Multiple sequence alignment - TraesCS6A01G370600

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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 TraesCS6A01G370600 chr6A 100.000 2908 0 0 1 2908 595482930 595480023 0.000000e+00 5371.0
1 TraesCS6A01G370600 chr6A 80.606 330 50 9 1141 1460 609160029 609159704 2.900000e-60 243.0
2 TraesCS6A01G370600 chr6A 82.456 171 28 2 1685 1854 609159428 609159259 6.490000e-32 148.0
3 TraesCS6A01G370600 chr6A 87.879 66 8 0 1546 1611 609159546 609159481 8.640000e-11 78.7
4 TraesCS6A01G370600 chr6A 100.000 28 0 0 1898 1925 595480999 595480972 5.000000e-03 52.8
5 TraesCS6A01G370600 chr6A 100.000 28 0 0 1932 1959 595481033 595481006 5.000000e-03 52.8
6 TraesCS6A01G370600 chr6D 89.896 1059 91 9 875 1930 449812529 449811484 0.000000e+00 1349.0
7 TraesCS6A01G370600 chr6D 87.918 778 49 20 2 744 449813396 449812629 0.000000e+00 874.0
8 TraesCS6A01G370600 chr6D 84.302 344 34 4 1932 2255 449811516 449811173 4.680000e-83 318.0
9 TraesCS6A01G370600 chr6D 86.598 291 24 4 2626 2908 449811096 449810813 1.010000e-79 307.0
10 TraesCS6A01G370600 chr6D 90.625 64 4 1 741 804 449812598 449812537 1.860000e-12 84.2
11 TraesCS6A01G370600 chr6D 88.235 51 2 4 1686 1732 452079100 452079050 1.130000e-04 58.4
12 TraesCS6A01G370600 chr6D 88.235 51 2 4 1686 1732 462406498 462406448 1.130000e-04 58.4
13 TraesCS6A01G370600 chr6B 86.520 1224 113 21 741 1930 681925221 681924016 0.000000e+00 1299.0
14 TraesCS6A01G370600 chr6B 90.090 999 60 19 1932 2907 681924048 681923066 0.000000e+00 1260.0
15 TraesCS6A01G370600 chr6B 81.806 742 69 34 29 747 681925948 681925250 1.960000e-156 562.0
16 TraesCS6A01G370600 chr4B 82.600 500 53 15 273 747 30805358 30804868 7.500000e-111 411.0
17 TraesCS6A01G370600 chr4B 81.289 481 58 15 291 747 498829395 498828923 7.660000e-96 361.0
18 TraesCS6A01G370600 chr1A 84.783 414 34 6 356 740 142890420 142890833 3.510000e-104 388.0
19 TraesCS6A01G370600 chr1A 87.687 268 28 4 2365 2628 434422942 434422676 1.010000e-79 307.0
20 TraesCS6A01G370600 chr1A 100.000 31 0 0 774 804 142890886 142890916 1.130000e-04 58.4
21 TraesCS6A01G370600 chr5A 81.733 427 51 13 817 1238 532463403 532462999 6.010000e-87 331.0
22 TraesCS6A01G370600 chr5A 88.213 263 30 1 2367 2628 566605368 566605106 2.180000e-81 313.0
23 TraesCS6A01G370600 chr5A 78.486 502 71 24 1416 1909 531891996 531892468 7.880000e-76 294.0
24 TraesCS6A01G370600 chr5A 78.287 502 73 24 1416 1909 532194612 532194139 1.020000e-74 291.0
25 TraesCS6A01G370600 chr5A 75.621 644 100 31 1332 1952 532462989 532462380 1.720000e-67 267.0
26 TraesCS6A01G370600 chr5A 81.893 243 19 13 1985 2204 531892462 531892702 6.400000e-42 182.0
27 TraesCS6A01G370600 chr5A 82.008 239 20 11 1990 2207 532194138 532193902 6.400000e-42 182.0
28 TraesCS6A01G370600 chr3A 88.679 265 29 1 2365 2628 706868067 706867803 3.620000e-84 322.0
29 TraesCS6A01G370600 chr2A 88.168 262 30 1 2368 2628 606574228 606574489 7.830000e-81 311.0
30 TraesCS6A01G370600 chr4D 89.157 249 25 2 2379 2626 120352394 120352147 2.810000e-80 309.0
31 TraesCS6A01G370600 chr2B 87.833 263 31 1 2367 2628 18809065 18809327 1.010000e-79 307.0
32 TraesCS6A01G370600 chr7D 87.786 262 31 1 2367 2627 96378914 96378653 3.640000e-79 305.0
33 TraesCS6A01G370600 chr7B 87.037 270 32 3 2361 2629 39930513 39930780 4.710000e-78 302.0
34 TraesCS6A01G370600 chr3D 77.046 562 45 24 214 747 578665576 578666081 2.240000e-61 246.0


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 TraesCS6A01G370600 chr6A 595480023 595482930 2907 True 1825.533333 5371 100.000000 1 2908 3 chr6A.!!$R1 2907
