.00 0.00 0.00 3.27
408 491 2.039462 GCCTTGGAAATGGGGGCT 59.961 61.111 0.00 0.00 39.68 5.19
412 498 1.959282 GCTATCTGCCTTGGAAATGGG 59.041 52.381 0.00 0.00 35.15 4.00
494 587 1.623811 GTCAAGGAGGAGGTACAAGCA 59.376 52.381 0.00 0.00 0.00 3.91
495 588 1.903183 AGTCAAGGAGGAGGTACAAGC 59.097 52.381 0.00 0.00 0.00 4.01
496 589 2.354203 GCAGTCAAGGAGGAGGTACAAG 60.354 54.545 0.00 0.00 0.00 3.16
498 591 1.203187 AGCAGTCAAGGAGGAGGTACA 60.203 52.381 0.00 0.00 0.00 2.90
532 629 2.655407 TCCTACCCCTCCCTATGATCTC 59.345 54.545 0.00 0.00 0.00 2.75
618 720 1.008449 AGGAGAGCTTGTAGGGCCTTA 59.992 52.381 13.45 0.00 0.00 2.69
683 785 4.883585 TGCCATTAGGATTGTGATTCTGTC 59.116 41.667 0.00 0.00 36.89 3.51
697 799 0.466189 AATCCAGCGGTGCCATTAGG 60.466 55.000 9.63 0.00 38.23 2.69
710 812 2.012673 CGAAGGCCTTCAAGAATCCAG 58.987 52.381 37.88 19.00 39.46 3.86
711 813 1.950484 GCGAAGGCCTTCAAGAATCCA 60.950 52.381 37.88 0.00 39.46 3.41
729 831 2.279741 TGAGCAAGCTAATTACCAGCG 58.720 47.619 0.00 0.00 43.97 5.18
753 856 2.809696 ACGTTCAAACCAAATAGGGACG 59.190 45.455 0.00 0.00 43.89 4.79
756 859 5.219633 CAAGAACGTTCAAACCAAATAGGG 58.780 41.667 28.78 0.73 43.89 3.53
818 924 4.209538 TGTATGGATTCAGGGCAAGAATG 58.790 43.478 8.16 0.00 35.93 2.67
819 925 4.524802 TGTATGGATTCAGGGCAAGAAT 57.475 40.909 3.68 3.68 38.35 2.40
843 949 3.131933 ACTCATCAGGATTCAGGAACGAG 59.868 47.826 0.00 0.00 0.00 4.18
849 955 2.502947 TCACCACTCATCAGGATTCAGG 59.497 50.000 0.00 0.00 0.00 3.86
851 957 4.964897 AGTATCACCACTCATCAGGATTCA 59.035 41.667 0.00 0.00 0.00 2.57
852 958 5.543507 AGTATCACCACTCATCAGGATTC 57.456 43.478 0.00 0.00 0.00 2.52
853 959 6.139671 ACTAGTATCACCACTCATCAGGATT 58.860 40.000 0.00 0.00 0.00 3.01
854 960 5.710646 ACTAGTATCACCACTCATCAGGAT 58.289 41.667 0.00 0.00 0.00 3.24
855 961 5.130705 ACTAGTATCACCACTCATCAGGA 57.869 43.478 0.00 0.00 0.00 3.86
856 962 4.279671 GGACTAGTATCACCACTCATCAGG 59.720 50.000 0.00 0.00 0.00 3.86
857 963 4.889995 TGGACTAGTATCACCACTCATCAG 59.110 45.833 0.00 0.00 0.00 2.90
858 964 4.867086 TGGACTAGTATCACCACTCATCA 58.133 43.478 0.00 0.00 0.00 3.07
859 965 5.133941 TCTGGACTAGTATCACCACTCATC 58.866 45.833 0.00 0.00 0.00 2.92
860 966 5.130705 TCTGGACTAGTATCACCACTCAT 57.869 43.478 0.00 0.00 0.00 2.90
861 967 4.586306 TCTGGACTAGTATCACCACTCA 57.414 45.455 0.00 0.00 0.00 3.41
