Multiple sequence alignment - TraesCS4A01G005200

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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 TraesCS4A01G005200 chr4A 100.000 2156 0 0 1 2156 3219212 3221367 0.000000e+00 3982.0
1 TraesCS4A01G005200 chr4A 100.000 141 0 0 2455 2595 3221666 3221806 7.120000e-66 261.0
2 TraesCS4A01G005200 chr4D 89.357 1663 114 32 1 1626 467999797 467998161 0.000000e+00 2032.0
3 TraesCS4A01G005200 chr4B 90.503 1074 57 22 589 1644 586331937 586330891 0.000000e+00 1376.0
4 TraesCS4A01G005200 chr4B 87.435 573 56 10 1 564 586332497 586331932 0.000000e+00 645.0
5 TraesCS4A01G005200 chr1D 85.319 361 40 9 1645 1993 370915120 370915479 6.830000e-96 361.0
6 TraesCS4A01G005200 chr1D 82.323 198 32 3 1645 1842 329670861 329670667 4.440000e-38 169.0
7 TraesCS4A01G005200 chr6D 84.848 363 42 9 1643 1993 89301371 89301010 1.140000e-93 353.0
8 TraesCS4A01G005200 chr6D 84.488 361 43 9 1645 1993 68091028 68091387 6.880000e-91 344.0
9 TraesCS4A01G005200 chr6D 94.118 51 2 1 2097 2146 68091490 68091540 2.770000e-10 76.8
10 TraesCS4A01G005200 chr3D 83.102 361 43 8 1645 1993 30945642 30945288 1.940000e-81 313.0
11 TraesCS4A01G005200 chr3D 79.585 289 52 5 1645 1931 595279543 595279826 1.570000e-47 200.0
12 TraesCS4A01G005200 chr3D 81.991 211 33 4 1644 1850 58539166 58538957 9.550000e-40 174.0
13 TraesCS4A01G005200 chr3D 92.308 39 3 0 244 282 57155229 57155267 3.610000e-04 56.5
14 TraesCS4A01G005200 chr2B 84.083 289 32 8 1645 1931 773077621 773077345 1.530000e-67 267.0
15 TraesCS4A01G005200 chr7D 80.072 276 48 5 1645 1918 634666337 634666067 5.660000e-47 198.0
16 TraesCS4A01G005200 chr7D 94.595 37 2 0 246 282 224474755 224474791 1.000000e-04 58.4
17 TraesCS4A01G005200 chr7D 100.000 30 0 0 253 282 588679997 588679968 3.610000e-04 56.5
18 TraesCS4A01G005200 chr6A 80.741 135 23 3 1786 1919 231702256 231702124 4.570000e-18 102.0
19 TraesCS4A01G005200 chr2D 89.583 48 5 0 236 283 79877545 79877498 7.750000e-06 62.1
20 TraesCS4A01G005200 chr7A 94.595 37 2 0 246 282 237952433 237952469 1.000000e-04 58.4
21 TraesCS4A01G005200 chr7A 100.000 30 0 0 253 282 4762861 4762832 3.610000e-04 56.5
22 TraesCS4A01G005200 chr3B 100.000 30 0 0 253 282 671380770 671380741 3.610000e-04 56.5


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 TraesCS4A01G005200 chr4A 3219212 3221806 2594 False 2121.5 3982 100.000 1 2595 2 chr4A.!!$F1 2594
1 TraesCS4A01G005200 chr4D 467998161 467999797 1636 True 2032.0 2032 89.357 1 1626 1 chr4D.!!$R1 1625
2 TraesCS4A01G005200 chr4B 586330891 586332497 1606 True 1010.5 1376 88.969 1 1644 2 chr4B.!!$R1 1643
3 TraesCS4A01G005200 chr6D 68091028 68091540 512 False 210.4 344 89.303 1645 2146 2 chr6D.!!$F1 501

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
417 426 0.109504 GCGCAGATACCGGAGAGATC 60.11 60.0 9.46 5.34 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1843 0.31716 TGCCACGTCAGTCTAACTGG 59.683 55.0 7.21 0.0 45.94 4.0 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
36 37 1.001641 CACTGGCAAGGGAGGGAAG 60.002 63.158 0.00 0.00 0.00 3.46
42 44 1.990060 CAAGGGAGGGAAGAGCGGA 60.990 63.158 0.00 0.00 0.00 5.54
67 70 1.559682 GTGAGGGAGGGAATAGCAACA 59.440 52.381 0.00 0.00 0.00 3.33
69 72 0.919710 AGGGAGGGAATAGCAACACC 59.080 55.000 0.00 0.00 0.00 4.16
75 78 1.208776 GGGAATAGCAACACCGGTAGT 59.791 52.381 6.87 5.15 0.00 2.73
91 94 2.745281 GGTAGTGTGAAATAAGGCGCAA 59.255 45.455 10.83 0.00 0.00 4.85
128 131 2.584391 GGTGAAGGAGGCGTGAGGT 61.584 63.158 0.00 0.00 0.00 3.85
139 142 0.525029 GCGTGAGGTAGCGACTTACC 60.525 60.000 0.00 0.00 42.84 2.85
169 172 5.777732 AGGATAGGATAACTAGCTCCAACAG 59.222 44.000 0.00 0.00 38.16 3.16
183 186 9.499479 CTAGCTCCAACAGAATATTGTATGATT 57.501 33.333 0.00 0.00 0.00 2.57
325 334 2.130193 ACAGGGGAGTATCATGCACAT 58.870 47.619 0.00 0.00 36.25 3.21
326 335 2.158711 ACAGGGGAGTATCATGCACATG 60.159 50.000 4.18 4.18 40.09 3.21
