Multiple sequence alignment - TraesCS2D01G543300

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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 TraesCS2D01G543300 chr2D 100.000 2513 0 0 1 2513 621266417 621263905 0.000000e+00 4641
1 TraesCS2D01G543300 chr2D 87.615 1518 134 33 622 2108 621313816 621312322 0.000000e+00 1712
2 TraesCS2D01G543300 chr2D 90.284 1266 100 14 781 2036 621140962 621139710 0.000000e+00 1635
3 TraesCS2D01G543300 chr2D 92.916 367 17 6 1 361 621150937 621150574 2.210000e-145 525
4 TraesCS2D01G543300 chr2D 86.269 386 50 3 2127 2512 537518932 537518550 1.390000e-112 416
5 TraesCS2D01G543300 chr2D 98.010 201 4 0 365 565 621150499 621150299 1.430000e-92 350
6 TraesCS2D01G543300 chr2D 97.701 174 4 0 557 730 621142816 621142643 1.460000e-77 300
7 TraesCS2D01G543300 chr2D 79.904 209 27 10 379 572 621314111 621313903 3.370000e-29 139
8 TraesCS2D01G543300 chr2B 89.250 1600 134 25 457 2036 762072289 762070708 0.000000e+00 1967
9 TraesCS2D01G543300 chr2B 86.061 1442 158 31 622 2035 762063528 762062102 0.000000e+00 1509
10 TraesCS2D01G543300 chr2B 87.895 380 37 4 2136 2512 587727696 587727323 2.970000e-119 438
11 TraesCS2D01G543300 chr2B 92.797 236 15 2 126 360 762072719 762072485 8.610000e-90 340
12 TraesCS2D01G543300 chr2B 97.143 105 2 1 365 469 762072409 762072306 2.570000e-40 176
13 TraesCS2D01G543300 chrUn 89.000 1600 138 25 457 2036 342645342 342643761 0.000000e+00 1945
14 TraesCS2D01G543300 chrUn 88.500 1600 136 32 457 2036 343020892 343019321 0.000000e+00 1892
15 TraesCS2D01G543300 chrUn 86.150 1444 158 30 622 2035 314618794 314617363 0.000000e+00 1520
16 TraesCS2D01G543300 chrUn 86.872 1234 140 17 817 2036 338975305 338976530 0.000000e+00 1362
17 TraesCS2D01G543300 chrUn 86.872 1234 140 17 817 2036 342893158 342894383 0.000000e+00 1362
18 TraesCS2D01G543300 chrUn 84.492 374 40 10 1 360 329050300 329049931 1.110000e-93 353
19 TraesCS2D01G543300 chrUn 97.980 99 1 1 371 469 342645456 342645359 1.200000e-38 171
20 TraesCS2D01G543300 chrUn 97.980 99 1 1 371 469 343021006 343020909 1.200000e-38 171
21 TraesCS2D01G543300 chr2A 89.650 1227 114 7 886 2101 753004565 753003341 0.000000e+00 1550
22 TraesCS2D01G543300 chr2A 95.187 374 17 1 365 738 753058746 753058374 7.740000e-165 590
23 TraesCS2D01G543300 chr2A 93.548 279 13 3 1 275 753059683 753059406 6.470000e-111 411
24 TraesCS2D01G543300 chr2A 79.070 215 26 13 379 574 752997207 752996993 2.030000e-26 130
25 TraesCS2D01G543300 chr2A 98.571 70 1 0 292 361 753058891 753058822 9.440000e-25 124
26 TraesCS2D01G543300 chr3B 88.267 375 42 2 2138 2512 827401561 827401189 4.930000e-122 448
27 TraesCS2D01G543300 chr3B 88.798 366 39 2 2138 2503 830789240 830789603 4.930000e-122 448
28 TraesCS2D01G543300 chr7D 86.579 380 47 3 2133 2512 26528138 26528513 1.390000e-112 416
29 TraesCS2D01G543300 chr1B 85.352 355 39 11 2155 2503 354661544 354661197 3.070000e-94 355
30 TraesCS2D01G543300 chr6A 83.516 364 49 9 2144 2503 409445339 409445695 1.860000e-86 329
31 TraesCS2D01G543300 chr4B 84.592 331 47 4 2136 2465 117279425 117279098 2.410000e-85 326
32 TraesCS2D01G543300 chr5A 81.766 351 55 9 2156 2503 487374135 487374479 4.090000e-73 285


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 TraesCS2D01G543300 chr2D 621263905 621266417 2512 True 4641.000000 4641 100.000000 1 2513 1 chr2D.!!$R2 2512
1 TraesCS2D01G543300 chr2D 621139710 621142816 3106 True 967.500000 1635 93.992500 557 2036 2 chr2D.!!$R3 1479
2 TraesCS2D01G543300 chr2D 621312322 621314111 1789 True 925.500000 1712 83.759500 379 2108 2 chr2D.!!$R5 1729
3 TraesCS2D01G543300 chr2D 621150299 621150937 638 True 437.500000 525 95.463000 1 565 2 chr2D.!!$R4 564
4 TraesCS2D01G543300 chr2B 762062102 762063528 1426 True 1509.000000 1509 86.061000 622 2035 1 chr2B.!!$R2 1413
5 TraesCS2D01G543300 chr2B 762070708 762072719 2011 True 827.666667 1967 93.063333 126 2036 3 chr2B.!!$R3 1910
6 TraesCS2D01G543300 chrUn 314617363 314618794 1431 True 1520.000000 1520 86.150000 622 2035 1 chrUn.!!$R1 1413
7 TraesCS2D01G543300 chrUn 338975305 338976530 1225 False 1362.000000 1362 86.872000 817 2036 1 chrUn.!!$F1 1219
8 TraesCS2D01G543300 chrUn 342893158 342894383 1225 False 1362.000000 1362 86.872000 817 2036 1 chrUn.!!$F2 1219
9 TraesCS2D01G543300 chrUn 342643761 342645456 1695 True 1058.000000 1945 93.490000 371 2036 2 chrUn.!!$R3 1665
10 TraesCS2D01G543300 chrUn 343019321 343021006 1685 True 1031.500000 1892 93.240000 371 2036 2 chrUn.!!$R4 1665
11 TraesCS2D01G543300 chr2A 753003341 753004565 1224 True 1550.000000 1550 89.650000 886 2101 1 chr2A.!!$R2 1215
12 TraesCS2D01G543300 chr2A 753058374 753059683 1309 True 375.000000 590 95.768667 1 738 3 chr2A.!!$R3 737

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
987 3292 0.459934 CTCTGCAAGCTCTCCTTCCG 60.46 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 4455 0.107703 CAGCCTTACCTGATGCCGAA 60.108 55.0 0.0 0.0 34.77 4.3 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
43 44 6.262193 TCGGTAGAAATTTGTTTTGGATCC 57.738 37.500 4.20 4.20 0.00 3.36