862 968 6.472686 AATTCTGGACTAGTATCACCACTC 57.527 41.667 0.00 0.00 0.00 3.51
864 970 8.038944 TGTTAAATTCTGGACTAGTATCACCAC 58.961 37.037 0.00 0.00 0.00 4.16
877 983 9.753674 AGGAATAACAATCTGTTAAATTCTGGA 57.246 29.630 11.79 0.00 44.84 3.86
888 994 9.965902 ACAGATAAGAAAGGAATAACAATCTGT 57.034 29.630 8.02 8.02 43.63 3.41
890 996 9.401058 CCACAGATAAGAAAGGAATAACAATCT 57.599 33.333 0.00 0.00 0.00 2.40
891 997 9.396022 TCCACAGATAAGAAAGGAATAACAATC 57.604 33.333 0.00 0.00 0.00 2.67
892 998 9.927081 ATCCACAGATAAGAAAGGAATAACAAT 57.073 29.630 0.00 0.00 0.00 2.71
894 1000 7.775093 CCATCCACAGATAAGAAAGGAATAACA 59.225 37.037 0.00 0.00 0.00 2.41
895 1001 7.229506 CCCATCCACAGATAAGAAAGGAATAAC 59.770 40.741 0.00 0.00 0.00 1.89
896 1002 7.091993 ACCCATCCACAGATAAGAAAGGAATAA 60.092 37.037 0.00 0.00 0.00 1.40
901 1007 4.510167 ACCCATCCACAGATAAGAAAGG 57.490 45.455 0.00 0.00 0.00 3.11
902 1008 6.094603 CAGAAACCCATCCACAGATAAGAAAG 59.905 42.308 0.00 0.00 0.00 2.62
903 1009 5.945784 CAGAAACCCATCCACAGATAAGAAA 59.054 40.000 0.00 0.00 0.00 2.52
905 1011 4.782691 TCAGAAACCCATCCACAGATAAGA 59.217 41.667 0.00 0.00 0.00 2.10
906 1012 4.878397 GTCAGAAACCCATCCACAGATAAG 59.122 45.833 0.00 0.00 0.00 1.73
907 1013 4.288366 TGTCAGAAACCCATCCACAGATAA 59.712 41.667 0.00 0.00 0.00 1.75
908 1014 3.843619 TGTCAGAAACCCATCCACAGATA 59.156 43.478 0.00 0.00 0.00 1.98
909 1015 2.644299 TGTCAGAAACCCATCCACAGAT 59.356 45.455 0.00 0.00 0.00 2.90
910 1016 2.038952 CTGTCAGAAACCCATCCACAGA 59.961 50.000 0.00 0.00 34.72 3.41
911 1017 2.430465 CTGTCAGAAACCCATCCACAG 58.570 52.381 0.00 0.00 0.00 3.66
912 1018 1.073763 CCTGTCAGAAACCCATCCACA 59.926 52.381 0.00 0.00 0.00 4.17
913 1019 1.351017 TCCTGTCAGAAACCCATCCAC 59.649 52.381 0.00 0.00 0.00 4.02
914 1020 1.630369 CTCCTGTCAGAAACCCATCCA 59.370 52.381 0.00 0.00 0.00 3.41
915 1021 1.909302 TCTCCTGTCAGAAACCCATCC 59.091 52.381 0.00 0.00 0.00 3.51
916 1022 3.604582 CTTCTCCTGTCAGAAACCCATC 58.395 50.000 0.00 0.00 31.86 3.51
917 1023 2.307098 CCTTCTCCTGTCAGAAACCCAT 59.693 50.000 0.00 0.00 31.86 4.00
921 1027 2.900546 TCCTCCTTCTCCTGTCAGAAAC 59.099 50.000 0.00 0.00 31.86 2.78
934 1040 3.641906 TCATAGGAATTCGGTCCTCCTTC 59.358 47.826 2.85 0.00 45.40 3.46
981 1087 8.694540 CCTTCCATTGGTCAACAAATATAATCA 58.305 33.333 1.86 0.00 43.46 2.57
