Multiple sequence alignment - TraesCS7A01G317100

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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 TraesCS7A01G317100 chr7A 100.000 4294 0 0 1 4294 455397214 455392921 0.000000e+00 7930
1 TraesCS7A01G317100 chr7A 86.179 246 28 2 1628 1867 34106282 34106037 1.180000e-65 261
2 TraesCS7A01G317100 chr7A 85.772 246 29 4 1628 1867 34519311 34519066 5.510000e-64 255
3 TraesCS7A01G317100 chr7A 84.553 246 32 4 1628 1867 512328944 512329189 5.550000e-59 239
4 TraesCS7A01G317100 chr7A 74.854 513 98 17 133 620 549788729 549789235 2.020000e-48 204
5 TraesCS7A01G317100 chr7D 95.305 2215 62 20 2111 4294 398719748 398717545 0.000000e+00 3476
6 TraesCS7A01G317100 chr7D 91.012 2025 145 15 4 2026 398722199 398720210 0.000000e+00 2697
7 TraesCS7A01G317100 chr7D 86.585 246 27 4 1628 1867 33754892 33755137 2.550000e-67 267
8 TraesCS7A01G317100 chr7D 86.250 240 33 0 1628 1867 34151394 34151155 1.180000e-65 261
9 TraesCS7A01G317100 chr7D 85.366 246 30 4 1628 1867 34011496 34011251 2.560000e-62 250
10 TraesCS7A01G317100 chr7D 84.959 246 31 5 1628 1867 34445267 34445512 1.190000e-60 244
11 TraesCS7A01G317100 chr7D 82.520 246 37 4 1628 1867 420742658 420742413 1.210000e-50 211
12 TraesCS7A01G317100 chr1A 77.888 502 107 4 133 634 386475766 386476263 4.170000e-80 309
13 TraesCS7A01G317100 chr1A 76.789 517 104 14 113 621 458533610 458533102 4.230000e-70 276
14 TraesCS7A01G317100 chr4A 86.531 245 27 4 1628 1866 691324135 691324379 9.160000e-67 265
15 TraesCS7A01G317100 chr4A 86.066 244 26 5 1628 1864 691247042 691247284 5.510000e-64 255
16 TraesCS7A01G317100 chr4A 86.522 230 25 4 1644 1867 691469822 691469593 9.220000e-62 248
17 TraesCS7A01G317100 chr4A 85.792 183 23 3 1163 1344 690881565 690881385 1.580000e-44 191
18 TraesCS7A01G317100 chr4A 85.326 184 26 1 1161 1344 691246754 691246936 5.670000e-44 189
19 TraesCS7A01G317100 chr4A 78.136 279 49 10 360 632 649346483 649346755 2.660000e-37 167
20 TraesCS7A01G317100 chr3D 75.697 502 111 10 114 611 427820579 427820085 1.540000e-59 241
21 TraesCS7A01G317100 chr7B 82.520 246 37 4 1628 1867 436787601 436787356 1.210000e-50 211
22 TraesCS7A01G317100 chr6D 83.556 225 29 7 1644 1864 310888063 310887843 2.020000e-48 204
23 TraesCS7A01G317100 chr6A 82.960 223 34 4 1644 1864 447178890 447178670 9.420000e-47 198
24 TraesCS7A01G317100 chr2A 76.786 336 74 4 123 457 377769985 377770317 7.330000e-43 185
25 TraesCS7A01G317100 chr6B 72.303 343 85 10 123 460 11175335 11174998 9.830000e-17 99


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 TraesCS7A01G317100 chr7A 455392921 455397214 4293 True 7930.0 7930 100.0000 1 4294 1 chr7A.!!$R3 4293
1 TraesCS7A01G317100 chr7A 549788729 549789235 506 False 204.0 204 74.8540 133 620 1 chr7A.!!$F2 487
2 TraesCS7A01G317100 chr7D 398717545 398722199 4654 True 3086.5 3476 93.1585 4 4294 2 chr7D.!!$R4 4290
3 TraesCS7A01G317100 chr1A 458533102 458533610 508 True 276.0 276 76.7890 113 621 1 chr1A.!!$R1 508
4 TraesCS7A01G317100 chr4A 691246754 691247284 530 False 222.0 255 85.6960 1161 1864 2 chr4A.!!$F3 703

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
884 912 0.033405 TCCGATCGTTTCTCCCTCCT 60.033 55.0 15.09 0.0 0.00 3.69 F
886 914 0.386113 CGATCGTTTCTCCCTCCTCC 59.614 60.0 7.03 0.0 0.00 4.30 F
1917 1951 0.466543 GCCACCATGGTACGGATACA 59.533 55.0 22.48 0.0 40.46 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2065 0.037303 CTGGATGGTGTCAAGGTGCT 59.963 55.0 0.0 0.0 0.00 4.40 R
2038 2072 0.038166 GGAAAGGCTGGATGGTGTCA 59.962 55.0 0.0 0.0 0.00 3.58 R
3424 3847 1.041447 AATCGGTAGTCTCCACCCCG 61.041 60.0 0.0 0.0 38.38 5.73 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
20 21 3.771577 TTAGCCCTAATTGCTCTAGGC 57.228 47.619 0.00 0.00 40.23 3.93
29 30 6.326375 CCTAATTGCTCTAGGCTTATCTACG 58.674 44.000 0.00 0.00 42.39 3.51
37 38 0.750850 GGCTTATCTACGCCAGTGGA 59.249 55.000 15.20 0.00 45.59 4.02
44 45 2.958818 TCTACGCCAGTGGATATCCTT 58.041 47.619 22.35 8.30 32.72 3.36
55 56 3.879892 GTGGATATCCTTTGCCTCTTGTC 59.120 47.826 22.35 0.00 36.82 3.18
58 59 0.693049 ATCCTTTGCCTCTTGTCGGT 59.307 50.000 0.00 0.00 0.00 4.69
63 64 2.045926 GCCTCTTGTCGGTGCCAT 60.046 61.111 0.00 0.00 0.00 4.40
64 65 1.220749 GCCTCTTGTCGGTGCCATA 59.779 57.895 0.00 0.00 0.00 2.74
67 68 1.066143 CCTCTTGTCGGTGCCATAGTT 60.066 52.381 0.00 0.00 0.00 2.24
69 70 1.621317 TCTTGTCGGTGCCATAGTTGA 59.379 47.619 0.00 0.00 0.00 3.18
78 79 1.138859 TGCCATAGTTGATCCACCTCG 59.861 52.381 0.00 0.00 0.00 4.63
87 88 1.340308 TGATCCACCTCGTCTTCGGTA 60.340 52.381 0.00 0.00 37.69 4.02
88 89 1.955080 GATCCACCTCGTCTTCGGTAT 59.045 52.381 0.00 0.00 37.69 2.73
