Multiple sequence alignment - TraesCS4A01G405600

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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 TraesCS4A01G405600 chr4A 100.000 2360 0 0 1 2360 678420226 678417867 0.000000e+00 4359
1 TraesCS4A01G405600 chr4A 83.602 372 55 2 994 1365 678376578 678376213 6.240000e-91 344
2 TraesCS4A01G405600 chr4A 82.552 384 49 7 993 1361 678408861 678408481 2.930000e-84 322
3 TraesCS4A01G405600 chr4A 79.221 385 62 5 996 1365 678373764 678373383 3.890000e-63 252
4 TraesCS4A01G405600 chr4A 77.957 372 60 15 997 1363 678340939 678340585 1.840000e-51 213
5 TraesCS4A01G405600 chr4A 76.762 383 47 19 996 1363 678370174 678369819 2.410000e-40 176
6 TraesCS4A01G405600 chr4A 83.173 208 5 16 1865 2043 678411910 678411704 1.880000e-36 163
7 TraesCS4A01G405600 chr4B 87.435 1536 95 49 463 1940 593351974 593350479 0.000000e+00 1677
8 TraesCS4A01G405600 chr4B 83.095 349 41 8 1028 1361 593347927 593347582 3.810000e-78 302
9 TraesCS4A01G405600 chr4B 78.740 381 51 12 1001 1366 593342707 593342342 6.560000e-56 228
10 TraesCS4A01G405600 chr4B 78.329 383 53 15 996 1363 593135973 593135606 1.100000e-53 220
11 TraesCS4A01G405600 chr4B 93.902 82 3 1 192 271 593353461 593353380 3.190000e-24 122
12 TraesCS4A01G405600 chr4D 85.592 1638 93 62 347 1931 471271151 471269604 0.000000e+00 1585
13 TraesCS4A01G405600 chr4D 79.750 400 50 16 979 1363 470856831 470856448 6.470000e-66 261
14 TraesCS4A01G405600 chr4D 78.500 400 64 11 984 1365 471212680 471212285 2.340000e-60 243
15 TraesCS4A01G405600 chr4D 77.285 383 45 18 996 1363 471153967 471153612 1.110000e-43 187
16 TraesCS4A01G405600 chr4D 89.600 125 10 3 163 287 471271501 471271380 3.140000e-34 156
17 TraesCS4A01G405600 chr4D 92.593 54 1 2 268 318 471271248 471271195 9.050000e-10 75
18 TraesCS4A01G405600 chr1B 91.429 280 2 1 2081 2360 29773300 29773043 4.790000e-97 364
19 TraesCS4A01G405600 chr1B 89.494 257 18 3 2088 2335 141642131 141641875 1.360000e-82 316
20 TraesCS4A01G405600 chr2B 91.941 273 0 1 2088 2360 10611903 10611653 1.720000e-96 363
21 TraesCS4A01G405600 chr6B 90.842 273 3 1 2088 2360 38067348 38067598 1.740000e-91 346
22 TraesCS4A01G405600 chr6D 90.947 243 16 6 2088 2326 76080875 76080635 2.930000e-84 322
23 TraesCS4A01G405600 chr1D 90.947 243 16 6 2088 2326 207149175 207148935 2.930000e-84 322
24 TraesCS4A01G405600 chr2D 90.574 244 17 6 2087 2326 427945994 427946235 3.780000e-83 318
25 TraesCS4A01G405600 chr3D 90.244 246 18 6 2085 2326 382819576 382819819 1.360000e-82 316
26 TraesCS4A01G405600 chr3D 90.535 243 17 6 2088 2326 554658265 554658505 1.360000e-82 316


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 TraesCS4A01G405600 chr4A 678417867 678420226 2359 True 4359.000000 4359 100.000000 1 2360 1 chr4A.!!$R2 2359
1 TraesCS4A01G405600 chr4A 678369819 678376578 6759 True 257.333333 344 79.861667 994 1365 3 chr4A.!!$R3 371
2 TraesCS4A01G405600 chr4A 678408481 678411910 3429 True 242.500000 322 82.862500 993 2043 2 chr4A.!!$R4 1050
3 TraesCS4A01G405600 chr4B 593347582 593353461 5879 True 700.333333 1677 88.144000 192 1940 3 chr4B.!!$R3 1748
4 TraesCS4A01G405600 chr4D 471269604 471271501 1897 True 605.333333 1585 89.261667 163 1931 3 chr4D.!!$R4 1768

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
523 1776 0.03213 GTCGTGCAAGTCTGTCAGGA 59.968 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 10078 0.03438 ATTCTGTCGGAGGAGGACGA 60.034 55.0 0.0 0.0 37.22 4.2 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
33 34 7.658179 TTATGCTATAGGATGAAAAAGAGCG 57.342 36.000 16.37 0.00 0.00 5.03
35 36 4.141711 TGCTATAGGATGAAAAAGAGCGGT 60.142 41.667 1.04 0.00 0.00 5.68
37 38 5.989777 GCTATAGGATGAAAAAGAGCGGTTA 59.010 40.000 1.04 0.00 0.00 2.85
38 39 6.146347 GCTATAGGATGAAAAAGAGCGGTTAG 59.854 42.308 1.04 0.00 0.00 2.34
67 68 3.047280 TCGGCGCATTGGACACAC 61.047 61.111 10.83 0.00 0.00 3.82
69 70 1.739929 CGGCGCATTGGACACACTA 60.740 57.895 10.83 0.00 0.00 2.74
72 73 1.966493 GCGCATTGGACACACTACCG 61.966 60.000 0.30 0.00 0.00 4.02
73 74 0.389296 CGCATTGGACACACTACCGA 60.389 55.000 0.00 0.00 0.00 4.69
75 76 1.933853 GCATTGGACACACTACCGATC 59.066 52.381 0.00 0.00 0.00 3.69
76 77 2.550978 CATTGGACACACTACCGATCC 58.449 52.381 0.00 0.00 0.00 3.36
78 79 1.634960 TGGACACACTACCGATCCAA 58.365 50.000 0.00 0.00 36.51 3.53
80 81 2.569853 TGGACACACTACCGATCCAAAT 59.430 45.455 0.00 0.00 36.51 2.32