327 336 1.422781 AGGGGAGTATCATGCACATGG 59.577 52.381 10.58 0.00 39.24 3.66
344 353 4.870426 CACATGGCACTATTCTACGAAACT 59.130 41.667 0.00 0.00 0.00 2.66
358 367 1.743394 CGAAACTTACCTCCCCAATGC 59.257 52.381 0.00 0.00 0.00 3.56
360 369 3.365472 GAAACTTACCTCCCCAATGCAT 58.635 45.455 0.00 0.00 0.00 3.96
364 373 3.785887 ACTTACCTCCCCAATGCATAAGA 59.214 43.478 0.00 0.00 0.00 2.10
394 403 7.488792 TCATACATTTCAGCAAAATTTCATCGG 59.511 33.333 0.00 0.00 35.32 4.18
398 407 2.161410 TCAGCAAAATTTCATCGGTCGG 59.839 45.455 0.00 0.00 0.00 4.79
399 408 1.135402 AGCAAAATTTCATCGGTCGGC 60.135 47.619 0.00 0.00 0.00 5.54
402 411 1.302383 AAATTTCATCGGTCGGCGCA 61.302 50.000 10.83 0.00 0.00 6.09
404 413 2.572095 ATTTCATCGGTCGGCGCAGA 62.572 55.000 10.83 8.36 0.00 4.26
413 422 3.592814 CGGCGCAGATACCGGAGA 61.593 66.667 9.46 0.00 45.74 3.71
417 426 0.109504 GCGCAGATACCGGAGAGATC 60.110 60.000 9.46 5.34 0.00 2.75
420 429 2.095466 CGCAGATACCGGAGAGATCTTC 60.095 54.545 9.46 4.34 0.00 2.87
421 430 2.230266 GCAGATACCGGAGAGATCTTCC 59.770 54.545 9.46 5.33 0.00 3.46
452 461 5.734855 AAATGCACGGTATCATACACTTC 57.265 39.130 0.00 0.00 0.00 3.01
463 472 7.011016 CGGTATCATACACTTCAGCAAAATGTA 59.989 37.037 0.00 0.00 0.00 2.29
468 477 5.689383 ACACTTCAGCAAAATGTAATCGT 57.311 34.783 0.00 0.00 0.00 3.73
479 488 4.778842 AATGTAATCGTTCGATGCAGAC 57.221 40.909 8.46 5.87 0.00 3.51
485 494 2.100631 GTTCGATGCAGACACCGGG 61.101 63.158 6.32 0.00 0.00 5.73
497 506 2.158519 AGACACCGGGGAGAATTTTTGT 60.159 45.455 12.96 0.00 0.00 2.83
498 507 2.626266 GACACCGGGGAGAATTTTTGTT 59.374 45.455 12.96 0.00 0.00 2.83
521 530 4.856487 TGAAAAAGAAACTTCAGCACGTTG 59.144 37.500 0.00 0.00 0.00 4.10
549 558 4.747108 CGCTGATTTCTTATCTACTGTGGG 59.253 45.833 0.00 0.00 0.00 4.61
590 599 6.042777 TGAATTATTGTAAGCGACAGGAGAG 58.957 40.000 0.00 0.00 39.88 3.20
593 602 1.905637 TGTAAGCGACAGGAGAGACA 58.094 50.000 0.00 0.00 32.86 3.41
594 603 1.540267 TGTAAGCGACAGGAGAGACAC 59.460 52.381 0.00 0.00 32.86 3.67
595 604 0.803117 TAAGCGACAGGAGAGACACG 59.197 55.000 0.00 0.00 0.00 4.49
597 606 1.154188 GCGACAGGAGAGACACGTC 60.154 63.158 0.00 0.00 0.00 4.34
601 611 0.315568 ACAGGAGAGACACGTCTTGC 59.684 55.000 0.38 0.00 40.61 4.01
617 627 5.116180 CGTCTTGCTCCCTATCACAATAAA 58.884 41.667 0.00 0.00 0.00 1.40
641 651 4.737855 AAGATAGCGTCCACATGTAAGT 57.262 40.909 0.00 0.00 0.00 2.24
658 668 3.870633 AAGTCGTGACTCATTAGGGTC 57.129 47.619 2.48 0.00 41.58 4.46
659 669 2.803956 AGTCGTGACTCATTAGGGTCA 58.196 47.619 0.00 0.00 36.92 4.02
660 670 3.366396 AGTCGTGACTCATTAGGGTCAT 58.634 45.455 1.08 0.00 43.07 3.06
661 671 3.381908 AGTCGTGACTCATTAGGGTCATC 59.618 47.826 1.08 0.00 43.07 2.92
662 672 3.381908 GTCGTGACTCATTAGGGTCATCT 59.618 47.826 1.08 0.00 43.07 2.90
669 679 6.841229 TGACTCATTAGGGTCATCTTATCTGT 59.159 38.462 0.00 0.00 37.52 3.41
676 686 6.597832 AGGGTCATCTTATCTGTACTATGC 57.402 41.667 0.00 0.00 0.00 3.14
707 717 0.869880 ACGGCGCTGCAAACTTTTTC 60.870 50.000 18.15 0.00 0.00 2.29
712 722 1.192980 CGCTGCAAACTTTTTCCATGC 59.807 47.619 0.00 0.00 37.52 4.06
823 840 4.363999 CGATGCCAACAAACCAAACTAAA 58.636 39.130 0.00 0.00 0.00 1.85
871 889 5.569441 CGCGTCTCTATATAACCATCAACAG 59.431 44.000 0.00 0.00 0.00 3.16
872 890 5.346281 GCGTCTCTATATAACCATCAACAGC 59.654 44.000 0.00 0.00 0.00 4.40
897 929 3.243636 GCCATACTTCTCCATTGCCATTG 60.244 47.826 0.00 0.00 0.00 2.82
898 930 3.956199 CCATACTTCTCCATTGCCATTGT 59.044 43.478 0.00 0.00 0.00 2.71
917 949 3.966154 TGTCGTTCTTCTCAGTTCTCAC 58.034 45.455 0.00 0.00 0.00 3.51
961 993 3.366440 AGGATCGAGCACGTATAAACC 57.634 47.619 1.84 0.00 40.69 3.27
978 1010 1.186200 ACCACGAGCAAGCATCTCTA 58.814 50.000 0.00 0.00 0.00 2.43
983 1015 4.398247 CACGAGCAAGCATCTCTAAAAAC 58.602 43.478 0.00 0.00 0.00 2.43
1017 1049 2.043227 GGGATGATTTCGAGGTCTCCT 58.957 52.381 12.63 0.00 36.03 3.69
1056 1088 3.560989 GGAGAGGCCCAGGATCAG 58.439 66.667 0.00 0.00 0.00 2.90
1057 1089 2.146061 GGAGAGGCCCAGGATCAGG 61.146 68.421 0.00 0.00 0.00 3.86