987 1093 4.093011 CCCCTTCCATTGGTCAACAAATA 58.907 43.478 1.86 0.00 43.46 1.40
1050 1159 1.590147 GATGTCGTCGTCCTTGGGT 59.410 57.895 0.00 0.00 0.00 4.51
1051 1160 1.153628 GGATGTCGTCGTCCTTGGG 60.154 63.158 12.94 0.00 44.12 4.12
1052 1161 1.153628 GGGATGTCGTCGTCCTTGG 60.154 63.158 18.43 0.00 46.08 3.61
1053 1162 1.153628 GGGGATGTCGTCGTCCTTG 60.154 63.158 18.43 0.00 46.08 3.61
1054 1163 2.707849 CGGGGATGTCGTCGTCCTT 61.708 63.158 18.43 0.00 46.08 3.36
1055 1164 3.138798 CGGGGATGTCGTCGTCCT 61.139 66.667 18.43 0.00 46.08 3.85
1056 1165 4.867599 GCGGGGATGTCGTCGTCC 62.868 72.222 11.94 11.94 46.10 4.79
1057 1166 4.867599 GGCGGGGATGTCGTCGTC 62.868 72.222 0.00 0.00 0.00 4.20
1253 1371 4.812476 TGGTTCCTCGATGCGGCG 62.812 66.667 0.51 0.51 0.00 6.46
1572 1708 4.020617 CAGAACCTGGCGAGGGCA 62.021 66.667 19.90 0.00 44.84 5.36
1591 1727 2.435586 CTCTGCCTTGAGCCACCG 60.436 66.667 0.00 0.00 42.71 4.94
1611 1747 2.124983 GCGATCCCTTGCAGCTCA 60.125 61.111 0.00 0.00 0.00 4.26
1734 1870 1.291877 CGAACGGGTTGAGGAAGCTG 61.292 60.000 0.00 0.00 41.07 4.24
1800 1936 2.958355 CACCCTGGTGTCAAACAAGATT 59.042 45.455 8.20 0.00 40.91 2.40
1820 1956 4.451150 GCCCGGCGATGTCTGACA 62.451 66.667 13.60 13.60 0.00 3.58
1824 1960 3.254024 AAACAGCCCGGCGATGTCT 62.254 57.895 9.30 0.00 0.00 3.41
1878 2014 1.747367 CCGCATTAGGCCGTCCAAA 60.747 57.895 0.00 0.00 40.31 3.28
1881 2017 2.895372 CACCGCATTAGGCCGTCC 60.895 66.667 0.00 0.00 40.31 4.79
1887 2023 1.789078 GCTCATGGCACCGCATTAGG 61.789 60.000 0.00 0.00 41.35 2.69
1890 2026 2.044650 AGCTCATGGCACCGCATT 60.045 55.556 8.58 0.00 44.79 3.56
1971 2107 4.489771 CCCCGGCCAAGCTTCGAT 62.490 66.667 2.24 0.00 0.00 3.59
1992 2128 2.746362 CTCGCTCTCCTTTTCAGCAATT 59.254 45.455 0.00 0.00 32.27 2.32
2109 2245 2.254459 CACTCCACATCTTCGACTTCG 58.746 52.381 0.00 0.00 41.45 3.79
2259 2398 1.344953 ATGGCTCCAACATAGGCCGA 61.345 55.000 0.00 0.00 46.72 5.54
2285 2424 1.081774 GACAGATCGATCGCCGGAG 60.082 63.158 19.33 0.00 39.14 4.63
2484 2623 0.107017 CCTCGCCTCCAATCCACAAT 60.107 55.000 0.00 0.00 0.00 2.71
2505 2644 5.186021 CAGTATGTTCTGTCTCAGGTACCTT 59.814 44.000 13.15 0.00 31.51 3.50
2538 2677 3.655777 TGATATCCAGTCCCAAATACCCC 59.344 47.826 0.00 0.00 0.00 4.95
2550 2689 1.662608 CTCGGCGCTGATATCCAGT 59.337 57.895 21.31 0.00 44.71 4.00
