Multiple sequence alignment - TraesCS2D01G469100

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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 TraesCS2D01G469100 chr2D 100.000 3845 0 0 1 3845 574348398 574344554 0.000000e+00 7101
1 TraesCS2D01G469100 chr2D 87.176 772 99 0 2068 2839 573852695 573853466 0.000000e+00 878
2 TraesCS2D01G469100 chr2D 90.576 191 16 1 3 191 90835205 90835015 6.380000e-63 252
3 TraesCS2D01G469100 chr2B 93.084 1923 69 16 1962 3845 690211462 690209565 0.000000e+00 2756
4 TraesCS2D01G469100 chr2B 91.596 940 40 16 559 1490 690212811 690211903 0.000000e+00 1262
5 TraesCS2D01G469100 chr2B 88.111 757 90 0 2083 2839 689715024 689715780 0.000000e+00 900
6 TraesCS2D01G469100 chr2B 94.947 376 14 2 1575 1947 690211819 690211446 5.540000e-163 584
7 TraesCS2D01G469100 chr2B 88.063 444 35 8 1 430 729060056 729060495 9.530000e-141 510
8 TraesCS2D01G469100 chr2A 94.353 1452 40 11 3 1433 712709129 712707699 0.000000e+00 2189
9 TraesCS2D01G469100 chr2A 92.214 1310 54 18 2163 3431 712702485 712701183 0.000000e+00 1810
10 TraesCS2D01G469100 chr2A 95.044 1029 31 9 1962 2973 712707385 712706360 0.000000e+00 1600
11 TraesCS2D01G469100 chr2A 86.658 772 103 0 2068 2839 712318038 712318809 0.000000e+00 856
12 TraesCS2D01G469100 chr2A 92.353 340 13 7 1615 1947 712707702 712707369 4.500000e-129 472
13 TraesCS2D01G469100 chr2A 93.796 274 7 4 2972 3238 712706201 712705931 1.660000e-108 403
14 TraesCS2D01G469100 chr2A 95.588 68 3 0 3238 3305 712705905 712705838 4.060000e-20 110
15 TraesCS2D01G469100 chr5A 83.024 754 122 4 2101 2851 646058656 646059406 0.000000e+00 678
16 TraesCS2D01G469100 chr5A 84.653 202 30 1 1613 1814 646058409 646058609 2.340000e-47 200
17 TraesCS2D01G469100 chr5D 82.846 752 123 5 2103 2851 519545809 519546557 0.000000e+00 669
18 TraesCS2D01G469100 chr5D 83.920 199 22 8 240 435 251427679 251427488 8.490000e-42 182
19 TraesCS2D01G469100 chr5B 82.672 756 121 7 2101 2851 654366430 654367180 0.000000e+00 662
20 TraesCS2D01G469100 chr5B 84.184 196 31 0 1613 1808 654366170 654366365 1.410000e-44 191
21 TraesCS2D01G469100 chr4D 86.858 487 62 2 3354 3839 37131925 37132410 9.390000e-151 544
22 TraesCS2D01G469100 chr3B 86.994 469 59 1 3356 3822 535653019 535653487 9.460000e-146 527
23 TraesCS2D01G469100 chr3B 81.333 450 60 16 1 430 672096630 672097075 1.020000e-90 344
24 TraesCS2D01G469100 chr3B 79.843 382 49 20 66 430 614570183 614569813 1.770000e-63 254
25 TraesCS2D01G469100 chr4B 86.458 480 61 4 3359 3837 315602326 315602802 1.220000e-144 523
26 TraesCS2D01G469100 chr6D 86.526 475 61 3 3365 3837 381989907 381990380 1.580000e-143 520
27 TraesCS2D01G469100 chr6D 88.532 436 33 7 1 423 287388022 287388453 2.650000e-141 512
28 TraesCS2D01G469100 chr1B 87.556 450 54 2 3359 3807 142057184 142056736 1.580000e-143 520
29 TraesCS2D01G469100 chr1B 77.561 410 67 21 40 433 654044601 654044201 1.390000e-54 224
30 TraesCS2D01G469100 chr6B 85.865 474 65 2 3365 3837 570958040 570958512 1.590000e-138 503
31 TraesCS2D01G469100 chr3D 85.331 484 68 3 3357 3839 600576808 600577289 7.420000e-137 497
32 TraesCS2D01G469100 chr3D 82.393 443 59 12 1 430 504053360 504053796 6.070000e-98 368
33 TraesCS2D01G469100 chr3D 82.000 450 57 14 1 430 58841923 58841478 1.020000e-95 361
34 TraesCS2D01G469100 chr3D 81.818 451 57 15 1 430 58989547 58989101 4.720000e-94 355