60 61 3.052186 GGATCCCAGGCTCTATATCCTCT 60.052 52.174 0.00 0.00 32.00 3.69
129 134 7.841915 AAAAATCCGAAAACAATTTCACACT 57.158 28.000 2.64 0.00 44.24 3.55
208 214 8.683774 CATTTCATTTAAAAAGCAAACACATGC 58.316 29.630 0.00 0.00 46.78 4.06
262 268 6.659242 AGTCCACAATATGAAAATCTTCCGTT 59.341 34.615 0.00 0.00 0.00 4.44
361 865 1.337071 AGTTGACGACGATCACTGTGT 59.663 47.619 7.79 0.00 0.00 3.72
362 866 2.551032 AGTTGACGACGATCACTGTGTA 59.449 45.455 7.79 0.00 0.00 2.90
363 867 2.606717 TGACGACGATCACTGTGTAC 57.393 50.000 7.79 2.68 0.00 2.90
731 1385 2.246719 ACAGCACAGTCAAGTCTTCC 57.753 50.000 0.00 0.00 0.00 3.46
738 1392 3.515502 CACAGTCAAGTCTTCCCATCCTA 59.484 47.826 0.00 0.00 0.00 2.94
739 1393 4.163078 CACAGTCAAGTCTTCCCATCCTAT 59.837 45.833 0.00 0.00 0.00 2.57
740 1394 4.785376 ACAGTCAAGTCTTCCCATCCTATT 59.215 41.667 0.00 0.00 0.00 1.73
741 1395 5.964477 ACAGTCAAGTCTTCCCATCCTATTA 59.036 40.000 0.00 0.00 0.00 0.98
742 1396 6.098982 ACAGTCAAGTCTTCCCATCCTATTAG 59.901 42.308 0.00 0.00 0.00 1.73
743 1397 5.071115 AGTCAAGTCTTCCCATCCTATTAGC 59.929 44.000 0.00 0.00 0.00 3.09
744 1398 4.348168 TCAAGTCTTCCCATCCTATTAGCC 59.652 45.833 0.00 0.00 0.00 3.93
745 1399 4.220861 AGTCTTCCCATCCTATTAGCCT 57.779 45.455 0.00 0.00 0.00 4.58
746 1400 3.906846 AGTCTTCCCATCCTATTAGCCTG 59.093 47.826 0.00 0.00 0.00 4.85
747 1401 3.648545 GTCTTCCCATCCTATTAGCCTGT 59.351 47.826 0.00 0.00 0.00 4.00
748 1402 4.838986 GTCTTCCCATCCTATTAGCCTGTA 59.161 45.833 0.00 0.00 0.00 2.74
749 1403 4.838986 TCTTCCCATCCTATTAGCCTGTAC 59.161 45.833 0.00 0.00 0.00 2.90
750 1404 4.207698 TCCCATCCTATTAGCCTGTACA 57.792 45.455 0.00 0.00 0.00 2.90
751 1405 4.160329 TCCCATCCTATTAGCCTGTACAG 58.840 47.826 16.34 16.34 0.00 2.74
779 2970 3.490761 CGTTTTGCTTGTGTTCCCATCTT 60.491 43.478 0.00 0.00 0.00 2.40
792 3076 5.221224 TGTTCCCATCTTCACAACATTCAAC 60.221 40.000 0.00 0.00 0.00 3.18
828 3114 1.728074 TACACGCACTCGACGCTTG 60.728 57.895 6.93 6.93 39.41 4.01
987 3292 0.459934 CTCTGCAAGCTCTCCTTCCG 60.460 60.000 0.00 0.00 0.00 4.30
996 3301 0.977395 CTCTCCTTCCGGTTCCAACT 59.023 55.000 0.00 0.00 0.00 3.16
1050 3355 2.517414 GCTGCCATGGCCATCCTA 59.483 61.111 33.44 13.22 41.09 2.94
1083 3388 0.672401 CGGCAATCTACAACGTGGGT 60.672 55.000 0.00 0.00 0.00 4.51
1281 3587 3.263425 ACTCCGGGAATGATGTTGTTACT 59.737 43.478 0.00 0.00 0.00 2.24
1288 3594 5.245531 GGAATGATGTTGTTACTCTCACCA 58.754 41.667 0.00 0.00 0.00 4.17
1307 3613 3.454573 CACCGGCACCCGCTACTA 61.455 66.667 0.00 0.00 46.86 1.82
1311 3617 1.457823 CCGGCACCCGCTACTACATA 61.458 60.000 0.00 0.00 46.86 2.29
1380 3686 2.041762 ATGCCAGGCTCCTCCTCA 59.958 61.111 14.15 0.00 45.52 3.86
1549 3860 1.666888 GCAGGCACATGTGTACTTTGC 60.667 52.381 26.01 21.64 0.00 3.68
1556 3868 4.092237 GCACATGTGTACTTTGCGTATGTA 59.908 41.667 26.01 0.00 0.00 2.29
1624 3936 9.679661 AGTTATGTGTATGTTGGACATATTCAA 57.320 29.630 4.29 0.00 42.39 2.69
1628 3941 7.815641 TGTGTATGTTGGACATATTCAAGTTG 58.184 34.615 4.29 0.00 42.39 3.16
1649 3962 6.256321 AGTTGTGTGTTTTGCTGATTCATTTC 59.744 34.615 0.00 0.00 0.00 2.17
1658 3976 7.389803 TTTGCTGATTCATTTCGGAGATTAA 57.610 32.000 0.00 0.00 35.04 1.40
1659 3977 7.572523 TTGCTGATTCATTTCGGAGATTAAT 57.427 32.000 0.00 0.00 35.04 1.40
1735 4053 2.285083 CCGTGAGAACCAACACTTTCA 58.715 47.619 0.00 0.00 35.23 2.69
1917 4241 2.676076 CAAAAATCCCGTCCTTTGCTG 58.324 47.619 0.00 0.00 0.00 4.41
1981 4307 1.064906 AGTCACCGTTATCGAGGGAGA 60.065 52.381 0.00 0.00 39.71 3.71
1982 4308 1.955080 GTCACCGTTATCGAGGGAGAT 59.045 52.381 0.00 0.00 35.76 2.75
2075 4407 3.503748 CGCTCTGAAGGACCAAAATTTCT 59.496 43.478 0.00 0.00 0.00 2.52
2076 4408 4.614535 CGCTCTGAAGGACCAAAATTTCTG 60.615 45.833 0.00 0.00 0.00 3.02
2080 4412 3.243839 TGAAGGACCAAAATTTCTGCTGC 60.244 43.478 0.00 0.00 0.00 5.25
2101 4433 1.696314 AGGCCCCATCCACCGTAAT 60.696 57.895 0.00 0.00 0.00 1.89
2104 4436 1.133730 GGCCCCATCCACCGTAATAAA 60.134 52.381 0.00 0.00 0.00 1.40
2106 4438 3.025262 GCCCCATCCACCGTAATAAAAA 58.975 45.455 0.00 0.00 0.00 1.94
2107 4439 3.181484 GCCCCATCCACCGTAATAAAAAC 60.181 47.826 0.00 0.00 0.00 2.43
2108 4440 4.017808 CCCCATCCACCGTAATAAAAACA 58.982 43.478 0.00 0.00 0.00 2.83
2109 4441 4.142337 CCCCATCCACCGTAATAAAAACAC 60.142 45.833 0.00 0.00 0.00 3.32
2110 4442 4.142337 CCCATCCACCGTAATAAAAACACC 60.142 45.833 0.00 0.00 0.00 4.16
2111 4443 4.703093 CCATCCACCGTAATAAAAACACCT 59.297 41.667 0.00 0.00 0.00 4.00
2112 4444 5.184287 CCATCCACCGTAATAAAAACACCTT 59.816 40.000 0.00 0.00 0.00 3.50
2113 4445 5.692613 TCCACCGTAATAAAAACACCTTG 57.307 39.130 0.00 0.00 0.00 3.61
2114 4446 4.519730 TCCACCGTAATAAAAACACCTTGG 59.480 41.667 0.00 0.00 0.00 3.61
2115 4447 4.321378 CCACCGTAATAAAAACACCTTGGG 60.321 45.833 0.00 0.00 0.00 4.12
2116 4448 3.256383 ACCGTAATAAAAACACCTTGGGC 59.744 43.478 0.00 0.00 0.00 5.36
2117 4449 3.494232 CGTAATAAAAACACCTTGGGCG 58.506 45.455 0.00 0.00 0.00 6.13
2118 4450 2.448926 AATAAAAACACCTTGGGCGC 57.551 45.000 0.00 0.00 0.00 6.53
2119 4451 1.333177 ATAAAAACACCTTGGGCGCA 58.667 45.000 10.83 0.00 0.00 6.09
2120 4452 1.333177 TAAAAACACCTTGGGCGCAT 58.667 45.000 10.83 0.00 0.00 4.73