90 91 0.384669 CCACCTCGTCTTCGGTATCC 59.615 60.000 0.00 0.00 37.69 2.59
97 98 2.173356 TCGTCTTCGGTATCCTTAGGGA 59.827 50.000 0.00 0.00 40.77 4.20
103 104 3.931317 TCGGTATCCTTAGGGAAATGGA 58.069 45.455 0.00 0.00 45.78 3.41
104 105 4.499472 TCGGTATCCTTAGGGAAATGGAT 58.501 43.478 0.00 0.00 45.78 3.41
111 112 3.371595 CCTTAGGGAAATGGATCACGGTT 60.372 47.826 0.00 0.00 33.58 4.44
112 113 2.128771 AGGGAAATGGATCACGGTTG 57.871 50.000 0.00 0.00 0.00 3.77
113 114 1.102978 GGGAAATGGATCACGGTTGG 58.897 55.000 0.00 0.00 0.00 3.77
117 118 1.285280 AATGGATCACGGTTGGAGGA 58.715 50.000 0.00 0.00 0.00 3.71
127 128 2.301009 ACGGTTGGAGGACTCGTTTTAT 59.699 45.455 0.00 0.00 0.00 1.40
162 164 3.935818 TTTGTCAGGGTTTGTGTCCTA 57.064 42.857 0.00 0.00 0.00 2.94
166 168 3.000727 GTCAGGGTTTGTGTCCTATTCG 58.999 50.000 0.00 0.00 0.00 3.34
168 170 2.027561 CAGGGTTTGTGTCCTATTCGGA 60.028 50.000 0.00 0.00 40.30 4.55
196 199 2.439156 GGCGGCTGCTTCCTGAAT 60.439 61.111 18.85 0.00 42.25 2.57
199 202 1.312815 GCGGCTGCTTCCTGAATATT 58.687 50.000 11.21 0.00 38.39 1.28
212 215 8.907885 GCTTCCTGAATATTGAATAAGGTTCTT 58.092 33.333 0.00 0.00 0.00 2.52
216 220 9.618890 CCTGAATATTGAATAAGGTTCTTCTCA 57.381 33.333 0.00 0.00 0.00 3.27
230 234 1.486726 CTTCTCATCTAGCCCCCGTTT 59.513 52.381 0.00 0.00 0.00 3.60
236 240 0.543410 TCTAGCCCCCGTTTCTGTGA 60.543 55.000 0.00 0.00 0.00 3.58
245 249 3.556213 CCCCGTTTCTGTGATGTGTCTAA 60.556 47.826 0.00 0.00 0.00 2.10
278 282 0.600255 CACGTGAAGGTGTGTCTCCC 60.600 60.000 10.90 0.00 33.24 4.30
282 286 1.347707 GTGAAGGTGTGTCTCCCATGA 59.652 52.381 0.00 0.00 0.00 3.07
294 319 4.286808 TGTCTCCCATGAATCTGTCTTTGA 59.713 41.667 0.00 0.00 0.00 2.69
323 348 2.224137 GCTCGGATCTGGTCATCATTCA 60.224 50.000 0.62 0.00 0.00 2.57
329 354 5.279156 CGGATCTGGTCATCATTCATCTACA 60.279 44.000 0.00 0.00 0.00 2.74
330 355 5.931146 GGATCTGGTCATCATTCATCTACAC 59.069 44.000 0.00 0.00 0.00 2.90
385 410 0.248012 TTACTCTTCATCGGCGGCAA 59.752 50.000 10.53 0.00 0.00 4.52
394 419 0.316841 ATCGGCGGCAATTGTTGTTT 59.683 45.000 10.53 0.00 0.00 2.83
395 420 0.318275 TCGGCGGCAATTGTTGTTTC 60.318 50.000 10.53 0.00 0.00 2.78
400 426 1.071568 CGGCAATTGTTGTTTCGTTGC 60.072 47.619 7.40 0.00 43.17 4.17
438 464 1.045407 TAGCACAACGACTTCCTGGT 58.955 50.000 0.00 0.00 0.00 4.00
445 471 3.926616 CAACGACTTCCTGGTTGTCTAT 58.073 45.455 15.52 5.51 37.01 1.98
492 518 4.148825 GGACGGGCGATGACAGCT 62.149 66.667 0.00 0.00 34.52 4.24
503 529 1.174712 ATGACAGCTGCACGCCTTTT 61.175 50.000 15.27 0.00 40.39 2.27
509 535 1.582968 CTGCACGCCTTTTGCTCAT 59.417 52.632 0.00 0.00 40.86 2.90
541 567 2.540515 CAGTCGTTGCTAGGTGGTATG 58.459 52.381 0.00 0.00 0.00 2.39
550 576 4.804597 TGCTAGGTGGTATGTAGATCTGT 58.195 43.478 5.18 0.00 0.00 3.41
556 582 9.688091 CTAGGTGGTATGTAGATCTGTATGTAT 57.312 37.037 5.18 0.00 0.00 2.29
557 583 8.958060 AGGTGGTATGTAGATCTGTATGTATT 57.042 34.615 5.18 0.00 0.00 1.89
603 631 8.771920 TTGTTGTACATCTACGATTGAAGATT 57.228 30.769 0.00 0.00 29.93 2.40
648 676 3.354089 AAAAAGCACTCATGAACCACG 57.646 42.857 0.00 0.00 0.00 4.94
655 683 3.179830 CACTCATGAACCACGTACTAGC 58.820 50.000 0.00 0.00 0.00 3.42
665 693 8.625786 TGAACCACGTACTAGCAATAGATATA 57.374 34.615 0.00 0.00 0.00 0.86
666 694 9.070179 TGAACCACGTACTAGCAATAGATATAA 57.930 33.333 0.00 0.00 0.00 0.98
689 717 7.670605 AAAAGGAATCATGATTCATGGATGT 57.329 32.000 36.93 20.20 46.77 3.06
742 770 0.256177 TGGCCGCTCTTCTCTCTCTA 59.744 55.000 0.00 0.00 0.00 2.43
884 912 0.033405 TCCGATCGTTTCTCCCTCCT 60.033 55.000 15.09 0.00 0.00 3.69
886 914 0.386113 CGATCGTTTCTCCCTCCTCC 59.614 60.000 7.03 0.00 0.00 4.30
887 915 0.753867 GATCGTTTCTCCCTCCTCCC 59.246 60.000 0.00 0.00 0.00 4.30
888 916 0.691413 ATCGTTTCTCCCTCCTCCCC 60.691 60.000 0.00 0.00 0.00 4.81
889 917 1.306226 CGTTTCTCCCTCCTCCCCT 60.306 63.158 0.00 0.00 0.00 4.79
927 955 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
928 956 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
929 957 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
930 958 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
931 959 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
932 960 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
933 961 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
934 962 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
935 963 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
936 964 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
937 965 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
938 966 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
939 967 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
