Multiple sequence alignment - TraesCS4D01G153800

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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 TraesCS4D01G153800 chr4D 100.000 2375 0 0 1 2375 196954011 196956385 0.000000e+00 4386.0
1 TraesCS4D01G153800 chr4D 92.857 784 55 1 653 1435 239784939 239784156 0.000000e+00 1136.0
2 TraesCS4D01G153800 chr4D 93.986 715 42 1 656 1369 225305682 225304968 0.000000e+00 1081.0
3 TraesCS4D01G153800 chr4D 93.218 693 37 4 794 1480 261222891 261222203 0.000000e+00 1011.0
4 TraesCS4D01G153800 chr4D 93.262 653 42 2 1 652 220962194 220961543 0.000000e+00 961.0
5 TraesCS4D01G153800 chr4D 92.496 653 47 2 1 652 220972555 220971904 0.000000e+00 933.0
6 TraesCS4D01G153800 chr4D 92.366 655 49 1 1 654 196912956 196913610 0.000000e+00 931.0
7 TraesCS4D01G153800 chr4D 90.687 655 60 1 1 654 141393247 141393901 0.000000e+00 870.0
8 TraesCS4D01G153800 chr4D 90.382 655 60 3 1 654 191552746 191552094 0.000000e+00 857.0
9 TraesCS4D01G153800 chr4D 90.244 656 60 4 1 654 171108939 171109592 0.000000e+00 854.0
10 TraesCS4D01G153800 chr4D 89.924 655 64 2 1 654 160125532 160124879 0.000000e+00 843.0
11 TraesCS4D01G153800 chr4D 88.294 299 26 7 2083 2375 338831802 338832097 1.350000e-92 350.0
12 TraesCS4D01G153800 chr4D 87.960 299 27 7 2083 2375 393157018 393156723 6.280000e-91 344.0
13 TraesCS4D01G153800 chr4D 88.333 240 22 3 1854 2087 1624539 1624300 1.390000e-72 283.0
14 TraesCS4D01G153800 chr4D 98.901 91 1 0 653 743 125892024 125892114 1.890000e-36 163.0
15 TraesCS4D01G153800 chr4D 95.522 67 3 0 1525 1591 196955469 196955535 8.980000e-20 108.0
16 TraesCS4D01G153800 chr4D 95.522 67 3 0 1459 1525 196955535 196955601 8.980000e-20 108.0
17 TraesCS4D01G153800 chr4D 91.429 70 1 1 1416 1480 239784152 239784083 9.040000e-15 91.6
18 TraesCS4D01G153800 chr6B 90.254 944 74 13 653 1591 429916214 429915284 0.000000e+00 1218.0
19 TraesCS4D01G153800 chr6B 80.000 425 50 21 1452 1853 429915359 429914947 5.000000e-72 281.0
20 TraesCS4D01G153800 chr6B 82.213 253 31 9 1611 1852 159275160 159274911 3.090000e-49 206.0
21 TraesCS4D01G153800 chr6B 85.075 201 25 4 1611 1808 2734559 2734757 1.440000e-47 200.0
22 TraesCS4D01G153800 chr3B 93.785 724 44 1 653 1375 715974438 715975161 0.000000e+00 1086.0
23 TraesCS4D01G153800 chr5A 93.251 726 46 2 653 1377 545036673 545037396 0.000000e+00 1066.0
24 TraesCS4D01G153800 chr1D 93.506 693 38 3 794 1480 417113815 417114506 0.000000e+00 1024.0
25 TraesCS4D01G153800 chr1D 87.625 299 28 7 2083 2375 433927387 433927092 2.920000e-89 339.0
26 TraesCS4D01G153800 chr3D 84.601 1091 100 42 794 1853 420359217 420360270 0.000000e+00 1022.0
27 TraesCS4D01G153800 chr3D 84.318 1033 86 36 794 1788 416552717 416553711 0.000000e+00 941.0
28 TraesCS4D01G153800 chr3D 91.077 650 55 3 1 648 337754172 337753524 0.000000e+00 876.0
29 TraesCS4D01G153800 chr3D 93.310 583 37 2 794 1375 571735411 571734830 0.000000e+00 859.0
