Multiple sequence alignment - TraesCS3A01G272200

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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 TraesCS3A01G272200 chr3A 100.000 4200 0 0 1 4200 501652784 501648585 0.000000e+00 7757.0
1 TraesCS3A01G272200 chr3A 93.697 238 14 1 3356 3592 501569073 501568836 5.160000e-94 355.0
2 TraesCS3A01G272200 chr3A 100.000 62 0 0 3971 4032 501648751 501648690 9.540000e-22 115.0
3 TraesCS3A01G272200 chr3A 100.000 62 0 0 4034 4095 501648814 501648753 9.540000e-22 115.0
4 TraesCS3A01G272200 chr3D 95.407 1154 37 10 1025 2176 376920914 376919775 0.000000e+00 1823.0
5 TraesCS3A01G272200 chr3D 96.051 1013 21 6 2258 3253 376919776 376918766 0.000000e+00 1631.0
6 TraesCS3A01G272200 chr3D 88.043 1012 69 22 1 988 376922200 376921217 0.000000e+00 1151.0
7 TraesCS3A01G272200 chr3B 92.836 1005 27 8 2261 3253 491520150 491519179 0.000000e+00 1415.0
8 TraesCS3A01G272200 chr3B 94.609 575 22 7 895 1463 491521390 491520819 0.000000e+00 881.0
9 TraesCS3A01G272200 chr3B 93.493 584 14 7 1595 2177 491520711 491520151 0.000000e+00 846.0
10 TraesCS3A01G272200 chr3B 86.226 530 46 15 305 814 491524757 491524235 2.210000e-152 549.0
11 TraesCS3A01G272200 chr3B 88.636 308 25 5 3 309 491533175 491532877 2.390000e-97 366.0
12 TraesCS3A01G272200 chr3B 96.552 87 3 0 2175 2261 492204386 492204472 1.220000e-30 145.0
13 TraesCS3A01G272200 chr3B 91.753 97 6 1 2166 2262 822221180 822221086 2.630000e-27 134.0
14 TraesCS3A01G272200 chr3B 91.753 97 6 1 2166 2262 822311536 822311442 2.630000e-27 134.0
15 TraesCS3A01G272200 chr4B 93.990 782 43 3 3255 4032 88865151 88864370 0.000000e+00 1181.0
16 TraesCS3A01G272200 chr4B 94.493 345 15 3 3252 3592 88851541 88851197 2.880000e-146 529.0
17 TraesCS3A01G272200 chr4B 94.611 167 9 0 4034 4200 88864431 88864265 4.170000e-65 259.0
18 TraesCS3A01G272200 chr4B 95.506 89 4 0 2175 2263 130615560 130615648 4.380000e-30 143.0
19 TraesCS3A01G272200 chr7A 88.761 783 82 5 3255 4032 647338054 647337273 0.000000e+00 953.0
20 TraesCS3A01G272200 chr7A 88.761 347 31 7 3252 3592 647316132 647315788 6.490000e-113 418.0
21 TraesCS3A01G272200 chr7A 91.346 104 8 1 2170 2273 129877027 129876925 1.570000e-29 141.0
22 TraesCS3A01G272200 chr7A 91.753 97 8 0 2174 2270 129876938 129877034 7.320000e-28 135.0
23 TraesCS3A01G272200 chr7A 93.103 87 6 0 2174 2260 155147899 155147985 1.230000e-25 128.0
24 TraesCS3A01G272200 chr7A 79.518 83 15 2 3941 4022 30385008 30385089 1.630000e-04 58.4
25 TraesCS3A01G272200 chr7A 92.105 38 3 0 4048 4085 30385052 30385089 2.000000e-03 54.7
26 TraesCS3A01G272200 chr6D 95.455 88 4 0 2178 2265 185090791 185090704 1.570000e-29 141.0
27 TraesCS3A01G272200 chr5D 89.623 106 10 1 2170 2275 354874356 354874460 2.630000e-27 134.0
28 TraesCS3A01G272200 chr5B 81.818 77 12 2 3947 4022 639529632 639529707 3.510000e-06 63.9
29 TraesCS3A01G272200 chr5B 87.500 48 5 1 4039 4085 639529660 639529707 2.000000e-03 54.7


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 TraesCS3A01G272200 chr3A 501648585 501652784 4199 True 7757.00 7757 100.0000 1 4200 1 chr3A.!!$R2 4199
1 TraesCS3A01G272200 chr3D 376918766 376922200 3434 True 1535.00 1823 93.1670 1 3253 3 chr3D.!!$R1 3252
2 TraesCS3A01G272200 chr3B 491519179 491524757 5578 True 922.75 1415 91.7910 305 3253 4 chr3B.!!$R4 2948
3 TraesCS3A01G272200 chr4B 88864265 88865151 886 True 720.00 1181 94.3005 3255 4200 2 chr4B.!!$R2 945
4 TraesCS3A01G272200 chr7A 647337273 647338054 781 True 953.00 953 88.7610 3255 4032 1 chr7A.!!$R3 777

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
703 725 0.037605 AACAAACTAGACCCCGAGCG 60.038 55.0 0.0 0.0 0.0 5.03 F
2189 5306 0.043637 AACCTATTCCCTCCGTCCCA 59.956 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 5360 0.635009 AATCTACTCCCTCCGTCCCA 59.365 55.0 0.0 0.0 0.0 4.37 R
4090 7232 0.038166 GAATTCACAGTGGGGGAGCA 59.962 55.0 0.0 0.0 0.0 4.26 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
128 129 6.594788 AATTGCATCATGTCCTTTGTAGTT 57.405 33.333 0.00 0.00 0.00 2.24
129 130 5.375417 TTGCATCATGTCCTTTGTAGTTG 57.625 39.130 0.00 0.00 0.00 3.16
131 132 4.455533 TGCATCATGTCCTTTGTAGTTGTC 59.544 41.667 0.00 0.00 0.00 3.18
134 135 4.304110 TCATGTCCTTTGTAGTTGTCGAC 58.696 43.478 9.11 9.11 0.00 4.20
142 143 6.015688 TCCTTTGTAGTTGTCGACTCTACATT 60.016 38.462 32.52 14.31 41.94 2.71
144 145 6.570672 TTGTAGTTGTCGACTCTACATTCT 57.429 37.500 32.52 17.45 41.94 2.40
146 147 6.609533 TGTAGTTGTCGACTCTACATTCTTC 58.390 40.000 30.59 16.10 38.98 2.87
