Multiple sequence alignment - TraesCS2D01G140800

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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 TraesCS2D01G140800 chr2D 100.000 2930 0 0 1 2930 83048993 83051922 0.000000e+00 5411.0
1 TraesCS2D01G140800 chr2D 97.625 379 8 1 1918 2295 83064291 83064669 0.000000e+00 649.0
2 TraesCS2D01G140800 chr2A 94.848 1087 47 6 829 1912 83691758 83690678 0.000000e+00 1688.0
3 TraesCS2D01G140800 chr2A 91.295 448 30 8 1235 1677 83746823 83747266 1.160000e-168 603.0
4 TraesCS2D01G140800 chr2A 95.851 241 8 2 1675 1914 83747442 83747681 3.540000e-104 388.0
5 TraesCS2D01G140800 chr2A 85.156 384 32 13 269 650 83692109 83691749 1.280000e-98 370.0
6 TraesCS2D01G140800 chr2A 81.967 244 21 7 317 560 83715511 83715731 4.990000e-43 185.0
7 TraesCS2D01G140800 chr2A 77.700 287 38 17 1629 1914 14900744 14900483 5.060000e-33 152.0
8 TraesCS2D01G140800 chr4A 96.373 1020 26 4 1918 2930 676201754 676200739 0.000000e+00 1668.0
9 TraesCS2D01G140800 chr4A 96.561 378 5 4 1918 2288 676197080 676196704 1.150000e-173 619.0
10 TraesCS2D01G140800 chr7D 96.161 1016 32 4 1918 2930 39733160 39734171 0.000000e+00 1653.0
11 TraesCS2D01G140800 chr7D 96.524 374 10 3 1918 2288 39737828 39738201 1.490000e-172 616.0
12 TraesCS2D01G140800 chr2B 93.534 1098 52 7 829 1914 134702370 134703460 0.000000e+00 1616.0
13 TraesCS2D01G140800 chr2B 86.343 432 40 12 34 449 134700945 134701373 1.240000e-123 453.0
14 TraesCS2D01G140800 chr2B 96.667 210 4 3 442 650 134702172 134702379 2.160000e-91 346.0
15 TraesCS2D01G140800 chr6A 95.196 1020 37 6 1918 2930 42337832 42336818 0.000000e+00 1602.0
16 TraesCS2D01G140800 chr6A 94.922 1024 36 8 1918 2930 42625182 42624164 0.000000e+00 1589.0
17 TraesCS2D01G140800 chr6A 96.441 562 20 0 2369 2930 42563982 42563421 0.000000e+00 928.0
18 TraesCS2D01G140800 chr7A 84.690 1032 122 27 1923 2930 7872165 7873184 0.000000e+00 998.0
19 TraesCS2D01G140800 chr7A 93.842 341 21 0 2590 2930 629815658 629815318 5.600000e-142 514.0
20 TraesCS2D01G140800 chr7A 90.027 371 21 6 2185 2543 629816024 629815658 1.590000e-127 466.0
21 TraesCS2D01G140800 chr7A 100.000 28 0 0 190 217 666597444 666597417 5.000000e-03 52.8
22 TraesCS2D01G140800 chrUn 96.637 565 19 0 2366 2930 397515048 397515612 0.000000e+00 939.0
23 TraesCS2D01G140800 chrUn 96.718 457 15 0 2474 2930 437834544 437835000 0.000000e+00 761.0
24 TraesCS2D01G140800 chrUn 80.351 911 140 26 1013 1914 18056834 18057714 0.000000e+00 654.0
25 TraesCS2D01G140800 chrUn 96.561 378 5 4 1918 2288 244956263 244955887 1.150000e-173 619.0
26 TraesCS2D01G140800 chrUn 84.105 497 75 2 1421 1914 238397473 238397968 7.350000e-131 477.0
27 TraesCS2D01G140800 chrUn 83.750 320 52 0 1595 1914 18025957 18025638 1.320000e-78 303.0
28 TraesCS2D01G140800 chr1D 96.296 378 7 3 1918 2288 13058034 13058411 5.370000e-172 614.0
29 TraesCS2D01G140800 chr6B 89.412 170 15 3 645 812 221189289 221189457 8.230000e-51 211.0
30 TraesCS2D01G140800 chr5D 89.412 170 15 3 645 812 423887461 423887293 8.230000e-51 211.0
31 TraesCS2D01G140800 chr5B 89.412 170 15 3 645 812 247548599 247548767 8.230000e-51 211.0
32 TraesCS2D01G140800 chr5B 89.412 170 15 3 645 812 484014232 484014064 8.230000e-51 211.0