30 TraesCS4D01G153800 chr3D 88.294 299 26 7 2083 2375 289596557 289596262 1.350000e-92 350.0
31 TraesCS4D01G153800 chr3D 87.960 299 27 7 2083 2375 593561323 593561028 6.280000e-91 344.0
32 TraesCS4D01G153800 chr3D 87.625 299 28 7 2083 2375 593539322 593539027 2.920000e-89 339.0
33 TraesCS4D01G153800 chr3D 83.714 350 31 12 1453 1790 213456966 213457301 8.250000e-80 307.0
34 TraesCS4D01G153800 chr5B 92.361 720 50 4 653 1369 189833854 189834571 0.000000e+00 1020.0
35 TraesCS4D01G153800 chr5B 88.333 240 22 3 1854 2087 122824555 122824316 1.390000e-72 283.0
36 TraesCS4D01G153800 chr1A 91.440 736 44 5 653 1369 168324541 168325276 0.000000e+00 992.0
37 TraesCS4D01G153800 chr2D 92.241 696 46 4 792 1480 397131307 397132001 0.000000e+00 979.0
38 TraesCS4D01G153800 chr2D 90.199 653 61 3 1 652 283243370 283242720 0.000000e+00 848.0
39 TraesCS4D01G153800 chr2D 89.030 237 20 3 1854 2084 410495151 410495387 2.990000e-74 289.0
40 TraesCS4D01G153800 chr2D 89.474 228 18 4 1563 1789 648996999 648997221 1.390000e-72 283.0
41 TraesCS4D01G153800 chr5D 90.748 735 50 8 653 1369 161384876 161384142 0.000000e+00 965.0
42 TraesCS4D01G153800 chr7B 91.311 633 35 7 862 1475 725311126 725311757 0.000000e+00 846.0
43 TraesCS4D01G153800 chr7B 88.055 293 30 3 2083 2375 147606746 147606459 2.260000e-90 342.0
44 TraesCS4D01G153800 chr4B 89.375 640 44 7 860 1480 200943406 200944040 0.000000e+00 784.0
45 TraesCS4D01G153800 chr4B 88.333 240 22 3 1854 2087 618361253 618361014 1.390000e-72 283.0
46 TraesCS4D01G153800 chrUn 93.678 522 31 2 1854 2375 316874440 316873921 0.000000e+00 780.0
47 TraesCS4D01G153800 chrUn 87.960 299 27 7 2083 2375 389663430 389663725 6.280000e-91 344.0
48 TraesCS4D01G153800 chr4A 87.965 565 49 5 935 1480 694217272 694217836 0.000000e+00 649.0
49 TraesCS4D01G153800 chr4A 87.560 209 23 2 1582 1789 24490307 24490513 3.050000e-59 239.0
50 TraesCS4D01G153800 chr7D 88.750 240 21 3 1854 2087 162828918 162828679 2.990000e-74 289.0
51 TraesCS4D01G153800 chr7D 88.382 241 22 3 1853 2087 556818208 556817968 3.860000e-73 285.0
52 TraesCS4D01G153800 chr7D 88.333 240 22 3 1854 2087 63900974 63901213 1.390000e-72 283.0
53 TraesCS4D01G153800 chr7D 86.134 238 22 10 1582 1815 152006730 152006500 1.820000e-61 246.0
54 TraesCS4D01G153800 chr7D 97.436 39 1 0 1434 1472 152006875 152006837 1.520000e-07 67.6
55 TraesCS4D01G153800 chr6D 88.608 237 21 3 1854 2084 11241812 11242048 1.390000e-72 283.0
56 TraesCS4D01G153800 chr7A 76.096 502 65 38 1378 1853 583704208 583704680 6.650000e-51 211.0
57 TraesCS4D01G153800 chr7A 93.671 79 1 1 1406 1480 56075333 56075411 5.360000e-22 115.0


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 TraesCS4D01G153800 chr4D 196954011 196956385 2374 False 1534.0 4386 97.014667 1 2375 3 chr4D.!!$F6 2374
1 TraesCS4D01G153800 chr4D 225304968 225305682 714 True 1081.0 1081 93.986000 656 1369 1 chr4D.!!$R6 713
2 TraesCS4D01G153800 chr4D 261222203 261222891 688 True 1011.0 1011 93.218000 794 1480 1 chr4D.!!$R7 686