81 82 3.195661 GGACACACTACCGATCCAAATC 58.804 50.000 0.00 0.00 0.00 2.17
82 83 3.118738 GGACACACTACCGATCCAAATCT 60.119 47.826 0.00 0.00 0.00 2.40
83 84 4.113354 GACACACTACCGATCCAAATCTC 58.887 47.826 0.00 0.00 0.00 2.75
84 85 3.513912 ACACACTACCGATCCAAATCTCA 59.486 43.478 0.00 0.00 0.00 3.27
86 87 4.935205 CACACTACCGATCCAAATCTCAAA 59.065 41.667 0.00 0.00 0.00 2.69
87 88 4.935808 ACACTACCGATCCAAATCTCAAAC 59.064 41.667 0.00 0.00 0.00 2.93
89 90 3.433306 ACCGATCCAAATCTCAAACCA 57.567 42.857 0.00 0.00 0.00 3.67
90 91 3.761897 ACCGATCCAAATCTCAAACCAA 58.238 40.909 0.00 0.00 0.00 3.67
91 92 3.506067 ACCGATCCAAATCTCAAACCAAC 59.494 43.478 0.00 0.00 0.00 3.77
92 93 3.119495 CCGATCCAAATCTCAAACCAACC 60.119 47.826 0.00 0.00 0.00 3.77
96 97 3.316868 TCCAAATCTCAAACCAACCGAAC 59.683 43.478 0.00 0.00 0.00 3.95
97 98 3.296628 CAAATCTCAAACCAACCGAACG 58.703 45.455 0.00 0.00 0.00 3.95
98 99 0.872388 ATCTCAAACCAACCGAACGC 59.128 50.000 0.00 0.00 0.00 4.84
99 100 1.161563 TCTCAAACCAACCGAACGCC 61.162 55.000 0.00 0.00 0.00 5.68
123 124 2.234300 GGACGGCCGATTGAAATAGA 57.766 50.000 35.90 0.00 0.00 1.98
124 125 1.865340 GGACGGCCGATTGAAATAGAC 59.135 52.381 35.90 7.29 0.00 2.59
128 129 3.754323 ACGGCCGATTGAAATAGACAAAA 59.246 39.130 35.90 0.00 0.00 2.44
129 130 4.216687 ACGGCCGATTGAAATAGACAAAAA 59.783 37.500 35.90 0.00 0.00 1.94
148 149 2.323968 AAAACAAACAAATGCGCCCT 57.676 40.000 4.18 0.00 0.00 5.19
149 150 2.323968 AAACAAACAAATGCGCCCTT 57.676 40.000 4.18 0.00 0.00 3.95
150 151 1.864565 AACAAACAAATGCGCCCTTC 58.135 45.000 4.18 0.00 0.00 3.46
151 152 0.318614 ACAAACAAATGCGCCCTTCG 60.319 50.000 4.18 0.00 42.12 3.79
154 155 0.387565 AACAAATGCGCCCTTCGTTT 59.612 45.000 4.18 0.00 41.07 3.60
155 156 0.318614 ACAAATGCGCCCTTCGTTTG 60.319 50.000 4.18 9.13 38.97 2.93
156 157 1.008361 CAAATGCGCCCTTCGTTTGG 61.008 55.000 4.18 0.00 41.07 3.28
158 159 1.862602 AATGCGCCCTTCGTTTGGAC 61.863 55.000 4.18 0.00 41.07 4.02
159 160 3.733960 GCGCCCTTCGTTTGGACC 61.734 66.667 0.00 0.00 41.07 4.46
160 161 2.032071 CGCCCTTCGTTTGGACCT 59.968 61.111 0.00 0.00 0.00 3.85
161 162 2.325082 CGCCCTTCGTTTGGACCTG 61.325 63.158 0.00 0.00 0.00 4.00
165 166 0.179029 CCTTCGTTTGGACCTGTGGT 60.179 55.000 0.00 0.00 39.44 4.16
184 185 2.825836 GGATGCACCTCCCTTGCG 60.826 66.667 0.00 0.00 43.34 4.85
310 460 0.717224 CGGTCCGGTTTAACATCGTG 59.283 55.000 2.34 0.00 0.00 4.35
311 461 1.799544 GGTCCGGTTTAACATCGTGT 58.200 50.000 0.00 0.00 0.00 4.49
313 463 1.136169 GTCCGGTTTAACATCGTGTGC 60.136 52.381 0.00 0.00 0.00 4.57
316 466 1.529438 CGGTTTAACATCGTGTGCAGT 59.471 47.619 0.00 0.00 0.00 4.40
317 467 2.732500 CGGTTTAACATCGTGTGCAGTA 59.267 45.455 0.00 0.00 0.00 2.74
318 468 3.181534 CGGTTTAACATCGTGTGCAGTAG 60.182 47.826 0.00 0.00 0.00 2.57
319 469 3.424433 GGTTTAACATCGTGTGCAGTAGC 60.424 47.826 0.00 0.00 42.57 3.58
336 486 2.969628 AGCCAGTACTGTACATGAGC 57.030 50.000 21.18 14.73 0.00 4.26
338 488 1.802880 GCCAGTACTGTACATGAGCCG 60.803 57.143 21.18 3.35 0.00 5.52
345 989 0.179111 TGTACATGAGCCGCTGTAGC 60.179 55.000 0.00 0.00 37.78 3.58
379 1023 2.050351 CCCAGCCGTATACGCTCG 60.050 66.667 19.86 12.36 38.18 5.03
387 1488 1.463805 CGTATACGCTCGGAACAGTG 58.536 55.000 13.08 0.00 0.00 3.66
403 1504 0.249699 AGTGCGACCGTTCACATGAA 60.250 50.000 0.00 0.00 35.76 2.57
407 1508 1.398451 GCGACCGTTCACATGAAGTTG 60.398 52.381 0.00 0.00 34.27 3.16
439 1540 2.961721 CGGTCGATCACATGGCCG 60.962 66.667 0.00 0.00 0.00 6.13
440 1541 2.588877 GGTCGATCACATGGCCGG 60.589 66.667 0.00 0.00 0.00 6.13
442 1543 4.889856 TCGATCACATGGCCGGCG 62.890 66.667 22.54 9.65 0.00 6.46
443 1544 4.889856 CGATCACATGGCCGGCGA 62.890 66.667 22.54 19.14 0.00 5.54
444 1545 2.513666 GATCACATGGCCGGCGAA 60.514 61.111 22.54 12.25 0.00 4.70
445 1546 2.823829 GATCACATGGCCGGCGAAC 61.824 63.158 22.54 7.39 0.00 3.95
467 1710 3.120199 CCCACAATATTCGCGAATCATCC 60.120 47.826 35.57 0.00 32.50 3.51
511 1764 6.401260 CCACGTATATAACTTTTTGTCGTGCA 60.401 38.462 0.00 0.00 42.64 4.57
513 1766 7.213706 CACGTATATAACTTTTTGTCGTGCAAG 59.786 37.037 0.00 0.00 39.22 4.01
514 1767 7.095523 ACGTATATAACTTTTTGTCGTGCAAGT 60.096 33.333 0.00 0.00 38.47 3.16
515 1768 7.421613 CGTATATAACTTTTTGTCGTGCAAGTC 59.578 37.037 0.00 0.00 38.47 3.01
516 1769 5.751243 ATAACTTTTTGTCGTGCAAGTCT 57.249 34.783 0.00 0.00 38.47 3.24
517 1770 3.405170 ACTTTTTGTCGTGCAAGTCTG 57.595 42.857 0.00 0.00 38.47 3.51
518 1771 2.747446 ACTTTTTGTCGTGCAAGTCTGT 59.253 40.909 0.00 0.00 38.47 3.41
