Multiple sequence alignment - TraesCS7D01G205800

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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 TraesCS7D01G205800 chr7D 100.000 2757 0 0 1 2757 163252263 163249507 0.000000e+00 5092.0
1 TraesCS7D01G205800 chr7D 89.390 1263 85 28 580 1815 163216035 163214795 0.000000e+00 1544.0
2 TraesCS7D01G205800 chr7D 85.294 816 102 13 1001 1805 163199875 163199067 0.000000e+00 826.0
3 TraesCS7D01G205800 chr7D 81.466 232 33 6 1 230 594159941 594159718 6.070000e-42 182.0
4 TraesCS7D01G205800 chr7D 84.264 197 17 5 276 460 163219255 163219061 2.180000e-41 180.0
5 TraesCS7D01G205800 chr7D 92.405 79 2 1 486 564 163219060 163218986 2.900000e-20 110.0
6 TraesCS7D01G205800 chr7D 84.848 66 7 2 230 294 524334692 524334755 2.290000e-06 63.9
7 TraesCS7D01G205800 chr7B 88.981 1815 146 30 970 2757 125356041 125354254 0.000000e+00 2194.0
8 TraesCS7D01G205800 chr7B 89.513 1354 85 23 478 1815 125363724 125362412 0.000000e+00 1661.0
9 TraesCS7D01G205800 chr7B 93.352 1083 56 5 856 1938 125244379 125243313 0.000000e+00 1587.0
10 TraesCS7D01G205800 chr7B 95.969 769 29 1 1170 1938 125313255 125312489 0.000000e+00 1247.0
11 TraesCS7D01G205800 chr7B 95.839 769 30 1 1170 1938 125280443 125279677 0.000000e+00 1242.0
12 TraesCS7D01G205800 chr7B 95.359 668 29 1 1271 1938 125221189 125220524 0.000000e+00 1061.0
13 TraesCS7D01G205800 chr7B 86.811 925 96 16 903 1807 125186655 125185737 0.000000e+00 1009.0
14 TraesCS7D01G205800 chr7B 88.677 786 69 13 1973 2757 125220529 125219763 0.000000e+00 941.0
15 TraesCS7D01G205800 chr7B 88.564 787 68 14 1973 2757 125279682 125278916 0.000000e+00 935.0
16 TraesCS7D01G205800 chr7B 88.437 787 70 13 1973 2757 125243318 125242551 0.000000e+00 929.0
17 TraesCS7D01G205800 chr7B 87.802 787 73 15 1973 2757 125312494 125311729 0.000000e+00 900.0
18 TraesCS7D01G205800 chr7B 86.187 847 54 25 475 1298 125208293 125207487 0.000000e+00 857.0
19 TraesCS7D01G205800 chr7B 81.716 536 28 23 488 986 125419972 125419470 1.550000e-102 383.0
20 TraesCS7D01G205800 chr7B 82.316 475 34 21 488 950 125356757 125356321 1.560000e-97 366.0
21 TraesCS7D01G205800 chr7B 91.321 265 15 3 1 264 125423274 125423017 3.380000e-94 355.0
22 TraesCS7D01G205800 chr7B 82.212 416 27 19 475 867 125244882 125244491 5.730000e-82 315.0
23 TraesCS7D01G205800 chr7B 82.212 416 27 19 475 867 125280937 125280546 5.730000e-82 315.0
24 TraesCS7D01G205800 chr7B 82.212 416 27 19 475 867 125314818 125314427 5.730000e-82 315.0
25 TraesCS7D01G205800 chr7B 84.649 228 20 4 760 986 125230790 125230577 2.150000e-51 213.0
26 TraesCS7D01G205800 chr7B 86.842 190 16 6 572 757 125231018 125230834 1.290000e-48 204.0
27 TraesCS7D01G205800 chr7B 94.697 132 4 2 626 757 125267138 125267010 4.660000e-48 202.0
28 TraesCS7D01G205800 chr7B 84.729 203 15 8 270 459 125231270 125231071 3.620000e-44 189.0
