Multiple sequence alignment - TraesCS2A01G453400

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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 TraesCS2A01G453400 chr2A 100.000 2321 0 0 1 2321 702936263 702938583 0.000000e+00 4287
1 TraesCS2A01G453400 chr2D 89.657 1750 98 49 398 2085 562231459 562233187 0.000000e+00 2152
2 TraesCS2A01G453400 chr2B 86.471 1567 109 50 820 2321 671901275 671902803 0.000000e+00 1624
3 TraesCS2A01G453400 chr2B 87.382 531 51 8 2 530 671900360 671900876 1.540000e-166 595
4 TraesCS2A01G453400 chr2B 91.071 56 4 1 2154 2209 671910943 671910997 8.890000e-10 75


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 TraesCS2A01G453400 chr2A 702936263 702938583 2320 False 4287.0 4287 100.0000 1 2321 1 chr2A.!!$F1 2320
1 TraesCS2A01G453400 chr2D 562231459 562233187 1728 False 2152.0 2152 89.6570 398 2085 1 chr2D.!!$F1 1687
2 TraesCS2A01G453400 chr2B 671900360 671902803 2443 False 1109.5 1624 86.9265 2 2321 2 chr2B.!!$F2 2319

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
790 792 0.035152 TTCGCCCAAGCATCTCACAT 60.035 50.0 0.0 0.0 39.83 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2241 0.658897 GGGTTTCGCTTGTTCGTTGA 59.341 50.0 0.0 0.0 0.0 3.18 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
47 49 2.438434 CCTGGGCCAAGGCGTAAG 60.438 66.667 15.12 2.45 43.06 2.34
54 56 1.305930 GCCAAGGCGTAAGGGTTCTG 61.306 60.000 0.00 0.00 38.28 3.02
64 66 2.486472 AAGGGTTCTGAGCATGACAG 57.514 50.000 12.19 12.19 0.00 3.51
72 74 3.705502 AGCATGACAGCTCCGTCT 58.294 55.556 0.00 0.00 42.18 4.18
74 76 1.812922 GCATGACAGCTCCGTCTGG 60.813 63.158 0.00 0.03 38.36 3.86
94 96 1.202698 GGGTGTCATACTCCATCAGCC 60.203 57.143 0.00 0.00 38.99 4.85
95 97 1.765314 GGTGTCATACTCCATCAGCCT 59.235 52.381 0.00 0.00 32.30 4.58
96 98 2.965831 GGTGTCATACTCCATCAGCCTA 59.034 50.000 0.00 0.00 32.30 3.93
98 100 3.006323 GTGTCATACTCCATCAGCCTAGG 59.994 52.174 3.67 3.67 0.00 3.02
99 101 3.235200 GTCATACTCCATCAGCCTAGGT 58.765 50.000 11.31 0.00 0.00 3.08
100 102 3.257127 GTCATACTCCATCAGCCTAGGTC 59.743 52.174 11.31 2.66 0.00 3.85
101 103 2.383442 TACTCCATCAGCCTAGGTCC 57.617 55.000 11.31 0.00 0.00 4.46
107 109 3.528370 CAGCCTAGGTCCGTCCGG 61.528 72.222 11.31 0.00 41.99 5.14
126 128 2.029073 CCGACGTGGCAAGTCAGT 59.971 61.111 28.32 7.35 38.46 3.41
130 132 0.861837 GACGTGGCAAGTCAGTTCTG 59.138 55.000 25.35 0.00 38.42 3.02
131 133 1.160329 ACGTGGCAAGTCAGTTCTGC 61.160 55.000 0.00 0.00 0.00 4.26
135 137 0.324943 GGCAAGTCAGTTCTGCCCTA 59.675 55.000 0.70 0.00 39.57 3.53
168 170 1.764723 TCAGGGTGTCATGATGCCTAG 59.235 52.381 15.25 9.86 0.00 3.02