35 TraesCS2D01G469100 chr3D 78.242 455 72 21 4 437 564803922 564803474 2.280000e-67 267
36 TraesCS2D01G469100 chr3A 87.857 420 32 11 26 430 586579604 586579189 3.480000e-130 475
37 TraesCS2D01G469100 chr1A 84.298 484 73 3 3356 3838 556758513 556758994 1.620000e-128 470
38 TraesCS2D01G469100 chr1A 80.645 434 73 9 1 430 361178329 361178755 3.700000e-85 326
39 TraesCS2D01G469100 chr1D 82.160 213 30 6 207 416 457085651 457085858 3.950000e-40 176


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 TraesCS2D01G469100 chr2D 574344554 574348398 3844 True 7101.000000 7101 100.000000 1 3845 1 chr2D.!!$R2 3844
1 TraesCS2D01G469100 chr2D 573852695 573853466 771 False 878.000000 878 87.176000 2068 2839 1 chr2D.!!$F1 771
2 TraesCS2D01G469100 chr2B 690209565 690212811 3246 True 1534.000000 2756 93.209000 559 3845 3 chr2B.!!$R1 3286
3 TraesCS2D01G469100 chr2B 689715024 689715780 756 False 900.000000 900 88.111000 2083 2839 1 chr2B.!!$F1 756
4 TraesCS2D01G469100 chr2A 712701183 712709129 7946 True 1097.333333 2189 93.891333 3 3431 6 chr2A.!!$R1 3428
5 TraesCS2D01G469100 chr2A 712318038 712318809 771 False 856.000000 856 86.658000 2068 2839 1 chr2A.!!$F1 771
6 TraesCS2D01G469100 chr5A 646058409 646059406 997 False 439.000000 678 83.838500 1613 2851 2 chr5A.!!$F1 1238
7 TraesCS2D01G469100 chr5D 519545809 519546557 748 False 669.000000 669 82.846000 2103 2851 1 chr5D.!!$F1 748
8 TraesCS2D01G469100 chr5B 654366170 654367180 1010 False 426.500000 662 83.428000 1613 2851 2 chr5B.!!$F1 1238

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
150 151 0.105760 ATCGAGTCCTGCCATCCTCT 60.106 55.0 0.00 0.00 0.00 3.69 F
1266 1291 0.041926 TCGATATCCGTACGTGCGTG 60.042 55.0 24.09 15.43 39.75 5.34 F
1942 1983 0.033642 TGCATGCATGTTGGGTGTTG 59.966 50.0 26.79 0.05 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1442 0.250513 AGGAAGAAGGTGATGGCGAC 59.749 55.000 0.00 0.0 0.00 5.19 R
2756 2798 1.741770 CCTGCCTGTCCGTTGTAGC 60.742 63.158 0.00 0.0 0.00 3.58 R
3312 8108 0.320771 CGTGAGCAGGCTTACAACCT 60.321 55.000 15.22 0.0 38.35 3.50 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
55 56 2.345760 TACTCCTCCGGTGTTCGCC 61.346 63.158 0.00 0.00 37.59 5.54
76 77 1.382557 TGCCCCCATCGCTCTTCTA 60.383 57.895 0.00 0.00 0.00 2.10
78 79 1.267121 GCCCCCATCGCTCTTCTATA 58.733 55.000 0.00 0.00 0.00 1.31
80 81 1.205893 CCCCCATCGCTCTTCTATAGC 59.794 57.143 0.00 0.00 36.60 2.97
150 151 0.105760 ATCGAGTCCTGCCATCCTCT 60.106 55.000 0.00 0.00 0.00 3.69
217 226 1.149148 GGAGCAGTTGTTCTTCCGAC 58.851 55.000 0.00 0.00 0.00 4.79
229 238 0.797249 CTTCCGACGTGACCGACATC 60.797 60.000 0.00 0.00 37.88 3.06
267 276 3.261137 AGGTTTTCGGTTTTTGGGTTTCA 59.739 39.130 0.00 0.00 0.00 2.69
271 280 5.803020 TTTCGGTTTTTGGGTTTCATTTG 57.197 34.783 0.00 0.00 0.00 2.32
272 281 4.473477 TCGGTTTTTGGGTTTCATTTGT 57.527 36.364 0.00 0.00 0.00 2.83
273 282 4.184629 TCGGTTTTTGGGTTTCATTTGTG 58.815 39.130 0.00 0.00 0.00 3.33
274 283 3.935828 CGGTTTTTGGGTTTCATTTGTGT 59.064 39.130 0.00 0.00 0.00 3.72
299 308 0.805614 TTGTTGTGTTGTCGTGGGTG 59.194 50.000 0.00 0.00 0.00 4.61
300 309 1.027255 TGTTGTGTTGTCGTGGGTGG 61.027 55.000 0.00 0.00 0.00 4.61
301 310 2.115911 TTGTGTTGTCGTGGGTGGC 61.116 57.895 0.00 0.00 0.00 5.01
302 311 2.203153 GTGTTGTCGTGGGTGGCT 60.203 61.111 0.00 0.00 0.00 4.75