2121 4453 0.033366 AAAAACACCTTGGGCGCATC 59.967 50.000 10.83 0.40 0.00 3.91
2122 4454 1.815817 AAAACACCTTGGGCGCATCC 61.816 55.000 10.83 1.84 0.00 3.51
2123 4455 2.713531 AAACACCTTGGGCGCATCCT 62.714 55.000 10.83 0.00 34.39 3.24
2124 4456 2.361610 CACCTTGGGCGCATCCTT 60.362 61.111 10.83 0.00 34.39 3.36
2125 4457 2.044946 ACCTTGGGCGCATCCTTC 60.045 61.111 10.83 0.00 34.39 3.46
2126 4458 3.204827 CCTTGGGCGCATCCTTCG 61.205 66.667 10.83 0.00 34.39 3.79
2127 4459 3.204827 CTTGGGCGCATCCTTCGG 61.205 66.667 10.83 0.00 34.39 4.30
2132 4464 2.896854 GCGCATCCTTCGGCATCA 60.897 61.111 0.30 0.00 0.00 3.07
2133 4465 2.890109 GCGCATCCTTCGGCATCAG 61.890 63.158 0.30 0.00 0.00 2.90
2134 4466 2.249535 CGCATCCTTCGGCATCAGG 61.250 63.158 0.00 0.00 0.00 3.86
2135 4467 1.153086 GCATCCTTCGGCATCAGGT 60.153 57.895 0.00 0.00 0.00 4.00
2136 4468 0.106708 GCATCCTTCGGCATCAGGTA 59.893 55.000 0.00 0.00 0.00 3.08
2137 4469 1.475034 GCATCCTTCGGCATCAGGTAA 60.475 52.381 0.00 0.00 0.00 2.85
2138 4470 2.487934 CATCCTTCGGCATCAGGTAAG 58.512 52.381 0.00 0.00 0.00 2.34
2139 4471 0.830648 TCCTTCGGCATCAGGTAAGG 59.169 55.000 0.00 0.00 38.44 2.69
2140 4472 0.815615 CCTTCGGCATCAGGTAAGGC 60.816 60.000 0.00 0.00 31.04 4.35
2141 4473 0.179000 CTTCGGCATCAGGTAAGGCT 59.821 55.000 0.00 0.00 0.00 4.58
2142 4474 0.107703 TTCGGCATCAGGTAAGGCTG 60.108 55.000 0.00 0.00 0.00 4.85
2143 4475 1.524621 CGGCATCAGGTAAGGCTGG 60.525 63.158 0.00 0.00 0.00 4.85
2144 4476 1.609783 GGCATCAGGTAAGGCTGGT 59.390 57.895 0.00 0.00 0.00 4.00
2145 4477 0.464554 GGCATCAGGTAAGGCTGGTC 60.465 60.000 0.00 0.00 0.00 4.02
2146 4478 0.253044 GCATCAGGTAAGGCTGGTCA 59.747 55.000 0.00 0.00 0.00 4.02
2147 4479 1.133976 GCATCAGGTAAGGCTGGTCAT 60.134 52.381 0.00 0.00 0.00 3.06
2148 4480 2.104792 GCATCAGGTAAGGCTGGTCATA 59.895 50.000 0.00 0.00 0.00 2.15
2149 4481 3.805108 GCATCAGGTAAGGCTGGTCATAG 60.805 52.174 0.00 0.00 0.00 2.23
2150 4482 3.116096 TCAGGTAAGGCTGGTCATAGT 57.884 47.619 0.00 0.00 0.00 2.12
2151 4483 2.766263 TCAGGTAAGGCTGGTCATAGTG 59.234 50.000 0.00 0.00 0.00 2.74
2152 4484 2.119495 AGGTAAGGCTGGTCATAGTGG 58.881 52.381 0.00 0.00 0.00 4.00
2153 4485 1.838077 GGTAAGGCTGGTCATAGTGGT 59.162 52.381 0.00 0.00 0.00 4.16
2154 4486 2.420129 GGTAAGGCTGGTCATAGTGGTG 60.420 54.545 0.00 0.00 0.00 4.17
2155 4487 1.656587 AAGGCTGGTCATAGTGGTGA 58.343 50.000 0.00 0.00 0.00 4.02
2156 4488 1.198713 AGGCTGGTCATAGTGGTGAG 58.801 55.000 0.00 0.00 0.00 3.51
2157 4489 0.905357 GGCTGGTCATAGTGGTGAGT 59.095 55.000 0.00 0.00 0.00 3.41
2158 4490 2.108168 GGCTGGTCATAGTGGTGAGTA 58.892 52.381 0.00 0.00 0.00 2.59
2159 4491 2.500098 GGCTGGTCATAGTGGTGAGTAA 59.500 50.000 0.00 0.00 0.00 2.24
2160 4492 3.522553 GCTGGTCATAGTGGTGAGTAAC 58.477 50.000 0.00 0.00 0.00 2.50
2161 4493 3.056107 GCTGGTCATAGTGGTGAGTAACA 60.056 47.826 0.00 0.00 0.00 2.41
2162 4494 4.383118 GCTGGTCATAGTGGTGAGTAACAT 60.383 45.833 0.00 0.00 0.00 2.71
2163 4495 5.163447 GCTGGTCATAGTGGTGAGTAACATA 60.163 44.000 0.00 0.00 0.00 2.29
2164 4496 6.463049 GCTGGTCATAGTGGTGAGTAACATAT 60.463 42.308 0.00 0.00 0.00 1.78
2165 4497 7.255836 GCTGGTCATAGTGGTGAGTAACATATA 60.256 40.741 0.00 0.00 0.00 0.86
2166 4498 7.948357 TGGTCATAGTGGTGAGTAACATATAC 58.052 38.462 0.00 0.00 0.00 1.47
2167 4499 7.783119 TGGTCATAGTGGTGAGTAACATATACT 59.217 37.037 0.00 0.00 0.00 2.12
2168 4500 9.293404 GGTCATAGTGGTGAGTAACATATACTA 57.707 37.037 0.00 0.00 0.00 1.82
2261 4593 9.797642 ATAGATGGTCTTATTTATTGTCATGCA 57.202 29.630 0.00 0.00 0.00 3.96
2262 4594 8.701908 AGATGGTCTTATTTATTGTCATGCAT 57.298 30.769 0.00 0.00 0.00 3.96
2263 4595 8.573885 AGATGGTCTTATTTATTGTCATGCATG 58.426 33.333 21.07 21.07 0.00 4.06
2264 4596 7.878547 TGGTCTTATTTATTGTCATGCATGA 57.121 32.000 25.42 25.42 0.00 3.07
2275 4607 3.198409 TCATGCATGACACATACTCCC 57.802 47.619 25.42 0.00 0.00 4.30
2276 4608 2.773661 TCATGCATGACACATACTCCCT 59.226 45.455 25.42 0.00 0.00 4.20
2277 4609 2.988010 TGCATGACACATACTCCCTC 57.012 50.000 0.00 0.00 0.00 4.30
2278 4610 1.486310 TGCATGACACATACTCCCTCC 59.514 52.381 0.00 0.00 0.00 4.30
2279 4611 1.539065 GCATGACACATACTCCCTCCG 60.539 57.143 0.00 0.00 0.00 4.63
2280 4612 1.757118 CATGACACATACTCCCTCCGT 59.243 52.381 0.00 0.00 0.00 4.69
2281 4613 1.933021 TGACACATACTCCCTCCGTT 58.067 50.000 0.00 0.00 0.00 4.44
2282 4614 1.822990 TGACACATACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
2283 4615 1.136500 GACACATACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
2284 4616 1.273098 ACACATACTCCCTCCGTTCCT 60.273 52.381 0.00 0.00 0.00 3.36
2285 4617 2.024655 ACACATACTCCCTCCGTTCCTA 60.025 50.000 0.00 0.00 0.00 2.94
2286 4618 3.028850 CACATACTCCCTCCGTTCCTAA 58.971 50.000 0.00 0.00 0.00 2.69
2287 4619 3.449737 CACATACTCCCTCCGTTCCTAAA 59.550 47.826 0.00 0.00 0.00 1.85
2288 4620 4.101119 CACATACTCCCTCCGTTCCTAAAT 59.899 45.833 0.00 0.00 0.00 1.40
2289 4621 5.303589 CACATACTCCCTCCGTTCCTAAATA 59.696 44.000 0.00 0.00 0.00 1.40
2290 4622 6.014499 CACATACTCCCTCCGTTCCTAAATAT 60.014 42.308 0.00 0.00 0.00 1.28
2291 4623 7.177921 CACATACTCCCTCCGTTCCTAAATATA 59.822 40.741 0.00 0.00 0.00 0.86