202 204 0.736053 GCCGGCCGTCATAAAAATGA 59.264 50.000 26.12 0.00 0.00 2.57
204 206 1.268539 CCGGCCGTCATAAAAATGAGC 60.269 52.381 26.12 0.00 0.00 4.26
262 264 8.341903 GGGTCCATTTTGTGTTTAATTTTGAAG 58.658 33.333 0.00 0.00 0.00 3.02
269 271 5.546526 TGTGTTTAATTTTGAAGATGGGCC 58.453 37.500 0.00 0.00 0.00 5.80
270 272 5.070981 TGTGTTTAATTTTGAAGATGGGCCA 59.929 36.000 9.61 9.61 0.00 5.36
277 279 2.766345 TGAAGATGGGCCAAATTTGC 57.234 45.000 11.89 8.18 0.00 3.68
306 308 1.064314 ACTAGGAGACATGCCTCGTCT 60.064 52.381 7.54 0.57 46.32 4.18
307 309 2.028130 CTAGGAGACATGCCTCGTCTT 58.972 52.381 7.54 0.00 43.72 3.01
308 310 0.820871 AGGAGACATGCCTCGTCTTC 59.179 55.000 2.71 0.19 43.72 2.87
309 311 0.526524 GGAGACATGCCTCGTCTTCG 60.527 60.000 2.71 0.00 43.72 3.79
310 312 0.171455 GAGACATGCCTCGTCTTCGT 59.829 55.000 0.00 0.00 43.72 3.85
311 313 0.171455 AGACATGCCTCGTCTTCGTC 59.829 55.000 0.00 0.00 40.89 4.20
312 314 0.171455 GACATGCCTCGTCTTCGTCT 59.829 55.000 0.00 0.00 38.33 4.18
313 315 0.603569 ACATGCCTCGTCTTCGTCTT 59.396 50.000 0.00 0.00 38.33 3.01
329 331 8.259872 GTCTTCGTCTTCAAAAGCAATAAAAAC 58.740 33.333 0.00 0.00 0.00 2.43
343 345 1.029681 AAAAACCACCGTGCTTCTCC 58.970 50.000 0.00 0.00 0.00 3.71
344 346 0.106918 AAAACCACCGTGCTTCTCCA 60.107 50.000 0.00 0.00 0.00 3.86
345 347 0.106918 AAACCACCGTGCTTCTCCAA 60.107 50.000 0.00 0.00 0.00 3.53
347 349 0.106918 ACCACCGTGCTTCTCCAAAA 60.107 50.000 0.00 0.00 0.00 2.44
348 350 1.028905 CCACCGTGCTTCTCCAAAAA 58.971 50.000 0.00 0.00 0.00 1.94
375 377 4.385358 AAGAAAAACACCGTGCAAGATT 57.615 36.364 0.00 0.00 0.00 2.40
378 380 3.626028 AAAACACCGTGCAAGATTCTC 57.374 42.857 0.00 0.00 0.00 2.87
381 383 2.094659 ACCGTGCAAGATTCTCGCG 61.095 57.895 0.00 0.00 0.00 5.87
384 386 1.746727 CGTGCAAGATTCTCGCGGAG 61.747 60.000 6.13 2.33 0.00 4.63
432 434 1.002366 GTCACGATGCAGTTAGCCTG 58.998 55.000 0.00 0.00 44.83 4.85
441 443 1.731720 CAGTTAGCCTGGAGTCAAGC 58.268 55.000 0.00 0.00 37.54 4.01
450 452 1.968540 GGAGTCAAGCCCACTGCAC 60.969 63.158 0.00 0.00 44.83 4.57
452 454 2.985847 GTCAAGCCCACTGCACCC 60.986 66.667 0.00 0.00 44.83 4.61
460 462 1.077930 CCACTGCACCCCTCATCTG 60.078 63.158 0.00 0.00 0.00 2.90
577 579 3.303135 TCAAGCTGAGTCGCCGGT 61.303 61.111 1.90 0.00 0.00 5.28
578 580 1.974875 TCAAGCTGAGTCGCCGGTA 60.975 57.895 1.90 0.00 0.00 4.02
579 581 1.141881 CAAGCTGAGTCGCCGGTAT 59.858 57.895 1.90 0.00 0.00 2.73
617 619 1.447314 GCCCGGATCTCGTCGTTTT 60.447 57.895 0.73 0.00 37.11 2.43
619 621 1.138047 CCCGGATCTCGTCGTTTTCG 61.138 60.000 0.73 0.00 39.32 3.46