1214 1246 2.010582 GCTGCCGACCTACAGGAGAG 62.011 65.000 1.29 0.00 38.94 3.20
1249 1281 0.332972 ATTCCTGGGCCTTGAGTTCC 59.667 55.000 4.53 0.00 0.00 3.62
1334 1366 6.529220 AGTAAGAAAGATCAGATATGCACCC 58.471 40.000 0.00 0.00 0.00 4.61
1456 1488 1.078848 GTGCCGGTCTCAGCAGATT 60.079 57.895 1.90 0.00 40.28 2.40
1469 1501 1.227497 CAGATTGCGAGGGAGGAGC 60.227 63.158 0.00 0.00 0.00 4.70
1579 1611 3.883462 CACGCGAGGGTGCAAATA 58.117 55.556 15.93 0.00 34.15 1.40
1638 1676 1.595489 GCAGTGAGCAAGTGACAAACG 60.595 52.381 0.00 0.00 44.79 3.60
1654 1692 6.018180 GTGACAAACGAAGGAGAGTAAATTGT 60.018 38.462 0.00 0.00 0.00 2.71
1656 1694 7.384115 TGACAAACGAAGGAGAGTAAATTGTAG 59.616 37.037 0.00 0.00 0.00 2.74
1664 1702 9.232473 GAAGGAGAGTAAATTGTAGAAAACCAT 57.768 33.333 0.00 0.00 0.00 3.55
1667 1705 9.178758 GGAGAGTAAATTGTAGAAAACCATCAT 57.821 33.333 0.00 0.00 0.00 2.45
1686 1724 7.158021 CCATCATTTTAAAGGTTAGGTTTGCA 58.842 34.615 0.00 0.00 0.00 4.08
1725 1763 7.346751 ACATTTTCTCTACACAAAACACCAT 57.653 32.000 0.00 0.00 0.00 3.55
1745 1783 5.890334 CCATATCTTGCGTAATGGTTTTGT 58.110 37.500 0.00 0.00 35.23 2.83
1773 1811 1.661821 CGATCGGCGAATCTGACCC 60.662 63.158 15.93 0.00 44.57 4.46
1780 1818 2.706890 GGCGAATCTGACCCTGTTAAA 58.293 47.619 0.00 0.00 0.00 1.52
1797 1835 7.362056 CCCTGTTAAATGAGTTTATGACAGGTG 60.362 40.741 19.92 12.95 46.09 4.00
1804 1842 1.143329 TTTATGACAGGTGGGGCCCA 61.143 55.000 24.76 24.76 38.26 5.36
1813 1851 2.208640 TGGGGCCCACCAGTTAGA 59.791 61.111 24.76 0.00 42.91 2.10
1850 1888 4.630069 GCTTAACATCTCACATGTAACGGT 59.370 41.667 0.00 0.00 0.00 4.83
1853 1891 4.471904 ACATCTCACATGTAACGGTGAT 57.528 40.909 0.00 0.00 42.62 3.06
1862 1900 4.693566 ACATGTAACGGTGATGTTTGGTAG 59.306 41.667 0.00 0.00 33.32 3.18
1868 1906 8.259411 TGTAACGGTGATGTTTGGTAGTATTAT 58.741 33.333 0.00 0.00 33.32 1.28
1913 1951 3.420893 GGTCCACATGTCATTGGAAGAA 58.579 45.455 14.54 0.00 43.67 2.52
1936 1985 0.036765 AAGCGTTCATCTTACCGCCA 60.037 50.000 0.00 0.00 46.85 5.69
1944 1993 3.387947 CTTACCGCCACCCGTCCT 61.388 66.667 0.00 0.00 34.38 3.85
1958 2007 3.695606 TCCTGAGCCGTGGCAGAC 61.696 66.667 14.29 4.84 44.88 3.51
2008 2101 4.021925 GCAGAGGCCCCTCGTTGT 62.022 66.667 0.00 0.00 46.90 3.32
2014 2107 2.280592 GCCCCTCGTTGTCGTTGT 60.281 61.111 0.00 0.00 38.33 3.32
2017 2110 2.654912 CCCTCGTTGTCGTTGTCGC 61.655 63.158 0.00 0.00 38.33 5.19
2018 2111 1.947146 CCTCGTTGTCGTTGTCGCA 60.947 57.895 0.00 0.00 38.33 5.10
2035 2128 3.884774 ACACCAAGGGCGAGGCAA 61.885 61.111 0.00 0.00 0.00 4.52
2036 2129 2.597217 CACCAAGGGCGAGGCAAA 60.597 61.111 0.00 0.00 0.00 3.68
2037 2130 2.282462 ACCAAGGGCGAGGCAAAG 60.282 61.111 0.00 0.00 0.00 2.77
2038 2131 2.034066 CCAAGGGCGAGGCAAAGA 59.966 61.111 0.00 0.00 0.00 2.52
2064 2157 4.530857 CCTGTCCGCCCGGCTAAG 62.531 72.222 8.05 0.00 34.68 2.18
2065 2158 4.530857 CTGTCCGCCCGGCTAAGG 62.531 72.222 8.05 1.24 34.68 2.69
2067 2160 4.222847 GTCCGCCCGGCTAAGGAG 62.223 72.222 8.05 0.00 32.82 3.69
2146 2239 3.925630 ATGCGCTGGTGGGTCTTGG 62.926 63.158 9.73 0.00 0.00 3.61
2147 2240 4.643387 GCGCTGGTGGGTCTTGGT 62.643 66.667 0.00 0.00 0.00 3.67
2148 2241 3.065306 CGCTGGTGGGTCTTGGTA 58.935 61.111 0.00 0.00 0.00 3.25
2149 2242 1.602237 CGCTGGTGGGTCTTGGTAT 59.398 57.895 0.00 0.00 0.00 2.73
2150 2243 0.035439 CGCTGGTGGGTCTTGGTATT 60.035 55.000 0.00 0.00 0.00 1.89
2151 2244 1.613255 CGCTGGTGGGTCTTGGTATTT 60.613 52.381 0.00 0.00 0.00 1.40
2152 2245 2.525368 GCTGGTGGGTCTTGGTATTTT 58.475 47.619 0.00 0.00 0.00 1.82
2153 2246 2.492088 GCTGGTGGGTCTTGGTATTTTC 59.508 50.000 0.00 0.00 0.00 2.29
2154 2247 2.747446 CTGGTGGGTCTTGGTATTTTCG 59.253 50.000 0.00 0.00 0.00 3.46
2155 2248 1.471287 GGTGGGTCTTGGTATTTTCGC 59.529 52.381 0.00 0.00 0.00 4.70
2471 2564 4.968197 GTCGGATAGACGCATCCC 57.032 61.111 5.88 0.00 41.38 3.85
2472 2565 1.289380 GTCGGATAGACGCATCCCC 59.711 63.158 5.88 0.00 41.38 4.81
2473 2566 2.258591 CGGATAGACGCATCCCCG 59.741 66.667 5.88 0.00 41.38 5.73
