Multiple sequence alignment - TraesCS7D01G295600

Loading Multiple Alignment...

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 TraesCS7D01G295600 chr7D 100.000 2530 0 0 1 2530 370516157 370518686 0.000000e+00 4673.0
1 TraesCS7D01G295600 chr7D 85.897 156 18 4 2062 2215 627566269 627566116 2.010000e-36 163.0
2 TraesCS7D01G295600 chr7D 78.906 128 23 4 283 409 129518345 129518221 1.610000e-12 84.2
3 TraesCS7D01G295600 chr1A 91.114 1508 93 23 472 1961 507001948 507003432 0.000000e+00 2004.0
4 TraesCS7D01G295600 chr1A 90.397 479 34 6 2062 2530 254729865 254729389 9.940000e-174 619.0
5 TraesCS7D01G295600 chr1A 94.574 129 6 1 347 474 254730627 254730499 5.520000e-47 198.0
6 TraesCS7D01G295600 chr1A 95.192 104 5 0 1954 2057 254730595 254730492 5.600000e-37 165.0
7 TraesCS7D01G295600 chr1D 89.013 1520 105 26 472 1961 410742357 410743844 0.000000e+00 1825.0
8 TraesCS7D01G295600 chr1D 91.875 480 27 6 2062 2530 11377187 11377665 0.000000e+00 660.0
9 TraesCS7D01G295600 chr1D 100.000 68 0 0 407 474 11376518 11376585 2.640000e-25 126.0
10 TraesCS7D01G295600 chr1B 88.620 1529 116 28 472 1952 553557263 553558781 0.000000e+00 1807.0
11 TraesCS7D01G295600 chr5D 91.632 478 30 4 2062 2530 134680969 134681445 0.000000e+00 652.0
12 TraesCS7D01G295600 chr5D 92.145 331 22 2 1 327 134679795 134680125 4.930000e-127 464.0
13 TraesCS7D01G295600 chr5D 84.168 499 47 13 2062 2530 166489037 166488541 2.970000e-124 455.0
14 TraesCS7D01G295600 chr5D 93.333 150 7 3 325 474 134680206 134680352 4.240000e-53 219.0
15 TraesCS7D01G295600 chr6A 91.004 478 30 7 2062 2528 151726442 151725967 1.280000e-177 632.0
16 TraesCS7D01G295600 chr6A 97.479 119 3 0 356 474 151727163 151727045 1.190000e-48 204.0
17 TraesCS7D01G295600 chr6A 85.859 99 9 5 298 395 493535265 493535359 1.600000e-17 100.0
18 TraesCS7D01G295600 chr6B 90.289 484 34 7 2057 2530 174676368 174675888 2.760000e-174 621.0
19 TraesCS7D01G295600 chr6B 98.319 119 2 0 356 474 174677074 174676956 2.550000e-50 209.0
20 TraesCS7D01G295600 chr5A 89.583 480 37 7 2062 2530 382610087 382609610 4.660000e-167 597.0
21 TraesCS7D01G295600 chr5A 96.639 119 4 0 356 474 382610808 382610690 5.520000e-47 198.0
22 TraesCS7D01G295600 chr5A 80.916 131 17 5 282 409 42399632 42399507 2.070000e-16 97.1
23 TraesCS7D01G295600 chr5A 85.000 100 8 5 298 395 123725088 123725182 7.450000e-16 95.3
24 TraesCS7D01G295600 chr4A 84.105 497 47 14 2062 2527 292836345 292836840 3.840000e-123 451.0
25 TraesCS7D01G295600 chr4A 80.503 159 19 8 2382 2530 644582230 644582074 7.400000e-21 111.0
26 TraesCS7D01G295600 chr4D 83.200 500 43 17 2062 2527 470789973 470790465 1.080000e-113 420.0
27 TraesCS7D01G295600 chr4B 81.481 135 18 5 283 415 285399099 285398970 1.240000e-18 104.0
28 TraesCS7D01G295600 chr5B 84.762 105 9 5 298 400 86077652 86077553 5.760000e-17 99.0
29 TraesCS7D01G295600 chr3B 82.727 110 12 6 2421 2524 376398346 376398238 9.640000e-15 91.6
30 TraesCS7D01G295600 chr2B 79.688 128 22 4 283 409 569462301 569462425 3.470000e-14 89.8


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 TraesCS7D01G295600 chr7D 370516157 370518686 2529 False 4673.000000 4673 100.000000 1 2530 1 chr7D.!!$F1 2529
1 TraesCS7D01G295600 chr1A 507001948 507003432 1484 False 2004.000000 2004 91.114000 472 1961 1 chr1A.!!$F1 1489