624 626 4.130281 CTCGTCGTTTTCGCCCGC 62.130 66.667 0.00 0.00 43.73 6.13
752 754 4.335647 CCAGAACCGCCCACAGCT 62.336 66.667 0.00 0.00 40.39 4.24
758 760 0.755327 AACCGCCCACAGCTTTCTTT 60.755 50.000 0.00 0.00 40.39 2.52
787 789 1.167851 CTTTTCGCCCAAGCATCTCA 58.832 50.000 0.00 0.00 39.83 3.27
790 792 0.035152 TTCGCCCAAGCATCTCACAT 60.035 50.000 0.00 0.00 39.83 3.21
850 963 2.436824 GGCCTCGAACCCTCTTGC 60.437 66.667 0.00 0.00 0.00 4.01
941 1054 2.041115 CACACCCTCGCTCTCTCGA 61.041 63.158 0.00 0.00 36.94 4.04
958 1072 3.759618 TCTCGAGTTCCTCTTCTTCTTCC 59.240 47.826 13.13 0.00 0.00 3.46
959 1073 2.826725 TCGAGTTCCTCTTCTTCTTCCC 59.173 50.000 0.00 0.00 0.00 3.97
979 1093 2.186384 CGAGCAAGGAGGAGGCTG 59.814 66.667 0.00 0.00 38.15 4.85
980 1094 2.124778 GAGCAAGGAGGAGGCTGC 60.125 66.667 0.00 0.00 38.15 5.25
981 1095 2.932194 AGCAAGGAGGAGGCTGCA 60.932 61.111 9.23 0.00 37.26 4.41
982 1096 2.268167 GAGCAAGGAGGAGGCTGCAT 62.268 60.000 9.23 0.00 38.15 3.96
983 1097 1.823041 GCAAGGAGGAGGCTGCATC 60.823 63.158 9.23 5.61 34.87 3.91
985 1099 2.739996 AAGGAGGAGGCTGCATCCG 61.740 63.158 25.57 0.00 43.22 4.18
986 1100 4.925861 GGAGGAGGCTGCATCCGC 62.926 72.222 25.55 25.55 42.02 5.54
988 1102 4.479993 AGGAGGCTGCATCCGCAC 62.480 66.667 25.57 4.01 45.36 5.34
1003 1127 3.129502 CACAGCCCTGCGTCATGG 61.130 66.667 0.00 0.00 0.00 3.66
1137 1261 3.310774 GCAACAGCGACATCTTCATGTAT 59.689 43.478 0.00 0.00 43.79 2.29
1322 1461 2.113433 TCTCCGTGGCGAGCTAGTC 61.113 63.158 0.00 0.00 0.00 2.59
1396 1538 1.003696 CTTGGGTTGAAGGAGGAGGAC 59.996 57.143 0.00 0.00 0.00 3.85
1406 1548 4.698625 AGGAGGACGCGGGGTTCT 62.699 66.667 12.47 5.58 37.11 3.01
1471 1618 5.619132 TCAATCTATTGATCTGCACAGGA 57.381 39.130 1.23 0.00 41.51 3.86
1473 1620 5.129980 TCAATCTATTGATCTGCACAGGACT 59.870 40.000 1.23 0.00 41.51 3.85
1477 1624 5.835280 TCTATTGATCTGCACAGGACTATCA 59.165 40.000 0.00 0.00 0.00 2.15
1479 1626 3.369175 TGATCTGCACAGGACTATCAGT 58.631 45.455 0.00 0.00 0.00 3.41
1480 1627 3.382865 TGATCTGCACAGGACTATCAGTC 59.617 47.826 0.00 0.00 44.32 3.51
1531 1684 0.256177 TTTTGGGGTTTGGGTTTGGC 59.744 50.000 0.00 0.00 0.00 4.52
1581 1734 2.350498 GCACCGTCGCTGTGTAATTATT 59.650 45.455 4.00 0.00 36.11 1.40
1590 1743 5.030295 CGCTGTGTAATTATTCAAGGCAAG 58.970 41.667 0.00 0.00 0.00 4.01
1616 1769 9.010366 GCGATGTAAAGTATTTCTCCAAATTTC 57.990 33.333 0.00 0.00 40.09 2.17
1673 1827 5.895636 ATGAGCATATTGTTTCGAACCAA 57.104 34.783 10.71 10.71 0.00 3.67
1696 1854 6.662755 AACAGATGTTGATGGTATGGTACAT 58.337 36.000 0.00 0.00 39.29 2.29
1697 1855 6.543465 AACAGATGTTGATGGTATGGTACATG 59.457 38.462 0.00 0.00 39.29 3.21