2474 2567 2.048127 GGATAGACGCATCCCCGC 60.048 66.667 0.81 0.00 38.91 6.13
2475 2568 2.574955 GGATAGACGCATCCCCGCT 61.575 63.158 0.81 0.00 38.91 5.52
2476 2569 1.373497 GATAGACGCATCCCCGCTG 60.373 63.158 0.00 0.00 0.00 5.18
2477 2570 1.806461 GATAGACGCATCCCCGCTGA 61.806 60.000 0.00 0.00 0.00 4.26
2478 2571 1.188219 ATAGACGCATCCCCGCTGAT 61.188 55.000 0.00 0.00 0.00 2.90
2479 2572 1.399744 TAGACGCATCCCCGCTGATT 61.400 55.000 0.00 0.00 0.00 2.57
2480 2573 2.514592 ACGCATCCCCGCTGATTG 60.515 61.111 0.00 0.00 0.00 2.67
2481 2574 3.957535 CGCATCCCCGCTGATTGC 61.958 66.667 0.00 0.00 38.57 3.56
2482 2575 2.829914 GCATCCCCGCTGATTGCA 60.830 61.111 0.00 0.00 43.06 4.08
2483 2576 3.113745 CATCCCCGCTGATTGCAC 58.886 61.111 0.00 0.00 43.06 4.57
2484 2577 1.750018 CATCCCCGCTGATTGCACA 60.750 57.895 0.00 0.00 43.06 4.57
2485 2578 1.750399 ATCCCCGCTGATTGCACAC 60.750 57.895 0.00 0.00 43.06 3.82
2486 2579 3.443045 CCCCGCTGATTGCACACC 61.443 66.667 0.00 0.00 43.06 4.16
2487 2580 2.360350 CCCGCTGATTGCACACCT 60.360 61.111 0.00 0.00 43.06 4.00
2488 2581 2.693762 CCCGCTGATTGCACACCTG 61.694 63.158 0.00 0.00 43.06 4.00
2489 2582 1.672030 CCGCTGATTGCACACCTGA 60.672 57.895 0.00 0.00 43.06 3.86
2490 2583 1.236616 CCGCTGATTGCACACCTGAA 61.237 55.000 0.00 0.00 43.06 3.02
2491 2584 0.167470 CGCTGATTGCACACCTGAAG 59.833 55.000 0.00 0.00 43.06 3.02
2492 2585 0.109412 GCTGATTGCACACCTGAAGC 60.109 55.000 0.00 0.00 42.31 3.86
2493 2586 0.524862 CTGATTGCACACCTGAAGCC 59.475 55.000 0.00 0.00 0.00 4.35
2494 2587 0.895100 TGATTGCACACCTGAAGCCC 60.895 55.000 0.00 0.00 0.00 5.19
2495 2588 0.895100 GATTGCACACCTGAAGCCCA 60.895 55.000 0.00 0.00 0.00 5.36
2496 2589 0.896940 ATTGCACACCTGAAGCCCAG 60.897 55.000 0.00 0.00 42.55 4.45
2497 2590 1.993701 TTGCACACCTGAAGCCCAGA 61.994 55.000 5.38 0.00 45.78 3.86
2498 2591 1.968540 GCACACCTGAAGCCCAGAC 60.969 63.158 5.38 0.00 45.78 3.51
2499 2592 1.757306 CACACCTGAAGCCCAGACT 59.243 57.895 5.38 0.00 45.78 3.24
2500 2593 0.109342 CACACCTGAAGCCCAGACTT 59.891 55.000 5.38 0.00 45.78 3.01
2501 2594 0.109342 ACACCTGAAGCCCAGACTTG 59.891 55.000 5.38 2.94 45.78 3.16
2502 2595 0.109342 CACCTGAAGCCCAGACTTGT 59.891 55.000 5.38 0.00 45.78 3.16
2503 2596 0.398318 ACCTGAAGCCCAGACTTGTC 59.602 55.000 5.38 0.00 45.78 3.18
2504 2597 0.322008 CCTGAAGCCCAGACTTGTCC 60.322 60.000 5.38 0.00 45.78 4.02
2505 2598 0.671781 CTGAAGCCCAGACTTGTCCG 60.672 60.000 0.00 0.00 45.78 4.79
2506 2599 1.118965 TGAAGCCCAGACTTGTCCGA 61.119 55.000 0.00 0.00 0.00 4.55
2507 2600 0.670854 GAAGCCCAGACTTGTCCGAC 60.671 60.000 0.00 0.00 0.00 4.79
2508 2601 1.407656 AAGCCCAGACTTGTCCGACA 61.408 55.000 0.00 0.00 0.00 4.35
2509 2602 1.070786 GCCCAGACTTGTCCGACAA 59.929 57.895 13.29 13.29 36.54 3.18
2510 2603 0.321653 GCCCAGACTTGTCCGACAAT 60.322 55.000 14.29 5.34 37.48 2.71
2511 2604 1.442769 CCCAGACTTGTCCGACAATG 58.557 55.000 14.29 9.87 37.48 2.82
2512 2605 1.270839 CCCAGACTTGTCCGACAATGT 60.271 52.381 14.29 13.56 37.48 2.71
2513 2606 1.800586 CCAGACTTGTCCGACAATGTG 59.199 52.381 14.29 12.21 37.48 3.21
2514 2607 1.800586 CAGACTTGTCCGACAATGTGG 59.199 52.381 14.29 5.66 37.48 4.17
2515 2608 0.517316 GACTTGTCCGACAATGTGGC 59.483 55.000 14.29 1.89 37.48 5.01
2516 2609 0.108585 ACTTGTCCGACAATGTGGCT 59.891 50.000 14.29 0.00 37.48 4.75
2517 2610 0.798776 CTTGTCCGACAATGTGGCTC 59.201 55.000 14.29 0.00 37.48 4.70
2518 2611 0.948623 TTGTCCGACAATGTGGCTCG 60.949 55.000 9.99 0.00 32.34 5.03
2519 2612 2.434185 TCCGACAATGTGGCTCGC 60.434 61.111 0.00 0.00 0.00 5.03
2520 2613 2.741985 CCGACAATGTGGCTCGCA 60.742 61.111 0.00 0.00 0.00 5.10
2521 2614 2.476051 CGACAATGTGGCTCGCAC 59.524 61.111 0.00 0.00 0.00 5.34
2522 2615 2.476051 GACAATGTGGCTCGCACG 59.524 61.111 0.00 0.00 0.00 5.34
2523 2616 3.651480 GACAATGTGGCTCGCACGC 62.651 63.158 0.00 0.00 0.00 5.34
2524 2617 4.799473 CAATGTGGCTCGCACGCG 62.799 66.667 3.53 3.53 41.35 6.01
2550 2643 1.645034 CGTAGGAAGGAGCACACATG 58.355 55.000 0.00 0.00 0.00 3.21