29 TraesCS7D01G205800 chr7B 84.236 203 16 8 270 459 125303511 125303312 1.690000e-42 183.0
30 TraesCS7D01G205800 chr7B 89.855 69 6 1 231 299 617827135 617827202 1.360000e-13 87.9
31 TraesCS7D01G205800 chr7B 100.000 29 0 0 2363 2391 727638284 727638312 1.000000e-03 54.7
32 TraesCS7D01G205800 chr7A 88.487 1798 117 32 1 1781 164394974 164393250 0.000000e+00 2091.0
33 TraesCS7D01G205800 chr7A 87.823 1240 100 22 610 1815 164182526 164181304 0.000000e+00 1406.0
34 TraesCS7D01G205800 chr7A 76.905 420 52 25 649 1053 163991452 163991063 2.170000e-46 196.0
35 TraesCS7D01G205800 chr7A 82.960 223 23 7 884 1096 164090995 164090778 1.300000e-43 187.0
36 TraesCS7D01G205800 chr7A 79.679 187 25 7 1 174 65090762 65090948 3.730000e-24 122.0
37 TraesCS7D01G205800 chr5B 84.028 432 44 17 2006 2425 523363146 523362728 2.570000e-105 392.0
38 TraesCS7D01G205800 chr5B 80.000 220 24 14 4 205 636660540 636660323 7.960000e-31 145.0
39 TraesCS7D01G205800 chr5B 85.526 76 9 2 234 307 672629655 672629580 8.190000e-11 78.7
40 TraesCS7D01G205800 chr2B 83.586 396 35 19 2002 2391 695000297 695000668 7.310000e-91 344.0
41 TraesCS7D01G205800 chr2B 79.394 330 49 9 2010 2336 172977625 172977938 5.980000e-52 215.0
42 TraesCS7D01G205800 chr2B 81.197 234 36 6 1 232 42238360 42238587 6.070000e-42 182.0
43 TraesCS7D01G205800 chrUn 82.212 416 27 19 475 867 332928375 332927984 5.730000e-82 315.0
44 TraesCS7D01G205800 chr3B 79.853 407 48 22 2007 2408 13366220 13365843 1.630000e-67 267.0
45 TraesCS7D01G205800 chr3B 85.294 68 10 0 1937 2004 412910339 412910406 1.370000e-08 71.3
46 TraesCS7D01G205800 chr1D 81.098 328 46 10 2010 2336 355836051 355835739 5.900000e-62 248.0
47 TraesCS7D01G205800 chr1D 90.816 98 9 0 1893 1990 59065501 59065404 6.200000e-27 132.0
48 TraesCS7D01G205800 chr1B 80.707 311 48 9 2457 2757 535556349 535556657 5.940000e-57 231.0
49 TraesCS7D01G205800 chr1B 78.750 240 29 15 1 232 631892267 631892042 1.030000e-29 141.0
50 TraesCS7D01G205800 chr1B 91.139 79 7 0 1912 1990 535556253 535556331 1.040000e-19 108.0
51 TraesCS7D01G205800 chr1B 85.227 88 10 3 231 316 673783187 673783273 1.360000e-13 87.9
52 TraesCS7D01G205800 chr3D 77.556 401 68 14 2003 2391 451373266 451373656 3.570000e-54 222.0
53 TraesCS7D01G205800 chr3D 79.747 237 28 15 1 231 419467733 419467955 1.320000e-33 154.0
54 TraesCS7D01G205800 chr6B 82.008 239 29 12 1 231 714327355 714327123 1.010000e-44 191.0
55 TraesCS7D01G205800 chr4B 85.311 177 23 2 1823 1999 71020488 71020661 2.180000e-41 180.0
56 TraesCS7D01G205800 chr4B 100.000 33 0 0 231 263 617690895 617690927 8.240000e-06 62.1
57 TraesCS7D01G205800 chr2A 78.750 240 29 16 1 232 584582126 584581901 1.030000e-29 141.0
58 TraesCS7D01G205800 chr2A 82.558 86 10 3 231 315 750531808 750531727 1.370000e-08 71.3
59 TraesCS7D01G205800 chr5A 83.186 113 16 2 231 342 558960309 558960199 1.750000e-17 100.0


