Multiple sequence alignment - TraesCS3B01G232900

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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 TraesCS3B01G232900 chr3B 100.000 2334 0 0 1 2334 358685816 358688149 0.000000e+00 4274.0
1 TraesCS3B01G232900 chr3B 93.012 644 20 11 1379 1999 358705453 358706094 0.000000e+00 917.0
2 TraesCS3B01G232900 chr3B 99.653 288 1 0 1996 2283 353776855 353777142 5.710000e-146 527.0
3 TraesCS3B01G232900 chr3B 99.306 288 2 0 1996 2283 353785323 353785610 2.660000e-144 521.0
4 TraesCS3B01G232900 chr3B 99.306 288 2 0 1996 2283 358695648 358695935 2.660000e-144 521.0
5 TraesCS3B01G232900 chr3B 100.000 29 0 0 1351 1379 355002221 355002193 1.000000e-03 54.7
6 TraesCS3B01G232900 chr2D 89.207 1362 139 5 1 1355 126957131 126958491 0.000000e+00 1694.0
7 TraesCS3B01G232900 chr2D 87.739 1362 159 5 1 1355 75164029 75165389 0.000000e+00 1583.0
8 TraesCS3B01G232900 chr2D 87.665 1362 158 7 1 1355 104915586 104916944 0.000000e+00 1576.0
9 TraesCS3B01G232900 chr2D 87.289 1361 164 6 1 1355 89201358 89200001 0.000000e+00 1546.0
10 TraesCS3B01G232900 chr5B 89.060 1362 141 6 1 1355 521394995 521396355 0.000000e+00 1683.0
11 TraesCS3B01G232900 chr5B 100.000 41 0 0 2294 2334 212973850 212973890 2.490000e-10 76.8
12 TraesCS3B01G232900 chr1B 88.399 1362 148 7 1 1355 684734539 684735897 0.000000e+00 1631.0
13 TraesCS3B01G232900 chr1B 100.000 41 0 0 2294 2334 198513813 198513853 2.490000e-10 76.8
14 TraesCS3B01G232900 chr1B 100.000 41 0 0 2294 2334 198520232 198520272 2.490000e-10 76.8
15 TraesCS3B01G232900 chr1A 87.555 1358 160 6 5 1355 260841570 260842925 0.000000e+00 1563.0
16 TraesCS3B01G232900 chr4D 86.995 1361 168 6 1 1355 463910329 463911686 0.000000e+00 1524.0
17 TraesCS3B01G232900 chr4A 86.720 1363 172 5 1 1355 438390310 438391671 0.000000e+00 1506.0
18 TraesCS3B01G232900 chrUn 92.122 622 46 3 1379 1999 271658636 271658017 0.000000e+00 874.0
19 TraesCS3B01G232900 chrUn 91.434 572 38 7 1379 1940 306960201 306960771 0.000000e+00 774.0
20 TraesCS3B01G232900 chrUn 100.000 41 0 0 2294 2334 191493942 191493982 2.490000e-10 76.8
21 TraesCS3B01G232900 chrUn 100.000 41 0 0 2294 2334 269169033 269169073 2.490000e-10 76.8
22 TraesCS3B01G232900 chrUn 100.000 28 0 0 1352 1379 55885107 55885080 4.000000e-03 52.8
23 TraesCS3B01G232900 chrUn 100.000 28 0 0 1352 1379 70676953 70676980 4.000000e-03 52.8
24 TraesCS3B01G232900 chrUn 100.000 28 0 0 1352 1379 210169154 210169127 4.000000e-03 52.8
25 TraesCS3B01G232900 chrUn 100.000 28 0 0 1352 1379 210636681 210636654 4.000000e-03 52.8
26 TraesCS3B01G232900 chrUn 100.000 28 0 0 1352 1379 258438050 258438023 4.000000e-03 52.8
27 TraesCS3B01G232900 chrUn 100.000 28 0 0 1352 1379 409786350 409786377 4.000000e-03 52.8
28 TraesCS3B01G232900 chr4B 92.233 618 46 2 1379 1995 297124233 297123617 0.000000e+00 874.0
29 TraesCS3B01G232900 chr4B 91.139 632 46 5 1377 1999 331949754 331949124 0.000000e+00 848.0
30 TraesCS3B01G232900 chr4B 90.291 618 58 2 1379 1995 244602293 244602909 0.000000e+00 808.0
31 TraesCS3B01G232900 chr4B 89.736 643 43 9 1379 1999 317944078 317944719 0.000000e+00 800.0
32 TraesCS3B01G232900 chr4B 93.295 522 35 0 1378 1899 245981784 245981263 0.000000e+00 771.0
33 TraesCS3B01G232900 chr2B 90.839 644 35 8 1379 1999 350348196 350348838 0.000000e+00 841.0
34 TraesCS3B01G232900 chr2B 88.975 644 29 5 1379 1999 194514210 194514834 0.000000e+00 758.0
35 TraesCS3B01G232900 chr2B 99.654 289 1 0 1995 2283 258645489 258645777 1.590000e-146 529.0