3 TraesCS4D01G153800 chr4D 220961543 220962194 651 True 961.0 961 93.262000 1 652 1 chr4D.!!$R4 651
4 TraesCS4D01G153800 chr4D 220971904 220972555 651 True 933.0 933 92.496000 1 652 1 chr4D.!!$R5 651
5 TraesCS4D01G153800 chr4D 196912956 196913610 654 False 931.0 931 92.366000 1 654 1 chr4D.!!$F4 653
6 TraesCS4D01G153800 chr4D 141393247 141393901 654 False 870.0 870 90.687000 1 654 1 chr4D.!!$F2 653
7 TraesCS4D01G153800 chr4D 191552094 191552746 652 True 857.0 857 90.382000 1 654 1 chr4D.!!$R3 653
8 TraesCS4D01G153800 chr4D 171108939 171109592 653 False 854.0 854 90.244000 1 654 1 chr4D.!!$F3 653
9 TraesCS4D01G153800 chr4D 160124879 160125532 653 True 843.0 843 89.924000 1 654 1 chr4D.!!$R2 653
10 TraesCS4D01G153800 chr4D 239784083 239784939 856 True 613.8 1136 92.143000 653 1480 2 chr4D.!!$R9 827
11 TraesCS4D01G153800 chr6B 429914947 429916214 1267 True 749.5 1218 85.127000 653 1853 2 chr6B.!!$R2 1200
12 TraesCS4D01G153800 chr3B 715974438 715975161 723 False 1086.0 1086 93.785000 653 1375 1 chr3B.!!$F1 722
13 TraesCS4D01G153800 chr5A 545036673 545037396 723 False 1066.0 1066 93.251000 653 1377 1 chr5A.!!$F1 724
14 TraesCS4D01G153800 chr1D 417113815 417114506 691 False 1024.0 1024 93.506000 794 1480 1 chr1D.!!$F1 686
15 TraesCS4D01G153800 chr3D 420359217 420360270 1053 False 1022.0 1022 84.601000 794 1853 1 chr3D.!!$F3 1059
16 TraesCS4D01G153800 chr3D 416552717 416553711 994 False 941.0 941 84.318000 794 1788 1 chr3D.!!$F2 994
17 TraesCS4D01G153800 chr3D 337753524 337754172 648 True 876.0 876 91.077000 1 648 1 chr3D.!!$R2 647
18 TraesCS4D01G153800 chr3D 571734830 571735411 581 True 859.0 859 93.310000 794 1375 1 chr3D.!!$R3 581
19 TraesCS4D01G153800 chr5B 189833854 189834571 717 False 1020.0 1020 92.361000 653 1369 1 chr5B.!!$F1 716
20 TraesCS4D01G153800 chr1A 168324541 168325276 735 False 992.0 992 91.440000 653 1369 1 chr1A.!!$F1 716
21 TraesCS4D01G153800 chr2D 397131307 397132001 694 False 979.0 979 92.241000 792 1480 1 chr2D.!!$F1 688
22 TraesCS4D01G153800 chr2D 283242720 283243370 650 True 848.0 848 90.199000 1 652 1 chr2D.!!$R1 651
23 TraesCS4D01G153800 chr5D 161384142 161384876 734 True 965.0 965 90.748000 653 1369 1 chr5D.!!$R1 716
24 TraesCS4D01G153800 chr7B 725311126 725311757 631 False 846.0 846 91.311000 862 1475 1 chr7B.!!$F1 613
25 TraesCS4D01G153800 chr4B 200943406 200944040 634 False 784.0 784 89.375000 860 1480 1 chr4B.!!$F1 620
26 TraesCS4D01G153800 chrUn 316873921 316874440 519 True 780.0 780 93.678000 1854 2375 1 chrUn.!!$R1 521
27 TraesCS4D01G153800 chr4A 694217272 694217836 564 False 649.0 649 87.965000 935 1480 1 chr4A.!!$F2 545

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
163 166 0.727793 GTGCGCATTAAACACACCGG 60.728 55.0 15.91 0.0 34.43 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1631 0.178992 TGCTCCCAGGTTCAAACAGG 60.179 55.0 0.0 0.0 0.0 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
145 148 2.281761 CTTTGCGGGCTGACAGGT 60.282 61.111 4.26 0.00 0.00 4.00