303 312 2.203139 TGTTGTCGTGGGTGGCTG 60.203 61.111 0.00 0.00 0.00 4.85
304 313 2.203153 GTTGTCGTGGGTGGCTGT 60.203 61.111 0.00 0.00 0.00 4.40
305 314 2.110213 TTGTCGTGGGTGGCTGTC 59.890 61.111 0.00 0.00 0.00 3.51
306 315 3.469863 TTGTCGTGGGTGGCTGTCC 62.470 63.158 0.00 0.00 0.00 4.02
307 316 3.626924 GTCGTGGGTGGCTGTCCT 61.627 66.667 0.00 0.00 0.00 3.85
308 317 3.311110 TCGTGGGTGGCTGTCCTC 61.311 66.667 0.00 0.00 0.00 3.71
309 318 3.314331 CGTGGGTGGCTGTCCTCT 61.314 66.667 0.00 0.00 0.00 3.69
310 319 2.348998 GTGGGTGGCTGTCCTCTG 59.651 66.667 0.00 0.00 0.00 3.35
311 320 2.930019 TGGGTGGCTGTCCTCTGG 60.930 66.667 0.00 0.00 0.00 3.86
312 321 2.607750 GGGTGGCTGTCCTCTGGA 60.608 66.667 0.00 0.00 0.00 3.86
331 340 1.125711 ACTAGCCGGGTGTGGAGTTT 61.126 55.000 18.40 0.00 0.00 2.66
353 362 1.865865 CTACACTGGTTGTTCGCAGT 58.134 50.000 0.00 0.00 39.91 4.40
408 417 9.284594 CTCTTCTTCTATAAAGCTATGATACGC 57.715 37.037 0.00 0.00 0.00 4.42
423 432 6.624352 ATGATACGCAATTTGCATACTCTT 57.376 33.333 20.56 7.29 45.36 2.85
587 597 9.965902 ATATTGTTTCTTCAGATTAGGAACAGT 57.034 29.630 0.00 0.00 41.02 3.55
640 650 1.891919 GCGGCGGCTGATTGGATAA 60.892 57.895 14.15 0.00 35.83 1.75
647 657 2.419990 CGGCTGATTGGATAAGGTGTGA 60.420 50.000 0.00 0.00 0.00 3.58
945 963 0.676184 CATTCTCCGCTAGCTAGCCA 59.324 55.000 34.27 22.32 46.34 4.75
1221 1246 3.325425 TGTTCCCTTCTTCGTTGGTATGA 59.675 43.478 0.00 0.00 0.00 2.15
1265 1290 0.870393 ATCGATATCCGTACGTGCGT 59.130 50.000 24.09 9.76 39.75 5.24
1266 1291 0.041926 TCGATATCCGTACGTGCGTG 60.042 55.000 24.09 15.43 39.75 5.34
1267 1292 1.594269 CGATATCCGTACGTGCGTGC 61.594 60.000 24.09 5.09 0.00 5.34
1448 1482 1.146041 AGGCAAGCACTTGTGTCGA 59.854 52.632 11.77 0.00 42.31 4.20
1449 1483 0.250467 AGGCAAGCACTTGTGTCGAT 60.250 50.000 11.77 0.00 42.31 3.59
1450 1484 0.166814 GGCAAGCACTTGTGTCGATC 59.833 55.000 11.77 0.00 42.31 3.69
1451 1485 0.179240 GCAAGCACTTGTGTCGATCG 60.179 55.000 9.36 9.36 42.31 3.69
1471 1505 1.323271 TGGACTCACCGCCTCAGATC 61.323 60.000 0.00 0.00 42.61 2.75
1475 1509 0.803768 CTCACCGCCTCAGATCAACG 60.804 60.000 0.00 0.00 0.00 4.10
1496 1530 9.820229 TCAACGTTGATTCAATAATTAACTCAC 57.180 29.630 26.53 0.00 38.68 3.51
1517 1551 9.706691 ACTCACTAATTTATATAACCCGACATG 57.293 33.333 0.00 0.00 0.00 3.21
1518 1552 9.151471 CTCACTAATTTATATAACCCGACATGG 57.849 37.037 0.00 0.00 37.55 3.66
1521 1555 9.498176 ACTAATTTATATAACCCGACATGGAAC 57.502 33.333 0.00 0.00 42.00 3.62
1543 1577 9.113876 GGAACACAAAATTAACTGATAAACTCG 57.886 33.333 0.00 0.00 0.00 4.18
1544 1578 9.659830 GAACACAAAATTAACTGATAAACTCGT 57.340 29.630 0.00 0.00 0.00 4.18
1545 1579 9.445786 AACACAAAATTAACTGATAAACTCGTG 57.554 29.630 0.00 0.00 0.00 4.35
1546 1580 8.617809 ACACAAAATTAACTGATAAACTCGTGT 58.382 29.630 0.00 0.00 0.00 4.49
1550 1584 8.524870 AAATTAACTGATAAACTCGTGTACGT 57.475 30.769 4.20 0.00 40.80 3.57
1551 1585 7.731556 ATTAACTGATAAACTCGTGTACGTC 57.268 36.000 4.20 0.00 40.80 4.34
1553 1587 3.503363 ACTGATAAACTCGTGTACGTCCA 59.497 43.478 4.20 0.00 40.80 4.02
1555 1589 4.417506 TGATAAACTCGTGTACGTCCATG 58.582 43.478 4.20 0.00 40.80 3.66
1557 1591 0.315886 AACTCGTGTACGTCCATGCA 59.684 50.000 4.20 0.00 40.80 3.96
1558 1592 0.388134 ACTCGTGTACGTCCATGCAC 60.388 55.000 4.20 0.00 40.80 4.57
1560 1594 4.563630 GTGTACGTCCATGCACGA 57.436 55.556 17.67 0.00 42.69 4.35