2559 2652 2.562912 GCACACATGCGTCCCTTG 59.437 61.111 0.00 0.00 43.33 3.61
2560 2653 2.562912 CACACATGCGTCCCTTGC 59.437 61.111 0.00 0.00 0.00 4.01
2561 2654 3.049674 ACACATGCGTCCCTTGCG 61.050 61.111 0.00 0.00 34.24 4.85
2562 2655 3.803082 CACATGCGTCCCTTGCGG 61.803 66.667 0.00 0.00 34.24 5.69
2583 2676 3.060000 GTGGGGCCGCACCTAAAC 61.060 66.667 36.25 15.23 39.10 2.01
2584 2677 3.253838 TGGGGCCGCACCTAAACT 61.254 61.111 20.22 0.00 39.10 2.66
2585 2678 2.437895 GGGGCCGCACCTAAACTC 60.438 66.667 16.21 0.00 39.10 3.01
2586 2679 2.437895 GGGCCGCACCTAAACTCC 60.438 66.667 0.00 0.00 39.10 3.85
2587 2680 2.818274 GGCCGCACCTAAACTCCG 60.818 66.667 0.00 0.00 34.51 4.63
2588 2681 2.263540 GCCGCACCTAAACTCCGA 59.736 61.111 0.00 0.00 0.00 4.55
2589 2682 2.098831 GCCGCACCTAAACTCCGAC 61.099 63.158 0.00 0.00 0.00 4.79
2590 2683 1.804326 CCGCACCTAAACTCCGACG 60.804 63.158 0.00 0.00 0.00 5.12
2591 2684 1.804326 CGCACCTAAACTCCGACGG 60.804 63.158 7.84 7.84 0.00 4.79
2592 2685 1.447314 GCACCTAAACTCCGACGGG 60.447 63.158 15.25 7.45 0.00 5.28
2593 2686 1.447314 CACCTAAACTCCGACGGGC 60.447 63.158 15.25 0.00 0.00 6.13
2594 2687 2.202703 CCTAAACTCCGACGGGCG 60.203 66.667 15.25 8.30 40.47 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.741915 CTCCCTCACTAGTTCCGCTC 59.258 60.000 0.00 0.00 0.00 5.03
42 44 3.310193 GCTATTCCCTCCCTCACTAGTT 58.690 50.000 0.00 0.00 0.00 2.24
67 70 2.675889 CGCCTTATTTCACACTACCGGT 60.676 50.000 13.98 13.98 0.00 5.28
69 72 1.326548 GCGCCTTATTTCACACTACCG 59.673 52.381 0.00 0.00 0.00 4.02
75 78 2.083774 CCTCTTGCGCCTTATTTCACA 58.916 47.619 4.18 0.00 0.00 3.58
91 94 4.917040 TCACCCTCTAGATCTACATCCTCT 59.083 45.833 0.00 0.00 0.00 3.69
128 131 6.002704 CCTATCCTTAGAAGGTAAGTCGCTA 58.997 44.000 8.17 0.00 46.54 4.26
139 142 7.891183 TGGAGCTAGTTATCCTATCCTTAGAAG 59.109 40.741 10.78 0.00 36.50 2.85
144 147 6.143915 TGTTGGAGCTAGTTATCCTATCCTT 58.856 40.000 10.78 0.00 36.50 3.36
157 160 9.499479 AATCATACAATATTCTGTTGGAGCTAG 57.501 33.333 0.00 0.00 0.00 3.42
288 291 7.345392 ACTCCCCTGTAATATAAGACCGTTTAA 59.655 37.037 0.00 0.00 0.00 1.52
295 298 7.982354 GCATGATACTCCCCTGTAATATAAGAC 59.018 40.741 0.00 0.00 0.00 3.01
297 300 7.766278 GTGCATGATACTCCCCTGTAATATAAG 59.234 40.741 0.00 0.00 0.00 1.73
305 308 1.583556 TGTGCATGATACTCCCCTGT 58.416 50.000 0.00 0.00 0.00 4.00
306 309 2.501261 CATGTGCATGATACTCCCCTG 58.499 52.381 6.32 0.00 41.20 4.45
307 310 1.422781 CCATGTGCATGATACTCCCCT 59.577 52.381 13.21 0.00 41.20 4.79
308 311 1.901591 CCATGTGCATGATACTCCCC 58.098 55.000 13.21 0.00 41.20 4.81
325 334 5.186409 AGGTAAGTTTCGTAGAATAGTGCCA 59.814 40.000 0.00 0.00 45.90 4.92
326 335 5.658468 AGGTAAGTTTCGTAGAATAGTGCC 58.342 41.667 0.00 0.00 45.90 5.01
327 336 5.747675 GGAGGTAAGTTTCGTAGAATAGTGC 59.252 44.000 0.00 0.00 45.90 4.40
337 346 2.878526 GCATTGGGGAGGTAAGTTTCGT 60.879 50.000 0.00 0.00 0.00 3.85
344 353 3.785887 ACTCTTATGCATTGGGGAGGTAA 59.214 43.478 3.54 0.00 0.00 2.85
387 396 1.730451 TATCTGCGCCGACCGATGAA 61.730 55.000 4.18 0.00 40.02 2.57
398 407 0.109504 GATCTCTCCGGTATCTGCGC 60.110 60.000 0.00 0.00 0.00 6.09
399 408 1.529226 AGATCTCTCCGGTATCTGCG 58.471 55.000 0.00 0.00 0.00 5.18
402 411 2.372504 TCGGAAGATCTCTCCGGTATCT 59.627 50.000 29.56 3.47 46.03 1.98
404 413 2.953284 TCGGAAGATCTCTCCGGTAT 57.047 50.000 29.56 3.30 46.03 2.73
428 437 6.150307 TGAAGTGTATGATACCGTGCATTTTT 59.850 34.615 0.00 0.00 0.00 1.94
437 446 5.794687 TTTTGCTGAAGTGTATGATACCG 57.205 39.130 0.00 0.00 0.00 4.02
438 447 7.088589 ACATTTTGCTGAAGTGTATGATACC 57.911 36.000 0.00 0.00 36.55 2.73
452 461 4.202959 GCATCGAACGATTACATTTTGCTG 59.797 41.667 6.98 0.00 31.62 4.41
463 472 1.359848 GGTGTCTGCATCGAACGATT 58.640 50.000 6.98 0.00 31.62 3.34
479 488 2.625790 TCAACAAAAATTCTCCCCGGTG 59.374 45.455 0.00 0.00 0.00 4.94
497 506 5.054390 ACGTGCTGAAGTTTCTTTTTCAA 57.946 34.783 0.00 0.00 33.30 2.69
498 507 4.695217 ACGTGCTGAAGTTTCTTTTTCA 57.305 36.364 0.00 0.00 32.75 2.69