168 169 7.337942 TCTTCTCTTGCATCTTAATTTTCCTCC 59.662 37.037 0.00 0.00 0.00 4.30
169 170 5.888161 TCTCTTGCATCTTAATTTTCCTCCC 59.112 40.000 0.00 0.00 0.00 4.30
170 171 5.831103 TCTTGCATCTTAATTTTCCTCCCT 58.169 37.500 0.00 0.00 0.00 4.20
171 172 6.256053 TCTTGCATCTTAATTTTCCTCCCTT 58.744 36.000 0.00 0.00 0.00 3.95
172 173 5.920193 TGCATCTTAATTTTCCTCCCTTG 57.080 39.130 0.00 0.00 0.00 3.61
173 174 5.579047 TGCATCTTAATTTTCCTCCCTTGA 58.421 37.500 0.00 0.00 0.00 3.02
184 185 6.485830 TTTCCTCCCTTGATACATCTAGTG 57.514 41.667 0.00 0.00 0.00 2.74
192 193 6.108687 CCTTGATACATCTAGTGCAGAAACA 58.891 40.000 0.00 0.00 36.67 2.83
193 194 6.765036 CCTTGATACATCTAGTGCAGAAACAT 59.235 38.462 0.00 0.00 36.67 2.71
209 210 6.376978 CAGAAACATCAGAAGACCAAACATC 58.623 40.000 0.00 0.00 0.00 3.06
218 219 2.233271 AGACCAAACATCCACAAGCTG 58.767 47.619 0.00 0.00 0.00 4.24
224 225 4.278170 CCAAACATCCACAAGCTGAACTAA 59.722 41.667 0.00 0.00 0.00 2.24
274 275 9.813446 CCTAATAACACGTAAGAACCTAAGATT 57.187 33.333 0.00 0.00 43.62 2.40
285 286 1.463444 ACCTAAGATTGTTGAACGCGC 59.537 47.619 5.73 0.00 0.00 6.86
287 288 0.800012 TAAGATTGTTGAACGCGCCC 59.200 50.000 5.73 0.00 0.00 6.13
290 291 0.318275 GATTGTTGAACGCGCCCAAA 60.318 50.000 5.73 0.00 0.00 3.28
297 298 0.524414 GAACGCGCCCAAATAACCTT 59.476 50.000 5.73 0.00 0.00 3.50
324 325 4.222145 AGGTTTAAAGAGTCGTATGAGCCA 59.778 41.667 0.00 0.00 0.00 4.75
359 361 5.122396 GCACAGTAGAACCTAAGATTGTTGG 59.878 44.000 0.00 0.00 0.00 3.77
389 392 0.251165 GCTGAAGGCAACACCCCTTA 60.251 55.000 0.00 0.00 42.56 2.69
402 405 2.161609 CACCCCTTACGAGAAATGTTGC 59.838 50.000 0.00 0.00 0.00 4.17
426 429 6.360329 CCAAACTGATACTTTGTTGTCGTAC 58.640 40.000 0.00 0.00 0.00 3.67
468 471 6.148264 GGAAGCACAAAAGAAAGAATCTCTG 58.852 40.000 0.00 0.00 37.42 3.35
494 497 8.398665 GGTGATAAGAACATTCTTGACAATACC 58.601 37.037 15.62 11.15 46.34 2.73
495 498 8.946085 GTGATAAGAACATTCTTGACAATACCA 58.054 33.333 15.62 0.00 46.34 3.25
510 513 4.386951 CCACCATCACCGTCGCCA 62.387 66.667 0.00 0.00 0.00 5.69
591 594 0.634465 AAACACCACAACCCCTTCCT 59.366 50.000 0.00 0.00 0.00 3.36
593 596 0.991355 ACACCACAACCCCTTCCTCA 60.991 55.000 0.00 0.00 0.00 3.86
602 623 0.753262 CCCCTTCCTCATGTAGGTCG 59.247 60.000 9.98 4.36 46.62 4.79
625 646 0.318441 CGTGATGCGGATAGGACCAT 59.682 55.000 0.00 0.00 36.85 3.55
634 655 3.557898 GCGGATAGGACCATGAATGACAT 60.558 47.826 0.00 0.00 40.17 3.06
637 658 5.380043 GGATAGGACCATGAATGACATTGT 58.620 41.667 5.14 0.00 37.53 2.71
641 662 5.327732 AGGACCATGAATGACATTGTCTTT 58.672 37.500 17.26 16.33 45.26 2.52
665 686 2.160013 CGTCGAGACTTTGCCGTAAAAG 60.160 50.000 1.56 5.72 41.91 2.27
703 725 0.037605 AACAAACTAGACCCCGAGCG 60.038 55.000 0.00 0.00 0.00 5.03
707 729 2.202756 CTAGACCCCGAGCGTTGC 60.203 66.667 0.00 0.00 0.00 4.17
755 777 3.927481 AAAAGGCGAGCAGGAGGCC 62.927 63.158 0.00 0.00 46.50 5.19
802 824 2.035632 CCTAGTGAAGGTCAGCTAGGG 58.964 57.143 17.41 7.10 40.52 3.53
803 825 1.410882 CTAGTGAAGGTCAGCTAGGGC 59.589 57.143 0.00 0.00 39.06 5.19
851 3659 9.847224 ATGGGAAAATATAGTAAGGTTGTACTG 57.153 33.333 0.00 0.00 35.85 2.74
852 3660 8.269317 TGGGAAAATATAGTAAGGTTGTACTGG 58.731 37.037 0.00 0.00 35.85 4.00
853 3661 7.228108 GGGAAAATATAGTAAGGTTGTACTGGC 59.772 40.741 0.00 0.00 35.85 4.85
854 3662 7.771826 GGAAAATATAGTAAGGTTGTACTGGCA 59.228 37.037 0.00 0.00 35.85 4.92
883 3705 1.773391 AGGAGGGAGGGGATGCATG 60.773 63.158 2.46 0.00 0.00 4.06
898 3720 0.733150 GCATGGGCCTACTCGTTTTC 59.267 55.000 4.53 0.00 0.00 2.29
954 3777 3.449918 CTCTTTCCTTCCCTCTCTCCTT 58.550 50.000 0.00 0.00 0.00 3.36
972 3795 5.380206 TCTCCTTCTATCCCCTTCTTATCCT 59.620 44.000 0.00 0.00 0.00 3.24
1328 4418 2.036992 CTCCTATTCCCTAGTGCTGCAG 59.963 54.545 10.11 10.11 0.00 4.41
1344 4434 4.397103 TGCTGCAGTTCATATTCAGGAAAG 59.603 41.667 16.64 0.00 0.00 2.62
1365 4455 8.585881 GGAAAGGAGTAGTTATGCTATATGACA 58.414 37.037 0.00 0.00 31.50 3.58
1417 4507 6.927416 TCCTTTCAGTTTCATCAATCCATTG 58.073 36.000 0.00 0.00 39.10 2.82
1465 4558 5.761726 ACATGTCACTATACAATGCTCATGG 59.238 40.000 0.00 0.00 34.88 3.66
1475 4568 2.280457 GCTCATGGCTCCCTACGC 60.280 66.667 0.00 0.00 38.06 4.42
1477 4570 1.365633 CTCATGGCTCCCTACGCTC 59.634 63.158 0.00 0.00 0.00 5.03
1482 4575 1.298667 GGCTCCCTACGCTCCAAAA 59.701 57.895 0.00 0.00 0.00 2.44
1483 4576 0.107165 GGCTCCCTACGCTCCAAAAT 60.107 55.000 0.00 0.00 0.00 1.82
1484 4577 1.140252 GGCTCCCTACGCTCCAAAATA 59.860 52.381 0.00 0.00 0.00 1.40
1485 4578 2.420967 GGCTCCCTACGCTCCAAAATAA 60.421 50.000 0.00 0.00 0.00 1.40
1490 4583 4.467082 TCCCTACGCTCCAAAATAAGTGTA 59.533 41.667 0.00 0.00 37.42 2.90