2574 2713 3.746949 GATCCTGCCGTGCTCCCTG 62.747 68.421 0.00 0.00 0.00 4.45
2733 2872 2.289694 GCTTGCTCCAGTGTTTCTAGGA 60.290 50.000 0.00 0.00 0.00 2.94
2973 3112 3.308188 CCTCAAAAAGAATACCGGGGTCT 60.308 47.826 6.32 1.58 0.00 3.85
2979 3118 3.181520 CGACAGCCTCAAAAAGAATACCG 60.182 47.826 0.00 0.00 0.00 4.02
3011 3150 7.218228 AGCACAATCATGTTCTCATTTAACA 57.782 32.000 0.00 0.00 40.85 2.41
3087 3226 6.376299 TCATCAATGCAAAGCAGAAGACTAAT 59.624 34.615 0.00 0.00 43.65 1.73
3090 3229 4.077108 TCATCAATGCAAAGCAGAAGACT 58.923 39.130 0.00 0.00 43.65 3.24
3112 3251 0.478507 CCACCTCCTTTCACCTGGTT 59.521 55.000 0.00 0.00 0.00 3.67
3129 3268 1.361204 TCATCCTCAAGGCAAGACCA 58.639 50.000 0.00 0.00 43.14 4.02
3130 3269 2.092753 TGATCATCCTCAAGGCAAGACC 60.093 50.000 0.00 0.00 39.61 3.85
3132 3271 2.573009 TGTGATCATCCTCAAGGCAAGA 59.427 45.455 0.00 0.00 34.44 3.02
3213 3352 3.895232 TTGGTTTTTGTTGGCAGCTTA 57.105 38.095 2.28 0.00 0.00 3.09
3303 3442 0.251077 CCTCAGCTTTCCTTGCCTGT 60.251 55.000 0.00 0.00 0.00 4.00
3342 3481 0.666274 GCGCCAAGCCAAGTTTTACC 60.666 55.000 0.00 0.00 40.81 2.85
3363 3502 1.264288 CCTGGACGCTGAGTTGTTTTC 59.736 52.381 0.00 0.00 0.00 2.29
3415 3554 1.091771 CCGCTGATCTTGCCGAACAT 61.092 55.000 0.00 0.00 0.00 2.71
3480 3619 6.318628 GTCTGAGTAGATAGACATATTGCCG 58.681 44.000 0.00 0.00 42.18 5.69
3525 3664 5.132502 TCTGATTTGAAGCCAAACAGAAGA 58.867 37.500 14.54 5.71 44.16 2.87
3628 3767 1.886313 AGCGCGAGAATGCCATGAG 60.886 57.895 12.10 0.00 0.00 2.90
3782 3921 0.179100 ATGCCAGATGAACTCGTCGG 60.179 55.000 0.00 5.81 36.99 4.79
3990 4129 2.270923 TCCGCGTCATCTCAGATTTTG 58.729 47.619 4.92 0.00 0.00 2.44
4115 4254 7.386059 TCAGACTAGCTATCTCAGTGATCTAG 58.614 42.308 0.00 0.00 36.47 2.43
4172 4316 6.072112 CTGTACACAGCAAGTTGGTTAAAT 57.928 37.500 4.45 0.00 37.15 1.40
4173 4317 5.493133 CTGTACACAGCAAGTTGGTTAAA 57.507 39.130 4.45 0.00 37.15 1.52
4220 4364 8.752766 TGCTCAGAATTTCATCAAAGAAAATC 57.247 30.769 0.00 0.00 40.54 2.17
4263 4409 2.234661 TCTCCAGGTCACATGTGTCATC 59.765 50.000 24.63 7.70 0.00 2.92
4293 4439 9.379791 CCCTCTGTAAAGAAATATAAGAACGTT 57.620 33.333 0.00 0.00 0.00 3.99
4294 4440 8.755977 TCCCTCTGTAAAGAAATATAAGAACGT 58.244 33.333 0.00 0.00 0.00 3.99
4295 4441 9.250624 CTCCCTCTGTAAAGAAATATAAGAACG 57.749 37.037 0.00 0.00 0.00 3.95