521 530 6.979238 ACAGTAGATAAGAAATCAGCGGTTAC 59.021 38.462 0.00 0.00 0.00 2.50
549 558 0.532573 TCAGATGTCTCCTTCGGTGC 59.467 55.000 0.00 0.00 0.00 5.01
553 562 8.648557 TTACAATAATTCAGATGTCTCCTTCG 57.351 34.615 0.00 0.00 0.00 3.79
590 599 1.476891 TGATAGGGAGCAAGACGTGTC 59.523 52.381 0.00 0.00 0.00 3.67
593 602 1.557099 TGTGATAGGGAGCAAGACGT 58.443 50.000 0.00 0.00 0.00 4.34
594 603 2.672961 TTGTGATAGGGAGCAAGACG 57.327 50.000 0.00 0.00 0.00 4.18
595 604 8.677148 TTATTTATTGTGATAGGGAGCAAGAC 57.323 34.615 0.00 0.00 0.00 3.01
597 606 9.342308 TCTTTATTTATTGTGATAGGGAGCAAG 57.658 33.333 0.00 0.00 0.00 4.01
617 627 6.817184 ACTTACATGTGGACGCTATCTTTAT 58.183 36.000 9.11 0.00 0.00 1.40
641 651 3.632333 AGATGACCCTAATGAGTCACGA 58.368 45.455 0.00 0.00 45.24 4.35
658 668 4.623167 GTGCCGCATAGTACAGATAAGATG 59.377 45.833 0.00 0.00 0.00 2.90
659 669 4.524714 AGTGCCGCATAGTACAGATAAGAT 59.475 41.667 0.00 0.00 0.00 2.40
660 670 3.889538 AGTGCCGCATAGTACAGATAAGA 59.110 43.478 0.00 0.00 0.00 2.10
661 671 3.983988 CAGTGCCGCATAGTACAGATAAG 59.016 47.826 0.00 0.00 0.00 1.73
662 672 3.383505 ACAGTGCCGCATAGTACAGATAA 59.616 43.478 0.00 0.00 0.00 1.75
669 679 4.513519 GCACAGTGCCGCATAGTA 57.486 55.556 15.27 0.00 37.42 1.82
690 700 0.529555 TGGAAAAAGTTTGCAGCGCC 60.530 50.000 2.29 0.00 0.00 6.53
696 706 3.062042 CAGGAGCATGGAAAAAGTTTGC 58.938 45.455 0.00 0.00 0.00 3.68
702 712 1.586028 GCGCAGGAGCATGGAAAAA 59.414 52.632 0.30 0.00 42.27 1.94
707 717 3.592814 CATGGCGCAGGAGCATGG 61.593 66.667 10.83 0.00 42.27 3.66
712 722 2.176273 GCTACACATGGCGCAGGAG 61.176 63.158 10.83 0.00 0.00 3.69
790 807 0.516877 TTGGCATCGCGAAAAGTGAG 59.483 50.000 15.24 0.00 43.34 3.51
823 840 0.110238 CAAGCTTGCACGCGTGTATT 60.110 50.000 36.80 22.66 35.19 1.89
871 889 1.869767 CAATGGAGAAGTATGGCGAGC 59.130 52.381 0.00 0.00 0.00 5.03
872 890 1.869767 GCAATGGAGAAGTATGGCGAG 59.130 52.381 0.00 0.00 0.00 5.03
897 929 3.966154 TGTGAGAACTGAGAAGAACGAC 58.034 45.455 0.00 0.00 0.00 4.34
898 930 3.004839 CCTGTGAGAACTGAGAAGAACGA 59.995 47.826 0.00 0.00 0.00 3.85
932 964 1.019278 TGCTCGATCCTTGAAACCGC 61.019 55.000 0.00 0.00 0.00 5.68
961 993 4.153117 AGTTTTTAGAGATGCTTGCTCGTG 59.847 41.667 0.00 0.00 37.46 4.35
978 1010 1.064952 CCGGCGAGACAACAAGTTTTT 59.935 47.619 9.30 0.00 0.00 1.94
983 1015 1.079127 ATCCCGGCGAGACAACAAG 60.079 57.895 9.30 0.00 0.00 3.16
1052 1084 0.975135 CGCCTGATCCTGATCCTGAT 59.025 55.000 4.76 0.00 37.02 2.90
1053 1085 1.117749 CCGCCTGATCCTGATCCTGA 61.118 60.000 4.76 0.00 37.02 3.86
1054 1086 1.370437 CCGCCTGATCCTGATCCTG 59.630 63.158 4.76 0.00 37.02 3.86
1055 1087 1.840650 CCCGCCTGATCCTGATCCT 60.841 63.158 4.76 0.00 37.02 3.24
1056 1088 2.746359 CCCGCCTGATCCTGATCC 59.254 66.667 4.76 0.00 37.02 3.36
1057 1089 1.838846 TCCCCGCCTGATCCTGATC 60.839 63.158 0.06 0.06 38.29 2.92
1194 1226 3.417275 CTCCTGTAGGTCGGCAGCG 62.417 68.421 0.00 0.00 36.34 5.18
1230 1262 0.332972 GGAACTCAAGGCCCAGGAAT 59.667 55.000 0.00 0.00 0.00 3.01
1234 1266 0.401738 TTCAGGAACTCAAGGCCCAG 59.598 55.000 0.00 0.00 34.60 4.45
1249 1281 1.003597 AGCAGAGGCAGCACTTCAG 60.004 57.895 0.00 0.00 44.61 3.02
1317 1349 3.582208 GAGGAGGGTGCATATCTGATCTT 59.418 47.826 0.00 0.00 0.00 2.40
1334 1366 8.937884 CAATAAGCATAGAGATTGAATGAGGAG 58.062 37.037 0.00 0.00 32.16 3.69
1446 1478 0.530211 CTCCCTCGCAATCTGCTGAG 60.530 60.000 0.00 11.17 42.25 3.35
1469 1501 2.563942 GATCTCGATCTCCCGCCG 59.436 66.667 0.00 0.00 35.04 6.46
1627 1665 3.821421 ACTCTCCTTCGTTTGTCACTT 57.179 42.857 0.00 0.00 0.00 3.16
1633 1671 7.884816 TCTACAATTTACTCTCCTTCGTTTG 57.115 36.000 0.00 0.00 0.00 2.93
1638 1676 8.617290 TGGTTTTCTACAATTTACTCTCCTTC 57.383 34.615 0.00 0.00 0.00 3.46
1656 1694 9.772973 AACCTAACCTTTAAAATGATGGTTTTC 57.227 29.630 12.47 0.00 40.84 2.29
1664 1702 9.449719 TTTTTGCAAACCTAACCTTTAAAATGA 57.550 25.926 12.39 0.00 0.00 2.57
1697 1735 8.784043 GGTGTTTTGTGTAGAGAAAATGTATCT 58.216 33.333 0.00 0.00 28.02 1.98