1561 1595 2.067616 GTGTACGTCCATGCACGAC 58.932 57.895 17.67 10.19 42.69 4.34
1562 1596 0.665068 GTGTACGTCCATGCACGACA 60.665 55.000 17.67 12.69 42.69 4.35
1563 1597 0.665068 TGTACGTCCATGCACGACAC 60.665 55.000 17.67 13.26 42.69 3.67
1564 1598 1.443025 TACGTCCATGCACGACACG 60.443 57.895 17.67 11.01 42.69 4.49
1565 1599 1.854163 TACGTCCATGCACGACACGA 61.854 55.000 17.67 0.00 42.69 4.35
1566 1600 1.805539 CGTCCATGCACGACACGAT 60.806 57.895 2.06 0.00 42.69 3.73
1570 1604 1.490693 CCATGCACGACACGATAGCC 61.491 60.000 0.00 0.00 42.67 3.93
1571 1605 1.588932 ATGCACGACACGATAGCCG 60.589 57.895 0.00 0.00 45.44 5.52
1572 1606 3.617538 GCACGACACGATAGCCGC 61.618 66.667 0.00 0.00 43.32 6.53
1573 1607 3.312504 CACGACACGATAGCCGCG 61.313 66.667 0.00 0.00 43.32 6.46
1590 1624 2.413634 CCGCGTGATAGGGAACAAAAAC 60.414 50.000 4.92 0.00 0.00 2.43
1592 1626 2.413634 GCGTGATAGGGAACAAAAACGG 60.414 50.000 0.00 0.00 0.00 4.44
1837 1871 7.611467 CCACCCATGCATGTTACTACAATATAT 59.389 37.037 24.58 0.00 37.91 0.86
1838 1872 8.453320 CACCCATGCATGTTACTACAATATATG 58.547 37.037 24.58 3.94 37.91 1.78
1839 1873 7.611467 ACCCATGCATGTTACTACAATATATGG 59.389 37.037 24.58 14.42 37.91 2.74
1900 1938 8.834465 ACTTATTGAGTGTGATGAGAATAATGC 58.166 33.333 0.00 0.00 37.17 3.56
1938 1979 2.634815 TTTTTGCATGCATGTTGGGT 57.365 40.000 26.79 0.00 0.00 4.51
1939 1980 1.880271 TTTTGCATGCATGTTGGGTG 58.120 45.000 26.79 2.44 0.00 4.61
1940 1981 0.757512 TTTGCATGCATGTTGGGTGT 59.242 45.000 26.79 0.00 0.00 4.16
1941 1982 0.757512 TTGCATGCATGTTGGGTGTT 59.242 45.000 26.79 0.00 0.00 3.32
1942 1983 0.033642 TGCATGCATGTTGGGTGTTG 59.966 50.000 26.79 0.05 0.00 3.33
1943 1984 0.317799 GCATGCATGTTGGGTGTTGA 59.682 50.000 26.79 0.00 0.00 3.18
1944 1985 1.670674 GCATGCATGTTGGGTGTTGAG 60.671 52.381 26.79 0.00 0.00 3.02
1945 1986 1.067425 CATGCATGTTGGGTGTTGAGG 60.067 52.381 18.91 0.00 0.00 3.86
1946 1987 0.106268 TGCATGTTGGGTGTTGAGGT 60.106 50.000 0.00 0.00 0.00 3.85
1947 1988 0.598065 GCATGTTGGGTGTTGAGGTC 59.402 55.000 0.00 0.00 0.00 3.85
1948 1989 1.247567 CATGTTGGGTGTTGAGGTCC 58.752 55.000 0.00 0.00 0.00 4.46
1949 1990 1.149101 ATGTTGGGTGTTGAGGTCCT 58.851 50.000 0.00 0.00 0.00 3.85
1950 1991 0.923358 TGTTGGGTGTTGAGGTCCTT 59.077 50.000 0.00 0.00 0.00 3.36
1951 1992 1.286553 TGTTGGGTGTTGAGGTCCTTT 59.713 47.619 0.00 0.00 0.00 3.11
1952 1993 2.291930 TGTTGGGTGTTGAGGTCCTTTT 60.292 45.455 0.00 0.00 0.00 2.27
1953 1994 2.358322 TGGGTGTTGAGGTCCTTTTC 57.642 50.000 0.00 0.00 0.00 2.29
1958 1999 4.891168 GGGTGTTGAGGTCCTTTTCTAAAA 59.109 41.667 0.00 0.00 0.00 1.52
2015 2056 2.688507 GTGATGAGATGACACGGTTGT 58.311 47.619 0.00 0.00 39.32 3.32
2499 2541 2.434185 GGCGTCCGCATCAAGACA 60.434 61.111 14.19 0.00 44.11 3.41
2524 2566 1.079658 AGAACTCCCCTACCAAGAGCT 59.920 52.381 0.00 0.00 0.00 4.09
2643 2685 1.973281 GTACGTCTCCGGGGTCACA 60.973 63.158 0.00 0.00 38.78 3.58
2676 2718 5.047566 TCAAGTTCAAGAACATCAAGGGA 57.952 39.130 14.69 0.00 43.47 4.20
2756 2798 0.730834 CTGCAGAACGTCGACCTCAG 60.731 60.000 8.42 5.23 0.00 3.35
2830 2872 1.971695 GTTGGCTACCAGCACCCAC 60.972 63.158 0.00 0.00 44.75 4.61
2839 2881 4.289101 AGCACCCACAGCCATGCA 62.289 61.111 0.00 0.00 40.63 3.96
2863 7618 0.956902 GACGTACGGCCAATTGGGTT 60.957 55.000 25.73 1.65 39.65 4.11
3052 7819 5.047943 AGTGGATTAGTGGCTCGTCATATAC 60.048 44.000 0.00 0.00 0.00 1.47