1 TraesCS6A01G370600 chr6D 449810813 449813396 2583 True 586.440000 1349 87.867800 2 2908 5 chr6D.!!$R3 2906
2 TraesCS6A01G370600 chr6B 681923066 681925948 2882 True 1040.333333 1299 86.138667 29 2907 3 chr6B.!!$R1 2878
3 TraesCS6A01G370600 chr5A 532462380 532463403 1023 True 299.000000 331 78.677000 817 1952 2 chr5A.!!$R3 1135
4 TraesCS6A01G370600 chr5A 531891996 531892702 706 False 238.000000 294 80.189500 1416 2204 2 chr5A.!!$F1 788
5 TraesCS6A01G370600 chr5A 532193902 532194612 710 True 236.500000 291 80.147500 1416 2207 2 chr5A.!!$R2 791
6 TraesCS6A01G370600 chr3D 578665576 578666081 505 False 246.000000 246 77.046000 214 747 1 chr3D.!!$F1 533

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
659 708 0.445436 GCGATTCTGCCACTCAAGTG 59.555 55.0 3.08 3.08 45.23 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2119 0.035458 GACCACAGGTTCAGGACTGG 59.965 60.0 0.0 0.0 39.0 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
26 30 3.308866 CAGCGGGTTTAATCTAGTTTCCG 59.691 47.826 6.92 6.92 39.26 4.30
34 38 7.201591 GGGTTTAATCTAGTTTCCGAAAGCTAC 60.202 40.741 0.00 0.00 0.00 3.58
53 57 2.227194 ACCCGTCTCCACAAACAAATC 58.773 47.619 0.00 0.00 0.00 2.17
257 280 2.107141 CGATTCCTCTGGCCGGAC 59.893 66.667 11.27 0.56 0.00 4.79
258 281 2.107141 GATTCCTCTGGCCGGACG 59.893 66.667 11.27 7.27 0.00 4.79
259 282 3.447025 GATTCCTCTGGCCGGACGG 62.447 68.421 11.02 11.02 38.57 4.79
260 283 3.976490 ATTCCTCTGGCCGGACGGA 62.976 63.158 20.38 20.38 37.50 4.69
265 288 4.271816 CTGGCCGGACGGAGATCG 62.272 72.222 12.16 0.00 45.88 3.69
266 289 4.807631 TGGCCGGACGGAGATCGA 62.808 66.667 15.99 0.00 42.43 3.59
267 290 3.296054 GGCCGGACGGAGATCGAT 61.296 66.667 15.99 0.00 42.43 3.59
271 294 1.601197 CGGACGGAGATCGATCCCT 60.601 63.158 21.66 4.15 42.43 4.20
276 299 1.979693 GGAGATCGATCCCTCCCCG 60.980 68.421 21.66 0.00 42.35 5.73
400 435 2.490217 CGCCTCTGTCGAATCGGT 59.510 61.111 1.76 0.00 0.00 4.69
403 445 1.874019 CCTCTGTCGAATCGGTGCG 60.874 63.158 1.76 0.00 0.00 5.34
430 472 4.204012 AGAGTAACTCGAGAGGGATGAAG 58.796 47.826 21.68 0.00 35.36 3.02
438 485 2.621055 CGAGAGGGATGAAGTACTCTGG 59.379 54.545 0.00 0.00 40.19 3.86
448 495 1.025647 AGTACTCTGGTCGCGTCTCC 61.026 60.000 5.77 8.39 0.00 3.71
469 516 3.603144 GATCTGAATCGCCTCTGGG 57.397 57.895 0.00 0.00 0.00 4.45
505 552 1.522900 GGGGAGAGGGGATTGATTGA 58.477 55.000 0.00 0.00 0.00 2.57
555 602 4.951254 TCGAATTGGCGGATATGTTCTAA 58.049 39.130 0.00 0.00 0.00 2.10
559 606 3.469008 TGGCGGATATGTTCTAAGGTG 57.531 47.619 0.00 0.00 0.00 4.00
572 619 1.206371 CTAAGGTGTTAGGTGTCCGGG 59.794 57.143 0.00 0.00 33.18 5.73
606 655 0.663153 AGAAATAATTCGGGCTGCGC 59.337 50.000 0.00 0.00 40.63 6.09
659 708 0.445436 GCGATTCTGCCACTCAAGTG 59.555 55.000 3.08 3.08 45.23 3.16
757 854 5.835819 TGTTAATCTGAAAACATTGGTGGGA 59.164 36.000 5.21 0.00 30.88 4.37
763 860 1.039856 AAACATTGGTGGGACTGTGC 58.960 50.000 0.00 0.00 0.00 4.57
765 862 2.034066 ATTGGTGGGACTGTGCGG 59.966 61.111 0.00 0.00 0.00 5.69
769 866 4.626081 GTGGGACTGTGCGGCTGT 62.626 66.667 0.00 0.00 0.00 4.40
770 867 4.624364 TGGGACTGTGCGGCTGTG 62.624 66.667 0.00 0.00 0.00 3.66
771 868 4.626081 GGGACTGTGCGGCTGTGT 62.626 66.667 0.00 0.00 0.00 3.72
772 869 3.349006 GGACTGTGCGGCTGTGTG 61.349 66.667 0.00 0.00 0.00 3.82
804 902 5.608437 TGGTTGAGAGCATCCTATTCCTTAT 59.392 40.000 0.00 0.00 35.36 1.73
805 903 6.169800 GGTTGAGAGCATCCTATTCCTTATC 58.830 44.000 0.00 0.00 33.66 1.75
806 904 6.169800 GTTGAGAGCATCCTATTCCTTATCC 58.830 44.000 0.00 0.00 33.66 2.59
