Multiple sequence alignment - TraesCS7B01G083000

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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 TraesCS7B01G083000 chr7B 100.000 2449 0 0 1 2449 93649725 93652173 0.000000e+00 4523.0
1 TraesCS7B01G083000 chr7B 90.766 1267 45 26 663 1874 94118631 94117382 0.000000e+00 1626.0
2 TraesCS7B01G083000 chr7B 86.293 1481 97 42 644 2067 93864350 93865781 0.000000e+00 1513.0
3 TraesCS7B01G083000 chr7B 88.289 1315 80 30 760 2018 93571366 93572662 0.000000e+00 1507.0
4 TraesCS7B01G083000 chr7B 91.581 1069 42 22 663 1692 94051075 94050016 0.000000e+00 1432.0
5 TraesCS7B01G083000 chr7B 87.327 1302 80 25 639 1874 157808153 157809435 0.000000e+00 1411.0
6 TraesCS7B01G083000 chr7B 91.132 1060 47 19 849 1874 94186390 94185344 0.000000e+00 1393.0
7 TraesCS7B01G083000 chr7B 97.015 335 2 1 2123 2449 93572686 93573020 7.650000e-155 556.0
8 TraesCS7B01G083000 chr7B 88.264 409 26 8 1684 2070 94049536 94049128 1.030000e-128 470.0
9 TraesCS7B01G083000 chr7B 86.937 222 20 4 2139 2352 157809629 157809849 8.750000e-60 241.0
10 TraesCS7B01G083000 chr7B 95.172 145 7 0 2216 2360 94142333 94142189 1.890000e-56 230.0
11 TraesCS7B01G083000 chr7B 94.483 145 8 0 2216 2360 94185105 94184961 8.810000e-55 224.0
12 TraesCS7B01G083000 chr7B 90.000 160 15 1 2200 2358 94049134 94048975 3.190000e-49 206.0
13 TraesCS7B01G083000 chr7B 88.421 95 6 3 2356 2448 94115362 94115271 2.570000e-20 110.0
14 TraesCS7B01G083000 chr7B 88.421 95 6 3 2356 2448 94142158 94142067 2.570000e-20 110.0
15 TraesCS7B01G083000 chr7B 88.636 88 5 3 2356 2441 94184930 94184846 4.310000e-18 102.0
16 TraesCS7B01G083000 chr7D 92.465 1128 49 9 768 1874 132156996 132158108 0.000000e+00 1580.0
17 TraesCS7B01G083000 chr7D 87.673 1371 94 17 804 2102 132830978 132829611 0.000000e+00 1526.0
18 TraesCS7B01G083000 chr7D 88.110 1270 90 21 644 1874 194129131 194130378 0.000000e+00 1452.0
19 TraesCS7B01G083000 chr7D 86.027 1417 114 29 741 2101 132740991 132742379 0.000000e+00 1443.0
20 TraesCS7B01G083000 chr7D 85.226 1435 121 33 721 2102 132747869 132749265 0.000000e+00 1391.0
21 TraesCS7B01G083000 chr7D 85.078 1414 117 46 761 2102 132135509 132136900 0.000000e+00 1356.0
22 TraesCS7B01G083000 chr7D 88.240 1165 66 31 757 1874 132764690 132763550 0.000000e+00 1327.0
23 TraesCS7B01G083000 chr7D 89.035 228 16 4 2139 2358 132136827 132137053 8.630000e-70 274.0
24 TraesCS7B01G083000 chr7D 84.753 223 26 4 1888 2102 132763503 132763281 1.470000e-52 217.0
25 TraesCS7B01G083000 chr7D 78.529 340 35 21 2137 2448 132158239 132158568 3.210000e-44 189.0
26 TraesCS7B01G083000 chr7D 78.485 330 40 17 2139 2448 132763355 132763037 1.160000e-43 187.0
27 TraesCS7B01G083000 chr7D 95.050 101 5 0 643 743 132156903 132157003 2.520000e-35 159.0
28 TraesCS7B01G083000 chr7D 87.097 62 5 3 2387 2448 132742497 132742555 1.570000e-07 67.6
29 TraesCS7B01G083000 chr7D 94.737 38 1 1 2412 2448 132138273 132138310 9.460000e-05 58.4
30 TraesCS7B01G083000 chr7A 88.000 1350 90 20 760 2042 130782302 130783646 0.000000e+00 1530.0
31 TraesCS7B01G083000 chr7A 87.812 1362 94 20 760 2054 131121633 131120277 0.000000e+00 1530.0
32 TraesCS7B01G083000 chr7A 86.048 1197 118 22 721 1874 131187723 131186533 0.000000e+00 1240.0