1698 1856 8.336873 AACAGATGTTGATGGTATGGTACATGG 61.337 40.741 0.00 0.00 39.29 3.66
1752 1927 1.266178 TGCCGTCCAAGAATCAGAGA 58.734 50.000 0.00 0.00 0.00 3.10
1775 1951 3.556775 CACAATTGTTTTCACTTGCCAGG 59.443 43.478 8.77 0.00 41.93 4.45
1779 1955 3.731652 TGTTTTCACTTGCCAGGATTG 57.268 42.857 0.00 0.00 0.00 2.67
1957 2165 9.914131 AAATCTCTGAAAAATACTAAACTTGGC 57.086 29.630 0.00 0.00 0.00 4.52
1989 2201 3.914426 ATCATGTACTGAACCAGGTCC 57.086 47.619 0.00 0.00 37.44 4.46
1991 2203 0.249398 ATGTACTGAACCAGGTCCGC 59.751 55.000 0.00 0.00 35.51 5.54
1992 2204 1.116536 TGTACTGAACCAGGTCCGCA 61.117 55.000 0.00 0.00 35.51 5.69
1993 2205 0.249398 GTACTGAACCAGGTCCGCAT 59.751 55.000 0.00 0.00 35.51 4.73
1998 2210 1.557371 TGAACCAGGTCCGCATATCAA 59.443 47.619 0.00 0.00 0.00 2.57
1999 2211 2.172505 TGAACCAGGTCCGCATATCAAT 59.827 45.455 0.00 0.00 0.00 2.57
2029 2241 5.166398 ACGAATACGAGGAAAACGAATCTT 58.834 37.500 0.00 0.00 42.66 2.40
2042 2254 2.096909 ACGAATCTTCAACGAACAAGCG 60.097 45.455 0.00 0.00 37.29 4.68
2049 2261 0.378962 CAACGAACAAGCGAAACCCA 59.621 50.000 0.00 0.00 34.83 4.51
2085 2298 4.142687 CGAATCGAGTAAACAAAAGGCCAT 60.143 41.667 5.01 0.00 0.00 4.40
2087 2300 2.227865 TCGAGTAAACAAAAGGCCATGC 59.772 45.455 5.01 0.00 0.00 4.06
2092 2305 1.999648 AACAAAAGGCCATGCAGAGA 58.000 45.000 5.01 0.00 0.00 3.10
2100 2313 3.371965 AGGCCATGCAGAGAAAATCAAT 58.628 40.909 5.01 0.00 0.00 2.57
2103 2316 3.795101 GCCATGCAGAGAAAATCAATTCG 59.205 43.478 0.00 0.00 34.46 3.34
2105 2318 5.271625 CCATGCAGAGAAAATCAATTCGAG 58.728 41.667 0.00 0.00 34.46 4.04
2108 2321 4.216042 TGCAGAGAAAATCAATTCGAGCAA 59.784 37.500 0.00 0.00 34.64 3.91
2111 2324 5.793952 CAGAGAAAATCAATTCGAGCAAGTG 59.206 40.000 0.00 0.00 34.46 3.16
2112 2325 5.471456 AGAGAAAATCAATTCGAGCAAGTGT 59.529 36.000 0.00 0.00 34.46 3.55
2113 2326 5.455392 AGAAAATCAATTCGAGCAAGTGTG 58.545 37.500 0.00 0.00 34.46 3.82
2115 2328 4.675190 AATCAATTCGAGCAAGTGTGAG 57.325 40.909 0.00 0.00 31.68 3.51
2116 2329 3.111853 TCAATTCGAGCAAGTGTGAGT 57.888 42.857 0.00 0.00 31.68 3.41
2117 2330 4.251543 TCAATTCGAGCAAGTGTGAGTA 57.748 40.909 0.00 0.00 31.68 2.59
2118 2331 4.627058 TCAATTCGAGCAAGTGTGAGTAA 58.373 39.130 0.00 0.00 31.68 2.24
2119 2332 5.053811 TCAATTCGAGCAAGTGTGAGTAAA 58.946 37.500 0.00 0.00 31.68 2.01
2120 2333 4.992381 ATTCGAGCAAGTGTGAGTAAAC 57.008 40.909 0.00 0.00 0.00 2.01
2121 2334 3.446310 TCGAGCAAGTGTGAGTAAACA 57.554 42.857 0.00 0.00 0.00 2.83
2122 2335 3.787785 TCGAGCAAGTGTGAGTAAACAA 58.212 40.909 0.00 0.00 0.00 2.83
2123 2336 4.185394 TCGAGCAAGTGTGAGTAAACAAA 58.815 39.130 0.00 0.00 0.00 2.83