2292 4624 7.731688 ACATACTCCCTCCGTTCCTAAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
2293 4625 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2294 4626 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2295 4627 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2296 4628 5.541484 TCCCTCCGTTCCTAAATATAAGTCC 59.459 44.000 0.00 0.00 0.00 3.85
2297 4629 5.543020 CCCTCCGTTCCTAAATATAAGTCCT 59.457 44.000 0.00 0.00 0.00 3.85
2298 4630 6.042897 CCCTCCGTTCCTAAATATAAGTCCTT 59.957 42.308 0.00 0.00 0.00 3.36
2299 4631 7.419865 CCCTCCGTTCCTAAATATAAGTCCTTT 60.420 40.741 0.00 0.00 0.00 3.11
2300 4632 7.991460 CCTCCGTTCCTAAATATAAGTCCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2336 4668 8.853077 AATGGACTACAACATATGGATGTATG 57.147 34.615 18.38 15.31 45.93 2.39
2337 4669 7.373617 TGGACTACAACATATGGATGTATGT 57.626 36.000 18.38 17.31 45.93 2.29
2338 4670 8.485578 TGGACTACAACATATGGATGTATGTA 57.514 34.615 18.38 11.27 45.93 2.29
2339 4671 8.585018 TGGACTACAACATATGGATGTATGTAG 58.415 37.037 22.20 22.20 45.93 2.74
2340 4672 8.803235 GGACTACAACATATGGATGTATGTAGA 58.197 37.037 26.03 8.59 45.93 2.59
2341 4673 9.627395 GACTACAACATATGGATGTATGTAGAC 57.373 37.037 26.03 21.22 45.93 2.59
2342 4674 9.143155 ACTACAACATATGGATGTATGTAGACA 57.857 33.333 26.03 7.65 45.93 3.41
2374 4706 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2375 4707 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2376 4708 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2377 4709 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2378 4710 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2379 4711 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2380 4712 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2381 4713 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2382 4714 3.684305 TCACTCATTTTGCTCCGTATGTG 59.316 43.478 0.00 0.00 0.00 3.21
2383 4715 3.009723 ACTCATTTTGCTCCGTATGTGG 58.990 45.455 0.00 0.00 0.00 4.17
2384 4716 3.009723 CTCATTTTGCTCCGTATGTGGT 58.990 45.455 0.00 0.00 0.00 4.16
2385 4717 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
2386 4718 2.552599 TTTTGCTCCGTATGTGGTCA 57.447 45.000 0.00 0.00 0.00 4.02
2387 4719 2.779755 TTTGCTCCGTATGTGGTCAT 57.220 45.000 0.00 0.00 38.00 3.06
2388 4720 2.779755 TTGCTCCGTATGTGGTCATT 57.220 45.000 0.00 0.00 35.70 2.57
2389 4721 2.779755 TGCTCCGTATGTGGTCATTT 57.220 45.000 0.00 0.00 35.70 2.32
2390 4722 2.355197 TGCTCCGTATGTGGTCATTTG 58.645 47.619 0.00 0.00 35.70 2.32
2391 4723 2.290008 TGCTCCGTATGTGGTCATTTGT 60.290 45.455 0.00 0.00 35.70 2.83
2392 4724 2.747446 GCTCCGTATGTGGTCATTTGTT 59.253 45.455 0.00 0.00 35.70 2.83
2393 4725 3.426159 GCTCCGTATGTGGTCATTTGTTG 60.426 47.826 0.00 0.00 35.70 3.33
2394 4726 3.078097 TCCGTATGTGGTCATTTGTTGG 58.922 45.455 0.00 0.00 35.70 3.77
2395 4727 3.078097 CCGTATGTGGTCATTTGTTGGA 58.922 45.455 0.00 0.00 35.70 3.53
2396 4728 3.504134 CCGTATGTGGTCATTTGTTGGAA 59.496 43.478 0.00 0.00 35.70 3.53
2397 4729 4.022762 CCGTATGTGGTCATTTGTTGGAAA 60.023 41.667 0.00 0.00 35.70 3.13
2398 4730 5.336372 CCGTATGTGGTCATTTGTTGGAAAT 60.336 40.000 0.00 0.00 35.70 2.17
2399 4731 5.799936 CGTATGTGGTCATTTGTTGGAAATC 59.200 40.000 0.00 0.00 35.70 2.17
2400 4732 6.349280 CGTATGTGGTCATTTGTTGGAAATCT 60.349 38.462 0.00 0.00 35.70 2.40
2401 4733 5.452078 TGTGGTCATTTGTTGGAAATCTC 57.548 39.130 0.00 0.00 0.00 2.75
2402 4734 5.139727 TGTGGTCATTTGTTGGAAATCTCT 58.860 37.500 0.00 0.00 0.00 3.10
2403 4735 6.303054 TGTGGTCATTTGTTGGAAATCTCTA 58.697 36.000 0.00 0.00 0.00 2.43
2404 4736 6.775142 TGTGGTCATTTGTTGGAAATCTCTAA 59.225 34.615 0.00 0.00 0.00 2.10
2405 4737 7.286546 TGTGGTCATTTGTTGGAAATCTCTAAA 59.713 33.333 0.00 0.00 0.00 1.85
2406 4738 8.141268 GTGGTCATTTGTTGGAAATCTCTAAAA 58.859 33.333 0.00 0.00 0.00 1.52
2407 4739 8.700051 TGGTCATTTGTTGGAAATCTCTAAAAA 58.300 29.630 0.00 0.00 0.00 1.94
2408 4740 9.196552 GGTCATTTGTTGGAAATCTCTAAAAAG 57.803 33.333 0.00 0.00 0.00 2.27
2409 4741 9.965824 GTCATTTGTTGGAAATCTCTAAAAAGA 57.034 29.630 0.00 0.00 0.00 2.52
2410 4742 9.965824 TCATTTGTTGGAAATCTCTAAAAAGAC 57.034 29.630 0.00 0.00 0.00 3.01
2411 4743 9.196552 CATTTGTTGGAAATCTCTAAAAAGACC 57.803 33.333 0.00 0.00 0.00 3.85
2412 4744 8.533569 TTTGTTGGAAATCTCTAAAAAGACCT 57.466 30.769 0.00 0.00 0.00 3.85
2413 4745 9.635404 TTTGTTGGAAATCTCTAAAAAGACCTA 57.365 29.630 0.00 0.00 0.00 3.08
2414 4746 9.807921 TTGTTGGAAATCTCTAAAAAGACCTAT 57.192 29.630 0.00 0.00 0.00 2.57
2429 4761 8.959705 AAAAGACCTATATTTAGAAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2430 4762 6.667558 AGACCTATATTTAGAAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2431 4763 6.379579 AGACCTATATTTAGAAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2432 4764 6.494146 AGACCTATATTTAGAAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2433 4765 6.141790 ACCTATATTTAGAAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2434 4766 7.300658 ACCTATATTTAGAAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2435 4767 7.450944 ACCTATATTTAGAAACGGAGGGAGTAG 59.549 40.741 0.00 0.00 0.00 2.57