3115 7884 2.000447 GCTTACCAGCTAAGTTGGTCG 59.000 52.381 9.83 4.74 43.44 4.79
3148 7917 0.108138 GTGTGGATCCGGAGTTGAGG 60.108 60.000 11.34 0.00 0.00 3.86
3173 7943 6.339587 TGGCAAAACCACCTATTAAGAAAG 57.660 37.500 0.00 0.00 46.36 2.62
3312 8108 5.943349 TTGATACGGTGAATTCCCTTCTA 57.057 39.130 2.27 0.00 34.75 2.10
3328 8124 3.526534 CTTCTAGGTTGTAAGCCTGCTC 58.473 50.000 0.00 0.00 37.54 4.26
3336 8132 1.275010 TGTAAGCCTGCTCACGATTCA 59.725 47.619 0.00 0.00 0.00 2.57
3418 8214 4.160252 TGCCAAAGAAAGAAGAAGCAGTTT 59.840 37.500 0.00 0.00 0.00 2.66
3422 8218 7.257722 CCAAAGAAAGAAGAAGCAGTTTGTAA 58.742 34.615 0.00 0.00 0.00 2.41
3429 8225 4.756084 AGAAGCAGTTTGTAATGAGCAC 57.244 40.909 0.00 0.00 0.00 4.40
3464 8260 5.428496 TGTCTTTTGAATGTGAGCTTCAG 57.572 39.130 0.00 0.00 34.33 3.02
3489 8285 1.686355 TCACGAAAGTTGGCACCAAT 58.314 45.000 5.22 0.00 46.40 3.16
3505 8301 5.449588 GGCACCAATAGATTGACACAGATTG 60.450 44.000 3.76 0.00 40.14 2.67
3515 8311 2.859165 ACACAGATTGTCCATTCGGT 57.141 45.000 0.00 0.00 29.79 4.69
3574 8370 3.396276 TCACATCTTGGAAGGGGTTGTTA 59.604 43.478 0.00 0.00 0.00 2.41
3619 8415 8.063200 TGAAATCCACTCGAAGAAACTAGATA 57.937 34.615 0.00 0.00 34.09 1.98
3620 8416 8.696374 TGAAATCCACTCGAAGAAACTAGATAT 58.304 33.333 0.00 0.00 34.09 1.63
3652 8448 3.463048 AGGTGGATTTTGAGAAGGCAT 57.537 42.857 0.00 0.00 0.00 4.40
3669 8465 3.956199 AGGCATATGACAAGGTCAAATGG 59.044 43.478 12.11 0.00 45.96 3.16
3681 8477 3.096092 GGTCAAATGGCCATTCCTACAA 58.904 45.455 30.74 10.33 40.23 2.41
3691 8487 1.406539 CATTCCTACAACAGGCCATGC 59.593 52.381 5.01 0.00 45.10 4.06
3724 8520 4.145052 GTTTGATGAAACCTGGAGGAAGT 58.855 43.478 0.00 0.00 36.24 3.01
3752 8548 4.281657 GACTCCTTTATCCAAAAGGGCAT 58.718 43.478 14.78 3.15 45.26 4.40
3777 8573 5.163205 TGTCGGGATTAAGGTGAATGATGAT 60.163 40.000 0.00 0.00 0.00 2.45
3793 8589 7.781219 TGAATGATGATGTGGGTCATTATTTCT 59.219 33.333 7.88 0.00 41.82 2.52
3826 8622 2.039879 GGCTTAAGACAAGGAGACCCAA 59.960 50.000 6.67 0.00 33.88 4.12
3839 8635 1.010793 AGACCCAATGTCCCCTATCCA 59.989 52.381 0.00 0.00 45.68 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.392445 ACCGTACATAGCGCTATAGAAGAG 59.608 45.833 28.57 17.53 0.00 2.85
72 73 3.124128 CGACCGTACATAGCGCTATAGAA 59.876 47.826 28.57 14.46 0.00 2.10
76 77 1.196354 GACGACCGTACATAGCGCTAT 59.804 52.381 24.15 24.15 0.00 2.97
78 79 1.354506 GACGACCGTACATAGCGCT 59.645 57.895 17.26 17.26 0.00 5.92
80 81 2.002401 GCGACGACCGTACATAGCG 61.002 63.158 0.00 0.00 41.15 4.26
267 276 5.525378 ACAACACAACAACAACAACACAAAT 59.475 32.000 0.00 0.00 0.00 2.32
271 280 3.118809 CGACAACACAACAACAACAACAC 59.881 43.478 0.00 0.00 0.00 3.32
272 281 3.243101 ACGACAACACAACAACAACAACA 60.243 39.130 0.00 0.00 0.00 3.33
273 282 3.118809 CACGACAACACAACAACAACAAC 59.881 43.478 0.00 0.00 0.00 3.32
274 283 3.300857 CACGACAACACAACAACAACAA 58.699 40.909 0.00 0.00 0.00 2.83
304 313 2.279073 CCCGGCTAGTCCAGAGGA 59.721 66.667 0.00 0.00 34.01 3.71
305 314 2.042843 ACCCGGCTAGTCCAGAGG 60.043 66.667 0.00 4.06 34.01 3.69
306 315 1.682684 ACACCCGGCTAGTCCAGAG 60.683 63.158 0.00 0.00 34.01 3.35
307 316 1.982395 CACACCCGGCTAGTCCAGA 60.982 63.158 0.00 0.00 34.01 3.86
308 317 2.579201 CACACCCGGCTAGTCCAG 59.421 66.667 0.00 0.00 34.01 3.86
309 318 3.000819 CCACACCCGGCTAGTCCA 61.001 66.667 0.00 0.00 34.01 4.02
310 319 2.682494 TCCACACCCGGCTAGTCC 60.682 66.667 0.00 0.00 0.00 3.85