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 TraesCS7D01G205800 chr7D 163249507 163252263 2756 True 5092.000000 5092 100.000000 1 2757 1 chr7D.!!$R2 2756
1 TraesCS7D01G205800 chr7D 163199067 163199875 808 True 826.000000 826 85.294000 1001 1805 1 chr7D.!!$R1 804
2 TraesCS7D01G205800 chr7D 163214795 163219255 4460 True 611.333333 1544 88.686333 276 1815 3 chr7D.!!$R4 1539
3 TraesCS7D01G205800 chr7B 125362412 125363724 1312 True 1661.000000 1661 89.513000 478 1815 1 chr7B.!!$R5 1337
4 TraesCS7D01G205800 chr7B 125354254 125356757 2503 True 1280.000000 2194 85.648500 488 2757 2 chr7B.!!$R11 2269
5 TraesCS7D01G205800 chr7B 125185737 125186655 918 True 1009.000000 1009 86.811000 903 1807 1 chr7B.!!$R1 904
6 TraesCS7D01G205800 chr7B 125219763 125221189 1426 True 1001.000000 1061 92.018000 1271 2757 2 chr7B.!!$R6 1486
7 TraesCS7D01G205800 chr7B 125242551 125244882 2331 True 943.666667 1587 88.000333 475 2757 3 chr7B.!!$R8 2282
8 TraesCS7D01G205800 chr7B 125207487 125208293 806 True 857.000000 857 86.187000 475 1298 1 chr7B.!!$R2 823
9 TraesCS7D01G205800 chr7B 125278916 125280937 2021 True 830.666667 1242 88.871667 475 2757 3 chr7B.!!$R9 2282
10 TraesCS7D01G205800 chr7B 125311729 125314818 3089 True 820.666667 1247 88.661000 475 2757 3 chr7B.!!$R10 2282
11 TraesCS7D01G205800 chr7B 125419470 125423274 3804 True 369.000000 383 86.518500 1 986 2 chr7B.!!$R12 985
12 TraesCS7D01G205800 chr7B 125230577 125231270 693 True 202.000000 213 85.406667 270 986 3 chr7B.!!$R7 716
13 TraesCS7D01G205800 chr7A 164393250 164394974 1724 True 2091.000000 2091 88.487000 1 1781 1 chr7A.!!$R4 1780
14 TraesCS7D01G205800 chr7A 164181304 164182526 1222 True 1406.000000 1406 87.823000 610 1815 1 chr7A.!!$R3 1205

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
45 46 0.5966 TCGTCTGTTTCACTCGTGCC 60.597 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 9395 1.13422 GGGCACCGAAGTGGATATTCA 60.134 52.381 0.0 0.0 44.69 2.57 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
41 42 1.792367 TGCAATCGTCTGTTTCACTCG 59.208 47.619 0.00 0.00 0.00 4.18
45 46 0.596600 TCGTCTGTTTCACTCGTGCC 60.597 55.000 0.00 0.00 0.00 5.01
125 126 6.349300 AGGATTAAATCATGTACGACTTGCT 58.651 36.000 0.00 0.00 0.00 3.91
126 127 6.258727 AGGATTAAATCATGTACGACTTGCTG 59.741 38.462 0.00 0.00 0.00 4.41
198 200 5.753438 TCTGGCTCGATCAATACAACAATAC 59.247 40.000 0.00 0.00 0.00 1.89
203 205 8.721478 GGCTCGATCAATACAACAATACAATAT 58.279 33.333 0.00 0.00 0.00 1.28
316 3160 7.063426 ACAATCACACTGAAACGTGTCTATATG 59.937 37.037 7.37 2.80 45.74 1.78
317 3161 6.020971 TCACACTGAAACGTGTCTATATGT 57.979 37.500 7.37 3.41 45.74 2.29
520 3393 5.106157 ACCCTCGCTTGAACAGAAAATAATG 60.106 40.000 0.00 0.00 0.00 1.90
564 3437 0.871722 TCGTCCCAAATTGAACTGCG 59.128 50.000 0.00 0.00 0.00 5.18
566 3439 1.135972 CGTCCCAAATTGAACTGCGAG 60.136 52.381 0.00 0.00 0.00 5.03