519 1772 3.181510 ACTTTTTGTCGTGCAAGTCTGTC 60.182 43.478 0.00 0.00 38.47 3.51
520 1773 2.017138 TTTGTCGTGCAAGTCTGTCA 57.983 45.000 0.00 0.00 38.47 3.58
521 1774 1.570813 TTGTCGTGCAAGTCTGTCAG 58.429 50.000 0.00 0.00 32.52 3.51
522 1775 0.249447 TGTCGTGCAAGTCTGTCAGG 60.249 55.000 0.00 0.00 0.00 3.86
523 1776 0.032130 GTCGTGCAAGTCTGTCAGGA 59.968 55.000 0.00 0.00 0.00 3.86
524 1777 0.032130 TCGTGCAAGTCTGTCAGGAC 59.968 55.000 0.00 0.00 36.56 3.85
631 1889 2.926242 ACGTCCATCCCAACGGGT 60.926 61.111 0.00 0.00 44.74 5.28
707 1965 4.157120 CTAGCCGTTGGACCCCGG 62.157 72.222 13.87 13.87 46.90 5.73
734 2015 1.079681 CGCTAACGGTAACCCTGCA 60.080 57.895 0.00 0.00 34.97 4.41
737 2018 1.722011 CTAACGGTAACCCTGCACTG 58.278 55.000 0.00 0.00 0.00 3.66
812 2093 4.178214 CGCCAATGACGCGCCATT 62.178 61.111 15.26 15.26 43.57 3.16
813 2094 2.818487 CGCCAATGACGCGCCATTA 61.818 57.895 20.34 0.00 43.57 1.90
830 2111 3.381590 CCATTAGCTAAACCCTTGCTTCC 59.618 47.826 10.85 0.00 38.15 3.46
882 2163 2.736236 CTCACAACTCGCAGCGCT 60.736 61.111 10.87 2.64 0.00 5.92
950 2254 4.112341 GTCGTCGCCGCCTACTGT 62.112 66.667 0.00 0.00 0.00 3.55
951 2255 3.807538 TCGTCGCCGCCTACTGTC 61.808 66.667 0.00 0.00 0.00 3.51
952 2256 3.812019 CGTCGCCGCCTACTGTCT 61.812 66.667 0.00 0.00 0.00 3.41
953 2257 2.102553 GTCGCCGCCTACTGTCTC 59.897 66.667 0.00 0.00 0.00 3.36
954 2258 2.045242 TCGCCGCCTACTGTCTCT 60.045 61.111 0.00 0.00 0.00 3.10
955 2259 1.677966 TCGCCGCCTACTGTCTCTT 60.678 57.895 0.00 0.00 0.00 2.85
956 2260 1.226717 CGCCGCCTACTGTCTCTTC 60.227 63.158 0.00 0.00 0.00 2.87
957 2261 1.658686 CGCCGCCTACTGTCTCTTCT 61.659 60.000 0.00 0.00 0.00 2.85
958 2262 1.390565 GCCGCCTACTGTCTCTTCTA 58.609 55.000 0.00 0.00 0.00 2.10
964 2268 4.381079 CGCCTACTGTCTCTTCTAAAGCTT 60.381 45.833 0.00 0.00 0.00 3.74
1218 5974 2.184322 GCTCCTTCCGCGATGACA 59.816 61.111 8.23 0.00 0.00 3.58
1221 5977 2.511600 CCTTCCGCGATGACACCC 60.512 66.667 8.23 0.00 0.00 4.61
1326 6082 3.470567 GTCAGCTTCGTCGCCGTG 61.471 66.667 0.00 0.00 35.01 4.94
1365 6121 2.487934 GCCGTCATGTTCTAGATGCAT 58.512 47.619 0.00 0.00 0.00 3.96
1366 6122 2.222678 GCCGTCATGTTCTAGATGCATG 59.777 50.000 22.08 22.08 40.76 4.06
1367 6123 2.222678 CCGTCATGTTCTAGATGCATGC 59.777 50.000 22.76 11.82 39.64 4.06
1411 6171 2.615493 CGGGAGTGCCACTCTGTTTTAT 60.615 50.000 23.23 0.00 44.46 1.40
1415 6175 4.095036 GGAGTGCCACTCTGTTTTATTAGC 59.905 45.833 23.23 0.00 44.46 3.09
1416 6176 3.684788 AGTGCCACTCTGTTTTATTAGCG 59.315 43.478 0.00 0.00 0.00 4.26
1425 6185 5.685841 TCTGTTTTATTAGCGCTGTTGTTC 58.314 37.500 22.90 5.75 0.00 3.18
1477 6238 3.430098 GGAGAGAGTGACATGACATGACC 60.430 52.174 22.19 12.85 0.00 4.02
1506 6267 7.095607 GCCATGTTATCTTGCTACATACTGTAC 60.096 40.741 0.00 0.00 31.64 2.90
1511 6272 3.066342 TCTTGCTACATACTGTACGCTCC 59.934 47.826 0.00 0.00 32.28 4.70
1557 7489 8.567948 TCTTTCATTTGTTACATTTGTCTCCTC 58.432 33.333 0.00 0.00 0.00 3.71
1558 7490 8.463930 TTTCATTTGTTACATTTGTCTCCTCT 57.536 30.769 0.00 0.00 0.00 3.69
1560 7492 6.655003 TCATTTGTTACATTTGTCTCCTCTCC 59.345 38.462 0.00 0.00 0.00 3.71
1569 7501 0.973496 GTCTCCTCTCCTGGGTGTCC 60.973 65.000 0.00 0.00 0.00 4.02
1580 7512 1.902508 CTGGGTGTCCTCTCTGCTTTA 59.097 52.381 0.00 0.00 0.00 1.85
1581 7513 2.503356 CTGGGTGTCCTCTCTGCTTTAT 59.497 50.000 0.00 0.00 0.00 1.40
1582 7514 2.912956 TGGGTGTCCTCTCTGCTTTATT 59.087 45.455 0.00 0.00 0.00 1.40
1583 7515 4.101114 TGGGTGTCCTCTCTGCTTTATTA 58.899 43.478 0.00 0.00 0.00 0.98
1611 7543 4.566759 TCGAGAAACTTTTCAGTCAGTGTG 59.433 41.667 4.58 0.00 39.61 3.82
1688 7623 1.565156 GAAATGCAGGCGTCGTCACA 61.565 55.000 0.00 0.00 0.00 3.58
1726 7661 9.787532 GATGCAGCATAGTAATTTTACTTTTCA 57.212 29.630 8.22 1.01 40.96 2.69
1751 7699 3.181479 GCGTTTCTTCCCTTTTGAGGTTT 60.181 43.478 0.00 0.00 0.00 3.27
1753 7701 4.097286 CGTTTCTTCCCTTTTGAGGTTTGA 59.903 41.667 0.00 0.00 0.00 2.69
1756 7704 3.573967 TCTTCCCTTTTGAGGTTTGATGC 59.426 43.478 0.00 0.00 0.00 3.91
1758 7706 1.613437 CCCTTTTGAGGTTTGATGCGT 59.387 47.619 0.00 0.00 0.00 5.24
1760 7708 2.574322 CTTTTGAGGTTTGATGCGTCG 58.426 47.619 0.58 0.00 0.00 5.12
1761 7709 0.237235 TTTGAGGTTTGATGCGTCGC 59.763 50.000 11.10 11.10 0.00 5.19
1762 7710 0.602638 TTGAGGTTTGATGCGTCGCT 60.603 50.000 19.50 3.67 0.00 4.93
1765 7713 1.132640 GGTTTGATGCGTCGCTGAC 59.867 57.895 19.50 9.98 0.00 3.51
1766 7714 1.565156 GGTTTGATGCGTCGCTGACA 61.565 55.000 19.50 12.42 32.09 3.58