940 968 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
941 969 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
942 970 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
943 971 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1043 1071 0.468029 CCTCCTCTCCTCCTCAGCTC 60.468 65.000 0.00 0.00 0.00 4.09
1073 1101 3.778265 AGCTCCAATCTATCTCCCTCTC 58.222 50.000 0.00 0.00 0.00 3.20
1082 1110 0.567182 ATCTCCCTCTCTCTGCCCAT 59.433 55.000 0.00 0.00 0.00 4.00
1086 1114 2.978278 CTCCCTCTCTCTGCCCATTTAT 59.022 50.000 0.00 0.00 0.00 1.40
1109 1137 3.311322 CAGCCTTTAACACACGAACTCAA 59.689 43.478 0.00 0.00 0.00 3.02
1146 1174 3.414136 AACCACTTCACGCAGGCCA 62.414 57.895 5.01 0.00 0.00 5.36
1157 1185 1.154225 GCAGGCCATCGTTTTGTCG 60.154 57.895 5.01 0.00 0.00 4.35
1199 1227 1.495951 GGTGAACGGTCAATCGTGC 59.504 57.895 3.77 0.00 43.07 5.34
1449 1477 6.742718 CGGTTCATGAAGCAAATAGTAGTTTG 59.257 38.462 30.87 11.05 41.02 2.93
1551 1579 4.399004 TTCTTGGATGGGTTGTTTTGTG 57.601 40.909 0.00 0.00 0.00 3.33
1555 1583 1.137872 GGATGGGTTGTTTTGTGCACA 59.862 47.619 17.42 17.42 0.00 4.57
1556 1584 2.200899 GATGGGTTGTTTTGTGCACAC 58.799 47.619 21.56 9.20 0.00 3.82
1867 1901 3.418714 GAGTACCGCCTCGACGAT 58.581 61.111 0.00 0.00 34.06 3.73
1879 1913 1.472878 CTCGACGATCCTTCTTCCACA 59.527 52.381 0.00 0.00 0.00 4.17
1917 1951 0.466543 GCCACCATGGTACGGATACA 59.533 55.000 22.48 0.00 40.46 2.29
1954 1988 1.883084 GGAGCTAATGCACCGACCG 60.883 63.158 0.00 0.00 39.93 4.79
2026 2060 2.366590 TGATAGGAGTACGAGCGTCCTA 59.633 50.000 9.56 9.56 45.08 2.94
2027 2061 2.522836 TAGGAGTACGAGCGTCCTAG 57.477 55.000 0.00 0.00 41.21 3.02
2028 2062 0.814812 AGGAGTACGAGCGTCCTAGC 60.815 60.000 0.00 0.00 39.03 3.42
2036 2070 1.817209 AGCGTCCTAGCTTAGCACC 59.183 57.895 7.07 0.00 46.80 5.01
2037 2071 0.684805 AGCGTCCTAGCTTAGCACCT 60.685 55.000 7.07 0.00 46.80 4.00
2038 2072 0.175989 GCGTCCTAGCTTAGCACCTT 59.824 55.000 7.07 0.00 0.00 3.50
2039 2073 1.927895 CGTCCTAGCTTAGCACCTTG 58.072 55.000 7.07 0.00 0.00 3.61
2040 2074 1.476891 CGTCCTAGCTTAGCACCTTGA 59.523 52.381 7.07 0.00 0.00 3.02
2041 2075 2.735762 CGTCCTAGCTTAGCACCTTGAC 60.736 54.545 7.07 4.83 0.00 3.18
2042 2076 2.233922 GTCCTAGCTTAGCACCTTGACA 59.766 50.000 7.07 0.00 0.00 3.58
2043 2077 2.233922 TCCTAGCTTAGCACCTTGACAC 59.766 50.000 7.07 0.00 0.00 3.67
2044 2078 2.622436 CTAGCTTAGCACCTTGACACC 58.378 52.381 7.07 0.00 0.00 4.16
2045 2079 0.764890 AGCTTAGCACCTTGACACCA 59.235 50.000 7.07 0.00 0.00 4.17
2046 2080 1.352352 AGCTTAGCACCTTGACACCAT 59.648 47.619 7.07 0.00 0.00 3.55
2047 2081 1.740025 GCTTAGCACCTTGACACCATC 59.260 52.381 0.00 0.00 0.00 3.51
2048 2082 2.359900 CTTAGCACCTTGACACCATCC 58.640 52.381 0.00 0.00 0.00 3.51
2049 2083 1.357137 TAGCACCTTGACACCATCCA 58.643 50.000 0.00 0.00 0.00 3.41
2050 2084 0.037303 AGCACCTTGACACCATCCAG 59.963 55.000 0.00 0.00 0.00 3.86
2051 2085 1.589716 GCACCTTGACACCATCCAGC 61.590 60.000 0.00 0.00 0.00 4.85
2052 2086 0.962356 CACCTTGACACCATCCAGCC 60.962 60.000 0.00 0.00 0.00 4.85
2053 2087 1.136329 ACCTTGACACCATCCAGCCT 61.136 55.000 0.00 0.00 0.00 4.58
2054 2088 0.038744 CCTTGACACCATCCAGCCTT 59.961 55.000 0.00 0.00 0.00 4.35
2055 2089 1.548582 CCTTGACACCATCCAGCCTTT 60.549 52.381 0.00 0.00 0.00 3.11
2056 2090 1.815003 CTTGACACCATCCAGCCTTTC 59.185 52.381 0.00 0.00 0.00 2.62
2057 2091 0.038166 TGACACCATCCAGCCTTTCC 59.962 55.000 0.00 0.00 0.00 3.13
2058 2092 0.329596 GACACCATCCAGCCTTTCCT 59.670 55.000 0.00 0.00 0.00 3.36
2059 2093 0.779997 ACACCATCCAGCCTTTCCTT 59.220 50.000 0.00 0.00 0.00 3.36
2060 2094 1.272147 ACACCATCCAGCCTTTCCTTC 60.272 52.381 0.00 0.00 0.00 3.46
2061 2095 0.332972 ACCATCCAGCCTTTCCTTCC 59.667 55.000 0.00 0.00 0.00 3.46
2062 2096 0.396278 CCATCCAGCCTTTCCTTCCC 60.396 60.000 0.00 0.00 0.00 3.97
2063 2097 0.396278 CATCCAGCCTTTCCTTCCCC 60.396 60.000 0.00 0.00 0.00 4.81
2064 2098 1.584717 ATCCAGCCTTTCCTTCCCCC 61.585 60.000 0.00 0.00 0.00 5.40
2079 2113 3.065462 CCCCCTCTCTCTCTATGCC 57.935 63.158 0.00 0.00 0.00 4.40
2080 2114 0.486879 CCCCCTCTCTCTCTATGCCT 59.513 60.000 0.00 0.00 0.00 4.75
2081 2115 1.713647 CCCCCTCTCTCTCTATGCCTA 59.286 57.143 0.00 0.00 0.00 3.93
2082 2116 2.291540 CCCCCTCTCTCTCTATGCCTAG 60.292 59.091 0.00 0.00 0.00 3.02
2083 2117 2.378547 CCCCTCTCTCTCTATGCCTAGT 59.621 54.545 0.00 0.00 0.00 2.57
2084 2118 3.561313 CCCCTCTCTCTCTATGCCTAGTC 60.561 56.522 0.00 0.00 0.00 2.59
2085 2119 3.330701 CCCTCTCTCTCTATGCCTAGTCT 59.669 52.174 0.00 0.00 0.00 3.24
2086 2120 4.565652 CCCTCTCTCTCTATGCCTAGTCTC 60.566 54.167 0.00 0.00 0.00 3.36
2087 2121 4.287067 CCTCTCTCTCTATGCCTAGTCTCT 59.713 50.000 0.00 0.00 0.00 3.10