311 320 1.542187 AACTCCACACCCGGCTAGTC 61.542 60.000 0.00 0.00 0.00 2.59
312 321 1.125711 AAACTCCACACCCGGCTAGT 61.126 55.000 0.00 0.00 0.00 2.57
313 322 0.036306 AAAACTCCACACCCGGCTAG 59.964 55.000 0.00 0.00 0.00 3.42
314 323 0.250553 CAAAACTCCACACCCGGCTA 60.251 55.000 0.00 0.00 0.00 3.93
331 340 0.941542 GCGAACAACCAGTGTAGCAA 59.058 50.000 0.00 0.00 40.60 3.91
353 362 3.748083 AGTACAAGACGACTACCACTCA 58.252 45.455 0.00 0.00 0.00 3.41
434 443 8.500753 TTAGTAGATGCACCGTGAAATAAATT 57.499 30.769 1.65 0.00 0.00 1.82
435 444 8.677148 ATTAGTAGATGCACCGTGAAATAAAT 57.323 30.769 1.65 0.00 0.00 1.40
502 511 6.910972 GCACTCAAGGTTAAACTTTGACTAAC 59.089 38.462 2.08 0.00 38.94 2.34
508 517 6.959671 TTTTGCACTCAAGGTTAAACTTTG 57.040 33.333 2.08 0.81 36.63 2.77
524 533 5.980715 TCCCTCGTTTCTTTTTATTTTGCAC 59.019 36.000 0.00 0.00 0.00 4.57
587 597 5.480073 TCATGATCATACGATGGTGGATGTA 59.520 40.000 8.15 0.00 29.66 2.29
640 650 5.964477 TCTAAACATAGATCCCTTCACACCT 59.036 40.000 0.00 0.00 0.00 4.00
647 657 6.444704 TCTGGTCTCTAAACATAGATCCCTT 58.555 40.000 0.00 0.00 0.00 3.95
957 975 4.473520 CGCCTCCTCACCCGCAAT 62.474 66.667 0.00 0.00 0.00 3.56
1221 1246 4.830826 TCGAGCACAACGTAGATCATAT 57.169 40.909 0.00 0.00 0.00 1.78
1265 1290 1.673993 ACCGCCAACATGAATCGCA 60.674 52.632 0.00 0.00 0.00 5.10
1266 1291 1.226379 CACCGCCAACATGAATCGC 60.226 57.895 0.00 0.00 0.00 4.58
1267 1292 1.226379 GCACCGCCAACATGAATCG 60.226 57.895 0.00 0.00 0.00 3.34
1268 1293 1.226379 CGCACCGCCAACATGAATC 60.226 57.895 0.00 0.00 0.00 2.52
1269 1294 2.876955 CGCACCGCCAACATGAAT 59.123 55.556 0.00 0.00 0.00 2.57
1404 1438 3.665675 GAAGGTGATGGCGACGGCT 62.666 63.158 22.70 7.99 39.81 5.52
1408 1442 0.250513 AGGAAGAAGGTGATGGCGAC 59.749 55.000 0.00 0.00 0.00 5.19
1448 1482 2.680352 AGGCGGTGAGTCCACGAT 60.680 61.111 7.64 0.00 44.09 3.73
1449 1483 3.371063 GAGGCGGTGAGTCCACGA 61.371 66.667 7.64 0.00 44.09 4.35
1450 1484 3.633094 CTGAGGCGGTGAGTCCACG 62.633 68.421 0.00 0.00 44.09 4.94
1451 1485 1.608717 ATCTGAGGCGGTGAGTCCAC 61.609 60.000 0.00 0.00 42.46 4.02
1471 1505 9.825972 AGTGAGTTAATTATTGAATCAACGTTG 57.174 29.630 22.35 22.35 29.60 4.10
1491 1525 9.706691 CATGTCGGGTTATATAAATTAGTGAGT 57.293 33.333 0.00 0.00 0.00 3.41
1492 1526 9.151471 CCATGTCGGGTTATATAAATTAGTGAG 57.849 37.037 0.00 0.00 0.00 3.51
1494 1528 9.496873 TTCCATGTCGGGTTATATAAATTAGTG 57.503 33.333 0.00 0.00 34.36 2.74
1495 1529 9.498176 GTTCCATGTCGGGTTATATAAATTAGT 57.502 33.333 0.00 0.00 34.36 2.24
1496 1530 9.496873 TGTTCCATGTCGGGTTATATAAATTAG 57.503 33.333 0.00 0.00 34.36 1.73
1498 1532 7.776030 TGTGTTCCATGTCGGGTTATATAAATT 59.224 33.333 0.00 0.00 34.36 1.82
1499 1533 7.284074 TGTGTTCCATGTCGGGTTATATAAAT 58.716 34.615 0.00 0.00 34.36 1.40
1500 1534 6.651086 TGTGTTCCATGTCGGGTTATATAAA 58.349 36.000 0.00 0.00 34.36 1.40
1502 1536 5.873146 TGTGTTCCATGTCGGGTTATATA 57.127 39.130 0.00 0.00 34.36 0.86
1504 1538 4.554960 TTGTGTTCCATGTCGGGTTATA 57.445 40.909 0.00 0.00 34.36 0.98
1505 1539 3.426787 TTGTGTTCCATGTCGGGTTAT 57.573 42.857 0.00 0.00 34.36 1.89
1506 1540 2.932855 TTGTGTTCCATGTCGGGTTA 57.067 45.000 0.00 0.00 34.36 2.85
1507 1541 2.060050 TTTGTGTTCCATGTCGGGTT 57.940 45.000 0.00 0.00 34.36 4.11
1508 1542 2.060050 TTTTGTGTTCCATGTCGGGT 57.940 45.000 0.00 0.00 34.36 5.28
1509 1543 3.658757 AATTTTGTGTTCCATGTCGGG 57.341 42.857 0.00 0.00 34.36 5.14