33 TraesCS7B01G083000 chr7A 90.258 893 63 12 643 1523 130891460 130892340 0.000000e+00 1146.0
34 TraesCS7B01G083000 chr7A 89.443 862 46 18 1032 1873 131109279 131108443 0.000000e+00 1046.0
35 TraesCS7B01G083000 chr7A 92.240 567 26 9 1314 1874 203697311 203697865 0.000000e+00 787.0
36 TraesCS7B01G083000 chr7A 86.084 618 40 18 1515 2102 130893568 130894169 7.440000e-175 623.0
37 TraesCS7B01G083000 chr7A 91.852 270 21 1 643 911 131109918 131109649 2.300000e-100 375.0
38 TraesCS7B01G083000 chr7A 86.996 223 21 1 1888 2102 131108395 131108173 6.760000e-61 244.0
39 TraesCS7B01G083000 chr7A 86.937 222 21 4 2139 2352 203698059 203698280 2.430000e-60 243.0
40 TraesCS7B01G083000 chr7A 86.364 220 22 2 1888 2099 210253296 210253515 1.460000e-57 233.0
41 TraesCS7B01G083000 chr7A 85.268 224 24 4 1888 2102 131186485 131186262 3.170000e-54 222.0
42 TraesCS7B01G083000 chr7A 93.836 146 8 1 2212 2357 130784831 130784975 4.100000e-53 219.0
43 TraesCS7B01G083000 chr7A 93.836 146 8 1 2212 2357 131119104 131118960 4.100000e-53 219.0
44 TraesCS7B01G083000 chr7A 78.635 337 35 16 2139 2448 210253445 210253771 3.210000e-44 189.0
45 TraesCS7B01G083000 chr7A 88.889 117 13 0 1959 2075 130784713 130784829 7.060000e-31 145.0
46 TraesCS7B01G083000 chr7A 88.889 117 13 0 1959 2075 131119222 131119106 7.060000e-31 145.0
47 TraesCS7B01G083000 chr3B 96.250 640 22 2 1 639 750414960 750415598 0.000000e+00 1048.0
48 TraesCS7B01G083000 chr3B 95.761 637 27 0 1 637 25481172 25481808 0.000000e+00 1027.0
49 TraesCS7B01G083000 chr3B 95.141 638 31 0 1 638 680348289 680347652 0.000000e+00 1007.0
50 TraesCS7B01G083000 chr3D 96.232 637 24 0 1 637 15103616 15102980 0.000000e+00 1044.0
51 TraesCS7B01G083000 chr3D 95.918 637 26 0 1 637 373998408 373997772 0.000000e+00 1033.0
52 TraesCS7B01G083000 chr5B 95.775 639 26 1 1 638 577360287 577359649 0.000000e+00 1029.0
53 TraesCS7B01G083000 chr2B 95.768 638 26 1 1 638 549943387 549942751 0.000000e+00 1027.0
54 TraesCS7B01G083000 chr1D 94.819 637 33 0 1 637 484442443 484441807 0.000000e+00 994.0
55 TraesCS7B01G083000 chrUn 94.255 644 32 3 1 640 33060889 33061531 0.000000e+00 979.0


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 TraesCS7B01G083000 chr7B 93649725 93652173 2448 False 4523.000000 4523 100.000000 1 2449 1 chr7B.!!$F1 2448
1 TraesCS7B01G083000 chr7B 93864350 93865781 1431 False 1513.000000 1513 86.293000 644 2067 1 chr7B.!!$F2 1423
2 TraesCS7B01G083000 chr7B 93571366 93573020 1654 False 1031.500000 1507 92.652000 760 2449 2 chr7B.!!$F3 1689
3 TraesCS7B01G083000 chr7B 94115271 94118631 3360 True 868.000000 1626 89.593500 663 2448 2 chr7B.!!$R2 1785
4 TraesCS7B01G083000 chr7B 157808153 157809849 1696 False 826.000000 1411 87.132000 639 2352 2 chr7B.!!$F4 1713
5 TraesCS7B01G083000 chr7B 94048975 94051075 2100 True 702.666667 1432 89.948333 663 2358 3 chr7B.!!$R1 1695
6 TraesCS7B01G083000 chr7B 94184846 94186390 1544 True 573.000000 1393 91.417000 849 2441 3 chr7B.!!$R4 1592
7 TraesCS7B01G083000 chr7D 132829611 132830978 1367 True 1526.000000 1526 87.673000 804 2102 1 chr7D.!!$R1 1298
8 TraesCS7B01G083000 chr7D 194129131 194130378 1247 False 1452.000000 1452 88.110000 644 1874 1 chr7D.!!$F2 1230
9 TraesCS7B01G083000 chr7D 132747869 132749265 1396 False 1391.000000 1391 85.226000 721 2102 1 chr7D.!!$F1 1381