2088 2122 5.482908 CTCTCTCTCTATGCCTAGTCTCTC 58.517 50.000 0.00 0.00 0.00 3.20
2089 2123 4.904853 TCTCTCTCTATGCCTAGTCTCTCA 59.095 45.833 0.00 0.00 0.00 3.27
2090 2124 4.968259 TCTCTCTATGCCTAGTCTCTCAC 58.032 47.826 0.00 0.00 0.00 3.51
2091 2125 4.658435 TCTCTCTATGCCTAGTCTCTCACT 59.342 45.833 0.00 0.00 39.41 3.41
2092 2126 4.713553 TCTCTATGCCTAGTCTCTCACTG 58.286 47.826 0.00 0.00 36.43 3.66
2093 2127 3.218453 TCTATGCCTAGTCTCTCACTGC 58.782 50.000 0.00 0.00 36.43 4.40
2094 2128 1.857965 ATGCCTAGTCTCTCACTGCA 58.142 50.000 0.00 0.00 38.16 4.41
2095 2129 0.891373 TGCCTAGTCTCTCACTGCAC 59.109 55.000 0.00 0.00 36.43 4.57
2096 2130 1.181786 GCCTAGTCTCTCACTGCACT 58.818 55.000 0.00 0.00 36.43 4.40
2097 2131 2.290960 TGCCTAGTCTCTCACTGCACTA 60.291 50.000 0.00 0.00 36.43 2.74
2098 2132 2.755655 GCCTAGTCTCTCACTGCACTAA 59.244 50.000 0.00 0.00 36.43 2.24
2099 2133 3.383185 GCCTAGTCTCTCACTGCACTAAT 59.617 47.826 0.00 0.00 36.43 1.73
2100 2134 4.736168 GCCTAGTCTCTCACTGCACTAATG 60.736 50.000 0.00 0.00 36.43 1.90
2101 2135 4.642437 CCTAGTCTCTCACTGCACTAATGA 59.358 45.833 0.00 0.00 36.43 2.57
2102 2136 5.301551 CCTAGTCTCTCACTGCACTAATGAT 59.698 44.000 0.00 0.00 36.43 2.45
2103 2137 5.674052 AGTCTCTCACTGCACTAATGATT 57.326 39.130 0.00 0.00 32.26 2.57
2104 2138 6.782082 AGTCTCTCACTGCACTAATGATTA 57.218 37.500 0.00 0.00 32.26 1.75
2105 2139 7.175347 AGTCTCTCACTGCACTAATGATTAA 57.825 36.000 0.00 0.00 32.26 1.40
2106 2140 7.615403 AGTCTCTCACTGCACTAATGATTAAA 58.385 34.615 0.00 0.00 32.26 1.52
2107 2141 7.547370 AGTCTCTCACTGCACTAATGATTAAAC 59.453 37.037 0.00 0.00 32.26 2.01
2108 2142 7.547370 GTCTCTCACTGCACTAATGATTAAACT 59.453 37.037 0.00 0.00 0.00 2.66
2109 2143 8.097038 TCTCTCACTGCACTAATGATTAAACTT 58.903 33.333 0.00 0.00 0.00 2.66
2383 2794 1.029947 TCTACTCCAGCGACGATGCA 61.030 55.000 7.77 0.00 37.31 3.96
2410 2821 1.487976 CAGATCCTGCACTACATGGGT 59.512 52.381 0.00 0.00 0.00 4.51
2653 3064 4.715523 CACCAACCCCACCGCGAT 62.716 66.667 8.23 0.00 0.00 4.58
2674 3085 3.083997 GGGATCACGGACTGGGCT 61.084 66.667 0.00 0.00 0.00 5.19
2689 3100 1.004440 GGCTATGATGGACCGGCTC 60.004 63.158 0.00 0.00 0.00 4.70
2951 3362 4.492570 CGTAACAACTGTAGCTGCTATTGC 60.493 45.833 13.20 4.76 40.20 3.56
2952 3363 2.359900 ACAACTGTAGCTGCTATTGCC 58.640 47.619 13.20 0.25 38.71 4.52
3039 3458 8.601476 ACAGTAAAAAGACTACAACGAGAAAAG 58.399 33.333 0.00 0.00 0.00 2.27
3126 3545 5.624159 AGATTGATGTGTGGAGAGAAAACA 58.376 37.500 0.00 0.00 0.00 2.83
3184 3603 1.469940 GGAGTATCACTGTCACCGCTG 60.470 57.143 0.00 0.00 36.25 5.18
3322 3745 1.943116 TTGTGGTGTGTGCAAGGTGC 61.943 55.000 0.00 0.00 45.29 5.01
3331 3754 4.895854 GCAAGGTGCGCAATTCAT 57.104 50.000 14.00 0.00 31.71 2.57
3385 3808 7.015098 TCTCTTCAAATTGTTGCCTGGAAATAA 59.985 33.333 0.00 0.00 34.50 1.40
3386 3809 7.504403 TCTTCAAATTGTTGCCTGGAAATAAA 58.496 30.769 0.26 0.00 34.50 1.40
3387 3810 7.656948 TCTTCAAATTGTTGCCTGGAAATAAAG 59.343 33.333 0.26 0.00 34.50 1.85
3389 3812 5.488262 AATTGTTGCCTGGAAATAAAGCT 57.512 34.783 0.26 0.00 0.00 3.74
3390 3813 3.940209 TGTTGCCTGGAAATAAAGCTG 57.060 42.857 0.00 0.00 0.00 4.24
3391 3814 3.495331 TGTTGCCTGGAAATAAAGCTGA 58.505 40.909 0.00 0.00 0.00 4.26
3392 3815 3.894427 TGTTGCCTGGAAATAAAGCTGAA 59.106 39.130 0.00 0.00 0.00 3.02
3416 3839 5.819991 AGATGGCCAAACTTTCTCATAGAA 58.180 37.500 10.96 0.00 31.28 2.10
3438 3861 2.664015 AGTAATCGGGGTGGAGACTAC 58.336 52.381 0.00 0.00 0.00 2.73
3453 3876 5.831525 TGGAGACTACCGATTTAGCTTCATA 59.168 40.000 0.00 0.00 0.00 2.15
3561 3985 1.448540 GTGACGACCATGGAGGCAG 60.449 63.158 21.47 6.93 43.14 4.85
3562 3986 2.187946 GACGACCATGGAGGCAGG 59.812 66.667 21.47 2.90 43.14 4.85
3575 3999 3.859414 GCAGGGGCGAGAGATGCT 61.859 66.667 0.00 0.00 34.10 3.79
3612 4036 1.170290 TCGCTTGTCGTGACAGGAGA 61.170 55.000 15.34 14.14 42.75 3.71
3622 4046 2.031682 CGTGACAGGAGAAAAAGGCAAG 60.032 50.000 0.00 0.00 0.00 4.01
3634 4058 9.056005 GGAGAAAAAGGCAAGTGAATTTAATTT 57.944 29.630 0.00 0.00 0.00 1.82
3643 4067 9.187455 GGCAAGTGAATTTAATTTTAAAGTCGA 57.813 29.630 14.74 5.57 45.50 4.20
3829 4259 2.489722 TGAGTCACTGATCTCCGTTCTG 59.510 50.000 0.00 0.00 0.00 3.02
3843 4273 3.578716 TCCGTTCTGGAGAGAGAAAACAT 59.421 43.478 0.00 0.00 43.74 2.71
3901 4331 4.696877 TGCTACATCATGGACACAGAAAAG 59.303 41.667 0.00 0.00 0.00 2.27
3904 4334 1.909700 TCATGGACACAGAAAAGGGC 58.090 50.000 0.00 0.00 0.00 5.19
3905 4335 1.425066 TCATGGACACAGAAAAGGGCT 59.575 47.619 0.00 0.00 0.00 5.19
3967 4398 6.187682 GGAGAGAGATCTTTAGATAGGGAGG 58.812 48.000 0.00 0.00 34.37 4.30
4026 4457 1.001760 GAGAGTAGTGCCCAGGGGA 59.998 63.158 7.91 0.00 37.50 4.81
4027 4458 1.002274 AGAGTAGTGCCCAGGGGAG 59.998 63.158 7.91 0.00 37.50 4.30