1494 4587 4.000988 ACGCTCCAAAATAAGTGTAGTGG 58.999 43.478 0.00 0.00 34.61 4.00
1495 4588 4.000988 CGCTCCAAAATAAGTGTAGTGGT 58.999 43.478 0.00 0.00 0.00 4.16
1499 4592 7.308109 CGCTCCAAAATAAGTGTAGTGGTTTTA 60.308 37.037 0.00 0.00 0.00 1.52
1554 4648 6.389906 ACATAAACTGTCAAAATTAGCTGCC 58.610 36.000 0.00 0.00 29.94 4.85
1562 4656 6.620678 TGTCAAAATTAGCTGCCAATAGTTC 58.379 36.000 0.00 0.00 0.00 3.01
1592 4686 7.272084 GTGAACGAAGATTCATGGAAATGAAAG 59.728 37.037 5.33 0.00 42.95 2.62
1627 4744 8.813643 ATACAAGAACGAAGCTAATATGGTAC 57.186 34.615 0.00 0.00 0.00 3.34
1721 4838 7.974675 TGTTTAGTGCTTATGCTCATTAAGAC 58.025 34.615 1.96 0.00 40.48 3.01
1749 4866 8.043113 TCAGCATGACTATCTTGTTTATGTTCT 58.957 33.333 0.00 0.00 42.56 3.01
1750 4867 8.121086 CAGCATGACTATCTTGTTTATGTTCTG 58.879 37.037 0.00 0.00 39.69 3.02
1787 4904 1.068585 GGCTTGCTTGCTTGCTTGT 59.931 52.632 9.28 0.00 0.00 3.16
1788 4905 1.219522 GGCTTGCTTGCTTGCTTGTG 61.220 55.000 9.28 0.00 0.00 3.33
1789 4906 0.529119 GCTTGCTTGCTTGCTTGTGT 60.529 50.000 3.47 0.00 0.00 3.72
1790 4907 1.205657 CTTGCTTGCTTGCTTGTGTG 58.794 50.000 3.47 0.00 0.00 3.82
1791 4908 0.531657 TTGCTTGCTTGCTTGTGTGT 59.468 45.000 3.47 0.00 0.00 3.72
1792 4909 0.179132 TGCTTGCTTGCTTGTGTGTG 60.179 50.000 3.47 0.00 0.00 3.82
1793 4910 0.179129 GCTTGCTTGCTTGTGTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
1794 4911 1.552226 CTTGCTTGCTTGTGTGTGTG 58.448 50.000 0.00 0.00 0.00 3.82
1795 4912 0.887247 TTGCTTGCTTGTGTGTGTGT 59.113 45.000 0.00 0.00 0.00 3.72
1796 4913 0.170784 TGCTTGCTTGTGTGTGTGTG 59.829 50.000 0.00 0.00 0.00 3.82
2001 5118 5.383476 CATATGAGAGGGAAAAATGAGCCT 58.617 41.667 0.00 0.00 0.00 4.58
2099 5216 4.689345 AGAATACCGTAGCACAGTGTTTTC 59.311 41.667 1.61 0.00 0.00 2.29
2177 5294 7.184862 ACCCATCTTGATTCTTGAAACCTATT 58.815 34.615 0.00 0.00 0.00 1.73
2178 5295 7.340487 ACCCATCTTGATTCTTGAAACCTATTC 59.660 37.037 0.00 0.00 0.00 1.75
2179 5296 7.201857 CCCATCTTGATTCTTGAAACCTATTCC 60.202 40.741 0.00 0.00 0.00 3.01
2180 5297 7.201857 CCATCTTGATTCTTGAAACCTATTCCC 60.202 40.741 0.00 0.00 0.00 3.97
2181 5298 7.032598 TCTTGATTCTTGAAACCTATTCCCT 57.967 36.000 0.00 0.00 0.00 4.20
2182 5299 7.112779 TCTTGATTCTTGAAACCTATTCCCTC 58.887 38.462 0.00 0.00 0.00 4.30
2183 5300 5.755849 TGATTCTTGAAACCTATTCCCTCC 58.244 41.667 0.00 0.00 0.00 4.30
2184 5301 3.906720 TCTTGAAACCTATTCCCTCCG 57.093 47.619 0.00 0.00 0.00 4.63
2185 5302 3.178865 TCTTGAAACCTATTCCCTCCGT 58.821 45.455 0.00 0.00 0.00 4.69
2186 5303 3.197116 TCTTGAAACCTATTCCCTCCGTC 59.803 47.826 0.00 0.00 0.00 4.79
2187 5304 1.835531 TGAAACCTATTCCCTCCGTCC 59.164 52.381 0.00 0.00 0.00 4.79
2188 5305 1.140452 GAAACCTATTCCCTCCGTCCC 59.860 57.143 0.00 0.00 0.00 4.46
2189 5306 0.043637 AACCTATTCCCTCCGTCCCA 59.956 55.000 0.00 0.00 0.00 4.37
2190 5307 0.267960 ACCTATTCCCTCCGTCCCAT 59.732 55.000 0.00 0.00 0.00 4.00
2191 5308 1.506418 ACCTATTCCCTCCGTCCCATA 59.494 52.381 0.00 0.00 0.00 2.74
2192 5309 2.090380 ACCTATTCCCTCCGTCCCATAA 60.090 50.000 0.00 0.00 0.00 1.90
2193 5310 3.182152 CCTATTCCCTCCGTCCCATAAT 58.818 50.000 0.00 0.00 0.00 1.28
2194 5311 4.202858 ACCTATTCCCTCCGTCCCATAATA 60.203 45.833 0.00 0.00 0.00 0.98
2195 5312 4.969359 CCTATTCCCTCCGTCCCATAATAT 59.031 45.833 0.00 0.00 0.00 1.28
2196 5313 6.141083 CCTATTCCCTCCGTCCCATAATATA 58.859 44.000 0.00 0.00 0.00 0.86
2197 5314 6.614087 CCTATTCCCTCCGTCCCATAATATAA 59.386 42.308 0.00 0.00 0.00 0.98
2198 5315 6.561519 ATTCCCTCCGTCCCATAATATAAG 57.438 41.667 0.00 0.00 0.00 1.73
2199 5316 5.279562 TCCCTCCGTCCCATAATATAAGA 57.720 43.478 0.00 0.00 0.00 2.10
2200 5317 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
2202 5319 4.421948 CTCCGTCCCATAATATAAGACGC 58.578 47.826 14.86 0.00 46.66 5.19
2203 5320 4.084287 TCCGTCCCATAATATAAGACGCT 58.916 43.478 14.86 0.00 46.66 5.07
2204 5321 4.525487 TCCGTCCCATAATATAAGACGCTT 59.475 41.667 14.86 0.00 46.66 4.68
2205 5322 5.011329 TCCGTCCCATAATATAAGACGCTTT 59.989 40.000 14.86 0.00 46.66 3.51
2206 5323 5.699458 CCGTCCCATAATATAAGACGCTTTT 59.301 40.000 14.86 0.00 46.66 2.27
2207 5324 6.204108 CCGTCCCATAATATAAGACGCTTTTT 59.796 38.462 14.86 0.00 46.66 1.94
2208 5325 7.069569 CGTCCCATAATATAAGACGCTTTTTG 58.930 38.462 10.06 0.00 43.07 2.44
2209 5326 7.042321 CGTCCCATAATATAAGACGCTTTTTGA 60.042 37.037 10.06 0.00 43.07 2.69
2210 5327 8.283291 GTCCCATAATATAAGACGCTTTTTGAG 58.717 37.037 0.00 0.00 0.00 3.02
2211 5328 8.208224 TCCCATAATATAAGACGCTTTTTGAGA 58.792 33.333 0.00 0.00 0.00 3.27
2212 5329 8.283291 CCCATAATATAAGACGCTTTTTGAGAC 58.717 37.037 0.00 0.00 0.00 3.36