36 TraesCS3B01G232900 chr2B 99.306 288 2 0 1996 2283 17977152 17977439 2.660000e-144 521.0
37 TraesCS3B01G232900 chr2B 99.306 288 2 0 1996 2283 17986805 17987092 2.660000e-144 521.0
38 TraesCS3B01G232900 chr2B 84.387 269 19 10 1753 1999 530164589 530164322 2.320000e-60 243.0
39 TraesCS3B01G232900 chr2B 92.035 113 6 3 1888 1999 194508477 194508367 3.110000e-34 156.0
40 TraesCS3B01G232900 chr7B 99.306 288 2 0 1996 2283 527584116 527584403 2.660000e-144 521.0
41 TraesCS3B01G232900 chr7B 98.962 289 3 0 1995 2283 670925901 670926189 3.440000e-143 518.0
42 TraesCS3B01G232900 chr7B 100.000 41 0 0 2294 2334 253469098 253469058 2.490000e-10 76.8
43 TraesCS3B01G232900 chr7B 100.000 41 0 0 2294 2334 253476050 253476010 2.490000e-10 76.8
44 TraesCS3B01G232900 chr3A 99.306 288 2 0 1996 2283 143922072 143922359 2.660000e-144 521.0
45 TraesCS3B01G232900 chr6B 100.000 41 0 0 2294 2334 471208526 471208486 2.490000e-10 76.8
46 TraesCS3B01G232900 chr6B 100.000 29 0 0 1351 1379 33352386 33352414 1.000000e-03 54.7
47 TraesCS3B01G232900 chr5A 100.000 41 0 0 2294 2334 699652963 699652923 2.490000e-10 76.8
48 TraesCS3B01G232900 chr5A 100.000 41 0 0 2294 2334 699661049 699661009 2.490000e-10 76.8
49 TraesCS3B01G232900 chr6D 100.000 28 0 0 1352 1379 12331220 12331247 4.000000e-03 52.8


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 TraesCS3B01G232900 chr3B 358685816 358688149 2333 False 4274 4274 100.000 1 2334 1 chr3B.!!$F3 2333
1 TraesCS3B01G232900 chr3B 358705453 358706094 641 False 917 917 93.012 1379 1999 1 chr3B.!!$F5 620
2 TraesCS3B01G232900 chr2D 126957131 126958491 1360 False 1694 1694 89.207 1 1355 1 chr2D.!!$F3 1354
3 TraesCS3B01G232900 chr2D 75164029 75165389 1360 False 1583 1583 87.739 1 1355 1 chr2D.!!$F1 1354
4 TraesCS3B01G232900 chr2D 104915586 104916944 1358 False 1576 1576 87.665 1 1355 1 chr2D.!!$F2 1354
5 TraesCS3B01G232900 chr2D 89200001 89201358 1357 True 1546 1546 87.289 1 1355 1 chr2D.!!$R1 1354
6 TraesCS3B01G232900 chr5B 521394995 521396355 1360 False 1683 1683 89.060 1 1355 1 chr5B.!!$F2 1354
7 TraesCS3B01G232900 chr1B 684734539 684735897 1358 False 1631 1631 88.399 1 1355 1 chr1B.!!$F3 1354
8 TraesCS3B01G232900 chr1A 260841570 260842925 1355 False 1563 1563 87.555 5 1355 1 chr1A.!!$F1 1350
9 TraesCS3B01G232900 chr4D 463910329 463911686 1357 False 1524 1524 86.995 1 1355 1 chr4D.!!$F1 1354
10 TraesCS3B01G232900 chr4A 438390310 438391671 1361 False 1506 1506 86.720 1 1355 1 chr4A.!!$F1 1354
11 TraesCS3B01G232900 chrUn 271658017 271658636 619 True 874 874 92.122 1379 1999 1 chrUn.!!$R5 620
12 TraesCS3B01G232900 chrUn 306960201 306960771 570 False 774 774 91.434 1379 1940 1 chrUn.!!$F4 561
13 TraesCS3B01G232900 chr4B 297123617 297124233 616 True 874 874 92.233 1379 1995 1 chr4B.!!$R2 616
14 TraesCS3B01G232900 chr4B 331949124 331949754 630 True 848 848 91.139 1377 1999 1 chr4B.!!$R3 622
15 TraesCS3B01G232900 chr4B 244602293 244602909 616 False 808 808 90.291 1379 1995 1 chr4B.!!$F1 616
16 TraesCS3B01G232900 chr4B 317944078 317944719 641 False 800 800 89.736 1379 1999 1 chr4B.!!$F2 620
17 TraesCS3B01G232900 chr4B 245981263 245981784 521 True 771 771 93.295 1378 1899 1 chr4B.!!$R1 521
18 TraesCS3B01G232900 chr2B 350348196 350348838 642 False 841 841 90.839 1379 1999 1 chr2B.!!$F5 620
19 TraesCS3B01G232900 chr2B 194514210 194514834 624 False 758 758 88.975 1379 1999 1 chr2B.!!$F3 620

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