156 159 1.729149 GCTGACAGGTGCGCATTAAAC 60.729 52.381 15.91 6.64 0.00 2.01
157 160 1.535028 CTGACAGGTGCGCATTAAACA 59.465 47.619 15.91 11.16 0.00 2.83
163 166 0.727793 GTGCGCATTAAACACACCGG 60.728 55.000 15.91 0.00 34.43 5.28
271 274 4.652822 GAGTGTCACCTATGGGTTTTTCT 58.347 43.478 0.00 0.00 44.73 2.52
274 277 3.572255 TGTCACCTATGGGTTTTTCTTGC 59.428 43.478 0.00 0.00 44.73 4.01
295 298 2.673200 GGAGAGGCTGCCATGTGGA 61.673 63.158 22.65 0.00 37.39 4.02
296 299 1.530771 GAGAGGCTGCCATGTGGAT 59.469 57.895 22.65 0.00 37.39 3.41
349 352 2.944557 CGCACTGATCGACGACGG 60.945 66.667 7.55 2.17 40.21 4.79
391 394 1.029681 GAAGTGGTTTGGCCTTCGTT 58.970 50.000 3.32 0.00 38.35 3.85
534 538 2.940514 TGGTCTTGGTCCCTCTGATA 57.059 50.000 0.00 0.00 0.00 2.15
580 584 8.085296 TCTCTTGATTTCTTGTACTCTGACTTC 58.915 37.037 0.00 0.00 0.00 3.01
612 616 3.628646 ATCTTGACCCCGTGCCTGC 62.629 63.158 0.00 0.00 0.00 4.85
912 917 5.182950 TCAAATAATCCATTTCGTGTGCTGT 59.817 36.000 0.00 0.00 34.49 4.40
997 1040 9.881649 CTATCATTTTCCTCATATGCTAGCTTA 57.118 33.333 17.23 14.54 0.00 3.09
1005 1049 7.382110 TCCTCATATGCTAGCTTAAGATGAAC 58.618 38.462 17.23 0.00 0.00 3.18
1144 1189 1.840635 AGCCATCTAGGAACAACTCCC 59.159 52.381 0.00 0.00 46.81 4.30
1321 1366 1.074752 GCGCAAGAAGTCTCAAGAGG 58.925 55.000 0.30 0.00 43.02 3.69
1480 1593 0.109342 ACCTGGGAGCACTTGTGAAG 59.891 55.000 4.79 0.00 0.00 3.02
1481 1594 0.109342 CCTGGGAGCACTTGTGAAGT 59.891 55.000 4.79 0.00 44.06 3.01
1483 1596 2.224523 CCTGGGAGCACTTGTGAAGTTA 60.225 50.000 4.79 0.00 40.46 2.24
1484 1597 3.560025 CCTGGGAGCACTTGTGAAGTTAT 60.560 47.826 4.79 0.00 40.46 1.89
1485 1598 3.411446 TGGGAGCACTTGTGAAGTTATG 58.589 45.455 4.79 0.00 40.46 1.90
1486 1599 3.181445 TGGGAGCACTTGTGAAGTTATGT 60.181 43.478 4.79 0.00 40.46 2.29
1487 1600 3.189287 GGGAGCACTTGTGAAGTTATGTG 59.811 47.826 4.79 0.00 40.46 3.21
1488 1601 3.189287 GGAGCACTTGTGAAGTTATGTGG 59.811 47.826 4.79 0.00 40.46 4.17
1489 1602 4.065088 GAGCACTTGTGAAGTTATGTGGA 58.935 43.478 4.79 0.00 40.46 4.02
1490 1603 4.655963 AGCACTTGTGAAGTTATGTGGAT 58.344 39.130 4.79 0.00 40.46 3.41
1491 1604 4.697352 AGCACTTGTGAAGTTATGTGGATC 59.303 41.667 4.79 0.00 40.46 3.36
1492 1605 4.697352 GCACTTGTGAAGTTATGTGGATCT 59.303 41.667 4.79 0.00 40.46 2.75
1493 1606 5.182001 GCACTTGTGAAGTTATGTGGATCTT 59.818 40.000 4.79 0.00 40.46 2.40
1494 1607 6.605849 CACTTGTGAAGTTATGTGGATCTTG 58.394 40.000 0.00 0.00 40.46 3.02
1495 1608 5.182001 ACTTGTGAAGTTATGTGGATCTTGC 59.818 40.000 0.00 0.00 39.04 4.01
1496 1609 4.910195 TGTGAAGTTATGTGGATCTTGCT 58.090 39.130 0.00 0.00 0.00 3.91
1497 1610 4.696877 TGTGAAGTTATGTGGATCTTGCTG 59.303 41.667 0.00 0.00 0.00 4.41
1498 1611 4.697352 GTGAAGTTATGTGGATCTTGCTGT 59.303 41.667 0.00 0.00 0.00 4.40
1499 1612 5.182001 GTGAAGTTATGTGGATCTTGCTGTT 59.818 40.000 0.00 0.00 0.00 3.16
1500 1613 5.769662 TGAAGTTATGTGGATCTTGCTGTTT 59.230 36.000 0.00 0.00 0.00 2.83
1501 1614 5.633830 AGTTATGTGGATCTTGCTGTTTG 57.366 39.130 0.00 0.00 0.00 2.93