1767 7715 0.234625 GTTTGATGCGTCGCTGACAA 59.765 50.000 19.50 17.19 32.09 3.18
1768 7716 0.940833 TTTGATGCGTCGCTGACAAA 59.059 45.000 19.50 21.26 32.09 2.83
1769 7717 0.940833 TTGATGCGTCGCTGACAAAA 59.059 45.000 19.50 0.00 32.09 2.44
1770 7718 0.940833 TGATGCGTCGCTGACAAAAA 59.059 45.000 19.50 0.00 32.09 1.94
1793 7752 1.471119 AGTAGGCGGTTCGATGAAGA 58.529 50.000 0.00 0.00 0.00 2.87
1794 7753 1.822990 AGTAGGCGGTTCGATGAAGAA 59.177 47.619 0.00 0.00 0.00 2.52
1831 7790 0.164647 GCTTACGCACTCAGCACAAG 59.835 55.000 0.00 0.00 46.13 3.16
1832 7791 1.783284 CTTACGCACTCAGCACAAGA 58.217 50.000 0.00 0.00 46.13 3.02
1835 7794 1.951130 CGCACTCAGCACAAGACGT 60.951 57.895 0.00 0.00 46.13 4.34
1836 7795 0.663269 CGCACTCAGCACAAGACGTA 60.663 55.000 0.00 0.00 46.13 3.57
1840 7799 3.865745 GCACTCAGCACAAGACGTAATAT 59.134 43.478 0.00 0.00 44.79 1.28
1842 7801 5.163854 GCACTCAGCACAAGACGTAATATTT 60.164 40.000 0.00 0.00 44.79 1.40
1843 7802 6.243551 CACTCAGCACAAGACGTAATATTTG 58.756 40.000 0.00 0.00 0.00 2.32
1909 7869 5.574830 TGAAACTTGTTTCAATCAACAACGG 59.425 36.000 21.90 0.00 40.88 4.44
1957 7938 7.819644 TCCTTTGTGAGTGTTGATTTATCATG 58.180 34.615 0.00 0.00 36.56 3.07
1958 7939 7.665145 TCCTTTGTGAGTGTTGATTTATCATGA 59.335 33.333 0.00 0.00 36.56 3.07
1970 7951 9.294030 GTTGATTTATCATGAATGAAACTGGTC 57.706 33.333 0.00 0.00 40.69 4.02
1971 7952 8.812513 TGATTTATCATGAATGAAACTGGTCT 57.187 30.769 0.00 0.00 40.69 3.85
1972 7953 8.896744 TGATTTATCATGAATGAAACTGGTCTC 58.103 33.333 0.00 0.00 40.69 3.36
1975 7956 4.582869 TCATGAATGAAACTGGTCTCAGG 58.417 43.478 0.00 0.00 38.37 3.86
1977 7958 4.705110 TGAATGAAACTGGTCTCAGGAA 57.295 40.909 0.00 0.00 44.99 3.36
1979 7960 5.445069 TGAATGAAACTGGTCTCAGGAAAA 58.555 37.500 0.00 0.00 44.99 2.29
2038 8191 4.990426 GCAAGCAAACTACATCAAAATGGT 59.010 37.500 0.00 0.00 37.19 3.55
2040 8193 6.813152 GCAAGCAAACTACATCAAAATGGTAT 59.187 34.615 0.00 0.00 37.19 2.73
2042 8195 6.332630 AGCAAACTACATCAAAATGGTATGC 58.667 36.000 0.00 0.00 37.19 3.14
2044 8197 6.034898 GCAAACTACATCAAAATGGTATGCAC 59.965 38.462 0.00 0.00 37.19 4.57
2047 8200 6.855836 ACTACATCAAAATGGTATGCACAAG 58.144 36.000 0.00 0.00 37.19 3.16
2049 8202 6.534475 ACATCAAAATGGTATGCACAAGAT 57.466 33.333 0.00 0.00 37.19 2.40
2050 8203 7.643569 ACATCAAAATGGTATGCACAAGATA 57.356 32.000 0.00 0.00 37.19 1.98
2051 8204 7.709947 ACATCAAAATGGTATGCACAAGATAG 58.290 34.615 0.00 0.00 37.19 2.08
2052 8205 7.340232 ACATCAAAATGGTATGCACAAGATAGT 59.660 33.333 0.00 0.00 37.19 2.12
2053 8206 7.320443 TCAAAATGGTATGCACAAGATAGTC 57.680 36.000 0.00 0.00 0.00 2.59
2056 8209 4.137116 TGGTATGCACAAGATAGTCCAC 57.863 45.455 0.00 0.00 0.00 4.02
2057 8210 3.123804 GGTATGCACAAGATAGTCCACG 58.876 50.000 0.00 0.00 0.00 4.94
2058 8211 3.430374 GGTATGCACAAGATAGTCCACGT 60.430 47.826 0.00 0.00 0.00 4.49
2060 8213 4.672587 ATGCACAAGATAGTCCACGTAT 57.327 40.909 0.00 0.00 0.00 3.06
2061 8214 5.784578 ATGCACAAGATAGTCCACGTATA 57.215 39.130 0.00 0.00 0.00 1.47
2064 8217 7.279750 TGCACAAGATAGTCCACGTATATTA 57.720 36.000 0.00 0.00 0.00 0.98
2066 8219 7.013942 TGCACAAGATAGTCCACGTATATTAGT 59.986 37.037 0.00 0.00 0.00 2.24
2076 8229 9.352191 AGTCCACGTATATTAGTAGTGAATTCT 57.648 33.333 7.05 0.00 35.03 2.40
2077 8230 9.962783 GTCCACGTATATTAGTAGTGAATTCTT 57.037 33.333 7.05 0.00 35.03 2.52
2110 9772 0.322187 CCCTCCGTCCCGAAAAACAT 60.322 55.000 0.00 0.00 0.00 2.71
2111 9773 0.802494 CCTCCGTCCCGAAAAACATG 59.198 55.000 0.00 0.00 0.00 3.21
2118 9780 0.179225 CCCGAAAAACATGTCGCGAG 60.179 55.000 10.24 0.00 35.93 5.03
2121 9783 0.454452 GAAAAACATGTCGCGAGGGC 60.454 55.000 10.24 0.00 0.00 5.19
2123 9785 1.169661 AAAACATGTCGCGAGGGCAA 61.170 50.000 10.24 0.00 39.92 4.52
2128 10033 1.400142 CATGTCGCGAGGGCAATTTTA 59.600 47.619 10.24 0.00 39.92 1.52
2133 10038 2.293677 TCGCGAGGGCAATTTTACAAAA 59.706 40.909 3.71 0.00 39.92 2.44
2135 10040 3.121160 CGCGAGGGCAATTTTACAAAAAC 60.121 43.478 0.00 0.00 39.92 2.43
2140 10045 4.165180 AGGGCAATTTTACAAAAACACCCT 59.835 37.500 14.24 14.24 40.06 4.34
2142 10047 5.008217 GGGCAATTTTACAAAAACACCCTTC 59.992 40.000 11.74 0.00 35.70 3.46
2147 10052 8.726068 CAATTTTACAAAAACACCCTTCAGTTT 58.274 29.630 0.00 0.00 39.46 2.66
2148 10053 7.892778 TTTTACAAAAACACCCTTCAGTTTC 57.107 32.000 0.00 0.00 36.98 2.78
2149 10054 6.844097 TTACAAAAACACCCTTCAGTTTCT 57.156 33.333 0.00 0.00 36.98 2.52
2150 10055 5.324784 ACAAAAACACCCTTCAGTTTCTC 57.675 39.130 0.00 0.00 36.98 2.87