4304 4450 8.667592 AGTTACTACTCCCTCTGTAAAGAAAT 57.332 34.615 0.00 0.00 0.00 2.17
4306 4452 8.389366 ACTAGTTACTACTCCCTCTGTAAAGAA 58.611 37.037 0.00 0.00 35.78 2.52
4307 4453 7.828223 CACTAGTTACTACTCCCTCTGTAAAGA 59.172 40.741 0.00 0.00 35.78 2.52
4308 4454 7.611079 ACACTAGTTACTACTCCCTCTGTAAAG 59.389 40.741 0.00 0.00 35.78 1.85
4309 4455 7.465116 ACACTAGTTACTACTCCCTCTGTAAA 58.535 38.462 0.00 0.00 35.78 2.01
4310 4456 7.025520 ACACTAGTTACTACTCCCTCTGTAA 57.974 40.000 0.00 0.00 35.78 2.41
4311 4457 6.633325 ACACTAGTTACTACTCCCTCTGTA 57.367 41.667 0.00 0.00 35.78 2.74
4312 4458 5.517620 ACACTAGTTACTACTCCCTCTGT 57.482 43.478 0.00 0.00 35.78 3.41
4313 4459 6.208994 ACAAACACTAGTTACTACTCCCTCTG 59.791 42.308 0.00 0.00 36.84 3.35
4314 4460 6.313324 ACAAACACTAGTTACTACTCCCTCT 58.687 40.000 0.00 0.00 36.84 3.69
4315 4461 6.587206 ACAAACACTAGTTACTACTCCCTC 57.413 41.667 0.00 0.00 36.84 4.30
4316 4462 6.990908 AACAAACACTAGTTACTACTCCCT 57.009 37.500 0.00 0.00 36.84 4.20
4317 4463 8.340443 CAAAAACAAACACTAGTTACTACTCCC 58.660 37.037 0.00 0.00 36.84 4.30
4318 4464 7.854422 GCAAAAACAAACACTAGTTACTACTCC 59.146 37.037 0.00 0.00 36.84 3.85
4319 4465 8.610035 AGCAAAAACAAACACTAGTTACTACTC 58.390 33.333 0.00 0.00 36.84 2.59
4325 4471 7.539366 GTGTTGAGCAAAAACAAACACTAGTTA 59.461 33.333 9.16 0.00 39.14 2.24
4346 4492 9.877178 ACATTATCTTCTAGGAGTAAAGTGTTG 57.123 33.333 0.00 0.00 0.00 3.33
4401 4547 2.554032 CAAGGGGTCACAAATCACAGAC 59.446 50.000 0.00 0.00 0.00 3.51
4461 4614 4.334552 TGCCAGACTAAATTCAGCATCAA 58.665 39.130 0.00 0.00 0.00 2.57
4481 4634 3.311966 GAGAACTTTGCTGGTGAAATGC 58.688 45.455 0.00 0.00 0.00 3.56
4526 4679 7.712205 AGCTGTTTTTGCTCTTGATTGTTTATT 59.288 29.630 0.00 0.00 35.67 1.40
4527 4680 7.212274 AGCTGTTTTTGCTCTTGATTGTTTAT 58.788 30.769 0.00 0.00 35.67 1.40
4528 4681 6.572519 AGCTGTTTTTGCTCTTGATTGTTTA 58.427 32.000 0.00 0.00 35.67 2.01
4549 4702 3.620488 TGTTTGTGACAAGGAAGAAGCT 58.380 40.909 0.00 0.00 34.69 3.74
4561 4714 3.064207 TGCCGACTAGATTGTTTGTGAC 58.936 45.455 0.00 0.00 0.00 3.67
4564 4717 2.066262 CGTGCCGACTAGATTGTTTGT 58.934 47.619 0.00 0.00 0.00 2.83
4602 4755 3.961729 CGACCTTCGTTTCCCCAC 58.038 61.111 0.00 0.00 34.72 4.61
4675 4828 2.426738 CAGAGGGCTGAGAGTACTTCAG 59.573 54.545 21.24 21.24 45.17 3.02