1502 1615 5.316167 AGTTATGTGGATCTTGCTGTTTGA 58.684 37.500 0.00 0.00 0.00 2.69
1503 1616 5.769662 AGTTATGTGGATCTTGCTGTTTGAA 59.230 36.000 0.00 0.00 0.00 2.69
1504 1617 4.778534 ATGTGGATCTTGCTGTTTGAAG 57.221 40.909 0.00 0.00 0.00 3.02
1505 1618 3.554934 TGTGGATCTTGCTGTTTGAAGT 58.445 40.909 0.00 0.00 0.00 3.01
1506 1619 3.953612 TGTGGATCTTGCTGTTTGAAGTT 59.046 39.130 0.00 0.00 0.00 2.66
1507 1620 5.129634 TGTGGATCTTGCTGTTTGAAGTTA 58.870 37.500 0.00 0.00 0.00 2.24
1508 1621 5.769662 TGTGGATCTTGCTGTTTGAAGTTAT 59.230 36.000 0.00 0.00 0.00 1.89
1509 1622 6.088824 GTGGATCTTGCTGTTTGAAGTTATG 58.911 40.000 0.00 0.00 0.00 1.90
1510 1623 5.769662 TGGATCTTGCTGTTTGAAGTTATGT 59.230 36.000 0.00 0.00 0.00 2.29
1518 1631 6.072508 TGCTGTTTGAAGTTATGTGGATCTTC 60.073 38.462 0.00 0.00 37.42 2.87
1567 1759 6.939730 TGAAGTTATGTGGATCTTGCTGTTTA 59.060 34.615 0.00 0.00 0.00 2.01
1575 1811 8.437360 TGTGGATCTTGCTGTTTATAGTTATG 57.563 34.615 0.00 0.00 0.00 1.90
1576 1812 8.046708 TGTGGATCTTGCTGTTTATAGTTATGT 58.953 33.333 0.00 0.00 0.00 2.29
1599 1835 8.437360 TGTGGATCTTGCTGTTTATAGTTATG 57.563 34.615 0.00 0.00 0.00 1.90
1605 1841 9.956720 ATCTTGCTGTTTATAGTTATGCATTTC 57.043 29.630 3.54 0.00 0.00 2.17
1666 1902 3.023832 CCGAGGCCCAAACAAGAATTAT 58.976 45.455 0.00 0.00 0.00 1.28
1696 1933 1.593296 CTTGGGCCTGAAAGCAGAGC 61.593 60.000 4.53 0.00 45.17 4.09
1702 1939 1.881498 GCCTGAAAGCAGAGCTGACTT 60.881 52.381 0.85 1.98 45.17 3.01
1703 1940 2.613977 GCCTGAAAGCAGAGCTGACTTA 60.614 50.000 0.85 0.00 45.17 2.24
1732 1971 4.101119 ACCTAGTCCGTATAAGCTTGCATT 59.899 41.667 9.86 0.00 0.00 3.56
1733 1972 5.057149 CCTAGTCCGTATAAGCTTGCATTT 58.943 41.667 9.86 0.00 0.00 2.32
1772 2011 3.876309 AGGCCCAAACAAGAACTAGAA 57.124 42.857 0.00 0.00 0.00 2.10
1797 2036 2.203625 GCTGTGGCCCCAAGGAAA 60.204 61.111 0.00 0.00 33.47 3.13
1798 2037 1.610379 GCTGTGGCCCCAAGGAAAT 60.610 57.895 0.00 0.00 33.47 2.17
1799 2038 1.194121 GCTGTGGCCCCAAGGAAATT 61.194 55.000 0.00 0.00 33.47 1.82
1808 2049 5.147767 GGCCCCAAGGAAATTGACTATAAT 58.852 41.667 0.00 0.00 41.83 1.28
1812 2053 9.528489 GCCCCAAGGAAATTGACTATAATAATA 57.472 33.333 0.00 0.00 41.83 0.98
1849 2099 7.727331 TGACAGAAAATAAAAGGCCAAATTG 57.273 32.000 5.01 0.00 0.00 2.32
1869 2119 1.880027 GTTGTGGAACTTGGGTGCTAG 59.120 52.381 0.00 0.00 38.04 3.42
1873 2123 0.324943 GGAACTTGGGTGCTAGCTGA 59.675 55.000 17.23 0.00 0.00 4.26
1927 2177 2.167487 TGTGGGTGTTCAAAAAGAAGCC 59.833 45.455 0.00 0.00 36.78 4.35
2032 2282 2.504175 ACACCTATTCACCCGTTGCTAT 59.496 45.455 0.00 0.00 0.00 2.97
2044 2294 3.476552 CCGTTGCTATAATGACCACCAT 58.523 45.455 0.00 0.00 36.99 3.55
2047 2297 4.574421 CGTTGCTATAATGACCACCATTCA 59.426 41.667 0.00 0.00 43.96 2.57
2071 2321 0.107017 TCCTTGCCTGCCTCTTATGC 60.107 55.000 0.00 0.00 0.00 3.14
2106 2356 6.044637 TCACCATAGTAGTAACCCAACCTTTT 59.955 38.462 0.00 0.00 0.00 2.27
2111 2361 2.036387 AGTAACCCAACCTTTTGTGCC 58.964 47.619 0.00 0.00 0.00 5.01
2112 2362 1.069513 GTAACCCAACCTTTTGTGCCC 59.930 52.381 0.00 0.00 0.00 5.36