33 TraesCS2D01G140800 chr4B 89.412 170 15 3 645 812 31736093 31735925 8.230000e-51 211.0
34 TraesCS2D01G140800 chr4B 84.615 65 10 0 174 238 391596220 391596284 6.780000e-07 65.8
35 TraesCS2D01G140800 chr1B 89.412 170 15 3 645 812 148280809 148280641 8.230000e-51 211.0
36 TraesCS2D01G140800 chr6D 88.824 170 16 3 645 812 95399669 95399837 3.830000e-49 206.0
37 TraesCS2D01G140800 chr6D 88.824 170 16 3 645 812 280654807 280654975 3.830000e-49 206.0
38 TraesCS2D01G140800 chr4D 88.824 170 16 3 645 812 26119251 26119083 3.830000e-49 206.0
39 TraesCS2D01G140800 chr3A 93.103 58 4 0 174 231 28263939 28263882 5.200000e-13 86.1
40 TraesCS2D01G140800 chr3B 91.667 48 4 0 183 230 828552408 828552361 1.880000e-07 67.6
41 TraesCS2D01G140800 chr5A 95.122 41 2 0 176 216 660210241 660210281 6.780000e-07 65.8


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 TraesCS2D01G140800 chr2D 83048993 83051922 2929 False 5411.0 5411 100.000000 1 2930 1 chr2D.!!$F1 2929
1 TraesCS2D01G140800 chr2A 83690678 83692109 1431 True 1029.0 1688 90.002000 269 1912 2 chr2A.!!$R2 1643
2 TraesCS2D01G140800 chr2A 83746823 83747681 858 False 495.5 603 93.573000 1235 1914 2 chr2A.!!$F2 679
3 TraesCS2D01G140800 chr4A 676196704 676201754 5050 True 1143.5 1668 96.467000 1918 2930 2 chr4A.!!$R1 1012
4 TraesCS2D01G140800 chr7D 39733160 39738201 5041 False 1134.5 1653 96.342500 1918 2930 2 chr7D.!!$F1 1012
5 TraesCS2D01G140800 chr2B 134700945 134703460 2515 False 805.0 1616 92.181333 34 1914 3 chr2B.!!$F1 1880
6 TraesCS2D01G140800 chr6A 42336818 42337832 1014 True 1602.0 1602 95.196000 1918 2930 1 chr6A.!!$R1 1012
7 TraesCS2D01G140800 chr6A 42624164 42625182 1018 True 1589.0 1589 94.922000 1918 2930 1 chr6A.!!$R3 1012
8 TraesCS2D01G140800 chr6A 42563421 42563982 561 True 928.0 928 96.441000 2369 2930 1 chr6A.!!$R2 561
9 TraesCS2D01G140800 chr7A 7872165 7873184 1019 False 998.0 998 84.690000 1923 2930 1 chr7A.!!$F1 1007
10 TraesCS2D01G140800 chr7A 629815318 629816024 706 True 490.0 514 91.934500 2185 2930 2 chr7A.!!$R2 745
11 TraesCS2D01G140800 chrUn 397515048 397515612 564 False 939.0 939 96.637000 2366 2930 1 chrUn.!!$F3 564
12 TraesCS2D01G140800 chrUn 18056834 18057714 880 False 654.0 654 80.351000 1013 1914 1 chrUn.!!$F1 901

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
123 124 0.236187 GCGTGTCGGCAACATGTTTA 59.764 50.0 8.77 0.0 45.19 2.01 F
636 1471 0.608640 GAGGAAGCTCAAGGACCGAA 59.391 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 1854 0.664767 AAGACTCGCTCTTGCACGTC 60.665 55.000 0.00 0.00 37.87 4.34 R
2323 3389 1.357690 GCGTGATCCACCATGCATG 59.642 57.895 20.19 20.19 45.68 4.06 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
19 20 3.019964 CTTGGTGCCACACTAAGCA 57.980 52.632 10.31 0.00 43.60 3.91
20 21 1.317613 CTTGGTGCCACACTAAGCAA 58.682 50.000 10.31 0.18 43.60 3.91
21 22 1.680735 CTTGGTGCCACACTAAGCAAA 59.319 47.619 10.31 0.00 43.60 3.68
22 23 1.769026 TGGTGCCACACTAAGCAAAA 58.231 45.000 0.00 0.00 41.48 2.44
23 24 2.315176 TGGTGCCACACTAAGCAAAAT 58.685 42.857 0.00 0.00 41.48 1.82
24 25 2.697751 TGGTGCCACACTAAGCAAAATT 59.302 40.909 0.00 0.00 41.48 1.82
25 26 3.133721 TGGTGCCACACTAAGCAAAATTT 59.866 39.130 0.00 0.00 41.48 1.82
26 27 3.494251 GGTGCCACACTAAGCAAAATTTG 59.506 43.478 0.57 0.57 41.48 2.32