2213 5330 9.046296 CCATAATATAAGACGCTTTTTGAGACT 57.954 33.333 0.00 0.00 0.00 3.24
2220 5337 9.953697 ATAAGACGCTTTTTGAGACTATACTAG 57.046 33.333 0.00 0.00 0.00 2.57
2221 5338 7.393841 AGACGCTTTTTGAGACTATACTAGT 57.606 36.000 0.00 0.00 42.86 2.57
2222 5339 7.251994 AGACGCTTTTTGAGACTATACTAGTG 58.748 38.462 5.39 0.00 39.59 2.74
2223 5340 6.921914 ACGCTTTTTGAGACTATACTAGTGT 58.078 36.000 5.39 0.39 39.59 3.55
2224 5341 7.028361 ACGCTTTTTGAGACTATACTAGTGTC 58.972 38.462 5.39 4.63 46.10 3.67
2251 5368 5.623956 AATGTCTTACATTATGGGACGGA 57.376 39.130 3.51 0.00 46.11 4.69
2252 5369 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
2253 5370 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
2254 5371 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2255 5372 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2256 5373 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2257 5374 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2258 5375 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2259 5376 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
2273 5390 8.503573 ACGGAGGGAGTAGATTATATCATCATA 58.496 37.037 0.00 0.00 0.00 2.15
2334 5453 4.744137 GCTGAGCTGACATACTGAACTATG 59.256 45.833 0.00 0.00 0.00 2.23
2598 5717 4.762289 TGTGTGCCCCAAAGTTTTATTT 57.238 36.364 0.00 0.00 0.00 1.40
2606 5725 7.332430 GTGCCCCAAAGTTTTATTTGTATTACC 59.668 37.037 0.00 0.00 38.28 2.85
2608 5727 8.044309 GCCCCAAAGTTTTATTTGTATTACCAT 58.956 33.333 0.00 0.00 38.28 3.55
2628 5747 9.806203 TTACCATGAATTTGAAATGCAGATAAG 57.194 29.630 4.69 0.00 0.00 1.73
2763 5890 2.808543 GGATTGTGTTCTCTGAAACGCT 59.191 45.455 13.40 0.81 39.74 5.07
2800 5930 9.588096 AGAAAATATCTTGTGTTTCTAAACCCT 57.412 29.630 3.27 0.00 38.28 4.34
2841 5971 6.588204 TCCTGTTAAGTGCTAGTTTTCTCAA 58.412 36.000 0.00 0.00 0.00 3.02
3245 6379 4.959839 AGGTGTAAATTTTGACCAGTGGTT 59.040 37.500 17.93 0.26 35.25 3.67
3246 6380 5.047188 GGTGTAAATTTTGACCAGTGGTTG 58.953 41.667 17.93 0.00 35.25 3.77
3247 6381 5.163499 GGTGTAAATTTTGACCAGTGGTTGA 60.163 40.000 17.93 5.29 35.25 3.18
3249 6383 4.670896 AAATTTTGACCAGTGGTTGAGG 57.329 40.909 17.93 0.00 35.25 3.86
3250 6384 2.818751 TTTTGACCAGTGGTTGAGGT 57.181 45.000 17.93 0.00 35.25 3.85
3251 6385 3.935818 TTTTGACCAGTGGTTGAGGTA 57.064 42.857 17.93 0.00 35.25 3.08
3252 6386 3.485463 TTTGACCAGTGGTTGAGGTAG 57.515 47.619 17.93 0.00 35.25 3.18
3253 6387 2.097110 TGACCAGTGGTTGAGGTAGT 57.903 50.000 17.93 0.00 35.25 2.73
3301 6435 1.220750 GGGGAGGTAGAGGGAGATCAA 59.779 57.143 0.00 0.00 0.00 2.57
3333 6468 2.506444 GGATCGAGGTAGACGAAGGAT 58.494 52.381 0.00 0.00 42.80 3.24
3374 6511 4.700213 AGCAAGAGAGAGAGTACAGAGTTC 59.300 45.833 0.00 0.00 0.00 3.01
3406 6546 1.632018 AATACAAGCTGCCCGGCCTA 61.632 55.000 7.03 0.00 0.00 3.93
3450 6590 4.701437 ATGGTCCTGGGCCCCACT 62.701 66.667 22.27 0.00 0.00 4.00
3557 6699 2.357517 CTTGCTGTCCGCCGTCTT 60.358 61.111 0.00 0.00 38.05 3.01
3560 6702 2.665185 GCTGTCCGCCGTCTTGTT 60.665 61.111 0.00 0.00 0.00 2.83
3585 6727 2.686835 GCAGCAGGAGAGGAGGGT 60.687 66.667 0.00 0.00 0.00 4.34
3594 6736 1.208293 GGAGAGGAGGGTGTGACATTC 59.792 57.143 0.00 0.00 0.00 2.67
3672 6814 3.370953 GCAGGACATTGTAGTTCTCCCAT 60.371 47.826 0.00 0.00 0.00 4.00
3750 6892 1.228124 CCCCTGCTTGACCAAACGA 60.228 57.895 0.00 0.00 0.00 3.85
3779 6921 0.823356 ATGGCTTGCGACACCAAGTT 60.823 50.000 4.13 0.00 43.17 2.66
3780 6922 1.008538 GGCTTGCGACACCAAGTTG 60.009 57.895 0.00 0.00 43.17 3.16
3806 6948 4.899239 GAGATCAGGTGGCGCCGG 62.899 72.222 23.90 11.68 43.70 6.13
3841 6983 2.772691 GGAGAGTAGTCCGGCGTGG 61.773 68.421 6.01 0.00 40.09 4.94
3891 7033 1.337728 GGGTGAATTTTGCTTTCCGGG 60.338 52.381 0.00 0.00 0.00 5.73
3911 7053 1.406887 GGGCAATTCGAGCTTGTAGGA 60.407 52.381 0.00 0.00 0.00 2.94
3943 7085 3.381590 CACCCGACTGATGATCTTGTAGA 59.618 47.826 0.00 0.00 0.00 2.59
3978 7120 2.046988 GCAAGTTTGGGGCATGGC 60.047 61.111 11.56 11.56 0.00 4.40
4032 7174 3.683802 CAATTTCAGAAGGACCTGCTCT 58.316 45.455 0.00 0.00 34.28 4.09
4033 7175 2.847327 TTTCAGAAGGACCTGCTCTG 57.153 50.000 14.76 14.76 38.34 3.35
4034 7176 0.979665 TTCAGAAGGACCTGCTCTGG 59.020 55.000 19.00 1.73 37.71 3.86
4035 7177 0.906756 TCAGAAGGACCTGCTCTGGG 60.907 60.000 19.00 1.39 37.71 4.45
4036 7178 2.270527 GAAGGACCTGCTCTGGGC 59.729 66.667 0.00 0.00 42.22 5.36
4051 7193 4.451150 GGCATGGCCGACTGACGA 62.451 66.667 8.35 0.00 45.77 4.20
4052 7194 3.188786 GCATGGCCGACTGACGAC 61.189 66.667 0.00 0.00 45.77 4.34
4053 7195 2.880879 CATGGCCGACTGACGACG 60.881 66.667 0.00 0.00 45.77 5.12