2124 2337 4.632251 TCGAGCAAGTGTGAGTAAACAAAA 59.368 37.500 0.00 0.00 0.00 2.44
2125 2338 5.295787 TCGAGCAAGTGTGAGTAAACAAAAT 59.704 36.000 0.00 0.00 0.00 1.82
2126 2339 5.621228 CGAGCAAGTGTGAGTAAACAAAATC 59.379 40.000 0.00 0.00 0.00 2.17
2127 2340 5.831997 AGCAAGTGTGAGTAAACAAAATCC 58.168 37.500 0.00 0.00 0.00 3.01
2128 2341 4.982295 GCAAGTGTGAGTAAACAAAATCCC 59.018 41.667 0.00 0.00 0.00 3.85
2129 2342 5.528870 CAAGTGTGAGTAAACAAAATCCCC 58.471 41.667 0.00 0.00 0.00 4.81
2130 2343 5.061721 AGTGTGAGTAAACAAAATCCCCT 57.938 39.130 0.00 0.00 0.00 4.79
2131 2344 6.195600 AGTGTGAGTAAACAAAATCCCCTA 57.804 37.500 0.00 0.00 0.00 3.53
2132 2345 6.607019 AGTGTGAGTAAACAAAATCCCCTAA 58.393 36.000 0.00 0.00 0.00 2.69
2133 2346 7.064229 AGTGTGAGTAAACAAAATCCCCTAAA 58.936 34.615 0.00 0.00 0.00 1.85
2134 2347 7.562088 AGTGTGAGTAAACAAAATCCCCTAAAA 59.438 33.333 0.00 0.00 0.00 1.52
2135 2348 8.198778 GTGTGAGTAAACAAAATCCCCTAAAAA 58.801 33.333 0.00 0.00 0.00 1.94
2166 2379 5.447624 TTAAGTAAACAAAGAGCCAAGGC 57.552 39.130 2.02 2.02 42.33 4.35
2169 2382 2.896745 AAACAAAGAGCCAAGGCAAG 57.103 45.000 14.40 0.64 44.88 4.01
2199 2412 9.630098 AAATCAAATCAAACATGATACACACTC 57.370 29.630 0.00 0.00 33.60 3.51
2203 2416 4.002982 TCAAACATGATACACACTCCAGC 58.997 43.478 0.00 0.00 0.00 4.85
2237 2450 6.127281 TGGAGGAAATCAAATCAACCATGATG 60.127 38.462 0.00 0.00 45.60 3.07
2245 2458 0.964860 TCAACCATGATGCCCCAACG 60.965 55.000 0.00 0.00 0.00 4.10
2267 2480 2.100631 CAATCCTCCGGCGTCACAC 61.101 63.158 6.01 0.00 0.00 3.82
2272 2485 4.337060 TCCGGCGTCACACTCGTG 62.337 66.667 6.01 0.00 45.08 4.35
2300 2513 7.088272 ACGCCTCAATTATTTTACTGTTTTCC 58.912 34.615 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.581637 CTTTCGCTAAAGAAAACGGGC 58.418 47.619 4.76 0.00 44.14 6.13
32 33 4.041762 CCCTTACGCCTTGGCCCA 62.042 66.667 0.00 0.00 0.00 5.36
33 34 3.578968 AACCCTTACGCCTTGGCCC 62.579 63.158 0.00 0.00 0.00 5.80
47 49 0.035630 AGCTGTCATGCTCAGAACCC 60.036 55.000 17.60 4.36 39.34 4.11
64 66 1.327690 TATGACACCCCAGACGGAGC 61.328 60.000 0.00 0.00 0.00 4.70
69 71 1.568504 TGGAGTATGACACCCCAGAC 58.431 55.000 0.00 0.00 0.00 3.51
72 74 2.118679 CTGATGGAGTATGACACCCCA 58.881 52.381 0.00 0.00 0.00 4.96
74 76 1.202698 GGCTGATGGAGTATGACACCC 60.203 57.143 0.00 0.00 0.00 4.61
111 113 0.861837 CAGAACTGACTTGCCACGTC 59.138 55.000 0.00 0.00 0.00 4.34
131 133 0.852842 TGATCAAGGGGCCATTAGGG 59.147 55.000 1.74 0.00 40.85 3.53
216 218 9.232882 TGGACCCCATTTAAACTAGTAATAGAT 57.767 33.333 3.83 0.00 0.00 1.98
235 237 6.768381 TCAAAATTAAACACAAAATGGACCCC 59.232 34.615 0.00 0.00 0.00 4.95