807 905 5.659503 TGAGAGCATCCTATTCCTTATCCT 58.340 41.667 0.00 0.00 33.66 3.24
808 906 6.087456 TGAGAGCATCCTATTCCTTATCCTT 58.913 40.000 0.00 0.00 33.66 3.36
809 907 7.248976 TGAGAGCATCCTATTCCTTATCCTTA 58.751 38.462 0.00 0.00 33.66 2.69
813 911 7.019388 AGCATCCTATTCCTTATCCTTAGTCA 58.981 38.462 0.00 0.00 0.00 3.41
825 923 7.934120 CCTTATCCTTAGTCAAAGATAGGTTGG 59.066 40.741 0.00 0.00 37.38 3.77
834 932 5.476945 GTCAAAGATAGGTTGGTTTGGTCAT 59.523 40.000 0.00 0.00 31.97 3.06
835 933 6.657541 GTCAAAGATAGGTTGGTTTGGTCATA 59.342 38.462 0.00 0.00 31.97 2.15
836 934 7.339466 GTCAAAGATAGGTTGGTTTGGTCATAT 59.661 37.037 0.00 0.00 31.97 1.78
837 935 7.339212 TCAAAGATAGGTTGGTTTGGTCATATG 59.661 37.037 0.00 0.00 31.97 1.78
838 936 6.575244 AGATAGGTTGGTTTGGTCATATGA 57.425 37.500 0.00 0.00 0.00 2.15
839 937 7.154191 AGATAGGTTGGTTTGGTCATATGAT 57.846 36.000 9.02 0.00 0.00 2.45
886 985 4.251268 ACCTTTCGACCATTAGTTAGTGC 58.749 43.478 0.00 0.00 0.00 4.40
977 1076 6.647334 TCACAATTCCAGAAACTTGCATAA 57.353 33.333 0.00 0.00 0.00 1.90
983 1082 5.947228 TCCAGAAACTTGCATAACTGAAG 57.053 39.130 0.00 0.00 0.00 3.02
993 1092 4.005650 TGCATAACTGAAGAGCCTCAAAG 58.994 43.478 0.00 0.00 0.00 2.77
1109 1209 4.418392 CAGATTTTGGTAAGCATCAGCAC 58.582 43.478 0.00 0.00 45.49 4.40
1110 1210 3.445096 AGATTTTGGTAAGCATCAGCACC 59.555 43.478 0.00 0.00 45.49 5.01
1118 1218 3.354948 AAGCATCAGCACCTAACATCA 57.645 42.857 0.00 0.00 45.49 3.07
1123 1223 1.347378 TCAGCACCTAACATCACAGCA 59.653 47.619 0.00 0.00 0.00 4.41
1163 1271 2.396590 TCCACGTTGCCTAAATCTCC 57.603 50.000 0.00 0.00 0.00 3.71
1171 1279 4.571176 CGTTGCCTAAATCTCCTTAACTCC 59.429 45.833 0.00 0.00 0.00 3.85
1177 1285 6.274579 CCTAAATCTCCTTAACTCCGTCTTC 58.725 44.000 0.00 0.00 0.00 2.87
1212 1323 3.692690 TCTTTATAACAACTGGTGGCCC 58.307 45.455 0.00 0.00 0.00 5.80
1240 1351 5.047847 TGACAGGTTAGAGACTTTTGTTCG 58.952 41.667 0.00 0.00 0.00 3.95
1242 1353 3.807622 CAGGTTAGAGACTTTTGTTCGCA 59.192 43.478 0.00 0.00 0.00 5.10
1243 1354 4.452455 CAGGTTAGAGACTTTTGTTCGCAT 59.548 41.667 0.00 0.00 0.00 4.73
1245 1356 6.147164 CAGGTTAGAGACTTTTGTTCGCATTA 59.853 38.462 0.00 0.00 0.00 1.90
1260 1371 5.811399 TCGCATTACCAAACCTTTATCTG 57.189 39.130 0.00 0.00 0.00 2.90
1261 1372 4.638421 TCGCATTACCAAACCTTTATCTGG 59.362 41.667 0.00 0.00 34.95 3.86
1268 1379 6.280855 ACCAAACCTTTATCTGGTAATTGC 57.719 37.500 0.00 0.00 40.42 3.56
1279 1391 4.985538 TCTGGTAATTGCTTTCAGGAGTT 58.014 39.130 0.00 0.00 0.00 3.01
1285 1397 7.084486 GGTAATTGCTTTCAGGAGTTTGTAAG 58.916 38.462 0.00 0.00 0.00 2.34
1336 1448 1.048601 ACCTCATACTACCCATGCCG 58.951 55.000 0.00 0.00 0.00 5.69
1398 1510 5.357878 TGTCAAATGAGAATGATGGGTAAGC 59.642 40.000 0.00 0.00 0.00 3.09
1409 1532 6.859112 ATGATGGGTAAGCGATTATCTAGT 57.141 37.500 3.38 0.00 0.00 2.57
1410 1533 7.956328 ATGATGGGTAAGCGATTATCTAGTA 57.044 36.000 3.38 0.00 0.00 1.82
1411 1534 7.154435 TGATGGGTAAGCGATTATCTAGTAC 57.846 40.000 3.38 0.00 0.00 2.73
1460 1595 5.567534 GCGTTATGAATCACGTTTGTCAAAT 59.432 36.000 0.40 0.00 38.70 2.32
1469 1605 6.169419 TCACGTTTGTCAAATCTGATGATC 57.831 37.500 0.40 0.00 33.05 2.92
1470 1606 5.017612 CACGTTTGTCAAATCTGATGATCG 58.982 41.667 0.40 0.00 33.05 3.69
1525 1661 3.430929 CCTTAGTGGCACAGATGGTACTC 60.431 52.174 21.41 0.00 41.80 2.59
1526 1662 1.644509 AGTGGCACAGATGGTACTCA 58.355 50.000 21.41 0.00 41.80 3.41
1543 1687 4.373156 ACTCATAACCTTTTCTGGCAGT 57.627 40.909 15.27 0.00 0.00 4.40
1579 1730 6.427853 CCATATCTAGATTTCAAACGATGGCA 59.572 38.462 11.25 0.00 0.00 4.92
1581 1732 5.545658 TCTAGATTTCAAACGATGGCAAC 57.454 39.130 0.00 0.00 0.00 4.17