2122 2372 2.426522 CTTTTGTGCCCGAAGATCTCA 58.573 47.619 0.00 0.00 0.00 3.27
2141 2391 4.977739 TCTCATGAATTAGGACCTGGGAAT 59.022 41.667 3.53 0.00 0.00 3.01
2161 2411 7.672239 TGGGAATAACAAGCTATTGGTTAAACT 59.328 33.333 0.00 0.00 40.97 2.66
2172 2422 7.180408 AGCTATTGGTTAAACTGAGGAGAGTAA 59.820 37.037 0.00 0.00 0.00 2.24
2179 2429 7.764901 GGTTAAACTGAGGAGAGTAATAAGTGG 59.235 40.741 0.00 0.00 0.00 4.00
2231 2481 1.284785 AGCTATAAGGCAGGTTGGCAA 59.715 47.619 0.00 0.00 46.46 4.52
2301 2551 6.014584 TCCTACAGAGCAGTCTTGAAATAACA 60.015 38.462 0.00 0.00 0.00 2.41
2309 2559 6.595716 AGCAGTCTTGAAATAACACACCTATC 59.404 38.462 0.00 0.00 0.00 2.08
2312 2562 7.819415 CAGTCTTGAAATAACACACCTATCTGA 59.181 37.037 0.00 0.00 0.00 3.27
2327 2577 5.749109 ACCTATCTGAGCTTCGATTTAAACG 59.251 40.000 4.32 0.00 0.00 3.60
2329 2579 5.704217 ATCTGAGCTTCGATTTAAACGTC 57.296 39.130 0.00 0.00 0.00 4.34
2343 2593 7.318439 CGATTTAAACGTCGTAGTCTATGAGAG 59.682 40.741 0.00 3.08 33.42 3.20
2353 2603 6.930164 TCGTAGTCTATGAGAGTTAGGTGATC 59.070 42.308 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 148 1.167155 ACCGGTGTGTTTAATGCGCA 61.167 50.000 14.96 14.96 0.00 6.09
156 159 1.464608 GATGTGACATTGACCGGTGTG 59.535 52.381 14.63 11.01 0.00 3.82
157 160 1.071542 TGATGTGACATTGACCGGTGT 59.928 47.619 14.63 2.45 0.00 4.16
163 166 3.610114 GCAACCAGTGATGTGACATTGAC 60.610 47.826 0.00 0.00 30.82 3.18
274 277 2.192443 CATGGCAGCCTCTCCCTG 59.808 66.667 14.15 0.00 0.00 4.45
295 298 3.200825 AGTGACTAAGTGGCAGCCATTAT 59.799 43.478 19.75 9.61 35.28 1.28
296 299 2.571653 AGTGACTAAGTGGCAGCCATTA 59.428 45.455 19.75 15.30 35.28 1.90
364 367 0.750249 CCAAACCACTTCACCAACCC 59.250 55.000 0.00 0.00 0.00 4.11
391 394 3.757941 TAGGGCCTGCCGGGACTA 61.758 66.667 18.53 0.00 44.42 2.59
534 538 2.270352 TTCGAAGGACCAACAAGCAT 57.730 45.000 0.00 0.00 0.00 3.79
612 616 0.108186 TCTGTTGCCCTGACTATGCG 60.108 55.000 0.00 0.00 0.00 4.73
636 640 1.029408 AGTGTCGCTGCAACAAACCA 61.029 50.000 0.00 0.00 0.00 3.67
912 917 4.817318 AACCAAGCAAGAGAAACCAAAA 57.183 36.364 0.00 0.00 0.00 2.44
997 1040 5.390613 CGCGTCCTTTATTTTGTTCATCTT 58.609 37.500 0.00 0.00 0.00 2.40
1005 1049 0.522495 CCGGCGCGTCCTTTATTTTG 60.522 55.000 4.51 0.00 0.00 2.44
1011 1056 4.747529 GGTACCGGCGCGTCCTTT 62.748 66.667 4.51 0.21 0.00 3.11
1276 1321 0.878523 TCAAGTTCCTTGTCGCGTGG 60.879 55.000 5.77 4.91 41.66 4.94
1321 1366 2.769095 AGTGGGCTAACTTCTCATCCTC 59.231 50.000 0.00 0.00 0.00 3.71
1353 1399 3.766545 TCAAACTGCCTTAGCTCCAAAT 58.233 40.909 0.00 0.00 40.80 2.32
1480 1593 5.627499 TCAAACAGCAAGATCCACATAAC 57.373 39.130 0.00 0.00 0.00 1.89
1481 1594 5.769662 ACTTCAAACAGCAAGATCCACATAA 59.230 36.000 0.00 0.00 0.00 1.90
1483 1596 4.147321 ACTTCAAACAGCAAGATCCACAT 58.853 39.130 0.00 0.00 0.00 3.21
1484 1597 3.554934 ACTTCAAACAGCAAGATCCACA 58.445 40.909 0.00 0.00 0.00 4.17
1485 1598 4.574599 AACTTCAAACAGCAAGATCCAC 57.425 40.909 0.00 0.00 0.00 4.02
1486 1599 5.769662 ACATAACTTCAAACAGCAAGATCCA 59.230 36.000 0.00 0.00 0.00 3.41