10 TraesCS7B01G083000 chr7D 132740991 132742555 1564 False 755.300000 1443 86.562000 741 2448 2 chr7D.!!$F5 1707
11 TraesCS7B01G083000 chr7D 132156903 132158568 1665 False 642.666667 1580 88.681333 643 2448 3 chr7D.!!$F4 1805
12 TraesCS7B01G083000 chr7D 132763037 132764690 1653 True 577.000000 1327 83.826000 757 2448 3 chr7D.!!$R2 1691
13 TraesCS7B01G083000 chr7D 132135509 132138310 2801 False 562.800000 1356 89.616667 761 2448 3 chr7D.!!$F3 1687
14 TraesCS7B01G083000 chr7A 130891460 130894169 2709 False 884.500000 1146 88.171000 643 2102 2 chr7A.!!$F2 1459
15 TraesCS7B01G083000 chr7A 131186262 131187723 1461 True 731.000000 1240 85.658000 721 2102 2 chr7A.!!$R3 1381
16 TraesCS7B01G083000 chr7A 130782302 130784975 2673 False 631.333333 1530 90.241667 760 2357 3 chr7A.!!$F1 1597
17 TraesCS7B01G083000 chr7A 131118960 131121633 2673 True 631.333333 1530 90.179000 760 2357 3 chr7A.!!$R2 1597
18 TraesCS7B01G083000 chr7A 131108173 131109918 1745 True 555.000000 1046 89.430333 643 2102 3 chr7A.!!$R1 1459
19 TraesCS7B01G083000 chr7A 203697311 203698280 969 False 515.000000 787 89.588500 1314 2352 2 chr7A.!!$F3 1038
20 TraesCS7B01G083000 chr3B 750414960 750415598 638 False 1048.000000 1048 96.250000 1 639 1 chr3B.!!$F2 638
21 TraesCS7B01G083000 chr3B 25481172 25481808 636 False 1027.000000 1027 95.761000 1 637 1 chr3B.!!$F1 636
22 TraesCS7B01G083000 chr3B 680347652 680348289 637 True 1007.000000 1007 95.141000 1 638 1 chr3B.!!$R1 637
23 TraesCS7B01G083000 chr3D 15102980 15103616 636 True 1044.000000 1044 96.232000 1 637 1 chr3D.!!$R1 636
24 TraesCS7B01G083000 chr3D 373997772 373998408 636 True 1033.000000 1033 95.918000 1 637 1 chr3D.!!$R2 636
25 TraesCS7B01G083000 chr5B 577359649 577360287 638 True 1029.000000 1029 95.775000 1 638 1 chr5B.!!$R1 637
26 TraesCS7B01G083000 chr2B 549942751 549943387 636 True 1027.000000 1027 95.768000 1 638 1 chr2B.!!$R1 637
27 TraesCS7B01G083000 chr1D 484441807 484442443 636 True 994.000000 994 94.819000 1 637 1 chr1D.!!$R1 636
28 TraesCS7B01G083000 chrUn 33060889 33061531 642 False 979.000000 979 94.255000 1 640 1 chrUn.!!$F1 639

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
919 953 0.04109 AAACCCCCTCCATTTCGCAT 59.959 50.0 0.0 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 4383 1.071542 TCAAGGTCGTTCATCAAGCCA 59.928 47.619 0.0 0.0 0.0 4.75 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
86 87 3.804036 TGACGAGTCCATCAAACACTTT 58.196 40.909 0.34 0.00 0.00 2.66
120 121 5.764686 TGTAAGTTTACTCGTGTAGTCTGGA 59.235 40.000 3.91 0.00 39.80 3.86
132 133 5.566032 CGTGTAGTCTGGACCATAGTTCAAA 60.566 44.000 0.00 0.00 28.39 2.69
154 159 8.668653 TCAAATAGCTTCAAATCTATATCCCCA 58.331 33.333 0.00 0.00 0.00 4.96
157 162 6.266131 AGCTTCAAATCTATATCCCCAACA 57.734 37.500 0.00 0.00 0.00 3.33
234 239 0.393944 ACATCTACTCGTGGGAGCGA 60.394 55.000 0.00 0.00 44.48 4.93
263 268 2.072874 ATTGGGCACTGTGGCTCACT 62.073 55.000 29.69 18.24 45.66 3.41
323 328 1.682702 CCTGTGCAGGTTATCCATGCA 60.683 52.381 9.96 10.90 43.61 3.96
329 334 3.213506 GCAGGTTATCCATGCATGTACA 58.786 45.455 24.58 9.14 37.60 2.90
400 405 4.634004 CCTTTTTATGATGGCGTCTACACA 59.366 41.667 8.40 0.00 0.00 3.72
465 470 1.968493 GGTGTAATCTCCGGATAGGCA 59.032 52.381 3.57 0.00 40.77 4.75
670 680 3.761752 ACCAAACGGTAGGAATTCATTGG 59.238 43.478 7.93 6.26 41.35 3.16