1592 1744 1.942657 CGATGGCAACTCTATTGTGGG 59.057 52.381 0.00 0.00 37.61 4.61
1612 1764 3.411446 GGACATCTGTGATGGACAAACA 58.589 45.455 11.55 0.00 32.80 2.83
1930 2092 1.227497 CAGCGCTTCATCCTCTCCC 60.227 63.158 7.50 0.00 0.00 4.30
1931 2093 2.279784 GCGCTTCATCCTCTCCCG 60.280 66.667 0.00 0.00 0.00 5.14
1932 2094 2.279784 CGCTTCATCCTCTCCCGC 60.280 66.667 0.00 0.00 0.00 6.13
1933 2095 2.279784 GCTTCATCCTCTCCCGCG 60.280 66.667 0.00 0.00 0.00 6.46
1934 2096 2.279784 CTTCATCCTCTCCCGCGC 60.280 66.667 0.00 0.00 0.00 6.86
1935 2097 3.798954 CTTCATCCTCTCCCGCGCC 62.799 68.421 0.00 0.00 0.00 6.53
1936 2098 4.841617 TCATCCTCTCCCGCGCCT 62.842 66.667 0.00 0.00 0.00 5.52
1937 2099 3.854669 CATCCTCTCCCGCGCCTT 61.855 66.667 0.00 0.00 0.00 4.35
1938 2100 3.541713 ATCCTCTCCCGCGCCTTC 61.542 66.667 0.00 0.00 0.00 3.46
1939 2101 4.761058 TCCTCTCCCGCGCCTTCT 62.761 66.667 0.00 0.00 0.00 2.85
1940 2102 4.521062 CCTCTCCCGCGCCTTCTG 62.521 72.222 0.00 0.00 0.00 3.02
1941 2103 3.452786 CTCTCCCGCGCCTTCTGA 61.453 66.667 0.00 0.00 0.00 3.27
1942 2104 2.759973 TCTCCCGCGCCTTCTGAT 60.760 61.111 0.00 0.00 0.00 2.90
1943 2105 2.279784 CTCCCGCGCCTTCTGATC 60.280 66.667 0.00 0.00 0.00 2.92
1944 2106 2.759973 TCCCGCGCCTTCTGATCT 60.760 61.111 0.00 0.00 0.00 2.75
1945 2107 2.279784 CCCGCGCCTTCTGATCTC 60.280 66.667 0.00 0.00 0.00 2.75
1946 2108 2.279784 CCGCGCCTTCTGATCTCC 60.280 66.667 0.00 0.00 0.00 3.71
1947 2109 2.496341 CGCGCCTTCTGATCTCCA 59.504 61.111 0.00 0.00 0.00 3.86
1948 2110 1.591059 CGCGCCTTCTGATCTCCAG 60.591 63.158 0.00 0.00 44.27 3.86
1949 2111 1.886777 GCGCCTTCTGATCTCCAGC 60.887 63.158 0.00 0.00 42.62 4.85
1950 2112 1.591059 CGCCTTCTGATCTCCAGCG 60.591 63.158 0.00 0.00 42.62 5.18
1951 2113 1.886777 GCCTTCTGATCTCCAGCGC 60.887 63.158 0.00 0.00 42.62 5.92
1952 2114 1.821936 CCTTCTGATCTCCAGCGCT 59.178 57.895 2.64 2.64 42.62 5.92
1953 2115 0.177604 CCTTCTGATCTCCAGCGCTT 59.822 55.000 7.50 0.00 42.62 4.68
1954 2116 1.569708 CTTCTGATCTCCAGCGCTTC 58.430 55.000 7.50 2.34 42.62 3.86
1955 2117 0.897621 TTCTGATCTCCAGCGCTTCA 59.102 50.000 7.50 8.05 42.62 3.02
1956 2118 1.117994 TCTGATCTCCAGCGCTTCAT 58.882 50.000 7.50 0.00 42.62 2.57
1957 2119 1.068281 TCTGATCTCCAGCGCTTCATC 59.932 52.381 7.50 7.44 42.62 2.92
1958 2120 0.105593 TGATCTCCAGCGCTTCATCC 59.894 55.000 7.50 0.00 0.00 3.51
1959 2121 0.105593 GATCTCCAGCGCTTCATCCA 59.894 55.000 7.50 0.00 0.00 3.41
1960 2122 0.106335 ATCTCCAGCGCTTCATCCAG 59.894 55.000 7.50 0.00 0.00 3.86
1961 2123 1.220206 CTCCAGCGCTTCATCCAGT 59.780 57.895 7.50 0.00 0.00 4.00
1962 2124 0.809241 CTCCAGCGCTTCATCCAGTC 60.809 60.000 7.50 0.00 0.00 3.51
1963 2125 1.817099 CCAGCGCTTCATCCAGTCC 60.817 63.158 7.50 0.00 0.00 3.85
1979 2141 0.759346 GTCCTGAACCTGTGGTCTGT 59.241 55.000 0.00 0.00 33.12 3.41
1994 2156 3.131396 GGTCTGTGTGTTTCTAGTGGTG 58.869 50.000 0.00 0.00 0.00 4.17
2179 2374 1.985473 ATCAGTCAGCTGTTTGCCAA 58.015 45.000 14.67 0.00 44.23 4.52
2210 2405 4.019858 TGCATACTCTGTCTAGCTTCTGT 58.980 43.478 0.00 0.00 0.00 3.41
2214 2409 1.742831 CTCTGTCTAGCTTCTGTCGCT 59.257 52.381 0.00 0.00 41.35 4.93
2217 2412 2.920490 CTGTCTAGCTTCTGTCGCTTTC 59.080 50.000 0.00 0.00 38.86 2.62
2263 2491 5.710513 ATGCATCTTGCTTTTTACTGACA 57.289 34.783 0.00 0.00 45.31 3.58
2264 2492 5.710513 TGCATCTTGCTTTTTACTGACAT 57.289 34.783 0.75 0.00 45.31 3.06
2265 2493 5.702865 TGCATCTTGCTTTTTACTGACATC 58.297 37.500 0.75 0.00 45.31 3.06
2266 2494 5.474532 TGCATCTTGCTTTTTACTGACATCT 59.525 36.000 0.75 0.00 45.31 2.90
2267 2495 5.798934 GCATCTTGCTTTTTACTGACATCTG 59.201 40.000 0.00 0.00 40.96 2.90