2436 4768 7.450944 CCTATATTTAGAAACGGAGGGAGTAGT 59.549 40.741 0.00 0.00 0.00 2.73
2437 4769 9.512588 CTATATTTAGAAACGGAGGGAGTAGTA 57.487 37.037 0.00 0.00 0.00 1.82
2438 4770 6.712179 ATTTAGAAACGGAGGGAGTAGTAG 57.288 41.667 0.00 0.00 0.00 2.57
2439 4771 2.377073 AGAAACGGAGGGAGTAGTAGC 58.623 52.381 0.00 0.00 0.00 3.58
2440 4772 2.097825 GAAACGGAGGGAGTAGTAGCA 58.902 52.381 0.00 0.00 0.00 3.49
2441 4773 2.456073 AACGGAGGGAGTAGTAGCAT 57.544 50.000 0.00 0.00 0.00 3.79
2442 4774 3.589951 AACGGAGGGAGTAGTAGCATA 57.410 47.619 0.00 0.00 0.00 3.14
2443 4775 3.589951 ACGGAGGGAGTAGTAGCATAA 57.410 47.619 0.00 0.00 0.00 1.90
2444 4776 3.220940 ACGGAGGGAGTAGTAGCATAAC 58.779 50.000 0.00 0.00 0.00 1.89
2445 4777 3.220110 CGGAGGGAGTAGTAGCATAACA 58.780 50.000 0.00 0.00 0.00 2.41
2446 4778 3.827302 CGGAGGGAGTAGTAGCATAACAT 59.173 47.826 0.00 0.00 0.00 2.71
2447 4779 4.281182 CGGAGGGAGTAGTAGCATAACATT 59.719 45.833 0.00 0.00 0.00 2.71
2448 4780 5.221461 CGGAGGGAGTAGTAGCATAACATTT 60.221 44.000 0.00 0.00 0.00 2.32
2449 4781 6.015688 CGGAGGGAGTAGTAGCATAACATTTA 60.016 42.308 0.00 0.00 0.00 1.40
2450 4782 7.309867 CGGAGGGAGTAGTAGCATAACATTTAT 60.310 40.741 0.00 0.00 0.00 1.40
2451 4783 8.376270 GGAGGGAGTAGTAGCATAACATTTATT 58.624 37.037 0.00 0.00 0.00 1.40
2473 4805 7.986085 ATTATGTTACGGTATCTACCTACGT 57.014 36.000 4.93 0.00 44.25 3.57
2474 4806 7.801716 TTATGTTACGGTATCTACCTACGTT 57.198 36.000 0.00 0.00 44.25 3.99
2475 4807 8.896320 TTATGTTACGGTATCTACCTACGTTA 57.104 34.615 0.00 0.00 44.25 3.18
2476 4808 6.598753 TGTTACGGTATCTACCTACGTTAC 57.401 41.667 0.00 0.00 44.25 2.50
2477 4809 6.346096 TGTTACGGTATCTACCTACGTTACT 58.654 40.000 0.00 0.00 44.25 2.24
2478 4810 7.494211 TGTTACGGTATCTACCTACGTTACTA 58.506 38.462 0.00 0.00 44.25 1.82
2479 4811 8.148351 TGTTACGGTATCTACCTACGTTACTAT 58.852 37.037 0.00 0.00 44.25 2.12
2480 4812 8.436200 GTTACGGTATCTACCTACGTTACTATG 58.564 40.741 0.00 0.00 44.25 2.23
2481 4813 6.759272 ACGGTATCTACCTACGTTACTATGA 58.241 40.000 0.00 0.00 44.25 2.15
2482 4814 6.647067 ACGGTATCTACCTACGTTACTATGAC 59.353 42.308 0.00 0.00 44.25 3.06
2483 4815 6.091441 CGGTATCTACCTACGTTACTATGACC 59.909 46.154 0.00 0.00 44.25 4.02
2484 4816 6.372937 GGTATCTACCTACGTTACTATGACCC 59.627 46.154 0.00 0.00 43.10 4.46
2485 4817 5.636903 TCTACCTACGTTACTATGACCCT 57.363 43.478 0.00 0.00 0.00 4.34
2486 4818 5.615289 TCTACCTACGTTACTATGACCCTC 58.385 45.833 0.00 0.00 0.00 4.30
2487 4819 4.516652 ACCTACGTTACTATGACCCTCT 57.483 45.455 0.00 0.00 0.00 3.69
2488 4820 4.459330 ACCTACGTTACTATGACCCTCTC 58.541 47.826 0.00 0.00 0.00 3.20
2489 4821 4.165758 ACCTACGTTACTATGACCCTCTCT 59.834 45.833 0.00 0.00 0.00 3.10
2490 4822 4.756135 CCTACGTTACTATGACCCTCTCTC 59.244 50.000 0.00 0.00 0.00 3.20
2491 4823 4.506937 ACGTTACTATGACCCTCTCTCT 57.493 45.455 0.00 0.00 0.00 3.10
2492 4824 4.453751 ACGTTACTATGACCCTCTCTCTC 58.546 47.826 0.00 0.00 0.00 3.20
2493 4825 4.164604 ACGTTACTATGACCCTCTCTCTCT 59.835 45.833 0.00 0.00 0.00 3.10
2494 4826 5.127491 CGTTACTATGACCCTCTCTCTCTT 58.873 45.833 0.00 0.00 0.00 2.85
2495 4827 5.237779 CGTTACTATGACCCTCTCTCTCTTC 59.762 48.000 0.00 0.00 0.00 2.87
2496 4828 6.362248 GTTACTATGACCCTCTCTCTCTTCT 58.638 44.000 0.00 0.00 0.00 2.85
2497 4829 5.466127 ACTATGACCCTCTCTCTCTTCTT 57.534 43.478 0.00 0.00 0.00 2.52
2498 4830 5.837829 ACTATGACCCTCTCTCTCTTCTTT 58.162 41.667 0.00 0.00 0.00 2.52
2499 4831 6.975949 ACTATGACCCTCTCTCTCTTCTTTA 58.024 40.000 0.00 0.00 0.00 1.85
2500 4832 7.415086 ACTATGACCCTCTCTCTCTTCTTTAA 58.585 38.462 0.00 0.00 0.00 1.52
2501 4833 8.065007 ACTATGACCCTCTCTCTCTTCTTTAAT 58.935 37.037 0.00 0.00 0.00 1.40
2502 4834 7.747809 ATGACCCTCTCTCTCTTCTTTAATT 57.252 36.000 0.00 0.00 0.00 1.40
2503 4835 7.560796 TGACCCTCTCTCTCTTCTTTAATTT 57.439 36.000 0.00 0.00 0.00 1.82
2504 4836 7.616313 TGACCCTCTCTCTCTTCTTTAATTTC 58.384 38.462 0.00 0.00 0.00 2.17
2505 4837 6.953101 ACCCTCTCTCTCTTCTTTAATTTCC 58.047 40.000 0.00 0.00 0.00 3.13
2506 4838 6.733334 ACCCTCTCTCTCTTCTTTAATTTCCT 59.267 38.462 0.00 0.00 0.00 3.36
2507 4839 7.047271 CCCTCTCTCTCTTCTTTAATTTCCTG 58.953 42.308 0.00 0.00 0.00 3.86
2508 4840 6.538381 CCTCTCTCTCTTCTTTAATTTCCTGC 59.462 42.308 0.00 0.00 0.00 4.85
2509 4841 6.410540 TCTCTCTCTTCTTTAATTTCCTGCC 58.589 40.000 0.00 0.00 0.00 4.85
2510 4842 6.013379 TCTCTCTCTTCTTTAATTTCCTGCCA 60.013 38.462 0.00 0.00 0.00 4.92
2511 4843 5.940470 TCTCTCTTCTTTAATTTCCTGCCAC 59.060 40.000 0.00 0.00 0.00 5.01
2512 4844 4.695455 TCTCTTCTTTAATTTCCTGCCACG 59.305 41.667 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.184287 GGGATCCAAAACAAATTTCTACCGA 59.816 40.000 15.23 0.00 0.00 4.69
43 44 6.322712 GGTTACATAGAGGATATAGAGCCTGG 59.677 46.154 0.00 0.00 43.32 4.45
129 134 3.063861 GCGTCAAACACATCTATGCATGA 59.936 43.478 10.16 5.36 0.00 3.07
185 191 7.312657 TGCATGTGTTTGCTTTTTAAATGAA 57.687 28.000 0.00 0.00 43.18 2.57
256 262 5.419788 TGCTACATAGAGACCTTTAACGGAA 59.580 40.000 4.76 0.00 0.00 4.30
262 268 7.253905 AGGTTTTGCTACATAGAGACCTTTA 57.746 36.000 0.00 0.00 0.00 1.85
594 1233 4.702131 AGATCCAAGTGTCCAAAGCATTAC 59.298 41.667 0.00 0.00 0.00 1.89