27 28 3.494251 GTGCCACACTAAGCAAAATTTGG 59.506 43.478 7.89 0.00 41.48 3.28
28 29 3.066380 GCCACACTAAGCAAAATTTGGG 58.934 45.455 7.89 0.00 0.00 4.12
29 30 3.663025 CCACACTAAGCAAAATTTGGGG 58.337 45.455 7.89 0.00 0.00 4.96
30 31 3.066380 CACACTAAGCAAAATTTGGGGC 58.934 45.455 7.89 0.00 0.00 5.80
31 32 2.038426 ACACTAAGCAAAATTTGGGGCC 59.962 45.455 7.89 0.00 0.00 5.80
32 33 2.302733 CACTAAGCAAAATTTGGGGCCT 59.697 45.455 0.84 0.00 0.00 5.19
108 109 3.740397 CACACCTGCCCATGCGTG 61.740 66.667 0.00 0.00 41.78 5.34
120 121 2.590291 TGCGTGTCGGCAACATGT 60.590 55.556 0.00 0.00 45.19 3.21
121 122 2.183504 TGCGTGTCGGCAACATGTT 61.184 52.632 4.92 4.92 45.19 2.71
122 123 1.008995 GCGTGTCGGCAACATGTTT 60.009 52.632 8.77 0.00 45.19 2.83
123 124 0.236187 GCGTGTCGGCAACATGTTTA 59.764 50.000 8.77 0.00 45.19 2.01
124 125 1.945207 CGTGTCGGCAACATGTTTAC 58.055 50.000 8.77 3.99 40.80 2.01
125 126 1.529438 CGTGTCGGCAACATGTTTACT 59.471 47.619 8.77 0.00 40.80 2.24
126 127 2.032377 CGTGTCGGCAACATGTTTACTT 60.032 45.455 8.77 0.00 40.80 2.24
127 128 3.547214 CGTGTCGGCAACATGTTTACTTT 60.547 43.478 8.77 0.00 40.80 2.66
128 129 4.318903 CGTGTCGGCAACATGTTTACTTTA 60.319 41.667 8.77 0.00 40.80 1.85
129 130 4.907582 GTGTCGGCAACATGTTTACTTTAC 59.092 41.667 8.77 3.75 40.80 2.01
164 165 3.426695 CGTTTGATCTCCTGCATGGTTTC 60.427 47.826 0.00 0.00 37.07 2.78
172 173 4.405358 TCTCCTGCATGGTTTCAAGTTTTT 59.595 37.500 0.00 0.00 37.07 1.94
225 252 8.956446 AATGTTTTATATTATGGGAGGAAGGG 57.044 34.615 0.00 0.00 0.00 3.95
233 260 2.735259 TGGGAGGAAGGGAGTAGTTT 57.265 50.000 0.00 0.00 0.00 2.66
281 308 2.734606 CCGTCGTATCAAGTTTCAGCAA 59.265 45.455 0.00 0.00 0.00 3.91
636 1471 0.608640 GAGGAAGCTCAAGGACCGAA 59.391 55.000 0.00 0.00 0.00 4.30
650 1485 2.165845 GGACCGAACACAGCATAGTACT 59.834 50.000 0.00 0.00 0.00 2.73
651 1486 3.436496 GACCGAACACAGCATAGTACTC 58.564 50.000 0.00 0.00 0.00 2.59
653 1488 3.179830 CCGAACACAGCATAGTACTCAC 58.820 50.000 0.00 0.00 0.00 3.51
654 1489 3.119459 CCGAACACAGCATAGTACTCACT 60.119 47.826 0.00 0.00 38.91 3.41
655 1490 4.099120 CGAACACAGCATAGTACTCACTC 58.901 47.826 0.00 0.00 36.14 3.51
656 1491 4.425520 GAACACAGCATAGTACTCACTCC 58.574 47.826 0.00 0.00 36.14 3.85
657 1492 2.423892 ACACAGCATAGTACTCACTCCG 59.576 50.000 0.00 0.00 36.14 4.63
658 1493 2.423892 CACAGCATAGTACTCACTCCGT 59.576 50.000 0.00 0.00 36.14 4.69
659 1494 3.090037 ACAGCATAGTACTCACTCCGTT 58.910 45.455 0.00 0.00 36.14 4.44
660 1495 3.128938 ACAGCATAGTACTCACTCCGTTC 59.871 47.826 0.00 0.00 36.14 3.95
661 1496 2.688958 AGCATAGTACTCACTCCGTTCC 59.311 50.000 0.00 0.00 36.14 3.62
662 1497 2.688958 GCATAGTACTCACTCCGTTCCT 59.311 50.000 0.00 0.00 36.14 3.36
663 1498 3.881688 GCATAGTACTCACTCCGTTCCTA 59.118 47.826 0.00 0.00 36.14 2.94
664 1499 4.337555 GCATAGTACTCACTCCGTTCCTAA 59.662 45.833 0.00 0.00 36.14 2.69
665 1500 5.163581 GCATAGTACTCACTCCGTTCCTAAA 60.164 44.000 0.00 0.00 36.14 1.85
666 1501 6.461231 GCATAGTACTCACTCCGTTCCTAAAT 60.461 42.308 0.00 0.00 36.14 1.40
667 1502 7.255381 GCATAGTACTCACTCCGTTCCTAAATA 60.255 40.741 0.00 0.00 36.14 1.40
668 1503 8.794553 CATAGTACTCACTCCGTTCCTAAATAT 58.205 37.037 0.00 0.00 36.14 1.28
670 1505 8.757982 AGTACTCACTCCGTTCCTAAATATAA 57.242 34.615 0.00 0.00 0.00 0.98
671 1506 8.848182 AGTACTCACTCCGTTCCTAAATATAAG 58.152 37.037 0.00 0.00 0.00 1.73