775 794 4.627467 CCTAATCGTATATCAAGCAGCACC 59.373 45.833 0.00 0.00 0.00 5.01
816 835 3.623906 CAGATCTTTCTGGAAGGCTCA 57.376 47.619 0.00 0.00 44.78 4.26
919 953 0.041090 AAACCCCCTCCATTTCGCAT 59.959 50.000 0.00 0.00 0.00 4.73
1183 1482 1.208614 GACGACGACTACAGCGGTT 59.791 57.895 0.00 0.00 0.00 4.44
1402 1753 0.039437 GAGGACGTCGCAACTCAGAA 60.039 55.000 9.92 0.00 0.00 3.02
1407 1758 1.954146 GTCGCAACTCAGAACGGCA 60.954 57.895 0.00 0.00 0.00 5.69
1677 3276 0.942962 CAAGATCAAGGCCGAGATGC 59.057 55.000 16.33 8.95 0.00 3.91
1828 4008 2.622470 TGATGTGGTCATGTTTGGTGTG 59.378 45.455 0.00 0.00 34.06 3.82
1830 4011 1.747924 TGTGGTCATGTTTGGTGTGTG 59.252 47.619 0.00 0.00 0.00 3.82
1905 4157 3.605461 CGCGAGTTTGGCATATGATGAAG 60.605 47.826 6.97 0.00 0.00 3.02
1979 4259 4.159321 TGTGAACTGATTTGGTGCTGAAAA 59.841 37.500 0.00 0.00 0.00 2.29
1981 4261 5.403466 GTGAACTGATTTGGTGCTGAAAATC 59.597 40.000 9.99 9.99 41.25 2.17
1996 4276 4.545610 TGAAAATCGTCATGAAACCTTGC 58.454 39.130 0.00 0.00 0.00 4.01
2035 4345 2.223044 GCGTGCTGGACTAAATTAGTGC 60.223 50.000 16.26 16.26 45.98 4.40
2040 4350 5.181245 GTGCTGGACTAAATTAGTGCTGAAA 59.819 40.000 26.57 15.35 45.97 2.69
2041 4351 5.945784 TGCTGGACTAAATTAGTGCTGAAAT 59.054 36.000 26.57 0.00 45.97 2.17
2042 4352 6.094048 TGCTGGACTAAATTAGTGCTGAAATC 59.906 38.462 26.57 14.16 45.97 2.17
2043 4353 6.662414 TGGACTAAATTAGTGCTGAAATCG 57.338 37.500 21.96 0.00 45.97 3.34
2044 4354 6.403049 TGGACTAAATTAGTGCTGAAATCGA 58.597 36.000 21.96 0.00 45.97 3.59
2045 4355 7.047891 TGGACTAAATTAGTGCTGAAATCGAT 58.952 34.615 21.96 0.00 45.97 3.59
2046 4356 7.224753 TGGACTAAATTAGTGCTGAAATCGATC 59.775 37.037 21.96 0.00 45.97 3.69
2047 4357 7.224753 GGACTAAATTAGTGCTGAAATCGATCA 59.775 37.037 15.92 0.00 42.95 2.92
2048 4358 8.668510 ACTAAATTAGTGCTGAAATCGATCAT 57.331 30.769 4.66 0.00 37.69 2.45
2049 4359 8.554528 ACTAAATTAGTGCTGAAATCGATCATG 58.445 33.333 4.66 0.00 37.69 3.07
2050 4360 6.932356 AATTAGTGCTGAAATCGATCATGT 57.068 33.333 0.00 0.00 0.00 3.21
2051 4361 8.437360 AAATTAGTGCTGAAATCGATCATGTA 57.563 30.769 0.00 0.00 0.00 2.29
2052 4362 6.828502 TTAGTGCTGAAATCGATCATGTAC 57.171 37.500 0.00 0.00 0.00 2.90
2053 4363 5.016051 AGTGCTGAAATCGATCATGTACT 57.984 39.130 0.00 2.24 0.00 2.73
2054 4364 4.807834 AGTGCTGAAATCGATCATGTACTG 59.192 41.667 0.00 0.00 29.57 2.74
2055 4365 4.568359 GTGCTGAAATCGATCATGTACTGT 59.432 41.667 0.00 0.00 0.00 3.55
2056 4366 4.567959 TGCTGAAATCGATCATGTACTGTG 59.432 41.667 0.00 0.00 0.00 3.66
2057 4367 4.568359 GCTGAAATCGATCATGTACTGTGT 59.432 41.667 0.00 0.00 0.00 3.72
2058 4368 5.063944 GCTGAAATCGATCATGTACTGTGTT 59.936 40.000 0.00 0.00 0.00 3.32
2059 4369 6.407475 TGAAATCGATCATGTACTGTGTTG 57.593 37.500 0.00 0.00 0.00 3.33
2060 4370 6.162777 TGAAATCGATCATGTACTGTGTTGA 58.837 36.000 0.00 0.00 0.00 3.18
2061 4371 6.818142 TGAAATCGATCATGTACTGTGTTGAT 59.182 34.615 0.00 0.00 0.00 2.57
2062 4372 7.334171 TGAAATCGATCATGTACTGTGTTGATT 59.666 33.333 0.00 3.70 31.72 2.57
2063 4373 6.594284 ATCGATCATGTACTGTGTTGATTG 57.406 37.500 0.00 8.96 33.22 2.67
2064 4374 5.478407 TCGATCATGTACTGTGTTGATTGT 58.522 37.500 12.47 0.00 33.53 2.71
2065 4375 5.576774 TCGATCATGTACTGTGTTGATTGTC 59.423 40.000 12.47 0.82 33.53 3.18
2066 4376 5.578336 CGATCATGTACTGTGTTGATTGTCT 59.422 40.000 0.00 0.00 0.00 3.41