2 TraesCS7D01G295600 chr1A 254729389 254730627 1238 True 327.333333 619 93.387667 347 2530 3 chr1A.!!$R1 2183
3 TraesCS7D01G295600 chr1D 410742357 410743844 1487 False 1825.000000 1825 89.013000 472 1961 1 chr1D.!!$F1 1489
4 TraesCS7D01G295600 chr1D 11376518 11377665 1147 False 393.000000 660 95.937500 407 2530 2 chr1D.!!$F2 2123
5 TraesCS7D01G295600 chr1B 553557263 553558781 1518 False 1807.000000 1807 88.620000 472 1952 1 chr1B.!!$F1 1480
6 TraesCS7D01G295600 chr5D 134679795 134681445 1650 False 445.000000 652 92.370000 1 2530 3 chr5D.!!$F1 2529
7 TraesCS7D01G295600 chr6A 151725967 151727163 1196 True 418.000000 632 94.241500 356 2528 2 chr6A.!!$R1 2172
8 TraesCS7D01G295600 chr6B 174675888 174677074 1186 True 415.000000 621 94.304000 356 2530 2 chr6B.!!$R1 2174
9 TraesCS7D01G295600 chr5A 382609610 382610808 1198 True 397.500000 597 93.111000 356 2530 2 chr5A.!!$R2 2174

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
605 752 0.329596 GCTCCAGTGGAAGGATGGTT 59.67 55.0 14.17 0.0 35.51 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2302 0.457035 CAGCGCCAGCCAATACATTT 59.543 50.0 2.29 0.0 46.67 2.32 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
26 27 0.840288 TTGTGCCCAGGCTCCTTCTA 60.840 55.000 10.58 0.00 42.51 2.10
52 53 1.209383 CGCGTCTCCTTCGTCTTCA 59.791 57.895 0.00 0.00 0.00 3.02
60 61 2.802816 CTCCTTCGTCTTCAACCAACAG 59.197 50.000 0.00 0.00 0.00 3.16
86 87 3.332919 GACCCCGTTTTAGTTCCTCTTC 58.667 50.000 0.00 0.00 0.00 2.87
96 97 3.194005 AGTTCCTCTTCGAAACAGCAA 57.806 42.857 0.00 0.00 0.00 3.91
99 100 2.912771 TCCTCTTCGAAACAGCAACAA 58.087 42.857 0.00 0.00 0.00 2.83
102 103 1.329292 TCTTCGAAACAGCAACAACCG 59.671 47.619 0.00 0.00 0.00 4.44
158 159 3.458287 AACTTCGGTTGTGGATGCATCC 61.458 50.000 34.71 34.71 40.96 3.51
169 170 1.211457 GGATGCATCCTCTCTTGTGGT 59.789 52.381 34.20 0.00 43.73 4.16
179 180 1.902508 TCTCTTGTGGTAGAAGGGCAG 59.097 52.381 0.00 0.00 0.00 4.85
205 206 5.989777 TCTGTAGACCTTGTACAAGAAAAGC 59.010 40.000 32.50 19.96 40.79 3.51
210 211 4.952460 ACCTTGTACAAGAAAAGCGACTA 58.048 39.130 32.50 0.00 40.79 2.59
213 214 6.485648 ACCTTGTACAAGAAAAGCGACTAAAT 59.514 34.615 32.50 0.00 40.79 1.40
336 424 7.225341 TGCAGCAGTTCAATGTATATTAGAGTG 59.775 37.037 0.00 0.00 0.00 3.51
354 442 8.894768 TTAGAGTGGAAAGAAGAGAAAAGAAG 57.105 34.615 0.00 0.00 0.00 2.85
505 652 1.419387 GGTGCCAGAGATATCTTGGCT 59.581 52.381 34.12 18.12 45.20 4.75
605 752 0.329596 GCTCCAGTGGAAGGATGGTT 59.670 55.000 14.17 0.00 35.51 3.67
612 759 2.576648 AGTGGAAGGATGGTTAAGGGTC 59.423 50.000 0.00 0.00 0.00 4.46
681 856 5.554437 TGATACCAAGGTAACAACAGACA 57.446 39.130 6.74 0.00 41.41 3.41
767 950 7.769220 ACTTATGCTTTGGAAGATTCAGATTG 58.231 34.615 0.00 0.00 0.00 2.67
797 989 6.041979 ACATTCTAAAAAGGCATCCTGTTGTT 59.958 34.615 0.00 0.00 30.34 2.83
802 995 3.350219 AAGGCATCCTGTTGTTCGTAT 57.650 42.857 0.00 0.00 32.13 3.06
837 1030 3.753797 TGTGTTTTGTAGTGTTGCACAGA 59.246 39.130 2.01 0.00 36.74 3.41
881 1074 0.767375 CATACATGGCTACCTGGGCT 59.233 55.000 0.00 0.00 0.00 5.19
966 1159 2.288666 TCTGTTGTGCAGTTCAACCTC 58.711 47.619 14.11 0.00 45.23 3.85
993 1186 1.808133 GCTCTAACTCCGCTTGATGGG 60.808 57.143 0.00 0.00 0.00 4.00
1056 1249 3.019564 GCCAACATTCTCTGTTAGCCAT 58.980 45.455 0.00 0.00 46.43 4.40
1100 1293 0.682532 TTGCTTCCACACACTTGCCA 60.683 50.000 0.00 0.00 0.00 4.92
1102 1295 0.242017 GCTTCCACACACTTGCCATC 59.758 55.000 0.00 0.00 0.00 3.51