672 1507 7.657023 ACTCACTCCGTTCCTAAATATAAGT 57.343 36.000 0.00 0.00 0.00 2.24
673 1508 7.714703 ACTCACTCCGTTCCTAAATATAAGTC 58.285 38.462 0.00 0.00 0.00 3.01
674 1509 7.560626 ACTCACTCCGTTCCTAAATATAAGTCT 59.439 37.037 0.00 0.00 0.00 3.24
675 1510 8.302515 TCACTCCGTTCCTAAATATAAGTCTT 57.697 34.615 0.00 0.00 0.00 3.01
676 1511 8.755977 TCACTCCGTTCCTAAATATAAGTCTTT 58.244 33.333 0.00 0.00 0.00 2.52
705 1540 8.833231 AAGATTTCATTATAGACCACATACGG 57.167 34.615 0.00 0.00 0.00 4.02
706 1541 8.190326 AGATTTCATTATAGACCACATACGGA 57.810 34.615 0.00 0.00 0.00 4.69
707 1542 8.816894 AGATTTCATTATAGACCACATACGGAT 58.183 33.333 0.00 0.00 0.00 4.18
708 1543 8.777865 ATTTCATTATAGACCACATACGGATG 57.222 34.615 5.94 5.94 39.16 3.51
710 1545 8.411991 TTCATTATAGACCACATACGGATGTA 57.588 34.615 14.23 0.00 44.82 2.29
711 1546 8.589701 TCATTATAGACCACATACGGATGTAT 57.410 34.615 14.23 4.48 44.82 2.29
712 1547 9.689501 TCATTATAGACCACATACGGATGTATA 57.310 33.333 14.23 4.47 44.82 1.47
718 1553 8.226819 AGACCACATACGGATGTATATAGATG 57.773 38.462 14.23 0.00 44.82 2.90
719 1554 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
720 1555 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
721 1556 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
722 1557 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
723 1558 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
724 1559 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
753 1588 8.798859 ATGTAGATTTACTCATTTTGCTCTGT 57.201 30.769 0.00 0.00 0.00 3.41
754 1589 9.890629 ATGTAGATTTACTCATTTTGCTCTGTA 57.109 29.630 0.00 0.00 0.00 2.74
755 1590 9.890629 TGTAGATTTACTCATTTTGCTCTGTAT 57.109 29.630 0.00 0.00 0.00 2.29
757 1592 8.798859 AGATTTACTCATTTTGCTCTGTATGT 57.201 30.769 0.00 0.00 0.00 2.29
758 1593 8.671921 AGATTTACTCATTTTGCTCTGTATGTG 58.328 33.333 0.00 0.00 0.00 3.21
759 1594 6.741992 TTACTCATTTTGCTCTGTATGTGG 57.258 37.500 0.00 0.00 0.00 4.17
760 1595 4.655963 ACTCATTTTGCTCTGTATGTGGT 58.344 39.130 0.00 0.00 0.00 4.16
761 1596 4.697352 ACTCATTTTGCTCTGTATGTGGTC 59.303 41.667 0.00 0.00 0.00 4.02
762 1597 4.009675 TCATTTTGCTCTGTATGTGGTCC 58.990 43.478 0.00 0.00 0.00 4.46
763 1598 3.500448 TTTTGCTCTGTATGTGGTCCA 57.500 42.857 0.00 0.00 0.00 4.02
764 1599 3.719268 TTTGCTCTGTATGTGGTCCAT 57.281 42.857 0.00 0.00 37.58 3.41
765 1600 4.835284 TTTGCTCTGTATGTGGTCCATA 57.165 40.909 0.00 0.00 34.86 2.74
766 1601 4.406648 TTGCTCTGTATGTGGTCCATAG 57.593 45.455 0.00 0.00 36.71 2.23
767 1602 3.374764 TGCTCTGTATGTGGTCCATAGT 58.625 45.455 0.00 0.00 36.71 2.12
768 1603 4.542697 TGCTCTGTATGTGGTCCATAGTA 58.457 43.478 0.00 0.00 36.71 1.82
769 1604 4.959839 TGCTCTGTATGTGGTCCATAGTAA 59.040 41.667 0.00 0.00 36.71 2.24
770 1605 5.423931 TGCTCTGTATGTGGTCCATAGTAAA 59.576 40.000 0.00 0.00 36.71 2.01
771 1606 6.070481 TGCTCTGTATGTGGTCCATAGTAAAA 60.070 38.462 0.00 0.00 36.71 1.52
772 1607 6.992715 GCTCTGTATGTGGTCCATAGTAAAAT 59.007 38.462 0.00 0.00 36.71 1.82
773 1608 7.171678 GCTCTGTATGTGGTCCATAGTAAAATC 59.828 40.741 0.00 0.00 36.71 2.17
774 1609 8.319057 TCTGTATGTGGTCCATAGTAAAATCT 57.681 34.615 0.00 0.00 36.71 2.40
775 1610 8.421784 TCTGTATGTGGTCCATAGTAAAATCTC 58.578 37.037 0.00 0.00 36.71 2.75
776 1611 8.319057 TGTATGTGGTCCATAGTAAAATCTCT 57.681 34.615 0.00 0.00 36.71 3.10