570 3443 2.083774 CCAAATTGAACTGCGAGGCTA 58.916 47.619 0.00 0.00 0.00 3.93
607 6419 2.794910 CACGCAGTAGATTTATCACCGG 59.205 50.000 0.00 0.00 41.61 5.28
608 6420 1.792949 CGCAGTAGATTTATCACCGGC 59.207 52.381 0.00 0.00 0.00 6.13
653 6475 2.403252 TCGCTTTCCCCTTCTGAATC 57.597 50.000 0.00 0.00 0.00 2.52
669 6492 0.597568 AATCACCGTCGGTAACACGA 59.402 50.000 18.38 10.33 41.53 4.35
837 6719 9.237846 GCACTATTTAATTAAGCTGTCAATTCC 57.762 33.333 0.00 0.00 0.00 3.01
967 7236 5.573337 AGAGATAATTCAAGGCAAAGCAC 57.427 39.130 0.00 0.00 0.00 4.40
979 7250 1.843992 CAAAGCACAAGAAGCCACAC 58.156 50.000 0.00 0.00 0.00 3.82
980 7251 1.134753 CAAAGCACAAGAAGCCACACA 59.865 47.619 0.00 0.00 0.00 3.72
981 7252 0.740737 AAGCACAAGAAGCCACACAC 59.259 50.000 0.00 0.00 0.00 3.82
982 7253 1.009675 GCACAAGAAGCCACACACG 60.010 57.895 0.00 0.00 0.00 4.49
983 7254 1.714899 GCACAAGAAGCCACACACGT 61.715 55.000 0.00 0.00 0.00 4.49
984 7255 1.577468 CACAAGAAGCCACACACGTA 58.423 50.000 0.00 0.00 0.00 3.57
985 7256 1.526887 CACAAGAAGCCACACACGTAG 59.473 52.381 0.00 0.00 0.00 3.51
1041 7323 1.678627 TGGATTAGCGTCTCTCTGCTC 59.321 52.381 0.00 0.00 42.48 4.26
1047 7329 0.796491 GCGTCTCTCTGCTCGTCTTG 60.796 60.000 0.00 0.00 0.00 3.02
1137 7419 3.432588 ACGTCGGTGAGGCTCGAG 61.433 66.667 8.45 8.45 36.00 4.04
1302 8625 2.936498 CAGGATGGCAGTAAGTTTACCG 59.064 50.000 0.00 0.00 34.19 4.02
1411 8753 2.426023 GTGTGGCAGTTCGAGGGT 59.574 61.111 0.00 0.00 0.00 4.34
1501 8843 1.504900 CACGCTCATGCTGCATGTT 59.495 52.632 34.14 18.65 41.98 2.71
1505 8847 1.130938 CGCTCATGCTGCATGTTTACA 59.869 47.619 34.14 18.67 41.98 2.41
1869 9220 5.929992 TCTACTCTATTTGTTGGTTGGTTCG 59.070 40.000 0.00 0.00 0.00 3.95
1870 9221 4.710324 ACTCTATTTGTTGGTTGGTTCGA 58.290 39.130 0.00 0.00 0.00 3.71
1873 9224 5.556915 TCTATTTGTTGGTTGGTTCGATCT 58.443 37.500 0.00 0.00 0.00 2.75
1931 9282 7.213178 ACTGTAGGATTCCCAAATCTACAAT 57.787 36.000 0.00 0.00 40.99 2.71
1932 9283 7.643123 ACTGTAGGATTCCCAAATCTACAATT 58.357 34.615 0.00 0.00 40.99 2.32
1933 9284 8.116026 ACTGTAGGATTCCCAAATCTACAATTT 58.884 33.333 0.00 0.00 40.99 1.82
1934 9285 8.893563 TGTAGGATTCCCAAATCTACAATTTT 57.106 30.769 0.00 0.00 40.99 1.82
1935 9286 8.748412 TGTAGGATTCCCAAATCTACAATTTTG 58.252 33.333 0.00 0.00 40.99 2.44
1936 9287 7.797121 AGGATTCCCAAATCTACAATTTTGT 57.203 32.000 0.00 1.08 40.99 2.83
1937 9288 8.206126 AGGATTCCCAAATCTACAATTTTGTT 57.794 30.769 0.63 0.00 40.99 2.83
1938 9289 8.659527 AGGATTCCCAAATCTACAATTTTGTTT 58.340 29.630 0.63 0.00 40.99 2.83
1939 9290 8.935844 GGATTCCCAAATCTACAATTTTGTTTC 58.064 33.333 0.63 0.00 40.99 2.78
1940 9291 9.487790 GATTCCCAAATCTACAATTTTGTTTCA 57.512 29.630 0.63 0.00 37.22 2.69
1941 9292 8.885494 TTCCCAAATCTACAATTTTGTTTCAG 57.115 30.769 0.63 0.00 42.35 3.02
1942 9293 8.017418 TCCCAAATCTACAATTTTGTTTCAGT 57.983 30.769 0.63 0.00 42.35 3.41
1943 9294 7.925483 TCCCAAATCTACAATTTTGTTTCAGTG 59.075 33.333 0.63 0.00 42.35 3.66