678 1332 1.223187 TTTCACGCGTTCCTTTCCTC 58.777 50.000 10.22 0.00 0.00 3.71
731 1385 4.543590 CCTGTACAGGCTAATAGGATGG 57.456 50.000 28.48 1.59 42.44 3.51
744 1398 1.463444 GCAAAACGTAGGCCTGTACAG 59.537 52.381 17.99 16.34 0.00 2.74
745 1399 1.071071 AGCAAAACGTAGGCCTGTACA 59.929 47.619 17.99 0.00 0.00 2.90
746 1400 1.804601 AGCAAAACGTAGGCCTGTAC 58.195 50.000 17.99 5.36 0.00 2.90
747 1401 2.147958 CAAGCAAAACGTAGGCCTGTA 58.852 47.619 17.99 0.00 0.00 2.74
748 1402 0.951558 CAAGCAAAACGTAGGCCTGT 59.048 50.000 17.99 1.70 0.00 4.00
749 1403 0.951558 ACAAGCAAAACGTAGGCCTG 59.048 50.000 17.99 0.87 0.00 4.85
750 1404 0.951558 CACAAGCAAAACGTAGGCCT 59.048 50.000 11.78 11.78 0.00 5.19
751 1405 0.666374 ACACAAGCAAAACGTAGGCC 59.334 50.000 0.00 0.00 0.00 5.19
752 1406 2.381589 GAACACAAGCAAAACGTAGGC 58.618 47.619 0.00 0.00 0.00 3.93
753 1407 2.287368 GGGAACACAAGCAAAACGTAGG 60.287 50.000 0.00 0.00 0.00 3.18
754 1408 2.356382 TGGGAACACAAGCAAAACGTAG 59.644 45.455 0.00 0.00 33.40 3.51
755 1409 2.366533 TGGGAACACAAGCAAAACGTA 58.633 42.857 0.00 0.00 33.40 3.57
756 1410 1.178276 TGGGAACACAAGCAAAACGT 58.822 45.000 0.00 0.00 33.40 3.99
779 2970 4.703645 TTTTGGACGTTGAATGTTGTGA 57.296 36.364 0.00 0.00 0.00 3.58
792 3076 2.811431 TGTACCTGCTTGATTTTGGACG 59.189 45.455 0.00 0.00 0.00 4.79
828 3114 0.028902 GAAACGTGTGAGGTTGGTGC 59.971 55.000 0.00 0.00 0.00 5.01
871 3157 8.813951 GGTCCTATTTATACTGTACAGGCTAAT 58.186 37.037 26.12 19.29 0.00 1.73
872 3158 7.234166 GGGTCCTATTTATACTGTACAGGCTAA 59.766 40.741 26.12 18.53 0.00 3.09
873 3159 6.723052 GGGTCCTATTTATACTGTACAGGCTA 59.277 42.308 26.12 14.02 0.00 3.93
874 3160 5.543020 GGGTCCTATTTATACTGTACAGGCT 59.457 44.000 26.12 15.00 0.00 4.58
875 3161 5.566230 CGGGTCCTATTTATACTGTACAGGC 60.566 48.000 26.12 0.00 0.00 4.85
876 3162 5.771666 TCGGGTCCTATTTATACTGTACAGG 59.228 44.000 26.12 6.74 0.00 4.00
877 3163 6.263842 TGTCGGGTCCTATTTATACTGTACAG 59.736 42.308 21.44 21.44 0.00 2.74
878 3164 6.039717 GTGTCGGGTCCTATTTATACTGTACA 59.960 42.308 0.00 0.00 0.00 2.90
987 3292 0.037975 CAGCCATTGCAGTTGGAACC 60.038 55.000 19.02 4.40 41.13 3.62
1281 3587 3.936203 GTGCCGGTGGTGGTGAGA 61.936 66.667 1.90 0.00 0.00 3.27
1437 3746 2.672996 ACATTGGTGGCAGCGGAC 60.673 61.111 12.58 0.00 0.00 4.79
1624 3936 4.717233 TGAATCAGCAAAACACACAACT 57.283 36.364 0.00 0.00 0.00 3.16
1628 3941 4.148696 CCGAAATGAATCAGCAAAACACAC 59.851 41.667 0.00 0.00 0.00 3.82
1667 3985 7.781056 ACAAATGTTGTACAAGACCAAAAGAT 58.219 30.769 8.98 0.00 43.27 2.40
1680 3998 4.961551 CGTGTGTCAAGACAAATGTTGTAC 59.038 41.667 4.20 0.00 45.52 2.90
1917 4241 2.017049 GAACATGTATGGCACTCCACC 58.983 52.381 0.00 0.00 46.92 4.61
1981 4307 1.529226 CGACTCCGATGGCTCTCTAT 58.471 55.000 0.00 0.00 38.22 1.98
1982 4308 0.535328 CCGACTCCGATGGCTCTCTA 60.535 60.000 0.00 0.00 38.22 2.43
2057 4389 4.553323 CAGCAGAAATTTTGGTCCTTCAG 58.447 43.478 0.00 0.00 0.00 3.02
2090 4422 5.184287 CCAAGGTGTTTTTATTACGGTGGAT 59.816 40.000 0.00 0.00 0.00 3.41
2096 4428 3.494232 CGCCCAAGGTGTTTTTATTACG 58.506 45.455 0.00 0.00 0.00 3.18
2101 4433 1.271102 GATGCGCCCAAGGTGTTTTTA 59.729 47.619 4.18 0.00 35.34 1.52
2104 4436 2.275380 GGATGCGCCCAAGGTGTTT 61.275 57.895 4.18 0.00 35.34 2.83
2106 4438 3.210012 AAGGATGCGCCCAAGGTGT 62.210 57.895 4.18 0.00 37.37 4.16
2107 4439 2.361610 AAGGATGCGCCCAAGGTG 60.362 61.111 4.18 0.00 37.37 4.00
2108 4440 2.044946 GAAGGATGCGCCCAAGGT 60.045 61.111 4.18 0.00 37.37 3.50
2109 4441 3.204827 CGAAGGATGCGCCCAAGG 61.205 66.667 4.18 0.00 37.37 3.61
2122 4454 0.179000 AGCCTTACCTGATGCCGAAG 59.821 55.000 0.00 0.00 0.00 3.79
2123 4455 0.107703 CAGCCTTACCTGATGCCGAA 60.108 55.000 0.00 0.00 34.77 4.30
2124 4456 1.522092 CAGCCTTACCTGATGCCGA 59.478 57.895 0.00 0.00 34.77 5.54
2125 4457 1.524621 CCAGCCTTACCTGATGCCG 60.525 63.158 0.00 0.00 34.77 5.69
2126 4458 0.464554 GACCAGCCTTACCTGATGCC 60.465 60.000 0.00 0.00 34.77 4.40
2127 4459 0.253044 TGACCAGCCTTACCTGATGC 59.747 55.000 0.00 0.00 34.77 3.91
2128 4460 3.389329 ACTATGACCAGCCTTACCTGATG 59.611 47.826 0.00 0.00 34.77 3.07
2129 4461 3.389329 CACTATGACCAGCCTTACCTGAT 59.611 47.826 0.00 0.00 34.77 2.90
2130 4462 2.766263 CACTATGACCAGCCTTACCTGA 59.234 50.000 0.00 0.00 34.77 3.86
2131 4463 2.158900 CCACTATGACCAGCCTTACCTG 60.159 54.545 0.00 0.00 0.00 4.00
2132 4464 2.119495 CCACTATGACCAGCCTTACCT 58.881 52.381 0.00 0.00 0.00 3.08
2133 4465 1.838077 ACCACTATGACCAGCCTTACC 59.162 52.381 0.00 0.00 0.00 2.85
2134 4466 2.500098 TCACCACTATGACCAGCCTTAC 59.500 50.000 0.00 0.00 0.00 2.34
2135 4467 2.766263 CTCACCACTATGACCAGCCTTA 59.234 50.000 0.00 0.00 0.00 2.69
2136 4468 1.556911 CTCACCACTATGACCAGCCTT 59.443 52.381 0.00 0.00 0.00 4.35
2137 4469 1.198713 CTCACCACTATGACCAGCCT 58.801 55.000 0.00 0.00 0.00 4.58
2138 4470 0.905357 ACTCACCACTATGACCAGCC 59.095 55.000 0.00 0.00 0.00 4.85
2139 4471 3.056107 TGTTACTCACCACTATGACCAGC 60.056 47.826 0.00 0.00 0.00 4.85
2140 4472 4.801330 TGTTACTCACCACTATGACCAG 57.199 45.455 0.00 0.00 0.00 4.00
2141 4473 7.783119 AGTATATGTTACTCACCACTATGACCA 59.217 37.037 0.00 0.00 0.00 4.02
2142 4474 8.179509 AGTATATGTTACTCACCACTATGACC 57.820 38.462 0.00 0.00 0.00 4.02