1107 1300 2.305635 TCCACACACTTGCCATCTGTAT 59.694 45.455 0.00 0.00 0.00 2.29
1115 1308 4.397103 CACTTGCCATCTGTATTGTGACAT 59.603 41.667 0.00 0.00 0.00 3.06
1143 1336 4.948847 TGGTGGACATAGATCGAAATGAG 58.051 43.478 11.41 0.00 0.00 2.90
1343 1735 4.322650 CCTGGAAAGACTCAAGGAAGAGAG 60.323 50.000 0.00 0.00 38.98 3.20
1352 1744 4.061596 CTCAAGGAAGAGAGTTCGCTTTT 58.938 43.478 0.00 0.00 36.14 2.27
1353 1745 4.058817 TCAAGGAAGAGAGTTCGCTTTTC 58.941 43.478 0.00 0.00 36.14 2.29
1414 1806 9.492730 ACCTGGTAATTTCCATTTCTAATTGAT 57.507 29.630 4.05 0.00 36.84 2.57
1502 1894 0.970937 CTCCCAACGTCCAGGAGCTA 60.971 60.000 13.61 0.00 40.75 3.32
1503 1895 0.325296 TCCCAACGTCCAGGAGCTAT 60.325 55.000 0.00 0.00 0.00 2.97
1642 2050 2.232941 AGGATCTACTCGCCGTGAAAAA 59.767 45.455 0.00 0.00 0.00 1.94
1682 2094 1.878102 CGATATGGAAAAGAGGGGCGG 60.878 57.143 0.00 0.00 0.00 6.13
1691 2103 1.198759 AAGAGGGGCGGCAAAGTAGA 61.199 55.000 12.47 0.00 0.00 2.59
1694 2106 1.002502 GGGGCGGCAAAGTAGAAGT 60.003 57.895 12.47 0.00 0.00 3.01
1724 2136 6.434596 TCATCCGTGTCTTAATGTTTGTTTG 58.565 36.000 0.00 0.00 0.00 2.93
1730 2144 8.714179 CCGTGTCTTAATGTTTGTTTGAGTATA 58.286 33.333 0.00 0.00 0.00 1.47
1756 2170 4.513692 TGTTTTATCTTGTGGAGTGGTTCG 59.486 41.667 0.00 0.00 0.00 3.95
1839 2263 3.191371 GTCAGACAAAATTACCTGGCTGG 59.809 47.826 14.71 9.11 46.86 4.85
1840 2264 3.181434 TCAGACAAAATTACCTGGCTGGT 60.181 43.478 20.36 20.36 46.86 4.00
1850 2274 1.467920 CCTGGCTGGTTCATTCCTTC 58.532 55.000 1.62 0.00 0.00 3.46
1925 2353 2.937149 GGTAATTCTTCTTGGACTCCGC 59.063 50.000 0.00 0.00 0.00 5.54
1927 2355 0.108138 ATTCTTCTTGGACTCCGCCG 60.108 55.000 0.00 0.00 0.00 6.46
1936 2365 1.139095 GACTCCGCCGAACTCGAAT 59.861 57.895 0.00 0.00 43.02 3.34
1958 2387 5.625568 TCCATCTGATGAGTGAATGTGAT 57.374 39.130 18.92 0.00 0.00 3.06
1960 2389 5.820947 TCCATCTGATGAGTGAATGTGATTG 59.179 40.000 18.92 0.00 0.00 2.67
1961 2390 5.589050 CCATCTGATGAGTGAATGTGATTGT 59.411 40.000 18.92 0.00 0.00 2.71
1962 2391 6.095021 CCATCTGATGAGTGAATGTGATTGTT 59.905 38.462 18.92 0.00 0.00 2.83
1963 2392 6.490566 TCTGATGAGTGAATGTGATTGTTG 57.509 37.500 0.00 0.00 0.00 3.33
1964 2393 5.999600 TCTGATGAGTGAATGTGATTGTTGT 59.000 36.000 0.00 0.00 0.00 3.32
1965 2394 7.160726 TCTGATGAGTGAATGTGATTGTTGTA 58.839 34.615 0.00 0.00 0.00 2.41
1966 2395 7.332678 TCTGATGAGTGAATGTGATTGTTGTAG 59.667 37.037 0.00 0.00 0.00 2.74
1967 2396 6.372381 TGATGAGTGAATGTGATTGTTGTAGG 59.628 38.462 0.00 0.00 0.00 3.18
1968 2397 4.455533 TGAGTGAATGTGATTGTTGTAGGC 59.544 41.667 0.00 0.00 0.00 3.93
1969 2398 4.655963 AGTGAATGTGATTGTTGTAGGCT 58.344 39.130 0.00 0.00 0.00 4.58
1970 2399 5.072741 AGTGAATGTGATTGTTGTAGGCTT 58.927 37.500 0.00 0.00 0.00 4.35
1971 2400 5.048504 AGTGAATGTGATTGTTGTAGGCTTG 60.049 40.000 0.00 0.00 0.00 4.01
1972 2401 3.855689 ATGTGATTGTTGTAGGCTTGC 57.144 42.857 0.00 0.00 0.00 4.01
1973 2402 2.580962 TGTGATTGTTGTAGGCTTGCA 58.419 42.857 0.00 0.00 0.00 4.08
1974 2403 2.954989 TGTGATTGTTGTAGGCTTGCAA 59.045 40.909 0.00 0.00 0.00 4.08
1975 2404 3.573538 TGTGATTGTTGTAGGCTTGCAAT 59.426 39.130 0.00 0.00 31.49 3.56
1976 2405 4.764308 TGTGATTGTTGTAGGCTTGCAATA 59.236 37.500 0.00 0.00 31.49 1.90
1977 2406 5.106197 TGTGATTGTTGTAGGCTTGCAATAG 60.106 40.000 0.00 0.00 31.49 1.73
1978 2407 5.009631 TGATTGTTGTAGGCTTGCAATAGT 58.990 37.500 0.00 0.00 31.49 2.12