1704 1742 8.918202 AGATATGGTGTTTTGTGTAGAGAAAA 57.082 30.769 0.00 0.00 0.00 2.29
1712 1750 3.568007 ACGCAAGATATGGTGTTTTGTGT 59.432 39.130 0.00 0.00 43.62 3.72
1713 1751 4.159377 ACGCAAGATATGGTGTTTTGTG 57.841 40.909 0.00 0.00 43.62 3.33
1715 1753 5.743398 CCATTACGCAAGATATGGTGTTTTG 59.257 40.000 0.00 0.00 42.58 2.44
1725 1763 9.182933 GTTTTTACAAAACCATTACGCAAGATA 57.817 29.630 1.31 0.00 43.62 1.98
1745 1783 2.296831 TCGCCGATCGATGGTTTTTA 57.703 45.000 18.66 0.00 43.16 1.52
1754 1792 1.359117 GGTCAGATTCGCCGATCGA 59.641 57.895 18.66 0.00 46.88 3.59
1755 1793 1.661821 GGGTCAGATTCGCCGATCG 60.662 63.158 8.51 8.51 40.15 3.69
1764 1802 8.960591 CATAAACTCATTTAACAGGGTCAGATT 58.039 33.333 0.00 0.00 33.98 2.40
1773 1811 7.362056 CCCACCTGTCATAAACTCATTTAACAG 60.362 40.741 0.00 0.00 33.98 3.16
1780 1818 2.357154 GCCCCACCTGTCATAAACTCAT 60.357 50.000 0.00 0.00 0.00 2.90
1797 1835 1.923909 AGTCTAACTGGTGGGCCCC 60.924 63.158 22.27 10.91 0.00 5.80
1804 1842 0.317479 GCCACGTCAGTCTAACTGGT 59.683 55.000 7.21 0.00 45.94 4.00
1805 1843 0.317160 TGCCACGTCAGTCTAACTGG 59.683 55.000 7.21 0.00 45.94 4.00
1810 1848 2.959372 CGGTGCCACGTCAGTCTA 59.041 61.111 0.00 0.00 0.00 2.59
1813 1851 2.372040 TTAAGCGGTGCCACGTCAGT 62.372 55.000 0.00 0.00 35.98 3.41
1862 1900 6.886459 AGGGCCACACATGATGATAATAATAC 59.114 38.462 6.18 0.00 0.00 1.89
1868 1906 4.507157 CCATAGGGCCACACATGATGATAA 60.507 45.833 6.18 0.00 0.00 1.75
1920 1958 1.087771 GGGTGGCGGTAAGATGAACG 61.088 60.000 0.00 0.00 0.00 3.95
2001 2094 1.198397 GTGCGACAACGACAACGAG 59.802 57.895 0.00 0.00 42.66 4.18
2004 2097 1.011574 GGTGTGCGACAACGACAAC 60.012 57.895 0.00 0.00 42.66 3.32
2006 2099 1.425267 CTTGGTGTGCGACAACGACA 61.425 55.000 0.00 0.00 39.05 4.35
2008 2101 1.885388 CCTTGGTGTGCGACAACGA 60.885 57.895 0.00 0.00 39.05 3.85
2017 2110 4.641645 TGCCTCGCCCTTGGTGTG 62.642 66.667 0.00 0.00 34.40 3.82
2018 2111 3.429372 TTTGCCTCGCCCTTGGTGT 62.429 57.895 0.00 0.00 34.40 4.16
2035 2128 4.070552 GACAGGCGGCGTCCTCTT 62.071 66.667 17.85 9.58 33.25 2.85
2048 2141 4.530857 CCTTAGCCGGGCGGACAG 62.531 72.222 14.39 8.00 37.50 3.51
2058 2151 3.741830 GACAGGCCGCTCCTTAGCC 62.742 68.421 0.00 0.00 44.75 3.93
2059 2152 2.202946 GACAGGCCGCTCCTTAGC 60.203 66.667 0.00 0.00 44.75 3.09
2060 2153 2.105128 CGACAGGCCGCTCCTTAG 59.895 66.667 0.00 0.00 44.75 2.18
2134 2227 2.785562 CGAAAATACCAAGACCCACCA 58.214 47.619 0.00 0.00 0.00 4.17
2454 2547 1.289380 GGGGATGCGTCTATCCGAC 59.711 63.158 5.77 0.00 46.19 4.79
2455 2548 2.265904 CGGGGATGCGTCTATCCGA 61.266 63.158 22.15 0.00 46.19 4.55
2456 2549 2.258591 CGGGGATGCGTCTATCCG 59.741 66.667 16.70 16.70 46.19 4.18
2457 2550 2.048127 GCGGGGATGCGTCTATCC 60.048 66.667 5.77 0.00 44.82 2.59
2458 2551 1.373497 CAGCGGGGATGCGTCTATC 60.373 63.158 5.77 0.00 40.67 2.08
2459 2552 1.188219 ATCAGCGGGGATGCGTCTAT 61.188 55.000 5.77 0.00 40.67 1.98
2460 2553 1.399744 AATCAGCGGGGATGCGTCTA 61.400 55.000 5.77 0.00 40.67 2.59
2461 2554 2.735772 AATCAGCGGGGATGCGTCT 61.736 57.895 5.77 0.00 40.67 4.18
2462 2555 2.203070 AATCAGCGGGGATGCGTC 60.203 61.111 0.00 0.00 40.67 5.19
2463 2556 2.514592 CAATCAGCGGGGATGCGT 60.515 61.111 0.00 0.00 40.67 5.24
2464 2557 3.957535 GCAATCAGCGGGGATGCG 61.958 66.667 0.00 0.00 40.67 4.73
2473 2566 0.109412 GCTTCAGGTGTGCAATCAGC 60.109 55.000 0.00 0.00 45.96 4.26
2474 2567 0.524862 GGCTTCAGGTGTGCAATCAG 59.475 55.000 0.00 0.00 0.00 2.90
2475 2568 0.895100 GGGCTTCAGGTGTGCAATCA 60.895 55.000 0.00 0.00 0.00 2.57
2476 2569 0.895100 TGGGCTTCAGGTGTGCAATC 60.895 55.000 0.00 0.00 0.00 2.67
2477 2570 0.896940 CTGGGCTTCAGGTGTGCAAT 60.897 55.000 0.00 0.00 39.76 3.56
2478 2571 1.529010 CTGGGCTTCAGGTGTGCAA 60.529 57.895 0.00 0.00 39.76 4.08
2479 2572 2.113774 CTGGGCTTCAGGTGTGCA 59.886 61.111 0.00 0.00 39.76 4.57
2480 2573 1.968540 GTCTGGGCTTCAGGTGTGC 60.969 63.158 7.54 0.00 43.53 4.57
2481 2574 0.109342 AAGTCTGGGCTTCAGGTGTG 59.891 55.000 7.54 0.00 43.53 3.82