777 1612 8.768397 TGTATGTGGTCCATAGTAAAATCTCTT 58.232 33.333 0.00 0.00 36.71 2.85
778 1613 9.262358 GTATGTGGTCCATAGTAAAATCTCTTC 57.738 37.037 0.00 0.00 36.71 2.87
779 1614 7.252612 TGTGGTCCATAGTAAAATCTCTTCA 57.747 36.000 0.00 0.00 0.00 3.02
780 1615 7.685481 TGTGGTCCATAGTAAAATCTCTTCAA 58.315 34.615 0.00 0.00 0.00 2.69
781 1616 8.160765 TGTGGTCCATAGTAAAATCTCTTCAAA 58.839 33.333 0.00 0.00 0.00 2.69
782 1617 9.010029 GTGGTCCATAGTAAAATCTCTTCAAAA 57.990 33.333 0.00 0.00 0.00 2.44
783 1618 9.581289 TGGTCCATAGTAAAATCTCTTCAAAAA 57.419 29.630 0.00 0.00 0.00 1.94
784 1619 9.841880 GGTCCATAGTAAAATCTCTTCAAAAAC 57.158 33.333 0.00 0.00 0.00 2.43
806 1641 9.955102 AAAACTTATATTTAAGAACGAGGGACT 57.045 29.630 9.58 0.00 39.20 3.85
814 1649 7.807977 TTTAAGAACGAGGGACTATATACGT 57.192 36.000 0.00 0.00 41.55 3.57
815 1650 5.686159 AAGAACGAGGGACTATATACGTG 57.314 43.478 0.00 0.00 41.55 4.49
816 1651 4.965814 AGAACGAGGGACTATATACGTGA 58.034 43.478 0.00 0.00 41.55 4.35
817 1652 5.558818 AGAACGAGGGACTATATACGTGAT 58.441 41.667 0.00 0.00 41.55 3.06
818 1653 5.642919 AGAACGAGGGACTATATACGTGATC 59.357 44.000 0.00 0.00 41.55 2.92
819 1654 5.163281 ACGAGGGACTATATACGTGATCT 57.837 43.478 0.00 0.00 41.55 2.75
820 1655 6.291648 ACGAGGGACTATATACGTGATCTA 57.708 41.667 0.00 0.00 41.55 1.98
821 1656 6.705302 ACGAGGGACTATATACGTGATCTAA 58.295 40.000 0.00 0.00 41.55 2.10
822 1657 7.164122 ACGAGGGACTATATACGTGATCTAAA 58.836 38.462 0.00 0.00 41.55 1.85
823 1658 7.663081 ACGAGGGACTATATACGTGATCTAAAA 59.337 37.037 0.00 0.00 41.55 1.52
824 1659 8.509690 CGAGGGACTATATACGTGATCTAAAAA 58.490 37.037 0.00 0.00 41.55 1.94
996 1832 1.064357 GAGAACCTCCGTCTCATCGAC 59.936 57.143 0.00 0.00 39.33 4.20
1018 1854 0.736325 GATGACCTCCAACGTGGACG 60.736 60.000 0.00 0.00 42.67 4.79
1019 1855 1.183030 ATGACCTCCAACGTGGACGA 61.183 55.000 6.12 0.00 42.67 4.20
1036 1872 1.081108 GACGTGCAAGAGCGAGTCT 60.081 57.895 6.65 0.00 46.23 3.24
1162 1998 0.179137 CGCTCTCAAGCCGTACATCA 60.179 55.000 0.00 0.00 46.34 3.07
1238 2074 4.020617 CCTCACCAGCTCCGGCAA 62.021 66.667 0.00 0.00 41.70 4.52
1354 2190 9.642343 ACTTGTAAGTCCACTGATATATACTCA 57.358 33.333 0.00 0.00 32.86 3.41
1362 2198 6.713450 TCCACTGATATATACTCAACGTAGCA 59.287 38.462 0.00 0.00 0.00 3.49
1614 2485 0.668535 AGAGCATGTACGCGCAGATA 59.331 50.000 5.73 0.00 36.85 1.98
1617 2488 1.607148 AGCATGTACGCGCAGATAGTA 59.393 47.619 5.73 0.00 36.85 1.82
1920 2969 2.464865 GATGCCATCGTCACTAGTGTC 58.535 52.381 21.99 15.74 0.00 3.67
2205 3262 6.763355 AGCACTTGACTGAATAAGAAGAAGA 58.237 36.000 0.00 0.00 0.00 2.87
2323 3389 1.375523 GTGGTGACCATGTCGGGAC 60.376 63.158 7.94 0.00 40.22 4.46
2324 3390 1.839296 TGGTGACCATGTCGGGACA 60.839 57.895 0.00 3.69 46.44 4.02
2490 3565 1.735973 CGATCCCGATGCTGACTCA 59.264 57.895 0.00 0.00 38.22 3.41
2768 3843 6.417327 CATGATTTCGAAAATCTCTCCTTCG 58.583 40.000 15.66 0.00 42.49 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.182537 TGCTTAGTGTGGCACCAAGT 59.817 50.000 16.26 2.65 35.97 3.16
1 2 1.317613 TTGCTTAGTGTGGCACCAAG 58.682 50.000 16.26 15.76 36.47 3.61
2 3 1.769026 TTTGCTTAGTGTGGCACCAA 58.231 45.000 16.26 7.89 38.23 3.67
3 4 1.769026 TTTTGCTTAGTGTGGCACCA 58.231 45.000 16.26 1.09 38.23 4.17
4 5 3.385193 AATTTTGCTTAGTGTGGCACC 57.615 42.857 16.26 6.59 38.23 5.01