182 184 1.184322 TGGCCCATTGACGCACAATT 61.184 50.0 0.0 0.0 45.6 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2061 0.108662 TGACGTGGCATCACTAGCAG 60.109 55.0 0.0 0.0 41.53 4.24 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
79 80 2.045885 AGGAAGATTGTGACCCCTAGGA 59.954 50.000 11.48 0.00 36.73 2.94
101 103 6.551227 AGGAGGGGACAATTATTATCAAAAGC 59.449 38.462 0.00 0.00 0.00 3.51
158 160 6.126390 TGGGATGAGGACATGATTAGACAAAT 60.126 38.462 0.00 0.00 36.82 2.32
182 184 1.184322 TGGCCCATTGACGCACAATT 61.184 50.000 0.00 0.00 45.60 2.32
338 340 1.444933 TCTAATGGGATGGGGCGAAT 58.555 50.000 0.00 0.00 0.00 3.34
392 394 4.015872 AGTTATCTTGTCCGGCAAAAGA 57.984 40.909 13.47 13.47 36.53 2.52
394 396 5.010282 AGTTATCTTGTCCGGCAAAAGATT 58.990 37.500 22.83 9.54 40.32 2.40
395 397 5.476945 AGTTATCTTGTCCGGCAAAAGATTT 59.523 36.000 22.83 10.06 40.32 2.17
396 398 4.871933 ATCTTGTCCGGCAAAAGATTTT 57.128 36.364 16.05 1.56 37.36 1.82
430 432 2.936498 GCGTACATTACATGGCACTCTT 59.064 45.455 0.00 0.00 33.60 2.85
435 437 4.202441 ACATTACATGGCACTCTTCCATC 58.798 43.478 0.00 0.00 42.11 3.51
472 474 4.561530 GCTAACAGACACATGAAGGTCTCA 60.562 45.833 13.74 5.13 42.22 3.27
486 488 1.276622 GTCTCACCCTCTTGCCCTAA 58.723 55.000 0.00 0.00 0.00 2.69
496 498 3.614092 CTCTTGCCCTAATTGCTCTCAA 58.386 45.455 0.00 0.00 36.51 3.02
535 537 3.679389 ACACATGCTTTTCCTCTGTAGG 58.321 45.455 0.00 0.00 45.21 3.18
558 560 3.312736 AGCAAAGGAGGTTTGGAAGAA 57.687 42.857 0.04 0.00 45.10 2.52
593 595 7.503230 TGGATGAGATTATTGATAAAGCTTGCA 59.497 33.333 0.00 0.00 0.00 4.08
646 648 6.729100 TGGAATACCTTCTACTTCTTCCAGAA 59.271 38.462 0.00 0.00 36.62 3.02
725 727 3.743132 TGGTACCTATGGTGGGAAAGAT 58.257 45.455 14.36 0.00 36.19 2.40
777 779 6.586463 CAGAATGCAAATCAGATATCAATGGC 59.414 38.462 5.32 6.75 0.00 4.40
787 789 5.105228 TCAGATATCAATGGCGATCATAGCA 60.105 40.000 5.32 0.00 34.44 3.49
829 831 1.745141 GCATCATCTCCAAAGGCGTCT 60.745 52.381 0.00 0.00 0.00 4.18
845 849 3.613030 GCGTCTATGAAAAAGGGGGTTA 58.387 45.455 0.00 0.00 0.00 2.85
891 895 5.048083 TGTGAAACTTAATGTTGATGCCTCC 60.048 40.000 0.00 0.00 39.13 4.30
972 976 5.201243 AGGTTTATTGTAGGAGGAAATGGC 58.799 41.667 0.00 0.00 0.00 4.40
975 979 6.071051 GGTTTATTGTAGGAGGAAATGGCAAA 60.071 38.462 0.00 0.00 0.00 3.68
988 992 8.133024 AGGAAATGGCAAAATTGACTATTGTA 57.867 30.769 0.01 0.00 37.03 2.41
1012 1016 2.105006 TGTTCTGATGGCTGAAGCTC 57.895 50.000 1.74 0.00 41.70 4.09
1017 1021 1.138464 CTGATGGCTGAAGCTCTAGCA 59.862 52.381 19.88 9.50 45.16 3.49
1095 1099 4.614475 ACTCAGACAATCTGGAGGTGATA 58.386 43.478 6.01 0.00 44.39 2.15
1118 1127 1.211212 TGCAGGATGGAGGACAATCAG 59.789 52.381 0.00 0.00 35.86 2.90
1142 1151 4.412270 CGGCGGCGGCAATTTTCA 62.412 61.111 32.59 0.00 42.47 2.69
1161 1170 4.623932 TCAAGGACTGCTTTCACTATGT 57.376 40.909 0.00 0.00 0.00 2.29
1169 1178 4.934001 ACTGCTTTCACTATGTCTGTGATG 59.066 41.667 0.00 0.00 42.95 3.07
1276 1285 0.322008 CAGACTGGTTTGAGGAGCCC 60.322 60.000 0.00 0.00 0.00 5.19
1313 1322 5.147330 ACTGATCCTCACAAACGATGTAA 57.853 39.130 0.00 0.00 41.46 2.41
1321 1330 6.537301 TCCTCACAAACGATGTAATGGTTATC 59.463 38.462 0.00 0.00 44.79 1.75
1330 1339 9.698309 AACGATGTAATGGTTATCTCTAATGAG 57.302 33.333 0.00 0.00 43.69 2.90
1373 1382 6.670695 AAAAACCAAGCTTCTCCAATACAT 57.329 33.333 0.00 0.00 0.00 2.29
1374 1383 7.775053 AAAAACCAAGCTTCTCCAATACATA 57.225 32.000 0.00 0.00 0.00 2.29
1375 1384 7.961326 AAAACCAAGCTTCTCCAATACATAT 57.039 32.000 0.00 0.00 0.00 1.78
1408 1417 0.393944 ATCCCTCGACTACTCGCACA 60.394 55.000 0.00 0.00 39.96 4.57
1455 1464 3.559811 CCAAGTGGACCAATGACATGAGA 60.560 47.826 0.00 0.00 37.39 3.27