2268 2496 6.348786 GCATCTTGCTTTTTACTGACATCTGA 60.349 38.462 0.00 0.00 40.96 3.27
2269 2497 7.587629 CATCTTGCTTTTTACTGACATCTGAA 58.412 34.615 0.00 0.00 0.00 3.02
2270 2498 6.959361 TCTTGCTTTTTACTGACATCTGAAC 58.041 36.000 0.00 0.00 0.00 3.18
2271 2499 6.542005 TCTTGCTTTTTACTGACATCTGAACA 59.458 34.615 0.00 0.00 0.00 3.18
2272 2500 6.691754 TGCTTTTTACTGACATCTGAACAA 57.308 33.333 0.00 0.00 0.00 2.83
2273 2501 7.094508 TGCTTTTTACTGACATCTGAACAAA 57.905 32.000 0.00 0.00 0.00 2.83
2274 2502 7.542890 TGCTTTTTACTGACATCTGAACAAAA 58.457 30.769 0.00 0.00 0.00 2.44
2275 2503 8.196771 TGCTTTTTACTGACATCTGAACAAAAT 58.803 29.630 0.00 0.00 0.00 1.82
2276 2504 8.482429 GCTTTTTACTGACATCTGAACAAAATG 58.518 33.333 0.00 0.00 0.00 2.32
2277 2505 7.928908 TTTTACTGACATCTGAACAAAATGC 57.071 32.000 0.00 0.00 0.00 3.56
2278 2506 6.631971 TTACTGACATCTGAACAAAATGCA 57.368 33.333 0.00 0.00 0.00 3.96
2279 2507 5.717078 ACTGACATCTGAACAAAATGCAT 57.283 34.783 0.00 0.00 0.00 3.96
2280 2508 5.706916 ACTGACATCTGAACAAAATGCATC 58.293 37.500 0.00 0.00 0.00 3.91
2281 2509 5.475909 ACTGACATCTGAACAAAATGCATCT 59.524 36.000 0.00 0.00 0.00 2.90
2282 2510 6.015688 ACTGACATCTGAACAAAATGCATCTT 60.016 34.615 0.00 0.00 0.00 2.40
2283 2511 6.153756 TGACATCTGAACAAAATGCATCTTG 58.846 36.000 11.24 11.24 0.00 3.02
2284 2512 4.927425 ACATCTGAACAAAATGCATCTTGC 59.073 37.500 12.71 0.00 45.29 4.01
2285 2513 4.859304 TCTGAACAAAATGCATCTTGCT 57.141 36.364 12.71 0.00 45.31 3.91
2286 2514 5.204409 TCTGAACAAAATGCATCTTGCTT 57.796 34.783 12.71 6.49 45.31 3.91
2287 2515 5.603596 TCTGAACAAAATGCATCTTGCTTT 58.396 33.333 12.71 0.53 45.31 3.51
2288 2516 5.464057 TCTGAACAAAATGCATCTTGCTTTG 59.536 36.000 12.71 14.52 45.31 2.77
2299 2527 4.082895 GCATCTTGCTTTGTCTGACTGATT 60.083 41.667 9.51 0.00 40.96 2.57
2334 2562 8.043113 TGATGCATAGTTTCTGTTCAGTTCTAT 58.957 33.333 0.00 4.74 0.00 1.98
2374 2602 8.791355 TCAAAAAGAAAAACTAAATACTCCGC 57.209 30.769 0.00 0.00 0.00 5.54
2377 2605 4.913784 AGAAAAACTAAATACTCCGCCCA 58.086 39.130 0.00 0.00 0.00 5.36
2383 2611 5.048846 ACTAAATACTCCGCCCATTTCAT 57.951 39.130 0.00 0.00 0.00 2.57
2388 2616 1.956477 ACTCCGCCCATTTCATAATGC 59.044 47.619 0.00 0.00 39.87 3.56
2391 2619 1.603678 CCGCCCATTTCATAATGCAGC 60.604 52.381 0.00 0.00 39.87 5.25
2512 2740 8.809159 AACTACGTCTTATGATGAATCTGATG 57.191 34.615 0.00 0.00 33.61 3.07
2585 2813 6.754193 TCAAAGTTTGTGAGGTTTGACTTTT 58.246 32.000 15.08 0.00 35.75 2.27
2631 2859 7.989741 ACATTATGAAACAGAGGGAGTATCTTG 59.010 37.037 0.00 0.00 33.73 3.02
2775 3011 8.757877 CCAGAATTTAATTTCCCTGGACAATAA 58.242 33.333 14.91 0.00 42.69 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.467803 ACTAGATTAAACCCGCTGATGC 58.532 45.455 0.00 0.00 0.00 3.91
26 30 0.606604 TGTGGAGACGGGTAGCTTTC 59.393 55.000 0.00 0.00 0.00 2.62
34 38 1.196808 CGATTTGTTTGTGGAGACGGG 59.803 52.381 0.00 0.00 0.00 5.28
94 104 2.962421 AGTTGGAGAAGGATCGGATCTC 59.038 50.000 16.96 8.31 39.06 2.75
144 154 8.744923 CCGGTGTTATTTTATTTTATTAACCGC 58.255 33.333 0.00 0.00 43.16 5.68
258 281 1.979693 CGGGGAGGGATCGATCTCC 60.980 68.421 21.75 20.95 46.57 3.71
259 282 1.979693 CCGGGGAGGGATCGATCTC 60.980 68.421 23.96 21.18 35.97 2.75
260 283 2.118513 CCGGGGAGGGATCGATCT 59.881 66.667 23.96 6.10 35.97 2.75
348 383 2.753043 ATCGACGGGTGCGTACCT 60.753 61.111 22.50 2.99 46.66 3.08
375 410 1.153939 CGACAGAGGCGGACAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
400 435 2.882876 GAGTTACTCTCGGCCGCA 59.117 61.111 23.51 8.58 33.25 5.69
430 472 1.428620 GGAGACGCGACCAGAGTAC 59.571 63.158 15.93 0.00 31.42 2.73
469 516 0.463833 CCCGGCTAACCTGATCCAAC 60.464 60.000 0.00 0.00 0.00 3.77