1944 9295 7.925483 CCCAAATCTACAATTTTGTTTCAGTGA 59.075 33.333 0.63 0.00 42.35 3.41
1945 9296 9.480053 CCAAATCTACAATTTTGTTTCAGTGAT 57.520 29.630 0.63 0.00 42.35 3.06
1953 9304 9.598517 ACAATTTTGTTTCAGTGATGTATTGTT 57.401 25.926 0.00 0.00 38.47 2.83
1956 9307 8.795786 TTTTGTTTCAGTGATGTATTGTTAGC 57.204 30.769 0.00 0.00 0.00 3.09
1957 9308 7.503521 TTGTTTCAGTGATGTATTGTTAGCA 57.496 32.000 0.00 0.00 0.00 3.49
1958 9309 7.686438 TGTTTCAGTGATGTATTGTTAGCAT 57.314 32.000 0.00 0.00 0.00 3.79
1959 9310 7.751732 TGTTTCAGTGATGTATTGTTAGCATC 58.248 34.615 0.00 0.00 39.37 3.91
1960 9311 7.607607 TGTTTCAGTGATGTATTGTTAGCATCT 59.392 33.333 0.00 0.00 39.58 2.90
1961 9312 8.454106 GTTTCAGTGATGTATTGTTAGCATCTT 58.546 33.333 0.00 0.00 39.58 2.40
1962 9313 7.543947 TCAGTGATGTATTGTTAGCATCTTG 57.456 36.000 0.00 0.00 39.58 3.02
1963 9314 7.330262 TCAGTGATGTATTGTTAGCATCTTGA 58.670 34.615 0.00 0.00 39.58 3.02
1964 9315 7.989170 TCAGTGATGTATTGTTAGCATCTTGAT 59.011 33.333 0.00 0.00 39.58 2.57
1965 9316 8.068380 CAGTGATGTATTGTTAGCATCTTGATG 58.932 37.037 6.27 6.27 39.58 3.07
1966 9317 7.772292 AGTGATGTATTGTTAGCATCTTGATGT 59.228 33.333 11.61 2.73 39.58 3.06
1967 9318 7.854422 GTGATGTATTGTTAGCATCTTGATGTG 59.146 37.037 11.61 0.00 39.58 3.21
1968 9319 7.769970 TGATGTATTGTTAGCATCTTGATGTGA 59.230 33.333 11.61 0.00 39.58 3.58
1969 9320 8.687292 ATGTATTGTTAGCATCTTGATGTGAT 57.313 30.769 11.61 2.51 0.00 3.06
1970 9321 9.783081 ATGTATTGTTAGCATCTTGATGTGATA 57.217 29.630 11.61 1.70 0.00 2.15
1971 9322 9.612066 TGTATTGTTAGCATCTTGATGTGATAA 57.388 29.630 11.61 6.69 0.00 1.75
2124 9543 5.450592 TTTGCAAGCAAGATGTTCATGTA 57.549 34.783 7.60 0.00 37.24 2.29
2125 9544 5.648178 TTGCAAGCAAGATGTTCATGTAT 57.352 34.783 2.89 0.00 0.00 2.29
2134 9553 7.031372 GCAAGATGTTCATGTATGTGATGTTT 58.969 34.615 0.00 0.00 0.00 2.83
2162 9581 5.461032 AAATTTGGCGAAGTTTGGACATA 57.539 34.783 1.20 0.00 0.00 2.29
2170 9589 3.522553 GAAGTTTGGACATACGAGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
2233 9652 8.006298 TGTTTTCAAATGTTTCTCACATACCT 57.994 30.769 0.00 0.00 46.23 3.08
2234 9653 7.920151 TGTTTTCAAATGTTTCTCACATACCTG 59.080 33.333 0.00 0.00 46.23 4.00
2277 9696 1.871039 CGAATGTCCAAACTTCACGGT 59.129 47.619 0.00 0.00 0.00 4.83
2305 9724 3.300857 CACGAGTATAACGCATCTGAGG 58.699 50.000 0.00 0.00 0.00 3.86
2380 9799 1.676006 GATTTACTGTTCATGCCCGGG 59.324 52.381 19.09 19.09 0.00 5.73
2385 9804 2.124151 GTTCATGCCCGGGCTCAT 60.124 61.111 43.34 28.62 42.51 2.90
2386 9805 2.189499 GTTCATGCCCGGGCTCATC 61.189 63.158 43.34 25.69 42.51 2.92
2387 9806 2.377810 TTCATGCCCGGGCTCATCT 61.378 57.895 43.34 21.28 42.51 2.90
2388 9807 2.593725 CATGCCCGGGCTCATCTG 60.594 66.667 43.34 27.32 42.51 2.90
2389 9808 2.769621 ATGCCCGGGCTCATCTGA 60.770 61.111 43.34 24.35 42.51 3.27
2390 9809 2.815945 ATGCCCGGGCTCATCTGAG 61.816 63.158 43.34 4.66 44.75 3.35
2391 9810 3.474570 GCCCGGGCTCATCTGAGT 61.475 66.667 38.76 0.00 43.85 3.41