4028 4459 1.001760 GAGTAGTGCCCAGGGGAGA 59.998 63.158 7.91 0.00 37.50 3.71
4029 4460 1.002274 AGTAGTGCCCAGGGGAGAG 59.998 63.158 7.91 0.00 37.50 3.20
4030 4461 2.365635 TAGTGCCCAGGGGAGAGC 60.366 66.667 7.91 0.00 37.50 4.09
4097 4529 2.096565 CGAGACATGCACAAGTCAACAG 60.097 50.000 15.53 3.32 37.23 3.16
4099 4531 3.136763 AGACATGCACAAGTCAACAGAG 58.863 45.455 15.53 0.00 37.23 3.35
4110 4542 2.281761 AACAGAGGGCGGCAACTG 60.282 61.111 24.62 24.62 36.58 3.16
4115 4547 4.101448 AGGGCGGCAACTGGCTAG 62.101 66.667 12.47 0.00 44.01 3.42
4117 4549 4.785453 GGCGGCAACTGGCTAGCT 62.785 66.667 15.72 0.00 42.65 3.32
4118 4550 3.198489 GCGGCAACTGGCTAGCTC 61.198 66.667 15.72 5.44 44.01 4.09
4119 4551 2.581354 CGGCAACTGGCTAGCTCT 59.419 61.111 15.72 0.00 44.01 4.09
4120 4552 1.816537 CGGCAACTGGCTAGCTCTA 59.183 57.895 15.72 0.60 44.01 2.43
4121 4553 0.528684 CGGCAACTGGCTAGCTCTAC 60.529 60.000 15.72 0.00 44.01 2.59
4124 4556 2.630580 GGCAACTGGCTAGCTCTACTAT 59.369 50.000 15.72 0.00 44.01 2.12
4129 4561 5.055265 ACTGGCTAGCTCTACTATCTGAA 57.945 43.478 15.72 0.00 0.00 3.02
4140 4572 6.568653 GCTCTACTATCTGAATCATGCACGTA 60.569 42.308 0.00 0.00 0.00 3.57
4202 4634 2.092968 GGAGGCATCATATCGGGCATTA 60.093 50.000 0.00 0.00 0.00 1.90
4209 4642 5.237344 GCATCATATCGGGCATTATTCTACC 59.763 44.000 0.00 0.00 0.00 3.18
4271 4704 4.376146 CCCCAGTGTTTATTTTTGTGTGG 58.624 43.478 0.00 0.00 0.00 4.17
4272 4705 4.141824 CCCCAGTGTTTATTTTTGTGTGGT 60.142 41.667 0.00 0.00 0.00 4.16
4276 4709 5.229052 CAGTGTTTATTTTTGTGTGGTCGTG 59.771 40.000 0.00 0.00 0.00 4.35
4277 4710 4.501198 GTGTTTATTTTTGTGTGGTCGTGG 59.499 41.667 0.00 0.00 0.00 4.94
4278 4711 3.357166 TTATTTTTGTGTGGTCGTGGC 57.643 42.857 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.771577 GCCTAGAGCAATTAGGGCTAA 57.228 47.619 9.40 0.00 42.78 3.09
20 21 4.707448 AGGATATCCACTGGCGTAGATAAG 59.293 45.833 23.81 0.00 38.89 1.73
29 30 1.133668 AGGCAAAGGATATCCACTGGC 60.134 52.381 28.42 28.42 42.13 4.85
33 34 3.879892 GACAAGAGGCAAAGGATATCCAC 59.120 47.826 23.81 9.67 38.89 4.02
37 38 2.505819 ACCGACAAGAGGCAAAGGATAT 59.494 45.455 0.00 0.00 0.00 1.63
38 39 1.906574 ACCGACAAGAGGCAAAGGATA 59.093 47.619 0.00 0.00 0.00 2.59
44 45 2.281484 GGCACCGACAAGAGGCAA 60.281 61.111 0.00 0.00 0.00 4.52
55 56 1.299541 GTGGATCAACTATGGCACCG 58.700 55.000 0.00 0.00 0.00 4.94
58 59 1.138859 CGAGGTGGATCAACTATGGCA 59.861 52.381 0.00 0.00 28.17 4.92
63 64 2.422479 CGAAGACGAGGTGGATCAACTA 59.578 50.000 0.00 0.00 42.66 2.24
64 65 1.202582 CGAAGACGAGGTGGATCAACT 59.797 52.381 0.00 0.00 42.66 3.16
67 68 0.611062 ACCGAAGACGAGGTGGATCA 60.611 55.000 0.00 0.00 42.66 2.92
69 70 1.955080 GATACCGAAGACGAGGTGGAT 59.045 52.381 0.00 0.00 41.51 3.41
78 79 5.298347 CATTTCCCTAAGGATACCGAAGAC 58.702 45.833 0.00 0.00 43.54 3.01
87 88 3.073062 CCGTGATCCATTTCCCTAAGGAT 59.927 47.826 0.00 0.00 43.54 3.24
88 89 2.438021 CCGTGATCCATTTCCCTAAGGA 59.562 50.000 0.00 0.00 41.88 3.36
90 91 3.560636 ACCGTGATCCATTTCCCTAAG 57.439 47.619 0.00 0.00 0.00 2.18
97 98 1.633432 TCCTCCAACCGTGATCCATTT 59.367 47.619 0.00 0.00 0.00 2.32
103 104 0.898789 ACGAGTCCTCCAACCGTGAT 60.899 55.000 0.00 0.00 31.85 3.06
104 105 1.111116 AACGAGTCCTCCAACCGTGA 61.111 55.000 0.00 0.00 33.48 4.35
111 112 6.942976 AGAAACATATAAAACGAGTCCTCCA 58.057 36.000 0.00 0.00 0.00 3.86
112 113 7.254017 CGAAGAAACATATAAAACGAGTCCTCC 60.254 40.741 0.00 0.00 0.00 4.30
113 114 7.487189 TCGAAGAAACATATAAAACGAGTCCTC 59.513 37.037 0.00 0.00 0.00 3.71
117 118 8.928270 ATCTCGAAGAAACATATAAAACGAGT 57.072 30.769 0.00 0.00 42.96 4.18
127 128 5.874810 CCCTGACAAATCTCGAAGAAACATA 59.125 40.000 0.00 0.00 34.09 2.29
147 149 2.027561 TCCGAATAGGACACAAACCCTG 60.028 50.000 0.00 0.00 45.98 4.45
162 164 0.458025 GCCGTCTCGTCTTTCCGAAT 60.458 55.000 0.00 0.00 36.24 3.34
166 168 2.506438 CCGCCGTCTCGTCTTTCC 60.506 66.667 0.00 0.00 0.00 3.13
168 170 3.681835 AGCCGCCGTCTCGTCTTT 61.682 61.111 0.00 0.00 0.00 2.52
185 188 8.055181 AGAACCTTATTCAATATTCAGGAAGCA 58.945 33.333 1.21 0.00 0.00 3.91
196 199 9.988815 GCTAGATGAGAAGAACCTTATTCAATA 57.011 33.333 0.00 0.00 31.13 1.90
199 202 6.183361 GGGCTAGATGAGAAGAACCTTATTCA 60.183 42.308 0.00 0.00 31.13 2.57
212 215 1.120530 GAAACGGGGGCTAGATGAGA 58.879 55.000 0.00 0.00 0.00 3.27
214 217 0.830648 CAGAAACGGGGGCTAGATGA 59.169 55.000 0.00 0.00 0.00 2.92
216 220 0.541863 CACAGAAACGGGGGCTAGAT 59.458 55.000 0.00 0.00 0.00 1.98
245 249 4.735132 CGTGCCCACCGACGATGT 62.735 66.667 0.00 0.00 37.81 3.06
278 282 5.909621 AACCCATCAAAGACAGATTCATG 57.090 39.130 0.00 0.00 0.00 3.07
282 286 4.154942 AGCAAACCCATCAAAGACAGATT 58.845 39.130 0.00 0.00 0.00 2.40