1979 2408 5.476599 TGATTGTTGTAGGCTTGCAATAGTT 59.523 36.000 0.00 0.00 31.49 2.24
1980 2409 5.782893 TTGTTGTAGGCTTGCAATAGTTT 57.217 34.783 0.00 0.00 31.49 2.66
1981 2410 6.885952 TTGTTGTAGGCTTGCAATAGTTTA 57.114 33.333 0.00 0.00 31.49 2.01
1982 2411 6.494893 TGTTGTAGGCTTGCAATAGTTTAG 57.505 37.500 0.00 0.00 31.49 1.85
1983 2412 6.234920 TGTTGTAGGCTTGCAATAGTTTAGA 58.765 36.000 0.00 0.00 31.49 2.10
1984 2413 6.884295 TGTTGTAGGCTTGCAATAGTTTAGAT 59.116 34.615 0.00 0.00 31.49 1.98
1985 2414 7.393234 TGTTGTAGGCTTGCAATAGTTTAGATT 59.607 33.333 0.00 0.00 31.49 2.40
1986 2415 7.320443 TGTAGGCTTGCAATAGTTTAGATTG 57.680 36.000 0.00 0.00 37.35 2.67
1987 2416 6.884295 TGTAGGCTTGCAATAGTTTAGATTGT 59.116 34.615 0.00 0.00 36.78 2.71
1988 2417 6.199937 AGGCTTGCAATAGTTTAGATTGTG 57.800 37.500 0.00 0.00 36.78 3.33
1989 2418 5.126061 AGGCTTGCAATAGTTTAGATTGTGG 59.874 40.000 0.00 0.00 36.78 4.17
1990 2419 5.343249 GCTTGCAATAGTTTAGATTGTGGG 58.657 41.667 0.00 0.00 36.78 4.61
1991 2420 5.679638 GCTTGCAATAGTTTAGATTGTGGGG 60.680 44.000 0.00 0.00 36.78 4.96
1992 2421 4.929479 TGCAATAGTTTAGATTGTGGGGT 58.071 39.130 0.00 0.00 36.78 4.95
1993 2422 5.329399 TGCAATAGTTTAGATTGTGGGGTT 58.671 37.500 0.00 0.00 36.78 4.11
1994 2423 6.486056 TGCAATAGTTTAGATTGTGGGGTTA 58.514 36.000 0.00 0.00 36.78 2.85
1995 2424 6.948886 TGCAATAGTTTAGATTGTGGGGTTAA 59.051 34.615 0.00 0.00 36.78 2.01
1996 2425 7.617723 TGCAATAGTTTAGATTGTGGGGTTAAT 59.382 33.333 0.00 0.00 36.78 1.40
1997 2426 7.920682 GCAATAGTTTAGATTGTGGGGTTAATG 59.079 37.037 0.00 0.00 36.78 1.90
1998 2427 9.184523 CAATAGTTTAGATTGTGGGGTTAATGA 57.815 33.333 0.00 0.00 31.00 2.57
1999 2428 9.762381 AATAGTTTAGATTGTGGGGTTAATGAA 57.238 29.630 0.00 0.00 0.00 2.57
2000 2429 9.762381 ATAGTTTAGATTGTGGGGTTAATGAAA 57.238 29.630 0.00 0.00 0.00 2.69
2001 2430 7.892609 AGTTTAGATTGTGGGGTTAATGAAAC 58.107 34.615 0.00 0.00 37.36 2.78
2002 2431 7.507616 AGTTTAGATTGTGGGGTTAATGAAACA 59.492 33.333 0.00 0.00 40.08 2.83
2003 2432 7.841282 TTAGATTGTGGGGTTAATGAAACAA 57.159 32.000 0.00 0.00 40.08 2.83
2004 2433 6.933514 AGATTGTGGGGTTAATGAAACAAT 57.066 33.333 8.43 8.43 40.06 2.71
2005 2434 7.315066 AGATTGTGGGGTTAATGAAACAATT 57.685 32.000 9.49 0.00 38.12 2.32
2006 2435 7.160726 AGATTGTGGGGTTAATGAAACAATTG 58.839 34.615 3.24 3.24 38.12 2.32
2007 2436 5.878406 TGTGGGGTTAATGAAACAATTGT 57.122 34.783 4.92 4.92 40.08 2.71
2008 2437 5.848406 TGTGGGGTTAATGAAACAATTGTC 58.152 37.500 12.39 0.49 40.08 3.18
2009 2438 5.221541 TGTGGGGTTAATGAAACAATTGTCC 60.222 40.000 12.39 5.85 40.08 4.02
2010 2439 4.284746 TGGGGTTAATGAAACAATTGTCCC 59.715 41.667 12.39 14.55 40.08 4.46
2011 2440 4.530553 GGGGTTAATGAAACAATTGTCCCT 59.469 41.667 20.89 7.39 40.08 4.20
2012 2441 5.717654 GGGGTTAATGAAACAATTGTCCCTA 59.282 40.000 20.89 7.26 40.08 3.53
2013 2442 6.127451 GGGGTTAATGAAACAATTGTCCCTAG 60.127 42.308 20.89 0.00 40.08 3.02
2014 2443 6.436218 GGGTTAATGAAACAATTGTCCCTAGT 59.564 38.462 12.39 1.31 40.08 2.57
2015 2444 7.039293 GGGTTAATGAAACAATTGTCCCTAGTT 60.039 37.037 12.39 0.62 40.08 2.24
2016 2445 8.364894 GGTTAATGAAACAATTGTCCCTAGTTT 58.635 33.333 12.39 0.00 40.08 2.66
2019 2448 8.706322 AATGAAACAATTGTCCCTAGTTTACT 57.294 30.769 12.39 0.00 33.04 2.24
2020 2449 8.706322 ATGAAACAATTGTCCCTAGTTTACTT 57.294 30.769 12.39 0.00 33.04 2.24
2021 2450 7.936584 TGAAACAATTGTCCCTAGTTTACTTG 58.063 34.615 12.39 0.00 33.04 3.16