2151 10056 4.159693 ACAAAAACACCCTTCAGTTTCTCC 59.840 41.667 0.00 0.00 36.98 3.71
2152 10057 2.658807 AACACCCTTCAGTTTCTCCC 57.341 50.000 0.00 0.00 0.00 4.30
2153 10058 0.396811 ACACCCTTCAGTTTCTCCCG 59.603 55.000 0.00 0.00 0.00 5.14
2154 10059 0.685097 CACCCTTCAGTTTCTCCCGA 59.315 55.000 0.00 0.00 0.00 5.14
2155 10060 0.685660 ACCCTTCAGTTTCTCCCGAC 59.314 55.000 0.00 0.00 0.00 4.79
2156 10061 0.036294 CCCTTCAGTTTCTCCCGACC 60.036 60.000 0.00 0.00 0.00 4.79
2157 10062 0.685097 CCTTCAGTTTCTCCCGACCA 59.315 55.000 0.00 0.00 0.00 4.02
2158 10063 1.071699 CCTTCAGTTTCTCCCGACCAA 59.928 52.381 0.00 0.00 0.00 3.67
2159 10064 2.486548 CCTTCAGTTTCTCCCGACCAAA 60.487 50.000 0.00 0.00 0.00 3.28
2160 10065 2.249844 TCAGTTTCTCCCGACCAAAC 57.750 50.000 0.00 0.00 0.00 2.93
2162 10067 0.109913 AGTTTCTCCCGACCAAACCC 59.890 55.000 0.00 0.00 31.50 4.11
2165 10070 4.323477 CTCCCGACCAAACCCGCA 62.323 66.667 0.00 0.00 0.00 5.69
2166 10071 4.629523 TCCCGACCAAACCCGCAC 62.630 66.667 0.00 0.00 0.00 5.34
2167 10072 4.636435 CCCGACCAAACCCGCACT 62.636 66.667 0.00 0.00 0.00 4.40
2168 10073 3.047877 CCGACCAAACCCGCACTC 61.048 66.667 0.00 0.00 0.00 3.51
2169 10074 3.047877 CGACCAAACCCGCACTCC 61.048 66.667 0.00 0.00 0.00 3.85
2172 10077 2.742372 CCAAACCCGCACTCCTCG 60.742 66.667 0.00 0.00 0.00 4.63
2173 10078 2.030562 CAAACCCGCACTCCTCGT 59.969 61.111 0.00 0.00 0.00 4.18
2174 10079 2.027625 CAAACCCGCACTCCTCGTC 61.028 63.158 0.00 0.00 0.00 4.20
2175 10080 3.569049 AAACCCGCACTCCTCGTCG 62.569 63.158 0.00 0.00 0.00 5.12
2177 10082 4.477975 CCCGCACTCCTCGTCGTC 62.478 72.222 0.00 0.00 0.00 4.20
2178 10083 4.477975 CCGCACTCCTCGTCGTCC 62.478 72.222 0.00 0.00 0.00 4.79
2179 10084 3.432588 CGCACTCCTCGTCGTCCT 61.433 66.667 0.00 0.00 0.00 3.85
2180 10085 2.486042 GCACTCCTCGTCGTCCTC 59.514 66.667 0.00 0.00 0.00 3.71
2181 10086 3.053849 GCACTCCTCGTCGTCCTCC 62.054 68.421 0.00 0.00 0.00 4.30
2182 10087 1.377463 CACTCCTCGTCGTCCTCCT 60.377 63.158 0.00 0.00 0.00 3.69
2183 10088 1.078285 ACTCCTCGTCGTCCTCCTC 60.078 63.158 0.00 0.00 0.00 3.71
2184 10089 1.820481 CTCCTCGTCGTCCTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
2185 10090 3.203412 CCTCGTCGTCCTCCTCCG 61.203 72.222 0.00 0.00 0.00 4.63
2191 10961 1.377612 TCGTCCTCCTCCGACAGAA 59.622 57.895 0.00 0.00 0.00 3.02
2194 10964 0.747852 GTCCTCCTCCGACAGAATCC 59.252 60.000 0.00 0.00 0.00 3.01
2195 10965 0.397254 TCCTCCTCCGACAGAATCCC 60.397 60.000 0.00 0.00 0.00 3.85
2196 10966 1.403687 CCTCCTCCGACAGAATCCCC 61.404 65.000 0.00 0.00 0.00 4.81
2197 10967 0.687757 CTCCTCCGACAGAATCCCCA 60.688 60.000 0.00 0.00 0.00 4.96
2199 10969 1.144936 CTCCGACAGAATCCCCAGC 59.855 63.158 0.00 0.00 0.00 4.85
2203 10973 1.817099 GACAGAATCCCCAGCTGCG 60.817 63.158 8.66 0.00 33.03 5.18
2335 11241 4.834453 CAGCTGCCTCCTGCTCCG 62.834 72.222 0.00 0.00 43.36 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.725148 CGCTCTTTTTCATCCTATAGCATAAAT 58.275 33.333 0.00 0.00 0.00 1.40
8 9 7.173218 CCGCTCTTTTTCATCCTATAGCATAAA 59.827 37.037 0.00 0.00 0.00 1.40
9 10 6.650807 CCGCTCTTTTTCATCCTATAGCATAA 59.349 38.462 0.00 0.00 0.00 1.90
10 11 6.166279 CCGCTCTTTTTCATCCTATAGCATA 58.834 40.000 0.00 0.00 0.00 3.14
11 12 4.999950 CCGCTCTTTTTCATCCTATAGCAT 59.000 41.667 0.00 0.00 0.00 3.79
13 14 4.381411 ACCGCTCTTTTTCATCCTATAGC 58.619 43.478 0.00 0.00 0.00 2.97
16 17 4.816925 GCTAACCGCTCTTTTTCATCCTAT 59.183 41.667 0.00 0.00 35.14 2.57
17 18 4.189231 GCTAACCGCTCTTTTTCATCCTA 58.811 43.478 0.00 0.00 35.14 2.94
18 19 3.010420 GCTAACCGCTCTTTTTCATCCT 58.990 45.455 0.00 0.00 35.14 3.24
19 20 2.097629 GGCTAACCGCTCTTTTTCATCC 59.902 50.000 0.00 0.00 39.13 3.51
49 50 3.047280 TGTGTCCAATGCGCCGAC 61.047 61.111 4.18 5.99 0.00 4.79
51 52 1.739929 TAGTGTGTCCAATGCGCCG 60.740 57.895 4.18 0.00 0.00 6.46
52 53 1.644786 GGTAGTGTGTCCAATGCGCC 61.645 60.000 4.18 0.00 0.00 6.53
53 54 1.794222 GGTAGTGTGTCCAATGCGC 59.206 57.895 0.00 0.00 0.00 6.09
54 55 0.389296 TCGGTAGTGTGTCCAATGCG 60.389 55.000 0.00 0.00 0.00 4.73
55 56 1.933853 GATCGGTAGTGTGTCCAATGC 59.066 52.381 0.00 0.00 0.00 3.56
56 57 2.093711 TGGATCGGTAGTGTGTCCAATG 60.094 50.000 0.00 0.00 36.12 2.82
58 59 1.634960 TGGATCGGTAGTGTGTCCAA 58.365 50.000 0.00 0.00 36.12 3.53
59 60 1.634960 TTGGATCGGTAGTGTGTCCA 58.365 50.000 0.00 0.00 37.20 4.02
60 61 2.754946 TTTGGATCGGTAGTGTGTCC 57.245 50.000 0.00 0.00 0.00 4.02
61 62 4.113354 GAGATTTGGATCGGTAGTGTGTC 58.887 47.826 0.00 0.00 37.37 3.67