555 602 0.114954 TACCCGGACACCTAACACCT 59.885 55.000 0.73 0.00 0.00 4.00
559 606 2.381911 TCTGATACCCGGACACCTAAC 58.618 52.381 0.73 0.00 0.00 2.34
572 619 8.507249 CGAATTATTTCTCCCCAATTCTGATAC 58.493 37.037 0.00 0.00 35.96 2.24
606 655 7.433719 AGAAAGAGACTCGAATCATAATTCACG 59.566 37.037 0.00 0.00 41.22 4.35
659 708 0.109913 TCCAGATGGCATCAGCATCC 59.890 55.000 27.93 0.92 44.61 3.51
681 742 0.592247 CGTGTGCAGCAACAGGAAAC 60.592 55.000 0.00 0.00 38.00 2.78
738 800 3.828451 CAGTCCCACCAATGTTTTCAGAT 59.172 43.478 0.00 0.00 0.00 2.90
757 854 0.462937 TAAACACACAGCCGCACAGT 60.463 50.000 0.00 0.00 0.00 3.55
763 860 1.577328 CCAGCCTAAACACACAGCCG 61.577 60.000 0.00 0.00 0.00 5.52
765 862 1.001378 CAACCAGCCTAAACACACAGC 60.001 52.381 0.00 0.00 0.00 4.40
768 865 2.808543 CTCTCAACCAGCCTAAACACAC 59.191 50.000 0.00 0.00 0.00 3.82
769 866 2.810400 GCTCTCAACCAGCCTAAACACA 60.810 50.000 0.00 0.00 0.00 3.72
770 867 1.807142 GCTCTCAACCAGCCTAAACAC 59.193 52.381 0.00 0.00 0.00 3.32
771 868 1.419762 TGCTCTCAACCAGCCTAAACA 59.580 47.619 0.00 0.00 35.89 2.83
772 869 2.185004 TGCTCTCAACCAGCCTAAAC 57.815 50.000 0.00 0.00 35.89 2.01
804 902 6.697641 AACCAACCTATCTTTGACTAAGGA 57.302 37.500 0.00 0.00 34.46 3.36
805 903 6.151144 CCAAACCAACCTATCTTTGACTAAGG 59.849 42.308 0.00 0.00 34.46 2.69
806 904 6.715264 ACCAAACCAACCTATCTTTGACTAAG 59.285 38.462 0.00 0.00 35.04 2.18
807 905 6.607019 ACCAAACCAACCTATCTTTGACTAA 58.393 36.000 0.00 0.00 0.00 2.24
808 906 6.183361 TGACCAAACCAACCTATCTTTGACTA 60.183 38.462 0.00 0.00 0.00 2.59
809 907 5.061721 ACCAAACCAACCTATCTTTGACT 57.938 39.130 0.00 0.00 0.00 3.41
813 911 7.410174 TCATATGACCAAACCAACCTATCTTT 58.590 34.615 0.00 0.00 0.00 2.52
835 933 7.991084 ATGACCGAATCACAATCATAATCAT 57.009 32.000 0.00 0.00 41.24 2.45
836 934 8.938906 CATATGACCGAATCACAATCATAATCA 58.061 33.333 0.00 0.00 41.24 2.57
837 935 8.393366 CCATATGACCGAATCACAATCATAATC 58.607 37.037 3.65 0.00 41.24 1.75
838 936 8.102676 TCCATATGACCGAATCACAATCATAAT 58.897 33.333 3.65 0.00 41.24 1.28
839 937 7.387673 GTCCATATGACCGAATCACAATCATAA 59.612 37.037 3.65 0.00 41.24 1.90
915 1014 7.655732 TCAAACACATTACGGACATCCTATATG 59.344 37.037 0.00 0.00 0.00 1.78
916 1015 7.656137 GTCAAACACATTACGGACATCCTATAT 59.344 37.037 0.00 0.00 0.00 0.86
917 1016 6.982141 GTCAAACACATTACGGACATCCTATA 59.018 38.462 0.00 0.00 0.00 1.31
921 1020 4.000988 AGTCAAACACATTACGGACATCC 58.999 43.478 0.00 0.00 0.00 3.51
977 1076 1.734655 TCCCTTTGAGGCTCTTCAGT 58.265 50.000 16.72 0.00 32.73 3.41
983 1082 1.373570 CATCGTTCCCTTTGAGGCTC 58.626 55.000 7.79 7.79 32.73 4.70
993 1092 1.069090 TGATAGCGCCATCGTTCCC 59.931 57.895 11.21 0.00 38.14 3.97
1065 1164 2.430694 CAATACGATCCCACCAGAGACA 59.569 50.000 0.00 0.00 0.00 3.41
1146 1254 4.935808 AGTTAAGGAGATTTAGGCAACGTG 59.064 41.667 0.00 0.00 46.39 4.49
1171 1279 0.445436 GCACATGCCTGAAGAAGACG 59.555 55.000 0.00 0.00 34.31 4.18
1177 1285 5.355071 TGTTATAAAGAGCACATGCCTGAAG 59.645 40.000 0.00 0.00 43.38 3.02
1212 1323 6.260936 ACAAAAGTCTCTAACCTGTCAACATG 59.739 38.462 0.00 0.00 0.00 3.21
1240 1351 5.914898 ACCAGATAAAGGTTTGGTAATGC 57.085 39.130 0.00 0.00 41.92 3.56
1245 1356 6.016555 AGCAATTACCAGATAAAGGTTTGGT 58.983 36.000 0.33 0.33 45.42 3.67
1260 1371 5.453567 ACAAACTCCTGAAAGCAATTACC 57.546 39.130 0.00 0.00 0.00 2.85
1261 1372 7.649057 ACTTACAAACTCCTGAAAGCAATTAC 58.351 34.615 0.00 0.00 0.00 1.89
1267 1378 6.430000 TGGATTACTTACAAACTCCTGAAAGC 59.570 38.462 0.00 0.00 0.00 3.51
1268 1379 7.979444 TGGATTACTTACAAACTCCTGAAAG 57.021 36.000 0.00 0.00 0.00 2.62