240 242 9.881529 CCATCTTCAAAATTAAACACAAAATGG 57.118 29.630 0.00 0.00 0.00 3.16
250 252 8.574737 CAAATTTGGCCCATCTTCAAAATTAAA 58.425 29.630 10.49 0.00 34.63 1.52
262 264 2.477845 AACAGCAAATTTGGCCCATC 57.522 45.000 19.47 1.96 0.00 3.51
269 271 7.168135 GTCTCCTAGTGAAAAACAGCAAATTTG 59.832 37.037 14.03 14.03 0.00 2.32
270 272 7.147915 TGTCTCCTAGTGAAAAACAGCAAATTT 60.148 33.333 0.00 0.00 0.00 1.82
277 279 4.154918 GGCATGTCTCCTAGTGAAAAACAG 59.845 45.833 0.00 0.00 0.00 3.16
306 308 7.009723 GTGGTTTTTATTGCTTTTGAAGACGAA 59.990 33.333 0.00 0.00 0.00 3.85
307 309 6.474102 GTGGTTTTTATTGCTTTTGAAGACGA 59.526 34.615 0.00 0.00 0.00 4.20
308 310 6.292114 GGTGGTTTTTATTGCTTTTGAAGACG 60.292 38.462 0.00 0.00 0.00 4.18
309 311 6.292114 CGGTGGTTTTTATTGCTTTTGAAGAC 60.292 38.462 0.00 0.00 0.00 3.01
310 312 5.751028 CGGTGGTTTTTATTGCTTTTGAAGA 59.249 36.000 0.00 0.00 0.00 2.87
311 313 5.522097 ACGGTGGTTTTTATTGCTTTTGAAG 59.478 36.000 0.00 0.00 0.00 3.02
312 314 5.292101 CACGGTGGTTTTTATTGCTTTTGAA 59.708 36.000 0.00 0.00 0.00 2.69
313 315 4.806247 CACGGTGGTTTTTATTGCTTTTGA 59.194 37.500 0.00 0.00 0.00 2.69
329 331 1.028905 TTTTTGGAGAAGCACGGTGG 58.971 50.000 10.60 0.00 0.00 4.61
345 347 6.017852 TGCACGGTGTTTTTCTTTTTCTTTTT 60.018 30.769 10.24 0.00 0.00 1.94
347 349 4.991687 TGCACGGTGTTTTTCTTTTTCTTT 59.008 33.333 10.24 0.00 0.00 2.52
348 350 4.561105 TGCACGGTGTTTTTCTTTTTCTT 58.439 34.783 10.24 0.00 0.00 2.52
349 351 4.181309 TGCACGGTGTTTTTCTTTTTCT 57.819 36.364 10.24 0.00 0.00 2.52
350 352 4.623595 TCTTGCACGGTGTTTTTCTTTTTC 59.376 37.500 10.24 0.00 0.00 2.29
356 358 3.964909 AGAATCTTGCACGGTGTTTTTC 58.035 40.909 10.24 6.65 0.00 2.29
361 363 1.291877 GCGAGAATCTTGCACGGTGT 61.292 55.000 17.14 0.00 40.38 4.16
362 364 1.421485 GCGAGAATCTTGCACGGTG 59.579 57.895 17.14 3.15 40.38 4.94
384 386 2.768769 GTAGGGGACTGGGGGCTC 60.769 72.222 0.00 0.00 43.88 4.70
391 393 4.162690 GCGGCTGGTAGGGGACTG 62.163 72.222 0.00 0.00 43.88 3.51
432 434 1.968540 GTGCAGTGGGCTTGACTCC 60.969 63.158 0.00 0.00 45.15 3.85
441 443 2.273449 GATGAGGGGTGCAGTGGG 59.727 66.667 0.00 0.00 0.00 4.61
450 452 0.763652 CCAGTGGATCAGATGAGGGG 59.236 60.000 1.68 0.00 0.00 4.79
452 454 1.693062 CTCCCAGTGGATCAGATGAGG 59.307 57.143 11.95 0.00 40.80 3.86
577 579 0.311790 GGGTCGCGTCGATGGTAATA 59.688 55.000 5.77 0.00 38.42 0.98
578 580 1.066918 GGGTCGCGTCGATGGTAAT 59.933 57.895 5.77 0.00 38.42 1.89
579 581 2.491152 GGGTCGCGTCGATGGTAA 59.509 61.111 5.77 0.00 38.42 2.85
657 659 2.715737 TTATGTTTTGTTCTGCGGCC 57.284 45.000 0.00 0.00 0.00 6.13
658 660 3.638484 ACTTTATGTTTTGTTCTGCGGC 58.362 40.909 0.00 0.00 0.00 6.53