2022 2451 7.776030 TGAAACAATTGTCCCTAGTTTACTTGA 59.224 33.333 12.39 0.00 33.04 3.02
2023 2452 8.528044 AAACAATTGTCCCTAGTTTACTTGAA 57.472 30.769 12.39 0.00 31.29 2.69
2024 2453 8.706322 AACAATTGTCCCTAGTTTACTTGAAT 57.294 30.769 12.39 0.00 0.00 2.57
2025 2454 8.336801 ACAATTGTCCCTAGTTTACTTGAATC 57.663 34.615 4.92 0.00 0.00 2.52
2026 2455 8.164070 ACAATTGTCCCTAGTTTACTTGAATCT 58.836 33.333 4.92 0.00 0.00 2.40
2027 2456 9.014297 CAATTGTCCCTAGTTTACTTGAATCTT 57.986 33.333 0.00 0.00 0.00 2.40
2028 2457 7.979444 TTGTCCCTAGTTTACTTGAATCTTG 57.021 36.000 0.00 0.00 0.00 3.02
2029 2458 5.938125 TGTCCCTAGTTTACTTGAATCTTGC 59.062 40.000 0.00 0.00 0.00 4.01
2030 2459 5.938125 GTCCCTAGTTTACTTGAATCTTGCA 59.062 40.000 0.00 0.00 0.00 4.08
2031 2460 6.092807 GTCCCTAGTTTACTTGAATCTTGCAG 59.907 42.308 0.00 0.00 0.00 4.41
2032 2461 6.013725 TCCCTAGTTTACTTGAATCTTGCAGA 60.014 38.462 0.00 0.00 0.00 4.26
2033 2462 6.655003 CCCTAGTTTACTTGAATCTTGCAGAA 59.345 38.462 0.00 0.00 0.00 3.02
2034 2463 7.337942 CCCTAGTTTACTTGAATCTTGCAGAAT 59.662 37.037 0.00 0.00 0.00 2.40
2035 2464 8.734386 CCTAGTTTACTTGAATCTTGCAGAATT 58.266 33.333 0.00 0.00 0.00 2.17
2042 2471 8.807667 ACTTGAATCTTGCAGAATTTAAAGTG 57.192 30.769 16.11 0.00 0.00 3.16
2043 2472 7.869429 ACTTGAATCTTGCAGAATTTAAAGTGG 59.131 33.333 16.11 0.00 0.00 4.00
2044 2473 7.288810 TGAATCTTGCAGAATTTAAAGTGGT 57.711 32.000 0.00 0.00 0.00 4.16
2045 2474 7.147312 TGAATCTTGCAGAATTTAAAGTGGTG 58.853 34.615 0.00 0.00 0.00 4.17
2046 2475 6.655078 ATCTTGCAGAATTTAAAGTGGTGT 57.345 33.333 0.00 0.00 0.00 4.16
2047 2476 7.759489 ATCTTGCAGAATTTAAAGTGGTGTA 57.241 32.000 0.00 0.00 0.00 2.90
2048 2477 7.759489 TCTTGCAGAATTTAAAGTGGTGTAT 57.241 32.000 0.00 0.00 0.00 2.29
2049 2478 7.592938 TCTTGCAGAATTTAAAGTGGTGTATG 58.407 34.615 0.00 0.00 0.00 2.39
2050 2479 5.708948 TGCAGAATTTAAAGTGGTGTATGC 58.291 37.500 0.00 0.00 0.00 3.14
2051 2480 5.242615 TGCAGAATTTAAAGTGGTGTATGCA 59.757 36.000 0.00 0.00 36.52 3.96
2052 2481 5.572896 GCAGAATTTAAAGTGGTGTATGCAC 59.427 40.000 5.22 5.22 44.53 4.57
2053 2482 6.570378 GCAGAATTTAAAGTGGTGTATGCACT 60.570 38.462 13.86 0.00 44.65 4.40
2054 2483 7.361713 GCAGAATTTAAAGTGGTGTATGCACTA 60.362 37.037 13.86 4.72 44.65 2.74
2055 2484 8.677300 CAGAATTTAAAGTGGTGTATGCACTAT 58.323 33.333 13.86 0.00 44.65 2.12
2056 2485 8.677300 AGAATTTAAAGTGGTGTATGCACTATG 58.323 33.333 13.86 0.00 44.65 2.23
2057 2486 6.751514 TTTAAAGTGGTGTATGCACTATGG 57.248 37.500 13.86 0.00 44.65 2.74
2058 2487 4.568072 AAAGTGGTGTATGCACTATGGA 57.432 40.909 13.86 0.00 44.65 3.41
2059 2488 4.778213 AAGTGGTGTATGCACTATGGAT 57.222 40.909 13.86 0.00 44.65 3.41
2060 2489 4.778213 AGTGGTGTATGCACTATGGATT 57.222 40.909 13.86 0.00 44.65 3.01
2240 2670 6.566079 AATCACATCATAAGAAGGTCAGGA 57.434 37.500 0.00 0.00 0.00 3.86
2243 2673 6.409704 TCACATCATAAGAAGGTCAGGAAAG 58.590 40.000 0.00 0.00 0.00 2.62
2245 2675 6.538021 CACATCATAAGAAGGTCAGGAAAGAG 59.462 42.308 0.00 0.00 0.00 2.85
2254 2686 4.223953 AGGTCAGGAAAGAGTAACACAGA 58.776 43.478 0.00 0.00 0.00 3.41
2312 2746 6.885735 ATTTCACCGTTTCTTCACAAAAAG 57.114 33.333 0.00 0.00 0.00 2.27
2315 2749 4.111916 CACCGTTTCTTCACAAAAAGCAT 58.888 39.130 0.00 0.00 0.00 3.79
2490 2933 8.925700 CCAAGAAGTCCAAATTACAAAAATAGC 58.074 33.333 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.244178 GAAGGAGACGCGAGGAGTTT 59.756 55.000 15.93 0.00 0.00 2.66