1279 1391 7.095910 CACAAAATGCCATGGATTACTTACAA 58.904 34.615 18.40 0.00 0.00 2.41
1336 1448 2.625314 GGAGCCCAGGAAAAATATGAGC 59.375 50.000 0.00 0.00 0.00 4.26
1398 1510 6.315891 GGCTACCAGGTAGTACTAGATAATCG 59.684 46.154 25.08 0.00 38.30 3.34
1436 1571 4.060288 TGACAAACGTGATTCATAACGC 57.940 40.909 0.00 0.00 43.49 4.84
1460 1595 7.378966 AGTAAAAACTGTTCTCGATCATCAGA 58.621 34.615 11.84 0.00 0.00 3.27
1525 1661 3.157087 ACCACTGCCAGAAAAGGTTATG 58.843 45.455 0.00 0.00 0.00 1.90
1526 1662 3.525800 ACCACTGCCAGAAAAGGTTAT 57.474 42.857 0.00 0.00 0.00 1.89
1579 1730 4.532126 TCACAGATGTCCCACAATAGAGTT 59.468 41.667 0.00 0.00 0.00 3.01
1581 1732 4.743057 TCACAGATGTCCCACAATAGAG 57.257 45.455 0.00 0.00 0.00 2.43
1592 1744 5.181811 TGAATGTTTGTCCATCACAGATGTC 59.818 40.000 6.29 0.78 35.97 3.06
1612 1764 6.672593 TCAAGGGAAGCAATAAGGTATGAAT 58.327 36.000 0.00 0.00 0.00 2.57
1685 1841 5.221402 TGCAGTGGTGAAATTGCATAAGAAA 60.221 36.000 0.00 0.00 41.23 2.52
1686 1842 4.280425 TGCAGTGGTGAAATTGCATAAGAA 59.720 37.500 0.00 0.00 41.23 2.52
1687 1843 3.825585 TGCAGTGGTGAAATTGCATAAGA 59.174 39.130 0.00 0.00 41.23 2.10
1701 1857 2.282674 CCACCTGCATGCAGTGGT 60.283 61.111 36.15 30.71 42.15 4.16
1751 1907 3.945434 GCGATGCTGCCCACGATG 61.945 66.667 12.62 0.00 0.00 3.84
1930 2092 1.591059 CTGGAGATCAGAAGGCGCG 60.591 63.158 0.00 0.00 46.18 6.86
1931 2093 1.886777 GCTGGAGATCAGAAGGCGC 60.887 63.158 0.00 0.00 46.18 6.53
1932 2094 1.591059 CGCTGGAGATCAGAAGGCG 60.591 63.158 0.00 0.57 46.18 5.52
1933 2095 1.886777 GCGCTGGAGATCAGAAGGC 60.887 63.158 0.00 0.00 46.18 4.35
1934 2096 0.177604 AAGCGCTGGAGATCAGAAGG 59.822 55.000 12.58 0.00 46.18 3.46
1935 2097 1.134877 TGAAGCGCTGGAGATCAGAAG 60.135 52.381 12.58 0.00 46.18 2.85
1936 2098 0.897621 TGAAGCGCTGGAGATCAGAA 59.102 50.000 12.58 0.00 46.18 3.02
1937 2099 1.068281 GATGAAGCGCTGGAGATCAGA 59.932 52.381 12.58 0.00 46.18 3.27
1938 2100 1.500108 GATGAAGCGCTGGAGATCAG 58.500 55.000 12.58 0.00 46.03 2.90
1939 2101 0.105593 GGATGAAGCGCTGGAGATCA 59.894 55.000 12.58 11.56 0.00 2.92
1940 2102 0.105593 TGGATGAAGCGCTGGAGATC 59.894 55.000 12.58 10.08 0.00 2.75
1941 2103 0.106335 CTGGATGAAGCGCTGGAGAT 59.894 55.000 12.58 0.00 0.00 2.75
1942 2104 1.260538 ACTGGATGAAGCGCTGGAGA 61.261 55.000 12.58 0.00 0.00 3.71
1943 2105 0.809241 GACTGGATGAAGCGCTGGAG 60.809 60.000 12.58 3.27 0.00 3.86
1944 2106 1.219124 GACTGGATGAAGCGCTGGA 59.781 57.895 12.58 0.00 0.00 3.86
1945 2107 1.817099 GGACTGGATGAAGCGCTGG 60.817 63.158 12.58 0.00 0.00 4.85
1946 2108 1.088340 CAGGACTGGATGAAGCGCTG 61.088 60.000 12.58 0.00 0.00 5.18
1947 2109 1.220206 CAGGACTGGATGAAGCGCT 59.780 57.895 2.64 2.64 0.00 5.92
1948 2110 0.391661 TTCAGGACTGGATGAAGCGC 60.392 55.000 0.00 0.00 31.93 5.92
1949 2111 1.363744 GTTCAGGACTGGATGAAGCG 58.636 55.000 0.00 0.00 36.16 4.68
1950 2112 1.743996 GGTTCAGGACTGGATGAAGC 58.256 55.000 0.00 1.89 43.96 3.86
1951 2113 2.304180 ACAGGTTCAGGACTGGATGAAG 59.696 50.000 0.00 0.00 39.00 3.02
1952 2114 2.038952 CACAGGTTCAGGACTGGATGAA 59.961 50.000 0.00 0.00 39.00 2.57
1953 2115 1.625315 CACAGGTTCAGGACTGGATGA 59.375 52.381 0.00 0.00 39.00 2.92
1954 2116 1.339438 CCACAGGTTCAGGACTGGATG 60.339 57.143 0.00 0.00 39.00 3.51
1955 2117 0.987294 CCACAGGTTCAGGACTGGAT 59.013 55.000 0.00 0.00 39.00 3.41
1956 2118 0.399949 ACCACAGGTTCAGGACTGGA 60.400 55.000 0.00 0.00 39.00 3.86
1957 2119 0.035458 GACCACAGGTTCAGGACTGG 59.965 60.000 0.00 0.00 39.00 4.00
1958 2120 1.051812 AGACCACAGGTTCAGGACTG 58.948 55.000 0.00 0.00 35.25 3.51
1959 2121 1.051812 CAGACCACAGGTTCAGGACT 58.948 55.000 0.00 0.00 35.25 3.85