2392 9811 2.503061 CCCGGGCTCATCTGAGTG 59.497 66.667 8.08 0.36 43.85 3.51
2393 9812 2.362369 CCCGGGCTCATCTGAGTGT 61.362 63.158 8.08 0.00 43.85 3.55
2394 9813 1.043116 CCCGGGCTCATCTGAGTGTA 61.043 60.000 8.08 0.00 43.85 2.90
2395 9814 0.103208 CCGGGCTCATCTGAGTGTAC 59.897 60.000 8.87 0.00 43.85 2.90
2396 9815 0.248661 CGGGCTCATCTGAGTGTACG 60.249 60.000 8.87 5.21 43.85 3.67
2431 9850 3.339141 CTGCTTCAGTTAGTTCCCCTTC 58.661 50.000 0.00 0.00 0.00 3.46
2448 9867 4.272261 CCCCTTCAAATTGTTTTTGGTTCG 59.728 41.667 0.00 0.00 0.00 3.95
2469 9888 5.767269 TCGATAACTGATCTCTTCATGCTC 58.233 41.667 0.00 0.00 32.72 4.26
2480 9899 0.527113 TTCATGCTCCATTGGCAACG 59.473 50.000 0.00 0.00 43.14 4.10
2496 9915 7.854934 TTGGCAACGTTTATTGTTGTATTAC 57.145 32.000 0.00 0.00 46.48 1.89
2561 9980 5.606348 TTTGTCCTGCCACATTTTACTTT 57.394 34.783 0.00 0.00 0.00 2.66
2607 10028 5.876460 TCTGTGACACATCCAATATGTTCAG 59.124 40.000 9.11 0.00 33.71 3.02
2618 10039 6.199376 TCCAATATGTTCAGGTACCTCACTA 58.801 40.000 12.84 6.87 0.00 2.74
2640 10061 9.869844 CACTAATTAGAAATTTAGAATGCTCCG 57.130 33.333 19.38 0.00 31.36 4.63
2655 10076 1.750682 GCTCCGCCCAATACATTTCCT 60.751 52.381 0.00 0.00 0.00 3.36
2672 10093 2.902608 TCCTAACTCAGGCTCTTTCCA 58.097 47.619 0.00 0.00 45.10 3.53
2687 10108 5.177696 GCTCTTTCCATACATCGGTTACATC 59.822 44.000 0.00 0.00 0.00 3.06
2688 10109 5.607477 TCTTTCCATACATCGGTTACATCC 58.393 41.667 0.00 0.00 0.00 3.51
2699 10120 1.361793 GTTACATCCGCCGTTGCTAA 58.638 50.000 0.00 0.00 34.43 3.09
2704 10125 1.151777 ATCCGCCGTTGCTAATGACG 61.152 55.000 0.00 0.00 38.90 4.35
2706 10127 1.343821 CGCCGTTGCTAATGACGAC 59.656 57.895 0.00 0.00 41.53 4.34
2732 10153 3.552604 TTTGCACGCTTCACCTATTTC 57.447 42.857 0.00 0.00 0.00 2.17
2733 10154 2.177394 TGCACGCTTCACCTATTTCA 57.823 45.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.627577 AGTGAAACAGACGATTGCAACTT 59.372 39.130 0.00 0.00 41.43 2.66
41 42 1.852157 TTCCCCCTCAGTCATGGCAC 61.852 60.000 0.00 0.00 0.00 5.01
45 46 2.814805 AACATTCCCCCTCAGTCATG 57.185 50.000 0.00 0.00 0.00 3.07
125 126 3.357203 AGCGAGAGATTTGGAGTAGACA 58.643 45.455 0.00 0.00 0.00 3.41
126 127 3.378742 TGAGCGAGAGATTTGGAGTAGAC 59.621 47.826 0.00 0.00 0.00 2.59
170 171 2.102925 TGTATTGATCGAGCCAGATGCA 59.897 45.455 0.00 0.00 44.83 3.96
264 3105 4.261801 CTCATTTCAATCCGTACCAAGGT 58.738 43.478 0.00 0.00 0.00 3.50
268 3109 4.545208 TCACTCATTTCAATCCGTACCA 57.455 40.909 0.00 0.00 0.00 3.25
343 3188 0.981277 ATAGACACCCACCCCCTTCG 60.981 60.000 0.00 0.00 0.00 3.79
345 3190 2.672703 TTATAGACACCCACCCCCTT 57.327 50.000 0.00 0.00 0.00 3.95
402 3258 3.202829 TGCGGGGATATTTGTAACTCC 57.797 47.619 0.00 0.00 0.00 3.85
520 3393 4.082733 GGCAAGGAGTTAAACAATGGAGAC 60.083 45.833 0.00 0.00 0.00 3.36
564 3437 2.508663 GGCGAACACGGTAGCCTC 60.509 66.667 0.00 0.00 45.67 4.70
570 3443 3.542676 TGTCCTGGCGAACACGGT 61.543 61.111 0.00 0.00 0.00 4.83