52 53 2.594592 GGGTCGCTGCTGTTGGTT 60.595 61.111 0.00 0.00 0.00 3.67
60 61 1.232621 AACTAAAACGGGGTCGCTGC 61.233 55.000 0.00 0.00 40.63 5.25
86 87 2.003443 CGCGGTTGTTGCTGTTTCG 61.003 57.895 0.00 0.00 0.00 3.46
96 97 0.032952 TGAACTTCTAGCGCGGTTGT 59.967 50.000 19.09 8.12 0.00 3.32
99 100 0.601558 TTCTGAACTTCTAGCGCGGT 59.398 50.000 17.70 17.70 0.00 5.68
102 103 2.416547 TGCAATTCTGAACTTCTAGCGC 59.583 45.455 0.00 0.00 0.00 5.92
158 159 1.902508 TGCCCTTCTACCACAAGAGAG 59.097 52.381 0.00 0.00 0.00 3.20
169 170 2.736347 GTCTACAGACCTGCCCTTCTA 58.264 52.381 0.00 0.00 39.07 2.10
201 202 9.403110 CCGTGTAATACTATATTTAGTCGCTTT 57.597 33.333 0.00 0.00 39.42 3.51
205 206 7.272084 GGCACCGTGTAATACTATATTTAGTCG 59.728 40.741 0.00 0.00 39.42 4.18
210 211 4.687483 GCGGCACCGTGTAATACTATATTT 59.313 41.667 11.27 0.00 42.09 1.40
213 214 2.030007 GGCGGCACCGTGTAATACTATA 60.030 50.000 11.27 0.00 42.09 1.31
216 217 1.153509 GGCGGCACCGTGTAATACT 60.154 57.895 11.27 0.00 42.09 2.12
276 281 3.694043 TTTGTACACTGCTAGGCATCA 57.306 42.857 0.00 0.00 38.13 3.07
336 424 8.840833 ACATACTCTTCTTTTCTCTTCTTTCC 57.159 34.615 0.00 0.00 0.00 3.13
346 434 7.020010 CACATCTGCAACATACTCTTCTTTTC 58.980 38.462 0.00 0.00 0.00 2.29
350 438 4.019860 ACCACATCTGCAACATACTCTTCT 60.020 41.667 0.00 0.00 0.00 2.85
351 439 4.093998 CACCACATCTGCAACATACTCTTC 59.906 45.833 0.00 0.00 0.00 2.87
353 441 3.603532 CACCACATCTGCAACATACTCT 58.396 45.455 0.00 0.00 0.00 3.24
354 442 2.096496 GCACCACATCTGCAACATACTC 59.904 50.000 0.00 0.00 34.56 2.59
505 652 1.077805 TCCCCGCAGTGGAGAAGTA 59.922 57.895 0.00 0.00 42.00 2.24
605 752 2.357760 GCAACACGCCGACCCTTA 60.358 61.111 0.00 0.00 32.94 2.69
681 856 7.023197 ACTGTAAATTTAAACTGTTGCGACT 57.977 32.000 5.50 0.00 0.00 4.18
767 950 6.753744 CAGGATGCCTTTTTAGAATGTTTAGC 59.246 38.462 0.00 0.00 0.00 3.09
783 969 2.027192 ACATACGAACAACAGGATGCCT 60.027 45.455 0.00 0.00 42.53 4.75
797 989 5.142061 ACACACCAGAATAACACATACGA 57.858 39.130 0.00 0.00 0.00 3.43
802 995 5.906113 ACAAAACACACCAGAATAACACA 57.094 34.783 0.00 0.00 0.00 3.72
837 1030 6.753279 GTGCATGTGCTGATGTTTTATATTGT 59.247 34.615 6.55 0.00 42.66 2.71
881 1074 3.009033 ACTGCTTGTACAAGATTGGCCTA 59.991 43.478 34.43 7.96 40.79 3.93
966 1159 4.047822 CAAGCGGAGTTAGAGCAAGATAG 58.952 47.826 0.00 0.00 0.00 2.08
1056 1249 6.554982 AGTGATTAGTGATTACCTGGCATAGA 59.445 38.462 0.00 0.00 0.00 1.98
1100 1293 7.121168 CCACCAAAGTTATGTCACAATACAGAT 59.879 37.037 0.00 0.00 31.70 2.90
1102 1295 6.429692 TCCACCAAAGTTATGTCACAATACAG 59.570 38.462 0.00 0.00 31.70 2.74
1107 1300 4.527944 TGTCCACCAAAGTTATGTCACAA 58.472 39.130 0.00 0.00 0.00 3.33
1115 1308 5.925506 TCGATCTATGTCCACCAAAGTTA 57.074 39.130 0.00 0.00 0.00 2.24
1164 1357 1.647346 ACAACGCACGAAGAAACAGA 58.353 45.000 0.00 0.00 0.00 3.41
1212 1543 2.922503 TCCACCTCTGCGGCTTGA 60.923 61.111 0.00 0.00 35.61 3.02
1502 1894 2.766313 TGCGCTTTCACAGAGTACAAT 58.234 42.857 9.73 0.00 0.00 2.71
1503 1895 2.232756 TGCGCTTTCACAGAGTACAA 57.767 45.000 9.73 0.00 0.00 2.41
1668 2076 1.877576 CTTTGCCGCCCCTCTTTTCC 61.878 60.000 0.00 0.00 0.00 3.13
1674 2084 0.744771 CTTCTACTTTGCCGCCCCTC 60.745 60.000 0.00 0.00 0.00 4.30
1682 2094 8.276325 CACGGATGATAAATACTTCTACTTTGC 58.724 37.037 0.00 0.00 0.00 3.68
1691 2103 9.832445 ACATTAAGACACGGATGATAAATACTT 57.168 29.630 0.00 0.00 0.00 2.24