660 662 8.673626 ATCATTACTTTATGTTTTGTTCTGCG 57.326 30.769 0.00 0.00 0.00 5.18
752 754 3.230976 GAAAAGCTGAGGGGGAAAGAAA 58.769 45.455 0.00 0.00 0.00 2.52
758 760 2.351276 GCGAAAAGCTGAGGGGGA 59.649 61.111 0.00 0.00 44.04 4.81
802 804 2.630580 TGCTTGGGCGGAAAGTTTTATT 59.369 40.909 0.00 0.00 42.25 1.40
804 806 1.338655 GTGCTTGGGCGGAAAGTTTTA 59.661 47.619 0.00 0.00 42.25 1.52
890 1003 2.896443 CTGAGGTTCGGAGGAGGC 59.104 66.667 0.00 0.00 0.00 4.70
898 1011 2.097038 CCGCTTGAGCTGAGGTTCG 61.097 63.158 0.00 0.00 39.32 3.95
942 1055 2.791347 GGGGGAAGAAGAAGAGGAAC 57.209 55.000 0.00 0.00 0.00 3.62
958 1072 3.474570 CTCCTCCTTGCTCGGGGG 61.475 72.222 4.52 4.52 46.87 5.40
959 1073 3.474570 CCTCCTCCTTGCTCGGGG 61.475 72.222 0.00 0.00 0.00 5.73
985 1099 3.807538 CATGACGCAGGGCTGTGC 61.808 66.667 0.00 2.71 44.38 4.57
986 1100 3.129502 CCATGACGCAGGGCTGTG 61.130 66.667 0.00 0.00 45.86 3.66
1305 1444 2.409651 GACTAGCTCGCCACGGAG 59.590 66.667 0.00 0.00 37.11 4.63
1341 1480 5.074115 ACATAGTTCCTACTAGCTAGCCAG 58.926 45.833 20.91 16.70 40.09 4.85
1342 1481 5.063017 ACATAGTTCCTACTAGCTAGCCA 57.937 43.478 20.91 8.01 40.09 4.75
1343 1482 5.415389 GGTACATAGTTCCTACTAGCTAGCC 59.585 48.000 20.91 4.71 40.09 3.93
1344 1483 5.415389 GGGTACATAGTTCCTACTAGCTAGC 59.585 48.000 20.91 6.62 40.09 3.42
1345 1484 6.781943 AGGGTACATAGTTCCTACTAGCTAG 58.218 44.000 19.44 19.44 40.09 3.42
1396 1538 3.419759 CGTCCAAAGAACCCCGCG 61.420 66.667 0.00 0.00 0.00 6.46
1406 1548 0.106918 AAGAACACTGGCCGTCCAAA 60.107 50.000 0.00 0.00 42.91 3.28
1471 1618 2.311463 CGGTGATCCTGGACTGATAGT 58.689 52.381 0.00 0.00 0.00 2.12
1473 1620 1.040646 GCGGTGATCCTGGACTGATA 58.959 55.000 0.00 0.00 0.00 2.15
1477 1624 3.461773 CCGCGGTGATCCTGGACT 61.462 66.667 19.50 0.00 0.00 3.85
1531 1684 1.202879 ACCCGCTCTCTCCTCTCATAG 60.203 57.143 0.00 0.00 0.00 2.23
1581 1734 2.778299 ACTTTACATCGCTTGCCTTGA 58.222 42.857 0.00 0.00 0.00 3.02
1590 1743 8.911247 AAATTTGGAGAAATACTTTACATCGC 57.089 30.769 0.00 0.00 31.18 4.58
1652 1805 4.517075 TGTTGGTTCGAAACAATATGCTCA 59.483 37.500 29.73 19.06 34.68 4.26
1656 1809 6.611381 ACATCTGTTGGTTCGAAACAATATG 58.389 36.000 29.73 29.05 37.10 1.78
1666 1820 3.476295 CCATCAACATCTGTTGGTTCG 57.524 47.619 19.84 5.25 46.32 3.95
1673 1827 5.692115 TGTACCATACCATCAACATCTGT 57.308 39.130 0.00 0.00 0.00 3.41
1685 1839 5.347620 TCAGTTGTACCATGTACCATACC 57.652 43.478 2.22 0.00 0.00 2.73
1687 1845 8.871629 AATTTTCAGTTGTACCATGTACCATA 57.128 30.769 2.22 0.00 0.00 2.74
1715 1882 4.142403 ACGGCAAATCGTTCATCATTTGAT 60.142 37.500 8.66 0.00 40.89 2.57