608 6420 2.907897 GATCCCTCCAACGCGGTGAG 62.908 65.000 28.95 20.07 35.57 3.51
618 6430 2.329267 AGCGATGTATTGATCCCTCCA 58.671 47.619 0.00 0.00 0.00 3.86
653 6475 1.207390 TTTTCGTGTTACCGACGGTG 58.793 50.000 29.55 12.35 36.19 4.94
837 6719 4.571919 TGTACCTTATGTTCGAAGTTGGG 58.428 43.478 0.00 0.23 0.00 4.12
979 7250 6.347402 GCCATTGGTACTTTATATGCTACGTG 60.347 42.308 4.26 0.00 0.00 4.49
980 7251 5.699458 GCCATTGGTACTTTATATGCTACGT 59.301 40.000 4.26 0.00 0.00 3.57
981 7252 5.932303 AGCCATTGGTACTTTATATGCTACG 59.068 40.000 4.26 0.00 0.00 3.51
982 7253 6.371825 GGAGCCATTGGTACTTTATATGCTAC 59.628 42.308 4.26 0.00 0.00 3.58
983 7254 6.272324 AGGAGCCATTGGTACTTTATATGCTA 59.728 38.462 4.26 0.00 24.41 3.49
984 7255 5.073691 AGGAGCCATTGGTACTTTATATGCT 59.926 40.000 4.26 0.00 24.41 3.79
985 7256 5.316987 AGGAGCCATTGGTACTTTATATGC 58.683 41.667 4.26 0.00 24.41 3.14
1041 7323 2.544359 CACGACGCCAACAAGACG 59.456 61.111 0.00 0.00 0.00 4.18
1047 7329 2.860293 CATGACCACGACGCCAAC 59.140 61.111 0.00 0.00 0.00 3.77
1302 8625 6.021596 CCAAACGAAGTACAACTAATGATGC 58.978 40.000 0.00 0.00 45.00 3.91
1354 8691 4.411013 AGCCCTGCAAGTAAAAGAAGATT 58.589 39.130 0.00 0.00 0.00 2.40
1363 8700 1.263356 AGTCGTAGCCCTGCAAGTAA 58.737 50.000 0.00 0.00 0.00 2.24
1531 8873 2.492090 GCATCCTCGACGAGCTGT 59.508 61.111 19.55 4.31 0.00 4.40
1663 9005 2.612212 CACGCCAAACTTGAAGTAGTGT 59.388 45.455 0.00 0.82 0.00 3.55
1908 9259 8.525290 AAATTGTAGATTTGGGAATCCTACAG 57.475 34.615 0.00 0.00 42.16 2.74
1931 9282 8.409371 TGCTAACAATACATCACTGAAACAAAA 58.591 29.630 0.00 0.00 0.00 2.44
1932 9283 7.935520 TGCTAACAATACATCACTGAAACAAA 58.064 30.769 0.00 0.00 0.00 2.83
1933 9284 7.503521 TGCTAACAATACATCACTGAAACAA 57.496 32.000 0.00 0.00 0.00 2.83
1934 9285 7.607607 AGATGCTAACAATACATCACTGAAACA 59.392 33.333 5.15 0.00 42.12 2.83
1935 9286 7.978982 AGATGCTAACAATACATCACTGAAAC 58.021 34.615 5.15 0.00 42.12 2.78
1936 9287 8.453320 CAAGATGCTAACAATACATCACTGAAA 58.547 33.333 5.15 0.00 42.12 2.69
1937 9288 7.823799 TCAAGATGCTAACAATACATCACTGAA 59.176 33.333 5.15 0.00 42.12 3.02
1938 9289 7.330262 TCAAGATGCTAACAATACATCACTGA 58.670 34.615 5.15 4.54 42.12 3.41
1939 9290 7.543947 TCAAGATGCTAACAATACATCACTG 57.456 36.000 5.15 2.54 42.12 3.66
1940 9291 7.772292 ACATCAAGATGCTAACAATACATCACT 59.228 33.333 9.85 0.00 42.12 3.41
1941 9292 7.854422 CACATCAAGATGCTAACAATACATCAC 59.146 37.037 9.85 0.00 42.12 3.06
1942 9293 7.769970 TCACATCAAGATGCTAACAATACATCA 59.230 33.333 9.85 0.00 42.12 3.07
1943 9294 8.146479 TCACATCAAGATGCTAACAATACATC 57.854 34.615 9.85 0.00 42.39 3.06
1944 9295 8.687292 ATCACATCAAGATGCTAACAATACAT 57.313 30.769 9.85 0.00 42.39 2.29
1945 9296 9.612066 TTATCACATCAAGATGCTAACAATACA 57.388 29.630 9.85 0.00 42.39 2.29
1991 9382 9.315525 GAAGTGGATATTCAGGAACTAACTAAC 57.684 37.037 0.00 0.00 36.02 2.34
1994 9385 6.407074 CCGAAGTGGATATTCAGGAACTAACT 60.407 42.308 0.00 0.00 42.00 2.24