1724 2136 9.601217 ACTCCACAAGATAAAACACATATACTC 57.399 33.333 0.00 0.00 0.00 2.59
1730 2144 5.385198 ACCACTCCACAAGATAAAACACAT 58.615 37.500 0.00 0.00 0.00 3.21
1756 2170 8.109391 GTCAATTTTACGTTTTAACCAACCAAC 58.891 33.333 0.00 0.00 0.00 3.77
1787 2201 3.005897 ACACACTGCTACTCAATTCGACT 59.994 43.478 0.00 0.00 0.00 4.18
1870 2298 4.023279 CAGCGCCAGCCAATACATTTTATA 60.023 41.667 2.29 0.00 46.67 0.98
1873 2301 1.135024 CAGCGCCAGCCAATACATTTT 60.135 47.619 2.29 0.00 46.67 1.82
1874 2302 0.457035 CAGCGCCAGCCAATACATTT 59.543 50.000 2.29 0.00 46.67 2.32
1876 2304 2.484062 GCAGCGCCAGCCAATACAT 61.484 57.895 2.29 0.00 46.67 2.29
1925 2353 2.871182 TCAGATGGATTCGAGTTCGG 57.129 50.000 1.26 0.00 40.29 4.30
1927 2355 4.744137 CACTCATCAGATGGATTCGAGTTC 59.256 45.833 10.67 0.00 37.23 3.01
1936 2365 5.625568 ATCACATTCACTCATCAGATGGA 57.374 39.130 10.67 0.00 0.00 3.41
1958 2387 5.782893 AAACTATTGCAAGCCTACAACAA 57.217 34.783 4.94 0.00 0.00 2.83
1960 2389 6.737254 TCTAAACTATTGCAAGCCTACAAC 57.263 37.500 4.94 0.00 0.00 3.32
1961 2390 7.393234 ACAATCTAAACTATTGCAAGCCTACAA 59.607 33.333 4.94 0.00 37.77 2.41
1962 2391 6.884295 ACAATCTAAACTATTGCAAGCCTACA 59.116 34.615 4.94 0.00 37.77 2.74
1963 2392 7.189512 CACAATCTAAACTATTGCAAGCCTAC 58.810 38.462 4.94 0.00 37.77 3.18
1964 2393 6.318648 CCACAATCTAAACTATTGCAAGCCTA 59.681 38.462 4.94 0.00 37.77 3.93
1965 2394 5.126061 CCACAATCTAAACTATTGCAAGCCT 59.874 40.000 4.94 0.00 37.77 4.58
1966 2395 5.343249 CCACAATCTAAACTATTGCAAGCC 58.657 41.667 4.94 0.00 37.77 4.35
1967 2396 5.343249 CCCACAATCTAAACTATTGCAAGC 58.657 41.667 4.94 0.00 37.77 4.01
1968 2397 5.418840 ACCCCACAATCTAAACTATTGCAAG 59.581 40.000 4.94 0.00 37.77 4.01
1969 2398 5.329399 ACCCCACAATCTAAACTATTGCAA 58.671 37.500 0.00 0.00 37.77 4.08
1970 2399 4.929479 ACCCCACAATCTAAACTATTGCA 58.071 39.130 0.00 0.00 37.77 4.08
1971 2400 5.914898 AACCCCACAATCTAAACTATTGC 57.085 39.130 0.00 0.00 37.77 3.56
1972 2401 9.184523 TCATTAACCCCACAATCTAAACTATTG 57.815 33.333 0.00 0.00 39.68 1.90
1973 2402 9.762381 TTCATTAACCCCACAATCTAAACTATT 57.238 29.630 0.00 0.00 0.00 1.73
1974 2403 9.762381 TTTCATTAACCCCACAATCTAAACTAT 57.238 29.630 0.00 0.00 0.00 2.12
1975 2404 9.016438 GTTTCATTAACCCCACAATCTAAACTA 57.984 33.333 0.00 0.00 0.00 2.24
1976 2405 7.507616 TGTTTCATTAACCCCACAATCTAAACT 59.492 33.333 0.00 0.00 35.81 2.66
1977 2406 7.662897 TGTTTCATTAACCCCACAATCTAAAC 58.337 34.615 0.00 0.00 35.81 2.01
1978 2407 7.841282 TGTTTCATTAACCCCACAATCTAAA 57.159 32.000 0.00 0.00 35.81 1.85
1979 2408 7.841282 TTGTTTCATTAACCCCACAATCTAA 57.159 32.000 0.00 0.00 35.81 2.10
1980 2409 8.310382 CAATTGTTTCATTAACCCCACAATCTA 58.690 33.333 0.00 0.00 34.52 1.98
1981 2410 6.933514 ATTGTTTCATTAACCCCACAATCT 57.066 33.333 0.00 0.00 35.81 2.40
1982 2411 6.934083 ACAATTGTTTCATTAACCCCACAATC 59.066 34.615 4.92 0.00 34.52 2.67
1983 2412 6.836242 ACAATTGTTTCATTAACCCCACAAT 58.164 32.000 4.92 0.00 36.61 2.71
1984 2413 6.240549 ACAATTGTTTCATTAACCCCACAA 57.759 33.333 4.92 0.00 35.81 3.33
1985 2414 5.221541 GGACAATTGTTTCATTAACCCCACA 60.222 40.000 13.36 0.00 35.81 4.17
1986 2415 5.234752 GGACAATTGTTTCATTAACCCCAC 58.765 41.667 13.36 0.00 35.81 4.61
1987 2416 4.284746 GGGACAATTGTTTCATTAACCCCA 59.715 41.667 13.36 0.00 35.81 4.96
1988 2417 4.530553 AGGGACAATTGTTTCATTAACCCC 59.469 41.667 19.07 17.15 35.81 4.95
1989 2418 5.738619 AGGGACAATTGTTTCATTAACCC 57.261 39.130 13.36 15.14 35.81 4.11