2235 4567 9.797642 TGCATGACAATAAATAAGACCATCTAT 57.202 29.630 0.00 0.00 0.00 1.98
2236 4568 9.797642 ATGCATGACAATAAATAAGACCATCTA 57.202 29.630 0.00 0.00 0.00 1.98
2237 4569 8.573885 CATGCATGACAATAAATAAGACCATCT 58.426 33.333 22.59 0.00 0.00 2.90
2238 4570 8.570488 TCATGCATGACAATAAATAAGACCATC 58.430 33.333 25.42 0.00 0.00 3.51
2239 4571 8.467963 TCATGCATGACAATAAATAAGACCAT 57.532 30.769 25.42 0.00 0.00 3.55
2240 4572 7.878547 TCATGCATGACAATAAATAAGACCA 57.121 32.000 25.42 0.00 0.00 4.02
2255 4587 2.773661 AGGGAGTATGTGTCATGCATGA 59.226 45.455 25.42 25.42 0.00 3.07
2256 4588 3.136763 GAGGGAGTATGTGTCATGCATG 58.863 50.000 21.07 21.07 0.00 4.06
2257 4589 2.105477 GGAGGGAGTATGTGTCATGCAT 59.895 50.000 0.00 0.00 0.00 3.96
2258 4590 1.486310 GGAGGGAGTATGTGTCATGCA 59.514 52.381 0.00 0.00 0.00 3.96
2259 4591 1.539065 CGGAGGGAGTATGTGTCATGC 60.539 57.143 0.00 0.00 0.00 4.06
2260 4592 1.757118 ACGGAGGGAGTATGTGTCATG 59.243 52.381 0.00 0.00 0.00 3.07
2261 4593 2.160721 ACGGAGGGAGTATGTGTCAT 57.839 50.000 0.00 0.00 0.00 3.06
2262 4594 1.822990 GAACGGAGGGAGTATGTGTCA 59.177 52.381 0.00 0.00 0.00 3.58
2263 4595 1.136500 GGAACGGAGGGAGTATGTGTC 59.864 57.143 0.00 0.00 0.00 3.67
2264 4596 1.192428 GGAACGGAGGGAGTATGTGT 58.808 55.000 0.00 0.00 0.00 3.72
2265 4597 1.486211 AGGAACGGAGGGAGTATGTG 58.514 55.000 0.00 0.00 0.00 3.21
2266 4598 3.393426 TTAGGAACGGAGGGAGTATGT 57.607 47.619 0.00 0.00 0.00 2.29
2267 4599 4.957684 ATTTAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
2268 4600 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
2269 4601 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2270 4602 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2271 4603 6.295180 GGACTTATATTTAGGAACGGAGGGAG 60.295 46.154 0.00 0.00 0.00 4.30
2272 4604 5.541484 GGACTTATATTTAGGAACGGAGGGA 59.459 44.000 0.00 0.00 0.00 4.20
2273 4605 5.543020 AGGACTTATATTTAGGAACGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
2274 4606 6.667558 AGGACTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
2275 4607 8.959705 AAAAGGACTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
2307 4639 9.693739 ACATCCATATGTTGTAGTCCATTTAAA 57.306 29.630 1.24 0.00 44.07 1.52
2310 4642 9.288576 CATACATCCATATGTTGTAGTCCATTT 57.711 33.333 16.38 1.83 44.07 2.32
2311 4643 8.439971 ACATACATCCATATGTTGTAGTCCATT 58.560 33.333 16.38 2.34 44.07 3.16
2312 4644 7.977818 ACATACATCCATATGTTGTAGTCCAT 58.022 34.615 16.38 3.57 44.07 3.41
2313 4645 7.373617 ACATACATCCATATGTTGTAGTCCA 57.626 36.000 16.38 1.84 44.07 4.02
2314 4646 8.803235 TCTACATACATCCATATGTTGTAGTCC 58.197 37.037 22.56 0.00 44.07 3.85
2315 4647 9.627395 GTCTACATACATCCATATGTTGTAGTC 57.373 37.037 22.56 18.41 44.07 2.59
2316 4648 9.143155 TGTCTACATACATCCATATGTTGTAGT 57.857 33.333 22.56 15.48 44.07 2.73
2352 4684 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2353 4685 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2354 4686 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2355 4687 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2356 4688 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2357 4689 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2358 4690 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2359 4691 4.154015 CACATACGGAGCAAAATGAGTGAA 59.846 41.667 0.00 0.00 0.00 3.18
2360 4692 3.684305 CACATACGGAGCAAAATGAGTGA 59.316 43.478 0.00 0.00 0.00 3.41
2361 4693 3.181507 CCACATACGGAGCAAAATGAGTG 60.182 47.826 0.00 0.00 0.00 3.51
2362 4694 3.009723 CCACATACGGAGCAAAATGAGT 58.990 45.455 0.00 0.00 0.00 3.41
2363 4695 3.009723 ACCACATACGGAGCAAAATGAG 58.990 45.455 0.00 0.00 0.00 2.90
2364 4696 3.006940 GACCACATACGGAGCAAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
2365 4697 2.746904 TGACCACATACGGAGCAAAATG 59.253 45.455 0.00 0.00 0.00 2.32
2366 4698 3.066291 TGACCACATACGGAGCAAAAT 57.934 42.857 0.00 0.00 0.00 1.82
2367 4699 2.552599 TGACCACATACGGAGCAAAA 57.447 45.000 0.00 0.00 0.00 2.44
2368 4700 2.779755 ATGACCACATACGGAGCAAA 57.220 45.000 0.00 0.00 34.71 3.68
2369 4701 2.746904 CAAATGACCACATACGGAGCAA 59.253 45.455 0.00 0.00 35.50 3.91
2370 4702 2.290008 ACAAATGACCACATACGGAGCA 60.290 45.455 0.00 0.00 35.50 4.26
2371 4703 2.356135 ACAAATGACCACATACGGAGC 58.644 47.619 0.00 0.00 35.50 4.70
2372 4704 3.126858 CCAACAAATGACCACATACGGAG 59.873 47.826 0.00 0.00 35.50 4.63
2373 4705 3.078097 CCAACAAATGACCACATACGGA 58.922 45.455 0.00 0.00 35.50 4.69
2374 4706 3.078097 TCCAACAAATGACCACATACGG 58.922 45.455 0.00 0.00 35.50 4.02
2375 4707 4.757799 TTCCAACAAATGACCACATACG 57.242 40.909 0.00 0.00 35.50 3.06
2376 4708 6.924111 AGATTTCCAACAAATGACCACATAC 58.076 36.000 0.00 0.00 35.50 2.39
2377 4709 6.947733 AGAGATTTCCAACAAATGACCACATA 59.052 34.615 0.00 0.00 35.50 2.29
2378 4710 5.776716 AGAGATTTCCAACAAATGACCACAT 59.223 36.000 0.00 0.00 38.50 3.21
2379 4711 5.139727 AGAGATTTCCAACAAATGACCACA 58.860 37.500 0.00 0.00 0.00 4.17
2380 4712 5.712152 AGAGATTTCCAACAAATGACCAC 57.288 39.130 0.00 0.00 0.00 4.16
2381 4713 7.831691 TTTAGAGATTTCCAACAAATGACCA 57.168 32.000 0.00 0.00 0.00 4.02