294 319 0.107017 CCAGATCCGAGCAAACCCAT 60.107 55.000 0.00 0.00 0.00 4.00
329 354 3.092301 TCCGATCTGAAGACACATGAGT 58.908 45.455 0.00 0.00 0.00 3.41
330 355 3.790152 TCCGATCTGAAGACACATGAG 57.210 47.619 0.00 0.00 0.00 2.90
385 410 1.476074 CAGCGCAACGAAACAACAAT 58.524 45.000 11.47 0.00 0.00 2.71
394 419 0.245266 TCATAGAACCAGCGCAACGA 59.755 50.000 11.47 0.00 0.00 3.85
395 420 0.647410 CTCATAGAACCAGCGCAACG 59.353 55.000 11.47 0.00 0.00 4.10
400 426 2.969628 AAGACCTCATAGAACCAGCG 57.030 50.000 0.00 0.00 0.00 5.18
438 464 8.946085 CCTGACAAAACTTGCTATAATAGACAA 58.054 33.333 0.00 0.00 0.00 3.18
445 471 5.412594 CAGAGCCTGACAAAACTTGCTATAA 59.587 40.000 0.00 0.00 32.44 0.98
472 498 1.813859 CTGTCATCGCCCGTCCTTA 59.186 57.895 0.00 0.00 0.00 2.69
474 500 4.148825 GCTGTCATCGCCCGTCCT 62.149 66.667 0.00 0.00 0.00 3.85
503 529 1.268625 CTGCAAGCACTGAAATGAGCA 59.731 47.619 0.00 0.00 0.00 4.26
509 535 1.063912 CAACGACTGCAAGCACTGAAA 59.936 47.619 0.00 0.00 37.60 2.69
577 605 8.948631 ATCTTCAATCGTAGATGTACAACAAT 57.051 30.769 0.00 0.00 45.12 2.71
579 607 9.863845 TTAATCTTCAATCGTAGATGTACAACA 57.136 29.630 0.00 0.00 45.12 3.33
631 659 2.037251 AGTACGTGGTTCATGAGTGCTT 59.963 45.455 0.00 0.00 0.00 3.91
632 660 1.618837 AGTACGTGGTTCATGAGTGCT 59.381 47.619 0.00 0.00 0.00 4.40
636 664 3.503827 TGCTAGTACGTGGTTCATGAG 57.496 47.619 0.00 0.00 0.00 2.90
665 693 7.670605 ACATCCATGAATCATGATTCCTTTT 57.329 32.000 34.65 19.75 43.81 2.27
666 694 7.670605 AACATCCATGAATCATGATTCCTTT 57.329 32.000 34.65 21.74 43.81 3.11
717 745 1.410882 AGAGAAGAGCGGCCAGTATTC 59.589 52.381 2.24 1.62 0.00 1.75
723 751 0.256177 TAGAGAGAGAAGAGCGGCCA 59.744 55.000 2.24 0.00 0.00 5.36
884 912 0.556380 AGGAGGAAGAGGAGAGGGGA 60.556 60.000 0.00 0.00 0.00 4.81
886 914 0.633921 TGAGGAGGAAGAGGAGAGGG 59.366 60.000 0.00 0.00 0.00 4.30
887 915 1.687996 GGTGAGGAGGAAGAGGAGAGG 60.688 61.905 0.00 0.00 0.00 3.69
888 916 1.287739 AGGTGAGGAGGAAGAGGAGAG 59.712 57.143 0.00 0.00 0.00 3.20
889 917 1.286553 GAGGTGAGGAGGAAGAGGAGA 59.713 57.143 0.00 0.00 0.00 3.71
927 955 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
928 956 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
929 957 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
930 958 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
931 959 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
932 960 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
933 961 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
934 962 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
935 963 6.068010 AGTAGAGAGAGAGAGAGAGAGAGAG 58.932 48.000 0.00 0.00 0.00 3.20
936 964 6.019656 AGTAGAGAGAGAGAGAGAGAGAGA 57.980 45.833 0.00 0.00 0.00 3.10
937 965 6.723298 AAGTAGAGAGAGAGAGAGAGAGAG 57.277 45.833 0.00 0.00 0.00 3.20
938 966 6.630413 GCAAAGTAGAGAGAGAGAGAGAGAGA 60.630 46.154 0.00 0.00 0.00 3.10
939 967 5.525378 GCAAAGTAGAGAGAGAGAGAGAGAG 59.475 48.000 0.00 0.00 0.00 3.20
940 968 5.045942 TGCAAAGTAGAGAGAGAGAGAGAGA 60.046 44.000 0.00 0.00 0.00 3.10
941 969 5.185454 TGCAAAGTAGAGAGAGAGAGAGAG 58.815 45.833 0.00 0.00 0.00 3.20
942 970 5.172687 TGCAAAGTAGAGAGAGAGAGAGA 57.827 43.478 0.00 0.00 0.00 3.10
943 971 5.393027 GGTTGCAAAGTAGAGAGAGAGAGAG 60.393 48.000 0.00 0.00 0.00 3.20
1073 1101 2.653234 AGGCTGATAAATGGGCAGAG 57.347 50.000 0.00 0.00 0.00 3.35
1082 1110 5.761234 AGTTCGTGTGTTAAAGGCTGATAAA 59.239 36.000 0.00 0.00 0.00 1.40
1086 1114 3.128349 GAGTTCGTGTGTTAAAGGCTGA 58.872 45.455 0.00 0.00 0.00 4.26
1109 1137 0.635009 TCTTCCAGGGACCGGTAGAT 59.365 55.000 7.34 0.00 0.00 1.98
1157 1185 5.285845 CGAGATGCTCATTGTTAGATCGATC 59.714 44.000 17.91 17.91 0.00 3.69
1357 1385 1.907739 CCATGGCGGGAGAAGAAGA 59.092 57.895 0.00 0.00 0.00 2.87
1449 1477 1.134946 AGTTTGCCACTTTGCACTGTC 59.865 47.619 0.00 0.00 41.88 3.51
1537 1565 1.470632 CGTGTGCACAAAACAACCCAT 60.471 47.619 23.59 0.00 0.00 4.00
1555 1583 5.038744 TTGATTTGTTCATCACGGGTACGT 61.039 41.667 0.00 0.00 44.14 3.57
1556 1584 3.433957 TTGATTTGTTCATCACGGGTACG 59.566 43.478 0.00 0.00 39.21 3.67
1798 1832 2.744709 GCGCGGCCCTTGTAGAAA 60.745 61.111 8.83 0.00 0.00 2.52
1917 1951 2.852449 TCCCCAATTGAGCTAGGTGATT 59.148 45.455 7.12 0.00 0.00 2.57
1952 1986 1.660104 GCAGCAAACAATTAATGGCGG 59.340 47.619 0.00 0.00 0.00 6.13
1954 1988 1.660104 CGGCAGCAAACAATTAATGGC 59.340 47.619 0.00 0.00 0.00 4.40
2026 2060 0.764890 TGGTGTCAAGGTGCTAAGCT 59.235 50.000 0.00 0.00 34.99 3.74
2027 2061 1.740025 GATGGTGTCAAGGTGCTAAGC 59.260 52.381 0.00 0.00 0.00 3.09
2028 2062 2.290260 TGGATGGTGTCAAGGTGCTAAG 60.290 50.000 0.00 0.00 0.00 2.18
2029 2063 1.702401 TGGATGGTGTCAAGGTGCTAA 59.298 47.619 0.00 0.00 0.00 3.09