1728 1896 1.737236 TGATTCTTGGACGGCAAATCG 59.263 47.619 0.00 0.00 0.00 3.34
1752 1927 4.183101 CTGGCAAGTGAAAACAATTGTGT 58.817 39.130 12.82 2.91 40.75 3.72
1779 1955 1.658409 GTTTTGTGGCACGAGCTGC 60.658 57.895 13.77 0.00 46.31 5.25
1837 2042 2.403132 ATTGGATGCGCTAGCTCCCC 62.403 60.000 16.58 11.45 45.42 4.81
1868 2073 1.804748 GAACTGCTTTCGGTTACAGGG 59.195 52.381 0.00 0.00 41.62 4.45
1957 2165 0.751277 TACATGATTTGCTGGGCCGG 60.751 55.000 8.39 8.39 0.00 6.13
1989 2201 9.946418 TCGTATTCGTATTTAAATTGATATGCG 57.054 29.630 5.91 13.84 38.33 4.73
1998 2210 9.086336 TCGTTTTCCTCGTATTCGTATTTAAAT 57.914 29.630 5.89 5.89 38.33 1.40
1999 2211 8.459521 TCGTTTTCCTCGTATTCGTATTTAAA 57.540 30.769 0.00 0.00 38.33 1.52
2029 2241 0.658897 GGGTTTCGCTTGTTCGTTGA 59.341 50.000 0.00 0.00 0.00 3.18
2042 2254 4.061596 TCGCCAAATGAAAATTGGGTTTC 58.938 39.130 7.36 0.00 46.03 2.78
2049 2261 5.059404 ACTCGATTCGCCAAATGAAAATT 57.941 34.783 0.00 0.00 0.00 1.82
2085 2298 3.752747 TGCTCGAATTGATTTTCTCTGCA 59.247 39.130 0.00 0.00 0.00 4.41
2087 2300 5.793952 CACTTGCTCGAATTGATTTTCTCTG 59.206 40.000 0.00 0.00 0.00 3.35
2092 2305 5.009010 ACTCACACTTGCTCGAATTGATTTT 59.991 36.000 0.00 0.00 0.00 1.82
2100 2313 3.787785 TGTTTACTCACACTTGCTCGAA 58.212 40.909 0.00 0.00 0.00 3.71
2103 2316 5.915196 GGATTTTGTTTACTCACACTTGCTC 59.085 40.000 0.00 0.00 0.00 4.26
2105 2318 4.982295 GGGATTTTGTTTACTCACACTTGC 59.018 41.667 0.00 0.00 0.00 4.01
2108 2321 5.061721 AGGGGATTTTGTTTACTCACACT 57.938 39.130 0.00 0.00 0.00 3.55
2135 2348 9.967346 GGCTCTTTGTTTACTTAATTCTTCTTT 57.033 29.630 0.00 0.00 0.00 2.52
2136 2349 9.131791 TGGCTCTTTGTTTACTTAATTCTTCTT 57.868 29.630 0.00 0.00 0.00 2.52
2137 2350 8.691661 TGGCTCTTTGTTTACTTAATTCTTCT 57.308 30.769 0.00 0.00 0.00 2.85
2138 2351 9.399403 CTTGGCTCTTTGTTTACTTAATTCTTC 57.601 33.333 0.00 0.00 0.00 2.87
2139 2352 8.360390 CCTTGGCTCTTTGTTTACTTAATTCTT 58.640 33.333 0.00 0.00 0.00 2.52
2140 2353 7.523873 GCCTTGGCTCTTTGTTTACTTAATTCT 60.524 37.037 4.11 0.00 0.00 2.40
2141 2354 6.586463 GCCTTGGCTCTTTGTTTACTTAATTC 59.414 38.462 4.11 0.00 0.00 2.17
2158 2371 1.076024 TGATTTCCTCTTGCCTTGGCT 59.924 47.619 13.18 0.00 0.00 4.75
2166 2379 8.997621 ATCATGTTTGATTTGATTTCCTCTTG 57.002 30.769 0.00 0.00 39.64 3.02
2169 2382 9.294030 GTGTATCATGTTTGATTTGATTTCCTC 57.706 33.333 0.00 0.00 42.61 3.71
2203 2416 1.078426 ATTTCCTCCACCTTCGGCG 60.078 57.895 0.00 0.00 0.00 6.46
2267 2480 2.004583 TAATTGAGGCGTTCCACGAG 57.995 50.000 0.00 0.00 46.05 4.18
2272 2485 6.190954 ACAGTAAAATAATTGAGGCGTTCC 57.809 37.500 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.