2004 9395 1.134220 GGGCACCGAAGTGGATATTCA 60.134 52.381 0.00 0.00 44.69 2.57
2033 9424 1.204146 ATACTGTTCACCGGGCTCAT 58.796 50.000 6.32 0.00 0.00 2.90
2114 9533 6.094719 GCACAAACATCACATACATGAACAT 58.905 36.000 0.00 0.00 30.82 2.71
2124 9543 5.505985 GCCAAATTTTGCACAAACATCACAT 60.506 36.000 9.26 0.00 0.00 3.21
2125 9544 4.201891 GCCAAATTTTGCACAAACATCACA 60.202 37.500 9.26 0.00 0.00 3.58
2134 9553 2.593346 ACTTCGCCAAATTTTGCACA 57.407 40.000 13.99 0.00 0.00 4.57
2183 9602 5.815740 ACACTGTTCTTACACGAATTTGTCT 59.184 36.000 0.00 0.00 0.00 3.41
2194 9613 8.085296 ACATTTGAAAACAACACTGTTCTTACA 58.915 29.630 0.00 0.00 45.25 2.41
2195 9614 8.460831 ACATTTGAAAACAACACTGTTCTTAC 57.539 30.769 0.00 0.00 45.25 2.34
2196 9615 9.482627 AAACATTTGAAAACAACACTGTTCTTA 57.517 25.926 0.00 0.00 45.25 2.10
2198 9617 7.872483 AGAAACATTTGAAAACAACACTGTTCT 59.128 29.630 0.00 0.00 45.25 3.01
2277 9696 5.751509 AGATGCGTTATACTCGTGCAAAATA 59.248 36.000 0.00 0.00 39.26 1.40
2380 9799 0.867753 CCGCGTACACTCAGATGAGC 60.868 60.000 4.92 0.00 45.79 4.26
2385 9804 2.986979 TGCCCGCGTACACTCAGA 60.987 61.111 4.92 0.00 0.00 3.27
2386 9805 2.809601 GTGCCCGCGTACACTCAG 60.810 66.667 18.33 0.00 33.92 3.35
2387 9806 4.367023 GGTGCCCGCGTACACTCA 62.367 66.667 22.82 2.64 36.99 3.41
2388 9807 3.869473 TTGGTGCCCGCGTACACTC 62.869 63.158 22.82 15.47 36.99 3.51
2389 9808 2.741486 ATTTGGTGCCCGCGTACACT 62.741 55.000 22.82 5.76 36.99 3.55
2390 9809 2.329614 ATTTGGTGCCCGCGTACAC 61.330 57.895 17.61 17.61 36.03 2.90
2391 9810 2.032834 ATTTGGTGCCCGCGTACA 59.967 55.556 4.92 0.00 0.00 2.90
2392 9811 2.483288 CATTTGGTGCCCGCGTAC 59.517 61.111 4.92 0.56 0.00 3.67
2408 9827 1.271379 GGGGAACTAACTGAAGCAGCA 60.271 52.381 0.00 0.00 34.37 4.41
2411 9830 2.708861 TGAAGGGGAACTAACTGAAGCA 59.291 45.455 0.00 0.00 0.00 3.91
2431 9850 8.346476 TCAGTTATCGAACCAAAAACAATTTG 57.654 30.769 0.00 0.00 36.08 2.32
2448 9867 5.851720 TGGAGCATGAAGAGATCAGTTATC 58.148 41.667 0.00 0.00 42.53 1.75
2469 9888 4.054671 ACAACAATAAACGTTGCCAATGG 58.945 39.130 0.00 0.00 46.14 3.16
2534 9953 7.378181 AGTAAAATGTGGCAGGACAAAAATAG 58.622 34.615 0.00 0.00 0.00 1.73
2561 9980 9.131791 ACAGAAGGCTTGTTCTCTTAATTTTTA 57.868 29.630 3.46 0.00 34.38 1.52
2640 10061 5.757850 CTGAGTTAGGAAATGTATTGGGC 57.242 43.478 0.00 0.00 0.00 5.36
2655 10076 5.451937 CGATGTATGGAAAGAGCCTGAGTTA 60.452 44.000 0.00 0.00 0.00 2.24
2699 10120 1.324435 CGTGCAAATGATCGTCGTCAT 59.676 47.619 0.00 4.98 40.44 3.06
2704 10125 1.128507 TGAAGCGTGCAAATGATCGTC 59.871 47.619 0.00 0.00 0.00 4.20
2706 10127 1.527696 GTGAAGCGTGCAAATGATCG 58.472 50.000 0.00 0.00 0.00 3.69
2732 10153 2.609459 GTCATGAGACAGGCCGTAAATG 59.391 50.000 0.00 4.14 44.34 2.32
2733 10154 2.420129 GGTCATGAGACAGGCCGTAAAT 60.420 50.000 0.00 0.00 46.80 1.40


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

AutoCloner maintained by Alex Coulton.