1999 2031 4.007644 CTGAGCAGCCCGGTGTGA 62.008 66.667 0.00 0.00 0.00 3.58
2000 2032 4.314440 TGAGCAGCCCGGTGTGAC 62.314 66.667 0.00 0.00 0.00 3.67
2010 2042 4.006357 GGTGTGACGCCCGGGTAA 62.006 66.667 24.63 1.90 0.00 2.85
2011 2043 2.266689 GTGTGACGCCCGGGTAAT 59.733 61.111 24.63 7.81 0.00 1.89
2012 2044 1.376295 GTGTGACGCCCGGGTAATT 60.376 57.895 24.63 3.28 0.00 1.40
2013 2045 0.108233 GTGTGACGCCCGGGTAATTA 60.108 55.000 24.63 1.26 0.00 1.40
2014 2046 0.612229 TGTGACGCCCGGGTAATTAA 59.388 50.000 24.63 1.06 0.00 1.40
2015 2047 1.292992 GTGACGCCCGGGTAATTAAG 58.707 55.000 24.63 7.55 0.00 1.85
2016 2048 0.462403 TGACGCCCGGGTAATTAAGC 60.462 55.000 24.63 3.29 0.00 3.09
2017 2049 0.179065 GACGCCCGGGTAATTAAGCT 60.179 55.000 24.63 0.00 0.00 3.74
2018 2050 1.069049 GACGCCCGGGTAATTAAGCTA 59.931 52.381 24.63 0.00 0.00 3.32
2019 2051 1.202568 ACGCCCGGGTAATTAAGCTAC 60.203 52.381 24.63 0.00 0.00 3.58
2020 2052 1.202557 CGCCCGGGTAATTAAGCTACA 60.203 52.381 24.63 0.00 0.00 2.74
2021 2053 2.490991 GCCCGGGTAATTAAGCTACAG 58.509 52.381 24.63 0.00 0.00 2.74
2022 2054 2.158856 GCCCGGGTAATTAAGCTACAGT 60.159 50.000 24.63 0.00 0.00 3.55
2023 2055 3.463944 CCCGGGTAATTAAGCTACAGTG 58.536 50.000 14.18 0.00 0.00 3.66
2024 2056 3.133362 CCCGGGTAATTAAGCTACAGTGA 59.867 47.826 14.18 0.00 0.00 3.41
2025 2057 4.202326 CCCGGGTAATTAAGCTACAGTGAT 60.202 45.833 14.18 0.00 0.00 3.06
2026 2058 4.989168 CCGGGTAATTAAGCTACAGTGATC 59.011 45.833 0.00 0.00 0.00 2.92
2027 2059 4.989168 CGGGTAATTAAGCTACAGTGATCC 59.011 45.833 0.00 0.00 0.00 3.36
2028 2060 5.221461 CGGGTAATTAAGCTACAGTGATCCT 60.221 44.000 0.00 0.00 0.00 3.24
2029 2061 6.224584 GGGTAATTAAGCTACAGTGATCCTC 58.775 44.000 0.00 0.00 0.00 3.71
2030 2062 6.042208 GGGTAATTAAGCTACAGTGATCCTCT 59.958 42.308 0.00 0.00 0.00 3.69
2031 2063 6.926272 GGTAATTAAGCTACAGTGATCCTCTG 59.074 42.308 11.74 11.74 38.68 3.35
2032 2064 2.977772 AAGCTACAGTGATCCTCTGC 57.022 50.000 12.83 2.62 36.50 4.26
2033 2065 2.157640 AGCTACAGTGATCCTCTGCT 57.842 50.000 12.83 4.46 36.50 4.24
2034 2066 3.304911 AGCTACAGTGATCCTCTGCTA 57.695 47.619 12.83 6.23 36.50 3.49
2035 2067 3.221771 AGCTACAGTGATCCTCTGCTAG 58.778 50.000 12.83 13.22 36.50 3.42
2036 2068 2.955660 GCTACAGTGATCCTCTGCTAGT 59.044 50.000 12.83 0.17 36.50 2.57
2037 2069 3.243367 GCTACAGTGATCCTCTGCTAGTG 60.243 52.174 12.83 0.00 36.50 2.74
2038 2070 3.093057 ACAGTGATCCTCTGCTAGTGA 57.907 47.619 12.83 0.00 36.50 3.41
2039 2071 3.641046 ACAGTGATCCTCTGCTAGTGAT 58.359 45.455 12.83 0.00 36.50 3.06
2040 2072 3.384146 ACAGTGATCCTCTGCTAGTGATG 59.616 47.826 12.83 0.00 36.50 3.07
2041 2073 2.364970 AGTGATCCTCTGCTAGTGATGC 59.635 50.000 0.00 0.00 0.00 3.91
2042 2074 1.690893 TGATCCTCTGCTAGTGATGCC 59.309 52.381 0.00 0.00 0.00 4.40
2043 2075 1.690893 GATCCTCTGCTAGTGATGCCA 59.309 52.381 0.00 0.00 0.00 4.92
2044 2076 0.826715 TCCTCTGCTAGTGATGCCAC 59.173 55.000 0.00 0.00 43.50 5.01
2052 2084 3.876300 GTGATGCCACGTCACCTC 58.124 61.111 8.44 0.00 39.99 3.85
2053 2085 2.094659 GTGATGCCACGTCACCTCG 61.095 63.158 8.44 0.00 39.99 4.63
2054 2086 2.272447 TGATGCCACGTCACCTCGA 61.272 57.895 0.00 0.00 34.70 4.04
2055 2087 1.141881 GATGCCACGTCACCTCGAT 59.858 57.895 0.00 0.00 34.70 3.59
2056 2088 0.460284 GATGCCACGTCACCTCGATT 60.460 55.000 0.00 0.00 34.70 3.34
2057 2089 0.821517 ATGCCACGTCACCTCGATTA 59.178 50.000 0.00 0.00 34.70 1.75
2058 2090 0.821517 TGCCACGTCACCTCGATTAT 59.178 50.000 0.00 0.00 34.70 1.28
2059 2091 2.025898 TGCCACGTCACCTCGATTATA 58.974 47.619 0.00 0.00 34.70 0.98