4059 7201 2.479650 CGACTGACGACGGAGGAC 59.520 66.667 0.00 0.00 45.77 3.85
4060 7202 2.033755 CGACTGACGACGGAGGACT 61.034 63.158 0.00 0.00 45.77 3.85
4061 7203 1.502640 GACTGACGACGGAGGACTG 59.497 63.158 0.00 0.00 0.00 3.51
4062 7204 2.179517 CTGACGACGGAGGACTGC 59.820 66.667 0.00 0.00 0.00 4.40
4063 7205 2.596338 TGACGACGGAGGACTGCA 60.596 61.111 0.00 0.00 0.00 4.41
4064 7206 2.126424 GACGACGGAGGACTGCAC 60.126 66.667 0.00 0.00 0.00 4.57
4065 7207 2.910479 ACGACGGAGGACTGCACA 60.910 61.111 0.00 0.00 0.00 4.57
4066 7208 2.214181 GACGACGGAGGACTGCACAT 62.214 60.000 0.00 0.00 0.00 3.21
4067 7209 0.963856 ACGACGGAGGACTGCACATA 60.964 55.000 0.00 0.00 0.00 2.29
4068 7210 0.385751 CGACGGAGGACTGCACATAT 59.614 55.000 0.00 0.00 0.00 1.78
4069 7211 1.858091 GACGGAGGACTGCACATATG 58.142 55.000 0.00 0.00 0.00 1.78
4070 7212 0.465705 ACGGAGGACTGCACATATGG 59.534 55.000 7.80 0.00 0.00 2.74
4071 7213 0.882042 CGGAGGACTGCACATATGGC 60.882 60.000 7.80 8.32 0.00 4.40
4072 7214 0.471617 GGAGGACTGCACATATGGCT 59.528 55.000 7.80 0.00 0.00 4.75
4073 7215 1.590932 GAGGACTGCACATATGGCTG 58.409 55.000 7.80 13.13 36.43 4.85
4074 7216 0.465097 AGGACTGCACATATGGCTGC 60.465 55.000 17.09 14.25 34.03 5.25
4075 7217 0.749091 GGACTGCACATATGGCTGCA 60.749 55.000 17.27 17.27 41.13 4.41
4076 7218 1.097232 GACTGCACATATGGCTGCAA 58.903 50.000 18.41 6.43 42.74 4.08
4077 7219 1.679680 GACTGCACATATGGCTGCAAT 59.320 47.619 18.41 11.23 42.74 3.56
4078 7220 2.100252 GACTGCACATATGGCTGCAATT 59.900 45.455 18.41 10.65 42.74 2.32
4079 7221 2.498481 ACTGCACATATGGCTGCAATTT 59.502 40.909 18.41 6.66 42.74 1.82
4080 7222 3.120792 CTGCACATATGGCTGCAATTTC 58.879 45.455 18.41 0.00 42.74 2.17
4081 7223 2.496470 TGCACATATGGCTGCAATTTCA 59.504 40.909 16.28 0.00 40.45 2.69
4082 7224 3.120792 GCACATATGGCTGCAATTTCAG 58.879 45.455 12.18 0.18 37.15 3.02
4083 7225 3.181484 GCACATATGGCTGCAATTTCAGA 60.181 43.478 9.43 0.00 36.19 3.27
4084 7226 4.678574 GCACATATGGCTGCAATTTCAGAA 60.679 41.667 9.43 0.00 36.19 3.02
4085 7227 5.041287 CACATATGGCTGCAATTTCAGAAG 58.959 41.667 9.43 0.00 36.19 2.85
4086 7228 4.098960 ACATATGGCTGCAATTTCAGAAGG 59.901 41.667 9.43 0.00 36.19 3.46
4087 7229 2.291209 TGGCTGCAATTTCAGAAGGA 57.709 45.000 9.43 0.00 36.19 3.36
4088 7230 1.888512 TGGCTGCAATTTCAGAAGGAC 59.111 47.619 9.43 0.00 36.19 3.85
4089 7231 1.203287 GGCTGCAATTTCAGAAGGACC 59.797 52.381 9.43 0.00 36.19 4.46
4090 7232 2.165998 GCTGCAATTTCAGAAGGACCT 58.834 47.619 9.43 0.00 36.19 3.85
4091 7233 2.094854 GCTGCAATTTCAGAAGGACCTG 60.095 50.000 9.43 0.00 36.19 4.00
4100 7242 2.936032 AAGGACCTGCTCCCCCAC 60.936 66.667 0.00 0.00 40.53 4.61
4126 7268 2.450609 TTCCCTCTCTGTACGTTTGC 57.549 50.000 0.00 0.00 0.00 3.68
4132 7274 0.319211 CTCTGTACGTTTGCGGTCCA 60.319 55.000 0.00 0.00 43.45 4.02
4133 7275 0.319083 TCTGTACGTTTGCGGTCCAT 59.681 50.000 0.00 0.00 43.45 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 9.838975 CTTGGCTTTTTGTTGTTTCTTTTAATT 57.161 25.926 0.00 0.00 0.00 1.40
68 69 9.225436 TCTTGGCTTTTTGTTGTTTCTTTTAAT 57.775 25.926 0.00 0.00 0.00 1.40
69 70 8.608844 TCTTGGCTTTTTGTTGTTTCTTTTAA 57.391 26.923 0.00 0.00 0.00 1.52
70 71 8.785329 ATCTTGGCTTTTTGTTGTTTCTTTTA 57.215 26.923 0.00 0.00 0.00 1.52
109 110 4.436050 CGACAACTACAAAGGACATGATGC 60.436 45.833 0.00 0.00 0.00 3.91
115 116 3.635373 AGAGTCGACAACTACAAAGGACA 59.365 43.478 19.50 0.00 38.74 4.02
128 129 5.620205 GCAAGAGAAGAATGTAGAGTCGACA 60.620 44.000 19.50 8.61 0.00 4.35
129 130 4.796312 GCAAGAGAAGAATGTAGAGTCGAC 59.204 45.833 7.70 7.70 0.00 4.20
131 132 4.738124 TGCAAGAGAAGAATGTAGAGTCG 58.262 43.478 0.00 0.00 0.00 4.18
134 135 8.939201 TTAAGATGCAAGAGAAGAATGTAGAG 57.061 34.615 0.00 0.00 0.00 2.43
142 143 7.337942 GGAGGAAAATTAAGATGCAAGAGAAGA 59.662 37.037 0.00 0.00 0.00 2.87
144 145 6.378280 GGGAGGAAAATTAAGATGCAAGAGAA 59.622 38.462 0.00 0.00 0.00 2.87
146 147 5.890419 AGGGAGGAAAATTAAGATGCAAGAG 59.110 40.000 0.00 0.00 0.00 2.85
168 169 6.108687 TGTTTCTGCACTAGATGTATCAAGG 58.891 40.000 0.00 0.00 34.80 3.61
169 170 7.493645 TGATGTTTCTGCACTAGATGTATCAAG 59.506 37.037 0.00 0.00 34.80 3.02
170 171 7.330262 TGATGTTTCTGCACTAGATGTATCAA 58.670 34.615 0.00 0.00 34.80 2.57
171 172 6.877236 TGATGTTTCTGCACTAGATGTATCA 58.123 36.000 0.00 0.00 34.80 2.15
172 173 7.205992 TCTGATGTTTCTGCACTAGATGTATC 58.794 38.462 0.00 0.00 34.80 2.24
173 174 7.117285 TCTGATGTTTCTGCACTAGATGTAT 57.883 36.000 0.00 0.00 34.80 2.29
184 185 4.036734 TGTTTGGTCTTCTGATGTTTCTGC 59.963 41.667 0.00 0.00 0.00 4.26
192 193 4.371624 TGTGGATGTTTGGTCTTCTGAT 57.628 40.909 0.00 0.00 0.00 2.90