5 6 3.494251 CCAAATTTTGCTTAGTGTGGCAC 59.506 43.478 11.55 11.55 38.23 5.01
6 7 3.494048 CCCAAATTTTGCTTAGTGTGGCA 60.494 43.478 3.50 0.00 36.62 4.92
7 8 3.066380 CCCAAATTTTGCTTAGTGTGGC 58.934 45.455 3.50 0.00 0.00 5.01
8 9 3.663025 CCCCAAATTTTGCTTAGTGTGG 58.337 45.455 3.50 0.00 0.00 4.17
9 10 3.066380 GCCCCAAATTTTGCTTAGTGTG 58.934 45.455 3.50 0.00 0.00 3.82
10 11 2.038426 GGCCCCAAATTTTGCTTAGTGT 59.962 45.455 3.50 0.00 0.00 3.55
11 12 2.302733 AGGCCCCAAATTTTGCTTAGTG 59.697 45.455 0.00 0.00 0.00 2.74
12 13 2.302733 CAGGCCCCAAATTTTGCTTAGT 59.697 45.455 0.00 0.00 0.00 2.24
13 14 2.566724 TCAGGCCCCAAATTTTGCTTAG 59.433 45.455 0.00 0.00 0.00 2.18
14 15 2.614259 TCAGGCCCCAAATTTTGCTTA 58.386 42.857 0.00 0.00 0.00 3.09
15 16 1.433121 TCAGGCCCCAAATTTTGCTT 58.567 45.000 0.00 0.00 0.00 3.91
16 17 1.279846 CATCAGGCCCCAAATTTTGCT 59.720 47.619 0.00 0.00 0.00 3.91
17 18 1.003464 ACATCAGGCCCCAAATTTTGC 59.997 47.619 0.00 0.00 0.00 3.68
18 19 2.355007 GGACATCAGGCCCCAAATTTTG 60.355 50.000 0.00 1.99 0.00 2.44
19 20 1.908619 GGACATCAGGCCCCAAATTTT 59.091 47.619 0.00 0.00 0.00 1.82
20 21 1.203288 TGGACATCAGGCCCCAAATTT 60.203 47.619 0.00 0.00 0.00 1.82
21 22 0.413037 TGGACATCAGGCCCCAAATT 59.587 50.000 0.00 0.00 0.00 1.82
22 23 0.324645 GTGGACATCAGGCCCCAAAT 60.325 55.000 0.00 0.00 0.00 2.32
23 24 1.076549 GTGGACATCAGGCCCCAAA 59.923 57.895 0.00 0.00 0.00 3.28
24 25 1.724148 TTGTGGACATCAGGCCCCAA 61.724 55.000 0.00 0.00 0.00 4.12
25 26 2.141011 CTTGTGGACATCAGGCCCCA 62.141 60.000 0.00 0.00 0.00 4.96
26 27 1.379044 CTTGTGGACATCAGGCCCC 60.379 63.158 0.00 0.00 0.00 5.80
27 28 0.251341 AACTTGTGGACATCAGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
28 29 0.883833 CAACTTGTGGACATCAGGCC 59.116 55.000 0.00 0.00 0.00 5.19
29 30 0.242017 GCAACTTGTGGACATCAGGC 59.758 55.000 0.00 0.00 0.00 4.85
30 31 1.608055 TGCAACTTGTGGACATCAGG 58.392 50.000 0.00 0.00 0.00 3.86
103 104 1.719725 AAACATGTTGCCGACACGCA 61.720 50.000 12.82 0.00 42.04 5.24
104 105 0.236187 TAAACATGTTGCCGACACGC 59.764 50.000 12.82 0.00 42.04 5.34
108 109 5.098218 TGTAAAGTAAACATGTTGCCGAC 57.902 39.130 12.82 8.29 0.00 4.79
116 117 5.351233 TTGCGGACTGTAAAGTAAACATG 57.649 39.130 0.00 0.00 0.00 3.21
117 118 5.529800 AGTTTGCGGACTGTAAAGTAAACAT 59.470 36.000 17.84 7.29 40.12 2.71
118 119 4.877251 AGTTTGCGGACTGTAAAGTAAACA 59.123 37.500 17.84 0.00 40.12 2.83
119 120 5.413969 AGTTTGCGGACTGTAAAGTAAAC 57.586 39.130 3.58 12.01 38.72 2.01
120 121 4.209703 CGAGTTTGCGGACTGTAAAGTAAA 59.790 41.667 5.29 0.00 36.16 2.01
121 122 3.737266 CGAGTTTGCGGACTGTAAAGTAA 59.263 43.478 5.29 0.00 36.16 2.24
122 123 3.243501 ACGAGTTTGCGGACTGTAAAGTA 60.244 43.478 5.29 0.00 36.16 2.24
123 124 2.132762 CGAGTTTGCGGACTGTAAAGT 58.867 47.619 5.00 5.00 38.36 2.66
124 125 2.132762 ACGAGTTTGCGGACTGTAAAG 58.867 47.619 0.00 0.00 32.55 1.85
125 126 2.228138 ACGAGTTTGCGGACTGTAAA 57.772 45.000 0.00 0.00 35.12 2.01
126 127 2.228138 AACGAGTTTGCGGACTGTAA 57.772 45.000 0.00 0.00 35.12 2.41
127 128 1.862201 CAAACGAGTTTGCGGACTGTA 59.138 47.619 14.63 0.00 42.66 2.74
128 129 0.655733 CAAACGAGTTTGCGGACTGT 59.344 50.000 14.63 0.00 42.66 3.55
129 130 0.934496 TCAAACGAGTTTGCGGACTG 59.066 50.000 20.32 0.41 46.92 3.51
207 234 7.372060 ACTACTCCCTTCCTCCCATAATATA 57.628 40.000 0.00 0.00 0.00 0.86