2060 2092 2.034179 TGCCACGTCACCTCGATTATAG 59.966 50.000 0.00 0.00 34.70 1.31
2061 2093 2.034305 GCCACGTCACCTCGATTATAGT 59.966 50.000 0.00 0.00 34.70 2.12
2062 2094 3.490419 GCCACGTCACCTCGATTATAGTT 60.490 47.826 0.00 0.00 34.70 2.24
2063 2095 4.042398 CCACGTCACCTCGATTATAGTTG 58.958 47.826 0.00 0.00 34.70 3.16
2064 2096 3.486108 CACGTCACCTCGATTATAGTTGC 59.514 47.826 0.00 0.00 34.70 4.17
2065 2097 3.380637 ACGTCACCTCGATTATAGTTGCT 59.619 43.478 0.00 0.00 34.70 3.91
2066 2098 4.577693 ACGTCACCTCGATTATAGTTGCTA 59.422 41.667 0.00 0.00 34.70 3.49
2067 2099 5.066893 ACGTCACCTCGATTATAGTTGCTAA 59.933 40.000 0.00 0.00 34.70 3.09
2068 2100 6.150318 CGTCACCTCGATTATAGTTGCTAAT 58.850 40.000 0.00 0.00 0.00 1.73
2069 2101 6.305877 CGTCACCTCGATTATAGTTGCTAATC 59.694 42.308 0.00 0.00 33.93 1.75
2070 2102 7.371936 GTCACCTCGATTATAGTTGCTAATCT 58.628 38.462 0.00 0.00 34.73 2.40
2071 2103 7.539366 GTCACCTCGATTATAGTTGCTAATCTC 59.461 40.741 0.00 0.00 34.73 2.75
2072 2104 6.524933 CACCTCGATTATAGTTGCTAATCTCG 59.475 42.308 0.00 0.00 34.73 4.04
2073 2105 6.430308 ACCTCGATTATAGTTGCTAATCTCGA 59.570 38.462 0.00 0.00 34.73 4.04
2074 2106 6.964370 CCTCGATTATAGTTGCTAATCTCGAG 59.036 42.308 5.93 5.93 35.19 4.04
2075 2107 7.361371 CCTCGATTATAGTTGCTAATCTCGAGT 60.361 40.741 13.13 0.00 34.45 4.18
2076 2108 7.872881 TCGATTATAGTTGCTAATCTCGAGTT 58.127 34.615 13.13 8.74 34.73 3.01
2077 2109 8.996271 TCGATTATAGTTGCTAATCTCGAGTTA 58.004 33.333 13.13 9.41 34.73 2.24
2078 2110 9.608617 CGATTATAGTTGCTAATCTCGAGTTAA 57.391 33.333 13.13 0.00 34.73 2.01
2082 2114 6.814076 AGTTGCTAATCTCGAGTTAATTCG 57.186 37.500 13.13 13.65 41.79 3.34
2083 2115 6.561614 AGTTGCTAATCTCGAGTTAATTCGA 58.438 36.000 20.10 20.10 46.41 3.71
2092 2124 5.691508 TCGAGTTAATTCGAAACCGATTC 57.308 39.130 19.25 0.00 45.69 2.52
2093 2125 5.162794 TCGAGTTAATTCGAAACCGATTCA 58.837 37.500 19.25 0.00 45.69 2.57
2094 2126 5.634439 TCGAGTTAATTCGAAACCGATTCAA 59.366 36.000 19.25 0.00 45.69 2.69
2095 2127 6.145858 TCGAGTTAATTCGAAACCGATTCAAA 59.854 34.615 19.25 0.00 45.69 2.69
2096 2128 6.959311 CGAGTTAATTCGAAACCGATTCAAAT 59.041 34.615 14.57 0.00 43.03 2.32
2097 2129 7.480542 CGAGTTAATTCGAAACCGATTCAAATT 59.519 33.333 14.57 5.54 43.03 1.82
2098 2130 8.669394 AGTTAATTCGAAACCGATTCAAATTC 57.331 30.769 0.00 0.00 36.37 2.17
2099 2131 8.293867 AGTTAATTCGAAACCGATTCAAATTCA 58.706 29.630 0.00 0.00 36.37 2.57
2100 2132 8.907685 GTTAATTCGAAACCGATTCAAATTCAA 58.092 29.630 0.00 0.00 36.37 2.69
2101 2133 7.938563 AATTCGAAACCGATTCAAATTCAAA 57.061 28.000 0.00 0.00 30.57 2.69
2102 2134 8.532977 AATTCGAAACCGATTCAAATTCAAAT 57.467 26.923 0.00 0.00 30.57 2.32
2103 2135 7.938563 TTCGAAACCGATTCAAATTCAAATT 57.061 28.000 0.00 0.00 37.96 1.82
2104 2136 7.938563 TCGAAACCGATTCAAATTCAAATTT 57.061 28.000 0.00 0.00 39.07 1.82
2105 2137 9.464714 TTCGAAACCGATTCAAATTCAAATTTA 57.535 25.926 0.00 0.00 37.96 1.40
2106 2138 9.464714 TCGAAACCGATTCAAATTCAAATTTAA 57.535 25.926 0.63 0.00 36.52 1.52
2213 2245 9.098355 TGTAGATGACACAGTTTTATAAGATGC 57.902 33.333 0.00 0.00 31.20 3.91
2214 2246 9.098355 GTAGATGACACAGTTTTATAAGATGCA 57.902 33.333 0.00 0.00 0.00 3.96
2215 2247 8.743085 AGATGACACAGTTTTATAAGATGCAT 57.257 30.769 0.00 0.00 0.00 3.96
2216 2248 9.836864 AGATGACACAGTTTTATAAGATGCATA 57.163 29.630 0.00 0.00 0.00 3.14
2310 2342 2.123640 CTCCCTCGTCTCCCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
2311 2343 2.944954 TCCCTCGTCTCCCTCCCA 60.945 66.667 0.00 0.00 0.00 4.37
2312 2344 2.443016 CCCTCGTCTCCCTCCCAG 60.443 72.222 0.00 0.00 0.00 4.45