2067 4377 6.454715 CGATCATGTACTGTGTTGATTGTCTG 60.455 42.308 0.00 0.00 0.00 3.51
2068 4378 5.852827 TCATGTACTGTGTTGATTGTCTGA 58.147 37.500 0.00 0.00 0.00 3.27
2069 4379 6.287525 TCATGTACTGTGTTGATTGTCTGAA 58.712 36.000 0.00 0.00 0.00 3.02
2070 4380 6.424812 TCATGTACTGTGTTGATTGTCTGAAG 59.575 38.462 0.00 0.00 0.00 3.02
2071 4381 5.670485 TGTACTGTGTTGATTGTCTGAAGT 58.330 37.500 0.00 0.00 0.00 3.01
2072 4382 6.112734 TGTACTGTGTTGATTGTCTGAAGTT 58.887 36.000 0.00 0.00 0.00 2.66
2073 4383 6.597672 TGTACTGTGTTGATTGTCTGAAGTTT 59.402 34.615 0.00 0.00 0.00 2.66
2074 4384 5.883661 ACTGTGTTGATTGTCTGAAGTTTG 58.116 37.500 0.00 0.00 0.00 2.93
2075 4385 5.163622 ACTGTGTTGATTGTCTGAAGTTTGG 60.164 40.000 0.00 0.00 0.00 3.28
2076 4386 4.044426 GTGTTGATTGTCTGAAGTTTGGC 58.956 43.478 0.00 0.00 0.00 4.52
2077 4387 3.953612 TGTTGATTGTCTGAAGTTTGGCT 59.046 39.130 0.00 0.00 0.00 4.75
2078 4388 4.402155 TGTTGATTGTCTGAAGTTTGGCTT 59.598 37.500 0.00 0.00 40.76 4.35
2079 4389 4.572985 TGATTGTCTGAAGTTTGGCTTG 57.427 40.909 0.00 0.00 37.59 4.01
2080 4390 4.206375 TGATTGTCTGAAGTTTGGCTTGA 58.794 39.130 0.00 0.00 37.59 3.02
2081 4391 4.828939 TGATTGTCTGAAGTTTGGCTTGAT 59.171 37.500 0.00 0.00 37.59 2.57
2082 4392 4.572985 TTGTCTGAAGTTTGGCTTGATG 57.427 40.909 0.00 0.00 37.59 3.07
2083 4393 3.819368 TGTCTGAAGTTTGGCTTGATGA 58.181 40.909 0.00 0.00 37.59 2.92
2084 4394 4.206375 TGTCTGAAGTTTGGCTTGATGAA 58.794 39.130 0.00 0.00 37.59 2.57
2085 4395 4.036734 TGTCTGAAGTTTGGCTTGATGAAC 59.963 41.667 0.00 0.00 37.59 3.18
2086 4396 3.250762 TCTGAAGTTTGGCTTGATGAACG 59.749 43.478 0.00 0.00 37.59 3.95
2087 4397 3.210227 TGAAGTTTGGCTTGATGAACGA 58.790 40.909 0.00 0.00 37.59 3.85
2088 4398 3.003275 TGAAGTTTGGCTTGATGAACGAC 59.997 43.478 0.00 0.00 37.59 4.34
2089 4399 1.880027 AGTTTGGCTTGATGAACGACC 59.120 47.619 0.00 0.00 0.00 4.79
2090 4400 1.880027 GTTTGGCTTGATGAACGACCT 59.120 47.619 0.00 0.00 0.00 3.85
2091 4401 2.270352 TTGGCTTGATGAACGACCTT 57.730 45.000 0.00 0.00 0.00 3.50
2092 4402 1.522668 TGGCTTGATGAACGACCTTG 58.477 50.000 0.00 0.00 0.00 3.61
2093 4403 1.071542 TGGCTTGATGAACGACCTTGA 59.928 47.619 0.00 0.00 0.00 3.02
2094 4404 2.290260 TGGCTTGATGAACGACCTTGAT 60.290 45.455 0.00 0.00 0.00 2.57
2095 4405 2.749621 GGCTTGATGAACGACCTTGATT 59.250 45.455 0.00 0.00 0.00 2.57
2096 4406 3.426695 GGCTTGATGAACGACCTTGATTG 60.427 47.826 0.00 0.00 0.00 2.67
2097 4407 3.189287 GCTTGATGAACGACCTTGATTGT 59.811 43.478 0.00 0.00 0.00 2.71
2098 4408 4.670221 GCTTGATGAACGACCTTGATTGTC 60.670 45.833 0.00 0.00 0.00 3.18
2099 4409 4.271696 TGATGAACGACCTTGATTGTCT 57.728 40.909 0.00 0.00 0.00 3.41
2100 4410 4.641396 TGATGAACGACCTTGATTGTCTT 58.359 39.130 0.00 0.00 0.00 3.01
2101 4411 5.789521 TGATGAACGACCTTGATTGTCTTA 58.210 37.500 0.00 0.00 0.00 2.10
2102 4412 6.406370 TGATGAACGACCTTGATTGTCTTAT 58.594 36.000 0.00 0.00 0.00 1.73
2103 4413 6.313658 TGATGAACGACCTTGATTGTCTTATG 59.686 38.462 0.00 0.00 0.00 1.90
2104 4414 5.789521 TGAACGACCTTGATTGTCTTATGA 58.210 37.500 0.00 0.00 0.00 2.15
2105 4415 6.227522 TGAACGACCTTGATTGTCTTATGAA 58.772 36.000 0.00 0.00 0.00 2.57
2106 4416 6.147164 TGAACGACCTTGATTGTCTTATGAAC 59.853 38.462 0.00 0.00 0.00 3.18
2107 4417 5.794894 ACGACCTTGATTGTCTTATGAACT 58.205 37.500 0.00 0.00 0.00 3.01
2108 4418 6.231211 ACGACCTTGATTGTCTTATGAACTT 58.769 36.000 0.00 0.00 0.00 2.66