2482 2575 0.109342 CAAGTCTGGGCTTCAGGTGT 59.891 55.000 7.54 0.00 43.53 4.16
2483 2576 0.109342 ACAAGTCTGGGCTTCAGGTG 59.891 55.000 7.54 6.56 43.53 4.00
2484 2577 0.398318 GACAAGTCTGGGCTTCAGGT 59.602 55.000 7.54 0.00 43.53 4.00
2485 2578 0.322008 GGACAAGTCTGGGCTTCAGG 60.322 60.000 0.00 0.00 43.53 3.86
2486 2579 0.671781 CGGACAAGTCTGGGCTTCAG 60.672 60.000 1.01 1.98 44.68 3.02
2487 2580 1.118965 TCGGACAAGTCTGGGCTTCA 61.119 55.000 9.03 0.00 36.64 3.02
2488 2581 0.670854 GTCGGACAAGTCTGGGCTTC 60.671 60.000 9.03 0.00 36.64 3.86
2489 2582 1.371558 GTCGGACAAGTCTGGGCTT 59.628 57.895 9.03 0.00 36.64 4.35
2490 2583 1.407656 TTGTCGGACAAGTCTGGGCT 61.408 55.000 19.07 0.00 32.34 5.19
2491 2584 0.321653 ATTGTCGGACAAGTCTGGGC 60.322 55.000 25.74 3.97 41.94 5.36
2492 2585 1.270839 ACATTGTCGGACAAGTCTGGG 60.271 52.381 25.74 14.03 41.94 4.45
2493 2586 1.800586 CACATTGTCGGACAAGTCTGG 59.199 52.381 25.74 15.47 41.94 3.86
2494 2587 1.800586 CCACATTGTCGGACAAGTCTG 59.199 52.381 25.74 21.11 41.94 3.51
2495 2588 1.878102 GCCACATTGTCGGACAAGTCT 60.878 52.381 25.74 9.38 41.94 3.24
2496 2589 0.517316 GCCACATTGTCGGACAAGTC 59.483 55.000 25.74 10.95 41.94 3.01
2497 2590 0.108585 AGCCACATTGTCGGACAAGT 59.891 50.000 25.74 20.04 41.94 3.16
2498 2591 0.798776 GAGCCACATTGTCGGACAAG 59.201 55.000 25.74 19.50 41.94 3.16
2499 2592 0.948623 CGAGCCACATTGTCGGACAA 60.949 55.000 24.32 24.32 42.95 3.18
2500 2593 1.374125 CGAGCCACATTGTCGGACA 60.374 57.895 6.76 6.76 0.00 4.02
2501 2594 2.740714 GCGAGCCACATTGTCGGAC 61.741 63.158 0.00 0.00 34.23 4.79
2502 2595 2.434185 GCGAGCCACATTGTCGGA 60.434 61.111 8.80 0.00 34.23 4.55
2503 2596 2.741985 TGCGAGCCACATTGTCGG 60.742 61.111 0.00 0.00 34.23 4.79
2504 2597 2.476051 GTGCGAGCCACATTGTCG 59.524 61.111 0.00 0.00 44.06 4.35
2505 2598 2.476051 CGTGCGAGCCACATTGTC 59.524 61.111 0.00 0.00 44.91 3.18
2506 2599 3.726517 GCGTGCGAGCCACATTGT 61.727 61.111 0.00 0.00 44.91 2.71
2507 2600 4.799473 CGCGTGCGAGCCACATTG 62.799 66.667 8.89 0.00 44.91 2.82
2521 2614 4.170062 TTCCTACGGACGCTCGCG 62.170 66.667 10.06 10.06 46.03 5.87
2522 2615 2.278013 CTTCCTACGGACGCTCGC 60.278 66.667 0.00 0.00 0.00 5.03
2523 2616 2.049475 CTCCTTCCTACGGACGCTCG 62.049 65.000 0.00 0.00 0.00 5.03
2524 2617 1.728672 CTCCTTCCTACGGACGCTC 59.271 63.158 0.00 0.00 0.00 5.03
2525 2618 2.416432 GCTCCTTCCTACGGACGCT 61.416 63.158 0.00 0.00 0.00 5.07
2526 2619 2.104530 GCTCCTTCCTACGGACGC 59.895 66.667 0.00 0.00 0.00 5.19
2527 2620 1.139095 GTGCTCCTTCCTACGGACG 59.861 63.158 0.00 0.00 0.00 4.79
2528 2621 0.108756 GTGTGCTCCTTCCTACGGAC 60.109 60.000 0.00 0.00 0.00 4.79
2529 2622 0.541063 TGTGTGCTCCTTCCTACGGA 60.541 55.000 0.00 0.00 0.00 4.69
2530 2623 0.537188 ATGTGTGCTCCTTCCTACGG 59.463 55.000 0.00 0.00 0.00 4.02
2531 2624 1.645034 CATGTGTGCTCCTTCCTACG 58.355 55.000 0.00 0.00 0.00 3.51
2543 2636 2.562912 GCAAGGGACGCATGTGTG 59.437 61.111 18.34 2.82 0.00 3.82
2544 2637 3.049674 CGCAAGGGACGCATGTGT 61.050 61.111 12.68 12.68 0.00 3.72
2566 2659 3.060000 GTTTAGGTGCGGCCCCAC 61.060 66.667 12.37 12.37 38.26 4.61
2567 2660 3.253838 AGTTTAGGTGCGGCCCCA 61.254 61.111 3.85 0.00 38.26 4.96
2568 2661 2.437895 GAGTTTAGGTGCGGCCCC 60.438 66.667 0.00 0.00 38.26 5.80
2569 2662 2.437895 GGAGTTTAGGTGCGGCCC 60.438 66.667 0.00 0.00 38.26 5.80
2570 2663 2.818274 CGGAGTTTAGGTGCGGCC 60.818 66.667 0.00 0.00 37.58 6.13
2571 2664 2.098831 GTCGGAGTTTAGGTGCGGC 61.099 63.158 0.00 0.00 0.00 6.53
2572 2665 1.804326 CGTCGGAGTTTAGGTGCGG 60.804 63.158 0.00 0.00 0.00 5.69
2573 2666 1.804326 CCGTCGGAGTTTAGGTGCG 60.804 63.158 4.91 0.00 0.00 5.34
2574 2667 1.447314 CCCGTCGGAGTTTAGGTGC 60.447 63.158 14.39 0.00 0.00 5.01
2575 2668 1.447314 GCCCGTCGGAGTTTAGGTG 60.447 63.158 14.39 0.00 0.00 4.00
2576 2669 2.976356 GCCCGTCGGAGTTTAGGT 59.024 61.111 14.39 0.00 0.00 3.08
2577 2670 2.202703 CGCCCGTCGGAGTTTAGG 60.203 66.667 14.39 0.00 33.78 2.69


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

AutoCloner maintained by Alex Coulton.