1487 1600 6.088824 CACATAACTTCAAACAGCAAGATCC 58.911 40.000 0.00 0.00 0.00 3.36
1488 1601 6.072508 TCCACATAACTTCAAACAGCAAGATC 60.073 38.462 0.00 0.00 0.00 2.75
1489 1602 5.769662 TCCACATAACTTCAAACAGCAAGAT 59.230 36.000 0.00 0.00 0.00 2.40
1490 1603 5.129634 TCCACATAACTTCAAACAGCAAGA 58.870 37.500 0.00 0.00 0.00 3.02
1491 1604 5.437289 TCCACATAACTTCAAACAGCAAG 57.563 39.130 0.00 0.00 0.00 4.01
1492 1605 5.769662 AGATCCACATAACTTCAAACAGCAA 59.230 36.000 0.00 0.00 0.00 3.91
1493 1606 5.316167 AGATCCACATAACTTCAAACAGCA 58.684 37.500 0.00 0.00 0.00 4.41
1494 1607 5.886960 AGATCCACATAACTTCAAACAGC 57.113 39.130 0.00 0.00 0.00 4.40
1495 1608 6.656693 AGGAAGATCCACATAACTTCAAACAG 59.343 38.462 0.00 0.00 39.61 3.16
1496 1609 6.430925 CAGGAAGATCCACATAACTTCAAACA 59.569 38.462 0.00 0.00 39.61 2.83
1497 1610 6.431234 ACAGGAAGATCCACATAACTTCAAAC 59.569 38.462 0.00 0.00 39.61 2.93
1498 1611 6.542821 ACAGGAAGATCCACATAACTTCAAA 58.457 36.000 0.00 0.00 39.61 2.69
1499 1612 6.126863 ACAGGAAGATCCACATAACTTCAA 57.873 37.500 0.00 0.00 39.61 2.69
1500 1613 5.762179 ACAGGAAGATCCACATAACTTCA 57.238 39.130 0.00 0.00 39.61 3.02
1501 1614 6.655003 TCAAACAGGAAGATCCACATAACTTC 59.345 38.462 0.00 0.00 39.61 3.01
1502 1615 6.542821 TCAAACAGGAAGATCCACATAACTT 58.457 36.000 0.00 0.00 39.61 2.66
1503 1616 6.126863 TCAAACAGGAAGATCCACATAACT 57.873 37.500 0.00 0.00 39.61 2.24
1504 1617 6.349363 GGTTCAAACAGGAAGATCCACATAAC 60.349 42.308 0.00 0.00 39.61 1.89
1505 1618 5.710099 GGTTCAAACAGGAAGATCCACATAA 59.290 40.000 0.00 0.00 39.61 1.90
1506 1619 5.014123 AGGTTCAAACAGGAAGATCCACATA 59.986 40.000 0.00 0.00 39.61 2.29
1507 1620 4.082125 GGTTCAAACAGGAAGATCCACAT 58.918 43.478 0.00 0.00 39.61 3.21
1508 1621 3.138283 AGGTTCAAACAGGAAGATCCACA 59.862 43.478 0.00 0.00 39.61 4.17
1509 1622 3.503748 CAGGTTCAAACAGGAAGATCCAC 59.496 47.826 0.00 0.00 39.61 4.02
1510 1623 3.498481 CCAGGTTCAAACAGGAAGATCCA 60.498 47.826 0.00 0.00 39.61 3.41
1518 1631 0.178992 TGCTCCCAGGTTCAAACAGG 60.179 55.000 0.00 0.00 0.00 4.00
1575 1811 7.012327 TGCATAACTATAAACAGCAAGATCCAC 59.988 37.037 0.00 0.00 0.00 4.02
1576 1812 7.053498 TGCATAACTATAAACAGCAAGATCCA 58.947 34.615 0.00 0.00 0.00 3.41
1599 1835 6.973229 ATTTTGCATAACTTCAGGAAATGC 57.027 33.333 9.23 9.23 42.52 3.56
1605 1841 7.703621 CAGGTTCATATTTTGCATAACTTCAGG 59.296 37.037 0.00 0.00 0.00 3.86
1710 1949 3.728076 TGCAAGCTTATACGGACTAGG 57.272 47.619 0.00 0.00 0.00 3.02
1711 1950 5.753438 TGAAATGCAAGCTTATACGGACTAG 59.247 40.000 0.00 0.00 0.00 2.57
1713 1952 4.513442 TGAAATGCAAGCTTATACGGACT 58.487 39.130 0.00 0.00 0.00 3.85
1714 1953 4.570772 TCTGAAATGCAAGCTTATACGGAC 59.429 41.667 0.00 0.00 0.00 4.79
1715 1954 4.765273 TCTGAAATGCAAGCTTATACGGA 58.235 39.130 0.00 0.00 0.00 4.69
1716 1955 5.484173 TTCTGAAATGCAAGCTTATACGG 57.516 39.130 0.00 0.00 0.00 4.02
1717 1956 7.975866 ATTTTCTGAAATGCAAGCTTATACG 57.024 32.000 0.00 0.00 34.26 3.06
1725 1964 7.041235 TGGCCTTTTTATTTTCTGAAATGCAAG 60.041 33.333 3.32 3.21 36.22 4.01