2109 4419 6.710744 ACGACCTTGATTGTCTTATGAACTTT 59.289 34.615 0.00 0.00 0.00 2.66
2110 4420 7.017645 CGACCTTGATTGTCTTATGAACTTTG 58.982 38.462 0.00 0.00 0.00 2.77
2111 4421 7.307989 CGACCTTGATTGTCTTATGAACTTTGT 60.308 37.037 0.00 0.00 0.00 2.83
2112 4422 7.875971 ACCTTGATTGTCTTATGAACTTTGTC 58.124 34.615 0.00 0.00 0.00 3.18
2113 4423 7.502226 ACCTTGATTGTCTTATGAACTTTGTCA 59.498 33.333 0.00 0.00 0.00 3.58
2114 4424 8.517878 CCTTGATTGTCTTATGAACTTTGTCAT 58.482 33.333 0.00 0.00 41.21 3.06
2115 4425 9.338291 CTTGATTGTCTTATGAACTTTGTCATG 57.662 33.333 0.00 0.00 38.69 3.07
2116 4426 8.620116 TGATTGTCTTATGAACTTTGTCATGA 57.380 30.769 0.00 0.00 38.69 3.07
2117 4427 9.065798 TGATTGTCTTATGAACTTTGTCATGAA 57.934 29.630 0.00 0.00 38.69 2.57
2118 4428 9.334693 GATTGTCTTATGAACTTTGTCATGAAC 57.665 33.333 0.00 0.00 38.69 3.18
2119 4429 8.450578 TTGTCTTATGAACTTTGTCATGAACT 57.549 30.769 0.00 0.00 38.69 3.01
2120 4430 8.450578 TGTCTTATGAACTTTGTCATGAACTT 57.549 30.769 0.00 0.00 38.69 2.66
2121 4431 8.902806 TGTCTTATGAACTTTGTCATGAACTTT 58.097 29.630 0.00 0.00 38.69 2.66
2122 4432 9.173939 GTCTTATGAACTTTGTCATGAACTTTG 57.826 33.333 0.00 0.00 38.69 2.77
2123 4433 8.902806 TCTTATGAACTTTGTCATGAACTTTGT 58.097 29.630 0.00 0.00 38.69 2.83
2124 4434 9.173939 CTTATGAACTTTGTCATGAACTTTGTC 57.826 33.333 0.00 0.00 38.69 3.18
2125 4435 6.507958 TGAACTTTGTCATGAACTTTGTCA 57.492 33.333 0.00 0.00 0.00 3.58
2126 4436 7.099266 TGAACTTTGTCATGAACTTTGTCAT 57.901 32.000 0.00 0.00 38.84 3.06
2127 4437 7.546358 TGAACTTTGTCATGAACTTTGTCATT 58.454 30.769 0.00 0.00 36.04 2.57
2128 4438 8.681806 TGAACTTTGTCATGAACTTTGTCATTA 58.318 29.630 0.00 0.00 36.04 1.90
2129 4439 9.515020 GAACTTTGTCATGAACTTTGTCATTAA 57.485 29.630 0.00 0.00 36.04 1.40
2214 4532 5.392767 TGAACTAGTCTTAAGCCAGTCTG 57.607 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 8.814038 AGATTTGAAGCTATTTGAACTATGGT 57.186 30.769 0.00 0.00 0.00 3.55
132 133 7.988937 TGTTGGGGATATAGATTTGAAGCTAT 58.011 34.615 6.72 6.72 40.42 2.97
154 159 2.343101 ACATGTTACGCGCACTATGTT 58.657 42.857 5.73 0.00 0.00 2.71
157 162 2.603110 CTGAACATGTTACGCGCACTAT 59.397 45.455 11.95 0.00 0.00 2.12
323 328 1.066605 GTACGGAGCCATCGTGTACAT 59.933 52.381 0.00 0.00 41.24 2.29
329 334 2.488355 CACGTACGGAGCCATCGT 59.512 61.111 21.06 2.39 43.64 3.73
670 680 7.033185 TGCTTTTCAAAGTTGGACTACTTTTC 58.967 34.615 8.74 0.00 43.85 2.29
718 729 2.349886 GTGCTAACCTTTGATCTGCTCG 59.650 50.000 0.00 0.00 0.00 5.03
775 794 1.398390 GAGGCCACAGCTTTACGATTG 59.602 52.381 5.01 0.00 39.73 2.67
816 835 0.613777 GACAGATCGGTTGGGGTCTT 59.386 55.000 0.00 0.00 0.00 3.01
919 953 3.371063 GTGGTGAGCGAGACGGGA 61.371 66.667 0.00 0.00 0.00 5.14
1183 1482 3.458163 GGGGATGACGAGGTCGCA 61.458 66.667 0.00 0.00 44.43 5.10
1402 1753 4.704103 TGGAGGAGAGGCTGCCGT 62.704 66.667 13.96 4.42 0.00 5.68
1407 1758 1.988956 CAGCAGTGGAGGAGAGGCT 60.989 63.158 0.00 0.00 0.00 4.58
1446 1800 4.641645 CTTGGCCACCCAGCGTCA 62.642 66.667 3.88 0.00 43.37 4.35
1472 1826 1.287815 CTTGAGGTACACCGCGTCA 59.712 57.895 4.92 0.00 42.08 4.35
1534 3124 2.054021 TCACCAGGATGTTCTTGTCCA 58.946 47.619 0.00 0.00 36.96 4.02
1677 3276 2.110967 CCCAGAGCACGCCATTCTG 61.111 63.158 0.95 0.95 38.41 3.02
1828 4008 3.181500 ACGAAGCAAAACAAGGAAGACAC 60.181 43.478 0.00 0.00 0.00 3.67