2313 2345 3.151022 CCTCGTCTCCCTCCCAGC 61.151 72.222 0.00 0.00 0.00 4.85
2314 2346 3.522731 CTCGTCTCCCTCCCAGCG 61.523 72.222 0.00 0.00 0.00 5.18
2332 2364 4.012895 CCGCCACTCGCAACACAC 62.013 66.667 0.00 0.00 37.30 3.82
2333 2365 3.268603 CGCCACTCGCAACACACA 61.269 61.111 0.00 0.00 37.30 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 5.301805 CCGCTTTTGATAATAATTGTCCCCT 59.698 40.000 0.00 0.00 0.00 4.79
90 92 3.016736 CAGGTCACCCGCTTTTGATAAT 58.983 45.455 0.00 0.00 35.12 1.28
101 103 1.078426 GGGTCAATCAGGTCACCCG 60.078 63.158 0.00 0.00 39.32 5.28
145 147 6.135454 TGGGCCACATAATTTGTCTAATCAT 58.865 36.000 0.00 0.00 36.00 2.45
158 160 0.322906 TGCGTCAATGGGCCACATAA 60.323 50.000 9.28 0.00 39.40 1.90
182 184 4.082787 GCGAAAGTGGGATTGAAAGAATCA 60.083 41.667 0.00 0.00 35.85 2.57
255 257 3.511934 AGTAAGCAGACCGAACTGAGAAT 59.488 43.478 11.76 0.00 39.94 2.40
264 266 0.888619 CCACAGAGTAAGCAGACCGA 59.111 55.000 0.00 0.00 0.00 4.69
313 315 3.947834 CGCCCCATCCCATTAGAATATTC 59.052 47.826 7.41 7.41 0.00 1.75
430 432 1.324740 CGAGTGTTACCCGGGATGGA 61.325 60.000 32.02 6.23 42.00 3.41
435 437 0.459063 GTTAGCGAGTGTTACCCGGG 60.459 60.000 22.25 22.25 0.00 5.73
472 474 1.002857 AGCAATTAGGGCAAGAGGGT 58.997 50.000 0.00 0.00 0.00 4.34
486 488 6.758886 CGTATCTTCTAAACCTTGAGAGCAAT 59.241 38.462 0.00 0.00 32.68 3.56
496 498 6.092259 GCATGTGTTTCGTATCTTCTAAACCT 59.908 38.462 0.00 0.00 32.18 3.50
535 537 3.636764 TCTTCCAAACCTCCTTTGCTTTC 59.363 43.478 0.00 0.00 38.40 2.62
558 560 7.878621 TCAATAATCTCATCCATCCCTAGTT 57.121 36.000 0.00 0.00 0.00 2.24
646 648 7.092174 TGGTACCCCATAATACTCAAATCTTGT 60.092 37.037 10.07 0.00 35.17 3.16
725 727 8.637986 AGTTAATTCCTTGTGCACTAATTTTCA 58.362 29.630 19.41 2.29 0.00 2.69
777 779 3.375782 TGGATGTGAGTGCTATGATCG 57.624 47.619 0.00 0.00 0.00 3.69
787 789 5.301551 TGCATTTACAAAGTTGGATGTGAGT 59.698 36.000 0.00 0.00 0.00 3.41
829 831 7.036425 AGGACAGTATTAACCCCCTTTTTCATA 60.036 37.037 0.00 0.00 0.00 2.15
845 849 3.797671 AACCCCTAGGAGGACAGTATT 57.202 47.619 19.81 3.38 37.67 1.89
891 895 4.202020 CCCTTCAGCATGTCATGATCAAAG 60.202 45.833 17.24 14.45 37.40 2.77
942 946 7.191593 TCCTCCTACAATAAACCTACCTTTC 57.808 40.000 0.00 0.00 0.00 2.62
972 976 8.450964 AGAACATCCGTACAATAGTCAATTTTG 58.549 33.333 0.00 0.00 0.00 2.44
975 979 7.327975 TCAGAACATCCGTACAATAGTCAATT 58.672 34.615 0.00 0.00 0.00 2.32
988 992 0.904649 TCAGCCATCAGAACATCCGT 59.095 50.000 0.00 0.00 0.00 4.69
1012 1016 4.458989 TGTTAGGCCAAATTTGAGTGCTAG 59.541 41.667 19.86 2.03 0.00 3.42
1017 1021 3.573967 CCAGTGTTAGGCCAAATTTGAGT 59.426 43.478 19.86 6.01 0.00 3.41
1095 1099 1.588239 TTGTCCTCCATCCTGCATCT 58.412 50.000 0.00 0.00 0.00 2.90
1142 1151 4.040952 ACAGACATAGTGAAAGCAGTCCTT 59.959 41.667 0.00 0.00 34.51 3.36
1161 1170 5.982890 TCTAGTCATGACAACATCACAGA 57.017 39.130 27.02 12.30 41.24 3.41
1169 1178 5.864474 AGTGTTCGAATCTAGTCATGACAAC 59.136 40.000 27.02 18.60 0.00 3.32
1251 1260 3.038280 TCCTCAAACCAGTCTGAAGTCA 58.962 45.455 0.00 0.00 0.00 3.41
1276 1285 8.737168 TGAGGATCAGTACAATTTCATTTAGG 57.263 34.615 0.00 0.00 42.56 2.69
1355 1364 5.240183 CACCATATGTATTGGAGAAGCTTGG 59.760 44.000 2.10 0.00 37.69 3.61
1356 1365 6.057533 TCACCATATGTATTGGAGAAGCTTG 58.942 40.000 2.10 0.00 37.69 4.01
1357 1366 6.252599 TCACCATATGTATTGGAGAAGCTT 57.747 37.500 0.00 0.00 37.69 3.74
1358 1367 5.894298 TCACCATATGTATTGGAGAAGCT 57.106 39.130 1.24 0.00 37.69 3.74
1359 1368 5.106396 GCATCACCATATGTATTGGAGAAGC 60.106 44.000 1.24 2.57 39.86 3.86