62 63 3.513912 TGAGATTTGGATCGGTAGTGTGT 59.486 43.478 0.00 0.00 37.37 3.72
63 64 4.123497 TGAGATTTGGATCGGTAGTGTG 57.877 45.455 0.00 0.00 37.37 3.82
64 65 4.819105 TTGAGATTTGGATCGGTAGTGT 57.181 40.909 0.00 0.00 37.37 3.55
67 68 4.513442 TGGTTTGAGATTTGGATCGGTAG 58.487 43.478 0.00 0.00 37.37 3.18
69 70 3.433306 TGGTTTGAGATTTGGATCGGT 57.567 42.857 0.00 0.00 37.37 4.69
72 73 3.756434 TCGGTTGGTTTGAGATTTGGATC 59.244 43.478 0.00 0.00 0.00 3.36
73 74 3.761897 TCGGTTGGTTTGAGATTTGGAT 58.238 40.909 0.00 0.00 0.00 3.41
75 76 3.638484 GTTCGGTTGGTTTGAGATTTGG 58.362 45.455 0.00 0.00 0.00 3.28
76 77 3.296628 CGTTCGGTTGGTTTGAGATTTG 58.703 45.455 0.00 0.00 0.00 2.32
78 79 1.265905 GCGTTCGGTTGGTTTGAGATT 59.734 47.619 0.00 0.00 0.00 2.40
80 81 1.161563 GGCGTTCGGTTGGTTTGAGA 61.162 55.000 0.00 0.00 0.00 3.27
81 82 1.281656 GGCGTTCGGTTGGTTTGAG 59.718 57.895 0.00 0.00 0.00 3.02
82 83 2.535788 CGGCGTTCGGTTGGTTTGA 61.536 57.895 0.00 0.00 34.75 2.69
83 84 2.051703 CGGCGTTCGGTTGGTTTG 60.052 61.111 0.00 0.00 34.75 2.93
105 106 2.546778 TGTCTATTTCAATCGGCCGTC 58.453 47.619 27.15 3.14 0.00 4.79
106 107 2.684001 TGTCTATTTCAATCGGCCGT 57.316 45.000 27.15 10.00 0.00 5.68
107 108 4.349663 TTTTGTCTATTTCAATCGGCCG 57.650 40.909 22.12 22.12 0.00 6.13
128 129 2.637947 AGGGCGCATTTGTTTGTTTTT 58.362 38.095 10.83 0.00 0.00 1.94
129 130 2.323968 AGGGCGCATTTGTTTGTTTT 57.676 40.000 10.83 0.00 0.00 2.43
130 131 2.209273 GAAGGGCGCATTTGTTTGTTT 58.791 42.857 10.83 0.00 0.00 2.83
131 132 1.864565 GAAGGGCGCATTTGTTTGTT 58.135 45.000 10.83 0.00 0.00 2.83
132 133 0.318614 CGAAGGGCGCATTTGTTTGT 60.319 50.000 10.83 0.00 0.00 2.83
134 135 0.387565 AACGAAGGGCGCATTTGTTT 59.612 45.000 19.18 8.31 46.04 2.83
135 136 0.387565 AAACGAAGGGCGCATTTGTT 59.612 45.000 19.18 19.18 46.04 2.83
137 138 1.008361 CCAAACGAAGGGCGCATTTG 61.008 55.000 10.83 10.06 46.04 2.32
141 142 2.975799 GTCCAAACGAAGGGCGCA 60.976 61.111 10.83 0.00 46.04 6.09
142 143 3.733960 GGTCCAAACGAAGGGCGC 61.734 66.667 0.00 0.00 46.04 6.53
145 146 0.889186 CCACAGGTCCAAACGAAGGG 60.889 60.000 0.00 0.00 0.00 3.95
146 147 0.179029 ACCACAGGTCCAAACGAAGG 60.179 55.000 0.00 0.00 0.00 3.46
148 149 1.384525 CAACCACAGGTCCAAACGAA 58.615 50.000 0.00 0.00 33.12 3.85
149 150 0.464735 CCAACCACAGGTCCAAACGA 60.465 55.000 0.00 0.00 33.12 3.85
150 151 0.464735 TCCAACCACAGGTCCAAACG 60.465 55.000 0.00 0.00 33.12 3.60
151 152 1.613437 CATCCAACCACAGGTCCAAAC 59.387 52.381 0.00 0.00 33.12 2.93
154 155 1.074775 GCATCCAACCACAGGTCCA 59.925 57.895 0.00 0.00 33.12 4.02
155 156 1.074775 TGCATCCAACCACAGGTCC 59.925 57.895 0.00 0.00 33.12 4.46
156 157 1.244019 GGTGCATCCAACCACAGGTC 61.244 60.000 0.00 0.00 33.12 3.85
158 159 0.962356 GAGGTGCATCCAACCACAGG 60.962 60.000 0.00 0.00 39.02 4.00
159 160 0.962356 GGAGGTGCATCCAACCACAG 60.962 60.000 1.24 0.00 39.34 3.66
160 161 1.074775 GGAGGTGCATCCAACCACA 59.925 57.895 1.24 0.00 39.34 4.17
161 162 1.678970 GGGAGGTGCATCCAACCAC 60.679 63.158 8.58 0.00 41.52 4.16
165 166 1.304381 GCAAGGGAGGTGCATCCAA 60.304 57.895 8.58 0.00 41.52 3.53
184 185 0.104304 AACGGGCTGTCGATACATCC 59.896 55.000 0.00 0.00 40.53 3.51
316 466 2.693591 GGCTCATGTACAGTACTGGCTA 59.306 50.000 26.12 12.06 34.19 3.93
317 467 1.482593 GGCTCATGTACAGTACTGGCT 59.517 52.381 26.12 9.42 34.19 4.75
318 468 1.802880 CGGCTCATGTACAGTACTGGC 60.803 57.143 26.12 18.08 34.19 4.85
319 469 1.802880 GCGGCTCATGTACAGTACTGG 60.803 57.143 26.12 8.66 34.19 4.00
338 488 4.735132 TCGCACGGTGGCTACAGC 62.735 66.667 10.60 1.93 41.58 4.40
362 1006 2.050351 CGAGCGTATACGGCTGGG 60.050 66.667 25.55 12.98 40.23 4.45
387 1488 0.865769 AACTTCATGTGAACGGTCGC 59.134 50.000 7.17 7.17 34.66 5.19
407 1508 1.004292 CGACCGTTTGTTTGTCTGGAC 60.004 52.381 0.00 0.00 0.00 4.02
442 1543 3.311322 TGATTCGCGAATATTGTGGGTTC 59.689 43.478 32.58 17.92 0.00 3.62
443 1544 3.275143 TGATTCGCGAATATTGTGGGTT 58.725 40.909 32.58 9.23 0.00 4.11
444 1545 2.912771 TGATTCGCGAATATTGTGGGT 58.087 42.857 32.58 10.04 0.00 4.51
445 1546 3.120199 GGATGATTCGCGAATATTGTGGG 60.120 47.826 32.58 0.00 0.00 4.61
446 1547 3.120199 GGGATGATTCGCGAATATTGTGG 60.120 47.826 32.58 0.00 0.00 4.17
447 1548 4.070581 GGGATGATTCGCGAATATTGTG 57.929 45.455 32.58 0.00 0.00 3.33
495 1739 4.393680 ACAGACTTGCACGACAAAAAGTTA 59.606 37.500 0.00 0.00 37.96 2.24
496 1740 3.190535 ACAGACTTGCACGACAAAAAGTT 59.809 39.130 0.00 0.00 37.96 2.66
497 1741 2.747446 ACAGACTTGCACGACAAAAAGT 59.253 40.909 0.00 0.00 37.96 2.66