193 194 3.855255 TGTGGATGTTTGGTCTTCTGA 57.145 42.857 0.00 0.00 0.00 3.27
209 210 3.126001 TGAGGTTAGTTCAGCTTGTGG 57.874 47.619 0.00 0.00 0.00 4.17
242 243 7.287235 AGGTTCTTACGTGTTATTAGGAGCTAT 59.713 37.037 0.00 0.00 0.00 2.97
244 245 5.421374 AGGTTCTTACGTGTTATTAGGAGCT 59.579 40.000 0.00 0.00 0.00 4.09
258 259 6.522761 CGTTCAACAATCTTAGGTTCTTACG 58.477 40.000 0.00 0.00 0.00 3.18
274 275 0.952280 TTATTTGGGCGCGTTCAACA 59.048 45.000 8.43 4.76 0.00 3.33
297 298 7.332678 GGCTCATACGACTCTTTAAACCTTTTA 59.667 37.037 0.00 0.00 0.00 1.52
324 325 3.156288 TCTACTGTGCTAGGAGTGTGT 57.844 47.619 0.00 0.00 38.60 3.72
359 361 1.339055 TGCCTTCAGCCATAGTGTGTC 60.339 52.381 0.00 0.00 42.71 3.67
402 405 5.418310 ACGACAACAAAGTATCAGTTTGG 57.582 39.130 10.36 0.00 41.55 3.28
426 429 1.215647 CGGTCTTCTTCCCCGACAG 59.784 63.158 0.00 0.00 44.41 3.51
446 449 5.595952 ACCAGAGATTCTTTCTTTTGTGCTT 59.404 36.000 0.00 0.00 33.74 3.91
468 471 8.398665 GGTATTGTCAAGAATGTTCTTATCACC 58.601 37.037 7.62 6.46 45.23 4.02
494 497 1.511318 TTTTGGCGACGGTGATGGTG 61.511 55.000 0.00 0.00 0.00 4.17
495 498 0.820074 TTTTTGGCGACGGTGATGGT 60.820 50.000 0.00 0.00 0.00 3.55
542 545 1.825474 AGATCGACGACTCCCATTGTT 59.175 47.619 0.00 0.00 0.00 2.83
591 594 1.099689 TCACGATGCGACCTACATGA 58.900 50.000 0.00 0.00 0.00 3.07
593 596 2.140065 CATCACGATGCGACCTACAT 57.860 50.000 0.00 0.00 31.39 2.29
613 634 3.751479 TGTCATTCATGGTCCTATCCG 57.249 47.619 0.00 0.00 0.00 4.18
625 646 5.692654 TCGACGTTAAAGACAATGTCATTCA 59.307 36.000 16.38 0.00 42.22 2.57
634 655 4.026310 GCAAAGTCTCGACGTTAAAGACAA 60.026 41.667 20.82 0.00 41.49 3.18
637 658 3.054878 GGCAAAGTCTCGACGTTAAAGA 58.945 45.455 0.00 0.00 36.20 2.52
641 662 0.311790 ACGGCAAAGTCTCGACGTTA 59.688 50.000 0.00 0.00 36.20 3.18
665 686 9.233232 AGTTTGTTTTTCATCTACGTTTGATTC 57.767 29.630 0.00 0.00 0.00 2.52
703 725 1.078637 GGGGGAACTACGGAGCAAC 60.079 63.158 0.00 0.00 0.00 4.17
755 777 1.839994 TGGCTTAGGTTGGATCTCCTG 59.160 52.381 12.46 1.96 35.51 3.86
864 3686 1.463018 ATGCATCCCCTCCCTCCTC 60.463 63.158 0.00 0.00 0.00 3.71
865 3687 1.773391 CATGCATCCCCTCCCTCCT 60.773 63.158 0.00 0.00 0.00 3.69
868 3690 2.780040 CCCATGCATCCCCTCCCT 60.780 66.667 0.00 0.00 0.00 4.20
872 3694 2.038438 TAGGCCCATGCATCCCCT 60.038 61.111 0.00 12.48 40.13 4.79
883 3705 1.450025 CAAGGAAAACGAGTAGGCCC 58.550 55.000 0.00 0.00 0.00 5.80
898 3720 0.612732 TTGCTCATGGGCTTCCAAGG 60.613 55.000 20.42 0.00 44.86 3.61
954 3777 5.137949 TGGAAGAGGATAAGAAGGGGATAGA 59.862 44.000 0.00 0.00 0.00 1.98
972 3795 2.683933 GGCGGGGAGAGTGGAAGA 60.684 66.667 0.00 0.00 0.00 2.87
998 3821 0.527565 CCACTGGCATTTCCTTTCGG 59.472 55.000 0.00 0.00 35.26 4.30
1392 4482 6.770746 ATGGATTGATGAAACTGAAAGGAG 57.229 37.500 0.00 0.00 39.30 3.69
1465 4558 2.614829 TATTTTGGAGCGTAGGGAGC 57.385 50.000 0.00 0.00 0.00 4.70
1501 4594 9.619316 CATCATAAATAAACTTCGTGGTTTGAA 57.381 29.630 14.92 1.70 39.39 2.69
1502 4595 9.004717 TCATCATAAATAAACTTCGTGGTTTGA 57.995 29.630 14.92 6.97 39.39 2.69
1503 4596 9.787532 ATCATCATAAATAAACTTCGTGGTTTG 57.212 29.630 14.92 2.97 39.39 2.93
1634 4751 6.762187 TGTTTACCAGATGTACGAGAACAAAA 59.238 34.615 0.00 0.00 28.43 2.44
1721 4838 6.765036 ACATAAACAAGATAGTCATGCTGAGG 59.235 38.462 0.00 0.00 0.00 3.86
1749 4866 2.486370 CCATGATACCAATACACCGGCA 60.486 50.000 0.00 0.00 0.00 5.69
1750 4867 2.151202 CCATGATACCAATACACCGGC 58.849 52.381 0.00 0.00 0.00 6.13
1787 4904 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1788 4905 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1789 4906 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1790 4907 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1791 4908 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1792 4909 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1793 4910 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1794 4911 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1795 4912 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
1796 4913 2.159626 GGTTACACACACACACACACAC 60.160 50.000 0.00 0.00 0.00 3.82
2099 5216 9.643693 AATGTTATGAACTTATTTGCCTTGAAG 57.356 29.630 0.00 0.00 0.00 3.02
2177 5294 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
2178 5295 4.142227 CGTCTTATATTATGGGACGGAGGG 60.142 50.000 17.59 0.46 43.69 4.30
2179 5296 4.677250 GCGTCTTATATTATGGGACGGAGG 60.677 50.000 22.36 6.98 46.26 4.30
2180 5297 4.158025 AGCGTCTTATATTATGGGACGGAG 59.842 45.833 22.36 7.20 46.26 4.63
2181 5298 4.084287 AGCGTCTTATATTATGGGACGGA 58.916 43.478 22.36 0.00 46.26 4.69