1830 4011 3.692791 ACGAAGCAAAACAAGGAAGAC 57.307 42.857 0.00 0.00 0.00 3.01
1905 4157 2.871633 CCAATTTCACCACCAAAGCAAC 59.128 45.455 0.00 0.00 0.00 4.17
1979 4259 3.057969 TCAGCAAGGTTTCATGACGAT 57.942 42.857 0.00 0.00 0.00 3.73
1981 4261 3.005554 AGATCAGCAAGGTTTCATGACG 58.994 45.455 0.00 0.00 0.00 4.35
1996 4276 3.372206 CACGCCAAACTTAAGGAGATCAG 59.628 47.826 7.53 0.00 0.00 2.90
2035 4345 6.311200 TCAACACAGTACATGATCGATTTCAG 59.689 38.462 0.00 0.00 0.00 3.02
2040 4350 6.108687 ACAATCAACACAGTACATGATCGAT 58.891 36.000 0.00 0.00 31.58 3.59
2041 4351 5.478407 ACAATCAACACAGTACATGATCGA 58.522 37.500 0.00 0.00 31.58 3.59
2042 4352 5.578336 AGACAATCAACACAGTACATGATCG 59.422 40.000 0.00 0.00 31.58 3.69
2043 4353 6.591448 TCAGACAATCAACACAGTACATGATC 59.409 38.462 0.00 0.00 31.58 2.92
2044 4354 6.466812 TCAGACAATCAACACAGTACATGAT 58.533 36.000 0.00 0.00 34.11 2.45
2045 4355 5.852827 TCAGACAATCAACACAGTACATGA 58.147 37.500 0.00 0.00 0.00 3.07
2046 4356 6.203530 ACTTCAGACAATCAACACAGTACATG 59.796 38.462 0.00 0.00 0.00 3.21
2047 4357 6.291377 ACTTCAGACAATCAACACAGTACAT 58.709 36.000 0.00 0.00 0.00 2.29
2048 4358 5.670485 ACTTCAGACAATCAACACAGTACA 58.330 37.500 0.00 0.00 0.00 2.90
2049 4359 6.604735 AACTTCAGACAATCAACACAGTAC 57.395 37.500 0.00 0.00 0.00 2.73
2050 4360 6.038161 CCAAACTTCAGACAATCAACACAGTA 59.962 38.462 0.00 0.00 0.00 2.74
2051 4361 5.163622 CCAAACTTCAGACAATCAACACAGT 60.164 40.000 0.00 0.00 0.00 3.55
2052 4362 5.276270 CCAAACTTCAGACAATCAACACAG 58.724 41.667 0.00 0.00 0.00 3.66
2053 4363 4.439974 GCCAAACTTCAGACAATCAACACA 60.440 41.667 0.00 0.00 0.00 3.72
2054 4364 4.044426 GCCAAACTTCAGACAATCAACAC 58.956 43.478 0.00 0.00 0.00 3.32
2055 4365 3.953612 AGCCAAACTTCAGACAATCAACA 59.046 39.130 0.00 0.00 0.00 3.33
2056 4366 4.574599 AGCCAAACTTCAGACAATCAAC 57.425 40.909 0.00 0.00 0.00 3.18
2057 4367 4.644234 TCAAGCCAAACTTCAGACAATCAA 59.356 37.500 0.00 0.00 36.04 2.57
2058 4368 4.206375 TCAAGCCAAACTTCAGACAATCA 58.794 39.130 0.00 0.00 36.04 2.57
2059 4369 4.836125 TCAAGCCAAACTTCAGACAATC 57.164 40.909 0.00 0.00 36.04 2.67
2060 4370 4.828939 TCATCAAGCCAAACTTCAGACAAT 59.171 37.500 0.00 0.00 36.04 2.71
2061 4371 4.206375 TCATCAAGCCAAACTTCAGACAA 58.794 39.130 0.00 0.00 36.04 3.18
2062 4372 3.819368 TCATCAAGCCAAACTTCAGACA 58.181 40.909 0.00 0.00 36.04 3.41
2063 4373 4.540824 GTTCATCAAGCCAAACTTCAGAC 58.459 43.478 0.00 0.00 36.04 3.51
2064 4374 3.250762 CGTTCATCAAGCCAAACTTCAGA 59.749 43.478 0.00 0.00 36.04 3.27
2065 4375 3.250762 TCGTTCATCAAGCCAAACTTCAG 59.749 43.478 0.00 0.00 36.04 3.02
2066 4376 3.003275 GTCGTTCATCAAGCCAAACTTCA 59.997 43.478 0.00 0.00 36.04 3.02
2067 4377 3.555518 GTCGTTCATCAAGCCAAACTTC 58.444 45.455 0.00 0.00 36.04 3.01
2068 4378 2.293399 GGTCGTTCATCAAGCCAAACTT 59.707 45.455 0.00 0.00 40.05 2.66
2069 4379 1.880027 GGTCGTTCATCAAGCCAAACT 59.120 47.619 0.00 0.00 0.00 2.66
2070 4380 1.880027 AGGTCGTTCATCAAGCCAAAC 59.120 47.619 0.00 0.00 0.00 2.93
2071 4381 2.270352 AGGTCGTTCATCAAGCCAAA 57.730 45.000 0.00 0.00 0.00 3.28
2072 4382 1.879380 CAAGGTCGTTCATCAAGCCAA 59.121 47.619 0.00 0.00 0.00 4.52
2073 4383 1.071542 TCAAGGTCGTTCATCAAGCCA 59.928 47.619 0.00 0.00 0.00 4.75
2074 4384 1.808411 TCAAGGTCGTTCATCAAGCC 58.192 50.000 0.00 0.00 0.00 4.35
2075 4385 3.189287 ACAATCAAGGTCGTTCATCAAGC 59.811 43.478 0.00 0.00 0.00 4.01