498 1742 3.181511 TGACAGACTTGCACGACAAAAAG 60.182 43.478 0.00 0.00 37.96 2.27
502 1755 1.570813 CTGACAGACTTGCACGACAA 58.429 50.000 0.00 0.00 36.62 3.18
518 1771 2.276116 GGAGGTGCTGTCGTCCTGA 61.276 63.158 8.00 0.00 38.75 3.86
519 1772 2.262915 GGAGGTGCTGTCGTCCTG 59.737 66.667 8.00 0.00 38.75 3.86
520 1773 2.118513 AGGAGGTGCTGTCGTCCT 59.881 61.111 10.75 10.75 44.56 3.85
521 1774 2.574399 GAGGAGGTGCTGTCGTCC 59.426 66.667 7.43 7.43 41.13 4.79
522 1775 2.574399 GGAGGAGGTGCTGTCGTC 59.426 66.667 0.00 0.00 0.00 4.20
523 1776 2.997897 GGGAGGAGGTGCTGTCGT 60.998 66.667 0.00 0.00 0.00 4.34
524 1777 4.135153 CGGGAGGAGGTGCTGTCG 62.135 72.222 0.00 0.00 0.00 4.35
552 1805 0.947180 CGTTGTGGTAGGTTCCCGTG 60.947 60.000 0.00 0.00 0.00 4.94
555 1808 1.673337 GCCGTTGTGGTAGGTTCCC 60.673 63.158 0.00 0.00 41.21 3.97
609 1862 1.740296 GTTGGGATGGACGTGACCG 60.740 63.158 0.00 0.00 40.83 4.79
631 1889 1.069090 GCGGATGCAATCGGGACTA 59.931 57.895 12.74 0.00 46.86 2.59
745 2026 2.033602 TCTGCGACGAGACCAGGA 59.966 61.111 0.00 0.00 0.00 3.86
798 2079 4.595629 GCTAATGGCGCGTCATTG 57.404 55.556 40.59 30.79 37.82 2.82
812 2093 1.283905 GGGGAAGCAAGGGTTTAGCTA 59.716 52.381 0.00 0.00 37.70 3.32
813 2094 0.039764 GGGGAAGCAAGGGTTTAGCT 59.960 55.000 0.00 0.00 41.03 3.32
882 2163 2.450243 GGGAGGGAGAGGTGTGGA 59.550 66.667 0.00 0.00 0.00 4.02
939 2243 1.390565 TAGAAGAGACAGTAGGCGGC 58.609 55.000 0.00 0.00 0.00 6.53
940 2244 3.735514 GCTTTAGAAGAGACAGTAGGCGG 60.736 52.174 0.00 0.00 0.00 6.13
943 2247 6.270064 GCTAAGCTTTAGAAGAGACAGTAGG 58.730 44.000 3.20 0.00 0.00 3.18
944 2248 6.127591 TGGCTAAGCTTTAGAAGAGACAGTAG 60.128 42.308 3.20 0.00 0.00 2.57
945 2249 5.715279 TGGCTAAGCTTTAGAAGAGACAGTA 59.285 40.000 3.20 0.00 0.00 2.74
946 2250 4.528596 TGGCTAAGCTTTAGAAGAGACAGT 59.471 41.667 3.20 0.00 0.00 3.55
947 2251 5.078411 TGGCTAAGCTTTAGAAGAGACAG 57.922 43.478 3.20 0.00 0.00 3.51
948 2252 5.078411 CTGGCTAAGCTTTAGAAGAGACA 57.922 43.478 3.20 1.52 0.00 3.41
964 2268 2.764128 CGGAGGGGAAGCTGGCTA 60.764 66.667 0.00 0.00 0.00 3.93
977 2281 3.177194 TTGGTGCTGGTGGACGGAG 62.177 63.158 0.00 0.00 35.23 4.63
1425 6185 7.852945 GCCTCTAAAAATGAATCTCGTTGTATG 59.147 37.037 0.00 0.00 0.00 2.39
1477 6238 5.762825 ATGTAGCAAGATAACATGGCAAG 57.237 39.130 0.00 0.00 32.74 4.01
1506 6267 7.621428 ATTCCATTAATAATGATCTGGAGCG 57.379 36.000 14.10 0.00 41.46 5.03
1549 6310 0.251832 GACACCCAGGAGAGGAGACA 60.252 60.000 0.00 0.00 0.00 3.41
1550 6311 0.973496 GGACACCCAGGAGAGGAGAC 60.973 65.000 0.00 0.00 0.00 3.36
1557 7489 1.612395 GCAGAGAGGACACCCAGGAG 61.612 65.000 0.00 0.00 33.88 3.69
1558 7490 1.610673 GCAGAGAGGACACCCAGGA 60.611 63.158 0.00 0.00 33.88 3.86
1560 7492 0.689623 AAAGCAGAGAGGACACCCAG 59.310 55.000 0.00 0.00 33.88 4.45
1569 7501 6.556212 TCTCGACTTGTAATAAAGCAGAGAG 58.444 40.000 7.45 0.00 37.73 3.20
1580 7512 7.494625 TGACTGAAAAGTTTCTCGACTTGTAAT 59.505 33.333 5.45 0.00 39.68 1.89
1581 7513 6.814644 TGACTGAAAAGTTTCTCGACTTGTAA 59.185 34.615 5.45 0.00 39.68 2.41
1582 7514 6.334989 TGACTGAAAAGTTTCTCGACTTGTA 58.665 36.000 5.45 0.00 39.68 2.41
1583 7515 5.175859 TGACTGAAAAGTTTCTCGACTTGT 58.824 37.500 5.45 0.00 39.68 3.16
1611 7543 1.440353 GCACACGTCGCATTTGACC 60.440 57.895 1.64 0.00 35.40 4.02
1715 7650 4.619437 AGAAACGCGGTGAAAAGTAAAA 57.381 36.364 12.47 0.00 0.00 1.52
1726 7661 0.666374 CAAAAGGGAAGAAACGCGGT 59.334 50.000 12.47 0.00 0.00 5.68
1751 7699 0.940833 TTTTTGTCAGCGACGCATCA 59.059 45.000 23.70 14.36 34.95 3.07
1768 7716 4.761975 TCATCGAACCGCCTACTATTTTT 58.238 39.130 0.00 0.00 0.00 1.94
1769 7717 4.395959 TCATCGAACCGCCTACTATTTT 57.604 40.909 0.00 0.00 0.00 1.82
1770 7718 4.098960 TCTTCATCGAACCGCCTACTATTT 59.901 41.667 0.00 0.00 0.00 1.40
1771 7719 3.635373 TCTTCATCGAACCGCCTACTATT 59.365 43.478 0.00 0.00 0.00 1.73
1772 7720 3.220110 TCTTCATCGAACCGCCTACTAT 58.780 45.455 0.00 0.00 0.00 2.12
1773 7721 2.646930 TCTTCATCGAACCGCCTACTA 58.353 47.619 0.00 0.00 0.00 1.82
1776 7724 1.546923 TGTTCTTCATCGAACCGCCTA 59.453 47.619 0.00 0.00 41.95 3.93
1793 7752 2.200899 GCAAAATCCAACTTGCGTGTT 58.799 42.857 0.00 0.00 38.66 3.32
1794 7753 1.851658 GCAAAATCCAACTTGCGTGT 58.148 45.000 0.00 0.00 38.66 4.49
1824 7783 7.094631 TCACTACAAATATTACGTCTTGTGCT 58.905 34.615 0.00 0.00 34.08 4.40
1898 7858 1.614996 TGCATCCACCGTTGTTGATT 58.385 45.000 0.00 0.00 0.00 2.57
1957 7938 6.391227 TTTTTCCTGAGACCAGTTTCATTC 57.609 37.500 0.00 0.00 38.74 2.67