2182 5299 4.451629 AGCGTCTTATATTATGGGACGG 57.548 45.455 22.36 12.20 46.26 4.79
2184 5301 8.149973 TCAAAAAGCGTCTTATATTATGGGAC 57.850 34.615 0.00 0.00 0.00 4.46
2185 5302 8.208224 TCTCAAAAAGCGTCTTATATTATGGGA 58.792 33.333 0.00 0.00 0.00 4.37
2186 5303 8.283291 GTCTCAAAAAGCGTCTTATATTATGGG 58.717 37.037 0.00 0.00 0.00 4.00
2187 5304 9.046296 AGTCTCAAAAAGCGTCTTATATTATGG 57.954 33.333 0.00 0.00 0.00 2.74
2194 5311 9.953697 CTAGTATAGTCTCAAAAAGCGTCTTAT 57.046 33.333 0.00 0.00 32.85 1.73
2226 5343 6.887545 TCCGTCCCATAATGTAAGACATTTTT 59.112 34.615 9.92 0.00 45.80 1.94
2227 5344 6.419791 TCCGTCCCATAATGTAAGACATTTT 58.580 36.000 9.92 0.33 45.80 1.82
2228 5345 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
2230 5347 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
2231 5348 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
2232 5349 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2233 5350 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2234 5351 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2235 5352 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2236 5353 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2237 5354 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2238 5355 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2239 5356 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2240 5357 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2241 5358 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2242 5359 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
2243 5360 0.635009 AATCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2244 5361 2.671896 TAATCTACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
2245 5362 5.507637 TGATATAATCTACTCCCTCCGTCC 58.492 45.833 0.00 0.00 0.00 4.79
2246 5363 6.829298 TGATGATATAATCTACTCCCTCCGTC 59.171 42.308 1.63 0.00 0.00 4.79
2247 5364 6.732487 TGATGATATAATCTACTCCCTCCGT 58.268 40.000 1.63 0.00 0.00 4.69
2248 5365 7.831691 ATGATGATATAATCTACTCCCTCCG 57.168 40.000 1.63 0.00 0.00 4.63
2334 5453 8.263940 TCTCTGCATTAACCTATGTAAAACAC 57.736 34.615 0.00 0.00 0.00 3.32
2598 5717 8.747471 TCTGCATTTCAAATTCATGGTAATACA 58.253 29.630 0.00 0.00 0.00 2.29
2763 5890 9.890629 ACACAAGATATTTTCTAGCTAACATGA 57.109 29.630 0.00 0.00 33.05 3.07
2800 5930 3.840666 ACAGGAGAGTAGGCAGATTCAAA 59.159 43.478 0.00 0.00 0.00 2.69
2841 5971 6.206634 TCACAGAAAGAGTAAATTTGGCGAAT 59.793 34.615 0.00 0.00 0.00 3.34
3056 6190 2.214216 ACGCTCCTAACACTGGGCA 61.214 57.895 0.00 0.00 0.00 5.36
3245 6379 0.963962 GGGTCGTGACAACTACCTCA 59.036 55.000 2.00 0.00 41.01 3.86
3246 6380 1.201880 GAGGGTCGTGACAACTACCTC 59.798 57.143 2.00 4.68 41.01 3.85
3247 6381 1.254954 GAGGGTCGTGACAACTACCT 58.745 55.000 2.00 0.00 41.01 3.08
3249 6383 2.731341 CGATGAGGGTCGTGACAACTAC 60.731 54.545 2.00 0.00 36.88 2.73
3250 6384 1.471287 CGATGAGGGTCGTGACAACTA 59.529 52.381 2.00 0.00 36.88 2.24
3251 6385 0.243907 CGATGAGGGTCGTGACAACT 59.756 55.000 2.00 0.00 36.88 3.16
3252 6386 0.736325 CCGATGAGGGTCGTGACAAC 60.736 60.000 2.00 0.00 39.89 3.32
3253 6387 0.896479 TCCGATGAGGGTCGTGACAA 60.896 55.000 2.00 0.00 39.89 3.18
3301 6435 0.187361 CTCGATCCCCTTCTCCTCCT 59.813 60.000 0.00 0.00 0.00 3.69
3333 6468 1.623811 GCTGAACAAGTCCCTCACCTA 59.376 52.381 0.00 0.00 0.00 3.08
3374 6511 5.726138 GCAGCTTGTATTCTGAATTCAGTCG 60.726 44.000 29.80 10.66 44.12 4.18
3406 6546 0.181114 ATATGCGTGTGTGAGGCCAT 59.819 50.000 5.01 0.00 34.34 4.40
3444 6584 1.485066 GGGTGTGTATGACTAGTGGGG 59.515 57.143 0.00 0.00 0.00 4.96
3450 6590 4.464951 CAGTTAGGTGGGTGTGTATGACTA 59.535 45.833 0.00 0.00 0.00 2.59
3492 6633 4.514585 ACAAGGGCCCACGTGCAA 62.515 61.111 27.56 0.00 0.00 4.08
3557 6699 0.682532 TCCTGCTGCAACCACAAACA 60.683 50.000 3.02 0.00 0.00 2.83
3560 6702 0.535780 CTCTCCTGCTGCAACCACAA 60.536 55.000 3.02 0.00 0.00 3.33
3585 6727 1.488705 AAGGAGGGGCGAATGTCACA 61.489 55.000 0.00 0.00 0.00 3.58
3750 6892 4.308526 CAAGCCATCTTGGAGCGT 57.691 55.556 0.00 0.00 44.53 5.07
3770 6912 2.101249 CTCACAATTGGCAACTTGGTGT 59.899 45.455 19.37 10.29 37.61 4.16
3779 6921 2.439409 CACCTGATCTCACAATTGGCA 58.561 47.619 10.83 0.00 0.00 4.92
3780 6922 1.747355 CCACCTGATCTCACAATTGGC 59.253 52.381 10.83 0.00 0.00 4.52
3806 6948 1.936547 CTCCAGTCTTTAATCAGCCGC 59.063 52.381 0.00 0.00 0.00 6.53
3808 6950 4.479786 ACTCTCCAGTCTTTAATCAGCC 57.520 45.455 0.00 0.00 0.00 4.85
3841 6983 3.482783 GTCGCAGCTCAAGCCGTC 61.483 66.667 0.00 0.00 43.38 4.79
3891 7033 1.017387 CCTACAAGCTCGAATTGCCC 58.983 55.000 9.36 0.00 0.00 5.36