1726 1965 6.769822 TGGCCTTTTTATTTTCTGAAATGCAA 59.230 30.769 3.32 0.00 36.22 4.08
1732 1971 5.304778 GCCTTGGCCTTTTTATTTTCTGAA 58.695 37.500 3.32 0.00 0.00 3.02
1733 1972 4.262851 GGCCTTGGCCTTTTTATTTTCTGA 60.263 41.667 22.47 0.00 0.00 3.27
1761 2000 7.308435 CCACAGCCTTTTTATTCTAGTTCTTG 58.692 38.462 0.00 0.00 0.00 3.02
1762 2001 6.071896 GCCACAGCCTTTTTATTCTAGTTCTT 60.072 38.462 0.00 0.00 0.00 2.52
1816 2057 9.428097 GCCTTTTATTTTCTGTCAAATCTCATT 57.572 29.630 0.00 0.00 0.00 2.57
1818 2059 7.015098 TGGCCTTTTATTTTCTGTCAAATCTCA 59.985 33.333 3.32 0.00 0.00 3.27
1819 2060 7.378181 TGGCCTTTTATTTTCTGTCAAATCTC 58.622 34.615 3.32 0.00 0.00 2.75
1821 2062 7.961325 TTGGCCTTTTATTTTCTGTCAAATC 57.039 32.000 3.32 0.00 0.00 2.17
1823 2064 8.619546 CAATTTGGCCTTTTATTTTCTGTCAAA 58.380 29.630 3.32 0.00 0.00 2.69
1824 2065 7.772757 ACAATTTGGCCTTTTATTTTCTGTCAA 59.227 29.630 3.32 0.00 0.00 3.18
1825 2066 7.278875 ACAATTTGGCCTTTTATTTTCTGTCA 58.721 30.769 3.32 0.00 0.00 3.58
1827 2068 7.555914 ACAACAATTTGGCCTTTTATTTTCTGT 59.444 29.630 3.32 0.00 37.00 3.41
1849 2099 1.880027 CTAGCACCCAAGTTCCACAAC 59.120 52.381 0.00 0.00 0.00 3.32
1906 2156 2.167487 GGCTTCTTTTTGAACACCCACA 59.833 45.455 0.00 0.00 0.00 4.17
1927 2177 7.716998 AGTTATCAATAGTACCATCAAGCCTTG 59.283 37.037 0.00 0.00 0.00 3.61
2047 2297 2.856000 AGGCAGGCAAGGACACCT 60.856 61.111 0.00 0.00 36.45 4.00
2050 2300 1.065199 CATAAGAGGCAGGCAAGGACA 60.065 52.381 0.00 0.00 0.00 4.02
2058 2308 4.613925 TGATAAGAGCATAAGAGGCAGG 57.386 45.455 0.00 0.00 0.00 4.85
2071 2321 9.915629 GGTTACTACTATGGTGAATGATAAGAG 57.084 37.037 0.00 0.00 0.00 2.85
2106 2356 1.194218 TCATGAGATCTTCGGGCACA 58.806 50.000 0.00 0.00 0.00 4.57
2111 2361 5.011533 AGGTCCTAATTCATGAGATCTTCGG 59.988 44.000 0.00 0.00 0.00 4.30
2112 2362 5.925397 CAGGTCCTAATTCATGAGATCTTCG 59.075 44.000 0.00 0.00 0.00 3.79
2122 2372 6.590656 TGTTATTCCCAGGTCCTAATTCAT 57.409 37.500 0.00 0.00 0.00 2.57
2141 2391 7.455058 TCCTCAGTTTAACCAATAGCTTGTTA 58.545 34.615 0.00 0.00 0.00 2.41
2161 2411 3.719871 TGGCCACTTATTACTCTCCTCA 58.280 45.455 0.00 0.00 0.00 3.86
2172 2422 3.928754 TCACCTAGAGATGGCCACTTAT 58.071 45.455 8.16 0.00 0.00 1.73
2179 2429 2.103771 TGCATCTTCACCTAGAGATGGC 59.896 50.000 16.69 11.30 38.72 4.40
2231 2481 6.263168 GCCAATAGAACTACATTAAGGCATGT 59.737 38.462 0.00 0.00 40.61 3.21
2274 2524 1.813178 TCAAGACTGCTCTGTAGGACG 59.187 52.381 0.00 0.00 0.00 4.79
2301 2551 4.744795 AAATCGAAGCTCAGATAGGTGT 57.255 40.909 4.57 0.00 35.65 4.16
2309 2559 3.364023 ACGACGTTTAAATCGAAGCTCAG 59.636 43.478 16.01 0.00 40.86 3.35
2312 2562 4.479619 ACTACGACGTTTAAATCGAAGCT 58.520 39.130 16.01 0.00 40.86 3.74
2327 2577 6.047870 TCACCTAACTCTCATAGACTACGAC 58.952 44.000 0.00 0.00 0.00 4.34
2329 2579 6.932400 AGATCACCTAACTCTCATAGACTACG 59.068 42.308 0.00 0.00 0.00 3.51
2343 2593 6.945938 TGAGCTTACTAGAGATCACCTAAC 57.054 41.667 0.00 0.00 37.17 2.34


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

AutoCloner maintained by Alex Coulton.