1960 2122 0.759346 ACAGACCACAGGTTCAGGAC 59.241 55.000 0.00 0.00 35.25 3.85
1961 2123 0.758734 CACAGACCACAGGTTCAGGA 59.241 55.000 0.00 0.00 35.25 3.86
1962 2124 0.469917 ACACAGACCACAGGTTCAGG 59.530 55.000 0.00 0.00 35.25 3.86
1963 2125 1.134401 ACACACAGACCACAGGTTCAG 60.134 52.381 0.00 0.00 35.25 3.02
1979 2141 1.270094 CGAGGCACCACTAGAAACACA 60.270 52.381 0.00 0.00 0.00 3.72
1994 2156 2.563179 TGATCCCTATTTCTAGCGAGGC 59.437 50.000 0.00 0.00 0.00 4.70
2146 2317 4.092091 GCTGACTGATAAGTTCAAGTTCCG 59.908 45.833 0.00 0.00 32.78 4.30
2179 2374 1.836166 ACAGAGTATGCAGTGATGCCT 59.164 47.619 0.00 0.00 0.00 4.75
2210 2405 4.519350 AGATATCATACTGACGGAAAGCGA 59.481 41.667 5.32 0.00 0.00 4.93
2214 2409 7.107639 TGTTCAGATATCATACTGACGGAAA 57.892 36.000 5.32 0.00 41.82 3.13
2217 2412 7.770801 TTTTGTTCAGATATCATACTGACGG 57.229 36.000 5.32 0.00 41.82 4.79
2255 2483 6.631971 TGCATTTTGTTCAGATGTCAGTAA 57.368 33.333 0.00 0.00 0.00 2.24
2256 2484 6.656270 AGATGCATTTTGTTCAGATGTCAGTA 59.344 34.615 0.00 0.00 0.00 2.74
2257 2485 5.475909 AGATGCATTTTGTTCAGATGTCAGT 59.524 36.000 0.00 0.00 0.00 3.41
2258 2486 5.950883 AGATGCATTTTGTTCAGATGTCAG 58.049 37.500 0.00 0.00 0.00 3.51
2259 2487 5.970317 AGATGCATTTTGTTCAGATGTCA 57.030 34.783 0.00 0.00 0.00 3.58
2260 2488 5.061808 GCAAGATGCATTTTGTTCAGATGTC 59.938 40.000 25.65 7.11 44.26 3.06
2261 2489 4.927425 GCAAGATGCATTTTGTTCAGATGT 59.073 37.500 25.65 0.00 44.26 3.06
2262 2490 5.450376 GCAAGATGCATTTTGTTCAGATG 57.550 39.130 25.65 4.69 44.26 2.90
2263 2491 8.167556 ACAAAGCAAGATGCATTTTGTTCAGAT 61.168 33.333 25.65 7.23 44.15 2.90
2264 2492 6.905342 ACAAAGCAAGATGCATTTTGTTCAGA 60.905 34.615 25.65 0.00 44.15 3.27
2265 2493 5.235616 ACAAAGCAAGATGCATTTTGTTCAG 59.764 36.000 25.65 18.77 44.15 3.02
2266 2494 5.117584 ACAAAGCAAGATGCATTTTGTTCA 58.882 33.333 25.65 0.00 44.15 3.18
2267 2495 5.464389 AGACAAAGCAAGATGCATTTTGTTC 59.536 36.000 25.65 17.43 45.50 3.18
2268 2496 5.235616 CAGACAAAGCAAGATGCATTTTGTT 59.764 36.000 25.65 19.64 45.50 2.83
2269 2497 4.748102 CAGACAAAGCAAGATGCATTTTGT 59.252 37.500 25.65 23.19 46.99 2.83
2276 2504 2.810274 TCAGTCAGACAAAGCAAGATGC 59.190 45.455 2.66 0.00 45.46 3.91
2277 2505 5.624344 AATCAGTCAGACAAAGCAAGATG 57.376 39.130 2.66 0.00 0.00 2.90
2278 2506 7.934855 ATTAATCAGTCAGACAAAGCAAGAT 57.065 32.000 2.66 0.00 0.00 2.40
2279 2507 7.663081 AGAATTAATCAGTCAGACAAAGCAAGA 59.337 33.333 2.66 0.00 0.00 3.02
2280 2508 7.749570 CAGAATTAATCAGTCAGACAAAGCAAG 59.250 37.037 2.66 0.00 0.00 4.01
2281 2509 7.229306 ACAGAATTAATCAGTCAGACAAAGCAA 59.771 33.333 2.66 0.00 0.00 3.91
2282 2510 6.712095 ACAGAATTAATCAGTCAGACAAAGCA 59.288 34.615 2.66 0.00 0.00 3.91
2283 2511 7.138692 ACAGAATTAATCAGTCAGACAAAGC 57.861 36.000 2.66 0.00 0.00 3.51
2284 2512 8.777413 TCAACAGAATTAATCAGTCAGACAAAG 58.223 33.333 2.66 0.00 0.00 2.77
2285 2513 8.675705 TCAACAGAATTAATCAGTCAGACAAA 57.324 30.769 2.66 0.00 0.00 2.83
2286 2514 8.724229 CATCAACAGAATTAATCAGTCAGACAA 58.276 33.333 2.66 0.00 0.00 3.18
2287 2515 7.148356 GCATCAACAGAATTAATCAGTCAGACA 60.148 37.037 2.66 0.00 0.00 3.41
2288 2516 7.148356 TGCATCAACAGAATTAATCAGTCAGAC 60.148 37.037 0.00 0.00 0.00 3.51
2299 2527 8.565896 ACAGAAACTATGCATCAACAGAATTA 57.434 30.769 0.19 0.00 0.00 1.40
2355 2583 4.913784 TGGGCGGAGTATTTAGTTTTTCT 58.086 39.130 0.00 0.00 0.00 2.52
2374 2602 1.067364 TGCGCTGCATTATGAAATGGG 59.933 47.619 9.73 0.00 42.39 4.00
2775 3011 3.143675 CTGTGCAGCCGTGAAGTAT 57.856 52.632 0.00 0.00 0.00 2.12
2776 3012 4.673403 CTGTGCAGCCGTGAAGTA 57.327 55.556 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.