1360 1369 5.121298 CGCATCACCATATGTATTGGAGAAG 59.879 44.000 1.24 0.00 37.39 2.85
1361 1370 4.996758 CGCATCACCATATGTATTGGAGAA 59.003 41.667 1.24 0.00 37.39 2.87
1362 1371 4.563374 CCGCATCACCATATGTATTGGAGA 60.563 45.833 1.24 0.00 38.07 3.71
1363 1372 3.686241 CCGCATCACCATATGTATTGGAG 59.314 47.826 1.24 0.00 37.69 3.86
1364 1373 3.326297 TCCGCATCACCATATGTATTGGA 59.674 43.478 1.24 0.00 37.69 3.53
1365 1374 3.673902 TCCGCATCACCATATGTATTGG 58.326 45.455 1.24 0.00 40.26 3.16
1366 1375 3.125829 GCTCCGCATCACCATATGTATTG 59.874 47.826 1.24 0.00 0.00 1.90
1367 1376 3.244526 TGCTCCGCATCACCATATGTATT 60.245 43.478 1.24 0.00 31.71 1.89
1368 1377 2.302733 TGCTCCGCATCACCATATGTAT 59.697 45.455 1.24 0.00 31.71 2.29
1369 1378 1.691434 TGCTCCGCATCACCATATGTA 59.309 47.619 1.24 0.00 31.71 2.29
1370 1379 0.469494 TGCTCCGCATCACCATATGT 59.531 50.000 1.24 0.00 31.71 2.29
1371 1380 3.310727 TGCTCCGCATCACCATATG 57.689 52.632 0.00 0.00 31.71 1.78
1408 1417 0.320771 GCGTTGGTGATGGAGTGTCT 60.321 55.000 0.00 0.00 0.00 3.41
1455 1464 4.164664 CGATGGCGCATGCACGTT 62.165 61.111 19.57 0.00 45.35 3.99
1995 2027 0.612229 TTAATTACCCGGGCGTCACA 59.388 50.000 24.08 0.00 0.00 3.58
1996 2028 1.292992 CTTAATTACCCGGGCGTCAC 58.707 55.000 24.08 0.00 0.00 3.67
1997 2029 0.462403 GCTTAATTACCCGGGCGTCA 60.462 55.000 24.08 1.25 0.00 4.35
1998 2030 0.179065 AGCTTAATTACCCGGGCGTC 60.179 55.000 24.08 0.83 0.00 5.19
1999 2031 1.122227 TAGCTTAATTACCCGGGCGT 58.878 50.000 24.08 4.08 0.00 5.68
2000 2032 1.202557 TGTAGCTTAATTACCCGGGCG 60.203 52.381 24.08 0.00 0.00 6.13
2001 2033 2.158856 ACTGTAGCTTAATTACCCGGGC 60.159 50.000 24.08 3.10 0.00 6.13
2002 2034 3.133362 TCACTGTAGCTTAATTACCCGGG 59.867 47.826 22.25 22.25 0.00 5.73
2003 2035 4.395959 TCACTGTAGCTTAATTACCCGG 57.604 45.455 0.00 0.00 0.00 5.73
2004 2036 4.989168 GGATCACTGTAGCTTAATTACCCG 59.011 45.833 0.00 0.00 0.00 5.28
2005 2037 6.042208 AGAGGATCACTGTAGCTTAATTACCC 59.958 42.308 0.00 0.00 37.82 3.69
2006 2038 6.926272 CAGAGGATCACTGTAGCTTAATTACC 59.074 42.308 0.00 0.00 37.82 2.85
2007 2039 6.422400 GCAGAGGATCACTGTAGCTTAATTAC 59.578 42.308 16.58 0.00 37.82 1.89
2008 2040 6.325028 AGCAGAGGATCACTGTAGCTTAATTA 59.675 38.462 16.58 0.00 37.82 1.40
2009 2041 5.130145 AGCAGAGGATCACTGTAGCTTAATT 59.870 40.000 16.58 0.00 37.82 1.40
2010 2042 4.653341 AGCAGAGGATCACTGTAGCTTAAT 59.347 41.667 16.58 0.00 37.82 1.40
2011 2043 4.026744 AGCAGAGGATCACTGTAGCTTAA 58.973 43.478 16.58 0.00 37.82 1.85
2012 2044 3.636679 AGCAGAGGATCACTGTAGCTTA 58.363 45.455 16.58 0.00 37.82 3.09
2013 2045 2.465813 AGCAGAGGATCACTGTAGCTT 58.534 47.619 16.58 1.30 37.82 3.74
2014 2046 2.157640 AGCAGAGGATCACTGTAGCT 57.842 50.000 16.58 0.00 37.82 3.32
2015 2047 2.955660 ACTAGCAGAGGATCACTGTAGC 59.044 50.000 16.58 6.48 37.82 3.58
2016 2048 4.203226 TCACTAGCAGAGGATCACTGTAG 58.797 47.826 16.58 16.67 37.82 2.74
2017 2049 4.236527 TCACTAGCAGAGGATCACTGTA 57.763 45.455 16.58 9.44 37.82 2.74
2018 2050 3.093057 TCACTAGCAGAGGATCACTGT 57.907 47.619 16.58 8.97 37.82 3.55
2019 2051 3.799574 GCATCACTAGCAGAGGATCACTG 60.800 52.174 12.74 12.74 37.82 3.66
2020 2052 2.364970 GCATCACTAGCAGAGGATCACT 59.635 50.000 0.00 0.00 37.82 3.41
2021 2053 2.547642 GGCATCACTAGCAGAGGATCAC 60.548 54.545 0.00 0.00 37.82 3.06
2022 2054 1.690893 GGCATCACTAGCAGAGGATCA 59.309 52.381 0.00 0.00 37.82 2.92
2023 2055 1.690893 TGGCATCACTAGCAGAGGATC 59.309 52.381 2.06 0.00 0.00 3.36
2024 2056 1.415659 GTGGCATCACTAGCAGAGGAT 59.584 52.381 0.00 0.00 40.58 3.24
2025 2057 0.826715 GTGGCATCACTAGCAGAGGA 59.173 55.000 0.00 0.00 40.58 3.71