636 1471 2.423892 CGGAGTGAGTACTATGCTGTGT 59.576 50.000 0.00 0.00 37.25 3.72
650 1485 7.893124 AGACTTATATTTAGGAACGGAGTGA 57.107 36.000 0.00 0.00 45.00 3.41
651 1486 8.943909 AAAGACTTATATTTAGGAACGGAGTG 57.056 34.615 0.00 0.00 45.00 3.51
679 1514 9.273016 CCGTATGTGGTCTATAATGAAATCTTT 57.727 33.333 0.00 0.00 0.00 2.52
680 1515 8.647796 TCCGTATGTGGTCTATAATGAAATCTT 58.352 33.333 0.00 0.00 0.00 2.40
681 1516 8.190326 TCCGTATGTGGTCTATAATGAAATCT 57.810 34.615 0.00 0.00 0.00 2.40
682 1517 8.873830 CATCCGTATGTGGTCTATAATGAAATC 58.126 37.037 0.00 0.00 0.00 2.17
683 1518 8.375506 ACATCCGTATGTGGTCTATAATGAAAT 58.624 33.333 0.00 0.00 44.79 2.17
684 1519 7.732025 ACATCCGTATGTGGTCTATAATGAAA 58.268 34.615 0.00 0.00 44.79 2.69
685 1520 7.297936 ACATCCGTATGTGGTCTATAATGAA 57.702 36.000 0.00 0.00 44.79 2.57
686 1521 6.911250 ACATCCGTATGTGGTCTATAATGA 57.089 37.500 0.00 0.00 44.79 2.57
692 1527 9.338622 CATCTATATACATCCGTATGTGGTCTA 57.661 37.037 3.56 0.00 45.99 2.59
693 1528 7.201830 GCATCTATATACATCCGTATGTGGTCT 60.202 40.741 3.56 0.00 45.99 3.85
694 1529 6.918569 GCATCTATATACATCCGTATGTGGTC 59.081 42.308 3.56 0.00 45.99 4.02
695 1530 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
696 1531 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
697 1532 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
727 1562 9.890629 ACAGAGCAAAATGAGTAAATCTACATA 57.109 29.630 0.00 0.00 0.00 2.29
728 1563 8.798859 ACAGAGCAAAATGAGTAAATCTACAT 57.201 30.769 0.00 0.00 0.00 2.29
729 1564 9.890629 ATACAGAGCAAAATGAGTAAATCTACA 57.109 29.630 0.00 0.00 0.00 2.74
731 1566 9.890629 ACATACAGAGCAAAATGAGTAAATCTA 57.109 29.630 0.00 0.00 0.00 1.98
732 1567 8.671921 CACATACAGAGCAAAATGAGTAAATCT 58.328 33.333 0.00 0.00 0.00 2.40
733 1568 7.912250 CCACATACAGAGCAAAATGAGTAAATC 59.088 37.037 0.00 0.00 0.00 2.17
734 1569 7.394359 ACCACATACAGAGCAAAATGAGTAAAT 59.606 33.333 0.00 0.00 0.00 1.40
735 1570 6.714810 ACCACATACAGAGCAAAATGAGTAAA 59.285 34.615 0.00 0.00 0.00 2.01
736 1571 6.237901 ACCACATACAGAGCAAAATGAGTAA 58.762 36.000 0.00 0.00 0.00 2.24
737 1572 5.804639 ACCACATACAGAGCAAAATGAGTA 58.195 37.500 0.00 0.00 0.00 2.59
738 1573 4.655963 ACCACATACAGAGCAAAATGAGT 58.344 39.130 0.00 0.00 0.00 3.41
739 1574 4.095483 GGACCACATACAGAGCAAAATGAG 59.905 45.833 0.00 0.00 0.00 2.90
740 1575 4.009675 GGACCACATACAGAGCAAAATGA 58.990 43.478 0.00 0.00 0.00 2.57
741 1576 3.758023 TGGACCACATACAGAGCAAAATG 59.242 43.478 0.00 0.00 0.00 2.32
742 1577 4.032960 TGGACCACATACAGAGCAAAAT 57.967 40.909 0.00 0.00 0.00 1.82
743 1578 3.500448 TGGACCACATACAGAGCAAAA 57.500 42.857 0.00 0.00 0.00 2.44
744 1579 3.719268 ATGGACCACATACAGAGCAAA 57.281 42.857 0.00 0.00 38.26 3.68
745 1580 3.774766 ACTATGGACCACATACAGAGCAA 59.225 43.478 0.00 0.00 41.03 3.91
746 1581 3.374764 ACTATGGACCACATACAGAGCA 58.625 45.455 0.00 0.00 41.03 4.26
747 1582 5.531122 TTACTATGGACCACATACAGAGC 57.469 43.478 0.00 0.00 41.03 4.09
748 1583 8.424918 AGATTTTACTATGGACCACATACAGAG 58.575 37.037 0.00 0.00 41.03 3.35
749 1584 8.319057 AGATTTTACTATGGACCACATACAGA 57.681 34.615 0.00 0.00 41.03 3.41
750 1585 8.424918 AGAGATTTTACTATGGACCACATACAG 58.575 37.037 0.00 0.00 41.03 2.74
751 1586 8.319057 AGAGATTTTACTATGGACCACATACA 57.681 34.615 0.00 0.00 41.03 2.29
752 1587 9.262358 GAAGAGATTTTACTATGGACCACATAC 57.738 37.037 0.00 0.00 41.03 2.39