1994 7975 9.720667 GCTTGCTAATTGTTCTTTTTCATTTTT 57.279 25.926 0.00 0.00 0.00 1.94
1995 7976 8.891720 TGCTTGCTAATTGTTCTTTTTCATTTT 58.108 25.926 0.00 0.00 0.00 1.82
1997 7978 8.436046 TTGCTTGCTAATTGTTCTTTTTCATT 57.564 26.923 0.00 0.00 0.00 2.57
1998 7979 8.337532 GTTTGCTTGCTAATTGTTCTTTTTCAT 58.662 29.630 0.00 0.00 0.00 2.57
1999 7980 7.548780 AGTTTGCTTGCTAATTGTTCTTTTTCA 59.451 29.630 0.00 0.00 0.00 2.69
2000 7981 7.909267 AGTTTGCTTGCTAATTGTTCTTTTTC 58.091 30.769 0.00 0.00 0.00 2.29
2018 8170 6.071447 TGCATACCATTTTGATGTAGTTTGCT 60.071 34.615 0.00 0.00 34.59 3.91
2038 8191 5.784578 ATACGTGGACTATCTTGTGCATA 57.215 39.130 0.00 0.00 40.21 3.14
2040 8193 5.784578 ATATACGTGGACTATCTTGTGCA 57.215 39.130 0.00 0.00 35.97 4.57
2050 8203 9.352191 AGAATTCACTACTAATATACGTGGACT 57.648 33.333 8.44 0.00 0.00 3.85
2051 8204 9.962783 AAGAATTCACTACTAATATACGTGGAC 57.037 33.333 8.44 0.00 0.00 4.02
2064 8217 9.654663 AGTATTTCGCTAAAAGAATTCACTACT 57.345 29.630 8.44 0.00 0.00 2.57
2066 8219 9.095065 GGAGTATTTCGCTAAAAGAATTCACTA 57.905 33.333 8.44 0.00 0.00 2.74
2081 8234 0.249363 GGACGGAGGGAGTATTTCGC 60.249 60.000 0.00 0.00 38.95 4.70
2110 9772 0.800012 GTAAAATTGCCCTCGCGACA 59.200 50.000 3.71 0.00 38.08 4.35
2111 9773 0.800012 TGTAAAATTGCCCTCGCGAC 59.200 50.000 3.71 0.00 38.08 5.19
2118 9780 4.456535 AGGGTGTTTTTGTAAAATTGCCC 58.543 39.130 11.85 11.85 34.89 5.36
2121 9783 7.841915 ACTGAAGGGTGTTTTTGTAAAATTG 57.158 32.000 0.00 0.00 0.00 2.32
2123 9785 8.318412 AGAAACTGAAGGGTGTTTTTGTAAAAT 58.682 29.630 0.00 0.00 36.64 1.82
2128 10033 4.159693 GGAGAAACTGAAGGGTGTTTTTGT 59.840 41.667 0.00 0.00 36.64 2.83
2133 10038 1.202770 CGGGAGAAACTGAAGGGTGTT 60.203 52.381 0.00 0.00 0.00 3.32
2135 10040 0.685097 TCGGGAGAAACTGAAGGGTG 59.315 55.000 0.00 0.00 34.75 4.61
2140 10045 2.567985 GTTTGGTCGGGAGAAACTGAA 58.432 47.619 0.00 0.00 42.89 3.02
2142 10047 1.235724 GGTTTGGTCGGGAGAAACTG 58.764 55.000 0.00 0.00 42.89 3.16
2147 10052 4.011517 GCGGGTTTGGTCGGGAGA 62.012 66.667 0.00 0.00 0.00 3.71
2148 10053 4.323477 TGCGGGTTTGGTCGGGAG 62.323 66.667 0.00 0.00 0.00 4.30
2149 10054 4.629523 GTGCGGGTTTGGTCGGGA 62.630 66.667 0.00 0.00 0.00 5.14
2150 10055 4.636435 AGTGCGGGTTTGGTCGGG 62.636 66.667 0.00 0.00 0.00 5.14
2151 10056 3.047877 GAGTGCGGGTTTGGTCGG 61.048 66.667 0.00 0.00 0.00 4.79
2152 10057 3.047877 GGAGTGCGGGTTTGGTCG 61.048 66.667 0.00 0.00 0.00 4.79
2153 10058 1.671379 GAGGAGTGCGGGTTTGGTC 60.671 63.158 0.00 0.00 0.00 4.02
2154 10059 2.430367 GAGGAGTGCGGGTTTGGT 59.570 61.111 0.00 0.00 0.00 3.67
2155 10060 2.742372 CGAGGAGTGCGGGTTTGG 60.742 66.667 0.00 0.00 0.00 3.28
2156 10061 2.027625 GACGAGGAGTGCGGGTTTG 61.028 63.158 0.00 0.00 0.00 2.93
2157 10062 2.342648 GACGAGGAGTGCGGGTTT 59.657 61.111 0.00 0.00 0.00 3.27
2158 10063 4.052229 CGACGAGGAGTGCGGGTT 62.052 66.667 0.00 0.00 0.00 4.11
2160 10065 4.477975 GACGACGAGGAGTGCGGG 62.478 72.222 0.00 0.00 0.00 6.13
2162 10067 3.384014 GAGGACGACGAGGAGTGCG 62.384 68.421 0.00 0.00 33.81 5.34
2165 10070 1.078285 GAGGAGGACGACGAGGAGT 60.078 63.158 0.00 0.00 0.00 3.85
2166 10071 1.820481 GGAGGAGGACGACGAGGAG 60.820 68.421 0.00 0.00 0.00 3.69
2167 10072 2.271497 GGAGGAGGACGACGAGGA 59.729 66.667 0.00 0.00 0.00 3.71
2168 10073 3.203412 CGGAGGAGGACGACGAGG 61.203 72.222 0.00 0.00 0.00 4.63
2169 10074 2.125229 TCGGAGGAGGACGACGAG 60.125 66.667 0.00 0.00 33.69 4.18
2173 10078 0.034380 ATTCTGTCGGAGGAGGACGA 60.034 55.000 0.00 0.00 37.22 4.20
2174 10079 0.382515 GATTCTGTCGGAGGAGGACG 59.617 60.000 0.00 0.00 37.22 4.79
2175 10080 0.747852 GGATTCTGTCGGAGGAGGAC 59.252 60.000 0.00 0.00 34.99 3.85
2176 10081 0.397254 GGGATTCTGTCGGAGGAGGA 60.397 60.000 0.00 0.00 0.00 3.71
2177 10082 1.403687 GGGGATTCTGTCGGAGGAGG 61.404 65.000 0.00 0.00 0.00 4.30
2178 10083 0.687757 TGGGGATTCTGTCGGAGGAG 60.688 60.000 0.00 0.00 0.00 3.69
2179 10084 0.687757 CTGGGGATTCTGTCGGAGGA 60.688 60.000 0.00 0.00 0.00 3.71
2180 10085 1.826024 CTGGGGATTCTGTCGGAGG 59.174 63.158 0.00 0.00 0.00 4.30
2181 10086 1.144936 GCTGGGGATTCTGTCGGAG 59.855 63.158 0.00 0.00 0.00 4.63
2182 10087 1.306141 AGCTGGGGATTCTGTCGGA 60.306 57.895 0.00 0.00 0.00 4.55
2183 10088 1.153289 CAGCTGGGGATTCTGTCGG 60.153 63.158 5.57 0.00 0.00 4.79
2184 10089 1.817099 GCAGCTGGGGATTCTGTCG 60.817 63.158 17.12 0.00 0.00 4.35
2185 10090 1.817099 CGCAGCTGGGGATTCTGTC 60.817 63.158 22.42 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.