2026 2058 0.529337 CGTGGCATCACTAGCAGAGG 60.529 60.000 0.00 0.00 41.53 3.69
2027 2059 0.174389 ACGTGGCATCACTAGCAGAG 59.826 55.000 0.00 0.00 41.53 3.35
2028 2060 0.173481 GACGTGGCATCACTAGCAGA 59.827 55.000 0.00 0.00 41.53 4.26
2029 2061 0.108662 TGACGTGGCATCACTAGCAG 60.109 55.000 0.00 0.00 41.53 4.24
2030 2062 0.389817 GTGACGTGGCATCACTAGCA 60.390 55.000 12.78 0.00 42.68 3.49
2031 2063 1.084370 GGTGACGTGGCATCACTAGC 61.084 60.000 17.94 1.78 44.88 3.42
2032 2064 0.532573 AGGTGACGTGGCATCACTAG 59.467 55.000 17.94 0.00 44.88 2.57
2033 2065 0.530744 GAGGTGACGTGGCATCACTA 59.469 55.000 17.94 0.00 44.88 2.74
2034 2066 1.293498 GAGGTGACGTGGCATCACT 59.707 57.895 17.94 6.94 44.88 3.41
2035 2067 2.094659 CGAGGTGACGTGGCATCAC 61.095 63.158 11.85 11.85 44.80 3.06
2036 2068 1.604147 ATCGAGGTGACGTGGCATCA 61.604 55.000 0.00 0.00 34.70 3.07
2037 2069 0.460284 AATCGAGGTGACGTGGCATC 60.460 55.000 0.00 0.00 34.70 3.91
2038 2070 0.821517 TAATCGAGGTGACGTGGCAT 59.178 50.000 0.00 0.00 34.70 4.40
2039 2071 0.821517 ATAATCGAGGTGACGTGGCA 59.178 50.000 0.00 0.00 34.70 4.92
2040 2072 2.034305 ACTATAATCGAGGTGACGTGGC 59.966 50.000 0.00 0.00 34.70 5.01
2041 2073 3.984508 ACTATAATCGAGGTGACGTGG 57.015 47.619 0.00 0.00 34.70 4.94
2042 2074 3.486108 GCAACTATAATCGAGGTGACGTG 59.514 47.826 0.00 0.00 33.11 4.49
2043 2075 3.380637 AGCAACTATAATCGAGGTGACGT 59.619 43.478 0.00 0.00 33.11 4.34
2044 2076 3.966154 AGCAACTATAATCGAGGTGACG 58.034 45.455 0.00 0.00 33.11 4.35
2045 2077 7.371936 AGATTAGCAACTATAATCGAGGTGAC 58.628 38.462 0.00 0.00 42.12 3.67
2046 2078 7.526142 AGATTAGCAACTATAATCGAGGTGA 57.474 36.000 0.00 0.00 42.12 4.02
2047 2079 6.524933 CGAGATTAGCAACTATAATCGAGGTG 59.475 42.308 0.00 0.00 42.12 4.00
2048 2080 6.430308 TCGAGATTAGCAACTATAATCGAGGT 59.570 38.462 0.00 0.00 42.12 3.85
2049 2081 6.843208 TCGAGATTAGCAACTATAATCGAGG 58.157 40.000 0.00 0.00 42.12 4.63
2050 2082 7.523219 ACTCGAGATTAGCAACTATAATCGAG 58.477 38.462 21.68 16.53 42.12 4.04
2051 2083 7.436430 ACTCGAGATTAGCAACTATAATCGA 57.564 36.000 21.68 0.00 42.12 3.59
2052 2084 9.608617 TTAACTCGAGATTAGCAACTATAATCG 57.391 33.333 21.68 0.00 42.12 3.34
2056 2088 9.608617 CGAATTAACTCGAGATTAGCAACTATA 57.391 33.333 21.68 0.00 41.44 1.31
2057 2089 8.350722 TCGAATTAACTCGAGATTAGCAACTAT 58.649 33.333 21.68 1.32 42.69 2.12
2058 2090 7.700505 TCGAATTAACTCGAGATTAGCAACTA 58.299 34.615 21.68 0.00 42.69 2.24
2059 2091 6.561614 TCGAATTAACTCGAGATTAGCAACT 58.438 36.000 21.68 0.00 42.69 3.16
2060 2092 6.807708 TCGAATTAACTCGAGATTAGCAAC 57.192 37.500 21.68 2.66 42.69 4.17
2078 2110 8.987890 AAATTTGAATTTGAATCGGTTTCGAAT 58.012 25.926 0.00 8.00 46.21 3.34
2079 2111 8.359060 AAATTTGAATTTGAATCGGTTTCGAA 57.641 26.923 0.00 0.00 41.60 3.71
2080 2112 7.938563 AAATTTGAATTTGAATCGGTTTCGA 57.061 28.000 1.14 0.00 42.03 3.71
2187 2219 9.098355 GCATCTTATAAAACTGTGTCATCTACA 57.902 33.333 0.00 0.00 35.06 2.74
2188 2220 9.098355 TGCATCTTATAAAACTGTGTCATCTAC 57.902 33.333 0.00 0.00 0.00 2.59
2189 2221 9.836864 ATGCATCTTATAAAACTGTGTCATCTA 57.163 29.630 0.00 0.00 0.00 1.98
2190 2222 8.743085 ATGCATCTTATAAAACTGTGTCATCT 57.257 30.769 0.00 0.00 0.00 2.90
2293 2325 2.123640 GGGAGGGAGACGAGGGAG 60.124 72.222 0.00 0.00 0.00 4.30
2294 2326 2.944954 TGGGAGGGAGACGAGGGA 60.945 66.667 0.00 0.00 0.00 4.20
2295 2327 2.443016 CTGGGAGGGAGACGAGGG 60.443 72.222 0.00 0.00 0.00 4.30
2296 2328 3.151022 GCTGGGAGGGAGACGAGG 61.151 72.222 0.00 0.00 0.00 4.63
2297 2329 3.522731 CGCTGGGAGGGAGACGAG 61.523 72.222 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.