1990 2419 7.462571 ACTAGGGACAATTGTTTCATTAACC 57.537 36.000 13.36 6.34 35.81 2.85
1993 2422 9.802039 AGTAAACTAGGGACAATTGTTTCATTA 57.198 29.630 13.36 4.21 33.63 1.90
1994 2423 8.706322 AGTAAACTAGGGACAATTGTTTCATT 57.294 30.769 13.36 5.09 33.63 2.57
1995 2424 8.576442 CAAGTAAACTAGGGACAATTGTTTCAT 58.424 33.333 13.36 8.69 33.63 2.57
1996 2425 7.776030 TCAAGTAAACTAGGGACAATTGTTTCA 59.224 33.333 13.36 0.00 33.63 2.69
1997 2426 8.161699 TCAAGTAAACTAGGGACAATTGTTTC 57.838 34.615 13.36 8.31 33.63 2.78
1998 2427 8.528044 TTCAAGTAAACTAGGGACAATTGTTT 57.472 30.769 13.36 3.64 35.43 2.83
1999 2428 8.706322 ATTCAAGTAAACTAGGGACAATTGTT 57.294 30.769 13.36 0.00 0.00 2.83
2000 2429 8.164070 AGATTCAAGTAAACTAGGGACAATTGT 58.836 33.333 11.78 11.78 0.00 2.71
2001 2430 8.567285 AGATTCAAGTAAACTAGGGACAATTG 57.433 34.615 3.24 3.24 0.00 2.32
2002 2431 9.014297 CAAGATTCAAGTAAACTAGGGACAATT 57.986 33.333 0.00 0.00 0.00 2.32
2003 2432 7.121315 GCAAGATTCAAGTAAACTAGGGACAAT 59.879 37.037 0.00 0.00 0.00 2.71
2004 2433 6.430000 GCAAGATTCAAGTAAACTAGGGACAA 59.570 38.462 0.00 0.00 0.00 3.18
2005 2434 5.938125 GCAAGATTCAAGTAAACTAGGGACA 59.062 40.000 0.00 0.00 0.00 4.02
2006 2435 5.938125 TGCAAGATTCAAGTAAACTAGGGAC 59.062 40.000 0.00 0.00 0.00 4.46
2007 2436 6.013725 TCTGCAAGATTCAAGTAAACTAGGGA 60.014 38.462 0.00 0.00 38.67 4.20
2008 2437 6.173339 TCTGCAAGATTCAAGTAAACTAGGG 58.827 40.000 0.00 0.00 38.67 3.53
2009 2438 7.672983 TTCTGCAAGATTCAAGTAAACTAGG 57.327 36.000 0.00 0.00 46.36 3.02
2016 2445 9.897744 CACTTTAAATTCTGCAAGATTCAAGTA 57.102 29.630 13.41 0.00 46.36 2.24
2017 2446 7.869429 CCACTTTAAATTCTGCAAGATTCAAGT 59.131 33.333 10.48 10.48 46.36 3.16
2018 2447 7.869429 ACCACTTTAAATTCTGCAAGATTCAAG 59.131 33.333 0.00 0.85 46.36 3.02
2019 2448 7.652909 CACCACTTTAAATTCTGCAAGATTCAA 59.347 33.333 0.00 0.00 46.36 2.69
2020 2449 7.147312 CACCACTTTAAATTCTGCAAGATTCA 58.853 34.615 0.00 0.00 46.36 2.57
2021 2450 7.147976 ACACCACTTTAAATTCTGCAAGATTC 58.852 34.615 0.00 0.00 46.36 2.52
2022 2451 7.054491 ACACCACTTTAAATTCTGCAAGATT 57.946 32.000 0.00 0.00 46.36 2.40
2023 2452 6.655078 ACACCACTTTAAATTCTGCAAGAT 57.345 33.333 0.00 0.00 46.36 2.40
2024 2453 7.592938 CATACACCACTTTAAATTCTGCAAGA 58.407 34.615 0.00 0.00 44.68 3.02
2025 2454 6.308766 GCATACACCACTTTAAATTCTGCAAG 59.691 38.462 0.00 0.00 0.00 4.01
2026 2455 6.155827 GCATACACCACTTTAAATTCTGCAA 58.844 36.000 0.00 0.00 0.00 4.08
2027 2456 5.242615 TGCATACACCACTTTAAATTCTGCA 59.757 36.000 0.00 0.00 32.84 4.41
2028 2457 5.572896 GTGCATACACCACTTTAAATTCTGC 59.427 40.000 0.00 0.00 41.21 4.26
2098 2528 6.597672 TCGAGCTGCTCCATCTTTTTAATTTA 59.402 34.615 22.97 0.00 0.00 1.40
2234 2664 5.602628 ACTTCTGTGTTACTCTTTCCTGAC 58.397 41.667 0.00 0.00 0.00 3.51
2240 2670 8.561738 TCTTTTGAACTTCTGTGTTACTCTTT 57.438 30.769 0.00 0.00 0.00 2.52
2243 2673 9.865484 GTTATCTTTTGAACTTCTGTGTTACTC 57.135 33.333 0.00 0.00 0.00 2.59
2254 2686 6.655078 AGTGCCATGTTATCTTTTGAACTT 57.345 33.333 0.00 0.00 0.00 2.66
2287 2720 7.514591 GCTTTTTGTGAAGAAACGGTGAAATAC 60.515 37.037 0.00 0.00 0.00 1.89
2303 2736 7.765360 AGAATTTGAACTTCATGCTTTTTGTGA 59.235 29.630 0.00 0.00 0.00 3.58
2415 2851 9.070179 AGTTTGTAATAAGTATTGAACCGGTTT 57.930 29.630 23.22 8.42 0.00 3.27


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

AutoCloner maintained by Alex Coulton.