2030 2064 1.278985 CTGGATGGTGTCAAGGTGCTA 59.721 52.381 0.00 0.00 0.00 3.49
2031 2065 0.037303 CTGGATGGTGTCAAGGTGCT 59.963 55.000 0.00 0.00 0.00 4.40
2032 2066 1.589716 GCTGGATGGTGTCAAGGTGC 61.590 60.000 0.00 0.00 0.00 5.01
2033 2067 0.962356 GGCTGGATGGTGTCAAGGTG 60.962 60.000 0.00 0.00 0.00 4.00
2034 2068 1.136329 AGGCTGGATGGTGTCAAGGT 61.136 55.000 0.00 0.00 0.00 3.50
2035 2069 0.038744 AAGGCTGGATGGTGTCAAGG 59.961 55.000 0.00 0.00 0.00 3.61
2036 2070 1.815003 GAAAGGCTGGATGGTGTCAAG 59.185 52.381 0.00 0.00 0.00 3.02
2037 2071 1.547675 GGAAAGGCTGGATGGTGTCAA 60.548 52.381 0.00 0.00 0.00 3.18
2038 2072 0.038166 GGAAAGGCTGGATGGTGTCA 59.962 55.000 0.00 0.00 0.00 3.58
2039 2073 0.329596 AGGAAAGGCTGGATGGTGTC 59.670 55.000 0.00 0.00 0.00 3.67
2040 2074 0.779997 AAGGAAAGGCTGGATGGTGT 59.220 50.000 0.00 0.00 0.00 4.16
2041 2075 1.467920 GAAGGAAAGGCTGGATGGTG 58.532 55.000 0.00 0.00 0.00 4.17
2042 2076 0.332972 GGAAGGAAAGGCTGGATGGT 59.667 55.000 0.00 0.00 0.00 3.55
2043 2077 0.396278 GGGAAGGAAAGGCTGGATGG 60.396 60.000 0.00 0.00 0.00 3.51
2044 2078 0.396278 GGGGAAGGAAAGGCTGGATG 60.396 60.000 0.00 0.00 0.00 3.51
2045 2079 1.584717 GGGGGAAGGAAAGGCTGGAT 61.585 60.000 0.00 0.00 0.00 3.41
2046 2080 2.238701 GGGGGAAGGAAAGGCTGGA 61.239 63.158 0.00 0.00 0.00 3.86
2047 2081 2.360585 GGGGGAAGGAAAGGCTGG 59.639 66.667 0.00 0.00 0.00 4.85
2061 2095 0.486879 AGGCATAGAGAGAGAGGGGG 59.513 60.000 0.00 0.00 0.00 5.40
2062 2096 2.378547 ACTAGGCATAGAGAGAGAGGGG 59.621 54.545 13.23 0.00 32.93 4.79
2063 2097 3.330701 AGACTAGGCATAGAGAGAGAGGG 59.669 52.174 13.23 0.00 32.93 4.30
2064 2098 4.287067 AGAGACTAGGCATAGAGAGAGAGG 59.713 50.000 13.23 0.00 32.93 3.69
2065 2099 5.012046 TGAGAGACTAGGCATAGAGAGAGAG 59.988 48.000 13.23 0.00 32.93 3.20
2066 2100 4.904853 TGAGAGACTAGGCATAGAGAGAGA 59.095 45.833 13.23 0.00 32.93 3.10
2067 2101 4.997395 GTGAGAGACTAGGCATAGAGAGAG 59.003 50.000 13.23 0.00 32.93 3.20
2068 2102 4.658435 AGTGAGAGACTAGGCATAGAGAGA 59.342 45.833 13.23 0.00 30.86 3.10
2069 2103 4.756642 CAGTGAGAGACTAGGCATAGAGAG 59.243 50.000 13.23 0.00 31.73 3.20
2070 2104 4.713553 CAGTGAGAGACTAGGCATAGAGA 58.286 47.826 13.23 0.00 31.73 3.10
2071 2105 3.253188 GCAGTGAGAGACTAGGCATAGAG 59.747 52.174 13.23 0.00 31.73 2.43
2072 2106 3.218453 GCAGTGAGAGACTAGGCATAGA 58.782 50.000 13.23 0.00 31.73 1.98
2073 2107 2.954989 TGCAGTGAGAGACTAGGCATAG 59.045 50.000 3.34 3.34 30.59 2.23
2074 2108 2.690497 GTGCAGTGAGAGACTAGGCATA 59.310 50.000 0.00 0.00 36.34 3.14
2075 2109 1.480137 GTGCAGTGAGAGACTAGGCAT 59.520 52.381 0.00 0.00 36.34 4.40
2076 2110 0.891373 GTGCAGTGAGAGACTAGGCA 59.109 55.000 0.00 0.00 32.57 4.75
2077 2111 1.181786 AGTGCAGTGAGAGACTAGGC 58.818 55.000 0.00 0.00 31.73 3.93
2078 2112 4.642437 TCATTAGTGCAGTGAGAGACTAGG 59.358 45.833 3.69 0.00 31.73 3.02
2079 2113 5.826601 TCATTAGTGCAGTGAGAGACTAG 57.173 43.478 3.69 0.00 31.73 2.57
2080 2114 6.782082 AATCATTAGTGCAGTGAGAGACTA 57.218 37.500 3.69 0.00 31.73 2.59
2081 2115 5.674052 AATCATTAGTGCAGTGAGAGACT 57.326 39.130 3.69 0.00 34.02 3.24
2082 2116 7.547370 AGTTTAATCATTAGTGCAGTGAGAGAC 59.453 37.037 3.69 0.00 0.00 3.36
2083 2117 7.615403 AGTTTAATCATTAGTGCAGTGAGAGA 58.385 34.615 3.69 0.00 0.00 3.10
2084 2118 7.840342 AGTTTAATCATTAGTGCAGTGAGAG 57.160 36.000 3.69 0.00 0.00 3.20
2085 2119 8.621532 AAAGTTTAATCATTAGTGCAGTGAGA 57.378 30.769 3.69 0.00 0.00 3.27
2086 2120 9.683069 AAAAAGTTTAATCATTAGTGCAGTGAG 57.317 29.630 3.69 0.00 0.00 3.51
2087 2121 9.677567 GAAAAAGTTTAATCATTAGTGCAGTGA 57.322 29.630 3.69 0.00 0.00 3.41
2088 2122 8.915654 GGAAAAAGTTTAATCATTAGTGCAGTG 58.084 33.333 3.69 0.00 0.00 3.66
2089 2123 8.637986 TGGAAAAAGTTTAATCATTAGTGCAGT 58.362 29.630 0.00 0.00 0.00 4.40
2090 2124 9.643693 ATGGAAAAAGTTTAATCATTAGTGCAG 57.356 29.630 0.00 0.00 0.00 4.41
2091 2125 9.421806 CATGGAAAAAGTTTAATCATTAGTGCA 57.578 29.630 0.00 0.00 0.00 4.57
2092 2126 9.423061 ACATGGAAAAAGTTTAATCATTAGTGC 57.577 29.630 0.00 0.00 0.00 4.40
2094 2128 9.423061 GCACATGGAAAAAGTTTAATCATTAGT 57.577 29.630 0.00 0.00 0.00 2.24
2095 2129 9.643693 AGCACATGGAAAAAGTTTAATCATTAG 57.356 29.630 0.00 0.00 0.00 1.73
2096 2130 9.995003 AAGCACATGGAAAAAGTTTAATCATTA 57.005 25.926 0.00 0.00 0.00 1.90
2097 2131 8.907222 AAGCACATGGAAAAAGTTTAATCATT 57.093 26.923 0.00 0.00 0.00 2.57
2098 2132 8.149647 TGAAGCACATGGAAAAAGTTTAATCAT 58.850 29.630 0.00 0.00 0.00 2.45
2099 2133 7.495901 TGAAGCACATGGAAAAAGTTTAATCA 58.504 30.769 0.00 0.00 0.00 2.57
2100 2134 7.945033 TGAAGCACATGGAAAAAGTTTAATC 57.055 32.000 0.00 0.00 0.00 1.75
2324 2735 1.228063 CCTTGCCCCCATCATCTCG 60.228 63.158 0.00 0.00 0.00 4.04