4676 4829 2.451490 CAGAGGGCTGAGAGTACTTCA 58.549 52.381 0.00 2.36 45.17 3.02
4677 4830 1.136110 GCAGAGGGCTGAGAGTACTTC 59.864 57.143 0.00 0.00 45.17 3.01
4678 4831 1.190643 GCAGAGGGCTGAGAGTACTT 58.809 55.000 0.00 0.00 45.17 2.24
4679 4832 0.040351 TGCAGAGGGCTGAGAGTACT 59.960 55.000 0.00 0.00 45.17 2.73
4680 4833 0.459489 CTGCAGAGGGCTGAGAGTAC 59.541 60.000 8.42 0.00 45.17 2.73
4681 4834 0.332972 TCTGCAGAGGGCTGAGAGTA 59.667 55.000 13.74 0.00 44.37 2.59
4691 4844 1.487976 TCCATTAGCCTTCTGCAGAGG 59.512 52.381 18.49 18.49 44.83 3.69
4700 4853 2.444388 TGAGCATCCATCCATTAGCCTT 59.556 45.455 0.00 0.00 0.00 4.35
4701 4854 2.060275 TGAGCATCCATCCATTAGCCT 58.940 47.619 0.00 0.00 0.00 4.58
4702 4855 2.157738 GTGAGCATCCATCCATTAGCC 58.842 52.381 0.00 0.00 0.00 3.93
4703 4856 2.812591 CAGTGAGCATCCATCCATTAGC 59.187 50.000 0.00 0.00 0.00 3.09
4704 4857 4.347360 TCAGTGAGCATCCATCCATTAG 57.653 45.455 0.00 0.00 0.00 1.73
4705 4858 4.776435 TTCAGTGAGCATCCATCCATTA 57.224 40.909 0.00 0.00 0.00 1.90
4706 4859 3.657398 TTCAGTGAGCATCCATCCATT 57.343 42.857 0.00 0.00 0.00 3.16
4707 4860 3.657398 TTTCAGTGAGCATCCATCCAT 57.343 42.857 0.00 0.00 0.00 3.41
4708 4861 3.438216 TTTTCAGTGAGCATCCATCCA 57.562 42.857 0.00 0.00 0.00 3.41
4709 4862 4.400251 TGAATTTTCAGTGAGCATCCATCC 59.600 41.667 0.00 0.00 32.50 3.51
4710 4863 5.571784 TGAATTTTCAGTGAGCATCCATC 57.428 39.130 0.00 0.00 32.50 3.51
4711 4864 5.681437 GCATGAATTTTCAGTGAGCATCCAT 60.681 40.000 0.00 0.00 41.08 3.41
4712 4865 4.381185 GCATGAATTTTCAGTGAGCATCCA 60.381 41.667 0.00 0.00 41.08 3.41
4713 4866 4.110482 GCATGAATTTTCAGTGAGCATCC 58.890 43.478 0.00 0.00 41.08 3.51
4714 4867 4.798907 CAGCATGAATTTTCAGTGAGCATC 59.201 41.667 0.00 0.00 41.08 3.91
4715 4868 4.381612 CCAGCATGAATTTTCAGTGAGCAT 60.382 41.667 0.00 0.00 41.08 3.79
4716 4869 3.057104 CCAGCATGAATTTTCAGTGAGCA 60.057 43.478 0.00 0.00 41.08 4.26
4717 4870 3.057033 ACCAGCATGAATTTTCAGTGAGC 60.057 43.478 0.00 1.53 41.08 4.26
4781 4935 4.158949 GCATGGCATTTATATCATGGCTGA 59.841 41.667 17.43 4.31 45.30 4.26
4782 4936 4.430007 GCATGGCATTTATATCATGGCTG 58.570 43.478 17.43 14.35 45.30 4.85
4783 4937 4.730949 GCATGGCATTTATATCATGGCT 57.269 40.909 17.43 5.68 45.30 4.75
4814 4968 2.730094 CCAGCACAACCAGGCAAC 59.270 61.111 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.