1510 1544 5.629020 CAGTTAATTTTGTGTTCCATGTCGG 59.371 40.000 0.00 0.00 0.00 4.79
1511 1545 6.434596 TCAGTTAATTTTGTGTTCCATGTCG 58.565 36.000 0.00 0.00 0.00 4.35
1512 1546 9.906660 TTATCAGTTAATTTTGTGTTCCATGTC 57.093 29.630 0.00 0.00 0.00 3.06
1516 1550 9.959749 GAGTTTATCAGTTAATTTTGTGTTCCA 57.040 29.630 0.00 0.00 0.00 3.53
1517 1551 9.113876 CGAGTTTATCAGTTAATTTTGTGTTCC 57.886 33.333 0.00 0.00 0.00 3.62
1518 1552 9.659830 ACGAGTTTATCAGTTAATTTTGTGTTC 57.340 29.630 0.00 0.00 0.00 3.18
1523 1557 9.246423 CGTACACGAGTTTATCAGTTAATTTTG 57.754 33.333 0.00 0.00 43.02 2.44
1525 1559 8.524870 ACGTACACGAGTTTATCAGTTAATTT 57.475 30.769 9.04 0.00 43.02 1.82
1526 1560 7.274250 GGACGTACACGAGTTTATCAGTTAATT 59.726 37.037 9.04 0.00 43.02 1.40
1527 1561 6.749118 GGACGTACACGAGTTTATCAGTTAAT 59.251 38.462 9.04 0.00 43.02 1.40
1528 1562 6.086222 GGACGTACACGAGTTTATCAGTTAA 58.914 40.000 9.04 0.00 43.02 2.01
1530 1564 4.022935 TGGACGTACACGAGTTTATCAGTT 60.023 41.667 9.04 0.00 43.02 3.16
1531 1565 3.503363 TGGACGTACACGAGTTTATCAGT 59.497 43.478 9.04 0.00 43.02 3.41
1532 1566 4.087510 TGGACGTACACGAGTTTATCAG 57.912 45.455 9.04 0.00 43.02 2.90
1533 1567 4.417506 CATGGACGTACACGAGTTTATCA 58.582 43.478 0.33 0.00 43.02 2.15
1534 1568 3.242248 GCATGGACGTACACGAGTTTATC 59.758 47.826 0.33 0.00 43.02 1.75
1535 1569 3.184541 GCATGGACGTACACGAGTTTAT 58.815 45.455 0.33 0.00 43.02 1.40
1536 1570 2.030096 TGCATGGACGTACACGAGTTTA 60.030 45.455 0.33 0.00 43.02 2.01
1540 1574 2.359792 GTGCATGGACGTACACGAG 58.640 57.895 0.33 0.00 43.02 4.18
1543 1577 0.665068 TGTCGTGCATGGACGTACAC 60.665 55.000 33.95 25.98 40.34 2.90
1544 1578 0.665068 GTGTCGTGCATGGACGTACA 60.665 55.000 33.95 30.23 40.34 2.90
1545 1579 1.670971 CGTGTCGTGCATGGACGTAC 61.671 60.000 33.95 29.62 40.34 3.67
1546 1580 1.443025 CGTGTCGTGCATGGACGTA 60.443 57.895 33.95 23.16 40.34 3.57
1547 1581 2.486636 ATCGTGTCGTGCATGGACGT 62.487 55.000 33.95 15.21 40.34 4.34
1548 1582 0.524604 TATCGTGTCGTGCATGGACG 60.525 55.000 31.03 31.03 40.83 4.79
1550 1584 0.527600 GCTATCGTGTCGTGCATGGA 60.528 55.000 5.98 0.00 34.91 3.41
1551 1585 1.490693 GGCTATCGTGTCGTGCATGG 61.491 60.000 5.98 0.00 34.91 3.66
1553 1587 1.588932 CGGCTATCGTGTCGTGCAT 60.589 57.895 0.00 0.00 0.00 3.96
1555 1589 3.617538 GCGGCTATCGTGTCGTGC 61.618 66.667 0.00 0.00 41.72 5.34
1562 1596 1.579932 CCTATCACGCGGCTATCGT 59.420 57.895 12.47 0.00 41.72 3.73
1563 1597 1.154016 CCCTATCACGCGGCTATCG 60.154 63.158 12.47 0.00 42.76 2.92
1564 1598 0.601558 TTCCCTATCACGCGGCTATC 59.398 55.000 12.47 0.00 0.00 2.08
1565 1599 0.317479 GTTCCCTATCACGCGGCTAT 59.683 55.000 12.47 2.91 0.00 2.97
1566 1600 1.038681 TGTTCCCTATCACGCGGCTA 61.039 55.000 12.47 0.00 0.00 3.93
1570 1604 2.723618 CGTTTTTGTTCCCTATCACGCG 60.724 50.000 3.53 3.53 0.00 6.01
1571 1605 2.413634 CCGTTTTTGTTCCCTATCACGC 60.414 50.000 0.00 0.00 0.00 5.34
1572 1606 2.160813 CCCGTTTTTGTTCCCTATCACG 59.839 50.000 0.00 0.00 0.00 4.35
1573 1607 3.189910 GTCCCGTTTTTGTTCCCTATCAC 59.810 47.826 0.00 0.00 0.00 3.06
1590 1624 5.812642 GCAGAACCATATATAATGAGTCCCG 59.187 44.000 0.00 0.00 0.00 5.14
1592 1626 6.820656 CCTGCAGAACCATATATAATGAGTCC 59.179 42.308 17.39 0.00 0.00 3.85
1837 1871 6.091441 GCATGTGTGTTTTGTTTTAGTTTCCA 59.909 34.615 0.00 0.00 0.00 3.53
1838 1872 6.091441 TGCATGTGTGTTTTGTTTTAGTTTCC 59.909 34.615 0.00 0.00 0.00 3.13