2383 2794 1.356124 AGTGCAGGATCTGGTCAAGT 58.644 50.000 0.00 0.00 31.21 3.16
2410 2821 3.921767 CTCCTGCTTGCACGAGCGA 62.922 63.158 5.94 0.00 45.64 4.93
2500 2911 1.523154 GCTTCATGAAACCGTGGCCA 61.523 55.000 9.88 0.00 0.00 5.36
2585 2996 2.000447 GACATTTCCGTCTCCTTTCGG 59.000 52.381 0.00 0.00 46.93 4.30
2589 3000 1.404315 GCTCGACATTTCCGTCTCCTT 60.404 52.381 0.00 0.00 33.54 3.36
2590 3001 0.173708 GCTCGACATTTCCGTCTCCT 59.826 55.000 0.00 0.00 33.54 3.69
2596 3007 2.849966 CTCGCGCTCGACATTTCCG 61.850 63.158 5.56 0.00 40.21 4.30
2653 3064 3.770040 CAGTCCGTGATCCCGCCA 61.770 66.667 0.00 0.00 0.00 5.69
2674 3085 1.792118 CGACGAGCCGGTCCATCATA 61.792 60.000 1.90 0.00 33.30 2.15
2689 3100 3.642778 ATTGAGGTGGGACGCGACG 62.643 63.158 15.93 0.00 41.51 5.12
2830 3241 3.855853 GCCCCTCCGAGAAGCCTC 61.856 72.222 0.00 0.00 36.08 4.70
3039 3458 8.722394 CGCTCTCCTTTATTATTATTTTCTCCC 58.278 37.037 0.00 0.00 0.00 4.30
3126 3545 7.217200 GCTTTAATCCCCTTTTCTTTCACTTT 58.783 34.615 0.00 0.00 0.00 2.66
3184 3603 2.128035 CAATAAGAGACGGGTGCGATC 58.872 52.381 0.00 0.00 0.00 3.69
3286 3709 7.532546 CACACCACAACAAACTATGTAATTACG 59.467 37.037 10.92 0.00 42.99 3.18
3296 3719 2.437413 TGCACACACCACAACAAACTA 58.563 42.857 0.00 0.00 0.00 2.24
3351 3774 6.638468 GGCAACAATTTGAAGAGAAGTTACTG 59.362 38.462 2.79 0.00 34.24 2.74
3385 3808 2.601905 AGTTTGGCCATCTTTCAGCTT 58.398 42.857 6.09 0.00 0.00 3.74
3386 3809 2.299326 AGTTTGGCCATCTTTCAGCT 57.701 45.000 6.09 0.00 0.00 4.24
3387 3810 3.006217 AGAAAGTTTGGCCATCTTTCAGC 59.994 43.478 36.94 24.77 45.15 4.26
3389 3812 4.214310 TGAGAAAGTTTGGCCATCTTTCA 58.786 39.130 36.94 27.14 45.15 2.69
3390 3813 4.853924 TGAGAAAGTTTGGCCATCTTTC 57.146 40.909 33.34 33.34 43.93 2.62
3391 3814 6.248433 TCTATGAGAAAGTTTGGCCATCTTT 58.752 36.000 26.07 26.07 34.68 2.52
3392 3815 5.819991 TCTATGAGAAAGTTTGGCCATCTT 58.180 37.500 6.09 12.18 0.00 2.40
3416 3839 3.614568 AGTCTCCACCCCGATTACTAT 57.385 47.619 0.00 0.00 0.00 2.12
3424 3847 1.041447 AATCGGTAGTCTCCACCCCG 61.041 60.000 0.00 0.00 38.38 5.73
3438 3861 5.743872 GGCAAAAAGTATGAAGCTAAATCGG 59.256 40.000 0.00 0.00 0.00 4.18
3453 3876 9.389755 AGTTAAACAAATTGTATGGCAAAAAGT 57.610 25.926 0.00 0.00 40.91 2.66
3561 3985 3.157252 TCCAGCATCTCTCGCCCC 61.157 66.667 0.00 0.00 0.00 5.80
3562 3986 2.107953 GTCCAGCATCTCTCGCCC 59.892 66.667 0.00 0.00 0.00 6.13
3649 4073 3.181477 CCATCCATCGATCTATGCCTCTC 60.181 52.174 9.92 0.00 0.00 3.20
3653 4082 3.726607 GATCCATCCATCGATCTATGCC 58.273 50.000 9.92 0.94 33.53 4.40
3829 4259 4.516698 TGTTGCTTGATGTTTTCTCTCTCC 59.483 41.667 0.00 0.00 0.00 3.71
3843 4273 3.888323 TGTCCAGCTTTTATGTTGCTTGA 59.112 39.130 0.00 0.00 34.51 3.02
3901 4331 3.078837 CTCTCTAGATCGACCTTAGCCC 58.921 54.545 0.00 0.00 0.00 5.19
3904 4334 7.214381 TCTTTCTCTCTCTAGATCGACCTTAG 58.786 42.308 0.00 0.00 0.00 2.18
3905 4335 7.127012 TCTTTCTCTCTCTAGATCGACCTTA 57.873 40.000 0.00 0.00 0.00 2.69
3937 4368 5.985175 TCTAAAGATCTCTCTCCCTCTCA 57.015 43.478 0.00 0.00 0.00 3.27
3967 4398 2.730094 CACTTGCCAGTTGCCACC 59.270 61.111 0.00 0.00 40.16 4.61
4026 4457 0.249784 CATATCGCACTGGCTGCTCT 60.250 55.000 0.00 0.00 44.64 4.09
4027 4458 0.249615 TCATATCGCACTGGCTGCTC 60.250 55.000 0.00 0.00 44.64 4.26
4028 4459 0.395686 ATCATATCGCACTGGCTGCT 59.604 50.000 0.00 0.00 44.64 4.24
4029 4460 1.728971 GTATCATATCGCACTGGCTGC 59.271 52.381 0.00 0.00 43.21 5.25
4030 4461 1.988467 CGTATCATATCGCACTGGCTG 59.012 52.381 0.00 0.00 38.10 4.85
4097 4529 4.096003 TAGCCAGTTGCCGCCCTC 62.096 66.667 0.00 0.00 42.71 4.30
4110 4542 6.563422 CATGATTCAGATAGTAGAGCTAGCC 58.437 44.000 12.13 2.81 36.79 3.93
4115 4547 4.620609 CGTGCATGATTCAGATAGTAGAGC 59.379 45.833 0.00 0.00 0.00 4.09
4116 4548 5.767269 ACGTGCATGATTCAGATAGTAGAG 58.233 41.667 14.17 0.00 0.00 2.43
4117 4549 5.774498 ACGTGCATGATTCAGATAGTAGA 57.226 39.130 14.17 0.00 0.00 2.59
4118 4550 6.799441 GTCTACGTGCATGATTCAGATAGTAG 59.201 42.308 14.17 0.00 0.00 2.57
4119 4551 6.565999 CGTCTACGTGCATGATTCAGATAGTA 60.566 42.308 14.17 0.00 34.11 1.82
4120 4552 5.524284 GTCTACGTGCATGATTCAGATAGT 58.476 41.667 14.17 0.00 0.00 2.12
4121 4553 4.614702 CGTCTACGTGCATGATTCAGATAG 59.385 45.833 14.17 2.03 34.11 2.08
4124 4556 2.797491 CGTCTACGTGCATGATTCAGA 58.203 47.619 14.17 6.56 34.11 3.27
4154 4586 0.036164 AAGTTGCATGGCCAGTACGA 59.964 50.000 13.05 0.00 0.00 3.43
4184 4616 4.202441 AGAATAATGCCCGATATGATGCC 58.798 43.478 0.00 0.00 0.00 4.40
4202 4634 2.762459 TCGGCGGGCAGGTAGAAT 60.762 61.111 7.21 0.00 0.00 2.40
4244 4677 6.014925 ACACAAAAATAAACACTGGGGGTATC 60.015 38.462 0.00 0.00 0.00 2.24
4253 4686 5.336744 CACGACCACACAAAAATAAACACT 58.663 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.