2076 4386 4.692625 AGACAATCAAGGTCGTTCATCAAG 59.307 41.667 0.00 0.00 40.20 3.02
2077 4387 4.641396 AGACAATCAAGGTCGTTCATCAA 58.359 39.130 0.00 0.00 40.20 2.57
2078 4388 4.271696 AGACAATCAAGGTCGTTCATCA 57.728 40.909 0.00 0.00 40.20 3.07
2079 4389 6.535150 TCATAAGACAATCAAGGTCGTTCATC 59.465 38.462 0.00 0.00 40.20 2.92
2080 4390 6.406370 TCATAAGACAATCAAGGTCGTTCAT 58.594 36.000 0.00 0.00 40.20 2.57
2081 4391 5.789521 TCATAAGACAATCAAGGTCGTTCA 58.210 37.500 0.00 0.00 40.20 3.18
2082 4392 6.369065 AGTTCATAAGACAATCAAGGTCGTTC 59.631 38.462 0.00 0.00 40.20 3.95
2083 4393 6.231211 AGTTCATAAGACAATCAAGGTCGTT 58.769 36.000 0.00 0.00 40.20 3.85
2084 4394 5.794894 AGTTCATAAGACAATCAAGGTCGT 58.205 37.500 0.00 0.00 40.20 4.34
2085 4395 6.727824 AAGTTCATAAGACAATCAAGGTCG 57.272 37.500 0.00 0.00 40.20 4.79
2086 4396 7.875971 ACAAAGTTCATAAGACAATCAAGGTC 58.124 34.615 0.00 0.00 35.50 3.85
2087 4397 7.502226 TGACAAAGTTCATAAGACAATCAAGGT 59.498 33.333 0.00 0.00 0.00 3.50
2088 4398 7.874940 TGACAAAGTTCATAAGACAATCAAGG 58.125 34.615 0.00 0.00 0.00 3.61
2089 4399 9.338291 CATGACAAAGTTCATAAGACAATCAAG 57.662 33.333 0.00 0.00 34.29 3.02
2090 4400 9.065798 TCATGACAAAGTTCATAAGACAATCAA 57.934 29.630 0.00 0.00 34.29 2.57
2091 4401 8.620116 TCATGACAAAGTTCATAAGACAATCA 57.380 30.769 0.00 0.00 34.29 2.57
2092 4402 9.334693 GTTCATGACAAAGTTCATAAGACAATC 57.665 33.333 0.00 0.00 34.29 2.67
2093 4403 9.071276 AGTTCATGACAAAGTTCATAAGACAAT 57.929 29.630 0.00 0.00 34.29 2.71
2094 4404 8.450578 AGTTCATGACAAAGTTCATAAGACAA 57.549 30.769 0.00 0.00 34.29 3.18
2095 4405 8.450578 AAGTTCATGACAAAGTTCATAAGACA 57.549 30.769 0.00 0.00 34.29 3.41
2096 4406 9.173939 CAAAGTTCATGACAAAGTTCATAAGAC 57.826 33.333 0.00 0.00 34.29 3.01
2097 4407 8.902806 ACAAAGTTCATGACAAAGTTCATAAGA 58.097 29.630 0.00 0.00 34.29 2.10
2098 4408 9.173939 GACAAAGTTCATGACAAAGTTCATAAG 57.826 33.333 0.00 0.00 34.29 1.73
2099 4409 8.681806 TGACAAAGTTCATGACAAAGTTCATAA 58.318 29.630 0.00 0.00 34.29 1.90
2100 4410 8.219546 TGACAAAGTTCATGACAAAGTTCATA 57.780 30.769 0.00 0.00 34.29 2.15
2101 4411 7.099266 TGACAAAGTTCATGACAAAGTTCAT 57.901 32.000 0.00 0.00 36.62 2.57
2102 4412 6.507958 TGACAAAGTTCATGACAAAGTTCA 57.492 33.333 0.00 0.00 0.00 3.18
2103 4413 7.992180 AATGACAAAGTTCATGACAAAGTTC 57.008 32.000 0.00 0.00 36.31 3.01
2104 4414 9.301153 GTTAATGACAAAGTTCATGACAAAGTT 57.699 29.630 0.00 0.00 36.31 2.66
2105 4415 8.686334 AGTTAATGACAAAGTTCATGACAAAGT 58.314 29.630 0.00 0.00 36.31 2.66
2106 4416 9.520204 AAGTTAATGACAAAGTTCATGACAAAG 57.480 29.630 0.00 0.00 36.31 2.77
2107 4417 9.868277 AAAGTTAATGACAAAGTTCATGACAAA 57.132 25.926 0.00 0.00 36.31 2.83
2139 4449 8.006298 AGTTCATGACAAATTTCACCACTAAA 57.994 30.769 0.00 0.00 0.00 1.85
2140 4450 7.581213 AGTTCATGACAAATTTCACCACTAA 57.419 32.000 0.00 0.00 0.00 2.24
2141 4451 7.581213 AAGTTCATGACAAATTTCACCACTA 57.419 32.000 0.00 0.00 0.00 2.74
2142 4452 6.469782 AAGTTCATGACAAATTTCACCACT 57.530 33.333 0.00 0.00 0.00 4.00
2143 4453 6.534793 ACAAAGTTCATGACAAATTTCACCAC 59.465 34.615 0.00 0.00 0.00 4.16
2144 4454 6.638610 ACAAAGTTCATGACAAATTTCACCA 58.361 32.000 0.00 0.00 0.00 4.17
2145 4455 7.538303 AACAAAGTTCATGACAAATTTCACC 57.462 32.000 0.00 0.00 0.00 4.02
2214 4532 3.449632 GACGAGAAAAGATAGACAGGCC 58.550 50.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.