753 1588 8.988060 TGAAGAGATTTTACTATGGACCACATA 58.012 33.333 0.00 0.00 41.03 2.29
754 1589 7.861629 TGAAGAGATTTTACTATGGACCACAT 58.138 34.615 0.00 0.00 43.68 3.21
755 1590 7.252612 TGAAGAGATTTTACTATGGACCACA 57.747 36.000 0.00 0.00 0.00 4.17
756 1591 8.561738 TTTGAAGAGATTTTACTATGGACCAC 57.438 34.615 0.00 0.00 0.00 4.16
757 1592 9.581289 TTTTTGAAGAGATTTTACTATGGACCA 57.419 29.630 0.00 0.00 0.00 4.02
758 1593 9.841880 GTTTTTGAAGAGATTTTACTATGGACC 57.158 33.333 0.00 0.00 0.00 4.46
780 1615 9.955102 AGTCCCTCGTTCTTAAATATAAGTTTT 57.045 29.630 0.00 0.00 39.65 2.43
788 1623 9.507329 ACGTATATAGTCCCTCGTTCTTAAATA 57.493 33.333 0.00 0.00 0.00 1.40
789 1624 8.295288 CACGTATATAGTCCCTCGTTCTTAAAT 58.705 37.037 0.00 0.00 0.00 1.40
790 1625 7.498900 TCACGTATATAGTCCCTCGTTCTTAAA 59.501 37.037 0.00 0.00 0.00 1.52
791 1626 6.992123 TCACGTATATAGTCCCTCGTTCTTAA 59.008 38.462 0.00 0.00 0.00 1.85
792 1627 6.524734 TCACGTATATAGTCCCTCGTTCTTA 58.475 40.000 0.00 0.00 0.00 2.10
793 1628 5.371526 TCACGTATATAGTCCCTCGTTCTT 58.628 41.667 0.00 0.00 0.00 2.52
794 1629 4.965814 TCACGTATATAGTCCCTCGTTCT 58.034 43.478 0.00 0.00 0.00 3.01
795 1630 5.642919 AGATCACGTATATAGTCCCTCGTTC 59.357 44.000 0.00 0.00 0.00 3.95
796 1631 5.558818 AGATCACGTATATAGTCCCTCGTT 58.441 41.667 0.00 0.00 0.00 3.85
797 1632 5.163281 AGATCACGTATATAGTCCCTCGT 57.837 43.478 0.00 0.00 0.00 4.18
798 1633 7.606858 TTTAGATCACGTATATAGTCCCTCG 57.393 40.000 0.00 0.00 0.00 4.63
925 1760 0.178973 TTGACGAGGTGGGTCTCTGA 60.179 55.000 0.00 0.00 35.45 3.27
927 1762 0.469331 TGTTGACGAGGTGGGTCTCT 60.469 55.000 0.00 0.00 35.45 3.10
967 1802 1.751927 GGAGGTTCTCGGCGTCCTA 60.752 63.158 6.85 0.00 37.76 2.94
996 1832 0.458543 CCACGTTGGAGGTCATCTCG 60.459 60.000 0.00 0.00 40.96 4.04
1018 1854 0.664767 AAGACTCGCTCTTGCACGTC 60.665 55.000 0.00 0.00 37.87 4.34
1019 1855 1.364171 AAGACTCGCTCTTGCACGT 59.636 52.632 0.00 0.00 37.87 4.49
1353 2189 3.728864 GCATGGAAATGAGTGCTACGTTG 60.729 47.826 0.00 0.00 34.85 4.10
1354 2190 2.420022 GCATGGAAATGAGTGCTACGTT 59.580 45.455 0.00 0.00 34.85 3.99
1355 2191 2.009774 GCATGGAAATGAGTGCTACGT 58.990 47.619 0.00 0.00 34.85 3.57
1356 2192 2.009051 TGCATGGAAATGAGTGCTACG 58.991 47.619 0.00 0.00 38.37 3.51
1362 2198 2.629137 TGTGCTTTGCATGGAAATGAGT 59.371 40.909 13.13 0.00 41.91 3.41
1914 2963 6.472016 TCAACAGGATTATTTGCTGACACTA 58.528 36.000 0.95 0.00 46.09 2.74
1915 2964 5.316167 TCAACAGGATTATTTGCTGACACT 58.684 37.500 0.95 0.00 46.09 3.55
1916 2965 5.627499 TCAACAGGATTATTTGCTGACAC 57.373 39.130 0.95 0.00 46.09 3.67
2255 3316 6.573289 GCAGGATCAGTTCTAACTCTTTCTCA 60.573 42.308 0.00 0.00 37.08 3.27
2323 3389 1.357690 GCGTGATCCACCATGCATG 59.642 57.895 20.19 20.19 45.68 4.06
2324 3390 3.831883 GCGTGATCCACCATGCAT 58.168 55.556 0.00 0.00 45.68 3.96
2326 3392 2.793946 GTGCGTGATCCACCATGC 59.206 61.111 0.00 0.00 46.35 4.06
2469 3544 3.527427 TCAGCATCGGGATCGCGT 61.527 61.111 28.38 15.13 36.13 6.01
2653 3728 3.900888 TCCTTGGCGGAGTCCTTT 58.099 55.556 7.77 0.00 36.69 3.11
2745 3820 6.341316 TCGAAGGAGAGATTTTCGAAATCAT 58.659 36.000 12.12 2.82 46.53 2.45
2768 3843 0.333312 TCCACTGTCTCTCCCTCCTC 59.667 60.000 0.00 0.00 0.00 3.71
2819 3894 1.002366 CCAAGTTCCTGAAGATCGCG 58.998 55.000 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.