1839 1873 7.054855 TGCATGTGTGTTTTGTTTTAGTTTC 57.945 32.000 0.00 0.00 0.00 2.78
1850 1884 9.323985 AGTATTTTGTAATTGCATGTGTGTTTT 57.676 25.926 0.00 0.00 0.00 2.43
1885 1919 9.793252 ATGTTTTACTTGCATTATTCTCATCAC 57.207 29.630 0.00 0.00 0.00 3.06
1930 1971 1.149101 AGGACCTCAACACCCAACAT 58.851 50.000 0.00 0.00 0.00 2.71
1931 1972 0.923358 AAGGACCTCAACACCCAACA 59.077 50.000 0.00 0.00 0.00 3.33
1932 1973 2.067365 AAAGGACCTCAACACCCAAC 57.933 50.000 0.00 0.00 0.00 3.77
1933 1974 2.243736 AGAAAAGGACCTCAACACCCAA 59.756 45.455 0.00 0.00 0.00 4.12
1934 1975 1.850345 AGAAAAGGACCTCAACACCCA 59.150 47.619 0.00 0.00 0.00 4.51
1935 1976 2.658807 AGAAAAGGACCTCAACACCC 57.341 50.000 0.00 0.00 0.00 4.61
1936 1977 6.459670 TTTTTAGAAAAGGACCTCAACACC 57.540 37.500 0.00 0.00 0.00 4.16
1958 1999 2.425312 TCACCTCAACACGCAACATTTT 59.575 40.909 0.00 0.00 0.00 1.82
2067 2109 9.838339 ATTTAGACATTTTAATCGTCAGATCCT 57.162 29.630 0.00 0.00 35.74 3.24
2068 2110 9.869844 CATTTAGACATTTTAATCGTCAGATCC 57.130 33.333 0.00 0.00 35.74 3.36
2400 2442 4.826404 TAGCGGCCGAGGCTACCA 62.826 66.667 33.48 0.00 41.80 3.25
2643 2685 5.152623 TCTTGAACTTGATGTCCTCGATT 57.847 39.130 0.00 0.00 0.00 3.34
2756 2798 1.741770 CCTGCCTGTCCGTTGTAGC 60.742 63.158 0.00 0.00 0.00 3.58
2830 2872 2.398498 GTACGTCTAGATGCATGGCTG 58.602 52.381 2.46 0.00 0.00 4.85
2839 2881 2.223971 CCAATTGGCCGTACGTCTAGAT 60.224 50.000 12.53 0.00 0.00 1.98
2863 7618 9.367444 CGCTAACTATAGAAGAAGAAAAAGGAA 57.633 33.333 6.78 0.00 0.00 3.36
3052 7819 4.356289 CGGGTGAAGGTTTGTTTAACTTG 58.644 43.478 0.00 0.00 36.93 3.16
3115 7884 5.112686 GGATCCACACATAGAAAGTGACTC 58.887 45.833 6.95 0.00 40.16 3.36
3286 8082 4.261801 AGGGAATTCACCGTATCAAACAG 58.738 43.478 3.45 0.00 0.00 3.16
3296 8092 3.270877 CAACCTAGAAGGGAATTCACCG 58.729 50.000 3.45 0.00 40.58 4.94
3312 8108 0.320771 CGTGAGCAGGCTTACAACCT 60.321 55.000 15.22 0.00 38.35 3.50
3328 8124 2.643551 AGCCCCATAGTTTGAATCGTG 58.356 47.619 0.00 0.00 0.00 4.35
3336 8132 5.515106 TGCAAACTAATAGCCCCATAGTTT 58.485 37.500 4.74 4.74 45.75 2.66
3418 8214 3.712016 TGGGCTAAAGTGCTCATTACA 57.288 42.857 0.00 0.00 38.69 2.41
3422 8218 4.796606 ACATATTGGGCTAAAGTGCTCAT 58.203 39.130 0.00 0.00 43.59 2.90
3429 8225 8.253113 ACATTCAAAAGACATATTGGGCTAAAG 58.747 33.333 0.00 0.00 0.00 1.85
3464 8260 4.083003 TGGTGCCAACTTTCGTGAATATTC 60.083 41.667 8.60 8.60 0.00 1.75
3515 8311 2.596338 TCTGACTCGGTCGCACCA 60.596 61.111 6.21 0.00 38.47 4.17
3535 8331 1.452833 GACTCCCAGGCATGAAGGC 60.453 63.158 0.00 0.00 44.61 4.35
3619 8415 4.598036 AATCCACCTTGAAGATCACCAT 57.402 40.909 0.00 0.00 0.00 3.55
3620 8416 4.387026 AAATCCACCTTGAAGATCACCA 57.613 40.909 0.00 0.00 0.00 4.17
3652 8448 3.448093 TGGCCATTTGACCTTGTCATA 57.552 42.857 0.00 0.00 42.40 2.15
3681 8477 2.361483 TTCATGCGCATGGCCTGT 60.361 55.556 41.21 11.29 42.61 4.00
3691 8487 1.462616 TCATCAAACCCCTTCATGCG 58.537 50.000 0.00 0.00 0.00 4.73
3715 8511 0.683504 GAGTCCGCCTACTTCCTCCA 60.684 60.000 0.00 0.00 0.00 3.86
3724 8520 2.464796 TGGATAAAGGAGTCCGCCTA 57.535 50.000 2.76 0.00 37.26 3.93
3752 8548 4.561500 TCATTCACCTTAATCCCGACAA 57.438 40.909 0.00 0.00 0.00 3.18
3777 8573 7.227873 TGTGAGTTTAGAAATAATGACCCACA 58.772 34.615 0.00 0.00 0.00 4.17
3793 8589 5.298989 TGTCTTAAGCCCTTGTGAGTTTA 57.701 39.130 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.