3943 7085 2.944129 TGCTTACAAGTTCTTTGGCCT 58.056 42.857 3.32 0.00 41.25 5.19
4034 7176 4.451150 TCGTCAGTCGGCCATGCC 62.451 66.667 2.24 0.00 46.75 4.40
4035 7177 3.188786 GTCGTCAGTCGGCCATGC 61.189 66.667 2.24 0.00 38.31 4.06
4036 7178 2.880879 CGTCGTCAGTCGGCCATG 60.881 66.667 2.24 0.00 41.52 3.66
4037 7179 4.129737 CCGTCGTCAGTCGGCCAT 62.130 66.667 2.24 0.00 41.58 4.40
4039 7181 4.477975 CTCCGTCGTCAGTCGGCC 62.478 72.222 0.00 0.00 46.13 6.13
4040 7182 4.477975 CCTCCGTCGTCAGTCGGC 62.478 72.222 0.00 0.00 46.13 5.54
4042 7184 2.033755 AGTCCTCCGTCGTCAGTCG 61.034 63.158 0.00 0.00 41.41 4.18
4043 7185 1.502640 CAGTCCTCCGTCGTCAGTC 59.497 63.158 0.00 0.00 0.00 3.51
4044 7186 2.627737 GCAGTCCTCCGTCGTCAGT 61.628 63.158 0.00 0.00 0.00 3.41
4045 7187 2.179517 GCAGTCCTCCGTCGTCAG 59.820 66.667 0.00 0.00 0.00 3.51
4046 7188 2.596338 TGCAGTCCTCCGTCGTCA 60.596 61.111 0.00 0.00 0.00 4.35
4047 7189 2.126424 GTGCAGTCCTCCGTCGTC 60.126 66.667 0.00 0.00 0.00 4.20
4048 7190 0.963856 TATGTGCAGTCCTCCGTCGT 60.964 55.000 0.00 0.00 0.00 4.34
4049 7191 0.385751 ATATGTGCAGTCCTCCGTCG 59.614 55.000 0.00 0.00 0.00 5.12
4050 7192 1.539065 CCATATGTGCAGTCCTCCGTC 60.539 57.143 1.24 0.00 0.00 4.79
4051 7193 0.465705 CCATATGTGCAGTCCTCCGT 59.534 55.000 1.24 0.00 0.00 4.69
4052 7194 0.882042 GCCATATGTGCAGTCCTCCG 60.882 60.000 10.27 0.00 0.00 4.63
4053 7195 0.471617 AGCCATATGTGCAGTCCTCC 59.528 55.000 15.63 0.00 0.00 4.30
4054 7196 1.590932 CAGCCATATGTGCAGTCCTC 58.409 55.000 15.63 0.00 0.00 3.71
4055 7197 0.465097 GCAGCCATATGTGCAGTCCT 60.465 55.000 12.18 0.00 39.62 3.85
4056 7198 0.749091 TGCAGCCATATGTGCAGTCC 60.749 55.000 15.02 3.80 44.70 3.85
4057 7199 2.784547 TGCAGCCATATGTGCAGTC 58.215 52.632 15.02 6.52 44.70 3.51
4061 7203 3.120792 CTGAAATTGCAGCCATATGTGC 58.879 45.455 10.56 10.56 40.29 4.57
4062 7204 4.642445 TCTGAAATTGCAGCCATATGTG 57.358 40.909 8.76 0.00 35.86 3.21
4063 7205 4.098960 CCTTCTGAAATTGCAGCCATATGT 59.901 41.667 8.76 0.00 35.86 2.29
4064 7206 4.340097 TCCTTCTGAAATTGCAGCCATATG 59.660 41.667 8.76 0.00 35.86 1.78
4065 7207 4.340381 GTCCTTCTGAAATTGCAGCCATAT 59.660 41.667 8.76 0.00 35.86 1.78
4066 7208 3.696051 GTCCTTCTGAAATTGCAGCCATA 59.304 43.478 8.76 0.00 35.86 2.74
4067 7209 2.494870 GTCCTTCTGAAATTGCAGCCAT 59.505 45.455 8.76 0.00 35.86 4.40
4068 7210 1.888512 GTCCTTCTGAAATTGCAGCCA 59.111 47.619 8.76 0.00 35.86 4.75
4069 7211 1.203287 GGTCCTTCTGAAATTGCAGCC 59.797 52.381 8.76 0.00 35.86 4.85
4070 7212 2.094854 CAGGTCCTTCTGAAATTGCAGC 60.095 50.000 8.76 0.00 36.93 5.25
4071 7213 2.094854 GCAGGTCCTTCTGAAATTGCAG 60.095 50.000 7.16 7.16 36.93 4.41
4072 7214 1.888512 GCAGGTCCTTCTGAAATTGCA 59.111 47.619 0.00 0.00 36.93 4.08
4073 7215 2.163211 GAGCAGGTCCTTCTGAAATTGC 59.837 50.000 0.00 0.00 36.93 3.56
4074 7216 2.751806 GGAGCAGGTCCTTCTGAAATTG 59.248 50.000 11.76 0.00 42.99 2.32
4075 7217 2.291217 GGGAGCAGGTCCTTCTGAAATT 60.291 50.000 18.34 0.00 46.06 1.82
4076 7218 1.283321 GGGAGCAGGTCCTTCTGAAAT 59.717 52.381 18.34 0.00 46.06 2.17
4077 7219 0.693049 GGGAGCAGGTCCTTCTGAAA 59.307 55.000 18.34 0.00 46.06 2.69
4078 7220 1.201429 GGGGAGCAGGTCCTTCTGAA 61.201 60.000 18.34 0.00 46.06 3.02
4079 7221 1.613630 GGGGAGCAGGTCCTTCTGA 60.614 63.158 18.34 0.00 46.06 3.27
4080 7222 2.674220 GGGGGAGCAGGTCCTTCTG 61.674 68.421 18.34 0.00 46.06 3.02
4081 7223 2.285743 GGGGGAGCAGGTCCTTCT 60.286 66.667 18.34 0.00 46.06 2.85
4082 7224 2.610859 TGGGGGAGCAGGTCCTTC 60.611 66.667 18.34 10.97 46.06 3.46
4083 7225 2.936032 GTGGGGGAGCAGGTCCTT 60.936 66.667 18.34 0.00 46.06 3.36
4084 7226 3.947041 AGTGGGGGAGCAGGTCCT 61.947 66.667 18.34 0.00 46.06 3.85
4085 7227 3.721706 CAGTGGGGGAGCAGGTCC 61.722 72.222 10.51 10.51 46.10 4.46
4086 7228 2.930562 ACAGTGGGGGAGCAGGTC 60.931 66.667 0.00 0.00 0.00 3.85
4087 7229 3.252284 CACAGTGGGGGAGCAGGT 61.252 66.667 0.00 0.00 0.00 4.00
4088 7230 1.856539 ATTCACAGTGGGGGAGCAGG 61.857 60.000 0.00 0.00 0.00 4.85
4089 7231 0.038744 AATTCACAGTGGGGGAGCAG 59.961 55.000 0.00 0.00 0.00 4.24
4090 7232 0.038166 GAATTCACAGTGGGGGAGCA 59.962 55.000 0.00 0.00 0.00 4.26
4091 7233 0.681243 GGAATTCACAGTGGGGGAGC 60.681 60.000 7.93 0.00 0.00 4.70
4100 7242 3.193691 ACGTACAGAGAGGGAATTCACAG 59.806 47.826 11.02 0.00 0.00 3.66
4126 7268 1.600957 GATGAAGCATCACATGGACCG 59.399 52.381 0.00 0.00 40.28 4.79
4132 7274 2.715046 ACAACGGATGAAGCATCACAT 58.285 42.857 9.37 0.00 42.13 3.21
4133 7275 2.183478 ACAACGGATGAAGCATCACA 57.817 45.000 9.37 0.00 42.13 3.58


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

AutoCloner maintained by Alex Coulton.