2382 4714 9.196552 CTTTTTAGAGATTTCCAACAAATGACC 57.803 33.333 0.00 0.00 0.00 4.02
2383 4715 9.965824 TCTTTTTAGAGATTTCCAACAAATGAC 57.034 29.630 0.00 0.00 0.00 3.06
2384 4716 9.965824 GTCTTTTTAGAGATTTCCAACAAATGA 57.034 29.630 0.00 0.00 0.00 2.57
2385 4717 9.196552 GGTCTTTTTAGAGATTTCCAACAAATG 57.803 33.333 0.00 0.00 0.00 2.32
2386 4718 9.147732 AGGTCTTTTTAGAGATTTCCAACAAAT 57.852 29.630 0.00 0.00 0.00 2.32
2387 4719 8.533569 AGGTCTTTTTAGAGATTTCCAACAAA 57.466 30.769 0.00 0.00 0.00 2.83
2388 4720 9.807921 ATAGGTCTTTTTAGAGATTTCCAACAA 57.192 29.630 0.00 0.00 0.00 2.83
2403 4735 9.392259 CCTCCGTTTCTAAATATAGGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2404 4736 7.991460 CCCTCCGTTTCTAAATATAGGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2405 4737 7.346436 TCCCTCCGTTTCTAAATATAGGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2406 4738 6.842807 TCCCTCCGTTTCTAAATATAGGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2407 4739 6.379579 TCCCTCCGTTTCTAAATATAGGTCT 58.620 40.000 0.00 0.00 0.00 3.85
2408 4740 6.267242 ACTCCCTCCGTTTCTAAATATAGGTC 59.733 42.308 0.00 0.00 0.00 3.85
2409 4741 6.141790 ACTCCCTCCGTTTCTAAATATAGGT 58.858 40.000 0.00 0.00 0.00 3.08
2410 4742 6.667558 ACTCCCTCCGTTTCTAAATATAGG 57.332 41.667 0.00 0.00 0.00 2.57
2411 4743 8.406730 ACTACTCCCTCCGTTTCTAAATATAG 57.593 38.462 0.00 0.00 0.00 1.31
2412 4744 9.512588 CTACTACTCCCTCCGTTTCTAAATATA 57.487 37.037 0.00 0.00 0.00 0.86
2413 4745 7.039853 GCTACTACTCCCTCCGTTTCTAAATAT 60.040 40.741 0.00 0.00 0.00 1.28
2414 4746 6.264067 GCTACTACTCCCTCCGTTTCTAAATA 59.736 42.308 0.00 0.00 0.00 1.40
2415 4747 5.068855 GCTACTACTCCCTCCGTTTCTAAAT 59.931 44.000 0.00 0.00 0.00 1.40
2416 4748 4.400567 GCTACTACTCCCTCCGTTTCTAAA 59.599 45.833 0.00 0.00 0.00 1.85
2417 4749 3.950395 GCTACTACTCCCTCCGTTTCTAA 59.050 47.826 0.00 0.00 0.00 2.10
2418 4750 3.054139 TGCTACTACTCCCTCCGTTTCTA 60.054 47.826 0.00 0.00 0.00 2.10
2419 4751 2.291411 TGCTACTACTCCCTCCGTTTCT 60.291 50.000 0.00 0.00 0.00 2.52
2420 4752 2.097825 TGCTACTACTCCCTCCGTTTC 58.902 52.381 0.00 0.00 0.00 2.78
2421 4753 2.226962 TGCTACTACTCCCTCCGTTT 57.773 50.000 0.00 0.00 0.00 3.60
2422 4754 2.456073 ATGCTACTACTCCCTCCGTT 57.544 50.000 0.00 0.00 0.00 4.44
2423 4755 3.220940 GTTATGCTACTACTCCCTCCGT 58.779 50.000 0.00 0.00 0.00 4.69
2424 4756 3.220110 TGTTATGCTACTACTCCCTCCG 58.780 50.000 0.00 0.00 0.00 4.63
2425 4757 5.810080 AATGTTATGCTACTACTCCCTCC 57.190 43.478 0.00 0.00 0.00 4.30
2459 4791 6.372937 GGGTCATAGTAACGTAGGTAGATACC 59.627 46.154 0.43 0.43 46.82 2.73
2460 4792 7.164803 AGGGTCATAGTAACGTAGGTAGATAC 58.835 42.308 0.00 0.00 0.00 2.24
2461 4793 7.236432 AGAGGGTCATAGTAACGTAGGTAGATA 59.764 40.741 0.00 0.00 0.00 1.98
2462 4794 6.044171 AGAGGGTCATAGTAACGTAGGTAGAT 59.956 42.308 0.00 0.00 0.00 1.98
2463 4795 5.367937 AGAGGGTCATAGTAACGTAGGTAGA 59.632 44.000 0.00 0.00 0.00 2.59
2464 4796 5.619220 AGAGGGTCATAGTAACGTAGGTAG 58.381 45.833 0.00 0.00 0.00 3.18
2465 4797 5.367937 AGAGAGGGTCATAGTAACGTAGGTA 59.632 44.000 0.00 0.00 0.00 3.08
2466 4798 4.165758 AGAGAGGGTCATAGTAACGTAGGT 59.834 45.833 0.00 0.00 0.00 3.08
2467 4799 4.716794 AGAGAGGGTCATAGTAACGTAGG 58.283 47.826 0.00 0.00 0.00 3.18
2468 4800 5.613329 AGAGAGAGGGTCATAGTAACGTAG 58.387 45.833 0.00 0.00 0.00 3.51
2469 4801 5.366186 AGAGAGAGAGGGTCATAGTAACGTA 59.634 44.000 0.00 0.00 0.00 3.57
2470 4802 4.164604 AGAGAGAGAGGGTCATAGTAACGT 59.835 45.833 0.00 0.00 0.00 3.99
2471 4803 4.710324 AGAGAGAGAGGGTCATAGTAACG 58.290 47.826 0.00 0.00 0.00 3.18
2472 4804 6.362248 AGAAGAGAGAGAGGGTCATAGTAAC 58.638 44.000 0.00 0.00 0.00 2.50
2473 4805 6.584471 AGAAGAGAGAGAGGGTCATAGTAA 57.416 41.667 0.00 0.00 0.00 2.24
2474 4806 6.584471 AAGAAGAGAGAGAGGGTCATAGTA 57.416 41.667 0.00 0.00 0.00 1.82
2475 4807 5.466127 AAGAAGAGAGAGAGGGTCATAGT 57.534 43.478 0.00 0.00 0.00 2.12
2476 4808 7.889873 TTAAAGAAGAGAGAGAGGGTCATAG 57.110 40.000 0.00 0.00 0.00 2.23
2477 4809 8.846423 AATTAAAGAAGAGAGAGAGGGTCATA 57.154 34.615 0.00 0.00 0.00 2.15
2478 4810 7.747809 AATTAAAGAAGAGAGAGAGGGTCAT 57.252 36.000 0.00 0.00 0.00 3.06
2479 4811 7.310734 GGAAATTAAAGAAGAGAGAGAGGGTCA 60.311 40.741 0.00 0.00 0.00 4.02
2480 4812 7.045416 GGAAATTAAAGAAGAGAGAGAGGGTC 58.955 42.308 0.00 0.00 0.00 4.46
2481 4813 6.733334 AGGAAATTAAAGAAGAGAGAGAGGGT 59.267 38.462 0.00 0.00 0.00 4.34
2482 4814 7.047271 CAGGAAATTAAAGAAGAGAGAGAGGG 58.953 42.308 0.00 0.00 0.00 4.30
2483 4815 6.538381 GCAGGAAATTAAAGAAGAGAGAGAGG 59.462 42.308 0.00 0.00 0.00 3.69
2484 4816 6.538381 GGCAGGAAATTAAAGAAGAGAGAGAG 59.462 42.308 0.00 0.00 0.00 3.20
2485 4817 6.013379 TGGCAGGAAATTAAAGAAGAGAGAGA 60.013 38.462 0.00 0.00 0.00 3.10
2486 4818 6.093357 GTGGCAGGAAATTAAAGAAGAGAGAG 59.907 42.308 0.00 0.00 0.00 3.20
2487 4819 5.940470 GTGGCAGGAAATTAAAGAAGAGAGA 59.060 40.000 0.00 0.00 0.00 3.10
2488 4820 5.163814 CGTGGCAGGAAATTAAAGAAGAGAG 60.164 44.000 0.00 0.00 0.00 3.20
2489 4821 4.695455 CGTGGCAGGAAATTAAAGAAGAGA 59.305 41.667 0.00 0.00 0.00 3.10
2490 4822 4.974591 CGTGGCAGGAAATTAAAGAAGAG 58.025 43.478 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.